pax_global_header00006660000000000000000000000064121161034520014505gustar00rootroot0000000000000052 comment=9bb5cba4f472b82e92aef1dd89f492ed421e3f2a genometools-1.5.1/000077500000000000000000000000001211610345200140445ustar00rootroot00000000000000genometools-1.5.1/.gitignore000066400000000000000000000015651211610345200160430ustar00rootroot00000000000000*.al1 *.bac *.bak *.bck *.bdx *.bsi *.bsr *.bwt *.core *.csv *.db *.des *.diff *.err *.esq *.fsp *.gcov *.kys *.lcp *.llv *.mbd *.mct *.md5 *.mem *.mer *.ois *.orig *.pbt *.polya *.polya.info *.prj *.pyc *.sds *.ssp *.sti1 *.suf *.swp *.tags* *.tis *~ .ccache .clang_complete .gdb_history .ycm_extra_conf.py /*.log /bin /dist /doc/devguide/*.aux /doc/devguide/*.log /doc/devguide/*.out /doc/devguide/*.toc /doc/manuals/*.aux /doc/manuals/*.bbl /doc/manuals/*.blg /doc/manuals/*.log /doc/manuals/*.out /doc/manuals/*.toc /doc/manuals/auto /lib /obj /testsuite/stest_stest_tests /testsuite/stest_testsuite LocalMakefile* TAGS cscope.* debug gthlicense.aux gthlicense.log gthlicense.pdf gthtestsuite massif.* nohup.out out src/external/hmmer* src/external/hmmer-2.3.2/squid/squid.h src/external/hmmer-2.3.2/squid/squidconf.h src/external/hmmer-2.3.2/src/config.h tags testdata/genomediff genometools-1.5.1/CHANGELOG000066400000000000000000000301361211610345200152610ustar00rootroot00000000000000changes in version 1.5.1 (2013-03-07) - bugfixes and cleanups - code generator script extended to create interface/implementation code - reference counting in GtAlphabet is now thread-safe - GtCodon, GtCodonIterator* now part of the API - GtFile, GtFileUtils APIs extended - GtDiscDistri now part of the API - GtMD5Encoder, GtMD5Fingerprint now part of the API - GtSeqIterator* now part of the API - multithreading interface now part of the API - GtTool, GtToolbox now part of the API - GtTransTable now part of the API - GtORFIterator now part of the API - GtFeatureStream moved to extended/, independent of Cairo presence - GtFeatureIndex and implementations moved to extended/, independent of Cairo presence changes in version 1.5.0 (2013-02-05) - bugfixes and cleanups - development tool `gt sain' added to run an induced suffix array sorting algorithm - the -typecheck option in the `gt gff3` and `gt gff3validator` tools now also validates parent (part-of) relationships, see -help output for details - new option -encseq besides -seqfile(s) and -regionmapping to select a encseq index as a sequence source - GtBioseq backend switched to GtEncseq - GtSeqCol is now an interface, GtEncseqCol added - GtRankedList added - GtSNPAnnotatorStream and `gt snpper' tool added - node sorting code is now aware of MD5 hash presence - compatibility with old Pango versions inproved - Lua updated to 5.1.5 - zlib updated to 1.2.7 changes in version 1.4.2 (2012-10-02) - bugfixes and cleanups - GFF3 parser now correctly handles GVF input - GtMD5Encoder added - GtRDB relational database wrapper added - database-backed feature index implementation added (SQLite, MySQL) - scripting bindings now support GtMetaNode and GtEOFNode - AnnotationSketch now uses Pango instead of the Cairo toy API for font rendering - `gt convertseq` tool has new options -contract{protein,dna}wc - `gt select` tool can use custom filters defined in Lua - `gt hop` tool added - LTRharvest is more space-efficient using streaming of indexes - LTR filtering, clustering and classification code added, used e.g. in the LTRsift software (http://www.zbh.uni-hamburg.de/LTRsift) - match iterators for BLAST and LAST added - CDS features with multiple parents are split in tidy-mode (if possible) - changed format for MD5 sequence IDs: It now uses md5:063b1024d68e26716b7f38caf958316f:1877523 instead of md5:063b1024d68e26716b7f38caf958316f. That is, the ``original'' sequence ID is kept after the MD5 hash. - `gt genomediff` tool has changed options and improved performance. - added tools for compression of short reads (with quality, fastq) either direct: tool `gt compreads compress` or using a reference genome: tool `gt compreads refcompress`. - improved running time and space requirements in suffix-prefix match computation - `gt chain2dim` has new option -global all, allowing for computing all best chains rather than a single best chain - add linear time functions to check the suffix array and the lcptable - added radixsort as new method when sorting buckets of suffixes changes in version 1.4.1 (2012-04-12) - the GFF3 parser now handles children which are defined before their parents - many small improvements to the GFF3 parser changes in version 1.4.0 (2012-04-02) - bugfixes and cleanups - the tool `gt mutate` has been renamed to `gt seqmutate`. The same functionality is still available with `gt mutate` in order not to break existing scripts. - `gt extractfeat` has new options -seqid and -target - `gt suffixerator` has new options -lcpdist, -genomediff - `gt readjoiner' toolbox added for sequence assembly - `gt encseq encode' has new option -lossless - `gt gff3 -tidy' recognizes and fixes more GFF3 errors - test suite is now multithreaded - added GtSamAlignment, GtSamfileIterator for SAM/BAM access - added GtHuffman*, GtGolomb*, GtEliasGamma* for integer encoding - added GtBit{In,Out}Stream - further optimizations in GtEncseq - ensure compatibility with GCC >=4.6 (as in Ubuntu oneiric) - BSD-licensed implementation is now used in GtRBTree - added GtRMQ class for efficient range minimum queries changes in version 1.3.9 (2011-07-02) - various bugfixes and cleanups - fix option -translate in `gt extractfeat` tool - mirroring and seqnum/filenum support added for gtruby/gtpython changes in version 1.3.8 (2011-06-16) - bugfixes and cleanups - GtEncseq completed, Lua bindings added - `gt encseq` toolbox added for encoded sequence handling - `gt suffixerator` and `gt packedindex mkindex` have new option -memlimit - `gt bed_to_gff3` has new options -o, -gzip, -bzip2 and -force - `gt gtf_to_gff3` has new options -o, -gzip, -bzip2 and -force - `gt splicesiteinfo` has new options -o, -gzip, -bzip2 and -force - `gt eval` has new options -o, -gzip, -bzip2 and -force - `gt gff3` has new option -show - `gt gff3_to_gtf` has new options -o, -gzip, -bzip2 and -force - file suffix of fingerprint tables has been changed from ".gt_bsf" to ".md5" - file suffix of bioseq index files has been changed from ".gt_bsi" to ".bsi" - file suffix of bioseq raw files has been changed from ".gt_bsr" to ".bsr" - the tool `gt filter` has been renamed to `gt select`. The same functionality is still available with `gt filter` in order not to break existing scripts - `gt id_to_md5` has new option -subtargetids changes in version 1.3.7 (2011-01-28) - bugfixes and cleanup - `gt suffixerator` now creates ssp/des/sds tables by default changes in version 1.3.6 (2011-01-07) - `gt stat` has new options -addintrons and -cdslengthdistri - the tool `gt bioseq` has been renamed to `gt seq` - `gt seq` has new options -o, -gzip, -bzip2 and -force - `gt stat` has new options -o, -gzip, -bzip2 and -force - `gt extractfeat` has new option -width - `gt splitfasta` has new option -width - `gt sequniq` has new option -width - `gt fingerprint` has new options -width, -o, -gzip, -bzip2 and -force - `gt mutate` has new options -width, -o, -gzip, -bzip2 and -force - `gt shredder` has new options -width, -o, -gzip, -bzip2 and -force - `gt seqfilter` has new options -width, -o, -gzip, -bzip2 and -force - `gt seqfilter` has new option -maxseqnum - new tool `gt seqtransform` added - `gt cds`, `gt extractfeat` and `gt splicesiteinfo` have new option -usedesc - new tools `gt md5_to_id` and `gt id_to_md5` added - `gt gff3` has new option -addids - `gt stat` has new option -source - `gt filter` has new option -source changes in version 1.3.5 (2010-07-12) - `gt gff3 -tidy` cleans up multi-features with different parents - `gt stat` shows number of multi-features - `gt gff3 -sort` joins sequence regions with the same ID - `gt cds` has new options -minorflen, -startcodon, and -finalstopcodon changes in version 1.3.4 (2009-11-19) - majority: bug fixes, cleanups - new tool `gt ltrdigest` added - new tool `gt convertseq` added - new tool `gt repfind` added - track order can be specified in AnnotationSketch - new gcc compatibility fixes - CustomStream and CustomVisitor base classes allow implementation of new functionality in {Ruby, Python} changes in version 1.3.3 (2009-07-10) - new tool `gt interfeat` added - new tool `gt mergefeat` added - new tool `gt dupfeat` added - `gt gff3 -tidy` cleans up features with duplicate attributes - new tool `gt ltrdigest` added changes in version 1.3.2 (2009-04-29) - bug fixes and cleanup changes in version 1.3.1 (2009-04-24) - `gt extractfeat` has new options -o, -gzip, and -bzip2 - `gt splitfasta` has new option -numfiles - new tool `gt sketch_page` added - `gt sketch` has new option -flattenfiles - bug fixes changes in version 1.3.0 (2008-12-03) - `gt bed_to_gff3` has new options -featuretype, -thicktype, and -blocktype - `gt sketch` has new option -input - many extensions and some changes to the C API. E.g., AnnotationSketch now allows one to define track selector functions and custom tracks. changes in version 1.2.2 (2008-11-04) - new tool `gt tallymer` added - new tool `gt congruence` added - the GenomeTools Python bindings (see gtpython/README) have been added - new tool `gt bed_to_gff3` added changes in version 1.2.1 (2008-11-03) - bug fixes changes in version 1.2.0 (2008-10-04) - `gt shredder` has new option -sample - `gt filter` has new options -targetbest and -maxgenescore - `gt gff3` has new option -typecheck - the GFF3 parser can handle embedded FASTA sequences - `gt gff3` has new option -width to format embedded FASTA sequences - new tool `gt gff3validator` has been added - `gt view` has been renamed to `gt sketch` - `gt gff3` has new option -tidy changes in version 1.1.2 (2008-07-04) - new tool `gt fingerprint` has been added - new tool `gt shredder` has been added - `gt stat` shows number of CDSs and protein-coding genes - `gt filter` has new options -hascds, -contain, and -targetstrand - `gt splitfasta` has new options -splitdesc and -force changes in version 1.1.1 (2008-04-11) - bug fixes changes in version 1.1.0 (2008-03-20) - `gt filter` has new optios -strand, -overlap, and -minaveragessp - new tool `gt mgth` has been added - new tool `gt seqfilter` has been added - new tool `gt sequniq` has been added changes in version 1.0.9 (2008-02-04): - `gt extractseq` has new options -frompos and -topos - bug fixes changes in version 1.0.8 (2007-12-13): - the GenomeTools Ruby bindings (see gtruby/README) have been added changes in version 1.0.7 (2007-11-27): - `gt view` has new option -addintrons - `gt stat` has new option -exonnumberdistri - `gt bioseq` has new option -seqlengthdistri changes in version 1.0.6 (2007-10-19): - new `gt extractseq` tool changes in version 1.0.5 (2007-10-17): - bug fixes changes in version 1.0.4 (2007-10-15): - `gt gff2` has new option -checkids (was the default behavior before) - new tool `gt chseqids` added which replaces the option -chseqids of the `gt gff3` tool - new `gt ltrharvest` tool - new `gt splicesiteinfo` tool - new `gt uniq` tool changes in version 1.0.3 (2007-09-12): - `gt view` can process multiple GFF3 files - the interactive mode has been improved (multiple line input, command line editing, similar to the Lua interpreter) - `gt gff3` has new option -offset - `gt gff3` has new option -offsetfile - `gt gff3` has new option -chseqids - all tools which process GFF3 files can read compressed GFF3 files, if the ending is correct (i.e., '.gz' for gzip compressed files and '.bz2' for bzip2 compressed files) changes in version 1.0.2 (2007-08-29): - `gt suffixerator` tool added - `gt mkfmindex` tool added - `gt uniquesub` tool added - bug fixes - new option -i added to `gt` changes in version 1.0.1 (2007-07-17): - undefined sequence-regions are added automatically - new feature types added - bug fixes changes in version 1.0.0: - `gt view` tool added (optional: compile with `make libgtview=yes`) - `gt eval` has new options -ltr and -ltrdelta which allow to evaluate LTR retrotransposon predictions instead of gene predictions - (from here on release numbers are synced with GenomeThreader) changes in version 0.7.5: - `gt splitfasta` runs faster and can process compressed files changes in version 0.7.4: - `gt gtf2gff3` has been renamed to `gt gtf_to_gff3` - new tool `gt gff3_to_gtf` has been added changes in version 0.7.3: - new exercise `gt exercise linearalign` added changes in version 0.7.2: - `gt splitfasta` tool added changes in version 0.7.1: - compilation output shortened - new functions added to libgtcore changes in version 0.7.0: - `gt eval` shows much more details - `gt cds` has new options -seqfile and -regionmapping (interface change) - `gt bioseq` can now read from stdin, too - `gt bioseq` has new option -gc-content - new tool `gt mutate` added - libgt has been split up into libgtcore and libgtext changes in version 0.6.9: - `gt stat` has new options -exonlengthdistri and -intronlengthdistri - `gt gff3` has new option -addintrons - a singular environment object and a memory allocator have been introduced changes in version 0.6.8: - Lua has been imported into the source tree - `gt extractfeat` has a new option -regionmapping - `gt bioseq` can be used with more then one sequence file - `gt filter` has a new option -seqid - `gt filter` has a new option -maxgenenum - the error() function has been removed - the GFF3 parser handles additional attributes genometools-1.5.1/CONTRIBUTORS000066400000000000000000000013701211610345200157250ustar00rootroot00000000000000The following contributors helped to develop GenomeTools. Please drop a note to gremme@zbh.uni-hamburg.de if I left someone out or missed something. - Stefan Bienert (patches) - Joachim Bonnet (Huffman/Golomb/Elias coding, GtBit{In,Out}Stream) - David Ellinghaus (parts of ltr/ subdirectory, ltrharvest tool) - Johannes Fischer (range minimum query code) - Giorgio Gonnella (codegen, simreads tool, readjoiner tools, patches) - Thomas Jahns (BitPackArray and BitPackString class, block-compressed FM-index) - Malte Mader (AnnotationSketch, sketch tool) - Brent Pedersen (python bindings, patches) - Christin Schaerfer (AnnotationSketch, sketch tool) - David Schmitz-Huebsch (mgth/ subdirectory, mgth tool) - Dirk Willrodt (genomediff tool, SAM/BAM, patches) genometools-1.5.1/INSTALL000066400000000000000000000110311211610345200150710ustar00rootroot00000000000000Building GenomeTools -------------------- Invoke GNU make, e.g.: $ make [argument ...] to build GenomeTools. You need at least version 3.80 of GNU make, you can check which version you have by invoking $ make --version On *BSD GNU make is often called ``gmake''. Possible arguments: - 64bit=yes to compile a 64-bit version (not available on all platforms) - opt=no to disable optimization - assert=no to disable assertions - amalgamation=yes to compile as an amalgamation - curses=no to disable the interactive Lua shell, dropping ncurses deps - cairo=no to disable AnnotationSketch, dropping Cairo/Pango deps - errorcheck=no to disable the handling of compiler warnings as errors - universal=yes to build a universal binary - with-hmmer=yes to add HMMER support to the LTRdigest tool Example call to build GenomeTools without assertions on a system where GNU make is called ``gmake'': $ gmake assert=no Please remember to always run `make cleanup` before rebuilding with changed make parameters! Building GenomeTools without the curses library: ------------------------------------------------ On systems without an installed curses library invoke make as above with the argument curses=no. Building GenomeTools without the sketch tool: --------------------------------------------- The AnnotationSketch engine requires the Cairo and Pango headers and libraries to be installed in order to build GenomeTools. Please consult your operating system's package manager for more information on how to install these. For example, on Debian the packages ``libcairo2-dev'' and ``libpango1.0-dev'' must be installed. If Cairo and/or Pango headers are not installed on the system, and AnnotationSketch support is not required, GenomeTools can be built without graphics support by invoking make as above with the argument cairo=no. Building GenomeTools with HMMER: -------------------------------- To enable protein domain search functionality in the ltrdigest tool please also append the with-hmmer=yes option to the make call. This option will make sure that a HMMER source package is downloaded and compiled along with the gt binary. Note that the wget executable must be available in the current PATH to do so (alternatively, you can download HMMER manually from ftp://selab.janelia.org/pub/software/hmmer/CURRENT/ and untar it in the src/external/ subdirectory). $ make with-hmmer=yes Building GenomeTools as a Universal Binary (on Mac OS X < v10.6): ----------------------------------------------------------------- Invoke make as above with the argument universal=yes. Note that on later Mac OS X systems (those with an Intel CPU) the universal=yes option is not required. Also, do not use it on Mac OS X 10.6 (Snow Leopard) or later as PowerPC support has since been discontinued. Thus trying to build a universal binary may lead to problems. Building GenomeTools on Windows (using Cygwin): ----------------------------------------------- Building GenomeTools with gcc on Windows occasionally results a warning regarding the '-fPIC' parameter. This can be ignored without problems. To ignore this warning, please append the errorcheck=no option to your make call. All other options given in this file can still be used. Testing GenomeTools (optional) ------------------------------ Call $ make test to make sure your GenomeTools build went fine. This step requires an installed Ruby 1.8 interpreter (see http://www.ruby-lang.org/en/ for informations on Ruby). Please note that all make options given during the compilation must be given in the `make test' invocation again. For example, if you compiled GenomeTools with the '64bit=yes cairo=no' options, the correct installation command would be: # make 64bit=yes cairo=no test Installing GenomeTools ---------------------- To install the ``gt'' binary and the ``libgenometools'' library (plus header files) on your system invoke $ make install Per default the files are installed under /usr/local. You can change this with the prefix argument. For example, to install under /usr, invoke # make prefix=/usr install Please note that all make options given during the compilation must be given in the `make install' invocation again. For example, if you compiled GenomeTools with the '64bit=yes cairo=no' options, the correct installation command would be: # make prefix=/usr 64bit=yes cairo=no install Omitting these options is likely to lead to problems during installation. Final note ----------- Please look at http://genometools.org for updates and report bugs if you encounter any. Enjoy! genometools-1.5.1/LICENSE000066400000000000000000000276401211610345200150620ustar00rootroot00000000000000All code of GenomeTools except src/core/msort.[ch], src/core/yarandom.[ch], and src/external/* is released under the following ICS license. It is functionally equivalent to a two-term BSD copyright with language removed that is made unnecessary by the Berne convention. See http://openbsd.org/policy.html for more information on copyrights. Copyright (c) 2003-2013 G. Gremme, S. Steinbiss, S. Kurtz, and CONTRIBUTORS Copyright (c) 2003-2013 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. 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Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu -------------------------------------------------------------------------------- The source in src/core/msort.[ch] is covered by the following license: Copyright (c) 1992, 1993 The Regents of the University of California. All rights reserved. This code is derived from software contributed to Berkeley by Peter McIlroy. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. genometools-1.5.1/Makefile000066400000000000000000001131671211610345200155150ustar00rootroot00000000000000# # Copyright (c) 2006-2013 Gordon Gremme # Copyright (c) 2008-2013 Sascha Steinbiss # Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # INCLUDEOPT:=-I$(CURDIR)/src -I$(CURDIR)/obj \ -I$(CURDIR)/src/external/zlib-1.2.7 \ -I$(CURDIR)/src/external/md5-1.1.2/src \ -I$(CURDIR)/src/external/lua-5.1.5/src \ -I$(CURDIR)/src/external/luafilesystem-1.5.0/src \ -I$(CURDIR)/src/external/lpeg-0.10.2 \ -I$(CURDIR)/src/external/expat-2.0.1/lib \ -I$(CURDIR)/src/external/bzip2-1.0.6 \ -I$(CURDIR)/src/external/libtecla-1.6.1 \ -I$(CURDIR)/src/external/samtools-0.1.18 \ -I$(CURDIR)/src/external/sqlite-3.7.10 ifeq ($(shell pkg-config --version > /dev/null 2> /dev/null; echo $$?),0) HAS_PKGCONFIG:=yes else HAS_PKGCONFIG:=no endif ifneq ($(cairo),no) ifeq ($(HAS_PKGCONFIG),yes) INCLUDEOPT+=$(shell pkg-config --cflags-only-I pango) \ $(shell pkg-config --cflags-only-I cairo) \ $(shell pkg-config --cflags-only-I pangocairo) \ $(shell pkg-config --cflags-only-I glib-2.0) endif endif # these variables are exported by the configuration script ifndef CC CC:=gcc endif ifndef CXX CXX:=g++ endif EXP_CFLAGS:=$(CFLAGS) EXP_LDFLAGS:=$(LDFLAGS) EXP_CXXFLAGS:=$(CXXFLAGS) EXP_CPPFLAGS:=$(CPPFLAGS) EXP_LDLIBS:=$(LIBS) -lm # ...while those starting with GT_ are for internal purposes only GT_CFLAGS:=-g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith # expat needs -DHAVE_MEMMOVE # lua needs -DLUA_USE_POSIX # tecla needs -DHAVE_CURSES_H -DHAVE_TERM_H -DUSE_TERMINFO # zlib needs -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN EXT_FLAGS:= -DHAVE_MEMMOVE -DLUA_USE_POSIX -DLUA_DL_DLOPEN \ -DHAVE_CURSES_H -DHAVE_TERM_H -DUSE_TERMINFO \ -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN EXP_CPPFLAGS+=-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 $(EXT_FLAGS) GT_CPPFLAGS:=$(INCLUDEOPT) GT_CXXFLAGS:=-g -pipe GT_LDFLAGS:=-Llib STEST_FLAGS:= EXP_LDFLAGS+=$(foreach dir, \ $(shell test -d /usr/local/lib && echo /usr/local/lib ; \ test -d /usr/X11R6/lib && echo /usr/X11R6/lib ; \ test -d /opt/local/lib && echo /opt/local/lib),-L$(dir)) BUILDSTAMP:=$(shell date +'"%Y-%m-%d %H:%M:%S"') # try to set RANLIB automatically SYSTEM:=$(shell uname -s) MACHINE:=$(shell uname -m) ifeq ($(SYSTEM),Darwin) RANLIB:=ranlib NO_STATIC_LINKING:=defined SHARED:=-dynamiclib -undefined dynamic_lookup SHARED_OBJ_NAME_EXT:=.dylib ifeq ($(universal),yes) MACHINE:="Universal_Binary" GT_CFLAGS+=-arch i386 -arch ppc -arch_errors_fatal GT_LDFLAGS+=-arch i386 -arch ppc -arch_errors_fatal endif ifeq ($(ppc),yes) MACHINE:="Power_Macintosh" GT_CFLAGS+=-arch ppc -arch_errors_fatal GT_LDFLAGS+=-arch ppc -arch_errors_fatal endif else SHARED_OBJ_NAME_EXT:=.so SHARED:=-shared endif # compiled executables GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c GTMAIN_OBJ:=$(GTMAIN_SRC:%.c=obj/%.o) GTMAIN_DEP:=$(GTMAIN_SRC:%.c=obj/%.d) EXAMPLES_SRC:=src/example.c EXAMPLES_DEP:=$(EXAMPLES_SRC:%.c=obj/%.d) SKPROTO_SRC:=src/skproto.c src/tools/gt_skproto.c SKPROTO_OBJ:=$(SKPROTO_SRC:%.c=obj/%.o) SKPROTO_DEP:=$(SKPROTO_SRC:%.c=obj/%.d) TOOLS_SRC:=$(wildcard src/tools/*.c) TOOLS_OBJ:=$(TOOLS_SRC:%.c=obj/%.o) TOOLS_DEP:=$(TOOLS_SRC:%.c=obj/%.d) EXPAT_DIR:=src/external/expat-2.0.1/lib LIBEXPAT_SRC:=$(EXPAT_DIR)/xmlparse.c $(EXPAT_DIR)/xmlrole.c \ $(EXPAT_DIR)/xmltok.c LIBEXPAT_OBJ:=$(LIBEXPAT_SRC:%.c=obj/%.o) LIBEXPAT_DEP:=$(LIBEXPAT_SRC:%.c=obj/%.d) LIBLUA_SRC=src/lualib.c\ src/external/md5-1.1.2/src/md5.c\ src/external/md5-1.1.2/src/md5lib.c\ src/external/md5-1.1.2/src/des56.c\ src/external/md5-1.1.2/src/ldes56.c\ src/external/luafilesystem-1.5.0/src/lfs.c\ src/external/lpeg-0.10.2/lpeg.c LIBLUA_OBJ:=$(LIBLUA_SRC:%.c=obj/%.o) LIBLUA_DEP:=$(LIBLUA_SRC:%.c=obj/%.d) LUAMAIN_SRC:=src/external/lua-5.1.5/etc/all.c LUAMAIN_OBJ:=$(LUAMAIN_SRC:%.c=obj/%.o) LUAMAIN_DEP:=$(LUAMAIN_SRC:%.c=obj/%.d) TECLA_DIR:=src/external/libtecla-1.6.1 LIBTECLA_SRC:=$(TECLA_DIR)/chrqueue.c $(TECLA_DIR)/cplfile.c \ $(TECLA_DIR)/cplmatch.c $(TECLA_DIR)/direader.c \ $(TECLA_DIR)/errmsg.c $(TECLA_DIR)/expand.c \ $(TECLA_DIR)/freelist.c $(TECLA_DIR)/getline.c \ $(TECLA_DIR)/hash.c $(TECLA_DIR)/history.c \ $(TECLA_DIR)/homedir.c $(TECLA_DIR)/ioutil.c \ $(TECLA_DIR)/keytab.c $(TECLA_DIR)/pathutil.c \ $(TECLA_DIR)/pcache.c $(TECLA_DIR)/stringrp.c \ $(TECLA_DIR)/strngmem.c $(TECLA_DIR)/version.c LIBTECLA_OBJ:=$(LIBTECLA_SRC:%.c=obj/%.o) LIBTECLA_DEP:=$(LIBTECLA_SRC:%.c=obj/%.d) BZ2_DIR:=src/external/bzip2-1.0.6 LIBBZ2_SRC:=$(BZ2_DIR)/blocksort.c $(BZ2_DIR)/huffman.c $(BZ2_DIR)/crctable.c \ $(BZ2_DIR)/randtable.c $(BZ2_DIR)/compress.c \ $(BZ2_DIR)/decompress.c $(BZ2_DIR)/bzlib.c LIBBZ2_OBJ:=$(LIBBZ2_SRC:%.c=obj/%.o) LIBBZ2_DEP:=$(LIBBZ2_SRC:%.c=obj/%.d) SQLITE3_DIR:=src/external/sqlite-3.7.10 SQLITE3_SRC:=$(SQLITE3_DIR)/sqlite3.c SQLITE3_OBJ:=$(SQLITE3_SRC:%.c=obj/%.o) SQLITE3_DEP:=$(SQLITE3_SRC:%.c=obj/%.d) HMMER_BASE:=src/external/hmmer-3.0 HMMER_DIR:=$(HMMER_BASE)/src HMMER_SRC:=$(HMMER_DIR)/emit.c $(HMMER_DIR)/build.c \ $(HMMER_DIR)/errors.c $(HMMER_DIR)/evalues.c \ $(HMMER_DIR)/eweight.c \ $(HMMER_DIR)/generic_decoding.c $(HMMER_DIR)/modelconfig.c \ $(HMMER_DIR)/generic_fwdback.c $(HMMER_DIR)/modelstats.c \ $(HMMER_DIR)/generic_msv.c $(HMMER_DIR)/mpisupport.c \ $(HMMER_DIR)/generic_null2.c $(HMMER_DIR)/p7_alidisplay.c \ $(HMMER_DIR)/generic_optacc.c $(HMMER_DIR)/p7_bg.c \ $(HMMER_DIR)/generic_stotrace.c $(HMMER_DIR)/p7_builder.c \ $(HMMER_DIR)/generic_viterbi.c $(HMMER_DIR)/p7_domaindef.c \ $(HMMER_DIR)/generic_vtrace.c $(HMMER_DIR)/p7_gmx.c \ $(HMMER_DIR)/h2_io.c $(HMMER_DIR)/p7_hmm.c \ $(HMMER_DIR)/heatmap.c $(HMMER_DIR)/p7_hmmfile.c \ $(HMMER_DIR)/p7_pipeline.c $(HMMER_DIR)/p7_prior.c \ $(HMMER_DIR)/p7_profile.c $(HMMER_DIR)/p7_spensemble.c \ $(HMMER_DIR)/hmmer.c $(HMMER_DIR)/p7_tophits.c \ $(HMMER_DIR)/p7_trace.c $(HMMER_DIR)/phmmer.c \ $(HMMER_DIR)/seqmodel.c $(HMMER_DIR)/tracealign.c \ $(HMMER_DIR)/logsum.c $(HMMER_DIR)/impl/decoding.c \ $(HMMER_DIR)/impl/optacc.c \ $(HMMER_DIR)/impl/fwdback.c $(HMMER_DIR)/impl/p7_omx.c \ $(HMMER_DIR)/impl/io.c $(HMMER_DIR)/impl/p7_oprofile.c \ $(HMMER_DIR)/impl/mpi.c $(HMMER_DIR)/impl/stotrace.c \ $(HMMER_DIR)/impl/msvfilter.c $(HMMER_DIR)/impl/vitfilter.c \ $(HMMER_DIR)/impl/null2.c HMMER_OBJ:=$(HMMER_SRC:%.c=%.o) EASEL_DIR:=$(HMMER_BASE)/easel EASEL_SRC:=$(EASEL_DIR)/easel.c $(EASEL_DIR)/esl_randomseq.c \ $(EASEL_DIR)/esl_alphabet.c $(EASEL_DIR)/esl_ratematrix.c \ $(EASEL_DIR)/esl_cluster.c $(EASEL_DIR)/esl_regexp.c \ $(EASEL_DIR)/esl_dirichlet.c $(EASEL_DIR)/esl_rootfinder.c \ $(EASEL_DIR)/esl_distance.c $(EASEL_DIR)/esl_scorematrix.c \ $(EASEL_DIR)/esl_dmatrix.c $(EASEL_DIR)/esl_sq.c \ $(EASEL_DIR)/esl_exponential.c $(EASEL_DIR)/esl_sqio_ascii.c \ $(EASEL_DIR)/esl_fileparser.c $(EASEL_DIR)/esl_sqio.c \ $(EASEL_DIR)/esl_gamma.c $(EASEL_DIR)/esl_sqio_ncbi.c \ $(EASEL_DIR)/esl_getopts.c $(EASEL_DIR)/esl_sse.c \ $(EASEL_DIR)/esl_gev.c $(EASEL_DIR)/esl_ssi.c \ $(EASEL_DIR)/esl_gumbel.c $(EASEL_DIR)/esl_stack.c \ $(EASEL_DIR)/esl_histogram.c $(EASEL_DIR)/esl_stats.c \ $(EASEL_DIR)/esl_hmm.c $(EASEL_DIR)/esl_stopwatch.c \ $(EASEL_DIR)/esl_hyperexp.c $(EASEL_DIR)/esl_stretchexp.c \ $(EASEL_DIR)/esl_keyhash.c \ $(EASEL_DIR)/esl_minimizer.c $(EASEL_DIR)/esl_threads.c \ $(EASEL_DIR)/esl_mixgev.c $(EASEL_DIR)/esl_tree.c \ $(EASEL_DIR)/esl_mpi.c $(EASEL_DIR)/esl_vectorops.c \ $(EASEL_DIR)/esl_msa.c $(EASEL_DIR)/esl_vmx.c \ $(EASEL_DIR)/esl_msacluster.c $(EASEL_DIR)/esl_weibull.c \ $(EASEL_DIR)/esl_msashuffle.c $(EASEL_DIR)/esl_workqueue.c \ $(EASEL_DIR)/esl_msaweight.c $(EASEL_DIR)/esl_wuss.c \ $(EASEL_DIR)/esl_normal.c $(EASEL_DIR)/esl_paml.c \ $(EASEL_DIR)/esl_random.c EASEL_OBJ:=$(EASEL_SRC:%.c=%.o) ZLIB_DIR:=src/external/zlib-1.2.7 ZLIB_SRC:=$(ZLIB_DIR)/adler32.c $(ZLIB_DIR)/compress.c $(ZLIB_DIR)/crc32.c \ $(ZLIB_DIR)/gzclose.c $(ZLIB_DIR)/gzlib.c $(ZLIB_DIR)/gzread.c \ $(ZLIB_DIR)/gzwrite.c $(ZLIB_DIR)/uncompr.c $(ZLIB_DIR)/deflate.c \ $(ZLIB_DIR)/trees.c $(ZLIB_DIR)/zutil.c $(ZLIB_DIR)/inflate.c \ $(ZLIB_DIR)/infback.c $(ZLIB_DIR)/inftrees.c $(ZLIB_DIR)/inffast.c ZLIB_OBJ:=$(ZLIB_SRC:%.c=obj/%.o) ZLIB_DEP:=$(ZLIB_SRC:%.c=obj/%.d) SAMTOOLS_DIR:=src/external/samtools-0.1.18 SAMTOOLS_SRC:=$(SAMTOOLS_DIR)/bgzf.c \ $(SAMTOOLS_DIR)/kstring.c \ $(SAMTOOLS_DIR)/bam_aux.c \ $(SAMTOOLS_DIR)/bam.c \ $(SAMTOOLS_DIR)/bam_import.c \ $(SAMTOOLS_DIR)/sam.c \ $(SAMTOOLS_DIR)/bam_index.c \ $(SAMTOOLS_DIR)/bam_pileup.c \ $(SAMTOOLS_DIR)/bam_lpileup.c \ $(SAMTOOLS_DIR)/bam_md.c \ $(SAMTOOLS_DIR)/razf.c \ $(SAMTOOLS_DIR)/faidx.c \ $(SAMTOOLS_DIR)/bedidx.c \ $(SAMTOOLS_DIR)/knetfile.c \ $(SAMTOOLS_DIR)/bam_sort.c \ $(SAMTOOLS_DIR)/sam_header.c \ $(SAMTOOLS_DIR)/bam_reheader.c \ $(SAMTOOLS_DIR)/kprobaln.c \ $(SAMTOOLS_DIR)/bam_cat.c SAMTOOLS_OBJ:=$(SAMTOOLS_SRC:%.c=obj/%.o) SAMTOOLS_DEP:=$(SAMTOOLS_SRC:%.c=obj/%.d) # add necessary shared lib dependencies then not building them ourselves ifeq ($(useshared),yes) DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ -llua5.1-filesystem -llua5.1-des56 -lbam else DEPLIBS:= endif EXP_LDLIBS += $(DEPLIBS) GTSHAREDLIB_LIBDEP += $(DEPLIBS) SERVER=satta@genometools.org WWWBASEDIR=/var/www/servers # process arguments ifeq ($(assert),no) EXP_CPPFLAGS += -DNDEBUG endif ifeq ($(cov),yes) export CCACHE_DISABLE # ccache cannot handle coverage objects GT_CFLAGS += -fprofile-arcs -ftest-coverage GT_LDFLAGS += -fprofile-arcs -ftest-coverage STEST_FLAGS += -gcov opt=no # hacks to link shared libs with cov=yes ifeq ($(SYSTEM),Linux) GT_LDFLAGS += -fprofile-arcs -ftest-coverage endif ifeq ($(MACHINE),amd64) GT_LDFLAGS += -fPIC endif endif ifneq ($(opt),no) ifeq ($(findstring clang,$(CC)),clang) ifeq ($(lto),yes) # clang/LLVM supports link-time optimization with -O4 # Note that on Linux this usually requires additional configuration of # LLVM! Consult http://llvm.org/docs/GoldPlugin.html if problems arise. GT_CFLAGS += -O4 GT_CXXFLAGS += -O4 else GT_CFLAGS += -O3 GT_CXXFLAGS += -O3 endif else GT_CFLAGS += -O3 GT_CXXFLAGS += -O3 endif endif ifeq ($(prof),yes) GT_CFLAGS += -pg GT_LDFLAGS += -pg endif ifeq ($(curl),yes) EXP_CPPFLAGS += -DCURLDEF GT_CPPFLAGS += -I/usr/include/curl -I/usr/local/include/curl EXP_LDLIBS += -lcurl endif ifneq ($(curses),no) EXP_CPPFLAGS += -DCURSES ifeq ($(findstring CYGWIN,$(SYSTEM)),CYGWIN) EXP_CPPFLAGS += $(shell pkg-config --cflags-only-I ncurses) endif EXP_LDLIBS += -lncurses GTLIBS := lib/libtecla.a endif ifdef testthreads STEST_FLAGS += -threads $(testthreads) endif ifdef gttestdata STEST_FLAGS += -gttestdata $(gttestdata) endif ifeq ($(memcheck),yes) STEST_FLAGS += -memcheck endif # system specific stuff (concerning 64bit compilation) ifeq ($(SYSTEM),Darwin) ifeq ($(64bit),yes) m64=yes else m32=yes endif endif ifeq ($(SYSTEM),Darwin) EXT_FLAGS += -DLUA_DL_DYLD else EXT_FLAGS += -DLUA_DL_DLOPEN ifneq ($(SYSTEM),FreeBSD) LUA_LDLIB:=-ldl EXP_LDLIBS += -ldl endif endif ifeq ($(64bit),yes) ifneq ($(MACHINE),x86_64) m64=yes endif BIT=64bit SPLINTD:=-D_LP64 else ifeq ($(MACHINE),x86_64) m32=yes endif BIT=32bit endif ifeq ($(m32),yes) GT_CFLAGS += -m32 HMMER_CFLAGS += -m32 GT_LDFLAGS += -m32 SQLITE_CFLAGS += -m32 endif ifeq ($(m64),yes) ifneq ($(MACHINE),ia64) ifneq ($(MACHINE),alpha) GT_CFLAGS += -m64 HMMER_CFLAGS += -m64 GT_LDFLAGS += -m64 SQLITE_CFLAGS += -m64 endif endif endif ifeq ($(findstring clang,$(CC)),clang) # do not complain about unnecessary options GT_CFLAGS += -Qunused-arguments -Wno-parentheses GT_CPPFLAGS += -Qunused-arguments -Wno-parentheses endif ifneq ($(sharedlib),no) SHARED_LIBGENOMETOOLS := lib/libgenometools$(SHARED_OBJ_NAME_EXT) endif LIBGENOMETOOLS_DIRS:= src/core \ src/extended \ src/gtlua \ src/match \ src/gth \ src/mgth \ src/ltr ifeq ($(with-hmmer),yes) LIBGENOMETOOLS_DIRS := src/external/hmmer-3.0 $(LIBGENOMETOOLS_DIRS) EXP_CPPFLAGS += -DHAVE_HMMER GT_CPPFLAGS += -I$(CURDIR)/$(HMMER_DIR) -I$(CURDIR)/$(EASEL_DIR) STEST_FLAGS += -hmmer HMMERADDTARGET = hmmerlibs endif ifneq ($(cairo),no) ifeq ($(SYSTEM),Darwin) EXP_LDFLAGS:= endif ifeq ($(HAS_PKGCONFIG),yes) GTSHAREDLIB_LIBDEP:= $(GTSHAREDLIB_LIBDEP) \ $(shell pkg-config --libs pango) \ $(shell pkg-config --libs cairo) \ $(shell pkg-config --libs pangocairo) EXP_LDLIBS:=$(EXP_LDLIBS) \ $(shell pkg-config --libs pango) \ $(shell pkg-config --libs cairo) \ $(shell pkg-config --libs pangocairo) endif ANNOTATIONSKETCH_EXAMPLES := bin/examples/sketch_constructed \ bin/examples/sketch_parsed_with_ctrack \ bin/examples/sketch_parsed_with_ordering \ bin/examples/sketch_parsed ANNOTATIONSKETCH_MANUAL := doc/manuals/annotationsketch.pdf LIBGENOMETOOLS_DIRS:=$(LIBGENOMETOOLS_DIRS) src/annotationsketch SKETCH_EXTRA_BINARIES := bin/examples/sketch_parsed \ bin/examples/sketch_constructed else EXP_CPPFLAGS += -DWITHOUT_CAIRO STEST_FLAGS += -nocairo CAIRO_FILTER_OUT:=src/gtlua/annotationsketch_lua.c \ src/gtlua/canvas_lua.c \ src/gtlua/diagram_lua.c \ src/gtlua/image_info_lua.c \ src/gtlua/layout_lua.c endif ifeq ($(threads),yes) EXP_CPPFLAGS += -DGT_THREADS_ENABLED EXP_LDLIBS += -lpthread GTSHAREDLIB_LIBDEP += -lpthread endif ifneq ($(with-sqlite),no) ifeq ($(useshared),yes) EXP_LDLIBS += -lsqlite3 GTSHAREDLIB_LIBDEP += -lsqlite3 else LIBGENOMETOOLS_DIRS := $(SQLITE3_DIR) $(LIBGENOMETOOLS_DIRS) GT_CPPFLAGS += -I$(CURDIR)/$(SQLITE3_DIR) OVERRIDELIBS += lib/libsqlite.a endif EXP_CPPFLAGS += -DHAVE_SQLITE -DSQLITE_THREADSAFE=1 EXP_LDLIBS += -lpthread ifneq ($(SYSTEM),FreeBSD) EXP_LDLIBS += -ldl endif STEST_FLAGS += -sqlite else SQLITE_FILTER_OUT:=src/extended/rdb_sqlite.c endif ifeq ($(with-mysql),yes) GTSHAREDLIB_LIBDEP:= $(GTSHAREDLIB_LIBDEP) -lmysqlclient EXP_CPPFLAGS += -DHAVE_MYSQL EXP_LDLIBS += -lmysqlclient else MYSQL_FILTER_OUT:=src/extended/rdb_mysql.c endif # the GenomeTools library LIBGENOMETOOLS_PRESRC:=$(filter-out src/ltr/pdom.c,\ $(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(wildcard $(DIR)/*.c))) # remove AnnotationSketch-only bindings LIBGENOMETOOLS_PRESRC:=$(filter-out $(CAIRO_FILTER_OUT),\ $(LIBGENOMETOOLS_PRESRC)) # remove MySQL-only files LIBGENOMETOOLS_PRESRC:=$(filter-out $(MYSQL_FILTER_OUT),\ $(LIBGENOMETOOLS_PRESRC)) # remove SQLite-only files LIBGENOMETOOLS_PRESRC:=$(filter-out $(SQLITE_FILTER_OUT),\ $(LIBGENOMETOOLS_PRESRC)) ifeq ($(amalgamation),yes) LIBGENOMETOOLS_SRC:=obj/amalgamation.c else LIBGENOMETOOLS_SRC:=$(LIBGENOMETOOLS_PRESRC) endif LIBGENOMETOOLS_OBJ:=$(LIBGENOMETOOLS_SRC:%.c=obj/%.o) LIBGENOMETOOLS_DEP:=$(LIBGENOMETOOLS_SRC:%.c=obj/%.d) ifneq ($(useshared),yes) LIBGENOMETOOLS_OBJ += $(LIBLUA_OBJ) \ $(LIBEXPAT_OBJ) \ $(SAMTOOLS_OBJ) \ $(LIBBZ2_OBJ) \ $(ZLIB_OBJ) LIBGENOMETOOLS_DEP += $(LIBLUA_DEP) \ $(LIBEXPAT_DEP) \ $(SAMTOOLS_DEP) \ $(LIBBZ2_DEP) \ $(ZLIB_DEP) endif ifneq ($(with-sqlite),no) ifneq ($(useshared),yes) LIBGENOMETOOLS_OBJ := $(LIBGENOMETOOLS_OBJ) lib/libsqlite.a endif endif ifeq ($(with-hmmer),yes) LIBGENOMETOOLS_SRC += src/ltr/pdom.c LIBGENOMETOOLS_OBJ += $(HMMER_OBJ) $(EASEL_OBJ) obj/src/ltr/pdom.o endif GT_CFLAGS_NO_WERROR:=$(GT_CFLAGS) -w ifneq ($(errorcheck),no) GT_CFLAGS += -Werror endif # set prefix for install target prefix ?= /usr/local ifdef DESTDIR prefix:=$(DESTDIR)$(prefix) endif # allow to set patch program patch ?= patch ifneq ($(useshared),yes) ADDITIONAL_BINARIES:=bin/lua else ADDITIONAL_BINARIES:= endif all: lib/libgenometools.a $(SHARED_LIBGENOMETOOLS) \ bin/skproto bin/gt bin/examples/custom_stream \ bin/examples/gff3sort bin/examples/gff3validator bin/examples/noop \ $(ANNOTATIONSKETCH_EXAMPLES) \ $(ADDITIONAL_BINARIES) lib/libexpat.a: $(LIBEXPAT_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @ar ru $@ $(LIBEXPAT_OBJ) ifdef RANLIB @$(RANLIB) $@ endif lib/libsqlite.a: $(SQLITE3_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @ar ru $@ $(SQLITE3_OBJ) ifdef RANLIB @$(RANLIB) $@ endif lib/libbz2.a: $(LIBBZ2_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @ar ru $@ $(LIBBZ2_OBJ) ifdef RANLIB @$(RANLIB) $@ endif $(HMMER_OBJ) $(EASEL_OBJ): hmmerlibs # HMMER libs must be built with -fPIC to support shared libs on AMD64 hmmerlibs: hmmer_get @echo "[build HMMER3]" @(cd $(HMMER_BASE) && CFLAGS=-O3\ -fPIC\ $(HMMER_CFLAGS) \ ./configure -q --enable-threads > /dev/null) @$(MAKE) -s -C $(HMMER_BASE) > /dev/null lib/libz.a: $(ZLIB_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @ar ru $@ $(ZLIB_OBJ) ifdef RANLIB @$(RANLIB) $@ endif lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @ar r $@ $(LIBGENOMETOOLS_OBJ) ifdef RANLIB @$(RANLIB) $@ endif ifneq ($(useshared),yes) ADDITIONAL_ZLIBS:=lib/libbz2.a lib/libz.a ADDITIONAL_SO_DEPS:=$(ADDITIONAL_ZLIBS) \ lib/libexpat.a endif lib/libgenometools$(SHARED_OBJ_NAME_EXT): obj/gt_config.h \ $(LIBGENOMETOOLS_OBJ) \ $(ADDITIONAL_SO_DEPS) \ $(ADDITIONAL_ZLIBS) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) $(LIBGENOMETOOLS_OBJ) \ -o $@ $(GTSHAREDLIB_LIBDEP) lib/libtecla.a: $(LIBTECLA_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @ar ru $@ $(LIBTECLA_OBJ) ifdef RANLIB @$(RANLIB) $@ endif define PROGRAM_template $(1): $(2) @echo "[link $$(@F)]" @test -d $$(@D) || mkdir -p $$(@D) @$$(CC) $$(EXP_LDFLAGS) $$(GT_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \ $$(filter-out $$(patsubst lib%.a,-l%,$$(notdir $$(OVERRIDELIBS))),\ $$(EXP_LDLIBS)) $$(OVERRIDELIBS) -o $$@ endef $(eval $(call PROGRAM_template, bin/skproto, $(SKPROTO_OBJ) \ lib/libgenometools.a \ $(ADDITIONAL_ZLIBS))) $(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \ lib/libgenometools.a \ $(GTLIBS) \ $(ADDITIONAL_ZLIBS))) $(eval $(call PROGRAM_template, bin/examples/custom_stream, \ obj/src/examples/custom_stream.o \ lib/libgenometools.a\ $(ADDITIONAL_ZLIBS))) $(eval $(call PROGRAM_template, bin/examples/gff3sort, \ obj/src/examples/gff3sort.o \ lib/libgenometools.a \ $(ADDITIONAL_ZLIBS))) $(eval $(call PROGRAM_template, bin/examples/gff3validator, \ obj/src/examples/gff3validator.o \ lib/libgenometools.a \ $(ADDITIONAL_ZLIBS))) $(eval $(call PROGRAM_template, bin/examples/noop, \ obj/src/examples/noop.o \ lib/libgenometools.a \ $(ADDITIONAL_ZLIBS))) $(eval $(call PROGRAM_template, bin/examples/sketch_constructed, \ obj/src/examples/sketch_constructed.o \ lib/libgenometools.a \ $(ADDITIONAL_ZLIBS))) $(eval $(call PROGRAM_template, bin/examples/sketch_parsed, \ obj/src/examples/sketch_parsed.o \ lib/libgenometools.a \ $(ADDITIONAL_ZLIBS))) $(eval $(call PROGRAM_template, bin/examples/sketch_parsed_with_ctrack, \ obj/src/examples/sketch_parsed_with_ctrack.o \ lib/libgenometools.a \ $(ADDITIONAL_ZLIBS))) $(eval $(call PROGRAM_template, bin/examples/sketch_parsed_with_ordering, \ obj/src/examples/sketch_parsed_with_ordering.o \ lib/libgenometools.a \ $(ADDITIONAL_ZLIBS))) bin/lua: $(LUAMAIN_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $^ -lm $(LUA_LDLIB) -o $@ obj/gt_config.h: VERSION @echo '[create $@]' @test -d $(@D) || mkdir -p $(@D) @(echo '#ifndef GT_CONFIG_H' ;\ echo '#define GT_CONFIG_H' ;\ echo '#define GT_BUILT $(BUILDSTAMP)' ;\ echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\ echo '#define GT_CFLAGS "$(EXP_CFLAGS) $(GT_CFLAGS)"' ;\ echo '$(EXP_CPPFLAGS) $(GT_CPPFLAGS)' | \ sed -e 's/\([^\]\)"/\1\\"/g' -e 's/^"/\\"/g' -e 's/$$/"/' \ -e 's/^/#define GT_CPPFLAGS "/'; \ echo '#define GT_VERSION "'`cat VERSION`\" ) > $@ @cat VERSION | \ sed 's/\([0-9]*\)\.[0-9]*\.[0-9]*/#define GT_MAJOR_VERSION \1/' >> $@ @cat VERSION | \ sed 's/[0-9]*\.\([0-9]*\)\.[0-9]*/#define GT_MINOR_VERSION \1/' >> $@ @cat VERSION | \ sed 's/[0-9]*\.[0-9]*\.\([0-9]*\)/#define GT_MICRO_VERSION \1/' >> $@ @echo '#endif' >> $@ obj/amalgamation.c: $(LIBGENOMETOOLS_PRESRC) @echo '[create $@]' @test -d $(@D) || mkdir -p $(@D) @scripts/create_amalgamation $(LIBGENOMETOOLS_PRESRC) > $@ bitpackstringop_Dependencies=src/core/bitpackstringop.template \ src/core/bitpackstringvectorreadop.gen \ src/core/bitpackstringvectorwriteop.gen \ scripts/template2c.pl src/core/bitpackstringop8.c: $(bitpackstringop_Dependencies) @echo '[rebuild $@]' @scripts/template2c.pl 8 $< src/core/checkbitpackstring8.c: \ src/core/checkbitpackstring.template scripts/template2c.pl @echo '[rebuild $@]' @scripts/template2c.pl 8 $< src/core/bitpackstringop16.c: $(bitpackstringop_Dependencies) @echo '[rebuild $@]' @scripts/template2c.pl 16 $< src/core/checkbitpackstring16.c: \ src/core/checkbitpackstring.template scripts/template2c.pl @echo '[rebuild $@]' @scripts/template2c.pl 16 $< src/core/bitpackstringop32.c: $(bitpackstringop_Dependencies) @echo '[rebuild $@]' @scripts/template2c.pl 32 $< src/core/checkbitpackstring32.c: \ src/core/checkbitpackstring.template scripts/template2c.pl @echo '[rebuild $@]' @scripts/template2c.pl 32 $< src/core/bitpackstringop64.c: $(bitpackstringop_Dependencies) @echo '[rebuild $@]' @scripts/template2c.pl 64 $< src/core/checkbitpackstring64.c: \ src/core/checkbitpackstring.template scripts/template2c.pl @echo '[rebuild $@]' @scripts/template2c.pl 64 $< src/core/checkbitpackstring-int.c: \ src/core/checkbitpackstring.template scripts/template2c.pl @echo '[rebuild $@]' @scripts/template2c.pl '-int' $< # If HMMER3 SIMD support is enabled, pdom.o must be compiled with additional # compiler flags. Get these from the HMMER3 Makefile so we don't # have to repeat what autoconf did. obj/src/ltr/pdom.o: src/ltr/pdom.c $(HMMERADDTARGET) @echo "[compile $(@F)]" @test -d $(@D) || mkdir -p $(@D) @$(CC) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) $(EXP_CFLAGS) \ $(filter-out -fomit-frame-pointer, \ ${shell grep -s "CFLAGS " $(HMMER_BASE)/Makefile | cut -f 2- -d "=" }) \ ${shell grep -s "SIMDFLAGS " $(HMMER_BASE)/Makefile | cut -f 2- -d "=" } \ $(GT_CFLAGS) $(3) @$(CC) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \ $(filter-out -fomit-frame-pointer, \ ${shell grep -s "CFLAGS " $(HMMER_BASE)/Makefile | cut -f 2- -d "=" }) \ ${shell grep -s "SIMDFLAGS " $(HMMER_BASE)/Makefile | cut -f 2- -d "=" } \ $(3) -MM -MP -MT $@ # SQLite needs special attention obj/$(SQLITE3_DIR)/%.o: $(SQLITE3_DIR)/%.c @echo "[compile $(@F)]" @test -d $(@D) || mkdir -p $(@D) @$(CC) -c $< -o $@ -DHAVE_MALLOC_USABLE_SIZE $(EXP_CPPFLAGS) \ $(GT_CPPFLAGS) $(EXP_CFLAGS) $(SQLITE_CFLAGS) -DSQLITE_ENABLE_UNLOCK_NOTIFY $(3) -fPIC @$(CC) -c $< -o $(@:.o=.d) -DHAVE_MALLOC_USABLE_SIZE $(EXP_CPPFLAGS) \ $(GT_CPPFLAGS) $(3) -MM -MP -MT $@ -fPIC define COMPILE_template $(1): $(2) @echo "[compile $$(@F)]" @test -d $$(@D) || mkdir -p $$(@D) @$$(CC) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GT_CPPFLAGS) $$(EXP_CFLAGS) \ $$(GT_CFLAGS) $(3) @$$(CC) -c $$< -o $$(@:.o=.d) $$(EXP_CPPFLAGS) $$(GT_CPPFLAGS) \ $(3) -MM -MP -MT $$@ endef obj/$(SAMTOOLS_DIR)/%.o: $(SAMTOOLS_DIR)/%.c @echo "[compile $(notdir $@)]" @test -d $(@D) || mkdir -p $(@D) @$(CC) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \ $(EXP_CFLAGS) $(GT_CFLAGS_NO_WERROR) @$(CC) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GT_CPPFLAGS) -MM -MP \ -MT $@ $(eval $(call COMPILE_template, obj/%.o, %.c)) obj/%.o: %.cxx @echo "[compile $@]" @test -d $(@D) || mkdir -p $(@D) @$(CXX) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \ $(EXP_CXXFLAGS) $(GT_CXXFLAGS) @$(CXX) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GT_CPPFLAGS) -MM -MP \ -MT $@ obj/%.o: %.cpp @echo "[compile $@]" @test -d $(@D) || mkdir -p $(@D) @$(CXX) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \ $(EXP_CXXFLAGS) $(GT_CXXFLAGS) @$(CXX) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) $(GT_CPPFLAGS) -MM -MP \ -MT $@ obj/src/core/versionfunc.o: obj/gt_config.h # read dependencies -include $(GTMAIN_DEP) \ $(EXAMPLES_DEP) \ $(SKPROTO_DEP) \ $(TOOLS_DEP) \ $(LUAMAIN_DEP) \ $(LIBTECLA_DEP) \ $(LIBBZ2_DEP) \ $(HMMER_DEP) \ $(ZLIB_DEP) \ $(SAMTOOLS_DEP) \ $(LIBGENOMETOOLS_DEP) \ obj/src/examples/custom_stream.d \ obj/src/examples/gff3sort.d \ obj/src/examples/gff3validator.d \ obj/src/examples/noop.d \ obj/src/examples/sketch_constructed.d \ obj/src/examples/sketch_parsed.d .PRECIOUS: $(HMMER_DIR)/%.c .SUFFIXES: .PHONY: dist srcdist release gt install docs manuals installwww push \ splint test clean cleanup hmmer_get VERSION:="`cat $(CURDIR)/VERSION`" SYSTEMNAME:="$(SYSTEM)_$(MACHINE)" GTDISTBASENAME:="gt-$(VERSION)-$(SYSTEMNAME)-${BIT}" DISTDIR:="$(CURDIR)/dist/$(SYSTEMNAME)" SCRIPTSDIR:="$(CURDIR)/scripts" GTDISTDIR:="$(DISTDIR)/$(GTDISTBASENAME)" dist: all manuals @echo "[build distribution]" @rm -rf $(GTDISTDIR) @rm -rf $(DISTDIR)/$(GTDISTBASENAME).tar.gz @mkdir -p $(GTDISTDIR)/bin $(GTDISTDIR)/doc @cp $(CURDIR)/doc/dist_readme.txt $(GTDISTDIR)/README @cp $(CURDIR)/LICENSE $(GTDISTDIR) @cp $(CURDIR)/CONTRIBUTORS $(GTDISTDIR) @cp $(CURDIR)/CHANGELOG $(GTDISTDIR) @cp $(CURDIR)/bin/gt $(GTDISTDIR)/bin @strip $(GTDISTDIR)/bin/gt @cp $(CURDIR)/doc/manuals/*.pdf $(GTDISTDIR)/doc @cp -r $(CURDIR)/gtdata $(GTDISTDIR) @cp -r $(CURDIR)/gtpython $(GTDISTDIR) @cp -r $(CURDIR)/gtruby $(GTDISTDIR) @$(MAKE) prefix=$(GTDISTDIR) install @cd $(DISTDIR) && $(SCRIPTSDIR)/tar_root.sh $(GTDISTBASENAME) @cd $(DISTDIR) && gzip -f -9 $(GTDISTBASENAME).tar @echo "$(DISTDIR)/$(GTDISTBASENAME).tar.gz" srcdist: git archive --format=tar --prefix=genometools-`cat VERSION`/ HEAD | \ gzip -9 > genometools-`cat VERSION`.tar.gz release: git tag "v`cat VERSION`" git archive --format=tar --prefix="genometools-`cat VERSION`"/ HEAD | \ gzip -9 > genometools-`cat VERSION`.tar.gz scp "genometools-`cat VERSION`.tar.gz" $(SERVER):$(WWWBASEDIR)/genometools.org/htdocs/pub git push --tags origin master git push --tags github master docs: bin/gt $(SKETCH_EXTRA_BINARIES) bin/gt gtscripts/gtdoc.lua -html $(CURDIR) \ > www/genometools.org/htdocs/libgenometools.html bin/gt gtscripts/gtdoc.lua -lua -html $(CURDIR) \ > www/genometools.org/htdocs/docs.html ifdef SKETCH_EXTRA_BINARIES bin/examples/sketch_parsed gtdata/sketch/default.style \ www/genometools.org/htdocs/images/parsed.png \ testdata/eden.gff3 bin/examples/sketch_parsed \ www/genometools.org/htdocs/annotationsketch/callbacks.style \ www/genometools.org/htdocs/images/callbacks.png \ www/genometools.org/htdocs/annotationsketch/callback_examples_with_score.gff3 bin/examples/sketch_constructed gtdata/sketch/default.style \ www/genometools.org/htdocs/images/constructed.png endif sed -nf scripts/incl.sed \ www/genometools.org/htdocs/examples_tmpl.html | \ sed 'N;N;s/\n//' > /tmp/tmp.sed.$$$$ && \ sed -f /tmp/tmp.sed.$$$$ \ www/genometools.org/htdocs/examples_tmpl.html > \ www/genometools.org/htdocs/examples.html; rm -f /tmp/tmp.sed.$$$$ bin/gt gtscripts/gtdoc.lua -tex $(CURDIR) \ > doc/manuals/api_reference.tex bin/gt gtscripts/gtdoc.lua -lua -tex $(CURDIR) \ > doc/manuals/gtscript_reference.tex $(MAKE) -C $(CURDIR)/doc/devguide doc/manuals/annotationsketch.pdf: docs $(MAKE) -C $(CURDIR)/doc/manuals annotationsketch manuals: $(ANNOTATIONSKETCH_MANUAL) $(MAKE) -C $(CURDIR)/doc/manuals installwww: # install genometools.org website rsync -rv www/genometools.org/ $(SERVER):$(WWWBASEDIR)/genometools.org push: git push origin master git push github master gt: bin/gt install: all test -d $(prefix)/bin || mkdir -p $(prefix)/bin cp bin/gt $(prefix)/bin cp -r gtdata $(prefix)/bin test -d $(prefix)/include/genometools/core \ || mkdir -p $(prefix)/include/genometools/core cp src/core/*_api.h $(prefix)/include/genometools/core test -d $(prefix)/include/genometools/extended \ || mkdir -p $(prefix)/include/genometools/extended cp src/extended/*_api.h $(prefix)/include/genometools/extended test -d $(prefix)/include/genometools/annotationsketch \ || mkdir -p $(prefix)/include/genometools/annotationsketch cp src/annotationsketch/*_api.h \ $(prefix)/include/genometools/annotationsketch test -d $(prefix)/include/genometools/ltr \ || mkdir -p $(prefix)/include/genometools/ltr cp src/ltr/*_api.h $(prefix)/include/genometools/ltr cp obj/gt_config.h $(prefix)/include/genometools cp src/genometools.h $(prefix)/include/genometools test -d $(prefix)/lib || mkdir -p $(prefix)/lib cp lib/libgenometools.a $(prefix)/lib ifdef RANLIB $(RANLIB) $(prefix)/lib/libgenometools.a endif cp lib/libgenometools$(SHARED_OBJ_NAME_EXT) $(prefix)/lib @echo '[build config script $(@F)]' sed -e 's!@CC@!$(CC)!' -e 's!@CFLAGS@!$(EXP_CFLAGS)!' \ -e 's!@CPPFLAGS@!$(subst ",\\",-I"$(prefix)/include" $(EXP_CPPFLAGS))!' \ -e 's!@CXX@!$(CXX)!' -e 's!@CXXFLAGS@!$(EXP_CXXFLAGS)!' \ -e 's!@LDFLAGS@!-L$(prefix)/lib $(EXP_LDFLAGS)!' \ -e 's!@LIBS@!$(EXP_LDLIBS)!' -e "s!@VERSION@!`cat VERSION`!" \ -e 's!@BUILDSTAMP@!$(BUILDSTAMP)!' \ -e 's!@SYSTEM@!$(SYSTEM)!' $(prefix)/bin/genometools-config chmod 755 $(prefix)/bin/genometools-config cflags: @echo ${GT_CFLAGS} splint: obj/gt_config.h splint -f $(CURDIR)/testdata/Splintoptions $(INCLUDEOPT) \ $(CURDIR)/src/*.c \ $(CURDIR)/src/core/*.c \ $(CURDIR)/src/extended/*.c \ $(CURDIR)/src/tools/*.c EISFILES=${shell ls ${CURDIR}/src/match/*.c | grep eis-} SKTOOLS=${shell grep -l Kurtz src/tools/*.c} SKCORE=${shell grep -l 'Stefan Kurtz' src/core/*.c} DWCORE=${shell grep -l Willrodt src/core/*.c} DWTOOLS=${shell grep -l Willrodt src/tools/*.c} GGTOOLS=${shell grep -l Gonnella src/tools/*.c} SKEXT=${shell grep -l 'Stefan Kurtz' src/extended/*.c} DWEXT=${shell grep -l Willrodt src/extended/*.c} GGEXT=${shell grep -l Gonnella src/extended/*.c} ALLSPLINT=${addprefix obj/,${notdir ${subst .c,.splint,\ ${filter-out ${EISFILES},${wildcard ${CURDIR}/src/match/*.c}}\ ${wildcard ${CURDIR}/src/ltr/*.c}\ ${SKTOOLS} ${SKCORE} ${SKEXT} \ ${DWTOOLS} ${DWCORE} ${DWEXT} \ ${GGTOOLS} ${GGEXT} }}} spgt:${ALLSPLINT} scgt: src_check src/core/* src_check src/match/* src_check src/ltr/* src_check src/extended/* src_check src/tools/* splintclean: find obj -name '*.splint' | xargs rm -f obj/%.splint: ${CURDIR}/src/match/%.c @echo "splint $<" @splint $(SPLINTD) $(EXP_CFLAGS) $(INCLUDEOPT) -f $(CURDIR)/testdata/SKsplintoptions $< @touch $@ obj/%.splint: ${CURDIR}/src/tools/%.c @echo "splint $<" @splint $(SPLINTD) $(EXP_CFLAGS) $(INCLUDEOPT) -f $(CURDIR)/testdata/SKsplintoptions $< @touch $@ obj/%.splint: ${CURDIR}/src/ltr/%.c @echo "splint $<" @splint $(SPLINTD) $(EXP_CFLAGS) $(INCLUDEOPT) -f $(CURDIR)/testdata/SKsplintoptions $< @touch $@ obj/%.splint: ${CURDIR}/src/core/%.c @echo "splint $<" @splint $(SPLINTD) $(EXP_CFLAGS) $(INCLUDEOPT) -f $(CURDIR)/testdata/SKsplintoptions $< @touch $@ obj/%.splint: ${CURDIR}/src/extended/%.c @echo "splint $<" @splint $(SPLINTD) $(EXP_CFLAGS) $(INCLUDEOPT) -f $(CURDIR)/testdata/SKsplintoptions $< @touch $@ DWHEADER=${filter-out %impl.h, ${shell find ${CURDIR} -name '*.h' | \ xargs grep -l Willrodt}} ALLHEADER=${addprefix obj/,${notdir ${subst .h,.check,\ ${DWHEADER}}}} headercheck:${ALLHEADER} headerclean: find obj -name '*.check' | xargs rm -f obj/%.check: ${CURDIR}/src/match/%.h @echo "check include $<" @src_check_header.rb $< @touch $@ obj/%.check: ${CURDIR}/src/tools/%.h @echo "check include $<" @src_check_header.rb $< @touch $@ obj/%.check: ${CURDIR}/src/ltr/%.h @echo "check include $<" @src_check_header.rb $< @touch $@ obj/%.check: ${CURDIR}/src/core/%.h @echo "check include $<" @src_check_header.rb $< @touch $@ obj/%.check: ${CURDIR}/src/extended/%.h @echo "check include $<" @src_check_header.rb $< @touch $@ obj/%.prepro: ${CURDIR}/src/match/%.c @echo "[generate $@]" $(CC) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \ $(EXP_CFLAGS) $(GT_CFLAGS) -E -g3 indent $@ obj/%.prepro: ${CURDIR}/src/tools/%.c @echo "[generate $@]" $(CC) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \ $(EXP_CFLAGS) $(GT_CFLAGS) -E -g3 indent $@ obj/%.prepro: ${CURDIR}/src/core/%.c @echo "[generate $@]" $(CC) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \ $(EXP_CFLAGS) $(GT_CFLAGS) -E -g3 indent $@ obj/%.prepro: ${CURDIR}/src/extended/%.c @echo "[generate $@]" $(CC) -c $< -o $@ $(EXP_CPPFLAGS) $(GT_CPPFLAGS) \ $(EXP_CFLAGS) $(GT_CFLAGS) -E -g3 indent $@ RUBY:=ruby test: all GT_MEM_BOOKKEEPING=on bin/gt -test cd testsuite && env -i GT_MEM_BOOKKEEPING=on MAKE=$(MAKE) PATH=$(PATH) \ CCACHE_DISABLE=yes HOME=$(HOME) \ $(RUBY) -I. testsuite.rb \ -testdata $(CURDIR)/testdata -bin $(CURDIR)/bin -cur $(CURDIR) \ -gtruby $(CURDIR)/gtruby $(STEST_FLAGS) clean: rm -rf obj rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests $(MAKE) -s -C $(CURDIR)/doc/devguide clean $(MAKE) -s -C $(CURDIR)/doc/manuals cleanup test -d "$(HMMER_BASE)" && $(MAKE) -s -C $(HMMER_BASE) clean || true cleangenerated: rm -f doc/manuals/api_reference.tex \ doc/manuals/gtscript_reference.tex find doc . -name "*.toc" -delete rm -f www/genometools.org/htdocs/images/callbacks.png \ www/genometools.org/htdocs/images/parsed.png \ www/genometools.org/htdocs/images/constructed.png \ doc/manuals/annotationsketch.pdf rm -f www/genometools.org/htdocs/docs.html \ www/genometools.org/htdocs/examples.html \ www/genometools.org/htdocs/libgenometools.html gtkviewer: @echo "[compile $(notdir $@)]" @$(CC) -o bin/examples/gtkviewer $(GT_CPPFLAGS) $(GT_LDFLAGS) \ src/examples/gtkviewer.c -lcairo `pkg-config --cflags --libs gtk+-2.0` \ -lgenometools cleanup: clean cleangenerated rm -rf lib bin rm -rf gtpython/build hmmer_get: @echo "[check for HMMER3]" @test ! -f "src/external/hmmer-3.0.tar.gz" && \ cd src/external && \ echo "[retrieve HMMER3]" && \ wget -q ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-3.0.tar.gz || true @test ! -d "$(HMMER_BASE)" && \ cd src/external && \ echo "[decompress HMMER3]" && \ tar -xzf hmmer-3.0.tar.gz || true genometools-1.5.1/README000066400000000000000000000033541211610345200147310ustar00rootroot00000000000000This directory contains the source code for GenomeTools (gt). Copyright (c) 2003-2013 G. Gremme, S. Steinbiss, S. Kurtz, and CONTRIBUTORS Copyright (c) 2003-2013 Center for Bioinformatics, University of Hamburg See LICENSE file or http://genometools.org/license.html for license details. The GenomeTools genome analysis system is a collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named ``gt''. It is based on a C library named ``libgenometools''. doc/ some documentation gtdata/ data needed by gt (during runtime) gtruby/ contains GenomeTools Ruby bindings (-> gtruby/README) gtpython/ contains GenomeTools Python bindings (-> gtpython/README) gtscripts/ some GenomeTools scripts (can be executed with gt) scripts/ scripts used for development src/ the C source code for gt itself and the runtime src/annotationsketch/ the C source code for AnnotationSketch src/core/ the C source code for the ``core'' part src/examples/ the C source code for some examples src/extended/ the C source code for the ``extended'' part src/external/ all C source code from external sources src/gtlua/ the C source code for the ``gtlua'' bindings src/ltr/ the C source code for the ``ltr'' part src/match/ the C source code for the ``match'' part src/mgth/ the C source code for the ``mgth'' part src/tools/ the C source code for all tools testdata/ the test data necessary for the test suite testsuite/ the test suite www/ the web site See INSTALL file for installation guidelines. genometools-1.5.1/VERSION000066400000000000000000000000061211610345200151100ustar00rootroot000000000000001.5.1 genometools-1.5.1/doc/000077500000000000000000000000001211610345200146115ustar00rootroot00000000000000genometools-1.5.1/doc/devguide/000077500000000000000000000000001211610345200164055ustar00rootroot00000000000000genometools-1.5.1/doc/devguide/.gitignore000066400000000000000000000000151211610345200203710ustar00rootroot00000000000000devguide.pdf genometools-1.5.1/doc/devguide/Makefile000077500000000000000000000006061211610345200200520ustar00rootroot00000000000000latexfile = devguide TEX = pdflatex $(latexfile).pdf : $(latexfile).tex while ($(TEX) --shell-escape $(latexfile) ; \ grep -q "Rerun to get cross" $(latexfile).log ) do true ; \ done pdf : $(latexfile).pdf $(latexfile).ps : $(latexfile).dvi dvips -o $(latexfile).ps $(latexfile).dvi ps : $(latexfile).ps clean: rm -f $(latexfile).pdf *.aux *.ps *.dvi *.log *.out *.toc *.bak genometools-1.5.1/doc/devguide/devguide.tex000066400000000000000000002330571211610345200207350ustar00rootroot00000000000000\documentclass[11pt,final]{article} \usepackage{a4wide} \usepackage{graphicx} % figures \usepackage{listings} % source code \usepackage{hyperref} % navigation \usepackage{booktabs} \usepackage[small]{caption} \usepackage{color} \usepackage{xspace} \usepackage{mathptmx} \setcounter{tocdepth}{1} \parindent0mm % this looks better in short paragraphs \definecolor{lightgray}{rgb}{.95,.95,.95} \definecolor{middlegray}{rgb}{.55,.55,.55} \lstset{ basicstyle=\footnotesize\ttfamily, keywordstyle=\bfseries\ttfamily, commentstyle=\color{middlegray}\ttfamily, tabsize=2, numbers=none, numberstyle=\tiny, numberblanklines=false, stepnumber=1, numbersep=10pt, language=C, xleftmargin=0pt, backgroundcolor=\color{lightgray} } \newcommand{\classname}[1]{\emph{#1}} \newcommand{\keyword}[1]{\lstinline{#1}} \newcommand{\Gt}[0]{\emph{GenomeTools}\xspace} \title{The \Gt Developer's Guide} \author{Sascha Steinbiss, Gordon Gremme and Stefan Kurtz\thanks{please send comments to: \texttt{steinbiss@zbh.uni-hamburg.de}}} \begin{document} \maketitle \tableofcontents \section{Introduction} This document describes design properties and coding guidelines for the \Gt genome analysis system. The goal of the \Gt environment is to provide a well understandable, comprehensive and most importantly reusable set of classes and modules to aid in the development of C-based bioinformatics applications. The expected gain in productivity is only possible to achieve if all components of the \Gt behave in a similar way -- or so to say -- in a way which is least surprising to the user (which is, in this case, a programmer). Thus we ask all developers contributing code to the \Gt to adhere to a common set of rules which make it easier for others to reuse the products of everyone's hard work. \section{Object-oriented design} \subsection{Classes} The central component type in \Gt is the \emph{class}. Structuring the C code into classes and modules gives us a unified design approach which simplifies thinking about design issues and avoids the code base becoming monolithic, a problem often encountered in C programs. \subsubsection{Simple classes} For most classes, a simple class suffices. A simple class is a class which does not inherit from other classes and from which no other classes inherit. Using mostly simple classes avoids the problems of large class hierarchies, namely the interdependence of classes which inherit from one another. The major advantage of simple classes over simple C structs is information hiding. \subsubsection{Implementing simple classes} \label {simpleclasses} We describe now how to implement a simple class using the string class \keyword{str.[ch]} of \Gt as an example. The interface to a class is always given in the \keyword{.h} header file (\keyword{str.h} in our example). To achieve information hiding the header file cannot contain implementation details of the class. The implementation can always be found in the corresponding \keyword{.c} file (\keyword{str.c} in our example). Therefore, we start with the following C construct to define our \keyword{GtStr} class in \keyword{str.h}: \begin{lstlisting} typedef struct GtStr GtStr; \end{lstlisting} This seldomly used feature of C introduces a new data type named \classname{GtStr} which is a synonym for the \keyword{struct GtStr} data type, which needs not to be known at this point. In the scope of the header file, the new data type \keyword{GtStr} cannot be used, since its size is unknown to the compiler at this point. Nevertheless, pointers of type \keyword{GtStr} can still be defined, because in C all pointers have the same size, regardless of their type. Using this fact, we can declare a constructor function: \begin{lstlisting} GtStr* gt_str_new(void); \end{lstlisting} which returns a new string object, and a destructor function \begin{lstlisting} void gt_str_delete(GtStr*); \end{lstlisting} which destroys a given string object. This gives us the basic structure of the string class header file: A new data type (which represents the class and its objects), a constructor function, and a destructor function. \begin{lstlisting} #ifndef STR_H #define STR_H /* the string class, string objects are strings which grow on demand */ typedef struct GtStr GtStr; GtStr* gt_str_new(void); void gt_str_delete(GtStr*); #endif \end{lstlisting} Now we look at the implementation side of the story, which can be found in the \keyword{str.c} file. At first, we include the \keyword{str.h} header file to make sure that the newly defined data type is known: \begin{lstlisting} #include "str.h" \end{lstlisting} Then we define \keyword{struct GtStr} which contains the actual data of a string object (the \emph{member variables} in object orientation lingo). \begin{lstlisting} struct GtStr { char *cstr; /* the actual string (always '\0' terminated) */ unsigned long length; /* currently used length (without trailing '\0') */ size_t allocated; /* currently allocated memory */ }; \end{lstlisting} Finally, we code the constructor \begin{lstlisting} GtStr* gt_str_new(void) { GtStr *s = gt_malloc(sizeof (GtStr)); /* create new string object */ s->cstr = gt_calloc(1, sizeof (char)); /* init the string with '\0' */ s->length = 0; /* set the initial length */ s->allocated = 1; /* set the initially allocated space */ return s; /* return the new string object */ } \end{lstlisting} and the destructor \begin{lstlisting} void gt_str_delete(GtStr *s) { if (!s) return; /* return without action if 's' is NULL */ gt_free(s->cstr); /* free the stored the C string */ gt_free(s); /* free the actual string object */ } \end{lstlisting} Our string class implementation so far looks like this \begin{lstlisting} #include "core/ma.h" #include "core/str.h" struct GtStr { char *cstr; /* the actual string (always '\0' terminated) */ unsigned long length; /* currently used length (without trailing '\0') */ size_t allocated; /* currently allocated memory */ }; GtStr* gt_str_new(void) { GtStr *s = gt_malloc(sizeof (GtStr)); /* create new string object */ s->cstr = gt_calloc(1, sizeof (char)); /* init the string with '\0' */ s->length = 0; /* set the initial length */ s->allocated = 1; /* set the initially allocated space */ return s; /* return the new string object */ } void gt_str_delete(GtStr *s) { if (!s) return; /* return without action if 's' is NULL */ gt_free(s->cstr); /* free the stored the C string */ gt_free(s); /* free the actual string object */ } \end{lstlisting} Since this string objects are pretty much useless so far, we define a couple more (object) methods in the header file \keyword{str.h} and the respective implementations in \keyword{str.c}. Because C does not allow the traditional \keyword{object.methodname()} syntax often used in object-oriented programming, we use the convention to pass the object always as the first argument to the function (\keyword{methodname(object, ...)}). To make it clear that a function is a method of a particular class \emph{classname}, we prefix the method name with \keyword{gt__}. That is, we get \keyword{gt__methodname(object, ...)} as the generic form of method names in C. The constructor is always called \keyword{gt__new()} and the destructor \keyword{gt__delete()}. See \keyword{str.c} for examples. \subsubsection{Class scaffold code generation} The boilerplate code needed to create the structure of a new class (header and C source) can be generated automatically to avoid typical copy-and-paste errors. In the \keyword{scripts/} subdirectory of the \Gt directory tree, there is a helper script to create header files and a C source file with an implementation scaffold for a given class name. Run \keyword{scripts/codegen help} to get more information about its usage. \subsection{Interfaces} Interfaces allow several classes with possibly different implementations to share a common set of methods that can be called independently of the actual implementing class. Each implementing class must adhere to the interface method signature (that is, the return type and the number and types of parameters) but is otherwise free to implement the method as liked. In addition to the common interface functions, a class can also have its own specific functions. To call an interface function, the object can simply be cast to the interface type, and to call an implementation-specific function, we cast it to the implementing type. The following section describes the technique used to implement interfaces in C such that objects can be cast from the interface type to the specific type without problems. Let's imagine we want an interface called \keyword{GtExample} which has a method \keyword{gt_example_run(GtExample*)}. This corresponds to the following header file \keyword{example.h} (source files are also available in the \Gt source distribution): \begin{lstlisting} #ifndef EXAMPLE_H #define EXAMPLE_H typedef struct GtExample GtExample; int gt_example_run(GtExample*); void gt_example_delete(GtExample*); #endif \end{lstlisting} Note that there is no \keyword{gt_example_new()} constructor function, as the constructors will be specific to the implementing classes. Otherwise, this header is not much different to the header files for a simple class. To make the methods implementable by more than one class, we need a \emph{class object} describing the interface-to-implementation mappings, that is, the specific functions to be called in the implementing class. This class definition is given in a \keyword{example_rep.h} header file, where ``rep'' stands for ``representation'': \begin{lstlisting} #ifndef EXAMPLE_REP_H #define EXAMPLE_REP_H #include #include "core/example.h" typedef struct GtExampleClass GtExampleClass; struct GtExampleClass { size_t size; int (*run)(GtExample*); void (*delete)(GtExample*); }; struct GtExample { const GtExampleClass *c_class; }; GtExample* gt_example_create(const GtExampleClass*); void* gt_example_cast(const GtExampleClass*, GtExample*); #endif \end{lstlisting} The \keyword{GtExampleClass} stores a function pointer to the specific function implementing the \keyword{gt_example_run()} interface method. We also define a \keyword{delete} function which is called when the implementing class needs to do additional cleanup when an object of it is deleted. Given a \keyword{GtExampleClass} filled with appropriate function pointers which match the signatures, the \keyword{gt_example_create()} function then creates an object which can be cast to both the interface type \keyword{GtExample*} as well as the implementing type. To accomplish this, the size of the implementing class is needed. The reason behind this will be explained below. Note that this header file is meant to be private, that is, it should only be included by code files which need to know about the interface-to-implementation mappings. It is then straightforward to write the \keyword{example.c} which both \begin{itemize} \item returns an object of the interface type, allocating memory to hold both a pointer to a \keyword{GtExampleClass} object (needed for calling methods in the interface context), and \item implements the interface methods by wrapping the implementation-specific function pointers given in the \keyword{GtExampleClass} object: \end{itemize} \begin{lstlisting} #include "example_rep.h" /* we need access to the class struct */ #include "core/ma.h" /* we need to allocate memory */ GtExample* gt_example_create(const GtExampleClass *ec) { GtExample *e = gt_calloc(1, ec->size); /* allocate memory */ e->c_class = ec; /* assign interface */ return e; } int gt_example_run(GtExample *e) { gt_assert(e && e->c_class && e->c_class->run); return e->c_class->run(e); /* call implementation-specific function */ } void gt_example_delete(GtExample *e) { if (!e) return; gt_assert(e && e->c_class); if (e->c_class->delete != NULL) { e->c_class->delete(e); /* delete implementation-specific members */ } gt_free(e); /* delete interface */ } \end{lstlisting} Now, let us have a look at how the implementing classes are written. Let's imagine we want class \keyword{GtExampleA} to implement the \keyword{GtExample} interface. Of course, we need a class header file \keyword{example_a.h} containing a constructor and destructor, just as described in section~\ref{simpleclasses}: \begin{lstlisting} #ifndef EXAMPLE_A_H #define EXAMPLE_A_H typedef struct GtExampleA GtExampleA; GtExample* gt_example_a_new(); #endif \end{lstlisting} An implementation of the \keyword{GtExampleA} class in the \keyword{example_a.c} source file then contains the code for the specific methods and their assignment to the interface mapping. First, we need to include the headers to be able to register our implementation-specific functions in the mapping struct: \begin{lstlisting} #include "example_a.h" #include "example_rep.h" \end{lstlisting} Then, we define our \keyword{GtExampleA} class as usual, but leave enough space for an instance of the interface class at the beginning of our definition: \begin{lstlisting} struct GtExampleA { GtExample parent_instance; unsigned long my_property; }; \end{lstlisting} By placing an instance of the interface at the beginning of our implementation, we allow the same pointer (to the beginning of the data structure) to be cast to \begin{enumerate} \item a pointer to a \keyword{GtExample} interface implementation, so it can be used safely with the \keyword{gt_example_*()} interface methods, restricting access to the interface members only, and \item a pointer to the \keyword{GtExampleA} data structure, which can safely be used with the \keyword{gt_example_a_*()} methods, ignoring the interface part and allowing access to the implementation member variables only. \end{enumerate} Figure~\ref{fig:interfacememlayout} illustrates this concept. \begin{figure} \begin{center} \includegraphics[width=.7\textwidth]{mlayout} \end{center} \caption{Memory layout used in the \keyword{GtExampleA} object starting at the memory location \keyword{e} implementing the \keyword{GtExample} interface.} \label{fig:interfacememlayout} \end{figure} In the rest of \keyword{example_a.c}, we then code our implementation of the \keyword{run} interface method: \begin{lstlisting} static int gt_example_a_run(GtExample *e) /* hidden from outside */ { GtExampleA *ea = (GtExampleA*) e; /* downcast to specific type */ printf("%lu", ea->my_property); /* run functionality */ return 0; } \end{lstlisting} Note that we cast our generic \keyword{GtExample*} pointer into a more specific \keyword{GtExampleA*} pointer. We can do this because we can now be sure that this function has been called on an object of the \keyword{GtExampleA} class. We can be sure because we have registered this method as an implementation of the \keyword{run} interface method by assigning it to the function pointer variable in the \keyword{GtExampleClass} structure: \begin{lstlisting} /* map static local method to interface */ const GtExampleClass* gt_example_a_class(void) { static const GtExampleClass ec = { sizeof (GtExampleA), gt_example_a_run, NULL }; return &ec; } \end{lstlisting} Note that we assign NULL to the \keyword{delete} function slot, because we do not allocate any memory inside the implementing class we need to free later. Have a look at the \keyword{example_b.*} files in the \Gt source distribution for an alternative implementation which allocates additional memory. We can then use the \keyword{GtExampleClass} returned by this function to write the \keyword{GtExampleA} constructor, which uses \keyword{gt_example_create()} to allocate the needed space, initializes the private members and returns the object: \begin{lstlisting} GtExample* gt_example_a_new(void) { GtExample *e = gt_example_create(gt_example_a_class()); GtExampleA *ea = (GtExampleA*) e; /* downcast to specific type */ ea->my_property = 3; /* access private implementation member */ return e; } \end{lstlisting} Now consider another implementation, \keyword{GtExampleB} which also implements this interface by creating a \keyword{GtExampleClass} with different implementation- specific function pointers (see the \keyword{example_b.*} files in the distribution). Combining these implementation with the interface headers now allows us to do the following: \begin{lstlisting} #include "example.h" /* include the interface header */ #include "example_a.h" /* include the implementation header */ #include "example_b.h" /* include another implementation header */ int main(int argc, char *argv[]) { GtExample *my_e = gt_example_a_new(); /* create GtExampleA object, but with interface type */ gt_example_run(my_e); /* call an interface method */ gt_example_delete(my_e); GtExample *my_e = gt_example_b_new(); /* create GtExampleB object, but with interface type */ gt_example_run(my_e); /* call an interface method */ gt_example_delete(my_e); return 0; } \end{lstlisting} That is, we can access two implementations via a common set of interface methods. \subsection{Modules} Modules bundle related functions which do not belong to a class. Examples: \begin{itemize} \item \keyword{dynalloc.h}, the low level module for dynamic allocation, e.g.\ used to implement arrays in \keyword{array.c} and the above-mentioned strings \item \keyword{sig.h}, bundles signal related functions (high level) \item \keyword{xansi.h}, contains wrappers for the standard ANSI C library \item \keyword{xposix.h}, contains wrappers for POSIX functions we use \end{itemize} When designing new code, it is not very often the case that one has to introduce new modules. Usually defining a new class is the better approach. \subsection{Unit tests} Classes and modules should contain a \keyword{gt__unit_test} function which performs a unit test of the class/module and returns 0 in case of success and -1 in case of failure. More information about how to write unit tests can be found in section~\ref{unittests}. \subsection{Tools} A \emph{tool} is the most high-level type of component \Gt has to offer. Tools are command line interface (CLI) applications linked into the single \keyword{gt} binary. They make use of helper classes like the \keyword{GtOptionParser} to make development of command line tools easier. Having a common interface for option parsing and error reporting ensures a consistent user experience across all \Gt tools, as they behave the same way when invoked from the command line. There are two possible code paths for defining and implementing a tool; only the newer approach will be described here. Simply put, a tool is just another object which needs to implement a special interface, providing callbacks for the \Gt runtime to call at predefined times during the tool's invocation. An example for a simple tool can be found in the \keyword{tools} subdirectory in the \keyword{gt_template.[ch]} files. First, a tool needs to define a structure to store its arguments. That is, every command line parameter needs to be represented by a member in the struct to store its value. For example, for a tool taking a boolean and a string parameter, we would need the following: \begin{lstlisting} typedef struct { bool bool_option; GtStr *str_option; } ExampleToolArguments; \end{lstlisting} The tool also requires an initializer function which prepares the argument structure for value assignment. For example, the \keyword{GtStr} in above example must be instantiated: \begin{lstlisting} static void* gt_example_tool_arguments_new(void) { ExampleToolArguments *arguments = gt_calloc(1, sizeof *arguments); arguments->str_option = gt_str_new(); return arguments; } \end{lstlisting} as well as a destructor function which deletes the argument objects, if necessary, and then frees the memory used for the argument struct: \begin{lstlisting} static void gt_example_tool_arguments_delete(void *tool_arguments) { ExampleToolArguments *arguments = tool_arguments; if (!arguments) return; gt_str_delete(arguments->str_option); gt_free(arguments); } \end{lstlisting} The argument structure is filled by an \emph{option parser}. An option parser is an object which gets passed an argument list, identifying parameter names and values and assigning them to the correct variables. It also handles the creation of a convenient help output by documenting the purpose of each option and its valid value range. See the interface documentation in \keyword{src/core/option.h} for a list of possible option types. A tool must contain a function returning an option parser object: \begin{lstlisting} static GtOptionParser* gt_example_tool_option_parser_new(void *tool_arguments) { ExampleToolArguments *arguments = tool_arguments; GtOptionParser *op; GtOption *option; gt_assert(arguments); /* initialize with one-liner */ op = gt_option_parser_new("[option ...] [file]", "This is an example tool for demonstration " "purposes."); /* -bool */ option = gt_option_new_bool("bool", "this is the boolean option", &arguments->bool_option, false); /* default value */ gt_option_parser_add_option(op, option); /* -string */ option = gt_option_new_string("string", "pass any string here", arguments->str_option, NULL); /* default value */ gt_option_parser_add_option(op, option); return op; } \end{lstlisting} The option parser already performs initial validation of the parameters. For example, it makes sure that a numeric parameter is not given a string value, that unsigned values are always positive or that probabilities stay between 0 and 1. In an error case, tool invocation is stopped and the appropriate error message is printed to \keyword{stderr}. For more sophisticated error checking, for example involving several parameters and their values at once, is is possible to write an argument checking function, which can set an error message in a \keyword{GtError} object (see~\ref{errors}) and return a non-zero return value if an error was found: \begin{lstlisting} static int gt_example_tool_arguments_check(GT_UNUSED int rest_argc, void *tool_arguments, GT_UNUSED GtError *err) { ExampleToolArguments *arguments = tool_arguments; int had_err = 0; gt_error_check(err); gt_assert(arguments); /* we assume that the string parameter must not be empty */ if (gt_str_length(arguments->str_option) == 0) { gt_error_set(err, "parameter 'string' must not be empty!"); had_err = -1; } return had_err; } \end{lstlisting} In most cases, however, this function is not necessary and needs not be implemented. The most important function which must be implemented in a tools is the runner. The runner calls the code that actually performs the tool's function and is the equivalent to the \keyword{main} function in a traditional C program. Its signature is very similar to a typical C \keyword{main} function as well, being passed the number of arguments \keyword{argc} and an array of argument strings \keyword{argv}.: \begin{lstlisting} static int gt_example_tool_runner(int argc, const char **argv, int parsed_args, void *tool_arguments, GT_UNUSED GtError *err) \end{lstlisting} In addition, it receives the number of arguments (\keyword{parsed_args}) which were already parsed by the option parser, thus specifying an offset in the argument array from which the rest of the arguments begin. That is, if the parameter string was \begin{lstlisting} -bool true -string foo bar baz \end{lstlisting} then \keyword{parsed_args} would be 4, as the \keyword{-bool} and \keyword{-string} options and their values have already been parsed, leaving \keyword{argv[parsed_args] = 'bar'} and \keyword{argv[parsed_args+1] = 'baz'} to be handled by the runner. The rest of the runner function could look like this: \begin{lstlisting} static int gt_example_tool_runner(int argc, const char **argv, int parsed_args, void *tool_arguments, GT_UNUSED GtError *err) { ExampleToolArguments *arguments = tool_arguments; int had_err = 0; gt_error_check(err); gt_assert(arguments); if (arguments->bool_option) printf("the bool option was set\n"); printf("the string was '%s', gt_str_get(arguments->bool_option)); return had_err; } \end{lstlisting} Finally, the functions described above are registered in the new tool object by using \keyword{gt_tool_new()} to create a new \keyword{GtTool} instance passing pointers to all the static callback functions. \begin{lstlisting} GtTool* gt_example_tool(void) { return gt_tool_new(gt_example_tool_arguments_new, gt_example_tool_arguments_delete, gt_example_tool_option_parser_new, gt_example_tool_arguments_check, gt_example_tool_runner); } \end{lstlisting} Let's assume that we have saved the implementation above in \keyword{tools/gt_example_tool.c}. We then make the \keyword{gt_example_tool()} function public by adding a \keyword{tools/gt_example_tool.c} header: \begin{lstlisting} #ifndef GT_EXAMPLE_TOOL_H #define GT_EXAMPLE_TOOL_H #include "core/tool_api.h" /* the example tool */ GtTool* gt_example_tool(void); #endif \end{lstlisting} This function can then be added to the \Gt toolbox by adding the following lines to \keyword{gtt.c}: \begin{lstlisting} ... #include "tools/gt_example_tool.h" ... GtToolbox* gtt_tools(void) { ... gt_toolbox_add_tool(tools, "example", gt_example_tool()); ... } \end{lstlisting} After compilation, we can then run our tool by calling \begin{lstlisting}[language=sh] $ gt example -bool true -string foo bar baz \end{lstlisting}%$ \section{Directory structure} All of these directories are given as subdirectories of the root directory of the \Gt source distribution. \begin{itemize} \item[\texttt{bin/}] This subdirectory contains the \Gt binary executable \texttt{gt} as dynamic and static variants as well as the example executables built from \texttt{src/examples}. This directory is only populated after a make run. Running \texttt{make cleanup} will remove its contents. \item[\texttt{doc/}] This subdirectory contains documentation such as this developer's guide, license information, format specifications, and the user manuals for the software tools included with the \Gt . \item[\texttt{gtdata/}] This subdirectory contains data needed for the \Gt to run which are not compiled into the \Gt binary itself, such as \begin{itemize} \item texts for the tool on-line help (in \texttt{gtdata/doc}), \item Lua code for documentation generation (in \texttt{gtdata/modules}), \item ontology definition files (in \texttt{gtdata/obo\_files}), \item \emph{AnnotationSketch} default (e.g.\ a default style file, in \texttt{gtdata/sketch}), and \item alphabet definition files for character mappings (in \texttt{gtdata/trans}). \end{itemize} \item[\texttt{gtpython/}] This subdirectory contains the Python bindings to selected parts of the \Gt library, as well as the Python test suite. See the \texttt{README} file in this directory for installation instructions. \item[\texttt{gtruby/}] This subdirectory contains the Ruby bindings to selected parts of the \Gt library. See the \texttt{README} file in this directory for installation instructions. \item[\texttt{gtscripts/}] This subdirectory contains a number of Lua scripts written using the \Gt Lua bindings; most prominently the \texttt{gtdoc.lua} script to generate the documentation. These scripts can be run using the \texttt{gt} executable, which is a Lua interpreter as well, by giving the script name instead of a tool name. \item[\texttt{lib/}] This subdirectory contains the \Gt static and dynamic libraries when built. \item[\texttt{obj/}] This subdirectory contains object files as they are created during \Gt compilation. \item[\texttt{scripts/}] This subdirectory contains useful scripts for \Gt developers. \item[\texttt{src/}] This subdirectory contains the main \Gt source tree. In particular, there is a number of subdirectories: \begin{itemize} \item the \texttt{src/annotationsketch} subdir contains \emph{AnnotationSketch} code for genome annotation drawing, \item the \texttt{src/core} subdir contains general code, i.e.\ basic data structures, memory management, file access, encoded sequences, sequence parsers, tool runtime, option parser, multithreading, etc., \item the \texttt{src/examples} subdir contains simple example applications built on \Gt (streams, or a GUI app), \item the \texttt{src/extended} subdir contain code for annotation handling and parsing, stream processing, alignment, chaining, etc., \item the \texttt{src/external} subdir contains third-party source code which is distributed with the \Gt source and built alongside the \Gt , \item the \texttt{src/gth} subdir with \emph{GenomeThreader} code, \item the \texttt{src/gtlua} subdir with Lua bindings for some of the \Gt classes and modules, \item the \texttt{src/ltr} subdir with LTR retrotransposon prediction and annotation code, \item the \texttt{src/match} subdir with code for index structure construction and access, short read mapping, matching algorithms etc., \item the \texttt{src/mgth} subdir contains \emph{MetaGenomeThreader} code, \item the \texttt{src/patches} subdirectory with platform-specific patches, and \item the \texttt{tools} subdir with code for all the tools included with \Gt . \end{itemize} \item[\texttt{testdata/}] This subdirectory contains test data used in the testsuite. Please refrain from storing large files ($>1$MB) in this directory, but use the \keyword{gttestdata} repo instead (see~\ref{gttestdata}). Special subdirectories: \begin{itemize} \item The \texttt{testdata/gtscripts} subdir contains test scripts used in the Lua test cases, \item the \texttt{testdata/gtruby} subdir contains test scripts used in the Ruby test cases, and \item the \texttt{testdata/gtpython} subdir contains test scripts used in the Python test cases. \end{itemize} \item[\texttt{testsuite/}] This subdirectory contains the test suite definitions as Ruby files as well as the test engine and temporary data created using test runs. After starting a test suite run, the \keyword{testsuite/stest_testsuite} subdirectory then contains a directory named \keyword{test} for each test, where \keyword{} is the test number. See~\ref{testdefinitions} for more details. \item[\texttt{www/}] This subdirectory contains the content of the \Gt website. \end{itemize} \section{Public APIs} In \Gt , we distinguish between \emph{public} and \emph{non-public} application programming interfaces (APIs). The API describes the classes and modules belonging to the \Gt and their methods and functions, in particular their signatures; that is, their name, return value, and number and types of their parameters. The public API is a subset of the \Gt library which is intended to be used by developers which do not belong to the \Gt core development team, and is fairly high-level at this point. To ensure compatibility with future versions of the \Gt library, the public API is supposed to be subject to as little change as possible. That is, interface changes should be made very sparsely, and interface design should `look forward' to make such changes unneccessary. For example, interface functions which could fail in theory should receive error handling facilities in their signature (such as a return code and a \keyword{GtError} object), even if their current (and maybe only) implementation cannot fail. This leaves room for implementations that \emph{may} fail without having to break the API when the new implementation finds its way into the \Gt . All public API functions for a given class must be declared in a prototype header file named \keyword{_api.h}. This header file must only include other public API headers. All of the public API header files are packaged to be distributed with the \Gt tarball and are installed into the given include path. That is, the functions defined in them are later accessible by including \keyword{genometools.h} only. It is important to note that all functions in the public header files must be properly documented (see section~\ref{documentation}). \section{Coding style} \subsection{General rules} \begin{itemize} \item No line in the source code must be longer than 80 characters. This allows proper formatting of the code. \item There must be not more than one consecutive empty line in the source code. \item Trailing spaces are disallowed. \item There must not be a comma at the beginning of a line. \item Unless it is at the end of a line, a comma should be followed by a space. Example: \begin{lstlisting} cmpfunc(gt_array_get(a, idx), gt_array_get(b, idx)); \end{lstlisting} instead of \begin{lstlisting} cmpfunc(gt_array_get(a,idx),gt_array_get(b,idx)); \end{lstlisting} \item The symbols `\keyword{=}', `\keyword{==}' und `\keyword{!=}' should be enclosed by spaces. That is, write \begin{lstlisting} i = 0; \end{lstlisting} instead of \begin{lstlisting} i=0; \end{lstlisting} \item There must be a space between the keywords \keyword{for}, \keyword{if}, \keyword{sizeof}, \keyword{switch}, \keyword{while} and \keyword{do} and the following parenthesis. \item The opening braces (\keyword{\{}) after the keywords \keyword{if}, \keyword{else}, \keyword{for}, \keyword{do}, and \keyword{while} should be on the same line as the keyword. \item The curly braces following an \keyword{if} or \keyword{else} expression should be omitted if the expression and the (single) following statement both fit on a single line. \item The keyword \keyword{else} should be placed on a separate line. \item Semantic blocks (statements inside loops, function definitions, etc.) must be indented by exactly two spaces w.r.t.\ the enclosing block. This explicitly means \emph{no tabs}, configure your editor! Here is an example: \begin{lstlisting} bool gt_array_equal(const GtArray *a, const GtArray *b, GtCompare cmpfunc) { unsigned long idx, size_a, size_b; int cmp; gt_assert(gt_array_elem_size(a) == gt_array_elem_size(b)); size_a = gt_array_size(a); size_b = gt_array_size(b); if (size_a < size_b) return false; if (size_a > size_b) return false; for (idx = 0; idx < size_a; idx++) { cmp = cmpfunc(gt_array_get(a, idx), gt_array_get(b, idx)); if (cmp != 0) return false; } return true; } \end{lstlisting} \item Use the \keyword{scripts/src_check} and \keyword{scripts/src_clean} scripts regularly to check your source code for style violations. \item Use the \keyword{scripts/pre-commit} git hook to automatically run a \keyword{src_check} before each commit. The commit will be canceled if errors are found.\\ To enable the git hook, copy the file \keyword{scripts/pre-commit} into the \keyword{.git/hooks} subdirectory of your \Gt repository. \item Static variables inside functions are not allowed. An exception are class structs, which must be static. \item All functions except those which should be callable publicly should be declared as \keyword{static}. All non-static functions must be documented in a header file. Think twice before making a function public. Its interface should be clean enough to be understood by someone who does not know implementation details! \item If a \Gt module or class exists for your particular need, use it instead of using more low-level means (e.g.\ try to use \keyword{GtFile} and friends for file access instead of \keyword{fopen()}/\keyword{fclose()}/\dots\ directly). Consult the documentation and the header files! \end{itemize} \subsection{Global variables} \begin{itemize} \item Generally, global variables are not allowed. \item There are exceptions in very rare cases, in which must be made sure that the content in question is initialized, synchronized for multithreaded use and properly cleaned up. Do not add global variables without talking to one of the core developers! \end{itemize} \subsection{Types} \begin{itemize} \item Use unsigned types whereever possible. We need to process large amount of data and we may need every bit to process it. \item Use \keyword{unsigned long} for sequence positions/lengths/offsets/\dots . The \keyword{unsigned long} type equals the word size on all common systems (i.e., it is 32-bit wide on 32-bit systems and 64-bit wide on 64-bit systems) which makes it ideal for most use cases. \item Use \keyword{GtStr} and \keyword{GtArray} instead of manipulating byte arrays directly if possible, especially when returning strings or item collections from a function. \end{itemize} \subsection{Naming rules} \begin{itemize} \item Class names must begin with \keyword{Gt}, e.g. \keyword{GtArray}, \keyword{GtNodeStream}. \item Class names may use camel case\footnote{\url{http://en.wikipedia.org/wiki/CamelCase}} if multiple words are required, e.g.\ \keyword{GtNodeStream}. \item Source and header files for a class must start with the class name in lowercase, without the \keyword{Gt} prefix. If camel case is used in the class name, use underscores in the respective file name, e.g.\ \keyword{GtNodeStream} $\to$ \keyword{node_stream.[ch]}. \item Variable names and function names must be all lower-case. \item Variable names and function names should use underscores to separate words (e.g. use the function name \keyword{get_first_five_chars} instead of \keyword{getfirstfivechars}). \item The names of public (i.e.\ non-static) functions must be prefixed by the string `\keyword{gt_}' to avoid namespace clashes when linking the \Gt library with third-party code. \item Class or module names must follow the `\keyword{gt_}' part in the function name. \item In method signatures, the object on which the method is called must always be the first argument of the method. That is, method \keyword{method} in class \keyword{GtClass} must be defined as: \begin{lstlisting} gt_class_method(GtClass*, ); \end{lstlisting} \end{itemize} \subsection{Copyright lines} \label{copyright} \begin{itemize} \item Every header and C source file must begin with a comment containing author and license information: \begin{lstlisting} /* Copyright (c) 2007-2010 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ \end{lstlisting} \item Each developer with substantial contributions (for example, by implementing new features, refactoring, or fixing bugs which require large rewrites) should give his/her name and email address, updating the given year ranges in the process. \item The "Center for Bioinformatics" copyright line is only required for developers employed by it, because only in this case the University gains any copyright. \end{itemize} \subsection{Header files} \begin{itemize} \item Use conditional inclusion to avoid including the same header file multiple times. Between the copyright header and the beginning of the declarations, put the following: \begin{lstlisting} #ifndef FILENAME_H #define FILENAME_H \end{lstlisting} and put an \begin{lstlisting} #endif \end{lstlisting} at the end of the header file. This causes the preprocessor to include the section between the \keyword{#ifndef} and \keyword{#endif} only once. \item The identifier to be \keyword{#define}d must be the filename of the header file in uppercase with all non-alphanumeric characters replaced by underscores. \end{itemize} \subsection{Comments and documentation} \label{documentation} \begin{itemize} \item Comments are written in plain C style (\keyword{/* ... */}). C++-style comments (\keyword{// ...}) are disallowed. \item The public API files (header files ending in \keyword{*_api.h}) are examined for automatic generation of API documentation. The following annotations are supported: \begin{itemize} \item Each type (e.g.\ class) should be directly preceded by a comment describing the purpose of the class. Example: \begin{lstlisting} /* objects are generic arrays for elements of a certain size which grow on demand. */ typedef struct GtArray GtArray; \end{lstlisting} \item Each function (method) should be directly preceded by a comment describing the purpose of the function, its preconditions, return value, and parameters. Example: \begin{lstlisting} /* Add element to . The size of must equal the given element size when the was created and is determined automatically with the operator. */ #define gt_array_add(array, elem) \ gt_array_add_elem(array, &(elem), sizeof (elem)) /* Add element with size to . must equal the given element size when the was created. Usually, this method is not used directly and the macro is used instead. */ void gt_array_add_elem(GtArray *array, void *elem, size_t size_of_elem); \end{lstlisting} \item Code keywords (parameters, class names, references to other functions) can be marked by putting them between angled brackets (\keyword{<}\dots\keyword{>}). Also, keywords can be marked as strong (bold) by putting them between three underscores (\keyword{___}\dots\keyword{___}) or emphasized (italic) by using two underscores (\keyword{__}\dots\keyword{__}). \end{itemize} \item The comment line should briefly describe \begin{itemize} \item what the method does (e.g.\ ``Calculates and returns X\dots'', ``Delivers the next element in order\dots'', ``Adds element X\dots''), \item what \emph{all} parameters are supposed to be (ideally given in the context of what the method does), \item what the return value is, \item potential side-effects, and \item if the function receives or returns a pointer, whether ownership is taken or retained for the accepted or returned memory (i.e.\ ``takes ownership of parameter X'' or ``X must be deleted by the caller''). \end{itemize} \item Do not group multiple functions beneath one comment line, even if they are largely similar and differ only in minor details. If required, repeat the comment above each function to ensure that both get an entry in the generated documentation. \item Stars (\keyword{*}) are \emph{not} to be continued on every line of the comment, as many editors like to do by default. Doing so anyway will lead to interspersed star symbols in the generated output. \item Please refrain from using other markup formats such as Doxygen or Javadoc style. It may look alright in the plain text, but will most certainly come out weird in the generated LaTeX or HTML documents. \item Use the \keyword{docs} target in the \Gt Makefile to build the API documentation, which is then found in \keyword{www/genometools.org/htdocs} subdirectory (libgenometools.html). \end{itemize} \subsection{Function pointers} \begin{itemize} \item Function pointer declarations used in public headers (e.g.\ to be used as method arguments) should always be \keyword{typedef}'ed to an identifier prefixed with \keyword{Gt}. An example: \begin{lstlisting} typedef int (*GtCompareWithData)(const void*, const void*, void *data); \end{lstlisting} The function pointer type can then be used in a sort function this way: \begin{lstlisting} void gt_qsort_r(void *a, size_t n, size_t es, void *data, GtCompareWithData cmp); \end{lstlisting} instead of: \begin{lstlisting} void gt_qsort_r(void *a, size_t n, size_t es, void *data, int (*cmp)(const void*, const void*, void *data)); \end{lstlisting} which makes the headers much harder to read. \item If callback functions need additional data to work, provide an additional \keyword{void*} pointer to pass external data to the callback function (as, for example, done with the \keyword{data} parameter in the function \keyword{gt_qsort_r()} above). Do not use global variables for that purpose! \end{itemize} \subsection{\texttt{\#define}s} \begin{itemize} \item Identifiers introduced by a \keyword{\#define} statement should be completely written in upper case letters. This also holds for the arguments of macros. \item Identifiers introduced by public \keyword{\#define}s should be prefixed with \keyword{GT_}. \item In public headers, \keyword{\#define} statements should only set constants. Macros defining code parts should only be used -- very sparingly -- locally within a class or module implementation. \end{itemize} \subsection{Information hiding} In \Gt, we try to adhere to object-oriented design guidelines. An integral part of these is the enforcement of \emph{information hiding} or \emph{encapsulation}, that is, making access to an object's internal state only possible through accessor functions. From this, it follows directly that the use of `open' structs, that is, C structures defined in public headers, is strongly discouraged! Structures (and structure member accesses) should only be implemented within a C file. This applies to both structures used to implement classes as well as structures used as auxiliary data structures. A notable exception are structs implementing classes which only act as containers, i.e.\ in which the only methods manipulating the members would be setter and getter methods (see \keyword{core/range_api.h}). However, even those structures should provide accessor, constructor and destructor methods so they can safely be created, accessed and deleted from scripting language bindings lacking support for proper C structure access. \section{Error handling} We distinguish between \emph{programming errors} and \emph{run-time errors}. Programming errors occur when the developer uses resources in an inherently erroneous way, e.g.\ passing a null pointer where a valid pointer is expected, passing incorrect length values to string comparison functions, or accessing uninitialised memory. This often happens because of incomplete documentation, or by running into ``corner cases'' which were overlooked. If undetected, they can lead to nasty bugs that are hard to track down. Other special cases are expected to come up sooner or later. For example, a user may specify a file name for input or output which is not readable or writable, or which does not exist. Typically, it is not intended to terminate program execution at that point, but to react in a graceful way (e.g.\ by creating a new file, reporting a proper error message, or asking for a different file name). These are run-time errors. \subsection{Programming errors} \begin{itemize} \item Use \keyword{gt_assert()} to check invariants in your program, that is, any conditions that you hold to be true for the following code to work properly. For example, in a function getting a pointer as a parameter which is to be dereferenced later, you should assert that the pointer is not \keyword{NULL} prior to dereferencing. Similarly, in a function that is supposed to never return a negative number, one should use \keyword{gt_assert()} to check this condition directly before the \keyword{return} statement. \item If the expression given to \keyword{gt_assert()} as a parameter evaluates to \keyword{false} (that is, 0, \keyword{false}, or \keyword{NULL}), the program will abort. \item Assertions can be disabled at compile time by passing the \keyword{assert=no} switch to the \keyword{make} call. If variables or parameters are only used in an assertion, disabling assertions may trigger this error message: \begin{lstlisting} error: unused parameter 'x' \end{lstlisting} or \begin{lstlisting} error: unused variable 'y' \end{lstlisting} Include \keyword{core/unused_api.h} and prefix the declaration of the offending identifier with \keyword{GT_UNUSED} to inform the compiler that this variable is intentionally unused. \end{itemize} \subsection{Run-time errors} \label{errors} \begin{itemize} \item Functions that are allowed to fail at run-time must return a negative error code or \texttt{NULL}. The code for successful execution should be 0 or a pointer different from \texttt{NULL}. Positive return values may be used as results. Such functions should also receive a \keyword{GtError} object as their last parameter, in order to store and propagate error messages. If a function may return an error code or \texttt{NULL}, \emph{always} check for this and handle the case accordingly. \item Use the \keyword{GtError} class (see \keyword{core/error_api.h}) for storing error messages and error status: \begin{lstlisting} char* get_first_five_chars(const char *str, GtError *err) { char *ret; if (strlen(str) < 5) { gt_error_set(err, "string '%s' is shorter than 5 characters", str); return NULL; } ret = gt_calloc(6, sizeof (char)); strncpy(ret, str, 5); return ret; } \end{lstlisting} \item Use a variable called \keyword{had_err} which is initialized to 0 and then assigned an error status such that an error is set when \keyword{had_err}$\neq 0$: \begin{lstlisting} int had_err = 0; const char *prefix; GtError *err = gt_error_new(); if ((prefix = get_first_five_chars("foo", err))) { /* go on with next step */ } else had_err = -1; if (!had_err) { ... } \end{lstlisting} \keyword{-1} should be used to store an error in the \keyword{had_err} variable. It is very idiomatic to write \keyword{if (had_err)...} or \keyword{if (!had_err)...}. \item Catch run-time errors and create error messages as close to their source as possible. \item The error object should always be the last parameter and should be named \keyword{err}. \end{itemize} \section{Memory management} \subsection{Allocation/deallocation} \begin{itemize} \item Space allocation is only allowed using the \keyword{gt_malloc()}, \keyword{gt_calloc()}, \keyword{gt_realloc()} functions in \keyword{core/ma_api.h}. Use \keyword{gt_free()} to deallocate memory. These methods are analog to \keyword{malloc(3)}, \keyword{calloc(3)} and \keyword{realloc(3)} from the C standard library, except that they never return \keyword{NULL} upon failure. \item The \keyword{gt_ma_get_space_peak()}, \keyword{gt_ma_show_space_peak()} and \keyword{gt_ma_check_space_leak()} functions in \keyword{core/ma_api.h} can be used to evaluate memory usage and check for memory leaks. \end{itemize} \subsection{Reference counting} Sometimes it is desired to have an object referenced by more than one other object, avoiding to \keyword{gt_free()} the object's memory until the last reference to the object has been dropped. In \Gt, \emph{reference counting} is used to implement this behaviour. That is, each object keeps the number of objects still keeping a reference on it in a local member variable. This is done by each referencing object calling the object's \keyword{ref()} method to announce that they now keep a reference, thus increasing the reference count. When the object reference is no longer needed, the usual \keyword{delete()} method is used. The \keyword{delete()} method checks and decreases the reference count and defers free'ing the object's memory until the object is not referenced by any other object any more. This makes reference counting a simple form of garbage collection. To add reference counting to a class, perform the following steps: \begin{itemize} \item Add an \keyword{unsigned int} counter variable called \keyword{reference_count} to the private member variables of the class; this variable must be initialized to 0 in the constructor. \item Consider a class \emph{GtFoo} to which we want to add reference counting capabilities. Then add a method \keyword{gt__ref()}, in this case \keyword{gt_foo_ref()} to the interface of the class: \begin{lstlisting} GtFoo* gt_foo_ref(GtFoo *f) { gt_assert(f); f->reference_count++; return f; } \end{lstlisting} \item In the destructor, check the reference count and only free the memory when necessary: \begin{lstlisting} void gt_foo_delete(GtFoo *f) { if (!f) return; if (f->reference_count) { f->reference_count--; return; } gt_free(f); } \end{lstlisting} \end{itemize} With reference counted classes, always use the \keyword{ref()} method when storing a reference to an object. That is, instead of writing \begin{lstlisting} void gt_bar_set_foo(GtBar *b, GtFoo *f) { b->value = f; } \end{lstlisting} use \begin{lstlisting} void gt_bar_set_foo(GtBar *b, GtFoo *f) { b->value = gt_foo_ref(f); } \end{lstlisting} Always remember to call \keyword{gt_foo_delete()} when the reference is no longer needed! For example, in the assignment above, a good place to do this is the destructor of the \keyword{GtBar} class. \subsection{Library initialization/finalization} Within the \Gt code, there are a number of global or static data which must be properly initialized before using any \Gt functionality, and space for which must be properly freed when done using the \Gt . This is usually done by the runtime by calling initializers when a tool is run using the \keyword{gt} binary. Now consider that \Gt can also be used as a library, called \keyword{libgenometools}. That means, it is possible to link an external code with the static or shared object file and call functions from there, without going through the tool runtime. It is now crucial that the necessary initializations have taken place before using functions, and that the required cleanup is done at the end. There are two functions in the \keyword{core/init.[ch]} module in \Gt used to accomplish this: \begin{itemize} \item \keyword{gt_lib_init()}, which initializes all static data and should be called before any other \Gt function, and \item \keyword{gt_lib_clean()}, which frees all static data. It returns 0 if no memory map, file pointer, or memory has been leaked and a value other than 0 otherwise. \end{itemize} It is also possible to make the cleanup happen automatically when the program using the library exits. This is done by calling \keyword{gt_lib_reg_atexit_func()} which registers an exit handler with the OS which will call \keyword{gt_lib_clean()} automatically. \section{Threads} The \Gt contain functions allowing developers to write their programs in a multi-threaded way, by wrapping the POSIX threads library \keyword{libpthread}. See \keyword{core/thread\_api.h} for more information. Any function with this signature: \begin{lstlisting} void* (*GtThreadFunc)(void *data); \end{lstlisting} can be enabled to be run concurrently by simply calling \begin{lstlisting} void *mythread(void *data) { ... } gt_multithread(mythread, NULL, err); \end{lstlisting} Some more useful information: \begin{itemize} \item For synchronization during parallel execution of multiple threads, \Gt provides classes for mutexes and read-write-locks. See \keyword{core/thread\_api.h} for a description of the interface of the \keyword{GtMutex} and \keyword{GtRWLock} classes. \item If code must be conditionally compiled depending on thread support, use \keyword{#ifdef} and friends with the \keyword{GT_THREADS_ENABLED} flag, which is set by the compiler via a \keyword{-D} option when threading support is enabled. \item Threading support is enabled at compile time by passing \keyword{threads=yes} to the \keyword{make} call. If threading support is not enabled, all \keyword{gt_multithread()} functions will run the thread function sequentially. \item If threading support is enabled, the number of concurrent jobs can be given using the \keyword{-j} parameter to the \keyword{gt} binary. That is, to have all multithreaded parts in the tool to be run use three threads at once, call the tool with \begin{lstlisting} $ gt -j 3 ... \end{lstlisting}%$ \end{itemize} \section{Testing and Debugging} \subsection{Testing on the code level -- the unit tests} \label{unittests} Unit test check whether classes and their methods behave correctly when used in a correct manner. The corresponding functions must be defined in the class implementation file (so they get access to the private member variables of the tested class) and adhere to the following interface: \begin{lstlisting} int (*UnitTestFunc)(GtError *err); \end{lstlisting} They must return 0 if the test was successful and -1 if the test has failed. The \keyword{gt_ensure} helper macro makes writing unit tests easier. To use it, \keyword{#include} the file \keyword{core/ensure.h}. Then write your unit test: \begin{lstlisting} int gt_class_unit_test(GtError *err) /* must be called 'err'! */ { int had_err = 0; gt_error_check(err); /* will abort if error was already set */ gt_ensure(had_err, 1 + 1 == 2); /* will succeed */ gt_ensure(had_err, 1 + 1 == 3); /* will fail */ return had_err; } \end{lstlisting} Similarly to \keyword{gt_assert()}, if the expression given to \keyword{gt_ensure()} as a second parameter evaluates to false, the test will fail with an error message, giving the location at which the first condition failed. Because \keyword{gt_ensure()} is implemented as a macro relying on certain naming conventions, it is mandatory that the \keyword{GtError} object passed to the test function is called \keyword{err}. The unit tests are added to the test suite in the function \keyword{gtt_unit_tests()} in \keyword{gtt.c} and loaded into the \Gt runtime in the function \keyword{gtr_register_components()} in \keyword{gtr.c}. That is, if your unit test function is \keyword{gt_class_unit_test()}, then you should \keyword{#include} the header \keyword{class.h} (which contains the function prototype) in \keyword{gtt.c} and add the following line in \keyword{gtt_unit_tests()}: \begin{lstlisting} gt_hashmap_add(unit_tests, "example class", gt_class_unit_test); \end{lstlisting} The tests registered in this hash table can be executed on the command line with: \begin{lstlisting}[language=sh] $ gt -test \end{lstlisting}%$ It is also possible to run a single test from the test suite by using the \keyword{-only} option: \begin{lstlisting}[language=sh] $ gt -test -only 'example class' \end{lstlisting}%$ \subsection{Testing on the tool level -- the test suite} While the unit tests check the correctness of the classes and modules on the code level, the Ruby-based test suite is used to run tests on the tools themselves. That means that they run tools with example data or invalid parameters and check whether they behave correctly by looking at error levels, error messages, and comparing output with reference data. Test data and reference data are stored in the \keyword{testdata/} directory of the \Gt source tree. Note that this directory is for smaller test data only. Large files, such as whole chromosome annotations go into another repository (see~\ref{gttestdata}). \subsubsection{Test definitions} \label{testdefinitions} Tests are defined in the \keyword{gt__include.rb} files in the \keyword{testsuite/} directory. They contain test definitions written in a Ruby-based domain specific language. Here is an example of a simple test: \begin{lstlisting}[language=Ruby] Name "gt cds test (description range)" Keywords "gt_cds usedesc" Test do run_test "#{$bin}gt cds -usedesc -seqfile " + "#{$testdata}gt_cds_test_descrange.fas " + "#{$testdata}gt_cds_test_descrange.in" run "diff #{$last_stdout} #{$testdata}/gt_cds_test_descrange.out" end \end{lstlisting}%$ This test runs the \keyword{gt cds} command with example data and compares its output on stdout with a reference file. Every test case must have a \keyword{name} and can have a set of \emph{keywords} associated with it, allowing for selective running of a subset of tests from all testsuites. Keywords are separated by spaces. The actual test code is given in the \keyword{Test} environment. Within this environment, one may use the following constructs to define test conditions: \begin{itemize} \item \keyword{run_test(runstring, options)}, where \begin{itemize} \item \keyword{runstring} is the tool commandline to run, and \item \keyword{options} are a hash specifying test constraints. The key \keyword{:retval} specifies the expected error code for this run (0 is the default). The option \keyword{:maxtime} specifies the maximal time in seconds that the started program may run before it is killed, resulting in a failed test (60 is the default). This allows one to detect infinite loops without stopping the testing progress. \end{itemize} This command runs the command specified in \keyword{runstring}, and causes the test to fail if the returned error code does not equal the expected one. \item \keyword{grep(file, pattern)} which searches for \keyword{pattern} in the file \keyword{file}, failing the test if there is no match. The pattern can be given as a regular expression. \item \keyword{run_ruby(rubyscript, options)} and \keyword{run_python(pythonscript, options)} can be used to run tests on external Ruby and Python scripts. \item Any Ruby code, such as custom functions, can be run inside the \keyword{Test} environment. To fail a test case manually, use the \keyword{failtest(msg)} command, where \keyword{msg} is the error message to fail with. \end{itemize} Inside test suite definitions, some useful paths are predefined to be conveniently used in test runs (like \keyword{$bin} and \keyword{$testdata} in the example above): \begin{itemize} \item \keyword{$testdata}, the path to the \keyword{testdata/} directory, \item \keyword{$gttestdata}, the path to the location of the \keyword{gttestdata} repository (see~\ref{gttestdata}), \item \keyword{$bin}, the path to the \Gt \keyword{bin/} directory, \item \keyword{$cur}, the path to the current test case directory (each test is run in a separate directory), \item \keyword{$transdir}, the path to the \keyword{gtdata/trans} directory, \item \keyword{$obodir}, the path to the \keyword{gtdata/obo_files} directory, \item \keyword{$gtruby}, the path to the \keyword{gtruby/} directory, \item \keyword{$gtpython}, the path to the \keyword{gtpython/} directory, \end{itemize} It is also possible to get the standard output and standard error contents of the last command run by referring to the files specified by \keyword{$last_stdout} and \keyword{$last_stderr}. Furthermore, each test commandline (let's say the $i$-th one in the test) creates a set of \keyword{run_}$i$ (contains the actual command which was run), \keyword{stdout_}$i$ (contains the standard output) an \keyword{stderr_}$i$ (contains the standard error output) files in the test directory (which is \keyword{testsuite/stest_testsuite/test}$n$\keyword{/}, where $n$ is the test number (printed in front of each test name). \subsubsection{The \keyword{gttestdata} repository} \label{gttestdata} Large test or reference data must not be placed into the \Gt \keyword{testdata/} directory because they would increase the size of the \Gt distribution too much. For such data there is a separate repository, which is available via Git: \begin{lstlisting}[language=sh] $ git clone git://genometools.org/gttestdata.git \end{lstlisting}%$ The location of the \keyword{gttestdata} repository must be given when running the testsuite (see below). If it is not given, make sure that test which depend on large test data are disabled (e.g. by placing them in an `\keyword{if $gttestdata}' clause).%$ \subsubsection{Running the testsuite} A comprehensive \Gt test run, containing both the unit tests and the tool tests, can be initiated by issuing \keyword{make test} in the \Gt directory. The following \keyword{make} switches influence the test runs: \begin{itemize} \item \keyword{memcheck=yes} enables memory access checking via \emph{valgrind}, \item \keyword{testthreads=} enables multithreaded testing with \keyword{} threads in parallel to speed up test runs, \item \keyword{gttestdata=} tells the test suite to look for large test data in \keyword{}. This must be where a copy of the \keyword{gttestdata} repository is installed. \end{itemize} The tool tests can also be run using the \keyword{testsuite/testsuite.rb} script. Use the \keyword{-keywords } parameter to only run these tests tagged with the given keywords. OR and AND operators can be used to specify the tests in a more detailed way. The \keyword{-select } parameter can be used to run only the one test with number \keyword{n}, and the \keyword{-threads } will run the testsuite with \keyword{n} threads in parallel. \subsection{Header inclusion dependencies} Often function prototypes in the \Gt header files use types declared in another header files. By mistake, it is possible to forget \keyword{#include}'ing the header files where the type is defined in the header using it. Note that this problem may never surface if the forgotten header is included in every C source file which includes the header file with the missing include statement. To address this, the script \keyword{scripts/src_check_header.rb} tries to include each header file given as a command line argument by itself in a C file and compile it. If dependencies are missing, the check will abort and output the compiler error message so the problem can be fixed. \subsection{Debug symbols} Compilation with debug symbols is enabled by default. To make sure that line numbers are correct when using a debugger, e.g. \keyword{gdb}, use the \keyword{opt=no} option in the \keyword{make} call to disable compile-time optimization. The \keyword{opt} option is enabled by default. \subsection{Profiling} To enable the generation of profiling output in the compiled binaries, use the \keyword{prof=yes} option in the \keyword{make} call. The \keyword{prof} option is disabled by default. Enabling this option makes the \Gt binary create a \keyword{gmon.out} file during each run, which can then be used for analysis using \emph{gprof}\footnote{See \url{http://sourceware.org/binutils/docs/gprof/index.html} for further information.}. \subsection{Logging} Use the \keyword{gt_log_*()} functions in \keyword{core/log_api.h} to log debug messages to the screen or files. Output of debugging information defined using these functions can then be enabled or disabled via the \keyword{-debug} option of the \keyword{gt} binary. That is, to run tool \keyword{mytool} with debug output enabled, run \begin{lstlisting} $ gt -debug mytool \end{lstlisting}%$ \section{Additional \keyword{make} parameters} \subsection{Additional targets} Simply running \emph{make} builds both the \keyword{gt} executable and the \Gt shared library. However, there are also other targets (besides the ones mentioned in the respective sections above) which can be built using the \Gt Makefile: \begin{itemize} \item \keyword{docs}, which builds API documentation as web pages in \keyword{www} and as \LaTeX\ source in \keyword{doc/}, \item \keyword{manuals}, which, in addition to the files created by \keyword{docs}, also creates manuals for some published tools in \Gt (see \keyword{doc/manuals}), \item \keyword{install}, which installs the compiled \Gt binaries, libraries and headers into the directory specified by the \keyword{prefix=} option, \item \keyword{dist}, which creates a tarball with a binary \Gt distribution, which will then reside in the \keyword{dist/} subdirectory of the \Gt root, \item \keyword{srcdist}, which creates a tarball with a source \Gt distribution, which will then reside in the working directory, \item \keyword{spgt}, which checks selected files in the \keyword{core/} and \keyword{match/} subdirectories using the splint static checker\footnote{\url{http://www.splint.org}}, using the rule set \keyword{testdata/SKsplintoptions}, \item \keyword{clean}, which removes all files created during the build and test processes, except the \keyword{lib} and \keyword{bin} directories, and \item \keyword{cleanup}, which even removes these. \end{itemize} \subsection{Additional options} There are additional \keyword{make} options which are also mentioned in the README file and which influence how the \Gt binaries are built: \begin{itemize} \item Use \keyword{amalgamation=yes} to compile \Gt as an \emph{amalgamation}. That means, all \Gt C source files are concatenated into a big source file, which is then compiled. This approach allows the compiler to perform more extensive optimizations during the compilation and may result in better performance. It is encouraged to check regularly whether compiling \Gt as an amalgamation still works, as name clashes in static functions can sometimes occur which compile fine when in separate files, but lead to errors in the amalgamation. This option is disabled by default. \item Use \keyword{errorcheck=no} to make the compilation process not stop when a warning is encountered. This option should only be used if necessary (e.g.\ when building \Gt on Windows). This option is enabled by default. \item Use \keyword{cairo=no} to disable Cairo support in the \emph{AnnotationSketch} component of \Gt . This is useful on systems on which there is no Cairo library present, and \emph{AnnotationSketch} is not needed. This option is enabled by default. \item The option \keyword{sharedlib=no} disables building of a \Gt shared library. This option is enabled by default. \item The option \keyword{static=yes} tries to link all dependencies of \Gt statically. This option is disabled by default. \item Use \keyword{curses=no} to disable ncurses support. Useful when there is no ncurses library on the target system. This option is enabled by default. \end{itemize} \section{Contributing code} For \Gt development, we use the distributed versioning system Git\footnote{For a good introduction to the use of the Git software itself, see the Git web site (\url{http://git-scm.com}) or read the following guide: Travis Swicegood. \emph{Pragmatic Version Control Using Git}. Pragmatic Bookshelf, ISBN 1934356158. We \emph{strongly} encourage future \Gt developers to familiarize themselves with Git before developing with the intent of submission!} to track changes and exchange new code. Thus a Git repository is necessary to both: \begin{itemize} \item obtain the latest development version of the \Gt , and \item contribute to the \Gt by submitting new code to the maintainers. \end{itemize} Be aware that, in this guide, we will not explain Git basic concepts, or how individual Git commands work in detail. Instead, we will shortly state what strategy is most effective when working in \Gt development. \subsection{Getting started} To get started with \Gt development, we recommend the following: \begin{enumerate} \item Install the Git version control system. \item Read the Git documentation. \item Clone the \Gt Git repository with: \begin{lstlisting}[language=sh] $ git clone git://genometools.org/genometools.git \end{lstlisting}%$ \item Start hacking on your own feature branch: \begin{lstlisting}[language=sh] $ cd genometools $ git checkout -b my_feature_branch_name \end{lstlisting} \item Have fun! \end{enumerate} \subsection{Basic Git configuration} Please set your username and email address correctly. If unconfigured, they are often based on the hostname of the workstation where a commit is done. This may not be -- and almost never is -- correct in typical development environments (i.e.\ \keyword{user@workstation.zbh.uni-hamburg.de} instead of \keyword{user@maildomain.org}). Use the \keyword{git config} commands while in your \Gt Git repository to set them to a correct value: \begin{lstlisting} $ git config user.name "Hans Mustermann" $ git config user.email "mustermann@maildomain.org" \end{lstlisting} \subsection{Tips for successful source management} \begin{itemize} \item Develop each major feature or try out bigger changes in a separate branch (the so-called \emph{feature branch}) dedicated only to that aspect. That makes it easier to combine or discard branches later on, without having to meddle with individual commits too much if something goes wrong. Creating, merging and deleting branches is cheap in Git! \item Always leave your \emph{master} branch untouched so code pulled from upstream (e.g.\ the official \Gt repository) does not get merged by accident. \item Branch off new feature branches from the \emph{master} branch only. That makes it easy to chain branches later via \keyword{git rebase} in any order. \item Try to keep commits atomic. Every commit should either add a single feature or fix a single bug. That makes two things easier: \begin{enumerate} \item Locating the exact commit which introduces a bug, e.g.\ using \keyword{git bisect}. If there are too many changes in one commit, bugs become more tedious to track down. \item Reverting single commits if new features introduce bugs. \end{enumerate} If you made several incomplete commits and want to reorder or combine them into one afterwards, use interactive rebasing via \keyword{git rebase -i}\footnote{See \url{http://book.git-scm.com/4_interactive_rebasing.html} for an explanation.}. \item Needless to say, every commit should compile cleanly. Again, bisecting can become very tedious if the code has to be fixed at each stop to get it to even compile. \item Try to avoid merges with upstream as much as possible to keep the history linear. Instead of merging, rebase your feature branches regularly against an updated \emph{master}: \begin{lstlisting}[language=sh] $ git branch * mybranch master $ git checkout master $ git pull origin <...> $ git checkout mybranch $ git rebase master <...> \end{lstlisting}%$ \item In the first line of the commit message, give a short description of the change contained in the commit. Please use active, present tense, e.g.\ ``add feature X'' or ``allow X to do Y''. Commit messages for commits that touch scripting language bindings should be prefixed with the language in question, e.g.\ ``gtpython: add bindings for GtFoo class''. \item For bugfixes for bugs also listed in the \Gt Lighthouse bug tracking web app\footnote{\url{http://genometools.lighthouseapp.com}}, commit messages can be used to update the ticket status. See the Lighthouse documentation\footnote{\url{http://help.lighthouseapp.com/faqs/ticket-workflow/ticket-keyword-updates}} for details. \end{itemize} \subsection{Submission of contributions} This section describes how to get your contributions noticed, reviewed and integrated into the main \Gt codebase. \subsubsection{Source code submission} To get your source code to be considered for inclusion into the \Gt official source tree, first you need a Git repository in a publicly accessible location. That may be a free public account on github (\url{http://www.github.com}, Gitorious (\url{http://gitorious.org}), etc., or a directory on a filesystem accessible by one of the core developers. Typically the \Gt maintainers pull from a branch provided in this location and specified by you. This is called a \emph{pull request}. Please specify the exact location to the repository as well as the branch name. A pull request can be sent to \centerline{\texttt{steinbiss@zbh.uni-hamburg.de}} or \centerline{\texttt{gremme@gmail.com}.} \textbf{Important:} Always rebase your feature branch against the current official \Gt master before requesting a pull (see above). Also, please check whether your code compiles cleanly, even with the \keyword{amalgamation=yes} and \keyword{assert=no} parameters enabled which may influence compilation success. Small changes can also be submitted as patches which must be applicable using \keyword{git apply}. You will then be credited in the commit message. Such patches can be created conveniently -- ready to be sent via mail -- via git only using \keyword{git format-patch} or \keyword{git diff}. \subsubsection{Test data submission} For submissions to the \keyword{gttestdata} repository, the same rules apply as for source code. Please provide a repository from which to pull a branch which has been rebased against the current \keyword{gttestdata} master before. Before adding any more test data to the repository, please make sure that the new data is absolutely necessary. That is, existing large sequence should be reused, for example when testing a sequence parser or the like. \subsubsection{Licensing} Note that the \Gt are free software, i.e.\ an open-source project. All code distributed with the \Gt is published under the ICS license, which can be viewed at \url{http://genometools.org/license.html}. Submission of code for inclusion into the \Gt implies your permission to publish your code under this license. 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Copyright (c) 2003-2013 G. Gremme, S. Steinbiss, S. Kurtz, and CONTRIBUTORS Copyright (c) 2003-2013 Center for Bioinformatics, University of Hamburg See LICENSE file or http://genometools.org/license.html for license details. The GenomeTools genome analysis system is a collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named ``gt''. It is based on a C library named ``libgenometools''. bin/ contains the binary file doc/ contains some PDF manuals include/ contains the genometools.h Header (in the genometools/ subdirectory) gtdata/ data needed by gt (during runtime) gtruby/ contains GenomeTools Ruby bindings (-> gtruby/README) gtpython/ contains GenomeTools Python bindings (-> gtpython/README) lib/ contains the libgenometools (as static and shared library) The GenomeTools source code can be downloaded from http://genometools.org For the ``gt'' binary an additional statically linked binary with the same name is contained in the directory bin/static/ (except for Mac OS X). Please try it, if the dynamically linked binary does not work on your system. genometools-1.5.1/doc/lgpl.txt000066400000000000000000000635041211610345200163200ustar00rootroot00000000000000 GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999 Copyright (C) 1991, 1999 Free Software Foundation, Inc. 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. [This is the first released version of the Lesser GPL. It also counts as the successor of the GNU Library Public License, version 2, hence the version number 2.1.] Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public Licenses are intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This license, the Lesser General Public License, applies to some specially designated software packages--typically libraries--of the Free Software Foundation and other authors who decide to use it. You can use it too, but we suggest you first think carefully about whether this license or the ordinary General Public License is the better strategy to use in any particular case, based on the explanations below. When we speak of free software, we are referring to freedom of use, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish); that you receive source code or can get it if you want it; that you can change the software and use pieces of it in new free programs; and that you are informed that you can do these things. To protect your rights, we need to make restrictions that forbid distributors to deny you these rights or to ask you to surrender these rights. 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To apply these terms, attach the following notices to the library. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Also add information on how to contact you by electronic and paper mail. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the library, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the library `Frob' (a library for tweaking knobs) written by James Random Hacker. , 1 April 1990 Ty Coon, President of Vice That's all there is to it! genometools-1.5.1/doc/license.template000066400000000000000000000022561211610345200177750ustar00rootroot00000000000000Below is an example license to be used for new code in GenomeTools, modeled after the ISC license. It is important to specify the year of the copyright. Additional years should be added with a dash, if possible (i.e., if the corresponding years are continuous), e.g., Copyright (c) 2003-2007 or with a comma, if not possible (i.e., if the corresponding years are not continuous), e.g., Copyright (c) 2003, 2007 /* Copyright (c) CCYY YOUR NAME HERE Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ genometools-1.5.1/doc/manuals/000077500000000000000000000000001211610345200162515ustar00rootroot00000000000000genometools-1.5.1/doc/manuals/.gitignore000066400000000000000000000002031211610345200202340ustar00rootroot00000000000000comment.cut *.pdf api_reference.tex gtscript_reference.tex U89959.fna read1.fna read2.fna tallymer-tmp.tex Q1.gz tagerator-tmp.tex genometools-1.5.1/doc/manuals/.ispell_american000066400000000000000000000022421211610345200214010ustar00rootroot00000000000000Arabidopsis BAC Bioinformatics FMindex Hamburg Kurtz Stefan acagttttttttttttacttta agttttttttttttactttat al bdx bsize cagttttttttttttactttat chromomsomes ctgacagtttttttttttta db dir dna ensembl esa fasta fmi fna genome gistaff gt gttttttttttttactttata gz gzipped indexname kurtz lh locfreq ls min mitrochondrial mkindex mup org packedindex pck prj queryfile querypos rev rw sapiens thaliana uniquesub AboutMatstat AboutUniquesub Mus actgtatctcaaaatataaa chr gcttgaagatcatgatccag ggaataaacatgtcattgag gggaataaacatgtcattgag matstat ms musculus subjectpos taattctatttttctttctt aagcttgctgctgca cdiff gcttgctg gcttgctgctgca maxocc nospecials pdiff sprank tagerator nowildcards BMC Genomics KUR NER Narechania STE TODO Tallymer Vmatch fp genomes genometools http idxname lcp maxmersize mbd mct mers mersize mersizes minmersize minocc nonunique nonuniquemulti occratio pl prefixlength preprocess qpos qseqnum queryfiles suf suffixerator tallymer tis tyr abspos dblength dbsequence dbstartpos edist nop ssp taglength tagnum tagseq tagstartpos tagsuffixseq withwildcards Choudhuri Embl Genbank genomic Giegerich hamburg IUB len Ohlebusch relpos repfind repidx REPuter seqnum Stoye Swissprot zbh genometools-1.5.1/doc/manuals/.ispell_british000066400000000000000000000016121211610345200212660ustar00rootroot00000000000000Abouelhoda AKO al allout analyzed args ataat Bioinformatics Boeke ca Center cerevisiae chr chrAll dbcluster del deletionscore des dna EKW Ellinghaus exdrop expr FASTA fsa gaaat genometools GenomeTools genomic gff GFF ggaat ggttc Gremme gt gtaat gttat gz gzip htbp http indexname insertionscore kim Kurtz lcp lLTR longoutput LTR ltrharvest LTRharvest LTRs matchscore maxdistltr maxlenltr maxLTRdistance maxLTRlength maxtsd maxTSDlength mindistltr minlenltr minLTRdistance minLTRlength minseedlength mintsd minTSDlength mis mismatchscore mkvtree motifmis motifmismatchesallowed novo nr nt Ohlebusch org outinner outputfile pl pred resultfile retrotransposon retrotransposons rLTR seedlength sequenceontology shtml sim similaritythreshold singlets stdout suf suffixerator Suffixerator tg tgca tis TSD TSDmaxlen TSDminlen TSDs Vanguri verbosemode vmatch Vmatch Voytas Willhoeft www xdrop Xdrop xdropbelowscore genometools-1.5.1/doc/manuals/Makefile000066400000000000000000000044221211610345200177130ustar00rootroot00000000000000ALL=readjoiner.pdf\ hop.pdf\ ltrharvest.pdf\ ltrdigest.pdf\ uniquesub.pdf\ matstat.pdf\ mgth.pdf\ packedindex.pdf\ repfind.pdf\ tallymer.pdf\ tagerator.pdf\ genomediff.pdf TALLYMERTMP=tallymer-tmp TAGERATORTMP=tagerator-tmp TESTDATA=../../testdata all:${ALL} annotationsketch: annotationsketch.pdf %.pdf:%.tex %-pdf.bbl -test -e $*-pdf.aux && mv $*-pdf.aux $*.aux -test -e $*-pdf.bbl && mv $*-pdf.bbl $*.bbl pdflatex $< pdflatex $< mv $*.aux $*-pdf.aux -test -e $*.bbl && mv $*.bbl $*-pdf.bbl .PRECIOUS: %-pdf.bbl %-dvi.bbl %-dvi.aux %-pdf.aux %-pdf.bbl: gtmanuals.bib %-pdf.aux -test -e $*-pdf.aux && mv $*-pdf.aux $*.aux -bibtex $* test -e $@ || touch $@ -diff $@ $*.bbl || mv $*.bbl $@ && rm -f $*.bbl mv $*.aux $*-pdf.aux %-pdf.aux: %.tex -test -e $@ && mv $@ $*.aux pdflatex $< && rm $*.pdf mv $*.aux $@ read1.fna:${TESTDATA}/at1MB head -n 6999 $< > $@ read2.fna:${TESTDATA}/at1MB echo ">" > $@ tail -n 6945 $< >> $@ U89959.fna:${TESTDATA}/U89959_genomic.fas cp $< $@ ${TALLYMERTMP}.tex:tallymer.tex read1.fna read2.fna U89959.fna ./findemptyoutfiles.sh ./execcommand.pl $< > $@ tallymer.pdf:${TALLYMERTMP}.tex pdflatex ${TALLYMERTMP} pdflatex ${TALLYMERTMP} mv ${TALLYMERTMP}.pdf $@ tallymer.dvi:${TALLYMERTMP}.tex latex ${TALLYMERTMP} latex ${TALLYMERTMP} mv ${TALLYMERTMP}.dvi $@ ${TAGERATORTMP}.tex:tagerator.tex pck-human.prj Q1.gz ./findemptyoutfiles.sh ./execcommand.pl $< > $@ pck-human.prj:${TESTDATA}/at1MB ../../bin/gt packedindex mkindex -dna -dir rev -parts 12 -bsize 10 \ -sprank -locfreq 32 -tis -ssp -indexname pck-human\ -db ${TESTDATA}/at1MB Q1.gz:${TESTDATA}/Q1.gz cp $< $@ tagerator.pdf:${TAGERATORTMP}.tex pdflatex ${TAGERATORTMP} pdflatex ${TAGERATORTMP} mv ${TAGERATORTMP}.pdf $@ tagerator.dvi:${TAGERATORTMP}.tex latex ${TAGERATORTMP} latex ${TAGERATORTMP} mv ${TAGERATORTMP}.dvi $@ #%.pdf:%.tex #pdflatex $< #pdflatex $< #%.dvi:%.tex #latex $< #latex $< clean: ${RM} *.aux *.log *.bbl *.blg *.dvi *.mer *.mct *.mbd comment.cut ${RM} *.out *.toc ${RM} U89959.fna read[12].fna ${RM} reads.al1 reads.esq reads.lcp reads.llv reads.prj reads.suf ${RM} ${TALLYMERTMP}.tex ${RM} ${TAGERATORTMP}.tex Q1.gz pck-human.* cleanup:clean ${RM} ${ALL} genometools-1.5.1/doc/manuals/annotationsketch.tex000066400000000000000000000760101211610345200223530ustar00rootroot00000000000000\documentclass[a4paper]{scrreprt} \usepackage{xcolor} % we use grey text here \usepackage{graphicx} % figures \usepackage{listings} % source code \usepackage{hyperref} % navigation \usepackage{mathptmx} \usepackage{verbatim} \usepackage{bold-extra} % bold keywords in listings \usepackage[small]{caption} % better-looking captions \parindent0mm % this looks better in short paragraphs \hyphenation{An-no-ta-tion-Sketch} % some colors \definecolor{arggrey}{gray}{.6} \definecolor{middlegray}{gray}{.5} \newcommand{\AnnotationSketch}{\emph{AnnotationSketch}\ } % listings style \lstset{ basicstyle=\scriptsize\ttfamily, keywordstyle=\bfseries\ttfamily, commentstyle=\color{middlegray}\ttfamily, showstringspaces=false, flexiblecolumns=false, tabsize=2, numbers=left, numberstyle=\tiny, numberblanklines=false, stepnumber=1, numbersep=10pt, xleftmargin=15pt } % this is a basic language definition for the listings package \lstdefinelanguage{Lua} { morecomment = [l]{--}, morecomment = [s]{--[*[}{]*]--}, morestring=[b]", morestring=[b]', sensitive = true, morekeywords = {and, break, do, else, elseif, end, for, function, if, local, nil, not, or, repeat, return, then, until, while} morekeywords=[2]{}, } \title{The \emph{AnnotationSketch} genome annotation drawing library} \subject{Supplementary Information} \author{Sascha Steinbiss, Gordon Gremme, Christin Sch\"arfer, Malte Mader\\ and Stefan Kurtz} \begin{document} \maketitle \tableofcontents \chapter{AnnotationSketch} \emph{AnnotationSketch} is a versatile and efficient C-based drawing library for GFF3-compatible genomic annotations. It is included in the \emph{GenomeTools} distribution. In addition to the native C interface, bindings to the Lua, Python and Ruby programming languages are provided. \section{Overview} \emph{AnnotationSketch} consists of several classes, which take part in three visualization \emph{phases} (see Fig. \ref{dataflow}). \begin{figure}[ht] \centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/dataflow.pdf}} \caption{Schematic of the data flow through the classes involved in image creation.} \label{dataflow} \end{figure} \subsection{Phase 1: Feature selection} The GFF3 input data are parsed into a directed acyclic graph (\emph{annotation graph}, see Fig. \ref{gfftree} for an example) whose nodes correspond to single features (i.e. lines from the GFF3 file). Consequently, edges in the graph represent the \emph{part-of} relationships between groups of genomic features according to the Sequence Ontology hierarchy. Note that GFF3 input files \emph{must} be valid according to the GFF3 specification to ensure that they can be read for \AnnotationSketch drawing or any other kind of manipulation using \emph{GenomeTools}. A validating GFF3 parser is available in \emph{GenomeTools} (and can be run using \texttt{gt gff3validator}). \begin{figure}[ht] \centering{\includegraphics[width=.9\textwidth]{../../www/genometools.org/htdocs/images/gfftree.pdf}} \caption{Example sequence region containing two genes in an annotation graph depicting the \emph{part-of} relationships between their components.} \label{gfftree} \end{figure} Each top-level node (which is a node without a parent) is then registered into a persistent \emph{FeatureIndex} object. The \emph{FeatureIndex} holds a collection of the top-level nodes of all features in each sequence region in an interval tree data structure that can be efficiently queried for features in a genomic region of interest. All child nodes of the top-level node are then available by the use of traversal functions. Alternatively, annotation graphs can be built by the user by creating each node explicitly and then connecting the nodes in a way such that the relationships are reflected in the graph structure (see examples section for example annotation graph building code). \subsection{Phase 2: Layout} The next step consists of processing the features (given via a \emph{FeatureIndex} or a simple array of top level nodes) into a \emph{Diagram} object which represents a single view of the annotations of a genomic region. First, semantic units are formed from the annotation subgraphs. This is done by building \emph{blocks} from connected features by grouping and overlaying them according to several user-defined collapsing options (see ``Collapsing''). By default, a separate \emph{track} is then created for each Sequence Ontology feature type. Alternatively, if more granularity in track assignment is desired, \emph{track selector} functions can be used to create tracks and assign blocks to them based on arbitrary feature characteristics. This is simply done by creating a unique identifier string per track. The \emph{Diagram} object can also be used to hold one or more \emph{custom tracks}, which allow users to develop their own graphical representations as plugins. The \emph{Diagram} is then prepared for image output by calculating a compact \emph{Layout} in which the \emph{Block} objects in a track are distributed into \emph{Line} objects, each containing non-overlapping blocks (see Fig. \ref{diagram}). The overall layout calculated this way tries to keep lines as compact as possible, minimising the amount of vertical space used. How new \emph{Lines} are created depends on the chosen implementation of the \emph{LineBreaker} interface, by default a \emph{Block} is pushed into a new \emph{Line} when either the \emph{Block} or its caption overlaps with another one. \begin{figure}[ht] \centering{\includegraphics[width=\textwidth]{../../www/genometools.org/htdocs/images/diagram.pdf}} \caption{The components of the \emph{Layout} class reflect sections of the resulting image.} \label{diagram} \end{figure} \subsection{Phase 3: Rendering} In the final phase, the \emph{Layout} object is used as a blueprint to create an image of a given type and size, considering user-defined options. The rendering process is invoked by calling the \texttt{sketch()} method of a \emph{Layout} object. All rendering logic is implemented in classes implementing the \emph{Canvas} interface, whose methods are called during traversal of the \emph{Layout} members. It encapsulates the state of a drawing and works independently of the chosen rendering back-end. Instead, rendering backend-dependent subclasses of \emph{Canvas} are closely tied to a specific implementation of the \emph{Graphics} interface, which provides methods to draw a number of primitives to a drawing surface abstraction. It wraps around the respective low-level graphics engine and allows for its easy extension or replacement. Currently, there is a \emph{Graphics} implementation for the Cairo 2D graphics library (\emph{GraphicsCairo}) and two \emph{Canvas} subclasses providing access to the image file formats supported by Cairo (\emph{CanvasCairoFile}) and to arbitrary Cairo contexts (\emph{CanvasCairoContext}, which directly accesses a \texttt{cairo\_t}). This class can be used, for example, to directly draw \emph{AnnotationSketch} output in any graphical environment which is supported by Cairo (\url{http://www.cairographics.org/manual/cairo-surfaces.html}). \subsection{Collapsing} By default, \emph{Lines} are grouped by the Sequence Ontology type associated with the top-level elements of their \emph{Blocks}, resulting in one track per type. To obtain a shorter yet concise output, tracks for parent types in the feature graph can be enabled to contain all the features of their child types. The features with the given type are then drawn on top of their parent features (e.g. all \emph{exon} and \emph{intron} features are placed into their parent \emph{mRNA} or \emph{gene} track). This process is called \emph{collapsing}. Collapsing can be enabled by setting the \texttt{collapse\_to\_parent} option for the respective child type to \texttt{true}, e.g. the following options: \begin{lstlisting}[language=Lua, showstringspaces=false,numbers=none,frame=single] config = { exon = { ..., collapse_to_parent = true, ..., }, intron = { ..., collapse_to_parent = true, ..., }, CDS = { ..., collapse_to_parent = true, ..., }, } \end{lstlisting} would lead to all features of the \emph{exon}, \emph{intron} and \emph{CDS} types collapsing into the \emph{mRNA} track (see Fig. \ref{collapsetypes} and \ref{cnn_large}). \begin{figure} \centering{\includegraphics[width=.3\textwidth]{../../www/genometools.org/htdocs/images/collapse_types.pdf}} \caption{Schematic of the relationships between the \emph{gene}, \emph{mRNA}, \emph{exon}, \emph{intron} and \emph{CDS} types and the colors of their representations in a diagram. The arrows illustrate how the relationships influence the collapsing process if collapsing is enabled for the \emph{exon}, \emph{intron} and \emph{CDS} types. In this example, they will be drawn on top of their parent \emph{mRNA} features.} \label{collapsetypes} \end{figure} \begin{figure} \centering{\includegraphics[width=\textwidth]{../../www/genometools.org/htdocs/images/cnn_large}} \caption{Example image of the \emph{cnn} and \emph{cbs} genes from \emph{Drosophila melanogaster} (Ensembl release 51, positions 9326816--9341000 on chromosome arm 2R) as drawn by \emph{AnnotationSketch}. At the bottom, the calculated GC content of the respective sequence is drawn via a custom track attached to the diagram. (a) shows a collapsed view in which all \emph{exon}, \emph{intron} and \emph{CDS} types are collapsed into their parent type's track. In contrast, (b) shows the \emph{cbs} gene with all collapsing options set to \texttt{false}, resulting in each type being drawn in its own track.} \label{cnn_large} \end{figure} \subsection{Styles} The Lua scripting language is used to provide user-defined settings. Settings can be imported from a script that is executed when loaded, thus eliminating the need for another parser. The Lua configuration data are made accessible to C via the \emph{Style} class. Configurable options include assignment of display styles to each feature type, spacer and margin sizes, and collapsing parameters. \par Instead of giving direct values, callback Lua functions can be used in some options to generate feature-dependent configuration settings at run-time. During layout and/or rendering, the \emph{GenomeNode} object for the feature to be rendered is passed to the callback function which can then be evaluated and the appropriate type can be returned. \par For example, setting the following options in the style file (or via the Lua bindings): \begin{lstlisting}[language=Lua, showstringspaces=false,numbers=left,frame=single] config = { ..., mRNA = { block_caption = function(gn) rng = gn:get_range() return string.format("%s/%s (%dbp, %d exons)", gn:get_attribute("Parent"), gn:get_attribute("ID"), rng:get_end() - rng:get_start() + 1, #(gn:get_exons())) end, ... }, exon = { -- Color definitions fill = function(gn) if gn:get_score() then aval = gn:get_score()*1.0 else aval = 0.0 end return {red=1.0, green=0.0, blue=0.0, alpha=aval} end, ... }, ... } \end{lstlisting} will result in a changed rendering (see Fig. \ref{callbacks}). The \texttt{block\_caption} function (line 4) overrides the default block naming scheme, allowing to set custom captions to each block depending on feature properties. Color definitions such as the \texttt{fill} setting (line 17) for a feature's fill color can also be individually styled using callbacks. In this case, the color intensity is shaded by the \emph{exon} feature's score value (e.g. given in a GFF file). \begin{figure} \centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/callbacks}} \caption{Example rendering using callback functions to enable custom block captions and score-dependent shading of exon features.} \label{callbacks} \end{figure} \section{The \texttt{gt sketch} tool} The \emph{GenomeTools} \texttt{gt} executable provides a new tool which uses the \emph{AnnotationSketch} library to create a drawing in PNG, PDF, PostScript or SVG format from GFF3 annotations. The annotations can be given by supplying one or more file names as command line arguments: \small \medskip \begin{verbatim} $ gt sketch output.png annotation.gff3 $ \end{verbatim} \normalsize \medskip or by receiving GFF3 data via the standard input, here prepared by the \texttt{gt gff3} tool (here called with the \texttt{-addintrons} option to automatically add intron features between exons): \small \medskip \begin{verbatim} $ gt gff3 -addintrons annotation.gff3 | gt sketch output.png $ \end{verbatim} \normalsize \medskip The region to create a diagram for can be specified in detail by using the \texttt{-seqid}, \texttt{-start} and \texttt{-end} parameters. For example, if the \emph{D. melanogaster} gene annotation is given in the \texttt{dmel\_annotation.gff3} file, use \small \medskip \begin{verbatim} $ gt sketch -format pdf -seqid 2R -start 9326816 -end 9332879 output.pdf \ dmel_annotation.gff3 $ \end{verbatim} \normalsize \medskip to plot a graphical representation of the \emph{cnn} and \emph{cbs} gene region from the \emph{FlyBase} default view in PDF format. The \texttt{-force} option can be used to force overwriting of an already existing output file. The \texttt{-pipe} option additionally allows passing the GFF3 input through the sketch tool via the standard output, allowing the intermediate visualisation of results in a longer pipeline of connected GFF3 tools. More command line options are available; their documentation can be viewed using the \texttt{-help} option. If an input file is not plotted due to parsing errors, \emph{GenomeTools} includes a strict GFF3 validator tool to check whether the input file is in valid GFF3 format. Simply run a command like the following: \small \medskip \begin{verbatim} $ gt gff3validator input_file.gff3 input is valid GFF3 $ \end{verbatim} \normalsize \medskip This validator also allows one to check the SO types occurring in a GFF3 file against a given OBO ontology file. This checking can be enabled by specifying the file as an argument to the \texttt{-typecheck} option. If the PDF, SVG and/or PostScript output format options are not available in the \texttt{gt} binary, the most likely cause is that PDF, SVG and/or PostScript support is disabled in your local \emph{Cairo} headers and thus also not available in your local \emph{Cairo} library. This issue is not directly related to \emph{AnnotationSketch} and can be resolved by recompiling the \emph{Cairo} library with the proper backend support enabled. \section{Dynamic track assignment} A special kind of function, called \emph{track selector function}, can be used to customise the \AnnotationSketch output by using arbitrary features of a block to assign blocks to tracks (and implicitly creating new tracks this way). \subsection{Default: Top level type decides track membership} By default, for each \emph{Block} in a \emph{Diagram}, its source filename and/or the type attribute of its top level element decides into which track the block is finally inserted during the layout phase. So by default, an annotation graph parsed from the GFF3 input file `example.gff3' with \emph{gene}, \emph{mRNA} and \emph{exon} type nodes will be rendered into two separate tracks (\emph{exon}$\to$\emph{mRNA} collapsing enabled, see Fig.~\ref{tsexample1}): \begin{itemize} \item \texttt{example.gff3|gene}, and \item \texttt{example.gff3|mRNA}. \end{itemize} We will call the second part (after the ``\texttt{|}'') of these track titles \emph{track identifier strings} in the rest of this document. \begin{figure}[ht] \centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect.png}} \caption{Default AnnotationSketch output for a simple GFF3 file with simple \emph{exon}$\to$\emph{mRNA} collapsing.} \label{tsexample1} \end{figure} While automatically determining tracks from the types actually present in the input annotations is convenient in many use cases, one could imagine cases in which more control about block handling may be desired. This leads to the question: How can one extract blocks with specific characteristics and assign them to a special track? The answer is simple: By overriding the default track identifier string, new tracks can be created and named on the fly as soon as a block satisfying user-defined rules is encountered. \subsection{Track selector functions} These rules take the form of \emph{track selector functions}. Basically, a track selector function is a function which takes a block reference as an argument, and returns an appropriate track identifier string. For example, in Python the default track selector function would look like this: \begin{lstlisting}[language=Python, showstringspaces=false,numbers=none,frame=single] def default_track_selector(block): return block.get_type() \end{lstlisting} This function simply returns a string representation of the type of a block's top level element, creating the tracks just like depicted in Fig. \ref{tsexample1}. For a very simple example, let's assume that we want to create separate tracks for all mRNAs on the plus strand and for all mRNAs on the minus strand. The idea now is to change the strand identifier for blocks of the \emph{mRNA} type to include the strand as additional information, thus creating different track identifiers for plus and minus strand features. In Python, this track selector function would construct a new string which contains both the type and the strand: \begin{lstlisting}[language=Python, showstringspaces=false,numbers=none,frame=single] def strand_track_selector(block): if block.get_type() == "mRNA": return "%s (%s strand)" % (block.get_type(), block.get_strand()) else: return block.get_type() \end{lstlisting} Using this track selector function would produce the desired result of separate tracks for the \emph{mRNA} features for each strand (see Fig. \ref{tsexample2}). \begin{figure}[ht] \centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect.png}} \caption{AnnotationSketch output with \texttt{strand\_track\_se\-lector()} track selector function. This image now shows separate tracks for plus and minus strand features.} \label{tsexample2} \end{figure} A track selector function can be set for a \emph{Diagram} object using the \texttt{diagram.set\_track\_se\-lec\-tor\_func()} method. In C, its argument is a pointer to a function of the signature \medskip \begin{verbatim} void (*GtTrackSelectorFunc)(GtBlock*, GtStr*, void*) \end{verbatim} \medskip where arbitrary data can be passed via the third \texttt{void*} argument. The Python \texttt{set\_track\_se\-lec\-tor\_func()} method directly accepts a Python function as an argument, while the Ruby version takes a Proc object: \begin{lstlisting}[language=Ruby, showstringspaces=false,numbers=none,frame=single] ... strand_track_selector = Proc.new { |block, data| "#{block.get_type} (#{block.get_strand} strand)" } ... diagram.set_track_selector_func(strand_track_selector) ... \end{lstlisting} Note that in Python and Ruby, it is also possible to reference data declared outside of the track selector function. For example, this can be used to filter blocks by pulling blocks whose description matches a pattern into a separate track: \begin{lstlisting}[language=Python, showstringspaces=false,numbers=none,frame=single] ... interesting_genes = ["First test gene", "another gene"] def filter_track_selector(block): if block.get_caption() in interesting_genes: return "interesting genes" else: return block.get_type() ... diagram.set_track_selector_func(filter_track_selector) ... \end{lstlisting} This code results in the image shown in Fig.~\ref{tsexample3} : \begin{figure}[ht] \centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect.png}} \caption{\AnnotationSketch output with \texttt{filter\_track\_selector()} track selector function. This image now shows a separate track for features with a specific caption.} \label{tsexample3} \end{figure} \section{Custom tracks} There are kinds of data which may be interesting to see together with annotation renderings, but that can not be expressed -- or only in a complicated way -- in GFF3 format. It may even be too difficult or counterintuitive to properly represent this data as typical \AnnotationSketch box graphics. For example, this may be sequence data, numerical sequence analysis results, or other kinds of data which does not fit into the simple ‘genomic feature’ scheme. For an example, see Fig. \ref{ctexample1}. \begin{figure}[ht] \centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct.png}} \caption{Example \AnnotationSketch output with a custom track at the bottom, displaying the GC content over a window size of 200 bp.} \label{ctexample1} \end{figure} With \emph{custom tracks}, \AnnotationSketch provides a mechanism to use the internal drawing functionality to create user-defined output which can be tailored to fit this kind of data. A custom track looks just like a normal \AnnotationSketch track, but is completely in control of the developer. While native \AnnotationSketch primitives such as boxes can of course be used, the author of a custom track is not restricted to the layout algorithm and can draw anything anywhere (as long as it is provided by the \emph{Graphics} class), taking arbitrary external data into account. \subsection{Anatomy of a custom track class} Simply put, custom tracks are classes which are derived from a \emph{CustomTrack} base class and must implement a set of mandatory methods: \begin{itemize} \item \texttt{get\_height()}: Returns the amount of vertical space (in pixels or points) the custom track will occupy in the final image. Must return a numeric value. \item \texttt{get\_title()}: Returns a title for the custom track which is displayed at the top of the track. Note that, unlike a track identifier string e.g. produced by a track selector function, the string returned by this function is not prepended by a file name. \item \texttt{render(graphics, ypos, range, style, error)}: Performs the actual rendering operations. As parameters, this function receives \begin{itemize} \item a \emph{Graphics} object to draw on, \item the vertical offset \emph{ypos} of the drawing area assigned to the custom track, \item the \emph{Range} of the sequence positions for which annotations are currently displayed, \item a \emph{Style} object which can be used to obtain style information specific to this custom track, and \item an \emph{Error} object which can be used to return an error message if the custom track needs to signal a problem. \end{itemize} \end{itemize} The \texttt{render()} method must return 0 if drawing was successful, or a negative value if an error occurred. Optionally, a \texttt{free()} method can be implemented if the subclass needs to clean up any private space allocated by itself. These methods are then called by the rendering code in AnnotationSketch when a Diagram containing a custom track is laid out and rendered. No other constraints apply on such a class besides that these methods are implemented (in the scripting language bindings, the parent classes' constructor must be called once). \subsection{Writing an example custom track} Let's suppose we are not satisfied with the display of single base features, such as transposable element insertion sites or SNPs. Instead of a single line denoting the feature location, we would like to have a small triangle pointing at the location. Suppose we also do not have this data in an annotation graph, so we cannot use the built-in rendering functions. It is straightforward to write a small custom track class which does this for us. This tutorial uses Python code for simplicity, but the general approach is common to all supported languages. First, we need to define a class inheriting from CustomTrack, call the parent constructor to register the functions and set instance variables for the triangle sidelength and a dictionary containing the feature positions and a description: \begin{lstlisting}[language=Python, showstringspaces=false,numbers=left,frame=single] class CustomTrackInsertions(CustomTrack): def __init__(self, sidelength, data): super(CustomTrackInsertions, self).__init__() self.sidelength = sidelength self.data = data \end{lstlisting} We define the height to be 20 pixels: \begin{lstlisting}[language=Python, firstnumber=6, showstringspaces=false,numbers=left,frame=single] def get_height(self): return 20 \end{lstlisting} As a track title, we set ``Insertion site'': \begin{lstlisting}[language=Python, firstnumber=8, showstringspaces=false,numbers=left,frame=single] def get_title(self): return "Insertion site" \end{lstlisting} The rendering code then calculates the triangle coordinates and draws the respective lines: \begin{lstlisting}[language=Python, firstnumber=10, showstringspaces=false,numbers=left,frame=single] def render(self, graphics, ypos, rng, style, error): height = (self.sidelength*math.sqrt(3))/2 margins = graphics.get_xmargins() red = Color(1, 0, 0, 0.7) for pos, desc in self.data.iteritems(): drawpos = margins + (float(pos)-rng.start)/(rng.end-rng.start+1) \ * (graphics.get_image_width()-2*margins) graphics.draw_line(drawpos-self.sidelength/2, ypos + height, \ drawpos, ypos, \ red, 1) graphics.draw_line(drawpos, ypos, \ drawpos+self.sidelength/2, ypos + height, \ red, 1) graphics.draw_line(drawpos-self.sidelength/2, ypos + height, \ drawpos+self.sidelength/2, ypos + height, \ red, 1) graphics.draw_text_centered(drawpos, ypos + height + 13, str(desc)) return 0 \end{lstlisting} For a Python custom track, that's it! No more code is necessary for this very simple custom track. We can now instantiate this class and attach the instance to a \emph{Diagram} object: \begin{lstlisting}[language=Python, showstringspaces=false,numbers=none,frame=single] ... diagram = Diagram(feature_index, seqid, range, style) ... ctt = CustomTrackInsertions(15, {2000:"foo", 4400:"bar", 8000:"baz"}) diagram.add_custom_track(ctt) ... \end{lstlisting} Running layout and drawing functions on this diagram then produces the desired image (see Fig.~\ref{ctexample2} \begin{figure}[ht] \centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_ct2.png}} \caption{The example insertion site custom track (at the bottom), displaying three sample data points.} \label{ctexample2} \end{figure} \section{Examples} This section will show how to use the \emph{AnnotationSketch} library in custom applications. As \emph{AnnotationSketch} is distributed as a part of \emph{GenomeTools}, its code is compiled into the \texttt{lib\-ge\-nome\-tools.so} shared library. Please refer to the INSTALL file inside the \emph{GenomeTools} distribution for installation instructions. For a general idea about how to use the library, a simple implementation of the GFF3 validator is included in the source package (see \texttt{src/examples/gff3validator.c}) as an example showing how to create \emph{GenomeTools}-based programs. In the same directory, there is also an appropriate \texttt{Makefile} to build and link this application against the installed shared library \texttt{libgenometools.so}. \subsection{Using \emph{AnnotationSketch} to draw annotations from a file} The following code examples (in C and Lua) illustrate how to produce an image from a given GFF3 file using \emph{AnnotationSketch}. The result is shown in Fig. \ref{parsed_img}. In essence, these code examples implement something like a simple version of the \texttt{gt sketch} tool from \emph{GenomeTools} without most command-line options. The C-based examples mentioned below are compiled along with the \emph{GenomeTools} library itself and available in the \texttt{bin/examples} directory. \begin{figure} \centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/parsed}} \caption{Example rendering of a GFF3 file with default style.} \label{parsed_img} \end{figure} \subsubsection{C code} (See \texttt{src/examples/sketch\_parsed.c} in the source distribution.) \lstinputlisting[language=C, breaklines=true, numbers=left, frame=single,]{../../src/examples/sketch_parsed.c} \subsubsection{Lua code} (See \texttt{gtscripts/sketch\_parsed.lua} in the source distribution. This example can be run by the command line \texttt{gt gtscripts/sketch\_parsed.lua }) \lstinputlisting[language=Lua, breaklines=true, numbers=left, frame=single,]{../../gtscripts/sketch_parsed.lua} \subsubsection{Ruby code} (See \texttt{gtruby/sketch\_parsed.rb} in the source distribution.) \lstinputlisting[language=Ruby, breaklines=true, numbers=left, frame=single,]{../../gtruby/sketch_parsed.rb} \subsubsection{Python code} (See \texttt{gtpython/sketch\_parsed.py} in the source distribution.) \lstinputlisting[language=Python, breaklines=true, numbers=left, frame=single,]{../../gtpython/sketch_parsed.py} \subsection{Using \emph{AnnotationSketch} to draw user-generated annotations} The following C code example illustrates how to produce an image from annotation graphs created by user code. The result is shown in Fig. \ref{constructed_img}. \begin{figure} \centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/constructed}} \caption{Example rendering of user-generated annotations with default style.} \label{constructed_img} \end{figure} \subsubsection{C code} (See \texttt{src/examples/sketch\_constructed.c} in the source distribution.) \lstinputlisting[language=C, breaklines=true, numbers=left, frame=single,]{../../src/examples/sketch_constructed.c} \subsubsection{Lua code} (See \texttt{gtscripts/sketch\_constructed.lua} in the source distribution. This example can be run by the command line \texttt{gt gtscripts/sketch\_constructed.lua }) \lstinputlisting[language=Lua, breaklines=true, numbers=left, frame=single,]{../../gtscripts/sketch_constructed.lua} \subsubsection{Ruby code} (See \texttt{gtruby/sketch\_constructed.rb} in the source distribution.) \lstinputlisting[language=Ruby, breaklines=true, numbers=left, frame=single,]{../../gtruby/sketch_constructed.rb} \subsubsection{Python code} (See \texttt{gtpython/sketch\_constructed.py} in the source distribution.) \lstinputlisting[language=Python, breaklines=true, numbers=left, frame=single,]{../../gtpython/sketch_constructed.py} \input{api_reference} %\input{gtscript_reference} \end{document} genometools-1.5.1/doc/manuals/execcommand.pl000077500000000000000000000043551211610345200211030ustar00rootroot00000000000000#!/usr/bin/env perl use strict; use warnings; unless(@ARGV) { print STDERR "Usage: $0 \n"; exit 1; } if((scalar @ARGV) eq 0) { print STDERR "$0: missing argument\n"; exit 1; } my($inputfile) = $ARGV[0]; unless ( -e $inputfile) { print STDERR "$0: file \"$inputfile\" does not exist\n"; exit 1; } unless ( open(INPUTFILEHANDLE, $inputfile) ) { print STDERR "Cannot open file \"$inputfile\""; exit 1; } while (my $in = ) { if($in =~ m/^\\EXECUTE\{([^\}]*)\}/) { runtheprogram($1); } else { print $in; } } sub determinemaxfilewidth { my ($filename) = @_; my $maxwidth = 0; my $width; unless(open(FILEHANDLE,$filename)) { print STDERR "Cannot open file \"$filename\"\n"; exit 1; } while(my $line = ) { $width = length $line; if($maxwidth < $width) { $maxwidth = $width; } } close(FILEHANDLE); return $maxwidth; } sub runtheprogram { my($argcommand) = @_; my(@argv) = split(' ',$argcommand); my $program = $argv[0]; my $outfileprefix = $argcommand; $outfileprefix =~ s/ \|.*//; # delete possible pipe at end $outfileprefix =~ s/\s+/-/g; # delete white spaces $outfileprefix =~ s/\*//g; # delete white spaces $outfileprefix =~ s/\'.*\'//g; # ' ' expressions my $outfilename = "output/${outfileprefix}" . ".out"; if(-f ${outfilename}) { print STDERR "# file ${outfilename} already exists\n"; } else { my $fh; my @skippipe = split(/\|/,$argcommand); unless(open($fh, ">" . $outfilename)) { print STDERR "Cannot open file $outfilename\n"; exit 1; } print $fh "\$ $skippipe[0]\n"; close($fh); push(@argv,'>>'); push(@argv,$outfilename); my $argstring = "../../bin/" . join(' ',@argv); print STDERR "run $argstring\n"; my($retcode) = system($argstring); $retcode = $? >> 8; if($retcode ne 0) { print STDERR "failure: $argstring\n"; unlink($outfilename); exit 1; } } my $maxwidth = determinemaxfilewidth($outfilename); my $env; if($maxwidth < 78) { $env = "footnotesize"; } else { $env = "scriptsize"; } print "\\begin{$env}"; print "\\verbatiminput{$outfilename}"; print "\\end{$env}\n"; } genometools-1.5.1/doc/manuals/findemptyoutfiles.sh000077500000000000000000000003161211610345200223620ustar00rootroot00000000000000#!/bin/sh for filename in `find output/ -name '*.out'` do filesize=`cat ${filename} | wc -l` if test $filesize -eq 1 then echo "Warning: ${filename} only contains one line" exit 1 fi done genometools-1.5.1/doc/manuals/genomediff.tex000066400000000000000000000304031211610345200210760ustar00rootroot00000000000000\documentclass[12pt,titlepage]{article} \usepackage[a4paper,top=30mm,bottom=30mm,left=20mm,right=20mm]{geometry} \usepackage[utf8]{inputenc} \usepackage{xspace} \usepackage{listings} \usepackage{optionman} \usepackage{url} \usepackage{booktabs} \usepackage{xcolor} %\usepackage[binary-units]{siunitx} %\usepackage{TheSansUHH} \newcommand{\Gdiff}{\textit{genomediff}\xspace} \newcommand{\Suff}{\textit{suffixerator}\xspace} \newcommand{\Mki}{\textit{packedindex}\xspace} \newcommand{\Encseq}{\textit{encseq}\xspace} \newcommand{\RGdiff}{\texttt{run\_genomediff.rb}\xspace} \newcommand{\GenomeTools}{\textit{GenomeTools}\xspace} \newcommand{\Gt}{\texttt{gt}\xspace} \newcommand{\Kr}{\ensuremath{K_r}\xspace} \newcommand{\Gtsuffixerator}{\texttt{gt suffixerator}\xspace} \newcommand{\Gtpackedindex}{\texttt{gt packedindex mkindex}\xspace} \newcommand{\ESA}{ESA\xspace} \newcommand{\FastA}{FASTA\xspace} \newcommand{\File}[1]{\texttt{\small #1}} \newcommand{\ShuS}{\textit{shustrings}\xspace} \lstset{language=bash, basicstyle=\ttfamily } \definecolor{darkgreen}{rgb}{0.3,0.5,0.3} \definecolor{darkblue}{rgb}{0.3,0.3,0.5} \definecolor{darkred}{rgb}{0.5,0.3,0.3} \lstdefinelanguage{LUA}{% sensitive=true,% columns=fixed,% keywordstyle=[1]{\color{darkblue}\bfseries},% keywordstyle=[2]{\color{darkgreen}\bfseries},% morekeywords=[1]{local,if,then,else,end,while,do, coroutine,yield},% Official LUA keywords morekeywords=[2]{units},% Your private keywords otherkeywords={.,=,~,*,>,:},% morestring=[b]",% stringstyle={\color{darkred}\itshape},% breaklines=true,% linewidth=\textwidth,% comment=[l]{--}% } \title{\Gdiff user manual} \author{\begin{tabular}{c} \textit{Dirk Willrodt}\\[1cm] Research Group for Genome Informatics\\ Center for Bioinformatics\\ University of Hamburg\\ Bundesstrasse 43\\ 20146 Hamburg\\ Germany\\[1cm] \url{willrodt@zbh.uni-hamburg.de}\\ \end{tabular}} \begin{document} %\tsuhhfamily \maketitle \section*{This Manual} Some text is highlighted by different fonts according to the following rules. \begin{itemize} \item \texttt{Typewriter font} is used for the names of software tools. \item \File{Small typewriter font} is used for file names. \item \begin{footnotesize}\texttt{Footnote sized typewriter font} \end{footnotesize} with a leading \begin{footnotesize}\texttt{'-'}\end{footnotesize} is used for program options. \item \Showoptionarg{small italic font} is used for the argument(s) of an option. \end{itemize} \section{Introduction} This document describes \Gdiff, a software tool for measuring evolutionary distances between sets of closely related genomes. These distances are Jukes-Cantor corrected divergence between the pairs of genomes, that is, the number of mutations per base between them. This distance is called \Kr and is based on so called \ShuS \cite{HAU:DOM:WIE:2008,HAU:PFA:DOM:WIE:2009,HAU:REE:PFA:2011}. The calculation of all pairwise distances is alignment free, but the resulting distances have the same biological meaning as if calculated with a multiple sequence alignment. This software is only able to process closely related distances, because \Kr is only reliable for distances $<0.5$. \Gdiff is written in C and it is based on the \GenomeTools library~\cite{genometools}. It is called as part of the single binary named \Gt. The source code can be compiled on 32-bit and 64-bit platforms without making any changes to the sources. \section{Building \Gdiff} \label{Building} As \Gdiff is part of the \GenomeTools software suite, a source distribution of \GenomeTools must be obtained, e.g.\@ via the \GenomeTools home page (\url{http://genometools.org}), and decompressed into a source directory: \begin{lstlisting} $ tar -xzvf genometools-X.X.X.tar.gz $ cd genometools-X.X.X \end{lstlisting} Where \lstinline!X.X.X! denotes the desired gt version. Then, it suffices to call \lstinline!make! to compile the source using the provided makefile. It is recommended to use the 64bit-version of the \GenomeTools executable if your system supports this. Pass the option \lstinline!64bit=yes! to enable 64 bit support. The option \lstinline!amalgamation=yes! allows the compiler to use better optimization. \begin{lstlisting} $ make 64bit=yes amalgamation=yes \end{lstlisting} After successful compilation, the \GenomeTools executable containing \Gdiff is available in the \File{bin} subfolder of the root directory of the uncompressed source. It can then be installed for system-wide use as follows (do this as root): \begin{lstlisting} $ make 64bit=yes amalgamation=yes install \end{lstlisting} Make sure to use the same options as for the compilation step when using the install target! If a \texttt{prefix=} option is appended to this line, a custom directory can be specified as the installation target directory, e.g.\@ \begin{lstlisting} $ make 64bit=yes amalgamation=yes install prefix=/home/user/gt \end{lstlisting} will install the \Gt binary in the \File{/home/user/gt/bin} directory. Please also consult the \File{README} and \File{INSTALL} files in the root directory of the uncompressed source tree for more information and troubleshooting advice. \section{Usage} \subsection{\Gdiff command line options} Since \Gdiff is part of \GenomeTools, it is invoked as follows: \texttt{gt genomediff [{\footnotesize options}] ({\small INDEX} | {\footnotesize -indexname} \textit{\footnotesize NAME} {\small SEQFILE SEQFILE [\ldots])}} where \File{INDEX} is the path without file extension of an encoded sequence containing the genomes to be compared and \Showoptionarg{NAME} is a name for an encoded sequence to be built from the given \texttt{\small SEQFILES}. A short description of all possible options is given in Table \ref{tab:gdopts}. \begin{table}[hbpt] \centering \caption{\Gdiff{} command line options} \begin{footnotesize} \label{tab:gdopts} \begin{tabular}{lp{0.6\textwidth}}\hline \Showoptiongroup{Input options} \Showoption{indextype} \Showoptionarg{type} & Specify type of index, one of: \Showoptionarg{esa\textbar{}pck\textbar{}encseq}. Where encseq is an encoded sequence and an enhanced suffix array will be constructed only in memory. default: \Showoptionarg{encseq}\\ \Showoption{unitfile} \Showoptionarg{filename} & Specifies genomic units, see below for description. default: undefined\\ \Showoptiongroup{Output options} \Showoption{indexname} \Showoptionarg{name} & Basename of encseq to construct. default: undefined\\ \Showoptiongroup{ESA options} \Showoption{mirrored} & Virtually append the reverse complement of each sequence default: \Showoptionarg{no}\\ \Showoption{pl} \Showoptionarg{n} & Specify prefix length for bucket sort recommendation: use without argument; then a reasonable prefix length is automatically determined. default: \Showoptionarg{0}\\ \Showoption{dc} \Showoptionarg{n} & Specify difference cover value. default: \Showoptionarg{0}\\ \Showoption{memlimit} \Showoptionarg{n} & Specify maximal amount of memory to be used during index construction (in bytes, the keywords 'MB' and 'GB' are allowed). default: undefined\\ \Showoptiongroup{Miscellaneous options} \Showoption{v} & Be verbose. default: \Showoptionarg{no}\\ \Showoption{help} & Display help for basic options and exit.\\ \Showoption{help+} & Display help for all options and exit.\\ \Showoption{version} & Display version information and exit.\\\hline \end{tabular} \end{footnotesize} \end{table} \begin{lstlisting}[% float=hbpt,% showlines=true,% frame=tb,% caption={Example unitfile: {\small The section '\texttt{units}' is mandatory, '\texttt{genome1/2}' are examples of names, filenames are paths as given on the command line or during index construction.} },% label={code:lua}, language=LUA] units = { genome1 = { "file1.fas", "file2.fas" }, genome2 = { "path/file3.fas", "file4.fas" } } \end{lstlisting} \subsection{Input files} The tool \Gdiff can handle three types of prepared indices. The first is an encoded sequence, which can be prepared by \Encseq. Given an encoded sequence, \Gdiff will build an enhanced suffix array in memory and calculate \Kr using that index. Second is an enhanced suffix array prepared by the tool \Suff (see \texttt{gt suffixerator -help}) and third a compressed FM-index build by the tool \Mki (see \texttt{gt packedindex mkindex -help}. The usage of FM-indices is not recommended, because calculation of \Kr takes significantly longer. Another way is to give the names of sequence files directly. Option \Showoption{-indexname} is mandatory in this case. The given name will be used to store an encoded sequence on disk. File format can be any sequence format supported by \GenomeTools. Either way, each given sequence file will be regarded as one genomic unit, regardless of the number of sequences inside that file. To give the genomic units other names than the filenames or to combine files to single genomic units one can give a unitfile with option \Showoption{-unitfile}. The format of an example unitfile is shown in Listing \ref{code:lua}. \subsection{Output} The output on the standard output stream consists of a line with the number of genomes or units that were compared. It is followed by a quadratic matrix of pairwise distances where each line consists of a file- or unitname and tabulator separated distance values. Depending on the options of the \Gt call there can be additional output where each line is prefixed by '\texttt{\# }' and additional output prefixed by'\texttt{debug: }' on the standard error stream. \section{Example} This section describes two example scenarios, the first being the comparison of multiple genomes organised in separate multiple \FastA-files and the second being the comparison of two genomes consisting of multiple files each. \subsection{Compare genomes in separate files} Consider three files \File{genome1.fas}, \File{genome2.fas} and \File{genome3.fas} each of which could contain multiple \FastA entries. Our machine has 2\,GiB RAM. Assuming the index construction would need 5\,GiB, we need to split it in at least three parts of equal size or restrict maximal memory requirements. The simplest way to calculate the distance matrix for these three genomes would be to call: \begin{lstlisting} gt genomediff -indexname 3genomes \ -memlimit 1500MB \ genome1.fas genome2.fas genome3.fas \end{lstlisting} \Showoption{-memlimit} should be reasonable less than available main memory. This will output the distance matrix on the terminal and store an encoded sequence with basename \File{3genomes} in the current directory. In order to save the results to a file use terminal redirection: \lstinline!gt genomediff ... > outfile!. The file \File{outfile} might look like this: \begin{verbatim} 3 genome1.fas 0.000000 0.115125 0.267473 genome2.fas 0.115125 0.000000 0.293082 genome3.fas 0.267473 0.293082 0.000000 \end{verbatim} This tabulator separated table can be used for example with \textit{Phylip} or \textit{R} to calculate a phylogenetic tree. Another way to calculate the same distances if an enhanced suffix array of the given files with name \File{3genomes\_idx} already exists on disk would be like this: \begin{lstlisting} gt genomediff -indextype esa 3genomes_idx > outfile \end{lstlisting} To reuse an existing encoded sequence just give the basename of it: \begin{lstlisting} gt genomediff 3genomes > outfile \end{lstlisting} \subsection{Compare two genomes in multiple files} Assume we have two genomes that consist of multiple chromosomes in separate files. For example, genome1 consists of \File{g1\_chr1.fas} and \File{g1\_chr2.fas} while the two files for genome2 are named accordingly. The unitfile could be organized like this: \begin{lstlisting}[language=lua] units = { genome1 = { "g1_chr1.fas", "g1_chr2.fas" }, genome2 = { "g2_chr1.fas", "g2_chr2.fas" } } \end{lstlisting} The name of the unitfile in our example will be \File{units}. Now we could call \Gdiff like this: \begin{lstlisting} gt genomediff -indexname 2genomes \ -unitfile units \ g1_chr1.fas g1_chr2.fas g2_chr1.fas g2.chr2.fas > output \end{lstlisting} File \File{output} could look like this: \begin{verbatim} 2 genome1 0.000000 0.115125 genome2 0.115125 0.000000 \end{verbatim} \section*{Bibliography} \bibliographystyle{unsrt} \bibliography{gtmanuals} \end{document} % vim:spell spelllang=en_gb genometools-1.5.1/doc/manuals/genomediff.tex.latexmain000066400000000000000000000004011211610345200230520ustar00rootroot00000000000000let g:Tex_ProjectSourceFiles = '' let g:Tex_Com_Gdiff = "\\Gdiff<++>" let g:Tex_Com_Encseq = "\\Encseq<++>" let g:Tex_Com_Suff = "\\Suff<++>" let g:Tex_Com_Mki = "\\Mki<++>" let g:Tex_Com_Gt = "\\Gt<++>" let g:Tex_Com_Kr = "\\Kr<++>" " vim:tw=0:syntax=vim genometools-1.5.1/doc/manuals/gtmanuals.bib000066400000000000000000000147201211610345200207260ustar00rootroot00000000000000% This file was created with JabRef 2.6. % Encoding: ISO8859_1 @MISC{oai:CiteSeerPSU:481302, author = {Paolo Ferragina and Giovanni Manzini}, title = {Opportunistic Data Structures with Applications}, month = sep # {~03}, year = {2000}, abstract = {In this paper we address the issue of compressing and indexing data. We devise a data structure whose space occupancy is a function of the entropy of the underlying data set. We call the data structure opportunistic since its space occupancy is decreased when the input is compressible and this space reduction is achieved at no significant slowdown in the query performance. More precisely, its space occupancy is optimal in an information-content sense because a text T [1, u] is stored using O(H k (T )) + o(1) bits per input symbol in the worst case, where H k (T ) is the kth order empirical entropy of T (the bound holds for any fixed k). Given an arbitrary string P [1; p], the opportunistic data structure allows one to search for the occ occurrences of P in T in O(p + occ log u) time (for any fixed > 0). If data are uncompressible we achieve the best space bound currently known [12]; on compressible data our solution improves the succinct suffix array of [12] and the classical suffix tree and suffix array data structures either in space or in query time or both.}, annote = {Paolo Ferragina (Universita di Pisa); Giovanni Manzini (Universita del Piemonte Orientale);}, bdsk-url-1 = {http://citeseer.ist.psu.edu/481302.html;%20%20%20%20http://butirro.di.unipi.it/FM-index/FM-pages/../../Latex/focs00.ps}, bibsource = {OAI-PMH server at cs1.ist.psu.edu}, citeseer-references = {oai:CiteSeerPSU:227724; oai:CiteSeerPSU:371352; oai:CiteSeerPSU:76182; oai:CiteSeerPSU:104285; oai:CiteSeerPSU:226353; oai:CiteSeerPSU:370410; oai:CiteSeerPSU:460358; oai:CiteSeerPSU:16136; oai:CiteSeerPSU:506611; oai:CiteSeerPSU:1331; oai:CiteSeerPSU:688013; oai:CiteSeerPSU:456171; oai:CiteSeerPSU:161058; oai:CiteSeerPSU:174195}, date-added = {2008-02-20 11:27:59 +0100}, date-modified = {2008-02-20 11:27:59 +0100}, language = {english}, oai = {oai:CiteSeerPSU:481302}, rights = {unrestricted}, url = {http://citeseer.ist.psu.edu/481302.html; http://butirro.di.unipi.it/FM-index/FM-pages/../../Latex/focs00.ps} } @ARTICLE{journals/talg/FerraginaMMN07, author = {Paolo Ferragina and Giovanni Manzini and Veli M{\"a}kinen and Gonzalo Navarro}, title = {Compressed representations of sequences and full-text indexes}, journal = {ACM Transactions on Algorithms}, year = {2007}, volume = {3}, number = {2}, bdsk-url-1 = {http://doi.acm.org/10.1145/1240233.1240243}, bibdate = {2007-10-23}, bibsource = {DBLP, http://dblp.uni-trier.de/db/journals/talg/talg3.html#FerraginaMMN07}, date-added = {2008-02-20 11:28:58 +0100}, date-modified = {2008-02-20 11:28:58 +0100}, url = {http://doi.acm.org/10.1145/1240233.1240243} } @MISC{genometools, author = {Gordon Gremme}, title = {The \textsc{GenomeTools} genome analysis system}, date-added = {2008-02-19 16:32:19 +0100}, date-modified = {2008-02-19 16:45:15 +0100}, note = {\url{http://genometools.org}}, url = {http://genometools.org} } @INPROCEEDINGS{HAU:DOM:WIE:2008, author = {Haubold, Bernhard and Domazet-Loso, Mirjana and Wiehe, Thomas}, title = {An Alignment-Free Distance Measure for Closely Related Genomes}, booktitle = {RECOMB-CG ’08: Proceedings of the international workshop on Comparative Genomics}, year = {2008}, pages = {87-99}, address = {Berlin, Heidelberg}, publisher = {Springer-Verlag}, doi = {http://dx.doi.org/10.1007/978-3-540-87989-3_7}, file = {:/home/willrodt/Documents/Paper/HauDomWie2008.pdf:PDF}, isbn = {978-3-540-87988-6}, location = {Paris, France}, owner = {willrodt}, timestamp = {2011.05.10} } @ARTICLE{HAU:PFA:DOM:WIE:2009, author = {Haubold, B. and Pfaffelhuber, P. and Domazet-Loso, M. and Wiehe, T.}, title = {Estimating Mutation Distances from Unaligned Genomes}, journal = {J. Comput. Biol.}, year = {2009}, volume = {16}, pages = {1487-1500}, month = {"Oct"}, file = {:/home/willrodt/Documents/Paper/HauPfaDomWie2009.pdf:PDF}, owner = {willrodt}, timestamp = {2011.05.10} } @ARTICLE{HAU:REE:PFA:2011, author = {Haubold, Bernhard and Reed, Floyd A. and Pfaffelhuber, Peter}, title = {Alignment-free estimation of nucleotide diversity}, journal = {Bioinformatics}, year = {2011}, volume = {27}, pages = {449-455}, number = {4}, abstract = {Motivation: Sequencing capacity is currently growing more rapidly than CPU speed, leading to an analysis bottleneck in many genome projects. Alignment-free sequence analysis methods tend to be more efficient than their alignment-based counterparts. They may, therefore, be important in the long run for keeping sequence analysis abreast with sequencing.Results: We derive and implement an alignment-free estimator of the number of pairwise mismatches, . Our implementation of , pim, is based on an enhanced suffix array and inherits the superior time and memory efficiency of this data structure. Simulations demonstrate that is accurate if mutations are distributed randomly along the chromosome. While real data often deviates from this ideal, remains useful for identifying regions of low genetic diversity using a sliding window approach. We demonstrate this by applying it to the complete genomes of 37 strains of Drosophila melanogaster, and to the genomes of two closely related Drosophila species, D.simulans and D.sechellia. In both cases, we detect the diversity minimum and discuss its biological implications.Availability: pim is written in standard C and its sources can be downloaded from http://guanine.evolbio.mpg.de/pim/.Contact: haubold@evolbio.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.}, doi = {10.1093/bioinformatics/btq689}, eprint = {http://bioinformatics.oxfordjournals.org/content/27/4/449.full.pdf+html}, file = {supplement:/home/willrodt/Documents/Paper/HauReePfa2011_supp.pdf:PDF;:/home/willrodt/Desktop/Paper/HauReePfa2011.pdf:PDF}, owner = {willrodt}, timestamp = {2012.01.26}, url = {http://bioinformatics.oxfordjournals.org/content/27/4/449.abstract} } @MISC{gttestdata, title = {\textsc{GenomeTools} test data set}, note = {\url{git://genometools.org/gttestdata.git}}, bdsk-url-1 = {http://www.genometools.org/askgordon}, date-added = {2008-02-19 01:42:22 +0100}, date-modified = {2008-02-19 17:04:35 +0100}, url = {git://genometools.org/gttestdata.git} } genometools-1.5.1/doc/manuals/hop.tex000066400000000000000000000250231211610345200175630ustar00rootroot00000000000000\documentclass[12pt,titlepage]{article} \usepackage[a4paper,top=30mm,bottom=30mm,left=20mm,right=20mm]{geometry} \usepackage{url} \usepackage{alltt} \usepackage{xspace} \usepackage{times} \usepackage{listings} \usepackage{bbm} \usepackage{verbatim} %\usepackage[dvips]{hyperref} \usepackage{optionman} \newcommand{\GenomeTools}{\textit{GenomeTools}\xspace} \newcommand{\Hop}{{HOP}\xspace} \newcommand{\Gtcmd}{\texttt{gt}\xspace} \newcommand{\Hopcmd}{\texttt{gt hop}\xspace} \newcommand{\minlen}{\ell} \title{\Huge{\Hop 1.0:\\ User manual.}\\[3mm] \Large{Reference-based homopolymer error correction.}} \author{\begin{tabular}{c} \textit{Giorgio Gonnella}\\ \textit{Stefan Kurtz}\\ \textit{Michael Beckstette}\\[2cm] Center for Bioinformatics\\ University of Hamburg\\ Bundesstrasse 43\\ 20146 Hamburg (Germany)\\[1cm] \url{gonnella@zbh.uni-hamburg.de}\\ \url{beckstette@zbh.uni-hamburg.de}\\ \url{kurtz@zbh.uni-hamburg.de}\\[1cm] \end{tabular}} \begin{document} \maketitle \section{Introduction} \label{Introduction} \Hop \cite{HOP} is a tool for the correction of homopolymer errors using a reference sequence. Homopolymer errors are particularly frequent in Roche 454 and IonTorrent sequencing data sets. \section{Installation} \Hop is provided as 64-bit binary distributions for Linux and Mac and as source code. The software is available from \url{http://zbh.uni-hamburg.de/hop} and will be included in future releases of \GenomeTools. \subsection{Binary distributions} In the binary distributions, the \texttt{bin} directory contains the \GenomeTools binary (\texttt{bin/gt}). The whole \GenomeTools is compiled into this single binary, including \Hop. On some systems (not MacOS) a statically-linked binary is also available under \texttt{bin/static/gt}. See also the \texttt{README} file. If desired, it may be possible to install the \GenomeTools binary system-wide by following the instructions contained in \texttt{INSTALL} file. \subsection{Source code distribution} The source code for \Hop is written in \texttt{C} and it is based on the \GenomeTools framework \cite{genometools}: as such, it is designed to be compilable on any POSIX-compliant operative systems. The compilation can be done using the \texttt{Makefile} provided with \GenomeTools. From the main directory of the sources, the following will compile \GenomeTools, including \Hop, as a 64bit binary: \begin{footnotesize} \begin{verbatim} > make 64bit=yes amalgamation=yes cairo=no curses=no \end{verbatim} \end{footnotesize} In principle it is possible to compile \Hop as a 32-bit binary, by leaving the \texttt{64bit=yes} flag out, however this is discouraged, if a 64-bit system is available. Furthermore, on some systems or using some particular compilers, it may be necessary to use the \texttt{errorcheck=no} option, if errors deriving from compiler warnings arise during the compilation. \subsection{Checking the installation of \Hop} After downloading \Hop or compiling it from the source code, you will have a single binary named \Gtcmd, comprising \Hop and other tools. \Hop can be executed, entering \texttt{gt hop} from the command line. Thus if everything went fine, and the \GenomeTools binary is in the command line path, the following will output an help text on the available options and command line syntax: \begin{footnotesize} \begin{verbatim} > gt hop -help \end{verbatim} \end{footnotesize} \subsection{External programs necessary for the \Hop pipeline} Besides \Hop you will need a read mapping tool. For our evaluation, we used \textit{bwa} (\url{http://bio-bwa.sourceforge.net/}), either using the aln/samse/sampe pipeline (for shorter reads, such as the IonTorrent reads) or the bwasw tool (for longer reads such as the 454 reads). More information can be obtained in the BWA manual page (\url{http://bio-bwa.sourceforge.net/bwa.shtml}). The output of the mapping tool must be, or must be converted into, in SAM/BAM format. Before feeding it into \Hop, the output must be sorted by reference coordinates. For this purpose, one can use the \textit{samtools} (\url{http://samtools.sourceforge.net/}) \texttt{sort} tool. For more information, see also the samtools manual page (\url{http://samtools.sourceforge.net/samtools.shtml}). \section{Preliminary steps} \subsection{1. Preparing the mapping using BWA and Samtools} \Hop corrects homopolymer errors based on a mapping of the reads to a reference sequence. This must be in SAM/BAM format and sorted by coordinate on the reference. It is usually quite easy to prepare the mapping as required. Say the reads to be corrected are \texttt{f\_reads.fastq} and \texttt{r\_reads.fastq}. Furthermore, the reference for the correction is in a Fasta file \texttt{refseq.fas}. Then, in the following example, the \texttt{bwa} tool will be used for the mapping in paired end mode and the results will be sorted using the \texttt{samtools} (as a side note, some of the commands could be combined using piping for an increased efficiency). \begin{footnotesize} \begin{verbatim} > bwa index refseq.fas > bwa aln -t 4 -o 3 -q 15 -f f_reads.sai refseq.fas f_reads.fastq > bwa aln -t 4 -o 3 -q 15 -f r_reads.sai refseq.fas r_reads.fastq > bwa sampe refseq.fas -f map.sam f_reads.sai r_reads.sai f_reads.fastq r_reads.fastq > samtools view -b -o map.bam -S map.sam > samtools sort map.sam sorted \end{verbatim} \end{footnotesize} The results of this pipeline will be in the \texttt{sorted.bam} BAM file, which will be used as an input mapping file for \Hop. \subsection{2. Preparing the reference sequence} The reference sequence is provided to \Hop in GtEncseq format. Converting a sequence in standard sequence formats such as Fasta into GtEncseq is very easy. The following will convert the sequence in \texttt{refseq.fas} into a GtEncseq (see also \texttt{gt encseq encode -help} for more information): \begin{footnotesize} \begin{verbatim} > gt encseq encode refseq.fas \end{verbatim} \end{footnotesize} If the reference comprises multiple sequences (e.g. contigs, or multiple chromosomes), it is important that the order of the sequences used for the encode step must be the same which is specified in the header of the SAM/BAM input file. This is usually not a problem, expecially if all reference sequences are contained in a single MultiFasta file, which is both used for the mapping tool and the generation of the GtEncseq. \section{Running \Hop} \Hop requires the following input: \begin{itemize} \item the mapping of the reads to the reference (sorted SAM/BAM file) \item the reference sequence (GtEncseq format) \item the uncorrected reads \end{itemize} The user shall choose one of the following correction modes:\\ \texttt{-aggressive}, \texttt{-moderate}, \texttt{-conservative} or \texttt{-expert}. The aggressive, moderate and conservative modes are three presets of different correction thresholds parameters. The aggressive mode will tend to correct more, but will be less precise. The conservative mode is the most precise, although more errors will remain. The expert mode allows to setup the parameters manually. For more information run \texttt{gt hop -help}. The following is an example of correction the reads in \texttt{f\_reads.fastq} and \texttt{r\_reads.fastq} using \Hop and a reference sequence contained in \texttt{refseq.fas}. The \texttt{-moderate} option will be used. \begin{footnotesize} \begin{verbatim} > gt hop -moderate -ref refseq.fas \ -map sorted.bam -reads f_reads.fastq r_reads.fastq \end{verbatim} \end{footnotesize} The output will be in this case in the two files \texttt{hop\_f\_reads.fastq} and \texttt{hop\_r\_reads.fastq}. The prefix added by \Hop (in this case \texttt{hop}, which is the default) can be changed using the \texttt{-outprefix} option. \section{Restricting corrections to coding sequences} If desired, it is possible to restrict corrections to coding sequences only. The idea is that coding sequences tend to be more conserved, thus homopolymer length differences of the reads to the reference are more likely to be errors in corrections. In other words, this will help increasing the precision of the correction (reduce false positives), but of course the overall sensitivity will be reduced, as only errors in coding sequences will be corrected. Currently, restricting to coding sequences is only available if a single reference sequence is used (that is no collection of sequences, such as contigs or multiple chromosomes). We plan to eliminate this limitation in future versions of \Hop. The annotation must be provided in \texttt{GFF} format, version 3. This is a standard annotation format. Furthermore, the annotation must be sorted by coordinate, which can be obtained using the \texttt{gt gff3} tool, using the \texttt{-sort} option. In the following example, the \texttt{refseq.gff} annotation will be used to restrict correction to coding sequences: \begin{footnotesize} \begin{verbatim} > gt gff3 -sort -o sorted.gff refseq.gff > gt hop -moderate -ref refseq.fas -ann sorted.gff \ -map sorted.bam -reads f_reads.fastq r_reads.fastq \end{verbatim} \end{footnotesize} The default behaviour when the \texttt{-ann} option is used, is to limit correction to homopolymers inside the \texttt{CDS} features. However, another feature type can be specified, e.g. \texttt{exon}, using the \texttt{-ft} option of \Hop. \subsection{Troubleshooting} In some cases, the GFF file may be slightly not conforming to the standard or suffer under some problems which disrupts parsing. In these cases, standard POSIX utilities can be sometimes be useful, to obtain a subset of the GFF file, which can be used for \Hop. In the following example, using \texttt{awk} and \texttt{sort}, a sorted subset of the \texttt{refseq.gff} annotation is prepared, and saved as \texttt{cdsonly.gff} which only contains the \texttt{CDS} features: \begin{footnotesize} \begin{verbatim} > echo '##gff-version 3' > cdsonly.gff > awk '$3 == "CDS"' refseq.gff | sort -k4 -n >> cdsonly.gff \end{verbatim} \end{footnotesize} \section{Help from the command line} Using \texttt{gt hop -help} will output more information regarding each command line option. Some command line options are used in \texttt{-expert} mode only. To output help also regarding these options use \texttt{gt hop -help+}. \begin{thebibliography}{1} \bibitem{genometools} Gremme, G. (2011). \newblock The \textsc{GenomeTools} genome analysis system. \url{http://genometools.org}. \bibitem{HOP} Gonnella G and Kurtz S and Beckstette M (2012). \newblock {HOP: a reference-based homopolymer error corrector.} \newblock {\em Submitted\/} \end{thebibliography} \end{document} genometools-1.5.1/doc/manuals/ltrdigest.tex000066400000000000000000000646401211610345200210060ustar00rootroot00000000000000\documentclass[12pt,titlepage]{article} \usepackage[a4paper,top=30mm,bottom=30mm,left=20mm,right=20mm]{geometry} \usepackage[utf8]{inputenc} \usepackage{url} \usepackage{alltt} \usepackage{xspace} \usepackage{times} \usepackage{listings} \usepackage{bbm} \usepackage{verbatim} \usepackage{optionman} \newcommand{\LTRdigest}{\textit{LTRdigest}\xspace} \newcommand{\GenomeTools}{\textit{GenomeTools}\xspace} \newcommand{\Suffixerator}{\textit{Suffixerator}\xspace} \newcommand{\GtLTRdigest}{\texttt{gt ltrdigest}\xspace} \newcommand{\Gt}{\texttt{gt}\xspace} \newcommand{\Gtsuffixerator}{\texttt{gt suffixerator}\xspace} \title{\LTRdigest User's Manual} \author{\begin{tabular}{c} \textit{Sascha Steinbiss}\\ \textit{Ute Willhoeft}\\ \textit{Gordon Gremme}\\ \textit{Stefan Kurtz}\\[1cm] Research Group for Genome Informatics\\ Center for Bioinformatics\\ University of Hamburg\\ Bundesstrasse 43\\ 20146 Hamburg\\ Germany\\[1cm] \url{steinbiss@zbh.uni-hamburg.de}\\[1cm] \begin{tabular}{p{0.8\textwidth}} In any documentation or publication about research using \LTRdigest please cite the following paper:\\[5mm] S.~Steinbiss, U.~Willhoeft, G.~Gremme and S.~Kurtz. Fine-grained annotation and classification of \emph{de novo} predicted LTR retrotransposons. \emph{Nucleic Acids Research} 2009, 37(21):7002--7013\\[1mm] \url{http://nar.oxfordjournals.org/cgi/content/full/37/21/7002} \end{tabular} \end{tabular}} \begin{document} \maketitle \section{Introduction} \label{Introduction} This document describes \LTRdigest , a software tool for identification and annotation of characteristic sequence features of LTR retrotransposons in predicted candidates, like those reported by\emph{LTRharvest}~\cite{EKW07}. In particular, \LTRdigest can be used to find \begin{itemize} \item protein domains, \item polypurine tracts (PPT) and \item primer binding sites (PBS) \end{itemize} inside a sequence region predicted to be a LTR retrotransposon. For this identification, \LTRdigest utilises a number of algorithms to create an annotation based on user-supplied constraints. For example, length and position values for possible features can be extensively parameterised, as can be algorithmic parameters like alignment scores and cut-off values. \LTRdigest computes the boundaries and attributes of the features that fit the user-supplied model and outputs them in GFF3 format~\cite{gff3} (in addition to the existing LTR retrotransposon annotation), as well as the corresponding sequences in multiple FASTA format. In addition, a tab-separated summary file is created that can conveniently and quickly browsed for results. \LTRdigest is written in C and it is based on the \GenomeTools library~\cite{genometools}. It is called as part of the single binary named \Gt. The source code can be compiled on 32-bit and 64-bit platforms without making any changes to the sources. It incorporates HMMER~\cite{hmmer}, a popular and widely used profile hidden Markov model package that is used for identification of protein domains, for example using pHMMs taken from the Pfam~\cite{pfam} database. The protein domain search is implemented to be run in a multi-threaded fashion, thus making use of modern multi-core computer systems. \section{Building \emph{LTRdigest}} \label{Building} As \LTRdigest is part of the \GenomeTools software suite, a source distribution of \GenomeTools must be obtained, e.g.\@ via the \GenomeTools home page (\url{http://genometools.org}), and decompressed into a source directory: \begin{verbatim} $ tar -xzvf genometools-X.X.X.tar.gz $ cd genometools-X.X.X \end{verbatim} Then, it suffices to call \texttt{make} to compile the source. To enable protein domain search functionality, please also append the \texttt{with-hmmer=yes} option to the \texttt{make} call. This option will make sure that a HMMER source package is downloaded and compiled along with the \Gt binary. Note that the \texttt{wget} executable must be available in the current PATH to do so (alternatively, you can download HMMER 2.3.2 manually from \texttt{ftp://selab.janelia.org/pub/software/hmmer/CURRENT/} and untar it in the \texttt{src/external/} subdirectory). \begin{verbatim} $ make with-hmmer=yes \end{verbatim}%$ If the \texttt{with-hmmer} option is not specified or set to \texttt{no}, protein domain finding functionality will be missing from the \LTRdigest program. If the build process reports an error due to an unavailable Cairo library, also append the \texttt{cairo=no} option to build the \Gt binary without Cairo support. This has no influence on the function of \LTRdigest . To enable multithreading support (that is, to speed up protein domain search by searching for multiple pHMMs at once), please also specify the \texttt{threads=yes} option to the \texttt{make} call: \begin{verbatim} $ make with-hmmer=yes threads=yes \end{verbatim}%$ After successful compilation, the \GenomeTools executable containing \LTRdigest can then be installed for system-wide use as follows: \begin{verbatim} $ make install \end{verbatim}%$ If a \texttt{prefix=} option is appended to this line, a custom directory can be specified as the installation target directory, e.g.\@ \begin{verbatim} $ make install prefix=/home/user/gt \end{verbatim}%$ %$ will install the \Gt binary in the \texttt{/home/user/gt/bin} directory. Please also consult the \texttt{README} and \texttt{INSTALL} files in the root directory of the uncompressed source tree for more information and troubleshooting advice. \section{Usage} \label{Usage} Some text is highlighted by different fonts according to the following rules. \begin{itemize} \item \texttt{Typewriter font} is used for the names of software tools. \item \texttt{\small{Small typewriter font}} is used for file names. \item \begin{footnotesize}\texttt{Footnote sized typewriter font} \end{footnotesize} with a leading \begin{footnotesize}\texttt{'-'}\end{footnotesize} is used for program options. \item \Showoptionarg{small italic font} is used for the argument(s) of an option. \end{itemize} \subsection{\LTRdigest command line options} Since \LTRdigest is part of \Gt, \LTRdigest is called as follows. \GtLTRdigest $[$\emph{options}$]$ \Showoptionarg{GFF3\_file} \Showoptionarg{indexname} where \emph{GFF3\_file} denotes the GFF3 input file and \emph{indexname} the name of an encoded sequence as created by the \Gtsuffixerator tool. An overview of all possible options with a short one-line description of each option is given in Table \ref{overviewOpt}. They can also be displayed when invoking \LTRdigest with the option \Showoption{help} or \Showoption{help+}. All options can be specified only once. To run the protein domain search in a parallel fashion, use the \Showoption{j} parameter to \texttt{gt} to specify the number of concurrent threads to use: \texttt{gt} \Showoption{j} 3 \texttt{ltrdigest} $[$\emph{options}$]$ \Showoptionarg{GFF3\_file} \Showoptionarg{indexname} \begin{table}[htbp] \caption{Overview of the \LTRdigest options sorted by categories.} \begin{footnotesize} \[ \renewcommand{\arraystretch}{0.89} \begin{tabular}{ll}\hline \Showoptiongroup{Input options} \emph{GFF3\_file}& specify the path to the GFF3 input file \\ \emph{indexname}& specify the path to the input sequences \\ \Showoptiongroup{Output options} \Showoption{outfileprefix}& specify prefix for sequence and tabular output files \\ \Showoption{o}& specify file to output result GFF3 into \\ \Showoption{gzip}& gzip-compress GFF3 output file specified by \Showoption{o} \\ \Showoption{bzip2}& bzip2-compress GFF3 output file specified by \Showoption{o} \\ \Showoption{force}& force output file to be overwritten \\ \Showoption{aaout}& output amino acid sequences for protein domain hits \\ \Showoption{aliout}& output HMMER amino acid alignments \\ \Showoption{seqnamelen}& set maximal length of sequence names in output FASTA headers\\ & (e.g.\@ for clustalw or similar tools) \\ \Showoptiongroup{PPT options} \Showoption{pptlen}& specify a range of acceptable PPT lengths \\ \Showoption{uboxlen}& specify a range of acceptable U-box lengths \\ \Showoption{pptradius}& specify region around 3' LTR beginning to search for PPT \\ \Showoption{pptrprob}& purine emission probability inside PPT \\ \Showoption{pptyprob}& pyrimidine emission probability inside PPT \\ \Showoption{pptaprob}& background A emission probability outside PPT \\ \Showoption{pptcprob}& background C emission probability outside PPT \\ \Showoption{pptgprob}& background G emission probability outside PPT \\ \Showoption{ppttprob}& background T emission probability outside PPT \\ \Showoption{pptuprob}& U/T emission probability inside U-box \\ \Showoptiongroup{PBS options} \Showoption{trnas}& tRNA library in multiple FASTA format \\ \Showoption{pbsalilen}& specify a range of acceptable PBS lengths \\ \Showoption{pbsoffset}& specify a range of acceptable PBS start distances from 3' end of 5' LTR \\ \Showoption{pbstrnaoffset}& specify a range of acceptable tRNA/PBS alignment offsets from tRNA 3' end \\ \Showoption{pbsmaxedist}& specify the maximal allowed unit edit distance in tRNA/PBS alignment \\ \Showoption{pbsradius}& specify region around 5' LTR end to search for PBS \\ \Showoptiongroup{Protein domain search options} \Showoption{hmms}& specify a list of pHMMs for domain search in HMMER2 format \\ \Showoption{pdomevalcutoff}& specify an E-value cutoff for pHMM search \\ \Showoption{maxgaplen}& maximum allowed chaining gap size between fragments (in amino acids) \\ \Showoptiongroup{Alignment options} \Showoption{pbsmatchscore}& specify matchscore for PBS/tRNA Smith-Waterman alignment \\ \Showoption{pbsmismatchscore}& specify mismatchscore for PBS/tRNA Smith-Waterman alignment \\ \Showoption{pbsinsertionscore}& specify insertionscore for PBS/tRNA Smith-Waterman alignment \\ \Showoption{pbsdeletionscore}& specify deletionscore for PBS/tRNA Smith-Waterman alignment \\ \Showoptiongroup{Miscellaneous options} \Showoption{v}& verbose mode \\ \Showoption{help}& show basic options \\ \Showoption{help+}& show basic and extended options \\ \hline \end{tabular} \] \end{footnotesize} \label{overviewOpt} \end{table} \newpage %%%% \subsection{Input parameters} \emph{GFF3\_file}\\ specifies the path to the GFF3 input file. It has to include at least position annotation for the LTR retrotransposon itself (\texttt{LTR\_retrotransposon} type) and the predicted LTRs (\texttt{long\_terminal\_repeat} type) because this information is needed to locate the favored positions of the features in question. The GFF3 file must also be sorted by position, which can be done using \GenomeTools :\\ \texttt{gt gff3} \Showoption{sort} \Showoptionarg{unsorted\_gff3\_file} \texttt{\symbol{62}} \Showoptionarg{sorted\_gff3\_file}\\ \emph{indexname}\\ specifies the index name of an encoded sequence file containing the sequences the GFF3 coordinates refer to. For each sequence in the encoded sequence file given as the second parameter, there must exist a sequence region in the GFF3 file named `\texttt{seq}\textit{i}' where $i$ is the (zero-based) index number of the corresponding sequence in the encoded sequence. For instance, all GFF3 feature coordinates for features on the first sequence in the index file must be on sequence region \texttt{seq0}, and so on. An encoded sequence can be created from a FASTA, GenBank or EMBL format file using the \Gtsuffixerator command:\\ \Gtsuffixerator \Showoption{tis} \Showoption{des} \Showoption{dna} \Showoption{ssp} \Showoption{db} \Showoptionarg{sequencefile} \Showoption{indexname} \Showoptionarg{indexname} %%%% \subsection{Output options} Results are reported in GFF3 format on stdout and can easily be written to a file using the notation \texttt{\symbol{62}} \Showoptionarg{GFF3\_resultfile} as in the following example: \GtLTRdigest $[$\emph{options}$]$ \Showoptionarg{GFF3\_file} \Showoptionarg{indexname} \texttt{\symbol{62}} \Showoptionarg{GFF3\_resultfile} \begin{Justshowoptions} \Option{outfileprefix}{\Showoptionarg{prefix}}{ If this option is given, a number of files containing further information will be created during the \LTRdigest\ run: \begin{itemize} \item \texttt{$<$prefix$>$\_tabout.csv} contains a tab-separated summary of the results that can, for example, be opened in a spreadsheet software or processed by a script. Each column is described in the file's header line and each row describes exactly one LTR retrotransposon candidate. \item \texttt{$<$prefix$>$\_conditions.csv} contains information about the parameters used in the current run for documentation purposes. \item \texttt{$<$prefix$>$\_pbs.fas} contains the PBS sequences identified in the current run in multiple FASTA format. \item \texttt{$<$prefix$>$\_ppt.fas} contains the PPT sequences identified in the current run in multiple FASTA format. \item The files \texttt{$<$prefix$>$\_5ltr.fas} and \texttt{$<$prefix$>$\_3ltr.fas} contain the 5' and 3' LTR sequences identified in the current run in multiple FASTA format. Please note: If the direction of the retrotransposon could be predicted, the files will contain the corresponding 3' and 5' LTR sequences. If no direction could be predicted, forward direction with regard to the original sequence will be assumed, i.e. the 'left' LTR will be considered the 5' LTR. \item Additionally, one \texttt{$<$prefix$>$\_pdom\_$<$domainname$>$.fas} file will be created per protein domain model given. This file contains the FASTA DNA sequences of the HMM matches to the LTR retrotransposon candidates. \end{itemize} In FASTA output files, each FASTA header contains position and sequence region information to match the hit to the corresponding LTR retrotransposon. } \Option{aaout}{\Showoptionarg{yes/no}}{ If this option is set to \Showoptionarg{yes}, one \texttt{$<$prefix$>$\_pdom\_$<$domainname$>$\_aa.fas} file will be created per protein domain model given. This file contains the (concatenated) FASTA amino acid sequences of the HMM matches to the LTR retrotransposon candidates. } \Option{aliout}{\Showoptionarg{yes/no}}{ If this option is set to \Showoptionarg{yes}, one \texttt{$<$prefix$>$\_pdom\_$<$domainname$>$.ali} file will be created per protein domain model given. This file contains alignment information for all matches to of the given protein domain model to the translations of all candidate. } \end{Justshowoptions} %%%% \subsection{PPT options} \begin{Justshowoptions} \Option{pptlen}{\Showoptionarg{$L_{min}$} \Showoptionarg{$L_{max}$}}{ Specify the minimum and maximum allowed lengths for PPT predictions. If a purine-rich region shorter than \Showoptionarg{$L_{min}$} or longer than \Showoptionarg{$L_{max}$} is found, it will be skipped. \\ \Showoptionarg{$L_{min}$} and \Showoptionarg{$L_{min}$} have to be positive integers. If this option is not selected, then \Showoptionarg{$L_{min}$} is set to $8$, \Showoptionarg{$L_{max}$} to 30. } \Option{uboxlen}{\Showoptionarg{$L_{min}$} \Showoptionarg{$L_{max}$}}{ Specify the minimum and maximum allowed lengths for U-box predictions. If a T-rich region preceding a PPT shorter than \Showoptionarg{$L_{min}$} or longer than \Showoptionarg{$L_{max}$} is found, it will be skipped.\\ \Showoptionarg{$L_{min}$} and \Showoptionarg{$L_{min}$} have to be positive integers. If this option is not selected, then \Showoptionarg{$L_{min}$} is set to $3$, \Showoptionarg{$L_{max}$} to 30. } \Option{pptradius}{\Showoptionarg{$r$}}{ Specify the area around the 3' LTR beginning ($l_{s}$) to be searched for PPTs, in other words, define the search interval $[l_{s}-r, l_{s}+r]$.\\ \Showoptionarg{$r$} has to be a positive integer. If this option is not selected, then \Showoptionarg{$r$} is set to 30. } \Option{pptrprob}{\Showoptionarg{$p_R$}}{ Specify the emission probability of a purine base (\texttt{A}/\texttt{G}) inside a PPT. This value must be a valid probability value ($0\leq p_R \leq 1$). If this option is not set, then \Showoptionarg{$p_R$} is set to 0.97. } \Option{pptyprob}{\Showoptionarg{$p_Y$}}{ Specify the emission probability of a pyrimidine base (\texttt{T}/\texttt{C}) inside a PPT. This value must be a valid probability value ($0\leq p_Y \leq 1$). If this option is not set, then \Showoptionarg{$p_Y$} is set to 0.03. } \Option{pptaprob}{\Showoptionarg{$p_A$}}{ Specify the background emission probability of an \texttt{A} base outside of PPT and U-box regions. This value must be a valid probability value ($0\leq p_A \leq 1$). If this option is not set, then \Showoptionarg{$p_A$} is set to 0.25. } \Option{pptcprob}{\Showoptionarg{$p_C$}}{ Specify the background emission probability of a \texttt{C} base outside of PPT and U-box regions. This value must be a valid probability value ($0\leq p_C \leq 1$). If this option is not set, then \Showoptionarg{$p_C$} is set to 0.25. } \Option{pptgprob}{\Showoptionarg{$p_G$}}{ Specify the background emission probability of a \texttt{G} base outside of PPT and U-box regions. This value must be a valid probability value ($0\leq p_G \leq 1$). If this option is not set, then \Showoptionarg{$p_G$} is set to 0.25. } \Option{ppttprob}{\Showoptionarg{$p_T$}}{ Specify the background emission probability of a \texttt{T} base outside of PPT and U-box regions. This value must be a valid probability value ($0\leq p_T \leq 1$). If this option is not set, then \Showoptionarg{$p_T$} is set to 0.25. } \end{Justshowoptions} Note that $\sum_{x \in \left\{A,C,G,T\right\}} p_x = 1$ must hold if the \Showoption{ppt\{a,c,g,t\}prob} options are used. \begin{Justshowoptions} \Option{pptuprob}{\Showoptionarg{$p_U$}}{ Specify the emission probability of a thymine base (\texttt{T}) inside a U-box. This value must be a valid probability value ($0 d$ will be skipped. Set this to 0 to accept exact matches only. It is also possible to fine-tune the results by adjusting the match/mismatch/indelscores used in the Smith-Waterman alignment (see below).\\ \Showoptionarg{$d$} has to be a positive integer. If this option is not selected, then \Showoptionarg{$d$} is set to 1. } \Option{pbsradius}{\Showoptionarg{$r$}}{ Specify the area around the 5' LTR end ($l_{e}$) to be searched for a PBS, in other words, define the search interval $[l_{e}-r, l_{e}+r]$.\\ \Showoptionarg{$r$} has to be a positive integer. If this option is not selected, then \Showoptionarg{$r$} is set to 30. } \Option{pbsmatchscore}{\Showoptionarg{$score_m$}}{ Specify the match score used in the PBS/tRNA Smith-Waterman alignment. Lower this value to discourage matches, increase this value to prefer matches.\\ \Showoptionarg{$score_m$} has to be an integer. If this option is not selected, then \Showoptionarg{$score_m$} is set to 5. } \Option{pbsmismatchscore}{\Showoptionarg{$score_{mm}$}}{ Specify the mismatch score used in the PBS/tRNA Smith-Waterman alignment. Lower this value to discourage mismatches, increase this value to prefer mismatches.\\ \Showoptionarg{$score_{mm}$} has to be an integer. If this option is not selected, then \Showoptionarg{$score_{mm}$} is set to -10. } \Option{pbsdeletionscore}{\Showoptionarg{$score_d$}}{ Specify the deletion score used in the PBS/tRNA Smith-Waterman alignment. Lower this value to discourage deletions, increase this value to prefer deletions.\\ \Showoptionarg{$score_d$} has to be an integer. If this option is not selected, then \Showoptionarg{$score_d$} is set to -20. } \Option{pbsinsertionscore}{\Showoptionarg{$score_i$}}{ Specify the insertion score used in the PBS/tRNA Smith-Waterman alignment. Lower this value to discourage insertions, increase this value to prefer insertions.\\ \Showoptionarg{$score_i$} has to be an integer. If this option is not selected, then \Showoptionarg{$score_i$} is set to -20. } \end{Justshowoptions} \subsection{Protein domain search options} \begin{Justshowoptions} \Option{hmms}{\Showoptionarg{$hmmfile_1, hmmfile_2, \dots, hmmfile_n$}}{ Specify a list of pHMM files in HMMER2 format. The pHMMs must be defined for the amino acid alphabet and follow the Plan7 specification. For example, pHMMs defining protein domains taken from the Pfam database can be used here. Every file must exist and be readable, otherwise an error is reported. If this option is not given, protein domain searching is skipped altogether. Please note that shell globbing can be used here to specify large numbers of files, e.g.\@ by using wildcards.} \Option{pdomevalcutoff}{\Showoptionarg{$c$}}{ Specify the E-value cutoff for HMMER searches. All hits that fail to meet this maximal e-value requirement are discarded.\\ \Showoptionarg{$c$} has to be a probability ($0 \leq c \leq 1$). If this option is not selected, then \Showoptionarg{$c$} is set to $10^{-6}$. } \end{Justshowoptions} \section{Example} This section describes an example session with \LTRdigest . For simplicity, we assume that a \emph{LTRharvest} run on a genome has already been performed and produced a \texttt{ltrs.gff3} file containing the basic GFF3 annotation describing LTR positions. The enhanced suffix array (ESA) index, any sequence output or the tabular standard output from \emph{LTRharvest} will not be needed. Instead, we require an encoded sequence representation of the original input sequence, in this example called \texttt{genome.fas}. This can be created using the \GenomeTools \Gtsuffixerator tool as follows: \texttt{gt suffixerator -tis -des -dna -ssp -db genome.fas -indexname genome.fas} This step creates additional files with the suffixes \texttt{.al1}, \texttt{.des}, \texttt{.esq}, \texttt{.prj} and \texttt{.ssp} in the sequence file directory. We will also assume that the HMM files to be used are called \texttt{HMM1.hmm}, \texttt{HMM2.hmm} and \texttt{HMM3.hmm}, we will be using a tRNA library called \texttt{tRNA.fas}, and we are running \LTRdigest on a dual-core system. We also want to restrict the PBS offset from the LTR end to a maximum of 3 nucleotides, while we want the PPT length to be at least 10 nucleotides. Finally, we want all output such as sequences written to files beginning with ``mygenome-ltrs''. First, sort the GFF3 output by position: \\[0.5cm] \texttt{gt gff3 -sort ltrs.gff3 $>$ ltrs\_sorted.gff3} \\[0.5cm] Then, the \LTRdigest run can be started with the following command line using the parameters above: \\[0.5cm] \texttt{gt -j 2 ltrdigest -pptlen 10 30 -pbsoffset 0 3 -trnas tRNA.fas \\-hmms HMM*.hmm -outfileprefix mygenome-ltrs ltrs\_sorted.gff3 genome.fas $>$ ltrs\_after\_ltrdigest.gff3} No screen output (except possible error messages) is produced since the GFF3 output on stdout is redirected to a file. Additionally, the files \texttt{mygenome\--ltrs\_conditions.csv}, \texttt{mygenome\--ltrs\_3ltr.fas}, \texttt{mygenome\--ltrs\_5ltr.fas}, \texttt{mygenome\--ltrs\_ppt.fas}, \texttt{mygenome\--ltrs\_pbs.fas}, \texttt{mygenome-\-ltrs\_tabout.csv} and one FASTA file for each of the HMM models will be created and updated during the computation. As the files are buffered, it may take a while before first output to these files can be observed. The calculation may be restarted with the same or changed parameters afterwards, overwriting the output files in the process. If it is desired to keep sequences etc. from each run, keep in mind to assign specific \texttt{-outfileprefix} values to each run. \bibliographystyle{unsrt} \begin{thebibliography}{1} \bibitem{EKW07} D.~Ellinghaus, S.~Kurtz, and U.~Willhoeft. \newblock \emph{LTRharvest}, an efficient and flexible software for de novo detection of \normalsize{LTR} retrotransposons. \newblock {\em BMC Bioinformatics} 9:18, 2008. \bibitem{gff3} L.~Stein. \newblock Generic Feature Format Version 3. \url{http://www.sequenceontology.org/gff3.shtml}. \bibitem{genometools} G.~Gremme. \newblock GenomeTools. \url{http://genometools.org}. \bibitem{pfam} R.D.~Finn, J.~Mistry, B.~Schuster-Boeckler, S.~Griffiths-Jones, V.~Hollich, T.~Lassmann,S.~Moxon, M.~Marshall, A.~Khanna, R.~Durbin, S.R.~Eddy, E.L.L.~Sonnhammer and A.~Bateman. \newblock Pfam: clans, web tools and services. \newblock {\em Nucleic Acids Research} (Database Issue), 34:D247-D251, 2006. \bibitem{hmmer} S.R.~Eddy. \newblock HMMER: Biosequence analysis using profile hidden Markov models. \url{http://hmmer.janelia.org}. \end{thebibliography} \end{document} genometools-1.5.1/doc/manuals/ltrharvest.tex000066400000000000000000000754011211610345200212000ustar00rootroot00000000000000\documentclass[12pt,titlepage]{article} \usepackage[a4paper,top=30mm,bottom=30mm,left=20mm,right=20mm]{geometry} \usepackage{url} \usepackage{alltt} \usepackage{xspace} \usepackage{times} \usepackage{listings} \usepackage{bbm} \usepackage{verbatim} %\usepackage[dvips]{hyperref} \usepackage{optionman} \newcommand{\LTRharvest}{\textit{LTRharvest}\xspace} \newcommand{\GenomeTools}{\textit{GenomeTools}\xspace} \newcommand{\Suffixerator}{\textit{Suffixerator}\xspace} \newcommand{\Gtltrharvest}{\texttt{gt ltrharvest}\xspace} \newcommand{\Gt}{\texttt{gt}\xspace} \newcommand{\Gtsuffixerator}{\texttt{gt suffixerator}\xspace} \title{\LTRharvest\\ a manual} \author{\begin{tabular}{c} \textit{David Ellinghaus}\\ \textit{Stefan Kurtz}\\ \textit{Ute Willhoeft}\\[1cm] Research Group for Genomeinformatics\\ Center for Bioinformatics\\ University of Hamburg\\ Bundesstrasse 43\\ 20146 Hamburg\\ Germany\\[1cm] \url{willhoeft@zbh.uni-hamburg.de}\\[1cm] \begin{tabular}{p{0.8\textwidth}} In any documentation or publication about research using \LTRharvest please cite the following paper:\\[5mm] D.~Ellinghaus, S.~Kurtz, and U.~Willhoeft. \LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons, BMC Bioinformatics 2008, 9:18\\[1mm] \url{http://www.biomedcentral.com/1471-2105/9/18} \end{tabular} \end{tabular}} \begin{document} \maketitle \section{Introduction} \label{Introduction} This document describes \LTRharvest \cite{LTRharvesturl}, a software tool for \textit{de novo} predictions of LTR retrotransposons in genomic sequences~\cite{EKW07}. \LTRharvest computes boundary positions of potential LTR retrotransposons on a persistent index structure of the genomic target sequence, the \textit{enhanced suffix array} \cite{AKO04}. Usually the genomic target sequence is a complete chromosomal DNA sequence in FASTA format. Nevertheless, every DNA sequence in (multiple) FASTA format can be passed to the software. For the prediction, \LTRharvest implements several filters. These are consecutively applied on the sequence data to reject candidates, which are not conform with sequence, length or distance features of LTR retrotransposons. Since these features are mostly species-specific, every filter can be switched on or switched off and is free for parameterisation of a certain LTR retrotransposon model. \LTRharvest is written in \texttt{C} and it is based on the \GenomeTools library \cite{genometools}. \LTRharvest is called as part of the single binary named \Gt. %The source code is single threaded and can be compiled on 32-bit and 64-bit %platforms without making any changes to the sources. \LTRharvest runs on an enhanced suffix array index, which is stored on files. This index needs to be constructed by the program \texttt{suffixerator}, which is also part of the \GenomeTools binary \Gt. \section{Usage} \label{Usage} Some text is highlighted by different fonts according to the following rules. \begin{itemize} \item \texttt{Typewriter font} is used for the names of software tools. \item \texttt{\small{Small typewriter font}} is used for file names. \item \begin{footnotesize}\texttt{Footnote sized typewriter font} \end{footnotesize} with a leading \begin{footnotesize}\texttt{'-'}\end{footnotesize} is used for program options. \item \Showoptionarg{small italic font} is used for the argument(s) of an option. \end{itemize} \subsection{The options of \LTRharvest} \label{Overview} Since \LTRharvest is part of \Gt, \LTRharvest is called as follows. \Gtltrharvest \Showoption{index} \Showoptionarg{indexname} $[$\emph{options}$]$ where \Showoptionarg{indexname} denotes the enhanced suffix array index of the target sequence(s) constructed by the program \Suffixerator. An overview of all possible options with a short one-line description of each option is given in Table \ref{overviewOpt}. All options can be specified only once. \begin{table}[htbp] \caption{Overview of the \LTRharvest options sorted by categories.} \begin{footnotesize} \[ \renewcommand{\arraystretch}{0.89} \begin{tabular}{ll}\hline \Showoptiongroup{Input options} \Showoption{index}& specify the name of the enhanced suffix array index \\ \Showoption{range}& specify the range in the input sequences to be searched for LTR retrotransposon candidates \\ \Showoptiongroup{Output options} \Showoption{out}& specify outputfilename for predictions in multiple FASTA format \\ \Showoption{gff3}& specify outputfilename for predictions in GFF3 format \\ \Showoption{outinner}& specify outputfilename for multiple FASTA file of the inner regions of predictions \\ \Showoptiongroup{Filter options} \Showoption{seed}& specify minimum seed length for exact maximal repeats \\ \Showoption{minlenltr}& specify minimum length for each LTR \\ \Showoption{maxlenltr}& specify maximum length for each LTR \\ \Showoption{mindistltr}& specify minimum distance of LTR startpositions \\ \Showoption{maxdistltr}& specify maximum distance of LTR startpositions \\ \Showoption{similar}& specify similaritythreshold in range [1..100\%] \\ \Showoption{mintsd}& specify minimum length for each TSD \\ \Showoption{maxtsd}& specify maximum length for each TSD (requires \Showoption{mintsd}) \\ \Showoption{motif}& specify palindromic motif consisting of 2 nucleotides startmotif + 2 nucleotides endmotif, \\ \Showoption{motifmis}& specify maximum number of mismatches in motif (requires \Showoption{motif}) \\ \Showoption{vic}& specify the number of nucleotides (to the left and to the right) \\ & that will be searched for TSDs and/or motifs around 5' and 3' boundary \\ \Showoption{overlaps}& specify no$|$best$|$all \\ \Showoptiongroup{Alignment options} \Showoption{xdrop}& specify xdrop value for seed extension \\ \Showoption{mat}& specify matchscore for seed extension \\ \Showoption{mis}& specify mismatchscore for seed extension \\ \Showoption{ins}& specify insertionscore for seed extension \\ \Showoption{del}& specify deletionscore for seed extension \\ \Showoptiongroup{Miscellaneous options} \Showoption{v}& verbose mode \\ \Showoption{longoutput}& additional motif/TSD output (requires \Showoption{mintsd} or \Showoption{motif}) \\ \Showoption{help}& show all options \\ \hline \end{tabular} %\input{ltrprogoptions} \] \end{footnotesize} \label{overviewOpt} \end{table} %%%% \subsection{Input options} \begin{Justshowoptions} \Option{index}{\Showoptionarg{indexname}}{ Specify the name of the enhanced suffix array index. The index must comprise the tables $\tt{suf}$, $\tt{lcp}$, $\tt{des}$ and $\tt{tis}$. An example of how the enhanced suffix array index is constructed with the program \Suffixerator can be found in section~\ref{Examples}. } \end{Justshowoptions} The option \Showoption{index} is mandatory. \begin{Justshowoptions} \Option{range}{\Showoptionarg{$x$ $y$}}{ Specify the range in the input sequence(s) to be searched for LTR retrotransposon candidates. That is, if $x=1000$ and $y=10000$ then candidates are only reported if they start after position 1000 and end before position 10000 in their respective sequence coordinates. If $x=y=0$ (default), then the whole sequences are searched. } \end{Justshowoptions} %%%% \subsection{Output options} Results are reported in tabular fashion on stdout and can easily be written to a file using the notation \texttt{\symbol{62}} \Showoptionarg{resultfile} as in the following: \Gtltrharvest \Showoption{index} \Showoptionarg{indexname} $[$\emph{options}$]$ \texttt{\symbol{62}} \Showoptionarg{resultfile} In addition, the following options write extra information to files \begin{Justshowoptions} \Option{out}{\Showoptionarg{outputfile}}{ Specify the name of a file where the predictions will be written to. Each prediction will be represented by an individual FASTA entry. } \Option{outinner}{\Showoptionarg{outputfile}}{ Specify the name of a file where the inner regions (the prediction sequences without the flanking LTR sequences) will be written to. Each prediction will be represented by an individual FASTA entry. } \Option{gff3}{\Showoptionarg{outputfile}}{ Specify the name of a file where the predictions will be written to. Each prediction will be represented by an individual GFF3~\cite{gff3} entry. } \end{Justshowoptions} %%%% \subsection{Filter options} The filter options provide the opportunity to exclude predictions with unwanted sequence, length or distance features. If a particular option is not set by the user, a default value for this options will be set, except for the options \Showoption{mintsd}, \Showoption{maxtsd} and \Showoption{motif}. Thus, if none of the filter options is set by the user, a prediction of LTR retrotransposons will be conducted without searching for target site duplications (TSD) or a particular LTR start-end motif. \begin{Justshowoptions} \Option{seed}{\Showoptionarg{$L_{ex}$}}{ Specify the minimum length for the exact maximal repeats. Only those repeats with the specified minimum length are analyzed in the process of finding candidate pairs. Exact maximal repeats of length below that threshold are not taken further into account. \Showoptionarg{$L_{ex}$} has to be a positive integer. If this option is not selected by the user, then \Showoptionarg{$L_{ex}$} is set to $30$ by default. } \Option{minlenltr}{\Showoptionarg{$L_{min}$}}{ Specify the minimum length of each LTR. \Showoptionarg{$L_{min}$} has to be specified as a positive integer. If this option is not selected by the user, then \Showoptionarg{$L_{min}$} is set to $100$ by default. } \Option{maxlenltr}{\Showoptionarg{$L_{max}$}}{ Specify the maximum length of each LTR. \Showoptionarg{$L_{max}$} has to be specified as a positive integer. If this option is not selected by the user, then \Showoptionarg{$L_{max}$} is set to $1000$ by default. } \Option{mindistltr}{\Showoptionarg{$D_{min}$}}{ Specify the minimum distance of LTR starting positions. \Showoptionarg{$D_{min}$} has to be specified as a positive integer. If this option is not selected by the user, then \Showoptionarg{$D_{min}$} is set to $1000$ by default. } \Option{maxdistltr}{\Showoptionarg{$D_{max}$}}{ Specify the maximum distance of LTR starting positions. \Showoptionarg{$D_{max}$} has to be specified as a positive integer. If this option is not selected by the user, then \Showoptionarg{$D_{max}$} is set to $15000$ by default. } \Option{similar}{\Showoptionarg{similaritythreshold}}{ Specify the minimum similarity value between the two LTRs. The argument \Showoptionarg{similaritythreshold} has to be chosen from the range [0,100] and means a percentage. If this option is not selected by the user, the default value is set to 85\%. } \Option{mintsd}{\Showoptionarg{TSDminlen}}{ If this option is selected, a search for target site duplications (TSDs) will be conducted with a minimum TSD length of \Showoptionarg{TSDminlen}. If this option is not selected by the user, a search for TSDs with minimum TSD length 4 will be conducted. If this option is set but no maximum TSD length is specified by the option \Showoption{maxtsd}, then the maximum TSD length is set to $20$ by default. } \Option{maxtsd}{\Showoptionarg{TSDmaxlen}}{ This option requires the option \Showoption{mintsd}. If this option is selected, a search for target site duplications (TSDs) will be conducted with a maximum TSD length of \Showoptionarg{TSDmaxlen}. } \Option{motif}{\Showoptionarg{expr}}{ Specify 2 nucleotides for the starting motif and 2 nucleotides for the ending motif at the beginning and the ending of each LTR, respectively. Only palindromic motif sequences - where the motif sequence is equal to its complementary sequence read backwards - %- of %nucleotides a(adenine), c(cytosine), g(guanine), t(thymine) are allowed, e.g. \Showoptionarg{tgca}. Type the nucleotides without any space separating them. If this option is not selected by the user, then candidate pairs will not be checked, if they contain a motif. If this options is set but no allowed number of mismatches is specified by the option \Showoption{motifmis}, then a search for the exact motif will be conducted. } \Option{motifmis}{\Showoptionarg{n}}{ This option requires the option \Showoption{motif}. Specify the allowed number of mismatches by the argument \Showoptionarg{n}. If this option is not set, then a search for the exact motif will be conducted. The non-negative integer \Showoptionarg{n} has to be chosen from the range $[0,3]$. } \Option{vic}{\Showoptionarg{l}}{ Specify the number of nucleotide positions \Showoptionarg{l} to the left and to the right (the vicinity), that will be searched for TSDs and/or one motif around the 5' and 3' predicted boundary of a LTR retrotransposon. This option has only an effect, if option \Showoption{mintsd} and/or option \Showoption{motif} is switched on. If this option is not selected by the user, the default value of $l$ is 60. } \Option{overlaps} {\Showoptionarg{no}$|$\Showoptionarg{best}$|$\Showoptionarg{all}}{ Specify the output with regard to nested and/or overlapping LTR retrotransposon predictions. If the argument \Showoptionarg{no} is selected, then neither nested nor overlapping predictions will be reported in the output. If the argument \Showoptionarg{best} is selected, then, in the case of two or more nested or overlapping predictions, solely the LTR retrotransposon prediction with the highest similarity between its LTRs will be reported. If the argument \Showoptionarg{all} is selected, then all LTR retrotransposon predictions will be reported whether there are nested and/or overlapping predictions or not. If this option is not selected by the user, the option with argument \Showoptionarg{best} is set by default. } \end{Justshowoptions} %%%% \subsection{Alignment options} An $X$-drop extension process permits the search for degenerated LTRs. The alignment options provide the opportunity to control this extension of the maximal repeat seeds. If a particular alignment option is not set by the user, a default value for this options will be set. \begin{Justshowoptions} \Option{xdrop}{\Showoptionarg{X}}{ Specify the xdrop value \Showoptionarg{X} for extending a seed repeat in both directions allowing for matches, mismatches, insertions, and deletions. The argument \Showoptionarg{X} must be a positive integer or $0$. The $X$-drop extension process stops as soon as the extension involving matches, mismatches, insertions, and deletions has a score smaller than $T-X$ where T denotes the largest score seen so far. If this option is not selected by the user, then \Showoptionarg{X} is set to $5$ by default. } \Option{mat}{\Showoptionarg{score}}{ Specify the positive match score for the $X$-drop extension process. If the option is not selected by the user, the default value is $2$. } \Option{mis}{\Showoptionarg{score}}{ Specify the negative mismatch score for the $X$-drop extension process. If this option is not selected by the user, the default value is $-2$. } \Option{ins}{\Showoptionarg{score}}{ Specify the negative insertion score for the $X$-drop extension process. If this option is not selected by the user, the default value is $-3$. } \Option{del}{\Showoptionarg{score}}{ Specify the negative deletion score for the $X$-drop extension process. If this option is not selected by the user, the default value is $-3$. } \end{Justshowoptions} %%%% \subsection{Miscellaneous options} \begin{Justshowoptions} \Option{v}{}{ This option enables the verbose mode. This means, that some more information about the processing will be printed to \texttt{stdout} during the run. This includes a long list of switched on or switched off options. } \Option{longoutput}{}{ This option additionally prints information about the detected TSD and/or the motif to \texttt{stdout}, if a search for TSD and/or for the motif has been selected by the user. This option requires the option \Showoption{mintsd} and/or \Showoption{motif}. } \Option{help}{}{ \LTRharvest will show a summary of all options on \texttt{stdout} and terminate with exit code $0$. } \end{Justshowoptions} %%%%%%%%%%%% \section{Examples} \label{Examples} In this section, example applications of \LTRharvest are presented. In Subsection~\ref{different-options}, examples for using different options of \LTRharvest are given. Subsection~\ref{Example-genome} then gives an example for the prediction of LTR retrotransposons on the entire \textit{S. cerevisiae} genome. In Subsection~\ref{ExampleCluster}, an example for a clustering process of the \LTRharvest output is shown. Please note that this step is not part of \LTRharvest and is carried out by %with a subsequent %clustering process of the predicted sequences using \textit{Vmatch}~\cite{vmatch}. %(which is not part of the \GenomeTools binary \Gt). \subsection{Using different options of \LTRharvest} \label{different-options} As target sequence file we use some FASTA file \texttt{\small{chr02.19970727.fsa.gz}} containing the \textit{S. cerevisiae} genome sequence, chromosome 2. Note that the file is a compressed file in gzip format (because of the ending \texttt{.gz}). This format can be handled by the program \Suffixerator. First, we create the enhanced suffix array. We invoke \Gtsuffixerator with options \Showoption{tis}, \Showoption{suf}, \Showoption{lcp}, \Showoption{des}, \Showoption{ssp} and \Showoption{sds} since \LTRharvest needs the corresponding tables. Furthermore, we specify \Showoption{dna}, as we process DNA-sequences. \begin{footnotesize} \begin{verbatim} $ gt suffixerator -db chr02.19970727.fsa.gz -indexname chr02.19970727.fsa -tis -suf -lcp -des -ssp -sds -dna # dna=yes # indexname="chr02.19970727.fsa" . . . # TIME overall 1.37 \end{verbatim} \end{footnotesize} Now we can use the index for \LTRharvest. The first example call will just use the default parameters for the filter and alignment options without searching for TSD or an LTR start-end motif. \begin{footnotesize} \begin{verbatim} $ gt ltrharvest -index chr02.19970727.fsa # args=-index chr02.19970727.fsa # predictions are reported in the following way # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR) l(rLTR) sim(LTRs) seq-nr # where: # s = starting position # e = ending position # l = length # ret = LTR-retrotransposon # lLTR = left LTR # rLTR = right LTR # sim = similarity # seq-nr = sequence number 259532 265448 5917 259532 259863 332 265117 265448 332 99.40 0 427672 430021 2350 427672 428170 499 429522 430021 500 91.60 0 29632 35597 5966 29632 29969 338 35259 35597 339 98.82 0 220989 226919 5931 220989 221339 351 226574 226919 346 97.15 0 \end{verbatim} \end{footnotesize} Each comment line starts with the comment symbol \#. Each non-comment line denotes a LTR retrotransposon prediction with starting and ending positions of the whole LTR retrotransposon, the left LTR instance and the right LTR instance, respectively. Furthermore, for each of these elements, the corresponding element length is reported as well as a percentage similarity of the two LTRs. The last integer of each line denotes the number of the input sequence, the LTR retrotransposon prediction occurs in. The input sequence numbers are counted from 0. Invoking \LTRharvest with the optional argument \Showoption{v} gives more information about enabled and disabled options as well as additional information about the enhanced suffix array index and time/space consumption. Moreover, specifying options \Showoption{out} and \Showoption{outinner} the run results in two multiple FASTA files. \begin{footnotesize} \begin{verbatim} $ gt ltrharvest -index chr02.19970727.fsa -v -out pred-chr02.fsa -outinner pred-inner-chr02.fsa # args=-index chr02.19970727.fsa -v -out pred-chr02.fsa -outinner pred-inner-chr02.fsa # user defined options and values: # verbosemode: On # indexname: chr02.19970727.fsa # outputfile: pred-chr02.fsa # outputfile inner region: pred-inner-chr02.fsa # xdropbelowscore: 5 # similaritythreshold: 85.00 # minseedlength: 30 # matchscore: 2 # mismatchscore: -2 # insertionscore: -3 # deletionscore: -3 # minLTRlength: 100 # maxLTRlength: 1000 # minLTRdistance: 1000 # maxLTRdistance: 15000 # overlaps: best # minTSDlength: 0 # maxTSDlength: 20 # palindromic motif: # motifmismatchesallowed: 4 # vicinity: 60 nt # predictions are reported in the following way # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR) l(rLTR) sim(LTRs) seq-nr # where: # s = starting position # e = ending position # l = length # ret = LTR-retrotransposon # lLTR = left LTR # rLTR = right LTR # sim = similarity # seq-nr = sequence number 259532 265448 5917 259532 259863 332 265117 265448 332 99.40 0 427672 430021 2350 427672 428170 499 429522 430021 500 91.60 0 29632 35597 5966 29632 29969 338 35259 35597 339 98.82 0 220989 226919 5931 220989 221339 351 226574 226919 346 97.15 0 \end{verbatim} \end{footnotesize} Searching additionally for TSD and a LTR start-end motif we use the options \Showoption{mintsd}, \Showoption{maxtsd}, \Showoption{motif} and \Showoption{motifmis}. \begin{footnotesize} \begin{verbatim} $ gt ltrharvest -index chr02.19970727.fsa -mintsd 5 -maxtsd 20 -motif tgca -motifmis 0 # args=-index chr02.19970727.fsa -mintsd 5 -maxtsd 20 -motif tgca -motifmis 0 # predictions are reported in the following way # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) s(rLTR) e(rLTR) l(rLTR) sim(LTRs) seq-nr # where: # s = starting position # e = ending position # l = length # ret = LTR-retrotransposon # lLTR = left LTR # rLTR = right LTR # sim = similarity # seq-nr = sequence number 259532 265448 5917 259532 259863 332 265117 265448 332 99.40 0 29632 35590 5959 29632 29963 332 35259 35590 332 99.70 0 220996 226911 5916 220996 221329 334 226575 226911 337 97.33 0 \end{verbatim} \end{footnotesize} Finally, if we are interested in the sequence and the length of the TSD as well as the sequence of the motif, we select the option \Showoption{longoutput}. This also is an example for specifying all filter and alignment options by the user. \begin{footnotesize} \begin{verbatim} $ gt ltrharvest -index chr02.19970727.fsa -seed 30 -xdrop 5 -mat 2 -mis -2 -ins -3 -del -3 -minlenltr 100 -maxlenltr 1000 -mindistltr 1000 -maxdistltr 15000 -similar 90.0 -overlaps all -mintsd 5 -maxtsd 20 -motif tgca -motifmis 0 -vic 60 -longoutput # args=-index chr02.19970727.fsa -seed 30 -xdrop 5 -mat 2 -mis -2 -ins -3 -del -3 -minlenltr 100 -maxlenltr 1000 -mindistltr 1000 -maxdistltr 15000 -similar 90.0 -overlaps all -mintsd 5 -maxtsd 20 -motif tgca -motifmis 0 -vic 60 -longoutput # predictions are reported in the following way # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) TSD l(TSD) m(lLTR) s(rLTR) e(rLTR) l(rLTR) TSD l(TSD) m(rLTR) sim(LTRs) seq-nr # where: # s = starting position # e = ending position # l = length # m = motif # ret = LTR-retrotransposon # lLTR = left LTR # rLTR = right LTR # TSD = target site duplication # sim = similarity # seq-nr = sequence number 259532 265448 5917 259532 259863 332 gtaat 5 tg..ca 265117 265448 332 gtaat 5 tg..ca 99.40 0 29632 35590 5959 29632 29963 332 ataat 5 tg..ca 35259 35590 332 ataat 5 tg..ca 99.70 0 220996 226911 5916 220996 221329 334 ggaat 5 tg..ca 226575 226911 337 ggaat 5 tg..ca 97.33 0 \end{verbatim} \end{footnotesize} \subsection{Predictions on the entire \textit{S.cerevisiae} genome} \label{Example-genome} As target sequences file we use some multiple FASTA file \texttt{\small{chrAll.19971001.fsa.gz}}, which contains all 16 chromosomal sequences of the release before Oct. 1st, 1997, probably used by Kim et al. in their comprehensive survey of retrotransposons~\cite{kim:1998}. First, we create the enhanced suffix array. We invoke \Gtsuffixerator with options \Showoption{tis}, \Showoption{suf}, \Showoption{lcp}, \Showoption{des}, since \LTRharvest needs the corresponding tables. Furthermore, we specify option \Showoption{dna}, as we are processing DNA sequences. \begin{footnotesize} \begin{verbatim} $ gt suffixerator -db chrAll.19971001.fsa.gz -indexname chrAll.19971001.fsa -tis -suf -lcp -des -sds -dna # dna=yes # indexname="chrAll.19971001.fsa" . . . # TIME overall 108.35 \end{verbatim} \end{footnotesize} Now we can use the index with \LTRharvest. In addition to the filter and alignment options, we choose option \Showoption{out} for printing the predicted LTR retrotransposon sequences to a file. \begin{footnotesize} \begin{verbatim} $ gt ltrharvest -index chrAll.19971001.fsa -seed 100 -minlenltr 100 -maxlenltr 1000 -mindistltr 1000 -maxdistltr 15000 -xdrop 5 -mat 2 -mis -2 -ins -3 -del -3 -similar 90.0 -overlaps best -mintsd 5 -maxtsd 20 -motif tgca -motifmis 0 -vic 60 -longoutput -out pred-chrAll.fsa # args=-index chrAll.19971001.fsa -seed 100 -minlenltr 100 -maxlenltr 1000 -mindistltr 1000 -maxdistltr 15000 -xdrop 5 -mat 2 -mis -2 -ins -3 -del -3 -similar 90.0 -overlaps best -mintsd 5 -maxtsd 20 -motif tgca -motifmis 0 -vic 60 -longoutput -out pred-chrAll.fsa # predictions are reported in the following way # s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR) TSD l(TSD) m(lLTR) s(rLTR) e(rLTR) l(rLTR) TSD l(TSD) m(rLTR) sim(LTRs) seq-nr # where: # s = starting position # e = ending position # l = length # m = motif # ret = LTR-retrotransposon # lLTR = left LTR # rLTR = right LTR # TSD = target site duplication # sim = similarity # seq-nr = sequence number 160239 166163 5925 160239 160575 337 ggttc 5 tg..ca 165827 166163 337 ggttc 5 tg..ca 100.00 0 29632 35590 5959 29632 29963 332 ataat 5 tg..ca 35259 35590 332 ataat 5 tg..ca 99.70 1 . . . 844407 850335 5929 844407 844744 338 gaaat 5 tg..ca 849998 850335 338 gaaat 5 tg..ca 100.00 15 56452 62375 5924 56452 56788 337 gttat 5 tg..ca 62039 62375 337 gttat 5 tg..ca 100.00 15 \end{verbatim} \end{footnotesize} \subsection{Sequence clustering of \LTRharvest output (optional)} \label{ExampleCluster} In addition to the prediction process done by \LTRharvest, a cluster analysis on the predicted sequences is recommended. Here, we choose the single linkage cluster analysis program from the \textit{Vmatch} software tool~\cite{vmatch} (which is not part of the \GenomeTools binary \Gt) in order to show how this task can be accomplished. An index needs to be constructed from the predicted sequences by the program \texttt{mkvtree} which is part of \textit{Vmatch}. \begin{footnotesize} \begin{verbatim} $ mkvtree -db pred-chrAll.fsa -dna -pl -allout -v reading file "pred-chrAll.fsa" ... . . . overall space peak: main=2.61 MB (10.01 bytes/symbol), secondary=0.53 MB \end{verbatim} \end{footnotesize} Now we can use \texttt{vmatch} (which is part of \textit{Vmatch}) to perform a clustering of the predicted sequences. A reasonable parameter set is given in Tab.~\ref{parameters-cluster-default}, page~\pageref{parameters-cluster-default}. See the \emph{Vmatch manual}~\cite{vmatch} for an explanation of the options. The following command computes clusters of all (database) sequences in \texttt{\small{pred-chrAll.fsa}}. Each cluster has a unique cluster number, followed by the sequence number contained in the cluster. \begin{footnotesize} \begin{verbatim} $ vmatch -dbcluster 95 7 Cluster-pred-chrAll -p -d -seedlength 50 -l 1101 -exdrop 9 pred-chrAll.fsa # args=-dbcluster 95 7 Cluster-pred-chrAll -p -d -seedlength 50 -l 1101 -exdrop 9 pred-chrAll.fsa # 3 clusters # 45 elements out of 46 (97.83%) are in clusters # 1 elements out of 46 (2.17%) are singlets # 1 cluster of size 2 # 1 cluster of size 3 # 1 cluster of size 40 0: 32 41 42 36 39 13 40 43 37 30 44 38 18 21 17 34 35 31 12 20 33 23 26 27 6 28 3 29 25 1 24 9 19 2 7 22 4 10 5 0 1: 8 15 11 2: 14 45 \end{verbatim} \end{footnotesize} %\bibliographystyle{plain} %\bibliography{references} \begin{thebibliography}{1} \bibitem{LTRharvesturl} \url{http://www.zbh.uni-hamburg.de/ltrharvest} \bibitem{gff3} \textsc{GFF3}, tab delimited file format for genome annotation. \url{http://www.sequenceontology.org/gff3.shtml}. \bibitem{AKO04} M.I. Abouelhoda, S.~Kurtz, and E.~Ohlebusch. \newblock Replacing suffix trees with enhanced suffix arrays. \newblock {\em Journal of Discrete Algorithms}, 2:53--86, 2004. \bibitem{EKW07} D.~Ellinghaus, S.~Kurtz, and U.~Willhoeft. \newblock \LTRharvest, an efficient and flexible software for de novo detection of \normalsize{LTR} retrotransposons. \newblock {\em BMC Bioinformatics}, 9:18, 2008. \bibitem{genometools} G.~Gremme. \newblock The \textsc{GenomeTools} genome analysis system. \url{http://genometools.org}. \bibitem{kim:1998} J.M. Kim, S.~Vanguri, J.D. Boeke, A.~Gabriel, and D.F. Voytas. \newblock Transposable elements and genome organisation: a comprehensive survey of retrotransposons revealed by the complete \textit{Saccharomyces cerevisiae} genome sequence. \newblock {\em Genome Research}, 8(5):464--478, 1998. \bibitem{vmatch} S.~Kurtz. \newblock The \textsc{Vmatch} large scale sequence analysis software. \url{http://www.vmatch.de}. \end{thebibliography} \begin{table} \caption{A default parameter set for \textit{Vmatch}'s single linkage clustering program.} \vspace{0.25cm} \begin{tabular}[h!]{lcl}\hline Parameter name & Value & Comment\\\hline dbcluster & 95 ($\lfloor(\frac{D_{min}}{D_{max}} \times 100)\rfloor + 1$) & Match covers at least 95\% of the smaller sequence and\\ & & (\textit{formula value})\% of the larger sequence\\ d & & Compute direct matches\\ p & & Compute palindromic matches\\ seedlength & 50 & Minimal length of the exact repeats\\ l & $D_{min} + L_{min}$ & Minimal length of matches\\ exdrop & 9 & Xdrop score when extending a seed in both directions\\\hline \end{tabular} \label{parameters-cluster-default} \end{table} \end{document} genometools-1.5.1/doc/manuals/matstat.tex000066400000000000000000000000461211610345200204500ustar00rootroot00000000000000\def\BuildMatstat{} \input{uniquesub} genometools-1.5.1/doc/manuals/mgth.tex000066400000000000000000000433601211610345200177400ustar00rootroot00000000000000\documentclass[12pt,titlepage]{article} \usepackage[a4paper,top=30mm,bottom=30mm,left=20mm,right=20mm]{geometry} \usepackage{url} \usepackage{alltt} \usepackage{xspace} \usepackage{times} \usepackage{listings} \usepackage{bbm} \usepackage{verbatim} \usepackage{optionman} \usepackage{graphicx} \usepackage{color} \input{dvipsnam.def} \newcommand{\MetagenomeThreader}{\textit{MetagenomeThreader}\xspace} \newcommand{\GenomeTools}{\textit{GenomeTools}\xspace} \newcommand{\nucleotide}{\textit{nucleotide}\xspace} \newcommand{\XMLFile}{\texttt{\small{BLAST-Filename}}\xspace} \newcommand{\MGFile}{\texttt{\small{Metagenome-Filename}}\xspace} \newcommand{\HitFile}{\texttt{\small{Hit-Sequence-Filename}}\xspace} \newcommand{\Gtmgth}{\texttt{gt mgth}\xspace} \newcommand{\Gt}{\texttt{gt}\xspace} \newcommand{\Attention}{\textbf{ATTENTION:}\xspace} \setlength{\tabcolsep}{2pt} \title{\MetagenomeThreader\\ a manual} \author{\begin{tabular}{c} \textit{David Schmitz-H\"{u}bsch}\\ \textit{Stefan Kurtz}\\[1cm] Research Group for Genomeinformatics\\ Center for Bioinformatics\\ University of Hamburg\\ Bundesstrasse 43\\ 20146 Hamburg\\ Germany\\[1cm] \end{tabular}} \begin{document} \maketitle \section{Introduction} \label{Introduction} This document describes the \MetagenomeThreader, a software tool for the prediction of genes in sequences of metagenome projects. The \MetagenomeThreader is based on the algorithem from Krause et al \cite{krause}. For the prediction of PCSs (Predicted Coding Sequences) the metagenome sequences are blasted against a nucleotide database and the resultig BLAST-hits are used to process a combined score for every position in a DNA-sequence. The combined score reflects the potential that a specific DNA-sequence position is a coding one. The \MetagenomeThreader is written in \texttt{C} and is based on the \GenomeTools library \cite{genometools}. \\ The \MetagenomeThreader is called as part of the single binary named \Gt. %The source code is single threaded and can be compiled on 32-bit and 64-bit %platforms without making any changes to the sources. \section{Usage} \label{Usage} \subsection{The meaning of used type of fonts} \label{Fonts} Some text is highlighted by different fonts according to the following rules. \begin{itemize} \item \texttt{Typewriter font} is used for the names of software tools. \item \texttt{\small{Small typewriter font}} is used for file names. \item \begin{footnotesize}\texttt{Footnote sized typewriter font} \end{footnotesize} with a leading \begin{footnotesize}\texttt{'-'}\end{footnotesize} is used for program options. \item \Showoptionarg{small italic font} is used for the argument(s) of an option. \end{itemize} \subsection{The functionality of the \MetagenomeThreader} \label{Functional} The \MetagenomeThreader needs 3 data sets, the metagenome sequences are also required. The BLAST-hits will then be generated through a BLAST of the metagenome-sequences against a nucleotide database such as nt from NCBI. \Attention Generating the BLAST-hits is not part of the \MetagenomeThreader and has to be done preliminary. The resulting BLAST-hits have to be saved in XML-format. If the BLAST-hits are generated, the hit-sequences can be achieved through the \MetagenomeThreader. In order to generate the hit-sequence file, the \MetagenomeThreader requires a local copy of the appropriate nucleotide database, such as nt from NCBI, which will be scanned during the \MetagenomeThreader processing. You can download a nucleotide database from \\ {\url{ftp://ftp.ncbi.nih.gov/blast/db/FASTA}} for example. \subsection{The Installation of the \MetagenomeThreader} \label{Install} The \MetagenomeThreader will be installed and is ready for use after the installation of the \GenomeTools (see \cite{genometools} for installation instructions). There are two different installation options for the \GenomeTools in relation to the \MetagenomeThreader. The standard installation installs the \\ \MetagenomeThreader without the cURL-module. If you prefer to install the \MetagenomeThreader including the cURL-module, you have to include the the command \texttt{make curl="yes"} during the \GenomeTools installation process. A connection to the internet is required to use the curl module. With the curl-module, the MetagenomeThreader will run an online query for missing hit-sequences, otherwise they will be ignored during the processing of the PCS's. \subsection{The Options of the \MetagenomeThreader} \label{Overview} Since \MetagenomeThreader is part of \Gt, the \MetagenomeThreader is called as following: \Gtmgth $[$\emph{options}$]$ \XMLFile \MGFile \HitFile \XMLFile denotes the XML formatted BLAST-hit file, \MGFile the FASTA formatted metagenome-sequences file and the \HitFile the FASTA formatted hit-sequences file. The \XMLFile has to be created with a BLAST-Program. Because of the dimension of the resulting files in metagenome projects, an online BLAST is neither advisable nor practicable. The hit-sequence file may be empty at the time of the first program call. All three files have to be provided at every program call and can also be zipped files (\texttt{\small{.gz}}). An overview of all possible options with a short descripton of each option is available in table \ref{overviewOpt}. All options can only be specified once. \begin{table}[htbp] \caption{Overview of the \MetagenomeThreader Options.} \begin{footnotesize} \[ \renewcommand{\arraystretch}{0.89} \begin{tabular}{p{2cm}p{14cm}}\hline \\ \Showoption{s}& specify score for a synonymic base exchange \\ \Showoption{n}& specify score for a nonsynonymic base exchange \\ \Showoption{b}& specify score for a blast-hit end within a query-sequence \\ \Showoption{q}& specify score for a stop-codon within a query-sequence \\ \Showoption{h}& specify score for a stop-codon within a hit-sequence \\ \Showoption{l}& specify score leaving a gene on forward/reverse strand or enter a gene on forward/reverse strand \\ \Showoption{p}& specify maximum span between coding-regions in the same reading frame resume as one prediction \\ \Showoption{f}& specify maximum span between coding-regions in different reading frames resume as coding-regions in the optimal reading-frame \\ \Showoption{o}& specify the database name for the fcgi-database used in the cURL-module \\ \Showoption{k}& specify the database name used for the hit-sequence extraction \\ \Showoption{t}& specify yes$|$no if a hit-sequence file exists \\ \Showoption{r}& specify 1$|$2$|$3 for the format of the output-file \\ \Showoption{a}& specify minimum length of the amino acid sequences in the result \\ \Showoption{d}& specify minimum percent-value for the different kinds in the hit-statistic output \\ \Showoption{e}& specify 1$|$2$|$3 for the use of alternative start-codons \\ \Showoption{m}& specify yes$|$no if the processing has to be based on homology - experimental \\ \Showoption{g}& specify yes$|$no for the \GenomeTools test modus - output without the creating date \\ \Showoption{x}& specify yes$|$no to extend PCSs to max length \\ \Showoption{version}& display version information and exit \\ \Showoption{help}& show all options \\ \hline \end{tabular} %\input{ltrprogoptions} \] \end{footnotesize} \label{overviewOpt} \end{table} %%%% \subsection{\MetagenomeThreader Options} \begin{Justshowoptions} \Option{s}{\Showoptionarg{score}}{ Specify the score for synonymic base exchanges. \Showoptionarg{score} has to be specified as a double. If this option is not selected by the user, then \Showoptionarg{score} is set to $1.00$ by default (recommended: positive score). } \Option{n}{\Showoptionarg{score}}{ Specify the score for nonsynonymic base exchanges. \Showoptionarg{score} has to be specified as a double. If this option is not selected by the user, then \Showoptionarg{score} is set to $-1.00$ by default (recommended: negative score). } \Option{b}{\Showoptionarg{score}}{ Specify the score for a blast-hit end within a query-sequence. \Showoptionarg{score} has to be specified as a double. If this option is not selected by the user, then \Showoptionarg{score} is set to $-10.00$ by default (recommended: negative score). } \Option{q}{\Showoptionarg{score}}{ Specify the score for a stop-codon in the query-sequence. \Showoptionarg{score} has to be specified as a negative double. If this option is not selected by the user, then \Showoptionarg{score} is set to $-2.00$ by default (recommended: negative score). } \Option{h}{\Showoptionarg{score}}{ Specify the score for a stop-codon in the hit-sequence. \Showoptionarg{score} has to be specified as a negative double. If this option is not selected by the user, then \Showoptionarg{score} is set to $-5.00$ by default (recommended: negative score). } \Option{l}{\Showoptionarg{score}}{ Specify the score for leaving a gene on forward/reverse strand or enter a gene on forward/reverse strand. The argument \Showoptionarg{score} has to be specified as a negative double. If this option is not selected by the user, the default value is set to $-2$ (recommended: negative score). } \Option{p}{\Showoptionarg{$S_{max}$}}{ Specify the maximum span between two coding-regions in the same reading frame in which they resume as one coding-region. The argument \Showoptionarg{$S_{max}$} has to be specified as a positive double. If this option is not selected by the user, \Showoptionarg{$S_{max}$} is set to $400.00$ by default. } \Option{f}{\Showoptionarg{$S_{max}$}}{ Specify the maximum span between coding-regions in different reading frames in which they resume as coding-regions in the optimal reading-frame. The argument \Showoptionarg{$S_{max}$} has to be specified as a positive double. If this option is not selected by the user, \Showoptionarg{$S_{max}$} is set to $200.00$ by default. } \Option{c}{\Showoptionarg{$DB_{name}$}}{ Specify the name of the database used in the cURL-Module. The argument \Showoptionarg{$DB_{name}$} has to be chosen as a valid database which you can find under \\ \mbox{\url{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?}}. If this option is not selected by the user, \Showoptionarg{$DB_{name}$} is set to \nucleotide by default. } \Option{o}{\Showoptionarg{output filename}}{ Specify the name of the resulting output-file where the predictions will be written to. Each prediction will be represented by an individual block (see chapter \ref{Examples}). If this option is not selected by the user, \Showoptionarg{output filename} is set to $output$ by default. } \Option{k}{\Showoptionarg{$DB_{Hit-Seq}$}}{ Specify the path to the hit-sequence database. The argument \Showoptionarg{$DB_{Hit-Seq}$} has to be chosen as a valid path to a valid database which you can find under \\ \mbox{\url{ftp://ftp.ncbi.nih.gov/blast/db/FASTA/}} for example. If this option is not selected by the user, \Showoptionarg{$DB_{Hit-Seq}$} is set to $nt.gz$ by default. } \Option{t}{\Showoptionarg{yes}$|$\Showoptionarg{no}}{ Specify if a hit-sequence file was already created (\Showoptionarg{yes}) or not created until now (\Showoptionarg{no}). If this option is not selected by the user, \Showoption{t} is set to \Showoptionarg{no} by default. \Attention If there is already a hit-sequence file and you do not use \Showoption{t} \Showoptionarg{yes} the existing hit-sequence file will be deleted. } \Option{r}{\Showoptionarg{1}$|$\Showoptionarg{2}$|$\Showoptionarg{3}}{ Specify the format for the output-file. You can choose between .txt (1), .html (2) und .xml (3) format. If this option is not selected by the user, the default value of $r$ is $1$. } \Option{a}{\Showoptionarg{$AA_{min}$}}{ Specify the minimum number of amino-acids in the amino-acid sequences in the output. Shorter amino-acid sequences will not appear in the output. The argument \Showoptionarg{$AA_{min}$} has to be chosen as a value higher or equal than 15. If this option is not selected by the user, the default value of $a$ is $15$. } \Option{d}{\Showoptionarg{$Stat_{min}$}}{ Specify the minimum percentage which the species must have to appear in the output-file in the statistic section. The argument \Showoptionarg{similaritythreshold} has to be chosen from the range [0.0,1.0] and means a percentage. If this option is not selected by the user, the default value of $d$ is $0.0$. } \Option{e}{\Showoptionarg{1}$|$\Showoptionarg{2}$|$\Showoptionarg{3}}{ Specify the format for the different start-codon modes. You can choose between (1): AUG, (2): AUG, CUG, GUG and (3): AUG, CUG, GUG, UUG. \Showoption{e} makes only sense if \Showoption{x} is set to \Showoptionarg{true}. If this option is not selected by the user, the default value of $e$ is $1$. } \Option{m}{\Showoptionarg{yes}$|$\Showoptionarg{no}}{ Specify the processing mode. If \Showoption{m} is set to \Showoptionarg{yes}, the specified scores are used if there are equal amino acids, otherwise they are used if the amino acids are different. The \Showoption{m} has only experimental status. Results are not checked. If this option is not selected by the user, the default value of $m$ is \Showoptionarg{no}. } \Option{g}{\Showoptionarg{yes}$|$\Showoptionarg{no}}{ Specify if the testmode should be used to make the results comparable in the \GenomeTools test suite. This option is not relevant for normal use of the \MetagenomeThreader. If this option is not selected by the user, the default value of $g$ is \Showoptionarg{no}. } \Option{x}{\Showoptionarg{yes}$|$\Showoptionarg{no}}{ Specify if the extended mode should be switched on. If \Showoption{x} is set to \Showoptionarg{yes} the processed PCSs will be extended to its max length in both directions. If this option is not selected by the user, the default value of $x$ is $no$. } \Option{help}{}{ \MetagenomeThreader will show a summary of all options on \texttt{stdout} and terminate with exit code $0$. } \Option{version}{}{ Shows the version of \GenomeTools. } \end{Justshowoptions} %%%%%%%%%%%% \section{Example of a Result from the \MetagenomeThreader} \label{Examples} \subsection{Header of the \MetagenomeThreader Result} \label{example-results} \renewcommand{\arraystretch}{1.15} \begin{tabular}{|p{4.5 cm}p{2,2 cm}|} \hline MetagenomeThreader& \\ Result 29.11.2007& \\ & \\ Parameter settings& \\ Synonymic Value:& 1.0000 \\ Non-Synonymic Value: &-1.0000 \\ Blast-Hit-End Value: &-10.0000 \\ Query Stop-Codon Value: &-2.0000 \\ Hit Stop-Codon Value: &-5.0000 \\ Frameshift-Span: &200.0000 \\ Prediction-Span: &400.0000 \\ Leavegene-Value: &-2.0000 \\ cURL-DB: &nucleotide \\ Output-Filename: &Metagenome \\ Output-Fileformat: &2 \\ (1/2/3)& \\ Hitfile: &1 \\ (yes=1/no=0)& \\ Min-Protein-Length &50 \\ (\textgreater=15)& \\ Min-Result-Percentage: &0.0000 \\ Extended-Modus &1 \\ (yes=1/no=0)& \\ Homology-Modus &0 \\ (yes=1/no=0)& \\ Codon-Modus &1 \\ (1/2/3)& \\ \hline \end{tabular} \begin{tabular}{l} Content: \\ - date of program execution \\ - used program parameters \end{tabular} \subsection{Sequence-Section of the \MetagenomeThreader result} \label{example-sequence} \begin{tabular}{|p{16.5 cm}p{0.5 cm}|} \hline Query-DNA-Entry Section&A \\ & \\ Query-DNA-Def: read\_11$\vert$beg$\vert$21$\vert$length$\vert$987$\vert$forward$\vert$NC\_000961$\vert$read\_12$\vert$chimeric$\vert$false$\vert$gi & \\ Query-DNA-Sequence& \\ \small{tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaaccatcccctcttattcaggagaagttttctgaactcttcaacatcctcga...}& \\ \hline \end{tabular} \begin{tabular}{|p{16.5 cm}p{0.5 cm}|} \hline Coding-DNA-Entry-Section&B \\ & \\ Coding-DNA& \\ \small{tataaaatagccaaatctgagcctaaaagcccttggatatccatgatttagaacgaaccatcccctcttattcaggagaagttttctgaactcttcaacatcctcga...}& \\ Protein-Sequence& \\ \small{MLLREVTREERKNFYTNEWKVKDIPDFIVKTLELREFGFDHSGEGPSDRKNQYTDIRDLEDYIRATA...}& \\ Hit-Information Section& \\ gi-nr: gi18892016 gi-def: \small{Pyrococcus furiosus DSM 3638, section 12 of 173... from: 6558 to: 7299}& \\ gi-nr: gi9453868 gi-def: \small{Pyrococcus furiosus priA gene for DNA primase... from: 1 to: 642}& \\ gi-nr: gi3342818 gi-def: \small{Thermophilic archaeon Bonch-Osmolovskaya primase... from: 21 to: 341}& \\ \hline \end{tabular} \begin{tabular}{p{1cm}p{15,7cm}} Content: \\ \mbox{- A:} &Output of the metagenome sequence and the metagenome sequence definition \\ \mbox{- B:} &for every PCS \\ & \begin{tabular}{p{0,1cm}p{14.9cm}} \mbox{-}& PCS DNA-sequence \\ \mbox{-}& PCS amino acid sequence \\ \mbox{-}& for the PCS processing used hit-definition \end{tabular} \end{tabular} \subsection{Statistic-Section of the \MetagenomeThreader result} \begin{tabular}{|r p{12.5 cm}|} \hline 0.7764& Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 \\ 0.7764& Salmonella typhimurium LT2, section 22 of 220 of the complete genome \\ 14.2553& Vibrio cholerae O395 chromosome 2, complete genome \\ 7.1809& Pyrococcus furiosus DSM 3638, section 12 of 173 of the complete genome \\ 0.2029& Escheria coli K12 MG1655, complete genome \\ \hline \end{tabular} \begin{tabular}{p{0,1cm}p{14cm}} Content: \\ - &percentage of hit-sequence length vs. length of all hit-sequences used for the PCS prediction \\ - &BLAST-hit definitions \end{tabular} In the HTML-format the GI-number of the BLAST-hits is a hyperlink to the linked NCBI entry. \Attention It is recommended that the hit-sequence file is stored at two different locations because if an existing hit-sequence file is used and the \MetagenomeThreader is called without \Showoption{t} \Showoptionarg{yes}, the hit-sequence file will be overwritten and a new scan of the nucleotide database and / or an online query of the hit-sequences has to be performed. %\bibliographystyle{plain} %\bibliography{references} \begin{thebibliography}{1} \bibitem{krause} L.~Krause \textit{et al}. \newblock Finding novel genes in bacterial communities isolated from the environment. \textit{Bioinformatics}, 22:e281-e289, 2006. \bibitem{genometools} G.~Gremme. \newblock The \textsc{GenomeTools} genome analysis system. \url{http://genometools.org}. \end{thebibliography} \end{document} genometools-1.5.1/doc/manuals/optionman.sty000066400000000000000000000030001211610345200210070ustar00rootroot00000000000000\usepackage{xspace} \newcommand{\Showoption}[1]{\mbox{\footnotesize \texttt{-#1}}} \newcommand{\Showoptiongroup}[1]{\hline\multicolumn{2}{c}{#1}\\[.2cm]} \newcommand{\Showoptionarg}[1]{\mbox{\footnotesize \textit{#1}}\index{#1@\textit{#1}}} \newcommand{\Showoptionalarg}[1]{\lbrack\Showoptionarg{#1}\rbrack} \newcommand{\Showoptionkey}[1]{\mbox{\footnotesize \texttt{#1}}} \newcommand{\Showrecentchange}[2]{\paragraph{#1; #2:}} \newcommand{\Option}[3]{% \item[\Showoption{#1}~#2]\mbox{}% \index{Option!\texttt{-#1}}% \\% #3} \newcommand{\Showformattype}[1]{\textsc{#1}\xspace} \newcommand{\Fasta}{\Showformattype{Fasta}} \newcommand{\Fastastart}[0]{\texttt{\symbol{62}}\xspace} \newenvironment{Showprogramwithoptions}[2]{ The program is called as follows: \par \noindent#1 [\emph{options}] \emph{indexname} \par #2 \par And here is a description of the options: \par \begin{list}{}{} }{\end{list}} \newenvironment{Showprogramwithoptionswithoutindex}[2]{ The program is called as follows: \par \noindent#1 \emph{options} \par #2 \par And here is a description of the options: \par \begin{list}{}{} }{\end{list}} \newenvironment{Justshowoptions}[0]{ \begin{list}{}{} }{\end{list}} \newcommand{\Helpoption}[0]{ \Option{help}{}{ Show a summary of all options and terminate with \index{exit code} exit code 0. } } \newenvironment{Output}{% \begin{scriptsize} \begin{alltt}}{% \end{alltt} \end{scriptsize}% \addvspace{-\medskipamount} } \parindent0pt \parskip5pt genometools-1.5.1/doc/manuals/output/000077500000000000000000000000001211610345200176115ustar00rootroot00000000000000gt-suffixerator--dna--pl--tis--suf--lcp--v--parts-4--db-read1.fna-read2.fna--indexname-reads.out000066400000000000000000000021371211610345200402340ustar00rootroot00000000000000genometools-1.5.1/doc/manuals/output$ gt suffixerator -dna -pl -tis -suf -lcp -v -parts 4 -db read1.fna read2.fna -indexname reads # dna=yes # indexname="reads" # prefixlength=automatic # storespecialcodes=false # parts=4 # inputfile[0]=read1.fna # inputfile[1]=read2.fna # indexname=reads # outtistab=true,outsuftab=true,outlcptab=true,outbwttab=false,outbcktab=false,outdestab=false # sizeof (Seqpos)=32 # specialranges of length 1: 17180 # specialranges of length 2: 764 # specialranges of length 3: 53 # specialranges of length 4: 9 # specialranges of length 5: 4 # init character encoding (uchar,241249 bytes,2.50 bits/symbol) # deliverchar=delivercharViauchartablesSpecialrange # specialcharacters=18923 # specialranges=18010 # realspecialranges=18010 # occurrences(a)=200061 # occurrences(c)=155192 # occurrences(g)=167557 # occurrences(t)=230643 # automatically determined prefixlength = 8 # sizeof (leftborder)=262148 # sizeof (countspecialcodes)=65536 # sizeof (distpfxidx)=21868 # widthofpart[0]=188406 # widthofpart[1]=188330 # widthofpart[2]=188355 # widthofpart[3]=188362 # space peak in megabytes: 1.42 # mmap space peak in megabytes: 0.00 genometools-1.5.1/doc/manuals/output/gt-tagerator--q-Q1.gz--maxocc-10--pck-pck-human.out000066400000000000000000000010071211610345200304250ustar00rootroot00000000000000$ gt tagerator -q Q1.gz -maxocc 10 -pck pck-human # computing matching statistics # indexname(pck)=pck-human # queryfile=Q1.gz # for each match show: tagnum tagseq dblength dbstartpos strand taglength # 0 15 aagcttgctgctgca 10 + 88693 9 + 88694 213545 8 + 25583 88695 213546 281700 325202 451235 747565 12 + 470064 11 + 470065 10 + 158315 363967 470066 501203 576660 729958 9 + 8 + 7 + 6 + 5 + 4 + 3 + 2 + 1 + 12 - 271321 11 - 271322 10 - 271323 9 - 217234 271324 762404 8 - 146318 216480 217235 271325 294145 762405 genometools-1.5.1/doc/manuals/output/gt-tagerator--q-Q1.gz--pck-pck-human--e-1--maxocc-5.out000066400000000000000000000010031211610345200310020ustar00rootroot00000000000000$ gt tagerator -q Q1.gz -pck pck-human -e 1 -maxocc 5 # computing prefix matches with up to 1 differences and at most 5 occurrences in the subject sequences # indexname(pck)=pck-human # queryfile=Q1.gz # for each match show: tagnum tagseq dblength dbstartpos strand taglength # 0 15 aagcttgctgctgca 8 1264 122 + 8 8 549 197 + 8 8 734 280 + 8 9 699 24 + 8 9 1060 311 + 8 9 1594 18 + 9 9 1475 90 + 9 9 1022 445 + 9 9 718 87 + 9 9 913 382 + 9 9 835 315 + 9 9 855 408 + 9 8 1534 258 + 7 8 1264 121 + 7 8 1476 281 + 7 genometools-1.5.1/doc/manuals/output/gt-tagerator--q-Q1.gz--pck-pck-human--e-2.out000066400000000000000000000010421211610345200273170ustar00rootroot00000000000000$ gt tagerator -q Q1.gz -pck pck-human -e 2 # computing complete matches with up to 2 differences # indexname(pck)=pck-human # queryfile=Q1.gz # for each match show: tagnum tagseq dblength dbstartpos strand # 0 aagcttgctgctgca 14 904 114 + 13 1439 224 + 13 1250 191 + 13 413 155 + 13 468 294 + 15 1158 74 + 14 227 311 + 13 1439 111 + 15 496 288 + 15 356 327 + 15 1690 336 + 13 1439 223 + 13 1250 190 + 14 1178 82 + 14 204 59 + 14 273 46 + 14 1156 136 + 14 803 343 + 15 1439 222 + 15 1250 189 + 15 803 342 + 16 1474 165 - # 1 atttgggactgtatctca gt-tallymer-mkindex--mersize-19--minocc-4--indexname-tyr-reads--counts--pl--esa-reads.out000066400000000000000000000004761211610345200375620ustar00rootroot00000000000000genometools-1.5.1/doc/manuals/output$ gt tallymer mkindex -scan -mersize 19 -minocc 4 -indexname tyr-reads -counts -pl -esa reads # construct mer buckets for prefixlength 4 # numofcodes = 256 # indexfilename = tyr-reads # alphasize = 4 # mersize = 19 # numofmers = 3166 # merbytes = 5 # space peak in megabytes: 0.06 # mmap space peak in megabytes: 3.93 genometools-1.5.1/doc/manuals/output/gt-tallymer-mkindex--mersize-19--minocc-40--esa-reads.out000066400000000000000000000010631211610345200317030ustar00rootroot00000000000000$ gt tallymer mkindex -scan -mersize 19 -minocc 40 -esa reads 1 444720 2 30886 3 3909 4 1397 5 640 6 335 7 111 8 172 9 39 10 16 11 9 12 82 13 27 14 53 15 27 16 11 17 12 18 17 19 21 20 36 21 27 22 13 23 2 24 5 25 12 26 11 27 6 28 13 29 4 31 1 32 5 33 1 34 9 35 10 36 9 37 8 38 4 39 11 40 8 ttcgacaacacccgtcaag tcggattcgacaacacccg tcgacaacacccgtcaagt tcatcggattcgacaacac cggattcgacaacacccgt cgacaacacccgtcaagtc catcggattcgacaacacc atcggattcgacaacaccc 41 2 gacaacacccgtcaagtcc acaacacccgtcaagtcca # space peak in megabytes: 0.06 # mmap space peak in megabytes: 3.93 gt-tallymer-occratio--output-unique-nonunique--mersizes-10-13-17--esa-reads.out000066400000000000000000000004741211610345200360070ustar00rootroot00000000000000genometools-1.5.1/doc/manuals/output$ gt tallymer occratio -scan -output unique nonunique -mersizes 10 13 17 -esa reads # distribution of unique mers 10 223755 13 465859 17 455449 # distribution of non unique mers (counting each non unique mer only once) 10 135526 13 49611 17 39769 # space peak in megabytes: 0.06 # mmap space peak in megabytes: 3.93 gt-tallymer-occratio--output-unique-nonunique--minmersize-10--maxmersize-20--esa-reads.out000066400000000000000000000007371211610345200403420ustar00rootroot00000000000000genometools-1.5.1/doc/manuals/output$ gt tallymer occratio -scan -output unique nonunique -minmersize 10 -maxmersize 20 -esa reads # distribution of unique mers 10 223755 11 373775 12 444083 13 465859 14 468735 15 465646 16 460791 17 455449 18 450049 19 444720 20 439532 # distribution of non unique mers (counting each non unique mer only once) 10 135526 11 92162 12 62347 13 49611 14 44618 15 42301 16 40867 17 39769 18 38815 19 37961 20 37166 # space peak in megabytes: 0.06 # mmap space peak in megabytes: 3.93 gt-tallymer-occratio--output-unique-relative--minmersize-10--maxmersize-20--esa-reads.out000066400000000000000000000005611211610345200401270ustar00rootroot00000000000000genometools-1.5.1/doc/manuals/output$ gt tallymer occratio -scan -output unique relative -minmersize 10 -maxmersize 20 -esa reads # distribution of unique mers 10 223755 0.623 11 373775 0.802 12 444083 0.877 13 465859 0.904 14 468735 0.913 15 465646 0.917 16 460791 0.919 17 455449 0.920 18 450049 0.921 19 444720 0.921 20 439532 0.922 # space peak in megabytes: 0.06 # mmap space peak in megabytes: 3.93 gt-tallymer-search--output-qseqnum-qpos-counts-sequence--tyr-tyr-reads--q-U89959.fna.out000066400000000000000000000015571211610345200377110ustar00rootroot00000000000000genometools-1.5.1/doc/manuals/output$ gt tallymer search -output qseqnum qpos counts sequence -tyr tyr-reads -q U89959.fna 0 +5966 4 tcttcttcttcttcttctt 0 +17269 14 atatatatatatatatata 0 +17270 12 tatatatatatatatatat 0 +17271 14 atatatatatatatatata 0 +17272 12 tatatatatatatatatat 0 +71281 6 tcatcatcatcatcatcat 0 +71282 4 catcatcatcatcatcatc 0 +71283 6 atcatcatcatcatcatca 0 +71284 6 tcatcatcatcatcatcat 0 +71285 4 catcatcatcatcatcatc 0 +71286 6 atcatcatcatcatcatca 0 +71287 6 tcatcatcatcatcatcat 0 +77815 14 atatatatatatatatata 0 +77816 12 tatatatatatatatatat 0 +77817 14 atatatatatatatatata 0 +77818 12 tatatatatatatatatat 0 +77819 14 atatatatatatatatata 0 +77820 12 tatatatatatatatatat 0 +77821 14 atatatatatatatatata 0 +77822 12 tatatatatatatatatat 0 +77823 14 atatatatatatatatata 0 +77824 12 tatatatatatatatatat 0 +77825 14 atatatatatatatatata 0 +77826 12 tatatatatatatatatat 0 +77827 14 atatatatatatatatata genometools-1.5.1/doc/manuals/packedindex.tex000066400000000000000000000376731211610345200212720ustar00rootroot00000000000000\documentclass[12pt,titlepage]{article} \usepackage[a4paper,top=30mm,bottom=30mm,left=20mm,right=20mm]{geometry} \usepackage{url} \usepackage{alltt} \usepackage{xspace} \usepackage{times} \usepackage{listings} \usepackage{bbm} \usepackage{verbatim} \usepackage{comment} \usepackage{optionman} \newcommand{\packedindex}{\textit{packedindex}\xspace} \newcommand{\GenomeTools}{\textit{GenomeTools}\xspace} \newcommand{\Suffixerator}{\textit{Suffixerator}\xspace} \newcommand{\Gt}{\texttt{gt}\xspace} \newcommand{\Gtsuffixerator}{\texttt{gt suffixerator}\xspace} \newcommand{\Gtpackedindex}{\texttt{gt packedindex}\xspace} \newcommand{\species}[1]{{\fontshape{it}\selectfont #1}}% \title{\packedindex manual} \author{\begin{tabular}{c} \textit{Thomas Jahns}\\ \textit{Stefan Kurtz}\\[1cm] Research Group for Genomeinformatics\\ Center for Bioinformatics\\ University of Hamburg\\ Bundesstrasse 43\\ 20146 Hamburg\\ Germany\\[1cm] \url{kurtz@zbh.uni-hamburg.de}\\[1cm] \begin{tabular}{p{0.8\textwidth}} % In any documentation or publication about research using \LTRharvest % please cite the following paper:\\[5mm] % D.~Ellinghaus, S.~Kurtz, and U.~Willhoeft. % \LTRharvest, an efficient and flexible software for de novo % detection of LTR retrotransposons. % BMC Bioinformatics 2008, 9:18 \end{tabular} \end{tabular}} \begin{document} \maketitle \section{Introduction} \label{Introduction} The \packedindex tools of the \GenomeTools package facilitate the creation of sequence index files which implement the FM index\cite{oai:CiteSeerPSU:481302} concept for biological sequences with some more recent features incorporated\cite{journals/talg/FerraginaMMN07}. The \packedindex routines and tools are written in \texttt{C} and are part of the \GenomeTools library \cite{genometools}. \packedindex methods are called as part of the single binary named \Gt. The \packedindex tools depend on routines of the \Suffixerator program to prepare the data stored in the index. Many command-line options are therefore the same. \section{Command line tools} \label{Usage} Some text is highlighted by different fonts according to the following rules. \newcommand{\toolname}[1]{\texttt{\bfseries #1}} \newcommand{\toolarg}[1]{\texttt{\itshape #1}} \newcommand{\tooloption}[1]{\texttt{-#1}} \newcommand{\tooloptionarg}[1]{\texttt{#1}} \begin{itemize} \item \toolname{toolname} is used for the names of software tools. \item \toolarg{filename} is used for file names. \item \tooloption{option} is used for program options. \item \tooloptionarg{argument} is used for the argument(s) of an option. \end{itemize} \subsection{The \packedindex tools} \label{Overview} The creation and integrity checks of the \packedindex tools are available as a sub-tool of \Gt. Each of those is called by giving \toolname{packedindex} as the first argument of the \toolname{gt} command-line. %\Gtltrharvest \Showoption{index} \Showoptionarg{indexname} $[$\emph{options}$]$% % %where \Showoptionarg{indexname} denotes the enhanced suffix array index of %the target sequence(s) constructed by the program \Suffixerator. %An overview of all possible options with a short one-line description of %each option is given in Table \ref{overviewOpt}. %All options can be specified only once. \subsubsection{Options common to all tools} \label{sec:packedindex:commonoptions} \begin{Justshowoptions} % \Option{v}{}{ % This option enables the verbose mode. This means, that some more information % about the processing will be printed to \texttt{stdout} during the run. % This includes a long list of switched on or switched off options. % } \Option{help}{}{ Prints a summary of available options to standard output and terminates with exit code $0$. } \Option{v}{}{ Turns on verbose progress information. } \Option{version}{}{ Displays \toolname{genometools} version information. } \end{Justshowoptions} \subsubsection{The creation of packedindex files} \label{sec:packedindex:mkindex} The command to build a \packedindex is \begin{quote} \ttfamily% \toolname{gt} \toolname{packedindex} \toolname{mkindex} [{\rmfamily Options}] \tooloption{db} \toolarg{sequenceinput...} \end{quote} The following options are specific to the \packedindex \toolname{mkindex} tool: \begin{table}[htbp] \caption{Overview of the \packedindex \toolname{mkindex} options.} \begin{footnotesize} \[ \renewcommand{\arraystretch}{0.89} \begin{tabular}{ll}\hline \Showoption{bsize}& specify the number of symbols joined in a block \\ \Showoption{blbuck}& specify number of blocks to join in a bucket \\ \Showoption{locfreq}& specify interval at which locate marks will be inserted \\ \Showoption{locbitmap}& force/deny use of the bitmap tagging method \\ \Showoption{sprank}& build source rank table so that regeneration of original sequence is possible without the usual gaps \\ \Showoption{sprankilog}& define log of interval used for the intermediate table \\ \hline \end{tabular} %\input{ltrprogoptions} \] \end{footnotesize} \label{tab:packedindex:mkindex:options} \end{table} Except for the output options \Showoption{suf}, \Showoption{lcp}, and \Showoption{bwt}, all other options are the same as used for the \toolname{suffixerator} tool. %%%% \begin{Justshowoptions} \Option{bsize}{\Showoptionarg{u}}{ Group \Showoptionarg{u} symbols in one block. While bigger blocks can speed up index access, the block size should be chosen so that \begin{displaymath} \alpha^u u\lceil\log_2 \alpha\rceil \end{displaymath} does not exceed the relevant cache size (typically of the 2nd level chache) of the system. The default of a block size of 8 results in a lookup-table size of 128kiB for the DNA alphabet. Systems with larger 2nd level cache like 4MiB on the Intel Core2 Duo might show improved performance when choosing block size 10. } \Option{blbuck}{\Showoptionarg{k}}{ Group this many blocks so that every atomic query of the index will on average require $\frac{k}{2}$ lookups of the block table (see option \Showoption{bsize}). While smaller blocks decrease query times, the corresponding increase in memory usage of the index will eventually defeat this effect. } \Option{locfreq}{\Showoptionarg{f}}{ Put location marks at interval \Showoptionarg{f} into the index. For a sequence of length $n$, $\frac{n}{f}\lceil\log_2n\rceil$ bits of storage will be required. Locate queries (i.e. finding the position of matches) will require $\frac{f}{2}$ operations. Again having an index that does not fit main memory will eventually defeat the speed gains of lower intervals. } \Option{locbitmap}{\Showoptionarg{yes} or \Showoptionarg{no}}{ Force/disable the use of a bitmap for locate marks. Finding marked positions will be faster if a bitmap is used but will require $n$ bits for a sequence of length $n$. If no locate bitmap is used, extra space usage will be $\frac{n}{f}\lceil\log_2uk\rceil$. By default the optimal value in terms of space usage will be chosen. } \Option{sprank}{\Showoptionarg{yes} or \Showoptionarg{no}}{ Normally special characters (N/X, separators and terminator) are encoding so that the reverse mapping required for context regeneration cannot pass over such symbols. If this option is given, an in-memory structure will be built to facilitate queries which allow to store necessary extra information in the index so that full context (the entire original sequence actually) can be regenerated. } \Option{sprankilog}{\Showoptionarg{$s$}}{ Set logarithm of interval used for the intermediate table (see \Showoption{sprank} option). Index creation might be faster if a lower value than the default $s = \log_2\log_2n$ is used and sufficient memory is available. Since every increment by 1 doubles the memory usage of the table (which is not stored itself in the index) during index construction two high values might actually slow index construction. } \Option{ctxilog}{\Showoptionarg{$c$}}{ Set logarithm of interval to use for the creation of a reverse lookup table. Said table will be stored alongside the index in a file with the same name prefix but suffix \toolarg{.$c$cxm} so that multiple reverse lookup accelerator tables can be stored for one index. So it's possible to load the one fitting available memory best later. The reverse lookup table is restricted to indices computed with the \Showoption{sprank} option. In those cases the index can replace the encoded sequence (stored in \toolarg{prefix.esq}) completely. The reverse suffix indices will be sampled at interval length $2^c$ } \end{Justshowoptions} %%%% \subsubsection{Building reverse lookup tables after index creation} \label{sec:packedindex:mkctxmap} The \toolname{mkctxmap} sub-tool facilitates late building of a reverse lookup table, it can use the \toolarg{prefix.suf} table as well as the locate information inside the packedindex structure (i.e. of any packedindex not constructed with \tooloption{locfreq} set to 0). The \toolname{mkctxmap} sub-tool only accepts the \tooloption{-ctxilog}, \tooloption{-v}, \tooloption{-version}, and \tooloption{-help} options already described for the \toolname{packedindex mkindex} tool. Given a previously computed suffix array or packedindex project \toolarg{chr01}, one can build an additional reverse lookup-table with interval 32 like this: \begin{footnotesize} \begin{verbatim} $ gt packedindex mkctxmap -ctxilog 5 chr01 \end{verbatim} \end{footnotesize} \subsubsection{Deriving packedindex files from a suffix array} \label{sec:packedindex:trsuftab} The \toolname{trsuftab} sub-tool will translate an index by reading suffix array and encoded sequence files. Thus the options specific to the packedindex properties are the same as previously shown~\ref{sec:packedindex:mkindex} but the suffixerator options are not available. Instead the latter are implicit in the properties of the suffix array and encoded sequence indices used as input for this tool. Thus to produce a packedindex with default options where a suffix array has already been created in chr01.\{prj$|$suf$|$esq\} use: \begin{footnotesize} \begin{verbatim} $ gt packedindex trsuftab chr01 \end{verbatim} \end{footnotesize} \subsubsection{packedindex integrity check tool} \label{sec:packedindex:chkintegrity} The integrity check tool is intended to verify that an index correctly represents the encoded BWT sequence. Therefore the .bwt file for the index project in question must have been generated as a prerequisite for this check. To check a \packedindex index file BWT sequence representation issue \begin{quote} \ttfamily% \toolname{gt} \toolname{packedindex} \toolname{chkintegrity} [{\rmfamily Options}] \toolarg{indexname} \end{quote} where \toolarg{indexname} refers to the name given previously on index creation (or automatically derived from the sequence input file set). The .bwt table file must have previously been generated with the \toolname{suffixerator} tool. See section~\ref{sec:packedindex:examples} for an example. \begin{table}[htbp] \caption{Overview of the \packedindex \toolname{chkintegrity} options.} \begin{footnotesize} \[ \renewcommand{\arraystretch}{0.89} \begin{tabular}{ll}\hline \Showoption{skip}& specify the number of symbols to skip before starting the comparison \\ \Showoption{ticks}& print a dot after this many symbols processed correctly \\ \Showoption{ext-rank-check}& do additional checks of rank query results \\ \hline \end{tabular} %\input{ltrprogoptions} \] \end{footnotesize} \label{tab:packedindex:chkintegrity:options} \end{table} \begin{Justshowoptions} \Option{skip}{\Showoptionarg{k}}{ Start the comparison \Showoptionarg{k} has to be a positive integer. If this option is not selected by the user, then \Showoptionarg{$L_{ex}$} is set to $30$ by default. } \Option{ticks}{\Showoptionarg{$k$}}{ As a form of progress meter, print a dot after $k$ symbols of the packedindex and the reference file (\toolarg{indexname.bwt}) compared equal and rank information was computed correctly. } \Option{ext-rank-check}{\Showoptionarg{yes$\|$no}}{ If yes, enables additional checks of the rank results, i.e. for all positions rank queries will be computed for all symbols of the alphabet and not only for the symbol for which the rank value changed in the reference. } \end{Justshowoptions} \subsubsection{Check \packedindex search accuracy tool} This check verifies that a packedindex correctly represents both the original sequence and correctly delivers the exact same search results as the suffix array. To check a \packedindex index file issue \begin{quote} \ttfamily% \toolname{gt} \toolname{packedindex} \toolname{chksearch} [{\rmfamily Options}] \toolarg{indexname} \end{quote} where \toolarg{indexname} refers to the name given previously on index creation (or automatically derived from the sequence input file set). The encoded sequence (\toolarg{.esq}) and suffix array table (\toolarg{.suf}) must have been previously generated with the \toolname{suffixerator} tool. \begin{table}[htbp] \caption{Overview of the \packedindex \toolname{chksearch} options.} \begin{footnotesize} \[ \renewcommand{\arraystretch}{0.89} \begin{tabular}{ll}\hline \Showoption{minpatlen}& shortest pattern length \\ \Showoption{maxpatlen}& longest pattern length \\ \Showoption{ticks}& print a dot after this many symbols processed correctly \\ \Showoption{nsamples}& generate this many patterns to search for \\ \Showoption{chksfxarray}& do additional checks of stored suffix array data \\ \hline \end{tabular} %\input{ltrprogoptions} \] \end{footnotesize} \label{tab:packedindex:chksearch:options} \end{table} \begin{Justshowoptions} \Option{minpatlen}{\Showoptionarg{$l$}}{ Perform searches for patterns that are at least of length $l$. } \Option{maxpatlen}{\Showoptionarg{$m$}}{ Perform searches for patterns that are at most of length $l$. } \Option{nsamples}{\Showoptionarg{$k$}}{ Generate $k$ patterns to search for, defaults to 1000. } \Option{chksfxarray}{\Showoptionarg{yes$\|$no}}{ Verify integrity of stored suffix array positions and test the regenerated context functionality if the index was constructed in a reversible fashion (option \Showoption{sprank} on index construction). In the latter case the test will take considerable time. } \Option{ticks}{\Showoptionarg{$k$}}{ Print a dot after this many searches completed correctly. If \Showoption{chksfxarray} is set, also prints a dot for every $k$ suffix array values compared. } \end{Justshowoptions} \section{Examples} \label{sec:packedindex:examples} \subsection{Create an index for sequence data from the \toolarg{gttestdata} repository\cite{gttestdata}} \label{sec:packedindex:examples:yeast} Amongst the more voluminous sequence data sets there is the \species{Saccharomyces cerevisiae} genome in the \toolarg{ltrharvest/s\_cer} sub-directory. This example will show how to build an index for chromosome 1 (file \toolarg{chr01.19960731.fsa.gz}). First compute the \packedindex index file (this assumes \toolarg{chr01.19960731.fsa.gz} has been copied/linked to the current directory and the gt binary is in the PATH): \begin{footnotesize} \begin{verbatim} $ gt packedindex mkindex -db chr01.19960731.fsa.gz -indexname chr01 -tis -des # TIME determining sequence length and number of special symbols 0.04 # TIME computing sequence encoding 0.04 [...] # TIME overall 0.71 $ \end{verbatim} \end{footnotesize} Then build the reference files that the index subsumes: \begin{footnotesize} \begin{verbatim} $ gt suffixerator -db chr01.19960731.fsa.gz -indexname chr01 -bwt -suf -des # TIME determining sequence length and number of special symbols 0.04 # TIME computing sequence encoding 0.04 [...] # TIME overall 0.31 $ \end{verbatim} \end{footnotesize} This index can then be verified or used in one of the tools supporting it. For integrity check use: \begin{footnotesize} \begin{verbatim} $ gt packedindex chkintegrity chr01 # Using index over sequence 230210 symbols long. [...] .. $ gt packedindex chksearch chr01 Using pre-computed sequence index. [...] Finished 1000 of 1000 matchings successfully. $ \end{verbatim} \end{footnotesize} \bibliographystyle{unsrt} \bibliography{gtmanuals} \end{document} genometools-1.5.1/doc/manuals/readjoiner.tex000066400000000000000000000437561211610345200211340ustar00rootroot00000000000000\documentclass[12pt,titlepage]{article} \usepackage[a4paper,top=30mm,bottom=30mm,left=20mm,right=20mm]{geometry} \usepackage{url} \usepackage{alltt} \usepackage{xspace} \usepackage{times} \usepackage{listings} \usepackage{bbm} \usepackage{verbatim} %\usepackage[dvips]{hyperref} \usepackage{optionman} \newcommand{\GenomeTools}{\textit{GenomeTools}\xspace} \newcommand{\Readjoiner}{\textit{Readjoiner}\xspace} \newcommand{\Rdjprefilter}{\textit{Readjoiner Prefilter}\xspace} \newcommand{\Rdjoverlap}{\textit{Readjoiner Overlap}\xspace} \newcommand{\Rdjassembly}{\textit{Readjoiner Assembly}\xspace} \newcommand{\Gtconvertseq}{\textit{Convertseq}\xspace} \newcommand{\Gtreadreads}{\textit{Readreads}\xspace} \newcommand{\Gtsuffixerator}{\textit{Suffixerator}\xspace} \newcommand{\Gtcmd}{\texttt{gt}\xspace} \newcommand{\Readjoinercmd}{\texttt{gt readjoiner}\xspace} \newcommand{\Rdjprefiltercmd}{\texttt{gt readjoiner prefilter}\xspace} \newcommand{\Rdjoverlapcmd}{\texttt{gt readjoiner overlap}\xspace} \newcommand{\Rdjassemblycmd}{\texttt{gt readjoiner assembly}\xspace} \newcommand{\Gtconvertseqcmd}{\texttt{gt convertseq}\xspace} \newcommand{\Gtreadreadscmd}{\texttt{gt dev readreads}\xspace} \newcommand{\Gtsuffixeratorcmd}{\texttt{gt suffixerator}\xspace} \newcommand{\minlen}{\ell} \title{\Huge{\Readjoiner 1.2:\\ User manual.}\\[3mm] \Large{A fast and memory efficient \\string graph-based sequence assembler.}} \author{\begin{tabular}{c} \textit{Giorgio Gonnella}\\ \textit{Stefan Kurtz}\\[2cm] Research Group for Genome Informatics\\ Center for Bioinformatics\\ University of Hamburg\\ Bundesstrasse 43\\ 20146 Hamburg (Germany)\\[1cm] \url{gonnella@zbh.uni-hamburg.de}\\ \url{kurtz@zbh.uni-hamburg.de}\\[1cm] \end{tabular}} \begin{document} \maketitle \section{Introduction} \label{Introduction} \Readjoiner is a software pipeline for the \textit{de novo} assembly of sequencing readsets, based on the assembly string graph framework \cite{MYE:2005}. \Readjoiner is written in \texttt{C} and it is based on the \GenomeTools library \cite{genometools}. It has no external library dependencies and may be compiled on any POSIX-compliant operative system. \Readjoiner is implemented as a collection of tools, all compiled in the single \GenomeTools binary named \Gtcmd. The \Readjoiner assembly pipeline consists in the following phases:\\[3mm] \begin{tabular}{lll} Phase & Tool & Description \\ \textit{Prefiltering} & \Rdjprefiltercmd & encode reads, remove contained and ambiguous\\ \textit{Overlap} & \Rdjoverlapcmd & determine all pairs suffix-prefix matches (SPMs) \\ \textit{Assembly} & \Rdjassemblycmd & build the string graph, output the contigs \\ \end{tabular} \Readjoiner can be installed either from a binary distribution or from the source code. In both cases, you will have the binary file \texttt{gt}. The rest of the manual assumes this binary is in the command line path. The \Readjoiner tools are run using the following syntax: \texttt{gt readjoiner }, where \texttt{} is either prefilter, overlap or assembly. The arguments are different, depending on the tool, however some options are common: \begin{itemize} \item \Showoption{help} will show an useful help message on the command line, with a summary of the most important options. \item \Showoption{help+} will show an expanded help message, in which further less common options are also listed. \item \Showoption{v} increases the verbosity. \item \Showoption{q} suppresses all output messages. \end{itemize} \subsection{Installation from the source code} For installation from the source code, please read the instruction in the \texttt{INSTALL} file (in the main directory of the sources). In most cases a 64-bit version is necessary, so make sure you use the \texttt{64bit=yes} make flag. External dependencies such as cairo and curses are not necessary for \Readjoiner, thus if you plan to use only \Readjoiner you may safely choose to use the \texttt{cairo=no curses=no} make flags. If you use the \texttt{amalgamation=yes} make flag, you will probably notice a significative speed-up, thus this option is reccomended. Further improvements in the runtime can be achieved by using \texttt{assert=no}: this skips all runtime assertions; if you encounter any problem by running \Readjoiner then you should (re-)compile using assertions before reporting a bug, as assertions are an useful source of information for the developer. Using the option \texttt{threads=yes} you can enable multithreading support. Currently the overlap phase can be run in parallel mode, thus this option is reccomended if \Readjoiner is run on a multi-core or multi-processor machine. \section{Error correction} Most sequencing technologies generate reads which contain technology-specific errors. For example, 454 and IonTorrent reads will contain mainly indels in homopolymeric regions, while Illumina reads will contain mainly substitution errors. An error correction prior to genome assembly is an essential step, and it is very important for Readjoiner, that the input reads have been already processed using an error correction tool. A number of stand-alone error correction tools exists: an example of a tool with a good performance on subsitution errors in Quake (Kelley et al., 2010). For homopolymer errors if a reference sequence is available, have a look to our error corrector HOP, also a part of GenomeTools. For susbtitution errors there is also an experimental support in Readjoiner of k-mer based error correction. If you want to try it, run \texttt{gt dev seqcorrect -help} for more information. %\newpage \section{Prefiltering} Readjoiner prefiltering step has the following functions: \begin{itemize} \item Remove ambiguity-containing reads \item Remove redundant information (duplicate and suffix/prefix reads) \item Encode the readset in GtEncseq format \end{itemize} \subsection{Describing the read set} The input to \Rdjprefilter consists of sequencing reads, in FastQ or Fasta format. The input is specified using the \Showoption{db} option, which takes multiple arguments, each argument describes a sequencing library. For single-end libraries, the corresponding argument of \Showoption{db} is simply the filename. Paired-end libraries are accepted in two variants: \textit{two-files} libraries, where a file contains the forward reads and a second file the reverse reads in the same order, and \textit{interleaved} libraries, consisting of a single file, where the first, third, fifth, etc sequences are the forward reads, the second, fourth, sixth, etc sequences are the reverse reads. For two-files libraries, the argument of \Showoption{db} is in the format \verb|::[,]| where \verb// are filenames, \verb|| is the average insert size and \verb|| is the standard deviation of insert sizes (which can be omitted if unknown). For interleaved libraries the library is specified as \verb|:[,]|. Some examples:\\[3mm] \begin{tabular}{p{0.5\textwidth}p{0.45\textwidth}} Argument of \Showoption{db} & Meaning:\\ \hline \Showoptionarg{se.fas} & single-end library (\texttt{se.fas})\\ \hline \Showoptionarg{pe.fastq:200} & interleaved paired-end library with average insert size of 200, standard deviation unknown\\ \hline \Showoptionarg{pe\_f.fastq:pe\_r.fastq:10000} & a paired-end library in two files, with average insert size of about 10kb, standard deviation unknown\\ \hline \Showoptionarg{se.fastq pe.fastq:180,20} & a single-end library plus an interleaved paired-end library with average insert size of 180, standard deviation 20\\ \hline \Showoptionarg{short.fastq:100 long\_f.fastq:long\_r.fastq:10000,1200 se.fastq} & an interleaved paired-end library with insert size 100 plus a two-files paired-end library with insert size 10000, standard deviation 1200, and a single-end library\\ \hline \end{tabular} %\newpage \subsection{Setting the read set name} The argument of the option \Showoption{readset} is the read set name. This will be used as basename for the output and intermediate files and must specified in subsequent calls to the \texttt{overlap} and \texttt{assembly} tools. \subsection{Contained reads} Duplicate reads and suffix/prefix reads (i.e. reads which are suffixes or prefixes of other reads) are contained reads, thus redundant sequence information, which is not represented in the string graph \cite{MYE:2005}. Furthermore, our overlap algorithm assumes that the read set is suffix-prefix-free, thus these reads are recognized and eliminated in the prefiltering phase. Reads are hereby considered from both strands, thus for example a reads which is equal to the reverse complement of another read is also removed. Internally contained reads (reads equal to an internal substring of other reads / reverse complement) are not identified here, but during the \Rdjoverlap step. In a paired-end library, if a read is contained, its mate pair is discarded too, to keep the library balanced. \subsection{Quality scores} Readjoiner supports the input formats FastQ and Fasta. The FastQ format is assumed to use the standard \textit{phred33} scores. As an alternative, \textit{phred64} scores are also supported; in this case the option \Showoption{phred64} must be specified. The only limitation is that it is not possible to mix libraries with \textit{phred33} scores and libraries with \textit{phred64} scores. The quality scores can be used for quality-based trimming. In order to activate this feature, the \Showoption{maxlow} option must be specified, with an argument $n$, which is the maximal number of low-quality bases acceptable in a read. If a read has more than $n$ low-quality bases, it is discarded. The definition of low-quality bases is any base whose associated quality score is at most $l$, where $l$ is an user-defined parameter, by default 3, which can be set using the \Showoption{lowqual} option. \subsection{Ambiguous base calls} Any read containing ambiguities is discarded as low-quality. If you want to keep reads containing ambuigities, you will have to split them at the ambiguity positions or permutate the ambiguities to a random non-ambiguous code using an external program or script. In a paired-end library, if a read is discarded, its mate pair is discarded too, so that the library is still balanced. %\newpage \section{The overlap phase} To construct the string graph, the suffix-prefix matches (SPM) among all pairs of reads must be calculated. Due to the small size of the DNA alphabet (4), small random matches from reads originating from different regions of the original DNA molecule are common. Thus, to avoid spurious matches a minimal match length pameter $\minlen$ is used. Transitive edges are not present in the final string graph \cite{MYE:2005}. \Rdjoverlap matching algorithm allows one to recognize which SPM would correspond to transitive edges in the graph. Thus the graph can be constructed only including the irreducible edges, requiring less memory. The \Rdjoverlap tool computes the list of suffix-prefix matches among all pairs of reads using a suffix sorting and scanning approach. Non-relevant suffixes are excluded, such as those shorter than $\minlen$ or without an initial $k$-mer matching a read or reverse complement of read. An index of the SPM-relevant suffixes is constructed during this phase. The index construction is partitioned in order to limit the space peak. \Readjoiner uses heuristics to automatically calculates a value for this parameter, which is usually a good choice.. However, a memory limit or number of parts can be given as a parameter to control this time vs.\ space tradeoff. If the binary has been compiled with multithreading support, you can specify the number of threads as follows: \texttt{gt -j readjoiner overlap }. \subsection{Running the \Rdjoverlap tool} The input to the \Readjoiner overlap tool is a prefix- and suffix-free readset in \GenomeTools encoded sequence format, usually the output of \Rdjprefilter. The following options shall be used: \begin{Justshowoptions} \Option{readset}{\Showoptionarg{readset}}{ Specify the readset name. The argument should be the same used for the prefilter tool.} \Option{l}{\Showoptionarg{minlen}}{ Specify the minimal SPM length parameter.} \end{Justshowoptions} The minimal SPM length parameter is an essential parameter of the procedure. A too large value will make the pipeline faster, but potentially miss some important matches. A too small value will make the pipeline too slow, and add too many spurious overlaps. We found that the ideal value is in the range $\approx 55-65$ for 100 bp reads. The assembly phase can be repeated using different values of the minimal SPM length, without repeating the overlap phase, as long as these values are larger than the value used in the overlap phase. Therefore, one can choose a little smaller value, e.g. $\approx 50$ during the overlap phase and then test the assembly phase using several values equal or larger than that. The output of the overlap phase consists in one or more \texttt{.spm} files, containing a binary encoded list of the non-redundant irreducible suffix-prefix matches in the readset. It is possible to manually examine the results, by converting this list a text format, using the following command: \texttt{gt readjoiner spmtest -readset -test showlist}. \section{The assembly phase} The \Rdjassembly tool constructs a string graph. Each non-contained read in the sequencing readset is represented by a pair of vertices modeling its two extremities (Begin and End vertices). Irreducible SPMs are represented by directed edges. Sequencing errors present in the reads lead to characteristic paths in the graph. The error-correction algorithms described in \cite{Edena} are implemented and can be applied to recognize dead ends and p-bubbles and remove them (option \Showoption{errors}). Finally the graph is traversed and sequences corresponding to unbranched paths are output. \subsection{Running the the \Rdjassembly tool} The input consists in SPM lists in \Readjoiner format which are the output of \Rdjoverlap. The following options shall be used: \begin{Justshowoptions} \Option{readset}{\Showoptionarg{readset}}{ Specify the readset name, This must be the same used in the overlap phase.} \Option{l}{\Showoptionarg{minlen}}{ (optional) Specify the minimal SPM length parameter. The value should be at least as high as the one used for \Rdjoverlap. If an higher value is used, shorter overlaps are not loaded in the string graph.} \Option{errors}{}{ Clean short dead ends and remove p-bubbles. This is reccomended} \Option{spmfiles}{\Showoptionarg{n}}{ If the overlap phase was run using muliple threads, this option is mandatory and should be set to the same number of threads used by the \Option{j} in the overlap phase. } \end{Justshowoptions} \section{Examples} Consider a dataset containing paired-end reads with an insert size of 1000bp (st.dev. 120bp) in the files \texttt{p\_f.fastq} and \texttt{p\_r.fastq} and single-end reads in the file \texttt{se.fastq}. This example assumes the reads have been previously error-corrected, otherwise the results will be probably very poor. The first step will be run by \Rdjprefilter. \begin{footnotesize} \begin{verbatim} > gt readjoiner prefilter -readset myreadset \ -db p_f.fastq:p_r.fastq:1000,120 se.fastq \end{verbatim} \end{footnotesize} The result is output in \GenomeTools encoded sequence format and consist in a \texttt{readset.esq} file. The encoded sequence can now be used as input for \Rdjoverlap. We will use a minimal SPM lenght of 50 for this example and suppose \Readjoiner has been compiled with multi-threading support and 8 cores are available. \begin{footnotesize} \begin{verbatim} > gt -j 8 readjoiner overlap -readset readset -l 50 \end{verbatim} \end{footnotesize} The output will be a set of files \texttt{readset..spm}, with N in the range 0 to 7, containing lists of irreducible non-redundant SPMs in \Readjoiner binary format. Note that the \Showoption{j} option is specified in a different position (between \texttt{gt} and \texttt{readjoiner}) than the other options. The next step consists in running the assembly phase using the \Rdjassembly tool. \begin{footnotesize} \begin{verbatim} > gt readjoiner assembly -spmfiles 8 -readset readset -l 60 \end{verbatim} \end{footnotesize} The \Showoption{spmfiles} option is only necessary if the overlap phase was run using multiple threads: we used the same value for \Showoption{spmfiles} which was used for the \Showoption{j} option in the overlap phase. We used an higher mimimal length value that the one used in the overlap phase. If the results are not satisfying, you can repeat the assembly phase using a smaller value, such as \Showoption{l} \Showoptionarg{50} or \Showoption{l} \Showoptionarg{55} (the minimum that can be used is the value used in the overlap phase) and a larger value, such as \Showoption{l} \Showoptionarg{65} or \Showoption{l} \Showoptionarg{70}. The results are contigs, which are saved in FASTA format in \texttt{readset.contigs.fas}. Basic statistics of the assembly results, such as the N50 value and the total length, are displayed in the standard output. \begin{thebibliography}{1} \bibitem{MYE:2005} Myers, EW. (2005). \newblock {{T}he fragment assembly string graph}. \newblock {\em Bioinformatics\/}, {21 Suppl 2}, 79--85. \bibitem{genometools} Gremme, G. (2011). \newblock The \textsc{GenomeTools} genome analysis system. \url{http://genometools.org}. \bibitem{AKO04} Abouelhoda MI, Kurtz S, and Ohlebusch E. \newblock Replacing suffix trees with enhanced suffix arrays. \newblock {\em Journal of Discrete Algorithms}, 2:53--86, 2004. \bibitem{Edena} Hernandez D, François P, Farinelli L, Osterås M, and Schrenzel J. (2008). \newblock De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. \newblock {\em Genome Res\/}, {18}(5), 802--809. \bibitem{Readjoiner} Gonnella G and Kurtz S (2012). \newblock {Readjoiner. A fast and memory efficient string graph-based sequence assembler.} \newblock {\em BMC Bioinformatics}, {13}:82. \end{thebibliography} \end{document} genometools-1.5.1/doc/manuals/repfind.tex000066400000000000000000000163541211610345200204330ustar00rootroot00000000000000\documentclass[12pt]{article} \usepackage[a4paper]{geometry} \usepackage{url} \usepackage{alltt} \usepackage{xspace} \usepackage{times} \usepackage{bbm} \usepackage{verbatim} \usepackage{ifthen} \usepackage{optionman} \newcommand{\Showrep}[2]{\begin{array}{@{}c@{}}#1\\ {#2} \end{array}} \newcommand{\Function}[3]{#1:#2\to#3} \newcommand{\Size}[1]{|#1|} \newcommand{\Iff}{if and only if\xspace} \newcommand{\Repfind}[0]{\texttt{\small repfind}\xspace} \newcommand{\Suffixerator}[0]{\texttt{\small suffixerator}\xspace} \newcommand{\Nats}{\textrm{I}\!\textrm{N}} \newcommand{\Substring}[3]{#1[#2..#3]} \newcommand{\Subchar}[2]{#1[#2]} \title{\texttt{repfind}: a program for finding exact maximal repeats\\ a manual} \author{\begin{tabular}{c} \textit{Stefan Kurtz}\\ Center for Bioinformatics,\\ University of Hamburg \end{tabular}} \begin{document} \maketitle This manual describes the options of the program \Repfind. It also gives some examples on how to use it. We postpone the definition of the basic notions to the appendix. \Repfind computes all maximal repeats in the input sequence represented by the given index, and echoes them to standard output. If an error occurs, then the program exits with exit code 1 or 2 (depending on the kind of error). Otherwise, the exit code is 0. The index is constructed by the \Suffixerator-program, which is, like \Repfind, part of the Genometools [1], an open source software for biological sequence analysis. The \Suffixerator-program can process files in Fasta, Embl, Genbank or Swissprot format. There can be more than one sequence in any indexed file. There are no special options necessary to tell the \Suffixerator-program the sequence format. It automatically detects the appropriate format. We recommend to use either the option \Showoption{dna} or \Showoption{protein}, depending on the kind of input sequences to be processed. However, if both of these options are missing \Suffixerator is in most cases able to automatically identify the kind of sequence. The input for DNA sequences may, besides the base symbols \(A\), \(C\), \(G\), or \(T\), contain IUB special characters \(R,Y,M,K,W,S,B,D,H,V,N\). None of the exact matches reported by \Repfind contains such a character as it does not match any character not even itself (at a different position). \Repfind implements a subset of the options of the repfind-program from the REPuter software suite. While \Repfind (as part of the GenomeTools) is open source, the REPuter software is closed source. \section{The Options} The program \Repfind is called as follows: \par \noindent\texttt{gt} \Repfind [\textit{options}] \Showoption{ii} \Showoptionarg{indexname} [\textit{options}] The options for \Repfind are as follows: \begin{Justshowoptions} \Option{l}{$\ell$}{ Specifies the length parameter $\ell$. This must be a positive integer smaller than the length of the input sequence. Only repeats of length at least \(\ell\) are reported. If this option is not used, then \(\ell=20\).} \Option{f}{}{Compute maximal forward repeats} \Option{r}{}{Compute maximal reversed repeats} \Option{scan}{}{scan the index rather than mapping it to main memory (as done in the default case). This option only has an effect for computing forward repeats.} \Option{ii}{$\Showoptionarg{indexname}$}{Use the index $\Showoptionarg{indexname}$. This is a mandatory option.} \Option{v}{}{Be verbose} \Option{help}{}{display help message and exit} \end{Justshowoptions} \subsection*{Important Remark} The user of the program should carefully choose the length parameter \(\ell\). The number of maximal repeats exponentially decreases with increasing \(\ell\). \section{Output Format}\label{Output} \Repfind reports maximal repeats \((\ell,i,j\) to the standard output. Each line of the output in the format \begin{verbatim} len seqnum1 relpos1 symbol len seqnum2 relpos2 \end{verbatim} where \begin{itemize} \item \texttt{S} is either the symbols \texttt{F} or \texttt{R}. \texttt{F} stands for forward repeats and \texttt{R} stands for reverse repeats. \item \texttt{len} is the length of maximal repeat, which is identical for the first and the second instance of the repeat. Thus the length is reported twice. \item \texttt{seqnum1} is the sequence number in which the first repeat instance occurs at position \texttt{relpos1}. \texttt{seqnum2} is the sequence number in which the second repeat instance occurs at position \texttt{relpos2}. The positions are counted beginning with 0. \end{itemize} Suppose the input sequence \(S=gagctcgagcgctgct\) is contained in the file \texttt{Repfind-example.fna}. Then \begin{footnotesize} \begin{verbatim} gt suffixerator -db repfinf-sample.seq -indexname repidx -dna -suf -tis -lcp -ssp -pl \end{verbatim} \end{footnotesize} creates the index named \texttt{repidx} required for \Repfind. This is called as follows: \begin{verbatim} gt repfind -f -r -l 4 -ii repidx \end{verbatim} gives the following output: \begin{verbatim} 4 0 0 F 4 0 6 4 1 14 R 4 0 12 4 1 11 R 4 0 9 10 1 0 R 10 0 0 5 0 5 R 5 2 7 9 0 0 R 9 2 2 \end{verbatim} So, for example there is a maximal repeat of length 4 on the forward strand. Both instances of the repeat are in sequence 0. The first instance begins are position 0 and the second at position 6. \section{Remarks} The programs has been extensively tested, and we are not aware of any bugs. If the user detects a bug or would like to suggest other options or features of the program, then please \texttt{kurtz@zbh.uni-hamburg.de} should be contacted. \section*{References} \begin{enumerate} \item[1] The GenomeTools genome analysis system \url{http://genometools.org}. \item[2] Kurtz, S., Choudhuri, J. V., Ohlebusch, E., Schleiermacher, C., Stoye, J., Giegerich, R. (2001). REPuter: The manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res., 29:4633–4642. \end{enumerate} \appendix \section{Basic Notions}\label{Basic} We consider a string \(S\) of length \(n\). We index the characters of \(S\) from \(0\) to \(n-1\), i.e.\ \(S=\Substring{S}{0}{n-1}\). By \(S^{-1}\) we denote the reverse of \(S\), i.e.\ the string \(u\) of length \(n\) such that \(\Subchar{u}{i}=\Subchar{S}{n-1-i}\) for any \(i\in[0,n-1]\). We define two different kinds of repeats: \begin{itemize} \item \((l,i,j)\) is a \emph{forward or direct repeat} \Iff\ \(i0\) means a positive number of differences. If this option is not used, then the program runs in \textit{ms}-mode, i.e.\ it computes the matching statistics for each short sequence tag. } \Option{nod}{}{ Do not compute direct matches, i.e.\ matches on the forward strand. If this option is not used, then matches are computed on the forward strand.} \Option{nop}{}{ Do not compute palindromic matches, i.e.\ matches on the reverse complemented strand. If this option is not used, then matches are computed on the reverse complemented strand.} \Option{maxocc}{$\Showoptionarg{t}$}{ Specify the maximum number of occurrences of exact prefix matches (in case of the matching statistics) or approximate prefix matches. } \Option{withwildcards}{}{ Output matches containing wildcard characters (e.g. N). This option cannot be used in any of the following cases: \begin{itemize} \item with option \Showoption{pck}, \item in the \textit{ms}-mode, \item for all modes with \(k=0\). \end{itemize} } \Option{best}{}{ For each tag, only show matches for the smallest possible distance. That is, if a tag has exact matches in the input index, then only exact matches are shown. If there are no exact matches, but matches with distance 1, then only these are shown. If there are no matches matches with distance 1 (and hence no exact matches), but with distance 2, then only these are shown etc. } \Option{output}{$\Showoptionarg{key}_{1}\ldots\Showoptionarg{key}_{q}$}{ Use combination of the following keywords to specify output according to the following table: \begin{center} \begin{tabular}{l|l} keyword & shows the following\\\hline tagnum & show ordinal number of tag\\ tagseq & show tag sequence\\ dblength & show length of match in database\\ dbstartpos& show start position of match in database\\ abspos & show absolute value of dbstartpos\\ dbsequence& show sequence of match\\ strand & show strand\\ edist & show edit distance\\ tagstartpos& show start position of match in tag (only for \Showoption{maxocc})\\ taglength & show length of match in tag (only for option \Showoption{maxocc})\\ tagsuffixseq& show suffix tag involved in match (only for option \Showoption{maxocc}) \end{tabular} \end{center} This option only has an effect when used in the cdiff-mode. If in cdiff mode this option is not used, then the output is such as if keywords \texttt{tagnum}, \texttt{tagseq}, \texttt{dblength}, \texttt{dbstartpos}, \texttt{strand} were used. } \Helpoption \end{Justshowoptions} The following conditions must be satisfied: \begin{enumerate} \item Option \Showoption{q} is mandatory. \item Either option \Showoption{pck} or \Showoption{esa} must be used. Both cannot be combined. \item If option \Showoption{e} is not used, then option \Showoption{maxocc} is required. \end{enumerate} \section{Examples} Suppose that in some directory, say \texttt{homo-sapiens}, we have 24 gzipped \Fasta files containing all 24 human chromomsomes. These may have been downloaded from \url{ftp://ftp.ensembl.org/pub/current_fasta/homo_sapiens_47_36i/dna}. In the first step, we construct the packed index for the entire human genome: \begin{Output} gt packedindex mkindex -dna -dir rev -parts 12 -bsize 10 -sprank -locfreq 32 -tis -ssp -indexname pck-human -db homo-sapiens/*.gz \end{Output} The program runs for little more than two hours and delivers an index \texttt{human-all} consisting of three files: \begin{Output} ls -lh human-all.* -rw-r----- 1 kurtz gistaff 37 2008-07-13 17:00 pck-human.al1 -rw-r----- 1 kurtz gistaff 2.6G 2008-07-13 19:22 pck-human.bdx -rw-r----- 1 kurtz gistaff 3.3K 2008-07-13 19:22 pck-human.prj \end{Output} Suppose that the compressed file \texttt{Q1.gz} contains short sequence tags in multiple \Fasta format. In a first call we run \Program in \textit{ms}-mode: \EXECUTE{gt tagerator -q Q1.gz -maxocc 10 -pck pck-human | head -n 25} The first line shortly reports the kind of computation performed. The second and third line give the name of the index containing the subject sequences. It is reported whether it is a packed index or an enhanced suffix array. Then, for each tag its length, say \(m\), and the tag \(p\) itself is shown, followed by a block of \(m\) lines each containing one integers. For all \(i\in[1,m]\), the first column in the \(i\)th line is the matching statistics length, say \(l\). This means that \(\Substring{p}{i}{i+l-1}\) is the maximum length prefix of \(\Substring{p}{i}{m}\) that occurs as a substring in the index. The second column gives the strand of the match: a \texttt{+} stands for the forward strand and a \texttt{-} for the reverse strand. If the number of occurrences of \(\Substring{p}{i}{i+l-1}\) is smaller than the maximum occurrence parameter (\(10\) in the above case), then all matching statistics positions are reported in ascending order. If it is larger than the maximum occurrence parameter, no positions are shown. So, for example, the sequence \texttt{gcttgctg} of length 8 starting at tag position 3 is the longest prefix of \texttt{gcttgctgctgca} that occurs as a substring in the index. It occurs at the positions 25583, 88695, 213546, etc. Note that the matching statistics lines for the forward strand are followed by the matching statistics block on the reverse strand. Note however, that the matching statistics positions are always reported with respect to the forward strand. In a second call, we run \Program in \textit{cdiff}-mode: \EXECUTE{gt tagerator -q Q1.gz -pck pck-human -e 2 | head -n 28} The first line shortly reports the kind of computation performed. The second and third line are as in the previous example. Then, for each tag its length and the tag itself is shown, followed by a block of lines each containing three integers and one of the symbols \texttt{+} or \texttt{-}, denoting the strand of the match. Each such triple of integers reports the length of an approximate match, the subject sequence in which the match occurs, and the relative position of the match in this sequence. For each start position only the shortest length is reported. If there are no approximate matches, then no such line appears. Note that the match always refers to the complete pattern. Our third example concerns the \textit{pdiff}-mode: \EXECUTE{gt tagerator -q Q1.gz -pck pck-human -e 1 -maxocc 5 | head -n 20} The output is similar as in the previous example, except that each match is reported by four integers with a sign between the first three and the last number. The first number reports the length of the approximate match, the second reports the subject sequence number in which the match occur, the third its relative position in the subject sequence. The last number reports the length of the prefix of the tag involved in the approximate match. Note that in some cases, the two length values are different. \end{document} genometools-1.5.1/doc/manuals/tallymer.tex000066400000000000000000000446141211610345200206350ustar00rootroot00000000000000\documentclass[12pt]{article} \usepackage[a4paper,top=20mm,bottom=20mm,left=20mm,right=20mm]{geometry} \usepackage{url} \usepackage{alltt} \usepackage{xspace} \usepackage{times} \usepackage{listings} \usepackage{bbm} \usepackage{verbatim} %\usepackage{prognames} \usepackage{optionman} \newcommand{\Filenamesuffix}[1]{\texttt{\small #1}\index{#1@\texttt{#1}}} \newcommand{\Programname}[1]{\texttt{\small #1}} \newcommand{\Tallymer}[0]{\Programname{tallymer}\xspace} \newcommand{\TYmkindex}[0]{\Programname{mkindex}\xspace} \newcommand{\TYsearch}[0]{\Programname{search}\xspace} \newcommand{\TYoccratio}[0]{\Programname{occratio}\xspace} \newcommand{\SFX}[0]{\Programname{suffixerator}\xspace} \newcommand{\SFXidx}[0]{\textit{suffixerator}-index\xspace} \newcommand{\Tyridx}[0]{\textit{tallymer}-index\xspace} \newcommand{\GT}[0]{\Programname{gt}\xspace} \newcommand{\Kmin}[0]{k_{\min}} \newcommand{\Kmax}[0]{k_{\max}} \newcommand{\Kstep}[0]{k_{step}} \newcommand{\Minmaxocctext}[2]{ Specify the #1\xspace occurrence number for which to output the $k$-mer sequences. That is, a $k$-mer is output, if it occurs #2\xspace $c$ times in the union of all sequences from the \SFXidx. When combined with option \Showoption{indexname}, this option specifies an occurrence constraint on the $k$-mers stored in the generated \Tyridx. That is, a $k$-mer is put into the \Tyridx, if it occurs #2\xspace $c$ times in the union of all sequences from the \SFXidx. } \newcommand{\Typrogintro}[1]{ \par \noindent\GT \Programname{tallymer} #1\xspace [\textit{options}] \Showoption{esa} \SFXidx [\textit{options}] \par The \SFXidx is an enhanced suffix array computed by the program \SFX, which is also part of the genometools-package. Currently, there is no \SFX-manual available, but in Section~\ref{Examples} we show how to call \SFX appropriately in the context of \Tallymer. The following options are available in #1:} \newcommand{\Esaoption}[0]{ \Option{esa}{\Showoptionarg{\SFXidx}}{ Specify the name of an \SFXidx computed by the \SFX-program using the output options \Showoption{suf}, \Showoption{lcp}, and \Showoption{tis}. This option is mandatory. }} \newcommand{\Scanoption}[0]{ \Option{scan}{}{ Sequentially read the \SFXidx. In the default case, the \SFXidx is mapped into main memory. This means that \SFXidx must not be larger than the available address space. So for a 32-bit machine, the index cannot be larger than 4~GB. When using this option, the \textsf{lcp}-table and the \textsf{suf}-table of the \SFXidx are sequentially scanned, so that only a small part of these tables reside in memory. This, of course, reduces the memory requirement of the program. Note that the sequence is still mapped completely into main memory as it is accessed in random order. This option is higly recommended for large data sizes. If you ever get an error like \texttt{gt tallymer occratio: error: fopen(): cannot open file 'reads.prj': No such file or directory} } then you should add this option. } \newcommand{\Standardoptions}[0]{ \Option{v}{~~~}{% Be verbose, that is, give reports about the different steps as well as the resource requirements of the computation. } \Option{version}{}{ Show the version of the program and exit. } \Option{help}{}{ display help and exit. } } \title{The tallymer software for counting, indexing, and searching $k$-mers\\ a manual} \author{Stefan Kurtz} \author{\begin{tabular}{c} \textit{Stefan Kurtz}\\ Center for Bioinformatics,\\ University of Hamburg \end{tabular}} \begin{document} \maketitle This manual describes the \textit{Tallymer}-software, a collection of programs for counting, indexing, and searching $k$-mers. For an introduction of the notions, concepts, and methods underlying the software, we refer the reader to \cite{KUR:NER:STE:WAR:2008}. \textit{Tallymer} is part of the genometools software (\url{http://genometools.org}). It is implemented as part of the \textit{gt}-binary and called as a subprogram. So to run \Tallymer, one has to call the \textit{gt}-binary with subprogram \texttt{tallymer}. \Tallymer itself has three subprograms \TYmkindex, \TYoccratio, and \TYsearch. These are described below. \section{\TYmkindex} The program \TYmkindex is used for counting and indexing \(k\)-mers for a fixed value of \(k\). It is called as follows: \par \Typrogintro{\TYmkindex} \begin{Justshowoptions} \Esaoption \Option{mersize}{$k$}{ Specify the size $k$ of the mers. That is, the program generates all substrings of length $k$ of the given input sequences, given as a \SFXidx If this option is missing, then the default value for $k$ is 20. } \Option{minocc}{$c$}{ \Minmaxocctext{minimum}{at least} } \Option{maxocc}{$c$}{ \Minmaxocctext{maximum}{at most} } \Option{pl}{$\Showoptionalarg{prefixlength}$}{ Specify the prefix length to construct a bucket boundary table for the generated \Tyridx. This additional table speeds up the search in the \Tyridx. This option only works for an alphabet of size 4, i.e.\ for the DNA alphabet. The argument \Showoptionarg{prefixlength} is optional. Hence it is denoted in square brackets. If the argument is omitted, then the value for \Showoptionarg{prefixlength} is automatically determined. More precisely, it is \(\left\lfloor\log_{4}\frac{n}{4}\right\rfloor\), where \(n\) is the total number of $k$-mers in the \Tyridx. } \Option{indexname}{\Showoptionarg{idxname}}{ Store the $k$-mers specified according to the options \Showoption{minocc} and \Showoption{maxocc} in the file named \Showoptionarg{idxname}\Filenamesuffix{.mer}. If option \Showoption{pl} is used, then additionally the bucket boundary table is stored in a file named \Showoptionarg{idxname}\Filenamesuffix{.mbd}. Using the option \Showoption{counts} (see below), an additional file \Showoptionarg{idxname}\Filenamesuffix{.mct} is generated. These file together make up the \Tyridx. } \Option{counts}{}{ Specify that \Showoptionarg{idxname}\Filenamesuffix{.mct} is generated storing the counts of the $k$-mers represented by the \Tyridx. This option can only be used together with option \Showoption{indexname} which also specifies prefix of the produced output file. This option is required if the program \TYsearch needs to report the $k$-mer-counts. } \Scanoption \Standardoptions \end{Justshowoptions} The following conditions must be satisfied: \begin{enumerate} \item Option \Showoption{pl} requires to also use option \Showoption{indexname}. \item Option \Showoption{counts} requires to also use option \Showoption{indexname}. \item Option \Showoption{indexname} requires to also use one of the options options \Showoption{minocc} and \Showoption{maxocc}. \end{enumerate} Note that the program ignores all $k$-mers not entirely consisting of wildcard characters (i.e. not \texttt{a}, \texttt{c}, \texttt{c}, and \texttt{g} in case of the DNA alphabet). \section{\TYoccratio} The program \TYoccratio is used to compute the occurrence ratios for a set of sequences represented by a \SFXidx It is called as follows: \par \Typrogintro{\TYoccratio} \begin{Justshowoptions} \Esaoption \Option{minmersize}{$\Kmin$}{ Specify the minimum size of the mers which are counted. That is, the program counts the number of unique and nonunique mers of length at least $\Kmin$. This option is mandatory if option \Showoption{mersizes} is not used.} \Option{maxmersize}{$\Kmax$}{ Specify the maximum size of the mers which are counted. That is, the program counts the number of unique and nonunique mers of length at most $\Kmax$. This option is mandatory if option \Showoption{mersizes} is not used.} \Option{step}{$\Kstep$}{ Specify the step size according to which the mer counts are output. That is, for all $k\in[\Kmin,\Kmin+\Kstep,\Kmin+2\Kstep,\ldots,\Kmax]$ the $k$-mer counts are output. If this option is not used, then $\Kstep$ is 1.} \Option{mersizes}{$k_{1}~k_{2}\ldots k_{q}$}{ Specify mer sizes $1\leq k_{1} GFF2 - GMOD

GFF2

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GFF2 is a supported format in GMOD, but it is now deprecated and if you have a choice you should use GFF3. Unfortunately, data is sometimes only available in GFF2 format. GFF2 has a number of shortcomings compared to GFF3. GFF2 can only represent 2 level feature hierarchies, while GFF3 can support arbitrary levels. GFF2 also does not require that column 3, the feature type, be part of the sequence ontology. It can be any string. This often led to quality control and data exchange problems.


Contents

GFF2 is Deprecated!

The GFF file format stands for "Gene Finding Format" and was invented at the Sanger Centre. It is easy to use, but it suffers from two main limitations (see the box).

Why GFF2 is harmful to your health

One of GFF2's problems is that it is only able to represent one level of nesting of features. This is mainly a problem when dealing with genes that have multiple alternatively-spliced transcripts. GFF2 is unable to deal with the three-level hierarchy of gene → transcript → exon. Most people get around this by declaring a series of transcripts and giving them similar names to indicate that they come from the same gene. The second limitation is that while GFF2 allows you to create two-level hierarchies, such as transcript → exon, it doesn't have any concept of the direction of the hierarchy. So it doesn't know whether the exon is a subfeature of the transcript, or vice-versa. This means you have to use "aggregators" to sort out the relationships. This is a major pain in the neck. For this reason, GFF2 format has been deprecated in favor of GFF3 format databases.

See GFF3 for more on the current version of GFF.

The GFF2 File Format

The GFF format is a flat tab-delimited file, each line of which corresponds to an annotation, or feature. Each line has nine columns and looks like this: 

Chr1  curated  CDS 365647  365963  .  +  1  Transcript "R119.7"

The 9 columns are as follows:

reference sequence
This is the ID of the sequence that is used to establish the coordinate system of the annotation. In the example above, the reference sequence is "Chr1".
source
The source of the annotation. This field describes how the annotation was derived. In the example above, the source is "curated" to indicate that the feature is the result of human curation. The names and versions of software programs are often used for the source field, as in "tRNAScan-SE/1.2".
method
The annotation method, also known as type. This field describes the type of the annotation, such as "CDS". Together the method and source describe the annotation type.
start position
The start of the annotation relative to the reference sequence.
stop position
The stop of the annotation relative to the reference sequence. Start is always less than or equal to stop.
score
For annotations that are associated with a numeric score (for example, a sequence similarity), this field describes the score. The score units are completely unspecified, but for sequence similarities, it is typically percent identity. Annotations that do not have a score can use "."
strand
For those annotations which are strand-specific, this field is the strand on which the annotation resides. It is "+" for the forward strand, "-" for the reverse strand, or "." for annotations that are not stranded.
phase
For annotations that are linked to proteins, this field describes the phase of the annotation on the codons. It is a number from 0 to 2, or "." for features that have no phase.
group
GFF provides a simple way of generating annotation hierarchies ("is composed of" relationships) by providing a group field. The group field contains the class and ID of an annotation which is the logical parent of the current one. In the example given above, the group is the Transcript named "R119.7".

The group field is also used to store information about the target of sequence similarity hits, and miscellaneous notes. See the next section for a description of how to describe similarity targets.

The sequences used to establish the coordinate system for annotations can correspond to sequenced clones, clone fragments, contigs or super-contigs.

In addition to a group ID, the GFF format allows annotations to have a group class. This makes sure that all groups are unique even if they happen to share the same name. For example, you can have a GenBank accession named AP001234 and a clone named AP001234 and distinguish between them by giving the first one a class of Accession and the second a class of Clone.

You should use double-quotes around the group name or class if it contains white space.

Creating a GFF2 table

The first 8 fields of the GFF2 format are easy to understand. The group field is a challenge. It is used in several distinct ways:

  • to group together a single sequence feature that spans a discontinuous range, such as a gapped alignment.
  • to name a feature, allowing it to be retrieved by name.
  • to add one or more notes to the annotation.
  • to add an alternative name

Using the Group field for simple features

For a simple feature that spans a single continuous range, choose a name and class for the object and give it a line in the GFF2 file that refers to its start and stop positions. 

Chr3   giemsa heterochromatin  4500000 6000000 . . .   Band 3q12.1

Using the Group field to group features that belong together

For a group of features that belong together, such as the exons in a transcript, choose a name and class for the object. Give each segment a separate line in the GFF2 file but use the same name for each line. For example: 

IV     curated exon    5506900 5506996 . + .   Transcript B0273.1
IV     curated exon    5506026 5506382 . + .   Transcript B0273.1
IV     curated exon    5506558 5506660 . + .   Transcript B0273.1
IV     curated exon    5506738 5506852 . + .   Transcript B0273.1

These four lines refer to a biological object of class "Transcript" and name B0273.1. Each of its parts uses the method "exon", source "curated". Once loaded, the user will be able to search the genome for this object by asking the browser to retrieve "Transcript:B0273.1". The browser can also be configured to allow the Transcript: prefix to be omitted.

You can extend the idiom for objects that have heterogeneous parts, such as a transcript that has 5' and 3' UTRs 

IV     curated  mRNA   5506800 5508917 . + .   Transcript B0273.1; Note "Zn-Finger"
IV     curated  5'UTR  5506800 5508999 . + .   Transcript B0273.1
IV     curated  exon   5506900 5506996 . + .   Transcript B0273.1
IV     curated  exon   5506026 5506382 . + .   Transcript B0273.1
IV     curated  exon   5506558 5506660 . + .   Transcript B0273.1
IV     curated  exon   5506738 5506852 . + .   Transcript B0273.1
IV     curated  3'UTR  5506852 5508917 . + .   Transcript B0273.1

In this example, there is a single feature with method "mRNA" that spans the entire range. It is grouped with subparts of type 5'UTR, 3'UTR and exon. They are all grouped together into a Transcript named B0273.1. Furthermore the mRNA feature has a note attached to it.

NOTE: The subparts of a feature are in absolute (chromosomal or contig) coordinates. It is not currently possible to define a feature in absolute coordinates and then to load its subparts using coordinates that are relative to the start of the feature.

Some annotations do not need to be individually named. For example, it is probably not useful to assign a unique name to each ALU repeat in a vertebrate genome. For these, just leave the Group field empty.

Using the Group field to add a note

The group field can be used to add one or more notes to an annotation. To do this, place a semicolon after the group name and add a Note field: 

Chr3 giemsa heterochromatin 4500000 6000000 . . . Band 3q12.1 ; Note "Marfan's syndrome"

You can add multiple Notes. Just separate them by semicolons: 

 Band 3q12.1 ; Note "Marfan's syndrome" ; Note "dystrophic dysplasia"

The Note should come AFTER the group type and name.

Using the Group field to add an alternative name

If you want the feature to be quickly searchable by an alternative name, you can add one or more Alias tags. A feature can have multiple aliases, and multiple features can share the same alias: 

Chr3 giemsa heterochromatin 4500000 6000000 . . . Band 3q12.1 ; Alias MFX

Searches for aliases will be both faster and more reliable than searches for keywords in notes, since the latter relies on whole-text search methods that vary somewhat from DBMS to DBMS.

Identifying the reference sequence

Each reference sequence in the GFF table must itself have an entry. This is necessary so that the length of the reference sequence is known.

For example, if "Chr1" is used as a reference sequence, then the GFF file should have an entry for it similar to this one: 

Chr1 assembly chromosome 1 14972282 . + . Sequence Chr1

This indicates that the reference sequence named "Chr1" has length 14972282 bp, method "chromosome" and source "assembly". In addition, as indicated by the group field, Chr1 has class "Sequence" and name "Chr1".

It is suggested that you use "Sequence" as the class name for all reference sequences, since this is the default class used by the Bio::DB::GFF module when no more specific class is requested. If you use a different class name, then be sure to indicate that fact with the "reference class" option (see below).


Sequence alignments

There are several cases in which an annotation indicates the relationship between two sequences. One common one is a similarity hit, where the annotation indicates an alignment. A second common case is a map assembly, in which the annotation indicates that a portion of a larger sequence is built up from one or more smaller ones.

Both cases are indicated by using the Target tag in the group field. For example, a typical similarity hit will look like this: 

Chr1 BLASTX similarity 76953 77108 132 + 0 Target Protein:SW:ABL_DROME 493 544

Here, the group field contains the Target tag, followed by an identifier for the biological object. The GFF format uses the notation Class:Name for the biological object, and even though this is stylistically inconsistent, that's the way it's done. The object identifier is followed by two integers indicating the start and stop of the alignment on the target sequence.

Unlike the main start and stop columns, it is possible for the target start to be greater than the target end. The previous example indicates that the the section of Chr1 from 76,953 to 77,108 aligns to the protein SW:ABL_DROME starting at position 493 and extending to position 544.

A similar notation is used for sequence assembly information as shown in this example: 

Chr1        assembly Link   10922906 11177731 . . . Target Sequence:LINK_H06O01 1 254826
LINK_H06O01 assembly Cosmid 32386    64122    . . . Target Sequence:F49B2       6 31742

This indicates that the region between bases 10922906 and 11177731 of Chr1 are composed of LINK_H06O01 from bp 1 to bp 254826. The region of LINK_H0601 between 32386 and 64122 is, in turn, composed of the bases 5 to 31742 of cosmid F49B2.


Dense quantitative data

If you have dense quantitative data, such as tiling array data, microarray expression data, ChIP-chip or ChIP-seq chromatin immunoprecipitation data, then you will probably want to create "Wiggle" format binary files, which represent the quantitative data in a compact format in external files. Use the wiggle2gff3.pl script, included in this distribution, to format and load this data. Run wiggle2gff3.pl -h for instructions.

Loading the GFF file into the database

Use the BioPerl script utilities bp_bulk_load_gff.pl, bp_load_gff.pl or (if you are brave) bp_fast_load_gff.pl to load the GFF file into the database. For example, if your database is a MySQL database on the local host named "dicty", you can load it into an empty database using bp_bulk_load_gff.pl like this: 

 bp_bulk_load_gff.pl -c -d dicty my_data.gff

To update existing databases, use either bp_load_gff.pl or bp_fast_load_gff.pl. The latter is somewhat experimental, so use with care.

Aggregators

It is not necessary to use aggregators with the Chado, BioSQL, or Bio::DB::SeqFeature::Store GBrowse Adaptors, or any other adaptor that is based on GFF3.

The Bio::DB::GFF adaptor (and only Bio::DB::GFF!) has a feature known as "aggregators". These are small software packages that recognize certain common feature types and convert them into complex biological objects. These aggregators make it possible to develop intelligent graphical representations of annotations, such as a gene that draws confirmed exons differently from predicted ones.

An aggregator typically creates a new composite feature with a different method than any of its components. For example, the standard "alignment" aggregator takes multiple alignments of method "similarity", groups them by their name, and returns a single feature of method "alignment".

The various aggregators are described in detail in the Bio::DB::GFF perldoc page. It is easy to write new aggregators, and also possible to define aggregators on the fly in the GBrowse configuration file. It is suggested that you use the sample GFF2 files from the yeast, drosophila and C. elegans projects to see what methods to use to achieve the desired results.

In addition to the standard aggregators that are distributed with BioPerl, GBrowse distributes several experimental and/or special-purpose aggregators:

match_gap
This aggregator is used for GFF3 style gapped alignments, in which there is a single feature of method 'match' with a 'Gap' attribute. This aggregator was contributed by Dmitri Bichko.
orf
This aggregator aggregates raw "ORF" features into "coding" features. It is basically identical to the "coding" aggregator, except that it looks for features of type "ORF" rather than "cds".
reftranscript
This aggregator was written to make the compound feature, "reftranscript" for use with GBrowse editing software developed outside of the GMOD development group. It can be used to aggregate "reftranscripts" from "refexons", loaded as second copy features. These features, in contrast to "transcripts", are usually implemented as features which cannot be edited and serve as starting point references for annotations added using GBrowse for feature visualization. Adding features to the compound feature, "reftranscript", can be done by adding to the "part_names" call (i.e. "refCDS").
waba_alignment
This aggregator handles the type of alignments produced by Jim Kent's WABA program, and was written to be compatible with the C. elegans GFF2 files. It aggregates the following feature types into an aggregate type of "waba_alignment":
  • nucleotide_match:waba_weak
  • nucleotide_match:waba_strong
  • nucleotide_match:waba_coding
wormbase_gene
This aggregator was written to be compatible with the C. elegans GFF2 files distributed by the Sanger Institute. It aggregates raw "CDS", "5'UTR", "3'UTR", "polyA" and "TSS" features into "transcript" features. For compatibility with the idiosyncrasies of the Sanger GFF2 format, it expects that the full range of the transcript is contained in a main feature of type "Sequence".
It is strongly recommended that for mirroring C. elegans annotations, you use the "processed_transcript" aggregator in conjunction with the GFF3 files found at:
ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF3

Converting GFF2 to GFF3

Converting a file from GFF2 to GFF3 format is problematic for several reasons. However, there are several GFF2 to GFF3 converters available on the web, but each makes specific assumptions about the GFF2 data that limit its applicability. GMOD does not endorse (or disparage) any particular converter. If you have GFF2 data from an external source, and they don't also provide it in GFF3 format, then you may be stuck with GFF2.

Some areas that need to be addressed by any GFF2 to GFF3 converter:

Column 3: Feature Type

If the GFF2 file does not use Sequence Ontology terms in column 3 then some sort of translation will need to be done on the types in the GFF2 to convert them to be SO terms.

Column 9: Group / Attributes

Column 9 has a slightly different format and is much more tightly defined in GFF3 than GFF2. Both require attention. GFF2 does not have any reserved attribute names, uses C style encoding/escaping of special characters, and has many other small differences.

Another big problem is that GFF2 supports only one level of feature nesting. While you can certainly reproduce this minimal nesting in GFF3, it would be better to also convert your feature representations to be multi-level at the time you migrate the data to GFF3. This is non-trivial.

Retrieved from "http://gmod.org/wiki/GFF2"
genometools-1.5.1/doc/notes/GO.format.obo-1_2.shtml000066400000000000000000001764751211610345200217670ustar00rootroot00000000000000 The OBO Flat File Format Specification, version 1.2 genometools-1.5.1/doc/notes/GTF22.html000066400000000000000000000425351211610345200174240ustar00rootroot00000000000000 GTF2.2: A Gene Annotation Format

GTF2.2: A Gene Annotation Format

(Revised Ensembl GTF)

Contents

Introduction

GTF stands for Gene transfer format. It borrows from GFF, but has additional structure that warrants a separate definition and format name.

Structure is as GFF, so the fields are:
<seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]

Here is a simple example with 3 translated exons. Order of rows is not important. 

381 Twinscan  CDS          380   401   .   +   0  gene_id "001"; transcript_id "001.1";
381 Twinscan  CDS          501   650   .   +   2  gene_id "001"; transcript_id "001.1";
381 Twinscan  CDS          700   707   .   +   2  gene_id "001"; transcript_id "001.1";
381 Twinscan  start_codon  380   382   .   +   0  gene_id "001"; transcript_id "001.1";
381 Twinscan  stop_codon   708   710   .   +   0  gene_id "001"; transcript_id "001.1";
The whitespace in this example is provided only for readability. In GTF, fields must be separated by a single TAB and no white space.

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GTF Field Definitions

<seqname>
The name of the sequence. Commonly, this is the chromosome ID or contig ID. Note that the coordinates used must be unique within each sequence name in all GTFs for an annotation set.

<source>
The source column should be a unique label indicating where the annotations came from --- typically the name of either a prediction program or a public database.

<feature>
The following feature types are required: "CDS", "start_codon", "stop_codon". The features "5UTR", "3UTR", "inter", "inter_CNS", "intron_CNS" and "exon" are optional. All other features will be ignored. The types must have the correct capitalization shown here.

CDS represents the coding sequence starting with the first translated codon and proceeding to the last translated codon. Unlike Genbank annotation, the stop codon is not included in the CDS for the terminal exon. The optional feature "5UTR" represents regions from the transcription start site or beginning of the known 5' UTR to the base before the start codon of the transcript. If this region is interrupted by introns then each exon or partial exon is annotated as a separate 5UTR feature. Similarly, "3UTR" represents regions after the stop codon and before the polyadenylation site or end of the known 3' untranslated region. Note that the UTR features can only be used to annotate portions of mRNA genes, not non-coding RNA genes.

The feature "exon" more generically describes any transcribed exon. Therefore, exon boundaries will be the transcription start site, splice donor, splice acceptor and poly-adenylation site. The start or stop codon will not necessarily lie on an exon boundary.

The "start_codon" feature is up to 3bp long in total and is included in the coordinates for the "CDS" features. The "stop_codon" feature similarly is up to 3bp long and is excluded from the coordinates for the "3UTR" features, if used.

The "start_codon" and "stop_codon" features are not required to be atomic; they may be interrupted by valid splice sites. A split start or stop codon appears as two distinct features. All "start_codon" and "stop_codon" features must have a 0,1,2 in the <frame> field indicating which part of the codon is represented by this feature. Contiguous start and stop codons will always have frame 0.

The "inter" feature describes an intergenic region, one which is by almost all accounts not transcribed. The "inter_CNS" feature describes an intergenic conserved noncoding sequence region. All of these should have an empty transcript_id attribute, since they are not transcribed and do not belong to any transcript. The "intron_CNS" feature describes a conserved noncoding sequence region within an intron of a transcript, and should have a transcript_id associated with it.

<start> <end>
Integer start and end coordinates of the feature relative to the beginning of the sequence named in <seqname>.  <start> must be less than or equal to <end>. Sequence numbering starts at 1. Values of <start> and <end> that extend outside the reference sequence are technically acceptable, but they are discouraged.

<score>
The score field indicates a degree of confidence in the feature's existence and coordinates. The value of this field has no global scale but may have relative significance when the <source> field indicates the prediction program used to create this annotation. It may be a floating point number or integer, and not necessary and may be replaced with a dot.

<frame>
0 indicates that the feature begins with a whole codon at the 5' most base. 1 means that there is one extra base (the third base of a codon) before the first whole codon and 2 means that there are two extra bases (the second and third bases of the codon) before the first codon. Note that for reverse strand features, the 5' most base is the <end> coordinate.

Here are the details excised from the GFF spec. Important: Note comment on reverse strand.

'0' indicates that the specified region is in frame, i.e. that its first base corresponds to the first base of a codon. '1' indicates that there is one extra base, i.e. that the second base of the region corresponds to the first base of a codon, and '2' means that the third base of the region is the first base of a codon. If the strand is '-', then the first base of the region is value of <end>, because the corresponding coding region will run from <end> to <start> on the reverse strand.

Frame is calculated as (3 - ((length-frame) mod 3)) mod 3.

  • (length-frame) is the length of the previous feature starting at the first whole codon (and thus the frame subtracted out).
  • (length-frame) mod 3 is the number of bases on the 3' end beyond the last whole codon of the previous feature.
  • 3-((length-frame) mod 3) is the number of bases left in the codon after removing those that are represented at the 3' end of the feature.
  • (3-((length-frame) mod 3)) mod 3 changes a 3 to a 0, since three bases makes a whole codon, and 1 and 2 are left unchanged.
[attributes]
All nine features have the same two mandatory attributes at the end of the record:
  • gene_id value;     A globally unique identifier for the genomic locus of the transcript. If empty, no gene is associated with this feature.
  • transcript_id value;     A globally unique identifier for the predicted transcript. If empty, no transcript is associated with this feature.
These attributes are designed for handling multiple transcripts from the same genomic region. Any other attributes or comments must appear after these two and will be ignored.

Attributes must end in a semicolon which must then be separated from the start of any subsequent attribute by exactly one space character (NOT a tab character).

Textual attributes should be surrounded by doublequotes.

These attributes are required even for non-mRNA transcribed regions such as "inter" and "inter_CNS" features.

[comments]
Comments begin with a hash ('#') and continue to the end of the line. Nothing beyond a hash will be parsed. These may occur anywhere in the file, including at the end of a feature line.

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Examples

Here is an example of a gene on the negative strand including UTR regions. Larger coordinates are 5' of smaller coordinates. Thus, the start codon is 3 bp with largest coordinates among all those bp that fall within the CDS regions. Note that the stop codon lies between the 3UTR and the CDS

140    Twinscan    inter         5141     8522     .    -    .    gene_id ""; transcript_id "";
140    Twinscan    inter_CNS     8523     9711     .    -    .    gene_id ""; transcript_id "";
140    Twinscan    inter         9712     13182    .    -    .    gene_id ""; transcript_id "";
140    Twinscan    3UTR          65149    65487    .    -    .    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    3UTR          66823    66992    .    -    .    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    stop_codon    66993    66995    .    -    0    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    CDS           66996    66999    .    -    1    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    intron_CNS    70103    70151    .    -    .    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    CDS           70207    70294    .    -    2    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    CDS           71696    71807    .    -    0    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    start_codon   71805    71806    .    -    0    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    start_codon   73222    73222    .    -    2    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    CDS           73222    73222    .    -    0    gene_id "140.000"; transcript_id "140.000.1";
140    Twinscan    5UTR          73223    73504    .    -    .    gene_id "140.000"; transcript_id "140.000.1";

Note the frames of the coding exons. For example:

  1. The first CDS (from 71807 to 71696) always has frame zero.
  2. Frame of the 1st CDS =0, length =112.  (3-((length - frame) mod 3)) mod 3  = 2, the frame of the 2nd CDS.
  3. Frame of the 2nd CDS=2, length=88. (3-((length - frame) mod 3)) mod 3  = 1, the frame of the terminal CDS.
  4. Alternatively, the frame of terminal CDS can be calculated without the rest of the gene. Length of the terminal CDS=4. length mod 3 =1, the frame of the terminal CDS.

Note the split start codon. The second start codon region has a frame of 2, since it is the second base, and has an accompanying CDS feature, since CDS always includes the start codon.

Here is an example in which the "exon" feature is used. It is a 5 exon gene with 3 translated exons.

381 Twinscan  exon         150   200   .   +   .  gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan  exon         300   401   .   +   .  gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan  CDS          380   401   .   +   0  gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan  exon         501   650   .   +   .  gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan  CDS          501   650   .   +   2  gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan  exon         700   800   .   +   .  gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan  CDS          700   707   .   +   2  gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan  exon         900  1000   .   +   .  gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan  start_codon  380   382   .   +   0  gene_id "381.000"; transcript_id "381.000.1";
381 Twinscan  stop_codon   708   710   .   +   0  gene_id "381.000"; transcript_id "381.000.1";

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Scripts and Resources

Several Perl scripts have been written for checking, parsing, correcting, and comparing GTF-formatted annotations. Most of the important ones are included the Eval package, which comes equipped with a GTF parsing Perl package GTF.pm.

The Eval documentation contains a complete code-level documentation of GTF.pm, suitable for able Perl programmers to create and parse GTF files.

The script validate_gtf.pl included in the Eval package is particularly useful for checking that your GTF annotation is consistent and well-formed. This can also be done over the web: Here are some more useful links:

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  genometools-1.5.1/doc/notes/TODO_libgtmatch.txt000066400000000000000000000027261211610345200214540ustar00rootroot00000000000000ma_get_space_peak() und das Makro env_ma_get_space_peak() die den space peak in Bytes zur"uckliefern. mrege genericfilenames into fbsadv, and finally replace genericfilename by genfilename (if not too slow). -------------------- store the special code information on a file and perform prefixlength many iterations to insert the suffixes: PRIO-low show space of different parts relative to all parts: PRIO-high add type Sequencelength: allows for small and large sequences in 32 bit mode. unsigned long in 64-bit mode: PRIO low use flexible fixed bits type to store integers: PRIO low use test sequence of length n where n % 4 \in [0,1,2,3] do not force -pl to be a mandatory argument, if left out, then it determined automatically. instead of determining the parts, the user should define a maximum amount of memory to be used. Then the number of parts are chosen such that this boundary is not exceeded. add advancement display, see Gordon's lib: 0% 1% ... 100% Sometimes I cannot set a default value when specifying the option, because the default value is determined after all other options are known and maybe some file is input replacing timer by some method which does not produce overflows. use encseq->totallength instead of the parameter totallength in bentleysedgewick output the ranges in sorted order w.r.t. the length add function to count the number of wildcards in a range. remove exits in library. add splintgoal for libgtmatch add prepro goal for libgtmatch genometools-1.5.1/doc/notes/css/000077500000000000000000000000001211610345200165315ustar00rootroot00000000000000genometools-1.5.1/doc/notes/css/so_style.css000066400000000000000000000176131211610345200211140ustar00rootroot00000000000000body { background: #eef3f9 url('../img/page_bg.gif') top left fixed; font-family: Verdana, Arial, Helvetica, Sans-Serif; font-size: 75%; /* text-align: center; */ margin: 15px 0 15px 0; } /* ------------------ typography ------------------ */ p, ul, ol { font-size: 1em; line-height: 1.5em; color: #3F322A; padding:0px; margin: 0 0 10px 0; } h1 { font-size: 2em; line-height: 1.3em; color: #420F0B; margin: 0 0 10px 0; padding: 0; } #header_left h1 { font-size: 2.3em; line-height: 1.4em; letter-spacing: -1px; color: #420F0B; margin: 0 0 0 0; padding: 0; } h2 { font-size: 1.75em; line-height: 1.3em; color: #420F0B; margin: 0 0 0px 0; padding: 0; } #header_left h2 { font-size: 1em; line-height: 1em; color: #5E9856; margin: 0 0 10px 0; padding: 0 0 0 3px; letter-spacing: 1px; } h3 { font-size: 1.5em; line-height: 1.3em; color: #420F0B; margin: 0 0 6px 0; padding: 0; } h4 { font-size: 1.25em; line-height: 1.1em; color: #5A703A; margin: 0 0 6px 0; padding: 0; } h5 { font-size: 1em; line-height: 1.3em; color: #420F0B; margin: 0 0 10px 0; padding: 0; } .code { font-size: 1.3em; margin: 20px; white-space: pre; font-family: monospace; } .autolist_name { font-weight: normal; } .autolist_synonym { font-style: italic; } .autolist_id { text-decoration: underline; } /* ------------------- tables ----------------- */ table { width: 90%; padding: 0px; border: 1px solid; margin: auto; margin-top: 10px; margin-bottom: 10px; } th { border: 1px solid; background-color: #CDCDCD; vertical-align: middle; padding: 3px; font-weight: bold; } td { border: 1px solid; vertical-align: middle; padding: 3px; } /* ------------------- hyperlinks ----------------- */ a, a:visited, a:active { background-color: transparent; color: #971903; text-decoration: none; } a:hover { background-color: transparent; color: #971903; text-decoration: underline; } #header_left A:link, #header_left A:visited, #header_left A:active { color: #EAEA9A; text-decoration: none; } #header_left A:hover { background-color: transparent; color: #FAF4E8; text-decoration: none; } #footer A:link, #footer A:visited, #footer A:active { background: transparent; color: #E6C581; text-decoration: none; padding-left: 5px; padding-right: 5px; } #footer A:hover { background: transparent; color: #E6C581; text-decoration: underline; } /* --------------- Ordered/Unordered Lists -------------- */ #main_content ul, #left_column ul, #right_column ul { margin-left: 6px; padding-left: 0px; list-style-type:none; margin-bottom: 15px; } #main_content li, #left_column li, #right_column li { padding-left: 10px; background: transparent url('../img/arrow.gif') 0 0.47em no-repeat; margin-bottom: .5em; } #main_content ol, #left_column ol, #right_column ol { margin-left: 0px; padding-left: 0px; } #main_content ol li, #left_column ol li, #right_column ol li { margin-left: 23px; padding-left: 0px; background: none; list-style-type: decimal; list-style-position: outside; } /* ----------------- horizontal menu bar ------------------ */ #navcontainer { text-align: center; } ul#navlist { margin: 12px 2px 12px 2px; padding: 0; font-family: arial; font-size: 1.4em; line-height: .8em; font-weight: bold; } #navlist li { display: inline; list-style-type: none; margin: 0; padding: 0; line-height: 1em; } #navlist a { padding:4px 8px 0px 8px; margin: 0; } #navlist a:link, #navlist a:visited { color: #fff; background-color: transparent; text-decoration: none; } #navlist a:hover { color: #fff; text-decoration: none; border-bottom:1px dotted white; } /* --------------------- page layout --------------------- */ #page_wrapper { background: #FFFFFF; /* can be percentage or fixed width. 745px wide is ideal for 800x600 screens */ /* width: 80%; */ width: 900px; border: 10px solid #FFFFFF; margin: 0 auto; } #header { height: 138px; background: #669ACC url('../img/header_bg.jpg') top left no-repeat; } #header_left { float: left; width: 300px; padding: 30px 20px 0px 20px; text-align: left; } #menu_bar { text-align: left; padding: 4px; margin:0; background: #3B6710 url('../img/menu_bg.jpg') top left repeat-x; } #breadcrumb { background: inherit; padding: 0; margin: 0px; text-align: left; border-bottom: 1px solid #DDD4C2; } #breadcrumb p { padding: 15px 10px 15px 10px; margin: 0; } #content_wrapper{ float: left; width: 100%; background: inherit; } #right_column { float: right; width: 23%; margin: 0px; border-left: 1px solid #DDD4C2; text-align: left; } #main_content{ overflow: auto; float: left; margin: 0; width: 75%; text-align: left; } .item { border: dotted 1px #DDD4C2; width: 95%; padding: 10px; margin: 10px; background: #eef3f9; } #export_bar{ margin: 0; padding: 0; width: 100%; text-align: left; } #footer { background-color: #4c7821; text-align: center; padding:0px; margin:0; border-top: 1px solid black; border-bottom: 1px solid black; } .logo { height: 50px; } #footer p { background-color: transparent; color: #C1BC9D; margin: 0px; padding: 20px 0 20px 0; } .footer_left { margin: 10px 0 10px 0; padding: 0px; display: inline; width: 25%; float: left; } .footer_center { margin: 0px 0 0px 0; padding: 0px; display: inline; width: 50%; float: left; } .footer_right { margin: 10px 0 10px 0; padding: 0px; display: inline; width: 25%; float: right; } .column_padding { /* margin to provide padding inside each side column */ overflow:auto; margin: 15px; } .main_padding { /* margin to provide padding inside main content area */ margin: 15px 15px 15px 10px; } /* ------------------------ other ------------------------- */ #img_frame { overflow: auto; width: 90%; border: 1px solid; background: inherit; padding: 0px; margin: auto; margin-top: 10px; margin-bottom: 10px; } /* img { padding: 10px; margin: 5px auto 5px; display: block; } */ .inline img { padding: 0; margin: 0; /* dislplay: inline; */ } blockquote { background-image: url(../img/quote.gif); background-repeat: no-repeat; background-position: 0px 0px; padding: 1px 0 1px 30px; margin: 0 30px 0 10px; } blockquote p { margin: 0 0 1em 0; padding: 0px; font-size: 1.1em; line-height: 1.4em; font-weight: bold; color: #6C5D53; } .note { width: 90%; margin: 5px auto 5px; padding: 5px 5px 5px 5px; border: 1px solid; font-size: 1em; background: silver; } .pub_citation { margin:10px; color: #6C5D53; } .pub_title { font-size: 1em; font-weight: bold; } .pub_author { font-style: oblique; } .pub_journal { } .float_right { float:right; margin: 5px 0 5px 10px; } .spacer { clear: both; } div.h_scroll { padding:5px; width:100%; overflow:auto; }genometools-1.5.1/doc/notes/deprecated.txt000066400000000000000000000263141211610345200206100ustar00rootroot00000000000000 /for sfx-blindtrie.c */ static void checkcurrentblindtrie(Blindtrie *blindtrie) { unsigned long suffixtable[6], idx, numofsuffixes, maxcommon; int retval; numofsuffixes = enumeratetrieleaves (blindtrie,&suffixtable[0], NULL, NULL); for (idx=1UL; idx < numofsuffixes; idx++) { maxcommon = 0; retval = gt_encseq_comparetwostringsgeneric( blindtrie->encseq, GT_ISDIRREVERSE(blindtrie->readmode) ? false : true, GT_ISDIRCOMPLEMENT(blindtrie->readmode) ? true : false, &maxcommon, suffixtable[idx-1], suffixtable[idx], 0); if (retval >= 0) { fprintf(stderr,"retval = %d, maxcommon = %u for idx = %lu\n", retval,maxcommon,idx); exit(GT_EXIT_PROGRAMMING_ERROR); } } } /* The following generalizes the previous in that the comparison of the sequences starts at offset . */ int gt_encseq_comparetwostringsgeneric(const GtEncseq *encseq, bool fwd, bool complement, unsigned long *maxcommon, unsigned long pos1, unsigned long pos2, unsigned long depth, unsigned long maxdepth) { unsigned long totallength = gt_encseq_total_length(encseq); int retval; bool leftspecial, rightspecial; if (fwd) { unsigned long endpos1, endpos2; if (maxdepth == 0) { endpos1 = endpos2 = totallength; } else { gt_assert(maxdepth >= depth); endpos1 = MIN(pos1 + maxdepth,totallength); endpos2 = MIN(pos2 + maxdepth,totallength); } if (pos1 + depth < endpos1 && pos2 + depth < endpos2) { retval = gt_encseq_comparetwostrings(encseq, fwd, complement, maxcommon, pos1+depth, pos2+depth, maxdepth == 0 ? 0 : (maxdepth - depth)); } else { retval = gt_encseq_comparewithonespecial( &leftspecial, &rightspecial, encseq, fwd, complement, pos1, pos2, depth, maxdepth); } } else { if (maxdepth > 0) { gt_assert(false); } if (pos1 >= depth && pos2 >= depth) { retval = gt_encseq_comparetwostrings(encseq, fwd, complement, maxcommon, pos1-depth, pos2-depth, maxdepth == 0 ? 0 : (maxdepth - depth)); } else { retval = gt_encseq_comparewithonespecial( &leftspecial, &rightspecial, encseq, fwd, complement, pos1, pos2, depth, maxdepth); } } *maxcommon += depth; return retval; } #undef FASTCOMPAREDEBUG #ifdef FASTCOMPAREDEBUG static void verifycomparestringresults(const GtEncseq *encseq, GtCommonunits *commonunits, bool fwd, bool complement, unsigned long pos1, unsigned long pos2, unsigned long depth, unsigned long maxdepth, int retval) { unsigned long lcp2 = 0; int retval2; retval2 = gt_encseq_comparetwostringsgeneric(encseq, fwd, complement, &lcp2, pos1, pos2, depth, maxdepth); if (retval != retval2) { fprintf(stderr,"line %d: retval = %d != %d = retval2\n",__LINE__, retval,retval2); fprintf(stderr,"pos1 = %lu, pos2 = %lu, depth = %lu, maxdepth = %lu " "lcp = %lu, lcp2 = %lu\n", pos1, pos2, depth, maxdepth, commonunits->finaldepth, lcp2); exit(GT_EXIT_PROGRAMMING_ERROR); } if (commonunits->finaldepth != lcp2) { fprintf(stderr,"line %d: pos1 = %lu, pos2 = %lu, depth = %lu, maxdepth=%lu " "lcp = %lu != %lu = lcp2\n", __LINE__, pos1, pos2, depth, maxdepth, commonunits->finaldepth, lcp2); exit(GT_EXIT_PROGRAMMING_ERROR); } } #endif #undef CHECKSUFFIXRANGE #ifdef CHECKSUFFIXRANGE static void checksuffixrange(const Bentsedgresources *bsr, unsigned long subbucketleft, unsigned long width, unsigned long depth, int line) { unsigned long idx, newdepth = depth, pos1, pos2; #ifdef SKDEBUG printf("checksuffixrange "); showsuffixrange(bsr, subbucketleft, width, depth); #endif for (idx=0; idxfwd) { pos1 = gt_suffixsortspace_get(bsr->sssp,subbucketleft,idx); pos2 = gt_suffixsortspace_get(bsr->sssp,subbucketleft,idx+1); } else { pos1 = GT_REVERSEPOS(gt_encseq_total_length(bsr->encseq), gt_suffixsortspace_get(bsr->sssp,subbucketleft, idx)); pos2 = GT_REVERSEPOS(gt_encseq_total_length(bsr->encseq), gt_suffixsortspace_get(bsr->sssp,subbucketleft, idx+1)); } (void) gt_encseq_comparetwostrings(bsr->encseq, bsr->fwd, bsr->complement, &newdepth, pos1, pos2, depth); if (depth > newdepth) { fprintf(stderr,"line %d: " "depth=%lu > %lu=newdepth\n", line, depth, newdepth); fprintf(stderr,"suffix %lu vs %lu\n", gt_suffixsortspace_get(bsr->sssp,subbucketleft,idx), gt_suffixsortspace_get(bsr->sssp,subbucketleft,idx+1)); fprintf(stderr,"in range of length %lu\n",width); exit(GT_EXIT_PROGRAMMING_ERROR); } } } #endif #ifdef FASTCOMPAREDEBUG verifycomparestringresults(encseq, commonunits, fwd, complement, fwd ? pos1 : GT_REVERSEPOS(encseq->totallength,pos1), fwd ? pos2 : GT_REVERSEPOS(encseq->totallength,pos2), depth, maxdepth, retval); #endif #ifdef FASTCOMPAREDEBUG verifycomparestringresults(encseq, commonunits, fwd, complement, fwd ? pos1 : GT_REVERSEPOS(encseq->totallength,pos1), fwd ? pos2 : GT_REVERSEPOS(encseq->totallength,pos2), depth, 0, retval); #endif static inline void writeLCPVal(const GtEncseq *encseq, GtReadmode readmode, unsigned long *dest, unsigned long a, unsigned long b) { #ifndef NDEBUG int cmp = #endif gt_encseq_comparetwosuffixes(encseq, readmode, dest, false, false, 0, a, b, NULL, NULL); #ifndef NDEBUG if (cmp > 0) { fprintf(stderr, ": cmp %lu %lu = %d", a, b, cmp); exit(GT_EXIT_PROGRAMMING_ERROR); } #endif } #ifdef WITHbruteforcelcpvalue static void showSuffixwithcode(FILE *fp,const Suffixwithcode *suffix) { char buffer[18+1]; gt_fromkmercode2string(buffer, suffix->code, 4, 8, "acgt"); fprintf(fp,"(startpos=%lu,code=%u,prefixindex=%u,\"%s\")", suffix->startpos, (unsigned int) suffix->code, suffix->prefixindex, buffer); } static unsigned long bruteforcelcpvalue(const GtEncseq *encseq, GtReadmode readmode, const Suffixwithcode *previoussuffix, const Suffixwithcode *currentsuffix, unsigned int minchanged, GtEncseqReader *esr1, GtEncseqReader *esr2) { unsigned long lcpvalue; unsigned int lcpvalue2; int cmp; cmp = gt_encseq_comparetwosuffixes(encseq, readmode, &lcpvalue, false, false, 0, previoussuffix->startpos, currentsuffix->startpos, esr1, esr2); if (cmp > 0) { fprintf(stderr,"cmp %lu %lu = %d, lcpval=%lu\n", previoussuffix->startpos, currentsuffix->startpos, cmp, lcpvalue); exit(GT_EXIT_PROGRAMMING_ERROR); } if (previoussuffix->code == currentsuffix->code) { gt_assert(lcpvalue == MIN(previoussuffix->prefixindex, currentsuffix->prefixindex)); } else { gt_assert(previoussuffix->code < currentsuffix->code); lcpvalue2 = MIN(minchanged,MIN(previoussuffix->prefixindex, currentsuffix->prefixindex)); if (lcpvalue != lcpvalue2) { fprintf(stderr,"lcpvalue = %lu != %u = lcpvalue2\n",lcpvalue,lcpvalue2); fprintf(stderr,"previoussuffix="); showSuffixwithcode(stderr,previoussuffix); fprintf(stderr,"\ncurrentsuffix="); showSuffixwithcode(stderr,currentsuffix); fprintf(stderr,"\n"); exit(GT_EXIT_PROGRAMMING_ERROR); } } return lcpvalue; } #endif genometools-1.5.1/doc/notes/gff3.shtml000066400000000000000000001663631211610345200176560ustar00rootroot00000000000000 The Sequence Ontology - Resources - GFF3

News

GENERIC FEATURE FORMAT VERSION 3


SUMMARY

Author: Lincoln Stein Date: 15 December 2010 Version: 1.20 Although there are many richer ways of representing genomic features via XML, the stubborn persistence of a variety of ad-hoc tab-delimited flat file formats declares the bioinformatics community's need for a simple format that can be modified with a text editor and processed with shell tools like grep. The GFF format, although widely used, has fragmented into multiple incompatible dialects. When asked why they have modified the published Sanger specification, bioinformaticists frequently answer that the format was insufficient for their needs, and they needed to extend it. The proposed GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats. The new format: 1) adds a mechanism for representing more than one level of hierarchical grouping of features and subfeatures. 2) separates the ideas of group membership and feature name/id 3) constrains the feature type field to be taken from a controlled vocabulary. 4) allows a single feature, such as an exon, to belong to more than one group at a time. 5) provides an explicit convention for pairwise alignments 6) provides an explicit convention for features that occupy disjunct regions

Online Validator

An online GFF3 validator is available at http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online It is limited to files of 3,000,000 lines or less. If you wish to validate larger files, please use the command-line version which can be downloaded from the same site.

DESCRIPTION OF THE FORMAT

The format consists of 9 columns, separated by tabs (NOT spaces). The following characters must be escaped using URL escaping conventions (%XX hex codes): tab newline carriage return control characters The following characters have reserved meanings and must be escaped when used in other contexts: ; (semicolon) = (equals) % (percent) & (ampersand) , (comma) Unescaped quotation marks, backslashes and other ad-hoc escaping conventions that have been added to the GFF format are explicitly forbidden Note that unescaped spaces are allowed within fields, meaning that parsers must split on tabs, not spaces. Undefined fields are replaced with the "." character, as described in the original GFF spec. Column 1: "seqid" The ID of the landmark used to establish the coordinate system for the current feature. IDs may contain any characters, but must escape any characters not in the set [a-zA-Z0-9.:^*$@!+_?-|]. In particular, IDs may not contain unescaped whitespace and must not begin with an unescaped ">". Column 2: "source" The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature. Typically this is the name of a piece of software, such as "Genescan" or a database name, such as "Genbank." In effect, the source is used to extend the feature ontology by adding a qualifier to the type creating a new composite type that is a subclass of the type in the type column. Column 3: "type" The type of the feature (previously called the "method"). This is constrained to be either: (a)a term from the "lite" version of the Sequence Ontology - SOFA, a term from the full Sequence Ontology - it must be an is_a child of sequence_feature (SO:0000110) or (c) a SOFA or SO accession number. The latter alternative is distinguished using the syntax SO:000000. Columns 4 & 5: "start" and "end" The start and end of the feature, in 1-based integer coordinates, relative to the landmark given in column 1. Start is always less than or equal to end. For features that cross the origin of a circular feature (e.g. most bacterial genomes, plasmids, and some viral genomes), the requirement for start to be less than or equal to end is satisfied by making end = the position of the end + the length of the landmark feature. For zero-length features, such as insertion sites, start equals end and the implied site is to the right of the indicated base in the direction of the landmark. Column 6: "score" The score of the feature, a floating point number. As in earlier versions of the format, the semantics of the score are ill-defined. It is strongly recommended that E-values be used for sequence similarity features, and that P-values be used for ab initio gene prediction features. Column 7: "strand" The strand of the feature. + for positive strand (relative to the landmark), - for minus strand, and . for features that are not stranded. In addition, ? can be used for features whose strandedness is relevant, but unknown. Column 8: "phase" For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon. In other words, a phase of "0" indicates that the next codon begins at the first base of the region described by the current line, a phase of "1" indicates that the next codon begins at the second base of this region, and a phase of "2" indicates that the codon begins at the third base of this region. This is NOT to be confused with the frame, which is simply start modulo 3. For forward strand features, phase is counted from the start field. For reverse strand features, phase is counted from the end field. The phase is REQUIRED for all CDS features. Column 9: "attributes" A list of feature attributes in the format tag=value. Multiple tag=value pairs are separated by semicolons. URL escaping rules are used for tags or values containing the following characters: ",=;". Spaces are allowed in this field, but tabs must be replaced with the %09 URL escape. These tags have predefined meanings: ID Indicates the ID of the feature. IDs for each feature must be unique within the scope of the GFF file. In the case of discontinuous features (i.e. a single feature that exists over multiple genomic locations) the same ID may appear on multiple lines. All lines that share an ID collectively represent a single feature. Name Display name for the feature. This is the name to be displayed to the user. Unlike IDs, there is no requirement that the Name be unique within the file. Alias A secondary name for the feature. It is suggested that this tag be used whenever a secondary identifier for the feature is needed, such as locus names and accession numbers. Unlike ID, there is no requirement that Alias be unique within the file. Parent Indicates the parent of the feature. A parent ID can be used to group exons into transcripts, transcripts into genes, an so forth. A feature may have multiple parents. Parent can *only* be used to indicate a partof relationship. Target Indicates the target of a nucleotide-to-nucleotide or protein-to-nucleotide alignment. The format of the value is "target_id start end [strand]", where strand is optional and may be "+" or "-". If the target_id contains spaces, they must be escaped as hex escape %20. Gap The alignment of the feature to the target if the two are not collinear (e.g. contain gaps). The alignment format is taken from the CIGAR format described in the Exonerate documentation. (http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/exonerate ?cvsroot=Ensembl). See "THE GAP ATTRIBUTE" for a description of this format. Derives_from Used to disambiguate the relationship between one feature and another when the relationship is a temporal one rather than a purely structural "part of" one. This is needed for polycistronic genes. See "PATHOLOGICAL CASES" for further discussion. Note A free text note. Dbxref A database cross reference. See the section "Ontology Associations and Db Cross References" for details on the format. Ontology_term A cross reference to an ontology term. See the section "Ontology Associations and Db Cross References" for details. Is_circular A flag to indicate whether a feature is circular. Multiple attributes of the same type are indicated by separating the values with the comma "," character, as in: Parent=AF2312,AB2812,abc-3 In addition to Parent, the Alias, Note, DBxref and Ontology_term attributes can have multiple values. Note that attribute names are case sensitive. "Parent" is not the same as "parent". All attributes that begin with an uppercase letter are reserved for later use. Attributes that begin with a lowercase letter can be used freely by applications.

THE CANONICAL GENE

Figure1

FIGURE 1


This section describes the representation of a protein-coding gene in GFF3. To illustrate how a canonical gene is represented, consider Figure 1 (figure1.png). This indicates a gene named EDEN extending from position 1000 to position 9000. It encodes three alternatively-spliced transcripts named EDEN.1, EDEN.2 and EDEN.3, the last of which has two alternative translational start sites leading to the generation of two protein coding sequences. There is also an identified transcriptional factor binding site located 50 bp upstream from the transcriptional start site of EDEN.1 and EDEN2. Here is how this gene should be described using GFF3: 0 ##gff-version 3 1 ##sequence-region ctg123 1 1497228 2 ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN 3 ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001 4 ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1 5 ctg123 . mRNA 1050 9000 . + . ID=mRNA00002;Parent=gene00001;Name=EDEN.2 6 ctg123 . mRNA 1300 9000 . + . ID=mRNA00003;Parent=gene00001;Name=EDEN.3 7 ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mRNA00003 8 ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mRNA00001,mRNA00002 9 ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mRNA00001,mRNA00003 10 ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA00003 11 ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA00003 12 ctg123 . CDS 1201 1500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1 13 ctg123 . CDS 3000 3902 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1 14 ctg123 . CDS 5000 5500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1 15 ctg123 . CDS 7000 7600 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1 16 ctg123 . CDS 1201 1500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2 17 ctg123 . CDS 5000 5500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2 18 ctg123 . CDS 7000 7600 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2 19 ctg123 . CDS 3301 3902 . + 0 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3 20 ctg123 . CDS 5000 5500 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3 21 ctg123 . CDS 7000 7600 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3 22 ctg123 . CDS 3391 3902 . + 0 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4 23 ctg123 . CDS 5000 5500 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4 24 ctg123 . CDS 7000 7600 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4 Lines beginning with ## are pragmas that provide meta-information about the document. Blank lines and lines beginning with a single # are ignored. Line 0 gives the GFF version using the ##gff-version pragma. Line 1 indicates the boundaries of the region being annotated (a 1,497,228 bp region named "ctg123") using the ##sequence-region pragma. Line 2 defines the boundaries of the gene. Column 9 of this line assigns the gene an ID of gene00001, and a human-readable name of EDEN. Because the gene is not part of a larger feature, it has no Parent. Line 3 annotates the transcriptional factor binding site. Since it is logically part of the gene, its Parent attribute is gene00001. Lines 4-6 define this gene's three spliced transcripts, one line for the full extent of each of the mRNAs. These features are necessary to act as parents for the four CDSs which derive from them, as well as the structural parents of the five exons in the alternative splicing set. Lines 7-11 identify the five exons. The Parent attributes indicate which mRNAs the exons belong to. Notice that several of the exons share the same parents, using the comma symbol to indicate multiple parentage. Lines 12-24 denote this gene's four CDSs. Each CDS belongs to one of the mRNAs. cds00003 and cds00004, which correspond to alternative start codons, belong to the same mRNA. Note that several of the features, including the gene, its mRNAs and the CDSs, all have Name attributes. This attributes assigns those features a public name, but is not mandatory. The ID attributes are only mandatory for those features that have children (the gene and mRNAs), or for those that span multiple lines. The IDs do not have meaning outside the file in which they reside. Hence, a slightly simplified version of this file would look like this: ##gff-version 3 ##sequence-region ctg123 1 1497228 ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN ctg123 . TF_binding_site 1000 1012 . + . Parent=gene00001 ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001 ctg123 . mRNA 1050 9000 . + . ID=mRNA00002;Parent=gene00001 ctg123 . mRNA 1300 9000 . + . ID=mRNA00003;Parent=gene00001 ctg123 . exon 1300 1500 . + . Parent=mRNA00003 ctg123 . exon 1050 1500 . + . Parent=mRNA00001,mRNA00002 ctg123 . exon 3000 3902 . + . Parent=mRNA00001,mRNA00003 ctg123 . exon 5000 5500 . + . Parent=mRNA00001,mRNA00002,mRNA00003 ctg123 . exon 7000 9000 . + . Parent=mRNA00001,mRNA00002,mRNA00003 ctg123 . CDS 1201 1500 . + 0 ID=cds00001;Parent=mRNA00001 ctg123 . CDS 3000 3902 . + 0 ID=cds00001;Parent=mRNA00001 ctg123 . CDS 5000 5500 . + 0 ID=cds00001;Parent=mRNA00001 ctg123 . CDS 7000 7600 . + 0 ID=cds00001;Parent=mRNA00001 ctg123 . CDS 1201 1500 . + 0 ID=cds00002;Parent=mRNA00002 ctg123 . CDS 5000 5500 . + 0 ID=cds00002;Parent=mRNA00002 ctg123 . CDS 7000 7600 . + 0 ID=cds00002;Parent=mRNA00002 ctg123 . CDS 3301 3902 . + 0 ID=cds00003;Parent=mRNA00003 ctg123 . CDS 5000 5500 . + 1 ID=cds00003;Parent=mRNA00003 ctg123 . CDS 7000 7600 . + 1 ID=cds00003;Parent=mRNA00003 ctg123 . CDS 3391 3902 . + 0 ID=cds00004;Parent=mRNA00003 ctg123 . CDS 5000 5500 . + 1 ID=cds00004;Parent=mRNA00003 ctg123 . CDS 7000 7600 . + 1 ID=cds00004;Parent=mRNA00003 NOTE 1 - SO or SOFA IDs: If using the SO (or SOFA) IDs rather than the short names1 ("mRNA" etc), use the following mappings: gene SO:0000704 mRNA SO:0000234 exon SO:0000147 cds SO:0000316 Other mRNA parts that you might wish to use are intron SO:0000188 (redundant with exon) polyA_sequence SO:0000610 (part of the three_prime_UTR) polyA_site SO:0000553 (part of the gene) five_prime_UTR SO:0000204 three_prime_UTR SO:0000205 NOTE 2 - "Orphan" exons CDSs, and other features. Ab initio gene prediction programs call hypothetical exons and CDS's that are attached to the genomic sequence and not necessarily to a known transcript. To handle these features, you may either (1) create a placeholder mRNA and use it as the parent for the exon and CDS subfeatures; or (2) attach the exons and CDSs directly to the gene. This is allowed by SO because of the transitive nature of the part_of relationship. NOTE 3 - UTRs, splice sites and translational start and stop sites. These are implied by the combination of exon and CDS and do not need to be explicitly annotated as part of the canonical gene. In the case of annotating predicted splice or translational start/stop sites independently of a particular gene, it is suggested that they be attached directly to the genomic sequence and not to a gene or a subpart of a gene. NOTE 4 - CDS features MUST have have a defined phase field. Otherwise it is not possible to infer the correct polypeptides corresponding to partially annotated genes. NOTE 5 - The START and STOP codons are included in the CDS. That is, if the locations of the start and stop codons are known, the first three base pairs of the CDS should correspond to the start codon and the last three correspond the stop codon.

CIRCULAR GENOMES

For a circular genome, the landmark feature should include Is_circular=true in column 9. In the example below, from bacteriophage f1, gene II extends across the origin from positions 6477-831. The feature end is given as length of the landmark feature, J02448, plus the distance from the origin to the end of gene II (6407 + 831 = 7238). ##gff-version 3 # organism Enterobacteria phage f1 # Note Bacteriophage f1, complete genome. J02448 GenBank region 1 6407 . + . ID=J02448;Name=J02448;Is_circular=true; J02448 GenBank CDS 6006 7238 . + 0 ID=geneII;Name=II;Note=protein II;

REPRESENTING SPLICED NON-CODING TRANSCRIPTS

For spliced non-coding transcripts, such as those produced by some processed snRNAs and viruses, use a parent feature of "noncoding_transcript" and a child of "exon."

PARENT (PART-OF) RELATIONSHIPS

The reserved Parent attribute can be used to establish a part-of relationship between two features. A feature that has the Parent attribute set is interpreted as asserting that it is a part of the specified Parent feature. Features must respect the Sequence Ontology Part-Of relationships. A Parent relationship between two features that is not one of the Part-Of relationships listed in SO should trigger a parse exception Similarly, a set of Parent relationships that would cause a cycle should also trigger an exception. The GFF3 format does not enforce a rule in which features must be wholly contained within the location of their parents, since some elements of the Sequence Ontology (e.g. enhancers in genes) allow for distant cis relationships.

THE GAP ATTRIBUTE

Protein and nucleotide alignment features typically consist of two sequences, the reference sequence and the "target", and are not always colinear. For example, consider the following alignment between an EST ("EST23") and a segment of the genome ("Chr3"): Chr3 (reference) 1 CAAGACCTAAACTGGAT-TCCAAT 23 EST23 (target) 1 CAAGACCT---CTGGATATCCAAT 21 Previous versions of the GFF format would represent this alignment as three colinear segments, but this made it difficult to reconstruct the gapped alignment. GFF3 recommends representing gapped alignments explicitly with the "Gap" attribute. The Gap attribute's format consists of a series of (operation,length) pairs separated by space characters, for example "M8 D3 M6". Each operation is a single-letter code: Code Operation ---- --------- M match I insert a gap into the reference sequence D insert a gap into the target (delete from reference) F frameshift forward in the reference sequence R frameshift reverse in the reference sequence In the alignment between EST23 and Chr3 shown above, Chr3 is the reference sequence referred to in the first column of the GFF3 file, and EST23 is the sequence referred to by the Target attribute. This gives a Gap string of "M8 D3 M6 I1 M6". The full GFF match line will read: Chr3 . Match 1 23 . . . ID=Match1;Target=EST23 1 21;Gap=M8 D3 M6 I1 M6 For protein to nucleotide matches, the M, I and D operations apply to amino acid residues in the target and nucleotide base pairs in the reference in a 1:3 residue. That is, "M2" means to match two amino residues in the target to six base pairs in the reference. Hence this alignment: 100 atgaaggag---gttattgcgaatgtcggcggt 1 M..K..E..V..V..I..-..N..V..G..G.. Corresponds to this GFF3 Line: ctg123 . nucleotide_to_protein 100 129 . + . ID=match008;Target=p101 1 10;Gap=M3 I1 M2 D1 M4 In addition, the Gap attribute provides <F>orward and <R>everse frameshift operators to allow for frameshifts in the alignment. These are in nucleotide coordinates: a forward frameshift skips forward the indicated number of base pairs, while a reverse frameshift moves backwards. Examples: 100 atgaaggag---gttattgaatgtcggcggt Gap=M3 I1 M2 F1 M4 1 M..K..E..V..V..I... N..V..G..G 100 atgaaggag---gttataatgtcggcggt Gap=M3 I1 M2 R1 M4 1 M..K..E..V..V..I. N..V..G..G

ALIGNMENTS

In the SO, an alignment between the reference sequence and another sequence is called a "match". In addition to the generic "match" type, there are the subclasses "cDNA_match," "EST_match," "translated_nucleotide_match," "nucleotide_to_protein_match," and "nucleotide_motif." Matches typically contain gaps; matches broken up by large gaps are usually called "HSPs" (high-scoring segment pair), and previous incarnations of GFF have handled gapped alignments by breaking up the alignment into a series of ungapped HSPs. The SO does not have an HSP type. Instead, gapped matches are represented as a single feature that occupies a discontinuous location on the reference sequence. Figure 2 shows the same gene as before, but with a new track added showing an alignment of a sequenced cDNA to the genome. For the purposes of illustration, we have shown the regions of alignment to be exact across the three exons of the second spliced transcript (EDEN.2).
Figure2

FIGURE 2

The recommended way to represent this alignment is with a single feature of type "cDNA_match" and a Gap attribute that indicates that the alignment is in three segments: ctg123 . cDNA_match 1050 9000 6.2e-45 + . ID=match00001;Target=cdna0123 12 2964;Gap=M451 D3499 M501 D1499 M2001 Parsed out, the Target attribute indicates that the sequence named "cdna0123" between bases 12 and 2964 (in cdna coordinates) aligns to bases 1050 to 9000 of ctg123. The Gap attribute is easier to read when spaces are inserted: M451 match 451 bases D3499 skip 3499 bases in the reference ctg123 sequence M501 match the next 501 bases D1499 skip 1499 bases in the reference ctg123 M2001 match the next 2001 bases Note that the matched region is 2953 bases, which corresponds exactly to the matching subsequence [12,2964] of the target. Extra bases in the cDNA which would cause gaps in the reference sequence would be indicated using the CIGAR "I" notation. Another important item to note is that the ID corresponds to the Match and not to the target sequence. This avoids the confusion that has occurred in previous incarnations of GFF which made it impossible to distinguish between a particular alignment of a target sequence to the genome and all alignments of a target sequence to the genome. A limitation of the Gap representation is that the entire alignment shares the same score (column 6). To give each component of the match a separate score, it can be broken across multiple lines as shown here: ctg123 . cDNA_match 1050 1500 5.8e-42 + . ID=match00001;Target=cdna0123 12 462 ctg123 . cDNA_match 5000 5500 8.1e-43 + . ID=match00001;Target=cdna0123 463 963 ctg123 . cDNA_match 7000 9000 1.4e-40 + . ID=match00001;Target=cdna0123 964 2964 Notice that the ID is the same across each of the three lines, indicating that these lines all refer to a single feature, the Match. Each aligning segment, however has a distinct score and Target region. The two types of representations can be mixed, allowing large aligned segments to have their own GFF line and score, while small gaps within them are represented using a Gap attribute. Matches can align to either the + or the - strand of the reference sequence. This should be denoted in the seventh column of the GFF line and *not* by changing the order of the start and end positions in the Target attribute. To illustrate this, Figure 3 adds an EST pair to the annotation. The two ESTs, mjm1123.5 and mum1123.3 correspond to 5' and 3' EST reads from the same cDNA clone. The following GFF3 lines describe them: ctg123 . EST_match 1200 3200 2.2e-30 + . ID=match00002;Target=mjm1123.5 5 506;Gap=M301 D1499 M201 ctg123 . EST_match 7000 9000 7.4e-32 - . ID=match00003;Target=mjm1123.3 1 502;Gap=M101 D1499 M401 Please note that the subsequence indicated by the Target always uses the coordinate system of the EST, regardless of the direction of the alignment. For the 3' EST, the seventh column contains a "-" to indicate that the match is to the reverse complement of ctg123. The Gap attribute does not change as a consequence of this reverse complementation, and is read from left to right in the usual manner. An application may wish to group the EST pair into a single feature. This can be accomplished by creating an implied cDNA_match that extends from the left end of the first EST to the right end of the last EST, and indicating that this cDNA match is the Parent of the two ESTs. The parts of the match use the SO "match_part" term. A match_part can be used as a subpart of any type of match. ctg123 . cDNA_match 1200 9000 . . . ID=cDNA00001 ctg123 . match_part 1200 3200 2.2e-30 + . ID=match00002;Parent=cDNA00001;Target=mjm1123.5 5 506;Gap=M301 D1499 M201 ctg123 . match_part 7000 9000 7.4e-32 - . ID=match00003;Parent=cDNA00001;Target=mjm1123.3 1 502;Gap=M101 D1499 M401
Figure3

FIGURE 3


TRANSCRIPT-RELATIVE ALIGNMENTS

The representation of strandedness in nucleotide-to-nucleotide and protein-to-nucleotide alignments is a common source of confusion in GFF files. This section will attempt to explain it. * Case #1: alignment to a + strand transcript Consider a pair of EST matches to the genome: ============================= genome -------------------> transcript ------> <---- EST_A (5') EST_B (3') EST_A is a 5' EST and its sequence (as represented in a FASTA file, for example) is in the same strand as the genomic sequence. It is represented as: ctg123 . EST_match 1000 1500 . + . ID=match001;Target=EST_A 1 500 + The strand field in column #7 is "+" indicating that the match is to the forward strand of the genome. The optional strand field in the Target attribute is also +, indicating that the alignment is to the plus strand of the implied underlying transcript. Let us now consider EST_B , which is a 3' EST. Its sequence as represented in the FASTA file aligns to the reverse complement of the genomic sequence. It is represented as: ctg123 . EST_match 2000 2500 . + . ID=match002;Target=EST_B 1 500 - The strand field in column #7 is "+" indicating that the match is to a transcript feature on the forward of the genome. The strand field in the Target attribute is -, indicating that the EST sequence should be reverse complemented in order to align to the underlying transcript. * Case #2: alignment to a - strand transcript Here is the opposite case: ============================= genome <-------------------- transcript ------> <---- EST_D (3') EST_C (5') In this case, the 5' EST_C aligns to the reverse complement of the forward strand of the genome, while the 3' EST_D aligns to the forward strand directly. These are represented as follows: ctg123 . EST_match 2000 2500 . - . ID=match001;Target=EST_C 1 500 + ctg123 . EST_match 1000 1500 . - . ID=match001;Target=EST_D 1 500 - The first line indicates that the transcript is on the - strand of the genome, and that EST_C aligns to the transcripts forward strand. The second line uses - in the 7th column to indicate that the transcript is on the minus strand, and - in the Target field to indicate that EST_D aligns to the minus strand of the transcript. =================================================================== Confused? Just remember that for purposes of display, the source and target strands will be multipled together. A +/+ or -/- alignment indicates that the reference sequence and the target sequence can be aligned directly. A +/- or -/+ alignment indicates that the target must be reverse complemented in order to align to the plus strand of the reference sequence. =================================================================== A similar rule applies to TBLASTX alignments, which rely on matching the six-frame translation of the source to the six-frame translation of the target. Consider the case of two genomes that align together in the forward direction, whose alignment is supported by translations of genes A and B, one of which is on the plus strand, and the other on the minus strand: =============================> genome X ------> <---- gene A gene B =============================> genome Y These two alignments will be represented as: X TBLASTX translated_nucleotide_match 1000 1500 . + . ID=matchA;Target=Y 500 1000 + X TBLASTX translated_nucleotide_match 2000 2500 . - . ID=matchB;Target=Y 1500 2000 - Note that the first alignment is +/+ and the second is -/-. Both indicate that the sequences of genomes X and Y can be aligned directly. Now we look at the case of two genomes that align in the antiparallel direction: =============================> genome X ------> <---- gene A gene B <============================= genome Y These two alignments will be represented as: X TBLASTX translated_nucleotide_match 1000 1500 . + . ID=matchA;Target=Y 500 1000 - X TBLASTX translated_nucleotide_match 2000 2500 . - . ID=matchB;Target=Y 1500 2000 + The first match indicates that a plus strand feature of genome X aligns to a minus strand feature of genome Y. The second match indicates that a minus strand feature of genome X aligns to a plus strand feature of genome Y. In both cases, the result is to align the plus strand of genome X to the minus strand of genome Y.

ONTOLOGY ASSOCIATIONS AND DB CROSS REFERENCES

Two reserved attributes, Ontology_term and Dbxref, can be used to establish links between a GFF3 feature and a data record contained in another database. Ontology_term is reserved for associations to ontologies, such as the Gene Ontology. Dbxref is used for all other cross references. While there is no firm boundary line between these two concepts, curators tend to treat ontology associations differently and hence ontology terms have been given their own reserved attribute label. The value of both Ontology_term and Dbxref is the ID of the cross referenced object in the form "DBTAG:ID". The DBTAG indicates which database the referenced object can be found in, and ID indicates the identifier of the object within that database. IDs can contain unescaped colons but DBTAGs cannot, so parsing code should split on the first colon encountered in the attribute value. The format of each type of ID varies from database to database. An authoritative list of databases, their DBTAGs, and the URL transformation rules that can be used to fetch the objects given their IDs can be found at this location: ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs Further details can be found here: ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs_spec Here are some common examples: * a dbxref to an EMBL sequence accession number: Dbxref="EMBL:AA816246" * a dbxref to an NCBI gi number: Dbxref="NCBI_gi:10727410" * a Ontology_term referring to a GO association Ontology_term="GO:0046703"

OTHER SYNTAX

Comments are preceded by the # symbol. Meta-data and directives are preceded by ##. The following directives are recognized: ##gff-version 3 The GFF version, always 3 in this spec. This directive must be present, and must be the topmost line of the file. ##sequence-region seqid start end The sequence segment referred to by this file, in the format "seqid start end". This element is optional, but strongly encouraged because it allows parsers to perform bounds checking on features. There may be multiple ##sequence-region directives, each corresponding to one of the reference sequences referred to in the body of the file. ##feature-ontology URI This directive indicates that the GFF3 file uses the ontology of feature types located at the indicated URI or URL. Multiple URIs may be added, in which case they are merged (or raise an exception if they cannot be merged). The URIs for the released sequence ontologies are: Release 1: 5/12/2004 http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.6 Release 2: 5/16/2005 http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12i Release 2.4.3 06/01/2010 SO: http://song.cvs.sourceforge.net/viewvc/*checkout*/song/ontology/so.obo?revision=1.263 SOFA: http://song.cvs.sourceforge.net/viewvc/*checkout*/song/ontology/sofa.obo?revision=1.217 Releases occur every two months for SO and SOFA. The repository for SO releases is here: http://sourceforge.net/projects/song/files/Sequence%20Ontology/ The repository for SOFA releases is here: http://sourceforge.net/projects/song/files/SO_Feature_Annotation/ This directive may occur several times per file. If no feature ontology is specified, then the most recent release of the Sequence Ontology is assumed. If multiple directives are given and a feature type is matched by multiple ontologies, the matching ontology included by the directive highest in the file wins the reference. The Sequence Ontology itself is always referenced last. The content referenced by URI must be in OBO or DAG-Edit format. ##attribute-ontology URI This directive indicates that the GFF3 uses the ontology of attribute names located at the indicated URI or URL. This directive may appear multiple times to load multiple URIs, in which case they are merged (or raise an exception if merging is not possible). Currently no formal attribute ontologies exist, so this attribute is for future extension. ##source-ontology URI This directive indicates that the GFF3 uses the ontology of source names located at the indicated URI or URL. This directive may appear multiple times to load multiple URIs, in which case they are merged (or raise an exception if merging is not possible). Currently no formal source ontologies exist, so this attribute is for future extension. ##species NCBI_Taxonomy_URI This directive indicates the species that the annotations apply to. The preferred format is a NCBI URL that points to the relevant species page in either of the following formats: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=6239 http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=Caenorhabditis+elegans ##genome-build source buildName The genome assembly build name used for the coordinates given in the file. Please specify the source of the assembly as well as its name. Examples (the parentheses are comments). ##genome-build NCBI B36 (human) ##genome-build WormBase ws110 (worm) ##genome-build FlyBase r4.1 (drosophila) ### This directive (three # signs in a row) indicates that all forward references to feature IDs that have been seen to this point have been resolved. After seeing this directive, a program that is processing the file serially can close off any open objects that it has created and return them, thereby allowing iterative access to the file. Otherwise, software cannot know that a feature has been fully populated by its subfeatures until the end of the file has been reached. It is recommended that complex features, such as the canonical gene, be terminated with the ### notation. ##FASTA This notation indicates that the annotation portion of the file is at an end and that the remainder of the file contains one or more sequences (nucleotide or protein) in FASTA format. This allows features and sequences to be bundled together. Example: ##gff-version 3 ##sequence-region ctg123 1 1497228 ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001 ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1 ctg123 . five_prime_UTR 1050 1200 . + . Parent=mRNA00001 ctg123 . CDS 1201 1500 . + 0 ID=cds00001;Parent=mRNA00001 ctg123 . CDS 3000 3902 . + 0 ID=cds00001;Parent=mRNA00001 ctg123 . CDS 5000 5500 . + 0 ID=cds00001;Parent=mRNA00001 ctg123 . CDS 7000 7600 . + 0 ID=cds00001;Parent=mRNA00001 ctg123 . three_prime_UTR 7601 9000 . + . Parent=mRNA00001 ctg123 . cDNA_match 1050 1500 5.8e-42 + . ID=match00001;Target=cdna0123+12+462 ctg123 . cDNA_match 5000 5500 8.1e-43 + . ID=match00001;Target=cdna0123+463+963 ctg123 . cDNA_match 7000 9000 1.4e-40 + . ID=match00001;Target=cdna0123+964+2964 ##FASTA >ctg123 cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc gtatttgatttgggtttactatcgaataatgagaattttcaggcttaggc ttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt aggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttag aatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattc ... >cnda0123 ttcaagtgctcagtcaatgtgattcacagtatgtcaccaaatattttggc agctttctcaagggatcaaaattatggatcattatggaatacctcggtgg aggctcagcgctcgatttaactaaaagtggaaagctggacgaaagtcata tcgctgtgattcttcgcgaaattttgaaaggtctcgagtatctgcatagt gaaagaaaaatccacagagatattaaaggagccaacgttttgttggaccg tcaaacagcggctgtaaaaatttgtgattatggttaaagg For backward-compatibility with the GFF version output by the Artemis tool, a GFF line that begins with the character > creates an implied ##FASTA directive.

PATHOLOGICAL CASES

The following section discusses how to represent "pathological" cases that arise in prokaryotic and eukaryotic genetics. Most of these have to do with organisms' endlessly creative ways of processing transcripts. a) Single exon genes This is the case in which a single unspliced transcript encodes a single CDS. ----->XXXXXXX*------> The preferred representation is to create a gene, a transcript, an exon and a CDS: ChrX . gene XXXX YYYY . + . ID=gene01;name=resA ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01 ChrX . exon XXXX YYYY . + . Parent=tran01 ChrX . CDS XXXX YYYY . + . Parent=tran01 Some groups will find this redundant. A valid alternative is to omit the exon feature: ChrX . gene XXXX YYYY . + . ID=gene01;name=resA ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01 ChrX . CDS XXXX YYYY . + . Parent=tran01 It is not recommended to parent the CDS directly onto the gene, because this will make it impossible to determine the UTRs (since the gene may validly include untranscribed regulatory regions). Also note that mixing the two styles, as in the case of an organism with both spliced and unspliced transcripts, is liable to lead to the confusion of people working with the GFF3 file. b) Polycistronic transcripts This is the case in which a single (possibly spliced) transcript encodes multiple open reading frames that generate independent protein products. ----->XXXXXXX*-->BBBBBB*--->ZZZZ*-->AAAAAA*----- Since the single transcript corresponds to multiple genes that can be identified by genetic analysis, the recommended solution here is to create four "gene" objects and make them the parent for a single transcript. The transcript will contain a single exon (in the unspliced case) and four separate CDSs: ChrX . gene XXXX YYYY . + . ID=gene01;name=resA ChrX . gene XXXX YYYY . + . ID=gene02;name=resB ChrX . gene XXXX YYYY . + . ID=gene03;name=resX ChrX . gene XXXX YYYY . + . ID=gene04;name=resZ ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01,gene02,gene03,gene04 ChrX . exon XXXX YYYY . + . ID=exon00001;Parent=tran01 ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene01 ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene02 ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene03 ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene04 To disambiguate the relationship between which genes encode which CDSs, you may use the Derives_from relationship. c) Gene containing an intein An intein occurs when a portion of the protein is spliced out and the two polypeptide fragments are rejoined to become a functional protein. The portion that is spliced out is called the "intein," and it may itself have intrinsic molecular activity: ----->XXXXXXyyyyyyyyyyXXXXXXX*------- (yyyyyy is the intein) The preferred representation is to create one gene, one transcript, one exon, and one CDS. The CDS produces a pre-polypeptide using the "Derives_from" tag, and this polypeptide in turn gives rise to two mature_polypeptides, one each for the intein and the flanking protein: ChrX . gene XXXX YYYY . + . ID=gene01;name=resA ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01 ChrX . exon XXXX YYYY . + . Parent=tran01 ChrX . CDS XXXX YYYY . + . ID=cds01;Parent=tran01 ChrX . polypeptide XXXX YYYY . + . ID=poly01;Derives_from=cds01 ChrX . mature_polypeptide XXXX YYYY . + . ID=poly02;Parent=poly01 ChrX . mature_polypeptide XXXX YYYY . + . ID=poly02;Parent=poly01 ChrX . intein XXXX YYYY . + . ID=poly03;Parent=poly01 Because the flanking mature_polypeptide has discontinuous coordinates on the genome, it appears twice with the same ID. If the intein is immediately degraded, you may not wish to annotate it explicitly, and its line would be deleted from the example. However, if it has molecular activity, it may correspond to a gene, in which case: ChrX . gene XXXX YYYY . + . ID=gene01;name=resA ChrX . gene XXXX YYYY . + . ID=gene02;name=inteinA ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01,gene02 ChrX . exon XXXX YYYY . + . Parent=tran01 ChrX . CDS XXXX YYYY . + . ID=cds01;Parent=tran01 ChrX . polypeptide XXXX YYYY . + . ID=poly01;Derives_from=cds01 ChrX . mature_polypeptide XXXX YYYY . + . ID=poly02;Parent=poly01;Derives_from=gene01 ChrX . mature_polypeptide XXXX YYYY . + . ID=poly02;Parent=poly01;Derives_from=gene01 ChrX . intein XXXX YYYY . + . ID=poly03;Parent=poly01;Derives_from=gene02 The term "polypeptide" is part of SO. The terms "mature_polypeptide" and "intein" are slated to be added in a pending release. d) Trans-spliced transcript This occurs when two genes contribute to a processed transcript via a trans-splicing reaction: spliced leader =======>----->XXXXXXX*------> The simplest way to represent this is to show the mRNA as being split across two discontinuous genomic locations: ChrX . gene XXXX YYYY . + . ID=gene01;name=my_gene ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01 ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01 ChrX . exon XXXX YYYY . + . Parent=tran01 ChrX . CDS XXXX YYYY . + . ID=cds01;Parent=tran01 However, this does not indicate which part of the transcript comes from the spliced leader. A preferred representation explicitly adds features for the spliced leader gene, the primary_transcript and the spliced_leader_RNA: ChrX . gene XXXX YYYY . + . ID=gene01;name=my_gene ChrX . gene XXXX YYYY . + . ID=gene02;name=leader_gene ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01,gene02 ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01,gene02 ChrX . primary_transcript XXXX YYYY . + . ID=pt01;Parent=tran01;Derives_from=gene01 ChrX . spliced_leader_RNA XXXX YYYY . + . ID=sl01;Parent=tran01;Derives_from=gene02 ChrX . exon XXXX YYYY . + . Parent=tran01 ChrX . CDS XXXX YYYY . + . ID=cds01;Parent=tran01 As shown here, the mRNA derives from two genes ("my_gene" and the leader gene) and occupies disjunct coordinates on the genome. The primary_transcript, which encodes the body of the mRNA, is part of (has as its Parent) this mRNA. The same relationship applies to the spliced leader RNA. The Derives_from relationship is used to indicate which genes produced the primary transcript and spliced leader respectively. The exon and CDS features follow in the normal fashion. e) Programmed frameshift This event occurs when the ribosome performs a programmed frameshift during translation in order to skip over an in-frame stop codon. The frameshift may occur forward or backward. -------------------------> mRNA ========== ============* CDS The representation of this is to make the CDS discontinuous: ChrX . gene XXXX YYYY . + . ID=gene01;name=my_gene ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01;Ontology_term=SO:1000069 ChrX . exon XXXX YYYY . + . Parent=tran01 ChrX . CDS XXXX YYYY 0 + . ID=cds01;Parent=tran01 ChrX . CDS YYYY-1 ZZZZ 1 + . ID=cds01;Parent=tran01 You will also need to adjust the phase field properly so that the CDS translates. It is suggested that the mRNA be tagged with the appropriate SO transcript attributes such as "minus_1_translational_frameshift" (SO:1000069). This will allow all such programmed frameshift mRNAs to be recovered with a query. The accession for "plus_1_translational_frameshift" is SO:1001263. f) An operon A classic operon occurs when the genes in a polycistronic transcript are co-regulated by cis-regulatory element(s): regulatory element * ================================================> operon ----->XXXXXXX*-->BBBBBB*--->ZZZZ*-->AAAAAA*----- It can be indicated in GFF3 in this way: ChrX . operon XXXX YYYY . + . ID=operon01;name=my_operon ChrX . promoter XXXX YYYY . + . Parent=operon01 ChrX . gene XXXX YYYY . + . ID=gene01;Parent=operon01;name=resA ChrX . gene XXXX YYYY . + . ID=gene02;Parent=operon01;name=resB ChrX . gene XXXX YYYY . + . ID=gene03;Parent=operon01;name=resX ChrX . gene XXXX YYYY . + . ID=gene04;Parent=operon01;name=resZ ChrX . mRNA XXXX YYYY . + . ID=tran01;Parent=gene01,gene02,gene03,gene04 ChrX . exon XXXX YYYY . + . ID=exon00001;Parent=tran01 ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene01 ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene02 ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene03 ChrX . CDS XXXX YYYY . + . Parent=tran01;Derives_from=gene04 The regulatory element ("promoter" in this example) is part of the operon via the Parent tag. The four genes are part of the operon, and the resulting mRNA is multiply-parented by the four genes, as in the earlier example. At the time of this writing, promoters and other cis-regulatory elements cannot be part_of an operon, but this restriction is being reconsidered.
Change Log: 1.20 Wed Dec 15 12:35:10 MST 2010 -Added language to the description of the ID attribute to clarify that discontinuous features can exist on multiple lines and share the same ID. 1.19 Tue Jul 6 12:51:26 MDT 2010 -Fixed coordinate errors in the EST_match and match_part examples in the 'Alignments' section. -Constrained multiple attribute values to the Parent, Alias, Note, DBxref and Ontology_term attributes. 1.18 June 24 2010 -Added the sections regarding circular genomes to the spec. 1.17 Wed June 2 2010 -Changed the spec to include Sequence Ontology (SO) sequence_feature terms in column 3 as well as SOFA terms. (SOFA is a subset of SO). 1.16 Tue May 25 10:06:38 MDT 2010 -Fixed more incorrect CDS phases throughout. -Changed (three|five)_prime_utr to (three|five)_prime_UTR throughout. -Changed (3'|5')-UTR to (three|five)_prime_UTR throughout. -Added ID attributes to CDS features (required for multiline features) in the FASTA pragma example. 1.15 Mon Aug 31 12:59:26 EDT 2009 -Fixed incorrect CDS phases in the canonical gene example. 1.14 Mon Aug 25 10:24:02 EDT 2008 -Add meta-directives for species and build number. 1.13 Wed May 23 10:31:01 EDT 2007 -Insist that CDS include the start and end codon. 1.12 Thu Apr 5 17:32:32 EDT 2007 -Use "match_part" as the subpart of cDNA_match in the paired EST example. -Phase is required for all CDS features. 1.11 Fri Dec 1 16:33:39 EST 2006 -Clarified definition of phase relative to reverse strand features 1.10 14 September 2006 -Reformatted for new SO web site. 1.09 Wed Sep 6 17:55:32 EDT 2006 -Information about the GFF3 validator. 1.08 Tue Jul 18 15:12:11 EDT 2006 -Added URLs for SO releases. 1.07 Wed May 24 21:59:02 EDT 2006 -Fixed description of phase (temporarily lost due to CVS glitches) 1.06 Wed May 24 11:44:22 EDT 2006 -Relaxed escaping rules. -Fixed typos found by Gordon Gremme. 1.05 Tue May 23 10:46:25 EDT 2006 -Fixed all IDs in the examples to make them internally consistent. Previously, some examples did not validate because of inconsistent numbers of zeroes in the identifiers (mRNA00001 vs mRNA0001).
genometools-1.5.1/gtdata/000077500000000000000000000000001211610345200153105ustar00rootroot00000000000000genometools-1.5.1/gtdata/doc/000077500000000000000000000000001211610345200160555ustar00rootroot00000000000000genometools-1.5.1/gtdata/doc/cds.lua000066400000000000000000000001411211610345200173250ustar00rootroot00000000000000if not gtdata_doc_dir then gtdata_doc_dir = "./" end dofile(gtdata_doc_dir.."regionmapping.lua") genometools-1.5.1/gtdata/doc/chseqids.lua000066400000000000000000000006061211610345200203650ustar00rootroot00000000000000print ([[ File format for mapping_file: The supplied mapping file defines a mapping table named ``chseqids''. It maps the sequence-regions given in the GFF3_file to other names. It can be defined as follows: chseqids = { chr1 = "seq1", chr2 = "seq2" } When this example is used, all sequence ids ``chr1'' will be changed to ``seq1'' and all sequence ids ``chr2'' to ``seq2''.]]) genometools-1.5.1/gtdata/doc/csa.lua000066400000000000000000000020701211610345200173250ustar00rootroot00000000000000print ([[ Example: -------- Let's assume we have a GFF3 file 'csa_example_spliced_alignments.gff3' containing the following four overlapping spliced alignments (represented as genes with exons as children): ]]) print(io.open(gtdata_doc_dir.."csa_example_spliced_alignments.gff3"):read("*a")) print([[ To compute the consensus spliced alignments we call: $ gt csa csa_example_spliced_alignments.gff3 Which returns: ]]) print(io.open(gtdata_doc_dir.."csa_example_consensus_spliced_alignments.gff3"):read("*a")) print([[ As one can see, they have been combined into a consensus spliced alignment (represented as genes with mRNAs as children which in turn have exons as children) with two alternative splice forms. The first and the third spliced alignment have been combined into the first alternative splice form (mRNA1) and the the second and the fourth spliced alignment into the second alternative splice form (mRNA2). As one can see, the second exon from the first alternative splice form ist shorter than the corresponding exon from the second alternative splice form.]]) genometools-1.5.1/gtdata/doc/csa_example_consensus_spliced_alignments.gff3000066400000000000000000000006711211610345200271350ustar00rootroot00000000000000##gff-version 3 ##sequence-region seq 1 290 seq gt csa gene 1 290 . + . ID=gene1 seq gt csa mRNA 1 290 . + . ID=mRNA1;Parent=gene1 seq gt csa exon 1 90 . + . Parent=mRNA1 seq gt csa exon 110 190 . + . Parent=mRNA1 seq gt csa exon 201 290 . + . Parent=mRNA1 seq gt csa mRNA 1 290 . + . ID=mRNA2;Parent=gene1 seq gt csa exon 1 90 . + . Parent=mRNA2 seq gt csa exon 101 190 . + . Parent=mRNA2 seq gt csa exon 201 290 . + . Parent=mRNA2 ### genometools-1.5.1/gtdata/doc/csa_example_spliced_alignments.gff3000066400000000000000000000011351211610345200250310ustar00rootroot00000000000000##gff-version 3 ##sequence-region seq 1 290 seq . gene 1 209 . + . ID=gene1 seq . exon 1 90 . + . Parent=gene1 seq . exon 110 190 . + . Parent=gene1 seq . exon 201 209 . + . Parent=gene1 ### seq . gene 1 290 . + . ID=gene2 seq . exon 1 90 . + . Parent=gene2 seq . exon 101 190 . + . Parent=gene2 seq . exon 201 290 . + . Parent=gene2 ### seq . gene 10 290 . + . ID=gene3 seq . exon 10 90 . + . Parent=gene3 seq . exon 110 190 . + . Parent=gene3 seq . exon 201 290 . + . Parent=gene3 ### seq . gene 181 290 . + . ID=gene4 seq . exon 181 190 . + . Parent=gene4 seq . exon 201 290 . + . Parent=gene4 ### genometools-1.5.1/gtdata/doc/eval.lua000066400000000000000000000010141211610345200175030ustar00rootroot00000000000000print ([[ The program shows sensitivity and specificity values for certain feature types (e.g., gene, mRNA, and exon). For some feature types the number of missing and wrong features of that type is also shown. Thereby, ``missing'' means the number of features of that type from the ``reference'' without overlap to a feature of that type from the ``prediction''. Vice versa, ``wrong'' denotes the number of features of that type from the ``prediction'' without overlap to a feature of that type from the ``reference''.]]) genometools-1.5.1/gtdata/doc/extractfeat.lua000066400000000000000000000001411211610345200210660ustar00rootroot00000000000000if not gtdata_doc_dir then gtdata_doc_dir = "./" end dofile(gtdata_doc_dir.."regionmapping.lua") genometools-1.5.1/gtdata/doc/extractseq.lua000066400000000000000000000052671211610345200207550ustar00rootroot00000000000000print ([[ The option -keys allows one to extract substrings or sequences from the given sequence file or from a fasta index. The substrings to be extracted are specified in a key file given as argument to this option. The key file must contain lines of the form k or k i j where k is a string (the key) and the optional i and j are positive integers such that i<=j. k is the key and the optional numbers i and j specify the first position of the substring and the last position of the substring to be extracted. The positions are counted from 1. If k is identical to the string between the first first and second occurrence of the symbol | in a fasta header, then the fasta header and the corresponding sequence is output. For example in the fasta header >tr|A0AQI4|A0AQI4_9ARCH Putative ammonia monooxygenase (Fragment) OS=uncultured archaeon GN=amoA PE=4 SV=1 the fasta key is A0AQI4. If i and j are both specified, then the corresponding substring is shown in fasta format. In the latter case the header of the fasta formatted sequence in the output begins with >k i j followed by the original original fasta header. If the sequence input are fasta files, then the following holds: - duplicated lines in the input file lead to only one sequence in the output - the sequences are output according to the order in the original sequence files - the formatting of the output can be controlled by the options -width, -o, -gzip, and -bzip2 If the sequence input comes from a fasta index (see below), the following holds: - option -width is required - option -o, -gzip and -bzip2 do not work - the sequences are output in the order the corresponding keys appear in the key file If the end of the argument list only contains one filename, say fastaindex, then it is checked if there is a file fastaindex.kys. This makes up part of the fasta index, which is contructed by calling the suffixerator tool as follows: gt suffixerator -protein -ssp -tis -des -sds -kys -indexname fastaindex -db inputfile1 [inputfile2 ..] This reads the protein sequence files given to the option -db and creates several files: - a file fastaindex.esq representing the sequence. - a file fastaindex.ssp specifying the sequence separator positions. - a file fastaindex.des showing the fasta headers line by line. - a file fastaindex.sds giving the sequence header delimiter positions. - a file fastaindex.kys containing the keys in the fasta files. For the suffixerator command to work, the keys of the form |key| in the fasta header must satisfy the following constraints: - they all have to be of the same length, not longer than 128, and not shorter than 1 - they have to appear in lexicographic order]]) genometools-1.5.1/gtdata/doc/fingerprint.lua000066400000000000000000000021641211610345200211120ustar00rootroot00000000000000print ([[ If neither option -check nor option -duplicates is used, the fingerprints for all sequences are shown on stdout. Examples: --------- Compute (unified) list of fingerprints: $ gt fingerprint U89959_ests.fas | sort | uniq > U89959_ests.checklist_uniq Compare fingerprints: $ gt fingerprint -check U89959_ests.checklist_uniq U89959_ests.fas 950b7715ab6cc030a8c810a0dba2dd33 only in sequence_file(s) Make sure a sequence file contains no duplicates (not the case here): $ gt fingerprint -duplicates U89959_ests.fas 950b7715ab6cc030a8c810a0dba2dd33 2 gt fingerprint: error: duplicates found: 1 out of 200 (0.500%) Extract sequence with given fingerprint: $ gt fingerprint -extract 6d3b4b9db4531cda588528f2c69c0a57 U89959_ests.fas >SQ;8720010 TTTTTTTTTTTTTTTTTCCTGACAAAACCCCAAGACTCAATTTAATCAATCCTCAAATTTACATGATACCAACGTAATGGGAGCTTAAAAATA Return values: -------------- 0 everything went fine (-check: the comparison was successful; -duplicates: no duplicates found) 1 an error occured (-check: the comparison was not successful; -duplicates: duplicates found)]]) genometools-1.5.1/gtdata/doc/genomediff.lua000066400000000000000000000014461211610345200206700ustar00rootroot00000000000000print ([[ The genomediff tool only accepts DNA input. When used with sequence files or encseq, an enhanced suffix array will be built in memory. The ESA will not be created completely, but construction will use -memlimit as a threshold and build it partwise, calculating the Shu-length for each part. File format for option -unitfile (lua): units = { genome1 = { "path/file1.fa", "file2.fa" }, genome2 = { "file3.fa", "path/file4.fa" } } Give the path to the files as they were given to the encseq tool! You can use gt encseq info INDEXNAME to get a list of files in an encoded sequence. Comment lines start with '--' and will be ignored. See GTDIR/testdata/genomediff/unitfile1.lua for an example. Options -pl -dc -memlimit are options to influence esa construction. ]]) -- vim: tw=78 genometools-1.5.1/gtdata/doc/gff3.lua000066400000000000000000000007771211610345200174200ustar00rootroot00000000000000print ([[ File format for option -offsetfile: The file supplied to option -offsetfile defines a mapping table named ``offsets''. It maps the sequence-regions given in the GFF3_file to offsets. It can be defined as follows: offsets = { chr1 = 1000, chr2 = 500 } When this example is used, all features with seqid ``chr1'' will be offset by 1000 and all features with seqid ``chr2'' by 500. If -offsetfile is used, offsets for all sequence-regions contained in the given GFF3 files must be defined.]]) genometools-1.5.1/gtdata/doc/gt.lua000066400000000000000000000007361211610345200172000ustar00rootroot00000000000000print ([[ Set the environment variable GT_MEM_BOOKKEEPING=on to enable memory bookkeeping (e.g., like this: env GT_MEM_BOOKKEEPING=on gt). Set the environment variable GT_ENV_OPTIONS=-spacepeak to show a spacepeak after program run. Set the environment variable GT_ENV_OPTIONS=-showtime to show processing times for some program parts if implemented. Combinations are possible. Running the `gt' binary with GT_ENV_OPTIONS=-help shows all possible ``environment options'')]]) genometools-1.5.1/gtdata/doc/hop.lua000066400000000000000000000027411211610345200173520ustar00rootroot00000000000000print ([[ Correction mode: One of the options -aggressive, -moderate, -conservative or -expert must be selected. The -aggressive, -moderate and -conservative modes are presets of the criteria by which it is decided if an observed discrepancy in homopolymer length between reference and a read shall be corrected or not. A description of the single criteria is provided by using the -help+ option. The presets are equivalent to the following settings: -aggressive -moderate -conservative -hmin 3 3 3 -read-hmin 1 1 2 -altmax 1.00 0.99 0.80 -refmin 0.00 0.00 0.10 -mapqmin 0 10 21 -covmin 1 1 1 -clenmax unlimited unlimited unlimited -allow-multiple yes yes no The aggressive mode tries to maximize the sensitivity, the conservative mode to minimize the false positives. An even more conservative set of corrections can be achieved using the -ann option (see -help+). The -expert mode allows to manually set each parameter; the default values are the same as in the -conservative mode. (Finally, for evaluation purposes only, the -state-of-truth mode can be used: this mode assumes that the target sequence of the sequencing has been specified as reference sequence and outputs an ideal list of corrections.)]]) genometools-1.5.1/gtdata/doc/id_to_md5.lua000066400000000000000000000001411211610345200204170ustar00rootroot00000000000000if not gtdata_doc_dir then gtdata_doc_dir = "./" end dofile(gtdata_doc_dir.."regionmapping.lua") genometools-1.5.1/gtdata/doc/luafilter.lua000066400000000000000000000012351211610345200205500ustar00rootroot00000000000000if not gtdata_doc_dir then gtdata_doc_dir = "./" end print ([[ File format for option -rule_files: The files supplied to option -rule_files define a function for filtering by user given criteria (see example below): ]]) print(io.open(gtdata_doc_dir.."luafilter_function.lua"):read("*a")) print([[The above function iterates over all children of 'gn' and checks whether there is a node of type 'exon'. If there is such a node the function returns 'false', indicating that the parent node 'gn' will not be sorted out.]]) print([[ NOTE:]]) print([[The function must be named 'filter' and must return 'false', indicating that the node survived the filtering process.]]) genometools-1.5.1/gtdata/doc/luafilter_function.lua000066400000000000000000000004001211610345200224460ustar00rootroot00000000000000function filter(gn) target = "exon" gfi = gt.feature_node_iterator_new(gn) curnode = gfi:next() while not(curnode == nil) do if (curnode:get_type() == target) then return false end curnode = gfi:next() end return true end genometools-1.5.1/gtdata/doc/magicmatch.lua000066400000000000000000000005631211610345200206610ustar00rootroot00000000000000print ([[ This tools implements parts of the functionality of MagicMatch which is described in the following paper M. Smith, V. Kunin, L. Goldovsky, A.J. Enright, and C.A. Ouzounis. MagicMatch -- cross-referencing sequence identifiers across databases. Bioinformatics, 21(16):3429-3430, 2005. It is mainly used for testing the underlying MD5 fingerprint machinery.]]) genometools-1.5.1/gtdata/doc/mutate.lua000066400000000000000000000012031211610345200200530ustar00rootroot00000000000000print ([[ For each position in the given sequences it is randomly determined with probability (mutation rate / 100) if the given position is mutated. If so, in 80% of the cases a substitution is performed, in 10% an insertion, and in 10% a deletion, respectively. For substitution and insertion events, the nucleotide is generated randomly without regard to the original nucleotide. That is, resubstitutions are possible. This procedure equals the one described on page 1867 of the following paper T.D. Wu and C.K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21(9):1859-1875, 2005.]]) genometools-1.5.1/gtdata/doc/readjoiner.lua000066400000000000000000000003421211610345200207010ustar00rootroot00000000000000print ([[ Please consult Readjoiner manual for more information. Tools: prefilter prepare the readset for Readjoiner overlap calculate suffix-prefix matches assembly construct string graph and output contigs]]) genometools-1.5.1/gtdata/doc/regionmapping.lua000066400000000000000000000014551211610345200214240ustar00rootroot00000000000000if not gtdata_doc_dir then gtdata_doc_dir = "./" end print ([[ File format for option -regionmapping: The file supplied to option -regionmapping defines a ``mapping''. A mapping maps the sequence-regions given in the GFF3_file to a sequence file containing the corresponding sequence. Mappings can be defined in one of the following two forms: ]]) print(io.open(gtdata_doc_dir.."regionmapping_table.lua"):read("*a")) print([[ or ]]) print(io.open(gtdata_doc_dir.."regionmapping_function.lua"):read("*a")) print([[ The first form defines a Lua (http://www.lua.org/) table named ``mapping'' which maps each sequence region to the corresponding sequence file. The second one defines a Lua function ``mapping'', which has to return the sequence file name when it is called with the sequence_region as argument.]]) genometools-1.5.1/gtdata/doc/regionmapping_function.lua000066400000000000000000000001241211610345200233210ustar00rootroot00000000000000function mapping(sequence_region) return "hs_ref_"..sequence_region..".fa.gz" end genometools-1.5.1/gtdata/doc/regionmapping_table.lua000066400000000000000000000001131211610345200225610ustar00rootroot00000000000000mapping = { chr1 = "hs_ref_chr1.fa.gz", chr2 = "hs_ref_chr2.fa.gz" } genometools-1.5.1/gtdata/doc/select.lua000066400000000000000000000001351211610345200200360ustar00rootroot00000000000000if not gtdata_doc_dir then gtdata_doc_dir = "./" end dofile(gtdata_doc_dir.."luafilter.lua") genometools-1.5.1/gtdata/doc/seqmutate.lua000066400000000000000000000012031211610345200205640ustar00rootroot00000000000000print ([[ For each position in the given sequences it is randomly determined with probability (mutation rate / 100) if the given position is mutated. If so, in 80% of the cases a substitution is performed, in 10% an insertion, and in 10% a deletion, respectively. For substitution and insertion events, the nucleotide is generated randomly without regard to the original nucleotide. That is, resubstitutions are possible. This procedure equals the one described on page 1867 of the following paper T.D. Wu and C.K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21(9):1859-1875, 2005.]]) genometools-1.5.1/gtdata/doc/shredder.lua000066400000000000000000000015271211610345200203650ustar00rootroot00000000000000print ([[ Each sequence given in sequence_file is shreddered into consecutive pieces of random length (between -minlength and -maxlength) until it is consumed. By this means the last shreddered fragment of a given sequence can be shorter than the argument to option -minlength. To get rid of such fragments use `gt seqfilter` (see example below). Examples: --------- Shredder a given BAC $ gt shredder U89959_genomic.fas > fragments.fas Shredder an EST collection into pieces between 50 and 100 bp and get rid of all (terminal) fragments shorter than 50 bp $ gt shredder -minlength 50 -maxlength 100 U89959_ests.fas \ | gt seqfilter -minlength 50 - > fragments.fas # 130 out of 1260 sequences have been removed (10.317%) Shredder an EST collection and show only random 10% of the resulting fragments $ gt shredder -sample 0.1 U89959_ests.fas]]) genometools-1.5.1/gtdata/doc/snpper.lua000066400000000000000000000001411211610345200200630ustar00rootroot00000000000000if not gtdata_doc_dir then gtdata_doc_dir = "./" end dofile(gtdata_doc_dir.."regionmapping.lua") genometools-1.5.1/gtdata/doc/splicesiteinfo.lua000066400000000000000000000001411211610345200215740ustar00rootroot00000000000000if not gtdata_doc_dir then gtdata_doc_dir = "./" end dofile(gtdata_doc_dir.."regionmapping.lua") genometools-1.5.1/gtdata/doc/uniq.lua000066400000000000000000000014711211610345200175370ustar00rootroot00000000000000print ([[ A depth-first traversal of a feature node graph starts at the top-level feature node (or pseudo-node) and explores as far along each branch as possible before backtracking. Let's assume that the feature nodes are stored in a list in the order of their traversal (called the ``feature node list''). Two feature node graphs are considered to be repeated if their feature node list (from the depth-first traversal) have the same length and each feature node pair (from both lists at the same position) is ``similar''. Two feature nodes are ``similar'', if they have the same sequence ID, feature type, range, strand, and phase. For such a repeated feature node graph the one with the higher score (of the top-level feature) is kept. If only one of the feature node graphs has a defined score, this one is kept.]]) genometools-1.5.1/gtdata/modules/000077500000000000000000000000001211610345200167605ustar00rootroot00000000000000genometools-1.5.1/gtdata/modules/external/000077500000000000000000000000001211610345200206025ustar00rootroot00000000000000genometools-1.5.1/gtdata/modules/external/cgilua/000077500000000000000000000000001211610345200220465ustar00rootroot00000000000000genometools-1.5.1/gtdata/modules/external/cgilua/authentication.lua000066400000000000000000000163361211610345200256010ustar00rootroot00000000000000-- CGILua authentication Module -- Author: Leonardo Godinho -- -- Offers a basic API for authentication assuming the presence of -- cgilua.POST.user, cgilua.POST.pass, cgilua.QUERY.logout, cgilua.QUERY[tokenName] -- -- The API consists in the functions -- check(username, passwd) - Checks if the pair username/passwd is authenticated by the configured method -- checkURL() - returns the URL for the checking script -- configure(options, methods) - configures the authentication framework (see /examples/authentication_conf.lua) -- logoutURL() - returns the URL for the logout page -- refURL() - returns the original URL being checked for authentication -- username() - returns the authenticated user if existent -- -- The authenticated user can be persisted by using a cookie or an ID in the URL -- -- $Id: authentication.lua,v 1.2 2007/12/05 19:41:13 carregal Exp $ local mime=require"mime" -- from LuaSocket local md5=require"md5" require"cgilua.cookies" local cgilua = cgilua local string = string local math = math local error = error module"cgilua.authentication" local authenticatedUser local configuration local _check -- check function provided by the configuration -- Callback functions to manipulate Tokens in the URL -- if not defined, CGILua standard URLs are assumed -- Returns the current token function getToken() return cgilua.QUERY[configuration.tokenName] end -- Sets the current token function setToken(token) cgilua.QUERY[configuration.tokenName] = token end -- Returns the current URL function currentURL() local script_name = cgilua.servervariable"SCRIPT_NAME" local path_info = cgilua.servervariable"PATH_INFO" or "" local query_string = cgilua.servervariable"QUERY_STRING" or "" if query_string ~= "" then query_string = "?"..query_string end return cgilua.mkabsoluteurl(script_name..path_info..query_string) end -- URL Base64 encoder and decoder functions -- (http://en.wikipedia.org/wiki/Base64) -- -- '=' is replaced by '' -- '+' and '/' are respectively replaced by '*' and '-' function encodeURLbase64(str) local b64str = mime.b64(str) local urlb64str = string.gsub(b64str,"=","") urlb64str = string.gsub(urlb64str,"+","*") urlb64str = string.gsub(urlb64str,"/","-") urlb64str = string.gsub(urlb64str," ","_") return urlb64str end function decodeURLbase64(urlb64str) local b64str = string.gsub(urlb64str,"*","+") b64str = string.gsub(b64str,"-","/") b64str = string.gsub(b64str,"_"," ") local b64strPadLen = math.fmod(4 - math.fmod(string.len(b64str), 4), 4) b64str = b64str..string.rep("=", b64strPadLen) local str = mime.unb64(b64str) return str end -- Returns the authenticated username or nil if no user is authenticated function username() if authenticatedUser == nil then local authenticatedUserData local token if configuration.tokenPersistence == "url" then token = getToken() elseif configuration.tokenPersistence == "cookie" then token = cgilua.cookies.get(configuration.tokenName) end if token then authenticatedUserData = md5.decrypt(decodeURLbase64(token), configuration.criptKey) -- check if IP in crypted data match with client IP local authenticatedUserIP = authenticatedUserData and string.gsub(authenticatedUserData, ",.*$","") or nil if authenticatedUserIP ~= cgilua.servervariable("REMOTE_ADDR") then return nil end authenticatedUser=authenticatedUserData and string.gsub(authenticatedUserData, "^.*,", "") or nil end end return authenticatedUser end -- encrypt the user IP and username for the user hash token local function cryptUserData() if authenticatedUser then local userData = cgilua.servervariable("REMOTE_ADDR") ..",".. authenticatedUser local cryptedUserData = encodeURLbase64(md5.crypt(userData, configuration.criptKey)) return cryptedUserData end end -- defines the logged user name and sets the user hash token local function setUser(username) authenticatedUser = username if username then local cryptedUserData = cryptUserData() if configuration.tokenPersistence == "url" then setToken(cryptedUserData) cgilua.cookies.delete(configuration.tokenName) -- removes an eventual previous cookie token elseif configuration.tokenPersistence == "cookie" then cgilua.cookies.set(configuration.tokenName, cryptedUserData) setToken() -- remove an eventual previous token from the URLs end end end -- User logout, clear everything function logout() setUser() cgilua.cookies.delete(configuration.tokenName) setToken() cgilua.QUERY.logout = nil end -- Checks if a user name/password is authenticated by the configured method -- if the user is authenticaded then login the user else logout the user -- returns true if the user has been succesfully authenticated or false plus -- an error message when the authentication fails function check(name, pass) name = name or cgilua.POST.user pass = pass or cgilua.POST.pass if name then -- Tries to authenticate the user using the configured method local retauth,errauth = _check(name, pass) if retauth then setUser(name) return true else logout() return false, errauth end else local authuser = username() if authuser then if cgilua.QUERY.logout ~= nil then logout() return false end end return authuser end end -- Returns a authentication URL with ref URL as a parameter, -- accepts an optional value for the logout action function checkURL(ref, tologout) local token if configuration.tokenPersistence == "url" then token = getToken() elseif configuration.tokenPersistence == "cookie" then token = cgilua.cookies.get(configuration.tokenName) end -- As HTTP header referer information can violate privacy, -- some browsers allow the user to disable the sending of referer information. -- Some proxy and firewall software will also filter out referer information, -- to avoid leaking the location of non-public websites. -- So we send the current URL as an URL parameter to the login URL. setToken() local args = {ref = ref or currentURL(), logout = tologout} if string.find(configuration.checkURL, "^https?:") then local params = "?"..urlcode.encodetable(args) return configuration.checkURL..params end return cgilua.mkabsoluteurl(cgilua.mkurlpath(configuration.checkURL, args)) end -- Returns the logout URL, based on the login URL function logoutURL() return checkURL(nil, 1) end -- Returns the referenced URL, the one supposed to be offered only for authenticated users function refURL() local url local baseURL = cgilua.QUERY.ref or configuration.checkURL if string.find(baseURL, "\?") then url = string.gsub(baseURL, "\?", "?"..configuration.tokenName.."="..cryptUserData().."&") else url = baseURL.."?"..configuration.tokenName.."="..cryptUserData() end return url end -- Sets the current configuration function configure(options, methods) configuration = options local method = methods[options.method] or {} if method.check then _check = method.check end if method.username then username = method.username end endgenometools-1.5.1/gtdata/modules/external/cgilua/cgilua.lua000066400000000000000000000514401211610345200240210ustar00rootroot00000000000000---------------------------------------------------------------------------- -- CGILua library. -- -- @release $Id: cgilua.lua,v 1.81 2008/05/19 18:13:36 carregal Exp $ ---------------------------------------------------------------------------- local _G, SAPI = _G, SAPI local urlcode = require"cgilua.urlcode" local lp = require"cgilua.lp" local lfs = require"lfs" local debug = require"debug" local assert, error, ipairs, select, tostring, type, unpack, xpcall = assert, error, ipairs, select, tostring, type, unpack, xpcall local pairs = pairs local gsub, format, strfind, strlower, strsub, match = string.gsub, string.format, string.find, string.lower, string.sub, string.match local setmetatable = setmetatable local _open = io.open local tinsert, tremove, concat = table.insert, table.remove, table.concat local foreachi = table.foreachi local date = os.date local os_tmpname = os.tmpname local getenv = os.getenv local remove = os.remove local seeall = package.seeall local setfenv = setfenv lp.setoutfunc ("cgilua.put") lp.setcompatmode (true) module ("cgilua") _COPYRIGHT = "Copyright (C) 2003 Kepler Project" _DESCRIPTION = "CGILua is a tool for creating dynamic Web pages and manipulating input data from forms" _VERSION = "CGILua 5.1.2" -- -- Internal state variables. local _default_errorhandler = debug.traceback local _errorhandler = _default_errorhandler local _default_erroroutput = function (msg) if type(msg) ~= "string" and type(msg) ~= "number" then msg = format ("bad argument #1 to 'error' (string expected, got %s)", type(msg)) end -- Logging error SAPI.Response.errorlog (msg) SAPI.Response.errorlog (" ") SAPI.Response.errorlog (SAPI.Request.servervariable"REMOTE_ADDR") SAPI.Response.errorlog (" ") SAPI.Response.errorlog (date()) SAPI.Response.errorlog ("\n") -- Building user message msg = gsub (gsub (msg, "\n", "
\n"), "\t", "  ") SAPI.Response.contenttype ("text/html") SAPI.Response.write ("CGILua Error" .. msg .. "") end local _erroroutput = _default_erroroutput local _default_maxfilesize = 512 * 1024 local _maxfilesize = _default_maxfilesize local _default_maxinput = 1024 * 1024 local _maxinput = _default_maxinput script_path = false -- -- Header functions ---------------------------------------------------------------------------- -- Sends a header. -- @param header String with the header. -- @param value String with the corresponding value. ---------------------------------------------------------------------------- function header(...) return SAPI.Response.header(...) end ---------------------------------------------------------------------------- -- Sends a Content-type header. -- @param type String with the type of the header. -- @param subtype String with the subtype of the header. ---------------------------------------------------------------------------- function contentheader (type, subtype) SAPI.Response.contenttype (type..'/'..subtype) end ---------------------------------------------------------------------------- -- Sends the HTTP header "text/html". ---------------------------------------------------------------------------- function htmlheader() SAPI.Response.contenttype ("text/html") end local htmlheader = htmlheader ---------------------------------------------------------------------------- -- Sends an HTTP header redirecting the browser to another URL -- @param url String with the URL. -- @param args Table with the arguments (optional). ---------------------------------------------------------------------------- function redirect (url, args) if strfind(url,"^https?:") then local params="" if args then params = "?"..urlcode.encodetable(args) end return SAPI.Response.redirect(url..params) else return SAPI.Response.redirect(mkabsoluteurl(mkurlpath(url,args))) end end ---------------------------------------------------------------------------- -- Returns a server variable -- @param name String with the name of the server variable. -- @return String with the value of the server variable. ---------------------------------------------------------------------------- function servervariable(...) return SAPI.Request.servervariable(...) end ---------------------------------------------------------------------------- -- Primitive error output function -- @param msg String (or number) with the message. -- @param level String with the error level (optional). ---------------------------------------------------------------------------- function errorlog (msg, level) local t = type(msg) if t == "string" or t == "number" then SAPI.Response.errorlog (msg, level) else error ("bad argument #1 to `cgilua.errorlog' (string expected, got "..t..")", 2) end end ---------------------------------------------------------------------------- -- Converts all its arguments to strings before sending them to the server. ---------------------------------------------------------------------------- function print (...) local args = { ... } for i = 1, select("#",...) do args[i] = tostring(args[i]) end SAPI.Response.write (concat(args,"\t")) SAPI.Response.write ("\n") end ---------------------------------------------------------------------------- -- Function 'put' sends its arguments (basically strings of HTML text) -- to the server -- Its basic implementation is to use Lua function 'write', which writes -- each of its arguments (strings or numbers) to file _OUTPUT (a file -- handle initialized with the file descriptor for stdout) -- @param s String (or number) with output. ---------------------------------------------------------------------------- function put (...) return SAPI.Response.write(...) end -- Returns the current errorhandler function _geterrorhandler(msg) return _errorhandler(msg) end -- -- Executes a function using the CGILua error handler. -- @param f Function to be called. -- function pcall (f) local results = {xpcall (f, _geterrorhandler)} local ok = results[1] tremove(results, 1) if ok then if #results == 0 then results = { true } end return unpack(results) else _erroroutput (unpack(results)) end end local function buildscriptenv() local env = { print = _M.print, write = _M.put } setmetatable(env, { __index = _G, __newindex = _G }) return env end ---------------------------------------------------------------------------- -- Execute a script -- If an error is found, Lua's error handler is called and this function -- does not return -- @param filename String with the name of the file to be processed. -- @return The result of the execution of the file. ---------------------------------------------------------------------------- function doscript (filename) local f, err = _G.loadfile(filename) if not f then error (format ("Cannot execute `%s'. Exiting.\n%s", filename, err)) else local env = buildscriptenv() setfenv(f, env) return pcall(f) end end ---------------------------------------------------------------------------- -- Execute the file if there is no "file error". -- If an error is found, and it is not a "file error", Lua 'error' -- is called and this function does not return -- @param filename String with the name of the file to be processed. -- @return The result of the execution of the file or nil (in case the -- file does not exists or if it cannot be opened). -- @return It could return an error message if the file cannot be opened. ---------------------------------------------------------------------------- function doif (filename) if not filename then return end -- no file local f, err = _open(filename) if not f then return nil, err end -- no file (or unreadable file) f:close() return doscript (filename) end --------------------------------------------------------------------------- -- Set the maximum "total" input size allowed (in bytes) -- @param nbytes Number of the maximum size (in bytes) of the whole POST data. --------------------------------------------------------------------------- function setmaxinput(nbytes) _maxinput = nbytes end --------------------------------------------------------------------------- -- Set the maximum size for an "uploaded" file (in bytes) -- Might be less or equal than _maxinput. -- @param nbytes Number of the maximum size (in bytes) of a file. --------------------------------------------------------------------------- function setmaxfilesize(nbytes) _maxfilesize = nbytes end -- Default path for temporary files tmp_path = _G.CGILUA_TMP or getenv("TEMP") or getenv ("TMP") or "/tmp" -- Default function for temporary names -- @returns a temporay name using os.tmpname tmpname = function() local tempname = os_tmpname() -- Lua os.tmpname returns a full path in Unix, but not in Windows -- so we strip the eventual prefix tempname = gsub(tempname, "(/tmp/)", "") return tempname end local _tmpfiles = {} --------------------------------------------------------------------------- -- Returns a temporary file in a directory using a name generator -- @param dir Base directory for the temporary file -- @param namefunction Name generator function --------------------------------------------------------------------------- function tmpfile(dir, namefunction) dir = dir or tmp_path namefunction = namefunction or tmpname local tempname = namefunction() local filename = dir.."/"..tempname local file, err = _open(filename, "wb+") if file then tinsert(_tmpfiles, {name = filename, file = file}) end return file, err end ---------------------------------------------------------------------------- -- Preprocess the content of a mixed HTML file and output a complete -- HTML document ( a 'Content-type' header is inserted before the -- preprocessed HTML ) -- @param filename String with the name of the file to be processed. -- @param env Optional environment ---------------------------------------------------------------------------- function handlelp (filename, env) env = env or buildscriptenv() htmlheader () lp.include (filename, env) end ---------------------------------------------------------------------------- -- Builds a handler that sends a header and the contents of the given file. -- Sends the contents of the file to the output without processing it. -- @param type String with the type of the header. -- @param subtype String with the subtype of the header. -- @return Function (which receives a filename as argument) that produces -- the header and copies the content of the given file. ---------------------------------------------------------------------------- function buildplainhandler (type, subtype) return function (filename) local fh, err = _open (filename, "rb") local contents = "" if fh then contents = fh:read("*a") fh:close() else error(err) end header("Content-Lenght", #contents) contentheader (type, subtype) put (contents) end end ---------------------------------------------------------------------------- -- Builds a handler that sends a header and the processed file. -- Processes the file as a Lua Page. -- @param type String with the type of the header. -- @param subtype String with the subtype of the header. -- @return Function (which receives a filename as argument) that produces -- the header and processes the given file. ---------------------------------------------------------------------------- function buildprocesshandler (type, subtype) return function (filename) local env = buildscriptenv() contentheader (type, subtype) lp.include (filename, env) end end ---------------------------------------------------------------------------- -- Builds the default handler table from cgilua.mime ---------------------------------------------------------------------------- local function buildhandlers() local mime = _G.require "cgilua.mime" for ext, mediatype in pairs(mime) do local t, st = match(mediatype, "([^/]*)/([^/]*)") addscripthandler(ext, buildplainhandler(t, st)) end end ---------------------------------------------------------------------------- -- Create an URL path to be used as a link to a CGILua script -- @param script String with the name of the script. -- @param args Table with arguments to script (optional). -- @return String in URL format. ---------------------------------------------------------------------------- function mkurlpath (script, args) -- URL-encode the parameters to be passed do the script local params = "" if args then params = "?"..urlcode.encodetable(args) end if strsub(script,1,1) == "/" then return urlpath .. script .. params else return urlpath .. script_vdir .. script .. params end end ---------------------------------------------------------------------------- -- Create an absolute URL containing the given URL path -- @param path String with the path. -- @param protocol String with the name of the protocol (default = "http"). -- @return String in URL format. ---------------------------------------------------------------------------- function mkabsoluteurl (path, protocol) protocol = protocol or "http" if path:sub(1,1) ~= '/' then path = '/'..path end return format("%s://%s:%s%s", protocol, servervariable"SERVER_NAME", servervariable"SERVER_PORT", path) end ---------------------------------------------------------------------------- -- Extract the "directory" and "file" parts of a path -- @param path String with a path. -- @return String with the directory part. -- @return String with the file part. ---------------------------------------------------------------------------- function splitonlast (path, sep) local dir,file = match(path,"^(.-)([^:/\\]*)$") return dir,file end splitpath = splitonlast -- compatibility with previous versions ---------------------------------------------------------------------------- -- Extracts the first and remaining parts of a path -- @param path separator (defaults to "/") -- @return String with the extracted part. -- @return String with the remaining path. ---------------------------------------------------------------------------- function splitonfirst(path, sep) local first, rest = match(path, "^/([^:/\\]*)(.*)") return first, rest end -- -- Define variables and build the cgilua.POST, cgilua.GET tables. -- local function getparams () requestmethod = servervariable"REQUEST_METHOD" -- Fill in the POST table. POST = {} if requestmethod == "POST" then post.parsedata { read = SAPI.Request.getpostdata, discardinput = ap and ap.discard_request_body, content_type = servervariable"CONTENT_TYPE", content_length = servervariable"CONTENT_LENGTH", maxinput = _maxinput, maxfilesize = _maxfilesize, args = POST, } end -- Fill in the QUERY table. QUERY = {} urlcode.parsequery (servervariable"QUERY_STRING", QUERY) end -- -- Stores all script handlers and the file extensions used to identify -- them. Loads the default local _script_handlers = {} -- -- Default handler. -- Sends the contents of the file to the output without processing it. -- This relies in the browser being able to discover the content type -- which is not reliable. -- @param filename String with the name of the file. -- local function default_handler (filename) local fh, err = _open (filename, "rb") local contents if fh then contents = fh:read("*a") fh:close() else error(err) end header("Content-Lenght", #contents) put ("\n") put (contents) end ---------------------------------------------------------------------------- -- Add a script handler. -- @param file_extension String with the lower-case extension of the script. -- @param func Function to handle this kind of scripts. ---------------------------------------------------------------------------- function addscripthandler (file_extension, func) assert (type(file_extension) == "string", "File extension must be a string") if strfind (file_extension, '%.', 1) then file_extension = strsub (file_extension, 2) end file_extension = strlower(file_extension) assert (type(func) == "function", "Handler must be a function") _script_handlers[file_extension] = func end --------------------------------------------------------------------------- -- Obtains the handler corresponding to the given script path. -- @param path String with a script path. -- @return Function that handles it or nil. ---------------------------------------------------------------------------- function getscripthandler (path) local i,f, ext = strfind (path, "%.([^.]+)$") return _script_handlers[strlower(ext or '')] end --------------------------------------------------------------------------- -- Execute the given path with the corresponding handler. -- @param path String with a script path. -- @return The returned values from the script. --------------------------------------------------------------------------- function handle (path) local h = getscripthandler (path) or default_handler return h (path) end --------------------------------------------------------------------------- -- Sets "errorhandler" function -- This function is called by Lua when an error occurs. -- It receives the error message generated by Lua and it is resposible -- for the final message which should be returned. -- @param Function. --------------------------------------------------------------------------- function seterrorhandler (f) local tf = type(f) if tf == "function" then _errorhandler = f else error (format ("Invalid type: expected `function', got `%s'", tf)) end end --------------------------------------------------------------------------- -- Defines the "erroroutput" function -- This function is called to generate the error output. -- @param Function. --------------------------------------------------------------------------- function seterroroutput (f) local tf = type(f) if tf == "function" then _erroroutput = f else error (format ("Invalid type: expected `function', got `%s'", tf)) end end -- -- Stores all close functions in order they are set. local _close_functions = { } --------------------------------------------------------------------------- -- Adds a function to be executed after the script. -- @param f Function to be registered. --------------------------------------------------------------------------- function addclosefunction (f) local tf = type(f) if tf == "function" then tinsert (_close_functions, f) else error (format ("Invalid type: expected `function', got `%s'", tf)) end end -- -- Close function. -- local function close() for i = #_close_functions, 1, -1 do _close_functions[i]() end end -- -- Stores all open functions in order they are set. local _open_functions = { } --------------------------------------------------------------------------- -- Adds a function to be executed before the script. -- @param f Function to be registered. --------------------------------------------------------------------------- function addopenfunction (f) local tf = type(f) if tf == "function" then tinsert (_open_functions, f) else error (format ("Invalid type: expected `function', got `%s'", tf)) end end -- -- Open function. -- Call all defined open-functions in the order they were created. -- local function open() for i = #_open_functions, 1, -1 do _open_functions[i]() end end -- -- Resets CGILua's state. -- local function reset () script_path = false _maxfilesize = _default_maxfilesize _maxinput = _default_maxinput -- Error Handling _errorhandler = _default_errorhandler _erroroutput = _default_erroroutput -- Handlers _script_handlers = {} _open_functions = {} _close_functions = {} -- clean temporary files foreachi(_tmpfiles, function (i, v) v.file:close() local _, err = remove(v.name) if err then error(err) end end) end --------------------------------------------------------------------------- -- Request processing. --------------------------------------------------------------------------- function main () SAPI = _G.SAPI buildhandlers() -- Default handler values addscripthandler ("lua", doscript) addscripthandler ("lp", handlelp) -- Looks for an optional loader module pcall (function () _G.require"cgilua.loader" end) -- post.lua needs to be loaded after cgilua.lua is compiled pcall (function () _G.require"cgilua.post" end) if loader then loader.init() end -- Build QUERY/POST tables if not pcall (getparams) then return nil end local result -- Executes the optional loader module if loader then loader.run() end -- Changing curent directory to the script's "physical" dir local curr_dir = lfs.currentdir () pcall (function () lfs.chdir (script_pdir) end) -- Opening functions pcall (open) -- Executes the script result, err = pcall (function () return handle (script_file) end) -- Closing functions pcall (close) -- Changing to original directory pcall (function () lfs.chdir (curr_dir) end) -- Cleanup reset () if result then -- script executed ok! return result end end genometools-1.5.1/gtdata/modules/external/cgilua/cookies.lua000066400000000000000000000062201211610345200242050ustar00rootroot00000000000000---------------------------------------------------------------------------- -- Cookies Library -- -- @release $Id: cookies.lua,v 1.8 2008/04/24 13:42:04 mascarenhas Exp $ ---------------------------------------------------------------------------- require"cgilua.urlcode" local error = error local format, gsub, strfind = string.format, string.gsub, string.find local date = os.date local escape, unescape = cgilua.urlcode.escape, cgilua.urlcode.unescape local function header(...) return SAPI.Response.header(...) end local function write(...) return SAPI.Response.write(...) end local function servervariable(...) return SAPI.Request.servervariable(...) end module ("cgilua.cookies") local function optional (what, name) if name ~= nil and name ~= "" then return format("; %s=%s", what, name) else return "" end end local function build (name, value, options) if not name or not value then error("cookie needs a name and a value") end local cookie = name .. "=" .. escape(value) options = options or {} if options.expires then local t = date("!%A, %d-%b-%Y %H:%M:%S GMT", options.expires) cookie = cookie .. optional("expires", t) end cookie = cookie .. optional("path", options.path) cookie = cookie .. optional("domain", options.domain) cookie = cookie .. optional("secure", options.secure) return cookie end ---------------------------------------------------------------------------- -- Sets a value to a cookie, with the given options. -- Generates a header "Set-Cookie", thus it can only be used in Lua Scripts. -- @param name String with the name of the cookie. -- @param value String with the value of the cookie. -- @param options Table with the options (optional). function set (name, value, options) header("Set-Cookie", build(name, value, options)) end ---------------------------------------------------------------------------- -- Sets a value to a cookie, with the given options. -- Generates an HTML META tag, thus it can be used in Lua Pages. -- @param name String with the name of the cookie. -- @param value String with the value of the cookie. -- @param options Table with the options (optional). function sethtml (name, value, options) write(format('', build(name, value, options))) end ---------------------------------------------------------------------------- -- Gets the value of a cookie. -- @param name String with the name of the cookie. -- @return String with the value associated with the cookie. function get (name) local cookies = servervariable"HTTP_COOKIE" or "" cookies = ";" .. cookies .. ";" cookies = gsub(cookies, "%s*;%s*", ";") -- remove extra spaces local pattern = ";" .. name .. "=(.-);" local _, __, value = strfind(cookies, pattern) return value and unescape(value) end ---------------------------------------------------------------------------- -- Deletes a cookie, by setting its value to "xxx". -- @param name String with the name of the cookie. -- @param options Table with the options (optional). function delete (name, options) options = options or {} options.expires = 1 set(name, "xxx", options) end genometools-1.5.1/gtdata/modules/external/cgilua/dispatcher.lua000066400000000000000000000041501211610345200246770ustar00rootroot00000000000000-- CGILua dispatcher module -- @release $Id: dispatcher.lua,v 1.8 2007/12/07 18:49:49 carregal Exp $ module(..., package.seeall) -- Checks if an URL matches a route pattern local function route_match(url, pattern) local params = {} local captures = string.gsub(pattern, "(/$[%w_-]+)", "/([^/]*)") local url_parts = {string.match(url, captures)} local i = 1 for name in string.gmatch(pattern, "/$([%w_-]+)") do params[name] = url_parts[i] i = i + 1 end return next(params) and params end local route_URLs = {} -- Maps the correct function for an URL local function route_map(url) for i, v in ipairs(route_URLs) do local pattern, f, name = unpack(v) local params = route_match(url, pattern) if params then return f, params end end end -- Returns an URL for a named route -- @param map_name Name associated with the map in the routed URL table. -- @param params Table of named parameters used in the URL map -- @param queryargs Optional table of named parameters used for the QUERY part of the URL function route_url(map_name, params, queryargs) local queryparams = "" if queryargs then queryparams = "?"..cgilua.urlcode.encodetable(queryargs) end for i, v in ipairs(route_URLs) do local pattern, f, name = unpack(v) if name == map_name then local url = string.gsub(pattern, "$([%w_-]+)", params) url = cgilua.urlpath.."/"..cgilua.app_name..url..queryparams return url end end end -- Defines the routing using a table of URLs maps or a single map -- a map defines a URL mask using $name to extract parameters, -- a function to be called with the extracted parameters and -- a name for the map when used with route_url -- @param table of maps or a single map function route(URLs) URLs = URLs or {} if type(URLs[1]) == "string" then -- accepts a single map as the only entry in a map table URLs = {URLs} end route_URLs = URLs f, args = route_map(cgilua.script_vpath) if f then return f(args) else error("Missing page parameters") end endgenometools-1.5.1/gtdata/modules/external/cgilua/loader.lua000066400000000000000000000066741211610345200240340ustar00rootroot00000000000000-- CGILua loader -- -- Assumes two global variables pointing to directories: -- CGILUA_CONF - CGILua configuration directory -- CGILUA_TMP - CGILua temporary files directory -- -- # $Id: loader.lua,v 1.7 2008/03/28 22:01:18 ignacio Exp $ require "lfs" module("cgilua.loader", package.seeall) function init() -- Loads the user configuration cgilua.doif (CGILUA_CONF.."/config.lua") end function run() local servervariable = cgilua.servervariable cgilua.script_vpath = cgilua.script_vpath or servervariable"PATH_INFO" if cgilua.script_vpath == nil or cgilua.script_vpath == "" then cgilua.script_vpath = "/" end local document_root = cgilua.pdir or servervariable"DOCUMENT_ROOT" if not cgilua.script_path then if CGILUA_ISDIRECT then -- the launcher is associated with scripts (Xavante, mod_lua or isapi usually) if servervariable"PATH_TRANSLATED" ~= "" then cgilua.script_path = servervariable"PATH_TRANSLATED" else cgilua.script_path = servervariable"SCRIPT_FILENAME" end else -- the launcher executable is present in the URL (CGI or FastCGI only) if document_root == nil or document_root == "" then -- tries to obtain documents_root from the server local path_info = cgilua.script_vpath if path_info == nil or path_info == "" or path_info == "/" then document_root = cgilua.pdir or servervariable"PATH_TRANSLATED" else if string.find(servervariable("SERVER_SOFTWARE"), "IIS") then path_info = string.gsub(path_info, "/", "\\") end document_root = cgilua.pdir or string.gsub(servervariable"PATH_TRANSLATED", path_info, "") end end if cgilua.use_executable_name then -- looks for a Lua script with the same name as the executable local _, name = cgilua.splitpath(servervariable"SCRIPT_NAME") name = string.gsub(name, "%.[^%.]-$","") if name and lfs.attributes(document_root.."/"..name..".lua") then cgilua.script_path = document_root.."/"..name..".lua" end else -- uses /index.lua then /index.lp as the default script if cgilua.script_vpath == "/" then if lfs.attributes(document_root.."/index.lua") then cgilua.script_vpath = "/index.lua" elseif lfs.attributes(document_root.."/index.lp") then cgilua.script_vpath = "/index.lp" else error("Kepler is correctly configured, but you didn't provide a script!") end end -- checks if PATH_INFO refers to a valid file and ajusts the settings accordingly local filepath, path_info = string.match (cgilua.script_vpath, "^([^%.]-%.[^/]+)(.*)") if filepath and lfs.attributes(document_root..filepath) then -- if one is found use it cgilua.script_path = document_root..filepath cgilua.script_vpath = path_info cgilua.urlpath = cgilua.urlpath or servervariable"SCRIPT_NAME"..filepath else -- otherwise go with the current PATH_INFO cgilua.script_path = document_root..cgilua.script_vpath end end end end -- define other cgilua vars so mkurlpath can work correctly if cgilua.script_vpath then cgilua.script_vdir = cgilua.splitpath (cgilua.script_vpath) cgilua.urlpath = cgilua.urlpath or servervariable"SCRIPT_NAME" else cgilua.script_vdir = cgilua.splitpath (servervariable"SCRIPT_NAME") cgilua.urlpath = cgilua.urlpath or "" end cgilua.script_pdir, cgilua.script_file = cgilua.splitpath (cgilua.script_path) end genometools-1.5.1/gtdata/modules/external/cgilua/lp.lua000066400000000000000000000105231211610345200231650ustar00rootroot00000000000000---------------------------------------------------------------------------- -- Lua Pages Template Preprocessor. -- -- @release $Id: lp.lua,v 1.13 2008/01/19 19:30:35 mascarenhas Exp $ ---------------------------------------------------------------------------- local assert, error, getfenv, loadstring, setfenv = assert, error, getfenv, loadstring, setfenv local find, format, gsub, strsub = string.find, string.format, string.gsub, string.sub local concat, tinsert = table.concat, table.insert local open = io.open module (...) ---------------------------------------------------------------------------- -- function to do output local outfunc = "io.write" -- accepts the old expression field: `$| |$' local compatmode = true -- -- Builds a piece of Lua code which outputs the (part of the) given string. -- @param s String. -- @param i Number with the initial position in the string. -- @param f Number with the final position in the string (default == -1). -- @return String with the correspondent Lua code which outputs the part of the string. -- local function out (s, i, f) s = strsub(s, i, f or -1) if s == "" then return s end -- we could use `%q' here, but this way we have better control s = gsub(s, "([\\\n\'])", "\\%1") -- substitute '\r' by '\'+'r' and let `loadstring' reconstruct it s = gsub(s, "\r", "\\r") return format(" %s('%s'); ", outfunc, s) end ---------------------------------------------------------------------------- -- Translate the template to Lua code. -- @param s String to translate. -- @return String with translated code. ---------------------------------------------------------------------------- function translate (s) s = gsub(s, "^#![^\n]+\n", "") if compatmode then s = gsub(s, "$|(.-)|%$", "") s = gsub(s, "", "") end s = gsub(s, "<%%(.-)%%>", "") local res = {} local start = 1 -- start of untranslated part in `s' while true do local ip, fp, target, exp, code = find(s, "<%?(%w*)[ \t]*(=?)(.-)%?>", start) if not ip then break end tinsert(res, out(s, start, ip-1)) if target ~= "" and target ~= "lua" then -- not for Lua; pass whole instruction to the output tinsert(res, out(s, ip, fp)) else if exp == "=" then -- expression? tinsert(res, format(" %s(%s);", outfunc, code)) else -- command tinsert(res, format(" %s ", code)) end end start = fp + 1 end tinsert(res, out(s, start)) return concat(res) end ---------------------------------------------------------------------------- -- Defines the name of the output function. -- @param f String with the name of the function which produces output. function setoutfunc (f) outfunc = f end ---------------------------------------------------------------------------- -- Turns on or off the compatibility with old CGILua 3.X behavior. -- @param c Boolean indicating if the compatibility mode should be used. function setcompatmode (c) compatmode = c end ---------------------------------------------------------------------------- -- Internal compilation cache. local cache = {} ---------------------------------------------------------------------------- -- Translates a template into a Lua function. -- Does NOT execute the resulting function. -- Uses a cache of templates. -- @param string String with the template to be translated. -- @param chunkname String with the name of the chunk, for debugging purposes. -- @return Function with the resulting translation. function compile (string, chunkname) local f, err = cache[string] if f then return f end f, err = loadstring (translate (string), chunkname) if not f then error (err, 3) end cache[string] = f return f end ---------------------------------------------------------------------------- -- Translates and executes a template in a given file. -- The translation creates a Lua function which will be executed in an -- optionally given environment. -- @param filename String with the name of the file containing the template. -- @param env Table with the environment to run the resulting function. function include (filename, env) -- read the whole contents of the file local fh = assert (open (filename)) local src = fh:read("*a") fh:close() -- translates the file into a function local prog = compile (src, '@'..filename) local _env if env then _env = getfenv (prog) setfenv (prog, env) end prog () end genometools-1.5.1/gtdata/modules/external/cgilua/mime.lua000066400000000000000000000124551211610345200235070ustar00rootroot00000000000000----------------------------------------------------------------------------- -- Xavante MIME types -- -- Authors: Javier Guerra and Andre Carregal -- Copyright (c) 2004-2007 Kepler Project -- -- $Id: mime.lua,v 1.1 2007/09/25 23:17:56 carregal Exp $ ----------------------------------------------------------------------------- -- Extracted from Apache's mime.types -- This file controls what Internet media types are sent to the client for -- given file extension(s). Sending the correct media type to the client -- is important so they know how to handle the content of the file. -- Extra types can either be added here or by using an AddType directive -- in your config files. For more information about Internet media types, -- please read RFC 2045, 2046, 2047, 2048, and 2077. The Internet media type -- registry is at . return { ez = "application/andrew-inset", atom = "application/atom+xml", hqx = "application/mac-binhex40", cpt = "application/mac-compactpro", mathml = "application/mathml+xml", doc = "application/msword", bin = "application/octet-stream", dms = "application/octet-stream", lha = "application/octet-stream", lzh = "application/octet-stream", exe = "application/octet-stream", class = "application/octet-stream", so = "application/octet-stream", dll = "application/octet-stream", dmg = "application/octet-stream", oda = "application/oda", ogg = "application/ogg", pdf = "application/pdf", ai = "application/postscript", eps = "application/postscript", ps = "application/postscript", rdf = "application/rdf+xml", smi = "application/smil", smil = "application/smil", gram = "application/srgs", grxml = "application/srgs+xml", mif = "application/vnd.mif", xul = "application/vnd.mozilla.xul+xml", xls = "application/vnd.ms-excel", ppt = "application/vnd.ms-powerpoint", rm = "application/vnd.rn-realmedia", wbxml = "application/vnd.wap.wbxml", wmlc = "application/vnd.wap.wmlc", wmlsc = "application/vnd.wap.wmlscriptc", vxml = "application/voicexml+xml", bcpio = "application/x-bcpio", vcd = "application/x-cdlink", pgn = "application/x-chess-pgn", cpio = "application/x-cpio", csh = "application/x-csh", dcr = "application/x-director", dir = "application/x-director", dxr = "application/x-director", dvi = "application/x-dvi", spl = "application/x-futuresplash", gtar = "application/x-gtar", hdf = "application/x-hdf", xhtml = "application/xhtml+xml", xht = "application/xhtml+xml", js = "application/x-javascript", skp = "application/x-koan", skd = "application/x-koan", skt = "application/x-koan", skm = "application/x-koan", latex = "application/x-latex", xml = "application/xml", xsl = "application/xml", dtd = "application/xml-dtd", nc = "application/x-netcdf", cdf = "application/x-netcdf", sh = "application/x-sh", shar = "application/x-shar", swf = "application/x-shockwave-flash", xslt = "application/xslt+xml", sit = "application/x-stuffit", sv4cpio = "application/x-sv4cpio", sv4crc = "application/x-sv4crc", tar = "application/x-tar", tcl = "application/x-tcl", tex = "application/x-tex", texinfo = "application/x-texinfo", texi = "application/x-texinfo", t = "application/x-troff", tr = "application/x-troff", roff = "application/x-troff", man = "application/x-troff-man", me = "application/x-troff-me", ms = "application/x-troff-ms", ustar = "application/x-ustar", src = "application/x-wais-source", zip = "application/zip", au = "audio/basic", snd = "audio/basic", mid = "audio/midi", midi = "audio/midi", kar = "audio/midi", mpga = "audio/mpeg", mp2 = "audio/mpeg", mp3 = "audio/mpeg", aif = "audio/x-aiff", aiff = "audio/x-aiff", aifc = "audio/x-aiff", m3u = "audio/x-mpegurl", ram = "audio/x-pn-realaudio", ra = "audio/x-pn-realaudio", wav = "audio/x-wav", pdb = "chemical/x-pdb", xyz = "chemical/x-xyz", bmp = "image/bmp", cgm = "image/cgm", gif = "image/gif", ief = "image/ief", jpeg = "image/jpeg", jpg = "image/jpeg", jpe = "image/jpeg", png = "image/png", svg = "image/svg+xml", svgz = "image/svg+xml", tiff = "image/tiff", tif = "image/tiff", djvu = "image/vnd.djvu", djv = "image/vnd.djvu", wbmp = "image/vnd.wap.wbmp", ras = "image/x-cmu-raster", ico = "image/x-icon", pnm = "image/x-portable-anymap", pbm = "image/x-portable-bitmap", pgm = "image/x-portable-graymap", ppm = "image/x-portable-pixmap", rgb = "image/x-rgb", xbm = "image/x-xbitmap", xpm = "image/x-xpixmap", xwd = "image/x-xwindowdump", igs = "model/iges", iges = "model/iges", msh = "model/mesh", mesh = "model/mesh", silo = "model/mesh", wrl = "model/vrml", vrml = "model/vrml", ics = "text/calendar", ifb = "text/calendar", css = "text/css", html = "text/html", htm = "text/html", asc = "text/plain", txt = "text/plain", rtx = "text/richtext", rtf = "text/rtf", sgml = "text/sgml", sgm = "text/sgml", tsv = "text/tab-separated-values", wml = "text/vnd.wap.wml", wmls = "text/vnd.wap.wmlscript", etx = "text/x-setext", mpeg = "video/mpeg", mpg = "video/mpeg", mpe = "video/mpeg", qt = "video/quicktime", mov = "video/quicktime", mxu = "video/vnd.mpegurl", avi = "video/x-msvideo", movie = "video/x-sgi-movie", ice = "x-conference/x-cooltalk", } genometools-1.5.1/gtdata/modules/external/cgilua/post.lua000066400000000000000000000225651211610345200235500ustar00rootroot00000000000000---------------------------------------------------------------------------- -- Process POST data. -- This library depends on some functions that read POST data and other -- HTTP information. A beginning is: -- require"post" -- local params = {} -- post.parsedata { -- read = ap.get_client_block or io.input, -- discardinput = ap.discard_request_body, -- content_type = ap.get_header"content-type" or os.getenv"CONTENT_TYPE", -- content_length = ap.get_header"content-length" or os.getenv"CONTENT_LENGTH", -- maxinput = 1024 * 1024, -- maxfilesize = 512 * 1024, -- args = params, -- } -- -- @release $Id: post.lua,v 1.17 2008/04/03 21:55:28 mascarenhas Exp $ ---------------------------------------------------------------------------- require"cgilua.readuntil" require"cgilua.urlcode" local assert, error, pairs, tonumber, tostring, type = assert, error, pairs, tonumber, tostring, type local getn, tinsert = table.getn, table.insert local format, gsub, strfind, strlower, strlen = string.format, string.gsub, string.find, string.lower, string.len local min = math.min local iterate = cgilua.readuntil.iterate local urlcode = cgilua.urlcode local tmpfile = cgilua.tmpfile -- environment for processing multipart/form-data input local boundary = nil -- boundary string that separates each 'part' of input local maxfilesize = nil -- maximum size for file upload local maxinput = nil -- maximum size of total POST data local inputfile = nil -- temporary file for inputting form-data local bytesleft = nil -- number of bytes yet to be read local content_type = nil -- request's content-type -- local functions local discardinput = nil -- discard all remaining input local readuntil = nil -- read until delimiter local read = nil -- basic read function module ("cgilua.post") -- -- Extract the boundary string from CONTENT_TYPE metavariable -- local function getboundary () local _,_,boundary = strfind (content_type, "boundary%=(.-)$") return "--"..boundary end -- -- Create a table containing the headers of a multipart/form-data field -- local function breakheaders (hdrdata) local headers = {} gsub (hdrdata, '([^%c%s:]+):%s+([^\n]+)', function(type,val) type = strlower(type) headers[type] = val end) return headers end -- -- Read the headers of the next multipart/form-data field -- -- This function returns a table containing the headers values. Each header -- value is indexed by the corresponding header "type". -- If end of input is reached (no more fields to process) it returns nil. -- local function readfieldheaders () local EOH = "\r\n\r\n" -- local hdrdata = "" local out = function (str) hdrdata = hdrdata..str end if readuntil (EOH, out) then -- parse headers return breakheaders (hdrdata) else -- no header found return nil end end -- -- Extract a field name (and possible filename) from its disposition header -- local function getfieldnames (headers) local disposition_hdr = headers["content-disposition"] local attrs = {} if disposition_hdr then gsub(disposition_hdr, ';%s*([^%s=]+)="(.-)"', function(attr, val) attrs[attr] = val end) else error("Error processing multipart/form-data.".. "\nMissing content-disposition header") end return attrs.name, attrs.filename end -- -- Read the contents of a 'regular' field to a string -- local function readfieldcontents () local value = "" local boundaryline = "\r\n"..boundary local out = function (str) value = value..str end if readuntil (boundaryline, out) then return value else error("Error processing multipart/form-data.\nUnexpected end of input\n") end end -- -- Read the contents of a 'file' field to a temporary file (file upload) -- local function fileupload (filename) -- create a temporary file for uploading the file field local file, err = tmpfile() if file == nil then discardinput(bytesleft) error("Cannot create a temporary file.\n"..err) end local bytesread = 0 local boundaryline = "\r\n"..boundary local out = function (str) local sl = strlen (str) if bytesread + sl > maxfilesize then discardinput (bytesleft) error (format ("Maximum file size (%d kbytes) exceeded while uploading `%s'", maxfilesize / 1024, filename)) end file:write (str) bytesread = bytesread + sl end if readuntil (boundaryline, out) then file:seek ("set", 0) return file, bytesread else error (format ("Error processing multipart/form-data.\nUnexpected end of input while uploading %s", filename)) end end -- -- Compose a file field 'value' -- local function filevalue (filehandle, filename, filesize, headers) -- the temporary file handle local value = { file = filehandle, filename = filename, filesize = filesize } -- copy additional header values for hdr, hdrval in pairs(headers) do if hdr ~= "content-disposition" then value[hdr] = hdrval end end return value end -- -- Process multipart/form-data -- -- This function receives the total size of the incoming multipart/form-data, -- the maximum size for a file upload, and a reference to a table where the -- form fields should be stored. -- -- For every field in the incoming form-data a (name=value) pair is -- inserted into the given table. [[name]] is the field name extracted -- from the content-disposition header. -- -- If a field is of type 'file' (i.e., a 'filename' attribute was found -- in its content-disposition header) a temporary file is created -- and the field contents are written to it. In this case, -- [[value]] has a table that contains the temporary file handle -- (key 'file') and the file name (key 'filename'). Optional headers -- included in the field description are also inserted into this table, -- as (header_type=value) pairs. -- -- If the field is not of type 'file', [[value]] contains the field -- contents. -- local function Main (inputsize, args) -- create a temporary file for processing input data local inputf,err = tmpfile() if inputf == nil then discardinput(inputsize) error("Cannot create a temporary file.\n"..err) end -- set the environment for processing the multipart/form-data inputfile = inputf bytesleft = inputsize maxfilesize = maxfilesize or inputsize boundary = getboundary() while true do -- read the next field header(s) local headers = readfieldheaders() if not headers then break end -- end of input -- get the name attributes for the form field (name and filename) local name, filename = getfieldnames(headers) -- get the field contents local value if filename then local filehandle, filesize = fileupload(filename) value = filevalue(filehandle, filename, filesize, headers) else value = readfieldcontents() end -- insert the form field into table [[args]] urlcode.insertfield(args, name, value) end end -- -- Initialize the library by setting the dependent functions: -- content_type = value of "Content-type" header -- content_length = value of "Content-length" header -- read = function that can read POST data -- discardinput (optional) = function that discard POST data -- maxinput (optional) = limit of POST data (in bytes) -- maxfilesize (optional) = limit of uploaded file(s) (in bytes) -- local function init (defs) assert (defs.read) read = defs.read readuntil = iterate (function () if bytesleft then if bytesleft <= 0 then return nil end local n = min (bytesleft, 2^13) -- 2^13 == 8192 local bytes = read (n) bytesleft = bytesleft - #bytes return bytes end end) if defs.discard_function then discardinput = defs.discardinput else discardinput = function (inputsize) readuntil ('\0', function()end) end end content_type = defs.content_type if defs.maxinput then maxinput = defs.maxinput end if defs.maxfilesize then maxfilesize = defs.maxfilesize end end ---------------------------------------------------------------------------- -- Parse the POST REQUEST incoming data according to its "content type" -- as defined by the metavariable CONTENT_TYPE (RFC CGI) -- -- An error is issued if the "total" size of the incoming data -- (defined by the metavariable CONTENT_LENGTH) exceeds the -- maximum input size allowed ---------------------------------------------------------------------------- function parsedata (defs) assert (type(defs.args) == "table", "field `args' must be a table") init (defs) -- get the "total" size of the incoming data local inputsize = tonumber(defs.content_length) or 0 if inputsize > maxinput then -- some Web Servers (like IIS) require that all the incoming data is read bytesleft = inputsize discardinput(inputsize) error(format("Total size of incoming data (%d KB) exceeds configured maximum (%d KB)", inputsize /1024, maxinput / 1024)) end -- process the incoming data according to its content type local contenttype = content_type if not contenttype then error("Undefined Media Type") end if strfind(contenttype, "x-www-form-urlencoded", 1, true) then urlcode.parsequery (read (inputsize), defs.args) elseif strfind(contenttype, "multipart/form-data", 1, true) then Main (inputsize, defs.args) elseif strfind (contenttype, "application/xml", 1, true) or strfind (contenttype, "text/xml", 1, true) or strfind (contenttype, "text/plain", 1, true) then tinsert (defs.args, read (inputsize)) else error("Unsupported Media Type: "..contenttype) end end genometools-1.5.1/gtdata/modules/external/cgilua/readuntil.lua000066400000000000000000000027231211610345200245440ustar00rootroot00000000000000---------------------------------------------------------------------------- -- Reads an input until a given character. -- -- @release $Id: readuntil.lua,v 1.5 2007/04/16 14:01:32 tomas Exp $ ---------------------------------------------------------------------------- local strsub, strfind, strlen = string.sub, string.find, string.len module ("cgilua.readuntil") ---------------------------------------------------------------------------- -- Creates a function which reads an input until a given character. -- @param inp Function which reads the input. -- @return Function which receives a delimiter character and an output -- function. ---------------------------------------------------------------------------- function iterate (inp) local current = "" return function (del, out) local dellen = strlen(del) local i, e while true do i, e = strfind(current, del, 1, 1) if i then break end local new = inp() if not new then break end do -- handle borders local endcurrent = strsub(current, -dellen+1) local border = endcurrent .. strsub(new, 1, dellen-1) if strlen(current) < dellen or strlen(new) < dellen or strfind(border, del, 1, 1) then -- move last part of `current' to new block current = strsub(current, 1, -dellen) new = endcurrent .. new end end out(current) current = new end out(strsub(current, 1, (i or 0) - 1)) current = strsub(current, (e or strlen(current)) + 1) return (i ~= nil) end end genometools-1.5.1/gtdata/modules/external/cgilua/serialize.lua000066400000000000000000000057171211610345200245520ustar00rootroot00000000000000---------------------------------------------------------------------------- -- Serialize tables. -- It works only for tables without cycles and without functions or -- userdata inside it. -- @release $Id: serialize.lua,v 1.7 2007/04/16 14:01:32 tomas Exp $ ---------------------------------------------------------------------------- local ipairs, pairs, type = ipairs, pairs, type local format = string.format local sort, tinsert = table.sort, table.insert -- local value = nil ---------------------------------------------------------------------------- -- Serializes a table. -- @param tab Table representing the session. -- @param outf Function used to generate the output. -- @param ind String with indentation pattern (default = ""). -- @param pre String with indentation prefix (default = ""). ---------------------------------------------------------------------------- local function tabledump (tab, outf, ind, pre) local sep_n, sep, _n = ",\n", ", ", "\n" if (not ind) or (ind == "") then ind = ""; sep_n = ", "; _n = "" end if not pre then pre = "" end outf ("{") local p = pre..ind -- prepare list of keys local keys = { boolean = {}, number = {}, string = {} } local total = 0 for key in pairs (tab) do total = total + 1 local t = type(key) if t == "string" then tinsert (keys.string, key) else keys[t][key] = true end end local many = total > 5 if not many then sep_n = sep; _n = " " end outf (_n) -- serialize entries with numeric keys if many then local _f,_s,_v = ipairs(tab) if _f(_s,_v) then outf (p) end end local num = keys.number local ok = false -- entries with automatic index for key, val in ipairs (tab) do value (val, outf, ind, p) outf (sep) num[key] = nil ok = true end if ok and many then outf (_n) end -- entries with explicit index for key in pairs (num) do if many then outf (p) end outf ("[") outf (key) outf ("] = ") value (tab[key], outf, ind, p) outf (sep_n) end -- serialize entries with boolean keys local tr = keys.boolean[true] if tr then outf (format ("%s[true] = ", many and p or '')) value (tab[true], outf, ind, p) outf (sep_n) end local fa = keys.boolean[false] if fa then outf (format ("%s[false] = ", many and p or '')) value (tab[false], outf, ind, p) outf (sep_n) end -- serialize entries with string keys sort (keys.string) for _, key in ipairs (keys.string) do outf (format ("%s[%q] = ", many and p or '', key)) value (tab[key], outf, ind, p) outf (sep_n) end if many then outf (pre) end outf ("}") end -- -- Serializes a value. -- value = function (v, outf, ind, pre) local t = type (v) if t == "string" then outf (format ("%q", v)) elseif t == "number" then outf (tostring(v)) elseif t == "boolean" then outf (tostring(v)) elseif t == "table" then tabledump (v, outf, ind, pre) else outf (format ("%q", tostring(v))) end end ---------------------------------------------------------------------------- cgilua.serialize = tabledump return tabledump genometools-1.5.1/gtdata/modules/external/cgilua/session.lua000066400000000000000000000162451211610345200242440ustar00rootroot00000000000000---------------------------------------------------------------------------- -- Session library. -- -- @release $Id: session.lua,v 1.29 2007/11/21 16:33:20 carregal Exp $ ---------------------------------------------------------------------------- local lfs = require"lfs" local serialize = require"cgilua.serialize" local assert, error, ipairs, _G, loadfile, next, tostring, type = assert, error, ipairs, _G, loadfile, next, tostring, type local format, gsub, strfind, strsub = string.format, string.gsub, string.find, string.sub local tinsert = table.insert local _open = io.open local remove, time = os.remove, os.time local mod, rand, randseed = math.mod, math.random, math.randomseed local attributes, dir, mkdir = lfs.attributes, lfs.dir, lfs.mkdir module ("cgilua.session") local INVALID_SESSION_ID = "Invalid session identification" ---------------------------------------------------------------------------- -- Internal state variables. local root_dir = nil local timeout = 10 * 60 -- 10 minutes -- -- Checks identifier's format. -- local function check_id (id) return id and (strfind (id, "^%d+$") ~= nil) end -- -- Produces a file name based on a session. -- @param id Session identification. -- @return String with the session file name. -- local function filename (id) return format ("%s/%s.lua", root_dir, id) end ---------------------------------------------------------------------------- -- Deletes a session. -- @param id Session identification. ---------------------------------------------------------------------------- function delete (id) if not check_id (id) then return nil, INVALID_SESSION_ID end remove (filename (id)) end -- -- Searches for a file in the root_dir -- local function find (file) local fh = _open (root_dir.."/"..file) if fh then fh:close () return true else return false end end -- -- Creates a new identifier. -- @return New identifier. -- local function new_id () return rand (999999999) end ---------------------------------------------------------------------------- -- Creates a new session identifier. -- @return Session identification. ---------------------------------------------------------------------------- function new () local id = new_id () if find (id..".lua") then repeat id = new_id (id) until not find (id..".lua") randseed (mod (id, 999999999)) end return id end ---------------------------------------------------------------------------- -- Changes the session identificator generator. -- @param func Function. ---------------------------------------------------------------------------- function setidgenerator (func) if type (func) == "function" then new_id = func end end ---------------------------------------------------------------------------- -- Loads data from a session. -- @param id Session identification. -- @return Table with session data or nil in case of error. -- @return In case of error, also returns the error message. ---------------------------------------------------------------------------- function load (id) if not check_id (id) then return nil, INVALID_SESSION_ID end local f, err = loadfile (filename (id)) if not f then return nil, err else return f() end end ---------------------------------------------------------------------------- -- Saves data to a session. -- @param id Session identification. -- @param data Table with session data to be saved. ---------------------------------------------------------------------------- function save (id, data) if not check_id (id) then return nil, INVALID_SESSION_ID end local fh = assert (_open (filename (id), "w+")) fh:write "return " serialize (data, function (s) fh:write(s) end) fh:close() end ---------------------------------------------------------------------------- -- Removes expired sessions. ---------------------------------------------------------------------------- function cleanup () local rem = {} local now = time () for file in dir (root_dir) do local attr = attributes(root_dir.."/"..file) if attr and attr.mode == 'file' then if attr.modification + timeout < now then tinsert (rem, file) end end end for _, file in ipairs (rem) do remove (root_dir.."/"..file) end end ---------------------------------------------------------------------------- -- Changes the session timeout. -- @param t Number of seconds to maintain a session. ---------------------------------------------------------------------------- function setsessiontimeout (t) if type (t) == "number" then timeout = t end end ---------------------------------------------------------------------------- -- Changes the session directory. -- @param path String with the new session directory. ---------------------------------------------------------------------------- function setsessiondir (path) path = gsub (path, "[/\\]$", "") -- Make sure the given path is a directory if not attributes (path, "mode") then assert (mkdir (path)) end -- Make sure it can create a new file in the given directory local test_file = path.."/".._G.cgilua.tmpname() local fh, err = _open (test_file, "w") if not fh then error ("Could not open a file in session directory: ".. tostring(err), 2) end fh:close () remove (test_file) root_dir = path end ---------------------------------------------------------------------------- local ID_NAME = "cgilua session identification" local id = nil ---------------------------------------------------------------------------- -- Destroys the session. ---------------------------------------------------------------------------- function destroy () data = {} -- removes data from session table to avoid recreation by `close' delete (id) end ---------------------------------------------------------------------------- -- Open user session. -- This function should be called before the script is executed. ---------------------------------------------------------------------------- function open () -- Redefine cgilua.mkurlpath to manage the session identification local mkurlpath = _G.cgilua.mkurlpath function _G.cgilua.mkurlpath (script, data) if not data then data = {} end data[ID_NAME] = id return mkurlpath (script, data) end cleanup() id = _G.cgilua.QUERY[ID_NAME] or new() if id then _G.cgilua.QUERY[ID_NAME] = nil _G.cgilua.session.data = load (id) or {} end end ---------------------------------------------------------------------------- -- Close user session. -- This function should be called after the script is executed. ---------------------------------------------------------------------------- function close () if next (_G.cgilua.session.data) then save (id, _G.cgilua.session.data) id = nil end end local already_enabled = false ---------------------------------------------------------------------------- -- Enables the use of sessions. -- This function must be called by every script that needs sessions. -- It just calls the `open' function and register the `close' function -- to be called at the end of the execution. ---------------------------------------------------------------------------- function _G.cgilua.enablesession () if already_enabled then -- avoid misuse when a script calls another one return else already_enabled = true end open () _G.cgilua.addclosefunction (close) end genometools-1.5.1/gtdata/modules/external/cgilua/urlcode.lua000066400000000000000000000066251211610345200242170ustar00rootroot00000000000000---------------------------------------------------------------------------- -- Utility functions for encoding/decoding of URLs. -- -- @release $Id: urlcode.lua,v 1.10 2008/01/21 16:11:32 carregal Exp $ ---------------------------------------------------------------------------- local ipairs, next, pairs, tonumber, type = ipairs, next, pairs, tonumber, type local string = string local table = table module ("cgilua.urlcode") ---------------------------------------------------------------------------- -- Decode an URL-encoded string (see RFC 2396) ---------------------------------------------------------------------------- function unescape (str) str = string.gsub (str, "+", " ") str = string.gsub (str, "%%(%x%x)", function(h) return string.char(tonumber(h,16)) end) str = string.gsub (str, "\r\n", "\n") return str end ---------------------------------------------------------------------------- -- URL-encode a string (see RFC 2396) ---------------------------------------------------------------------------- function escape (str) str = string.gsub (str, "\n", "\r\n") str = string.gsub (str, "([^0-9a-zA-Z ])", -- locale independent function (c) return string.format ("%%%02X", string.byte(c)) end) str = string.gsub (str, " ", "+") return str end ---------------------------------------------------------------------------- -- Insert a (name=value) pair into table [[args]] -- @param args Table to receive the result. -- @param name Key for the table. -- @param value Value for the key. -- Multi-valued names will be represented as tables with numerical indexes -- (in the order they came). ---------------------------------------------------------------------------- function insertfield (args, name, value) if not args[name] then args[name] = value else local t = type (args[name]) if t == "string" then args[name] = { args[name], value, } elseif t == "table" then table.insert (args[name], value) else error ("CGILua fatal error (invalid args table)!") end end end ---------------------------------------------------------------------------- -- Parse url-encoded request data -- (the query part of the script URL or url-encoded post data) -- -- Each decoded (name=value) pair is inserted into table [[args]] -- @param query String to be parsed. -- @param args Table where to store the pairs. ---------------------------------------------------------------------------- function parsequery (query, args) if type(query) == "string" then local insertfield, unescape = insertfield, unescape string.gsub (query, "([^&=]+)=([^&=]*)&?", function (key, val) insertfield (args, unescape(key), unescape(val)) end) end end ---------------------------------------------------------------------------- -- URL-encode the elements of a table creating a string to be used in a -- URL for passing data/parameters to another script -- @param args Table where to extract the pairs (name=value). -- @return String with the resulting encoding. ---------------------------------------------------------------------------- function encodetable (args) if args == nil or next(args) == nil then -- no args or empty args? return "" end local strp = "" for key, vals in pairs(args) do if type(vals) ~= "table" then vals = {vals} end for i,val in ipairs(vals) do strp = strp.."&"..escape(key).."="..escape(val) end end -- remove first & return string.sub(strp,2) end genometools-1.5.1/gtdata/modules/external/md5.lua000066400000000000000000000016141211610345200217740ustar00rootroot00000000000000---------------------------------------------------------------------------- -- $Id: md5.lua,v 1.4 2006/08/21 19:24:21 carregal Exp $ ---------------------------------------------------------------------------- local core = require"md5.core" local string = require"string" local pairs = _G.pairs local assert = _G.assert local md5 = _G.md5 module ("md5") -- export md5.core to md5 for k, v in pairs(core) do if k ~= "_M" and k ~= "_NAME" and k~= "_PACKAGE" then assert(not md5[k]) -- symbol is undefined md5[k] = v -- export symbol end end ---------------------------------------------------------------------------- -- @param k String with original message. -- @return String with the md5 hash value converted to hexadecimal digits function sumhexa (k) k = core.sum(k) return (string.gsub(k, ".", function (c) return string.format("%02x", string.byte(c)) end)) end genometools-1.5.1/gtdata/modules/external/re.lua000066400000000000000000000122711211610345200217160ustar00rootroot00000000000000-- $Id: re.lua,v 1.32 2008/10/09 20:25:06 roberto Exp $ local m = require"lpeg" local _G = _G local tonumber, type, print, error = tonumber, type, print, error local mt = getmetatable(m.P(0)) module "re" local any = m.P(1) -- Pre-defined names Predef = { nl = m.P"\n" } local I = m.P(function (s,i) print(i, s:sub(1, i-1)); return i end) local function getdef (id, Defs) local c = Defs and Defs[id] if not c then error("undefined name: " .. id) end return c end local function patt_error (s, i) local msg = (#s < i + 20) and s:sub(i) or s:sub(i,i+20) .. "..." msg = ("pattern error near '%s'"):format(msg) error(msg, 2) end local function mult (p, n) local np = m.P(true) while n >= 1 do if n%2 >= 1 then np = np * p end p = p * p n = n/2 end return np end local function equalcap (s, i, c) if type(c) ~= "string" then return nil end local e = #c + i if s:sub(i, e - 1) == c then return e else return nil end end local S = (m.S(" \t\n") + "--" * (any - m.S"\n")^0)^0 local name = m.R("AZ", "az") * m.R("AZ", "az", "09")^0 local exp_follow = m.P"/" + ")" + "}" + ":}" + "~}" + name + -1 name = m.C(name) -- identifiers only have meaning in a given environment local Identifier = name * m.Carg(1) local num = m.C(m.R"09"^1) * S / tonumber local String = "'" * m.C((any - "'")^0) * "'" + '"' * m.C((any - '"')^0) * '"' local Cat = "%" * Identifier / function (c,Defs) local cat = Defs and Defs[c] or Predef[c] if not cat then error ("name '" .. c .. "' undefined") end return cat end local Range = m.Cs(any * (m.P"-"/"") * (any - "]")) / m.R local item = Cat + Range + m.C(any) local Class = "[" * (m.C(m.P"^"^-1)) -- optional complement symbol * m.Cf(item * (item - "]")^0, mt.__add) / function (c, p) return c == "^" and any - p or p end * "]" local function adddef (t, k, Defs, exp) if t[k] then error("'"..k.."' already defined as a rule") else t[k] = exp end return t end local function firstdef (n, Defs, r) return adddef({n}, n, Defs, r) end local exp = m.P{ "Exp", Exp = S * ( m.V"Grammar" + m.Cf(m.V"Seq" * ("/" * S * m.V"Seq")^0, mt.__add) ); Seq = m.Cf(m.Cc(m.P"") * m.V"Prefix"^0 , mt.__mul) * (#exp_follow + patt_error); Prefix = "&" * S * m.V"Prefix" / mt.__len + "!" * S * m.V"Prefix" / mt.__unm + m.V"Suffix"; Suffix = m.Cf(m.V"Primary" * S * ( ( m.P"+" * m.Cc(1, mt.__pow) + m.P"*" * m.Cc(0, mt.__pow) + m.P"?" * m.Cc(-1, mt.__pow) + "^" * ( m.Cg(num * m.Cc(mult)) + m.Cg(m.C(m.S"+-" * m.R"09"^1) * m.Cc(mt.__pow)) ) + "->" * S * ( m.Cg(String * m.Cc(mt.__div)) + m.P"{}" * m.Cc(nil, m.Ct) + m.Cg(Identifier / getdef * m.Cc(mt.__div)) ) + "=>" * S * m.Cg(Identifier / getdef * m.Cc(m.Cmt)) ) * S )^0, function (a,b,f) return f(a,b) end ); Primary = "(" * m.V"Exp" * ")" + String / m.P + Class + Cat + "{:" * (name * ":" + m.Cc(nil)) * m.V"Exp" * ":}" / function (n, p) return m.Cg(p, n) end + "=" * name / function (n) return m.Cmt(m.Cb(n), equalcap) end + m.P"{}" / m.Cp + "{~" * m.V"Exp" * "~}" / m.Cs + "{" * m.V"Exp" * "}" / m.C + m.P"." * m.Cc(any) + "<" * name * ">" / m.V; Definition = Identifier * S * '<-' * m.V"Exp"; Grammar = m.Cf(m.V"Definition" / firstdef * m.Cg(m.V"Definition")^0, adddef) / m.P } local pattern = S * exp / m.P * (-any + patt_error) function compile (p, defs) if m.type(p) == "pattern" then return p end -- already compiled local cp = pattern:match(p, 1, defs) if not cp then error("incorrect pattern", 3) end return cp end local mem local fmem local gmem local mt = {__mode = "v"} function match (s, p, i) local cp = mem[p] if not cp then cp = compile(p) mem[p] = cp end return cp:match(s, i or 1) end function find (s, p, i) local cp = fmem[p] if not cp then cp = compile(p) cp = m.P{ m.Cp() * cp + 1 * m.V(1) } fmem[p] = cp end return cp:match(s, i or 1) end function gsub (s, p, rep) gmem[p] = gmem[p] or {} local cp = gmem[p][rep] if not cp then cp = compile(p) cp = m.Cs((cp / rep + 1)^0) gmem[p][rep] = cp end return cp:match(s) end function updatelocale () m.locale(Predef) Predef.a = Predef.alpha Predef.c = Predef.cntrl Predef.d = Predef.digit Predef.g = Predef.graph Predef.l = Predef.lower Predef.p = Predef.punct Predef.s = Predef.space Predef.u = Predef.upper Predef.w = Predef.alnum Predef.x = Predef.xdigit Predef.A = any - Predef.a Predef.C = any - Predef.c Predef.D = any - Predef.d Predef.G = any - Predef.g Predef.L = any - Predef.l Predef.P = any - Predef.p Predef.S = any - Predef.s Predef.U = any - Predef.u Predef.W = any - Predef.w Predef.X = any - Predef.x mem = {} -- restart memoization fmem = {} gmem = {} _G.setmetatable(mem, mt) _G.setmetatable(fmem, mt) _G.setmetatable(gmem, mt) end updatelocale() genometools-1.5.1/gtdata/modules/fileutils.lua000066400000000000000000000046501211610345200214700ustar00rootroot00000000000000--[[ Copyright (c) 2007-2008 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) require 'lfs' -- returns true if file with exists, false otherwise function file_exists(filename) assert(filename) if lfs.attributes(filename, "mode") then return true else return false end end local function has_mode(filename, mode) assert(filename and mode) local attr, err = lfs.attributes(filename, "mode") assert(attr, err) if attr == mode then return true else return false end end -- returns true if file with is a directory, false otherwise function is_dir(filename) assert(filename) return has_mode(filename, "directory") end -- returns true if file with is a regular file, false otherwise function is_regular_file(filename) assert(filename) return has_mode(filename, "file") end local function is_regular_file_with_ending(filename, ending) assert(filename and ending) local pattern = "%" .. ending .. "$" if string.find(filename, pattern) and is_regular_file(filename) then return true else return false end end -- returns true if file with is a header file, false otherwise function is_header(filename) assert(filename) return is_regular_file_with_ending(filename, ".h") end -- returns true if file with is an API header file, false otherwise function is_api_header(filename) assert(filename) return is_regular_file_with_ending(filename, "_api.h") end -- returns true if file with is a Lua file, false otherwise function is_lua_file(filename) assert(filename) return is_regular_file_with_ending(filename, ".lua") end genometools-1.5.1/gtdata/modules/gtdoclib.lua000066400000000000000000000023731211610345200212570ustar00rootroot00000000000000--[[ Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) require 'gtmodulehelper' -- all gtdoc modules which should be loaded local gtdocmodules = { "fileutils", "gtdoclib.docbase", "gtdoclib.docparser", "gtdoclib.docvisitorhtml", "gtdoclib.docvisitorlatex", "gtdoclib.docvisitortxt" } gtmodulehelper.load_modules(gtdocmodules); genometools-1.5.1/gtdata/modules/gtdoclib/000077500000000000000000000000001211610345200205475ustar00rootroot00000000000000genometools-1.5.1/gtdata/modules/gtdoclib/class.lp000066400000000000000000000000741211610345200222120ustar00rootroot00000000000000

Class <%=classname%>

genometools-1.5.1/gtdata/modules/gtdoclib/class_comments.lp000066400000000000000000000001211211610345200241100ustar00rootroot00000000000000<% for _, comment in ipairs(comments) do %>

<%= comment %>

<% end %>
genometools-1.5.1/gtdata/modules/gtdoclib/class_comments_latex.lp000066400000000000000000000001371211610345200253140ustar00rootroot00000000000000<% for _, comment in ipairs(comments) do %> <%= comment %> <% end %> \subsubsection*{Methods} genometools-1.5.1/gtdata/modules/gtdoclib/class_latex.lp000066400000000000000000000000661211610345200234100ustar00rootroot00000000000000\section{Class <%=classname%>} \label{<%=classname%>} genometools-1.5.1/gtdata/modules/gtdoclib/classes.lp000066400000000000000000000001661211610345200225440ustar00rootroot00000000000000

Classes

    <%for _, class in ipairs(classes) do%>
  • <%=class%> <%end%>
genometools-1.5.1/gtdata/modules/gtdoclib/classes_latex.lp000066400000000000000000000002551211610345200237400ustar00rootroot00000000000000\section*{Table of Classes} \begin{itemize} <%for _, class in ipairs(classes) do%> \item Class \texttt{<%=class%>}\dotfill page \pageref{<%=class%>} <%end%> \end{itemize} genometools-1.5.1/gtdata/modules/gtdoclib/docbase.lua000066400000000000000000000164641211610345200226650ustar00rootroot00000000000000--[[ Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) require 'stringext' local w = require 'warning' DocBase = {} function DocBase:new() o = {} o.classes = {} o.classcomments = {} o.modules = {} o.moduledefs = {} o.solefuncs = {} setmetatable(o, self) self.__index = self return o end function DocBase:add_class(classname, comments, be_verbose) assert(classname) if be_verbose then print("class added: " .. classname) end self.classes[classname] = self.classes[classname] or {} self.classcomments[classname] = comments end function DocBase:add_module(modulename, be_verbose) assert(modulename) if be_verbose then print("module added: " .. modulename) end self.modules[modulename] = self.modules[modulename] or {} end function DocBase:add_method(funcret, funcname, funcargs, comment, be_verbose) assert(funcname and comment) local desc = {} -- remove ``GenomeTools_'' prefix which is used to extend exported C classes desc.rval = funcret desc.name = string.gsub(funcname, "^GenomeTools_", "") desc.args = funcargs desc.comment = comment if be_verbose then print("method added: " .. desc.name) end if self.last_module then self.modules[self.last_module][#self.modules[self.last_module] + 1] = desc return end local classname, match funcname = string.lower(string.gsub(desc.name, "_", "")) for class_to_search in pairs(self.classes) do local class_to_match = "^" .. string.lower(string.gsub(class_to_search, "_", "")) if be_verbose then print("match class: " .. class_to_match .. funcname) end match = string.match(funcname, class_to_match) if match then if not classname or string.len(match) > string.len(classname) then classname = class_to_search end end end if be_verbose and classname then print("classname found: " .. classname) end -- if this is a valid classname, try to store method in class if classname and self.classes[classname] then self.classes[classname][#self.classes[classname] + 1] = desc else self.solefuncs[#self.solefuncs + 1] = desc end end local function method_keyword(ast, be_verbose) for i, keyword in ipairs(ast) do if be_verbose then print("Try: " .. keyword) end if keyword == "function" then if be_verbose then print("Return: " .. i) end return i end end return 0 end function DocBase:process_ast(ast, be_verbose) assert(ast) for _, v in ipairs(ast) do if type(v) == "table" then self:process_ast(v, be_verbose) else local keyword = ast[1] if be_verbose then print("keyword: " .. keyword) end if keyword == "class" then o.last_module = nil local comments if #ast > 2 then comments = {} for i = 2, #ast - 1 do if be_verbose then print("add class comment: " .. ast[i]) end comments[#comments + 1] = ast[i] end end self["add_" .. ast[1]](self, ast[#ast], comments, be_verbose) break elseif keyword == "module" then self.last_module = ast[2] self["add_" .. ast[1]](self, ast[2], be_verbose) elseif keyword == "funcdef" then if be_verbose then print("funcdef keyword found") end if self.last_module then desc = {} desc.name = ast[3] desc.comment = ast[2] self.moduledefs[self.last_module] = self.moduledefs[self.last_module] or {} self.moduledefs[self.last_module][#self.moduledefs[self.last_module] + 1] = desc end break elseif keyword == "comment" then local funcpos = method_keyword(ast, be_verbose) local complete_comment = "" if funcpos > 0 then assert(funcpos > 2) assert(#ast == funcpos + 2 or #ast == funcpos + 3) if be_verbose then print("function found!") end if ast[2] == "undefined" then w.warning("undefined comment") else complete_comment = table.concat(ast, "", 2, funcpos-1) complete_comment = string.strip(complete_comment) end self:add_method(ast[funcpos+1], ast[funcpos+2], ast[funcpos+3], complete_comment, be_verbose) break elseif be_verbose then print("no function found!") end end end end end function DocBase:accept(visitor) assert(visitor) local method_names = {} -- visit all classes local sorted_classes = {} for classname in pairs(self.classes) do if #self.classes[classname] > 0 then sorted_classes[#sorted_classes + 1] = classname end end table.sort(sorted_classes) if visitor.visit_classes then visitor:visit_classes(sorted_classes) end -- visit all modules local sorted_modules = {} for modulename in pairs(self.modules) do if #self.modules[modulename] > 0 or #self.moduledefs[modulename] > 0 then sorted_modules[#sorted_modules + 1] = modulename end end table.sort(sorted_modules) if visitor.visit_modules then visitor:visit_modules(sorted_modules) end -- visit sole functions for _, funcdesc in ipairs(self.solefuncs) do if visitor.visit_sole_function then visitor:visit_sole_function(funcdesc) else visitor:visit_method(funcdesc) end method_names[#method_names + 1] = funcdesc.name end -- visit each class for _, classname in ipairs(sorted_classes) do visitor:visit_class(classname, self.classcomments[classname]) -- visit methods for class for _, method in ipairs(self.classes[classname]) do visitor:visit_method(method) method_names[#method_names + 1] = method.name end end -- visit each module if visitor.visit_module then for _, modulename in ipairs(sorted_modules) do visitor:visit_module(modulename) -- visit funcdefs for module if self.moduledefs[modulename] then for _, funcdef in ipairs(self.moduledefs[modulename]) do visitor:visit_funcdef(funcdef) end end -- visit functions for module for _, method in ipairs(self.modules[modulename]) do visitor:visit_method(method) method_names[#method_names + 1] = method.name end end end -- visit all method names (for index construction) if visitor.visit_index then table.sort(method_names) visitor:visit_index(method_names) end end genometools-1.5.1/gtdata/modules/gtdoclib/docparser.lua000066400000000000000000000173111211610345200232370ustar00rootroot00000000000000--[[ Copyright (c) 2008, 2011 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) require 'lpeg' require 'fileutils' DocParser = {} -- Common Lexical Elements local Any = lpeg.P(1) local Newline = lpeg.S("\n") local Whitespace = lpeg.S(" \t\n") local OptionalSpace = Whitespace^0 local Space = Whitespace^1 local Semicolon = lpeg.S(";") local DefineSeparator = lpeg.S("\\") -- Lexical Elements of Lua local LuaLongCommentStart = lpeg.P("--[[") local LuaLongCommentEnd = lpeg.P("]]") local LuaLongComment = lpeg.Cc("long comment") * lpeg.C(LuaLongCommentStart * (Any - LuaLongCommentEnd)^0 * LuaLongCommentEnd) local LuaShortCommentStart = lpeg.P("--") local LuaShortCommentEnd = Newline local LuaShortCommentLine = OptionalSpace * LuaShortCommentStart * lpeg.C((Any - LuaShortCommentEnd)^0) * LuaShortCommentEnd local LuaShortComment = lpeg.Cc("comment") * LuaShortCommentLine^1 local LuaOptionalComment = LuaShortComment + lpeg.Cc("comment") * lpeg.Cc("undefined") local LuaCommentStart = LuaLongCommentStart + LuaShortCommentStart local LuaEnd = lpeg.P("end") local LuaLocalFunction = lpeg.P("local") * OptionalSpace * lpeg.P("function") * OptionalSpace * lpeg.P(Any - lpeg.P("("))^1 * lpeg.P("(") * (Any - lpeg.P(")"))^0 * lpeg.P(")") local LuaGlobalFunction = -lpeg.P("local") * OptionalSpace * lpeg.C(lpeg.P("function")) * OptionalSpace * lpeg.Cc("") * lpeg.C(lpeg.P(Any - lpeg.P("("))^1) * lpeg.P("(") * lpeg.C((Any - lpeg.P(")"))^0) * lpeg.P(")") local ExportLuaMethod = lpeg.Ct(LuaOptionalComment * LuaGlobalFunction) local CodeStop = LuaCommentStart + LuaLocalFunction + LuaGlobalFunction local LuaCode = lpeg.Cc("code") * lpeg.C((Any - CodeStop)^1) -- Lexical Elements of (Lua) C local Character = lpeg.R("AZ", "az") + lpeg.R("09") + lpeg.P("_") + lpeg.P("*") local CCommentStart = lpeg.P("/*") local CCommentEnd = lpeg.P("*/") local ExportLuaCComment = CCommentStart * lpeg.P(" exports the ") * lpeg.Ct(lpeg.Cc("class") * lpeg.C(Character^1)) * (Any - lpeg.P("to Lua:"))^1 * lpeg.P("to Lua:") * ExportLuaMethod^0 * (Any - CCommentEnd)^0 * CCommentEnd local CComment = CCommentStart * (Any - CCommentEnd)^0 * CCommentEnd local CCode = (Any - CCommentStart)^1 -- Lexical Elements of (pure) C local Ifndef = lpeg.P("#ifndef") * Whitespace * Character^1 * Newline local Define = lpeg.P("#define") * Whitespace * Character^1 * Newline local Endif = lpeg.P("#endif") * Newline^0 local Include = lpeg.P("#include") * (Any - Newline)^1 * Newline local ClassTypedef = lpeg.Ct(lpeg.Cc("class") * (CCommentStart * lpeg.C((Any - CCommentEnd)^0) * CCommentEnd)^0 * Newline^0 * ((lpeg.P("typedef") * Space * (lpeg.P("struct") + lpeg.P("enum")) * Space * Character^1 * Space * lpeg.C(Character^1)) + (lpeg.P("typedef") * Space * lpeg.P("char*") * Space * lpeg.C(lpeg.P("GtTagValueMap")))) * OptionalSpace * Semicolon) local FunctionTypedef = lpeg.Ct(lpeg.Cc("funcdef") * (CCommentStart * lpeg.C((Any - CCommentEnd)^0) * CCommentEnd) * Newline^0 * lpeg.P("typedef") * Space * lpeg.C((Any - Semicolon)^1) * Semicolon) local TypedefStruct = lpeg.P("typedef struct") * (Any - Semicolon)^1 * Semicolon local OptionalWord = (Character^1 * Space)^-1 local Function = lpeg.Cc("function") * lpeg.C(Character^1 * Space * OptionalWord) * lpeg.C(lpeg.P(Any - lpeg.P("("))^1) * lpeg.P("(") * lpeg.C((Any - lpeg.P(")"))^1) * lpeg.P(")") * (Any - Semicolon)^0 * Semicolon local ExportedComment = lpeg.Cc("comment") * CCommentStart * lpeg.C((Any - CCommentEnd)^0) * CCommentEnd local ExportedDefine = lpeg.Cc("function") * lpeg.C("#define") * Space * lpeg.C(lpeg.P(Any - lpeg.P("("))^1) * lpeg.P("(") * lpeg.C((Any - lpeg.P(")"))^1) * lpeg.P(")") * OptionalSpace * DefineSeparator local ExportedPlainDefine = lpeg.Cc("function") * lpeg.C("#define") * Space * lpeg.C(lpeg.P(Any - (DefineSeparator + Space))^1) * OptionalSpace * DefineSeparator local ExportCMethod = lpeg.Ct(ExportedComment * Newline^0 * Function) local ExportCDefine = lpeg.Ct(ExportedComment * Newline^0 * (ExportedDefine+ ExportedPlainDefine)) local ModuleDef = lpeg.Ct(lpeg.Cc("module") * CCommentStart * Space * lpeg.C(Character^1) * Space * lpeg.P("module") * Space * CCommentEnd) -- Lua Grammar local Elem, Start = lpeg.V"Elem", lpeg.V"Start" local LuaGrammar = lpeg.P{ Start, Start = lpeg.Ct(Elem^0); Elem = ExportLuaMethod + LuaLongComment + LuaShortComment + Space + LuaLocalFunction + LuaCode; } LuaGrammar = LuaGrammar * -1 -- Lua C Grammar local LuaCGrammar = lpeg.P{ Start, Start = lpeg.Ct(Elem^0); Elem = lpeg.Ct(ExportLuaCComment) + CComment + Space + CCode; } LuaCGrammar = LuaCGrammar * -1 -- CGrammar local CGrammar = lpeg.P{ Start, -- Start = lpeg.Ct(CComment * Newline^0 * Ifndef * Define * Elem^0 * Endif); Start = lpeg.Ct(CComment * Newline^0 * Ifndef * Define * Elem^0); Elem = ClassTypedef + ModuleDef + ExportCDefine + ExportCMethod + Space + Include + lpeg.C(TypedefStruct) + FunctionTypedef + CCode + CComment; } CGrammar = CGrammar * -1 function DocParser:new() o = {} o.lua_c_pattern = LuaCGrammar o.lua_pattern = LuaGrammar o.c_pattern = CGrammar setmetatable(o, self) self.__index = self return o end function DocParser:parse(filename, be_verbose, is_lua) assert(filename) assert(is_header(filename) or is_lua_file(filename)) if be_verbose then print("parsing " .. filename) end local file, err = io.open(filename, "r") assert(file, err) local filecontent = file:read("*a") if is_header(filename) then if is_lua then return lpeg.match(self.lua_c_pattern, filecontent) else return lpeg.match(self.c_pattern, filecontent) end else assert(is_lua_file(filename)) return lpeg.match(self.lua_pattern, filecontent) end end genometools-1.5.1/gtdata/modules/gtdoclib/docvisitorhtml.lua000066400000000000000000000066701211610345200243350ustar00rootroot00000000000000--[[ Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) lp = require 'cgilua/lp' DocVisitorHTML = {} local template_dir function DocVisitorHTML:new(template_path, header) assert(template_path and header) template_dir = template_path o = {} setmetatable(o, self) self.__index = self o.header = header return o end local function include(template, env) assert(template) local template_path = template_dir .. template env = env or {} env.io = io env.os = os env.ipairs = ipairs return lp.include(template_path, env) end local function codify(str) assert(str) local res = string.gsub(str, "<<(.-)>>", "@@%1@@") res = string.gsub(res, "<(.-)>", "%1") res = string.gsub(res, "@@(.-)@@", "<%1>") res = string.gsub(res, " ([%a_][%a%d_%.]-%(%))", " %1") res = string.gsub(res, "___(.-)___", "%1") return string.gsub(res, "__(.-)__", "%1") end local function paragraphify(str) assert(str) return string.gsub(str, "\n\n", "

") end function DocVisitorHTML:show_header() include(self.header) end function DocVisitorHTML:visit_classes(classes) assert(classes) include("classes.lp", { classes = classes }) end function DocVisitorHTML:visit_modules(modules) assert(modules) include("modules.lp", { modules = modules }) end function DocVisitorHTML:visit_class(classname, comments) assert(classname) include("class.lp", { classname = classname }) if comments then for i, _ in ipairs(comments) do comments[i] = paragraphify(codify(comments[i])) end include("class_comments.lp", { comments = comments }) end end function DocVisitorHTML:visit_module(modulename) assert(modulename) include("module.lp", { modulename = modulename }) end local sole_function_visited = false function DocVisitorHTML:visit_sole_function(desc) if not sole_function_visited then include("sole_function.lp") sole_function_visited = true end self:visit_method(desc) end function DocVisitorHTML:visit_method(desc) assert(desc) local name local prototype = desc.name if desc.rval then name = desc.rval .. " " .. desc.name else name = desc.rval end include("method.lp", { name = name, args = desc.args, comment = codify(desc.comment), prototype = prototype }) end function DocVisitorHTML:visit_funcdef(desc) assert(desc) include("funcdef.lp", { name = desc.name, comment = codify(desc.comment) }) end function DocVisitorHTML:visit_index(names) assert(names) include("index.lp", { names = names }) end function DocVisitorHTML:show_footer() include("footer.lp") end genometools-1.5.1/gtdata/modules/gtdoclib/docvisitorlatex.lua000066400000000000000000000077001211610345200245010ustar00rootroot00000000000000--[[ Copyright (c) 2008 Sascha Steinbiss Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) lp = require 'cgilua/lp' DocVisitorLaTeX = {} local template_dir function DocVisitorLaTeX:new(template_path, header) assert(template_path and header) template_dir = template_path o = {} setmetatable(o, self) self.__index = self o.header = header return o end local function include(template, env) assert(template) local template_path = template_dir .. template env = env or {} env.io = io env.os = os env.ipairs = ipairs return lp.include(template_path, env) end local function trim(s) return (string.gsub(s, "^%s*(.-)%s*$", "%1")) end local function codify(str) if (str == nil) then str = "" end str = trim(str) local res = string.gsub(str, "\\", "$\\backslash$") res = string.gsub(res, "<<([^ ]-)>>", "@@%1@@") res = string.gsub(res, "<([^ ]-)>", "\\texttt{%1}") res = string.gsub(res, "@@([^ ]-)@@", "\\texttt{<%1>}") res = string.gsub(res, "\->", "$\\to$") res = string.gsub(res, ">", "$>$") res = string.gsub(res, "<", "$<$") res = string.gsub(res, " ([%a_][%a%d_%.]-%(%))", "\\texttt{%1}") res = string.gsub(res, "___(.-)___", " \\textbf{%1}") res = string.gsub(res, "__(.-)__", "\\emph{%1}") res = string.gsub(res, "_", "\\_") res = string.gsub(res, "#", "\\#") return res end local function paragraphify(str) assert(str) return string.gsub(str, "\n\n", "\\\\") end function DocVisitorLaTeX:show_header() include(self.header) end function DocVisitorLaTeX:visit_classes(classes) assert(classes) include("classes_latex.lp", { classes = classes }) end function DocVisitorLaTeX:visit_modules(modules) assert(modules) if (#modules == 0) then return end include("modules_latex.lp", { modules = modules }) end function DocVisitorLaTeX:visit_class(classname, comments) assert(classname) include("class_latex.lp", { classname = codify(classname) }) if comments then for i, _ in ipairs(comments) do comments[i] = paragraphify(codify(comments[i])) end include("class_comments_latex.lp", { comments = comments }) end end function DocVisitorLaTeX:visit_module(modulename) assert(modulename) include("module_latex.lp", { modulename = modulename }) end local sole_function_visited = false function DocVisitorLaTeX:visit_sole_function(desc) if not sole_function_visited then include("sole_function_latex.lp") sole_function_visited = true end self:visit_method(desc) end function DocVisitorLaTeX:visit_method(desc) assert(desc) local name local prototype = desc.name if desc.rval then name = desc.rval .. " " .. desc.name else name = desc.rval end include("method_latex.lp", { name = codify(name), args = codify(desc.args), comment = paragraphify(codify(desc.comment)), prototype = codify(prototype) }) end function DocVisitorLaTeX:visit_funcdef(desc) assert(desc) include("funcdef_latex.lp", { name = codify(desc.name), comment = paragraphify(codify(desc.comment)) }) end function DocVisitorLaTeX:visit_index(names) end function DocVisitorLaTeX:show_footer() include("footer_latex.lp") end genometools-1.5.1/gtdata/modules/gtdoclib/docvisitortxt.lua000066400000000000000000000037441211610345200242070ustar00rootroot00000000000000--[[ Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) DocVisitorTxt = {} function DocVisitorTxt:new() o = {} setmetatable(o, self) self.__index = self return o end function DocVisitorTxt:visit_modules(modules) print("modules:") for _, mod in ipairs(modules) do print(mod) end end function DocVisitorTxt:visit_class(classname, comments) assert(classname) io.write(string.format("class: %s\n", classname)) if comments then print("comments: " .. table.concat(comments)) end end function DocVisitorTxt:visit_module(modulename) assert(modulename) io.write(string.format("module: %s\n", modulename)) end function DocVisitorTxt:visit_method(desc) assert(desc) if desc.args then io.write(string.format("method:\n%s\n%s(%s)\n", desc.comment, desc.name, desc.args)) else io.write(string.format("method:\n%s\n%s\n", desc.comment, desc.name)) end end function DocVisitorTxt:visit_funcdef(desc) assert(desc) io.write(string.format("fundef:\n%s\n%s\n", desc.comment, desc.name)) end function DocVisitorTxt:visit_index(names) assert(names) print("index:") for _, name in ipairs(names) do print(name) end end genometools-1.5.1/gtdata/modules/gtdoclib/footer.lp000066400000000000000000000013771211610345200224120ustar00rootroot00000000000000

genometools-1.5.1/gtdata/modules/gtdoclib/footer_latex.lp000066400000000000000000000000011211610345200235660ustar00rootroot00000000000000 genometools-1.5.1/gtdata/modules/gtdoclib/funcdef.lp000066400000000000000000000000621211610345200225140ustar00rootroot00000000000000<%=name%>

<%=comment%>

genometools-1.5.1/gtdata/modules/gtdoclib/funcdef_latex.lp000066400000000000000000000002001211610345200237030ustar00rootroot00000000000000\begin{minipage}{\textwidth} \vspace{3mm} \texttt{<%=name%>}\\[-.4cm] \hangindent3em \hangafter=0 <%=comment%> \end{minipage} genometools-1.5.1/gtdata/modules/gtdoclib/gtscript_header.lp000066400000000000000000000053251211610345200242600ustar00rootroot00000000000000 gtscript documentation

gtscript documentation

This document describes the gtscript API. gtscript is basically Lua (an embeddable scripting language) plus parts of the GenomeTools C libraries exported to Lua. Because the GenomeTools binary gt contains an embedded Lua interpreter, gtscript files can be executed with the gt binary. The parts of the GenomeTools C libraries exported to Lua (the gtscript API) are described here, for a documentation of Lua itself and its APIs, please refer to the Lua reference manual.

See the index for an alphabetical list of all available interfaces.

Notes

  • You have to add require 'gtlua' to your script in order to load the parts of the gtscript API which are implemented in gtscript itself.
  • By default, all functions of the gtscript API are contained in the gt table. That is, you have to prepend all functions calls with ``gt.''. For example, write gt.show() to call the show() function documented below. You can use gt.export() or gt.re() to export the gt table to the global environment, which makes the prepending unnecessary (but clutters your global environment).
  • If a function is documented as ``returns an array'', this means that the function returns a table where only consecutive integer keys from 1 on are used and which can be traversed with the ipairs() function.
genometools-1.5.1/gtdata/modules/gtdoclib/gtscript_header_latex.lp000066400000000000000000000030131211610345200254450ustar00rootroot00000000000000\chapter{gtscript Reference} This chapter describes the \texttt{gtscript} API. \texttt{gtscript} is basically Lua (an embeddable scripting language) plus parts of the \emph{GenomeTools} C libraries exported to Lua. Because the \emph{GenomeTools} binary \texttt{gt} contains an embedded Lua interpreter, \texttt{gtscript} files can be executed with the \texttt{gt} binary. The parts of the \emph{GenomeTools} C libraries exported to Lua (the gtscript API) are described here, for a documentation of Lua itself and its APIs, please refer to the Lua reference manual. See the index for an alphabetical list of all available interfaces. \section*{Notes} \begin{itemize} \item You have to add \texttt{require 'gtlua'} to your script in order to load the parts of the \texttt{gtscript} API which are implemented in \texttt{gtscript} itself. \item By default, all functions of the \texttt{gtscript} API are contained in the \texttt{gt} table. That is, you have to prepend all functions calls with ``\texttt{gt}.''. For example, write \texttt{gt.show()} to call the \texttt{show()} function documented below. You can use \texttt{gt.export()} or \texttt{gt.re()} to export the \texttt{gt} table to the global environment, which makes the prepending unnecessary (but clutters your global environment). \item If a function is documented as ``returns an array'', this means that the function returns a table where only consecutive integer keys from 1 on are used and which can be traversed with the \texttt{ipairs()} function. \end{itemize} genometools-1.5.1/gtdata/modules/gtdoclib/index.lp000066400000000000000000000002101211610345200222040ustar00rootroot00000000000000

Index

<%for _, name in ipairs(names) do%> <%= name%>
<%end%> genometools-1.5.1/gtdata/modules/gtdoclib/libgenometools_header.lp000066400000000000000000000024101211610345200254330ustar00rootroot00000000000000 GenomeTools C API

GenomeTools C API

This document describes the GenomeTools C API (that is, all public interfaces which are part of libgenometools).

See the index for an alphabetical list of all available interfaces.

genometools-1.5.1/gtdata/modules/gtdoclib/libgenometools_header_latex.lp000066400000000000000000000000301211610345200266240ustar00rootroot00000000000000\chapter{API Reference} genometools-1.5.1/gtdata/modules/gtdoclib/method.lp000066400000000000000000000002531211610345200223640ustar00rootroot00000000000000 <%=func%>

<%=comment%>

genometools-1.5.1/gtdata/modules/gtdoclib/method_latex.lp000066400000000000000000000002761211610345200235660ustar00rootroot00000000000000\begin{minipage}{\textwidth} \vspace{3mm} \texttt{<%=name%><%if args ~= "" then %>(\textcolor{arggrey}{<%=args%>})<%end%>}\\[-.4cm] \hangindent3em \hangafter=0 <%=comment%> \end{minipage} genometools-1.5.1/gtdata/modules/gtdoclib/module.lp000066400000000000000000000000771211610345200223750ustar00rootroot00000000000000

Module <%=modulename%>

genometools-1.5.1/gtdata/modules/gtdoclib/module_latex.lp000066400000000000000000000000711211610345200235640ustar00rootroot00000000000000\section{Module <%=modulename%>} \label{<%=modulename%>} genometools-1.5.1/gtdata/modules/gtdoclib/modules.lp000066400000000000000000000001711211610345200225530ustar00rootroot00000000000000

Modules

    <%for _, module in ipairs(modules) do%>
  • <%=module%> <%end%>
genometools-1.5.1/gtdata/modules/gtdoclib/modules_latex.lp000066400000000000000000000002611211610345200237500ustar00rootroot00000000000000\section*{Table of Modules} \begin{itemize} <%for _, module in ipairs(modules) do%> \item Module \texttt{<%=module%>}\dotfill page \pageref{<%=module%>} <%end%> \end{itemize} genometools-1.5.1/gtdata/modules/gtdoclib/sole_function.lp000066400000000000000000000000301211610345200237440ustar00rootroot00000000000000

Sole functions

genometools-1.5.1/gtdata/modules/gtdoclib/sole_function_latex.lp000066400000000000000000000000311211610345200251420ustar00rootroot00000000000000\section{Sole functions} genometools-1.5.1/gtdata/modules/gtlua.lua000066400000000000000000000043161211610345200206030ustar00rootroot00000000000000--[[ Copyright (c) 2007-2008 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] local modname = ... module(modname, package.seeall) require 'gt' -- all GenomeTools modules which should be loaded local gtmodules = { "fileutils", "gtlua.feature_index", "gtlua.genome_features", "gtlua.genome_node", "gtlua.helper", "gtlua.range" } -- everything that will be exported to the gt table local gtexport = {} local function load_module(mod) assert(mod) local t = require(mod) for k, v in pairs(t) do if k ~= "_M" and k ~= "_NAME" and k~= "_PACKAGE" then assert(not gtexport[k]) -- symbol is undefined gtexport[k] = v -- record symbol for export end end end local function load_modules(modules) assert(modules) -- load all modules for _, mod in ipairs(modules) do load_module(mod) end -- export all symbols for k, v in pairs(gtexport) do assert(not gt[k]) -- symbol is undefined gt[k] = v -- export symbol end end -- Reload module. function reload() -- remove all exported symbols from gt table for k in pairs(gtexport) do gt[k] = nil end -- mark all packages as unloaded for _, mod in ipairs(gtmodules) do package.loaded[mod] = nil end package.loaded[modname] = nil -- reload require(modname) end -- register reload() function in gt table gt.reload = reload load_modules(gtmodules) genometools-1.5.1/gtdata/modules/gtlua/000077500000000000000000000000001211610345200200745ustar00rootroot00000000000000genometools-1.5.1/gtdata/modules/gtlua/feature_index.lua000066400000000000000000000103071211610345200234220ustar00rootroot00000000000000--[[ Copyright (c) 2007-2008 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) require "gtlua.genome_features" -- XXX: remove if statement if libannotationsketch is always compiled in if GenomeTools_feature_index then -- Computes the coverage for the sequence ID . The optional -- parameter denotes the maximal distance two features can be apart without -- creating a new Range. Returns an array of Ranges denoting parts the of -- covered by features. function GenomeTools_feature_index:get_coverage(seqid, maxdist) assert(seqid) local maxdist = maxdist or 0 local features = self:get_features_for_seqid(seqid) local starpos, endpos local minstartpos = nil local maxendpos = nil local ranges = {} local coverage = {} -- collect all feature ranges for i, feature in ipairs(features) do ranges[#ranges+1] = feature:get_range() end -- sort feature ranges ranges = gt.ranges_sort(ranges) -- compute and store coverage for i, range in ipairs(ranges) do startpos, endpos = range:get_start(), range:get_end() if i == 1 then minstartpos = startpos maxendpos = endpos else -- assert(startpos >= minstartpos) if (startpos > maxendpos + maxdist) then -- new region started coverage[#coverage+1] = gt.range_new(minstartpos, maxendpos) minstartpos = startpos maxendpos = endpos else -- continue old region maxendpos = (endpos > maxendpos) and endpos or maxendpos end end end -- add last region coverage[#coverage+1] = gt.range_new(minstartpos, maxendpos) return coverage end -- Returns an array of Ranges denoting parts of which are covered by -- at least one marked feature. Internally, get_coverage() is called and the -- is passed along. function GenomeTools_feature_index:get_marked_regions(seqid, maxdist) assert(seqid, "missing seqid argument") local coverage = self:get_coverage(seqid, maxdist) local marked = {} for _,range in ipairs(coverage) do local features = feature_index:get_features_for_range(seqid, range) if gt.features_contain_marked(features) then marked[#marked+1] = range end end return marked end -- Render to PNG file for in with optional . -- If no is given os.tmpname() is called to create one. -- Returns name of written PNG file. function GenomeTools_feature_index:render_to_png(seqid, range, png_file, width) assert(seqid and range) png_file = png_file or os.tmpname() if not width then width = 1600 end local diagram = gt.diagram_new(self, seqid, range) local render = gt.render_new() render:to_png(diagram, png_file, width) return png_file end -- Show all sequence IDs. function GenomeTools_feature_index:show_seqids() for _,seqid in ipairs(feature_index:get_seqids()) do print(seqid) end end -- Returns all features from . function GenomeTools_feature_index:get_all_features() local seqids = self:get_seqids() local all_features = {} for _, seqid in ipairs(seqids) do local seqid_features = self:get_features_for_seqid(seqid) for _, feature in ipairs(seqid_features) do all_features[#all_features + 1] = feature end end return all_features end end genometools-1.5.1/gtdata/modules/gtlua/genome_features.lua000066400000000000000000000077761211610345200237700ustar00rootroot00000000000000--[[ Copyright (c) 2007-2008 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) -- Returns true if the given array of contains a marked feature, -- false otherwise. function features_contain_marked(features) assert(features) for _, feature in ipairs(features) do if feature:contains_marked() then return true end end return false end -- Print the given array of to stdout. function features_show(features) assert(features) local gff3_visitor = gt.gff3_visitor_new() for _, features in ipairs(features) do features:show(gff3_visitor) end end -- Return all marked (an array) as an array or nil if -- contains no marked features. function features_get_marked(features) assert(features) local marked_features = nil if features_contain_marked(features) then marked_features = {} for _, feature in ipairs(features) do if feature:contains_marked() then local gni = gt.genome_node_iterator_new(feature) local node = gni:next() while node do if node:is_marked() then marked_features[#marked_features + 1] = node end node = gni:next() end end end end return marked_features end -- Print all marked (an array) to stdout. function features_show_marked(features) assert(features) if features_contain_marked(features) then for _, feature in ipairs(features) do feature:show_marked() end end end local function create_gene_from_mRNA(mRNA) assert(mRNA) assert(mRNA:get_type() == "mRNA") local gene = gt.genome_feature_new(mRNA:get_seqid(), "gene", mRNA:get_range(), mRNA:get_strand()) gene:set_source(mRNA:get_source()) local gni = gt.genome_node_iterator_new_direct(mRNA) local old_child = gni:next() while (old_child) do local new_child = gt.genome_feature_new(old_child:get_seqid(), old_child:get_type(), old_child:get_range(), old_child:get_strand()) new_child:set_source(old_child:get_source()) gene:is_part_of_genome_node(new_child) old_child = gni:next() end return gene end -- Return an array of genome features which contains a separate gene feature for -- each mRNA in . function features_mRNAs2genes(in_features) assert(in_features) local out_features = {} for _, in_feature in ipairs(in_features) do if in_feature:get_type() == "gene" then local gni = gt.genome_node_iterator_new_direct(in_feature) local child = gni:next() while (child) do if child:get_type() == "mRNA" then out_features[#out_features + 1] = create_gene_from_mRNA(child) end child = gni:next() end end end return out_features end -- Return an array with the sequences of the given features. function features_extract_sequences(features, type, join, region_mapping) local sequences = {} for _, feature in ipairs(features) do local sequence = feature:extract_sequence(type, join, region_mapping) if type then sequences[#sequences + 1] = sequence end end return sequences end genometools-1.5.1/gtdata/modules/gtlua/genome_node.lua000066400000000000000000000026551211610345200230660ustar00rootroot00000000000000--[[ Copyright (c) 2007-2008 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) -- Show genome node on stdout (using the optional ). function GenomeTools_genome_node:show(gff3_visitor) local gff3_visitor = gff3_visitor or gt.gff3_visitor_new() self:accept(gff3_visitor) end -- Show marked parts of genome node on stdout. function GenomeTools_genome_node:show_marked() if self:contains_marked() then local gni = gt.genome_node_iterator_new(self) local gn = gni:next() while gn do if gn:is_marked() then gn:output_leading() print("") end gn = gni:next() end end end genometools-1.5.1/gtdata/modules/gtlua/helper.lua000066400000000000000000000035741211610345200220670ustar00rootroot00000000000000--[[ Copyright (c) 2007-2008 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) -- Export the content of table to the global environment. function export() for k,v in pairs(gt) do _G[k] = v end end -- Call external 'display' program for file . function display(filename) assert(filename and gt.file_exists(filename)) if os.execute("display " .. filename) ~= 0 then io.stdout:write("\nexit (type 'y' to confirm)? ") if io.stdin:read() == "y" then print("bye") os.exit(0) end end end -- Show all keys and values of table . function show_table(tbl) assert(tbl) for k,v in pairs(tbl) do print(string.format("k=%s, v=%s", k, type(v))) end end -- Show content of the table. function show(all) local a = {} for k in pairs(gt) do a[#a+1] = k end table.sort(a) for i,v in pairs(a) do if all then print(string.format("%s (%s)", v, type(gt[v]))) else print(v) end end end -- Reload the module and export its content to the global environment. function re() gt.reload() gt.export() end genometools-1.5.1/gtdata/modules/gtlua/range.lua000066400000000000000000000020021211610345200216650ustar00rootroot00000000000000--[[ Copyright (c) 2007-2008 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) -- Show range on stdout. function GenomeTools_range:show() print(string.format("%u, %u", self:get_start(), self:get_end())) end genometools-1.5.1/gtdata/modules/gtmodulehelper.lua000066400000000000000000000021651211610345200225070ustar00rootroot00000000000000--[[ Copyright (c) 2007-2008 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) function load_modules(modules) assert(modules) for _, mod in ipairs(modules) do local t = require(mod) for k, v in pairs(t) do if k ~= "_M" and k ~= "_NAME" and k~= "_PACKAGE" then _G[k] = v end end end end genometools-1.5.1/gtdata/modules/stringext.lua000066400000000000000000000020651211610345200215150ustar00rootroot00000000000000--[[ Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] require 'string' -- Removes all leading and trailing spaces from and returns the result. function string.strip(str) local res = string.gsub(str, "^%s+", "") res = string.gsub(res, "%s+$", "") return res end genometools-1.5.1/gtdata/modules/warning.lua000066400000000000000000000017611211610345200211350ustar00rootroot00000000000000--[[ Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] module(..., package.seeall) function warning(warnmsg, ...) assert(warnmsg) io.stderr:write(string.format("warning: " .. warnmsg .. "\n", ...)) end genometools-1.5.1/gtdata/obo_files/000077500000000000000000000000001211610345200172515ustar00rootroot00000000000000genometools-1.5.1/gtdata/obo_files/so-xp.obo000066400000000000000000026746721211610345200210500ustar00rootroot00000000000000format-version: 1.2 date: 14:11:2012 16:46 saved-by: kareneilbeck auto-generated-by: OBO-Edit 2.1.1-beta7 subsetdef: biosapiens "biosapiens protein feature ontology" subsetdef: DBVAR "database of genomic structural variation" subsetdef: SOFA "SO feature annotation" synonymtypedef: aa1 "amino acid 1 letter code" synonymtypedef: aa3 "amino acid 3 letter code" synonymtypedef: AAMOD "amino acid modification" synonymtypedef: BS "biosapiens" synonymtypedef: dbsnp "dbsnp variant terms" synonymtypedef: dbvar "DBVAR" synonymtypedef: ebi_variants "ensembl variant terms" synonymtypedef: RNAMOD "RNA modification" EXACT default-namespace: sequence remark: autogenerated-by: DAG-Edit version 1.417\nsaved-by: eilbeck\ndate: Tue May 11 15:18:44 PDT 2004\nversion: $Revision: 1.45 $ ontology: so-xp.obo [Term] id: SO:0000000 name: Sequence_Ontology subset: SOFA is_obsolete: true [Term] id: SO:0000001 name: region def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke] subset: SOFA synonym: "sequence" EXACT [] is_a: SO:0000110 ! sequence_feature disjoint_from: SO:0000699 ! junction [Term] id: SO:0000002 name: sequence_secondary_structure def: "A folded sequence." [SO:ke] synonym: "sequence secondary structure" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000003 name: G_quartet def: "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract] synonym: "G quartet" EXACT [] synonym: "G tetrad" EXACT [] synonym: "G-quadruplex" EXACT [] synonym: "G-quartet" EXACT [] synonym: "G-tetrad" EXACT [] synonym: "G_quadruplex" EXACT [] synonym: "guanine tetrad" EXACT [] xref: http://en.wikipedia.org/wiki/G-quadruplex "wiki" is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000004 name: interior_coding_exon subset: SOFA synonym: "interior coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:0000005 name: satellite_DNA def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "satellite DNA" EXACT [] xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki" is_a: SO:0000705 ! tandem_repeat [Term] id: SO:0000006 name: PCR_product def: "A region amplified by a PCR reaction." [SO:ke] comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406. subset: SOFA synonym: "amplicon" RELATED [] synonym: "PCR product" EXACT [] xref: http://en.wikipedia.org/wiki/RAPD "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000007 name: read_pair def: "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls] subset: SOFA synonym: "mate pair" EXACT [] synonym: "read-pair" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000149 ! contig relationship: part_of SO:0001790 ! paired_end_fragment [Term] id: SO:0000008 name: gene_sensu_your_favorite_organism is_obsolete: true [Term] id: SO:0000009 name: gene_class is_obsolete: true [Term] id: SO:0000010 name: protein_coding synonym: "protein-coding" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000011 name: non_protein_coding synonym: "non protein-coding" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000012 name: scRNA_primary_transcript def: "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html] synonym: "scRNA primary transcript" EXACT [] synonym: "scRNA transcript" EXACT [] synonym: "small cytoplasmic RNA" RELATED [] synonym: "small cytoplasmic RNA transcript" EXACT [] synonym: "small_cytoplasmic_RNA" RELATED [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000013 name: scRNA def: "A small non coding RNA sequence, present in the cytoplasm." [SO:ke] subset: SOFA synonym: "small cytoplasmic RNA" EXACT [] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000012 ! scRNA_primary_transcript [Term] id: SO:0000014 name: INR_motif def: "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867] comment: Binds TAF1, TAF2. synonym: "DMp2" RELATED [] synonym: "initiator" EXACT [] synonym: "initiator motif" EXACT [] synonym: "INR motif" EXACT [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter [Term] id: SO:0000015 name: DPE_motif def: "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867] comment: Binds TAF6, TAF9. synonym: "CRWMGCGWKCGCTTS" NARROW [] synonym: "downstream core promoter element" EXACT [] synonym: "DPE motif" EXACT [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter [Term] id: SO:0000016 name: BREu_motif def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867] comment: Binds TFIIB. synonym: "B-recognition element" EXACT [] synonym: "BRE motif" EXACT [] synonym: "BREu" RELATED [] synonym: "BREu motif" EXACT [] synonym: "TFIIB recognition element" RELATED [] synonym: "transcription factor B-recognition element" EXACT [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter [Term] id: SO:0000017 name: PSE_motif def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739] synonym: "proximal sequence element" EXACT [] synonym: "PSE motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000167 ! promoter [Term] id: SO:0000018 name: linkage_group def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046] synonym: "linkage group" EXACT [] xref: http://en.wikipedia.org/wiki/Linkage_group "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000020 name: RNA_internal_loop def: "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke] synonym: "RNA internal loop" EXACT [] is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000021 name: asymmetric_RNA_internal_loop def: "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke] synonym: "asymmetric RNA internal loop" EXACT [] is_a: SO:0000020 ! RNA_internal_loop [Term] id: SO:0000022 name: A_minor_RNA_motif def: "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke] synonym: "A minor RNA motif" EXACT [] is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000023 name: K_turn_RNA_motif def: "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke] synonym: "K turn RNA motif" EXACT [] synonym: "K-turn" EXACT [] synonym: "kink turn" EXACT [] synonym: "kink-turn motif" EXACT [] xref: http://en.wikipedia.org/wiki/K-turn "wiki" is_a: SO:0000021 ! asymmetric_RNA_internal_loop [Term] id: SO:0000024 name: sarcin_like_RNA_motif def: "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662] synonym: "sarcin like RNA motif" EXACT [] synonym: "sarcin/ricin domain" EXACT [] synonym: "sarcin/ricin loop" EXACT [] synonym: "sarcin/ricin RNA domain" EXACT [] is_a: SO:0000021 ! asymmetric_RNA_internal_loop [Term] id: SO:0000025 name: symmetric_RNA_internal_loop def: "An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke] synonym: "A-minor RNA motif" EXACT [] is_a: SO:0000020 ! RNA_internal_loop [Term] id: SO:0000026 name: RNA_junction_loop synonym: "RNA junction loop" EXACT [] is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000027 name: RNA_hook_turn synonym: "hook turn" RELATED [] synonym: "hook-turn motif" EXACT [] synonym: "RNA hook turn" EXACT [] is_a: SO:0000026 ! RNA_junction_loop [Term] id: SO:0000028 name: base_pair synonym: "base pair" EXACT [] xref: http://en.wikipedia.org/wiki/Base_pair "wiki" is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000029 name: WC_base_pair def: "The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293] synonym: "canonical base pair" EXACT [] synonym: "Watson Crick base pair" EXACT [] synonym: "Watson-Crick base pair" RELATED [] synonym: "Watson-Crick pair" EXACT [] synonym: "WC base pair" EXACT [] is_a: SO:0000028 ! base_pair [Term] id: SO:0000030 name: sugar_edge_base_pair def: "A type of non-canonical base-pairing." [PMID:12177293] synonym: "sugar edge base pair" EXACT [] is_a: SO:0000028 ! base_pair [Term] id: SO:0000031 name: aptamer def: "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu] xref: http://en.wikipedia.org/wiki/Aptamer "wiki" is_a: SO:0000696 ! oligo [Term] id: SO:0000032 name: DNA_aptamer def: "DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu] synonym: "DNA aptamer" EXACT [] is_a: SO:0000031 ! aptamer [Term] id: SO:0000033 name: RNA_aptamer def: "RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu] synonym: "RNA aptamer" EXACT [] is_a: SO:0000031 ! aptamer [Term] id: SO:0000034 name: morpholino_oligo def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/] synonym: "morphant" BROAD [] synonym: "morpholino" EXACT [] synonym: "morpholino oligo" EXACT [] is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001183 ! morpholino_backbone relationship: has_quality SO:0001183 ! morpholino_backbone [Term] id: SO:0000035 name: riboswitch def: "A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954] synonym: "riboswitch RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Riboswitch "wiki" is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000036 name: matrix_attachment_site def: "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma] synonym: "MAR" EXACT [] synonym: "matrix association region" EXACT [] synonym: "matrix attachment region" EXACT [] synonym: "matrix attachment site" EXACT [] synonym: "nuclear matrix association region" EXACT [] synonym: "nuclear matrix attachment site" EXACT [] synonym: "S/MAR" EXACT [] synonym: "S/MAR element" RELATED [] synonym: "scaffold attachment site" EXACT [] synonym: "scaffold matrix attachment region" EXACT [] synonym: "SMAR" EXACT [] xref: http://en.wikipedia.org/wiki/Matrix_attachment_site "wiki" is_a: SO:0000626 ! chromosomal_regulatory_element [Term] id: SO:0000037 name: locus_control_region def: "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma] synonym: "LCR" EXACT [] synonym: "locus control element" RELATED [] synonym: "locus control region" EXACT [] xref: http://en.wikipedia.org/wiki/Locus_control_region "wiki" is_a: SO:0000727 ! CRM [Term] id: SO:0000038 name: match_set def: "A collection of match parts." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000039 name: match_part def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke] subset: SOFA synonym: "match part" EXACT [] is_a: SO:0001410 ! experimental_feature relationship: part_of SO:0000343 ! match [Term] id: SO:0000040 name: genomic_clone def: "A clone of a DNA region of a genome." [SO:ma] synonym: "genomic clone" EXACT [] is_a: SO:0000151 ! clone intersection_of: SO:0000151 ! clone intersection_of: has_quality SO:0000991 ! genomic_DNA relationship: has_quality SO:0000991 ! genomic_DNA [Term] id: SO:0000041 name: sequence_operation def: "An operation that can be applied to a sequence, that results in a change." [SO:ke] synonym: "sequence operation" EXACT [] is_obsolete: true [Term] id: SO:0000042 name: pseudogene_attribute def: "An attribute of a pseudogene (SO:0000336)." [SO:ma] synonym: "pseudogene attribute" EXACT [] is_obsolete: true [Term] id: SO:0000043 name: processed_pseudogene def: "A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp] comment: Please not the synonym R psi M uses the spelled out form of the greek letter. synonym: "processed pseudogene" EXACT [] synonym: "pseudogene by reverse transcription" RELATED [] synonym: "R psi G" RELATED [] synonym: "retropseudogene" EXACT [] is_a: SO:0000336 ! pseudogene [Term] id: SO:0000044 name: pseudogene_by_unequal_crossing_over def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke] synonym: "pseudogene by unequal crossing over" EXACT [] is_a: SO:0001760 ! non_processed_pseudogene [Term] id: SO:0000045 name: delete def: "To remove a subsection of sequence." [SO:ke] is_obsolete: true [Term] id: SO:0000046 name: insert def: "To insert a subsection of sequence." [SO:ke] is_obsolete: true [Term] id: SO:0000047 name: invert def: "To invert a subsection of sequence." [SO:ke] is_obsolete: true [Term] id: SO:0000048 name: substitute def: "To substitute a subsection of sequence for another." [SO:ke] is_obsolete: true [Term] id: SO:0000049 name: translocate def: "To translocate a subsection of sequence." [SO:ke] is_obsolete: true [Term] id: SO:0000050 name: gene_part def: "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000051 name: probe def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma] xref: http://en.wikipedia.org/wiki/Hybridization_probe "wiki" is_a: SO:0000696 ! oligo [Term] id: SO:0000052 name: assortment_derived_deficiency synonym: "assortment-derived_deficiency" RELATED [] is_obsolete: true [Term] id: SO:0000053 name: sequence_variant_affecting_regulatory_region def: "A sequence_variant_effect which changes the regulatory region of a gene." [SO:ke] comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting regulatory region" RELATED [] synonym: "sequence variant affecting regulatory region" EXACT [] is_obsolete: true replaced_by: SO:0001556 [Term] id: SO:0000054 name: aneuploid def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke] xref: http://en.wikipedia.org/wiki/Aneuploid "wiki" is_a: SO:1000182 ! chromosome_number_variation [Term] id: SO:0000055 name: hyperploid def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke] xref: http://en.wikipedia.org/wiki/Hyperploid "wiki" is_a: SO:0000054 ! aneuploid [Term] id: SO:0000056 name: hypoploid def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke] xref: http://en.wikipedia.org/wiki/Hypoploid "wiki" is_a: SO:0000054 ! aneuploid [Term] id: SO:0000057 name: operator def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma] subset: SOFA synonym: "operator segment" EXACT [] xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki" is_a: SO:0000752 ! gene_group_regulatory_region [Term] id: SO:0000058 name: assortment_derived_aneuploid synonym: "assortment-derived_aneuploid" RELATED [] is_obsolete: true [Term] id: SO:0000059 name: nuclease_binding_site def: "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb] subset: SOFA synonym: "nuclease binding site" EXACT [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site [Term] id: SO:0000060 name: compound_chromosome_arm comment: FLAG - this term is should probably be a part of rather than an is_a. synonym: "compound chromosome arm" EXACT [] is_a: SO:1000042 ! compound_chromosome [Term] id: SO:0000061 name: restriction_enzyme_binding_site def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb] comment: A region of a molecule that binds to a restriction enzyme. synonym: "restriction endonuclease binding site" EXACT [] synonym: "restriction enzyme binding site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0000062 name: deficient_intrachromosomal_transposition def: "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual] synonym: "deficient intrachromosomal transposition" EXACT [] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000041 ! intrachromosomal_transposition intersection_of: SO:1000041 ! intrachromosomal_transposition intersection_of: has_part SO:0000159 ! deletion relationship: has_part SO:0000159 ! deletion [Term] id: SO:0000063 name: deficient_interchromosomal_transposition def: "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke] synonym: "deficient interchromosomal transposition" EXACT [] is_a: SO:1000155 ! interchromosomal_transposition [Term] id: SO:0000064 name: gene_by_transcript_attribute comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004. is_obsolete: true [Term] id: SO:0000065 name: free_chromosome_arm def: "A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke] synonym: "free chromosome arm" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:0000066 name: gene_by_polyadenylation_attribute is_obsolete: true [Term] id: SO:0000067 name: gene_to_gene_feature synonym: "gene to gene feature" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000068 name: overlapping def: "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke] is_a: SO:0000067 ! gene_to_gene_feature [Term] id: SO:0000069 name: inside_intron def: "An attribute to describe a gene when it is located within the intron of another gene." [SO:ke] synonym: "inside intron" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000070 name: inside_intron_antiparallel def: "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke] synonym: "inside intron antiparallel" EXACT [] is_a: SO:0000069 ! inside_intron [Term] id: SO:0000071 name: inside_intron_parallel def: "An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke] synonym: "inside intron parallel" EXACT [] is_a: SO:0000069 ! inside_intron [Term] id: SO:0000072 name: end_overlapping_gene is_obsolete: true [Term] id: SO:0000073 name: five_prime_three_prime_overlap def: "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke] synonym: "five prime-three prime overlap" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000074 name: five_prime_five_prime_overlap def: "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke] synonym: "five prime-five prime overlap" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000075 name: three_prime_three_prime_overlap def: "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke] synonym: "three prime-three prime overlap" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000076 name: three_prime_five_prime_overlap def: "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke] synonym: "5' 3' overlap" EXACT [] synonym: "three prime five prime overlap" EXACT [] is_a: SO:0000068 ! overlapping [Term] id: SO:0000077 name: antisense def: "A region sequence that is complementary to a sequence of messenger RNA." [SO:ke] xref: http://en.wikipedia.org/wiki/Antisense "wiki" is_a: SO:0000068 ! overlapping [Term] id: SO:0000078 name: polycistronic_transcript def: "A transcript that is polycistronic." [SO:xp] synonym: "polycistronic transcript" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000880 ! polycistronic relationship: has_quality SO:0000880 ! polycistronic [Term] id: SO:0000079 name: dicistronic_transcript def: "A transcript that is dicistronic." [SO:ke] synonym: "dicistronic transcript" EXACT [] is_a: SO:0000078 ! polycistronic_transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000879 ! dicistronic relationship: has_quality SO:0000879 ! dicistronic [Term] id: SO:0000080 name: operon_member synonym: "operon member" EXACT [] is_a: SO:0000081 ! gene_array_member [Term] id: SO:0000081 name: gene_array_member synonym: "gene array member" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000082 name: processed_transcript_attribute is_obsolete: true [Term] id: SO:0000083 name: macronuclear_sequence synonym: "macronuclear sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000084 name: micronuclear_sequence synonym: "micronuclear sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000085 name: gene_by_genome_location is_obsolete: true [Term] id: SO:0000086 name: gene_by_organelle_of_genome is_obsolete: true [Term] id: SO:0000087 name: nuclear_gene def: "A gene from nuclear sequence." [SO:xp] synonym: "nuclear gene" EXACT [] xref: http://en.wikipedia.org/wiki/Nuclear_gene "wiki" is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000738 ! nuclear_sequence relationship: has_origin SO:0000738 ! nuclear_sequence [Term] id: SO:0000088 name: mt_gene def: "A gene located in mitochondrial sequence." [SO:xp] synonym: "mitochondrial gene" EXACT [] synonym: "mt gene" EXACT [] xref: http://en.wikipedia.org/wiki/Mitochondrial_gene "wiki" is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000737 ! mitochondrial_sequence relationship: has_origin SO:0000737 ! mitochondrial_sequence [Term] id: SO:0000089 name: kinetoplast_gene def: "A gene located in kinetoplast sequence." [SO:xp] synonym: "kinetoplast gene" EXACT [] is_a: SO:0000088 ! mt_gene intersection_of: SO:0000088 ! mt_gene intersection_of: has_origin SO:0000741 ! kinetoplast relationship: has_origin SO:0000741 ! kinetoplast [Term] id: SO:0000090 name: plastid_gene def: "A gene from plastid sequence." [SO:xp] synonym: "plastid gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000740 ! plastid_sequence relationship: has_origin SO:0000740 ! plastid_sequence [Term] id: SO:0000091 name: apicoplast_gene def: "A gene from apicoplast sequence." [SO:xp] synonym: "apicoplast gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000743 ! apicoplast_sequence relationship: has_origin SO:0000743 ! apicoplast_sequence [Term] id: SO:0000092 name: ct_gene def: "A gene from chloroplast sequence." [SO:xp] synonym: "chloroplast gene" EXACT [] synonym: "ct gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000745 ! chloroplast_sequence relationship: has_origin SO:0000745 ! chloroplast_sequence [Term] id: SO:0000093 name: chromoplast_gene def: "A gene from chromoplast_sequence." [SO:xp] synonym: "chromoplast gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000744 ! chromoplast_sequence relationship: has_origin SO:0000744 ! chromoplast_sequence [Term] id: SO:0000094 name: cyanelle_gene def: "A gene from cyanelle sequence." [SO:xp] synonym: "cyanelle gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000746 ! cyanelle_sequence relationship: has_origin SO:0000746 ! cyanelle_sequence [Term] id: SO:0000095 name: leucoplast_gene def: "A plastid gene from leucoplast sequence." [SO:xp] synonym: "leucoplast gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000747 ! leucoplast_sequence relationship: has_origin SO:0000747 ! leucoplast_sequence [Term] id: SO:0000096 name: proplastid_gene def: "A gene from proplastid sequence." [SO:ke] synonym: "proplastid gene" EXACT [] is_a: SO:0000090 ! plastid_gene intersection_of: SO:0000090 ! plastid_gene intersection_of: has_origin SO:0000748 ! proplastid_sequence relationship: has_origin SO:0000748 ! proplastid_sequence [Term] id: SO:0000097 name: nucleomorph_gene def: "A gene from nucleomorph sequence." [SO:xp] synonym: "nucleomorph gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000739 ! nucleomorphic_sequence relationship: has_origin SO:0000739 ! nucleomorphic_sequence [Term] id: SO:0000098 name: plasmid_gene def: "A gene from plasmid sequence." [SO:xp] synonym: "plasmid gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000749 ! plasmid_location relationship: has_origin SO:0000749 ! plasmid_location [Term] id: SO:0000099 name: proviral_gene def: "A gene from proviral sequence." [SO:xp] synonym: "proviral gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_origin SO:0000751 ! proviral_location relationship: has_origin SO:0000751 ! proviral_location [Term] id: SO:0000100 name: endogenous_retroviral_gene def: "A proviral gene with origin endogenous retrovirus." [SO:xp] synonym: "endogenous retroviral gene" EXACT [] is_a: SO:0000099 ! proviral_gene intersection_of: SO:0000099 ! proviral_gene intersection_of: has_origin SO:0000903 ! endogenous_retroviral_sequence relationship: has_origin SO:0000903 ! endogenous_retroviral_sequence [Term] id: SO:0000101 name: transposable_element def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html] subset: SOFA synonym: "transposable element" EXACT [] synonym: "transposon" EXACT [] xref: http://en.wikipedia.org/wiki/Transposable_element "wiki" is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000102 name: expressed_sequence_match def: "A match to an EST or cDNA sequence." [SO:ke] subset: SOFA synonym: "expressed sequence match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000103 name: clone_insert_end def: "The end of the clone insert." [SO:ke] subset: SOFA synonym: "clone insert end" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000104 name: polypeptide alt_id: SO:0000358 def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute. subset: SOFA synonym: "protein" EXACT [] xref: http://en.wikipedia.org/wiki/Polypeptide "wiki" is_a: SO:0001411 ! biological_region relationship: derives_from SO:0000316 ! CDS [Term] id: SO:0000105 name: chromosome_arm def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152] synonym: "chromosome arm" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000106 name: non_capped_primary_transcript is_obsolete: true [Term] id: SO:0000107 name: sequencing_primer synonym: "sequencing primer" EXACT [] is_a: SO:0000112 ! primer [Term] id: SO:0000108 name: mRNA_with_frameshift def: "An mRNA with a frameshift." [SO:xp] synonym: "frameshifted mRNA" EXACT [] synonym: "mRNA with frameshift" EXACT [] is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000865 ! frameshift relationship: has_quality SO:0000865 ! frameshift [Term] id: SO:0000109 name: sequence_variant_obs def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] subset: SOFA synonym: "mutation" RELATED [] is_obsolete: true [Term] id: SO:0000110 name: sequence_feature def: "An extent of biological sequence." [SO:ke] subset: SOFA synonym: "located sequence feature" RELATED [] synonym: "located_sequence_feature" EXACT [] synonym: "sequence feature" EXACT [] disjoint_from: SO:0000240 ! chromosome_variation disjoint_from: SO:0000400 ! sequence_attribute [Term] id: SO:0000111 name: transposable_element_gene def: "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke] synonym: "transposable element gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: part_of SO:0000101 ! transposable_element relationship: part_of SO:0000101 ! transposable_element [Term] id: SO:0000112 name: primer def: "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke] subset: SOFA synonym: "DNA primer" EXACT [] synonym: "primer oligonucleotide" EXACT [] synonym: "primer polynucleotide" EXACT [] synonym: "primer sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki" is_a: SO:0000441 ! ss_oligo [Term] id: SO:0000113 name: proviral_region def: "A viral sequence which has integrated into a host genome." [SO:ke] subset: SOFA synonym: "proviral region" EXACT [] synonym: "proviral sequence" RELATED [] is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000114 name: methylated_cytosine def: "A methylated deoxy-cytosine." [SO:ke] subset: SOFA synonym: "methylated C" EXACT [] synonym: "methylated cytosine" EXACT [] synonym: "methylated cytosine base" EXACT [] synonym: "methylated cytosine residue" EXACT [] synonym: "methylated_C" EXACT [] is_a: SO:0000306 ! methylated_DNA_base_feature [Term] id: SO:0000115 name: transcript_feature is_obsolete: true [Term] id: SO:0000116 name: edited def: "An attribute describing a sequence that is modified by editing." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000117 name: transcript_with_readthrough_stop_codon is_obsolete: true [Term] id: SO:0000118 name: transcript_with_translational_frameshift def: "A transcript with a translational frameshift." [SO:xp] synonym: "transcript with translational frameshift" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000887 ! translationally_frameshifted relationship: has_quality SO:0000887 ! translationally_frameshifted [Term] id: SO:0000119 name: regulated def: "An attribute to describe a sequence that is regulated." [SO:ke] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000120 name: protein_coding_primary_transcript def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke] comment: May contain introns. subset: SOFA synonym: "pre mRNA" RELATED [] synonym: "protein coding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000121 name: forward_primer def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "DNA forward primer" EXACT [] synonym: "forward DNA primer" EXACT [] synonym: "forward primer" EXACT [] synonym: "forward primer oligo" EXACT [] synonym: "forward primer oligonucleotide" EXACT [] synonym: "forward primer polynucleotide" EXACT [] synonym: "forward primer sequence" EXACT [] is_a: SO:0000112 ! primer intersection_of: SO:0000112 ! primer intersection_of: has_quality SO:0001030 ! forward relationship: has_quality SO:0001030 ! forward [Term] id: SO:0000122 name: RNA_sequence_secondary_structure def: "A folded RNA sequence." [SO:ke] synonym: "RNA sequence secondary structure" EXACT [] is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000123 name: transcriptionally_regulated def: "An attribute describing a gene that is regulated at transcription." [SO:ma] comment: By:. synonym: "transcriptionally regulated" EXACT [] is_a: SO:0000119 ! regulated [Term] id: SO:0000124 name: transcriptionally_constitutive def: "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke] synonym: "transcriptionally constitutive" EXACT [] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000125 name: transcriptionally_induced def: "An inducer molecule is required for transcription to occur." [SO:ke] synonym: "transcriptionally induced" EXACT [] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000126 name: transcriptionally_repressed def: "A repressor molecule is required for transcription to stop." [SO:ke] synonym: "transcriptionally repressed" EXACT [] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000127 name: silenced_gene def: "A gene that is silenced." [SO:xp] synonym: "silenced gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000893 ! silenced relationship: has_quality SO:0000893 ! silenced [Term] id: SO:0000128 name: gene_silenced_by_DNA_modification def: "A gene that is silenced by DNA modification." [SO:xp] synonym: "gene silenced by DNA modification" EXACT [] is_a: SO:0000127 ! silenced_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000894 ! silenced_by_DNA_modification relationship: has_quality SO:0000894 ! silenced_by_DNA_modification [Term] id: SO:0000129 name: gene_silenced_by_DNA_methylation def: "A gene that is silenced by DNA methylation." [SO:xp] synonym: "gene silenced by DNA methylation" EXACT [] synonym: "methylation-silenced gene" EXACT [] is_a: SO:0000128 ! gene_silenced_by_DNA_modification intersection_of: SO:0000128 ! gene_silenced_by_DNA_modification intersection_of: has_quality SO:0000895 ! silenced_by_DNA_methylation relationship: has_quality SO:0000895 ! silenced_by_DNA_methylation [Term] id: SO:0000130 name: post_translationally_regulated def: "An attribute describing a gene that is regulated after it has been translated." [SO:ke] synonym: "post translationally regulated" EXACT [] synonym: "post-translationally regulated" EXACT [] is_a: SO:0000119 ! regulated [Term] id: SO:0000131 name: translationally_regulated def: "An attribute describing a gene that is regulated as it is translated." [SO:ke] synonym: "translationally regulated" EXACT [] is_a: SO:0000119 ! regulated [Term] id: SO:0000132 name: reverse_primer def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "DNA reverse primer" EXACT [] synonym: "reverse DNA primer" EXACT [] synonym: "reverse primer" EXACT [] synonym: "reverse primer oligo" EXACT [] synonym: "reverse primer oligonucleotide" EXACT [] synonym: "reverse primer sequence" EXACT [] is_a: SO:0000112 ! primer intersection_of: SO:0000112 ! primer intersection_of: has_quality SO:0001031 ! reverse relationship: has_quality SO:0001031 ! reverse [Term] id: SO:0000133 name: epigenetically_modified def: "This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke] synonym: "epigenetically modified" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000134 name: genomically_imprinted def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke] synonym: "genomically imprinted" EXACT [] synonym: "imprinted" BROAD [] xref: http:http://en.wikipedia.org/wiki/Genomic_imprinting "wiki" is_a: SO:0000119 ! regulated is_a: SO:0000133 ! epigenetically_modified [Term] id: SO:0000135 name: maternally_imprinted def: "The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] synonym: "maternally imprinted" EXACT [] is_a: SO:0000134 ! genomically_imprinted [Term] id: SO:0000136 name: paternally_imprinted def: "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] synonym: "paternally imprinted" EXACT [] is_a: SO:0000134 ! genomically_imprinted [Term] id: SO:0000137 name: allelically_excluded def: "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke] comment: Examples are x-inactivation and immunoglobulin formation. synonym: "allelically excluded" EXACT [] is_a: SO:0000133 ! epigenetically_modified [Term] id: SO:0000138 name: gene_rearranged_at_DNA_level def: "An epigenetically modified gene, rearranged at the DNA level." [SO:xp] synonym: "gene rearranged at DNA level" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene intersection_of: SO:0000898 ! epigenetically_modified_gene intersection_of: has_quality SO:0000904 ! rearranged_at_DNA_level relationship: has_quality SO:0000904 ! rearranged_at_DNA_level [Term] id: SO:0000139 name: ribosome_entry_site def: "Region in mRNA where ribosome assembles." [SO:ke] subset: SOFA synonym: "ribosome entry site" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000204 ! five_prime_UTR [Term] id: SO:0000140 name: attenuator def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as] subset: SOFA synonym: "attenuator sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Attenuator "wiki" is_a: SO:0001680 ! translation_regulatory_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000141 name: terminator def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "terminator sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki" is_a: SO:0001679 ! transcription_regulatory_region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000142 name: DNA_sequence_secondary_structure def: "A folded DNA sequence." [SO:ke] synonym: "DNA sequence secondary structure" EXACT [] is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000143 name: assembly_component def: "A region of known length which may be used to manufacture a longer region." [SO:ke] subset: SOFA synonym: "assembly component" EXACT [] is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000144 name: primary_transcript_attribute is_obsolete: true [Term] id: SO:0000145 name: recoded_codon def: "A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp] synonym: "recoded codon" EXACT [] is_a: SO:0000360 ! codon [Term] id: SO:0000146 name: capped def: "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000147 name: exon def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Exon "wiki" is_a: SO:0000833 ! transcript_region [Term] id: SO:0000148 name: supercontig def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls] subset: SOFA synonym: "scaffold" RELATED [] is_a: SO:0001876 ! partial_genomic_sequence_assembly relationship: part_of SO:0000719 ! ultracontig [Term] id: SO:0000149 name: contig def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls] subset: SOFA xref: http://en.wikipedia.org/wiki/Contig "wiki" is_a: SO:0000143 ! assembly_component is_a: SO:0000353 ! sequence_assembly relationship: part_of SO:0000148 ! supercontig [Term] id: SO:0000150 name: read def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd] subset: SOFA is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000149 ! contig [Term] id: SO:0000151 name: clone def: "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke] subset: SOFA xref: http:http://en.wikipedia.org/wiki/Clone_(genetics) "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000152 name: YAC def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "yeast artificial chromosome" EXACT [] is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000153 name: BAC def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "bacterial artificial chromosome" EXACT [] is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000154 name: PAC def: "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome. synonym: "P1" EXACT [] synonym: "P1 artificial chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000155 name: plasmid def: "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "plasmid sequence" EXACT [] is_a: SO:0001235 ! replicon [Term] id: SO:0000156 name: cosmid def: "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma] comment: Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "cosmid vector" EXACT [] xref: http://en.wikipedia.org/wiki/Cosmid "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000157 name: phagemid def: "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma] synonym: "phagemid vector" RELATED [] xref: http://en.wikipedia.org/wiki/Phagemid "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000158 name: fosmid def: "A cloning vector that utilizes the E. coli F factor." [SO:ma] comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996. synonym: "fosmid vector" RELATED [] xref: http://en.wikipedia.org/wiki/Fosmid "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000159 name: deletion alt_id: SO:1000033 def: "The point at which one or more contiguous nucleotides were excised." [SO:ke] subset: SOFA synonym: "deleted_sequence" EXACT [] synonym: "nucleotide deletion" EXACT [] synonym: "nucleotide_deletion" EXACT [] xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki" xref: loinc:LA6692-3 "Deletion" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:0000160 name: lambda_clone def: "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] is_obsolete: true [Term] id: SO:0000161 name: methylated_adenine def: "A modified base in which adenine has been methylated." [SO:ke] subset: SOFA synonym: "methylated A" EXACT [] synonym: "methylated adenine" EXACT [] synonym: "methylated adenine base" EXACT [] synonym: "methylated adenine residue" EXACT [] synonym: "methylated_A" EXACT [] is_a: SO:0000306 ! methylated_DNA_base_feature [Term] id: SO:0000162 name: splice_site def: "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke] comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery. subset: SOFA synonym: "splice site" EXACT [] xref: http://en.wikipedia.org/wiki/Splice_site "wiki" is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000163 name: five_prime_cis_splice_site def: "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] subset: SOFA synonym: "5' splice site" EXACT [] synonym: "donor" RELATED [] synonym: "donor splice site" EXACT [] synonym: "five prime splice site" EXACT [] synonym: "splice donor site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000164 name: three_prime_cis_splice_site def: "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] subset: SOFA synonym: "3' splice site" RELATED [] synonym: "acceptor" RELATED [] synonym: "acceptor splice site" EXACT [] synonym: "splice acceptor site" EXACT [] synonym: "three prime splice site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000165 name: enhancer def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO. subset: SOFA xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki" is_a: SO:0000727 ! CRM [Term] id: SO:0000166 name: enhancer_bound_by_factor def: "An enhancer bound by a factor." [SO:xp] synonym: "enhancer bound by factor" EXACT [] is_a: SO:0000165 ! enhancer intersection_of: SO:0000165 ! enhancer intersection_of: has_quality SO:0000277 ! bound_by_factor relationship: has_quality SO:0000277 ! bound_by_factor [Term] id: SO:0000167 name: promoter def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. subset: SOFA synonym: "promoter sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Promoter "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000168 name: restriction_enzyme_cut_site def: "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma] is_obsolete: true [Term] id: SO:0000169 name: RNApol_I_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke] synonym: "pol I promoter" EXACT [] synonym: "polymerase I promoter" EXACT [] synonym: "RNA polymerase A promoter" EXACT [] synonym: "RNApol I promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000170 name: RNApol_II_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke] synonym: "pol II promoter" RELATED [] synonym: "polymerase II promoter" EXACT [] synonym: "RNA polymerase B promoter" EXACT [] synonym: "RNApol II promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000171 name: RNApol_III_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke] synonym: "pol III promoter" EXACT [] synonym: "polymerase III promoter" EXACT [] synonym: "RNA polymerase C promoter" EXACT [] synonym: "RNApol III promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000172 name: CAAT_signal def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "CAAT box" EXACT [] synonym: "CAAT signal" EXACT [] synonym: "CAAT-box" EXACT [] xref: http://en.wikipedia.org/wiki/CAAT_box "wiki" is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000173 name: GC_rich_promoter_region def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "GC rich promoter region" EXACT [] synonym: "GC-rich region" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000174 name: TATA_box def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867] comment: Binds TBP. synonym: "Goldstein-Hogness box" EXACT [] synonym: "TATA box" EXACT [] xref: http://en.wikipedia.org/wiki/TATA_box "wiki" is_a: SO:0001660 ! core_promoter_element [Term] id: SO:0000175 name: minus_10_signal def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "-10 signal" EXACT [] synonym: "minus 10 signal" EXACT [] synonym: "Pribnow box" EXACT [] synonym: "Pribnow Schaller box" EXACT [] synonym: "Pribnow-Schaller box" EXACT [] xref: http://en.wikipedia.org/wiki/Pribnow_box "wiki" is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70 relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf [Term] id: SO:0000176 name: minus_35_signal def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "-35 signal" EXACT [] synonym: "minus 35 signal" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70 relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf [Term] id: SO:0000177 name: cross_genome_match def: "A nucleotide match against a sequence from another organism." [SO:ma] subset: SOFA synonym: "cross genome match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000178 name: operon def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Operon "wiki" is_a: SO:0005855 ! gene_group [Term] id: SO:0000179 name: clone_insert_start def: "The start of the clone insert." [SO:ke] subset: SOFA synonym: "clone insert start" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000180 name: retrotransposon def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r] synonym: "class I" RELATED [] synonym: "class I transposon" EXACT [] synonym: "retrotransposon element" EXACT [] xref: http://en.wikipedia.org/wiki/Retrotransposon "wiki" is_a: SO:0000101 ! transposable_element [Term] id: SO:0000181 name: translated_nucleotide_match def: "A match against a translated sequence." [SO:ke] subset: SOFA synonym: "translated nucleotide match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000182 name: DNA_transposon def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke] synonym: "class II" RELATED [] synonym: "class II transposon" EXACT [] synonym: "DNA transposon" EXACT [] is_a: SO:0000101 ! transposable_element [Term] id: SO:0000183 name: non_transcribed_region def: "A region of the gene which is not transcribed." [SO:ke] subset: SOFA synonym: "non transcribed region" EXACT [] synonym: "non-transcribed sequence" EXACT [] synonym: "nontranscribed region" EXACT [] synonym: "nontranscribed sequence" EXACT [] is_a: SO:0000842 ! gene_component_region [Term] id: SO:0000184 name: U2_intron def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511] comment: May have either GT-AG or AT-AG 5' and 3' boundaries. synonym: "U2 intron" EXACT [] is_a: SO:0000662 ! spliceosomal_intron [Term] id: SO:0000185 name: primary_transcript def: "A transcript that in its initial state requires modification to be functional." [SO:ma] subset: SOFA synonym: "precursor RNA" EXACT [] synonym: "primary transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki" is_a: SO:0000673 ! transcript [Term] id: SO:0000186 name: LTR_retrotransposon def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke] synonym: "long terminal repeat retrotransposon" EXACT [] synonym: "LTR retrotransposon" EXACT [] is_a: SO:0000180 ! retrotransposon [Term] id: SO:0000187 name: repeat_family def: "A group of characterized repeat sequences." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000188 name: intron def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Intron "wiki" is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000189 name: non_LTR_retrotransposon def: "A retrotransposon without long terminal repeat sequences." [SO:ke] synonym: "non LTR retrotransposon" EXACT [] is_a: SO:0000180 ! retrotransposon [Term] id: SO:0000190 name: five_prime_intron synonym: "5' intron" EXACT [] synonym: "5' intron sequence" EXACT [] synonym: "five prime intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000191 name: interior_intron synonym: "interior intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000192 name: three_prime_intron synonym: "3' intron" EXACT [] synonym: "3' intron sequence" RELATED [] synonym: "three prime intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000193 name: RFLP_fragment def: "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj] subset: SOFA synonym: "restriction fragment length polymorphism" EXACT [] synonym: "RFLP" EXACT [] synonym: "RFLP fragment" EXACT [] xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki" is_a: SO:0000412 ! restriction_fragment [Term] id: SO:0000194 name: LINE_element def: "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] synonym: "LINE" EXACT [] synonym: "LINE element" EXACT [] synonym: "Long interspersed element" EXACT [] synonym: "Long interspersed nuclear element" EXACT [] is_a: SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000195 name: coding_exon def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke] subset: SOFA synonym: "coding exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000196 name: five_prime_coding_exon_coding_region def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm] subset: SOFA synonym: "five prime exon coding region" EXACT [] is_a: SO:0001215 ! coding_region_of_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000197 name: three_prime_coding_exon_coding_region def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm] subset: SOFA synonym: "three prime exon coding region" EXACT [] is_a: SO:0001215 ! coding_region_of_exon relationship: part_of SO:0000202 ! three_prime_coding_exon [Term] id: SO:0000198 name: noncoding_exon def: "An exon that does not contain any codons." [SO:ke] subset: SOFA synonym: "noncoding exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000199 name: translocation def: "A region of nucleotide sequence that has translocated to a new position." [SO:ke] subset: DBVAR synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "translocated sequence" EXACT [] is_a: SO:0001059 ! sequence_alteration [Term] id: SO:0000200 name: five_prime_coding_exon def: "The 5' most coding exon." [SO:ke] subset: SOFA synonym: "5' coding exon" EXACT [] synonym: "five prime coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:0000201 name: interior_exon def: "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547] synonym: "interior exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000202 name: three_prime_coding_exon def: "The coding exon that is most 3-prime on a given transcript." [SO:ma] synonym: "3' coding exon" RELATED [] synonym: "three prime coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:0000203 name: UTR def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke] subset: SOFA synonym: "untranslated region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000204 name: five_prime_UTR def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "5' UTR" EXACT [] synonym: "five prime UTR" EXACT [] synonym: "five_prime_untranslated_region" EXACT [] xref: http://en.wikipedia.org/wiki/5'_UTR "wiki" is_a: SO:0000203 ! UTR [Term] id: SO:0000205 name: three_prime_UTR def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "three prime untranslated region" EXACT [] synonym: "three prime UTR" EXACT [] xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki" is_a: SO:0000203 ! UTR [Term] id: SO:0000206 name: SINE_element def: "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke] synonym: "Short interspersed element" EXACT [] synonym: "Short interspersed nuclear element" EXACT [] synonym: "SINE element" EXACT [] xref: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element "wiki" is_a: SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000207 name: simple_sequence_length_variation synonym: "simple sequence length polymorphism" RELATED [] synonym: "simple sequence length variation" EXACT [] synonym: "SSLP" RELATED [] is_a: SO:0000248 ! sequence_length_variation [Term] id: SO:0000208 name: terminal_inverted_repeat_element def: "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] synonym: "terminal inverted repeat element" EXACT [] synonym: "TIR element" EXACT [] is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000209 name: rRNA_primary_transcript def: "A primary transcript encoding a ribosomal RNA." [SO:ke] subset: SOFA synonym: "ribosomal RNA primary transcript" EXACT [] synonym: "rRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000210 name: tRNA_primary_transcript def: "A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke] synonym: "tRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000211 name: alanine_tRNA_primary_transcript def: "A primary transcript encoding alanyl tRNA." [SO:ke] synonym: "alanine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000212 name: arginine_tRNA_primary_transcript def: "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke] synonym: "arginine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000213 name: asparagine_tRNA_primary_transcript def: "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke] synonym: "asparagine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000214 name: aspartic_acid_tRNA_primary_transcript def: "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke] synonym: "aspartic acid tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000215 name: cysteine_tRNA_primary_transcript def: "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke] synonym: "cysteine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000216 name: glutamic_acid_tRNA_primary_transcript def: "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke] synonym: "glutamic acid tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000217 name: glutamine_tRNA_primary_transcript def: "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke] synonym: "glutamine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000218 name: glycine_tRNA_primary_transcript def: "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke] synonym: "glycine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000219 name: histidine_tRNA_primary_transcript def: "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke] synonym: "histidine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000220 name: isoleucine_tRNA_primary_transcript def: "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke] synonym: "isoleucine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000221 name: leucine_tRNA_primary_transcript def: "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke] synonym: "leucine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000222 name: lysine_tRNA_primary_transcript def: "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke] synonym: "lysine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000223 name: methionine_tRNA_primary_transcript def: "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke] synonym: "methionine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000224 name: phenylalanine_tRNA_primary_transcript def: "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke] synonym: "phenylalanine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000225 name: proline_tRNA_primary_transcript def: "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke] synonym: "proline tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000226 name: serine_tRNA_primary_transcript def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke] synonym: "serine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000227 name: threonine_tRNA_primary_transcript def: "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke] synonym: "threonine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000228 name: tryptophan_tRNA_primary_transcript def: "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke] synonym: "tryptophan tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000229 name: tyrosine_tRNA_primary_transcript def: "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke] synonym: "tyrosine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000230 name: valine_tRNA_primary_transcript def: "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke] synonym: "valine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000231 name: snRNA_primary_transcript def: "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke] synonym: "snRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000232 name: snoRNA_primary_transcript def: "A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke] synonym: "snoRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000233 name: mature_transcript def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke] comment: A processed transcript cannot contain introns. subset: SOFA synonym: "mature transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki" is_a: SO:0000673 ! transcript relationship: derives_from SO:0000185 ! primary_transcript [Term] id: SO:0000234 name: mRNA def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "messenger RNA" EXACT [] xref: http://en.wikipedia.org/wiki/MRNA "wiki" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000235 name: TF_binding_site def: "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke] subset: SOFA synonym: "TF binding site" EXACT [] synonym: "transcription factor binding site" EXACT [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0000236 name: ORF def: "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma] comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "open reading frame" EXACT [] is_a: SO:0000717 ! reading_frame [Term] id: SO:0000237 name: transcript_attribute synonym: "transcript attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000238 name: foldback_element def: "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] synonym: "foldback element" EXACT [] synonym: "long inverted repeat element" RELATED [] synonym: "LVR element" RELATED [] is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000239 name: flanking_region def: "The sequences extending on either side of a specific region." [SO:ke] subset: SOFA synonym: "flanking region" EXACT [] is_a: SO:0001412 ! topologically_defined_region [Term] id: SO:0000240 name: chromosome_variation synonym: "chromosome variation" EXACT [] is_a: SO:0001507 ! variant_collection disjoint_from: SO:0000400 ! sequence_attribute relationship: part_of SO:0001524 ! chromosomally_aberrant_genome [Term] id: SO:0000241 name: internal_UTR def: "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm] synonym: "internal UTR" EXACT [] is_a: SO:0000203 ! UTR [Term] id: SO:0000242 name: untranslated_region_polycistronic_mRNA def: "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke] synonym: "untranslated region polycistronic mRNA" EXACT [] is_a: SO:0000203 ! UTR [Term] id: SO:0000243 name: internal_ribosome_entry_site def: "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke] synonym: "internal ribosomal entry sequence" EXACT [] synonym: "internal ribosomal entry site" EXACT [] synonym: "internal ribosome entry sequence" RELATED [] synonym: "internal ribosome entry site" EXACT [] synonym: "IRES" EXACT [] xref: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site "wiki" is_a: SO:0000139 ! ribosome_entry_site [Term] id: SO:0000244 name: four_cutter_restriction_site synonym: "4-cutter_restriction_site" RELATED [] synonym: "four-cutter_restriction_sit" RELATED [] is_obsolete: true [Term] id: SO:0000245 name: mRNA_by_polyadenylation_status is_obsolete: true [Term] id: SO:0000246 name: polyadenylated def: "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000247 name: mRNA_not_polyadenylated is_obsolete: true [Term] id: SO:0000248 name: sequence_length_variation synonym: "sequence length variation" EXACT [] is_a: SO:1000002 ! substitution [Term] id: SO:0000249 name: six_cutter_restriction_site synonym: "6-cutter_restriction_site" RELATED [] synonym: "six-cutter_restriction_site" RELATED [] is_obsolete: true [Term] id: SO:0000250 name: modified_RNA_base_feature def: "A post_transcriptionally modified base." [SO:ke] synonym: "modified RNA base feature" EXACT [] is_a: SO:0001236 ! base [Term] id: SO:0000251 name: eight_cutter_restriction_site synonym: "8-cutter_restriction_site" RELATED [] synonym: "eight-cutter_restriction_site" RELATED [] is_obsolete: true [Term] id: SO:0000252 name: rRNA def: "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732] subset: SOFA synonym: "ribosomal ribonucleic acid" EXACT [] synonym: "ribosomal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000253 name: tRNA def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "transfer ribonucleic acid" RELATED [] synonym: "transfer RNA" RELATED [] xref: http://en.wikipedia.org/wiki/TRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000254 name: alanyl_tRNA def: "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke] synonym: "alanyl tRNA" EXACT [] synonym: "alanyl-transfer ribonucleic acid" EXACT [] synonym: "alanyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000211 ! alanine_tRNA_primary_transcript [Term] id: SO:0000255 name: rRNA_small_subunit_primary_transcript def: "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke] synonym: "rRNA small subunit primary transcript" EXACT [] is_a: SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000256 name: asparaginyl_tRNA def: "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke] synonym: "asparaginyl tRNA" EXACT [] synonym: "asparaginyl-transfer ribonucleic acid" EXACT [] synonym: "asparaginyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000213 ! asparagine_tRNA_primary_transcript [Term] id: SO:0000257 name: aspartyl_tRNA def: "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke] synonym: "aspartyl tRNA" EXACT [] synonym: "aspartyl-transfer ribonucleic acid" EXACT [] synonym: "aspartyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000214 ! aspartic_acid_tRNA_primary_transcript [Term] id: SO:0000258 name: cysteinyl_tRNA def: "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke] synonym: "cysteinyl tRNA" EXACT [] synonym: "cysteinyl-transfer ribonucleic acid" EXACT [] synonym: "cysteinyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000215 ! cysteine_tRNA_primary_transcript [Term] id: SO:0000259 name: glutaminyl_tRNA def: "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke] synonym: "glutaminyl tRNA" EXACT [] synonym: "glutaminyl-transfer ribonucleic acid" EXACT [] synonym: "glutaminyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000216 ! glutamic_acid_tRNA_primary_transcript [Term] id: SO:0000260 name: glutamyl_tRNA def: "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke] synonym: "glutamyl tRNA" EXACT [] synonym: "glutamyl-transfer ribonucleic acid" EXACT [] synonym: "glutamyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000217 ! glutamine_tRNA_primary_transcript [Term] id: SO:0000261 name: glycyl_tRNA def: "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke] synonym: "glycyl tRNA" EXACT [] synonym: "glycyl-transfer ribonucleic acid" RELATED [] synonym: "glycyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000218 ! glycine_tRNA_primary_transcript [Term] id: SO:0000262 name: histidyl_tRNA def: "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke] synonym: "histidyl tRNA" EXACT [] synonym: "histidyl-transfer ribonucleic acid" EXACT [] synonym: "histidyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000219 ! histidine_tRNA_primary_transcript [Term] id: SO:0000263 name: isoleucyl_tRNA def: "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke] synonym: "isoleucyl tRNA" EXACT [] synonym: "isoleucyl-transfer ribonucleic acid" EXACT [] synonym: "isoleucyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000220 ! isoleucine_tRNA_primary_transcript [Term] id: SO:0000264 name: leucyl_tRNA def: "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke] synonym: "leucyl tRNA" EXACT [] synonym: "leucyl-transfer ribonucleic acid" EXACT [] synonym: "leucyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000221 ! leucine_tRNA_primary_transcript [Term] id: SO:0000265 name: lysyl_tRNA def: "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke] synonym: "lysyl tRNA" EXACT [] synonym: "lysyl-transfer ribonucleic acid" EXACT [] synonym: "lysyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000222 ! lysine_tRNA_primary_transcript [Term] id: SO:0000266 name: methionyl_tRNA def: "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke] synonym: "methionyl tRNA" EXACT [] synonym: "methionyl-transfer ribonucleic acid" EXACT [] synonym: "methionyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000223 ! methionine_tRNA_primary_transcript [Term] id: SO:0000267 name: phenylalanyl_tRNA def: "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke] synonym: "phenylalanyl tRNA" EXACT [] synonym: "phenylalanyl-transfer ribonucleic acid" EXACT [] synonym: "phenylalanyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000224 ! phenylalanine_tRNA_primary_transcript [Term] id: SO:0000268 name: prolyl_tRNA def: "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke] synonym: "prolyl tRNA" EXACT [] synonym: "prolyl-transfer ribonucleic acid" EXACT [] synonym: "prolyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000225 ! proline_tRNA_primary_transcript [Term] id: SO:0000269 name: seryl_tRNA def: "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke] synonym: "seryl tRNA" EXACT [] synonym: "seryl-transfer ribonucleic acid" RELATED [] synonym: "seryl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000226 ! serine_tRNA_primary_transcript [Term] id: SO:0000270 name: threonyl_tRNA def: "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke] synonym: "threonyl tRNA" EXACT [] synonym: "threonyl-transfer ribonucleic acid" EXACT [] synonym: "threonyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000227 ! threonine_tRNA_primary_transcript [Term] id: SO:0000271 name: tryptophanyl_tRNA def: "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke] synonym: "tryptophanyl tRNA" EXACT [] synonym: "tryptophanyl-transfer ribonucleic acid" EXACT [] synonym: "tryptophanyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000228 ! tryptophan_tRNA_primary_transcript [Term] id: SO:0000272 name: tyrosyl_tRNA def: "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke] synonym: "tyrosyl tRNA" EXACT [] synonym: "tyrosyl-transfer ribonucleic acid" EXACT [] synonym: "tyrosyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000229 ! tyrosine_tRNA_primary_transcript [Term] id: SO:0000273 name: valyl_tRNA def: "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke] synonym: "valyl tRNA" EXACT [] synonym: "valyl-transfer ribonucleic acid" EXACT [] synonym: "valyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000230 ! valine_tRNA_primary_transcript [Term] id: SO:0000274 name: snRNA def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "small nuclear RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SnRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000231 ! snRNA_primary_transcript [Term] id: SO:0000275 name: snoRNA def: "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc] subset: SOFA synonym: "small nucleolar RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SnoRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000276 name: miRNA def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000] subset: SOFA synonym: "micro RNA" EXACT [] synonym: "microRNA" EXACT [] xref: http://en.wikipedia.org/wiki/MiRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA relationship: derives_from SO:0000647 ! miRNA_primary_transcript [Term] id: SO:0000277 name: bound_by_factor def: "An attribute describing a sequence that is bound by another molecule." [SO:ke] comment: Formerly called transcript_by_bound_factor. synonym: "bound by factor" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000278 name: transcript_bound_by_nucleic_acid def: "A transcript that is bound by a nucleic acid." [SO:xp] comment: Formerly called transcript_by_bound_nucleic_acid. synonym: "transcript bound by nucleic acid" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000876 ! bound_by_nucleic_acid relationship: has_quality SO:0000876 ! bound_by_nucleic_acid [Term] id: SO:0000279 name: transcript_bound_by_protein def: "A transcript that is bound by a protein." [SO:xp] comment: Formerly called transcript_by_bound_protein. synonym: "transcript bound by protein" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000875 ! bound_by_protein relationship: has_quality SO:0000875 ! bound_by_protein [Term] id: SO:0000280 name: engineered_gene def: "A gene that is engineered." [SO:xp] synonym: "engineered gene" EXACT [] is_a: SO:0000704 ! gene is_a: SO:0000804 ! engineered_region intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000281 name: engineered_foreign_gene def: "A gene that is engineered and foreign." [SO:xp] synonym: "engineered foreign gene" EXACT [] is_a: SO:0000280 ! engineered_gene is_a: SO:0000285 ! foreign_gene is_a: SO:0000805 ! engineered_foreign_region intersection_of: SO:0000280 ! engineered_gene intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000282 name: mRNA_with_minus_1_frameshift def: "An mRNA with a minus 1 frameshift." [SO:xp] synonym: "mRNA with minus 1 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000866 ! minus_1_frameshift relationship: has_quality SO:0000866 ! minus_1_frameshift [Term] id: SO:0000283 name: engineered_foreign_transposable_element_gene def: "A transposable_element that is engineered and foreign." [SO:xp] synonym: "engineered foreign transposable element gene" EXACT [] is_a: SO:0000111 ! transposable_element_gene is_a: SO:0000281 ! engineered_foreign_gene intersection_of: SO:0000111 ! transposable_element_gene intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000284 name: type_I_enzyme_restriction_site def: "The recognition site is bipartite and interrupted." [http://www.promega.com] is_obsolete: true [Term] id: SO:0000285 name: foreign_gene def: "A gene that is foreign." [SO:xp] synonym: "foreign gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000286 name: long_terminal_repeat def: "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "direct terminal repeat" RELATED [] synonym: "long terminal repeat" EXACT [] synonym: "LTR" EXACT [] xref: http://en.wikipedia.org/wiki/Long_terminal_repeat "wiki" is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000186 ! LTR_retrotransposon [Term] id: SO:0000287 name: fusion_gene def: "A gene that is a fusion." [SO:xp] synonym: "fusion gene" EXACT [] xref: http://en.wikipedia.org/wiki/Fusion_gene "wiki" is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000806 ! fusion relationship: has_quality SO:0000806 ! fusion [Term] id: SO:0000288 name: engineered_fusion_gene def: "A fusion gene that is engineered." [SO:xp] synonym: "engineered fusion gene" EXACT [] is_a: SO:0000280 ! engineered_gene is_a: SO:0000287 ! fusion_gene intersection_of: SO:0000287 ! fusion_gene intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000289 name: microsatellite def: "A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem." [http://www.informatics.jax.org/silver/glossary.shtml] subset: SOFA synonym: "microsatellite locus" EXACT [] synonym: "microsatellite marker" EXACT [] synonym: "VNTR" EXACT [] xref: http://en.wikipedia.org/wiki/Microsatellite "wiki" is_a: SO:0000005 ! satellite_DNA [Term] id: SO:0000290 name: dinucleotide_repeat_microsatellite_feature synonym: "dinucleotide repeat microsatellite" EXACT [] synonym: "dinucleotide repeat microsatellite feature" EXACT [] synonym: "dinucleotide repeat microsatellite locus" EXACT [] synonym: "dinucleotide repeat microsatellite marker" EXACT [] is_a: SO:0000289 ! microsatellite [Term] id: SO:0000291 name: trinucleotide_repeat_microsatellite_feature synonym: "dinucleotide repeat microsatellite marker" RELATED [] synonym: "rinucleotide repeat microsatellite" EXACT [] synonym: "trinucleotide repeat microsatellite feature" EXACT [] synonym: "trinucleotide repeat microsatellite locus" EXACT [] is_a: SO:0000289 ! microsatellite [Term] id: SO:0000292 name: repetitive_element is_obsolete: true [Term] id: SO:0000293 name: engineered_foreign_repetitive_element def: "A repetitive element that is engineered and foreign." [SO:xp] synonym: "engineered foreign repetitive element" EXACT [] is_a: SO:0000657 ! repeat_region is_a: SO:0000805 ! engineered_foreign_region intersection_of: SO:0000657 ! repeat_region intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000294 name: inverted_repeat def: "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke] subset: SOFA synonym: "inverted repeat" EXACT [] synonym: "inverted repeat sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000295 name: U12_intron def: "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511] comment: May have either GT-AC or AT-AC 5' and 3' boundaries. synonym: "U12 intron" EXACT [] synonym: "U12-dependent intron" EXACT [] is_a: SO:0000662 ! spliceosomal_intron [Term] id: SO:0000296 name: origin_of_replication def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "ori" EXACT [] synonym: "origin of replication" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki" is_a: SO:0001411 ! biological_region relationship: part_of SO:0001235 ! replicon [Term] id: SO:0000297 name: D_loop def: "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "D-loop" EXACT [] synonym: "displacement loop" RELATED [] xref: http://en.wikipedia.org/wiki/D_loop "wiki" is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000298 name: recombination_feature synonym: "recombination feature" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000299 name: specific_recombination_site synonym: "specific recombination site" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000300 name: recombination_feature_of_rearranged_gene synonym: "recombination feature of rearranged gene" EXACT [] is_a: SO:0000299 ! specific_recombination_site [Term] id: SO:0000301 name: vertebrate_immune_system_gene_recombination_feature synonym: "vertebrate immune system gene recombination feature" EXACT [] is_a: SO:0000300 ! recombination_feature_of_rearranged_gene [Term] id: SO:0000302 name: J_gene_recombination_feature def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J gene recombination feature" EXACT [] synonym: "J-RS" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000303 name: clip def: "Part of the primary transcript that is clipped off during processing." [SO:ke] subset: SOFA is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000304 name: type_II_enzyme_restriction_site def: "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." [http://www.promega.com] is_obsolete: true [Term] id: SO:0000305 name: modified_DNA_base def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Modified base:. subset: SOFA synonym: "modified base site" EXACT [] is_a: SO:0001236 ! base is_a: SO:0001720 ! epigenetically_modified_region [Term] id: SO:0000306 name: methylated_DNA_base_feature def: "A nucleotide modified by methylation." [SO:ke] subset: SOFA synonym: "methylated base feature" EXACT [] is_a: SO:0000305 ! modified_DNA_base [Term] id: SO:0000307 name: CpG_island def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd] subset: SOFA synonym: "CG island" EXACT [] synonym: "CpG island" EXACT [] xref: http://en.wikipedia.org/wiki/CpG_island "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000308 name: sequence_feature_locating_method is_obsolete: true [Term] id: SO:0000309 name: computed_feature is_obsolete: true [Term] id: SO:0000310 name: predicted_ab_initio_computation is_obsolete: true [Term] id: SO:0000311 name: computed_feature_by_similarity def: "." [SO:ma] comment: similar to: is_obsolete: true [Term] id: SO:0000312 name: experimentally_determined def: "Attribute to describe a feature that has been experimentally verified." [SO:ke] synonym: "experimentally determined" EXACT [] is_a: SO:0000789 ! validated [Term] id: SO:0000313 name: stem_loop alt_id: SO:0000019 def: "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "RNA_hairpin_loop" EXACT [] synonym: "stem loop" EXACT [] synonym: "stem-loop" EXACT [] xref: http://en.wikipedia.org/wiki/Stem_loop "wiki" is_a: SO:0000122 ! RNA_sequence_secondary_structure [Term] id: SO:0000314 name: direct_repeat def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke] subset: SOFA synonym: "direct repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000315 name: TSS def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] subset: SOFA synonym: "transcription start site" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000316 name: CDS def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] subset: SOFA synonym: "coding sequence" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000317 name: cDNA_clone def: "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "cDNA clone" EXACT [] is_a: SO:0000151 ! clone intersection_of: SO:0000151 ! clone intersection_of: has_quality SO:0000756 ! cDNA relationship: has_quality SO:0000756 ! cDNA [Term] id: SO:0000318 name: start_codon def: "First codon to be translated by a ribosome." [SO:ke] subset: SOFA synonym: "initiation codon" EXACT [] synonym: "start codon" EXACT [] xref: http://en.wikipedia.org/wiki/Start_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000319 name: stop_codon def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke] subset: SOFA synonym: "stop codon" EXACT [] xref: http://en.wikipedia.org/wiki/Stop_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000320 name: intronic_splice_enhancer def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke] synonym: "intronic splice enhancer" EXACT [] is_a: SO:0000344 ! splice_enhancer is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000321 name: mRNA_with_plus_1_frameshift def: "An mRNA with a plus 1 frameshift." [SO:ke] synonym: "mRNA with plus 1 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000868 ! plus_1_frameshift relationship: has_quality SO:0000868 ! plus_1_frameshift [Term] id: SO:0000322 name: nuclease_hypersensitive_site synonym: "nuclease hypersensitive site" EXACT [] is_a: SO:0000684 ! nuclease_sensitive_site [Term] id: SO:0000323 name: coding_start def: "The first base to be translated into protein." [SO:ke] synonym: "coding start" EXACT [] synonym: "translation initiation site" EXACT [] synonym: "translation start" RELATED [] is_a: SO:0000851 ! CDS_region [Term] id: SO:0000324 name: tag def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke] subset: SOFA is_a: SO:0000696 ! oligo [Term] id: SO:0000325 name: rRNA_large_subunit_primary_transcript def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke] subset: SOFA synonym: "35S rRNA primary transcript" EXACT [] synonym: "rRNA large subunit primary transcript" EXACT [] is_a: SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000326 name: SAGE_tag def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract] subset: SOFA synonym: "SAGE tag" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000327 name: coding_end def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke] synonym: "coding end" EXACT [] synonym: "translation termination site" EXACT [] synonym: "translation_end" EXACT [] is_a: SO:0000851 ! CDS_region [Term] id: SO:0000328 name: microarray_oligo synonym: "microarray oligo" EXACT [] synonym: "microarray oligonucleotide" EXACT [] is_a: SO:0000051 ! probe [Term] id: SO:0000329 name: mRNA_with_plus_2_frameshift def: "An mRNA with a plus 2 frameshift." [SO:xp] synonym: "mRNA with plus 2 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000869 ! plus_2_framshift relationship: has_quality SO:0000869 ! plus_2_framshift [Term] id: SO:0000330 name: conserved_region def: "Region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "conserved region" EXACT [] xref: http://en.wikipedia.org/wiki/Conserved_region "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000331 name: STS def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com] subset: SOFA synonym: "sequence tag site" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000332 name: coding_conserved_region def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "coding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000333 name: exon_junction def: "The boundary between two exons in a processed transcript." [SO:ke] subset: SOFA synonym: "exon junction" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000334 name: nc_conserved_region def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "nc conserved region" EXACT [] synonym: "noncoding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000335 name: mRNA_with_minus_2_frameshift def: "A mRNA with a minus 2 frameshift." [SO:ke] synonym: "mRNA with minus 2 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift intersection_of: SO:0000108 ! mRNA_with_frameshift intersection_of: has_quality SO:0000867 ! minus_2_frameshift relationship: has_quality SO:0000867 ! minus_2_frameshift [Term] id: SO:0000336 name: pseudogene def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] subset: SOFA xref: http://en.wikipedia.org/wiki/Pseudogene "wiki" is_a: SO:0001411 ! biological_region relationship: non_functional_homolog_of SO:0000704 ! gene [Term] id: SO:0000337 name: RNAi_reagent def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd] subset: SOFA synonym: "RNAi reagent" EXACT [] is_a: SO:0000442 ! ds_oligo [Term] id: SO:0000338 name: MITE def: "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083] synonym: "miniature inverted repeat transposable element" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000339 name: recombination_hotspot def: "A region in a genome which promotes recombination." [SO:rd] synonym: "recombination hotspot" EXACT [] xref: http://en.wikipedia.org/wiki/Recombination_hotspot "wiki" is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000340 name: chromosome def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Chromosome "wiki" is_a: SO:0001235 ! replicon [Term] id: SO:0000341 name: chromosome_band def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma] subset: SOFA synonym: "chromosome band" EXACT [] synonym: "cytoband" EXACT [] synonym: "cytological band" EXACT [] xref: http://en.wikipedia.org/wiki/Cytological_band "wiki" is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000342 name: site_specific_recombination_target_region synonym: "site specific recombination target region" EXACT [] is_a: SO:0000299 ! specific_recombination_site [Term] id: SO:0000343 name: match def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000344 name: splice_enhancer def: "Region of a transcript that regulates splicing." [SO:ke] subset: SOFA synonym: "splice enhancer" EXACT [] is_a: SO:0001056 ! splicing_regulatory_region [Term] id: SO:0000345 name: EST def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "expressed sequence tag" EXACT [] is_a: SO:0000324 ! tag relationship: derives_from SO:0000234 ! mRNA [Term] id: SO:0000346 name: loxP_site synonym: "Cre-recombination target region" RELATED [] synonym: "loxP site" EXACT [] is_a: SO:0000947 ! resolution_site [Term] id: SO:0000347 name: nucleotide_match def: "A match against a nucleotide sequence." [SO:ke] subset: SOFA synonym: "nucleotide match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000348 name: nucleic_acid def: "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb] synonym: "nucleic acid" EXACT [] xref: http://en.wikipedia.org/wiki/Nucleic_acid "wiki" is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000349 name: protein_match def: "A match against a protein sequence." [SO:ke] subset: SOFA synonym: "protein match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000350 name: FRT_site def: "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma] synonym: "FLP recombination target region" EXACT [] synonym: "FRT site" EXACT [] is_a: SO:0000948 ! inversion_site [Term] id: SO:0000351 name: synthetic_sequence def: "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma] synonym: "synthetic sequence" EXACT [] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000352 name: DNA def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb] is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0000353 name: sequence_assembly def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] subset: SOFA synonym: "sequence assembly" EXACT [] xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki" is_a: SO:0001248 ! assembly [Term] id: SO:0000354 name: group_1_intron_homing_endonuclease_target_region def: "A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke] synonym: "group 1 intron homing endonuclease target region" EXACT [] is_a: SO:0000684 ! nuclease_sensitive_site [Term] id: SO:0000355 name: haplotype_block def: "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma] synonym: "haplotype block" EXACT [] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000356 name: RNA def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0000357 name: flanked def: "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000359 name: floxed def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke] xref: http://en.wikipedia.org/wiki/Floxed "wiki" is_a: SO:0000357 ! flanked [Term] id: SO:0000360 name: codon def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Codon "wiki" is_a: SO:0000851 ! CDS_region [Term] id: SO:0000361 name: FRT_flanked def: "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke] synonym: "FRT flanked" EXACT [] is_a: SO:0000357 ! flanked [Term] id: SO:0000362 name: invalidated_by_chimeric_cDNA def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma] synonym: "invalidated by chimeric cDNA" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000363 name: floxed_gene def: "A transgene that is floxed." [SO:xp] synonym: "floxed gene" EXACT [] is_a: SO:0000902 ! transgene intersection_of: SO:0000902 ! transgene intersection_of: has_quality SO:0000359 ! floxed relationship: has_quality SO:0000359 ! floxed [Term] id: SO:0000364 name: transposable_element_flanking_region def: "The region of sequence surrounding a transposable element." [SO:ke] synonym: "transposable element flanking region" EXACT [] is_a: SO:0000239 ! flanking_region [Term] id: SO:0000365 name: integron def: "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as] xref: http://en.wikipedia.org/wiki/Integron "wiki" is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000366 name: insertion_site def: "The junction where an insertion occurred." [SO:ke] subset: SOFA synonym: "insertion site" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000367 name: attI_site def: "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as] synonym: "attI site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0000365 ! integron [Term] id: SO:0000368 name: transposable_element_insertion_site def: "The junction in a genome where a transposable_element has inserted." [SO:ke] subset: SOFA synonym: "transposable element insertion site" EXACT [] is_a: SO:0000366 ! insertion_site [Term] id: SO:0000369 name: integrase_coding_region is_obsolete: true [Term] id: SO:0000370 name: small_regulatory_ncRNA def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma] subset: SOFA synonym: "small regulatory ncRNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000371 name: conjugative_transposon def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html] synonym: "conjugative transposon" EXACT [] is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000372 name: enzymatic_RNA def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. subset: SOFA synonym: "enzymatic RNA" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0001185 ! enzymatic relationship: has_quality SO:0001185 ! enzymatic [Term] id: SO:0000373 name: recombinationally_inverted_gene def: "A recombinationally rearranged gene by inversion." [SO:xp] synonym: "recombinationally inverted gene" EXACT [] is_a: SO:0000456 ! recombinationally_rearranged_gene intersection_of: SO:0000456 ! recombinationally_rearranged_gene intersection_of: has_quality SO:1000036 ! inversion relationship: has_quality SO:1000036 ! inversion [Term] id: SO:0000374 name: ribozyme def: "An RNA with catalytic activity." [SO:ma] subset: SOFA xref: http://en.wikipedia.org/wiki/Ribozyme "wiki" is_a: SO:0000372 ! enzymatic_RNA intersection_of: SO:0000372 ! enzymatic_RNA intersection_of: has_quality SO:0001186 ! ribozymic relationship: has_quality SO:0001186 ! ribozymic [Term] id: SO:0000375 name: rRNA_5_8S def: "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002] subset: SOFA synonym: "5.8S LSU rRNA" EXACT [] synonym: "5.8S ribosomal RNA" EXACT [] synonym: "5.8S rRNA" EXACT [] synonym: "rRNA 5 8S" EXACT [] xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000376 name: RNA_6S def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013] synonym: "6S RNA" EXACT [] synonym: "RNA 6S" EXACT [] xref: http://en.wikipedia.org/wiki/6S_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000377 name: CsrB_RsmB_RNA def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018] synonym: "CsrB RsmB RNA" EXACT [] synonym: "CsrB-RsmB RNA" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000378 name: DsrA_RNA def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014] synonym: "DsrA RNA" EXACT [] xref: http://en.wikipedia.org/wiki/DsrA_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000379 name: GcvB_RNA def: "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022] synonym: "GcvB RNA" EXACT [] xref: http://en.wikipedia.org/wiki/GcvB_RNA "wiki" is_a: SO:0000378 ! DsrA_RNA [Term] id: SO:0000380 name: hammerhead_ribozyme def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805] subset: SOFA synonym: "hammerhead ribozyme" EXACT [] xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki" is_a: SO:0000715 ! RNA_motif intersection_of: SO:0000715 ! RNA_motif intersection_of: has_quality SO:0001186 ! ribozymic relationship: has_quality SO:0001186 ! ribozymic [Term] id: SO:0000381 name: group_IIA_intron synonym: "group IIA intron" EXACT [] is_a: SO:0000603 ! group_II_intron [Term] id: SO:0000382 name: group_IIB_intron synonym: "group IIB intron" EXACT [] is_a: SO:0000603 ! group_II_intron [Term] id: SO:0000383 name: MicF_RNA def: "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033] synonym: "MicF RNA" EXACT [] xref: http://en.wikipedia.org/wiki/MicF_RNA "wiki" is_a: SO:0000644 ! antisense_RNA [Term] id: SO:0000384 name: OxyS_RNA def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035] synonym: "OxyS RNA" EXACT [] xref: http://en.wikipedia.org/wiki/OxyS_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000385 name: RNase_MRP_RNA def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030] subset: SOFA synonym: "RNase MRP RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000386 name: RNase_P_RNA def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010] subset: SOFA synonym: "RNase P RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000387 name: RprA_RNA def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034] synonym: "RprA RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RprA_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000388 name: RRE_RNA def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036] synonym: "RRE RNA" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000389 name: spot_42_RNA def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021] synonym: "spot-42 RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Spot_42_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000390 name: telomerase_RNA def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025] subset: SOFA synonym: "telomerase RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000391 name: U1_snRNA def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003] subset: SOFA synonym: "small nuclear RNA U1" EXACT [RSC:cb] synonym: "snRNA U1" EXACT [RSC:cb] synonym: "U1 small nuclear RNA" EXACT [RSC:cb] synonym: "U1 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000392 name: U2_snRNA def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004] subset: SOFA synonym: "small nuclear RNA U2" EXACT [RSC:CB] synonym: "snRNA U2" EXACT [RSC:CB] synonym: "U2 small nuclear RNA" EXACT [RSC:CB] synonym: "U2 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000393 name: U4_snRNA def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U4" EXACT [RSC:cb] synonym: "snRNA U4" EXACT [RSC:cb] synonym: "U4 small nuclear RNA" EXACT [RSC:cb] synonym: "U4 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000394 name: U4atac_snRNA def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455] subset: SOFA synonym: "small nuclear RNA U4atac" EXACT [RSC:cb] synonym: "snRNA U4atac" EXACT [RSC:cb] synonym: "U4atac small nuclear RNA" EXACT [RSC:cb] synonym: "U4atac snRNA" EXACT [] is_a: SO:0000274 ! snRNA [Term] id: SO:0000395 name: U5_snRNA def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020] subset: SOFA synonym: "small nuclear RNA U5" EXACT [RSC:cb] synonym: "snRNA U5" EXACT [RSC:cb] synonym: "U5 small nuclear RNA" EXACT [RSC:cb] synonym: "U5 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000396 name: U6_snRNA def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U6" EXACT [RSC:cb] synonym: "snRNA U6" EXACT [RSC:cb] synonym: "U6 small nuclear RNA" EXACT [RSC:cb] synonym: "U6 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000397 name: U6atac_snRNA def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract] subset: SOFA synonym: "snRNA U6atac" EXACT [RSC:cb] synonym: "U6atac small nuclear RNA" EXACT [RSC:cb] synonym: "U6atac snRNA" EXACT [RSC:cb] is_a: SO:0000274 ! snRNA [Term] id: SO:0000398 name: U11_snRNA def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129] subset: SOFA synonym: "small nuclear RNA U11" EXACT [RSC:cb] synonym: "snRNA U11" EXACT [RSC:cb] synonym: "U11 small nuclear RNA" EXACT [RSC:cb] synonym: "U11 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000399 name: U12_snRNA def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007] subset: SOFA synonym: "small nuclear RNA U12" EXACT [RSC:cb] synonym: "snRNA U12" EXACT [RSC:cb] synonym: "U12 small nuclear RNA" EXACT [RSC:cb] synonym: "U12 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000400 name: sequence_attribute def: "An attribute describes a quality of sequence." [SO:ke] synonym: "sequence attribute" EXACT [] [Term] id: SO:0000401 name: gene_attribute synonym: "gene attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000402 name: enhancer_attribute is_obsolete: true [Term] id: SO:0000403 name: U14_snoRNA alt_id: SO:0005839 def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119] comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. subset: SOFA synonym: "small nucleolar RNA U14" EXACT [] synonym: "snoRNA U14" EXACT [] synonym: "U14 small nucleolar RNA" EXACT [] synonym: "U14 snoRNA" EXACT [] is_a: SO:0000593 ! C_D_box_snoRNA relationship: derives_from SO:0005837 ! U14_snoRNA_primary_transcript [Term] id: SO:0000404 name: vault_RNA def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006] subset: SOFA synonym: "vault RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000405 name: Y_RNA def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019] subset: SOFA synonym: "Y RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Y_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000406 name: twintron def: "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908] xref: http://en.wikipedia.org/wiki/Twintron "wiki" is_a: SO:0000188 ! intron [Term] id: SO:0000407 name: rRNA_18S def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "18S ribosomal RNA" EXACT [] synonym: "18S rRNA" EXACT [] synonym: "rRNA 18S" EXACT [] xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki" is_a: SO:0000650 ! small_subunit_rRNA [Term] id: SO:0000408 name: site def: "The interbase position where something (eg an aberration) occurred." [SO:ke] is_obsolete: true [Term] id: SO:0000409 name: binding_site alt_id: BS:00033 def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] comment: See GO:0005488 : binding. subset: biosapiens subset: SOFA synonym: "binding_or_interaction_site" EXACT [] synonym: "site" RELATED [] xref: http://en.wikipedia.org/wiki/Binding_site "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000410 name: protein_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke] comment: See GO:0042277 : peptide binding. subset: SOFA synonym: "protein binding site" EXACT [] is_a: SO:0000409 ! binding_site [Term] id: SO:0000411 name: rescue_region def: "A region that rescues." [SO:xp] synonym: "rescue fragment" EXACT [] synonym: "rescue region" EXACT [] synonym: "rescue segment" RELATED [] is_a: SO:0000695 ! reagent intersection_of: SO:0000695 ! reagent intersection_of: has_quality SO:0000814 ! rescue relationship: has_quality SO:0000814 ! rescue [Term] id: SO:0000412 name: restriction_fragment def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke] subset: SOFA synonym: "restriction fragment" EXACT [] xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki" is_a: SO:0000143 ! assembly_component [Term] id: SO:0000413 name: sequence_difference def: "A region where the sequence differs from that of a specified sequence." [SO:ke] subset: SOFA synonym: "sequence difference" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000414 name: invalidated_by_genomic_contamination def: "An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke] synonym: "invalidated by genomic contamination" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000415 name: invalidated_by_genomic_polyA_primed_cDNA def: "An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke] synonym: "invalidated by genomic polyA primed cDNA" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000416 name: invalidated_by_partial_processing def: "An attribute to describe a feature that is invalidated due to partial processing." [SO:ke] synonym: "invalidated by partial processing" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000417 name: polypeptide_domain alt_id: BS:00012 alt_id: BS:00134 alt_id: SO:0001069 def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR] comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains. subset: biosapiens synonym: "ca_bind" RELATED BS [uniprot:feature_type] synonym: "DNA_bind" RELATED BS [uniprot:feature_type] synonym: "domain" BROAD BS [uniprot:feature_type] synonym: "np_bind" RELATED BS [uniprot:feature_type] synonym: "polypeptide domain" EXACT [] synonym: "polypeptide_structural_domain" EXACT BS [] synonym: "structural domain" BROAD BS [] synonym: "zn_fing" RELATED BS [uniprot:feature_type] is_a: SO:0001070 ! polypeptide_structural_region is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0000418 name: signal_peptide alt_id: BS:00159 def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence. subset: biosapiens subset: SOFA synonym: "signal" RELATED [uniprot:feature_type] synonym: "signal peptide" EXACT [] synonym: "signal peptide coding sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki" is_a: SO:0001527 ! peptide_localization_signal relationship: part_of SO:0001062 ! propeptide [Term] id: SO:0000419 name: mature_protein_region alt_id: BS:00149 def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb] comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification. subset: biosapiens subset: SOFA synonym: "chain" RELATED [uniprot:feature_type] synonym: "mature peptide" RELATED [] synonym: "mature protein region" EXACT [] is_a: SO:0000839 ! polypeptide_region relationship: part_of SO:0001063 ! immature_peptide_region [Term] id: SO:0000420 name: five_prime_terminal_inverted_repeat synonym: "5' TIR" EXACT [] synonym: "five prime terminal inverted repeat" EXACT [] is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000421 name: three_prime_terminal_inverted_repeat synonym: "3' TIR" EXACT [] synonym: "three prime terminal inverted repeat" EXACT [] is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000422 name: U5_LTR_region synonym: "U5 long terminal repeat region" EXACT [] synonym: "U5 LTR region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000423 name: R_LTR_region synonym: "R long terminal repeat region" EXACT [] synonym: "R LTR region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000424 name: U3_LTR_region synonym: "U3 long terminal repeat region" EXACT [] synonym: "U3 LTR region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000425 name: five_prime_LTR synonym: "5' long terminal repeat" EXACT [] synonym: "5' LTR" EXACT [] synonym: "five prime LTR" EXACT [] is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0000426 name: three_prime_LTR synonym: "3' long terminal repeat" EXACT [] synonym: "3' LTR" EXACT [] synonym: "three prime LTR" EXACT [] is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0000427 name: R_five_prime_LTR_region synonym: "R 5' long term repeat region" EXACT [] synonym: "R five prime LTR region" EXACT [] is_a: SO:0000423 ! R_LTR_region is_a: SO:0000850 ! five_prime_LTR_component [Term] id: SO:0000428 name: U5_five_prime_LTR_region synonym: "U5 5' long terminal repeat region" EXACT [] synonym: "U5 five prime LTR region" EXACT [] is_a: SO:0000422 ! U5_LTR_region is_a: SO:0000850 ! five_prime_LTR_component [Term] id: SO:0000429 name: U3_five_prime_LTR_region synonym: "U3 5' long term repeat region" EXACT [] synonym: "U3 five prime LTR region" EXACT [] is_a: SO:0000424 ! U3_LTR_region is_a: SO:0000850 ! five_prime_LTR_component [Term] id: SO:0000430 name: R_three_prime_LTR_region synonym: "R 3' long terminal repeat region" EXACT [] synonym: "R three prime LTR region" EXACT [] is_a: SO:0000849 ! three_prime_LTR_component [Term] id: SO:0000431 name: U3_three_prime_LTR_region synonym: "U3 3' long terminal repeat region" EXACT [] synonym: "U3 three prime LTR region" EXACT [] is_a: SO:0000849 ! three_prime_LTR_component [Term] id: SO:0000432 name: U5_three_prime_LTR_region synonym: "U5 3' long terminal repeat region" EXACT [] synonym: "U5 three prime LTR region" EXACT [] is_a: SO:0000849 ! three_prime_LTR_component [Term] id: SO:0000433 name: non_LTR_retrotransposon_polymeric_tract def: "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke] synonym: "non LTR retrotransposon polymeric tract" EXACT [] is_a: SO:0000657 ! repeat_region is_a: SO:0000840 ! repeat_component relationship: part_of SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000434 name: target_site_duplication def: "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html] synonym: "target site duplication" EXACT [] is_a: SO:0000314 ! direct_repeat intersection_of: SO:0000314 ! direct_repeat intersection_of: derives_from SO:0000101 ! transposable_element relationship: derives_from SO:0000101 ! transposable_element [Term] id: SO:0000435 name: RR_tract def: "A polypurine tract within an LTR_retrotransposon." [SO:ke] synonym: "LTR retrotransposon poly purine tract" RELATED [] synonym: "RR tract" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0000186 ! LTR_retrotransposon [Term] id: SO:0000436 name: ARS def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma] subset: SOFA synonym: "autonomously replicating sequence" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000437 name: assortment_derived_duplication is_obsolete: true [Term] id: SO:0000438 name: gene_not_polyadenylated is_obsolete: true [Term] id: SO:0000439 name: inverted_ring_chromosome synonym: "inverted ring chromosome" EXACT [] is_a: SO:1000030 ! chromosomal_inversion is_a: SO:1000045 ! ring_chromosome [Term] id: SO:0000440 name: vector_replicon def: "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "vector" EXACT [] synonym: "vector replicon" EXACT [] xref: http://en.wikipedia.org/wiki/Vector_(molecular_biology) "wiki" is_a: SO:0001235 ! replicon relationship: part_of SO:0000151 ! clone [Term] id: SO:0000441 name: ss_oligo def: "A single stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "single strand oligo" EXACT [] synonym: "single strand oligonucleotide" EXACT [] synonym: "single stranded oligonucleotide" EXACT [] synonym: "ss oligo" EXACT [] synonym: "ss oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000442 name: ds_oligo def: "A double stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "double stranded oligonucleotide" EXACT [] synonym: "ds oligo" EXACT [] synonym: "ds-oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000443 name: polymer_attribute def: "An attribute to describe the kind of biological sequence." [SO:ke] synonym: "polymer attribute" EXACT [] is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000444 name: three_prime_noncoding_exon def: "Non-coding exon in the 3' UTR." [SO:ke] synonym: "three prime noncoding exon" EXACT [] is_a: SO:0000198 ! noncoding_exon [Term] id: SO:0000445 name: five_prime_noncoding_exon def: "Non-coding exon in the 5' UTR." [SO:ke] synonym: "5' nc exon" EXACT [] synonym: "5' non coding exon" EXACT [] synonym: "five prime noncoding exon" EXACT [] is_a: SO:0000198 ! noncoding_exon [Term] id: SO:0000446 name: UTR_intron def: "Intron located in the untranslated region." [SO:ke] synonym: "UTR intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000447 name: five_prime_UTR_intron def: "An intron located in the 5' UTR." [SO:ke] synonym: "five prime UTR intron" EXACT [] is_a: SO:0000446 ! UTR_intron [Term] id: SO:0000448 name: three_prime_UTR_intron def: "An intron located in the 3' UTR." [SO:ke] synonym: "three prime UTR intron" EXACT [] is_a: SO:0000446 ! UTR_intron [Term] id: SO:0000449 name: random_sequence def: "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components." [SO:ma] synonym: "random sequence" EXACT [] is_a: SO:0000351 ! synthetic_sequence [Term] id: SO:0000450 name: interband def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma] synonym: "chromosome interband" RELATED [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000451 name: gene_with_polyadenylated_mRNA def: "A gene that encodes a polyadenylated mRNA." [SO:xp] synonym: "gene with polyadenylated mRNA" EXACT [] is_a: SO:0001217 ! protein_coding_gene intersection_of: SO:0001217 ! protein_coding_gene intersection_of: transcribed_to SO:0000871 ! polyadenylated_mRNA relationship: transcribed_to SO:0000871 ! polyadenylated_mRNA [Term] id: SO:0000452 name: transgene_attribute is_obsolete: true [Term] id: SO:0000453 name: chromosomal_transposition def: "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke] synonym: "chromosomal transposition" EXACT [] synonym: "transposition" NARROW [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:0000454 name: rasiRNA def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284] subset: SOFA synonym: "repeat associated small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RasiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000455 name: gene_with_mRNA_with_frameshift def: "A gene that encodes an mRNA with a frameshift." [SO:xp] synonym: "gene with mRNA with frameshift" EXACT [] is_a: SO:0001217 ! protein_coding_gene intersection_of: SO:0001217 ! protein_coding_gene intersection_of: has_quality SO:0000865 ! frameshift relationship: has_quality SO:0000865 ! frameshift [Term] id: SO:0000456 name: recombinationally_rearranged_gene def: "A gene that is recombinationally rearranged." [SO:ke] synonym: "recombinationally rearranged gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000940 ! recombinationally_rearranged relationship: has_quality SO:0000940 ! recombinationally_rearranged [Term] id: SO:0000457 name: interchromosomal_duplication def: "A chromosome duplication involving an insertion from another chromosome." [SO:ke] synonym: "interchromosomal duplication" EXACT [] is_a: SO:1000037 ! chromosomal_duplication [Term] id: SO:0000458 name: D_gene_segment def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D gene" EXACT [] synonym: "D-GENE" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000459 name: gene_with_trans_spliced_transcript def: "A gene with a transcript that is trans-spliced." [SO:xp] synonym: "gene with trans spliced transcript" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: transcribed_to SO:0000479 ! trans_spliced_transcript relationship: transcribed_to SO:0000479 ! trans_spliced_transcript [Term] id: SO:0000460 name: vertebrate_immunoglobulin_T_cell_receptor_segment comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'. synonym: "vertebrate immunoglobulin T cell receptor segment" EXACT [] synonym: "vertebrate_immunoglobulin/T-cell receptor gene" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000461 name: inversion_derived_bipartite_deficiency def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km] synonym: "inversion derived bipartite deficiency" EXACT [] is_a: SO:1000029 ! chromosomal_deletion [Term] id: SO:0000462 name: pseudogenic_region def: "A non-functional descendent of a functional entity." [SO:cjm] subset: SOFA synonym: "pseudogenic region" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000463 name: encodes_alternately_spliced_transcripts def: "A gene that encodes more than one transcript." [SO:ke] synonym: "encodes alternately spliced transcripts" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000464 name: decayed_exon def: "A non-functional descendant of an exon." [SO:ke] subset: SOFA synonym: "decayed exon" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000147 ! exon [Term] id: SO:0000465 name: inversion_derived_deficiency_plus_duplication def: "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km] synonym: "inversion derived deficiency plus duplication" EXACT [] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000466 name: V_gene_segment def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V gene" EXACT [] synonym: "V-GENE" EXACT [] synonym: "variable_gene" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000467 name: post_translationally_regulated_by_protein_stability def: "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke] synonym: "post translationally regulated by protein stability" EXACT [] synonym: "post-translationally regulated by protein stability" EXACT [] is_a: SO:0000130 ! post_translationally_regulated [Term] id: SO:0000468 name: golden_path_fragment def: "One of the pieces of sequence that make up a golden path." [SO:rd] subset: SOFA synonym: "golden path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000688 ! golden_path [Term] id: SO:0000469 name: post_translationally_regulated_by_protein_modification def: "An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke] synonym: "post translationally regulated by protein modification" EXACT [] synonym: "post-translationally regulated by protein modification" EXACT [] is_a: SO:0000130 ! post_translationally_regulated [Term] id: SO:0000470 name: J_gene_segment def: "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J gene" EXACT [] synonym: "J-GENE" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000471 name: autoregulated def: "The gene product is involved in its own transcriptional regulation." [SO:ke] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000472 name: tiling_path def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm] subset: SOFA synonym: "tiling path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000473 name: negatively_autoregulated def: "The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke] synonym: "negatively autoregulated" EXACT [] is_a: SO:0000126 ! transcriptionally_repressed is_a: SO:0000471 ! autoregulated [Term] id: SO:0000474 name: tiling_path_fragment def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke] subset: SOFA synonym: "tiling path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000472 ! tiling_path [Term] id: SO:0000475 name: positively_autoregulated def: "The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke] synonym: "positively autoregulated" EXACT [] is_a: SO:0000125 ! transcriptionally_induced is_a: SO:0000471 ! autoregulated [Term] id: SO:0000476 name: contig_read def: "A DNA sequencer read which is part of a contig." [SO:ke] synonym: "contig read" EXACT [] is_a: SO:0000150 ! read [Term] id: SO:0000477 name: polycistronic_gene def: "A gene that is polycistronic." [SO:ke] is_obsolete: true [Term] id: SO:0000478 name: C_gene_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "C gene" EXACT [] synonym: "C_GENE" EXACT [] synonym: "constant gene" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000479 name: trans_spliced_transcript def: "A transcript that is trans-spliced." [SO:xp] synonym: "trans spliced transcript" EXACT [] synonym: "trans-spliced transcript" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000870 ! trans_spliced relationship: has_quality SO:0000870 ! trans_spliced [Term] id: SO:0000480 name: tiling_path_clone def: "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke] synonym: "tiling path clone" EXACT [] is_a: SO:0000151 ! clone is_a: SO:0000474 ! tiling_path_fragment [Term] id: SO:0000481 name: terminal_inverted_repeat def: "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke] synonym: "terminal inverted repeat" EXACT [] synonym: "TIR" EXACT [] is_a: SO:0000294 ! inverted_repeat relationship: part_of SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000482 name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster synonym: "vertebrate immunoglobulin T cell receptor gene cluster" EXACT [] synonym: "vertebrate_immunoglobulin/T-cell receptor gene cluster" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000483 name: nc_primary_transcript def: "A primary transcript that is never translated into a protein." [SO:ke] subset: SOFA synonym: "nc primary transcript" EXACT [] synonym: "noncoding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000484 name: three_prime_coding_exon_noncoding_region def: "The sequence of the 3' exon that is not coding." [SO:ke] subset: SOFA synonym: "three prime coding exon noncoding region" EXACT [] synonym: "three_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon relationship: part_of SO:0000202 ! three_prime_coding_exon [Term] id: SO:0000485 name: DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(DJ)-J-CLUSTER" EXACT [] synonym: "DJ J cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000486 name: five_prime_coding_exon_noncoding_region def: "The sequence of the 5' exon preceding the start codon." [SO:ke] subset: SOFA synonym: "five prime coding exon noncoding region" EXACT [] synonym: "five_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000487 name: VDJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VDJ)-J-C-CLUSTER" EXACT [] synonym: "VDJ J C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000488 name: VDJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VDJ)-J-CLUSTER" EXACT [] synonym: "VDJ J cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000489 name: VJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VJ)-C-CLUSTER" RELATED [] synonym: "VJ C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000490 name: VJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VJ)-J-C-CLUSTER" EXACT [] synonym: "VJ J C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000491 name: VJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VJ)-J-CLUSTER" EXACT [] synonym: "VJ J cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000492 name: D_gene_recombination_feature synonym: "D gene recombination feature" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000493 name: three_prime_D_heptamer def: "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-HEPTAMER" EXACT [] synonym: "three prime D heptamer" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence [Term] id: SO:0000494 name: three_prime_D_nonamer def: "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-NOMAMER" EXACT [] synonym: "three prime D nonamer" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence [Term] id: SO:0000495 name: three_prime_D_spacer def: "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-SPACER" EXACT [] synonym: "three prime D spacer" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence [Term] id: SO:0000496 name: five_prime_D_heptamer def: "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'D-HEPTAMER" EXACT [] synonym: "five prime D heptamer" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000497 name: five_prime_D_nonamer def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'D-NONAMER" EXACT [] synonym: "five prime D nonamer" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000498 name: five_prime_D_spacer def: "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'-SPACER" EXACT [] synonym: "five prime D spacer" EXACT [] synonym: "five prime D-spacer" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000499 name: virtual_sequence def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke] subset: SOFA synonym: "virtual sequence" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000500 name: Hoogsteen_base_pair def: "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293] synonym: "Hoogsteen base pair" EXACT [] xref: http://en.wikipedia.org/wiki/Hoogsteen_base_pair "wiki" is_a: SO:0000028 ! base_pair [Term] id: SO:0000501 name: reverse_Hoogsteen_base_pair def: "A type of non-canonical base-pairing." [SO:ke] synonym: "reverse Hoogsteen base pair" EXACT [] is_a: SO:0000028 ! base_pair [Term] id: SO:0000502 name: transcribed_region def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke] comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being. subset: SOFA is_obsolete: true [Term] id: SO:0000503 name: alternately_spliced_gene_encodeing_one_transcript is_obsolete: true [Term] id: SO:0000504 name: D_DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ C cluster" EXACT [] synonym: "D-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000505 name: D_DJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ cluster" EXACT [] synonym: "D-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000506 name: D_DJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ J C cluster" EXACT [] synonym: "D-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000507 name: pseudogenic_exon def: "A non functional descendant of an exon, part of a pseudogene." [SO:ke] comment: This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. synonym: "pseudogenic exon" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000147 ! exon relationship: part_of SO:0000516 ! pseudogenic_transcript [Term] id: SO:0000508 name: D_DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ J cluster" EXACT [] synonym: "D-(DJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000509 name: D_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D J C cluster" EXACT [] synonym: "D-J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000510 name: VD_gene_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V_D_GENE" EXACT [] synonym: "VD gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000511 name: J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J C cluster" EXACT [] synonym: "J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000512 name: inversion_derived_deficiency_plus_aneuploid def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] synonym: "inversion derived deficiency plus aneuploid" EXACT [] is_a: SO:1000029 ! chromosomal_deletion [Term] id: SO:0000513 name: J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J cluster" EXACT [] synonym: "J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000514 name: J_nonamer def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J nonamer" EXACT [] synonym: "J-NONAMER" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000302 ! J_gene_recombination_feature [Term] id: SO:0000515 name: J_heptamer def: "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J heptamer" EXACT [] synonym: "J-HEPTAMER" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000302 ! J_gene_recombination_feature [Term] id: SO:0000516 name: pseudogenic_transcript def: "A non functional descendant of a transcript, part of a pseudogene." [SO:ke] comment: This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. synonym: "pseudogenic transcript" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000673 ! transcript relationship: part_of SO:0000336 ! pseudogene [Term] id: SO:0000517 name: J_spacer def: "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J spacer" EXACT [] synonym: "J-SPACER" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000302 ! J_gene_recombination_feature [Term] id: SO:0000518 name: V_DJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ cluster" EXACT [] synonym: "V-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000519 name: V_DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ J cluster" EXACT [] synonym: "V-(DJ)-J-CLUSTER" RELATED [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000520 name: V_VDJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ C cluster" EXACT [] synonym: "V-(VDJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000521 name: V_VDJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ cluster" EXACT [] synonym: "V-(VDJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000522 name: V_VDJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ J cluster" EXACT [] synonym: "V-(VDJ)-J-CLUSTER" RELATED [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000523 name: V_VJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ C cluster" EXACT [] synonym: "V-(VJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000524 name: V_VJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ cluster" EXACT [] synonym: "V-(VJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000525 name: V_VJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ J cluster" EXACT [] synonym: "V-(VJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000526 name: V_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V cluster" EXACT [] synonym: "V-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment [Term] id: SO:0000527 name: V_D_DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ C cluster" EXACT [] synonym: "V-D-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000528 name: V_D_DJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ cluster" EXACT [] synonym: "V-D-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000529 name: V_D_DJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ J C cluster" EXACT [] synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000530 name: V_D_DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ J cluster" EXACT [] synonym: "V-D-(DJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000531 name: V_D_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D J C cluster" EXACT [] synonym: "V-D-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000532 name: V_D_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D J cluster" EXACT [] synonym: "V-D-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000533 name: V_heptamer def: "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V heptamer" EXACT [] synonym: "V-HEPTAMER" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000538 ! V_gene_recombination_feature [Term] id: SO:0000534 name: V_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V J cluster" EXACT [] synonym: "V-J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000535 name: V_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V J C cluster" EXACT [] synonym: "V-J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000536 name: V_nonamer def: "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V nonamer" EXACT [] synonym: "V-NONAMER" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000538 ! V_gene_recombination_feature [Term] id: SO:0000537 name: V_spacer def: "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V spacer" EXACT [] synonym: "V-SPACER" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000538 ! V_gene_recombination_feature [Term] id: SO:0000538 name: V_gene_recombination_feature def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V gene recombination feature" EXACT [] synonym: "V-RS" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000539 name: DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(DJ)-C-CLUSTER" EXACT [] synonym: "DJ C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000540 name: DJ_J_C_cluster def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(DJ)-J-C-CLUSTER" EXACT [] synonym: "DJ J C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000541 name: VDJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VDJ)-C-CLUSTER" EXACT [] synonym: "VDJ C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000542 name: V_DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ C cluster" EXACT [] synonym: "V-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000543 name: alternately_spliced_gene_encoding_greater_than_one_transcript is_obsolete: true [Term] id: SO:0000544 name: helitron def: "A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569] synonym: "ISCR" RELATED [] xref: http://en.wikipedia.org/wiki/Helitron "wiki" is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000545 name: recoding_pseudoknot def: "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937] synonym: "recoding pseudoknot" EXACT [] is_a: SO:0000591 ! pseudoknot relationship: part_of SO:1001268 ! recoding_stimulatory_region [Term] id: SO:0000546 name: designed_sequence synonym: "designed sequence" EXACT [] is_a: SO:0000351 ! synthetic_sequence [Term] id: SO:0000547 name: inversion_derived_bipartite_duplication def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km] synonym: "inversion derived bipartite duplication" EXACT [] is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000548 name: gene_with_edited_transcript def: "A gene that encodes a transcript that is edited." [SO:xp] synonym: "gene with edited transcript" EXACT [] is_a: SO:0001217 ! protein_coding_gene intersection_of: SO:0001217 ! protein_coding_gene intersection_of: transcribed_to SO:0000873 ! edited_transcript relationship: transcribed_to SO:0000873 ! edited_transcript [Term] id: SO:0000549 name: inversion_derived_duplication_plus_aneuploid def: "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] synonym: "inversion derived duplication plus aneuploid" EXACT [] is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000550 name: aneuploid_chromosome def: "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke] comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila. synonym: "aneuploid chromosome" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:0000551 name: polyA_signal_sequence def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "poly(A) signal" EXACT [] synonym: "polyA signal sequence" EXACT [] synonym: "polyadenylation termination signal" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0000552 name: Shine_Dalgarno_sequence def: "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh] comment: Not found in Eukaryotic sequence. synonym: "five prime ribosome binding site" EXACT [] synonym: "RBS" RELATED [] synonym: "Shine Dalgarno sequence" EXACT [] synonym: "Shine-Dalgarno sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence "wiki" is_a: SO:0000139 ! ribosome_entry_site [Term] id: SO:0000553 name: polyA_site alt_id: SO:0001430 def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "polyA cleavage site" EXACT [] synonym: "polyA junction" EXACT [] synonym: "polyA site" EXACT [] synonym: "polyA_junction" EXACT [] synonym: "polyadenylation site" RELATED [] is_a: SO:0000699 ! junction relationship: part_of SO:0000205 ! three_prime_UTR relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000554 name: assortment_derived_deficiency_plus_duplication is_obsolete: true [Term] id: SO:0000555 name: five_prime_clip def: "5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "5' clip" RELATED [] synonym: "five prime clip" EXACT [] is_a: SO:0000303 ! clip [Term] id: SO:0000556 name: five_prime_D_recombination_signal_sequence def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'RS" EXACT [] synonym: "five prime D recombination signal sequence" EXACT [] synonym: "five prime D-recombination signal sequence" EXACT [] is_a: SO:0000492 ! D_gene_recombination_feature [Term] id: SO:0000557 name: three_prime_clip def: "3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "3'-clip" EXACT [] synonym: "three prime clip" EXACT [] is_a: SO:0000303 ! clip [Term] id: SO:0000558 name: C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "C cluster" EXACT [] synonym: "C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000559 name: D_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D cluster" EXACT [] synonym: "D-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment [Term] id: SO:0000560 name: D_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D J cluster" EXACT [] synonym: "D-J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000561 name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene def: "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "HEPTAMER" RELATED [] synonym: "heptamer of recombination feature of vertebrate immune system gene" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000562 name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene synonym: "nonamer of recombination feature of vertebrate immune system gene" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000563 name: vertebrate_immune_system_gene_recombination_spacer synonym: "vertebrate immune system gene recombination spacer" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000564 name: V_DJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ J C cluster" EXACT [] synonym: "V-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000565 name: V_VDJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ J C cluster" EXACT [] synonym: "V-(VDJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000566 name: V_VJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ J C cluster" EXACT [] synonym: "V-(VJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000567 name: inversion_derived_aneuploid_chromosome def: "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km] synonym: "inversion derived aneuploid chromosome" EXACT [] is_a: SO:0000550 ! aneuploid_chromosome [Term] id: SO:0000568 name: bidirectional_promoter synonym: "bidirectional promoter" EXACT [] is_a: SO:0000167 ! promoter [Term] id: SO:0000569 name: retrotransposed alt_id: SO:0100042 def: "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke] comment: GO:0003964 RNA-directed DNA polymerase activity. xref: http://en.wikipedia.org/wiki/Retrotransposed "wiki" is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000570 name: three_prime_D_recombination_signal_sequence def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-RS" EXACT [] synonym: "three prime D recombination signal sequence" EXACT [] synonym: "three_prime_D-recombination_signal_sequence" EXACT [] is_a: SO:0000492 ! D_gene_recombination_feature [Term] id: SO:0000571 name: miRNA_encoding synonym: "miRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000572 name: DJ_gene_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D-J-GENE" EXACT [] synonym: "DJ gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000573 name: rRNA_encoding synonym: "rRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000574 name: VDJ_gene_segment def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V-D-J-GENE" EXACT [] synonym: "VDJ gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000575 name: scRNA_encoding synonym: "scRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000576 name: VJ_gene_segment def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V-J-GENE" EXACT [] synonym: "VJ gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000577 name: centromere def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Centromere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000578 name: snoRNA_encoding synonym: "snoRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000579 name: edited_transcript_feature def: "A locatable feature on a transcript that is edited." [SO:ma] synonym: "edited transcript feature" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000580 name: methylation_guide_snoRNA_primary_transcript def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke] synonym: "methylation guide snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000581 name: cap def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] subset: SOFA xref: http://en.wikipedia.org/wiki/5%27_cap "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000582 name: rRNA_cleavage_snoRNA_primary_transcript def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke] synonym: "rRNA cleavage snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000583 name: pre_edited_region def: "The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "pre edited region" EXACT [] synonym: "pre-edited region" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000584 name: tmRNA def: "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023] synonym: "10Sa RNA" RELATED [] synonym: "ssrA" RELATED [] xref: http://en.wikipedia.org/wiki/TmRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000585 name: C_D_box_snoRNA_encoding synonym: "C/D box snoRNA encoding" EXACT [] is_a: SO:0000578 ! snoRNA_encoding [Term] id: SO:0000586 name: tmRNA_primary_transcript def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke] synonym: "10Sa RNA primary transcript" RELATED [] synonym: "ssrA RNA primary transcript" RELATED [] synonym: "tmRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000587 name: group_I_intron def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028] comment: GO:0000372. subset: SOFA synonym: "group I intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000588 name: autocatalytically_spliced_intron def: "A self spliced intron." [SO:ke] subset: SOFA synonym: "autocatalytically spliced intron" EXACT [] is_a: SO:0000188 ! intron intersection_of: SO:0000188 ! intron intersection_of: has_quality SO:0001186 ! ribozymic relationship: has_quality SO:0001186 ! ribozymic [Term] id: SO:0000589 name: SRP_RNA_primary_transcript def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke] synonym: "SRP RNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000590 name: SRP_RNA def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017] subset: SOFA synonym: "7S RNA" RELATED [] synonym: "signal recognition particle RNA" RELATED [] synonym: "SRP RNA" EXACT [] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000589 ! SRP_RNA_primary_transcript [Term] id: SO:0000591 name: pseudoknot def: "A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb] xref: http://en.wikipedia.org/wiki/Pseudoknot "wiki" is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000592 name: H_pseudoknot def: "A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract] synonym: "classical pseudoknot" EXACT [] synonym: "H pseudoknot" EXACT [] synonym: "H-pseudoknot" EXACT [] synonym: "H-type pseudoknot" EXACT [] synonym: "hairpin-type pseudoknot" EXACT [] is_a: SO:0000591 ! pseudoknot [Term] id: SO:0000593 name: C_D_box_snoRNA def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] subset: SOFA synonym: "box C/D snoRNA" EXACT [] synonym: "C D box snoRNA" EXACT [] synonym: "C/D box snoRNA" EXACT [] is_a: SO:0000275 ! snoRNA relationship: derives_from SO:0000595 ! C_D_box_snoRNA_primary_transcript [Term] id: SO:0000594 name: H_ACA_box_snoRNA def: "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] synonym: "box H/ACA snoRNA" EXACT [] synonym: "H ACA box snoRNA" EXACT [] synonym: "H/ACA box snoRNA" EXACT [] is_a: SO:0000275 ! snoRNA relationship: derives_from SO:0000596 ! H_ACA_box_snoRNA_primary_transcript [Term] id: SO:0000595 name: C_D_box_snoRNA_primary_transcript def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke] synonym: "C/D box snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000596 name: H_ACA_box_snoRNA_primary_transcript def: "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke] synonym: "H ACA box snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000597 name: transcript_edited_by_U_insertion/deletion def: "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html] is_obsolete: true [Term] id: SO:0000598 name: edited_by_C_insertion_and_dinucleotide_insertion synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED [] is_obsolete: true [Term] id: SO:0000599 name: edited_by_C_to_U_substitution is_obsolete: true [Term] id: SO:0000600 name: edited_by_A_to_I_substitution is_obsolete: true [Term] id: SO:0000601 name: edited_by_G_addition is_obsolete: true [Term] id: SO:0000602 name: guide_RNA def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html] subset: SOFA synonym: "gRNA" EXACT [] synonym: "guide RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000603 name: group_II_intron def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml] comment: GO:0000373. subset: SOFA synonym: "group II intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000604 name: editing_block def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "editing block" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000605 name: intergenic_region def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "intergenic region" EXACT [] xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000606 name: editing_domain def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "editing domain" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000607 name: unedited_region def: "The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "unedited region" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000608 name: H_ACA_box_snoRNA_encoding synonym: "H ACA box snoRNA encoding" EXACT [] is_a: SO:0000578 ! snoRNA_encoding [Term] id: SO:0000609 name: oligo_U_tail def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/] synonym: "oligo U tail" EXACT [] is_a: SO:0001411 ! biological_region relationship: adjacent_to SO:0000602 ! guide_RNA [Term] id: SO:0000610 name: polyA_sequence def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] subset: SOFA synonym: "polyA sequence" EXACT [] is_a: SO:0001411 ! biological_region relationship: adjacent_to SO:0000234 ! mRNA [Term] id: SO:0000611 name: branch_site def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke] subset: SOFA synonym: "branch point" EXACT [] synonym: "branch site" EXACT [] synonym: "branch_point" EXACT [] is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000612 name: polypyrimidine_tract def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888] subset: SOFA synonym: "polypyrimidine tract" EXACT [] xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki" is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000613 name: bacterial_RNApol_promoter def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke] synonym: "bacterial RNApol promoter" EXACT [] is_a: SO:0000752 ! gene_group_regulatory_region is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000614 name: bacterial_terminator def: "A terminator signal for bacterial transcription." [SO:ke] synonym: "bacterial terminator" EXACT [] is_a: SO:0000141 ! terminator is_a: SO:0000752 ! gene_group_regulatory_region [Term] id: SO:0000615 name: terminator_of_type_2_RNApol_III_promoter def: "A terminator signal for RNA polymerase III transcription." [SO:ke] synonym: "terminator of type 2 RNApol III promoter" EXACT [] is_a: SO:0000951 ! eukaryotic_terminator [Term] id: SO:0000616 name: transcription_end_site def: "The base where transcription ends." [SO:ke] subset: SOFA synonym: "transcription end site" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000617 name: RNApol_III_promoter_type_1 synonym: "RNApol III promoter type 1" EXACT [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000618 name: RNApol_III_promoter_type_2 synonym: "RNApol III promoter type 2" EXACT [] synonym: "tRNA promoter" RELATED [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000619 name: A_box def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke] comment: Binds TFIIIC. synonym: "A-box" EXACT [] xref: http://en.wikipedia.org/wiki/A-box "wiki" is_a: SO:0001660 ! core_promoter_element [Term] id: SO:0000620 name: B_box def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke] comment: Binds TFIIIC. synonym: "B-box" EXACT [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 [Term] id: SO:0000621 name: RNApol_III_promoter_type_3 synonym: "RNApol III promoter type 3" EXACT [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000622 name: C_box def: "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke] synonym: "C-box" EXACT [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 [Term] id: SO:0000623 name: snRNA_encoding synonym: "snRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000624 name: telomere def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma] subset: SOFA synonym: "telomeric DNA" EXACT [] synonym: "telomeric sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Telomere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000625 name: silencer def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki" is_a: SO:0000727 ! CRM [Term] id: SO:0000626 name: chromosomal_regulatory_element synonym: "chromosomal regulatory element" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000627 name: insulator def: "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative] subset: SOFA synonym: "insulator element" EXACT [] xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000628 name: chromosomal_structural_element subset: SOFA synonym: "chromosomal structural element" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000629 name: five_prime_open_reading_frame synonym: "five prime open reading frame" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000204 ! five_prime_UTR [Term] id: SO:0000630 name: upstream_AUG_codon def: "A start codon upstream of the ORF." [SO:ke] synonym: "upstream AUG codon" EXACT [] is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000203 ! UTR [Term] id: SO:0000631 name: polycistronic_primary_transcript def: "A primary transcript encoding for more than one gene product." [SO:ke] synonym: "polycistronic primary transcript" EXACT [] is_a: SO:0000078 ! polycistronic_transcript is_a: SO:0000185 ! primary_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: has_quality SO:0000880 ! polycistronic relationship: has_quality SO:0000880 ! polycistronic [Term] id: SO:0000632 name: monocistronic_primary_transcript def: "A primary transcript encoding for one gene product." [SO:ke] synonym: "monocistronic primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript is_a: SO:0000665 ! monocistronic_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: has_quality SO:0000878 ! monocistronic relationship: has_quality SO:0000878 ! monocistronic [Term] id: SO:0000633 name: monocistronic_mRNA def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd] synonym: "monocistronic mRNA" EXACT [] synonym: "monocistronic processed transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA "wiki" is_a: SO:0000234 ! mRNA is_a: SO:0000665 ! monocistronic_transcript intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000878 ! monocistronic relationship: has_quality SO:0000878 ! monocistronic [Term] id: SO:0000634 name: polycistronic_mRNA def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd] synonym: "polycistronic mRNA" EXACT [] synonym: "polycistronic processed transcript" RELATED [] xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA "wiki" is_a: SO:0000078 ! polycistronic_transcript is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000880 ! polycistronic relationship: has_quality SO:0000880 ! polycistronic [Term] id: SO:0000635 name: mini_exon_donor_RNA def: "A primary transcript that donates the spliced leader to other mRNA." [SO:ke] synonym: "mini exon donor RNA" EXACT [] synonym: "mini-exon donor RNA" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000636 name: spliced_leader_RNA synonym: "mini-exon" RELATED [] synonym: "spliced leader RNA" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000635 ! mini_exon_donor_RNA [Term] id: SO:0000637 name: engineered_plasmid def: "A plasmid that is engineered." [SO:xp] synonym: "engineered plasmid" EXACT [] synonym: "engineered plasmid gene" RELATED [] is_a: SO:0000155 ! plasmid is_a: SO:0000804 ! engineered_region intersection_of: SO:0000155 ! plasmid intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000638 name: transcribed_spacer_region def: "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html] synonym: "transcribed spacer region" EXACT [] is_a: SO:0000838 ! rRNA_primary_transcript_region [Term] id: SO:0000639 name: internal_transcribed_spacer_region def: "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke] synonym: "internal transcribed spacer region" EXACT [] is_a: SO:0000638 ! transcribed_spacer_region [Term] id: SO:0000640 name: external_transcribed_spacer_region def: "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke] synonym: "external transcribed spacer region" EXACT [] is_a: SO:0000638 ! transcribed_spacer_region [Term] id: SO:0000641 name: tetranucleotide_repeat_microsatellite_feature synonym: "tetranucleotide repeat microsatellite feature" EXACT [] is_a: SO:0000289 ! microsatellite [Term] id: SO:0000642 name: SRP_RNA_encoding synonym: "SRP RNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000643 name: minisatellite def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml] subset: SOFA xref: http://en.wikipedia.org/wiki/Minisatellite "wiki" is_a: SO:0000005 ! satellite_DNA [Term] id: SO:0000644 name: antisense_RNA def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke] subset: SOFA synonym: "antisense RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000645 ! antisense_primary_transcript [Term] id: SO:0000645 name: antisense_primary_transcript def: "The reverse complement of the primary transcript." [SO:ke] subset: SOFA synonym: "antisense primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000646 name: siRNA def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000] subset: SOFA synonym: "small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000647 name: miRNA_primary_transcript def: "A primary transcript encoding a micro RNA." [SO:ke] synonym: "micro RNA primary transcript" EXACT [] synonym: "miRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000648 name: stRNA_primary_transcript def: "A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke] synonym: "small temporal RNA primary transcript" EXACT [] synonym: "stRNA primary transcript" EXACT [] is_a: SO:0000647 ! miRNA_primary_transcript [Term] id: SO:0000649 name: stRNA def: "Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512] subset: SOFA synonym: "small temporal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/StRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000650 name: small_subunit_rRNA def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "small subunit rRNA" EXACT [] synonym: "SSU RNA" EXACT [RSC:cb] synonym: "SSU rRNA" EXACT [RSC:cb] is_a: SO:0000252 ! rRNA relationship: derives_from SO:0000255 ! rRNA_small_subunit_primary_transcript [Term] id: SO:0000651 name: large_subunit_rRNA def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke] subset: SOFA synonym: "large subunit rRNA" EXACT [] synonym: "LSU RNA" EXACT [RSC:cb] synonym: "LSU rRNA" EXACT [RSC:cb] is_a: SO:0000252 ! rRNA relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript [Term] id: SO:0000652 name: rRNA_5S def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001] subset: SOFA synonym: "5S LSU rRNA" EXACT [] synonym: "5S ribosomal RNA" EXACT [] synonym: "5S rRNA" EXACT [] synonym: "rRNA 5S" EXACT [] xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000653 name: rRNA_28S def: "A component of the large ribosomal subunit." [SO:ke] subset: SOFA synonym: "28S LSU rRNA" EXACT [] synonym: "28S ribosomal RNA" EXACT [] synonym: "28S rRNA" EXACT [] synonym: "rRNA 28S" EXACT [] xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000654 name: maxicircle_gene def: "A mitochondrial gene located in a maxicircle." [SO:xp] synonym: "maxi-circle gene" EXACT [] synonym: "maxicircle gene" EXACT [] is_a: SO:0000089 ! kinetoplast_gene intersection_of: SO:0000089 ! kinetoplast_gene intersection_of: part_of SO:0000742 ! maxicircle relationship: part_of SO:0000742 ! maxicircle [Term] id: SO:0000655 name: ncRNA def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. subset: SOFA synonym: "noncoding RNA" EXACT [] xref: http://en.wikipedia.org/wiki/NcRNA "wiki" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000656 name: stRNA_encoding synonym: "stRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000657 name: repeat_region def: "A region of sequence containing one or more repeat units." [SO:ke] subset: SOFA synonym: "repeat region" EXACT [] is_a: SO:0001411 ! biological_region relationship: has_part SO:0000726 ! repeat_unit [Term] id: SO:0000658 name: dispersed_repeat def: "A repeat that is located at dispersed sites in the genome." [SO:ke] subset: SOFA synonym: "dispersed repeat" EXACT [] synonym: "interspersed repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000659 name: tmRNA_encoding synonym: "tmRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000660 name: DNA_invertase_target_sequence is_obsolete: true [Term] id: SO:0000661 name: intron_attribute is_obsolete: true [Term] id: SO:0000662 name: spliceosomal_intron def: "An intron which is spliced by the spliceosome." [SO:ke] comment: GO:0000398. subset: SOFA synonym: "spliceosomal intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000663 name: tRNA_encoding synonym: "tRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000664 name: introgressed_chromosome_region synonym: "introgressed chromosome region" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000665 name: monocistronic_transcript def: "A transcript that is monocistronic." [SO:xp] synonym: "monocistronic transcript" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000878 ! monocistronic relationship: has_quality SO:0000878 ! monocistronic [Term] id: SO:0000666 name: mobile_intron def: "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke] synonym: "mobile intron" EXACT [] is_a: SO:0000188 ! intron is_a: SO:0001037 ! mobile_genetic_element intersection_of: SO:0000188 ! intron intersection_of: has_quality SO:0001234 ! mobile relationship: has_quality SO:0001234 ! mobile [Term] id: SO:0000667 name: insertion alt_id: SO:1000034 def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] subset: DBVAR subset: SOFA synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "nucleotide insertion" EXACT [] synonym: "nucleotide_insertion" EXACT [] xref: loinc:LA6687-3 "Insertion" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:0000668 name: EST_match def: "A match against an EST sequence." [SO:ke] subset: SOFA synonym: "EST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000669 name: sequence_rearrangement_feature synonym: "sequence rearrangement feature" EXACT [] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000670 name: chromosome_breakage_sequence def: "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma] synonym: "chromosome breakage sequence" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000671 name: internal_eliminated_sequence def: "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma] synonym: "internal eliminated sequence" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000672 name: macronucleus_destined_segment def: "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma] synonym: "macronucleus destined segment" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000673 name: transcript def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] subset: SOFA xref: http://en.wikipedia.org/wiki/RNA "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0000674 name: non_canonical_splice_site def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke] synonym: "non canonical splice site" EXACT [] synonym: "non-canonical splice site" EXACT [] is_obsolete: true consider: SO:0000678 consider: SO:0000679 [Term] id: SO:0000675 name: canonical_splice_site def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke] synonym: "canonical splice site" EXACT [] is_obsolete: true consider: SO:0000676 consider: SO:0000677 [Term] id: SO:0000676 name: canonical_three_prime_splice_site def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke] synonym: "canonical 3' splice site" EXACT [] synonym: "canonical three prime splice site" EXACT [] is_a: SO:0000164 ! three_prime_cis_splice_site [Term] id: SO:0000677 name: canonical_five_prime_splice_site def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke] synonym: "canonical 5' splice site" EXACT [] synonym: "canonical five prime splice site" EXACT [] is_a: SO:0000163 ! five_prime_cis_splice_site [Term] id: SO:0000678 name: non_canonical_three_prime_splice_site def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke] synonym: "non canonical 3' splice site" RELATED [] synonym: "non canonical three prime splice site" EXACT [] synonym: "non-canonical three prime splice site" EXACT [] is_a: SO:0000164 ! three_prime_cis_splice_site [Term] id: SO:0000679 name: non_canonical_five_prime_splice_site def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke] synonym: "non canonical 5' splice site" EXACT [] synonym: "non canonical five prime splice site" EXACT [] synonym: "non-canonical five prime splice site" EXACT [] is_a: SO:0000163 ! five_prime_cis_splice_site [Term] id: SO:0000680 name: non_canonical_start_codon def: "A start codon that is not the usual AUG sequence." [SO:ke] synonym: "non ATG start codon" EXACT [] synonym: "non canonical start codon" EXACT [] synonym: "non-canonical start codon" EXACT [] is_a: SO:0000318 ! start_codon [Term] id: SO:0000681 name: aberrant_processed_transcript def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke] synonym: "aberrant processed transcript" EXACT [] is_a: SO:0000673 ! transcript [Term] id: SO:0000682 name: splicing_feature is_obsolete: true [Term] id: SO:0000683 name: exonic_splice_enhancer def: "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract] synonym: "exonic splice enhancer" EXACT [] is_a: SO:0000344 ! splice_enhancer [Term] id: SO:0000684 name: nuclease_sensitive_site def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma] subset: SOFA synonym: "nuclease sensitive site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0000685 name: DNAseI_hypersensitive_site synonym: "DHS" EXACT [] synonym: "DNAseI hypersensitive site" EXACT [] is_a: SO:0000322 ! nuclease_hypersensitive_site [Term] id: SO:0000686 name: translocation_element def: "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma] synonym: "translocation element" EXACT [] is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:0000687 name: deletion_junction def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke] subset: SOFA synonym: "deletion junction" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000688 name: golden_path def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls] subset: SOFA synonym: "golden path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000689 name: cDNA_match def: "A match against cDNA sequence." [SO:ke] subset: SOFA synonym: "cDNA match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000690 name: gene_with_polycistronic_transcript def: "A gene that encodes a polycistronic transcript." [SO:xp] synonym: "gene with polycistronic transcript" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: transcribed_to SO:0000078 ! polycistronic_transcript relationship: transcribed_to SO:0000078 ! polycistronic_transcript [Term] id: SO:0000691 name: cleaved_initiator_methionine alt_id: BS:00067 def: "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR] subset: biosapiens synonym: "cleaved initiator methionine" EXACT [] synonym: "init_met" RELATED [uniprot:feature_type] synonym: "initiator methionine" RELATED [] is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0000692 name: gene_with_dicistronic_transcript def: "A gene that encodes a dicistronic transcript." [SO:xp] synonym: "gene with dicistronic transcript" EXACT [] is_a: SO:0000690 ! gene_with_polycistronic_transcript intersection_of: SO:0000690 ! gene_with_polycistronic_transcript intersection_of: transcribed_to SO:0000079 ! dicistronic_transcript relationship: transcribed_to SO:0000079 ! dicistronic_transcript [Term] id: SO:0000693 name: gene_with_recoded_mRNA def: "A gene that encodes an mRNA that is recoded." [SO:xp] synonym: "gene with recoded mRNA" EXACT [] is_a: SO:0001217 ! protein_coding_gene intersection_of: SO:0001217 ! protein_coding_gene intersection_of: has_quality SO:0000881 ! recoded relationship: has_quality SO:0000881 ! recoded [Term] id: SO:0000694 name: SNP def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb] subset: SOFA synonym: "single nucleotide polymorphism" EXACT [] is_a: SO:0001483 ! SNV [Term] id: SO:0000695 name: reagent def: "A sequence used in experiment." [SO:ke] comment: Requested by Lynn Crosby, jan 2006. subset: SOFA is_a: SO:0001409 ! biomaterial_region [Term] id: SO:0000696 name: oligo def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] subset: SOFA synonym: "oligonucleotide" EXACT [] xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000697 name: gene_with_stop_codon_read_through def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp] synonym: "gene with stop codon read through" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA intersection_of: SO:0000693 ! gene_with_recoded_mRNA intersection_of: has_part SO:0000883 ! stop_codon_read_through relationship: has_part SO:0000883 ! stop_codon_read_through [Term] id: SO:0000698 name: gene_with_stop_codon_redefined_as_pyrrolysine def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp] synonym: "gene with stop codon redefined as pyrrolysine" EXACT [] is_a: SO:0000697 ! gene_with_stop_codon_read_through intersection_of: SO:0000693 ! gene_with_recoded_mRNA intersection_of: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine relationship: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine [Term] id: SO:0000699 name: junction def: "A sequence_feature with an extent of zero." [SO:ke] comment: A junction is a boundary between regions. A boundary has an extent of zero. subset: SOFA synonym: "boundary" EXACT [] synonym: "breakpoint" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0000700 name: remark def: "A comment about the sequence." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000701 name: possible_base_call_error def: "A region of sequence where the validity of the base calling is questionable." [SO:ke] subset: SOFA synonym: "possible base call error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000702 name: possible_assembly_error def: "A region of sequence where there may have been an error in the assembly." [SO:ke] subset: SOFA synonym: "possible assembly error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000703 name: experimental_result_region def: "A region of sequence implicated in an experimental result." [SO:ke] subset: SOFA synonym: "experimental result region" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000704 name: gene def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. subset: SOFA xref: http://en.wikipedia.org/wiki/Gene "wiki" is_a: SO:0001411 ! biological_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000705 name: tandem_repeat def: "Two or more adjcent copies of a region (of length greater than 1)." [SO:ke] subset: SOFA synonym: "tandem repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki" xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html is_a: SO:0000657 ! repeat_region [Term] id: SO:0000706 name: trans_splice_acceptor_site def: "The 3' splice site of the acceptor primary transcript." [SO:ke] comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans. subset: SOFA synonym: "3' trans splice site" RELATED [] synonym: "trans splice acceptor site" EXACT [] is_a: SO:0001420 ! trans_splice_site [Term] id: SO:0000707 name: trans_splice_donor_site def: "The 5' five prime splice site region of the donor RNA." [SO:ke] comment: SL RNA contains a donor site. synonym: "5 prime trans splice site" RELATED [] synonym: "trans splice donor site" EXACT [] synonym: "trans-splice donor site" EXACT [] is_a: SO:0001420 ! trans_splice_site [Term] id: SO:0000708 name: SL1_acceptor_site def: "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw] synonym: "SL1 acceptor site" EXACT [] is_a: SO:0000706 ! trans_splice_acceptor_site [Term] id: SO:0000709 name: SL2_acceptor_site def: "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL2 acceptor site" EXACT [] is_a: SO:0000706 ! trans_splice_acceptor_site [Term] id: SO:0000710 name: gene_with_stop_codon_redefined_as_selenocysteine def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp] synonym: "gene with stop codon redefined as selenocysteine" EXACT [] is_a: SO:0000697 ! gene_with_stop_codon_read_through intersection_of: SO:0000697 ! gene_with_stop_codon_read_through intersection_of: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine relationship: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine [Term] id: SO:0000711 name: gene_with_mRNA_recoded_by_translational_bypass def: "A gene with mRNA recoded by translational bypass." [SO:xp] synonym: "gene with mRNA recoded by translational bypass" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA intersection_of: SO:0001217 ! protein_coding_gene intersection_of: has_quality SO:0000886 ! recoded_by_translational_bypass relationship: has_quality SO:0000886 ! recoded_by_translational_bypass [Term] id: SO:0000712 name: gene_with_transcript_with_translational_frameshift def: "A gene encoding a transcript that has a translational frameshift." [SO:xp] synonym: "gene with transcript with translational frameshift" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA intersection_of: SO:0000693 ! gene_with_recoded_mRNA intersection_of: has_quality SO:0000887 ! translationally_frameshifted relationship: has_quality SO:0000887 ! translationally_frameshifted [Term] id: SO:0000713 name: DNA_motif def: "A motif that is active in the DNA form of the sequence." [SO:ke] synonym: "DNA motif" EXACT [] xref: http://en.wikipedia.org/wiki/DNA_motif "wiki" is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000714 name: nucleotide_motif def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke] subset: SOFA synonym: "nucleotide motif" EXACT [] is_a: SO:0001683 ! sequence_motif [Term] id: SO:0000715 name: RNA_motif def: "A motif that is active in RNA sequence." [SO:ke] subset: SOFA synonym: "RNA motif" EXACT [] is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000716 name: dicistronic_mRNA def: "An mRNA that has the quality dicistronic." [SO:ke] synonym: "dicistronic mRNA" EXACT [] synonym: "dicistronic processed transcript" RELATED [] is_a: SO:0000079 ! dicistronic_transcript is_a: SO:0000634 ! polycistronic_mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000879 ! dicistronic relationship: has_quality SO:0000879 ! dicistronic [Term] id: SO:0000717 name: reading_frame def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb] comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop. subset: SOFA synonym: "reading frame" EXACT [] xref: http://en.wikipedia.org/wiki/Reading_frame "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000718 name: blocked_reading_frame def: "A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons." [SGD:rb] comment: Term requested by Rama from SGD. synonym: "blocked reading frame" EXACT [] is_a: SO:0000717 ! reading_frame [Term] id: SO:0000719 name: ultracontig def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG] subset: SOFA synonym: "superscaffold" RELATED [] is_a: SO:0001876 ! partial_genomic_sequence_assembly [Term] id: SO:0000720 name: foreign_transposable_element def: "A transposable element that is foreign." [SO:ke] comment: requested by Michael on 19 Nov 2004. synonym: "foreign transposable element" EXACT [] is_a: SO:0000101 ! transposable_element intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000721 name: gene_with_dicistronic_primary_transcript def: "A gene that encodes a dicistronic primary transcript." [SO:xp] comment: Requested by Michael, 19 nov 2004. synonym: "gene with dicistronic primary transcript" EXACT [] is_a: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: transcribed_to SO:1001197 ! dicistronic_primary_transcript relationship: transcribed_to SO:1001197 ! dicistronic_primary_transcript [Term] id: SO:0000722 name: gene_with_dicistronic_mRNA def: "A gene that encodes a polycistronic mRNA." [SO:xp] comment: Requested by MA nov 19 2004. synonym: "gene with dicistronic mRNA" EXACT [] synonym: "gene with dicistronic processed transcript" EXACT [] is_a: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: SO:0000692 ! gene_with_dicistronic_transcript intersection_of: transcribed_to SO:0000716 ! dicistronic_mRNA relationship: transcribed_to SO:0000716 ! dicistronic_mRNA [Term] id: SO:0000723 name: iDNA def: "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma] synonym: "intervening DNA" EXACT [] xref: http://en.wikipedia.org/wiki/IDNA "wiki" is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000724 name: oriT def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "origin of transfer" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki" is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000725 name: transit_peptide alt_id: BS:00055 def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Added to bring SO inline with the embl ddbj genbank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle. subset: biosapiens subset: SOFA synonym: "signal" RELATED [] synonym: "transit" RELATED [uniprot:feature_type] synonym: "transit peptide" EXACT [] is_a: SO:0001527 ! peptide_localization_signal [Term] id: SO:0000726 name: repeat_unit def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke] comment: Added to comply with the feature table. A single repeat. synonym: "repeat unit" EXACT [] xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html is_a: SO:0001411 ! biological_region [Term] id: SO:0000727 name: CRM def: "A regulatory_region where more than 1 TF_binding_site together are regulatorily active." [SO:SG] comment: Requested by Stepen Grossmann Dec 2004. subset: SOFA synonym: "cis regulatory module" EXACT [] synonym: "TF module" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region intersection_of: SO:0001055 ! transcriptional_cis_regulatory_region intersection_of: has_part SO:0000235 ! TF_binding_site relationship: has_part SO:0000235 ! TF_binding_site [Term] id: SO:0000728 name: intein def: "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke] comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein. synonym: "protein intron" RELATED [] xref: http://en.wikipedia.org/wiki/Intein "wiki" is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0000729 name: intein_containing def: "An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke] synonym: "intein containing" EXACT [] is_a: SO:0000010 ! protein_coding [Term] id: SO:0000730 name: gap def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke] subset: SOFA is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000353 ! sequence_assembly [Term] id: SO:0000731 name: fragmentary def: "An attribute to describe a feature that is incomplete." [SO:ke] comment: Term added because of request by MO people. synonym: "fragment" EXACT [] is_a: SO:0000905 ! status [Term] id: SO:0000732 name: predicted def: "An attribute describing an unverified region." [SO:ke] xref: http://en.wikipedia.org/wiki/Predicted "wiki" is_a: SO:0000905 ! status [Term] id: SO:0000733 name: feature_attribute def: "An attribute describing a located_sequence_feature." [SO:ke] synonym: "feature attribute" EXACT [] is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000734 name: exemplar_mRNA def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php] comment: Added for the MO people. synonym: "exemplar mRNA" EXACT [] is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000864 ! exemplar relationship: has_quality SO:0000864 ! exemplar [Term] id: SO:0000735 name: sequence_location synonym: "sequence location" EXACT [] is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000736 name: organelle_sequence synonym: "organelle sequence" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000737 name: mitochondrial_sequence comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "mitochondrial sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000738 name: nuclear_sequence synonym: "nuclear sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000739 name: nucleomorphic_sequence synonym: "nucleomorphic sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000740 name: plastid_sequence synonym: "plastid sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000741 name: kinetoplast alt_id: SO:0000826 def: "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species." [PMID:8395055] synonym: "kinetoplast_chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/Kinetoplast "wiki" is_a: SO:0001026 ! genome intersection_of: SO:0001260 ! sequence_collection intersection_of: has_part SO:0000742 ! maxicircle intersection_of: has_part SO:0000980 ! minicircle relationship: has_part SO:0000742 ! maxicircle relationship: has_part SO:0000980 ! minicircle [Term] id: SO:0000742 name: maxicircle alt_id: SO:0000827 def: "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055] synonym: "maxicircle_chromosome" EXACT [] is_a: SO:0001235 ! replicon [Term] id: SO:0000743 name: apicoplast_sequence synonym: "apicoplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000744 name: chromoplast_sequence synonym: "chromoplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000745 name: chloroplast_sequence synonym: "chloroplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000746 name: cyanelle_sequence synonym: "cyanelle sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000747 name: leucoplast_sequence synonym: "leucoplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000748 name: proplastid_sequence synonym: "proplastid sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000749 name: plasmid_location synonym: "plasmid location" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000750 name: amplification_origin def: "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma] synonym: "amplification origin" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000751 name: proviral_location synonym: "proviral location" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000752 name: gene_group_regulatory_region subset: SOFA synonym: "gene group regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000753 name: clone_insert def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke] subset: SOFA synonym: "clone insert" EXACT [] is_a: SO:0000695 ! reagent relationship: part_of SO:0000151 ! clone [Term] id: SO:0000754 name: lambda_vector def: "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] synonym: "lambda vector" EXACT [] is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000755 name: plasmid_vector synonym: "plasmid vector" EXACT [] xref: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors "wiki" is_a: SO:0000440 ! vector_replicon intersection_of: SO:0001235 ! replicon intersection_of: derives_from SO:0000155 ! plasmid relationship: derives_from SO:0000155 ! plasmid [Term] id: SO:0000756 name: cDNA def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma] synonym: "complementary DNA" EXACT [] xref: http://en.wikipedia.org/wiki/CDNA "wiki" is_a: SO:0000352 ! DNA [Term] id: SO:0000757 name: single_stranded_cDNA synonym: "single strand cDNA" EXACT [] synonym: "single stranded cDNA" EXACT [] synonym: "single-strand cDNA" RELATED [] is_a: SO:0000756 ! cDNA [Term] id: SO:0000758 name: double_stranded_cDNA synonym: "double strand cDNA" RELATED [] synonym: "double stranded cDNA" EXACT [] synonym: "double-strand cDNA" RELATED [] is_a: SO:0000756 ! cDNA [Term] id: SO:0000759 name: plasmid_clone is_obsolete: true [Term] id: SO:0000760 name: YAC_clone is_obsolete: true [Term] id: SO:0000761 name: phagemid_clone is_obsolete: true [Term] id: SO:0000762 name: PAC_clone synonym: "P1_clone" RELATED [] is_obsolete: true [Term] id: SO:0000763 name: fosmid_clone is_obsolete: true [Term] id: SO:0000764 name: BAC_clone is_obsolete: true [Term] id: SO:0000765 name: cosmid_clone is_obsolete: true [Term] id: SO:0000766 name: pyrrolysyl_tRNA def: "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke] synonym: "pyrrolysyl tRNA" EXACT [] synonym: "pyrrolysyl-transfer ribonucleic acid" EXACT [] synonym: "pyrrolysyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0001178 ! pyrrolysine_tRNA_primary_transcript [Term] id: SO:0000767 name: clone_insert_start is_obsolete: true [Term] id: SO:0000768 name: episome def: "A plasmid that may integrate with a chromosome." [SO:ma] is_a: SO:0000155 ! plasmid [Term] id: SO:0000769 name: tmRNA_coding_piece def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962] comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005. synonym: "tmRNA coding piece" EXACT [] is_a: SO:0000847 ! tmRNA_region [Term] id: SO:0000770 name: tmRNA_acceptor_piece def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw] comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005. synonym: "tmRNA acceptor piece" EXACT [] is_a: SO:0000847 ! tmRNA_region [Term] id: SO:0000771 name: QTL def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/] comment: Added in respose to request by Simon Twigger November 14th 2005. synonym: "quantitative trait locus" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000772 name: genomic_island def: "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke] comment: Genomic islands are transmissible elements characterized by large size (>10kb). synonym: "genomic island" EXACT [] xref: http://en.wikipedia.org/wiki/Genomic_island "wiki" is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000773 name: pathogenic_island def: "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke] comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. synonym: "pathogenic island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000774 name: metabolic_island def: "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands. synonym: "metabolic island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000775 name: adaptive_island def: "An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke] comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. synonym: "adaptive island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000776 name: symbiosis_island def: "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149. synonym: "symbiosis island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000777 name: pseudogenic_rRNA def: "A non functional descendent of an rRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "pseudogenic rRNA" EXACT [] is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0000778 name: pseudogenic_tRNA def: "A non functional descendent of a tRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "pseudogenic tRNA" EXACT [] is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0000779 name: engineered_episome def: "An episome that is engineered." [SO:xp] comment: Requested by Lynn Crosby Jan 2006. synonym: "engineered episome" EXACT [] is_a: SO:0000637 ! engineered_plasmid is_a: SO:0000768 ! episome intersection_of: SO:0000768 ! episome intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000780 name: transposable_element_attribute comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs is_obsolete: true [Term] id: SO:0000781 name: transgenic def: "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000782 name: natural def: "An attribute describing a feature that occurs in nature." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000783 name: engineered def: "An attribute to describe a region that was modified in vitro." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000784 name: foreign def: "An attribute to describe a region from another species." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000785 name: cloned_region comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions. synonym: "cloned region" EXACT [] synonym: "cloned segment" EXACT [] is_a: SO:0000695 ! reagent relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000786 name: reagent_attribute comment: Added jan 2006 by KE. synonym: "reagent attribute" EXACT [] is_obsolete: true [Term] id: SO:0000787 name: clone_attribute is_obsolete: true [Term] id: SO:0000788 name: cloned is_obsolete: true [Term] id: SO:0000789 name: validated def: "An attribute to describe a feature that has been proven." [SO:ke] is_a: SO:0000905 ! status [Term] id: SO:0000790 name: invalidated def: "An attribute describing a feature that is invalidated." [SO:ke] is_a: SO:0000905 ! status [Term] id: SO:0000791 name: cloned_genomic is_obsolete: true [Term] id: SO:0000792 name: cloned_cDNA is_obsolete: true [Term] id: SO:0000793 name: engineered_DNA is_obsolete: true [Term] id: SO:0000794 name: engineered_rescue_region def: "A rescue region that is engineered." [SO:xp] synonym: "engineered rescue fragment" EXACT [] synonym: "engineered rescue region" EXACT [] synonym: "engineered rescue segment" EXACT [] is_a: SO:0000411 ! rescue_region is_a: SO:0000804 ! engineered_region intersection_of: SO:0000411 ! rescue_region intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000795 name: rescue_mini_gene def: "A mini_gene that rescues." [SO:xp] synonym: "rescue mini gene" EXACT [] synonym: "rescue mini-gene" EXACT [] is_a: SO:0000815 ! mini_gene intersection_of: SO:0000815 ! mini_gene intersection_of: has_quality SO:0000814 ! rescue relationship: has_quality SO:0000814 ! rescue [Term] id: SO:0000796 name: transgenic_transposable_element def: "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc] comment: Modified as requested by Lynn - FB. May 2007. synonym: "transgenic transposable element" EXACT [] is_a: SO:0000101 ! transposable_element intersection_of: SO:0000101 ! transposable_element intersection_of: derives_from SO:0000151 ! clone intersection_of: has_quality SO:0000781 ! transgenic relationship: derives_from SO:0000151 ! clone relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0000797 name: natural_transposable_element def: "TE that exists (or existed) in nature." [FB:mc] synonym: "natural transposable element" EXACT [] is_a: SO:0000101 ! transposable_element is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000782 ! natural relationship: has_quality SO:0000782 ! natural [Term] id: SO:0000798 name: engineered_transposable_element def: "TE that has been modified by manipulations in vitro." [FB:mc] synonym: "engineered transposable element" EXACT [] is_a: SO:0000101 ! transposable_element is_a: SO:0000804 ! engineered_region intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000799 name: engineered_foreign_transposable_element def: "A transposable_element that is engineered and foreign." [FB:mc] synonym: "engineered foreign transposable element" EXACT [] is_a: SO:0000720 ! foreign_transposable_element is_a: SO:0000798 ! engineered_transposable_element is_a: SO:0000805 ! engineered_foreign_region intersection_of: SO:0000101 ! transposable_element intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000800 name: assortment_derived_duplication def: "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm] synonym: "assortment derived duplication" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000801 name: assortment_derived_deficiency_plus_duplication def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm] synonym: "assortment derived deficiency plus duplication" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000802 name: assortment_derived_deficiency def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm] synonym: "assortment-derived deficiency" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000803 name: assortment_derived_aneuploid def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm] synonym: "assortment derived aneuploid" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000804 name: engineered_region def: "A region that is engineered." [SO:xp] synonym: "construct" EXACT [] synonym: "engineered region" EXACT [] synonym: "engineered sequence" EXACT [] is_a: SO:0001409 ! biomaterial_region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000805 name: engineered_foreign_region def: "A region that is engineered and foreign." [SO:xp] synonym: "engineered foreign region" EXACT [] is_a: SO:0000804 ! engineered_region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000783 ! engineered intersection_of: has_quality SO:0000784 ! foreign relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000806 name: fusion is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000807 name: engineered_tag def: "A tag that is engineered." [SO:xp] synonym: "engineered tag" EXACT [] is_a: SO:0000324 ! tag is_a: SO:0000804 ! engineered_region intersection_of: SO:0000324 ! tag intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000808 name: validated_cDNA_clone def: "A cDNA clone that has been validated." [SO:xp] synonym: "validated cDNA clone" EXACT [] is_a: SO:0000317 ! cDNA_clone intersection_of: SO:0000317 ! cDNA_clone intersection_of: has_quality SO:0000789 ! validated relationship: has_quality SO:0000789 ! validated [Term] id: SO:0000809 name: invalidated_cDNA_clone def: "A cDNA clone that is invalid." [SO:xp] synonym: "invalidated cDNA clone" EXACT [] is_a: SO:0000317 ! cDNA_clone intersection_of: SO:0000317 ! cDNA_clone intersection_of: has_quality SO:0000790 ! invalidated relationship: has_quality SO:0000790 ! invalidated [Term] id: SO:0000810 name: chimeric_cDNA_clone def: "A cDNA clone invalidated because it is chimeric." [SO:xp] synonym: "chimeric cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA relationship: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA [Term] id: SO:0000811 name: genomically_contaminated_cDNA_clone def: "A cDNA clone invalidated by genomic contamination." [SO:xp] synonym: "genomically contaminated cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000414 ! invalidated_by_genomic_contamination relationship: has_quality SO:0000414 ! invalidated_by_genomic_contamination [Term] id: SO:0000812 name: polyA_primed_cDNA_clone def: "A cDNA clone invalidated by polyA priming." [SO:xp] synonym: "polyA primed cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA relationship: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA [Term] id: SO:0000813 name: partially_processed_cDNA_clone def: "A cDNA invalidated clone by partial processing." [SO:xp] synonym: "partially processed cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone intersection_of: SO:0000809 ! invalidated_cDNA_clone intersection_of: has_quality SO:0000416 ! invalidated_by_partial_processing relationship: has_quality SO:0000416 ! invalidated_by_partial_processing [Term] id: SO:0000814 name: rescue def: "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000815 name: mini_gene def: "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143] synonym: "mini gene" EXACT [] is_a: SO:0000236 ! ORF [Term] id: SO:0000816 name: rescue_gene def: "A gene that rescues." [SO:xp] synonym: "rescue gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000814 ! rescue relationship: has_quality SO:0000814 ! rescue [Term] id: SO:0000817 name: wild_type def: "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke] synonym: "wild type" EXACT [] xref: http://en.wikipedia.org/wiki/Wild_type "wiki" xref: loinc:LA9658-1 "wild type" is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000818 name: wild_type_rescue_gene def: "A gene that rescues." [SO:xp] synonym: "wild type rescue gene" EXACT [] is_a: SO:0000816 ! rescue_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000817 ! wild_type relationship: has_quality SO:0000817 ! wild_type [Term] id: SO:0000819 name: mitochondrial_chromosome def: "A chromosome originating in a mitochondria." [SO:xp] synonym: "mitochondrial chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000737 ! mitochondrial_sequence relationship: has_origin SO:0000737 ! mitochondrial_sequence [Term] id: SO:0000820 name: chloroplast_chromosome def: "A chromosome originating in a chloroplast." [SO:xp] synonym: "chloroplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000745 ! chloroplast_sequence relationship: has_origin SO:0000745 ! chloroplast_sequence [Term] id: SO:0000821 name: chromoplast_chromosome def: "A chromosome originating in a chromoplast." [SO:xp] synonym: "chromoplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000744 ! chromoplast_sequence relationship: has_origin SO:0000744 ! chromoplast_sequence [Term] id: SO:0000822 name: cyanelle_chromosome def: "A chromosome originating in a cyanelle." [SO:xp] synonym: "cyanelle chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000746 ! cyanelle_sequence relationship: has_origin SO:0000746 ! cyanelle_sequence [Term] id: SO:0000823 name: leucoplast_chromosome def: "A chromosome with origin in a leucoplast." [SO:xp] synonym: "leucoplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000747 ! leucoplast_sequence relationship: has_origin SO:0000747 ! leucoplast_sequence [Term] id: SO:0000824 name: macronuclear_chromosome def: "A chromosome originating in a macronucleus." [SO:xp] synonym: "macronuclear chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000083 ! macronuclear_sequence relationship: has_origin SO:0000083 ! macronuclear_sequence [Term] id: SO:0000825 name: micronuclear_chromosome def: "A chromosome originating in a micronucleus." [SO:xp] synonym: "micronuclear chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000084 ! micronuclear_sequence relationship: has_origin SO:0000084 ! micronuclear_sequence [Term] id: SO:0000828 name: nuclear_chromosome def: "A chromosome originating in a nucleus." [SO:xp] synonym: "nuclear chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000738 ! nuclear_sequence relationship: has_origin SO:0000738 ! nuclear_sequence [Term] id: SO:0000829 name: nucleomorphic_chromosome def: "A chromosome originating in a nucleomorph." [SO:xp] synonym: "nucleomorphic chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000739 ! nucleomorphic_sequence relationship: has_origin SO:0000739 ! nucleomorphic_sequence [Term] id: SO:0000830 name: chromosome_part def: "A region of a chromosome." [SO:ke] comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. subset: SOFA synonym: "chromosome part" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0000831 name: gene_member_region def: "A region of a gene." [SO:ke] comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. subset: SOFA synonym: "gene member region" EXACT [] is_a: SO:0001411 ! biological_region relationship: member_of SO:0000704 ! gene [Term] id: SO:0000832 name: promoter_region def: "A region of sequence which is part of a promoter." [SO:ke] comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000833 name: transcript_region def: "A region of a transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "transcript region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000834 name: mature_transcript_region def: "A region of a mature transcript." [SO:ke] comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. subset: SOFA synonym: "mature transcript region" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000835 name: primary_transcript_region def: "A part of a primary transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "primary transcript region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000185 ! primary_transcript [Term] id: SO:0000836 name: mRNA_region def: "A region of an mRNA." [SO:cb] comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root. subset: SOFA synonym: "mRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000837 name: UTR_region def: "A region of UTR." [SO:ke] comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root. subset: SOFA synonym: "UTR region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000838 name: rRNA_primary_transcript_region def: "A region of an rRNA primary transcript." [SO:ke] comment: To allow transcribed_spacer_region to have a path to the root. synonym: "rRNA primary transcript region" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000839 name: polypeptide_region alt_id: BS:00124 alt_id: BS:00331 def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] comment: Added to allow the polypeptide regions to have is_a paths back to the root. subset: biosapiens subset: SOFA synonym: "positional" RELATED [] synonym: "positional polypeptide feature" RELATED [] synonym: "region" NARROW [uniprot:feature_type] synonym: "region or site annotation" RELATED [] synonym: "site" NARROW [uniprot:feature_type] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000840 name: repeat_component def: "A region of a repeated sequence." [SO:ke] comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root. synonym: "repeat component" EXACT [] is_a: SO:0001412 ! topologically_defined_region [Term] id: SO:0000841 name: spliceosomal_intron_region def: "A region within an intron." [SO:ke] comment: A terms added to allow the parts of introns to have is_a paths to the root. subset: SOFA synonym: "spliceosomal intron region" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000662 ! spliceosomal_intron [Term] id: SO:0000842 name: gene_component_region subset: SOFA synonym: "gene component region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000704 ! gene [Term] id: SO:0000843 name: bacterial_RNApol_promoter_region def: "A region which is part of a bacterial RNA polymerase promoter." [SO:ke] comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000844 name: RNApol_II_promoter_region def: "A region of sequence which is a promoter for RNA polymerase II." [SO:ke] comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000845 name: RNApol_III_promoter_type_1_region def: "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke] comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000846 name: RNApol_III_promoter_type_2_region def: "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke] comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000847 name: tmRNA_region def: "A region of a tmRNA." [SO:cb] comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root. synonym: "tmRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000584 ! tmRNA [Term] id: SO:0000848 name: LTR_component synonym: "long term repeat component" EXACT [] synonym: "LTR component" EXACT [] is_a: SO:0000840 ! repeat_component relationship: part_of SO:0000286 ! long_terminal_repeat [Term] id: SO:0000849 name: three_prime_LTR_component synonym: "3' long terminal repeat component" EXACT [] synonym: "three prime LTR component" EXACT [] is_a: SO:0000848 ! LTR_component relationship: part_of SO:0000426 ! three_prime_LTR [Term] id: SO:0000850 name: five_prime_LTR_component synonym: "5' long term repeat component" EXACT [] synonym: "five prime LTR component" EXACT [] is_a: SO:0000848 ! LTR_component relationship: part_of SO:0000425 ! five_prime_LTR [Term] id: SO:0000851 name: CDS_region def: "A region of a CDS." [SO:cb] subset: SOFA synonym: "CDS region" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000316 ! CDS [Term] id: SO:0000852 name: exon_region def: "A region of an exon." [RSC:cb] subset: SOFA synonym: "exon region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000147 ! exon [Term] id: SO:0000853 name: homologous_region def: "A region that is homologous to another region." [SO:ke] synonym: "homolog" EXACT [] synonym: "homologous region" EXACT [] synonym: "homologue" EXACT [] xref: http://en.wikipedia.org/wiki/Homology_(biology) "wiki" is_a: SO:0000330 ! conserved_region intersection_of: SO:0000330 ! conserved_region intersection_of: has_quality SO:0000857 ! homologous relationship: has_quality SO:0000857 ! homologous [Term] id: SO:0000854 name: paralogous_region def: "A homologous_region that is paralogous to another region." [SO:ke] comment: A term to be used in conjunction with the paralogous_to relationship. synonym: "paralog" EXACT [] synonym: "paralogous region" EXACT [] synonym: "paralogue" EXACT [] xref: http://en.wikipedia.org/wiki/Paralog#Paralogy "wiki" is_a: SO:0000853 ! homologous_region intersection_of: SO:0000853 ! homologous_region intersection_of: has_quality SO:0000859 ! paralogous relationship: has_quality SO:0000859 ! paralogous [Term] id: SO:0000855 name: orthologous_region def: "A homologous_region that is orthologous to another region." [SO:ke] comment: This term should be used in conjunction with the similarity relationships defined in SO. synonym: "ortholog" EXACT [] synonym: "orthologous region" EXACT [] synonym: "orthologue" EXACT [] xref: http://en.wikipedia.org/wiki/Ortholog#Orthology "wiki" is_a: SO:0000853 ! homologous_region intersection_of: SO:0000853 ! homologous_region intersection_of: has_quality SO:0000858 ! orthologous relationship: has_quality SO:0000858 ! orthologous [Term] id: SO:0000856 name: conserved is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000857 name: homologous def: "Similarity due to common ancestry." [SO:ke] is_a: SO:0000856 ! conserved [Term] id: SO:0000858 name: orthologous def: "An attribute describing a kind of homology where divergence occured after a speciation event." [SO:ke] is_a: SO:0000857 ! homologous [Term] id: SO:0000859 name: paralogous def: "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke] is_a: SO:0000857 ! homologous [Term] id: SO:0000860 name: syntenic def: "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke] xref: http://en.wikipedia.org/wiki/Syntenic "wiki" is_a: SO:0000856 ! conserved [Term] id: SO:0000861 name: capped_primary_transcript def: "A primary transcript that is capped." [SO:xp] synonym: "capped primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript intersection_of: SO:0000185 ! primary_transcript intersection_of: adjacent_to SO:0000581 ! cap intersection_of: has_quality SO:0000146 ! capped relationship: adjacent_to SO:0000581 ! cap relationship: has_quality SO:0000146 ! capped [Term] id: SO:0000862 name: capped_mRNA def: "An mRNA that is capped." [SO:xp] synonym: "capped mRNA" EXACT [] is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: adjacent_to SO:0000581 ! cap intersection_of: has_quality SO:0000146 ! capped relationship: adjacent_to SO:0000581 ! cap relationship: has_quality SO:0000146 ! capped [Term] id: SO:0000863 name: mRNA_attribute def: "An attribute describing an mRNA feature." [SO:ke] synonym: "mRNA attribute" EXACT [] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000864 name: exemplar def: "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000865 name: frameshift def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke] xref: http://en.wikipedia.org/wiki/Frameshift "wiki" is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000866 name: minus_1_frameshift def: "A frameshift caused by deleting one base." [SO:ke] synonym: "minus 1 frameshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000867 name: minus_2_frameshift def: "A frameshift caused by deleting two bases." [SO:ke] synonym: "minus 2 frameshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000868 name: plus_1_frameshift def: "A frameshift caused by inserting one base." [SO:ke] synonym: "plus 1 frameshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000869 name: plus_2_framshift def: "A frameshift caused by inserting two bases." [SO:ke] synonym: "plus 2 framshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000870 name: trans_spliced def: "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke] synonym: "trans-spliced" EXACT [] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000871 name: polyadenylated_mRNA def: "An mRNA that is polyadenylated." [SO:xp] synonym: "polyadenylated mRNA" EXACT [] is_a: SO:0000234 ! mRNA intersection_of: SO:0000234 ! mRNA intersection_of: adjacent_to SO:0000610 ! polyA_sequence intersection_of: has_quality SO:0000246 ! polyadenylated relationship: adjacent_to SO:0000610 ! polyA_sequence relationship: has_quality SO:0000246 ! polyadenylated [Term] id: SO:0000872 name: trans_spliced_mRNA def: "An mRNA that is trans-spliced." [SO:xp] synonym: "trans-spliced mRNA" EXACT [] is_a: SO:0000234 ! mRNA is_a: SO:0000479 ! trans_spliced_transcript intersection_of: SO:0000234 ! mRNA intersection_of: adjacent_to SO:0000636 ! spliced_leader_RNA intersection_of: has_quality SO:0000870 ! trans_spliced relationship: adjacent_to SO:0000636 ! spliced_leader_RNA relationship: has_quality SO:0000870 ! trans_spliced [Term] id: SO:0000873 name: edited_transcript def: "A transcript that is edited." [SO:ke] synonym: "edited transcript" EXACT [] is_a: SO:0000673 ! transcript intersection_of: SO:0000673 ! transcript intersection_of: has_quality SO:0000116 ! edited relationship: guided_by SO:0000602 ! guide_RNA relationship: has_part SO:0000977 ! anchor_binding_site relationship: has_quality SO:0000116 ! edited [Term] id: SO:0000874 name: edited_transcript_by_A_to_I_substitution def: "A transcript that has been edited by A to I substitution." [SO:ke] synonym: "edited transcript by A to I substitution" EXACT [] is_a: SO:0000873 ! edited_transcript [Term] id: SO:0000875 name: bound_by_protein def: "An attribute describing a sequence that is bound by a protein." [SO:ke] synonym: "bound by protein" EXACT [] is_a: SO:0000277 ! bound_by_factor [Term] id: SO:0000876 name: bound_by_nucleic_acid def: "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke] synonym: "bound by nucleic acid" EXACT [] is_a: SO:0000277 ! bound_by_factor [Term] id: SO:0000877 name: alternatively_spliced def: "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke] synonym: "alternatively spliced" EXACT [] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000878 name: monocistronic def: "An attribute describing a sequence that contains the code for one gene product." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000879 name: dicistronic def: "An attribute describing a sequence that contains the code for two gene products." [SO:ke] is_a: SO:0000880 ! polycistronic [Term] id: SO:0000880 name: polycistronic def: "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000881 name: recoded def: "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000882 name: codon_redefined def: "An attribute describing the alteration of codon meaning." [SO:ke] synonym: "codon redefined" EXACT [] is_a: SO:0000881 ! recoded [Term] id: SO:0000883 name: stop_codon_read_through def: "A stop codon redefined to be a new amino acid." [SO:ke] synonym: "stop codon read through" EXACT [] synonym: "stop codon readthrough" RELATED [] is_a: SO:0000145 ! recoded_codon [Term] id: SO:0000884 name: stop_codon_redefined_as_pyrrolysine def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke] synonym: "stop codon redefined as pyrrolysine" EXACT [] is_a: SO:0000883 ! stop_codon_read_through [Term] id: SO:0000885 name: stop_codon_redefined_as_selenocysteine def: "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke] synonym: "stop codon redefined as selenocysteine" EXACT [] is_a: SO:0000883 ! stop_codon_read_through [Term] id: SO:0000886 name: recoded_by_translational_bypass def: "Recoded mRNA where a block of nucleotides is not translated." [SO:ke] synonym: "recoded by translational bypass" EXACT [] is_a: SO:0000881 ! recoded [Term] id: SO:0000887 name: translationally_frameshifted def: "Recoding by frameshifting a particular site." [SO:ke] synonym: "translationally frameshifted" EXACT [] is_a: SO:0000881 ! recoded [Term] id: SO:0000888 name: maternally_imprinted_gene def: "A gene that is maternally_imprinted." [SO:xp] synonym: "maternally imprinted gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000135 ! maternally_imprinted relationship: has_quality SO:0000135 ! maternally_imprinted [Term] id: SO:0000889 name: paternally_imprinted_gene def: "A gene that is paternally imprinted." [SO:xp] synonym: "paternally imprinted gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000136 ! paternally_imprinted relationship: has_quality SO:0000136 ! paternally_imprinted [Term] id: SO:0000890 name: post_translationally_regulated_gene def: "A gene that is post translationally regulated." [SO:xp] synonym: "post translationally regulated gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000130 ! post_translationally_regulated relationship: has_quality SO:0000130 ! post_translationally_regulated [Term] id: SO:0000891 name: negatively_autoregulated_gene def: "A gene that is negatively autoreguated." [SO:xp] synonym: "negatively autoregulated gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000473 ! negatively_autoregulated relationship: has_quality SO:0000473 ! negatively_autoregulated [Term] id: SO:0000892 name: positively_autoregulated_gene def: "A gene that is positively autoregulated." [SO:xp] synonym: "positively autoregulated gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000475 ! positively_autoregulated relationship: has_quality SO:0000475 ! positively_autoregulated [Term] id: SO:0000893 name: silenced def: "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke] xref: http://en.wikipedia.org/wiki/Silenced "wiki" is_a: SO:0000126 ! transcriptionally_repressed [Term] id: SO:0000894 name: silenced_by_DNA_modification def: "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke] synonym: "silenced by DNA modification" EXACT [] is_a: SO:0000893 ! silenced [Term] id: SO:0000895 name: silenced_by_DNA_methylation def: "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke] synonym: "silenced by DNA methylation" EXACT [] is_a: SO:0000894 ! silenced_by_DNA_modification [Term] id: SO:0000896 name: translationally_regulated_gene def: "A gene that is translationally regulated." [SO:xp] synonym: "translationally regulated gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000131 ! translationally_regulated relationship: has_quality SO:0000131 ! translationally_regulated [Term] id: SO:0000897 name: allelically_excluded_gene def: "A gene that is allelically_excluded." [SO:xp] synonym: "allelically excluded gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene intersection_of: SO:0000898 ! epigenetically_modified_gene intersection_of: has_quality SO:0000137 ! allelically_excluded relationship: has_quality SO:0000137 ! allelically_excluded [Term] id: SO:0000898 name: epigenetically_modified_gene def: "A gene that is epigenetically modified." [SO:ke] synonym: "epigenetically modified gene" EXACT [] is_a: SO:0000704 ! gene is_a: SO:0001720 ! epigenetically_modified_region intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000133 ! epigenetically_modified relationship: has_quality SO:0000133 ! epigenetically_modified [Term] id: SO:0000899 name: nuclear_mitochondrial def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke] synonym: "nuclear mitochondrial" EXACT [] is_obsolete: true [Term] id: SO:0000900 name: processed def: "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." [SO:ke] is_obsolete: true [Term] id: SO:0000901 name: unequally_crossed_over def: "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke] synonym: "unequally crossed over" EXACT [] is_obsolete: true [Term] id: SO:0000902 name: transgene def: "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp] xref: http://en.wikipedia.org/wiki/Transgene "wiki" is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000781 ! transgenic relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0000903 name: endogenous_retroviral_sequence synonym: "endogenous retroviral sequence" EXACT [] is_a: SO:0000751 ! proviral_location [Term] id: SO:0000904 name: rearranged_at_DNA_level def: "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke] synonym: "rearranged at DNA level" EXACT [] is_a: SO:0000133 ! epigenetically_modified [Term] id: SO:0000905 name: status def: "An attribute describing the status of a feature, based on the available evidence." [SO:ke] comment: This term is the hypernym of attributes and should not be annotated to. is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000906 name: independently_known def: "Attribute to describe a feature that is independently known - not predicted." [SO:ke] synonym: "independently known" EXACT [] is_a: SO:0000905 ! status [Term] id: SO:0000907 name: supported_by_sequence_similarity def: "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke] synonym: "supported by sequence similarity" EXACT [] is_a: SO:0000732 ! predicted [Term] id: SO:0000908 name: supported_by_domain_match def: "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke] synonym: "supported by domain match" EXACT [] is_a: SO:0000907 ! supported_by_sequence_similarity [Term] id: SO:0000909 name: supported_by_EST_or_cDNA def: "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke] synonym: "supported by EST or cDNA" EXACT [] is_a: SO:0000907 ! supported_by_sequence_similarity [Term] id: SO:0000910 name: orphan is_a: SO:0000732 ! predicted [Term] id: SO:0000911 name: predicted_by_ab_initio_computation def: "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke] synonym: "predicted by ab initio computation" EXACT [] is_a: SO:0000732 ! predicted [Term] id: SO:0000912 name: asx_turn alt_id: BS:00203 def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0000913 name: cloned_cDNA_insert def: "A clone insert made from cDNA." [SO:xp] synonym: "cloned cDNA insert" EXACT [] is_a: SO:0000753 ! clone_insert intersection_of: SO:0000753 ! clone_insert intersection_of: has_quality SO:0000756 ! cDNA relationship: has_quality SO:0000756 ! cDNA [Term] id: SO:0000914 name: cloned_genomic_insert def: "A clone insert made from genomic DNA." [SO:xp] synonym: "cloned genomic insert" EXACT [] is_a: SO:0000753 ! clone_insert intersection_of: SO:0000753 ! clone_insert intersection_of: has_quality SO:0000991 ! genomic_DNA relationship: has_quality SO:0000991 ! genomic_DNA [Term] id: SO:0000915 name: engineered_insert def: "A clone insert that is engineered." [SO:xp] synonym: "engineered insert" EXACT [] is_a: SO:0000753 ! clone_insert is_a: SO:0000804 ! engineered_region intersection_of: SO:0000753 ! clone_insert intersection_of: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000916 name: edit_operation synonym: "edit operation" EXACT [] is_obsolete: true [Term] id: SO:0000917 name: insert_U def: "An edit to insert a U." [SO:ke] comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. synonym: "insert U" EXACT [] is_obsolete: true [Term] id: SO:0000918 name: delete_U def: "An edit to delete a uridine." [SO:ke] comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. synonym: "delete U" EXACT [] is_obsolete: true [Term] id: SO:0000919 name: substitute_A_to_I def: "An edit to substitute an I for an A." [SO:ke] synonym: "substitute A to I" EXACT [] is_obsolete: true [Term] id: SO:0000920 name: insert_C def: "An edit to insert a cytidine." [SO:ke] synonym: "insert C" EXACT [] is_obsolete: true [Term] id: SO:0000921 name: insert_dinucleotide def: "An edit to insert a dinucleotide." [SO:ke] synonym: "insert dinucleotide" EXACT [] is_obsolete: true [Term] id: SO:0000922 name: substitute_C_to_U def: "An edit to substitute an U for a C." [SO:ke] synonym: "substitute C to U" EXACT [] is_obsolete: true [Term] id: SO:0000923 name: insert_G def: "An edit to insert a G." [SO:ke] synonym: "insert G" EXACT [] is_obsolete: true [Term] id: SO:0000924 name: insert_GC def: "An edit to insert a GC dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert GC" EXACT [] is_obsolete: true [Term] id: SO:0000925 name: insert_GU def: "An edit to insert a GU dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert GU" EXACT [] is_obsolete: true [Term] id: SO:0000926 name: insert_CU def: "An edit to insert a CU dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert CU" EXACT [] is_obsolete: true [Term] id: SO:0000927 name: insert_AU def: "An edit to insert a AU dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert AU" EXACT [] is_obsolete: true [Term] id: SO:0000928 name: insert_AA def: "An edit to insert a AA dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert AA" EXACT [] is_obsolete: true [Term] id: SO:0000929 name: edited_mRNA def: "An mRNA that is edited." [SO:xp] synonym: "edited mRNA" EXACT [] is_a: SO:0000234 ! mRNA is_a: SO:0000873 ! edited_transcript intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000116 ! edited relationship: has_quality SO:0000116 ! edited [Term] id: SO:0000930 name: guide_RNA_region def: "A region of guide RNA." [SO:ma] synonym: "guide RNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000602 ! guide_RNA [Term] id: SO:0000931 name: anchor_region def: "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk] synonym: "anchor region" EXACT [] is_a: SO:0000930 ! guide_RNA_region [Term] id: SO:0000932 name: pre_edited_mRNA synonym: "pre-edited mRNA" EXACT [] is_a: SO:0000120 ! protein_coding_primary_transcript [Term] id: SO:0000933 name: intermediate def: "An attribute to describe a feature between stages of processing." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000934 name: miRNA_target_site def: "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds] synonym: "miRNA target site" EXACT [] is_a: SO:0001655 ! nucleotide_binding_site [Term] id: SO:0000935 name: edited_CDS def: "A CDS that is edited." [SO:xp] synonym: "edited CDS" EXACT [] is_a: SO:0000316 ! CDS intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000116 ! edited relationship: has_quality SO:0000116 ! edited [Term] id: SO:0000936 name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment synonym: "vertebrate immunoglobulin T cell receptor rearranged segment" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000937 name: vertebrate_immune_system_feature is_obsolete: true [Term] id: SO:0000938 name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster synonym: "vertebrate immunoglobulin T cell receptor rearranged gene cluster" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000939 name: vertebrate_immune_system_gene_recombination_signal_feature synonym: "vertebrate immune system gene recombination signal feature" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000940 name: recombinationally_rearranged synonym: "recombinationally rearranged" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000941 name: recombinationally_rearranged_vertebrate_immune_system_gene def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp] synonym: "recombinationally rearranged vertebrate immune system gene" EXACT [] is_a: SO:0000456 ! recombinationally_rearranged_gene [Term] id: SO:0000942 name: attP_site def: "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as] synonym: "attP site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0001042 ! phage_sequence [Term] id: SO:0000943 name: attB_site def: "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as] synonym: "attB site" EXACT [] is_a: SO:0000946 ! integration_excision_site [Term] id: SO:0000944 name: attL_site def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as] synonym: "attBP'" RELATED [] synonym: "attL site" RELATED [] is_a: SO:0000946 ! integration_excision_site [Term] id: SO:0000945 name: attR_site def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as] synonym: "attPB'" RELATED [] synonym: "attR site" EXACT [] is_a: SO:0000946 ! integration_excision_site [Term] id: SO:0000946 name: integration_excision_site def: "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as] synonym: "attachment site" RELATED [] synonym: "integration excision site" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000947 name: resolution_site def: "A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as] synonym: "res site" EXACT [] synonym: "resolution site" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000948 name: inversion_site def: "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma] comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase. synonym: "inversion site" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000949 name: dif_site def: "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as] synonym: "dif site" EXACT [] is_a: SO:0000947 ! resolution_site [Term] id: SO:0000950 name: attC_site def: "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as] synonym: "attC site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0000365 ! integron [Term] id: SO:0000951 name: eukaryotic_terminator synonym: "eukaryotic terminator" EXACT [] is_a: SO:0000141 ! terminator [Term] id: SO:0000952 name: oriV def: "An origin of vegetative replication in plasmids and phages." [SO:as] synonym: "origin of vegetative replication" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000953 name: oriC def: "An origin of bacterial chromosome replication." [SO:as] synonym: "origin of bacterial chromosome replication" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000954 name: DNA_chromosome def: "Structural unit composed of a self-replicating, DNA molecule." [SO:ma] synonym: "DNA chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_quality SO:0000352 ! DNA relationship: has_quality SO:0000352 ! DNA [Term] id: SO:0000955 name: double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma] synonym: "double stranded DNA chromosome" EXACT [] is_a: SO:0000954 ! DNA_chromosome intersection_of: SO:0000954 ! DNA_chromosome intersection_of: has_quality SO:0000985 ! double relationship: has_quality SO:0000985 ! double [Term] id: SO:0000956 name: single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma] synonym: "single stranded DNA chromosome" EXACT [] is_a: SO:0000954 ! DNA_chromosome intersection_of: SO:0000954 ! DNA_chromosome intersection_of: has_quality SO:0000984 ! single relationship: has_quality SO:0000984 ! single [Term] id: SO:0000957 name: linear_double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma] synonym: "linear double stranded DNA chromosome" EXACT [] is_a: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000958 name: circular_double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma] synonym: "circular double stranded DNA chromosome" EXACT [] is_a: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: SO:0000955 ! double_stranded_DNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000959 name: linear_single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma] synonym: "linear single stranded DNA chromosome" EXACT [] is_a: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000960 name: circular_single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] synonym: "circular single stranded DNA chromosome" EXACT [] is_a: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: SO:0000956 ! single_stranded_DNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000961 name: RNA_chromosome def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma] synonym: "RNA chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_quality SO:0000356 ! RNA relationship: has_quality SO:0000356 ! RNA [Term] id: SO:0000962 name: single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma] synonym: "single stranded RNA chromosome" EXACT [] is_a: SO:0000961 ! RNA_chromosome intersection_of: SO:0000961 ! RNA_chromosome intersection_of: has_quality SO:0000984 ! single relationship: has_quality SO:0000984 ! single [Term] id: SO:0000963 name: linear_single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma] synonym: "linear single stranded RNA chromosome" EXACT [] is_a: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000964 name: linear_double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma] synonym: "linear double stranded RNA chromosome" EXACT [] is_a: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: has_quality SO:0000987 ! linear relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000965 name: double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma] synonym: "double stranded RNA chromosome" EXACT [] is_a: SO:0000961 ! RNA_chromosome intersection_of: SO:0000961 ! RNA_chromosome intersection_of: has_quality SO:0000985 ! double relationship: has_quality SO:0000985 ! double [Term] id: SO:0000966 name: circular_single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] synonym: "circular single stranded RNA chromosome" EXACT [] is_a: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: SO:0000962 ! single_stranded_RNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000967 name: circular_double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma] synonym: "circular double stranded RNA chromosome" EXACT [] is_a: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: SO:0000965 ! double_stranded_RNA_chromosome intersection_of: has_quality SO:0000988 ! circular relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000968 name: sequence_replication_mode comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961. synonym: "sequence replication mode" EXACT [] is_obsolete: true [Term] id: SO:0000969 name: rolling_circle comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581. synonym: "rolling circle" EXACT [] xref: http://en.wikipedia.org/wiki/Rolling_circle "wiki" is_obsolete: true [Term] id: SO:0000970 name: theta_replication comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582 synonym: "theta replication" EXACT [] is_obsolete: true [Term] id: SO:0000971 name: DNA_replication_mode comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260. synonym: "DNA replication mode" EXACT [] is_obsolete: true [Term] id: SO:0000972 name: RNA_replication_mode comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961. synonym: "RNA replication mode" EXACT [] is_obsolete: true [Term] id: SO:0000973 name: insertion_sequence def: "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as] synonym: "insertion sequence" EXACT [] synonym: "IS" RELATED [] xref: http://en.wikipedia.org/wiki/Insertion_sequence "wiki" is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000975 name: minicircle_gene synonym: "minicircle gene" EXACT [] is_a: SO:0000089 ! kinetoplast_gene intersection_of: SO:0000089 ! kinetoplast_gene intersection_of: part_of SO:0000980 ! minicircle relationship: part_of SO:0000980 ! minicircle [Term] id: SO:0000976 name: cryptic def: "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000977 name: anchor_binding_site comment: Part of an edited transcript only. synonym: "anchor binding site" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000978 name: template_region def: "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk] synonym: "information region" EXACT [] synonym: "template region" EXACT [] is_a: SO:0000930 ! guide_RNA_region [Term] id: SO:0000979 name: gRNA_encoding def: "A non-protein_coding gene that encodes a guide_RNA." [SO:ma] synonym: "gRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000980 name: minicircle alt_id: SO:0000974 def: "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055] synonym: "minicircle_chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/Minicircle "wiki" is_a: SO:0001235 ! replicon [Term] id: SO:0000981 name: rho_dependent_bacterial_terminator synonym: "rho dependent bacterial terminator" EXACT [] is_a: SO:0000614 ! bacterial_terminator [Term] id: SO:0000982 name: rho_independent_bacterial_terminator synonym: "rho independent bacterial terminator" EXACT [] is_a: SO:0000614 ! bacterial_terminator [Term] id: SO:0000983 name: strand_attribute comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "strand attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000984 name: single comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. is_a: SO:0000983 ! strand_attribute [Term] id: SO:0000985 name: double comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. is_a: SO:0000983 ! strand_attribute [Term] id: SO:0000986 name: topology_attribute comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "topology attribute" EXACT [] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000987 name: linear def: "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "two-ended" RELATED [] is_a: SO:0000986 ! topology_attribute disjoint_from: SO:0000988 ! circular [Term] id: SO:0000988 name: circular def: "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "zero-ended" RELATED [] is_a: SO:0000986 ! topology_attribute [Term] id: SO:0000989 name: class_II_RNA def: "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] synonym: "class II RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000990 name: class_I_RNA def: "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577. synonym: "class I RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000991 name: genomic_DNA comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "genomic DNA" EXACT [] is_a: SO:0000352 ! DNA [Term] id: SO:0000992 name: BAC_cloned_genomic_insert comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006. synonym: "BAC cloned genomic insert" EXACT [] is_a: SO:0000914 ! cloned_genomic_insert intersection_of: SO:0000914 ! cloned_genomic_insert intersection_of: derives_from SO:0000153 ! BAC relationship: derives_from SO:0000153 ! BAC [Term] id: SO:0000993 name: consensus comment: Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA. is_a: SO:0000905 ! status [Term] id: SO:0000994 name: consensus_region comment: DO not obsolete without considering MGED mapping. synonym: "consensus region" EXACT [] is_a: SO:0001410 ! experimental_feature intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0000993 ! consensus relationship: has_quality SO:0000993 ! consensus [Term] id: SO:0000995 name: consensus_mRNA comment: DO not obsolete without considering MGED mapping. synonym: "consensus mRNA" EXACT [] is_a: SO:0000234 ! mRNA is_a: SO:0000994 ! consensus_region intersection_of: SO:0000234 ! mRNA intersection_of: has_quality SO:0000993 ! consensus relationship: has_quality SO:0000993 ! consensus [Term] id: SO:0000996 name: predicted_gene comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "predicted gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000732 ! predicted relationship: has_quality SO:0000732 ! predicted [Term] id: SO:0000997 name: gene_fragment comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "gene fragment" EXACT [] is_a: SO:0000842 ! gene_component_region intersection_of: SO:0000842 ! gene_component_region intersection_of: has_quality SO:0000731 ! fragmentary relationship: has_quality SO:0000731 ! fragmentary [Term] id: SO:0000998 name: recursive_splice_site def: "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661] synonym: "recursive splice site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000999 name: BAC_end def: "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke] comment: Requested by Keith Boroevich December, 2006. synonym: "BAC end" EXACT [] synonym: "BAC end sequence" EXACT [] synonym: "BES" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000153 ! BAC [Term] id: SO:0001000 name: rRNA_16S def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "16S ribosomal RNA" EXACT [] synonym: "16S rRNA" RELATED [] synonym: "16S SSU RNA" EXACT [] synonym: "rRNA 16S" EXACT [] xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki" is_a: SO:0000650 ! small_subunit_rRNA [Term] id: SO:0001001 name: rRNA_23S def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke] subset: SOFA synonym: "23S LSU rRNA" EXACT [] synonym: "23S ribosomal RNA" RELATED [] synonym: "23S rRNA" EXACT [] synonym: "rRNA 23S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001002 name: rRNA_25S def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb] subset: SOFA synonym: "25S LSU rRNA" EXACT [] synonym: "25S ribosomal RNA" EXACT [] synonym: "25S rRNA" EXACT [] synonym: "rRNA 25S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001003 name: solo_LTR def: "A recombination product between the 2 LTR of the same element." [SO:ke] comment: Requested by Hadi Quesneville January 2007. synonym: "solo LTR" EXACT [] is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0001004 name: low_complexity synonym: "low complexity" EXACT [] is_a: SO:0000905 ! status [Term] id: SO:0001005 name: low_complexity_region synonym: "low complexity region" EXACT [] is_a: SO:0001410 ! experimental_feature intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0001004 ! low_complexity relationship: has_quality SO:0001004 ! low_complexity [Term] id: SO:0001006 name: prophage def: "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\"." [GOC:jl] xref: http://en.wikipedia.org/wiki/Prophage "wiki" is_a: SO:0000113 ! proviral_region [Term] id: SO:0001007 name: cryptic_prophage def: "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." [GOC:jl] comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site. synonym: "cryptic prophage" EXACT [] xref: http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w is_a: SO:0000772 ! genomic_island [Term] id: SO:0001008 name: tetraloop def: "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke] xref: http://en.wikipedia.org/wiki/Tetraloop "wiki" is_a: SO:0000313 ! stem_loop [Term] id: SO:0001009 name: DNA_constraint_sequence def: "A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\]&dispmax=50] synonym: "DNA constraint" EXACT [] synonym: "DNA constraint sequence" EXACT [] is_a: SO:0000442 ! ds_oligo [Term] id: SO:0001010 name: i_motif def: "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739] synonym: "i motif" EXACT [] synonym: "short intercalated motif" EXACT [] is_a: SO:0000142 ! DNA_sequence_secondary_structure [Term] id: SO:0001011 name: PNA_oligo def: "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke] synonym: "peptide nucleic acid" EXACT [] synonym: "PNA oligo" EXACT [] xref: http://en.wikipedia.org/wiki/Peptide_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001184 ! PNA relationship: has_quality SO:0001184 ! PNA [Term] id: SO:0001012 name: DNAzyme def: "A DNA sequence with catalytic activity." [SO:cb] comment: Added by request from Colin Batchelor. synonym: "catalytic DNA" EXACT [] synonym: "deoxyribozyme" RELATED [] synonym: "DNA enzyme" EXACT [] is_a: SO:0000696 ! oligo intersection_of: SO:0000696 ! oligo intersection_of: has_quality SO:0001185 ! enzymatic relationship: has_quality SO:0001185 ! enzymatic [Term] id: SO:0001013 name: MNP def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431] synonym: "multiple nucleotide polymorphism" RELATED [] is_a: SO:1000002 ! substitution [Term] id: SO:0001014 name: intron_domain comment: Requested by Colin Batchelor, Feb 2007. synonym: "intron domain" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000188 ! intron [Term] id: SO:0001015 name: wobble_base_pair def: "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617] synonym: "wobble base pair" EXACT [] synonym: "wobble pair" EXACT [] xref: http://en.wikipedia.org/wiki/Wobble_base_pair "wiki" is_a: SO:0000028 ! base_pair [Term] id: SO:0001016 name: internal_guide_sequence def: "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb] synonym: "IGS" EXACT [] synonym: "internal guide sequence" EXACT [] is_a: SO:0001014 ! intron_domain relationship: part_of SO:0000587 ! group_I_intron [Term] id: SO:0001017 name: silent_mutation def: "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke] comment: Added in March 2007 in after meeting with pharmgkb. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc. synonym: "silent mutation" EXACT [] xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki" xref: loinc:LA6700-4 "Silent" is_a: SO:0001878 ! feature_variant [Term] id: SO:0001018 name: epitope def: "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb] comment: Requested by Trish Whetzel. xref: http://en.wikipedia.org/wiki/Epitope "wiki" is_a: SO:0000409 ! binding_site [Term] id: SO:0001019 name: copy_number_variation def: "A variation that increases or decreases the copy number of a given region." [SO:ke] subset: SOFA synonym: "CNP" EXACT [] synonym: "CNV" EXACT [] synonym: "copy number polymorphism" EXACT [] synonym: "copy number variation" EXACT [] xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki" is_a: SO:0001059 ! sequence_alteration [Term] id: SO:0001020 name: sequence_variant_affecting_copy_number comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting copy number" EXACT [] synonym: "sequence variant affecting copy number" EXACT [] is_obsolete: true replaced_by: SO:0001563 [Term] id: SO:0001021 name: chromosome_breakpoint alt_id: SO:0001242 synonym: "aberration breakpoint" EXACT [] synonym: "aberration_junction" EXACT [] synonym: "chromosome breakpoint" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0001022 name: inversion_breakpoint def: "The point within a chromosome where an inversion begins or ends." [SO:cb] synonym: "inversion breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001023 name: allele def: "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop] synonym: "allelomorph" EXACT [] xref: http://en.wikipedia.org/wiki/Allele "wiki" is_a: SO:0001507 ! variant_collection relationship: variant_of SO:0000704 ! gene [Term] id: SO:0001024 name: haplotype def: "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop] xref: http://en.wikipedia.org/wiki/Haplotype "wiki" is_a: SO:0001507 ! variant_collection relationship: variant_of SO:0000355 ! haplotype_block [Term] id: SO:0001025 name: polymorphic_sequence_variant def: "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop] synonym: "polymorphic sequence variant" EXACT [] is_a: SO:0001023 ! allele [Term] id: SO:0001026 name: genome def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop] xref: http://en.wikipedia.org/wiki/Genome "wiki" is_a: SO:0001260 ! sequence_collection intersection_of: SO:0001260 ! sequence_collection intersection_of: has_part SO:0001235 ! replicon relationship: has_part SO:0001235 ! replicon [Term] id: SO:0001027 name: genotype def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop] xref: http://en.wikipedia.org/wiki/Genotype "wiki" is_a: SO:0001507 ! variant_collection relationship: variant_of SO:0001026 ! genome [Term] id: SO:0001028 name: diplotype def: "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop] is_a: SO:0001507 ! variant_collection [Term] id: SO:0001029 name: direction_attribute synonym: "direction attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001030 name: forward def: "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke] is_a: SO:0001029 ! direction_attribute [Term] id: SO:0001031 name: reverse def: "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke] is_a: SO:0001029 ! direction_attribute [Term] id: SO:0001032 name: mitochondrial_DNA comment: This terms is used by MO. synonym: "mitochondrial DNA" EXACT [] synonym: "mtDNA" EXACT [] xref: http://en.wikipedia.org/wiki/Mitochondrial_DNA "wiki" is_a: SO:0000737 ! mitochondrial_sequence intersection_of: SO:0000737 ! mitochondrial_sequence intersection_of: has_quality SO:0000352 ! DNA relationship: has_quality SO:0000352 ! DNA [Term] id: SO:0001033 name: chloroplast_DNA comment: This term is used by MO. synonym: "chloroplast DNA" EXACT [] is_a: SO:0000745 ! chloroplast_sequence intersection_of: SO:0000745 ! chloroplast_sequence intersection_of: has_quality SO:0000352 ! DNA relationship: has_quality SO:0000352 ! DNA [Term] id: SO:0001034 name: mirtron def: "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma] comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns. is_a: SO:0001014 ! intron_domain [Term] id: SO:0001035 name: piRNA def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke] synonym: "piwi-associated RNA" EXACT [] xref: http://en.wikipedia.org/wiki/PiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0001036 name: arginyl_tRNA def: "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke] synonym: "arginyl tRNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000212 ! arginine_tRNA_primary_transcript [Term] id: SO:0001037 name: mobile_genetic_element def: "A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355] subset: SOFA synonym: "MGE" EXACT [] synonym: "mobile genetic element" EXACT [] xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki" is_a: SO:0001411 ! biological_region intersection_of: SO:0000001 ! region intersection_of: has_quality SO:0001234 ! mobile relationship: has_quality SO:0001234 ! mobile [Term] id: SO:0001038 name: extrachromosomal_mobile_genetic_element def: "An MGE that is not integrated into the host chromosome." [SO:ke] synonym: "extrachromosomal mobile genetic element" EXACT [] is_a: SO:0001037 ! mobile_genetic_element [Term] id: SO:0001039 name: integrated_mobile_genetic_element def: "An MGE that is integrated into the host chromosome." [SO:ke] subset: SOFA synonym: "integrated mobile genetic element" EXACT [] is_a: SO:0001037 ! mobile_genetic_element [Term] id: SO:0001040 name: integrated_plasmid def: "A plasmid sequence that is integrated within the host chromosome." [SO:ke] synonym: "integrated plasmid" EXACT [] is_a: SO:0001039 ! integrated_mobile_genetic_element intersection_of: SO:0001039 ! integrated_mobile_genetic_element intersection_of: derives_from SO:0000155 ! plasmid relationship: derives_from SO:0000155 ! plasmid [Term] id: SO:0001041 name: viral_sequence def: "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke] comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct. synonym: "viral sequence" EXACT [] synonym: "virus sequence" EXACT [] is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element is_a: SO:0001235 ! replicon [Term] id: SO:0001042 name: phage_sequence def: "The nucleotide sequence of a virus that infects bacteria." [SO:ke] synonym: "bacteriophage" EXACT [] synonym: "phage" EXACT [] synonym: "phage sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Bacteriophage "wiki" is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001043 name: attCtn_site def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at] synonym: "attCtn site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0000371 ! conjugative_transposon [Term] id: SO:0001044 name: nuclear_mt_pseudogene def: "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp] comment: Definition change requested by Val, 3172757. synonym: "nuclear mitochondrial pseudogene" EXACT [] synonym: "nuclear mt pseudogene" EXACT [] synonym: "NUMT" EXACT [] xref: http://en.wikipedia.org/wiki/Numt "wikipedia" is_a: SO:0001760 ! non_processed_pseudogene [Term] id: SO:0001045 name: cointegrated_plasmid def: "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at] synonym: "cointegrated plasmid" EXACT [] synonym: "cointegrated replicon" EXACT [] is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0001046 name: IRLinv_site def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at] synonym: "IRLinv site" EXACT [] is_a: SO:0001048 ! inversion_site_part relationship: part_of SO:0000948 ! inversion_site [Term] id: SO:0001047 name: IRRinv_site def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at] synonym: "IRRinv site" EXACT [] is_a: SO:0001048 ! inversion_site_part relationship: part_of SO:0000948 ! inversion_site [Term] id: SO:0001048 name: inversion_site_part def: "A region located within an inversion site." [SO:ke] comment: A term created to allow the parts of an inversion site have an is_a path back to the root. synonym: "inversion site part" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0001049 name: defective_conjugative_transposon def: "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane] synonym: "defective conjugative transposon" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0001050 name: repeat_fragment def: "A portion of a repeat, interrupted by the insertion of another element." [SO:ke] comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats. synonym: "repeat fragment" EXACT [] is_a: SO:0000840 ! repeat_component relationship: part_of SO:0001649 ! nested_repeat [Term] id: SO:0001051 name: nested_region is_obsolete: true [Term] id: SO:0001052 name: nested_repeat is_obsolete: true [Term] id: SO:0001053 name: nested_transposon is_obsolete: true [Term] id: SO:0001054 name: transposon_fragment def: "A portion of a transposon, interrupted by the insertion of another element." [SO:ke] synonym: "transposon fragment" EXACT [] is_a: SO:0000840 ! repeat_component relationship: part_of SO:0001648 ! nested_transposon [Term] id: SO:0001055 name: transcriptional_cis_regulatory_region def: "A regulatory_region that modulates the transcription of a gene or genes." [SO:regcreative] subset: SOFA synonym: "transcriptional cis regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0001056 name: splicing_regulatory_region def: "A regulatory_region that modulates splicing." [SO:ke] subset: SOFA synonym: "splicing regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0001057 name: enhanceosome is_obsolete: true [Term] id: SO:0001058 name: promoter_targeting_sequence def: "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative] synonym: "promoter targeting sequence" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0001059 name: sequence_alteration alt_id: SO:1000004 alt_id: SO:1000007 def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] comment: Merged with partially characterized change in nucleotide sequence. subset: SOFA synonym: "partially characterised change in DNA sequence" NARROW [] synonym: "partially_characterised_change_in_DNA_sequence" NARROW [] synonym: "sequence alteration" EXACT [] synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0001060 name: sequence_variant def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] synonym: "sequence variant" EXACT [] [Term] id: SO:0001061 name: propeptide_cleavage_site alt_id: BS:00063 def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR] comment: Discrete. subset: biosapiens synonym: "propeptide cleavage site" EXACT [] is_a: SO:0100011 ! cleaved_peptide_region relationship: part_of SO:0001062 ! propeptide [Term] id: SO:0001062 name: propeptide alt_id: BS:00077 def: "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "propep" RELATED [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Propeptide "wiki" is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0001063 name: immature_peptide_region alt_id: BS:00129 def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR] comment: Range. subset: biosapiens subset: SOFA synonym: "immature peptide region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001064 name: active_peptide alt_id: BS:00076 def: "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual] comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length. subset: biosapiens synonym: "active peptide" EXACT [] synonym: "peptide" BROAD [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Peptide "wiki" is_a: SO:0000419 ! mature_protein_region [Term] id: SO:0001066 name: compositionally_biased_region_of_peptide alt_id: BS:00068 def: "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "compbias" RELATED [uniprot:feature_type] synonym: "compositional bias" RELATED [] synonym: "compositionally biased" RELATED [] synonym: "compositionally biased region of peptide" RELATED [] synonym: "compositionally_biased_region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001067 name: polypeptide_motif alt_id: BS:00032 def: "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "motif" BROAD [uniprot:feature_type] synonym: "polypeptide motif" EXACT [] is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0001068 name: polypeptide_repeat alt_id: BS:00070 def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "polypeptide repeat" EXACT [] synonym: "repeat" RELATED [uniprot:feature_type] is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0001070 name: polypeptide_structural_region alt_id: BS:00337 def: "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb] comment: Range. subset: biosapiens synonym: "polypeptide structural region" EXACT [] synonym: "structural_region" RELATED [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001071 name: membrane_structure alt_id: BS:00128 def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "membrane structure" EXACT [] is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0001072 name: extramembrane_polypeptide_region alt_id: BS:00154 def: "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb] comment: Range. subset: biosapiens synonym: "extramembrane" RELATED BS [] synonym: "extramembrane polypeptide region" EXACT [] synonym: "extramembrane_region" RELATED BS [] synonym: "topo_dom" RELATED BS [uniprot:feature_type] is_a: SO:0001070 ! polypeptide_structural_region relationship: part_of SO:0001071 ! membrane_structure [Term] id: SO:0001073 name: cytoplasmic_polypeptide_region alt_id: BS:00145 def: "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "cytoplasm_location" EXACT BS [] synonym: "cytoplasmic polypeptide region" EXACT [] synonym: "inside" RELATED BS [] is_a: SO:0001072 ! extramembrane_polypeptide_region [Term] id: SO:0001074 name: non_cytoplasmic_polypeptide_region alt_id: BS:00144 def: "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb] comment: This could be inside an organelle within the cell. subset: biosapiens synonym: "non cytoplasmic polypeptide region" EXACT [] synonym: "non_cytoplasm_location" EXACT BS [] synonym: "outside" RELATED BS [] is_a: SO:0001072 ! extramembrane_polypeptide_region [Term] id: SO:0001075 name: intramembrane_polypeptide_region alt_id: BS:00156 def: "Polypeptide region present in the lipid bilayer." [EBIBS:GAR] subset: biosapiens synonym: "intramembrane" RELATED BS [] synonym: "intramembrane polypeptide region" EXACT [] is_a: SO:0001070 ! polypeptide_structural_region relationship: part_of SO:0001071 ! membrane_structure [Term] id: SO:0001076 name: membrane_peptide_loop alt_id: BS:00155 def: "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "membrane peptide loop" EXACT [] synonym: "membrane_loop" RELATED BS [] is_a: SO:0001075 ! intramembrane_polypeptide_region [Term] id: SO:0001077 name: transmembrane_polypeptide_region alt_id: BS:00158 def: "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual] subset: biosapiens synonym: "transmem" RELATED BS [uniprot:feature_type] synonym: "transmembrane" RELATED BS [] synonym: "transmembrane polypeptide region" EXACT [] is_a: SO:0001075 ! intramembrane_polypeptide_region [Term] id: SO:0001078 name: polypeptide_secondary_structure alt_id: BS:00003 def: "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR] comment: Biosapien term was secondary_structure. subset: biosapiens synonym: "2nary structure" RELATED BS [] synonym: "polypeptide secondary structure" EXACT [] synonym: "secondary structure" RELATED BS [] synonym: "secondary structure region" RELATED BS [] synonym: "secondary_structure" RELATED BS [] xref: http://en.wikipedia.org/wiki/Secondary_structure "wiki" is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0001079 name: polypeptide_structural_motif alt_id: BS:0000338 def: "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR] subset: biosapiens synonym: "polypeptide structural motif" RELATED [] synonym: "structural_motif" RELATED BS [] xref: http://en.wikipedia.org/wiki/Structural_motif "wiki" is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0001080 name: coiled_coil alt_id: BS:00041 def: "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "coiled" RELATED BS [uniprot:feature_type] synonym: "coiled coil" EXACT [] xref: http://en.wikipedia.org/wiki/Coiled_coil "wiki" is_a: SO:0001079 ! polypeptide_structural_motif [Term] id: SO:0001081 name: helix_turn_helix alt_id: BS:00147 def: "A motif comprising two helices separated by a turn." [EBIBS:GAR] subset: biosapiens synonym: "helix turn helix" EXACT [] synonym: "helix-turn-helix" EXACT [] synonym: "HTH" RELATED BS [] is_a: SO:0001079 ! polypeptide_structural_motif relationship: has_part SO:0001114 ! peptide_helix relationship: has_part SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001082 name: polypeptide_sequencing_information alt_id: BS:00125 def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "sequencing_information" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0001083 name: non_adjacent_residues alt_id: BS:00182 def: "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual] subset: biosapiens synonym: "non consecutive" EXACT [] synonym: "non_cons" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001084 name: non_terminal_residue alt_id: BS:00072 def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "non terminal" EXACT [] synonym: "non_ter" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001085 name: sequence_conflict alt_id: BS:00069 def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "conflict" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001086 name: sequence_uncertainty alt_id: BS:00181 def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual] subset: biosapiens synonym: "unsure" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001087 name: cross_link alt_id: BS:00178 def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual] subset: biosapiens synonym: "cross link" EXACT [] synonym: "crosslink" RELATED [] is_obsolete: true [Term] id: SO:0001088 name: disulfide_bond alt_id: BS:00028 def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual] comment: 2 discreet & joined. subset: biosapiens synonym: "disulfid" RELATED [] synonym: "disulfide" RELATED [] synonym: "disulfide bond" RELATED [] synonym: "disulphide" EXACT [] synonym: "disulphide bond" RELATED [] is_obsolete: true [Term] id: SO:0001089 name: post_translationally_modified_region alt_id: BS:00052 def: "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "mod_res" EXACT [uniprot:feature_type] synonym: "modified residue" EXACT [] synonym: "post_translational_modification" EXACT [] xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki" is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0001090 name: covalent_binding_site alt_id: BS:00246 def: "Binding involving a covalent bond." [EBIBS:GAR] subset: biosapiens synonym: "covalent binding site" EXACT [] is_obsolete: true [Term] id: SO:0001091 name: non_covalent_binding_site alt_id: BS:00029 def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR] comment: Discrete. subset: biosapiens synonym: "binding" RELATED [uniprot:curation] synonym: "binding site" RELATED [] synonym: "non covalent binding site" EXACT [] is_obsolete: true [Term] id: SO:0001092 name: polypeptide_metal_contact alt_id: BS:00027 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual] comment: Residue is part of a binding site for a metal ion. subset: biosapiens synonym: "metal_binding" RELATED [] is_a: SO:0001656 ! metal_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001093 name: protein_protein_contact alt_id: BS:00131 def: "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual] subset: biosapiens synonym: "protein protein contact" EXACT [] synonym: "protein protein contact site" EXACT [] synonym: "protein_protein_interaction" RELATED [] xref: http://en.wikipedia.org/wiki/Protein_protein_interaction "wiki" is_a: SO:0000410 ! protein_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001094 name: polypeptide_calcium_ion_contact_site alt_id: BS:00186 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR] comment: Residue involved in contact with calcium. subset: biosapiens synonym: "ca bind" RELATED [] synonym: "Ca_contact_site" EXACT [] synonym: "polypeptide calcium ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001095 name: polypeptide_cobalt_ion_contact_site alt_id: BS:00136 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Co_contact_site" EXACT [] synonym: "polypeptide cobalt ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001096 name: polypeptide_copper_ion_contact_site alt_id: BS:00146 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Cu_contact_site" EXACT [] synonym: "polypeptide copper ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001097 name: polypeptide_iron_ion_contact_site alt_id: BS:00137 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Fe_contact_site" EXACT [] synonym: "polypeptide iron ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001098 name: polypeptide_magnesium_ion_contact_site alt_id: BS:00187 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Mg_contact_site" EXACT [] synonym: "polypeptide magnesium ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001099 name: polypeptide_manganese_ion_contact_site alt_id: BS:00140 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Mn_contact_site" EXACT [] synonym: "polypeptide manganese ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001100 name: polypeptide_molybdenum_ion_contact_site alt_id: BS:00141 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Mo_contact_site" EXACT [] synonym: "polypeptide molybdenum ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001101 name: polypeptide_nickel_ion_contact_site alt_id: BS:00142 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR] subset: biosapiens synonym: "Ni_contact_site" EXACT [] synonym: "polypeptide nickel ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001102 name: polypeptide_tungsten_ion_contact_site alt_id: BS:00143 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "polypeptide tungsten ion contact site" EXACT [] synonym: "W_contact_site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001103 name: polypeptide_zinc_ion_contact_site alt_id: BS:00185 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "polypeptide zinc ion contact site" EXACT [] synonym: "Zn_contact_site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001104 name: catalytic_residue alt_id: BS:00026 def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "act_site" RELATED [uniprot:feature_type] synonym: "active site residue" EXACT [] synonym: "catalytic residue" EXACT [] is_a: SO:0001237 ! amino_acid relationship: part_of SO:0100019 ! polypeptide_catalytic_motif [Term] id: SO:0001105 name: polypeptide_ligand_contact alt_id: BS:00157 def: "Residues which interact with a ligand." [EBIBS:GAR] subset: biosapiens synonym: "polypeptide ligand contact" EXACT [] synonym: "protein-ligand interaction" RELATED [] is_a: SO:0001657 ! ligand_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001106 name: asx_motif alt_id: BS:00202 def: "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx motif" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001107 name: beta_bulge alt_id: BS:00208 def: "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge" EXACT [] xref: http://en.wikipedia.org/wiki/Beta_bulge "wiki" is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001108 name: beta_bulge_loop alt_id: BS:00209 def: "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge loop" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001109 name: beta_bulge_loop_five alt_id: BS:00210 def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge loop five" EXACT [] is_a: SO:0001108 ! beta_bulge_loop [Term] id: SO:0001110 name: beta_bulge_loop_six alt_id: BS:00211 def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge loop six" EXACT [] is_a: SO:0001108 ! beta_bulge_loop [Term] id: SO:0001111 name: beta_strand alt_id: BS:00042 def: "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "strand" RELATED BS [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Beta_sheet "wiki" is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001112 name: antiparallel_beta_strand alt_id: BS:0000341 def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "antiparallel beta strand" EXACT [] is_a: SO:0001111 ! beta_strand [Term] id: SO:0001113 name: parallel_beta_strand alt_id: BS:00151 def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "parallel beta strand" EXACT [] is_a: SO:0001111 ! beta_strand [Term] id: SO:0001114 name: peptide_helix alt_id: BS:00152 def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "helix" RELATED BS [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001115 name: left_handed_peptide_helix alt_id: BS:00222 def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR] subset: biosapiens synonym: "helix-l" RELATED [] synonym: "left handed helix" EXACT [] is_a: SO:0001114 ! peptide_helix [Term] id: SO:0001116 name: right_handed_peptide_helix alt_id: BS:0000339 def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR] subset: biosapiens synonym: "helix" RELATED BS [] synonym: "right handed helix" EXACT [] is_a: SO:0001114 ! peptide_helix [Term] id: SO:0001117 name: alpha_helix alt_id: BS:00040 def: "The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "a-helix" RELATED BS [] synonym: "helix" RELATED BS [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Alpha_helix "wiki" is_a: SO:0001116 ! right_handed_peptide_helix [Term] id: SO:0001118 name: pi_helix alt_id: BS:00153 def: "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "pi helix" EXACT [] xref: http://en.wikipedia.org/wiki/Pi_helix "wiki" is_a: SO:0001116 ! right_handed_peptide_helix [Term] id: SO:0001119 name: three_ten_helix alt_id: BS:0000340 def: "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "3(10) helix" EXACT [] synonym: "3-10 helix" EXACT [] synonym: "310 helix" EXACT [] synonym: "three ten helix" EXACT [] xref: http://en.wikipedia.org/wiki/310_helix "wiki" is_a: SO:0001116 ! right_handed_peptide_helix [Term] id: SO:0001120 name: polypeptide_nest_motif alt_id: BS:00223 def: "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "nest" RELATED BS [] synonym: "nest_motif" EXACT [] synonym: "polypeptide nest motif" RELATED [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001121 name: polypeptide_nest_left_right_motif alt_id: BS:00224 def: "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "nest_left_right" EXACT [] synonym: "nest_lr" EXACT [] synonym: "polypeptide nest left right motif" EXACT [] is_a: SO:0001120 ! polypeptide_nest_motif [Term] id: SO:0001122 name: polypeptide_nest_right_left_motif alt_id: BS:00225 def: "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "nest_right_left" EXACT [] synonym: "nest_rl" EXACT [] synonym: "polypeptide nest right left motif" EXACT [] is_a: SO:0001120 ! polypeptide_nest_motif [Term] id: SO:0001123 name: schellmann_loop alt_id: BS:00226 def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "paperclip" RELATED BS [] synonym: "paperclip loop" RELATED [] synonym: "schellmann loop" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001124 name: schellmann_loop_seven alt_id: BS:00228 def: "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "schellmann loop seven" EXACT [] synonym: "seven-residue schellmann loop" EXACT [] is_a: SO:0001123 ! schellmann_loop [Term] id: SO:0001125 name: schellmann_loop_six alt_id: BS:00227 def: "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "schellmann loop six" EXACT [] synonym: "six-residue schellmann loop" EXACT [] is_a: SO:0001123 ! schellmann_loop [Term] id: SO:0001126 name: serine_threonine_motif alt_id: BS:00229 def: "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "serine/threonine motif" EXACT [] synonym: "st motif" EXACT [] synonym: "st_motif" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001127 name: serine_threonine_staple_motif alt_id: BS:00230 def: "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "serine threonine staple motif" EXACT [] synonym: "st_staple" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001128 name: polypeptide_turn_motif alt_id: BS:00148 def: "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type] comment: Range. subset: biosapiens synonym: "turn" RELATED BS [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001129 name: asx_turn_left_handed_type_one alt_id: BS:00206 def: "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn left handed type one" EXACT [] synonym: "asx_turn_il" RELATED [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001130 name: asx_turn_left_handed_type_two alt_id: BS:00204 def: "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn left handed type two" EXACT [] synonym: "asx_turn_iil" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001131 name: asx_turn_right_handed_type_two alt_id: BS:00205 def: "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn right handed type two" EXACT [] synonym: "asx_turn_iir" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001132 name: asx_turn_right_handed_type_one alt_id: BS:00207 def: "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn type right handed type one" EXACT [] synonym: "asx_turn_ir" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001133 name: beta_turn alt_id: BS:00212 def: "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001134 name: beta_turn_left_handed_type_one alt_id: BS:00215 def: "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn left handed type one" EXACT [] synonym: "beta_turn_il" EXACT [] synonym: "type I' beta turn" EXACT [] synonym: "type I' turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001135 name: beta_turn_left_handed_type_two alt_id: BS:00213 def: "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn left handed type two" EXACT [] synonym: "beta_turn_iil" EXACT [] synonym: "type II' beta turn" EXACT [] synonym: "type II' turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001136 name: beta_turn_right_handed_type_one alt_id: BS:00216 def: "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn right handed type one" EXACT [] synonym: "beta_turn_ir" EXACT [] synonym: "type I beta turn" EXACT [] synonym: "type I turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001137 name: beta_turn_right_handed_type_two alt_id: BS:00214 def: "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn right handed type two" EXACT [] synonym: "beta_turn_iir" EXACT [] synonym: "type II beta turn" EXACT [] synonym: "type II turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001138 name: gamma_turn alt_id: BS:00219 def: "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "gamma turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001139 name: gamma_turn_classic alt_id: BS:00220 def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "classic gamma turn" EXACT [] synonym: "gamma turn classic" EXACT [] is_a: SO:0001138 ! gamma_turn [Term] id: SO:0001140 name: gamma_turn_inverse alt_id: BS:00221 def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "gamma turn inverse" EXACT [] is_a: SO:0001138 ! gamma_turn [Term] id: SO:0001141 name: serine_threonine_turn alt_id: BS:00231 def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "serine/threonine turn" EXACT [] synonym: "st_turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001142 name: st_turn_left_handed_type_one alt_id: BS:00234 def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn left handed type one" EXACT [] synonym: "st_turn_il" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001143 name: st_turn_left_handed_type_two alt_id: BS:00232 def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn left handed type two" EXACT [] synonym: "st_turn_iil" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001144 name: st_turn_right_handed_type_one alt_id: BS:00235 def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn right handed type one" EXACT [] synonym: "st_turn_ir" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001145 name: st_turn_right_handed_type_two alt_id: BS:00233 def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn right handed type two" EXACT [] synonym: "st_turn_iir" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001146 name: polypeptide_variation_site alt_id: BS:00336 def: "A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke] comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations. subset: biosapiens synonym: "sequence_variations" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001147 name: natural_variant_site alt_id: BS:00071 def: "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "natural_variant" BROAD [] synonym: "sequence variation" BROAD [] synonym: "variant" BROAD [uniprot:feature_type] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001148 name: mutated_variant_site alt_id: BS:00036 def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "mutagen" EXACT BS [uniprot:feature_type] synonym: "mutagenesis" EXACT [] synonym: "mutated_site" EXACT [] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001149 name: alternate_sequence_site alt_id: BS:00073 alt_id: SO:0001065 def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "alternative_sequence" EXACT [] synonym: "isoform" NARROW [] synonym: "sequence variation" NARROW [] synonym: "var_seq" EXACT [uniprot:feature_type] synonym: "varsplic" NARROW [] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001150 name: beta_turn_type_six def: "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb] subset: biosapiens synonym: "beta turn type six" EXACT [] synonym: "cis-proline loop" EXACT [] synonym: "type VI beta turn" EXACT [] synonym: "type VI turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001151 name: beta_turn_type_six_a def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] subset: biosapiens synonym: "beta turn type six a" EXACT [] synonym: "type VIa beta turn" EXACT [] synonym: "type VIa turn" EXACT [] is_a: SO:0001150 ! beta_turn_type_six [Term] id: SO:0001152 name: beta_turn_type_six_a_one subset: biosapiens synonym: "beta turn type six a one" EXACT [] synonym: "type VIa1 beta turn" EXACT [] synonym: "type VIa1 turn" EXACT [] is_a: SO:0001151 ! beta_turn_type_six_a [Term] id: SO:0001153 name: beta_turn_type_six_a_two subset: biosapiens synonym: "beta turn type six a two" EXACT [] synonym: "type VIa2 beta turn" EXACT [] synonym: "type VIa2 turn" EXACT [] is_a: SO:0001151 ! beta_turn_type_six_a [Term] id: SO:0001154 name: beta_turn_type_six_b def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] subset: biosapiens synonym: "beta turn type six b" EXACT [] synonym: "type VIb beta turn" EXACT [] synonym: "type VIb turn" EXACT [] is_a: SO:0001150 ! beta_turn_type_six [Term] id: SO:0001155 name: beta_turn_type_eight def: "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb] subset: biosapiens synonym: "beta turn type eight" EXACT [] synonym: "type VIII beta turn" EXACT [] synonym: "type VIII turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001156 name: DRE_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576] comment: This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10. synonym: "DRE motif" EXACT [] synonym: "NDM4" EXACT [] synonym: "WATCGATW_motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001157 name: DMv4_motif def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576] synonym: "directional motif v4" EXACT [] synonym: "DMv4" EXACT [] synonym: "DMv4 motif" EXACT [] synonym: "motif 1 element" EXACT [] synonym: "promoter motif 1" EXACT [] synonym: "YGGTCACATR" NARROW [] is_a: SO:0001659 ! promoter_element [Term] id: SO:0001158 name: E_box_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941] synonym: "AWCAGCTGWT" NARROW [] synonym: "E box motif" EXACT [] synonym: "generic E box motif" EXACT [] synonym: "NDM5" RELATED [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001159 name: DMv5_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941] synonym: "directional motif v5" EXACT [] synonym: "DMv5" EXACT [] synonym: "DMv5 motif" EXACT [] synonym: "KTYRGTATWTTT" NARROW [] synonym: "promoter motif 6" RELATED [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001160 name: DMv3_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941] synonym: "directional motif v3" EXACT [] synonym: "DMv3" EXACT [] synonym: "DMv3 motif" EXACT [] synonym: "KNNCAKCNCTRNY" NARROW [] synonym: "promoter motif 7" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001161 name: DMv2_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941] synonym: "directional motif v2" EXACT [] synonym: "DMv2" EXACT [] synonym: "DMv2 motif" EXACT [] synonym: "MKSYGGCARCGSYSS" NARROW [] synonym: "promoter motif 8" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001162 name: MTE def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867] synonym: "CSARCSSAACGS" NARROW [] synonym: "motif ten element" EXACT [] synonym: "motif_ten_element" EXACT [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter [Term] id: SO:0001163 name: INR1_motif def: "A promoter motif with consensus sequence TCATTCG." [PMID:16827941] synonym: "directional motif p3" EXACT [] synonym: "directional promoter motif 3" EXACT [] synonym: "DMp3" EXACT [] synonym: "INR1 motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001164 name: DPE1_motif def: "A promoter motif with consensus sequence CGGACGT." [PMID:16827941] synonym: "directional motif 5" EXACT [] synonym: "directional promoter motif 5" RELATED [] synonym: "DMp5" EXACT [] synonym: "DPE1 motif" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001165 name: DMv1_motif def: "A promoter motif with consensus sequence CARCCCT." [PMID:16827941] synonym: "directional promoter motif v1" RELATED [] synonym: "DMv1" RELATED [] synonym: "DMv1 motif" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001166 name: GAGA_motif def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941] synonym: "GAGA" EXACT [] synonym: "GAGA motif" EXACT [] synonym: "NDM1" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001167 name: NDM2_motif def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941] synonym: "NDM2" EXACT [] synonym: "NDM2 motif" EXACT [] synonym: "non directional promoter motif 2" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001168 name: NDM3_motif def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941] synonym: "NDM3" EXACT [] synonym: "NDM3 motif" EXACT [] synonym: "non directional motif 3" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001169 name: ds_RNA_viral_sequence def: "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke] synonym: "double stranded RNA virus sequence" EXACT [] synonym: "ds RNA viral sequence" EXACT [] is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001170 name: polinton def: "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396] synonym: "maverick element" RELATED [] is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0001171 name: rRNA_21S def: "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb] synonym: "21S LSU rRNA" EXACT [] synonym: "21S ribosomal RNA" EXACT [] synonym: "21S rRNA" EXACT [] synonym: "rRNA 21S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001172 name: tRNA_region def: "A region of a tRNA." [RSC:cb] synonym: "tRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000253 ! tRNA [Term] id: SO:0001173 name: anticodon_loop def: "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207] synonym: "anti-codon loop" EXACT [] synonym: "anticodon loop" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001174 name: anticodon def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb] synonym: "anti-codon" EXACT [] xref: http://en.wikipedia.org/wiki/Anticodon "wiki" is_a: SO:0001172 ! tRNA_region relationship: part_of SO:0001173 ! anticodon_loop [Term] id: SO:0001175 name: CCA_tail def: "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207] synonym: "CCA sequence" EXACT [] synonym: "CCA tail" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001176 name: DHU_loop def: "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920] synonym: "D loop" RELATED [] synonym: "DHU loop" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001177 name: T_loop def: "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207] synonym: "T loop" EXACT [] synonym: "TpsiC loop" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001178 name: pyrrolysine_tRNA_primary_transcript def: "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb] synonym: "pyrrolysine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0001179 name: U3_snoRNA def: "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012] comment: The definition is most of the old definition for snoRNA (SO:0000275). synonym: "small nucleolar RNA U3" EXACT [] synonym: "snoRNA U3" EXACT [] synonym: "U3 small nucleolar RNA" EXACT [] synonym: "U3 snoRNA" EXACT [] xref: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 "wiki" is_a: SO:0000593 ! C_D_box_snoRNA [Term] id: SO:0001180 name: AU_rich_element def: "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223] synonym: "ARE" RELATED [] synonym: "AU rich element" EXACT [] synonym: "AU-rich element" EXACT [] xref: http://en.wikipedia.org/wiki/AU-rich_element "wiki" is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000205 ! three_prime_UTR [Term] id: SO:0001181 name: Bruno_response_element def: "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231] comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B. synonym: "BRE" RELATED [] synonym: "Bruno response element" EXACT [] is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000205 ! three_prime_UTR [Term] id: SO:0001182 name: iron_responsive_element def: "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843] synonym: "IRE" EXACT [] synonym: "iron responsive element" EXACT [] xref: http://en.wikipedia.org/wiki/Iron_responsive_element "wiki" is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000203 ! UTR [Term] id: SO:0001183 name: morpholino_backbone def: "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb] comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead. synonym: "morpholino backbone" EXACT [] xref: http://en.wikipedia.org/wiki/Morpholino "wiki" is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001184 name: PNA def: "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb] comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead. synonym: "peptide nucleic acid" RELATED [] is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001185 name: enzymatic def: "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead. is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001186 name: ribozymic def: "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb] comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead. is_a: SO:0001185 ! enzymatic [Term] id: SO:0001187 name: pseudouridylation_guide_snoRNA def: "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] comment: Has RNA pseudouridylation guide activity (GO:0030558). synonym: "pseudouridylation guide snoRNA" EXACT [] is_a: SO:0000594 ! H_ACA_box_snoRNA [Term] id: SO:0001188 name: LNA def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010] comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001189 name: LNA_oligo def: "An oligo composed of LNA residues." [RSC:cb] synonym: "LNA oligo" EXACT [] synonym: "locked nucleic acid" EXACT [] xref: http://en.wikipedia.org/wiki/Locked_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001188 ! LNA relationship: has_quality SO:0001188 ! LNA [Term] id: SO:0001190 name: TNA def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019] comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001191 name: TNA_oligo def: "An oligo composed of TNA residues." [RSC:cb] synonym: "threose nucleic acid" EXACT [] synonym: "TNA oligo" EXACT [] xref: http://en.wikipedia.org/wiki/Threose_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001190 ! TNA relationship: has_quality SO:0001190 ! TNA [Term] id: SO:0001192 name: GNA def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015] comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001193 name: GNA_oligo def: "An oligo composed of GNA residues." [RSC:cb] synonym: "glycerol nucleic acid" EXACT [] synonym: "glycol nucleic acid" EXACT [] synonym: "GNA oligo" EXACT [] xref: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo intersection_of: SO:0001247 ! synthetic_oligo intersection_of: has_quality SO:0001192 ! GNA relationship: has_quality SO:0001192 ! GNA [Term] id: SO:0001194 name: R_GNA def: "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016] comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead. synonym: "R GNA" EXACT [] is_a: SO:0001192 ! GNA [Term] id: SO:0001195 name: R_GNA_oligo def: "An oligo composed of (R)-GNA residues." [RSC:cb] synonym: "(R)-glycerol nucleic acid" EXACT [] synonym: "(R)-glycol nucleic acid" EXACT [] synonym: "R GNA oligo" EXACT [] is_a: SO:0001193 ! GNA_oligo intersection_of: SO:0001193 ! GNA_oligo intersection_of: has_quality SO:0001194 ! R_GNA relationship: has_quality SO:0001194 ! R_GNA [Term] id: SO:0001196 name: S_GNA def: "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017] comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead. synonym: "S GNA" EXACT [] is_a: SO:0001192 ! GNA [Term] id: SO:0001197 name: S_GNA_oligo def: "An oligo composed of (S)-GNA residues." [RSC:cb] synonym: "(S)-glycerol nucleic acid" EXACT [] synonym: "(S)-glycol nucleic acid" EXACT [] synonym: "S GNA oligo" EXACT [] is_a: SO:0001193 ! GNA_oligo intersection_of: SO:0001193 ! GNA_oligo intersection_of: has_quality SO:0001196 ! S_GNA relationship: has_quality SO:0001196 ! S_GNA [Term] id: SO:0001198 name: ds_DNA_viral_sequence def: "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke] synonym: "double stranded DNA virus" EXACT [] synonym: "ds DNA viral sequence" EXACT [] is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001199 name: ss_RNA_viral_sequence def: "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke] synonym: "single strand RNA virus" EXACT [] synonym: "ss RNA viral sequence" EXACT [] is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001200 name: negative_sense_ssRNA_viral_sequence def: "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke] synonym: "negative sense single stranded RNA virus" RELATED [] synonym: "negative sense ssRNA viral sequence" EXACT [] is_a: SO:0001199 ! ss_RNA_viral_sequence [Term] id: SO:0001201 name: positive_sense_ssRNA_viral_sequence def: "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke] synonym: "positive sense single stranded RNA virus" RELATED [] synonym: "positive sense ssRNA viral sequence" EXACT [] is_a: SO:0001199 ! ss_RNA_viral_sequence [Term] id: SO:0001202 name: ambisense_ssRNA_viral_sequence def: "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke] synonym: "ambisense single stranded RNA virus" EXACT [] synonym: "ambisense ssRNA viral sequence" EXACT [] is_a: SO:0001199 ! ss_RNA_viral_sequence [Term] id: SO:0001203 name: RNA_polymerase_promoter def: "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "RNA polymerase promoter" EXACT [] is_a: SO:0000167 ! promoter [Term] id: SO:0001204 name: Phage_RNA_Polymerase_Promoter def: "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "Phage RNA Polymerase Promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0001205 name: SP6_RNA_Polymerase_Promoter def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "SP6 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001206 name: T3_RNA_Polymerase_Promoter def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "T3 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001207 name: T7_RNA_Polymerase_Promoter def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "T7 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001208 name: five_prime_EST def: "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] synonym: "5' EST" EXACT [] synonym: "five prime EST" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001209 name: three_prime_EST def: "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] synonym: "3' EST" EXACT [] synonym: "three prime EST" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001210 name: translational_frameshift def: "The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] synonym: "ribosomal frameshift" EXACT [] synonym: "translational frameshift" EXACT [] xref: http://en.wikipedia.org/wiki/Translational_frameshift "wiki" is_a: SO:0000836 ! mRNA_region [Term] id: SO:0001211 name: plus_1_translational_frameshift def: "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] synonym: "plus 1 ribosomal frameshift" EXACT [] synonym: "plus 1 translational frameshift" EXACT [] is_a: SO:0001210 ! translational_frameshift [Term] id: SO:0001212 name: plus_2_translational_frameshift def: "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] synonym: "plus 2 ribosomal frameshift" EXACT [] synonym: "plus 2 translational frameshift" EXACT [] is_a: SO:0001210 ! translational_frameshift [Term] id: SO:0001213 name: group_III_intron def: "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794] comment: GO:0000374. synonym: "group III intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_III_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0001214 name: noncoding_region_of_exon def: "The maximal intersection of exon and UTR." [SO:ke] comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding. subset: SOFA synonym: "noncoding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001215 name: coding_region_of_exon def: "The region of an exon that encodes for protein sequence." [SO:ke] comment: An exon containing either a start or stop codon will be partially coding and partially non coding. subset: SOFA synonym: "coding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001216 name: endonuclease_spliced_intron def: "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke] synonym: "endonuclease spliced intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0001217 name: protein_coding_gene synonym: "protein coding gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000010 ! protein_coding relationship: has_quality SO:0000010 ! protein_coding [Term] id: SO:0001218 name: transgenic_insertion def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm] synonym: "transgenic insertion" EXACT [] is_a: SO:0000667 ! insertion intersection_of: SO:0000667 ! insertion intersection_of: has_quality SO:0000781 ! transgenic relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0001219 name: retrogene is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000569 ! retrotransposed relationship: has_quality SO:0000569 ! retrotransposed [Term] id: SO:0001220 name: silenced_by_RNA_interference def: "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb] comment: RNA interference is GO:0016246. synonym: "silenced by RNA interference" EXACT [] is_a: SO:0000893 ! silenced [Term] id: SO:0001221 name: silenced_by_histone_modification def: "An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb] comment: Histone modification is GO:0016570. synonym: "silenced by histone modification" EXACT [] is_a: SO:0000893 ! silenced [Term] id: SO:0001222 name: silenced_by_histone_methylation def: "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb] comment: Histone methylation is GO:0016571. synonym: "silenced by histone methylation" EXACT [] is_a: SO:0001221 ! silenced_by_histone_modification [Term] id: SO:0001223 name: silenced_by_histone_deacetylation def: "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb] comment: Histone deacetylation is GO:0016573. synonym: "silenced by histone deacetylation" EXACT [] is_a: SO:0001221 ! silenced_by_histone_modification [Term] id: SO:0001224 name: gene_silenced_by_RNA_interference def: "A gene that is silenced by RNA interference." [SO:xp] synonym: "gene silenced by RNA interference" EXACT [] synonym: "RNA interference silenced gene" EXACT [] synonym: "RNAi silenced gene" EXACT [] is_a: SO:0000127 ! silenced_gene intersection_of: SO:0000127 ! silenced_gene intersection_of: has_quality SO:0001220 ! silenced_by_RNA_interference relationship: has_quality SO:0001220 ! silenced_by_RNA_interference [Term] id: SO:0001225 name: gene_silenced_by_histone_modification def: "A gene that is silenced by histone modification." [SO:xp] synonym: "gene silenced by histone modification" EXACT [] is_a: SO:0000127 ! silenced_gene intersection_of: SO:0000127 ! silenced_gene intersection_of: has_quality SO:0001221 ! silenced_by_histone_modification relationship: has_quality SO:0001221 ! silenced_by_histone_modification [Term] id: SO:0001226 name: gene_silenced_by_histone_methylation def: "A gene that is silenced by histone methylation." [SO:xp] synonym: "gene silenced by histone methylation" EXACT [] is_a: SO:0001225 ! gene_silenced_by_histone_modification intersection_of: SO:0001225 ! gene_silenced_by_histone_modification intersection_of: has_quality SO:0001222 ! silenced_by_histone_methylation relationship: has_quality SO:0001222 ! silenced_by_histone_methylation [Term] id: SO:0001227 name: gene_silenced_by_histone_deacetylation def: "A gene that is silenced by histone deacetylation." [SO:xp] synonym: "gene silenced by histone deacetylation" EXACT [] is_a: SO:0001225 ! gene_silenced_by_histone_modification intersection_of: SO:0001225 ! gene_silenced_by_histone_modification intersection_of: has_quality SO:0001223 ! silenced_by_histone_deacetylation relationship: has_quality SO:0001223 ! silenced_by_histone_deacetylation [Term] id: SO:0001228 name: dihydrouridine def: "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb] synonym: "D" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Dihydrouridine "wiki" xref: RNAMOD:051 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001229 name: pseudouridine def: "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb] comment: The free molecule is CHEBI:17802. synonym: "Y" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Pseudouridine "wiki" xref: RNAMOD:050 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001230 name: inosine def: "A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb] comment: The free molecule is CHEBI:17596. synonym: "I" RELATED [] synonym: "RNAMOD:017" RELATED [] xref: http://en.wikipedia.org/wiki/Inosine "wiki" is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001231 name: seven_methylguanine def: "A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb] comment: The free molecule is CHEBI:2274. synonym: "7-methylguanine" EXACT [] synonym: "seven methylguanine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001232 name: ribothymidine def: "A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb] comment: The free molecule is CHEBI:30832. is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001233 name: methylinosine def: "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb] is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001234 name: mobile def: "An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb] xref: http://en.wikipedia.org/wiki/Mobile "wiki" is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001235 name: replicon def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] subset: SOFA xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001236 name: base def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Nucleobase "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001237 name: amino_acid def: "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb] comment: Probably in the future this will cross reference to Chebi. synonym: "amino acid" EXACT [] xref: http://en.wikipedia.org/wiki/Amino_acid "wiki" is_a: SO:0001411 ! biological_region relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0001238 name: major_TSS synonym: "major transcription start site" EXACT [] synonym: "major TSS" EXACT [] is_a: SO:0000315 ! TSS [Term] id: SO:0001239 name: minor_TSS synonym: "minor TSS" EXACT [] is_a: SO:0000315 ! TSS [Term] id: SO:0001240 name: TSS_region def: "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw] synonym: "TSS region" EXACT [] is_a: SO:0000842 ! gene_component_region relationship: has_part SO:0000315 ! TSS [Term] id: SO:0001241 name: encodes_alternate_transcription_start_sites synonym: "encodes alternate transcription start sites" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0001243 name: miRNA_primary_transcript_region def: "A part of an miRNA primary_transcript." [SO:ke] synonym: "miRNA primary transcript region" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0001244 name: pre_miRNA def: "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure." [SO:ke] synonym: "pre-miRNA" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region relationship: part_of SO:0000647 ! miRNA_primary_transcript [Term] id: SO:0001245 name: miRNA_stem def: "The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] synonym: "miRNA stem" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region relationship: part_of SO:0001244 ! pre_miRNA [Term] id: SO:0001246 name: miRNA_loop def: "The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] synonym: "miRNA loop" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region relationship: part_of SO:0001244 ! pre_miRNA [Term] id: SO:0001247 name: synthetic_oligo def: "An oligo composed of synthetic nucleotides." [SO:ke] synonym: "synthetic oligo" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0001248 name: assembly def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0001249 name: fragment_assembly def: "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke] synonym: "fragment assembly" EXACT [] synonym: "physical map" EXACT [] is_a: SO:0001248 ! assembly [Term] id: SO:0001250 name: fingerprint_map def: "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke] synonym: "BACmap" EXACT [] synonym: "fingerprint map" EXACT [] synonym: "FPC" EXACT [] synonym: "FPCmap" EXACT [] synonym: "restriction map" EXACT [] is_a: SO:0001249 ! fragment_assembly relationship: has_part SO:0000412 ! restriction_fragment [Term] id: SO:0001251 name: STS_map def: "An STS map is a physical map organized by the unique STS landmarks." [SO:ke] synonym: "STS map" EXACT [] is_a: SO:0001249 ! fragment_assembly relationship: has_part SO:0000331 ! STS [Term] id: SO:0001252 name: RH_map def: "A radiation hybrid map is a physical map." [SO:ke] synonym: "radiation hybrid map" EXACT [] synonym: "RH map" EXACT [] is_a: SO:0001249 ! fragment_assembly relationship: has_part SO:0000331 ! STS [Term] id: SO:0001253 name: sonicate_fragment def: "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke] synonym: "sonicate fragment" EXACT [] is_a: SO:0000143 ! assembly_component [Term] id: SO:0001254 name: polyploid def: "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke] xref: http://en.wikipedia.org/wiki/Polyploid "wiki" is_a: SO:1000182 ! chromosome_number_variation [Term] id: SO:0001255 name: autopolyploid def: "A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke] xref: http://en.wikipedia.org/wiki/Autopolyploid "wiki" is_a: SO:0001254 ! polyploid [Term] id: SO:0001256 name: allopolyploid def: "A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke] xref: http://en.wikipedia.org/wiki/Allopolyploid "wiki" is_a: SO:0001254 ! polyploid [Term] id: SO:0001257 name: homing_endonuclease_binding_site def: "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke] synonym: "homing endonuclease binding site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0001258 name: octamer_motif def: "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662] comment: Nature. 1986 Oct 16-22;323(6089):640-3. synonym: "octamer motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001259 name: apicoplast_chromosome def: "A chromosome originating in an apicoplast." [SO:xp] synonym: "apicoplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome intersection_of: SO:0000340 ! chromosome intersection_of: has_origin SO:0000743 ! apicoplast_sequence relationship: has_origin SO:0000743 ! apicoplast_sequence [Term] id: SO:0001260 name: sequence_collection def: "A collection of discontinuous sequences." [SO:ke] synonym: "sequence collection" EXACT [] [Term] id: SO:0001261 name: overlapping_feature_set def: "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke] comment: This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA. synonym: "overlapping feature set" EXACT [] is_a: SO:0000703 ! experimental_result_region [Term] id: SO:0001262 name: overlapping_EST_set def: "A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke] synonym: "overlapping EST set" EXACT [] is_a: SO:0001261 ! overlapping_feature_set relationship: has_part SO:0000345 ! EST [Term] id: SO:0001263 name: ncRNA_gene synonym: "ncRNA gen" EXACT [] synonym: "ncRNA gene" EXACT [] synonym: "non-coding RNA gene" RELATED [] is_a: SO:0000704 ! gene [Term] id: SO:0001264 name: gRNA_gene synonym: "gRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000979 ! gRNA_encoding relationship: has_quality SO:0000979 ! gRNA_encoding [Term] id: SO:0001265 name: miRNA_gene synonym: "miRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000571 ! miRNA_encoding relationship: has_quality SO:0000571 ! miRNA_encoding [Term] id: SO:0001266 name: scRNA_gene synonym: "scRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000575 ! scRNA_encoding relationship: has_quality SO:0000575 ! scRNA_encoding [Term] id: SO:0001267 name: snoRNA_gene synonym: "snoRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000578 ! snoRNA_encoding relationship: has_quality SO:0000578 ! snoRNA_encoding [Term] id: SO:0001268 name: snRNA_gene synonym: "snRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0001263 ! ncRNA_gene relationship: has_quality SO:0001263 ! ncRNA_gene [Term] id: SO:0001269 name: SRP_RNA_gene synonym: "SRP RNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000642 ! SRP_RNA_encoding relationship: has_quality SO:0000642 ! SRP_RNA_encoding [Term] id: SO:0001270 name: stRNA_gene synonym: "stRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000656 ! stRNA_encoding relationship: has_quality SO:0000656 ! stRNA_encoding [Term] id: SO:0001271 name: tmRNA_gene synonym: "tmRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000659 ! tmRNA_encoding relationship: has_quality SO:0000659 ! tmRNA_encoding [Term] id: SO:0001272 name: tRNA_gene synonym: "tRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene intersection_of: SO:0001263 ! ncRNA_gene intersection_of: has_quality SO:0000663 ! tRNA_encoding relationship: has_quality SO:0000663 ! tRNA_encoding [Term] id: SO:0001273 name: modified_adenosine def: "A modified adenine is an adenine base feature that has been altered." [SO:ke] synonym: "modified adenosine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001274 name: modified_inosine def: "A modified inosine is an inosine base feature that has been altered." [SO:ke] synonym: "modified inosine" EXACT [] is_a: SO:0001230 ! inosine [Term] id: SO:0001275 name: modified_cytidine def: "A modified cytidine is a cytidine base feature which has been altered." [SO:ke] synonym: "modified cytidine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001276 name: modified_guanosine synonym: "modified guanosine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001277 name: modified_uridine synonym: "modified uridine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001278 name: one_methylinosine def: "1-methylinosine is a modified insosine." [http://library.med.utah.edu/RNAmods/] synonym: "1-methylinosine" EXACT [] synonym: "m1I" EXACT RNAMOD [] synonym: "one methylinosine" EXACT [] xref: RNAMOD:018 is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001279 name: one_two_prime_O_dimethylinosine def: "1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] synonym: "1,2'-O-dimethylinosine" EXACT [] synonym: "m'Im" EXACT RNAMOD [] synonym: "one two prime O dimethylinosine" EXACT [] xref: RNAMOD:019 is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001280 name: two_prime_O_methylinosine def: "2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylinosine" EXACT [] synonym: "Im" EXACT RNAMOD [] synonym: "two prime O methylinosine" EXACT [] xref: RNAMOD:081 is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001281 name: three_methylcytidine def: "3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "3-methylcytidine" EXACT [] synonym: "m3C" EXACT RNAMOD [] synonym: "three methylcytidine" EXACT [] xref: RNAMOD:020 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001282 name: five_methylcytidine def: "5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylcytidine" EXACT [] synonym: "five methylcytidine" EXACT [] synonym: "m5C" EXACT RNAMOD [] xref: RNAMOD:021 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001283 name: two_prime_O_methylcytidine def: "2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylcytidine" EXACT [] synonym: "Cm" EXACT RNAMOD [] synonym: "two prime O methylcytidine" EXACT [] xref: RNAMOD:022 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001284 name: two_thiocytidine def: "2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "2-thiocytidine" EXACT [] synonym: "s2C" EXACT RNAMOD [] synonym: "two thiocytidine" EXACT [] xref: RNAMOD:023 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001285 name: N4_acetylcytidine def: "N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "ac4C" EXACT RNAMOD [] synonym: "N4 acetylcytidine" EXACT [] synonym: "N4-acetylcytidine" EXACT [] xref: RNAMOD:024 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001286 name: five_formylcytidine def: "5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-formylcytidine" EXACT [] synonym: "f5C" EXACT RNAMOD [] synonym: "five formylcytidine" EXACT [] xref: RNAMOD:025 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001287 name: five_two_prime_O_dimethylcytidine def: "5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5,2'-O-dimethylcytidine" EXACT [] synonym: "five two prime O dimethylcytidine" EXACT [] synonym: "m5Cm" EXACT RNAMOD [] xref: RNAMOD:026 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001288 name: N4_acetyl_2_prime_O_methylcytidine def: "N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "ac4Cm" EXACT RNAMOD [] synonym: "N4 acetyl 2 prime O methylcytidine" EXACT [] synonym: "N4-acetyl-2'-O-methylcytidine" EXACT [] xref: RNAMOD:027 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001289 name: lysidine def: "Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "k2C" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Lysidine "wiki" xref: RNAMOD:028 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001290 name: N4_methylcytidine def: "N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "m4C" EXACT RNAMOD [] synonym: "N4 methylcytidine" EXACT [] synonym: "N4-methylcytidine" EXACT [] xref: RNAMOD:082 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001291 name: N4_2_prime_O_dimethylcytidine def: "N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "m4Cm" EXACT RNAMOD [] synonym: "N4 2 prime O dimethylcytidine" EXACT [] synonym: "N4,2'-O-dimethylcytidine" EXACT [] xref: RNAMOD:083 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001292 name: five_hydroxymethylcytidine def: "5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-hydroxymethylcytidine" EXACT [] synonym: "five hydroxymethylcytidine" EXACT [] synonym: "hm5C" EXACT RNAMOD [] xref: RNAMOD:084 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001293 name: five_formyl_two_prime_O_methylcytidine def: "5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-formyl-2'-O-methylcytidine" EXACT [] synonym: "f5Cm" EXACT RNAMOD [] synonym: "five formyl two prime O methylcytidine" EXACT [] xref: RNAMOD:095 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001294 name: N4_N4_2_prime_O_trimethylcytidine def: "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "m42Cm" EXACT RNAMOD [] synonym: "N4,N4,2'-O-trimethylcytidine" EXACT [] xref: RNAMOD:107 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001295 name: one_methyladenosine def: "1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "1-methyladenosine" EXACT [] synonym: "m1A" EXACT RNAMOD [] synonym: "one methyladenosine" EXACT [] xref: RNAMOD:001 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001296 name: two_methyladenosine def: "2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methyladenosine" EXACT [] synonym: "m2A" EXACT RNAMOD [] synonym: "two methyladenosine" EXACT [] xref: RNAMOD:002 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001297 name: N6_methyladenosine def: "N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m6A" EXACT RNAMOD [] synonym: "N6 methyladenosine" EXACT [] synonym: "N6-methyladenosine" EXACT [] xref: RNAMOD:003 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001298 name: two_prime_O_methyladenosine def: "2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methyladenosine" EXACT [] synonym: "Am" EXACT RNAMOD [] synonym: "two prime O methyladenosine" EXACT [] xref: RNAMOD:004 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001299 name: two_methylthio_N6_methyladenosine def: "2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-methyladenosine" EXACT [] synonym: "ms2m6A" EXACT RNAMOD [] synonym: "two methylthio N6 methyladenosine" EXACT [] xref: RNAMOD:005 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001300 name: N6_isopentenyladenosine def: "N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "i6A" EXACT RNAMOD [] synonym: "N6 isopentenyladenosine" EXACT [] synonym: "N6-isopentenyladenosine" EXACT [] xref: RNAMOD:006 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001301 name: two_methylthio_N6_isopentenyladenosine def: "2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-isopentenyladenosine" EXACT [] synonym: "ms2i6A" EXACT RNAMOD [] synonym: "two methylthio N6 isopentenyladenosine" EXACT [] xref: RNAMOD:007 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001302 name: N6_cis_hydroxyisopentenyl_adenosine def: "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "io6A" EXACT RNAMOD [] synonym: "N6 cis hydroxyisopentenyl adenosine" EXACT [] synonym: "N6-(cis-hydroxyisopentenyl)adenosine" EXACT [] xref: RNAMOD:008 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001303 name: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine def: "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine" EXACT [] synonym: "ms2io6A" EXACT RNAMOD [] synonym: "two methylthio N6 cis hydroxyisopentenyl adenosine" EXACT [] xref: RNAMOD:009 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001304 name: N6_glycinylcarbamoyladenosine def: "N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "g6A" EXACT RNAMOD [] synonym: "N6 glycinylcarbamoyladenosine" EXACT [] synonym: "N6-glycinylcarbamoyladenosine" EXACT [] xref: RNAMOD:010 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001305 name: N6_threonylcarbamoyladenosine def: "N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "N6 threonylcarbamoyladenosine" EXACT [] synonym: "N6-threonylcarbamoyladenosine" EXACT [] synonym: "t6A" EXACT RNAMOD [] xref: RNAMOD:011 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001306 name: two_methylthio_N6_threonyl_carbamoyladenosine def: "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-threonyl carbamoyladenosine" EXACT [] synonym: "ms2t6A" EXACT RNAMOD [] synonym: "two methylthio N6 threonyl carbamoyladenosine" EXACT [] xref: RNAMOD:012 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001307 name: N6_methyl_N6_threonylcarbamoyladenosine def: "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m6t6A" EXACT RNAMOD [] synonym: "N6 methyl N6 threonylcarbamoyladenosine" EXACT [] synonym: "N6-methyl-N6-threonylcarbamoyladenosine" EXACT [] xref: RNAMOD:013 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001308 name: N6_hydroxynorvalylcarbamoyladenosine def: "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "hn6A" EXACT RNAMOD [] synonym: "N6 hydroxynorvalylcarbamoyladenosine" EXACT [] synonym: "N6-hydroxynorvalylcarbamoyladenosine" EXACT [] xref: RNAMOD:014 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001309 name: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine def: "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine" EXACT [] synonym: "ms2hn6A" EXACT RNAMOD [] synonym: "two methylthio N6 hydroxynorvalyl carbamoyladenosine" EXACT [] xref: RNAMOD:015 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001310 name: two_prime_O_ribosyladenosine_phosphate def: "2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-ribosyladenosine (phosphate)" EXACT [] synonym: "Ar(p)" EXACT RNAMOD [] synonym: "two prime O ribosyladenosine phosphate" EXACT [] xref: RNAMOD:016 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001311 name: N6_N6_dimethyladenosine def: "N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m62A" EXACT RNAMOD [] synonym: "N6,N6-dimethyladenosine" EXACT [] xref: RNAMOD:080 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001312 name: N6_2_prime_O_dimethyladenosine def: "N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m6Am" EXACT RNAMOD [] synonym: "N6 2 prime O dimethyladenosine" EXACT [] synonym: "N6,2'-O-dimethyladenosine" EXACT [] xref: RNAMOD:088 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001313 name: N6_N6_2_prime_O_trimethyladenosine def: "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m62Am" EXACT RNAMOD [] synonym: "N6,N6,2'-O-trimethyladenosine" EXACT [] xref: RNAMOD:089 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001314 name: one_two_prime_O_dimethyladenosine def: "1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "1,2'-O-dimethyladenosine" EXACT [] synonym: "m1Am" EXACT RNAMOD [] synonym: "one two prime O dimethyladenosine" EXACT [] xref: RNAMOD:097 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001315 name: N6_acetyladenosine def: "N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "ac6A" EXACT RNAMOD [] synonym: "N6 acetyladenosine" EXACT [] synonym: "N6-acetyladenosine" EXACT [] xref: RNAMOD:102 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001316 name: seven_deazaguanosine def: "7-deazaguanosine is a moddified guanosine." [http://library.med.utah.edu/RNAmods/] synonym: "7-deazaguanosine" RELATED [] synonym: "seven deazaguanosine" EXACT [] is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001317 name: queuosine def: "Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "Q" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Queuosine "wiki" xref: RNAMOD:043 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001318 name: epoxyqueuosine def: "Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "eQ" EXACT RNAMOD [] xref: RNAMOD:044 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001319 name: galactosyl_queuosine def: "Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "galactosyl queuosine" EXACT [] synonym: "galactosyl-queuosine" EXACT [] synonym: "galQ" EXACT RNAMOD [] xref: RNAMOD:045 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001320 name: mannosyl_queuosine def: "Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "mannosyl queuosine" EXACT [] synonym: "mannosyl-queuosine" EXACT [] synonym: "manQ" EXACT RNAMOD [] xref: RNAMOD:046 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001321 name: seven_cyano_seven_deazaguanosine def: "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "7-cyano-7-deazaguanosine" EXACT [] synonym: "preQ0" EXACT RNAMOD [] synonym: "seven cyano seven deazaguanosine" EXACT [] xref: RNAMOD:047 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001322 name: seven_aminomethyl_seven_deazaguanosine def: "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "7-aminomethyl-7-deazaguanosine" EXACT [] synonym: "preQ1" EXACT RNAMOD [] synonym: "seven aminomethyl seven deazaguanosine" EXACT [] xref: RNAMOD:048 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001323 name: archaeosine def: "Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "G+" EXACT RNAMOD [] xref: RNAMOD:049 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001324 name: one_methylguanosine def: "1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1-methylguanosine" EXACT [] synonym: "m1G" EXACT RNAMOD [] synonym: "one methylguanosine" EXACT [] xref: RNAMOD:029 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001325 name: N2_methylguanosine def: "N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2G" EXACT RNAMOD [] synonym: "N2 methylguanosine" EXACT [] synonym: "N2-methylguanosine" EXACT [] xref: RNAMOD:030 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001326 name: seven_methylguanosine def: "7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "7-methylguanosine" EXACT [] synonym: "m7G" EXACT RNAMOD [] synonym: "seven methylguanosine" EXACT [] xref: RNAMOD:031 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001327 name: two_prime_O_methylguanosine def: "2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylguanosine" EXACT [] synonym: "Gm" EXACT RNAMOD [] synonym: "two prime O methylguanosine" EXACT [] xref: RNAMOD:032 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001328 name: N2_N2_dimethylguanosine def: "N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m22G" EXACT RNAMOD [] synonym: "N2,N2-dimethylguanosine" EXACT [] xref: RNAMOD:033 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001329 name: N2_2_prime_O_dimethylguanosine def: "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2Gm" EXACT RNAMOD [] synonym: "N2 2 prime O dimethylguanosine" EXACT [] synonym: "N2,2'-O-dimethylguanosine" EXACT [] xref: RNAMOD:034 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001330 name: N2_N2_2_prime_O_trimethylguanosine def: "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m22Gmv" EXACT RNAMOD [] synonym: "N2,N2,2'-O-trimethylguanosine" EXACT [] xref: RNAMOD:035 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001331 name: two_prime_O_ribosylguanosine_phosphate def: "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-ribosylguanosine (phosphate)" EXACT [] synonym: "Gr(p)" EXACT RNAMOD [] synonym: "two prime O ribosylguanosine phosphate" EXACT [] xref: RNAMOD:036 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001332 name: wybutosine def: "Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "yW" EXACT RNAMOD [] xref: RNAMOD:037 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001333 name: peroxywybutosine def: "Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "o2yW" EXACT RNAMOD [] xref: RNAMOD:038 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001334 name: hydroxywybutosine def: "Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "OHyW" EXACT RNAMOD [] xref: RNAMOD:039 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001335 name: undermodified_hydroxywybutosine def: "Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "OHyW*" EXACT RNAMOD [] synonym: "undermodified hydroxywybutosine" EXACT [] xref: RNAMOD:040 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001336 name: wyosine def: "Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "IMG" EXACT RNAMOD [] xref: RNAMOD:041 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001337 name: methylwyosine def: "Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "mimG" EXACT RNAMOD [] xref: RNAMOD:042 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001338 name: N2_7_dimethylguanosine def: "N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2,7G" EXACT RNAMOD [] synonym: "N2 7 dimethylguanosine" EXACT [] synonym: "N2,7-dimethylguanosine" EXACT [] xref: RNAMOD:090 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001339 name: N2_N2_7_trimethylguanosine def: "N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2,2,7G" EXACT RNAMOD [] synonym: "N2,N2,7-trimethylguanosine" EXACT [] xref: RNAMOD:091 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001340 name: one_two_prime_O_dimethylguanosine def: "1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1,2'-O-dimethylguanosine" EXACT [] synonym: "m1Gm" EXACT RNAMOD [] synonym: "one two prime O dimethylguanosine" EXACT [] xref: RNAMOD:096 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001341 name: four_demethylwyosine def: "4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "4-demethylwyosine" EXACT [] synonym: "four demethylwyosine" EXACT [] synonym: "imG-14" EXACT RNAMOD [] xref: RNAMOD:100 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001342 name: isowyosine def: "Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "imG2" EXACT RNAMOD [] xref: RNAMOD:101 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001343 name: N2_7_2prirme_O_trimethylguanosine def: "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2,7Gm" EXACT RNAMOD [] synonym: "N2 7 2prirme O trimethylguanosine" EXACT [] synonym: "N2,7,2'-O-trimethylguanosine" EXACT [] xref: RNAMOD:106 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001344 name: five_methyluridine def: "5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methyluridine" EXACT [] synonym: "five methyluridine" EXACT [] synonym: "m5U" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/5-methyluridine "wiki" xref: RNAMOD:052 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001345 name: two_prime_O_methyluridine def: "2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methyluridine" EXACT [] synonym: "two prime O methyluridine" EXACT [] synonym: "Um" EXACT RNAMOD [] xref: RNAMOD:053 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001346 name: five_two_prime_O_dimethyluridine def: "5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5,2'-O-dimethyluridine" EXACT [] synonym: "five two prime O dimethyluridine" EXACT [] synonym: "m5Um" EXACT RNAMOD [] xref: RNAMOD:054 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001347 name: one_methylpseudouridine def: "1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1-methylpseudouridine" EXACT [] synonym: "m1Y" EXACT RNAMOD [] synonym: "one methylpseudouridine" EXACT [] xref: RNAMOD:055 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001348 name: two_prime_O_methylpseudouridine def: "2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylpseudouridine" EXACT [] synonym: "two prime O methylpseudouridine" EXACT [] synonym: "Ym" EXACT RNAMOD [] xref: RNAMOD:056 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001349 name: two_thiouridine def: "2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2-thiouridine" EXACT [] synonym: "s2U" EXACT RNAMOD [] synonym: "two thiouridine" EXACT [] xref: RNAMOD:057 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001350 name: four_thiouridine def: "4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "4-thiouridine" EXACT [] synonym: "four thiouridine" EXACT [] synonym: "s4U" EXACT RNAMOD [] xref: RNAMOD:058 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001351 name: five_methyl_2_thiouridine def: "5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methyl-2-thiouridine" EXACT [] synonym: "five methyl 2 thiouridine" EXACT [] synonym: "m5s2U" EXACT RNAMOD [] xref: RNAMOD:059 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001352 name: two_thio_two_prime_O_methyluridine def: "2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2-thio-2'-O-methyluridine" EXACT [] synonym: "s2Um" EXACT RNAMOD [] synonym: "two thio two prime O methyluridine" EXACT [] xref: RNAMOD:060 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001353 name: three_three_amino_three_carboxypropyl_uridine def: "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3-(3-amino-3-carboxypropyl)uridine" EXACT [] synonym: "acp3U" EXACT RNAMOD [] xref: RNAMOD:061 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001354 name: five_hydroxyuridine def: "5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-hydroxyuridine" EXACT [] synonym: "five hydroxyuridine" EXACT [] synonym: "ho5U" EXACT RNAMOD [] xref: RNAMOD:060 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001355 name: five_methoxyuridine def: "5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxyuridine" EXACT [] synonym: "five methoxyuridine" EXACT [] synonym: "mo5U" EXACT RNAMOD [] xref: RNAMOD:063 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001356 name: uridine_five_oxyacetic_acid def: "Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "cmo5U" EXACT RNAMOD [] synonym: "uridine 5-oxyacetic acid" EXACT [] synonym: "uridine five oxyacetic acid" EXACT [] xref: RNAMOD:064 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001357 name: uridine_five_oxyacetic_acid_methyl_ester def: "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "mcmo5U" EXACT RNAMOD [] synonym: "uridine 5-oxyacetic acid methyl ester" EXACT [] synonym: "uridine five oxyacetic acid methyl ester" EXACT [] xref: RNAMOD:065 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001358 name: five_carboxyhydroxymethyl_uridine def: "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(carboxyhydroxymethyl)uridine" EXACT [] synonym: "chm5U" EXACT RNAMOD [] synonym: "five carboxyhydroxymethyl uridine" EXACT [] xref: RNAMOD:066 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001359 name: five_carboxyhydroxymethyl_uridine_methyl_ester def: "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(carboxyhydroxymethyl)uridine methyl ester" EXACT [] synonym: "five carboxyhydroxymethyl uridine methyl ester" EXACT [] synonym: "mchm5U" EXACT RNAMOD [] xref: RNAMOD:067 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001360 name: five_methoxycarbonylmethyluridine def: "Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxycarbonylmethyluridine" EXACT [] synonym: "five methoxycarbonylmethyluridine" EXACT [] synonym: "mcm5U" EXACT RNAMOD [] xref: RNAMOD:068 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001361 name: five_methoxycarbonylmethyl_two_prime_O_methyluridine def: "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxycarbonylmethyl-2'-O-methyluridine" EXACT [] synonym: "five methoxycarbonylmethyl two prime O methyluridine" EXACT [] synonym: "mcm5Um" EXACT RNAMOD [] xref: RNAMOD:069 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001362 name: five_methoxycarbonylmethyl_two_thiouridine def: "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxycarbonylmethyl-2-thiouridine" EXACT [] synonym: "five methoxycarbonylmethyl two thiouridine" EXACT [] synonym: "mcm5s2U" EXACT RNAMOD [] xref: RNAMOD:070 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001363 name: five_aminomethyl_two_thiouridine def: "5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-aminomethyl-2-thiouridine" EXACT [] synonym: "five aminomethyl two thiouridine" EXACT [] synonym: "nm5s2U" EXACT RNAMOD [] xref: RNAMOD:071 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001364 name: five_methylaminomethyluridine def: "5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylaminomethyluridine" EXACT [] synonym: "five methylaminomethyluridine" EXACT [] synonym: "mnm5U" EXACT RNAMOD [] xref: RNAMOD:072 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001365 name: five_methylaminomethyl_two_thiouridine def: "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylaminomethyl-2-thiouridine" EXACT [] synonym: "five methylaminomethyl two thiouridine" EXACT [] synonym: "mnm5s2U" EXACT RNAMOD [] xref: RNAMOD:073 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001366 name: five_methylaminomethyl_two_selenouridine def: "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylaminomethyl-2-selenouridine" EXACT [] synonym: "five methylaminomethyl two selenouridine" EXACT [] synonym: "mnm5se2U" EXACT RNAMOD [] xref: RNAMOD:074 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001367 name: five_carbamoylmethyluridine def: "5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carbamoylmethyluridine" EXACT [] synonym: "five carbamoylmethyluridine" EXACT [] synonym: "ncm5U" EXACT RNAMOD [] xref: RNAMOD:075 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001368 name: five_carbamoylmethyl_two_prime_O_methyluridine def: "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carbamoylmethyl-2'-O-methyluridine" EXACT [] synonym: "five carbamoylmethyl two prime O methyluridine" EXACT [] synonym: "ncm5Um" EXACT RNAMOD [] xref: RNAMOD:076 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001369 name: five_carboxymethylaminomethyluridine def: "5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethylaminomethyluridine" EXACT [] synonym: "cmnm5U" EXACT RNAMOD [] synonym: "five carboxymethylaminomethyluridine" EXACT [] xref: RNAMOD:077 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001370 name: five_carboxymethylaminomethyl_two_prime_O_methyluridine def: "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethylaminomethyl- 2'-O-methyluridine" EXACT [] synonym: "cmnm5Um" EXACT RNAMOD [] synonym: "five carboxymethylaminomethyl two prime O methyluridine" EXACT [] xref: RNAMOD:078 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001371 name: five_carboxymethylaminomethyl_two_thiouridine def: "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethylaminomethyl-2-thiouridine" EXACT [] synonym: "cmnm5s2U" EXACT RNAMOD [] synonym: "five carboxymethylaminomethyl two thiouridine" EXACT [] xref: RNAMOD:079 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001372 name: three_methyluridine def: "3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3-methyluridine" EXACT [] synonym: "m3U" EXACT RNAMOD [] synonym: "three methyluridine" EXACT [] xref: RNAMOD:085 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001373 name: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine def: "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine" EXACT [] synonym: "m1acp3Y" EXACT RNAMOD [] xref: RNAMOD:086 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001374 name: five_carboxymethyluridine def: "5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethyluridine" EXACT [] synonym: "cm5U" EXACT RNAMOD [] synonym: "five carboxymethyluridine" EXACT [] xref: RNAMOD:087 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001375 name: three_two_prime_O_dimethyluridine def: "3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3,2'-O-dimethyluridine" EXACT [] synonym: "m3Um" EXACT RNAMOD [] synonym: "three two prime O dimethyluridine" EXACT [] xref: RNAMOD:092 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001376 name: five_methyldihydrouridine def: "5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methyldihydrouridine" EXACT [] synonym: "five methyldihydrouridine" EXACT [] synonym: "m5D" EXACT RNAMOD [] xref: RNAMOD:093 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001377 name: three_methylpseudouridine def: "3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3-methylpseudouridine" EXACT [] synonym: "m3Y" EXACT RNAMOD [] synonym: "three methylpseudouridine" EXACT [] xref: RNAMOD:094 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001378 name: five_taurinomethyluridine def: "5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-taurinomethyluridine" EXACT [] synonym: "five taurinomethyluridine" EXACT [] synonym: "tm5U" EXACT RNAMOD [] xref: RNAMOD:098 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001379 name: five_taurinomethyl_two_thiouridine def: "5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-taurinomethyl-2-thiouridine" EXACT [] synonym: "five taurinomethyl two thiouridine" EXACT [] synonym: "tm5s2U" EXACT RNAMOD [] xref: RNAMOD:099 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001380 name: five_isopentenylaminomethyl_uridine def: "5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(isopentenylaminomethyl)uridine" EXACT [] synonym: "five isopentenylaminomethyl uridine" EXACT [] synonym: "inm5U" EXACT RNAMOD [] xref: RNAMOD:103 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001381 name: five_isopentenylaminomethyl_two_thiouridine def: "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(isopentenylaminomethyl)- 2-thiouridine" EXACT [] synonym: "five isopentenylaminomethyl two thiouridine" EXACT [] synonym: "inm5s2U" EXACT RNAMOD [] xref: RNAMOD:104 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001382 name: five_isopentenylaminomethyl_two_prime_O_methyluridine def: "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(isopentenylaminomethyl)- 2'-O-methyluridine" EXACT [] synonym: "five isopentenylaminomethyl two prime O methyluridine" EXACT [] synonym: "inm5Um" EXACT RNAMOD [] xref: RNAMOD:105 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001383 name: histone_binding_site def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke] synonym: "histone binding site" EXACT [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site [Term] id: SO:0001384 name: CDS_fragment synonym: "CDS fragment" EXACT [] synonym: "incomplete CDS" EXACT [] is_a: SO:0000316 ! CDS intersection_of: SO:0000316 ! CDS intersection_of: has_quality SO:0000731 ! fragmentary relationship: has_quality SO:0000731 ! fragmentary [Term] id: SO:0001385 name: modified_amino_acid_feature def: "A post translationally modified amino acid feature." [SO:ke] synonym: "modified amino acid feature" EXACT [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001386 name: modified_glycine def: "A post translationally modified glycine amino acid feature." [SO:ke] synonym: "ModGly" EXACT AAMOD [] synonym: "modified glycine" EXACT [] xref: MOD:00908 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001387 name: modified_L_alanine def: "A post translationally modified alanine amino acid feature." [SO:ke] synonym: "ModAla" EXACT AAMOD [] synonym: "modified L alanine" EXACT [] synonym: "modified L-alanine" EXACT [] xref: MOD:00901 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001388 name: modified_L_asparagine def: "A post translationally modified asparagine amino acid feature." [SO:ke] synonym: "ModAsn" EXACT AAMOD [] synonym: "modified L asparagine" EXACT [] synonym: "modified L-asparagine" EXACT [] xref: MOD:00903 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001389 name: modified_L_aspartic_acid def: "A post translationally modified aspartic acid amino acid feature." [SO:ke] synonym: "ModAsp" EXACT AAMOD [] synonym: "modified L aspartic acid" EXACT [] synonym: "modified L-aspartic acid" EXACT [] xref: MOD:00904 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001390 name: modified_L_cysteine def: "A post translationally modified cysteine amino acid feature." [SO:ke] synonym: "ModCys" EXACT AAMOD [] synonym: "modified L cysteine" EXACT [] synonym: "modified L-cysteine" EXACT [] xref: MOD:00905 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001391 name: modified_L_glutamic_acid synonym: "ModGlu" EXACT AAMOD [] synonym: "modified L glutamic acid" EXACT [] synonym: "modified L-glutamic acid" EXACT [] xref: MOD:00906 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001392 name: modified_L_threonine def: "A post translationally modified threonine amino acid feature." [SO:ke] synonym: "modified L threonine" EXACT [] synonym: "modified L-threonine" EXACT [] synonym: "ModThr" EXACT AAMOD [] xref: MOD:00917 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001393 name: modified_L_tryptophan def: "A post translationally modified tryptophan amino acid feature." [SO:ke] synonym: "modified L tryptophan" EXACT [] synonym: "modified L-tryptophan" EXACT [] synonym: "ModTrp" EXACT AAMOD [] xref: MOD:00918 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001394 name: modified_L_glutamine def: "A post translationally modified glutamine amino acid feature." [SO:ke] synonym: "ModGln" EXACT [] synonym: "modified L glutamine" EXACT [] synonym: "modified L-glutamine" EXACT [] xref: MOD:00907 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001395 name: modified_L_methionine def: "A post translationally modified methionine amino acid feature." [SO:ke] synonym: "modified L methionine" EXACT [] synonym: "modified L-methionine" EXACT [] synonym: "ModMet" EXACT AAMOD [] xref: MOD:00913 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001396 name: modified_L_isoleucine def: "A post translationally modified isoleucine amino acid feature." [SO:ke] synonym: "modified L isoleucine" EXACT [] synonym: "modified L-isoleucine" EXACT [] synonym: "ModIle" EXACT AAMOD [] xref: MOD:00910 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001397 name: modified_L_phenylalanine def: "A post translationally modified phenylalanine amino acid feature." [SO:ke] synonym: "modified L phenylalanine" EXACT [] synonym: "modified L-phenylalanine" EXACT [] synonym: "ModPhe" EXACT AAMOD [] xref: MOD:00914 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001398 name: modified_L_histidine def: "A post translationally modified histidie amino acid feature." [SO:ke] synonym: "ModHis" EXACT [] synonym: "modified L histidine" EXACT [] synonym: "modified L-histidine" EXACT [] xref: MOD:00909 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001399 name: modified_L_serine def: "A post translationally modified serine amino acid feature." [SO:ke] synonym: "modified L serine" EXACT [] synonym: "modified L-serine" EXACT [] synonym: "MosSer" EXACT AAMOD [] xref: MOD:00916 "http://www.psidev.info/index.php?q=node/104" is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001400 name: modified_L_lysine def: "A post translationally modified lysine amino acid feature." [SO:ke] synonym: "modified L lysine" EXACT [] synonym: "modified L-lysine" EXACT [] synonym: "ModLys" EXACT AAMOD [] xref: MOD:00912 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001401 name: modified_L_leucine def: "A post translationally modified leucine amino acid feature." [SO:ke] synonym: "modified L leucine" EXACT [] synonym: "modified L-leucine " EXACT [] synonym: "ModLeu" EXACT AAMOD [] xref: MOD:00911 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001402 name: modified_L_selenocysteine def: "A post translationally modified selenocysteine amino acid feature." [SO:ke] synonym: "modified L selenocysteine" EXACT [] synonym: "modified L-selenocysteine" EXACT [] xref: MOD:01158 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001403 name: modified_L_valine def: "A post translationally modified valine amino acid feature." [SO:ke] synonym: "modified L valine" EXACT [] synonym: "modified L-valine" EXACT [] synonym: "ModVal" EXACT AAMOD [] xref: MOD:00920 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001404 name: modified_L_proline def: "A post translationally modified proline amino acid feature." [SO:ke] synonym: "modified L proline" EXACT [] synonym: "modified L-proline " EXACT [] synonym: "ModPro" EXACT AAMOD [] xref: MOD:00915 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001405 name: modified_L_tyrosine def: "A post translationally modified tyrosine amino acid feature." [SO:ke] synonym: "modified L tyrosine" EXACT [] synonym: "modified L-tyrosine" EXACT [] synonym: "ModTry" EXACT AAMOD [] xref: MOD:00919 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001406 name: modified_L_arginine def: "A post translationally modified arginine amino acid feature." [SO:ke] synonym: "ModArg" EXACT AAMOD [] synonym: "modified L arginine" EXACT [] synonym: "modified L-arginine" EXACT [] xref: MOD:00902 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001407 name: peptidyl def: "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0001408 name: cleaved_for_gpi_anchor_region def: "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh] synonym: "cleaved for gpi anchor region" EXACT [] is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0001409 name: biomaterial_region def: "A region which is intended for use in an experiment." [SO:cb] subset: SOFA synonym: "biomaterial region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001410 name: experimental_feature def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] subset: SOFA synonym: "analysis feature" RELATED [] synonym: "experimental output artefact" EXACT [] synonym: "experimental_output_artefact" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001411 name: biological_region def: "A region defined by its disposition to be involved in a biological process." [SO:cb] subset: SOFA synonym: "biological region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001412 name: topologically_defined_region def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb] subset: SOFA synonym: "topologically defined region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001413 name: translocation_breakpoint def: "The point within a chromosome where a translocation begins or ends." [SO:cb] synonym: "translocation breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001414 name: insertion_breakpoint def: "The point within a chromosome where a insertion begins or ends." [SO:cb] synonym: "insertion breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001415 name: deletion_breakpoint def: "The point within a chromosome where a deletion begins or ends." [SO:cb] synonym: "deletion breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001416 name: five_prime_flanking_region def: "A flanking region located five prime of a specific region." [SO:chado] synonym: "5' flanking region" RELATED [] synonym: "five prime flanking region" EXACT [] is_a: SO:0000239 ! flanking_region [Term] id: SO:0001417 name: three_prime_flanking_region def: "A flanking region located three prime of a specific region." [SO:chado] synonym: "3' flanking region" RELATED [] synonym: "three prime flanking region" EXACT [] is_a: SO:0000239 ! flanking_region [Term] id: SO:0001418 name: transcribed_fragment def: "An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke] comment: Term requested by the MODencode group. synonym: "transcribed fragment" EXACT [] synonym: "transfrag" RELATED [] is_a: SO:0001410 ! experimental_feature [Term] id: SO:0001419 name: cis_splice_site def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke] subset: SOFA synonym: "cis splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001420 name: trans_splice_site def: "Primary transcript region bordering trans-splice junction." [SO:ke] subset: SOFA synonym: "trans splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001421 name: splice_junction def: "The boundary between an intron and an exon." [SO:ke] synonym: "splice boundary" EXACT [] synonym: "splice junction" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0001422 name: conformational_switch def: "A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke] comment: MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999. synonym: "polypeptide conformational switch" EXACT [] is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0001423 name: dye_terminator_read def: "A read produced by the dye terminator method of sequencing." [SO:ke] synonym: "dye terminator read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001424 name: pyrosequenced_read def: "A read produced by pyrosequencing technology." [SO:ke] comment: An example is a read produced by Roche 454 technology. synonym: "pyorsequenced read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001425 name: ligation_based_read def: "A read produced by ligation based sequencing technologies." [SO:ke] comment: An example of this kind of read is one produced by ABI SOLiD. synonym: "ligation based read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001426 name: polymerase_synthesis_read def: "A read produced by the polymerase based sequence by synthesis method." [SO:ke] comment: An example is a read produced by Illumina technology. synonym: "polymerase synthesis read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001427 name: cis_regulatory_frameshift_element def: "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd] synonym: "cis regulatory frameshift element" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0001428 name: expressed_sequence_assembly def: "A sequence assembly derived from expressed sequences." [SO:ke] comment: From tracker [ 2372385 ] expressed_sequence_assembly. synonym: "expressed sequence assembly" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0001429 name: DNA_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke] synonym: "DNA binding site" EXACT [] is_a: SO:0001655 ! nucleotide_binding_site [Term] id: SO:0001431 name: cryptic_gene def: "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke] synonym: "cryptic gene" EXACT [] is_a: SO:0000704 ! gene intersection_of: SO:0000704 ! gene intersection_of: has_quality SO:0000976 ! cryptic relationship: has_quality SO:0000976 ! cryptic [Term] id: SO:0001432 name: sequence_variant_affecting_polyadenylation comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting polyadenylation" RELATED [] synonym: "sequence variant affecting polyadenylation" EXACT [] is_obsolete: true replaced_by: SO:0001545 [Term] id: SO:0001433 name: three_prime_RACE_clone def: "A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw] synonym: "3' RACE clone" RELATED [] is_a: SO:0000317 ! cDNA_clone [Term] id: SO:0001434 name: cassette_pseudogene def: "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke] comment: Requested by the Trypanosome community. synonym: "cassette pseudogene" EXACT [] synonym: "cassette type psedogene" RELATED [] is_a: SO:0001760 ! non_processed_pseudogene [Term] id: SO:0001435 name: alanine comment: A place holder for a cross product with chebi. synonym: "A" EXACT aa1 [] synonym: "Ala" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001436 name: valine comment: A place holder for a cross product with chebi. synonym: "V" EXACT aa1 [] synonym: "Val" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001437 name: leucine comment: A place holder for a cross product with chebi. synonym: "L" EXACT aa1 [] synonym: "Leu" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001438 name: isoleucine comment: A place holder for a cross product with chebi. synonym: "I" EXACT aa1 [] synonym: "Ile" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001439 name: proline comment: A place holder for a cross product with chebi. synonym: "P" EXACT aa1 [] synonym: "Pro" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001440 name: tryptophan comment: A place holder for a cross product with chebi. synonym: "Trp" EXACT aa3 [] synonym: "W" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001441 name: phenylalanine comment: A place holder for a cross product with chebi. synonym: "F" EXACT aa1 [] synonym: "Phe" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001442 name: methionine comment: A place holder for a cross product with chebi. synonym: "M" EXACT aa1 [] synonym: "Met" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001443 name: glycine comment: A place holder for a cross product with chebi. synonym: "G" EXACT aa1 [] synonym: "Gly" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001444 name: serine comment: A place holder for a cross product with chebi. synonym: "S" EXACT aa1 [] synonym: "Ser" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001445 name: threonine comment: A place holder for a cross product with chebi. synonym: "T" EXACT aa1 [] synonym: "Thr" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001446 name: tyrosine comment: A place holder for a cross product with chebi. synonym: "Tyr" EXACT aa3 [] synonym: "Y" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001447 name: cysteine comment: A place holder for a cross product with chebi. synonym: "C" EXACT aa1 [] synonym: "Cys" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001448 name: glutamine comment: A place holder for a cross product with chebi. synonym: "Gln" EXACT aa3 [] synonym: "Q" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001449 name: asparagine comment: A place holder for a cross product with chebi. synonym: "Asn" EXACT aa3 [] synonym: "N" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001450 name: lysine comment: A place holder for a cross product with chebi. synonym: "K" EXACT aa1 [] synonym: "Lys" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001451 name: arginine comment: A place holder for a cross product with chebi. synonym: "Arg" EXACT aa3 [] synonym: "R" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001452 name: histidine comment: A place holder for a cross product with chebi. synonym: "H" EXACT aa1 [] synonym: "His" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001453 name: aspartic_acid comment: A place holder for a cross product with chebi. synonym: "Asp" EXACT aa3 [] synonym: "aspartic acid" EXACT [] synonym: "D" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001454 name: glutamic_acid comment: A place holder for a cross product with chebi. synonym: "E" EXACT aa1 [] synonym: "Glu" EXACT aa3 [] synonym: "glutamic acid" EXACT [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001455 name: selenocysteine comment: A place holder for a cross product with chebi. synonym: "Sec" EXACT aa3 [] synonym: "U" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001456 name: pyrrolysine comment: A place holder for a cross product with chebi. synonym: "O" EXACT aa1 [] synonym: "Pyl" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001457 name: transcribed_cluster def: "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke] comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157. synonym: "transcribed cluster" EXACT [] synonym: "unigene cluster" RELATED [] is_a: SO:0001410 ! experimental_feature relationship: has_part SO:0000695 ! reagent [Term] id: SO:0001458 name: unigene_cluster def: "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke] comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157. synonym: "unigene cluster" RELATED [] is_a: SO:0001457 ! transcribed_cluster [Term] id: SO:0001459 name: CRISPR def: "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd] synonym: "Clustered_Regularly_Interspaced_Short_Palindromic_Repeat" EXACT [] synonym: "CRISPR element" EXACT [] xref: http:en.wikipedia.org/wiki/CRISPR is_a: SO:0000314 ! direct_repeat [Term] id: SO:0001460 name: insulator_binding_site def: "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] comment: See tracker ID 2060908. synonym: "insulator binding site" RELATED [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site relationship: part_of SO:0000627 ! insulator [Term] id: SO:0001461 name: enhancer_binding_site def: "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] synonym: "enhancer binding site" RELATED [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site relationship: part_of SO:0000165 ! enhancer [Term] id: SO:0001462 name: contig_collection def: "A collection of contigs." [SO:ke] comment: See tracker ID: 2138359. synonym: "contig collection" EXACT [] is_a: SO:0001085 ! sequence_conflict is_a: SO:0001260 ! sequence_collection intersection_of: SO:0001085 ! sequence_conflict intersection_of: has_part SO:0000149 ! contig relationship: has_part SO:0000149 ! contig [Term] id: SO:0001463 name: lincRNA def: "A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke] synonym: "large intervening non-coding RNA" EXACT [] synonym: "long intergenic non-coding RNA" EXACT [] is_a: SO:0001877 ! lnc_RNA [Term] id: SO:0001464 name: UST def: "An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw] synonym: "UTR sequence tag" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001465 name: three_prime_UST def: "A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw] synonym: "3' UST" RELATED [] is_a: SO:0001464 ! UST [Term] id: SO:0001466 name: five_prime_UST def: "An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw] synonym: "5' UST" RELATED [] is_a: SO:0001464 ! UST [Term] id: SO:0001467 name: RST def: "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw] synonym: "RACE sequence tag" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001468 name: three_prime_RST def: "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw] synonym: "3' RST" EXACT [] is_a: SO:0001467 ! RST [Term] id: SO:0001469 name: five_prime_RST def: "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw] synonym: "5' RST" RELATED [] is_a: SO:0001467 ! RST [Term] id: SO:0001470 name: UST_match def: "A match against an UST sequence." [SO:nlw] synonym: "UST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0001471 name: RST_match def: "A match against an RST sequence." [SO:nlw] synonym: "RST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0001472 name: primer_match def: "A nucleotide match to a primer sequence." [SO:nlw] synonym: "primer match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0001473 name: miRNA_antiguide def: "A region of the pri miRNA that basepairs with the guide to form the hairpin." [SO:ke] synonym: "miRNA antiguide " EXACT [] synonym: "miRNA passenger strand" EXACT [] synonym: "miRNA star" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region created_by: kareneilbeck creation_date: 2009-05-27T03:35:43Z [Term] id: SO:0001474 name: trans_splice_junction def: "The boundary between the spliced leader and the first exon of the mRNA." [SO:ke] synonym: "trans-splice junction" EXACT [] is_a: SO:0000699 ! junction created_by: kareneilbeck creation_date: 2009-07-13T04:50:49Z [Term] id: SO:0001475 name: outron def: "A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke] is_a: SO:0000835 ! primary_transcript_region created_by: kareneilbeck creation_date: 2009-07-14T11:36:08Z [Term] id: SO:0001476 name: natural_plasmid def: "A plasmid that occurs naturally." [SO:xp] synonym: "natural plasmid" EXACT [] is_a: SO:0000155 ! plasmid is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element intersection_of: SO:0000155 ! plasmid intersection_of: has_quality SO:0000782 ! natural relationship: has_quality SO:0000782 ! natural created_by: kareneilbeck creation_date: 2009-09-01T03:43:06Z [Term] id: SO:0001477 name: gene_trap_construct def: "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh] synonym: "gene trap construct" EXACT [] is_a: SO:0000637 ! engineered_plasmid created_by: kareneilbeck creation_date: 2009-09-01T03:49:09Z [Term] id: SO:0001478 name: promoter_trap_construct def: "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh] synonym: "promoter trap construct" EXACT [] is_a: SO:0000637 ! engineered_plasmid created_by: kareneilbeck creation_date: 2009-09-01T03:52:01Z [Term] id: SO:0001479 name: enhancer_trap_construct def: "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh] synonym: "enhancer trap construct" EXACT [] is_a: SO:0000637 ! engineered_plasmid created_by: kareneilbeck creation_date: 2009-09-01T03:53:26Z [Term] id: SO:0001480 name: PAC_end def: "A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh] synonym: "PAC end" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000154 ! PAC created_by: kareneilbeck creation_date: 2009-09-09T05:18:12Z [Term] id: SO:0001481 name: RAPD def: "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh] synonym: "Random Amplification Polymorphic DNA" EXACT [] is_a: SO:0000006 ! PCR_product created_by: kareneilbeck creation_date: 2009-09-09T05:26:10Z [Term] id: SO:0001482 name: shadow_enhancer synonym: "shadow enhancer" EXACT [] is_a: SO:0000165 ! enhancer created_by: kareneilbeck creation_date: 2009-09-09T05:29:29Z [Term] id: SO:0001483 name: SNV def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm] subset: SOFA synonym: "single nucleotide variant" EXACT [] is_a: SO:1000002 ! substitution created_by: kareneilbeck creation_date: 2009-10-08T11:37:49Z [Term] id: SO:0001484 name: X_element_combinatorial_repeat def: "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html] comment: X element combinatorial repeats contain Tbf1p binding sites,\nand possible functions include a role in telomerase-independent telomere\nmaintenance via recombination or as a barrier against transcriptional\nsilencing. These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. synonym: "X element combinatorial repeat" EXACT [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-10T11:03:37Z [Term] id: SO:0001485 name: Y_prime_element def: "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. synonym: "Y' element" EXACT [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-10T12:08:57Z [Term] id: SO:0001486 name: standard_draft def: "The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126] synonym: "standard draft" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:48:32Z [Term] id: SO:0001487 name: high_quality_draft def: "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126] synonym: "high quality draft" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:52:36Z [Term] id: SO:0001488 name: improved_high_quality_draft def: "The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126] synonym: "improved high quality draft" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:54:35Z [Term] id: SO:0001489 name: annotation_directed_improved_draft def: "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126] synonym: "annotation directed improvement" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:57:10Z [Term] id: SO:0001490 name: noncontiguous_finished def: "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126] synonym: "non contiguous finished" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T01:01:07Z [Term] id: SO:0001491 name: finished_genome def: "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126] synonym: "finished" EXACT [] synonym: "finished genome" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T01:04:43Z [Term] id: SO:0001492 name: intronic_regulatory_region def: "A regulatory region that is part of an intron." [SO:ke] synonym: "intronic regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region relationship: part_of SO:0000188 ! intron created_by: kareneilbeck creation_date: 2009-11-08T02:48:02Z [Term] id: SO:0001493 name: centromere_DNA_Element_I def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. synonym: "CDEI" EXACT [] synonym: "Centromere DNA Element I" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001794 ! point_centromere created_by: kareneilbeck creation_date: 2009-11-09T05:47:23Z [Term] id: SO:0001494 name: centromere_DNA_Element_II def: "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. synonym: "CDEII" EXACT [] synonym: "centromere DNA Element II" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001794 ! point_centromere created_by: kareneilbeck creation_date: 2009-11-09T05:51:26Z [Term] id: SO:0001495 name: centromere_DNA_Element_III def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. synonym: "CDEIII" EXACT [] synonym: "centromere DNA Element III" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001794 ! point_centromere created_by: kareneilbeck creation_date: 2009-11-09T05:54:47Z [Term] id: SO:0001496 name: telomeric_repeat def: "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065] comment: The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739. synonym: "telomeric repeat" EXACT [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-09T06:00:42Z [Term] id: SO:0001497 name: X_element def: "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence] comment: Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. synonym: "X element" RELATED [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-10T10:56:54Z [Term] id: SO:0001498 name: YAC_end def: "A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke] synonym: "YAC end" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000152 ! YAC created_by: kareneilbeck creation_date: 2009-11-19T11:07:18Z [Term] id: SO:0001499 name: whole_genome_sequence_status def: "The status of whole genome sequence." [DOI:10.1126] comment: This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms. synonym: "whole genome sequence status" EXACT [] is_a: SO:0000905 ! status created_by: kareneilbeck creation_date: 2009-10-23T12:47:47Z [Term] id: SO:0001500 name: heritable_phenotypic_marker def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene] synonym: "heritable phenotypic marker" EXACT [] synonym: "phenotypic marker" EXACT [] is_a: SO:0001645 ! genetic_marker created_by: kareneilbeck creation_date: 2009-12-07T01:50:55Z [Term] id: SO:0001501 name: peptide_collection def: "A collection of peptide sequences." [BBOP:nlw] comment: Term requested via tracker ID: 2910829. synonym: "peptide collection" EXACT [] synonym: "peptide set" EXACT [] is_a: SO:0001260 ! sequence_collection intersection_of: SO:0001260 ! sequence_collection intersection_of: has_part SO:0000104 ! polypeptide relationship: has_part SO:0000104 ! polypeptide created_by: kareneilbeck creation_date: 2009-12-11T10:58:58Z [Term] id: SO:0001502 name: high_identity_region def: "An experimental feature with high sequence identity to another sequence." [SO:ke] comment: Requested by tracker ID: 2902685. synonym: "high identity region" EXACT [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2009-12-11T11:06:05Z [Term] id: SO:0001503 name: processed_transcript def: "A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen] comment: Ensembl and Vega also use this term name. Requested by Howard Deen of MGI. synonym: "processed transcript" EXACT [] is_a: SO:0000673 ! transcript created_by: kareneilbeck creation_date: 2009-12-21T05:37:14Z [Term] id: SO:0001504 name: assortment_derived_variation def: "A chromosome variation derived from an event during meiosis." [SO:ke] synonym: "assortment derived variation" RELATED [] is_a: SO:0000240 ! chromosome_variation created_by: kareneilbeck creation_date: 2010-03-02T05:03:18Z [Term] id: SO:0001505 name: reference_genome def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke] synonym: "reference genome" RELATED [] is_a: SO:0001026 ! genome created_by: kareneilbeck creation_date: 2010-03-03T02:10:03Z [Term] id: SO:0001506 name: variant_genome def: "A collection of sequences (often chromosomes) of an individual." [SO:ke] synonym: "variant genome" RELATED [] is_a: SO:0001026 ! genome created_by: kareneilbeck creation_date: 2010-03-03T02:11:25Z [Term] id: SO:0001507 name: variant_collection def: "A collection of one or more sequences of an individual." [SO:ke] synonym: "variant collection" RELATED [] is_a: SO:0001260 ! sequence_collection intersection_of: SO:0001260 ! sequence_collection intersection_of: has_part SO:0001059 ! sequence_alteration relationship: has_part SO:0001059 ! sequence_alteration created_by: kareneilbeck creation_date: 2010-03-03T02:13:28Z [Term] id: SO:0001508 name: alteration_attribute synonym: "alteration attribute" EXACT [] is_a: SO:0000733 ! feature_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:53:23Z [Term] id: SO:0001509 name: chromosomal_variation_attribute synonym: "chromosomal variation attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:54:30Z [Term] id: SO:0001510 name: intrachromosomal is_a: SO:0001509 ! chromosomal_variation_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:55:25Z [Term] id: SO:0001511 name: interchromosomal is_a: SO:0001509 ! chromosomal_variation_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:55:43Z [Term] id: SO:0001512 name: insertion_attribute def: "A quality of a chromosomal insertion,." [SO:ke] synonym: "insertion attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:55:56Z [Term] id: SO:0001513 name: tandem is_a: SO:0001512 ! insertion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:56:37Z [Term] id: SO:0001514 name: direct def: "A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke] is_a: SO:0001512 ! insertion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:56:49Z [Term] id: SO:0001515 name: inverted def: "A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke] is_a: SO:0001512 ! insertion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:57:40Z [Term] id: SO:0001516 name: free def: "The quality of a duplication where the new region exists independently of the original." [SO:ke] is_a: SO:0001523 ! duplication_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:57:51Z [Term] id: SO:0001517 name: inversion_attribute synonym: "inversion attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:10Z [Term] id: SO:0001518 name: pericentric is_a: SO:0001517 ! inversion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:24Z [Term] id: SO:0001519 name: paracentric is_a: SO:0001517 ! inversion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:35Z [Term] id: SO:0001520 name: translocaton_attribute synonym: "translocation attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:47Z [Term] id: SO:0001521 name: reciprocal is_a: SO:0001520 ! translocaton_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:59:34Z [Term] id: SO:0001522 name: insertional is_a: SO:0001520 ! translocaton_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:59:51Z [Term] id: SO:0001523 name: duplication_attribute synonym: "duplication attribute" RELATED [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-05T01:56:33Z [Term] id: SO:0001524 name: chromosomally_aberrant_genome synonym: "chromosomally aberrant genome" RELATED [] is_a: SO:0001506 ! variant_genome created_by: kareneilbeck creation_date: 2010-03-05T02:21:00Z [Term] id: SO:0001525 name: assembly_error_correction def: "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke] synonym: "assembly error correction" RELATED [] is_a: SO:0000413 ! sequence_difference created_by: kareneilbeck creation_date: 2010-03-09T02:16:31Z [Term] id: SO:0001526 name: base_call_error_correction def: "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke] synonym: "base call error correction" RELATED [] is_a: SO:0000413 ! sequence_difference created_by: kareneilbeck creation_date: 2010-03-09T02:18:07Z [Term] id: SO:0001527 name: peptide_localization_signal def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke] subset: SOFA synonym: "localization signal" RELATED [] synonym: "peptide localization signal" EXACT [] is_a: SO:0000839 ! polypeptide_region created_by: kareneilbeck creation_date: 2010-03-11T02:15:05Z [Term] id: SO:0001528 name: nuclear_localization_signal def: "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke] synonym: "NLS" EXACT [] xref: http://en.wikipedia.org/wiki/Nuclear_localization_signal "wikipedia" is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:16:38Z [Term] id: SO:0001529 name: endosomal_localization_signal def: "A polypeptide region that targets a polypeptide to the endosome." [SO:ke] synonym: "endosomal localization signal" EXACT [] is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:20:58Z [Term] id: SO:0001530 name: lysosomal_localization_signal def: "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke] synonym: "lysosomal localization signal" EXACT [] is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:24:10Z [Term] id: SO:0001531 name: nuclear_export_signal def: "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke] synonym: "NES" EXACT [] synonym: "nuclear export signal" EXACT [] xref: http://en.wikipedia.org/wiki/Nuclear_export_signal is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:25:25Z [Term] id: SO:0001532 name: recombination_signal_sequence def: "A region recognized by a recombinase." [SO:ke] synonym: "recombination signal sequence" RELATED [] xref: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences "wikipedia" is_a: SO:0000299 ! specific_recombination_site created_by: kareneilbeck creation_date: 2010-03-11T03:16:47Z [Term] id: SO:0001533 name: cryptic_splice_site def: "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke] synonym: "cryptic splice signal" RELATED [] synonym: "cryptic splice site" EXACT [] is_a: SO:0000162 ! splice_site created_by: kareneilbeck creation_date: 2010-03-11T03:25:06Z [Term] id: SO:0001534 name: nuclear_rim_localization_signal def: "A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke] synonym: "nuclear rim localization signal" RELATED [] xref: PMID:16027110 is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T03:31:30Z [Term] id: SO:0001535 name: p_element def: "A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke] synonym: "P element" RELATED [] is_a: SO:0000182 ! DNA_transposon created_by: kareneilbeck creation_date: 2010-03-12T03:40:33Z [Term] id: SO:0001536 name: functional_variant def: "A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke] synonym: "functional variant" EXACT [] is_a: SO:0001060 ! sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T11:30:25Z [Term] id: SO:0001537 name: structural_variant def: "A sequence variant that changes one or more sequence features." [SO:ke] synonym: "structural variant" RELATED [] is_a: SO:0001060 ! sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T11:31:01Z [Term] id: SO:0001538 name: transcript_function_variant def: "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcript function variant" EXACT [] is_a: SO:0001536 ! functional_variant created_by: kareneilbeck creation_date: 2010-03-22T11:32:58Z [Term] id: SO:0001539 name: translational_product_function_variant def: "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke] synonym: "translational product variant" EXACT [] is_a: SO:0001536 ! functional_variant created_by: kareneilbeck creation_date: 2010-03-22T11:46:15Z [Term] id: SO:0001540 name: level_of_transcript_variant def: "A sequence variant which alters the level of a transcript." [SO:ke] synonym: "level of transcript variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:47:07Z [Term] id: SO:0001541 name: decreased_transcript_level_variant def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] synonym: "decreased transcript level" EXACT [] is_a: SO:0001540 ! level_of_transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T11:47:47Z [Term] id: SO:0001542 name: increased_transcript_level_variant def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] synonym: "increased transcript level variant" EXACT [] is_a: SO:0001540 ! level_of_transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T11:48:17Z [Term] id: SO:0001543 name: transcript_processing_variant def: "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcript processing variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:48:48Z [Term] id: SO:0001544 name: editing_variant def: "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke] synonym: "editing variant" EXACT [] is_a: SO:0001543 ! transcript_processing_variant created_by: kareneilbeck creation_date: 2010-03-22T11:49:25Z [Term] id: SO:0001545 name: polyadenylation_variant def: "A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke] synonym: "polyadenylation variant" EXACT [] is_a: SO:0001543 ! transcript_processing_variant created_by: kareneilbeck creation_date: 2010-03-22T11:49:40Z [Term] id: SO:0001546 name: transcript_stability_variant def: "A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcript stability variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:50:01Z [Term] id: SO:0001547 name: decreased_transcript_stability_variant def: "A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke] synonym: "decrease transcript stability variant" EXACT [] is_a: SO:0001546 ! transcript_stability_variant created_by: kareneilbeck creation_date: 2010-03-22T11:50:23Z [Term] id: SO:0001548 name: increased_transcript_stability_variant def: "A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke] synonym: "increased transcript stability variant" EXACT [] is_a: SO:0001546 ! transcript_stability_variant created_by: kareneilbeck creation_date: 2010-03-22T11:50:39Z [Term] id: SO:0001549 name: transcription_variant def: "A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcription variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:51:26Z [Term] id: SO:0001550 name: rate_of_transcription_variant def: "A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke] synonym: "rate of transcription variant" EXACT [] is_a: SO:0001549 ! transcription_variant created_by: kareneilbeck creation_date: 2010-03-22T11:51:50Z [Term] id: SO:0001551 name: increased_transcription_rate_variant def: "A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke] synonym: "increased transcription rate variant" EXACT [] is_a: SO:0001550 ! rate_of_transcription_variant created_by: kareneilbeck creation_date: 2010-03-22T11:52:17Z [Term] id: SO:0001552 name: decreased_transcription_rate_variant def: "A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke] synonym: "decreased transcription rate variant" EXACT [] is_a: SO:0001550 ! rate_of_transcription_variant created_by: kareneilbeck creation_date: 2010-03-22T11:52:43Z [Term] id: SO:0001553 name: translational_product_level_variant def: "A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke] synonym: "translational product level variant" EXACT [] is_a: SO:0001539 ! translational_product_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:53:32Z [Term] id: SO:0001554 name: polypeptide_function_variant def: "A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke] synonym: "polypeptide function variant" EXACT [] is_a: SO:0001539 ! translational_product_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:53:54Z [Term] id: SO:0001555 name: decreased_translational_product_level def: "A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke] synonym: "decrease translational product level" EXACT [] is_a: SO:0001553 ! translational_product_level_variant created_by: kareneilbeck creation_date: 2010-03-22T11:54:25Z [Term] id: SO:0001556 name: increased_translational_product_level def: "A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke] synonym: "increase translational product level" EXACT [] is_a: SO:0001553 ! translational_product_level_variant created_by: kareneilbeck creation_date: 2010-03-22T11:55:25Z [Term] id: SO:0001557 name: polypeptide_gain_of_function_variant def: "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke] synonym: "polypeptide gain of function variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:56:12Z [Term] id: SO:0001558 name: polypeptide_localization_variant def: "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke] synonym: "polypeptide localization variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:56:37Z [Term] id: SO:0001559 name: polypeptide_loss_of_function_variant def: "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke] synonym: "polypeptide loss of function variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:56:58Z [Term] id: SO:0001560 name: inactive_ligand_binding_site def: "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke] synonym: "inactive ligand binding site" EXACT [] is_a: SO:0001559 ! polypeptide_loss_of_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:58:00Z [Term] id: SO:0001561 name: polypeptide_partial_loss_of_function def: "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke] synonym: "polypeptide partial loss of function" EXACT [] is_a: SO:0001559 ! polypeptide_loss_of_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:58:32Z [Term] id: SO:0001562 name: polypeptide_post_translational_processing_variant def: "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke] synonym: "polypeptide post translational processing variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:59:06Z [Term] id: SO:0001563 name: copy_number_change def: "A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke] synonym: "copy number change" EXACT [] is_a: SO:0001537 ! structural_variant created_by: kareneilbeck creation_date: 2010-03-22T02:27:33Z [Term] id: SO:0001564 name: gene_variant def: "A sequence variant where the structure of the gene is changed." [SO:ke] synonym: "gene structure variant" EXACT [] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-22T02:28:01Z [Term] id: SO:0001565 name: gene_fusion def: "A sequence variant whereby a two genes have become joined." [SO:ke] synonym: "gene fusion" EXACT [] is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:28:28Z [Term] id: SO:0001566 name: regulatory_region_variant def: "A sequence variant located within a regulatory region." [SO:ke] comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl. synonym: "regulatory region variant" EXACT [] synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-22T02:28:48Z [Term] id: SO:0001567 name: stop_retained_variant def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke] synonym: "stop retained variant" EXACT [] is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001819 ! synonymous_variant created_by: kareneilbeck creation_date: 2010-04-19T05:02:30Z [Term] id: SO:0001568 name: splicing_variant def: "A sequence variant that changes the process of splicing." [SO:ke] synonym: "splicing variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:29:22Z [Term] id: SO:0001569 name: cryptic_splice_site_variant def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "cryptic splice site activation" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:29:41Z [Term] id: SO:0001570 name: cryptic_splice_acceptor def: "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke] synonym: "cryptic splice acceptor" EXACT [] is_a: SO:0001569 ! cryptic_splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:30:11Z [Term] id: SO:0001571 name: cryptic_splice_donor def: "A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke] synonym: "cryptic splice donor" EXACT [] is_a: SO:0001569 ! cryptic_splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:30:35Z [Term] id: SO:0001572 name: exon_loss def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke] synonym: "exon loss" EXACT [] is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:09Z [Term] id: SO:0001573 name: intron_gain def: "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "intron gain" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:25Z [Term] id: SO:0001574 name: splice_acceptor_variant def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke] synonym: "splice acceptor variant" EXACT [] is_a: SO:0001629 ! splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:52Z [Term] id: SO:0001575 name: splice_donor_variant def: "A splice variant that changes the2 base region at the 5' end of an intron." [SO:ke] synonym: "splice donor variant" EXACT [] is_a: SO:0001629 ! splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:32:10Z [Term] id: SO:0001576 name: transcript_variant def: "A sequence variant that changes the structure of the transcript." [SO:ke] synonym: "transcript variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:32:41Z [Term] id: SO:0001577 name: complex_transcript_variant def: "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html] comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. synonym: "complex transcript variant" EXACT [] synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "complext change in transcript" EXACT [] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T02:33:03Z [Term] id: SO:0001578 name: stop_lost def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke] comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon. synonym: "stop codon lost" EXACT [] synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001650 ! inframe_variant is_a: SO:0001907 ! feature_elongation created_by: kareneilbeck creation_date: 2010-03-23T03:46:42Z [Term] id: SO:0001579 name: transcript_sequence_variant synonym: "transcript sequence variant" EXACT [] is_obsolete: true [Term] id: SO:0001580 name: coding_sequence_variant alt_id: SO:0001581 def: "A sequence variant that changes the coding sequence." [SO:ke] synonym: "coding sequence variant" EXACT [] synonym: "coding variant" EXACT [] synonym: "codon variant" EXACT [] synonym: "codon_variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001791 ! exon_variant created_by: kareneilbeck creation_date: 2010-03-22T02:34:36Z [Term] id: SO:0001582 name: initiator_codon_variant def: "A codon variant that changes at least one base of the first codon of a transcript." [SO:ke] synonym: "initiatior codon variant" EXACT [] synonym: "initiator codon change" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html xref: loinc:LA6695-6 "Initiating Methionine" is_a: SO:0001650 ! inframe_variant created_by: kareneilbeck creation_date: 2010-03-22T02:35:18Z [Term] id: SO:0001583 name: missense_variant alt_id: SO:0001584 alt_id: SO:0001783 def: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke] comment: EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution. synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "missense codon" EXACT [] synonym: "non synonymous codon" EXACT [] synonym: "non synonymous variant" EXACT [] synonym: "non_synonymous_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html xref: http://en.wikipedia.org/wiki/Missense_mutation xref: loinc:LA6698-0 "Missense" is_a: SO:0001650 ! inframe_variant created_by: kareneilbeck creation_date: 2010-03-22T02:35:49Z [Term] id: SO:0001585 name: conservative_missense_variant def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke] synonym: "conservative missense codon" EXACT [] synonym: "conservative missense variant" EXACT [] synonym: "neutral missense codon" RELATED [] synonym: "quiet missense codon" RELATED [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001583 ! missense_variant created_by: kareneilbeck creation_date: 2010-03-22T02:36:40Z [Term] id: SO:0001586 name: non_conservative_missense_variant def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke] synonym: "non conservative missense codon" EXACT [] synonym: "non conservative missense variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001583 ! missense_variant created_by: kareneilbeck creation_date: 2010-03-22T02:37:16Z [Term] id: SO:0001587 name: stop_gained def: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke] comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence). synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "nonsense codon" EXACT [] synonym: "stop codon gained" RELATED [] synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] xref: loinc:LA6699-8 "Nonsense" is_a: SO:0001650 ! inframe_variant is_a: SO:0001906 ! feature_truncation created_by: kareneilbeck creation_date: 2010-03-22T02:37:52Z [Term] id: SO:0001589 name: frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke] comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift. synonym: "frameshift variant" EXACT [] synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] xref: loinc:LA6694-9 "Frameshift" is_a: SO:0001818 ! protein_altering_variant created_by: kareneilbeck creation_date: 2010-03-22T02:40:19Z [Term] id: SO:0001590 name: terminator_codon_variant alt_id: SO:0001625 def: "A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke] comment: The terminal codon may be the terminator, or in an incomplete transcript the last available codon. synonym: "terminal codon variant" EXACT [] synonym: "terminal_codon_variant" EXACT [] synonym: "terminator codon variant" EXACT [] xref: loinc:LA6700-2 "Stop Codon Mutation" is_a: SO:0001580 ! coding_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:40:37Z [Term] id: SO:0001591 name: frame_restoring_variant def: "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke] synonym: "frame restoring variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:41:09Z [Term] id: SO:0001592 name: minus_1_frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] synonym: "-1 frameshift variant" EXACT [] synonym: "minus 1 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:41:30Z [Term] id: SO:0001593 name: minus_2_frameshift_variant synonym: "-2 frameshift variant" EXACT [] synonym: "minus 2 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:41:52Z [Term] id: SO:0001594 name: plus_1_frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] synonym: "+1 frameshift variant" EXACT [] synonym: "plus 1 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:42:06Z [Term] id: SO:0001595 name: plus_2_frameshift_variant synonym: "+2 frameshift variant" EXACT [] synonym: "plus 2 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:42:23Z [Term] id: SO:0001596 name: transcript_secondary_structure_variant def: "A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke] synonym: "transcript secondary structure variant" EXACT [] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T02:43:18Z [Term] id: SO:0001597 name: compensatory_transcript_secondary_structure_variant def: "A secondary structure variant that compensate for the change made by a previous variant." [SO:ke] synonym: "compensatory transcript secondary structure variant" EXACT [] is_a: SO:0001596 ! transcript_secondary_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:43:54Z [Term] id: SO:0001598 name: translational_product_structure_variant def: "A sequence variant within the transcript that changes the structure of the translational product." [SO:ke] synonym: "translational product structure variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:44:17Z [Term] id: SO:0001599 name: 3D_polypeptide_structure_variant def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke] synonym: "3D polypeptide structure variant" EXACT [] is_a: SO:0001598 ! translational_product_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:44:46Z [Term] id: SO:0001600 name: complex_3D_structural_variant def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke] synonym: "complex 3D structural variant" EXACT [] is_a: SO:0001599 ! 3D_polypeptide_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:45:13Z [Term] id: SO:0001601 name: conformational_change_variant def: "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke] synonym: "conformational change variant" EXACT [] is_a: SO:0001599 ! 3D_polypeptide_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:45:48Z [Term] id: SO:0001602 name: complex_change_of_translational_product_variant synonym: "complex change of translational product variant" EXACT [] is_a: SO:0001598 ! translational_product_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:46:54Z [Term] id: SO:0001603 name: polypeptide_sequence_variant def: "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke] synonym: "polypeptide sequence variant" EXACT [] is_a: SO:0001598 ! translational_product_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:47:13Z [Term] id: SO:0001604 name: amino_acid_deletion def: "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke] synonym: "amino acid deletion" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:47:36Z [Term] id: SO:0001605 name: amino_acid_insertion def: "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke] synonym: "amino acid insertion" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:47:56Z [Term] id: SO:0001606 name: amino_acid_substitution def: "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke] synonym: "amino acid substitution" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:48:17Z [Term] id: SO:0001607 name: conservative_amino_acid_substitution def: "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke] synonym: "conservative amino acid substitution" EXACT [] is_a: SO:0001606 ! amino_acid_substitution created_by: kareneilbeck creation_date: 2010-03-22T02:48:57Z [Term] id: SO:0001608 name: non_conservative_amino_acid_substitution def: "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke] synonym: "non conservative amino acid substitution" EXACT [] is_a: SO:0001606 ! amino_acid_substitution created_by: kareneilbeck creation_date: 2010-03-22T02:49:23Z [Term] id: SO:0001609 name: elongated_polypeptide def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke] synonym: "elongated polypeptide" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:49:52Z [Term] id: SO:0001610 name: elongated_polypeptide_C_terminal def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] synonym: "elongated polypeptide C terminal" EXACT [] is_a: SO:0001609 ! elongated_polypeptide created_by: kareneilbeck creation_date: 2010-03-22T02:50:20Z [Term] id: SO:0001611 name: elongated_polypeptide_N_terminal def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] synonym: "elongated polypeptide N terminal" EXACT [] is_a: SO:0001609 ! elongated_polypeptide created_by: kareneilbeck creation_date: 2010-03-22T02:50:31Z [Term] id: SO:0001612 name: elongated_in_frame_polypeptide_C_terminal def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] synonym: "elongated in frame polypeptide C terminal" EXACT [] is_a: SO:0001610 ! elongated_polypeptide_C_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:51:05Z [Term] id: SO:0001613 name: elongated_out_of_frame_polypeptide_C_terminal def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] synonym: "elongated polypeptide out of frame C terminal" EXACT [] is_a: SO:0001610 ! elongated_polypeptide_C_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:51:20Z [Term] id: SO:0001614 name: elongated_in_frame_polypeptide_N_terminal_elongation def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] synonym: "elongated in frame polypeptide N terminal" EXACT [] is_a: SO:0001611 ! elongated_polypeptide_N_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:51:49Z [Term] id: SO:0001615 name: elongated_out_of_frame_polypeptide_N_terminal def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] synonym: "elongated out of frame N terminal" EXACT [] is_a: SO:0001611 ! elongated_polypeptide_N_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:52:05Z [Term] id: SO:0001616 name: polypeptide_fusion def: "A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke] synonym: "polypeptide fusion" EXACT [] is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:52:43Z [Term] id: SO:0001617 name: polypeptide_truncation def: "A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke] synonym: "polypeptide truncation" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:53:07Z [Term] id: SO:0001618 name: inactive_catalytic_site def: "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke] synonym: "inactive catalytic site" EXACT [] is_a: SO:0001560 ! inactive_ligand_binding_site created_by: kareneilbeck creation_date: 2010-03-22T03:06:14Z [Term] id: SO:0001619 name: nc_transcript_variant def: "A transcript variant of a non coding RNA gene." [SO:ke] comment: Within non-coding gene - Located within a gene that does not code for a protein. synonym: "nc transcript variant" EXACT [] synonym: "non coding transcript variant" EXACT [] synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:16:23Z [Term] id: SO:0001620 name: mature_miRNA_variant def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke] comment: EBI term: Within mature miRNA - Located within a microRNA. synonym: "mature miRNA variant" EXACT [] synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001619 ! nc_transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:16:58Z [Term] id: SO:0001621 name: NMD_transcript_variant def: "A variant in a transcript that is the target of NMD." [SO:ke] synonym: "NMD transcript variant" EXACT [] synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:20:40Z [Term] id: SO:0001622 name: UTR_variant def: "A transcript variant that is located within the UTR." [SO:ke] synonym: "UTR variant" EXACT [] synonym: "UTR_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:22:58Z [Term] id: SO:0001623 name: 5_prime_UTR_variant def: "A UTR variant of the 5' UTR." [SO:ke] comment: EBI term: 5prime UTR variations - In 5prime UTR (untranslated region). synonym: "5'UTR variant" EXACT [] synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "five prime UTR variant" EXACT [] synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001622 ! UTR_variant created_by: kareneilbeck creation_date: 2010-03-23T11:23:29Z [Term] id: SO:0001624 name: 3_prime_UTR_variant def: "A UTR variant of the 3' UTR." [SO:ke] comment: EBI term 3prime UTR variations - In 3prime UTR. synonym: "3'UTR variant" EXACT [] synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "three prime UTR variant" EXACT [] synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001622 ! UTR_variant created_by: kareneilbeck creation_date: 2010-03-23T11:23:54Z [Term] id: SO:0001626 name: incomplete_terminal_codon_variant def: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke] comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown. synonym: "incomplete terminal codon variant" EXACT [] synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001650 ! inframe_variant created_by: kareneilbeck creation_date: 2010-03-23T03:51:15Z [Term] id: SO:0001627 name: intron_variant def: "A transcript variant occurring within an intron." [SO:ke] comment: EBI term: Intronic variations - In intron. synonym: "intron variant" EXACT [] synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T03:52:38Z [Term] id: SO:0001628 name: intergenic_variant def: "A sequence variant located in the intergenic region, between genes." [SO:ke] comment: EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript. synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "intergenic variant" EXACT [] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-23T05:07:37Z [Term] id: SO:0001629 name: splice_site_variant def: "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html] comment: EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger. synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "splice site variant" EXACT [] is_a: SO:0001627 ! intron_variant created_by: kareneilbeck creation_date: 2010-03-24T09:42:00Z [Term] id: SO:0001630 name: splice_region_variant def: "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html] comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron. synonym: "splice region variant" EXACT [] synonym: "splice_region_variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-24T09:46:02Z [Term] id: SO:0001631 name: upstream_gene_variant def: "A sequence variant located 5' of a gene." [SO:ke] comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. synonym: "upstream gene variant" EXACT [] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-24T09:49:13Z [Term] id: SO:0001632 name: downstream_gene_variant def: "A sequence variant located 3' of a gene." [SO:ke] comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. synonym: "downstream gene variant" EXACT [] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-24T09:49:38Z [Term] id: SO:0001633 name: 5KB_downstream_variant def: "A sequence variant located within 5 KB of the end of a gene." [SO:ke] comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript. synonym: "5KB downstream variant" EXACT [] synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "within 5KB downstream" RELATED [] is_a: SO:0001632 ! downstream_gene_variant created_by: kareneilbeck creation_date: 2010-03-24T09:50:16Z [Term] id: SO:0001634 name: 500B_downstream_variant def: "A sequence variant located within a half KB of the end of a gene." [SO:ke] synonym: "500B downstream variant" EXACT [] synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001633 ! 5KB_downstream_variant created_by: kareneilbeck creation_date: 2010-03-24T09:50:42Z [Term] id: SO:0001635 name: 5KB_upstream_variant def: "A sequence variant located within 5KB 5' of a gene." [SO:ke] comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript. synonym: "5kb upstream variant" EXACT [] synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001631 ! upstream_gene_variant created_by: kareneilbeck creation_date: 2010-03-24T09:51:06Z [Term] id: SO:0001636 name: 2KB_upstream_variant def: "A sequence variant located within 2KB 5' of a gene." [SO:ke] synonym: "2KB upstream variant" EXACT [] synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001635 ! 5KB_upstream_variant created_by: kareneilbeck creation_date: 2010-03-24T09:51:22Z [Term] id: SO:0001637 name: rRNA_gene def: "A gene that encodes for ribosomal RNA." [SO:ke] synonym: "rRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:10:32Z [Term] id: SO:0001638 name: piRNA_gene def: "A gene that encodes for an piwi associated RNA." [SO:ke] synonym: "piRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:11:36Z [Term] id: SO:0001639 name: RNase_P_RNA_gene def: "A gene that encodes an RNase P RNA." [SO:ke] synonym: "RNase P RNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:13:23Z [Term] id: SO:0001640 name: RNase_MRP_RNA_gene def: "A gene that encodes a RNase_MRP_RNA." [SO:ke] synonym: "RNase MRP RNA gene" RELATED [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:13:58Z [Term] id: SO:0001641 name: lincRNA_gene def: "A gene that encodes large intervening non-coding RNA." [SO:ke] synonym: "lincRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:14:24Z [Term] id: SO:0001642 name: mathematically_defined_repeat def: "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill] comment: Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.). synonym: "mathematically defined repeat" EXACT [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2010-05-03T11:50:14Z [Term] id: SO:0001643 name: telomerase_RNA_gene def: "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke] synonym: "Telomerase RNA component" EXACT [] synonym: "telomerase RNA gene" EXACT [] synonym: "TERC" EXACT [] xref: http:http://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia" is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-05-18T05:26:38Z [Term] id: SO:0001644 name: targeting_vector def: "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467] synonym: "targeting vector" RELATED [] is_a: SO:0000440 ! vector_replicon is_a: SO:0000804 ! engineered_region intersection_of: SO:0000440 ! vector_replicon intersection_of: has_part SO:0000853 ! homologous_region intersection_of: has_quality SO:0000783 ! engineered relationship: has_part SO:0000853 ! homologous_region relationship: has_quality SO:0000783 ! engineered created_by: kareneilbeck creation_date: 2010-05-28T02:05:25Z [Term] id: SO:0001645 name: genetic_marker def: "A measurable sequence feature that varies within a population." [SO:db] synonym: "genetic marker" RELATED [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-05-28T02:33:07Z [Term] id: SO:0001646 name: DArT_marker def: "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke] synonym: "DArT marker" EXACT [] is_a: SO:0001645 ! genetic_marker created_by: kareneilbeck creation_date: 2010-05-28T02:34:43Z [Term] id: SO:0001647 name: kozak_sequence def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke] subset: SOFA synonym: "kozak consensus" EXACT [] synonym: "kozak consensus sequence" EXACT [] synonym: "kozak sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia" is_a: SO:0000139 ! ribosome_entry_site created_by: kareneilbeck creation_date: 2010-06-07T03:12:20Z [Term] id: SO:0001648 name: nested_transposon def: "A transposon that is disrupted by the insertion of another element." [SO:ke] synonym: "nested transposon" EXACT [] is_a: SO:0000101 ! transposable_element created_by: kareneilbeck creation_date: 2010-06-23T03:22:57Z [Term] id: SO:0001649 name: nested_repeat def: "A repeat that is disrupted by the insertion of another element." [SO:ke] synonym: "nested repeat" RELATED [] is_a: SO:0000657 ! repeat_region created_by: kareneilbeck creation_date: 2010-06-23T03:24:55Z [Term] id: SO:0001650 name: inframe_variant def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke] synonym: "cds-indel" EXACT dbsnp [] synonym: "inframe variant" EXACT [] is_a: SO:0001818 ! protein_altering_variant created_by: kareneilbeck creation_date: 2010-07-19T01:24:44Z [Term] id: SO:0001653 name: retinoic_acid_responsive_element def: "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671] synonym: "RARE" EXACT [] synonym: "retinoic acid responsive element" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000167 ! promoter created_by: kareneilbeck creation_date: 2010-08-03T10:46:12Z [Term] id: SO:0001654 name: nucleotide_to_protein_binding_site def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] subset: SOFA synonym: "nucleotide to protein binding site" RELATED [] is_a: SO:0000410 ! protein_binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:26:05Z [Term] id: SO:0001655 name: nucleotide_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb] comment: See GO:0000166 : nucleotide binding. synonym: "nucleotide binding site" EXACT [] is_a: SO:0000409 ! binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:30:04Z [Term] id: SO:0001656 name: metal_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb] comment: See GO:0046872 : metal ion binding. synonym: "metal binding site" RELATED [] is_a: SO:0000409 ! binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:31:42Z [Term] id: SO:0001657 name: ligand_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke] synonym: "ligand binding site" EXACT [] is_a: SO:0000409 ! binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:32:58Z [Term] id: SO:0001658 name: nested_tandem_repeat def: "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF] comment: Tracker ID: 3052459. synonym: "nested tandem repeat" EXACT [] synonym: "NTR" EXACT [] is_a: SO:0001649 ! nested_repeat created_by: kareneilbeck creation_date: 2010-08-26T09:36:16Z [Term] id: SO:0001659 name: promoter_element synonym: "promoter element" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: overlaps SO:0000235 ! TF_binding_site created_by: kareneilbeck creation_date: 2010-10-01T11:48:32Z [Term] id: SO:0001660 name: core_promoter_element synonym: "core promoter element" EXACT [] synonym: "general transcription factor binding site" RELATED [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2010-10-01T11:49:03Z [Term] id: SO:0001661 name: RNA_polymerase_II_TATA_box def: "A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867] synonym: "RNA polymerase II TATA box" EXACT [] is_a: SO:0000174 ! TATA_box relationship: part_of SO:0001669 ! RNApol_II_core_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:42:12Z [Term] id: SO:0001662 name: RNA_polymerase_III_TATA_box def: "A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke] synonym: "RNA polymerase III TATA box" EXACT [] is_a: SO:0000174 ! TATA_box relationship: part_of SO:0000171 ! RNApol_III_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:43:16Z [Term] id: SO:0001663 name: BREd_motif def: "A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867] synonym: "BREd" EXACT [] synonym: "BREd motif" RELATED [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:49:55Z [Term] id: SO:0001664 name: DCE def: "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867] synonym: "downstream core element" RELATED [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:56:41Z [Term] id: SO:0001665 name: DCE_SI def: "A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke] synonym: "DCE SI" RELATED [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001664 ! DCE created_by: kareneilbeck creation_date: 2010-10-01T03:00:10Z [Term] id: SO:0001666 name: DCE_SII def: "A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke] synonym: "DCE SII" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001664 ! DCE created_by: kareneilbeck creation_date: 2010-10-01T03:00:30Z [Term] id: SO:0001667 name: DCE_SIII def: "A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke] synonym: "DCE SIII" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001664 ! DCE created_by: kareneilbeck creation_date: 2010-10-01T03:00:44Z [Term] id: SO:0001668 name: proximal_promoter_element synonym: "proximal promoter element" RELATED [] synonym: "specific transcription factor binding site" RELATED [] is_a: SO:0001678 ! regulatory_promoter_element created_by: kareneilbeck creation_date: 2010-10-01T03:10:23Z [Term] id: SO:0001669 name: RNApol_II_core_promoter def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867] synonym: "RNApol II core promoter" EXACT [] is_a: SO:0000170 ! RNApol_II_promoter created_by: kareneilbeck creation_date: 2010-10-01T03:13:41Z [Term] id: SO:0001670 name: distal_promoter_element synonym: "distal promoter element" RELATED [] is_a: SO:0001678 ! regulatory_promoter_element created_by: kareneilbeck creation_date: 2010-10-01T03:21:08Z [Term] id: SO:0001671 name: bacterial_RNApol_promoter_sigma_70 synonym: "bacterial RNA polymerase promoter sigma 70" EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2010-10-06T01:41:34Z [Term] id: SO:0001672 name: bacterial_RNApol_promoter_sigma54 synonym: "bacterial RNA polymerase promoter sigma54" EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2010-10-06T01:42:37Z [Term] id: SO:0001673 name: minus_12_signal def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] synonym: "minus 12 signal" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54 created_by: kareneilbeck creation_date: 2010-10-06T01:44:57Z [Term] id: SO:0001674 name: minus_24_signal def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] synonym: "minus 24 signal" RELATED [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54 created_by: kareneilbeck creation_date: 2010-10-06T01:45:24Z [Term] id: SO:0001675 name: A_box_type_1 def: "An A box within an RNA polymerase III type 1 promoter." [SO:ke] comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. synonym: "A box type 1" RELATED [] is_a: SO:0000619 ! A_box relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 created_by: kareneilbeck creation_date: 2010-10-06T05:43:43Z [Term] id: SO:0001676 name: A_box_type_2 def: "An A box within an RNA polymerase III type 2 promoter." [SO:ke] comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. synonym: "A box type 2" RELATED [] is_a: SO:0000619 ! A_box relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 created_by: kareneilbeck creation_date: 2010-10-06T05:44:18Z [Term] id: SO:0001677 name: intermediate_element def: "A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659] synonym: "IE" EXACT [] synonym: "intermediate element" RELATED [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 created_by: kareneilbeck creation_date: 2010-10-06T05:52:03Z [Term] id: SO:0001678 name: regulatory_promoter_element def: "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659] synonym: "regulatory promoter element" RELATED [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2010-10-07T04:39:48Z [Term] id: SO:0001679 name: transcription_regulatory_region def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke] subset: SOFA synonym: "transcription regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:49:35Z [Term] id: SO:0001680 name: translation_regulatory_region def: "A regulatory region that is involved in the control of the process of translation." [SO:ke] synonym: "translation regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:52:45Z [Term] id: SO:0001681 name: recombination_regulatory_region def: "A regulatory region that is involved in the control of the process of recombination." [SO:ke] synonym: "recombination regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:53:35Z [Term] id: SO:0001682 name: replication_regulatory_region def: "A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke] synonym: "replication regulatory region" RELATED [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:54:09Z [Term] id: SO:0001683 name: sequence_motif def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif] subset: SOFA synonym: "sequence motif" RELATED [] xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia" is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-10-14T04:13:22Z [Term] id: SO:0001684 name: experimental_feature_attribute def: "An attribute of an experimentally derived feature." [SO:ke] synonym: "experimental feature attribute" RELATED [] is_a: SO:0000733 ! feature_attribute created_by: kareneilbeck creation_date: 2010-10-28T02:22:23Z [Term] id: SO:0001685 name: score def: "The score of an experimentally derived feature such as a p-value." [SO:ke] is_a: SO:0001684 ! experimental_feature_attribute created_by: kareneilbeck creation_date: 2010-10-28T02:23:16Z [Term] id: SO:0001686 name: quality_value def: "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke] synonym: "quality value" RELATED [] is_a: SO:0001684 ! experimental_feature_attribute created_by: kareneilbeck creation_date: 2010-10-28T02:24:11Z [Term] id: SO:0001687 name: restriction_enzyme_recognition_site def: "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke] synonym: "restriction endonuclease recognition site" EXACT [] synonym: "restriction enzyme recognition site" EXACT [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-10-29T12:29:57Z [Term] id: SO:0001688 name: restriction_enzyme_cleavage_junction def: "The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke] synonym: "restriction enzyme cleavage junction" EXACT [] is_a: SO:0000699 ! junction created_by: kareneilbeck creation_date: 2010-10-29T12:35:02Z [Term] id: SO:0001689 name: five_prime_restriction_enzyme_junction def: "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke] synonym: "5' restriction enzyme junction" EXACT [] is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:36:24Z [Term] id: SO:0001690 name: three_prime_restriction_enzyme_junction synonym: "3' restriction enzyme junction" EXACT [] is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:37:52Z [Term] id: SO:0001691 name: blunt_end_restriction_enzyme_cleavage_site synonym: "blunt end restriction enzyme cleavage site" EXACT [] is_a: SO:0001687 ! restriction_enzyme_recognition_site created_by: kareneilbeck creation_date: 2010-10-29T12:39:53Z [Term] id: SO:0001692 name: sticky_end_restriction_enzyme_cleavage_site synonym: "sticky end restriction enzyme cleavage site" RELATED [] is_a: SO:0001687 ! restriction_enzyme_recognition_site created_by: kareneilbeck creation_date: 2010-10-29T12:40:50Z [Term] id: SO:0001693 name: blunt_end_restriction_enzyme_cleavage_junction def: "A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke] synonym: "blunt end restriction enzyme cleavage site" RELATED [] is_a: SO:0001688 ! restriction_enzyme_cleavage_junction relationship: part_of SO:0001691 ! blunt_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:43:14Z [Term] id: SO:0001694 name: single_strand_restriction_enzyme_cleavage_site def: "A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke] synonym: "single strand restriction enzyme cleavage site" RELATED [] is_a: SO:0001688 ! restriction_enzyme_cleavage_junction created_by: kareneilbeck creation_date: 2010-10-29T12:44:48Z [Term] id: SO:0001695 name: restriction_enzyme_single_strand_overhang def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke] synonym: "single strand overhang" EXACT [] synonym: "sticky end" RELATED [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:48:35Z [Term] id: SO:0001696 name: experimentally_defined_binding_region def: "A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke] synonym: "experimentally defined binding region" RELATED [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2010-11-02T11:39:59Z [Term] id: SO:0001697 name: ChIP_seq_region def: "A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke] synonym: "ChIP seq region" RELATED [] is_a: SO:0001696 ! experimentally_defined_binding_region relationship: contains SO:0000410 ! protein_binding_site created_by: kareneilbeck creation_date: 2010-11-02T11:43:07Z [Term] id: SO:0001698 name: ASPE_primer def: "\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801] synonym: "allele specific primer extension primer" EXACT [] synonym: "ASPE primer" EXACT [] is_a: SO:0000112 ! primer created_by: kareneilbeck creation_date: 2010-11-11T03:25:21Z [Term] id: SO:0001699 name: dCAPS_primer def: "A primer with one or more mis-matches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033] synonym: "dCAPS primer" EXACT [] synonym: "derived cleaved amplified polymorphic primer" EXACT [] is_a: SO:0000112 ! primer created_by: kareneilbeck creation_date: 2010-11-11T03:27:09Z [Term] id: SO:0001700 name: histone_modification def: "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone] synonym: "histone modification" EXACT [] synonym: "histone modification site" RELATED [] is_a: SO:0001089 ! post_translationally_modified_region is_a: SO:0001720 ! epigenetically_modified_region intersection_of: SO:0001089 ! post_translationally_modified_region intersection_of: has_quality SO:0000133 ! epigenetically_modified relationship: has_quality SO:0000133 ! epigenetically_modified created_by: kareneilbeck creation_date: 2010-03-31T10:22:08Z [Term] id: SO:0001701 name: histone_methylation_site def: "A histone modification site where the modification is the methylation of the residue." [SO:ke] synonym: "histone methylation" EXACT [] synonym: "histone methylation site" EXACT [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-03-31T10:23:02Z [Term] id: SO:0001702 name: histone_acetylation_site def: "A histone modification where the modification is the acylation of the residue." [SO:ke] synonym: "histone acetylation" EXACT [] synonym: "histone acetylatoin site" EXACT [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-03-31T10:23:27Z [Term] id: SO:0001703 name: H3K9_acetylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K9 acetylation site" EXACT [] synonym: "H3K9Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:25:05Z [Term] id: SO:0001704 name: H3K14_acetylation_site def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K14 acetylation site" EXACT [] synonym: "H3K14Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:25:53Z [Term] id: SO:0001705 name: H3K4_monomethylation_site def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K4 mono-methylation site" EXACT [] synonym: "H3K4me1" RELATED [] is_a: SO:0001734 ! H3K4_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:28:14Z [Term] id: SO:0001706 name: H3K4_trimethylation def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K4 tri-methylation" EXACT [] synonym: "H3K4me3" RELATED [] is_a: SO:0001734 ! H3K4_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:29:12Z [Term] id: SO:0001707 name: H3K9_trimethylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K9 tri-methylation site" EXACT [] synonym: "H3K9Me3" RELATED [] is_a: SO:0001736 ! H3K9_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:30:34Z [Term] id: SO:0001708 name: H3K27_monomethylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H2K27 mono-methylation site" EXACT [] synonym: "H2K27Me1" RELATED [] is_a: SO:0001732 ! H3K27_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:31:54Z [Term] id: SO:0001709 name: H3K27_trimethylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K27 tri-methylation site" EXACT [] synonym: "H3K27Me3" RELATED [] is_a: SO:0001732 ! H3K27_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:32:41Z [Term] id: SO:0001710 name: H3K79_monomethylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K79 mono-methylation site" EXACT [] synonym: "H3K79me1" RELATED [] is_a: SO:0001735 ! H3K79_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:33:42Z [Term] id: SO:0001711 name: H3K79_dimethylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K79 di-methylation site" EXACT [] synonym: "H3K79Me2" RELATED [] is_a: SO:0001735 ! H3K79_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:34:39Z [Term] id: SO:0001712 name: H3K79_trimethylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K79 tri-methylation site" EXACT [] synonym: "H3K79Me3" RELATED [] is_a: SO:0001735 ! H3K79_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:35:30Z [Term] id: SO:0001713 name: H4K20_monomethylation_site def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H34histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H4K20 mono-methylation site" EXACT [] synonym: "H4K20Me1" RELATED [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:36:43Z [Term] id: SO:0001714 name: H2BK5_monomethylation_site def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H2BK5 mono-methylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:38:12Z [Term] id: SO:0001715 name: ISRE def: "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac] comment: Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. synonym: "interferon stimulated response element" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region created_by: kareneilbeck creation_date: 2010-04-05T11:15:08Z [Term] id: SO:0001716 name: histone_ubiqitination_site def: "A histone modification site where ubiquitin may be added." [SO:ke] synonym: "histone ubiquitination site" RELATED [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-04-13T10:12:18Z [Term] id: SO:0001717 name: H2B_ubiquitination_site def: "A histone modification site on H2B where ubiquitin may be added." [SO:ke] synonym: "H2BUbiq" RELATED [] is_a: SO:0001716 ! histone_ubiqitination_site created_by: kareneilbeck creation_date: 2010-04-13T10:13:28Z [Term] id: SO:0001718 name: H3K18_acetylation_site def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] synonym: "H3K18 acetylation site" EXACT [] synonym: "H3K18Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:39:35Z [Term] id: SO:0001719 name: H3K23_acylation_site def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] synonym: "H3K23 acylation site" RELATED [] synonym: "H3K23Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:42:45Z [Term] id: SO:0001720 name: epigenetically_modified_region def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke] subset: SOFA synonym: "epigenetically modified region" RELATED [] is_a: SO:0001411 ! biological_region intersection_of: SO:0001411 ! biological_region intersection_of: has_quality SO:0000133 ! epigenetically_modified relationship: has_quality SO:0000133 ! epigenetically_modified created_by: kareneilbeck creation_date: 2010-03-27T12:02:29Z [Term] id: SO:0001721 name: H3K27_acylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] synonym: "H3K27 acylation site" EXACT [] synonym: "H3K27Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:44:09Z [Term] id: SO:0001722 name: H3K36_monomethylation_site def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke] synonym: "H3K36 mono-methylation site" EXACT [] synonym: "H3K36. synonym: "transcriptionally regulated" EXACT [] is_a: SO:0000119 ! regulated [Term] id: SO:0000124 name: transcriptionally_constitutive def: "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke] synonym: "transcriptionally constitutive" EXACT [] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000125 name: transcriptionally_induced def: "An inducer molecule is required for transcription to occur." [SO:ke] synonym: "transcriptionally induced" EXACT [] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000126 name: transcriptionally_repressed def: "A repressor molecule is required for transcription to stop." [SO:ke] synonym: "transcriptionally repressed" EXACT [] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000127 name: silenced_gene def: "A gene that is silenced." [SO:xp] synonym: "silenced gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000893 ! silenced [Term] id: SO:0000128 name: gene_silenced_by_DNA_modification def: "A gene that is silenced by DNA modification." [SO:xp] synonym: "gene silenced by DNA modification" EXACT [] is_a: SO:0000127 ! silenced_gene relationship: has_quality SO:0000894 ! silenced_by_DNA_modification [Term] id: SO:0000129 name: gene_silenced_by_DNA_methylation def: "A gene that is silenced by DNA methylation." [SO:xp] synonym: "gene silenced by DNA methylation" EXACT [] synonym: "methylation-silenced gene" EXACT [] is_a: SO:0000128 ! gene_silenced_by_DNA_modification relationship: has_quality SO:0000895 ! silenced_by_DNA_methylation [Term] id: SO:0000130 name: post_translationally_regulated def: "An attribute describing a gene that is regulated after it has been translated." [SO:ke] synonym: "post translationally regulated" EXACT [] synonym: "post-translationally regulated" EXACT [] is_a: SO:0000119 ! regulated [Term] id: SO:0000131 name: translationally_regulated def: "An attribute describing a gene that is regulated as it is translated." [SO:ke] synonym: "translationally regulated" EXACT [] is_a: SO:0000119 ! regulated [Term] id: SO:0000132 name: reverse_primer def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "DNA reverse primer" EXACT [] synonym: "reverse DNA primer" EXACT [] synonym: "reverse primer" EXACT [] synonym: "reverse primer oligo" EXACT [] synonym: "reverse primer oligonucleotide" EXACT [] synonym: "reverse primer sequence" EXACT [] is_a: SO:0000112 ! primer relationship: has_quality SO:0001031 ! reverse [Term] id: SO:0000133 name: epigenetically_modified def: "This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke] synonym: "epigenetically modified" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000134 name: genomically_imprinted def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke] synonym: "genomically imprinted" EXACT [] synonym: "imprinted" BROAD [] xref: http:http://en.wikipedia.org/wiki/Genomic_imprinting "wiki" is_a: SO:0000119 ! regulated is_a: SO:0000133 ! epigenetically_modified [Term] id: SO:0000135 name: maternally_imprinted def: "The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] synonym: "maternally imprinted" EXACT [] is_a: SO:0000134 ! genomically_imprinted [Term] id: SO:0000136 name: paternally_imprinted def: "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke] synonym: "paternally imprinted" EXACT [] is_a: SO:0000134 ! genomically_imprinted [Term] id: SO:0000137 name: allelically_excluded def: "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke] comment: Examples are x-inactivation and immunoglobulin formation. synonym: "allelically excluded" EXACT [] is_a: SO:0000133 ! epigenetically_modified [Term] id: SO:0000138 name: gene_rearranged_at_DNA_level def: "An epigenetically modified gene, rearranged at the DNA level." [SO:xp] synonym: "gene rearranged at DNA level" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene relationship: has_quality SO:0000904 ! rearranged_at_DNA_level [Term] id: SO:0000139 name: ribosome_entry_site def: "Region in mRNA where ribosome assembles." [SO:ke] subset: SOFA synonym: "ribosome entry site" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000204 ! five_prime_UTR [Term] id: SO:0000140 name: attenuator def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as] subset: SOFA synonym: "attenuator sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Attenuator "wiki" is_a: SO:0001680 ! translation_regulatory_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000141 name: terminator def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "terminator sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki" is_a: SO:0001679 ! transcription_regulatory_region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000142 name: DNA_sequence_secondary_structure def: "A folded DNA sequence." [SO:ke] synonym: "DNA sequence secondary structure" EXACT [] is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000143 name: assembly_component def: "A region of known length which may be used to manufacture a longer region." [SO:ke] subset: SOFA synonym: "assembly component" EXACT [] is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000144 name: primary_transcript_attribute is_obsolete: true [Term] id: SO:0000145 name: recoded_codon def: "A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp] synonym: "recoded codon" EXACT [] is_a: SO:0000360 ! codon [Term] id: SO:0000146 name: capped def: "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000147 name: exon def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Exon "wiki" is_a: SO:0000833 ! transcript_region [Term] id: SO:0000148 name: supercontig def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls] subset: SOFA synonym: "scaffold" RELATED [] is_a: SO:0001876 ! partial_genomic_sequence_assembly relationship: part_of SO:0000719 ! ultracontig [Term] id: SO:0000149 name: contig def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls] subset: SOFA xref: http://en.wikipedia.org/wiki/Contig "wiki" is_a: SO:0000143 ! assembly_component is_a: SO:0000353 ! sequence_assembly relationship: part_of SO:0000148 ! supercontig [Term] id: SO:0000150 name: read def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd] subset: SOFA is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000149 ! contig [Term] id: SO:0000151 name: clone def: "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke] subset: SOFA xref: http:http://en.wikipedia.org/wiki/Clone_(genetics) "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000152 name: YAC def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "yeast artificial chromosome" EXACT [] is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000153 name: BAC def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "bacterial artificial chromosome" EXACT [] is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000154 name: PAC def: "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome. synonym: "P1" EXACT [] synonym: "P1 artificial chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000155 name: plasmid def: "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "plasmid sequence" EXACT [] is_a: SO:0001235 ! replicon [Term] id: SO:0000156 name: cosmid def: "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma] comment: Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "cosmid vector" EXACT [] xref: http://en.wikipedia.org/wiki/Cosmid "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000157 name: phagemid def: "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma] synonym: "phagemid vector" RELATED [] xref: http://en.wikipedia.org/wiki/Phagemid "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000158 name: fosmid def: "A cloning vector that utilizes the E. coli F factor." [SO:ma] comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996. synonym: "fosmid vector" RELATED [] xref: http://en.wikipedia.org/wiki/Fosmid "wiki" is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000159 name: deletion alt_id: SO:1000033 def: "The point at which one or more contiguous nucleotides were excised." [SO:ke] subset: SOFA synonym: "deleted_sequence" EXACT [] synonym: "nucleotide deletion" EXACT [] synonym: "nucleotide_deletion" EXACT [] xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki" xref: loinc:LA6692-3 "Deletion" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:0000160 name: lambda_clone def: "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] is_obsolete: true [Term] id: SO:0000161 name: methylated_adenine def: "A modified base in which adenine has been methylated." [SO:ke] subset: SOFA synonym: "methylated A" EXACT [] synonym: "methylated adenine" EXACT [] synonym: "methylated adenine base" EXACT [] synonym: "methylated adenine residue" EXACT [] synonym: "methylated_A" EXACT [] is_a: SO:0000306 ! methylated_DNA_base_feature [Term] id: SO:0000162 name: splice_site def: "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke] comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery. subset: SOFA synonym: "splice site" EXACT [] xref: http://en.wikipedia.org/wiki/Splice_site "wiki" is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000163 name: five_prime_cis_splice_site def: "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] subset: SOFA synonym: "5' splice site" EXACT [] synonym: "donor" RELATED [] synonym: "donor splice site" EXACT [] synonym: "five prime splice site" EXACT [] synonym: "splice donor site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000164 name: three_prime_cis_splice_site def: "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke] subset: SOFA synonym: "3' splice site" RELATED [] synonym: "acceptor" RELATED [] synonym: "acceptor splice site" EXACT [] synonym: "splice acceptor site" EXACT [] synonym: "three prime splice site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000165 name: enhancer def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO. subset: SOFA xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki" is_a: SO:0000727 ! CRM [Term] id: SO:0000166 name: enhancer_bound_by_factor def: "An enhancer bound by a factor." [SO:xp] synonym: "enhancer bound by factor" EXACT [] is_a: SO:0000165 ! enhancer relationship: has_quality SO:0000277 ! bound_by_factor [Term] id: SO:0000167 name: promoter def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. subset: SOFA synonym: "promoter sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Promoter "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000168 name: restriction_enzyme_cut_site def: "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma] is_obsolete: true [Term] id: SO:0000169 name: RNApol_I_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke] synonym: "pol I promoter" EXACT [] synonym: "polymerase I promoter" EXACT [] synonym: "RNA polymerase A promoter" EXACT [] synonym: "RNApol I promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000170 name: RNApol_II_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke] synonym: "pol II promoter" RELATED [] synonym: "polymerase II promoter" EXACT [] synonym: "RNA polymerase B promoter" EXACT [] synonym: "RNApol II promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000171 name: RNApol_III_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke] synonym: "pol III promoter" EXACT [] synonym: "polymerase III promoter" EXACT [] synonym: "RNA polymerase C promoter" EXACT [] synonym: "RNApol III promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000172 name: CAAT_signal def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "CAAT box" EXACT [] synonym: "CAAT signal" EXACT [] synonym: "CAAT-box" EXACT [] xref: http://en.wikipedia.org/wiki/CAAT_box "wiki" is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000173 name: GC_rich_promoter_region def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "GC rich promoter region" EXACT [] synonym: "GC-rich region" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0000174 name: TATA_box def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867] comment: Binds TBP. synonym: "Goldstein-Hogness box" EXACT [] synonym: "TATA box" EXACT [] xref: http://en.wikipedia.org/wiki/TATA_box "wiki" is_a: SO:0001660 ! core_promoter_element [Term] id: SO:0000175 name: minus_10_signal def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "-10 signal" EXACT [] synonym: "minus 10 signal" EXACT [] synonym: "Pribnow box" EXACT [] synonym: "Pribnow Schaller box" EXACT [] synonym: "Pribnow-Schaller box" EXACT [] xref: http://en.wikipedia.org/wiki/Pribnow_box "wiki" is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70 relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf [Term] id: SO:0000176 name: minus_35_signal def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "-35 signal" EXACT [] synonym: "minus 35 signal" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70 relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf [Term] id: SO:0000177 name: cross_genome_match def: "A nucleotide match against a sequence from another organism." [SO:ma] subset: SOFA synonym: "cross genome match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000178 name: operon def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Operon "wiki" is_a: SO:0005855 ! gene_group [Term] id: SO:0000179 name: clone_insert_start def: "The start of the clone insert." [SO:ke] subset: SOFA synonym: "clone insert start" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000180 name: retrotransposon def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r] synonym: "class I" RELATED [] synonym: "class I transposon" EXACT [] synonym: "retrotransposon element" EXACT [] xref: http://en.wikipedia.org/wiki/Retrotransposon "wiki" is_a: SO:0000101 ! transposable_element [Term] id: SO:0000181 name: translated_nucleotide_match def: "A match against a translated sequence." [SO:ke] subset: SOFA synonym: "translated nucleotide match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0000182 name: DNA_transposon def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke] synonym: "class II" RELATED [] synonym: "class II transposon" EXACT [] synonym: "DNA transposon" EXACT [] is_a: SO:0000101 ! transposable_element [Term] id: SO:0000183 name: non_transcribed_region def: "A region of the gene which is not transcribed." [SO:ke] subset: SOFA synonym: "non transcribed region" EXACT [] synonym: "non-transcribed sequence" EXACT [] synonym: "nontranscribed region" EXACT [] synonym: "nontranscribed sequence" EXACT [] is_a: SO:0000842 ! gene_component_region [Term] id: SO:0000184 name: U2_intron def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511] comment: May have either GT-AG or AT-AG 5' and 3' boundaries. synonym: "U2 intron" EXACT [] is_a: SO:0000662 ! spliceosomal_intron [Term] id: SO:0000185 name: primary_transcript def: "A transcript that in its initial state requires modification to be functional." [SO:ma] subset: SOFA synonym: "precursor RNA" EXACT [] synonym: "primary transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki" is_a: SO:0000673 ! transcript [Term] id: SO:0000186 name: LTR_retrotransposon def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke] synonym: "long terminal repeat retrotransposon" EXACT [] synonym: "LTR retrotransposon" EXACT [] is_a: SO:0000180 ! retrotransposon [Term] id: SO:0000187 name: repeat_family def: "A group of characterized repeat sequences." [SO:ke] subset: SOFA is_obsolete: true [Term] id: SO:0000188 name: intron def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Intron "wiki" is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000189 name: non_LTR_retrotransposon def: "A retrotransposon without long terminal repeat sequences." [SO:ke] synonym: "non LTR retrotransposon" EXACT [] is_a: SO:0000180 ! retrotransposon [Term] id: SO:0000190 name: five_prime_intron synonym: "5' intron" EXACT [] synonym: "5' intron sequence" EXACT [] synonym: "five prime intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000191 name: interior_intron synonym: "interior intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000192 name: three_prime_intron synonym: "3' intron" EXACT [] synonym: "3' intron sequence" RELATED [] synonym: "three prime intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000193 name: RFLP_fragment def: "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj] subset: SOFA synonym: "restriction fragment length polymorphism" EXACT [] synonym: "RFLP" EXACT [] synonym: "RFLP fragment" EXACT [] xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki" is_a: SO:0000412 ! restriction_fragment [Term] id: SO:0000194 name: LINE_element def: "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] synonym: "LINE" EXACT [] synonym: "LINE element" EXACT [] synonym: "Long interspersed element" EXACT [] synonym: "Long interspersed nuclear element" EXACT [] is_a: SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000195 name: coding_exon def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke] subset: SOFA synonym: "coding exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000196 name: five_prime_coding_exon_coding_region def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm] subset: SOFA synonym: "five prime exon coding region" EXACT [] is_a: SO:0001215 ! coding_region_of_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000197 name: three_prime_coding_exon_coding_region def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm] subset: SOFA synonym: "three prime exon coding region" EXACT [] is_a: SO:0001215 ! coding_region_of_exon relationship: part_of SO:0000202 ! three_prime_coding_exon [Term] id: SO:0000198 name: noncoding_exon def: "An exon that does not contain any codons." [SO:ke] subset: SOFA synonym: "noncoding exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000199 name: translocation def: "A region of nucleotide sequence that has translocated to a new position." [SO:ke] subset: DBVAR synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "translocated sequence" EXACT [] is_a: SO:0001059 ! sequence_alteration [Term] id: SO:0000200 name: five_prime_coding_exon def: "The 5' most coding exon." [SO:ke] subset: SOFA synonym: "5' coding exon" EXACT [] synonym: "five prime coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:0000201 name: interior_exon def: "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547] synonym: "interior exon" EXACT [] is_a: SO:0000147 ! exon [Term] id: SO:0000202 name: three_prime_coding_exon def: "The coding exon that is most 3-prime on a given transcript." [SO:ma] synonym: "3' coding exon" RELATED [] synonym: "three prime coding exon" EXACT [] is_a: SO:0000195 ! coding_exon [Term] id: SO:0000203 name: UTR def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke] subset: SOFA synonym: "untranslated region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000204 name: five_prime_UTR def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "5' UTR" EXACT [] synonym: "five prime UTR" EXACT [] synonym: "five_prime_untranslated_region" EXACT [] xref: http://en.wikipedia.org/wiki/5'_UTR "wiki" is_a: SO:0000203 ! UTR [Term] id: SO:0000205 name: three_prime_UTR def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "three prime untranslated region" EXACT [] synonym: "three prime UTR" EXACT [] xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki" is_a: SO:0000203 ! UTR [Term] id: SO:0000206 name: SINE_element def: "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke] synonym: "Short interspersed element" EXACT [] synonym: "Short interspersed nuclear element" EXACT [] synonym: "SINE element" EXACT [] xref: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element "wiki" is_a: SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000207 name: simple_sequence_length_variation synonym: "simple sequence length polymorphism" RELATED [] synonym: "simple sequence length variation" EXACT [] synonym: "SSLP" RELATED [] is_a: SO:0000248 ! sequence_length_variation [Term] id: SO:0000208 name: terminal_inverted_repeat_element def: "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] synonym: "terminal inverted repeat element" EXACT [] synonym: "TIR element" EXACT [] is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000209 name: rRNA_primary_transcript def: "A primary transcript encoding a ribosomal RNA." [SO:ke] subset: SOFA synonym: "ribosomal RNA primary transcript" EXACT [] synonym: "rRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000210 name: tRNA_primary_transcript def: "A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke] synonym: "tRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000211 name: alanine_tRNA_primary_transcript def: "A primary transcript encoding alanyl tRNA." [SO:ke] synonym: "alanine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000212 name: arginine_tRNA_primary_transcript def: "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke] synonym: "arginine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000213 name: asparagine_tRNA_primary_transcript def: "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke] synonym: "asparagine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000214 name: aspartic_acid_tRNA_primary_transcript def: "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke] synonym: "aspartic acid tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000215 name: cysteine_tRNA_primary_transcript def: "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke] synonym: "cysteine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000216 name: glutamic_acid_tRNA_primary_transcript def: "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke] synonym: "glutamic acid tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000217 name: glutamine_tRNA_primary_transcript def: "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke] synonym: "glutamine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000218 name: glycine_tRNA_primary_transcript def: "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke] synonym: "glycine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000219 name: histidine_tRNA_primary_transcript def: "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke] synonym: "histidine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000220 name: isoleucine_tRNA_primary_transcript def: "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke] synonym: "isoleucine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000221 name: leucine_tRNA_primary_transcript def: "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke] synonym: "leucine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000222 name: lysine_tRNA_primary_transcript def: "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke] synonym: "lysine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000223 name: methionine_tRNA_primary_transcript def: "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke] synonym: "methionine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000224 name: phenylalanine_tRNA_primary_transcript def: "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke] synonym: "phenylalanine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000225 name: proline_tRNA_primary_transcript def: "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke] synonym: "proline tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000226 name: serine_tRNA_primary_transcript def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke] synonym: "serine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000227 name: threonine_tRNA_primary_transcript def: "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke] synonym: "threonine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000228 name: tryptophan_tRNA_primary_transcript def: "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke] synonym: "tryptophan tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000229 name: tyrosine_tRNA_primary_transcript def: "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke] synonym: "tyrosine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000230 name: valine_tRNA_primary_transcript def: "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke] synonym: "valine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000231 name: snRNA_primary_transcript def: "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke] synonym: "snRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000232 name: snoRNA_primary_transcript def: "A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke] synonym: "snoRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000233 name: mature_transcript def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke] comment: A processed transcript cannot contain introns. subset: SOFA synonym: "mature transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki" is_a: SO:0000673 ! transcript relationship: derives_from SO:0000185 ! primary_transcript [Term] id: SO:0000234 name: mRNA def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "messenger RNA" EXACT [] xref: http://en.wikipedia.org/wiki/MRNA "wiki" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000235 name: TF_binding_site def: "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke] subset: SOFA synonym: "TF binding site" EXACT [] synonym: "transcription factor binding site" EXACT [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0000236 name: ORF def: "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma] comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "open reading frame" EXACT [] is_a: SO:0000717 ! reading_frame [Term] id: SO:0000237 name: transcript_attribute synonym: "transcript attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000238 name: foldback_element def: "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf] synonym: "foldback element" EXACT [] synonym: "long inverted repeat element" RELATED [] synonym: "LVR element" RELATED [] is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000239 name: flanking_region def: "The sequences extending on either side of a specific region." [SO:ke] subset: SOFA synonym: "flanking region" EXACT [] is_a: SO:0001412 ! topologically_defined_region [Term] id: SO:0000240 name: chromosome_variation synonym: "chromosome variation" EXACT [] is_a: SO:0001507 ! variant_collection disjoint_from: SO:0000400 ! sequence_attribute relationship: part_of SO:0001524 ! chromosomally_aberrant_genome [Term] id: SO:0000241 name: internal_UTR def: "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm] synonym: "internal UTR" EXACT [] is_a: SO:0000203 ! UTR [Term] id: SO:0000242 name: untranslated_region_polycistronic_mRNA def: "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke] synonym: "untranslated region polycistronic mRNA" EXACT [] is_a: SO:0000203 ! UTR [Term] id: SO:0000243 name: internal_ribosome_entry_site def: "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke] synonym: "internal ribosomal entry sequence" EXACT [] synonym: "internal ribosomal entry site" EXACT [] synonym: "internal ribosome entry sequence" RELATED [] synonym: "internal ribosome entry site" EXACT [] synonym: "IRES" EXACT [] xref: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site "wiki" is_a: SO:0000139 ! ribosome_entry_site [Term] id: SO:0000244 name: four_cutter_restriction_site synonym: "4-cutter_restriction_site" RELATED [] synonym: "four-cutter_restriction_sit" RELATED [] is_obsolete: true [Term] id: SO:0000245 name: mRNA_by_polyadenylation_status is_obsolete: true [Term] id: SO:0000246 name: polyadenylated def: "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000247 name: mRNA_not_polyadenylated is_obsolete: true [Term] id: SO:0000248 name: sequence_length_variation synonym: "sequence length variation" EXACT [] is_a: SO:1000002 ! substitution [Term] id: SO:0000249 name: six_cutter_restriction_site synonym: "6-cutter_restriction_site" RELATED [] synonym: "six-cutter_restriction_site" RELATED [] is_obsolete: true [Term] id: SO:0000250 name: modified_RNA_base_feature def: "A post_transcriptionally modified base." [SO:ke] synonym: "modified RNA base feature" EXACT [] is_a: SO:0001236 ! base [Term] id: SO:0000251 name: eight_cutter_restriction_site synonym: "8-cutter_restriction_site" RELATED [] synonym: "eight-cutter_restriction_site" RELATED [] is_obsolete: true [Term] id: SO:0000252 name: rRNA def: "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732] subset: SOFA synonym: "ribosomal ribonucleic acid" EXACT [] synonym: "ribosomal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000253 name: tRNA def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "transfer ribonucleic acid" RELATED [] synonym: "transfer RNA" RELATED [] xref: http://en.wikipedia.org/wiki/TRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0000254 name: alanyl_tRNA def: "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke] synonym: "alanyl tRNA" EXACT [] synonym: "alanyl-transfer ribonucleic acid" EXACT [] synonym: "alanyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000211 ! alanine_tRNA_primary_transcript [Term] id: SO:0000255 name: rRNA_small_subunit_primary_transcript def: "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke] synonym: "rRNA small subunit primary transcript" EXACT [] is_a: SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000256 name: asparaginyl_tRNA def: "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke] synonym: "asparaginyl tRNA" EXACT [] synonym: "asparaginyl-transfer ribonucleic acid" EXACT [] synonym: "asparaginyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000213 ! asparagine_tRNA_primary_transcript [Term] id: SO:0000257 name: aspartyl_tRNA def: "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke] synonym: "aspartyl tRNA" EXACT [] synonym: "aspartyl-transfer ribonucleic acid" EXACT [] synonym: "aspartyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000214 ! aspartic_acid_tRNA_primary_transcript [Term] id: SO:0000258 name: cysteinyl_tRNA def: "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke] synonym: "cysteinyl tRNA" EXACT [] synonym: "cysteinyl-transfer ribonucleic acid" EXACT [] synonym: "cysteinyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000215 ! cysteine_tRNA_primary_transcript [Term] id: SO:0000259 name: glutaminyl_tRNA def: "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke] synonym: "glutaminyl tRNA" EXACT [] synonym: "glutaminyl-transfer ribonucleic acid" EXACT [] synonym: "glutaminyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000216 ! glutamic_acid_tRNA_primary_transcript [Term] id: SO:0000260 name: glutamyl_tRNA def: "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke] synonym: "glutamyl tRNA" EXACT [] synonym: "glutamyl-transfer ribonucleic acid" EXACT [] synonym: "glutamyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000217 ! glutamine_tRNA_primary_transcript [Term] id: SO:0000261 name: glycyl_tRNA def: "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke] synonym: "glycyl tRNA" EXACT [] synonym: "glycyl-transfer ribonucleic acid" RELATED [] synonym: "glycyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000218 ! glycine_tRNA_primary_transcript [Term] id: SO:0000262 name: histidyl_tRNA def: "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke] synonym: "histidyl tRNA" EXACT [] synonym: "histidyl-transfer ribonucleic acid" EXACT [] synonym: "histidyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000219 ! histidine_tRNA_primary_transcript [Term] id: SO:0000263 name: isoleucyl_tRNA def: "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke] synonym: "isoleucyl tRNA" EXACT [] synonym: "isoleucyl-transfer ribonucleic acid" EXACT [] synonym: "isoleucyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000220 ! isoleucine_tRNA_primary_transcript [Term] id: SO:0000264 name: leucyl_tRNA def: "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke] synonym: "leucyl tRNA" EXACT [] synonym: "leucyl-transfer ribonucleic acid" EXACT [] synonym: "leucyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000221 ! leucine_tRNA_primary_transcript [Term] id: SO:0000265 name: lysyl_tRNA def: "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke] synonym: "lysyl tRNA" EXACT [] synonym: "lysyl-transfer ribonucleic acid" EXACT [] synonym: "lysyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000222 ! lysine_tRNA_primary_transcript [Term] id: SO:0000266 name: methionyl_tRNA def: "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke] synonym: "methionyl tRNA" EXACT [] synonym: "methionyl-transfer ribonucleic acid" EXACT [] synonym: "methionyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000223 ! methionine_tRNA_primary_transcript [Term] id: SO:0000267 name: phenylalanyl_tRNA def: "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke] synonym: "phenylalanyl tRNA" EXACT [] synonym: "phenylalanyl-transfer ribonucleic acid" EXACT [] synonym: "phenylalanyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000224 ! phenylalanine_tRNA_primary_transcript [Term] id: SO:0000268 name: prolyl_tRNA def: "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke] synonym: "prolyl tRNA" EXACT [] synonym: "prolyl-transfer ribonucleic acid" EXACT [] synonym: "prolyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000225 ! proline_tRNA_primary_transcript [Term] id: SO:0000269 name: seryl_tRNA def: "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke] synonym: "seryl tRNA" EXACT [] synonym: "seryl-transfer ribonucleic acid" RELATED [] synonym: "seryl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000226 ! serine_tRNA_primary_transcript [Term] id: SO:0000270 name: threonyl_tRNA def: "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke] synonym: "threonyl tRNA" EXACT [] synonym: "threonyl-transfer ribonucleic acid" EXACT [] synonym: "threonyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000227 ! threonine_tRNA_primary_transcript [Term] id: SO:0000271 name: tryptophanyl_tRNA def: "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke] synonym: "tryptophanyl tRNA" EXACT [] synonym: "tryptophanyl-transfer ribonucleic acid" EXACT [] synonym: "tryptophanyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000228 ! tryptophan_tRNA_primary_transcript [Term] id: SO:0000272 name: tyrosyl_tRNA def: "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke] synonym: "tyrosyl tRNA" EXACT [] synonym: "tyrosyl-transfer ribonucleic acid" EXACT [] synonym: "tyrosyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000229 ! tyrosine_tRNA_primary_transcript [Term] id: SO:0000273 name: valyl_tRNA def: "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke] synonym: "valyl tRNA" EXACT [] synonym: "valyl-transfer ribonucleic acid" EXACT [] synonym: "valyl-transfer RNA" RELATED [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000230 ! valine_tRNA_primary_transcript [Term] id: SO:0000274 name: snRNA def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "small nuclear RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SnRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000231 ! snRNA_primary_transcript [Term] id: SO:0000275 name: snoRNA def: "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc] subset: SOFA synonym: "small nucleolar RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SnoRNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000276 name: miRNA def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:12592000] subset: SOFA synonym: "micro RNA" EXACT [] synonym: "microRNA" EXACT [] xref: http://en.wikipedia.org/wiki/MiRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA relationship: derives_from SO:0000647 ! miRNA_primary_transcript [Term] id: SO:0000277 name: bound_by_factor def: "An attribute describing a sequence that is bound by another molecule." [SO:ke] comment: Formerly called transcript_by_bound_factor. synonym: "bound by factor" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000278 name: transcript_bound_by_nucleic_acid def: "A transcript that is bound by a nucleic acid." [SO:xp] comment: Formerly called transcript_by_bound_nucleic_acid. synonym: "transcript bound by nucleic acid" EXACT [] is_a: SO:0000673 ! transcript relationship: has_quality SO:0000876 ! bound_by_nucleic_acid [Term] id: SO:0000279 name: transcript_bound_by_protein def: "A transcript that is bound by a protein." [SO:xp] comment: Formerly called transcript_by_bound_protein. synonym: "transcript bound by protein" EXACT [] is_a: SO:0000673 ! transcript relationship: has_quality SO:0000875 ! bound_by_protein [Term] id: SO:0000280 name: engineered_gene def: "A gene that is engineered." [SO:xp] synonym: "engineered gene" EXACT [] is_a: SO:0000704 ! gene is_a: SO:0000804 ! engineered_region relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000281 name: engineered_foreign_gene def: "A gene that is engineered and foreign." [SO:xp] synonym: "engineered foreign gene" EXACT [] is_a: SO:0000280 ! engineered_gene is_a: SO:0000285 ! foreign_gene is_a: SO:0000805 ! engineered_foreign_region relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000282 name: mRNA_with_minus_1_frameshift def: "An mRNA with a minus 1 frameshift." [SO:xp] synonym: "mRNA with minus 1 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift relationship: has_quality SO:0000866 ! minus_1_frameshift [Term] id: SO:0000283 name: engineered_foreign_transposable_element_gene def: "A transposable_element that is engineered and foreign." [SO:xp] synonym: "engineered foreign transposable element gene" EXACT [] is_a: SO:0000111 ! transposable_element_gene is_a: SO:0000281 ! engineered_foreign_gene relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000284 name: type_I_enzyme_restriction_site def: "The recognition site is bipartite and interrupted." [http://www.promega.com] is_obsolete: true [Term] id: SO:0000285 name: foreign_gene def: "A gene that is foreign." [SO:xp] synonym: "foreign gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000286 name: long_terminal_repeat def: "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "direct terminal repeat" RELATED [] synonym: "long terminal repeat" EXACT [] synonym: "LTR" EXACT [] xref: http://en.wikipedia.org/wiki/Long_terminal_repeat "wiki" is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000186 ! LTR_retrotransposon [Term] id: SO:0000287 name: fusion_gene def: "A gene that is a fusion." [SO:xp] synonym: "fusion gene" EXACT [] xref: http://en.wikipedia.org/wiki/Fusion_gene "wiki" is_a: SO:0000704 ! gene relationship: has_quality SO:0000806 ! fusion [Term] id: SO:0000288 name: engineered_fusion_gene def: "A fusion gene that is engineered." [SO:xp] synonym: "engineered fusion gene" EXACT [] is_a: SO:0000280 ! engineered_gene is_a: SO:0000287 ! fusion_gene relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000289 name: microsatellite def: "A repeat_region containing repeat_units (2 to 4 bp) that is repeated multiple times in tandem." [http://www.informatics.jax.org/silver/glossary.shtml] subset: SOFA synonym: "microsatellite locus" EXACT [] synonym: "microsatellite marker" EXACT [] synonym: "VNTR" EXACT [] xref: http://en.wikipedia.org/wiki/Microsatellite "wiki" is_a: SO:0000005 ! satellite_DNA [Term] id: SO:0000290 name: dinucleotide_repeat_microsatellite_feature synonym: "dinucleotide repeat microsatellite" EXACT [] synonym: "dinucleotide repeat microsatellite feature" EXACT [] synonym: "dinucleotide repeat microsatellite locus" EXACT [] synonym: "dinucleotide repeat microsatellite marker" EXACT [] is_a: SO:0000289 ! microsatellite [Term] id: SO:0000291 name: trinucleotide_repeat_microsatellite_feature synonym: "dinucleotide repeat microsatellite marker" RELATED [] synonym: "rinucleotide repeat microsatellite" EXACT [] synonym: "trinucleotide repeat microsatellite feature" EXACT [] synonym: "trinucleotide repeat microsatellite locus" EXACT [] is_a: SO:0000289 ! microsatellite [Term] id: SO:0000292 name: repetitive_element is_obsolete: true [Term] id: SO:0000293 name: engineered_foreign_repetitive_element def: "A repetitive element that is engineered and foreign." [SO:xp] synonym: "engineered foreign repetitive element" EXACT [] is_a: SO:0000657 ! repeat_region is_a: SO:0000805 ! engineered_foreign_region relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000294 name: inverted_repeat def: "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke] subset: SOFA synonym: "inverted repeat" EXACT [] synonym: "inverted repeat sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000295 name: U12_intron def: "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511] comment: May have either GT-AC or AT-AC 5' and 3' boundaries. synonym: "U12 intron" EXACT [] synonym: "U12-dependent intron" EXACT [] is_a: SO:0000662 ! spliceosomal_intron [Term] id: SO:0000296 name: origin_of_replication def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "ori" EXACT [] synonym: "origin of replication" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki" is_a: SO:0001411 ! biological_region relationship: part_of SO:0001235 ! replicon [Term] id: SO:0000297 name: D_loop def: "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "D-loop" EXACT [] synonym: "displacement loop" RELATED [] xref: http://en.wikipedia.org/wiki/D_loop "wiki" is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000298 name: recombination_feature synonym: "recombination feature" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000299 name: specific_recombination_site synonym: "specific recombination site" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000300 name: recombination_feature_of_rearranged_gene synonym: "recombination feature of rearranged gene" EXACT [] is_a: SO:0000299 ! specific_recombination_site [Term] id: SO:0000301 name: vertebrate_immune_system_gene_recombination_feature synonym: "vertebrate immune system gene recombination feature" EXACT [] is_a: SO:0000300 ! recombination_feature_of_rearranged_gene [Term] id: SO:0000302 name: J_gene_recombination_feature def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J gene recombination feature" EXACT [] synonym: "J-RS" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000303 name: clip def: "Part of the primary transcript that is clipped off during processing." [SO:ke] subset: SOFA is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000304 name: type_II_enzyme_restriction_site def: "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." [http://www.promega.com] is_obsolete: true [Term] id: SO:0000305 name: modified_DNA_base def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Modified base:. subset: SOFA synonym: "modified base site" EXACT [] is_a: SO:0001236 ! base is_a: SO:0001720 ! epigenetically_modified_region [Term] id: SO:0000306 name: methylated_DNA_base_feature def: "A nucleotide modified by methylation." [SO:ke] subset: SOFA synonym: "methylated base feature" EXACT [] is_a: SO:0000305 ! modified_DNA_base [Term] id: SO:0000307 name: CpG_island def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd] subset: SOFA synonym: "CG island" EXACT [] synonym: "CpG island" EXACT [] xref: http://en.wikipedia.org/wiki/CpG_island "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000308 name: sequence_feature_locating_method is_obsolete: true [Term] id: SO:0000309 name: computed_feature is_obsolete: true [Term] id: SO:0000310 name: predicted_ab_initio_computation is_obsolete: true [Term] id: SO:0000311 name: computed_feature_by_similarity def: "." [SO:ma] comment: similar to: is_obsolete: true [Term] id: SO:0000312 name: experimentally_determined def: "Attribute to describe a feature that has been experimentally verified." [SO:ke] synonym: "experimentally determined" EXACT [] is_a: SO:0000789 ! validated [Term] id: SO:0000313 name: stem_loop alt_id: SO:0000019 def: "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "RNA_hairpin_loop" EXACT [] synonym: "stem loop" EXACT [] synonym: "stem-loop" EXACT [] xref: http://en.wikipedia.org/wiki/Stem_loop "wiki" is_a: SO:0000122 ! RNA_sequence_secondary_structure [Term] id: SO:0000314 name: direct_repeat def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke] subset: SOFA synonym: "direct repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000315 name: TSS def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] subset: SOFA synonym: "transcription start site" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000316 name: CDS def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] subset: SOFA synonym: "coding sequence" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000317 name: cDNA_clone def: "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "cDNA clone" EXACT [] is_a: SO:0000151 ! clone relationship: has_quality SO:0000756 ! cDNA [Term] id: SO:0000318 name: start_codon def: "First codon to be translated by a ribosome." [SO:ke] subset: SOFA synonym: "initiation codon" EXACT [] synonym: "start codon" EXACT [] xref: http://en.wikipedia.org/wiki/Start_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000319 name: stop_codon def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke] subset: SOFA synonym: "stop codon" EXACT [] xref: http://en.wikipedia.org/wiki/Stop_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000320 name: intronic_splice_enhancer def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke] synonym: "intronic splice enhancer" EXACT [] is_a: SO:0000344 ! splice_enhancer is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000321 name: mRNA_with_plus_1_frameshift def: "An mRNA with a plus 1 frameshift." [SO:ke] synonym: "mRNA with plus 1 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift relationship: has_quality SO:0000868 ! plus_1_frameshift [Term] id: SO:0000322 name: nuclease_hypersensitive_site synonym: "nuclease hypersensitive site" EXACT [] is_a: SO:0000684 ! nuclease_sensitive_site [Term] id: SO:0000323 name: coding_start def: "The first base to be translated into protein." [SO:ke] synonym: "coding start" EXACT [] synonym: "translation initiation site" EXACT [] synonym: "translation start" RELATED [] is_a: SO:0000851 ! CDS_region [Term] id: SO:0000324 name: tag def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke] subset: SOFA is_a: SO:0000696 ! oligo [Term] id: SO:0000325 name: rRNA_large_subunit_primary_transcript def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke] subset: SOFA synonym: "35S rRNA primary transcript" EXACT [] synonym: "rRNA large subunit primary transcript" EXACT [] is_a: SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000326 name: SAGE_tag def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract] subset: SOFA synonym: "SAGE tag" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000327 name: coding_end def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke] synonym: "coding end" EXACT [] synonym: "translation termination site" EXACT [] synonym: "translation_end" EXACT [] is_a: SO:0000851 ! CDS_region [Term] id: SO:0000328 name: microarray_oligo synonym: "microarray oligo" EXACT [] synonym: "microarray oligonucleotide" EXACT [] is_a: SO:0000051 ! probe [Term] id: SO:0000329 name: mRNA_with_plus_2_frameshift def: "An mRNA with a plus 2 frameshift." [SO:xp] synonym: "mRNA with plus 2 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift relationship: has_quality SO:0000869 ! plus_2_framshift [Term] id: SO:0000330 name: conserved_region def: "Region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "conserved region" EXACT [] xref: http://en.wikipedia.org/wiki/Conserved_region "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000331 name: STS def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com] subset: SOFA synonym: "sequence tag site" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000332 name: coding_conserved_region def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "coding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000333 name: exon_junction def: "The boundary between two exons in a processed transcript." [SO:ke] subset: SOFA synonym: "exon junction" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000334 name: nc_conserved_region def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "nc conserved region" EXACT [] synonym: "noncoding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000335 name: mRNA_with_minus_2_frameshift def: "A mRNA with a minus 2 frameshift." [SO:ke] synonym: "mRNA with minus 2 frameshift" EXACT [] is_a: SO:0000108 ! mRNA_with_frameshift relationship: has_quality SO:0000867 ! minus_2_frameshift [Term] id: SO:0000336 name: pseudogene def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] subset: SOFA xref: http://en.wikipedia.org/wiki/Pseudogene "wiki" is_a: SO:0001411 ! biological_region relationship: non_functional_homolog_of SO:0000704 ! gene [Term] id: SO:0000337 name: RNAi_reagent def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd] subset: SOFA synonym: "RNAi reagent" EXACT [] is_a: SO:0000442 ! ds_oligo [Term] id: SO:0000338 name: MITE def: "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083] synonym: "miniature inverted repeat transposable element" EXACT [] is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000339 name: recombination_hotspot def: "A region in a genome which promotes recombination." [SO:rd] synonym: "recombination hotspot" EXACT [] xref: http://en.wikipedia.org/wiki/Recombination_hotspot "wiki" is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000340 name: chromosome def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Chromosome "wiki" is_a: SO:0001235 ! replicon [Term] id: SO:0000341 name: chromosome_band def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma] subset: SOFA synonym: "chromosome band" EXACT [] synonym: "cytoband" EXACT [] synonym: "cytological band" EXACT [] xref: http://en.wikipedia.org/wiki/Cytological_band "wiki" is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000342 name: site_specific_recombination_target_region synonym: "site specific recombination target region" EXACT [] is_a: SO:0000299 ! specific_recombination_site [Term] id: SO:0000343 name: match def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000344 name: splice_enhancer def: "Region of a transcript that regulates splicing." [SO:ke] subset: SOFA synonym: "splice enhancer" EXACT [] is_a: SO:0001056 ! splicing_regulatory_region [Term] id: SO:0000345 name: EST def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "expressed sequence tag" EXACT [] is_a: SO:0000324 ! tag relationship: derives_from SO:0000234 ! mRNA [Term] id: SO:0000346 name: loxP_site synonym: "Cre-recombination target region" RELATED [] synonym: "loxP site" EXACT [] is_a: SO:0000947 ! resolution_site [Term] id: SO:0000347 name: nucleotide_match def: "A match against a nucleotide sequence." [SO:ke] subset: SOFA synonym: "nucleotide match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000348 name: nucleic_acid def: "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb] synonym: "nucleic acid" EXACT [] xref: http://en.wikipedia.org/wiki/Nucleic_acid "wiki" is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000349 name: protein_match def: "A match against a protein sequence." [SO:ke] subset: SOFA synonym: "protein match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000350 name: FRT_site def: "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma] synonym: "FLP recombination target region" EXACT [] synonym: "FRT site" EXACT [] is_a: SO:0000948 ! inversion_site [Term] id: SO:0000351 name: synthetic_sequence def: "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma] synonym: "synthetic sequence" EXACT [] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000352 name: DNA def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb] is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0000353 name: sequence_assembly def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] subset: SOFA synonym: "sequence assembly" EXACT [] xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki" is_a: SO:0001248 ! assembly [Term] id: SO:0000354 name: group_1_intron_homing_endonuclease_target_region def: "A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke] synonym: "group 1 intron homing endonuclease target region" EXACT [] is_a: SO:0000684 ! nuclease_sensitive_site [Term] id: SO:0000355 name: haplotype_block def: "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma] synonym: "haplotype block" EXACT [] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000356 name: RNA def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0000357 name: flanked def: "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000359 name: floxed def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke] xref: http://en.wikipedia.org/wiki/Floxed "wiki" is_a: SO:0000357 ! flanked [Term] id: SO:0000360 name: codon def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Codon "wiki" is_a: SO:0000851 ! CDS_region [Term] id: SO:0000361 name: FRT_flanked def: "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke] synonym: "FRT flanked" EXACT [] is_a: SO:0000357 ! flanked [Term] id: SO:0000362 name: invalidated_by_chimeric_cDNA def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma] synonym: "invalidated by chimeric cDNA" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000363 name: floxed_gene def: "A transgene that is floxed." [SO:xp] synonym: "floxed gene" EXACT [] is_a: SO:0000902 ! transgene relationship: has_quality SO:0000359 ! floxed [Term] id: SO:0000364 name: transposable_element_flanking_region def: "The region of sequence surrounding a transposable element." [SO:ke] synonym: "transposable element flanking region" EXACT [] is_a: SO:0000239 ! flanking_region [Term] id: SO:0000365 name: integron def: "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as] xref: http://en.wikipedia.org/wiki/Integron "wiki" is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000366 name: insertion_site def: "The junction where an insertion occurred." [SO:ke] subset: SOFA synonym: "insertion site" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000367 name: attI_site def: "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as] synonym: "attI site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0000365 ! integron [Term] id: SO:0000368 name: transposable_element_insertion_site def: "The junction in a genome where a transposable_element has inserted." [SO:ke] subset: SOFA synonym: "transposable element insertion site" EXACT [] is_a: SO:0000366 ! insertion_site [Term] id: SO:0000369 name: integrase_coding_region is_obsolete: true [Term] id: SO:0000370 name: small_regulatory_ncRNA def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma] subset: SOFA synonym: "small regulatory ncRNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000371 name: conjugative_transposon def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html] synonym: "conjugative transposon" EXACT [] is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000372 name: enzymatic_RNA def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. subset: SOFA synonym: "enzymatic RNA" EXACT [] is_a: SO:0000673 ! transcript relationship: has_quality SO:0001185 ! enzymatic [Term] id: SO:0000373 name: recombinationally_inverted_gene def: "A recombinationally rearranged gene by inversion." [SO:xp] synonym: "recombinationally inverted gene" EXACT [] is_a: SO:0000456 ! recombinationally_rearranged_gene relationship: has_quality SO:1000036 ! inversion [Term] id: SO:0000374 name: ribozyme def: "An RNA with catalytic activity." [SO:ma] subset: SOFA xref: http://en.wikipedia.org/wiki/Ribozyme "wiki" is_a: SO:0000372 ! enzymatic_RNA relationship: has_quality SO:0001186 ! ribozymic [Term] id: SO:0000375 name: rRNA_5_8S def: "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002] subset: SOFA synonym: "5.8S LSU rRNA" EXACT [] synonym: "5.8S ribosomal RNA" EXACT [] synonym: "5.8S rRNA" EXACT [] synonym: "rRNA 5 8S" EXACT [] xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000376 name: RNA_6S def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013] synonym: "6S RNA" EXACT [] synonym: "RNA 6S" EXACT [] xref: http://en.wikipedia.org/wiki/6S_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000377 name: CsrB_RsmB_RNA def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018] synonym: "CsrB RsmB RNA" EXACT [] synonym: "CsrB-RsmB RNA" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000378 name: DsrA_RNA def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014] synonym: "DsrA RNA" EXACT [] xref: http://en.wikipedia.org/wiki/DsrA_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000379 name: GcvB_RNA def: "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022] synonym: "GcvB RNA" EXACT [] xref: http://en.wikipedia.org/wiki/GcvB_RNA "wiki" is_a: SO:0000378 ! DsrA_RNA [Term] id: SO:0000380 name: hammerhead_ribozyme def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805] subset: SOFA synonym: "hammerhead ribozyme" EXACT [] xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki" is_a: SO:0000715 ! RNA_motif relationship: has_quality SO:0001186 ! ribozymic [Term] id: SO:0000381 name: group_IIA_intron synonym: "group IIA intron" EXACT [] is_a: SO:0000603 ! group_II_intron [Term] id: SO:0000382 name: group_IIB_intron synonym: "group IIB intron" EXACT [] is_a: SO:0000603 ! group_II_intron [Term] id: SO:0000383 name: MicF_RNA def: "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033] synonym: "MicF RNA" EXACT [] xref: http://en.wikipedia.org/wiki/MicF_RNA "wiki" is_a: SO:0000644 ! antisense_RNA [Term] id: SO:0000384 name: OxyS_RNA def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035] synonym: "OxyS RNA" EXACT [] xref: http://en.wikipedia.org/wiki/OxyS_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000385 name: RNase_MRP_RNA def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030] subset: SOFA synonym: "RNase MRP RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000386 name: RNase_P_RNA def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010] subset: SOFA synonym: "RNase P RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000387 name: RprA_RNA def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034] synonym: "RprA RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RprA_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000388 name: RRE_RNA def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036] synonym: "RRE RNA" EXACT [] is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000389 name: spot_42_RNA def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021] synonym: "spot-42 RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Spot_42_RNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000390 name: telomerase_RNA def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025] subset: SOFA synonym: "telomerase RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000391 name: U1_snRNA def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003] subset: SOFA synonym: "small nuclear RNA U1" EXACT [RSC:cb] synonym: "snRNA U1" EXACT [RSC:cb] synonym: "U1 small nuclear RNA" EXACT [RSC:cb] synonym: "U1 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000392 name: U2_snRNA def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004] subset: SOFA synonym: "small nuclear RNA U2" EXACT [RSC:CB] synonym: "snRNA U2" EXACT [RSC:CB] synonym: "U2 small nuclear RNA" EXACT [RSC:CB] synonym: "U2 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000393 name: U4_snRNA def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U4" EXACT [RSC:cb] synonym: "snRNA U4" EXACT [RSC:cb] synonym: "U4 small nuclear RNA" EXACT [RSC:cb] synonym: "U4 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000394 name: U4atac_snRNA def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455] subset: SOFA synonym: "small nuclear RNA U4atac" EXACT [RSC:cb] synonym: "snRNA U4atac" EXACT [RSC:cb] synonym: "U4atac small nuclear RNA" EXACT [RSC:cb] synonym: "U4atac snRNA" EXACT [] is_a: SO:0000274 ! snRNA [Term] id: SO:0000395 name: U5_snRNA def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020] subset: SOFA synonym: "small nuclear RNA U5" EXACT [RSC:cb] synonym: "snRNA U5" EXACT [RSC:cb] synonym: "U5 small nuclear RNA" EXACT [RSC:cb] synonym: "U5 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000396 name: U6_snRNA def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U6" EXACT [RSC:cb] synonym: "snRNA U6" EXACT [RSC:cb] synonym: "U6 small nuclear RNA" EXACT [RSC:cb] synonym: "U6 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000397 name: U6atac_snRNA def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract] subset: SOFA synonym: "snRNA U6atac" EXACT [RSC:cb] synonym: "U6atac small nuclear RNA" EXACT [RSC:cb] synonym: "U6atac snRNA" EXACT [RSC:cb] is_a: SO:0000274 ! snRNA [Term] id: SO:0000398 name: U11_snRNA def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129] subset: SOFA synonym: "small nuclear RNA U11" EXACT [RSC:cb] synonym: "snRNA U11" EXACT [RSC:cb] synonym: "U11 small nuclear RNA" EXACT [RSC:cb] synonym: "U11 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000399 name: U12_snRNA def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007] subset: SOFA synonym: "small nuclear RNA U12" EXACT [RSC:cb] synonym: "snRNA U12" EXACT [RSC:cb] synonym: "U12 small nuclear RNA" EXACT [RSC:cb] synonym: "U12 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000400 name: sequence_attribute def: "An attribute describes a quality of sequence." [SO:ke] synonym: "sequence attribute" EXACT [] [Term] id: SO:0000401 name: gene_attribute synonym: "gene attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000402 name: enhancer_attribute is_obsolete: true [Term] id: SO:0000403 name: U14_snoRNA alt_id: SO:0005839 def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119] comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. subset: SOFA synonym: "small nucleolar RNA U14" EXACT [] synonym: "snoRNA U14" EXACT [] synonym: "U14 small nucleolar RNA" EXACT [] synonym: "U14 snoRNA" EXACT [] is_a: SO:0000593 ! C_D_box_snoRNA relationship: derives_from SO:0005837 ! U14_snoRNA_primary_transcript [Term] id: SO:0000404 name: vault_RNA def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006] subset: SOFA synonym: "vault RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000405 name: Y_RNA def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019] subset: SOFA synonym: "Y RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Y_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000406 name: twintron def: "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908] xref: http://en.wikipedia.org/wiki/Twintron "wiki" is_a: SO:0000188 ! intron [Term] id: SO:0000407 name: rRNA_18S def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "18S ribosomal RNA" EXACT [] synonym: "18S rRNA" EXACT [] synonym: "rRNA 18S" EXACT [] xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki" is_a: SO:0000650 ! small_subunit_rRNA [Term] id: SO:0000408 name: site def: "The interbase position where something (eg an aberration) occurred." [SO:ke] is_obsolete: true [Term] id: SO:0000409 name: binding_site alt_id: BS:00033 def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] comment: See GO:0005488 : binding. subset: biosapiens subset: SOFA synonym: "binding_or_interaction_site" EXACT [] synonym: "site" RELATED [] xref: http://en.wikipedia.org/wiki/Binding_site "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000410 name: protein_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke] comment: See GO:0042277 : peptide binding. subset: SOFA synonym: "protein binding site" EXACT [] is_a: SO:0000409 ! binding_site [Term] id: SO:0000411 name: rescue_region def: "A region that rescues." [SO:xp] synonym: "rescue fragment" EXACT [] synonym: "rescue region" EXACT [] synonym: "rescue segment" RELATED [] is_a: SO:0000695 ! reagent relationship: has_quality SO:0000814 ! rescue [Term] id: SO:0000412 name: restriction_fragment def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke] subset: SOFA synonym: "restriction fragment" EXACT [] xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki" is_a: SO:0000143 ! assembly_component [Term] id: SO:0000413 name: sequence_difference def: "A region where the sequence differs from that of a specified sequence." [SO:ke] subset: SOFA synonym: "sequence difference" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000414 name: invalidated_by_genomic_contamination def: "An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke] synonym: "invalidated by genomic contamination" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000415 name: invalidated_by_genomic_polyA_primed_cDNA def: "An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke] synonym: "invalidated by genomic polyA primed cDNA" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000416 name: invalidated_by_partial_processing def: "An attribute to describe a feature that is invalidated due to partial processing." [SO:ke] synonym: "invalidated by partial processing" EXACT [] is_a: SO:0000790 ! invalidated [Term] id: SO:0000417 name: polypeptide_domain alt_id: BS:00012 alt_id: BS:00134 alt_id: SO:0001069 def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR] comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains. subset: biosapiens synonym: "ca_bind" RELATED BS [uniprot:feature_type] synonym: "DNA_bind" RELATED BS [uniprot:feature_type] synonym: "domain" BROAD BS [uniprot:feature_type] synonym: "np_bind" RELATED BS [uniprot:feature_type] synonym: "polypeptide domain" EXACT [] synonym: "polypeptide_structural_domain" EXACT BS [] synonym: "structural domain" BROAD BS [] synonym: "zn_fing" RELATED BS [uniprot:feature_type] is_a: SO:0001070 ! polypeptide_structural_region is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0000418 name: signal_peptide alt_id: BS:00159 def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence. subset: biosapiens subset: SOFA synonym: "signal" RELATED [uniprot:feature_type] synonym: "signal peptide" EXACT [] synonym: "signal peptide coding sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki" is_a: SO:0001527 ! peptide_localization_signal relationship: part_of SO:0001062 ! propeptide [Term] id: SO:0000419 name: mature_protein_region alt_id: BS:00149 def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb] comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification. subset: biosapiens subset: SOFA synonym: "chain" RELATED [uniprot:feature_type] synonym: "mature peptide" RELATED [] synonym: "mature protein region" EXACT [] is_a: SO:0000839 ! polypeptide_region relationship: part_of SO:0001063 ! immature_peptide_region [Term] id: SO:0000420 name: five_prime_terminal_inverted_repeat synonym: "5' TIR" EXACT [] synonym: "five prime terminal inverted repeat" EXACT [] is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000421 name: three_prime_terminal_inverted_repeat synonym: "3' TIR" EXACT [] synonym: "three prime terminal inverted repeat" EXACT [] is_a: SO:0000481 ! terminal_inverted_repeat [Term] id: SO:0000422 name: U5_LTR_region synonym: "U5 long terminal repeat region" EXACT [] synonym: "U5 LTR region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000423 name: R_LTR_region synonym: "R long terminal repeat region" EXACT [] synonym: "R LTR region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000424 name: U3_LTR_region synonym: "U3 long terminal repeat region" EXACT [] synonym: "U3 LTR region" EXACT [] is_a: SO:0000848 ! LTR_component [Term] id: SO:0000425 name: five_prime_LTR synonym: "5' long terminal repeat" EXACT [] synonym: "5' LTR" EXACT [] synonym: "five prime LTR" EXACT [] is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0000426 name: three_prime_LTR synonym: "3' long terminal repeat" EXACT [] synonym: "3' LTR" EXACT [] synonym: "three prime LTR" EXACT [] is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0000427 name: R_five_prime_LTR_region synonym: "R 5' long term repeat region" EXACT [] synonym: "R five prime LTR region" EXACT [] is_a: SO:0000423 ! R_LTR_region is_a: SO:0000850 ! five_prime_LTR_component [Term] id: SO:0000428 name: U5_five_prime_LTR_region synonym: "U5 5' long terminal repeat region" EXACT [] synonym: "U5 five prime LTR region" EXACT [] is_a: SO:0000422 ! U5_LTR_region is_a: SO:0000850 ! five_prime_LTR_component [Term] id: SO:0000429 name: U3_five_prime_LTR_region synonym: "U3 5' long term repeat region" EXACT [] synonym: "U3 five prime LTR region" EXACT [] is_a: SO:0000424 ! U3_LTR_region is_a: SO:0000850 ! five_prime_LTR_component [Term] id: SO:0000430 name: R_three_prime_LTR_region synonym: "R 3' long terminal repeat region" EXACT [] synonym: "R three prime LTR region" EXACT [] is_a: SO:0000849 ! three_prime_LTR_component [Term] id: SO:0000431 name: U3_three_prime_LTR_region synonym: "U3 3' long terminal repeat region" EXACT [] synonym: "U3 three prime LTR region" EXACT [] is_a: SO:0000849 ! three_prime_LTR_component [Term] id: SO:0000432 name: U5_three_prime_LTR_region synonym: "U5 3' long terminal repeat region" EXACT [] synonym: "U5 three prime LTR region" EXACT [] is_a: SO:0000849 ! three_prime_LTR_component [Term] id: SO:0000433 name: non_LTR_retrotransposon_polymeric_tract def: "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke] synonym: "non LTR retrotransposon polymeric tract" EXACT [] is_a: SO:0000657 ! repeat_region is_a: SO:0000840 ! repeat_component relationship: part_of SO:0000189 ! non_LTR_retrotransposon [Term] id: SO:0000434 name: target_site_duplication def: "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html] synonym: "target site duplication" EXACT [] is_a: SO:0000314 ! direct_repeat relationship: derives_from SO:0000101 ! transposable_element [Term] id: SO:0000435 name: RR_tract def: "A polypurine tract within an LTR_retrotransposon." [SO:ke] synonym: "LTR retrotransposon poly purine tract" RELATED [] synonym: "RR tract" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0000186 ! LTR_retrotransposon [Term] id: SO:0000436 name: ARS def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma] subset: SOFA synonym: "autonomously replicating sequence" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000437 name: assortment_derived_duplication is_obsolete: true [Term] id: SO:0000438 name: gene_not_polyadenylated is_obsolete: true [Term] id: SO:0000439 name: inverted_ring_chromosome synonym: "inverted ring chromosome" EXACT [] is_a: SO:1000030 ! chromosomal_inversion is_a: SO:1000045 ! ring_chromosome [Term] id: SO:0000440 name: vector_replicon def: "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "vector" EXACT [] synonym: "vector replicon" EXACT [] xref: http://en.wikipedia.org/wiki/Vector_(molecular_biology) "wiki" is_a: SO:0001235 ! replicon relationship: part_of SO:0000151 ! clone [Term] id: SO:0000441 name: ss_oligo def: "A single stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "single strand oligo" EXACT [] synonym: "single strand oligonucleotide" EXACT [] synonym: "single stranded oligonucleotide" EXACT [] synonym: "ss oligo" EXACT [] synonym: "ss oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000442 name: ds_oligo def: "A double stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "double stranded oligonucleotide" EXACT [] synonym: "ds oligo" EXACT [] synonym: "ds-oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000443 name: polymer_attribute def: "An attribute to describe the kind of biological sequence." [SO:ke] synonym: "polymer attribute" EXACT [] is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000444 name: three_prime_noncoding_exon def: "Non-coding exon in the 3' UTR." [SO:ke] synonym: "three prime noncoding exon" EXACT [] is_a: SO:0000198 ! noncoding_exon [Term] id: SO:0000445 name: five_prime_noncoding_exon def: "Non-coding exon in the 5' UTR." [SO:ke] synonym: "5' nc exon" EXACT [] synonym: "5' non coding exon" EXACT [] synonym: "five prime noncoding exon" EXACT [] is_a: SO:0000198 ! noncoding_exon [Term] id: SO:0000446 name: UTR_intron def: "Intron located in the untranslated region." [SO:ke] synonym: "UTR intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000447 name: five_prime_UTR_intron def: "An intron located in the 5' UTR." [SO:ke] synonym: "five prime UTR intron" EXACT [] is_a: SO:0000446 ! UTR_intron [Term] id: SO:0000448 name: three_prime_UTR_intron def: "An intron located in the 3' UTR." [SO:ke] synonym: "three prime UTR intron" EXACT [] is_a: SO:0000446 ! UTR_intron [Term] id: SO:0000449 name: random_sequence def: "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components." [SO:ma] synonym: "random sequence" EXACT [] is_a: SO:0000351 ! synthetic_sequence [Term] id: SO:0000450 name: interband def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma] synonym: "chromosome interband" RELATED [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000451 name: gene_with_polyadenylated_mRNA def: "A gene that encodes a polyadenylated mRNA." [SO:xp] synonym: "gene with polyadenylated mRNA" EXACT [] is_a: SO:0001217 ! protein_coding_gene relationship: transcribed_to SO:0000871 ! polyadenylated_mRNA [Term] id: SO:0000452 name: transgene_attribute is_obsolete: true [Term] id: SO:0000453 name: chromosomal_transposition def: "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke] synonym: "chromosomal transposition" EXACT [] synonym: "transposition" NARROW [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:0000454 name: rasiRNA def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284] subset: SOFA synonym: "repeat associated small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RasiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000455 name: gene_with_mRNA_with_frameshift def: "A gene that encodes an mRNA with a frameshift." [SO:xp] synonym: "gene with mRNA with frameshift" EXACT [] is_a: SO:0001217 ! protein_coding_gene relationship: has_quality SO:0000865 ! frameshift [Term] id: SO:0000456 name: recombinationally_rearranged_gene def: "A gene that is recombinationally rearranged." [SO:ke] synonym: "recombinationally rearranged gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000940 ! recombinationally_rearranged [Term] id: SO:0000457 name: interchromosomal_duplication def: "A chromosome duplication involving an insertion from another chromosome." [SO:ke] synonym: "interchromosomal duplication" EXACT [] is_a: SO:1000037 ! chromosomal_duplication [Term] id: SO:0000458 name: D_gene_segment def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D gene" EXACT [] synonym: "D-GENE" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000459 name: gene_with_trans_spliced_transcript def: "A gene with a transcript that is trans-spliced." [SO:xp] synonym: "gene with trans spliced transcript" EXACT [] is_a: SO:0000704 ! gene relationship: transcribed_to SO:0000479 ! trans_spliced_transcript [Term] id: SO:0000460 name: vertebrate_immunoglobulin_T_cell_receptor_segment comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'. synonym: "vertebrate immunoglobulin T cell receptor segment" EXACT [] synonym: "vertebrate_immunoglobulin/T-cell receptor gene" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000461 name: inversion_derived_bipartite_deficiency def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km] synonym: "inversion derived bipartite deficiency" EXACT [] is_a: SO:1000029 ! chromosomal_deletion [Term] id: SO:0000462 name: pseudogenic_region def: "A non-functional descendent of a functional entity." [SO:cjm] subset: SOFA synonym: "pseudogenic region" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000463 name: encodes_alternately_spliced_transcripts def: "A gene that encodes more than one transcript." [SO:ke] synonym: "encodes alternately spliced transcripts" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0000464 name: decayed_exon def: "A non-functional descendant of an exon." [SO:ke] subset: SOFA synonym: "decayed exon" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000147 ! exon [Term] id: SO:0000465 name: inversion_derived_deficiency_plus_duplication def: "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km] synonym: "inversion derived deficiency plus duplication" EXACT [] is_a: SO:1000029 ! chromosomal_deletion is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000466 name: V_gene_segment def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V gene" EXACT [] synonym: "V-GENE" EXACT [] synonym: "variable_gene" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000467 name: post_translationally_regulated_by_protein_stability def: "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke] synonym: "post translationally regulated by protein stability" EXACT [] synonym: "post-translationally regulated by protein stability" EXACT [] is_a: SO:0000130 ! post_translationally_regulated [Term] id: SO:0000468 name: golden_path_fragment def: "One of the pieces of sequence that make up a golden path." [SO:rd] subset: SOFA synonym: "golden path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000688 ! golden_path [Term] id: SO:0000469 name: post_translationally_regulated_by_protein_modification def: "An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke] synonym: "post translationally regulated by protein modification" EXACT [] synonym: "post-translationally regulated by protein modification" EXACT [] is_a: SO:0000130 ! post_translationally_regulated [Term] id: SO:0000470 name: J_gene_segment def: "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J gene" EXACT [] synonym: "J-GENE" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000471 name: autoregulated def: "The gene product is involved in its own transcriptional regulation." [SO:ke] is_a: SO:0000123 ! transcriptionally_regulated [Term] id: SO:0000472 name: tiling_path def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm] subset: SOFA synonym: "tiling path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000473 name: negatively_autoregulated def: "The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke] synonym: "negatively autoregulated" EXACT [] is_a: SO:0000126 ! transcriptionally_repressed is_a: SO:0000471 ! autoregulated [Term] id: SO:0000474 name: tiling_path_fragment def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke] subset: SOFA synonym: "tiling path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000472 ! tiling_path [Term] id: SO:0000475 name: positively_autoregulated def: "The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke] synonym: "positively autoregulated" EXACT [] is_a: SO:0000125 ! transcriptionally_induced is_a: SO:0000471 ! autoregulated [Term] id: SO:0000476 name: contig_read def: "A DNA sequencer read which is part of a contig." [SO:ke] synonym: "contig read" EXACT [] is_a: SO:0000150 ! read [Term] id: SO:0000477 name: polycistronic_gene def: "A gene that is polycistronic." [SO:ke] is_obsolete: true [Term] id: SO:0000478 name: C_gene_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "C gene" EXACT [] synonym: "C_GENE" EXACT [] synonym: "constant gene" EXACT [] is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment [Term] id: SO:0000479 name: trans_spliced_transcript def: "A transcript that is trans-spliced." [SO:xp] synonym: "trans spliced transcript" EXACT [] synonym: "trans-spliced transcript" EXACT [] is_a: SO:0000673 ! transcript relationship: has_quality SO:0000870 ! trans_spliced [Term] id: SO:0000480 name: tiling_path_clone def: "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke] synonym: "tiling path clone" EXACT [] is_a: SO:0000151 ! clone is_a: SO:0000474 ! tiling_path_fragment [Term] id: SO:0000481 name: terminal_inverted_repeat def: "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke] synonym: "terminal inverted repeat" EXACT [] synonym: "TIR" EXACT [] is_a: SO:0000294 ! inverted_repeat relationship: part_of SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000482 name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster synonym: "vertebrate immunoglobulin T cell receptor gene cluster" EXACT [] synonym: "vertebrate_immunoglobulin/T-cell receptor gene cluster" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000483 name: nc_primary_transcript def: "A primary transcript that is never translated into a protein." [SO:ke] subset: SOFA synonym: "nc primary transcript" EXACT [] synonym: "noncoding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000484 name: three_prime_coding_exon_noncoding_region def: "The sequence of the 3' exon that is not coding." [SO:ke] subset: SOFA synonym: "three prime coding exon noncoding region" EXACT [] synonym: "three_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon relationship: part_of SO:0000202 ! three_prime_coding_exon [Term] id: SO:0000485 name: DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(DJ)-J-CLUSTER" EXACT [] synonym: "DJ J cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000486 name: five_prime_coding_exon_noncoding_region def: "The sequence of the 5' exon preceding the start codon." [SO:ke] subset: SOFA synonym: "five prime coding exon noncoding region" EXACT [] synonym: "five_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000487 name: VDJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VDJ)-J-C-CLUSTER" EXACT [] synonym: "VDJ J C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000488 name: VDJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VDJ)-J-CLUSTER" EXACT [] synonym: "VDJ J cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000489 name: VJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VJ)-C-CLUSTER" RELATED [] synonym: "VJ C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000490 name: VJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VJ)-J-C-CLUSTER" EXACT [] synonym: "VJ J C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000491 name: VJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VJ)-J-CLUSTER" EXACT [] synonym: "VJ J cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000492 name: D_gene_recombination_feature synonym: "D gene recombination feature" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000493 name: three_prime_D_heptamer def: "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-HEPTAMER" EXACT [] synonym: "three prime D heptamer" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence [Term] id: SO:0000494 name: three_prime_D_nonamer def: "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-NOMAMER" EXACT [] synonym: "three prime D nonamer" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence [Term] id: SO:0000495 name: three_prime_D_spacer def: "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-SPACER" EXACT [] synonym: "three prime D spacer" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence [Term] id: SO:0000496 name: five_prime_D_heptamer def: "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'D-HEPTAMER" EXACT [] synonym: "five prime D heptamer" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000497 name: five_prime_D_nonamer def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'D-NONAMER" EXACT [] synonym: "five prime D nonamer" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000498 name: five_prime_D_spacer def: "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'-SPACER" EXACT [] synonym: "five prime D spacer" EXACT [] synonym: "five prime D-spacer" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence [Term] id: SO:0000499 name: virtual_sequence def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke] subset: SOFA synonym: "virtual sequence" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000500 name: Hoogsteen_base_pair def: "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293] synonym: "Hoogsteen base pair" EXACT [] xref: http://en.wikipedia.org/wiki/Hoogsteen_base_pair "wiki" is_a: SO:0000028 ! base_pair [Term] id: SO:0000501 name: reverse_Hoogsteen_base_pair def: "A type of non-canonical base-pairing." [SO:ke] synonym: "reverse Hoogsteen base pair" EXACT [] is_a: SO:0000028 ! base_pair [Term] id: SO:0000502 name: transcribed_region def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke] comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being. subset: SOFA is_obsolete: true [Term] id: SO:0000503 name: alternately_spliced_gene_encodeing_one_transcript is_obsolete: true [Term] id: SO:0000504 name: D_DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ C cluster" EXACT [] synonym: "D-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000505 name: D_DJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ cluster" EXACT [] synonym: "D-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000506 name: D_DJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ J C cluster" EXACT [] synonym: "D-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000507 name: pseudogenic_exon def: "A non functional descendant of an exon, part of a pseudogene." [SO:ke] comment: This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. synonym: "pseudogenic exon" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000147 ! exon relationship: part_of SO:0000516 ! pseudogenic_transcript [Term] id: SO:0000508 name: D_DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D DJ J cluster" EXACT [] synonym: "D-(DJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000509 name: D_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D J C cluster" EXACT [] synonym: "D-J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000510 name: VD_gene_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V_D_GENE" EXACT [] synonym: "VD gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000511 name: J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J C cluster" EXACT [] synonym: "J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000512 name: inversion_derived_deficiency_plus_aneuploid def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] synonym: "inversion derived deficiency plus aneuploid" EXACT [] is_a: SO:1000029 ! chromosomal_deletion [Term] id: SO:0000513 name: J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J cluster" EXACT [] synonym: "J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000514 name: J_nonamer def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J nonamer" EXACT [] synonym: "J-NONAMER" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000302 ! J_gene_recombination_feature [Term] id: SO:0000515 name: J_heptamer def: "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J heptamer" EXACT [] synonym: "J-HEPTAMER" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000302 ! J_gene_recombination_feature [Term] id: SO:0000516 name: pseudogenic_transcript def: "A non functional descendant of a transcript, part of a pseudogene." [SO:ke] comment: This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations. synonym: "pseudogenic transcript" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000673 ! transcript relationship: part_of SO:0000336 ! pseudogene [Term] id: SO:0000517 name: J_spacer def: "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "J spacer" EXACT [] synonym: "J-SPACER" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000302 ! J_gene_recombination_feature [Term] id: SO:0000518 name: V_DJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ cluster" EXACT [] synonym: "V-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000519 name: V_DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ J cluster" EXACT [] synonym: "V-(DJ)-J-CLUSTER" RELATED [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000520 name: V_VDJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ C cluster" EXACT [] synonym: "V-(VDJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000521 name: V_VDJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ cluster" EXACT [] synonym: "V-(VDJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000522 name: V_VDJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ J cluster" EXACT [] synonym: "V-(VDJ)-J-CLUSTER" RELATED [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000523 name: V_VJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ C cluster" EXACT [] synonym: "V-(VJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000524 name: V_VJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ cluster" EXACT [] synonym: "V-(VJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000525 name: V_VJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ J cluster" EXACT [] synonym: "V-(VJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000526 name: V_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V cluster" EXACT [] synonym: "V-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment [Term] id: SO:0000527 name: V_D_DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ C cluster" EXACT [] synonym: "V-D-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000528 name: V_D_DJ_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ cluster" EXACT [] synonym: "V-D-(DJ)-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000529 name: V_D_DJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ J C cluster" EXACT [] synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000530 name: V_D_DJ_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D DJ J cluster" EXACT [] synonym: "V-D-(DJ)-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000531 name: V_D_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D J C cluster" EXACT [] synonym: "V-D-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000532 name: V_D_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V D J cluster" EXACT [] synonym: "V-D-J-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000533 name: V_heptamer def: "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V heptamer" EXACT [] synonym: "V-HEPTAMER" EXACT [] is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000538 ! V_gene_recombination_feature [Term] id: SO:0000534 name: V_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V J cluster" EXACT [] synonym: "V-J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000535 name: V_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V J C cluster" EXACT [] synonym: "V-J-C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000536 name: V_nonamer def: "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V nonamer" EXACT [] synonym: "V-NONAMER" EXACT [] is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene relationship: part_of SO:0000538 ! V_gene_recombination_feature [Term] id: SO:0000537 name: V_spacer def: "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V spacer" EXACT [] synonym: "V-SPACER" EXACT [] is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer relationship: part_of SO:0000538 ! V_gene_recombination_feature [Term] id: SO:0000538 name: V_gene_recombination_feature def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V gene recombination feature" EXACT [] synonym: "V-RS" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000539 name: DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(DJ)-C-CLUSTER" EXACT [] synonym: "DJ C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000540 name: DJ_J_C_cluster def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(DJ)-J-C-CLUSTER" EXACT [] synonym: "DJ J C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000541 name: VDJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "(VDJ)-C-CLUSTER" EXACT [] synonym: "VDJ C cluster" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000542 name: V_DJ_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ C cluster" EXACT [] synonym: "V-(DJ)-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000543 name: alternately_spliced_gene_encoding_greater_than_one_transcript is_obsolete: true [Term] id: SO:0000544 name: helitron def: "A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569] synonym: "ISCR" RELATED [] xref: http://en.wikipedia.org/wiki/Helitron "wiki" is_a: SO:0000182 ! DNA_transposon [Term] id: SO:0000545 name: recoding_pseudoknot def: "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937] synonym: "recoding pseudoknot" EXACT [] is_a: SO:0000591 ! pseudoknot relationship: part_of SO:1001268 ! recoding_stimulatory_region [Term] id: SO:0000546 name: designed_sequence synonym: "designed sequence" EXACT [] is_a: SO:0000351 ! synthetic_sequence [Term] id: SO:0000547 name: inversion_derived_bipartite_duplication def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km] synonym: "inversion derived bipartite duplication" EXACT [] is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000548 name: gene_with_edited_transcript def: "A gene that encodes a transcript that is edited." [SO:xp] synonym: "gene with edited transcript" EXACT [] is_a: SO:0001217 ! protein_coding_gene relationship: transcribed_to SO:0000873 ! edited_transcript [Term] id: SO:0000549 name: inversion_derived_duplication_plus_aneuploid def: "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km] synonym: "inversion derived duplication plus aneuploid" EXACT [] is_a: SO:1000038 ! intrachromosomal_duplication [Term] id: SO:0000550 name: aneuploid_chromosome def: "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke] comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila. synonym: "aneuploid chromosome" EXACT [] is_a: SO:1000183 ! chromosome_structure_variation [Term] id: SO:0000551 name: polyA_signal_sequence def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "poly(A) signal" EXACT [] synonym: "polyA signal sequence" EXACT [] synonym: "polyadenylation termination signal" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0000552 name: Shine_Dalgarno_sequence def: "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh] comment: Not found in Eukaryotic sequence. synonym: "five prime ribosome binding site" EXACT [] synonym: "RBS" RELATED [] synonym: "Shine Dalgarno sequence" EXACT [] synonym: "Shine-Dalgarno sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence "wiki" is_a: SO:0000139 ! ribosome_entry_site [Term] id: SO:0000553 name: polyA_site alt_id: SO:0001430 def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "polyA cleavage site" EXACT [] synonym: "polyA junction" EXACT [] synonym: "polyA site" EXACT [] synonym: "polyA_junction" EXACT [] synonym: "polyadenylation site" RELATED [] is_a: SO:0000699 ! junction relationship: part_of SO:0000205 ! three_prime_UTR relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000554 name: assortment_derived_deficiency_plus_duplication is_obsolete: true [Term] id: SO:0000555 name: five_prime_clip def: "5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "5' clip" RELATED [] synonym: "five prime clip" EXACT [] is_a: SO:0000303 ! clip [Term] id: SO:0000556 name: five_prime_D_recombination_signal_sequence def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "5'RS" EXACT [] synonym: "five prime D recombination signal sequence" EXACT [] synonym: "five prime D-recombination signal sequence" EXACT [] is_a: SO:0000492 ! D_gene_recombination_feature [Term] id: SO:0000557 name: three_prime_clip def: "3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] synonym: "3'-clip" EXACT [] synonym: "three prime clip" EXACT [] is_a: SO:0000303 ! clip [Term] id: SO:0000558 name: C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "C cluster" EXACT [] synonym: "C-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000478 ! C_gene_segment [Term] id: SO:0000559 name: D_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D cluster" EXACT [] synonym: "D-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment [Term] id: SO:0000560 name: D_J_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D J cluster" EXACT [] synonym: "D-J-CLUSTER" EXACT [] is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster relationship: has_part SO:0000458 ! D_gene_segment relationship: has_part SO:0000470 ! J_gene_segment [Term] id: SO:0000561 name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene def: "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "HEPTAMER" RELATED [] synonym: "heptamer of recombination feature of vertebrate immune system gene" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000562 name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene synonym: "nonamer of recombination feature of vertebrate immune system gene" EXACT [] is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature [Term] id: SO:0000563 name: vertebrate_immune_system_gene_recombination_spacer synonym: "vertebrate immune system gene recombination spacer" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000564 name: V_DJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V DJ J C cluster" EXACT [] synonym: "V-(DJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000572 ! DJ_gene_segment [Term] id: SO:0000565 name: V_VDJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VDJ J C cluster" EXACT [] synonym: "V-(VDJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000574 ! VDJ_gene_segment [Term] id: SO:0000566 name: V_VJ_J_C_cluster def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V VJ J C cluster" EXACT [] synonym: "V-(VJ)-J-C-CLUSTER" EXACT [] is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster relationship: has_part SO:0000466 ! V_gene_segment relationship: has_part SO:0000470 ! J_gene_segment relationship: has_part SO:0000478 ! C_gene_segment relationship: has_part SO:0000576 ! VJ_gene_segment [Term] id: SO:0000567 name: inversion_derived_aneuploid_chromosome def: "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km] synonym: "inversion derived aneuploid chromosome" EXACT [] is_a: SO:0000550 ! aneuploid_chromosome [Term] id: SO:0000568 name: bidirectional_promoter synonym: "bidirectional promoter" EXACT [] is_a: SO:0000167 ! promoter [Term] id: SO:0000569 name: retrotransposed alt_id: SO:0100042 def: "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke] comment: GO:0003964 RNA-directed DNA polymerase activity. xref: http://en.wikipedia.org/wiki/Retrotransposed "wiki" is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000570 name: three_prime_D_recombination_signal_sequence def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "3'D-RS" EXACT [] synonym: "three prime D recombination signal sequence" EXACT [] synonym: "three_prime_D-recombination_signal_sequence" EXACT [] is_a: SO:0000492 ! D_gene_recombination_feature [Term] id: SO:0000571 name: miRNA_encoding synonym: "miRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000572 name: DJ_gene_segment def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "D-J-GENE" EXACT [] synonym: "DJ gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000573 name: rRNA_encoding synonym: "rRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000574 name: VDJ_gene_segment def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V-D-J-GENE" EXACT [] synonym: "VDJ gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000575 name: scRNA_encoding synonym: "scRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000576 name: VJ_gene_segment def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#] synonym: "V-J-GENE" EXACT [] synonym: "VJ gene" EXACT [] is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment [Term] id: SO:0000577 name: centromere def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Centromere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000578 name: snoRNA_encoding synonym: "snoRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000579 name: edited_transcript_feature def: "A locatable feature on a transcript that is edited." [SO:ma] synonym: "edited transcript feature" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000580 name: methylation_guide_snoRNA_primary_transcript def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke] synonym: "methylation guide snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000581 name: cap def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] subset: SOFA xref: http://en.wikipedia.org/wiki/5%27_cap "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000582 name: rRNA_cleavage_snoRNA_primary_transcript def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke] synonym: "rRNA cleavage snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000583 name: pre_edited_region def: "The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "pre edited region" EXACT [] synonym: "pre-edited region" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000584 name: tmRNA def: "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023] synonym: "10Sa RNA" RELATED [] synonym: "ssrA" RELATED [] xref: http://en.wikipedia.org/wiki/TmRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000585 name: C_D_box_snoRNA_encoding synonym: "C/D box snoRNA encoding" EXACT [] is_a: SO:0000578 ! snoRNA_encoding [Term] id: SO:0000586 name: tmRNA_primary_transcript def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke] synonym: "10Sa RNA primary transcript" RELATED [] synonym: "ssrA RNA primary transcript" RELATED [] synonym: "tmRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000587 name: group_I_intron def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028] comment: GO:0000372. subset: SOFA synonym: "group I intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000588 name: autocatalytically_spliced_intron def: "A self spliced intron." [SO:ke] subset: SOFA synonym: "autocatalytically spliced intron" EXACT [] is_a: SO:0000188 ! intron relationship: has_quality SO:0001186 ! ribozymic [Term] id: SO:0000589 name: SRP_RNA_primary_transcript def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke] synonym: "SRP RNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000590 name: SRP_RNA def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017] subset: SOFA synonym: "7S RNA" RELATED [] synonym: "signal recognition particle RNA" RELATED [] synonym: "SRP RNA" EXACT [] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000589 ! SRP_RNA_primary_transcript [Term] id: SO:0000591 name: pseudoknot def: "A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb] xref: http://en.wikipedia.org/wiki/Pseudoknot "wiki" is_a: SO:0000002 ! sequence_secondary_structure [Term] id: SO:0000592 name: H_pseudoknot def: "A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract] synonym: "classical pseudoknot" EXACT [] synonym: "H pseudoknot" EXACT [] synonym: "H-pseudoknot" EXACT [] synonym: "H-type pseudoknot" EXACT [] synonym: "hairpin-type pseudoknot" EXACT [] is_a: SO:0000591 ! pseudoknot [Term] id: SO:0000593 name: C_D_box_snoRNA def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] subset: SOFA synonym: "box C/D snoRNA" EXACT [] synonym: "C D box snoRNA" EXACT [] synonym: "C/D box snoRNA" EXACT [] is_a: SO:0000275 ! snoRNA relationship: derives_from SO:0000595 ! C_D_box_snoRNA_primary_transcript [Term] id: SO:0000594 name: H_ACA_box_snoRNA def: "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] synonym: "box H/ACA snoRNA" EXACT [] synonym: "H ACA box snoRNA" EXACT [] synonym: "H/ACA box snoRNA" EXACT [] is_a: SO:0000275 ! snoRNA relationship: derives_from SO:0000596 ! H_ACA_box_snoRNA_primary_transcript [Term] id: SO:0000595 name: C_D_box_snoRNA_primary_transcript def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke] synonym: "C/D box snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000596 name: H_ACA_box_snoRNA_primary_transcript def: "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke] synonym: "H ACA box snoRNA primary transcript" EXACT [] is_a: SO:0000232 ! snoRNA_primary_transcript [Term] id: SO:0000597 name: transcript_edited_by_U_insertion/deletion def: "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html] is_obsolete: true [Term] id: SO:0000598 name: edited_by_C_insertion_and_dinucleotide_insertion synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED [] is_obsolete: true [Term] id: SO:0000599 name: edited_by_C_to_U_substitution is_obsolete: true [Term] id: SO:0000600 name: edited_by_A_to_I_substitution is_obsolete: true [Term] id: SO:0000601 name: edited_by_G_addition is_obsolete: true [Term] id: SO:0000602 name: guide_RNA def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html] subset: SOFA synonym: "gRNA" EXACT [] synonym: "guide RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000603 name: group_II_intron def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml] comment: GO:0000373. subset: SOFA synonym: "group II intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000604 name: editing_block def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "editing block" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000605 name: intergenic_region def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "intergenic region" EXACT [] xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000606 name: editing_domain def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "editing domain" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000607 name: unedited_region def: "The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx] synonym: "unedited region" EXACT [] is_a: SO:0000579 ! edited_transcript_feature [Term] id: SO:0000608 name: H_ACA_box_snoRNA_encoding synonym: "H ACA box snoRNA encoding" EXACT [] is_a: SO:0000578 ! snoRNA_encoding [Term] id: SO:0000609 name: oligo_U_tail def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/] synonym: "oligo U tail" EXACT [] is_a: SO:0001411 ! biological_region relationship: adjacent_to SO:0000602 ! guide_RNA [Term] id: SO:0000610 name: polyA_sequence def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] subset: SOFA synonym: "polyA sequence" EXACT [] is_a: SO:0001411 ! biological_region relationship: adjacent_to SO:0000234 ! mRNA [Term] id: SO:0000611 name: branch_site def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke] subset: SOFA synonym: "branch point" EXACT [] synonym: "branch site" EXACT [] synonym: "branch_point" EXACT [] is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000612 name: polypyrimidine_tract def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888] subset: SOFA synonym: "polypyrimidine tract" EXACT [] xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki" is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000613 name: bacterial_RNApol_promoter def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke] synonym: "bacterial RNApol promoter" EXACT [] is_a: SO:0000752 ! gene_group_regulatory_region is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0000614 name: bacterial_terminator def: "A terminator signal for bacterial transcription." [SO:ke] synonym: "bacterial terminator" EXACT [] is_a: SO:0000141 ! terminator is_a: SO:0000752 ! gene_group_regulatory_region [Term] id: SO:0000615 name: terminator_of_type_2_RNApol_III_promoter def: "A terminator signal for RNA polymerase III transcription." [SO:ke] synonym: "terminator of type 2 RNApol III promoter" EXACT [] is_a: SO:0000951 ! eukaryotic_terminator [Term] id: SO:0000616 name: transcription_end_site def: "The base where transcription ends." [SO:ke] subset: SOFA synonym: "transcription end site" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000617 name: RNApol_III_promoter_type_1 synonym: "RNApol III promoter type 1" EXACT [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000618 name: RNApol_III_promoter_type_2 synonym: "RNApol III promoter type 2" EXACT [] synonym: "tRNA promoter" RELATED [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000619 name: A_box def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke] comment: Binds TFIIIC. synonym: "A-box" EXACT [] xref: http://en.wikipedia.org/wiki/A-box "wiki" is_a: SO:0001660 ! core_promoter_element [Term] id: SO:0000620 name: B_box def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke] comment: Binds TFIIIC. synonym: "B-box" EXACT [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 [Term] id: SO:0000621 name: RNApol_III_promoter_type_3 synonym: "RNApol III promoter type 3" EXACT [] is_a: SO:0000171 ! RNApol_III_promoter [Term] id: SO:0000622 name: C_box def: "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke] synonym: "C-box" EXACT [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 [Term] id: SO:0000623 name: snRNA_encoding synonym: "snRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000624 name: telomere def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma] subset: SOFA synonym: "telomeric DNA" EXACT [] synonym: "telomeric sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Telomere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000625 name: silencer def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki" is_a: SO:0000727 ! CRM [Term] id: SO:0000626 name: chromosomal_regulatory_element synonym: "chromosomal regulatory element" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000627 name: insulator def: "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative] subset: SOFA synonym: "insulator element" EXACT [] xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000628 name: chromosomal_structural_element subset: SOFA synonym: "chromosomal structural element" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000629 name: five_prime_open_reading_frame synonym: "five prime open reading frame" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000204 ! five_prime_UTR [Term] id: SO:0000630 name: upstream_AUG_codon def: "A start codon upstream of the ORF." [SO:ke] synonym: "upstream AUG codon" EXACT [] is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000203 ! UTR [Term] id: SO:0000631 name: polycistronic_primary_transcript def: "A primary transcript encoding for more than one gene product." [SO:ke] synonym: "polycistronic primary transcript" EXACT [] is_a: SO:0000078 ! polycistronic_transcript is_a: SO:0000185 ! primary_transcript relationship: has_quality SO:0000880 ! polycistronic [Term] id: SO:0000632 name: monocistronic_primary_transcript def: "A primary transcript encoding for one gene product." [SO:ke] synonym: "monocistronic primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript is_a: SO:0000665 ! monocistronic_transcript relationship: has_quality SO:0000878 ! monocistronic [Term] id: SO:0000633 name: monocistronic_mRNA def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd] synonym: "monocistronic mRNA" EXACT [] synonym: "monocistronic processed transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA "wiki" is_a: SO:0000234 ! mRNA is_a: SO:0000665 ! monocistronic_transcript relationship: has_quality SO:0000878 ! monocistronic [Term] id: SO:0000634 name: polycistronic_mRNA def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd] synonym: "polycistronic mRNA" EXACT [] synonym: "polycistronic processed transcript" RELATED [] xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA "wiki" is_a: SO:0000078 ! polycistronic_transcript is_a: SO:0000234 ! mRNA relationship: has_quality SO:0000880 ! polycistronic [Term] id: SO:0000635 name: mini_exon_donor_RNA def: "A primary transcript that donates the spliced leader to other mRNA." [SO:ke] synonym: "mini exon donor RNA" EXACT [] synonym: "mini-exon donor RNA" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000636 name: spliced_leader_RNA synonym: "mini-exon" RELATED [] synonym: "spliced leader RNA" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000635 ! mini_exon_donor_RNA [Term] id: SO:0000637 name: engineered_plasmid def: "A plasmid that is engineered." [SO:xp] synonym: "engineered plasmid" EXACT [] synonym: "engineered plasmid gene" RELATED [] is_a: SO:0000155 ! plasmid is_a: SO:0000804 ! engineered_region relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000638 name: transcribed_spacer_region def: "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html] synonym: "transcribed spacer region" EXACT [] is_a: SO:0000838 ! rRNA_primary_transcript_region [Term] id: SO:0000639 name: internal_transcribed_spacer_region def: "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke] synonym: "internal transcribed spacer region" EXACT [] is_a: SO:0000638 ! transcribed_spacer_region [Term] id: SO:0000640 name: external_transcribed_spacer_region def: "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke] synonym: "external transcribed spacer region" EXACT [] is_a: SO:0000638 ! transcribed_spacer_region [Term] id: SO:0000641 name: tetranucleotide_repeat_microsatellite_feature synonym: "tetranucleotide repeat microsatellite feature" EXACT [] is_a: SO:0000289 ! microsatellite [Term] id: SO:0000642 name: SRP_RNA_encoding synonym: "SRP RNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000643 name: minisatellite def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml] subset: SOFA xref: http://en.wikipedia.org/wiki/Minisatellite "wiki" is_a: SO:0000005 ! satellite_DNA [Term] id: SO:0000644 name: antisense_RNA def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke] subset: SOFA synonym: "antisense RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000645 ! antisense_primary_transcript [Term] id: SO:0000645 name: antisense_primary_transcript def: "The reverse complement of the primary transcript." [SO:ke] subset: SOFA synonym: "antisense primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000646 name: siRNA def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000] subset: SOFA synonym: "small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000647 name: miRNA_primary_transcript def: "A primary transcript encoding a micro RNA." [SO:ke] synonym: "micro RNA primary transcript" EXACT [] synonym: "miRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000648 name: stRNA_primary_transcript def: "A primary transcript encoding a small temporal mRNA (SO:0000649)." [SO:ke] synonym: "small temporal RNA primary transcript" EXACT [] synonym: "stRNA primary transcript" EXACT [] is_a: SO:0000647 ! miRNA_primary_transcript [Term] id: SO:0000649 name: stRNA def: "Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512] subset: SOFA synonym: "small temporal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/StRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000650 name: small_subunit_rRNA def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "small subunit rRNA" EXACT [] synonym: "SSU RNA" EXACT [RSC:cb] synonym: "SSU rRNA" EXACT [RSC:cb] is_a: SO:0000252 ! rRNA relationship: derives_from SO:0000255 ! rRNA_small_subunit_primary_transcript [Term] id: SO:0000651 name: large_subunit_rRNA def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke] subset: SOFA synonym: "large subunit rRNA" EXACT [] synonym: "LSU RNA" EXACT [RSC:cb] synonym: "LSU rRNA" EXACT [RSC:cb] is_a: SO:0000252 ! rRNA relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript [Term] id: SO:0000652 name: rRNA_5S def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001] subset: SOFA synonym: "5S LSU rRNA" EXACT [] synonym: "5S ribosomal RNA" EXACT [] synonym: "5S rRNA" EXACT [] synonym: "rRNA 5S" EXACT [] xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000653 name: rRNA_28S def: "A component of the large ribosomal subunit." [SO:ke] subset: SOFA synonym: "28S LSU rRNA" EXACT [] synonym: "28S ribosomal RNA" EXACT [] synonym: "28S rRNA" EXACT [] synonym: "rRNA 28S" EXACT [] xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000654 name: maxicircle_gene def: "A mitochondrial gene located in a maxicircle." [SO:xp] synonym: "maxi-circle gene" EXACT [] synonym: "maxicircle gene" EXACT [] is_a: SO:0000089 ! kinetoplast_gene relationship: part_of SO:0000742 ! maxicircle [Term] id: SO:0000655 name: ncRNA def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. subset: SOFA synonym: "noncoding RNA" EXACT [] xref: http://en.wikipedia.org/wiki/NcRNA "wiki" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000656 name: stRNA_encoding synonym: "stRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000657 name: repeat_region def: "A region of sequence containing one or more repeat units." [SO:ke] subset: SOFA synonym: "repeat region" EXACT [] is_a: SO:0001411 ! biological_region relationship: has_part SO:0000726 ! repeat_unit [Term] id: SO:0000658 name: dispersed_repeat def: "A repeat that is located at dispersed sites in the genome." [SO:ke] subset: SOFA synonym: "dispersed repeat" EXACT [] synonym: "interspersed repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000659 name: tmRNA_encoding synonym: "tmRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000660 name: DNA_invertase_target_sequence is_obsolete: true [Term] id: SO:0000661 name: intron_attribute is_obsolete: true [Term] id: SO:0000662 name: spliceosomal_intron def: "An intron which is spliced by the spliceosome." [SO:ke] comment: GO:0000398. subset: SOFA synonym: "spliceosomal intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000663 name: tRNA_encoding synonym: "tRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000664 name: introgressed_chromosome_region synonym: "introgressed chromosome region" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000665 name: monocistronic_transcript def: "A transcript that is monocistronic." [SO:xp] synonym: "monocistronic transcript" EXACT [] is_a: SO:0000673 ! transcript relationship: has_quality SO:0000878 ! monocistronic [Term] id: SO:0000666 name: mobile_intron def: "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke] synonym: "mobile intron" EXACT [] is_a: SO:0000188 ! intron is_a: SO:0001037 ! mobile_genetic_element relationship: has_quality SO:0001234 ! mobile [Term] id: SO:0000667 name: insertion alt_id: SO:1000034 def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] subset: DBVAR subset: SOFA synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "nucleotide insertion" EXACT [] synonym: "nucleotide_insertion" EXACT [] xref: loinc:LA6687-3 "Insertion" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:0000668 name: EST_match def: "A match against an EST sequence." [SO:ke] subset: SOFA synonym: "EST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000669 name: sequence_rearrangement_feature synonym: "sequence rearrangement feature" EXACT [] is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000670 name: chromosome_breakage_sequence def: "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma] synonym: "chromosome breakage sequence" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000671 name: internal_eliminated_sequence def: "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma] synonym: "internal eliminated sequence" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000672 name: macronucleus_destined_segment def: "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma] synonym: "macronucleus destined segment" EXACT [] is_a: SO:0000669 ! sequence_rearrangement_feature [Term] id: SO:0000673 name: transcript def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] subset: SOFA xref: http://en.wikipedia.org/wiki/RNA "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0000674 name: non_canonical_splice_site def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke] synonym: "non canonical splice site" EXACT [] synonym: "non-canonical splice site" EXACT [] is_obsolete: true consider: SO:0000678 consider: SO:0000679 [Term] id: SO:0000675 name: canonical_splice_site def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke] synonym: "canonical splice site" EXACT [] is_obsolete: true consider: SO:0000676 consider: SO:0000677 [Term] id: SO:0000676 name: canonical_three_prime_splice_site def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke] synonym: "canonical 3' splice site" EXACT [] synonym: "canonical three prime splice site" EXACT [] is_a: SO:0000164 ! three_prime_cis_splice_site [Term] id: SO:0000677 name: canonical_five_prime_splice_site def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke] synonym: "canonical 5' splice site" EXACT [] synonym: "canonical five prime splice site" EXACT [] is_a: SO:0000163 ! five_prime_cis_splice_site [Term] id: SO:0000678 name: non_canonical_three_prime_splice_site def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke] synonym: "non canonical 3' splice site" RELATED [] synonym: "non canonical three prime splice site" EXACT [] synonym: "non-canonical three prime splice site" EXACT [] is_a: SO:0000164 ! three_prime_cis_splice_site [Term] id: SO:0000679 name: non_canonical_five_prime_splice_site def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke] synonym: "non canonical 5' splice site" EXACT [] synonym: "non canonical five prime splice site" EXACT [] synonym: "non-canonical five prime splice site" EXACT [] is_a: SO:0000163 ! five_prime_cis_splice_site [Term] id: SO:0000680 name: non_canonical_start_codon def: "A start codon that is not the usual AUG sequence." [SO:ke] synonym: "non ATG start codon" EXACT [] synonym: "non canonical start codon" EXACT [] synonym: "non-canonical start codon" EXACT [] is_a: SO:0000318 ! start_codon [Term] id: SO:0000681 name: aberrant_processed_transcript def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke] synonym: "aberrant processed transcript" EXACT [] is_a: SO:0000673 ! transcript [Term] id: SO:0000682 name: splicing_feature is_obsolete: true [Term] id: SO:0000683 name: exonic_splice_enhancer def: "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract] synonym: "exonic splice enhancer" EXACT [] is_a: SO:0000344 ! splice_enhancer [Term] id: SO:0000684 name: nuclease_sensitive_site def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma] subset: SOFA synonym: "nuclease sensitive site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0000685 name: DNAseI_hypersensitive_site synonym: "DHS" EXACT [] synonym: "DNAseI hypersensitive site" EXACT [] is_a: SO:0000322 ! nuclease_hypersensitive_site [Term] id: SO:0000686 name: translocation_element def: "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma] synonym: "translocation element" EXACT [] is_a: SO:1000044 ! chromosomal_translocation [Term] id: SO:0000687 name: deletion_junction def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke] subset: SOFA synonym: "deletion junction" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000688 name: golden_path def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls] subset: SOFA synonym: "golden path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000689 name: cDNA_match def: "A match against cDNA sequence." [SO:ke] subset: SOFA synonym: "cDNA match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000690 name: gene_with_polycistronic_transcript def: "A gene that encodes a polycistronic transcript." [SO:xp] synonym: "gene with polycistronic transcript" EXACT [] is_a: SO:0000704 ! gene relationship: transcribed_to SO:0000078 ! polycistronic_transcript [Term] id: SO:0000691 name: cleaved_initiator_methionine alt_id: BS:00067 def: "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR] subset: biosapiens synonym: "cleaved initiator methionine" EXACT [] synonym: "init_met" RELATED [uniprot:feature_type] synonym: "initiator methionine" RELATED [] is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0000692 name: gene_with_dicistronic_transcript def: "A gene that encodes a dicistronic transcript." [SO:xp] synonym: "gene with dicistronic transcript" EXACT [] is_a: SO:0000690 ! gene_with_polycistronic_transcript relationship: transcribed_to SO:0000079 ! dicistronic_transcript [Term] id: SO:0000693 name: gene_with_recoded_mRNA def: "A gene that encodes an mRNA that is recoded." [SO:xp] synonym: "gene with recoded mRNA" EXACT [] is_a: SO:0001217 ! protein_coding_gene relationship: has_quality SO:0000881 ! recoded [Term] id: SO:0000694 name: SNP def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb] subset: SOFA synonym: "single nucleotide polymorphism" EXACT [] is_a: SO:0001483 ! SNV [Term] id: SO:0000695 name: reagent def: "A sequence used in experiment." [SO:ke] comment: Requested by Lynn Crosby, jan 2006. subset: SOFA is_a: SO:0001409 ! biomaterial_region [Term] id: SO:0000696 name: oligo def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] subset: SOFA synonym: "oligonucleotide" EXACT [] xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000697 name: gene_with_stop_codon_read_through def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp] synonym: "gene with stop codon read through" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA relationship: has_part SO:0000883 ! stop_codon_read_through [Term] id: SO:0000698 name: gene_with_stop_codon_redefined_as_pyrrolysine def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp] synonym: "gene with stop codon redefined as pyrrolysine" EXACT [] is_a: SO:0000697 ! gene_with_stop_codon_read_through relationship: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine [Term] id: SO:0000699 name: junction def: "A sequence_feature with an extent of zero." [SO:ke] comment: A junction is a boundary between regions. A boundary has an extent of zero. subset: SOFA synonym: "boundary" EXACT [] synonym: "breakpoint" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0000700 name: remark def: "A comment about the sequence." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000701 name: possible_base_call_error def: "A region of sequence where the validity of the base calling is questionable." [SO:ke] subset: SOFA synonym: "possible base call error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000702 name: possible_assembly_error def: "A region of sequence where there may have been an error in the assembly." [SO:ke] subset: SOFA synonym: "possible assembly error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000703 name: experimental_result_region def: "A region of sequence implicated in an experimental result." [SO:ke] subset: SOFA synonym: "experimental result region" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000704 name: gene def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. subset: SOFA xref: http://en.wikipedia.org/wiki/Gene "wiki" is_a: SO:0001411 ! biological_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000705 name: tandem_repeat def: "Two or more adjcent copies of a region (of length greater than 1)." [SO:ke] subset: SOFA synonym: "tandem repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki" xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html is_a: SO:0000657 ! repeat_region [Term] id: SO:0000706 name: trans_splice_acceptor_site def: "The 3' splice site of the acceptor primary transcript." [SO:ke] comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans. subset: SOFA synonym: "3' trans splice site" RELATED [] synonym: "trans splice acceptor site" EXACT [] is_a: SO:0001420 ! trans_splice_site [Term] id: SO:0000707 name: trans_splice_donor_site def: "The 5' five prime splice site region of the donor RNA." [SO:ke] comment: SL RNA contains a donor site. synonym: "5 prime trans splice site" RELATED [] synonym: "trans splice donor site" EXACT [] synonym: "trans-splice donor site" EXACT [] is_a: SO:0001420 ! trans_splice_site [Term] id: SO:0000708 name: SL1_acceptor_site def: "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw] synonym: "SL1 acceptor site" EXACT [] is_a: SO:0000706 ! trans_splice_acceptor_site [Term] id: SO:0000709 name: SL2_acceptor_site def: "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw] synonym: "SL2 acceptor site" EXACT [] is_a: SO:0000706 ! trans_splice_acceptor_site [Term] id: SO:0000710 name: gene_with_stop_codon_redefined_as_selenocysteine def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp] synonym: "gene with stop codon redefined as selenocysteine" EXACT [] is_a: SO:0000697 ! gene_with_stop_codon_read_through relationship: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine [Term] id: SO:0000711 name: gene_with_mRNA_recoded_by_translational_bypass def: "A gene with mRNA recoded by translational bypass." [SO:xp] synonym: "gene with mRNA recoded by translational bypass" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA relationship: has_quality SO:0000886 ! recoded_by_translational_bypass [Term] id: SO:0000712 name: gene_with_transcript_with_translational_frameshift def: "A gene encoding a transcript that has a translational frameshift." [SO:xp] synonym: "gene with transcript with translational frameshift" EXACT [] is_a: SO:0000693 ! gene_with_recoded_mRNA relationship: has_quality SO:0000887 ! translationally_frameshifted [Term] id: SO:0000713 name: DNA_motif def: "A motif that is active in the DNA form of the sequence." [SO:ke] synonym: "DNA motif" EXACT [] xref: http://en.wikipedia.org/wiki/DNA_motif "wiki" is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000714 name: nucleotide_motif def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke] subset: SOFA synonym: "nucleotide motif" EXACT [] is_a: SO:0001683 ! sequence_motif [Term] id: SO:0000715 name: RNA_motif def: "A motif that is active in RNA sequence." [SO:ke] subset: SOFA synonym: "RNA motif" EXACT [] is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000716 name: dicistronic_mRNA def: "An mRNA that has the quality dicistronic." [SO:ke] synonym: "dicistronic mRNA" EXACT [] synonym: "dicistronic processed transcript" RELATED [] is_a: SO:0000079 ! dicistronic_transcript is_a: SO:0000634 ! polycistronic_mRNA relationship: has_quality SO:0000879 ! dicistronic [Term] id: SO:0000717 name: reading_frame def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb] comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop. subset: SOFA synonym: "reading frame" EXACT [] xref: http://en.wikipedia.org/wiki/Reading_frame "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000718 name: blocked_reading_frame def: "A reading_frame that is interrupted by one or more stop codons; usually identified through intergenomic sequence comparisons." [SGD:rb] comment: Term requested by Rama from SGD. synonym: "blocked reading frame" EXACT [] is_a: SO:0000717 ! reading_frame [Term] id: SO:0000719 name: ultracontig def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG] subset: SOFA synonym: "superscaffold" RELATED [] is_a: SO:0001876 ! partial_genomic_sequence_assembly [Term] id: SO:0000720 name: foreign_transposable_element def: "A transposable element that is foreign." [SO:ke] comment: requested by Michael on 19 Nov 2004. synonym: "foreign transposable element" EXACT [] is_a: SO:0000101 ! transposable_element relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000721 name: gene_with_dicistronic_primary_transcript def: "A gene that encodes a dicistronic primary transcript." [SO:xp] comment: Requested by Michael, 19 nov 2004. synonym: "gene with dicistronic primary transcript" EXACT [] is_a: SO:0000692 ! gene_with_dicistronic_transcript relationship: transcribed_to SO:1001197 ! dicistronic_primary_transcript [Term] id: SO:0000722 name: gene_with_dicistronic_mRNA def: "A gene that encodes a polycistronic mRNA." [SO:xp] comment: Requested by MA nov 19 2004. synonym: "gene with dicistronic mRNA" EXACT [] synonym: "gene with dicistronic processed transcript" EXACT [] is_a: SO:0000692 ! gene_with_dicistronic_transcript relationship: transcribed_to SO:0000716 ! dicistronic_mRNA [Term] id: SO:0000723 name: iDNA def: "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma] synonym: "intervening DNA" EXACT [] xref: http://en.wikipedia.org/wiki/IDNA "wiki" is_a: SO:0000298 ! recombination_feature [Term] id: SO:0000724 name: oriT def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "origin of transfer" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki" is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000725 name: transit_peptide alt_id: BS:00055 def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Added to bring SO inline with the embl ddbj genbank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle. subset: biosapiens subset: SOFA synonym: "signal" RELATED [] synonym: "transit" RELATED [uniprot:feature_type] synonym: "transit peptide" EXACT [] is_a: SO:0001527 ! peptide_localization_signal [Term] id: SO:0000726 name: repeat_unit def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke] comment: Added to comply with the feature table. A single repeat. synonym: "repeat unit" EXACT [] xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html is_a: SO:0001411 ! biological_region [Term] id: SO:0000727 name: CRM def: "A regulatory_region where more than 1 TF_binding_site together are regulatorily active." [SO:SG] comment: Requested by Stepen Grossmann Dec 2004. subset: SOFA synonym: "cis regulatory module" EXACT [] synonym: "TF module" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region relationship: has_part SO:0000235 ! TF_binding_site [Term] id: SO:0000728 name: intein def: "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke] comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein. synonym: "protein intron" RELATED [] xref: http://en.wikipedia.org/wiki/Intein "wiki" is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0000729 name: intein_containing def: "An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke] synonym: "intein containing" EXACT [] is_a: SO:0000010 ! protein_coding [Term] id: SO:0000730 name: gap def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke] subset: SOFA is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000353 ! sequence_assembly [Term] id: SO:0000731 name: fragmentary def: "An attribute to describe a feature that is incomplete." [SO:ke] comment: Term added because of request by MO people. synonym: "fragment" EXACT [] is_a: SO:0000905 ! status [Term] id: SO:0000732 name: predicted def: "An attribute describing an unverified region." [SO:ke] xref: http://en.wikipedia.org/wiki/Predicted "wiki" is_a: SO:0000905 ! status [Term] id: SO:0000733 name: feature_attribute def: "An attribute describing a located_sequence_feature." [SO:ke] synonym: "feature attribute" EXACT [] is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000734 name: exemplar_mRNA def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php] comment: Added for the MO people. synonym: "exemplar mRNA" EXACT [] is_a: SO:0000234 ! mRNA relationship: has_quality SO:0000864 ! exemplar [Term] id: SO:0000735 name: sequence_location synonym: "sequence location" EXACT [] is_a: SO:0000400 ! sequence_attribute [Term] id: SO:0000736 name: organelle_sequence synonym: "organelle sequence" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000737 name: mitochondrial_sequence comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "mitochondrial sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000738 name: nuclear_sequence synonym: "nuclear sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000739 name: nucleomorphic_sequence synonym: "nucleomorphic sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000740 name: plastid_sequence synonym: "plastid sequence" EXACT [] is_a: SO:0000736 ! organelle_sequence [Term] id: SO:0000741 name: kinetoplast alt_id: SO:0000826 def: "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxi circles, located near the base of the flagellum of some protozoan species." [PMID:8395055] synonym: "kinetoplast_chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/Kinetoplast "wiki" is_a: SO:0001026 ! genome relationship: has_part SO:0000742 ! maxicircle relationship: has_part SO:0000980 ! minicircle [Term] id: SO:0000742 name: maxicircle alt_id: SO:0000827 def: "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055] synonym: "maxicircle_chromosome" EXACT [] is_a: SO:0001235 ! replicon [Term] id: SO:0000743 name: apicoplast_sequence synonym: "apicoplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000744 name: chromoplast_sequence synonym: "chromoplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000745 name: chloroplast_sequence synonym: "chloroplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000746 name: cyanelle_sequence synonym: "cyanelle sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000747 name: leucoplast_sequence synonym: "leucoplast sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000748 name: proplastid_sequence synonym: "proplastid sequence" EXACT [] is_a: SO:0000740 ! plastid_sequence [Term] id: SO:0000749 name: plasmid_location synonym: "plasmid location" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000750 name: amplification_origin def: "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma] synonym: "amplification origin" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000751 name: proviral_location synonym: "proviral location" EXACT [] is_a: SO:0000735 ! sequence_location [Term] id: SO:0000752 name: gene_group_regulatory_region subset: SOFA synonym: "gene group regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000753 name: clone_insert def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke] subset: SOFA synonym: "clone insert" EXACT [] is_a: SO:0000695 ! reagent relationship: part_of SO:0000151 ! clone [Term] id: SO:0000754 name: lambda_vector def: "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8] synonym: "lambda vector" EXACT [] is_a: SO:0000440 ! vector_replicon [Term] id: SO:0000755 name: plasmid_vector synonym: "plasmid vector" EXACT [] xref: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors "wiki" is_a: SO:0000440 ! vector_replicon relationship: derives_from SO:0000155 ! plasmid [Term] id: SO:0000756 name: cDNA def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma] synonym: "complementary DNA" EXACT [] xref: http://en.wikipedia.org/wiki/CDNA "wiki" is_a: SO:0000352 ! DNA [Term] id: SO:0000757 name: single_stranded_cDNA synonym: "single strand cDNA" EXACT [] synonym: "single stranded cDNA" EXACT [] synonym: "single-strand cDNA" RELATED [] is_a: SO:0000756 ! cDNA [Term] id: SO:0000758 name: double_stranded_cDNA synonym: "double strand cDNA" RELATED [] synonym: "double stranded cDNA" EXACT [] synonym: "double-strand cDNA" RELATED [] is_a: SO:0000756 ! cDNA [Term] id: SO:0000759 name: plasmid_clone is_obsolete: true [Term] id: SO:0000760 name: YAC_clone is_obsolete: true [Term] id: SO:0000761 name: phagemid_clone is_obsolete: true [Term] id: SO:0000762 name: PAC_clone synonym: "P1_clone" RELATED [] is_obsolete: true [Term] id: SO:0000763 name: fosmid_clone is_obsolete: true [Term] id: SO:0000764 name: BAC_clone is_obsolete: true [Term] id: SO:0000765 name: cosmid_clone is_obsolete: true [Term] id: SO:0000766 name: pyrrolysyl_tRNA def: "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke] synonym: "pyrrolysyl tRNA" EXACT [] synonym: "pyrrolysyl-transfer ribonucleic acid" EXACT [] synonym: "pyrrolysyl-transfer RNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0001178 ! pyrrolysine_tRNA_primary_transcript [Term] id: SO:0000767 name: clone_insert_start is_obsolete: true [Term] id: SO:0000768 name: episome def: "A plasmid that may integrate with a chromosome." [SO:ma] is_a: SO:0000155 ! plasmid [Term] id: SO:0000769 name: tmRNA_coding_piece def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962] comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005. synonym: "tmRNA coding piece" EXACT [] is_a: SO:0000847 ! tmRNA_region [Term] id: SO:0000770 name: tmRNA_acceptor_piece def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw] comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005. synonym: "tmRNA acceptor piece" EXACT [] is_a: SO:0000847 ! tmRNA_region [Term] id: SO:0000771 name: QTL def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/] comment: Added in respose to request by Simon Twigger November 14th 2005. synonym: "quantitative trait locus" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000772 name: genomic_island def: "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke] comment: Genomic islands are transmissible elements characterized by large size (>10kb). synonym: "genomic island" EXACT [] xref: http://en.wikipedia.org/wiki/Genomic_island "wiki" is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0000773 name: pathogenic_island def: "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke] comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. synonym: "pathogenic island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000774 name: metabolic_island def: "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands. synonym: "metabolic island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000775 name: adaptive_island def: "An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke] comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker. synonym: "adaptive island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000776 name: symbiosis_island def: "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke] comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149. synonym: "symbiosis island" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0000777 name: pseudogenic_rRNA def: "A non functional descendent of an rRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "pseudogenic rRNA" EXACT [] is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0000778 name: pseudogenic_tRNA def: "A non functional descendent of a tRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "pseudogenic tRNA" EXACT [] is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0000779 name: engineered_episome def: "An episome that is engineered." [SO:xp] comment: Requested by Lynn Crosby Jan 2006. synonym: "engineered episome" EXACT [] is_a: SO:0000637 ! engineered_plasmid is_a: SO:0000768 ! episome relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000780 name: transposable_element_attribute comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs is_obsolete: true [Term] id: SO:0000781 name: transgenic def: "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000782 name: natural def: "An attribute describing a feature that occurs in nature." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000783 name: engineered def: "An attribute to describe a region that was modified in vitro." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000784 name: foreign def: "An attribute to describe a region from another species." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000785 name: cloned_region comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions. synonym: "cloned region" EXACT [] synonym: "cloned segment" EXACT [] is_a: SO:0000695 ! reagent relationship: part_of SO:0000753 ! clone_insert [Term] id: SO:0000786 name: reagent_attribute comment: Added jan 2006 by KE. synonym: "reagent attribute" EXACT [] is_obsolete: true [Term] id: SO:0000787 name: clone_attribute is_obsolete: true [Term] id: SO:0000788 name: cloned is_obsolete: true [Term] id: SO:0000789 name: validated def: "An attribute to describe a feature that has been proven." [SO:ke] is_a: SO:0000905 ! status [Term] id: SO:0000790 name: invalidated def: "An attribute describing a feature that is invalidated." [SO:ke] is_a: SO:0000905 ! status [Term] id: SO:0000791 name: cloned_genomic is_obsolete: true [Term] id: SO:0000792 name: cloned_cDNA is_obsolete: true [Term] id: SO:0000793 name: engineered_DNA is_obsolete: true [Term] id: SO:0000794 name: engineered_rescue_region def: "A rescue region that is engineered." [SO:xp] synonym: "engineered rescue fragment" EXACT [] synonym: "engineered rescue region" EXACT [] synonym: "engineered rescue segment" EXACT [] is_a: SO:0000411 ! rescue_region is_a: SO:0000804 ! engineered_region relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000795 name: rescue_mini_gene def: "A mini_gene that rescues." [SO:xp] synonym: "rescue mini gene" EXACT [] synonym: "rescue mini-gene" EXACT [] is_a: SO:0000815 ! mini_gene relationship: has_quality SO:0000814 ! rescue [Term] id: SO:0000796 name: transgenic_transposable_element def: "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc] comment: Modified as requested by Lynn - FB. May 2007. synonym: "transgenic transposable element" EXACT [] is_a: SO:0000101 ! transposable_element relationship: derives_from SO:0000151 ! clone relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0000797 name: natural_transposable_element def: "TE that exists (or existed) in nature." [FB:mc] synonym: "natural transposable element" EXACT [] is_a: SO:0000101 ! transposable_element is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element relationship: has_quality SO:0000782 ! natural [Term] id: SO:0000798 name: engineered_transposable_element def: "TE that has been modified by manipulations in vitro." [FB:mc] synonym: "engineered transposable element" EXACT [] is_a: SO:0000101 ! transposable_element is_a: SO:0000804 ! engineered_region relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000799 name: engineered_foreign_transposable_element def: "A transposable_element that is engineered and foreign." [FB:mc] synonym: "engineered foreign transposable element" EXACT [] is_a: SO:0000720 ! foreign_transposable_element is_a: SO:0000798 ! engineered_transposable_element is_a: SO:0000805 ! engineered_foreign_region relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000800 name: assortment_derived_duplication def: "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm] synonym: "assortment derived duplication" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000801 name: assortment_derived_deficiency_plus_duplication def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm] synonym: "assortment derived deficiency plus duplication" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000802 name: assortment_derived_deficiency def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm] synonym: "assortment-derived deficiency" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000803 name: assortment_derived_aneuploid def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm] synonym: "assortment derived aneuploid" EXACT [] is_a: SO:0001504 ! assortment_derived_variation [Term] id: SO:0000804 name: engineered_region def: "A region that is engineered." [SO:xp] synonym: "construct" EXACT [] synonym: "engineered region" EXACT [] synonym: "engineered sequence" EXACT [] is_a: SO:0001409 ! biomaterial_region relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000805 name: engineered_foreign_region def: "A region that is engineered and foreign." [SO:xp] synonym: "engineered foreign region" EXACT [] is_a: SO:0000804 ! engineered_region relationship: has_quality SO:0000783 ! engineered relationship: has_quality SO:0000784 ! foreign [Term] id: SO:0000806 name: fusion is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000807 name: engineered_tag def: "A tag that is engineered." [SO:xp] synonym: "engineered tag" EXACT [] is_a: SO:0000324 ! tag is_a: SO:0000804 ! engineered_region relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000808 name: validated_cDNA_clone def: "A cDNA clone that has been validated." [SO:xp] synonym: "validated cDNA clone" EXACT [] is_a: SO:0000317 ! cDNA_clone relationship: has_quality SO:0000789 ! validated [Term] id: SO:0000809 name: invalidated_cDNA_clone def: "A cDNA clone that is invalid." [SO:xp] synonym: "invalidated cDNA clone" EXACT [] is_a: SO:0000317 ! cDNA_clone relationship: has_quality SO:0000790 ! invalidated [Term] id: SO:0000810 name: chimeric_cDNA_clone def: "A cDNA clone invalidated because it is chimeric." [SO:xp] synonym: "chimeric cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone relationship: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA [Term] id: SO:0000811 name: genomically_contaminated_cDNA_clone def: "A cDNA clone invalidated by genomic contamination." [SO:xp] synonym: "genomically contaminated cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone relationship: has_quality SO:0000414 ! invalidated_by_genomic_contamination [Term] id: SO:0000812 name: polyA_primed_cDNA_clone def: "A cDNA clone invalidated by polyA priming." [SO:xp] synonym: "polyA primed cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone relationship: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA [Term] id: SO:0000813 name: partially_processed_cDNA_clone def: "A cDNA invalidated clone by partial processing." [SO:xp] synonym: "partially processed cDNA clone" EXACT [] is_a: SO:0000809 ! invalidated_cDNA_clone relationship: has_quality SO:0000416 ! invalidated_by_partial_processing [Term] id: SO:0000814 name: rescue def: "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000815 name: mini_gene def: "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143] synonym: "mini gene" EXACT [] is_a: SO:0000236 ! ORF [Term] id: SO:0000816 name: rescue_gene def: "A gene that rescues." [SO:xp] synonym: "rescue gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000814 ! rescue [Term] id: SO:0000817 name: wild_type def: "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke] synonym: "wild type" EXACT [] xref: http://en.wikipedia.org/wiki/Wild_type "wiki" xref: loinc:LA9658-1 "wild type" is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000818 name: wild_type_rescue_gene def: "A gene that rescues." [SO:xp] synonym: "wild type rescue gene" EXACT [] is_a: SO:0000816 ! rescue_gene relationship: has_quality SO:0000817 ! wild_type [Term] id: SO:0000819 name: mitochondrial_chromosome def: "A chromosome originating in a mitochondria." [SO:xp] synonym: "mitochondrial chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000737 ! mitochondrial_sequence [Term] id: SO:0000820 name: chloroplast_chromosome def: "A chromosome originating in a chloroplast." [SO:xp] synonym: "chloroplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000745 ! chloroplast_sequence [Term] id: SO:0000821 name: chromoplast_chromosome def: "A chromosome originating in a chromoplast." [SO:xp] synonym: "chromoplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000744 ! chromoplast_sequence [Term] id: SO:0000822 name: cyanelle_chromosome def: "A chromosome originating in a cyanelle." [SO:xp] synonym: "cyanelle chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000746 ! cyanelle_sequence [Term] id: SO:0000823 name: leucoplast_chromosome def: "A chromosome with origin in a leucoplast." [SO:xp] synonym: "leucoplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000747 ! leucoplast_sequence [Term] id: SO:0000824 name: macronuclear_chromosome def: "A chromosome originating in a macronucleus." [SO:xp] synonym: "macronuclear chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000083 ! macronuclear_sequence [Term] id: SO:0000825 name: micronuclear_chromosome def: "A chromosome originating in a micronucleus." [SO:xp] synonym: "micronuclear chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000084 ! micronuclear_sequence [Term] id: SO:0000828 name: nuclear_chromosome def: "A chromosome originating in a nucleus." [SO:xp] synonym: "nuclear chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000738 ! nuclear_sequence [Term] id: SO:0000829 name: nucleomorphic_chromosome def: "A chromosome originating in a nucleomorph." [SO:xp] synonym: "nucleomorphic chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000739 ! nucleomorphic_sequence [Term] id: SO:0000830 name: chromosome_part def: "A region of a chromosome." [SO:ke] comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. subset: SOFA synonym: "chromosome part" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0000831 name: gene_member_region def: "A region of a gene." [SO:ke] comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. subset: SOFA synonym: "gene member region" EXACT [] is_a: SO:0001411 ! biological_region relationship: member_of SO:0000704 ! gene [Term] id: SO:0000832 name: promoter_region def: "A region of sequence which is part of a promoter." [SO:ke] comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000833 name: transcript_region def: "A region of a transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "transcript region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000834 name: mature_transcript_region def: "A region of a mature transcript." [SO:ke] comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. subset: SOFA synonym: "mature transcript region" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000835 name: primary_transcript_region def: "A part of a primary transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "primary transcript region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000185 ! primary_transcript [Term] id: SO:0000836 name: mRNA_region def: "A region of an mRNA." [SO:cb] comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root. subset: SOFA synonym: "mRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000837 name: UTR_region def: "A region of UTR." [SO:ke] comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root. subset: SOFA synonym: "UTR region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000838 name: rRNA_primary_transcript_region def: "A region of an rRNA primary transcript." [SO:ke] comment: To allow transcribed_spacer_region to have a path to the root. synonym: "rRNA primary transcript region" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000839 name: polypeptide_region alt_id: BS:00124 alt_id: BS:00331 def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] comment: Added to allow the polypeptide regions to have is_a paths back to the root. subset: biosapiens subset: SOFA synonym: "positional" RELATED [] synonym: "positional polypeptide feature" RELATED [] synonym: "region" NARROW [uniprot:feature_type] synonym: "region or site annotation" RELATED [] synonym: "site" NARROW [uniprot:feature_type] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000840 name: repeat_component def: "A region of a repeated sequence." [SO:ke] comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root. synonym: "repeat component" EXACT [] is_a: SO:0001412 ! topologically_defined_region [Term] id: SO:0000841 name: spliceosomal_intron_region def: "A region within an intron." [SO:ke] comment: A terms added to allow the parts of introns to have is_a paths to the root. subset: SOFA synonym: "spliceosomal intron region" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000662 ! spliceosomal_intron [Term] id: SO:0000842 name: gene_component_region subset: SOFA synonym: "gene component region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000704 ! gene [Term] id: SO:0000843 name: bacterial_RNApol_promoter_region def: "A region which is part of a bacterial RNA polymerase promoter." [SO:ke] comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000844 name: RNApol_II_promoter_region def: "A region of sequence which is a promoter for RNA polymerase II." [SO:ke] comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000845 name: RNApol_III_promoter_type_1_region def: "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke] comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000846 name: RNApol_III_promoter_type_2_region def: "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke] comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root. is_obsolete: true [Term] id: SO:0000847 name: tmRNA_region def: "A region of a tmRNA." [SO:cb] comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root. synonym: "tmRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000584 ! tmRNA [Term] id: SO:0000848 name: LTR_component synonym: "long term repeat component" EXACT [] synonym: "LTR component" EXACT [] is_a: SO:0000840 ! repeat_component relationship: part_of SO:0000286 ! long_terminal_repeat [Term] id: SO:0000849 name: three_prime_LTR_component synonym: "3' long terminal repeat component" EXACT [] synonym: "three prime LTR component" EXACT [] is_a: SO:0000848 ! LTR_component relationship: part_of SO:0000426 ! three_prime_LTR [Term] id: SO:0000850 name: five_prime_LTR_component synonym: "5' long term repeat component" EXACT [] synonym: "five prime LTR component" EXACT [] is_a: SO:0000848 ! LTR_component relationship: part_of SO:0000425 ! five_prime_LTR [Term] id: SO:0000851 name: CDS_region def: "A region of a CDS." [SO:cb] subset: SOFA synonym: "CDS region" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000316 ! CDS [Term] id: SO:0000852 name: exon_region def: "A region of an exon." [RSC:cb] subset: SOFA synonym: "exon region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000147 ! exon [Term] id: SO:0000853 name: homologous_region def: "A region that is homologous to another region." [SO:ke] synonym: "homolog" EXACT [] synonym: "homologous region" EXACT [] synonym: "homologue" EXACT [] xref: http://en.wikipedia.org/wiki/Homology_(biology) "wiki" is_a: SO:0000330 ! conserved_region relationship: has_quality SO:0000857 ! homologous [Term] id: SO:0000854 name: paralogous_region def: "A homologous_region that is paralogous to another region." [SO:ke] comment: A term to be used in conjunction with the paralogous_to relationship. synonym: "paralog" EXACT [] synonym: "paralogous region" EXACT [] synonym: "paralogue" EXACT [] xref: http://en.wikipedia.org/wiki/Paralog#Paralogy "wiki" is_a: SO:0000853 ! homologous_region relationship: has_quality SO:0000859 ! paralogous [Term] id: SO:0000855 name: orthologous_region def: "A homologous_region that is orthologous to another region." [SO:ke] comment: This term should be used in conjunction with the similarity relationships defined in SO. synonym: "ortholog" EXACT [] synonym: "orthologous region" EXACT [] synonym: "orthologue" EXACT [] xref: http://en.wikipedia.org/wiki/Ortholog#Orthology "wiki" is_a: SO:0000853 ! homologous_region relationship: has_quality SO:0000858 ! orthologous [Term] id: SO:0000856 name: conserved is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000857 name: homologous def: "Similarity due to common ancestry." [SO:ke] is_a: SO:0000856 ! conserved [Term] id: SO:0000858 name: orthologous def: "An attribute describing a kind of homology where divergence occured after a speciation event." [SO:ke] is_a: SO:0000857 ! homologous [Term] id: SO:0000859 name: paralogous def: "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke] is_a: SO:0000857 ! homologous [Term] id: SO:0000860 name: syntenic def: "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke] xref: http://en.wikipedia.org/wiki/Syntenic "wiki" is_a: SO:0000856 ! conserved [Term] id: SO:0000861 name: capped_primary_transcript def: "A primary transcript that is capped." [SO:xp] synonym: "capped primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript relationship: adjacent_to SO:0000581 ! cap relationship: has_quality SO:0000146 ! capped [Term] id: SO:0000862 name: capped_mRNA def: "An mRNA that is capped." [SO:xp] synonym: "capped mRNA" EXACT [] is_a: SO:0000234 ! mRNA relationship: adjacent_to SO:0000581 ! cap relationship: has_quality SO:0000146 ! capped [Term] id: SO:0000863 name: mRNA_attribute def: "An attribute describing an mRNA feature." [SO:ke] synonym: "mRNA attribute" EXACT [] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000864 name: exemplar def: "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000865 name: frameshift def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke] xref: http://en.wikipedia.org/wiki/Frameshift "wiki" is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000866 name: minus_1_frameshift def: "A frameshift caused by deleting one base." [SO:ke] synonym: "minus 1 frameshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000867 name: minus_2_frameshift def: "A frameshift caused by deleting two bases." [SO:ke] synonym: "minus 2 frameshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000868 name: plus_1_frameshift def: "A frameshift caused by inserting one base." [SO:ke] synonym: "plus 1 frameshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000869 name: plus_2_framshift def: "A frameshift caused by inserting two bases." [SO:ke] synonym: "plus 2 framshift" EXACT [] is_a: SO:0000865 ! frameshift [Term] id: SO:0000870 name: trans_spliced def: "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke] synonym: "trans-spliced" EXACT [] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000871 name: polyadenylated_mRNA def: "An mRNA that is polyadenylated." [SO:xp] synonym: "polyadenylated mRNA" EXACT [] is_a: SO:0000234 ! mRNA relationship: adjacent_to SO:0000610 ! polyA_sequence relationship: has_quality SO:0000246 ! polyadenylated [Term] id: SO:0000872 name: trans_spliced_mRNA def: "An mRNA that is trans-spliced." [SO:xp] synonym: "trans-spliced mRNA" EXACT [] is_a: SO:0000234 ! mRNA is_a: SO:0000479 ! trans_spliced_transcript relationship: adjacent_to SO:0000636 ! spliced_leader_RNA relationship: has_quality SO:0000870 ! trans_spliced [Term] id: SO:0000873 name: edited_transcript def: "A transcript that is edited." [SO:ke] synonym: "edited transcript" EXACT [] is_a: SO:0000673 ! transcript relationship: guided_by SO:0000602 ! guide_RNA relationship: has_part SO:0000977 ! anchor_binding_site relationship: has_quality SO:0000116 ! edited [Term] id: SO:0000874 name: edited_transcript_by_A_to_I_substitution def: "A transcript that has been edited by A to I substitution." [SO:ke] synonym: "edited transcript by A to I substitution" EXACT [] is_a: SO:0000873 ! edited_transcript [Term] id: SO:0000875 name: bound_by_protein def: "An attribute describing a sequence that is bound by a protein." [SO:ke] synonym: "bound by protein" EXACT [] is_a: SO:0000277 ! bound_by_factor [Term] id: SO:0000876 name: bound_by_nucleic_acid def: "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke] synonym: "bound by nucleic acid" EXACT [] is_a: SO:0000277 ! bound_by_factor [Term] id: SO:0000877 name: alternatively_spliced def: "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke] synonym: "alternatively spliced" EXACT [] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000878 name: monocistronic def: "An attribute describing a sequence that contains the code for one gene product." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000879 name: dicistronic def: "An attribute describing a sequence that contains the code for two gene products." [SO:ke] is_a: SO:0000880 ! polycistronic [Term] id: SO:0000880 name: polycistronic def: "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke] is_a: SO:0000237 ! transcript_attribute [Term] id: SO:0000881 name: recoded def: "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke] is_a: SO:0000863 ! mRNA_attribute [Term] id: SO:0000882 name: codon_redefined def: "An attribute describing the alteration of codon meaning." [SO:ke] synonym: "codon redefined" EXACT [] is_a: SO:0000881 ! recoded [Term] id: SO:0000883 name: stop_codon_read_through def: "A stop codon redefined to be a new amino acid." [SO:ke] synonym: "stop codon read through" EXACT [] synonym: "stop codon readthrough" RELATED [] is_a: SO:0000145 ! recoded_codon [Term] id: SO:0000884 name: stop_codon_redefined_as_pyrrolysine def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke] synonym: "stop codon redefined as pyrrolysine" EXACT [] is_a: SO:0000883 ! stop_codon_read_through [Term] id: SO:0000885 name: stop_codon_redefined_as_selenocysteine def: "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke] synonym: "stop codon redefined as selenocysteine" EXACT [] is_a: SO:0000883 ! stop_codon_read_through [Term] id: SO:0000886 name: recoded_by_translational_bypass def: "Recoded mRNA where a block of nucleotides is not translated." [SO:ke] synonym: "recoded by translational bypass" EXACT [] is_a: SO:0000881 ! recoded [Term] id: SO:0000887 name: translationally_frameshifted def: "Recoding by frameshifting a particular site." [SO:ke] synonym: "translationally frameshifted" EXACT [] is_a: SO:0000881 ! recoded [Term] id: SO:0000888 name: maternally_imprinted_gene def: "A gene that is maternally_imprinted." [SO:xp] synonym: "maternally imprinted gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene relationship: has_quality SO:0000135 ! maternally_imprinted [Term] id: SO:0000889 name: paternally_imprinted_gene def: "A gene that is paternally imprinted." [SO:xp] synonym: "paternally imprinted gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene relationship: has_quality SO:0000136 ! paternally_imprinted [Term] id: SO:0000890 name: post_translationally_regulated_gene def: "A gene that is post translationally regulated." [SO:xp] synonym: "post translationally regulated gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000130 ! post_translationally_regulated [Term] id: SO:0000891 name: negatively_autoregulated_gene def: "A gene that is negatively autoreguated." [SO:xp] synonym: "negatively autoregulated gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000473 ! negatively_autoregulated [Term] id: SO:0000892 name: positively_autoregulated_gene def: "A gene that is positively autoregulated." [SO:xp] synonym: "positively autoregulated gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000475 ! positively_autoregulated [Term] id: SO:0000893 name: silenced def: "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke] xref: http://en.wikipedia.org/wiki/Silenced "wiki" is_a: SO:0000126 ! transcriptionally_repressed [Term] id: SO:0000894 name: silenced_by_DNA_modification def: "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke] synonym: "silenced by DNA modification" EXACT [] is_a: SO:0000893 ! silenced [Term] id: SO:0000895 name: silenced_by_DNA_methylation def: "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke] synonym: "silenced by DNA methylation" EXACT [] is_a: SO:0000894 ! silenced_by_DNA_modification [Term] id: SO:0000896 name: translationally_regulated_gene def: "A gene that is translationally regulated." [SO:xp] synonym: "translationally regulated gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000131 ! translationally_regulated [Term] id: SO:0000897 name: allelically_excluded_gene def: "A gene that is allelically_excluded." [SO:xp] synonym: "allelically excluded gene" EXACT [] is_a: SO:0000898 ! epigenetically_modified_gene relationship: has_quality SO:0000137 ! allelically_excluded [Term] id: SO:0000898 name: epigenetically_modified_gene def: "A gene that is epigenetically modified." [SO:ke] synonym: "epigenetically modified gene" EXACT [] is_a: SO:0000704 ! gene is_a: SO:0001720 ! epigenetically_modified_region relationship: has_quality SO:0000133 ! epigenetically_modified [Term] id: SO:0000899 name: nuclear_mitochondrial def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke] synonym: "nuclear mitochondrial" EXACT [] is_obsolete: true [Term] id: SO:0000900 name: processed def: "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." [SO:ke] is_obsolete: true [Term] id: SO:0000901 name: unequally_crossed_over def: "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke] synonym: "unequally crossed over" EXACT [] is_obsolete: true [Term] id: SO:0000902 name: transgene def: "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp] xref: http://en.wikipedia.org/wiki/Transgene "wiki" is_a: SO:0000704 ! gene relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0000903 name: endogenous_retroviral_sequence synonym: "endogenous retroviral sequence" EXACT [] is_a: SO:0000751 ! proviral_location [Term] id: SO:0000904 name: rearranged_at_DNA_level def: "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke] synonym: "rearranged at DNA level" EXACT [] is_a: SO:0000133 ! epigenetically_modified [Term] id: SO:0000905 name: status def: "An attribute describing the status of a feature, based on the available evidence." [SO:ke] comment: This term is the hypernym of attributes and should not be annotated to. is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000906 name: independently_known def: "Attribute to describe a feature that is independently known - not predicted." [SO:ke] synonym: "independently known" EXACT [] is_a: SO:0000905 ! status [Term] id: SO:0000907 name: supported_by_sequence_similarity def: "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke] synonym: "supported by sequence similarity" EXACT [] is_a: SO:0000732 ! predicted [Term] id: SO:0000908 name: supported_by_domain_match def: "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke] synonym: "supported by domain match" EXACT [] is_a: SO:0000907 ! supported_by_sequence_similarity [Term] id: SO:0000909 name: supported_by_EST_or_cDNA def: "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke] synonym: "supported by EST or cDNA" EXACT [] is_a: SO:0000907 ! supported_by_sequence_similarity [Term] id: SO:0000910 name: orphan is_a: SO:0000732 ! predicted [Term] id: SO:0000911 name: predicted_by_ab_initio_computation def: "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke] synonym: "predicted by ab initio computation" EXACT [] is_a: SO:0000732 ! predicted [Term] id: SO:0000912 name: asx_turn alt_id: BS:00203 def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0000913 name: cloned_cDNA_insert def: "A clone insert made from cDNA." [SO:xp] synonym: "cloned cDNA insert" EXACT [] is_a: SO:0000753 ! clone_insert relationship: has_quality SO:0000756 ! cDNA [Term] id: SO:0000914 name: cloned_genomic_insert def: "A clone insert made from genomic DNA." [SO:xp] synonym: "cloned genomic insert" EXACT [] is_a: SO:0000753 ! clone_insert relationship: has_quality SO:0000991 ! genomic_DNA [Term] id: SO:0000915 name: engineered_insert def: "A clone insert that is engineered." [SO:xp] synonym: "engineered insert" EXACT [] is_a: SO:0000753 ! clone_insert is_a: SO:0000804 ! engineered_region relationship: has_quality SO:0000783 ! engineered [Term] id: SO:0000916 name: edit_operation synonym: "edit operation" EXACT [] is_obsolete: true [Term] id: SO:0000917 name: insert_U def: "An edit to insert a U." [SO:ke] comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. synonym: "insert U" EXACT [] is_obsolete: true [Term] id: SO:0000918 name: delete_U def: "An edit to delete a uridine." [SO:ke] comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. synonym: "delete U" EXACT [] is_obsolete: true [Term] id: SO:0000919 name: substitute_A_to_I def: "An edit to substitute an I for an A." [SO:ke] synonym: "substitute A to I" EXACT [] is_obsolete: true [Term] id: SO:0000920 name: insert_C def: "An edit to insert a cytidine." [SO:ke] synonym: "insert C" EXACT [] is_obsolete: true [Term] id: SO:0000921 name: insert_dinucleotide def: "An edit to insert a dinucleotide." [SO:ke] synonym: "insert dinucleotide" EXACT [] is_obsolete: true [Term] id: SO:0000922 name: substitute_C_to_U def: "An edit to substitute an U for a C." [SO:ke] synonym: "substitute C to U" EXACT [] is_obsolete: true [Term] id: SO:0000923 name: insert_G def: "An edit to insert a G." [SO:ke] synonym: "insert G" EXACT [] is_obsolete: true [Term] id: SO:0000924 name: insert_GC def: "An edit to insert a GC dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert GC" EXACT [] is_obsolete: true [Term] id: SO:0000925 name: insert_GU def: "An edit to insert a GU dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert GU" EXACT [] is_obsolete: true [Term] id: SO:0000926 name: insert_CU def: "An edit to insert a CU dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert CU" EXACT [] is_obsolete: true [Term] id: SO:0000927 name: insert_AU def: "An edit to insert a AU dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert AU" EXACT [] is_obsolete: true [Term] id: SO:0000928 name: insert_AA def: "An edit to insert a AA dinucleotide." [SO:ke] comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs. synonym: "insert AA" EXACT [] is_obsolete: true [Term] id: SO:0000929 name: edited_mRNA def: "An mRNA that is edited." [SO:xp] synonym: "edited mRNA" EXACT [] is_a: SO:0000234 ! mRNA is_a: SO:0000873 ! edited_transcript relationship: has_quality SO:0000116 ! edited [Term] id: SO:0000930 name: guide_RNA_region def: "A region of guide RNA." [SO:ma] synonym: "guide RNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000602 ! guide_RNA [Term] id: SO:0000931 name: anchor_region def: "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk] synonym: "anchor region" EXACT [] is_a: SO:0000930 ! guide_RNA_region [Term] id: SO:0000932 name: pre_edited_mRNA synonym: "pre-edited mRNA" EXACT [] is_a: SO:0000120 ! protein_coding_primary_transcript [Term] id: SO:0000933 name: intermediate def: "An attribute to describe a feature between stages of processing." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000934 name: miRNA_target_site def: "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds] synonym: "miRNA target site" EXACT [] is_a: SO:0001655 ! nucleotide_binding_site [Term] id: SO:0000935 name: edited_CDS def: "A CDS that is edited." [SO:xp] synonym: "edited CDS" EXACT [] is_a: SO:0000316 ! CDS relationship: has_quality SO:0000116 ! edited [Term] id: SO:0000936 name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment synonym: "vertebrate immunoglobulin T cell receptor rearranged segment" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000937 name: vertebrate_immune_system_feature is_obsolete: true [Term] id: SO:0000938 name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster synonym: "vertebrate immunoglobulin T cell receptor rearranged gene cluster" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000939 name: vertebrate_immune_system_gene_recombination_signal_feature synonym: "vertebrate immune system gene recombination signal feature" EXACT [] is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature [Term] id: SO:0000940 name: recombinationally_rearranged synonym: "recombinationally rearranged" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000941 name: recombinationally_rearranged_vertebrate_immune_system_gene def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp] synonym: "recombinationally rearranged vertebrate immune system gene" EXACT [] is_a: SO:0000456 ! recombinationally_rearranged_gene [Term] id: SO:0000942 name: attP_site def: "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as] synonym: "attP site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0001042 ! phage_sequence [Term] id: SO:0000943 name: attB_site def: "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as] synonym: "attB site" EXACT [] is_a: SO:0000946 ! integration_excision_site [Term] id: SO:0000944 name: attL_site def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as] synonym: "attBP'" RELATED [] synonym: "attL site" RELATED [] is_a: SO:0000946 ! integration_excision_site [Term] id: SO:0000945 name: attR_site def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as] synonym: "attPB'" RELATED [] synonym: "attR site" EXACT [] is_a: SO:0000946 ! integration_excision_site [Term] id: SO:0000946 name: integration_excision_site def: "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as] synonym: "attachment site" RELATED [] synonym: "integration excision site" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000947 name: resolution_site def: "A region specifically recognised by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as] synonym: "res site" EXACT [] synonym: "resolution site" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000948 name: inversion_site def: "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma] comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase. synonym: "inversion site" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0000949 name: dif_site def: "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as] synonym: "dif site" EXACT [] is_a: SO:0000947 ! resolution_site [Term] id: SO:0000950 name: attC_site def: "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as] synonym: "attC site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0000365 ! integron [Term] id: SO:0000951 name: eukaryotic_terminator synonym: "eukaryotic terminator" EXACT [] is_a: SO:0000141 ! terminator [Term] id: SO:0000952 name: oriV def: "An origin of vegetative replication in plasmids and phages." [SO:as] synonym: "origin of vegetative replication" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000953 name: oriC def: "An origin of bacterial chromosome replication." [SO:as] synonym: "origin of bacterial chromosome replication" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000954 name: DNA_chromosome def: "Structural unit composed of a self-replicating, DNA molecule." [SO:ma] synonym: "DNA chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_quality SO:0000352 ! DNA [Term] id: SO:0000955 name: double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma] synonym: "double stranded DNA chromosome" EXACT [] is_a: SO:0000954 ! DNA_chromosome relationship: has_quality SO:0000985 ! double [Term] id: SO:0000956 name: single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma] synonym: "single stranded DNA chromosome" EXACT [] is_a: SO:0000954 ! DNA_chromosome relationship: has_quality SO:0000984 ! single [Term] id: SO:0000957 name: linear_double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma] synonym: "linear double stranded DNA chromosome" EXACT [] is_a: SO:0000955 ! double_stranded_DNA_chromosome relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000958 name: circular_double_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma] synonym: "circular double stranded DNA chromosome" EXACT [] is_a: SO:0000955 ! double_stranded_DNA_chromosome relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000959 name: linear_single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma] synonym: "linear single stranded DNA chromosome" EXACT [] is_a: SO:0000956 ! single_stranded_DNA_chromosome relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000960 name: circular_single_stranded_DNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] synonym: "circular single stranded DNA chromosome" EXACT [] is_a: SO:0000956 ! single_stranded_DNA_chromosome relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000961 name: RNA_chromosome def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma] synonym: "RNA chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_quality SO:0000356 ! RNA [Term] id: SO:0000962 name: single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma] synonym: "single stranded RNA chromosome" EXACT [] is_a: SO:0000961 ! RNA_chromosome relationship: has_quality SO:0000984 ! single [Term] id: SO:0000963 name: linear_single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma] synonym: "linear single stranded RNA chromosome" EXACT [] is_a: SO:0000962 ! single_stranded_RNA_chromosome relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000964 name: linear_double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma] synonym: "linear double stranded RNA chromosome" EXACT [] is_a: SO:0000965 ! double_stranded_RNA_chromosome relationship: has_quality SO:0000987 ! linear [Term] id: SO:0000965 name: double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma] synonym: "double stranded RNA chromosome" EXACT [] is_a: SO:0000961 ! RNA_chromosome relationship: has_quality SO:0000985 ! double [Term] id: SO:0000966 name: circular_single_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma] synonym: "circular single stranded RNA chromosome" EXACT [] is_a: SO:0000962 ! single_stranded_RNA_chromosome relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000967 name: circular_double_stranded_RNA_chromosome def: "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma] synonym: "circular double stranded RNA chromosome" EXACT [] is_a: SO:0000965 ! double_stranded_RNA_chromosome relationship: has_quality SO:0000988 ! circular [Term] id: SO:0000968 name: sequence_replication_mode comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961. synonym: "sequence replication mode" EXACT [] is_obsolete: true [Term] id: SO:0000969 name: rolling_circle comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581. synonym: "rolling circle" EXACT [] xref: http://en.wikipedia.org/wiki/Rolling_circle "wiki" is_obsolete: true [Term] id: SO:0000970 name: theta_replication comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582 synonym: "theta replication" EXACT [] is_obsolete: true [Term] id: SO:0000971 name: DNA_replication_mode comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260. synonym: "DNA replication mode" EXACT [] is_obsolete: true [Term] id: SO:0000972 name: RNA_replication_mode comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961. synonym: "RNA replication mode" EXACT [] is_obsolete: true [Term] id: SO:0000973 name: insertion_sequence def: "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as] synonym: "insertion sequence" EXACT [] synonym: "IS" RELATED [] xref: http://en.wikipedia.org/wiki/Insertion_sequence "wiki" is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0000975 name: minicircle_gene synonym: "minicircle gene" EXACT [] is_a: SO:0000089 ! kinetoplast_gene relationship: part_of SO:0000980 ! minicircle [Term] id: SO:0000976 name: cryptic def: "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000977 name: anchor_binding_site comment: Part of an edited transcript only. synonym: "anchor binding site" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000978 name: template_region def: "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk] synonym: "information region" EXACT [] synonym: "template region" EXACT [] is_a: SO:0000930 ! guide_RNA_region [Term] id: SO:0000979 name: gRNA_encoding def: "A non-protein_coding gene that encodes a guide_RNA." [SO:ma] synonym: "gRNA encoding" EXACT [] is_a: SO:0000011 ! non_protein_coding [Term] id: SO:0000980 name: minicircle alt_id: SO:0000974 def: "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055] synonym: "minicircle_chromosome" EXACT [] xref: http://en.wikipedia.org/wiki/Minicircle "wiki" is_a: SO:0001235 ! replicon [Term] id: SO:0000981 name: rho_dependent_bacterial_terminator synonym: "rho dependent bacterial terminator" EXACT [] is_a: SO:0000614 ! bacterial_terminator [Term] id: SO:0000982 name: rho_independent_bacterial_terminator synonym: "rho independent bacterial terminator" EXACT [] is_a: SO:0000614 ! bacterial_terminator [Term] id: SO:0000983 name: strand_attribute comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "strand attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0000984 name: single comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. is_a: SO:0000983 ! strand_attribute [Term] id: SO:0000985 name: double comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. is_a: SO:0000983 ! strand_attribute [Term] id: SO:0000986 name: topology_attribute comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "topology attribute" EXACT [] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0000987 name: linear def: "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "two-ended" RELATED [] is_a: SO:0000986 ! topology_attribute disjoint_from: SO:0000988 ! circular [Term] id: SO:0000988 name: circular def: "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb] comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006. synonym: "zero-ended" RELATED [] is_a: SO:0000986 ! topology_attribute [Term] id: SO:0000989 name: class_II_RNA def: "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] synonym: "class II RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000990 name: class_I_RNA def: "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696] comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577. synonym: "class I RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000991 name: genomic_DNA comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "genomic DNA" EXACT [] is_a: SO:0000352 ! DNA [Term] id: SO:0000992 name: BAC_cloned_genomic_insert comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006. synonym: "BAC cloned genomic insert" EXACT [] is_a: SO:0000914 ! cloned_genomic_insert relationship: derives_from SO:0000153 ! BAC [Term] id: SO:0000993 name: consensus comment: Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA. is_a: SO:0000905 ! status [Term] id: SO:0000994 name: consensus_region comment: DO not obsolete without considering MGED mapping. synonym: "consensus region" EXACT [] is_a: SO:0001410 ! experimental_feature relationship: has_quality SO:0000993 ! consensus [Term] id: SO:0000995 name: consensus_mRNA comment: DO not obsolete without considering MGED mapping. synonym: "consensus mRNA" EXACT [] is_a: SO:0000234 ! mRNA is_a: SO:0000994 ! consensus_region relationship: has_quality SO:0000993 ! consensus [Term] id: SO:0000996 name: predicted_gene comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "predicted gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000732 ! predicted [Term] id: SO:0000997 name: gene_fragment comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. synonym: "gene fragment" EXACT [] is_a: SO:0000842 ! gene_component_region relationship: has_quality SO:0000731 ! fragmentary [Term] id: SO:0000998 name: recursive_splice_site def: "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661] synonym: "recursive splice site" EXACT [] is_a: SO:0001419 ! cis_splice_site [Term] id: SO:0000999 name: BAC_end def: "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke] comment: Requested by Keith Boroevich December, 2006. synonym: "BAC end" EXACT [] synonym: "BAC end sequence" EXACT [] synonym: "BES" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000153 ! BAC [Term] id: SO:0001000 name: rRNA_16S def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "16S ribosomal RNA" EXACT [] synonym: "16S rRNA" RELATED [] synonym: "16S SSU RNA" EXACT [] synonym: "rRNA 16S" EXACT [] xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki" is_a: SO:0000650 ! small_subunit_rRNA [Term] id: SO:0001001 name: rRNA_23S def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke] subset: SOFA synonym: "23S LSU rRNA" EXACT [] synonym: "23S ribosomal RNA" RELATED [] synonym: "23S rRNA" EXACT [] synonym: "rRNA 23S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001002 name: rRNA_25S def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb] subset: SOFA synonym: "25S LSU rRNA" EXACT [] synonym: "25S ribosomal RNA" EXACT [] synonym: "25S rRNA" EXACT [] synonym: "rRNA 25S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001003 name: solo_LTR def: "A recombination product between the 2 LTR of the same element." [SO:ke] comment: Requested by Hadi Quesneville January 2007. synonym: "solo LTR" EXACT [] is_a: SO:0000286 ! long_terminal_repeat [Term] id: SO:0001004 name: low_complexity synonym: "low complexity" EXACT [] is_a: SO:0000905 ! status [Term] id: SO:0001005 name: low_complexity_region synonym: "low complexity region" EXACT [] is_a: SO:0001410 ! experimental_feature relationship: has_quality SO:0001004 ! low_complexity [Term] id: SO:0001006 name: prophage def: "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\"." [GOC:jl] xref: http://en.wikipedia.org/wiki/Prophage "wiki" is_a: SO:0000113 ! proviral_region [Term] id: SO:0001007 name: cryptic_prophage def: "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." [GOC:jl] comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site. synonym: "cryptic prophage" EXACT [] xref: http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w is_a: SO:0000772 ! genomic_island [Term] id: SO:0001008 name: tetraloop def: "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke] xref: http://en.wikipedia.org/wiki/Tetraloop "wiki" is_a: SO:0000313 ! stem_loop [Term] id: SO:0001009 name: DNA_constraint_sequence def: "A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\]&dispmax=50] synonym: "DNA constraint" EXACT [] synonym: "DNA constraint sequence" EXACT [] is_a: SO:0000442 ! ds_oligo [Term] id: SO:0001010 name: i_motif def: "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739] synonym: "i motif" EXACT [] synonym: "short intercalated motif" EXACT [] is_a: SO:0000142 ! DNA_sequence_secondary_structure [Term] id: SO:0001011 name: PNA_oligo def: "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke] synonym: "peptide nucleic acid" EXACT [] synonym: "PNA oligo" EXACT [] xref: http://en.wikipedia.org/wiki/Peptide_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo relationship: has_quality SO:0001184 ! PNA [Term] id: SO:0001012 name: DNAzyme def: "A DNA sequence with catalytic activity." [SO:cb] comment: Added by request from Colin Batchelor. synonym: "catalytic DNA" EXACT [] synonym: "deoxyribozyme" RELATED [] synonym: "DNA enzyme" EXACT [] is_a: SO:0000696 ! oligo relationship: has_quality SO:0001185 ! enzymatic [Term] id: SO:0001013 name: MNP def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431] synonym: "multiple nucleotide polymorphism" RELATED [] is_a: SO:1000002 ! substitution [Term] id: SO:0001014 name: intron_domain comment: Requested by Colin Batchelor, Feb 2007. synonym: "intron domain" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000188 ! intron [Term] id: SO:0001015 name: wobble_base_pair def: "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617] synonym: "wobble base pair" EXACT [] synonym: "wobble pair" EXACT [] xref: http://en.wikipedia.org/wiki/Wobble_base_pair "wiki" is_a: SO:0000028 ! base_pair [Term] id: SO:0001016 name: internal_guide_sequence def: "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb] synonym: "IGS" EXACT [] synonym: "internal guide sequence" EXACT [] is_a: SO:0001014 ! intron_domain relationship: part_of SO:0000587 ! group_I_intron [Term] id: SO:0001017 name: silent_mutation def: "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke] comment: Added in March 2007 in after meeting with pharmgkb. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc. synonym: "silent mutation" EXACT [] xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki" xref: loinc:LA6700-4 "Silent" is_a: SO:0001878 ! feature_variant [Term] id: SO:0001018 name: epitope def: "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb] comment: Requested by Trish Whetzel. xref: http://en.wikipedia.org/wiki/Epitope "wiki" is_a: SO:0000409 ! binding_site [Term] id: SO:0001019 name: copy_number_variation def: "A variation that increases or decreases the copy number of a given region." [SO:ke] subset: SOFA synonym: "CNP" EXACT [] synonym: "CNV" EXACT [] synonym: "copy number polymorphism" EXACT [] synonym: "copy number variation" EXACT [] xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki" is_a: SO:0001059 ! sequence_alteration [Term] id: SO:0001020 name: sequence_variant_affecting_copy_number comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting copy number" EXACT [] synonym: "sequence variant affecting copy number" EXACT [] is_obsolete: true replaced_by: SO:0001563 [Term] id: SO:0001021 name: chromosome_breakpoint alt_id: SO:0001242 synonym: "aberration breakpoint" EXACT [] synonym: "aberration_junction" EXACT [] synonym: "chromosome breakpoint" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0001022 name: inversion_breakpoint def: "The point within a chromosome where an inversion begins or ends." [SO:cb] synonym: "inversion breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001023 name: allele def: "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop] synonym: "allelomorph" EXACT [] xref: http://en.wikipedia.org/wiki/Allele "wiki" is_a: SO:0001507 ! variant_collection relationship: variant_of SO:0000704 ! gene [Term] id: SO:0001024 name: haplotype def: "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop] xref: http://en.wikipedia.org/wiki/Haplotype "wiki" is_a: SO:0001507 ! variant_collection relationship: variant_of SO:0000355 ! haplotype_block [Term] id: SO:0001025 name: polymorphic_sequence_variant def: "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop] synonym: "polymorphic sequence variant" EXACT [] is_a: SO:0001023 ! allele [Term] id: SO:0001026 name: genome def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop] xref: http://en.wikipedia.org/wiki/Genome "wiki" is_a: SO:0001260 ! sequence_collection relationship: has_part SO:0001235 ! replicon [Term] id: SO:0001027 name: genotype def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop] xref: http://en.wikipedia.org/wiki/Genotype "wiki" is_a: SO:0001507 ! variant_collection relationship: variant_of SO:0001026 ! genome [Term] id: SO:0001028 name: diplotype def: "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop] is_a: SO:0001507 ! variant_collection [Term] id: SO:0001029 name: direction_attribute synonym: "direction attribute" EXACT [] is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001030 name: forward def: "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke] is_a: SO:0001029 ! direction_attribute [Term] id: SO:0001031 name: reverse def: "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke] is_a: SO:0001029 ! direction_attribute [Term] id: SO:0001032 name: mitochondrial_DNA comment: This terms is used by MO. synonym: "mitochondrial DNA" EXACT [] synonym: "mtDNA" EXACT [] xref: http://en.wikipedia.org/wiki/Mitochondrial_DNA "wiki" is_a: SO:0000737 ! mitochondrial_sequence relationship: has_quality SO:0000352 ! DNA [Term] id: SO:0001033 name: chloroplast_DNA comment: This term is used by MO. synonym: "chloroplast DNA" EXACT [] is_a: SO:0000745 ! chloroplast_sequence relationship: has_quality SO:0000352 ! DNA [Term] id: SO:0001034 name: mirtron def: "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma] comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns. is_a: SO:0001014 ! intron_domain [Term] id: SO:0001035 name: piRNA def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke] synonym: "piwi-associated RNA" EXACT [] xref: http://en.wikipedia.org/wiki/PiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0001036 name: arginyl_tRNA def: "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke] synonym: "arginyl tRNA" EXACT [] is_a: SO:0000253 ! tRNA relationship: derives_from SO:0000212 ! arginine_tRNA_primary_transcript [Term] id: SO:0001037 name: mobile_genetic_element def: "A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355] subset: SOFA synonym: "MGE" EXACT [] synonym: "mobile genetic element" EXACT [] xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki" is_a: SO:0001411 ! biological_region relationship: has_quality SO:0001234 ! mobile [Term] id: SO:0001038 name: extrachromosomal_mobile_genetic_element def: "An MGE that is not integrated into the host chromosome." [SO:ke] synonym: "extrachromosomal mobile genetic element" EXACT [] is_a: SO:0001037 ! mobile_genetic_element [Term] id: SO:0001039 name: integrated_mobile_genetic_element def: "An MGE that is integrated into the host chromosome." [SO:ke] subset: SOFA synonym: "integrated mobile genetic element" EXACT [] is_a: SO:0001037 ! mobile_genetic_element [Term] id: SO:0001040 name: integrated_plasmid def: "A plasmid sequence that is integrated within the host chromosome." [SO:ke] synonym: "integrated plasmid" EXACT [] is_a: SO:0001039 ! integrated_mobile_genetic_element relationship: derives_from SO:0000155 ! plasmid [Term] id: SO:0001041 name: viral_sequence def: "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke] comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct. synonym: "viral sequence" EXACT [] synonym: "virus sequence" EXACT [] is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element is_a: SO:0001235 ! replicon [Term] id: SO:0001042 name: phage_sequence def: "The nucleotide sequence of a virus that infects bacteria." [SO:ke] synonym: "bacteriophage" EXACT [] synonym: "phage" EXACT [] synonym: "phage sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Bacteriophage "wiki" is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001043 name: attCtn_site def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at] synonym: "attCtn site" EXACT [] is_a: SO:0000946 ! integration_excision_site relationship: part_of SO:0000371 ! conjugative_transposon [Term] id: SO:0001044 name: nuclear_mt_pseudogene def: "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp] comment: Definition change requested by Val, 3172757. synonym: "nuclear mitochondrial pseudogene" EXACT [] synonym: "nuclear mt pseudogene" EXACT [] synonym: "NUMT" EXACT [] xref: http://en.wikipedia.org/wiki/Numt "wikipedia" is_a: SO:0001760 ! non_processed_pseudogene [Term] id: SO:0001045 name: cointegrated_plasmid def: "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at] synonym: "cointegrated plasmid" EXACT [] synonym: "cointegrated replicon" EXACT [] is_a: SO:0001039 ! integrated_mobile_genetic_element [Term] id: SO:0001046 name: IRLinv_site def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at] synonym: "IRLinv site" EXACT [] is_a: SO:0001048 ! inversion_site_part relationship: part_of SO:0000948 ! inversion_site [Term] id: SO:0001047 name: IRRinv_site def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at] synonym: "IRRinv site" EXACT [] is_a: SO:0001048 ! inversion_site_part relationship: part_of SO:0000948 ! inversion_site [Term] id: SO:0001048 name: inversion_site_part def: "A region located within an inversion site." [SO:ke] comment: A term created to allow the parts of an inversion site have an is_a path back to the root. synonym: "inversion site part" EXACT [] is_a: SO:0000342 ! site_specific_recombination_target_region [Term] id: SO:0001049 name: defective_conjugative_transposon def: "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane] synonym: "defective conjugative transposon" EXACT [] is_a: SO:0000772 ! genomic_island [Term] id: SO:0001050 name: repeat_fragment def: "A portion of a repeat, interrupted by the insertion of another element." [SO:ke] comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats. synonym: "repeat fragment" EXACT [] is_a: SO:0000840 ! repeat_component relationship: part_of SO:0001649 ! nested_repeat [Term] id: SO:0001051 name: nested_region is_obsolete: true [Term] id: SO:0001052 name: nested_repeat is_obsolete: true [Term] id: SO:0001053 name: nested_transposon is_obsolete: true [Term] id: SO:0001054 name: transposon_fragment def: "A portion of a transposon, interrupted by the insertion of another element." [SO:ke] synonym: "transposon fragment" EXACT [] is_a: SO:0000840 ! repeat_component relationship: part_of SO:0001648 ! nested_transposon [Term] id: SO:0001055 name: transcriptional_cis_regulatory_region def: "A regulatory_region that modulates the transcription of a gene or genes." [SO:regcreative] subset: SOFA synonym: "transcriptional cis regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0001056 name: splicing_regulatory_region def: "A regulatory_region that modulates splicing." [SO:ke] subset: SOFA synonym: "splicing regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0001057 name: enhanceosome is_obsolete: true [Term] id: SO:0001058 name: promoter_targeting_sequence def: "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative] synonym: "promoter targeting sequence" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0001059 name: sequence_alteration alt_id: SO:1000004 alt_id: SO:1000007 def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] comment: Merged with partially characterized change in nucleotide sequence. subset: SOFA synonym: "partially characterised change in DNA sequence" NARROW [] synonym: "partially_characterised_change_in_DNA_sequence" NARROW [] synonym: "sequence alteration" EXACT [] synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0001060 name: sequence_variant def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke] synonym: "sequence variant" EXACT [] [Term] id: SO:0001061 name: propeptide_cleavage_site alt_id: BS:00063 def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR] comment: Discrete. subset: biosapiens synonym: "propeptide cleavage site" EXACT [] is_a: SO:0100011 ! cleaved_peptide_region relationship: part_of SO:0001062 ! propeptide [Term] id: SO:0001062 name: propeptide alt_id: BS:00077 def: "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "propep" RELATED [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Propeptide "wiki" is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0001063 name: immature_peptide_region alt_id: BS:00129 def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR] comment: Range. subset: biosapiens subset: SOFA synonym: "immature peptide region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001064 name: active_peptide alt_id: BS:00076 def: "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual] comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length. subset: biosapiens synonym: "active peptide" EXACT [] synonym: "peptide" BROAD [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Peptide "wiki" is_a: SO:0000419 ! mature_protein_region [Term] id: SO:0001066 name: compositionally_biased_region_of_peptide alt_id: BS:00068 def: "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "compbias" RELATED [uniprot:feature_type] synonym: "compositional bias" RELATED [] synonym: "compositionally biased" RELATED [] synonym: "compositionally biased region of peptide" RELATED [] synonym: "compositionally_biased_region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001067 name: polypeptide_motif alt_id: BS:00032 def: "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "motif" BROAD [uniprot:feature_type] synonym: "polypeptide motif" EXACT [] is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0001068 name: polypeptide_repeat alt_id: BS:00070 def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "polypeptide repeat" EXACT [] synonym: "repeat" RELATED [uniprot:feature_type] is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0001070 name: polypeptide_structural_region alt_id: BS:00337 def: "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb] comment: Range. subset: biosapiens synonym: "polypeptide structural region" EXACT [] synonym: "structural_region" RELATED [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001071 name: membrane_structure alt_id: BS:00128 def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "membrane structure" EXACT [] is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0001072 name: extramembrane_polypeptide_region alt_id: BS:00154 def: "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb] comment: Range. subset: biosapiens synonym: "extramembrane" RELATED BS [] synonym: "extramembrane polypeptide region" EXACT [] synonym: "extramembrane_region" RELATED BS [] synonym: "topo_dom" RELATED BS [uniprot:feature_type] is_a: SO:0001070 ! polypeptide_structural_region relationship: part_of SO:0001071 ! membrane_structure [Term] id: SO:0001073 name: cytoplasmic_polypeptide_region alt_id: BS:00145 def: "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "cytoplasm_location" EXACT BS [] synonym: "cytoplasmic polypeptide region" EXACT [] synonym: "inside" RELATED BS [] is_a: SO:0001072 ! extramembrane_polypeptide_region [Term] id: SO:0001074 name: non_cytoplasmic_polypeptide_region alt_id: BS:00144 def: "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb] comment: This could be inside an organelle within the cell. subset: biosapiens synonym: "non cytoplasmic polypeptide region" EXACT [] synonym: "non_cytoplasm_location" EXACT BS [] synonym: "outside" RELATED BS [] is_a: SO:0001072 ! extramembrane_polypeptide_region [Term] id: SO:0001075 name: intramembrane_polypeptide_region alt_id: BS:00156 def: "Polypeptide region present in the lipid bilayer." [EBIBS:GAR] subset: biosapiens synonym: "intramembrane" RELATED BS [] synonym: "intramembrane polypeptide region" EXACT [] is_a: SO:0001070 ! polypeptide_structural_region relationship: part_of SO:0001071 ! membrane_structure [Term] id: SO:0001076 name: membrane_peptide_loop alt_id: BS:00155 def: "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "membrane peptide loop" EXACT [] synonym: "membrane_loop" RELATED BS [] is_a: SO:0001075 ! intramembrane_polypeptide_region [Term] id: SO:0001077 name: transmembrane_polypeptide_region alt_id: BS:00158 def: "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual] subset: biosapiens synonym: "transmem" RELATED BS [uniprot:feature_type] synonym: "transmembrane" RELATED BS [] synonym: "transmembrane polypeptide region" EXACT [] is_a: SO:0001075 ! intramembrane_polypeptide_region [Term] id: SO:0001078 name: polypeptide_secondary_structure alt_id: BS:00003 def: "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR] comment: Biosapien term was secondary_structure. subset: biosapiens synonym: "2nary structure" RELATED BS [] synonym: "polypeptide secondary structure" EXACT [] synonym: "secondary structure" RELATED BS [] synonym: "secondary structure region" RELATED BS [] synonym: "secondary_structure" RELATED BS [] xref: http://en.wikipedia.org/wiki/Secondary_structure "wiki" is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0001079 name: polypeptide_structural_motif alt_id: BS:0000338 def: "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR] subset: biosapiens synonym: "polypeptide structural motif" RELATED [] synonym: "structural_motif" RELATED BS [] xref: http://en.wikipedia.org/wiki/Structural_motif "wiki" is_a: SO:0001070 ! polypeptide_structural_region [Term] id: SO:0001080 name: coiled_coil alt_id: BS:00041 def: "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "coiled" RELATED BS [uniprot:feature_type] synonym: "coiled coil" EXACT [] xref: http://en.wikipedia.org/wiki/Coiled_coil "wiki" is_a: SO:0001079 ! polypeptide_structural_motif [Term] id: SO:0001081 name: helix_turn_helix alt_id: BS:00147 def: "A motif comprising two helices separated by a turn." [EBIBS:GAR] subset: biosapiens synonym: "helix turn helix" EXACT [] synonym: "helix-turn-helix" EXACT [] synonym: "HTH" RELATED BS [] is_a: SO:0001079 ! polypeptide_structural_motif relationship: has_part SO:0001114 ! peptide_helix relationship: has_part SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001082 name: polypeptide_sequencing_information alt_id: BS:00125 def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "sequencing_information" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0001083 name: non_adjacent_residues alt_id: BS:00182 def: "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual] subset: biosapiens synonym: "non consecutive" EXACT [] synonym: "non_cons" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001084 name: non_terminal_residue alt_id: BS:00072 def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "non terminal" EXACT [] synonym: "non_ter" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001085 name: sequence_conflict alt_id: BS:00069 def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "conflict" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001086 name: sequence_uncertainty alt_id: BS:00181 def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual] subset: biosapiens synonym: "unsure" EXACT [uniprot:feature_type] is_a: SO:0001082 ! polypeptide_sequencing_information [Term] id: SO:0001087 name: cross_link alt_id: BS:00178 def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual] subset: biosapiens synonym: "cross link" EXACT [] synonym: "crosslink" RELATED [] is_obsolete: true [Term] id: SO:0001088 name: disulfide_bond alt_id: BS:00028 def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual] comment: 2 discreet & joined. subset: biosapiens synonym: "disulfid" RELATED [] synonym: "disulfide" RELATED [] synonym: "disulfide bond" RELATED [] synonym: "disulphide" EXACT [] synonym: "disulphide bond" RELATED [] is_obsolete: true [Term] id: SO:0001089 name: post_translationally_modified_region alt_id: BS:00052 def: "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "mod_res" EXACT [uniprot:feature_type] synonym: "modified residue" EXACT [] synonym: "post_translational_modification" EXACT [] xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki" is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0001090 name: covalent_binding_site alt_id: BS:00246 def: "Binding involving a covalent bond." [EBIBS:GAR] subset: biosapiens synonym: "covalent binding site" EXACT [] is_obsolete: true [Term] id: SO:0001091 name: non_covalent_binding_site alt_id: BS:00029 def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR] comment: Discrete. subset: biosapiens synonym: "binding" RELATED [uniprot:curation] synonym: "binding site" RELATED [] synonym: "non covalent binding site" EXACT [] is_obsolete: true [Term] id: SO:0001092 name: polypeptide_metal_contact alt_id: BS:00027 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual] comment: Residue is part of a binding site for a metal ion. subset: biosapiens synonym: "metal_binding" RELATED [] is_a: SO:0001656 ! metal_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001093 name: protein_protein_contact alt_id: BS:00131 def: "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual] subset: biosapiens synonym: "protein protein contact" EXACT [] synonym: "protein protein contact site" EXACT [] synonym: "protein_protein_interaction" RELATED [] xref: http://en.wikipedia.org/wiki/Protein_protein_interaction "wiki" is_a: SO:0000410 ! protein_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001094 name: polypeptide_calcium_ion_contact_site alt_id: BS:00186 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR] comment: Residue involved in contact with calcium. subset: biosapiens synonym: "ca bind" RELATED [] synonym: "Ca_contact_site" EXACT [] synonym: "polypeptide calcium ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001095 name: polypeptide_cobalt_ion_contact_site alt_id: BS:00136 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Co_contact_site" EXACT [] synonym: "polypeptide cobalt ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001096 name: polypeptide_copper_ion_contact_site alt_id: BS:00146 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Cu_contact_site" EXACT [] synonym: "polypeptide copper ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001097 name: polypeptide_iron_ion_contact_site alt_id: BS:00137 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Fe_contact_site" EXACT [] synonym: "polypeptide iron ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001098 name: polypeptide_magnesium_ion_contact_site alt_id: BS:00187 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Mg_contact_site" EXACT [] synonym: "polypeptide magnesium ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001099 name: polypeptide_manganese_ion_contact_site alt_id: BS:00140 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Mn_contact_site" EXACT [] synonym: "polypeptide manganese ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001100 name: polypeptide_molybdenum_ion_contact_site alt_id: BS:00141 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "Mo_contact_site" EXACT [] synonym: "polypeptide molybdenum ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001101 name: polypeptide_nickel_ion_contact_site alt_id: BS:00142 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR] subset: biosapiens synonym: "Ni_contact_site" EXACT [] synonym: "polypeptide nickel ion contact site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001102 name: polypeptide_tungsten_ion_contact_site alt_id: BS:00143 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "polypeptide tungsten ion contact site" EXACT [] synonym: "W_contact_site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001103 name: polypeptide_zinc_ion_contact_site alt_id: BS:00185 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb] subset: biosapiens synonym: "polypeptide zinc ion contact site" EXACT [] synonym: "Zn_contact_site" EXACT [] is_a: SO:0001092 ! polypeptide_metal_contact [Term] id: SO:0001104 name: catalytic_residue alt_id: BS:00026 def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "act_site" RELATED [uniprot:feature_type] synonym: "active site residue" EXACT [] synonym: "catalytic residue" EXACT [] is_a: SO:0001237 ! amino_acid relationship: part_of SO:0100019 ! polypeptide_catalytic_motif [Term] id: SO:0001105 name: polypeptide_ligand_contact alt_id: BS:00157 def: "Residues which interact with a ligand." [EBIBS:GAR] subset: biosapiens synonym: "polypeptide ligand contact" EXACT [] synonym: "protein-ligand interaction" RELATED [] is_a: SO:0001657 ! ligand_binding_site is_a: SO:0100002 ! molecular_contact_region [Term] id: SO:0001106 name: asx_motif alt_id: BS:00202 def: "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx motif" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001107 name: beta_bulge alt_id: BS:00208 def: "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge" EXACT [] xref: http://en.wikipedia.org/wiki/Beta_bulge "wiki" is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001108 name: beta_bulge_loop alt_id: BS:00209 def: "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge loop" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001109 name: beta_bulge_loop_five alt_id: BS:00210 def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge loop five" EXACT [] is_a: SO:0001108 ! beta_bulge_loop [Term] id: SO:0001110 name: beta_bulge_loop_six alt_id: BS:00211 def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta bulge loop six" EXACT [] is_a: SO:0001108 ! beta_bulge_loop [Term] id: SO:0001111 name: beta_strand alt_id: BS:00042 def: "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "strand" RELATED BS [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Beta_sheet "wiki" is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001112 name: antiparallel_beta_strand alt_id: BS:0000341 def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "antiparallel beta strand" EXACT [] is_a: SO:0001111 ! beta_strand [Term] id: SO:0001113 name: parallel_beta_strand alt_id: BS:00151 def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "parallel beta strand" EXACT [] is_a: SO:0001111 ! beta_strand [Term] id: SO:0001114 name: peptide_helix alt_id: BS:00152 def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "helix" RELATED BS [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001115 name: left_handed_peptide_helix alt_id: BS:00222 def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR] subset: biosapiens synonym: "helix-l" RELATED [] synonym: "left handed helix" EXACT [] is_a: SO:0001114 ! peptide_helix [Term] id: SO:0001116 name: right_handed_peptide_helix alt_id: BS:0000339 def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR] subset: biosapiens synonym: "helix" RELATED BS [] synonym: "right handed helix" EXACT [] is_a: SO:0001114 ! peptide_helix [Term] id: SO:0001117 name: alpha_helix alt_id: BS:00040 def: "The helix has 3.6 residues per turn which corersponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "a-helix" RELATED BS [] synonym: "helix" RELATED BS [uniprot:feature_type] xref: http://en.wikipedia.org/wiki/Alpha_helix "wiki" is_a: SO:0001116 ! right_handed_peptide_helix [Term] id: SO:0001118 name: pi_helix alt_id: BS:00153 def: "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "pi helix" EXACT [] xref: http://en.wikipedia.org/wiki/Pi_helix "wiki" is_a: SO:0001116 ! right_handed_peptide_helix [Term] id: SO:0001119 name: three_ten_helix alt_id: BS:0000340 def: "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "3(10) helix" EXACT [] synonym: "3-10 helix" EXACT [] synonym: "310 helix" EXACT [] synonym: "three ten helix" EXACT [] xref: http://en.wikipedia.org/wiki/310_helix "wiki" is_a: SO:0001116 ! right_handed_peptide_helix [Term] id: SO:0001120 name: polypeptide_nest_motif alt_id: BS:00223 def: "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "nest" RELATED BS [] synonym: "nest_motif" EXACT [] synonym: "polypeptide nest motif" RELATED [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001121 name: polypeptide_nest_left_right_motif alt_id: BS:00224 def: "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "nest_left_right" EXACT [] synonym: "nest_lr" EXACT [] synonym: "polypeptide nest left right motif" EXACT [] is_a: SO:0001120 ! polypeptide_nest_motif [Term] id: SO:0001122 name: polypeptide_nest_right_left_motif alt_id: BS:00225 def: "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "nest_right_left" EXACT [] synonym: "nest_rl" EXACT [] synonym: "polypeptide nest right left motif" EXACT [] is_a: SO:0001120 ! polypeptide_nest_motif [Term] id: SO:0001123 name: schellmann_loop alt_id: BS:00226 def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "paperclip" RELATED BS [] synonym: "paperclip loop" RELATED [] synonym: "schellmann loop" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001124 name: schellmann_loop_seven alt_id: BS:00228 def: "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "schellmann loop seven" EXACT [] synonym: "seven-residue schellmann loop" EXACT [] is_a: SO:0001123 ! schellmann_loop [Term] id: SO:0001125 name: schellmann_loop_six alt_id: BS:00227 def: "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "schellmann loop six" EXACT [] synonym: "six-residue schellmann loop" EXACT [] is_a: SO:0001123 ! schellmann_loop [Term] id: SO:0001126 name: serine_threonine_motif alt_id: BS:00229 def: "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "serine/threonine motif" EXACT [] synonym: "st motif" EXACT [] synonym: "st_motif" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001127 name: serine_threonine_staple_motif alt_id: BS:00230 def: "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "serine threonine staple motif" EXACT [] synonym: "st_staple" EXACT [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001128 name: polypeptide_turn_motif alt_id: BS:00148 def: "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type] comment: Range. subset: biosapiens synonym: "turn" RELATED BS [] is_a: SO:0001078 ! polypeptide_secondary_structure [Term] id: SO:0001129 name: asx_turn_left_handed_type_one alt_id: BS:00206 def: "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn left handed type one" EXACT [] synonym: "asx_turn_il" RELATED [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001130 name: asx_turn_left_handed_type_two alt_id: BS:00204 def: "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn left handed type two" EXACT [] synonym: "asx_turn_iil" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001131 name: asx_turn_right_handed_type_two alt_id: BS:00205 def: "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn right handed type two" EXACT [] synonym: "asx_turn_iir" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001132 name: asx_turn_right_handed_type_one alt_id: BS:00207 def: "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "asx turn type right handed type one" EXACT [] synonym: "asx_turn_ir" EXACT [] is_a: SO:0000912 ! asx_turn [Term] id: SO:0001133 name: beta_turn alt_id: BS:00212 def: "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001134 name: beta_turn_left_handed_type_one alt_id: BS:00215 def: "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn left handed type one" EXACT [] synonym: "beta_turn_il" EXACT [] synonym: "type I' beta turn" EXACT [] synonym: "type I' turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001135 name: beta_turn_left_handed_type_two alt_id: BS:00213 def: "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn left handed type two" EXACT [] synonym: "beta_turn_iil" EXACT [] synonym: "type II' beta turn" EXACT [] synonym: "type II' turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001136 name: beta_turn_right_handed_type_one alt_id: BS:00216 def: "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn right handed type one" EXACT [] synonym: "beta_turn_ir" EXACT [] synonym: "type I beta turn" EXACT [] synonym: "type I turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001137 name: beta_turn_right_handed_type_two alt_id: BS:00214 def: "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "beta turn right handed type two" EXACT [] synonym: "beta_turn_iir" EXACT [] synonym: "type II beta turn" EXACT [] synonym: "type II turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001138 name: gamma_turn alt_id: BS:00219 def: "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "gamma turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001139 name: gamma_turn_classic alt_id: BS:00220 def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "classic gamma turn" EXACT [] synonym: "gamma turn classic" EXACT [] is_a: SO:0001138 ! gamma_turn [Term] id: SO:0001140 name: gamma_turn_inverse alt_id: BS:00221 def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "gamma turn inverse" EXACT [] is_a: SO:0001138 ! gamma_turn [Term] id: SO:0001141 name: serine_threonine_turn alt_id: BS:00231 def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "serine/threonine turn" EXACT [] synonym: "st_turn" EXACT [] is_a: SO:0001128 ! polypeptide_turn_motif [Term] id: SO:0001142 name: st_turn_left_handed_type_one alt_id: BS:00234 def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn left handed type one" EXACT [] synonym: "st_turn_il" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001143 name: st_turn_left_handed_type_two alt_id: BS:00232 def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn left handed type two" EXACT [] synonym: "st_turn_iil" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001144 name: st_turn_right_handed_type_one alt_id: BS:00235 def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn right handed type one" EXACT [] synonym: "st_turn_ir" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001145 name: st_turn_right_handed_type_two alt_id: BS:00233 def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/] subset: biosapiens synonym: "st turn right handed type two" EXACT [] synonym: "st_turn_iir" EXACT [] is_a: SO:0001141 ! serine_threonine_turn [Term] id: SO:0001146 name: polypeptide_variation_site alt_id: BS:00336 def: "A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke] comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations. subset: biosapiens synonym: "sequence_variations" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001147 name: natural_variant_site alt_id: BS:00071 def: "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "natural_variant" BROAD [] synonym: "sequence variation" BROAD [] synonym: "variant" BROAD [uniprot:feature_type] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001148 name: mutated_variant_site alt_id: BS:00036 def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "mutagen" EXACT BS [uniprot:feature_type] synonym: "mutagenesis" EXACT [] synonym: "mutated_site" EXACT [] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001149 name: alternate_sequence_site alt_id: BS:00073 alt_id: SO:0001065 def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "alternative_sequence" EXACT [] synonym: "isoform" NARROW [] synonym: "sequence variation" NARROW [] synonym: "var_seq" EXACT [uniprot:feature_type] synonym: "varsplic" NARROW [] is_a: SO:0001146 ! polypeptide_variation_site [Term] id: SO:0001150 name: beta_turn_type_six def: "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb] subset: biosapiens synonym: "beta turn type six" EXACT [] synonym: "cis-proline loop" EXACT [] synonym: "type VI beta turn" EXACT [] synonym: "type VI turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001151 name: beta_turn_type_six_a def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] subset: biosapiens synonym: "beta turn type six a" EXACT [] synonym: "type VIa beta turn" EXACT [] synonym: "type VIa turn" EXACT [] is_a: SO:0001150 ! beta_turn_type_six [Term] id: SO:0001152 name: beta_turn_type_six_a_one subset: biosapiens synonym: "beta turn type six a one" EXACT [] synonym: "type VIa1 beta turn" EXACT [] synonym: "type VIa1 turn" EXACT [] is_a: SO:0001151 ! beta_turn_type_six_a [Term] id: SO:0001153 name: beta_turn_type_six_a_two subset: biosapiens synonym: "beta turn type six a two" EXACT [] synonym: "type VIa2 beta turn" EXACT [] synonym: "type VIa2 turn" EXACT [] is_a: SO:0001151 ! beta_turn_type_six_a [Term] id: SO:0001154 name: beta_turn_type_six_b def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb] subset: biosapiens synonym: "beta turn type six b" EXACT [] synonym: "type VIb beta turn" EXACT [] synonym: "type VIb turn" EXACT [] is_a: SO:0001150 ! beta_turn_type_six [Term] id: SO:0001155 name: beta_turn_type_eight def: "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb] subset: biosapiens synonym: "beta turn type eight" EXACT [] synonym: "type VIII beta turn" EXACT [] synonym: "type VIII turn" EXACT [] is_a: SO:0001133 ! beta_turn [Term] id: SO:0001156 name: DRE_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576] comment: This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10. synonym: "DRE motif" EXACT [] synonym: "NDM4" EXACT [] synonym: "WATCGATW_motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001157 name: DMv4_motif def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576] synonym: "directional motif v4" EXACT [] synonym: "DMv4" EXACT [] synonym: "DMv4 motif" EXACT [] synonym: "motif 1 element" EXACT [] synonym: "promoter motif 1" EXACT [] synonym: "YGGTCACATR" NARROW [] is_a: SO:0001659 ! promoter_element [Term] id: SO:0001158 name: E_box_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941] synonym: "AWCAGCTGWT" NARROW [] synonym: "E box motif" EXACT [] synonym: "generic E box motif" EXACT [] synonym: "NDM5" RELATED [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001159 name: DMv5_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941] synonym: "directional motif v5" EXACT [] synonym: "DMv5" EXACT [] synonym: "DMv5 motif" EXACT [] synonym: "KTYRGTATWTTT" NARROW [] synonym: "promoter motif 6" RELATED [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001160 name: DMv3_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941] synonym: "directional motif v3" EXACT [] synonym: "DMv3" EXACT [] synonym: "DMv3 motif" EXACT [] synonym: "KNNCAKCNCTRNY" NARROW [] synonym: "promoter motif 7" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001161 name: DMv2_motif def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941] synonym: "directional motif v2" EXACT [] synonym: "DMv2" EXACT [] synonym: "DMv2 motif" EXACT [] synonym: "MKSYGGCARCGSYSS" NARROW [] synonym: "promoter motif 8" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001162 name: MTE def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867] synonym: "CSARCSSAACGS" NARROW [] synonym: "motif ten element" EXACT [] synonym: "motif_ten_element" EXACT [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter [Term] id: SO:0001163 name: INR1_motif def: "A promoter motif with consensus sequence TCATTCG." [PMID:16827941] synonym: "directional motif p3" EXACT [] synonym: "directional promoter motif 3" EXACT [] synonym: "DMp3" EXACT [] synonym: "INR1 motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001164 name: DPE1_motif def: "A promoter motif with consensus sequence CGGACGT." [PMID:16827941] synonym: "directional motif 5" EXACT [] synonym: "directional promoter motif 5" RELATED [] synonym: "DMp5" EXACT [] synonym: "DPE1 motif" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001165 name: DMv1_motif def: "A promoter motif with consensus sequence CARCCCT." [PMID:16827941] synonym: "directional promoter motif v1" RELATED [] synonym: "DMv1" RELATED [] synonym: "DMv1 motif" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001166 name: GAGA_motif def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941] synonym: "GAGA" EXACT [] synonym: "GAGA motif" EXACT [] synonym: "NDM1" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001167 name: NDM2_motif def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941] synonym: "NDM2" EXACT [] synonym: "NDM2 motif" EXACT [] synonym: "non directional promoter motif 2" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001168 name: NDM3_motif def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941] synonym: "NDM3" EXACT [] synonym: "NDM3 motif" EXACT [] synonym: "non directional motif 3" EXACT [] is_a: SO:0001659 ! promoter_element relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001169 name: ds_RNA_viral_sequence def: "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke] synonym: "double stranded RNA virus sequence" EXACT [] synonym: "ds RNA viral sequence" EXACT [] is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001170 name: polinton def: "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396] synonym: "maverick element" RELATED [] is_a: SO:0000208 ! terminal_inverted_repeat_element [Term] id: SO:0001171 name: rRNA_21S def: "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb] synonym: "21S LSU rRNA" EXACT [] synonym: "21S ribosomal RNA" EXACT [] synonym: "21S rRNA" EXACT [] synonym: "rRNA 21S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001172 name: tRNA_region def: "A region of a tRNA." [RSC:cb] synonym: "tRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000253 ! tRNA [Term] id: SO:0001173 name: anticodon_loop def: "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207] synonym: "anti-codon loop" EXACT [] synonym: "anticodon loop" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001174 name: anticodon def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb] synonym: "anti-codon" EXACT [] xref: http://en.wikipedia.org/wiki/Anticodon "wiki" is_a: SO:0001172 ! tRNA_region relationship: part_of SO:0001173 ! anticodon_loop [Term] id: SO:0001175 name: CCA_tail def: "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207] synonym: "CCA sequence" EXACT [] synonym: "CCA tail" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001176 name: DHU_loop def: "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920] synonym: "D loop" RELATED [] synonym: "DHU loop" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001177 name: T_loop def: "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207] synonym: "T loop" EXACT [] synonym: "TpsiC loop" EXACT [] is_a: SO:0001172 ! tRNA_region [Term] id: SO:0001178 name: pyrrolysine_tRNA_primary_transcript def: "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb] synonym: "pyrrolysine tRNA primary transcript" EXACT [] is_a: SO:0000210 ! tRNA_primary_transcript [Term] id: SO:0001179 name: U3_snoRNA def: "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012] comment: The definition is most of the old definition for snoRNA (SO:0000275). synonym: "small nucleolar RNA U3" EXACT [] synonym: "snoRNA U3" EXACT [] synonym: "U3 small nucleolar RNA" EXACT [] synonym: "U3 snoRNA" EXACT [] xref: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 "wiki" is_a: SO:0000593 ! C_D_box_snoRNA [Term] id: SO:0001180 name: AU_rich_element def: "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223] synonym: "ARE" RELATED [] synonym: "AU rich element" EXACT [] synonym: "AU-rich element" EXACT [] xref: http://en.wikipedia.org/wiki/AU-rich_element "wiki" is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000205 ! three_prime_UTR [Term] id: SO:0001181 name: Bruno_response_element def: "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231] comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B. synonym: "BRE" RELATED [] synonym: "Bruno response element" EXACT [] is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000205 ! three_prime_UTR [Term] id: SO:0001182 name: iron_responsive_element def: "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843] synonym: "IRE" EXACT [] synonym: "iron responsive element" EXACT [] xref: http://en.wikipedia.org/wiki/Iron_responsive_element "wiki" is_a: SO:0000837 ! UTR_region relationship: part_of SO:0000203 ! UTR [Term] id: SO:0001183 name: morpholino_backbone def: "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb] comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead. synonym: "morpholino backbone" EXACT [] xref: http://en.wikipedia.org/wiki/Morpholino "wiki" is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001184 name: PNA def: "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb] comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead. synonym: "peptide nucleic acid" RELATED [] is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001185 name: enzymatic def: "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead. is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001186 name: ribozymic def: "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb] comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead. is_a: SO:0001185 ! enzymatic [Term] id: SO:0001187 name: pseudouridylation_guide_snoRNA def: "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565] comment: Has RNA pseudouridylation guide activity (GO:0030558). synonym: "pseudouridylation guide snoRNA" EXACT [] is_a: SO:0000594 ! H_ACA_box_snoRNA [Term] id: SO:0001188 name: LNA def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010] comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001189 name: LNA_oligo def: "An oligo composed of LNA residues." [RSC:cb] synonym: "LNA oligo" EXACT [] synonym: "locked nucleic acid" EXACT [] xref: http://en.wikipedia.org/wiki/Locked_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo relationship: has_quality SO:0001188 ! LNA [Term] id: SO:0001190 name: TNA def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019] comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001191 name: TNA_oligo def: "An oligo composed of TNA residues." [RSC:cb] synonym: "threose nucleic acid" EXACT [] synonym: "TNA oligo" EXACT [] xref: http://en.wikipedia.org/wiki/Threose_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo relationship: has_quality SO:0001190 ! TNA [Term] id: SO:0001192 name: GNA def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015] comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead. is_a: SO:0000348 ! nucleic_acid [Term] id: SO:0001193 name: GNA_oligo def: "An oligo composed of GNA residues." [RSC:cb] synonym: "glycerol nucleic acid" EXACT [] synonym: "glycol nucleic acid" EXACT [] synonym: "GNA oligo" EXACT [] xref: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid "wiki" is_a: SO:0001247 ! synthetic_oligo relationship: has_quality SO:0001192 ! GNA [Term] id: SO:0001194 name: R_GNA def: "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016] comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead. synonym: "R GNA" EXACT [] is_a: SO:0001192 ! GNA [Term] id: SO:0001195 name: R_GNA_oligo def: "An oligo composed of (R)-GNA residues." [RSC:cb] synonym: "(R)-glycerol nucleic acid" EXACT [] synonym: "(R)-glycol nucleic acid" EXACT [] synonym: "R GNA oligo" EXACT [] is_a: SO:0001193 ! GNA_oligo relationship: has_quality SO:0001194 ! R_GNA [Term] id: SO:0001196 name: S_GNA def: "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017] comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead. synonym: "S GNA" EXACT [] is_a: SO:0001192 ! GNA [Term] id: SO:0001197 name: S_GNA_oligo def: "An oligo composed of (S)-GNA residues." [RSC:cb] synonym: "(S)-glycerol nucleic acid" EXACT [] synonym: "(S)-glycol nucleic acid" EXACT [] synonym: "S GNA oligo" EXACT [] is_a: SO:0001193 ! GNA_oligo relationship: has_quality SO:0001196 ! S_GNA [Term] id: SO:0001198 name: ds_DNA_viral_sequence def: "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke] synonym: "double stranded DNA virus" EXACT [] synonym: "ds DNA viral sequence" EXACT [] is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001199 name: ss_RNA_viral_sequence def: "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke] synonym: "single strand RNA virus" EXACT [] synonym: "ss RNA viral sequence" EXACT [] is_a: SO:0001041 ! viral_sequence [Term] id: SO:0001200 name: negative_sense_ssRNA_viral_sequence def: "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke] synonym: "negative sense single stranded RNA virus" RELATED [] synonym: "negative sense ssRNA viral sequence" EXACT [] is_a: SO:0001199 ! ss_RNA_viral_sequence [Term] id: SO:0001201 name: positive_sense_ssRNA_viral_sequence def: "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke] synonym: "positive sense single stranded RNA virus" RELATED [] synonym: "positive sense ssRNA viral sequence" EXACT [] is_a: SO:0001199 ! ss_RNA_viral_sequence [Term] id: SO:0001202 name: ambisense_ssRNA_viral_sequence def: "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke] synonym: "ambisense single stranded RNA virus" EXACT [] synonym: "ambisense ssRNA viral sequence" EXACT [] is_a: SO:0001199 ! ss_RNA_viral_sequence [Term] id: SO:0001203 name: RNA_polymerase_promoter def: "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "RNA polymerase promoter" EXACT [] is_a: SO:0000167 ! promoter [Term] id: SO:0001204 name: Phage_RNA_Polymerase_Promoter def: "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "Phage RNA Polymerase Promoter" EXACT [] is_a: SO:0001203 ! RNA_polymerase_promoter [Term] id: SO:0001205 name: SP6_RNA_Polymerase_Promoter def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "SP6 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001206 name: T3_RNA_Polymerase_Promoter def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "T3 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001207 name: T7_RNA_Polymerase_Promoter def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb] synonym: "T7 RNA Polymerase Promoter" EXACT [] is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter [Term] id: SO:0001208 name: five_prime_EST def: "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] synonym: "5' EST" EXACT [] synonym: "five prime EST" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001209 name: three_prime_EST def: "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html] synonym: "3' EST" EXACT [] synonym: "three prime EST" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001210 name: translational_frameshift def: "The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] synonym: "ribosomal frameshift" EXACT [] synonym: "translational frameshift" EXACT [] xref: http://en.wikipedia.org/wiki/Translational_frameshift "wiki" is_a: SO:0000836 ! mRNA_region [Term] id: SO:0001211 name: plus_1_translational_frameshift def: "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] synonym: "plus 1 ribosomal frameshift" EXACT [] synonym: "plus 1 translational frameshift" EXACT [] is_a: SO:0001210 ! translational_frameshift [Term] id: SO:0001212 name: plus_2_translational_frameshift def: "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke] synonym: "plus 2 ribosomal frameshift" EXACT [] synonym: "plus 2 translational frameshift" EXACT [] is_a: SO:0001210 ! translational_frameshift [Term] id: SO:0001213 name: group_III_intron def: "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794] comment: GO:0000374. synonym: "group III intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_III_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0001214 name: noncoding_region_of_exon def: "The maximal intersection of exon and UTR." [SO:ke] comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding. subset: SOFA synonym: "noncoding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001215 name: coding_region_of_exon def: "The region of an exon that encodes for protein sequence." [SO:ke] comment: An exon containing either a start or stop codon will be partially coding and partially non coding. subset: SOFA synonym: "coding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001216 name: endonuclease_spliced_intron def: "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke] synonym: "endonuclease spliced intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0001217 name: protein_coding_gene synonym: "protein coding gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000010 ! protein_coding [Term] id: SO:0001218 name: transgenic_insertion def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm] synonym: "transgenic insertion" EXACT [] is_a: SO:0000667 ! insertion relationship: has_quality SO:0000781 ! transgenic [Term] id: SO:0001219 name: retrogene is_a: SO:0000704 ! gene relationship: has_quality SO:0000569 ! retrotransposed [Term] id: SO:0001220 name: silenced_by_RNA_interference def: "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb] comment: RNA interference is GO:0016246. synonym: "silenced by RNA interference" EXACT [] is_a: SO:0000893 ! silenced [Term] id: SO:0001221 name: silenced_by_histone_modification def: "An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb] comment: Histone modification is GO:0016570. synonym: "silenced by histone modification" EXACT [] is_a: SO:0000893 ! silenced [Term] id: SO:0001222 name: silenced_by_histone_methylation def: "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb] comment: Histone methylation is GO:0016571. synonym: "silenced by histone methylation" EXACT [] is_a: SO:0001221 ! silenced_by_histone_modification [Term] id: SO:0001223 name: silenced_by_histone_deacetylation def: "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb] comment: Histone deacetylation is GO:0016573. synonym: "silenced by histone deacetylation" EXACT [] is_a: SO:0001221 ! silenced_by_histone_modification [Term] id: SO:0001224 name: gene_silenced_by_RNA_interference def: "A gene that is silenced by RNA interference." [SO:xp] synonym: "gene silenced by RNA interference" EXACT [] synonym: "RNA interference silenced gene" EXACT [] synonym: "RNAi silenced gene" EXACT [] is_a: SO:0000127 ! silenced_gene relationship: has_quality SO:0001220 ! silenced_by_RNA_interference [Term] id: SO:0001225 name: gene_silenced_by_histone_modification def: "A gene that is silenced by histone modification." [SO:xp] synonym: "gene silenced by histone modification" EXACT [] is_a: SO:0000127 ! silenced_gene relationship: has_quality SO:0001221 ! silenced_by_histone_modification [Term] id: SO:0001226 name: gene_silenced_by_histone_methylation def: "A gene that is silenced by histone methylation." [SO:xp] synonym: "gene silenced by histone methylation" EXACT [] is_a: SO:0001225 ! gene_silenced_by_histone_modification relationship: has_quality SO:0001222 ! silenced_by_histone_methylation [Term] id: SO:0001227 name: gene_silenced_by_histone_deacetylation def: "A gene that is silenced by histone deacetylation." [SO:xp] synonym: "gene silenced by histone deacetylation" EXACT [] is_a: SO:0001225 ! gene_silenced_by_histone_modification relationship: has_quality SO:0001223 ! silenced_by_histone_deacetylation [Term] id: SO:0001228 name: dihydrouridine def: "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb] synonym: "D" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Dihydrouridine "wiki" xref: RNAMOD:051 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001229 name: pseudouridine def: "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb] comment: The free molecule is CHEBI:17802. synonym: "Y" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Pseudouridine "wiki" xref: RNAMOD:050 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001230 name: inosine def: "A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb] comment: The free molecule is CHEBI:17596. synonym: "I" RELATED [] synonym: "RNAMOD:017" RELATED [] xref: http://en.wikipedia.org/wiki/Inosine "wiki" is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001231 name: seven_methylguanine def: "A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb] comment: The free molecule is CHEBI:2274. synonym: "7-methylguanine" EXACT [] synonym: "seven methylguanine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001232 name: ribothymidine def: "A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb] comment: The free molecule is CHEBI:30832. is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001233 name: methylinosine def: "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb] is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001234 name: mobile def: "An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb] xref: http://en.wikipedia.org/wiki/Mobile "wiki" is_a: SO:0000733 ! feature_attribute [Term] id: SO:0001235 name: replicon def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] subset: SOFA xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001236 name: base def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Nucleobase "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001237 name: amino_acid def: "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb] comment: Probably in the future this will cross reference to Chebi. synonym: "amino acid" EXACT [] xref: http://en.wikipedia.org/wiki/Amino_acid "wiki" is_a: SO:0001411 ! biological_region relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0001238 name: major_TSS synonym: "major transcription start site" EXACT [] synonym: "major TSS" EXACT [] is_a: SO:0000315 ! TSS [Term] id: SO:0001239 name: minor_TSS synonym: "minor TSS" EXACT [] is_a: SO:0000315 ! TSS [Term] id: SO:0001240 name: TSS_region def: "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw] synonym: "TSS region" EXACT [] is_a: SO:0000842 ! gene_component_region relationship: has_part SO:0000315 ! TSS [Term] id: SO:0001241 name: encodes_alternate_transcription_start_sites synonym: "encodes alternate transcription start sites" EXACT [] is_a: SO:0000401 ! gene_attribute [Term] id: SO:0001243 name: miRNA_primary_transcript_region def: "A part of an miRNA primary_transcript." [SO:ke] synonym: "miRNA primary transcript region" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0001244 name: pre_miRNA def: "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin sructure." [SO:ke] synonym: "pre-miRNA" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region relationship: part_of SO:0000647 ! miRNA_primary_transcript [Term] id: SO:0001245 name: miRNA_stem def: "The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] synonym: "miRNA stem" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region relationship: part_of SO:0001244 ! pre_miRNA [Term] id: SO:0001246 name: miRNA_loop def: "The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke] synonym: "miRNA loop" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region relationship: part_of SO:0001244 ! pre_miRNA [Term] id: SO:0001247 name: synthetic_oligo def: "An oligo composed of synthetic nucleotides." [SO:ke] synonym: "synthetic oligo" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0001248 name: assembly def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0001249 name: fragment_assembly def: "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke] synonym: "fragment assembly" EXACT [] synonym: "physical map" EXACT [] is_a: SO:0001248 ! assembly [Term] id: SO:0001250 name: fingerprint_map def: "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke] synonym: "BACmap" EXACT [] synonym: "fingerprint map" EXACT [] synonym: "FPC" EXACT [] synonym: "FPCmap" EXACT [] synonym: "restriction map" EXACT [] is_a: SO:0001249 ! fragment_assembly relationship: has_part SO:0000412 ! restriction_fragment [Term] id: SO:0001251 name: STS_map def: "An STS map is a physical map organized by the unique STS landmarks." [SO:ke] synonym: "STS map" EXACT [] is_a: SO:0001249 ! fragment_assembly relationship: has_part SO:0000331 ! STS [Term] id: SO:0001252 name: RH_map def: "A radiation hybrid map is a physical map." [SO:ke] synonym: "radiation hybrid map" EXACT [] synonym: "RH map" EXACT [] is_a: SO:0001249 ! fragment_assembly relationship: has_part SO:0000331 ! STS [Term] id: SO:0001253 name: sonicate_fragment def: "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke] synonym: "sonicate fragment" EXACT [] is_a: SO:0000143 ! assembly_component [Term] id: SO:0001254 name: polyploid def: "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke] xref: http://en.wikipedia.org/wiki/Polyploid "wiki" is_a: SO:1000182 ! chromosome_number_variation [Term] id: SO:0001255 name: autopolyploid def: "A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke] xref: http://en.wikipedia.org/wiki/Autopolyploid "wiki" is_a: SO:0001254 ! polyploid [Term] id: SO:0001256 name: allopolyploid def: "A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke] xref: http://en.wikipedia.org/wiki/Allopolyploid "wiki" is_a: SO:0001254 ! polyploid [Term] id: SO:0001257 name: homing_endonuclease_binding_site def: "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke] synonym: "homing endonuclease binding site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0001258 name: octamer_motif def: "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662] comment: Nature. 1986 Oct 16-22;323(6089):640-3. synonym: "octamer motif" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000170 ! RNApol_II_promoter [Term] id: SO:0001259 name: apicoplast_chromosome def: "A chromosome originating in an apicoplast." [SO:xp] synonym: "apicoplast chromosome" EXACT [] is_a: SO:0000340 ! chromosome relationship: has_origin SO:0000743 ! apicoplast_sequence [Term] id: SO:0001260 name: sequence_collection def: "A collection of discontinuous sequences." [SO:ke] synonym: "sequence collection" EXACT [] [Term] id: SO:0001261 name: overlapping_feature_set def: "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke] comment: This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA. synonym: "overlapping feature set" EXACT [] is_a: SO:0000703 ! experimental_result_region [Term] id: SO:0001262 name: overlapping_EST_set def: "A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke] synonym: "overlapping EST set" EXACT [] is_a: SO:0001261 ! overlapping_feature_set relationship: has_part SO:0000345 ! EST [Term] id: SO:0001263 name: ncRNA_gene synonym: "ncRNA gen" EXACT [] synonym: "ncRNA gene" EXACT [] synonym: "non-coding RNA gene" RELATED [] is_a: SO:0000704 ! gene [Term] id: SO:0001264 name: gRNA_gene synonym: "gRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000979 ! gRNA_encoding [Term] id: SO:0001265 name: miRNA_gene synonym: "miRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000571 ! miRNA_encoding [Term] id: SO:0001266 name: scRNA_gene synonym: "scRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000575 ! scRNA_encoding [Term] id: SO:0001267 name: snoRNA_gene synonym: "snoRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000578 ! snoRNA_encoding [Term] id: SO:0001268 name: snRNA_gene synonym: "snRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0001263 ! ncRNA_gene [Term] id: SO:0001269 name: SRP_RNA_gene synonym: "SRP RNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000642 ! SRP_RNA_encoding [Term] id: SO:0001270 name: stRNA_gene synonym: "stRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000656 ! stRNA_encoding [Term] id: SO:0001271 name: tmRNA_gene synonym: "tmRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000659 ! tmRNA_encoding [Term] id: SO:0001272 name: tRNA_gene synonym: "tRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene relationship: has_quality SO:0000663 ! tRNA_encoding [Term] id: SO:0001273 name: modified_adenosine def: "A modified adenine is an adenine base feature that has been altered." [SO:ke] synonym: "modified adenosine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001274 name: modified_inosine def: "A modified inosine is an inosine base feature that has been altered." [SO:ke] synonym: "modified inosine" EXACT [] is_a: SO:0001230 ! inosine [Term] id: SO:0001275 name: modified_cytidine def: "A modified cytidine is a cytidine base feature which has been altered." [SO:ke] synonym: "modified cytidine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001276 name: modified_guanosine synonym: "modified guanosine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001277 name: modified_uridine synonym: "modified uridine" EXACT [] is_a: SO:0000250 ! modified_RNA_base_feature [Term] id: SO:0001278 name: one_methylinosine def: "1-methylinosine is a modified insosine." [http://library.med.utah.edu/RNAmods/] synonym: "1-methylinosine" EXACT [] synonym: "m1I" EXACT RNAMOD [] synonym: "one methylinosine" EXACT [] xref: RNAMOD:018 is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001279 name: one_two_prime_O_dimethylinosine def: "1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] synonym: "1,2'-O-dimethylinosine" EXACT [] synonym: "m'Im" EXACT RNAMOD [] synonym: "one two prime O dimethylinosine" EXACT [] xref: RNAMOD:019 is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001280 name: two_prime_O_methylinosine def: "2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylinosine" EXACT [] synonym: "Im" EXACT RNAMOD [] synonym: "two prime O methylinosine" EXACT [] xref: RNAMOD:081 is_a: SO:0001274 ! modified_inosine [Term] id: SO:0001281 name: three_methylcytidine def: "3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "3-methylcytidine" EXACT [] synonym: "m3C" EXACT RNAMOD [] synonym: "three methylcytidine" EXACT [] xref: RNAMOD:020 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001282 name: five_methylcytidine def: "5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylcytidine" EXACT [] synonym: "five methylcytidine" EXACT [] synonym: "m5C" EXACT RNAMOD [] xref: RNAMOD:021 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001283 name: two_prime_O_methylcytidine def: "2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylcytidine" EXACT [] synonym: "Cm" EXACT RNAMOD [] synonym: "two prime O methylcytidine" EXACT [] xref: RNAMOD:022 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001284 name: two_thiocytidine def: "2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "2-thiocytidine" EXACT [] synonym: "s2C" EXACT RNAMOD [] synonym: "two thiocytidine" EXACT [] xref: RNAMOD:023 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001285 name: N4_acetylcytidine def: "N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "ac4C" EXACT RNAMOD [] synonym: "N4 acetylcytidine" EXACT [] synonym: "N4-acetylcytidine" EXACT [] xref: RNAMOD:024 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001286 name: five_formylcytidine def: "5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-formylcytidine" EXACT [] synonym: "f5C" EXACT RNAMOD [] synonym: "five formylcytidine" EXACT [] xref: RNAMOD:025 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001287 name: five_two_prime_O_dimethylcytidine def: "5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5,2'-O-dimethylcytidine" EXACT [] synonym: "five two prime O dimethylcytidine" EXACT [] synonym: "m5Cm" EXACT RNAMOD [] xref: RNAMOD:026 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001288 name: N4_acetyl_2_prime_O_methylcytidine def: "N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "ac4Cm" EXACT RNAMOD [] synonym: "N4 acetyl 2 prime O methylcytidine" EXACT [] synonym: "N4-acetyl-2'-O-methylcytidine" EXACT [] xref: RNAMOD:027 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001289 name: lysidine def: "Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "k2C" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Lysidine "wiki" xref: RNAMOD:028 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001290 name: N4_methylcytidine def: "N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "m4C" EXACT RNAMOD [] synonym: "N4 methylcytidine" EXACT [] synonym: "N4-methylcytidine" EXACT [] xref: RNAMOD:082 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001291 name: N4_2_prime_O_dimethylcytidine def: "N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "m4Cm" EXACT RNAMOD [] synonym: "N4 2 prime O dimethylcytidine" EXACT [] synonym: "N4,2'-O-dimethylcytidine" EXACT [] xref: RNAMOD:083 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001292 name: five_hydroxymethylcytidine def: "5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-hydroxymethylcytidine" EXACT [] synonym: "five hydroxymethylcytidine" EXACT [] synonym: "hm5C" EXACT RNAMOD [] xref: RNAMOD:084 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001293 name: five_formyl_two_prime_O_methylcytidine def: "5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "5-formyl-2'-O-methylcytidine" EXACT [] synonym: "f5Cm" EXACT RNAMOD [] synonym: "five formyl two prime O methylcytidine" EXACT [] xref: RNAMOD:095 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001294 name: N4_N4_2_prime_O_trimethylcytidine def: "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/] synonym: "m42Cm" EXACT RNAMOD [] synonym: "N4,N4,2'-O-trimethylcytidine" EXACT [] xref: RNAMOD:107 is_a: SO:0001275 ! modified_cytidine [Term] id: SO:0001295 name: one_methyladenosine def: "1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "1-methyladenosine" EXACT [] synonym: "m1A" EXACT RNAMOD [] synonym: "one methyladenosine" EXACT [] xref: RNAMOD:001 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001296 name: two_methyladenosine def: "2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methyladenosine" EXACT [] synonym: "m2A" EXACT RNAMOD [] synonym: "two methyladenosine" EXACT [] xref: RNAMOD:002 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001297 name: N6_methyladenosine def: "N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m6A" EXACT RNAMOD [] synonym: "N6 methyladenosine" EXACT [] synonym: "N6-methyladenosine" EXACT [] xref: RNAMOD:003 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001298 name: two_prime_O_methyladenosine def: "2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methyladenosine" EXACT [] synonym: "Am" EXACT RNAMOD [] synonym: "two prime O methyladenosine" EXACT [] xref: RNAMOD:004 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001299 name: two_methylthio_N6_methyladenosine def: "2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-methyladenosine" EXACT [] synonym: "ms2m6A" EXACT RNAMOD [] synonym: "two methylthio N6 methyladenosine" EXACT [] xref: RNAMOD:005 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001300 name: N6_isopentenyladenosine def: "N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "i6A" EXACT RNAMOD [] synonym: "N6 isopentenyladenosine" EXACT [] synonym: "N6-isopentenyladenosine" EXACT [] xref: RNAMOD:006 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001301 name: two_methylthio_N6_isopentenyladenosine def: "2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-isopentenyladenosine" EXACT [] synonym: "ms2i6A" EXACT RNAMOD [] synonym: "two methylthio N6 isopentenyladenosine" EXACT [] xref: RNAMOD:007 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001302 name: N6_cis_hydroxyisopentenyl_adenosine def: "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "io6A" EXACT RNAMOD [] synonym: "N6 cis hydroxyisopentenyl adenosine" EXACT [] synonym: "N6-(cis-hydroxyisopentenyl)adenosine" EXACT [] xref: RNAMOD:008 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001303 name: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine def: "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine" EXACT [] synonym: "ms2io6A" EXACT RNAMOD [] synonym: "two methylthio N6 cis hydroxyisopentenyl adenosine" EXACT [] xref: RNAMOD:009 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001304 name: N6_glycinylcarbamoyladenosine def: "N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "g6A" EXACT RNAMOD [] synonym: "N6 glycinylcarbamoyladenosine" EXACT [] synonym: "N6-glycinylcarbamoyladenosine" EXACT [] xref: RNAMOD:010 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001305 name: N6_threonylcarbamoyladenosine def: "N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "N6 threonylcarbamoyladenosine" EXACT [] synonym: "N6-threonylcarbamoyladenosine" EXACT [] synonym: "t6A" EXACT RNAMOD [] xref: RNAMOD:011 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001306 name: two_methylthio_N6_threonyl_carbamoyladenosine def: "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-threonyl carbamoyladenosine" EXACT [] synonym: "ms2t6A" EXACT RNAMOD [] synonym: "two methylthio N6 threonyl carbamoyladenosine" EXACT [] xref: RNAMOD:012 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001307 name: N6_methyl_N6_threonylcarbamoyladenosine def: "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m6t6A" EXACT RNAMOD [] synonym: "N6 methyl N6 threonylcarbamoyladenosine" EXACT [] synonym: "N6-methyl-N6-threonylcarbamoyladenosine" EXACT [] xref: RNAMOD:013 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001308 name: N6_hydroxynorvalylcarbamoyladenosine def: "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "hn6A" EXACT RNAMOD [] synonym: "N6 hydroxynorvalylcarbamoyladenosine" EXACT [] synonym: "N6-hydroxynorvalylcarbamoyladenosine" EXACT [] xref: RNAMOD:014 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001309 name: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine def: "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine" EXACT [] synonym: "ms2hn6A" EXACT RNAMOD [] synonym: "two methylthio N6 hydroxynorvalyl carbamoyladenosine" EXACT [] xref: RNAMOD:015 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001310 name: two_prime_O_ribosyladenosine_phosphate def: "2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-ribosyladenosine (phosphate)" EXACT [] synonym: "Ar(p)" EXACT RNAMOD [] synonym: "two prime O ribosyladenosine phosphate" EXACT [] xref: RNAMOD:016 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001311 name: N6_N6_dimethyladenosine def: "N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m62A" EXACT RNAMOD [] synonym: "N6,N6-dimethyladenosine" EXACT [] xref: RNAMOD:080 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001312 name: N6_2_prime_O_dimethyladenosine def: "N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m6Am" EXACT RNAMOD [] synonym: "N6 2 prime O dimethyladenosine" EXACT [] synonym: "N6,2'-O-dimethyladenosine" EXACT [] xref: RNAMOD:088 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001313 name: N6_N6_2_prime_O_trimethyladenosine def: "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "m62Am" EXACT RNAMOD [] synonym: "N6,N6,2'-O-trimethyladenosine" EXACT [] xref: RNAMOD:089 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001314 name: one_two_prime_O_dimethyladenosine def: "1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "1,2'-O-dimethyladenosine" EXACT [] synonym: "m1Am" EXACT RNAMOD [] synonym: "one two prime O dimethyladenosine" EXACT [] xref: RNAMOD:097 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001315 name: N6_acetyladenosine def: "N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/] synonym: "ac6A" EXACT RNAMOD [] synonym: "N6 acetyladenosine" EXACT [] synonym: "N6-acetyladenosine" EXACT [] xref: RNAMOD:102 is_a: SO:0001273 ! modified_adenosine [Term] id: SO:0001316 name: seven_deazaguanosine def: "7-deazaguanosine is a moddified guanosine." [http://library.med.utah.edu/RNAmods/] synonym: "7-deazaguanosine" RELATED [] synonym: "seven deazaguanosine" EXACT [] is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001317 name: queuosine def: "Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "Q" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/Queuosine "wiki" xref: RNAMOD:043 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001318 name: epoxyqueuosine def: "Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "eQ" EXACT RNAMOD [] xref: RNAMOD:044 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001319 name: galactosyl_queuosine def: "Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "galactosyl queuosine" EXACT [] synonym: "galactosyl-queuosine" EXACT [] synonym: "galQ" EXACT RNAMOD [] xref: RNAMOD:045 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001320 name: mannosyl_queuosine def: "Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "mannosyl queuosine" EXACT [] synonym: "mannosyl-queuosine" EXACT [] synonym: "manQ" EXACT RNAMOD [] xref: RNAMOD:046 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001321 name: seven_cyano_seven_deazaguanosine def: "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "7-cyano-7-deazaguanosine" EXACT [] synonym: "preQ0" EXACT RNAMOD [] synonym: "seven cyano seven deazaguanosine" EXACT [] xref: RNAMOD:047 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001322 name: seven_aminomethyl_seven_deazaguanosine def: "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "7-aminomethyl-7-deazaguanosine" EXACT [] synonym: "preQ1" EXACT RNAMOD [] synonym: "seven aminomethyl seven deazaguanosine" EXACT [] xref: RNAMOD:048 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001323 name: archaeosine def: "Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/] synonym: "G+" EXACT RNAMOD [] xref: RNAMOD:049 is_a: SO:0001316 ! seven_deazaguanosine [Term] id: SO:0001324 name: one_methylguanosine def: "1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1-methylguanosine" EXACT [] synonym: "m1G" EXACT RNAMOD [] synonym: "one methylguanosine" EXACT [] xref: RNAMOD:029 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001325 name: N2_methylguanosine def: "N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2G" EXACT RNAMOD [] synonym: "N2 methylguanosine" EXACT [] synonym: "N2-methylguanosine" EXACT [] xref: RNAMOD:030 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001326 name: seven_methylguanosine def: "7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "7-methylguanosine" EXACT [] synonym: "m7G" EXACT RNAMOD [] synonym: "seven methylguanosine" EXACT [] xref: RNAMOD:031 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001327 name: two_prime_O_methylguanosine def: "2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylguanosine" EXACT [] synonym: "Gm" EXACT RNAMOD [] synonym: "two prime O methylguanosine" EXACT [] xref: RNAMOD:032 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001328 name: N2_N2_dimethylguanosine def: "N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m22G" EXACT RNAMOD [] synonym: "N2,N2-dimethylguanosine" EXACT [] xref: RNAMOD:033 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001329 name: N2_2_prime_O_dimethylguanosine def: "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2Gm" EXACT RNAMOD [] synonym: "N2 2 prime O dimethylguanosine" EXACT [] synonym: "N2,2'-O-dimethylguanosine" EXACT [] xref: RNAMOD:034 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001330 name: N2_N2_2_prime_O_trimethylguanosine def: "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m22Gmv" EXACT RNAMOD [] synonym: "N2,N2,2'-O-trimethylguanosine" EXACT [] xref: RNAMOD:035 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001331 name: two_prime_O_ribosylguanosine_phosphate def: "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-ribosylguanosine (phosphate)" EXACT [] synonym: "Gr(p)" EXACT RNAMOD [] synonym: "two prime O ribosylguanosine phosphate" EXACT [] xref: RNAMOD:036 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001332 name: wybutosine def: "Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "yW" EXACT RNAMOD [] xref: RNAMOD:037 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001333 name: peroxywybutosine def: "Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "o2yW" EXACT RNAMOD [] xref: RNAMOD:038 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001334 name: hydroxywybutosine def: "Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "OHyW" EXACT RNAMOD [] xref: RNAMOD:039 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001335 name: undermodified_hydroxywybutosine def: "Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "OHyW*" EXACT RNAMOD [] synonym: "undermodified hydroxywybutosine" EXACT [] xref: RNAMOD:040 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001336 name: wyosine def: "Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "IMG" EXACT RNAMOD [] xref: RNAMOD:041 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001337 name: methylwyosine def: "Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "mimG" EXACT RNAMOD [] xref: RNAMOD:042 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001338 name: N2_7_dimethylguanosine def: "N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2,7G" EXACT RNAMOD [] synonym: "N2 7 dimethylguanosine" EXACT [] synonym: "N2,7-dimethylguanosine" EXACT [] xref: RNAMOD:090 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001339 name: N2_N2_7_trimethylguanosine def: "N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2,2,7G" EXACT RNAMOD [] synonym: "N2,N2,7-trimethylguanosine" EXACT [] xref: RNAMOD:091 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001340 name: one_two_prime_O_dimethylguanosine def: "1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1,2'-O-dimethylguanosine" EXACT [] synonym: "m1Gm" EXACT RNAMOD [] synonym: "one two prime O dimethylguanosine" EXACT [] xref: RNAMOD:096 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001341 name: four_demethylwyosine def: "4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "4-demethylwyosine" EXACT [] synonym: "four demethylwyosine" EXACT [] synonym: "imG-14" EXACT RNAMOD [] xref: RNAMOD:100 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001342 name: isowyosine def: "Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "imG2" EXACT RNAMOD [] xref: RNAMOD:101 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001343 name: N2_7_2prirme_O_trimethylguanosine def: "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "m2,7Gm" EXACT RNAMOD [] synonym: "N2 7 2prirme O trimethylguanosine" EXACT [] synonym: "N2,7,2'-O-trimethylguanosine" EXACT [] xref: RNAMOD:106 is_a: SO:0001276 ! modified_guanosine [Term] id: SO:0001344 name: five_methyluridine def: "5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methyluridine" EXACT [] synonym: "five methyluridine" EXACT [] synonym: "m5U" EXACT RNAMOD [] xref: http://en.wikipedia.org/wiki/5-methyluridine "wiki" xref: RNAMOD:052 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001345 name: two_prime_O_methyluridine def: "2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methyluridine" EXACT [] synonym: "two prime O methyluridine" EXACT [] synonym: "Um" EXACT RNAMOD [] xref: RNAMOD:053 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001346 name: five_two_prime_O_dimethyluridine def: "5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5,2'-O-dimethyluridine" EXACT [] synonym: "five two prime O dimethyluridine" EXACT [] synonym: "m5Um" EXACT RNAMOD [] xref: RNAMOD:054 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001347 name: one_methylpseudouridine def: "1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1-methylpseudouridine" EXACT [] synonym: "m1Y" EXACT RNAMOD [] synonym: "one methylpseudouridine" EXACT [] xref: RNAMOD:055 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001348 name: two_prime_O_methylpseudouridine def: "2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2'-O-methylpseudouridine" EXACT [] synonym: "two prime O methylpseudouridine" EXACT [] synonym: "Ym" EXACT RNAMOD [] xref: RNAMOD:056 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001349 name: two_thiouridine def: "2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2-thiouridine" EXACT [] synonym: "s2U" EXACT RNAMOD [] synonym: "two thiouridine" EXACT [] xref: RNAMOD:057 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001350 name: four_thiouridine def: "4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "4-thiouridine" EXACT [] synonym: "four thiouridine" EXACT [] synonym: "s4U" EXACT RNAMOD [] xref: RNAMOD:058 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001351 name: five_methyl_2_thiouridine def: "5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methyl-2-thiouridine" EXACT [] synonym: "five methyl 2 thiouridine" EXACT [] synonym: "m5s2U" EXACT RNAMOD [] xref: RNAMOD:059 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001352 name: two_thio_two_prime_O_methyluridine def: "2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "2-thio-2'-O-methyluridine" EXACT [] synonym: "s2Um" EXACT RNAMOD [] synonym: "two thio two prime O methyluridine" EXACT [] xref: RNAMOD:060 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001353 name: three_three_amino_three_carboxypropyl_uridine def: "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3-(3-amino-3-carboxypropyl)uridine" EXACT [] synonym: "acp3U" EXACT RNAMOD [] xref: RNAMOD:061 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001354 name: five_hydroxyuridine def: "5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-hydroxyuridine" EXACT [] synonym: "five hydroxyuridine" EXACT [] synonym: "ho5U" EXACT RNAMOD [] xref: RNAMOD:060 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001355 name: five_methoxyuridine def: "5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxyuridine" EXACT [] synonym: "five methoxyuridine" EXACT [] synonym: "mo5U" EXACT RNAMOD [] xref: RNAMOD:063 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001356 name: uridine_five_oxyacetic_acid def: "Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "cmo5U" EXACT RNAMOD [] synonym: "uridine 5-oxyacetic acid" EXACT [] synonym: "uridine five oxyacetic acid" EXACT [] xref: RNAMOD:064 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001357 name: uridine_five_oxyacetic_acid_methyl_ester def: "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "mcmo5U" EXACT RNAMOD [] synonym: "uridine 5-oxyacetic acid methyl ester" EXACT [] synonym: "uridine five oxyacetic acid methyl ester" EXACT [] xref: RNAMOD:065 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001358 name: five_carboxyhydroxymethyl_uridine def: "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(carboxyhydroxymethyl)uridine" EXACT [] synonym: "chm5U" EXACT RNAMOD [] synonym: "five carboxyhydroxymethyl uridine" EXACT [] xref: RNAMOD:066 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001359 name: five_carboxyhydroxymethyl_uridine_methyl_ester def: "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(carboxyhydroxymethyl)uridine methyl ester" EXACT [] synonym: "five carboxyhydroxymethyl uridine methyl ester" EXACT [] synonym: "mchm5U" EXACT RNAMOD [] xref: RNAMOD:067 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001360 name: five_methoxycarbonylmethyluridine def: "Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxycarbonylmethyluridine" EXACT [] synonym: "five methoxycarbonylmethyluridine" EXACT [] synonym: "mcm5U" EXACT RNAMOD [] xref: RNAMOD:068 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001361 name: five_methoxycarbonylmethyl_two_prime_O_methyluridine def: "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxycarbonylmethyl-2'-O-methyluridine" EXACT [] synonym: "five methoxycarbonylmethyl two prime O methyluridine" EXACT [] synonym: "mcm5Um" EXACT RNAMOD [] xref: RNAMOD:069 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001362 name: five_methoxycarbonylmethyl_two_thiouridine def: "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methoxycarbonylmethyl-2-thiouridine" EXACT [] synonym: "five methoxycarbonylmethyl two thiouridine" EXACT [] synonym: "mcm5s2U" EXACT RNAMOD [] xref: RNAMOD:070 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001363 name: five_aminomethyl_two_thiouridine def: "5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-aminomethyl-2-thiouridine" EXACT [] synonym: "five aminomethyl two thiouridine" EXACT [] synonym: "nm5s2U" EXACT RNAMOD [] xref: RNAMOD:071 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001364 name: five_methylaminomethyluridine def: "5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylaminomethyluridine" EXACT [] synonym: "five methylaminomethyluridine" EXACT [] synonym: "mnm5U" EXACT RNAMOD [] xref: RNAMOD:072 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001365 name: five_methylaminomethyl_two_thiouridine def: "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylaminomethyl-2-thiouridine" EXACT [] synonym: "five methylaminomethyl two thiouridine" EXACT [] synonym: "mnm5s2U" EXACT RNAMOD [] xref: RNAMOD:073 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001366 name: five_methylaminomethyl_two_selenouridine def: "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methylaminomethyl-2-selenouridine" EXACT [] synonym: "five methylaminomethyl two selenouridine" EXACT [] synonym: "mnm5se2U" EXACT RNAMOD [] xref: RNAMOD:074 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001367 name: five_carbamoylmethyluridine def: "5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carbamoylmethyluridine" EXACT [] synonym: "five carbamoylmethyluridine" EXACT [] synonym: "ncm5U" EXACT RNAMOD [] xref: RNAMOD:075 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001368 name: five_carbamoylmethyl_two_prime_O_methyluridine def: "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carbamoylmethyl-2'-O-methyluridine" EXACT [] synonym: "five carbamoylmethyl two prime O methyluridine" EXACT [] synonym: "ncm5Um" EXACT RNAMOD [] xref: RNAMOD:076 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001369 name: five_carboxymethylaminomethyluridine def: "5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethylaminomethyluridine" EXACT [] synonym: "cmnm5U" EXACT RNAMOD [] synonym: "five carboxymethylaminomethyluridine" EXACT [] xref: RNAMOD:077 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001370 name: five_carboxymethylaminomethyl_two_prime_O_methyluridine def: "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethylaminomethyl- 2'-O-methyluridine" EXACT [] synonym: "cmnm5Um" EXACT RNAMOD [] synonym: "five carboxymethylaminomethyl two prime O methyluridine" EXACT [] xref: RNAMOD:078 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001371 name: five_carboxymethylaminomethyl_two_thiouridine def: "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethylaminomethyl-2-thiouridine" EXACT [] synonym: "cmnm5s2U" EXACT RNAMOD [] synonym: "five carboxymethylaminomethyl two thiouridine" EXACT [] xref: RNAMOD:079 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001372 name: three_methyluridine def: "3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3-methyluridine" EXACT [] synonym: "m3U" EXACT RNAMOD [] synonym: "three methyluridine" EXACT [] xref: RNAMOD:085 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001373 name: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine def: "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine" EXACT [] synonym: "m1acp3Y" EXACT RNAMOD [] xref: RNAMOD:086 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001374 name: five_carboxymethyluridine def: "5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-carboxymethyluridine" EXACT [] synonym: "cm5U" EXACT RNAMOD [] synonym: "five carboxymethyluridine" EXACT [] xref: RNAMOD:087 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001375 name: three_two_prime_O_dimethyluridine def: "3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3,2'-O-dimethyluridine" EXACT [] synonym: "m3Um" EXACT RNAMOD [] synonym: "three two prime O dimethyluridine" EXACT [] xref: RNAMOD:092 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001376 name: five_methyldihydrouridine def: "5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-methyldihydrouridine" EXACT [] synonym: "five methyldihydrouridine" EXACT [] synonym: "m5D" EXACT RNAMOD [] xref: RNAMOD:093 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001377 name: three_methylpseudouridine def: "3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "3-methylpseudouridine" EXACT [] synonym: "m3Y" EXACT RNAMOD [] synonym: "three methylpseudouridine" EXACT [] xref: RNAMOD:094 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001378 name: five_taurinomethyluridine def: "5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-taurinomethyluridine" EXACT [] synonym: "five taurinomethyluridine" EXACT [] synonym: "tm5U" EXACT RNAMOD [] xref: RNAMOD:098 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001379 name: five_taurinomethyl_two_thiouridine def: "5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-taurinomethyl-2-thiouridine" EXACT [] synonym: "five taurinomethyl two thiouridine" EXACT [] synonym: "tm5s2U" EXACT RNAMOD [] xref: RNAMOD:099 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001380 name: five_isopentenylaminomethyl_uridine def: "5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(isopentenylaminomethyl)uridine" EXACT [] synonym: "five isopentenylaminomethyl uridine" EXACT [] synonym: "inm5U" EXACT RNAMOD [] xref: RNAMOD:103 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001381 name: five_isopentenylaminomethyl_two_thiouridine def: "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(isopentenylaminomethyl)- 2-thiouridine" EXACT [] synonym: "five isopentenylaminomethyl two thiouridine" EXACT [] synonym: "inm5s2U" EXACT RNAMOD [] xref: RNAMOD:104 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001382 name: five_isopentenylaminomethyl_two_prime_O_methyluridine def: "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/] synonym: "5-(isopentenylaminomethyl)- 2'-O-methyluridine" EXACT [] synonym: "five isopentenylaminomethyl two prime O methyluridine" EXACT [] synonym: "inm5Um" EXACT RNAMOD [] xref: RNAMOD:105 is_a: SO:0001277 ! modified_uridine [Term] id: SO:0001383 name: histone_binding_site def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke] synonym: "histone binding site" EXACT [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site [Term] id: SO:0001384 name: CDS_fragment synonym: "CDS fragment" EXACT [] synonym: "incomplete CDS" EXACT [] is_a: SO:0000316 ! CDS relationship: has_quality SO:0000731 ! fragmentary [Term] id: SO:0001385 name: modified_amino_acid_feature def: "A post translationally modified amino acid feature." [SO:ke] synonym: "modified amino acid feature" EXACT [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001386 name: modified_glycine def: "A post translationally modified glycine amino acid feature." [SO:ke] synonym: "ModGly" EXACT AAMOD [] synonym: "modified glycine" EXACT [] xref: MOD:00908 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001387 name: modified_L_alanine def: "A post translationally modified alanine amino acid feature." [SO:ke] synonym: "ModAla" EXACT AAMOD [] synonym: "modified L alanine" EXACT [] synonym: "modified L-alanine" EXACT [] xref: MOD:00901 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001388 name: modified_L_asparagine def: "A post translationally modified asparagine amino acid feature." [SO:ke] synonym: "ModAsn" EXACT AAMOD [] synonym: "modified L asparagine" EXACT [] synonym: "modified L-asparagine" EXACT [] xref: MOD:00903 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001389 name: modified_L_aspartic_acid def: "A post translationally modified aspartic acid amino acid feature." [SO:ke] synonym: "ModAsp" EXACT AAMOD [] synonym: "modified L aspartic acid" EXACT [] synonym: "modified L-aspartic acid" EXACT [] xref: MOD:00904 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001390 name: modified_L_cysteine def: "A post translationally modified cysteine amino acid feature." [SO:ke] synonym: "ModCys" EXACT AAMOD [] synonym: "modified L cysteine" EXACT [] synonym: "modified L-cysteine" EXACT [] xref: MOD:00905 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001391 name: modified_L_glutamic_acid synonym: "ModGlu" EXACT AAMOD [] synonym: "modified L glutamic acid" EXACT [] synonym: "modified L-glutamic acid" EXACT [] xref: MOD:00906 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001392 name: modified_L_threonine def: "A post translationally modified threonine amino acid feature." [SO:ke] synonym: "modified L threonine" EXACT [] synonym: "modified L-threonine" EXACT [] synonym: "ModThr" EXACT AAMOD [] xref: MOD:00917 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001393 name: modified_L_tryptophan def: "A post translationally modified tryptophan amino acid feature." [SO:ke] synonym: "modified L tryptophan" EXACT [] synonym: "modified L-tryptophan" EXACT [] synonym: "ModTrp" EXACT AAMOD [] xref: MOD:00918 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001394 name: modified_L_glutamine def: "A post translationally modified glutamine amino acid feature." [SO:ke] synonym: "ModGln" EXACT [] synonym: "modified L glutamine" EXACT [] synonym: "modified L-glutamine" EXACT [] xref: MOD:00907 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001395 name: modified_L_methionine def: "A post translationally modified methionine amino acid feature." [SO:ke] synonym: "modified L methionine" EXACT [] synonym: "modified L-methionine" EXACT [] synonym: "ModMet" EXACT AAMOD [] xref: MOD:00913 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001396 name: modified_L_isoleucine def: "A post translationally modified isoleucine amino acid feature." [SO:ke] synonym: "modified L isoleucine" EXACT [] synonym: "modified L-isoleucine" EXACT [] synonym: "ModIle" EXACT AAMOD [] xref: MOD:00910 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001397 name: modified_L_phenylalanine def: "A post translationally modified phenylalanine amino acid feature." [SO:ke] synonym: "modified L phenylalanine" EXACT [] synonym: "modified L-phenylalanine" EXACT [] synonym: "ModPhe" EXACT AAMOD [] xref: MOD:00914 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001398 name: modified_L_histidine def: "A post translationally modified histidie amino acid feature." [SO:ke] synonym: "ModHis" EXACT [] synonym: "modified L histidine" EXACT [] synonym: "modified L-histidine" EXACT [] xref: MOD:00909 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001399 name: modified_L_serine def: "A post translationally modified serine amino acid feature." [SO:ke] synonym: "modified L serine" EXACT [] synonym: "modified L-serine" EXACT [] synonym: "MosSer" EXACT AAMOD [] xref: MOD:00916 "http://www.psidev.info/index.php?q=node/104" is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001400 name: modified_L_lysine def: "A post translationally modified lysine amino acid feature." [SO:ke] synonym: "modified L lysine" EXACT [] synonym: "modified L-lysine" EXACT [] synonym: "ModLys" EXACT AAMOD [] xref: MOD:00912 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001401 name: modified_L_leucine def: "A post translationally modified leucine amino acid feature." [SO:ke] synonym: "modified L leucine" EXACT [] synonym: "modified L-leucine " EXACT [] synonym: "ModLeu" EXACT AAMOD [] xref: MOD:00911 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001402 name: modified_L_selenocysteine def: "A post translationally modified selenocysteine amino acid feature." [SO:ke] synonym: "modified L selenocysteine" EXACT [] synonym: "modified L-selenocysteine" EXACT [] xref: MOD:01158 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001403 name: modified_L_valine def: "A post translationally modified valine amino acid feature." [SO:ke] synonym: "modified L valine" EXACT [] synonym: "modified L-valine" EXACT [] synonym: "ModVal" EXACT AAMOD [] xref: MOD:00920 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001404 name: modified_L_proline def: "A post translationally modified proline amino acid feature." [SO:ke] synonym: "modified L proline" EXACT [] synonym: "modified L-proline " EXACT [] synonym: "ModPro" EXACT AAMOD [] xref: MOD:00915 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001405 name: modified_L_tyrosine def: "A post translationally modified tyrosine amino acid feature." [SO:ke] synonym: "modified L tyrosine" EXACT [] synonym: "modified L-tyrosine" EXACT [] synonym: "ModTry" EXACT AAMOD [] xref: MOD:00919 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001406 name: modified_L_arginine def: "A post translationally modified arginine amino acid feature." [SO:ke] synonym: "ModArg" EXACT AAMOD [] synonym: "modified L arginine" EXACT [] synonym: "modified L-arginine" EXACT [] xref: MOD:00902 is_a: SO:0001385 ! modified_amino_acid_feature [Term] id: SO:0001407 name: peptidyl def: "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke] is_a: SO:0000443 ! polymer_attribute [Term] id: SO:0001408 name: cleaved_for_gpi_anchor_region def: "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh] synonym: "cleaved for gpi anchor region" EXACT [] is_a: SO:0100011 ! cleaved_peptide_region [Term] id: SO:0001409 name: biomaterial_region def: "A region which is intended for use in an experiment." [SO:cb] subset: SOFA synonym: "biomaterial region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001410 name: experimental_feature def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] subset: SOFA synonym: "analysis feature" RELATED [] synonym: "experimental output artefact" EXACT [] synonym: "experimental_output_artefact" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001411 name: biological_region def: "A region defined by its disposition to be involved in a biological process." [SO:cb] subset: SOFA synonym: "biological region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001412 name: topologically_defined_region def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb] subset: SOFA synonym: "topologically defined region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001413 name: translocation_breakpoint def: "The point within a chromosome where a translocation begins or ends." [SO:cb] synonym: "translocation breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001414 name: insertion_breakpoint def: "The point within a chromosome where a insertion begins or ends." [SO:cb] synonym: "insertion breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001415 name: deletion_breakpoint def: "The point within a chromosome where a deletion begins or ends." [SO:cb] synonym: "deletion breakpoint" EXACT [] is_a: SO:0001021 ! chromosome_breakpoint [Term] id: SO:0001416 name: five_prime_flanking_region def: "A flanking region located five prime of a specific region." [SO:chado] synonym: "5' flanking region" RELATED [] synonym: "five prime flanking region" EXACT [] is_a: SO:0000239 ! flanking_region [Term] id: SO:0001417 name: three_prime_flanking_region def: "A flanking region located three prime of a specific region." [SO:chado] synonym: "3' flanking region" RELATED [] synonym: "three prime flanking region" EXACT [] is_a: SO:0000239 ! flanking_region [Term] id: SO:0001418 name: transcribed_fragment def: "An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke] comment: Term requested by the MODencode group. synonym: "transcribed fragment" EXACT [] synonym: "transfrag" RELATED [] is_a: SO:0001410 ! experimental_feature [Term] id: SO:0001419 name: cis_splice_site def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke] subset: SOFA synonym: "cis splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001420 name: trans_splice_site def: "Primary transcript region bordering trans-splice junction." [SO:ke] subset: SOFA synonym: "trans splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001421 name: splice_junction def: "The boundary between an intron and an exon." [SO:ke] synonym: "splice boundary" EXACT [] synonym: "splice junction" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0001422 name: conformational_switch def: "A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke] comment: MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999. synonym: "polypeptide conformational switch" EXACT [] is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0001423 name: dye_terminator_read def: "A read produced by the dye terminator method of sequencing." [SO:ke] synonym: "dye terminator read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001424 name: pyrosequenced_read def: "A read produced by pyrosequencing technology." [SO:ke] comment: An example is a read produced by Roche 454 technology. synonym: "pyorsequenced read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001425 name: ligation_based_read def: "A read produced by ligation based sequencing technologies." [SO:ke] comment: An example of this kind of read is one produced by ABI SOLiD. synonym: "ligation based read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001426 name: polymerase_synthesis_read def: "A read produced by the polymerase based sequence by synthesis method." [SO:ke] comment: An example is a read produced by Illumina technology. synonym: "polymerase synthesis read" RELATED [] is_a: SO:0000150 ! read [Term] id: SO:0001427 name: cis_regulatory_frameshift_element def: "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd] synonym: "cis regulatory frameshift element" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0001428 name: expressed_sequence_assembly def: "A sequence assembly derived from expressed sequences." [SO:ke] comment: From tracker [ 2372385 ] expressed_sequence_assembly. synonym: "expressed sequence assembly" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0001429 name: DNA_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke] synonym: "DNA binding site" EXACT [] is_a: SO:0001655 ! nucleotide_binding_site [Term] id: SO:0001431 name: cryptic_gene def: "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke] synonym: "cryptic gene" EXACT [] is_a: SO:0000704 ! gene relationship: has_quality SO:0000976 ! cryptic [Term] id: SO:0001432 name: sequence_variant_affecting_polyadenylation comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. synonym: "mutation affecting polyadenylation" RELATED [] synonym: "sequence variant affecting polyadenylation" EXACT [] is_obsolete: true replaced_by: SO:0001545 [Term] id: SO:0001433 name: three_prime_RACE_clone def: "A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw] synonym: "3' RACE clone" RELATED [] is_a: SO:0000317 ! cDNA_clone [Term] id: SO:0001434 name: cassette_pseudogene def: "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke] comment: Requested by the Trypanosome community. synonym: "cassette pseudogene" EXACT [] synonym: "cassette type psedogene" RELATED [] is_a: SO:0001760 ! non_processed_pseudogene [Term] id: SO:0001435 name: alanine comment: A place holder for a cross product with chebi. synonym: "A" EXACT aa1 [] synonym: "Ala" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001436 name: valine comment: A place holder for a cross product with chebi. synonym: "V" EXACT aa1 [] synonym: "Val" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001437 name: leucine comment: A place holder for a cross product with chebi. synonym: "L" EXACT aa1 [] synonym: "Leu" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001438 name: isoleucine comment: A place holder for a cross product with chebi. synonym: "I" EXACT aa1 [] synonym: "Ile" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001439 name: proline comment: A place holder for a cross product with chebi. synonym: "P" EXACT aa1 [] synonym: "Pro" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001440 name: tryptophan comment: A place holder for a cross product with chebi. synonym: "Trp" EXACT aa3 [] synonym: "W" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001441 name: phenylalanine comment: A place holder for a cross product with chebi. synonym: "F" EXACT aa1 [] synonym: "Phe" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001442 name: methionine comment: A place holder for a cross product with chebi. synonym: "M" EXACT aa1 [] synonym: "Met" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001443 name: glycine comment: A place holder for a cross product with chebi. synonym: "G" EXACT aa1 [] synonym: "Gly" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001444 name: serine comment: A place holder for a cross product with chebi. synonym: "S" EXACT aa1 [] synonym: "Ser" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001445 name: threonine comment: A place holder for a cross product with chebi. synonym: "T" EXACT aa1 [] synonym: "Thr" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001446 name: tyrosine comment: A place holder for a cross product with chebi. synonym: "Tyr" EXACT aa3 [] synonym: "Y" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001447 name: cysteine comment: A place holder for a cross product with chebi. synonym: "C" EXACT aa1 [] synonym: "Cys" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001448 name: glutamine comment: A place holder for a cross product with chebi. synonym: "Gln" EXACT aa3 [] synonym: "Q" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001449 name: asparagine comment: A place holder for a cross product with chebi. synonym: "Asn" EXACT aa3 [] synonym: "N" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001450 name: lysine comment: A place holder for a cross product with chebi. synonym: "K" EXACT aa1 [] synonym: "Lys" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001451 name: arginine comment: A place holder for a cross product with chebi. synonym: "Arg" EXACT aa3 [] synonym: "R" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001452 name: histidine comment: A place holder for a cross product with chebi. synonym: "H" EXACT aa1 [] synonym: "His" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001453 name: aspartic_acid comment: A place holder for a cross product with chebi. synonym: "Asp" EXACT aa3 [] synonym: "aspartic acid" EXACT [] synonym: "D" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001454 name: glutamic_acid comment: A place holder for a cross product with chebi. synonym: "E" EXACT aa1 [] synonym: "Glu" EXACT aa3 [] synonym: "glutamic acid" EXACT [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001455 name: selenocysteine comment: A place holder for a cross product with chebi. synonym: "Sec" EXACT aa3 [] synonym: "U" EXACT aa1 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001456 name: pyrrolysine comment: A place holder for a cross product with chebi. synonym: "O" EXACT aa1 [] synonym: "Pyl" EXACT aa3 [] is_a: SO:0001237 ! amino_acid [Term] id: SO:0001457 name: transcribed_cluster def: "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke] comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157. synonym: "transcribed cluster" EXACT [] synonym: "unigene cluster" RELATED [] is_a: SO:0001410 ! experimental_feature relationship: has_part SO:0000695 ! reagent [Term] id: SO:0001458 name: unigene_cluster def: "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke] comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157. synonym: "unigene cluster" RELATED [] is_a: SO:0001457 ! transcribed_cluster [Term] id: SO:0001459 name: CRISPR def: "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd] synonym: "Clustered_Regularly_Interspaced_Short_Palindromic_Repeat" EXACT [] synonym: "CRISPR element" EXACT [] xref: http:en.wikipedia.org/wiki/CRISPR is_a: SO:0000314 ! direct_repeat [Term] id: SO:0001460 name: insulator_binding_site def: "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] comment: See tracker ID 2060908. synonym: "insulator binding site" RELATED [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site relationship: part_of SO:0000627 ! insulator [Term] id: SO:0001461 name: enhancer_binding_site def: "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] synonym: "enhancer binding site" RELATED [] is_a: SO:0001654 ! nucleotide_to_protein_binding_site relationship: part_of SO:0000165 ! enhancer [Term] id: SO:0001462 name: contig_collection def: "A collection of contigs." [SO:ke] comment: See tracker ID: 2138359. synonym: "contig collection" EXACT [] is_a: SO:0001085 ! sequence_conflict is_a: SO:0001260 ! sequence_collection relationship: has_part SO:0000149 ! contig [Term] id: SO:0001463 name: lincRNA def: "A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke] synonym: "large intervening non-coding RNA" EXACT [] synonym: "long intergenic non-coding RNA" EXACT [] is_a: SO:0001877 ! lnc_RNA [Term] id: SO:0001464 name: UST def: "An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw] synonym: "UTR sequence tag" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001465 name: three_prime_UST def: "A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw] synonym: "3' UST" RELATED [] is_a: SO:0001464 ! UST [Term] id: SO:0001466 name: five_prime_UST def: "An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw] synonym: "5' UST" RELATED [] is_a: SO:0001464 ! UST [Term] id: SO:0001467 name: RST def: "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw] synonym: "RACE sequence tag" EXACT [] is_a: SO:0000345 ! EST [Term] id: SO:0001468 name: three_prime_RST def: "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw] synonym: "3' RST" EXACT [] is_a: SO:0001467 ! RST [Term] id: SO:0001469 name: five_prime_RST def: "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw] synonym: "5' RST" RELATED [] is_a: SO:0001467 ! RST [Term] id: SO:0001470 name: UST_match def: "A match against an UST sequence." [SO:nlw] synonym: "UST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0001471 name: RST_match def: "A match against an RST sequence." [SO:nlw] synonym: "RST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0001472 name: primer_match def: "A nucleotide match to a primer sequence." [SO:nlw] synonym: "primer match" EXACT [] is_a: SO:0000347 ! nucleotide_match [Term] id: SO:0001473 name: miRNA_antiguide def: "A region of the pri miRNA that basepairs with the guide to form the hairpin." [SO:ke] synonym: "miRNA antiguide " EXACT [] synonym: "miRNA passenger strand" EXACT [] synonym: "miRNA star" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region created_by: kareneilbeck creation_date: 2009-05-27T03:35:43Z [Term] id: SO:0001474 name: trans_splice_junction def: "The boundary between the spliced leader and the first exon of the mRNA." [SO:ke] synonym: "trans-splice junction" EXACT [] is_a: SO:0000699 ! junction created_by: kareneilbeck creation_date: 2009-07-13T04:50:49Z [Term] id: SO:0001475 name: outron def: "A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke] is_a: SO:0000835 ! primary_transcript_region created_by: kareneilbeck creation_date: 2009-07-14T11:36:08Z [Term] id: SO:0001476 name: natural_plasmid def: "A plasmid that occurs naturally." [SO:xp] synonym: "natural plasmid" EXACT [] is_a: SO:0000155 ! plasmid is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element relationship: has_quality SO:0000782 ! natural created_by: kareneilbeck creation_date: 2009-09-01T03:43:06Z [Term] id: SO:0001477 name: gene_trap_construct def: "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh] synonym: "gene trap construct" EXACT [] is_a: SO:0000637 ! engineered_plasmid created_by: kareneilbeck creation_date: 2009-09-01T03:49:09Z [Term] id: SO:0001478 name: promoter_trap_construct def: "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh] synonym: "promoter trap construct" EXACT [] is_a: SO:0000637 ! engineered_plasmid created_by: kareneilbeck creation_date: 2009-09-01T03:52:01Z [Term] id: SO:0001479 name: enhancer_trap_construct def: "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh] synonym: "enhancer trap construct" EXACT [] is_a: SO:0000637 ! engineered_plasmid created_by: kareneilbeck creation_date: 2009-09-01T03:53:26Z [Term] id: SO:0001480 name: PAC_end def: "A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh] synonym: "PAC end" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000154 ! PAC created_by: kareneilbeck creation_date: 2009-09-09T05:18:12Z [Term] id: SO:0001481 name: RAPD def: "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh] synonym: "Random Amplification Polymorphic DNA" EXACT [] is_a: SO:0000006 ! PCR_product created_by: kareneilbeck creation_date: 2009-09-09T05:26:10Z [Term] id: SO:0001482 name: shadow_enhancer synonym: "shadow enhancer" EXACT [] is_a: SO:0000165 ! enhancer created_by: kareneilbeck creation_date: 2009-09-09T05:29:29Z [Term] id: SO:0001483 name: SNV def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm] subset: SOFA synonym: "single nucleotide variant" EXACT [] is_a: SO:1000002 ! substitution created_by: kareneilbeck creation_date: 2009-10-08T11:37:49Z [Term] id: SO:0001484 name: X_element_combinatorial_repeat def: "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html] comment: X element combinatorial repeats contain Tbf1p binding sites,\nand possible functions include a role in telomerase-independent telomere\nmaintenance via recombination or as a barrier against transcriptional\nsilencing. These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. synonym: "X element combinatorial repeat" EXACT [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-10T11:03:37Z [Term] id: SO:0001485 name: Y_prime_element def: "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. synonym: "Y' element" EXACT [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-10T12:08:57Z [Term] id: SO:0001486 name: standard_draft def: "The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126] synonym: "standard draft" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:48:32Z [Term] id: SO:0001487 name: high_quality_draft def: "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126] synonym: "high quality draft" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:52:36Z [Term] id: SO:0001488 name: improved_high_quality_draft def: "The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126] synonym: "improved high quality draft" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:54:35Z [Term] id: SO:0001489 name: annotation_directed_improved_draft def: "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126] synonym: "annotation directed improvement" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T12:57:10Z [Term] id: SO:0001490 name: noncontiguous_finished def: "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126] synonym: "non contiguous finished" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T01:01:07Z [Term] id: SO:0001491 name: finished_genome def: "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126] synonym: "finished" EXACT [] synonym: "finished genome" EXACT [] is_a: SO:0001499 ! whole_genome_sequence_status created_by: kareneilbeck creation_date: 2009-10-23T01:04:43Z [Term] id: SO:0001492 name: intronic_regulatory_region def: "A regulatory region that is part of an intron." [SO:ke] synonym: "intronic regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region relationship: part_of SO:0000188 ! intron created_by: kareneilbeck creation_date: 2009-11-08T02:48:02Z [Term] id: SO:0001493 name: centromere_DNA_Element_I def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. synonym: "CDEI" EXACT [] synonym: "Centromere DNA Element I" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001794 ! point_centromere created_by: kareneilbeck creation_date: 2009-11-09T05:47:23Z [Term] id: SO:0001494 name: centromere_DNA_Element_II def: "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. synonym: "CDEII" EXACT [] synonym: "centromere DNA Element II" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001794 ! point_centromere created_by: kareneilbeck creation_date: 2009-11-09T05:51:26Z [Term] id: SO:0001495 name: centromere_DNA_Element_III def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754] comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699. synonym: "CDEIII" EXACT [] synonym: "centromere DNA Element III" EXACT [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0001794 ! point_centromere created_by: kareneilbeck creation_date: 2009-11-09T05:54:47Z [Term] id: SO:0001496 name: telomeric_repeat def: "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065] comment: The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739. synonym: "telomeric repeat" EXACT [] is_a: SO:0000657 ! repeat_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-09T06:00:42Z [Term] id: SO:0001497 name: X_element def: "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence] comment: Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. synonym: "X element" RELATED [] is_a: SO:0000330 ! conserved_region relationship: part_of SO:0000624 ! telomere created_by: kareneilbeck creation_date: 2009-11-10T10:56:54Z [Term] id: SO:0001498 name: YAC_end def: "A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke] synonym: "YAC end" EXACT [] is_a: SO:0000150 ! read relationship: part_of SO:0000152 ! YAC created_by: kareneilbeck creation_date: 2009-11-19T11:07:18Z [Term] id: SO:0001499 name: whole_genome_sequence_status def: "The status of whole genome sequence." [DOI:10.1126] comment: This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms. synonym: "whole genome sequence status" EXACT [] is_a: SO:0000905 ! status created_by: kareneilbeck creation_date: 2009-10-23T12:47:47Z [Term] id: SO:0001500 name: heritable_phenotypic_marker def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene] synonym: "heritable phenotypic marker" EXACT [] synonym: "phenotypic marker" EXACT [] is_a: SO:0001645 ! genetic_marker created_by: kareneilbeck creation_date: 2009-12-07T01:50:55Z [Term] id: SO:0001501 name: peptide_collection def: "A collection of peptide sequences." [BBOP:nlw] comment: Term requested via tracker ID: 2910829. synonym: "peptide collection" EXACT [] synonym: "peptide set" EXACT [] is_a: SO:0001260 ! sequence_collection relationship: has_part SO:0000104 ! polypeptide created_by: kareneilbeck creation_date: 2009-12-11T10:58:58Z [Term] id: SO:0001502 name: high_identity_region def: "An experimental feature with high sequence identity to another sequence." [SO:ke] comment: Requested by tracker ID: 2902685. synonym: "high identity region" EXACT [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2009-12-11T11:06:05Z [Term] id: SO:0001503 name: processed_transcript def: "A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen] comment: Ensembl and Vega also use this term name. Requested by Howard Deen of MGI. synonym: "processed transcript" EXACT [] is_a: SO:0000673 ! transcript created_by: kareneilbeck creation_date: 2009-12-21T05:37:14Z [Term] id: SO:0001504 name: assortment_derived_variation def: "A chromosome variation derived from an event during meiosis." [SO:ke] synonym: "assortment derived variation" RELATED [] is_a: SO:0000240 ! chromosome_variation created_by: kareneilbeck creation_date: 2010-03-02T05:03:18Z [Term] id: SO:0001505 name: reference_genome def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke] synonym: "reference genome" RELATED [] is_a: SO:0001026 ! genome created_by: kareneilbeck creation_date: 2010-03-03T02:10:03Z [Term] id: SO:0001506 name: variant_genome def: "A collection of sequences (often chromosomes) of an individual." [SO:ke] synonym: "variant genome" RELATED [] is_a: SO:0001026 ! genome created_by: kareneilbeck creation_date: 2010-03-03T02:11:25Z [Term] id: SO:0001507 name: variant_collection def: "A collection of one or more sequences of an individual." [SO:ke] synonym: "variant collection" RELATED [] is_a: SO:0001260 ! sequence_collection relationship: has_part SO:0001059 ! sequence_alteration created_by: kareneilbeck creation_date: 2010-03-03T02:13:28Z [Term] id: SO:0001508 name: alteration_attribute synonym: "alteration attribute" EXACT [] is_a: SO:0000733 ! feature_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:53:23Z [Term] id: SO:0001509 name: chromosomal_variation_attribute synonym: "chromosomal variation attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:54:30Z [Term] id: SO:0001510 name: intrachromosomal is_a: SO:0001509 ! chromosomal_variation_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:55:25Z [Term] id: SO:0001511 name: interchromosomal is_a: SO:0001509 ! chromosomal_variation_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:55:43Z [Term] id: SO:0001512 name: insertion_attribute def: "A quality of a chromosomal insertion,." [SO:ke] synonym: "insertion attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:55:56Z [Term] id: SO:0001513 name: tandem is_a: SO:0001512 ! insertion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:56:37Z [Term] id: SO:0001514 name: direct def: "A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke] is_a: SO:0001512 ! insertion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:56:49Z [Term] id: SO:0001515 name: inverted def: "A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke] is_a: SO:0001512 ! insertion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:57:40Z [Term] id: SO:0001516 name: free def: "The quality of a duplication where the new region exists independently of the original." [SO:ke] is_a: SO:0001523 ! duplication_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:57:51Z [Term] id: SO:0001517 name: inversion_attribute synonym: "inversion attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:10Z [Term] id: SO:0001518 name: pericentric is_a: SO:0001517 ! inversion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:24Z [Term] id: SO:0001519 name: paracentric is_a: SO:0001517 ! inversion_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:35Z [Term] id: SO:0001520 name: translocaton_attribute synonym: "translocation attribute" EXACT [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:58:47Z [Term] id: SO:0001521 name: reciprocal is_a: SO:0001520 ! translocaton_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:59:34Z [Term] id: SO:0001522 name: insertional is_a: SO:0001520 ! translocaton_attribute created_by: kareneilbeck creation_date: 2010-03-04T02:59:51Z [Term] id: SO:0001523 name: duplication_attribute synonym: "duplication attribute" RELATED [] is_a: SO:0001508 ! alteration_attribute created_by: kareneilbeck creation_date: 2010-03-05T01:56:33Z [Term] id: SO:0001524 name: chromosomally_aberrant_genome synonym: "chromosomally aberrant genome" RELATED [] is_a: SO:0001506 ! variant_genome created_by: kareneilbeck creation_date: 2010-03-05T02:21:00Z [Term] id: SO:0001525 name: assembly_error_correction def: "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke] synonym: "assembly error correction" RELATED [] is_a: SO:0000413 ! sequence_difference created_by: kareneilbeck creation_date: 2010-03-09T02:16:31Z [Term] id: SO:0001526 name: base_call_error_correction def: "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke] synonym: "base call error correction" RELATED [] is_a: SO:0000413 ! sequence_difference created_by: kareneilbeck creation_date: 2010-03-09T02:18:07Z [Term] id: SO:0001527 name: peptide_localization_signal def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke] subset: SOFA synonym: "localization signal" RELATED [] synonym: "peptide localization signal" EXACT [] is_a: SO:0000839 ! polypeptide_region created_by: kareneilbeck creation_date: 2010-03-11T02:15:05Z [Term] id: SO:0001528 name: nuclear_localization_signal def: "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke] synonym: "NLS" EXACT [] xref: http://en.wikipedia.org/wiki/Nuclear_localization_signal "wikipedia" is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:16:38Z [Term] id: SO:0001529 name: endosomal_localization_signal def: "A polypeptide region that targets a polypeptide to the endosome." [SO:ke] synonym: "endosomal localization signal" EXACT [] is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:20:58Z [Term] id: SO:0001530 name: lysosomal_localization_signal def: "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke] synonym: "lysosomal localization signal" EXACT [] is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:24:10Z [Term] id: SO:0001531 name: nuclear_export_signal def: "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke] synonym: "NES" EXACT [] synonym: "nuclear export signal" EXACT [] xref: http://en.wikipedia.org/wiki/Nuclear_export_signal is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T02:25:25Z [Term] id: SO:0001532 name: recombination_signal_sequence def: "A region recognized by a recombinase." [SO:ke] synonym: "recombination signal sequence" RELATED [] xref: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences "wikipedia" is_a: SO:0000299 ! specific_recombination_site created_by: kareneilbeck creation_date: 2010-03-11T03:16:47Z [Term] id: SO:0001533 name: cryptic_splice_site def: "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke] synonym: "cryptic splice signal" RELATED [] synonym: "cryptic splice site" EXACT [] is_a: SO:0000162 ! splice_site created_by: kareneilbeck creation_date: 2010-03-11T03:25:06Z [Term] id: SO:0001534 name: nuclear_rim_localization_signal def: "A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke] synonym: "nuclear rim localization signal" RELATED [] xref: PMID:16027110 is_a: SO:0001527 ! peptide_localization_signal created_by: kareneilbeck creation_date: 2010-03-11T03:31:30Z [Term] id: SO:0001535 name: p_element def: "A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke] synonym: "P element" RELATED [] is_a: SO:0000182 ! DNA_transposon created_by: kareneilbeck creation_date: 2010-03-12T03:40:33Z [Term] id: SO:0001536 name: functional_variant def: "A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke] synonym: "functional variant" EXACT [] is_a: SO:0001060 ! sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T11:30:25Z [Term] id: SO:0001537 name: structural_variant def: "A sequence variant that changes one or more sequence features." [SO:ke] synonym: "structural variant" RELATED [] is_a: SO:0001060 ! sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T11:31:01Z [Term] id: SO:0001538 name: transcript_function_variant def: "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcript function variant" EXACT [] is_a: SO:0001536 ! functional_variant created_by: kareneilbeck creation_date: 2010-03-22T11:32:58Z [Term] id: SO:0001539 name: translational_product_function_variant def: "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke] synonym: "translational product variant" EXACT [] is_a: SO:0001536 ! functional_variant created_by: kareneilbeck creation_date: 2010-03-22T11:46:15Z [Term] id: SO:0001540 name: level_of_transcript_variant def: "A sequence variant which alters the level of a transcript." [SO:ke] synonym: "level of transcript variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:47:07Z [Term] id: SO:0001541 name: decreased_transcript_level_variant def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] synonym: "decreased transcript level" EXACT [] is_a: SO:0001540 ! level_of_transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T11:47:47Z [Term] id: SO:0001542 name: increased_transcript_level_variant def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke] synonym: "increased transcript level variant" EXACT [] is_a: SO:0001540 ! level_of_transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T11:48:17Z [Term] id: SO:0001543 name: transcript_processing_variant def: "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcript processing variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:48:48Z [Term] id: SO:0001544 name: editing_variant def: "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke] synonym: "editing variant" EXACT [] is_a: SO:0001543 ! transcript_processing_variant created_by: kareneilbeck creation_date: 2010-03-22T11:49:25Z [Term] id: SO:0001545 name: polyadenylation_variant def: "A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke] synonym: "polyadenylation variant" EXACT [] is_a: SO:0001543 ! transcript_processing_variant created_by: kareneilbeck creation_date: 2010-03-22T11:49:40Z [Term] id: SO:0001546 name: transcript_stability_variant def: "A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcript stability variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:50:01Z [Term] id: SO:0001547 name: decreased_transcript_stability_variant def: "A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke] synonym: "decrease transcript stability variant" EXACT [] is_a: SO:0001546 ! transcript_stability_variant created_by: kareneilbeck creation_date: 2010-03-22T11:50:23Z [Term] id: SO:0001548 name: increased_transcript_stability_variant def: "A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke] synonym: "increased transcript stability variant" EXACT [] is_a: SO:0001546 ! transcript_stability_variant created_by: kareneilbeck creation_date: 2010-03-22T11:50:39Z [Term] id: SO:0001549 name: transcription_variant def: "A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke] synonym: "transcription variant" EXACT [] is_a: SO:0001538 ! transcript_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:51:26Z [Term] id: SO:0001550 name: rate_of_transcription_variant def: "A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke] synonym: "rate of transcription variant" EXACT [] is_a: SO:0001549 ! transcription_variant created_by: kareneilbeck creation_date: 2010-03-22T11:51:50Z [Term] id: SO:0001551 name: increased_transcription_rate_variant def: "A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke] synonym: "increased transcription rate variant" EXACT [] is_a: SO:0001550 ! rate_of_transcription_variant created_by: kareneilbeck creation_date: 2010-03-22T11:52:17Z [Term] id: SO:0001552 name: decreased_transcription_rate_variant def: "A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke] synonym: "decreased transcription rate variant" EXACT [] is_a: SO:0001550 ! rate_of_transcription_variant created_by: kareneilbeck creation_date: 2010-03-22T11:52:43Z [Term] id: SO:0001553 name: translational_product_level_variant def: "A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke] synonym: "translational product level variant" EXACT [] is_a: SO:0001539 ! translational_product_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:53:32Z [Term] id: SO:0001554 name: polypeptide_function_variant def: "A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke] synonym: "polypeptide function variant" EXACT [] is_a: SO:0001539 ! translational_product_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:53:54Z [Term] id: SO:0001555 name: decreased_translational_product_level def: "A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke] synonym: "decrease translational product level" EXACT [] is_a: SO:0001553 ! translational_product_level_variant created_by: kareneilbeck creation_date: 2010-03-22T11:54:25Z [Term] id: SO:0001556 name: increased_translational_product_level def: "A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke] synonym: "increase translational product level" EXACT [] is_a: SO:0001553 ! translational_product_level_variant created_by: kareneilbeck creation_date: 2010-03-22T11:55:25Z [Term] id: SO:0001557 name: polypeptide_gain_of_function_variant def: "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke] synonym: "polypeptide gain of function variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:56:12Z [Term] id: SO:0001558 name: polypeptide_localization_variant def: "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke] synonym: "polypeptide localization variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:56:37Z [Term] id: SO:0001559 name: polypeptide_loss_of_function_variant def: "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke] synonym: "polypeptide loss of function variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:56:58Z [Term] id: SO:0001560 name: inactive_ligand_binding_site def: "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke] synonym: "inactive ligand binding site" EXACT [] is_a: SO:0001559 ! polypeptide_loss_of_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:58:00Z [Term] id: SO:0001561 name: polypeptide_partial_loss_of_function def: "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke] synonym: "polypeptide partial loss of function" EXACT [] is_a: SO:0001559 ! polypeptide_loss_of_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:58:32Z [Term] id: SO:0001562 name: polypeptide_post_translational_processing_variant def: "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke] synonym: "polypeptide post translational processing variant" EXACT [] is_a: SO:0001554 ! polypeptide_function_variant created_by: kareneilbeck creation_date: 2010-03-22T11:59:06Z [Term] id: SO:0001563 name: copy_number_change def: "A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke] synonym: "copy number change" EXACT [] is_a: SO:0001537 ! structural_variant created_by: kareneilbeck creation_date: 2010-03-22T02:27:33Z [Term] id: SO:0001564 name: gene_variant def: "A sequence variant where the structure of the gene is changed." [SO:ke] synonym: "gene structure variant" EXACT [] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-22T02:28:01Z [Term] id: SO:0001565 name: gene_fusion def: "A sequence variant whereby a two genes have become joined." [SO:ke] synonym: "gene fusion" EXACT [] is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:28:28Z [Term] id: SO:0001566 name: regulatory_region_variant def: "A sequence variant located within a regulatory region." [SO:ke] comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl. synonym: "regulatory region variant" EXACT [] synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-22T02:28:48Z [Term] id: SO:0001567 name: stop_retained_variant def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke] synonym: "stop retained variant" EXACT [] is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001819 ! synonymous_variant created_by: kareneilbeck creation_date: 2010-04-19T05:02:30Z [Term] id: SO:0001568 name: splicing_variant def: "A sequence variant that changes the process of splicing." [SO:ke] synonym: "splicing variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:29:22Z [Term] id: SO:0001569 name: cryptic_splice_site_variant def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "cryptic splice site activation" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:29:41Z [Term] id: SO:0001570 name: cryptic_splice_acceptor def: "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke] synonym: "cryptic splice acceptor" EXACT [] is_a: SO:0001569 ! cryptic_splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:30:11Z [Term] id: SO:0001571 name: cryptic_splice_donor def: "A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke] synonym: "cryptic splice donor" EXACT [] is_a: SO:0001569 ! cryptic_splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:30:35Z [Term] id: SO:0001572 name: exon_loss def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke] synonym: "exon loss" EXACT [] is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:09Z [Term] id: SO:0001573 name: intron_gain def: "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] synonym: "intron gain" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:25Z [Term] id: SO:0001574 name: splice_acceptor_variant def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke] synonym: "splice acceptor variant" EXACT [] is_a: SO:0001629 ! splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:31:52Z [Term] id: SO:0001575 name: splice_donor_variant def: "A splice variant that changes the2 base region at the 5' end of an intron." [SO:ke] synonym: "splice donor variant" EXACT [] is_a: SO:0001629 ! splice_site_variant created_by: kareneilbeck creation_date: 2010-03-22T02:32:10Z [Term] id: SO:0001576 name: transcript_variant def: "A sequence variant that changes the structure of the transcript." [SO:ke] synonym: "transcript variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:32:41Z [Term] id: SO:0001577 name: complex_transcript_variant def: "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html] comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. synonym: "complex transcript variant" EXACT [] synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "complext change in transcript" EXACT [] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T02:33:03Z [Term] id: SO:0001578 name: stop_lost def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke] comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon. synonym: "stop codon lost" EXACT [] synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001650 ! inframe_variant is_a: SO:0001907 ! feature_elongation created_by: kareneilbeck creation_date: 2010-03-23T03:46:42Z [Term] id: SO:0001579 name: transcript_sequence_variant synonym: "transcript sequence variant" EXACT [] is_obsolete: true [Term] id: SO:0001580 name: coding_sequence_variant alt_id: SO:0001581 def: "A sequence variant that changes the coding sequence." [SO:ke] synonym: "coding sequence variant" EXACT [] synonym: "coding variant" EXACT [] synonym: "codon variant" EXACT [] synonym: "codon_variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001791 ! exon_variant created_by: kareneilbeck creation_date: 2010-03-22T02:34:36Z [Term] id: SO:0001582 name: initiator_codon_variant def: "A codon variant that changes at least one base of the first codon of a transcript." [SO:ke] synonym: "initiatior codon variant" EXACT [] synonym: "initiator codon change" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html xref: loinc:LA6695-6 "Initiating Methionine" is_a: SO:0001650 ! inframe_variant created_by: kareneilbeck creation_date: 2010-03-22T02:35:18Z [Term] id: SO:0001583 name: missense_variant alt_id: SO:0001584 alt_id: SO:0001783 def: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke] comment: EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution. synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "missense codon" EXACT [] synonym: "non synonymous codon" EXACT [] synonym: "non synonymous variant" EXACT [] synonym: "non_synonymous_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html xref: http://en.wikipedia.org/wiki/Missense_mutation xref: loinc:LA6698-0 "Missense" is_a: SO:0001650 ! inframe_variant created_by: kareneilbeck creation_date: 2010-03-22T02:35:49Z [Term] id: SO:0001585 name: conservative_missense_variant def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke] synonym: "conservative missense codon" EXACT [] synonym: "conservative missense variant" EXACT [] synonym: "neutral missense codon" RELATED [] synonym: "quiet missense codon" RELATED [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001583 ! missense_variant created_by: kareneilbeck creation_date: 2010-03-22T02:36:40Z [Term] id: SO:0001586 name: non_conservative_missense_variant def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke] synonym: "non conservative missense codon" EXACT [] synonym: "non conservative missense variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001583 ! missense_variant created_by: kareneilbeck creation_date: 2010-03-22T02:37:16Z [Term] id: SO:0001587 name: stop_gained def: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke] comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence). synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "nonsense codon" EXACT [] synonym: "stop codon gained" RELATED [] synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] xref: loinc:LA6699-8 "Nonsense" is_a: SO:0001650 ! inframe_variant is_a: SO:0001906 ! feature_truncation created_by: kareneilbeck creation_date: 2010-03-22T02:37:52Z [Term] id: SO:0001589 name: frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke] comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift. synonym: "frameshift variant" EXACT [] synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] xref: loinc:LA6694-9 "Frameshift" is_a: SO:0001818 ! protein_altering_variant created_by: kareneilbeck creation_date: 2010-03-22T02:40:19Z [Term] id: SO:0001590 name: terminator_codon_variant alt_id: SO:0001625 def: "A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke] comment: The terminal codon may be the terminator, or in an incomplete transcript the last available codon. synonym: "terminal codon variant" EXACT [] synonym: "terminal_codon_variant" EXACT [] synonym: "terminator codon variant" EXACT [] xref: loinc:LA6700-2 "Stop Codon Mutation" is_a: SO:0001580 ! coding_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:40:37Z [Term] id: SO:0001591 name: frame_restoring_variant def: "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke] synonym: "frame restoring variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:41:09Z [Term] id: SO:0001592 name: minus_1_frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] synonym: "-1 frameshift variant" EXACT [] synonym: "minus 1 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:41:30Z [Term] id: SO:0001593 name: minus_2_frameshift_variant synonym: "-2 frameshift variant" EXACT [] synonym: "minus 2 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:41:52Z [Term] id: SO:0001594 name: plus_1_frameshift_variant def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535] synonym: "+1 frameshift variant" EXACT [] synonym: "plus 1 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:42:06Z [Term] id: SO:0001595 name: plus_2_frameshift_variant synonym: "+2 frameshift variant" EXACT [] synonym: "plus 2 frameshift variant" EXACT [] is_a: SO:0001589 ! frameshift_variant created_by: kareneilbeck creation_date: 2010-03-22T02:42:23Z [Term] id: SO:0001596 name: transcript_secondary_structure_variant def: "A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke] synonym: "transcript secondary structure variant" EXACT [] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-22T02:43:18Z [Term] id: SO:0001597 name: compensatory_transcript_secondary_structure_variant def: "A secondary structure variant that compensate for the change made by a previous variant." [SO:ke] synonym: "compensatory transcript secondary structure variant" EXACT [] is_a: SO:0001596 ! transcript_secondary_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:43:54Z [Term] id: SO:0001598 name: translational_product_structure_variant def: "A sequence variant within the transcript that changes the structure of the translational product." [SO:ke] synonym: "translational product structure variant" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001564 ! gene_variant created_by: kareneilbeck creation_date: 2010-03-22T02:44:17Z [Term] id: SO:0001599 name: 3D_polypeptide_structure_variant def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke] synonym: "3D polypeptide structure variant" EXACT [] is_a: SO:0001598 ! translational_product_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:44:46Z [Term] id: SO:0001600 name: complex_3D_structural_variant def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke] synonym: "complex 3D structural variant" EXACT [] is_a: SO:0001599 ! 3D_polypeptide_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:45:13Z [Term] id: SO:0001601 name: conformational_change_variant def: "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke] synonym: "conformational change variant" EXACT [] is_a: SO:0001599 ! 3D_polypeptide_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:45:48Z [Term] id: SO:0001602 name: complex_change_of_translational_product_variant synonym: "complex change of translational product variant" EXACT [] is_a: SO:0001598 ! translational_product_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:46:54Z [Term] id: SO:0001603 name: polypeptide_sequence_variant def: "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke] synonym: "polypeptide sequence variant" EXACT [] is_a: SO:0001598 ! translational_product_structure_variant created_by: kareneilbeck creation_date: 2010-03-22T02:47:13Z [Term] id: SO:0001604 name: amino_acid_deletion def: "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke] synonym: "amino acid deletion" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:47:36Z [Term] id: SO:0001605 name: amino_acid_insertion def: "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke] synonym: "amino acid insertion" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:47:56Z [Term] id: SO:0001606 name: amino_acid_substitution def: "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke] synonym: "amino acid substitution" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:48:17Z [Term] id: SO:0001607 name: conservative_amino_acid_substitution def: "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke] synonym: "conservative amino acid substitution" EXACT [] is_a: SO:0001606 ! amino_acid_substitution created_by: kareneilbeck creation_date: 2010-03-22T02:48:57Z [Term] id: SO:0001608 name: non_conservative_amino_acid_substitution def: "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke] synonym: "non conservative amino acid substitution" EXACT [] is_a: SO:0001606 ! amino_acid_substitution created_by: kareneilbeck creation_date: 2010-03-22T02:49:23Z [Term] id: SO:0001609 name: elongated_polypeptide def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke] synonym: "elongated polypeptide" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:49:52Z [Term] id: SO:0001610 name: elongated_polypeptide_C_terminal def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] synonym: "elongated polypeptide C terminal" EXACT [] is_a: SO:0001609 ! elongated_polypeptide created_by: kareneilbeck creation_date: 2010-03-22T02:50:20Z [Term] id: SO:0001611 name: elongated_polypeptide_N_terminal def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] synonym: "elongated polypeptide N terminal" EXACT [] is_a: SO:0001609 ! elongated_polypeptide created_by: kareneilbeck creation_date: 2010-03-22T02:50:31Z [Term] id: SO:0001612 name: elongated_in_frame_polypeptide_C_terminal def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] synonym: "elongated in frame polypeptide C terminal" EXACT [] is_a: SO:0001610 ! elongated_polypeptide_C_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:51:05Z [Term] id: SO:0001613 name: elongated_out_of_frame_polypeptide_C_terminal def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke] synonym: "elongated polypeptide out of frame C terminal" EXACT [] is_a: SO:0001610 ! elongated_polypeptide_C_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:51:20Z [Term] id: SO:0001614 name: elongated_in_frame_polypeptide_N_terminal_elongation def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] synonym: "elongated in frame polypeptide N terminal" EXACT [] is_a: SO:0001611 ! elongated_polypeptide_N_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:51:49Z [Term] id: SO:0001615 name: elongated_out_of_frame_polypeptide_N_terminal def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke] synonym: "elongated out of frame N terminal" EXACT [] is_a: SO:0001611 ! elongated_polypeptide_N_terminal created_by: kareneilbeck creation_date: 2010-03-22T02:52:05Z [Term] id: SO:0001616 name: polypeptide_fusion def: "A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke] synonym: "polypeptide fusion" EXACT [] is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:52:43Z [Term] id: SO:0001617 name: polypeptide_truncation def: "A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke] synonym: "polypeptide truncation" EXACT [] xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html is_a: SO:0001603 ! polypeptide_sequence_variant created_by: kareneilbeck creation_date: 2010-03-22T02:53:07Z [Term] id: SO:0001618 name: inactive_catalytic_site def: "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke] synonym: "inactive catalytic site" EXACT [] is_a: SO:0001560 ! inactive_ligand_binding_site created_by: kareneilbeck creation_date: 2010-03-22T03:06:14Z [Term] id: SO:0001619 name: nc_transcript_variant def: "A transcript variant of a non coding RNA gene." [SO:ke] comment: Within non-coding gene - Located within a gene that does not code for a protein. synonym: "nc transcript variant" EXACT [] synonym: "non coding transcript variant" EXACT [] synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:16:23Z [Term] id: SO:0001620 name: mature_miRNA_variant def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke] comment: EBI term: Within mature miRNA - Located within a microRNA. synonym: "mature miRNA variant" EXACT [] synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001619 ! nc_transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:16:58Z [Term] id: SO:0001621 name: NMD_transcript_variant def: "A variant in a transcript that is the target of NMD." [SO:ke] synonym: "NMD transcript variant" EXACT [] synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:20:40Z [Term] id: SO:0001622 name: UTR_variant def: "A transcript variant that is located within the UTR." [SO:ke] synonym: "UTR variant" EXACT [] synonym: "UTR_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T11:22:58Z [Term] id: SO:0001623 name: 5_prime_UTR_variant def: "A UTR variant of the 5' UTR." [SO:ke] comment: EBI term: 5prime UTR variations - In 5prime UTR (untranslated region). synonym: "5'UTR variant" EXACT [] synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "five prime UTR variant" EXACT [] synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001622 ! UTR_variant created_by: kareneilbeck creation_date: 2010-03-23T11:23:29Z [Term] id: SO:0001624 name: 3_prime_UTR_variant def: "A UTR variant of the 3' UTR." [SO:ke] comment: EBI term 3prime UTR variations - In 3prime UTR. synonym: "3'UTR variant" EXACT [] synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "three prime UTR variant" EXACT [] synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001622 ! UTR_variant created_by: kareneilbeck creation_date: 2010-03-23T11:23:54Z [Term] id: SO:0001626 name: incomplete_terminal_codon_variant def: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke] comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown. synonym: "incomplete terminal codon variant" EXACT [] synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001590 ! terminator_codon_variant is_a: SO:0001650 ! inframe_variant created_by: kareneilbeck creation_date: 2010-03-23T03:51:15Z [Term] id: SO:0001627 name: intron_variant def: "A transcript variant occurring within an intron." [SO:ke] comment: EBI term: Intronic variations - In intron. synonym: "intron variant" EXACT [] synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001576 ! transcript_variant created_by: kareneilbeck creation_date: 2010-03-23T03:52:38Z [Term] id: SO:0001628 name: intergenic_variant def: "A sequence variant located in the intergenic region, between genes." [SO:ke] comment: EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript. synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "intergenic variant" EXACT [] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-23T05:07:37Z [Term] id: SO:0001629 name: splice_site_variant def: "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html] comment: EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger. synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "splice site variant" EXACT [] is_a: SO:0001627 ! intron_variant created_by: kareneilbeck creation_date: 2010-03-24T09:42:00Z [Term] id: SO:0001630 name: splice_region_variant def: "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html] comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron. synonym: "splice region variant" EXACT [] synonym: "splice_region_variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001568 ! splicing_variant created_by: kareneilbeck creation_date: 2010-03-24T09:46:02Z [Term] id: SO:0001631 name: upstream_gene_variant def: "A sequence variant located 5' of a gene." [SO:ke] comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. synonym: "upstream gene variant" EXACT [] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-24T09:49:13Z [Term] id: SO:0001632 name: downstream_gene_variant def: "A sequence variant located 3' of a gene." [SO:ke] comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references. synonym: "downstream gene variant" EXACT [] is_a: SO:0001878 ! feature_variant created_by: kareneilbeck creation_date: 2010-03-24T09:49:38Z [Term] id: SO:0001633 name: 5KB_downstream_variant def: "A sequence variant located within 5 KB of the end of a gene." [SO:ke] comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript. synonym: "5KB downstream variant" EXACT [] synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] synonym: "within 5KB downstream" RELATED [] is_a: SO:0001632 ! downstream_gene_variant created_by: kareneilbeck creation_date: 2010-03-24T09:50:16Z [Term] id: SO:0001634 name: 500B_downstream_variant def: "A sequence variant located within a half KB of the end of a gene." [SO:ke] synonym: "500B downstream variant" EXACT [] synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001633 ! 5KB_downstream_variant created_by: kareneilbeck creation_date: 2010-03-24T09:50:42Z [Term] id: SO:0001635 name: 5KB_upstream_variant def: "A sequence variant located within 5KB 5' of a gene." [SO:ke] comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript. synonym: "5kb upstream variant" EXACT [] synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html] is_a: SO:0001631 ! upstream_gene_variant created_by: kareneilbeck creation_date: 2010-03-24T09:51:06Z [Term] id: SO:0001636 name: 2KB_upstream_variant def: "A sequence variant located within 2KB 5' of a gene." [SO:ke] synonym: "2KB upstream variant" EXACT [] synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd] is_a: SO:0001635 ! 5KB_upstream_variant created_by: kareneilbeck creation_date: 2010-03-24T09:51:22Z [Term] id: SO:0001637 name: rRNA_gene def: "A gene that encodes for ribosomal RNA." [SO:ke] synonym: "rRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:10:32Z [Term] id: SO:0001638 name: piRNA_gene def: "A gene that encodes for an piwi associated RNA." [SO:ke] synonym: "piRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:11:36Z [Term] id: SO:0001639 name: RNase_P_RNA_gene def: "A gene that encodes an RNase P RNA." [SO:ke] synonym: "RNase P RNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:13:23Z [Term] id: SO:0001640 name: RNase_MRP_RNA_gene def: "A gene that encodes a RNase_MRP_RNA." [SO:ke] synonym: "RNase MRP RNA gene" RELATED [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:13:58Z [Term] id: SO:0001641 name: lincRNA_gene def: "A gene that encodes large intervening non-coding RNA." [SO:ke] synonym: "lincRNA gene" EXACT [] is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-04-21T10:14:24Z [Term] id: SO:0001642 name: mathematically_defined_repeat def: "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill] comment: Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.). synonym: "mathematically defined repeat" EXACT [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2010-05-03T11:50:14Z [Term] id: SO:0001643 name: telomerase_RNA_gene def: "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke] synonym: "Telomerase RNA component" EXACT [] synonym: "telomerase RNA gene" EXACT [] synonym: "TERC" EXACT [] xref: http:http://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia" is_a: SO:0001263 ! ncRNA_gene created_by: kareneilbeck creation_date: 2010-05-18T05:26:38Z [Term] id: SO:0001644 name: targeting_vector def: "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467] synonym: "targeting vector" RELATED [] is_a: SO:0000440 ! vector_replicon is_a: SO:0000804 ! engineered_region relationship: has_part SO:0000853 ! homologous_region relationship: has_quality SO:0000783 ! engineered created_by: kareneilbeck creation_date: 2010-05-28T02:05:25Z [Term] id: SO:0001645 name: genetic_marker def: "A measurable sequence feature that varies within a population." [SO:db] synonym: "genetic marker" RELATED [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-05-28T02:33:07Z [Term] id: SO:0001646 name: DArT_marker def: "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke] synonym: "DArT marker" EXACT [] is_a: SO:0001645 ! genetic_marker created_by: kareneilbeck creation_date: 2010-05-28T02:34:43Z [Term] id: SO:0001647 name: kozak_sequence def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke] subset: SOFA synonym: "kozak consensus" EXACT [] synonym: "kozak consensus sequence" EXACT [] synonym: "kozak sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia" is_a: SO:0000139 ! ribosome_entry_site created_by: kareneilbeck creation_date: 2010-06-07T03:12:20Z [Term] id: SO:0001648 name: nested_transposon def: "A transposon that is disrupted by the insertion of another element." [SO:ke] synonym: "nested transposon" EXACT [] is_a: SO:0000101 ! transposable_element created_by: kareneilbeck creation_date: 2010-06-23T03:22:57Z [Term] id: SO:0001649 name: nested_repeat def: "A repeat that is disrupted by the insertion of another element." [SO:ke] synonym: "nested repeat" RELATED [] is_a: SO:0000657 ! repeat_region created_by: kareneilbeck creation_date: 2010-06-23T03:24:55Z [Term] id: SO:0001650 name: inframe_variant def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke] synonym: "cds-indel" EXACT dbsnp [] synonym: "inframe variant" EXACT [] is_a: SO:0001818 ! protein_altering_variant created_by: kareneilbeck creation_date: 2010-07-19T01:24:44Z [Term] id: SO:0001653 name: retinoic_acid_responsive_element def: "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671] synonym: "RARE" EXACT [] synonym: "retinoic acid responsive element" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0000167 ! promoter created_by: kareneilbeck creation_date: 2010-08-03T10:46:12Z [Term] id: SO:0001654 name: nucleotide_to_protein_binding_site def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] subset: SOFA synonym: "nucleotide to protein binding site" RELATED [] is_a: SO:0000410 ! protein_binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:26:05Z [Term] id: SO:0001655 name: nucleotide_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb] comment: See GO:0000166 : nucleotide binding. synonym: "nucleotide binding site" EXACT [] is_a: SO:0000409 ! binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:30:04Z [Term] id: SO:0001656 name: metal_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb] comment: See GO:0046872 : metal ion binding. synonym: "metal binding site" RELATED [] is_a: SO:0000409 ! binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:31:42Z [Term] id: SO:0001657 name: ligand_binding_site def: "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke] synonym: "ligand binding site" EXACT [] is_a: SO:0000409 ! binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:32:58Z [Term] id: SO:0001658 name: nested_tandem_repeat def: "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF] comment: Tracker ID: 3052459. synonym: "nested tandem repeat" EXACT [] synonym: "NTR" EXACT [] is_a: SO:0001649 ! nested_repeat created_by: kareneilbeck creation_date: 2010-08-26T09:36:16Z [Term] id: SO:0001659 name: promoter_element synonym: "promoter element" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: overlaps SO:0000235 ! TF_binding_site created_by: kareneilbeck creation_date: 2010-10-01T11:48:32Z [Term] id: SO:0001660 name: core_promoter_element synonym: "core promoter element" EXACT [] synonym: "general transcription factor binding site" RELATED [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2010-10-01T11:49:03Z [Term] id: SO:0001661 name: RNA_polymerase_II_TATA_box def: "A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867] synonym: "RNA polymerase II TATA box" EXACT [] is_a: SO:0000174 ! TATA_box relationship: part_of SO:0001669 ! RNApol_II_core_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:42:12Z [Term] id: SO:0001662 name: RNA_polymerase_III_TATA_box def: "A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke] synonym: "RNA polymerase III TATA box" EXACT [] is_a: SO:0000174 ! TATA_box relationship: part_of SO:0000171 ! RNApol_III_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:43:16Z [Term] id: SO:0001663 name: BREd_motif def: "A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867] synonym: "BREd" EXACT [] synonym: "BREd motif" RELATED [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:49:55Z [Term] id: SO:0001664 name: DCE def: "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867] synonym: "downstream core element" RELATED [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0001669 ! RNApol_II_core_promoter created_by: kareneilbeck creation_date: 2010-10-01T02:56:41Z [Term] id: SO:0001665 name: DCE_SI def: "A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke] synonym: "DCE SI" RELATED [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001664 ! DCE created_by: kareneilbeck creation_date: 2010-10-01T03:00:10Z [Term] id: SO:0001666 name: DCE_SII def: "A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke] synonym: "DCE SII" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001664 ! DCE created_by: kareneilbeck creation_date: 2010-10-01T03:00:30Z [Term] id: SO:0001667 name: DCE_SIII def: "A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke] synonym: "DCE SIII" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001664 ! DCE created_by: kareneilbeck creation_date: 2010-10-01T03:00:44Z [Term] id: SO:0001668 name: proximal_promoter_element synonym: "proximal promoter element" RELATED [] synonym: "specific transcription factor binding site" RELATED [] is_a: SO:0001678 ! regulatory_promoter_element created_by: kareneilbeck creation_date: 2010-10-01T03:10:23Z [Term] id: SO:0001669 name: RNApol_II_core_promoter def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867] synonym: "RNApol II core promoter" EXACT [] is_a: SO:0000170 ! RNApol_II_promoter created_by: kareneilbeck creation_date: 2010-10-01T03:13:41Z [Term] id: SO:0001670 name: distal_promoter_element synonym: "distal promoter element" RELATED [] is_a: SO:0001678 ! regulatory_promoter_element created_by: kareneilbeck creation_date: 2010-10-01T03:21:08Z [Term] id: SO:0001671 name: bacterial_RNApol_promoter_sigma_70 synonym: "bacterial RNA polymerase promoter sigma 70" EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2010-10-06T01:41:34Z [Term] id: SO:0001672 name: bacterial_RNApol_promoter_sigma54 synonym: "bacterial RNA polymerase promoter sigma54" EXACT [] is_a: SO:0000613 ! bacterial_RNApol_promoter created_by: kareneilbeck creation_date: 2010-10-06T01:42:37Z [Term] id: SO:0001673 name: minus_12_signal def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] synonym: "minus 12 signal" EXACT [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54 created_by: kareneilbeck creation_date: 2010-10-06T01:44:57Z [Term] id: SO:0001674 name: minus_24_signal def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472] synonym: "minus 24 signal" RELATED [] is_a: SO:0000713 ! DNA_motif relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54 created_by: kareneilbeck creation_date: 2010-10-06T01:45:24Z [Term] id: SO:0001675 name: A_box_type_1 def: "An A box within an RNA polymerase III type 1 promoter." [SO:ke] comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. synonym: "A box type 1" RELATED [] is_a: SO:0000619 ! A_box relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 created_by: kareneilbeck creation_date: 2010-10-06T05:43:43Z [Term] id: SO:0001676 name: A_box_type_2 def: "An A box within an RNA polymerase III type 2 promoter." [SO:ke] comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true. synonym: "A box type 2" RELATED [] is_a: SO:0000619 ! A_box relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2 created_by: kareneilbeck creation_date: 2010-10-06T05:44:18Z [Term] id: SO:0001677 name: intermediate_element def: "A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659] synonym: "IE" EXACT [] synonym: "intermediate element" RELATED [] is_a: SO:0001660 ! core_promoter_element relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1 created_by: kareneilbeck creation_date: 2010-10-06T05:52:03Z [Term] id: SO:0001678 name: regulatory_promoter_element def: "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659] synonym: "regulatory promoter element" RELATED [] is_a: SO:0001659 ! promoter_element created_by: kareneilbeck creation_date: 2010-10-07T04:39:48Z [Term] id: SO:0001679 name: transcription_regulatory_region def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke] subset: SOFA synonym: "transcription regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:49:35Z [Term] id: SO:0001680 name: translation_regulatory_region def: "A regulatory region that is involved in the control of the process of translation." [SO:ke] synonym: "translation regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:52:45Z [Term] id: SO:0001681 name: recombination_regulatory_region def: "A regulatory region that is involved in the control of the process of recombination." [SO:ke] synonym: "recombination regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:53:35Z [Term] id: SO:0001682 name: replication_regulatory_region def: "A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke] synonym: "replication regulatory region" RELATED [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:54:09Z [Term] id: SO:0001683 name: sequence_motif def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif] subset: SOFA synonym: "sequence motif" RELATED [] xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia" is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-10-14T04:13:22Z [Term] id: SO:0001684 name: experimental_feature_attribute def: "An attribute of an experimentally derived feature." [SO:ke] synonym: "experimental feature attribute" RELATED [] is_a: SO:0000733 ! feature_attribute created_by: kareneilbeck creation_date: 2010-10-28T02:22:23Z [Term] id: SO:0001685 name: score def: "The score of an experimentally derived feature such as a p-value." [SO:ke] is_a: SO:0001684 ! experimental_feature_attribute created_by: kareneilbeck creation_date: 2010-10-28T02:23:16Z [Term] id: SO:0001686 name: quality_value def: "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke] synonym: "quality value" RELATED [] is_a: SO:0001684 ! experimental_feature_attribute created_by: kareneilbeck creation_date: 2010-10-28T02:24:11Z [Term] id: SO:0001687 name: restriction_enzyme_recognition_site def: "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke] synonym: "restriction endonuclease recognition site" EXACT [] synonym: "restriction enzyme recognition site" EXACT [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-10-29T12:29:57Z [Term] id: SO:0001688 name: restriction_enzyme_cleavage_junction def: "The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke] synonym: "restriction enzyme cleavage junction" EXACT [] is_a: SO:0000699 ! junction created_by: kareneilbeck creation_date: 2010-10-29T12:35:02Z [Term] id: SO:0001689 name: five_prime_restriction_enzyme_junction def: "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke] synonym: "5' restriction enzyme junction" EXACT [] is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:36:24Z [Term] id: SO:0001690 name: three_prime_restriction_enzyme_junction synonym: "3' restriction enzyme junction" EXACT [] is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:37:52Z [Term] id: SO:0001691 name: blunt_end_restriction_enzyme_cleavage_site synonym: "blunt end restriction enzyme cleavage site" EXACT [] is_a: SO:0001687 ! restriction_enzyme_recognition_site created_by: kareneilbeck creation_date: 2010-10-29T12:39:53Z [Term] id: SO:0001692 name: sticky_end_restriction_enzyme_cleavage_site synonym: "sticky end restriction enzyme cleavage site" RELATED [] is_a: SO:0001687 ! restriction_enzyme_recognition_site created_by: kareneilbeck creation_date: 2010-10-29T12:40:50Z [Term] id: SO:0001693 name: blunt_end_restriction_enzyme_cleavage_junction def: "A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke] synonym: "blunt end restriction enzyme cleavage site" RELATED [] is_a: SO:0001688 ! restriction_enzyme_cleavage_junction relationship: part_of SO:0001691 ! blunt_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:43:14Z [Term] id: SO:0001694 name: single_strand_restriction_enzyme_cleavage_site def: "A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke] synonym: "single strand restriction enzyme cleavage site" RELATED [] is_a: SO:0001688 ! restriction_enzyme_cleavage_junction created_by: kareneilbeck creation_date: 2010-10-29T12:44:48Z [Term] id: SO:0001695 name: restriction_enzyme_single_strand_overhang def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke] synonym: "single strand overhang" EXACT [] synonym: "sticky end" RELATED [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site created_by: kareneilbeck creation_date: 2010-10-29T12:48:35Z [Term] id: SO:0001696 name: experimentally_defined_binding_region def: "A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke] synonym: "experimentally defined binding region" RELATED [] is_a: SO:0001410 ! experimental_feature created_by: kareneilbeck creation_date: 2010-11-02T11:39:59Z [Term] id: SO:0001697 name: ChIP_seq_region def: "A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke] synonym: "ChIP seq region" RELATED [] is_a: SO:0001696 ! experimentally_defined_binding_region relationship: contains SO:0000410 ! protein_binding_site created_by: kareneilbeck creation_date: 2010-11-02T11:43:07Z [Term] id: SO:0001698 name: ASPE_primer def: "\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801] synonym: "allele specific primer extension primer" EXACT [] synonym: "ASPE primer" EXACT [] is_a: SO:0000112 ! primer created_by: kareneilbeck creation_date: 2010-11-11T03:25:21Z [Term] id: SO:0001699 name: dCAPS_primer def: "A primer with one or more mis-matches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033] synonym: "dCAPS primer" EXACT [] synonym: "derived cleaved amplified polymorphic primer" EXACT [] is_a: SO:0000112 ! primer created_by: kareneilbeck creation_date: 2010-11-11T03:27:09Z [Term] id: SO:0001700 name: histone_modification def: "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone] synonym: "histone modification" EXACT [] synonym: "histone modification site" RELATED [] is_a: SO:0001089 ! post_translationally_modified_region is_a: SO:0001720 ! epigenetically_modified_region relationship: has_quality SO:0000133 ! epigenetically_modified created_by: kareneilbeck creation_date: 2010-03-31T10:22:08Z [Term] id: SO:0001701 name: histone_methylation_site def: "A histone modification site where the modification is the methylation of the residue." [SO:ke] synonym: "histone methylation" EXACT [] synonym: "histone methylation site" EXACT [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-03-31T10:23:02Z [Term] id: SO:0001702 name: histone_acetylation_site def: "A histone modification where the modification is the acylation of the residue." [SO:ke] synonym: "histone acetylation" EXACT [] synonym: "histone acetylatoin site" EXACT [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-03-31T10:23:27Z [Term] id: SO:0001703 name: H3K9_acetylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K9 acetylation site" EXACT [] synonym: "H3K9Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:25:05Z [Term] id: SO:0001704 name: H3K14_acetylation_site def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K14 acetylation site" EXACT [] synonym: "H3K14Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:25:53Z [Term] id: SO:0001705 name: H3K4_monomethylation_site def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K4 mono-methylation site" EXACT [] synonym: "H3K4me1" RELATED [] is_a: SO:0001734 ! H3K4_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:28:14Z [Term] id: SO:0001706 name: H3K4_trimethylation def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K4 tri-methylation" EXACT [] synonym: "H3K4me3" RELATED [] is_a: SO:0001734 ! H3K4_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:29:12Z [Term] id: SO:0001707 name: H3K9_trimethylation_site def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K9 tri-methylation site" EXACT [] synonym: "H3K9Me3" RELATED [] is_a: SO:0001736 ! H3K9_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:30:34Z [Term] id: SO:0001708 name: H3K27_monomethylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H2K27 mono-methylation site" EXACT [] synonym: "H2K27Me1" RELATED [] is_a: SO:0001732 ! H3K27_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:31:54Z [Term] id: SO:0001709 name: H3K27_trimethylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K27 tri-methylation site" EXACT [] synonym: "H3K27Me3" RELATED [] is_a: SO:0001732 ! H3K27_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:32:41Z [Term] id: SO:0001710 name: H3K79_monomethylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K79 mono-methylation site" EXACT [] synonym: "H3K79me1" RELATED [] is_a: SO:0001735 ! H3K79_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:33:42Z [Term] id: SO:0001711 name: H3K79_dimethylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K79 di-methylation site" EXACT [] synonym: "H3K79Me2" RELATED [] is_a: SO:0001735 ! H3K79_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:34:39Z [Term] id: SO:0001712 name: H3K79_trimethylation_site def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H3K79 tri-methylation site" EXACT [] synonym: "H3K79Me3" RELATED [] is_a: SO:0001735 ! H3K79_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:35:30Z [Term] id: SO:0001713 name: H4K20_monomethylation_site def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H34histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H4K20 mono-methylation site" EXACT [] synonym: "H4K20Me1" RELATED [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:36:43Z [Term] id: SO:0001714 name: H2BK5_monomethylation_site def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone] synonym: "H2BK5 mono-methylation site" EXACT [] is_a: SO:0001701 ! histone_methylation_site created_by: kareneilbeck creation_date: 2010-03-31T10:38:12Z [Term] id: SO:0001715 name: ISRE def: "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac] comment: Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term. synonym: "interferon stimulated response element" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region created_by: kareneilbeck creation_date: 2010-04-05T11:15:08Z [Term] id: SO:0001716 name: histone_ubiqitination_site def: "A histone modification site where ubiquitin may be added." [SO:ke] synonym: "histone ubiquitination site" RELATED [] is_a: SO:0001700 ! histone_modification created_by: kareneilbeck creation_date: 2010-04-13T10:12:18Z [Term] id: SO:0001717 name: H2B_ubiquitination_site def: "A histone modification site on H2B where ubiquitin may be added." [SO:ke] synonym: "H2BUbiq" RELATED [] is_a: SO:0001716 ! histone_ubiqitination_site created_by: kareneilbeck creation_date: 2010-04-13T10:13:28Z [Term] id: SO:0001718 name: H3K18_acetylation_site def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] synonym: "H3K18 acetylation site" EXACT [] synonym: "H3K18Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:39:35Z [Term] id: SO:0001719 name: H3K23_acylation_site def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] synonym: "H3K23 acylation site" RELATED [] synonym: "H3K23Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:42:45Z [Term] id: SO:0001720 name: epigenetically_modified_region def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke] subset: SOFA synonym: "epigenetically modified region" RELATED [] is_a: SO:0001411 ! biological_region relationship: has_quality SO:0000133 ! epigenetically_modified created_by: kareneilbeck creation_date: 2010-03-27T12:02:29Z [Term] id: SO:0001721 name: H3K27_acylation_site def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke] synonym: "H3K27 acylation site" EXACT [] synonym: "H3K27Ac" RELATED [] is_a: SO:0001702 ! histone_acetylation_site created_by: kareneilbeck creation_date: 2010-04-13T10:44:09Z [Term] id: SO:0001722 name: H3K36_monomethylation_site def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke] synonym: "H3K36 mono-methylation site" EXACT [] synonym: "H3K36. subset: SOFA synonym: "modified base site" EXACT [] is_a: SO:0001236 ! base is_a: SO:0001720 ! epigenetically_modified_region [Term] id: SO:0000306 name: methylated_DNA_base_feature namespace: sequence def: "A nucleotide modified by methylation." [SO:ke] subset: SOFA synonym: "methylated base feature" EXACT [] is_a: SO:0000305 ! modified_DNA_base [Term] id: SO:0000307 name: CpG_island namespace: sequence def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd] subset: SOFA synonym: "CG island" EXACT [] synonym: "CpG island" EXACT [] xref: http://en.wikipedia.org/wiki/CpG_island "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000314 name: direct_repeat namespace: sequence def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-----GCTGA." [SO:ke] subset: SOFA synonym: "direct repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000315 name: TSS namespace: sequence def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] subset: SOFA synonym: "transcription start site" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000316 name: CDS namespace: sequence def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma] subset: SOFA synonym: "coding sequence" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000318 name: start_codon namespace: sequence def: "First codon to be translated by a ribosome." [SO:ke] subset: SOFA synonym: "initiation codon" EXACT [] synonym: "start codon" EXACT [] xref: http://en.wikipedia.org/wiki/Start_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000319 name: stop_codon namespace: sequence def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke] subset: SOFA synonym: "stop codon" EXACT [] xref: http://en.wikipedia.org/wiki/Stop_codon "wiki" is_a: SO:0000360 ! codon [Term] id: SO:0000324 name: tag namespace: sequence def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke] subset: SOFA is_a: SO:0000696 ! oligo [Term] id: SO:0000325 name: rRNA_large_subunit_primary_transcript namespace: sequence def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke] subset: SOFA synonym: "35S rRNA primary transcript" EXACT [] synonym: "rRNA large subunit primary transcript" EXACT [] is_a: SO:0000209 ! rRNA_primary_transcript [Term] id: SO:0000326 name: SAGE_tag namespace: sequence def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract] subset: SOFA synonym: "SAGE tag" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000330 name: conserved_region namespace: sequence def: "Region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "conserved region" EXACT [] xref: http://en.wikipedia.org/wiki/Conserved_region "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000331 name: STS namespace: sequence def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com] subset: SOFA synonym: "sequence tag site" EXACT [] is_a: SO:0000324 ! tag [Term] id: SO:0000332 name: coding_conserved_region namespace: sequence def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "coding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000333 name: exon_junction namespace: sequence def: "The boundary between two exons in a processed transcript." [SO:ke] subset: SOFA synonym: "exon junction" EXACT [] is_a: SO:0000699 ! junction relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000334 name: nc_conserved_region namespace: sequence def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "nc conserved region" EXACT [] synonym: "noncoding conserved region" EXACT [] is_a: SO:0000330 ! conserved_region [Term] id: SO:0000336 name: pseudogene namespace: sequence def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] subset: SOFA xref: http://en.wikipedia.org/wiki/Pseudogene "wiki" is_a: SO:0001411 ! biological_region relationship: non_functional_homolog_of SO:0000704 ! gene [Term] id: SO:0000337 name: RNAi_reagent namespace: sequence def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd] subset: SOFA synonym: "RNAi reagent" EXACT [] is_a: SO:0000442 ! ds_oligo [Term] id: SO:0000340 name: chromosome namespace: sequence def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA xref: http://en.wikipedia.org/wiki/Chromosome "wiki" is_a: SO:0001235 ! replicon [Term] id: SO:0000341 name: chromosome_band namespace: sequence def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma] subset: SOFA synonym: "chromosome band" EXACT [] synonym: "cytoband" EXACT [] synonym: "cytological band" EXACT [] xref: http://en.wikipedia.org/wiki/Cytological_band "wiki" is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000343 name: match namespace: sequence def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000344 name: splice_enhancer namespace: sequence def: "Region of a transcript that regulates splicing." [SO:ke] subset: SOFA synonym: "splice enhancer" EXACT [] is_a: SO:0001056 ! splicing_regulatory_region [Term] id: SO:0000345 name: EST namespace: sequence def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "expressed sequence tag" EXACT [] is_a: SO:0000324 ! tag relationship: derives_from SO:0000234 ! mRNA [Term] id: SO:0000347 name: nucleotide_match namespace: sequence def: "A match against a nucleotide sequence." [SO:ke] subset: SOFA synonym: "nucleotide match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000349 name: protein_match namespace: sequence def: "A match against a protein sequence." [SO:ke] subset: SOFA synonym: "protein match" EXACT [] is_a: SO:0000343 ! match [Term] id: SO:0000353 name: sequence_assembly namespace: sequence def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma] subset: SOFA synonym: "sequence assembly" EXACT [] xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki" is_a: SO:0001248 ! assembly [Term] id: SO:0000360 name: codon namespace: sequence def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Codon "wiki" is_a: SO:0000851 ! CDS_region [Term] id: SO:0000366 name: insertion_site namespace: sequence def: "The junction where an insertion occurred." [SO:ke] subset: SOFA synonym: "insertion site" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000368 name: transposable_element_insertion_site namespace: sequence def: "The junction in a genome where a transposable_element has inserted." [SO:ke] subset: SOFA synonym: "transposable element insertion site" EXACT [] is_a: SO:0000366 ! insertion_site [Term] id: SO:0000370 name: small_regulatory_ncRNA namespace: sequence def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma] subset: SOFA synonym: "small regulatory ncRNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000372 name: enzymatic_RNA namespace: sequence def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb] comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts. subset: SOFA synonym: "enzymatic RNA" EXACT [] is_a: SO:0000673 ! transcript [Term] id: SO:0000374 name: ribozyme namespace: sequence def: "An RNA with catalytic activity." [SO:ma] subset: SOFA xref: http://en.wikipedia.org/wiki/Ribozyme "wiki" is_a: SO:0000372 ! enzymatic_RNA [Term] id: SO:0000375 name: rRNA_5_8S namespace: sequence def: "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002] subset: SOFA synonym: "5.8S LSU rRNA" EXACT [] synonym: "5.8S ribosomal RNA" EXACT [] synonym: "5.8S rRNA" EXACT [] synonym: "rRNA 5 8S" EXACT [] xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000380 name: hammerhead_ribozyme namespace: sequence def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805] subset: SOFA synonym: "hammerhead ribozyme" EXACT [] xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki" is_a: SO:0000715 ! RNA_motif [Term] id: SO:0000385 name: RNase_MRP_RNA namespace: sequence def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030] subset: SOFA synonym: "RNase MRP RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000386 name: RNase_P_RNA namespace: sequence def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010] subset: SOFA synonym: "RNase P RNA" EXACT [] is_a: SO:0000655 ! ncRNA [Term] id: SO:0000390 name: telomerase_RNA namespace: sequence def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025] subset: SOFA synonym: "telomerase RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000391 name: U1_snRNA namespace: sequence def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003] subset: SOFA synonym: "small nuclear RNA U1" EXACT [RSC:cb] synonym: "snRNA U1" EXACT [RSC:cb] synonym: "U1 small nuclear RNA" EXACT [RSC:cb] synonym: "U1 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000392 name: U2_snRNA namespace: sequence def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004] subset: SOFA synonym: "small nuclear RNA U2" EXACT [RSC:CB] synonym: "snRNA U2" EXACT [RSC:CB] synonym: "U2 small nuclear RNA" EXACT [RSC:CB] synonym: "U2 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000393 name: U4_snRNA namespace: sequence def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U4" EXACT [RSC:cb] synonym: "snRNA U4" EXACT [RSC:cb] synonym: "U4 small nuclear RNA" EXACT [RSC:cb] synonym: "U4 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000394 name: U4atac_snRNA namespace: sequence def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455] subset: SOFA synonym: "small nuclear RNA U4atac" EXACT [RSC:cb] synonym: "snRNA U4atac" EXACT [RSC:cb] synonym: "U4atac small nuclear RNA" EXACT [RSC:cb] synonym: "U4atac snRNA" EXACT [] is_a: SO:0000274 ! snRNA [Term] id: SO:0000395 name: U5_snRNA namespace: sequence def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020] subset: SOFA synonym: "small nuclear RNA U5" EXACT [RSC:cb] synonym: "snRNA U5" EXACT [RSC:cb] synonym: "U5 small nuclear RNA" EXACT [RSC:cb] synonym: "U5 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000396 name: U6_snRNA namespace: sequence def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015] subset: SOFA synonym: "small nuclear RNA U6" EXACT [RSC:cb] synonym: "snRNA U6" EXACT [RSC:cb] synonym: "U6 small nuclear RNA" EXACT [RSC:cb] synonym: "U6 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000397 name: U6atac_snRNA namespace: sequence def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract] subset: SOFA synonym: "snRNA U6atac" EXACT [RSC:cb] synonym: "U6atac small nuclear RNA" EXACT [RSC:cb] synonym: "U6atac snRNA" EXACT [RSC:cb] is_a: SO:0000274 ! snRNA [Term] id: SO:0000398 name: U11_snRNA namespace: sequence def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129] subset: SOFA synonym: "small nuclear RNA U11" EXACT [RSC:cb] synonym: "snRNA U11" EXACT [RSC:cb] synonym: "U11 small nuclear RNA" EXACT [RSC:cb] synonym: "U11 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000399 name: U12_snRNA namespace: sequence def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007] subset: SOFA synonym: "small nuclear RNA U12" EXACT [RSC:cb] synonym: "snRNA U12" EXACT [RSC:cb] synonym: "U12 small nuclear RNA" EXACT [RSC:cb] synonym: "U12 snRNA" EXACT [] xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki" is_a: SO:0000274 ! snRNA [Term] id: SO:0000403 name: U14_snoRNA namespace: sequence alt_id: SO:0005839 def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119] comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. subset: SOFA synonym: "small nucleolar RNA U14" EXACT [] synonym: "snoRNA U14" EXACT [] synonym: "U14 small nucleolar RNA" EXACT [] synonym: "U14 snoRNA" EXACT [] is_a: SO:0000593 ! C_D_box_snoRNA [Term] id: SO:0000404 name: vault_RNA namespace: sequence def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006] subset: SOFA synonym: "vault RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000405 name: Y_RNA namespace: sequence def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019] subset: SOFA synonym: "Y RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Y_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000407 name: rRNA_18S namespace: sequence def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "18S ribosomal RNA" EXACT [] synonym: "18S rRNA" EXACT [] synonym: "rRNA 18S" EXACT [] xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki" is_a: SO:0000650 ! small_subunit_rRNA [Term] id: SO:0000409 name: binding_site namespace: sequence alt_id: BS:00033 def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke] comment: See GO:0005488 : binding. subset: biosapiens subset: SOFA synonym: "binding_or_interaction_site" EXACT [] synonym: "site" RELATED [] xref: http://en.wikipedia.org/wiki/Binding_site "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000410 name: protein_binding_site namespace: sequence def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke] comment: See GO:0042277 : peptide binding. subset: SOFA synonym: "protein binding site" EXACT [] is_a: SO:0000409 ! binding_site [Term] id: SO:0000412 name: restriction_fragment namespace: sequence def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke] subset: SOFA synonym: "restriction fragment" EXACT [] xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki" is_a: SO:0000143 ! assembly_component [Term] id: SO:0000413 name: sequence_difference namespace: sequence def: "A region where the sequence differs from that of a specified sequence." [SO:ke] subset: SOFA synonym: "sequence difference" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000418 name: signal_peptide namespace: sequence alt_id: BS:00159 def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence. subset: biosapiens subset: SOFA synonym: "signal" RELATED [uniprot:feature_type] synonym: "signal peptide" EXACT [] synonym: "signal peptide coding sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki" is_a: SO:0001527 ! peptide_localization_signal relationship: part_of SO:0100011 ! cleaved_peptide_region [Term] id: SO:0000419 name: mature_protein_region namespace: sequence alt_id: BS:00149 def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb] comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification. subset: biosapiens subset: SOFA synonym: "chain" RELATED [uniprot:feature_type] synonym: "mature peptide" RELATED [] synonym: "mature protein region" EXACT [] is_a: SO:0000839 ! polypeptide_region relationship: part_of SO:0001063 ! immature_peptide_region [Term] id: SO:0000436 name: ARS namespace: sequence def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma] subset: SOFA synonym: "autonomously replicating sequence" EXACT [] is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000441 name: ss_oligo namespace: sequence def: "A single stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "single strand oligo" EXACT [] synonym: "single strand oligonucleotide" EXACT [] synonym: "single stranded oligonucleotide" EXACT [] synonym: "ss oligo" EXACT [] synonym: "ss oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000442 name: ds_oligo namespace: sequence def: "A double stranded oligonucleotide." [SO:ke] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "double stranded oligonucleotide" EXACT [] synonym: "ds oligo" EXACT [] synonym: "ds-oligonucleotide" EXACT [] is_a: SO:0000696 ! oligo [Term] id: SO:0000454 name: rasiRNA namespace: sequence def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284] subset: SOFA synonym: "repeat associated small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RasiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000462 name: pseudogenic_region namespace: sequence def: "A non-functional descendent of a functional entity." [SO:cjm] subset: SOFA synonym: "pseudogenic region" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000464 name: decayed_exon namespace: sequence def: "A non-functional descendant of an exon." [SO:ke] subset: SOFA synonym: "decayed exon" EXACT [] is_a: SO:0000462 ! pseudogenic_region relationship: non_functional_homolog_of SO:0000147 ! exon [Term] id: SO:0000468 name: golden_path_fragment namespace: sequence def: "One of the pieces of sequence that make up a golden path." [SO:rd] subset: SOFA synonym: "golden path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000688 ! golden_path [Term] id: SO:0000472 name: tiling_path namespace: sequence def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm] subset: SOFA synonym: "tiling path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000474 name: tiling_path_fragment namespace: sequence def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke] subset: SOFA synonym: "tiling path fragment" EXACT [] is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000472 ! tiling_path [Term] id: SO:0000483 name: nc_primary_transcript namespace: sequence def: "A primary transcript that is never translated into a protein." [SO:ke] subset: SOFA synonym: "nc primary transcript" EXACT [] synonym: "noncoding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000484 name: three_prime_coding_exon_noncoding_region namespace: sequence def: "The sequence of the 3' exon that is not coding." [SO:ke] subset: SOFA synonym: "three prime coding exon noncoding region" EXACT [] synonym: "three_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon relationship: part_of SO:0000195 ! coding_exon [Term] id: SO:0000486 name: five_prime_coding_exon_noncoding_region namespace: sequence def: "The sequence of the 5' exon preceding the start codon." [SO:ke] subset: SOFA synonym: "five prime coding exon noncoding region" EXACT [] synonym: "five_prime_exon_noncoding_region" EXACT [] is_a: SO:0001214 ! noncoding_region_of_exon relationship: part_of SO:0000200 ! five_prime_coding_exon [Term] id: SO:0000499 name: virtual_sequence namespace: sequence def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke] subset: SOFA synonym: "virtual sequence" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000502 name: transcribed_region namespace: sequence def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke] comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being. subset: SOFA is_obsolete: true [Term] id: SO:0000551 name: polyA_signal_sequence namespace: sequence def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "poly(A) signal" EXACT [] synonym: "polyA signal sequence" EXACT [] synonym: "polyadenylation termination signal" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0000553 name: polyA_site namespace: sequence alt_id: SO:0001430 def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "polyA cleavage site" EXACT [] synonym: "polyA junction" EXACT [] synonym: "polyA site" EXACT [] synonym: "polyA_junction" EXACT [] synonym: "polyadenylation site" RELATED [] is_a: SO:0000699 ! junction relationship: part_of SO:0000205 ! three_prime_UTR relationship: part_of SO:0000233 ! mature_transcript [Term] id: SO:0000577 name: centromere namespace: sequence def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Centromere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000581 name: cap namespace: sequence def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html] subset: SOFA xref: http://en.wikipedia.org/wiki/5%27_cap "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000587 name: group_I_intron namespace: sequence def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028] comment: GO:0000372. subset: SOFA synonym: "group I intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000588 name: autocatalytically_spliced_intron namespace: sequence def: "A self spliced intron." [SO:ke] subset: SOFA synonym: "autocatalytically spliced intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000590 name: SRP_RNA namespace: sequence def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017] subset: SOFA synonym: "7S RNA" RELATED [] synonym: "signal recognition particle RNA" RELATED [] synonym: "SRP RNA" EXACT [] is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000483 ! nc_primary_transcript [Term] id: SO:0000593 name: C_D_box_snoRNA namespace: sequence def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] subset: SOFA synonym: "box C/D snoRNA" EXACT [] synonym: "C D box snoRNA" EXACT [] synonym: "C/D box snoRNA" EXACT [] is_a: SO:0000275 ! snoRNA [Term] id: SO:0000602 name: guide_RNA namespace: sequence def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html] subset: SOFA synonym: "gRNA" EXACT [] synonym: "guide RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000603 name: group_II_intron namespace: sequence def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml] comment: GO:0000373. subset: SOFA synonym: "group II intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000605 name: intergenic_region namespace: sequence def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "intergenic region" EXACT [] xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000610 name: polyA_sequence namespace: sequence def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke] subset: SOFA synonym: "polyA sequence" EXACT [] is_a: SO:0001411 ! biological_region relationship: adjacent_to SO:0000234 ! mRNA [Term] id: SO:0000611 name: branch_site namespace: sequence def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke] subset: SOFA synonym: "branch point" EXACT [] synonym: "branch site" EXACT [] synonym: "branch_point" EXACT [] is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000612 name: polypyrimidine_tract namespace: sequence def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888] subset: SOFA synonym: "polypyrimidine tract" EXACT [] xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki" is_a: SO:0000841 ! spliceosomal_intron_region [Term] id: SO:0000616 name: transcription_end_site namespace: sequence def: "The base where transcription ends." [SO:ke] subset: SOFA synonym: "transcription end site" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000624 name: telomere namespace: sequence def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma] subset: SOFA synonym: "telomeric DNA" EXACT [] synonym: "telomeric sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Telomere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000625 name: silencer namespace: sequence def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki" is_a: SO:0000727 ! CRM [Term] id: SO:0000627 name: insulator namespace: sequence def: "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative] subset: SOFA synonym: "insulator element" EXACT [] xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000628 name: chromosomal_structural_element namespace: sequence subset: SOFA synonym: "chromosomal structural element" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000643 name: minisatellite namespace: sequence def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml] subset: SOFA xref: http://en.wikipedia.org/wiki/Minisatellite "wiki" is_a: SO:0000005 ! satellite_DNA [Term] id: SO:0000644 name: antisense_RNA namespace: sequence def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke] subset: SOFA synonym: "antisense RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki" is_a: SO:0000655 ! ncRNA relationship: derives_from SO:0000645 ! antisense_primary_transcript [Term] id: SO:0000645 name: antisense_primary_transcript namespace: sequence def: "The reverse complement of the primary transcript." [SO:ke] subset: SOFA synonym: "antisense primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000646 name: siRNA namespace: sequence def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000] subset: SOFA synonym: "small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SiRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000649 name: stRNA namespace: sequence def: "Non-coding RNAs of about 21 nucleotides in length that regulate temporal development; first discovered in C. elegans." [PMID:11081512] subset: SOFA synonym: "small temporal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/StRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000650 name: small_subunit_rRNA namespace: sequence def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "small subunit rRNA" EXACT [] synonym: "SSU RNA" EXACT [RSC:cb] synonym: "SSU rRNA" EXACT [RSC:cb] is_a: SO:0000252 ! rRNA [Term] id: SO:0000651 name: large_subunit_rRNA namespace: sequence def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke] subset: SOFA synonym: "large subunit rRNA" EXACT [] synonym: "LSU RNA" EXACT [RSC:cb] synonym: "LSU rRNA" EXACT [RSC:cb] is_a: SO:0000252 ! rRNA relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript [Term] id: SO:0000652 name: rRNA_5S namespace: sequence def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001] subset: SOFA synonym: "5S LSU rRNA" EXACT [] synonym: "5S ribosomal RNA" EXACT [] synonym: "5S rRNA" EXACT [] synonym: "rRNA 5S" EXACT [] xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000653 name: rRNA_28S namespace: sequence def: "A component of the large ribosomal subunit." [SO:ke] subset: SOFA synonym: "28S LSU rRNA" EXACT [] synonym: "28S ribosomal RNA" EXACT [] synonym: "28S rRNA" EXACT [] synonym: "rRNA 28S" EXACT [] xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki" is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0000655 name: ncRNA namespace: sequence def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. subset: SOFA synonym: "noncoding RNA" EXACT [] xref: http://en.wikipedia.org/wiki/NcRNA "wiki" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000657 name: repeat_region namespace: sequence def: "A region of sequence containing one or more repeat units." [SO:ke] subset: SOFA synonym: "repeat region" EXACT [] is_a: SO:0001411 ! biological_region relationship: has_part SO:0001411 ! biological_region [Term] id: SO:0000658 name: dispersed_repeat namespace: sequence def: "A repeat that is located at dispersed sites in the genome." [SO:ke] subset: SOFA synonym: "dispersed repeat" EXACT [] synonym: "interspersed repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki" is_a: SO:0000657 ! repeat_region [Term] id: SO:0000662 name: spliceosomal_intron namespace: sequence def: "An intron which is spliced by the spliceosome." [SO:ke] comment: GO:0000398. subset: SOFA synonym: "spliceosomal intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000667 name: insertion namespace: sequence alt_id: SO:1000034 def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke] subset: DBVAR subset: SOFA synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] synonym: "nucleotide insertion" EXACT [] synonym: "nucleotide_insertion" EXACT [] xref: loinc:LA6687-3 "Insertion" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:0000668 name: EST_match namespace: sequence def: "A match against an EST sequence." [SO:ke] subset: SOFA synonym: "EST match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000673 name: transcript namespace: sequence def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] subset: SOFA xref: http://en.wikipedia.org/wiki/RNA "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0000684 name: nuclease_sensitive_site namespace: sequence def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma] subset: SOFA synonym: "nuclease sensitive site" EXACT [] is_a: SO:0000059 ! nuclease_binding_site [Term] id: SO:0000687 name: deletion_junction namespace: sequence def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke] subset: SOFA synonym: "deletion junction" EXACT [] is_a: SO:0000699 ! junction [Term] id: SO:0000688 name: golden_path namespace: sequence def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls] subset: SOFA synonym: "golden path" EXACT [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000689 name: cDNA_match namespace: sequence def: "A match against cDNA sequence." [SO:ke] subset: SOFA synonym: "cDNA match" EXACT [] is_a: SO:0000102 ! expressed_sequence_match [Term] id: SO:0000694 name: SNP namespace: sequence def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb] subset: SOFA synonym: "single nucleotide polymorphism" EXACT [] is_a: SO:0001483 ! SNV [Term] id: SO:0000695 name: reagent namespace: sequence def: "A sequence used in experiment." [SO:ke] comment: Requested by Lynn Crosby, jan 2006. subset: SOFA is_a: SO:0001409 ! biomaterial_region [Term] id: SO:0000696 name: oligo namespace: sequence def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma] subset: SOFA synonym: "oligonucleotide" EXACT [] xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki" is_a: SO:0000695 ! reagent [Term] id: SO:0000699 name: junction namespace: sequence def: "A sequence_feature with an extent of zero." [SO:ke] comment: A junction is a boundary between regions. A boundary has an extent of zero. subset: SOFA synonym: "boundary" EXACT [] synonym: "breakpoint" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0000700 name: remark namespace: sequence def: "A comment about the sequence." [SO:ke] subset: SOFA is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000701 name: possible_base_call_error namespace: sequence def: "A region of sequence where the validity of the base calling is questionable." [SO:ke] subset: SOFA synonym: "possible base call error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000702 name: possible_assembly_error namespace: sequence def: "A region of sequence where there may have been an error in the assembly." [SO:ke] subset: SOFA synonym: "possible assembly error" EXACT [] is_a: SO:0000413 ! sequence_difference [Term] id: SO:0000703 name: experimental_result_region namespace: sequence def: "A region of sequence implicated in an experimental result." [SO:ke] subset: SOFA synonym: "experimental result region" EXACT [] is_a: SO:0000700 ! remark [Term] id: SO:0000704 name: gene namespace: sequence def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. subset: SOFA xref: http://en.wikipedia.org/wiki/Gene "wiki" is_a: SO:0001411 ! biological_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000705 name: tandem_repeat namespace: sequence def: "Two or more adjcent copies of a region (of length greater than 1)." [SO:ke] subset: SOFA synonym: "tandem repeat" EXACT [] xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki" xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html is_a: SO:0000657 ! repeat_region [Term] id: SO:0000706 name: trans_splice_acceptor_site namespace: sequence def: "The 3' splice site of the acceptor primary transcript." [SO:ke] comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans. subset: SOFA synonym: "3' trans splice site" RELATED [] synonym: "trans splice acceptor site" EXACT [] is_a: SO:0001420 ! trans_splice_site [Term] id: SO:0000714 name: nucleotide_motif namespace: sequence def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke] subset: SOFA synonym: "nucleotide motif" EXACT [] is_a: SO:0001683 ! sequence_motif [Term] id: SO:0000715 name: RNA_motif namespace: sequence def: "A motif that is active in RNA sequence." [SO:ke] subset: SOFA synonym: "RNA motif" EXACT [] is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000717 name: reading_frame namespace: sequence def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb] comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop. subset: SOFA synonym: "reading frame" EXACT [] xref: http://en.wikipedia.org/wiki/Reading_frame "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000719 name: ultracontig namespace: sequence def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG] subset: SOFA synonym: "superscaffold" RELATED [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000724 name: oriT namespace: sequence def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] subset: SOFA synonym: "origin of transfer" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki" is_a: SO:0000296 ! origin_of_replication [Term] id: SO:0000725 name: transit_peptide namespace: sequence alt_id: BS:00055 def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] comment: Added to bring SO inline with the embl ddbj genbank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle. subset: biosapiens subset: SOFA synonym: "signal" RELATED [] synonym: "transit" RELATED [uniprot:feature_type] synonym: "transit peptide" EXACT [] is_a: SO:0001527 ! peptide_localization_signal [Term] id: SO:0000727 name: CRM namespace: sequence def: "A regulatory_region where more than 1 TF_binding_site together are regulatorily active." [SO:SG] comment: Requested by Stepen Grossmann Dec 2004. subset: SOFA synonym: "cis regulatory module" EXACT [] synonym: "TF module" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region intersection_of: SO:0001055 ! transcriptional_cis_regulatory_region intersection_of: has_part SO:0000235 ! TF_binding_site relationship: has_part SO:0000235 ! TF_binding_site [Term] id: SO:0000730 name: gap namespace: sequence def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke] subset: SOFA is_a: SO:0000143 ! assembly_component relationship: part_of SO:0000353 ! sequence_assembly [Term] id: SO:0000752 name: gene_group_regulatory_region namespace: sequence subset: SOFA synonym: "gene group regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region relationship: member_of SO:0005855 ! gene_group [Term] id: SO:0000753 name: clone_insert namespace: sequence def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke] subset: SOFA synonym: "clone insert" EXACT [] is_a: SO:0000695 ! reagent relationship: part_of SO:0000151 ! clone [Term] id: SO:0000777 name: pseudogenic_rRNA namespace: sequence def: "A non functional descendent of an rRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "pseudogenic rRNA" EXACT [] is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0000778 name: pseudogenic_tRNA namespace: sequence def: "A non functional descendent of a tRNA." [SO:ke] comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations. subset: SOFA synonym: "pseudogenic tRNA" EXACT [] is_a: SO:0000462 ! pseudogenic_region [Term] id: SO:0000830 name: chromosome_part namespace: sequence def: "A region of a chromosome." [SO:ke] comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. subset: SOFA synonym: "chromosome part" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000340 ! chromosome [Term] id: SO:0000831 name: gene_member_region namespace: sequence def: "A region of a gene." [SO:ke] comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. subset: SOFA synonym: "gene member region" EXACT [] is_a: SO:0001411 ! biological_region relationship: member_of SO:0000704 ! gene [Term] id: SO:0000833 name: transcript_region namespace: sequence def: "A region of a transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "transcript region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000673 ! transcript [Term] id: SO:0000834 name: mature_transcript_region namespace: sequence def: "A region of a mature transcript." [SO:ke] comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. subset: SOFA synonym: "mature transcript region" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000835 name: primary_transcript_region namespace: sequence def: "A part of a primary transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "primary transcript region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000185 ! primary_transcript [Term] id: SO:0000836 name: mRNA_region namespace: sequence def: "A region of an mRNA." [SO:cb] comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root. subset: SOFA synonym: "mRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region relationship: part_of SO:0000234 ! mRNA [Term] id: SO:0000837 name: UTR_region namespace: sequence def: "A region of UTR." [SO:ke] comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root. subset: SOFA synonym: "UTR region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000839 name: polypeptide_region namespace: sequence alt_id: BS:00124 alt_id: BS:00331 def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] comment: Added to allow the polypeptide regions to have is_a paths back to the root. subset: biosapiens subset: SOFA synonym: "positional" RELATED [] synonym: "positional polypeptide feature" RELATED [] synonym: "region" NARROW [uniprot:feature_type] synonym: "region or site annotation" RELATED [] synonym: "site" NARROW [uniprot:feature_type] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000104 ! polypeptide [Term] id: SO:0000841 name: spliceosomal_intron_region namespace: sequence def: "A region within an intron." [SO:ke] comment: A terms added to allow the parts of introns to have is_a paths to the root. subset: SOFA synonym: "spliceosomal intron region" EXACT [] is_a: SO:0000835 ! primary_transcript_region relationship: part_of SO:0000662 ! spliceosomal_intron [Term] id: SO:0000842 name: gene_component_region namespace: sequence subset: SOFA synonym: "gene component region" EXACT [] is_a: SO:0001411 ! biological_region relationship: part_of SO:0000704 ! gene [Term] id: SO:0000851 name: CDS_region namespace: sequence def: "A region of a CDS." [SO:cb] subset: SOFA synonym: "CDS region" EXACT [] is_a: SO:0000836 ! mRNA_region relationship: part_of SO:0000316 ! CDS [Term] id: SO:0000852 name: exon_region namespace: sequence def: "A region of an exon." [RSC:cb] subset: SOFA synonym: "exon region" EXACT [] is_a: SO:0000833 ! transcript_region relationship: part_of SO:0000147 ! exon [Term] id: SO:0001000 name: rRNA_16S namespace: sequence def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke] subset: SOFA synonym: "16S ribosomal RNA" EXACT [] synonym: "16S rRNA" RELATED [] synonym: "16S SSU RNA" EXACT [] synonym: "rRNA 16S" EXACT [] xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki" is_a: SO:0000650 ! small_subunit_rRNA [Term] id: SO:0001001 name: rRNA_23S namespace: sequence def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke] subset: SOFA synonym: "23S LSU rRNA" EXACT [] synonym: "23S ribosomal RNA" RELATED [] synonym: "23S rRNA" EXACT [] synonym: "rRNA 23S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001002 name: rRNA_25S namespace: sequence def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb] subset: SOFA synonym: "25S LSU rRNA" EXACT [] synonym: "25S ribosomal RNA" EXACT [] synonym: "25S rRNA" EXACT [] synonym: "rRNA 25S" EXACT [] is_a: SO:0000651 ! large_subunit_rRNA [Term] id: SO:0001019 name: copy_number_variation namespace: sequence def: "A variation that increases or decreases the copy number of a given region." [SO:ke] subset: SOFA synonym: "CNP" EXACT [] synonym: "CNV" EXACT [] synonym: "copy number polymorphism" EXACT [] synonym: "copy number variation" EXACT [] xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki" is_a: SO:0001059 ! sequence_alteration [Term] id: SO:0001037 name: mobile_genetic_element namespace: sequence def: "A nucleotide region with either intra-genome or intracellular moblity, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355] subset: SOFA synonym: "MGE" EXACT [] synonym: "mobile genetic element" EXACT [] xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001039 name: integrated_mobile_genetic_element namespace: sequence def: "An MGE that is integrated into the host chromosome." [SO:ke] subset: SOFA synonym: "integrated mobile genetic element" EXACT [] is_a: SO:0001037 ! mobile_genetic_element [Term] id: SO:0001055 name: transcriptional_cis_regulatory_region namespace: sequence def: "A regulatory_region that modulates the transcription of a gene or genes." [SO:regcreative] subset: SOFA synonym: "transcriptional cis regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0001056 name: splicing_regulatory_region namespace: sequence def: "A regulatory_region that modulates splicing." [SO:ke] subset: SOFA synonym: "splicing regulatory region" EXACT [] is_a: SO:0001679 ! transcription_regulatory_region [Term] id: SO:0001059 name: sequence_alteration namespace: sequence alt_id: SO:1000004 alt_id: SO:1000007 def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke] comment: Merged with partially characterized change in nucleotide sequence. subset: SOFA synonym: "partially characterised change in DNA sequence" NARROW [] synonym: "partially_characterised_change_in_DNA_sequence" NARROW [] synonym: "sequence alteration" EXACT [] synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0001063 name: immature_peptide_region namespace: sequence alt_id: BS:00129 def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR] comment: Range. subset: biosapiens subset: SOFA synonym: "immature peptide region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:0001214 name: noncoding_region_of_exon namespace: sequence def: "The maximal intersection of exon and UTR." [SO:ke] comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding. subset: SOFA synonym: "noncoding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001215 name: coding_region_of_exon namespace: sequence def: "The region of an exon that encodes for protein sequence." [SO:ke] comment: An exon containing either a start or stop codon will be partially coding and partially non coding. subset: SOFA synonym: "coding region of exon" EXACT [] is_a: SO:0000852 ! exon_region [Term] id: SO:0001235 name: replicon namespace: sequence def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207] subset: SOFA xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001236 name: base namespace: sequence def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Nucleobase "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001248 name: assembly namespace: sequence def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0001409 name: biomaterial_region namespace: sequence def: "A region which is intended for use in an experiment." [SO:cb] subset: SOFA synonym: "biomaterial region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001410 name: experimental_feature namespace: sequence def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] subset: SOFA synonym: "analysis feature" RELATED [] synonym: "experimental output artefact" EXACT [] synonym: "experimental_output_artefact" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001411 name: biological_region namespace: sequence def: "A region defined by its disposition to be involved in a biological process." [SO:cb] subset: SOFA synonym: "biological region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001412 name: topologically_defined_region namespace: sequence def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb] subset: SOFA synonym: "topologically defined region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001419 name: cis_splice_site namespace: sequence def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke] subset: SOFA synonym: "cis splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001420 name: trans_splice_site namespace: sequence def: "Primary transcript region bordering trans-splice junction." [SO:ke] subset: SOFA synonym: "trans splice site" EXACT [] is_a: SO:0000162 ! splice_site [Term] id: SO:0001483 name: SNV namespace: sequence def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm] subset: SOFA synonym: "single nucleotide variant" EXACT [] is_a: SO:1000002 ! substitution created_by: kareneilbeck creation_date: 2009-10-08T11:37:49Z [Term] id: SO:0001527 name: peptide_localization_signal namespace: sequence def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke] subset: SOFA synonym: "localization signal" RELATED [] synonym: "peptide localization signal" EXACT [] is_a: SO:0000839 ! polypeptide_region created_by: kareneilbeck creation_date: 2010-03-11T02:15:05Z [Term] id: SO:0001647 name: kozak_sequence namespace: sequence def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke] subset: SOFA synonym: "kozak consensus" EXACT [] synonym: "kozak consensus sequence" EXACT [] synonym: "kozak sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia" is_a: SO:0000139 ! ribosome_entry_site created_by: kareneilbeck creation_date: 2010-06-07T03:12:20Z [Term] id: SO:0001654 name: nucleotide_to_protein_binding_site namespace: sequence def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] subset: SOFA synonym: "nucleotide to protein binding site" RELATED [] is_a: SO:0000410 ! protein_binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:26:05Z [Term] id: SO:0001679 name: transcription_regulatory_region namespace: sequence def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke] subset: SOFA synonym: "transcription regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-10-12T03:49:35Z [Term] id: SO:0001683 name: sequence_motif namespace: sequence def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif] subset: SOFA synonym: "sequence motif" RELATED [] xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia" is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-10-14T04:13:22Z [Term] id: SO:0001720 name: epigenetically_modified_region namespace: sequence def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke] subset: SOFA synonym: "epigenetically modified region" RELATED [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-03-27T12:02:29Z [Term] id: SO:0001790 name: paired_end_fragment namespace: sequence def: "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke] subset: SOFA synonym: "paired end fragment" EXACT [] is_a: SO:0000143 ! assembly_component created_by: kareneilbeck creation_date: 2011-04-14T01:48:20Z [Term] id: SO:0005836 name: regulatory_region namespace: sequence def: "A region of sequence that is involved in the control of a biological process." [SO:ke] subset: SOFA synonym: "regulatory region" EXACT [] xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0005855 name: gene_group namespace: sequence def: "A collection of related genes." [SO:ma] subset: SOFA synonym: "gene group" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0100011 name: cleaved_peptide_region namespace: sequence def: "The cleaved_peptide_regon is the a region of peptide sequence that is cleaved during maturation." [EBIBS:GAR] comment: Range. subset: biosapiens subset: SOFA synonym: "cleaved peptide region" EXACT [] is_a: SO:0000839 ! polypeptide_region relationship: part_of SO:0001063 ! immature_peptide_region [Term] id: SO:1000002 name: substitution namespace: sequence def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke] subset: SOFA xref: loinc:LA6690-7 "Substitution" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:1000005 name: complex_substitution namespace: sequence def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: SOFA synonym: "complex substitution" EXACT [] is_a: SO:1000002 ! substitution [Term] id: SO:1000008 name: point_mutation namespace: sequence def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop] subset: SOFA synonym: "point mutation" EXACT [] xref: http://en.wikipedia.org/wiki/Point_mutation "wiki" is_a: SO:0001483 ! SNV [Term] id: SO:1000036 name: inversion namespace: sequence def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html] subset: DBVAR subset: SOFA synonym: "inversion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/] xref: loinc:LA6689-9 "Inversion" is_a: SO:0001059 ! sequence_alteration is_a: SO:0001411 ! biological_region [Term] id: SO:1001284 name: regulon namespace: sequence def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732] subset: SOFA xref: http://en.wikipedia.org/wiki/Regulon "wiki" is_a: SO:0005855 ! gene_group [Term] id: SO:2000061 name: databank_entry namespace: sequence def: "The sequence referred to by an entry in a databank such as Genbank or SwissProt." [SO:ke] subset: SOFA synonym: "accession" RELATED [] synonym: "databank entry" EXACT [] is_a: SO:0000695 ! reagent [Typedef] id: adjacent_to name: adjacent_to namespace: sequence def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap." [PMID:20226267, SO:ke] subset: SOFA [Typedef] id: associated_with name: associated_with namespace: sequence comment: This relationship is vague and up for discussion. [Typedef] id: complete_evidence_for_feature name: complete_evidence_for_feature namespace: sequence def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke] comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. is_transitive: true is_a: evidence_for_feature ! evidence_for_feature [Typedef] id: connects_on name: connects_on namespace: sequence def: "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z." [PMID:20226267] comment: Example: A splice_junction connects_on exon, exon, mature_transcript. created_by: kareneilbeck creation_date: 2010-10-14T01:38:51Z [Typedef] id: contained_by name: contained_by namespace: sequence def: "X contained_by Y iff X starts after start of Y and X ends before end of Y." [PMID:20226267] comment: The inverse is contains. Example: intein contained_by immature_peptide_region. is_transitive: true created_by: kareneilbeck creation_date: 2010-10-14T01:26:16Z [Typedef] id: contains name: contains namespace: sequence def: "The inverse of contained_by." [PMID:20226267] comment: Example: pre_miRNA contains miRNA_loop. is_transitive: true created_by: kareneilbeck creation_date: 2010-10-14T01:32:15Z [Typedef] id: derives_from name: derives_from namespace: sequence subset: SOFA is_transitive: true [Typedef] id: disconnected_from name: disconnected_from namespace: sequence def: "X is disconnected_from Y iff it is not the case that X overlaps Y." [PMID:20226267] created_by: kareneilbeck creation_date: 2010-10-14T01:42:10Z [Typedef] id: edited_from name: edited_from namespace: sequence created_by: kareneilbeck creation_date: 2009-08-19T02:19:45Z [Typedef] id: edited_to name: edited_to namespace: sequence created_by: kareneilbeck creation_date: 2009-08-19T02:19:11Z [Typedef] id: evidence_for_feature name: evidence_for_feature namespace: sequence def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke] comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222. is_transitive: true [Typedef] id: exemplar_of name: exemplar_of namespace: sequence def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke] comment: Tracker id: 2594157. [Typedef] id: finished_by name: finished_by namespace: sequence def: "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." [PMID:20226267] comment: Example CDS finished_by stop_codon. created_by: kareneilbeck creation_date: 2010-10-14T01:45:45Z [Typedef] id: finishes name: finishes namespace: sequence def: "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." [PMID:20226267] comment: Example: stop_codon finishes CDS. created_by: kareneilbeck creation_date: 2010-10-14T02:17:53Z [Typedef] id: gained name: gained namespace: sequence def: "X gained Y if X is a variant_of X' and Y part of X but not X'." [SO:ke] comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence. created_by: kareneilbeck creation_date: 2011-06-28T12:51:10Z [Typedef] id: genome_of name: genome_of namespace: sequence [Typedef] id: guided_by name: guided_by namespace: sequence created_by: kareneilbeck creation_date: 2009-08-19T02:27:04Z [Typedef] id: guides name: guides namespace: sequence created_by: kareneilbeck creation_date: 2009-08-19T02:27:24Z [Typedef] id: has_integral_part name: has_integral_part namespace: sequence def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1] comment: Example: mRNA has_integral_part CDS. is_a: has_part ! has_part created_by: kareneilbeck creation_date: 2009-08-19T12:01:46Z [Typedef] id: has_origin name: has_origin namespace: sequence [Typedef] id: has_part name: has_part namespace: sequence def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1] comment: Example: operon has_part gene. [Typedef] id: has_quality name: has_quality namespace: sequence comment: The relationship between a feature and an attribute. [Typedef] id: homologous_to name: homologous_to namespace: sequence subset: SOFA is_symmetric: true is_a: similar_to ! similar_to [Typedef] id: integral_part_of name: integral_part_of namespace: sequence def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1] comment: Example: exon integral_part_of transcript. is_a: part_of ! part_of created_by: kareneilbeck creation_date: 2009-08-19T12:03:28Z [Typedef] id: is_consecutive_sequence_of name: is_consecutive_sequence_of namespace: sequence def: "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical)." [PMID:20226267] comment: Example: region is consecutive_sequence of base. created_by: kareneilbeck creation_date: 2010-10-14T02:19:48Z [Typedef] id: lost name: lost namespace: sequence def: "X lost Y if X is a variant_of X' and Y part of X' but not X." [SO:ke] comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence. created_by: kareneilbeck creation_date: 2011-06-28T12:53:16Z [Typedef] id: maximally_overlaps name: maximally_overlaps namespace: sequence def: "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." [PMID:20226267] comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR. created_by: kareneilbeck creation_date: 2010-10-14T01:34:48Z [Typedef] id: member_of name: member_of namespace: sequence comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444. subset: SOFA is_transitive: true is_a: part_of ! part_of [Typedef] id: non_functional_homolog_of name: non_functional_homolog_of namespace: sequence def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke] subset: SOFA is_a: homologous_to ! homologous_to [Typedef] id: orthologous_to name: orthologous_to namespace: sequence subset: SOFA is_symmetric: true is_a: homologous_to ! homologous_to [Typedef] id: overlaps name: overlaps namespace: sequence def: "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." [PMID:20226267] comment: Example: coding_exon overlaps CDS. created_by: kareneilbeck creation_date: 2010-10-14T01:33:15Z [Typedef] id: paralogous_to name: paralogous_to namespace: sequence subset: SOFA is_symmetric: true is_a: homologous_to ! homologous_to [Typedef] id: part_of name: part_of namespace: sequence def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: amino_acid part_of polypeptide. subset: SOFA is_transitive: true [Typedef] id: partial_evidence_for_feature name: partial_evidence_for_feature namespace: sequence def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke] is_a: evidence_for_feature ! evidence_for_feature [Typedef] id: position_of name: position_of namespace: sequence [Typedef] id: processed_from name: processed_from namespace: sequence def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1] comment: Example: miRNA processed_from miRNA_primary_transcript. created_by: kareneilbeck creation_date: 2009-08-19T12:14:00Z [Typedef] id: processed_into name: processed_into namespace: sequence def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: miRNA_primary_transcript processed into miRNA. created_by: kareneilbeck creation_date: 2009-08-19T12:15:02Z [Typedef] id: recombined_from name: recombined_from namespace: sequence created_by: kareneilbeck creation_date: 2009-08-19T02:21:03Z [Typedef] id: recombined_to name: recombined_to namespace: sequence created_by: kareneilbeck creation_date: 2009-08-19T02:20:07Z [Typedef] id: sequence_of name: sequence_of namespace: sequence [Typedef] id: similar_to name: similar_to namespace: sequence subset: SOFA is_symmetric: true [Typedef] id: started_by name: started_by namespace: sequence def: "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." [PMID:20226267] comment: Example: CDS started_by start_codon. created_by: kareneilbeck creation_date: 2010-10-14T01:43:55Z [Typedef] id: starts name: starts namespace: sequence def: "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." [PMID:20226267] comment: Example: start_codon starts CDS. created_by: kareneilbeck creation_date: 2010-10-14T01:47:53Z [Typedef] id: trans_spliced_from name: trans_spliced_from namespace: sequence created_by: kareneilbeck creation_date: 2009-08-19T02:22:14Z [Typedef] id: trans_spliced_to name: trans_spliced_to namespace: sequence created_by: kareneilbeck creation_date: 2009-08-19T02:22:00Z [Typedef] id: transcribed_from name: transcribed_from namespace: sequence def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: primary_transcript transcribed_from gene. created_by: kareneilbeck creation_date: 2009-08-19T12:05:39Z [Typedef] id: transcribed_to name: transcribed_to namespace: sequence def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1] comment: Example: gene transcribed_to primary_transcript. created_by: kareneilbeck creation_date: 2009-08-19T12:08:24Z [Typedef] id: translates_to name: translates_to namespace: sequence def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1] comment: Example: codon translates_to amino_acid. created_by: kareneilbeck creation_date: 2009-08-19T12:11:53Z [Typedef] id: translation_of name: translation_of namespace: sequence def: "X is translation of Y if X is translated by ribosome to create Y." [http://precedings.nature.com/documents/3495/version/1] comment: Example: Polypeptide translation_of CDS. created_by: kareneilbeck creation_date: 2009-08-19T12:09:59Z [Typedef] id: variant_of name: variant_of namespace: sequence def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop] comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith. genometools-1.5.1/gtdata/sketch/000077500000000000000000000000001211610345200165715ustar00rootroot00000000000000genometools-1.5.1/gtdata/sketch/default.style000066400000000000000000000251001211610345200212750ustar00rootroot00000000000000--[[ This is the GenomeTools annotation viewer config file. All options must be set inside the 'style' table. All items in this table must be tables, called 'sections'. Typically there is one section per feature type. Color definitions ----------------- Colors are given as RGB triplets {red=,green=,blue=(,alpha=)} where is a decimal value between 0 and 1. The alpha value is optional, as a default 0.5 will be used. Global format settings ---------------------- Global settings, such as margins, spacers, etc. are found at the end of this file, in the "format" section. ]]-- style = { gene = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=0.9, green=0.9, blue=1.0}, style = "box", -- Collapsing options collapse_to_parent = false, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = nil, }, -------------------------------------- mRNA = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=0.4, green=0.5, blue=0.6}, style = "box", -- Collapsing options collapse_to_parent = false, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = nil, }, -------------------------------------- exon = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=0.6, green=0.6, blue=0.9}, style = "box", -- Collapsing options collapse_to_parent = true, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = nil, }, -------------------------------------- CDS = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=0.9, green=0.9, blue=0.2}, style = "box", -- Collapsing options collapse_to_parent = true, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = nil, }, -------------------------------------- TF_binding_site = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=0.8, green=0.6, blue=0.6}, style = "box", -- Collapsing options collapse_to_parent = false, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = nil, }, -------------------------------------- intron = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=1.0, green=1.0, blue=1.0}, style = "caret", -- Collapsing options collapse_to_parent = true, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = nil, }, -------------------------------------- repeat_region = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=0.8, green=0.3, blue=0.3}, style = "box", -- Collapsing options collapse_to_parent = false, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = 0, }, -------------------------------------- LTR_retrotransposon = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=0.8, green=0.5, blue=0.5}, style = "box", -- Collapsing options collapse_to_parent = false, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = nil, }, -------------------------------------- long_terminal_repeat = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=0.9, green=0.9, blue=0.4}, style = "box", -- Collapsing options collapse_to_parent = true, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = nil, }, target_site_duplication = { max_show_width = 0, }, -------------------------------------- protein_match = { -- Color definitions stroke = {red=0.0, green=0.0, blue=0.0, alpha = 1.0}, stroke_marked = {red=1.0, green=0.0, blue=0.0}, fill = {red=0.1, green=0.1, blue=0.5}, style = "box", -- Collapsing options collapse_to_parent = true, split_lines = true, -- Caption options max_capt_show_width= nil, -- Display this track only if the viewport is not wider than this -- number of nucleotides. Set to 0 to disable type track. max_show_width = nil, }, -------------------------------------- five_prime_cis_splice_site = { collapse_to_parent = true, }, -------------------------------------- five_prime_splice_site = { collapse_to_parent = true, }, -------------------------------------- three_prime_cis_splice_site = { collapse_to_parent = true, }, -------------------------------------- three_prime_splice_site = { collapse_to_parent = true, }, -------------------------------------- expressed_sequence_match = { fill = {red=0.2, green=0.2, blue=0.8}, max_show_width = 10000, max_num_lines = 10, max_capt_show_width= 5000, }, -------------------------------------- binding_site = { fill = {red=0.7, green=0.2, blue=0.8}, max_show_width = 10000, max_num_lines = 10, max_capt_show_width= 10000, }, -------------------------------------- SNP = { fill = {red=0.1, green=0.8, blue=0.8}, max_show_width = 10000, max_num_lines = 10, max_capt_show_width= 10000, }, -------------------------------------- deletion = { fill = {red=0.1, green=0.8, blue=0.8}, max_show_width = nil, max_num_lines = 10, max_capt_show_width= 10000, }, -------------------------------------- chromosome = { fill = {red=0.1, green=0.8, blue=0.8}, max_show_width = nil, max_num_lines = 10, }, -------------------------------------- substitution = { fill = {red=1.0, green=0.1, blue=0.05}, max_show_width = 10000, max_num_lines = 10, max_capt_show_width= 1000, }, -------------------------------------- BED_feature = { fill = {red=0.0, green=0.1, blue=0.0}, style = "box", }, -------------------------------------- BED_thick_feature = { fill = {red=0.0, green=0.5, blue=0.0}, style = "box", collapse_to_parent = true, }, -------------------------------------- BED_block = { fill = {red=0.0, green=1.0, blue=0.0}, style = "box", collapse_to_parent = true, }, -------------------------------------- GC_content = { -- this is for a custom track stroke = {red=0.2, green=0.2, blue=1.0, alpha = 0.4}, }, -------------------------------------- -- Defines various format options for drawing. format = { -- Set the following three settings to 'false' to globally disable them. split_lines = true, -- generally enable splitting show_block_captions = true, -- generally show captions show_track_captions = true, -- generally show track captions margins = 30, -- space left and right of diagram, in pixels bar_height = 16, -- height of a feature bar, in pixels bar_vspace = 10, -- space between feature bars, in pixels track_vspace = 15, -- space between tracks, in pixels ruler_font_size = 8, -- size of scale labels ruler_space = 20, -- space between ruler and first track block_caption_font_size = 8, -- size of block captions block_caption_space = 7, -- space between blocks and their captions track_caption_font_size = 8, -- size of track captions track_caption_space = 7, -- space between tracks and their captions arrow_width = 6, -- width of feature arrowheads, in pixels stroke_width = .5, -- width of outlines, in pixels unit = "bp", -- basepair unit, e.g. "bp" ruler_left_text = "5'", -- text left of the ruler axis ruler_right_text = "3'", -- text right of the ruler axis stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels show_grid = true, -- shows light vertical lines for orientation min_len_block = 20 , -- minimum length of a block in which single elements are shown track_title_color = {red=0.7, green=0.7, blue=0.7, alpha = 1.0}, default_stroke_color = {red=0.1, green=0.1, blue=0.1, alpha = 1.0}, background_color = {red=1.0, green=1.0, blue=1.0, alpha = 1.0}, }, } genometools-1.5.1/gtdata/trans/000077500000000000000000000000001211610345200164375ustar00rootroot00000000000000genometools-1.5.1/gtdata/trans/TransAnum000066400000000000000000000002031211610345200202650ustar00rootroot000000000000000 1 2 3 4 5 6 7 8 9 aA bB cC dD eE fF gG hH iI jJ kK lL mM nN oO pP qQ rR sS tT uU vV wW xX yY zZ !@#$%^&*()_-+=\|{}[];:'",<.>/?`~ genometools-1.5.1/gtdata/trans/TransDNA000066400000000000000000000000451211610345200177730ustar00rootroot00000000000000aA cC gG tTuU nsywrkvbdhmNSYWRKVBDHM genometools-1.5.1/gtdata/trans/TransDNAX000066400000000000000000000000471211610345200201250ustar00rootroot00000000000000aA cC gG tTuU nsywrkvbdhmxNSYWRKVBDHMX genometools-1.5.1/gtdata/trans/TransDNAX2000066400000000000000000000000471211610345200202070ustar00rootroot00000000000000A C G TU acgtunsywrkvbdhmxNSYWRKVBDHMX genometools-1.5.1/gtdata/trans/TransDNA_CBNP000066400000000000000000000000531211610345200205740ustar00rootroot00000000000000aA cC gG tT nsywrkvbdhmNSYWRKVBDHMxpofXPOF genometools-1.5.1/gtdata/trans/TransDNAall000066400000000000000000000000711211610345200204630ustar00rootroot00000000000000aA cC gG tT unsywrkvbdhmlifeqpxzojUNSYWRKVBDHMLIFEQPXZJO genometools-1.5.1/gtdata/trans/TransDNAlowermask000066400000000000000000000000471211610345200217220ustar00rootroot00000000000000A C G TU acgtunsywrkvbdhmxNSYWRKVBDHMX genometools-1.5.1/gtdata/trans/TransMass000066400000000000000000000002531211610345200202750ustar00rootroot00000000000000# 24-character amino acid alphabet in upper case # in addition to the usual 20 aminoacids, we have the following # B O X Z G A S P V T C LIX N O B D Q K Z E M H F R Y W * genometools-1.5.1/gtdata/trans/TransProt11000066400000000000000000000002221211610345200204540ustar00rootroot00000000000000# 11-character alphabet as defined by Volker Brendel # * and - are for stop codon LVIFJ i KR + ED - AG s ST o NQ n YW a P p H h M m C c XUBZO*- x genometools-1.5.1/gtdata/trans/TransProt12000066400000000000000000000003251211610345200204610ustar00rootroot00000000000000# 12-character alphabet defined by Volker Brendel # * is for a stop codon. It is an extra character but not a wildcard. LVIFlvif i KRkr + EDed - AGag s STst o NQnq n YWyw a Pp p Hh h Mm m Cc c *- * XUBZJOxubzjo x genometools-1.5.1/gtdata/trans/TransProt2000066400000000000000000000001531211610345200203770ustar00rootroot00000000000000# 2-character hydrophobic alphabet # O (hydrophobic), I (hydrophilic) AFILMPVWJ I CDEGHKNQRSTY O XUBZO*- x genometools-1.5.1/gtdata/trans/TransProt20000066400000000000000000000001421211610345200204550ustar00rootroot00000000000000# 20-character amino acid alphabet in upper case L V I F K R E D A G S T N Q Y W P H M C XUBZJO*- genometools-1.5.1/gtdata/trans/TransProt21000066400000000000000000000003221211610345200204560ustar00rootroot00000000000000# 21-character amino acid alphabet in capital and lower case # * denotes refers to stop codon and is extra character but not wildcard Ll Vv Ii Ff Kk Rr Ee Dd Aa Gg Ss Tt Nn Qq Yy Ww Pp Hh Mm Cc *- XUBZJOxubzjo genometools-1.5.1/gtdata/trans/TransProt3000066400000000000000000000001671211610345200204050ustar00rootroot00000000000000# 3-character structural alphabet # A (ambivalent), E (external), I (internal) ACGPSTWY A RNDQEHK E ILMFVJ I XUBZO*- X genometools-1.5.1/gtdata/trans/TransProt3B000066400000000000000000000001041211610345200204760ustar00rootroot00000000000000# 3-character charge alphabet DE A HKR C ACFGILMNPQSTVWYJ N XUBZO*- genometools-1.5.1/gtdata/trans/TransProt4000066400000000000000000000002011211610345200203730ustar00rootroot00000000000000# 4-character functional alphabet # A (acidic), C (basic), H (hydrophobic), P (polar) DE A HKR C AFILMPVWJ H CGNQSTY P XUBZO*- x genometools-1.5.1/gtdata/trans/TransProt4B000066400000000000000000000001121211610345200204760ustar00rootroot00000000000000# 4-character Stanfel alphabet ACGILMPSTVJ A DENQ C FWY D HKR E XUBZO*- X genometools-1.5.1/gtdata/trans/TransProt6000066400000000000000000000001201211610345200203750ustar00rootroot00000000000000# 6-character Dayhoff alphabet C A AGPST C DENQ D HKR E ILMVJ F FWY G XUBZO*- X genometools-1.5.1/gtdata/trans/TransProt7000066400000000000000000000001221211610345200204000ustar00rootroot00000000000000# 7-character Sneath alphabet ILVJ A AGP C MNQ D CST E DE F KR G FHWY H XUBZO*- X genometools-1.5.1/gtdata/trans/TransProt8000066400000000000000000000002761211610345200204130ustar00rootroot00000000000000# 8-character chemical alphabet # A (acidic), L (aliphatic), M (amide), R (aromatic) # C (basic), H (hydroxyl), I (imino), S (sulphur) DE A AGILVJ L NQ M FWY R RHK C ST H P I CM S XUBZO*- X genometools-1.5.1/gtdata/trans/TransProtall000066400000000000000000000003471211610345200210130ustar00rootroot00000000000000# simple mapping for protein sequences with all alphabet characters # * is for a stop codon. It is an extra character but not a wildcard. LVIFlvif i KRkr + EDed - AGag s STst o NQnq n YWyw a Pp p Hh h Mm m Cc c *- * XUBZJOxubzjo x genometools-1.5.1/gtdata/trans/Transab000066400000000000000000000000061211610345200177500ustar00rootroot00000000000000a b * genometools-1.5.1/gtpython/000077500000000000000000000000001211610345200157205ustar00rootroot00000000000000genometools-1.5.1/gtpython/README000066400000000000000000000017031211610345200166010ustar00rootroot00000000000000This directory contains the GenomeTools Python bindings. To use them, you have to add the following line to your Python script: from gt import * It is also possible to import single classes from the 'core', 'extended' and 'annotationsketch' sub-packages, e.g. from gt.extended.feature_node import FeatureNode Make sure that this directory is added to the PYTHONPATH environment variable. Alternatively, run python setup.py install to install the 'gt' package on this system (must be root). Furthermore, you have to make sure that the GenomeTools shared libraries can be be found by the dlopen(3) system call. For example, by adding the lib/ subdirectory of GenomeTools to your LD_LIBRARY_PATH environment variable. Alternatively, use "make install" in the genometools directory for a system-wide installation of libgenometools. For examples on how to use these bindings, please refer to the scripts in the subdirectory testdata/gtpython/ of GenomeTools. genometools-1.5.1/gtpython/gt/000077500000000000000000000000001211610345200163325ustar00rootroot00000000000000genometools-1.5.1/gtpython/gt/__init__.py000066400000000000000000000024141211610345200204440ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # import sys try: import ctypes except ImportError: sys.stderr.write("The ctypes package could not be found. ") sys.stderr.write("Please make sure it can be imported by Python.") sys.exit(1) try: from annotationsketch import * except AttributeError: # fail gracefully when AnnotationSketch symbols are not present pass from core import * from extended import * genometools-1.5.1/gtpython/gt/annotationsketch/000077500000000000000000000000001211610345200217065ustar00rootroot00000000000000genometools-1.5.1/gtpython/gt/annotationsketch/__init__.py000066400000000000000000000031271211610345200240220ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from block import * from canvas import * from color import * from custom_track import * from diagram import * from feature_index import * from feature_stream import * from graphics import * from image_info import * from layout import * from rec_map import * from style import * try: Block.register(gtlib) CanvasCairoFileBase.register(gtlib) CustomTrack.register(gtlib) Diagram.register(gtlib) #DiagramFromArray.register(gtlib) FeatureIndex.register(gtlib) Graphics.register(gtlib) ImageInfo.register(gtlib) Layout.register(gtlib) RecMap.register(gtlib) Style.register(gtlib) except AttributeError: # fail gracefully when AnnotationSketch symbols are not present pass genometools-1.5.1/gtpython/gt/annotationsketch/block.py000066400000000000000000000077511211610345200233640ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.error import gterror from gt.core.gtrange import Range from gt.core.gtstr import Str from gt.extended.strand import strandchars from gt.extended.feature_node import FeatureNode class Block(object): def __init__(self, ptr): if ptr == 0 or ptr == None: gterror("Block pointer cannot be NULL (was: " + str(ptr) + ")") self.block = gtlib.gt_block_ref(ptr) self._as_parameter_ = self.block def __del__(self): try: gtlib.gt_block_delete(self.block) except AttributeError: pass def get_range(self): r = gtlib.gt_block_get_range(self.block) return (r.start, r.end) def get_type(self): return gtlib.gt_block_get_type(self.block) def has_only_one_fullsize_element(self): return gtlib.gt_block_has_only_one_fullsize_element(self.block) == \ 1 def merge(self, block2): gtlib.gt_block_merge(self.block, block2) def clone(self): return Block(gtlib.gt_block_clone(self.block)) def get_caption(self): s = Str(gtlib.gt_block_get_caption(self.block)) return str(s) def set_strand(self, strand): if not strand in strandchars: gterror("Invalid strand '%s' -- must be one of %s" % (strand, strandchars)) gtlib.gt_block_set_strand(self.block, strandchars.index(strand)) def get_strand(self): return strandchars[gtlib.gt_block_get_strand(self.block)] def get_top_level_feature(self): f = gtlib.gt_block_get_top_level_feature(self.block) if f != 0: return FeatureNode.create_from_ptr(f, True) else: return None def get_size(self): return gtlib.gt_block_get_size(self.block) def from_param(cls, obj): if not isinstance(obj, Block): raise TypeError, "argument must be a Block" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_char_p, c_void_p, c_int gtlib.gt_block_get_range.restype = Range gtlib.gt_block_get_range.argtypes = [c_void_p] gtlib.gt_block_get_type.restype = c_char_p gtlib.gt_block_get_type.argtypes = [c_void_p] gtlib.gt_block_has_only_one_fullsize_element.argtypes = [c_void_p] gtlib.gt_block_merge.argtypes = [c_void_p, Block] gtlib.gt_block_clone.restype = c_void_p gtlib.gt_block_clone.argtypes = [c_void_p] gtlib.gt_block_set_caption_visibility.argtypes = [c_void_p, c_int] gtlib.gt_block_caption_is_visible.argtypes = [c_void_p] gtlib.gt_block_get_caption.restype = c_void_p gtlib.gt_block_get_caption.argtypes = [c_void_p] gtlib.gt_block_set_strand.argtypes = [c_void_p, c_int] gtlib.gt_block_get_strand.restype = c_int gtlib.gt_block_get_strand.argtypes = [c_void_p] gtlib.gt_block_get_top_level_feature.restype = c_void_p gtlib.gt_block_get_top_level_feature.argtypes = [c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/annotationsketch/canvas.py000066400000000000000000000111471211610345200235370ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.annotationsketch.style import Style from gt.annotationsketch.image_info import ImageInfo from gt.core.error import Error, gterror from gt.core.gtstr import Str GRAPHICS_PDF = 0 GRAPHICS_PNG = 1 GRAPHICS_PS = 2 GRAPHICS_SVG = 3 class Canvas: def __init__(self, *args): raise NotImplementedError, \ 'Please call the constructor of a Canvas implementation.' def __del__(self): try: gtlib.gt_canvas_delete(self.canvas) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, Canvas): raise TypeError, "argument must be a Canvas" return obj._as_parameter_ from_param = classmethod(from_param) class CanvasCairoFileBase(Canvas): def from_param(cls, obj): if not isinstance(obj, CanvasCairoFile): raise TypeError, "argument must be a CanvasCairoFile" return obj._as_parameter_ from_param = classmethod(from_param) def to_file(self, filename): err = Error() rval = gtlib.gt_canvas_cairo_file_to_file(self.canvas, filename, err) if rval != 0: gterror(err) def to_stream(self): from ctypes import string_at str = Str(None) gtlib.gt_canvas_cairo_file_to_stream(self.canvas, str) return string_at(str.get_mem(), str.length()) def register(cls, gtlib): from ctypes import c_char_p, c_void_p, c_ulong, c_int gtlib.gt_canvas_cairo_file_to_file.restype = c_int gtlib.gt_canvas_cairo_file_to_file.argtypes = [c_void_p, c_char_p, Error] gtlib.gt_canvas_cairo_file_to_stream.restype = c_char_p gtlib.gt_canvas_cairo_file_to_stream.argtypes = [c_void_p, Str] gtlib.gt_canvas_cairo_file_new.restype = c_void_p gtlib.gt_canvas_cairo_file_new.argtypes = [Style, c_int, c_ulong, c_ulong, ImageInfo] register = classmethod(register) class CanvasCairoFile(CanvasCairoFileBase): def __init__(self, style, width, height, ii=None): err = Error() canvas = gtlib.gt_canvas_cairo_file_new(style, GRAPHICS_PNG, width, height, ii, err) if canvas == None: gterror(err) self.canvas = canvas self._as_parameter_ = self.canvas class CanvasCairoFilePNG(CanvasCairoFileBase): def __init__(self, style, width, height, ii=None): err = Error() canvas = gtlib.gt_canvas_cairo_file_new(style, GRAPHICS_PNG, width, height, ii, err) if canvas == None: gterror(err) self.canvas = canvas self._as_parameter_ = self.canvas class CanvasCairoFilePDF(CanvasCairoFileBase): def __init__(self, style, width, height, ii=None): err = Error() canvas = gtlib.gt_canvas_cairo_file_new(style, GRAPHICS_PDF, width, height, ii, err) if canvas == None: gterror(err) self.canvas = canvas self._as_parameter_ = self.canvas class CanvasCairoFilePS(CanvasCairoFileBase): def __init__(self, style, width, height, ii=None): err = Error() canvas = gtlib.gt_canvas_cairo_file_new(style, GRAPHICS_PS, width, height, ii, err) if canvas == None: gterror(err) self.canvas = canvas self._as_parameter_ = self.canvas class CanvasCairoFileSVG(CanvasCairoFileBase): def __init__(self, style, width, height, ii=None): err = Error() canvas = gtlib.gt_canvas_cairo_file_new(style, GRAPHICS_SVG, width, height, ii, err) if canvas == None: gterror(err) self.canvas = canvas self._as_parameter_ = self.canvas genometools-1.5.1/gtpython/gt/annotationsketch/color.py000066400000000000000000000021301211610345200233720ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from ctypes import Structure, c_double class Color(Structure): _fields_ = [("red", c_double), ("green", c_double), ("blue", c_double), ("alpha", c_double)] genometools-1.5.1/gtpython/gt/annotationsketch/custom_track.py000066400000000000000000000060631211610345200247630ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008-2009 Sascha Steinbiss # Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from ctypes import CFUNCTYPE, POINTER, c_char_p, c_void_p, c_int, c_ulong from gt.dlload import gtlib from gt.annotationsketch.color import Color from gt.annotationsketch.style import Style from gt.annotationsketch.graphics import Graphics from gt.core.error import Error, gterror from gt.core.gtrange import Range from gt.core.gtstr import Str RenderFunc = CFUNCTYPE(c_int, c_void_p, c_ulong, POINTER(Range), c_void_p, c_void_p) TitleFunc = CFUNCTYPE(c_int, c_void_p, c_void_p) HeightFunc = CFUNCTYPE(c_ulong, c_void_p) FreeFunc = CFUNCTYPE(c_void_p, c_void_p) class CustomTrack(object): def __init__(self): # create callbacks to C script wrapper def get_title_w(ptr, str): s = Str(str) title = self.get_title() s.append_cstr(title) return 0 self.get_title_cb = TitleFunc(get_title_w) def get_height_w(ptr): return self.get_height() self.get_height_cb = HeightFunc(get_height_w) def render_w(graphics, ypos, rng, sty, err): g = Graphics(graphics) s = Style(sty) e = Error(err) return self.render(g, ypos, rng.contents, s, e) self.render_cb = RenderFunc(render_w) def free_w(ptr): self.free() self.free_cb = FreeFunc(free_w) self.ctt = gtlib.gt_custom_track_script_wrapper_new(self.render_cb, self.get_height_cb, self.get_title_cb, self.free_cb) self._as_parameter_ = self.ctt def __del__(self): try: gtlib.gt_custom_track_delete(self.ctt) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, CustomTrack): raise TypeError, "argument must be a CustomTrack" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_char_p, c_void_p, c_int, POINTER gtlib.gt_custom_track_script_wrapper_new.restype = c_void_p gtlib.gt_custom_track_script_wrapper_new.argtypes = [RenderFunc, HeightFunc, TitleFunc, FreeFunc] register = classmethod(register) genometools-1.5.1/gtpython/gt/annotationsketch/custom_track_example.py000066400000000000000000000031251211610345200264720ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.annotationsketch.custom_track import CustomTrack from gt.annotationsketch.color import Color from gt.core.gtrange import Range class CustomTrackExample(CustomTrack): def __init__(self): super(CustomTrackExample, self).__init__() def get_height(self): return 50 def get_title(self): return "Sample track drawn by a Python script" def render(self, graphics, ypos, rng, style, error): from random import random data = [] for i in range(0, 120): data.append(random()) graphics.draw_curve_data(graphics.get_xmargins(), ypos, Color(0, 0, 1, .6), data, 120, Range(0, 1), 40) return 0 genometools-1.5.1/gtpython/gt/annotationsketch/diagram.py000066400000000000000000000100701211610345200236620ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from ctypes import CFUNCTYPE, c_char_p, c_void_p, c_int from gt.dlload import gtlib from gt.annotationsketch.block import Block from gt.annotationsketch.canvas import Canvas from gt.annotationsketch.custom_track import CustomTrack from gt.annotationsketch.style import Style from gt.core.array import Array from gt.core.error import Error, gterror from gt.core.gtrange import Range from gt.core.gtstr import Str from gt.extended.feature_index import FeatureIndex from gt.extended.feature_node import FeatureNode TrackSelectorFunc = CFUNCTYPE(c_void_p, c_void_p, c_void_p, c_void_p) class Diagram: def from_array(arr, rng, style): from ctypes import byref, sizeof if rng.start > rng.end: gterror("range.start > range.end") gtarr = Array.create(sizeof(c_void_p), False) for i in arr: if not isinstance(i, FeatureNode): gterror("Diagram array must only contain FeatureNodes!") gtarr.add(i) diagram = gtlib.gt_diagram_new_from_array(gtarr, byref(rng), style) return Diagram(diagram) from_array = staticmethod(from_array) def from_index(feature_index, seqid, rng, style): from ctypes import byref err = Error() if rng.start > rng.end: gterror("range.start > range.end") diagram = gtlib.gt_diagram_new(feature_index, seqid, byref(rng), style, err) if err.is_set(): gterror(err) return Diagram(diagram) from_index = staticmethod(from_index) def __init__(self, ptr): self.diagram = ptr self._as_parameter_ = self.diagram def __del__(self): try: gtlib.gt_diagram_delete(self.diagram) except AttributeError: pass def set_track_selector_func(self, func): def trackselector(block_ptr, string_ptr, data_ptr): b = Block(block_ptr) string = Str(string_ptr) ret = func(b) if not ret: gterror("Track selector callback function must return a string!") string.append_cstr(ret) self.tsf_cb = TrackSelectorFunc(trackselector) self.tsf = trackselector gtlib.gt_diagram_set_track_selector_func(self.diagram, self.tsf_cb) def add_custom_track(self, ct): gtlib.gt_diagram_add_custom_track(self.diagram, ct) def from_param(cls, obj): if not isinstance(obj, Diagram): raise TypeError, "argument must be a Diagram" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_char_p, c_void_p, POINTER gtlib.gt_diagram_new.restype = c_void_p gtlib.gt_diagram_new.argtypes = [FeatureIndex, c_char_p, POINTER(Range), Style, Error] gtlib.gt_diagram_set_track_selector_func.argtypes = [c_void_p, TrackSelectorFunc] gtlib.gt_diagram_add_custom_track.argtypes = [c_void_p, CustomTrack] gtlib.gt_diagram_new_from_array.restype = c_void_p gtlib.gt_diagram_new_from_array.argtypes = [Array, POINTER(Range), Style] register = classmethod(register) genometools-1.5.1/gtpython/gt/annotationsketch/feature_index.py000066400000000000000000000017621211610345200251100ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2013 Sascha Steinbiss # Copyright (c) 2013 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # import warnings warnings.warn("deprecated", DeprecationWarning) from gt.extended.feature_index import * genometools-1.5.1/gtpython/gt/annotationsketch/feature_stream.py000066400000000000000000000017631211610345200252750ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2013 Sascha Steinbiss # Copyright (c) 2013 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # import warnings warnings.warn("deprecated", DeprecationWarning) from gt.extended.feature_stream import * genometools-1.5.1/gtpython/gt/annotationsketch/graphics.py000066400000000000000000000267641211610345200240770ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008-2010 Sascha Steinbiss # Copyright (c) 2008-2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.annotationsketch.color import Color from gt.core.array import Array from gt.core.error import Error, gterror from gt.core.gtrange import Range from gt.core.gtstr import Str GRAPHICS_PDF = 0 GRAPHICS_PNG = 1 GRAPHICS_PS = 2 GRAPHICS_SVG = 3 ARROW_LEFT = 0 ARROW_RIGHT = 1 ARROW_BOTH = 2 ARROW_NONE = 3 class Graphics: def __init__(self, p): self.g = p self.own = False self._as_parameter_ = self.g def __del__(self): if self.own: try: gtlib.gt_graphics_delete(self.g) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, Graphics): raise TypeError, "argument must be a Graphics" return obj._as_parameter_ from_param = classmethod(from_param) def draw_text(self, x, y, text): gtlib.gt_graphics_draw_text(self.g, x, y, text) def draw_text_centered(self, x, y, text): gtlib.gt_graphics_draw_text_centered(self.g, x, y, text) def draw_text_right(self, x, y, text): gtlib.gt_graphics_draw_text_right(self.g, x, y, text) def draw_colored_text(self, x, y, color, text): gtlib.gt_graphics_draw_colored_text(self.g, x, y, color, text) def get_image_height(self): return gtlib.gt_graphics_get_image_height(self.g) def get_image_width(self): return gtlib.gt_graphics_get_image_width(self.g) def get_text_height(self): return gtlib.gt_graphics_get_text_height(self.g) def get_text_width(self, txt): return gtlib.gt_graphics_get_text_width(self.g, txt) def set_margins(self, xmargs, ymargs): gtlib.gt_graphics_set_margins(self.g, xmargs, ymargs) def get_xmargins(self): return gtlib.gt_graphics_get_xmargins(self.g) def get_ymargins(self): return gtlib.gt_graphics_get_ymargins(self.g) def draw_line(self, x, y, xto, yto, color, stroke_width): gtlib.gt_graphics_draw_line(self.g, x, y, xto, yto, color, stroke_width) def draw_horizontal_line(self, x, y, color, width, stroke_width): gtlib.gt_graphics_draw_horizontal_line(self.g, x, y, color, width, stroke_width) def draw_vertical_line(self, x, y, color, length, stroke_width): gtlib.gt_graphics_draw_vertical_line(self.g, x, y, color, length, stroke_width) def draw_box( self, x, y, width, height, fillcolor, astatus, awidth, swidth, scolor, dashed, ): if dashed: d_int = 1 else: d_int = 0 gtlib.gt_graphics_draw_box( self.g, x, y, width, height, fillcolor, astatus, awidth, swidth, scolor, d_int, ) def draw_dashes( self, x, y, width, height, astatus, awidth, swidth, scolor, ): gtlib.gt_graphics_draw_dashes( self.g, x, y, width, height, astatus, awidth, swidth, scolor, ) def draw_caret( self, x, y, width, height, astatus, awidth, swidth, scolor, ): gtlib.gt_graphics_draw_caret( self.g, x, y, width, height, astatus, awidth, swidth, scolor, ) def draw_rectangle( self, x, y, filled, fcolor, stroked, scolor, swidth, width, height, ): if filled: f_int = 1 else: f_int = 0 if stroked: s_int = 1 else: s_int = 0 gtlib.gt_graphics_draw_rectangle( self.g, x, y, f_int, fcolor, s_int, scolor, swidth, width, height, ) def draw_arrowhead(self, x, y, color, status): gtlib.gt_graphics_draw_arrowhead(self.g, x, y, color, status) def draw_curve_data(self, x, y, color, data, ndata, valrange, height): from ctypes import c_double NDblArr = c_double * ndata cdata = NDblArr() for i in range(0, ndata): cdata[i] = data[i] gtlib.gt_graphics_draw_curve_data(self.g, x, y, color, cdata, ndata, valrange, height) def to_file(self, filename): err = Error() if gtlib.gt_graphics_save_to_file(self.g, filename, err) < 0: gterror(err) def to_stream(self): from ctypes import string_at s = Str(None) gtlib.gt_graphics_save_to_stream(self.g, s) return string_at(s.get_mem(), s.length()) def get_text_height(self): return gtlib.gt_graphics_get_text_height(self.g) def get_text_width(self, text): return gtlib.gt_graphics_get_text_width(self.g, text) def register(cls, gtlib): from ctypes import c_char_p, c_void_p, c_int, POINTER, c_double, \ c_ulong gtlib.gt_graphics_draw_text.argtypes = [c_void_p, c_double, c_double, c_char_p] gtlib.gt_graphics_draw_text_right.argtypes = [c_void_p, c_double, c_double, c_char_p] gtlib.gt_graphics_draw_text_centered.argtypes = [c_void_p, c_double, c_double, c_char_p] gtlib.gt_graphics_draw_colored_text.argtypes = [c_void_p, c_double, c_double, Color, c_char_p] gtlib.gt_graphics_get_image_height.restype = c_double gtlib.gt_graphics_get_image_height.argtypes = [c_void_p] gtlib.gt_graphics_get_image_width.restype = c_double gtlib.gt_graphics_get_image_width.argtypes = [c_void_p] gtlib.gt_graphics_get_text_height.restype = c_double gtlib.gt_graphics_get_text_height.argtypes = [c_void_p] gtlib.gt_graphics_get_text_width.restype = c_double gtlib.gt_graphics_get_text_width.argtypes = [c_void_p, c_char_p] gtlib.gt_graphics_set_margins.argtypes = [c_void_p, c_double, c_double] gtlib.gt_graphics_get_xmargins.restype = c_double gtlib.gt_graphics_get_xmargins.argtypes = [c_void_p] gtlib.gt_graphics_get_ymargins.restype = c_double gtlib.gt_graphics_get_ymargins.argtypes = [c_void_p] gtlib.gt_graphics_draw_vertical_line.argtypes = [c_void_p, c_double, c_double, Color, c_double, c_double] gtlib.gt_graphics_draw_line.argtypes = [c_void_p, c_double, c_double, c_double, c_double, Color, c_double] gtlib.gt_graphics_draw_horizontal_line.argtypes = [c_void_p, c_double, c_double, Color, c_double, c_double] gtlib.gt_graphics_draw_box.argtypes = [ c_void_p, c_double, c_double, c_double, c_double, Color, c_int, c_double, c_double, Color, c_int, ] gtlib.gt_graphics_draw_dashes.argtypes = [ c_void_p, c_double, c_double, c_double, c_double, c_int, c_double, c_double, Color, ] gtlib.gt_graphics_draw_caret.argtypes = [ c_void_p, c_double, c_double, c_double, c_double, c_int, c_double, c_double, Color, ] gtlib.gt_graphics_draw_rectangle.argtypes = [ c_void_p, c_double, c_double, c_int, Color, c_int, Color, c_double, c_double, c_double, ] gtlib.gt_graphics_draw_arrowhead.argtypes = [c_void_p, c_double, c_double, Color, c_int] gtlib.gt_graphics_draw_curve_data.argtypes = [c_void_p, c_double, c_double, Color, c_void_p, c_ulong, Range, c_ulong] gtlib.gt_graphics_save_to_file.restype = c_int gtlib.gt_graphics_save_to_file.argtypes = [c_void_p, c_char_p, Error] gtlib.gt_graphics_save_to_stream.argtypes = [c_void_p, Str] register = classmethod(register) class GraphicsCairo(Graphics): def __init__(self, p): self.g = p self.own = False self._as_parameter_ = self.g def from_param(cls, obj): if not isinstance(obj, GraphicsCairo): raise TypeError, "argument must be a GraphicsCairo" return obj._as_parameter_ from_param = classmethod(from_param) class GraphicsCairoPNG(GraphicsCairo): def __init__(self, width, height): self.g = gtlib.gt_graphics_cairo_new(GRAPHICS_PNG, width, height) self.own = True self._as_parameter_ = self.g def from_param(cls, obj): if not isinstance(obj, GraphicsCairoPNG): raise TypeError, "argument must be a GraphicsCairoPNG" return obj._as_parameter_ from_param = classmethod(from_param) class GraphicsCairoPDF(GraphicsCairo): def __init__(self, width, height): self.g = gtlib.gt_graphics_cairo_new(GRAPHICS_PDF, width, height) self.own = True self._as_parameter_ = self.g def from_param(cls, obj): if not isinstance(obj, GraphicsCairoPDF): raise TypeError, "argument must be a GraphicsCairoPDF" return obj._as_parameter_ from_param = classmethod(from_param) class GraphicsCairoPS(GraphicsCairo): def __init__(self, width, height): self.g = gtlib.gt_graphics_cairo_new(GRAPHICS_PS, width, height) self.own = True self._as_parameter_ = self.g def from_param(cls, obj): if not isinstance(obj, GraphicsCairoPS): raise TypeError, "argument must be a GraphicsCairoPS" return obj._as_parameter_ from_param = classmethod(from_param) class GraphicsCairoSVG(GraphicsCairo): def __init__(self, width, height): self.g = gtlib.gt_graphics_cairo_new(GRAPHICS_SVG, width, height) self.own = True self._as_parameter_ = self.g def from_param(cls, obj): if not isinstance(obj, GraphicsCairoSVG): raise TypeError, "argument must be a GraphicsCairoSVG" return obj._as_parameter_ from_param = classmethod(from_param) genometools-1.5.1/gtpython/gt/annotationsketch/image_info.py000066400000000000000000000063601211610345200243620ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.annotationsketch.rec_map import RecMap import math class ImageInfo: def __init__(self): self.ii = gtlib.gt_image_info_new() self._as_parameter_ = self.ii self.hotspots = None def __del__(self): try: gtlib.gt_image_info_delete(self.ii) except AttributeError: pass def from_param(cls, obj): if not (isinstance(obj, ImageInfo) or obj == None): raise TypeError, "argument must be an ImageInfo" if obj == None: return None return obj._as_parameter_ from_param = classmethod(from_param) def get_height(self): return gtlib.gt_image_info_get_height(self.ii) def num_of_rec_maps(self): return gtlib.gt_image_info_num_of_rec_maps(self.ii) def compare_hotspots(cls, hs1, hs2): if hs1[2] - hs1[0] + 1 > hs2[2] - hs2[0] + 1: return 1 elif hs1[2] - hs1[0] + 1 == hs2[2] - hs2[0] + 1: if hs1[3] > hs2[3]: return 1 elif hs1[3] == hs2[3]: return 0 else: return -1 else: return -1 compare_hotspots = classmethod(compare_hotspots) def each_hotspot(self): if not self.hotspots: self.hotspots = [] for i in range(self.num_of_rec_maps()): rm = RecMap(gtlib.gt_image_info_get_rec_map(self.ii, i)) self.hotspots.append([math.floor(rm.get_northwest_x()), math.floor(rm.get_northwest_y()), math.floor(rm.get_southeast_x()), math.floor(rm.get_southeast_y()), rm.get_genome_feature()]) self.hotspots.sort(ImageInfo.compare_hotspots) for hs in self.hotspots: yield (hs[0], hs[1], hs[2], hs[3], hs[4]) def register(cls, gtlib): from ctypes import c_void_p, c_ulong, c_uint gtlib.gt_image_info_get_rec_map.restype = c_void_p gtlib.gt_image_info_get_rec_map.argtypes = [c_void_p, c_ulong] gtlib.gt_image_info_num_of_rec_maps.restype = c_ulong gtlib.gt_image_info_num_of_rec_maps.argtypes = [c_void_p] gtlib.gt_image_info_get_height.restype = c_uint gtlib.gt_image_info_get_height.argtypes = [c_void_p] gtlib.gt_image_info_new.restype = c_void_p register = classmethod(register) genometools-1.5.1/gtpython/gt/annotationsketch/layout.py000066400000000000000000000065241211610345200236040ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008-2009 Sascha Steinbiss # Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.annotationsketch.canvas import Canvas from gt.annotationsketch.diagram import Diagram from gt.annotationsketch.style import Style from gt.core.error import Error, gterror from ctypes import c_ulong, c_void_p, c_int, c_char_p, CFUNCTYPE, byref, \ POINTER, c_double TrackOrderingFunc = CFUNCTYPE(c_int, c_char_p, c_char_p, c_void_p) class Layout: def __init__(self, diagram, width, style): err = Error() self.layout = gtlib.gt_layout_new(diagram, width, style, err) if err.is_set(): gterror(err) self._as_parameter_ = self.layout def __del__(self): try: gtlib.gt_layout_delete(self.layout) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, Layout): raise TypeError, "argument must be a Layout" return obj._as_parameter_ from_param = classmethod(from_param) def sketch(self, canvas): err = Error() had_err = gtlib.gt_layout_sketch(self.layout, canvas, err) if err.is_set(): gterror(err) def get_height(self): err = Error() height = c_ulong() gtlib.gt_layout_get_height(self.layout, byref(height), err) if err.is_set(): gterror(err) return height.value def set_track_ordering_func(self, func): def trackorderer(s1, s2, data_ptr): ret = func(s1, s2) try: if ret is None: raise ValueError else: ret = int(ret) except ValueError: gterror("Track ordering function must return a number!") return ret self.tof_cb = TrackOrderingFunc(trackorderer) self.tof = trackorderer gtlib.gt_layout_set_track_ordering_func(self.layout, self.tof_cb) def register(cls, gtlib): gtlib.gt_layout_new.restype = c_void_p gtlib.gt_layout_new.argtypes = [Diagram, c_ulong, Style] gtlib.gt_layout_sketch.restype = c_int gtlib.gt_layout_sketch.argtypes = [c_void_p, Canvas, Error] gtlib.gt_layout_set_track_ordering_func.argtypes = [c_void_p, TrackOrderingFunc] gtlib.gt_layout_get_height.restype = c_int gtlib.gt_layout_get_height.argtypes = [c_void_p, POINTER(c_ulong), Error] register = classmethod(register) genometools-1.5.1/gtpython/gt/annotationsketch/rec_map.py000066400000000000000000000053701211610345200236730ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.feature_node import FeatureNode class RecMap: def __init__(self, rm): self.rm = rm self._as_parameter_ = self.rm def from_param(cls, obj): if not isinstance(obj, RecMap): raise TypeError, "argument must be a RecMap" return obj._as_parameter_ from_param = classmethod(from_param) def get_northwest_x(self): return gtlib.gt_rec_map_get_northwest_x(self.rm) def get_northwest_y(self): return gtlib.gt_rec_map_get_northwest_y(self.rm) def get_southeast_x(self): return gtlib.gt_rec_map_get_southeast_x(self.rm) def get_southeast_y(self): return gtlib.gt_rec_map_get_southeast_y(self.rm) def get_genome_feature(self): #refcount only this FeatureNode! return FeatureNode.create_from_ptr(gtlib.gt_rec_map_get_genome_feature(self.rm), True) def has_omitted_children(self): return gtlib.gt_rec_map_has_omitted_children(self.rm) == 1 def register(cls, gtlib): from ctypes import c_int, c_void_p, c_double gtlib.gt_rec_map_get_northwest_x.restype = c_double gtlib.gt_rec_map_get_northwest_x.argtypes = [c_void_p] gtlib.gt_rec_map_get_northwest_y.restype = c_double gtlib.gt_rec_map_get_northwest_y.argtypes = [c_void_p] gtlib.gt_rec_map_get_southeast_x.restype = c_double gtlib.gt_rec_map_get_southeast_x.argtypes = [c_void_p] gtlib.gt_rec_map_get_southeast_y.restype = c_double gtlib.gt_rec_map_get_southeast_y.argtypes = [c_void_p] gtlib.gt_rec_map_get_genome_feature.restype = c_void_p gtlib.gt_rec_map_get_genome_feature.argtypes = [c_void_p] gtlib.gt_rec_map_has_omitted_children.restype = c_int gtlib.gt_rec_map_has_omitted_children.argtypes = [c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/annotationsketch/style.py000066400000000000000000000141711211610345200234240ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008-2010 Sascha Steinbiss # Copyright (c) 2008-2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib, CollectFunc from gt.annotationsketch.color import Color from gt.core.error import Error, gterror from gt.core.gtstr import Str from gt.core.str_array import StrArray from gt.extended.genome_node import GenomeNode STYLE_OK = 0 STYLE_NOT_SET = 1 STYLE_ERROR = 2 class Style: def __init__(self, ptr=None): if ptr: self.style = ptr self.own = False else: e = Error() self.style = gtlib.gt_style_new(e) if self.style == 0 or self.style == None: gterror(e) self.own = True self._as_parameter_ = self.style def __del__(self): if self.own: try: gtlib.gt_style_delete(self.style) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, Style): raise TypeError, "argument must be a Style" return obj._as_parameter_ from_param = classmethod(from_param) def load_file(self, filename): err = Error() rval = gtlib.gt_style_load_file(self.style, filename, err) if rval != 0: gterror(err) def load_str(self, string): err = Error() strg = Str(str(string.encode("utf-8"))) rval = gtlib.gt_style_load_str(self.style, strg, err) if rval != 0: gterror(err) def to_str(self): err = Error() string = Str() if gtlib.gt_style_to_str(self.style, string, err) == 0: return str(string) else: gterror(err) def clone(self): sty = Style() str = self.to_str() sty.load_str(str) return sty def get_color(self, section, key, gn=None): from ctypes import byref color = Color() err = Error() rval = gtlib.gt_style_get_color(self.style, section, key, byref(color),\ gn, err) if rval == STYLE_OK: return color elif rval == STYLE_NOT_SET: return None elif rval == STYLE_ERROR: gterror(err) def set_color(self, section, key, color): from ctypes import byref gtlib.gt_style_set_color(self.style, section, key, byref(color)) def get_cstr(self, section, key, gn=None): string = Str() err = Error() rval = gtlib.gt_style_get_str(self.style, section, key, string, gn, err) if rval == STYLE_OK: return str(string) elif rval == STYLE_NOT_SET: return None elif rval == STYLE_ERROR: gterror(err) def set_cstr(self, section, key, value): string = Str(str(value.encode("utf-8"))) gtlib.gt_style_set_str(self.style, section, key, string) def get_num(self, section, key, gn=None): from ctypes import c_double, byref double = c_double() err = Error() rval = gtlib.gt_style_get_num(self.style, section, key, byref(double), \ gn, err) if rval == STYLE_OK: return double.value elif rval == STYLE_NOT_SET: return None elif rval == STYLE_ERROR: gterror(err) def set_num(self, section, key, number): from ctypes import c_double num = c_double(number) gtlib.gt_style_set_num(self.style, section, key, num) def get_bool(self, section, key, gn=None): from ctypes import byref, c_int bool = c_int() err = Error() rval = gtlib.gt_style_get_bool(self.style, section, key, byref(bool), \ gn, err) if rval == STYLE_OK: if bool.value == 1: return True else: return False elif rval == STYLE_NOT_SET: return None elif rval == STYLE_ERROR: gterror(err) def set_bool(self, section, key, val): if val == True: gtlib.gt_style_set_bool(self.style, section, key, 1) else: gtlib.gt_style_set_bool(self.style, section, key, 0) def unset(self, section, key): gtlib.gt_style_unset(self.style, section, key) def register(cls, gtlib): from ctypes import c_char_p, c_double, c_float, c_void_p, \ POINTER, c_int gtlib.gt_style_get_bool.restype = c_int gtlib.gt_style_get_bool.argtypes = [c_void_p, c_char_p, c_char_p, POINTER(c_int), c_void_p] gtlib.gt_style_get_num.restype = c_int gtlib.gt_style_get_num.argtypes = [c_void_p, c_char_p, c_char_p, POINTER(c_double), c_void_p] gtlib.gt_style_get_str.restype = c_int gtlib.gt_style_get_str.argtypes = [c_void_p, c_char_p, c_char_p, Str, c_void_p] gtlib.gt_style_get_color.restype = c_int gtlib.gt_style_get_color.argtypes = [c_void_p, c_char_p, c_char_p, POINTER(Color), c_void_p] gtlib.gt_style_load_str.argtypes = [c_void_p, Str, Error] gtlib.gt_style_load_file.argtypes = [c_void_p, c_char_p, Error] gtlib.gt_style_unset.argtypes = [c_void_p, c_char_p, c_char_p] gtlib.gt_style_to_str.argtypes = [c_void_p, Str, Error] register = classmethod(register) genometools-1.5.1/gtpython/gt/core/000077500000000000000000000000001211610345200172625ustar00rootroot00000000000000genometools-1.5.1/gtpython/gt/core/__init__.py000066400000000000000000000024261211610345200213770ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from array import * from alphabet import * from encseq import * from error import * from gtrange import * from gtstr import * from str_array import * from warning import * Alphabet.register(gtlib) Array.register(gtlib) Encseq.register(gtlib) EncseqEncoder.register(gtlib) EncseqBuilder.register(gtlib) EncseqReader.register(gtlib) Error.register(gtlib) Str.register(gtlib) StrArray.register(gtlib) genometools-1.5.1/gtpython/gt/core/alphabet.py000066400000000000000000000132111211610345200214120ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2010 Sascha Steinbiss # Copyright (c) 2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.error import Error, gterror from gt.core.gtstr import Str from gt.core.str_array import StrArray from ctypes import c_ulong, c_uint, c_int, c_char_p, c_void_p, c_char, c_ubyte import os.path class Alphabet: def create_dna(): return Alphabet(gtlib.gt_alphabet_new_dna(), True) create_dna = staticmethod(create_dna) def create_protein(): return Alphabet(gtlib.gt_alphabet_new_protein(), True) create_protein = staticmethod(create_protein) def create_empty(): return Alphabet(gtlib.gt_alphabet_new_empty(), True) create_empty = staticmethod(create_empty) def create_from_file(indexname): if not os.path.exists(indexname + ".al1"): raise IOError, ("file not found: %s" % (indexname + ".al1")) e = Error() a_ptr = gtlib.gt_alphabet_new_from_file(str(indexname), e) a = Alphabet(a_ptr, True) if a == None: gterror(e) else: return a create_from_file = staticmethod(create_from_file) def create_from_sequence(seqfilenames): if not isinstance(seqfilenames, list): raise TypeError, "argument must be a list of strings" e = Error() sa = StrArray() for f in seqfilenames: if not os.path.exists(f): raise IOError, ("file not found: %s" % f) sa.add(str(f)) a_ptr = gtlib.gt_alphabet_new_from_sequence(sa, e) a = Alphabet(a_ptr, True) if a == None: gterror(e) else: return a create_from_sequence = staticmethod(create_from_sequence) def __init__(self, alpha, own=False): if own: self.alpha = alpha; else: self.alpha = gtlib.gt_alphabet_ref(alpha); self._as_parameter_ = self.alpha def __del__(self): try: gtlib.gt_alphabet_delete(self.slpha) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, Alphabet): raise TypeError, "argument must be an Alphabet" return obj._as_parameter_ from_param = classmethod(from_param) def size(self): return gtlib.gt_alphabet_size(self.alpha) def num_of_chars(self): return gtlib.gt_alphabet_num_of_chars(self.alpha) def encode(self, plainchar): if not self.valid_input(plainchar): gterror("No valid input character: %c" % plainchar) return gtlib.gt_alphabet_encode(self.alpha, plainchar) def decode(self, encodedchar): return gtlib.gt_alphabet_decode(self.alpha, encodedchar) def decode_seq(self, encoded): encstr = (c_ubyte*len(encoded))(*encoded) str_p = gtlib.gt_alphabet_decode_seq_to_str(self.alpha, encstr, len(encstr)) s = Str(str_p) return str(s) def valid_input(self, plainchar): if gtlib.gt_alphabet_valid_input(self.alpha, plainchar) == 1: return True else: return False def is_dna(self): if gtlib.gt_alphabet_is_dna(self.alpha) == 1: return True else: return False def is_protein(self): if gtlib.gt_alphabet_is_protein(self.alpha) == 1: return True else: return False def register(cls, gtlib): gtlib.gt_alphabet_new_from_sequence.restype = c_void_p gtlib.gt_alphabet_new_from_sequence.argtypes = [StrArray, Error] gtlib.gt_alphabet_new_dna.restype = c_void_p gtlib.gt_alphabet_new_dna.argtypes = [] gtlib.gt_alphabet_new_protein.restype = c_void_p gtlib.gt_alphabet_new_protein.argtypes = [] gtlib.gt_alphabet_new_empty.restype = c_void_p gtlib.gt_alphabet_new_empty.argtypes = [] gtlib.gt_alphabet_new_from_file.restype = c_void_p gtlib.gt_alphabet_new_from_file.argtypes = [c_char_p, Error] gtlib.gt_alphabet_ref.restype = c_void_p gtlib.gt_alphabet_ref.argtypes = [c_void_p] gtlib.gt_alphabet_size.restype = c_uint gtlib.gt_alphabet_size.argtypes = [c_void_p] gtlib.gt_alphabet_num_of_chars.restype = c_uint gtlib.gt_alphabet_num_of_chars.argtypes = [c_void_p] gtlib.gt_alphabet_encode.restype = c_ubyte gtlib.gt_alphabet_encode.argtypes = [c_void_p, c_char] gtlib.gt_alphabet_decode.restype = c_char gtlib.gt_alphabet_decode.argtypes = [c_void_p, c_ubyte] gtlib.gt_alphabet_valid_input.restype = c_int gtlib.gt_alphabet_valid_input.argtypes = [c_void_p, c_char] gtlib.gt_alphabet_is_dna.restype = c_int gtlib.gt_alphabet_is_dna.argtypes = [c_void_p] gtlib.gt_alphabet_is_protein.restype = c_int gtlib.gt_alphabet_is_protein.argtypes = [c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/core/array.py000066400000000000000000000046231211610345200207570ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib class Array: def create(size=None, own=True): if size is None: from ctypes import c_void_p, sizeof size = sizeof(c_void_p) return Array(gtlib.gt_array_new(size), own) create = staticmethod(create) def __init__(self, arr, own=False): self.array = arr self._as_parameter_ = self.array self.own = own def __del__(self): if self.own: try: gtlib.gt_array_delete(self.array) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, Array): raise TypeError, "argument must be an Array" return obj._as_parameter_ from_param = classmethod(from_param) def get(self, i): return gtlib.gt_array_get(self.array, i).contents def size(self): return gtlib.gt_array_size(self.array) def add(self, val): gtlib.gt_array_add_ptr(self.array, val._as_parameter_) def register(cls, gtlib): from ctypes import c_void_p, c_uint, c_ulong, POINTER gtlib.gt_array_new.restype = c_void_p gtlib.gt_array_new.argtypes = [c_uint] gtlib.gt_array_ref.restype = c_void_p gtlib.gt_array_ref.argtypes = [c_void_p] gtlib.gt_array_get.restype = POINTER(c_void_p) gtlib.gt_array_get.argtypes = [c_ulong] gtlib.gt_array_size.restype = c_ulong gtlib.gt_array_add_ptr.argtypes = [c_void_p, c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/core/encseq.py000066400000000000000000000426511211610345200211220ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2010-2011 Sascha Steinbiss # Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.alphabet import Alphabet from gt.core.error import Error, gterror from gt.core.readmode import * from gt.core.str_array import StrArray from gt.core.gtstr import Str import os from ctypes import Structure, c_ulong, c_uint, c_int, c_char_p, c_void_p, \ POINTER, byref, c_uint32, c_uint64, string_at, \ create_string_buffer, c_ubyte, c_char def int2bool(val): if val == 0: return False else: return True class Seqinfo(Structure): _fields_ = [("startpos", c_ulong), ("length", c_ulong)] class EncseqEncoder: def __init__(self): self.ee = gtlib.gt_encseq_encoder_new() self._as_parameter_ = self.ee def __del__(self): try: gtlib.gt_encseq_encoder_delete(self.ee) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, EncseqEncoder): raise TypeError, "argument must be an EncseqEncoder object" return obj._as_parameter_ from_param = classmethod(from_param) def set_representation_type(self, sat): gtlib.gt_encseq_encoder_set_access_type(self.ee, Str(str(sat.encode("utf-8")))) def set_symbolmap_file(self, fn): gtlib.gt_encseq_encoder_set_symbolmap_file(self.ee, Str(str(fn.encode("utf-8")))) def enable_description_support(self): gtlib.gt_encseq_encoder_enable_description_support(self.ee) def disable_description_support(self): gtlib.gt_encseq_encoder_disable_description_support(self.ee) def enable_multiseq_support(self): gtlib.gt_encseq_encoder_enable_multiseq_support(self.ee) def disable_multiseq_support(self): gtlib.gt_encseq_encoder_disable_multiseq_support(self.ee) def create_des_tab(self): gtlib.gt_encseq_encoder_create_des_tab(self.ee) def do_not_create_des_tab(self): gtlib.gt_encseq_encoder_do_not_create_des_tab(self.ee) def create_ssp_tab(self): gtlib.gt_encseq_encoder_create_ssp_tab(self.ee) def do_not_create_ssp_tab(self): gtlib.gt_encseq_encoder_do_not_create_ssp_tab(self.ee) def create_sds_tab(self): gtlib.gt_encseq_encoder_create_sds_tab(self.ee) def do_not_create_sds_tab(self): gtlib.gt_encseq_encoder_do_not_create_sds_tab(self.ee) def set_input_protein(self): gtlib.gt_encseq_encoder_set_input_protein(self.ee) def set_input_dna(self): gtlib.gt_encseq_encoder_set_input_dna(self.ee) def encode(self, seqfiles, indexname): if not isinstance(seqfiles, list): raise TypeError, "argument must be a list of strings" if len(seqfiles) == 0: raise Error, "list of input sequence files must be non-empty" sa = StrArray() for f in seqfiles: if not os.path.exists(str(f)): raise IOError, ("file not found: %s" % str(f)) sa.add(str(f)) err = Error() esptr = gtlib.gt_encseq_encoder_encode(self.ee, sa, str(indexname), err) if esptr != 0: gterror(err) def register(cls, gtlib): gtlib.gt_encseq_encoder_encode.argtypes = [c_void_p, StrArray, \ c_char_p, Error] register = classmethod(register) class EncseqLoader: def __init__(self): self.el = gtlib.gt_encseq_loader_new() self._as_parameter_ = self.el self.destab = True self.ssptab = True self.sdstab = True def __del__(self): try: gtlib.gt_encseq_loader_delete(self.el) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, EncseqLoader): raise TypeError, "argument must be an EncseqLoader object" return obj._as_parameter_ from_param = classmethod(from_param) def require_description_support(self): self.destab = True self.sdstab = True gtlib.gt_encseq_loader_require_description_support(self.el) def drop_description_support(self): self.destab = False self.sdstab = False gtlib.gt_encseq_loader_drop_description_support(self.el) def require_multiseq_support(self): self.ssptab = True gtlib.gt_encseq_loader_require_multiseq_support(self.el) def drop_multiseq_support(self): self.ssptab = False gtlib.gt_encseq_loader_drop_multiseq_support(self.el) def require_des_tab(self): self.destab = True gtlib.gt_encseq_loader_require_des_tab(self.el) def do_not_require_des_tab(self): self.destab = False gtlib.gt_encseq_loader_do_not_require_des_tab(self.el) def require_ssp_tab(self): self.ssptab = True gtlib.gt_encseq_loader_require_ssp_tab(self.el) def do_not_require_ssp_tab(self): self.ssptab = False gtlib.gt_encseq_encoder_do_not_require_ssp_tab(self.el) def require_sds_tab(self): self.sdstab = True gtlib.gt_encseq_loader_require_sds_tab(self.el) def do_not_require_sds_tab(self): self.sdstab = False gtlib.gt_encseq_loader_do_not_require_sds_tab(self.el) def load(self, indexname): if not os.path.exists(indexname+".esq"): raise IOError, ("file not found: %s" % indexname+".esq") if self.destab and not os.path.exists(indexname+".des"): raise IOError, ("file not found: %s" % indexname+".des") # not required in every case (equallength seqs) #if self.ssptab and not os.path.exists(indexname+".ssp"): # raise IOError, ("file not found: %s" % indexname+".ssp") if self.sdstab and not os.path.exists(indexname+".sds"): raise IOError, ("file not found: %s" % indexname+".sds") err = Error() esptr = gtlib.gt_encseq_loader_load(self.el, str(indexname), err) if not esptr: gterror(err) return Encseq(esptr, True) class EncseqBuilder: def __init__(self, a): self.eb = gtlib.gt_encseq_builder_new(a) self._as_parameter_ = self.eb def __del__(self): try: gtlib.gt_encseq_builder_delete(self.eb) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, EncseqBuilder): raise TypeError, "argument must be an EncseqBuilder object" return obj._as_parameter_ from_param = classmethod(from_param) def enable_description_support(self): gtlib.gt_encseq_builder_enable_description_support(self.eb) def disable_description_support(self): gtlib.gt_encseq_builder_disable_description_support(self.eb) def enable_multiseq_support(self): gtlib.gt_encseq_builder_enable_multiseq_support(self.eb) def disable_multiseq_support(self): gtlib.gt_encseq_builder_disable_multiseq_support(self.eb) def create_des_tab(self): gtlib.gt_encseq_builder_create_des_tab(self.eb) def do_not_create_des_tab(self): gtlib.gt_encseq_builder_do_not_create_des_tab(self.eb) def create_ssp_tab(self): gtlib.gt_encseq_builder_create_ssp_tab(self.eb) def do_not_create_ssp_tab(self): gtlib.gt_encseq_builder_do_not_create_ssp_tab(self.eb) def create_sds_tab(self): gtlib.gt_encseq_builder_create_sds_tab(self.eb) def do_not_create_sds_tab(self): gtlib.gt_encseq_builder_do_not_create_sds_tab(self.eb) def enable_range_iterator(self): gtlib.gt_encseq_builder_enable_range_iterator(self.eb) def disable_range_iterator(self): gtlib.gt_encseq_builder_disable_range_iterator(self.eb) def add_string(self, string, desc = ''): string = str(string) gtlib.gt_encseq_builder_add_cstr(self.eb, string, len(string), desc) def build(self): err = Error() esptr = gtlib.gt_encseq_builder_build(self.eb, err) if not esptr: gterror(err) return Encseq(esptr, True) def register(cls, gtlib): gtlib.gt_encseq_builder_new.argtypes = [Alphabet] gtlib.gt_encseq_builder_add_cstr.argtypes = [c_void_p, c_char_p, \ c_ulong, c_char_p] register = classmethod(register) class EncseqReader: def __init__(self, ptr, own=False): self.er = ptr self._as_parameter_ = self.er self.own = own def __del__(self): if self.own: try: gtlib.gt_encseq_reader_delete(self.er) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, EncseqReader): raise TypeError, "argument must be an EncseqReader" return obj._as_parameter_ def next_encoded_char(self): return gtlib.gt_encseq_reader_next_encoded_char(self.er) def next_decoded_char(self): return gtlib.gt_encseq_reader_next_decoded_char(self.er) from_param = classmethod(from_param) def register(cls, gtlib): gtlib.gt_encseq_reader_next_encoded_char.restype = c_ubyte gtlib.gt_encseq_reader_next_encoded_char.argtypes = [c_void_p] gtlib.gt_encseq_reader_next_decoded_char.restype = c_char gtlib.gt_encseq_reader_next_decoded_char.argtypes = [c_void_p] register = classmethod(register) class Encseq: def __init__(self, ptr, own=False): self.encseq = ptr self._as_parameter_ = self.encseq self.own = own def __del__(self): if self.own: try: gtlib.gt_encseq_delete(self.encseq) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, Encseq): raise TypeError, "argument must be an Encseq" return obj._as_parameter_ from_param = classmethod(from_param) def num_of_sequences(self): return gtlib.gt_encseq_num_of_sequences(self.encseq) def num_of_files(self): return gtlib.gt_encseq_num_of_files(self.encseq) def description(self, num): if not num < self.num_of_sequences(): gterror("invalid sequence number %d" % num) desclen = c_ulong() str_addr = gtlib.gt_encseq_description(self.encseq, byref(desclen), num) return str(string_at(str_addr, desclen.value)) def total_length(self): return gtlib.gt_encseq_total_length(self.encseq) def get_encoded_char(self, pos, readmode=0): if readmode < 0 or readmode > 3: gterror("invalid readmode!") return gtlib.gt_encseq_get_encoded_char(self.encseq, pos, readmode) def get_decoded_char(self, pos, readmode=0): if readmode < 0 or readmode > 3: gterror("invalid readmode!") return gtlib.gt_encseq_get_decoded_char(self.encseq, pos, readmode) def alphabet(self): a = gtlib.gt_encseq_alphabet(self.encseq) if not a: return None return Alphabet(a) def seqstartpos(self, num): if not num < self.num_of_sequences(): gterror("invalid sequence number %d" % num) return gtlib.gt_encseq_seqstartpos(self.encseq, num) def filestartpos(self, num): if not num < self.num_of_files(): gterror("invalid file number %d" % num) return gtlib.gt_encseq_filestartpos(self.encseq, num) def seqlength(self, num): if not num < self.num_of_sequences(): gterror("invalid sequence number %d" % num) return gtlib.gt_encseq_seqlength(self.encseq, num) def effective_filelength(self, num): if not num < self.num_of_files(): gterror("invalid file number %d" % num) return gtlib.gt_encseq_effective_filelength(self.encseq, num) def filenames(self, num): arr = StrArray(gtlib.gt_encseq_filenames(seld.encseq)) return arr.to_list() def create_reader_with_readmode(self, readmode, startpos): if readmode < 0 or readmode > 3: gterror("invalid readmode!") if startpos < 0 or startpos >= self.total_length(): gterror("invalid startposition: %d (allowed: %d-%d)" % (startpos, 0, self.total_length()-1)) er = gtlib.gt_encseq_create_reader_with_readmode(self.encseq, readmode, startpos) return EncseqReader(er, True) def extract_encoded(self, start, end): if start < 0 or end >= self.total_length(): gterror("invalid coordinates: %d-%d (allowed: %d-%d)" % (start, end, 0, self.total_length()-1)) buf = (c_ubyte * (end-start+1))() gtlib.gt_encseq_extract_encoded(self.encseq, buf, start, end) return buf def extract_decoded(self, start, end): if start < 0 or end >= self.total_length(): gterror("invalid coordinates: %d-%d (allowed: %d-%d)" % (start, end, 0, self.total_length()-1)) buf = (c_char * (end-start+1))() gtlib.gt_encseq_extract_decoded(self.encseq, buf, start, end) return string_at(buf, end-start+1) def seqnum(self, pos): if pos < 0 or pos >= self.total_length(): gterror("invalid position: %d (allowed: %d-%d)" % (pos, 0, self.total_length()-1)) return gtlib.gt_encseq_seqnum(self.encseq, pos) def filenum(self, pos): if pos < 0 or pos >= self.total_length(): gterror("invalid position: %d (allowed: %d-%d)" % (pos, 0, self.total_length()-1)) return gtlib.gt_encseq_filenum(self.encseq, pos) def mirror(self): if self.is_mirrored(): gterror("encoded sequence is already mirrored") err = Error() ret = gtlib.gt_encseq_mirror(self.encseq, err) if ret < 0: gterror(err) def unmirror(self): if not self.is_mirrored(): gterror("encoded sequence is not mirrored") err = Error() gtlib.gt_encseq_unmirror(self.encseq) def is_mirrored(self): return int2bool(gtlib.gt_encseq_is_mirrored(self.encseq)) def register(cls, gtlib): gtlib.gt_encseq_num_of_sequences.restype = c_ulong gtlib.gt_encseq_num_of_sequences.argtypes = [c_void_p] gtlib.gt_encseq_num_of_files.restype = c_ulong gtlib.gt_encseq_num_of_files.argtypes = [c_void_p] gtlib.gt_encseq_total_length.restype = c_ulong gtlib.gt_encseq_total_length.argtypes = [c_void_p] gtlib.gt_encseq_description.restype = c_char_p gtlib.gt_encseq_description.argtypes = [c_void_p, POINTER(c_ulong), \ c_ulong] gtlib.gt_encseq_get_encoded_char.restype = c_ubyte gtlib.gt_encseq_get_encoded_char.argtypes = [c_void_p, c_ulong, c_int] gtlib.gt_encseq_get_decoded_char.restype = c_char gtlib.gt_encseq_get_decoded_char.argtypes = [c_void_p, c_ulong, c_int] gtlib.gt_encseq_alphabet.restype = c_void_p gtlib.gt_encseq_alphabet.argtypes = [c_void_p] gtlib.gt_encseq_seqstartpos.restype = c_ulong gtlib.gt_encseq_seqstartpos.argtypes = [c_void_p, c_ulong] gtlib.gt_encseq_seqlength.restype = c_ulong gtlib.gt_encseq_seqlength.argtypes = [c_void_p, c_ulong] gtlib.gt_encseq_effective_filelength.restype = c_uint64 gtlib.gt_encseq_effective_filelength.argtypes = [c_void_p, c_ulong] gtlib.gt_encseq_extract_encoded.argtypes = [c_void_p, \ POINTER(c_ubyte), \ c_ulong, c_ulong] gtlib.gt_encseq_extract_decoded.argtypes = [c_void_p, c_char_p, \ c_ulong, c_ulong] gtlib.gt_encseq_mirror.restype = c_int gtlib.gt_encseq_mirror.argtypes = [c_void_p] gtlib.gt_encseq_unmirror.argtypes = [c_void_p] gtlib.gt_encseq_is_mirrored.restype = c_int gtlib.gt_encseq_is_mirrored.argtypes = [c_void_p] gtlib.gt_encseq_filestartpos.restype = c_ulong gtlib.gt_encseq_filestartpos.argtypes = [c_void_p, c_ulong] gtlib.gt_encseq_seqnum.restype = c_ulong gtlib.gt_encseq_seqnum.argtypes = [c_void_p, c_ulong] gtlib.gt_encseq_filenum.restype = c_ulong gtlib.gt_encseq_filenum.argtypes = [c_void_p, c_ulong] gtlib.gt_encseq_filenames.restype = c_void_p gtlib.gt_encseq_filenames.argtypes = [c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/core/error.py000066400000000000000000000047731211610345200210000ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib class GTError(RuntimeError): pass class Error: def __init__(self, ptr=None): if ptr: self.error = ptr self.own = False else: self.error = gtlib.gt_error_new() self.own = True self._as_parameter_ = self.error def __del__(self): if self.own: try: gtlib.gt_error_delete(self.error) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, Error): raise TypeError, "argument must be an Error" return obj._as_parameter_ from_param = classmethod(from_param) def get(self): return gtlib.gt_error_get(self.error) def set(self, errmsg): return gtlib.gt_error_set_nonvariadic(self.error, str(errmsg)) def is_set(self): return gtlib.gt_error_is_set(self.error) == 1 def unset(self): gtlib.gt_error_unset(self.error) def register(cls, gtlib): from ctypes import c_void_p, c_char_p, c_int gtlib.gt_error_new.restype = c_void_p gtlib.gt_error_get.restype = c_char_p gtlib.gt_error_is_set.restype = c_int gtlib.gt_error_get.argtypes = [c_void_p] gtlib.gt_error_set_nonvariadic.argtypes = [c_void_p, c_char_p] gtlib.gt_error_is_set.argtypes = [c_void_p] gtlib.gt_error_unset.argtypes = [c_void_p] register = classmethod(register) def gterror(err): if isinstance(err, Error): raise GTError, "GenomeTools error: " + err.get() else: raise GTError, "GenomeTools error: " + err genometools-1.5.1/gtpython/gt/core/gtrange.py000066400000000000000000000034141211610345200212650ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008-2010 Sascha Steinbiss # Copyright (c) 2008-2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.error import gterror from ctypes import Structure, c_ulong class Range(Structure): _fields_ = [("w_start", c_ulong), ("w_end", c_ulong)] def __init__(self, start = 0, end = 0): if start > end or start < 0 or end < 0: gterror("range error: start > end!") super(Range, self).__init__(start, end) def _get_start(self): return self.w_start def _set_start(self, val): if val > self.end or not val >= 0: gterror("Invalid range start component: %d" % val) self.w_start = val start = property(_get_start, _set_start) def _get_end(self): return self.w_end def _set_end(self, val): if val < self.start or not val >= 0: gterror("Invalid range end component: %d" % val) self.w_end = val end = property(_get_end, _set_end) genometools-1.5.1/gtpython/gt/core/gtstr.py000066400000000000000000000046251211610345200210060ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib class Str: def __init__(self, s=None): if s == None or isinstance(s, str): self.strg = gtlib.gt_str_new_cstr(s) self.own = True else: self.strg = s self.own = False self._as_parameter_ = self.strg def __del__(self): if self.own: try: gtlib.gt_str_delete(self.strg) except AttributeError: pass def __str__(self): return str(gtlib.gt_str_get(self.strg)) def reset(self): gtlib.gt_str_reset(self.strg) def from_param(cls, obj): if not isinstance(obj, Str): raise TypeError, "argument must be a Str" return obj._as_parameter_ from_param = classmethod(from_param) def append_cstr(self, string): gtlib.gt_str_append_cstr(self.strg, string) def length(self): return gtlib.gt_str_length(self.strg) def get_mem(self): return gtlib.gt_str_get_mem(self.strg) def register(cls, gtlib): from ctypes import c_void_p, c_char_p, c_ulong gtlib.gt_str_new.restype = c_void_p gtlib.gt_str_new_cstr.restype = c_void_p gtlib.gt_str_new_cstr.argtypes = [c_char_p] gtlib.gt_str_append_cstr.argtypes = [c_void_p, c_char_p] gtlib.gt_str_get.restype = c_char_p gtlib.gt_str_get_mem.restype = c_void_p gtlib.gt_str_length.restype = c_ulong gtlib.gt_str_reset.argtypes = [c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/core/readmode.py000066400000000000000000000016731211610345200214230ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2010 Sascha Steinbiss # Copyright (c) 2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # FORWARD = 0 REVERSE = 1 COMPL = 2 REVCOMPL = 3 genometools-1.5.1/gtpython/gt/core/str_array.py000066400000000000000000000044651211610345200216530ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib class StrArray: def __init__(self, arr=None): if not arr: self.strarr = gtlib.gt_str_array_new() else: self.strarr = gtlib.gt_str_array_ref(arr) self._as_parameter_ = self.strarr def __del__(self): try: gtlib.gt_str_array_delete(self.strarr) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, StrArray): raise TypeError, "argument must be a StrArray" return obj._as_parameter_ from_param = classmethod(from_param) def to_list(self): result = [] for i in range(gtlib.gt_str_array_size(self.strarr)): result.append(gtlib.gt_str_array_get(self.strarr, i)) return result def size(self): return gtlib.gt_str_array_size(self.strarr) def get(self, i): return gtlib.gt_str_array_get(self.strarr, i) def add(self, s): gtlib.gt_str_array_add_cstr(self.strarr, str(s)) def register(cls, gtlib): from ctypes import c_void_p, c_char_p, c_ulong gtlib.gt_str_array_add_cstr.argtypes = [c_void_p, c_char_p] gtlib.gt_str_array_get.restype = c_char_p gtlib.gt_str_array_get.argtypes = [c_void_p, c_ulong] gtlib.gt_str_array_size.restype = c_ulong gtlib.gt_str_array_add_cstr.argtypes = [c_void_p, c_char_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/core/warning.py000066400000000000000000000023341211610345200213030ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2010 Sascha Steinbiss # Copyright (c) 2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib def warning_disable(): gtlib.gt_warning_disable() def warning_enable_default(): from ctypes import CFUNCTYPE, c_void_p, c_char_p, addressof defhand = CFUNCTYPE(None, c_void_p, c_char_p, c_char_p).in_dll(gtlib, "gt_warning_default_handler") gtlib.gt_warning_set_handler(addressof(defhand), None) genometools-1.5.1/gtpython/gt/dlload.py000066400000000000000000000023561211610345200201510ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from ctypes import CDLL, CFUNCTYPE, c_char_p, c_void_p import sys # inspired by the ruby bindings, maybe there is a better way if sys.platform == "darwin": soext = ".dylib" else: soext = ".so" gtlib = CDLL("libgenometools" + soext) gtlib.gt_lib_init() gtlib.gt_lib_reg_atexit_func() CollectFunc = CFUNCTYPE(c_void_p, c_char_p, c_char_p, c_void_p) genometools-1.5.1/gtpython/gt/extended/000077500000000000000000000000001211610345200201325ustar00rootroot00000000000000genometools-1.5.1/gtpython/gt/extended/__init__.py000066400000000000000000000036211211610345200222450ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008-2012 Sascha Steinbiss # Copyright (c) 2008-2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from comment_node import * from feature_node import * from custom_stream import * from custom_stream_example import * from custom_visitor import * from genome_node import * from genome_stream import * from gff3_in_stream import * from gff3_out_stream import * from gff3_visitor import * from node_visitor import * from region_node import * from sequence_node import * from add_introns_stream import * from inter_feature_stream import * from dup_feature_stream import * from merge_feature_stream import * from rdb import * from anno_db import * CommentNode.register(gtlib) GenomeNode.register(gtlib) RegionNode.register(gtlib) SequenceNode.register(gtlib) MetaNode.register(gtlib) EOFNode.register(gtlib) CustomStream.register(gtlib) FeatureNode.register(gtlib) FeatureNodeIterator.register(gtlib) GFF3InStream.register(gtlib) AddIntronsStream.register(gtlib) InterFeatureStream.register(gtlib) DuplicateFeatureStream.register(gtlib) MergeFeatureStream.register(gtlib) RDBSqlite.register(gtlib) AnnoDBSchema.register(gtlib) genometools-1.5.1/gtpython/gt/extended/add_introns_stream.py000066400000000000000000000031251211610345200243640ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.genome_stream import GenomeStream class AddIntronsStream(GenomeStream): def __init__(self, genome_stream): self.gs = gtlib.gt_add_introns_stream_new(genome_stream) self._as_parameter_ = self.gs def from_param(cls, obj): if not isinstance(obj, AddIntronsStream): raise TypeError, "argument must be a AddIntronsStream" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_void_p gtlib.gt_add_introns_stream_new.restype = c_void_p gtlib.gt_add_introns_stream_new.argtypes = [GenomeStream] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/anno_db.py000066400000000000000000000052051211610345200221060ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2012 Sascha Steinbiss # Copyright (c) 2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.error import Error, gterror from gt.extended.rdb import RDB from gt.annotationsketch.feature_index import FeatureIndexFromPtr class AnnoDBSchema: def __init__(self, *args): raise NotImplementedError, \ 'Please call the constructor of an AnnoDBSchema implementation.' def __del__(self): try: gtlib.gt_anno_db_schema_delete(self.ads) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, AnnoDBSchema): raise TypeError, "argument must be an AnnoDBSchema" return obj._as_parameter_ from_param = classmethod(from_param) def get_feature_index(self, rdb): err = Error() fi = gtlib.gt_anno_db_schema_get_feature_index(self.ads, rdb, err) if fi == None: gterror(err) return FeatureIndexFromPtr(fi) def register(cls, gtlib): from ctypes import c_void_p gtlib.gt_anno_db_schema_get_feature_index.restype = c_void_p gtlib.gt_anno_db_schema_get_feature_index.argtypes = [c_void_p, RDB, Error] register = classmethod(register) class AnnoDBGFFLike(AnnoDBSchema): def __init__(self): err = Error() ads = gtlib.gt_anno_db_gfflike_new() if ads == None: gterror(err) self.ads = ads self._as_parameter_ = self.ads def from_param(cls, obj): if not isinstance(obj, AnnoDBGFFLike): raise TypeError, "argument must be an AnnoDBGFFLike" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_void_p gtlib.gt_anno_db_gfflike_new.restype = c_void_p register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/comment_node.py000066400000000000000000000031611211610345200231540ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.genome_node import GenomeNode class CommentNode(GenomeNode): def __init__(self): pass @classmethod def create_new(cls, comment): fn = gtlib.gt_comment_node_new(str(comment)) n = cls.create_from_ptr(fn, True) return n def get_comment(self): return gtlib.gt_comment_node_get_comment(self.gn) def register(cls, gtlib): from ctypes import c_char_p, c_void_p gtlib.gt_comment_node_new.restype = c_void_p gtlib.gt_comment_node_new.argtypes = [c_char_p] gtlib.gt_comment_node_get_comment.restype = c_char_p gtlib.gt_comment_node_get_comment.argtypes = [c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/custom_stream.py000066400000000000000000000050461211610345200233760ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from ctypes import CFUNCTYPE, c_void_p, c_int, POINTER from gt.dlload import gtlib from gt.core.error import Error, gterror, GTError from gt.extended.genome_stream import GenomeStream NextFunc = CFUNCTYPE(c_int, POINTER(c_void_p), c_void_p) FreeFunc = CFUNCTYPE(c_void_p, c_void_p) class CustomStream(GenomeStream): def __init__(self): try: self.next except AttributeError: gterror("%s does not implement mandatory method 'next'!" \ % self.__class__.__name__) def next_w(nodepp, err): error = Error(err) try: nextnode = self.next() if nextnode: nodepp[0] = nextnode.gn else: nodepp[0] = None return 0 except Error, errmsg: error.set(str(errmsg)) return -1 self.next_cb = NextFunc(next_w) def free_w(ptr): self.free() self.free_cb = FreeFunc(free_w) self.gs = gtlib.gt_script_wrapper_stream_new(self.next_cb, self.free_cb) self._as_parameter_ = self.gs def from_param(cls, obj): if not isinstance(obj, CustomStream): raise TypeError, "argument must be a CustomStream" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_char_p, c_void_p, c_int, POINTER gtlib.gt_script_wrapper_stream_new.restype = c_void_p gtlib.gt_script_wrapper_stream_new.argtypes = [NextFunc, FreeFunc] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/custom_stream_example.py000066400000000000000000000035461211610345200251140ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.core.error import GTError from gt.extended.custom_stream import CustomStream from gt.extended.custom_visitor_example import CustomVisitorExample from gt.extended.feature_node import FeatureNode # This is an example custom stream implementation in Python. # It applies a CustomVisitorExample to each node read from the input stream. # For example, it can be used like this: # # ins = GFF3InStream("somefile.gff3") # cs = CustomStreamExample(ins) # outs = GFF3OutStream(cs) # outs.pull() # # Please raise a GTError if a user error in the stream is to be signaled. # This will ensure that error handling is done properly in the underlying C # code. class CustomStreamExample(CustomStream): def __init__(self, instream): CustomStream.__init__(self) self.instream = instream self.visitor = CustomVisitorExample() def next(self): node = self.instream.next_tree() if node: node.accept(self.visitor) return node genometools-1.5.1/gtpython/gt/extended/custom_visitor.py000066400000000000000000000117301211610345200235770ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009-2012 Sascha Steinbiss # Copyright (c) 2009-2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.node_visitor import NodeVisitor from ctypes import CFUNCTYPE, c_void_p, c_int, POINTER from gt.extended.feature_node import FeatureNode from gt.extended.region_node import RegionNode from gt.extended.sequence_node import SequenceNode from gt.extended.comment_node import CommentNode from gt.extended.eof_node import EOFNode from gt.extended.meta_node import MetaNode from gt.core.error import Error, GTError CommentNodeFunc = CFUNCTYPE(c_int, c_void_p, c_void_p) FeatureNodeFunc = CFUNCTYPE(c_int, c_void_p, c_void_p) RegionNodeFunc = CFUNCTYPE(c_int, c_void_p, c_void_p) SequenceNodeFunc = CFUNCTYPE(c_int, c_void_p, c_void_p) MetaNodeFunc = CFUNCTYPE(c_int, c_void_p, c_void_p) EOFNodeFunc = CFUNCTYPE(c_int, c_void_p, c_void_p) FreeFunc = CFUNCTYPE(c_void_p, c_void_p) class CustomVisitor(NodeVisitor): def __init__(self): def feature_node_w(fn_p, err_p): fn = FeatureNode.create_from_ptr(fn_p) err = Error(err_p) try: try: self.visit_feature_node(fn) except AttributeError: pass return 0 except GTError, errmsg: err.set(str(errmsg)) return -1 self.feature_node_cb = FeatureNodeFunc(feature_node_w) def sequence_node_w(sn_p, err_p): sn = SequenceNode.create_from_ptr(sn_p) err = Error(err_p) try: try: self.visit_sequence_node(sn) except AttributeError: pass return 0 except GTError, errmsg: err.set(str(errmsg)) return -1 self.sequence_node_cb = SequenceNodeFunc(sequence_node_w) def region_node_w(rn_p, err_p): rn = RegionNode.create_from_ptr(rn_p) err = Error(err_p) try: try: self.visit_region_node(rn) except AttributeError: pass return 0 except GTError, errmsg: err.set(str(errmsg)) return -1 self.region_node_cb = RegionNodeFunc(region_node_w) def comment_node_w(cn_p, err_p): cn = CommentNode.create_from_ptr(cn_p) err = Error(err_p) try: try: self.visit_comment_node(cn) except AttributeError: pass return 0 except GTError, errmsg: err.set(str(errmsg)) return -1 self.comment_node_cb = CommentNodeFunc(comment_node_w) def eof_node_w(en_p, err_p): en = EOFNode.create_from_ptr(en_p) err = Error(err_p) try: try: self.visit_eof_node(en) except AttributeError: pass return 0 except GTError, errmsg: err.set(str(errmsg)) return -1 self.eof_node_cb = EOFNodeFunc(eof_node_w) def meta_node_w(mn_p, err_p): mn = EOFNode.create_from_ptr(mn_p) err = Error(err_p) try: try: self.visit_meta_node(mn) except AttributeError: pass return 0 except GTError, errmsg: err.set(str(errmsg)) return -1 self.meta_node_cb = MetaNodeFunc(meta_node_w) self.gv = gtlib.gt_script_wrapper_visitor_new(self.comment_node_cb, \ self.feature_node_cb, \ self.region_node_cb, \ self.sequence_node_cb, \ self.meta_node_cb, \ self.eof_node_cb, \ None) self._as_parameter_ = self.gv genometools-1.5.1/gtpython/gt/extended/custom_visitor_example.py000066400000000000000000000036021211610345200253110ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.core.error import GTError from gt.extended.custom_visitor import CustomVisitor from gt.extended.feature_node import FeatureNode # This is an example custom visitor implementation in Python. # It adds a new subfeature to the visited node. # # For each node type, there is an accompanying visit_*_node method which is # called when a node of this type is visited. If a method is missing, then the # corresponding node type is ignored. # # Please raise a GTError if a user error in the visitor is to be signaled. # This will ensure that error handling is done properly in the underlying C # code. class CustomVisitorExample(CustomVisitor): def __init__(self): CustomVisitor.__init__(self) def visit_feature_node(self, fn): new_child = FeatureNode.create_new(fn.get_seqid(), "bar", 100, 1000, "+") fn.add_child(new_child) def visit_region_node(self, rn): pass def visit_comment_node(self, cn): pass def visit_sequence_node(self, sn): pass genometools-1.5.1/gtpython/gt/extended/dup_feature_stream.py000066400000000000000000000031411211610345200243610ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Brent Pedersen # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.genome_stream import GenomeStream class DuplicateFeatureStream(GenomeStream): def __init__(self, genome_stream, dest_type, source_type): self.gs = gtlib.gt_dup_feature_stream_new(genome_stream, dest_type, source_type) self._as_parameter_ = self.gs def from_param(cls, obj): if not isinstance(obj, DuplicateFeatureStream): raise TypeError, "argument must be a DuplicateFeatureStream" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_void_p, c_char_p gtlib.gt_dup_feature_stream_new.restype = c_void_p gtlib.gt_dup_feature_stream_new.argtypes = [GenomeStream, c_char_p, c_char_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/eof_node.py000066400000000000000000000025421211610345200222650ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2012 Sascha Steinbiss # Copyright (c) 2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.genome_node import GenomeNode from gt.core.gtstr import Str class EOFNode(GenomeNode): def __init__(self): pass @classmethod def create_new(cls): fn = gtlib.gt_eof_node_new() n = cls.create_from_ptr(fn, True) return n def register(cls, gtlib): from ctypes import c_void_p, c_char_p gtlib.gt_eof_node_new.restype = c_void_p register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/feature_index.py000066400000000000000000000132241211610345200233300ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.array import Array from gt.core.error import Error, gterror from gt.core.gtrange import Range from gt.core.str_array import StrArray from gt.extended.feature_node import FeatureNode class FeatureIndex: def __init__(self, *args): raise NotImplementedError, \ 'Please call the constructor of a FeatureIndex implementation.' def __del__(self): try: gtlib.gt_feature_index_delete(self.fi) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, FeatureIndex): raise TypeError, "argument must be a FeatureIndex" return obj._as_parameter_ from_param = classmethod(from_param) def get_features_for_seqid(self, seqid): err = Error() result = [] rval = gtlib.gt_feature_index_get_features_for_seqid(self.fi, seqid, err) if rval: a = Array(rval, True) for i in range(a.size()): fptr = gtlib.gt_genome_node_ref(a.get(i)) result.append(FeatureNode.create_from_ptr(fptr)) return result else: gterror(err) return result def add_gff3file(self, filename): err = Error() rval = gtlib.gt_feature_index_add_gff3file(self.fi, filename, err) if rval != 0: gterror(err) def has_seqid(self, seqid): from ctypes import c_int, byref val = c_int() err = Error() ret = gtlib.gt_feature_index_has_seqid(self.fi, byref(val), seqid, err) if ret != 0: gterror(err) else: return (val.value > 0) def get_first_seqid(self): err = Error() str = gtlib.gt_feature_index_get_first_seqid(self.fi, err) if str == None: gterror(err) return str def get_seqids(self): result = [] err = Error() stra = StrArray(gtlib.gt_feature_index_get_seqids(self.fi, err)) if stra == None: gterror(err) for i in range(stra.size()): result.append(stra.get(i)) return result def get_range_for_seqid(self, seqid): from ctypes import byref err = Error() if self.has_seqid(seqid) == 0: gterror("feature_index does not contain seqid") range = Range() rval = gtlib.gt_feature_index_get_range_for_seqid(self.fi, byref(range), seqid, err) if rval != 0: gterror(err) return range def get_features_for_range(self, start, end, seqid): from ctypes import byref a = Array.create() err = Error() rng = Range(start, end) rval = gtlib.gt_feature_index_get_features_for_range(self.fi, a, seqid, byref(rng), err) if rval != 0: gterror(err) result = [] for i in range(a.size()): fptr = gtlib.gt_genome_node_ref(a.get(i)) result.append(FeatureNode.create_from_ptr(fptr)) return result def register(cls, gtlib): from ctypes import c_char_p, c_void_p, c_int, POINTER gtlib.gt_feature_index_get_features_for_seqid.restype = c_void_p gtlib.gt_feature_index_add_gff3file.argtypes = [c_void_p, c_char_p, Error] gtlib.gt_feature_index_get_first_seqid.restype = c_char_p gtlib.gt_feature_index_get_first_seqid.argtypes = [c_void_p, Error] gtlib.gt_feature_index_get_seqids.restype = c_int gtlib.gt_feature_index_get_first_seqid.argtypes = [c_void_p, Error] gtlib.gt_feature_index_has_seqid.restype = c_int gtlib.gt_feature_index_has_seqid.argtypes = [c_void_p, POINTER(c_int), c_char_p, Error] gtlib.gt_feature_index_get_range_for_seqid.argtypes = [c_void_p, POINTER(Range), c_char_p] gtlib.gt_feature_index_get_features_for_range.argtypes = [c_void_p, Array, c_char_p, POINTER(Range), Error] register = classmethod(register) class FeatureIndexMemory(FeatureIndex): def __init__(self): self.fi = gtlib.gt_feature_index_memory_new() self._as_parameter_ = self.fi def from_param(cls, obj): if not isinstance(obj, FeatureIndexMemory): raise TypeError, "argument must be a FeatureIndexMemory" return obj._as_parameter_ from_param = classmethod(from_param) class FeatureIndexFromPtr(FeatureIndex): def __init__(self, ptr): self.fi = ptr self._as_parameter_ = self.fi def from_param(cls, obj): if not isinstance(obj, FeatureIndexFromPtr): raise TypeError, "argument must be a FeatureIndexFromPtr" return obj._as_parameter_ from_param = classmethod(from_param) genometools-1.5.1/gtpython/gt/extended/feature_node.py000066400000000000000000000213151211610345200231460ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008-2009 Sascha Steinbiss # Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib, CollectFunc from gt.core.error import Error, gterror from gt.core.gtstr import Str from gt.core.str_array import StrArray from gt.extended.genome_node import GenomeNode from gt.props import cachedproperty class FeatureNode(GenomeNode): def __init__(self): self.depth_first = True pass @classmethod def create_new(cls, seqid, type, start, end, strand): from gt.extended.strand import strandchars if not strand in strandchars: gterror("Invalid strand '%s' -- must be one of %s" % (strand, strandchars)) s = Str(str(seqid.encode("utf-8"))) fn = gtlib.gt_feature_node_new(s, type, start, end, \ strandchars.index(strand)) n = cls.create_from_ptr(fn, True) n.depth_first = True return n def update_attrs(self): attribs = {} def py_collect_func(tag, val, data): attribs[tag] = val collect_func = CollectFunc(py_collect_func) gtlib.gt_feature_node_foreach_attribute(self.gn, collect_func, None) return attribs def add_child(self, node): ownid = str(self.get_seqid()) newid = str(node.get_seqid()) if (ownid != newid): gterror("cannot add node with sequence region '%s' to node with sequence region '%s'" % (ownid, newid)) else: gtlib.gt_feature_node_add_child(self.gn, node) def from_param(cls, obj): if not isinstance(obj, FeatureNode): raise TypeError, "argument must be a FeatureNode" return obj._as_parameter_ from_param = classmethod(from_param) def get_source(self): return gtlib.gt_feature_node_get_source(self.gn) def set_source(self, source): s = Str(str(source.encode("utf-8"))) gtlib.gt_feature_node_set_source(self.gn, s) source = cachedproperty(get_source, set_source) def get_type(self): return gtlib.gt_feature_node_get_type(self.gn) def set_type(self, type): gtlib.gt_feature_node_set_type(self.gn, type) type = cachedproperty(get_type, set_type) def has_type(self, type): return gtlib.gt_feature_node_has_type(self.gn, type) == 1 def set_strand(self, strand): from gt.extended.strand import strandchars if not strand in strandchars: gterror("Invalid strand '%s' -- must be one of %s" % (strand, strandchars)) gtlib.gt_feature_node_set_strand(self.gn, strandchars.index(strand)) def get_strand(self): from gt.extended.strand import strandchars return strandchars[gtlib.gt_feature_node_get_strand(self.gn)] strand = cachedproperty(get_strand, set_strand) def get_phase(self): return gtlib.gt_feature_node_get_phase(self.gn) def set_phase(self, phase): return gtlib.gt_feature_node_set_phase(self.gn, phase) phase = cachedproperty(get_phase, set_phase) def score_is_defined(self): return gtlib.gt_feature_node_score_is_defined(self.gn) == 1 def get_score(self): if gtlib.gt_feature_node_score_is_defined(self.gn) == 1: return gtlib.gt_feature_node_get_score(self.gn) else: return None def set_score(self, score): gtlib.gt_feature_node_set_score(self.gn, score) def unset_score(self): gtlib.gt_feature_node_unset_score(self.gn) score = cachedproperty(get_score, set_score, unset_score) def get_attribute(self, attrib): return gtlib.gt_feature_node_get_attribute(self.gn, attrib) def add_attribute(self, attrib, value): if attrib == "" or value == "": gterror("attribute keys or values must not be empty!") gtlib.gt_feature_node_add_attribute(self.gn, attrib, value) def each_attribute(self): attribs = self.update_attrs() for (tag, val) in attribs.iteritems(): yield (tag, val) def get_attribs(self): return dict(self.each_attribute()) attribs = property(get_attribs) def register(cls, gtlib): from ctypes import c_char_p, c_float, c_int, c_int, c_void_p, \ c_ulong, c_float gtlib.gt_feature_node_new.restype = c_void_p gtlib.gt_feature_node_new.argtypes = [Str, c_char_p, c_ulong, c_ulong, c_int] gtlib.gt_feature_node_add_child.argtypes = [c_void_p, FeatureNode] gtlib.gt_feature_node_set_source.argtypes = [c_void_p, Str] gtlib.gt_feature_node_get_source.restype = c_char_p gtlib.gt_feature_node_get_source.argtypes = [c_void_p] gtlib.gt_feature_node_get_type.restype = c_char_p gtlib.gt_feature_node_get_type.argtypes = [c_void_p] gtlib.gt_feature_node_has_type.restype = c_int gtlib.gt_feature_node_has_type.argtypes = [c_void_p, c_char_p] gtlib.gt_feature_node_get_score.restype = c_float gtlib.gt_feature_node_get_score.argtypes = [c_void_p] gtlib.gt_feature_node_set_score.argtypes = [c_void_p, c_float] gtlib.gt_feature_node_get_phase.restype = c_int gtlib.gt_feature_node_get_phase.argtypes = [c_void_p] gtlib.gt_feature_node_set_phase.argtypes = [c_void_p, c_int] gtlib.gt_feature_node_score_is_defined.restype = c_int gtlib.gt_feature_node_score_is_defined.argtypes = [c_void_p] gtlib.gt_feature_node_get_strand.restype = c_int gtlib.gt_feature_node_get_strand.argtypes = [c_void_p] gtlib.gt_feature_node_set_strand.argtypes = [c_void_p, c_int] gtlib.gt_feature_node_unset_score.argtypes = [c_void_p] gtlib.gt_feature_node_add_attribute.argtypes = [c_void_p, c_char_p, c_char_p] gtlib.gt_feature_node_get_attribute.restype = c_char_p gtlib.gt_feature_node_get_attribute.argtypes = [c_void_p, c_char_p] register = classmethod(register) def traverse(self, it): f = it.next() while f is not None: yield f f = it.next() def __iter__(self): if self.depth_first: it = FeatureNodeIteratorDepthFirst(self) else: it = FeatureNodeIteratorDirect(self) return self.traverse(it) def __call__(self, method=None): if str(method).lower() == 'direct': it = FeatureNodeIteratorDirect(self) else: it = FeatureNodeIteratorDepthFirst(self) return self.traverse(it) def traverse_dfs(self): it = FeatureNodeIteratorDepthFirst(self) return self.traverse(it) def traverse_direct(self): it = FeatureNodeIteratorDirect(self) return self.traverse(it) class FeatureNodeIterator(object): def next(self): ret = gtlib.gt_feature_node_iterator_next(self.i) if ret != None: return FeatureNode.create_from_ptr(ret) return ret def __del__(self): try: gtlib.gt_feature_node_iterator_delete(self.i) except AttributeError: pass def register(cls, gtlib): from ctypes import c_void_p gtlib.gt_feature_node_iterator_new.restype = c_void_p gtlib.gt_feature_node_iterator_new.argtypes = [FeatureNode] gtlib.gt_feature_node_iterator_new_direct.restype = c_void_p gtlib.gt_feature_node_iterator_new_direct.argtypes = [FeatureNode] gtlib.gt_feature_node_iterator_next.restype = c_void_p register = classmethod(register) class FeatureNodeIteratorDepthFirst(FeatureNodeIterator): """ includes the node itself """ def __init__(self, node): self.i = gtlib.gt_feature_node_iterator_new(node) self._as_parameter_ = self.i class FeatureNodeIteratorDirect(FeatureNodeIterator): def __init__(self, node): self.i = gtlib.gt_feature_node_iterator_new_direct(node) self._as_parameter_ = self.i genometools-1.5.1/gtpython/gt/extended/feature_stream.py000066400000000000000000000032431211610345200235140ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.annotationsketch.feature_index import FeatureIndex from gt.extended.genome_stream import GenomeStream class FeatureStream(GenomeStream): def __init__(self, genome_stream, feature_index): self.gs = gtlib.gt_feature_stream_new(genome_stream, feature_index) self._as_parameter_ = self.gs def from_param(cls, obj): if not isinstance(obj, FeatureStream): raise TypeError, "argument must be a FeatureStream" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): gtlib.gt_feature_stream_new.restype = c_void_p gtlib.gt_feature_stream_new.argtypes = [GenomeStream, FeatureIndex] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/genome_node.py000066400000000000000000000107031211610345200227640ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008-2009 Sascha Steinbiss # Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.error import Error, gterror from gt.extended.node_visitor import NodeVisitor from gt.core.gtstr import Str from gt.props import cachedproperty class GenomeNode(object): def __init__(self): pass @classmethod def create_from_ptr(cls, node_ptr, newref=False): if node_ptr == 0 or node_ptr == None: gterror("GenomeNode pointer cannot be NULL (was: " + str(node_ptr) + ")") n = cls() if newref: n.own = True n.gn = gtlib.gt_genome_node_ref(node_ptr) else: n.own = False n.gn = node_ptr n._as_parameter_ = n.gn return n def __repr__(self): c = self.__class__.__name__ return "%s(start=%i, end=%i, seqid=\"%s\")" % (c, self.start, self.end, self.seqid) def __del__(self): if self.own: try: gtlib.gt_genome_node_delete(self.gn) except AttributeError: pass def __eq__(self, node): try: return self.gn == node.gn except AttributeError: return False def from_param(cls, obj): if not isinstance(obj, GenomeNode): raise TypeError, "argument must be a GenomeNode" return obj._as_parameter_ from_param = classmethod(from_param) def get_range(self): return (gtlib.gt_genome_node_get_start(self.gn), gtlib.gt_genome_node_get_end(self.gn)) range = property(get_range) def get_seqid(self): strptr = gtlib.gt_genome_node_get_seqid(self.gn) if strptr: return str(Str(strptr)) else: return None seqid = cachedproperty(get_seqid) def get_start(self): if not self.__class__.__name__ == "EOFNode": return gtlib.gt_genome_node_get_start(self.gn) else: return None start = cachedproperty(get_start) def get_end(self): if not self.__class__.__name__ == "EOFNode": return gtlib.gt_genome_node_get_end(self.gn) else: return None end = cachedproperty(get_end) def get_filename(self): return gtlib.gt_genome_node_get_filename(self.gn) filename = property(get_filename) def get_line_number(self): return gtlib.gt_genome_node_get_line_number(self.gn) line_number = property(get_line_number) def accept(self, visitor): err = Error() rval = gtlib.gt_genome_node_accept(self.gn, visitor, err) if rval != 0: gterror(err) def register(cls, gtlib): from ctypes import c_char_p, c_ulong, c_int, c_void_p, c_uint gtlib.gt_genome_node_get_filename.restype = c_char_p gtlib.gt_genome_node_get_filename.argtypes = [c_void_p] gtlib.gt_genome_node_get_start.restype = c_ulong gtlib.gt_genome_node_get_start.argtypes = [c_void_p] gtlib.gt_genome_node_get_end.restype = c_ulong gtlib.gt_genome_node_get_end.argtypes = [c_void_p] gtlib.gt_genome_node_get_seqid.argtypes = [c_void_p] gtlib.gt_genome_node_get_seqid.restype = c_void_p gtlib.gt_genome_node_get_filename.argtypes = [c_void_p] gtlib.gt_genome_node_get_filename.restype = c_char_p gtlib.gt_genome_node_get_line_number.argtypes = [c_void_p] gtlib.gt_genome_node_get_line_number.restype = c_uint gtlib.gt_genome_node_accept.restype = c_int gtlib.gt_genome_node_accept.argtypes = [c_void_p, NodeVisitor, Error] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/genome_stream.py000066400000000000000000000040361211610345200233340ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.error import Error, gterror from gt.extended.genome_node import GenomeNode from ctypes import byref, c_void_p class GenomeStream: def __init__(self, *args): raise NotImplementedError, \ 'Please call the constructor of a GenomeStream implementation.' def __del__(self): try: gtlib.gt_node_stream_delete(self.gs) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, GenomeStream): raise TypeError, "argument must be a GenomeStream" return obj._as_parameter_ from_param = classmethod(from_param) def next_tree(self): err = Error() genome_node = c_void_p() rval = gtlib.gt_node_stream_next(self.gs, byref(genome_node), err) if rval != 0: gterror(err) if genome_node.value == None: return None else: return GenomeNode.create_from_ptr(genome_node.value) def pull(self): err = Error() rval = gtlib.gt_node_stream_pull(self.gs, err) if rval != 0: gterror(err) genometools-1.5.1/gtpython/gt/extended/gff3_in_stream.py000066400000000000000000000041161211610345200233740ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.error import gterror from gt.core.str_array import StrArray from gt.extended.genome_stream import GenomeStream class GFF3InStream(GenomeStream): def __init__(self, filename): try: p = open(filename) tmp = p.readline() p.close() except: gterror("File " + filename + " not readable!") self.gs = gtlib.gt_gff3_in_stream_new_sorted(filename, 0) self._as_parameter_ = self.gs def from_param(cls, obj): if not isinstance(obj, GFF3InStream): raise TypeError, "argument must be a GFF3InStream" return obj._as_parameter_ from_param = classmethod(from_param) def get_used_types(self): str_array_ptr = gtlib.gt_gff3_in_stream_get_used_types(self.gs) used_types = StrArray(str_array_ptr) return used_types.to_list() def register(cls, gtlib): from ctypes import c_char_p, c_int, c_void_p gtlib.gt_gff3_in_stream_new_sorted.argtypes = [c_char_p, c_int] gtlib.gt_gff3_in_stream_get_used_types.restype = c_void_p gtlib.gt_gff3_in_stream_new_sorted.restype = c_void_p register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/gff3_out_stream.py000066400000000000000000000025511211610345200235760ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.genome_stream import GenomeStream class GFF3OutStream(GenomeStream): def __init__(self, genome_stream): self.gs = gtlib.gt_gff3_out_stream_new(genome_stream, None) self._as_parameter_ = self.gs def from_param(cls, obj): if not isinstance(obj, GFF3OutStream): raise TypeError, "argument must be a GFF3OutStream" return obj._as_parameter_ from_param = classmethod(from_param) genometools-1.5.1/gtpython/gt/extended/gff3_visitor.py000066400000000000000000000021471211610345200231140ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.node_visitor import NodeVisitor class GFF3Visitor(NodeVisitor): def __init__(self): self.gv = gtlib.gt_gff3_visitor_new(None) self._as_parameter_ = self.gv genometools-1.5.1/gtpython/gt/extended/inter_feature_stream.py000066400000000000000000000031341211610345200247140ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Brent Pedersen # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.genome_stream import GenomeStream class InterFeatureStream(GenomeStream): def __init__(self, genome_stream, surround_type, new_type): self.gs = gtlib.gt_inter_feature_stream_new(genome_stream, surround_type, new_type) self._as_parameter_ = self.gs def from_param(cls, obj): if not isinstance(obj, InterFeatureStream): raise TypeError, "argument must be a InterFeatureStream" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_void_p, c_char_p gtlib.gt_inter_feature_stream_new.restype = c_void_p gtlib.gt_inter_feature_stream_new.argtypes = [GenomeStream, c_char_p, c_char_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/merge_feature_stream.py000066400000000000000000000030151211610345200246700ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Brent Pedersen # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.genome_stream import GenomeStream class MergeFeatureStream(GenomeStream): def __init__(self, genome_stream): self.gs = gtlib.gt_merge_feature_stream_new(genome_stream) self._as_parameter_ = self.gs def from_param(cls, obj): if not isinstance(obj, MergeFeatureStream): raise TypeError, "argument must be a MergeFeatureStream" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_void_p gtlib.gt_merge_feature_stream_new.restype = c_void_p gtlib.gt_merge_feature_stream_new.argtypes = [GenomeStream] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/meta_node.py000066400000000000000000000035501211610345200224420ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2012 Sascha Steinbiss # Copyright (c) 2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.genome_node import GenomeNode from gt.core.gtstr import Str class MetaNode(GenomeNode): def __init__(self): pass @classmethod def create_new(cls, directive, data): fn = gtlib.gt_meta_node_new(str(directive), str(data)) n = cls.create_from_ptr(fn, True) return n def get_directive(self): return str(gtlib.gt_meta_node_get_directive(self.gn)) def get_data(self): return str(gtlib.gt_meta_node_get_data(self.gn)) def register(cls, gtlib): from ctypes import c_void_p, c_char_p gtlib.gt_meta_node_new.restype = c_void_p gtlib.gt_meta_node_new.argtypes = [c_char_p, c_char_p] gtlib.gt_meta_node_get_directive.restype = c_char_p gtlib.gt_meta_node_get_directive.argtypes = [c_void_p] gtlib.gt_meta_node_get_data.restype = c_char_p gtlib.gt_meta_node_get_data.argtypes = [c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/node_visitor.py000066400000000000000000000025471211610345200232200ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib class NodeVisitor(object): def __init__(self): raise NotImplementedError, \ 'Please call the constructor of a NodeVisitor implementation.' def __del__(self): gtlib.gt_node_visitor_delete(self.gv) def from_param(cls, obj): if not isinstance(obj, NodeVisitor): raise TypeError, "argument must be a NodeVisitor" return obj._as_parameter_ from_param = classmethod(from_param) genometools-1.5.1/gtpython/gt/extended/rdb.py000066400000000000000000000041231211610345200212530ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2012 Sascha Steinbiss # Copyright (c) 2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.error import Error, gterror class RDB: def __init__(self, *args): raise NotImplementedError, \ 'Please call the constructor of a RDB implementation.' def __del__(self): try: gtlib.gt_rdb_delete(self.rdb) except AttributeError: pass def from_param(cls, obj): if not isinstance(obj, RDB): raise TypeError, "argument must be a RDB" return obj._as_parameter_ from_param = classmethod(from_param) class RDBSqlite(RDB): def __init__(self, filename): err = Error() rdb = gtlib.gt_rdb_sqlite_new(filename, err) if rdb == None: gterror(err) self.rdb = rdb self._as_parameter_ = self.rdb def from_param(cls, obj): if not isinstance(obj, RDBSqlite): raise TypeError, "argument must be a RDBSqlite" return obj._as_parameter_ from_param = classmethod(from_param) def register(cls, gtlib): from ctypes import c_char_p, c_void_p gtlib.gt_rdb_sqlite_new.restype = c_void_p gtlib.gt_rdb_sqlite_new.argtypes = [c_char_p, c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/region_node.py000066400000000000000000000030561211610345200230000ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.extended.genome_node import GenomeNode from gt.core.gtstr import Str class RegionNode(GenomeNode): def __init__(self): pass @classmethod def create_new(cls, seqid, start, end): if start > end: raise "start > end" seq_str = Str(str(seqid)) fn = gtlib.gt_region_node_new(seq_str, start, end) n = cls.create_from_ptr(fn, True) return n def register(cls, gtlib): from ctypes import c_ulong, c_void_p gtlib.gt_region_node_new.restype = c_void_p gtlib.gt_region_node_new.argtypes = [Str, c_ulong, c_ulong] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/sequence_node.py000066400000000000000000000044361211610345200233300ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.dlload import gtlib from gt.core.gtstr import Str from gt.extended.genome_node import GenomeNode class SequenceNode(GenomeNode): def __init__(self): pass @classmethod def create_new(cls, description, sequence): seq_str = Str(str(sequence.encode("utf-8"))) fn = gtlib.gt_sequence_node_new(description, seq_str) n = cls.create_from_ptr(fn, True) return n def get_description(self): return gtlib.gt_sequence_node_get_description(self.gn) def get_sequence(self): seq = gtlib.gt_sequence_node_get_sequence(self.gn) if seq: return str(seq) else: return "" def get_sequence_length(self): return gtlib.gt_sequence_node_get_sequence_length(self.gn) def register(cls, gtlib): from ctypes import c_char_p, c_void_p, c_ulong gtlib.gt_sequence_node_new.restype = c_void_p gtlib.gt_sequence_node_new.argtypes = [c_char_p, Str] gtlib.gt_sequence_node_get_description.restype = c_char_p gtlib.gt_sequence_node_get_description.argtypes = [c_void_p] gtlib.gt_sequence_node_get_sequence.restype = c_char_p gtlib.gt_sequence_node_get_sequence.argtypes = [c_void_p] gtlib.gt_sequence_node_get_sequence_length.restype = c_ulong gtlib.gt_sequence_node_get_sequence_length.argtypes = [c_void_p] register = classmethod(register) genometools-1.5.1/gtpython/gt/extended/strand.py000066400000000000000000000016451211610345200220050ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # strandchars = ['+', '-', '.'] genometools-1.5.1/gtpython/gt/props.py000066400000000000000000000044411211610345200200520ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- class cachedproperty(object): ''' >>> class C(object): ... def __init__(self, x): ... self._x = x ... def get_x(self): ... print "getting x" ... return self._x ... ... def set_x(self, newx): ... print "setting x with %s" % newx ... self._x = newx ... def del_x(self): ... self._x = "i am deleted" ... ... x = cachedproperty(get_x, set_x, del_x) ... other_x = cachedproperty(get_x, set_x) >>> c = C(5) >>> c.x getting x 5 # cached. >>> c.x 5 >>> c.x, c.y = 6, 7 setting x with 6 # uncached. >>> c.x getting x 6 >>> c.x, c.y (6, 7) >>> c.y = 35 >>> c.x, c.y (6, 35) # ok with multiple instances. >>> d = C(4) >>> d.x getting x 4 >>> c.x 6 >>> c.other_x = 7 setting x with 7 >>> c.get_x() getting x 7 >>> del c.x >>> c.x getting x \'i am deleted\' >>> c.set_x(22) setting x with 22 # but the property cant konw about it... >>> c.x \'i am deleted\' ''' __slots__ = ("fget", "fset", "fdel", "n") def __init__(self, fget=None, fset=None, fdel=None): self.fget = fget self.fset = fset self.fdel = fdel self.n = "__" + fget.__name__ def __get__(self, o, otype=None): if o is None: return None if self.n in o.__dict__: return (o.__dict__)[self.n] result = (o.__dict__)[self.n] = self.fget(o) return result def __set__(self, o, value): if self.fset is None: raise AttributeError, "unsettable %s (with %s)" % (self.n, value) else: if o == 22: print self.n, o, value if self.n in o.__dict__: del (o.__dict__)[self.n] self.fset(o, value) def __delete__(self, o): if self.fdel is None: raise AttributeError, "undeletable %s (with %s)" % (self.n, value) else: if self.n in o.__dict__: del (o.__dict__)[self.n] self.fdel(o) if __name__ == "__main__": import doctest doctest.testmod() genometools-1.5.1/gtpython/setup.cfg000066400000000000000000000000471211610345200175420ustar00rootroot00000000000000[nosetests] with-doctest=1 verbosity=2 genometools-1.5.1/gtpython/setup.py000066400000000000000000000005541211610345200174360ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from distutils.core import setup setup(name='GenomeTools', version='0.1', description= 'Python bindings for GenomeTools', author='Sascha Steinbiss', author_email='steinbiss@zbh.uni-hamburg.de', url= 'http://www.genometools.org ', packages=['gt', 'gt.core', 'gt.annotationsketch', 'gt.extended']) genometools-1.5.1/gtpython/sketch_constructed.py000066400000000000000000000027541211610345200222000ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from gt.core import * from gt.extended import * from gt.annotationsketch import * from gt.annotationsketch.custom_track import CustomTrack from gt.core.gtrange import Range import sys if __name__ == "__main__": if len(sys.argv) != 3: sys.stderr.write("Usage: " + (sys.argv)[0] + " style_file PNG_file\n") sys.exit(1) seqid = "chromosome_21" nodes = [] # construct a gene on the forward strand with two exons gene = FeatureNode.create_new(seqid, "gene", 100, 900, "+") exon = FeatureNode.create_new(seqid, "exon", 100, 200, "+") gene.add_child(exon) intron = FeatureNode.create_new(seqid, "intron", 201, 799, "+") gene.add_child(intron) exon = FeatureNode.create_new(seqid, "exon", 800, 900, "+") gene.add_child(exon) # construct a single-exon gene on the reverse strand # (within the intron of the forward strand gene) reverse_gene = FeatureNode.create_new(seqid, "gene", 400, 600, "-") reverse_exon = FeatureNode.create_new(seqid, "exon", 400, 600, "-") reverse_gene.add_child(reverse_exon) pngfile = (sys.argv)[2] style = Style() style.load_file((sys.argv)[1]) diagram = Diagram.from_array([gene, reverse_gene], Range(1, 1000), style) layout = Layout(diagram, 600, style) height = layout.get_height() canvas = CanvasCairoFile(style, 600, height) layout.sketch(canvas) canvas.to_file(pngfile) genometools-1.5.1/gtpython/sketch_parsed.py000066400000000000000000000021631211610345200211130ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from gt.annotationsketch import * from gt.core.gtrange import Range import sys if __name__ == "__main__": if len(sys.argv) != 4: sys.stderr.write("Usage: " + (sys.argv)[0] + " Style_file PNG_file GFF3_file\n") sys.stderr.write("Create PNG representation of GFF3 annotation file.") sys.exit(1) pngfile = (sys.argv)[2] # load style file style = Style() style.load_file((sys.argv)[1]) # create feature index feature_index = FeatureIndexMemory() # add GFF3 file to index feature_index.add_gff3file((sys.argv)[3]) # create diagram for first sequence ID in feature index seqid = feature_index.get_first_seqid() range = feature_index.get_range_for_seqid(seqid) diagram = Diagram.from_index(feature_index, seqid, range, style) # create layout layout = Layout(diagram, 600, style) height = layout.get_height() # create canvas canvas = CanvasCairoFile(style, 600, height) # sketch layout on canvas layout.sketch(canvas) # write canvas to file canvas.to_file(pngfile) genometools-1.5.1/gtpython/tests/000077500000000000000000000000001211610345200170625ustar00rootroot00000000000000genometools-1.5.1/gtpython/tests/__init__.py000066400000000000000000000005551211610345200212000ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from test_alphabet import * from test_commentnode import * from test_customvisitor import * from test_encseq import * from test_featurenode import * from test_metanode import * from test_sequencenode import * from test_iterators import * from test_stream import * from test_range import * import unittest unittest.main() genometools-1.5.1/gtpython/tests/test_alphabet.py000066400000000000000000000135101211610345200222530ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright (c) 2010 Sascha Steinbiss # Copyright (c) 2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # from gt.core import * import unittest import tempfile import os import string class AlphabetTest(unittest.TestCase): def setUp(self): self.dnaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False) self.dnaseqfile.write(">seq1\nagtccagctgtcagctagcgggcccgatgatatttt") self.aaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False) self.aaseqfile.write(">seq1\nMVHFTAEEKAAVTSLWSKMNVEEAGGEALG") self.dnaal1file = tempfile.NamedTemporaryFile(mode="w", suffix=".al1", \ delete=False) self.dnaal1file.write("aA\ncC\ngG\ntTuU\nnsywrkvbdhmNSYWRKVBDHM\n") self.aaal1file = tempfile.NamedTemporaryFile(mode="w", suffix=".al1", \ delete=False) self.aaal1file.write("L\nV\nI\nF\nK\nR\nE\nD\nA\nG\nS\nT\nN\nQ\nY\nW\nP\nH\nM\nC\nXUBZO*- x\n") self.dnaseqfile.close() self.aaseqfile.close() self.dnaal1file.close() self.aaal1file.close() def tearDown(self): os.unlink(self.dnaseqfile.name) os.unlink(self.aaseqfile.name) os.unlink(self.dnaal1file.name) os.unlink(self.aaal1file.name) def dna_encodedecode(self, a_dna): # test DNA alphabet dnachars = { 0 : ('A', 'a'), 1 : ('C','c'), 2 : ('G','g'), \ 3 : ('T','t'), 254 : ('N','n')} # encoding should yield the correct code independent of case for idx, c in dnachars.items(): self.assertEqual(a_dna.encode(c[0]), idx) self.assertEqual(a_dna.decode(a_dna.encode(c[0])), c[1]) self.assertEqual(a_dna.encode(c[1]), idx) self.assertEqual(a_dna.decode(a_dna.encode(c[1])), c[1]) # invalid input should raise an exception self.assertRaises(GTError, a_dna.encode, 'Z') teststr = "agtccagctgtcagctagcgggcccgatgatatttt" # encode string 'by hand' encodedstr = [a_dna.encode(c) for c in teststr] # ensure that string is ok self.assertEqual(a_dna.decode_seq(encodedstr), teststr) def protein_encodedecode(self, a_protein): # test AA alphabet aas = "LVIFKREDAGSTNQYWPHMC" aachars = {} for idx, c in enumerate(aas): aachars[idx] = (string.upper(c), string.lower(c)) #print aachars wcs = ('X','x','U','u','B','b','Z','z','O','*','-') # encoding should yield the correct code independent of case for idx, c in aachars.items(): self.assertEqual(a_protein.encode(c[0]), idx) self.assertEqual(a_protein.decode(a_protein.encode(c[0])), c[0]) # invalid input should raise an exception self.assertRaises(GTError, a_protein.encode, '&') teststr = "MVHFTAEEKAAVTSLWSKMNVEEAGGEALG" # encode string 'by hand' encodedstr = [a_protein.encode(c) for c in teststr] # ensure that string is ok self.assertEqual(a_protein.decode_seq(encodedstr), teststr) def test_dna_newcreated(self): a_dna = Alphabet.create_dna() self.dna_encodedecode(a_dna) def test_dna_fromsequence(self): a_dna = Alphabet.create_from_sequence([self.dnaseqfile.name]) self.dna_encodedecode(a_dna) def test_dna_fromsequence_fail(self): self.assertRaises(TypeError, Alphabet.create_from_sequence, \ self.dnaseqfile.name) def test_dna_fromal1file(self): indexname = self.dnaal1file.name.rsplit('.',1)[0] a_dna = Alphabet.create_from_file(indexname) self.dna_encodedecode(a_dna) def test_dna_fromal1file_fail(self): self.assertRaises(IOError, Alphabet.create_from_file, "nonexisting") def test_aa_newcreated(self): a_protein = Alphabet.create_protein() self.protein_encodedecode(a_protein) def test_aa_isdna(self): a_protein = Alphabet.create_protein() self.assertTrue(a_protein.is_protein()) self.assertFalse(a_protein.is_dna()) def test_isdna(self): a_protein = Alphabet.create_dna() self.assertFalse(a_protein.is_protein()) self.assertTrue(a_protein.is_dna()) def test_aa_fromsequence(self): a_protein = Alphabet.create_from_sequence([self.aaseqfile.name]) self.protein_encodedecode(a_protein) def test_aa_fromsequence_fail(self): self.assertRaises(TypeError, Alphabet.create_from_sequence, \ self.aaseqfile.name) def test_aa_fromsequence_fail_2(self): self.assertRaises(IOError, Alphabet.create_from_sequence, \ ["nonexisting"]) def test_aa_fromal1file(self): indexname = self.aaal1file.name.rsplit('.',1)[0] a_protein = Alphabet.create_from_file(indexname) self.protein_encodedecode(a_protein) def test_aa_fromal1file_fail(self): self.assertRaises(IOError, Alphabet.create_from_file, "nonexisting") if __name__ == "__main__": unittest.main() genometools-1.5.1/gtpython/tests/test_commentnode.py000066400000000000000000000011301211610345200227760ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import unittest from gt import CommentNode, Str class CommentNodeTestCase(unittest.TestCase): def setUp(self): self.fn = CommentNode.create_new("testcomment") self.fn2 = CommentNode.create_new(333) def test_repr(self): self.assertEqual(str(self.fn), 'CommentNode(start=0, end=0, seqid="None")') def test_get_comment(self): self.assertEqual(self.fn.get_comment(), 'testcomment') self.assertEqual(self.fn2.get_comment(), '333') if __name__ == "__main__": unittest.main() genometools-1.5.1/gtpython/tests/test_customvisitor.py000066400000000000000000000054621211610345200234340ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import unittest from gt import FeatureNode, CommentNode, SequenceNode, RegionNode, \ CustomVisitor, MetaNode, EOFNode,FeatureNodeIteratorDepthFirst, \ GTError class TestVisitor(CustomVisitor): def __init__(self): CustomVisitor.__init__(self) self.sn = None self.rn = None self.cn = None self.en = None self.mn = None def visit_feature_node(self, fn): new_child = FeatureNode.create_new(fn.get_seqid(), "bar", 100, 1000, "+") fn.add_child(new_child) def visit_region_node(self, rn): self.rn = rn def visit_comment_node(self, cn): self.cn = cn def visit_sequence_node(self, sn): self.sn = sn def visit_meta_node(self, mn): self.mn = mn def visit_eof_node(self, en): self.en = en class ErrorTestVisitor(CustomVisitor): def __init__(self): CustomVisitor.__init__(self) def visit_feature_node(self, fn): raise GTError class CustomVisitorTestCase(unittest.TestCase): def setUp(self): self.fn = FeatureNode.create_new("foo", "gene", 100, 10000, "+") self.cn = CommentNode.create_new("comment") self.rn = RegionNode.create_new("foo", 100, 2000) self.sn = SequenceNode.create_new("foo", "AGATATAGA") self.en = EOFNode.create_new() self.mn = MetaNode.create_new("foo", "bar") self.tv = TestVisitor() self.etv = ErrorTestVisitor() def test_accept_feature_node(self): self.fn.accept(self.tv) dfi = FeatureNodeIteratorDepthFirst(self.fn) f = dfi.next() nodes = [] while f: nodes.append(f) f = dfi.next() self.assertEqual(nodes[1].get_type(), "bar") self.assertRaises(GTError, self.fn.accept, self.etv) self.cn.accept(self.etv) self.sn.accept(self.etv) self.rn.accept(self.etv) def test_accept_sequence_node(self): self.assertNotEqual(self.tv.sn, self.sn) self.sn.accept(self.tv) self.assertEqual(self.tv.sn, self.sn) def test_accept_region_node(self): self.assertNotEqual(self.tv.rn, self.rn) self.rn.accept(self.tv) self.assertEqual(self.tv.rn, self.rn) def test_accept_comment_node(self): self.assertNotEqual(self.tv.cn, self.cn) self.cn.accept(self.tv) self.assertEqual(self.tv.cn, self.cn) def test_accept_eof_node(self): self.assertNotEqual(self.tv.en, self.en) self.en.accept(self.tv) self.assertEqual(self.tv.en, self.en) def test_accept_meta_node(self): self.assertNotEqual(self.tv.mn, self.mn) self.mn.accept(self.tv) self.assertEqual(self.tv.mn, self.mn) if __name__ == "__main__": unittest.main() genometools-1.5.1/gtpython/tests/test_encseq.py000077500000000000000000000266771211610345200217760ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from gt.core.encseq import * from gt.core.error import GTError from gt.core import readmode import unittest import tempfile import sys, os import string class EncodedsequenceTest(unittest.TestCase): def setUp(self): self.dnaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False) self.dseq1 = "agtccagctgtcagctagcgggcccgatgatatttt" self.dseq2 = "gtgctgtac" self.dseq3 = "gtacagcac" self.dseq4 = "aaaatatcatcgggcccgctagctgacagctggact" self.dnaseqfile.write(">seq1\n"+self.dseq1+"\n") self.dnaseqfile.write(">seq2\n"+self.dseq2+"\n") self.aaseqfile = tempfile.NamedTemporaryFile(mode="w", delete=False) self.aaseq1 = "MVHFTAEEKAAVTSLWSKMNVEEAGGEALG" self.aaseq2 = "KMNAVE" self.aaseqfile.write(">seq1\n"+self.aaseq1+"\n") self.aaseqfile.write(">seq2\n"+self.aaseq2+"\n") self.dnaseqfile.close() self.aaseqfile.close() self.idxsuffixes = ['esq','des','ssp','sds'] def tearDown(self): os.unlink(self.dnaseqfile.name) os.unlink(self.aaseqfile.name) def create_es(self, indexname): ee = EncseqEncoder() return ee.encode([self.dnaseqfile.name], indexname) def create_es_protein(self, indexname): ee = EncseqEncoder() return ee.encode([self.aaseqfile.name], indexname) def create_mem(self): a = Alphabet.create_dna() eb = EncseqBuilder(a) eb.enable_description_support() eb.enable_multiseq_support() eb.add_string(self.dseq1, 'seq1') eb.add_string(self.dseq2, 'seq2') return eb.build() def create_mem_protein(self): a = Alphabet.create_protein() eb = EncseqBuilder(a) eb.enable_description_support() eb.enable_multiseq_support() eb.add_string(self.aaseq1, 'seq1') eb.add_string(self.aaseq2, 'seq2') return eb.build() def delete_idx(self, indexname): for suf in self.idxsuffixes: os.unlink(indexname+"."+suf) def test_create_new(self): val = self.create_es("foo") for suf in self.idxsuffixes: self.assertTrue(os.path.isfile("foo."+suf)) self.delete_idx("foo") def test_create_mapped(self): self.create_es("foo_mapped") el = EncseqLoader() es = el.load("foo_mapped") self.assertNotEqual(es, None) self.delete_idx("foo_mapped") def test_map_fail(self): el = EncseqLoader() self.assertRaises(IOError, el.load, "foo_fail") def test_dna(self): self.create_es("foo") el = EncseqLoader() es = el.load("foo") self.run_test_descriptions(es) self.run_test_get_encoded_char(es, self.dseq1, self.dseq2, self.dseq3, self.dseq4) self.run_test_num_seqs(es) self.run_test_num_files(es) self.run_test_seq_length(es) self.run_test_seq_startpos(es) self.run_test_seq_substr_encoded(es, self.dseq1, self.dseq2, self.dseq3, self.dseq4) self.run_test_seq_substr_plain(es, self.dseq1, self.dseq2, self.dseq3, self.dseq4) self.run_test_seq_substr_sequential(es, self.dseq1, self.dseq2, self.dseq3, self.dseq4) self.run_test_total_length(es) self.delete_idx("foo") es = self.create_mem() self.run_test_descriptions(es) self.run_test_get_encoded_char(es, self.dseq1, self.dseq2, self.dseq3, self.dseq4) self.run_test_num_seqs(es) self.run_test_num_files_mem(es) self.run_test_seq_length(es) self.run_test_seq_substr_encoded(es, self.dseq1, self.dseq2, self.dseq3, self.dseq4) self.run_test_seq_substr_plain(es, self.dseq1, self.dseq2, self.dseq3, self.dseq4) self.run_test_seq_substr_sequential(es, self.dseq1, self.dseq2, self.dseq3, self.dseq4) self.run_test_total_length(es) def test_protein(self): self.create_es_protein("foo") el = EncseqLoader() es = el.load("foo") self.run_test_descriptions(es) self.run_test_get_encoded_char(es, self.aaseq1, self.aaseq2, None, None) self.run_test_num_seqs(es) self.run_test_num_files(es) self.run_test_seq_startpos_protein(es) self.run_test_seq_length_protein(es) self.run_test_file_length_protein(es) self.run_test_seq_substr_encoded(es, self.aaseq1, self.aaseq2, None, None) self.run_test_seq_substr_plain(es, self.aaseq1, self.aaseq2, None, None) self.run_test_seq_substr_sequential(es, self.aaseq1, self.aaseq2, None, None) self.run_test_total_length_protein(es) self.delete_idx("foo") es = self.create_mem_protein() self.run_test_descriptions(es) self.run_test_get_encoded_char(es, self.aaseq1, self.aaseq2, None, None) self.run_test_num_seqs(es) self.run_test_num_files_mem(es) self.run_test_seq_length_protein(es) self.run_test_seq_substr_encoded(es, self.aaseq1, self.aaseq2, None, None) self.run_test_seq_substr_plain(es, self.aaseq1, self.aaseq2, None, None) self.run_test_seq_substr_sequential(es, self.aaseq1, self.aaseq2, None, None) self.run_test_total_length_protein(es) def run_test_num_seqs(self, es): self.assertEquals(es.num_of_sequences(), 2) if es.alphabet().is_dna(): es.mirror() self.assertEquals(es.num_of_sequences(), 4) es.unmirror() def run_test_num_files(self, es): self.assertEquals(es.num_of_files(), 1) if es.alphabet().is_dna(): es.mirror() self.assertEquals(es.num_of_files(), 1) es.unmirror() def run_test_num_files_mem(self, es): self.assertEquals(es.num_of_files(), 1) if es.alphabet().is_dna(): es.mirror() self.assertEquals(es.num_of_files(), 1) es.unmirror() def run_test_descriptions(self, es): self.assertRaises(GTError, es.description, 2) self.assertEquals(es.description(0), "seq1") self.assertEquals(es.description(1), "seq2") if es.alphabet().is_dna(): es.mirror() self.assertRaises(GTError, es.description, 5) self.assertEquals(es.description(2), "seq2") self.assertEquals(es.description(3), "seq1") es.unmirror() def run_test_total_length(self, es): self.assertEquals(es.total_length(), 46) if es.alphabet().is_dna(): es.mirror() self.assertEquals(es.total_length(), 93) es.unmirror() def run_test_total_length_protein(self, es): self.assertEquals(es.total_length(), 37) def run_test_get_encoded_char(self, es, seq1, seq2, seq3, seq4): a = es.alphabet() for i, c in enumerate(seq1): encchar = es.get_encoded_char(i, readmode.FORWARD) self.assertEquals(a.decode(encchar), c) for i, c in enumerate(seq2[::-1]): encchar = es.get_encoded_char(i, readmode.REVERSE) self.assertEquals(a.decode(encchar), c) if es.alphabet().is_dna(): es.mirror() for i, c in enumerate(seq3): encchar = es.get_encoded_char(47+i, readmode.FORWARD) self.assertEquals(a.decode(encchar), c) for i, c in enumerate(seq4[::-1]): encchar = es.get_encoded_char(i, readmode.REVERSE) self.assertEquals(a.decode(encchar), c) es.unmirror() def run_test_seq_startpos(self, es): self.assertEquals(es.seqstartpos(0), 0) self.assertEquals(es.seqstartpos(1), 37) def run_test_seq_startpos_protein(self, es): self.assertEquals(es.seqstartpos(0), 0) self.assertEquals(es.seqstartpos(1), 31) def run_test_seq_length(self, es): self.assertEquals(es.seqlength(0), 36) self.assertEquals(es.seqlength(1), 9) def run_test_file_length(self, es): self.assertEquals(es.effective_filelength(0), 46) def run_test_seq_length_protein(self, es): self.assertEquals(es.seqlength(0), 30) self.assertEquals(es.seqlength(1), 6) def run_test_file_length_protein(self, es): self.assertEquals(es.effective_filelength(0), 37) def run_test_seq_substr_encoded(self, es, seq1, seq2, seq3, seq4): start = 3 end = 13 res = es.extract_encoded(start, end) a = es.alphabet() for i in range(start, end): self.assertEquals(a.decode(res[i-start]), seq1[i]) start = 0 end = 5 ssp = es.seqstartpos(1) res = es.extract_encoded(ssp+start, ssp+end) for i in range(start, end): self.assertEquals(a.decode(res[i-start]), seq2[i]) if es.alphabet().is_dna(): es.mirror() start = 3 end = 8 ssp = es.seqstartpos(2) res = es.extract_encoded(ssp+start, ssp+end) for i in range(start, end): self.assertEquals(a.decode(res[i-start]), seq3[i]) start = 0 end = 5 ssp = es.seqstartpos(3) res = es.extract_encoded(ssp+start, ssp+end) for i in range(start, end): self.assertEquals(a.decode(res[i-start]), seq4[i]) es.unmirror() def run_test_seq_substr_plain(self, es, seq1, seq2, seq3, seq4): start = 3 end = 13 self.assertEquals(es.extract_decoded(start, end), seq1[start:end+1]) start = 0 end = 5 ssp = es.seqstartpos(1) self.assertEquals(es.extract_decoded(ssp+start, ssp+end), \ seq2[start:end+1]) if es.alphabet().is_dna(): es.mirror() start = 3 end = 8 ssp = es.seqstartpos(2) res = es.extract_encoded(ssp+start, ssp+end) for i in range(start, end): self.assertEquals(es.extract_decoded(ssp+start, ssp+end), \ seq3[start:end+1]) start = 0 end = 5 ssp = es.seqstartpos(3) res = es.extract_encoded(ssp+start, ssp+end) for i in range(start, end): self.assertEquals(es.extract_decoded(ssp+start, ssp+end), \ seq4[start:end+1]) es.unmirror() def run_test_seq_substr_sequential(self, es, seq1, seq2, seq3, seq4): start = 3 end = 13 er = es.create_reader_with_readmode(readmode.FORWARD, start) a = es.alphabet() for i in range(start, end): self.assertEquals(a.decode(er.next_encoded_char()), seq1[i]) start = es.seqstartpos(1) end = start + 5 er = es.create_reader_with_readmode(readmode.FORWARD, start) for i in range(start-start, end-start): self.assertEquals(a.decode(er.next_encoded_char()), seq2[i]) if es.alphabet().is_dna(): es.mirror() start = es.seqstartpos(2) end = start + 5 er = es.create_reader_with_readmode(readmode.FORWARD, start) for i in range(start-start, end-start): self.assertEquals(a.decode(er.next_encoded_char()), seq3[i]) start = es.seqstartpos(3) end = start + 5 er = es.create_reader_with_readmode(readmode.FORWARD, start) for i in range(start-start, end-start): self.assertEquals(a.decode(er.next_encoded_char()), seq4[i]) es.unmirror() if __name__ == "__main__": unittest.main() genometools-1.5.1/gtpython/tests/test_featurenode.py000066400000000000000000000120671211610345200230020ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import unittest from gt import FeatureNode, FeatureNodeIteratorDepthFirst, GenomeNode class FeatureNodeTestCase(unittest.TestCase): def setUp(self): self.fn = FeatureNode.create_new("test", "type", 100, 500, "+") def test_repr(self): self.assertEqual(str(self.fn), 'FeatureNode(start=100, end=500, seqid="test")') def test_score(self): fn = self.fn self.assert_(not fn.score_is_defined()) fn.set_score(2) self.assert_(fn.score_is_defined()) self.assertEqual(2, fn.get_score()) fn.unset_score() self.assert_(not fn.score_is_defined()) def test_type(self): fn = self.fn self.assert_(not fn.has_type("foo")) self.assert_(fn.has_type("type")) def test_strand(self): fn = self.fn self.assertEqual(fn.get_strand(), "+") def test_seqid(self): fn = self.fn self.assertEqual(fn.seqid, "test") def test_start_end(self): fn = self.fn self.assertEqual(fn.start, 100) self.assertEqual(fn.end, 500) def test_attributes(self): fn = self.fn fn.add_attribute("test", "testval") fn.add_attribute("test2", "testval2") self.assert_("test" in fn.attribs) self.assert_("test2" in fn.attribs) nattrs = 0 for (tag, val) in fn.each_attribute(): self.assertEqual(val, fn.get_attribute(tag)) nattrs += 1 self.assertEqual(nattrs, 2) class TestFeatureNodeChildren(unittest.TestCase): def setUp(self): self.fn = FeatureNode.create_new("test", "type", 100, 500, "+") self.fn2 = FeatureNode.create_new("test", "type2", 200, 300, "+") self.fn.add_child(self.fn2) def test_phase(self): fn = self.fn self.assertEqual(fn.get_phase(), 3) fn.set_phase(0) self.assertEqual(fn.get_phase(), 0) def test_fni(self): fn = self.fn fni = FeatureNodeIteratorDepthFirst(fn) num_features = 0 tfn = fni.next() while tfn: tfn = fni.next() num_features += 1 self.assertEqual(num_features, 2) fn3 = FeatureNode.create_new("test", "type3", 250, 300, "+") fn.add_child(fn3) fni = FeatureNodeIteratorDepthFirst(fn) num_features = 0 tfn = fni.next() while tfn: num_features += 1 tfn = fni.next() self.assertEqual(num_features, 3) def test_iterator(self): fn = self.fn fn3 = FeatureNode.create_new("test", "type3", 250, 300, "+") fn4 = FeatureNode.create_new("test", "type4", 250, 300, "+") fn.add_child(fn3) fn.add_child(fn4) # try object as iterator types = [] for i, f in enumerate(fn): types.append(f.type) self.assertEqual(types, ["type", "type2", "type3", "type4"], types) self.assert_(i == 3, i) # try iterator method types = [] for i, f in enumerate(fn.traverse_dfs()): types.append(f.type) self.assertEqual(types, ["type", "type2", "type3", "type4"], types) self.assert_(i == 3, i) # try callable object as iterator types = [] for i, f in enumerate(fn(method="depth_first")): types.append(f.type) self.assertEqual(types, ["type", "type2", "type3", "type4"], types) self.assert_(i == 3, i) # direct types = [] for i, f in enumerate(fn(method="direct")): types.append(f.type) self.assertEqual(types, ["type2", "type3", "type4"], types) self.assert_(i == 2, i) types = [] for i, f in enumerate(fn.traverse_direct()): types.append(f.type) self.assertEqual(types, ["type2", "type3", "type4"], types) self.assert_(i == 2, i) fn.depth_first = False types = [] for i, f in enumerate(fn): types.append(f.type) self.assertEqual(types, ["type2", "type3", "type4"], types) self.assert_(i == 2, i) class TestFeatureNodeProperties(unittest.TestCase): def setUp(self): self.fn = FeatureNode.create_new("test", "type", 100, 500, "+") def test_strand(self): fn = self.fn self.assertEqual("+", fn.strand) fn.strand = "-" self.assertEqual("-", fn.strand) def test_score(self): fn = self.fn self.assert_(not fn.score_is_defined()) fn.score = 2 self.assert_(fn.score_is_defined()) self.assertEqual(2, fn.get_score()) self.assertEqual(2, fn.score) fn.set_score(4) self.assertEqual(2, fn.score) def test_range(self): fn = self.fn self.assertEqual((100, 500), fn.range) def test_conversion(self): fn = self.fn g = GenomeNode.create_from_ptr(fn.gn, True) self.assertEqual((100, 500), g.range) f2 = FeatureNode.create_from_ptr(g.gn, True) self.assertEqual((100, 500), f2.range) if __name__ == "__main__": unittest.main() genometools-1.5.1/gtpython/tests/test_iterators.py000066400000000000000000000044651211610345200225200ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import unittest import gt import os op = os.path datadir = op.abspath(op.join(op.dirname(__file__), "..", "..", "testdata")) """ ### 1877523 gth gene 25221 26100 1 + . ID=gene12;Target=8690053 1 521 + 1877523 gth exon 25221 25310 1 + . Parent=gene12 1877523 gth five_prime_cis_splice_site 25311 25312 0.993 + . Parent=gene12 1877523 gth three_prime_cis_splice_site 25508 25509 0.439 + . Parent=gene12 1877523 gth exon 25510 25626 1 + . Parent=gene12 1877523 gth five_prime_cis_splice_site 25627 25628 0.998 + . Parent=gene12 1877523 gth three_prime_cis_splice_site 25711 25712 0.996 + . Parent=gene12 1877523 gth exon 25713 25841 1 + . Parent=gene12 1877523 gth five_prime_cis_splice_site 25842 25843 0.63 + . Parent=gene12 1877523 gth three_prime_cis_splice_site 25914 25915 0.926 + . Parent=gene12 1877523 gth exon 25916 26100 1 + . Parent=gene12 ### """ class FeatureNodeIteratorTest(unittest.TestCase): def setUp(self): fi = gt.FeatureIndexMemory() self.gff_file = op.join(datadir, "U89959_sas.gff3") fi.add_gff3file(self.gff_file) self.fi = fi self.feature = fi.get_features_for_range(25000, 26000, '1877523')[0] def test_depth_first(self): dfi = gt.FeatureNodeIteratorDepthFirst(self.feature) found = dfi.next() self.assertEqual(found.get_attribute("ID"), "gene12") self.assertEqual(found.type, "gene") found = dfi.next() self.assertEqual(found.type, 'exon') found = dfi.next() self.assertEqual(found.type, 'five_prime_cis_splice_site') found = dfi.next() found = dfi.next() self.assertEqual(found.type, 'exon') def test_direct(self): di = gt.FeatureNodeIteratorDirect(self.feature) found = di.next() types = {} while found: types[found.type] = 1 found = di.next() #self.assert_('gene' in types) self.assert_('exon' in types) self.assert_('five_prime_cis_splice_site' in types) self.assert_('three_prime_cis_splice_site' in types) self.assertEqual(found, None) if __name__ == "__main__": unittest.main() genometools-1.5.1/gtpython/tests/test_metanode.py000066400000000000000000000011221211610345200222630ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import unittest from gt import MetaNode, Str class MetaNodeTestCase(unittest.TestCase): def setUp(self): self.fn = MetaNode.create_new("test", "data") self.fn2 = MetaNode.create_new(333, 444) def test_get_directive(self): self.assertEqual(self.fn.get_directive(), 'test') self.assertEqual(self.fn2.get_directive(), '333') def test_get_data(self): self.assertEqual(self.fn.get_data(), 'data') self.assertEqual(self.fn2.get_data(), '444') if __name__ == "__main__": unittest.main() genometools-1.5.1/gtpython/tests/test_range.py000066400000000000000000000026761211610345200216020ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import unittest from gt import Range, GTError class RangeTestCase(unittest.TestCase): def test_newrng(self): rng = Range(10, 100) self.assertEqual(rng.start, 10) self.assertEqual(rng.end, 100) rng = Range(10, 10) rng = Range(0, 0) rng = Range() self.assertEqual(rng.start, 0) self.assertEqual(rng.end, 0) def test_invalidrng(self): self.assertRaises(GTError, Range, 100, 10) self.assertRaises(GTError, Range, -10, 100) self.assertRaises(GTError, Range, -10, -100) self.assertRaises(GTError, Range, 10, -100) def test_setgetrng(self): rng = Range(10, 100) # change start/end values rng.start = 20 self.assertEqual(rng.start, 20) self.assertEqual(rng.end, 100) rng.end = 200 self.assertEqual(rng.start, 20) self.assertEqual(rng.end, 200) # change start/end to invalid value def setend(rng, val): rng.end = val def setstart(rng, val): rng.start = val # 20 > 10 self.assertRaises(GTError, setend, rng, 10) self.assertEqual(rng.start, 20) self.assertEqual(rng.end, 200) # 300 > 200 self.assertRaises(GTError, setstart, rng, 300) self.assertEqual(rng.start, 20) self.assertEqual(rng.end, 200) if __name__ == "__main__": unittest.main() genometools-1.5.1/gtpython/tests/test_sequencenode.py000066400000000000000000000014011211610345200231450ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import unittest from gt import SequenceNode, Str class SequenceNodeTestCase(unittest.TestCase): def setUp(self): self.fn = SequenceNode.create_new("testdesc", "AGATATAGA") def test_repr(self): self.assertEqual(str(self.fn), 'SequenceNode(start=0, end=0, seqid="testdesc")') def test_get_sequence(self): self.assertEqual(self.fn.get_sequence(), 'AGATATAGA') def test_get_sequence_length(self): self.assertEqual(len(self.fn.get_sequence()), \ self.fn.get_sequence_length()) def test_get_description(self): self.assertEqual(self.fn.get_description(), 'testdesc') if __name__ == "__main__": unittest.main() genometools-1.5.1/gtpython/tests/test_stream.py000066400000000000000000000060141211610345200217670ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import unittest import gt import os op = os.path datadir = op.abspath(op.join(op.dirname(__file__), "..", "..", "testdata")) class StreamTest(unittest.TestCase): def setUp(self): self.gff_file = op.join(datadir, "U89959_sas.gff3") self.ins = gt.GFF3InStream(self.gff_file) def test_pull(self): add_introns_stream = gt.AddIntronsStream(self.ins) fi = gt.FeatureIndexMemory() gt.FeatureStream(add_introns_stream, fi).pull() self.assert_('1877523' in fi.get_seqids()) class TestDuplicateStream(unittest.TestCase): def setUp(self): self.gff_file = op.join(datadir, "addintrons.gff3") self.ins = gt.GFF3InStream(self.gff_file) def test_dup(self): fi = gt.FeatureIndexMemory() gt.FeatureStream(gt.DuplicateFeatureStream(self.ins, "intron", "exon"), fi).pull() f = fi.get_features_for_seqid('ctg123') dfi = gt.FeatureNodeIteratorDepthFirst(f[0]) f = dfi.next() types = set([]) while f: types.update([f.type]) f = dfi.next() self.assert_('intron' in types, types) class TestMergeStream(unittest.TestCase): def setUp(self): self.gff_file = op.join(datadir, "mergefeat.gff3") self.ins = gt.GFF3InStream(self.gff_file) def test_merge(self): fi = gt.FeatureIndexMemory() gt.FeatureStream(gt.MergeFeatureStream(self.ins), fi).pull() f = fi.get_features_for_seqid('seq1') self.assertEqual(len(f), 1) dfi = gt.FeatureNodeIteratorDirect(f[0]) sub = dfi.next() self.assertEqual(None, dfi.next()) self.assertEqual(sub.start, 1000) self.assertEqual(sub.end, 10000) class TestInterFeat(unittest.TestCase): def setUp(self): self.gff_file = op.join(datadir, "addintrons.gff3") self.ins = gt.GFF3InStream(self.gff_file) def test_inter(self): fi = gt.FeatureIndexMemory() gt.FeatureStream(gt.InterFeatureStream(self.ins, "exon", "intron"), fi).pull() f = fi.get_features_for_seqid('ctg123') dfi = gt.FeatureNodeIteratorDepthFirst(f[0]) f = dfi.next() types = set([]) while f: types.update([f.type]) f = dfi.next() self.assert_('intron' in types, types) class TestCustomExample(unittest.TestCase): def setUp(self): self.gff_file = op.join(datadir, "eden.gff3") self.ins = gt.GFF3InStream(self.gff_file) def test_inter(self): fi = gt.FeatureIndexMemory() gt.FeatureStream(gt.CustomStreamExample(self.ins), fi).pull() f = fi.get_features_for_seqid('ctg123') dfi = gt.FeatureNodeIteratorDepthFirst(f[0]) f = dfi.next() types = set([]) while f: types.update([f.type]) f = dfi.next() self.assert_('bar' in types, types) if __name__ == "__main__": unittest.main() genometools-1.5.1/gtruby/000077500000000000000000000000001211610345200153605ustar00rootroot00000000000000genometools-1.5.1/gtruby/README000066400000000000000000000012651211610345200162440ustar00rootroot00000000000000This directory contains the GenomeTools Ruby bindings. To be able to use them, you have to add the following line to your Ruby script: require 'gtruby' and make sure that this directory is added to the ruby load-path variable ($:). Either by calling ruby with the option -I or by adding this directory to the RUBYLIB environment variable. Furthermore, you have to make sure that the GenomeTools shared libraries can be be found by the dlopen(3) system call. For example, by adding the lib/ subdirectory of GenomeTools to your LD_LIBRARY_PATH environment variable. For examples on how to use these bindings, please refer to the scripts in the subdirectory testdata/gtruby/ of GenomeTools. genometools-1.5.1/gtruby/annotationsketch.rb000066400000000000000000000025071211610345200212650ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # begin require 'annotationsketch/block' require 'annotationsketch/canvas' require 'annotationsketch/custom_track' require 'annotationsketch/style' require 'annotationsketch/diagram' require 'annotationsketch/graphics' require 'annotationsketch/image_info' require 'annotationsketch/layout' require 'annotationsketch/rec_map' rescue RuntimeError # fail gracefully when AnnotationSketch symbols are not present raise unless $!.to_s.match(/can't find the symbol/) end genometools-1.5.1/gtruby/annotationsketch/000077500000000000000000000000001211610345200207345ustar00rootroot00000000000000genometools-1.5.1/gtruby/annotationsketch/block.rb000066400000000000000000000051341211610345200223560ustar00rootroot00000000000000# # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' module GT extend DL::Importable gtdlload "libgenometools" extern "GtBlock* gt_block_ref(GtBlock*)" extern "GtRange* gt_block_get_range_ptr(const GtBlock*)" extern "const char* gt_block_get_type(const GtBlock*)" extern "bool gt_block_has_only_one_fullsize_element(const GtBlock*)" extern "void gt_block_merge(GtBlock*, GtBlock*)" extern "GtBlock* gt_block_clone(GtBlock*)" extern "void gt_block_set_strand(GtBlock*, int)" extern "GtFeatureNode* gt_block_get_top_level_feature(const GtBlock*)" extern "int gt_block_get_strand(const GtBlock*)" extern "unsigned long gt_block_get_size(const GtBlock*)" extern "void gt_block_delete(GtBlock*)" STRANDCHARS = ['+', '-', '.'] class Block def initialize(ptr) @block = GT.gt_block_ref(ptr) @block.free = GT::symbol("gt_block_delete", "0P") end def get_range ptr = GT.gt_block_get_range_ptr(@block) ptr.struct!("LL", :start, :stop) (ptr[:start]..ptr[:stop]) end def has_only_one_fullsize_element GT.gt_block_has_only_one_fullsize_element(@block) end def get_type GT.gt_block_get_type(@block) end def merge(block) GT.gt_block_merge(@block, block) end def clone Block.new(GT.gt_block_clone(@block)) end def set_strand(strand) if !GT::STRANDCHARS.include?(strand) GT::gterror("Invalid strand: '#{strand}'") end GT.gt_block_set_strand(@block, GT::STRANDCHARS.index(strand)) end def get_strand GT::STRANDCHARS[GT.gt_block_get_strand(@block)] end def get_size GT::gt_block_get_size(@block) end def to_ptr @block end end end genometools-1.5.1/gtruby/annotationsketch/canvas.rb000066400000000000000000000136721211610345200225450ustar00rootroot00000000000000# # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' require 'annotationsketch/graphics' require 'core/str' module GT extend DL::Importable gtdlload "libgenometools" extern "GtCanvas* gt_canvas_cairo_file_new(GtStyle*, int, unsigned int, " + \ "unsigned int, GtImageInfo*, " + \ "GtError*)" extern "int gt_canvas_cairo_file_to_file(GtCanvasCairoFile*, const char*, " + "GtError*)" extern "int gt_canvas_cairo_file_to_stream(GtCanvasCairoFile*, GtStr*)" extern "void gt_canvas_delete(GtCanvas*)" class Canvas def initialize(*) raise(NotImplementedError, "Please call the constructor of a " + "#{self.class} implementation.") end end class CanvasCairoFileBase < Canvas def initialize(*) raise(NotImplementedError, "Please call the constructor of a " + "#{self.class} implementation.") end def to_file(filename) err = GT::Error.new() rval = GT.gt_canvas_cairo_file_to_file(@canvas, filename, err.to_ptr) if rval != 0 then GT.gterror(err) end end def to_stream() str = GT::Str.new(nil) GT.gt_canvas_cairo_file_to_stream(@canvas, str.to_ptr) str.get_mem.to_s(str.length) end def to_ptr @canvas end end class CanvasCairoFile < CanvasCairoFileBase def initialize(style, width, height, ii = nil) err = GT::Error.new if ii.nil? then @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_PNG, \ width, height, GT::NULL, \ err.to_ptr) else @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_PNG, \ width, height, ii.to_ptr, \ err.to_ptr) end if @canvas == GT::NULL or @canvas == nil then GT.gterror(err) else @canvas.free = GT::symbol("gt_canvas_delete", "0P") end end end class CanvasCairoFilePNG < CanvasCairoFileBase def initialize(style, width, height, ii = nil) err = GT::Error.new if ii.nil? then @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_PNG, \ width, height, GT::NULL, \ err.to_ptr) else @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_PNG, \ width, height, ii.to_ptr, \ err.to_ptr) end if @canvas == GT::NULL or @canvas == nil then GT.gterror(err) else @canvas.free = GT::symbol("gt_canvas_delete", "0P") end end end class CanvasCairoFilePS < CanvasCairoFileBase def initialize(style, width, height, ii = nil) err = GT::Error.new if ii.nil? then @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_PS, \ width, height, GT::NULL, \ err.to_ptr) else @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_PS, \ width, height, ii.to_ptr, \ err.to_ptr) end if @canvas == GT::NULL or @canvas == nil then GT.gterror(err) else @canvas.free = GT::symbol("gt_canvas_delete", "0P") end end end class CanvasCairoFileSVG < CanvasCairoFileBase def initialize(style, width, height, ii = nil) err = GT::Error.new if ii.nil? then @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_SVG, \ width, height, GT::NULL, \ err.to_ptr) else @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_SVG, \ width, height, ii.to_ptr, \ err.to_ptr) end if @canvas == GT::NULL or @canvas == nil then GT.gterror(err) else @canvas.free = GT::symbol("gt_canvas_delete", "0P") end end end class CanvasCairoFilePDF < CanvasCairoFileBase def initialize(style, width, height, ii = nil) err = GT::Error.new if ii.nil? then @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_PDF, \ width, height, GT::NULL, \ err.to_ptr) else @canvas = GT.gt_canvas_cairo_file_new(style.style, GT::GRAPHICS_PDF, \ width, height, ii.to_ptr, \ err.to_ptr) end if @canvas == GT::NULL or @canvas == nil then GT.gterror(err) else @canvas.free = GT::symbol("gt_canvas_delete", "0P") end end end end genometools-1.5.1/gtruby/annotationsketch/color.rb000066400000000000000000000017351211610345200224050ustar00rootroot00000000000000# # Copyright (c) 2008 Gordon Gremme # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/struct' module GT Color = struct [ "double red", "double green", "double blue", "double alpha" ] end genometools-1.5.1/gtruby/annotationsketch/custom_track.rb000066400000000000000000000060401211610345200237570ustar00rootroot00000000000000# # Copyright (c) 2008-2009 Sascha Steinbiss # Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' module GT extend DL::Importable gtdlload "libgenometools" extern "GtCustomTrack* gt_custom_track_script_wrapper_new(void*, void*, void*, void*)" class CustomTrack def initialize() @get_height = DL.callback("L") do ret = self.get_height() if ret.nil? or !ret.is_a?(Numeric) then GT::gterror("custom track get_height() method must " + \ "return a numeric value!") end ret end @get_title = DL.callback("0PP") do |ptr, str_ptr| ret = self.get_title() s = GT::Str.new(str_ptr) if ret.nil? or !ret.to_s.is_a?(String) then GT::gterror("custom track get_title() method must " + \ "return a string!") end s.append_cstr(ret) end @render = DL.callback("IPLPPP") do |g, ypos, rng, sty, err| rng.struct!("LL", :start, :end) range = (rng[:start]..rng[:end]) ret = self.render(GT::Graphics.new(g), ypos, range, \ GT::Style.new(sty), GT::Error.new(err)) if ret.nil? or !ret.is_a?(Numeric) then GT::gterror("custom track render() method must " + \ "return a numeric value!") end ret end @free = DL.callback("0") do self.free() end @ct = GT.gt_custom_track_script_wrapper_new(@render, \ @get_height, \ @get_title, \ @free) @ct.free = GT::symbol("gt_custom_track_delete", "0P") end def to_ptr @ct end end end genometools-1.5.1/gtruby/annotationsketch/custom_track_example.rb000066400000000000000000000026141211610345200254750ustar00rootroot00000000000000# # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' require 'annotationsketch/custom_track' module GT extend DL::Importable gtdlload "libgenometools" class CustomTrackExample < CustomTrack def get_height 50 end def get_title "Sample track drawn by a Ruby script" end def render(g, ypos, rng, sty, err) data = [] 120.times do data.push(rand()) end g.draw_curve_data(g.get_xmargins(), ypos, [0,0,1,0.6].pack("DDDD").to_ptr, data, 120, 0, 1, 40) 0 end end end genometools-1.5.1/gtruby/annotationsketch/diagram.rb000066400000000000000000000072201211610345200226660ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'annotationsketch/block' require 'core/array' require 'core/range' module GT extend DL::Importable gtdlload "libgenometools" extern "GtDiagram* gt_diagram_new(GtFeatureIndex*, const char*, " + \ "const GtRange*, GtStyle*, GtError*)" extern "GtDiagram* gt_diagram_new_from_array(GtArray*, " + \ "const GtRange*, GtStyle*)" extern "void gt_diagram_set_track_selector_func(GtDiagram*, void*, void*)" extern "void gt_diagram_add_custom_track(GtDiagram*, GtCustomTrack*)" extern "void gt_diagram_delete(GtDiagram*)" class Diagram attr_reader :diagram def self.from_index(feature_index, seqid, range, style) err = GT::Error.new() if range.start > range.end GT.gterror("range.start > range.end") end if feature_index.nil? then GT.gterror("feature index must not be nil!") end if seqid.nil? then GT.gterror("seqid must not be nil!") end if !style.is_a?(GT::Style) then GT.gterror("'style' parameter must be a Style object!") end diagram = GT.gt_diagram_new(feature_index, seqid, range.to_ptr, style, err) if diagram.nil? then GT::gterror(err) end return GT::Diagram.new(diagram) end def self.from_array(array, range, style) if range.start > range.end GT.gterror("range.start > range.end") end gtarr = GT::Array.create(DL.sizeof("P"), false) array.each do |i| if !i.is_a?(GT::FeatureNode) then GT::gterror("Diagram array must only contain FeatureNodes!") end gtarr.add(i) end diagram = GT.gt_diagram_new_from_array(gtarr, range.to_ptr, style) return GT::Diagram.new(diagram) end def initialize(ptr) @diagram = ptr @diagram.free = GT::symbol("gt_diagram_delete", "0P") # callback_releaser = Proc.new do # DL.remove_callback(@tsf) unless @tsf.nil # end # ObjectSpace.define_finalizer(self, callback_releaser) end def set_track_selector_func(proc) @tsf = DL.callback('0PPP') do |b_ptr, string_ptr, data_ptr| b = GT::Block.new(b_ptr) string = GT::Str.new(string_ptr) s = proc.call(b, data_ptr) if (s.nil?) then GT::gterror("Track selector callback must return a string!") else string.append_cstr(s) end end GT.gt_diagram_set_track_selector_func(@diagram, @tsf, GT::NULL) end def release_track_selector_func DL.remove_callback(@tsf) end def add_custom_track(ct) GT.gt_diagram_add_custom_track(@diagram, ct) end def to_ptr @diagram end end end genometools-1.5.1/gtruby/annotationsketch/feature_index.rb000066400000000000000000000015761211610345200241140ustar00rootroot00000000000000# # Copyright (c) 2013 Sascha Steinbiss # Copyright (c) 2013 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'extended/feature_index' genometools-1.5.1/gtruby/annotationsketch/feature_stream.rb000066400000000000000000000015771211610345200243010ustar00rootroot00000000000000# # Copyright (c) 2013 Sascha Steinbiss # Copyright (c) 2013 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'extended/feature_stream' genometools-1.5.1/gtruby/annotationsketch/graphics.rb000066400000000000000000000222621211610345200230650ustar00rootroot00000000000000# # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy.to_f, modify.to_f, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'dl/struct' require 'gthelper' module GT extend DL::Importable gtdlload "libgenometools" extern "void gt_graphics_draw_text_p(GtGraphics*, void*)" extern "void gt_graphics_draw_text_clip_p(GtGraphics*, void*)" extern "void gt_graphics_draw_text_centered_p(GtGraphics*, void*)" extern "void gt_graphics_draw_text_right_p(GtGraphics*, void*)" extern "void gt_graphics_draw_colored_text_p(GtGraphics*, void*)" extern "double gt_graphics_get_text_height(GtGraphics*)" extern "double gt_graphics_get_text_width(GtGraphics*, const char*)" extern "double gt_graphics_get_image_width(GtGraphics*)" extern "double gt_graphics_get_image_height(GtGraphics*)" extern "void gt_graphics_set_margins_p(GtGraphics*, void*)" extern "double gt_graphics_get_xmargins(GtGraphics*)" extern "double gt_graphics_get_ymargins(GtGraphics*)" extern "void gt_graphics_draw_horizontal_line_p(GtGraphics*, void*)" extern "void gt_graphics_draw_vertical_line_p(GtGraphics*, void*)" extern "void gt_graphics_draw_line_p(GtGraphics*, void*)" extern "void gt_graphics_draw_box_p(GtGraphics*, void*)" extern "void gt_graphics_draw_dashes_p(GtGraphics*, void*)" extern "void gt_graphics_draw_caret_p(GtGraphics*, void*)" extern "void gt_graphics_draw_rectangle_p(GtGraphics*, void*)" extern "void gt_graphics_draw_arrowhead_p(GtGraphics*, void*)" extern "void gt_graphics_draw_curve_data_p(GtGraphics*, void*, double*, unsigned long, unsigned long, unsigned long, unsigned long)" extern "int gt_graphics_save_to_file(const GtGraphics*, const char*, GtError*)" extern "void gt_graphics_save_to_stream(const GtGraphics*, GtStr*)" extern "void gt_graphics_delete(GtGraphics*)" extern "GtGraphics* gt_graphics_cairo_new(int, unsigned int, unsigned int)" GRAPHICS_PDF = 0 GRAPHICS_PNG = 1 GRAPHICS_PS = 2 GRAPHICS_SVG = 3 ARROW_LEFT = 0 ARROW_RIGHT = 1 ARROW_BOTH = 2 ARROW_NONE = 3 class Graphics def initialize(ptr) @g = ptr end def draw_text(x, y, text) ptr = [x.to_f, y.to_f, text].pack("DDp").to_ptr GT.gt_graphics_draw_text_p(@g, ptr) end def draw_text_centered(x, y, text) ptr = [x.to_f, y.to_f, text].pack("DDp").to_ptr GT.gt_graphics_draw_text_centered_p(@g, ptr) end def draw_text_right(x, y, text) ptr = [x.to_f, y.to_f, text].pack("DDp").to_ptr GT.gt_graphics_draw_text_right_p(@g, ptr) end def draw_colored_text(x, y, color, text) color.struct!("DDDD", :r, :g, :b, :a) params = [x.to_f, y.to_f, color[:r], color[:g], color[:b], \ color[:a], text] GT.gt_graphics_draw_colored_text_p(@g, params.pack("DDDDDDp").to_ptr) end def get_image_height GT.gt_graphics_get_image_height(@g) end def get_image_width GT.gt_graphics_get_image_width(@g) end def get_text_height GT.gt_graphics_get_text_height(@g) end def get_text_width(txt) GT.gt_graphics_get_text_width(@g, txt) end def set_margins(xmargs, ymargs) ptr = [xmargs.to_f, ymargs.to_f].pack("DD").to_ptr GT.gt_graphics_set_margins_p(@g, ptr) end def get_xmargins GT.gt_graphics_get_xmargins(@g) end def get_ymargins GT.gt_graphics_get_ymargins(@g) end def draw_line(x, y, xto, yto, color, stroke_width) color.struct!("DDDD", :r, :g, :b, :a) params = [x.to_f, y.to_f, xto.to_f, yto.to_f, color[:r], color[:g], \ color[:b], color[:a], stroke_width.to_f ] GT.gt_graphics_draw_line_p(@g, params.pack("DDDDDDDDD").to_ptr) end def draw_horizontal_line(x, y, color, width, stroke_width) color.struct!("DDDD", :r, :g, :b, :a) params = [x.to_f, y.to_f, color[:r], color[:g], color[:b], color[:a], \ width.to_f, stroke_width.to_f] GT.gt_graphics_draw_horizontal_line_p(@g, params.pack("DDDDDDDD").to_ptr) end def draw_vertical_line(x, y, color, len, stroke_width) color.struct!("DDDD", :r, :g, :b, :a) params = [x.to_f, y.to_f, color[:r], color[:g], color[:b], color[:a], \ len.to_f, stroke_width.to_f] GT.gt_graphics_draw_vertical_line_p(@g, params.pack("DDDDDDDD").to_ptr) end def draw_box(x, y, width, height, fillcolor, astatus, awidth, swidth, \ scolor, dashed) fillcolor.struct!("DDDD", :r, :g, :b, :a) scolor.struct!("DDDD", :r, :g, :b, :a) if dashed then d_int = 1 else d_int = 0 end params = [x.to_f, y.to_f, width.to_f, height.to_f, fillcolor[:r], \ fillcolor[:g], fillcolor[:b], fillcolor[:a], awidth.to_f, \ swidth.to_f, scolor[:r],scolor[:g], scolor[:b], scolor[:a], \ d_int, astatus] GT.gt_graphics_draw_box_p(@g, params.pack("DDDDDDDDDDDDDDii").to_ptr) end def draw_dashes(x, y, width, height, astatus, awidth, swidth, scolor) scolor.struct!("DDDD", :r, :g, :b, :a) params = [x.to_f, y.to_f, width.to_f, height.to_f, awidth.to_f, \ swidth.to_f, scolor[:r],scolor[:g], scolor[:b], scolor[:a], \ astatus] GT.gt_graphics_draw_dashes_p(@g, params.pack("DDDDDDDDDDi").to_ptr) end def draw_caret(x, y, width, height, astatus, awidth, swidth, scolor) scolor.struct!("DDDD", :r, :g, :b, :a) params = [x.to_f, y.to_f, width.to_f, height.to_f, awidth, swidth, \ scolor[:r],scolor[:g], scolor[:b], scolor[:a], astatus] GT.gt_graphics_draw_caret_p(@g, params.pack("DDDDDDDDDDi").to_ptr) end def draw_rectangle(x, y, filled, fcolor, stroked, scolor, swidth, \ width, height) scolor.struct!("DDDD", :r, :g, :b, :a) fcolor.struct!("DDDD", :r, :g, :b, :a) if filled then f_int = 1 else f_int = 0 end if stroked then s_int = 1 else s_int = 0 end params = [x.to_f, y.to_f, fcolor[:r], fcolor[:g], fcolor[:b], fcolor[:a],\ scolor[:r], scolor[:g], scolor[:b], scolor[:a], swidth, width, \ height, f_int.to_i, s_int.to_i ] GT.gt_graphics_draw_rectangle_p(@g, params.pack("DDDDDDDDDDDDDii").to_ptr) end def draw_arrowhead(x, y, color, status) color.struct!("DDDD", :r, :g, :b, :a) params = [x.to_f, y.to_f, color[:r], color[:g], color[:b], color[:a], \ status] GT.gt_graphics_draw_arrowhead_p(@g, params.pack("DDDDDDi").to_ptr) end def draw_curve_data(x, y, color, data, ndata, s, e, height) color.struct!("DDDD", :r, :g, :b, :a) params = [x.to_f, y.to_f, color[:r], color[:g], color[:b], color[:a]] GT.gt_graphics_draw_curve_data_p(@g, params.pack("DDDDDD").to_ptr, \ data.to_ptr, s, e, ndata, height) end def to_file(filename) err = GT::Error.new() if GT.gt_graphics_save_to_file(@g, filename, err) < 0 then GT::gterror(err) end end def to_stream str = GT::Str.new() GT.gt_graphics_save_to_stream(@g, str) str.get_mem.to_s(str.length) end def get_text_height GT.gt_graphics_get_text_height(@g) end def get_text_width(text) GT.gt_graphics_get_text_width(@g, text) end def to_ptr @g end end class GraphicsCairo < Graphics end class GraphicsCairoPDF < GraphicsCairo def initialize(width, height) @g = GT.gt_graphics_cairo_new(GT::GRAPHICS_PDF, width, height) @g.free = GT::symbol("gt_graphics_delete", "0P") end end class GraphicsCairoPNG < GraphicsCairo def initialize(width, height) @g = GT.gt_graphics_cairo_new(GT::GRAPHICS_PNG, width, height) @g.free = GT::symbol("gt_graphics_delete", "0P") end end class GraphicsCairoPS < GraphicsCairo def initialize(width, height) @g = GT.gt_graphics_cairo_new(GT::GRAPHICS_PS, width, height) @g.free = GT::symbol("gt_graphics_delete", "0P") end end class GraphicsCairoSVG < GraphicsCairo def initialize(width, height) @g = GT.gt_graphics_cairo_new(GT::GRAPHICS_SVG, width, height) @g.free = GT::symbol("gt_graphics_delete", "0P") end end end genometools-1.5.1/gtruby/annotationsketch/image_info.rb000066400000000000000000000050431211610345200233600ustar00rootroot00000000000000# # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'dl/struct' require 'gthelper' require 'extended/feature_node' require 'annotationsketch/rec_map' module GT extend DL::Importable gtdlload "libgenometools" extern "GtImageInfo* gt_image_info_new()" extern "unsigned int gt_image_info_get_height(GtImageInfo*)" extern "unsigned long gt_image_info_num_of_rec_maps(GtImageInfo*)" extern "const GtRecMap* gt_image_info_get_rec_map(GtImageInfo*, " + "unsigned long)" extern "void gt_image_info_delete(GtImageInfo*)" class ImageInfo attr_reader :image_info def initialize() @image_info = GT.gt_image_info_new() @image_info.free = GT::symbol("gt_image_info_delete", "0P") end def get_height() GT.gt_image_info_get_height(@image_info) end def num_of_rec_maps() GT.gt_image_info_num_of_rec_maps(@image_info) end def each_hotspot() if @hotspots.nil? then @hotspots = [] 0.upto(self.num_of_rec_maps()-1) do |i| rm = GT::RecMap.new(GT.gt_image_info_get_rec_map(@image_info, i)) @hotspots.push([rm.get_northwest_x.to_i, \ rm.get_northwest_y.to_i, \ rm.get_southeast_x.to_i, \ rm.get_southeast_y.to_i, \ rm.get_genome_feature]) end @hotspots.sort!{|hs1,hs2| if hs1[2]-hs1[0]+1 == hs2[2]-hs2[0]+1 then hs1[3] <=> hs2[3] else hs1[2]-hs1[0]+1 <=> hs2[2]-hs2[0]+1 end } end @hotspots.each do |hs| yield hs[0],hs[1],hs[2],hs[3],hs[4] end end def to_ptr @image_info end end end genometools-1.5.1/gtruby/annotationsketch/layout.rb000066400000000000000000000053031211610345200225770ustar00rootroot00000000000000# # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' module GT extend DL::Importable gtdlload "libgenometools" extern "GtLayout* gt_layout_new(GtDiagram*, unsigned int, GtStyle*, " + \ "GtError*)" extern "int gt_layout_get_height(GtLayout*, unsigned long*, " + \ "GtError*)" extern "int gt_layout_sketch(GtLayout*, GtCanvas*, GtError*)" extern "void gt_layout_set_track_ordering_func(GtLayout*, " + \ "void*, void*)" extern "void gt_layout_delete(GtCanvas*)" class Layout UlongParam = GT.struct [ "GtUlong val" ] def initialize(diagram, width, style) err = GT::Error.new() @layout = GT.gt_layout_new(diagram, width, style, err) if @layout.nil? then GT::gterror(err) end @layout.free = GT::symbol("gt_layout_delete", "0P") end def get_height() err = GT::Error.new() height = UlongParam.malloc had_err = GT.gt_layout_get_height(@layout, height, err) if had_err < 0 then GT::gterror(err) end return height.val end def sketch(canvas) err = GT::Error.new() had_err = GT.gt_layout_sketch(@layout, canvas, err.to_ptr) if had_err < 0 or err.is_set? then GT::gterror(err) end end def set_track_ordering_func(proc) @tof = DL.callback('ISSP') do |s1, s2, data_ptr| r = proc.call(s1, s2) if (!r.is_a?(Numeric)) then GT::gterror("Track ordering callback must return a number!") end r.to_i end GT.gt_layout_set_track_ordering_func(@layout, @tof, GT::NULL) end def release_track_ordering_func DL.remove_callback(@tof) end def to_ptr @layout end end end genometools-1.5.1/gtruby/annotationsketch/rec_map.rb000066400000000000000000000036471211610345200227010ustar00rootroot00000000000000# # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'gthelper' module GT extend DL::Importable typealias "bool", "ibool" extern "double gt_rec_map_get_northwest_x(const GtRecMap*)" extern "double gt_rec_map_get_northwest_y(const GtRecMap*)" extern "double gt_rec_map_get_southeast_x(const GtRecMap*)" extern "double gt_rec_map_get_southeast_y(const GtRecMap*)" extern "const GtFeatureNode* gt_rec_map_get_genome_feature(const GtRecMap*)" extern "bool gt_rec_map_has_omitted_children(const GtRecMap*)" class RecMap def initialize(rm) @rm = rm end def get_northwest_x GT::gt_rec_map_get_northwest_x(@rm) end def get_northwest_y GT::gt_rec_map_get_northwest_y(@rm) end def get_southeast_x GT::gt_rec_map_get_southeast_x(@rm) end def get_southeast_y GT::gt_rec_map_get_southeast_y(@rm) end def get_genome_feature #refcount only this FeatureNode! GT::FeatureNode.new(GT::gt_rec_map_get_genome_feature(@rm), true) end def has_omitted_children GT::gt_rec_map_has_omitted_children(@gn) end end end genometools-1.5.1/gtruby/annotationsketch/style.rb000066400000000000000000000130371211610345200224250ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2008-2010 Sascha Steinbiss # Copyright (c) 2007-2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'gthelper' require 'core/error' require 'annotationsketch/color' module GT extend DL::Importable gtdlload "libgenometools" STYLE_OK = 0 STYLE_NOT_SET = 1 STYLE_ERROR = 2 # looks weird, but apparently the way to pass proper pointers to external # functions DoubleArg = struct [ "double val" ] typealias "bool", "ibool" # same as above BoolArg = struct [ "bool val" ] extern "GtStyle* gt_style_new(GtError*)" extern "int gt_style_load_file(GtStyle*, const char*, GtError*)" extern "int gt_style_load_str(GtStyle*, GtStr*, GtError*)" extern "int gt_style_to_str(const GtStyle*, GtStr*, GtError*)" extern "int gt_style_get_color(GtStyle*, const char*, const char*, GtColor*, " + "GenomeNode*, GtError*)" extern "void gt_style_set_color(GtStyle*, const char*, const char*, GtColor*)" extern "int gt_style_get_str(const GtStyle*, const char*, " + "const char*, GtStr*, GtGenomeNode*, GtError*)" extern "void gt_style_set_str(GtStyle*, const char*, const char*, GtStr*)" extern "int gt_style_get_num(const GtStyle*, const char*, " + "const char*, double*, GtGenomeNode*, GtError*)" extern "void gt_style_set_num_p(GtStyle*, const char*, const char*, double*)" extern "int gt_style_get_bool(const GtStyle*, const char*, " + "const char*, bool*, GtGenomeNode*, GtError*)" extern "void gt_style_set_bool(GtStyle*, const char*, const char*, bool)" extern "void gt_style_unset(GtStyle*, const char*, const char*)" extern "void gt_style_delete(GtStyle*)" class Style attr_reader :style def initialize(s = nil) err = GT::Error.new() if s.nil? then @style = GT.gt_style_new(err.to_ptr) @style.free = GT::symbol("gt_style_delete", "0P") else @style = s end if not @style then GT.gterror(err) end end def load_file(filename) err = GT::Error.new() rval = GT.gt_style_load_file(@style, filename, err.to_ptr) if rval != 0 then GT.gterror(err) end end def load_str(str) err = GT::Error.new() str = GT::Str.new(str) rval = GT.gt_style_load_str(@style, str.to_ptr, err.to_ptr) if rval != 0 then GT.gterror(err) end end def to_str() err = GT::Error.new() str = GT::Str.new(nil) if GT.gt_style_to_str(@style, str.to_ptr, err.to_ptr) == 0 str.to_s else GT.gterror(err) end end def clone sty = GT::Style.new() str = self.to_str() sty.load_str(str) sty end def get_color(section, key, gn = GT::NULL) color = GT::Color.malloc err = GT::Error.new case GT.gt_style_get_color(@style, section, key, color, gn, err.to_ptr) when STYLE_OK then color when STYLE_NOT_SET then nil when STYLE_ERROR then GT.gterror(err) end end def set_color(section, key, color) GT.gt_style_set_color(@style, section, key, color) end def get_cstr(section, key, gn = GT::NULL) str = GT::Str.new(nil) err = GT::Error.new case GT.gt_style_get_str(@style, section, key, str, gn, err.to_ptr) when STYLE_OK then str.to_s when STYLE_NOT_SET then nil when STYLE_ERROR then GT.gterror(err) end end def set_cstr(section, key, value) str = GT::Str.new(value) GT.gt_style_set_str(@style, section, key, str) end def get_num(section, key, gn = GT::NULL) double = DoubleArg.malloc err = GT::Error.new case GT.gt_style_get_num(@style, section, key, double, gn, err.to_ptr) when STYLE_OK then double.val when STYLE_NOT_SET then nil when STYLE_ERROR then GT.gterror(err) end end def set_num(section, key, number) num = number.to_f double = DoubleArg.malloc double.val = num GT.gt_style_set_num_p(@style, section, key, double) end def get_bool(section, key, gn = GT::NULL) bool = BoolArg.malloc err = GT::Error.new case GT.gt_style_get_bool(@style, section, key, bool, gn, err.to_ptr) when STYLE_OK then bool.val when STYLE_NOT_SET then nil when STYLE_ERROR then GT.gterror(err) end end def set_bool(section, key, val) GT.gt_style_set_bool(@style, section, key, val) end def unset(section, key) GT.gt_style_unset(@style, section, key) end def to_ptr @style end end end genometools-1.5.1/gtruby/core.rb000066400000000000000000000020421211610345200166330ustar00rootroot00000000000000# # Copyright (c) 2007 Gordon Gremme # Copyright (c) 2007 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'core/allocators' require 'core/alphabet' require 'core/array' require 'core/encseq' require 'core/error' require 'core/range' require 'core/readmode' require 'core/str' require 'core/str_array' genometools-1.5.1/gtruby/core/000077500000000000000000000000001211610345200163105ustar00rootroot00000000000000genometools-1.5.1/gtruby/core/allocators.rb000066400000000000000000000017761211610345200210130ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' module GT extend DL::Importable gtdlload "libgenometools" extern "void gt_lib_init()" extern "void gt_lib_reg_atexit_func()" end genometools-1.5.1/gtruby/core/alphabet.rb000066400000000000000000000105551211610345200204230ustar00rootroot00000000000000# # Copyright (c) 2010 Sascha Steinbiss # Copyright (c) 2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'core/str' require 'core/str_array' module GT extend DL::Importable gtdlload "libgenometools" typealias "bool", "ibool" typealias "GtUchar", "unsigned char" extern "GtAlphabet* gt_alphabet_new_from_sequence(const GtStrArray*, GtError*)" extern "GtAlphabet* gt_alphabet_new_dna()" extern "GtAlphabet* gt_alphabet_new_protein()" extern "GtAlphabet* gt_alphabet_new_empty()" extern "GtAlphabet* gt_alphabet_new_from_file(const char*, GtError*)" extern "GtAlphabet* gt_alphabet_guess(const char*, unsigned long)" extern "GtAlphabet* gt_alphabet_ref(GtAlphabet*)" extern "void gt_alphabet_delete(GtAlphabet*)" extern "unsigned int gt_alphabet_num_of_chars(const GtAlphabet*)" extern "unsigned int gt_alphabet_size(const GtAlphabet*)" extern "const void* gt_alphabet_characters(const GtAlphabet*)" extern "int gt_alphabet_is_protein(const GtAlphabet*)" extern "int gt_alphabet_is_dna(const GtAlphabet*)" extern "int gt_alphabet_valid_input(const GtAlphabet*, char)" extern "GtUchar gt_alphabet_encode(const GtAlphabet*, char)" extern "char gt_alphabet_decode(const GtAlphabet*, GtUchar)" extern "GtStr* gt_alphabet_decode_seq_to_str(const GtAlphabet*, const GtUchar*, unsigned long)" class Alphabet def self.create_dna return Alphabet.new(GT.gt_alphabet_new_dna()) end def self.create_protein return Alphabet.new(GT.gt_alphabet_new_protein()) end def self.create_from_file(filename) err = Error.new aptr = GT.gt_alphabet_new_from_file(filename.to_str, err.to_ptr) if aptr == GT::NULL GT.gterror(err) else return Alphabet.new(aptr) end end def self.create_from_sequence(files) files = files.to_a if files.length == 0 then GT.gterror("list of input sequence files must be non-empty") end sa = StrArray.new files.each do |f| fn = f.to_s if (!File.exists?(fn)) GT.gterror("file not found: #{fn}") end sa.add(fn) end err = Error.new aptr = GT.gt_alphabet_new_from_sequence(sa, err) if aptr == GT::NULL GT.gterror(err) else return Alphabet.new(aptr) end end def initialize(aptr, own = true) if own then @alpha = aptr else @alpha = GT.gt_alphabet_ref(aptr) end @alpha.free = GT::symbol("gt_alphabet_delete", "0P") end def size GT.gt_alphabet_size(@alpha) end def num_of_chars GT.gt_alphabet_num_of_chars(@alpha) end def valid_input(char) GT.gt_alphabet_valid_input(@alpha, char) != 0 end def is_dna? GT.gt_alphabet_is_dna(@alpha) != 0 end def is_protein? GT.gt_alphabet_is_protein(@alpha) != 0 end def characters ptr = GT.gt_alphabet_characters(@alpha) ptr.to_a('C', self.num_of_chars).collect{|c| c.chr} end def encode(char) if !self.valid_input(char) then GT.gterror("#{char} is not a valid input character!") end return GT.gt_alphabet_encode(@alpha, char) end def decode(char) return GT.gt_alphabet_decode(@alpha, char).chr end def decode_seq(arr) strptr = GT.gt_alphabet_decode_seq_to_str(@alpha, arr.pack('C*'), \ arr.length) Str.new(strptr).to_s end def to_ptr @alpha end end end genometools-1.5.1/gtruby/core/array.rb000066400000000000000000000034371211610345200177620ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' module GT extend DL::Importable gtdlload "libgenometools" typealias "size_t", "unsigned long" extern "GtArray* gt_array_new(size_t)" extern "void* gt_array_get(const GtArray*, unsigned long)" extern "void gt_array_add_ptr(GtArray*, void*)" extern "unsigned long gt_array_size(const GtArray*)" extern "void gt_array_delete(GtArray*)" class Array def self.create(size = nil, own = true) if size.nil? then size = DL::sizeof("P") end return GT::Array.new(GT.gt_array_new(size), own) end def initialize(array_ptr, own = false) @array = array_ptr if own then @array.free = GT::symbol("gt_array_delete", "0P") end end def get(idx) GT.gt_array_get(@array, idx).ptr end def add(val) GT.gt_array_add_ptr(@array, val.to_ptr) end def size GT.gt_array_size(@array) end def to_ptr @array end end end genometools-1.5.1/gtruby/core/encseq.rb000066400000000000000000000501721211610345200201200ustar00rootroot00000000000000# # Copyright (c) 2010 Sascha Steinbiss # Copyright (c) 2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'core/alphabet' require 'core/error' require 'core/readmode' require 'core/str' require 'dl/struct' require 'dl' module GT extend DL::Importable gtdlload "libgenometools" extern "GtEncseqEncoder* gt_encseq_encoder_new()" extern "int gt_encseq_encoder_use_representation(GtEncseqEncoder*, GtStr*, GtError*)" extern "int gt_encseq_encoder_use_symbolmap_file(GtEncseqEncoder*, GtStr*, GtError*)" extern "void gt_encseq_encoder_enable_description_support(GtEncseqEncoder*)" extern "void gt_encseq_encoder_disable_description_support(GtEncseqEncoder*)" extern "void gt_encseq_encoder_enable_multiseq_support(GtEncseqEncoder*)" extern "void gt_encseq_encoder_disable_multiseq_support(GtEncseqEncoder*)" extern "void gt_encseq_encoder_create_des_tab(GtEncseqEncoder*)" extern "void gt_encseq_encoder_do_not_create_des_tab(GtEncseqEncoder*)" extern "void gt_encseq_encoder_create_ssp_tab(GtEncseqEncoder*)" extern "void gt_encseq_encoder_do_not_create_ssp_tab(GtEncseqEncoder*)" extern "void gt_encseq_encoder_create_sds_tab(GtEncseqEncoder*)" extern "void gt_encseq_encoder_do_not_create_sds_tab(GtEncseqEncoder*)" extern "void gt_encseq_encoder_set_input_dna(GtEncseqEncoder*)" extern "void gt_encseq_encoder_set_input_protein(GtEncseqEncoder*)" extern "int gt_encseq_encoder_encode(GtEncseqEncoder*, GtStrArray*, const char*, GtError*)" extern "void gt_encseq_encoder_delete(GtEncseqEncoder*)" extern "GtEncseqLoader* gt_encseq_loader_new()" extern "void gt_encseq_loader_require_description_support(GtEncseqLoader*)" extern "void gt_encseq_loader_drop_description_support(GtEncseqLoader*)" extern "void gt_encseq_loader_require_multiseq_support(GtEncseqLoader*)" extern "void gt_encseq_loader_drop_multiseq_support(GtEncseqLoader*)" extern "void gt_encseq_loader_require_des_tab(GtEncseqLoader*)" extern "void gt_encseq_loader_do_not_require_des_tab(GtEncseqLoader*)" extern "void gt_encseq_loader_require_ssp_tab(GtEncseqLoader*)" extern "void gt_encseq_loader_do_not_require_ssp_tab(GtEncseqLoader*)" extern "void gt_encseq_loader_require_sds_tab(GtEncseqLoader*)" extern "void gt_encseq_loader_do_not_require_sds_tab(GtEncseqLoader*)" extern "GtEncseq* gt_encseq_loader_load(GtEncseqLoader*, const char*, GtError*)" extern "void gt_encseq_loader_delete(GtEncseqLoader*)" extern "GtEncseqBuilder* gt_encseq_builder_new(GtAlphabet*)" extern "void gt_encseq_builder_enable_description_support(GtEncseqBuilder*)" extern "void gt_encseq_builder_disable_description_support(GtEncseqBuilder*)" extern "void gt_encseq_builder_enable_multiseq_support(GtEncseqBuilder*)" extern "void gt_encseq_builder_disable_multiseq_support(GtEncseqBuilder*)" extern "void gt_encseq_builder_create_des_tab(GtEncseqBuilder*)" extern "void gt_encseq_builder_do_not_create_des_tab(GtEncseqBuilder*)" extern "void gt_encseq_builder_create_ssp_tab(GtEncseqBuilder*)" extern "void gt_encseq_builder_do_not_create_ssp_tab(GtEncseqBuilder*)" extern "void gt_encseq_builder_create_sds_tab(GtEncseqBuilder*)" extern "void gt_encseq_builder_do_not_create_sds_tab(GtEncseqBuilder*)" extern "void gt_encseq_builder_add_cstr(GtEncseqBuilder*,const char*, unsigned long, const char*)" extern "void gt_encseq_builder_add_encoded(GtEncseqBuilder*, const GtUchar*, unsigned long, const char*)" extern "GtEncseq* gt_encseq_builder_build(GtEncseqBuilder*, GtError*)" extern "void gt_encseq_builder_reset(GtEncseqBuilder*)" extern "void gt_encseq_builder_delete(GtEncseqBuilder*)" typealias "GtUchar", "unsigned char" typealias "GtUlong", "unsigned long" typealias "GtReadmode", "int" extern "void gt_encseq_total_length_p(const GtEncseq*, unsigned long*)" extern "void gt_encseq_num_of_sequences_p(const GtEncseq*, unsigned long*)" extern "void gt_encseq_num_of_files_p(const GtEncseq*, unsigned long*)" extern "GtUchar gt_encseq_get_encoded_char_p(const GtEncseq*, unsigned long*, GtReadmode)" extern "char gt_encseq_get_decoded_char_p(const GtEncseq*, unsigned long*, GtReadmode)" extern "void gt_encseq_extract_encoded_p(const GtEncseq*, GtUchar*, GtRange*)" extern "void gt_encseq_extract_decoded_p(const GtEncseq*, void*, GtRange*)" extern "void gt_encseq_seqlength_p(const GtEncseq*, unsigned long*, unsigned long*)" extern "void gt_encseq_seqnum_p(const GtEncseq*, unsigned long*, unsigned long*)" extern "void gt_encseq_filenum_p(const GtEncseq*, unsigned long*, unsigned long*)" extern "void gt_encseq_seqstartpos_p(const GtEncseq *, unsigned long*, unsigned long*)" extern "void gt_encseq_filestartpos_p(const GtEncseq *, unsigned long*, unsigned long*)" extern "void* gt_encseq_description_p(const GtEncseq*, unsigned long*, unsigned long*)" extern "void gt_encseq_effective_filelength_p(const GtEncseq*, void*, unsigned long*)" extern "GtEncseqReader* gt_encseq_create_reader_with_readmode_p(const GtEncseq*, GtReadmode, unsigned long*)" extern "const GtStrArray* gt_encseq_filenames(const GtEncseq*)" extern "GtAlphabet* gt_encseq_alphabet(const GtEncseq*)" extern "int gt_encseq_mirror(GtEncseq*, GtError*)" extern "void gt_encseq_unmirror(GtEncseq*)" extern "int gt_encseq_is_mirrored(GtEncseq*)" extern "void gt_encseq_delete(GtEncseq*)" extern "GtUchar gt_encseq_reader_next_encoded_char(GtEncseqReader*)" extern "char gt_encseq_reader_next_decoded_char(GtEncseqReader*)" extern "void gt_encseq_reader_delete(GtEncseqReader*)" class EncseqEncoder def initialize(eenc = nil, own = true) if eenc.nil? then @eenc = GT.gt_encseq_encoder_new() else @eenc = eenc end if own then @eenc.free = GT::symbol("gt_encseq_encoder_delete", "0P") end end def use_representation(sat) strsat = Str.new(sat) err = Error.new if (GT.gt_encseq_encoder_use_representation(@eenc, strsat, err) != 0) GT.gterror(err) end end def use_symbolmap_file(smap) strsmap = Str.new(smap) err = Error.new if (GT.gt_encseq_encoder_use_symbolmap_file(@eenc, strsmap, err) != 0) GT.gterror(err) end end def enable_description_support GT.gt_encseq_encoder_enable_description_support(@eenc) end def disable_description_support GT.gt_encseq_encoder_disable_description_support(@eenc) end def enable_multiseq_support GT.gt_encseq_encoder_enable_multiseq_support(@eenc) end def disable_multiseq_support GT.gt_encseq_encoder_disable_multiseq_support(@eenc) end def create_des_tab GT.gt_encseq_encoder_create_des_tab(@eenc) end def do_not_create_des_tab GT.gt_encseq_encoder_do_not_create_des_tab(@eenc) end def create_ssp_tab GT.gt_encseq_encoder_create_ssp_tab(@eenc) end def do_not_create_ssp_tab GT.gt_encseq_encoder_do_not_create_ssp_tab(@eenc) end def create_sds_tab GT.gt_encseq_encoder_create_sds_tab(@eenc) end def do_not_create_sds_tab GT.gt_encseq_encoder_do_not_create_sds_tab(@eenc) end def set_input_dna GT.gt_encseq_encoder_set_input_dna(@eenc) end def set_input_protein GT.gt_encseq_encoder_set_input_protein(@eenc) end def encode(files, indexname) files = files.to_a if files.length == 0 then GT.gterror("list of input sequence files must be non-empty") end sa = StrArray.new files.each do |f| fn = f.to_s if (!File.exists?(fn)) GT.gterror("file not found: #{fn}") end sa.add(fn) end err = Error.new rval = GT.gt_encseq_encoder_encode(@eenc, sa.to_ptr, indexname.to_s, \ err.to_ptr) if rval != 0 then GT.gterror(err) end end def to_ptr @eenc end end class EncseqLoader def initialize(eldr = nil, own = true) if eldr.nil? then @eldr = GT.gt_encseq_loader_new() else @eldr = eldr end if own then @eldr.free = GT::symbol("gt_encseq_loader_delete", "0P") end @destab = true @ssptab = true @sdstab = true end def require_description_support @destab = true @sdstab = true GT.gt_encseq_loader_require_description_support(@eldr) end def drop_description_support @destab = false @sdstab = false GT.gt_encseq_loader_drop_description_support(@eldr) end def require_multiseq_support @ssptab = true GT.gt_encseq_loader_require_multiseq_support(@eldr) end def drop_multiseq_support @ssptab = false GT.gt_encseq_loader_drop_multiseq_support(@eldr) end def require_des_tab @destab = true GT.gt_encseq_loader_require_des_tab(@eldr) end def do_not_require_des_tab @destab = false GT.gt_encseq_loader_do_not_require_des_tab(@eldr) end def require_ssp_tab @ssptab = true GT.gt_encseq_loader_require_ssp_tab(@eldr) end def do_not_require_ssp_tab @ssptab = false GT.gt_encseq_loader_do_not_require_ssp_tab(@eldr) end def require_sds_tab @sdstab = true GT.gt_encseq_loader_require_sds_tab(@eldr) end def do_not_require_sds_tab @sdstab = false GT.gt_encseq_loader_do_not_require_sds_tab(@eldr) end def enable_range_iterator GT.gt_encseq_loader_enable_range_iterator(@eldr) end def disable_range_iterator GT.gt_encseq_loader_disable_range_iterator(@eldr) end def load(indexname) if !File.exists?("#{indexname}.esq") then GT.gterror("file not found: #{indexname}.esq") end if @destab and !File.exists?("#{indexname}.des") then GT.gterror("file not found: #{indexname}.des") end # not required in every case (equallength seqs) #if @ssptab and !File.exists?("#{indexname}.ssp") then # GT.gterror("file not found: #{indexname}.ssp") #end if @sdstab and !File.exists?("#{indexname}.sds") then GT.gterror("file not found: #{indexname}.sds") end err = Error.new rval = GT.gt_encseq_loader_load(@eldr, indexname.to_s, err.to_ptr) if rval == GT::NULL then GT.gterror(err) end Encseq.new(rval, true) end def to_ptr @eldr end end class EncseqBuilder def self.create(alphabet) if !alphabet.is_a?(Alphabet) then GT.gterror("argument must be an Alphabet") end EncseqBuilder.new(GT.gt_encseq_builder_new(alphabet.to_ptr)) end def initialize(ebld, own = true) @ebld = ebld if own then @ebld.free = GT::symbol("gt_encseq_builder_delete", "0P") end end def enable_description_support GT.gt_encseq_builder_enable_description_support(@ebld) end def disable_description_support GT.gt_encseq_builder_disable_description_support(@ebld) end def enable_multiseq_support GT.gt_encseq_builder_enable_multiseq_support(@ebld) end def disable_multiseq_support GT.gt_encseq_builder_disable_multiseq_support(@ebld) end def create_des_tab GT.gt_encseq_builder_create_des_tab(@ebld) end def do_not_create_des_tab GT.gt_encseq_builder_do_not_create_des_tab(@ebld) end def create_ssp_tab GT.gt_encseq_builder_create_ssp_tab(@ebld) end def do_not_create_ssp_tab GT.gt_encseq_builder_do_not_create_ssp_tab(@ebld) end def create_sds_tab GT.gt_encseq_builder_create_sds_tab(@ebld) end def do_not_create_sds_tab GT.gt_encseq_builder_do_not_create_sds_tab(@ebld) end def add_string(string, desc = '') str = string.to_s GT.gt_encseq_builder_add_cstr(@ebld, str, str.length, desc) end def build err = Error.new rval = GT.gt_encseq_builder_build(@ebld, err.to_ptr) if rval == GT::NULL then GT.gterror(err) end Encseq.new(rval, true) end def to_ptr @ebld end end UlongParam = struct [ "GtUlong val" ] SeqInfo = struct [ "GtUlong startpos", "GtUlong length" ] class Encseq attr_reader :num_of_sequences, :num_of_files, :total_length def initialize(encseq, own = true) @encseq = encseq @num_of_sequences = self._num_of_sequences @num_of_files = self._num_of_files @total_length = self._total_length if own then @encseq.free = GT::symbol("gt_encseq_delete", "0P") end end def to_ptr @encseq end def _num_of_sequences n = DL::malloc(GT::NATIVEULONGSIZE) GT.gt_encseq_num_of_sequences_p(@encseq, n) return n[0, n.size].unpack("L!")[0] end def _num_of_files n = DL::malloc(GT::NATIVEULONGSIZE) GT.gt_encseq_num_of_files_p(@encseq, n) return n[0, n.size].unpack("L!")[0] end def description(num) num = num.to_i if num >= @num_of_sequences then GT.gterror("invalid sequence number #{num}") end len = DL::malloc(GT::NATIVEULONGSIZE) n = [num].pack("L!") charptr = GT.gt_encseq_description_p(@encseq, len, n) lval = len[0, len.size].unpack("L!")[0] if lval > 0 and charptr != GT::NULL then charptr.to_s(lval) else "" end end def get_encoded_char(pos, readmode = GT::READMODE_FORWARD) if readmode < 0 or readmode > 3 then GT.gterror("invalid readmode!") end p = [pos.to_i].pack("L!") return GT.gt_encseq_get_encoded_char_p(@encseq, p, readmode) end def get_decoded_char(pos, readmode = GT::READMODE_FORWARD) if readmode < 0 or readmode > 3 then GT.gterror("invalid readmode!") end p = [pos.to_i].pack("L!") return GT.gt_encseq_get_decoded_char_p(@encseq, p, readmode) end def _total_length n = DL::malloc(GT::NATIVEULONGSIZE) GT.gt_encseq_total_length_p(@encseq, n) return n[0, n.size].unpack("L!")[0] end def alphabet aptr = GT.gt_encseq_alphabet(@encseq) if aptr == GT::NULL then nil else Alphabet.new(aptr, false) end end def seqlength(num) if num >= @num_of_sequences then GT.gterror("invalid sequence number #{num}") end n = [num.to_i].pack("L!") l = DL::malloc(GT::NATIVEULONGSIZE) GT.gt_encseq_seqlength_p(@encseq, n, l) return l[0, l.size].unpack("L!")[0] end def effective_filelength(num) if num >= @num_of_files then GT.gterror("invalid file number #{num}") end n = UlongParam.malloc n.val = num.to_i # 64-bit size hardcoded res = DL::malloc(8) GT.gt_encseq_effective_filelength_p(@encseq, res, n) # 64-bit size hardcoded res[0, 8].unpack("Q")[0] end def seqstartpos(num) if num >= @num_of_sequences then GT.gterror("invalid sequence number #{num}") end n = [num.to_i].pack("L!") l = DL::malloc(GT::NATIVEULONGSIZE) GT.gt_encseq_seqstartpos_p(@encseq, n, l) return l[0, l.size].unpack("L!")[0] end def filestartpos(num) if num >= @num_of_files then GT.gterror("invalid file number #{num}") end n = [num.to_i].pack("L!") l = DL::malloc(GT::NATIVEULONGSIZE) GT.gt_encseq_filestartpos_p(@encseq, n, l) return l[0, l.size].unpack("L!")[0] end def create_reader_with_readmode(readmode, startpos) if readmode < 0 or readmode > 3 then GT.gterror("invalid readmode!") end if startpos < 0 or startpos >= @total_length then gterror("invalid start position: #{startpos} " + \ "(allowed: 0-#{total_length-1})") end p = [startpos.to_i].pack("L!") er_ptr = GT.gt_encseq_create_reader_with_readmode_p(@encseq, readmode, p) return EncseqReader.new(er_ptr) end def extract_encoded(start, stop) if start < 0 or stop >= @total_length then GT.gterror("invalid coordinates: #{start}-#{stop} " + \ "(allowed: 0-#{@total_length-1})") end buf = DL.malloc(DL::sizeof('C') * (stop-start+1)) r = GT::Range.new(start, stop) GT.gt_encseq_extract_encoded_p(@encseq, buf, r) buf.to_a('C') end def extract_decoded(start, stop) if start < 0 or stop >= @total_length then GT.gterror("invalid coordinates: #{start}-#{stop} " + \ "(allowed: 0-#{@total_length-1})") end buf = DL.malloc(DL::sizeof('C') * (stop-start+1)) r = GT::Range.new(start, stop) GT.gt_encseq_extract_decoded_p(@encseq, buf, r) buf.to_s(stop-start+1) end def mirrored? if GT.gt_encseq_is_mirrored(@encseq) == 1 then true else false end end def mirror if self.mirrored? then GT.gterror("encoded sequence is already mirrored") end err = Error.new rval = GT.gt_encseq_mirror(@encseq, err.to_ptr) if rval < 0 then GT.gterror(err) end @num_of_sequences = self._num_of_sequences @total_length = self._total_length end def unmirror if !self.mirrored? then GT.gterror("encoded sequence is not mirrored") end GT.gt_encseq_unmirror(@encseq) @num_of_sequences = self._num_of_sequences @total_length = self._total_length end def seqnum(pos) if pos < 0 or pos >= @total_length then GT.gterror("invalid coordinates: #{start}-#{stop} " + \ "(allowed: 0-#{@total_length-1})") end n = [pos.to_i].pack("L!") l = DL::malloc(GT::NATIVEULONGSIZE) GT.gt_encseq_seqnum_p(@encseq, l, n) return l[0, l.size].unpack("L!")[0] end def filenum(pos) if pos < 0 or pos >= @total_length then GT.gterror("invalid coordinates: #{start}-#{stop} " + \ "(allowed: 0-#{@total_length-1})") end n = [pos.to_i].pack("L!") l = DL::malloc(GT::NATIVEULONGSIZE) GT.gt_encseq_filenum_p(@encseq, l, n) return l[0, l.size].unpack("L!")[0] end def filenames sa = GT::StrArray.new(GT.gt_encseq_filenames(@encseq), false) sa.to_a end end class EncseqReader def initialize(er, own = true) @er = er if own then @er.free = GT::symbol("gt_encseq_reader_delete", "0P") end end def next_encoded_char return GT.gt_encseq_reader_next_encoded_char(@er) end def next_decoded_char return GT.gt_encseq_reader_next_decoded_char(@er) end def to_ptr @er end end end genometools-1.5.1/gtruby/core/error.rb000066400000000000000000000033601211610345200177700ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' module GT extend DL::Importable gtdlload "libgenometools" extern "GtError* gt_error_new()" extern "const char* gt_error_get(const GtError*)" extern "ibool gt_error_is_set(const GtError*)" extern "const char* gt_error_get(const GtError*)" extern "void gt_error_set_nonvariadic(GtError*, const char*)" extern "void gt_error_unset(GtError*)" extern "void gt_error_delete(GtError*)" class Error def initialize(e = nil) if e.nil? then @error = GT.gt_error_new() @error.free = GT::symbol("gt_error_delete", "0P") else @error = e end end def get GT.gt_error_get(@error) end def set(str) GT.gt_error_set_nonvariadic(@error, str.to_s) end def is_set? GT.gt_error_is_set(@error) end def unset GT.gt_error_unset(@error) end def to_ptr @error end end end genometools-1.5.1/gtruby/core/range.rb000066400000000000000000000033351211610345200177350ustar00rootroot00000000000000# # Copyright (c) 2007 Gordon Gremme # Copyright (c) 2007 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # module GT class Range def initialize(start, stop) set(start, stop) end def set(start, stop) if start.nil? or stop.nil? or start > stop or start < 0 or stop < 0 then GT.gterror("range error: start > end!") end @start = start # 'end' is a reserved token in Ruby and cannot be used as an identifier @stop = stop end def start @start end def start=(val) if val > @stop or not val >= 0 then GT.gterror("Invalid range start component: %d" % val) end @start = val end def Range.malloc Range.new() end def end @stop end def end=(val) if val < @start or not val >= 0 then GT.gterror("Invalid range end component: %d" % val) end @stop = val end def to_ptr (@mem = [@start, @stop].pack("L_L_")).to_ptr end end end genometools-1.5.1/gtruby/core/readmode.rb000066400000000000000000000017131211610345200204170ustar00rootroot00000000000000# # Copyright (c) 2010 Sascha Steinbiss # Copyright (c) 2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # module GT READMODE_FORWARD = 0 READMODE_REVERSE = 1 READMODE_COMPL = 2 READMODE_REVCOMPL = 3 end genometools-1.5.1/gtruby/core/str.rb000066400000000000000000000042401211610345200174450ustar00rootroot00000000000000# # Copyright (c) 2008 Gordon Gremme # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' module GT extend DL::Importable gtdlload "libgenometools" extern "GtStr* gt_str_new()" extern "GtStr* gt_str_new_cstr(const char*)" extern "void* gt_str_get_mem(const GtStr*)" extern "void gt_str_append_str(GtStr*, const GtStr*)" extern "void gt_str_append_cstr(GtStr*, const char*)" # we declare the return value as const char* instead of char*, because # otherwise dl/import wrongly assumes that it has responsibility for the # returned memory region (which leads to a double free()) extern "const char* gt_str_get(const GtStr*)" extern "unsigned long gt_str_length(const GtStr*)" extern "void gt_str_delete(GtStr*)" class Str def initialize(cstr) if cstr.is_a?(String) then @str = GT.gt_str_new_cstr(cstr) @str.free = GT::symbol("gt_str_delete", "0P") elsif cstr.is_a?(DL::PtrData) then @str = cstr else @str = GT.gt_str_new() @str.free = GT::symbol("gt_str_delete", "0P") end end def append_str(str) GT.gt_str_append_str(@str, str) end def append_cstr(cstr) GT.gt_str_append_cstr(@str, cstr) end def to_s GT.gt_str_get(@str) end def get_mem GT.gt_str_get_mem(@str) end def to_ptr @str end def length GT.gt_str_length(@str) end end end genometools-1.5.1/gtruby/core/str_array.rb000066400000000000000000000035761211610345200206560ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' module GT extend DL::Importable gtdlload "libgenometools" extern "GtStrArray* gt_str_array_new()" extern "void gt_str_array_add_cstr(GtStrArray*, const char*)" extern "const char* gt_str_array_get(const GtStrArray*, unsigned long)" extern "unsigned long gt_str_array_size(const GtStrArray*)" extern "void gt_str_array_delete(GtStrArray*)" class StrArray attr_reader :str_array def initialize(str_array_ptr = GT.gt_str_array_new(), own = true) @str_array = str_array_ptr if own != false then @str_array.free = GT::symbol("gt_str_array_delete", "0P") end end def add_list(list) list.each { |cstr| GT.gt_str_array_add_cstr(@str_array, cstr.to_s) } end def add(string) GT.gt_str_array_add_cstr(@str_array, string.to_s) end def to_a strings = [] 1.upto(GT.gt_str_array_size(@str_array)) do |i| strings.push(GT.gt_str_array_get(@str_array, i-1)) end strings end def to_ptr @str_array end end end genometools-1.5.1/gtruby/extended.rb000066400000000000000000000025751211610345200175160ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'extended/add_introns_stream' require 'extended/anno_db' require 'extended/comment_node' require 'extended/custom_stream' require 'extended/custom_visitor' require 'extended/eof_node' require 'extended/feature_index' require 'extended/feature_node' require 'extended/feature_stream' require 'extended/gff3_in_stream' require 'extended/gff3_out_stream' require 'extended/gff3_visitor' require 'extended/meta_node' require 'extended/rdb' require 'extended/region_node' require 'extended/sequence_node' require 'extended/type_checker' genometools-1.5.1/gtruby/extended/000077500000000000000000000000001211610345200171605ustar00rootroot00000000000000genometools-1.5.1/gtruby/extended/add_introns_stream.rb000066400000000000000000000023521211610345200233660ustar00rootroot00000000000000# # Copyright (c) 2008 Gordon Gremme # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'extended/genome_stream' module GT extend DL::Importable gtdlload "libgenometools" extern "GtNodeStream* gt_add_introns_stream_new(GtNodeStream*)" class AddIntronsStream < GenomeStream def initialize(in_stream) @genome_stream = GT.gt_add_introns_stream_new(in_stream) @genome_stream.free = GT::symbol("gt_node_stream_delete", "0P") end end end genometools-1.5.1/gtruby/extended/anno_db.rb000066400000000000000000000040101211610345200211000ustar00rootroot00000000000000# # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'extended/feature_index' module GT extend DL::Importable gtdlload "libgenometools" extern "GtAnnoDBSchema* gt_anno_db_gfflike_new()" extern "GtFeatureIndex* gt_anno_db_schema_get_feature_index(GtAnnoDBSchema*, GtRDB*, GtError*)" extern "void gt_anno_db_schema_delete(GtAnnoDBSchema*) " class AnnoDBSchema def initialize(*) raise(NotImplementedError, "Please call the constructor of a " + "#{self.class} implementation.") end def to_ptr @adb end def get_feature_index(rdb) err = GT::Error.new() fi = GT.gt_anno_db_schema_get_feature_index(@adb, rdb.to_ptr, err) if fi.nil? then GT::gterror(err) end GT::FeatureIndexFromPtr.new(fi) end end class AnnoDBGFFlike < AnnoDBSchema def initialize() err = GT::Error.new() @adb = GT.gt_anno_db_gfflike_new() if @adb.nil? then GT::gterror(err) end @adb.free = GT::symbol("gt_anno_db_schema_delete", "0P") end end end genometools-1.5.1/gtruby/extended/comment_node.rb000066400000000000000000000026311211610345200221560ustar00rootroot00000000000000# # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' module GT extend DL::Importable gtdlload "libgenometools" extern "GtCommentNode* gt_comment_node_new(const char*)" extern "const char* gt_comment_node_get_comment(const GtCommentNode*)" class CommentNode < GenomeNode def self.create(comment) newfn = GT.gt_comment_node_new(comment.to_s) return GT::CommentNode.new(newfn, true) end def initialize(gn, newref=false) super(gn, newref) end def get_comment return GT.gt_comment_node_get_comment(@genome_node) end end end genometools-1.5.1/gtruby/extended/custom_stream.rb000066400000000000000000000035641211610345200224020ustar00rootroot00000000000000# # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'gthelper' require 'extended/genome_stream' require 'dl/struct' module GT extend DL::Importable gtdlload "libgenometools" extern "GtNodeStream* gt_script_wrapper_stream_new(void*, void*)" class CustomStream < GenomeStream def initialize() if !public_methods.include?("next") then GT::gterror "#{self.class} must implement 'next' method" end @next_cb = DL.callback("IPP") do |gn_ptr, err_ptr| rval = 0 begin node = self.next gn_ptr.struct!("P", :val) if !node.nil? then GT.gt_genome_node_ref(node) gn_ptr[:val] = node.to_ptr else gn_ptr[:val] = nil end rescue => errmsg Error.new(err_ptr).set(errmsg) rval = -1 end rval end @genome_stream = GT.gt_script_wrapper_stream_new(@next_cb, nil) @genome_stream.free = GT::symbol("gt_node_stream_delete", "0P") end def to_ptr @genome_stream end end end genometools-1.5.1/gtruby/extended/custom_stream_example.rb000066400000000000000000000023351211610345200241100ustar00rootroot00000000000000# # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'extended/custom_stream' require 'extended/custom_visitor_example' module GT class CustomStreamExample < CustomStream def initialize(instream) super() @instream = instream @visitor = CustomVisitorExample.new end def next node = @instream.next_tree if node then node.accept(@visitor) end node end end end genometools-1.5.1/gtruby/extended/custom_visitor.rb000066400000000000000000000070251211610345200226020ustar00rootroot00000000000000# # Copyright (c) 2009-2012 Sascha Steinbiss # Copyright (c) 2009-2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' require 'extended/comment_node' require 'extended/eof_node' require 'extended/feature_node' require 'extended/meta_node' require 'extended/sequence_node' require 'extended/region_node' module GT extend DL::Importable gtdlload "libgenometools" extern "GtNodeVisitor* gt_script_wrapper_visitor_new(void*, void*, void*, void*, void*, void*, void*)" class CustomVisitor def visitor_func_generic(node_class, node_ptr, err_ptr, method_name) node = node_class.new(node_ptr, true) err = GT::Error.new(err_ptr) begin begin ret = self.send("visit_#{method_name}_node", node) rescue NoMethodError ret = 0 end rescue Error => msg err.set(msg) ret = -1 end if ret.nil? 0 else begin Integer(ret) rescue err.set("Function 'visit_#{method_name}_node' of class " + \ "'#{self.class}' must return an integer or nil!") 1 end end end def initialize() @feature_node_cb = DL.callback("IPP") do |fn_ptr, err_ptr| self.visitor_func_generic(GT::FeatureNode, fn_ptr, err_ptr, "feature") end @comment_node_cb = DL.callback("IPP") do |cn_ptr, err_ptr| self.visitor_func_generic(GT::CommentNode, cn_ptr, err_ptr, "comment") end @region_node_cb = DL.callback("IPP") do |rn_ptr, err_ptr| self.visitor_func_generic(GT::RegionNode, rn_ptr, err_ptr, "region") end @sequence_node_cb = DL.callback("IPP") do |sn_ptr, err_ptr| self.visitor_func_generic(GT::CommentNode, sn_ptr, err_ptr, "sequence") end @meta_node_cb = DL.callback("IPP") do |mn_ptr, err_ptr| self.visitor_func_generic(GT::MetaNode, mn_ptr, err_ptr, "meta") end @eof_node_cb = DL.callback("IPP") do |en_ptr, err_ptr| self.visitor_func_generic(GT::EOFNode, en_ptr, err_ptr, "eof") end @genome_visitor = GT.gt_script_wrapper_visitor_new(@comment_node_cb, @feature_node_cb, @region_node_cb, @sequence_node_cb, @meta_node_cb, @eof_node_cb, nil) @genome_visitor.free = GT::symbol("gt_node_visitor_delete", "0P") end def to_ptr @genome_visitor end end end genometools-1.5.1/gtruby/extended/custom_visitor_example.rb000066400000000000000000000023151211610345200243120ustar00rootroot00000000000000# # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'extended/custom_visitor' module GT class CustomVisitorExample < CustomVisitor def initialize() super end def visit_feature_node(feature_node) new_node = GT::FeatureNode.create(feature_node.get_seqid, "test", \ 100, 1000, '+') feature_node.add_child(new_node) 0 end end end genometools-1.5.1/gtruby/extended/eof_node.rb000066400000000000000000000023441211610345200212660ustar00rootroot00000000000000# # Copyright (c) 2012 Sascha Steinbiss # Copyright (c) 2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' require 'extended/genome_node' module GT extend DL::Importable gtdlload "libgenometools" extern "GtGenomeNode* gt_eof_node_new()" class EOFNode < GenomeNode def self.create newfn = GT.gt_eof_node_new() return GT::EOFNode.new(newfn, true) end def initialize(gn, newref=false) super(gn, newref) end end end genometools-1.5.1/gtruby/extended/feature_index.rb000066400000000000000000000131051211610345200223270ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2008-2010 Sascha Steinbiss # Copyright (c) 2007-2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'core/array' require 'core/range' require 'core/str_array' module GT extend DL::Importable gtdlload "libgenometools" typealias "bool", "ibool" extern "GtFeatureIndex* gt_feature_index_memory_new()" extern "void gt_feature_index_delete(GtFeatureIndex*)" extern "int gt_feature_index_add_gff3file(GtFeatureIndex*, " + "const char*, " + "GtError*)" extern "GtArray* gt_feature_index_get_features_for_seqid(Gt_FeatureIndex*, " + "const char*, " + "GtError*)" extern "char* gt_feature_index_get_first_seqid(const GtFeatureIndex*, " + "GtError*)" extern "GtStrArray* gt_feature_index_get_seqids(const GtFeatureIndex*, " + "GtError*)" extern "int gt_feature_index_get_range_for_seqid(GtFeatureIndex*, " + "GtRange*, const char*, " + "GtError*)" extern "int gt_feature_index_has_seqid(const GtFeatureIndex*, int*, " + "const char*, GtError*)" extern "int gt_feature_index_get_features_for_range(GtFeatureIndex*, GtArray*, const char*, const GtRange*, GtError*)" class FeatureIndex attr_reader :feature_index def initialize(*) raise(NotImplementedError, "Please call the constructor of a " + "#{self.class} implementation.") end def get_features_for_seqid(seqid) err = GT::Error.new() rval = GT.gt_feature_index_get_features_for_seqid(@feature_index, seqid, \ err) if rval then a = GT::Array.new(rval) result = [] 1.upto(a.size) do |i| fn = GT::FeatureNode.new(GT.gt_genome_node_ref(a.get(i-1))) result.push(fn) end result else GT.gterror(err) end end def get_features_for_range(start, stop, seqid) a = Array.create() err = Error.new() rng = Range.new(start, stop) rval = GT::gt_feature_index_get_features_for_range(@feature_index, a, \ seqid, rng.to_ptr, err) if rval != 0 then GT.gterror(err) end result = [] 1.upto(a.size) do |i| fn = GT::FeatureNode.new(GT.gt_genome_node_ref(a.get(i-1))) result.push(fn) end result end def add_gff3file(filename) err = GT::Error.new() rval = GT.gt_feature_index_add_gff3file(@feature_index, filename, \ err.to_ptr) if rval != 0 then GT.gterror(err) end end def get_first_seqid err = Error.new() val = GT.gt_feature_index_get_first_seqid(@feature_index, err.to_ptr) if val.nil? then GT.gterror(err) end val end def get_seqids err = Error.new() sap = GT.gt_feature_index_get_seqids(@feature_index, err.to_ptr) if sap.nil? then GT.gterror(err) end GT::StrArray.new(sap).to_a end def has_seqid?(seqid) err = Error.new() val = (GT::struct ["bool val"]).malloc rval = GT.gt_feature_index_has_seqid(@feature_index, val, seqid, err) if rval != 0 then GT.gterror(err) else return (val.val == true) end end def get_range_for_seqid(seqid) err = Error.new() if not self.has_seqid?(seqid) then GT.gterror("feature_index does not contain seqid") end range = DL::malloc(DL::sizeof("LL")) rval = GT.gt_feature_index_get_range_for_seqid(@feature_index, range, \ seqid, err) if rval != 0 then GT.gterror(err) else range.struct!("LL", :start, :stop) Range.new(range[:start],range[:stop]) end end def to_ptr @feature_index end end class FeatureIndexMemory < FeatureIndex def initialize @feature_index = GT.gt_feature_index_memory_new() @feature_index.free = GT::symbol("gt_feature_index_delete", "0P") end end class FeatureIndexFromPtr < FeatureIndex def initialize(ptr, own = false) @feature_index = ptr if own then @feature_index.free = GT::symbol("gt_feature_index_delete", "0P") end end end end genometools-1.5.1/gtruby/extended/feature_node.rb000066400000000000000000000163751211610345200221610ustar00rootroot00000000000000# # Copyright (c) 2008 Sascha Steinbiss # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' require 'core/str' require 'extended/genome_node' module GT extend DL::Importable gtdlload "libgenometools" typealias "bool", "ibool" typealias "GtStrand", "int" typealias "GtPhase", "int" extern "GtGenomeNode* gt_feature_node_new(GtStr*, const char*, unsigned long, unsigned long, GtStrand)" extern "void gt_feature_node_add_child(GtFeatureNode*, GtFeatureNode*)" extern "const char* gt_feature_node_get_source(GtFeatureNode*)" extern "void gt_feature_node_set_source(GtFeatureNode*, GtStr*)" extern "const char* gt_feature_node_get_type(GtFeatureNode*)" extern "bool gt_feature_node_has_type(GtFeatureNode*, const char*)" extern "bool gt_feature_node_score_is_defined(const GtFeatureNode*)" extern "float gt_feature_node_get_score(const GtFeatureNode*)" extern "void gt_feature_node_set_score(GtFeatureNode*, float)" extern "void gt_feature_node_unset_score(GtFeatureNode*)" extern "GtStrand gt_feature_node_get_strand(GtFeatureNode*)" extern "void gt_feature_node_set_strand(GtFeatureNode*, GtStrand)" extern "GtPhase gt_feature_node_get_phase(GtFeatureNode*)" extern "void gt_feature_node_set_phase(GtFeatureNode*, GtPhase)" extern "const char* gt_feature_node_get_attribute(GtFeatureNode*, const char*)" extern "void gt_feature_node_add_attribute(GtFeatureNode*, const char*, const char*)" extern "void gt_feature_node_foreach_attribute(GtFeatureNode*, void*, void*)" #callback to populate attribute list def collect_attrib(tag, val, data) GT.gt_str_array_add_cstr(data, tag) GT.gt_str_array_add_cstr(data, val) end COLLECTFUNC = callback "void collect_attrib(const char*, const char*, void*)" class FeatureNode < GenomeNode def self.create(seqid, type, start, stop, strand) s = GT::Str.new(seqid) if !GT::STRANDCHARS.include?(strand) GT::gterror("Invalid strand: '#{strand}'") end newfn = GT.gt_feature_node_new(s, type, start, stop, \ GT::STRANDCHARS.index(strand)) return GT::FeatureNode.new(newfn, true) end def initialize(gn, newref=false) super(gn, newref) end def add_child(node) if self.get_seqid != node.get_seqid GT::gterror("nodes must have identical sequence regions! " + \ "(was: '#{self.get_seqid}' vs. '#{node.get_seqid}'") end GT.gt_feature_node_add_child(@genome_node, node) end def get_source GT.gt_feature_node_get_source(@genome_node) end def set_source(source) GT.gt_feature_node_set_source(@genome_node, source.to_s) end def update_attribs attribs = GT::StrArray.new GT.gt_feature_node_foreach_attribute(@genome_node, COLLECTFUNC, attribs) attr_a = attribs.to_a @attribs = {} while not attr_a.empty? do @attribs[attr_a.shift] = attr_a.shift end end def get_type GT.gt_feature_node_get_type(@genome_node) end def has_type?(type) GT.gt_feature_node_has_type(@genome_node, type.to_s) end def score_is_defined? GT.gt_feature_node_score_is_defined(@genome_node) end def get_score if GT.gt_feature_node_score_is_defined(@genome_node) then GT.gt_feature_node_get_score(@genome_node) else nil end end def set_score(score) GT.gt_feature_node_set_score(@genome_node, score.to_f) end def unset_score GT.gt_feature_node_unset_score(@genome_node) end def get_strand GT.gt_feature_node_get_strand(@genome_node) end def set_strand if !GT::STRANDCHARS.include?(strand) GT::gterror("Invalid strand: '#{strand}'") end GT.gt_feature_node_set_strand(GT::STRANDCHARS.index(strand)) end def get_phase GT.gt_feature_node_get_phase(@genome_node) end def set_phase(phase) if phase.to_i > 3 then GT::gterror("Invalid phase: '#{phase}'") end GT.gt_feature_node_set_phase(@genome_node, phase.to_i) end def get_attribute(attrib) if @attribs.nil? self.update_attribs end @attribs[attrib] end def add_attribute(tag, val) if tag.to_s == "" or val.to_s == "" then gterror("Attribute keys or values must not be empty!") end GT.gt_feature_node_add_attribute(@genome_node, tag.to_s, val.to_s) self.update_attribs end def each_attribute if @attribs.nil? self.update_attribs end @attribs.each_pair do |tag, val| yield tag, val end end def traverse(it) tfn = it.next while !tfn.nil? do yield tfn tfn = it.next end end def traverse_dfs self.traverse(GT::FeatureNodeIteratorDepthFirst.new(self)) do |n| yield n end end def traverse_direct self.traverse(GT::FeatureNodeIteratorDirect.new(self)) do |n| yield n end end def to_ptr @genome_node end end extern "GtFeatureNode* gt_feature_node_iterator_next(GtFeatureNodeIterator*)" extern "void gt_feature_node_iterator_delete(GtFeatureNodeIterator*)" extern "GtFeatureNodeIterator* gt_feature_node_iterator_new(const GtFeatureNode*)" extern "GtFeatureNodeIterator* gt_feature_node_iterator_new_direct(const GtFeatureNode*)" class FeatureNodeIterator def next ret = GT.gt_feature_node_iterator_next(@i) if !ret.nil? then GT::FeatureNode.new(ret, true) else nil end end end class FeatureNodeIteratorDepthFirst < FeatureNodeIterator def initialize(node) @i = GT.gt_feature_node_iterator_new(node) @i.free = GT::symbol("gt_feature_node_iterator_delete", "0P") end end class FeatureNodeIteratorDirect < FeatureNodeIterator def initialize(node) @i = GT.gt_feature_node_iterator_new_direct(node) @i.free = GT::symbol("gt_feature_node_iterator_delete", "0P") end end end genometools-1.5.1/gtruby/extended/feature_stream.rb000066400000000000000000000025201211610345200225120ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'extended/genome_stream' module GT extend DL::Importable gtdlload "libgenometools" extern "GtNodeStream* gt_feature_stream_new(GtNodeStream*, GtFeatureIndex*)" class FeatureStream < GenomeStream def initialize(genome_stream, feature_index) @genome_stream = GT.gt_feature_stream_new(genome_stream, feature_index) @genome_stream.free = GT::symbol("gt_node_stream_delete", "0P") end end end genometools-1.5.1/gtruby/extended/genome_node.rb000066400000000000000000000051351211610345200217700ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2007-2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'gthelper' require 'core/str' module GT extend DL::Importable gtdlload "libgenometools" extern "int gt_genome_node_accept(GtGenomeNode*, GenomeVisitor*, GtError*)" extern "GtGenomeNode* gt_genome_node_ref(GtGenomeNode*)" extern "GtStr* gt_genome_node_get_seqid(GtGenomeNode*)" extern "unsigned long gt_genome_node_get_start(GtGenomeNode*)" extern "unsigned long gt_genome_node_get_end(GtGenomeNode*)" extern "const char* gt_genome_node_get_filename(GtGenomeNode*)" extern "unsigned int gt_genome_node_get_line_number(GtGenomeNode*)" extern "void gt_genome_node_delete(GtGenomeNode*)" class GenomeNode attr_reader :genome_node def initialize(node_ptr, newref=false) if newref then @genome_node = GT.gt_genome_node_ref(node_ptr) else @genome_node = node_ptr end @genome_node.free = GT::symbol("gt_genome_node_delete", "0P") end def ==(node) (node.genome_node == @genome_node) end def get_range (GT::gt_genome_node_get_start(@genome_node)..\ GT::gt_genome_node_get_end(@genome_node)) end def get_filename GT.gt_genome_node_get_filename(@genome_node) end def get_line_number GT.gt_genome_node_get_line_number(@genome_node) end def to_ptr @genome_node end def get_seqid str = GT::Str.new(GT.gt_genome_node_get_seqid(@genome_node)) if !str.nil? then str.to_s else "" end end def accept(visitor) err = GT::Error.new() rval = GT.gt_genome_node_accept(@genome_node, visitor.to_ptr, err.to_ptr) if rval != 0 GT.gterror(err) end end end end genometools-1.5.1/gtruby/extended/genome_stream.rb000066400000000000000000000033731211610345200223400ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2007-2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'gthelper' require 'core/error' require 'extended/genome_node' module GT extend DL::Importable gtdlload "libgenometools" extern "int gt_node_stream_next(GtNodeStream*, GtGenomeNode**, GtError*)" class GenomeStream def initialize(*) raise(NotImplementedError, "Please call the constructor of a " + "#{self.class} implementation.") end def next_tree err = GT::Error.new() genome_node = DL::PtrData.new(0) genome_node.free = DL::FREE rval = GT.gt_node_stream_next(@genome_stream, genome_node.ref, err.to_ptr) if rval != 0 then GT.gterror(err) end if genome_node.null? then return nil end GT::GenomeNode.new(genome_node) end def to_ptr @genome_stream end end end genometools-1.5.1/gtruby/extended/gff3_in_stream.rb000066400000000000000000000051741211610345200224020ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2012 Sascha Steinbiss # Copyright (c) 2007-2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'gthelper' require 'core/str_array' require 'extended/genome_stream' module GT extend DL::Importable gtdlload "libgenometools" typealias "bool", "ibool" extern "GtNodeStream* gt_gff3_in_stream_new_sorted(const char*)" extern "GtNodeStream* gt_gff3_in_stream_new_unsorted(int, const char**)" extern "GtStrArray* gt_gff3_in_stream_get_used_types(GtNodeStream*)" extern "void gt_gff3_in_stream_enable_strict_mode(GtGFF3InStream*)" extern "void gt_gff3_in_stream_enable_tidy_mode(GtGFF3InStream*)" extern "void gt_gff3_in_stream_set_type_checker(GtNodeStream*, GtTypeChecker*)" class GFF3InStream < GenomeStream def initialize(filename, sorted = true) if not File.readable?(filename) GT.gterror("file '#{filename}' not readable") end if sorted then @genome_stream = GT.gt_gff3_in_stream_new_sorted(filename.to_s) else @genome_stream = GT.gt_gff3_in_stream_new_unsorted(1, [filename.to_s]) end @genome_stream.free = GT::symbol("gt_node_stream_delete", "0P") end def get_used_types str_array_ptr = GT.gt_gff3_in_stream_get_used_types(@genome_stream) used_types = GT::StrArray.new(str_array_ptr) used_types.to_a end def enable_strict_mode GT.gt_gff3_in_stream_enable_strict_mode(@genome_stream) end def enable_tidy_mode GT.gt_gff3_in_stream_enable_tidy_mode(@genome_stream) end def set_type_checker(checker) if !checker.is_a?(GT::TypeChecker) then GT.gterror("'checker' parameter must be a TypeChecker object!") end GT.gt_gff3_in_stream_set_type_checker(@genome_stream, checker) end end end genometools-1.5.1/gtruby/extended/gff3_out_stream.rb000066400000000000000000000023741211610345200226020ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'extended/genome_stream' module GT extend DL::Importable gtdlload "libgenometools" extern "GtNodeStream* gt_gff3_out_stream_new(GtNodeStream*, GtGenFile*)" class GFF3OutStream < GenomeStream def initialize(in_stream) @genome_stream = GT.gt_gff3_out_stream_new(in_stream, nil) @genome_stream.free = GT::symbol("gt_node_stream_delete", "0P") end end end genometools-1.5.1/gtruby/extended/gff3_visitor.rb000066400000000000000000000023571211610345200221200ustar00rootroot00000000000000# # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'gtdlload' require 'extended/genome_stream' module GT extend DL::Importable gtdlload "libgenometools" extern "GtNodeVisitor* gt_gff3_visitor_new(GtFile*)" class GFF3Visitor def initialize @genome_visitor = GT.gt_gff3_visitor_new(nil) @genome_visitor.free = GT::symbol("gt_node_visitor_delete", "0P") end def to_ptr @genome_visitor end end end genometools-1.5.1/gtruby/extended/meta_node.rb000066400000000000000000000030721211610345200214420ustar00rootroot00000000000000# # Copyright (c) 2012 Sascha Steinbiss # Copyright (c) 2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' module GT extend DL::Importable gtdlload "libgenometools" extern "GtGenomeNode* gt_meta_node_new(const char*, const char*)" extern "const char* gt_meta_node_get_directive(const GtMetaNode*)" extern "const char* gt_meta_node_get_data(const GtMetaNode*)" class MetaNode < GenomeNode def self.create(directive, data) newfn = GT.gt_meta_node_new(directive.to_s, data.to_s) return GT::MetaNode.new(newfn, true) end def initialize(gn, newref=false) super(gn, newref) end def get_directive return GT.gt_meta_node_get_directive(@genome_node) end def get_data return GT.gt_meta_node_get_data(@genome_node) end end end genometools-1.5.1/gtruby/extended/rdb.rb000066400000000000000000000037111211610345200202560ustar00rootroot00000000000000# # Copyright (c) 2009-2012 Sascha Steinbiss # Copyright (c) 2009-2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' module GT extend DL::Importable gtdlload "libgenometools" extern "GtRDB* gt_rdb_sqlite_new(const char*, GtError*)" begin extern "GtRDB* gt_rdb_mysql_new(const char*, unsigned int, const char*, const char*, const char*, GtError*)" rescue end class RDB def initialize(*) raise(NotImplementedError, "Please call the constructor of a " + "#{self.class} implementation.") end def to_ptr @rdb end end class RDBSqlite < RDB def initialize(dbpath) err = GT::Error.new() @rdb = GT.gt_rdb_sqlite_new(dbpath, err) if @rdb.nil? then GT::gterror(err) end @rdb.free = GT::symbol("gt_rdb_delete", "0P") end end class RDBMySQL < RDB def initialize(server, port, db, user, pass) err = GT::Error.new() @rdb = GT.gt_rdb_mysql_new(server, port, db, user, pass, err) if @rdb.nil? then GT::gterror(err) end @rdb.free = GT::symbol("gt_rdb_delete", "0P") end end end genometools-1.5.1/gtruby/extended/region_node.rb000066400000000000000000000027421211610345200220020ustar00rootroot00000000000000# # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' require "core/str" module GT extend DL::Importable gtdlload "libgenometools" extern "GtRegionNode* gt_region_node_new(GtStr*, unsigned long, unsigned long)" class RegionNode < GenomeNode def self.create(seqid, start, stop) unless start <= stop raise(ArgumentError, "start (#{start}) > stop (#{stop})") else newrn = GT.gt_region_node_new(GT::Str.new(seqid.to_s), start, stop) return GT::RegionNode.new(newrn, true) end end def initialize(gn, newref=false) super(gn, newref) end end end genometools-1.5.1/gtruby/extended/sequence_node.rb000066400000000000000000000037111211610345200223240ustar00rootroot00000000000000# # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' require "core/str" module GT extend DL::Importable gtdlload "libgenometools" extern "GtGenomeNode* gt_sequence_node_new(const char*, GtStr*)" extern "const char* gt_sequence_node_get_description(const GtSequenceNode*)" extern "const char* gt_sequence_node_get_sequence(const GtSequenceNode*)" extern "unsigned long gt_sequence_node_get_sequence_length(const GtSequenceNode*)" class SequenceNode < GenomeNode def self.create(description, sequence) newsn = GT.gt_sequence_node_new(description.to_s, \ GT::Str.new(sequence.to_s)) return GT::SequenceNode.new(newsn, true) end def initialize(gn, newref=false) super(gn, newref) end def get_description return GT.gt_sequence_node_get_description(@genome_node) end def get_sequence (seq = GT.gt_sequence_node_get_sequence(@genome_node)) ? seq : "" end def get_sequence_length return GT.gt_sequence_node_get_sequence_length(@genome_node) end end end genometools-1.5.1/gtruby/extended/type_checker.rb000066400000000000000000000044351211610345200221600ustar00rootroot00000000000000# # Copyright (c) 2012 Sascha Steinbiss # Copyright (c) 2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' require 'gthelper' require 'core/error' module GT extend DL::Importable gtdlload "libgenometools" extern "GtTypeChecker* gt_type_checker_ref(GtTypeChecker*)" extern "bool gt_type_checker_is_valid(GtTypeChecker*, const char*)" extern "void gt_type_checker_delete(GtTypeChecker*)" extern "GtTypeChecker* gt_type_checker_obo_new(const char*, GtError*)" extern "GtTypeChecker* gt_type_checker_builtin_new()" class TypeChecker def initialize(*) raise(NotImplementedError, "Please call the constructor of a " + "#{self.class} implementation.") end def is_valid?(type) rval = GT.gt_type_checker_is_valid(@checker, type) return rval end def to_ptr @checker end end class TypeCheckerBuiltin < TypeChecker def initialize @checker = GT.gt_type_checker_builtin_new() @checker.free = GT::symbol("gt_type_checker_delete", "0P") end end class TypeCheckerOBO < TypeChecker def initialize(filename) if !File.exist?(filename) or File.directory?(filename) \ or !File.readable?(filename) GT.gterror("invalid file: #{filename}") end err = GT::Error.new @checker = GT.gt_type_checker_obo_new(filename, err.to_ptr) if @checker == GT::NULL or @checker == nil then GT.gterror(err) else @checker.free = GT::symbol("gt_type_checker_delete", "0P") end end end end genometools-1.5.1/gtruby/gtdlload.rb000066400000000000000000000022741211610345200175040ustar00rootroot00000000000000# # Copyright (c) 2008 Gordon Gremme # Copyright (c) 2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'dl/import' module GT # XXX: Does anybody have a better idea for this mess? def GT.gtdlload(basename) if not $GT_SYSTEM then $GT_SYSTEM=`uname -s`.chomp end if $GT_SYSTEM == "Darwin" then dlload basename + ".dylib" else dlload basename + ".so" end end # a NULL pointer NULL = DL::PtrData.new(0) end genometools-1.5.1/gtruby/gthelper.rb000066400000000000000000000023021211610345200175140ustar00rootroot00000000000000# # Copyright (c) 2007 Gordon Gremme # Copyright (c) 2007 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'core/error' module GT class GTError < RuntimeError end # this is needed because DL is unaware of the native ulong size NATIVEULONGSIZE = [0].pack('L!').size def GT.gterror(err) if err.class == GT::Error then raise GTError, "GenomeTools error: #{err.get}" else raise GTError, "GenomeTools error: " + err end end end genometools-1.5.1/gtruby/gtruby.rb000066400000000000000000000020251211610345200172200ustar00rootroot00000000000000# # Copyright (c) 2007 Gordon Gremme # Copyright (c) 2007 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # # the GenomeTools Ruby bindings require 'gthelper' require 'core' require 'extended' require 'annotationsketch' # initialize library globals GT::gt_lib_init() GT::gt_lib_reg_atexit_func() genometools-1.5.1/gtruby/sketch_constructed.rb000066400000000000000000000021221211610345200216000ustar00rootroot00000000000000require 'gtruby' if ARGV.size != 2 then STDERR.puts "Usage: #{$0} style_file PNG_file" exit(1) end seqid = "chromosome_21" # construct a gene on the forward strand with two exons gene = GT::FeatureNode.create(seqid, "gene", 100, 900, "+") exon = GT::FeatureNode.create(seqid, "exon", 100, 200, "+") gene.add_child(exon) intron = GT::FeatureNode.create(seqid, "intron", 201, 799, "+") gene.add_child(intron) exon = GT::FeatureNode.create(seqid, "exon", 800, 900, "+") gene.add_child(exon) # construct a single-exon gene on the reverse strand # (within the intron of the forward strand gene) reverse_gene = GT::FeatureNode.create(seqid, "gene", 400, 600, "-") reverse_exon = GT::FeatureNode.create(seqid, "exon", 400, 600, "-") reverse_gene.add_child(reverse_exon) pngfile = ARGV[1] style = GT::Style.new() style.load_file(ARGV[0]) rng = GT::Range.new(1, 1000) diagram = GT::Diagram.from_array([gene, reverse_gene], rng, style) layout = GT::Layout.new(diagram, 600, style) canvas = GT::CanvasCairoFile.new(style, 600, layout.get_height, nil) layout.sketch(canvas) canvas.to_file(pngfile) genometools-1.5.1/gtruby/sketch_parsed.rb000066400000000000000000000016471211610345200205340ustar00rootroot00000000000000require 'gtruby' if ARGV.size != 3 then STDERR.puts "Usage: #{$0} style_file PNG_file GFF3_file" STDERR.puts "Create PNG representation of GFF3 annotation file." exit(1) end (stylefile, pngfile, gff3file) = ARGV # load style file style = GT::Style.new() style.load_file(stylefile) # create feature index feature_index = GT::FeatureIndexMemory.new() # add GFF3 file to index feature_index.add_gff3file(gff3file) # create diagram for first sequence ID in feature index seqid = feature_index.get_first_seqid() range = feature_index.get_range_for_seqid(seqid) diagram = GT::Diagram.from_index(feature_index, seqid, range, style) # create layout for given width layout = GT::Layout.new(diagram, 800, style) # create canvas with given width and computed height canvas = GT::CanvasCairoFile.new(style, 800, layout.get_height, nil) # sketch layout on canvas layout.sketch(canvas) # write canvas to file canvas.to_file(pngfile) genometools-1.5.1/gtscripts/000077500000000000000000000000001211610345200160665ustar00rootroot00000000000000genometools-1.5.1/gtscripts/display.lua000066400000000000000000000027551211610345200202470ustar00rootroot00000000000000--[[ Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] require 'gtlua' function usage() io.stderr:write(string.format("Usage: %s PNG_dir\n", arg[0])) io.stderr:write("Display numbered PNG files in PNG_dir.\n") os.exit(1) end if #arg == 1 then png_dir = arg[1] -- make sure png_dir is a directory rval, err = lfs.attributes(png_dir, "mode") if rval ~= "directory" then io.stderr:write(string.format("PNG_dir '%s' is not a directory\n", png_dir)) os.exit(1) end else usage() end filenumber = 1 while (true) do local filename = png_dir .. "/" .. filenumber .. ".png" if gt.file_exists(filename) then gt.display(filename) filenumber = filenumber + 1 else break end end genometools-1.5.1/gtscripts/evalviz.lua000066400000000000000000000057101211610345200202540ustar00rootroot00000000000000--[[ Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] require 'gtlua' require 'lfs' function usage() io.stderr:write(string.format("Usage: %s PNG_dir reality_file " .. "prediction_file\n", arg[0])) io.stderr:write("Evaluate prediction_file against reality_file and write " .. "out PNGs to PNG_dir.\n") os.exit(1) end if #arg == 3 then png_dir = arg[1] reality_file = arg[2] prediction_file = arg[3] -- make sure png_dir is a directory or create it rval, err = lfs.attributes(png_dir, "mode") if rval then if rval ~= "directory" then io.stderr:write(string.format("PNG_dir '%s' is not a directory\n", png_dir)) os.exit(1) end else -- not successfull, try to create directory rval, err = lfs.mkdir(png_dir) if not rval then io.stderr:write(string.format("could not create directory '%s': %s", png_dir, err)) os.exit(1) end end else usage() end function write_marked_regions(seqid, filenumber, maxdist) assert(seqid) local marked = feature_index:get_marked_regions(seqid, maxdist) for _,range in ipairs(marked) do local filename = png_dir .. "/" .. filenumber .. ".png" io.write(string.format("writing file '%s'\n", filename)) feature_index:render_to_png(seqid, range, filename, width) filenumber = filenumber + 1 end return filenumber end -- process input files reality_stream = gt.gff3_in_stream_new_sorted(reality_file) prediction_stream = gt.gff3_in_stream_new_sorted(prediction_file) stream_evaluator = gt.stream_evaluator_new(reality_stream, prediction_stream) feature_index = gt.feature_index_memory_new() feature_visitor = gt.feature_visitor_new(feature_index) stream_evaluator:evaluate(feature_visitor) stream_evaluator:show() -- write results filenumber = 1 width = 1600 for _, seqid in ipairs(feature_index:get_seqids()) do print(string.format("seqid '%s'", seqid)) filenumber = write_marked_regions(seqid, filenumber) end -- get ready for interactive mode fi = feature_index features = fi:get_all_features() marked_features = gt.features_get_marked(features) gt.export() genometools-1.5.1/gtscripts/gtdoc.lua000066400000000000000000000107701211610345200176760ustar00rootroot00000000000000--[[ Copyright (c) 2008-2011 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] require 'gtdoclib' function usage() io.stderr:write(string.format("Usage: [-html] [-lua] [-tex] [-v] %s " .. "gt_home\n", arg[0])) io.stderr:write("Generate documentation for the GenomeTools home " .. "directory gt_home.\n") os.exit(1) end local be_verbose = false local in_mode = "C" local out_mode = "txt" local file_mode = false local file_list = {} if #arg >= 1 then while #arg >= 1 and string.match(arg[1], "^-") do if string.match(arg[1], "^-f") then file_mode = true table.remove(arg, 1) while #arg > 1 and not string.match(arg[1], "^-") do file_list[#file_list+1] = arg[1] table.remove(arg, 1) end elseif string.match(arg[1], "^-h") then out_mode = "html" table.remove(arg, 1) elseif string.match(arg[1], "^-t") then out_mode = "latex" table.remove(arg, 1) elseif string.match(arg[1], "^-l") then in_mode = "Lua" table.remove(arg, 1) elseif string.match(arg[1], "^-v") then be_verbose = true table.remove(arg, 1) end end if #arg == 1 then gt_home = arg[1] else usage() end else usage() end local template_path = gt_home .. "/gtdata/modules/gtdoclib/" local export_C = { "src/core", "src/extended", "src/annotationsketch" } local export_Lua = { "src/gtlua", "gtdata/modules/gtlua.lua", "gtdata/modules/gtlua" } local doc_parser = DocParser:new() local doc_base = DocBase:new() local function show_rec_array(array, depth) assert(array) for _, v in ipairs(array) do if type(v) == "table" then print("") show_rec_array(v, depth + 2) else local indent = string.rep(".", depth) print(string.format("%s%s", indent, v)) end end end local function process_file(filename, be_verbose, is_lua) assert(filename) if (is_lua and (is_header(filename) or is_lua_file(filename))) or (not is_lua and is_api_header(filename)) then local ast = doc_parser:parse(filename, be_verbose, is_lua) if ast and be_verbose then print("showing ast:") show_rec_array(ast, 0) end if ast then doc_base:process_ast(ast, be_verbose) end end end local export = nil local is_lua = nil if in_mode == "C" then export = export_C is_lua = false else assert(in_mode == "Lua") export = export_Lua is_lua = true end assert(export) if file_mode then for _, f in ipairs(file_list) do local filename = gt_home .. "/" .. f process_file(filename, be_verbose, is_lua) end else for _, v in ipairs(export) do local filename = gt_home .. "/" .. v if is_dir(filename) then for f in lfs.dir(filename) do local filename = filename .. "/" .. f process_file(filename, be_verbose, is_lua) end else process_file(filename, be_verbose, is_lua) end end end local doc_visitor if out_mode == "txt" then doc_visitor = DocVisitorTxt:new() doc_base:accept(doc_visitor) elseif out_mode == "latex" then local header if in_mode == "C" then header = "libgenometools_header_latex.lp" else header = "gtscript_header_latex.lp" end doc_visitor = DocVisitorLaTeX:new(template_path, header) doc_visitor:show_header() doc_base:accept(doc_visitor) doc_visitor:show_footer() else assert(out_mode == "html") local header if in_mode == "C" then header = "libgenometools_header.lp" else header = "gtscript_header.lp" end doc_visitor = DocVisitorHTML:new(template_path, header) doc_visitor:show_header() doc_base:accept(doc_visitor) doc_visitor:show_footer() end genometools-1.5.1/gtscripts/repgen.lua000066400000000000000000000037031211610345200200540ustar00rootroot00000000000000--[[ Copyright (c) 2012 Stefan Kurtz Copyright (c) 2012 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] require 'gtlua' function usage() io.stderr:write(string.format("Usage: %s \n" , arg[0])) os.exit(1) end function outputmulticseq(indent, linewidth, times) for i = 1, times-1 do io.write('c') if indent >= linewidth then io.write('\n') indent = 0 else indent = indent + 1 end end return indent end function outputrepetitivesequence(iter) indent = 1; linewidth = 70; midseq = "acaccaccc" io.write(string.format(">%s for i=%d\na","ac^{i^2}acac^2ac^3 ... ac^ia",iter)) indent = outputmulticseq(indent,linewidth,iter * iter) assert (indent < linewidth) if indent + string.len(midseq) > linewidth then rest = linewidth - indent io.write(string.format("%*.*s\n",rest,rest,midseq)) if rest < string.len(midseq) then io.write(string.format("%s",midseq + rest)) end indent = 0 else io.write(string.format("acaccaccc")) indent = indent + string.len(midseq) end indent = outputmulticseq(indent,linewidth,iter) io.write("\n") end if #arg == 1 then i = arg[1] outputrepetitivesequence(i) else usage() end gt.export() genometools-1.5.1/gtscripts/sketch_constructed.lua000066400000000000000000000024051211610345200224700ustar00rootroot00000000000000function usage() io.stderr:write(string.format("Usage: %s Style_file PNG_file\n", arg[0])) os.exit(1) end if #arg == 2 then style_file = arg[1] png_file = arg[2] else usage() end -- load style file dofile(style_file) -- construct the example features seqid = "chromosome_21" nodes = {} -- construct a gene on the forward strand with two exons gene = gt.feature_node_new(seqid, "gene", 100, 900, "+") exon = gt.feature_node_new(seqid, "exon", 100, 200, "+") gene:add_child(exon) intron = gt.feature_node_new(seqid, "intron", 201, 799, "+") gene:add_child(intron) exon = gt.feature_node_new(seqid, "exon", 800, 900, "+") gene:add_child(exon) nodes[1] = gene -- construct a single-exon gene on the reverse strand -- (within the intron of the forward strand gene) reverse_gene = gt.feature_node_new(seqid, "gene", 400, 600, "-") reverse_exon = gt.feature_node_new(seqid, "exon", 400, 600, "-") reverse_gene:add_child(reverse_exon) nodes[2] = reverse_gene -- create diagram diagram = gt.diagram_new_from_array(nodes, 1, 1000) layout = gt.layout_new(diagram, 600) height = layout:get_height() -- create canvas canvas = gt.canvas_cairo_file_new_png(600, height, nil) -- sketch layout on canvas layout:sketch(canvas) -- write canvas to file canvas:to_file(png_file) genometools-1.5.1/gtscripts/sketch_parsed.lua000066400000000000000000000016441211610345200214150ustar00rootroot00000000000000function usage() io.stderr:write(string.format("Usage: %s Style_file PNG_file GFF3_file\n", arg[0])) io.stderr:write("Create PNG representation of GFF3 annotation file.\n") os.exit(1) end if #arg == 3 then style_file = arg[1] png_file = arg[2] gff3_file = arg[3] else usage() end -- load style file dofile(style_file) -- create feature index feature_index = gt.feature_index_memory_new() -- add GFF3 file to index feature_index:add_gff3file(gff3_file) -- create diagram for first sequence ID in feature index seqid = feature_index:get_first_seqid() range = feature_index:get_range_for_seqid(seqid) diagram = gt.diagram_new(feature_index, seqid, range) -- create layout layout = gt.layout_new(diagram, 600) height = layout:get_height() -- create canvas canvas = gt.canvas_cairo_file_new_png(600, height, nil) -- sketch layout on canvas layout:sketch(canvas) -- write canvas to file canvas:to_file(png_file) genometools-1.5.1/scripts/000077500000000000000000000000001211610345200155335ustar00rootroot00000000000000genometools-1.5.1/scripts/DW-pre-commit000077500000000000000000000010141211610345200200410ustar00rootroot00000000000000#!/bin/sh # copy this file to .git/hooks (i.e., overwrite the file .git/hooks/pre-commit) # to perform source checks before commits FILES=`git diff --cached --name-status HEAD | \ awk '$1 != "R" && $1 != "D" { print $2 }' | \ grep -v -e 'src/external' | \ grep -e '.*\.c$' -e '.*\.h$'` make -j8 curses=no cairo=no CFLAGS+=-fstrict-aliasing opt=no 64bit=yes CC='ccache gcc' [ $? -eq 0 ] && make -j8 spgt [ $? -eq 0 ] && if [ ${#FILES} -gt 0 ] then $PWD/scripts/src_check $FILES else exit 0 fi genometools-1.5.1/scripts/Suffixerator-calls.rb000077500000000000000000000010711211610345200216370ustar00rootroot00000000000000#!/usr/bin/env ruby require 'Suffixerator-table' numofargs = ARGV.length if numofargs != 2 STDERR.puts "Usage: $0 " exit 1 end program = ARGV[0] dbdna = ARGV[1] def makesystemcall(argstring) if system(argstring) STDERR.puts "# success #{argstring}" else STDERR.puts "system \"#{argstring}\" failed: errorcode #{$?}" exit 1 end end arglisttable = makesuffixeratorarglisttable(dbdna) arglisttable.each do |argstring| makesystemcall(program + " " + argstring) end STDERR.puts "# number of calls was #{arglisttable.length}" genometools-1.5.1/scripts/Suffixerator-table.rb000066400000000000000000001702141211610345200216330ustar00rootroot00000000000000def makesuffixeratorarglisttable(dbdna) arglisttable = [ " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 8 -locfreq 4", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 8 -locfreq 8", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 8 -locfreq 16", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 8 -locfreq 32", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 9 -locfreq 4", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 9 -locfreq 8", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 9 -locfreq 16", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 9 -locfreq 32", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 10 -locfreq 4", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 10 -locfreq 8", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 10 -locfreq 16", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 -blbuck 10 -locfreq 32", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 8 -locfreq 4", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 8 -locfreq 8", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 8 -locfreq 16", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 8 -locfreq 32", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 9 -locfreq 4", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 9 -locfreq 8", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 9 -locfreq 16", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 9 -locfreq 32", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 10 -locfreq 4", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 10 -locfreq 8", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 10 -locfreq 16", " -dna -db #{dbdna} -bck -pl -tis -bsize 9 -blbuck 10 -locfreq 32", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 8 -locfreq 4", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 8 -locfreq 8", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 8 -locfreq 16", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 8 -locfreq 32", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 9 -locfreq 4", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 9 -locfreq 8", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 9 -locfreq 16", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 9 -locfreq 32", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 10 -locfreq 4", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 10 -locfreq 8", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 10 -locfreq 16", " -dna -db #{dbdna} -bck -pl -tis -bsize 10 -blbuck 10 -locfreq 32", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 8 -locfreq 4", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 8 -locfreq 8", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 8 -locfreq 16", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 8 -locfreq 32", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 9 -locfreq 4", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 9 -locfreq 8", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 9 -locfreq 16", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 9 -locfreq 32", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 10 -locfreq 4", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 10 -locfreq 8", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 10 -locfreq 16", " -dna -db #{dbdna} -bck -pl -bsize 8 -blbuck 10 -locfreq 32", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 8 -locfreq 4", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 8 -locfreq 8", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 8 -locfreq 16", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 8 -locfreq 32", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 9 -locfreq 4", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 9 -locfreq 8", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 9 -locfreq 16", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 9 -locfreq 32", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 10 -locfreq 4", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 10 -locfreq 8", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 10 -locfreq 16", " -dna -db #{dbdna} -bck -pl -bsize 9 -blbuck 10 -locfreq 32", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 8 -locfreq 4", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 8 -locfreq 8", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 8 -locfreq 16", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 8 -locfreq 32", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 9 -locfreq 4", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 9 -locfreq 8", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 9 -locfreq 16", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 9 -locfreq 32", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 10 -locfreq 4", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 10 -locfreq 8", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 10 -locfreq 16", " -dna -db #{dbdna} -bck -pl -bsize 10 -blbuck 10 -locfreq 32", " -dna -db #{dbdna} -bck -pl -tis -bsize 8 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-blbuck 9 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 9 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 9 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 10 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 10 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 10 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 10 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 8 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 8 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 8 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 8 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 9 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 9 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 9 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 9 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 10 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 10 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 10 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 8 -blbuck 10 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 8 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 8 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 8 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 8 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 9 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 9 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 9 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 9 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 10 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 10 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 10 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 9 -blbuck 10 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 8 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 8 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 8 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 8 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 9 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 9 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 9 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 9 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 10 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 10 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 10 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -tis -bsize 10 -blbuck 10 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 8 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 8 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 8 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 8 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 9 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 9 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 9 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 9 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 10 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 10 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 10 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 8 -blbuck 10 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 8 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 8 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 8 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 8 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 9 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 9 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 9 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 9 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 10 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 10 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 10 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 9 -blbuck 10 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 8 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 8 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 8 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 8 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 9 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 9 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 9 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 9 -locfreq 32", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 10 -locfreq 4", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 10 -locfreq 8", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 10 -locfreq 16", " -smap TransDNA -db #{dbdna} -pl -bsize 10 -blbuck 10 -locfreq 32", ] return arglisttable end genometools-1.5.1/scripts/add_revcmp.rb000077500000000000000000000032431211610345200201710ustar00rootroot00000000000000#!/usr/bin/env ruby class Sequence attr_reader :sequence, :length, :fasta_id attr_writer :sequence, :length, :fasta_id def initialize() @length = 0 @sequence = "" @fasta_id = "" end def read_sequence(file) if !File.exists?(file) raise "The specified file #{file} does not exist." end File.open(file) do |line| #read first line str = line.gets.chomp if (str =~ /^>.*$/) then #FASTA file, read header properly @fasta_id = str else #no FASTA file, but plain sequence @sequence = str @length = str.length end #read the rest of the file while nextline = line.gets nextline.chomp! @sequence = @sequence + nextline @length += nextline.length end end end end def revcomp(seq) seq.tr("aAcCgGtTnN","tTgGcCaAnN").reverse end class MSA attr_reader :seqs, :length, :cons def initialize(file) if !File.exists?(file) raise "The specified file #{file} does not exist." end @file = file @length = 0 @seqs = [] self.read end def read text = File.read(@file) text = text.split('>') text[1..text.length-1].each do |item| seq_components = item.split(/\n/) fasta_id=seq_components[0] sequence = seq_components[1..seq_components.length-1] seqObj = Sequence.new() seqObj.fasta_id = fasta_id seqObj.sequence = sequence.join seqObj.length = seqObj.sequence.length @seqs.push(seqObj) end @length = @seqs[0].length end end m = MSA.new(ARGV[0]) l = 0 m.seqs.each do |s| puts ">#{s.fasta_id}" puts "#{s.sequence}" l += s.length end m.seqs.reverse.each do |s| puts ">#{s.fasta_id}" puts "#{revcomp(s.sequence)}" end puts genometools-1.5.1/scripts/alloutputoptions.rb000077500000000000000000000014071211610345200215320ustar00rootroot00000000000000#!/usr/bin/env ruby def turnwheels(outlist) numofalphabets = outlist.length wheelspace = Array.new alphasizes = Array.new 0.upto(numofalphabets-1) do |z| alphasizes[z] = 2 wheelspace[z] = 0 end z = numofalphabets-1 while true output = false 0.upto(numofalphabets-1) do |i| if wheelspace[i] == 1 output = true print " #{outlist[i]}" end end if output puts "" end stop = false while not stop wheelspace[z] = wheelspace[z]+1 if wheelspace[z] == alphasizes[z] wheelspace[z] = 0 if z == 0 return end z = z - 1 else z = numofalphabets-1 stop = true end end end end turnwheels(["-tis","-suf","-bwt","-lcp"]) genometools-1.5.1/scripts/appendsuffix.rb000077500000000000000000000065701211610345200205670ustar00rootroot00000000000000#!/usr/bin/ruby # # Copyright (c) 2011 Giorgio Gonnella # Copyright (c) 2011 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # usage = <<-end_usage Usage: #$0 [+] Find macro names, function names and typedefs in a C file (templatefilename) and append "_" followed by the specified suffix to these identifiers and to further identifiers specified as optional arguments. end_usage if ARGV.size < 2 || !File.exists?(ARGV[0]) puts usage exit end class IdentifiersCollection attr_reader :macros, :functions, :types def initialize(c_code) uncommented = delcomments(c_code) toplevel = delblocks(uncommented) @macros = findmacronames(toplevel) notpreproc_toplevel = delpreproc(toplevel) @functions = findfunctionnames(notpreproc_toplevel) @types = findtypes(notpreproc_toplevel) end private def delcomments(input) output = "" prevc = nil state = :code input.each_byte do |c| if state == :comment state = :code if c == ?/ and prevc == ?* else if c == ?* and prevc == ?/ state = :comment output.chop! else output << c end end prevc = c end return output end def delblocks(uncommented) output = "" level = 0 uncommented.each_byte do |c| level += 1 if c == ?{ output << c if level == 0 level -= 1 if c == ?} end return output end def delpreproc(input) state = :notpreproc prevc = nil output = "" input.each_byte do |c| if state == :preproc state = :notpreproc if c == ?\n and prevc != ?\\ else if c == ?# state = :preproc else output << c end end prevc = c end return output end def findmacronames(toplevel) toplevel.scan(/#\s*define\s(\w+)/).flatten end def findfunctionnames(notpreproc_toplevel) notpreproc_toplevel.scan(/(\w+)\s*\([^\*].*?\)/m).flatten end def findtypes(notpreproc_toplevel) notpreproc_toplevel.scan(/typedef\s+[^;]*\s+(\w+)\s*;/m).flatten end end class CCode def initialize(c_code) @code = c_code @ids = IdentifiersCollection.new(c_code) end def append_suffix!(suffix, more_identifiers = []) ids = more_identifiers [:macros, :functions, :types].each do |idtype| ids += @ids.send(idtype) end ids.each do |id| @code.gsub!(/(\W+)(#{id})(\W+)/m) {"#$1#$2_#{suffix}#$3"} end end def to_s @code end end input = IO.read(ARGV.shift) suffix = ARGV.shift more_identifiers = ARGV code = CCode.new(input) code.append_suffix!(suffix, more_identifiers) print code genometools-1.5.1/scripts/blat2gff3000077500000000000000000000040701211610345200172340ustar00rootroot00000000000000#!/usr/bin/env ruby # # Copyright (c) 2006-2007 Gordon Gremme # Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'getoptlong' $:.push(File.dirname($0)) require 'gff3' # parse options opts = GetoptLong.new( [ "--max-mismatches", "-m", GetoptLong::REQUIRED_ARGUMENT ] ) max_mismatches = nil opts.each do |opt, arg| raise if opt != "--max-mismatches" max_mismatches = arg.to_i end # read input sequences = {} ARGF.each do |line| matches, misMatches, repMatches, nCount, qNumInsert, qBaseInsert, \ tNumInsert, tBaseInsert, strand, qName, qSize, qStart, qEnd, tName, tSize, \ tStart, tEnd, blockCount, blockSizes, qStarts, tStarts = line.split if not max_mismatches or misMatches.to_i <= max_mismatches then if sequences[tName] then sequences[tName].update_range(tStart.to_i, tEnd.to_i) else sequences[tName] = Sequence.new(tStart.to_i, tEnd.to_i) end gene = Gene.new(Range.new(tStart.to_i + 1, tEnd.to_i + 1), strand[0..0].to_s) exon_start_pos = tStarts.split(',') exon_sizes = blockSizes.split(',') 1.upto(blockCount.to_i) do |i| gene.add_exon(Range.new(exon_start_pos[i-1].to_i + 1, \ exon_start_pos[i-1].to_i + exon_sizes[i-1].to_i)); end sequences[tName].add_gene(gene); end end # output gff3_output(sequences, "blat") genometools-1.5.1/scripts/calcmonosize.rb000077500000000000000000000025421211610345200205540ustar00rootroot00000000000000#!/usr/bin/env ruby # compute the size of the representation of a monotone sequence of integers # the representation is described in author = # Gonnella, G. and Kurtz, S. # Readjoiner: a fast and memory efficient string graph-based sequence assembler # BMC Bioinformatics, 13, http://www.biomedcentral.com/1471-2105/13/82, # 2012 def log2(v) return Math.log(v)/Math.log(2.0) end def monotonesize(numofelems,maxvalue,trace=false) beta = log2 maxvalue.ceil minbits = nil mindelta = nil extra = nil 0.upto(beta) do |delta| bits = numofelems * delta + 2 ** (beta-delta) if trace puts "delta=#{delta},beta=#{beta},bits=#{bits/8}" end if minbits.nil? or bits < minbits minbits = bits mindelta = delta extra = 2 ** (beta-delta) end end return mindelta, minbits, extra end [10,20,30,40,50].each do |elems| numofelems = elems * 100000 [10,20,30,40,50].each do |maxval| maxvalue = numofelems * maxval mindelta, minbits, extra = monotonesize(numofelems,maxvalue) print "#{numofelems} #{maxvalue} #{mindelta} #{minbits} " printf("%.2f\n",minbits/numofelems.to_f) end end maxvalue = 2329908870 numofelems = 2492653 mindelta, minbits, extra = monotonesize(numofelems,maxvalue,true) print "#{numofelems} #{maxvalue} #{mindelta} #{minbits} " printf("%.2f %u %u\n",minbits/numofelems.to_f,minbits/8,extra/8) genometools-1.5.1/scripts/callrununique.sh000077500000000000000000000017501211610345200207640ustar00rootroot00000000000000#!/bin/sh # # Copyright (c) 2009 Stefan Kurtz # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. set -e -x cd testsuite AT=../testdata/at1MB U8=../testdata/U89959_genomic.fas ../scripts/rununique.sh ../bin/gt 10 20 ${U8} ${AT} cd .. genometools-1.5.1/scripts/calltestcase.sh000077500000000000000000000002401211610345200205350ustar00rootroot00000000000000#!/bin/sh if test $# -ne 1 then echo "Usage: $0 " exit 1 fi cd testsuite env -i ./testsuite.rb -gttestdata ${GTTESTDATA} -keywords ${1} cd .. genometools-1.5.1/scripts/check_api_includes000077500000000000000000000001311211610345200212500ustar00rootroot00000000000000#!/bin/bash find src/ -name '*_api.h' | xargs grep include | grep '"' | grep -v 'api.h"' genometools-1.5.1/scripts/check_core_includes000077500000000000000000000001351211610345200214330ustar00rootroot00000000000000#!/bin/bash find src/core -name '*.h' | xargs grep '#include' | grep '"' | egrep -v '"core/' genometools-1.5.1/scripts/checkchains.rb000077500000000000000000000022351211610345200203300ustar00rootroot00000000000000#!/usr/bin/env ruby def runchain2dimvschain2dim(args,matchfile) system "cat #{matchfile} | ../scripts/rf2of.rb > tmp.of" system "../bin/gt chain2dim " + args + " -m tmp.of > gtchain.out" system "chain2dim.x " + args + " tmp.of > vschain.out" system "cmp -s gtchain.out vschain.out" end params = ["-global", "-silent -global", "-local -wf 1.8", "-local -wf 0.5", "-local -maxgap 20", "-local 2b", "-local 55p -silent", "-global gc", "-global ov", "-global gc -wf 1.5", "-global ov -wf 1.8", "-global -maxgap 10", "-global gc -wf 1.5 -maxgap 10", "-global ov -wf 1.8 -maxgap 10", "-local", "-local 2p", "-local 20", "-local 2p -wf 1.8", "-local 2b -wf 1.8", "-local 20 -wf 1.8", "-local -wf 1.8 -maxgap 20", "-local 2p -wf 1.8 -maxgap 10", "-local 2b -wf 1.8 -maxgap 10", "-local 20 -wf 1.8 -maxgap 10"] resultdir="#{ENV['GTTESTDATA']}/repfind-result" Dir.foreach("#{resultdir}") do |matchfile| if matchfile.match(/^\S+\.fna-\S+\.fna.result$/) params.each do |args| runchain2dimvschain2dim(args,"#{resultdir}/#{matchfile}") end end end system "rm -f tmp.of gtchain.out vschain.out" genometools-1.5.1/scripts/checklcp.sh000077500000000000000000000003011211610345200176400ustar00rootroot00000000000000#!/bin/sh set -e -x if test $# -ne 1 then echo "Usage: $0 " exit 1 fi gt suffixerator -db $1 -dna -suf -tis -lcp -indexname sideeff gt dev sfxmap -lcp -tis -suf -esa sideeff genometools-1.5.1/scripts/checkmaxpairs.sh000077500000000000000000000020701211610345200207130ustar00rootroot00000000000000#!/bin/sh #set -e -x usage() { echo "Usage: $0 minlength [-q query] file1 [file2 ...]" } checkerror() { $1 if test $? -ne 0 then echo "failure: ${1}" exit 1 fi } cleanhashlines() { TMPFILE=`mktemp TMP.XXXXXX` || exit 1 sed -e '/^#/d' $1 > ${TMPFILE} mv ${TMPFILE} $1 } if test $# -lt 2 then usage exit 1 fi queryfile="" minlength=$1 if test "$2" = "-q" then if test $# -lt 4 then usage exit 1 fi queryfile=$3 shift shift fi shift filenames=$* for filename in ${filenames} do echo "$0 ${minlength} ${filename}" checkerror "../bin/gt suffixerator -algbds 3 43 120 -db ${filename} -indexname sfxidx -dna -suf -tis -lcp -pl" if test "X${queryfile}" = "X" then checkerror "../bin/gt repfind -l ${minlength} -ii sfxidx" > result.mp cleanhashlines result.mp else checkerror "../bin/gt repfind -l ${minlength} -q ${queryfile} -ii sfxidx" > result.mp cleanhashlines result.mp fi resultfile="${GTTESTDATA}/repfind-result/`basename ${filename}`.result" checkerror "cmp -s ${resultfile} result.mp" done genometools-1.5.1/scripts/checktallymer.sh000077500000000000000000000036671211610345200207350ustar00rootroot00000000000000#!/bin/sh checkerror() { if test $? -ne 0 then echo "failure: ${cmd}" exit 1 else echo "run ${cmd}" fi } cerr() { $* if [ $? -ne 0 ] then echo "failure: $*" exit 1 fi } if test $# -ne 1 then echo "Usage: $0 " exit 1 fi mersize=20 inputfile=$1 outoptions="-counts -pl -mersize ${mersize} -minocc 2 -maxocc 30" #PRECMD="valgrind.sh" PRECMD="env -i" cerr "bin/gt suffixerator -sat direct -db ${inputfile} -algbds 3 43 120 -tis -suf -lcp -pl -dna -indexname sfxidx" cmd="env -i bin/gt tallymer mkindex -test -mersize ${mersize} -esa sfxidx" ${cmd} > tmp1 checkerror cerr "mkvtree.x -db ${inputfile} -tis -suf -lcp -pl -dna -indexname mkvidx" cmd="tallymer-mkindex -mersize ${mersize} mkvidx" ${cmd} > tmp2 checkerror grep -v '^#' tmp2 > tmp2.2 mv tmp2.2 tmp2 cerr "cmp -s tmp1 tmp2" rm -f tmp[12] cmd="tallymer-mkindex ${outoptions} -indexname mkv-tyr-index mkvidx" ${cmd} checkerror cmd="${PRECMD} bin/gt tallymer mkindex ${outoptions} -indexname tyr-index -esa sfxidx" ${cmd} checkerror if test -s tyr-index.mct then cmd="${PRECMD} bin/gt tallymer search -strand fp -output qseqnum qpos counts sequence -test -tyr tyr-index -q ${AT}" ${cmd} > tmp1 checkerror cmd="tallymer-search -strand fp -output qseqnum qpos counts sequence mkv-tyr-index ${AT}" ${cmd} > tmp2 checkerror grep -v '^#' tmp2 > tmp2.2 mv tmp2.2 tmp2 cerr "cmp -s tmp1 tmp2" if test ${inputfile} = "testdata/Duplicate.fna" then echo "skip ${inputfile}" else cmd="${PRECMD} bin/gt tallymer occratio -minmersize 10 -maxmersize 500 -esa sfxidx -output total unique nonunique nonuniquemulti relative" ${cmd} > tmp1 checkerror grep -v '^#' tmp1 > tmp1.2 mv tmp1.2 tmp1 cmd="tallymer-occratio -minmersize 10 -maxmersize 500 -output total unique nonunique nonuniquemulti relative mkvidx" ${cmd} > tmp2 checkerror grep -v '^#' tmp2 > tmp2.2 mv tmp2.2 tmp2 cerr "cmp -s tmp1 tmp2" fi fi rm -f tmp[12] genometools-1.5.1/scripts/checkunique.sh000077500000000000000000000003541211610345200204000ustar00rootroot00000000000000#!/bin/sh set -e -x if test $# -lt 4 then echo "Usage: $0 ..." exit 1 fi rununique.sh ../bin/gt $* | grep -v '^#' > shit rununique-test.sh $* | grep -v '^#' > shit-test diff shit shit-test genometools-1.5.1/scripts/class_gen.rb000077500000000000000000000173451211610345200200330ustar00rootroot00000000000000#!/usr/bin/env ruby # # Copyright (c) 2013 Dirk Willrodt # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # # # # # create a new abstract class, or uses an abstract class to start an # implementation of it. # see src/core/example_rep.h # src/core/example.[ch] # for abstract class example and src/core/example_a.[ch] # src/core/example_b.[ch] # for implementations thereof. require 'optparse' require 'ostruct' require "erb" $:.unshift File.join(File.dirname(__FILE__), ".") require "codegen_module.rb" $CONFIG = ENV["GT_CODEGEN_CONFIG"] || "~/.gitconfig" module ClassGenOpts def self.parse(args) options = OpenStruct.new options.editor = "editor" options.create = true options.force = false options.refcount = true opts = OptionParser.new() opts.program_name = File.basename($0) opts.version = 0 , 1 opts.release = 1 opts.banner = "USAGE: #{opts.program_name} [options] dirname basename" opts.separator "" opts.separator "editor will open during file-creation, after editing, safe" opts.separator "the file, more files will be created based on that file" opts.separator "" opts.separator "Specific options:" opts.on("--editor EDITOR", "Your editor of choice to edit source code, ", "defaults to 'editor' which is only set on ", "Debion style systems" ) do |editor| options.editor = editor end opts.on("-f", "--force", "overwrite files if they already exist. _rep.h ", "file can be reused with --no-create.") do |force| options.force = force end opts.on("--[no-]create", "defaults to --create, will overwrite _rep.h ", "file if it exists (with --force). Otherwise ", "it will try to reopen it for editing. ", "(usufull if something went wrong in the first ", "step)" ) do |create| options.create = create end opts.on("--[no-]refcount", "add reference counting to the class interface ", "defaults to true.") do |refcount| options.refcount = refcount end opts.separator "" opts.separator "Common options" opts.on("-h", "--help", "print this help end exit") do puts opts exit end opts.on("--version", "print version and exit") do puts opts.ver exit end opts.parse!(args) if (args.length != 2) CodeGen.perror "wrong number of arguments\n" + opts end options.subdir = args[0] options.dirname = File.join "src", options.subdir if options.classname options.basename = File.join(options.dirname, File.basename(options.classname) + "_" + args[1]) else options.basename = File.join options.dirname, args[1] end return options end end def create_rep_file(options) repfile = File.new(options.repname, 'w') repfile << CodeGen.create_license guard_macro = File.basename(options.repname).gsub(/\./, '_').upcase fkt_pref = options.fkt_pref classN = options.classN subdir = options.subdir content = ERB.new($repfile).result(binding) repfile << ERB.new($hwrapper).result(binding) repfile.close end def fill_out_files(options) repfile = File.readlines(options.repname) options.functions = CodeGen.extract_functions_from_rep(options.classN, repfile) repfile.each_with_index do |line, idx| next unless line.match /XX\w+XX/ if line.match /XXfunctionNamesXX/ repfile[idx] = [] options.functions.each do |func, parameters| repfile[idx].push " #{options.classN}#{func} #{ func.gsub(/(^|[a-z])([A-Z])/) do replace = "" replace += $1 + '_' if $1.length > 0 replace += $2.downcase end};\n" end end if line.match /XXfunctionPtrXX/ repfile[idx] = [] indent = repfile[idx-1][/^.*\(/].length options.functions.each do |func, parameters| repfile[idx].push "#{' ' * indent}#{options.classN}#{func},\n" end repfile[idx][-1] = repfile[idx][-1].chomp.chop + ");\n" end end repfile.flatten! newfile = File.new(options.repname, 'w') newfile << repfile.join newfile.close end def create_interface_header(options) options.interfacename = options.basename + ".h" if File.exist?(options.interfacename) and not options.force CodeGen.perror "file #{options.interfacename} already exists\n" + "use --force to overwrite, with --no-create to reuse\n" + "(#$0 -h for details)" end i_file = File.new(options.interfacename, 'w') i_file << CodeGen.create_license classN = options.classN fkt_pref = options.fkt_pref functions = options.functions max_type_len = 0 max_type_len = "#{classN} *".length if options.refcount functions.each do |func, parameters| max_type_len = parameters[0].length if max_type_len < parameters[0].length end content = ERB.new($interface_header).result(binding) guard_macro = File.basename(options.interfacename).gsub(/\./, '_').upcase i_file << ERB.new($hwrapper).result(binding) end def create_interface_code(options) options.interfacename = options.basename + ".c" if File.exist?(options.interfacename) and not options.force CodeGen.perror "file #{options.interfacename} already exists\n" + "use --force to overwrite, with --no-create to reuse\n" + "(#$0 -h for details)" end i_code_file = File.new(options.interfacename, 'w') i_code_file << CodeGen.create_license classN = options.classN fkt_pref = options.fkt_pref functions = options.functions interface_funcs = "" functions.each do |func, paras| next if func == 'DeleteFunc' type = paras.shift interface_funcs += ERB.new($interface_func).result(binding) end create_func = ERB.new($create_func).result(binding) ref_func = ERB.new($ref_func).result(binding) cast_func = ERB.new($cast_func).result(binding) delete_func = ERB.new($delete_func).result(binding) class_new_fkt = ERB.new($class_new_fkt).result(binding) subdir = options.subdir i_code_file << ERB.new($interface_file).result(binding) i_code_file.close end begin options = ClassGenOpts.parse(ARGV); rescue OptionParser::InvalidOption => e CodeGen.perror e.message end options.repname = "#{options.basename}_rep.h" options.fkt_pref = File.basename(options.repname, '_rep.h') options.classN = CodeGen.filename2classname(options.basename) if File.exist?(options.repname) if not options.force CodeGen.perror "file #{options.repname} already exists\n" + "use --force to overwrite, with --no-create to reuse\n" + "(#$0 -h for details)" else if options.create create_rep_file(options) end end else create_rep_file(options) end system("#{options.editor} #{options.repname}") if options.create fill_out_files(options) else repfile = File.readlines(options.repname) options.functions = CodeGen.extract_functions_from_rep(options.classN, repfile) end create_interface_header(options) create_interface_code(options) genometools-1.5.1/scripts/class_implement.rb000077500000000000000000000103411211610345200212410ustar00rootroot00000000000000#!/usr/bin/env ruby # # Copyright (c) 2013 Dirk Willrodt # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # # # # # creates an implementation skeleton of an abstract class # see src/core/example_rep.h # src/core/example.[ch] # for abstract class example and src/core/example_a.[ch] # src/core/example_b.[ch] # for implementations thereof. require 'optparse' require 'ostruct' require 'pp' require "erb" $:.unshift File.join(File.dirname(__FILE__), ".") require "codegen_module.rb" module ClassGenOpts def self.parse(args) options = OpenStruct.new options.force = false opts = OptionParser.new() opts.program_name = File.basename($0) opts.version = 0 , 1 opts.release = 1 opts.banner = "USAGE: #{opts.program_name} [options] dirname classname basename" opts.separator "" opts.separator "dirname + classname gives the path to the abstract class," opts.separator "basename will be added to classname for files of" opts.separator "implemetation" opts.separator "" opts.separator "Specific options:" opts.on("-f", "--force", "overwrite files if they already exist.") do |force| options.force = force end opts.separator "" opts.separator "Common options" opts.on("-h", "--help", "print this help end exit") do puts opts exit end opts.on("--version", "print version and exit") do puts opts.ver exit end opts.parse!(args) if (args.length != 3) CodeGen.perror "wrong number of arguments\n" + opts end options.dirname = File.join "src", args[0] options.classbase = File.join options.dirname, args[1] options.basename = options.classbase + '_' + args[2] if (File.exist?(options.basename + '.h') or File.exist?(options.basename + '.c')) and not options.force CodeGen.perror "Either or both file(s) #{options.basename}.[ch]\n" + "already exist. Use --force to overwrite.\n" + "(#{opts.program_name} -h for details)" end return options end end def create_header(options) h_file = File.new(options.basename + '.h', 'w') h_file << CodeGen.create_license classbase = options.classbase[4..-1] guard_macro = File.basename(options.basename).upcase + '_H' cvar= File.basename(options.classbase) icvar= File.basename(options.basename) fkt_pref = "gt_" + cvar ifkt_pref = "gt_" + icvar classN = CodeGen.filename2classname(options.classbase) iclassN = CodeGen.filename2classname(options.basename) content = ERB.new($implement_header).result(binding) h_file << ERB.new($hwrapper).result(binding) h_file.close end def create_src(options) src_file = File.new(options.basename + '.c', 'w') src_file << CodeGen.create_license classbase = options.classbase[/[^\/]+\/(.+)$/, 1] basename = options.basename[/[^\/]+\/(.+)$/, 1] classN = CodeGen.filename2classname(options.classbase) iclassN = CodeGen.filename2classname(options.basename) cvar= File.basename(options.classbase) icvar= File.basename(options.basename) fkt_pref = "gt_" + cvar ifkt_pref = "gt_" + icvar repfile = File.readlines(options.classbase + "_rep.h") functions = CodeGen.extract_functions_from_rep(classN,repfile) funcnames = [] cvar= File.basename(options.classbase) icvar= File.basename(options.basename) src_file << ERB.new($implement_src).result(binding) src_file.close end begin options = ClassGenOpts.parse(ARGV); rescue OptionParser::InvalidOption => e CodeGen.perror e.message end create_header(options) create_src(options) genometools-1.5.1/scripts/cleanpp.sh000077500000000000000000000010001211610345200175030ustar00rootroot00000000000000#!/bin/sh # clean all files comprising the different kind of indexes rm -f *.ssp rm -f *.llv rm -f *.llv2 rm -f *.skp rm -f *.al[12] rm -f *.des rm -f *.prj rm -f *.lcp rm -f *.lcp2 rm -f *.suf rm -f *.tis rm -f *.ois rm -f *.bwt rm -f *.bck rm -f *.sds rm -f *.kys rm -f *.iso rm -f *.sti rm -f *.sti1 rm -f *.cld rm -f *.cld1 rm -f *.crf rm -f *.cfr rm -f *.lsf rm -f *.mer rm -f *.mbd rm -f *.mct rm -f *.esq rm -f *.bdx rm -f *.fma rm -f *.fmd rm -f *.pbt rm -f *.md5 rm -f *.[1-9]cxm genometools-1.5.1/scripts/cmpdbfile.sh000077500000000000000000000015021211610345200200150ustar00rootroot00000000000000#!/bin/sh if test $# -lt 1 then echo "Usage: $0 " exit 1 fi checkerror() { $1 if test $? -ne 0 then echo "failure: ${1}" exit 1 fi } comparefiles() { TMPFILE1=`mktemp ../testsuite/TMP.XXXXXX` || exit 1 egrep -v 'prefixlength|integersize|readmode|realspecialranges' $1 > ${TMPFILE1} TMPFILE2=`mktemp ../testsuite/TMP.XXXXXX` || exit 1 egrep -v 'prefixlength|integersize|readmode|realspecialranges' $2 > ${TMPFILE2} checkerror "cmp -s ${TMPFILE1} ${TMPFILE2}" rm -f ${TMPFILE1} ${TMPFILE2} } options="$*" checkerror "../bin/gt suffixerator -algbds 3 43 120 -indexname /tmp/idx-sfx -des ${options}" MKVTREE="/Users/stefan/bin-ops/i686-apple-darwin/mkvtree.x" checkerror "${MKVTREE} -indexname /tmp/idx-mkv -dna ${options}" echo "XXX ${options}" comparefiles /tmp/idx-mkv.prj /tmp/idx-sfx.prj genometools-1.5.1/scripts/cmplcpintervals.sh000077500000000000000000000022371211610345200213040ustar00rootroot00000000000000#!/bin/sh checkerror() { if test $? -ne 0 then echo "failure: ${cmd}" exit 1 fi } if test $# -eq 1 then filenamelist="$1" else filenamelist=`find testdata/ -name '[A-Z]*.fna'` fi for filename in ${filenamelist} do echo "${filename}" cmd="env -i bin/gt suffixerator -tis -suf -lcp -dna -indexname sfx -db ${filename}" ${cmd} checkerror cmd="env -i RUBYLIB=gtruby LD_LIBRARY_PATH=lib scripts/lcpintervals.rb --itv sfx" ${cmd} > itvs.result1 checkerror cmd="env -i bin/gt dev sfxmap -enumlcpitvs -esa sfx" ${cmd} > itvs.result2 checkerror cmd="cmp -s itvs.result1 itvs.result2" ${cmd} checkerror cmd="env -i RUBYLIB=gtruby LD_LIBRARY_PATH=lib scripts/lcpintervals.rb --tree sfx" ${cmd} > itvtree.result1 checkerror cmd="env -i bin/gt dev sfxmap -enumlcpitvtree -esa sfx" ${cmd} > itvtree.result2 checkerror cmd="env -i bin/gt dev sfxmap -enumlcpitvtreeBU -esa sfx" ${cmd} > itvtree.result3 checkerror cmd="cmp -s itvtree.result1 itvtree.result2" ${cmd} checkerror cmd="cmp -s itvtree.result2 itvtree.result3" ${cmd} checkerror done rm -f itvs.result1 itvs.result2 rm -f itvtree.result1 itvtree.result2 itvtree.result3 genometools-1.5.1/scripts/code_templates.rb000066400000000000000000000232751211610345200210610ustar00rootroot00000000000000 $license = <<-END_LICENSE /* Copyright (c) <%=year%> <%=name%> <<%=email%>> Copyright (c) <%=year%> Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ END_LICENSE $repfile = <<-END_REPFILE #include #include "<%=subdir%>/<%=fkt_pref%>.h" typedef struct <%=classN%>Class <%=classN%>Class; typedef struct <%=classN%>Members <%=classN%>Members; /* TODO: add typedefs for functions here */ /* examples showcasing coding convention: typedef unsigned int (*<%=classN%>FooFunc)(<%=classN%>*, unsigned long*); typedef int *(*<%=classN%>BarFunc)(<%=classN%>*, unsigned long); */ typedef void (*<%=classN%>DeleteFunc)(<%=classN%>*); struct <%=classN%> { const <%=classN%>Class *c_class; <%=classN%>Members *members; }; struct <%=classN%>Class { size_t size; /* XXfunctionNamesXX do not change will be replaced by function names */ }; struct <%=classN%>Members {<% if options.refcount %>\n unsigned long refcount;<% end %> }; const <%=classN%>Class* gt_<%=fkt_pref%>_class_new(size_t size, <%= " "*(classN.length + fkt_pref.length + 26) %>\ /* XXfunctionPtrXX do not change */); <%=classN%>* gt_<%=fkt_pref%>_create(const <%=classN%>Class*); void*<%= ' ' * (classN.length + 8) %>\ gt_<%=fkt_pref%>_cast(const <%=classN%>Class*, <%= ' ' * (classN.length + fkt_pref.length + 22) %><%=classN%>*); END_REPFILE $hwrapper = <<-END_HWRAPPER #ifndef <%=guard_macro%> #define <%=guard_macro%> <%=content%> #endif END_HWRAPPER $gt_class_c = <<-END_GT_CLASS_C #include "core/ma.h" struct <%=klass%> { }; <%=creatordecl%> { <%=klass%> *<%=basename%>; <%=basename%> = gt_malloc(sizeof (<%=klass%>)); return <%=basename%>; } <%=destructordecl%> { gt_free(<%=basename%>); } END_GT_CLASS_C $gt_class_h = <<-END_GT_CLASS_H typedef struct <%=klass%> <%=klass%>; <%=creatordecl%>; <%=destructordecl%>; END_GT_CLASS_H $interface_header = <<-INTERFACE_HEADER /* Abstract class <%=classN%>, TODO: add documentation */ typedef struct <%=classN%> <%=classN%>; <% if options.refcount %>\ /* Increases the reference count of the <<%=classN%>>. */ <%=classN%>*<%=' '*(max_type_len - 1 - classN.length)%>\ gt_<%=fkt_pref%>_ref(<%=classN%> *<%=fkt_pref%>);\ <% end %>\ <%functions.each do |func, parameters| %> /* TODO: document and add parameter names */ <% type =parameters[0] + ' '*(max_type_len - parameters[0].length) %>\ <% type = type.gsub(/ [*]/, '* ') funcname = type + 'gt_' + fkt_pref + '_' + func[0..-5].gsub(/(^|.)([A-Z])/) do rep = '' rep = $1+'_' if $1.length >0 rep += $2.downcase end + '(' %>\ <%=funcname%>\ <% parameters[1..-1].each_with_index do |parameter, idx|%>\ <% if idx > 0 %>, <%= ' ' * funcname.length%>\ <% end %>\ <% if parameter[-1] == '*' %>\ <% puts parameter %>\ <%= parameter.chop%> *\ <% else %>\ <%= parameter%>\ <% end %>\ <% if parameter.match /^\#{classN}\\*$/ %>\ <%= fkt_pref %>\ <% else %>\ para<%=idx%> /*TODO: name*/\ <% end %>\ <% end %>);\ <%end %> INTERFACE_HEADER $ref_func = <<-REF_FUNC <%=classN%> *gt_<%=fkt_pref%>_ref(<%=classN%> *<%=fkt_pref%>) { gt_assert(<%=fkt_pref%>); <%=fkt_pref%>->members->refcount++; return <%=fkt_pref%>; } REF_FUNC $create_func = <<-CREATE_FUNC <%=classN%> *gt_<%=fkt_pref%>_create(const <%=classN%>Class *<%=fkt_pref%>_c) { <%=classN%> *<%=fkt_pref%>; gt_assert(<%=fkt_pref%>_c && <%=fkt_pref%>_c->size); <%=fkt_pref%> = gt_calloc((size_t) 1, <%=fkt_pref%>_c->size); <%=fkt_pref%>->c_class = <%=fkt_pref%>_c; <%=fkt_pref%>->members = gt_calloc((size_t) 1, sizeof (<%=classN%>Members)); return <%=fkt_pref%>; } CREATE_FUNC $cast_func = <<-CAST_FUNC void *gt_<%=fkt_pref%>_cast(GT_UNUSED const <%=classN%>Class *<%=fkt_pref%>_c, <%=' ' * (fkt_pref.length + 15)%><%=classN%> *<%=fkt_pref%>) { gt_assert(<%=fkt_pref%>_c && <%=fkt_pref%> && <%=fkt_pref%>->c_class == <%=fkt_pref%>_c); return <%=fkt_pref%>; } CAST_FUNC $delete_func = <<-DELETE_FUNC void gt_<%=fkt_pref%>_delete(<%=classN%> *<%=fkt_pref%>) { if (<%=fkt_pref%> != NULL) { <% if options.refcount %>\ if (<%=fkt_pref%>->members->refcount) { <%=fkt_pref%>->members->refcount--; return; } <%end %>\ gt_assert(<%=fkt_pref%>->c_class); if (<%=fkt_pref%>->c_class->delete_func != NULL) <%=fkt_pref%>->c_class->delete_func(<%=fkt_pref%>); gt_free(<%=fkt_pref%>->members); gt_free(<%=fkt_pref%>); } } DELETE_FUNC $interface_func = <<-INTERFACE_FUNC <%funcname = type + 'gt_' + fkt_pref + '_' + func[0..-5].gsub(/(^|.)([A-Z])/) do rep = '' rep = $1+'_' if $1.length >0 rep += $2.downcase end + '(' %> <%=funcname %>\ <%paras.each_with_index do |para,idx| %>\ <% if idx > 0 %>, <%= ' ' * (funcname.length) %>\ <% end %>\ <% if para[-1] == '*' %>\ <%= para.chop %> *\ <% else %>\ <%= para %>\ <% end %>\ <% if para.match /^\#{classN}\\*$/ %>\ <%= fkt_pref %>\ <% else %>\ para<%=idx%> /*TODO: name*/\ <% end %>\ <%end %>) { gt_assert(<%=fkt_pref%> != NULL); gt_assert(<%=fkt_pref%>->c_class != NULL); if (<%=fkt_pref%>->c_class->\ <%=func.gsub(/(^|.)([A-Z])/) do rep = '' rep = $1+'_' if $1.length >0 rep += $2.downcase \ end %> != NULL) return <%=fkt_pref%>->c_class->\ <%=func.gsub(/(^|.)([A-Z])/) do rep = '' rep = $1+'_' if $1.length >0 rep += $2.downcase \ end %>(\ <%paras.each_with_index do |para,idx| %>\ <% if idx > 0 %>, <%= ' ' * (func.length + fkt_pref.length + 23) %>\ <% end%>\ <% if para.match /^\#{classN}\\*$/ %>\ <%= fkt_pref %>\ <% else %>\ para<%=idx%> /*TODO: name*/\ <% end %>\ <%end %>); return\ <%if type.match /[*]/ %>\ NULL;\ <%elsif type.match /void/ %>\ ;\ <%else %>\ 0;\ <%end %> /* TODO: check if default return value is sane */ } INTERFACE_FUNC $class_new_fkt = <<-CLASS_NEW_FKT const <%=classN%>Class *gt_<%=fkt_pref%>_class_new(size_t size\ <%functions.each do |func, paras| %>, <%= ' ' * (27 + classN.length + fkt_pref.length)%>\ <%=classN%><%=func%> <%=func.gsub(/(^|.)([A-Z])/) do rep = '' rep = $1+'_' if $1.length > 0 rep += $2.downcase end%>\ <%end %>) { <%=classN%>Class *<%=fkt_pref%>_c = gt_malloc(sizeof (*<%=fkt_pref%>_c); <%=fkt_pref%>_c->size = size; <%functions.each do |func, paras| %>\ <% name = func.gsub(/(^|.)([A-Z])/) do rep = '' rep = $1+'_' if $1.length >0 rep += $2.downcase end %>\ <%=fkt_pref%>_c-><%=name%> = <%=name%>; <%end %>\ return <%=fkt_pref%>_c; } CLASS_NEW_FKT $interface_file = <<-INTERFACE_CODE #include "<%=subdir%>/<%=fkt_pref%>_rep.h" #include "core/assert_api.h" #include "core/ma.h" #include "core/unused_api.h" <%=create_func%> <% if options.refcount %>\ <%=ref_func%> <% end %>\ <%=cast_func%>\ <%=interface_funcs%> <%=class_new_fkt%> <%=delete_func%> INTERFACE_CODE $implement_header = <<-IMPLEMENT_HEADER #include "<%=classbase%>.h" /* Class <<%=iclassN%>>, Implements the <<%=classN%>> interface. TODO: add documentation */ typedef struct <%=iclassN%> <%=iclassN%>; /* Return a new <<%=classN%>> object, the implementation beeing of type <<%=iclassN%>>. TODO: add documentation */ <%=classN%>* <%=ifkt_pref%>_new(void /*TODO: add parameters*/); /* TODO: add prototypes of implementation <<%=iclassN%>> only functions */ IMPLEMENT_HEADER $implement_src = <<-IMPLEMENT_SRC #include "<%=classbase%>_rep.h" #include "<%=basename%>.h" #include "core/unused_api.h" struct <%=iclassN%> { <%=classN%> parent_instance; /* TODO: add implementation members */ }; <%functions.each do |func, parameters| %>\ <% type = parameters[0] %>\ <% funcnames << ifkt_pref + '_' + func[0..-5].gsub(/(^|.)([A-Z])/) do rep = '' rep = $1+'_' if $1.length >0 rep += $2.downcase end funcname = type + funcnames[-1] + '(' %>\ static <%=funcname%>\ <% parameters[1..-1].each_with_index do |parameter, idx|%>\ <% if idx > 0 %>, <%= ' ' * (funcname.length + 7)%>\ <% end %>GT_UNUSED \ <% if parameter[-1] == '*' %>\ <%= parameter.chop%> *\ <% else %>\ <%= parameter%>\ <% end %>\ <% if parameter.match /^\#{classN}\\*$/ %>\ <%= icvar %>\ <% else %>\ para<%=idx%> /*TODO: name*/\ <% end %>\ <% end %>) { /* TODO: add functionality */ return\ <% if type.match /[*]/ %>\ NULL;\ <% elsif type.match /void/ %>\ ;\ <% else %>\ 0;\ <% end %> /* TODO: check if default return value is sane */ } <%end %>\ /* TODO: implement <<%=iclassN%>> only functions */ /* map static local methods to interface */ const <%=classN%>Class* <%=ifkt_pref%>_class(void) { static const <%=classN%>Class *this_c = NULL; if (this_c == NULL) { this_c = <%=fkt_pref%>_class_new(sizeof (<%=iclassN%>), <%funcnames.each_with_index do |name,idx| %>\ <% if idx > 0 %>\ , <% end %>\ <%= ' ' * (fkt_pref.length + 24) %><%=name%>\ <%end %>); } return this_c; } #define <%=ifkt_pref%>_cast(cvar) \\ <%=fkt_pref%>_cast(<%=ifkt_pref%>_class(), cvar) <%=classN%>* <%=ifkt_pref%>_new(void /* TODO: add parameters */) { <%=classN%> *<%=cvar%>; <%=iclassN%> *<%=icvar%>; <%=cvar%> = <%=fkt_pref%>_create(<%=ifkt_pref%>_class()); <%=icvar%> = <%=ifkt_pref%>_cast(<%=cvar%>); /* TODO: initialise */ return <%=cvar%>; } IMPLEMENT_SRC genometools-1.5.1/scripts/codegen000077500000000000000000000123601211610345200170670ustar00rootroot00000000000000#!/usr/bin/env ruby # # Copyright (c) 2009-2010 Giorgio Gonnella # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require "erb" $:.unshift File.join(File.dirname(__FILE__), ".") require "codegen_module.rb" $help = <<-END_HELP \nCode generator for: - header file (license, ifndef/def/endif) - module files (header file and c file including the header) - class files (h and c files, basic skeleton) - tool files (based on tools/gt_template.[ch]) It requires name and email of the user, that are expected to be found in the [user] section of the user-specific git configuration file (#$GITCONFIG). You may specify another file using the env variable GT_CODEGEN_CONFIG. Usage: #$0 header|module|class|tool where is the directory under src where the files are written and has no gt_ prefix and is written in lower case, and if it consists of multiple words they are connected_with_underscores e.g. #$0 tool tools xyz #$0 header core abc_def There is absolutely no guarantee that the results are correct. Existing files are not overwritten or modified. Report bugs to . END_HELP def find_src_directory scripts_dir = File.dirname(File.expand_path($0)) src_dir = File.join(scripts_dir, "..", "src") return File.expand_path(src_dir) end def parse_args generators = %w{header module class tool help} CodeGen.perror("not enough arguments") if ARGV.size < 1 generator = ARGV[0] if (generator=="help") puts($help) exit(0) end CodeGen.perror("generator #{generator} unknown") if !generators.include?(generator) CodeGen.perror("not enough arguments") if ARGV.size < 3 CodeGen.perror("too many arguments") if ARGV.size > 3 path = File.join(find_src_directory, ARGV[1]) CodeGen.perror("Directory #{path} not found") if !File.directory?(path) basename = ARGV[2] return generator, path, basename end def check_file(path, basename, extension) filename = File.join(path, basename+"."+extension) CodeGen.perror("File #{filename} exists already") if File.exist?(filename) end def write_file(path, basename, extension, content) filename = File.join(path, basename+"."+extension) file = File.open(filename, "w+") puts File.expand_path(file.path) file.puts(content) file.close end def gen_header(path, basename, content = "") guard_macro = basename.upcase+"_H" header = $license + "\n" + ERB.new($hwrapper).result(binding) check_file(path, basename, "h") write_file(path, basename, "h", header) end def gen_module(path, basename, ccontent = "\n", hcontent = "") code = $license + "\n" + "#include \"#{File.basename(path)}/#{basename}.h\"" + ccontent check_file(path, basename, "c") gen_header(path, basename, hcontent) write_file(path, basename, "c", code) end def gen_class(path, basename) prefix = "gt_#{basename}_" klass = "Gt"+basename.gsub(/(^|_)(.)/){$2.upcase} creatordecl = "#{klass} *#{prefix}new(void)" destructordecl = "void #{prefix}delete(#{klass} *#{basename})" gen_module(path, basename, ERB.new($gt_class_c).result(binding), ERB.new($gt_class_h).result(binding)) end def prepare_tool_c(path, basename) tools_dir = File.join(find_src_directory, "tools") gt_template_c = File.expand_path(File.join(tools_dir, "gt_template.c")) CodeGen.perror("File #{gt_template_c} not found") if !File.exists?(gt_template_c) # skip license template: c_template = IO.read(gt_template_c) c_template =~ /(.*?)(#include.*)/m c_template = $2 structprefix = "Gt"+basename.gsub(/(^|_)(.)/){$2.upcase} c_template.gsub!("template", basename) c_template.gsub!("Template", structprefix) return $license + "\n" + c_template end def prepare_tool_h(path, basename) tools_dir = File.join(find_src_directory, "tools") gt_template_h = File.expand_path(File.join(tools_dir, "gt_template.h")) CodeGen.perror("File #{gt_template_h} not found") if !File.exists?(gt_template_h) h_template = IO.read(gt_template_h) # skip license template: h_template =~ /(.*?)(#ifndef.*)/m h_template = $2 h_template.gsub!("TEMPLATE", basename.upcase) h_template.gsub!("template", basename) return $license + "\n" + h_template end def gen_tool(path, basename) check_file(path, "gt_"+basename, "h") check_file(path, "gt_"+basename, "c") write_file(path, "gt_"+basename, "h", prepare_tool_h(path, basename)) write_file(path, "gt_"+basename, "c", prepare_tool_c(path, basename)) end # main generator, path, basename = parse_args name, email = CodeGen.find_user_data year = Time.now.year $license = ERB.new($license).result send("gen_#{generator}", path, basename) genometools-1.5.1/scripts/codegen_module.rb000066400000000000000000000031111211610345200210250ustar00rootroot00000000000000$:.unshift File.join(File.dirname(__FILE__), ".") require "code_templates.rb" $GITCONFIG = ENV["GT_CODEGEN_CONFIG"] || "~/.gitconfig" module CodeGen def CodeGen.perror(msg) STDERR.puts "#$0: error: #{msg}" STDERR.puts "Use '#$0 help' to print usage instructions" exit(1) end def CodeGen.find_user_data configfile = File.expand_path($GITCONFIG) if File.exist?(configfile) name = nil email = nil File.open(configfile) do |f| while (line = f.gets) && (!name||!email) do name = $1 if !name && line =~ /\s*name\s*=\s*(.*)\s*\n/ email = $1 if !email && line =~ /\s*email\s*=\s*(.*)\s*\n/ end end return name, email else self.perror("#$GITCONFIG file not found") exit end end def CodeGen.create_license name, email = CodeGen.find_user_data year = Time.now.year ERB.new($license).result(binding) end def CodeGen.filename2classname(filename) "Gt" + File.basename(filename).gsub(/(^|_)(.)/){$2.upcase} end def CodeGen.extract_functions_from_rep(classN, repfile) get_parameters=false functions = Hash.new repfile.each do |line| if line.match /^typedef (\S+( \S+)* \*?)\(\*#{classN}(\w+)\)/ functions[$3] = [$1] get_parameters = $3 end if get_parameters line.scan /(\w+(\s\w+)*[*]?)(,|\);)/ do |parameter| functions[get_parameters].push parameter[0] end get_parameters = false if line.match /\);/ end break if line.match /^struct #{classN}/ end return functions end end genometools-1.5.1/scripts/comparesfx.sh000077500000000000000000000003731211610345200202440ustar00rootroot00000000000000#!/bin/sh for filename in `scripts/enumseqfiles.sh` do # echo "${filename}" bin/gt suffixerator -db ${filename} -tis -v > tmp1 /local/kurtz/tallymer-test/bin/gt suffixerator -algbds 3 43 120 -db ${filename} -tis -v > tmp2 diff tmp1 tmp2 done genometools-1.5.1/scripts/create_amalgamation000077500000000000000000000001211211610345200214300ustar00rootroot00000000000000#!/bin/sh -e for FILE in $* do echo "$FILE\"" | sed 's%src/%#include "%' done genometools-1.5.1/scripts/ctags.sh000077500000000000000000000030451211610345200171750ustar00rootroot00000000000000#!/bin/sh # # Copyright (c) 2007-2008 Gordon Gremme # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # # try to differntiate between Exuberant Ctags and BSD Ctags ctags --version > /dev/null if [ $? -eq 0 ] then exuberantopts="--c++-kinds=+p --fields=+iaSKlm --extra=+q" fi # make a new tags file ctags -w ${exuberantopts} \ src/*.[ch] \ src/annotationsketch/*.[ch] \ src/core/*.[ch] \ src/examples/*.[ch] \ src/extended/*.[ch] \ src/gtlua/*.[ch] \ src/gth/*.[ch] \ src/ltr/*.[ch] \ src/match/*.[ch] \ src/mgth/*.[ch] \ src/tools/*.[ch] \ testsuite/*.rb \ scripts/*.rb genometools-1.5.1/scripts/diff-cover.rb000077500000000000000000000040751211610345200201150ustar00rootroot00000000000000#!/usr/bin/env ruby def copy(v,r) return Array.new(r) {v} end def partialsums(bseq) sum = 0 l = [0] bseq.each do |b| sum += b l = l.push(sum) end return l end def checkcover(v,psum,i) psum.each do |j| psum.each do |k| if (k-j) % v == i return true end end end return false end def checkallcover(v,psum) 0.upto(v-1) do |i| if not checkcover(v,psum,i) STDERR.puts "cannot find difference elements for #{i} in #{v}-cover" exit(1) end end end def diff_cover(check,logmod) dc = case logmod when 0 then [0] when 1 then [0,1] when 2 then [0,1,2] when 3 then [0,1,2,4] when 4 then [0,1,2,5,8] when 5 then [0,1,2,3,7,11,19] when 6 then [0,1,2,5,14,16,34,42,59] when 7 then [0,1,3,7,17,40,55,64,75,85,104,109,117] when 8 then [0,1,3,7,12,20,30,44,65,80,89,96,114, 122,128,150,196,197,201,219] else v = 2**logmod r = 0 while 24*r*r+36*r+13 < v r += 1 end bseq = copy(1,r) + copy(r+1,1) + copy(2*r+1,r) + copy(4*r+3,2*r+1) + copy(2*r+2,r+1) + copy(1,r) psum = partialsums(bseq) if check checkallcover(v,psum) end partialsums(bseq) end return dc end def usage() STDERR.puts "Usage: #{$0} [check] " exit(1) end check=false if ARGV.length == 1 maxcover=ARGV[0].to_i else if ARGV.length == 2 if ARGV[0] == 'check' check=true maxcover=ARGV[0].to_i else usage() end else usage() end end def formtype(dc,cflag) dc.collect {|a| "#{cflag}(" + a.to_s + ")"} end puts "static Diffvalue differencecovertab[] =" puts "{" lentab = [] 0.upto(maxcover) do |logmod| dc = diff_cover(check,logmod) lentab = lentab.push(dc.length) print " /* #{2**logmod} */ " + formtype(dc,"UScast").join(",") if logmod == maxcover puts "" else puts ", " end end puts "};" puts "" puts "static Diffrank differencecoversizes[]" puts " = {" + formtype(lentab,"UCcast").join(",") + "};" genometools-1.5.1/scripts/do.sh000077500000000000000000000010111211610345200164650ustar00rootroot00000000000000#!/bin/sh checkerror() { if test $? -ne 0 then echo "failure: ${cmd}" exit 1 else echo "okay: ${cmd}" fi } for cmpcharbychar in 0 1 do for dir in fwd rev cpl rcl do extra="" if cmpcharbychar -eq 1 then extra="-cmpcharbychar" fi cmd="gt suffixerator -dir ${dir} -algbds 3 43 120 -parts 5 -dna -v -pl -bck -tis -suf -lcp -bwt -des -db ${AT} -showtime ${extra}" ${cmd} checkerror cmd="gt dev sfxmap -tis -suf -lcp -bwt -des -esa at1MB" ${cmd} checkerror done done genometools-1.5.1/scripts/dos2unix000077500000000000000000000001671211610345200172400ustar00rootroot00000000000000#!/usr/bin/env ruby regex = /\r\n/ newstring = "\n" ARGF.each{ |line| line.gsub!( regex, newstring ) puts line } genometools-1.5.1/scripts/dwmake.rb000077500000000000000000000054261211610345200173420ustar00rootroot00000000000000#!/usr/bin/env ruby # # Copyright (c) 2010 Stefan Kurtz # Copyright (c) 2010 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # require 'ostruct' require 'optparse' require 'fileutils' def usage(opts,msg) STDERR.puts "#{$0}: #{msg}\n#{opts.to_s}" exit 1 end def parseargs(argv) options = OpenStruct.new options.m64 = false options.speed = false options.prof = false options.ddd = false options.threads = false opts = OptionParser.new opts.on("-m","--m64","compile 64 bit binary") do |x| options.m64 = true end opts.on("-s","--speed","optimize for speed") do |x| if options.ddd usage(opts,"-d and -s exclusive") end options.speed = true end opts.on("-p","--prof","compile for profiling") do |x| options.prof = true end opts.on("-d","--ddd","compile for debugging (no opt)") do |x| if options.speed usage(opts,"-d and -s exclusive") end options.ddd = true end opts.on("-j [n]", Integer, "number of processes for make") do |x| options.threads = true options.j = x || "" end rest = opts.parse(argv) if not rest.empty? usage(opts,"unnecessary arguments: #{rest}") exit 1 end return options end def makecompilerflags(fp,options) fp.print "all:\n\t\${MAKE} curses=no cairo=no" fp.print " CFLAGS+=-fstrict-aliasing" if options.ddd fp.print " opt=no" end if options.speed fp.print " assert=no amalgamation=yes" end if options.m64 fp.print " 64bit=yes" end if options.prof fp.print " prof=yes" end if options.threads fp.print " -j#{options.j}" end fp.puts " CC='ccache clang'" end if File.exists?('LocalMakefile') FileUtils.mv('LocalMakefile','LocalMakefile.previous') end options = parseargs(ARGV) File.open('LocalMakefile',"w") do |fp| makecompilerflags(fp,options) end if File.exists?('LocalMakefile.previous') and not FileUtils.compare_file('LocalMakefile','LocalMakefile.previous') STDERR.puts "Current and previous LocalMakefile files differ: first " + "remove them" exit 1 end system("make -f LocalMakefile") genometools-1.5.1/scripts/encodesql2gff3000077500000000000000000000034541211610345200202740ustar00rootroot00000000000000#!/usr/bin/env ruby # # Copyright (c) 2006-2007, 2012 Gordon Gremme # Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # $:.push(File.dirname($0)) require 'gff3' # read input sequences = {} ARGF.each do |line| bin, name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds, score, name2, cdsStartStat, cdsEndStat, exonFrames = line.split if sequences[chrom] then sequences[chrom].update_range(txStart.to_i+1, txEnd.to_i) else sequences[chrom] = Sequence.new(txStart.to_i+1, txEnd.to_i) end gene = Gene.new(Range.new(txStart.to_i+1, txEnd.to_i), strand) gene.name = name gene.attributes = { "Name2" => name2 } if (cdsStart.to_i > 0 and cdsEnd.to_i > 0) then gene.cds_pos = Range.new(cdsStart.to_i+1, cdsEnd.to_i) end exon_start_pos = exonStarts.split(',') exon_end_pos = exonEnds.split(',') 1.upto(exonCount.to_i) do |i| gene.add_exon(Range.new(exon_start_pos[i-1].to_i+1, exon_end_pos[i-1].to_i)); end sequences[chrom].add_gene(gene); end # output gff3_output(sequences, "ENCODE") genometools-1.5.1/scripts/enumseqfiles.sh000077500000000000000000000002411211610345200205670ustar00rootroot00000000000000#!/bin/sh find testdata ${GTTESTDATA} -type f \( -name '*.fsa.gz' -o\ -name '*.fna' -o\ -name '*.fsa' \) genometools-1.5.1/scripts/esq-in-bytes.sh000077500000000000000000000004711211610345200204140ustar00rootroot00000000000000#!/bin/sh set -e -x # set GTDIR as paht of genometools directory for filename in `${GTDIR}/scripts/findfasta.rb` do gt encseq encode -ssp no -sds no -md5 no -des no -no_esq_header \ -showstats -sat direct -indexname seq $filename # Now do something with the sequence ls -l seq.esq done genometools-1.5.1/scripts/evalsfxrun.sh000077500000000000000000000070141211610345200202710ustar00rootroot00000000000000#!/bin/bash # set -e -x if test $# -ne 1 then echo "Usage: $0 [small|all]" exit 1 fi if test "${PROJECT}XXX" = "XXX" then echo "$0: environment variable PROJECT not defined" exit 1 fi repetitivefiles="mfd paradoxus" case $1 in small) allfiles="at1MB ecoli1 ecoli2 yeast mfd" ;; all) allfiles="at1MB ecoli1 ecoli2 yeast mfd dmel human2 human22 paradoxus" ;; *) allfiles=$1 ;; esac code2file() { case $1 in at1MB) echo "${GTDIR}/testdata/at1MB";; mfd) echo "${HOME}/seqcmpprojects/MouthFootDisease/mfdallpart.fna.gz";; yeast) echo "${HOME}/seqcmpprojects/yeast.fna.gz";; human2) echo "${PROJECT}/genomes/primate/H_sapiens-build36.54-2009/Homo_sapiens.NCBI36.54.dna.chromosome.02.fa.gz";; human22) echo "${PROJECT}/genomes/primate/H_sapiens-build36.54-2009/Homo_sapiens.NCBI36.54.dna.chromosome.22.fa.gz";; dmel) echo "${HOME}/seqcmpprojects/d_mel.fna.gz";; ecoli1) echo "${PROJECT}/genomes/Bacteria/Escherichia_coli_K12/NC_000913.fna";; ecoli2) echo "${PROJECT}/genomes/Bacteria/Ecoli_O157_H7/AE005174.fna";; swiss1MB) echo "${GTTESTDATA}/swissprot/swiss1MB";; paradoxus) echo "${HOME}/seqcmpprojects/S-paradoxus.fna.gz";; *) echo "$0: illegal filecode $1" exit 1;; esac } checkrepetitive() { filename=$1 for cfc in $repetitivefiles do if test ${cfc} == ${filename} then return 1 fi done return 0 } suffixerator() { fc=$1 filename=`code2file $1` shift printf "# RUN $fc sfx $*\n" GT_ENV_OPTIONS=-showtime ${RUNNER} ${GTDIR}/bin/gt suffixerator -v -indexname sfx-id -tis -suf -db ${filename} $* | egrep '# TIME overall|# space peak' } sainesq() { fc=$1 filename=`code2file $1` shift printf "# RUN ${fc} sainesq\n" ${GTDIR}/bin/gt encseq encode -indexname sfx-id ${filename} GT_ENV_OPTIONS=-showtime ${RUNNER} ${GTDIR}/bin/gt dev sain -esq sfx-id | egrep '# TIME overall|# space peak' } sainfile() { fc=$1 filename=`code2file $1` shift printf "# RUN ${fc} sainfile\n" GT_ENV_OPTIONS=-showtime ${RUNNER} ${GTDIR}/bin/gt dev sain -file ${filename} | egrep '# TIME overall|# space peak' } sais() { fc=$1 filename=`code2file $1` shift printf "# RUN ${fc} sais-lite\n" ${ETC}/Ccode/SAIS-lite/sais.x ${filename} | egrep '# TIME overall|# space peak' } afconstruct() { fc=$1 filename=`code2file $1` shift printf "# RUN ${fc} afconstruct\n" Structatordir=${HOME}/Software/Structator1.1 TMPFILE=`mktemp /tmp/fastafile.XXXXXX` echo ${filename} | egrep '\.gz$' > /dev/null if test $? -eq 0 then cmd="gzip -c -d ${filename}" else cmd="cat ${filename}" fi ${cmd} > ${TMPFILE} if test $? -ne 0 then echo "Failure: ${cmd}" exit 1 fi ${Structatordir}/construct/afconstruct ${TMPFILE} -suf -alph ${Structatordir}/testdata/rna.alphab -time | egrep '# TIME overall' } mkesa() { fc=$1 printf "# RUN $fc mkesa\n" filename=`code2file $1` runmkesa-sfx.sh ${filename} } for rfc in $allfiles do fn=`code2file ${rfc}` if test ! -f ${fn} then echo "$0: ${fn} does not exist" exit 1 fi done # suffixerator ecoli2 -sat uint32 -dc 128 # exit 0 echo "# DATE `date +%Y-%m-%d-%H:%M`" echo "# HOSTNAME `hostname`" for rfc in $allfiles do checkrepetitive ${rfc} if test $? -eq 0 then suffixerator ${rfc} "" fi for dc in 32 128 256 do suffixerator ${rfc} -dc ${dc} done sainesq ${rfc} sainfile ${rfc} sais ${rfc} mkesa ${rfc} afconstruct ${rfc} rm -f sfx-id.* mkesa-idx.* done genometools-1.5.1/scripts/expand_license000077500000000000000000000062461211610345200204520ustar00rootroot00000000000000#!/usr/bin/env lua --[[ Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. ]] function usage() io.stderr:write(string.format("Usage: %s source_file [...]\n", arg[0])) io.stderr:write("Expand license string to full license in given source files.\n") os.exit(1) end if #arg == 0 then usage() end local tmpfile = "tempfile.txt" -- not nice, but ``pure'' lua doesn't have mktemp local license_string = [[ See LICENSE file or http://genometools.org/license.html for license details.]] local license_string_script = [[ # See LICENSE file or http://genometools.org/license.html for license details.]] local license_full = [[ Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.]] local license_full_script = [[ # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.]] for index, file in ipairs(arg) do io.output(tmpfile) for line in io.lines(file) do line = string.gsub(line, license_string, license_full) line = string.gsub(line, license_string_script, license_full_script) io.write(line) io.write("\n") end rval, err = os.rename(tmpfile, file) if not rval then error(err) end end genometools-1.5.1/scripts/failure.sh000077500000000000000000000012051211610345200175170ustar00rootroot00000000000000#!/bin/sh set -e -x if test $# -ne 3 then echo "Usage: $0 " exit 1 fi reference=$1 query=$2 threshold=$3 # exec in gt root dir # mkvtree.x -db ${reference} -indexname esa-mkv -dna -pl -lcp -suf -tis # vstree2tex.x -tis -suf -s esa-mkv > tmp.tex # gt suffixerator -tis -suf -dna -pl -db ${reference} -indexname esa-fwd # gt tagerator -e 2 -maxocc 20 -rw -esa esa-fwd -q ${query} gt packedindex mkindex -ssp -tis -indexname pck-rev -db ${reference} -sprank -dna -pl -bsize 10 -locfreq 32 -dir rev gt prebwt -maxdepth 4 -pck pck-rev gt tagerator -rw -best -e ${threshold} -pck pck-rev -q ${query} genometools-1.5.1/scripts/findfasta.rb000077500000000000000000000030401211610345200200170ustar00rootroot00000000000000#!/usr/bin/ruby def listdirectory(directory) # prepare regexp for entries to ignore # saves time for repeated regexp use, since it stays the same ignore_dirs = Regexp.compile(/^\.\.?$/) stack = Array.new stack.push(directory) while not stack.empty? d = stack.pop Dir.foreach(d) do |entry| if not ignore_dirs.match(entry) if File.stat("#{d}/#{entry}").file? yield "#{d}/#{entry}" else stack.push("#{d}/#{entry}") end end end end end def listselected(dirname,excludelist) suffixes = ["fastq","fasta","fna","fa","fsa.gz","fsa","FASTA.gz","FASTA"] listdirectory(dirname) do |filename| suffixes.each do |suffix| if filename.match(/\.#{suffix}$/) and not excludelist.member?(File.basename(filename)) yield filename end end end end testdata_exclude = ["solid_color_reads.fastq", "test2_wrong_begin.fastq", "test9_uneven_length.fastq", "test7_empty_seq.fastq", "test6_premature_end.fastq", "test4_different_seqlengths.fastq", "test3_different_seqnames.fastq", "corruptpatternfile.fna", "sw100K1.fsa", "sw100K2.fsa"] listselected("testdata",testdata_exclude) do |filename| puts filename end if ENV.has_key?("GTTESTDATA") gttestdata_exclude = ["trembl-section.fsa.gz"] listselected(ENV["GTTESTDATA"],gttestdata_exclude) do |filename| puts filename end end genometools-1.5.1/scripts/fmt_embl.rb000077500000000000000000000041751211610345200176570ustar00rootroot00000000000000#!/usr/bin/env ruby # # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # def each_seq(filename) File.open(filename) do |file| (farr = file.read.split(">")).each do |fitem| seq = fitem.split("\n") fline = seq.shift next if fline.nil? sequence = seq.collect{|l| l.chomp}.join yield fline, sequence end end end if ARGV.length != 1 then STDERR.puts "Usage: #{$0} " exit 1 end j=0 begin each_seq(ARGV[0]) do |header, seq| # break up headers into words and create description lines not longer than # 70 characters of length hlines = [[]] llen = 0 lineno = 0 header.chomp.split(/\s+/).each do |word| if llen + word.length + 1 > 70 hlines.push([]) lineno += 1 llen = 0 end hlines[lineno].push(word) llen += word.length + 1 end i=1 puts "ID sequence#{j}" puts "XX" hlines.each do |hline| puts "DE #{hline.join(" ")}" end puts "XX" puts "SQ" print " " seq.each_byte do |c| putc c if i % 10 == 0 then print " " end if i % 60 == 0 then printf("%9s\n ", i) end i += 1 end printf(' '*(80-i%60-(i%60)/10-13) + "%9d\n", i-1) puts "//\n\n" j+=1 end rescue StandardError => msg STDERR.puts "Error: #{msg}" exit 1 end genometools-1.5.1/scripts/fmt_gbk.rb000077500000000000000000000042731211610345200175020ustar00rootroot00000000000000#!/usr/bin/env ruby # # Copyright (c) 2009 Sascha Steinbiss # Copyright (c) 2009 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # def each_seq(filename) File.open(filename) do |file| (farr = file.read.split(">")).each do |fitem| seq = fitem.split("\n") fline = seq.shift next if fline.nil? sequence = seq.collect{|l| l.chomp}.join yield fline, sequence end end end if ARGV.length != 1 then STDERR.puts "Usage: #{$0} " exit 1 end j=0 begin each_seq(ARGV[0]) do |header, seq| # break up headers into words and create description lines not longer than # 70 characters of length hlines = [[]] llen = 0 lineno = 0 header.chomp.split(/\s+/).each do |word| if llen + word.length + 1 > 65 hlines.push([]) lineno += 1 llen = 0 end hlines[lineno].push(word) llen += word.length + 1 end puts "LOCUS sequence#{j}" first = true hlines.each do |hline| if first then print "DEFINITION " first = false else print " " end puts "#{hline.join(" ")}" end puts "ORIGIN " i=1 print " 1 " seq.each_byte do |c| putc c if i % 10 == 0 then print " " end if i % 60 == 0 then printf("\n%9s ", i+1) end i += 1 end puts "\n//\n" j+=1 end rescue StandardError => msg STDERR.puts "Error: #{msg}" exit 1 end genometools-1.5.1/scripts/gdb-stack.sh000077500000000000000000000004051211610345200177300ustar00rootroot00000000000000#!/bin/sh if test $# -eq 0 then echo "Usage: $0 " exit 1 fi TMPFILE=`mktemp -t tmpfile.XXXXXX` shift echo "break exit" >> ${TMPFILE} echo "run $*" >> ${TMPFILE} echo "bt" >> ${TMPFILE} cat ${TMPFILE} | gdb ${GTDIR}/bin/gt rm -f ${TMPFILE} genometools-1.5.1/scripts/gen-esa-bottomup.rb000077500000000000000000000414311211610345200212540ustar00rootroot00000000000000#!/usr/bin/env ruby require 'ostruct' require 'optparse' def usage(opts,msg) STDERR.puts "#{$0}: #{msg}\n#{opts.to_s}" exit 1 end def parseargs(argv) options = OpenStruct.new options.key = nil options.usefile = false options.absolute = false options.with_process_branching = true options.with_process_lcpinterval = true options.process_lastvalue = true options.withlastfrompreviousbucket = false options.gtlcpvaluetypeset = false options.nodeclarations = false options.additionaluint32bucket = false opts = OptionParser.new opts.on("-k","--key STRING","use given key as suffix for all symbols") do |x| options.key = x end opts.on("--reader","generate code for the esa-reader") do |x| options.usefile = true end opts.on("--absolute","use absolute start positions to address suffixes") do |x| options.absolute = true end opts.on("--no_process_branchingedge","no processbranchingedge function") do |x| options.with_process_branching = false end opts.on("--no_process_lcpinterval","no processlcpinterval function") do |x| options.with_process_lcpinterval = false end opts.on("--no_process_lastvalue","no proceccing of lastsuftabvalue") do |x| options.process_lastvalue = false end opts.on("--gtlcpvaluetypeset","use GtLcpvaluetype for lcp type") do |x| options.gtlcpvaluetypeset = true end opts.on("--withlastfrompreviousbucket","process last value from previous bucket") do |x| options.withlastfrompreviousbucket = true end opts.on("--additionaluint32bucket","add uint32-bucket argument") do |x| options.additionaluint32bucket = true end opts.on("--no_declarations","do not output declarations") do |x| options.nodeclarations = true end rest = opts.parse(argv) if not rest.empty? usage(opts,"superfluous arguments") end if options.key.nil? usage(opts,"option --key is mandatory") end return options end def processleafedgeargs(options) if options.absolute return "unsigned long, /* position */" else return "unsigned long, /* seqnum */ unsigned long, /* relpos */" end end def spacer(width) s = "" 0.upto(width-1) do |idx| s += " " end return s end def previoussuffix_expr_get(width,variable,options) if options.absolute return variable + "," else return "gt_seqnumrelpos_decode_seqnum(snrp,#{variable}), #{" " * width} gt_seqnumrelpos_decode_relpos(snrp,#{variable})," end end def previoussuffix_param_get(width,options) return previoussuffix_expr_get(width,"previoussuffix",options) end def processbranching_call1(key,options) if options.with_process_branching return "if (processbranchingedge_#{key}(firstedge, TOP_ESA_BOTTOMUP_#{key}.lcp, &TOP_ESA_BOTTOMUP_#{key}.info, lastinterval->lcp, lastinterval->rb - lastinterval->lb + 1, &lastinterval->info, bustate, err) != 0) { haserr = true; }" else return "/* no call to processbranchingedge_#{key} */" end end def processbranching_call2(key,options) if options.with_process_branching return "unsigned long lastintervallcp = lastinterval->lcp, lastintervalrb = lastinterval->rb; PUSH_ESA_BOTTOMUP_#{key}(lcpvalue,lastintervallb); if (processbranchingedge_#{key}(true, TOP_ESA_BOTTOMUP_#{key}.lcp, &TOP_ESA_BOTTOMUP_#{key}.info, lastintervallcp, lastintervalrb - lastintervallb + 1, NULL, bustate, err) != 0) { haserr = true; }" else return "PUSH_ESA_BOTTOMUP_#{key}(lcpvalue,lastintervallb);" end end def processlcpinterval_decl(key,options) if options.with_process_lcpinterval return "static int processlcpinterval_#{key}(unsigned long, GtBUinfo_#{key} *, GtBUstate_#{key} *, GtError *err);" else return "/* no declaration of processlcpinterval_#{key} */" end end def processlcpinterval_call1(key,options) if options.with_process_lcpinterval return "if (processlcpinterval_#{key}(lastinterval->lcp, &lastinterval->info, bustate, err) != 0) { haserr = true; }" else return "/* no call to processlcpinterval_#{key} */" end end def processlcpinterval_call2(key,options) if options.with_process_lcpinterval return "if (processlcpinterval_#{key}(TOP_ESA_BOTTOMUP_#{key}.lcp, &TOP_ESA_BOTTOMUP_#{key}.info, bustate, err) != 0) { haserr = true; }" else return "/* no call to processlcpinterval_#{key} */" end end def showidxexpr(options) if options.withlastfrompreviousbucket return "idx + bustate->idxoffset" else return "idx" end end def process_suf_lcp(key,options) print <nextfreeGtBUItvinfo > 0); if (lcpvalue <= TOP_ESA_BOTTOMUP_#{key}.lcp) { if (TOP_ESA_BOTTOMUP_#{key}.lcp > 0 || !firstedgefromroot) { firstedge = false; } else { firstedge = true; firstedgefromroot = false; } if (processleafedge_#{key}(firstedge, TOP_ESA_BOTTOMUP_#{key}.lcp, &TOP_ESA_BOTTOMUP_#{key}.info, #{previoussuffix_param_get(14,options)} bustate, err) != 0) { haserr = true; } } gt_assert(lastinterval == NULL); while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_#{key}.lcp) { lastinterval = POP_ESA_BOTTOMUP_#{key}; lastinterval->rb = #{showidxexpr(options)}; #{processlcpinterval_call1(key,options)} if (lcpvalue <= TOP_ESA_BOTTOMUP_#{key}.lcp) { if (TOP_ESA_BOTTOMUP_#{key}.lcp > 0 || !firstedgefromroot) { firstedge = false; } else { firstedge = true; firstedgefromroot = false; } #{processbranching_call1(key,options)} lastinterval = NULL; } } if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_#{key}.lcp) { if (lastinterval != NULL) { unsigned long lastintervallb = lastinterval->lb; #{processbranching_call2(key,options)} lastinterval = NULL; } else { PUSH_ESA_BOTTOMUP_#{key}(lcpvalue,#{showidxexpr(options)}); if (processleafedge_#{key}(true, TOP_ESA_BOTTOMUP_#{key}.lcp, &TOP_ESA_BOTTOMUP_#{key}.info, #{previoussuffix_param_get(16,options)} bustate, err) != 0) { haserr = true; } } } END_OF_FILE end def lastsuftabvalue_fromarray(options) if not options.usefile return "unsigned long lastsuftabvalue = bucketofsuffixes[numberofsuffixes-1];" else return "/* no assignment to lastsuftabvalue */" end end def lastsuftabvalue_get(key,options) if options.process_lastvalue print <nextfreeGtBUItvinfo > 0); if (!haserr && TOP_ESA_BOTTOMUP_#{key}.lcp > 0) { #{lastsuftabvalue_fromarray(options)} if (processleafedge_#{key}(false, TOP_ESA_BOTTOMUP_#{key}.lcp, &TOP_ESA_BOTTOMUP_#{key}.info, #{previoussuffix_expr_get(12,"lastsuftabvalue",options)} bustate, err) != 0) { haserr = true; } else { TOP_ESA_BOTTOMUP_#{key}.rb = #{showidxexpr(options)}; #{processlcpinterval_call2(key,options)} } } END_OF_FILE else print <previousbucketlastsuffix = #{accessbucketofsuffixes("numberofsuffixes-1",options)} bustate->firstedgefromroot = firstedgefromroot; } END_OF_FILE end end def seqnumrelpos_include(options) if not options.absolute return "#include \"seqnumrelpos.h\"" else return "/* no include for seqnumrelpos.h */" end end def processbranchingedge_decl(key,options) if options.with_process_branching return "static int processbranchingedge_#{key}(bool firstsucc, unsigned long, GtBUinfo_#{key} *, unsigned long, unsigned long, GtBUinfo_#{key} *, GtBUstate_#{key} *, GtError *);" else return "/* no declaration of processbranchingedge_#{key} */" end end def return_snrp_decl(options) if not options.absolute return "const GtSeqnumrelpos *snrp," else return "/* no parameter snrp */" end end def lcptype(options) if options.gtlcpvaluetypeset return "const GtLcpvaluetype" else return "const uint16_t" end end def additionaluint32bucket(options) if options.additionaluint32bucket return "const uint32_t *bucketofsuffixes_uint32,\n" + (" " * 24) + lcptype(options) else return "#{lcptype(options)}" end end def accessbucketofsuffixes(idx,options) if options.additionaluint32bucket return "bucketofsuffixes != NULL ? bucketofsuffixes[#{idx}] : (unsigned long) bucketofsuffixes_uint32[#{idx}];" else return "bucketofsuffixes[#{idx}];" end end def formatargv(argv) s = "\n #{argv[0]} #{argv[1]}" argv.each_with_index do |arg,i| if i > 1 s += "\n " + argv[i] end end return s end def initfirstinterval(key,options) if options.withlastfrompreviousbucket print <previousbucketlastsuffix == ULONG_MAX) { PUSH_ESA_BOTTOMUP_#{key}(0,0); firstedgefromroot = true; } else { firstedgefromroot = bustate->firstedgefromroot; } END_OF_FILE else print < Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ /* THIS FILE IS GENERATED by\n #{$0}#{formatargv(ARGV)}. DO NOT EDIT. */ #include #include "core/ma.h" #include "esa-seqread.h" #{seqnumrelpos_include(options)} END_OF_FILE if not options.nodeclarations print <spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1] #define POP_ESA_BOTTOMUP_#{key}\\ (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo)) #define PUSH_ESA_BOTTOMUP_#{key}(LCP,LB)\\ if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\\ {\\ gt_assert(stack->nextfreeGtBUItvinfo ==\\ stack->allocatedGtBUItvinfo);\\ stack->spaceGtBUItvinfo\\ = allocateBUstack_#{key}(stack->spaceGtBUItvinfo,\\ stack->allocatedGtBUItvinfo,\\ stack->allocatedGtBUItvinfo+incrementstacksize,\\ bustate);\\ stack->allocatedGtBUItvinfo += incrementstacksize;\\ }\\ gt_assert(stack->spaceGtBUItvinfo != NULL);\\ stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\\ stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\\ stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo++].rb = ULONG_MAX typedef struct { unsigned long lcp, lb, rb; GtBUinfo_#{key} info; } GtBUItvinfo_#{key}; typedef struct { GtBUItvinfo_#{key} *spaceGtBUItvinfo; unsigned long allocatedGtBUItvinfo, nextfreeGtBUItvinfo; } GtArrayGtBUItvinfo_#{key}; GtArrayGtBUItvinfo_#{key} *gt_GtArrayGtBUItvinfo_new_#{key}(void) { GtArrayGtBUItvinfo_#{key} *stack = gt_malloc(sizeof (*stack)); stack->spaceGtBUItvinfo = NULL; stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0; return stack; } void gt_GtArrayGtBUItvinfo_delete_#{key}(GtArrayGtBUItvinfo_#{key} *stack, GtBUstate_#{key} *state) { unsigned long idx; for (idx=0; idxallocatedGtBUItvinfo; idx++) { freeBUinfo_#{key}(&stack->spaceGtBUItvinfo[idx].info,state); } gt_free(stack->spaceGtBUItvinfo); gt_free(stack); } static GtBUItvinfo_#{key} *allocateBUstack_#{key}(GtBUItvinfo_#{key} *ptr, unsigned long currentallocated, unsigned long allocated, GtBUstate_#{key} *state) { unsigned long idx; GtBUItvinfo_#{key} *itvinfo; itvinfo = gt_realloc(ptr,sizeof (*itvinfo) * allocated); gt_assert(allocated > currentallocated); for (idx=currentallocated; idxfirstedgefromroot; END_OF_FILE process_suf_lcp(key,options) print <firstedgefromroot = firstedgefromroot; } return haserr ? -1 : 0; } END_OF_FILE end if options.usefile print < 0); for (idx = 0; !haserr && idx < numberofsuffixes-1; idx++) { lcpvalue = (unsigned long) lcptab_bucket[idx+1]; previoussuffix = #{accessbucketofsuffixes("idx",options)} END_OF_FILE end process_suf_lcp(key,options) puts " }" lastsuftabvalue_get(key,options) if options.usefile puts " gt_GtArrayGtBUItvinfo_delete_#{key}(stack,bustate);" elsif options.process_lastvalue puts " stack->nextfreeGtBUItvinfo = 0; /* empty the stack */" end puts " return haserr ? -1 : 0;" puts "}" genometools-1.5.1/scripts/gen-esa-bottomup.sh000077500000000000000000000020241211610345200212560ustar00rootroot00000000000000#!/bin/sh TEMPLATE=src/match/esa-bottomup SC=scripts/gen-esa-bottomup.rb ${SC} --key maxpairs --reader --absolute \ --no_process_lcpinterval > ${TEMPLATE}-maxpairs.inc ${SC} --key spmsk --no_process_branchingedge > ${TEMPLATE}-spmsk.inc ${SC} --key rdjcv --reader --absolute \ --no_process_lcpinterval > ${TEMPLATE}-rdjcv.inc ${SC} --key rdjce --reader --absolute \ --no_process_lcpinterval > ${TEMPLATE}-rdjce.inc ${SC} --key errfind --reader --absolute > ${TEMPLATE}-errfind.inc ${SC} --key spmeq --no_process_lcpinterval > ${TEMPLATE}-spmeq.inc ${SC} --key spmvar > ${TEMPLATE}-spmvar.inc ${SC} --key shulen --reader --absolute \ --no_process_lcpinterval > ${TEMPLATE}-shulen.inc ${SC} --key shulen --gtlcpvaluetypeset --absolute --no_process_lastvalue \ --no_process_lcpinterval \ --withlastfrompreviousbucket \ --additionaluint32bucket \ --no_declarations > ${TEMPLATE}-shulen-RAM.inc genometools-1.5.1/scripts/gen-radixsort-ip.rb000077500000000000000000000252011211610345200212570ustar00rootroot00000000000000#!/usr/bin/env ruby require 'ostruct' require 'optparse' def usage(opts,msg) STDERR.puts "#{$0}: #{msg}\n#{opts.to_s}" exit 1 end def parseargs(argv) options = OpenStruct.new options.ulong = true opts = OptionParser.new opts.on("--ulongpair","generate code sorting pairs of ulongs") do |x| options.ulong = false end rest = opts.parse(argv) if not rest.empty? usage(opts,"superfluous arguments") end return options end def makekey(options) if options.ulong return "ulong" else return "ulongpair" end end def maketype(options) if options.ulong return "unsigned long" else return "GtUlongPair" end end def derefptr(ptr,options) if options.ulong return "*#{ptr}" else return "#{ptr}->a" end end def derefval(val,options) if options.ulong return "#{val}" else return "#{val}.a" end end options = parseargs(ARGV) print <values.#{makekey(options)}ptr[(binnum << rbuf->log_bufsize) + (unsigned long) rbuf->nextidx[binnum]]; } static void gt_radixsort_#{makekey(options)}_bin_update(#{maketype(options)} *target, GtRadixbuffer *rbuf, unsigned long binnum, #{maketype(options)} value) { unsigned long binoffset = binnum << rbuf->log_bufsize; rbuf->values.#{makekey(options)}ptr[binoffset + (unsigned long) rbuf->nextidx[binnum]] = value; if ((unsigned long) rbuf->nextidx[binnum] < rbuf->buf_size - 1) { rbuf->nextidx[binnum]++; } else { unsigned long j; #{maketype(options)} *wtargetptr, *rtargetptr, *rend, *valptr; wtargetptr = target + rbuf->endofbin[binnum] - (rbuf->buf_size - 1); rtargetptr = wtargetptr + rbuf->buf_size; rend = target + rbuf->startofbin[binnum+1]; valptr = rbuf->values.#{makekey(options)}ptr + binoffset; for (j=0; jbuf_size; j++) { *wtargetptr++ = *valptr; if (rtargetptr < rend) { *valptr = *rtargetptr++; } valptr++; } rbuf->nextidx[binnum] = 0; } rbuf->endofbin[binnum]++; } static void gt_radixsort_#{makekey(options)}_cached_shuffle(GtRadixbuffer *rbuf, #{maketype(options)} *source, GtCountbasetype len, size_t rightshift) { unsigned long binoffset, binnum, bufoffset, nextbin, firstnonemptybin = UINT8_MAX+1; GtCountbasetype *count, previouscount, current; #{maketype(options)} *sp, *spend = source + len; rbuf->countcached++; count = rbuf->startofbin; /* use same memory for count and startofbin */ for (binnum = 0; binnum <= UINT8_MAX; binnum++) { count[binnum] = 0; rbuf->nextidx[binnum] = 0; } for (sp = source; sp < spend; sp++) { count[GT_RADIX_KEY(UINT8_MAX,rightshift,#{derefptr("sp",options)})]++; } for (bufoffset = 0, binoffset = 0, binnum = 0; binnum <= UINT8_MAX; bufoffset += rbuf->buf_size, binoffset += count[binnum], binnum++) { unsigned long j; const unsigned long end = MIN(rbuf->buf_size,(unsigned long) count[binnum]); if (firstnonemptybin == UINT8_MAX+1 && end > 0) { firstnonemptybin = binnum; } for (j=0; jvalues.#{makekey(options)}ptr[bufoffset + j] = source[binoffset + j]; } } previouscount = count[0]; rbuf->startofbin[0] = rbuf->endofbin[0] = 0; nextbin = 0; for (binnum = 1UL; binnum <= UINT8_MAX; binnum++) { GtCountbasetype tmp = rbuf->startofbin[binnum-1] + previouscount; previouscount = count[binnum]; rbuf->startofbin[binnum] = rbuf->endofbin[binnum] = tmp; } /* to simplify compution of bin end */ rbuf->startofbin[UINT8_MAX+1] = len; for (current = 0, binnum = firstnonemptybin; current < len; binnum = nextbin - 1) { #{maketype(options)} currentvalue = gt_radixsort_#{makekey(options)}_bin_get(rbuf,binnum); while (true) { binnum = GT_RADIX_KEY(UINT8_MAX,rightshift,#{derefval("currentvalue",options)}); if (current != rbuf->endofbin[binnum]) { #{maketype(options)} tmp = currentvalue; currentvalue = gt_radixsort_#{makekey(options)}_bin_get(rbuf,binnum); gt_radixsort_#{makekey(options)}_bin_update(source,rbuf,binnum,tmp); } else { break; } } gt_radixsort_#{makekey(options)}_bin_update(source,rbuf,binnum,currentvalue); current++; /* skip over empty bins */ while (nextbin <= UINT8_MAX && current >= rbuf->startofbin[nextbin]) { nextbin++; } /* skip over full bins */ while (nextbin <= UINT8_MAX && rbuf->endofbin[nextbin-1] == rbuf->startofbin[nextbin]) { nextbin++; } if (current < rbuf->endofbin[nextbin-1]) { current = rbuf->endofbin[nextbin-1]; } } for (binnum = 0; binnum <= UINT8_MAX; binnum++) { unsigned long bufleft = (unsigned long) rbuf->nextidx[binnum]; if (bufleft > 0) { unsigned long j; #{maketype(options)} *targetptr, *valptr; valptr = rbuf->values.#{makekey(options)}ptr + (binnum << rbuf->log_bufsize); targetptr = source + rbuf->startofbin[binnum+1] - bufleft; for (j=0; j < bufleft; j++) { targetptr[j] = valptr[j]; } } } } static void gt_radixsort_#{makekey(options)}_uncached_shuffle(GtRadixbuffer *rbuf, #{maketype(options)} *source, GtCountbasetype len, size_t rightshift) { unsigned long binnum, nextbin; #{maketype(options)} *sp, *spend = source + len; GtCountbasetype current, previouscount, *count; rbuf->countuncached++; count = rbuf->startofbin; /* use same memory for count and startofbin */ for (binnum = 0; binnum <= UINT8_MAX; binnum++) { count[binnum] = 0; rbuf->nextidx[binnum] = 0; } for (sp = source; sp < spend; sp++) { count[GT_RADIX_KEY(UINT8_MAX,rightshift,#{derefptr("sp",options)})]++; } previouscount = count[0]; rbuf->startofbin[0] = rbuf->endofbin[0] = 0; nextbin = 0; for (binnum = 1UL; binnum <= UINT8_MAX; binnum++) { GtCountbasetype tmp = rbuf->startofbin[binnum-1] + previouscount; previouscount = count[binnum]; rbuf->startofbin[binnum] = rbuf->endofbin[binnum] = tmp; } /* to simplify compution of bin end */ rbuf->startofbin[UINT8_MAX+1] = len; for (current = 0; current < len; /* Nothing */) { #{maketype(options)} currentvalue = source[current]; GtCountbasetype *binptr; while (true) { binptr = rbuf->endofbin + GT_RADIX_KEY(UINT8_MAX,rightshift,#{derefval("currentvalue",options)}); if (current != *binptr) { #{maketype(options)} tmp = currentvalue; currentvalue = source[*binptr]; source[*binptr] = tmp; (*binptr)++; } else { break; } } source[current++] = currentvalue; (*binptr)++; /* skip over empty bins */ while (nextbin <= UINT8_MAX && current >= rbuf->startofbin[nextbin]) { nextbin++; } /* skip over full bins */ while (nextbin <= UINT8_MAX && rbuf->endofbin[nextbin-1] == rbuf->startofbin[nextbin]) { nextbin++; } if (current < rbuf->endofbin[nextbin-1]) { current = rbuf->endofbin[nextbin-1]; } } } static void gt_radixsort_#{makekey(options)}_shuffle(GtRadixbuffer *rbuf, #{maketype(options)} *source, GtCountbasetype len, size_t rightshift) { ((unsigned long) len > rbuf->cachesize ? gt_radixsort_#{makekey(options)}_cached_shuffle : gt_radixsort_#{makekey(options)}_uncached_shuffle) (rbuf,source,len,rightshift); } static void gt_radixsort_#{makekey(options)}_inplace_insertionsort(#{maketype(options)} *a, GtCountbasetype a_size) { #{maketype(options)} *optr, *iptr, *end = a + a_size; for (optr = a + 1; optr < end; optr++) { if (#{derefptr("optr",options)} < #{derefptr("(optr-1)",options)}) { #{maketype(options)} currentElement = *optr; *optr = *(optr-1); for (iptr = optr-1; iptr > a && #{derefval("currentElement",options)} < #{derefptr("(iptr-1)",options)}; iptr--) { *iptr = *(iptr-1); } *iptr = currentElement; } } } static void gt_radixsort_#{makekey(options)}_process_bin( GtStackGtRadixsort_stackelem *stack, GtRadixbuffer *rbuf, #{maketype(options)} *source, size_t shift) { unsigned long binnum; for (binnum = 0; binnum <= UINT8_MAX; binnum++) { GtCountbasetype width = rbuf->endofbin[binnum] - rbuf->startofbin[binnum]; if (width >= (GtCountbasetype) 2) { #{maketype(options)} *ptr = source + rbuf->startofbin[binnum]; if (width == (GtCountbasetype) 2) { if (#{derefptr("ptr",options)} > #{derefptr("(ptr+1)",options)}) { #{maketype(options)} tmp = *ptr; *ptr = *(ptr+1); *(ptr+1) = tmp; } } else { if (width <= (GtCountbasetype) 32) { rbuf->countinsertionsort++; gt_radixsort_#{makekey(options)}_inplace_insertionsort(ptr,width); } else { GtRadixsort_stackelem tmpstackelem; tmpstackelem.left.#{makekey(options)}ptr = ptr; tmpstackelem.len = width; tmpstackelem.shift = shift - CHAR_BIT; GT_STACK_PUSH(stack,tmpstackelem); } } } } } static void gt_radixsort_#{makekey(options)}_sub_inplace(GtRadixbuffer *rbuf, GtStackGtRadixsort_stackelem *stack) { GtRadixsort_stackelem currentstackelem; while (!GT_STACK_ISEMPTY(stack)) { currentstackelem = GT_STACK_POP(stack); gt_radixsort_#{makekey(options)}_shuffle(rbuf,currentstackelem.left.#{makekey(options)}ptr, currentstackelem.len, currentstackelem.shift); if (currentstackelem.shift > 0) { (void) gt_radixsort_#{makekey(options)}_process_bin(stack,rbuf, currentstackelem.left.#{makekey(options)}ptr, currentstackelem.shift); } } } END_OF_FILE genometools-1.5.1/scripts/gen-radixsort-ip.sh000077500000000000000000000002071211610345200212650ustar00rootroot00000000000000#!/bin/sh gen-radixsort-ip.rb > src/core/radixsort-ip-ulong.inc gen-radixsort-ip.rb --ulongpair > src/core/radixsort-ip-ulongpair.inc genometools-1.5.1/scripts/generate_hmmer_squid_h000077500000000000000000000003031211610345200221530ustar00rootroot00000000000000#!/bin/sh -e sed -e 's/#include /#include \ #include /'\ -e 's/@SQD_UINT16@/uint16_t/'\ -e 's/@SQD_UINT32@/uint32_t/'\ -e 's/@SQD_UINT64@/uint64_t/' $1 genometools-1.5.1/scripts/generate_hmmer_squidconf_h000077500000000000000000000015111211610345200230230ustar00rootroot00000000000000#!/bin/sh -e sed -e 's/#undef SQUID_VERSION/#define SQUID_VERSION "1.9g"/'\ -e 's/#undef SQUID_RELCODE/#define SQUID_RELCODE "squid1_9g"/'\ -e 's/#undef SQUID_DATE/#define SQUID_DATE "January 2003"/'\ -e 's/#undef SQUID_COPYRIGHT/#define SQUID_COPYRIGHT "Copyright (C) 1992-2003 HHMI\/Washington University School of Medicine"/'\ -e 's/#undef SQUID_LICENSE/#define SQUID_LICENSE "Freely distributed under the GNU General Public License (GPL)"/'\ -e 's/SIZEOF_UNSIGNED_SHORT 0/SIZEOF_UNSIGNED_SHORT 2/'\ -e 's/SIZEOF_UNSIGNED_INT 0/SIZEOF_UNSIGNED_INT 4/'\ -e 's/#define SIZEOF_UNSIGNED_LONG 0/#ifdef _LP64\ #define SIZEOF_UNSIGNED_LONG 8\ #else\ #define SIZEOF_UNSIGNED_LONG 4\ #endif/'\ -e 's/SIZEOF_UNSIGNED_LONG_LONG 0/SIZEOF_UNSIGNED_LONG_LONG 8/' $1 genometools-1.5.1/scripts/genlengthsorted.rb000077500000000000000000000017741211610345200212700ustar00rootroot00000000000000#!/usr/bin/env ruby # generate random DNA sequence of approx. the given totallength, such that the # sequence are ordered according to their length, with the shortest sequences # coming first. Stefan Kurtz, September 2012 if ARGV.length != 1 STDERR.puts "Usage: #{$0} " exit 1 end srand=37739292920 def randseq(width,len) seq = "" currentwidth=0 0.upto(len-1) do |idx| r = rand(3) cc = ['a','c','g','t'][rand(4)] seq += "#{cc}" if currentwidth < width currentwidth+=1 else seq += "\n" currentwidth=0 end end return seq.chomp end totallength = ARGV[0].to_i currentlen = 100 currentseqnum = 0 seqnumofthislength = 1 + rand(10) sumlen = 0 seqnum = 0 while sumlen < totallength puts ">sequence #{seqnum} of length #{currentlen}\n#{randseq(70,currentlen)}" seqnum+=1 sumlen += currentlen if currentseqnum < seqnumofthislength currentseqnum+=1 else currentseqnum=0 seqnumofthislength = 1 + rand(10) currentlen += 43 end end genometools-1.5.1/scripts/genomediff.rb000066400000000000000000000176421211610345200201750ustar00rootroot00000000000000# # Copyright (c) 2010 Dirk Willrodt # Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # # common functions for genomediff scripts # require 'tempfile' require 'fileutils' module Genomediff def Genomediff.reduceN(file,removeN) alphabet = [?a, ?A, ?c, ?C, ?g, ?G, ?t, ?T] newline = [?\n] charcount = 0 header = false wildcard = false first = true newfile = "" dirname = File.dirname(file) File.open(file, 'r') {|fp| basename = File.basename(file, ".*") newfile = File.join(dirname, basename + "_redN.fas") #return newfile if File.exist?(newfile) File.open(newfile, 'w') {|nfp| while cc = fp.getc if charcount == 80 nfp.putc ?\n charcount = 0 end if not header and cc == ?> header = true nfp.putc ?\n unless first first = false nfp.putc cc next elsif header if cc == ?\n header = false charcount = 0 end nfp.putc cc next end if cc == ?\n next end if not wildcard and not alphabet.include?(cc) wildcard = true unless removeN nfp.putc ?N charcount += 1 end next elsif wildcard if alphabet.include?(cc) wildcard = false nfp.putc cc charcount += 1 next end else nfp.putc cc charcount += 1 end end nfp.putc ?\n } } exit 1 unless File.exist?(newfile) return newfile end def Genomediff.reverse_and_concat(file) tf = Tempfile.new("gt_rev") tmpfile = tf.path tf.close dirname = File.dirname(file) `$GTDIR/bin/gt \ convertseq -o #{tmpfile} \ -force -r #{file}` basename = File.basename(file, ".*") newfile = File.join(dirname, basename + "_plus_rev.fas") `cat #{file} #{tmpfile} > #{newfile}` exit 1 unless File.exist?(newfile) File.unlink(tmpfile) return newfile end def Genomediff.pck_index(files,idxname,parameter) return `$GTDIR/bin/gt \ packedindex mkindex \ -mirrored \ -dna -dir rev -ssp -sprank -pl \ -db #{files} \ -indexname #{idxname} \ #{parameter}` end def Genomediff.esa_index(files,idxname,parameter) return `$GTDIR/bin/gt suffixerator \ -mirrored \ -dna -suf -tis -lcp -ssp \ -db #{files} \ -indexname #{idxname} \ #{parameter}` end def Genomediff.pck_genomediff(idxname,parameter) return `$GTDIR/bin/gt genomediff \ -indextype pck #{parameter} #{idxname}` end def Genomediff.esa_genomediff(idxname,parameter) return `$GTDIR/bin/gt genomediff \ -indextype esa #{parameter} #{idxname}` end end module Eval def Eval.pck_index(code, revfiles, log_fp, verbose, bsize, parts) puts "# INDEX PCK" if verbose idxname = File.join(File.dirname(revfiles[0]), code+"_pck") log_fp.puts "# RUN #{code} -pck -parts #{parts} -bsize #{bsize}" puts "# RUN #{code} -pck -parts"+ " #{parts} -bsize #{bsize}" if verbose output = Genomediff.pck_index(revfiles.join(" "),bsize,parts,idxname) /^# TIME overall \d+.\d+.*$/.match output log_fp.puts $& /^# space peak .*$/.match output log_fp.puts $& puts output if verbose return idxname end def Eval.esa_index(code, revfiles, log_fp, verbose, parts) puts "# INDEX ESA" if verbose m = code.match(/(\d+_\d+)_(\d+\.\d+)_(\d+)/) filecode, div, n = m[1], m[2], m[3] idxname = File.join(File.dirname(revfiles[0]), code+"_esa") log_fp.puts "# RUN #{filecode} d:#{div} n:#{n} -parts #{parts}" puts "# RUN #{filecode} d:#{div} n:#{n}"+ " -esa" if verbose output = Genomediff.esa_index(revfiles.join(" "),parts,idxname) /^# TIME overall \d+.\d+.*$/.match output log_fp.puts $& /^# space peak .*$/.match output log_fp.puts $& puts output if verbose return idxname end def Eval.pck_genomediff(code, idxname, parameter, log_fp, verbose) puts "# GENOMEDIFF PCK" if verbose m = code.match(/(\d+_\d+)_(\d+\.\d+)_(\d+)/) filecode, div, n = m[1], m[2], m[3] log_fp.puts "# RUN #{filecode} d:#{div} n:#{n} #{parameter}" puts "# RUN #{filecode} d:#{div} n:#{n} #{parameter}" if verbose output = Genomediff.pck_genomediff(idxname,parameter) /^# TIME overall \d+.\d+.*$/.match output log_fp.puts $& /^# space peak .*$/.match output log_fp.puts $& /^# mmap .*$/.match output log_fp.puts $& puts output if verbose end def Eval.esa_genomediff(code, idxname, parameter, log_fp, verbose) puts "# GENOMEDIFF ESA" if verbose m = code.match(/(\d+_\d+)_(\d+\.\d+)_(\d+)/) filecode, div, n = m[1], m[2], m[3] log_fp.puts "# RUN #{filecode} d:#{div} n:#{n} #{parameter}" puts "# RUN #{filecode} d:#{div} n:#{n} #{parameter}" if verbose output = Genomediff.esa_genomediff(idxname,parameter) /^# TIME overall \d+.\d+.*$/.match output log_fp.puts $& /^# space peak .*$/.match output log_fp.puts $& /^# mmap .*$/.match output log_fp.puts $& puts output if verbose end def Eval.run_pck_index_creation(code, revfiles, log_fp, verbose) self.pck_index(code, revfiles, log_fp, verbose, 8, 1) end def Eval.run_pck_index_bsize(code, revfiles, log_fp, verbose, bsize) self.pck_index(code, revfiles, log_fp, verbose, bsize, 1) end def Eval.run_pck_index_parts(code, revfiles, log_fp, verbose, parts) self.pck_index(code, revfiles, log_fp, verbose, 8, parts) end def Eval.run_esa_index_creation(code, revfiles, log_fp, verbose) self.esa_index(code, revfiles, log_fp, verbose, 1) end def Eval.run_esa_index_parts(code, revfiles, log_fp, verbose,parts) self.esa_index(code, revfiles, log_fp, verbose, parts) end def Eval.run_genomediff_pck(code, idxname, parameter, log_fp, verbose) parameter += " -v " if verbose self.pck_genomediff(code, idxname, parameter, log_fp, verbose) end def Eval.run_genomediff_esa(code, idxname, parameter, log_fp, verbose) parameter += " -v " if verbose self.esa_genomediff(code, idxname, parameter, log_fp, verbose) end end genometools-1.5.1/scripts/genswtest.sh000077500000000000000000000021741211610345200201210ustar00rootroot00000000000000#!/bin/sh VSTREEBIN=/projects/vstree/bin/i686-pc-linux-gnu if test ! -d ${VSTREEBIN} then VSTREEBIN=/Users/stefan/vstree/bin/i686-apple-darwin fi set -e -x if test $# -ne 4 then echo "Usage: $0 <# refseq> <# query seq> " exit 1 fi # modify the following if you need larger files. # but only use an extractfile that does not contain wildcard characters, # i.e. N etc. extractfile=testdata/U89959_genomic.fas lines=$1 seqref=$2 seqquery=$3 threshold=$4 createseq() { TMPFILE=`mktemp gt-test.XXXXXX` || exit 1 echo ">$3 -n $1" > ${TMPFILE}.extract grep -v '^>' ${extractfile} | $3 -n $1 >> ${TMPFILE}.extract gt mutate -rate 10 ${TMPFILE}.extract | grep -v '^#' > ${TMPFILE}.mut ${VSTREEBIN}/mkvtree -db ${TMPFILE}.mut -indexname ${TMPFILE} -ois -tis -dna ${VSTREEBIN}/vsubseqselect -minlength 100 -maxlength 200 -snum $2 ${TMPFILE} |\ grep -v '^#' | gawk '/.*/ {print ">\n" $1}' rm -f ${TMPFILE}.* } createseq $lines $seqref head > gt-test-refer createseq $lines $seqquery tail > gt-test-query scripts/failure.sh gt-test-refer gt-test-query ${threshold} genometools-1.5.1/scripts/gff3.rb000077500000000000000000000056001211610345200167110ustar00rootroot00000000000000# # Copyright (c) 2006-2007 Gordon Gremme # Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # class Gene def initialize(range, strand) @range = range if not (strand == '+' or strand == '-') then raise "'#{strand}' is not a valid strand" end @strand = strand @exons = [] end def add_exon(range) @exons.push(range) end attr_reader :range, :strand, :exons attr_accessor :name, :attributes, :cds_pos end class Sequence def initialize(start_pos, end_pos) @start_pos = start_pos @end_pos = end_pos @genes = [] end def update_range(start_pos, end_pos) @start_pos = start_pos if start_pos < @start_pos @end_pos = end_pos if end_pos > @end_pos end def add_gene(gene) @genes.push(gene) end attr_accessor :start_pos, :end_pos attr_reader :genes end def gff3_output(sequences, source) gene_number = 1 puts "##gff-version 3" sequences.each do |name, seq| puts "##sequence-region #{name} #{seq.start_pos} #{seq.end_pos}" seq.genes.each do |gene| print "#{name} #{source} gene #{gene.range.begin} "+ "#{gene.range.end} . #{gene.strand} . "+ "ID=gene#{gene_number}" if gene.name then print ";Name=#{gene.name}" end if gene.attributes then gene.attributes.each do |attr_name, attr_value| print ";#{attr_name}=#{attr_value}" end end print "\n" exon_number = 1 gene.exons.each do |exon| puts "#{name} #{source} exon #{exon.begin} #{exon.end} "+ ". #{gene.strand} . Parent=gene#{gene_number}" if (gene.cds_pos) then max_start = gene.cds_pos.begin > exon.begin ? gene.cds_pos.begin \ : exon.begin min_end = gene.cds_pos.end < exon.end ? gene.cds_pos.end : exon.end if (gene.cds_pos.begin <= exon.end and gene.cds_pos.end >= exon.begin) then puts "#{name} #{source} CDS " + "#{max_start} #{min_end} . #{gene.strand} . Parent=gene#{gene_number}" end end end gene_number += 1 end puts "###" end end genometools-1.5.1/scripts/gff3tidy_all000077500000000000000000000024471211610345200200370ustar00rootroot00000000000000#!/bin/sh # # Copyright (c) 2010 Gordon Gremme # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # if [ $# -lt 1 ] then echo "Usage: `basename $0` file [...]" >&2 echo "Apply \"gt gff3 -tidy\" to each \"file\" and replace it afterwards." >&2 echo "The original \"file\" is saved as \"file.bac\"." >&2 exit 1 fi for FILE in $* do TMPFILE=`mktemp` cp $FILE $FILE.bac gt gff3 -tidy $FILE > $TMPFILE if [ $? -eq 0 ] then # gt gff3 -tidy call succeeded -> overwrite file mv -f $TMPFILE $FILE else echo "`basename $0`: gt gff3 -tidy command failed, removing tmpfile" rm -f $TMPFILE fi done genometools-1.5.1/scripts/gmap2gff3000077500000000000000000000106131211610345200172360ustar00rootroot00000000000000#!/usr/bin/env ruby # # Copyright (c) 2006-2007 Gordon Gremme # Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # $:.push(File.dirname($0)) require 'gff3' class Scanner def initialize(input) @input = input @line_buf = nil end def peek if @line_buf then return @line_buf end @line_buf = @input.gets end def gets if @line_buf then buf = @line_buf @line_buf = nil return buf end @input.gets end def lineno @input.lineno end def filename @input.filename end end class GMAPParser def initialize(sequences) @sequences = sequences @current_accession = nil @current_strand = nil end def parse(scanner) while scanner.peek if scanner.gets =~ /^>/ then if parse_paths(scanner) then parse_alignment(scanner) end end end end private def parse_paths(scanner) line = scanner.gets if line =~ /^Paths/ then # XXX: change parser to handle multiple paths if line =~ /^Paths \(1\):/ then while line = scanner.gets do if line =~ /Genomic pos:/ then if line =~ /^.*\(([+-])/ then @current_strand = $1 else raise "could not parse strand on line #{scanner.lineno} of " + "file #{scanner.filename}" end elsif line =~ /Accessions:/ then accession_parts = line.split(':') @current_accession = accession_parts[1].strip return true end end elsif line !~ /^Paths \(0\):/ STDERR.puts "warning: skipping multiple path alignment on line " + "#{scanner.lineno} of file #{scanner.filename}" return false end else raise "expecting 'Paths' on line #{scanner.lineno} of file " + "#{scanner.filename}" end end def parse_alignment(scanner) while line = scanner.gets do if line =~ /^Alignments:/ then # skip two lines scanner.gets scanner.gets exons = [] while (line = scanner.gets) =~ /:/ do # process all alignment lines line =~ /^.*:(\d+)-(\d+)/ exon = Range.new($1.to_i, $2.to_i) if exon.begin > exon.end then exon = Range.new(exon.end, exon.begin) end exons.push(exon) end if exons.size == 0 then raise "could not parse exon up to line #{scanner.lineno} in file " + "#{scanner.filename}" end # construct gene exon_border = [] exon_border.push(exons.first.begin) exon_border.push(exons.first.end) exon_border.push(exons.last.begin) exon_border.push(exons.last.end) gene_range = Range.new(exon_border.min, exon_border.max) raise if gene_range.begin > gene_range.end if current_sequence = @sequences[@current_accession] then # the current sequence exists already -> make sure it is maximal current_sequence.update_range(gene_range.begin, gene_range.end) else # the current sequence does not exist -> add it @sequences[@current_accession] = Sequence.new(gene_range.begin, gene_range.end) end current_sequence = @sequences[@current_accession] gene = Gene.new(gene_range, @current_strand) exons.each { |exon| gene.add_exon(exon) } current_sequence.add_gene(gene) return end end end end # read input sequences = {} gmap_parser = GMAPParser.new(sequences) gmap_parser.parse(Scanner.new(ARGF)) # output gff3_output(sequences, "gmap") genometools-1.5.1/scripts/gprof-run.sh000077500000000000000000000005511211610345200200120ustar00rootroot00000000000000#!/bin/sh Yeast=`ls ${GTTESTDATA}/ltrharvest/s_cer/chr[01][0-9].*.gz` bin/gt packedindex mkindex -sprank -tis -dna -pl -bsize 10 -locfreq 32 -dir rev\ -db ${Yeast}\ -indexname pck-yeast env -i GT_MEM_BOOKKEEPING=off time bin/gt tagerator -rw -pck pck-yeast -k 2\ -t yeast.1000 > tmp.prot gprof bin/gt gmon.out genometools-1.5.1/scripts/gtgrep.sh000077500000000000000000000002641211610345200173640ustar00rootroot00000000000000#!/bin/sh egrep "$@" src/match/*\ src/ltr/*\ src/mgth/*\ src/tools/*.[ch]\ src/*.[ch]\ scripts/*\ testsuite/*.rb genometools-1.5.1/scripts/gthclean.sh000077500000000000000000000024201211610345200176550ustar00rootroot00000000000000#!/bin/sh # # Copyright (c) 2004-2008, 2012 Gordon Gremme # Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # # clean (i.e., remove!) all files comprising the index constructed by mkvtree # and all *.polya and *.polya.info files constructed by gth # furthermore, all bioseq files (*.bsi, *.bsr, and *.md5) are removed rm -f *.ssp *.llv *.skp *.al[12] *.des *.prj *.lcp *.suf rm -f *.tis *.ois *.bwt *.bck *.sds *.iso *.sti *.sti1 *.cld rm -f *.cld1 *.crf *.cfr *.lsf rm -f *.polya *.polya.info rm -f *.bsi *.bsr *.md5 genometools-1.5.1/scripts/gthcleanrec.sh000077500000000000000000000025521211610345200203550ustar00rootroot00000000000000#!/bin/sh -e # # Copyright (c) 2004-2008, 2012 Gordon Gremme # Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # # descend recursively in all subdirectries of the current directory and # clean (i.e., remove!) all files comprising the index constructed by mkvtree # and all *.polya and *.polya.info files constructed by gth # furthermore, all bioseq files (*.bsi, *.bsr, and *.md5) are removed SUFFIXES="ssp llv skp al1 al2 des prj lcp suf tis ois bwt bck sds iso sti sti1 cld cld1 crf cfr lsf polya polya.info bsi bsr md5" for SUFFIX in $SUFFIXES do find . -name "*.$SUFFIX" -print0 | xargs -0 rm -f done genometools-1.5.1/scripts/hop.sh000077500000000000000000000523111211610345200166620ustar00rootroot00000000000000#!/bin/bash # # Copyright (c) 2012 Giorgio Gonnella # Copyright (c) 2012 Center for Bioinformatics, University of Hamburg # # Permission to use, copy, modify, and distribute this software for any # purpose with or without fee is hereby granted, provided that the above # copyright notice and this permission notice appear in all copies. # # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES # WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR # ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES # WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN # ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # # hardcoded values: NOGFF='--' # default values: BWA=${BWA:=bwa} GT=${GT:=gt} SAMTOOLS=${SAMTOOLS:=samtools} HOP_PARAMS=${HOP_PARAMS:=""} BWA_PARAMS=${BWA_PARAMS:="-t 4"} USESW=${USESW:=""} # command line parameters: USG=" (|$NOGFF) []" ACTION=$1 if [[ "$ACTION" =~ "eval" ]]; then USG="eval " USG="$USG (|$NOGFF) []" SGENOME=$2 shift fi GENOME=$2 ANNOTATION=$3 READS=$4 MATES=$5 MAP="${READS}.${GENOME}" MAPM="${MATES}.${GENOME}" function show_globals { echo "USG=$USG" echo "ACTION=$ACTION" echo "SGENOME=$SGENOME" echo "GENOME=$GENOME" echo "ANNOTATION=$ANNOTATION" echo "READS=$READS" echo "MATES=$MATES" echo "MAP=$MAP" echo "MAPM=$MAPM" } function f_help_header { echo "Reference-based correction of homopolymer length in sequencing reads." echo echo " Usage: $0 $USG" echo } function f_help_footer { echo echo "Important: this script only works correctly if all files are located" echo " in the working directory where the script is called" echo " (you can use symbolic links, of course)" echo echo "Further parameters can be optionally passed using env variables:" echo " - BWA path to bwa binary (default: $BWA)" echo " - SAMTOOLS path to samtools binary (default: $SAMTOOLS)" echo " - GT path to GenomeTools binary (default: $GT)" echo " - BWA_PARAMS parameters for bwa aln (default: $BWA_PARAMS)" echo " - HOP_PARAMS parameters for hop (default: $HOP_PARAMS)" echo " - USESW set to \"TRUE\" to use bwa bwasw instead of bwa aln" echo " - SHOWONLY set to \"TRUE\" to echo commands, without executing" } function f_shorthelp { f_help_header echo "Use \"$0 help\" for more information." } function f_help { f_help_header echo " - is one of the following:" echo echo " prepare prepare the data necessary for the correction" echo " (index preparation, mapping, sorting, etc)" echo echo " correct run the homopolymer error correction tool;" echo " (for single-end reads, reads are output in a " echo " single file and are usually sorted differently " echo " than in the original file;" echo " if paired-end reads are used, the sorting " echo " order is conserved, at cost of a longer running " echo " time and an higher memory requirement)" echo echo " clean remove index, mapping results and intermediate files" echo " (DISCLAIMER: this may have unintended effects, as" echo " it deletes files solely based on their filename)" echo echo " run prepare, correct and clean" echo echo " stats collect statistics for each correction position" echo " (useful for debugging and evaluation," echo " it may be slow and require lot of memory)" echo echo " eval-help more information about evaluation actions;" echo echo " help shows this message" echo echo " - is a single sequence Fasta file which" echo " contains the reference against which the correction is done" echo echo " - CDS.gff contains the annotation of ;" echo " instead of a filename '$NOGFF' can be specified; in this case," echo " homopolymer are corrected in the whole sequence instead of only " echo " in coding regions" echo echo " - contains the reads to correct" echo echo " - contains the mate pairs (if available)" f_help_footer } function f_eval_help { f_help_header echo " - is one of the following:" echo echo " eval evaluate corrections to reads of a known genome" echo echo " eval-make-true prepare a set of \"true\" corrections" echo " for reads which have been sequenced from " echo " " echo echo " eval-prepare prepare for the evaluation of corrections " echo " against " echo echo " eval-help show this message" echo echo " - is a single sequence Fasta file which" echo " contains the genome that has been sequenced" echo echo " - is a single sequence Fasta file which" echo " contains the reference against which the correction is done" echo echo " - CDS.gff contains the annotation of genome.fas;" echo " instead of a filename '$NOGFF' can be specified; in this case," echo " homopolymer are corrected in the whole sequence instead of only " echo " in coding regions; this is however not reccomended" echo echo " - contains the reads to correct" echo echo " - contains the mate pairs (if available)" echo echo "Before using eval, both eval-make-true and eval-prepare must be called." f_help_footer } function f_die { f_shorthelp exit $E_BADARGS } function f_index { echo "==== Create bwa genome index..." CMD="$BWA index $GENOME" echo echo $CMD if [ "$SHOWONLY" != "TRUE" ]; then $CMD; fi echo } function f_map { if [ "$USESW" == "TRUE" ]; then echo "==== Map reads to the genome using bwasw..." echo CMD="$BWA bwasw ${BWA_PARAMS} $GENOME $READS" echo $CMD '>' $MAP.sam if [ "$SHOWONLY" != "TRUE" ]; then $CMD > $MAP.sam; fi else echo "==== Map reads to the genome using bwa..." echo CMD="$BWA aln ${BWA_PARAMS} $GENOME $READS" echo $CMD '>' $MAP.sai if [ "$SHOWONLY" != "TRUE" ]; then $CMD > $MAP.sai; fi if [ "$MATES" != "" ]; then CMD1="$BWA aln ${BWA_PARAMS} $GENOME $MATES" CMD2="$BWA sampe $GENOME $MAP.sai $MAPM.sai $READS $MATES" echo $CMD1 '>' $MAPM.sai echo $CMD2 '>' $MAP.sam if [ "$SHOWONLY" != "TRUE" ]; then $CMD1 > $MAPM.sai $CMD2 > $MAP.sam fi else CMD="$BWA samse $GENOME $MAP.sai $READS" echo $CMD '>' $MAP.sam if [ "$SHOWONLY" != "TRUE" ]; then $CMD > $MAP.sam; fi fi fi echo } function f_sortmap { echo "==== Sort the mapping results using samtools..." echo CMD1="$SAMTOOLS view -Shu $MAP.sam" CMD2="$SAMTOOLS sort $MAP.bam sorted.$MAP" echo $CMD1 '>' $MAP.bam echo $CMD2 if [ "$SHOWONLY" != "TRUE" ]; then $CMD1 > $MAP.bam $CMD2 fi echo } function f_sortgff { echo "==== Process and sort the annotation..." echo awk '$3 == "CDS" \ {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t." }' \ $ANNOTATION > tmp_1.$ANNOTATION echo "##gff-version 3" > tmp_2.$ANNOTATION sort -k4 -n tmp_1.$ANNOTATION >> tmp_2.$ANNOTATION $GT gff3 -tidy -force -o sorted.$ANNOTATION tmp_2.$ANNOTATION rm tmp_1.$ANNOTATION rm tmp_2.$ANNOTATION echo } function f_encode { echo echo "==== Encode genome in GtEncseq format..." echo CMD="$GT encseq encode -v $GENOME" echo $CMD if [ "$SHOWONLY" != "TRUE" ]; then $CMD; fi echo } function f_prepare { f_index f_map f_sortmap f_encode if [ "$ANNOTATION" != "$NOGFF" ]; then f_sortgff; fi } function f_correct { echo "==== Correct homopolymers..." echo if [ "$ANNOTATION" != "$NOGFF" ]; then HOP_PARAMS="-ann sorted.$ANNOTATION $HOP_PARAMS" fi if [ "$MATES" != "" -o "$USESW" == "TRUE" ]; then HOP_PARAMS="-reads $READS $MATES $HOP_PARAMS" else HOP_PARAMS="-o hop_$READS $HOP_PARAMS" fi CMD="$GT hop -v -ref $GENOME -map sorted.$MAP.bam $HOP_PARAMS" echo $CMD if [ "$SHOWONLY" != "TRUE" ]; then $CMD; fi echo echo "==== done " echo echo "corrected reads: hop_$READS" echo } function f_clean { rm -f $GENOME.amb $GENOME.ann $GENOME.bwt $GENOME.pac $GENOME.sa rm -f $MAP.sai $MAP.sam rm -f $MAP.bam sorted.$MAP.bam rm -f $GENOME.esq $GENOME.des $GENOME.md5 $GENOME.sds if [ "$ANNOTATION" != "$NOGFF" ]; then rm -f sorted.$ANNOTATION fi if [ "$MATES" != "" ]; then rm -f $MAPM.sai fi } function f_run { f_prepare f_correct f_clean } # position of fields in correction stats output table declare -A FIELD FIELD[R_HPOS]='$1' FIELD[EDIT]='$2' FIELD[S_HPOS]='$3' FIELD[S_HEND]='$4' FIELD[S_CHAR]='$5' FIELD[S_OR]='$6' FIELD[C_LEN]='$7' FIELD[COVERAGE]='$8' FIELD[R_HLEN]='$9' FIELD[R_SUPP]='$10' FIELD[S_HLEN]='$11' FIELD[A_HLEN]='$12' FIELD[A_SUPP]='$13' FIELD[S_MAPQ]='$14' FIELD[S_Q_BEF]='$15' FIELD[S_Q_FIRST]='$16' FIELD[S_Q_MIN]='$17' FIELD[S_Q_AVE]='$18' FIELD[S_Q_MAX]='$19' FIELD[S_Q_RANGE]='$20' FIELD[S_Q_LAST]='$21' FIELD[S_Q_AFT]='$22' FIELD[S_QUAL]='$23' FIELD[S_ID]='$24' FIELD[C_CLASS]='$25' # combined fields FIELD[EDIT_OP]="${FIELD[EDIT]}\"-\"${FIELD[S_CHAR]}" FIELD[MULTIEDIT_OP]="${FIELD[EDIT]}\"-\"${FIELD[S_CHAR]}\"-\"${FIELD[C_LEN]}" FIELD[A_HLEN_DIFF]="${FIELD[A_HLEN]}-${FIELD[R_HLEN]}" FIELD[S_HLEN_DIFF]="${FIELD[S_HLEN]}-${FIELD[R_HLEN]}" FIELD[NON_C_LEN]="(${FIELD[S_HLEN]}>${FIELD[R_HLEN]}?${FIELD[S_HLEN]}-${FIELD[R_HLEN]}:${FIELD[R_HLEN]}-${FIELD[S_HLEN]})-${FIELD[C_LEN]}" FIELD[A_SUPP_DIFF]="${FIELD[A_SUPP]}-${FIELD[R_SUPP]}" function f_pos_stats { count_all () { RETVAL=`grep '^'$2 $1 | wc -l`; } count_all_pos () { RETVAL=`awk '/^'$2'/ && ('${FIELD[S_HEND]}' == "'$3'")' $1 \ | wc -l`; } count () { RETVAL=`awk '/^'$2'/ && ('${FIELD[S_CHAR]}' == "'$3'")' $1 | wc -l`; } count_pos () { RETVAL=`awk '/^'$2'/ && ('${FIELD[S_HEND]}' == "'$3'") \ && ('${FIELD[S_CHAR]}' == "'$4'")' $1 | wc -l`; } nof_seq_long () { RETVAL=`grep "^$2--$2" $1 | awk '{ print $2 }'` if [ "$RETVAL" == "" ]; then RETVAL=0; fi; } OUTFILE=$2 MAX_READ_LEN=`grep 'maximum length' $3 | awk '{ print $4 }'` NOFSEQ=`grep 'sequences' $3 | awk '{ print $2 }'` nof_seq_long $3 1; S=$RETVAL P=`echo "$S / $NOFSEQ" | bc -l` rm -f $OUTFILE touch $OUTFILE echo \ "# pos: last position in original read of corrected homopolymer (1-based)"\ >> $OUTFILE echo \ "# %reads: percent of reads which are at least as long as pos" >> $OUTFILE echo "# (ins|del): insertions, deletions in read" >> $OUTFILE echo "# (ins|del)[ACGT]: insertions, deletions in read of symbol" >> $OUTFILE H="# pos\t%reads\tedits\tins\tdel" H="$H\tinsA\tinsC\tinsG\tinsT\tdelA\tdelC\tdelG\tdelT" echo -e "$H" >> $OUTFILE count_all $1 I; I=$RETVAL count_all $1 D; D=$RETVAL A=$[$I+ $D] count $1 I a; Ia=$RETVAL count $1 I c; Ic=$RETVAL count $1 I g; Ig=$RETVAL count $1 I t; It=$RETVAL count $1 D a; Da=$RETVAL count $1 D c; Dc=$RETVAL count $1 D g; Dg=$RETVAL count $1 D t; Dt=$RETVAL echo -e "all\t100.00\t$A\t$I\t$D\t$Ia\t$Ic\t$Ig\t$It\t$Da\t$Dc\t$Dg\t$Dt" \ >> $OUTFILE for ((i = 2; i < $MAX_READ_LEN; i++)); do nof_seq_long $3 $i S=$[$RETVAL+$S] P=`echo "(1.0 - ($S / $NOFSEQ)) * 100" | bc -l` count_all_pos $1 I $i; I=$RETVAL count_all_pos $1 D $i; D=$RETVAL A=$[$I+ $D] count_pos $1 I $i a; Ia=$RETVAL count_pos $1 D $i a; Da=$RETVAL count_pos $1 I $i c; Ic=$RETVAL count_pos $1 D $i c; Dc=$RETVAL count_pos $1 I $i g; Ig=$RETVAL count_pos $1 D $i g; Dg=$RETVAL count_pos $1 I $i t; It=$RETVAL count_pos $1 D $i t; Dt=$RETVAL printf "$i\t%.2f\t$A\t$I\t$D\t$Ia\t$Ic\t$Ig\t$It\t$Da\t$Dc\t$Dg\t$Dt\n" $P \ >> $OUTFILE done } function f_edits_per_read { grep -v '^#' $1 | awk '{ print '${FIELD[S_ID]}' }' | sort | uniq -c > $MAP~tmpfile echo "# edited reads: `cat $MAP~tmpfile | wc -l`" >> $1 t=0 for ((i=1;i<10;i++)); do c=`awk ' $1 == '$i $MAP~tmpfile | wc -l` if [ $c == 0 ]; then break else t=$[$t+($c*$i)] echo -e "# reads edited $i time(s): $c" >> $1 fi done echo -e "# total edits: $t" >> $1 rm $MAP~tmpfile } function f_stats { echo "==== Collecting correction statistics..." if [ "$ANNOTATION" != "$NOGFF" ]; then HOP_PARAMS="-ann sorted.$ANNOTATION $HOP_PARAMS" fi if [ "$MAKETRUE" == "TRUE" ]; then HOP_PARAMS="-state-of-truth $HOP_PARAMS" else HOP_PARAMS="-stats $HOP_PARAMS" fi if [ "$MATES" != "" -o "$USESW" == "TRUE" ]; then HOP_PARAMS="-reads $READS $MATES $HOP_PARAMS" else HOP_PARAMS="-o hop_$READS $HOP_PARAMS" fi CMD="$GT hop -v -ref $GENOME -map sorted.$MAP.bam $HOP_PARAMS" echo "$CMD" '>' $MAP.hop_stats if [ "$SHOWONLY" != "TRUE" ]; then $CMD > $MAP.hop_stats echo f_edits_per_read $MAP.hop_stats fi echo "==== done " echo echo "correction statistics: $MAP.hop_stats" echo } stats2eds () { grep -v '^#' $MAP.hop_stats | awk '{ printf("%-30s\t%-5s\t%s\t%s\n", \ '${FIELD[S_ID]}', '${FIELD[S_HEND]}', \ '${FIELD[EDIT]}', '${FIELD[C_LEN]}') }' | sort > $MAP.eds } function f_eval_make_true { GENOME=$SGENOME MAP="${READS}.${GENOME}" MAPM="${MATES}.${GENOME}" ANNOTATION=$NOGFF if [ "$NOMAP" != "TRUE" ]; then f_prepare; fi MAKETRUE="TRUE" f_stats if [ "$SHOWONLY" != "TRUE" ]; then stats2eds; fi } function f_eval_prepare { f_prepare } function f_eval_mark { echo "==== Mark hop_stats lines using evaluation results" SMAP="${READS}.${SGENOME}" diff $SMAP.eds $MAP.eds | grep '^>' | sort > $MAP.fp ruby -e " fp = IO.read('$MAP.fp').split(%Q[\n]) S_ID = %Q[${FIELD[S_ID]}][1..-1].to_i - 1 S_HEND = %Q[${FIELD[S_HEND]}][1..-1].to_i - 1 fp = fp.map{|x| x = x.split; %Q[#{x[1]} #{x[2]}]} infile = File.new('$MAP.hop_stats') outfile = File.new('$MAP.hop_stats_eval', 'w') infile.each do |line| line.chomp! if line =~ /^# coordinates/ outfile.puts %Q[# c_class = classification of correction ]+ %Q[(TP=true positive; FP=false positive)] outfile.puts line elsif line =~ /^# edit\sr_hpos/ outfile.puts %Q[#{line}\tc_class] elsif line =~ /^#/ outfile.puts line else splitted = line.split if (fp.include?(%Q[#{splitted[S_ID]} #{splitted[S_HEND]}])) outfile.puts %Q[#{line}\tFP] else outfile.puts %Q[#{line}\tTP] end end end " echo "marked hop_stats: $MAP.hop_stats_eval" } function f_eval_proc_marked { awk ${FIELD[C_CLASS]}' == "FP"' $MAP.hop_stats_eval > $MAP.hop_stats_FP awk ${FIELD[C_CLASS]}' == "TP"' $MAP.hop_stats_eval > $MAP.hop_stats_TP echo "false positive only stats: $MAP.hop_stats_FP" echo "true positive only stats: $MAP.hop_stats_TP" QUANT_MEASURES="S_HPOS S_HEND C_LEN COVERAGE R_HLEN R_SUPP S_HLEN" QUANT_MEASURES="${QUANT_MEASURES} A_HLEN A_SUPP S_MAPQ S_Q_BEF S_Q_FIRST" QUANT_MEASURES="${QUANT_MEASURES} S_Q_MIN S_Q_AVE S_Q_MAX S_Q_RANGE S_Q_LAST" QUANT_MEASURES="${QUANT_MEASURES} S_Q_AFT A_HLEN_DIFF S_HLEN_DIFF NON_C_LEN" QUANT_MEASURES="${QUANT_MEASURES} A_SUPP_DIFF" for MEASURE in ${QUANT_MEASURES}; do awk '{print int('${FIELD[$MEASURE]}')}' $MAP.hop_stats_FP \ | sort -n | uniq -c > $MAP.hop_FP_${MEASURE}_distri awk '{print int('${FIELD[$MEASURE]}')}' $MAP.hop_stats_TP \ | sort -n | uniq -c > $MAP.hop_TP_${MEASURE}_distri done QUAL_MEASURES="S_CHAR EDIT S_OR EDIT_OP MULTIEDIT_OP" for MEASURE in ${QUAL_MEASURES}; do awk '{print '${FIELD[$MEASURE]}'}' $MAP.hop_stats_FP \ | sort | uniq -c > $MAP.hop_FP_${MEASURE}_distri awk '{print '${FIELD[$MEASURE]}'}' $MAP.hop_stats_TP \ | sort | uniq -c > $MAP.hop_TP_${MEASURE}_distri done MEASURES="${QUAL_MEASURES} ${QUANT_MEASURES}" for MEASURE in $MEASURES; do ruby -e " f = File.open('$MAP.hop_${MEASURE}_distri', 'w') tp={} fp={} IO.read(%Q[$MAP.hop_TP_${MEASURE}_distri]).split(%Q[\n]). each{|x| x=x.split; tp[x[1]]=x[0]; fp[x[1]]=0} IO.read(%Q[$MAP.hop_FP_${MEASURE}_distri]).split(%Q[\n]). each{|x| x=x.split; fp[x[1]]=x[0]; tp[x[1]]||=0} f.printf(%Q[${MEASURE}\tALL\tTP\tFP\tTPR\tFPR\n]) keys = tp.keys if (keys[0].to_i.to_s == keys[0]) keys = keys.sort_by {|x| x.to_i} else keys.sort! end keys.each do |k| f.printf(%Q[#{k}\t%s\t%s\t%s\t%.2f\t%.2f\n], tp[k].to_i + fp[k].to_i, tp[k], fp[k], tp[k].to_f * 100 / (tp[k].to_f+fp[k].to_f), fp[k].to_f * 100 / (tp[k].to_f+fp[k].to_f)) end f.close " echo "${MEASURE} distribution: $MAP.hop_${MEASURE}_distri" done } function f_eval_stats { SMAP="${READS}.${SGENOME}" EDSDIFF="$SMAP.$GENOME.eds_diff" INFO="$SMAP.$GENOME.eval" diff $SMAP.eds $MAP.eds > $EDSDIFF CORR=`cat $MAP.eds | wc -l` ERR=`cat $SMAP.eds | wc -l` FN=`grep '^<' $EDSDIFF | wc -l` FP=`grep '^>' $EDSDIFF | wc -l` TP=$[$CORR-$FP] GENOMEDESC=`head -n 1 $GENOME` SGENOMEDESC=`head -n 1 $SGENOME` echo "==== Computing evaluation statistics..." echo | tee $INFO echo "Statistics of the correction of:" | tee -a $INFO if [ "$MATES" == "" ];then echo "- reads: $READS" | tee -a $INFO else echo "- reads: $READS + $MATES" | tee -a $INFO fi echo "- state of truth based upon: $SGENOMEDESC" | tee -a $INFO echo | tee -a $INFO MIN_HLEN=`grep -P -o "(?<=Distribution of homopolymers of length >= )\d+" \ $MAP.hop_stats` if [ "$MIN_HLEN" == "" ]; then MIN_HLEN="n.a."; fi NOF_READS=`grep -P -o "(?<=segments in SAM file:)\s+\d+" \ $MAP.hop_stats | grep -P -o "\d+"` NOF_NMAP=`grep -P -o "(?<=not mapping:)\s+\d+" \ $MAP.hop_stats | grep -P -o "\d+"` if [ "$NOF_READS" != "" -a "$NOF_NMAP" != "" ]; then NOF_MAP=$[$NOF_READS - $NOF_NMAP] else NOF_MAP="n.a." fi if [ "$NOF_READS" == "" ]; then NOF_READS="n.a."; fi if [ "$NOF_NMAP" == "" ]; then NOF_NMAP="n.a."; fi echo "Correction parameters:" | tee -a $INFO echo "- reference for correction: $GENOMEDESC" | tee -a $INFO if [ "$ANNOTATION" != "$NOGFF" ]; then echo "- annotation: $ANNOTATION" | tee -a $INFO else echo "- annotation: none" | tee -a $INFO fi echo "- minimal homopol. length: ${MIN_HLEN}" | tee -a $INFO echo | tee -a $INFO echo "Mapping results:" | tee -a $INFO echo "- total reads: $NOF_READS" | tee -a $INFO echo "- mapping: $NOF_MAP" | tee -a $INFO echo "- not mapping: $NOF_NMAP" | tee -a $INFO echo | tee -a $INFO echo "Correction results:" | tee -a $INFO echo "- homopol. errors: $ERR" | tee -a $INFO echo "- corrected homopol.: $CORR" | tee -a $INFO echo "- true positives: $TP" | tee -a $INFO echo "- false positives: $FP" | tee -a $INFO echo "- false negatives: $FN" | tee -a $INFO SN=`echo "$TP * 100 / ($TP + $FN)" | bc -l` PR=`echo "$TP * 100 / ($TP + $FP)" | bc -l` printf -- "- sensitivity: %.2f %%\n" $SN | tee -a $INFO printf -- "- precision: %.2f %%\n" $PR | tee -a $INFO echo | tee -a $INFO echo "==== done " echo echo "evaluation statistics: $INFO" echo } function f_eval { f_stats if [ "$SHOWONLY" != "TRUE" ]; then stats2eds f_eval_stats fi } function f_dists { echo "==== Computing distributions..." echo $GT seqstat -distlen -b 1 $READS $MATES >| $READS.lendist $GT seqstat -distlen -b 1 hop_$READS >| hop_$READS.lendist f_pos_stats $MAP.hop_stats $MAP.hop_pos_stats $READS.lendist echo echo "==== done " echo echo "original reads length distribution: $READS.lendist" echo "corrected reads length distribution: hop_$READS.lendist" echo "corrections per read position: $MAP.hop_pos_stats" echo } if [ "$ACTION" != "help" -a "$ACTION" != "eval-help" ]; then if [ $# -lt 4 -o $# -gt 5 ]; then f_die; fi fi case "$ACTION" in 'prepare') f_prepare ;; 'correct') f_correct ;; 'clean') f_clean ;; 'run') f_run ;; 'stats') f_stats ;; 'dists') f_dists ;; 'help') f_help ;; 'eval-help') f_eval_help ;; 'eval-make-true') f_eval_make_true ;; 'eval-prepare') f_eval_prepare ;; 'eval') f_eval ;; # parts of other actions: 'index') f_index ;; 'map') f_map ;; 'sortmap') f_sortmap ;; 'encode') f_encode ;; 'sortgff') f_sortgff ;; 'eval-stats') f_eval_stats ;; 'eval-mark') f_eval_mark ;; 'eval-proc-marked') f_eval_proc_marked ;; *) f_die ;; esac genometools-1.5.1/scripts/incl.sed000066400000000000000000000001041211610345200171500ustar00rootroot00000000000000/ this is a SNP <----- */ if (gt_range_overlap(&new_rng, &sas->cur_gene_range)) { /* it falls into the currently observed range */ gt_queue_add(sas->snps, gt_genome_node_ref((GtGenomeNode*) fn)); } else { /* SNP outside a gene, this cluster is done add to out queue and start serving */ gt_assert(gt_queue_size(sas->outqueue) == 0); had_err = snp_annotator_stream_process_current_gene(sas, err); gt_queue_add(sas->outqueue, mygn); if (gt_queue_size(sas->outqueue) > 0) { *gn = (GtGenomeNode*) gt_queue_get(sas->outqueue); complete_cluster = true; } } } else if (type == gene_type) { /* -----> this is a gene <----- */ if (gt_array_size(sas->cur_gene_set) == 0UL) { /* new overlapping gene cluster */ addgn = gt_genome_node_ref(mygn); gt_array_add(sas->cur_gene_set, addgn); sas->cur_gene_range = gt_genome_node_get_range(mygn); } else { if (gt_range_overlap(&new_rng, &sas->cur_gene_range)) { /* gene overlaps with current one, add to cluster */ addgn = gt_genome_node_ref(mygn); gt_array_add(sas->cur_gene_set, addgn); sas->cur_gene_range = gt_range_join(&sas->cur_gene_range, &new_rng); } else { /* finish current cluster and start a new one */ had_err = snp_annotator_stream_process_current_gene(sas, err); if (!had_err) { addgn = gt_genome_node_ref(mygn); gt_array_add(sas->cur_gene_set, addgn); sas->cur_gene_range = gt_genome_node_get_range(mygn); } if (gt_queue_size(sas->outqueue) > 0) { *gn = (GtGenomeNode*) gt_queue_get(sas->outqueue); complete_cluster = true; } } } /* from now on, genes are kept in gene cluster arrays only */ gt_genome_node_delete(mygn); } } else { /* meta node */ had_err = snp_annotator_stream_process_current_gene(sas, err); if (!had_err) { gt_queue_add(sas->outqueue, mygn); } if (gt_queue_size(sas->outqueue) > 0) { *gn = (GtGenomeNode*) gt_queue_get(sas->outqueue); complete_cluster = true; } } } return had_err; } static void snp_annotator_stream_free(GtNodeStream *ns) { unsigned long i; GtSNPAnnotatorStream *sas; if (!ns) return; sas = gt_snp_annotator_stream_cast(ns); gt_region_mapping_delete(sas->rmap); while (gt_queue_size(sas->snps) > 0) { gt_genome_node_delete((GtGenomeNode*) gt_queue_get(sas->snps)); } while (gt_queue_size(sas->outqueue) > 0) { gt_genome_node_delete((GtGenomeNode*) gt_queue_get(sas->outqueue)); } for (i = 0; i < gt_array_size(sas->instreams); i++) { gt_node_stream_delete(*(GtNodeStream**) gt_array_get(sas->instreams, i)); } for (i = 0; i < gt_array_size(sas->cur_gene_set); i++) { gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(sas->cur_gene_set, i)); } gt_array_delete(sas->cur_gene_set); gt_node_stream_delete(sas->merge_stream); gt_array_delete(sas->instreams); gt_queue_delete(sas->snps); gt_queue_delete(sas->outqueue); } const GtNodeStreamClass* gt_snp_annotator_stream_class(void) { static const GtNodeStreamClass *nsc = NULL; gt_class_alloc_lock_enter(); if (!nsc) { nsc = gt_node_stream_class_new(sizeof (GtSNPAnnotatorStream), snp_annotator_stream_free, snp_annotator_stream_next); } gt_class_alloc_lock_leave(); return nsc; } GtNodeStream* gt_snp_annotator_stream_new(GtNodeStream *gvf_stream, GtNodeStream *gff_stream, GtTransTable *trans_table, GtRegionMapping *rmap) { GtSNPAnnotatorStream *sas; GtNodeStream *ns; gt_assert(gvf_stream && gff_stream && rmap); ns = gt_node_stream_create(gt_snp_annotator_stream_class(), true); sas = gt_snp_annotator_stream_cast(ns); sas->instreams = gt_array_new(sizeof (GtNodeStream*)); (void) gt_node_stream_ref(gvf_stream); gt_array_add(sas->instreams, gvf_stream); (void) gt_node_stream_ref(gff_stream); gt_array_add(sas->instreams, gff_stream); sas->cur_gene_set = gt_array_new(sizeof (GtFeatureNode*)); sas->merge_stream = gt_merge_stream_new(sas->instreams); sas->rmap = gt_region_mapping_ref(rmap); sas->cur_gene_range.start = sas->cur_gene_range.end = GT_UNDEF_ULONG; sas->snps = gt_queue_new(); sas->outqueue = gt_queue_new(); sas->tt = trans_table; return ns; } genometools-1.5.1/src/extended/snp_annotator_stream.h000066400000000000000000000030051211610345200230420ustar00rootroot00000000000000/* Copyright (c) 2012-2013 Sascha Steinbiss Copyright (c) 2012-2013 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SNP_ANNOTATOR_STREAM_H #define SNP_ANNOTATOR_STREAM_H #include "core/trans_table_api.h" #include "extended/node_stream_api.h" #include "extended/region_mapping_api.h" /* implements the ``genome stream'' interface */ typedef struct GtSNPAnnotatorStream GtSNPAnnotatorStream; const GtNodeStreamClass* gt_snp_annotator_stream_class(void); GtNodeStream* gt_snp_annotator_stream_new(GtNodeStream *gvf_stream, GtNodeStream *gff_stream, GtTransTable *trans_table, GtRegionMapping *rmap); #endif genometools-1.5.1/src/extended/snp_annotator_visitor.c000066400000000000000000000351601211610345200232500ustar00rootroot00000000000000/* Copyright (c) 2013 Sascha Steinbiss Copyright (c) 2013 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "core/codon_api.h" #include "core/complement.h" #include "core/cstr_api.h" #include "core/hashmap.h" #include "core/log.h" #include "core/ma_api.h" #include "core/strand_api.h" #include "core/symbol.h" #include "core/trans_table.h" #include "core/undef_api.h" #include "core/unused_api.h" #include "core/warning_api.h" #include "extended/feature_node_iterator_api.h" #include "extended/feature_type.h" #include "extended/gff3_defines.h" #include "extended/node_visitor_api.h" #include "extended/region_mapping_api.h" #include "extended/reverse_api.h" #include "extended/snp_annotator_visitor.h" struct GtSNPAnnotatorVisitor { const GtNodeVisitor parent_instance; GtFeatureNode *gene; GtRegionMapping *rmap; GtHashmap *rnaseqs; GtTransTable *tt; bool own_tt; const char *mRNA_type, *CDS_type, *SNV_type, *SNP_type; }; #define GT_SNP_MISSENSE_EFFECT "non_conservative_missense_variant" #define GT_SNP_NONSENSE_EFFECT "stop_gained" #define GT_SNP_STOP_LOST_EFFECT "stop_lost" #define GT_SNP_SYNONYMOUS_AMINO_EFFECT "synonymous_variant" #define GT_SNP_SYNONYMOUS_STOP_EFFECT "stop_retained_variant" #define snp_annotator_visitor_cast(GV)\ gt_node_visitor_cast(gt_snp_annotator_visitor_class(), GV) static void snp_annotator_visitor_free(GtNodeVisitor *nv) { GtSNPAnnotatorVisitor *sav; if (!nv) return; sav = snp_annotator_visitor_cast(nv); gt_genome_node_delete((GtGenomeNode*) sav->gene); if (sav->own_tt) gt_trans_table_delete(sav->tt); gt_region_mapping_delete(sav->rmap); gt_hashmap_delete(sav->rnaseqs); } static int snp_annotator_classify_snp(GtSNPAnnotatorVisitor *sav, GtFeatureNode *mRNA, GtFeatureNode *snp, unsigned long variant_pos, unsigned long variant_idx, char variant_char, #ifndef NDEBUG GT_UNUSED char reference_char, #endif GT_UNUSED GtError *err) { int had_err = 0; char *mrnaseq; const char *variant_effect = NULL; gt_assert(mRNA && snp && sav); gt_log_log("processing variant char %c for SNP %s\n", variant_char, gt_feature_node_get_attribute(snp, "Dbxref")); mrnaseq = gt_hashmap_get(sav->rnaseqs, mRNA); gt_assert(mrnaseq); if (mrnaseq) { char codon[3], variant_codon[3]; GtStr *effect_string; char oldamino, newamino; GT_UNUSED unsigned long mrnalen; unsigned long startpos = variant_pos / GT_CODON_LENGTH, variantoffset = variant_pos % GT_CODON_LENGTH; mrnalen = strlen(mrnaseq); gt_assert(variant_pos < mrnalen); variant_codon[0] = codon[0] = mrnaseq[3*startpos]; variant_codon[1] = codon[1] = mrnaseq[3*startpos+1]; variant_codon[2] = codon[2] = mrnaseq[3*startpos+2]; variant_codon[variantoffset] = variant_char; #ifndef NDEBUG gt_assert(toupper(codon[variantoffset]) == toupper(reference_char)); #endif if (gt_trans_table_is_stop_codon(sav->tt, codon[0], codon[1], codon[2])) { if (gt_trans_table_is_stop_codon(sav->tt, variant_codon[0], variant_codon[1], variant_codon[2])) { variant_effect = gt_symbol(GT_SNP_SYNONYMOUS_STOP_EFFECT); } else { variant_effect = gt_symbol(GT_SNP_STOP_LOST_EFFECT); } } else { if (gt_trans_table_is_stop_codon(sav->tt, variant_codon[0], variant_codon[1], variant_codon[2])) { variant_effect = gt_symbol(GT_SNP_NONSENSE_EFFECT); } else { had_err = gt_trans_table_translate_codon(sav->tt, codon[0], codon[1], codon[2], &oldamino, err); if (!had_err) { had_err = gt_trans_table_translate_codon(sav->tt, variant_codon[0], variant_codon[1], variant_codon[2], &newamino, err); } if (!had_err) { if (newamino == oldamino) { variant_effect = gt_symbol(GT_SNP_SYNONYMOUS_AMINO_EFFECT); } else { variant_effect = gt_symbol(GT_SNP_MISSENSE_EFFECT); } } } } if (!had_err) { const char *var_attrib; gt_assert(variant_effect != NULL); if ((var_attrib = gt_feature_node_get_attribute(snp, GT_GVF_VARIANT_EFFECT))) { effect_string = gt_str_new_cstr(var_attrib); gt_str_append_cstr(effect_string, ","); gt_str_append_cstr(effect_string, variant_effect); } else { effect_string = gt_str_new_cstr(variant_effect); } gt_str_append_cstr(effect_string, " "); gt_str_append_ulong(effect_string, variant_idx); gt_str_append_cstr(effect_string, " "); gt_str_append_cstr(effect_string, gt_feature_node_get_type(mRNA)); gt_str_append_cstr(effect_string, " "); gt_str_append_cstr(effect_string, gt_feature_node_get_attribute(mRNA, GT_GFF_ID)); gt_feature_node_set_attribute(snp, GT_GVF_VARIANT_EFFECT, gt_str_get(effect_string)); gt_str_reset(effect_string); gt_str_delete(effect_string); } } return had_err; } static int snp_annotator_visitor_feature_node(GtNodeVisitor *nv, GtFeatureNode *fn, GtError *err) { int had_err = 0; GtSNPAnnotatorVisitor *sav; GtFeatureNodeIterator *fni, *mrnafni; GtFeatureNode *curnode, *curnode2; GtRange snp_rng; gt_error_check(err); sav = snp_annotator_visitor_cast(nv); /* ignore non-nodes */ if (!fn) return 0; /* only process SNPs */ if (!(gt_feature_node_get_type(fn) == sav->SNV_type || gt_feature_node_get_type(fn) == sav->SNP_type)) { return 0; } fni = gt_feature_node_iterator_new_direct(sav->gene); snp_rng = gt_genome_node_get_range((GtGenomeNode*) fn); while (!had_err && (curnode = gt_feature_node_iterator_next(fni))) { if (gt_feature_node_get_type(curnode) == sav->mRNA_type) { GtStrand mrna_strand = gt_feature_node_get_strand(curnode); #ifndef NDEBUG const char *refstr; #endif unsigned long mrnasnppos = 0; mrnafni = gt_feature_node_iterator_new(curnode); while (!had_err && (curnode2 = gt_feature_node_iterator_next(mrnafni))) { if (gt_feature_node_get_type(curnode2) == sav->CDS_type) { GtRange cds_rng = gt_genome_node_get_range((GtGenomeNode*) curnode2); if (gt_range_overlap(&snp_rng, &cds_rng)) { char *mRNA, origchar; char *variantchars, *variantptr = NULL; GT_UNUSED char *refchars, *refptr = NULL; mRNA = (char*) gt_hashmap_get(sav->rnaseqs, curnode); gt_assert(mRNA); gt_assert(snp_rng.start >= cds_rng.start); mrnasnppos += (snp_rng.start - cds_rng.start); if (mrna_strand == GT_STRAND_REVERSE) mrnasnppos = strlen(mRNA) - mrnasnppos - 1; gt_assert(mrnasnppos < strlen(mRNA)); origchar = mRNA[mrnasnppos]; #ifndef NDEBUG refstr = refptr = gt_cstr_dup(gt_feature_node_get_attribute(fn, GT_GVF_REFERENCE_SEQ)); if (!had_err && refstr) { if (gt_feature_node_get_strand(curnode) == GT_STRAND_REVERSE) { int rval = gt_complement(&origchar, origchar, err); gt_assert(rval == 0); } gt_assert(toupper(origchar) == toupper(refstr[0])); } #endif variantchars = variantptr = gt_cstr_dup( gt_feature_node_get_attribute(fn, GT_GVF_VARIANT_SEQ)); if (!had_err && variantchars) { unsigned long i = 0; while (!had_err && (*variantchars != ';' && *variantchars != '\0')) { if (*variantchars != ',' && *variantchars != origchar) { char variantchar = *variantchars; #ifndef NDEBUG char refchar = refstr[0]; if (!had_err && mrna_strand == GT_STRAND_REVERSE) had_err = gt_complement(&refchar, refchar, err); #endif if (!had_err && mrna_strand == GT_STRAND_REVERSE) had_err = gt_complement(&variantchar, variantchar, err); if (!had_err) { had_err = snp_annotator_classify_snp(sav, curnode, fn, mrnasnppos, i++, variantchar, #ifndef NDEBUG refchar, #endif err); } } else if (*variantchars == origchar) { i++; } variantchars++; } gt_free(variantptr); gt_free(refptr); } } else { mrnasnppos += gt_range_length(&cds_rng); } } } gt_feature_node_iterator_delete(mrnafni); } } gt_feature_node_iterator_delete(fni); return had_err; } const GtNodeVisitorClass* gt_snp_annotator_visitor_class() { static GtNodeVisitorClass *nvc = NULL; gt_class_alloc_lock_enter(); if (!nvc) { nvc = gt_node_visitor_class_new(sizeof (GtSNPAnnotatorVisitor), snp_annotator_visitor_free, NULL, snp_annotator_visitor_feature_node, NULL, NULL, NULL); } gt_class_alloc_lock_leave(); return nvc; } static int gt_snp_annotator_visitor_prepare_gene(GtSNPAnnotatorVisitor *sav, GtError *err) { GtFeatureNodeIterator *fni, *mrnafni; GtFeatureNode *curnode, *last_mRNA = NULL; GtStr *mrnaseq, *seqid; int had_err = 0; mrnaseq = gt_str_new(); seqid = gt_genome_node_get_seqid((GtGenomeNode*) sav->gene); fni = gt_feature_node_iterator_new(sav->gene); while (!had_err && (curnode = gt_feature_node_iterator_next(fni))) { if (gt_feature_node_get_type(curnode) == sav->mRNA_type) { GtFeatureNode *curnode2; if (last_mRNA) { char *mrna_charseq = gt_calloc(gt_str_length(mrnaseq)+1, sizeof (char)); (void) strncpy(mrna_charseq, gt_str_get(mrnaseq), gt_str_length(mrnaseq)); if (gt_feature_node_get_strand(sav->gene) == GT_STRAND_REVERSE) { had_err = gt_reverse_complement(mrna_charseq, gt_str_length(mrnaseq), err); } if (!had_err) { gt_hashmap_add(sav->rnaseqs, last_mRNA, mrna_charseq); last_mRNA = curnode; gt_str_reset(mrnaseq); } } else last_mRNA = curnode; if (!had_err) { mrnafni = gt_feature_node_iterator_new(curnode); while (!had_err && (curnode2 = gt_feature_node_iterator_next(mrnafni))) { if (gt_feature_node_get_type(curnode2) == sav->CDS_type) { char *tmp; GtRange rng = gt_genome_node_get_range((GtGenomeNode*) curnode2); had_err = gt_region_mapping_get_sequence(sav->rmap, &tmp, seqid, rng.start, rng.end, err); if (!had_err) { gt_str_append_cstr_nt(mrnaseq, tmp, gt_range_length(&rng)); gt_free(tmp); } } } gt_feature_node_iterator_delete(mrnafni); } } } if (!had_err && last_mRNA) { char *mrna_charseq = gt_calloc(gt_str_length(mrnaseq)+1, sizeof (char)); (void) strncpy(mrna_charseq, gt_str_get(mrnaseq), gt_str_length(mrnaseq)); if (gt_feature_node_get_strand(sav->gene) == GT_STRAND_REVERSE) { had_err = gt_reverse_complement(mrna_charseq, gt_str_length(mrnaseq), err); } if (!had_err) { gt_hashmap_add(sav->rnaseqs, last_mRNA, mrna_charseq); } } gt_feature_node_iterator_delete(fni); gt_str_delete(mrnaseq); return had_err; } GtNodeVisitor* gt_snp_annotator_visitor_new(GtFeatureNode *gene, GtTransTable *trans_table, GtRegionMapping *rmap, GtError *err) { GtNodeVisitor *nv; GtSNPAnnotatorVisitor *sav; gt_assert(gene && gt_feature_node_get_type(gene) == gt_symbol(gt_ft_gene)); nv = gt_node_visitor_create(gt_snp_annotator_visitor_class()); sav = snp_annotator_visitor_cast(nv); sav->gene = (GtFeatureNode*) gt_genome_node_ref((GtGenomeNode*) gene); sav->rmap = gt_region_mapping_ref(rmap); sav->mRNA_type = gt_symbol(gt_ft_mRNA); sav->CDS_type = gt_symbol(gt_ft_CDS); sav->SNV_type = gt_symbol(gt_ft_SNV); sav->SNP_type = gt_symbol(gt_ft_SNP); sav->rnaseqs = gt_hashmap_new(GT_HASH_DIRECT, NULL, gt_free_func); if (trans_table) { sav->tt = trans_table; sav->own_tt = false; } else { sav->tt = gt_trans_table_new_standard(err); sav->own_tt = true; } if (!sav->tt || gt_snp_annotator_visitor_prepare_gene(sav, err) != 0) { gt_node_visitor_delete(nv); return NULL; } return nv; } genometools-1.5.1/src/extended/snp_annotator_visitor.h000066400000000000000000000030211211610345200232440ustar00rootroot00000000000000/* Copyright (c) 2013 Sascha Steinbiss Copyright (c) 2013 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SNP_ANNOTATOR_VISITOR_H #define SNP_ANNOTATOR_VISITOR_H /* Implements the interface. */ typedef struct GtSNPAnnotatorVisitor GtSNPAnnotatorVisitor; #include "core/error_api.h" #include "core/trans_table_api.h" #include "extended/region_mapping_api.h" #include "extended/node_visitor_api.h" const GtNodeVisitorClass* gt_snp_annotator_visitor_class(void); GtNodeVisitor* gt_snp_annotator_visitor_new(GtFeatureNode *gene, GtTransTable *trans_table, GtRegionMapping *rmap, GtError *err); #endif genometools-1.5.1/src/extended/sort_stream.c000066400000000000000000000106411211610345200211430ustar00rootroot00000000000000/* Copyright (c) 2006-2011 Gordon Gremme Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/array.h" #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "extended/eof_node.h" #include "extended/genome_node.h" #include "extended/node_stream_api.h" #include "extended/sort_stream.h" struct GtSortStream { const GtNodeStream parent_instance; GtNodeStream *in_stream; unsigned long idx; GtArray *nodes; bool sorted; }; #define gt_sort_stream_cast(GS)\ gt_node_stream_cast(gt_sort_stream_class(), GS); static int gt_sort_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) { GtSortStream *sort_stream; GtGenomeNode *node, *eofn; int had_err = 0; gt_error_check(err); sort_stream = gt_sort_stream_cast(ns); if (!sort_stream->sorted) { while (!(had_err = gt_node_stream_next(sort_stream->in_stream, &node, err)) && node) { if ((eofn = gt_eof_node_try_cast(node))) gt_genome_node_delete(eofn); /* get rid of EOF nodes */ else gt_array_add(sort_stream->nodes, node); } if (!had_err) { gt_genome_nodes_sort_stable(sort_stream->nodes); sort_stream->sorted = true; } } if (!had_err) { gt_assert(sort_stream->sorted); if (sort_stream->idx < gt_array_size(sort_stream->nodes)) { *gn = *(GtGenomeNode**) gt_array_get(sort_stream->nodes, sort_stream->idx); sort_stream->idx++; /* join region nodes with the same sequence ID */ if (gt_region_node_try_cast(*gn)) { GtRange range_a, range_b; while (sort_stream->idx < gt_array_size(sort_stream->nodes)) { node = *(GtGenomeNode**) gt_array_get(sort_stream->nodes, sort_stream->idx); if (!gt_region_node_try_cast(node) || gt_str_cmp(gt_genome_node_get_seqid(*gn), gt_genome_node_get_seqid(node))) { /* the next node is not a region node with the same ID */ break; } range_a = gt_genome_node_get_range(*gn); range_b = gt_genome_node_get_range(node); range_a = gt_range_join(&range_a, &range_b); gt_genome_node_set_range(*gn, &range_a); gt_genome_node_delete(node); sort_stream->idx++; } } return 0; } } if (!had_err) { gt_array_reset(sort_stream->nodes); *gn = NULL; } return had_err; } static void gt_sort_stream_free(GtNodeStream *ns) { unsigned long i; GtSortStream *sort_stream = gt_sort_stream_cast(ns); for (i = sort_stream->idx; i < gt_array_size(sort_stream->nodes); i++) { gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(sort_stream->nodes, i)); } gt_array_delete(sort_stream->nodes); gt_node_stream_delete(sort_stream->in_stream); } const GtNodeStreamClass* gt_sort_stream_class(void) { static const GtNodeStreamClass *nsc = NULL; gt_class_alloc_lock_enter(); if (!nsc) { nsc = gt_node_stream_class_new(sizeof (GtSortStream), gt_sort_stream_free, gt_sort_stream_next); } gt_class_alloc_lock_leave(); return nsc; } GtNodeStream* gt_sort_stream_new(GtNodeStream *in_stream) { GtNodeStream *ns = gt_node_stream_create(gt_sort_stream_class(), true); GtSortStream *sort_stream = gt_sort_stream_cast(ns); gt_assert(in_stream); sort_stream->in_stream = gt_node_stream_ref(in_stream); sort_stream->sorted = false; sort_stream->idx = 0; sort_stream->nodes = gt_array_new(sizeof (GtGenomeNode*)); return ns; } genometools-1.5.1/src/extended/sort_stream.h000066400000000000000000000017761211610345200211610ustar00rootroot00000000000000/* Copyright (c) 2006-2007, 2011 Gordon Gremme Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SORT_STREAM_H #define SORT_STREAM_H #include "extended/sort_stream_api.h" const GtNodeStreamClass* gt_sort_stream_class(void); #endif genometools-1.5.1/src/extended/sort_stream_api.h000066400000000000000000000025151211610345200220020ustar00rootroot00000000000000/* Copyright (c) 2006-2007, 2011 Gordon Gremme Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SORT_STREAM_API_H #define SORT_STREAM_API_H #include "extended/node_stream_api.h" /* Implements the interface. A sorts the objects it retrieves from its node source. */ typedef struct GtSortStream GtSortStream; /* Create a which sorts the genome nodes it retrieves from and returns them unmodified, but in sorted order. */ GtNodeStream* gt_sort_stream_new(GtNodeStream *in_stream); #endif genometools-1.5.1/src/extended/splice_site_info_stream.c000066400000000000000000000077751211610345200235100ustar00rootroot00000000000000/* Copyright (c) 2007-2011 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "extended/genome_node.h" #include "extended/node_stream_api.h" #include "extended/splice_site_info_stream.h" #include "extended/splice_site_info_visitor.h" struct GtSpliceSiteInfoStream { const GtNodeStream parent_instance; GtNodeStream *in_stream; GtNodeVisitor *splice_site_info_visitor; }; #define gt_splice_site_info_stream_cast(GS)\ gt_node_stream_cast(gt_splice_site_info_stream_class(), GS) static int gt_splice_site_info_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) { GtSpliceSiteInfoStream *ssis; int had_err; gt_error_check(err); ssis = gt_splice_site_info_stream_cast(ns); had_err = gt_node_stream_next(ssis->in_stream, gn, err); if (!had_err) { gt_assert(ssis->splice_site_info_visitor); if (*gn) { had_err = gt_genome_node_accept(*gn, ssis->splice_site_info_visitor, err); if (had_err) { /* we own the node -> delete it */ gt_genome_node_delete(*gn); *gn = NULL; } } } return had_err; } static void gt_splice_site_info_stream_free(GtNodeStream *ns) { GtSpliceSiteInfoStream *ssis = gt_splice_site_info_stream_cast(ns); gt_node_visitor_delete(ssis->splice_site_info_visitor); gt_node_stream_delete(ssis->in_stream); } const GtNodeStreamClass* gt_splice_site_info_stream_class(void) { static const GtNodeStreamClass *nsc = NULL; gt_class_alloc_lock_enter(); if (!nsc) { nsc = gt_node_stream_class_new(sizeof (GtSpliceSiteInfoStream), gt_splice_site_info_stream_free, gt_splice_site_info_stream_next); } gt_class_alloc_lock_leave(); return nsc; } GtNodeStream* gt_splice_site_info_stream_new(GtNodeStream *in_stream, GtRegionMapping *rm) { GtNodeStream *ns = gt_node_stream_create(gt_splice_site_info_stream_class(), false); GtSpliceSiteInfoStream *ssis = gt_splice_site_info_stream_cast(ns); ssis->in_stream = gt_node_stream_ref(in_stream); ssis->splice_site_info_visitor = gt_splice_site_info_visitor_new(rm); return ns; } bool gt_splice_site_info_stream_show(GtNodeStream *ns, GtFile *outfp) { GtSpliceSiteInfoStream *ssis; gt_assert(ns); ssis = gt_splice_site_info_stream_cast(ns); return gt_splice_site_info_visitor_show(ssis->splice_site_info_visitor, outfp); } bool gt_splice_site_info_stream_intron_processed(GtNodeStream *ns) { GtSpliceSiteInfoStream *ssis; gt_assert(ns); ssis = gt_splice_site_info_stream_cast(ns); return gt_splice_site_info_visitor_intron_processed(ssis ->splice_site_info_visitor); } bool gt_splice_site_info_stream_show_canonical(GtNodeStream *ns, bool show_gc) { GtSpliceSiteInfoStream *ssis; gt_assert(ns); ssis = gt_splice_site_info_stream_cast(ns); return gt_splice_site_info_visitor_show_canonical(ssis ->splice_site_info_visitor, show_gc); } genometools-1.5.1/src/extended/splice_site_info_stream.h000066400000000000000000000034141211610345200234770ustar00rootroot00000000000000/* Copyright (c) 2007-2011 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SPLICE_SITE_INFO_STREAM_H #define SPLICE_SITE_INFO_STREAM_H #include #include "extended/node_stream_api.h" #include "extended/region_mapping_api.h" /* implements the ``genome_stream'' interface */ typedef struct GtSpliceSiteInfoStream GtSpliceSiteInfoStream; const GtNodeStreamClass* gt_splice_site_info_stream_class(void); /* Create a GtSpliceSiteInfoStream, takes ownership of . */ GtNodeStream* gt_splice_site_info_stream_new(GtNodeStream *in_stream, GtRegionMapping *region_mapping); /* Returns if an intron has been processed, otherwise */ bool gt_splice_site_info_stream_show(GtNodeStream*, GtFile*); bool gt_splice_site_info_stream_intron_processed(GtNodeStream*); bool gt_splice_site_info_stream_show_canonical(GtNodeStream*, bool show_gc); #endif genometools-1.5.1/src/extended/splice_site_info_visitor.c000066400000000000000000000177111211610345200237030ustar00rootroot00000000000000/* Copyright (c) 2007-2010 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "core/fasta.h" #include "core/ma_api.h" #include "core/string_distri.h" #include "core/unused_api.h" #include "core/warning_api.h" #include "core/xansi_api.h" #include "extended/feature_node_iterator_api.h" #include "extended/feature_type.h" #include "extended/node_visitor_api.h" #include "extended/splice_site_info_visitor.h" #include "extended/reverse_api.h" struct GtSpliceSiteInfoVisitor { const GtNodeVisitor parent_instance; GtRegionMapping *region_mapping; GtStringDistri *splicesites, *donorsites, *acceptorsites; bool show, intron_processed; }; #define splice_site_info_visitor_cast(GV)\ gt_node_visitor_cast(gt_splice_site_info_visitor_class(), GV) static void splice_site_info_visitor_free(GtNodeVisitor *nv) { GtSpliceSiteInfoVisitor *splice_site_info_visitor; gt_assert(nv); splice_site_info_visitor = splice_site_info_visitor_cast(nv); gt_region_mapping_delete(splice_site_info_visitor->region_mapping); gt_string_distri_delete(splice_site_info_visitor->splicesites); gt_string_distri_delete(splice_site_info_visitor->donorsites); gt_string_distri_delete(splice_site_info_visitor->acceptorsites); } static int process_intron(GtSpliceSiteInfoVisitor *ssiv, GtGenomeNode *intron, GtError *err) { char *sequence = NULL; GtStrand strand; GtRange range; char site[5]; GtStr *seqid; int had_err = 0; gt_error_check(err); gt_assert(ssiv && intron); ssiv->intron_processed = true; range = gt_genome_node_get_range(intron); gt_assert(range.start); /* 1-based coordinates */ if (gt_range_length(&range) >= 4) { seqid = gt_genome_node_get_seqid(intron); had_err = gt_region_mapping_get_sequence(ssiv->region_mapping, &sequence, seqid, range.start, range.end, err); if (!had_err) { strand = gt_feature_node_get_strand((GtFeatureNode*) intron); if (strand == GT_STRAND_FORWARD || strand == GT_STRAND_REVERSE) { /* fill site */ site[0] = tolower(sequence[0]); site[1] = tolower(sequence[1]); site[2] = tolower(sequence[gt_range_length(&range)-2]); site[3] = tolower(sequence[gt_range_length(&range)-1]); site[4] = '\0'; if (strand == GT_STRAND_REVERSE) had_err = gt_reverse_complement(site, 4, err); if (!had_err) { /* add site to distributions */ gt_string_distri_add(ssiv->splicesites, site); gt_string_distri_add(ssiv->acceptorsites, site + 2); site[2] = '\0'; gt_string_distri_add(ssiv->donorsites, site); ssiv->show = true; } } else { gt_warning("skipping intron with unknown orientation " "(file '%s', line %u)", gt_genome_node_get_filename(intron), gt_genome_node_get_line_number(intron)); } gt_free(sequence); } } return had_err; } static int splice_site_info_visitor_feature_node(GtNodeVisitor *nv, GtFeatureNode *fn, GtError *err) { GtSpliceSiteInfoVisitor *ssiv; GtFeatureNodeIterator *fni; GtFeatureNode *node; int had_err = 0; gt_error_check(err); ssiv = splice_site_info_visitor_cast(nv); gt_assert(ssiv->region_mapping); fni = gt_feature_node_iterator_new(fn); while (!had_err && (node = gt_feature_node_iterator_next(fni))) { if (gt_feature_node_has_type((GtFeatureNode*) node, gt_ft_intron)) had_err = process_intron(ssiv, (GtGenomeNode*) node, err); } gt_feature_node_iterator_delete(fni); return had_err; } const GtNodeVisitorClass* gt_splice_site_info_visitor_class() { static const GtNodeVisitorClass *nvc = NULL; gt_class_alloc_lock_enter(); if (!nvc) { nvc = gt_node_visitor_class_new(sizeof (GtSpliceSiteInfoVisitor), splice_site_info_visitor_free, NULL, splice_site_info_visitor_feature_node, NULL, NULL, NULL); } gt_class_alloc_lock_leave(); return nvc; } GtNodeVisitor* gt_splice_site_info_visitor_new(GtRegionMapping *rm) { GtNodeVisitor *nv; GtSpliceSiteInfoVisitor *ssiv; gt_assert(rm); nv = gt_node_visitor_create(gt_splice_site_info_visitor_class()); ssiv = splice_site_info_visitor_cast(nv); ssiv->region_mapping = rm; ssiv->splicesites = gt_string_distri_new(); ssiv->acceptorsites = gt_string_distri_new(); ssiv->donorsites = gt_string_distri_new(); return nv; } static void showsplicesite(const char *string, unsigned long occurrences, double probability, GT_UNUSED void *unused) { gt_assert(string && strlen(string) == 4); gt_xputchar(string[0]); gt_xputchar(string[1]); gt_xputchar('-'); gt_xputchar(string[2]); gt_xputchar(string[3]); printf(": %6.2f%% (n=%lu)\n", probability * 100.0, occurrences); } static void showsinglesite(const char *string, unsigned long occurrences, double probability, GT_UNUSED void *unused) { gt_assert(string && strlen(string) == 2); printf("%s: %6.2f%% (n=%lu)\n", string, probability * 100.0, occurrences); } bool gt_splice_site_info_visitor_show(GtNodeVisitor *nv, GtFile *outfp) { GtSpliceSiteInfoVisitor *ssiv; gt_assert(nv); ssiv = splice_site_info_visitor_cast(nv); if (ssiv->show) { /* show splice sites */ gt_file_xprintf(outfp, "splice site distribution (for introns >= 4bp)\n"); gt_string_distri_foreach(ssiv->splicesites, showsplicesite, outfp); gt_xputchar('\n'); /* show donor sites */ gt_file_xprintf(outfp, "donor site distribution (for introns >= 4bp)\n"); gt_string_distri_foreach(ssiv->donorsites, showsinglesite, outfp); gt_xputchar('\n'); /* show acceptor sites */ gt_file_xprintf(outfp, "acceptor site distribution (for introns >= 4bp)\n"); gt_string_distri_foreach(ssiv->acceptorsites, showsinglesite, outfp); } return ssiv->intron_processed; } bool gt_splice_site_info_visitor_intron_processed(GtNodeVisitor *nv) { GtSpliceSiteInfoVisitor *ssiv; gt_assert(nv); ssiv = splice_site_info_visitor_cast(nv); return ssiv->intron_processed; } bool gt_splice_site_info_visitor_show_canonical(GtNodeVisitor *nv, bool show_gc) { GtSpliceSiteInfoVisitor *ssiv; bool canonical_shown = false; gt_assert(nv); ssiv = splice_site_info_visitor_cast(nv); if (ssiv->show) { unsigned long occ; if ((occ = gt_string_distri_get(ssiv->splicesites, "gtag"))) { printf("gt-ag: %6.2f%% (n=%lu)\n", gt_string_distri_get_prob(ssiv->splicesites, "gtag") * 100.0, occ); canonical_shown = true; } if (show_gc && (occ = gt_string_distri_get(ssiv->splicesites, "gcag"))) { printf("gc-ag: %6.2f%% (n=%lu)\n", gt_string_distri_get_prob(ssiv->splicesites, "gcag") * 100.0, occ); canonical_shown = true; } } return canonical_shown; } genometools-1.5.1/src/extended/splice_site_info_visitor.h000066400000000000000000000031231211610345200237000ustar00rootroot00000000000000/* Copyright (c) 2007-2011 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SPLICE_SITE_INFO_VISITOR_H #define SPLICE_SITE_INFO_VISITOR_H /* Implements the interface. */ typedef struct GtSpliceSiteInfoVisitor GtSpliceSiteInfoVisitor; #include #include "extended/node_visitor.h" #include "extended/region_mapping_api.h" const GtNodeVisitorClass* gt_splice_site_info_visitor_class(void); /* takes ownership of */ GtNodeVisitor* gt_splice_site_info_visitor_new(GtRegionMapping *rm); bool gt_splice_site_info_visitor_show(GtNodeVisitor*, GtFile*); bool gt_splice_site_info_visitor_intron_processed(GtNodeVisitor*); bool gt_splice_site_info_visitor_show_canonical(GtNodeVisitor*, bool show_gc); #endif genometools-1.5.1/src/extended/splicedseq.c000066400000000000000000000112611211610345200207340ustar00rootroot00000000000000/* Copyright (c) 2006-2007 Gordon Gremme Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include "core/array.h" #include "core/ensure.h" #include "core/ma.h" #include "core/str.h" #include "extended/reverse_api.h" #include "extended/splicedseq.h" struct Splicedseq { GtStr *splicedseq; GtArray *positionmapping; bool forward; }; Splicedseq* gt_splicedseq_new(void) { Splicedseq *ss = gt_malloc(sizeof (Splicedseq)); ss->splicedseq = gt_str_new(); ss->positionmapping = gt_array_new(sizeof (unsigned long)); ss->forward = true; return ss; } void gt_splicedseq_add(Splicedseq *ss, unsigned long start, unsigned long end, const char *original_sequence) { unsigned long i; gt_assert(ss && start <= end && original_sequence); gt_str_append_cstr_nt(ss->splicedseq, original_sequence, end - start + 1); /* make sure elements are added in ascending order */ gt_assert(!gt_array_size(ss->positionmapping) || start > *(unsigned long*) gt_array_get_last(ss->positionmapping)); for (i = start; i <= end; i++) gt_array_add(ss->positionmapping, i); } char* gt_splicedseq_get(const Splicedseq *ss) { return gt_str_get(ss->splicedseq); } bool gt_splicedseq_pos_is_border(const Splicedseq *ss, unsigned long pos) { gt_assert(ss && gt_str_length(ss->splicedseq) == gt_array_size(ss->positionmapping)); gt_assert(pos < gt_str_length(ss->splicedseq)); /* legal position */ if (ss->forward && pos + 1 < gt_array_size(ss->positionmapping) && *(unsigned long*) gt_array_get(ss->positionmapping, pos) + 1 != *(unsigned long*) gt_array_get(ss->positionmapping, pos+1)) { return true; } if (!ss->forward && pos && *(unsigned long*) gt_array_get(ss->positionmapping, pos-1) - 1 != *(unsigned long*) gt_array_get(ss->positionmapping, pos)) { return true; } return false; } unsigned long gt_splicedseq_map(const Splicedseq *ss, unsigned long pos) { gt_assert(ss && gt_str_length(ss->splicedseq) == gt_array_size(ss->positionmapping)); gt_assert(pos < gt_str_length(ss->splicedseq)); /* legal position */ return *(unsigned long*) gt_array_get(ss->positionmapping, pos); } unsigned long gt_splicedseq_length(const Splicedseq *ss) { gt_assert(ss); return gt_str_length(ss->splicedseq); } int gt_splicedseq_reverse(Splicedseq *ss, GtError *err) { int had_err; gt_error_check(err); gt_assert(ss); had_err = gt_reverse_complement(gt_str_get(ss->splicedseq), gt_str_length(ss->splicedseq), err); if (!had_err) { gt_array_reverse(ss->positionmapping); ss->forward = !ss->forward; } return had_err; } void gt_splicedseq_reset(Splicedseq *ss) { gt_assert(ss); gt_str_reset(ss->splicedseq); gt_array_reset(ss->positionmapping); ss->forward = true; } static int check_splicedseq(Splicedseq *ss, GtError *err) { /*0123456789*/ static char *origseq = "aaccaagtga", *splicedseq = "ccgtg"; int had_err = 0; gt_error_check(err); gt_splicedseq_add(ss, 2, 3, origseq + 2); gt_splicedseq_add(ss, 6, 8, origseq + 6); gt_ensure(had_err, strcmp(gt_splicedseq_get(ss), splicedseq) == 0); gt_ensure(had_err, !gt_splicedseq_pos_is_border(ss, 0)); gt_ensure(had_err, gt_splicedseq_pos_is_border(ss, 1)); gt_ensure(had_err, !gt_splicedseq_pos_is_border(ss, 2)); gt_ensure(had_err, !gt_splicedseq_pos_is_border(ss, 3)); gt_ensure(had_err, !gt_splicedseq_pos_is_border(ss, 4)); return had_err; } int gt_splicedseq_unit_test(GtError *err) { Splicedseq *ss; int had_err = 0; gt_error_check(err); ss = gt_splicedseq_new(); had_err = check_splicedseq(ss, err); if (!had_err) { gt_splicedseq_reset(ss); had_err = check_splicedseq(ss, err); } gt_splicedseq_delete(ss); return had_err; } void gt_splicedseq_delete(Splicedseq *ss) { if (!ss) return; gt_str_delete(ss->splicedseq); gt_array_delete(ss->positionmapping); gt_free(ss); } genometools-1.5.1/src/extended/splicedseq.h000066400000000000000000000033521211610345200207430ustar00rootroot00000000000000/* Copyright (c) 2006-2007 Gordon Gremme Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SPLICEDSEQ_H #define SPLICEDSEQ_H #include typedef struct Splicedseq Splicedseq; Splicedseq* gt_splicedseq_new(void); /* adds an ``exon'' to the spliced sequence */ void gt_splicedseq_add(Splicedseq*, unsigned long start, unsigned long end, const char *original_sequence); char* gt_splicedseq_get(const Splicedseq*); bool gt_splicedseq_pos_is_border(const Splicedseq*, unsigned long); /* maps the given position back to the original coordinate system */ unsigned long gt_splicedseq_map(const Splicedseq*, unsigned long); unsigned long gt_splicedseq_length(const Splicedseq*); int gt_splicedseq_reverse(Splicedseq*, GtError*); void gt_splicedseq_reset(Splicedseq*); int gt_splicedseq_unit_test(GtError*); void gt_splicedseq_delete(Splicedseq*); #endif genometools-1.5.1/src/extended/sspliced_alignment.c000066400000000000000000000061101211610345200224410ustar00rootroot00000000000000/* Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/cstr_api.h" #include "core/ma.h" #include "extended/sspliced_alignment.h" struct GtSSplicedAlignment { char *id; bool forward; GtArray *exons; /* the exon ranges */ }; GtSSplicedAlignment* gt_sspliced_alignment_new(const char *id, bool forward) { GtSSplicedAlignment *sa; gt_assert(id); sa = gt_malloc(sizeof *sa); sa->id = gt_cstr_dup(id); sa->forward = forward; sa->exons = gt_array_new(sizeof (GtRange)); return sa; } void gt_sspliced_alignment_delete(GtSSplicedAlignment *sa) { if (!sa) return; gt_array_delete(sa->exons); gt_free(sa->id); gt_free(sa); } bool gt_sspliced_alignment_is_forward(const GtSSplicedAlignment *sa) { gt_assert(sa); return sa->forward; } void gt_sspliced_alignment_add_exon(GtSSplicedAlignment *sa, GtRange exon) { gt_assert(sa); gt_array_add(sa->exons, exon); } unsigned long gt_sspliced_alignment_num_of_exons(const GtSSplicedAlignment *sa) { gt_assert(sa); return gt_array_size(sa->exons); } GtRange gt_sspliced_alignment_get_exon(const GtSSplicedAlignment *sa, unsigned long exon_number) { gt_assert(sa); return *(GtRange*) gt_array_get(sa->exons, exon_number); } GtRange gt_sspliced_alignment_genomic_range(const GtSSplicedAlignment *sa) { GtRange range; gt_assert(sa); gt_assert(gt_array_size(sa->exons)); range.start = ((GtRange*) gt_array_get_first(sa->exons))->start; range.end = ((GtRange*) gt_array_get_last(sa->exons))->end; return range; } static int range_compare_long_first(GtRange range_a, GtRange range_b) { gt_assert(range_a.start <= range_a.end && range_b.start <= range_b.end); if ((range_a.start == range_b.start) && (range_a.end == range_b.end)) return 0; /* range_a == range_b */ if ((range_a.start < range_b.start) || ((range_a.start == range_b.start) && (range_a.end > range_b.end))) return -1; /* range_a < range_b */ return 1; /* range_a > range_b */ } int gt_sspliced_alignment_compare_ptr(const GtSSplicedAlignment **sa_a, const GtSSplicedAlignment **sa_b) { GtRange range_a, range_b; range_a = gt_sspliced_alignment_genomic_range(*sa_a); range_b = gt_sspliced_alignment_genomic_range(*sa_b); return range_compare_long_first(range_a, range_b); } genometools-1.5.1/src/extended/sspliced_alignment.h000066400000000000000000000041231211610345200224500ustar00rootroot00000000000000/* Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SSPLICED_ALIGNMENT_H #define SSPLICED_ALIGNMENT_H #include #include "core/range.h" /* the simple spliced alignment class */ typedef struct GtSSplicedAlignment GtSSplicedAlignment; GtSSplicedAlignment* gt_sspliced_alignment_new(const char *id, bool forward); void gt_sspliced_alignment_delete(GtSSplicedAlignment*); bool gt_sspliced_alignment_is_forward(const GtSSplicedAlignment*); void gt_sspliced_alignment_add_exon(GtSSplicedAlignment*, GtRange); unsigned long gt_sspliced_alignment_num_of_exons(const GtSSplicedAlignment*); GtRange gt_sspliced_alignment_get_exon(const GtSSplicedAlignment*, unsigned long exon_number); GtRange gt_sspliced_alignment_genomic_range(const GtSSplicedAlignment*); int gt_sspliced_alignment_compare_ptr(const GtSSplicedAlignment**, const GtSSplicedAlignment**); #endif genometools-1.5.1/src/extended/sspliced_alignment_parsing.c000066400000000000000000000100511211610345200241630ustar00rootroot00000000000000/* Copyright (c) 2005-2008 Gordon Gremme Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/fa.h" #include "core/str.h" #include "extended/sspliced_alignment.h" #include "extended/sspliced_alignment_parsing.h" #define DELIMITER ',' #define FORWARDSTRANDCHAR '+' #define REVERSESTRANDCHAR '-' static int parse_input_line(GtSSplicedAlignment **alignment, const char *line, unsigned long line_length, GtError *err) { long leftpos, rightpos; unsigned long i = 0; GtRange exon; GtStr *id; int had_err = 0; gt_error_check(err); #define CHECKLINELENGTH\ if (!had_err && i >= line_length) { \ gt_error_set(err, "incomplete input line\n" \ "line=%s", line); \ return had_err = -1; \ } /* init */ id = gt_str_new(); *alignment = NULL; /* parsing id */ while (!had_err) { CHECKLINELENGTH; if (line[i] == DELIMITER) { /* reference id has been saved, skip this character and break */ i++; CHECKLINELENGTH; break; } else { /* save this character of the reference id */ gt_str_append_char(id, line[i]); } /* increase counter */ i++; } /* parsing orientation */ if (line[i] == FORWARDSTRANDCHAR) *alignment = gt_sspliced_alignment_new(gt_str_get(id), true); else if (line[i] == REVERSESTRANDCHAR) *alignment = gt_sspliced_alignment_new(gt_str_get(id), false); else { gt_error_set(err, "wrong formatted input line, orientation must be %c or %c\n" "line=%s", FORWARDSTRANDCHAR, REVERSESTRANDCHAR, line); had_err = -1; } i++; CHECKLINELENGTH; if (!had_err && line[i] != DELIMITER) { gt_error_set(err, "incomplete input line\nline=%s", line); had_err = -1; } while (!had_err) { if (line[i] == DELIMITER) { i++; CHECKLINELENGTH; if (!had_err && sscanf(line+i, "%ld-%ld", &leftpos, &rightpos) != 2) { gt_error_set(err, "incomplete input line\nline=%s", line); had_err = -1; } if (!had_err) { /* save exon */ exon.start = leftpos; exon.end = rightpos; gt_sspliced_alignment_add_exon(*alignment, exon); } } i++; if (i >= line_length) break; } if (had_err) gt_sspliced_alignment_delete(*alignment); else { /* alignment contains at least one exon */ gt_assert(gt_sspliced_alignment_num_of_exons(*alignment)); } gt_str_delete(id); return had_err; } int gt_sspliced_alignment_parse(GtArray *spliced_alignments, const char *filename, GtError *err) { FILE *input_file; GtSSplicedAlignment *sa; int had_err = 0; GtStr *line; gt_error_check(err); line = gt_str_new(); input_file = gt_fa_xfopen(filename, "r"); while (!had_err && gt_str_read_next_line(line, input_file) != EOF) { /* parse input line and save result in spliced alignment */ had_err = parse_input_line(&sa, gt_str_get(line), gt_str_length(line), err); if (!had_err) { /* store spliced alignment */ gt_array_add(spliced_alignments, sa); /* reset array */ gt_str_reset(line); } } gt_fa_xfclose(input_file); gt_str_delete(line); return had_err; } genometools-1.5.1/src/extended/sspliced_alignment_parsing.h000066400000000000000000000021531211610345200241740ustar00rootroot00000000000000/* Copyright (c) 2005-2008 Gordon Gremme Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SSPLICED_ALIGNMENT_PARSING_H #define SSPLICED_ALIGNMENT_PARSING_H #include "core/error.h" int gt_sspliced_alignment_parse(GtArray *spliced_alignments, const char *filename, GtError*); #endif genometools-1.5.1/src/extended/stat_stream.c000066400000000000000000000072021211610345200211260ustar00rootroot00000000000000/* Copyright (c) 2007-2011 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "extended/eof_node.h" #include "extended/genome_node.h" #include "extended/stat_stream_api.h" #include "extended/stat_visitor.h" #include "extended/node_stream_api.h" struct GtStatStream { const GtNodeStream parent_instance; GtNodeStream *in_stream; GtNodeVisitor *stat_visitor; unsigned long number_of_DAGs; }; const GtNodeStreamClass* gt_stat_stream_class(void); #define stat_stream_cast(GS)\ gt_node_stream_cast(gt_stat_stream_class(), GS) static int stat_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) { GtStatStream *stat_stream; int had_err; gt_error_check(err); stat_stream = stat_stream_cast(ns); had_err = gt_node_stream_next(stat_stream->in_stream, gn, err); if (!had_err) { gt_assert(stat_stream->stat_visitor); if (*gn) { if (!gt_eof_node_try_cast(*gn)) /* do not count EOF nodes */ stat_stream->number_of_DAGs++; had_err = gt_genome_node_accept(*gn, stat_stream->stat_visitor, err); gt_assert(!had_err); /* the status visitor is sane */ } } return had_err; } static void stat_stream_free(GtNodeStream *ns) { GtStatStream *stat_stream = stat_stream_cast(ns); gt_node_visitor_delete(stat_stream->stat_visitor); gt_node_stream_delete(stat_stream->in_stream); } const GtNodeStreamClass* gt_stat_stream_class(void) { static const GtNodeStreamClass *nsc = NULL; gt_class_alloc_lock_enter(); if (!nsc) { nsc = gt_node_stream_class_new(sizeof (GtStatStream), stat_stream_free, stat_stream_next); } gt_class_alloc_lock_leave(); return nsc; } GtNodeStream* gt_stat_stream_new(GtNodeStream *in_stream, bool gene_length_distri, bool gene_score_distri, bool exon_length_distri, bool exon_number_distri, bool intron_length_distri, bool cds_length_distri, bool used_sources) { GtNodeStream *ns = gt_node_stream_create(gt_stat_stream_class(), false); GtStatStream *ss = stat_stream_cast(ns); ss->in_stream = gt_node_stream_ref(in_stream); ss->stat_visitor = gt_stat_visitor_new(gene_length_distri, gene_score_distri, exon_length_distri, exon_number_distri, intron_length_distri, cds_length_distri, used_sources); return ns; } void gt_stat_stream_show_stats(GtStatStream *ss, GtFile *outfp) { gt_file_xprintf(outfp, "parsed genome node DAGs: %lu\n", ss->number_of_DAGs); gt_stat_visitor_show_stats(ss->stat_visitor, outfp); } genometools-1.5.1/src/extended/stat_stream_api.h000066400000000000000000000047101211610345200217650ustar00rootroot00000000000000/* Copyright (c) 2007-2011 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef STAT_STREAM_API_H #define STAT_STREAM_API_H #include #include "core/file_api.h" #include "extended/node_stream_api.h" /* Implements the interface. A gathers statistics about the objects it retrieves from its node source and passes them along unmodified. */ typedef struct GtStatStream GtStatStream; /* Create a object which gathers statistics about the objects it retrieves from its and returns them unmodified. Besides the basic statistics, statistics about the following distributions can be gathered, if the corresponding argument equals : , , , , , . If equals , it is recorded which source tags have been encountered. */ GtNodeStream* gt_stat_stream_new(GtNodeStream *in_stream, bool gene_length_distribution, bool gene_score_distribution, bool exon_length_distribution, bool exon_number_distribution, bool intron_length_distribution, bool cds_length_distribution, bool used_sources); /* Write the statistics gathered by to . */ void gt_stat_stream_show_stats(GtStatStream *stat_stream, GtFile *outfp); #endif genometools-1.5.1/src/extended/stat_visitor.c000066400000000000000000000257131211610345200213410ustar00rootroot00000000000000/* Copyright (c) 2006-2011 Gordon Gremme Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "core/cstr_table_api.h" #include "core/disc_distri_api.h" #include "core/unused_api.h" #include "extended/feature_node.h" #include "extended/node_visitor_api.h" #include "extended/stat_visitor.h" struct GtStatVisitor { const GtNodeVisitor parent_instance; unsigned long number_of_sequence_regions, number_of_multi_features, number_of_genes, number_of_protein_coding_genes, number_of_mRNAs, number_of_protein_coding_mRNAs, number_of_exons, number_of_CDSs, number_of_LTR_retrotransposons, exon_number_for_distri, cds_length_for_distri; unsigned long long total_length_of_sequence_regions; GtDiscDistri *gene_length_distribution, *gene_score_distribution, *exon_length_distribution, *exon_number_distribution, *intron_length_distribution, *cds_length_distribution; GtCstrTable *used_sources; }; #define stat_visitor_cast(GV)\ gt_node_visitor_cast(gt_stat_visitor_class(), GV) static void stat_visitor_free(GtNodeVisitor *nv) { GtStatVisitor *sv = stat_visitor_cast(nv); gt_cstr_table_delete(sv->used_sources); gt_disc_distri_delete(sv->cds_length_distribution); gt_disc_distri_delete(sv->intron_length_distribution); gt_disc_distri_delete(sv->exon_number_distribution); gt_disc_distri_delete(sv->exon_length_distribution); gt_disc_distri_delete(sv->gene_score_distribution); gt_disc_distri_delete(sv->gene_length_distribution); } static int add_exon_or_cds_number(GtFeatureNode *fn, void *data, GT_UNUSED GtError *err) { GtStatVisitor *sv = (GtStatVisitor*) data; gt_error_check(err); gt_assert(sv && fn); if (gt_feature_node_has_type(fn, gt_ft_exon)) sv->exon_number_for_distri++; else if (gt_feature_node_has_type(fn, gt_ft_CDS)) { GtRange range = gt_genome_node_get_range((GtGenomeNode*) fn); sv->cds_length_for_distri += gt_range_length(&range); } return 0; } static void compute_source_statistics(GtFeatureNode *fn, GtCstrTable *used_sources) { const char *source; gt_assert(fn && used_sources); source = gt_feature_node_get_source(fn); if (!gt_cstr_table_get(used_sources, source)) gt_cstr_table_add(used_sources, source); } static void compute_type_statistics(GtFeatureNode *fn, GtStatVisitor *sv) { GtRange range; gt_assert(fn && sv); if (gt_feature_node_has_type(fn, gt_ft_gene)) { sv->number_of_genes++; if (gt_feature_node_has_CDS(fn)) sv->number_of_protein_coding_genes++; if (sv->gene_length_distribution) { range = gt_genome_node_get_range((GtGenomeNode*) fn); gt_disc_distri_add(sv->gene_length_distribution, gt_range_length(&range)); } if (sv->gene_score_distribution) { gt_disc_distri_add(sv->gene_score_distribution, gt_feature_node_get_score(fn) * 100.0); } } else if (gt_feature_node_has_type(fn, gt_ft_mRNA)) { sv->number_of_mRNAs++; if (gt_feature_node_has_CDS(fn)) sv->number_of_protein_coding_mRNAs++; } else if (gt_feature_node_has_type(fn, gt_ft_exon)) { sv->number_of_exons++; if (sv->exon_length_distribution) { range = gt_genome_node_get_range((GtGenomeNode*) fn); gt_disc_distri_add(sv->exon_length_distribution, gt_range_length(&range)); } } else if (gt_feature_node_has_type(fn, gt_ft_CDS)) { sv->number_of_CDSs++; } else if (gt_feature_node_has_type(fn, gt_ft_intron)) { if (sv->intron_length_distribution) { range = gt_genome_node_get_range((GtGenomeNode*) fn); gt_disc_distri_add(sv->intron_length_distribution, gt_range_length(&range)); } } else if (gt_feature_node_has_type(fn, gt_ft_LTR_retrotransposon)) { sv->number_of_LTR_retrotransposons++; } } static int compute_statistics(GtFeatureNode *fn, void *data, GtError *err) { GtStatVisitor *sv; GT_UNUSED int rval; gt_error_check(err); gt_assert(data); sv = (GtStatVisitor*) data; if (gt_feature_node_is_multi(fn) && gt_feature_node_get_multi_representative(fn) == fn) { sv->number_of_multi_features++; } if (sv->used_sources) compute_source_statistics(fn, sv->used_sources); compute_type_statistics(fn, sv); if (sv->exon_number_distribution || sv->cds_length_distribution) { sv->exon_number_for_distri = 0; sv->cds_length_for_distri = 0; rval = gt_feature_node_traverse_direct_children(fn, sv, add_exon_or_cds_number, err); gt_assert(!rval); /* add_exon_or_cds_number() is sane */ if (sv->exon_number_distribution && sv->exon_number_for_distri) { gt_disc_distri_add(sv->exon_number_distribution, sv->exon_number_for_distri); } if (sv->cds_length_distribution && sv->cds_length_for_distri) { gt_disc_distri_add(sv->cds_length_distribution, sv->cds_length_for_distri); } } return 0; } static int stat_visitor_feature_node(GtNodeVisitor *nv, GtFeatureNode *fn, GtError *err) { GtStatVisitor *sv; gt_error_check(err); sv = stat_visitor_cast(nv); return gt_feature_node_traverse_children(fn, sv, compute_statistics, false, err); } static int stat_visitor_region_node(GtNodeVisitor *nv, GtRegionNode *rn, GT_UNUSED GtError *err) { GtStatVisitor *sv; GtRange range; gt_error_check(err); sv = stat_visitor_cast(nv); sv->number_of_sequence_regions++; range = gt_genome_node_get_range((GtGenomeNode*) rn); sv->total_length_of_sequence_regions += gt_range_length(&range); return 0; } const GtNodeVisitorClass* gt_stat_visitor_class() { static const GtNodeVisitorClass *nvc = NULL; gt_class_alloc_lock_enter(); if (!nvc) { nvc = gt_node_visitor_class_new(sizeof (GtStatVisitor), stat_visitor_free, NULL, stat_visitor_feature_node, stat_visitor_region_node, NULL, NULL); } gt_class_alloc_lock_leave(); return nvc; } GtNodeVisitor* gt_stat_visitor_new(bool gene_length_distri, bool gene_score_distri, bool exon_length_distri, bool exon_number_distri, bool intron_length_distri, bool cds_length_distri, bool used_sources) { GtNodeVisitor *nv = gt_node_visitor_create(gt_stat_visitor_class()); GtStatVisitor *sv = stat_visitor_cast(nv); if (gene_length_distri) sv->gene_length_distribution = gt_disc_distri_new(); if (gene_score_distri) sv->gene_score_distribution = gt_disc_distri_new(); if (exon_length_distri) sv->exon_length_distribution = gt_disc_distri_new(); if (exon_number_distri) sv->exon_number_distribution = gt_disc_distri_new(); if (intron_length_distri) sv->intron_length_distribution = gt_disc_distri_new(); if (cds_length_distri) sv->cds_length_distribution = gt_disc_distri_new(); if (used_sources) sv->used_sources = gt_cstr_table_new(); return nv; } void gt_stat_visitor_show_stats(GtNodeVisitor *nv, GtFile *outfp) { GtStatVisitor *sv = stat_visitor_cast(nv); if (sv->number_of_sequence_regions) { gt_file_xprintf(outfp, "sequence regions: %lu (total length: %llu)\n", sv->number_of_sequence_regions, sv->total_length_of_sequence_regions); } if (sv->number_of_multi_features) { gt_file_xprintf(outfp, "multi-features: %lu\n", sv->number_of_multi_features); } if (sv->number_of_genes) gt_file_xprintf(outfp, "genes: %lu\n", sv->number_of_genes); if (sv->number_of_protein_coding_genes) { gt_file_xprintf(outfp, "protein-coding genes: %lu\n", sv->number_of_protein_coding_genes); } if (sv->number_of_mRNAs) gt_file_xprintf(outfp, "mRNAs: %lu\n", sv->number_of_mRNAs); if (sv->number_of_protein_coding_mRNAs) { gt_file_xprintf(outfp, "protein-coding mRNAs: %lu\n", sv->number_of_protein_coding_mRNAs); } if (sv->number_of_exons) gt_file_xprintf(outfp, "exons: %lu\n", sv->number_of_exons); if (sv->number_of_CDSs) gt_file_xprintf(outfp, "CDSs: %lu\n", sv->number_of_CDSs); if (sv->number_of_LTR_retrotransposons) { gt_file_xprintf(outfp, "LTR_retrotransposons: %lu\n", sv->number_of_LTR_retrotransposons); } if (sv->gene_length_distribution) { gt_file_xprintf(outfp, "gene length distribution:\n"); gt_disc_distri_show(sv->gene_length_distribution, outfp); } if (sv->gene_score_distribution) { gt_file_xprintf(outfp, "gene score distribution:\n"); gt_disc_distri_show(sv->gene_score_distribution, outfp); } if (sv->exon_length_distribution) { gt_file_xprintf(outfp, "exon length distribution:\n"); gt_disc_distri_show(sv->exon_length_distribution, outfp); } if (sv->exon_number_distribution) { gt_file_xprintf(outfp, "exon number distribution:\n"); gt_disc_distri_show(sv->exon_number_distribution, outfp); } if (sv->intron_length_distribution) { gt_file_xprintf(outfp, "intron length distribution:\n"); gt_disc_distri_show(sv->intron_length_distribution, outfp); } if (sv->cds_length_distribution) { gt_file_xprintf(outfp, "CDS length distribution:\n"); gt_disc_distri_show(sv->cds_length_distribution, outfp); } if (sv->used_sources) { GtStrArray *sources; unsigned long i; gt_file_xprintf(outfp, "used source tags:\n"); sources = gt_cstr_table_get_all(sv->used_sources); for (i = 0; i < gt_str_array_size(sources); i++) gt_file_xprintf(outfp, "%s\n", gt_str_array_get(sources, i)); gt_str_array_delete(sources); } } genometools-1.5.1/src/extended/stat_visitor.h000066400000000000000000000032371211610345200213430ustar00rootroot00000000000000/* Copyright (c) 2006-2011 Gordon Gremme Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef STAT_VISITOR_H #define STAT_VISITOR_H /* Implements the interface, gathers statistics. */ typedef struct GtStatVisitor GtStatVisitor; #include "extended/node_visitor.h" const GtNodeVisitorClass* gt_stat_visitor_class(void); GtNodeVisitor* gt_stat_visitor_new(bool gene_length_distri, bool gene_score_distri, bool exon_length_distri, bool exon_number_distri, bool intron_length_distri, bool cds_length_distri, bool used_sources); void gt_stat_visitor_show_stats(GtNodeVisitor*, GtFile*); #endif genometools-1.5.1/src/extended/stream_evaluator.c000066400000000000000000002064331211610345200221640ustar00rootroot00000000000000/* Copyright (c) 2006-2011 Gordon Gremme Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/bsearch.h" #include "core/cstr_api.h" #include "core/hashmap.h" #include "core/log.h" #include "core/ma.h" #include "core/unused_api.h" #include "core/warning_api.h" #include "core/xansi_api.h" #include "extended/evaluator.h" #include "extended/gff3_output.h" #include "extended/stream_evaluator.h" #include "extended/transcript_evaluators.h" #include "extended/transcript_exons.h" #include "extended/transcript_used_exons.h" typedef struct { unsigned long TP, FP, FN; } NucEval; struct GtStreamEvaluator { GtNodeStream *reference, *prediction; bool nuceval, evalLTR; unsigned long LTRdelta; GtHashmap *slots; /* sequence id -> slot */ GtEvaluator *mRNA_gene_evaluator, *CDS_gene_evaluator, *mRNA_mRNA_evaluator, *CDS_mRNA_evaluator, *LTR_evaluator; GtTranscriptEvaluators *mRNA_exon_evaluators, *mRNA_exon_evaluators_collapsed, *CDS_exon_evaluators, *CDS_exon_evaluators_collapsed; unsigned long missing_genes, wrong_genes, missing_mRNAs, wrong_mRNAs, missing_LTRs, wrong_LTRs; NucEval mRNA_nucleotides, CDS_nucleotides; }; typedef struct { GtArray *genes_forward, *genes_reverse, *mRNAs_forward, *mRNAs_reverse, *LTRs; GtTranscriptExons *mRNA_exons_forward, *mRNA_exons_reverse, *CDS_exons_forward, *CDS_exons_reverse; GtTranscriptCounts *mRNA_counts_forward, *mRNA_counts_reverse, *CDS_counts_forward, *CDS_counts_reverse; GtRange real_range; unsigned long FP_mRNA_nucleotides_forward, FP_mRNA_nucleotides_reverse, FP_CDS_nucleotides_forward, FP_CDS_nucleotides_reverse; GtBittab *real_mRNA_nucleotides_forward, *pred_mRNA_nucleotides_forward, *real_mRNA_nucleotides_reverse, *pred_mRNA_nucleotides_reverse, *real_CDS_nucleotides_forward, *pred_CDS_nucleotides_forward, *real_CDS_nucleotides_reverse, *pred_CDS_nucleotides_reverse, *true_mRNA_genes_forward, *true_mRNA_genes_reverse, *true_CDS_genes_forward, *true_CDS_genes_reverse, *true_mRNA_mRNAs_forward, *true_mRNA_mRNAs_reverse, *true_CDS_mRNAs_forward, *true_CDS_mRNAs_reverse, *true_LTRs, *overlapped_genes_forward, *overlapped_genes_reverse, *overlapped_mRNAs_forward, *overlapped_mRNAs_reverse, *overlapped_LTRs; GtTranscriptBittabs *mRNA_exon_bittabs_forward, *mRNA_exon_bittabs_reverse, *CDS_exon_bittabs_forward, *CDS_exon_bittabs_reverse; GtTranscriptUsedExons *used_mRNA_exons_forward, *used_mRNA_exons_reverse, *used_CDS_exons_forward, *used_CDS_exons_reverse; } Slot; typedef struct { Slot *slot; bool nuceval, verbose; } ProcessRealFeatureInfo; typedef struct { Slot *slot; bool nuceval, verbose, exondiff, exondiffcollapsed; unsigned long LTRdelta; GtEvaluator *mRNA_gene_evaluator, *CDS_gene_evaluator, *mRNA_mRNA_evaluator, *CDS_mRNA_evaluator, *LTR_evaluator; GtTranscriptEvaluators *mRNA_exon_evaluators, *mRNA_exon_evaluators_collapsed, *CDS_exon_evaluators, *CDS_exon_evaluators_collapsed; unsigned long *wrong_genes, *wrong_mRNAs, *wrong_LTRs; } ProcessPredictedFeatureInfo; static Slot* slot_new(bool nuceval, GtRange range) { unsigned long length; Slot *s = gt_calloc(1, sizeof (Slot)); length = gt_range_length(&range); s->genes_forward = gt_array_new(sizeof (GtGenomeNode*)); s->genes_reverse = gt_array_new(sizeof (GtGenomeNode*)); s->mRNAs_forward = gt_array_new(sizeof (GtGenomeNode*)); s->mRNAs_reverse = gt_array_new(sizeof (GtGenomeNode*)); s->LTRs = gt_array_new(sizeof (GtGenomeNode*)); s->mRNA_exons_forward = gt_transcript_exons_new(); s->mRNA_exons_reverse = gt_transcript_exons_new(); s->CDS_exons_forward = gt_transcript_exons_new(); s->CDS_exons_reverse = gt_transcript_exons_new(); if (nuceval) { s->real_range = range; s->real_mRNA_nucleotides_forward = gt_bittab_new(length); s->pred_mRNA_nucleotides_forward = gt_bittab_new(length); s->real_mRNA_nucleotides_reverse = gt_bittab_new(length); s->pred_mRNA_nucleotides_reverse = gt_bittab_new(length); s->real_CDS_nucleotides_forward = gt_bittab_new(length); s->pred_CDS_nucleotides_forward = gt_bittab_new(length); s->real_CDS_nucleotides_reverse = gt_bittab_new(length); s->pred_CDS_nucleotides_reverse = gt_bittab_new(length); } s->used_mRNA_exons_forward = gt_transcript_used_exons_new(); s->used_mRNA_exons_reverse = gt_transcript_used_exons_new(); s->used_CDS_exons_forward = gt_transcript_used_exons_new(); s->used_CDS_exons_reverse = gt_transcript_used_exons_new(); return s; } static void slot_delete(Slot *s) { unsigned long i; gt_assert(s); for (i = 0; i < gt_array_size(s->genes_forward); i++) gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(s->genes_forward, i)); gt_array_delete(s->genes_forward); for (i = 0; i < gt_array_size(s->genes_reverse); i++) gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(s->genes_reverse, i)); gt_array_delete(s->genes_reverse); for (i = 0; i < gt_array_size(s->mRNAs_forward); i++) gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(s->mRNAs_forward, i)); gt_array_delete(s->mRNAs_forward); for (i = 0; i < gt_array_size(s->mRNAs_reverse); i++) gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(s->mRNAs_reverse, i)); gt_array_delete(s->mRNAs_reverse); for (i = 0; i < gt_array_size(s->LTRs); i++) gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(s->LTRs, i)); gt_array_delete(s->LTRs); gt_transcript_exons_delete(s->mRNA_exons_forward); gt_transcript_exons_delete(s->mRNA_exons_reverse); gt_transcript_exons_delete(s->CDS_exons_forward); gt_transcript_exons_delete(s->CDS_exons_reverse); gt_transcript_counts_delete(s->mRNA_counts_forward); gt_transcript_counts_delete(s->mRNA_counts_reverse); gt_transcript_counts_delete(s->CDS_counts_forward); gt_transcript_counts_delete(s->CDS_counts_reverse); gt_bittab_delete(s->real_mRNA_nucleotides_forward); gt_bittab_delete(s->pred_mRNA_nucleotides_forward); gt_bittab_delete(s->real_mRNA_nucleotides_reverse); gt_bittab_delete(s->pred_mRNA_nucleotides_reverse); gt_bittab_delete(s->real_CDS_nucleotides_forward); gt_bittab_delete(s->pred_CDS_nucleotides_forward); gt_bittab_delete(s->real_CDS_nucleotides_reverse); gt_bittab_delete(s->pred_CDS_nucleotides_reverse); gt_bittab_delete(s->true_mRNA_genes_forward); gt_bittab_delete(s->true_mRNA_genes_reverse); gt_bittab_delete(s->true_CDS_genes_forward); gt_bittab_delete(s->true_CDS_genes_reverse); gt_bittab_delete(s->true_mRNA_mRNAs_forward); gt_bittab_delete(s->true_mRNA_mRNAs_reverse); gt_bittab_delete(s->true_CDS_mRNAs_forward); gt_bittab_delete(s->true_CDS_mRNAs_reverse); gt_bittab_delete(s->true_LTRs); gt_bittab_delete(s->overlapped_genes_forward); gt_bittab_delete(s->overlapped_genes_reverse); gt_bittab_delete(s->overlapped_mRNAs_forward); gt_bittab_delete(s->overlapped_mRNAs_reverse); gt_bittab_delete(s->overlapped_LTRs); gt_transcript_bittabs_delete(s->mRNA_exon_bittabs_forward); gt_transcript_bittabs_delete(s->mRNA_exon_bittabs_reverse); gt_transcript_bittabs_delete(s->CDS_exon_bittabs_forward); gt_transcript_bittabs_delete(s->CDS_exon_bittabs_reverse); gt_transcript_used_exons_delete(s->used_mRNA_exons_forward); gt_transcript_used_exons_delete(s->used_mRNA_exons_reverse); gt_transcript_used_exons_delete(s->used_CDS_exons_forward); gt_transcript_used_exons_delete(s->used_CDS_exons_reverse); gt_free(s); } GtStreamEvaluator* gt_stream_evaluator_new(GtNodeStream *reference, GtNodeStream *prediction, bool nuceval, bool evalLTR, unsigned long LTRdelta) { GtStreamEvaluator *evaluator = gt_calloc(1, sizeof (GtStreamEvaluator)); evaluator->reference = gt_node_stream_ref(reference); evaluator->prediction = gt_node_stream_ref(prediction); evaluator->nuceval = nuceval; evaluator->evalLTR = evalLTR; evaluator->LTRdelta = LTRdelta; evaluator->slots = gt_hashmap_new(GT_HASH_STRING, gt_free_func, (GtFree) slot_delete); evaluator->mRNA_gene_evaluator = gt_evaluator_new(); evaluator->CDS_gene_evaluator = gt_evaluator_new(); evaluator->mRNA_mRNA_evaluator = gt_evaluator_new(); evaluator->CDS_mRNA_evaluator = gt_evaluator_new(); evaluator->LTR_evaluator = gt_evaluator_new(); evaluator->mRNA_exon_evaluators = gt_transcript_evaluators_new(); evaluator->mRNA_exon_evaluators_collapsed = gt_transcript_evaluators_new(); evaluator->CDS_exon_evaluators = gt_transcript_evaluators_new(); evaluator->CDS_exon_evaluators_collapsed = gt_transcript_evaluators_new(); return evaluator; } static int set_actuals_and_sort_them(GT_UNUSED void *key, void *value, void *data, GT_UNUSED GtError *err) { GtStreamEvaluator *se = (GtStreamEvaluator*) data; Slot *s = (Slot*) value; gt_error_check(err); gt_assert(key && value && data); /* set actual genes */ gt_evaluator_add_actual(se->mRNA_gene_evaluator, gt_array_size(s->genes_forward)); gt_evaluator_add_actual(se->mRNA_gene_evaluator, gt_array_size(s->genes_reverse)); gt_evaluator_add_actual(se->CDS_gene_evaluator, gt_array_size(s->genes_forward)); gt_evaluator_add_actual(se->CDS_gene_evaluator, gt_array_size(s->genes_reverse)); /* set actual mRNAs */ gt_evaluator_add_actual(se->mRNA_mRNA_evaluator, gt_array_size(s->mRNAs_forward)); gt_evaluator_add_actual(se->mRNA_mRNA_evaluator, gt_array_size(s->mRNAs_reverse)); gt_evaluator_add_actual(se->CDS_mRNA_evaluator, gt_array_size(s->mRNAs_forward)); gt_evaluator_add_actual(se->CDS_mRNA_evaluator, gt_array_size(s->mRNAs_reverse)); /* set actual LTRs */ gt_evaluator_add_actual(se->LTR_evaluator, gt_array_size(s->LTRs)); /* set actual exons (before uniq!) */ gt_transcript_evaluators_add_actuals(se->mRNA_exon_evaluators, s->mRNA_exons_forward); gt_transcript_evaluators_add_actuals(se->mRNA_exon_evaluators, s->mRNA_exons_reverse); gt_transcript_evaluators_add_actuals(se->CDS_exon_evaluators, s->CDS_exons_forward); gt_transcript_evaluators_add_actuals(se->CDS_exon_evaluators, s->CDS_exons_reverse); /* sort genes */ gt_genome_nodes_sort(s->genes_forward); gt_genome_nodes_sort(s->genes_reverse); /* sort mRNAs */ gt_genome_nodes_sort(s->mRNAs_forward); gt_genome_nodes_sort(s->mRNAs_reverse); /* sort LTRs */ gt_genome_nodes_sort(s->LTRs); /* sort exons */ gt_transcript_exons_sort(s->mRNA_exons_forward); gt_transcript_exons_sort(s->mRNA_exons_reverse); gt_transcript_exons_sort(s->CDS_exons_forward); gt_transcript_exons_sort(s->CDS_exons_reverse); /* determine true exons */ s->mRNA_counts_forward = gt_transcript_exons_uniq_in_place_count(s->mRNA_exons_forward); s->mRNA_counts_reverse = gt_transcript_exons_uniq_in_place_count(s->mRNA_exons_reverse); s->CDS_counts_forward = gt_transcript_exons_uniq_in_place_count(s->CDS_exons_forward); s->CDS_counts_reverse = gt_transcript_exons_uniq_in_place_count(s->CDS_exons_reverse); /* set actual exons for the collapsed case (after uniq!) */ gt_transcript_evaluators_add_actuals(se->mRNA_exon_evaluators_collapsed, s->mRNA_exons_forward); gt_transcript_evaluators_add_actuals(se->mRNA_exon_evaluators_collapsed, s->mRNA_exons_reverse); gt_transcript_evaluators_add_actuals(se->CDS_exon_evaluators_collapsed, s->CDS_exons_forward); gt_transcript_evaluators_add_actuals(se->CDS_exon_evaluators_collapsed, s->CDS_exons_reverse); /* make sure that the genes are sorted */ gt_assert(gt_genome_nodes_are_sorted(s->genes_forward)); gt_assert(gt_genome_nodes_are_sorted(s->genes_reverse)); /* make sure that the mRNAs are sorted */ gt_assert(gt_genome_nodes_are_sorted(s->mRNAs_forward)); gt_assert(gt_genome_nodes_are_sorted(s->mRNAs_reverse)); /* make sure that the LTRs are sorted */ gt_assert(gt_genome_nodes_are_sorted(s->LTRs)); /* make sure that the exons are sorted */ gt_assert(gt_transcript_exons_are_sorted(s->mRNA_exons_forward)); gt_assert(gt_transcript_exons_are_sorted(s->mRNA_exons_reverse)); gt_assert(gt_transcript_exons_are_sorted(s->CDS_exons_forward)); gt_assert(gt_transcript_exons_are_sorted(s->CDS_exons_reverse)); /* init true bittabs */ s->true_mRNA_genes_forward = gt_array_size(s->genes_forward) ? gt_bittab_new(gt_array_size(s->genes_forward)) : NULL; s->true_mRNA_genes_reverse = gt_array_size(s->genes_reverse) ? gt_bittab_new(gt_array_size(s->genes_reverse)) : NULL; s->true_CDS_genes_forward = gt_array_size(s->genes_forward) ? gt_bittab_new(gt_array_size(s->genes_forward)) : NULL; s->true_CDS_genes_reverse = gt_array_size(s->genes_reverse) ? gt_bittab_new(gt_array_size(s->genes_reverse)) : NULL; s->true_mRNA_mRNAs_forward = gt_array_size(s->mRNAs_forward) ? gt_bittab_new(gt_array_size(s->mRNAs_forward)) : NULL; s->true_mRNA_mRNAs_reverse = gt_array_size(s->mRNAs_reverse) ? gt_bittab_new(gt_array_size(s->mRNAs_reverse)) : NULL; s->true_CDS_mRNAs_forward = gt_array_size(s->mRNAs_forward) ? gt_bittab_new(gt_array_size(s->mRNAs_forward)) : NULL; s->true_CDS_mRNAs_reverse = gt_array_size(s->mRNAs_reverse) ? gt_bittab_new(gt_array_size(s->mRNAs_reverse)) : NULL; s->true_LTRs = gt_array_size(s->LTRs) ? gt_bittab_new(gt_array_size(s->LTRs)) : NULL; /* init overlap bittabs */ s->overlapped_genes_forward = gt_array_size(s->genes_forward) ? gt_bittab_new(gt_array_size(s->genes_forward)) : NULL; s->overlapped_genes_reverse = gt_array_size(s->genes_reverse) ? gt_bittab_new(gt_array_size(s->genes_reverse)) : NULL; s->overlapped_mRNAs_forward = gt_array_size(s->mRNAs_forward) ? gt_bittab_new(gt_array_size(s->mRNAs_forward)) : NULL; s->overlapped_mRNAs_reverse = gt_array_size(s->mRNAs_reverse) ? gt_bittab_new(gt_array_size(s->mRNAs_reverse)) : NULL; s->overlapped_LTRs = gt_array_size(s->LTRs) ? gt_bittab_new(gt_array_size(s->LTRs)) : NULL; /* init bittabs (for collapsed exons) */ s->mRNA_exon_bittabs_forward = gt_transcript_exons_create_bittabs(s->mRNA_exons_forward); s->mRNA_exon_bittabs_reverse = gt_transcript_exons_create_bittabs(s->mRNA_exons_reverse); s->CDS_exon_bittabs_forward = gt_transcript_exons_create_bittabs(s->CDS_exons_forward); s->CDS_exon_bittabs_reverse = gt_transcript_exons_create_bittabs(s->CDS_exons_reverse); return 0; } static void add_real_exon(GtTranscriptExons *te, GtRange range, GtFeatureNode *fn) { gt_assert(te); gt_array_add(gt_transcript_exons_get_all(te), range); switch (gt_feature_node_get_transcriptfeaturetype(fn)) { case TRANSCRIPT_FEATURE_TYPE_UNDETERMINED: gt_warning("type of feature (single, initial, internal, or terminal) " "given on line %u in file \"%s\" could not be determined, " "because the feature has no Parent attribute. Treating it as " "single.", gt_genome_node_get_line_number((GtGenomeNode*) fn), gt_genome_node_get_filename((GtGenomeNode*) fn)); /*@fallthrough@*/ case TRANSCRIPT_FEATURE_TYPE_SINGLE: gt_array_add(gt_transcript_exons_get_single(te), range); break; case TRANSCRIPT_FEATURE_TYPE_INITIAL: gt_array_add(gt_transcript_exons_get_initial(te), range); break; case TRANSCRIPT_FEATURE_TYPE_INTERNAL: gt_array_add(gt_transcript_exons_get_internal(te), range); break; case TRANSCRIPT_FEATURE_TYPE_TERMINAL: gt_array_add(gt_transcript_exons_get_terminal(te), range); break; } } static void add_nucleotide_exon(GtBittab *nucleotides, GtRange range, GtRange real_range, unsigned long *FP) { unsigned long i; gt_assert(nucleotides); for (i = range.start; i <= range.end; i++) { if (gt_range_within(&real_range, i)) { gt_assert(i >= real_range.start); gt_bittab_set_bit(nucleotides, i - real_range.start); } else { gt_assert(FP); (*FP)++; } } } static int process_real_feature(GtFeatureNode *fn, void *data, GT_UNUSED GtError *err) { ProcessRealFeatureInfo *info = (ProcessRealFeatureInfo*) data; GtGenomeNode *gn_ref; GtRange range; gt_error_check(err); gt_assert(fn && data); if (gt_feature_node_has_type(fn, gt_ft_gene)) { switch (gt_feature_node_get_strand(fn)) { case GT_STRAND_FORWARD: gn_ref = gt_genome_node_ref((GtGenomeNode*) fn); gt_array_add(info->slot->genes_forward, gn_ref); break; case GT_STRAND_REVERSE: gn_ref = gt_genome_node_ref((GtGenomeNode*) fn); gt_array_add(info->slot->genes_reverse, gn_ref); break; default: if (info->verbose) { fprintf(stderr, "skipping real gene with unknown orientation " "(line %u)\n", gt_genome_node_get_line_number((GtGenomeNode*) fn)); } } } else if (gt_feature_node_has_type(fn, gt_ft_mRNA)) { switch (gt_feature_node_get_strand(fn)) { case GT_STRAND_FORWARD: gn_ref = gt_genome_node_ref((GtGenomeNode*) fn); gt_array_add(info->slot->mRNAs_forward, gn_ref); break; case GT_STRAND_REVERSE: gn_ref = gt_genome_node_ref((GtGenomeNode*) fn); gt_array_add(info->slot->mRNAs_reverse, gn_ref); break; default: if (info->verbose) { fprintf(stderr, "skipping real mRNA with unknown orientation " "(line %u)\n", gt_genome_node_get_line_number((GtGenomeNode*) fn)); } } } else if (gt_feature_node_has_type(fn, gt_ft_LTR_retrotransposon)) { gn_ref = gt_genome_node_ref((GtGenomeNode*) fn); gt_array_add(info->slot->LTRs, gn_ref); } else if (gt_feature_node_has_type(fn, gt_ft_CDS)) { range = gt_genome_node_get_range((GtGenomeNode*) fn); switch (gt_feature_node_get_strand(fn)) { case GT_STRAND_FORWARD: add_real_exon(info->slot->CDS_exons_forward, range, fn); /* nucleotide level */ if (info->nuceval) { add_nucleotide_exon(info->slot->real_CDS_nucleotides_forward, range, info->slot->real_range, NULL); } break; case GT_STRAND_REVERSE: add_real_exon(info->slot->CDS_exons_reverse, range, fn); /* nucleotide level */ if (info->nuceval) { add_nucleotide_exon(info->slot->real_CDS_nucleotides_reverse, range, info->slot->real_range, NULL); } break; default: if (info->verbose) { fprintf(stderr, "skipping real CDS exon with unknown orientation " "(line %u)\n", gt_genome_node_get_line_number((GtGenomeNode*) fn)); } } } else if (gt_feature_node_has_type(fn, gt_ft_exon)) { range = gt_genome_node_get_range((GtGenomeNode*) fn); switch (gt_feature_node_get_strand(fn)) { case GT_STRAND_FORWARD: add_real_exon(info->slot->mRNA_exons_forward, range, fn); /* nucleotide level */ if (info->nuceval) { add_nucleotide_exon(info->slot->real_mRNA_nucleotides_forward, range, info->slot->real_range, NULL); } break; case GT_STRAND_REVERSE: add_real_exon(info->slot->mRNA_exons_reverse, range, fn); /* nucleotide level */ if (info->nuceval) { add_nucleotide_exon(info->slot->real_mRNA_nucleotides_reverse, range, info->slot->real_range, NULL); } break; default: if (info->verbose) { fprintf(stderr, "skipping real mRNA exon with unknown orientation " "(line %u)\n", gt_genome_node_get_line_number((GtGenomeNode*) fn)); } } } return 0; } typedef struct { GtArray *exons; const char *feature_type; } StoreExonFeatureInfo; static int store_exon(GtFeatureNode *fn, void *data, GT_UNUSED GtError *err) { StoreExonFeatureInfo *info = (StoreExonFeatureInfo*) data; GtRange range; gt_error_check(err); gt_assert(fn && info); if (gt_feature_node_has_type(fn, info->feature_type)) { range = gt_genome_node_get_range((GtGenomeNode*) fn); gt_array_add(info->exons, range); } return 0; } static bool mRNAs_are_equal(GtGenomeNode *gn_1, GtGenomeNode *gn_2, const char *feature_type) { GtArray *exons_1, *exons_2; StoreExonFeatureInfo info; bool equal; GT_UNUSED int had_err; gt_assert(gn_1 && gn_2 && feature_type); /* init */ exons_1 = gt_array_new(sizeof (GtRange)); exons_2 = gt_array_new(sizeof (GtRange)); /* get exon ranges */ info.exons = exons_1; info.feature_type = feature_type; had_err = gt_feature_node_traverse_children(gt_feature_node_cast(gn_1), &info, store_exon, false, NULL); gt_assert(!had_err); /* cannot happen, store_exon() is sane */ info.exons = exons_2; had_err = gt_feature_node_traverse_children(gt_feature_node_cast(gn_2), &info, store_exon, false, NULL); gt_assert(!had_err); /* cannot happen, store_exon() is sane */ /* sort exon ranges */ gt_ranges_sort(exons_1); gt_ranges_sort(exons_2); /* compare exon ranges */ equal = gt_ranges_are_equal(exons_1, exons_2); /* free */ gt_array_delete(exons_1); gt_array_delete(exons_2); return equal; } typedef struct { GtArray *exons, *mRNAs; const char *feature_type; } StoreGeneFeatureInfo; static int store_gene_feature(GtFeatureNode *fn, void *data, GT_UNUSED GtError *err) { StoreGeneFeatureInfo *info = (StoreGeneFeatureInfo*) data; GtRange range; gt_error_check(err); gt_assert(fn && info); if (gt_feature_node_has_type(fn, gt_ft_mRNA)) gt_array_add(info->mRNAs, fn); else if (gt_feature_node_has_type(fn, info->feature_type)) { range = gt_genome_node_get_range((GtGenomeNode*) fn); gt_array_add(info->exons, range); } return 0; } static bool genes_are_equal(GtGenomeNode *gn_1, GtGenomeNode *gn_2, const char *feature_type) { GtArray *exons_1, *exons_2, *mRNAs_1, *mRNAs_2; StoreGeneFeatureInfo info; unsigned long i; bool equal; GT_UNUSED int had_err; gt_assert(gn_1 && gn_2 && feature_type); /* init */ exons_1 = gt_array_new(sizeof (GtRange)); exons_2 = gt_array_new(sizeof (GtRange)); mRNAs_1 = gt_array_new(sizeof (GtGenomeNode*)); mRNAs_2 = gt_array_new(sizeof (GtGenomeNode*)); /* get (direct) gene features */ info.exons = exons_1; info.mRNAs = mRNAs_1; info.feature_type = feature_type; had_err = gt_feature_node_traverse_direct_children(gt_feature_node_cast(gn_1), &info, store_gene_feature, NULL); gt_assert(!had_err); /* cannot happen, store_gene_feature() is sane */ info.exons = exons_2; info.mRNAs = mRNAs_2; had_err = gt_feature_node_traverse_direct_children(gt_feature_node_cast(gn_2), &info, store_gene_feature, NULL); gt_assert(!had_err); /* cannot happen, store_gene_feature() is sane */ /* sort exon ranges */ gt_ranges_sort(exons_1); gt_ranges_sort(exons_2); /* compare exon ranges */ equal = gt_ranges_are_equal(exons_1, exons_2); /* compare mRNAs, if necessary */ if (equal && gt_array_size(mRNAs_1) == gt_array_size(mRNAs_2)) { /* sort mRNAs */ gt_genome_nodes_sort(mRNAs_1); gt_genome_nodes_sort(mRNAs_2); for (i = 0; i < gt_array_size(mRNAs_1); i++) { gt_assert(equal); equal = mRNAs_are_equal(*(GtGenomeNode**) gt_array_get(mRNAs_1, i), *(GtGenomeNode**) gt_array_get(mRNAs_2, i), feature_type); if (!equal) break; } } /* free */ gt_array_delete(exons_1); gt_array_delete(exons_2); gt_array_delete(mRNAs_1); gt_array_delete(mRNAs_2); return equal; } static void store_predicted_exon(GtTranscriptEvaluators *te, GtFeatureNode *fn) { gt_assert(te && fn); gt_evaluator_add_predicted(gt_transcript_evaluators_get_all(te), 1); switch (gt_feature_node_get_transcriptfeaturetype(fn)) { case TRANSCRIPT_FEATURE_TYPE_UNDETERMINED: gt_warning("type of feature (single, initial, internal, or terminal) " "given on line %u in file \"%s\" could not be determined, " "because the feature has no Parent attribute. Treating it as " "single.", gt_genome_node_get_line_number((GtGenomeNode*) fn), gt_genome_node_get_filename((GtGenomeNode*) fn)); /*@fallthrough@*/ case TRANSCRIPT_FEATURE_TYPE_SINGLE: gt_evaluator_add_predicted(gt_transcript_evaluators_get_single(te), 1); break; case TRANSCRIPT_FEATURE_TYPE_INITIAL: gt_evaluator_add_predicted(gt_transcript_evaluators_get_initial(te), 1); break; case TRANSCRIPT_FEATURE_TYPE_INTERNAL: gt_evaluator_add_predicted(gt_transcript_evaluators_get_internal(te), 1); break; case TRANSCRIPT_FEATURE_TYPE_TERMINAL: gt_evaluator_add_predicted(gt_transcript_evaluators_get_terminal(te), 1); break; } } /* adds exon only if necessary */ static void add_predicted_collapsed(GtDlist *used_exons, GtRange *predicted_range, GtEvaluator *exon_evaluator_collapsed) { GtRange *used_range; if (!gt_dlist_find(used_exons, predicted_range)) { used_range = gt_malloc(sizeof (GtRange)); used_range->start = predicted_range->start; used_range->end = predicted_range->end; gt_dlist_add(used_exons, used_range); gt_evaluator_add_predicted(exon_evaluator_collapsed, 1); } } static void store_predicted_exon_collapsed(GtTranscriptUsedExons *used_exons, GtRange *predicted_range, GtTranscriptEvaluators *te, GtFeatureNode *fn) { add_predicted_collapsed(gt_transcript_used_exons_get_all(used_exons), predicted_range, gt_transcript_evaluators_get_all(te)); switch (gt_feature_node_get_transcriptfeaturetype(fn)) { case TRANSCRIPT_FEATURE_TYPE_UNDETERMINED: /* we do not show a warning here, because store_predicted_exon() has been called before and already shown one */ case TRANSCRIPT_FEATURE_TYPE_SINGLE: add_predicted_collapsed(gt_transcript_used_exons_get_single(used_exons), predicted_range, gt_transcript_evaluators_get_single(te)); break; case TRANSCRIPT_FEATURE_TYPE_INITIAL: add_predicted_collapsed(gt_transcript_used_exons_get_initial(used_exons), predicted_range, gt_transcript_evaluators_get_initial(te)); break; case TRANSCRIPT_FEATURE_TYPE_INTERNAL: add_predicted_collapsed(gt_transcript_used_exons_get_internal(used_exons), predicted_range, gt_transcript_evaluators_get_internal(te)); break; case TRANSCRIPT_FEATURE_TYPE_TERMINAL: add_predicted_collapsed(gt_transcript_used_exons_get_terminal(used_exons), predicted_range, gt_transcript_evaluators_get_terminal(te)); break; } } static void mark_and_show_false_exon(GtFeatureNode *fn, bool exondiff) { gt_feature_node_mark(fn); /* mark false exons */ if (exondiff) { gt_gff3_output_leading(fn, NULL); printf(".\n"); } } static void determine_true_exon(GtFeatureNode *fn, GtStrand predicted_strand, bool exondiff, bool exondiffcollapsed, GtRange *predicted_range, GtArray *exons_forward, GtArray *exons_reverse, GtArray *true_exons_forward, GtArray *true_exons_reverse, GtBittab *true_exons_forward_collapsed, GtBittab *true_exons_reverse_collapsed, GtEvaluator *exon_evaluator, GtEvaluator *exon_evaluator_collapsed) { GtRange *actual_range; unsigned long num, *ctr_ptr; if ((actual_range = bsearch(predicted_range, predicted_strand == GT_STRAND_FORWARD ? gt_array_get_space(exons_forward) : gt_array_get_space(exons_reverse), predicted_strand == GT_STRAND_FORWARD ? gt_array_size(exons_forward) : gt_array_size(exons_reverse), sizeof (GtRange), (GtCompare) gt_range_compare))) { if (predicted_strand == GT_STRAND_FORWARD) { num = actual_range - (GtRange*) gt_array_get_space(exons_forward); ctr_ptr = gt_array_get(true_exons_forward, num); if (*ctr_ptr) { (*ctr_ptr)--; gt_evaluator_add_true(exon_evaluator); } else mark_and_show_false_exon(fn, exondiff); if (true_exons_forward_collapsed && !gt_bittab_bit_is_set(true_exons_forward_collapsed, num)) { gt_bittab_set_bit(true_exons_forward_collapsed, num); gt_evaluator_add_true(exon_evaluator_collapsed); } } else { num = actual_range - (GtRange*) gt_array_get_space(exons_reverse); ctr_ptr = gt_array_get(true_exons_reverse, num); if (*ctr_ptr) { (*ctr_ptr)--; gt_evaluator_add_true(exon_evaluator); } else mark_and_show_false_exon(fn, exondiff); if (true_exons_reverse_collapsed && !gt_bittab_bit_is_set(true_exons_reverse_collapsed, num)) { gt_bittab_set_bit(true_exons_reverse_collapsed, num); gt_evaluator_add_true(exon_evaluator_collapsed); } } } else { mark_and_show_false_exon(fn, exondiff); if (exondiffcollapsed) { gt_gff3_output_leading(fn, NULL); printf(".\n"); } } } static void store_true_exon(GtFeatureNode *fn, GtStrand predicted_strand, GtRange *predicted_range, bool exondiff, bool exondiffcollapsed, GtTranscriptExons *exons_forward, GtTranscriptExons *exons_reverse, GtTranscriptCounts *counts_forward, GtTranscriptCounts *counts_reverse, GtTranscriptBittabs *exon_bittabs_forward, GtTranscriptBittabs *exon_bittabs_reverse, GtTranscriptEvaluators *exon_evaluators, GtTranscriptEvaluators *exon_evaluators_collapsed) { gt_assert(fn && predicted_range && exons_forward && exons_reverse); determine_true_exon(fn, predicted_strand, exondiff, exondiffcollapsed, predicted_range, gt_transcript_exons_get_all(exons_forward), gt_transcript_exons_get_all(exons_reverse), gt_transcript_counts_get_all(counts_forward), gt_transcript_counts_get_all(counts_reverse), gt_transcript_bittabs_get_all(exon_bittabs_forward), gt_transcript_bittabs_get_all(exon_bittabs_reverse), gt_transcript_evaluators_get_all(exon_evaluators), gt_transcript_evaluators_get_all( exon_evaluators_collapsed)); switch (gt_feature_node_get_transcriptfeaturetype(fn)) { case TRANSCRIPT_FEATURE_TYPE_UNDETERMINED: case TRANSCRIPT_FEATURE_TYPE_SINGLE: determine_true_exon(fn, predicted_strand, exondiff, exondiffcollapsed, predicted_range, gt_transcript_exons_get_single(exons_forward), gt_transcript_exons_get_single(exons_reverse), gt_transcript_counts_get_single(counts_forward), gt_transcript_counts_get_single(counts_reverse), gt_transcript_bittabs_get_single( exon_bittabs_forward), gt_transcript_bittabs_get_single( exon_bittabs_reverse), gt_transcript_evaluators_get_single(exon_evaluators), gt_transcript_evaluators_get_single( exon_evaluators_collapsed)); break; case TRANSCRIPT_FEATURE_TYPE_INITIAL: determine_true_exon(fn, predicted_strand, exondiff, exondiffcollapsed, predicted_range, gt_transcript_exons_get_initial(exons_forward), gt_transcript_exons_get_initial(exons_reverse), gt_transcript_counts_get_initial(counts_forward), gt_transcript_counts_get_initial(counts_reverse), gt_transcript_bittabs_get_initial( exon_bittabs_forward), gt_transcript_bittabs_get_initial( exon_bittabs_reverse), gt_transcript_evaluators_get_initial(exon_evaluators), gt_transcript_evaluators_get_initial( exon_evaluators_collapsed)); break; case TRANSCRIPT_FEATURE_TYPE_INTERNAL: determine_true_exon(fn, predicted_strand, exondiff, exondiffcollapsed, predicted_range, gt_transcript_exons_get_internal(exons_forward), gt_transcript_exons_get_internal(exons_reverse), gt_transcript_counts_get_internal(counts_forward), gt_transcript_counts_get_internal(counts_reverse), gt_transcript_bittabs_get_internal( exon_bittabs_forward), gt_transcript_bittabs_get_internal( exon_bittabs_reverse), gt_transcript_evaluators_get_internal( exon_evaluators), gt_transcript_evaluators_get_internal( exon_evaluators_collapsed)); break; case TRANSCRIPT_FEATURE_TYPE_TERMINAL: determine_true_exon(fn, predicted_strand, exondiff, exondiffcollapsed, predicted_range, gt_transcript_exons_get_terminal(exons_forward), gt_transcript_exons_get_terminal(exons_reverse), gt_transcript_counts_get_terminal(counts_forward), gt_transcript_counts_get_terminal(counts_reverse), gt_transcript_bittabs_get_terminal( exon_bittabs_forward), gt_transcript_bittabs_get_terminal( exon_bittabs_reverse), gt_transcript_evaluators_get_terminal( exon_evaluators), gt_transcript_evaluators_get_terminal( exon_evaluators_collapsed)); break; } } typedef bool (*FeaturesAreEqualFunc)(GtGenomeNode *gn_1, GtGenomeNode *gn_2, const char *feature_type); static void compare_features(GtArray *real_genome_nodes, GtFeatureNode *fn, GtArray *genes_forward, GtArray *genes_reverse, GtBittab *true_genes_forward, GtBittab *true_genes_reverse, GtEvaluator *gene_evaluator, FeaturesAreEqualFunc features_are_equal, const char *feature_type) { GtStrand predicted_strand; GtGenomeNode **real_gn; unsigned long i, num; gt_assert(real_genome_nodes && fn && genes_forward && genes_reverse); gt_assert(gene_evaluator && features_are_equal && feature_type); predicted_strand = gt_feature_node_get_strand(fn); for (i = 0; i < gt_array_size(real_genome_nodes); i++) { real_gn = *(GtGenomeNode***) gt_array_get(real_genome_nodes, i); if (features_are_equal((GtGenomeNode*) fn, *real_gn, feature_type)) { if (predicted_strand == GT_STRAND_FORWARD) { num = real_gn - (GtGenomeNode**) gt_array_get_space(genes_forward); if (!gt_bittab_bit_is_set(true_genes_forward, num)) { gt_bittab_set_bit(true_genes_forward, num); gt_evaluator_add_true(gene_evaluator); /*@loopbreak@*/ break; } } else { num = real_gn - (GtGenomeNode**) gt_array_get_space(genes_reverse); if (!gt_bittab_bit_is_set(true_genes_reverse, num)) { gt_bittab_set_bit(true_genes_reverse, num); gt_evaluator_add_true(gene_evaluator); /*@loopbreak@*/ break; } } } } } static int process_predicted_feature(GtFeatureNode *fn, void *data, GT_UNUSED GtError *err) { ProcessPredictedFeatureInfo *info = (ProcessPredictedFeatureInfo*) data; GtRange predicted_range; unsigned long i, num; GtStrand predicted_strand; GtArray *real_genome_nodes; GtGenomeNode **real_gn; gt_error_check(err); gt_assert(fn && data); predicted_range = gt_genome_node_get_range((GtGenomeNode*) fn); predicted_strand = gt_feature_node_get_strand(fn); real_genome_nodes = gt_array_new(sizeof (GtGenomeNode**)); if (gt_feature_node_has_type(fn, gt_ft_gene)) { /* store predicted gene */ gt_evaluator_add_predicted(info->mRNA_gene_evaluator, 1); gt_evaluator_add_predicted(info->CDS_gene_evaluator, 1); /* determine true gene */ switch (predicted_strand) { case GT_STRAND_FORWARD: case GT_STRAND_REVERSE: gt_bsearch_all_mark(real_genome_nodes, &fn, predicted_strand == GT_STRAND_FORWARD ? gt_array_get_space(info->slot->genes_forward) : gt_array_get_space(info->slot->genes_reverse), predicted_strand == GT_STRAND_FORWARD ? gt_array_size(info->slot->genes_forward) : gt_array_size(info->slot->genes_reverse), sizeof (GtGenomeNode*), (GtCompareWithData) gt_genome_node_compare_with_data, NULL, predicted_strand == GT_STRAND_FORWARD ? info->slot->overlapped_genes_forward : info->slot->overlapped_genes_reverse); if (gt_array_size(real_genome_nodes)) { /* gene(s) with the same range found -> check if they are equal */ compare_features(real_genome_nodes, fn, info->slot->genes_forward, info->slot->genes_reverse, info->slot->true_mRNA_genes_forward, info->slot->true_mRNA_genes_reverse, info->mRNA_gene_evaluator, genes_are_equal, gt_ft_exon); compare_features(real_genome_nodes, fn, info->slot->genes_forward, info->slot->genes_reverse, info->slot->true_CDS_genes_forward, info->slot->true_CDS_genes_reverse, info->CDS_gene_evaluator, genes_are_equal, gt_ft_CDS); } else { /* no gene with the same range found -> check if this is a wrong gene */ if (!gt_feature_node_overlaps_nodes_mark(fn, predicted_strand == GT_STRAND_FORWARD ? info->slot->genes_forward : info->slot->genes_reverse, predicted_strand == GT_STRAND_FORWARD ? info->slot->overlapped_genes_forward : info->slot->overlapped_genes_reverse)) { (*info->wrong_genes)++; } } break; default: if (info->verbose) { fprintf(stderr, "skipping predicted gene with unknown orientation " "(line %u)\n", gt_genome_node_get_line_number((GtGenomeNode*) fn)); } } } else if (gt_feature_node_has_type(fn, gt_ft_mRNA)) { /* store predicted mRNA */ gt_evaluator_add_predicted(info->mRNA_mRNA_evaluator, 1); gt_evaluator_add_predicted(info->CDS_mRNA_evaluator, 1); /* determine true mRNA */ switch (predicted_strand) { case GT_STRAND_FORWARD: case GT_STRAND_REVERSE: gt_bsearch_all_mark(real_genome_nodes, &fn, predicted_strand == GT_STRAND_FORWARD ? gt_array_get_space(info->slot->mRNAs_forward) : gt_array_get_space(info->slot->mRNAs_reverse), predicted_strand == GT_STRAND_FORWARD ? gt_array_size(info->slot->mRNAs_forward) : gt_array_size(info->slot->mRNAs_reverse), sizeof (GtGenomeNode*), (GtCompareWithData) gt_genome_node_compare_with_data, NULL, predicted_strand == GT_STRAND_FORWARD ? info->slot->overlapped_mRNAs_forward : info->slot->overlapped_mRNAs_reverse); if (gt_array_size(real_genome_nodes)) { /* mRNA(s) with the same range found -> check if they are equal */ compare_features(real_genome_nodes, fn, info->slot->mRNAs_forward, info->slot->mRNAs_reverse, info->slot->true_mRNA_mRNAs_forward, info->slot->true_mRNA_mRNAs_reverse, info->mRNA_mRNA_evaluator, mRNAs_are_equal, gt_ft_exon); compare_features(real_genome_nodes, fn, info->slot->mRNAs_forward, info->slot->mRNAs_reverse, info->slot->true_CDS_mRNAs_forward, info->slot->true_CDS_mRNAs_reverse, info->CDS_mRNA_evaluator, mRNAs_are_equal, gt_ft_CDS); } else { /* no mRNA with the same range found -> check if this is a wrong mRNA */ if (!gt_feature_node_overlaps_nodes_mark(fn, predicted_strand == GT_STRAND_FORWARD ? info->slot->mRNAs_forward : info->slot->mRNAs_reverse, predicted_strand == GT_STRAND_FORWARD ? info->slot->overlapped_mRNAs_forward : info->slot->overlapped_mRNAs_reverse)) { (*info->wrong_mRNAs)++; } } break; default: if (info->verbose) { fprintf(stderr, "skipping predicted mRNA with unknown orientation " "(line %u)\n", gt_genome_node_get_line_number((GtGenomeNode*) fn)); } } } else if (gt_feature_node_has_type(fn, gt_ft_LTR_retrotransposon)) { /* store predicted LTR */ gt_evaluator_add_predicted(info->LTR_evaluator, 1); /* determine true LTR */ gt_bsearch_all_mark(real_genome_nodes, &fn, gt_array_get_space(info->slot->LTRs), gt_array_size(info->slot->LTRs), sizeof (GtGenomeNode*), (GtCompareWithData) gt_genome_node_compare_delta, &info->LTRdelta, info->slot->overlapped_LTRs); if (gt_array_size(real_genome_nodes)) { for (i = 0; i < gt_array_size(real_genome_nodes); i++) { real_gn = *(GtGenomeNode***) gt_array_get(real_genome_nodes, i); num = real_gn - (GtGenomeNode**) gt_array_get_space(info->slot->LTRs); if (!gt_bittab_bit_is_set(info->slot->true_LTRs, num)) { gt_bittab_set_bit(info->slot->true_LTRs, num); gt_evaluator_add_true(info->LTR_evaluator); /*@loopbreak@*/ break; } } } else { /* no LTR with the same range found -> check if this is a wrong LTR */ if (!gt_feature_node_overlaps_nodes_mark(fn, info->slot->LTRs, info->slot->overlapped_LTRs)) { (*info->wrong_LTRs)++; } } } else if (gt_feature_node_has_type(fn, gt_ft_exon)) { /* store predicted exon (mRNA level)*/ store_predicted_exon(info->mRNA_exon_evaluators, fn); /* store predicted exon (mRNA level, collapsed) */ store_predicted_exon_collapsed(predicted_strand == GT_STRAND_FORWARD ? info->slot->used_mRNA_exons_forward : info->slot->used_mRNA_exons_reverse, &predicted_range, info->mRNA_exon_evaluators_collapsed, fn); /* determine true exon (mRNA level)*/ switch (predicted_strand) { case GT_STRAND_FORWARD: case GT_STRAND_REVERSE: store_true_exon(fn, predicted_strand, &predicted_range, info->exondiff, info->exondiffcollapsed, info->slot->mRNA_exons_forward, info->slot->mRNA_exons_reverse, info->slot->mRNA_counts_forward, info->slot->mRNA_counts_reverse, info->slot->mRNA_exon_bittabs_forward, info->slot->mRNA_exon_bittabs_reverse, info->mRNA_exon_evaluators, info->mRNA_exon_evaluators_collapsed); /* nucleotide level */ if (info->nuceval) { add_nucleotide_exon(predicted_strand == GT_STRAND_FORWARD ? info->slot->pred_mRNA_nucleotides_forward : info->slot->pred_mRNA_nucleotides_reverse, predicted_range, info->slot->real_range, predicted_strand == GT_STRAND_FORWARD ? &info->slot->FP_mRNA_nucleotides_forward : &info->slot->FP_mRNA_nucleotides_reverse); } break; default: if (info->verbose) { fprintf(stderr, "skipping predicted exon with unknown orientation " "(line %u)\n", gt_genome_node_get_line_number((GtGenomeNode*) fn)); } } } else if (gt_feature_node_has_type(fn, gt_ft_CDS)) { /* store predicted exon (CDS level)*/ store_predicted_exon(info->CDS_exon_evaluators, fn); /* store predicted exon (CDS level, collapsed) */ store_predicted_exon_collapsed(predicted_strand == GT_STRAND_FORWARD ? info->slot->used_CDS_exons_forward : info->slot->used_CDS_exons_reverse, &predicted_range, info->CDS_exon_evaluators_collapsed, fn); /* determine true exon (CDS level) */ switch (predicted_strand) { case GT_STRAND_FORWARD: case GT_STRAND_REVERSE: store_true_exon(fn, predicted_strand, &predicted_range, info->exondiff, info->exondiffcollapsed, info->slot->CDS_exons_forward, info->slot->CDS_exons_reverse, info->slot->CDS_counts_forward, info->slot->CDS_counts_reverse, info->slot->CDS_exon_bittabs_forward, info->slot->CDS_exon_bittabs_reverse, info->CDS_exon_evaluators, info->CDS_exon_evaluators_collapsed); /* nucleotide level */ if (info->nuceval) { add_nucleotide_exon(predicted_strand == GT_STRAND_FORWARD ? info->slot->pred_CDS_nucleotides_forward : info->slot->pred_CDS_nucleotides_reverse, predicted_range, info->slot->real_range, predicted_strand == GT_STRAND_FORWARD ? &info->slot->FP_CDS_nucleotides_forward : &info->slot->FP_CDS_nucleotides_reverse); } break; default: if (info->verbose) { fprintf(stderr, "skipping predicted exon with unknown orientation " "(line %u)\n", gt_genome_node_get_line_number((GtGenomeNode*) fn)); } } } gt_array_delete(real_genome_nodes); return 0; } static int determine_missing_features(GT_UNUSED void *key, void *value, void *data, GT_UNUSED GtError *err) { GtStreamEvaluator *se = (GtStreamEvaluator*) data; Slot *slot = (Slot*) value; gt_error_check(err); gt_assert(key && value && data); if (slot->overlapped_genes_forward) { se->missing_genes += gt_bittab_size(slot->overlapped_genes_forward) - gt_bittab_count_set_bits(slot->overlapped_genes_forward); } if (slot->overlapped_genes_reverse) { se->missing_genes += gt_bittab_size(slot->overlapped_genes_reverse) - gt_bittab_count_set_bits(slot->overlapped_genes_reverse); } if (slot->overlapped_mRNAs_forward) { se->missing_mRNAs += gt_bittab_size(slot->overlapped_mRNAs_forward) - gt_bittab_count_set_bits(slot->overlapped_mRNAs_forward); } if (slot->overlapped_mRNAs_reverse) { se->missing_mRNAs += gt_bittab_size(slot->overlapped_mRNAs_reverse) - gt_bittab_count_set_bits(slot->overlapped_mRNAs_reverse); } if (slot->overlapped_LTRs) { se->missing_LTRs += gt_bittab_size(slot->overlapped_LTRs) - gt_bittab_count_set_bits(slot->overlapped_LTRs); } return 0; } static void add_nucleotide_values(NucEval *nucleotides, GtBittab *real, GtBittab *pred, GtBittab *tmp, const char *level) { gt_assert(nucleotides && real && pred && tmp); if (gt_log_enabled()) { gt_log_log("%s", level); gt_log_log("reference:"); gt_bittab_show(real, gt_log_fp()); gt_log_log("prediction:"); gt_bittab_show(pred, gt_log_fp()); } /* real & pred = TP */ gt_bittab_and(tmp, real, pred); nucleotides->TP += gt_bittab_count_set_bits(tmp); /* ~real & pred = FP */; gt_bittab_complement(tmp, real); gt_bittab_and_equal(tmp, pred); nucleotides->FP += gt_bittab_count_set_bits(tmp); /* real & ~pred = FN */ gt_bittab_complement(tmp, pred); gt_bittab_and_equal(tmp, real); nucleotides->FN += gt_bittab_count_set_bits(tmp); } static int compute_nucleotides_values(GT_UNUSED void *key, void *value, void *data, GT_UNUSED GtError *err) { GtStreamEvaluator *se = (GtStreamEvaluator*) data; Slot *slot = (Slot*) value; GtBittab *tmp; gt_error_check(err); gt_assert(key && value && data); /* add ``out of range'' FPs */ se->mRNA_nucleotides.FP += slot->FP_mRNA_nucleotides_forward; se->mRNA_nucleotides.FP += slot->FP_mRNA_nucleotides_reverse; se->CDS_nucleotides.FP += slot->FP_CDS_nucleotides_forward; se->CDS_nucleotides.FP += slot->FP_CDS_nucleotides_reverse; /* add other values */ tmp = gt_bittab_new(gt_range_length(&slot->real_range)); add_nucleotide_values(&se->mRNA_nucleotides, slot->real_mRNA_nucleotides_forward, slot->pred_mRNA_nucleotides_forward, tmp, "mRNA forward"); add_nucleotide_values(&se->mRNA_nucleotides, slot->real_mRNA_nucleotides_reverse, slot->pred_mRNA_nucleotides_reverse, tmp, "mRNA reverse"); add_nucleotide_values(&se->CDS_nucleotides, slot->real_CDS_nucleotides_forward, slot->pred_CDS_nucleotides_forward, tmp, "CDS forward"); add_nucleotide_values(&se->CDS_nucleotides, slot->real_CDS_nucleotides_reverse, slot->pred_CDS_nucleotides_reverse, tmp, "CDS reverse"); gt_bittab_delete(tmp); return 0; } int gt_stream_evaluator_evaluate(GtStreamEvaluator *se, bool verbose, bool exondiff, bool exondiffcollapsed, GtNodeVisitor *nv, GtError *err) { GtGenomeNode *gn; GtFeatureNode *fn; Slot *slot; ProcessRealFeatureInfo real_info; ProcessPredictedFeatureInfo predicted_info; int had_err; gt_error_check(err); gt_assert(se); /* init */ real_info.nuceval = se->nuceval; real_info.verbose = verbose; predicted_info.nuceval = se->nuceval; predicted_info.verbose = verbose; predicted_info.exondiff = exondiff; predicted_info.exondiffcollapsed = exondiffcollapsed; predicted_info.LTRdelta = se->LTRdelta; predicted_info.mRNA_gene_evaluator = se->mRNA_gene_evaluator; predicted_info.CDS_gene_evaluator = se->CDS_gene_evaluator; predicted_info.mRNA_mRNA_evaluator = se->mRNA_mRNA_evaluator; predicted_info.CDS_mRNA_evaluator = se->CDS_mRNA_evaluator; predicted_info.LTR_evaluator = se->LTR_evaluator; predicted_info.mRNA_exon_evaluators = se->mRNA_exon_evaluators; predicted_info.mRNA_exon_evaluators_collapsed = se->mRNA_exon_evaluators_collapsed; predicted_info.CDS_exon_evaluators = se->CDS_exon_evaluators; predicted_info.CDS_exon_evaluators_collapsed = se->CDS_exon_evaluators_collapsed; predicted_info.wrong_genes = &se->wrong_genes; predicted_info.wrong_mRNAs = &se->wrong_mRNAs; predicted_info.wrong_LTRs = &se->wrong_LTRs; /* process the reference stream completely */ while (!(had_err = gt_node_stream_next(se->reference, &gn, err)) && gn) { if (gt_region_node_try_cast(gn)) { /* each sequence region gets its own ``slot'' */ if (!(slot = gt_hashmap_get(se->slots, gt_str_get(gt_genome_node_get_seqid(gn))))) { slot = slot_new(se->nuceval, gt_genome_node_get_range(gn)); gt_hashmap_add(se->slots, gt_cstr_dup(gt_str_get(gt_genome_node_get_seqid(gn))), slot); } gt_assert(slot); } /* we consider only genome features */ if ((fn = gt_feature_node_try_cast(gn))) { /* each sequence must have its own ``slot'' at this point */ slot = gt_hashmap_get(se->slots, gt_str_get(gt_genome_node_get_seqid(gn))); gt_assert(slot); /* store the exons */ real_info.slot = slot; gt_feature_node_determine_transcripttypes(fn); had_err = gt_feature_node_traverse_children(fn, &real_info, process_real_feature, false, NULL); gt_assert(!had_err); /* cannot happen, process_real_feature() is sane */ } if (nv) gt_genome_node_accept(gn, nv, err); gt_genome_node_delete(gn); } /* set the actuals and sort them */ if (!had_err) { had_err = gt_hashmap_foreach(se->slots, set_actuals_and_sort_them, se, NULL); gt_assert(!had_err); /* set_actuals_and_sort_them() is sane */ } /* process the prediction stream */ if (!had_err) { while (!(had_err = gt_node_stream_next(se->prediction, &gn, err)) && gn) { /* we consider only genome features */ if ((fn = gt_feature_node_try_cast(gn))) { /* get (real) slot */ slot = gt_hashmap_get(se->slots, gt_str_get(gt_genome_node_get_seqid(gn))); if (slot) { predicted_info.slot = slot; gt_feature_node_determine_transcripttypes(fn); had_err = gt_feature_node_traverse_children(fn, &predicted_info, process_predicted_feature, false, NULL); gt_assert(!had_err); /* cannot happen, process_predicted_feature() is sane */ } else { /* we got no (real) slot */ gt_warning("sequence id \"%s\" (with predictions) not given in " "reference", gt_str_get(gt_genome_node_get_seqid(gn))); } } if (nv) had_err = gt_genome_node_accept(gn, nv, err); gt_genome_node_delete(gn); } } /* determine the missing mRNAs */ if (!had_err) { had_err = gt_hashmap_foreach(se->slots, determine_missing_features, se, NULL); gt_assert(!had_err); /* determine_missing_features() is sane */ } /* compute the nucleotides values */ if (!had_err && se->nuceval) { had_err = gt_hashmap_foreach(se->slots, compute_nucleotides_values, se, NULL); gt_assert(!had_err); /* compute_nucleotides_values() is sane */ } return had_err; } static void show_transcript_values(GtTranscriptEvaluators *te, const char *level, const char *additional_info, GtFile *outfp) { gt_assert(te); gt_file_xprintf(outfp, "exon sensitivity (%s level, all%s): ", level, additional_info); gt_evaluator_show_sensitivity(gt_transcript_evaluators_get_all(te), outfp); gt_file_xfputc('\n', outfp); gt_file_xprintf(outfp, "exon specificity (%s level, all%s): ", level, additional_info); gt_evaluator_show_specificity(gt_transcript_evaluators_get_all(te), outfp); gt_file_xfputc('\n', outfp); gt_file_xprintf(outfp, "exon sensitivity (%s level, single%s): ", level, additional_info); gt_evaluator_show_sensitivity(gt_transcript_evaluators_get_single(te), outfp); gt_file_xfputc('\n', outfp); gt_file_xprintf(outfp, "exon specificity (%s level, single%s): ", level, additional_info ); gt_evaluator_show_specificity(gt_transcript_evaluators_get_single(te), outfp); gt_file_xfputc('\n', outfp); gt_file_xprintf(outfp, "exon sensitivity (%s level, initial%s): ", level, additional_info); gt_evaluator_show_sensitivity(gt_transcript_evaluators_get_initial(te), outfp); gt_file_xfputc('\n', outfp); gt_file_xprintf(outfp, "exon specificity (%s level, initial%s): ", level, additional_info); gt_evaluator_show_specificity(gt_transcript_evaluators_get_initial(te), outfp); gt_file_xfputc('\n', outfp); gt_file_xprintf(outfp, "exon sensitivity (%s level, internal%s): ", level, additional_info); gt_evaluator_show_sensitivity(gt_transcript_evaluators_get_internal(te), outfp); gt_file_xfputc('\n', outfp); gt_file_xprintf(outfp, "exon specificity (%s level, internal%s): ", level, additional_info); gt_evaluator_show_specificity(gt_transcript_evaluators_get_internal(te), outfp); gt_file_xfputc('\n', outfp); gt_file_xprintf(outfp, "exon sensitivity (%s level, terminal%s): ", level, additional_info); gt_evaluator_show_sensitivity(gt_transcript_evaluators_get_terminal(te), outfp); gt_file_xfputc('\n', outfp); gt_file_xprintf(outfp, "exon specificity (%s level, terminal%s): ", level, additional_info); gt_evaluator_show_specificity(gt_transcript_evaluators_get_terminal(te), outfp); gt_file_xfputc('\n', outfp); } static void show_nucleotide_values(NucEval *nucleotides, const char *level, GtFile *outfp) { double sensitivity = 1.0, specificity = 1.0; gt_assert(nucleotides && level); if (nucleotides->TP || nucleotides->FN) { sensitivity = (double) nucleotides->TP / (nucleotides->TP + nucleotides->FN); } if (nucleotides->TP || nucleotides->FP) { specificity = (double) nucleotides->TP / (nucleotides->TP + nucleotides->FP); } gt_file_xprintf(outfp, "nucleotide sensitivity (%s level): %6.2f%% " "(TP=%lu/(TP=%lu + FN=%lu))\n", level, sensitivity * 100.0, nucleotides->TP, nucleotides->TP, nucleotides->FN); gt_file_xprintf(outfp, "nucleotide specificity (%s level): %6.2f%% " "(TP=%lu/(TP=%lu + FP=%lu))\n", level, specificity * 100.0, nucleotides->TP, nucleotides->TP, nucleotides->FP); } void gt_stream_evaluator_show(GtStreamEvaluator *se, GtFile *outfp) { gt_assert(se); if (!se->evalLTR) { /* gene level */ gt_file_xprintf(outfp, "gene sensitivity (mRNA level): "); gt_evaluator_show_sensitivity(se->mRNA_gene_evaluator, outfp); gt_file_xprintf(outfp, " (missing genes: %lu)\n", se->missing_genes); gt_file_xprintf(outfp, "gene specificity (mRNA level): "); gt_evaluator_show_specificity(se->mRNA_gene_evaluator, outfp); gt_file_xprintf(outfp, " (wrong genes: %lu)\n", se->wrong_genes); gt_file_xprintf(outfp, "gene sensitivity (CDS level): "); gt_evaluator_show_sensitivity(se->CDS_gene_evaluator, outfp); gt_file_xprintf(outfp, " (missing genes: %lu)\n", se->missing_genes); gt_file_xprintf(outfp, "gene specificity (CDS level): "); gt_evaluator_show_specificity(se->CDS_gene_evaluator, outfp); gt_file_xprintf(outfp, " (wrong genes: %lu)\n", se->wrong_genes); /* mRNA level */ gt_file_xprintf(outfp, "mRNA sensitivity (mRNA level): "); gt_evaluator_show_sensitivity(se->mRNA_mRNA_evaluator, outfp); gt_file_xprintf(outfp, " (missing mRNAs: %lu)\n", se->missing_mRNAs); gt_file_xprintf(outfp, "mRNA specificity (mRNA level): "); gt_evaluator_show_specificity(se->mRNA_mRNA_evaluator, outfp); gt_file_xprintf(outfp, " (wrong mRNAs: %lu)\n", se->wrong_mRNAs); gt_file_xprintf(outfp, "mRNA sensitivity (CDS level): "); gt_evaluator_show_sensitivity(se->CDS_mRNA_evaluator, outfp); gt_file_xprintf(outfp, " (missing mRNAs: %lu)\n", se->missing_mRNAs); gt_file_xprintf(outfp, "mRNA specificity (CDS level): "); gt_evaluator_show_specificity(se->CDS_mRNA_evaluator, outfp); gt_file_xprintf(outfp, " (wrong mRNAs: %lu)\n", se->wrong_mRNAs); /* mRNA exon level */ show_transcript_values(se->mRNA_exon_evaluators, "mRNA", "", outfp); show_transcript_values(se->mRNA_exon_evaluators_collapsed, "mRNA", ", collapsed", outfp); /* CDS exon level */ show_transcript_values(se->CDS_exon_evaluators, "CDS", "", outfp); show_transcript_values(se->CDS_exon_evaluators_collapsed, "CDS", ", collapsed", outfp); if (se->nuceval) { /* mRNA nucleotide level */ show_nucleotide_values(&se->mRNA_nucleotides, "mRNA", outfp); /* CDS nucleotide level */ show_nucleotide_values(&se->CDS_nucleotides, "CDS", outfp); } } else { /* LTR_retrotransposon prediction */ gt_file_xprintf(outfp, "LTR_retrotransposon sensitivity: "); gt_evaluator_show_sensitivity(se->LTR_evaluator, outfp); gt_file_xprintf(outfp, " (missing LTRs: %lu)\n", se->missing_LTRs); gt_file_xprintf(outfp, "LTR_retrotransposon specificity: "); gt_evaluator_show_specificity(se->LTR_evaluator, outfp); gt_file_xprintf(outfp, " (wrong LTRs: %lu)\n", se->wrong_LTRs); } } void gt_stream_evaluator_delete(GtStreamEvaluator *se) { if (!se) return; gt_node_stream_delete(se->reference); gt_node_stream_delete(se->prediction); gt_hashmap_delete(se->slots); gt_evaluator_delete(se->mRNA_gene_evaluator); gt_evaluator_delete(se->CDS_gene_evaluator); gt_evaluator_delete(se->mRNA_mRNA_evaluator); gt_evaluator_delete(se->CDS_mRNA_evaluator); gt_evaluator_delete(se->LTR_evaluator); gt_transcript_evaluators_delete(se->mRNA_exon_evaluators); gt_transcript_evaluators_delete(se->mRNA_exon_evaluators_collapsed); gt_transcript_evaluators_delete(se->CDS_exon_evaluators); gt_transcript_evaluators_delete(se->CDS_exon_evaluators_collapsed); gt_free(se); } genometools-1.5.1/src/extended/stream_evaluator.h000066400000000000000000000034741211610345200221710ustar00rootroot00000000000000/* Copyright (c) 2006-2011 Gordon Gremme Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef STREAM_EVALUATOR_H #define STREAM_EVALUATOR_H #include "extended/node_stream_api.h" #include "extended/node_visitor_api.h" typedef struct GtStreamEvaluator GtStreamEvaluator; GtStreamEvaluator* gt_stream_evaluator_new(GtNodeStream *reference, GtNodeStream *prediction, bool nuceval, bool evalLTR, unsigned long LTRdelta); /* if is not NULL, it visits all nodes from reference and the prediction */ int gt_stream_evaluator_evaluate(GtStreamEvaluator*, bool verbose, bool exondiff, bool exondiffcollapsed, GtNodeVisitor *nv, GtError*); void gt_stream_evaluator_show(GtStreamEvaluator*, GtFile*); void gt_stream_evaluator_delete(GtStreamEvaluator*); #endif genometools-1.5.1/src/extended/string_matching.c000066400000000000000000000221531211610345200217620ustar00rootroot00000000000000/* Copyright (c) 2006-2009 Gordon Gremme Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include #include "core/assert_api.h" #include "core/bittab.h" #include "core/ensure.h" #include "core/ma.h" #include "core/mathsupport.h" #include "core/undef_api.h" #include "extended/string_matching.h" #define STRING_MATCHING_NUM_OF_TESTS 256 #define STRING_MATCHING_MAX_STRING_LENGTH 100000 #define STRING_MATCHING_MAX_PATTERN_LENGTH 66 void gt_string_matching_bmh(const char *s, unsigned long n, const char *p, unsigned long m, GtProcessMatch process_match, void *data) { unsigned long i, j, pos, d[UCHAR_MAX]; gt_assert(s && p); if (m > n || !m || !n) /* no match possible */ return; /* preprocessing */ for (i = 0; i < UCHAR_MAX; i++) d[i] = m; for (j = 0; j < m-1; j++) d[(unsigned) p[j]] = m-(j+1); /* searching */ pos = 0; while (pos <= n-m) { j = m; while (j > 0 && s[pos+j-1] == p[j-1]) j--; if (j == 0 && process_match) { if (process_match(pos, data)) return; } pos += d[(unsigned) s[pos+m-1]]; } } static unsigned long* compute_prefixtab(const char *p, unsigned long m) { unsigned long i, vlen = 0, *prefixtab; char b; gt_assert(p); prefixtab = gt_malloc(sizeof (unsigned long) * (m+1)); prefixtab[0] = GT_UNDEF_ULONG; /* paranoia */ if (m) prefixtab[1] = 0; for (i = 2; i <= m; i++) { b = p[i-1]; while (vlen > 0 && p[vlen] != b) vlen = prefixtab[vlen]; if (p[vlen] == b) vlen++; prefixtab[i] = vlen; } return prefixtab; } unsigned long gt_string_matching_kmp(const char *s, unsigned long n, const char *p, unsigned long m, GtProcessMatch process_match, void *data) { unsigned long *prefixtab, j = 0, /* position in s corresponding to the first character in p */ cpl = 0; /* length of common prefix of s[j]..s[n-1] and p */ char b, c; gt_assert(s && p); if (!m || !n) /* no match possible */ return 0; prefixtab = compute_prefixtab(p, m); while (j + cpl < n) { if (cpl == m) { /* case (1) */ if (process_match) { if (process_match(j, data)) break; } j = j + cpl - prefixtab[cpl]; cpl = prefixtab[cpl]; } else { /* case (2) */ b = s[j+cpl]; c = p[cpl]; if (b != c) { if (cpl > 0) { j = j + cpl - prefixtab[cpl]; /* case (2a) */ cpl = prefixtab[cpl]; } else j++; /* case (2b) */ } else cpl++; /* case (2c) */ } } /* do not miss match at the last possible position */ if (cpl == m && process_match) process_match(j, data); gt_free(prefixtab); return cpl; } void gt_string_matching_shift_and(const char *s, unsigned long n, const char *p, unsigned long m, GtProcessMatch process_match, void *data) { GtBittab *D, *B[UCHAR_MAX] = { NULL }; unsigned long i, j; gt_assert(s && p); if (m > n || !m || !n) /* no match possible */ return; /* preprocessing */ for (j = 0; j < m; j++) { if (!B[(unsigned) p[j]]) B[(unsigned) p[j]] = gt_bittab_new(m); gt_bittab_set_bit(B[(unsigned) p[j]], j); } /* searching */ D = gt_bittab_new(m); for (i = 0; i < n; i++) { gt_bittab_shift_left_equal(D); gt_bittab_set_bit(D, 0); if (B[(unsigned) s[i]]) gt_bittab_and_equal(D, B[(unsigned) s[i]]); else gt_bittab_unset(D); if (gt_bittab_bit_is_set(D, m - 1) && process_match) { if (process_match(i - m + 1, data)) break; } } /* free */ for (i = 0; i < UCHAR_MAX; i++) gt_bittab_delete(B[i]); gt_bittab_delete(D); } void gt_string_matching_brute_force(const char *s, unsigned long n, const char *p, unsigned long m, GtProcessMatch process_match, void *data) { unsigned long i; gt_assert(s && p); if (m > n || !m || !n) /* no match possible */ return; for (i = 0; i <= n - m; i++) { unsigned long j = 0; while (j < m && s[i+j] == p[j]) j++; if (j == m && process_match) { if (process_match(i, data)) break; } } } static bool store_first_match(unsigned long pos, void *data) { unsigned long *match = data; gt_assert(match); *match = pos; return true; } static bool store_match(unsigned long pos, void *data) { GtArray *positions = data; gt_assert(positions); gt_array_add(positions, pos); return false; } int gt_string_matching_unit_test(GtError *err) { char s[STRING_MATCHING_MAX_STRING_LENGTH+1], p[STRING_MATCHING_MAX_PATTERN_LENGTH+1], *text = "foo"; GtArray *brute_force_matches, *bmh_matches, *kmp_matches, *shift_and_matches; unsigned long i, brute_force_match, bmh_match, kmp_match, shift_and_match; int had_err = 0; gt_error_check(err); brute_force_matches = gt_array_new(sizeof (unsigned long)); bmh_matches = gt_array_new(sizeof (unsigned long)); kmp_matches = gt_array_new(sizeof (unsigned long)); shift_and_matches = gt_array_new(sizeof (unsigned long)); /* match the empty pattern */ gt_string_matching_brute_force(text, strlen(text), "", 0, store_match, brute_force_matches); gt_string_matching_bmh(text, strlen(text), "", 0, store_match, bmh_matches); gt_string_matching_kmp(text, strlen(text), "", 0, store_match, kmp_matches); gt_string_matching_shift_and(text, strlen(text), "", 0, store_match, shift_and_matches); gt_ensure(had_err, !gt_array_size(brute_force_matches)); gt_ensure(had_err, !gt_array_size(bmh_matches)); gt_ensure(had_err, !gt_array_size(kmp_matches)); gt_ensure(had_err, !gt_array_size(shift_and_matches)); for (i = 0; !had_err && i < STRING_MATCHING_NUM_OF_TESTS; i++) { unsigned long j, n, m; /* generate random string and pattern */ n = gt_rand_max(STRING_MATCHING_MAX_STRING_LENGTH); m = gt_rand_max(STRING_MATCHING_MAX_PATTERN_LENGTH); for (j = 0; j < n; j++) s[j] = gt_rand_char(); s[n] = '\0'; for (j = 0; j < m; j++) p[j] = gt_rand_char(); p[m] = '\0'; /* matching (first match) */ brute_force_match = GT_UNDEF_ULONG; bmh_match = GT_UNDEF_ULONG; kmp_match = GT_UNDEF_ULONG; shift_and_match = GT_UNDEF_ULONG; gt_string_matching_brute_force(s, n, p, m, store_first_match, &brute_force_match); gt_string_matching_bmh(s, n, p, m, store_first_match, &bmh_match); gt_string_matching_kmp(s, n, p, m, store_first_match, &kmp_match); gt_string_matching_shift_and(s, n, p, m, store_first_match, &shift_and_match); /* comparing (first match) */ gt_ensure(had_err, brute_force_match == bmh_match); gt_ensure(had_err, brute_force_match == kmp_match); gt_ensure(had_err, brute_force_match == shift_and_match); /* matching (all matches) */ gt_string_matching_brute_force(s, n, p, m, store_match, brute_force_matches); gt_string_matching_bmh(s, n, p, m, store_match, bmh_matches); gt_string_matching_kmp(s, n, p, m, store_match, kmp_matches); gt_string_matching_shift_and(s, n, p, m, store_match, shift_and_matches); /* comparing (all matches) */ gt_ensure(had_err, gt_array_size(brute_force_matches) == gt_array_size(bmh_matches)); gt_ensure(had_err, gt_array_size(brute_force_matches) == gt_array_size(kmp_matches)); gt_ensure(had_err, gt_array_size(brute_force_matches) == gt_array_size(shift_and_matches)); gt_ensure(had_err, !gt_array_cmp(brute_force_matches, bmh_matches)); gt_ensure(had_err, !gt_array_cmp(brute_force_matches, kmp_matches)); gt_ensure(had_err, !gt_array_cmp(brute_force_matches, shift_and_matches)); /* reset */ gt_array_reset(brute_force_matches); gt_array_reset(bmh_matches); gt_array_reset(kmp_matches); gt_array_reset(shift_and_matches); } gt_array_delete(shift_and_matches); gt_array_delete(bmh_matches); gt_array_delete(kmp_matches); gt_array_delete(brute_force_matches); return had_err; } genometools-1.5.1/src/extended/string_matching.h000066400000000000000000000042431211610345200217670ustar00rootroot00000000000000/* Copyright (c) 2006-2008 Gordon Gremme Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef STRING_MATCHING_H #define STRING_MATCHING_H #include /* Gets called for every match. If it returns true, the matching is stopped. */ typedef bool (*GtProcessMatch)(unsigned long pos, void *data); /* Boyer-Moore-Horspool alg. (O(n*m) time worst-case; sublinear on average). */ void gt_string_matching_bmh(const char *s, unsigned long n, const char *p, unsigned long m, GtProcessMatch, void *data); /* Knuth-Morris-Pratt algorithm (O(n+m) time). Returns the last common prefix length.*/ unsigned long gt_string_matching_kmp(const char *s, unsigned long n, const char *p, unsigned long m, GtProcessMatch, void *data); /* Shift-And algorithm (O(n*(m/|w|) time, |w| is the word size). */ void gt_string_matching_shift_and(const char *s, unsigned long n, const char *p, unsigned long m, GtProcessMatch, void *data); /* Brute Force algorithm (O(n*m) time worst-case). */ void gt_string_matching_brute_force(const char *s, unsigned long n, const char *p, unsigned long m, GtProcessMatch, void *data); int gt_string_matching_unit_test(GtError*); #endif genometools-1.5.1/src/extended/swalign.c000066400000000000000000000145741211610345200202560ustar00rootroot00000000000000/* Copyright (c) 2007-2009 Gordon Gremme Copyright (c) 2007-2009 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include "core/array2dim_api.h" #include "core/assert_api.h" #include "core/chardef.h" #include "core/minmax.h" #include "core/undef_api.h" #include "extended/swalign.h" typedef struct { unsigned long x, y; } Coordinate; typedef struct { long score; bool max_replacement, max_deletion, max_insertion; } DPentry; static void swalign_fill_table(DPentry **dptable, const GtUchar *u, unsigned long ulen, const GtUchar *v, unsigned long vlen, const int **scores, int deletion_score, int insertion_score, Coordinate *max_coordinate, unsigned int u_alpha_size, unsigned int v_alpha_size) { unsigned long i, j; long maxscore, repscore, delscore, insscore, overall_maxscore = LONG_MIN; gt_assert(dptable && u && ulen && v && vlen && max_coordinate && u_alpha_size && v_alpha_size); for (j = 1; j <= vlen; j++) { for (i = 1; i <= ulen; i++) { int uval, vval; uval = (int) ((u[i-1] == WILDCARD) ? u_alpha_size - 1 : u[i-1]); vval = (int) ((v[j-1] == WILDCARD) ? v_alpha_size - 1 : v[j-1]); repscore = dptable[i-1][j-1].score + scores[uval][vval]; delscore = dptable[i-1][j].score + deletion_score; insscore = dptable[i][j-1].score + insertion_score; maxscore = MAX(MAX(MAX(repscore, delscore), insscore), 0); dptable[i][j].score = maxscore; dptable[i][j].max_replacement = (maxscore == repscore) ? true : false; dptable[i][j].max_deletion = (maxscore == delscore) ? true : false; dptable[i][j].max_insertion = (maxscore == insscore) ? true : false; if (maxscore > overall_maxscore) { overall_maxscore = maxscore; max_coordinate->x = i; max_coordinate->y = j; } } } } static Coordinate traceback(GtAlignment *a, DPentry **dptable, unsigned long i, unsigned long j) { Coordinate start_coordinate = { GT_UNDEF_ULONG, GT_UNDEF_ULONG }; gt_assert(a && dptable); while (dptable[i][j].score) { gt_assert(dptable[i][j].score > 0); start_coordinate.x = i; start_coordinate.y = j; if (dptable[i][j].max_replacement) { gt_alignment_add_replacement(a); i--; j--; } else if (dptable[i][j].max_deletion) { gt_alignment_add_deletion(a); i--;; } else if (dptable[i][j].max_insertion) { gt_alignment_add_insertion(a); j--; } } gt_assert(start_coordinate.x != GT_UNDEF_ULONG); gt_assert(start_coordinate.y != GT_UNDEF_ULONG); return start_coordinate; } static GtAlignment* smith_waterman_align(const char *u_orig, const char *v_orig, const GtUchar *u_enc, const GtUchar *v_enc, unsigned long u_len, unsigned long v_len, const int **scores, int deletion_score, int insertion_score, const GtAlphabet *u_alpha, const GtAlphabet *v_alpha) { gt_assert(u_orig && v_orig && u_enc && v_enc && u_len && v_len && scores && u_alpha && v_alpha); Coordinate alignment_start, alignment_end = { GT_UNDEF_ULONG, GT_UNDEF_ULONG }; GtRange urange, vrange; DPentry **dptable; GtAlignment *a = NULL; gt_array2dim_calloc(dptable, u_len+1, v_len+1); swalign_fill_table(dptable, u_enc, u_len, v_enc, v_len, scores, deletion_score, insertion_score, &alignment_end, gt_alphabet_size(u_alpha), gt_alphabet_size(v_alpha)); gt_assert(alignment_end.x != GT_UNDEF_ULONG); gt_assert(alignment_end.y != GT_UNDEF_ULONG); if (dptable[alignment_end.x][alignment_end.y].score) { /* construct only an alignment if a (positive) score was computed */ a = gt_alignment_new(); alignment_start = traceback(a, dptable, alignment_end.x, alignment_end.y); /* transform the positions in the DP matrix to sequence positions */ urange.start = --alignment_start.x; vrange.start = --alignment_start.y; urange.end = --alignment_end.x; vrange.end = --alignment_end.y; /* employ sequence positions to set alignment sequences */ gt_alignment_set_seqs(a, (const GtUchar *) (u_orig + alignment_start.x), alignment_end.x - alignment_start.x + 1, (const GtUchar *) (v_orig + alignment_start.y), alignment_end.y - alignment_start.y + 1); gt_alignment_set_urange(a, urange); gt_alignment_set_vrange(a, vrange); } gt_array2dim_delete(dptable); return a; } GtAlignment* gt_swalign(GtSeq *u, GtSeq *v, const GtScoreFunction *sf) { gt_assert(u && v && sf); return smith_waterman_align(gt_seq_get_orig(u), gt_seq_get_orig(v), gt_seq_get_encoded(u), gt_seq_get_encoded(v), gt_seq_length(u), gt_seq_length(v), gt_score_function_get_scores(sf), gt_score_function_get_deletion_score(sf), gt_score_function_get_insertion_score(sf), gt_seq_get_alphabet(u), gt_seq_get_alphabet(v)); } genometools-1.5.1/src/extended/swalign.h000066400000000000000000000023271211610345200202540ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef SWALIGN_H #define SWALIGN_H #include "core/score_function.h" #include "core/seq.h" #include "extended/alignment.h" /* (locally) align and (Smith-Waterman algorithm ) with the given score function and return one optimal Alignment. If no such alignment was found, NULL is returned. */ GtAlignment* gt_swalign(GtSeq *u, GtSeq *v, const GtScoreFunction*); #endif genometools-1.5.1/src/extended/tag_value_map.c000066400000000000000000000271451211610345200214140ustar00rootroot00000000000000/* Copyright (c) 2008-2011 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include #include "core/ma.h" #include "core/ensure.h" #include "core/unused_api.h" #include "core/xansi_api.h" #include "extended/tag_value_map.h" /* The GtTagValueMap is implemented as a simple char* which points to a memory region organized as follows: tag\0value\0tag\0value\0\0 */ GtTagValueMap gt_tag_value_map_new(const char *tag, const char *value) { GtTagValueMap map; size_t tag_len, value_len; gt_assert(tag && value); tag_len = strlen(tag); value_len = strlen(value); gt_assert(tag_len && value_len); map = gt_malloc((tag_len + 1 + value_len + 1 + 1) * sizeof *map); memcpy(map, tag, tag_len + 1); memcpy(map + tag_len + 1, value, value_len + 1); map[tag_len + 1 + value_len + 1] = '\0'; return map; } /* Stores map length in if the return value equals NULL (i.e., if not value has been found) and does not equal NULL. */ static char* get_value(const GtTagValueMap map, const char *tag, size_t *map_len) { char *map_ptr; const char *tag_ptr; /* search for equal tag */ map_ptr = map; tag_ptr = tag; for (;;) { while (*map_ptr == *tag_ptr++) { if (*map_ptr++ == '\0') return map_ptr; /* match found -> return value */ } /* no match found */ while (*map_ptr++ != '\0'); /* go to next value */ if (*map_ptr == '\0') break; /* no next value found */ /* reset tag pointer */ tag_ptr = tag; } if (map_len) *map_len = map_ptr - map; /* save map length */ return NULL; } static size_t get_map_len(const GtTagValueMap map) { const char *map_ptr = map; for (;;) { if ((*map_ptr++ == '\0') && (*map_ptr++ == '\0')) break; } return map_ptr - map - 1; } void gt_tag_value_map_add(GtTagValueMap *map, const char *tag, const char *value) { size_t tag_len, value_len, map_len = 0; GT_UNUSED const char *tag_already_used; gt_assert(map && *map && tag && value); tag_len = strlen(tag); value_len = strlen(value); gt_assert(tag_len && value_len); /* determine current map length */ tag_already_used = get_value(*map, tag, &map_len); gt_assert(!tag_already_used); /* map does not contain given already */ /* allocate additional space */ *map = gt_realloc(*map, map_len + tag_len + 1 + value_len + 1 + 1); /* store new tag/value pair */ memcpy(*map + map_len, tag, tag_len + 1); memcpy(*map + map_len + tag_len + 1, value, value_len + 1); (*map)[map_len + tag_len + 1 + value_len + 1] = '\0'; } void gt_tag_value_map_remove(GtTagValueMap *map, const char *tag) { size_t tag_len, value_len, map_len; char *value; gt_assert(map && tag); tag_len = strlen(tag); gt_assert(tag_len); /* determine value for given tag */ value = get_value(*map, tag, NULL); gt_assert(value); map_len = get_map_len(*map); value_len = strlen(value); /* move memory from end position of value to start position of tag */ memmove(value - tag_len - 1, value + value_len + 1, map_len - ((size_t) value - (size_t) *map + value_len)); *map = gt_realloc(*map, map_len - (tag_len + 1 + value_len + 1) + 1); gt_assert((*map)[map_len - (tag_len + 1 + value_len + 1)] == '\0'); } void gt_tag_value_map_set(GtTagValueMap *map, const char *tag, const char *new_value) { size_t old_value_len, new_value_len, map_len = 0; char *old_value; gt_assert(map && *map && tag && new_value); gt_assert(strlen(tag)); new_value_len = strlen(new_value); gt_assert(new_value_len); /* determine current map length */ old_value = get_value(*map, tag, &map_len); if (!old_value) return gt_tag_value_map_add(map, tag, new_value); /* tag already used -> replace it */ old_value_len = strlen(old_value); map_len = get_map_len(*map); if (new_value_len < old_value_len) { memcpy(old_value, new_value, new_value_len); memmove(old_value + new_value_len, old_value + old_value_len, map_len - ((size_t) old_value - (size_t) *map + old_value_len) + 1); *map = gt_realloc(*map, map_len - (old_value_len - new_value_len) + 1); } else if (new_value_len == old_value_len) { memcpy(old_value, new_value, new_value_len); } else { /* (new_value_len > old_value_len) */ *map = gt_realloc(*map, map_len + (new_value_len - old_value_len) + 1); /* determine old_value again, realloc() might have moved it */ old_value = get_value(*map, tag, &map_len); gt_assert(old_value); memmove(old_value + new_value_len, old_value + old_value_len, map_len - ((size_t) old_value - (size_t) *map + old_value_len) + 1); memcpy(old_value, new_value, new_value_len); } gt_assert((*map)[map_len - old_value_len + new_value_len] == '\0'); } const char* gt_tag_value_map_get(const GtTagValueMap map, const char *tag) { gt_assert(map && tag && strlen(tag)); return get_value(map, tag, NULL); } void gt_tag_value_map_foreach(const GtTagValueMap map, GtTagValueMapIteratorFunc func, void *data) { const char *map_ptr, *tag; gt_assert(map && func); map_ptr = map; do { /* the map has at least one tag/value pair */ tag = map_ptr; while (*map_ptr++ != '\0'); /* skip tag and \0 */ func(tag, map_ptr /* value */, data); while (*map_ptr++ != '\0'); /* skip value and \0 */ } while (*map_ptr != '\0'); } void gt_tag_value_map_show(const GtTagValueMap map) { bool null_terminator_read = false; const char *map_ptr; gt_assert(map); map_ptr = map; for (;;) { if (*map_ptr == '\0') { printf("\\0"); if (null_terminator_read) break; else null_terminator_read = true; } else { gt_xputchar(*map_ptr); null_terminator_read = false; } map_ptr++; } gt_xputchar('\n'); } int gt_tag_value_map_example(GT_UNUSED GtError *err) { GtTagValueMap map; gt_error_check(err); map = gt_tag_value_map_new("tag 1", "value 1"); gt_tag_value_map_add(&map, "tag 2", "value 2"); gt_tag_value_map_add(&map, "tag 3", "value 3"); gt_assert(!gt_tag_value_map_get(map, "unused tag")); gt_assert(!strcmp(gt_tag_value_map_get(map, "tag 1"), "value 1")); gt_assert(!strcmp(gt_tag_value_map_get(map, "tag 2"), "value 2")); gt_assert(!strcmp(gt_tag_value_map_get(map, "tag 3"), "value 3")); gt_tag_value_map_delete(map); return 0; } static GtTagValueMap create_filled_tag_value_list(void) { GtTagValueMap map = gt_tag_value_map_new("tag 1", "value 1"); gt_tag_value_map_add(&map, "tag 2", "value 2"); gt_tag_value_map_add(&map, "tag 3", "value 3"); gt_assert(!gt_tag_value_map_get(map, "unused tag")); gt_assert(!strcmp(gt_tag_value_map_get(map, "tag 1"), "value 1")); gt_assert(!strcmp(gt_tag_value_map_get(map, "tag 2"), "value 2")); gt_assert(!strcmp(gt_tag_value_map_get(map, "tag 3"), "value 3")); return map; } int gt_tag_value_map_unit_test(GtError *err) { GtTagValueMap map; int had_err = 0; gt_error_check(err); /* test gt_tag_value_map_set() (new tags are shorter than old tags) */ map = create_filled_tag_value_list(); gt_tag_value_map_set(&map, "tag 1", "val X"); gt_tag_value_map_set(&map, "tag 2", "val Y"); gt_tag_value_map_set(&map, "tag 3", "val Z"); gt_ensure(had_err, !gt_tag_value_map_get(map, "unused tag")); gt_ensure(had_err, !strcmp(gt_tag_value_map_get(map, "tag 1"), "val X")); gt_ensure(had_err, !strcmp(gt_tag_value_map_get(map, "tag 2"), "val Y")); gt_ensure(had_err, !strcmp(gt_tag_value_map_get(map, "tag 3"), "val Z")); gt_tag_value_map_delete(map); /* test gt_tag_value_map_set() (new tags have same length) */ if (!had_err) { map = create_filled_tag_value_list(); gt_tag_value_map_set(&map, "tag 1", "value X"); gt_tag_value_map_set(&map, "tag 2", "value Y"); gt_tag_value_map_set(&map, "tag 3", "value Z"); gt_ensure(had_err, !gt_tag_value_map_get(map, "unused tag")); gt_ensure(had_err, !strcmp(gt_tag_value_map_get(map, "tag 1"), "value X")); gt_ensure(had_err, !strcmp(gt_tag_value_map_get(map, "tag 2"), "value Y")); gt_ensure(had_err, !strcmp(gt_tag_value_map_get(map, "tag 3"), "value Z")); gt_tag_value_map_delete(map); } /* test gt_tag_value_map_set() (new tags are longer than old tags) */ if (!had_err) { map = create_filled_tag_value_list(); gt_tag_value_map_set(&map, "tag 1", "value XXX"); gt_tag_value_map_set(&map, "tag 2", "value YYY"); gt_tag_value_map_set(&map, "tag 3", "value ZZZ"); gt_ensure(had_err, !gt_tag_value_map_get(map, "unused tag")); gt_ensure(had_err, !strcmp(gt_tag_value_map_get(map, "tag 1"), "value XXX")); gt_ensure(had_err, !strcmp(gt_tag_value_map_get(map, "tag 2"), "value YYY")); gt_ensure(had_err, !strcmp(gt_tag_value_map_get(map, "tag 3"), "value ZZZ")); gt_tag_value_map_delete(map); } /* test gt_tag_value_map_remove() (remove first tag)*/ if (!had_err) { size_t old_map_len, new_map_len; map = create_filled_tag_value_list(); gt_tag_value_map_set(&map, "tag 1", "value XXX"); gt_tag_value_map_set(&map, "tag 2", "value YYY"); gt_tag_value_map_set(&map, "tag 3", "value ZZZ"); old_map_len = get_map_len(map); gt_tag_value_map_remove(&map, "tag 1"); new_map_len = get_map_len(map); gt_ensure(had_err, !gt_tag_value_map_get(map, "unused tag")); gt_ensure(had_err, !(old_map_len - new_map_len - strlen("tag 1") - 1 - strlen("value XXX") -1)); gt_tag_value_map_delete(map); } /* test gt_tag_value_map_remove() (remove middle tag)*/ if (!had_err) { size_t old_map_len, new_map_len; map = create_filled_tag_value_list(); gt_tag_value_map_set(&map, "tag 1", "value XXX"); gt_tag_value_map_set(&map, "tag 2", "value YYY"); gt_tag_value_map_set(&map, "tag 3", "value ZZZ"); old_map_len = get_map_len(map); gt_tag_value_map_remove(&map, "tag 2"); new_map_len = get_map_len(map); gt_ensure(had_err, !gt_tag_value_map_get(map, "unused tag")); gt_ensure(had_err, !(old_map_len - new_map_len - strlen("tag 2") - 1 - strlen("value YYY") -1)); gt_tag_value_map_delete(map); } /* test gt_tag_value_map_remove() (remove last tag)*/ if (!had_err) { size_t old_map_len, new_map_len; map = create_filled_tag_value_list(); gt_tag_value_map_set(&map, "tag 1", "value XXX"); gt_tag_value_map_set(&map, "tag 2", "value YYY"); gt_tag_value_map_set(&map, "tag 3", "value ZZZ"); old_map_len = get_map_len(map); gt_tag_value_map_remove(&map, "tag 3"); new_map_len = get_map_len(map); gt_ensure(had_err, !gt_tag_value_map_get(map, "unused tag")); gt_ensure(had_err, !(old_map_len - new_map_len - strlen("tag 3") - 1 - strlen("value ZZZ") -1)); gt_tag_value_map_delete(map); } return had_err; } void gt_tag_value_map_delete(GtTagValueMap map) { if (!map) return; gt_free(map); } genometools-1.5.1/src/extended/tag_value_map.h000066400000000000000000000020611211610345200214070ustar00rootroot00000000000000/* Copyright (c) 2008-2011 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TAG_VALUE_MAP_H #define TAG_VALUE_MAP_H #include "extended/tag_value_map_api.h" void gt_tag_value_map_show(const GtTagValueMap); int gt_tag_value_map_unit_test(GtError*); #endif genometools-1.5.1/src/extended/tag_value_map_api.h000066400000000000000000000066201211610345200222450ustar00rootroot00000000000000/* Copyright (c) 2008-2011 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TAG_VALUE_MAP_API_H #define TAG_VALUE_MAP_API_H #include "core/error_api.h" /* A very simple tag/value map absolutely optimized for space (i.e., memory consumption) on the cost of time. Basically, each read/write access costs O(n) time, whereas n denotes the accumulated length of all tags and values contained in the map. Tags and values cannot have length 0. The implementation as a char* shines through (also to save one additional memory allocation), therefore the usage is a little bit different compared to other __GenomeTools__ classes. See the implementation of for an ussage example. */ typedef char* GtTagValueMap; /* Iterator function used to iterate over tag/value maps. A / pair and user are given as arguments. */ typedef void (*GtTagValueMapIteratorFunc)(const char *tag, const char *value, void *data); /* Return a new object which stores the given / pair. */ GtTagValueMap gt_tag_value_map_new(const char *tag, const char *value); /* Add / pair to . must not contain the given already! */ void gt_tag_value_map_add(GtTagValueMap *tag_value_map, const char *tag, const char *value); /* Set the given in to . */ void gt_tag_value_map_set(GtTagValueMap *tag_value_map, const char *tag, const char *value); /* Return value corresponding to from . If does not contain such a value, is returned. */ const char* gt_tag_value_map_get(const GtTagValueMap tag_value_map, const char *tag); /* Removes the given from . must contain the given already! */ void gt_tag_value_map_remove(GtTagValueMap *tag_value_map, const char *tag); /* Apply to each tag/value pair contained in and pass along. */ void gt_tag_value_map_foreach(const GtTagValueMap tag_value_map, GtTagValueMapIteratorFunc iterator_func, void *data); /* Implements an example useage of a tag/value map. */ int gt_tag_value_map_example(GtError *err); /* Delete . */ void gt_tag_value_map_delete(GtTagValueMap tag_value_map); #endif genometools-1.5.1/src/extended/targetbest_select_stream.c000066400000000000000000000155711211610345200236660ustar00rootroot00000000000000/* Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "core/cstr_api.h" #include "core/dlist.h" #include "core/hashmap.h" #include "core/ma.h" #include "core/undef_api.h" #include "core/unused_api.h" #include "extended/feature_node.h" #include "extended/genome_node.h" #include "extended/gff3_defines.h" #include "extended/gff3_parser.h" #include "extended/node_stream_api.h" #include "extended/targetbest_select_stream.h" struct GtTargetbestSelectStream { const GtNodeStream parent_instance; GtNodeStream *in_stream; GtDlist *trees; GtDlistelem *next; GtHashmap *target_to_elem; /* maps the target ids to GtDlist elements */ bool in_stream_processed; }; #define targetbest_select_stream_cast(GS)\ gt_node_stream_cast(gt_targetbest_select_stream_class(), GS); static void build_key(GtStr *key, GtFeatureNode *feature, GtStr *target_id) { gt_assert(key && feature && target_id); gt_str_reset(key); gt_str_append_str(key, gt_genome_node_get_seqid((GtGenomeNode*) feature)); gt_str_append_char(key, '\t'); /* cannot occur in seqid or target_id */ gt_str_append_str(key, target_id); } static void include_feature(GtDlist *trees, GtHashmap *target_to_elem, GtFeatureNode *feature, GtStr *key) { gt_dlist_add(trees, feature); gt_hashmap_add(target_to_elem, gt_cstr_dup(gt_str_get(key)), gt_dlist_last(trees)); } static void remove_elem(GtDlistelem *elem, GtDlist *trees, GtHashmap *target_to_elem, GtStr *key) { GtGenomeNode *node = gt_dlistelem_get_data(elem); gt_genome_node_delete(node); gt_dlist_remove(trees, elem); gt_hashmap_remove(target_to_elem, gt_str_get(key)); } static void replace_previous_elem(GtDlistelem *previous_elem, GtFeatureNode *current_feature, GtDlist *trees, GtHashmap *target_to_elem, GtStr *key) { remove_elem(previous_elem, trees, target_to_elem, key); include_feature(trees, target_to_elem, current_feature, key); } static void select_targetbest(GtFeatureNode *current_feature, GtDlist *trees, GtHashmap *target_to_elem) { unsigned long num_of_targets; GtDlistelem *previous_elem; GtStr *first_target_id; const char *target; GT_UNUSED int had_err; gt_assert(current_feature && trees); target = gt_feature_node_get_attribute(current_feature, GT_GFF_TARGET); gt_assert(target); first_target_id = gt_str_new(); had_err = gt_gff3_parser_parse_target_attributes(target, &num_of_targets, first_target_id, NULL, NULL, "", 0, NULL); gt_assert(!had_err); if (num_of_targets == 1) { GtStr *key = gt_str_new(); build_key(key, current_feature, first_target_id); if (!(previous_elem = gt_hashmap_get(target_to_elem, gt_str_get(key)))) { /* element with this target_id not included yet -> include it */ include_feature(trees, target_to_elem, current_feature, key); } else { GtFeatureNode *previous_feature = gt_dlistelem_get_data(previous_elem); /* element with this target_id included already -> compare them */ if (gt_feature_node_get_score(current_feature) > gt_feature_node_get_score(previous_feature)) { /* current feature is better -> replace previous feature */ replace_previous_elem(previous_elem, current_feature, trees, target_to_elem, key); } else /* current feature is not better -> remove it */ gt_genome_node_delete((GtGenomeNode*) current_feature); } gt_str_delete(key); } else gt_dlist_add(trees, current_feature); gt_str_delete(first_target_id); } static int targetbest_select_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) { GtTargetbestSelectStream *tfs; GtGenomeNode *node; int had_err = 0; gt_error_check(err); tfs = targetbest_select_stream_cast(ns); if (!tfs->in_stream_processed) { while (!(had_err = gt_node_stream_next(tfs->in_stream, &node, err)) && node) { if (gt_feature_node_try_cast(node) && gt_feature_node_get_attribute((GtFeatureNode*) node, "Target")) { select_targetbest((GtFeatureNode*) node, tfs->trees, tfs->target_to_elem); } else gt_dlist_add(tfs->trees, node); } tfs->next = gt_dlist_first(tfs->trees); tfs->in_stream_processed = true; } if (!had_err) { gt_assert(tfs->in_stream_processed); if (tfs->next) { *gn = gt_dlistelem_get_data(tfs->next); tfs->next = gt_dlistelem_next(tfs->next); } else *gn = NULL; return 0; } return had_err; } static void targetbest_select_stream_free(GtNodeStream *ns) { GtTargetbestSelectStream *tfs = targetbest_select_stream_cast(ns); for (; tfs->next != NULL; tfs->next = gt_dlistelem_next(tfs->next)) gt_genome_node_delete(gt_dlistelem_get_data(tfs->next)); gt_dlist_delete(tfs->trees); gt_hashmap_delete(tfs->target_to_elem); gt_node_stream_delete(tfs->in_stream); } const GtNodeStreamClass* gt_targetbest_select_stream_class(void) { static const GtNodeStreamClass *nsc = NULL; gt_class_alloc_lock_enter(); if (!nsc) { nsc = gt_node_stream_class_new(sizeof (GtTargetbestSelectStream), targetbest_select_stream_free, targetbest_select_stream_next); } gt_class_alloc_lock_leave(); return nsc; } GtNodeStream* gt_targetbest_select_stream_new(GtNodeStream *in_stream) { GtTargetbestSelectStream *tfs; GtNodeStream *ns; gt_assert(in_stream); ns = gt_node_stream_create(gt_targetbest_select_stream_class(), gt_node_stream_is_sorted(in_stream)); tfs = targetbest_select_stream_cast(ns); tfs->in_stream = gt_node_stream_ref(in_stream); tfs->in_stream_processed = false; tfs->trees = gt_dlist_new(NULL); tfs->target_to_elem = gt_hashmap_new(GT_HASH_STRING, gt_free_func, NULL); return ns; } genometools-1.5.1/src/extended/targetbest_select_stream.h000066400000000000000000000023141211610345200236620ustar00rootroot00000000000000/* Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TARGETBEST_SELECT_STREAM_H #define TARGETBEST_SELECT_STREAM_H #include "extended/node_stream_api.h" /* implements the ``genome stream'' interface */ typedef struct GtTargetbestSelectStream GtTargetbestSelectStream; const GtNodeStreamClass* gt_targetbest_select_stream_class(void); GtNodeStream* gt_targetbest_select_stream_new(GtNodeStream*); #endif genometools-1.5.1/src/extended/tidy_region_node_stream.c000066400000000000000000000067401211610345200235020ustar00rootroot00000000000000/* Copyright (c) 2012 Sascha Steinbiss Copyright (c) 2012 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "extended/feature_node.h" #include "extended/tidy_region_node_stream.h" #include "extended/tidy_region_node_visitor.h" #include "extended/node_stream_api.h" struct GtTidyRegionNodeStream { const GtNodeStream parent_instance; GtNodeStream *in_stream; GtNodeVisitor *tidy_region_node_visitor; bool queued; }; #define gt_tidy_region_node_stream_cast(GS)\ gt_node_stream_cast(gt_tidy_region_node_stream_class(), GS); static int tidy_region_node_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) { GtTidyRegionNodeStream *ais; int had_err = 0; gt_error_check(err); ais = gt_tidy_region_node_stream_cast(ns); if (!ais->queued) { /* no nodes in the buffer -> get new nodes */ while (!(had_err = gt_node_stream_next(ais->in_stream, gn, err)) && *gn) { gt_assert(*gn && !had_err); had_err = gt_genome_node_accept(*gn, ais->tidy_region_node_visitor, err); if (had_err) { /* we own the node -> delete it */ gt_genome_node_delete(*gn); *gn = NULL; break; } } if (!had_err) { ais->queued = true; } } if (!had_err) { if (gt_tidy_region_node_visitor_node_buffer_size( ais->tidy_region_node_visitor)) { *gn = gt_tidy_region_node_visitor_get_node(ais->tidy_region_node_visitor); } } return had_err; } static void tidy_region_node_stream_free(GtNodeStream *ns) { GtTidyRegionNodeStream *ais = gt_tidy_region_node_stream_cast(ns); gt_node_visitor_delete(ais->tidy_region_node_visitor); gt_node_stream_delete(ais->in_stream); } const GtNodeStreamClass* gt_tidy_region_node_stream_class(void) { static const GtNodeStreamClass *nsc = NULL; gt_class_alloc_lock_enter(); if (!nsc) { nsc = gt_node_stream_class_new(sizeof (GtTidyRegionNodeStream), tidy_region_node_stream_free, tidy_region_node_stream_next); } gt_class_alloc_lock_leave(); return nsc; } GtNodeStream* gt_tidy_region_node_stream_new(GtNodeStream *in_stream) { GtTidyRegionNodeStream *tidy_region_node_stream; GtNodeStream *ns; gt_assert(in_stream); ns = gt_node_stream_create(gt_tidy_region_node_stream_class(), false); tidy_region_node_stream = gt_tidy_region_node_stream_cast(ns); tidy_region_node_stream->in_stream = gt_node_stream_ref(in_stream); tidy_region_node_stream->tidy_region_node_visitor = gt_tidy_region_node_visitor_new(); tidy_region_node_stream->queued = false; return ns; } genometools-1.5.1/src/extended/tidy_region_node_stream.h000066400000000000000000000023471211610345200235060ustar00rootroot00000000000000/* Copyright (c) 2012 Sascha Steinbiss Copyright (c) 2012 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TIDY_REGION_NODE_STREAM_H #define TIDY_REGION_NODE_STREAM_H #include "core/strand_api.h" #include "extended/node_stream_api.h" /* implements the ``genome stream'' interface */ typedef struct GtTidyRegionNodeStream GtTidyRegionNodeStream; const GtNodeStreamClass* gt_tidy_region_node_stream_class(void); GtNodeStream* gt_tidy_region_node_stream_new(GtNodeStream*); #endif genometools-1.5.1/src/extended/tidy_region_node_visitor.c000066400000000000000000000164421211610345200237060ustar00rootroot00000000000000/* Copyright (c) 2012 Sascha Steinbiss Copyright (c) 2012 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "core/cstr_api.h" #include "core/hashmap.h" #include "core/ma_api.h" #include "core/minmax.h" #include "core/queue.h" #include "core/undef_api.h" #include "core/unused_api.h" #include "core/warning_api.h" #include "extended/tidy_region_node_visitor.h" #include "extended/feature_node_iterator_api.h" #include "extended/node_visitor_api.h" struct GtTidyRegionNodeVisitor { const GtNodeVisitor parent_instance; GtQueue *node_buffer; GtHashmap *region_nodes; }; #define tidy_region_node_visitor_cast(GV)\ gt_node_visitor_cast(gt_tidy_region_node_visitor_class(), GV) static void tidy_region_node_visitor_free(GtNodeVisitor *nv) { GtTidyRegionNodeVisitor *tidy_region_node_visitor = tidy_region_node_visitor_cast(nv); gt_hashmap_delete(tidy_region_node_visitor->region_nodes); gt_queue_delete(tidy_region_node_visitor->node_buffer); } static int tidy_region_node_visitor_feature_node(GtNodeVisitor *nv, GtFeatureNode *fn, GT_UNUSED GtError *err) { GtTidyRegionNodeVisitor *trnv; GtFeatureNodeIterator *fni; GtFeatureNode *node; GtGenomeNode *sr; GtRange range = {0, 0}, sr_range, joined_range = {0, 0}; bool first = true; int had_err = 0; const char *seqid; trnv = tidy_region_node_visitor_cast(nv); seqid = gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*) fn)); fni = gt_feature_node_iterator_new(fn); while ((node = gt_feature_node_iterator_next(fni))) { GtRange node_range = gt_genome_node_get_range((GtGenomeNode*) node); if (first) { range = node_range; first = false; } else range = gt_range_join(&range, &node_range); } gt_feature_node_iterator_delete(fni); sr = gt_hashmap_get(trnv->region_nodes, seqid); if (!sr) { gt_error_set(err, "seqid '%s' on line %u in file \"%s\" has not been " "defined yet", seqid, gt_genome_node_get_line_number((GtGenomeNode*) fn), gt_genome_node_get_filename((GtGenomeNode*) fn)); had_err = -1; } if (!had_err) { gt_assert(sr); sr_range = gt_genome_node_get_range(sr); joined_range = gt_range_join(&range, &sr_range); gt_genome_node_set_range(sr, &joined_range); gt_queue_add(trnv->node_buffer, fn); } return 0; } static int tidy_region_node_visitor_region_node(GtNodeVisitor *nv, GtRegionNode *rn, GT_UNUSED GtError *err) { GtTidyRegionNodeVisitor *trnv; const char *seqid; gt_error_check(err); trnv = tidy_region_node_visitor_cast(nv); seqid = gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*) rn)); gt_assert(seqid); if (!gt_hashmap_get(trnv->region_nodes, seqid)) { gt_hashmap_add(trnv->region_nodes, gt_cstr_dup(seqid), gt_genome_node_ref((GtGenomeNode*) rn)); gt_assert(gt_hashmap_get(trnv->region_nodes, seqid)); } gt_queue_add(trnv->node_buffer, rn); return 0; } static int tidy_region_node_visitor_sequence_node(GtNodeVisitor *nv, GtSequenceNode *sn, GT_UNUSED GtError *err) { GtTidyRegionNodeVisitor *trnv; gt_error_check(err); trnv = tidy_region_node_visitor_cast(nv); gt_queue_add(trnv->node_buffer, sn); return 0; } static int tidy_region_node_visitor_comment_node(GtNodeVisitor *nv, GtCommentNode *cn, GT_UNUSED GtError *err) { GtTidyRegionNodeVisitor *trnv; gt_error_check(err); trnv = tidy_region_node_visitor_cast(nv); gt_queue_add(trnv->node_buffer, cn); return 0; } static int tidy_region_node_visitor_meta_node(GtNodeVisitor *nv, GtMetaNode *mn, GT_UNUSED GtError *err) { GtTidyRegionNodeVisitor *trnv; gt_error_check(err); trnv = tidy_region_node_visitor_cast(nv); gt_queue_add(trnv->node_buffer, mn); return 0; } static int tidy_region_node_visitor_eof_node(GtNodeVisitor *nv, GtEOFNode *en, GT_UNUSED GtError *err) { GtTidyRegionNodeVisitor *trnv; gt_error_check(err); trnv = tidy_region_node_visitor_cast(nv); gt_queue_add(trnv->node_buffer, en); return 0; } const GtNodeVisitorClass* gt_tidy_region_node_visitor_class() { static GtNodeVisitorClass *nvc = NULL; gt_class_alloc_lock_enter(); if (!nvc) { nvc = gt_node_visitor_class_new(sizeof (GtTidyRegionNodeVisitor), tidy_region_node_visitor_free, tidy_region_node_visitor_comment_node, tidy_region_node_visitor_feature_node, tidy_region_node_visitor_region_node, tidy_region_node_visitor_sequence_node, tidy_region_node_visitor_eof_node); gt_node_visitor_class_set_meta_node_func(nvc, tidy_region_node_visitor_meta_node); } gt_class_alloc_lock_leave(); return nvc; } GtNodeVisitor* gt_tidy_region_node_visitor_new(void) { GtNodeVisitor *nv; GtTidyRegionNodeVisitor *tidy_region_node_visitor; nv = gt_node_visitor_create(gt_tidy_region_node_visitor_class()); tidy_region_node_visitor = tidy_region_node_visitor_cast(nv); tidy_region_node_visitor->node_buffer = gt_queue_new(); tidy_region_node_visitor->region_nodes = gt_hashmap_new(GT_HASH_STRING, gt_free_func, (GtFree) gt_genome_node_delete); return nv; } unsigned long gt_tidy_region_node_visitor_node_buffer_size(GtNodeVisitor *nv) { GtTidyRegionNodeVisitor *tidy_region_node_visitor = tidy_region_node_visitor_cast(nv); return gt_queue_size(tidy_region_node_visitor->node_buffer); } GtGenomeNode* gt_tidy_region_node_visitor_get_node(GtNodeVisitor *nv) { GtTidyRegionNodeVisitor *tidy_region_node_visitor = tidy_region_node_visitor_cast(nv); return gt_queue_get(tidy_region_node_visitor->node_buffer); } genometools-1.5.1/src/extended/tidy_region_node_visitor.h000066400000000000000000000025141211610345200237060ustar00rootroot00000000000000/* Copyright (c) 2012 Sascha Steinbiss Copyright (c) 2012 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TIDY_REGION_NODE_VISITOR_H #define TIDY_REGION_NODE_VISITOR_H /* Implements the interface. */ typedef struct GtTidyRegionNodeVisitor GtTidyRegionNodeVisitor; #include "extended/node_visitor.h" const GtNodeVisitorClass* gt_tidy_region_node_visitor_class(void); GtNodeVisitor* gt_tidy_region_node_visitor_new(void); unsigned long gt_tidy_region_node_visitor_node_buffer_size(GtNodeVisitor*); GtGenomeNode* gt_tidy_region_node_visitor_get_node(GtNodeVisitor*); #endif genometools-1.5.1/src/extended/toolbox.c000066400000000000000000000074121211610345200202710ustar00rootroot00000000000000/* Copyright (c) 2007-2011 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include "core/hashmap.h" #include "core/ma.h" #include "core/unused_api.h" #include "core/xansi_api.h" #include "extended/toolbox.h" struct GtToolbox { GtHashmap *tools; }; typedef struct { GtTool *tool; GtToolfunc toolfunc; bool hidden; } GtToolinfo; GtToolinfo* gt_toolinfo_new(void) { return gt_calloc(1, sizeof (GtToolinfo)); } void gt_toolinfo_delete(GtToolinfo *toolinfo) { if (!toolinfo) return; gt_tool_delete(toolinfo->tool); gt_free(toolinfo); } GtToolbox* gt_toolbox_new(void) { GtToolbox *tb; tb = gt_malloc(sizeof (GtToolbox)); tb->tools = gt_hashmap_new(GT_HASH_STRING, NULL, (GtFree) gt_toolinfo_delete); return tb; } void gt_toolbox_add_tool(GtToolbox *tb, const char *toolname, GtTool *tool) { GtToolinfo *toolinfo; gt_assert(tb && tb->tools); toolinfo = gt_toolinfo_new(); toolinfo->tool= tool; gt_hashmap_add(tb->tools, (char*) toolname, toolinfo); } void gt_toolbox_add_hidden_tool(GtToolbox *tb, const char *toolname, GtTool *tool) { GtToolinfo *toolinfo; gt_assert(tb && tb->tools); toolinfo = gt_toolinfo_new(); toolinfo->tool= tool; toolinfo->hidden = true; gt_hashmap_add(tb->tools, (char*) toolname, toolinfo); } GtTool* gt_toolbox_get_tool(GtToolbox *tb, const char *toolname) { GtToolinfo *toolinfo; gt_assert(tb && tb->tools); toolinfo = gt_hashmap_get(tb->tools, toolname); if (toolinfo) return toolinfo->tool; return NULL; } bool gt_toolbox_has_tool(const GtToolbox *tb, const char *toolname) { gt_assert(tb && tb->tools); if (gt_hashmap_get(tb->tools, toolname)) return true; return false; } void gt_toolbox_add(GtToolbox *tb, const char *toolname, GtToolfunc toolfunc) { GtToolinfo *toolinfo; gt_assert(tb && tb->tools); toolinfo = gt_toolinfo_new(); toolinfo->toolfunc = toolfunc; gt_hashmap_add(tb->tools, (char*) toolname, toolinfo); } GtToolfunc gt_toolbox_get(const GtToolbox *tb, const char *toolname) { GtToolinfo *toolinfo; gt_assert(tb && tb->tools); toolinfo = gt_hashmap_get(tb->tools, toolname); if (toolinfo) return toolinfo->toolfunc; return NULL; } static int show_tool_name(void *key, void *value, GT_UNUSED void *data, GT_UNUSED GtError *err) { GtToolinfo *toolinfo = value; gt_error_check(err); gt_assert(key && value); if (!toolinfo->hidden) gt_xputs(key); return 0; } int gt_toolbox_show(GT_UNUSED const char *progname, void *toolbox, GT_UNUSED GtError *err) { GtToolbox *tb; GT_UNUSED int had_err = 0; gt_error_check(err); gt_assert(toolbox); tb = (GtToolbox*) toolbox; printf("\nTools:\n\n"); had_err = gt_hashmap_foreach_in_key_order(tb->tools, show_tool_name, NULL, NULL); gt_assert(!had_err); /* show_tool_name() is sane */ return 0; } void gt_toolbox_delete(GtToolbox *tb) { if (!tb) return; gt_hashmap_delete(tb->tools); gt_free(tb); } genometools-1.5.1/src/extended/toolbox.h000066400000000000000000000024761211610345200203030ustar00rootroot00000000000000/* Copyright (c) 2007-2011 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TOOLBOX_H #define TOOLBOX_H #include "core/error.h" #include "core/tool_api.h" #include "extended/toolbox_api.h" /* deprecated */ typedef int (*GtToolfunc)(int argc, const char **argv, GtError*); /* deprecated */ bool gt_toolbox_has_tool(const GtToolbox*, const char *toolname); /* deprecated */ void gt_toolbox_add(GtToolbox*, const char *toolname, GtToolfunc); /* deprecated */ GtToolfunc gt_toolbox_get(const GtToolbox*, const char *toolname); #endif genometools-1.5.1/src/extended/toolbox_api.h000066400000000000000000000041761211610345200211330ustar00rootroot00000000000000/* Copyright (c) 2007-2011 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TOOLBOX_API_H #define TOOLBOX_API_H #include "core/error_api.h" #include "core/tool_api.h" /* The class groups several tools into one and can be used to structure GenomeTools into sensible sets of subtools. */ typedef struct GtToolbox GtToolbox; /* Return a new empty . */ GtToolbox* gt_toolbox_new(void); /* Add with name to . Takes ownership of . */ void gt_toolbox_add_tool(GtToolbox *toolbox, const char *toolname, GtTool *tool); /* Add (hidden) with name to . Hidden tools are not shown in the output of . Takes ownership of . */ void gt_toolbox_add_hidden_tool(GtToolbox *toolbox, const char *toolname, GtTool *tool); /* Get with name from . Returns NULL if tool does not exist in . */ GtTool* gt_toolbox_get_tool(GtToolbox *toolbox, const char *toolname); /* Show all tools in except the hidden ones. Intended to be used as an argument to . */ int gt_toolbox_show(const char *progname, void *toolbox, GtError*); /* Deletes . */ void gt_toolbox_delete(GtToolbox *toolbox); #endif genometools-1.5.1/src/extended/transcript_bittabs.c000066400000000000000000000054601211610345200225050ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/ma.h" #include "extended/transcript_bittabs.h" struct GtTranscriptBittabs { GtBittab *gt_bittab_all, *gt_bittab_single, *gt_bittab_initial, *gt_bittab_internal, *gt_bittab_terminal; }; GtTranscriptBittabs* gt_transcript_bittabs_new(unsigned long size_all, unsigned long size_single, unsigned long size_initial, unsigned long size_internal, unsigned long size_terminal) { GtTranscriptBittabs *tb = gt_calloc(1, sizeof (GtTranscriptBittabs)); if (size_all) tb->gt_bittab_all = gt_bittab_new(size_all); if (size_single) tb->gt_bittab_single = gt_bittab_new(size_single); if (size_initial) tb->gt_bittab_initial = gt_bittab_new(size_initial); if (size_internal) tb->gt_bittab_internal = gt_bittab_new(size_internal); if (size_terminal) tb->gt_bittab_terminal = gt_bittab_new(size_all); return tb; } GtBittab* gt_transcript_bittabs_get_all(const GtTranscriptBittabs *tb) { gt_assert(tb); return tb->gt_bittab_all; } GtBittab* gt_transcript_bittabs_get_single(const GtTranscriptBittabs *tb) { gt_assert(tb); return tb->gt_bittab_single; } GtBittab* gt_transcript_bittabs_get_initial(const GtTranscriptBittabs *tb) { gt_assert(tb); return tb->gt_bittab_initial; } GtBittab* gt_transcript_bittabs_get_internal(const GtTranscriptBittabs *tb) { gt_assert(tb); return tb->gt_bittab_internal; } GtBittab* gt_transcript_bittabs_get_terminal(const GtTranscriptBittabs *tb) { gt_assert(tb); return tb->gt_bittab_terminal; } void gt_transcript_bittabs_delete(GtTranscriptBittabs *tb) { if (!tb) return; gt_bittab_delete(tb->gt_bittab_all); gt_bittab_delete(tb->gt_bittab_single); gt_bittab_delete(tb->gt_bittab_initial); gt_bittab_delete(tb->gt_bittab_internal); gt_bittab_delete(tb->gt_bittab_terminal); gt_free(tb); } genometools-1.5.1/src/extended/transcript_bittabs.h000066400000000000000000000045141211610345200225110ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TRANSCRIPT_BITTABS_H #define TRANSCRIPT_BITTABS_H #include "core/bittab.h" /* a container class for transcript bittabs */ typedef struct GtTranscriptBittabs GtTranscriptBittabs; /* create an empy container */ GtTranscriptBittabs* gt_transcript_bittabs_new(unsigned long size_all, unsigned long size_single, unsigned long size_initial, unsigned long size_internal, unsigned long size_terminal); /* return the bittab for all exons */ GtBittab* gt_transcript_bittabs_get_all(const GtTranscriptBittabs*); /* return the bittab for single exons */ GtBittab* gt_transcript_bittabs_get_single(const GtTranscriptBittabs*); /* return the bittab for initial exons */ GtBittab* gt_transcript_bittabs_get_initial(const GtTranscriptBittabs*); /* return the bittab for internal exons */ GtBittab* gt_transcript_bittabs_get_internal(const GtTranscriptBittabs*); /* return the bittab for terminal exons */ GtBittab* gt_transcript_bittabs_get_terminal(const GtTranscriptBittabs*); void gt_transcript_bittabs_delete(GtTranscriptBittabs*); #endif genometools-1.5.1/src/extended/transcript_counts.c000066400000000000000000000055141211610345200223700ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/ma.h" #include "extended/transcript_counts.h" struct GtTranscriptCounts { GtArray *exon_array_all, *exon_array_single, *exon_array_initial, *exon_array_internal, *exon_array_terminal; }; GtTranscriptCounts* gt_transcript_counts_new(void) { GtTranscriptCounts *tc = gt_calloc(1, sizeof (GtTranscriptCounts)); return tc; } GtArray* gt_transcript_counts_get_all(const GtTranscriptCounts *tc) { gt_assert(tc); return tc->exon_array_all; } void gt_transcript_counts_set_all(GtTranscriptCounts *tc, GtArray *counts) { gt_assert(tc && counts); tc->exon_array_all = counts; } GtArray* gt_transcript_counts_get_single(const GtTranscriptCounts *tc) { gt_assert(tc); return tc->exon_array_single; } void gt_transcript_counts_set_single(GtTranscriptCounts *tc, GtArray *counts) { gt_assert(tc && counts); tc->exon_array_single = counts; } GtArray* gt_transcript_counts_get_initial(const GtTranscriptCounts *tc) { gt_assert(tc); return tc->exon_array_initial; } void gt_transcript_counts_set_initial(GtTranscriptCounts *tc, GtArray *counts) { gt_assert(tc && counts); tc->exon_array_initial = counts; } GtArray* gt_transcript_counts_get_internal(const GtTranscriptCounts *tc) { gt_assert(tc); return tc->exon_array_internal; } void gt_transcript_counts_set_internal(GtTranscriptCounts *tc, GtArray *counts) { gt_assert(tc && counts); tc->exon_array_internal = counts; } GtArray* gt_transcript_counts_get_terminal(const GtTranscriptCounts *tc) { gt_assert(tc); return tc->exon_array_terminal; } void gt_transcript_counts_set_terminal(GtTranscriptCounts *tc, GtArray *counts) { gt_assert(tc && counts); tc->exon_array_terminal = counts; } void gt_transcript_counts_delete(GtTranscriptCounts *tc) { if (!tc) return; gt_array_delete(tc->exon_array_all); gt_array_delete(tc->exon_array_single); gt_array_delete(tc->exon_array_initial); gt_array_delete(tc->exon_array_internal); gt_array_delete(tc->exon_array_terminal); gt_free(tc); } genometools-1.5.1/src/extended/transcript_counts.h000066400000000000000000000042441211610345200223740ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TRANSCRIPT_COUNTS_H #define TRANSCRIPT_COUNTS_H #include "core/array.h" /* a container class for transcript count arrays */ typedef struct GtTranscriptCounts GtTranscriptCounts; /* create an empy container */ GtTranscriptCounts* gt_transcript_counts_new(void); /* return the count array for all exons */ GtArray* gt_transcript_counts_get_all(const GtTranscriptCounts*); void gt_transcript_counts_set_all(GtTranscriptCounts*, GtArray*); /* return the count array for single exons */ GtArray* gt_transcript_counts_get_single(const GtTranscriptCounts*); void gt_transcript_counts_set_single(GtTranscriptCounts*, GtArray*); /* return the count array for initial exons */ GtArray* gt_transcript_counts_get_initial(const GtTranscriptCounts*); void gt_transcript_counts_set_initial(GtTranscriptCounts*, GtArray*); /* return the count array for internal exons */ GtArray* gt_transcript_counts_get_internal(const GtTranscriptCounts*); void gt_transcript_counts_set_internal(GtTranscriptCounts*, GtArray*); /* return the count array for terminal exons */ GtArray* gt_transcript_counts_get_terminal(const GtTranscriptCounts*); void gt_transcript_counts_set_terminal(GtTranscriptCounts*, GtArray*); void gt_transcript_counts_delete(GtTranscriptCounts*); #endif genometools-1.5.1/src/extended/transcript_evaluators.c000066400000000000000000000072721211610345200232450ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/ma.h" #include "extended/transcript_evaluators.h" struct GtTranscriptEvaluators { GtEvaluator *exon_evaluator_all, *exon_evaluator_single, *exon_evaluator_initial, *exon_evaluator_internal, *exon_evaluator_terminal; }; GtTranscriptEvaluators* gt_transcript_evaluators_new(void) { GtTranscriptEvaluators *te = gt_malloc(sizeof (GtTranscriptEvaluators)); te->exon_evaluator_all = gt_evaluator_new(); te->exon_evaluator_single = gt_evaluator_new(); te->exon_evaluator_initial = gt_evaluator_new(); te->exon_evaluator_internal = gt_evaluator_new(); te->exon_evaluator_terminal = gt_evaluator_new(); return te; } GtEvaluator* gt_transcript_evaluators_get_all(const GtTranscriptEvaluators *te) { gt_assert(te); return te->exon_evaluator_all; } GtEvaluator* gt_transcript_evaluators_get_single(const GtTranscriptEvaluators *te) { gt_assert(te); return te->exon_evaluator_single; } GtEvaluator* gt_transcript_evaluators_get_initial(const GtTranscriptEvaluators *te) { gt_assert(te); return te->exon_evaluator_initial; } GtEvaluator* gt_transcript_evaluators_get_internal(const GtTranscriptEvaluators *te) { gt_assert(te); return te->exon_evaluator_internal; } GtEvaluator* gt_transcript_evaluators_get_terminal(const GtTranscriptEvaluators *te) { gt_assert(te); return te->exon_evaluator_terminal; } void gt_transcript_evaluators_add_actuals(const GtTranscriptEvaluators *evaluators, const GtTranscriptExons *exons) { gt_assert(evaluators && exons); gt_evaluator_add_actual(evaluators->exon_evaluator_all, gt_array_size(gt_transcript_exons_get_all(exons))); gt_evaluator_add_actual(evaluators->exon_evaluator_single, gt_array_size(gt_transcript_exons_get_single(exons))); gt_evaluator_add_actual(evaluators->exon_evaluator_initial, gt_array_size(gt_transcript_exons_get_initial(exons))); gt_evaluator_add_actual(evaluators->exon_evaluator_internal, gt_array_size(gt_transcript_exons_get_internal(exons))); gt_evaluator_add_actual(evaluators->exon_evaluator_terminal, gt_array_size(gt_transcript_exons_get_terminal(exons))); } void gt_transcript_evaluators_delete(GtTranscriptEvaluators *te) { if (!te) return; gt_evaluator_delete(te->exon_evaluator_all); gt_evaluator_delete(te->exon_evaluator_single); gt_evaluator_delete(te->exon_evaluator_initial); gt_evaluator_delete(te->exon_evaluator_internal); gt_evaluator_delete(te->exon_evaluator_terminal); gt_free(te); } genometools-1.5.1/src/extended/transcript_evaluators.h000066400000000000000000000046131211610345200232460ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TRANSCRIPT_EVALUATORS_H #define TRANSCRIPT_EVALUATORS_H #include "extended/evaluator.h" #include "extended/transcript_exons.h" /* a container class for transcript evaluators */ typedef struct GtTranscriptEvaluators GtTranscriptEvaluators; GtTranscriptEvaluators* gt_transcript_evaluators_new(void); /* return the evaluator for all exons */ GtEvaluator* gt_transcript_evaluators_get_all(const GtTranscriptEvaluators*); /* return the evaluator for single exons */ GtEvaluator* gt_transcript_evaluators_get_single(const GtTranscriptEvaluators*); /* return the evaluator for initial exons */ GtEvaluator* gt_transcript_evaluators_get_initial(const GtTranscriptEvaluators*); /* return the evaluator for internal exons */ GtEvaluator* gt_transcript_evaluators_get_internal(const GtTranscriptEvaluators*); /* return the evaluator for terminal exons */ GtEvaluator* gt_transcript_evaluators_get_terminal(const GtTranscriptEvaluators*); void gt_transcript_evaluators_add_actuals(const GtTranscriptEvaluators*, const GtTranscriptExons*); void gt_transcript_evaluators_delete(GtTranscriptEvaluators*); #endif genometools-1.5.1/src/extended/transcript_exons.c000066400000000000000000000107171211610345200222120ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/ma.h" #include "core/range.h" #include "extended/transcript_exons.h" struct GtTranscriptExons { GtArray *exon_array_all, *exon_array_single, *exon_array_initial, *exon_array_internal, *exon_array_terminal; }; GtTranscriptExons* gt_transcript_exons_new(void) { GtTranscriptExons *te = gt_malloc(sizeof (GtTranscriptExons)); te->exon_array_all = gt_array_new(sizeof (GtRange)); te->exon_array_single = gt_array_new(sizeof (GtRange)); te->exon_array_initial = gt_array_new(sizeof (GtRange)); te->exon_array_internal = gt_array_new(sizeof (GtRange)); te->exon_array_terminal = gt_array_new(sizeof (GtRange)); return te; } GtArray* gt_transcript_exons_get_all(const GtTranscriptExons *te) { gt_assert(te); return te->exon_array_all; } GtArray* gt_transcript_exons_get_single(const GtTranscriptExons *te) { gt_assert(te); return te->exon_array_single; } GtArray* gt_transcript_exons_get_initial(const GtTranscriptExons *te) { gt_assert(te); return te->exon_array_initial; } GtArray* gt_transcript_exons_get_internal(const GtTranscriptExons *te) { gt_assert(te); return te->exon_array_internal; } GtArray* gt_transcript_exons_get_terminal(const GtTranscriptExons *te) { gt_assert(te); return te->exon_array_terminal; } void gt_transcript_exons_sort(const GtTranscriptExons *te) { gt_assert(te); gt_ranges_sort(te->exon_array_all); gt_ranges_sort(te->exon_array_single); gt_ranges_sort(te->exon_array_initial); gt_ranges_sort(te->exon_array_internal); gt_ranges_sort(te->exon_array_terminal); } GtTranscriptCounts* gt_transcript_exons_uniq_in_place_count(GtTranscriptExons *te) { GtTranscriptCounts *tc; GtArray *counts; gt_assert(te); tc = gt_transcript_counts_new(); counts = gt_ranges_uniq_in_place_count(te->exon_array_all); gt_transcript_counts_set_all(tc, counts); counts = gt_ranges_uniq_in_place_count(te->exon_array_single); gt_transcript_counts_set_single(tc, counts); counts = gt_ranges_uniq_in_place_count(te->exon_array_initial); gt_transcript_counts_set_initial(tc, counts); counts = gt_ranges_uniq_in_place_count(te->exon_array_internal); gt_transcript_counts_set_internal(tc, counts); counts = gt_ranges_uniq_in_place_count(te->exon_array_terminal); gt_transcript_counts_set_terminal(tc, counts); return tc; } bool gt_transcript_exons_are_sorted(const GtTranscriptExons *te) { gt_assert(te); if (!gt_ranges_are_sorted(te->exon_array_all)) return false; if (!gt_ranges_are_sorted(te->exon_array_single)) return false; if (!gt_ranges_are_sorted(te->exon_array_initial)) return false; if (!gt_ranges_are_sorted(te->exon_array_internal)) return false; if (!gt_ranges_are_sorted(te->exon_array_terminal)) return false; return true; } GtTranscriptBittabs* gt_transcript_exons_create_bittabs(const GtTranscriptExons *te) { gt_assert(te); return gt_transcript_bittabs_new(gt_array_size(te->exon_array_all), gt_array_size(te->exon_array_single), gt_array_size(te->exon_array_initial), gt_array_size(te->exon_array_internal), gt_array_size(te->exon_array_terminal)); } void gt_transcript_exons_delete(GtTranscriptExons *te) { if (!te) return; gt_array_delete(te->exon_array_all); gt_array_delete(te->exon_array_single); gt_array_delete(te->exon_array_initial); gt_array_delete(te->exon_array_internal); gt_array_delete(te->exon_array_terminal); gt_free(te); } genometools-1.5.1/src/extended/transcript_exons.h000066400000000000000000000041771211610345200222220ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TRANSCRIPT_EXONS_H #define TRANSCRIPT_EXONS_H #include "extended/transcript_bittabs.h" #include "extended/transcript_counts.h" /* a container class for transcript exon arrays */ typedef struct GtTranscriptExons GtTranscriptExons; GtTranscriptExons* gt_transcript_exons_new(void); /* return the exon array for all exons */ GtArray* gt_transcript_exons_get_all(const GtTranscriptExons*); /* return the exon array for single exons */ GtArray* gt_transcript_exons_get_single(const GtTranscriptExons*); /* return the exon array for initial exons */ GtArray* gt_transcript_exons_get_initial(const GtTranscriptExons*); /* return the exon array for internal exons */ GtArray* gt_transcript_exons_get_internal(const GtTranscriptExons*); /* return the exon array for terminal exons */ GtArray* gt_transcript_exons_get_terminal(const GtTranscriptExons*); void gt_transcript_exons_sort(const GtTranscriptExons*); GtTranscriptCounts* gt_transcript_exons_uniq_in_place_count(GtTranscriptExons*); bool gt_transcript_exons_are_sorted(const GtTranscriptExons*); GtTranscriptBittabs* gt_transcript_exons_create_bittabs(const GtTranscriptExons*); void gt_transcript_exons_delete(GtTranscriptExons*); #endif genometools-1.5.1/src/extended/transcript_feature_type.h000066400000000000000000000022021211610345200235450ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TRANSCRIPT_FEATURE_TYPE_H #define TRANSCRIPT_FEATURE_TYPE_H typedef enum { TRANSCRIPT_FEATURE_TYPE_SINGLE, TRANSCRIPT_FEATURE_TYPE_INITIAL, TRANSCRIPT_FEATURE_TYPE_INTERNAL, TRANSCRIPT_FEATURE_TYPE_TERMINAL, TRANSCRIPT_FEATURE_TYPE_UNDETERMINED } GtTranscriptFeatureType; #endif genometools-1.5.1/src/extended/transcript_used_exons.c000066400000000000000000000055351211610345200232340ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/ma.h" #include "core/range.h" #include "extended/transcript_used_exons.h" struct GtTranscriptUsedExons { GtDlist *used_exons_all, *used_exons_single, *used_exons_initial, *used_exons_internal, *used_exons_terminal; }; GtTranscriptUsedExons* gt_transcript_used_exons_new(void) { GtTranscriptUsedExons *tue = gt_malloc(sizeof (GtTranscriptUsedExons)); tue->used_exons_all = gt_dlist_new((GtCompare) gt_range_compare); tue->used_exons_single = gt_dlist_new((GtCompare) gt_range_compare); tue->used_exons_initial = gt_dlist_new((GtCompare) gt_range_compare); tue->used_exons_internal = gt_dlist_new((GtCompare) gt_range_compare); tue->used_exons_terminal = gt_dlist_new((GtCompare) gt_range_compare); return tue; } GtDlist* gt_transcript_used_exons_get_all(GtTranscriptUsedExons *tue) { gt_assert(tue); return tue->used_exons_all; } GtDlist* gt_transcript_used_exons_get_single(GtTranscriptUsedExons *tue) { gt_assert(tue); return tue->used_exons_single; } GtDlist* gt_transcript_used_exons_get_initial(GtTranscriptUsedExons *tue) { gt_assert(tue); return tue->used_exons_initial; } GtDlist* gt_transcript_used_exons_get_internal(GtTranscriptUsedExons *tue) { gt_assert(tue); return tue->used_exons_internal; } GtDlist* gt_transcript_used_exons_get_terminal(GtTranscriptUsedExons *tue) { gt_assert(tue); return tue->used_exons_terminal; } static void used_gt_dlist_delete(GtDlist *used_list) { GtDlistelem *dlistelem; for (dlistelem = gt_dlist_first(used_list); dlistelem != NULL; dlistelem = gt_dlistelem_next(dlistelem)) { gt_free(gt_dlistelem_get_data(dlistelem)); } gt_dlist_delete(used_list); } void gt_transcript_used_exons_delete(GtTranscriptUsedExons *tue) { if (!tue) return; used_gt_dlist_delete(tue->used_exons_all); used_gt_dlist_delete(tue->used_exons_single); used_gt_dlist_delete(tue->used_exons_initial); used_gt_dlist_delete(tue->used_exons_internal); used_gt_dlist_delete(tue->used_exons_terminal); gt_free(tue); } genometools-1.5.1/src/extended/transcript_used_exons.h000066400000000000000000000030111211610345200232240ustar00rootroot00000000000000/* Copyright (c) 2007 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TRANSCRIPT_USED_EXONS_H #define TRANSCRIPT_USED_EXONS_H #include "core/dlist.h" typedef struct GtTranscriptUsedExons GtTranscriptUsedExons; GtTranscriptUsedExons* gt_transcript_used_exons_new(void); GtDlist* gt_transcript_used_exons_get_all(GtTranscriptUsedExons*); GtDlist* gt_transcript_used_exons_get_single(GtTranscriptUsedExons*); GtDlist* gt_transcript_used_exons_get_initial(GtTranscriptUsedExons*); GtDlist* gt_transcript_used_exons_get_internal(GtTranscriptUsedExons*); GtDlist* gt_transcript_used_exons_get_terminal(GtTranscriptUsedExons*); void gt_transcript_used_exons_delete(GtTranscriptUsedExons*); #endif genometools-1.5.1/src/extended/type_checker.c000066400000000000000000000056151211610345200212530ustar00rootroot00000000000000/* Copyright (c) 2008, 2012 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/ma.h" #include "core/unused_api.h" #include "extended/type_checker_rep.h" GtTypeChecker* gt_type_checker_create(const GtTypeCheckerClass *type_checker_class) { GtTypeChecker *type_checker; gt_assert(type_checker_class && type_checker_class->size); type_checker = gt_calloc(1, type_checker_class->size); type_checker->c_class = type_checker_class; return type_checker; } GtTypeChecker* gt_type_checker_ref(GtTypeChecker *type_checker) { gt_assert(type_checker); type_checker->reference_count++; return type_checker; } const char* gt_type_checker_description(GtTypeChecker *type_checker) { gt_assert(type_checker && type_checker->c_class && type_checker->c_class->description); return type_checker->c_class->description(type_checker); } bool gt_type_checker_is_valid(GtTypeChecker *type_checker, const char *type) { gt_assert(type_checker && type_checker->c_class && type_checker->c_class->is_valid); return type_checker->c_class->is_valid(type_checker, type); } bool gt_type_checker_is_partof(GtTypeChecker *type_checker, const char *parent_type, const char *child_type) { gt_assert(type_checker && type_checker->c_class && type_checker->c_class->is_partof); return type_checker->c_class->is_partof(type_checker, parent_type, child_type); } void gt_type_checker_delete(GtTypeChecker *type_checker) { if (!type_checker) return; if (type_checker->reference_count) { type_checker->reference_count--; return; } gt_assert(type_checker->c_class); if (type_checker->c_class->free) type_checker->c_class->free(type_checker); gt_free(type_checker); } void* gt_type_checker_cast(GT_UNUSED const GtTypeCheckerClass *type_checker_class, GtTypeChecker *type_checker) { gt_assert(type_checker_class && type_checker && type_checker->c_class == type_checker_class); return type_checker; } genometools-1.5.1/src/extended/type_checker.h000066400000000000000000000017701211610345200212560ustar00rootroot00000000000000/* Copyright (c) 2008, 2011 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TYPE_CHECKER_H #define TYPE_CHECKER_H #include "extended/type_checker_api.h" typedef struct GtTypeCheckerClass GtTypeCheckerClass; #endif genometools-1.5.1/src/extended/type_checker_api.h000066400000000000000000000037371211610345200221140ustar00rootroot00000000000000/* Copyright (c) 2008, 2011-2012 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TYPE_CHECKER_API_H #define TYPE_CHECKER_API_H /* The interface, allows one to check the validity of (genome feature) types. */ typedef struct GtTypeChecker GtTypeChecker; /* Increase the reference count for and return it. */ GtTypeChecker* gt_type_checker_ref(GtTypeChecker *type_checker); /* Return description of . */ const char* gt_type_checker_description(GtTypeChecker *type_checker); /* Return if is a valid type for the given , otherwise. */ bool gt_type_checker_is_valid(GtTypeChecker *type_checker, const char *type); /* Return if is partof , otherwise. */ bool gt_type_checker_is_partof(GtTypeChecker *type_checker, const char *parent_type, const char *child_type); /* Decrease the reference count for or delete it, if this was the last reference. */ void gt_type_checker_delete(GtTypeChecker *type_checker); #endif genometools-1.5.1/src/extended/type_checker_builtin.c000066400000000000000000000071121211610345200227730ustar00rootroot00000000000000/* Copyright (c) 2008, 2012-2013 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include #include "core/assert_api.h" #include "core/hashtable.h" #include "core/ma.h" #include "core/strcmp.h" #include "extended/type_checker_builtin.h" #include "extended/type_checker_rep.h" struct GtTypeCheckerBuiltin { const GtTypeChecker parent_instance; }; #define gt_type_checker_builtin_cast(FTF)\ gt_type_checker_cast(gt_type_checker_builtin_class(), FTF) static const char *gt_feature_node_type_strings[] = { "CDS", "EST_match", "LTR_retrotransposon", "SNP", "TF_binding_site", "cDNA_match", "exon", "five_prime_UTR", "five_prime_cis_splice_site", "gene", "intron", "inverted_repeat", "long_terminal_repeat", "mRNA", "protein_match", "repeat_region", "target_site_duplication", "three_prime_UTR", "three_prime_cis_splice_site", "transcript", "undefined" }; static const char* type_checker_builtin_find_type(const char *gft_string) { void *result; gt_assert(gft_string); /* do not convert undefined string */ gt_assert(strcmp(gft_string, "undefined")); result = bsearch(&gft_string, gt_feature_node_type_strings, sizeof (gt_feature_node_type_strings) / sizeof (gt_feature_node_type_strings[0]), sizeof (char*), gt_strcmpptr); if (result) return *(char**) result; return NULL; } static const char* gt_type_checker_builtin_description(GT_UNUSED GtTypeChecker *tc) { gt_assert(tc); return "built-in"; } static bool gt_type_checker_builtin_is_valid(GT_UNUSED GtTypeChecker *tc, const char *type) { gt_assert(tc && type); return type_checker_builtin_find_type(type) ? true : false; } static bool gt_type_checker_builtin_is_partof(GT_UNUSED GtTypeChecker *tc, GT_UNUSED const char *parent_type, GT_UNUSED const char *child_type) { gt_assert(tc && parent_type && child_type); return true; } const GtTypeCheckerClass* gt_type_checker_builtin_class(void) { static const GtTypeCheckerClass gt_type_checker_class = { sizeof (GtTypeCheckerBuiltin), gt_type_checker_builtin_description, gt_type_checker_builtin_is_valid, gt_type_checker_builtin_is_partof, NULL }; return >_type_checker_class; } GtTypeChecker* gt_type_checker_builtin_new(void) { GT_UNUSED GtTypeCheckerBuiltin *type_checker_builtin; GtTypeChecker *type_checker; type_checker = gt_type_checker_create(gt_type_checker_builtin_class()); type_checker_builtin = gt_type_checker_builtin_cast(type_checker); return type_checker; } genometools-1.5.1/src/extended/type_checker_builtin.h000066400000000000000000000022671211610345200230060ustar00rootroot00000000000000/* Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TYPE_CHECKER_BUILTIN_H #define TYPE_CHECKER_BUILTIN_H #include "extended/type_checker.h" /* Implements the GtTypeChecker interface with built-in types. */ typedef struct GtTypeCheckerBuiltin GtTypeCheckerBuiltin; const GtTypeCheckerClass* gt_type_checker_builtin_class(void); GtTypeChecker* gt_type_checker_builtin_new(); #endif genometools-1.5.1/src/extended/type_checker_obo.c000066400000000000000000000120331211610345200221020ustar00rootroot00000000000000/* Copyright (c) 2008, 2012 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include "core/cstr_api.h" #include "core/cstr_table.h" #include "core/ma.h" #include "extended/obo_parse_tree.h" #include "extended/type_checker_obo.h" #include "extended/type_checker_rep.h" #include "extended/type_graph.h" struct GtTypeCheckerOBO { const GtTypeChecker parent_instance; GtStr *description; GtCstrTable *feature_node_types; GtTypeGraph *type_graph; }; #define gt_type_checker_obo_cast(FTF)\ gt_type_checker_cast(gt_type_checker_obo_class(), FTF) static void gt_type_checker_obo_free(GtTypeChecker *tc) { GtTypeCheckerOBO *tco = gt_type_checker_obo_cast(tc); gt_type_graph_delete(tco->type_graph); gt_cstr_table_delete(tco->feature_node_types); gt_str_delete(tco->description); } static const char* gt_type_checker_obo_description(GtTypeChecker *tc) { GtTypeCheckerOBO *tco; gt_assert(tc); tco = gt_type_checker_obo_cast(tc); return gt_str_get(tco->description); } static bool gt_type_checker_obo_is_valid(GtTypeChecker *tc, const char *type) { GtTypeCheckerOBO *tco; gt_assert(tc && type); tco = gt_type_checker_obo_cast(tc); return gt_cstr_table_get(tco->feature_node_types, type) ? true : false; } static bool gt_type_checker_obo_is_partof(GtTypeChecker *tc, const char *parent_type, const char *child_type) { GtTypeCheckerOBO *tco; gt_assert(tc && parent_type && child_type); tco = gt_type_checker_obo_cast(tc); return gt_type_graph_is_partof(tco->type_graph, parent_type, child_type); } const GtTypeCheckerClass* gt_type_checker_obo_class(void) { static const GtTypeCheckerClass gt_type_checker_class = { sizeof (GtTypeCheckerOBO), gt_type_checker_obo_description, gt_type_checker_obo_is_valid, gt_type_checker_obo_is_partof, gt_type_checker_obo_free }; return >_type_checker_class; } static void add_feature_node_from_tree(GtTypeCheckerOBO *tco, GtOBOParseTree *obo_parse_tree, unsigned long stanza_num, const char *stanza_key) { const char *value; gt_assert(tco && obo_parse_tree && stanza_key); value = gt_obo_parse_tree_get_stanza_value(obo_parse_tree, stanza_num, stanza_key); /* do not add values multiple times (possible for "name" values) */ if (!gt_cstr_table_get(tco->feature_node_types, value)) gt_cstr_table_add(tco->feature_node_types, value); else puts(value); } static int create_feature_nodes(GtTypeCheckerOBO *tco, const char *obo_file_path, GtError *err) { GtOBOParseTree *obo_parse_tree; unsigned long i; gt_error_check(err); gt_assert(tco && obo_file_path); if ((obo_parse_tree = gt_obo_parse_tree_new(obo_file_path, err))) { for (i = 0; i < gt_obo_parse_tree_num_of_stanzas(obo_parse_tree); i++) { if (!strcmp(gt_obo_parse_tree_get_stanza_type(obo_parse_tree, i), "Term")) { const char *is_obsolete = gt_obo_parse_tree_get_stanza_value(obo_parse_tree, i, "is_obsolete"); /* do not add obsolete types */ if (!is_obsolete || strcmp(is_obsolete, "true")) { const GtOBOStanza *stanza; add_feature_node_from_tree(tco, obo_parse_tree, i, "id"); add_feature_node_from_tree(tco, obo_parse_tree, i, "name"); stanza = gt_obo_parse_tree_get_stanza(obo_parse_tree, i); gt_type_graph_add_stanza(tco->type_graph, stanza); } } } gt_obo_parse_tree_delete(obo_parse_tree); return 0; } return -1; } GtTypeChecker* gt_type_checker_obo_new(const char *obo_file_path, GtError *err) { GtTypeCheckerOBO *tco; GtTypeChecker *tc; gt_error_check(err); gt_assert(obo_file_path); tc = gt_type_checker_create(gt_type_checker_obo_class()); tco = gt_type_checker_obo_cast(tc); tco->description= gt_str_new_cstr("OBO file "); gt_str_append_cstr(tco->description, obo_file_path); tco->feature_node_types = gt_cstr_table_new(); tco->type_graph = gt_type_graph_new(); if (create_feature_nodes(tco, obo_file_path, err)) { gt_type_checker_delete(tc); return NULL; } return tc; } genometools-1.5.1/src/extended/type_checker_obo.h000066400000000000000000000020401211610345200221040ustar00rootroot00000000000000/* Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TYPE_CHECKER_OBO_H #define TYPE_CHECKER_OBO_H #include "extended/type_checker_obo_api.h" #include "extended/type_checker.h" const GtTypeCheckerClass* gt_type_checker_obo_class(void); #endif genometools-1.5.1/src/extended/type_checker_obo_api.h000066400000000000000000000025201211610345200227400ustar00rootroot00000000000000/* Copyright (c) 2008, 2011 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TYPE_CHECKER_OBO_API_H #define TYPE_CHECKER_OBO_API_H #include "extended/type_checker_api.h" /* Implements the interface with types from an OBO file. */ typedef struct GtTypeCheckerOBO GtTypeCheckerOBO; /* Create a new for OBO file with given . If the OBO file cannot be parsed correctly, is returned and is set correspondingly. */ GtTypeChecker* gt_type_checker_obo_new(const char *obo_file_path, GtError *err); #endif genometools-1.5.1/src/extended/type_checker_rep.h000066400000000000000000000031041211610345200221150ustar00rootroot00000000000000/* Copyright (c) 2008, 2012 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TYPE_CHECKER_REP_H #define TYPE_CHECKER_REP_H #include #include "core/cstr_table.h" #include "extended/feature_type.h" #include "extended/type_checker.h" struct GtTypeCheckerClass { size_t size; const char* (*description)(GtTypeChecker*); bool (*is_valid)(GtTypeChecker*, const char *type); bool (*is_partof)(GtTypeChecker*, const char *parent_type, const char *child_type); void (*free)(GtTypeChecker*); }; struct GtTypeChecker { const GtTypeCheckerClass *c_class; unsigned int reference_count; }; GtTypeChecker* gt_type_checker_create(const GtTypeCheckerClass*); void* gt_type_checker_cast(const GtTypeCheckerClass*, GtTypeChecker*); #endif genometools-1.5.1/src/extended/type_graph.c000066400000000000000000000156461211610345200207550ustar00rootroot00000000000000/* Copyright (c) 2012-2013 Gordon Gremme Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include "core/array_api.h" #include "core/bool_matrix.h" #include "core/cstr_api.h" #include "core/hashmap_api.h" #include "core/ma_api.h" #include "core/symbol_api.h" #include "extended/type_graph.h" #include "extended/type_node.h" #define PART_OF "part_of" #define MEMBER_OF "member_of" #define INTEGRAL_PART_OF "integral_part_of" struct GtTypeGraph { GtHashmap *name2id, /* maps from name to SO ID */ *nodemap; /* maps SO ID to actual node */ GtArray *nodes; GtBoolMatrix *part_of_out_edges, *part_of_in_edges; bool ready; }; GtTypeGraph* gt_type_graph_new(void) { GtTypeGraph *type_graph = gt_malloc(sizeof (GtTypeGraph)); type_graph->name2id = gt_hashmap_new(GT_HASH_DIRECT, NULL, NULL); type_graph->nodemap = gt_hashmap_new(GT_HASH_DIRECT, NULL, NULL); type_graph->nodes = gt_array_new(sizeof (GtTypeNode*)); type_graph->part_of_out_edges = gt_bool_matrix_new(); type_graph->part_of_in_edges = gt_bool_matrix_new(); type_graph->ready = false; return type_graph; } void gt_type_graph_delete(GtTypeGraph *type_graph) { unsigned long i; if (!type_graph) return; gt_bool_matrix_delete(type_graph->part_of_in_edges); gt_bool_matrix_delete(type_graph->part_of_out_edges); for (i = 0; i < gt_array_size(type_graph->nodes); i++) gt_type_node_delete(*(GtTypeNode**) gt_array_get(type_graph->nodes, i)); gt_array_delete(type_graph->nodes); gt_hashmap_delete(type_graph->nodemap); gt_hashmap_delete(type_graph->name2id); gt_free(type_graph); } void gt_type_graph_add_stanza(GtTypeGraph *type_graph, const GtOBOStanza *stanza) { const char *id_value, *name_value; unsigned long i, size; GtTypeNode *node; GtStr *buf; gt_assert(type_graph && stanza && !type_graph->ready); gt_assert(gt_obo_stanza_size(stanza, "id") == 1); gt_assert(gt_obo_stanza_size(stanza, "name") == 1); id_value = gt_symbol(gt_obo_stanza_get_value(stanza, "id", 0)); name_value = gt_symbol(gt_obo_stanza_get_value(stanza, "name", 0)); gt_assert(id_value); gt_assert(name_value); gt_assert(!gt_hashmap_get(type_graph->nodemap, id_value)); node = gt_type_node_new(gt_array_size(type_graph->nodes), id_value); gt_hashmap_add(type_graph->name2id, (char*) name_value, (char*) id_value); gt_hashmap_add(type_graph->nodemap, (char*) id_value, node); gt_array_add(type_graph->nodes, node); buf = gt_str_new(); /* store is_a entries in node, if necessary */ if ((size = gt_obo_stanza_size(stanza, "is_a"))) { for (i = 0; i < size; i++) { const char *id = gt_obo_stanza_get_value(stanza, "is_a", i); gt_str_reset(buf); gt_str_append_cstr_nt(buf, id, strcspn(id, " \n")); gt_type_node_is_a_add(node, gt_symbol(gt_str_get(buf))); } } /* store part_of entries in node, if necessary */ if ((size = gt_obo_stanza_size(stanza, "relationship"))) { for (i = 0; i < size; i++) { const char *rel = gt_obo_stanza_get_value(stanza, "relationship", i); gt_str_reset(buf); /* match part_of */ if (!strncmp(rel, PART_OF, strlen(PART_OF))) { const char *part_of = rel + strlen(PART_OF) + 1; gt_str_append_cstr_nt(buf, part_of, strcspn(part_of, " \n")); gt_type_node_part_of_add(node, gt_symbol(gt_str_get(buf))); continue; } /* match member_of */ if (!strncmp(rel, MEMBER_OF, strlen(MEMBER_OF))) { const char *member_of = rel + strlen(MEMBER_OF) + 1; gt_str_append_cstr_nt(buf, member_of, strcspn(member_of, " \n")); gt_type_node_part_of_add(node, gt_symbol(gt_str_get(buf))); continue; } /* match integral_part_of */ if (!strncmp(rel, INTEGRAL_PART_OF, strlen(INTEGRAL_PART_OF))) { const char *integral_part_of = rel + strlen(INTEGRAL_PART_OF) + 1; gt_str_append_cstr_nt(buf, integral_part_of, strcspn(integral_part_of, " \n")); gt_type_node_part_of_add(node, gt_symbol(gt_str_get(buf))); } } } gt_str_delete(buf); } static void create_vertices(GtTypeGraph *type_graph) { unsigned long i, j; GtTypeNode *parent; const char *id; gt_assert(type_graph && !type_graph->ready); /* iterate over nodes */ for (i = 0; i < gt_array_size(type_graph->nodes); i++) { GtTypeNode *node = *(GtTypeNode**) gt_array_get(type_graph->nodes, i); /* process is_a parents */ for (j = 0; j < gt_type_node_is_a_size(node); j++) { id = gt_type_node_is_a_get(node, j); parent = gt_hashmap_get(type_graph->nodemap, id); gt_assert(parent); gt_type_node_add_is_a_vertex(node, parent); } /* process part_of parents */ for (j = 0; j < gt_type_node_part_of_size(node); j++) { id = gt_type_node_part_of_get(node, j); parent = gt_hashmap_get(type_graph->nodemap, id); gt_assert(parent); gt_bool_matrix_set(type_graph->part_of_out_edges, gt_type_node_num(node), gt_type_node_num(parent), true); gt_bool_matrix_set(type_graph->part_of_in_edges, gt_type_node_num(parent), gt_type_node_num(node), true); } } } bool gt_type_graph_is_partof(GtTypeGraph *type_graph, const char *parent_type, const char *child_type) { const char *parent_id, *child_id; GtTypeNode *child_node; gt_assert(type_graph && parent_type && child_type); /* make sure graph is built */ if (!type_graph->ready) { create_vertices(type_graph); type_graph->ready = true; } /* get parent ID, if the type is not mappable to an ID, assume it is the ID */ if (!(parent_id = gt_hashmap_get(type_graph->name2id, parent_type))) parent_id = parent_type; /* get child ID, if the type is not mappable to an ID, assmue it is the ID */ if (!(child_id = gt_hashmap_get(type_graph->name2id, child_type))) child_id = child_type; /* get child node */ child_node = gt_hashmap_get(type_graph->nodemap, child_id); gt_assert(child_node); /* check for parent */ return gt_type_node_has_parent(child_node, parent_id, type_graph->part_of_out_edges, type_graph->part_of_in_edges, type_graph->nodes); } genometools-1.5.1/src/extended/type_graph.h000066400000000000000000000024651211610345200207550ustar00rootroot00000000000000/* Copyright (c) 2012-2013 Gordon Gremme Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TYPE_GRAPH_H #define TYPE_GRAPH_H #include "extended/obo_stanza.h" typedef struct GtTypeGraph GtTypeGraph; GtTypeGraph* gt_type_graph_new(void); void gt_type_graph_delete(GtTypeGraph *type_graph); void gt_type_graph_add_stanza(GtTypeGraph *type_graph, const GtOBOStanza *obo_stanza); bool gt_type_graph_is_partof(GtTypeGraph *type_graph, const char *parent_type, const char *child_type); #endif genometools-1.5.1/src/extended/type_node.c000066400000000000000000000150231211610345200205660ustar00rootroot00000000000000/* Copyright (c) 2012-2013 Gordon Gremme Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include #include "core/array_api.h" #include "core/hashmap_api.h" #include "core/log_api.h" #include "core/ma_api.h" #include "extended/type_node.h" struct GtTypeNode { unsigned long num; const char *id; GtArray *is_a_list, *part_of_list; GtArray *is_a_out_edges; GtHashmap *cache; }; GtTypeNode* gt_type_node_new(unsigned long num, const char *id) { GtTypeNode *node = gt_calloc(1, sizeof *node); node->num = num; node->id = id; return node; } void gt_type_node_delete(GtTypeNode *type_node) { if (!type_node) return; gt_hashmap_delete(type_node->cache); gt_array_delete(type_node->is_a_out_edges); gt_array_delete(type_node->part_of_list); gt_array_delete(type_node->is_a_list); gt_free(type_node); } unsigned long gt_type_node_num(const GtTypeNode *type_node) { gt_assert(type_node); return type_node->num; } void gt_type_node_is_a_add(GtTypeNode *type_node, const char *id) { gt_assert(type_node && id); if (!type_node->is_a_list) type_node->is_a_list = gt_array_new(sizeof (const char*)); gt_array_add(type_node->is_a_list, id); } const char* gt_type_node_is_a_get(const GtTypeNode *type_node, unsigned long idx) { gt_assert(type_node && idx < gt_type_node_is_a_size(type_node)); return *(const char**) gt_array_get(type_node->is_a_list, idx); } unsigned long gt_type_node_is_a_size(const GtTypeNode *type_node) { gt_assert(type_node); return (type_node->is_a_list) ? gt_array_size(type_node->is_a_list) : 0; } void gt_type_node_part_of_add(GtTypeNode *type_node, const char *id) { gt_assert(type_node && id); if (!type_node->part_of_list) type_node->part_of_list = gt_array_new(sizeof (const char*)); gt_array_add(type_node->part_of_list, id); } const char* gt_type_node_part_of_get(const GtTypeNode *type_node, unsigned long idx) { gt_assert(type_node && idx < gt_type_node_part_of_size(type_node)); return *(const char**) gt_array_get(type_node->part_of_list, idx); } unsigned long gt_type_node_part_of_size(const GtTypeNode *type_node) { gt_assert(type_node); return (type_node->part_of_list) ? gt_array_size(type_node->part_of_list) : 0; } void gt_type_node_add_is_a_vertex(GtTypeNode *src, const GtTypeNode *dst) { gt_assert(src && dst); if (!src->is_a_out_edges) src->is_a_out_edges = gt_array_new(sizeof (GtTypeNode*)); gt_array_add(src->is_a_out_edges, dst); } static void create_transitive_part_of_edges(GtTypeNode *node, GtBoolMatrix *part_of_out_edges, GtBoolMatrix *part_of_in_edges, GtArray *node_stack) { unsigned long i, j; if (gt_array_size(node_stack)) { for (i = gt_bool_matrix_get_first_column(part_of_in_edges, node->num); i != gt_bool_matrix_get_last_column(part_of_in_edges, node->num); i = gt_bool_matrix_get_next_column(part_of_in_edges, node->num, i)) { for (j = 0; j < gt_array_size(node_stack); j++) { GtTypeNode *child = *(GtTypeNode**) gt_array_get(node_stack, j); gt_bool_matrix_set(part_of_out_edges, i, child->num, true); gt_bool_matrix_set(part_of_in_edges, child->num, i, true); } } } gt_array_add(node_stack, node); for (i = 0; i < gt_array_size(node->is_a_out_edges); i++) { GtTypeNode *parent = *(GtTypeNode**) gt_array_get(node->is_a_out_edges, i); create_transitive_part_of_edges(parent, part_of_out_edges, part_of_in_edges, node_stack); } gt_array_pop(node_stack); } bool gt_type_node_has_parent(GtTypeNode *node, const char *id, GtBoolMatrix *part_of_out_edges, GtBoolMatrix *part_of_in_edges, GtArray *node_list) { GtArray *node_stack; GtTypeNode *parent; unsigned long i; bool *result; gt_assert(node && id); gt_log_log("check if node %s has parent %s", node->id, id); /* try cache */ if (node->cache) { if ((result = gt_hashmap_get(node->cache, id))) return *result; } else node->cache = gt_hashmap_new(GT_HASH_DIRECT, NULL, gt_free_func); result = gt_malloc(sizeof (bool)); /* no cache hit found */ if (node->id == id) { *result = true; gt_hashmap_add(node->cache, (char*) id, result); gt_log_log("return true"); return true; } /* create transitive part_of edges */ node_stack = gt_array_new(sizeof (GtTypeNode*)); create_transitive_part_of_edges(node, part_of_out_edges, part_of_in_edges, node_stack); gt_assert(!gt_array_size(node_stack)); gt_array_delete(node_stack); /* traversal of part_of out edges */ for (i = gt_bool_matrix_get_first_column(part_of_out_edges, node->num); i != gt_bool_matrix_get_last_column(part_of_out_edges, node->num); i = gt_bool_matrix_get_next_column(part_of_out_edges, node->num, i)) { parent = *(GtTypeNode**) gt_array_get(node_list, i); if (gt_type_node_has_parent(parent, id, part_of_out_edges, part_of_in_edges, node_list)) { *result = true; gt_hashmap_add(node->cache, (char*) id, result); gt_log_log("return true"); return true; } } /* traversal of is_a out edges */ for (i = 0; i < gt_array_size(node->is_a_out_edges); i++) { parent = *(GtTypeNode**) gt_array_get(node->is_a_out_edges, i); if (gt_type_node_has_parent(parent, id, part_of_out_edges, part_of_in_edges, node_list)) { *result = true; gt_hashmap_add(node->cache, (char*) id, result); gt_log_log("return true"); return true; } } /* no result found */ *result = false; gt_hashmap_add(node->cache, (char*) id, result); return false; } genometools-1.5.1/src/extended/type_node.h000066400000000000000000000035041211610345200205740ustar00rootroot00000000000000/* Copyright (c) 2012-2013 Gordon Gremme Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TYPE_NODE_H #define TYPE_NODE_H #include "core/bool_matrix.h" typedef struct GtTypeNode GtTypeNode; GtTypeNode* gt_type_node_new(unsigned long num, const char *id); void gt_type_node_delete(GtTypeNode*); unsigned long gt_type_node_num(const GtTypeNode*); void gt_type_node_is_a_add(GtTypeNode*, const char*); const char* gt_type_node_is_a_get(const GtTypeNode*, unsigned long); unsigned long gt_type_node_is_a_size(const GtTypeNode*); void gt_type_node_part_of_add(GtTypeNode*, const char*); const char* gt_type_node_part_of_get(const GtTypeNode*, unsigned long); unsigned long gt_type_node_part_of_size(const GtTypeNode*); void gt_type_node_add_is_a_vertex(GtTypeNode *src, const GtTypeNode *dst); bool gt_type_node_has_parent(GtTypeNode*, const char *id, GtBoolMatrix *part_of_out_edges, GtBoolMatrix *part_of_in_edges, GtArray *node_list); #endif genometools-1.5.1/src/extended/typecheck_info.c000066400000000000000000000114311211610345200215710ustar00rootroot00000000000000/* Copyright (c) 2013 Gordon Gremme Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/cstr_api.h" #include "core/error.h" #include "core/fileutils.h" #include "core/gtdatapath.h" #include "core/ma_api.h" #include "extended/typecheck_info.h" #include "extended/type_checker_builtin.h" #include "extended/type_checker_obo.h" struct GtTypecheckInfo { GtStr *typecheck; GtOption *typecheck_option; bool typecheck_built_in; }; GtTypecheckInfo* gt_typecheck_info_new(void) { GtTypecheckInfo *tci = gt_calloc(1, sizeof *tci); tci->typecheck = gt_str_new(); return tci; } void gt_typecheck_info_delete(GtTypecheckInfo *tci) { if (!tci) return; gt_option_delete(tci->typecheck_option); gt_str_delete(tci->typecheck); gt_free(tci); } void gt_typecheck_info_register_options(GtTypecheckInfo *tci, GtOptionParser *op) { GtOption *typecheck_option, *built_in_option; gt_assert(tci && op); gt_assert(!tci->typecheck_option); /* can only called once */ /* -typecheck */ typecheck_option = gt_option_new_string("typecheck", "check GFF3 types against \"id\" and " "\"name\" tags in given OBO file and validate parent " "(part-of) relationships.\nIf no argument is given, " "the sofa.obo file from the gtdata/obo_files " "directory is used.\nIf an argument is given, it is " "used as an OBO filename.\nIn the case that such a " "file does not exist '.obo' is added to the argument " "and loading the resulting filename from the " "gtdata/obo_files directory is attempted.", tci->typecheck, NULL); gt_option_argument_is_optional(typecheck_option); gt_option_parser_add_option(op, typecheck_option); tci->typecheck_option = gt_option_ref(typecheck_option); /* -typecheck-built-in */ built_in_option = gt_option_new_bool("typecheck-built-in", "use built-in type checker", &tci->typecheck_built_in, false); gt_option_is_development_option(built_in_option); gt_option_parser_add_option(op, built_in_option); gt_option_exclude(typecheck_option, built_in_option); } bool gt_typecheck_info_option_used(const GtTypecheckInfo *tci) { gt_assert(tci && tci->typecheck_option); if (gt_option_is_set(tci->typecheck_option) || tci->typecheck_built_in) return true; return false; } static GtStr* get_obo_path(GtError *err) { const char *progname; GtStr *obo_path, *prog; gt_error_check(err); progname = gt_error_get_progname(err); gt_assert(progname != NULL); prog = gt_str_new(); gt_str_append_cstr_nt(prog, progname, gt_cstr_length_up_to_char(progname, ' ')); obo_path = gt_get_gtdata_path(gt_str_get(prog), err); if (obo_path) gt_str_append_cstr(obo_path, "/obo_files/"); gt_str_delete(prog); return obo_path; } GtTypeChecker* gt_typecheck_info_create_type_checker(const GtTypecheckInfo *tci, GtError *err) { GtTypeChecker *type_checker = NULL; int had_err = 0; gt_error_check(err); gt_assert(tci); if (tci->typecheck_built_in) type_checker = gt_type_checker_builtin_new(); else { GtStr *obo_file; gt_assert(gt_option_is_set(tci->typecheck_option)); if (!gt_str_length(tci->typecheck)) { /* a. */ if (!(obo_file = get_obo_path(err))) had_err = -1; if (!had_err) gt_str_append_cstr(obo_file, "sofa.obo"); } else if (gt_file_exists(gt_str_get(tci->typecheck))) { /* b. */ obo_file = gt_str_new_cstr(gt_str_get(tci->typecheck)); } else { /* c. */ if (!(obo_file = get_obo_path(err))) had_err = -1; if (!had_err) { gt_str_append_str(obo_file, tci->typecheck); gt_str_append_cstr(obo_file, ".obo"); } } if (!had_err) type_checker = gt_type_checker_obo_new(gt_str_get(obo_file), err); gt_str_delete(obo_file); } return type_checker; } genometools-1.5.1/src/extended/typecheck_info.h000066400000000000000000000026261211610345200216040ustar00rootroot00000000000000/* Copyright (c) 2013 Gordon Gremme Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef TYPECHECK_INFO_H #define TYPECHECK_INFO_H #include "core/option_api.h" #include "extended/type_checker_api.h" typedef struct GtTypecheckInfo GtTypecheckInfo; GtTypecheckInfo* gt_typecheck_info_new(void); void gt_typecheck_info_delete(GtTypecheckInfo*); void gt_typecheck_info_register_options(GtTypecheckInfo*, GtOptionParser*); bool gt_typecheck_info_option_used(const GtTypecheckInfo*); GtTypeChecker* gt_typecheck_info_create_type_checker(const GtTypecheckInfo*, GtError *err); #endif genometools-1.5.1/src/extended/uint64hashtable.c000066400000000000000000000237131211610345200216120ustar00rootroot00000000000000/* Copyright (c) 2011 Giorgio Gonnella Copyright (c) 2011 Stefan Kurtz Copyright (c) 2011 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/ensure.h" #include "core/log.h" #include "core/ma.h" #include "core/hashtable.h" /* gt_uint64_key_mul_hash */ #include "core/spacecalc.h" #include "core/format64.h" #include "core/qsort_r_api.h" #include "core/timer_api.h" #include "extended/uint64hashtable.h" #include "extended/uint64hashtable_primes.h" #define GT_UINT64TABLE_TOO_LARGE \ "fatal: no prime number larger than %lu in lookup table\n" \ "developers: modify scripts/makeprimestable.sh to create a larger table\n" #define GT_UINT64TABLE_NOFPRIMES \ (sizeof (gt_uint64hashtable_primes) / sizeof (gt_uint64hashtable_primes[0])) #define GT_UINT64TABLE_LARGEST_PRIME \ gt_uint64hashtable_primes[GT_UINT64TABLE_NOFPRIMES - 1UL] /* if n is in lookup table return it; * otherwise return first element in lookup table larger than n */ static size_t gt_uint64hashtable_get_size(size_t n) { size_t u, l, i, k, k_i; k = n; if (k > (size_t)GT_UINT64TABLE_LARGEST_PRIME) { fprintf(stderr, GT_UINT64TABLE_TOO_LARGE, (unsigned long)k); exit(1); } if (k < (size_t)gt_uint64hashtable_primes[0]) { return (size_t)gt_uint64hashtable_primes[0]; } l = 0; u = GT_UINT64TABLE_NOFPRIMES - (size_t)1; do { i = (l + u) >> 1; gt_assert(u >= l); if (u - l == (size_t)1) { return ((size_t)gt_uint64hashtable_primes[l] == k) ? k : (size_t)gt_uint64hashtable_primes[u]; } k_i = (size_t)gt_uint64hashtable_primes[i]; if (k < k_i) { u = i; } else if (k > k_i) { l = i; } else { return k_i; } } while (true); gt_assert(false); /* this point should never be reached */ return 0; } typedef struct { uint64_t key; unsigned long count; } GtUint64hashstoredvalue; static int compareGtUint64hashstoredvalue(const void *a,const void *b, void *data) { GtUint64hashstoredvalue *hspace = (GtUint64hashstoredvalue *) data; uint32_t va = *(const uint32_t *) a; uint32_t vb = *(const uint32_t *) b; if (hspace[va].key < hspace[vb].key) { return -1; } if (hspace[va].key > hspace[vb].key) { return 1; } gt_assert(false); return 0; } struct GtUint64hashtable { GtUint64hashstoredvalue *hspace; uint32_t *sortedhspace; size_t alloc; unsigned long countcollisions, zero_count, allentries; bool zero_occurs; }; GtUint64hashtable *gt_uint64hashtable_new(size_t nof_elements) { GtUint64hashtable *table; const double loadfactor = 1.30; table = gt_malloc(sizeof (*table)); table->countcollisions = 0; table->allentries = 0; table->zero_occurs = false; table->zero_count = 0; table->alloc = gt_uint64hashtable_get_size((size_t)(1 + loadfactor * (double) nof_elements)); table->hspace = gt_calloc(table->alloc, sizeof (*table->hspace)); return table; } void gt_uint64hashtable_delete(GtUint64hashtable *table) { if (table != NULL) { gt_free(table->hspace); gt_free(table); } } static inline size_t gt_uint64hashtable_h1(uint64_t key, size_t table_size) { return (size_t) gt_uint64_key_mul_hash(key) % table_size; } static inline size_t gt_uint64hashtable_h2(uint64_t key, size_t table_size) { return (size_t) 1 + (size_t) gt_uint64_key_mul_hash(key) % (table_size - 1); } bool gt_uint64hashtable_search(GtUint64hashtable *table, uint64_t key, bool insert_if_not_found) { gt_assert(table != NULL); if (key > 0) { size_t pos, hashadd = 0, iteration; const uint64_t emptymark = 0; #ifndef NDEBUG size_t first_pos; #endif pos = gt_uint64hashtable_h1(key, table->alloc); #ifndef NDEBUG first_pos = pos; #endif for (iteration = 0; iteration < table->alloc; iteration++) { gt_assert(pos < table->alloc); if (table->hspace[pos].key == emptymark) { if (insert_if_not_found) { table->allentries++; table->hspace[pos].key = key; table->hspace[pos].count++; } return false; } if (table->hspace[pos].key == key) { gt_assert(table->hspace[pos].count > 0); table->hspace[pos].count++; return true; } table->countcollisions++; if (hashadd == 0) { hashadd = gt_uint64hashtable_h2(key, table->alloc); } gt_assert(hashadd > 0); pos += hashadd; if (pos >= table->alloc) { pos -= table->alloc; } gt_assert(pos != first_pos); } fprintf(stderr, "function %s, file %s, line %d.\n" "Cannot find empty slot in hashtable: " "This is probably a bug, please report it.\n", __func__, __FILE__, __LINE__); exit(GT_EXIT_PROGRAMMING_ERROR); } else { if (!table->zero_occurs) { if (insert_if_not_found) { table->zero_occurs = true; table->zero_count++; } return false; } else { gt_assert(table->zero_count > 0); table->zero_count++; return true; } } } unsigned long gt_uint64hashtable_insertionindex(GtUint64hashtable *table, uint64_t key) { gt_assert(table != NULL); if (key > 0) { size_t pos, hashadd = 0, iteration; const uint64_t emptymark = 0; #ifndef NDEBUG size_t first_pos; #endif pos = gt_uint64hashtable_h1(key, table->alloc); #ifndef NDEBUG first_pos = pos; #endif for (iteration = 0; iteration < table->alloc; iteration++) { gt_assert(pos < table->alloc); if (table->hspace[pos].key == emptymark) { return ULONG_MAX; } if (table->hspace[pos].key == key) { gt_assert(table->hspace[pos].count > 0); return --table->hspace[pos].count; } table->countcollisions++; if (hashadd == 0) { hashadd = gt_uint64hashtable_h2(key, table->alloc); } gt_assert(hashadd > 0); pos += hashadd; if (pos >= table->alloc) { pos -= table->alloc; } gt_assert(pos != first_pos); } fprintf(stderr, "function %s, file %s, line %d.\n" "Cannot find empty slot in hashtable: " "This is probably a bug, please report it.\n", __func__, __FILE__, __LINE__); exit(GT_EXIT_PROGRAMMING_ERROR); } else { gt_assert(table->zero_occurs); gt_assert(table->zero_count > 0); return --table->zero_count; } } unsigned long gt_uint64hashtable_countsum_get(const GtUint64hashtable *table) { size_t idx; unsigned long sumcount = 0; for (idx=0; idx < table->alloc; idx++) { if (table->hspace[idx].count > 0) { sumcount += table->hspace[idx].count; } } return sumcount + table->zero_count; } unsigned long gt_uint64hashtable_partialsums(GtUint64hashtable *table, GtTimer *timer) { size_t idx, next = 0; unsigned long psum, maxsize = 0; table->sortedhspace = gt_malloc((size_t) table->allentries * sizeof (*table->sortedhspace)); if (timer != NULL) { gt_timer_show_progress(timer, "sorting the hashkeys",stdout); } for (idx = 0; idx < table->alloc; idx++) { if (table->hspace[idx].count > 0) { gt_assert(next < (size_t) table->allentries); table->sortedhspace[next++] = idx; if (maxsize < table->hspace[idx].count) { maxsize = table->hspace[idx].count; } } } gt_qsort_r(table->sortedhspace,next,sizeof (*table->sortedhspace), table->hspace,compareGtUint64hashstoredvalue); gt_assert(next > 0); if (table->zero_occurs) { table->hspace[table->sortedhspace[0]].count += table->zero_count; } if (timer != NULL) { gt_timer_show_progress(timer, "computing partial sums",stdout); } for (idx = (size_t) 1; idx < next; idx++) { table->hspace[table->sortedhspace[idx]].count += table->hspace[table->sortedhspace[idx-1]].count; } psum = table->hspace[table->sortedhspace[next-1]].count; gt_free(table->sortedhspace); return psum; } int gt_uint64hashtable_unit_test(GtError *err) { int had_err = 0; GtUint64hashtable *table = NULL; bool found; size_t i, nof_elements; gt_error_check(err); table = gt_uint64hashtable_new(0); gt_ensure(had_err, table != NULL); found = gt_uint64hashtable_search(table, (uint64_t)7, false); gt_ensure(had_err, !found); found = gt_uint64hashtable_search(table, (uint64_t)7, true); gt_ensure(had_err, !found); found = gt_uint64hashtable_search(table, (uint64_t)7, true); gt_ensure(had_err, found); gt_uint64hashtable_delete(table); nof_elements = (size_t)10000; table = gt_uint64hashtable_new(nof_elements); gt_ensure(had_err, table != NULL); for (i = 0; i < nof_elements; i++) { found = gt_uint64hashtable_search(table, (uint64_t)i, true); gt_ensure(had_err, !found); } for (i = 0; i < nof_elements; i++) { found = gt_uint64hashtable_search(table, (uint64_t)i, true); gt_ensure(had_err, found); } gt_uint64hashtable_delete(table); return had_err; } genometools-1.5.1/src/extended/uint64hashtable.h000066400000000000000000000040531211610345200216130ustar00rootroot00000000000000/* Copyright (c) 2011 Giorgio Gonnella Copyright (c) 2011 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef UINT64HASHTABLE_H #define UINT64HASHTABLE_H #include #include "core/timer_api.h" #include "core/error.h" /* An hash table of uint64_t values without any associated information */ typedef struct GtUint64hashtable GtUint64hashtable; /* Create a new with space for at least values */ GtUint64hashtable* gt_uint64hashtable_new(size_t nof_elements); /* Deletes a and frees all associated memory */ void gt_uint64hashtable_delete(GtUint64hashtable *table); /* Searches key in table; returns true if found, false otherwise; * if insert_if_not_found is true, key is added to the table if not already * contained */ bool gt_uint64hashtable_search(GtUint64hashtable *table, uint64_t key, bool insert_if_not_found); unsigned long gt_uint64hashtable_countsum_get(const GtUint64hashtable *table); unsigned long gt_uint64hashtable_partialsums(GtUint64hashtable *table, GtTimer *timer); unsigned long gt_uint64hashtable_insertionindex(GtUint64hashtable *table, uint64_t key); int gt_uint64hashtable_unit_test(GtError *err); #endif genometools-1.5.1/src/extended/uint64hashtable_primes.h000066400000000000000000001171671211610345200232050ustar00rootroot00000000000000#ifndef UINT64HASHTABLE_PRIMES_H #define UINT64HASHTABLE_PRIMES_H static const unsigned long gt_uint64hashtable_primes[] = { 1048583UL, 5242891UL, 9437203UL, 13631539UL, 17825867UL, 22020181UL, 26214511UL, 30408817UL, 34603141UL, 38797457UL, 42991769UL, 47186099UL, 51380429UL, 55574737UL, 59769067UL, 63963371UL, 68157689UL, 72352001UL, 76546331UL, 80740651UL, 84934973UL, 89129297UL, 93323621UL, 97517939UL, 101712269UL, 105906587UL, 110100919UL, 114295231UL, 118489619UL, 122683927UL, 126878249UL, 131072587UL, 135266891UL, 139461209UL, 143655529UL, 147849847UL, 152044199UL, 156238519UL, 160432823UL, 164627137UL, 168821447UL, 173015753UL, 177210071UL, 181404389UL, 185598701UL, 189793027UL, 193987361UL, 198181693UL, 202376003UL, 206570333UL, 210764669UL, 214958977UL, 219153281UL, 223347601UL, 227541907UL, 231736229UL, 235930579UL, 240124883UL, 244319197UL, 248513501UL, 252707813UL, 256902119UL, 261096449UL, 265290757UL, 269485067UL, 273679381UL, 277873691UL, 282068071UL, 286262387UL, 290456711UL, 294651047UL, 298845353UL, 303039707UL, 307234043UL, 311428391UL, 315622717UL, 319817021UL, 324011357UL, 328205687UL, 332399999UL, 336594331UL, 340788667UL, 344982997UL, 349177319UL, 353371637UL, 357565991UL, 361760327UL, 365954647UL, 370148963UL, 374343287UL, 378537647UL, 382731977UL, 386926327UL, 391120637UL, 395314943UL, 399509267UL, 403703579UL, 407897887UL, 412092209UL, 416286589UL, 420480899UL, 424675219UL, 428869541UL, 433063847UL, 437258167UL, 441452477UL, 445646791UL, 449841109UL, 454035427UL, 458229731UL, 462424063UL, 466618387UL, 470812703UL, 475007009UL, 479201329UL, 483395641UL, 487589981UL, 491784301UL, 495978629UL, 500172949UL, 504367289UL, 508561601UL, 512755913UL, 516950243UL, 521144549UL, 525338867UL, 529533181UL, 533727487UL, 537921847UL, 542116163UL, 546310481UL, 550504807UL, 554699111UL, 558893443UL, 563087773UL, 567282077UL, 571476391UL, 575670701UL, 579865021UL, 584059351UL, 588253663UL, 592447997UL, 596642309UL, 600836617UL, 605030929UL, 609225259UL, 613419563UL, 617613869UL, 621808177UL, 626002483UL, 630196811UL, 634391119UL, 638585429UL, 642779737UL, 646974059UL, 651168373UL, 655362679UL, 659557009UL, 663751367UL, 667945679UL, 672139987UL, 676334299UL, 680528603UL, 684722911UL, 688917223UL, 693111533UL, 697305853UL, 701500193UL, 705694499UL, 709888843UL, 714083177UL, 718277503UL, 722471819UL, 726666131UL, 730860437UL, 735054751UL, 739249067UL, 743443373UL, 747637691UL, 751832063UL, 756026377UL, 760220687UL, 764415059UL, 768609367UL, 772803673UL, 776998037UL, 781192361UL, 785386699UL, 789581017UL, 793775351UL, 797969693UL, 802164017UL, 806358323UL, 810552641UL, 814746983UL, 818941297UL, 823135603UL, 827329907UL, 831524263UL, 835718567UL, 839912881UL, 844107191UL, 848301499UL, 852495863UL, 856690201UL, 860884529UL, 865078853UL, 869273159UL, 873467477UL, 877661843UL, 881856193UL, 886050499UL, 890244833UL, 894439151UL, 898633457UL, 902827771UL, 907022099UL, 911216407UL, 915410711UL, 919605019UL, 923799341UL, 927993653UL, 932187961UL, 936382277UL, 940576591UL, 944770921UL, 948965239UL, 953159551UL, 957353869UL, 961548197UL, 965742527UL, 969936883UL, 974131211UL, 978325529UL, 982519847UL, 986714173UL, 990908509UL, 995102831UL, 999297151UL, 1003491527UL, 1007685841UL, 1011880153UL, 1016074471UL, 1020268801UL, 1024463117UL, 1028657453UL, 1032851801UL, 1037046133UL, 1041240443UL, 1045434751UL, 1049629099UL, 1053823409UL, 1058017721UL, 1062212033UL, 1066406377UL, 1070600723UL, 1074795041UL, 1078989367UL, 1083183683UL, 1087378001UL, 1091572343UL, 1095766649UL, 1099960957UL, 1104155263UL, 1108349581UL, 1112543893UL, 1116738199UL, 1120932511UL, 1125126823UL, 1129321147UL, 1133515483UL, 1137709823UL, 1141904131UL, 1146098491UL, 1150292809UL, 1154487127UL, 1158681439UL, 1162875773UL, 1167070087UL, 1171264399UL, 1175458703UL, 1179653009UL, 1183847317UL, 1188041623UL, 1192235929UL, 1196430241UL, 1200624569UL, 1204818889UL, 1209013199UL, 1213207517UL, 1217401831UL, 1221596221UL, 1225790569UL, 1229984879UL, 1234179203UL, 1238373527UL, 1242567841UL, 1246762151UL, 1250956459UL, 1255150781UL, 1259345089UL, 1263539401UL, 1267733717UL, 1271928071UL, 1276122377UL, 1280316757UL, 1284511073UL, 1288705469UL, 1292899787UL, 1297094111UL, 1301288431UL, 1305482747UL, 1309677067UL, 1313871371UL, 1318065691UL, 1322260001UL, 1326454307UL, 1330648651UL, 1334842961UL, 1339037279UL, 1343231587UL, 1347425909UL, 1351620269UL, 1355814589UL, 1360008913UL, 1364203223UL, 1368397531UL, 1372591873UL, 1376786179UL, 1380980507UL, 1385174827UL, 1389369139UL, 1393563469UL, 1397757797UL, 1401952103UL, 1406146429UL, 1410340733UL, 1414535063UL, 1418729381UL, 1422923687UL, 1427117999UL, 1431312307UL, 1435506661UL, 1439700967UL, 1443895273UL, 1448089603UL, 1452283909UL, 1456478251UL, 1460672567UL, 1464866881UL, 1469061199UL, 1473255503UL, 1477449811UL, 1481644123UL, 1485838429UL, 1490032741UL, 1494227047UL, 1498421357UL, 1502615729UL, 1506810037UL, 1511004367UL, 1515198673UL, 1519392977UL, 1523587291UL, 1527781597UL, 1531975901UL, 1536170213UL, 1540364587UL, 1544558891UL, 1548753223UL, 1552947547UL, 1557141853UL, 1561336199UL, 1565530507UL, 1569724817UL, 1573919147UL, 1578113461UL, 1582307803UL, 1586502107UL, 1590696413UL, 1594890727UL, 1599085069UL, 1603279373UL, 1607473691UL, 1611667999UL, 1615862317UL, 1620056687UL, 1624251023UL, 1628445341UL, 1632639653UL, 1636833973UL, 1641028289UL, 1645222609UL, 1649416943UL, 1653611251UL, 1657805557UL, 1661999881UL, 1666194193UL, 1670388497UL, 1674582853UL, 1678777171UL, 1682971481UL, 1687165787UL, 1691360123UL, 1695554437UL, 1699748779UL, 1703943103UL, 1708137413UL, 1712331739UL, 1716526043UL, 1720720357UL, 1724914669UL, 1729108993UL, 1733303309UL, 1737497669UL, 1741692011UL, 1745886319UL, 1750080677UL, 1754275007UL, 1758469343UL, 1762663691UL, 1766857997UL, 1771052303UL, 1775246633UL, 1779440941UL, 1783635263UL, 1787829611UL, 1792023917UL, 1796218247UL, 1800412589UL, 1804606897UL, 1808801257UL, 1812995567UL, 1817189897UL, 1821384203UL, 1825578527UL, 1829772853UL, 1833967171UL, 1838161511UL, 1842355849UL, 1846550191UL, 1850744507UL, 1854938893UL, 1859133197UL, 1863327503UL, 1867521827UL, 1871716139UL, 1875910453UL, 1880104813UL, 1884299143UL, 1888493447UL, 1892687759UL, 1896882073UL, 1901076389UL, 1905270713UL, 1909465043UL, 1913659361UL, 1917853681UL, 1922047997UL, 1926242309UL, 1930436617UL, 1934630927UL, 1938825241UL, 1943019557UL, 1947213869UL, 1951408253UL, 1955602567UL, 1959796957UL, 1963991269UL, 1968185573UL, 1972379887UL, 1976574221UL, 1980768551UL, 1984962871UL, 1989157201UL, 1993351517UL, 1997545877UL, 2001740197UL, 2005934501UL, 2010128831UL, 2014323137UL, 2018517451UL, 2022711773UL, 2026906099UL, 2031100411UL, 2035294717UL, 2039489021UL, 2043683329UL, 2047877707UL, 2052072013UL, 2056266343UL, 2060460671UL, 2064654997UL, 2068849309UL, 2073043619UL, 2077237927UL, 2081432257UL, 2085626563UL, 2089820893UL, 2094015221UL, 2098209541UL, 2102403917UL, 2106598283UL, 2110792601UL, 2114986961UL, 2119181269UL, 2123375587UL, 2127569921UL, 2131764253UL, 2135958563UL, 2140152887UL, 2144347229UL, 2148541537UL, 2152735847UL, 2156930203UL, 2161124509UL, 2165318851UL, 2169513161UL, 2173707541UL, 2177901857UL, 2182096177UL, 2186290487UL, 2190484817UL, 2194679191UL, 2198873513UL, 2203067821UL, 2207262143UL, 2211456491UL, 2215650797UL, 2219845129UL, 2224039457UL, 2228233771UL, 2232428087UL, 2236622489UL, 2240816843UL, 2245011151UL, 2249205473UL, 2253399787UL, 2257594091UL, 2261788457UL, 2265982777UL, 2270177083UL, 2274371413UL, 2278565797UL, 2282760107UL, 2286954419UL, 2291148733UL, 2295343081UL, 2299537403UL, 2303731711UL, 2307926041UL, 2312120347UL, 2316314717UL, 2320509041UL, 2324703349UL, 2328897691UL, 2333091997UL, 2337286313UL, 2341480633UL, 2345674937UL, 2349869257UL, 2354063561UL, 2358257911UL, 2362452221UL, 2366646533UL, 2370840853UL, 2375035231UL, 2379229553UL, 2383423879UL, 2387618197UL, 2391812503UL, 2396006863UL, 2400201169UL, 2404395473UL, 2408589791UL, 2412784123UL, 2416978441UL, 2421172801UL, 2425367129UL, 2429561471UL, 2433755783UL, 2437950089UL, 2442144427UL, 2446338733UL, 2450533093UL, 2454727397UL, 2458921709UL, 2463116057UL, 2467310387UL, 2471504747UL, 2475699067UL, 2479893371UL, 2484087703UL, 2488282007UL, 2492476319UL, 2496670637UL, 2500864963UL, 2505059311UL, 2509253633UL, 2513447957UL, 2517642263UL, 2521836613UL, 2526030919UL, 2530225223UL, 2534419529UL, 2538613837UL, 2542808141UL, 2547002449UL, 2551196761UL, 2555391071UL, 2559585403UL, 2563779719UL, 2567974027UL, 2572168337UL, 2576362661UL, 2580556997UL, 2584751303UL, 2588945609UL, 2593139917UL, 2597334241UL, 2601528563UL, 2605722907UL, 2609917253UL, 2614111601UL, 2618305967UL, 2622500281UL, 2626694641UL, 2630888963UL, 2635083271UL, 2639277611UL, 2643471947UL, 2647666261UL, 2651860567UL, 2656054883UL, 2660249197UL, 2664443503UL, 2668637831UL, 2672832137UL, 2677026463UL, 2681220811UL, 2685415121UL, 2689609427UL, 2693803741UL, 2697998111UL, 2702192417UL, 2706386729UL, 2710581043UL, 2714775361UL, 2718969667UL, 2723163977UL, 2727358289UL, 2731552609UL, 2735746933UL, 2739941299UL, 2744135623UL, 2748329933UL, 2752524251UL, 2756718577UL, 2760912883UL, 2765107201UL, 2769301511UL, 2773495831UL, 2777690171UL, 2781884503UL, 2786078809UL, 2790273149UL, 2794467527UL, 2798661857UL, 2802856169UL, 2807050487UL, 2811244861UL, 2815439213UL, 2819633533UL, 2823827837UL, 2828022179UL, 2832216487UL, 2836410809UL, 2840605121UL, 2844799429UL, 2848993733UL, 2853188053UL, 2857382357UL, 2861576701UL, 2865771019UL, 2869965331UL, 2874159641UL, 2878353949UL, 2882548267UL, 2886742571UL, 2890936883UL, 2895131191UL, 2899325497UL, 2903519803UL, 2907714109UL, 2911908463UL, 2916102797UL, 2920297117UL, 2924491459UL, 2928685777UL, 2932880087UL, 2937074407UL, 2941268731UL, 2945463041UL, 2949657371UL, 2953851689UL, 2958046001UL, 2962240319UL, 2966434661UL, 2970628979UL, 2974823297UL, 2979017611UL, 2983211927UL, 2987406239UL, 2991600583UL, 2995794887UL, 2999989217UL, 3004183547UL, 3008377877UL, 3012572183UL, 3016766491UL, 3020960807UL, 3025155163UL, 3029349497UL, 3033543803UL, 3037738117UL, 3041932427UL, 3046126757UL, 3050321083UL, 3054515389UL, 3058709707UL, 3062904011UL, 3067098341UL, 3071292661UL, 3075486989UL, 3079681307UL, 3083875651UL, 3088069961UL, 3092264267UL, 3096458579UL, 3100652897UL, 3104847203UL, 3109041511UL, 3113235883UL, 3117430201UL, 3121624531UL, 3125818921UL, 3130013231UL, 3134207561UL, 3138401887UL, 3142596211UL, 3146790527UL, 3150984847UL, 3155179171UL, 3159373489UL, 3163567807UL, 3167762113UL, 3171956423UL, 3176150741UL, 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THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/ensure.h" #include "core/ma.h" #include "extended/union_find.h" #define UNION_FIND_TEST_SIZE 1024 typedef struct { unsigned long parent, rank; } GtUnionFindElement; struct GtUnionFind { GtUnionFindElement *elems; unsigned long num_of_elems; }; GtUnionFind* gt_union_find_new(unsigned long num_of_elems) { GtUnionFind *uf; unsigned long i; gt_assert(num_of_elems); uf = gt_malloc(sizeof *uf); uf->elems = gt_calloc(sizeof (GtUnionFindElement), num_of_elems); for (i = 0; i < num_of_elems; i++) uf->elems[i].parent = i; uf->num_of_elems = num_of_elems; return uf; } void gt_union_find_delete(GtUnionFind *uf) { if (!uf) return; gt_free(uf->elems); gt_free(uf); } unsigned long gt_union_find_find(GtUnionFind *uf, unsigned long elem) { gt_assert(uf && elem < uf->num_of_elems); if (elem != uf->elems[elem].parent) /* path compression */ uf->elems[elem].parent = gt_union_find_find(uf, uf->elems[elem].parent); return uf->elems[elem].parent; } void gt_union_find_union(GtUnionFind *uf, unsigned long elem_a, unsigned long elem_b) { unsigned long x, y; gt_assert(uf && elem_a < uf->num_of_elems && elem_b < uf->num_of_elems); x = gt_union_find_find(uf, elem_a); y = gt_union_find_find(uf, elem_b); uf->elems[y].parent = x; /* union-by-rank heuristic if (uf->elems[x].rank > uf->elems[y].rank) uf->elems[y].parent = x; else { uf->elems[x].parent = y; if (uf->elems[x].rank == uf->elems[y].rank) uf->elems[y].rank++; } */ } int gt_union_find_unit_test(GtError *err) { unsigned long i; GtUnionFind *uf; int had_err = 0; gt_error_check(err); /* one element */ uf = gt_union_find_new(1); gt_ensure(had_err, gt_union_find_find(uf, 0) == 0); gt_union_find_delete(uf); /* two elements */ if (!had_err) { uf = gt_union_find_new(2); gt_ensure(had_err, gt_union_find_find(uf, 0) != gt_union_find_find(uf, 1)); gt_union_find_union(uf, 0, 1); gt_ensure(had_err, gt_union_find_find(uf, 0) == gt_union_find_find(uf, 1)); gt_union_find_delete(uf); } /* many elements */ if (!had_err) { uf = gt_union_find_new(UNION_FIND_TEST_SIZE); for (i = 1; !had_err && i < UNION_FIND_TEST_SIZE; i++) gt_ensure(had_err, gt_union_find_find(uf, 0) != gt_union_find_find(uf, i)); for (i = 1; !had_err && i < UNION_FIND_TEST_SIZE; i++) gt_union_find_union(uf, 0, i); for (i = 1; !had_err && i < UNION_FIND_TEST_SIZE; i++) gt_ensure(had_err, gt_union_find_find(uf, 0) == gt_union_find_find(uf, i)); gt_union_find_delete(uf); } return had_err; } genometools-1.5.1/src/extended/union_find.h000066400000000000000000000036751211610345200207470ustar00rootroot00000000000000/* Copyright (c) 2008 Gordon Gremme Copyright (c) 2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef UNION_FIND_H #define UNION_FIND_H #include "core/error.h" /* This class implements the union-find data structure (with union-by-rank heuristic and path compression). For a description see for example page 446 to page 449 of the book T.H. Cormen, C.E. Leiserson and R.L. Rivest. Introduction to Algorithms. MIT Press: Cambridge, MA, 1990. */ typedef struct GtUnionFind GtUnionFind; /* Create a new union-find data structures representing many elements (numbered from 0 up to - 1) contained in disjoined sets. */ GtUnionFind* gt_union_find_new(unsigned long num_of_elems); /* Delete the given union-find data structure. */ void gt_union_find_delete(GtUnionFind*); /* Find the representative set for the given . */ unsigned long gt_union_find_find(GtUnionFind*, unsigned long elem); /* Union the set containing with the set containing . */ void gt_union_find_union(GtUnionFind*, unsigned long elem_a, unsigned long elem_b); int gt_union_find_unit_test(GtError*); #endif genometools-1.5.1/src/extended/uniq_stream.c000066400000000000000000000126121211610345200211300ustar00rootroot00000000000000/* Copyright (c) 2007-2008 Gordon Gremme Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/assert_api.h" #include "core/class_alloc_lock.h" #include "core/undef_api.h" #include "extended/feature_node.h" #include "extended/feature_node_iterator_api.h" #include "extended/node_stream_api.h" #include "extended/uniq_stream.h" struct GtUniqStream{ const GtNodeStream parent_instance; GtNodeStream *in_stream; GtGenomeNode *first_node, *second_node; }; #define uniq_stream_cast(GS)\ gt_node_stream_cast(gt_uniq_stream_class(), GS) static bool nodes_are_equal_feature_trees(GtGenomeNode *first_node, GtGenomeNode *second_node) { bool equal = false; GtFeatureNodeIterator *fni_a, *fni_b; GtFeatureNode *fn_a, *fn_b; fn_a = gt_feature_node_try_cast(first_node); fn_b = gt_feature_node_try_cast(second_node); if (fn_a && fn_b) { fni_a = gt_feature_node_iterator_new((GtFeatureNode*) first_node); fni_b = gt_feature_node_iterator_new((GtFeatureNode*) second_node); for (fn_a = gt_feature_node_iterator_next(fni_a), fn_b = gt_feature_node_iterator_next(fni_b); fn_a && fn_b; fn_a = gt_feature_node_iterator_next(fni_a), fn_b = gt_feature_node_iterator_next(fni_b)) { if (!fn_b || !gt_feature_node_is_similar(fn_a, fn_b)) break; } fn_b = (GtFeatureNode*) gt_feature_node_iterator_next(fni_b); if (!fn_a && !fn_b) equal = true; gt_feature_node_iterator_delete(fni_a); gt_feature_node_iterator_delete(fni_b); return equal; } return false; } static bool uniq(GtGenomeNode **first_node, GtGenomeNode **second_node) { bool first_score_is_defined, second_score_is_defined; float first_score = 0.0, second_score = 0.0; gt_assert(*first_node && *second_node); if (nodes_are_equal_feature_trees(*first_node, *second_node)) { if ((first_score_is_defined = gt_feature_node_score_is_defined((GtFeatureNode*) *first_node))) { first_score = gt_feature_node_get_score((GtFeatureNode*) *first_node); } if ((second_score_is_defined = gt_feature_node_score_is_defined((GtFeatureNode*) *second_node))) { second_score = gt_feature_node_get_score((GtFeatureNode*) *second_node); } if ((!first_score_is_defined && !second_score_is_defined) || (first_score_is_defined && !second_score_is_defined) || (first_score_is_defined && second_score_is_defined && first_score >= second_score)) { /* keep first node */ gt_genome_node_delete(*second_node); } else { /* keep second node */ gt_genome_node_delete(*first_node); *first_node = *second_node; } *second_node = NULL; return true; } return false; } static int uniq_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) { GtUniqStream *us; int had_err; gt_error_check(err); us = uniq_stream_cast(ns); gt_assert(!us->second_node); /* the second buffer is always empty when this function is called */ if (!us->first_node) { /* both buffers are empty */ had_err = gt_node_stream_next(us->in_stream, &us->first_node, err); if (had_err) return had_err; if (!us->first_node) { *gn = NULL; return 0; } } /* uniq loop */ for (;;) { gt_assert(us->first_node && !us->second_node); had_err = gt_node_stream_next(us->in_stream, &us->second_node, err); if (!had_err && us->second_node) { if (!uniq(&us->first_node, &us->second_node)) break; /* no uniq possible */ } else break; } /* serve node */ if (!had_err) { gt_assert(us->first_node); *gn = us->first_node; us->first_node = us->second_node; us->second_node = NULL; } return had_err; } static void uniq_stream_free(GtNodeStream *ns) { GtUniqStream *us = uniq_stream_cast(ns); gt_genome_node_delete(us->first_node); gt_genome_node_delete(us->second_node); gt_node_stream_delete(us->in_stream); } const GtNodeStreamClass* gt_uniq_stream_class(void) { static const GtNodeStreamClass *nsc = NULL; gt_class_alloc_lock_enter(); if (!nsc) { nsc = gt_node_stream_class_new(sizeof (GtUniqStream), uniq_stream_free, uniq_stream_next); } gt_class_alloc_lock_leave(); return nsc; } GtNodeStream* gt_uniq_stream_new(GtNodeStream *in_stream) { GtNodeStream *ns; GtUniqStream *us; gt_assert(in_stream && gt_node_stream_is_sorted(in_stream)); ns = gt_node_stream_create(gt_uniq_stream_class(), true); us = uniq_stream_cast(ns); us->in_stream = gt_node_stream_ref(in_stream); return ns; } genometools-1.5.1/src/extended/uniq_stream.h000066400000000000000000000017641211610345200211430ustar00rootroot00000000000000/* Copyright (c) 2007, 2011 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef UNIQ_STREAM_H #define UNIQ_STREAM_H #include "extended/uniq_stream_api.h" const GtNodeStreamClass* gt_uniq_stream_class(void); #endif genometools-1.5.1/src/extended/uniq_stream_api.h000066400000000000000000000033361211610345200217710ustar00rootroot00000000000000/* Copyright (c) 2007, 2011 Gordon Gremme Copyright (c) 2007 Center for Bioinformatics, University of Hamburg Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef UNIQ_STREAM_API_H #define UNIQ_STREAM_API_H #include "extended/node_stream_api.h" /* Implements the interface. A filters out repeated features it retrieves from its node source. */ typedef struct GtUniqStream GtUniqStream; /* Create a object which filters out repeated feature node graphs it retrieves from the sorted and return all other nodes. Two feature node graphs are considered to be __repeated__ if they have the same depth-first traversal and each corresponding feature node pair is similar according to the method. For such a repeated feature node graph the one with the higher score (of the top-level feature) is kept. If only one of the feature node graphs has a defined score, this one is kept. */ GtNodeStream* gt_uniq_stream_new(GtNodeStream*); #endif genometools-1.5.1/src/extended/visitor_stream.c000066400000000000000000000052401211610345200216520ustar00rootroot00000000000000/* Copyright (c) 2010 Gordon Gremme Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #include "core/class_alloc_lock.h" #include "extended/feature_node.h" #include "extended/node_stream_api.h" #include "extended/visitor_stream.h" struct GtVisitorStream { const GtNodeStream parent_instance; GtNodeStream *in_stream; GtNodeVisitor *visitor; }; #define visitor_stream_cast(GS)\ gt_node_stream_cast(gt_visitor_stream_class(), GS) static int visitor_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) { GtVisitorStream *visitor_stream; int had_err; gt_error_check(err); visitor_stream = visitor_stream_cast(ns); had_err = gt_node_stream_next(visitor_stream->in_stream, gn, err); if (!had_err && *gn) had_err = gt_genome_node_accept(*gn, visitor_stream->visitor, err); if (had_err) { /* we own the node -> delete it */ gt_genome_node_delete(*gn); *gn = NULL; } return had_err; } static void visitor_stream_free(GtNodeStream *ns) { GtVisitorStream *visitor_stream = visitor_stream_cast(ns); gt_node_visitor_delete(visitor_stream->visitor); gt_node_stream_delete(visitor_stream->in_stream); } const GtNodeStreamClass* gt_visitor_stream_class(void) { static const GtNodeStreamClass *nsc = NULL; gt_class_alloc_lock_enter(); if (!nsc) { nsc = gt_node_stream_class_new(sizeof (GtVisitorStream), visitor_stream_free, visitor_stream_next); } gt_class_alloc_lock_leave(); return nsc; } GtNodeStream* gt_visitor_stream_new(GtNodeStream *in_stream, GtNodeVisitor *visitor) { GtVisitorStream *visitor_stream; GtNodeStream *ns; ns = gt_node_stream_create(gt_visitor_stream_class(), gt_node_stream_is_sorted(in_stream)); visitor_stream = visitor_stream_cast(ns); visitor_stream->in_stream = gt_node_stream_ref(in_stream); visitor_stream->visitor = visitor; return ns; } genometools-1.5.1/src/extended/visitor_stream.h000066400000000000000000000016631211610345200216640ustar00rootroot00000000000000/* Copyright (c) 2010-2011 Gordon Gremme Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef VISITOR_STREAM_H #define VISITOR_STREAM_H #include "extended/visitor_stream_api.h" const GtNodeStreamClass* gt_visitor_stream_class(void); #endif genometools-1.5.1/src/extended/visitor_stream_api.h000066400000000000000000000025621211610345200225140ustar00rootroot00000000000000/* Copyright (c) 2010-2011 Gordon Gremme Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. */ #ifndef VISITOR_STREAM_API_H #define VISITOR_STREAM_API_H #include #include "extended/node_stream_api.h" #include "extended/node_visitor_api.h" /* Implements the interface. */ typedef struct GtVisitorStream GtVisitorStream; /* Create a new , takes ownership of . This stream applies to each node which passes through it. Can be used to implement all streams with such a functionality. */ GtNodeStream* gt_visitor_stream_new(GtNodeStream *in_stream, GtNodeVisitor *node_visitor); #endif genometools-1.5.1/src/external/000077500000000000000000000000001211610345200164555ustar00rootroot00000000000000genometools-1.5.1/src/external/bzip2-1.0.6/000077500000000000000000000000001211610345200201435ustar00rootroot00000000000000genometools-1.5.1/src/external/bzip2-1.0.6/CHANGES000066400000000000000000000262311211610345200211420ustar00rootroot00000000000000 ------------------------------------------------------------------ This file is part of bzip2/libbzip2, a program and library for lossless, block-sorting data compression. bzip2/libbzip2 version 1.0.6 of 6 September 2010 Copyright (C) 1996-2010 Julian Seward Please read the WARNING, DISCLAIMER and PATENTS sections in the README file. This program is released under the terms of the license contained in the file LICENSE. ------------------------------------------------------------------ 0.9.0 ~~~~~ First version. 0.9.0a ~~~~~~ Removed 'ranlib' from Makefile, since most modern Unix-es don't need it, or even know about it. 0.9.0b ~~~~~~ Fixed a problem with error reporting in bzip2.c. This does not effect the library in any way. Problem is: versions 0.9.0 and 0.9.0a (of the program proper) compress and decompress correctly, but give misleading error messages (internal panics) when an I/O error occurs, instead of reporting the problem correctly. This shouldn't give any data loss (as far as I can see), but is confusing. Made the inline declarations disappear for non-GCC compilers. 0.9.0c ~~~~~~ Fixed some problems in the library pertaining to some boundary cases. This makes the library behave more correctly in those situations. The fixes apply only to features (calls and parameters) not used by bzip2.c, so the non-fixedness of them in previous versions has no effect on reliability of bzip2.c. In bzlib.c: * made zero-length BZ_FLUSH work correctly in bzCompress(). * fixed bzWrite/bzRead to ignore zero-length requests. * fixed bzread to correctly handle read requests after EOF. * wrong parameter order in call to bzDecompressInit in bzBuffToBuffDecompress. Fixed. In compress.c: * changed setting of nGroups in sendMTFValues() so as to do a bit better on small files. This _does_ effect bzip2.c. 0.9.5a ~~~~~~ Major change: add a fallback sorting algorithm (blocksort.c) to give reasonable behaviour even for very repetitive inputs. Nuked --repetitive-best and --repetitive-fast since they are no longer useful. Minor changes: mostly a whole bunch of small changes/ bugfixes in the driver (bzip2.c). Changes pertaining to the user interface are: allow decompression of symlink'd files to stdout decompress/test files even without .bz2 extension give more accurate error messages for I/O errors when compressing/decompressing to stdout, don't catch control-C read flags from BZIP2 and BZIP environment variables decline to break hard links to a file unless forced with -f allow -c flag even with no filenames preserve file ownerships as far as possible make -s -1 give the expected block size (100k) add a flag -q --quiet to suppress nonessential warnings stop decoding flags after --, so files beginning in - can be handled resolved inconsistent naming: bzcat or bz2cat ? bzip2 --help now returns 0 Programming-level changes are: fixed syntax error in GET_LL4 for Borland C++ 5.02 let bzBuffToBuffDecompress return BZ_DATA_ERROR{_MAGIC} fix overshoot of mode-string end in bzopen_or_bzdopen wrapped bzlib.h in #ifdef __cplusplus ... extern "C" { ... } close file handles under all error conditions added minor mods so it compiles with DJGPP out of the box fixed Makefile so it doesn't give problems with BSD make fix uninitialised memory reads in dlltest.c 0.9.5b ~~~~~~ Open stdin/stdout in binary mode for DJGPP. 0.9.5c ~~~~~~ Changed BZ_N_OVERSHOOT to be ... + 2 instead of ... + 1. The + 1 version could cause the sorted order to be wrong in some extremely obscure cases. Also changed setting of quadrant in blocksort.c. 0.9.5d ~~~~~~ The only functional change is to make bzlibVersion() in the library return the correct string. This has no effect whatsoever on the functioning of the bzip2 program or library. Added a couple of casts so the library compiles without warnings at level 3 in MS Visual Studio 6.0. Included a Y2K statement in the file Y2K_INFO. All other changes are minor documentation changes. 1.0 ~~~ Several minor bugfixes and enhancements: * Large file support. The library uses 64-bit counters to count the volume of data passing through it. bzip2.c is now compiled with -D_FILE_OFFSET_BITS=64 to get large file support from the C library. -v correctly prints out file sizes greater than 4 gigabytes. All these changes have been made without assuming a 64-bit platform or a C compiler which supports 64-bit ints, so, except for the C library aspect, they are fully portable. * Decompression robustness. The library/program should be robust to any corruption of compressed data, detecting and handling _all_ corruption, instead of merely relying on the CRCs. What this means is that the program should never crash, given corrupted data, and the library should always return BZ_DATA_ERROR. * Fixed an obscure race-condition bug only ever observed on Solaris, in which, if you were very unlucky and issued control-C at exactly the wrong time, both input and output files would be deleted. * Don't run out of file handles on test/decompression when large numbers of files have invalid magic numbers. * Avoid library namespace pollution. Prefix all exported symbols with BZ2_. * Minor sorting enhancements from my DCC2000 paper. * Advance the version number to 1.0, so as to counteract the (false-in-this-case) impression some people have that programs with version numbers less than 1.0 are in some way, experimental, pre-release versions. * Create an initial Makefile-libbz2_so to build a shared library. Yes, I know I should really use libtool et al ... * Make the program exit with 2 instead of 0 when decompression fails due to a bad magic number (ie, an invalid bzip2 header). Also exit with 1 (as the manual claims :-) whenever a diagnostic message would have been printed AND the corresponding operation is aborted, for example bzip2: Output file xx already exists. When a diagnostic message is printed but the operation is not aborted, for example bzip2: Can't guess original name for wurble -- using wurble.out then the exit value 0 is returned, unless some other problem is also detected. I think it corresponds more closely to what the manual claims now. 1.0.1 ~~~~~ * Modified dlltest.c so it uses the new BZ2_ naming scheme. * Modified makefile-msc to fix minor build probs on Win2k. * Updated README.COMPILATION.PROBLEMS. There are no functionality changes or bug fixes relative to version 1.0.0. This is just a documentation update + a fix for minor Win32 build problems. For almost everyone, upgrading from 1.0.0 to 1.0.1 is utterly pointless. Don't bother. 1.0.2 ~~~~~ A bug fix release, addressing various minor issues which have appeared in the 18 or so months since 1.0.1 was released. Most of the fixes are to do with file-handling or documentation bugs. To the best of my knowledge, there have been no data-loss-causing bugs reported in the compression/decompression engine of 1.0.0 or 1.0.1. Note that this release does not improve the rather crude build system for Unix platforms. The general plan here is to autoconfiscate/ libtoolise 1.0.2 soon after release, and release the result as 1.1.0 or perhaps 1.2.0. That, however, is still just a plan at this point. Here are the changes in 1.0.2. Bug-reporters and/or patch-senders in parentheses. * Fix an infinite segfault loop in 1.0.1 when a directory is encountered in -f (force) mode. (Trond Eivind Glomsrod, Nicholas Nethercote, Volker Schmidt) * Avoid double fclose() of output file on certain I/O error paths. (Solar Designer) * Don't fail with internal error 1007 when fed a long stream (> 48MB) of byte 251. Also print useful message suggesting that 1007s may be caused by bad memory. (noticed by Juan Pedro Vallejo, fixed by me) * Fix uninitialised variable silly bug in demo prog dlltest.c. (Jorj Bauer) * Remove 512-MB limitation on recovered file size for bzip2recover on selected platforms which support 64-bit ints. At the moment all GCC supported platforms, and Win32. (me, Alson van der Meulen) * Hard-code header byte values, to give correct operation on platforms using EBCDIC as their native character set (IBM's OS/390). (Leland Lucius) * Copy file access times correctly. (Marty Leisner) * Add distclean and check targets to Makefile. (Michael Carmack) * Parameterise use of ar and ranlib in Makefile. Also add $(LDFLAGS). (Rich Ireland, Bo Thorsen) * Pass -p (create parent dirs as needed) to mkdir during make install. (Jeremy Fusco) * Dereference symlinks when copying file permissions in -f mode. (Volker Schmidt) * Majorly simplify implementation of uInt64_qrm10. (Bo Lindbergh) * Check the input file still exists before deleting the output one, when aborting in cleanUpAndFail(). (Joerg Prante, Robert Linden, Matthias Krings) Also a bunch of patches courtesy of Philippe Troin, the Debian maintainer of bzip2: * Wrapper scripts (with manpages): bzdiff, bzgrep, bzmore. * Spelling changes and minor enhancements in bzip2.1. * Avoid race condition between creating the output file and setting its interim permissions safely, by using fopen_output_safely(). No changes to bzip2recover since there is no issue with file permissions there. * do not print senseless report with -v when compressing an empty file. * bzcat -f works on non-bzip2 files. * do not try to escape shell meta-characters on unix (the shell takes care of these). * added --fast and --best aliases for -1 -9 for gzip compatibility. 1.0.3 (15 Feb 05) ~~~~~~~~~~~~~~~~~ Fixes some minor bugs since the last version, 1.0.2. * Further robustification against corrupted compressed data. There are currently no known bitstreams which can cause the decompressor to crash, loop or access memory which does not belong to it. If you are using bzip2 or the library to decompress bitstreams from untrusted sources, an upgrade to 1.0.3 is recommended. This fixes CAN-2005-1260. * The documentation has been converted to XML, from which html and pdf can be derived. * Various minor bugs in the documentation have been fixed. * Fixes for various compilation warnings with newer versions of gcc, and on 64-bit platforms. * The BZ_NO_STDIO cpp symbol was not properly observed in 1.0.2. This has been fixed. 1.0.4 (20 Dec 06) ~~~~~~~~~~~~~~~~~ Fixes some minor bugs since the last version, 1.0.3. * Fix file permissions race problem (CAN-2005-0953). * Avoid possible segfault in BZ2_bzclose. From Coverity's NetBSD scan. * 'const'/prototype cleanups in the C code. * Change default install location to /usr/local, and handle multiple 'make install's without error. * Sanitise file names more carefully in bzgrep. Fixes CAN-2005-0758 to the extent that applies to bzgrep. * Use 'mktemp' rather than 'tempfile' in bzdiff. * Tighten up a couple of assertions in blocksort.c following automated analysis. * Fix minor doc/comment bugs. 1.0.5 (10 Dec 07) ~~~~~~~~~~~~~~~~~ Security fix only. Fixes CERT-FI 20469 as it applies to bzip2. 1.0.6 (6 Sept 10) ~~~~~~~~~~~~~~~~~ * Security fix for CVE-2010-0405. This was reported by Mikolaj Izdebski. * Make the documentation build on Ubuntu 10.04 genometools-1.5.1/src/external/bzip2-1.0.6/LICENSE000066400000000000000000000035551211610345200211600ustar00rootroot00000000000000 -------------------------------------------------------------------------- This program, "bzip2", the associated library "libbzip2", and all documentation, are copyright (C) 1996-2010 Julian R Seward. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 3. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 4. The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Julian Seward, jseward@bzip.org bzip2/libbzip2 version 1.0.6 of 6 September 2010 -------------------------------------------------------------------------- genometools-1.5.1/src/external/bzip2-1.0.6/Makefile000066400000000000000000000142361211610345200216110ustar00rootroot00000000000000# ------------------------------------------------------------------ # This file is part of bzip2/libbzip2, a program and library for # lossless, block-sorting data compression. # # bzip2/libbzip2 version 1.0.6 of 6 September 2010 # Copyright (C) 1996-2010 Julian Seward # # Please read the WARNING, DISCLAIMER and PATENTS sections in the # README file. # # This program is released under the terms of the license contained # in the file LICENSE. # ------------------------------------------------------------------ SHELL=/bin/sh # To assist in cross-compiling CC=gcc AR=ar RANLIB=ranlib LDFLAGS= BIGFILES=-D_FILE_OFFSET_BITS=64 CFLAGS=-Wall -Winline -O2 -g $(BIGFILES) # Where you want it installed when you do 'make install' PREFIX=/usr/local OBJS= blocksort.o \ huffman.o \ crctable.o \ randtable.o \ compress.o \ decompress.o \ bzlib.o all: libbz2.a bzip2 bzip2recover test bzip2: libbz2.a bzip2.o $(CC) $(CFLAGS) $(LDFLAGS) -o bzip2 bzip2.o -L. -lbz2 bzip2recover: bzip2recover.o $(CC) $(CFLAGS) $(LDFLAGS) -o bzip2recover bzip2recover.o libbz2.a: $(OBJS) rm -f libbz2.a $(AR) cq libbz2.a $(OBJS) @if ( test -f $(RANLIB) -o -f /usr/bin/ranlib -o \ -f /bin/ranlib -o -f /usr/ccs/bin/ranlib ) ; then \ echo $(RANLIB) libbz2.a ; \ $(RANLIB) libbz2.a ; \ fi check: test test: bzip2 @cat words1 ./bzip2 -1 < sample1.ref > sample1.rb2 ./bzip2 -2 < sample2.ref > sample2.rb2 ./bzip2 -3 < sample3.ref > sample3.rb2 ./bzip2 -d < sample1.bz2 > sample1.tst ./bzip2 -d < sample2.bz2 > sample2.tst ./bzip2 -ds < sample3.bz2 > sample3.tst cmp sample1.bz2 sample1.rb2 cmp sample2.bz2 sample2.rb2 cmp sample3.bz2 sample3.rb2 cmp sample1.tst sample1.ref cmp sample2.tst sample2.ref cmp sample3.tst sample3.ref @cat words3 install: bzip2 bzip2recover if ( test ! -d $(PREFIX)/bin ) ; then mkdir -p $(PREFIX)/bin ; fi if ( test ! -d $(PREFIX)/lib ) ; then mkdir -p $(PREFIX)/lib ; fi if ( test ! -d $(PREFIX)/man ) ; then mkdir -p $(PREFIX)/man ; fi if ( test ! -d $(PREFIX)/man/man1 ) ; then mkdir -p $(PREFIX)/man/man1 ; fi if ( test ! -d $(PREFIX)/include ) ; then mkdir -p $(PREFIX)/include ; fi cp -f bzip2 $(PREFIX)/bin/bzip2 cp -f bzip2 $(PREFIX)/bin/bunzip2 cp -f bzip2 $(PREFIX)/bin/bzcat cp -f bzip2recover $(PREFIX)/bin/bzip2recover chmod a+x $(PREFIX)/bin/bzip2 chmod a+x $(PREFIX)/bin/bunzip2 chmod a+x $(PREFIX)/bin/bzcat chmod a+x $(PREFIX)/bin/bzip2recover cp -f bzip2.1 $(PREFIX)/man/man1 chmod a+r $(PREFIX)/man/man1/bzip2.1 cp -f bzlib.h $(PREFIX)/include chmod a+r $(PREFIX)/include/bzlib.h cp -f libbz2.a $(PREFIX)/lib chmod a+r $(PREFIX)/lib/libbz2.a cp -f bzgrep $(PREFIX)/bin/bzgrep ln -s -f $(PREFIX)/bin/bzgrep $(PREFIX)/bin/bzegrep ln -s -f $(PREFIX)/bin/bzgrep $(PREFIX)/bin/bzfgrep chmod a+x $(PREFIX)/bin/bzgrep cp -f bzmore $(PREFIX)/bin/bzmore ln -s -f $(PREFIX)/bin/bzmore $(PREFIX)/bin/bzless chmod a+x $(PREFIX)/bin/bzmore cp -f bzdiff $(PREFIX)/bin/bzdiff ln -s -f $(PREFIX)/bin/bzdiff $(PREFIX)/bin/bzcmp chmod a+x $(PREFIX)/bin/bzdiff cp -f bzgrep.1 bzmore.1 bzdiff.1 $(PREFIX)/man/man1 chmod a+r $(PREFIX)/man/man1/bzgrep.1 chmod a+r $(PREFIX)/man/man1/bzmore.1 chmod a+r $(PREFIX)/man/man1/bzdiff.1 echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzegrep.1 echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzfgrep.1 echo ".so man1/bzmore.1" > $(PREFIX)/man/man1/bzless.1 echo ".so man1/bzdiff.1" > $(PREFIX)/man/man1/bzcmp.1 clean: rm -f *.o libbz2.a bzip2 bzip2recover \ sample1.rb2 sample2.rb2 sample3.rb2 \ sample1.tst sample2.tst sample3.tst blocksort.o: blocksort.c @cat words0 $(CC) $(CFLAGS) -c blocksort.c huffman.o: huffman.c $(CC) $(CFLAGS) -c huffman.c crctable.o: crctable.c $(CC) $(CFLAGS) -c crctable.c randtable.o: randtable.c $(CC) $(CFLAGS) -c randtable.c compress.o: compress.c $(CC) $(CFLAGS) -c compress.c decompress.o: decompress.c $(CC) $(CFLAGS) -c decompress.c bzlib.o: bzlib.c $(CC) $(CFLAGS) -c bzlib.c bzip2.o: bzip2.c $(CC) $(CFLAGS) -c bzip2.c bzip2recover.o: bzip2recover.c $(CC) $(CFLAGS) -c bzip2recover.c distclean: clean rm -f manual.ps manual.html manual.pdf DISTNAME=bzip2-1.0.6 dist: check manual rm -f $(DISTNAME) ln -s -f . $(DISTNAME) tar cvf $(DISTNAME).tar \ $(DISTNAME)/blocksort.c \ $(DISTNAME)/huffman.c \ $(DISTNAME)/crctable.c \ $(DISTNAME)/randtable.c \ $(DISTNAME)/compress.c \ $(DISTNAME)/decompress.c \ $(DISTNAME)/bzlib.c \ $(DISTNAME)/bzip2.c \ $(DISTNAME)/bzip2recover.c \ $(DISTNAME)/bzlib.h \ $(DISTNAME)/bzlib_private.h \ $(DISTNAME)/Makefile \ $(DISTNAME)/LICENSE \ $(DISTNAME)/bzip2.1 \ $(DISTNAME)/bzip2.1.preformatted \ $(DISTNAME)/bzip2.txt \ $(DISTNAME)/words0 \ $(DISTNAME)/words1 \ $(DISTNAME)/words2 \ $(DISTNAME)/words3 \ $(DISTNAME)/sample1.ref \ $(DISTNAME)/sample2.ref \ $(DISTNAME)/sample3.ref \ $(DISTNAME)/sample1.bz2 \ $(DISTNAME)/sample2.bz2 \ $(DISTNAME)/sample3.bz2 \ $(DISTNAME)/dlltest.c \ $(DISTNAME)/manual.html \ $(DISTNAME)/manual.pdf \ $(DISTNAME)/manual.ps \ $(DISTNAME)/README \ $(DISTNAME)/README.COMPILATION.PROBLEMS \ $(DISTNAME)/README.XML.STUFF \ $(DISTNAME)/CHANGES \ $(DISTNAME)/libbz2.def \ $(DISTNAME)/libbz2.dsp \ $(DISTNAME)/dlltest.dsp \ $(DISTNAME)/makefile.msc \ $(DISTNAME)/unzcrash.c \ $(DISTNAME)/spewG.c \ $(DISTNAME)/mk251.c \ $(DISTNAME)/bzdiff \ $(DISTNAME)/bzdiff.1 \ $(DISTNAME)/bzmore \ $(DISTNAME)/bzmore.1 \ $(DISTNAME)/bzgrep \ $(DISTNAME)/bzgrep.1 \ $(DISTNAME)/Makefile-libbz2_so \ $(DISTNAME)/bz-common.xsl \ $(DISTNAME)/bz-fo.xsl \ $(DISTNAME)/bz-html.xsl \ $(DISTNAME)/bzip.css \ $(DISTNAME)/entities.xml \ $(DISTNAME)/manual.xml \ $(DISTNAME)/format.pl \ $(DISTNAME)/xmlproc.sh gzip -v $(DISTNAME).tar # For rebuilding the manual from sources on my SuSE 9.1 box MANUAL_SRCS= bz-common.xsl bz-fo.xsl bz-html.xsl bzip.css \ entities.xml manual.xml manual: manual.html manual.ps manual.pdf manual.ps: $(MANUAL_SRCS) ./xmlproc.sh -ps manual.xml manual.pdf: $(MANUAL_SRCS) ./xmlproc.sh -pdf manual.xml manual.html: $(MANUAL_SRCS) ./xmlproc.sh -html manual.xml genometools-1.5.1/src/external/bzip2-1.0.6/Makefile-libbz2_so000066400000000000000000000033061211610345200234700ustar00rootroot00000000000000 # This Makefile builds a shared version of the library, # libbz2.so.1.0.6, with soname libbz2.so.1.0, # at least on x86-Linux (RedHat 7.2), # with gcc-2.96 20000731 (Red Hat Linux 7.1 2.96-98). # Please see the README file for some important info # about building the library like this. # ------------------------------------------------------------------ # This file is part of bzip2/libbzip2, a program and library for # lossless, block-sorting data compression. # # bzip2/libbzip2 version 1.0.6 of 6 September 2010 # Copyright (C) 1996-2010 Julian Seward # # Please read the WARNING, DISCLAIMER and PATENTS sections in the # README file. # # This program is released under the terms of the license contained # in the file LICENSE. # ------------------------------------------------------------------ SHELL=/bin/sh CC=gcc BIGFILES=-D_FILE_OFFSET_BITS=64 CFLAGS=-fpic -fPIC -Wall -Winline -O2 -g $(BIGFILES) OBJS= blocksort.o \ huffman.o \ crctable.o \ randtable.o \ compress.o \ decompress.o \ bzlib.o all: $(OBJS) $(CC) -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 $(OBJS) $(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.1.0.6 rm -f libbz2.so.1.0 ln -s libbz2.so.1.0.6 libbz2.so.1.0 clean: rm -f $(OBJS) bzip2.o libbz2.so.1.0.6 libbz2.so.1.0 bzip2-shared blocksort.o: blocksort.c $(CC) $(CFLAGS) -c blocksort.c huffman.o: huffman.c $(CC) $(CFLAGS) -c huffman.c crctable.o: crctable.c $(CC) $(CFLAGS) -c crctable.c randtable.o: randtable.c $(CC) $(CFLAGS) -c randtable.c compress.o: compress.c $(CC) $(CFLAGS) -c compress.c decompress.o: decompress.c $(CC) $(CFLAGS) -c decompress.c bzlib.o: bzlib.c $(CC) $(CFLAGS) -c bzlib.c genometools-1.5.1/src/external/bzip2-1.0.6/README000066400000000000000000000166361211610345200210370ustar00rootroot00000000000000 This is the README for bzip2/libzip2. This version is fully compatible with the previous public releases. ------------------------------------------------------------------ This file is part of bzip2/libbzip2, a program and library for lossless, block-sorting data compression. bzip2/libbzip2 version 1.0.6 of 6 September 2010 Copyright (C) 1996-2010 Julian Seward Please read the WARNING, DISCLAIMER and PATENTS sections in this file. This program is released under the terms of the license contained in the file LICENSE. ------------------------------------------------------------------ Complete documentation is available in Postscript form (manual.ps), PDF (manual.pdf) or html (manual.html). A plain-text version of the manual page is available as bzip2.txt. HOW TO BUILD -- UNIX Type 'make'. This builds the library libbz2.a and then the programs bzip2 and bzip2recover. Six self-tests are run. If the self-tests complete ok, carry on to installation: To install in /usr/local/bin, /usr/local/lib, /usr/local/man and /usr/local/include, type make install To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type make install PREFIX=/xxx/yyy If you are (justifiably) paranoid and want to see what 'make install' is going to do, you can first do make -n install or make -n install PREFIX=/xxx/yyy respectively. The -n instructs make to show the commands it would execute, but not actually execute them. HOW TO BUILD -- UNIX, shared library libbz2.so. Do 'make -f Makefile-libbz2_so'. This Makefile seems to work for Linux-ELF (RedHat 7.2 on an x86 box), with gcc. I make no claims that it works for any other platform, though I suspect it probably will work for most platforms employing both ELF and gcc. bzip2-shared, a client of the shared library, is also built, but not self-tested. So I suggest you also build using the normal Makefile, since that conducts a self-test. A second reason to prefer the version statically linked to the library is that, on x86 platforms, building shared objects makes a valuable register (%ebx) unavailable to gcc, resulting in a slowdown of 10%-20%, at least for bzip2. Important note for people upgrading .so's from 0.9.0/0.9.5 to version 1.0.X. All the functions in the library have been renamed, from (eg) bzCompress to BZ2_bzCompress, to avoid namespace pollution. Unfortunately this means that the libbz2.so created by Makefile-libbz2_so will not work with any program which used an older version of the library. I do encourage library clients to make the effort to upgrade to use version 1.0, since it is both faster and more robust than previous versions. HOW TO BUILD -- Windows 95, NT, DOS, Mac, etc. It's difficult for me to support compilation on all these platforms. My approach is to collect binaries for these platforms, and put them on the master web site (http://www.bzip.org). Look there. However (FWIW), bzip2-1.0.X is very standard ANSI C and should compile unmodified with MS Visual C. If you have difficulties building, you might want to read README.COMPILATION.PROBLEMS. At least using MS Visual C++ 6, you can build from the unmodified sources by issuing, in a command shell: nmake -f makefile.msc (you may need to first run the MSVC-provided script VCVARS32.BAT so as to set up paths to the MSVC tools correctly). VALIDATION Correct operation, in the sense that a compressed file can always be decompressed to reproduce the original, is obviously of paramount importance. To validate bzip2, I used a modified version of Mark Nelson's churn program. Churn is an automated test driver which recursively traverses a directory structure, using bzip2 to compress and then decompress each file it encounters, and checking that the decompressed data is the same as the original. Please read and be aware of the following: WARNING: This program and library (attempts to) compress data by performing several non-trivial transformations on it. Unless you are 100% familiar with *all* the algorithms contained herein, and with the consequences of modifying them, you should NOT meddle with the compression or decompression machinery. Incorrect changes can and very likely *will* lead to disastrous loss of data. DISCLAIMER: I TAKE NO RESPONSIBILITY FOR ANY LOSS OF DATA ARISING FROM THE USE OF THIS PROGRAM/LIBRARY, HOWSOEVER CAUSED. Every compression of a file implies an assumption that the compressed file can be decompressed to reproduce the original. Great efforts in design, coding and testing have been made to ensure that this program works correctly. However, the complexity of the algorithms, and, in particular, the presence of various special cases in the code which occur with very low but non-zero probability make it impossible to rule out the possibility of bugs remaining in the program. DO NOT COMPRESS ANY DATA WITH THIS PROGRAM UNLESS YOU ARE PREPARED TO ACCEPT THE POSSIBILITY, HOWEVER SMALL, THAT THE DATA WILL NOT BE RECOVERABLE. That is not to say this program is inherently unreliable. Indeed, I very much hope the opposite is true. bzip2/libbzip2 has been carefully constructed and extensively tested. PATENTS: To the best of my knowledge, bzip2/libbzip2 does not use any patented algorithms. However, I do not have the resources to carry out a patent search. Therefore I cannot give any guarantee of the above statement. WHAT'S NEW IN 0.9.0 (as compared to 0.1pl2) ? * Approx 10% faster compression, 30% faster decompression * -t (test mode) is a lot quicker * Can decompress concatenated compressed files * Programming interface, so programs can directly read/write .bz2 files * Less restrictive (BSD-style) licensing * Flag handling more compatible with GNU gzip * Much more documentation, i.e., a proper user manual * Hopefully, improved portability (at least of the library) WHAT'S NEW IN 0.9.5 ? * Compression speed is much less sensitive to the input data than in previous versions. Specifically, the very slow performance caused by repetitive data is fixed. * Many small improvements in file and flag handling. * A Y2K statement. WHAT'S NEW IN 1.0.0 ? See the CHANGES file. WHAT'S NEW IN 1.0.2 ? See the CHANGES file. WHAT'S NEW IN 1.0.3 ? See the CHANGES file. WHAT'S NEW IN 1.0.4 ? See the CHANGES file. WHAT'S NEW IN 1.0.5 ? See the CHANGES file. WHAT'S NEW IN 1.0.6 ? See the CHANGES file. I hope you find bzip2 useful. Feel free to contact me at jseward@bzip.org if you have any suggestions or queries. Many people mailed me with comments, suggestions and patches after the releases of bzip-0.15, bzip-0.21, and bzip2 versions 0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1, 1.0.2 and 1.0.3, and the changes in bzip2 are largely a result of this feedback. I thank you for your comments. bzip2's "home" is http://www.bzip.org/ Julian Seward jseward@bzip.org Cambridge, UK. 18 July 1996 (version 0.15) 25 August 1996 (version 0.21) 7 August 1997 (bzip2, version 0.1) 29 August 1997 (bzip2, version 0.1pl2) 23 August 1998 (bzip2, version 0.9.0) 8 June 1999 (bzip2, version 0.9.5) 4 Sept 1999 (bzip2, version 0.9.5d) 5 May 2000 (bzip2, version 1.0pre8) 30 December 2001 (bzip2, version 1.0.2pre1) 15 February 2005 (bzip2, version 1.0.3) 20 December 2006 (bzip2, version 1.0.4) 10 December 2007 (bzip2, version 1.0.5) 6 Sept 2010 (bzip2, version 1.0.6) genometools-1.5.1/src/external/bzip2-1.0.6/README.COMPILATION.PROBLEMS000066400000000000000000000047171211610345200240330ustar00rootroot00000000000000------------------------------------------------------------------ This file is part of bzip2/libbzip2, a program and library for lossless, block-sorting data compression. bzip2/libbzip2 version 1.0.6 of 6 September 2010 Copyright (C) 1996-2010 Julian Seward Please read the WARNING, DISCLAIMER and PATENTS sections in the README file. This program is released under the terms of the license contained in the file LICENSE. ------------------------------------------------------------------ bzip2-1.0.6 should compile without problems on the vast majority of platforms. Using the supplied Makefile, I've built and tested it myself for x86-linux and amd64-linux. With makefile.msc, Visual C++ 6.0 and nmake, you can build a native Win32 version too. Large file support seems to work correctly on at least on amd64-linux. When I say "large file" I mean a file of size 2,147,483,648 (2^31) bytes or above. Many older OSs can't handle files above this size, but many newer ones can. Large files are pretty huge -- most files you'll encounter are not Large Files. Early versions of bzip2 (0.1, 0.9.0, 0.9.5) compiled on a wide variety of platforms without difficulty, and I hope this version will continue in that tradition. However, in order to support large files, I've had to include the define -D_FILE_OFFSET_BITS=64 in the Makefile. This can cause problems. The technique of adding -D_FILE_OFFSET_BITS=64 to get large file support is, as far as I know, the Recommended Way to get correct large file support. For more details, see the Large File Support Specification, published by the Large File Summit, at http://ftp.sas.com/standards/large.file As a general comment, if you get compilation errors which you think are related to large file support, try removing the above define from the Makefile, ie, delete the line BIGFILES=-D_FILE_OFFSET_BITS=64 from the Makefile, and do 'make clean ; make'. This will give you a version of bzip2 without large file support, which, for most applications, is probably not a problem. Alternatively, try some of the platform-specific hints listed below. You can use the spewG.c program to generate huge files to test bzip2's large file support, if you are feeling paranoid. Be aware though that any compilation problems which affect bzip2 will also affect spewG.c, alas. AIX: I have reports that for large file support, you need to specify -D_LARGE_FILES rather than -D_FILE_OFFSET_BITS=64. I have not tested this myself. genometools-1.5.1/src/external/bzip2-1.0.6/README.XML.STUFF000066400000000000000000000025241211610345200223530ustar00rootroot00000000000000 ---------------------------------------------------------------- This file is part of bzip2/libbzip2, a program and library for lossless, block-sorting data compression. bzip2/libbzip2 version 1.0.6 of 6 September 2010 Copyright (C) 1996-2010 Julian Seward Please read the WARNING, DISCLAIMER and PATENTS sections in the README file. This program is released under the terms of the license contained in the file LICENSE. ---------------------------------------------------------------- The script xmlproc.sh takes an xml file as input, and processes it to create .pdf, .html or .ps output. It uses format.pl, a perl script to format 
 blocks nicely,
 and add CDATA tags so writers do not have to use eg. < 

The file "entities.xml" must be edited to reflect current
version, year, etc.


Usage:

  ./xmlproc.sh -v manual.xml
  Validates an xml file to ensure no dtd-compliance errors

  ./xmlproc.sh -html manual.xml
  Output: manual.html

  ./xmlproc.sh -pdf manual.xml
  Output: manual.pdf

  ./xmlproc.sh -ps manual.xml
  Output: manual.ps


Notum bene: 
- pdfxmltex barfs if given a filename with an underscore in it

- xmltex won't work yet - there's a bug in passivetex
    which we are all waiting for Sebastian to fix.
  So we are going the xml -> pdf -> ps route for the time being,
    using pdfxmltex.
genometools-1.5.1/src/external/bzip2-1.0.6/blocksort.c000066400000000000000000000737461211610345200223320ustar00rootroot00000000000000
/*-------------------------------------------------------------*/
/*--- Block sorting machinery                               ---*/
/*---                                           blocksort.c ---*/
/*-------------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


#include "bzlib_private.h"

/*---------------------------------------------*/
/*--- Fallback O(N log(N)^2) sorting        ---*/
/*--- algorithm, for repetitive blocks      ---*/
/*---------------------------------------------*/

/*---------------------------------------------*/
static 
__inline__
void fallbackSimpleSort ( UInt32* fmap, 
                          UInt32* eclass, 
                          Int32   lo, 
                          Int32   hi )
{
   Int32 i, j, tmp;
   UInt32 ec_tmp;

   if (lo == hi) return;

   if (hi - lo > 3) {
      for ( i = hi-4; i >= lo; i-- ) {
         tmp = fmap[i];
         ec_tmp = eclass[tmp];
         for ( j = i+4; j <= hi && ec_tmp > eclass[fmap[j]]; j += 4 )
            fmap[j-4] = fmap[j];
         fmap[j-4] = tmp;
      }
   }

   for ( i = hi-1; i >= lo; i-- ) {
      tmp = fmap[i];
      ec_tmp = eclass[tmp];
      for ( j = i+1; j <= hi && ec_tmp > eclass[fmap[j]]; j++ )
         fmap[j-1] = fmap[j];
      fmap[j-1] = tmp;
   }
}


/*---------------------------------------------*/
#define fswap(zz1, zz2) \
   { Int32 zztmp = zz1; zz1 = zz2; zz2 = zztmp; }

#define fvswap(zzp1, zzp2, zzn)       \
{                                     \
   Int32 yyp1 = (zzp1);               \
   Int32 yyp2 = (zzp2);               \
   Int32 yyn  = (zzn);                \
   while (yyn > 0) {                  \
      fswap(fmap[yyp1], fmap[yyp2]);  \
      yyp1++; yyp2++; yyn--;          \
   }                                  \
}


#define fmin(a,b) ((a) < (b)) ? (a) : (b)

#define fpush(lz,hz) { stackLo[sp] = lz; \
                       stackHi[sp] = hz; \
                       sp++; }

#define fpop(lz,hz) { sp--;              \
                      lz = stackLo[sp];  \
                      hz = stackHi[sp]; }

#define FALLBACK_QSORT_SMALL_THRESH 10
#define FALLBACK_QSORT_STACK_SIZE   100


static
void fallbackQSort3 ( UInt32* fmap, 
                      UInt32* eclass,
                      Int32   loSt, 
                      Int32   hiSt )
{
   Int32 unLo, unHi, ltLo, gtHi, n, m;
   Int32 sp, lo, hi;
   UInt32 med, r, r3;
   Int32 stackLo[FALLBACK_QSORT_STACK_SIZE];
   Int32 stackHi[FALLBACK_QSORT_STACK_SIZE];

   r = 0;

   sp = 0;
   fpush ( loSt, hiSt );

   while (sp > 0) {

      AssertH ( sp < FALLBACK_QSORT_STACK_SIZE - 1, 1004 );

      fpop ( lo, hi );
      if (hi - lo < FALLBACK_QSORT_SMALL_THRESH) {
         fallbackSimpleSort ( fmap, eclass, lo, hi );
         continue;
      }

      /* Random partitioning.  Median of 3 sometimes fails to
         avoid bad cases.  Median of 9 seems to help but 
         looks rather expensive.  This too seems to work but
         is cheaper.  Guidance for the magic constants 
         7621 and 32768 is taken from Sedgewick's algorithms
         book, chapter 35.
      */
      r = ((r * 7621) + 1) % 32768;
      r3 = r % 3;
      if (r3 == 0) med = eclass[fmap[lo]]; else
      if (r3 == 1) med = eclass[fmap[(lo+hi)>>1]]; else
                   med = eclass[fmap[hi]];

      unLo = ltLo = lo;
      unHi = gtHi = hi;

      while (1) {
         while (1) {
            if (unLo > unHi) break;
            n = (Int32)eclass[fmap[unLo]] - (Int32)med;
            if (n == 0) { 
               fswap(fmap[unLo], fmap[ltLo]); 
               ltLo++; unLo++; 
               continue; 
            };
            if (n > 0) break;
            unLo++;
         }
         while (1) {
            if (unLo > unHi) break;
            n = (Int32)eclass[fmap[unHi]] - (Int32)med;
            if (n == 0) { 
               fswap(fmap[unHi], fmap[gtHi]); 
               gtHi--; unHi--; 
               continue; 
            };
            if (n < 0) break;
            unHi--;
         }
         if (unLo > unHi) break;
         fswap(fmap[unLo], fmap[unHi]); unLo++; unHi--;
      }

      AssertD ( unHi == unLo-1, "fallbackQSort3(2)" );

      if (gtHi < ltLo) continue;

      n = fmin(ltLo-lo, unLo-ltLo); fvswap(lo, unLo-n, n);
      m = fmin(hi-gtHi, gtHi-unHi); fvswap(unLo, hi-m+1, m);

      n = lo + unLo - ltLo - 1;
      m = hi - (gtHi - unHi) + 1;

      if (n - lo > hi - m) {
         fpush ( lo, n );
         fpush ( m, hi );
      } else {
         fpush ( m, hi );
         fpush ( lo, n );
      }
   }
}

#undef fmin
#undef fpush
#undef fpop
#undef fswap
#undef fvswap
#undef FALLBACK_QSORT_SMALL_THRESH
#undef FALLBACK_QSORT_STACK_SIZE


/*---------------------------------------------*/
/* Pre:
      nblock > 0
      eclass exists for [0 .. nblock-1]
      ((UChar*)eclass) [0 .. nblock-1] holds block
      ptr exists for [0 .. nblock-1]

   Post:
      ((UChar*)eclass) [0 .. nblock-1] holds block
      All other areas of eclass destroyed
      fmap [0 .. nblock-1] holds sorted order
      bhtab [ 0 .. 2+(nblock/32) ] destroyed
*/

#define       SET_BH(zz)  bhtab[(zz) >> 5] |= (1 << ((zz) & 31))
#define     CLEAR_BH(zz)  bhtab[(zz) >> 5] &= ~(1 << ((zz) & 31))
#define     ISSET_BH(zz)  (bhtab[(zz) >> 5] & (1 << ((zz) & 31)))
#define      WORD_BH(zz)  bhtab[(zz) >> 5]
#define UNALIGNED_BH(zz)  ((zz) & 0x01f)

static
void fallbackSort ( UInt32* fmap, 
                    UInt32* eclass, 
                    UInt32* bhtab,
                    Int32   nblock,
                    Int32   verb )
{
   Int32 ftab[257];
   Int32 ftabCopy[256];
   Int32 H, i, j, k, l, r, cc, cc1;
   Int32 nNotDone;
   Int32 nBhtab;
   UChar* eclass8 = (UChar*)eclass;

   /*--
      Initial 1-char radix sort to generate
      initial fmap and initial BH bits.
   --*/
   if (verb >= 4)
      VPrintf0 ( "        bucket sorting ...\n" );
   for (i = 0; i < 257;    i++) ftab[i] = 0;
   for (i = 0; i < nblock; i++) ftab[eclass8[i]]++;
   for (i = 0; i < 256;    i++) ftabCopy[i] = ftab[i];
   for (i = 1; i < 257;    i++) ftab[i] += ftab[i-1];

   for (i = 0; i < nblock; i++) {
      j = eclass8[i];
      k = ftab[j] - 1;
      ftab[j] = k;
      fmap[k] = i;
   }

   nBhtab = 2 + (nblock / 32);
   for (i = 0; i < nBhtab; i++) bhtab[i] = 0;
   for (i = 0; i < 256; i++) SET_BH(ftab[i]);

   /*--
      Inductively refine the buckets.  Kind-of an
      "exponential radix sort" (!), inspired by the
      Manber-Myers suffix array construction algorithm.
   --*/

   /*-- set sentinel bits for block-end detection --*/
   for (i = 0; i < 32; i++) { 
      SET_BH(nblock + 2*i);
      CLEAR_BH(nblock + 2*i + 1);
   }

   /*-- the log(N) loop --*/
   H = 1;
   while (1) {

      if (verb >= 4) 
         VPrintf1 ( "        depth %6d has ", H );

      j = 0;
      for (i = 0; i < nblock; i++) {
         if (ISSET_BH(i)) j = i;
         k = fmap[i] - H; if (k < 0) k += nblock;
         eclass[k] = j;
      }

      nNotDone = 0;
      r = -1;
      while (1) {

	 /*-- find the next non-singleton bucket --*/
         k = r + 1;
         while (ISSET_BH(k) && UNALIGNED_BH(k)) k++;
         if (ISSET_BH(k)) {
            while (WORD_BH(k) == 0xffffffff) k += 32;
            while (ISSET_BH(k)) k++;
         }
         l = k - 1;
         if (l >= nblock) break;
         while (!ISSET_BH(k) && UNALIGNED_BH(k)) k++;
         if (!ISSET_BH(k)) {
            while (WORD_BH(k) == 0x00000000) k += 32;
            while (!ISSET_BH(k)) k++;
         }
         r = k - 1;
         if (r >= nblock) break;

         /*-- now [l, r] bracket current bucket --*/
         if (r > l) {
            nNotDone += (r - l + 1);
            fallbackQSort3 ( fmap, eclass, l, r );

            /*-- scan bucket and generate header bits-- */
            cc = -1;
            for (i = l; i <= r; i++) {
               cc1 = eclass[fmap[i]];
               if (cc != cc1) { SET_BH(i); cc = cc1; };
            }
         }
      }

      if (verb >= 4) 
         VPrintf1 ( "%6d unresolved strings\n", nNotDone );

      H *= 2;
      if (H > nblock || nNotDone == 0) break;
   }

   /*-- 
      Reconstruct the original block in
      eclass8 [0 .. nblock-1], since the
      previous phase destroyed it.
   --*/
   if (verb >= 4)
      VPrintf0 ( "        reconstructing block ...\n" );
   j = 0;
   for (i = 0; i < nblock; i++) {
      while (ftabCopy[j] == 0) j++;
      ftabCopy[j]--;
      eclass8[fmap[i]] = (UChar)j;
   }
   AssertH ( j < 256, 1005 );
}

#undef       SET_BH
#undef     CLEAR_BH
#undef     ISSET_BH
#undef      WORD_BH
#undef UNALIGNED_BH


/*---------------------------------------------*/
/*--- The main, O(N^2 log(N)) sorting       ---*/
/*--- algorithm.  Faster for "normal"       ---*/
/*--- non-repetitive blocks.                ---*/
/*---------------------------------------------*/

/*---------------------------------------------*/
static
__inline__
Bool mainGtU ( UInt32  i1, 
               UInt32  i2,
               UChar*  block, 
               UInt16* quadrant,
               UInt32  nblock,
               Int32*  budget )
{
   Int32  k;
   UChar  c1, c2;
   UInt16 s1, s2;

   AssertD ( i1 != i2, "mainGtU" );
   /* 1 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 2 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 3 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 4 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 5 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 6 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 7 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 8 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 9 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 10 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 11 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;
   /* 12 */
   c1 = block[i1]; c2 = block[i2];
   if (c1 != c2) return (c1 > c2);
   i1++; i2++;

   k = nblock + 8;

   do {
      /* 1 */
      c1 = block[i1]; c2 = block[i2];
      if (c1 != c2) return (c1 > c2);
      s1 = quadrant[i1]; s2 = quadrant[i2];
      if (s1 != s2) return (s1 > s2);
      i1++; i2++;
      /* 2 */
      c1 = block[i1]; c2 = block[i2];
      if (c1 != c2) return (c1 > c2);
      s1 = quadrant[i1]; s2 = quadrant[i2];
      if (s1 != s2) return (s1 > s2);
      i1++; i2++;
      /* 3 */
      c1 = block[i1]; c2 = block[i2];
      if (c1 != c2) return (c1 > c2);
      s1 = quadrant[i1]; s2 = quadrant[i2];
      if (s1 != s2) return (s1 > s2);
      i1++; i2++;
      /* 4 */
      c1 = block[i1]; c2 = block[i2];
      if (c1 != c2) return (c1 > c2);
      s1 = quadrant[i1]; s2 = quadrant[i2];
      if (s1 != s2) return (s1 > s2);
      i1++; i2++;
      /* 5 */
      c1 = block[i1]; c2 = block[i2];
      if (c1 != c2) return (c1 > c2);
      s1 = quadrant[i1]; s2 = quadrant[i2];
      if (s1 != s2) return (s1 > s2);
      i1++; i2++;
      /* 6 */
      c1 = block[i1]; c2 = block[i2];
      if (c1 != c2) return (c1 > c2);
      s1 = quadrant[i1]; s2 = quadrant[i2];
      if (s1 != s2) return (s1 > s2);
      i1++; i2++;
      /* 7 */
      c1 = block[i1]; c2 = block[i2];
      if (c1 != c2) return (c1 > c2);
      s1 = quadrant[i1]; s2 = quadrant[i2];
      if (s1 != s2) return (s1 > s2);
      i1++; i2++;
      /* 8 */
      c1 = block[i1]; c2 = block[i2];
      if (c1 != c2) return (c1 > c2);
      s1 = quadrant[i1]; s2 = quadrant[i2];
      if (s1 != s2) return (s1 > s2);
      i1++; i2++;

      if (i1 >= nblock) i1 -= nblock;
      if (i2 >= nblock) i2 -= nblock;

      k -= 8;
      (*budget)--;
   }
      while (k >= 0);

   return False;
}


/*---------------------------------------------*/
/*--
   Knuth's increments seem to work better
   than Incerpi-Sedgewick here.  Possibly
   because the number of elems to sort is
   usually small, typically <= 20.
--*/
static
Int32 incs[14] = { 1, 4, 13, 40, 121, 364, 1093, 3280,
                   9841, 29524, 88573, 265720,
                   797161, 2391484 };

static
void mainSimpleSort ( UInt32* ptr,
                      UChar*  block,
                      UInt16* quadrant,
                      Int32   nblock,
                      Int32   lo, 
                      Int32   hi, 
                      Int32   d,
                      Int32*  budget )
{
   Int32 i, j, h, bigN, hp;
   UInt32 v;

   bigN = hi - lo + 1;
   if (bigN < 2) return;

   hp = 0;
   while (incs[hp] < bigN) hp++;
   hp--;

   for (; hp >= 0; hp--) {
      h = incs[hp];

      i = lo + h;
      while (True) {

         /*-- copy 1 --*/
         if (i > hi) break;
         v = ptr[i];
         j = i;
         while ( mainGtU ( 
                    ptr[j-h]+d, v+d, block, quadrant, nblock, budget 
                 ) ) {
            ptr[j] = ptr[j-h];
            j = j - h;
            if (j <= (lo + h - 1)) break;
         }
         ptr[j] = v;
         i++;

         /*-- copy 2 --*/
         if (i > hi) break;
         v = ptr[i];
         j = i;
         while ( mainGtU ( 
                    ptr[j-h]+d, v+d, block, quadrant, nblock, budget 
                 ) ) {
            ptr[j] = ptr[j-h];
            j = j - h;
            if (j <= (lo + h - 1)) break;
         }
         ptr[j] = v;
         i++;

         /*-- copy 3 --*/
         if (i > hi) break;
         v = ptr[i];
         j = i;
         while ( mainGtU ( 
                    ptr[j-h]+d, v+d, block, quadrant, nblock, budget 
                 ) ) {
            ptr[j] = ptr[j-h];
            j = j - h;
            if (j <= (lo + h - 1)) break;
         }
         ptr[j] = v;
         i++;

         if (*budget < 0) return;
      }
   }
}


/*---------------------------------------------*/
/*--
   The following is an implementation of
   an elegant 3-way quicksort for strings,
   described in a paper "Fast Algorithms for
   Sorting and Searching Strings", by Robert
   Sedgewick and Jon L. Bentley.
--*/

#define mswap(zz1, zz2) \
   { Int32 zztmp = zz1; zz1 = zz2; zz2 = zztmp; }

#define mvswap(zzp1, zzp2, zzn)       \
{                                     \
   Int32 yyp1 = (zzp1);               \
   Int32 yyp2 = (zzp2);               \
   Int32 yyn  = (zzn);                \
   while (yyn > 0) {                  \
      mswap(ptr[yyp1], ptr[yyp2]);    \
      yyp1++; yyp2++; yyn--;          \
   }                                  \
}

static 
__inline__
UChar mmed3 ( UChar a, UChar b, UChar c )
{
   UChar t;
   if (a > b) { t = a; a = b; b = t; };
   if (b > c) { 
      b = c;
      if (a > b) b = a;
   }
   return b;
}

#define mmin(a,b) ((a) < (b)) ? (a) : (b)

#define mpush(lz,hz,dz) { stackLo[sp] = lz; \
                          stackHi[sp] = hz; \
                          stackD [sp] = dz; \
                          sp++; }

#define mpop(lz,hz,dz) { sp--;             \
                         lz = stackLo[sp]; \
                         hz = stackHi[sp]; \
                         dz = stackD [sp]; }


#define mnextsize(az) (nextHi[az]-nextLo[az])

#define mnextswap(az,bz)                                        \
   { Int32 tz;                                                  \
     tz = nextLo[az]; nextLo[az] = nextLo[bz]; nextLo[bz] = tz; \
     tz = nextHi[az]; nextHi[az] = nextHi[bz]; nextHi[bz] = tz; \
     tz = nextD [az]; nextD [az] = nextD [bz]; nextD [bz] = tz; }


#define MAIN_QSORT_SMALL_THRESH 20
#define MAIN_QSORT_DEPTH_THRESH (BZ_N_RADIX + BZ_N_QSORT)
#define MAIN_QSORT_STACK_SIZE 100

static
void mainQSort3 ( UInt32* ptr,
                  UChar*  block,
                  UInt16* quadrant,
                  Int32   nblock,
                  Int32   loSt, 
                  Int32   hiSt, 
                  Int32   dSt,
                  Int32*  budget )
{
   Int32 unLo, unHi, ltLo, gtHi, n, m, med;
   Int32 sp, lo, hi, d;

   Int32 stackLo[MAIN_QSORT_STACK_SIZE];
   Int32 stackHi[MAIN_QSORT_STACK_SIZE];
   Int32 stackD [MAIN_QSORT_STACK_SIZE];

   Int32 nextLo[3];
   Int32 nextHi[3];
   Int32 nextD [3];

   sp = 0;
   mpush ( loSt, hiSt, dSt );

   while (sp > 0) {

      AssertH ( sp < MAIN_QSORT_STACK_SIZE - 2, 1001 );

      mpop ( lo, hi, d );
      if (hi - lo < MAIN_QSORT_SMALL_THRESH || 
          d > MAIN_QSORT_DEPTH_THRESH) {
         mainSimpleSort ( ptr, block, quadrant, nblock, lo, hi, d, budget );
         if (*budget < 0) return;
         continue;
      }

      med = (Int32) 
            mmed3 ( block[ptr[ lo         ]+d],
                    block[ptr[ hi         ]+d],
                    block[ptr[ (lo+hi)>>1 ]+d] );

      unLo = ltLo = lo;
      unHi = gtHi = hi;

      while (True) {
         while (True) {
            if (unLo > unHi) break;
            n = ((Int32)block[ptr[unLo]+d]) - med;
            if (n == 0) { 
               mswap(ptr[unLo], ptr[ltLo]); 
               ltLo++; unLo++; continue; 
            };
            if (n >  0) break;
            unLo++;
         }
         while (True) {
            if (unLo > unHi) break;
            n = ((Int32)block[ptr[unHi]+d]) - med;
            if (n == 0) { 
               mswap(ptr[unHi], ptr[gtHi]); 
               gtHi--; unHi--; continue; 
            };
            if (n <  0) break;
            unHi--;
         }
         if (unLo > unHi) break;
         mswap(ptr[unLo], ptr[unHi]); unLo++; unHi--;
      }

      AssertD ( unHi == unLo-1, "mainQSort3(2)" );

      if (gtHi < ltLo) {
         mpush(lo, hi, d+1 );
         continue;
      }

      n = mmin(ltLo-lo, unLo-ltLo); mvswap(lo, unLo-n, n);
      m = mmin(hi-gtHi, gtHi-unHi); mvswap(unLo, hi-m+1, m);

      n = lo + unLo - ltLo - 1;
      m = hi - (gtHi - unHi) + 1;

      nextLo[0] = lo;  nextHi[0] = n;   nextD[0] = d;
      nextLo[1] = m;   nextHi[1] = hi;  nextD[1] = d;
      nextLo[2] = n+1; nextHi[2] = m-1; nextD[2] = d+1;

      if (mnextsize(0) < mnextsize(1)) mnextswap(0,1);
      if (mnextsize(1) < mnextsize(2)) mnextswap(1,2);
      if (mnextsize(0) < mnextsize(1)) mnextswap(0,1);

      AssertD (mnextsize(0) >= mnextsize(1), "mainQSort3(8)" );
      AssertD (mnextsize(1) >= mnextsize(2), "mainQSort3(9)" );

      mpush (nextLo[0], nextHi[0], nextD[0]);
      mpush (nextLo[1], nextHi[1], nextD[1]);
      mpush (nextLo[2], nextHi[2], nextD[2]);
   }
}

#undef mswap
#undef mvswap
#undef mpush
#undef mpop
#undef mmin
#undef mnextsize
#undef mnextswap
#undef MAIN_QSORT_SMALL_THRESH
#undef MAIN_QSORT_DEPTH_THRESH
#undef MAIN_QSORT_STACK_SIZE


/*---------------------------------------------*/
/* Pre:
      nblock > N_OVERSHOOT
      block32 exists for [0 .. nblock-1 +N_OVERSHOOT]
      ((UChar*)block32) [0 .. nblock-1] holds block
      ptr exists for [0 .. nblock-1]

   Post:
      ((UChar*)block32) [0 .. nblock-1] holds block
      All other areas of block32 destroyed
      ftab [0 .. 65536 ] destroyed
      ptr [0 .. nblock-1] holds sorted order
      if (*budget < 0), sorting was abandoned
*/

#define BIGFREQ(b) (ftab[((b)+1) << 8] - ftab[(b) << 8])
#define SETMASK (1 << 21)
#define CLEARMASK (~(SETMASK))

static
void mainSort ( UInt32* ptr, 
                UChar*  block,
                UInt16* quadrant, 
                UInt32* ftab,
                Int32   nblock,
                Int32   verb,
                Int32*  budget )
{
   Int32  i, j, k, ss, sb;
   Int32  runningOrder[256];
   Bool   bigDone[256];
   Int32  copyStart[256];
   Int32  copyEnd  [256];
   UChar  c1;
   Int32  numQSorted;
   UInt16 s;
   if (verb >= 4) VPrintf0 ( "        main sort initialise ...\n" );

   /*-- set up the 2-byte frequency table --*/
   for (i = 65536; i >= 0; i--) ftab[i] = 0;

   j = block[0] << 8;
   i = nblock-1;
   for (; i >= 3; i -= 4) {
      quadrant[i] = 0;
      j = (j >> 8) | ( ((UInt16)block[i]) << 8);
      ftab[j]++;
      quadrant[i-1] = 0;
      j = (j >> 8) | ( ((UInt16)block[i-1]) << 8);
      ftab[j]++;
      quadrant[i-2] = 0;
      j = (j >> 8) | ( ((UInt16)block[i-2]) << 8);
      ftab[j]++;
      quadrant[i-3] = 0;
      j = (j >> 8) | ( ((UInt16)block[i-3]) << 8);
      ftab[j]++;
   }
   for (; i >= 0; i--) {
      quadrant[i] = 0;
      j = (j >> 8) | ( ((UInt16)block[i]) << 8);
      ftab[j]++;
   }

   /*-- (emphasises close relationship of block & quadrant) --*/
   for (i = 0; i < BZ_N_OVERSHOOT; i++) {
      block   [nblock+i] = block[i];
      quadrant[nblock+i] = 0;
   }

   if (verb >= 4) VPrintf0 ( "        bucket sorting ...\n" );

   /*-- Complete the initial radix sort --*/
   for (i = 1; i <= 65536; i++) ftab[i] += ftab[i-1];

   s = block[0] << 8;
   i = nblock-1;
   for (; i >= 3; i -= 4) {
      s = (s >> 8) | (block[i] << 8);
      j = ftab[s] -1;
      ftab[s] = j;
      ptr[j] = i;
      s = (s >> 8) | (block[i-1] << 8);
      j = ftab[s] -1;
      ftab[s] = j;
      ptr[j] = i-1;
      s = (s >> 8) | (block[i-2] << 8);
      j = ftab[s] -1;
      ftab[s] = j;
      ptr[j] = i-2;
      s = (s >> 8) | (block[i-3] << 8);
      j = ftab[s] -1;
      ftab[s] = j;
      ptr[j] = i-3;
   }
   for (; i >= 0; i--) {
      s = (s >> 8) | (block[i] << 8);
      j = ftab[s] -1;
      ftab[s] = j;
      ptr[j] = i;
   }

   /*--
      Now ftab contains the first loc of every small bucket.
      Calculate the running order, from smallest to largest
      big bucket.
   --*/
   for (i = 0; i <= 255; i++) {
      bigDone     [i] = False;
      runningOrder[i] = i;
   }

   {
      Int32 vv;
      Int32 h = 1;
      do h = 3 * h + 1; while (h <= 256);
      do {
         h = h / 3;
         for (i = h; i <= 255; i++) {
            vv = runningOrder[i];
            j = i;
            while ( BIGFREQ(runningOrder[j-h]) > BIGFREQ(vv) ) {
               runningOrder[j] = runningOrder[j-h];
               j = j - h;
               if (j <= (h - 1)) goto zero;
            }
            zero:
            runningOrder[j] = vv;
         }
      } while (h != 1);
   }

   /*--
      The main sorting loop.
   --*/

   numQSorted = 0;

   for (i = 0; i <= 255; i++) {

      /*--
         Process big buckets, starting with the least full.
         Basically this is a 3-step process in which we call
         mainQSort3 to sort the small buckets [ss, j], but
         also make a big effort to avoid the calls if we can.
      --*/
      ss = runningOrder[i];

      /*--
         Step 1:
         Complete the big bucket [ss] by quicksorting
         any unsorted small buckets [ss, j], for j != ss.  
         Hopefully previous pointer-scanning phases have already
         completed many of the small buckets [ss, j], so
         we don't have to sort them at all.
      --*/
      for (j = 0; j <= 255; j++) {
         if (j != ss) {
            sb = (ss << 8) + j;
            if ( ! (ftab[sb] & SETMASK) ) {
               Int32 lo = ftab[sb]   & CLEARMASK;
               Int32 hi = (ftab[sb+1] & CLEARMASK) - 1;
               if (hi > lo) {
                  if (verb >= 4)
                     VPrintf4 ( "        qsort [0x%x, 0x%x]   "
                                "done %d   this %d\n",
                                ss, j, numQSorted, hi - lo + 1 );
                  mainQSort3 ( 
                     ptr, block, quadrant, nblock, 
                     lo, hi, BZ_N_RADIX, budget 
                  );   
                  numQSorted += (hi - lo + 1);
                  if (*budget < 0) return;
               }
            }
            ftab[sb] |= SETMASK;
         }
      }

      AssertH ( !bigDone[ss], 1006 );

      /*--
         Step 2:
         Now scan this big bucket [ss] so as to synthesise the
         sorted order for small buckets [t, ss] for all t,
         including, magically, the bucket [ss,ss] too.
         This will avoid doing Real Work in subsequent Step 1's.
      --*/
      {
         for (j = 0; j <= 255; j++) {
            copyStart[j] =  ftab[(j << 8) + ss]     & CLEARMASK;
            copyEnd  [j] = (ftab[(j << 8) + ss + 1] & CLEARMASK) - 1;
         }
         for (j = ftab[ss << 8] & CLEARMASK; j < copyStart[ss]; j++) {
            k = ptr[j]-1; if (k < 0) k += nblock;
            c1 = block[k];
            if (!bigDone[c1])
               ptr[ copyStart[c1]++ ] = k;
         }
         for (j = (ftab[(ss+1) << 8] & CLEARMASK) - 1; j > copyEnd[ss]; j--) {
            k = ptr[j]-1; if (k < 0) k += nblock;
            c1 = block[k];
            if (!bigDone[c1]) 
               ptr[ copyEnd[c1]-- ] = k;
         }
      }

      AssertH ( (copyStart[ss]-1 == copyEnd[ss])
                || 
                /* Extremely rare case missing in bzip2-1.0.0 and 1.0.1.
                   Necessity for this case is demonstrated by compressing 
                   a sequence of approximately 48.5 million of character 
                   251; 1.0.0/1.0.1 will then die here. */
                (copyStart[ss] == 0 && copyEnd[ss] == nblock-1),
                1007 )

      for (j = 0; j <= 255; j++) ftab[(j << 8) + ss] |= SETMASK;

      /*--
         Step 3:
         The [ss] big bucket is now done.  Record this fact,
         and update the quadrant descriptors.  Remember to
         update quadrants in the overshoot area too, if
         necessary.  The "if (i < 255)" test merely skips
         this updating for the last bucket processed, since
         updating for the last bucket is pointless.

         The quadrant array provides a way to incrementally
         cache sort orderings, as they appear, so as to 
         make subsequent comparisons in fullGtU() complete
         faster.  For repetitive blocks this makes a big
         difference (but not big enough to be able to avoid
         the fallback sorting mechanism, exponential radix sort).

         The precise meaning is: at all times:

            for 0 <= i < nblock and 0 <= j <= nblock

            if block[i] != block[j], 

               then the relative values of quadrant[i] and 
                    quadrant[j] are meaningless.

               else {
                  if quadrant[i] < quadrant[j]
                     then the string starting at i lexicographically
                     precedes the string starting at j

                  else if quadrant[i] > quadrant[j]
                     then the string starting at j lexicographically
                     precedes the string starting at i

                  else
                     the relative ordering of the strings starting
                     at i and j has not yet been determined.
               }
      --*/
      bigDone[ss] = True;

      if (i < 255) {
         Int32 bbStart  = ftab[ss << 8] & CLEARMASK;
         Int32 bbSize   = (ftab[(ss+1) << 8] & CLEARMASK) - bbStart;
         Int32 shifts   = 0;

         while ((bbSize >> shifts) > 65534) shifts++;

         for (j = bbSize-1; j >= 0; j--) {
            Int32 a2update     = ptr[bbStart + j];
            UInt16 qVal        = (UInt16)(j >> shifts);
            quadrant[a2update] = qVal;
            if (a2update < BZ_N_OVERSHOOT)
               quadrant[a2update + nblock] = qVal;
         }
         AssertH ( ((bbSize-1) >> shifts) <= 65535, 1002 );
      }

   }

   if (verb >= 4)
      VPrintf3 ( "        %d pointers, %d sorted, %d scanned\n",
                 nblock, numQSorted, nblock - numQSorted );
}

#undef BIGFREQ
#undef SETMASK
#undef CLEARMASK


/*---------------------------------------------*/
/* Pre:
      nblock > 0
      arr2 exists for [0 .. nblock-1 +N_OVERSHOOT]
      ((UChar*)arr2)  [0 .. nblock-1] holds block
      arr1 exists for [0 .. nblock-1]

   Post:
      ((UChar*)arr2) [0 .. nblock-1] holds block
      All other areas of block destroyed
      ftab [ 0 .. 65536 ] destroyed
      arr1 [0 .. nblock-1] holds sorted order
*/
void BZ2_blockSort ( EState* s )
{
   UInt32* ptr    = s->ptr; 
   UChar*  block  = s->block;
   UInt32* ftab   = s->ftab;
   Int32   nblock = s->nblock;
   Int32   verb   = s->verbosity;
   Int32   wfact  = s->workFactor;
   UInt16* quadrant;
   Int32   budget;
   Int32   budgetInit;
   Int32   i;

   if (nblock < 10000) {
      fallbackSort ( s->arr1, s->arr2, ftab, nblock, verb );
   } else {
      /* Calculate the location for quadrant, remembering to get
         the alignment right.  Assumes that &(block[0]) is at least
         2-byte aligned -- this should be ok since block is really
         the first section of arr2.
      */
      i = nblock+BZ_N_OVERSHOOT;
      if (i & 1) i++;
      quadrant = (UInt16*)(&(block[i]));

      /* (wfact-1) / 3 puts the default-factor-30
         transition point at very roughly the same place as 
         with v0.1 and v0.9.0.  
         Not that it particularly matters any more, since the
         resulting compressed stream is now the same regardless
         of whether or not we use the main sort or fallback sort.
      */
      if (wfact < 1  ) wfact = 1;
      if (wfact > 100) wfact = 100;
      budgetInit = nblock * ((wfact-1) / 3);
      budget = budgetInit;

      mainSort ( ptr, block, quadrant, ftab, nblock, verb, &budget );
      if (verb >= 3) 
         VPrintf3 ( "      %d work, %d block, ratio %5.2f\n",
                    budgetInit - budget,
                    nblock, 
                    (float)(budgetInit - budget) /
                    (float)(nblock==0 ? 1 : nblock) ); 
      if (budget < 0) {
         if (verb >= 2) 
            VPrintf0 ( "    too repetitive; using fallback"
                       " sorting algorithm\n" );
         fallbackSort ( s->arr1, s->arr2, ftab, nblock, verb );
      }
   }

   s->origPtr = -1;
   for (i = 0; i < s->nblock; i++)
      if (ptr[i] == 0)
         { s->origPtr = i; break; };

   AssertH( s->origPtr != -1, 1003 );
}


/*-------------------------------------------------------------*/
/*--- end                                       blocksort.c ---*/
/*-------------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/bz-common.xsl000066400000000000000000000020411211610345200225710ustar00rootroot00000000000000 



 



 
 
   
    
      
     
  




set       toc,title
book      toc,title,figure,table,example,equation
chapter   toc,title
section   toc
sect1     toc
sect2     toc
sect3     toc
sect4     nop
sect5     nop
qandaset  toc
qandadiv  nop
appendix  toc,title
article/appendix  nop
article   toc,title
preface   toc,title
reference toc,title



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genometools-1.5.1/src/external/bzip2-1.0.6/bz-html.xsl000066400000000000000000000012061211610345200222470ustar00rootroot00000000000000 
 ]>










  
  



genometools-1.5.1/src/external/bzip2-1.0.6/bzdiff000066400000000000000000000041201211610345200213270ustar00rootroot00000000000000#!/bin/sh
# sh is buggy on RS/6000 AIX 3.2. Replace above line with #!/bin/ksh

# Bzcmp/diff wrapped for bzip2, 
# adapted from zdiff by Philippe Troin  for Debian GNU/Linux.

# Bzcmp and bzdiff are used to invoke the cmp or the  diff  pro-
# gram  on compressed files.  All options specified are passed
# directly to cmp or diff.  If only 1 file is specified,  then
# the  files  compared  are file1 and an uncompressed file1.gz.
# If two files are specified, then they are  uncompressed  (if
# necessary) and fed to cmp or diff.  The exit status from cmp
# or diff is preserved.

PATH="/usr/bin:/bin:$PATH"; export PATH
prog=`echo $0 | sed 's|.*/||'`
case "$prog" in
  *cmp) comp=${CMP-cmp}   ;;
  *)    comp=${DIFF-diff} ;;
esac

OPTIONS=
FILES=
for ARG
do
    case "$ARG" in
    -*)	OPTIONS="$OPTIONS $ARG";;
     *)	if test -f "$ARG"; then
            FILES="$FILES $ARG"
        else
            echo "${prog}: $ARG not found or not a regular file"
	    exit 1
        fi ;;
    esac
done
if test -z "$FILES"; then
	echo "Usage: $prog [${comp}_options] file [file]"
	exit 1
fi
tmp=`mktemp ${TMPDIR:-/tmp}/bzdiff.XXXXXXXXXX` || {
      echo 'cannot create a temporary file' >&2
      exit 1
}
set $FILES
if test $# -eq 1; then
	FILE=`echo "$1" | sed 's/.bz2$//'`
	bzip2 -cd "$FILE.bz2" | $comp $OPTIONS - "$FILE"
	STAT="$?"

elif test $# -eq 2; then
	case "$1" in
        *.bz2)
                case "$2" in
	        *.bz2)
			F=`echo "$2" | sed 's|.*/||;s|.bz2$||'`
                        bzip2 -cdfq "$2" > $tmp
                        bzip2 -cdfq "$1" | $comp $OPTIONS - $tmp
                        STAT="$?"
			/bin/rm -f $tmp;;

                *)      bzip2 -cdfq "$1" | $comp $OPTIONS - "$2"
                        STAT="$?";;
                esac;;
        *)      case "$2" in
	        *.bz2)
                        bzip2 -cdfq "$2" | $comp $OPTIONS "$1" -
                        STAT="$?";;
                *)      $comp $OPTIONS "$1" "$2"
                        STAT="$?";;
                esac;;
	esac
        exit "$STAT"
else
	echo "Usage: $prog [${comp}_options] file [file]"
	exit 1
fi
genometools-1.5.1/src/external/bzip2-1.0.6/bzdiff.1000066400000000000000000000016011211610345200214670ustar00rootroot00000000000000\"Shamelessly copied from zmore.1 by Philippe Troin 
\"for Debian GNU/Linux
.TH BZDIFF 1
.SH NAME
bzcmp, bzdiff \- compare bzip2 compressed files
.SH SYNOPSIS
.B bzcmp
[ cmp_options ] file1
[ file2 ]
.br
.B bzdiff
[ diff_options ] file1
[ file2 ]
.SH DESCRIPTION
.I  Bzcmp
and 
.I bzdiff
are used to invoke the
.I cmp
or the
.I diff
program on bzip2 compressed files.  All options specified are passed
directly to
.I cmp
or
.IR diff "."
If only 1 file is specified, then the files compared are
.I file1
and an uncompressed
.IR file1 ".bz2."
If two files are specified, then they are uncompressed if necessary and fed to
.I cmp
or
.IR diff "."
The exit status from 
.I cmp
or
.I diff
is preserved.
.SH "SEE ALSO"
cmp(1), diff(1), bzmore(1), bzless(1), bzgrep(1), bzip2(1)
.SH BUGS
Messages from the
.I cmp
or
.I diff
programs refer to temporary filenames instead of those specified.
genometools-1.5.1/src/external/bzip2-1.0.6/bzgrep000066400000000000000000000032151211610345200213600ustar00rootroot00000000000000#!/bin/sh

# Bzgrep wrapped for bzip2, 
# adapted from zgrep by Philippe Troin  for Debian GNU/Linux.
## zgrep notice:
## zgrep -- a wrapper around a grep program that decompresses files as needed
## Adapted from a version sent by Charles Levert 

PATH="/usr/bin:$PATH"; export PATH

prog=`echo $0 | sed 's|.*/||'`
case "$prog" in
	*egrep)	grep=${EGREP-egrep}	;;
	*fgrep)	grep=${FGREP-fgrep}	;;
	*)	grep=${GREP-grep}	;;
esac
pat=""
while test $# -ne 0; do
  case "$1" in
  -e | -f) opt="$opt $1"; shift; pat="$1"
           if test "$grep" = grep; then  # grep is buggy with -e on SVR4
             grep=egrep
           fi;;
  -A | -B) opt="$opt $1 $2"; shift;;
  -*)	   opt="$opt $1";;
   *)      if test -z "$pat"; then
	     pat="$1"
	   else
	     break;
           fi;;
  esac
  shift
done

if test -z "$pat"; then
  echo "grep through bzip2 files"
  echo "usage: $prog [grep_options] pattern [files]"
  exit 1
fi

list=0
silent=0
op=`echo "$opt" | sed -e 's/ //g' -e 's/-//g'`
case "$op" in
  *l*) list=1
esac
case "$op" in
  *h*) silent=1
esac

if test $# -eq 0; then
  bzip2 -cdfq | $grep $opt "$pat"
  exit $?
fi

res=0
for i do
  if test -f "$i"; then :; else if test -f "$i.bz2"; then i="$i.bz2"; fi; fi
  if test $list -eq 1; then
    bzip2 -cdfq "$i" | $grep $opt "$pat" 2>&1 > /dev/null && echo $i
    r=$?
  elif test $# -eq 1 -o $silent -eq 1; then
    bzip2 -cdfq "$i" | $grep $opt "$pat"
    r=$?
  else
    j=${i//\\/\\\\}
    j=${j//|/\\|}
    j=${j//&/\\&}
    j=`printf "%s" "$j" | tr '\n' ' '`
    bzip2 -cdfq "$i" | $grep $opt "$pat" | sed "s|^|${j}:|"
    r=$?
  fi
  test "$r" -ne 0 && res="$r"
done
exit $res
genometools-1.5.1/src/external/bzip2-1.0.6/bzgrep.1000066400000000000000000000024211211610345200215150ustar00rootroot00000000000000\"Shamelessly copied from zmore.1 by Philippe Troin 
\"for Debian GNU/Linux
.TH BZGREP 1
.SH NAME
bzgrep, bzfgrep, bzegrep \- search possibly bzip2 compressed files for a regular expression
.SH SYNOPSIS
.B bzgrep
[ grep_options ]
.BI  [\ -e\ ] " pattern"
.IR filename ".\|.\|."
.br
.B bzegrep
[ egrep_options ]
.BI  [\ -e\ ] " pattern"
.IR filename ".\|.\|."
.br
.B bzfgrep
[ fgrep_options ]
.BI  [\ -e\ ] " pattern"
.IR filename ".\|.\|."
.SH DESCRIPTION
.IR  Bzgrep
is used to invoke the
.I grep
on bzip2-compressed files. All options specified are passed directly to
.I grep.
If no file is specified, then the standard input is decompressed
if necessary and fed to grep.
Otherwise the given files are uncompressed if necessary and fed to
.I grep.
.PP
If
.I bzgrep
is invoked as
.I bzegrep
or
.I bzfgrep
then
.I egrep
or
.I fgrep
is used instead of
.I grep.
If the GREP environment variable is set,
.I bzgrep
uses it as the
.I grep
program to be invoked. For example:

    for sh:  GREP=fgrep  bzgrep string files
    for csh: (setenv GREP fgrep; bzgrep string files)
.SH AUTHOR
Charles Levert (charles@comm.polymtl.ca). Adapted to bzip2 by Philippe
Troin  for Debian GNU/Linux.
.SH "SEE ALSO"
grep(1), egrep(1), fgrep(1), bzdiff(1), bzmore(1), bzless(1), bzip2(1)
genometools-1.5.1/src/external/bzip2-1.0.6/bzip.css000066400000000000000000000033221211610345200216210ustar00rootroot00000000000000/* Colours:
#74240f  dark brown      h1, h2, h3, h4
#336699  medium blue     links
#339999  turquoise       link hover colour
#202020  almost black    general text
#761596  purple          md5sum text
#626262  dark gray       pre border
#eeeeee  very light gray pre background
#f2f2f9  very light blue nav table background
#3366cc  medium blue     nav table border
*/

a, a:link, a:visited, a:active { color: #336699; }
a:hover { color: #339999; }

body { font: 80%/126% sans-serif; }
h1, h2, h3, h4 { color: #74240f; }

dt { color: #336699; font-weight: bold }
dd { 
 margin-left: 1.5em; 
 padding-bottom: 0.8em;
}

/* -- ruler -- */
div.hr_blue { 
  height:  3px; 
  background:#ffffff url("/images/hr_blue.png") repeat-x; }
div.hr_blue hr { display:none; }

/* release styles */
#release p { margin-top: 0.4em; }
#release .md5sum { color: #761596; }


/* ------ styles for docs|manuals|howto ------ */
/* -- lists -- */
ul  { 
 margin:     0px 4px 16px 16px;
 padding:    0px;
 list-style: url("/images/li-blue.png"); 
}
ul li { 
 margin-bottom: 10px;
}
ul ul	{ 
 list-style-type:  none; 
 list-style-image: none; 
 margin-left:      0px; 
}

/* header / footer nav tables */
table.nav {
 border:     solid 1px #3366cc;
 background: #f2f2f9;
 background-color: #f2f2f9;
 margin-bottom: 0.5em;
}
/* don't have underlined links in chunked nav menus */
table.nav a { text-decoration: none; }
table.nav a:hover { text-decoration: underline; }
table.nav td { font-size: 85%; }

code, tt, pre { font-size: 120%; }
code, tt { color: #761596; }

div.literallayout, pre.programlisting, pre.screen {
 color:      #000000;
 padding:    0.5em;
 background: #eeeeee;
 border:     1px solid #626262;
 background-color: #eeeeee;
 margin: 4px 0px 4px 0px; 
}
genometools-1.5.1/src/external/bzip2-1.0.6/bzip2.1000066400000000000000000000376001211610345200212610ustar00rootroot00000000000000.PU
.TH bzip2 1
.SH NAME
bzip2, bunzip2 \- a block-sorting file compressor, v1.0.6
.br
bzcat \- decompresses files to stdout
.br
bzip2recover \- recovers data from damaged bzip2 files

.SH SYNOPSIS
.ll +8
.B bzip2
.RB [ " \-cdfkqstvzVL123456789 " ]
[
.I "filenames \&..."
]
.ll -8
.br
.B bunzip2
.RB [ " \-fkvsVL " ]
[ 
.I "filenames \&..."
]
.br
.B bzcat
.RB [ " \-s " ]
[ 
.I "filenames \&..."
]
.br
.B bzip2recover
.I "filename"

.SH DESCRIPTION
.I bzip2
compresses files using the Burrows-Wheeler block sorting
text compression algorithm, and Huffman coding.  Compression is
generally considerably better than that achieved by more conventional
LZ77/LZ78-based compressors, and approaches the performance of the PPM
family of statistical compressors.

The command-line options are deliberately very similar to 
those of 
.I GNU gzip, 
but they are not identical.

.I bzip2
expects a list of file names to accompany the
command-line flags.  Each file is replaced by a compressed version of
itself, with the name "original_name.bz2".  
Each compressed file
has the same modification date, permissions, and, when possible,
ownership as the corresponding original, so that these properties can
be correctly restored at decompression time.  File name handling is
naive in the sense that there is no mechanism for preserving original
file names, permissions, ownerships or dates in filesystems which lack
these concepts, or have serious file name length restrictions, such as
MS-DOS.

.I bzip2
and
.I bunzip2
will by default not overwrite existing
files.  If you want this to happen, specify the \-f flag.

If no file names are specified,
.I bzip2
compresses from standard
input to standard output.  In this case,
.I bzip2
will decline to
write compressed output to a terminal, as this would be entirely
incomprehensible and therefore pointless.

.I bunzip2
(or
.I bzip2 \-d) 
decompresses all
specified files.  Files which were not created by 
.I bzip2
will be detected and ignored, and a warning issued.  
.I bzip2
attempts to guess the filename for the decompressed file 
from that of the compressed file as follows:

       filename.bz2    becomes   filename
       filename.bz     becomes   filename
       filename.tbz2   becomes   filename.tar
       filename.tbz    becomes   filename.tar
       anyothername    becomes   anyothername.out

If the file does not end in one of the recognised endings, 
.I .bz2, 
.I .bz, 
.I .tbz2
or
.I .tbz, 
.I bzip2 
complains that it cannot
guess the name of the original file, and uses the original name
with
.I .out
appended.

As with compression, supplying no
filenames causes decompression from 
standard input to standard output.

.I bunzip2 
will correctly decompress a file which is the
concatenation of two or more compressed files.  The result is the
concatenation of the corresponding uncompressed files.  Integrity
testing (\-t) 
of concatenated 
compressed files is also supported.

You can also compress or decompress files to the standard output by
giving the \-c flag.  Multiple files may be compressed and
decompressed like this.  The resulting outputs are fed sequentially to
stdout.  Compression of multiple files 
in this manner generates a stream
containing multiple compressed file representations.  Such a stream
can be decompressed correctly only by
.I bzip2 
version 0.9.0 or
later.  Earlier versions of
.I bzip2
will stop after decompressing
the first file in the stream.

.I bzcat
(or
.I bzip2 -dc) 
decompresses all specified files to
the standard output.

.I bzip2
will read arguments from the environment variables
.I BZIP2
and
.I BZIP,
in that order, and will process them
before any arguments read from the command line.  This gives a 
convenient way to supply default arguments.

Compression is always performed, even if the compressed 
file is slightly
larger than the original.  Files of less than about one hundred bytes
tend to get larger, since the compression mechanism has a constant
overhead in the region of 50 bytes.  Random data (including the output
of most file compressors) is coded at about 8.05 bits per byte, giving
an expansion of around 0.5%.

As a self-check for your protection, 
.I 
bzip2
uses 32-bit CRCs to
make sure that the decompressed version of a file is identical to the
original.  This guards against corruption of the compressed data, and
against undetected bugs in
.I bzip2
(hopefully very unlikely).  The
chances of data corruption going undetected is microscopic, about one
chance in four billion for each file processed.  Be aware, though, that
the check occurs upon decompression, so it can only tell you that
something is wrong.  It can't help you 
recover the original uncompressed
data.  You can use 
.I bzip2recover
to try to recover data from
damaged files.

Return values: 0 for a normal exit, 1 for environmental problems (file
not found, invalid flags, I/O errors, &c), 2 to indicate a corrupt
compressed file, 3 for an internal consistency error (eg, bug) which
caused
.I bzip2
to panic.

.SH OPTIONS
.TP
.B \-c --stdout
Compress or decompress to standard output.
.TP
.B \-d --decompress
Force decompression.  
.I bzip2, 
.I bunzip2 
and
.I bzcat 
are
really the same program, and the decision about what actions to take is
done on the basis of which name is used.  This flag overrides that
mechanism, and forces 
.I bzip2
to decompress.
.TP
.B \-z --compress
The complement to \-d: forces compression, regardless of the
invocation name.
.TP
.B \-t --test
Check integrity of the specified file(s), but don't decompress them.
This really performs a trial decompression and throws away the result.
.TP
.B \-f --force
Force overwrite of output files.  Normally,
.I bzip2 
will not overwrite
existing output files.  Also forces 
.I bzip2 
to break hard links
to files, which it otherwise wouldn't do.

bzip2 normally declines to decompress files which don't have the
correct magic header bytes.  If forced (-f), however, it will pass
such files through unmodified.  This is how GNU gzip behaves.
.TP
.B \-k --keep
Keep (don't delete) input files during compression
or decompression.
.TP
.B \-s --small
Reduce memory usage, for compression, decompression and testing.  Files
are decompressed and tested using a modified algorithm which only
requires 2.5 bytes per block byte.  This means any file can be
decompressed in 2300k of memory, albeit at about half the normal speed.

During compression, \-s selects a block size of 200k, which limits
memory use to around the same figure, at the expense of your compression
ratio.  In short, if your machine is low on memory (8 megabytes or
less), use \-s for everything.  See MEMORY MANAGEMENT below.
.TP
.B \-q --quiet
Suppress non-essential warning messages.  Messages pertaining to
I/O errors and other critical events will not be suppressed.
.TP
.B \-v --verbose
Verbose mode -- show the compression ratio for each file processed.
Further \-v's increase the verbosity level, spewing out lots of
information which is primarily of interest for diagnostic purposes.
.TP
.B \-L --license -V --version
Display the software version, license terms and conditions.
.TP
.B \-1 (or \-\-fast) to \-9 (or \-\-best)
Set the block size to 100 k, 200 k ..  900 k when compressing.  Has no
effect when decompressing.  See MEMORY MANAGEMENT below.
The \-\-fast and \-\-best aliases are primarily for GNU gzip 
compatibility.  In particular, \-\-fast doesn't make things
significantly faster.  
And \-\-best merely selects the default behaviour.
.TP
.B \--
Treats all subsequent arguments as file names, even if they start
with a dash.  This is so you can handle files with names beginning
with a dash, for example: bzip2 \-- \-myfilename.
.TP
.B \--repetitive-fast --repetitive-best
These flags are redundant in versions 0.9.5 and above.  They provided
some coarse control over the behaviour of the sorting algorithm in
earlier versions, which was sometimes useful.  0.9.5 and above have an
improved algorithm which renders these flags irrelevant.

.SH MEMORY MANAGEMENT
.I bzip2 
compresses large files in blocks.  The block size affects
both the compression ratio achieved, and the amount of memory needed for
compression and decompression.  The flags \-1 through \-9
specify the block size to be 100,000 bytes through 900,000 bytes (the
default) respectively.  At decompression time, the block size used for
compression is read from the header of the compressed file, and
.I bunzip2
then allocates itself just enough memory to decompress
the file.  Since block sizes are stored in compressed files, it follows
that the flags \-1 to \-9 are irrelevant to and so ignored
during decompression.

Compression and decompression requirements, 
in bytes, can be estimated as:

       Compression:   400k + ( 8 x block size )

       Decompression: 100k + ( 4 x block size ), or
                      100k + ( 2.5 x block size )

Larger block sizes give rapidly diminishing marginal returns.  Most of
the compression comes from the first two or three hundred k of block
size, a fact worth bearing in mind when using
.I bzip2
on small machines.
It is also important to appreciate that the decompression memory
requirement is set at compression time by the choice of block size.

For files compressed with the default 900k block size,
.I bunzip2
will require about 3700 kbytes to decompress.  To support decompression
of any file on a 4 megabyte machine, 
.I bunzip2
has an option to
decompress using approximately half this amount of memory, about 2300
kbytes.  Decompression speed is also halved, so you should use this
option only where necessary.  The relevant flag is -s.

In general, try and use the largest block size memory constraints allow,
since that maximises the compression achieved.  Compression and
decompression speed are virtually unaffected by block size.

Another significant point applies to files which fit in a single block
-- that means most files you'd encounter using a large block size.  The
amount of real memory touched is proportional to the size of the file,
since the file is smaller than a block.  For example, compressing a file
20,000 bytes long with the flag -9 will cause the compressor to
allocate around 7600k of memory, but only touch 400k + 20000 * 8 = 560
kbytes of it.  Similarly, the decompressor will allocate 3700k but only
touch 100k + 20000 * 4 = 180 kbytes.

Here is a table which summarises the maximum memory usage for different
block sizes.  Also recorded is the total compressed size for 14 files of
the Calgary Text Compression Corpus totalling 3,141,622 bytes.  This
column gives some feel for how compression varies with block size.
These figures tend to understate the advantage of larger block sizes for
larger files, since the Corpus is dominated by smaller files.

           Compress   Decompress   Decompress   Corpus
    Flag     usage      usage       -s usage     Size

     -1      1200k       500k         350k      914704
     -2      2000k       900k         600k      877703
     -3      2800k      1300k         850k      860338
     -4      3600k      1700k        1100k      846899
     -5      4400k      2100k        1350k      845160
     -6      5200k      2500k        1600k      838626
     -7      6100k      2900k        1850k      834096
     -8      6800k      3300k        2100k      828642
     -9      7600k      3700k        2350k      828642

.SH RECOVERING DATA FROM DAMAGED FILES
.I bzip2
compresses files in blocks, usually 900kbytes long.  Each
block is handled independently.  If a media or transmission error causes
a multi-block .bz2
file to become damaged, it may be possible to
recover data from the undamaged blocks in the file.

The compressed representation of each block is delimited by a 48-bit
pattern, which makes it possible to find the block boundaries with
reasonable certainty.  Each block also carries its own 32-bit CRC, so
damaged blocks can be distinguished from undamaged ones.

.I bzip2recover
is a simple program whose purpose is to search for
blocks in .bz2 files, and write each block out into its own .bz2 
file.  You can then use
.I bzip2 
\-t
to test the
integrity of the resulting files, and decompress those which are
undamaged.

.I bzip2recover
takes a single argument, the name of the damaged file, 
and writes a number of files "rec00001file.bz2",
"rec00002file.bz2", etc, containing the  extracted  blocks.
The  output  filenames  are  designed  so  that the use of
wildcards in subsequent processing -- for example,  
"bzip2 -dc  rec*file.bz2 > recovered_data" -- processes the files in
the correct order.

.I bzip2recover
should be of most use dealing with large .bz2
files,  as  these will contain many blocks.  It is clearly
futile to use it on damaged single-block  files,  since  a
damaged  block  cannot  be recovered.  If you wish to minimise 
any potential data loss through media  or  transmission errors, 
you might consider compressing with a smaller
block size.

.SH PERFORMANCE NOTES
The sorting phase of compression gathers together similar strings in the
file.  Because of this, files containing very long runs of repeated
symbols, like "aabaabaabaab ..."  (repeated several hundred times) may
compress more slowly than normal.  Versions 0.9.5 and above fare much
better than previous versions in this respect.  The ratio between
worst-case and average-case compression time is in the region of 10:1.
For previous versions, this figure was more like 100:1.  You can use the
\-vvvv option to monitor progress in great detail, if you want.

Decompression speed is unaffected by these phenomena.

.I bzip2
usually allocates several megabytes of memory to operate
in, and then charges all over it in a fairly random fashion.  This means
that performance, both for compressing and decompressing, is largely
determined by the speed at which your machine can service cache misses.
Because of this, small changes to the code to reduce the miss rate have
been observed to give disproportionately large performance improvements.
I imagine 
.I bzip2
will perform best on machines with very large caches.

.SH CAVEATS
I/O error messages are not as helpful as they could be.
.I bzip2
tries hard to detect I/O errors and exit cleanly, but the details of
what the problem is sometimes seem rather misleading.

This manual page pertains to version 1.0.6 of
.I bzip2.  
Compressed data created by this version is entirely forwards and
backwards compatible with the previous public releases, versions
0.1pl2, 0.9.0, 0.9.5, 1.0.0, 1.0.1, 1.0.2 and above, but with the following
exception: 0.9.0 and above can correctly decompress multiple
concatenated compressed files.  0.1pl2 cannot do this; it will stop
after decompressing just the first file in the stream.

.I bzip2recover
versions prior to 1.0.2 used 32-bit integers to represent
bit positions in compressed files, so they could not handle compressed
files more than 512 megabytes long.  Versions 1.0.2 and above use
64-bit ints on some platforms which support them (GNU supported
targets, and Windows).  To establish whether or not bzip2recover was
built with such a limitation, run it without arguments.  In any event
you can build yourself an unlimited version if you can recompile it
with MaybeUInt64 set to be an unsigned 64-bit integer.



.SH AUTHOR
Julian Seward, jsewardbzip.org.

http://www.bzip.org

The ideas embodied in
.I bzip2
are due to (at least) the following
people: Michael Burrows and David Wheeler (for the block sorting
transformation), David Wheeler (again, for the Huffman coder), Peter
Fenwick (for the structured coding model in the original
.I bzip,
and many refinements), and Alistair Moffat, Radford Neal and Ian Witten
(for the arithmetic coder in the original
.I bzip).  
I am much
indebted for their help, support and advice.  See the manual in the
source distribution for pointers to sources of documentation.  Christian
von Roques encouraged me to look for faster sorting algorithms, so as to
speed up compression.  Bela Lubkin encouraged me to improve the
worst-case compression performance.  
Donna Robinson XMLised the documentation.
The bz* scripts are derived from those of GNU gzip.
Many people sent patches, helped
with portability problems, lent machines, gave advice and were generally
helpful.
genometools-1.5.1/src/external/bzip2-1.0.6/bzip2.1.preformatted000066400000000000000000000507071211610345200237570ustar00rootroot00000000000000bzip2(1)                                                 bzip2(1)



NNAAMMEE
       bzip2, bunzip2 − a block‐sorting file compressor, v1.0.6
       bzcat − decompresses files to stdout
       bzip2recover − recovers data from damaged bzip2 files


SSYYNNOOPPSSIISS
       bbzziipp22 [ −−ccddffkkqqssttvvzzVVLL112233445566778899 ] [ _f_i_l_e_n_a_m_e_s _._._.  ]
       bbuunnzziipp22 [ −−ffkkvvssVVLL ] [ _f_i_l_e_n_a_m_e_s _._._.  ]
       bbzzccaatt [ −−ss ] [ _f_i_l_e_n_a_m_e_s _._._.  ]
       bbzziipp22rreeccoovveerr _f_i_l_e_n_a_m_e


DDEESSCCRRIIPPTTIIOONN
       _b_z_i_p_2  compresses  files  using  the Burrows‐Wheeler block
       sorting text compression algorithm,  and  Huffman  coding.
       Compression  is  generally  considerably  better than that
       achieved by more conventional LZ77/LZ78‐based compressors,
       and  approaches  the performance of the PPM family of sta­
       tistical compressors.

       The command‐line options are deliberately very similar  to
       those of _G_N_U _g_z_i_p_, but they are not identical.

       _b_z_i_p_2  expects  a list of file names to accompany the com­
       mand‐line flags.  Each file is replaced  by  a  compressed
       version  of  itself,  with  the  name "original_name.bz2".
       Each compressed file has the same modification date,  per­
       missions, and, when possible, ownership as the correspond­
       ing original, so that these properties  can  be  correctly
       restored  at  decompression  time.   File name handling is
       naive in the sense that there is no mechanism for preserv­
       ing  original file names, permissions, ownerships or dates
       in filesystems which lack these concepts, or have  serious
       file name length restrictions, such as MS‐DOS.

       _b_z_i_p_2  and  _b_u_n_z_i_p_2 will by default not overwrite existing
       files.  If you want this to happen, specify the −f flag.

       If no file names  are  specified,  _b_z_i_p_2  compresses  from
       standard  input  to  standard output.  In this case, _b_z_i_p_2
       will decline to write compressed output to a terminal,  as
       this  would  be  entirely  incomprehensible  and therefore
       pointless.

       _b_u_n_z_i_p_2 (or _b_z_i_p_2 _−_d_) decompresses  all  specified  files.
       Files which were not created by _b_z_i_p_2 will be detected and
       ignored, and a warning issued.  _b_z_i_p_2  attempts  to  guess
       the  filename  for  the decompressed file from that of the
       compressed file as follows:

              filename.bz2    becomes   filename
              filename.bz     becomes   filename
              filename.tbz2   becomes   filename.tar
              filename.tbz    becomes   filename.tar
              anyothername    becomes   anyothername.out

       If the file does not end in one of the recognised endings,
       _._b_z_2_,  _._b_z_,  _._t_b_z_2 or _._t_b_z_, _b_z_i_p_2 complains that it cannot
       guess the name of the original file, and uses the original
       name with _._o_u_t appended.

       As  with compression, supplying no filenames causes decom­
       pression from standard input to standard output.

       _b_u_n_z_i_p_2 will correctly decompress a file which is the con­
       catenation of two or more compressed files.  The result is
       the concatenation of the corresponding uncompressed files.
       Integrity testing (−t) of concatenated compressed files is
       also supported.

       You can also compress or decompress files to the  standard
       output  by giving the −c flag.  Multiple files may be com­
       pressed and decompressed like this.  The resulting outputs
       are  fed  sequentially to stdout.  Compression of multiple
       files in this manner generates a stream containing  multi­
       ple compressed file representations.  Such a stream can be
       decompressed correctly only  by  _b_z_i_p_2  version  0.9.0  or
       later.   Earlier  versions of _b_z_i_p_2 will stop after decom­
       pressing the first file in the stream.

       _b_z_c_a_t (or _b_z_i_p_2 _‐_d_c_) decompresses all specified  files  to
       the standard output.

       _b_z_i_p_2  will  read arguments from the environment variables
       _B_Z_I_P_2 and _B_Z_I_P_, in  that  order,  and  will  process  them
       before  any  arguments  read  from the command line.  This
       gives a convenient way to supply default arguments.

       Compression is always performed, even  if  the  compressed
       file  is slightly larger than the original.  Files of less
       than about one hundred bytes tend to get larger, since the
       compression  mechanism  has  a  constant  overhead  in the
       region of 50 bytes.  Random data (including the output  of
       most  file  compressors)  is  coded at about 8.05 bits per
       byte, giving an expansion of around 0.5%.

       As a self‐check for your  protection,  _b_z_i_p_2  uses  32‐bit
       CRCs  to make sure that the decompressed version of a file
       is identical to the original.  This guards against corrup­
       tion  of  the compressed data, and against undetected bugs
       in _b_z_i_p_2 (hopefully very unlikely).  The chances  of  data
       corruption  going  undetected  is  microscopic,  about one
       chance in four billion for each file processed.  Be aware,
       though,  that  the  check occurs upon decompression, so it
       can only tell you that something is wrong.  It can’t  help
       you  recover  the original uncompressed data.  You can use
       _b_z_i_p_2_r_e_c_o_v_e_r to try to recover data from damaged files.

       Return values: 0 for a normal exit,  1  for  environmental
       problems  (file not found, invalid flags, I/O errors, &c),
       2 to indicate a corrupt compressed file, 3 for an internal
       consistency error (eg, bug) which caused _b_z_i_p_2 to panic.


OOPPTTIIOONNSS
       −−cc ‐‐‐‐ssttddoouutt
              Compress or decompress to standard output.

       −−dd ‐‐‐‐ddeeccoommpprreessss
              Force  decompression.  _b_z_i_p_2_, _b_u_n_z_i_p_2 and _b_z_c_a_t are
              really the same program,  and  the  decision  about
              what  actions to take is done on the basis of which
              name is used.  This flag overrides that  mechanism,
              and forces _b_z_i_p_2 to decompress.

       −−zz ‐‐‐‐ccoommpprreessss
              The   complement   to   −d:   forces   compression,
              regardless of the invocation name.

       −−tt ‐‐‐‐tteesstt
              Check integrity of the specified file(s), but don’t
              decompress  them.   This  really  performs  a trial
              decompression and throws away the result.

       −−ff ‐‐‐‐ffoorrccee
              Force overwrite of output files.   Normally,  _b_z_i_p_2
              will  not  overwrite  existing  output files.  Also
              forces _b_z_i_p_2 to break hard links to files, which it
              otherwise wouldn’t do.

              bzip2  normally  declines to decompress files which
              don’t have the  correct  magic  header  bytes.   If
              forced  (‐f),  however,  it  will  pass  such files
              through unmodified.  This is how GNU gzip  behaves.

       −−kk ‐‐‐‐kkeeeepp
              Keep  (don’t delete) input files during compression
              or decompression.

       −−ss ‐‐‐‐ssmmaallll
              Reduce memory usage, for compression, decompression
              and  testing.   Files  are  decompressed and tested
              using a modified algorithm which only requires  2.5
              bytes  per  block byte.  This means any file can be
              decompressed in 2300k of memory,  albeit  at  about
              half the normal speed.

              During  compression,  −s  selects  a  block size of
              200k, which limits memory use to  around  the  same
              figure,  at  the expense of your compression ratio.
              In short, if your  machine  is  low  on  memory  (8
              megabytes  or  less),  use  −s for everything.  See
              MEMORY MANAGEMENT below.

       −−qq ‐‐‐‐qquuiieett
              Suppress non‐essential warning messages.   Messages
              pertaining  to I/O errors and other critical events
              will not be suppressed.

       −−vv ‐‐‐‐vveerrbboossee
              Verbose mode ‐‐ show the compression ratio for each
              file  processed.   Further  −v’s  increase the ver­
              bosity level, spewing out lots of information which
              is primarily of interest for diagnostic purposes.

       −−LL ‐‐‐‐lliicceennssee ‐‐VV ‐‐‐‐vveerrssiioonn
              Display  the  software  version,  license terms and
              conditions.

       −−11 ((oorr −−−−ffaasstt)) ttoo −−99 ((oorr −−−−bbeesstt))
              Set the block size to 100 k, 200 k ..  900  k  when
              compressing.   Has  no  effect  when decompressing.
              See MEMORY MANAGEMENT below.  The −−fast and −−best
              aliases  are  primarily for GNU gzip compatibility.
              In particular, −−fast doesn’t make things  signifi­
              cantly  faster.   And  −−best  merely  selects  the
              default behaviour.

       −−‐‐     Treats all subsequent arguments as file names, even
              if they start with a dash.  This is so you can han­
              dle files with names beginning  with  a  dash,  for
              example: bzip2 −‐ −myfilename.

       −−‐‐rreeppeettiittiivvee‐‐ffaasstt ‐‐‐‐rreeppeettiittiivvee‐‐bbeesstt
              These  flags  are  redundant  in versions 0.9.5 and
              above.  They provided some coarse control over  the
              behaviour  of the sorting algorithm in earlier ver­
              sions, which was sometimes useful.  0.9.5 and above
              have  an  improved  algorithm  which  renders these
              flags irrelevant.


MMEEMMOORRYY MMAANNAAGGEEMMEENNTT
       _b_z_i_p_2 compresses large files in blocks.   The  block  size
       affects  both  the  compression  ratio  achieved,  and the
       amount of memory needed for compression and decompression.
       The  flags  −1  through  −9  specify  the block size to be
       100,000 bytes through 900,000 bytes (the default)  respec­
       tively.   At  decompression  time, the block size used for
       compression is read from  the  header  of  the  compressed
       file, and _b_u_n_z_i_p_2 then allocates itself just enough memory
       to decompress the file.  Since block sizes are  stored  in
       compressed  files,  it follows that the flags −1 to −9 are
       irrelevant to and so ignored during decompression.

       Compression and decompression requirements, in bytes,  can
       be estimated as:

              Compression:   400k + ( 8 x block size )

              Decompression: 100k + ( 4 x block size ), or
                             100k + ( 2.5 x block size )

       Larger  block  sizes  give  rapidly  diminishing  marginal
       returns.  Most of the compression comes from the first two
       or  three hundred k of block size, a fact worth bearing in
       mind when using _b_z_i_p_2  on  small  machines.   It  is  also
       important  to  appreciate  that  the  decompression memory
       requirement is set at compression time by  the  choice  of
       block size.

       For  files  compressed  with  the default 900k block size,
       _b_u_n_z_i_p_2 will require about 3700 kbytes to decompress.   To
       support decompression of any file on a 4 megabyte machine,
       _b_u_n_z_i_p_2 has an option to  decompress  using  approximately
       half this amount of memory, about 2300 kbytes.  Decompres­
       sion speed is also halved, so you should use  this  option
       only where necessary.  The relevant flag is ‐s.

       In general, try and use the largest block size memory con­
       straints  allow,  since  that  maximises  the  compression
       achieved.   Compression and decompression speed are virtu­
       ally unaffected by block size.

       Another significant point applies to files which fit in  a
       single  block  ‐‐  that  means  most files you’d encounter
       using a large block  size.   The  amount  of  real  memory
       touched is proportional to the size of the file, since the
       file is smaller than a block.  For example, compressing  a
       file  20,000  bytes  long  with the flag ‐9 will cause the
       compressor to allocate around 7600k of  memory,  but  only
       touch 400k + 20000 * 8 = 560 kbytes of it.  Similarly, the
       decompressor will allocate 3700k but  only  touch  100k  +
       20000 * 4 = 180 kbytes.

       Here  is a table which summarises the maximum memory usage
       for different block sizes.  Also  recorded  is  the  total
       compressed  size for 14 files of the Calgary Text Compres­
       sion Corpus totalling 3,141,622 bytes.  This column  gives
       some  feel  for  how  compression  varies with block size.
       These figures tend to understate the advantage  of  larger
       block  sizes  for  larger files, since the Corpus is domi­
       nated by smaller files.

                  Compress   Decompress   Decompress   Corpus
           Flag     usage      usage       ‐s usage     Size

            ‐1      1200k       500k         350k      914704
            ‐2      2000k       900k         600k      877703
            ‐3      2800k      1300k         850k      860338
            ‐4      3600k      1700k        1100k      846899
            ‐5      4400k      2100k        1350k      845160
            ‐6      5200k      2500k        1600k      838626
            ‐7      6100k      2900k        1850k      834096
            ‐8      6800k      3300k        2100k      828642
            ‐9      7600k      3700k        2350k      828642


RREECCOOVVEERRIINNGG DDAATTAA FFRROOMM DDAAMMAAGGEEDD FFIILLEESS
       _b_z_i_p_2 compresses files in blocks, usually 900kbytes  long.
       Each block is handled independently.  If a media or trans­
       mission error causes a multi‐block  .bz2  file  to  become
       damaged,  it  may  be  possible  to  recover data from the
       undamaged blocks in the file.

       The compressed representation of each block  is  delimited
       by  a  48‐bit pattern, which makes it possible to find the
       block boundaries with reasonable  certainty.   Each  block
       also  carries its own 32‐bit CRC, so damaged blocks can be
       distinguished from undamaged ones.

       _b_z_i_p_2_r_e_c_o_v_e_r is a  simple  program  whose  purpose  is  to
       search  for blocks in .bz2 files, and write each block out
       into its own .bz2 file.  You can then use _b_z_i_p_2 −t to test
       the integrity of the resulting files, and decompress those
       which are undamaged.

       _b_z_i_p_2_r_e_c_o_v_e_r takes a single argument, the name of the dam­
       aged    file,    and    writes    a    number   of   files
       "rec00001file.bz2",  "rec00002file.bz2",  etc,  containing
       the   extracted   blocks.   The   output   filenames   are
       designed  so  that the use of wildcards in subsequent pro­
       cessing  ‐‐ for example, "bzip2 ‐dc  rec*file.bz2 > recov­
       ered_data" ‐‐ processes the files in the correct order.

       _b_z_i_p_2_r_e_c_o_v_e_r should be of most use dealing with large .bz2
       files,  as  these will contain many blocks.  It is clearly
       futile to use it on damaged single‐block  files,  since  a
       damaged  block  cannot  be recovered.  If you wish to min­
       imise any potential data loss through media  or  transmis­
       sion errors, you might consider compressing with a smaller
       block size.


PPEERRFFOORRMMAANNCCEE NNOOTTEESS
       The sorting phase of compression gathers together  similar
       strings  in  the  file.  Because of this, files containing
       very long runs of  repeated  symbols,  like  "aabaabaabaab
       ..."   (repeated  several hundred times) may compress more
       slowly than normal.  Versions 0.9.5 and  above  fare  much
       better  than previous versions in this respect.  The ratio
       between worst‐case and average‐case compression time is in
       the  region  of  10:1.  For previous versions, this figure
       was more like 100:1.  You can use the −vvvv option to mon­
       itor progress in great detail, if you want.

       Decompression speed is unaffected by these phenomena.

       _b_z_i_p_2  usually  allocates  several  megabytes of memory to
       operate in, and then charges all over it in a fairly  ran­
       dom  fashion.   This means that performance, both for com­
       pressing and decompressing, is largely determined  by  the
       speed  at  which  your  machine  can service cache misses.
       Because of this, small changes to the code to  reduce  the
       miss  rate  have  been observed to give disproportionately
       large performance improvements.  I imagine _b_z_i_p_2 will per­
       form best on machines with very large caches.


CCAAVVEEAATTSS
       I/O  error  messages  are not as helpful as they could be.
       _b_z_i_p_2 tries hard to detect I/O errors  and  exit  cleanly,
       but  the  details  of  what  the problem is sometimes seem
       rather misleading.

       This manual page pertains to version 1.0.6 of _b_z_i_p_2_.  Com­
       pressed  data created by this version is entirely forwards
       and  backwards  compatible  with   the   previous   public
       releases,  versions  0.1pl2,  0.9.0,  0.9.5, 1.0.0, 1.0.1, 
       1.0.2 and above, but with the  following  exception: 0.9.0
       and above can  correctly decompress  multiple concatenated
       compressed files.  0.1pl2  cannot do this;  it  will  stop 
       after  decompressing just the first file in the stream.

       _b_z_i_p_2_r_e_c_o_v_e_r  versions prior to 1.0.2 used 32‐bit integers
       to represent bit positions in compressed  files,  so  they
       could  not handle compressed files more than 512 megabytes
       long.  Versions 1.0.2 and above use 64‐bit  ints  on  some
       platforms  which  support them (GNU supported targets, and
       Windows).  To establish whether or  not  bzip2recover  was
       built  with  such  a limitation, run it without arguments.
       In any event you can build yourself an  unlimited  version
       if  you  can  recompile  it  with MaybeUInt64 set to be an
       unsigned 64‐bit integer.




AAUUTTHHOORR
       Julian Seward, jsewardbzip.org.

       http://www.bzip.org

       The ideas embodied in _b_z_i_p_2 are due to (at least) the fol­
       lowing  people: Michael Burrows and David Wheeler (for the
       block sorting transformation), David Wheeler  (again,  for
       the Huffman coder), Peter Fenwick (for the structured cod­
       ing model in the original _b_z_i_p_, and many refinements), and
       Alistair  Moffat,  Radford  Neal  and  Ian Witten (for the
       arithmetic  coder  in  the  original  _b_z_i_p_)_.   I  am  much
       indebted for their help, support and advice.  See the man­
       ual in the source distribution for pointers to sources  of
       documentation.  Christian von Roques encouraged me to look
       for faster sorting algorithms, so as to speed up  compres­
       sion.  Bela Lubkin encouraged me to improve the worst‐case
       compression performance.  Donna Robinson XMLised the docu­
       mentation.   The bz* scripts are derived from those of GNU
       gzip.  Many people sent patches, helped  with  portability
       problems,  lent  machines,  gave advice and were generally
       helpful.



                                                         bzip2(1)
genometools-1.5.1/src/external/bzip2-1.0.6/bzip2.c000066400000000000000000001622741211610345200213510ustar00rootroot00000000000000
/*-----------------------------------------------------------*/
/*--- A block-sorting, lossless compressor        bzip2.c ---*/
/*-----------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


/* Place a 1 beside your platform, and 0 elsewhere.
   Generic 32-bit Unix.
   Also works on 64-bit Unix boxes.
   This is the default.
*/
#define BZ_UNIX      1

/*--
  Win32, as seen by Jacob Navia's excellent
  port of (Chris Fraser & David Hanson)'s excellent
  lcc compiler.  Or with MS Visual C.
  This is selected automatically if compiled by a compiler which
  defines _WIN32, not including the Cygwin GCC.
--*/
#define BZ_LCCWIN32  0

#if defined(_WIN32) && !defined(__CYGWIN__)
#undef  BZ_LCCWIN32
#define BZ_LCCWIN32 1
#undef  BZ_UNIX
#define BZ_UNIX 0
#endif


/*---------------------------------------------*/
/*--
  Some stuff for all platforms.
--*/

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include "bzlib.h"

#define ERROR_IF_EOF(i)       { if ((i) == EOF)  ioError(); }
#define ERROR_IF_NOT_ZERO(i)  { if ((i) != 0)    ioError(); }
#define ERROR_IF_MINUS_ONE(i) { if ((i) == (-1)) ioError(); }


/*---------------------------------------------*/
/*--
   Platform-specific stuff.
--*/

#if BZ_UNIX
#   include 
#   include 
#   include 
#   include 
#   include 
#   include 

#   define PATH_SEP    '/'
#   define MY_LSTAT    lstat
#   define MY_STAT     stat
#   define MY_S_ISREG  S_ISREG
#   define MY_S_ISDIR  S_ISDIR

#   define APPEND_FILESPEC(root, name) \
      root=snocString((root), (name))

#   define APPEND_FLAG(root, name) \
      root=snocString((root), (name))

#   define SET_BINARY_MODE(fd) /**/

#   ifdef __GNUC__
#      define NORETURN __attribute__ ((noreturn))
#   else
#      define NORETURN /**/
#   endif

#   ifdef __DJGPP__
#     include 
#     include 
#     undef MY_LSTAT
#     undef MY_STAT
#     define MY_LSTAT stat
#     define MY_STAT stat
#     undef SET_BINARY_MODE
#     define SET_BINARY_MODE(fd)                        \
        do {                                            \
           int retVal = setmode ( fileno ( fd ),        \
                                  O_BINARY );           \
           ERROR_IF_MINUS_ONE ( retVal );               \
        } while ( 0 )
#   endif

#   ifdef __CYGWIN__
#     include 
#     include 
#     undef SET_BINARY_MODE
#     define SET_BINARY_MODE(fd)                        \
        do {                                            \
           int retVal = setmode ( fileno ( fd ),        \
                                  O_BINARY );           \
           ERROR_IF_MINUS_ONE ( retVal );               \
        } while ( 0 )
#   endif
#endif /* BZ_UNIX */



#if BZ_LCCWIN32
#   include 
#   include 
#   include 

#   define NORETURN       /**/
#   define PATH_SEP       '\\'
#   define MY_LSTAT       _stat
#   define MY_STAT        _stat
#   define MY_S_ISREG(x)  ((x) & _S_IFREG)
#   define MY_S_ISDIR(x)  ((x) & _S_IFDIR)

#   define APPEND_FLAG(root, name) \
      root=snocString((root), (name))

#   define APPEND_FILESPEC(root, name)                \
      root = snocString ((root), (name))

#   define SET_BINARY_MODE(fd)                        \
      do {                                            \
         int retVal = setmode ( fileno ( fd ),        \
                                O_BINARY );           \
         ERROR_IF_MINUS_ONE ( retVal );               \
      } while ( 0 )

#endif /* BZ_LCCWIN32 */


/*---------------------------------------------*/
/*--
  Some more stuff for all platforms :-)
--*/

typedef char            Char;
typedef unsigned char   Bool;
typedef unsigned char   UChar;
typedef int             Int32;
typedef unsigned int    UInt32;
typedef short           Int16;
typedef unsigned short  UInt16;
                                       
#define True  ((Bool)1)
#define False ((Bool)0)

/*--
  IntNative is your platform's `native' int size.
  Only here to avoid probs with 64-bit platforms.
--*/
typedef int IntNative;


/*---------------------------------------------------*/
/*--- Misc (file handling) data decls             ---*/
/*---------------------------------------------------*/

Int32   verbosity;
Bool    keepInputFiles, smallMode, deleteOutputOnInterrupt;
Bool    forceOverwrite, testFailsExist, unzFailsExist, noisy;
Int32   numFileNames, numFilesProcessed, blockSize100k;
Int32   exitValue;

/*-- source modes; F==file, I==stdin, O==stdout --*/
#define SM_I2O           1
#define SM_F2O           2
#define SM_F2F           3

/*-- operation modes --*/
#define OM_Z             1
#define OM_UNZ           2
#define OM_TEST          3

Int32   opMode;
Int32   srcMode;

#define FILE_NAME_LEN 1034

Int32   longestFileName;
Char    inName [FILE_NAME_LEN];
Char    outName[FILE_NAME_LEN];
Char    tmpName[FILE_NAME_LEN];
Char    *progName;
Char    progNameReally[FILE_NAME_LEN];
FILE    *outputHandleJustInCase;
Int32   workFactor;

static void    panic                 ( const Char* ) NORETURN;
static void    ioError               ( void )        NORETURN;
static void    outOfMemory           ( void )        NORETURN;
static void    configError           ( void )        NORETURN;
static void    crcError              ( void )        NORETURN;
static void    cleanUpAndFail        ( Int32 )       NORETURN;
static void    compressedStreamEOF   ( void )        NORETURN;

static void    copyFileName ( Char*, Char* );
static void*   myMalloc     ( Int32 );
static void    applySavedFileAttrToOutputFile ( IntNative fd );



/*---------------------------------------------------*/
/*--- An implementation of 64-bit ints.  Sigh.    ---*/
/*--- Roll on widespread deployment of ANSI C9X ! ---*/
/*---------------------------------------------------*/

typedef
   struct { UChar b[8]; } 
   UInt64;


static
void uInt64_from_UInt32s ( UInt64* n, UInt32 lo32, UInt32 hi32 )
{
   n->b[7] = (UChar)((hi32 >> 24) & 0xFF);
   n->b[6] = (UChar)((hi32 >> 16) & 0xFF);
   n->b[5] = (UChar)((hi32 >> 8)  & 0xFF);
   n->b[4] = (UChar) (hi32        & 0xFF);
   n->b[3] = (UChar)((lo32 >> 24) & 0xFF);
   n->b[2] = (UChar)((lo32 >> 16) & 0xFF);
   n->b[1] = (UChar)((lo32 >> 8)  & 0xFF);
   n->b[0] = (UChar) (lo32        & 0xFF);
}


static
double uInt64_to_double ( UInt64* n )
{
   Int32  i;
   double base = 1.0;
   double sum  = 0.0;
   for (i = 0; i < 8; i++) {
      sum  += base * (double)(n->b[i]);
      base *= 256.0;
   }
   return sum;
}


static
Bool uInt64_isZero ( UInt64* n )
{
   Int32 i;
   for (i = 0; i < 8; i++)
      if (n->b[i] != 0) return 0;
   return 1;
}


/* Divide *n by 10, and return the remainder.  */
static 
Int32 uInt64_qrm10 ( UInt64* n )
{
   UInt32 rem, tmp;
   Int32  i;
   rem = 0;
   for (i = 7; i >= 0; i--) {
      tmp = rem * 256 + n->b[i];
      n->b[i] = tmp / 10;
      rem = tmp % 10;
   }
   return rem;
}


/* ... and the Whole Entire Point of all this UInt64 stuff is
   so that we can supply the following function.
*/
static
void uInt64_toAscii ( char* outbuf, UInt64* n )
{
   Int32  i, q;
   UChar  buf[32];
   Int32  nBuf   = 0;
   UInt64 n_copy = *n;
   do {
      q = uInt64_qrm10 ( &n_copy );
      buf[nBuf] = q + '0';
      nBuf++;
   } while (!uInt64_isZero(&n_copy));
   outbuf[nBuf] = 0;
   for (i = 0; i < nBuf; i++) 
      outbuf[i] = buf[nBuf-i-1];
}


/*---------------------------------------------------*/
/*--- Processing of complete files and streams    ---*/
/*---------------------------------------------------*/

/*---------------------------------------------*/
static 
Bool myfeof ( FILE* f )
{
   Int32 c = fgetc ( f );
   if (c == EOF) return True;
   ungetc ( c, f );
   return False;
}


/*---------------------------------------------*/
static 
void compressStream ( FILE *stream, FILE *zStream )
{
   BZFILE* bzf = NULL;
   UChar   ibuf[5000];
   Int32   nIbuf;
   UInt32  nbytes_in_lo32, nbytes_in_hi32;
   UInt32  nbytes_out_lo32, nbytes_out_hi32;
   Int32   bzerr, bzerr_dummy, ret;

   SET_BINARY_MODE(stream);
   SET_BINARY_MODE(zStream);

   if (ferror(stream)) goto errhandler_io;
   if (ferror(zStream)) goto errhandler_io;

   bzf = BZ2_bzWriteOpen ( &bzerr, zStream, 
                           blockSize100k, verbosity, workFactor );   
   if (bzerr != BZ_OK) goto errhandler;

   if (verbosity >= 2) fprintf ( stderr, "\n" );

   while (True) {

      if (myfeof(stream)) break;
      nIbuf = fread ( ibuf, sizeof(UChar), 5000, stream );
      if (ferror(stream)) goto errhandler_io;
      if (nIbuf > 0) BZ2_bzWrite ( &bzerr, bzf, (void*)ibuf, nIbuf );
      if (bzerr != BZ_OK) goto errhandler;

   }

   BZ2_bzWriteClose64 ( &bzerr, bzf, 0, 
                        &nbytes_in_lo32, &nbytes_in_hi32,
                        &nbytes_out_lo32, &nbytes_out_hi32 );
   if (bzerr != BZ_OK) goto errhandler;

   if (ferror(zStream)) goto errhandler_io;
   ret = fflush ( zStream );
   if (ret == EOF) goto errhandler_io;
   if (zStream != stdout) {
      Int32 fd = fileno ( zStream );
      if (fd < 0) goto errhandler_io;
      applySavedFileAttrToOutputFile ( fd );
      ret = fclose ( zStream );
      outputHandleJustInCase = NULL;
      if (ret == EOF) goto errhandler_io;
   }
   outputHandleJustInCase = NULL;
   if (ferror(stream)) goto errhandler_io;
   ret = fclose ( stream );
   if (ret == EOF) goto errhandler_io;

   if (verbosity >= 1) {
      if (nbytes_in_lo32 == 0 && nbytes_in_hi32 == 0) {
	 fprintf ( stderr, " no data compressed.\n");
      } else {
	 Char   buf_nin[32], buf_nout[32];
	 UInt64 nbytes_in,   nbytes_out;
	 double nbytes_in_d, nbytes_out_d;
	 uInt64_from_UInt32s ( &nbytes_in, 
			       nbytes_in_lo32, nbytes_in_hi32 );
	 uInt64_from_UInt32s ( &nbytes_out, 
			       nbytes_out_lo32, nbytes_out_hi32 );
	 nbytes_in_d  = uInt64_to_double ( &nbytes_in );
	 nbytes_out_d = uInt64_to_double ( &nbytes_out );
	 uInt64_toAscii ( buf_nin, &nbytes_in );
	 uInt64_toAscii ( buf_nout, &nbytes_out );
	 fprintf ( stderr, "%6.3f:1, %6.3f bits/byte, "
		   "%5.2f%% saved, %s in, %s out.\n",
		   nbytes_in_d / nbytes_out_d,
		   (8.0 * nbytes_out_d) / nbytes_in_d,
		   100.0 * (1.0 - nbytes_out_d / nbytes_in_d),
		   buf_nin,
		   buf_nout
		 );
      }
   }

   return;

   errhandler:
   BZ2_bzWriteClose64 ( &bzerr_dummy, bzf, 1, 
                        &nbytes_in_lo32, &nbytes_in_hi32,
                        &nbytes_out_lo32, &nbytes_out_hi32 );
   switch (bzerr) {
      case BZ_CONFIG_ERROR:
         configError(); break;
      case BZ_MEM_ERROR:
         outOfMemory (); break;
      case BZ_IO_ERROR:
         errhandler_io:
         ioError(); break;
      default:
         panic ( "compress:unexpected error" );
   }

   panic ( "compress:end" );
   /*notreached*/
}



/*---------------------------------------------*/
static 
Bool uncompressStream ( FILE *zStream, FILE *stream )
{
   BZFILE* bzf = NULL;
   Int32   bzerr, bzerr_dummy, ret, nread, streamNo, i;
   UChar   obuf[5000];
   UChar   unused[BZ_MAX_UNUSED];
   Int32   nUnused;
   void*   unusedTmpV;
   UChar*  unusedTmp;

   nUnused = 0;
   streamNo = 0;

   SET_BINARY_MODE(stream);
   SET_BINARY_MODE(zStream);

   if (ferror(stream)) goto errhandler_io;
   if (ferror(zStream)) goto errhandler_io;

   while (True) {

      bzf = BZ2_bzReadOpen ( 
               &bzerr, zStream, verbosity, 
               (int)smallMode, unused, nUnused
            );
      if (bzf == NULL || bzerr != BZ_OK) goto errhandler;
      streamNo++;

      while (bzerr == BZ_OK) {
         nread = BZ2_bzRead ( &bzerr, bzf, obuf, 5000 );
         if (bzerr == BZ_DATA_ERROR_MAGIC) goto trycat;
         if ((bzerr == BZ_OK || bzerr == BZ_STREAM_END) && nread > 0)
            fwrite ( obuf, sizeof(UChar), nread, stream );
         if (ferror(stream)) goto errhandler_io;
      }
      if (bzerr != BZ_STREAM_END) goto errhandler;

      BZ2_bzReadGetUnused ( &bzerr, bzf, &unusedTmpV, &nUnused );
      if (bzerr != BZ_OK) panic ( "decompress:bzReadGetUnused" );

      unusedTmp = (UChar*)unusedTmpV;
      for (i = 0; i < nUnused; i++) unused[i] = unusedTmp[i];

      BZ2_bzReadClose ( &bzerr, bzf );
      if (bzerr != BZ_OK) panic ( "decompress:bzReadGetUnused" );

      if (nUnused == 0 && myfeof(zStream)) break;
   }

   closeok:
   if (ferror(zStream)) goto errhandler_io;
   if (stream != stdout) {
      Int32 fd = fileno ( stream );
      if (fd < 0) goto errhandler_io;
      applySavedFileAttrToOutputFile ( fd );
   }
   ret = fclose ( zStream );
   if (ret == EOF) goto errhandler_io;

   if (ferror(stream)) goto errhandler_io;
   ret = fflush ( stream );
   if (ret != 0) goto errhandler_io;
   if (stream != stdout) {
      ret = fclose ( stream );
      outputHandleJustInCase = NULL;
      if (ret == EOF) goto errhandler_io;
   }
   outputHandleJustInCase = NULL;
   if (verbosity >= 2) fprintf ( stderr, "\n    " );
   return True;

   trycat: 
   if (forceOverwrite) {
      rewind(zStream);
      while (True) {
      	 if (myfeof(zStream)) break;
      	 nread = fread ( obuf, sizeof(UChar), 5000, zStream );
      	 if (ferror(zStream)) goto errhandler_io;
      	 if (nread > 0) fwrite ( obuf, sizeof(UChar), nread, stream );
      	 if (ferror(stream)) goto errhandler_io;
      }
      goto closeok;
   }
  
   errhandler:
   BZ2_bzReadClose ( &bzerr_dummy, bzf );
   switch (bzerr) {
      case BZ_CONFIG_ERROR:
         configError(); break;
      case BZ_IO_ERROR:
         errhandler_io:
         ioError(); break;
      case BZ_DATA_ERROR:
         crcError();
      case BZ_MEM_ERROR:
         outOfMemory();
      case BZ_UNEXPECTED_EOF:
         compressedStreamEOF();
      case BZ_DATA_ERROR_MAGIC:
         if (zStream != stdin) fclose(zStream);
         if (stream != stdout) fclose(stream);
         if (streamNo == 1) {
            return False;
         } else {
            if (noisy)
            fprintf ( stderr, 
                      "\n%s: %s: trailing garbage after EOF ignored\n",
                      progName, inName );
            return True;       
         }
      default:
         panic ( "decompress:unexpected error" );
   }

   panic ( "decompress:end" );
   return True; /*notreached*/
}


/*---------------------------------------------*/
static 
Bool testStream ( FILE *zStream )
{
   BZFILE* bzf = NULL;
   Int32   bzerr, bzerr_dummy, ret, nread, streamNo, i;
   UChar   obuf[5000];
   UChar   unused[BZ_MAX_UNUSED];
   Int32   nUnused;
   void*   unusedTmpV;
   UChar*  unusedTmp;

   nUnused = 0;
   streamNo = 0;

   SET_BINARY_MODE(zStream);
   if (ferror(zStream)) goto errhandler_io;

   while (True) {

      bzf = BZ2_bzReadOpen ( 
               &bzerr, zStream, verbosity, 
               (int)smallMode, unused, nUnused
            );
      if (bzf == NULL || bzerr != BZ_OK) goto errhandler;
      streamNo++;

      while (bzerr == BZ_OK) {
         nread = BZ2_bzRead ( &bzerr, bzf, obuf, 5000 );
         if (bzerr == BZ_DATA_ERROR_MAGIC) goto errhandler;
      }
      if (bzerr != BZ_STREAM_END) goto errhandler;

      BZ2_bzReadGetUnused ( &bzerr, bzf, &unusedTmpV, &nUnused );
      if (bzerr != BZ_OK) panic ( "test:bzReadGetUnused" );

      unusedTmp = (UChar*)unusedTmpV;
      for (i = 0; i < nUnused; i++) unused[i] = unusedTmp[i];

      BZ2_bzReadClose ( &bzerr, bzf );
      if (bzerr != BZ_OK) panic ( "test:bzReadGetUnused" );
      if (nUnused == 0 && myfeof(zStream)) break;

   }

   if (ferror(zStream)) goto errhandler_io;
   ret = fclose ( zStream );
   if (ret == EOF) goto errhandler_io;

   if (verbosity >= 2) fprintf ( stderr, "\n    " );
   return True;

   errhandler:
   BZ2_bzReadClose ( &bzerr_dummy, bzf );
   if (verbosity == 0) 
      fprintf ( stderr, "%s: %s: ", progName, inName );
   switch (bzerr) {
      case BZ_CONFIG_ERROR:
         configError(); break;
      case BZ_IO_ERROR:
         errhandler_io:
         ioError(); break;
      case BZ_DATA_ERROR:
         fprintf ( stderr,
                   "data integrity (CRC) error in data\n" );
         return False;
      case BZ_MEM_ERROR:
         outOfMemory();
      case BZ_UNEXPECTED_EOF:
         fprintf ( stderr,
                   "file ends unexpectedly\n" );
         return False;
      case BZ_DATA_ERROR_MAGIC:
         if (zStream != stdin) fclose(zStream);
         if (streamNo == 1) {
          fprintf ( stderr, 
                    "bad magic number (file not created by bzip2)\n" );
            return False;
         } else {
            if (noisy)
            fprintf ( stderr, 
                      "trailing garbage after EOF ignored\n" );
            return True;       
         }
      default:
         panic ( "test:unexpected error" );
   }

   panic ( "test:end" );
   return True; /*notreached*/
}


/*---------------------------------------------------*/
/*--- Error [non-] handling grunge                ---*/
/*---------------------------------------------------*/

/*---------------------------------------------*/
static
void setExit ( Int32 v )
{
   if (v > exitValue) exitValue = v;
}


/*---------------------------------------------*/
static 
void cadvise ( void )
{
   if (noisy)
   fprintf (
      stderr,
      "\nIt is possible that the compressed file(s) have become corrupted.\n"
        "You can use the -tvv option to test integrity of such files.\n\n"
        "You can use the `bzip2recover' program to attempt to recover\n"
        "data from undamaged sections of corrupted files.\n\n"
    );
}


/*---------------------------------------------*/
static 
void showFileNames ( void )
{
   if (noisy)
   fprintf (
      stderr,
      "\tInput file = %s, output file = %s\n",
      inName, outName 
   );
}


/*---------------------------------------------*/
static 
void cleanUpAndFail ( Int32 ec )
{
   IntNative      retVal;
   struct MY_STAT statBuf;

   if ( srcMode == SM_F2F 
        && opMode != OM_TEST
        && deleteOutputOnInterrupt ) {

      /* Check whether input file still exists.  Delete output file
         only if input exists to avoid loss of data.  Joerg Prante, 5
         January 2002.  (JRS 06-Jan-2002: other changes in 1.0.2 mean
         this is less likely to happen.  But to be ultra-paranoid, we
         do the check anyway.)  */
      retVal = MY_STAT ( inName, &statBuf );
      if (retVal == 0) {
         if (noisy)
            fprintf ( stderr, 
                      "%s: Deleting output file %s, if it exists.\n",
                      progName, outName );
         if (outputHandleJustInCase != NULL)
            fclose ( outputHandleJustInCase );
         retVal = remove ( outName );
         if (retVal != 0)
            fprintf ( stderr,
                      "%s: WARNING: deletion of output file "
                      "(apparently) failed.\n",
                      progName );
      } else {
         fprintf ( stderr,
                   "%s: WARNING: deletion of output file suppressed\n",
                    progName );
         fprintf ( stderr,
                   "%s:    since input file no longer exists.  Output file\n",
                   progName );
         fprintf ( stderr,
                   "%s:    `%s' may be incomplete.\n",
                   progName, outName );
         fprintf ( stderr, 
                   "%s:    I suggest doing an integrity test (bzip2 -tv)"
                   " of it.\n",
                   progName );
      }
   }

   if (noisy && numFileNames > 0 && numFilesProcessed < numFileNames) {
      fprintf ( stderr, 
                "%s: WARNING: some files have not been processed:\n"
                "%s:    %d specified on command line, %d not processed yet.\n\n",
                progName, progName,
                numFileNames, numFileNames - numFilesProcessed );
   }
   setExit(ec);
   exit(exitValue);
}


/*---------------------------------------------*/
static 
void panic ( const Char* s )
{
   fprintf ( stderr,
             "\n%s: PANIC -- internal consistency error:\n"
             "\t%s\n"
             "\tThis is a BUG.  Please report it to me at:\n"
             "\tjseward@bzip.org\n",
             progName, s );
   showFileNames();
   cleanUpAndFail( 3 );
}


/*---------------------------------------------*/
static 
void crcError ( void )
{
   fprintf ( stderr,
             "\n%s: Data integrity error when decompressing.\n",
             progName );
   showFileNames();
   cadvise();
   cleanUpAndFail( 2 );
}


/*---------------------------------------------*/
static 
void compressedStreamEOF ( void )
{
  if (noisy) {
    fprintf ( stderr,
	      "\n%s: Compressed file ends unexpectedly;\n\t"
	      "perhaps it is corrupted?  *Possible* reason follows.\n",
	      progName );
    perror ( progName );
    showFileNames();
    cadvise();
  }
  cleanUpAndFail( 2 );
}


/*---------------------------------------------*/
static 
void ioError ( void )
{
   fprintf ( stderr,
             "\n%s: I/O or other error, bailing out.  "
             "Possible reason follows.\n",
             progName );
   perror ( progName );
   showFileNames();
   cleanUpAndFail( 1 );
}


/*---------------------------------------------*/
static 
void mySignalCatcher ( IntNative n )
{
   fprintf ( stderr,
             "\n%s: Control-C or similar caught, quitting.\n",
             progName );
   cleanUpAndFail(1);
}


/*---------------------------------------------*/
static 
void mySIGSEGVorSIGBUScatcher ( IntNative n )
{
   if (opMode == OM_Z)
      fprintf ( 
      stderr,
      "\n%s: Caught a SIGSEGV or SIGBUS whilst compressing.\n"
      "\n"
      "   Possible causes are (most likely first):\n"
      "   (1) This computer has unreliable memory or cache hardware\n"
      "       (a surprisingly common problem; try a different machine.)\n"
      "   (2) A bug in the compiler used to create this executable\n"
      "       (unlikely, if you didn't compile bzip2 yourself.)\n"
      "   (3) A real bug in bzip2 -- I hope this should never be the case.\n"
      "   The user's manual, Section 4.3, has more info on (1) and (2).\n"
      "   \n"
      "   If you suspect this is a bug in bzip2, or are unsure about (1)\n"
      "   or (2), feel free to report it to me at: jseward@bzip.org.\n"
      "   Section 4.3 of the user's manual describes the info a useful\n"
      "   bug report should have.  If the manual is available on your\n"
      "   system, please try and read it before mailing me.  If you don't\n"
      "   have the manual or can't be bothered to read it, mail me anyway.\n"
      "\n",
      progName );
      else
      fprintf ( 
      stderr,
      "\n%s: Caught a SIGSEGV or SIGBUS whilst decompressing.\n"
      "\n"
      "   Possible causes are (most likely first):\n"
      "   (1) The compressed data is corrupted, and bzip2's usual checks\n"
      "       failed to detect this.  Try bzip2 -tvv my_file.bz2.\n"
      "   (2) This computer has unreliable memory or cache hardware\n"
      "       (a surprisingly common problem; try a different machine.)\n"
      "   (3) A bug in the compiler used to create this executable\n"
      "       (unlikely, if you didn't compile bzip2 yourself.)\n"
      "   (4) A real bug in bzip2 -- I hope this should never be the case.\n"
      "   The user's manual, Section 4.3, has more info on (2) and (3).\n"
      "   \n"
      "   If you suspect this is a bug in bzip2, or are unsure about (2)\n"
      "   or (3), feel free to report it to me at: jseward@bzip.org.\n"
      "   Section 4.3 of the user's manual describes the info a useful\n"
      "   bug report should have.  If the manual is available on your\n"
      "   system, please try and read it before mailing me.  If you don't\n"
      "   have the manual or can't be bothered to read it, mail me anyway.\n"
      "\n",
      progName );

   showFileNames();
   if (opMode == OM_Z)
      cleanUpAndFail( 3 ); else
      { cadvise(); cleanUpAndFail( 2 ); }
}


/*---------------------------------------------*/
static 
void outOfMemory ( void )
{
   fprintf ( stderr,
             "\n%s: couldn't allocate enough memory\n",
             progName );
   showFileNames();
   cleanUpAndFail(1);
}


/*---------------------------------------------*/
static 
void configError ( void )
{
   fprintf ( stderr,
             "bzip2: I'm not configured correctly for this platform!\n"
             "\tI require Int32, Int16 and Char to have sizes\n"
             "\tof 4, 2 and 1 bytes to run properly, and they don't.\n"
             "\tProbably you can fix this by defining them correctly,\n"
             "\tand recompiling.  Bye!\n" );
   setExit(3);
   exit(exitValue);
}


/*---------------------------------------------------*/
/*--- The main driver machinery                   ---*/
/*---------------------------------------------------*/

/* All rather crufty.  The main problem is that input files
   are stat()d multiple times before use.  This should be
   cleaned up. 
*/

/*---------------------------------------------*/
static 
void pad ( Char *s )
{
   Int32 i;
   if ( (Int32)strlen(s) >= longestFileName ) return;
   for (i = 1; i <= longestFileName - (Int32)strlen(s); i++)
      fprintf ( stderr, " " );
}


/*---------------------------------------------*/
static 
void copyFileName ( Char* to, Char* from ) 
{
   if ( strlen(from) > FILE_NAME_LEN-10 )  {
      fprintf (
         stderr,
         "bzip2: file name\n`%s'\n"
         "is suspiciously (more than %d chars) long.\n"
         "Try using a reasonable file name instead.  Sorry! :-)\n",
         from, FILE_NAME_LEN-10
      );
      setExit(1);
      exit(exitValue);
   }

  strncpy(to,from,FILE_NAME_LEN-10);
  to[FILE_NAME_LEN-10]='\0';
}


/*---------------------------------------------*/
static 
Bool fileExists ( Char* name )
{
   FILE *tmp   = fopen ( name, "rb" );
   Bool exists = (tmp != NULL);
   if (tmp != NULL) fclose ( tmp );
   return exists;
}


/*---------------------------------------------*/
/* Open an output file safely with O_EXCL and good permissions.
   This avoids a race condition in versions < 1.0.2, in which
   the file was first opened and then had its interim permissions
   set safely.  We instead use open() to create the file with
   the interim permissions required. (--- --- rw-).

   For non-Unix platforms, if we are not worrying about
   security issues, simple this simply behaves like fopen.
*/
static
FILE* fopen_output_safely ( Char* name, const char* mode )
{
#  if BZ_UNIX
   FILE*     fp;
   IntNative fh;
   fh = open(name, O_WRONLY|O_CREAT|O_EXCL, S_IWUSR|S_IRUSR);
   if (fh == -1) return NULL;
   fp = fdopen(fh, mode);
   if (fp == NULL) close(fh);
   return fp;
#  else
   return fopen(name, mode);
#  endif
}


/*---------------------------------------------*/
/*--
  if in doubt, return True
--*/
static 
Bool notAStandardFile ( Char* name )
{
   IntNative      i;
   struct MY_STAT statBuf;

   i = MY_LSTAT ( name, &statBuf );
   if (i != 0) return True;
   if (MY_S_ISREG(statBuf.st_mode)) return False;
   return True;
}


/*---------------------------------------------*/
/*--
  rac 11/21/98 see if file has hard links to it
--*/
static 
Int32 countHardLinks ( Char* name )
{  
   IntNative      i;
   struct MY_STAT statBuf;

   i = MY_LSTAT ( name, &statBuf );
   if (i != 0) return 0;
   return (statBuf.st_nlink - 1);
}


/*---------------------------------------------*/
/* Copy modification date, access date, permissions and owner from the
   source to destination file.  We have to copy this meta-info off
   into fileMetaInfo before starting to compress / decompress it,
   because doing it afterwards means we get the wrong access time.

   To complicate matters, in compress() and decompress() below, the
   sequence of tests preceding the call to saveInputFileMetaInfo()
   involves calling fileExists(), which in turn establishes its result
   by attempting to fopen() the file, and if successful, immediately
   fclose()ing it again.  So we have to assume that the fopen() call
   does not cause the access time field to be updated.

   Reading of the man page for stat() (man 2 stat) on RedHat 7.2 seems
   to imply that merely doing open() will not affect the access time.
   Therefore we merely need to hope that the C library only does
   open() as a result of fopen(), and not any kind of read()-ahead
   cleverness.

   It sounds pretty fragile to me.  Whether this carries across
   robustly to arbitrary Unix-like platforms (or even works robustly
   on this one, RedHat 7.2) is unknown to me.  Nevertheless ...  
*/
#if BZ_UNIX
static 
struct MY_STAT fileMetaInfo;
#endif

static 
void saveInputFileMetaInfo ( Char *srcName )
{
#  if BZ_UNIX
   IntNative retVal;
   /* Note use of stat here, not lstat. */
   retVal = MY_STAT( srcName, &fileMetaInfo );
   ERROR_IF_NOT_ZERO ( retVal );
#  endif
}


static 
void applySavedTimeInfoToOutputFile ( Char *dstName )
{
#  if BZ_UNIX
   IntNative      retVal;
   struct utimbuf uTimBuf;

   uTimBuf.actime = fileMetaInfo.st_atime;
   uTimBuf.modtime = fileMetaInfo.st_mtime;

   retVal = utime ( dstName, &uTimBuf );
   ERROR_IF_NOT_ZERO ( retVal );
#  endif
}

static 
void applySavedFileAttrToOutputFile ( IntNative fd )
{
#  if BZ_UNIX
   IntNative retVal;

   retVal = fchmod ( fd, fileMetaInfo.st_mode );
   ERROR_IF_NOT_ZERO ( retVal );

   (void) fchown ( fd, fileMetaInfo.st_uid, fileMetaInfo.st_gid );
   /* chown() will in many cases return with EPERM, which can
      be safely ignored.
   */
#  endif
}


/*---------------------------------------------*/
static 
Bool containsDubiousChars ( Char* name )
{
#  if BZ_UNIX
   /* On unix, files can contain any characters and the file expansion
    * is performed by the shell.
    */
   return False;
#  else /* ! BZ_UNIX */
   /* On non-unix (Win* platforms), wildcard characters are not allowed in 
    * filenames.
    */
   for (; *name != '\0'; name++)
      if (*name == '?' || *name == '*') return True;
   return False;
#  endif /* BZ_UNIX */
}


/*---------------------------------------------*/
#define BZ_N_SUFFIX_PAIRS 4

const Char* zSuffix[BZ_N_SUFFIX_PAIRS] 
   = { ".bz2", ".bz", ".tbz2", ".tbz" };
const Char* unzSuffix[BZ_N_SUFFIX_PAIRS] 
   = { "", "", ".tar", ".tar" };

static 
Bool hasSuffix ( Char* s, const Char* suffix )
{
   Int32 ns = strlen(s);
   Int32 nx = strlen(suffix);
   if (ns < nx) return False;
   if (strcmp(s + ns - nx, suffix) == 0) return True;
   return False;
}

static 
Bool mapSuffix ( Char* name, 
                 const Char* oldSuffix, 
                 const Char* newSuffix )
{
   if (!hasSuffix(name,oldSuffix)) return False;
   name[strlen(name)-strlen(oldSuffix)] = 0;
   strcat ( name, newSuffix );
   return True;
}


/*---------------------------------------------*/
static 
void compress ( Char *name )
{
   FILE  *inStr;
   FILE  *outStr;
   Int32 n, i;
   struct MY_STAT statBuf;

   deleteOutputOnInterrupt = False;

   if (name == NULL && srcMode != SM_I2O)
      panic ( "compress: bad modes\n" );

   switch (srcMode) {
      case SM_I2O: 
         copyFileName ( inName, (Char*)"(stdin)" );
         copyFileName ( outName, (Char*)"(stdout)" ); 
         break;
      case SM_F2F: 
         copyFileName ( inName, name );
         copyFileName ( outName, name );
         strcat ( outName, ".bz2" ); 
         break;
      case SM_F2O: 
         copyFileName ( inName, name );
         copyFileName ( outName, (Char*)"(stdout)" ); 
         break;
   }

   if ( srcMode != SM_I2O && containsDubiousChars ( inName ) ) {
      if (noisy)
      fprintf ( stderr, "%s: There are no files matching `%s'.\n",
                progName, inName );
      setExit(1);
      return;
   }
   if ( srcMode != SM_I2O && !fileExists ( inName ) ) {
      fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
                progName, inName, strerror(errno) );
      setExit(1);
      return;
   }
   for (i = 0; i < BZ_N_SUFFIX_PAIRS; i++) {
      if (hasSuffix(inName, zSuffix[i])) {
         if (noisy)
         fprintf ( stderr, 
                   "%s: Input file %s already has %s suffix.\n",
                   progName, inName, zSuffix[i] );
         setExit(1);
         return;
      }
   }
   if ( srcMode == SM_F2F || srcMode == SM_F2O ) {
      MY_STAT(inName, &statBuf);
      if ( MY_S_ISDIR(statBuf.st_mode) ) {
         fprintf( stderr,
                  "%s: Input file %s is a directory.\n",
                  progName,inName);
         setExit(1);
         return;
      }
   }
   if ( srcMode == SM_F2F && !forceOverwrite && notAStandardFile ( inName )) {
      if (noisy)
      fprintf ( stderr, "%s: Input file %s is not a normal file.\n",
                progName, inName );
      setExit(1);
      return;
   }
   if ( srcMode == SM_F2F && fileExists ( outName ) ) {
      if (forceOverwrite) {
	 remove(outName);
      } else {
	 fprintf ( stderr, "%s: Output file %s already exists.\n",
		   progName, outName );
	 setExit(1);
	 return;
      }
   }
   if ( srcMode == SM_F2F && !forceOverwrite &&
        (n=countHardLinks ( inName )) > 0) {
      fprintf ( stderr, "%s: Input file %s has %d other link%s.\n",
                progName, inName, n, n > 1 ? "s" : "" );
      setExit(1);
      return;
   }

   if ( srcMode == SM_F2F ) {
      /* Save the file's meta-info before we open it.  Doing it later
         means we mess up the access times. */
      saveInputFileMetaInfo ( inName );
   }

   switch ( srcMode ) {

      case SM_I2O:
         inStr = stdin;
         outStr = stdout;
         if ( isatty ( fileno ( stdout ) ) ) {
            fprintf ( stderr,
                      "%s: I won't write compressed data to a terminal.\n",
                      progName );
            fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
                              progName, progName );
            setExit(1);
            return;
         };
         break;

      case SM_F2O:
         inStr = fopen ( inName, "rb" );
         outStr = stdout;
         if ( isatty ( fileno ( stdout ) ) ) {
            fprintf ( stderr,
                      "%s: I won't write compressed data to a terminal.\n",
                      progName );
            fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
                              progName, progName );
            if ( inStr != NULL ) fclose ( inStr );
            setExit(1);
            return;
         };
         if ( inStr == NULL ) {
            fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
                      progName, inName, strerror(errno) );
            setExit(1);
            return;
         };
         break;

      case SM_F2F:
         inStr = fopen ( inName, "rb" );
         outStr = fopen_output_safely ( outName, "wb" );
         if ( outStr == NULL) {
            fprintf ( stderr, "%s: Can't create output file %s: %s.\n",
                      progName, outName, strerror(errno) );
            if ( inStr != NULL ) fclose ( inStr );
            setExit(1);
            return;
         }
         if ( inStr == NULL ) {
            fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
                      progName, inName, strerror(errno) );
            if ( outStr != NULL ) fclose ( outStr );
            setExit(1);
            return;
         };
         break;

      default:
         panic ( "compress: bad srcMode" );
         break;
   }

   if (verbosity >= 1) {
      fprintf ( stderr,  "  %s: ", inName );
      pad ( inName );
      fflush ( stderr );
   }

   /*--- Now the input and output handles are sane.  Do the Biz. ---*/
   outputHandleJustInCase = outStr;
   deleteOutputOnInterrupt = True;
   compressStream ( inStr, outStr );
   outputHandleJustInCase = NULL;

   /*--- If there was an I/O error, we won't get here. ---*/
   if ( srcMode == SM_F2F ) {
      applySavedTimeInfoToOutputFile ( outName );
      deleteOutputOnInterrupt = False;
      if ( !keepInputFiles ) {
         IntNative retVal = remove ( inName );
         ERROR_IF_NOT_ZERO ( retVal );
      }
   }

   deleteOutputOnInterrupt = False;
}


/*---------------------------------------------*/
static 
void uncompress ( Char *name )
{
   FILE  *inStr;
   FILE  *outStr;
   Int32 n, i;
   Bool  magicNumberOK;
   Bool  cantGuess;
   struct MY_STAT statBuf;

   deleteOutputOnInterrupt = False;

   if (name == NULL && srcMode != SM_I2O)
      panic ( "uncompress: bad modes\n" );

   cantGuess = False;
   switch (srcMode) {
      case SM_I2O: 
         copyFileName ( inName, (Char*)"(stdin)" );
         copyFileName ( outName, (Char*)"(stdout)" ); 
         break;
      case SM_F2F: 
         copyFileName ( inName, name );
         copyFileName ( outName, name );
         for (i = 0; i < BZ_N_SUFFIX_PAIRS; i++)
            if (mapSuffix(outName,zSuffix[i],unzSuffix[i]))
               goto zzz; 
         cantGuess = True;
         strcat ( outName, ".out" );
         break;
      case SM_F2O: 
         copyFileName ( inName, name );
         copyFileName ( outName, (Char*)"(stdout)" ); 
         break;
   }

   zzz:
   if ( srcMode != SM_I2O && containsDubiousChars ( inName ) ) {
      if (noisy)
      fprintf ( stderr, "%s: There are no files matching `%s'.\n",
                progName, inName );
      setExit(1);
      return;
   }
   if ( srcMode != SM_I2O && !fileExists ( inName ) ) {
      fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
                progName, inName, strerror(errno) );
      setExit(1);
      return;
   }
   if ( srcMode == SM_F2F || srcMode == SM_F2O ) {
      MY_STAT(inName, &statBuf);
      if ( MY_S_ISDIR(statBuf.st_mode) ) {
         fprintf( stderr,
                  "%s: Input file %s is a directory.\n",
                  progName,inName);
         setExit(1);
         return;
      }
   }
   if ( srcMode == SM_F2F && !forceOverwrite && notAStandardFile ( inName )) {
      if (noisy)
      fprintf ( stderr, "%s: Input file %s is not a normal file.\n",
                progName, inName );
      setExit(1);
      return;
   }
   if ( /* srcMode == SM_F2F implied && */ cantGuess ) {
      if (noisy)
      fprintf ( stderr, 
                "%s: Can't guess original name for %s -- using %s\n",
                progName, inName, outName );
      /* just a warning, no return */
   }   
   if ( srcMode == SM_F2F && fileExists ( outName ) ) {
      if (forceOverwrite) {
	remove(outName);
      } else {
        fprintf ( stderr, "%s: Output file %s already exists.\n",
                  progName, outName );
        setExit(1);
        return;
      }
   }
   if ( srcMode == SM_F2F && !forceOverwrite &&
        (n=countHardLinks ( inName ) ) > 0) {
      fprintf ( stderr, "%s: Input file %s has %d other link%s.\n",
                progName, inName, n, n > 1 ? "s" : "" );
      setExit(1);
      return;
   }

   if ( srcMode == SM_F2F ) {
      /* Save the file's meta-info before we open it.  Doing it later
         means we mess up the access times. */
      saveInputFileMetaInfo ( inName );
   }

   switch ( srcMode ) {

      case SM_I2O:
         inStr = stdin;
         outStr = stdout;
         if ( isatty ( fileno ( stdin ) ) ) {
            fprintf ( stderr,
                      "%s: I won't read compressed data from a terminal.\n",
                      progName );
            fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
                              progName, progName );
            setExit(1);
            return;
         };
         break;

      case SM_F2O:
         inStr = fopen ( inName, "rb" );
         outStr = stdout;
         if ( inStr == NULL ) {
            fprintf ( stderr, "%s: Can't open input file %s:%s.\n",
                      progName, inName, strerror(errno) );
            if ( inStr != NULL ) fclose ( inStr );
            setExit(1);
            return;
         };
         break;

      case SM_F2F:
         inStr = fopen ( inName, "rb" );
         outStr = fopen_output_safely ( outName, "wb" );
         if ( outStr == NULL) {
            fprintf ( stderr, "%s: Can't create output file %s: %s.\n",
                      progName, outName, strerror(errno) );
            if ( inStr != NULL ) fclose ( inStr );
            setExit(1);
            return;
         }
         if ( inStr == NULL ) {
            fprintf ( stderr, "%s: Can't open input file %s: %s.\n",
                      progName, inName, strerror(errno) );
            if ( outStr != NULL ) fclose ( outStr );
            setExit(1);
            return;
         };
         break;

      default:
         panic ( "uncompress: bad srcMode" );
         break;
   }

   if (verbosity >= 1) {
      fprintf ( stderr, "  %s: ", inName );
      pad ( inName );
      fflush ( stderr );
   }

   /*--- Now the input and output handles are sane.  Do the Biz. ---*/
   outputHandleJustInCase = outStr;
   deleteOutputOnInterrupt = True;
   magicNumberOK = uncompressStream ( inStr, outStr );
   outputHandleJustInCase = NULL;

   /*--- If there was an I/O error, we won't get here. ---*/
   if ( magicNumberOK ) {
      if ( srcMode == SM_F2F ) {
         applySavedTimeInfoToOutputFile ( outName );
         deleteOutputOnInterrupt = False;
         if ( !keepInputFiles ) {
            IntNative retVal = remove ( inName );
            ERROR_IF_NOT_ZERO ( retVal );
         }
      }
   } else {
      unzFailsExist = True;
      deleteOutputOnInterrupt = False;
      if ( srcMode == SM_F2F ) {
         IntNative retVal = remove ( outName );
         ERROR_IF_NOT_ZERO ( retVal );
      }
   }
   deleteOutputOnInterrupt = False;

   if ( magicNumberOK ) {
      if (verbosity >= 1)
         fprintf ( stderr, "done\n" );
   } else {
      setExit(2);
      if (verbosity >= 1)
         fprintf ( stderr, "not a bzip2 file.\n" ); else
         fprintf ( stderr,
                   "%s: %s is not a bzip2 file.\n",
                   progName, inName );
   }

}


/*---------------------------------------------*/
static 
void testf ( Char *name )
{
   FILE *inStr;
   Bool allOK;
   struct MY_STAT statBuf;

   deleteOutputOnInterrupt = False;

   if (name == NULL && srcMode != SM_I2O)
      panic ( "testf: bad modes\n" );

   copyFileName ( outName, (Char*)"(none)" );
   switch (srcMode) {
      case SM_I2O: copyFileName ( inName, (Char*)"(stdin)" ); break;
      case SM_F2F: copyFileName ( inName, name ); break;
      case SM_F2O: copyFileName ( inName, name ); break;
   }

   if ( srcMode != SM_I2O && containsDubiousChars ( inName ) ) {
      if (noisy)
      fprintf ( stderr, "%s: There are no files matching `%s'.\n",
                progName, inName );
      setExit(1);
      return;
   }
   if ( srcMode != SM_I2O && !fileExists ( inName ) ) {
      fprintf ( stderr, "%s: Can't open input %s: %s.\n",
                progName, inName, strerror(errno) );
      setExit(1);
      return;
   }
   if ( srcMode != SM_I2O ) {
      MY_STAT(inName, &statBuf);
      if ( MY_S_ISDIR(statBuf.st_mode) ) {
         fprintf( stderr,
                  "%s: Input file %s is a directory.\n",
                  progName,inName);
         setExit(1);
         return;
      }
   }

   switch ( srcMode ) {

      case SM_I2O:
         if ( isatty ( fileno ( stdin ) ) ) {
            fprintf ( stderr,
                      "%s: I won't read compressed data from a terminal.\n",
                      progName );
            fprintf ( stderr, "%s: For help, type: `%s --help'.\n",
                              progName, progName );
            setExit(1);
            return;
         };
         inStr = stdin;
         break;

      case SM_F2O: case SM_F2F:
         inStr = fopen ( inName, "rb" );
         if ( inStr == NULL ) {
            fprintf ( stderr, "%s: Can't open input file %s:%s.\n",
                      progName, inName, strerror(errno) );
            setExit(1);
            return;
         };
         break;

      default:
         panic ( "testf: bad srcMode" );
         break;
   }

   if (verbosity >= 1) {
      fprintf ( stderr, "  %s: ", inName );
      pad ( inName );
      fflush ( stderr );
   }

   /*--- Now the input handle is sane.  Do the Biz. ---*/
   outputHandleJustInCase = NULL;
   allOK = testStream ( inStr );

   if (allOK && verbosity >= 1) fprintf ( stderr, "ok\n" );
   if (!allOK) testFailsExist = True;
}


/*---------------------------------------------*/
static 
void license ( void )
{
   fprintf ( stderr,

    "bzip2, a block-sorting file compressor.  "
    "Version %s.\n"
    "   \n"
    "   Copyright (C) 1996-2010 by Julian Seward.\n"
    "   \n"
    "   This program is free software; you can redistribute it and/or modify\n"
    "   it under the terms set out in the LICENSE file, which is included\n"
    "   in the bzip2-1.0.6 source distribution.\n"
    "   \n"
    "   This program is distributed in the hope that it will be useful,\n"
    "   but WITHOUT ANY WARRANTY; without even the implied warranty of\n"
    "   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n"
    "   LICENSE file for more details.\n"
    "   \n",
    BZ2_bzlibVersion()
   );
}


/*---------------------------------------------*/
static 
void usage ( Char *fullProgName )
{
   fprintf (
      stderr,
      "bzip2, a block-sorting file compressor.  "
      "Version %s.\n"
      "\n   usage: %s [flags and input files in any order]\n"
      "\n"
      "   -h --help           print this message\n"
      "   -d --decompress     force decompression\n"
      "   -z --compress       force compression\n"
      "   -k --keep           keep (don't delete) input files\n"
      "   -f --force          overwrite existing output files\n"
      "   -t --test           test compressed file integrity\n"
      "   -c --stdout         output to standard out\n"
      "   -q --quiet          suppress noncritical error messages\n"
      "   -v --verbose        be verbose (a 2nd -v gives more)\n"
      "   -L --license        display software version & license\n"
      "   -V --version        display software version & license\n"
      "   -s --small          use less memory (at most 2500k)\n"
      "   -1 .. -9            set block size to 100k .. 900k\n"
      "   --fast              alias for -1\n"
      "   --best              alias for -9\n"
      "\n"
      "   If invoked as `bzip2', default action is to compress.\n"
      "              as `bunzip2',  default action is to decompress.\n"
      "              as `bzcat', default action is to decompress to stdout.\n"
      "\n"
      "   If no file names are given, bzip2 compresses or decompresses\n"
      "   from standard input to standard output.  You can combine\n"
      "   short flags, so `-v -4' means the same as -v4 or -4v, &c.\n"
#     if BZ_UNIX
      "\n"
#     endif
      ,

      BZ2_bzlibVersion(),
      fullProgName
   );
}


/*---------------------------------------------*/
static 
void redundant ( Char* flag )
{
   fprintf ( 
      stderr, 
      "%s: %s is redundant in versions 0.9.5 and above\n",
      progName, flag );
}


/*---------------------------------------------*/
/*--
  All the garbage from here to main() is purely to
  implement a linked list of command-line arguments,
  into which main() copies argv[1 .. argc-1].

  The purpose of this exercise is to facilitate 
  the expansion of wildcard characters * and ? in 
  filenames for OSs which don't know how to do it
  themselves, like MSDOS, Windows 95 and NT.

  The actual Dirty Work is done by the platform-
  specific macro APPEND_FILESPEC.
--*/

typedef
   struct zzzz {
      Char        *name;
      struct zzzz *link;
   }
   Cell;


/*---------------------------------------------*/
static 
void *myMalloc ( Int32 n )
{
   void* p;

   p = malloc ( (size_t)n );
   if (p == NULL) outOfMemory ();
   return p;
}


/*---------------------------------------------*/
static 
Cell *mkCell ( void )
{
   Cell *c;

   c = (Cell*) myMalloc ( sizeof ( Cell ) );
   c->name = NULL;
   c->link = NULL;
   return c;
}


/*---------------------------------------------*/
static 
Cell *snocString ( Cell *root, Char *name )
{
   if (root == NULL) {
      Cell *tmp = mkCell();
      tmp->name = (Char*) myMalloc ( 5 + strlen(name) );
      strcpy ( tmp->name, name );
      return tmp;
   } else {
      Cell *tmp = root;
      while (tmp->link != NULL) tmp = tmp->link;
      tmp->link = snocString ( tmp->link, name );
      return root;
   }
}


/*---------------------------------------------*/
static 
void addFlagsFromEnvVar ( Cell** argList, Char* varName ) 
{
   Int32 i, j, k;
   Char *envbase, *p;

   envbase = getenv(varName);
   if (envbase != NULL) {
      p = envbase;
      i = 0;
      while (True) {
         if (p[i] == 0) break;
         p += i;
         i = 0;
         while (isspace((Int32)(p[0]))) p++;
         while (p[i] != 0 && !isspace((Int32)(p[i]))) i++;
         if (i > 0) {
            k = i; if (k > FILE_NAME_LEN-10) k = FILE_NAME_LEN-10;
            for (j = 0; j < k; j++) tmpName[j] = p[j];
            tmpName[k] = 0;
            APPEND_FLAG(*argList, tmpName);
         }
      }
   }
}


/*---------------------------------------------*/
#define ISFLAG(s) (strcmp(aa->name, (s))==0)

IntNative main ( IntNative argc, Char *argv[] )
{
   Int32  i, j;
   Char   *tmp;
   Cell   *argList;
   Cell   *aa;
   Bool   decode;

   /*-- Be really really really paranoid :-) --*/
   if (sizeof(Int32) != 4 || sizeof(UInt32) != 4  ||
       sizeof(Int16) != 2 || sizeof(UInt16) != 2  ||
       sizeof(Char)  != 1 || sizeof(UChar)  != 1)
      configError();

   /*-- Initialise --*/
   outputHandleJustInCase  = NULL;
   smallMode               = False;
   keepInputFiles          = False;
   forceOverwrite          = False;
   noisy                   = True;
   verbosity               = 0;
   blockSize100k           = 9;
   testFailsExist          = False;
   unzFailsExist           = False;
   numFileNames            = 0;
   numFilesProcessed       = 0;
   workFactor              = 30;
   deleteOutputOnInterrupt = False;
   exitValue               = 0;
   i = j = 0; /* avoid bogus warning from egcs-1.1.X */

   /*-- Set up signal handlers for mem access errors --*/
   signal (SIGSEGV, mySIGSEGVorSIGBUScatcher);
#  if BZ_UNIX
#  ifndef __DJGPP__
   signal (SIGBUS,  mySIGSEGVorSIGBUScatcher);
#  endif
#  endif

   copyFileName ( inName,  (Char*)"(none)" );
   copyFileName ( outName, (Char*)"(none)" );

   copyFileName ( progNameReally, argv[0] );
   progName = &progNameReally[0];
   for (tmp = &progNameReally[0]; *tmp != '\0'; tmp++)
      if (*tmp == PATH_SEP) progName = tmp + 1;


   /*-- Copy flags from env var BZIP2, and 
        expand filename wildcards in arg list.
   --*/
   argList = NULL;
   addFlagsFromEnvVar ( &argList,  (Char*)"BZIP2" );
   addFlagsFromEnvVar ( &argList,  (Char*)"BZIP" );
   for (i = 1; i <= argc-1; i++)
      APPEND_FILESPEC(argList, argv[i]);


   /*-- Find the length of the longest filename --*/
   longestFileName = 7;
   numFileNames    = 0;
   decode          = True;
   for (aa = argList; aa != NULL; aa = aa->link) {
      if (ISFLAG("--")) { decode = False; continue; }
      if (aa->name[0] == '-' && decode) continue;
      numFileNames++;
      if (longestFileName < (Int32)strlen(aa->name) )
         longestFileName = (Int32)strlen(aa->name);
   }


   /*-- Determine source modes; flag handling may change this too. --*/
   if (numFileNames == 0)
      srcMode = SM_I2O; else srcMode = SM_F2F;


   /*-- Determine what to do (compress/uncompress/test/cat). --*/
   /*-- Note that subsequent flag handling may change this. --*/
   opMode = OM_Z;

   if ( (strstr ( progName, "unzip" ) != 0) ||
        (strstr ( progName, "UNZIP" ) != 0) )
      opMode = OM_UNZ;

   if ( (strstr ( progName, "z2cat" ) != 0) ||
        (strstr ( progName, "Z2CAT" ) != 0) ||
        (strstr ( progName, "zcat" ) != 0)  ||
        (strstr ( progName, "ZCAT" ) != 0) )  {
      opMode = OM_UNZ;
      srcMode = (numFileNames == 0) ? SM_I2O : SM_F2O;
   }


   /*-- Look at the flags. --*/
   for (aa = argList; aa != NULL; aa = aa->link) {
      if (ISFLAG("--")) break;
      if (aa->name[0] == '-' && aa->name[1] != '-') {
         for (j = 1; aa->name[j] != '\0'; j++) {
            switch (aa->name[j]) {
               case 'c': srcMode          = SM_F2O; break;
               case 'd': opMode           = OM_UNZ; break;
               case 'z': opMode           = OM_Z; break;
               case 'f': forceOverwrite   = True; break;
               case 't': opMode           = OM_TEST; break;
               case 'k': keepInputFiles   = True; break;
               case 's': smallMode        = True; break;
               case 'q': noisy            = False; break;
               case '1': blockSize100k    = 1; break;
               case '2': blockSize100k    = 2; break;
               case '3': blockSize100k    = 3; break;
               case '4': blockSize100k    = 4; break;
               case '5': blockSize100k    = 5; break;
               case '6': blockSize100k    = 6; break;
               case '7': blockSize100k    = 7; break;
               case '8': blockSize100k    = 8; break;
               case '9': blockSize100k    = 9; break;
               case 'V':
               case 'L': license();            break;
               case 'v': verbosity++; break;
               case 'h': usage ( progName );
                         exit ( 0 );
                         break;
               default:  fprintf ( stderr, "%s: Bad flag `%s'\n",
                                   progName, aa->name );
                         usage ( progName );
                         exit ( 1 );
                         break;
            }
         }
      }
   }
   
   /*-- And again ... --*/
   for (aa = argList; aa != NULL; aa = aa->link) {
      if (ISFLAG("--")) break;
      if (ISFLAG("--stdout"))            srcMode          = SM_F2O;  else
      if (ISFLAG("--decompress"))        opMode           = OM_UNZ;  else
      if (ISFLAG("--compress"))          opMode           = OM_Z;    else
      if (ISFLAG("--force"))             forceOverwrite   = True;    else
      if (ISFLAG("--test"))              opMode           = OM_TEST; else
      if (ISFLAG("--keep"))              keepInputFiles   = True;    else
      if (ISFLAG("--small"))             smallMode        = True;    else
      if (ISFLAG("--quiet"))             noisy            = False;   else
      if (ISFLAG("--version"))           license();                  else
      if (ISFLAG("--license"))           license();                  else
      if (ISFLAG("--exponential"))       workFactor = 1;             else 
      if (ISFLAG("--repetitive-best"))   redundant(aa->name);        else
      if (ISFLAG("--repetitive-fast"))   redundant(aa->name);        else
      if (ISFLAG("--fast"))              blockSize100k = 1;          else
      if (ISFLAG("--best"))              blockSize100k = 9;          else
      if (ISFLAG("--verbose"))           verbosity++;                else
      if (ISFLAG("--help"))              { usage ( progName ); exit ( 0 ); }
         else
         if (strncmp ( aa->name, "--", 2) == 0) {
            fprintf ( stderr, "%s: Bad flag `%s'\n", progName, aa->name );
            usage ( progName );
            exit ( 1 );
         }
   }

   if (verbosity > 4) verbosity = 4;
   if (opMode == OM_Z && smallMode && blockSize100k > 2) 
      blockSize100k = 2;

   if (opMode == OM_TEST && srcMode == SM_F2O) {
      fprintf ( stderr, "%s: -c and -t cannot be used together.\n",
                progName );
      exit ( 1 );
   }

   if (srcMode == SM_F2O && numFileNames == 0)
      srcMode = SM_I2O;

   if (opMode != OM_Z) blockSize100k = 0;

   if (srcMode == SM_F2F) {
      signal (SIGINT,  mySignalCatcher);
      signal (SIGTERM, mySignalCatcher);
#     if BZ_UNIX
      signal (SIGHUP,  mySignalCatcher);
#     endif
   }

   if (opMode == OM_Z) {
     if (srcMode == SM_I2O) {
        compress ( NULL );
     } else {
        decode = True;
        for (aa = argList; aa != NULL; aa = aa->link) {
           if (ISFLAG("--")) { decode = False; continue; }
           if (aa->name[0] == '-' && decode) continue;
           numFilesProcessed++;
           compress ( aa->name );
        }
     }
   } 
   else

   if (opMode == OM_UNZ) {
      unzFailsExist = False;
      if (srcMode == SM_I2O) {
         uncompress ( NULL );
      } else {
         decode = True;
         for (aa = argList; aa != NULL; aa = aa->link) {
            if (ISFLAG("--")) { decode = False; continue; }
            if (aa->name[0] == '-' && decode) continue;
            numFilesProcessed++;
            uncompress ( aa->name );
         }      
      }
      if (unzFailsExist) { 
         setExit(2); 
         exit(exitValue);
      }
   } 

   else {
      testFailsExist = False;
      if (srcMode == SM_I2O) {
         testf ( NULL );
      } else {
         decode = True;
         for (aa = argList; aa != NULL; aa = aa->link) {
	    if (ISFLAG("--")) { decode = False; continue; }
            if (aa->name[0] == '-' && decode) continue;
            numFilesProcessed++;
            testf ( aa->name );
	 }
      }
      if (testFailsExist && noisy) {
         fprintf ( stderr,
           "\n"
           "You can use the `bzip2recover' program to attempt to recover\n"
           "data from undamaged sections of corrupted files.\n\n"
         );
         setExit(2);
         exit(exitValue);
      }
   }

   /* Free the argument list memory to mollify leak detectors 
      (eg) Purify, Checker.  Serves no other useful purpose.
   */
   aa = argList;
   while (aa != NULL) {
      Cell* aa2 = aa->link;
      if (aa->name != NULL) free(aa->name);
      free(aa);
      aa = aa2;
   }

   return exitValue;
}


/*-----------------------------------------------------------*/
/*--- end                                         bzip2.c ---*/
/*-----------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/bzip2.txt000066400000000000000000000450541211610345200217420ustar00rootroot00000000000000
NAME
       bzip2, bunzip2 - a block-sorting file compressor, v1.0.6
       bzcat - decompresses files to stdout
       bzip2recover - recovers data from damaged bzip2 files


SYNOPSIS
       bzip2 [ -cdfkqstvzVL123456789 ] [ filenames ...  ]
       bunzip2 [ -fkvsVL ] [ filenames ...  ]
       bzcat [ -s ] [ filenames ...  ]
       bzip2recover filename


DESCRIPTION
       bzip2  compresses  files  using  the Burrows-Wheeler block
       sorting text compression algorithm,  and  Huffman  coding.
       Compression  is  generally  considerably  better than that
       achieved by more conventional LZ77/LZ78-based compressors,
       and  approaches  the performance of the PPM family of sta-
       tistical compressors.

       The command-line options are deliberately very similar  to
       those of GNU gzip, but they are not identical.

       bzip2  expects  a list of file names to accompany the com-
       mand-line flags.  Each file is replaced  by  a  compressed
       version  of  itself,  with  the  name "original_name.bz2".
       Each compressed file has the same modification date,  per-
       missions, and, when possible, ownership as the correspond-
       ing original, so that these properties  can  be  correctly
       restored  at  decompression  time.   File name handling is
       naive in the sense that there is no mechanism for preserv-
       ing  original file names, permissions, ownerships or dates
       in filesystems which lack these concepts, or have  serious
       file name length restrictions, such as MS-DOS.

       bzip2  and  bunzip2 will by default not overwrite existing
       files.  If you want this to happen, specify the -f flag.

       If no file names  are  specified,  bzip2  compresses  from
       standard  input  to  standard output.  In this case, bzip2
       will decline to write compressed output to a terminal,  as
       this  would  be  entirely  incomprehensible  and therefore
       pointless.

       bunzip2 (or bzip2 -d) decompresses  all  specified  files.
       Files which were not created by bzip2 will be detected and
       ignored, and a warning issued.  bzip2  attempts  to  guess
       the  filename  for  the decompressed file from that of the
       compressed file as follows:

              filename.bz2    becomes   filename
              filename.bz     becomes   filename
              filename.tbz2   becomes   filename.tar
              filename.tbz    becomes   filename.tar
              anyothername    becomes   anyothername.out

       If the file does not end in one of the recognised endings,
       .bz2,  .bz,  .tbz2 or .tbz, bzip2 complains that it cannot
       guess the name of the original file, and uses the original
       name with .out appended.

       As  with compression, supplying no filenames causes decom-
       pression from standard input to standard output.

       bunzip2 will correctly decompress a file which is the con-
       catenation of two or more compressed files.  The result is
       the concatenation of the corresponding uncompressed files.
       Integrity testing (-t) of concatenated compressed files is
       also supported.

       You can also compress or decompress files to the  standard
       output  by giving the -c flag.  Multiple files may be com-
       pressed and decompressed like this.  The resulting outputs
       are  fed  sequentially to stdout.  Compression of multiple
       files in this manner generates a stream containing  multi-
       ple compressed file representations.  Such a stream can be
       decompressed correctly only  by  bzip2  version  0.9.0  or
       later.   Earlier  versions of bzip2 will stop after decom-
       pressing the first file in the stream.

       bzcat (or bzip2 -dc) decompresses all specified  files  to
       the standard output.

       bzip2  will  read arguments from the environment variables
       BZIP2 and BZIP, in  that  order,  and  will  process  them
       before  any  arguments  read  from the command line.  This
       gives a convenient way to supply default arguments.

       Compression is always performed, even  if  the  compressed
       file  is slightly larger than the original.  Files of less
       than about one hundred bytes tend to get larger, since the
       compression  mechanism  has  a  constant  overhead  in the
       region of 50 bytes.  Random data (including the output  of
       most  file  compressors)  is  coded at about 8.05 bits per
       byte, giving an expansion of around 0.5%.

       As a self-check for your  protection,  bzip2  uses  32-bit
       CRCs  to make sure that the decompressed version of a file
       is identical to the original.  This guards against corrup-
       tion  of  the compressed data, and against undetected bugs
       in bzip2 (hopefully very unlikely).  The chances  of  data
       corruption  going  undetected  is  microscopic,  about one
       chance in four billion for each file processed.  Be aware,
       though,  that  the  check occurs upon decompression, so it
       can only tell you that something is wrong.  It can't  help
       you  recover  the original uncompressed data.  You can use
       bzip2recover to try to recover data from damaged files.

       Return values: 0 for a normal exit,  1  for  environmental
       problems  (file not found, invalid flags, I/O errors, &c),
       2 to indicate a corrupt compressed file, 3 for an internal
       consistency error (eg, bug) which caused bzip2 to panic.


OPTIONS
       -c --stdout
              Compress or decompress to standard output.

       -d --decompress
              Force  decompression.  bzip2, bunzip2 and bzcat are
              really the same program,  and  the  decision  about
              what  actions to take is done on the basis of which
              name is used.  This flag overrides that  mechanism,
              and forces bzip2 to decompress.

       -z --compress
              The   complement   to   -d:   forces   compression,
              regardless of the invocation name.

       -t --test
              Check integrity of the specified file(s), but don't
              decompress  them.   This  really  performs  a trial
              decompression and throws away the result.

       -f --force
              Force overwrite of output files.   Normally,  bzip2
              will  not  overwrite  existing  output files.  Also
              forces bzip2 to break hard links to files, which it
              otherwise wouldn't do.

              bzip2  normally  declines to decompress files which
              don't have the  correct  magic  header  bytes.   If
              forced  (-f),  however,  it  will  pass  such files
              through unmodified.  This is how GNU gzip  behaves.

       -k --keep
              Keep  (don't delete) input files during compression
              or decompression.

       -s --small
              Reduce memory usage, for compression, decompression
              and  testing.   Files  are  decompressed and tested
              using a modified algorithm which only requires  2.5
              bytes  per  block byte.  This means any file can be
              decompressed in 2300k of memory,  albeit  at  about
              half the normal speed.

              During  compression,  -s  selects  a  block size of
              200k, which limits memory use to  around  the  same
              figure,  at  the expense of your compression ratio.
              In short, if your  machine  is  low  on  memory  (8
              megabytes  or  less),  use  -s for everything.  See
              MEMORY MANAGEMENT below.

       -q --quiet
              Suppress non-essential warning messages.   Messages
              pertaining  to I/O errors and other critical events
              will not be suppressed.

       -v --verbose
              Verbose mode -- show the compression ratio for each
              file  processed.   Further  -v's  increase the ver-
              bosity level, spewing out lots of information which
              is primarily of interest for diagnostic purposes.

       -L --license -V --version
              Display  the  software  version,  license terms and
              conditions.

       -1 (or --fast) to -9 (or --best)
              Set the block size to 100 k, 200 k ..  900  k  when
              compressing.   Has  no  effect  when decompressing.
              See MEMORY MANAGEMENT below.  The --fast and --best
              aliases  are  primarily for GNU gzip compatibility.
              In particular, --fast doesn't make things  signifi-
              cantly  faster.   And  --best  merely  selects  the
              default behaviour.

       --     Treats all subsequent arguments as file names, even
              if they start with a dash.  This is so you can han-
              dle files with names beginning  with  a  dash,  for
              example: bzip2 -- -myfilename.

       --repetitive-fast --repetitive-best
              These  flags  are  redundant  in versions 0.9.5 and
              above.  They provided some coarse control over  the
              behaviour  of the sorting algorithm in earlier ver-
              sions, which was sometimes useful.  0.9.5 and above
              have  an  improved  algorithm  which  renders these
              flags irrelevant.


MEMORY MANAGEMENT
       bzip2 compresses large files in blocks.   The  block  size
       affects  both  the  compression  ratio  achieved,  and the
       amount of memory needed for compression and decompression.
       The  flags  -1  through  -9  specify  the block size to be
       100,000 bytes through 900,000 bytes (the default)  respec-
       tively.   At  decompression  time, the block size used for
       compression is read from  the  header  of  the  compressed
       file, and bunzip2 then allocates itself just enough memory
       to decompress the file.  Since block sizes are  stored  in
       compressed  files,  it follows that the flags -1 to -9 are
       irrelevant to and so ignored during decompression.

       Compression and decompression requirements, in bytes,  can
       be estimated as:

              Compression:   400k + ( 8 x block size )

              Decompression: 100k + ( 4 x block size ), or
                             100k + ( 2.5 x block size )

       Larger  block  sizes  give  rapidly  diminishing  marginal
       returns.  Most of the compression comes from the first two
       or  three hundred k of block size, a fact worth bearing in
       mind when using bzip2  on  small  machines.   It  is  also
       important  to  appreciate  that  the  decompression memory
       requirement is set at compression time by  the  choice  of
       block size.

       For  files  compressed  with  the default 900k block size,
       bunzip2 will require about 3700 kbytes to decompress.   To
       support decompression of any file on a 4 megabyte machine,
       bunzip2 has an option to  decompress  using  approximately
       half this amount of memory, about 2300 kbytes.  Decompres-
       sion speed is also halved, so you should use  this  option
       only where necessary.  The relevant flag is -s.

       In general, try and use the largest block size memory con-
       straints  allow,  since  that  maximises  the  compression
       achieved.   Compression and decompression speed are virtu-
       ally unaffected by block size.

       Another significant point applies to files which fit in  a
       single  block  --  that  means  most files you'd encounter
       using a large block  size.   The  amount  of  real  memory
       touched is proportional to the size of the file, since the
       file is smaller than a block.  For example, compressing  a
       file  20,000  bytes  long  with the flag -9 will cause the
       compressor to allocate around 7600k of  memory,  but  only
       touch 400k + 20000 * 8 = 560 kbytes of it.  Similarly, the
       decompressor will allocate 3700k but  only  touch  100k  +
       20000 * 4 = 180 kbytes.

       Here  is a table which summarises the maximum memory usage
       for different block sizes.  Also  recorded  is  the  total
       compressed  size for 14 files of the Calgary Text Compres-
       sion Corpus totalling 3,141,622 bytes.  This column  gives
       some  feel  for  how  compression  varies with block size.
       These figures tend to understate the advantage  of  larger
       block  sizes  for  larger files, since the Corpus is domi-
       nated by smaller files.

                  Compress   Decompress   Decompress   Corpus
           Flag     usage      usage       -s usage     Size

            -1      1200k       500k         350k      914704
            -2      2000k       900k         600k      877703
            -3      2800k      1300k         850k      860338
            -4      3600k      1700k        1100k      846899
            -5      4400k      2100k        1350k      845160
            -6      5200k      2500k        1600k      838626
            -7      6100k      2900k        1850k      834096
            -8      6800k      3300k        2100k      828642
            -9      7600k      3700k        2350k      828642


RECOVERING DATA FROM DAMAGED FILES
       bzip2 compresses files in blocks, usually 900kbytes  long.
       Each block is handled independently.  If a media or trans-
       mission error causes a multi-block  .bz2  file  to  become
       damaged,  it  may  be  possible  to  recover data from the
       undamaged blocks in the file.

       The compressed representation of each block  is  delimited
       by  a  48-bit pattern, which makes it possible to find the
       block boundaries with reasonable  certainty.   Each  block
       also  carries its own 32-bit CRC, so damaged blocks can be
       distinguished from undamaged ones.

       bzip2recover is a  simple  program  whose  purpose  is  to
       search  for blocks in .bz2 files, and write each block out
       into its own .bz2 file.  You can then use bzip2 -t to test
       the integrity of the resulting files, and decompress those
       which are undamaged.

       bzip2recover takes a single argument, the name of the dam-
       aged    file,    and    writes    a    number   of   files
       "rec00001file.bz2",  "rec00002file.bz2",  etc,  containing
       the   extracted   blocks.   The   output   filenames   are
       designed  so  that the use of wildcards in subsequent pro-
       cessing  -- for example, "bzip2 -dc  rec*file.bz2 > recov-
       ered_data" -- processes the files in the correct order.

       bzip2recover should be of most use dealing with large .bz2
       files,  as  these will contain many blocks.  It is clearly
       futile to use it on damaged single-block  files,  since  a
       damaged  block  cannot  be recovered.  If you wish to min-
       imise any potential data loss through media  or  transmis-
       sion errors, you might consider compressing with a smaller
       block size.


PERFORMANCE NOTES
       The sorting phase of compression gathers together  similar
       strings  in  the  file.  Because of this, files containing
       very long runs of  repeated  symbols,  like  "aabaabaabaab
       ..."   (repeated  several hundred times) may compress more
       slowly than normal.  Versions 0.9.5 and  above  fare  much
       better  than previous versions in this respect.  The ratio
       between worst-case and average-case compression time is in
       the  region  of  10:1.  For previous versions, this figure
       was more like 100:1.  You can use the -vvvv option to mon-
       itor progress in great detail, if you want.

       Decompression speed is unaffected by these phenomena.

       bzip2  usually  allocates  several  megabytes of memory to
       operate in, and then charges all over it in a fairly  ran-
       dom  fashion.   This means that performance, both for com-
       pressing and decompressing, is largely determined  by  the
       speed  at  which  your  machine  can service cache misses.
       Because of this, small changes to the code to  reduce  the
       miss  rate  have  been observed to give disproportionately
       large performance improvements.  I imagine bzip2 will per-
       form best on machines with very large caches.


CAVEATS
       I/O  error  messages  are not as helpful as they could be.
       bzip2 tries hard to detect I/O errors  and  exit  cleanly,
       but  the  details  of  what  the problem is sometimes seem
       rather misleading.

       This manual page pertains to version 1.0.6 of bzip2.  Com-
       pressed  data created by this version is entirely forwards
       and  backwards  compatible  with   the   previous   public
       releases,  versions  0.1pl2,  0.9.0,  0.9.5, 1.0.0, 1.0.1,
       1.0.2 and above, but with the  following  exception: 0.9.0
       and above can  correctly decompress  multiple concatenated
       compressed files.  0.1pl2  cannot do this;  it  will  stop
       after  decompressing just the first file in the stream.

       bzip2recover  versions prior to 1.0.2 used 32-bit integers
       to represent bit positions in compressed  files,  so  they
       could  not handle compressed files more than 512 megabytes
       long.  Versions 1.0.2 and above use 64-bit  ints  on  some
       platforms  which  support them (GNU supported targets, and
       Windows).  To establish whether or  not  bzip2recover  was
       built  with  such  a limitation, run it without arguments.
       In any event you can build yourself an  unlimited  version
       if  you  can  recompile  it  with MaybeUInt64 set to be an
       unsigned 64-bit integer.


AUTHOR
       Julian Seward, jsewardbzip.org.

       http://www.bzip.org

       The ideas embodied in bzip2 are due to (at least) the fol-
       lowing  people: Michael Burrows and David Wheeler (for the
       block sorting transformation), David Wheeler  (again,  for
       the Huffman coder), Peter Fenwick (for the structured cod-
       ing model in the original bzip, and many refinements), and
       Alistair  Moffat,  Radford  Neal  and  Ian Witten (for the
       arithmetic  coder  in  the  original  bzip).   I  am  much
       indebted for their help, support and advice.  See the man-
       ual in the source distribution for pointers to sources  of
       documentation.  Christian von Roques encouraged me to look
       for faster sorting algorithms, so as to speed up  compres-
       sion.  Bela Lubkin encouraged me to improve the worst-case
       compression performance.  Donna Robinson XMLised the docu-
       mentation.   The bz* scripts are derived from those of GNU
       gzip.  Many people sent patches, helped  with  portability
       problems,  lent  machines,  gave advice and were generally
       helpful.

genometools-1.5.1/src/external/bzip2-1.0.6/bzip2recover.c000066400000000000000000000351141211610345200227270ustar00rootroot00000000000000/*-----------------------------------------------------------*/
/*--- Block recoverer program for bzip2                   ---*/
/*---                                      bzip2recover.c ---*/
/*-----------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */

/* This program is a complete hack and should be rewritten properly.
	 It isn't very complicated. */

#include 
#include 
#include 
#include 


/* This program records bit locations in the file to be recovered.
   That means that if 64-bit ints are not supported, we will not
   be able to recover .bz2 files over 512MB (2^32 bits) long.
   On GNU supported platforms, we take advantage of the 64-bit
   int support to circumvent this problem.  Ditto MSVC.

   This change occurred in version 1.0.2; all prior versions have
   the 512MB limitation.
*/
#ifdef __GNUC__
   typedef  unsigned long long int  MaybeUInt64;
#  define MaybeUInt64_FMT "%Lu"
#else
#ifdef _MSC_VER
   typedef  unsigned __int64  MaybeUInt64;
#  define MaybeUInt64_FMT "%I64u"
#else
   typedef  unsigned int   MaybeUInt64;
#  define MaybeUInt64_FMT "%u"
#endif
#endif

typedef  unsigned int   UInt32;
typedef  int            Int32;
typedef  unsigned char  UChar;
typedef  char           Char;
typedef  unsigned char  Bool;
#define True    ((Bool)1)
#define False   ((Bool)0)


#define BZ_MAX_FILENAME 2000

Char inFileName[BZ_MAX_FILENAME];
Char outFileName[BZ_MAX_FILENAME];
Char progName[BZ_MAX_FILENAME];

MaybeUInt64 bytesOut = 0;
MaybeUInt64 bytesIn  = 0;


/*---------------------------------------------------*/
/*--- Header bytes                                ---*/
/*---------------------------------------------------*/

#define BZ_HDR_B 0x42                         /* 'B' */
#define BZ_HDR_Z 0x5a                         /* 'Z' */
#define BZ_HDR_h 0x68                         /* 'h' */
#define BZ_HDR_0 0x30                         /* '0' */
 

/*---------------------------------------------------*/
/*--- I/O errors                                  ---*/
/*---------------------------------------------------*/

/*---------------------------------------------*/
static void readError ( void )
{
   fprintf ( stderr,
             "%s: I/O error reading `%s', possible reason follows.\n",
            progName, inFileName );
   perror ( progName );
   fprintf ( stderr, "%s: warning: output file(s) may be incomplete.\n",
             progName );
   exit ( 1 );
}


/*---------------------------------------------*/
static void writeError ( void )
{
   fprintf ( stderr,
             "%s: I/O error reading `%s', possible reason follows.\n",
            progName, inFileName );
   perror ( progName );
   fprintf ( stderr, "%s: warning: output file(s) may be incomplete.\n",
             progName );
   exit ( 1 );
}


/*---------------------------------------------*/
static void mallocFail ( Int32 n )
{
   fprintf ( stderr,
             "%s: malloc failed on request for %d bytes.\n",
            progName, n );
   fprintf ( stderr, "%s: warning: output file(s) may be incomplete.\n",
             progName );
   exit ( 1 );
}


/*---------------------------------------------*/
static void tooManyBlocks ( Int32 max_handled_blocks )
{
   fprintf ( stderr,
             "%s: `%s' appears to contain more than %d blocks\n",
            progName, inFileName, max_handled_blocks );
   fprintf ( stderr,
             "%s: and cannot be handled.  To fix, increase\n",
             progName );
   fprintf ( stderr, 
             "%s: BZ_MAX_HANDLED_BLOCKS in bzip2recover.c, and recompile.\n",
             progName );
   exit ( 1 );
}



/*---------------------------------------------------*/
/*--- Bit stream I/O                              ---*/
/*---------------------------------------------------*/

typedef
   struct {
      FILE*  handle;
      Int32  buffer;
      Int32  buffLive;
      Char   mode;
   }
   BitStream;


/*---------------------------------------------*/
static BitStream* bsOpenReadStream ( FILE* stream )
{
   BitStream *bs = malloc ( sizeof(BitStream) );
   if (bs == NULL) mallocFail ( sizeof(BitStream) );
   bs->handle = stream;
   bs->buffer = 0;
   bs->buffLive = 0;
   bs->mode = 'r';
   return bs;
}


/*---------------------------------------------*/
static BitStream* bsOpenWriteStream ( FILE* stream )
{
   BitStream *bs = malloc ( sizeof(BitStream) );
   if (bs == NULL) mallocFail ( sizeof(BitStream) );
   bs->handle = stream;
   bs->buffer = 0;
   bs->buffLive = 0;
   bs->mode = 'w';
   return bs;
}


/*---------------------------------------------*/
static void bsPutBit ( BitStream* bs, Int32 bit )
{
   if (bs->buffLive == 8) {
      Int32 retVal = putc ( (UChar) bs->buffer, bs->handle );
      if (retVal == EOF) writeError();
      bytesOut++;
      bs->buffLive = 1;
      bs->buffer = bit & 0x1;
   } else {
      bs->buffer = ( (bs->buffer << 1) | (bit & 0x1) );
      bs->buffLive++;
   };
}


/*---------------------------------------------*/
/*--
   Returns 0 or 1, or 2 to indicate EOF.
--*/
static Int32 bsGetBit ( BitStream* bs )
{
   if (bs->buffLive > 0) {
      bs->buffLive --;
      return ( ((bs->buffer) >> (bs->buffLive)) & 0x1 );
   } else {
      Int32 retVal = getc ( bs->handle );
      if ( retVal == EOF ) {
         if (errno != 0) readError();
         return 2;
      }
      bs->buffLive = 7;
      bs->buffer = retVal;
      return ( ((bs->buffer) >> 7) & 0x1 );
   }
}


/*---------------------------------------------*/
static void bsClose ( BitStream* bs )
{
   Int32 retVal;

   if ( bs->mode == 'w' ) {
      while ( bs->buffLive < 8 ) {
         bs->buffLive++;
         bs->buffer <<= 1;
      };
      retVal = putc ( (UChar) (bs->buffer), bs->handle );
      if (retVal == EOF) writeError();
      bytesOut++;
      retVal = fflush ( bs->handle );
      if (retVal == EOF) writeError();
   }
   retVal = fclose ( bs->handle );
   if (retVal == EOF) {
      if (bs->mode == 'w') writeError(); else readError();
   }
   free ( bs );
}


/*---------------------------------------------*/
static void bsPutUChar ( BitStream* bs, UChar c )
{
   Int32 i;
   for (i = 7; i >= 0; i--)
      bsPutBit ( bs, (((UInt32) c) >> i) & 0x1 );
}


/*---------------------------------------------*/
static void bsPutUInt32 ( BitStream* bs, UInt32 c )
{
   Int32 i;

   for (i = 31; i >= 0; i--)
      bsPutBit ( bs, (c >> i) & 0x1 );
}


/*---------------------------------------------*/
static Bool endsInBz2 ( Char* name )
{
   Int32 n = strlen ( name );
   if (n <= 4) return False;
   return
      (name[n-4] == '.' &&
       name[n-3] == 'b' &&
       name[n-2] == 'z' &&
       name[n-1] == '2');
}


/*---------------------------------------------------*/
/*---                                             ---*/
/*---------------------------------------------------*/

/* This logic isn't really right when it comes to Cygwin. */
#ifdef _WIN32
#  define  BZ_SPLIT_SYM  '\\'  /* path splitter on Windows platform */
#else
#  define  BZ_SPLIT_SYM  '/'   /* path splitter on Unix platform */
#endif

#define BLOCK_HEADER_HI  0x00003141UL
#define BLOCK_HEADER_LO  0x59265359UL

#define BLOCK_ENDMARK_HI 0x00001772UL
#define BLOCK_ENDMARK_LO 0x45385090UL

/* Increase if necessary.  However, a .bz2 file with > 50000 blocks
   would have an uncompressed size of at least 40GB, so the chances
   are low you'll need to up this.
*/
#define BZ_MAX_HANDLED_BLOCKS 50000

MaybeUInt64 bStart [BZ_MAX_HANDLED_BLOCKS];
MaybeUInt64 bEnd   [BZ_MAX_HANDLED_BLOCKS];
MaybeUInt64 rbStart[BZ_MAX_HANDLED_BLOCKS];
MaybeUInt64 rbEnd  [BZ_MAX_HANDLED_BLOCKS];

Int32 main ( Int32 argc, Char** argv )
{
   FILE*       inFile;
   FILE*       outFile;
   BitStream*  bsIn, *bsWr;
   Int32       b, wrBlock, currBlock, rbCtr;
   MaybeUInt64 bitsRead;

   UInt32      buffHi, buffLo, blockCRC;
   Char*       p;

   strcpy ( progName, argv[0] );
   inFileName[0] = outFileName[0] = 0;

   fprintf ( stderr, 
             "bzip2recover 1.0.6: extracts blocks from damaged .bz2 files.\n" );

   if (argc != 2) {
      fprintf ( stderr, "%s: usage is `%s damaged_file_name'.\n",
                        progName, progName );
      switch (sizeof(MaybeUInt64)) {
         case 8:
            fprintf(stderr, 
                    "\trestrictions on size of recovered file: None\n");
            break;
         case 4:
            fprintf(stderr, 
                    "\trestrictions on size of recovered file: 512 MB\n");
            fprintf(stderr, 
                    "\tto circumvent, recompile with MaybeUInt64 as an\n"
                    "\tunsigned 64-bit int.\n");
            break;
         default:
            fprintf(stderr, 
                    "\tsizeof(MaybeUInt64) is not 4 or 8 -- "
                    "configuration error.\n");
            break;
      }
      exit(1);
   }

   if (strlen(argv[1]) >= BZ_MAX_FILENAME-20) {
      fprintf ( stderr, 
                "%s: supplied filename is suspiciously (>= %d chars) long.  Bye!\n",
                progName, (int)strlen(argv[1]) );
      exit(1);
   }

   strcpy ( inFileName, argv[1] );

   inFile = fopen ( inFileName, "rb" );
   if (inFile == NULL) {
      fprintf ( stderr, "%s: can't read `%s'\n", progName, inFileName );
      exit(1);
   }

   bsIn = bsOpenReadStream ( inFile );
   fprintf ( stderr, "%s: searching for block boundaries ...\n", progName );

   bitsRead = 0;
   buffHi = buffLo = 0;
   currBlock = 0;
   bStart[currBlock] = 0;

   rbCtr = 0;

   while (True) {
      b = bsGetBit ( bsIn );
      bitsRead++;
      if (b == 2) {
         if (bitsRead >= bStart[currBlock] &&
            (bitsRead - bStart[currBlock]) >= 40) {
            bEnd[currBlock] = bitsRead-1;
            if (currBlock > 0)
               fprintf ( stderr, "   block %d runs from " MaybeUInt64_FMT 
                                 " to " MaybeUInt64_FMT " (incomplete)\n",
                         currBlock,  bStart[currBlock], bEnd[currBlock] );
         } else
            currBlock--;
         break;
      }
      buffHi = (buffHi << 1) | (buffLo >> 31);
      buffLo = (buffLo << 1) | (b & 1);
      if ( ( (buffHi & 0x0000ffff) == BLOCK_HEADER_HI 
             && buffLo == BLOCK_HEADER_LO)
           || 
           ( (buffHi & 0x0000ffff) == BLOCK_ENDMARK_HI 
             && buffLo == BLOCK_ENDMARK_LO)
         ) {
         if (bitsRead > 49) {
            bEnd[currBlock] = bitsRead-49;
         } else {
            bEnd[currBlock] = 0;
         }
         if (currBlock > 0 &&
	     (bEnd[currBlock] - bStart[currBlock]) >= 130) {
            fprintf ( stderr, "   block %d runs from " MaybeUInt64_FMT 
                              " to " MaybeUInt64_FMT "\n",
                      rbCtr+1,  bStart[currBlock], bEnd[currBlock] );
            rbStart[rbCtr] = bStart[currBlock];
            rbEnd[rbCtr] = bEnd[currBlock];
            rbCtr++;
         }
         if (currBlock >= BZ_MAX_HANDLED_BLOCKS)
            tooManyBlocks(BZ_MAX_HANDLED_BLOCKS);
         currBlock++;

         bStart[currBlock] = bitsRead;
      }
   }

   bsClose ( bsIn );

   /*-- identified blocks run from 1 to rbCtr inclusive. --*/

   if (rbCtr < 1) {
      fprintf ( stderr,
                "%s: sorry, I couldn't find any block boundaries.\n",
                progName );
      exit(1);
   };

   fprintf ( stderr, "%s: splitting into blocks\n", progName );

   inFile = fopen ( inFileName, "rb" );
   if (inFile == NULL) {
      fprintf ( stderr, "%s: can't open `%s'\n", progName, inFileName );
      exit(1);
   }
   bsIn = bsOpenReadStream ( inFile );

   /*-- placate gcc's dataflow analyser --*/
   blockCRC = 0; bsWr = 0;

   bitsRead = 0;
   outFile = NULL;
   wrBlock = 0;
   while (True) {
      b = bsGetBit(bsIn);
      if (b == 2) break;
      buffHi = (buffHi << 1) | (buffLo >> 31);
      buffLo = (buffLo << 1) | (b & 1);
      if (bitsRead == 47+rbStart[wrBlock]) 
         blockCRC = (buffHi << 16) | (buffLo >> 16);

      if (outFile != NULL && bitsRead >= rbStart[wrBlock]
                          && bitsRead <= rbEnd[wrBlock]) {
         bsPutBit ( bsWr, b );
      }

      bitsRead++;

      if (bitsRead == rbEnd[wrBlock]+1) {
         if (outFile != NULL) {
            bsPutUChar ( bsWr, 0x17 ); bsPutUChar ( bsWr, 0x72 );
            bsPutUChar ( bsWr, 0x45 ); bsPutUChar ( bsWr, 0x38 );
            bsPutUChar ( bsWr, 0x50 ); bsPutUChar ( bsWr, 0x90 );
            bsPutUInt32 ( bsWr, blockCRC );
            bsClose ( bsWr );
         }
         if (wrBlock >= rbCtr) break;
         wrBlock++;
      } else
      if (bitsRead == rbStart[wrBlock]) {
         /* Create the output file name, correctly handling leading paths. 
            (31.10.2001 by Sergey E. Kusikov) */
         Char* split;
         Int32 ofs, k;
         for (k = 0; k < BZ_MAX_FILENAME; k++) 
            outFileName[k] = 0;
         strcpy (outFileName, inFileName);
         split = strrchr (outFileName, BZ_SPLIT_SYM);
         if (split == NULL) {
            split = outFileName;
         } else {
            ++split;
	 }
	 /* Now split points to the start of the basename. */
         ofs  = split - outFileName;
         sprintf (split, "rec%5d", wrBlock+1);
         for (p = split; *p != 0; p++) if (*p == ' ') *p = '0';
         strcat (outFileName, inFileName + ofs);

         if ( !endsInBz2(outFileName)) strcat ( outFileName, ".bz2" );

         fprintf ( stderr, "   writing block %d to `%s' ...\n",
                           wrBlock+1, outFileName );

         outFile = fopen ( outFileName, "wb" );
         if (outFile == NULL) {
            fprintf ( stderr, "%s: can't write `%s'\n",
                      progName, outFileName );
            exit(1);
         }
         bsWr = bsOpenWriteStream ( outFile );
         bsPutUChar ( bsWr, BZ_HDR_B );    
         bsPutUChar ( bsWr, BZ_HDR_Z );    
         bsPutUChar ( bsWr, BZ_HDR_h );    
         bsPutUChar ( bsWr, BZ_HDR_0 + 9 );
         bsPutUChar ( bsWr, 0x31 ); bsPutUChar ( bsWr, 0x41 );
         bsPutUChar ( bsWr, 0x59 ); bsPutUChar ( bsWr, 0x26 );
         bsPutUChar ( bsWr, 0x53 ); bsPutUChar ( bsWr, 0x59 );
      }
   }

   fprintf ( stderr, "%s: finished\n", progName );
   return 0;
}



/*-----------------------------------------------------------*/
/*--- end                                  bzip2recover.c ---*/
/*-----------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/bzlib.c000066400000000000000000001317451211610345200214240ustar00rootroot00000000000000
/*-------------------------------------------------------------*/
/*--- Library top-level functions.                          ---*/
/*---                                               bzlib.c ---*/
/*-------------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */

/* CHANGES
   0.9.0    -- original version.
   0.9.0a/b -- no changes in this file.
   0.9.0c   -- made zero-length BZ_FLUSH work correctly in bzCompress().
     fixed bzWrite/bzRead to ignore zero-length requests.
     fixed bzread to correctly handle read requests after EOF.
     wrong parameter order in call to bzDecompressInit in
     bzBuffToBuffDecompress.  Fixed.
*/

#include "bzlib_private.h"
#include "core/unused_api.h"

/*---------------------------------------------------*/
/*--- Compression stuff                           ---*/
/*---------------------------------------------------*/


/*---------------------------------------------------*/
#ifndef BZ_NO_STDIO
void BZ2_bz__AssertH__fail ( int errcode )
{
   fprintf(stderr, 
      "\n\nbzip2/libbzip2: internal error number %d.\n"
      "This is a bug in bzip2/libbzip2, %s.\n"
      "Please report it to me at: jseward@bzip.org.  If this happened\n"
      "when you were using some program which uses libbzip2 as a\n"
      "component, you should also report this bug to the author(s)\n"
      "of that program.  Please make an effort to report this bug;\n"
      "timely and accurate bug reports eventually lead to higher\n"
      "quality software.  Thanks.  Julian Seward, 10 December 2007.\n\n",
      errcode,
      BZ2_bzlibVersion()
   );

   if (errcode == 1007) {
   fprintf(stderr,
      "\n*** A special note about internal error number 1007 ***\n"
      "\n"
      "Experience suggests that a common cause of i.e. 1007\n"
      "is unreliable memory or other hardware.  The 1007 assertion\n"
      "just happens to cross-check the results of huge numbers of\n"
      "memory reads/writes, and so acts (unintendedly) as a stress\n"
      "test of your memory system.\n"
      "\n"
      "I suggest the following: try compressing the file again,\n"
      "possibly monitoring progress in detail with the -vv flag.\n"
      "\n"
      "* If the error cannot be reproduced, and/or happens at different\n"
      "  points in compression, you may have a flaky memory system.\n"
      "  Try a memory-test program.  I have used Memtest86\n"
      "  (www.memtest86.com).  At the time of writing it is free (GPLd).\n"
      "  Memtest86 tests memory much more thorougly than your BIOSs\n"
      "  power-on test, and may find failures that the BIOS doesn't.\n"
      "\n"
      "* If the error can be repeatably reproduced, this is a bug in\n"
      "  bzip2, and I would very much like to hear about it.  Please\n"
      "  let me know, and, ideally, save a copy of the file causing the\n"
      "  problem -- without which I will be unable to investigate it.\n"
      "\n"
   );
   }

   exit(3);
}
#endif


/*---------------------------------------------------*/
static
int bz_config_ok ( void )
{
   if (sizeof(int)   != 4) return 0;
   if (sizeof(short) != 2) return 0;
   if (sizeof(char)  != 1) return 0;
   return 1;
}


/*---------------------------------------------------*/
static
void* default_bzalloc ( GT_UNUSED void* opaque, Int32 items, Int32 size )
{
   void* v = malloc ( items * size );
   return v;
}

static
void default_bzfree ( GT_UNUSED void* opaque, void* addr )
{
   if (addr != NULL) free ( addr );
}


/*---------------------------------------------------*/
static
void prepare_new_block ( EState* s )
{
   Int32 i;
   s->nblock = 0;
   s->numZ = 0;
   s->state_out_pos = 0;
   BZ_INITIALISE_CRC ( s->blockCRC );
   for (i = 0; i < 256; i++) s->inUse[i] = False;
   s->blockNo++;
}


/*---------------------------------------------------*/
static
void init_RL ( EState* s )
{
   s->state_in_ch  = 256;
   s->state_in_len = 0;
}


static
Bool isempty_RL ( EState* s )
{
   if (s->state_in_ch < 256 && s->state_in_len > 0)
      return False; else
      return True;
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzCompressInit) 
                    ( bz_stream* strm, 
                     int        blockSize100k,
                     int        verbosity,
                     int        workFactor )
{
   Int32   n;
   EState* s;

   if (!bz_config_ok()) return BZ_CONFIG_ERROR;

   if (strm == NULL || 
       blockSize100k < 1 || blockSize100k > 9 ||
       workFactor < 0 || workFactor > 250)
     return BZ_PARAM_ERROR;

   if (workFactor == 0) workFactor = 30;
   if (strm->bzalloc == NULL) strm->bzalloc = default_bzalloc;
   if (strm->bzfree == NULL) strm->bzfree = default_bzfree;

   s = BZALLOC( sizeof(EState) );
   if (s == NULL) return BZ_MEM_ERROR;
   s->strm = strm;

   s->arr1 = NULL;
   s->arr2 = NULL;
   s->ftab = NULL;

   n       = 100000 * blockSize100k;
   s->arr1 = BZALLOC( n                  * sizeof(UInt32) );
   s->arr2 = BZALLOC( (n+BZ_N_OVERSHOOT) * sizeof(UInt32) );
   s->ftab = BZALLOC( 65537              * sizeof(UInt32) );

   if (s->arr1 == NULL || s->arr2 == NULL || s->ftab == NULL) {
      if (s->arr1 != NULL) BZFREE(s->arr1);
      if (s->arr2 != NULL) BZFREE(s->arr2);
      if (s->ftab != NULL) BZFREE(s->ftab);
      if (s       != NULL) BZFREE(s);
      return BZ_MEM_ERROR;
   }

   s->blockNo           = 0;
   s->state             = BZ_S_INPUT;
   s->mode              = BZ_M_RUNNING;
   s->combinedCRC       = 0;
   s->blockSize100k     = blockSize100k;
   s->nblockMAX         = 100000 * blockSize100k - 19;
   s->verbosity         = verbosity;
   s->workFactor        = workFactor;

   s->block             = (UChar*)s->arr2;
   s->mtfv              = (UInt16*)s->arr1;
   s->zbits             = NULL;
   s->ptr               = (UInt32*)s->arr1;

   strm->state          = s;
   strm->total_in_lo32  = 0;
   strm->total_in_hi32  = 0;
   strm->total_out_lo32 = 0;
   strm->total_out_hi32 = 0;
   init_RL ( s );
   prepare_new_block ( s );
   return BZ_OK;
}


/*---------------------------------------------------*/
static
void add_pair_to_block ( EState* s )
{
   Int32 i;
   UChar ch = (UChar)(s->state_in_ch);
   for (i = 0; i < s->state_in_len; i++) {
      BZ_UPDATE_CRC( s->blockCRC, ch );
   }
   s->inUse[s->state_in_ch] = True;
   switch (s->state_in_len) {
      case 1:
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         break;
      case 2:
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         break;
      case 3:
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         break;
      default:
         s->inUse[s->state_in_len-4] = True;
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         s->block[s->nblock] = (UChar)ch; s->nblock++;
         s->block[s->nblock] = ((UChar)(s->state_in_len-4));
         s->nblock++;
         break;
   }
}


/*---------------------------------------------------*/
static
void flush_RL ( EState* s )
{
   if (s->state_in_ch < 256) add_pair_to_block ( s );
   init_RL ( s );
}


/*---------------------------------------------------*/
#define ADD_CHAR_TO_BLOCK(zs,zchh0)               \
{                                                 \
   UInt32 zchh = (UInt32)(zchh0);                 \
   /*-- fast track the common case --*/           \
   if (zchh != zs->state_in_ch &&                 \
       zs->state_in_len == 1) {                   \
      UChar ch = (UChar)(zs->state_in_ch);        \
      BZ_UPDATE_CRC( zs->blockCRC, ch );          \
      zs->inUse[zs->state_in_ch] = True;          \
      zs->block[zs->nblock] = (UChar)ch;          \
      zs->nblock++;                               \
      zs->state_in_ch = zchh;                     \
   }                                              \
   else                                           \
   /*-- general, uncommon cases --*/              \
   if (zchh != zs->state_in_ch ||                 \
      zs->state_in_len == 255) {                  \
      if (zs->state_in_ch < 256)                  \
         add_pair_to_block ( zs );                \
      zs->state_in_ch = zchh;                     \
      zs->state_in_len = 1;                       \
   } else {                                       \
      zs->state_in_len++;                         \
   }                                              \
}


/*---------------------------------------------------*/
static
Bool copy_input_until_stop ( EState* s )
{
   Bool progress_in = False;

   if (s->mode == BZ_M_RUNNING) {

      /*-- fast track the common case --*/
      while (True) {
         /*-- block full? --*/
         if (s->nblock >= s->nblockMAX) break;
         /*-- no input? --*/
         if (s->strm->avail_in == 0) break;
         progress_in = True;
         ADD_CHAR_TO_BLOCK ( s, (UInt32)(*((UChar*)(s->strm->next_in))) ); 
         s->strm->next_in++;
         s->strm->avail_in--;
         s->strm->total_in_lo32++;
         if (s->strm->total_in_lo32 == 0) s->strm->total_in_hi32++;
      }

   } else {

      /*-- general, uncommon case --*/
      while (True) {
         /*-- block full? --*/
         if (s->nblock >= s->nblockMAX) break;
         /*-- no input? --*/
         if (s->strm->avail_in == 0) break;
         /*-- flush/finish end? --*/
         if (s->avail_in_expect == 0) break;
         progress_in = True;
         ADD_CHAR_TO_BLOCK ( s, (UInt32)(*((UChar*)(s->strm->next_in))) ); 
         s->strm->next_in++;
         s->strm->avail_in--;
         s->strm->total_in_lo32++;
         if (s->strm->total_in_lo32 == 0) s->strm->total_in_hi32++;
         s->avail_in_expect--;
      }
   }
   return progress_in;
}


/*---------------------------------------------------*/
static
Bool copy_output_until_stop ( EState* s )
{
   Bool progress_out = False;

   while (True) {

      /*-- no output space? --*/
      if (s->strm->avail_out == 0) break;

      /*-- block done? --*/
      if (s->state_out_pos >= s->numZ) break;

      progress_out = True;
      *(s->strm->next_out) = s->zbits[s->state_out_pos];
      s->state_out_pos++;
      s->strm->avail_out--;
      s->strm->next_out++;
      s->strm->total_out_lo32++;
      if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
   }

   return progress_out;
}


/*---------------------------------------------------*/
static
Bool handle_compress ( bz_stream* strm )
{
   Bool progress_in  = False;
   Bool progress_out = False;
   EState* s = strm->state;
   
   while (True) {

      if (s->state == BZ_S_OUTPUT) {
         progress_out |= copy_output_until_stop ( s );
         if (s->state_out_pos < s->numZ) break;
         if (s->mode == BZ_M_FINISHING && 
             s->avail_in_expect == 0 &&
             isempty_RL(s)) break;
         prepare_new_block ( s );
         s->state = BZ_S_INPUT;
         if (s->mode == BZ_M_FLUSHING && 
             s->avail_in_expect == 0 &&
             isempty_RL(s)) break;
      }

      if (s->state == BZ_S_INPUT) {
         progress_in |= copy_input_until_stop ( s );
         if (s->mode != BZ_M_RUNNING && s->avail_in_expect == 0) {
            flush_RL ( s );
            BZ2_compressBlock ( s, (Bool)(s->mode == BZ_M_FINISHING) );
            s->state = BZ_S_OUTPUT;
         }
         else
         if (s->nblock >= s->nblockMAX) {
            BZ2_compressBlock ( s, False );
            s->state = BZ_S_OUTPUT;
         }
         else
         if (s->strm->avail_in == 0) {
            break;
         }
      }

   }

   return progress_in || progress_out;
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzCompress) ( bz_stream *strm, int action )
{
   Bool progress;
   EState* s;
   if (strm == NULL) return BZ_PARAM_ERROR;
   s = strm->state;
   if (s == NULL) return BZ_PARAM_ERROR;
   if (s->strm != strm) return BZ_PARAM_ERROR;

   preswitch:
   switch (s->mode) {

      case BZ_M_IDLE:
         return BZ_SEQUENCE_ERROR;

      case BZ_M_RUNNING:
         if (action == BZ_RUN) {
            progress = handle_compress ( strm );
            return progress ? BZ_RUN_OK : BZ_PARAM_ERROR;
         } 
         else
	 if (action == BZ_FLUSH) {
            s->avail_in_expect = strm->avail_in;
            s->mode = BZ_M_FLUSHING;
            goto preswitch;
         }
         else
         if (action == BZ_FINISH) {
            s->avail_in_expect = strm->avail_in;
            s->mode = BZ_M_FINISHING;
            goto preswitch;
         }
         else 
            return BZ_PARAM_ERROR;

      case BZ_M_FLUSHING:
         if (action != BZ_FLUSH) return BZ_SEQUENCE_ERROR;
         if (s->avail_in_expect != s->strm->avail_in) 
            return BZ_SEQUENCE_ERROR;
         progress = handle_compress ( strm );
         if (s->avail_in_expect > 0 || !isempty_RL(s) ||
             s->state_out_pos < s->numZ) return BZ_FLUSH_OK;
         s->mode = BZ_M_RUNNING;
         return BZ_RUN_OK;

      case BZ_M_FINISHING:
         if (action != BZ_FINISH) return BZ_SEQUENCE_ERROR;
         if (s->avail_in_expect != s->strm->avail_in) 
            return BZ_SEQUENCE_ERROR;
         progress = handle_compress ( strm );
         if (!progress) return BZ_SEQUENCE_ERROR;
         if (s->avail_in_expect > 0 || !isempty_RL(s) ||
             s->state_out_pos < s->numZ) return BZ_FINISH_OK;
         s->mode = BZ_M_IDLE;
         return BZ_STREAM_END;
   }
   return BZ_OK; /*--not reached--*/
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzCompressEnd)  ( bz_stream *strm )
{
   EState* s;
   if (strm == NULL) return BZ_PARAM_ERROR;
   s = strm->state;
   if (s == NULL) return BZ_PARAM_ERROR;
   if (s->strm != strm) return BZ_PARAM_ERROR;

   if (s->arr1 != NULL) BZFREE(s->arr1);
   if (s->arr2 != NULL) BZFREE(s->arr2);
   if (s->ftab != NULL) BZFREE(s->ftab);
   BZFREE(strm->state);

   strm->state = NULL;   

   return BZ_OK;
}


/*---------------------------------------------------*/
/*--- Decompression stuff                         ---*/
/*---------------------------------------------------*/

/*---------------------------------------------------*/
int BZ_API(BZ2_bzDecompressInit) 
                     ( bz_stream* strm, 
                       int        verbosity,
                       int        small )
{
   DState* s;

   if (!bz_config_ok()) return BZ_CONFIG_ERROR;

   if (strm == NULL) return BZ_PARAM_ERROR;
   if (small != 0 && small != 1) return BZ_PARAM_ERROR;
   if (verbosity < 0 || verbosity > 4) return BZ_PARAM_ERROR;

   if (strm->bzalloc == NULL) strm->bzalloc = default_bzalloc;
   if (strm->bzfree == NULL) strm->bzfree = default_bzfree;

   s = BZALLOC( sizeof(DState) );
   if (s == NULL) return BZ_MEM_ERROR;
   s->strm                  = strm;
   strm->state              = s;
   s->state                 = BZ_X_MAGIC_1;
   s->bsLive                = 0;
   s->bsBuff                = 0;
   s->calculatedCombinedCRC = 0;
   strm->total_in_lo32      = 0;
   strm->total_in_hi32      = 0;
   strm->total_out_lo32     = 0;
   strm->total_out_hi32     = 0;
   s->smallDecompress       = (Bool)small;
   s->ll4                   = NULL;
   s->ll16                  = NULL;
   s->tt                    = NULL;
   s->currBlockNo           = 0;
   s->verbosity             = verbosity;

   return BZ_OK;
}


/*---------------------------------------------------*/
/* Return  True iff data corruption is discovered.
   Returns False if there is no problem.
*/
static
Bool unRLE_obuf_to_output_FAST ( DState* s )
{
   UChar k1;

   if (s->blockRandomised) {

      while (True) {
         /* try to finish existing run */
         while (True) {
            if (s->strm->avail_out == 0) return False;
            if (s->state_out_len == 0) break;
            *( (UChar*)(s->strm->next_out) ) = s->state_out_ch;
            BZ_UPDATE_CRC ( s->calculatedBlockCRC, s->state_out_ch );
            s->state_out_len--;
            s->strm->next_out++;
            s->strm->avail_out--;
            s->strm->total_out_lo32++;
            if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
         }

         /* can a new run be started? */
         if (s->nblock_used == s->save_nblock+1) return False;
               
         /* Only caused by corrupt data stream? */
         if (s->nblock_used > s->save_nblock+1)
            return True;
   
         s->state_out_len = 1;
         s->state_out_ch = s->k0;
         BZ_GET_FAST(k1); BZ_RAND_UPD_MASK; 
         k1 ^= BZ_RAND_MASK; s->nblock_used++;
         if (s->nblock_used == s->save_nblock+1) continue;
         if (k1 != s->k0) { s->k0 = k1; continue; };
   
         s->state_out_len = 2;
         BZ_GET_FAST(k1); BZ_RAND_UPD_MASK; 
         k1 ^= BZ_RAND_MASK; s->nblock_used++;
         if (s->nblock_used == s->save_nblock+1) continue;
         if (k1 != s->k0) { s->k0 = k1; continue; };
   
         s->state_out_len = 3;
         BZ_GET_FAST(k1); BZ_RAND_UPD_MASK; 
         k1 ^= BZ_RAND_MASK; s->nblock_used++;
         if (s->nblock_used == s->save_nblock+1) continue;
         if (k1 != s->k0) { s->k0 = k1; continue; };
   
         BZ_GET_FAST(k1); BZ_RAND_UPD_MASK; 
         k1 ^= BZ_RAND_MASK; s->nblock_used++;
         s->state_out_len = ((Int32)k1) + 4;
         BZ_GET_FAST(s->k0); BZ_RAND_UPD_MASK; 
         s->k0 ^= BZ_RAND_MASK; s->nblock_used++;
      }

   } else {

      /* restore */
      UInt32        c_calculatedBlockCRC = s->calculatedBlockCRC;
      UChar         c_state_out_ch       = s->state_out_ch;
      Int32         c_state_out_len      = s->state_out_len;
      Int32         c_nblock_used        = s->nblock_used;
      Int32         c_k0                 = s->k0;
      UInt32*       c_tt                 = s->tt;
      UInt32        c_tPos               = s->tPos;
      char*         cs_next_out          = s->strm->next_out;
      unsigned int  cs_avail_out         = s->strm->avail_out;
      Int32         ro_blockSize100k     = s->blockSize100k;
      /* end restore */

      UInt32       avail_out_INIT = cs_avail_out;
      Int32        s_save_nblockPP = s->save_nblock+1;
      unsigned int total_out_lo32_old;

      while (True) {

         /* try to finish existing run */
         if (c_state_out_len > 0) {
            while (True) {
               if (cs_avail_out == 0) goto return_notr;
               if (c_state_out_len == 1) break;
               *( (UChar*)(cs_next_out) ) = c_state_out_ch;
               BZ_UPDATE_CRC ( c_calculatedBlockCRC, c_state_out_ch );
               c_state_out_len--;
               cs_next_out++;
               cs_avail_out--;
            }
            s_state_out_len_eq_one:
            {
               if (cs_avail_out == 0) { 
                  c_state_out_len = 1; goto return_notr;
               };
               *( (UChar*)(cs_next_out) ) = c_state_out_ch;
               BZ_UPDATE_CRC ( c_calculatedBlockCRC, c_state_out_ch );
               cs_next_out++;
               cs_avail_out--;
            }
         }   
         /* Only caused by corrupt data stream? */
         if (c_nblock_used > s_save_nblockPP)
            return True;

         /* can a new run be started? */
         if (c_nblock_used == s_save_nblockPP) {
            c_state_out_len = 0; goto return_notr;
         };   
         c_state_out_ch = c_k0;
         BZ_GET_FAST_C(k1); c_nblock_used++;
         if (k1 != c_k0) { 
            c_k0 = k1; goto s_state_out_len_eq_one; 
         };
         if (c_nblock_used == s_save_nblockPP) 
            goto s_state_out_len_eq_one;
   
         c_state_out_len = 2;
         BZ_GET_FAST_C(k1); c_nblock_used++;
         if (c_nblock_used == s_save_nblockPP) continue;
         if (k1 != c_k0) { c_k0 = k1; continue; };
   
         c_state_out_len = 3;
         BZ_GET_FAST_C(k1); c_nblock_used++;
         if (c_nblock_used == s_save_nblockPP) continue;
         if (k1 != c_k0) { c_k0 = k1; continue; };
   
         BZ_GET_FAST_C(k1); c_nblock_used++;
         c_state_out_len = ((Int32)k1) + 4;
         BZ_GET_FAST_C(c_k0); c_nblock_used++;
      }

      return_notr:
      total_out_lo32_old = s->strm->total_out_lo32;
      s->strm->total_out_lo32 += (avail_out_INIT - cs_avail_out);
      if (s->strm->total_out_lo32 < total_out_lo32_old)
         s->strm->total_out_hi32++;

      /* save */
      s->calculatedBlockCRC = c_calculatedBlockCRC;
      s->state_out_ch       = c_state_out_ch;
      s->state_out_len      = c_state_out_len;
      s->nblock_used        = c_nblock_used;
      s->k0                 = c_k0;
      s->tt                 = c_tt;
      s->tPos               = c_tPos;
      s->strm->next_out     = cs_next_out;
      s->strm->avail_out    = cs_avail_out;
      /* end save */
   }
   return False;
}



/*---------------------------------------------------*/
__inline__ Int32 BZ2_indexIntoF ( Int32 indx, Int32 *cftab )
{
   Int32 nb, na, mid;
   nb = 0;
   na = 256;
   do {
      mid = (nb + na) >> 1;
      if (indx >= cftab[mid]) nb = mid; else na = mid;
   }
   while (na - nb != 1);
   return nb;
}


/*---------------------------------------------------*/
/* Return  True iff data corruption is discovered.
   Returns False if there is no problem.
*/
static
Bool unRLE_obuf_to_output_SMALL ( DState* s )
{
   UChar k1;

   if (s->blockRandomised) {

      while (True) {
         /* try to finish existing run */
         while (True) {
            if (s->strm->avail_out == 0) return False;
            if (s->state_out_len == 0) break;
            *( (UChar*)(s->strm->next_out) ) = s->state_out_ch;
            BZ_UPDATE_CRC ( s->calculatedBlockCRC, s->state_out_ch );
            s->state_out_len--;
            s->strm->next_out++;
            s->strm->avail_out--;
            s->strm->total_out_lo32++;
            if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
         }
   
         /* can a new run be started? */
         if (s->nblock_used == s->save_nblock+1) return False;

         /* Only caused by corrupt data stream? */
         if (s->nblock_used > s->save_nblock+1)
            return True;
   
         s->state_out_len = 1;
         s->state_out_ch = s->k0;
         BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK; 
         k1 ^= BZ_RAND_MASK; s->nblock_used++;
         if (s->nblock_used == s->save_nblock+1) continue;
         if (k1 != s->k0) { s->k0 = k1; continue; };
   
         s->state_out_len = 2;
         BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK; 
         k1 ^= BZ_RAND_MASK; s->nblock_used++;
         if (s->nblock_used == s->save_nblock+1) continue;
         if (k1 != s->k0) { s->k0 = k1; continue; };
   
         s->state_out_len = 3;
         BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK; 
         k1 ^= BZ_RAND_MASK; s->nblock_used++;
         if (s->nblock_used == s->save_nblock+1) continue;
         if (k1 != s->k0) { s->k0 = k1; continue; };
   
         BZ_GET_SMALL(k1); BZ_RAND_UPD_MASK; 
         k1 ^= BZ_RAND_MASK; s->nblock_used++;
         s->state_out_len = ((Int32)k1) + 4;
         BZ_GET_SMALL(s->k0); BZ_RAND_UPD_MASK; 
         s->k0 ^= BZ_RAND_MASK; s->nblock_used++;
      }

   } else {

      while (True) {
         /* try to finish existing run */
         while (True) {
            if (s->strm->avail_out == 0) return False;
            if (s->state_out_len == 0) break;
            *( (UChar*)(s->strm->next_out) ) = s->state_out_ch;
            BZ_UPDATE_CRC ( s->calculatedBlockCRC, s->state_out_ch );
            s->state_out_len--;
            s->strm->next_out++;
            s->strm->avail_out--;
            s->strm->total_out_lo32++;
            if (s->strm->total_out_lo32 == 0) s->strm->total_out_hi32++;
         }
   
         /* can a new run be started? */
         if (s->nblock_used == s->save_nblock+1) return False;

         /* Only caused by corrupt data stream? */
         if (s->nblock_used > s->save_nblock+1)
            return True;
   
         s->state_out_len = 1;
         s->state_out_ch = s->k0;
         BZ_GET_SMALL(k1); s->nblock_used++;
         if (s->nblock_used == s->save_nblock+1) continue;
         if (k1 != s->k0) { s->k0 = k1; continue; };
   
         s->state_out_len = 2;
         BZ_GET_SMALL(k1); s->nblock_used++;
         if (s->nblock_used == s->save_nblock+1) continue;
         if (k1 != s->k0) { s->k0 = k1; continue; };
   
         s->state_out_len = 3;
         BZ_GET_SMALL(k1); s->nblock_used++;
         if (s->nblock_used == s->save_nblock+1) continue;
         if (k1 != s->k0) { s->k0 = k1; continue; };
   
         BZ_GET_SMALL(k1); s->nblock_used++;
         s->state_out_len = ((Int32)k1) + 4;
         BZ_GET_SMALL(s->k0); s->nblock_used++;
      }

   }
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzDecompress) ( bz_stream *strm )
{
   Bool    corrupt;
   DState* s;
   if (strm == NULL) return BZ_PARAM_ERROR;
   s = strm->state;
   if (s == NULL) return BZ_PARAM_ERROR;
   if (s->strm != strm) return BZ_PARAM_ERROR;

   while (True) {
      if (s->state == BZ_X_IDLE) return BZ_SEQUENCE_ERROR;
      if (s->state == BZ_X_OUTPUT) {
         if (s->smallDecompress)
            corrupt = unRLE_obuf_to_output_SMALL ( s ); else
            corrupt = unRLE_obuf_to_output_FAST  ( s );
         if (corrupt) return BZ_DATA_ERROR;
         if (s->nblock_used == s->save_nblock+1 && s->state_out_len == 0) {
            BZ_FINALISE_CRC ( s->calculatedBlockCRC );
            if (s->verbosity >= 3) 
               VPrintf2 ( " {0x%08x, 0x%08x}", s->storedBlockCRC, 
                          s->calculatedBlockCRC );
            if (s->verbosity >= 2) VPrintf0 ( "]" );
            if (s->calculatedBlockCRC != s->storedBlockCRC)
               return BZ_DATA_ERROR;
            s->calculatedCombinedCRC 
               = (s->calculatedCombinedCRC << 1) | 
                    (s->calculatedCombinedCRC >> 31);
            s->calculatedCombinedCRC ^= s->calculatedBlockCRC;
            s->state = BZ_X_BLKHDR_1;
         } else {
            return BZ_OK;
         }
      }
      if (s->state >= BZ_X_MAGIC_1) {
         Int32 r = BZ2_decompress ( s );
         if (r == BZ_STREAM_END) {
            if (s->verbosity >= 3)
               VPrintf2 ( "\n    combined CRCs: stored = 0x%08x, computed = 0x%08x", 
                          s->storedCombinedCRC, s->calculatedCombinedCRC );
            if (s->calculatedCombinedCRC != s->storedCombinedCRC)
               return BZ_DATA_ERROR;
            return r;
         }
         if (s->state != BZ_X_OUTPUT) return r;
      }
   }

   AssertH ( 0, 6001 );

   return 0;  /*NOTREACHED*/
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzDecompressEnd)  ( bz_stream *strm )
{
   DState* s;
   if (strm == NULL) return BZ_PARAM_ERROR;
   s = strm->state;
   if (s == NULL) return BZ_PARAM_ERROR;
   if (s->strm != strm) return BZ_PARAM_ERROR;

   if (s->tt   != NULL) BZFREE(s->tt);
   if (s->ll16 != NULL) BZFREE(s->ll16);
   if (s->ll4  != NULL) BZFREE(s->ll4);

   BZFREE(strm->state);
   strm->state = NULL;

   return BZ_OK;
}


#ifndef BZ_NO_STDIO
/*---------------------------------------------------*/
/*--- File I/O stuff                              ---*/
/*---------------------------------------------------*/

#define BZ_SETERR(eee)                    \
{                                         \
   if (bzerror != NULL) *bzerror = eee;   \
   if (bzf != NULL) bzf->lastErr = eee;   \
}

typedef 
   struct {
      FILE*     handle;
      Char      buf[BZ_MAX_UNUSED];
      Int32     bufN;
      Bool      writing;
      bz_stream strm;
      Int32     lastErr;
      Bool      initialisedOk;
   }
   bzFile;


/*---------------------------------------------*/
static Bool myfeof ( FILE* f )
{
   Int32 c = fgetc ( f );
   if (c == EOF) return True;
   ungetc ( c, f );
   return False;
}


/*---------------------------------------------------*/
BZFILE* BZ_API(BZ2_bzWriteOpen) 
                    ( int*  bzerror,      
                      FILE* f, 
                      int   blockSize100k, 
                      int   verbosity,
                      int   workFactor )
{
   Int32   ret;
   bzFile* bzf = NULL;

   BZ_SETERR(BZ_OK);

   if (f == NULL ||
       (blockSize100k < 1 || blockSize100k > 9) ||
       (workFactor < 0 || workFactor > 250) ||
       (verbosity < 0 || verbosity > 4))
      { BZ_SETERR(BZ_PARAM_ERROR); return NULL; };

   if (ferror(f))
      { BZ_SETERR(BZ_IO_ERROR); return NULL; };

   bzf = malloc ( sizeof(bzFile) );
   if (bzf == NULL)
      { BZ_SETERR(BZ_MEM_ERROR); return NULL; };

   BZ_SETERR(BZ_OK);
   bzf->initialisedOk = False;
   bzf->bufN          = 0;
   bzf->handle        = f;
   bzf->writing       = True;
   bzf->strm.bzalloc  = NULL;
   bzf->strm.bzfree   = NULL;
   bzf->strm.opaque   = NULL;

   if (workFactor == 0) workFactor = 30;
   ret = BZ2_bzCompressInit ( &(bzf->strm), blockSize100k, 
                              verbosity, workFactor );
   if (ret != BZ_OK)
      { BZ_SETERR(ret); free(bzf); return NULL; };

   bzf->strm.avail_in = 0;
   bzf->initialisedOk = True;
   return bzf;   
}



/*---------------------------------------------------*/
void BZ_API(BZ2_bzWrite)
             ( int*    bzerror, 
               BZFILE* b, 
               void*   buf, 
               int     len )
{
   Int32 n, n2, ret;
   bzFile* bzf = (bzFile*)b;

   BZ_SETERR(BZ_OK);
   if (bzf == NULL || buf == NULL || len < 0)
      { BZ_SETERR(BZ_PARAM_ERROR); return; };
   if (!(bzf->writing))
      { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
   if (ferror(bzf->handle))
      { BZ_SETERR(BZ_IO_ERROR); return; };

   if (len == 0)
      { BZ_SETERR(BZ_OK); return; };

   bzf->strm.avail_in = len;
   bzf->strm.next_in  = buf;

   while (True) {
      bzf->strm.avail_out = BZ_MAX_UNUSED;
      bzf->strm.next_out = bzf->buf;
      ret = BZ2_bzCompress ( &(bzf->strm), BZ_RUN );
      if (ret != BZ_RUN_OK)
         { BZ_SETERR(ret); return; };

      if (bzf->strm.avail_out < BZ_MAX_UNUSED) {
         n = BZ_MAX_UNUSED - bzf->strm.avail_out;
         n2 = fwrite ( (void*)(bzf->buf), sizeof(UChar), 
                       n, bzf->handle );
         if (n != n2 || ferror(bzf->handle))
            { BZ_SETERR(BZ_IO_ERROR); return; };
      }

      if (bzf->strm.avail_in == 0)
         { BZ_SETERR(BZ_OK); return; };
   }
}


/*---------------------------------------------------*/
void BZ_API(BZ2_bzWriteClose)
                  ( int*          bzerror, 
                    BZFILE*       b, 
                    int           abandon,
                    unsigned int* nbytes_in,
                    unsigned int* nbytes_out )
{
   BZ2_bzWriteClose64 ( bzerror, b, abandon, 
                        nbytes_in, NULL, nbytes_out, NULL );
}


void BZ_API(BZ2_bzWriteClose64)
                  ( int*          bzerror, 
                    BZFILE*       b, 
                    int           abandon,
                    unsigned int* nbytes_in_lo32,
                    unsigned int* nbytes_in_hi32,
                    unsigned int* nbytes_out_lo32,
                    unsigned int* nbytes_out_hi32 )
{
   Int32   n, n2, ret;
   bzFile* bzf = (bzFile*)b;

   if (bzf == NULL)
      { BZ_SETERR(BZ_OK); return; };
   if (!(bzf->writing))
      { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
   if (ferror(bzf->handle))
      { BZ_SETERR(BZ_IO_ERROR); return; };

   if (nbytes_in_lo32 != NULL) *nbytes_in_lo32 = 0;
   if (nbytes_in_hi32 != NULL) *nbytes_in_hi32 = 0;
   if (nbytes_out_lo32 != NULL) *nbytes_out_lo32 = 0;
   if (nbytes_out_hi32 != NULL) *nbytes_out_hi32 = 0;

   if ((!abandon) && bzf->lastErr == BZ_OK) {
      while (True) {
         bzf->strm.avail_out = BZ_MAX_UNUSED;
         bzf->strm.next_out = bzf->buf;
         ret = BZ2_bzCompress ( &(bzf->strm), BZ_FINISH );
         if (ret != BZ_FINISH_OK && ret != BZ_STREAM_END)
            { BZ_SETERR(ret); return; };

         if (bzf->strm.avail_out < BZ_MAX_UNUSED) {
            n = BZ_MAX_UNUSED - bzf->strm.avail_out;
            n2 = fwrite ( (void*)(bzf->buf), sizeof(UChar), 
                          n, bzf->handle );
            if (n != n2 || ferror(bzf->handle))
               { BZ_SETERR(BZ_IO_ERROR); return; };
         }

         if (ret == BZ_STREAM_END) break;
      }
   }

   if ( !abandon && !ferror ( bzf->handle ) ) {
      fflush ( bzf->handle );
      if (ferror(bzf->handle))
         { BZ_SETERR(BZ_IO_ERROR); return; };
   }

   if (nbytes_in_lo32 != NULL)
      *nbytes_in_lo32 = bzf->strm.total_in_lo32;
   if (nbytes_in_hi32 != NULL)
      *nbytes_in_hi32 = bzf->strm.total_in_hi32;
   if (nbytes_out_lo32 != NULL)
      *nbytes_out_lo32 = bzf->strm.total_out_lo32;
   if (nbytes_out_hi32 != NULL)
      *nbytes_out_hi32 = bzf->strm.total_out_hi32;

   BZ_SETERR(BZ_OK);
   BZ2_bzCompressEnd ( &(bzf->strm) );
   free ( bzf );
}


/*---------------------------------------------------*/
BZFILE* BZ_API(BZ2_bzReadOpen) 
                   ( int*  bzerror, 
                     FILE* f, 
                     int   verbosity,
                     int   small,
                     void* unused,
                     int   nUnused )
{
   bzFile* bzf = NULL;
   int     ret;

   BZ_SETERR(BZ_OK);

   if (f == NULL || 
       (small != 0 && small != 1) ||
       (verbosity < 0 || verbosity > 4) ||
       (unused == NULL && nUnused != 0) ||
       (unused != NULL && (nUnused < 0 || nUnused > BZ_MAX_UNUSED)))
      { BZ_SETERR(BZ_PARAM_ERROR); return NULL; };

   if (ferror(f))
      { BZ_SETERR(BZ_IO_ERROR); return NULL; };

   bzf = malloc ( sizeof(bzFile) );
   if (bzf == NULL) 
      { BZ_SETERR(BZ_MEM_ERROR); return NULL; };

   BZ_SETERR(BZ_OK);

   bzf->initialisedOk = False;
   bzf->handle        = f;
   bzf->bufN          = 0;
   bzf->writing       = False;
   bzf->strm.bzalloc  = NULL;
   bzf->strm.bzfree   = NULL;
   bzf->strm.opaque   = NULL;
   
   while (nUnused > 0) {
      bzf->buf[bzf->bufN] = *((UChar*)(unused)); bzf->bufN++;
      unused = ((void*)( 1 + ((UChar*)(unused))  ));
      nUnused--;
   }

   ret = BZ2_bzDecompressInit ( &(bzf->strm), verbosity, small );
   if (ret != BZ_OK)
      { BZ_SETERR(ret); free(bzf); return NULL; };

   bzf->strm.avail_in = bzf->bufN;
   bzf->strm.next_in  = bzf->buf;

   bzf->initialisedOk = True;
   return bzf;   
}


/*---------------------------------------------------*/
void BZ_API(BZ2_bzReadClose) ( int *bzerror, BZFILE *b )
{
   bzFile* bzf = (bzFile*)b;

   BZ_SETERR(BZ_OK);
   if (bzf == NULL)
      { BZ_SETERR(BZ_OK); return; };

   if (bzf->writing)
      { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };

   if (bzf->initialisedOk)
      (void)BZ2_bzDecompressEnd ( &(bzf->strm) );
   free ( bzf );
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzRead) 
           ( int*    bzerror, 
             BZFILE* b, 
             void*   buf, 
             int     len )
{
   Int32   n, ret;
   bzFile* bzf = (bzFile*)b;

   BZ_SETERR(BZ_OK);

   if (bzf == NULL || buf == NULL || len < 0)
      { BZ_SETERR(BZ_PARAM_ERROR); return 0; };

   if (bzf->writing)
      { BZ_SETERR(BZ_SEQUENCE_ERROR); return 0; };

   if (len == 0)
      { BZ_SETERR(BZ_OK); return 0; };

   bzf->strm.avail_out = len;
   bzf->strm.next_out = buf;

   while (True) {

      if (ferror(bzf->handle)) 
         { BZ_SETERR(BZ_IO_ERROR); return 0; };

      if (bzf->strm.avail_in == 0 && !myfeof(bzf->handle)) {
         n = fread ( bzf->buf, sizeof(UChar), 
                     BZ_MAX_UNUSED, bzf->handle );
         if (ferror(bzf->handle))
            { BZ_SETERR(BZ_IO_ERROR); return 0; };
         bzf->bufN = n;
         bzf->strm.avail_in = bzf->bufN;
         bzf->strm.next_in = bzf->buf;
      }

      ret = BZ2_bzDecompress ( &(bzf->strm) );

      if (ret != BZ_OK && ret != BZ_STREAM_END)
         { BZ_SETERR(ret); return 0; };

      if (ret == BZ_OK && myfeof(bzf->handle) && 
          bzf->strm.avail_in == 0 && bzf->strm.avail_out > 0)
         { BZ_SETERR(BZ_UNEXPECTED_EOF); return 0; };

      if (ret == BZ_STREAM_END)
         { BZ_SETERR(BZ_STREAM_END);
           return len - bzf->strm.avail_out; };
      if (bzf->strm.avail_out == 0)
         { BZ_SETERR(BZ_OK); return len; };
      
   }

   return 0; /*not reached*/
}


/*---------------------------------------------------*/
void BZ_API(BZ2_bzReadGetUnused) 
                     ( int*    bzerror, 
                       BZFILE* b, 
                       void**  unused, 
                       int*    nUnused )
{
   bzFile* bzf = (bzFile*)b;
   if (bzf == NULL)
      { BZ_SETERR(BZ_PARAM_ERROR); return; };
   if (bzf->lastErr != BZ_STREAM_END)
      { BZ_SETERR(BZ_SEQUENCE_ERROR); return; };
   if (unused == NULL || nUnused == NULL)
      { BZ_SETERR(BZ_PARAM_ERROR); return; };

   BZ_SETERR(BZ_OK);
   *nUnused = bzf->strm.avail_in;
   *unused = bzf->strm.next_in;
}
#endif


/*---------------------------------------------------*/
/*--- Misc convenience stuff                      ---*/
/*---------------------------------------------------*/

/*---------------------------------------------------*/
int BZ_API(BZ2_bzBuffToBuffCompress) 
                         ( char*         dest, 
                           unsigned int* destLen,
                           char*         source, 
                           unsigned int  sourceLen,
                           int           blockSize100k, 
                           int           verbosity, 
                           int           workFactor )
{
   bz_stream strm;
   int ret;

   if (dest == NULL || destLen == NULL || 
       source == NULL ||
       blockSize100k < 1 || blockSize100k > 9 ||
       verbosity < 0 || verbosity > 4 ||
       workFactor < 0 || workFactor > 250) 
      return BZ_PARAM_ERROR;

   if (workFactor == 0) workFactor = 30;
   strm.bzalloc = NULL;
   strm.bzfree = NULL;
   strm.opaque = NULL;
   ret = BZ2_bzCompressInit ( &strm, blockSize100k, 
                              verbosity, workFactor );
   if (ret != BZ_OK) return ret;

   strm.next_in = source;
   strm.next_out = dest;
   strm.avail_in = sourceLen;
   strm.avail_out = *destLen;

   ret = BZ2_bzCompress ( &strm, BZ_FINISH );
   if (ret == BZ_FINISH_OK) goto output_overflow;
   if (ret != BZ_STREAM_END) goto errhandler;

   /* normal termination */
   *destLen -= strm.avail_out;   
   BZ2_bzCompressEnd ( &strm );
   return BZ_OK;

   output_overflow:
   BZ2_bzCompressEnd ( &strm );
   return BZ_OUTBUFF_FULL;

   errhandler:
   BZ2_bzCompressEnd ( &strm );
   return ret;
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzBuffToBuffDecompress) 
                           ( char*         dest, 
                             unsigned int* destLen,
                             char*         source, 
                             unsigned int  sourceLen,
                             int           small,
                             int           verbosity )
{
   bz_stream strm;
   int ret;

   if (dest == NULL || destLen == NULL || 
       source == NULL ||
       (small != 0 && small != 1) ||
       verbosity < 0 || verbosity > 4) 
          return BZ_PARAM_ERROR;

   strm.bzalloc = NULL;
   strm.bzfree = NULL;
   strm.opaque = NULL;
   ret = BZ2_bzDecompressInit ( &strm, verbosity, small );
   if (ret != BZ_OK) return ret;

   strm.next_in = source;
   strm.next_out = dest;
   strm.avail_in = sourceLen;
   strm.avail_out = *destLen;

   ret = BZ2_bzDecompress ( &strm );
   if (ret == BZ_OK) goto output_overflow_or_eof;
   if (ret != BZ_STREAM_END) goto errhandler;

   /* normal termination */
   *destLen -= strm.avail_out;
   BZ2_bzDecompressEnd ( &strm );
   return BZ_OK;

   output_overflow_or_eof:
   if (strm.avail_out > 0) {
      BZ2_bzDecompressEnd ( &strm );
      return BZ_UNEXPECTED_EOF;
   } else {
      BZ2_bzDecompressEnd ( &strm );
      return BZ_OUTBUFF_FULL;
   };      

   errhandler:
   BZ2_bzDecompressEnd ( &strm );
   return ret; 
}


/*---------------------------------------------------*/
/*--
   Code contributed by Yoshioka Tsuneo (tsuneo@rr.iij4u.or.jp)
   to support better zlib compatibility.
   This code is not _officially_ part of libbzip2 (yet);
   I haven't tested it, documented it, or considered the
   threading-safeness of it.
   If this code breaks, please contact both Yoshioka and me.
--*/
/*---------------------------------------------------*/

/*---------------------------------------------------*/
/*--
   return version like "0.9.5d, 4-Sept-1999".
--*/
const char * BZ_API(BZ2_bzlibVersion)(void)
{
   return BZ_VERSION;
}


#ifndef BZ_NO_STDIO
/*---------------------------------------------------*/

#if defined(_WIN32) || defined(OS2) || defined(MSDOS)
#   include 
#   include 
#   define SET_BINARY_MODE(file) setmode(fileno(file),O_BINARY)
#else
#   define SET_BINARY_MODE(file)
#endif
static
BZFILE * bzopen_or_bzdopen
               ( const char *path,   /* no use when bzdopen */
                 int fd,             /* no use when bzdopen */
                 const char *mode,
                 int open_mode)      /* bzopen: 0, bzdopen:1 */
{
   int    bzerr;
   char   unused[BZ_MAX_UNUSED];
   int    blockSize100k = 9;
   int    writing       = 0;
   char   mode2[10]     = "";
   FILE   *fp           = NULL;
   BZFILE *bzfp         = NULL;
   int    verbosity     = 0;
   int    workFactor    = 30;
   int    smallMode     = 0;
   int    nUnused       = 0; 

   if (mode == NULL) return NULL;
   while (*mode) {
      switch (*mode) {
      case 'r':
         writing = 0; break;
      case 'w':
         writing = 1; break;
      case 's':
         smallMode = 1; break;
      default:
         if (isdigit((int)(*mode))) {
            blockSize100k = *mode-BZ_HDR_0;
         }
      }
      mode++;
   }
   strcat(mode2, writing ? "w" : "r" );
   strcat(mode2,"b");   /* binary mode */

   if (open_mode==0) {
      if (path==NULL || strcmp(path,"")==0) {
        fp = (writing ? stdout : stdin);
        SET_BINARY_MODE(fp);
      } else {
        fp = fopen(path,mode2);
      }
   } else {
#ifdef BZ_STRICT_ANSI
      fp = NULL;
#else
      fp = fdopen(fd,mode2);
#endif
   }
   if (fp == NULL) return NULL;

   if (writing) {
      /* Guard against total chaos and anarchy -- JRS */
      if (blockSize100k < 1) blockSize100k = 1;
      if (blockSize100k > 9) blockSize100k = 9; 
      bzfp = BZ2_bzWriteOpen(&bzerr,fp,blockSize100k,
                             verbosity,workFactor);
   } else {
      bzfp = BZ2_bzReadOpen(&bzerr,fp,verbosity,smallMode,
                            unused,nUnused);
   }
   if (bzfp == NULL) {
      if (fp != stdin && fp != stdout) fclose(fp);
      return NULL;
   }
   return bzfp;
}


/*---------------------------------------------------*/
/*--
   open file for read or write.
      ex) bzopen("file","w9")
      case path="" or NULL => use stdin or stdout.
--*/
BZFILE * BZ_API(BZ2_bzopen)
               ( const char *path,
                 const char *mode )
{
   return bzopen_or_bzdopen(path,-1,mode,/*bzopen*/0);
}


/*---------------------------------------------------*/
BZFILE * BZ_API(BZ2_bzdopen)
               ( int fd,
                 const char *mode )
{
   return bzopen_or_bzdopen(NULL,fd,mode,/*bzdopen*/1);
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzread) (BZFILE* b, void* buf, int len )
{
   int bzerr, nread;
   if (((bzFile*)b)->lastErr == BZ_STREAM_END) return 0;
   nread = BZ2_bzRead(&bzerr,b,buf,len);
   if (bzerr == BZ_OK || bzerr == BZ_STREAM_END) {
      return nread;
   } else {
      return -1;
   }
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzwrite) (BZFILE* b, void* buf, int len )
{
   int bzerr;

   BZ2_bzWrite(&bzerr,b,buf,len);
   if(bzerr == BZ_OK){
      return len;
   }else{
      return -1;
   }
}


/*---------------------------------------------------*/
int BZ_API(BZ2_bzflush) (GT_UNUSED BZFILE *b)
{
   /* do nothing now... */
   return 0;
}


/*---------------------------------------------------*/
void BZ_API(BZ2_bzclose) (BZFILE* b)
{
   int bzerr;
   FILE *fp;
   
   if (b==NULL) {return;}
   fp = ((bzFile *)b)->handle;
   if(((bzFile*)b)->writing){
      BZ2_bzWriteClose(&bzerr,b,0,NULL,NULL);
      if(bzerr != BZ_OK){
         BZ2_bzWriteClose(NULL,b,1,NULL,NULL);
      }
   }else{
      BZ2_bzReadClose(&bzerr,b);
   }
   if(fp!=stdin && fp!=stdout){
      fclose(fp);
   }
}


/*---------------------------------------------------*/
/*--
   return last error code 
--*/
static const char *bzerrorstrings[] = {
       "OK"
      ,"SEQUENCE_ERROR"
      ,"PARAM_ERROR"
      ,"MEM_ERROR"
      ,"DATA_ERROR"
      ,"DATA_ERROR_MAGIC"
      ,"IO_ERROR"
      ,"UNEXPECTED_EOF"
      ,"OUTBUFF_FULL"
      ,"CONFIG_ERROR"
      ,"???"   /* for future */
      ,"???"   /* for future */
      ,"???"   /* for future */
      ,"???"   /* for future */
      ,"???"   /* for future */
      ,"???"   /* for future */
};


const char * BZ_API(BZ2_bzerror) (BZFILE *b, int *errnum)
{
   int err = ((bzFile *)b)->lastErr;

   if(err>0) err = 0;
   *errnum = err;
   return bzerrorstrings[err*-1];
}
#endif


/*-------------------------------------------------------------*/
/*--- end                                           bzlib.c ---*/
/*-------------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/bzlib.h000066400000000000000000000141451211610345200214230ustar00rootroot00000000000000
/*-------------------------------------------------------------*/
/*--- Public header file for the library.                   ---*/
/*---                                               bzlib.h ---*/
/*-------------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


#ifndef _BZLIB_H
#define _BZLIB_H

#ifdef __cplusplus
extern "C" {
#endif

#define BZ_RUN               0
#define BZ_FLUSH             1
#define BZ_FINISH            2

#define BZ_OK                0
#define BZ_RUN_OK            1
#define BZ_FLUSH_OK          2
#define BZ_FINISH_OK         3
#define BZ_STREAM_END        4
#define BZ_SEQUENCE_ERROR    (-1)
#define BZ_PARAM_ERROR       (-2)
#define BZ_MEM_ERROR         (-3)
#define BZ_DATA_ERROR        (-4)
#define BZ_DATA_ERROR_MAGIC  (-5)
#define BZ_IO_ERROR          (-6)
#define BZ_UNEXPECTED_EOF    (-7)
#define BZ_OUTBUFF_FULL      (-8)
#define BZ_CONFIG_ERROR      (-9)

typedef 
   struct {
      char *next_in;
      unsigned int avail_in;
      unsigned int total_in_lo32;
      unsigned int total_in_hi32;

      char *next_out;
      unsigned int avail_out;
      unsigned int total_out_lo32;
      unsigned int total_out_hi32;

      void *state;

      void *(*bzalloc)(void *,int,int);
      void (*bzfree)(void *,void *);
      void *opaque;
   } 
   bz_stream;


#ifndef BZ_IMPORT
#define BZ_EXPORT
#endif

#ifndef BZ_NO_STDIO
/* Need a definitition for FILE */
#include 
#endif

#ifdef _WIN32
#   include 
#   ifdef small
      /* windows.h define small to char */
#      undef small
#   endif
#   ifdef BZ_EXPORT
#   define BZ_API(func) WINAPI func
#   define BZ_EXTERN extern
#   else
   /* import windows dll dynamically */
#   define BZ_API(func) (WINAPI * func)
#   define BZ_EXTERN
#   endif
#else
#   define BZ_API(func) func
#   define BZ_EXTERN extern
#endif


/*-- Core (low-level) library functions --*/

BZ_EXTERN int BZ_API(BZ2_bzCompressInit) ( 
      bz_stream* strm, 
      int        blockSize100k, 
      int        verbosity, 
      int        workFactor 
   );

BZ_EXTERN int BZ_API(BZ2_bzCompress) ( 
      bz_stream* strm, 
      int action 
   );

BZ_EXTERN int BZ_API(BZ2_bzCompressEnd) ( 
      bz_stream* strm 
   );

BZ_EXTERN int BZ_API(BZ2_bzDecompressInit) ( 
      bz_stream *strm, 
      int       verbosity, 
      int       small
   );

BZ_EXTERN int BZ_API(BZ2_bzDecompress) ( 
      bz_stream* strm 
   );

BZ_EXTERN int BZ_API(BZ2_bzDecompressEnd) ( 
      bz_stream *strm 
   );



/*-- High(er) level library functions --*/

#ifndef BZ_NO_STDIO
#define BZ_MAX_UNUSED 5000

typedef void BZFILE;

BZ_EXTERN BZFILE* BZ_API(BZ2_bzReadOpen) ( 
      int*  bzerror,   
      FILE* f, 
      int   verbosity, 
      int   small,
      void* unused,    
      int   nUnused 
   );

BZ_EXTERN void BZ_API(BZ2_bzReadClose) ( 
      int*    bzerror, 
      BZFILE* b 
   );

BZ_EXTERN void BZ_API(BZ2_bzReadGetUnused) ( 
      int*    bzerror, 
      BZFILE* b, 
      void**  unused,  
      int*    nUnused 
   );

BZ_EXTERN int BZ_API(BZ2_bzRead) ( 
      int*    bzerror, 
      BZFILE* b, 
      void*   buf, 
      int     len 
   );

BZ_EXTERN BZFILE* BZ_API(BZ2_bzWriteOpen) ( 
      int*  bzerror,      
      FILE* f, 
      int   blockSize100k, 
      int   verbosity, 
      int   workFactor 
   );

BZ_EXTERN void BZ_API(BZ2_bzWrite) ( 
      int*    bzerror, 
      BZFILE* b, 
      void*   buf, 
      int     len 
   );

BZ_EXTERN void BZ_API(BZ2_bzWriteClose) ( 
      int*          bzerror, 
      BZFILE*       b, 
      int           abandon, 
      unsigned int* nbytes_in, 
      unsigned int* nbytes_out 
   );

BZ_EXTERN void BZ_API(BZ2_bzWriteClose64) ( 
      int*          bzerror, 
      BZFILE*       b, 
      int           abandon, 
      unsigned int* nbytes_in_lo32, 
      unsigned int* nbytes_in_hi32, 
      unsigned int* nbytes_out_lo32, 
      unsigned int* nbytes_out_hi32
   );
#endif


/*-- Utility functions --*/

BZ_EXTERN int BZ_API(BZ2_bzBuffToBuffCompress) ( 
      char*         dest, 
      unsigned int* destLen,
      char*         source, 
      unsigned int  sourceLen,
      int           blockSize100k, 
      int           verbosity, 
      int           workFactor 
   );

BZ_EXTERN int BZ_API(BZ2_bzBuffToBuffDecompress) ( 
      char*         dest, 
      unsigned int* destLen,
      char*         source, 
      unsigned int  sourceLen,
      int           small, 
      int           verbosity 
   );


/*--
   Code contributed by Yoshioka Tsuneo (tsuneo@rr.iij4u.or.jp)
   to support better zlib compatibility.
   This code is not _officially_ part of libbzip2 (yet);
   I haven't tested it, documented it, or considered the
   threading-safeness of it.
   If this code breaks, please contact both Yoshioka and me.
--*/

BZ_EXTERN const char * BZ_API(BZ2_bzlibVersion) (
      void
   );

#ifndef BZ_NO_STDIO
BZ_EXTERN BZFILE * BZ_API(BZ2_bzopen) (
      const char *path,
      const char *mode
   );

BZ_EXTERN BZFILE * BZ_API(BZ2_bzdopen) (
      int        fd,
      const char *mode
   );
         
BZ_EXTERN int BZ_API(BZ2_bzread) (
      BZFILE* b, 
      void* buf, 
      int len 
   );

BZ_EXTERN int BZ_API(BZ2_bzwrite) (
      BZFILE* b, 
      void*   buf, 
      int     len 
   );

BZ_EXTERN int BZ_API(BZ2_bzflush) (
      BZFILE* b
   );

BZ_EXTERN void BZ_API(BZ2_bzclose) (
      BZFILE* b
   );

BZ_EXTERN const char * BZ_API(BZ2_bzerror) (
      BZFILE *b, 
      int    *errnum
   );
#endif

#ifdef __cplusplus
}
#endif

#endif

/*-------------------------------------------------------------*/
/*--- end                                           bzlib.h ---*/
/*-------------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/bzlib_private.h000066400000000000000000000316741211610345200231630ustar00rootroot00000000000000
/*-------------------------------------------------------------*/
/*--- Private header file for the library.                  ---*/
/*---                                       bzlib_private.h ---*/
/*-------------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


#ifndef _BZLIB_PRIVATE_H
#define _BZLIB_PRIVATE_H

#include 

#ifndef BZ_NO_STDIO
#include 
#include 
#include 
#endif

#include "bzlib.h"



/*-- General stuff. --*/

#define BZ_VERSION  "1.0.6, 6-Sept-2010"

typedef char            Char;
typedef unsigned char   Bool;
typedef unsigned char   UChar;
typedef int             Int32;
typedef unsigned int    UInt32;
typedef short           Int16;
typedef unsigned short  UInt16;

#define True  ((Bool)1)
#define False ((Bool)0)

#ifndef __GNUC__
#define __inline__  /* */
#endif 

#ifndef BZ_NO_STDIO

extern void BZ2_bz__AssertH__fail ( int errcode );
#define AssertH(cond,errcode) \
   { if (!(cond)) BZ2_bz__AssertH__fail ( errcode ); }

#if BZ_DEBUG
#define AssertD(cond,msg) \
   { if (!(cond)) {       \
      fprintf ( stderr,   \
        "\n\nlibbzip2(debug build): internal error\n\t%s\n", msg );\
      exit(1); \
   }}
#else
#define AssertD(cond,msg) /* */
#endif

#define VPrintf0(zf) \
   fprintf(stderr,zf)
#define VPrintf1(zf,za1) \
   fprintf(stderr,zf,za1)
#define VPrintf2(zf,za1,za2) \
   fprintf(stderr,zf,za1,za2)
#define VPrintf3(zf,za1,za2,za3) \
   fprintf(stderr,zf,za1,za2,za3)
#define VPrintf4(zf,za1,za2,za3,za4) \
   fprintf(stderr,zf,za1,za2,za3,za4)
#define VPrintf5(zf,za1,za2,za3,za4,za5) \
   fprintf(stderr,zf,za1,za2,za3,za4,za5)

#else

extern void bz_internal_error ( int errcode );
#define AssertH(cond,errcode) \
   { if (!(cond)) bz_internal_error ( errcode ); }
#define AssertD(cond,msg)                do { } while (0)
#define VPrintf0(zf)                     do { } while (0)
#define VPrintf1(zf,za1)                 do { } while (0)
#define VPrintf2(zf,za1,za2)             do { } while (0)
#define VPrintf3(zf,za1,za2,za3)         do { } while (0)
#define VPrintf4(zf,za1,za2,za3,za4)     do { } while (0)
#define VPrintf5(zf,za1,za2,za3,za4,za5) do { } while (0)

#endif


#define BZALLOC(nnn) (strm->bzalloc)(strm->opaque,(nnn),1)
#define BZFREE(ppp)  (strm->bzfree)(strm->opaque,(ppp))


/*-- Header bytes. --*/

#define BZ_HDR_B 0x42   /* 'B' */
#define BZ_HDR_Z 0x5a   /* 'Z' */
#define BZ_HDR_h 0x68   /* 'h' */
#define BZ_HDR_0 0x30   /* '0' */
  
/*-- Constants for the back end. --*/

#define BZ_MAX_ALPHA_SIZE 258
#define BZ_MAX_CODE_LEN    23

#define BZ_RUNA 0
#define BZ_RUNB 1

#define BZ_N_GROUPS 6
#define BZ_G_SIZE   50
#define BZ_N_ITERS  4

#define BZ_MAX_SELECTORS (2 + (900000 / BZ_G_SIZE))



/*-- Stuff for randomising repetitive blocks. --*/

extern Int32 BZ2_rNums[512];

#define BZ_RAND_DECLS                          \
   Int32 rNToGo;                               \
   Int32 rTPos                                 \

#define BZ_RAND_INIT_MASK                      \
   s->rNToGo = 0;                              \
   s->rTPos  = 0                               \

#define BZ_RAND_MASK ((s->rNToGo == 1) ? 1 : 0)

#define BZ_RAND_UPD_MASK                       \
   if (s->rNToGo == 0) {                       \
      s->rNToGo = BZ2_rNums[s->rTPos];         \
      s->rTPos++;                              \
      if (s->rTPos == 512) s->rTPos = 0;       \
   }                                           \
   s->rNToGo--;



/*-- Stuff for doing CRCs. --*/

extern UInt32 BZ2_crc32Table[256];

#define BZ_INITIALISE_CRC(crcVar)              \
{                                              \
   crcVar = 0xffffffffL;                       \
}

#define BZ_FINALISE_CRC(crcVar)                \
{                                              \
   crcVar = ~(crcVar);                         \
}

#define BZ_UPDATE_CRC(crcVar,cha)              \
{                                              \
   crcVar = (crcVar << 8) ^                    \
            BZ2_crc32Table[(crcVar >> 24) ^    \
                           ((UChar)cha)];      \
}



/*-- States and modes for compression. --*/

#define BZ_M_IDLE      1
#define BZ_M_RUNNING   2
#define BZ_M_FLUSHING  3
#define BZ_M_FINISHING 4

#define BZ_S_OUTPUT    1
#define BZ_S_INPUT     2

#define BZ_N_RADIX 2
#define BZ_N_QSORT 12
#define BZ_N_SHELL 18
#define BZ_N_OVERSHOOT (BZ_N_RADIX + BZ_N_QSORT + BZ_N_SHELL + 2)




/*-- Structure holding all the compression-side stuff. --*/

typedef
   struct {
      /* pointer back to the struct bz_stream */
      bz_stream* strm;

      /* mode this stream is in, and whether inputting */
      /* or outputting data */
      Int32    mode;
      Int32    state;

      /* remembers avail_in when flush/finish requested */
      UInt32   avail_in_expect;

      /* for doing the block sorting */
      UInt32*  arr1;
      UInt32*  arr2;
      UInt32*  ftab;
      Int32    origPtr;

      /* aliases for arr1 and arr2 */
      UInt32*  ptr;
      UChar*   block;
      UInt16*  mtfv;
      UChar*   zbits;

      /* for deciding when to use the fallback sorting algorithm */
      Int32    workFactor;

      /* run-length-encoding of the input */
      UInt32   state_in_ch;
      Int32    state_in_len;
      BZ_RAND_DECLS;

      /* input and output limits and current posns */
      Int32    nblock;
      Int32    nblockMAX;
      Int32    numZ;
      Int32    state_out_pos;

      /* map of bytes used in block */
      Int32    nInUse;
      Bool     inUse[256];
      UChar    unseqToSeq[256];

      /* the buffer for bit stream creation */
      UInt32   bsBuff;
      Int32    bsLive;

      /* block and combined CRCs */
      UInt32   blockCRC;
      UInt32   combinedCRC;

      /* misc administratium */
      Int32    verbosity;
      Int32    blockNo;
      Int32    blockSize100k;

      /* stuff for coding the MTF values */
      Int32    nMTF;
      Int32    mtfFreq    [BZ_MAX_ALPHA_SIZE];
      UChar    selector   [BZ_MAX_SELECTORS];
      UChar    selectorMtf[BZ_MAX_SELECTORS];

      UChar    len     [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
      Int32    code    [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
      Int32    rfreq   [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
      /* second dimension: only 3 needed; 4 makes index calculations faster */
      UInt32   len_pack[BZ_MAX_ALPHA_SIZE][4];

   }
   EState;



/*-- externs for compression. --*/

extern void 
BZ2_blockSort ( EState* );

extern void 
BZ2_compressBlock ( EState*, Bool );

extern void 
BZ2_bsInitWrite ( EState* );

extern void 
BZ2_hbAssignCodes ( Int32*, UChar*, Int32, Int32, Int32 );

extern void 
BZ2_hbMakeCodeLengths ( UChar*, Int32*, Int32, Int32 );



/*-- states for decompression. --*/

#define BZ_X_IDLE        1
#define BZ_X_OUTPUT      2

#define BZ_X_MAGIC_1     10
#define BZ_X_MAGIC_2     11
#define BZ_X_MAGIC_3     12
#define BZ_X_MAGIC_4     13
#define BZ_X_BLKHDR_1    14
#define BZ_X_BLKHDR_2    15
#define BZ_X_BLKHDR_3    16
#define BZ_X_BLKHDR_4    17
#define BZ_X_BLKHDR_5    18
#define BZ_X_BLKHDR_6    19
#define BZ_X_BCRC_1      20
#define BZ_X_BCRC_2      21
#define BZ_X_BCRC_3      22
#define BZ_X_BCRC_4      23
#define BZ_X_RANDBIT     24
#define BZ_X_ORIGPTR_1   25
#define BZ_X_ORIGPTR_2   26
#define BZ_X_ORIGPTR_3   27
#define BZ_X_MAPPING_1   28
#define BZ_X_MAPPING_2   29
#define BZ_X_SELECTOR_1  30
#define BZ_X_SELECTOR_2  31
#define BZ_X_SELECTOR_3  32
#define BZ_X_CODING_1    33
#define BZ_X_CODING_2    34
#define BZ_X_CODING_3    35
#define BZ_X_MTF_1       36
#define BZ_X_MTF_2       37
#define BZ_X_MTF_3       38
#define BZ_X_MTF_4       39
#define BZ_X_MTF_5       40
#define BZ_X_MTF_6       41
#define BZ_X_ENDHDR_2    42
#define BZ_X_ENDHDR_3    43
#define BZ_X_ENDHDR_4    44
#define BZ_X_ENDHDR_5    45
#define BZ_X_ENDHDR_6    46
#define BZ_X_CCRC_1      47
#define BZ_X_CCRC_2      48
#define BZ_X_CCRC_3      49
#define BZ_X_CCRC_4      50



/*-- Constants for the fast MTF decoder. --*/

#define MTFA_SIZE 4096
#define MTFL_SIZE 16



/*-- Structure holding all the decompression-side stuff. --*/

typedef
   struct {
      /* pointer back to the struct bz_stream */
      bz_stream* strm;

      /* state indicator for this stream */
      Int32    state;

      /* for doing the final run-length decoding */
      UChar    state_out_ch;
      Int32    state_out_len;
      Bool     blockRandomised;
      BZ_RAND_DECLS;

      /* the buffer for bit stream reading */
      UInt32   bsBuff;
      Int32    bsLive;

      /* misc administratium */
      Int32    blockSize100k;
      Bool     smallDecompress;
      Int32    currBlockNo;
      Int32    verbosity;

      /* for undoing the Burrows-Wheeler transform */
      Int32    origPtr;
      UInt32   tPos;
      Int32    k0;
      Int32    unzftab[256];
      Int32    nblock_used;
      Int32    cftab[257];
      Int32    cftabCopy[257];

      /* for undoing the Burrows-Wheeler transform (FAST) */
      UInt32   *tt;

      /* for undoing the Burrows-Wheeler transform (SMALL) */
      UInt16   *ll16;
      UChar    *ll4;

      /* stored and calculated CRCs */
      UInt32   storedBlockCRC;
      UInt32   storedCombinedCRC;
      UInt32   calculatedBlockCRC;
      UInt32   calculatedCombinedCRC;

      /* map of bytes used in block */
      Int32    nInUse;
      Bool     inUse[256];
      Bool     inUse16[16];
      UChar    seqToUnseq[256];

      /* for decoding the MTF values */
      UChar    mtfa   [MTFA_SIZE];
      Int32    mtfbase[256 / MTFL_SIZE];
      UChar    selector   [BZ_MAX_SELECTORS];
      UChar    selectorMtf[BZ_MAX_SELECTORS];
      UChar    len  [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];

      Int32    limit  [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
      Int32    base   [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
      Int32    perm   [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
      Int32    minLens[BZ_N_GROUPS];

      /* save area for scalars in the main decompress code */
      Int32    save_i;
      Int32    save_j;
      Int32    save_t;
      Int32    save_alphaSize;
      Int32    save_nGroups;
      Int32    save_nSelectors;
      Int32    save_EOB;
      Int32    save_groupNo;
      Int32    save_groupPos;
      Int32    save_nextSym;
      Int32    save_nblockMAX;
      Int32    save_nblock;
      Int32    save_es;
      Int32    save_N;
      Int32    save_curr;
      Int32    save_zt;
      Int32    save_zn; 
      Int32    save_zvec;
      Int32    save_zj;
      Int32    save_gSel;
      Int32    save_gMinlen;
      Int32*   save_gLimit;
      Int32*   save_gBase;
      Int32*   save_gPerm;

   }
   DState;



/*-- Macros for decompression. --*/

#define BZ_GET_FAST(cccc)                     \
    /* c_tPos is unsigned, hence test < 0 is pointless. */ \
    if (s->tPos >= (UInt32)100000 * (UInt32)s->blockSize100k) return True; \
    s->tPos = s->tt[s->tPos];                 \
    cccc = (UChar)(s->tPos & 0xff);           \
    s->tPos >>= 8;

#define BZ_GET_FAST_C(cccc)                   \
    /* c_tPos is unsigned, hence test < 0 is pointless. */ \
    if (c_tPos >= (UInt32)100000 * (UInt32)ro_blockSize100k) return True; \
    c_tPos = c_tt[c_tPos];                    \
    cccc = (UChar)(c_tPos & 0xff);            \
    c_tPos >>= 8;

#define SET_LL4(i,n)                                          \
   { if (((i) & 0x1) == 0)                                    \
        s->ll4[(i) >> 1] = (s->ll4[(i) >> 1] & 0xf0) | (n); else    \
        s->ll4[(i) >> 1] = (s->ll4[(i) >> 1] & 0x0f) | ((n) << 4);  \
   }

#define GET_LL4(i)                             \
   ((((UInt32)(s->ll4[(i) >> 1])) >> (((i) << 2) & 0x4)) & 0xF)

#define SET_LL(i,n)                          \
   { s->ll16[i] = (UInt16)(n & 0x0000ffff);  \
     SET_LL4(i, n >> 16);                    \
   }

#define GET_LL(i) \
   (((UInt32)s->ll16[i]) | (GET_LL4(i) << 16))

#define BZ_GET_SMALL(cccc)                            \
    /* c_tPos is unsigned, hence test < 0 is pointless. */ \
    if (s->tPos >= (UInt32)100000 * (UInt32)s->blockSize100k) return True; \
    cccc = BZ2_indexIntoF ( s->tPos, s->cftab );    \
    s->tPos = GET_LL(s->tPos);


/*-- externs for decompression. --*/

extern Int32 
BZ2_indexIntoF ( Int32, Int32* );

extern Int32 
BZ2_decompress ( DState* );

extern void 
BZ2_hbCreateDecodeTables ( Int32*, Int32*, Int32*, UChar*,
                           Int32,  Int32, Int32 );


#endif


/*-- BZ_NO_STDIO seems to make NULL disappear on some platforms. --*/

#ifdef BZ_NO_STDIO
#ifndef NULL
#define NULL 0
#endif
#endif


/*-------------------------------------------------------------*/
/*--- end                                   bzlib_private.h ---*/
/*-------------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/bzmore000066400000000000000000000023531211610345200213670ustar00rootroot00000000000000#!/bin/sh

# Bzmore wrapped for bzip2, 
# adapted from zmore by Philippe Troin  for Debian GNU/Linux.

PATH="/usr/bin:$PATH"; export PATH

prog=`echo $0 | sed 's|.*/||'`
case "$prog" in
	*less)	more=less	;;
	*)	more=more       ;;
esac

if test "`echo -n a`" = "-n a"; then
  # looks like a SysV system:
  n1=''; n2='\c'
else
  n1='-n'; n2=''
fi
oldtty=`stty -g 2>/dev/null`
if stty -cbreak 2>/dev/null; then
  cb='cbreak'; ncb='-cbreak'
else
  # 'stty min 1' resets eof to ^a on both SunOS and SysV!
  cb='min 1 -icanon'; ncb='icanon eof ^d'
fi
if test $? -eq 0 -a -n "$oldtty"; then
   trap 'stty $oldtty 2>/dev/null; exit' 0 2 3 5 10 13 15
else
   trap 'stty $ncb echo 2>/dev/null; exit' 0 2 3 5 10 13 15
fi

if test $# = 0; then
    if test -t 0; then
	echo usage: $prog files...
    else
	bzip2 -cdfq | eval $more
    fi
else
    FIRST=1
    for FILE
    do
	if test $FIRST -eq 0; then
		echo $n1 "--More--(Next file: $FILE)$n2"
		stty $cb -echo 2>/dev/null
		ANS=`dd bs=1 count=1 2>/dev/null` 
		stty $ncb echo 2>/dev/null
		echo " "
		if test "$ANS" = 'e' -o "$ANS" = 'q'; then
			exit
		fi
	fi
	if test "$ANS" != 's'; then
		echo "------> $FILE <------"
		bzip2 -cdfq "$FILE" | eval $more
	fi
	if test -t; then
		FIRST=0
	fi
    done
fi
genometools-1.5.1/src/external/bzip2-1.0.6/bzmore.1000066400000000000000000000103261211610345200215250ustar00rootroot00000000000000.\"Shamelessly copied from zmore.1 by Philippe Troin 
.\"for Debian GNU/Linux
.TH BZMORE 1
.SH NAME
bzmore, bzless \- file perusal filter for crt viewing of bzip2 compressed text
.SH SYNOPSIS
.B bzmore
[ name ...  ]
.br
.B bzless
[ name ...  ]
.SH NOTE
In the following description,
.I bzless
and
.I less
can be used interchangeably with
.I bzmore
and
.I more.
.SH DESCRIPTION
.I  Bzmore
is a filter which allows examination of compressed or plain text files
one screenful at a time on a soft-copy terminal.
.I bzmore
works on files compressed with
.I bzip2
and also on uncompressed files.
If a file does not exist,
.I bzmore
looks for a file of the same name with the addition of a .bz2 suffix.
.PP
.I Bzmore
normally pauses after each screenful, printing --More--
at the bottom of the screen.
If the user then types a carriage return, one more line is displayed.
If the user hits a space,
another screenful is displayed.  Other possibilities are enumerated later.
.PP
.I Bzmore
looks in the file
.I /etc/termcap
to determine terminal characteristics,
and to determine the default window size.
On a terminal capable of displaying 24 lines,
the default window size is 22 lines.
Other sequences which may be typed when
.I bzmore
pauses, and their effects, are as follows (\fIi\fP is an optional integer
argument, defaulting to 1) :
.PP
.IP \fIi\|\fP
display
.I i
more lines, (or another screenful if no argument is given)
.PP
.IP ^D
display 11 more lines (a ``scroll'').
If
.I i
is given, then the scroll size is set to \fIi\|\fP.
.PP
.IP d
same as ^D (control-D)
.PP
.IP \fIi\|\fPz
same as typing a space except that \fIi\|\fP, if present, becomes the new
window size.  Note that the window size reverts back to the default at the
end of the current file.
.PP
.IP \fIi\|\fPs
skip \fIi\|\fP lines and print a screenful of lines
.PP
.IP \fIi\|\fPf
skip \fIi\fP screenfuls and print a screenful of lines
.PP
.IP "q or Q"
quit reading the current file; go on to the next (if any)
.PP
.IP "e or q"
When the prompt --More--(Next file: 
.IR file )
is printed, this command causes bzmore to exit.
.PP
.IP s
When the prompt --More--(Next file: 
.IR file )
is printed, this command causes bzmore to skip the next file and continue.
.PP 
.IP =
Display the current line number.
.PP
.IP \fIi\|\fP/expr
search for the \fIi\|\fP-th occurrence of the regular expression \fIexpr.\fP
If the pattern is not found,
.I bzmore
goes on to the next file (if any).
Otherwise, a screenful is displayed, starting two lines before the place
where the expression was found.
The user's erase and kill characters may be used to edit the regular
expression.
Erasing back past the first column cancels the search command.
.PP
.IP \fIi\|\fPn
search for the \fIi\|\fP-th occurrence of the last regular expression entered.
.PP
.IP !command
invoke a shell with \fIcommand\|\fP. 
The character `!' in "command" are replaced with the
previous shell command.  The sequence "\\!" is replaced by "!".
.PP
.IP ":q or :Q"
quit reading the current file; go on to the next (if any)
(same as q or Q).
.PP
.IP .
(dot) repeat the previous command.
.PP
The commands take effect immediately, i.e., it is not necessary to
type a carriage return.
Up to the time when the command character itself is given,
the user may hit the line kill character to cancel the numerical
argument being formed.
In addition, the user may hit the erase character to redisplay the
--More-- message.
.PP
At any time when output is being sent to the terminal, the user can
hit the quit key (normally control\-\\).
.I Bzmore
will stop sending output, and will display the usual --More--
prompt.
The user may then enter one of the above commands in the normal manner.
Unfortunately, some output is lost when this is done, due to the
fact that any characters waiting in the terminal's output queue
are flushed when the quit signal occurs.
.PP
The terminal is set to
.I noecho
mode by this program so that the output can be continuous.
What you type will thus not show on your terminal, except for the / and !
commands.
.PP
If the standard output is not a teletype, then
.I bzmore
acts just like
.I bzcat,
except that a header is printed before each file.
.SH FILES
.DT
/etc/termcap		Terminal data base
.SH "SEE ALSO"
more(1), less(1), bzip2(1), bzdiff(1), bzgrep(1)
genometools-1.5.1/src/external/bzip2-1.0.6/compress.c000066400000000000000000000501211211610345200221410ustar00rootroot00000000000000
/*-------------------------------------------------------------*/
/*--- Compression machinery (not incl block sorting)        ---*/
/*---                                            compress.c ---*/
/*-------------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


/* CHANGES
    0.9.0    -- original version.
    0.9.0a/b -- no changes in this file.
    0.9.0c   -- changed setting of nGroups in sendMTFValues() 
                so as to do a bit better on small files
*/

#include "bzlib_private.h"


/*---------------------------------------------------*/
/*--- Bit stream I/O                              ---*/
/*---------------------------------------------------*/

/*---------------------------------------------------*/
void BZ2_bsInitWrite ( EState* s )
{
   s->bsLive = 0;
   s->bsBuff = 0;
}


/*---------------------------------------------------*/
static
void bsFinishWrite ( EState* s )
{
   while (s->bsLive > 0) {
      s->zbits[s->numZ] = (UChar)(s->bsBuff >> 24);
      s->numZ++;
      s->bsBuff <<= 8;
      s->bsLive -= 8;
   }
}


/*---------------------------------------------------*/
#define bsNEEDW(nz)                           \
{                                             \
   while (s->bsLive >= 8) {                   \
      s->zbits[s->numZ]                       \
         = (UChar)(s->bsBuff >> 24);          \
      s->numZ++;                              \
      s->bsBuff <<= 8;                        \
      s->bsLive -= 8;                         \
   }                                          \
}


/*---------------------------------------------------*/
static
__inline__
void bsW ( EState* s, Int32 n, UInt32 v )
{
   bsNEEDW ( n );
   s->bsBuff |= (v << (32 - s->bsLive - n));
   s->bsLive += n;
}


/*---------------------------------------------------*/
static
void bsPutUInt32 ( EState* s, UInt32 u )
{
   bsW ( s, 8, (u >> 24) & 0xffL );
   bsW ( s, 8, (u >> 16) & 0xffL );
   bsW ( s, 8, (u >>  8) & 0xffL );
   bsW ( s, 8,  u        & 0xffL );
}


/*---------------------------------------------------*/
static
void bsPutUChar ( EState* s, UChar c )
{
   bsW( s, 8, (UInt32)c );
}


/*---------------------------------------------------*/
/*--- The back end proper                         ---*/
/*---------------------------------------------------*/

/*---------------------------------------------------*/
static
void makeMaps_e ( EState* s )
{
   Int32 i;
   s->nInUse = 0;
   for (i = 0; i < 256; i++)
      if (s->inUse[i]) {
         s->unseqToSeq[i] = s->nInUse;
         s->nInUse++;
      }
}


/*---------------------------------------------------*/
static
void generateMTFValues ( EState* s )
{
   UChar   yy[256];
   Int32   i, j;
   Int32   zPend;
   Int32   wr;
   Int32   EOB;

   /* 
      After sorting (eg, here),
         s->arr1 [ 0 .. s->nblock-1 ] holds sorted order,
         and
         ((UChar*)s->arr2) [ 0 .. s->nblock-1 ] 
         holds the original block data.

      The first thing to do is generate the MTF values,
      and put them in
         ((UInt16*)s->arr1) [ 0 .. s->nblock-1 ].
      Because there are strictly fewer or equal MTF values
      than block values, ptr values in this area are overwritten
      with MTF values only when they are no longer needed.

      The final compressed bitstream is generated into the
      area starting at
         (UChar*) (&((UChar*)s->arr2)[s->nblock])

      These storage aliases are set up in bzCompressInit(),
      except for the last one, which is arranged in 
      compressBlock().
   */
   UInt32* ptr   = s->ptr;
   UChar* block  = s->block;
   UInt16* mtfv  = s->mtfv;

   makeMaps_e ( s );
   EOB = s->nInUse+1;

   for (i = 0; i <= EOB; i++) s->mtfFreq[i] = 0;

   wr = 0;
   zPend = 0;
   for (i = 0; i < s->nInUse; i++) yy[i] = (UChar) i;

   for (i = 0; i < s->nblock; i++) {
      UChar ll_i;
      AssertD ( wr <= i, "generateMTFValues(1)" );
      j = ptr[i]-1; if (j < 0) j += s->nblock;
      ll_i = s->unseqToSeq[block[j]];
      AssertD ( ll_i < s->nInUse, "generateMTFValues(2a)" );

      if (yy[0] == ll_i) { 
         zPend++;
      } else {

         if (zPend > 0) {
            zPend--;
            while (True) {
               if (zPend & 1) {
                  mtfv[wr] = BZ_RUNB; wr++; 
                  s->mtfFreq[BZ_RUNB]++; 
               } else {
                  mtfv[wr] = BZ_RUNA; wr++; 
                  s->mtfFreq[BZ_RUNA]++; 
               }
               if (zPend < 2) break;
               zPend = (zPend - 2) / 2;
            };
            zPend = 0;
         }
         {
            register UChar  rtmp;
            register UChar* ryy_j;
            register UChar  rll_i;
            rtmp  = yy[1];
            yy[1] = yy[0];
            ryy_j = &(yy[1]);
            rll_i = ll_i;
            while ( rll_i != rtmp ) {
               register UChar rtmp2;
               ryy_j++;
               rtmp2  = rtmp;
               rtmp   = *ryy_j;
               *ryy_j = rtmp2;
            };
            yy[0] = rtmp;
            j = ryy_j - &(yy[0]);
            mtfv[wr] = j+1; wr++; s->mtfFreq[j+1]++;
         }

      }
   }

   if (zPend > 0) {
      zPend--;
      while (True) {
         if (zPend & 1) {
            mtfv[wr] = BZ_RUNB; wr++; 
            s->mtfFreq[BZ_RUNB]++; 
         } else {
            mtfv[wr] = BZ_RUNA; wr++; 
            s->mtfFreq[BZ_RUNA]++; 
         }
         if (zPend < 2) break;
         zPend = (zPend - 2) / 2;
      };
      zPend = 0;
   }

   mtfv[wr] = EOB; wr++; s->mtfFreq[EOB]++;

   s->nMTF = wr;
}


/*---------------------------------------------------*/
#define BZ_LESSER_ICOST  0
#define BZ_GREATER_ICOST 15

static
void sendMTFValues ( EState* s )
{
   Int32 v, t, i, j, gs, ge, totc, bt, bc, iter;
   Int32 nSelectors, alphaSize, minLen, maxLen, selCtr;
   Int32 nGroups, nBytes;

   /*--
   UChar  len [BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
   is a global since the decoder also needs it.

   Int32  code[BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
   Int32  rfreq[BZ_N_GROUPS][BZ_MAX_ALPHA_SIZE];
   are also globals only used in this proc.
   Made global to keep stack frame size small.
   --*/


   UInt16 cost[BZ_N_GROUPS];
   Int32  fave[BZ_N_GROUPS];

   UInt16* mtfv = s->mtfv;

   if (s->verbosity >= 3)
      VPrintf3( "      %d in block, %d after MTF & 1-2 coding, "
                "%d+2 syms in use\n", 
                s->nblock, s->nMTF, s->nInUse );

   alphaSize = s->nInUse+2;
   for (t = 0; t < BZ_N_GROUPS; t++)
      for (v = 0; v < alphaSize; v++)
         s->len[t][v] = BZ_GREATER_ICOST;

   /*--- Decide how many coding tables to use ---*/
   AssertH ( s->nMTF > 0, 3001 );
   if (s->nMTF < 200)  nGroups = 2; else
   if (s->nMTF < 600)  nGroups = 3; else
   if (s->nMTF < 1200) nGroups = 4; else
   if (s->nMTF < 2400) nGroups = 5; else
                       nGroups = 6;

   /*--- Generate an initial set of coding tables ---*/
   { 
      Int32 nPart, remF, tFreq, aFreq;

      nPart = nGroups;
      remF  = s->nMTF;
      gs = 0;
      while (nPart > 0) {
         tFreq = remF / nPart;
         ge = gs-1;
         aFreq = 0;
         while (aFreq < tFreq && ge < alphaSize-1) {
            ge++;
            aFreq += s->mtfFreq[ge];
         }

         if (ge > gs 
             && nPart != nGroups && nPart != 1 
             && ((nGroups-nPart) % 2 == 1)) {
            aFreq -= s->mtfFreq[ge];
            ge--;
         }

         if (s->verbosity >= 3)
            VPrintf5( "      initial group %d, [%d .. %d], "
                      "has %d syms (%4.1f%%)\n",
                      nPart, gs, ge, aFreq, 
                      (100.0 * (float)aFreq) / (float)(s->nMTF) );
 
         for (v = 0; v < alphaSize; v++)
            if (v >= gs && v <= ge) 
               s->len[nPart-1][v] = BZ_LESSER_ICOST; else
               s->len[nPart-1][v] = BZ_GREATER_ICOST;
 
         nPart--;
         gs = ge+1;
         remF -= aFreq;
      }
   }

   /*--- 
      Iterate up to BZ_N_ITERS times to improve the tables.
   ---*/
   for (iter = 0; iter < BZ_N_ITERS; iter++) {

      for (t = 0; t < nGroups; t++) fave[t] = 0;

      for (t = 0; t < nGroups; t++)
         for (v = 0; v < alphaSize; v++)
            s->rfreq[t][v] = 0;

      /*---
        Set up an auxiliary length table which is used to fast-track
	the common case (nGroups == 6). 
      ---*/
      if (nGroups == 6) {
         for (v = 0; v < alphaSize; v++) {
            s->len_pack[v][0] = (s->len[1][v] << 16) | s->len[0][v];
            s->len_pack[v][1] = (s->len[3][v] << 16) | s->len[2][v];
            s->len_pack[v][2] = (s->len[5][v] << 16) | s->len[4][v];
	 }
      }

      nSelectors = 0;
      totc = 0;
      gs = 0;
      while (True) {

         /*--- Set group start & end marks. --*/
         if (gs >= s->nMTF) break;
         ge = gs + BZ_G_SIZE - 1; 
         if (ge >= s->nMTF) ge = s->nMTF-1;

         /*-- 
            Calculate the cost of this group as coded
            by each of the coding tables.
         --*/
         for (t = 0; t < nGroups; t++) cost[t] = 0;

         if (nGroups == 6 && 50 == ge-gs+1) {
            /*--- fast track the common case ---*/
            register UInt32 cost01, cost23, cost45;
            register UInt16 icv;
            cost01 = cost23 = cost45 = 0;

#           define BZ_ITER(nn)                \
               icv = mtfv[gs+(nn)];           \
               cost01 += s->len_pack[icv][0]; \
               cost23 += s->len_pack[icv][1]; \
               cost45 += s->len_pack[icv][2]; \

            BZ_ITER(0);  BZ_ITER(1);  BZ_ITER(2);  BZ_ITER(3);  BZ_ITER(4);
            BZ_ITER(5);  BZ_ITER(6);  BZ_ITER(7);  BZ_ITER(8);  BZ_ITER(9);
            BZ_ITER(10); BZ_ITER(11); BZ_ITER(12); BZ_ITER(13); BZ_ITER(14);
            BZ_ITER(15); BZ_ITER(16); BZ_ITER(17); BZ_ITER(18); BZ_ITER(19);
            BZ_ITER(20); BZ_ITER(21); BZ_ITER(22); BZ_ITER(23); BZ_ITER(24);
            BZ_ITER(25); BZ_ITER(26); BZ_ITER(27); BZ_ITER(28); BZ_ITER(29);
            BZ_ITER(30); BZ_ITER(31); BZ_ITER(32); BZ_ITER(33); BZ_ITER(34);
            BZ_ITER(35); BZ_ITER(36); BZ_ITER(37); BZ_ITER(38); BZ_ITER(39);
            BZ_ITER(40); BZ_ITER(41); BZ_ITER(42); BZ_ITER(43); BZ_ITER(44);
            BZ_ITER(45); BZ_ITER(46); BZ_ITER(47); BZ_ITER(48); BZ_ITER(49);

#           undef BZ_ITER

            cost[0] = cost01 & 0xffff; cost[1] = cost01 >> 16;
            cost[2] = cost23 & 0xffff; cost[3] = cost23 >> 16;
            cost[4] = cost45 & 0xffff; cost[5] = cost45 >> 16;

         } else {
	    /*--- slow version which correctly handles all situations ---*/
            for (i = gs; i <= ge; i++) { 
               UInt16 icv = mtfv[i];
               for (t = 0; t < nGroups; t++) cost[t] += s->len[t][icv];
            }
         }
 
         /*-- 
            Find the coding table which is best for this group,
            and record its identity in the selector table.
         --*/
         bc = 999999999; bt = -1;
         for (t = 0; t < nGroups; t++)
            if (cost[t] < bc) { bc = cost[t]; bt = t; };
         totc += bc;
         fave[bt]++;
         s->selector[nSelectors] = bt;
         nSelectors++;

         /*-- 
            Increment the symbol frequencies for the selected table.
          --*/
         if (nGroups == 6 && 50 == ge-gs+1) {
            /*--- fast track the common case ---*/

#           define BZ_ITUR(nn) s->rfreq[bt][ mtfv[gs+(nn)] ]++

            BZ_ITUR(0);  BZ_ITUR(1);  BZ_ITUR(2);  BZ_ITUR(3);  BZ_ITUR(4);
            BZ_ITUR(5);  BZ_ITUR(6);  BZ_ITUR(7);  BZ_ITUR(8);  BZ_ITUR(9);
            BZ_ITUR(10); BZ_ITUR(11); BZ_ITUR(12); BZ_ITUR(13); BZ_ITUR(14);
            BZ_ITUR(15); BZ_ITUR(16); BZ_ITUR(17); BZ_ITUR(18); BZ_ITUR(19);
            BZ_ITUR(20); BZ_ITUR(21); BZ_ITUR(22); BZ_ITUR(23); BZ_ITUR(24);
            BZ_ITUR(25); BZ_ITUR(26); BZ_ITUR(27); BZ_ITUR(28); BZ_ITUR(29);
            BZ_ITUR(30); BZ_ITUR(31); BZ_ITUR(32); BZ_ITUR(33); BZ_ITUR(34);
            BZ_ITUR(35); BZ_ITUR(36); BZ_ITUR(37); BZ_ITUR(38); BZ_ITUR(39);
            BZ_ITUR(40); BZ_ITUR(41); BZ_ITUR(42); BZ_ITUR(43); BZ_ITUR(44);
            BZ_ITUR(45); BZ_ITUR(46); BZ_ITUR(47); BZ_ITUR(48); BZ_ITUR(49);

#           undef BZ_ITUR

         } else {
	    /*--- slow version which correctly handles all situations ---*/
            for (i = gs; i <= ge; i++)
               s->rfreq[bt][ mtfv[i] ]++;
         }

         gs = ge+1;
      }
      if (s->verbosity >= 3) {
         VPrintf2 ( "      pass %d: size is %d, grp uses are ", 
                   iter+1, totc/8 );
         for (t = 0; t < nGroups; t++)
            VPrintf1 ( "%d ", fave[t] );
         VPrintf0 ( "\n" );
      }

      /*--
        Recompute the tables based on the accumulated frequencies.
      --*/
      /* maxLen was changed from 20 to 17 in bzip2-1.0.3.  See 
         comment in huffman.c for details. */
      for (t = 0; t < nGroups; t++)
         BZ2_hbMakeCodeLengths ( &(s->len[t][0]), &(s->rfreq[t][0]), 
                                 alphaSize, 17 /*20*/ );
   }


   AssertH( nGroups < 8, 3002 );
   AssertH( nSelectors < 32768 &&
            nSelectors <= (2 + (900000 / BZ_G_SIZE)),
            3003 );


   /*--- Compute MTF values for the selectors. ---*/
   {
      UChar pos[BZ_N_GROUPS], ll_i, tmp2, tmp;
      for (i = 0; i < nGroups; i++) pos[i] = i;
      for (i = 0; i < nSelectors; i++) {
         ll_i = s->selector[i];
         j = 0;
         tmp = pos[j];
         while ( ll_i != tmp ) {
            j++;
            tmp2 = tmp;
            tmp = pos[j];
            pos[j] = tmp2;
         };
         pos[0] = tmp;
         s->selectorMtf[i] = j;
      }
   };

   /*--- Assign actual codes for the tables. --*/
   for (t = 0; t < nGroups; t++) {
      minLen = 32;
      maxLen = 0;
      for (i = 0; i < alphaSize; i++) {
         if (s->len[t][i] > maxLen) maxLen = s->len[t][i];
         if (s->len[t][i] < minLen) minLen = s->len[t][i];
      }
      AssertH ( !(maxLen > 17 /*20*/ ), 3004 );
      AssertH ( !(minLen < 1),  3005 );
      BZ2_hbAssignCodes ( &(s->code[t][0]), &(s->len[t][0]), 
                          minLen, maxLen, alphaSize );
   }

   /*--- Transmit the mapping table. ---*/
   { 
      Bool inUse16[16];
      for (i = 0; i < 16; i++) {
          inUse16[i] = False;
          for (j = 0; j < 16; j++)
             if (s->inUse[i * 16 + j]) inUse16[i] = True;
      }
     
      nBytes = s->numZ;
      for (i = 0; i < 16; i++)
         if (inUse16[i]) bsW(s,1,1); else bsW(s,1,0);

      for (i = 0; i < 16; i++)
         if (inUse16[i])
            for (j = 0; j < 16; j++) {
               if (s->inUse[i * 16 + j]) bsW(s,1,1); else bsW(s,1,0);
            }

      if (s->verbosity >= 3) 
         VPrintf1( "      bytes: mapping %d, ", s->numZ-nBytes );
   }

   /*--- Now the selectors. ---*/
   nBytes = s->numZ;
   bsW ( s, 3, nGroups );
   bsW ( s, 15, nSelectors );
   for (i = 0; i < nSelectors; i++) { 
      for (j = 0; j < s->selectorMtf[i]; j++) bsW(s,1,1);
      bsW(s,1,0);
   }
   if (s->verbosity >= 3)
      VPrintf1( "selectors %d, ", s->numZ-nBytes );

   /*--- Now the coding tables. ---*/
   nBytes = s->numZ;

   for (t = 0; t < nGroups; t++) {
      Int32 curr = s->len[t][0];
      bsW ( s, 5, curr );
      for (i = 0; i < alphaSize; i++) {
         while (curr < s->len[t][i]) { bsW(s,2,2); curr++; /* 10 */ };
         while (curr > s->len[t][i]) { bsW(s,2,3); curr--; /* 11 */ };
         bsW ( s, 1, 0 );
      }
   }

   if (s->verbosity >= 3)
      VPrintf1 ( "code lengths %d, ", s->numZ-nBytes );

   /*--- And finally, the block data proper ---*/
   nBytes = s->numZ;
   selCtr = 0;
   gs = 0;
   while (True) {
      if (gs >= s->nMTF) break;
      ge = gs + BZ_G_SIZE - 1; 
      if (ge >= s->nMTF) ge = s->nMTF-1;
      AssertH ( s->selector[selCtr] < nGroups, 3006 );

      if (nGroups == 6 && 50 == ge-gs+1) {
            /*--- fast track the common case ---*/
            UInt16 mtfv_i;
            UChar* s_len_sel_selCtr 
               = &(s->len[s->selector[selCtr]][0]);
            Int32* s_code_sel_selCtr
               = &(s->code[s->selector[selCtr]][0]);

#           define BZ_ITAH(nn)                      \
               mtfv_i = mtfv[gs+(nn)];              \
               bsW ( s,                             \
                     s_len_sel_selCtr[mtfv_i],      \
                     s_code_sel_selCtr[mtfv_i] )

            BZ_ITAH(0);  BZ_ITAH(1);  BZ_ITAH(2);  BZ_ITAH(3);  BZ_ITAH(4);
            BZ_ITAH(5);  BZ_ITAH(6);  BZ_ITAH(7);  BZ_ITAH(8);  BZ_ITAH(9);
            BZ_ITAH(10); BZ_ITAH(11); BZ_ITAH(12); BZ_ITAH(13); BZ_ITAH(14);
            BZ_ITAH(15); BZ_ITAH(16); BZ_ITAH(17); BZ_ITAH(18); BZ_ITAH(19);
            BZ_ITAH(20); BZ_ITAH(21); BZ_ITAH(22); BZ_ITAH(23); BZ_ITAH(24);
            BZ_ITAH(25); BZ_ITAH(26); BZ_ITAH(27); BZ_ITAH(28); BZ_ITAH(29);
            BZ_ITAH(30); BZ_ITAH(31); BZ_ITAH(32); BZ_ITAH(33); BZ_ITAH(34);
            BZ_ITAH(35); BZ_ITAH(36); BZ_ITAH(37); BZ_ITAH(38); BZ_ITAH(39);
            BZ_ITAH(40); BZ_ITAH(41); BZ_ITAH(42); BZ_ITAH(43); BZ_ITAH(44);
            BZ_ITAH(45); BZ_ITAH(46); BZ_ITAH(47); BZ_ITAH(48); BZ_ITAH(49);

#           undef BZ_ITAH

      } else {
	 /*--- slow version which correctly handles all situations ---*/
         for (i = gs; i <= ge; i++) {
            bsW ( s, 
                  s->len  [s->selector[selCtr]] [mtfv[i]],
                  s->code [s->selector[selCtr]] [mtfv[i]] );
         }
      }


      gs = ge+1;
      selCtr++;
   }
   AssertH( selCtr == nSelectors, 3007 );

   if (s->verbosity >= 3)
      VPrintf1( "codes %d\n", s->numZ-nBytes );
}


/*---------------------------------------------------*/
void BZ2_compressBlock ( EState* s, Bool is_last_block )
{
   if (s->nblock > 0) {

      BZ_FINALISE_CRC ( s->blockCRC );
      s->combinedCRC = (s->combinedCRC << 1) | (s->combinedCRC >> 31);
      s->combinedCRC ^= s->blockCRC;
      if (s->blockNo > 1) s->numZ = 0;

      if (s->verbosity >= 2)
         VPrintf4( "    block %d: crc = 0x%08x, "
                   "combined CRC = 0x%08x, size = %d\n",
                   s->blockNo, s->blockCRC, s->combinedCRC, s->nblock );

      BZ2_blockSort ( s );
   }

   s->zbits = (UChar*) (&((UChar*)s->arr2)[s->nblock]);

   /*-- If this is the first block, create the stream header. --*/
   if (s->blockNo == 1) {
      BZ2_bsInitWrite ( s );
      bsPutUChar ( s, BZ_HDR_B );
      bsPutUChar ( s, BZ_HDR_Z );
      bsPutUChar ( s, BZ_HDR_h );
      bsPutUChar ( s, (UChar)(BZ_HDR_0 + s->blockSize100k) );
   }

   if (s->nblock > 0) {

      bsPutUChar ( s, 0x31 ); bsPutUChar ( s, 0x41 );
      bsPutUChar ( s, 0x59 ); bsPutUChar ( s, 0x26 );
      bsPutUChar ( s, 0x53 ); bsPutUChar ( s, 0x59 );

      /*-- Now the block's CRC, so it is in a known place. --*/
      bsPutUInt32 ( s, s->blockCRC );

      /*-- 
         Now a single bit indicating (non-)randomisation. 
         As of version 0.9.5, we use a better sorting algorithm
         which makes randomisation unnecessary.  So always set
         the randomised bit to 'no'.  Of course, the decoder
         still needs to be able to handle randomised blocks
         so as to maintain backwards compatibility with
         older versions of bzip2.
      --*/
      bsW(s,1,0);

      bsW ( s, 24, s->origPtr );
      generateMTFValues ( s );
      sendMTFValues ( s );
   }


   /*-- If this is the last block, add the stream trailer. --*/
   if (is_last_block) {

      bsPutUChar ( s, 0x17 ); bsPutUChar ( s, 0x72 );
      bsPutUChar ( s, 0x45 ); bsPutUChar ( s, 0x38 );
      bsPutUChar ( s, 0x50 ); bsPutUChar ( s, 0x90 );
      bsPutUInt32 ( s, s->combinedCRC );
      if (s->verbosity >= 2)
         VPrintf1( "    final combined CRC = 0x%08x\n   ", s->combinedCRC );
      bsFinishWrite ( s );
   }
}


/*-------------------------------------------------------------*/
/*--- end                                        compress.c ---*/
/*-------------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/crctable.c000066400000000000000000000113221211610345200220650ustar00rootroot00000000000000
/*-------------------------------------------------------------*/
/*--- Table for doing CRCs                                  ---*/
/*---                                            crctable.c ---*/
/*-------------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


#include "bzlib_private.h"

/*--
  I think this is an implementation of the AUTODIN-II,
  Ethernet & FDDI 32-bit CRC standard.  Vaguely derived
  from code by Rob Warnock, in Section 51 of the
  comp.compression FAQ.
--*/

UInt32 BZ2_crc32Table[256] = {

   /*-- Ugly, innit? --*/

   0x00000000L, 0x04c11db7L, 0x09823b6eL, 0x0d4326d9L,
   0x130476dcL, 0x17c56b6bL, 0x1a864db2L, 0x1e475005L,
   0x2608edb8L, 0x22c9f00fL, 0x2f8ad6d6L, 0x2b4bcb61L,
   0x350c9b64L, 0x31cd86d3L, 0x3c8ea00aL, 0x384fbdbdL,
   0x4c11db70L, 0x48d0c6c7L, 0x4593e01eL, 0x4152fda9L,
   0x5f15adacL, 0x5bd4b01bL, 0x569796c2L, 0x52568b75L,
   0x6a1936c8L, 0x6ed82b7fL, 0x639b0da6L, 0x675a1011L,
   0x791d4014L, 0x7ddc5da3L, 0x709f7b7aL, 0x745e66cdL,
   0x9823b6e0L, 0x9ce2ab57L, 0x91a18d8eL, 0x95609039L,
   0x8b27c03cL, 0x8fe6dd8bL, 0x82a5fb52L, 0x8664e6e5L,
   0xbe2b5b58L, 0xbaea46efL, 0xb7a96036L, 0xb3687d81L,
   0xad2f2d84L, 0xa9ee3033L, 0xa4ad16eaL, 0xa06c0b5dL,
   0xd4326d90L, 0xd0f37027L, 0xddb056feL, 0xd9714b49L,
   0xc7361b4cL, 0xc3f706fbL, 0xceb42022L, 0xca753d95L,
   0xf23a8028L, 0xf6fb9d9fL, 0xfbb8bb46L, 0xff79a6f1L,
   0xe13ef6f4L, 0xe5ffeb43L, 0xe8bccd9aL, 0xec7dd02dL,
   0x34867077L, 0x30476dc0L, 0x3d044b19L, 0x39c556aeL,
   0x278206abL, 0x23431b1cL, 0x2e003dc5L, 0x2ac12072L,
   0x128e9dcfL, 0x164f8078L, 0x1b0ca6a1L, 0x1fcdbb16L,
   0x018aeb13L, 0x054bf6a4L, 0x0808d07dL, 0x0cc9cdcaL,
   0x7897ab07L, 0x7c56b6b0L, 0x71159069L, 0x75d48ddeL,
   0x6b93dddbL, 0x6f52c06cL, 0x6211e6b5L, 0x66d0fb02L,
   0x5e9f46bfL, 0x5a5e5b08L, 0x571d7dd1L, 0x53dc6066L,
   0x4d9b3063L, 0x495a2dd4L, 0x44190b0dL, 0x40d816baL,
   0xaca5c697L, 0xa864db20L, 0xa527fdf9L, 0xa1e6e04eL,
   0xbfa1b04bL, 0xbb60adfcL, 0xb6238b25L, 0xb2e29692L,
   0x8aad2b2fL, 0x8e6c3698L, 0x832f1041L, 0x87ee0df6L,
   0x99a95df3L, 0x9d684044L, 0x902b669dL, 0x94ea7b2aL,
   0xe0b41de7L, 0xe4750050L, 0xe9362689L, 0xedf73b3eL,
   0xf3b06b3bL, 0xf771768cL, 0xfa325055L, 0xfef34de2L,
   0xc6bcf05fL, 0xc27dede8L, 0xcf3ecb31L, 0xcbffd686L,
   0xd5b88683L, 0xd1799b34L, 0xdc3abdedL, 0xd8fba05aL,
   0x690ce0eeL, 0x6dcdfd59L, 0x608edb80L, 0x644fc637L,
   0x7a089632L, 0x7ec98b85L, 0x738aad5cL, 0x774bb0ebL,
   0x4f040d56L, 0x4bc510e1L, 0x46863638L, 0x42472b8fL,
   0x5c007b8aL, 0x58c1663dL, 0x558240e4L, 0x51435d53L,
   0x251d3b9eL, 0x21dc2629L, 0x2c9f00f0L, 0x285e1d47L,
   0x36194d42L, 0x32d850f5L, 0x3f9b762cL, 0x3b5a6b9bL,
   0x0315d626L, 0x07d4cb91L, 0x0a97ed48L, 0x0e56f0ffL,
   0x1011a0faL, 0x14d0bd4dL, 0x19939b94L, 0x1d528623L,
   0xf12f560eL, 0xf5ee4bb9L, 0xf8ad6d60L, 0xfc6c70d7L,
   0xe22b20d2L, 0xe6ea3d65L, 0xeba91bbcL, 0xef68060bL,
   0xd727bbb6L, 0xd3e6a601L, 0xdea580d8L, 0xda649d6fL,
   0xc423cd6aL, 0xc0e2d0ddL, 0xcda1f604L, 0xc960ebb3L,
   0xbd3e8d7eL, 0xb9ff90c9L, 0xb4bcb610L, 0xb07daba7L,
   0xae3afba2L, 0xaafbe615L, 0xa7b8c0ccL, 0xa379dd7bL,
   0x9b3660c6L, 0x9ff77d71L, 0x92b45ba8L, 0x9675461fL,
   0x8832161aL, 0x8cf30badL, 0x81b02d74L, 0x857130c3L,
   0x5d8a9099L, 0x594b8d2eL, 0x5408abf7L, 0x50c9b640L,
   0x4e8ee645L, 0x4a4ffbf2L, 0x470cdd2bL, 0x43cdc09cL,
   0x7b827d21L, 0x7f436096L, 0x7200464fL, 0x76c15bf8L,
   0x68860bfdL, 0x6c47164aL, 0x61043093L, 0x65c52d24L,
   0x119b4be9L, 0x155a565eL, 0x18197087L, 0x1cd86d30L,
   0x029f3d35L, 0x065e2082L, 0x0b1d065bL, 0x0fdc1becL,
   0x3793a651L, 0x3352bbe6L, 0x3e119d3fL, 0x3ad08088L,
   0x2497d08dL, 0x2056cd3aL, 0x2d15ebe3L, 0x29d4f654L,
   0xc5a92679L, 0xc1683bceL, 0xcc2b1d17L, 0xc8ea00a0L,
   0xd6ad50a5L, 0xd26c4d12L, 0xdf2f6bcbL, 0xdbee767cL,
   0xe3a1cbc1L, 0xe760d676L, 0xea23f0afL, 0xeee2ed18L,
   0xf0a5bd1dL, 0xf464a0aaL, 0xf9278673L, 0xfde69bc4L,
   0x89b8fd09L, 0x8d79e0beL, 0x803ac667L, 0x84fbdbd0L,
   0x9abc8bd5L, 0x9e7d9662L, 0x933eb0bbL, 0x97ffad0cL,
   0xafb010b1L, 0xab710d06L, 0xa6322bdfL, 0xa2f33668L,
   0xbcb4666dL, 0xb8757bdaL, 0xb5365d03L, 0xb1f740b4L
};


/*-------------------------------------------------------------*/
/*--- end                                        crctable.c ---*/
/*-------------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/decompress.c000066400000000000000000000506671211610345200224710ustar00rootroot00000000000000
/*-------------------------------------------------------------*/
/*--- Decompression machinery                               ---*/
/*---                                          decompress.c ---*/
/*-------------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


#include "bzlib_private.h"


/*---------------------------------------------------*/
static
void makeMaps_d ( DState* s )
{
   Int32 i;
   s->nInUse = 0;
   for (i = 0; i < 256; i++)
      if (s->inUse[i]) {
         s->seqToUnseq[s->nInUse] = i;
         s->nInUse++;
      }
}


/*---------------------------------------------------*/
#define RETURN(rrr)                               \
   { retVal = rrr; goto save_state_and_return; };

#define GET_BITS(lll,vvv,nnn)                     \
   case lll: s->state = lll;                      \
   while (True) {                                 \
      if (s->bsLive >= nnn) {                     \
         UInt32 v;                                \
         v = (s->bsBuff >>                        \
             (s->bsLive-nnn)) & ((1 << nnn)-1);   \
         s->bsLive -= nnn;                        \
         vvv = v;                                 \
         break;                                   \
      }                                           \
      if (s->strm->avail_in == 0) RETURN(BZ_OK);  \
      s->bsBuff                                   \
         = (s->bsBuff << 8) |                     \
           ((UInt32)                              \
              (*((UChar*)(s->strm->next_in))));   \
      s->bsLive += 8;                             \
      s->strm->next_in++;                         \
      s->strm->avail_in--;                        \
      s->strm->total_in_lo32++;                   \
      if (s->strm->total_in_lo32 == 0)            \
         s->strm->total_in_hi32++;                \
   }

#define GET_UCHAR(lll,uuu)                        \
   GET_BITS(lll,uuu,8)

#define GET_BIT(lll,uuu)                          \
   GET_BITS(lll,uuu,1)

/*---------------------------------------------------*/
#define GET_MTF_VAL(label1,label2,lval)           \
{                                                 \
   if (groupPos == 0) {                           \
      groupNo++;                                  \
      if (groupNo >= nSelectors)                  \
         RETURN(BZ_DATA_ERROR);                   \
      groupPos = BZ_G_SIZE;                       \
      gSel = s->selector[groupNo];                \
      gMinlen = s->minLens[gSel];                 \
      gLimit = &(s->limit[gSel][0]);              \
      gPerm = &(s->perm[gSel][0]);                \
      gBase = &(s->base[gSel][0]);                \
   }                                              \
   groupPos--;                                    \
   zn = gMinlen;                                  \
   GET_BITS(label1, zvec, zn);                    \
   while (1) {                                    \
      if (zn > 20 /* the longest code */)         \
         RETURN(BZ_DATA_ERROR);                   \
      if (zvec <= gLimit[zn]) break;              \
      zn++;                                       \
      GET_BIT(label2, zj);                        \
      zvec = (zvec << 1) | zj;                    \
   };                                             \
   if (zvec - gBase[zn] < 0                       \
       || zvec - gBase[zn] >= BZ_MAX_ALPHA_SIZE)  \
      RETURN(BZ_DATA_ERROR);                      \
   lval = gPerm[zvec - gBase[zn]];                \
}


/*---------------------------------------------------*/
Int32 BZ2_decompress ( DState* s )
{
   UChar      uc;
   Int32      retVal;
   Int32      minLen, maxLen;
   bz_stream* strm = s->strm;

   /* stuff that needs to be saved/restored */
   Int32  i;
   Int32  j;
   Int32  t;
   Int32  alphaSize;
   Int32  nGroups;
   Int32  nSelectors;
   Int32  EOB;
   Int32  groupNo;
   Int32  groupPos;
   Int32  nextSym;
   Int32  nblockMAX;
   Int32  nblock;
   Int32  es;
   Int32  N;
   Int32  curr;
   Int32  zt;
   Int32  zn; 
   Int32  zvec;
   Int32  zj;
   Int32  gSel;
   Int32  gMinlen;
   Int32* gLimit;
   Int32* gBase;
   Int32* gPerm;

   if (s->state == BZ_X_MAGIC_1) {
      /*initialise the save area*/
      s->save_i           = 0;
      s->save_j           = 0;
      s->save_t           = 0;
      s->save_alphaSize   = 0;
      s->save_nGroups     = 0;
      s->save_nSelectors  = 0;
      s->save_EOB         = 0;
      s->save_groupNo     = 0;
      s->save_groupPos    = 0;
      s->save_nextSym     = 0;
      s->save_nblockMAX   = 0;
      s->save_nblock      = 0;
      s->save_es          = 0;
      s->save_N           = 0;
      s->save_curr        = 0;
      s->save_zt          = 0;
      s->save_zn          = 0;
      s->save_zvec        = 0;
      s->save_zj          = 0;
      s->save_gSel        = 0;
      s->save_gMinlen     = 0;
      s->save_gLimit      = NULL;
      s->save_gBase       = NULL;
      s->save_gPerm       = NULL;
   }

   /*restore from the save area*/
   i           = s->save_i;
   j           = s->save_j;
   t           = s->save_t;
   alphaSize   = s->save_alphaSize;
   nGroups     = s->save_nGroups;
   nSelectors  = s->save_nSelectors;
   EOB         = s->save_EOB;
   groupNo     = s->save_groupNo;
   groupPos    = s->save_groupPos;
   nextSym     = s->save_nextSym;
   nblockMAX   = s->save_nblockMAX;
   nblock      = s->save_nblock;
   es          = s->save_es;
   N           = s->save_N;
   curr        = s->save_curr;
   zt          = s->save_zt;
   zn          = s->save_zn; 
   zvec        = s->save_zvec;
   zj          = s->save_zj;
   gSel        = s->save_gSel;
   gMinlen     = s->save_gMinlen;
   gLimit      = s->save_gLimit;
   gBase       = s->save_gBase;
   gPerm       = s->save_gPerm;

   retVal = BZ_OK;

   switch (s->state) {

      GET_UCHAR(BZ_X_MAGIC_1, uc);
      if (uc != BZ_HDR_B) RETURN(BZ_DATA_ERROR_MAGIC);

      GET_UCHAR(BZ_X_MAGIC_2, uc);
      if (uc != BZ_HDR_Z) RETURN(BZ_DATA_ERROR_MAGIC);

      GET_UCHAR(BZ_X_MAGIC_3, uc)
      if (uc != BZ_HDR_h) RETURN(BZ_DATA_ERROR_MAGIC);

      GET_BITS(BZ_X_MAGIC_4, s->blockSize100k, 8)
      if (s->blockSize100k < (BZ_HDR_0 + 1) || 
          s->blockSize100k > (BZ_HDR_0 + 9)) RETURN(BZ_DATA_ERROR_MAGIC);
      s->blockSize100k -= BZ_HDR_0;

      if (s->smallDecompress) {
         s->ll16 = BZALLOC( s->blockSize100k * 100000 * sizeof(UInt16) );
         s->ll4  = BZALLOC( 
                      ((1 + s->blockSize100k * 100000) >> 1) * sizeof(UChar) 
                   );
         if (s->ll16 == NULL || s->ll4 == NULL) RETURN(BZ_MEM_ERROR);
      } else {
         s->tt  = BZALLOC( s->blockSize100k * 100000 * sizeof(Int32) );
         if (s->tt == NULL) RETURN(BZ_MEM_ERROR);
      }

      GET_UCHAR(BZ_X_BLKHDR_1, uc);

      if (uc == 0x17) goto endhdr_2;
      if (uc != 0x31) RETURN(BZ_DATA_ERROR);
      GET_UCHAR(BZ_X_BLKHDR_2, uc);
      if (uc != 0x41) RETURN(BZ_DATA_ERROR);
      GET_UCHAR(BZ_X_BLKHDR_3, uc);
      if (uc != 0x59) RETURN(BZ_DATA_ERROR);
      GET_UCHAR(BZ_X_BLKHDR_4, uc);
      if (uc != 0x26) RETURN(BZ_DATA_ERROR);
      GET_UCHAR(BZ_X_BLKHDR_5, uc);
      if (uc != 0x53) RETURN(BZ_DATA_ERROR);
      GET_UCHAR(BZ_X_BLKHDR_6, uc);
      if (uc != 0x59) RETURN(BZ_DATA_ERROR);

      s->currBlockNo++;
      if (s->verbosity >= 2)
         VPrintf1 ( "\n    [%d: huff+mtf ", s->currBlockNo );
 
      s->storedBlockCRC = 0;
      GET_UCHAR(BZ_X_BCRC_1, uc);
      s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
      GET_UCHAR(BZ_X_BCRC_2, uc);
      s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
      GET_UCHAR(BZ_X_BCRC_3, uc);
      s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);
      GET_UCHAR(BZ_X_BCRC_4, uc);
      s->storedBlockCRC = (s->storedBlockCRC << 8) | ((UInt32)uc);

      GET_BITS(BZ_X_RANDBIT, s->blockRandomised, 1);

      s->origPtr = 0;
      GET_UCHAR(BZ_X_ORIGPTR_1, uc);
      s->origPtr = (s->origPtr << 8) | ((Int32)uc);
      GET_UCHAR(BZ_X_ORIGPTR_2, uc);
      s->origPtr = (s->origPtr << 8) | ((Int32)uc);
      GET_UCHAR(BZ_X_ORIGPTR_3, uc);
      s->origPtr = (s->origPtr << 8) | ((Int32)uc);

      if (s->origPtr < 0)
         RETURN(BZ_DATA_ERROR);
      if (s->origPtr > 10 + 100000*s->blockSize100k) 
         RETURN(BZ_DATA_ERROR);

      /*--- Receive the mapping table ---*/
      for (i = 0; i < 16; i++) {
         GET_BIT(BZ_X_MAPPING_1, uc);
         if (uc == 1) 
            s->inUse16[i] = True; else 
            s->inUse16[i] = False;
      }

      for (i = 0; i < 256; i++) s->inUse[i] = False;

      for (i = 0; i < 16; i++)
         if (s->inUse16[i])
            for (j = 0; j < 16; j++) {
               GET_BIT(BZ_X_MAPPING_2, uc);
               if (uc == 1) s->inUse[i * 16 + j] = True;
            }
      makeMaps_d ( s );
      if (s->nInUse == 0) RETURN(BZ_DATA_ERROR);
      alphaSize = s->nInUse+2;

      /*--- Now the selectors ---*/
      GET_BITS(BZ_X_SELECTOR_1, nGroups, 3);
      if (nGroups < 2 || nGroups > 6) RETURN(BZ_DATA_ERROR);
      GET_BITS(BZ_X_SELECTOR_2, nSelectors, 15);
      if (nSelectors < 1) RETURN(BZ_DATA_ERROR);
      for (i = 0; i < nSelectors; i++) {
         j = 0;
         while (True) {
            GET_BIT(BZ_X_SELECTOR_3, uc);
            if (uc == 0) break;
            j++;
            if (j >= nGroups) RETURN(BZ_DATA_ERROR);
         }
         s->selectorMtf[i] = j;
      }

      /*--- Undo the MTF values for the selectors. ---*/
      {
         UChar pos[BZ_N_GROUPS], tmp, v;
         for (v = 0; v < nGroups; v++) pos[v] = v;
   
         for (i = 0; i < nSelectors; i++) {
            v = s->selectorMtf[i];
            tmp = pos[v];
            while (v > 0) { pos[v] = pos[v-1]; v--; }
            pos[0] = tmp;
            s->selector[i] = tmp;
         }
      }

      /*--- Now the coding tables ---*/
      for (t = 0; t < nGroups; t++) {
         GET_BITS(BZ_X_CODING_1, curr, 5);
         for (i = 0; i < alphaSize; i++) {
            while (True) {
               if (curr < 1 || curr > 20) RETURN(BZ_DATA_ERROR);
               GET_BIT(BZ_X_CODING_2, uc);
               if (uc == 0) break;
               GET_BIT(BZ_X_CODING_3, uc);
               if (uc == 0) curr++; else curr--;
            }
            s->len[t][i] = curr;
         }
      }

      /*--- Create the Huffman decoding tables ---*/
      for (t = 0; t < nGroups; t++) {
         minLen = 32;
         maxLen = 0;
         for (i = 0; i < alphaSize; i++) {
            if (s->len[t][i] > maxLen) maxLen = s->len[t][i];
            if (s->len[t][i] < minLen) minLen = s->len[t][i];
         }
         BZ2_hbCreateDecodeTables ( 
            &(s->limit[t][0]), 
            &(s->base[t][0]), 
            &(s->perm[t][0]), 
            &(s->len[t][0]),
            minLen, maxLen, alphaSize
         );
         s->minLens[t] = minLen;
      }

      /*--- Now the MTF values ---*/

      EOB      = s->nInUse+1;
      nblockMAX = 100000 * s->blockSize100k;
      groupNo  = -1;
      groupPos = 0;

      for (i = 0; i <= 255; i++) s->unzftab[i] = 0;

      /*-- MTF init --*/
      {
         Int32 ii, jj, kk;
         kk = MTFA_SIZE-1;
         for (ii = 256 / MTFL_SIZE - 1; ii >= 0; ii--) {
            for (jj = MTFL_SIZE-1; jj >= 0; jj--) {
               s->mtfa[kk] = (UChar)(ii * MTFL_SIZE + jj);
               kk--;
            }
            s->mtfbase[ii] = kk + 1;
         }
      }
      /*-- end MTF init --*/

      nblock = 0;
      GET_MTF_VAL(BZ_X_MTF_1, BZ_X_MTF_2, nextSym);

      while (True) {

         if (nextSym == EOB) break;

         if (nextSym == BZ_RUNA || nextSym == BZ_RUNB) {

            es = -1;
            N = 1;
            do {
               /* Check that N doesn't get too big, so that es doesn't
                  go negative.  The maximum value that can be
                  RUNA/RUNB encoded is equal to the block size (post
                  the initial RLE), viz, 900k, so bounding N at 2
                  million should guard against overflow without
                  rejecting any legitimate inputs. */
               if (N >= 2*1024*1024) RETURN(BZ_DATA_ERROR);
               if (nextSym == BZ_RUNA) es = es + (0+1) * N; else
               if (nextSym == BZ_RUNB) es = es + (1+1) * N;
               N = N * 2;
               GET_MTF_VAL(BZ_X_MTF_3, BZ_X_MTF_4, nextSym);
            }
               while (nextSym == BZ_RUNA || nextSym == BZ_RUNB);

            es++;
            uc = s->seqToUnseq[ s->mtfa[s->mtfbase[0]] ];
            s->unzftab[uc] += es;

            if (s->smallDecompress)
               while (es > 0) {
                  if (nblock >= nblockMAX) RETURN(BZ_DATA_ERROR);
                  s->ll16[nblock] = (UInt16)uc;
                  nblock++;
                  es--;
               }
            else
               while (es > 0) {
                  if (nblock >= nblockMAX) RETURN(BZ_DATA_ERROR);
                  s->tt[nblock] = (UInt32)uc;
                  nblock++;
                  es--;
               };

            continue;

         } else {

            if (nblock >= nblockMAX) RETURN(BZ_DATA_ERROR);

            /*-- uc = MTF ( nextSym-1 ) --*/
            {
               Int32 ii, jj, kk, pp, lno, off;
               UInt32 nn;
               nn = (UInt32)(nextSym - 1);

               if (nn < MTFL_SIZE) {
                  /* avoid general-case expense */
                  pp = s->mtfbase[0];
                  uc = s->mtfa[pp+nn];
                  while (nn > 3) {
                     Int32 z = pp+nn;
                     s->mtfa[(z)  ] = s->mtfa[(z)-1];
                     s->mtfa[(z)-1] = s->mtfa[(z)-2];
                     s->mtfa[(z)-2] = s->mtfa[(z)-3];
                     s->mtfa[(z)-3] = s->mtfa[(z)-4];
                     nn -= 4;
                  }
                  while (nn > 0) { 
                     s->mtfa[(pp+nn)] = s->mtfa[(pp+nn)-1]; nn--; 
                  };
                  s->mtfa[pp] = uc;
               } else { 
                  /* general case */
                  lno = nn / MTFL_SIZE;
                  off = nn % MTFL_SIZE;
                  pp = s->mtfbase[lno] + off;
                  uc = s->mtfa[pp];
                  while (pp > s->mtfbase[lno]) { 
                     s->mtfa[pp] = s->mtfa[pp-1]; pp--; 
                  };
                  s->mtfbase[lno]++;
                  while (lno > 0) {
                     s->mtfbase[lno]--;
                     s->mtfa[s->mtfbase[lno]] 
                        = s->mtfa[s->mtfbase[lno-1] + MTFL_SIZE - 1];
                     lno--;
                  }
                  s->mtfbase[0]--;
                  s->mtfa[s->mtfbase[0]] = uc;
                  if (s->mtfbase[0] == 0) {
                     kk = MTFA_SIZE-1;
                     for (ii = 256 / MTFL_SIZE-1; ii >= 0; ii--) {
                        for (jj = MTFL_SIZE-1; jj >= 0; jj--) {
                           s->mtfa[kk] = s->mtfa[s->mtfbase[ii] + jj];
                           kk--;
                        }
                        s->mtfbase[ii] = kk + 1;
                     }
                  }
               }
            }
            /*-- end uc = MTF ( nextSym-1 ) --*/

            s->unzftab[s->seqToUnseq[uc]]++;
            if (s->smallDecompress)
               s->ll16[nblock] = (UInt16)(s->seqToUnseq[uc]); else
               s->tt[nblock]   = (UInt32)(s->seqToUnseq[uc]);
            nblock++;

            GET_MTF_VAL(BZ_X_MTF_5, BZ_X_MTF_6, nextSym);
            continue;
         }
      }

      /* Now we know what nblock is, we can do a better sanity
         check on s->origPtr.
      */
      if (s->origPtr < 0 || s->origPtr >= nblock)
         RETURN(BZ_DATA_ERROR);

      /*-- Set up cftab to facilitate generation of T^(-1) --*/
      /* Check: unzftab entries in range. */
      for (i = 0; i <= 255; i++) {
         if (s->unzftab[i] < 0 || s->unzftab[i] > nblock)
            RETURN(BZ_DATA_ERROR);
      }
      /* Actually generate cftab. */
      s->cftab[0] = 0;
      for (i = 1; i <= 256; i++) s->cftab[i] = s->unzftab[i-1];
      for (i = 1; i <= 256; i++) s->cftab[i] += s->cftab[i-1];
      /* Check: cftab entries in range. */
      for (i = 0; i <= 256; i++) {
         if (s->cftab[i] < 0 || s->cftab[i] > nblock) {
            /* s->cftab[i] can legitimately be == nblock */
            RETURN(BZ_DATA_ERROR);
         }
      }
      /* Check: cftab entries non-descending. */
      for (i = 1; i <= 256; i++) {
         if (s->cftab[i-1] > s->cftab[i]) {
            RETURN(BZ_DATA_ERROR);
         }
      }

      s->state_out_len = 0;
      s->state_out_ch  = 0;
      BZ_INITIALISE_CRC ( s->calculatedBlockCRC );
      s->state = BZ_X_OUTPUT;
      if (s->verbosity >= 2) VPrintf0 ( "rt+rld" );

      if (s->smallDecompress) {

         /*-- Make a copy of cftab, used in generation of T --*/
         for (i = 0; i <= 256; i++) s->cftabCopy[i] = s->cftab[i];

         /*-- compute the T vector --*/
         for (i = 0; i < nblock; i++) {
            uc = (UChar)(s->ll16[i]);
            SET_LL(i, s->cftabCopy[uc]);
            s->cftabCopy[uc]++;
         }

         /*-- Compute T^(-1) by pointer reversal on T --*/
         i = s->origPtr;
         j = GET_LL(i);
         do {
            Int32 tmp = GET_LL(j);
            SET_LL(j, i);
            i = j;
            j = tmp;
         }
            while (i != s->origPtr);

         s->tPos = s->origPtr;
         s->nblock_used = 0;
         if (s->blockRandomised) {
            BZ_RAND_INIT_MASK;
            BZ_GET_SMALL(s->k0); s->nblock_used++;
            BZ_RAND_UPD_MASK; s->k0 ^= BZ_RAND_MASK; 
         } else {
            BZ_GET_SMALL(s->k0); s->nblock_used++;
         }

      } else {

         /*-- compute the T^(-1) vector --*/
         for (i = 0; i < nblock; i++) {
            uc = (UChar)(s->tt[i] & 0xff);
            s->tt[s->cftab[uc]] |= (i << 8);
            s->cftab[uc]++;
         }

         s->tPos = s->tt[s->origPtr] >> 8;
         s->nblock_used = 0;
         if (s->blockRandomised) {
            BZ_RAND_INIT_MASK;
            BZ_GET_FAST(s->k0); s->nblock_used++;
            BZ_RAND_UPD_MASK; s->k0 ^= BZ_RAND_MASK; 
         } else {
            BZ_GET_FAST(s->k0); s->nblock_used++;
         }

      }

      RETURN(BZ_OK);



    endhdr_2:

      GET_UCHAR(BZ_X_ENDHDR_2, uc);
      if (uc != 0x72) RETURN(BZ_DATA_ERROR);
      GET_UCHAR(BZ_X_ENDHDR_3, uc);
      if (uc != 0x45) RETURN(BZ_DATA_ERROR);
      GET_UCHAR(BZ_X_ENDHDR_4, uc);
      if (uc != 0x38) RETURN(BZ_DATA_ERROR);
      GET_UCHAR(BZ_X_ENDHDR_5, uc);
      if (uc != 0x50) RETURN(BZ_DATA_ERROR);
      GET_UCHAR(BZ_X_ENDHDR_6, uc);
      if (uc != 0x90) RETURN(BZ_DATA_ERROR);

      s->storedCombinedCRC = 0;
      GET_UCHAR(BZ_X_CCRC_1, uc);
      s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
      GET_UCHAR(BZ_X_CCRC_2, uc);
      s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
      GET_UCHAR(BZ_X_CCRC_3, uc);
      s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);
      GET_UCHAR(BZ_X_CCRC_4, uc);
      s->storedCombinedCRC = (s->storedCombinedCRC << 8) | ((UInt32)uc);

      s->state = BZ_X_IDLE;
      RETURN(BZ_STREAM_END);

      default: AssertH ( False, 4001 );
   }

   AssertH ( False, 4002 );

   save_state_and_return:

   s->save_i           = i;
   s->save_j           = j;
   s->save_t           = t;
   s->save_alphaSize   = alphaSize;
   s->save_nGroups     = nGroups;
   s->save_nSelectors  = nSelectors;
   s->save_EOB         = EOB;
   s->save_groupNo     = groupNo;
   s->save_groupPos    = groupPos;
   s->save_nextSym     = nextSym;
   s->save_nblockMAX   = nblockMAX;
   s->save_nblock      = nblock;
   s->save_es          = es;
   s->save_N           = N;
   s->save_curr        = curr;
   s->save_zt          = zt;
   s->save_zn          = zn;
   s->save_zvec        = zvec;
   s->save_zj          = zj;
   s->save_gSel        = gSel;
   s->save_gMinlen     = gMinlen;
   s->save_gLimit      = gLimit;
   s->save_gBase       = gBase;
   s->save_gPerm       = gPerm;

   return retVal;   
}


/*-------------------------------------------------------------*/
/*--- end                                      decompress.c ---*/
/*-------------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/dlltest.c000066400000000000000000000104621211610345200217650ustar00rootroot00000000000000/*
   minibz2
      libbz2.dll test program.
      by Yoshioka Tsuneo (tsuneo@rr.iij4u.or.jp)
      This file is Public Domain.  Welcome any email to me.

   usage: minibz2 [-d] [-{1,2,..9}] [[srcfilename] destfilename]
*/

#define BZ_IMPORT
#include 
#include 
#include "bzlib.h"
#ifdef _WIN32
#include 
#endif


#ifdef _WIN32

#define BZ2_LIBNAME "libbz2-1.0.2.DLL" 

#include 
static int BZ2DLLLoaded = 0;
static HINSTANCE BZ2DLLhLib;
int BZ2DLLLoadLibrary(void)
{
   HINSTANCE hLib;

   if(BZ2DLLLoaded==1){return 0;}
   hLib=LoadLibrary(BZ2_LIBNAME);
   if(hLib == NULL){
      fprintf(stderr,"Can't load %s\n",BZ2_LIBNAME);
      return -1;
   }
   BZ2_bzlibVersion=GetProcAddress(hLib,"BZ2_bzlibVersion");
   BZ2_bzopen=GetProcAddress(hLib,"BZ2_bzopen");
   BZ2_bzdopen=GetProcAddress(hLib,"BZ2_bzdopen");
   BZ2_bzread=GetProcAddress(hLib,"BZ2_bzread");
   BZ2_bzwrite=GetProcAddress(hLib,"BZ2_bzwrite");
   BZ2_bzflush=GetProcAddress(hLib,"BZ2_bzflush");
   BZ2_bzclose=GetProcAddress(hLib,"BZ2_bzclose");
   BZ2_bzerror=GetProcAddress(hLib,"BZ2_bzerror");

   if (!BZ2_bzlibVersion || !BZ2_bzopen || !BZ2_bzdopen
       || !BZ2_bzread || !BZ2_bzwrite || !BZ2_bzflush
       || !BZ2_bzclose || !BZ2_bzerror) {
      fprintf(stderr,"GetProcAddress failed.\n");
      return -1;
   }
   BZ2DLLLoaded=1;
   BZ2DLLhLib=hLib;
   return 0;

}
int BZ2DLLFreeLibrary(void)
{
   if(BZ2DLLLoaded==0){return 0;}
   FreeLibrary(BZ2DLLhLib);
   BZ2DLLLoaded=0;
}
#endif /* WIN32 */

void usage(void)
{
   puts("usage: minibz2 [-d] [-{1,2,..9}] [[srcfilename] destfilename]");
}

int main(int argc,char *argv[])
{
   int decompress = 0;
   int level = 9;
   char *fn_r = NULL;
   char *fn_w = NULL;

#ifdef _WIN32
   if(BZ2DLLLoadLibrary()<0){
      fprintf(stderr,"Loading of %s failed.  Giving up.\n", BZ2_LIBNAME);
      exit(1);
   }
   printf("Loading of %s succeeded.  Library version is %s.\n",
          BZ2_LIBNAME, BZ2_bzlibVersion() );
#endif
   while(++argv,--argc){
      if(**argv =='-' || **argv=='/'){
         char *p;

         for(p=*argv+1;*p;p++){
            if(*p=='d'){
               decompress = 1;
            }else if('1'<=*p && *p<='9'){
               level = *p - '0';
            }else{
               usage();
               exit(1);
            }
         }
      }else{
         break;
      }
   }
   if(argc>=1){
      fn_r = *argv;
      argc--;argv++;
   }else{
      fn_r = NULL;
   }
   if(argc>=1){
      fn_w = *argv;
      argc--;argv++;
   }else{
      fn_w = NULL;
   }
   {
      int len;
      char buff[0x1000];
      char mode[10];

      if(decompress){
         BZFILE *BZ2fp_r = NULL;
         FILE *fp_w = NULL;

         if(fn_w){
            if((fp_w = fopen(fn_w,"wb"))==NULL){
               printf("can't open [%s]\n",fn_w);
               perror("reason:");
               exit(1);
            }
         }else{
            fp_w = stdout;
         }
         if((fn_r == NULL && (BZ2fp_r = BZ2_bzdopen(fileno(stdin),"rb"))==NULL)
            || (fn_r != NULL && (BZ2fp_r = BZ2_bzopen(fn_r,"rb"))==NULL)){
            printf("can't bz2openstream\n");
            exit(1);
         }
         while((len=BZ2_bzread(BZ2fp_r,buff,0x1000))>0){
            fwrite(buff,1,len,fp_w);
         }
         BZ2_bzclose(BZ2fp_r);
         if(fp_w != stdout) fclose(fp_w);
      }else{
         BZFILE *BZ2fp_w = NULL;
         FILE *fp_r = NULL;

         if(fn_r){
            if((fp_r = fopen(fn_r,"rb"))==NULL){
               printf("can't open [%s]\n",fn_r);
               perror("reason:");
               exit(1);
            }
         }else{
            fp_r = stdin;
         }
         mode[0]='w';
         mode[1] = '0' + level;
         mode[2] = '\0';

         if((fn_w == NULL && (BZ2fp_w = BZ2_bzdopen(fileno(stdout),mode))==NULL)
            || (fn_w !=NULL && (BZ2fp_w = BZ2_bzopen(fn_w,mode))==NULL)){
            printf("can't bz2openstream\n");
            exit(1);
         }
         while((len=fread(buff,1,0x1000,fp_r))>0){
            BZ2_bzwrite(BZ2fp_w,buff,len);
         }
         BZ2_bzclose(BZ2fp_w);
         if(fp_r!=stdin)fclose(fp_r);
      }
   }
#ifdef _WIN32
   BZ2DLLFreeLibrary();
#endif
   return 0;
}
genometools-1.5.1/src/external/bzip2-1.0.6/dlltest.dsp000066400000000000000000000066741211610345200223430ustar00rootroot00000000000000# Microsoft Developer Studio Project File - Name="dlltest" - Package Owner=<4>
# Microsoft Developer Studio Generated Build File, Format Version 5.00
# ** ҏWȂł **

# TARGTYPE "Win32 (x86) Console Application" 0x0103

CFG=dlltest - Win32 Debug
!MESSAGE ͗LҲ̧قł͂܂B ۼުĂނ邽߂ɂ NMAKE gpĂB
!MESSAGE [Ҳ̧ق̴߰] ނgpĎsĂ
!MESSAGE 
!MESSAGE NMAKE /f "dlltest.mak".
!MESSAGE 
!MESSAGE NMAKE ̎sɍ\wł܂
!MESSAGE  ײݏϸۂ̐ݒ`܂B:
!MESSAGE 
!MESSAGE NMAKE /f "dlltest.mak" CFG="dlltest - Win32 Debug"
!MESSAGE 
!MESSAGE I”\ Ӱ:
!MESSAGE 
!MESSAGE "dlltest - Win32 Release" ("Win32 (x86) Console Application" p)
!MESSAGE "dlltest - Win32 Debug" ("Win32 (x86) Console Application" p)
!MESSAGE 

# Begin Project
# PROP Scc_ProjName ""
# PROP Scc_LocalPath ""
CPP=cl.exe
RSC=rc.exe

!IF  "$(CFG)" == "dlltest - Win32 Release"

# PROP BASE Use_MFC 0
# PROP BASE Use_Debug_Libraries 0
# PROP BASE Output_Dir "Release"
# PROP BASE Intermediate_Dir "Release"
# PROP BASE Target_Dir ""
# PROP Use_MFC 0
# PROP Use_Debug_Libraries 0
# PROP Output_Dir "Release"
# PROP Intermediate_Dir "Release"
# PROP Ignore_Export_Lib 0
# PROP Target_Dir ""
# ADD BASE CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
# ADD CPP /nologo /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
# ADD BASE RSC /l 0x411 /d "NDEBUG"
# ADD RSC /l 0x411 /d "NDEBUG"
BSC32=bscmake.exe
# ADD BASE BSC32 /nologo
# ADD BSC32 /nologo
LINK32=link.exe
# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386
# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /machine:I386 /out:"minibz2.exe"

!ELSEIF  "$(CFG)" == "dlltest - Win32 Debug"

# PROP BASE Use_MFC 0
# PROP BASE Use_Debug_Libraries 1
# PROP BASE Output_Dir "dlltest_"
# PROP BASE Intermediate_Dir "dlltest_"
# PROP BASE Target_Dir ""
# PROP Use_MFC 0
# PROP Use_Debug_Libraries 1
# PROP Output_Dir "dlltest_"
# PROP Intermediate_Dir "dlltest_"
# PROP Ignore_Export_Lib 0
# PROP Target_Dir ""
# ADD BASE CPP /nologo /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
# ADD CPP /nologo /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_CONSOLE" /D "_MBCS" /YX /FD /c
# ADD BASE RSC /l 0x411 /d "_DEBUG"
# ADD RSC /l 0x411 /d "_DEBUG"
BSC32=bscmake.exe
# ADD BASE BSC32 /nologo
# ADD BSC32 /nologo
LINK32=link.exe
# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /pdbtype:sept
# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:console /debug /machine:I386 /out:"minibz2.exe" /pdbtype:sept

!ENDIF 

# Begin Target

# Name "dlltest - Win32 Release"
# Name "dlltest - Win32 Debug"
# Begin Source File

SOURCE=.\bzlib.h
# End Source File
# Begin Source File

SOURCE=.\dlltest.c
# End Source File
# End Target
# End Project
genometools-1.5.1/src/external/bzip2-1.0.6/entities.xml000066400000000000000000000003601211610345200225100ustar00rootroot00000000000000








genometools-1.5.1/src/external/bzip2-1.0.6/format.pl000077500000000000000000000032311211610345200217720ustar00rootroot00000000000000#!/usr/bin/perl -w
#
# ------------------------------------------------------------------
# This file is part of bzip2/libbzip2, a program and library for
# lossless, block-sorting data compression.
#
# bzip2/libbzip2 version 1.0.6 of 6 September 2010
# Copyright (C) 1996-2010 Julian Seward 
#
# Please read the WARNING, DISCLAIMER and PATENTS sections in the 
# README file.
#
# This program is released under the terms of the license contained
# in the file LICENSE.
# ------------------------------------------------------------------
#
use strict;

# get command line values:
if ( $#ARGV !=1 ) {
    die "Usage:  $0 xml_infile xml_outfile\n";
}

my $infile = shift;
# check infile exists
die "Can't find file \"$infile\""
  unless -f $infile;
# check we can read infile
if (! -r $infile) {
    die "Can't read input $infile\n";
}
# check we can open infile
open( INFILE,"<$infile" ) or 
    die "Can't input $infile $!";

#my $outfile = 'fmt-manual.xml';
my $outfile = shift;
#print "Infile: $infile, Outfile: $outfile\n";
# check we can write to outfile
open( OUTFILE,">$outfile" ) or 
    die "Can't output $outfile $! for writing";

my ($prev, $curr, $str);
$prev = ''; $curr = '';
while (  ) {

		print OUTFILE $prev;
    $prev = $curr;
    $curr = $_;
    $str = '';

    if ( $prev =~ /$|$/ ) {
        chomp $prev;
        $curr = join( '', $prev, "|<\/screen>/ ) {
        chomp $prev;
        $curr = join( '', $prev, "]]>", $curr );
				$prev = '';
        next;
    }
}
print OUTFILE $curr;
close INFILE;
close OUTFILE;
exit;
genometools-1.5.1/src/external/bzip2-1.0.6/huffman.c000066400000000000000000000155171211610345200217440ustar00rootroot00000000000000
/*-------------------------------------------------------------*/
/*--- Huffman coding low-level stuff                        ---*/
/*---                                             huffman.c ---*/
/*-------------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


#include "bzlib_private.h"

/*---------------------------------------------------*/
#define WEIGHTOF(zz0)  ((zz0) & 0xffffff00)
#define DEPTHOF(zz1)   ((zz1) & 0x000000ff)
#define MYMAX(zz2,zz3) ((zz2) > (zz3) ? (zz2) : (zz3))

#define ADDWEIGHTS(zw1,zw2)                           \
   (WEIGHTOF(zw1)+WEIGHTOF(zw2)) |                    \
   (1 + MYMAX(DEPTHOF(zw1),DEPTHOF(zw2)))

#define UPHEAP(z)                                     \
{                                                     \
   Int32 zz, tmp;                                     \
   zz = z; tmp = heap[zz];                            \
   while (weight[tmp] < weight[heap[zz >> 1]]) {      \
      heap[zz] = heap[zz >> 1];                       \
      zz >>= 1;                                       \
   }                                                  \
   heap[zz] = tmp;                                    \
}

#define DOWNHEAP(z)                                   \
{                                                     \
   Int32 zz, yy, tmp;                                 \
   zz = z; tmp = heap[zz];                            \
   while (True) {                                     \
      yy = zz << 1;                                   \
      if (yy > nHeap) break;                          \
      if (yy < nHeap &&                               \
          weight[heap[yy+1]] < weight[heap[yy]])      \
         yy++;                                        \
      if (weight[tmp] < weight[heap[yy]]) break;      \
      heap[zz] = heap[yy];                            \
      zz = yy;                                        \
   }                                                  \
   heap[zz] = tmp;                                    \
}


/*---------------------------------------------------*/
void BZ2_hbMakeCodeLengths ( UChar *len, 
                             Int32 *freq,
                             Int32 alphaSize,
                             Int32 maxLen )
{
   /*--
      Nodes and heap entries run from 1.  Entry 0
      for both the heap and nodes is a sentinel.
   --*/
   Int32 nNodes, nHeap, n1, n2, i, j, k;
   Bool  tooLong;

   Int32 heap   [ BZ_MAX_ALPHA_SIZE + 2 ];
   Int32 weight [ BZ_MAX_ALPHA_SIZE * 2 ];
   Int32 parent [ BZ_MAX_ALPHA_SIZE * 2 ]; 

   for (i = 0; i < alphaSize; i++)
      weight[i+1] = (freq[i] == 0 ? 1 : freq[i]) << 8;

   while (True) {

      nNodes = alphaSize;
      nHeap = 0;

      heap[0] = 0;
      weight[0] = 0;
      parent[0] = -2;

      for (i = 1; i <= alphaSize; i++) {
         parent[i] = -1;
         nHeap++;
         heap[nHeap] = i;
         UPHEAP(nHeap);
      }

      AssertH( nHeap < (BZ_MAX_ALPHA_SIZE+2), 2001 );
   
      while (nHeap > 1) {
         n1 = heap[1]; heap[1] = heap[nHeap]; nHeap--; DOWNHEAP(1);
         n2 = heap[1]; heap[1] = heap[nHeap]; nHeap--; DOWNHEAP(1);
         nNodes++;
         parent[n1] = parent[n2] = nNodes;
         weight[nNodes] = ADDWEIGHTS(weight[n1], weight[n2]);
         parent[nNodes] = -1;
         nHeap++;
         heap[nHeap] = nNodes;
         UPHEAP(nHeap);
      }

      AssertH( nNodes < (BZ_MAX_ALPHA_SIZE * 2), 2002 );

      tooLong = False;
      for (i = 1; i <= alphaSize; i++) {
         j = 0;
         k = i;
         while (parent[k] >= 0) { k = parent[k]; j++; }
         len[i-1] = j;
         if (j > maxLen) tooLong = True;
      }
      
      if (! tooLong) break;

      /* 17 Oct 04: keep-going condition for the following loop used
         to be 'i < alphaSize', which missed the last element,
         theoretically leading to the possibility of the compressor
         looping.  However, this count-scaling step is only needed if
         one of the generated Huffman code words is longer than
         maxLen, which up to and including version 1.0.2 was 20 bits,
         which is extremely unlikely.  In version 1.0.3 maxLen was
         changed to 17 bits, which has minimal effect on compression
         ratio, but does mean this scaling step is used from time to
         time, enough to verify that it works.

         This means that bzip2-1.0.3 and later will only produce
         Huffman codes with a maximum length of 17 bits.  However, in
         order to preserve backwards compatibility with bitstreams
         produced by versions pre-1.0.3, the decompressor must still
         handle lengths of up to 20. */

      for (i = 1; i <= alphaSize; i++) {
         j = weight[i] >> 8;
         j = 1 + (j / 2);
         weight[i] = j << 8;
      }
   }
}


/*---------------------------------------------------*/
void BZ2_hbAssignCodes ( Int32 *code,
                         UChar *length,
                         Int32 minLen,
                         Int32 maxLen,
                         Int32 alphaSize )
{
   Int32 n, vec, i;

   vec = 0;
   for (n = minLen; n <= maxLen; n++) {
      for (i = 0; i < alphaSize; i++)
         if (length[i] == n) { code[i] = vec; vec++; };
      vec <<= 1;
   }
}


/*---------------------------------------------------*/
void BZ2_hbCreateDecodeTables ( Int32 *limit,
                                Int32 *base,
                                Int32 *perm,
                                UChar *length,
                                Int32 minLen,
                                Int32 maxLen,
                                Int32 alphaSize )
{
   Int32 pp, i, j, vec;

   pp = 0;
   for (i = minLen; i <= maxLen; i++)
      for (j = 0; j < alphaSize; j++)
         if (length[j] == i) { perm[pp] = j; pp++; };

   for (i = 0; i < BZ_MAX_CODE_LEN; i++) base[i] = 0;
   for (i = 0; i < alphaSize; i++) base[length[i]+1]++;

   for (i = 1; i < BZ_MAX_CODE_LEN; i++) base[i] += base[i-1];

   for (i = 0; i < BZ_MAX_CODE_LEN; i++) limit[i] = 0;
   vec = 0;

   for (i = minLen; i <= maxLen; i++) {
      vec += (base[i+1] - base[i]);
      limit[i] = vec-1;
      vec <<= 1;
   }
   for (i = minLen + 1; i <= maxLen; i++)
      base[i] = ((limit[i-1] + 1) << 1) - base[i];
}


/*-------------------------------------------------------------*/
/*--- end                                         huffman.c ---*/
/*-------------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/libbz2.def000066400000000000000000000010051211610345200220030ustar00rootroot00000000000000LIBRARY			LIBBZ2
DESCRIPTION		"libbzip2: library for data compression"
EXPORTS
	BZ2_bzCompressInit
	BZ2_bzCompress
	BZ2_bzCompressEnd
	BZ2_bzDecompressInit
	BZ2_bzDecompress
	BZ2_bzDecompressEnd
	BZ2_bzReadOpen
	BZ2_bzReadClose
	BZ2_bzReadGetUnused
	BZ2_bzRead
	BZ2_bzWriteOpen
	BZ2_bzWrite
	BZ2_bzWriteClose
	BZ2_bzWriteClose64
	BZ2_bzBuffToBuffCompress
	BZ2_bzBuffToBuffDecompress
	BZ2_bzlibVersion
	BZ2_bzopen
	BZ2_bzdopen
	BZ2_bzread
	BZ2_bzwrite
	BZ2_bzflush
	BZ2_bzclose
	BZ2_bzerror
genometools-1.5.1/src/external/bzip2-1.0.6/libbz2.dsp000066400000000000000000000102361211610345200220410ustar00rootroot00000000000000# Microsoft Developer Studio Project File - Name="libbz2" - Package Owner=<4>
# Microsoft Developer Studio Generated Build File, Format Version 5.00
# ** ҏWȂł **

# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102

CFG=libbz2 - Win32 Debug
!MESSAGE ͗LҲ̧قł͂܂B ۼުĂނ邽߂ɂ NMAKE gpĂB
!MESSAGE [Ҳ̧ق̴߰] ނgpĎsĂ
!MESSAGE 
!MESSAGE NMAKE /f "libbz2.mak".
!MESSAGE 
!MESSAGE NMAKE ̎sɍ\wł܂
!MESSAGE  ײݏϸۂ̐ݒ`܂B:
!MESSAGE 
!MESSAGE NMAKE /f "libbz2.mak" CFG="libbz2 - Win32 Debug"
!MESSAGE 
!MESSAGE I”\ Ӱ:
!MESSAGE 
!MESSAGE "libbz2 - Win32 Release" ("Win32 (x86) Dynamic-Link Library" p)
!MESSAGE "libbz2 - Win32 Debug" ("Win32 (x86) Dynamic-Link Library" p)
!MESSAGE 

# Begin Project
# PROP Scc_ProjName ""
# PROP Scc_LocalPath ""
CPP=cl.exe
MTL=midl.exe
RSC=rc.exe

!IF  "$(CFG)" == "libbz2 - Win32 Release"

# PROP BASE Use_MFC 0
# PROP BASE Use_Debug_Libraries 0
# PROP BASE Output_Dir "Release"
# PROP BASE Intermediate_Dir "Release"
# PROP BASE Target_Dir ""
# PROP Use_MFC 0
# PROP Use_Debug_Libraries 0
# PROP Output_Dir "Release"
# PROP Intermediate_Dir "Release"
# PROP Ignore_Export_Lib 0
# PROP Target_Dir ""
# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c
# ADD CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /YX /FD /c
# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /o NUL /win32
# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /o NUL /win32
# ADD BASE RSC /l 0x411 /d "NDEBUG"
# ADD RSC /l 0x411 /d "NDEBUG"
BSC32=bscmake.exe
# ADD BASE BSC32 /nologo
# ADD BSC32 /nologo
LINK32=link.exe
# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /machine:I386
# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /machine:I386 /out:"libbz2.dll"

!ELSEIF  "$(CFG)" == "libbz2 - Win32 Debug"

# PROP BASE Use_MFC 0
# PROP BASE Use_Debug_Libraries 1
# PROP BASE Output_Dir "Debug"
# PROP BASE Intermediate_Dir "Debug"
# PROP BASE Target_Dir ""
# PROP Use_MFC 0
# PROP Use_Debug_Libraries 1
# PROP Output_Dir "Debug"
# PROP Intermediate_Dir "Debug"
# PROP Ignore_Export_Lib 0
# PROP Target_Dir ""
# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /YX /FD /c
# ADD CPP /nologo /MTd /W3 /Gm /GX /Zi /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /YX /FD /c
# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /o NUL /win32
# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /o NUL /win32
# ADD BASE RSC /l 0x411 /d "_DEBUG"
# ADD RSC /l 0x411 /d "_DEBUG"
BSC32=bscmake.exe
# ADD BASE BSC32 /nologo
# ADD BSC32 /nologo
LINK32=link.exe
# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /debug /machine:I386 /pdbtype:sept
# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /subsystem:windows /dll /debug /machine:I386 /out:"libbz2.dll" /pdbtype:sept

!ENDIF 

# Begin Target

# Name "libbz2 - Win32 Release"
# Name "libbz2 - Win32 Debug"
# Begin Source File

SOURCE=.\blocksort.c
# End Source File
# Begin Source File

SOURCE=.\bzlib.c
# End Source File
# Begin Source File

SOURCE=.\bzlib.h
# End Source File
# Begin Source File

SOURCE=.\bzlib_private.h
# End Source File
# Begin Source File

SOURCE=.\compress.c
# End Source File
# Begin Source File

SOURCE=.\crctable.c
# End Source File
# Begin Source File

SOURCE=.\decompress.c
# End Source File
# Begin Source File

SOURCE=.\huffman.c
# End Source File
# Begin Source File

SOURCE=.\libbz2.def
# End Source File
# Begin Source File

SOURCE=.\randtable.c
# End Source File
# End Target
# End Project
genometools-1.5.1/src/external/bzip2-1.0.6/makefile.msc000066400000000000000000000031171211610345200224260ustar00rootroot00000000000000# Makefile for Microsoft Visual C++ 6.0
# usage: nmake -f makefile.msc
# K.M. Syring (syring@gsf.de)
# Fixed up by JRS for bzip2-0.9.5d release.

CC=cl
CFLAGS= -DWIN32 -MD -Ox -D_FILE_OFFSET_BITS=64 -nologo

OBJS= blocksort.obj  \
      huffman.obj    \
      crctable.obj   \
      randtable.obj  \
      compress.obj   \
      decompress.obj \
      bzlib.obj

all: lib bzip2 test

bzip2: lib
	$(CC) $(CFLAGS) -o bzip2 bzip2.c libbz2.lib setargv.obj
	$(CC) $(CFLAGS) -o bzip2recover bzip2recover.c

lib: $(OBJS)
	lib /out:libbz2.lib $(OBJS)

test: bzip2
	type words1
	.\\bzip2 -1  < sample1.ref > sample1.rb2
	.\\bzip2 -2  < sample2.ref > sample2.rb2
	.\\bzip2 -3  < sample3.ref > sample3.rb2
	.\\bzip2 -d  < sample1.bz2 > sample1.tst
	.\\bzip2 -d  < sample2.bz2 > sample2.tst
	.\\bzip2 -ds < sample3.bz2 > sample3.tst
	@echo All six of the fc's should find no differences.
	@echo If fc finds an error on sample3.bz2, this could be
	@echo because WinZip's 'TAR file smart CR/LF conversion'
	@echo is too clever for its own good.  Disable this option.
	@echo The correct size for sample3.ref is 120,244.  If it
	@echo is 150,251, WinZip has messed it up.
	fc sample1.bz2 sample1.rb2 
	fc sample2.bz2 sample2.rb2
	fc sample3.bz2 sample3.rb2
	fc sample1.tst sample1.ref
	fc sample2.tst sample2.ref
	fc sample3.tst sample3.ref



clean: 
	del *.obj
	del libbz2.lib 
	del bzip2.exe
	del bzip2recover.exe
	del sample1.rb2 
	del sample2.rb2 
	del sample3.rb2
	del sample1.tst 
	del sample2.tst
	del sample3.tst

.c.obj: 
	$(CC) $(CFLAGS) -c $*.c -o $*.obj

genometools-1.5.1/src/external/bzip2-1.0.6/mk251.c000066400000000000000000000016271211610345200211540ustar00rootroot00000000000000
/* Spew out a long sequence of the byte 251.  When fed to bzip2
   versions 1.0.0 or 1.0.1, causes it to die with internal error
   1007 in blocksort.c.  This assertion misses an extremely rare
   case, which is fixed in this version (1.0.2) and above.
*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


#include 

int main ()
{
   int i;
   for (i = 0; i < 48500000 ; i++)
     putchar(251);
   return 0;
}
genometools-1.5.1/src/external/bzip2-1.0.6/randtable.c000066400000000000000000000074241211610345200222520ustar00rootroot00000000000000
/*-------------------------------------------------------------*/
/*--- Table for randomising repetitive blocks               ---*/
/*---                                           randtable.c ---*/
/*-------------------------------------------------------------*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


#include "bzlib_private.h"


/*---------------------------------------------*/
Int32 BZ2_rNums[512] = { 
   619, 720, 127, 481, 931, 816, 813, 233, 566, 247, 
   985, 724, 205, 454, 863, 491, 741, 242, 949, 214, 
   733, 859, 335, 708, 621, 574, 73, 654, 730, 472, 
   419, 436, 278, 496, 867, 210, 399, 680, 480, 51, 
   878, 465, 811, 169, 869, 675, 611, 697, 867, 561, 
   862, 687, 507, 283, 482, 129, 807, 591, 733, 623, 
   150, 238, 59, 379, 684, 877, 625, 169, 643, 105, 
   170, 607, 520, 932, 727, 476, 693, 425, 174, 647, 
   73, 122, 335, 530, 442, 853, 695, 249, 445, 515, 
   909, 545, 703, 919, 874, 474, 882, 500, 594, 612, 
   641, 801, 220, 162, 819, 984, 589, 513, 495, 799, 
   161, 604, 958, 533, 221, 400, 386, 867, 600, 782, 
   382, 596, 414, 171, 516, 375, 682, 485, 911, 276, 
   98, 553, 163, 354, 666, 933, 424, 341, 533, 870, 
   227, 730, 475, 186, 263, 647, 537, 686, 600, 224, 
   469, 68, 770, 919, 190, 373, 294, 822, 808, 206, 
   184, 943, 795, 384, 383, 461, 404, 758, 839, 887, 
   715, 67, 618, 276, 204, 918, 873, 777, 604, 560, 
   951, 160, 578, 722, 79, 804, 96, 409, 713, 940, 
   652, 934, 970, 447, 318, 353, 859, 672, 112, 785, 
   645, 863, 803, 350, 139, 93, 354, 99, 820, 908, 
   609, 772, 154, 274, 580, 184, 79, 626, 630, 742, 
   653, 282, 762, 623, 680, 81, 927, 626, 789, 125, 
   411, 521, 938, 300, 821, 78, 343, 175, 128, 250, 
   170, 774, 972, 275, 999, 639, 495, 78, 352, 126, 
   857, 956, 358, 619, 580, 124, 737, 594, 701, 612, 
   669, 112, 134, 694, 363, 992, 809, 743, 168, 974, 
   944, 375, 748, 52, 600, 747, 642, 182, 862, 81, 
   344, 805, 988, 739, 511, 655, 814, 334, 249, 515, 
   897, 955, 664, 981, 649, 113, 974, 459, 893, 228, 
   433, 837, 553, 268, 926, 240, 102, 654, 459, 51, 
   686, 754, 806, 760, 493, 403, 415, 394, 687, 700, 
   946, 670, 656, 610, 738, 392, 760, 799, 887, 653, 
   978, 321, 576, 617, 626, 502, 894, 679, 243, 440, 
   680, 879, 194, 572, 640, 724, 926, 56, 204, 700, 
   707, 151, 457, 449, 797, 195, 791, 558, 945, 679, 
   297, 59, 87, 824, 713, 663, 412, 693, 342, 606, 
   134, 108, 571, 364, 631, 212, 174, 643, 304, 329, 
   343, 97, 430, 751, 497, 314, 983, 374, 822, 928, 
   140, 206, 73, 263, 980, 736, 876, 478, 430, 305, 
   170, 514, 364, 692, 829, 82, 855, 953, 676, 246, 
   369, 970, 294, 750, 807, 827, 150, 790, 288, 923, 
   804, 378, 215, 828, 592, 281, 565, 555, 710, 82, 
   896, 831, 547, 261, 524, 462, 293, 465, 502, 56, 
   661, 821, 976, 991, 658, 869, 905, 758, 745, 193, 
   768, 550, 608, 933, 378, 286, 215, 979, 792, 961, 
   61, 688, 793, 644, 986, 403, 106, 366, 905, 644, 
   372, 567, 466, 434, 645, 210, 389, 550, 919, 135, 
   780, 773, 635, 389, 707, 100, 626, 958, 165, 504, 
   920, 176, 193, 713, 857, 265, 203, 50, 668, 108, 
   645, 990, 626, 197, 510, 357, 358, 850, 858, 364, 
   936, 638
};


/*-------------------------------------------------------------*/
/*--- end                                       randtable.c ---*/
/*-------------------------------------------------------------*/
genometools-1.5.1/src/external/bzip2-1.0.6/spewG.c000066400000000000000000000033021211610345200213720ustar00rootroot00000000000000
/* spew out a thoroughly gigantic file designed so that bzip2
   can compress it reasonably rapidly.  This is to help test
   support for large files (> 2GB) in a reasonable amount of time.
   I suggest you use the undocumented --exponential option to
   bzip2 when compressing the resulting file; this saves a bit of
   time.  Note: *don't* bother with --exponential when compressing 
   Real Files; it'll just waste a lot of CPU time :-)
   (but is otherwise harmless).
*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
	 ------------------------------------------------------------------ */


#define _FILE_OFFSET_BITS 64

#include 
#include 

/* The number of megabytes of junk to spew out (roughly) */
#define MEGABYTES 5000

#define N_BUF 1000000
char buf[N_BUF];

int main ( int argc, char** argv )
{
   int ii, kk, p;
   srandom(1);
   setbuffer ( stdout, buf, N_BUF );
   for (kk = 0; kk < MEGABYTES * 515; kk+=3) {
      p = 25+random()%50;
      for (ii = 0; ii < p; ii++)
         printf ( "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" );
      for (ii = 0; ii < p-1; ii++)
         printf ( "bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb" );
      for (ii = 0; ii < p+1; ii++)
         printf ( "ccccccccccccccccccccccccccccccccccccc" );
   }
   fflush(stdout);
   return 0;
}
genometools-1.5.1/src/external/bzip2-1.0.6/unzcrash.c000066400000000000000000000071031211610345200221450ustar00rootroot00000000000000
/* A test program written to test robustness to decompression of
   corrupted data.  Usage is 
       unzcrash filename
   and the program will read the specified file, compress it (in memory),
   and then repeatedly decompress it, each time with a different bit of
   the compressed data inverted, so as to test all possible one-bit errors.
   This should not cause any invalid memory accesses.  If it does, 
   I want to know about it!

   PS.  As you can see from the above description, the process is
   incredibly slow.  A file of size eg 5KB will cause it to run for
   many hours.
*/

/* ------------------------------------------------------------------
   This file is part of bzip2/libbzip2, a program and library for
   lossless, block-sorting data compression.

   bzip2/libbzip2 version 1.0.6 of 6 September 2010
   Copyright (C) 1996-2010 Julian Seward 

   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
   README file.

   This program is released under the terms of the license contained
   in the file LICENSE.
   ------------------------------------------------------------------ */


#include 
#include 
#include "bzlib.h"

#define M_BLOCK 1000000

typedef unsigned char uchar;

#define M_BLOCK_OUT (M_BLOCK + 1000000)
uchar inbuf[M_BLOCK];
uchar outbuf[M_BLOCK_OUT];
uchar zbuf[M_BLOCK + 600 + (M_BLOCK / 100)];

int nIn, nOut, nZ;

static char *bzerrorstrings[] = {
       "OK"
      ,"SEQUENCE_ERROR"
      ,"PARAM_ERROR"
      ,"MEM_ERROR"
      ,"DATA_ERROR"
      ,"DATA_ERROR_MAGIC"
      ,"IO_ERROR"
      ,"UNEXPECTED_EOF"
      ,"OUTBUFF_FULL"
      ,"???"   /* for future */
      ,"???"   /* for future */
      ,"???"   /* for future */
      ,"???"   /* for future */
      ,"???"   /* for future */
      ,"???"   /* for future */
};

void flip_bit ( int bit )
{
   int byteno = bit / 8;
   int bitno  = bit % 8;
   uchar mask = 1 << bitno;
   //fprintf ( stderr, "(byte %d  bit %d  mask %d)",
   //          byteno, bitno, (int)mask );
   zbuf[byteno] ^= mask;
}

int main ( int argc, char** argv )
{
   FILE* f;
   int   r;
   int   bit;
   int   i;

   if (argc != 2) {
      fprintf ( stderr, "usage: unzcrash filename\n" );
      return 1;
   }

   f = fopen ( argv[1], "r" );
   if (!f) {
      fprintf ( stderr, "unzcrash: can't open %s\n", argv[1] );
      return 1;
   }

   nIn = fread ( inbuf, 1, M_BLOCK, f );
   fprintf ( stderr, "%d bytes read\n", nIn );

   nZ = M_BLOCK;
   r = BZ2_bzBuffToBuffCompress (
         zbuf, &nZ, inbuf, nIn, 9, 0, 30 );

   assert (r == BZ_OK);
   fprintf ( stderr, "%d after compression\n", nZ );

   for (bit = 0; bit < nZ*8; bit++) {
      fprintf ( stderr, "bit %d  ", bit );
      flip_bit ( bit );
      nOut = M_BLOCK_OUT;
      r = BZ2_bzBuffToBuffDecompress (
            outbuf, &nOut, zbuf, nZ, 0, 0 );
      fprintf ( stderr, " %d  %s ", r, bzerrorstrings[-r] );

      if (r != BZ_OK) {
         fprintf ( stderr, "\n" );
      } else {
         if (nOut != nIn) {
           fprintf(stderr, "nIn/nOut mismatch %d %d\n", nIn, nOut );
           return 1;
         } else {
           for (i = 0; i < nOut; i++)
             if (inbuf[i] != outbuf[i]) { 
                fprintf(stderr, "mismatch at %d\n", i ); 
                return 1; 
           }
           if (i == nOut) fprintf(stderr, "really ok!\n" );
         }
      }

      flip_bit ( bit );
   }

#if 0
   assert (nOut == nIn);
   for (i = 0; i < nOut; i++) {
     if (inbuf[i] != outbuf[i]) {
        fprintf ( stderr, "difference at %d !\n", i );
        return 1;
     }
   }
#endif

   fprintf ( stderr, "all ok\n" );
   return 0;
}
genometools-1.5.1/src/external/bzip2-1.0.6/words0000066400000000000000000000005701211610345200213060ustar00rootroot00000000000000
If compilation produces errors, or a large number of warnings,
please read README.COMPILATION.PROBLEMS -- you might be able to
adjust the flags in this Makefile to improve matters.

Also in README.COMPILATION.PROBLEMS are some hints that may help
if your build produces an executable which is unable to correctly
handle so-called 'large files' -- files of size 2GB or more.

genometools-1.5.1/src/external/bzip2-1.0.6/words1000066400000000000000000000001471211610345200213070ustar00rootroot00000000000000
Doing 6 tests (3 compress, 3 uncompress) ...
If there's a problem, things might stop at this point.
 
genometools-1.5.1/src/external/bzip2-1.0.6/words2000066400000000000000000000002721211610345200213070ustar00rootroot00000000000000
Checking test results.  If any of the four "cmp"s which follow
report any differences, something is wrong.  If you can't easily
figure out what, please let me know (jseward@bzip.org).

genometools-1.5.1/src/external/bzip2-1.0.6/words3000066400000000000000000000016611211610345200213130ustar00rootroot00000000000000
If you got this far and the 'cmp's didn't complain, it looks
like you're in business.  

To install in /usr/local/bin, /usr/local/lib, /usr/local/man and 
/usr/local/include, type

   make install

To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type 

   make install PREFIX=/xxx/yyy

If you are (justifiably) paranoid and want to see what 'make install'
is going to do, you can first do

   make -n install                      or
   make -n install PREFIX=/xxx/yyy      respectively.

The -n instructs make to show the commands it would execute, but
not actually execute them.

Instructions for use are in the preformatted manual page, in the file
bzip2.txt.  For more detailed documentation, read the full manual.  
It is available in Postscript form (manual.ps), PDF form (manual.pdf),
and HTML form (manual.html).

You can also do "bzip2 --help" to see some helpful information. 
"bzip2 -L" displays the software license.

genometools-1.5.1/src/external/bzip2-1.0.6/xmlproc.sh000077500000000000000000000055441211610345200221760ustar00rootroot00000000000000#!/bin/bash
# see the README file for usage etc.
#
# ------------------------------------------------------------------
#  This file is part of bzip2/libbzip2, a program and library for
#  lossless, block-sorting data compression.
#
#  bzip2/libbzip2 version 1.0.6 of 6 September 2010
#  Copyright (C) 1996-2010 Julian Seward 
#
#  Please read the WARNING, DISCLAIMER and PATENTS sections in the 
#  README file.
#
#  This program is released under the terms of the license contained
#  in the file LICENSE.
# ----------------------------------------------------------------


usage() {
  echo '';
  echo 'Usage: xmlproc.sh -[option] ';
  echo 'Specify a target from:';
  echo '-v      verify xml file conforms to dtd';
  echo '-html   output in html format (single file)';
  echo '-ps     output in postscript format';
  echo '-pdf    output in pdf format';
  exit;
}

if test $# -ne 2; then
  usage
fi
# assign the variable for the output type
action=$1; shift
# assign the output filename
xmlfile=$1; shift
# and check user input it correct
if !(test -f $xmlfile); then
  echo "No such file: $xmlfile";
  exit;
fi
# some other stuff we will use
OUT=output
xsl_fo=bz-fo.xsl
xsl_html=bz-html.xsl

basename=$xmlfile
basename=${basename//'.xml'/''}

fofile="${basename}.fo"
htmlfile="${basename}.html"
pdffile="${basename}.pdf"
psfile="${basename}.ps"
xmlfmtfile="${basename}.fmt"

# first process the xmlfile with CDATA tags
./format.pl $xmlfile $xmlfmtfile
# so the shell knows where the catalogs live
export XML_CATALOG_FILES=/etc/xml/catalog

# post-processing tidy up
cleanup() {
  echo "Cleaning up: $@" 
  while [ $# != 0 ]
  do
    arg=$1; shift;
    echo "  deleting $arg";
    rm $arg
  done
}

case $action in
  -v)
   flags='--noout --xinclude --noblanks --postvalid'
   dtd='--dtdvalid http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd'
   xmllint $flags $dtd $xmlfmtfile 2> $OUT 
   egrep 'error' $OUT 
   rm $OUT
  ;;

  -html)
   echo "Creating $htmlfile ..."
   xsltproc --nonet --xinclude  -o $htmlfile $xsl_html $xmlfmtfile
   cleanup $xmlfmtfile
  ;;

  -pdf)
   echo "Creating $pdffile ..."
   xsltproc --nonet --xinclude -o $fofile $xsl_fo $xmlfmtfile
   pdfxmltex $fofile >$OUT $OUT $OUT $OUT $OUT $OUT $OUT $OUT $OUT >BBDDBBHHJJMMLLPPTTQQWWYYZZ^^\\``bbggiijjoollqqvvttyy{{~~‰ÊŎƐǒȕʙ˙̟ϡϢѥҩөԭֱױصڻݼ,#	H*\ȰÇ#JHŋ3jȱǏ CIɓ(S\ɲ˗0%2Is"j.3RO% @s"QJH@FQ0ᣤ P`O QECeܐ
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/XwEk7r8BW*!0i9sa΄lulv$ W(
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ejq3:3Tā'-qwgS5!;6#t@4qrAC7@,	(:3W#P3W1F':<e&@P0x0`@P;i{PY8-+7W$
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GM 1@1Ep@{bl;RmdJ"M>"G@(	kSٵjl۶n;genometools-1.5.1/src/external/cgilua-5.1.3/doc/br/index.html000066400000000000000000000213321211610345200235310ustar00rootroot00000000000000


    CGILua: geração de scripts para a Web usando Lua
    
	





	


	
	
CGILua

	
Geração de scripts para a Web usando Lua


 



	
 






Visão geral


O CGILua é uma ferramenta que permite criar páginas Web dinâmicas e manipular a inserção de dados por meio de formulários Web. O CGILua permite separar o tratamento dos dados e a lógica do processo de geração de páginas, facilitando o desenvolvimento de aplicativos Web em Lua.

Uma das vantagens do CGILua é sua capacidade de abstrair o servidor Web utilizado. Você pode desenvolver um aplicativo em CGILua para um servidor Web e executá-lo em qualquer outro servidor Web compatível com CGILua. 



O CGILua é um software livre que usa a mesma licença da Lua 5.0.



Status


A versão atual é a 5.0.



Download



O download do CGILua pode ser feito em código fonte na sua página no LuaForge.




Histórico




    
Versão 5.0 [23 de julho de 2005]

    

    
    
        
  • A distribuição do CGILua passa a incluir apenas os arquivos Lua. Os disparadores foram movidos para o Kepler.
    • 
        
  • A biblioteca Stable passou a ser distribuída com VEnv.
    • 
        
  • Correção de um problema de upload de arquivo nos disparadores CGI e Xavante.
    • 
        
  • cgilua.lp.include() passa a aceitar um ambiente com o qual executa o arquivo preprocessado.
    • 
    

    

    
Versão 5.0 beta 2 [23 de dezembro de 2004]

    

    
    
      
  • Correção de problema de distribuição: stable.lua estava ausente
    • 
    

    

    
Versão 5.0 beta [15 de dezembro de 2004]

    

    
    
        
  • Novos disparadores ISAPI e Servlet.
    • 
        
  • Novos recursos de tratamento de erros.
    • 
        
  • Novo recurso de dados persistentes (Stable).
    • 
        
  • Uso do modelo de pacote de Lua 5.1.
    • 
        
  • API de usuário Session mais simples.
    • 
        
  • Correções de pequenos problemas
    • 
    

    

  
Versão 5.0 alfa 3 [8 de junho de 2004]

  

  
Versão 5.0 alfa [21 de abril de 2004]

  





Incompatibilidade com versões anteriores do CGILua (4.0 e 3.x)



    
    
  • O CGILua 5.0 usa o Lua 5.0.
    • 
    
  • A tabela cgi passou a permitir valores do tipo tabela. Consulte Recebimento de parâmetros para obter uma explicação detalhada.
    • 
    
  • As tags de templates foram alteradas. Consulte Lua Pages para obter uma explicação detalhada.
    • 
    
  • O uso de chamadas getenv para obter variáveis CGI deve ser substituído por chamadas cgilua.servervariable.
    • 




Créditos




    
CGILua 5.0

    
O CGILua 5.0 foi totalmente reelaborado por Roberto Ierusalimschy, André Carregal e Tomás Guisasola, como parte do Projeto Kepler. A implementação é compatível com a Lua 5.0 e foi codificada por Tomás Guisasola, com as valiosas contribuições de Ana Lúcia de Moura, Fábio Mascarenhas e Danilo Tuler. O desenvolvimento do CGILua 5.0 foi patrocinado pela Fábrica Digital, pela FINEP e pelo CNPq.

    
    
CGILua 4.0

    
Ana Lúcia de Moura adaptou o CGILua 3.2 para Lua 4.0, reimplementou alguns trechos do código e acrescentou alguns aperfeiçoamentos, mas essa versão não foi distribuída oficialmente.

    
    
CGILua 3.x

    
O CGILua surgiu como a evolução de um sistema originário desenvolvido por Renato Ferreira Borges e André Clínio no TeCGraf. Na época (circa 1995) não estavam disponíveis ferramentas em CGI e tudo era feito com scripts de shell!
 Porém, a principal contribuição ao CGILua 3 foi dada por Anna Hester, que consolidou toda a ferramenta e desenvolveu uma distribuição consistente com as versões 3.1 e 3.2 (o número foi um esforço para seguir os números de versão da Lua). Essa versão foi amplamente utilizada em uma grande variedade de sistemas.






Fale conosco


Para obter mais informações, entre em contato. Seus comentários são importantes!




 


 



	
XHTML 1.0 válido!

	
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genometools-1.5.1/src/external/cgilua-5.1.3/doc/br/libraries.html000066400000000000000000000205451211610345200244030ustar00rootroot00000000000000


    CGILua: geração de scripts para a Web usando Lua
    
	





	


	
	
CGILua

	
Geração de scripts para a Web usando Lua


 



	
 





Visão geral



O CGILua inclui um conjunto de bibliotecas externas que permite o tratamento de cookies, dados serializados e sessões. Para usar essas bibliotecas, basta usar a instrução require para solicitá-las no arquivo config.lua do CGILua.



Cookies




    
cgilua.cookies.get (name)

    
Obtém o valor do cookie com o name fornecido.
 Retorna uma string com o valor do cookie.

    
    
cgilua.cookies.set (name, value[, options])

    
Define o valor value do cookie com um name dado. Os nomes e valores de campos na tabela options são usados nos atributos do cookie. Esta função deve ser chamada antes do envio dos cabeçalhos HTTP e antes da geração de qualquer resultado.
 Não retorna nada.

    
    
cgilua.cookies.sethtml (name, value[, options])

    
Define o valor value do cookie com um name dado. Esta função gera um elemento HTML <meta>, assim, ela deve ser chamada depois de produzida a tag HTML <head> e antes da tag </head> correspondente.
 Não retorna nada.

    
    
cgilua.cookies.delete (name[, options])

    
Exclui um cookie com um name dado (define o valor como xxx).
 Não retorna nada.








Serialize




    
cgilua.serialize (table, outfunc[, indent[, prefix]])

    
Serializa uma table usando outfunc como a função usada para gerar o resultado; indent como uma string opcional com o padrão de identação; prefix como uma string opcional com o prefixo de identação (usado para armazenar o recuo real entre as chamadas recursivas).
 Observe que há algumas restrições: os valores dos tipos function e userdata não podem ser serializados; as tabelas que contêm ciclos também não podem ser serializadas.
 Não retorna nada.








Session




    
cgilua.session.close ()

    
Fecha a sessão de usuário. Salva todos os dados em cgilua.session.data no sistema de armazenamento em uso (normalmente, o sistema de arquivos). Esta função deve ser chamada depois que o script terminar de ser executado. Para garantir que isso ocorra, recomenda-se usar a addclosefunction no arquivo de configuração.
 Não retorna nada.

    
    
cgilua.session.data

    
Tabela que contém os dados sobre a sessão de usuário.

    
    
cgilua.session.delete (id)

    
Exclui uma sessão. O argumento id é o identificador da sessão.
 Não retorna nada.

    
    
cgilua.session.load (id)

    
Carrega dados de uma sessão. O argumento id é o identificador da sessão.
 Retorna uma tabela com os dados da sessão ou nil seguido de uma mensagem de erro.

    
    
cgilua.session.new ()

    
Cria um novo identificador de sessão.
 Retorna o novo identificador de sessão.

    
    
cgilua.session.open ()

    
Abre a sessão de usuário. Cria a tabela cgilua.session.data. Esta função deve ser chamada imediatamente antes da execução do script, mas após o processamento dos cabeçalhos da solicitação. Para garantir que isso ocorra, recomenda-se usar a addopenfunction no arquivo de configuração.
 Não retorna nada.

    
    
cgilua.session.save (id, data)

    
Salva data em uma sessão com um id.
 Não retorna nada.

    
    
cgilua.session.setsessiondir (path)

    
Define o diretório temporário da sessão. O argumento path é uma string com o novo diretório.
 Não retorna nada.





 


 



	
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    CGILua: geração de scripts para a Web usando Lua
    
	





	


	
	
CGILua

	
Geração de scripts para a Web usando Lua


 



	
 





Licença



O CGILua é um software livre: ele pode ser usado com fins acadêmicos e comerciais sem custo algum. Não há royalties ou restrições do tipo "copyleft" da GNU. O CGILua é classificado como um software Open Source (código aberto). Suas licenças são compatíveis com GPL. O CGILua não é de domínio público e o Kepler Project mantém o seu direito autoral. Os detalhes legais estão listados abaixo.



A idéia da licença é a de que você fique livre para usar o CGILua com qualquer objetivo sem incorrer em despesas e sem ter que pedir autorização para isso. Nossa única exigência é que, caso você realmente use o CGILua, então, o devido crédito seja dado por meio da inclusão do aviso de copyright apropriado em seu produto ou na documentação correspondente.



A biblioteca do CGILua foi desenvolvida e implementada por Roberto Ierusalimschy, André Carregal e Tomás Guisasola. A implementação não deriva de softwares licenciados.






Copyright © 2003-2005 The Kepler Project.



Por meio deste, concede-se permissão gratuita a qualquer pessoa que obtenha uma cópia deste software e dos arquivos da documentação associada (o "Software") para trabalhar com o Software sem restrições, incluindo, sem limitação, os direitos de usar, copiar, modificar, mesclar, publicar, distribuir, sublicenciar e/ou vender cópias do Software, e de permitir a pessoas a quem o Software seja fornecido de assim fazê-lo, sujeitando-se às seguintes condições:



O aviso de copyright acima e esta permissão devem ser incluídos em todas as cópias ou em partes significativas do Software.



O SOFTWARE É FORNECIDO "NO ESTADO EM QUE ESTIVER", SEM GARANTIAS DE QUALQUER TIPO, EXPLÍCITAS OU IMPLÍCITAS, INCLUINDO, SEM LIMITAÇÃO, AS GARANTIAS DE COMERCIALIZAÇÃO, ADEQUAÇÃO A UM DETERMINADO OBJETIVO E NÃO INFRAÇÃO. EM CIRCUNSTÂNCIA ALGUMA OS AUTORES OU OS DETENTORES DO COPYRIGHT SERÃO CONSIDERADOS RESPONSÁVEIS POR QUAISQUER REIVINDICAÇÕES, DANOS OU OUTRAS RESPONSABILIDADES, POR MEIO DE CONTRATO, DANOS OU OUTROS RELACIONADOS OU EM DECORRÊNCIA DO USO DO SOFTWARE OU OUTRAS AÇÕES NO MESMO.



 


 



	
XHTML 1.0 válido!

	
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    CGILua: geração de scripts para a Web usando Lua
    
	





	


	
	
CGILua

	
Geração de scripts para a Web usando Lua


 



	
 





Introdução



O CGILua usa Lua como a linguagem de scripts do servidor para criar páginas Web dinâmicas. O CGILua oferece suporte a Lua Scripts puros e a Lua Pages (.lp). Um Lua Script é, basicamente, um programa em Lua que cria todo o conteúdo de uma página Web e o retorna para o cliente. Uma Lua Page é um arquivo de texto com marcações (HTML, XML etc.) que incorpora código Lua usando algumas tags especiais. Essas tags são processadas pelo CGILua e a página resultante é retornada para o cliente.



Os Lua Scripts e as Lua Pages são igualmente fáceis de usar e a opção por um deles depende, primariamente, das características da página resultante. Enquanto as Lua Pages são mais convenientes para separar a lógica e o formato, os Lua Scripts são mais adequados para criar páginas de estrutura mais simples, mas que requeiram uma quantidade significativamente maior de processamento interno.



Ao permitir a combinação desses dois métodos, o CGILua dá aos desenvolvedores de aplicativos Web uma maior flexibilidade quando os dois requisitos estão presentes. Para obter uma descrição detalhada de ambos os métodos de criação de scripts e alguns exemplos práticos, consulte Lua Scripts e Lua Pages.



A arquitetura do CGILua é dividida em duas camadas. O nível inferior é representado pela API do servidor (SAPI) e o mais alto, pela API do próprio CGILua. SAPI é a interface entre o servidor Web e a API do CGILua, precisando portanto ser implementada em cada servidor Web e método de disparo empregado.



O CGILua e a API do CGILua são implementados usando-se apenas a SAPI e são totalmente transportáveis entre disparadores e os servidores Web compatíveis. Dessa maneira, qualquer Lua Script ou Lua Page pode ser usada por qualquer disparador.



Instalação



O CGILua segue o modelo de pacotes de Lua 5.1 e, conseqüentemente, precisa ser "instalado". Consulte a seção Configuração do Compat-5.1 para obter informações sobre como instalar corretamente o módulo.




Configuração



O CGILua 5.0 oferece um único arquivo de configuração, chamado config.lua, e um conjunto de funções para alterar a configuração padrão do CGILua. Esse arquivo pode ser colocado em qualquer lugar em LUA_PATH para facilitar a atualização do CGILua sem a substituição do config.lua existente.



Alguns usos do config.lua são:




    
Tratadores de scripts

    
Você pode adicionar novos tratadores de CGILua usando cgilua.addscripthandler (consulte também cgilua.buildplainhandler e cgilua.buildprocesshandler para obter as funções que criam tratadores simples).
    

    
Tamanhos de dados POST

    
Altere os limites de tamanho dos dados POST usando cgilua.setmaxinput e cgilua.setmaxfilesize.
    

    
Abertura e fechamento de funções

    
Você pode adicionar suas funções ao ciclo de vida útil do CGILua usando cgilua.addopenfunction e cgilua.addclosefunction. Essas funções são executadas imediatamente antes e depois da execução do script, mesmo quando ocorrer um erro no processamento do script.





Tratamento de erros



Há três funções para tratamento de erros no CGILua:



A função cgilua.seterrorhandler define o tratador de erro, uma função chamada pela Lua logo após ocorrer um erro. O tratador de erro tem acesso à pilha de execução antes da ocorrência do erro, assim, ele pode gerar uma mensagem de erro usando as informações da pilha. Lua também possui uma função para fazer isso: debug.traceback.



A função cgilua.seterroroutput define a função que decide o que deve ser feito com a mensagem de erro. Ele pode ser enviado para o cliente, gravado em um arquivo de log ou enviado para um endereço de email (com a ajuda do LuaSocket ou do LuaLogging, por exemplo).



A função cgilua.errorlog é fornecida para gravar diretamente no arquivo de log de erros do servidor HTTP.



Lua Scripts



Os Lua Scripts são arquivos de texto que contêm código Lua válido. Esse estilo de uso adota uma forma de programação para Web mais "rústica", na qual um programa é responsável pela geração da página resultante. Os Lua Scripts têm a extensão padrão .lua.



Para gerar um documento Web (HTML, XML, WML, CSS etc.) válido, o Lua Script deve obedecer a uma ordem esperada pelo HTTP para produzir a saída, primeiro enviando os cabeçalhos corretos e, depois, enviando o conteúdo real do documento.



O CGILua tem algumas funções que facilitam essas tarefas, por exemplo, cgilua.htmlheader para produzir o cabeçalho de um documento HTML e cgilua.put para enviar o conteúdo do documento (ou parte dele).



Por exemplo, um documento HTML que exiba a frase "Olá mundo!" pode ser gerado com este Lua Script:



cgilua.htmlheader()
cgilua.put([[
<html>
<head>
  <title>Olá mundo</title>
</head>
<body>
  <strong>Olá mundo!</strong>
</body>
</html>]])




Observe que o exemplo acima gera uma página "fixa": embora ela seja gerada no momento da execução, a página não contém informações "variáveis". Isso significa que o mesmo documento poderia ser gerado diretamente com um simples arquivo HTML estático. No entanto, os Lua Scripts são especialmente úteis quando o documento contém informações que não sejam conhecidas de antemão ou que mudem de acordo com os parâmetros passados. Nesse caso, é necessário gerar uma página "dinâmica".



Outro exemplo fácil pode ser mostrado, desta vez, usando uma estrutura de controle Lua, variáveis e o operador de concatenação:



cgilua.htmlheader()

if cgi.language == 'english' then
  greeting = 'Hello World!'
elseif cgi.language == 'portuguese' then
  greeting = 'Olá Mundo!'
else
  greeting = '[unknown language]'
end

cgilua.put('<html>')  
cgilua.put('<head>')
cgilua.put('  <title>'..greeting..'</title>')
cgilua.put('</head>')
cgilua.put('<body>')
cgilua.put('  <strong>'..greeting..'</strong>')
cgilua.put('</body>')
cgilua.put('</html>')




No exemplo acima, o uso de cgi.language indica que language foi passado para o Lua Script como um parâmetro do CGILua, oriundo de um campo de formulário HTML (via POST) ou da URL usada para ativá-lo (via GET). O CGILua decodifica automaticamente esses parâmetros para que você possa usá-los à vontade em Lua Scripts e Lua Pages.



Lua Pages



Uma Lua Page é um arquivo de modelo (template) com texto que será processado pelo CGILua antes de o servidor HTTP enviá-lo para o cliente. O CGILua não processa o texto, ele procura algumas marcações especiais que inserem o código Lua no arquivo. Depois que essas marcações são processadas e mescladas no arquivo de template, os resultados são enviados para o cliente.



As Lua Pages têm a extensão padrão .lp. Elas são uma maneira mais simples de criar uma página dinâmica porque eliminam a necessidade de enviar os cabeçalhos HTTP. Em geral, Lua Pages são páginas HTML, portanto, o CGILua envia automaticamente o cabeçalho HTML.



Como há algumas restrições quanto aos usos de cabeçalhos HTTP, ocasionalmente, será preciso usar um Lua Script em vez de uma Lua Page.



As marcações fundamentais de uma Lua Page são:




    
<?lua chunk ?>

    
Processa e mescla os resultados da execução do chunk Lua, no qual a marcação está localizada no template. A forma alternativa <% chunk %> também pode ser usada.

    
    
<?lua= expression ?>

    
Processa e mescla a avaliação de uma expression em Lua, na qual a marcação está localizada no template. A forma alternativa <%= expression %> também pode ser usada.





Observe que a marcação de término não pode estar dentro de um chunk de código ou uma expressão Lua, mesmo que esteja entre aspas. O pré-processador de Lua Pages apenas faz substituições globais no template, procurando um par correspondente de marcações e gerando o código Lua correspondente para obter o mesmo resultado que o Lua Script equivalente.
 


O segundo exemplo da seção anterior pode ser escrito usando uma Lua Page como esta:



<html>
<?lua
if cgi.language == 'english' then
  greeting = 'Hello World!'
elseif cgi.language == 'portuguese' then
  greeting = 'Olá Mundo!'
else
  greeting = '[unknown language]'
end
?>
<head>
  <title><%= greeting %></title>
</head>
<body>
  <>strong<%= greeting %></strong>
</body>
</html>




As tags HTML e as tags de Lua Page podem ser livremente intercambiadas. Porém, como ocorre em outras linguagens de template, considera-se uma boa prática não usar lógica Lua explícita em templates. A abordagem recomendada é usar apenas chamadas de funções que retornam chunks de conteúdo, dessa forma, nesse exemplo, pressupondo-se que a função getGreeting tenha sido definida em outro ponto como



function getGreeting()
  local greeting
  if cgi.language == 'english' then
    greeting = 'Hello World!'
  elseif cgi.language == 'portuguese' then
    greeting = 'Olá Mundo!'
  else
    greeting = '[unknown language]'
  end
  return greeting
end




a Lua Page poderia ser reescrita desta maneira:



<html>
<head>
  <title><%= getGreeting() %></title>
</head>
<body>
  <strong><%= getGreeting() %></strong>
</body>
</html>




Recebimento de parâmetros: a tabela cgi



O CGILua oferece uma maneira unificada de acessar dados passados para os scripts no método HTTP usado (GET ou POST). Independentemente do método usado no cliente, todos os parâmetros serão fornecidos dentro da tabela cgi.



Normalmente, todos os tipos de parâmetros estarão disponíveis como strings. Se o valor de um parâmetro for um número, ele será convertido na representação de string correspondente.



Há apenas duas exceções nas quais o valor será uma tabela Lua. O primeiro caso ocorre em uploads de arquivos, no qual a tabela correspondente terá estes campos:




    
filename

    
o nome do arquivo como fornecido pelo cliente.

    
    
filesize

    
o tamanho do arquivo em bytes.

    
    
file

    
o handler do arquivo temporário. O arquivo deve ser copiado porque o CGILua o removerá após a conclusão do script.





O outro caso que usa tabelas Lua ocorre quando há mais de um valor associado ao mesmo nome de parâmetro. Isso acontece no caso de uma lista de seleção com vários valores; mas também ocorre quando o formulário tiver dois ou mais elementos com o mesmo atributo name (possivelmente porque um estava em um formulário e o outro, na query string). Todos os valores serão inseridos em uma tabela indexada, na ordem em que foram tratados.



 


 



	
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genometools-1.5.1/src/external/cgilua-5.1.3/doc/br/reference.html000066400000000000000000000470421211610345200243660ustar00rootroot00000000000000


    CGILua: geração de scripts para a Web usando Lua
    
	





	


	
	
CGILua

	
Geração de scripts para a Web usando Lua


 



	
 






Cabeçalhos



As funções de cabeçalho são usadas para alterar os cabeçalhos de resposta HTTP e consistem em:




    
cgilua.contentheader (type, subtype)

    
Envia um cabeçalho Content-type com os valores dados de tipo e subtipo.
 Ambos os argumentos são strings: type é o tipo do cabeçalho; subtype é o subtipo do cabeçalho.
 Não retorna nada.

    
    
cgilua.header (header, value)

    
Envia um cabeçalho genérico. Esta função não deve ser usada para gerar um cabeçalho Content-type ou Location.
 Ambos os argumentos são strings: header é o nome do cabeçalho e value, seu valor.
 Não retorna nada.


    
cgilua.htmlheader ()

    
Envia o cabeçalho de um arquivo HTML (Content-type: text/html).
 Não retorna nada.

    
    
cgilua.redirect (url, args)

    
Envia o cabeçalho para forçar o redirecionamento para a URL dada, adicionando os parâmetros na tabela args relativos à nova URL.
 O primeiro argumento (url) é a URL à qual o navegador deve ser redirecionado; o segundo (args) é uma tabela opcional que pode conter pares nome = valor que serão codificados para formar um URL válido (consulte a função cgilua.urlcode.encodetable).
 Não retorna nada.






Geração de conteúdo



As funções de geração de conteúdo são usadas para produzir texto para a resposta e gerar URLs no formato do CGILua. Elas consistem em:




    
cgilua.mkabsoluteurl (path)

    
Cria uma URL absoluta contendo path da URL dada.
 Retorna a URL absoluta resultante.

    
    
cgilua.mkurlpath (script [, args])

    
Cria o caminho de uma URL a ser usado como link para um script CGILua usando a tabela opcional de argumentos (args). Os argumentos são usados na URL como parâmetros de string de consulta.
 Retorna a URL resultante.

    
    
cgilua.put (string)

    
Envia a string dada para o cliente.
 Não retorna nada.





Lua Pages



As funções de Lua Pages são usadas para processar templates Lua Pages e definir o comportamento desse processamento. Elas consistem em:




    
cgilua.handlelp (filename)

    
Equivale a cgilua.lp.include, mas envia o cabeçalho HTML antes do arquivo pré-processado.
 Não retorna nada.


    
cgilua.lp.include (filename)

    
Pré-processa um template Lua Page (fornecido por filename) e envia o resultado para o cliente.
 Não retorna nada.

    
    
cgilua.lp.setcompatmode (boolean)

    
Ativa e desativa o modo de compatibilidade. A ativação fará com que o pré-processador de Lua Pages entenda as estruturas de campos de expressão e campos de código usadas por versões anteriores do CGILua.
 Não retorna nada.

    
    
cgilua.lp.setoutfunc (funcname)

    
Define o nome da função de resultado de templates. O pré-processador Lua Pages gera chamadas para a função com o funcname fornecido (uma string).
 Não retorna nada.

    
    
cgilua.lp.translate (string)

    
Usa o pré-processador Lua Pages para gerar uma string correspondente ao código Lua que executa expressões e/ou chunks em Lua dentro da string fornecida.
 Retorna uma string com o código Lua resultante.






Variáveis do CGILua



As variáveis do CGILua oferecem informações sobre o script em processamento e as variáveis de ambiente do CGI. Elas consistem em atributos e funções:




    
cgilua.script_file

    
O nome do arquivo do script em execução. Obtido de cgilua.script_path.

    
    
cgilua.script_path

    
O caminho completo do arquivo do script em execução. Esta variável normalmente é igual à variável de ambiente do CGI PATH_TRANSLATED.

    
    
cgilua.script_pdir

    
O diretório do script em execução. Obtido de cgilua.script_path.

    
    
cgilua.script_vdir

    
O diretório virtual do script em execução. Obtido de cgilua.script_vpath.

    
    
cgilua.script_vpath

    
O caminho virtual completo do arquivo do script em execução. Equivale à variável de ambiente do CGI PATH_INFO.

    
    
cgilua.servervariable (varname)

    
Retorna uma string com o valor da variável de ambiente do CGI que corresponde a varname. Para obter uma lista das variáveis do CGI, consulte SAPI.Request.servervariable.

    
    
cgilua.urlpath

    
O nome do script. Equivale à variável de ambiente do CGI SCRIPT_NAME.





Tratamento de erros



As funções de tratamento de erros do CGILua permitem a redefinição de como os erros são tratados e apresentados ao usuário. Elas consistem em:




    
cgilua.errorlog (string)

    
Envia a string dada para o arquivo de log de erros.
 Não retorna nada.

    
    
cgilua.seterrorhandler (func)

    
Define a tratador de erros como func. Esta função é chamada pela Lua quando ocorre um erro. Ela recebe a mensagem de erro gerada pela Lua e é responsável por gerar e retornar o erro correto que deve ser usado pelo CGILua.
 Não retorna nada.

    
    
cgilua.seterroroutput (func)

    
Define a função responsável pela apresentação de erros como func. Esta função é chamada pela Lua para gerar o resultado do erro.
 Não retorna nada.





Comportamento do CGILua



O comportamento do CGILua pode ser configurado com o uso deste conjunto de funções:




    
cgilua.addclosefunction (func)

    
Define uma função (func) para ser chamada após a execução do CGILua.
 Não retorna nada.

    
    
cgilua.addopenfunction (func)

    
Define uma função (func) para ser chamada antes da execução do CGILua.
 Não retorna nada.


    
cgilua.addscripthandler (ext, func)

    
Define uma função (func) para pré-processar os arquivos com uma determinada extensão (ext). A configuração padrão usa cgilua.doscript para processar Lua Scripts (arquivos .lua) e cgilua.handlelp para processar Lua Pages (arquivos .lp).
 Não retorna nada.


    
cgilua.buildplainhandler (type, subtype)

    
Cria um tratador de scripts que envia o cabeçalho fornecido e o arquivo sem formatação solicitado. O cabeçalho Content-type é formado pelos dois argumentos; a função criada recebe um nome de arquivo como único argumento e retorna o nome de arquivo dado sem alterações.
 Retorna uma função.

    
    
cgilua.buildprocesshandler (type, subtype)

    
Cria um tratador de scripts que envia o cabeçalho fornecido e o arquivo processado solicitado. O cabeçalho Content-type é formado pelos dois argumentos; a função criada recebe um nome de arquivo como único argumento e retorna o nome de arquivo dado pré-processado pela função cgilua.lp.include.
 Retorna uma função.

    
    
cgilua.setlibdir (dir)

    
Define o diretório de bibliotecas padrão do CGILua. Esse valor é usado para criar o LUA_PATH usado pela função require (require é redefinida pelo CGILua).
 Não retorna nada.

    
    
cgilua.setmaxfilesize (size)

    
Define o tamanho máximo (em bytes) de cada arquivo cujo upload seja feito. Esse valor é limitado pelo tamanho máximo de entrada total (consulte cgilua.setmaxinput). Esta função só passa a vigorar se usada antes do processamento dos dados de POST, portanto, seu uso em scripts é irrelevante.
 Não retorna nada.

    
    
cgilua.setmaxinput (size)

    
Define o tamanho de entrada total máxima permitido (em bytes). Esta função só passa a vigorar se usada antes do processamento dos dados de POST, portanto, seu uso em scripts é irrelevante.
 Não retorna nada.





Funções de codificação de URL



As funções de codificação do CGILua permitem que o processamento de strings de URL seja feito de maneira simples:




    
cgilua.urlcode.encodetable (table)

    
Codifica em formato URL os elementos de uma tabela, criando uma string usada como URL para informar dados/parâmetros a outro script.
 Retorna uma string representando a tabela de argumentos codificada.

    
    
cgilua.urlcode.escape (string)

    
Codifica em formato URL uma string.
 Retorna a string codificada.

    
    
cgilua.urlcode.insertfield (args, name, value)

    
Adiciona o valor (value) fornecido ao campo indexado por um nome (nome) na tabela args. Se o campo já tiver um valor, será transformado em uma tabela com esse valor no índice 1 e o novo valor no índice 2. Outros valores serão acrescentados no final da parte array da tabela criada.
 Não retorna nada.

    
    
cgilua.urlcode.parsequery (query, args)

    
Analisa os dados codificados em formato URL do pedido. Isso pode ser a parte query da URL do script ou dos dados POST codificados em URL. Cada par nome = valor codificado é inserido na tabela args.
 Não retorna nada.

    
    
cgilua.urlcode.unescape (string)

    
Decodifica uma string que usa o formato URL.
 Retorna a string decodificada.





Funções auxiliares




    
cgilua.doscript (filepath)

    
Executa um arquivo (dado por filepath). Gera um erro se ocorrer. Em caso de êxito, retorna os valores retornados pela execução.

    
    
cgilua.pack (...)

    
Retorna uma nova tabela que armazena todos os argumentos passados.

    
    
cgilua.splitpath (path)

    
Retorna duas strings com as partes "diretório" e "arquivo" do path fornecido.





Índice alfabético


addclosefunction
 addopenfunction
 addscripthandler
 buildplainhandler
 buildprocesshandler
 contentheader
 doscript
 encodetable (urlcode)
 errorlog
 escape (urlcode)
 header
 htmlheader
 include (lp)
 insertfield (urlcode)
 mkabsoluteurl
 mkurlpath
 pack
 parsequery (urlcode)
 handlelp
 lp
 put
 redirect
 script_file
 script_path
 script_pdir
 script_vdir
 script_vpath
 servervariable
 setcompatmode (lp)
 seterrorhandler
 seterroroutput
 setlibdir
 setmaxfilesize
 setmaxinput
 setoutfunc (lp)
 splitpath
 urlcode
 unescape (urlcode)
 urlpath



 


 



	
XHTML 1.0 válido!

	
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genometools-1.5.1/src/external/cgilua-5.1.3/doc/br/sapi.html000066400000000000000000000260371211610345200233650ustar00rootroot00000000000000


    CGILua: geração de scripts para a Web usando Lua
    
	





	


	
	
CGILua

	
Geração de scripts para a Web usando Lua


 



	
 





API do servidor



A API do servidor (SAPI) é um conjunto de funções que abstrai o servidor Web e o disparador usado. Um disparador de SAPI é o mecanismo que permite a um servidor Web executar e comunicar-se com o CGILua e os aplicativos Web. A SAPI permite a abstração de uma série de detalhes internos, fazendo com que o CGILua seja muito mais portátil, já que transportar o CGILua para uma nova plataforma significa simplesmente escrever um disparador de SAPI para a plataforma de destino.



No momento, o CGILua oferece suporte a Apache, Microsoft IIS, Tomcat e Xavante como servidores Web, e a CGI, FastCGI, mod_lua, ISAPI e servlets como disparadores.



As funções são separadas em dois pacotes: SAPI.Request e SAPI.Response:




    
SAPI.Request.getpostdata ([n])

    
Obtém um bloco de dados de POST. O parâmetro opcional n é o número de bytes para ler (o tamanho de bloco padrão será usado se nenhum parâmetro for informado).
 Retorna o bloco como uma string Lua.

    
    
SAPI.Request.servervariable (string)

    
Obtém o valor de uma variável de ambiente do servidor. O argumento pode ser uma das variáveis CGI definidas, embora nem todos os servidores implementem o conjunto completo de variáveis. O conjunto consiste em:

    
    
        
  • AUTH_TYPE - se o servidor suportar autenticação de usuário e o script estiver protegido, este é o método de autenticação específico ao protocolo usado para validar o usuário.
    • 
        
        
  • CONTENT_LENGTH - o tamanho do conteúdo como fornecido pelo cliente.
    • 
        
        
  • CONTENT_TYPE - para consultas que têm informações anexadas, por exemplo, HTTP POST e PUT, este é o tipo de conteúdo dos dados.
    • 
        
        
  • GATEWAY_INTERFACE - a revisão da especificação CGI com a qual esse servidor é compatível. Formato: CGI/revisão
    • 
        
        
  • PATH_INFO - informações adicionais sobre o caminho, conforme fornecidas pelo cliente. Em outras palavras, os scripts podem ser acessados por meio dos respectivos nomes de caminho virtual, seguidos de informações adicionais no final desse caminho. As informações adicionais são enviadas como PATH_INFO. Essas informações devem ser decodificadas pelo servidor se vierem de uma URL antes de serem passadas para o script CGI.
    • 
        
        
  • PATH_TRANSLATED - o servidor fornece uma versão convertida de PATH_INFO, que realiza quaisquer mapeamentos de virtual para físico no caminho.
    • 
        
        
  • QUERY_STRING - as informações inseridas após o "?" na URL que fez referência a esse script. Essas são as informações da consulta e não devem ser decodificadas. Esta variável deve ser sempre definida quando houver informações da consulta, qualquer que seja a decodificação da linha de comando.
    • 
        
        
  • REMOTE_ADDR - o endereço IP do host remoto que faz o pedido.
    • 
        
        
  • REMOTE_HOST - o nome do host que faz o pedido. Se o servidor não tiver essas informações, ele define REMOTE_ADDR e não define esta variável.
    • 
        
        
  • REMOTE_IDENT - se o servidor HTTP oferecer suporte à identificação RFC 931, esta variável será definida com o nome do usuário remoto recuperado do servidor. O uso desta variável deve ser limitado apenas à conexão.
    • 
        
        
  • REMOTE_USER - se o servidor oferecer suporte à autenticação de usuário e o script estiver protegido, este é o nome de usuário com o qual eles foram autenticados.
    • 
        
        
  • REQUEST_METHOD - o método com o qual o pedido foi feito. Para HTTP, isto equivale a "GET", "HEAD", "POST" etc.
    • 
        
        
  • SCRIPT_NAME - um caminho virtual para o script em execução, usado em URLs auto-referentes.
    • 
        
        
  • SERVER_NAME - o nome do host do servidor, o alias do DNS ou o endereço IP como exibido em URLs auto-referentes.
    • 
        
        
  • SERVER_PORT - o número da porta à qual o pedido foi enviado.
    • 
        
        
  • SERVER_PROTOCOL - o nome e a revisão do protocolo de informações com o qual este pedido foi enviado. Formato: protocolo/revisão
    • 
        
        
  • SERVER_SOFTWARE - o nome e a versão do software do servidor Web que responde ao pedido (e executa o gateway). Formato: nome/versão
    • 
    

    Além desses, as linhas do cabeçalho recebidas do cliente, se houver, são colocadas no ambiente com o prefixo HTTP_ seguido do nome do cabeçalho. Quaisquer caracteres - (hífen) no nome do cabeçalho são alterados para caracteres _ (sublinhado). O servidor pode excluir quaisquer cabeçalhos que já tenha processado, por exemplo, Authorization, Content-type e Content-length. Se necessário, o servidor pode optar por excluir todos ou qualquer um desses cabeçalhos se a inclusão exceder algum limite do ambiente do sistema.

    Retorna uma string.


    
SAPI.Response.contenttype (string)

    
Envia o cabeçalho Content-type para o cliente. A string fornecida está na forma "tipo/subtipo". Esta função deve ser chamada antes que qualquer saída seja enviada com o uso de SAPI.Response.write.
 Não retorna nada.

    
    
SAPI.Response.errorlog (string)

    
Gera uma saída de erro usando a string fornecida.
 Não retorna nada.


    
SAPI.Response.header (header, value)

    
Envia um cabeçalho genérico para o cliente. O primeiro argumento deve ser o nome do cabeçalho, por exemplo, "Set-Cookie". O segundo deve ser o valor. Esta função não deve ser usada em substituição às funções SAPI.Response.contenttype ou SAPI.Response.redirect.
 Não retorna nada.


    
SAPI.Response.redirect (url)

    
Envia o cabeçalho Location para o cliente. A url fornecida deve ser uma string.
 Não retorna nada.

  
    
SAPI.Response.write (string)

    
Gera uma saída usando a string fornecida.
 Não retorna nada.





 


 



	
XHTML 1.0 válido!

	
$Id: sapi.html,v 1.3 2005/11/03 18:48:57 carregal Exp $


 


 


 
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    CGILua: Building Web Scripts with Lua
    
	





	


	
	
CGILua

	
Building Web Scripts with Lua


 



	
 






Overview


CGILua is a tool for creating dynamic Web pages and manipulating input data
from Web forms. CGILua allows the separation of logic and data handling from
the generation of pages, making it easy to develop web applications with Lua.





One of advantages of CGILua is its abstraction of the underlying Web server.
CGILua can be used with a variety of Web servers and, for each server, with
different launchers. A launcher is responsible for the interaction of CGILua
and the Web server, for example using ISAPI on IIS or mod_lua on Apache.
The reference implementation of CGILua launchers is
Kepler.





CGILua is free software and uses the same license
as Lua 5.1.




Status



Current version is 5.1.3



Download



CGILua source code can be downloaded from its
LuaForge page



You can also install CGILua using LuaRocks:



luarocks install cgilua


	

History




    
Version 5.1.2 [9/Mar/2009]

	
    
		
  • Strips utf-8 BOM from templates in lp.include
    • 
		
  • Fixed reentrancy bug
    • 
		
  • Fixed reset of cgilua.urlpath
    • 
	

	
    
Version 5.1.2 [19/May/2008]

	

	
    
        
  • Added the cgilua.authentication module
    • 
        
  • cgilua.print now separates arguments with tabs,
        like Lua print
    • 
        
  • Now print and write are aliases to cgilua.print
        and cgilua.put.
    • 
		
  • Now strips an eventual #! from top of Lua Pages files
    • 
		
  • CGILua can now process sequential requests in the same Lua state
    • 
        
  • Better error handling. Wraps error message in valid HTML
    • 
        
  • Bug fixed: CGILua was ignoring CGILUA_TMP in Windows
    • 
		
  • Corrected the URL handling for the dispatcher (bug found by Ronaldo Sugii)
    • 
		
  • Better URL handling for different locales
    • 
        
  • Handling multiple values in the generated URL (patch by Matt Campbell)
    • 
		
  • Fixed file handle leak in loader.lua
    • 
		
  • Fixed bug [#2630] - Including new files (bug found by Bruno Massa)
    • 
    

    

    
	
Version 5.1.1 [21/Nov/2007]

	

	
    
		
  • Changed the security policy for scripts. Now scripts have access to all Lua globals,
		including the debug and os packages. It is up to the application
		developer to choose what policy to use
    • 
        
  • If you are using Kepler, it is strongly suggested that you replace your previous CGILua config.lua
        file with the new one installed by Kepler and then merge the differences
    • 
        
  • Added the cgilua.dispatcher module
    • 
		
  • Added default handlers for a set of MIME types. The default handlers return
		only the content-type and conten-lenght headers for the files.
    • 
		
  • Added functions cgilua.splitonfirst and
		cgilua.splitonlast
    • 
		
  • Added functions cgilua.tmpfile and
		cgilua.tmpname
    • 
		
  • Changed the use of "/test" for the session temporary directory
		checking (bug found by Yuri Takhteyev)
    • 
		
  • Corrected the use of cgilua.QUERY in the session handling (bug found by Jim Madsen)
    • 
		
  • Better handling of "application/xml" POST content types (patch by Ignacio Burgueño)
    • 
		
  • Fixed
		Bug [#1910] -
		Bug in byte accounting in post.lua (found by Greg Bell)
    • 
	

	

	
    
Version 5.1.0 [23/Aug/2007]

    

    
    
        
  • Uses Lua 5.1
    • 
        
  • Added function cgilua.print (that uses
        tostring on its parameters)
    • 
        
  • Added a generic dispatcher and the concept of CGILua Apps
    • 
        
  • Replaced the cgi table used until CGILua 5.0 by two others
        cgilua.QUERY and cgilua.POST)
    • 
        
  • Added fake "package" table to enable the user/programmer
        to create modules with global visibility
    • 
        
  • Bug fix: return of HTTP status code
    • 
        
  • Bug fix: close method was recreating the session file
    • 
        
  • Correcting how LP handles strings with CR characters
        (Lua 5.0 would not mind, but Lua 5.1 does)
    • 
        
  • Fixed a bug with lighttpd
    • 
    

    


    
Version 5.0.1 [20/Sep/2006]

    

    
    
        
  • Uses Compat-5.1 Release 5.
    • 
        
  • Caches Lua Pages template strings.
    • 
        
  • New configuration examples.
    • 
        
  • Improvements in the Session library.
    • 
        
  • Removed the debug package from the user scripts environment.
    • 
        
  • POST handling bug fixes (related to the text/plain content type).
    • 
    

    



    
Version 5.0 [23/Jul/2005]

    

    
    
        
  • CGILua distribution includes now only the Lua files, the launchers
        have been moved to Kepler.
    • 
        
  • The Stable
        library is now distributed with VEnv.
    • 
        
  • Fixed a file upload bug in the CGI and Xavante launchers.
    • 
        
  • cgilua.lp.include() now accepts an environment to run
        the preprocessed file in it.
    • 
    

    

    
    
Version 5.0 beta 2 [23/Dec/2004]

    

    
    
      
  • Distribution bug fix: stable.lua was missing
    • 
    

    

    
    
Version 5.0 beta [15/Dec/2004]

    

    
    
        
  • New ISAPI and Servlet Launchers.
    • 
        
  • New Error Handling features.
    • 
        
  • New persistent data feature (Stable).
    • 
        
  • Uses the package model
        for Lua 5.1.
    • 
        
  • Simpler User Session API.
    • 
        
  • Small bug corrections
    • 
    

    

    
    
Version 5.0 alpha 3 [8/Jun/2004]

    


    
Version 5.0 alpha [21/Apr/2004]

    





Incompatibility with previous CGILua versions (5.0, 4.0 and 3.x)



    
    
  • CGILua 5.1 uses Lua 5.1.
    • 
    
  • The cgi table is now deprecated. See
    Receiving parameters for a more
    detailed explanation.
    • 
    
  • The template tags have changed. See
    Lua pages for a more detailed
    explanation.
    • 
    
  • The use of getenv calls to obtain CGI variables
    should be replaced by
    cgilua.servervariable
    calls.
    • 




Credits




    
CGILua 5.1

    

    CGILua 5.1 is being maintained by André Carregal and
    Tomás Guisasola with contributions from Fábio Mascarenhas
    and others from the Kepler mailing list.
    

    
    
CGILua 5.0

    
CGILua 5.0 was completely redesigned by Roberto Ierusalimschy,
    André Carregal and Tomás Guisasola as part of the
    Kepler Project.
    The implementation is compatible with Lua 5.0 and was coded by
    Tomás Guisasola with invaluable contributions by Ana
    Lúcia de Moura, Fábio Mascarenhas and Danilo Tuler.
    CGILua 5.0 development was sponsored by
    Fábrica Digital,
    FINEP and
    CNPq.

    
    
CGILua 4.0

    
Ana Lúcia de Moura adapted CGILua 3.2 to Lua 4.0,
    reimplemented some code and added a few improvements but this
    version was not officially distributed.

    
    
CGILua 3.x

    
CGILua was born as the evolution of an early system developed by
    Renato Ferreira Borges and André Clínio at
    TeCGraf.
    At the time (circa 1995) there were no CGI tools available and everything
    was done with shell scripts!

    However, the main contribution to CGILua 3 was done by Anna Hester, who
    consolidated the whole tool and developed a consistent distribution
    with versions 3.1 and 3.2 (the number was an effort to follow
    Lua version numbers). This version was widely used on a great
    variety of systems.






Contact us




For more information please
contact us.
Comments are welcome!





You can also reach other CGILua developers and users on the Kepler
Project mailing list.




 


 



	
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CGILua

	
Building Web Scripts with Lua


 



	
 





Overview



CGILua includes a set of external libraries that allows the handling
of authentication, cookies, dispatching, serialized data and sessions.
To use these libraries just require them in your CGILua config.lua or script file.



Authentication




    
cgilua.authentication.check (username, passwd)

    
Checks if the pair username/passwd is authenticated by the configured method.

    Returns true if succesfull or nil plus an error message if not.


    
cgilua.authentication.checkURL ()

    
Returns the URL for the checking script. The checking script receives the current URL
    as the ref parameter. It is up to the checking script to ask for user credentials,
    check if the user has the expected credentials
    (using cgilua.authentication.check (username, passwd)
    if implementing the checking script using CGILua), and redirect to the original URL
    (using the ref parameter or
    cgilua.authentication.refURL() if implementing the checking script using CGILua).


    
cgilua.authentication.configure (options, methods)

    
Configures the authentication framework (see /examples/authentication_conf.lua in CVS for more
    information).

    
    
cgilua.authentication.logoutURL ()

    
Returns the URL for the logout script.


    
cgilua.authentication.refURL ()

    
Returns the URL for the page that orignally required authentication. Used in checking scripts
    that use CGILua. Other checking scripts can use the ref parameter.


    
cgilua.authentication.username ()

    
Returns the authenticated user or nil if no user is currently authenticated.





Cookies




    
cgilua.cookies.get (name)

    
Gets the value of the cookie with the given name.

    Returns a string with the value of the cookie.

    
    
cgilua.cookies.set (name, value[, options])

    
Sets the value of the cookie with a given name.
    The optional table options is used togive the values of
    the cookies attributes: expires, path, domain, secure. This function
    should be called before the HTTP headers are sent and before any output
    is generated, so it must not be used inside a Lua Page.

    This function sends a cookie with the response. If you need to create
    a cookie inside the generated response or if the cookie needs to be set
    inside the client, use cgilua.cookies.sethtml instead.

    Returns nothing.

    
    
cgilua.cookies.sethtml (name, value[, options])

    
Sets the value of the cookie with a given name.
    The optional table options is used to give the values of
    the cookies attributes: expires, path, domain, secure.

    This function generates a <meta> HTML element so it
    should be called after the <head> HTML tag and before
    the corresponding </head>.

    This function creates a cookie in the client, if you need to send the cookie
    with the response use cgilua.cookies.set instead.

    Returns nothing.

    
    
cgilua.cookies.delete (name[, options])

    
Deletes a cookie with a given name (setting its value
    to xxx).
    This function should be called
    before the HTTP headers are sent and before any output is generated.

    Returns nothing.








Dispatcher




    
cgilua.dispatch.route (urlmaps)

    
Defines the routing using a table of URLs maps or a single map.
    A map defines a URL mask using $name patterns to extract parameters,
    a function to be called with the extracted parameters and a name for the map when used
    with cgilua.dispatch.route_url.
    

    
    
cgilua.dispatch.route_url (mapname, parameters, query)

    
Returns an URL for a named route map.
    mapname defines the name associated with
    the map in the original routed URL table sent to cgilua.dispatch.route.
    params defines a table of named parameters used to fill the URL pattern.
    query defines an optional table of named parameters used for the QUERY part of the URL.
    








Serialize




    
cgilua.serialize (table, outfunc[, indent[, prefix]])

    
Serializes a table using outfunc as the function
    to be used to generate the output; indent as an optional string
    with the indentation pattern; prefix as an optional string with
    the indentation prefix (it is used to store the actual indentation between the
    recursion calls).

    Some restrictions must be noted: values of types function and
    userdata are not serialized; tables with cycles are not serialized.

    Returns nothing.








Session




    
cgilua.session.close ()

    
Closes the user session. Saves all data in cgilua.session.data
    to the storage system being used (usually the filesystem). This function
    should be called after the end of the script execution. A recommended way
    to ensure that is to use
    addclosefunction
    in the configuration file.

    Returns nothing.

    
    
cgilua.session.data

    
Table which holds the user session data.

    
    
cgilua.session.delete (id)

    
Deletes a session. The argument id is the session identifier.

    Returns nothing.

    
    
cgilua.session.destroy ()

    
Destroys the current session.

    Returns nothing.

    
    
cgilua.session.load (id)

    
Loads data from a session. The argument id is the session
    identifier.

    Returns a table with session data or nil followed by an error
    message.

    
    
cgilua.session.new ()

    
Creates a new session identifier.

    Returns the new session identifier.

    
    
cgilua.session.open ()

    
Opens the user session. Creates the table cgilua.session.data.
    This function should be called just before the execution of the script,
    but after the processing of the request's headers. A recommended way to
    ensure that is to use addopenfunction
    in the configuration file.

    Returns nothing.

    
    
cgilua.session.save (id, data)

    
Saves data to a session with an id.

    Returns nothing.

    
    
cgilua.session.setsessiondir (path)

    
Defines the session temporary directory.
    Argument path is a string with the new directory.

    Returns nothing.





 


 



	
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Building Web Scripts with Lua


 



	
 





License



CGILua is free software: it can be used for both academic and commercial
purposes at absolutely no cost. There are no royalties or GNU-like "copyleft"
restrictions. CGILua qualifies as
Open Source
software. Its licenses are compatible with
GPL. CGILua is not in
the public domain and the
Kepler Project keep its copyright.
The legal details are below.



The spirit of the license is that you are free to use CGILua for any purpose
at no cost without having to ask us. The only requirement is that if you do use
CGILua, then you should give us credit by including the appropriate copyright
notice somewhere in your product or its documentation.



The CGILua library is designed and implemented by Roberto Ierusalimschy,
André Carregal and Tomás Guisasola. The implementation is not
derived from licensed software.






Copyright © 2003 Kepler Project.



Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is furnished to do
so, subject to the following conditions:



The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.



THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



 


 


 


 


 


 


 



 


 



	
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CGILua

	
Building Web Scripts with Lua


 



	
 





Introduction




CGILua uses Lua as a server-side scripting
language for creating dynamic Web pages. Both pure
Lua Scripts and
Lua Pages (LP) are supported by CGILua.
A Lua Script is essentially a Lua program that creates the whole contents of
a web page and returns it to the client. A Lua Page is a conventional
markup text (HTML, XML etc) file that embeds Lua code using some special
tags. Those tags are processed by CGILua and resulting page is returned to the
client.



Lua Scripts and Lua Pages are equally easy to use, and choosing one of them
basically depends on the characteristics of the resulting page. While Lua
Pages are more convenient for the separation of logic and format, Lua Scripts
are more adequate for creating pages that are simpler in terms of its structure,
but require a more significative amount of internal processing.



Allowing these two methods to be intermixed, CGILua provides Web applications
developers with great flexibility when both requirements are present. For a
detailed description of both scripting methods and some examples of
their use see Lua Scripts and
Lua Pages.



Architecture




CGILua architecture is divided in two layers. The lower level is represented
by the Server API (SAPI) and the higher level is
represented by the CGILua API itself. SAPI is the interface between the web server
and the CGILua API, so it needs to be implemented for each Web server and launching
method used.





A launcher is responsible for the interaction of CGILua and the Web server,
implementing SAPI for example using ISAPI on IIS or mod_lua on Apache.
The reference implementation of CGILua launchers is
Kepler.





The CGILua API is implemented using only SAPI and is totally portable
over different launchers and their supporting Web servers. This way any Lua Script
or Lua Page can be used by any launcher.




Request life cycle




CGILua processes requests using a CGI metaphor (even if the launcher is not based
on CGI) and requests have a life cycle that can be customized by the programmer.
The CGILua request life cycle consists in the following sequence of steps for each
request:




    
    
  1. Add default handlers such as LuaScripts and Lua Pages and commom file formats.
    2. 
    
  2. Execute the config.lua file, allowing the customization of the next steps.
    3. 
    
  3. Build the cgilua.POST and cgilua.QUERY tables (processing POST and QUERY data).
    4. 
    
  4. Change to user script directory.
    5. 
    
  5. Execute the registered open functions.
    6. 
    
  6. Execute the requested script with the correct environment.
    7. 
    
  7. Execute the registered close functions.
    8. 
    
  8. Change back to the original directory
    9. 





Editing the config.lua file one can customize the CGILua behaviour.
One typical use would be registering the open and close functions
in order to change the request processing behavior.
With this customization it is possible to implement new features like
session management and private library directories as shown in section
Configuration, or even to implement new
abstractions over the whole CGILua way of live, like MVC-frameworks such as Orbit.




Installation




CGILua follows the
package model
for Lua 5.1, therefore it should be "installed" in your package.path.




You can also install CGILua using LuaRocks:



luarocks install cgilua


	

Configuration




The Kepler distribution of CGILua 5.1 offers a single configuration file, called config.lua.
This file can be used to alter the default CGILua behaviour and is located in the Kepler configuration directory.




Some of the uses of config.lua customization are:




    
Script Handlers

    
A handler is responsible for the response of a request.
    You can add new CGILua handlers using
    cgilua.addscripthandler
    (see also cgilua.buildplainhandler
    and cgilua.buildprocesshandler
    for functions that build simple handlers).
    

    
    
POST Data Sizes

    
You can change the POST data size limits using
    cgilua.setmaxinput and
    cgilua.setmaxfilesize.
    

    
    
Opening and Closing Functions

    
You can add your functions to the life cycle of CGILua using
    cgilua.addopenfunction and
    cgilua.addclosefunction.
    These functions are executed just before and just after the script execution,
    even when an error occurs in the script processing.







In particular, the opening and closing functions are useful for different things.
Some examples of the use of such functions in config.lua are shown next.





Previous versions of CGILua loaded a env.lua file from the
script directory before processing it. To emulate this with CGILua 5.1 you can
use something like:




cgilua.addopenfunction (function ()
	cgilua.doif ("env.lua")
end)





If every script needs to load a module (such as the sessions library), you can do:




require"cgilua.session"
cgilua.session.setsessiondir(CGILUA_TMP)
cgilua.addopenfunction (cgilua.session.open)
cgilua.addclosefunction (cgilua.session.close)





Note that the function cgilua.addopenfunction
must be used to call cgilua.session.open because this function
needs to change the cgi table (see section
Receiving parameters
for more information on this special table)
which is not yet available during the execution of the config.lua
file (see the Request life cycle).





When some scripts may use the library but others may not,
you could define an "enabling" function (which should be called at the
very beginning of each script that needs to use sessions):




require"cgilua.session"
cgilua.session.setsessiondir(CGILUA_TMP)
cgilua.enablesession = function ()
	cgilua.session.open ()
	cgilua.addclosefunction (cgilua.session.close)
end





Sometimes you need to configure a private libraries directory for each application
hosted in the server. This configuration allows the function require
to find packages installed in the private directory and in the system directory
but not in other application's private directory. To implement this you could do:




local app_lib_dir = {
	["/virtual/path/"] = "/absolute/path/lib/",
}
local package = package
cgilua.addopenfunction (function ()
	local app = app_lib_dir[cgilua.script_vdir]
	if app then
		package.path = app..'/?.lua'..';'..package.path
	end
end)




Lua Scripts




Lua Scripts are text files containing valid Lua code. This style of usage
adopts a more "raw" form of web programming, where a program is responsible
for the entire generation of the resulting page. Lua Scripts have a default
.lua extension.





To generate a valid web document (HTML, XML, WML, CSS etc) the Lua Script
must follow the expected HTTP order to produce its output, first sending the
correct headers and then sending the
actual document contents.





CGILua offers some functions to ease these tasks, such as
cgilua.htmlheader to
produce the header for a HTML document and
cgilua.put to send the document
contents (or part of it).





For example, a HTML document which displays the sentence "Hello World!" can
be generated with the following Lua Script:




cgilua.htmlheader()
cgilua.put([[
<html>
<head>
  <title>Hello World</title>
</head>
<body>
  <strong>Hello World!</strong>
</body>
</html>]])





It should be noted that the above example generates a "fixed" page: even
though the page is generated at execution time there is no "variable"
information. That means that the very same document could be generated directly
with a simple static HTML file. However, Lua Scripts become especially useful
when the document contains information which is not known beforehand or changes
according to passed parameters, and it is necessary to generate a "dynamic" page.





Another easy example can be shown, this time using a Lua control structure,
variables, and the concatenation operator:




cgilua.htmlheader()  

if cgilua.QUERY.language == 'english' then
  greeting = 'Hello World!'
elseif cgilua.QUERY.language == 'portuguese' then
  greeting = 'Olá Mundo!'
else
  greeting = '[unknown language]'
end

cgilua.put('<html>')  
cgilua.put('<head>')
cgilua.put('  <title>'..greeting..'</title>')
cgilua.put('</head>')
cgilua.put('<body>')
cgilua.put('  <strong>'..greeting..'</strong>')
cgilua.put('</body>')
cgilua.put('</html>')





In the above example the use of cgilua.QUERY.language indicates
that language was passed to the Lua Script as a
CGILua parameter, coming from the URL used to activate it
(via GET). If you were using a form, the parameter would be available in
cgilua.POST.language. CGILua automatically decodes such
QUERY and POST parameters so you can use them at will on your
Lua Scripts and Lua Pages.




Lua Pages




A Lua Page is a text template file which will be processed by CGILua
before the HTTP server sends it to the client. CGILua does not
process the text itself but look for some special markups that include Lua
code into the file. After all those markups are processed and merged with the
template file, the results are sent to the client.





Lua Pages have a default .lp extension. They are a simpler
way to make a dynamic page because there is no need to send the HTTP headers.
Usually Lua Pages are HTML pages so CGILua sends the HTML header automatically.





Since there are some restrictions on the uses of HTTP headers sometimes
a Lua Script will have to be used instead of a Lua Page.




The fundamental Lua Page markups are:




    
<?lua chunk ?>

    
Processes and merges the Lua chunk execution results where
    the markup is located in the template. The alternative form
    <% chunk %> can also be used.

    
    
<?lua= expression ?>

    
Processes and merges the Lua expression evaluation where the
    markup is located in the template. The alternative form
    <%= expression %> can also be used.






Note that the ending mark could not appear inside a Lua chunk or Lua
expression even inside quotes. The Lua Pages pre-processor just makes global
substitutions on the template, searching for a matching pair of markups and
generating the corresponding Lua code to achieve the same result as the
equivalent Lua Script.

 



The second example on the previous section could be written using a
Lua Page like:




<html>
<?lua
if cgilua.QUERY.language == 'english' then
  greeting = 'Hello World!'
elseif cgilua.QUERY.language == 'portuguese' then
  greeting = 'Olá Mundo!'
else
  greeting = '[unknown language]'
end
?>
<head>
  <title><%= greeting %></title>
</head>
<body>
  <strong><%= greeting %></strong>
</body>
</html>





HTML tags and Lua Page tags can be freely intermixed. However, as on other
template languages, it's considered a best practice to not use explicit
Lua logic on templates.
The recommended aproach is to use only function calls that returns content
chunks, so in this example, assuming that function getGreeting
was definied in file functions.lua as follows:




function getGreeting()
  local greeting
  if cgilua.QUERY.language == 'english' then
    greeting = 'Hello World!'
  elseif cgilua.QUERY.language == 'portuguese' then
    greeting = 'Olá Mundo!'
  else
    greeting = '[unknown language]'
  end
  return greeting
end




the Lua Page could be rewriten as:



<?lua
assert (loadfile"functions.lua")()
?>
<html>
<head>
  <title><%= getGreeting() %></title>
</head>
<body>
  <strong><%= getGreeting() %></strong>
</body>
</html>





Another interesting feature of Lua Pages is the intermixing of Lua and HTML.
It is very usual to have a list of values in a table, iterate over the list
and show the items on the page.





A Lua Script could do that using a loop like:




cgilua.put("<ul>")
for i, item in ipairs(list) do
    cgilua.put("<li>"..item.."</li>")
end
cgilua.put("</ul>")





The equivalent loop in Lua Page would be:




<ul>
    <% for i, item in ipairs(list) do %>
    <li><%= item %></li>
    <% end %>
</ul>




Receiving parameters: the QUERY and POST tables




CGILua offers both types of request parameters (QUERY strings and POST data) in the
cgilua.QUERY and cgilua.POST tables.





Usually all types of parameters will be available as strings. If the value of
a parameter is a number, it will be converted to its string representation.





There are only two exceptions where the value will be a Lua table. The first
case occurs on file uploads, where the corresponding table will have the
following fields:





    
filename

    
the file name as given by the client.

    
    
filesize

    
the file size in bytes.

    
    
file

    
the temporary file handle. The file must be copied
    because CGILua will remove it after the script ends.






The other case that uses Lua tables occurs when
there is more than one value associated with the same parameter
name. This happens in the case of a selection list with multiple values; but it
also occurs when the form (of the referrer) had two or more
elements with the same name attribute (maybe because one was on a
form and another was in the query string). All values will be inserted
in an indexed table in the order in which they are handled.




Dispatching




If you want to use more sophisticated URLs, the Kepler distribution includes a dispatching script
called app.lua that can be used to handle URLs in the format
.../app.lua/app_name/path_info in a standard way.
URLs in this format are said to refer to CGILua spplications, which consists in a standard loading
sequence for web applications using CGILua and app.lua as their dispatcher:




    
    
  • there is an app_name as the start of path_info
    • 
    
  • there is an init.lua file in CGILUA_APPS/app_name
    • 
    
  • changes the current directory to CGILUA_APPS/app_name
    • 
    
  • sets cgilua.app_name to app_name
    • 
    
  • adds CGILUA_APPS/app_name/lua to the start of package.path
    • 
    
  • executes init.lua
    • 





CGILua applications usually need to dispatch their actions using the remaining path_info and for that
they can use cgilua.dispatcher as a helper library. The example below uses it to dispatch URLs that
follow a convention similar to Rails. Let's assume that this is a
init.lua file in the CGILUA_APPS/blog directory:




require"cgilua.dispatcher"
return cgilua.dispatcher.route{"/$controller/$action/$ID", handle, "rails"}





In this example URLs like .../app.lua/blog/post/edit/2 would result in the function handle
being called as




handle({controller="post", action="edit", ID="2"})





the handle function would then decide how to proceed depending on the parameters received and generate
the corresponding response using CGILua functions or a template engine like Lua Pages or Cosmo.





Note that this example does not include error handling for invalid URLs or default values.




Authentication




CGILua offers a simple but useful authentication mechanism that can be shared by different CGILua applications
or even applications developed in other platforms. The authentication mechanism is based on HTTP redirections
and assumes three different participants.





The first one is the controller script, which is responsible for centralizing the user authentication control
and deciding if the application should continue depending on a user being logged in or not. An example of such
controller would be the app.lua dispatcher script distributed with Kepler. As most of the controllers
would do, it checks for the presence of an authenticated user and redirects to the checking script when that fails:




-- checks for authenticated users
if not cgilua.authentication.username() then
    cgilua.redirect(cgilua.authentication.checkURL())
else
    -- continues with the application flow
end




If your application is not handled by a single script like one using app.lua then you would need
to repeat this check in every script that requires authenticated users.




The second participant in the authentication mechanism is the checking script. This script should ask for user
credentials, check them using the adequate method and redirect back to the original URL if the user was succesfully
authenticated.





One simple example of such a checking script is the one found in /examples/check.lua in CGILua CVS,
but usually a checking script implemented in CGILua would do the following:




-- Checking script example
-- Assumes that the login form will use two fields called username and pass

local username = cgilua.POST.username
local pass = cgilua.POST.pass
local logged, err, logoutURL

if cgilua.authentication then
    logged, err = cgilua.authentication.check(username, pass)
    username = cgilua.authentication.username() or ""
    logoutURL = cgilua.authentication.logoutURL()
else
    logged = false
    err = "No authentication configured!"
    username = ""
end

if logged and username then
    -- goes back to the application
	cgilua.redirect(cgilua.authentication.refURL())
else
    err = err or ""
    -- displays the login form which submits to this same script
	cgilua.htmlheader()
	cgilua.lp.include ("login.lp", {
        logged = logged, errorMsg = err, username = username,
        cgilua = cgilua, logoutURL = logoutURL})
end





The login form for this example can be fount at /examples/login.lp in CGILua CVS and consists of:




<% if logged then %>
<p>User <%= username %> logged in</p>
<a href="<%= logoutURL %>">Logout</a>
<% else %>
<p style="color:#ff0000"><%= errorMsg %> </p>
<form method="post" action="" >
    User name: <input name="username" maxlength="20" size="20" value="<%= username %>" ><br />
    Password: <input name="pass" type="password" maxlength="20" size="20"><br />
    <input type="submit" value="Login">
    <input type="reset" value="Reset">
</form>
<% end %>





Finally the third participant in the authentication process is the configuration file. This file is used to
set the authentication method and other details. Each method has it's set of parameters and defines a
check callback used by CGILua during the authentication process.
See /examples/authentication_conf.lua for configuration examples using database, LDAP and Web server
authentication methods. 




Error Handling



There are three functions for error handling in CGILua:




The function
cgilua.seterrorhandler
defines the error handler, a function called by Lua when an error has
just occurred. The error handler has access to the execution stack before the
error is thrown so it can build an error message using stack information.
Lua also provides a function to do that: debug.traceback.





The function
cgilua.seterroroutput
defines the function that decides what to do with the error message. It could
be sent to the client's browser, written to a log file or sent to an e-mail
address (with the help of
LuaSocket or 
LuaLogging for example).





The function
cgilua.errorlog
is provided to write directly to the http server error log file.





An useful example of its use could be handling unexpected errors.
Customizing unexpected error messages to the end user but giving all the
information to the application's developers is the goal of the following
piece of code:




local ip = cgilua.servervariable"REMOTE_ADDR"
local developers_machines = {
	["192.168.0.20"] = true,
	["192.168.0.27"] = true,
	["192.168.0.30"] = true,
}
local function mail (s)
	require"cgilua.serialize"
	require"socket.smtp"
	-- Build the message
	local msg = {}
	table.insert (msg, tostring(s))
	-- Tries to obtain the REFERER URL
	table.insert (msg, tostring (cgilua.servervariable"HTTP_REFERER"))
	table.insert (msg, cgilua.servervariable"SERVER_NAME"..
		cgilua.servervariable"SCRIPT_NAME")
	-- CGI parameters
	table.insert (msg, "CGI")
	cgilua.serialize(cgi, function (s) table.insert (msg, s) end)
	table.insert (msg, tostring (os.date()))
	table.insert (msg, tostring (ip))
	table.insert (msg, "Cookies:")
	table.insert (msg, tostring (cgilua.servervariable"HTTP_COOKIE" or "no cookies"))
	-- Formats message according to LuaSocket-2.0b3
	local source = socket.smtp.message {
		headers = { subject = "Script Error", },
		body = table.concat (msg, '\n'),
	}
	-- Sends the message
	local r, e = socket.smtp.send {
		from = "sender@my.domain.net",
		rcpt = "developers@my.domain.net",
		source = source,
	}
end
if developers_machines[ip] then
	-- Developer's error treatment: write to the display
	cgilua.seterroroutput (function (msg)
		cgilua.errorlog (msg)
		cgilua.errorlog (cgilua.servervariable"REMOTE_ADDR")
		cgilua.errorlog (os.date())
		cgilua.htmlheader ()
		msg = string.gsub (string.gsub (msg, "\n", "<br>\n"), "\t", "  ")
		cgilua.put (msg)
	end)
else
	-- User's error treatment: shows a standard page and sends an e-mail to
	-- the developer
	cgilua.seterroroutput (function (s)
		cgilua.htmlheader ()
		cgilua.put"<h1>An error occurred</h1>\n"
		cgilua.put"The responsible is being informed."
		mail (s)
	end)
end





The message is written to the browser if the request comes from one of
the developer's machines. If it is not the case, a simple polite message
is given to the user and a message is sent to the developer's e-mail account
containing all possible information to help reproduce the situation.




 


 



	
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    CGILua: Building Web Scripts with Lua
    
	





	


	
	
CGILua

	
Building Web Scripts with Lua


 



	
 






Headers



Headers functions are used to change the HTTP response headers and consist of:




    
cgilua.contentheader (type, subtype)

    
Sends a Content-type header with the given values of type and
    sub-type.

    Both arguments are strings: type is the header type;
    subtype is the header sub-type.

    Returns nothing.

    
    
cgilua.header (header, value)

    
Sends a generic header. This function should not be used to
    generate a Content-type nor a Location header because
    some launchers/web-servers use different functions for this purpose.

    Both arguments are strings: header is the name of the header;
    value is its value.

    Returns nothing.


    
cgilua.htmlheader ()

    
Sends the header of an HTML file (Content-type: text/html).

    Returns nothing.

    
    
cgilua.redirect (url, args)

    
Sends the header to force a redirection to the given URL adding the
    parameters in table args to the new URL.

    The first argument (url) is the URL the browser should be
    redirected to; the second one (args) is an optional table
    which could have pairs name = value that will be encoded to form
    a valid URL (see function cgilua.urlcode.encodetable).

    Returns nothing.






Content Generation



Content generation functions are used to output text to the response and to
generate URLs in the CGILua format. They consist of:




    
cgilua.mkabsoluteurl (path)

    
Creates an absolute URL containing the given URL path.

    Returns the resulting absolute URL.

    
    
cgilua.mkurlpath (script [, args])

    
Creates an URL path to be used as a link to a CGILua script
    using the optional table of arguments (args). The arguments are
    used in the URL as query string parameters.

    Returns the resulting URL.


    
cgilua.print (...)

    
Sends the given arguments to the client. This function converts all its
    arguments to strings before sending them to the server thus it does not
    raises errors like cgilua.put.

    Returns nothing.


    
cgilua.put (...)

    
Sends the given arguments to the client. This function should
    always be used; do not use Lua's print or io.write
    for output otherwise your script may not work for every launching method.

    Returns nothing.





Lua Pages



Lua Pages functions are used to process Lua Pages templates and to define the
behavior of this processing. They consist of:




    
cgilua.handlelp (filename[, env])

    
Equivalent to cgilua.lp.include but
    sends the HTML header before the pre-processed file.

    Returns nothing.

    
    
cgilua.lp.compile (string)

    
Compile a piece of code given as a string into a Lua function.
    The string is translated with
    cgilua.lp.translate
    into another string which is transformed into a function with
    loadstring.
    The resulting function is cached internaly and reused if the same piece of
    code is given.

    Returns a function.


    
cgilua.lp.include (filename[, env])

    
Pre-processes a Lua Page template (given by filename) and sends the results
    to the client. The file content is processed by cgilua.lp.compile
    and no headers are sent. If an optional environment table is passed, the file is executed with this
    environment instead of the global one. This can be used to sandbox your scripts.

    Returns nothing.

    
    
cgilua.lp.setcompatmode (boolean)

    
Turns on or off the compatibility mode. Turning it on will make the
    Lua Pages preprocessor understand the expression fields and
    code fields structures used by previous versions of CGILua.

    Default value: true

    Returns nothing.

    
    
cgilua.lp.setoutfunc (funcname)

    
Defines the name of the output function for templates. The Lua Pages
    preprocessor will generate calls to the function with the given
    funcname (a string).

    Returns nothing.

    
    
cgilua.lp.translate (string)

    
Uses the Lua Pages preprocessor to generate a string corresponding to
    the Lua code that executes the Lua chunks and/or expressions inside the
    given string.

    Returns a string with the resulting Lua code.






CGILua Variables



CGILua Variables offers information about the script being processed and
the CGI environment variables depending
on the Web server and launcher used.
They consist of both atributes and functions:




    
cgilua.script_file

    
The file name of the running script. Obtained from
    cgilua.script_path.

    
    
cgilua.script_path

    
The complete path of the running script. This variable is usually the
    same as the CGI environment variable
    PATH_TRANSLATED.

    
    
cgilua.script_pdir

    
The directory of the running script. Obtained from
    cgilua.script_path.

    
    
cgilua.script_vdir

    
The virtual directory of the running script. Obtained from
    cgilua.script_vpath.

    
    
cgilua.script_vpath

    
The complete virtual path of the running script. Equivalent to the
    CGI environment variable
    PATH_INFO.

    
    
cgilua.servervariable (varname)

    
Returns a string with the value of the CGI environment variable
    correspoding to varname. For a list of CGI variables please refer to
    SAPI.Request.servervariable


    
cgilua.tmp_path

    
The directory used by cgilua.tmpfile.
    Obtained by checking os.getenv("TEMP"), os.getenv ("TMP") and
    "/tmp" in that order.

    
    
cgilua.urlpath

    
The name of the script. Equivalent to the
    CGI environment variable
    SCRIPT_NAME.





Error Handling



CGILua error handling functions allow the redefinition of how errors are
handled and presented to the user. The consist of:




    
cgilua.errorlog (string)

    
Sends the given string to the error log file.

    Returns nothing.

    
    
cgilua.seterrorhandler (func)

    
Sets the error handler function to func.
    This function is called by Lua when an error occurs. It receives the error
    message generated by Lua and it is responsible for generating and returning
    the correct error message to be used by CGILua.

    Returns nothing.

    
    
cgilua.seterroroutput (func)

    
Sets the error output function to func.
    This function is called by Lua to generate the error output itself.

    Returns nothing.





CGILua behavior



The behavior of CGILua can be configured using this set of functions:




    
cgilua.addclosefunction (func)

    
Defines a function (func) to be called after the execution
    of the script requested.

    Returns nothing.

    
    
cgilua.addopenfunction (func)

    
Defines a function (func) to be called before the execution
    of the script requested.

    Returns nothing.


    
cgilua.addscripthandler (ext, func)

    
Defines a function (func) to pre-process files with a
    certain extension (ext). The default configuration uses
    cgilua.doscript to process Lua Scripts
    (.lua files) and cgilua.handlelp
    to process Lua Pages (.lp files).

    Returns nothing.


    
cgilua.buildplainhandler (type, subtype)

    
Creates a script handler that sends the given header and the plain
    file requested. The Content-type header is formed by the two arguments;
    the created function will receive a filename as its only argument
    and will return the given filename untouched.

    Returns a function.

    
    
cgilua.buildprocesshandler (type, subtype)

    
Creates a script handler that sends the given header and the
    processed file requested. The Content-type header is formed by the
    two arguments; the created function will receive a filename as its
    only argument and will return the given filename pre-processed by the
    function cgilua.lp.include.

    Returns a function.

    
    
cgilua.setmaxfilesize (size)

    
Sets the maximum size (in bytes) for each uploaded file.
    This value is bounded by the maximum total input size (see
    cgilua.setmaxinput). This function only takes
    effect if used before POST data is processed, therefore its use in scripts
    are meaningless.

    Returns nothing.

    
    
cgilua.setmaxinput (size)

    
Sets the maximum total input size allowed (in bytes).
    This function only takes efect if used before POST data is processed,
    therefore its use in scripts are meaningless.

    Returns nothing.





URL encoding functions



CGILua enconding functions allow the processing of URL strings in a simple way:




    
cgilua.urlcode.encodetable (table)

    
URL-encode the elements of a table creating a
    string to be used as a URL for passing data/parameters to another script.

    Returns a string representing the encoded argument table.

    
    
cgilua.urlcode.escape (string)

    
URL-encode a string.

    Returns the encoded string.

    
    
cgilua.urlcode.insertfield (args, name, value)

    
Adds the given value to the field indexed by name
    in the args table. If the field already has a value, it is
    transformed into a table with this value at index 1 and
    the new value at index 2. Other values will be added at
    the end of the array-part of the created table.

    Returns nothing.

    
    
cgilua.urlcode.parsequery (query, args)

    
Parse URL-encoded request data. This could be the query
    part of the script URL or URL-encoded POST data. Each decoded
    name = value pair is inserted into the args table.

    Returns nothing.

    
    
cgilua.urlcode.unescape (string)

    
URL-decodes a string.

    Returns the decoded string.





Auxiliar functions




    
cgilua.doif (filepath)

    
Executes a file (given by filepath) if it exists. 
    Returns the values returned by the execution, or
    nil followed by an error message if the file does not exists.


    
cgilua.doscript (filepath)

    
Executes a file (given by filepath). Raises an error if it
    occurs. In case of success, returns the values returned by the execution.


    
cgilua.pack (...)

    
Returns a new table with all the passed arguments stored in it.


    
cgilua.splitfirst (path)

    
Returns two strings with the "first directory" and the "remaining paht" of the given
    path string splitted on the first separator ("/" or "\").

    
    
cgilua.splitonlast (path)

    
Returns two strings with the "directory path" and "file" parts of the given
    path string splitted on the last separator ("/" or "\").
    This function used to be called cgilua.splitpath and still can be accessed by
    this name for compatibility reasons. cgilua.splitpath may be deprecated in future
    versions.

    
    
cgilua.tmpfile (dir[, namefunction])

    
Returns a temporary file in the cgilua.tmp_path directory
    using an optional name generator. If the name generator function is not passed,
    cgilua.tmpname is used. The file is removed by CGILua after the request has been
    processed.


    
cgilua.tmpname ()

    
Returns a temporary name using an adjusted version of os.tmpname.





Alphabetic Index


addclosefunction

addopenfunction

addscripthandler

buildplainhandler

buildprocesshandler

contentheader

doif

doscript

encodetable (urlcode)

errorlog

escape (urlcode)

header

htmlheader

include (lp)

insertfield (urlcode)

mkabsoluteurl

mkurlpath

pack

parsequery (urlcode)

handlelp

lp

print

put

redirect

script_file

script_path

script_pdir

script_vdir

script_vpath

servervariable

setcompatmode (lp)

seterrorhandler

seterroroutput

setlibdir

setmaxfilesize

setmaxinput

setoutfunc (lp)

splitonfirst

splitonlast

tmpfile

tmpname

tmp_path

urlcode

unescape (urlcode)

urlpath



 


 



	
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genometools-1.5.1/src/external/cgilua-5.1.3/doc/us/sapi.html000066400000000000000000000243031211610345200234030ustar00rootroot00000000000000


    CGILua: Building Web Scripts with Lua
    
	





	


	
	
CGILua

	
Building Web Scripts with Lua


 



	
 





Server API



The Server API (SAPI) allows the abstraction of a series of internal web server details
and allows CGILua to be used over WSAPI.
Kepler is the reference implementation of WSAPI and currently supports Apache,
Microsoft IIS and Xavante as Web servers, and CGI, FastCGI, as WSAPI connectors.
Xavante has a native WSAPI connector.





The SAPI API is separated into two packages:
SAPI.Request and SAPI.Response.





The SAPI.Request package offers two functions:





    
SAPI.Request.getpostdata ([n])

    
Gets a block of POST data. The optional parameter n is
    the number of bytes to read (a default block size is used if no parameter is
    passed).

    Returns the block as a Lua string.

    
    
SAPI.Request.servervariable (varname)

    
Gets the value of a server environment variable. The argument can be
    one of the defined
    CGI Variables, although
    not all servers implements the full set of variables. The set consists of:

    
    
        
  • AUTH_TYPE - If the server supports
        user authentication, and the script is protected, this is the
        protocol-specific authentication method used to validate the user.
    • 
        
        
  • CONTENT_LENGTH - The length of the
        content itself as given by the client.
    • 
        
        
  • CONTENT_TYPE - For queries which
        have attached information, such as HTTP POST and PUT, this is the
        content type of the data.
    • 
        
        
  • GATEWAY_INTERFACE - The revision of
        the CGI specification to which this server complies.
        Format: CGI/revision
    • 
        
        
  • PATH_INFO - The extra path
        information, as given by the client. In other words, scripts can be
        accessed by their virtual pathname, followed by extra information at
        the end of this path. The extra information is sent as PATH_INFO.
        This information should be decoded by the server if it comes from a
        URL before it is passed to the CGI script.
    • 
        
        
  • PATH_TRANSLATED - The server provides
        a translated version of PATH_INFO, which takes the path and does any
        virtual-to-physical mapping to it.
    • 
        
        
  • QUERY_STRING - The information which
        follows the "?" in the URL which referenced this script. This is the
        query information. It should not be decoded in any fashion. This variable
        should always be set when there is query information, regardless of
        command line decoding.
    • 
        
        
  • REMOTE_ADDR - The IP address of the
        remote host making the request.
    • 
        
        
  • REMOTE_HOST - The hostname making
        the request. If the server does not have this information, it should
        set REMOTE_ADDR and leave this unset.
    • 
        
        
  • REMOTE_IDENT - If the HTTP server
        supports RFC 931 identification, then this variable will be set to the
        remote user name retrieved from the server. Usage of this variable
        should be limited to logging only.
    • 
        
        
  • REMOTE_USER - If the server supports
        user authentication, and the script is protected, this is the username
        they have authenticated as.
    • 
        
        
  • REQUEST_METHOD - The method with which
        the request was made. For HTTP, this is "GET", "HEAD", "POST", etc.
    • 
        
        
  • SCRIPT_NAME - A virtual path to the
        script being executed, used for self-referencing URLs.
    • 
        
        
  • SERVER_NAME - The server's hostname,
        DNS alias, or IP address as it would appear in self-referencing URLs.
    • 
        
        
  • SERVER_PORT - The port number to which
        the request was sent.
    • 
        
        
  • SERVER_PROTOCOL - The name and revision
        of the information protcol this request came in with.
        Format: protocol/revision
    • 
        
        
  • SERVER_SOFTWARE - The name and version
        of the web server software answering the request (and running the gateway).
        Format: name/version
    • 
    

    In addition to these, the header lines received from the client, if any, are
    placed into the environment with the prefix HTTP_ followed by the
    header name. Any - characters in the header name are changed to
    _ characters. The server may exclude any headers which it has
    already processed, such as Authorization, Content-type, and
    Content-length. If necessary, the server may choose to exclude any
    or all of these headers if including them would exceed any system environment
    limits.

    Returns a string.






And the SAPI.Response package offers five functions:





    
SAPI.Response.contenttype (header)

    
Sends the Content-type header to the client. The given
    header should be in the form "type/subtype".
    This function must be called before any output is sent using
    SAPI.Response.write.

    Returns nothing.

    
    
SAPI.Response.errorlog (message)

    
Generates error output using the given string or number.

    Returns nothing.


    
SAPI.Response.header (header, value)

    
Sends a generic header to the client. The first argument must be the
    header name, such as "Set-Cookie". The second argument should be its value.
    This function should not be used to replace the
    SAPI.Response.contenttype nor the
    SAPI.Response.redirect functions.

    Returns nothing.


    
SAPI.Response.redirect (url)

    
Sends the Location header to the client. The given url
    should be a string.

    Returns nothing.

  
    
SAPI.Response.write (...)

    
Generates output using the given arguments.
    The arguments must be strings or numbers.

    Returns nothing.





 


 



	
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$Id: sapi.html,v 1.33 2009/02/06 00:56:06 carregal Exp $


 


 


 
genometools-1.5.1/src/external/cgilua-5.1.3/examples/000077500000000000000000000000001211610345200222015ustar00rootroot00000000000000genometools-1.5.1/src/external/cgilua-5.1.3/examples/authentication_conf.lua000066400000000000000000000066551211610345200267440ustar00rootroot00000000000000----------------------------
-- Authentication configuration file
-- 
-- Defines the method and details of the authentication mechanism
--
-- $Id: authentication_conf.lua,v 1.1 2007/12/05 18:40:17 carregal Exp $
----------------------------

require"cgilua.authentication"

local options = {
    -- Authentication method: "simpledatabase", "webserver", "ldap", "test"
    method = "test",
    
    -- How Authentication is stored on the client
    -- This directive can be "cookie" or "url"
    tokenPersistence="url",
    
    -- Name used for the token persitence
    tokenName = "userhash",
    
    -- The criptografic key to encode user information on cookies and URLs
    criptKey="sfdtdyedbbg",
    
    -- Where to redirect when authentication is needed
    -- checkURL="https://remotehost/sso/authenticate", -- absolute URL
    checkURL="check.lua", -- authentication controller used by app.lua
}

--
-- Simple database authentication parameters
--
options.simpledatabase = {
    driver="mysql",  -- "mysql","oracle","odbc"
    sourcename="users",
    dbusername="root",
    dbpassword="pass",
    passwd_hash_function=(require"md5") and md5.sumhexa, -- for MD5 encription
        -- passwd_hash_function = function(arg) return arg end , -- for no encription
    users_table="Users",
    user_name_field="Name",
    pass_field="Password",
}

--
-- Web Server authentication parameters
--
options.webserver = {
    user_env_var="REMOTE_USER", -- if supports RFC 931 use "REMOTE_IDENT"
}

--
-- LDAP authentication parameters
--
options.ldap = {
    host="127.0.0.1", -- accepts host:port
    usetls=false,
    --baseDN="ou=People,dc=example,dc=com",
    baseDN="dc=example,dc=com",
    RDNatributeName="cn",
}


local methods = {
    simpledatabase = {},
    webserver = {},
    ldap = {},
    test = {},
}

--
-- Simple database authentication method
--
methods.simpledatabase.check = function(username,userpasswd)
    local simpledatabase = options.simpledatabase
    require ("luasql."..simpledatabase.driver)

    local query = "SELECT "..simpledatabase.pass_field.." FROM "..simpledatabase.users_table.." WHERE "..simpledatabase.user_name_field.." = '"..username.."'"
    local conn,err = luasql[simpledatabase.driver]:connect(simpledatabase.sourcename,simpledatabase.dbusername,simpledatabase.dbpassword)
    if conn == nil then
        return false, err
    end
    local cur=conn:execute(query)
    local row=cur:fetch()
    local retpasswd=row[simpledatabase.pass_field]
    local passwdhash=simpledatabase.passwd_hash_function(userpasswd)
    if retpasswd==passwdhash then
        return true
    end
    return false, "Username and password do not match."
end


--
-- Web Server authentication method
--
methods.webserver.user = function ()
	return cgilua.servervariable (options.webserver.user_env_var)
end


--
-- LDAP authentication method
--
methods.ldap.check = function(username,userpasswd)
    require"lualdap"
	local ld,err = options.lualdap.open_simple (options.ldap.host,
                options.ldap.RDNatributeName.."="..username..","..options.ldap.baseDN,
		        userpasswd, options.ldap.usetls)
	if ld~=nil then
		return true
	else
	    return false, err
    end
end

--
-- Test authentication method
--
methods.test.check = function(username,userpasswd)
    if (username == "admin") and (userpasswd == "admin") then
        return true
    else
        return false, "Wrong user/password combination!"
    end
end

cgilua.authentication.configure(options, methods)genometools-1.5.1/src/external/cgilua-5.1.3/examples/check.lua000066400000000000000000000013711211610345200237630ustar00rootroot00000000000000-- Checking script example
-- Assumes that the login form will use two fields called username and pass

local username = cgilua.POST.username
local pass = cgilua.POST.pass
local logged, err, logoutURL

if cgilua.authentication then
    logged, err = cgilua.authentication.check(username, pass)
    username = cgilua.authentication.username() or ""
    logoutURL = cgilua.authentication.logoutURL()
else
    logged = false
    err = "No authentication configured!"
    username = ""
end

if logged and username then
	cgilua.redirect(cgilua.authentication.refURL())
else
    err = err or ""

	cgilua.htmlheader()
	cgilua.lp.include ("login.lp", {
        logged = logged, errorMsg = err, username = username,
        cgilua = cgilua, logoutURL = logoutURL})
end

genometools-1.5.1/src/external/cgilua-5.1.3/examples/login.lp000066400000000000000000000011011211610345200236370ustar00rootroot00000000000000

Login



    <% if logged then %>
    
User <%= username %> logged in

    Logout
    <% else %>
    
<%= errorMsg %> 

    

        User name: 

        Password: 

        
        
    

    <% end %>

genometools-1.5.1/src/external/cgilua-5.1.3/rockspec/000077500000000000000000000000001211610345200221745ustar00rootroot00000000000000genometools-1.5.1/src/external/cgilua-5.1.3/rockspec/cgilua-5.1.2-1.rockspec000066400000000000000000000015451211610345200257770ustar00rootroot00000000000000package = "CGILua"

version = "5.1.2-1"

source = {
   url = "http://luaforge.net/frs/download.php/3398/cgilua-5.1.2.tar.gz"
}

description = {
   summary = "Tool for creating dynamic Web pages and manipulating data from Web forms",
   detailed = [[
      CGILua allows the separation of logic and data handling from the
      generation of pages, making it easy to develop web applications with
      Lua. CGILua can be used with a variety of Web servers and, for each
      server, with different launchers. A launcher is responsible for the
      interaction of CGILua and the Web server, for example using ISAPI on
      IIS or mod_lua on Apache. 
   ]]
}

dependencies = {
   "lua >= 5.1",
   "luafilesystem >= 1.4.1",
}

build = {
   type = "make",
   build_pass = false,
   install_target = "install",
   install_variables = {
      LUA_DIR = "$(LUADIR)"
   }
}
genometools-1.5.1/src/external/cgilua-5.1.3/rockspec/cgilua-5.1.2-2.rockspec000066400000000000000000000015451211610345200260000ustar00rootroot00000000000000package = "CGILua"

version = "5.1.2-2"

source = {
   url = "http://luaforge.net/frs/download.php/3398/cgilua-5.1.2.tar.gz"
}

description = {
   summary = "Tool for creating dynamic Web pages and manipulating data from Web forms",
   detailed = [[
      CGILua allows the separation of logic and data handling from the
      generation of pages, making it easy to develop web applications with
      Lua. CGILua can be used with a variety of Web servers and, for each
      server, with different launchers. A launcher is responsible for the
      interaction of CGILua and the Web server, for example using ISAPI on
      IIS or mod_lua on Apache. 
   ]]
}

dependencies = {
   "lua >= 5.1",
   "luafilesystem >= 1.4.1",
}

build = {
   type = "make",
   build_pass = false,
   install_target = "install",
   install_variables = {
      LUA_DIR = "$(LUADIR)"
   }
}
genometools-1.5.1/src/external/cgilua-5.1.3/rockspec/cgilua-5.1.2rc1-1.rockspec000066400000000000000000000015341211610345200264030ustar00rootroot00000000000000package = "CGILua"

version = "5.1.2rc1-1"

description = {
   summary = "Tool for creating dynamic Web pages and manipulating data from Web forms",
   detailed = [[
      CGILua allows the separation of logic and data handling from the
      generation of pages, making it easy to develop web applications with
      Lua. CGILua can be used with a variety of Web servers and, for each
      server, with different launchers. A launcher is responsible for the
      interaction of CGILua and the Web server, for example using ISAPI on
      IIS or mod_lua on Apache. 
   ]]
}

dependencies = {
   "lua >= 5.1",
   "luafilesystem 1.4.1rc1",
}

source = {
   url = "http://cgilua.luaforge.net/cgilua-5.1.2rc1.tar.gz"
}

build = {
   type = "make",
   build_pass = false,
   install_target = "install",
   install_variables = {
      LUA_DIR = "$(LUADIR)"
   }
}
genometools-1.5.1/src/external/cgilua-5.1.3/rockspec/cgilua-5.1.3-1.rockspec000066400000000000000000000025231211610345200257750ustar00rootroot00000000000000package = "CGILua"

version = "5.1.3-1"

source = {
   url = "http://luaforge.net/frs/download.php/3398/cgilua-5.1.3.tar.gz"
}

description = {
   summary = "Tool for creating dynamic Web pages and manipulating data from Web forms",
   detailed = [[
      CGILua allows the separation of logic and data handling from the
      generation of pages, making it easy to develop web applications with
      Lua. CGILua can be used with a variety of Web servers and, for each
      server, with different launchers. A launcher is responsible for the
      interaction of CGILua and the Web server, for example using ISAPI on
      IIS or mod_lua on Apache. 
   ]]
}

dependencies = {
   "lua >= 5.1",
   "luafilesystem >= 1.4.1",
}

local CGILUA_LUAS = { "src/cgilua/authentication.lua", 
      "src/cgilua/cookies.lua", 
      "src/cgilua/dispatcher.lua", 
      "src/cgilua/loader.lua", 
      "src/cgilua/lp.lua", 
      "src/cgilua/mime.lua", 
      "src/cgilua/post.lua", 
      "src/cgilua/readuntil.lua", 
      "src/cgilua/serialize.lua", 
      "src/cgilua/session.lua", 
      "src/cgilua/urlcode.lua" }

build = {
   type = "module",
   modules = {
     cgilua = "src/cgilua/cgilua.lua"
   }
}

for i = 1, #CGILUA_LUAS do
    local file = CGILUA_LUAS[i]
    local mod = "cgilua." .. file:match("^src/cgilua/([^%.]+)%.lua$")
    build.modules[mod] = file
end
genometools-1.5.1/src/external/cgilua-5.1.3/rockspec/cgilua-cvs-2.rockspec000066400000000000000000000015451211610345200261300ustar00rootroot00000000000000package = "CGILua"
version = "cvs-2"
source = {
   url = "cvs://:pserver:anonymous:@cvs.luaforge.net:/cvsroot/cgilua",
   cvs_tag = "HEAD",
}
description = {
   summary = "Tool for creating dynamic Web pages and manipulating data from Web forms",
   detailed = [[
      CGILua allows the separation of logic and data handling from the
      generation of pages, making it easy to develop web applications with
      Lua. CGILua can be used with a variety of Web servers and, for each
      server, with different launchers. A launcher is responsible for the
      interaction of CGILua and the Web server, for example using ISAPI on
      IIS or mod_lua on Apache. 
   ]]
}
dependencies = {
   "lua >= 5.1",
   "luafilesystem > 1.0",
   "luasocket >= 2.0"
}
build = {
   type = "make",
   build_pass = false,
   install_variables = {
      LUA_DIR = "$(LUADIR)"
   }
}
genometools-1.5.1/src/external/cgilua-5.1.3/rockspec/cgilua-cvs-3.rockspec000066400000000000000000000016021211610345200261230ustar00rootroot00000000000000package = "CGILua"

version = "cvs-3"

description = {
   summary = "Tool for creating dynamic Web pages and manipulating data from Web forms",
   detailed = [[
      CGILua allows the separation of logic and data handling from the
      generation of pages, making it easy to develop web applications with
      Lua. CGILua can be used with a variety of Web servers and, for each
      server, with different launchers. A launcher is responsible for the
      interaction of CGILua and the Web server, for example using ISAPI on
      IIS or mod_lua on Apache. 
   ]]
}

dependencies = {
   "lua >= 5.1",
   "luafilesystem cvs",
}

source = {
   url = "cvs://:pserver:anonymous@cvs.luaforge.net:/cvsroot/cgilua",
   cvs_tag = "HEAD",
   dir = "cgilua"
}

build = {
   type = "make",
   build_pass = false,
   install_target = "install",
   install_variables = {
      LUA_DIR = "$(LUADIR)"
   }
}
genometools-1.5.1/src/external/cgilua-5.1.3/rockspec/cgilua-cvs-4.rockspec000066400000000000000000000025601211610345200261300ustar00rootroot00000000000000package = "CGILua"

version = "cvs-4"

description = {
   summary = "Tool for creating dynamic Web pages and manipulating data from Web forms",
   detailed = [[
      CGILua allows the separation of logic and data handling from the
      generation of pages, making it easy to develop web applications with
      Lua. CGILua can be used with a variety of Web servers and, for each
      server, with different launchers. A launcher is responsible for the
      interaction of CGILua and the Web server, for example using ISAPI on
      IIS or mod_lua on Apache. 
   ]]
}

dependencies = {
   "lua >= 5.1",
   "luafilesystem cvs",
}

source = {
   url = "cvs://:pserver:anonymous@cvs.luaforge.net:/cvsroot/cgilua",
   cvs_tag = "HEAD",
   dir = "cgilua"
}

local CGILUA_LUAS = { "src/cgilua/authentication.lua", 
      "src/cgilua/cookies.lua", 
      "src/cgilua/dispatcher.lua", 
      "src/cgilua/loader.lua", 
      "src/cgilua/lp.lua", 
      "src/cgilua/mime.lua", 
      "src/cgilua/post.lua", 
      "src/cgilua/readuntil.lua", 
      "src/cgilua/serialize.lua", 
      "src/cgilua/session.lua", 
      "src/cgilua/urlcode.lua" }

build = {
   type = "module",
   modules = {
     cgilua = "src/cgilua/cgilua.lua"
   }
}

for i = 1, #CGILUA_LUAS do
    local file = CGILUA_LUAS[i]
    local mod = "cgilua." .. file:match("^src/cgilua/([^%.]+)%.lua$")
    build.modules[mod] = file
end
genometools-1.5.1/src/external/cgilua-5.1.3/src/000077500000000000000000000000001211610345200211525ustar00rootroot00000000000000genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/000077500000000000000000000000001211610345200224165ustar00rootroot00000000000000genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/authentication.lua000066400000000000000000000163361211610345200261510ustar00rootroot00000000000000-- CGILua authentication Module
-- Author: Leonardo Godinho
--
-- Offers a basic API for authentication assuming the presence of 
-- cgilua.POST.user, cgilua.POST.pass, cgilua.QUERY.logout, cgilua.QUERY[tokenName]
--
-- The API consists in the functions
--   check(username, passwd) - Checks if the pair username/passwd is authenticated by the configured method
--   checkURL() - returns the URL for the checking script
--   configure(options, methods) - configures the authentication framework (see /examples/authentication_conf.lua)
--   logoutURL() - returns the URL for the logout page
--   refURL() - returns the original URL being checked for authentication
--   username() - returns the authenticated user if existent
--
-- The authenticated user can be persisted by using a cookie or an ID in the URL
--
-- $Id: authentication.lua,v 1.2 2007/12/05 19:41:13 carregal Exp $


local mime=require"mime" -- from LuaSocket
local md5=require"md5"
require"cgilua.cookies"

local cgilua = cgilua
local string = string
local math = math
local error = error

module"cgilua.authentication"

local authenticatedUser
local configuration
local _check -- check function provided by the configuration

-- Callback functions to manipulate Tokens in the URL
-- if not defined, CGILua standard URLs are assumed

-- Returns the current token
function getToken()
    return cgilua.QUERY[configuration.tokenName]
end

-- Sets the current token
function setToken(token)
    cgilua.QUERY[configuration.tokenName] = token
end
    
-- Returns the current URL
function currentURL()
    local script_name = cgilua.servervariable"SCRIPT_NAME"
    local path_info = cgilua.servervariable"PATH_INFO" or ""
    local query_string = cgilua.servervariable"QUERY_STRING" or ""
    if query_string ~= "" then
        query_string = "?"..query_string
    end
    return cgilua.mkabsoluteurl(script_name..path_info..query_string)
end

-- URL Base64 encoder and decoder functions
-- (http://en.wikipedia.org/wiki/Base64)
--
-- '=' is replaced by ''
-- '+' and '/' are respectively replaced by '*' and '-'
function encodeURLbase64(str)
	local b64str = mime.b64(str)
	local urlb64str = string.gsub(b64str,"=","")
	urlb64str = string.gsub(urlb64str,"+","*")
	urlb64str = string.gsub(urlb64str,"/","-")
	urlb64str = string.gsub(urlb64str," ","_")
	return urlb64str
end

function decodeURLbase64(urlb64str)
	local b64str = string.gsub(urlb64str,"*","+")
	b64str = string.gsub(b64str,"-","/")
	b64str = string.gsub(b64str,"_"," ")
	local b64strPadLen = math.fmod(4 - math.fmod(string.len(b64str), 4), 4)
	b64str = b64str..string.rep("=", b64strPadLen)
	local str = mime.unb64(b64str)
	return str
end

-- Returns the authenticated username or nil if no user is authenticated
function username()
	if authenticatedUser == nil then
		local authenticatedUserData
        local token
		if configuration.tokenPersistence == "url" then
            token = getToken()
		elseif configuration.tokenPersistence == "cookie" then
			token = cgilua.cookies.get(configuration.tokenName)
		end
        if token then
            authenticatedUserData = md5.decrypt(decodeURLbase64(token), configuration.criptKey)
            -- check if IP in crypted data match with client IP
            local authenticatedUserIP = authenticatedUserData and string.gsub(authenticatedUserData, ",.*$","") or nil
            if authenticatedUserIP ~= cgilua.servervariable("REMOTE_ADDR") then
                return nil
            end
            authenticatedUser=authenticatedUserData and string.gsub(authenticatedUserData, "^.*,", "") or nil
        end
	end
	return authenticatedUser
end

-- encrypt the user IP and username for the user hash token
local function cryptUserData()
    if authenticatedUser then
        local userData = cgilua.servervariable("REMOTE_ADDR") ..",".. authenticatedUser
        local cryptedUserData = encodeURLbase64(md5.crypt(userData, configuration.criptKey))
        return cryptedUserData
    end
end

-- defines the logged user name and sets the user hash token
local function setUser(username)
	authenticatedUser = username
    if username then
        local cryptedUserData = cryptUserData()
        if configuration.tokenPersistence == "url" then
            setToken(cryptedUserData)
            cgilua.cookies.delete(configuration.tokenName) -- removes an eventual previous cookie token
        elseif configuration.tokenPersistence == "cookie" then
            cgilua.cookies.set(configuration.tokenName, cryptedUserData)
            setToken() -- remove an eventual previous token from the URLs
        end
    end
end

-- User logout, clear everything
function logout()
    setUser()
    cgilua.cookies.delete(configuration.tokenName)
    setToken()
    cgilua.QUERY.logout = nil
end

-- Checks if a user name/password is authenticated by the configured method
-- if the user is authenticaded then login the user else logout the user
-- returns true if the user has been succesfully authenticated or false plus
-- an error message when the authentication fails
function check(name, pass)
    name = name or cgilua.POST.user
    pass = pass or cgilua.POST.pass
	if name then
        -- Tries to authenticate the user using the configured method
		local retauth,errauth = _check(name, pass)
		if  retauth then
			setUser(name)
			return true
		else
			logout()
			return false, errauth
		end
	else
		local authuser = username()
		if authuser then
			if cgilua.QUERY.logout ~= nil then
				logout()
				return false
			end
		end
		return authuser
	end
end

-- Returns a authentication URL with ref URL as a parameter,
-- accepts an optional value for the logout action
function checkURL(ref, tologout)
    local token
    if configuration.tokenPersistence == "url" then
        token = getToken()
    elseif configuration.tokenPersistence == "cookie" then
        token = cgilua.cookies.get(configuration.tokenName)
    end

    -- As HTTP header referer information can violate privacy, 
    -- some browsers allow the user to disable the sending of referer information.
    -- Some proxy and firewall software will also filter out referer information,
    -- to avoid leaking the location of non-public websites.
    -- So we send the current URL as an URL parameter to the login URL.     
	setToken()
	local args = {ref = ref or currentURL(), logout = tologout}
	if string.find(configuration.checkURL, "^https?:") then
		local params = "?"..urlcode.encodetable(args)
		return configuration.checkURL..params
	end
	return cgilua.mkabsoluteurl(cgilua.mkurlpath(configuration.checkURL, args))
end

-- Returns the logout URL, based on the login URL
function logoutURL()
	return checkURL(nil, 1)
end

-- Returns the referenced URL, the one supposed to be offered only for authenticated users
function refURL()
    local url
    local baseURL = cgilua.QUERY.ref or configuration.checkURL
    if string.find(baseURL, "\?") then
        url = string.gsub(baseURL, "\?", "?"..configuration.tokenName.."="..cryptUserData().."&")
    else
        url = baseURL.."?"..configuration.tokenName.."="..cryptUserData()
    end
	return url
end

-- Sets the current configuration
function configure(options, methods)
    configuration = options
    local method = methods[options.method] or {}
    
    if method.check then
        _check = method.check
    end
    if method.username then
        username = method.username
    end
endgenometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/cgilua.lua000066400000000000000000000517421211610345200243760ustar00rootroot00000000000000----------------------------------------------------------------------------
-- CGILua library.
--
-- @release $Id: cgilua.lua,v 1.84 2009/03/09 22:03:24 carregal Exp $
----------------------------------------------------------------------------

local _G, SAPI = _G, SAPI
local urlcode = require"cgilua.urlcode"
local lp = require"cgilua.lp"
local lfs = require"lfs"
local debug = require"debug"
local assert, error, ipairs, select, tostring, type, unpack, xpcall = assert, error, ipairs, select, tostring, type, unpack, xpcall
local pairs = pairs
local gsub, format, strfind, strlower, strsub, match = string.gsub, string.format, string.find, string.lower, string.sub, string.match
local setmetatable = setmetatable
local _open = io.open
local tinsert, tremove, concat = table.insert, table.remove, table.concat
local foreachi = table.foreachi
local date = os.date
local os_tmpname = os.tmpname
local getenv = os.getenv
local remove = os.remove
local seeall = package.seeall
local setfenv = setfenv

lp.setoutfunc ("cgilua.put")
lp.setcompatmode (true)

module ("cgilua")

_COPYRIGHT = "Copyright (C) 2003 Kepler Project"
_DESCRIPTION = "CGILua is a tool for creating dynamic Web pages and manipulating input data from forms"
_VERSION = "CGILua 5.1.3"
--
-- Internal state variables.
local _default_errorhandler = debug.traceback
local _errorhandler = _default_errorhandler
local _default_erroroutput = function (msg)

    if type(msg) ~= "string" and type(msg) ~= "number" then
        msg = format ("bad argument #1 to 'error' (string expected, got %s)", type(msg))
    end
  
	-- Logging error
	SAPI.Response.errorlog (msg)
	SAPI.Response.errorlog (" ")

	SAPI.Response.errorlog (SAPI.Request.servervariable"REMOTE_ADDR")
	SAPI.Response.errorlog (" ")

	SAPI.Response.errorlog (date())
	SAPI.Response.errorlog ("\n")

	-- Building user message
	msg = gsub (gsub (msg, "\n", "
\n"), "\t", "  ")
	SAPI.Response.contenttype ("text/html")
	SAPI.Response.write ("CGILua Error" .. msg .. "")
end
local _erroroutput = _default_erroroutput
local _default_maxfilesize = 512 * 1024
local _maxfilesize = _default_maxfilesize
local _default_maxinput = 1024 * 1024
local _maxinput = _default_maxinput
script_path = false

--
-- Header functions

----------------------------------------------------------------------------
-- Sends a header.
-- @param header String with the header.
-- @param value String with the corresponding value.
----------------------------------------------------------------------------
function header(...)
   return SAPI.Response.header(...)
end

----------------------------------------------------------------------------
-- Sends a Content-type header.
-- @param type String with the type of the header.
-- @param subtype String with the subtype of the header.
----------------------------------------------------------------------------
function contentheader (type, subtype)
	SAPI.Response.contenttype (type..'/'..subtype)
end

----------------------------------------------------------------------------
-- Sends the HTTP header "text/html".
----------------------------------------------------------------------------
function htmlheader()
	SAPI.Response.contenttype ("text/html")
end
local htmlheader = htmlheader

----------------------------------------------------------------------------
-- Sends an HTTP header redirecting the browser to another URL
-- @param url String with the URL.
-- @param args Table with the arguments (optional).
----------------------------------------------------------------------------
function redirect (url, args)
	if strfind(url,"^https?:") then
		local params=""
		if args then
			params = "?"..urlcode.encodetable(args)
		end
		return SAPI.Response.redirect(url..params)
	else
		return SAPI.Response.redirect(mkabsoluteurl(mkurlpath(url,args)))
	end
end

----------------------------------------------------------------------------
-- Returns a server variable
-- @param name String with the name of the server variable.
-- @return String with the value of the server variable.
----------------------------------------------------------------------------
function servervariable(...)
   return SAPI.Request.servervariable(...)
end

----------------------------------------------------------------------------
-- Primitive error output function
-- @param msg String (or number) with the message.
-- @param level String with the error level (optional).
----------------------------------------------------------------------------
function errorlog (msg, level)
	local t = type(msg)
	if t == "string" or t == "number" then
		SAPI.Response.errorlog (msg, level)
	else
		error ("bad argument #1 to `cgilua.errorlog' (string expected, got "..t..")", 2)
	end
end

----------------------------------------------------------------------------
-- Converts all its arguments to strings before sending them to the server.
----------------------------------------------------------------------------
function print (...)
	local args = { ... }
	for i = 1, select("#",...) do
		args[i] = tostring(args[i])
	end
	SAPI.Response.write (concat(args,"\t"))
	SAPI.Response.write ("\n")
end

----------------------------------------------------------------------------
-- Function 'put' sends its arguments (basically strings of HTML text)
--  to the server
-- Its basic implementation is to use Lua function 'write', which writes
--  each of its arguments (strings or numbers) to file _OUTPUT (a file
--  handle initialized with the file descriptor for stdout)
-- @param s String (or number) with output.
----------------------------------------------------------------------------
function put (...)
   return SAPI.Response.write(...)
end

-- Returns the current errorhandler
function _geterrorhandler(msg)
    return _errorhandler(msg)
end

--
-- Executes a function using the CGILua error handler.
-- @param f Function to be called.
--
function pcall (f)
	local results = {xpcall (f, _geterrorhandler)}
	local ok = results[1]
	tremove(results, 1)
	if ok then
	        if #results == 0 then results = { true } end
		return unpack(results)
	else
		_erroroutput (unpack(results))
	end
end

local function buildscriptenv()
  local env = { print = _M.print, write = _M.put }
  setmetatable(env, { __index = _G, __newindex = _G })
  return env
end

----------------------------------------------------------------------------
-- Execute a script
--  If an error is found, Lua's error handler is called and this function
--  does not return
-- @param filename String with the name of the file to be processed.
-- @return The result of the execution of the file.
----------------------------------------------------------------------------
function doscript (filename)
  local f, err = _G.loadfile(filename)
  if not f then
    error (format ("Cannot execute `%s'. Exiting.\n%s", filename, err))
  else
    local env = buildscriptenv()
    setfenv(f, env)
    return pcall(f)
  end
end

----------------------------------------------------------------------------
-- Execute the file if there is no "file error".
--  If an error is found, and it is not a "file error", Lua 'error'
--  is called and this function does not return
-- @param filename String with the name of the file to be processed.
-- @return The result of the execution of the file or nil (in case the
--	file does not exists or if it cannot be opened).
-- @return It could return an error message if the file cannot be opened.
----------------------------------------------------------------------------
function doif (filename)
	if not filename then return end    -- no file
	local f, err = _open(filename)
	if not f then return nil, err end    -- no file (or unreadable file)
	f:close()
	return doscript (filename)
end

---------------------------------------------------------------------------
-- Set the maximum "total" input size allowed (in bytes)
-- @param nbytes Number of the maximum size (in bytes) of the whole POST data.
---------------------------------------------------------------------------
function setmaxinput(nbytes)
	_maxinput = nbytes
end

---------------------------------------------------------------------------
-- Set the maximum size for an "uploaded" file (in bytes)
-- Might be less or equal than _maxinput.
-- @param nbytes Number of the maximum size (in bytes) of a file.
---------------------------------------------------------------------------
function setmaxfilesize(nbytes)
	_maxfilesize = nbytes
end


-- Default path for temporary files
tmp_path = _G.CGILUA_TMP or getenv("TEMP") or getenv ("TMP") or "/tmp"

-- Default function for temporary names
-- @returns a temporay name using os.tmpname
tmpname = function()
    local tempname = os_tmpname()
    -- Lua os.tmpname returns a full path in Unix, but not in Windows
    -- so we strip the eventual prefix
    tempname = gsub(tempname, "(/tmp/)", "")
    return tempname
end

local _tmpfiles = {}

---------------------------------------------------------------------------
-- Returns a temporary file in a directory using a name generator
-- @param dir Base directory for the temporary file
-- @param namefunction Name generator function
---------------------------------------------------------------------------
function tmpfile(dir, namefunction)
    dir = dir or tmp_path
    namefunction = namefunction or tmpname
    local tempname = namefunction()
    local filename = dir.."/"..tempname
    local file, err = _open(filename, "wb+")
    if file then
        tinsert(_tmpfiles, {name = filename, file = file})
    end
    return file, err
end


----------------------------------------------------------------------------
-- Preprocess the content of a mixed HTML file and output a complete
--   HTML document ( a 'Content-type' header is inserted before the
--   preprocessed HTML )
-- @param filename String with the name of the file to be processed.
-- @param env Optional environment
----------------------------------------------------------------------------
function handlelp (filename, env)
  env = env or buildscriptenv()
  htmlheader ()
  lp.include (filename, env)
end

----------------------------------------------------------------------------
-- Builds a handler that sends a header and the contents of the given file.
-- Sends the contents of the file to the output without processing it.
-- @param type String with the type of the header.
-- @param subtype String with the subtype of the header.
-- @return Function (which receives a filename as argument) that produces
--	the header and copies the content of the given file.
----------------------------------------------------------------------------
function buildplainhandler (type, subtype)
	return function (filename)
		local fh, err = _open (filename, "rb")
        local contents = ""
        if fh then
            contents = fh:read("*a")
            fh:close()
        else
            error(err)
        end
        header("Content-Lenght", #contents)
		contentheader (type, subtype)
		put (contents)
	end
end

----------------------------------------------------------------------------
-- Builds a handler that sends a header and the processed file.
-- Processes the file as a Lua Page.
-- @param type String with the type of the header.
-- @param subtype String with the subtype of the header.
-- @return Function (which receives a filename as argument) that produces
--	the header and processes the given file.
----------------------------------------------------------------------------
function buildprocesshandler (type, subtype)
	return function (filename)
		 local env = buildscriptenv()
		 contentheader (type, subtype)
		 lp.include (filename, env)
	end
end

----------------------------------------------------------------------------
-- Builds the default handler table from cgilua.mime
----------------------------------------------------------------------------
local function buildhandlers()
    local mime = _G.require "cgilua.mime"
    for ext, mediatype in pairs(mime) do
        local t, st = match(mediatype, "([^/]*)/([^/]*)")
        addscripthandler(ext, buildplainhandler(t, st))
    end
end

----------------------------------------------------------------------------
-- Create an URL path to be used as a link to a CGILua script
-- @param script String with the name of the script.
-- @param args Table with arguments to script (optional).
-- @return String in URL format.
----------------------------------------------------------------------------
function mkurlpath (script, args)
	-- URL-encode the parameters to be passed do the script
	local params = ""
	if args then
		params = "?"..urlcode.encodetable(args)
	end
	if strsub(script,1,1) == "/" then
		return urlpath .. script .. params
	else
		return urlpath .. script_vdir .. script .. params
	end
end

----------------------------------------------------------------------------
-- Create an absolute URL containing the given URL path
-- @param path String with the path.
-- @param protocol String with the name of the protocol (default = "http").
-- @return String in URL format.
----------------------------------------------------------------------------
function mkabsoluteurl (path, protocol)
	protocol = protocol or "http"
	if path:sub(1,1) ~= '/' then
		path = '/'..path
	end
	return format("%s://%s:%s%s",
		protocol,
		servervariable"SERVER_NAME",
		servervariable"SERVER_PORT",
		path)
end

----------------------------------------------------------------------------
-- Extract the "directory" and "file" parts of a path
-- @param path String with a path.
-- @return String with the directory part.
-- @return String with the file part.
----------------------------------------------------------------------------
function splitonlast (path, sep)
	local dir,file = match(path,"^(.-)([^:/\\]*)$")
	return dir,file
end

splitpath = splitonlast -- compatibility with previous versions

----------------------------------------------------------------------------
-- Extracts the first and remaining parts of a path
-- @param path separator (defaults to "/")
-- @return String with the extracted part.
-- @return String with the remaining path.
----------------------------------------------------------------------------
function splitonfirst(path, sep)
    local first, rest = match(path, "^/([^:/\\]*)(.*)")
    return first, rest
end

--
-- Define variables and build the cgilua.POST, cgilua.GET tables.
--
local function getparams ()
    requestmethod = servervariable"REQUEST_METHOD"
	-- Fill in the POST table.
	POST = {}
	if  requestmethod == "POST" then
		post.parsedata {
			read = SAPI.Request.getpostdata,
			discardinput = ap and ap.discard_request_body,
			content_type = servervariable"CONTENT_TYPE",
			content_length = servervariable"CONTENT_LENGTH",
			maxinput = _maxinput,
			maxfilesize = _maxfilesize,
			args = POST,
		}
	end
	-- Fill in the QUERY table.
	QUERY = {}
	urlcode.parsequery (servervariable"QUERY_STRING", QUERY)
end

--
-- Stores all script handlers and the file extensions used to identify
-- them. Loads the default 
local _script_handlers = {}
--
-- Default handler.
-- Sends the contents of the file to the output without processing it.
-- This relies in the browser being able to discover the content type
-- which is not reliable.
-- @param filename String with the name of the file.
--
local function default_handler (filename)
	local fh, err = _open (filename, "rb")
    local contents
    if fh then
        contents = fh:read("*a")
        fh:close()
    else
        error(err)
    end
    header("Content-Lenght", #contents)
    put ("\n")
	put (contents)
end

----------------------------------------------------------------------------
-- Add a script handler.
-- @param file_extension String with the lower-case extension of the script.
-- @param func Function to handle this kind of scripts.
----------------------------------------------------------------------------
function addscripthandler (file_extension, func)
	assert (type(file_extension) == "string", "File extension must be a string")
	if strfind (file_extension, '%.', 1) then
		file_extension = strsub (file_extension, 2)
	end
	file_extension = strlower(file_extension)
	assert (type(func) == "function", "Handler must be a function")

	_script_handlers[file_extension] = func
end

---------------------------------------------------------------------------
-- Obtains the handler corresponding to the given script path.
-- @param path String with a script path.
-- @return Function that handles it or nil.
----------------------------------------------------------------------------
function getscripthandler (path)
	local i,f, ext = strfind (path, "%.([^.]+)$")
	return _script_handlers[strlower(ext or '')]
end

---------------------------------------------------------------------------
-- Execute the given path with the corresponding handler.
-- @param path String with a script path.
-- @return The returned values from the script.
---------------------------------------------------------------------------
function handle (path)
	local h = getscripthandler (path) or default_handler
    return h (path)
end

---------------------------------------------------------------------------
-- Sets "errorhandler" function
-- This function is called by Lua when an error occurs.
-- It receives the error message generated by Lua and it is resposible
-- for the final message which should be returned.
-- @param Function.
---------------------------------------------------------------------------
function seterrorhandler (f)
	local tf = type(f)
	if tf == "function" then
		_errorhandler = f
	else
		error (format ("Invalid type: expected `function', got `%s'", tf))
	end
end

---------------------------------------------------------------------------
-- Defines the "erroroutput" function
-- This function is called to generate the error output.
-- @param Function.
---------------------------------------------------------------------------
function seterroroutput (f)
	local tf = type(f)
	if tf == "function" then
		_erroroutput = f
	else
		error (format ("Invalid type: expected `function', got `%s'", tf))
	end
end

--
-- Stores all close functions in order they are set.
local _close_functions = {
}

---------------------------------------------------------------------------
-- Adds a function to be executed after the script.
-- @param f Function to be registered.
---------------------------------------------------------------------------
function addclosefunction (f)
	local tf = type(f)
	if tf == "function" then
		tinsert (_close_functions, f)
	else
		error (format ("Invalid type: expected `function', got `%s'", tf))
	end
end

--
-- Close function.
--
local function close()
	for i = #_close_functions, 1, -1 do
		_close_functions[i]()
	end
end

--
-- Stores all open functions in order they are set.
local _open_functions = {
}

---------------------------------------------------------------------------
-- Adds a function to be executed before the script.
-- @param f Function to be registered.
---------------------------------------------------------------------------
function addopenfunction (f)
	local tf = type(f)
	if tf == "function" then
		tinsert (_open_functions, f)
	else
		error (format ("Invalid type: expected `function', got `%s'", tf))
	end
end

--
-- Open function.
-- Call all defined open-functions in the order they were created.
--
local function open()
	for i = #_open_functions, 1, -1 do
		_open_functions[i]()
	end
end

--
-- Resets CGILua's state.
--
local function reset ()
	script_path = false
        script_vpath, pdir, use_executable_name, urlpath, script_vdir, script_pdir,
          script_file, authentication, app_name = 
               nil, nil, nil, nil, nil, nil, nil, nil, nil
	_maxfilesize = _default_maxfilesize
	_maxinput = _default_maxinput
	-- Error Handling
	_errorhandler = _default_errorhandler
	_erroroutput = _default_erroroutput
	-- Handlers
	_script_handlers = {}
	_open_functions = {}
	_close_functions = {}
    -- clean temporary files
    foreachi(_tmpfiles, function (i, v)
        v.file:close()
        local _, err = remove(v.name)
        if err then
            error(err)
        end
    end)
end

---------------------------------------------------------------------------
-- Request processing.
---------------------------------------------------------------------------
function main ()
        SAPI = _G.SAPI
	buildhandlers()    
	-- Default handler values
	addscripthandler ("lua", doscript)
	addscripthandler ("lp", handlelp)
	-- Looks for an optional loader module
	pcall (function () _G.require"cgilua.loader" end)

	-- post.lua needs to be loaded after cgilua.lua is compiled
	pcall (function () _G.require"cgilua.post" end)

	if loader then
		loader.init()
	end
    
	-- Build QUERY/POST tables
	if not pcall (getparams) then return nil end

	local result
	-- Executes the optional loader module
	if loader then
		loader.run()
	end

	-- Changing curent directory to the script's "physical" dir
	local curr_dir = lfs.currentdir ()
	pcall (function () lfs.chdir (script_pdir) end)

	-- Opening functions
	pcall (open)

	-- Executes the script
	result, err = pcall (function () return handle (script_file) end)
    
	-- Closing functions
	pcall (close)
	-- Changing to original directory
	pcall (function () lfs.chdir (curr_dir) end)

	-- Cleanup
	reset ()
	if result then -- script executed ok!
		return result
	end
end
genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/cookies.lua000066400000000000000000000062201211610345200245550ustar00rootroot00000000000000----------------------------------------------------------------------------
-- Cookies Library
--
-- @release $Id: cookies.lua,v 1.8 2008/04/24 13:42:04 mascarenhas Exp $
----------------------------------------------------------------------------

require"cgilua.urlcode"

local error = error
local format, gsub, strfind = string.format, string.gsub, string.find
local date = os.date
local escape, unescape = cgilua.urlcode.escape, cgilua.urlcode.unescape
local function header(...)
   return SAPI.Response.header(...)
end
local function write(...)
   return SAPI.Response.write(...)
end
local function servervariable(...)
   return SAPI.Request.servervariable(...)
end

module ("cgilua.cookies")

local function optional (what, name)
  if name ~= nil and name ~= "" then
    return format("; %s=%s", what, name)
  else
    return ""
  end
end


local function build (name, value, options)
  if not name or not value then
    error("cookie needs a name and a value")
  end
  local cookie = name .. "=" .. escape(value)
  options = options or {}
  if options.expires then
    local t = date("!%A, %d-%b-%Y %H:%M:%S GMT", options.expires)
    cookie = cookie .. optional("expires", t)
  end
  cookie = cookie .. optional("path", options.path)
  cookie = cookie .. optional("domain", options.domain)
  cookie = cookie .. optional("secure", options.secure)
  return cookie
end


----------------------------------------------------------------------------
-- Sets a value to a cookie, with the given options.
-- Generates a header "Set-Cookie", thus it can only be used in Lua Scripts.
-- @param name String with the name of the cookie.
-- @param value String with the value of the cookie.
-- @param options Table with the options (optional).

function set (name, value, options)
  header("Set-Cookie", build(name, value, options))
end


----------------------------------------------------------------------------
-- Sets a value to a cookie, with the given options.
-- Generates an HTML META tag, thus it can be used in Lua Pages.
-- @param name String with the name of the cookie.
-- @param value String with the value of the cookie.
-- @param options Table with the options (optional).

function sethtml (name, value, options)
  write(format('', 
                build(name, value, options)))
end


----------------------------------------------------------------------------
-- Gets the value of a cookie.
-- @param name String with the name of the cookie.
-- @return String with the value associated with the cookie.

function get (name)
  local cookies = servervariable"HTTP_COOKIE" or ""
  cookies = ";" .. cookies .. ";"
  cookies = gsub(cookies, "%s*;%s*", ";")   -- remove extra spaces
  local pattern = ";" .. name .. "=(.-);"
  local _, __, value = strfind(cookies, pattern)
  return value and unescape(value)
end


----------------------------------------------------------------------------
-- Deletes a cookie, by setting its value to "xxx".
-- @param name String with the name of the cookie.
-- @param options Table with the options (optional).

function delete (name, options)
  options = options or {}
  options.expires = 1
  set(name, "xxx", options)
end
genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/dispatcher.lua000066400000000000000000000041501211610345200252470ustar00rootroot00000000000000-- CGILua dispatcher module
-- @release $Id: dispatcher.lua,v 1.8 2007/12/07 18:49:49 carregal Exp $

module(..., package.seeall)

-- Checks if an URL matches a route pattern
local function route_match(url, pattern) 
    local params = {}
    local captures = string.gsub(pattern, "(/$[%w_-]+)", "/([^/]*)")
    local url_parts = {string.match(url, captures)}
    local i = 1
    for name in string.gmatch(pattern, "/$([%w_-]+)") do
        params[name] = url_parts[i]
        i = i + 1
    end
    return next(params) and params
end

local route_URLs = {}

-- Maps the correct function for an URL
local function route_map(url) 
    for i, v in ipairs(route_URLs) do
        local pattern, f, name = unpack(v)
        local params = route_match(url, pattern)
        if params then 
            return f, params 
        end
    end
end

-- Returns an URL for a named route
-- @param map_name Name associated with the map in the routed URL table.
-- @param params Table of named parameters used in the URL map
-- @param queryargs Optional table of named parameters used for the QUERY part of the URL
function route_url(map_name, params, queryargs)
	local queryparams = ""
	if queryargs then
		queryparams = "?"..cgilua.urlcode.encodetable(queryargs)
	end
	for i, v in ipairs(route_URLs) do
        local pattern, f, name = unpack(v)
        if name == map_name then
            local url = string.gsub(pattern, "$([%w_-]+)", params)
            url = cgilua.urlpath.."/"..cgilua.app_name..url..queryparams
            return url
        end
    end
end

-- Defines the routing using a table of URLs maps or a single map
-- a map defines a URL mask using $name to extract parameters,
-- a function to be called with the extracted parameters and
-- a name for the map when used with route_url
-- @param table of maps or a single map
function route(URLs)
	URLs = URLs or {}
	if type(URLs[1]) == "string" then
		-- accepts a single map as the only entry in a map table
		URLs = {URLs}
	end
    route_URLs = URLs
    f, args = route_map(cgilua.script_vpath)

    if f then
        return f(args)
    else
        error("Missing page parameters")
    end
endgenometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/loader.lua000066400000000000000000000066741211610345200244040ustar00rootroot00000000000000-- CGILua loader
--
-- Assumes two global variables pointing to directories:
--  CGILUA_CONF - CGILua configuration directory
--  CGILUA_TMP  - CGILua temporary files directory
--
-- # $Id: loader.lua,v 1.7 2008/03/28 22:01:18 ignacio Exp $

require "lfs"

module("cgilua.loader", package.seeall)

function init()
   -- Loads the user configuration
   cgilua.doif (CGILUA_CONF.."/config.lua")
end

function run()
   local servervariable = cgilua.servervariable
   cgilua.script_vpath = cgilua.script_vpath or servervariable"PATH_INFO"

   if cgilua.script_vpath == nil or cgilua.script_vpath == "" then
      cgilua.script_vpath = "/"
   end

   local document_root = cgilua.pdir or servervariable"DOCUMENT_ROOT"

   if not cgilua.script_path then
      if CGILUA_ISDIRECT then -- the launcher is associated with scripts (Xavante, mod_lua or isapi usually)
	 if servervariable"PATH_TRANSLATED" ~= "" then
	    cgilua.script_path = servervariable"PATH_TRANSLATED"
	 else
	    cgilua.script_path = servervariable"SCRIPT_FILENAME"
	 end
      else -- the launcher executable is present in the URL (CGI or FastCGI only)
	 if document_root == nil or document_root == "" then
	    -- tries to obtain documents_root from the server
	    local path_info = cgilua.script_vpath
	    if path_info == nil or path_info == "" or path_info == "/" then
	       document_root = cgilua.pdir or servervariable"PATH_TRANSLATED"
	    else
	       if string.find(servervariable("SERVER_SOFTWARE"), "IIS") then
		  path_info = string.gsub(path_info, "/", "\\")
	       end
	       document_root = cgilua.pdir or string.gsub(servervariable"PATH_TRANSLATED", path_info, "")
	    end
	 end
	 if cgilua.use_executable_name then
	    -- looks for a Lua script with the same name as the executable
	    local _, name = cgilua.splitpath(servervariable"SCRIPT_NAME")
	    name = string.gsub(name, "%.[^%.]-$","")
		if name and lfs.attributes(document_root.."/"..name..".lua") then
			cgilua.script_path = document_root.."/"..name..".lua"
		end
	 else
	    -- uses /index.lua then /index.lp as the default script
	    if cgilua.script_vpath == "/" then
	       if lfs.attributes(document_root.."/index.lua") then
		  cgilua.script_vpath = "/index.lua"
	       elseif lfs.attributes(document_root.."/index.lp") then
		  cgilua.script_vpath = "/index.lp"
	       else
		  error("Kepler is correctly configured, but you didn't provide a script!")
	       end                    
	    end
	    -- checks if PATH_INFO refers to a valid file and ajusts the settings accordingly
	    local filepath, path_info = string.match (cgilua.script_vpath, "^([^%.]-%.[^/]+)(.*)")
	    if filepath and lfs.attributes(document_root..filepath) then
	       -- if one is found use it
	       cgilua.script_path = document_root..filepath
	       cgilua.script_vpath = path_info
	       cgilua.urlpath = cgilua.urlpath or servervariable"SCRIPT_NAME"..filepath
	    else
	       -- otherwise go with the current PATH_INFO
	       cgilua.script_path = document_root..cgilua.script_vpath
	    end
	 end
      end
   end
   
   -- define other cgilua vars so mkurlpath can work correctly
   if cgilua.script_vpath then
      cgilua.script_vdir = cgilua.splitpath (cgilua.script_vpath)
      cgilua.urlpath = cgilua.urlpath or servervariable"SCRIPT_NAME"
   else
      cgilua.script_vdir = cgilua.splitpath (servervariable"SCRIPT_NAME")
      cgilua.urlpath = cgilua.urlpath or ""
   end

   cgilua.script_pdir, cgilua.script_file = cgilua.splitpath (cgilua.script_path)
end
genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/lp.lua000066400000000000000000000107101211610345200235330ustar00rootroot00000000000000----------------------------------------------------------------------------
-- Lua Pages Template Preprocessor.
--
-- @release $Id: lp.lua,v 1.15 2008/12/11 17:40:24 mascarenhas Exp $
----------------------------------------------------------------------------

local assert, error, getfenv, loadstring, setfenv = assert, error, getfenv, loadstring, setfenv
local find, format, gsub, strsub, char = string.find, string.format, string.gsub, string.sub, string.char
local concat, tinsert = table.concat, table.insert
local open = io.open

module (...)

----------------------------------------------------------------------------
-- function to do output
local outfunc = "io.write"
-- accepts the old expression field: `$|  |$'
local compatmode = true

--
-- Builds a piece of Lua code which outputs the (part of the) given string.
-- @param s String.
-- @param i Number with the initial position in the string.
-- @param f Number with the final position in the string (default == -1).
-- @return String with the correspondent Lua code which outputs the part of the string.
--
local function out (s, i, f)
	s = strsub(s, i, f or -1)
	if s == "" then return s end
	-- we could use `%q' here, but this way we have better control
	s = gsub(s, "([\\\n\'])", "\\%1")
	-- substitute '\r' by '\'+'r' and let `loadstring' reconstruct it
	s = gsub(s, "\r", "\\r")
	return format(" %s('%s'); ", outfunc, s)
end


----------------------------------------------------------------------------
-- Translate the template to Lua code.
-- @param s String to translate.
-- @return String with translated code.
----------------------------------------------------------------------------
function translate (s)
        s = gsub(s, "^#![^\n]+\n", "")
	if compatmode then
		s = gsub(s, "$|(.-)|%$", "")
		s = gsub(s, "", "")
	end
	s = gsub(s, "<%%(.-)%%>", "")
	local res = {}
	local start = 1   -- start of untranslated part in `s'
	while true do
		local ip, fp, target, exp, code = find(s, "<%?(%w*)[ \t]*(=?)(.-)%?>", start)
		if not ip then break end
		tinsert(res, out(s, start, ip-1))
		if target ~= "" and target ~= "lua" then
			-- not for Lua; pass whole instruction to the output
			tinsert(res, out(s, ip, fp))
		else
			if exp == "=" then   -- expression?
				tinsert(res, format(" %s(%s);", outfunc, code))
			else  -- command
				tinsert(res, format(" %s ", code))
			end
		end
		start = fp + 1
	end
	tinsert(res, out(s, start))
	return concat(res)
end


----------------------------------------------------------------------------
-- Defines the name of the output function.
-- @param f String with the name of the function which produces output.

function setoutfunc (f)
	outfunc = f
end

----------------------------------------------------------------------------
-- Turns on or off the compatibility with old CGILua 3.X behavior.
-- @param c Boolean indicating if the compatibility mode should be used.

function setcompatmode (c)
	compatmode = c
end

----------------------------------------------------------------------------
-- Internal compilation cache.

local cache = {}

----------------------------------------------------------------------------
-- Translates a template into a Lua function.
-- Does NOT execute the resulting function.
-- Uses a cache of templates.
-- @param string String with the template to be translated.
-- @param chunkname String with the name of the chunk, for debugging purposes.
-- @return Function with the resulting translation.

function compile (string, chunkname)
	local f, err = cache[string]
	if f then return f end
	f, err = loadstring (translate (string), chunkname)
	if not f then error (err, 3) end
	cache[string] = f
	return f
end

----------------------------------------------------------------------------
-- Translates and executes a template in a given file.
-- The translation creates a Lua function which will be executed in an
-- optionally given environment.
-- @param filename String with the name of the file containing the template.
-- @param env Table with the environment to run the resulting function.
local BOM = char(239) .. char(187) .. char(191)

function include (filename, env)
	-- read the whole contents of the file
	local fh = assert (open (filename))
	local src = fh:read("*a")
	fh:close()
	if src:sub(1,3) == BOM then src = src:sub(4) end
	-- translates the file into a function
	local prog = compile (src, '@'..filename)
	local _env
	if env then
		_env = getfenv (prog)
		setfenv (prog, env)
	end
	prog ()
end
genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/mime.lua000066400000000000000000000124551211610345200240570ustar00rootroot00000000000000-----------------------------------------------------------------------------
-- Xavante MIME types
--
-- Authors: Javier Guerra and Andre Carregal
-- Copyright (c) 2004-2007 Kepler Project
--
-- $Id: mime.lua,v 1.1 2007/09/25 23:17:56 carregal Exp $
-----------------------------------------------------------------------------

-- Extracted from Apache's mime.types
-- This file controls what Internet media types are sent to the client for
-- given file extension(s).  Sending the correct media type to the client
-- is important so they know how to handle the content of the file.
-- Extra types can either be added here or by using an AddType directive
-- in your config files. For more information about Internet media types,
-- please read RFC 2045, 2046, 2047, 2048, and 2077.  The Internet media type
-- registry is at .

return {
  ez = "application/andrew-inset",
  atom = "application/atom+xml",
  hqx = "application/mac-binhex40",
  cpt = "application/mac-compactpro",
  mathml = "application/mathml+xml",
  doc = "application/msword",
  bin = "application/octet-stream",
  dms = "application/octet-stream",
  lha = "application/octet-stream",
  lzh = "application/octet-stream",
  exe = "application/octet-stream",
  class = "application/octet-stream",
  so = "application/octet-stream",
  dll = "application/octet-stream",
  dmg = "application/octet-stream",
  oda = "application/oda",
  ogg = "application/ogg",
  pdf = "application/pdf",
  ai = "application/postscript",
  eps = "application/postscript",
  ps = "application/postscript",
  rdf = "application/rdf+xml",
  smi = "application/smil",
  smil = "application/smil",
  gram = "application/srgs",
  grxml = "application/srgs+xml",
  mif = "application/vnd.mif",
  xul = "application/vnd.mozilla.xul+xml",
  xls = "application/vnd.ms-excel",
  ppt = "application/vnd.ms-powerpoint",
  rm = "application/vnd.rn-realmedia",
  wbxml = "application/vnd.wap.wbxml",
  wmlc = "application/vnd.wap.wmlc",
  wmlsc = "application/vnd.wap.wmlscriptc",
  vxml = "application/voicexml+xml",
  bcpio = "application/x-bcpio",
  vcd = "application/x-cdlink",
  pgn = "application/x-chess-pgn",
  cpio = "application/x-cpio",
  csh = "application/x-csh",
  dcr = "application/x-director",
  dir = "application/x-director",
  dxr = "application/x-director",
  dvi = "application/x-dvi",
  spl = "application/x-futuresplash",
  gtar = "application/x-gtar",
  hdf = "application/x-hdf",
  xhtml = "application/xhtml+xml",
  xht = "application/xhtml+xml",
  js = "application/x-javascript",
  skp = "application/x-koan",
  skd = "application/x-koan",
  skt = "application/x-koan",
  skm = "application/x-koan",
  latex = "application/x-latex",
  xml = "application/xml",
  xsl = "application/xml",
  dtd = "application/xml-dtd",
  nc = "application/x-netcdf",
  cdf = "application/x-netcdf",
  sh = "application/x-sh",
  shar = "application/x-shar",
  swf = "application/x-shockwave-flash",
  xslt = "application/xslt+xml",
  sit = "application/x-stuffit",
  sv4cpio = "application/x-sv4cpio",
  sv4crc = "application/x-sv4crc",
  tar = "application/x-tar",
  tcl = "application/x-tcl",
  tex = "application/x-tex",
  texinfo = "application/x-texinfo",
  texi = "application/x-texinfo",
  t = "application/x-troff",
  tr = "application/x-troff",
  roff = "application/x-troff",
  man = "application/x-troff-man",
  me = "application/x-troff-me",
  ms = "application/x-troff-ms",
  ustar = "application/x-ustar",
  src = "application/x-wais-source",
  zip = "application/zip",
  au = "audio/basic",
  snd = "audio/basic",
  mid = "audio/midi",
  midi = "audio/midi",
  kar = "audio/midi",
  mpga = "audio/mpeg",
  mp2 = "audio/mpeg",
  mp3 = "audio/mpeg",
  aif = "audio/x-aiff",
  aiff = "audio/x-aiff",
  aifc = "audio/x-aiff",
  m3u = "audio/x-mpegurl",
  ram = "audio/x-pn-realaudio",
  ra = "audio/x-pn-realaudio",
  wav = "audio/x-wav",
  pdb = "chemical/x-pdb",
  xyz = "chemical/x-xyz",
  bmp = "image/bmp",
  cgm = "image/cgm",
  gif = "image/gif",
  ief = "image/ief",
  jpeg = "image/jpeg",
  jpg = "image/jpeg",
  jpe = "image/jpeg",
  png = "image/png",
  svg = "image/svg+xml",
  svgz = "image/svg+xml",
  tiff = "image/tiff",
  tif = "image/tiff",
  djvu = "image/vnd.djvu",
  djv = "image/vnd.djvu",
  wbmp = "image/vnd.wap.wbmp",
  ras = "image/x-cmu-raster",
  ico = "image/x-icon",
  pnm = "image/x-portable-anymap",
  pbm = "image/x-portable-bitmap",
  pgm = "image/x-portable-graymap",
  ppm = "image/x-portable-pixmap",
  rgb = "image/x-rgb",
  xbm = "image/x-xbitmap",
  xpm = "image/x-xpixmap",
  xwd = "image/x-xwindowdump",
  igs = "model/iges",
  iges = "model/iges",
  msh = "model/mesh",
  mesh = "model/mesh",
  silo = "model/mesh",
  wrl = "model/vrml",
  vrml = "model/vrml",
  ics = "text/calendar",
  ifb = "text/calendar",
  css = "text/css",
  html = "text/html",
  htm = "text/html",
  asc = "text/plain",
  txt = "text/plain",
  rtx = "text/richtext",
  rtf = "text/rtf",
  sgml = "text/sgml",
  sgm = "text/sgml",
  tsv = "text/tab-separated-values",
  wml = "text/vnd.wap.wml",
  wmls = "text/vnd.wap.wmlscript",
  etx = "text/x-setext",
  mpeg = "video/mpeg",
  mpg = "video/mpeg",
  mpe = "video/mpeg",
  qt = "video/quicktime",
  mov = "video/quicktime",
  mxu = "video/vnd.mpegurl",
  avi = "video/x-msvideo",
  movie = "video/x-sgi-movie",
  ice = "x-conference/x-cooltalk",
}
genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/post.lua000066400000000000000000000225651211610345200241200ustar00rootroot00000000000000----------------------------------------------------------------------------
-- Process POST data.
-- This library depends on some functions that read POST data and other
-- HTTP information.  A beginning is:
--	require"post"
--	local params = {}
--	post.parsedata {
--		read = ap.get_client_block or io.input,
--		discardinput = ap.discard_request_body,
--		content_type = ap.get_header"content-type" or os.getenv"CONTENT_TYPE",
--		content_length = ap.get_header"content-length" or os.getenv"CONTENT_LENGTH",
--		maxinput = 1024 * 1024,
--		maxfilesize = 512 * 1024,
--		args = params,
--	}
--
-- @release $Id: post.lua,v 1.17 2008/04/03 21:55:28 mascarenhas Exp $
----------------------------------------------------------------------------

require"cgilua.readuntil"
require"cgilua.urlcode"

local assert, error, pairs, tonumber, tostring, type = assert, error, pairs, tonumber, tostring, type
local getn, tinsert = table.getn, table.insert
local format, gsub, strfind, strlower, strlen = string.format, string.gsub, string.find, string.lower, string.len
local min = math.min
local iterate = cgilua.readuntil.iterate
local urlcode = cgilua.urlcode
local tmpfile = cgilua.tmpfile

-- environment for processing multipart/form-data input
local boundary = nil      -- boundary string that separates each 'part' of input
local maxfilesize = nil   -- maximum size for file upload
local maxinput = nil      -- maximum size of total POST data
local inputfile = nil     -- temporary file for inputting form-data
local bytesleft = nil     -- number of bytes yet to be read
local content_type = nil  -- request's content-type
-- local functions
local discardinput = nil  -- discard all remaining input
local readuntil = nil     -- read until delimiter
local read = nil          -- basic read function

module ("cgilua.post")

--
-- Extract the boundary string from CONTENT_TYPE metavariable
--
local function getboundary ()
  local _,_,boundary = strfind (content_type, "boundary%=(.-)$")
  return  "--"..boundary 
end

--
-- Create a table containing the headers of a multipart/form-data field
--
local function breakheaders (hdrdata)
  local headers = {}
  gsub (hdrdata, '([^%c%s:]+):%s+([^\n]+)', function(type,val)
    type = strlower(type)
    headers[type] = val
  end)
  return headers
end

--
-- Read the headers of the next multipart/form-data field 
--
--  This function returns a table containing the headers values. Each header
--  value is indexed by the corresponding header "type". 
--  If end of input is reached (no more fields to process) it returns nil.
--
local function readfieldheaders ()
	local EOH = "\r\n\r\n" -- 
	local hdrdata = ""
	local out = function (str) hdrdata = hdrdata..str end
	if readuntil (EOH, out) then
		-- parse headers
		return breakheaders (hdrdata)
	else
		-- no header found
		return nil
	end
end

--
-- Extract a field name (and possible filename) from its disposition header
--
local function getfieldnames (headers)
  local disposition_hdr = headers["content-disposition"]
  local attrs = {}
  if disposition_hdr then
    gsub(disposition_hdr, ';%s*([^%s=]+)="(.-)"', function(attr, val)
	   attrs[attr] = val
         end)
  else
    error("Error processing multipart/form-data."..
          "\nMissing content-disposition header")
  end
  return attrs.name, attrs.filename
end

--
-- Read the contents of a 'regular' field to a string
--
local function readfieldcontents ()
	local value = ""
	local boundaryline = "\r\n"..boundary
	local out = function (str) value = value..str end
	if readuntil (boundaryline, out) then
		return value
	else
		error("Error processing multipart/form-data.\nUnexpected end of input\n")
	end
end

--
-- Read the contents of a 'file' field to a temporary file (file upload)
--
local function fileupload (filename)
	-- create a temporary file for uploading the file field
	local file, err = tmpfile()
	if file == nil then
		discardinput(bytesleft)
		error("Cannot create a temporary file.\n"..err)
	end      
	local bytesread = 0
	local boundaryline = "\r\n"..boundary
	local out = function (str)
		local sl = strlen (str)
		if bytesread + sl > maxfilesize then
			discardinput (bytesleft)
			error (format ("Maximum file size (%d kbytes) exceeded while uploading `%s'", maxfilesize / 1024, filename))
		end
		file:write (str)
		bytesread = bytesread + sl
	end
	if readuntil (boundaryline, out) then
		file:seek ("set", 0)
		return file, bytesread
	else
		error (format ("Error processing multipart/form-data.\nUnexpected end of input while uploading %s", filename))
	end
end

--
-- Compose a file field 'value' 
--
local function filevalue (filehandle, filename, filesize, headers)
  -- the temporary file handle
  local value = { file = filehandle,
                  filename = filename,
                  filesize = filesize }
  -- copy additional header values
  for hdr, hdrval in pairs(headers) do
    if hdr ~= "content-disposition" then
      value[hdr] = hdrval
    end
  end
  return value
end

--
-- Process multipart/form-data 
--
-- This function receives the total size of the incoming multipart/form-data, 
-- the maximum size for a file upload, and a reference to a table where the 
-- form fields should be stored.
--
-- For every field in the incoming form-data a (name=value) pair is 
-- inserted into the given table. [[name]] is the field name extracted
-- from the content-disposition header.
--
-- If a field is of type 'file' (i.e., a 'filename' attribute was found
-- in its content-disposition header) a temporary file is created 
-- and the field contents are written to it. In this case,
-- [[value]] has a table that contains the temporary file handle 
-- (key 'file') and the file name (key 'filename'). Optional headers
-- included in the field description are also inserted into this table,
-- as (header_type=value) pairs.
--
-- If the field is not of type 'file', [[value]] contains the field 
-- contents.
--
local function Main (inputsize, args)

	-- create a temporary file for processing input data
	local inputf,err = tmpfile()
	if inputf == nil then
		discardinput(inputsize)
		error("Cannot create a temporary file.\n"..err)
	end

	-- set the environment for processing the multipart/form-data
	inputfile = inputf
	bytesleft = inputsize
	maxfilesize = maxfilesize or inputsize 
	boundary = getboundary()

	while true do
		-- read the next field header(s)
		local headers = readfieldheaders()
		if not headers then break end	-- end of input

		-- get the name attributes for the form field (name and filename)
		local name, filename = getfieldnames(headers)

		-- get the field contents
		local value
		if filename then
			local filehandle, filesize = fileupload(filename)
			value = filevalue(filehandle, filename, filesize, headers)
		else
			value = readfieldcontents()
		end

		-- insert the form field into table [[args]]
		urlcode.insertfield(args, name, value)
	end
end

--
-- Initialize the library by setting the dependent functions:
--	content_type            = value of "Content-type" header
--	content_length          = value of "Content-length" header
--	read                    = function that can read POST data
--	discardinput (optional) = function that discard POST data
--	maxinput (optional)     = limit of POST data (in bytes)
--	maxfilesize (optional)  = limit of uploaded file(s) (in bytes)
--
local function init (defs)
	assert (defs.read)
	read = defs.read
	readuntil = iterate (function ()
        if bytesleft then
            if bytesleft <= 0 then return nil end
            local n = min (bytesleft, 2^13) -- 2^13 == 8192
            local bytes = read (n)
            bytesleft = bytesleft - #bytes
            return bytes
        end
	end)
	if defs.discard_function then
		discardinput = defs.discardinput
	else
		discardinput = function (inputsize)
			readuntil ('\0', function()end)
		end
	end
	content_type = defs.content_type
	if defs.maxinput then
		maxinput = defs.maxinput
	end
	if defs.maxfilesize then
		maxfilesize = defs.maxfilesize
	end
end

----------------------------------------------------------------------------
-- Parse the POST REQUEST incoming data according to its "content type"
-- as defined by the metavariable CONTENT_TYPE (RFC CGI)
--
--  An error is issued if the "total" size of the incoming data
--   (defined by the metavariable CONTENT_LENGTH) exceeds the
--   maximum input size allowed
----------------------------------------------------------------------------
function parsedata (defs)
	assert (type(defs.args) == "table", "field `args' must be a table")
	init (defs)
	-- get the "total" size of the incoming data
	local inputsize = tonumber(defs.content_length) or 0
	if inputsize > maxinput then
		-- some Web Servers (like IIS) require that all the incoming data is read 
		bytesleft = inputsize
		discardinput(inputsize)
		error(format("Total size of incoming data (%d KB) exceeds configured maximum (%d KB)",
			inputsize /1024, maxinput / 1024))
	end

	-- process the incoming data according to its content type
	local contenttype = content_type
	if not contenttype then
		error("Undefined Media Type") 
	end
	if strfind(contenttype, "x-www-form-urlencoded", 1, true) then
		urlcode.parsequery (read (inputsize), defs.args)
	elseif strfind(contenttype, "multipart/form-data", 1, true) then
		Main (inputsize, defs.args)
	elseif strfind (contenttype, "application/xml", 1, true) or strfind (contenttype, "text/xml", 1, true) or strfind (contenttype, "text/plain", 1, true) then
		tinsert (defs.args, read (inputsize))
	else
		error("Unsupported Media Type: "..contenttype)
	end
end
genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/readuntil.lua000066400000000000000000000027231211610345200251140ustar00rootroot00000000000000----------------------------------------------------------------------------
-- Reads an input until a given character.
--
-- @release $Id: readuntil.lua,v 1.5 2007/04/16 14:01:32 tomas Exp $
----------------------------------------------------------------------------

local strsub, strfind, strlen = string.sub, string.find, string.len

module ("cgilua.readuntil")

----------------------------------------------------------------------------
-- Creates a function which reads an input until a given character.
-- @param inp Function which reads the input.
-- @return Function which receives a delimiter character and an output
--	function.
----------------------------------------------------------------------------
function iterate (inp)
	local current = ""
	return function (del, out)
		local dellen = strlen(del) 
		local i, e
		while true do
			i, e = strfind(current, del, 1, 1)
			if i then break end
			local new = inp()
			if not new then break end
			do	 -- handle borders
				local endcurrent = strsub(current, -dellen+1)
				local border = endcurrent .. strsub(new, 1, dellen-1)
				if strlen(current) < dellen or strlen(new) < dellen or
					 strfind(border, del, 1, 1) then
					-- move last part of `current' to new block
					current = strsub(current, 1, -dellen)
					new = endcurrent .. new
				end
			end
			out(current)
			current = new
		end
		out(strsub(current, 1, (i or 0) - 1))
		current = strsub(current, (e or strlen(current)) + 1)
		return (i ~= nil)
	end
end
genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/serialize.lua000066400000000000000000000057171211610345200251220ustar00rootroot00000000000000----------------------------------------------------------------------------
-- Serialize tables.
-- It works only for tables without cycles and without functions or
-- userdata inside it.
-- @release $Id: serialize.lua,v 1.7 2007/04/16 14:01:32 tomas Exp $
----------------------------------------------------------------------------

local ipairs, pairs, type = ipairs, pairs, type
local format = string.format
local sort, tinsert = table.sort, table.insert

--
local value = nil

----------------------------------------------------------------------------
-- Serializes a table.
-- @param tab Table representing the session.
-- @param outf Function used to generate the output.
-- @param ind String with indentation pattern (default = "").
-- @param pre String with indentation prefix (default = "").
----------------------------------------------------------------------------
local function tabledump (tab, outf, ind, pre)
	local sep_n, sep, _n = ",\n", ", ", "\n"
	if (not ind) or (ind == "") then ind = ""; sep_n = ", "; _n = "" end
	if not pre then pre = "" end
	outf ("{")
	local p = pre..ind
	-- prepare list of keys
	local keys = { boolean = {}, number = {}, string = {} }
	local total = 0
	for key in pairs (tab) do
		total = total + 1
		local t = type(key)
		if t == "string" then
			tinsert (keys.string, key)
		else
			keys[t][key] = true
		end
	end
	local many = total > 5
	if not many then sep_n = sep; _n = " " end
	outf (_n)
	-- serialize entries with numeric keys
	if many then
		local _f,_s,_v = ipairs(tab)
		if _f(_s,_v) then outf (p) end
	end
	local num = keys.number
	local ok = false
	-- entries with automatic index
	for key, val in ipairs (tab) do
		value (val, outf, ind, p)
		outf (sep)
		num[key] = nil
		ok = true
	end
	if ok and many then outf (_n) end
	-- entries with explicit index
	for key in pairs (num) do
		if many then outf (p) end
		outf ("[")
		outf (key)
		outf ("] = ")
		value (tab[key], outf, ind, p)
		outf (sep_n)
	end
	-- serialize entries with boolean keys
	local tr = keys.boolean[true]
	if tr then
		outf (format ("%s[true] = ", many and p or ''))
		value (tab[true], outf, ind, p)
		outf (sep_n)
	end
	local fa = keys.boolean[false]
	if fa then
		outf (format ("%s[false] = ", many and p or ''))
		value (tab[false], outf, ind, p)
		outf (sep_n)
	end
	-- serialize entries with string keys
	sort (keys.string)
	for _, key in ipairs (keys.string) do
		outf (format ("%s[%q] = ", many and p or '', key))
		value (tab[key], outf, ind, p)
		outf (sep_n)
	end
	if many then outf (pre) end
	outf ("}")
end


--
-- Serializes a value.
--
value = function (v, outf, ind, pre)
	local t = type (v)
	if t == "string" then
		outf (format ("%q", v))
	elseif t == "number" then
		outf (tostring(v))
	elseif t == "boolean" then
		outf (tostring(v))
	elseif t == "table" then
		tabledump (v, outf, ind, pre)
	else
		outf (format ("%q", tostring(v)))
	end
end

----------------------------------------------------------------------------
cgilua.serialize = tabledump

return tabledump
genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/session.lua000066400000000000000000000162451211610345200246140ustar00rootroot00000000000000----------------------------------------------------------------------------
-- Session library.
--
-- @release $Id: session.lua,v 1.29 2007/11/21 16:33:20 carregal Exp $
----------------------------------------------------------------------------

local lfs = require"lfs"
local serialize = require"cgilua.serialize"

local assert, error, ipairs, _G, loadfile, next, tostring, type = assert, error, ipairs, _G, loadfile, next, tostring, type
local format, gsub, strfind, strsub = string.format, string.gsub, string.find, string.sub
local tinsert = table.insert
local _open = io.open
local remove, time = os.remove, os.time
local mod, rand, randseed = math.mod, math.random, math.randomseed
local attributes, dir, mkdir = lfs.attributes, lfs.dir, lfs.mkdir

module ("cgilua.session")

local INVALID_SESSION_ID = "Invalid session identification"

----------------------------------------------------------------------------
-- Internal state variables.
local root_dir = nil
local timeout = 10 * 60 -- 10 minutes

--
-- Checks identifier's format.
--
local function check_id (id)
	return id and (strfind (id, "^%d+$") ~= nil)
end

--
-- Produces a file name based on a session.
-- @param id Session identification.
-- @return String with the session file name.
--
local function filename (id)
	return format ("%s/%s.lua", root_dir, id)
end

----------------------------------------------------------------------------
-- Deletes a session.
-- @param id Session identification.
----------------------------------------------------------------------------
function delete (id)
	if not check_id (id) then
		return nil, INVALID_SESSION_ID
	end
	remove (filename (id))
end

--
-- Searches for a file in the root_dir
--
local function find (file)
	local fh = _open (root_dir.."/"..file)
	if fh then
		fh:close ()
		return true
	else
		return false
	end
end

--
-- Creates a new identifier.
-- @return New identifier.
--
local function new_id ()
	return rand (999999999)
end

----------------------------------------------------------------------------
-- Creates a new session identifier.
-- @return Session identification.
----------------------------------------------------------------------------
function new ()
	local id = new_id ()
	if find (id..".lua") then
		repeat
			id = new_id (id)
		until not find (id..".lua")
		randseed (mod (id, 999999999))
	end
	return id
end

----------------------------------------------------------------------------
-- Changes the session identificator generator.
-- @param func Function.
----------------------------------------------------------------------------
function setidgenerator (func)
	if type (func) == "function" then
		new_id = func
	end
end

----------------------------------------------------------------------------
-- Loads data from a session.
-- @param id Session identification.
-- @return Table with session data or nil in case of error.
-- @return In case of error, also returns the error message.
----------------------------------------------------------------------------
function load (id)
	if not check_id (id) then
		return nil, INVALID_SESSION_ID
	end
	local f, err = loadfile (filename (id))
	if not f then
		return nil, err
	else
		return f()
	end
end

----------------------------------------------------------------------------
-- Saves data to a session.
-- @param id Session identification.
-- @param data Table with session data to be saved.
----------------------------------------------------------------------------
function save (id, data)
	if not check_id (id) then
		return nil, INVALID_SESSION_ID
	end
	local fh = assert (_open (filename (id), "w+"))
	fh:write "return "
	serialize (data, function (s) fh:write(s) end)
	fh:close()
end

----------------------------------------------------------------------------
-- Removes expired sessions.
----------------------------------------------------------------------------
function cleanup ()
	local rem = {}
	local now = time ()
	for file in dir (root_dir) do
		local attr = attributes(root_dir.."/"..file)
		if attr and attr.mode == 'file' then
			if attr.modification + timeout < now then
				tinsert (rem, file)
			end
		end
	end
	for _, file in ipairs (rem) do
		remove (root_dir.."/"..file)
	end
end

----------------------------------------------------------------------------
-- Changes the session timeout.
-- @param t Number of seconds to maintain a session.
----------------------------------------------------------------------------
function setsessiontimeout (t)
	if type (t) == "number" then
		timeout = t
	end
end

----------------------------------------------------------------------------
-- Changes the session directory.
-- @param path String with the new session directory.
----------------------------------------------------------------------------
function setsessiondir (path)
	path = gsub (path, "[/\\]$", "")
	-- Make sure the given path is a directory
	if not attributes (path, "mode") then
		assert (mkdir (path))
	end
	-- Make sure it can create a new file in the given directory
	local test_file = path.."/".._G.cgilua.tmpname()
	local fh, err = _open (test_file, "w")
	if not fh then
		error ("Could not open a file in session directory: "..
			tostring(err), 2)
	end
	fh:close ()
	remove (test_file)
	root_dir = path
end

----------------------------------------------------------------------------
local ID_NAME = "cgilua session identification"
local id = nil

----------------------------------------------------------------------------
-- Destroys the session.
----------------------------------------------------------------------------
function destroy ()
	data = {} -- removes data from session table to avoid recreation by `close'
	delete (id)
end

----------------------------------------------------------------------------
-- Open user session.
-- This function should be called before the script is executed.
----------------------------------------------------------------------------
function open ()
	-- Redefine cgilua.mkurlpath to manage the session identification
	local mkurlpath = _G.cgilua.mkurlpath
	function _G.cgilua.mkurlpath (script, data)
		if not data then
			data = {}
		end
		data[ID_NAME] = id
		return mkurlpath (script, data)
	end

	cleanup()

	id = _G.cgilua.QUERY[ID_NAME] or new()
	if id then
		_G.cgilua.QUERY[ID_NAME] = nil
		_G.cgilua.session.data = load (id) or {}
	end
end

----------------------------------------------------------------------------
-- Close user session.
-- This function should be called after the script is executed.
----------------------------------------------------------------------------
function close ()
	if next (_G.cgilua.session.data) then
		save (id, _G.cgilua.session.data)
		id = nil
	end
end

local already_enabled = false
----------------------------------------------------------------------------
-- Enables the use of sessions.
-- This function must be called by every script that needs sessions.
-- It just calls the `open' function and register the `close' function
-- to be called at the end of the execution.
----------------------------------------------------------------------------
function _G.cgilua.enablesession ()
	if already_enabled then -- avoid misuse when a script calls another one
		return
	else
		already_enabled = true
	end
	open ()
	_G.cgilua.addclosefunction (close)
end

genometools-1.5.1/src/external/cgilua-5.1.3/src/cgilua/urlcode.lua000066400000000000000000000066251211610345200245670ustar00rootroot00000000000000----------------------------------------------------------------------------
-- Utility functions for encoding/decoding of URLs.
--
-- @release $Id: urlcode.lua,v 1.10 2008/01/21 16:11:32 carregal Exp $
----------------------------------------------------------------------------

local ipairs, next, pairs, tonumber, type = ipairs, next, pairs, tonumber, type
local string = string
local table = table

module ("cgilua.urlcode")

----------------------------------------------------------------------------
-- Decode an URL-encoded string (see RFC 2396)
----------------------------------------------------------------------------
function unescape (str)
	str = string.gsub (str, "+", " ")
	str = string.gsub (str, "%%(%x%x)", function(h) return string.char(tonumber(h,16)) end)
	str = string.gsub (str, "\r\n", "\n")
	return str
end

----------------------------------------------------------------------------
-- URL-encode a string (see RFC 2396)
----------------------------------------------------------------------------
function escape (str)
	str = string.gsub (str, "\n", "\r\n")
	str = string.gsub (str, "([^0-9a-zA-Z ])", -- locale independent
		function (c) return string.format ("%%%02X", string.byte(c)) end)
	str = string.gsub (str, " ", "+")
	return str
end

----------------------------------------------------------------------------
-- Insert a (name=value) pair into table [[args]]
-- @param args Table to receive the result.
-- @param name Key for the table.
-- @param value Value for the key.
-- Multi-valued names will be represented as tables with numerical indexes
--	(in the order they came).
----------------------------------------------------------------------------
function insertfield (args, name, value)
	if not args[name] then
		args[name] = value
	else
		local t = type (args[name])
		if t == "string" then
			args[name] = {
				args[name],
				value,
			}
		elseif t == "table" then
			table.insert (args[name], value)
		else
			error ("CGILua fatal error (invalid args table)!")
		end
	end
end

----------------------------------------------------------------------------
-- Parse url-encoded request data 
--   (the query part of the script URL or url-encoded post data)
--
--  Each decoded (name=value) pair is inserted into table [[args]]
-- @param query String to be parsed.
-- @param args Table where to store the pairs.
----------------------------------------------------------------------------
function parsequery (query, args)
	if type(query) == "string" then
		local insertfield, unescape = insertfield, unescape
		string.gsub (query, "([^&=]+)=([^&=]*)&?",
			function (key, val)
				insertfield (args, unescape(key), unescape(val))
			end)
	end
end

----------------------------------------------------------------------------
-- URL-encode the elements of a table creating a string to be used in a
--   URL for passing data/parameters to another script
-- @param args Table where to extract the pairs (name=value).
-- @return String with the resulting encoding.
----------------------------------------------------------------------------
function encodetable (args)
  if args == nil or next(args) == nil then   -- no args or empty args?
    return ""
  end
  local strp = ""
 for key, vals in pairs(args) do
    if type(vals) ~= "table" then
      vals = {vals}
    end
    for i,val in ipairs(vals) do
      strp = strp.."&"..escape(key).."="..escape(val)
    end
  end
  -- remove first & 
  return string.sub(strp,2)
end

genometools-1.5.1/src/external/cgilua-5.1.3/tests/000077500000000000000000000000001211610345200215255ustar00rootroot00000000000000genometools-1.5.1/src/external/cgilua-5.1.3/tests/Makefile000066400000000000000000000005041211610345200231640ustar00rootroot00000000000000# $Id: Makefile,v 1.5 2004/11/08 16:39:51 tomas Exp $

T= test

include ../config

V= 1.0a
#DIST_DIR=../$(PKG)/$T

SRCS= test_main.html test_main.lua test_main.lp test_cookies.lua test_cookies.lp

clean cgi fcgi mod:

cgiinstall fcgiinstall modinstall:

dist dist_dir:
	mkdir -p $(DIST_DIR)
	cp $(SRCS) Makefile $(DIST_DIR)
genometools-1.5.1/src/external/cgilua-5.1.3/tests/download.lua000066400000000000000000000030161211610345200240370ustar00rootroot00000000000000#!/usr/local/bin/lua

require"luasocket"

function receive (connection)
	connection:settimeout(0)
	local s, status = connection:receive (2^10)
	if status == "timeout" then
		coroutine.yield (connection)
	end
	return s, status
end

function download (host, file, outfile)
	--local f = assert (io.open (outfile, "w"))
	local c = assert (socket.connect (host, 80))
	c:send ("GET "..file.." HTTP/1.0\r\n\r\n")
	while true do
		local s, status = receive (c)
		--f:write (s)
		if status == "closed" then
			break
		end
	end
	c:close()
	--f:close()
end

local threads = {}
function get (host, file, outfile)
	print (string.format ("Downloading %s from %s to %s", file, host, outfile))
	local co = coroutine.create (function ()
		return download (host, file, outfile)
	end)
	table.insert (threads, co)
end

function dispatcher ()
	while true do
		local n = table.getn (threads)
		if n == 0 then
			break
		end
		local connections = {}
		for i = 1, n do
			local status, res = coroutine.resume (threads[i])
			if not res then
				table.remove (threads, i)
				break
			else
				table.insert (connections, res)
			end
		end
		if table.getn (connections) == n then
			socket.select (connections)
		end
	end
end

local url = arg[1]
if not url then
	print (string.format ("usage: %s url [times]", arg[0]))
	os.exit()
end
local times = arg[2] or 5

url = string.gsub (url, "^http.?://", "")
local _, _, host, file = string.find (url, "^([^/]+)(/.*)")
local _, _, fn = string.find (file, "([^/]+)$")

for i = 1, times do
	get (host, file, fn..i)
end

dispatcher ()
genometools-1.5.1/src/external/cgilua-5.1.3/tests/env.lua000066400000000000000000000013011211610345200230130ustar00rootroot00000000000000-- This file should be executed before any script in this directory
-- according to the configuration (cgilua/conf.lua).

pcall (cgilua.enablesession)

local put, mkurlpath = cgilua.put, cgilua.mkurlpath

cgilua.addclosefunction (function ()
	put [[



Main]]
	for _, test in ipairs{
			{ "Get", "test_main.lua", {ab = "cd", ef = "gh"} },
			{ "Cookies", "test_cookies.lua", },
			{ "FileSystem", "test_fs.lua", },
			{ "Libraries", "test_lib.lua", },
			{ "Session", "test_session.lua", },
			{ "Variables", "test_variables.lp", },
		} do
		put (string.format (' · %s',
			mkurlpath (test[2], test[3]), test[1]))
	end
	put [[
]]
end)
genometools-1.5.1/src/external/cgilua-5.1.3/tests/overview.lp000066400000000000000000000032731211610345200237350ustar00rootroot00000000000000

CGILua installation overview



CGILua installation overview




  

    Version
    Copyright
    Description
  


  

    <%= tostring(_G[l[2]]) %>
    
    
  


  


  

    <%= idx(p,"VERSION") %>
    <%= idx(p,"COPYRIGHT") %>
    <%= idx(p,"DESCRIPTION") %>
  







genometools-1.5.1/src/external/cgilua-5.1.3/tests/prepara_sql2.lua000066400000000000000000000013161211610345200246240ustar00rootroot00000000000000#!/usr/local/bin/lua
-- Prepara o 2o. teste de acesso ao banco de dados.
-- Sao criadas duas tabelas com uma chave estrangeira ligando-as.

MAX_ROWS = arg[1] or 10

require"postgres"

local env = assert (luasql.postgres ())
local conn = assert (env:connect ("luasql-test", "tomas"))

-- Apaga restos de outros testes.
conn:execute "drop table t2"
conn:execute "drop table t1"

-- Criando as tabelas.
assert (conn:execute [[create table t1 (
	a int,
	b int
)]])
assert (conn:execute [[create table t2 (
	c int,
	d int
)]])

-- Preenchedo as tabelas.
for i = 1, MAX_ROWS do
	local ii = 2*i
	assert (conn:execute (string.format ([[
insert into t1 values (%d, %d);
insert into t2 values (%d, %d);]],
		ii, i, ii, i)))
end
genometools-1.5.1/src/external/cgilua-5.1.3/tests/tcgi1.lua000066400000000000000000000005311211610345200232360ustar00rootroot00000000000000-- $Id: tcgi1.lua,v 1.1 2004/03/25 19:31:05 tomas Exp $

io.stdout:write"Content-type: text/html\n\n"

for i,v in pairs{"QUERY_STRING", } do
	io.stdout:write (string.format ("%s = %s", v, os.getenv(v) or ' '))
end
io.stdout:write "
\n"

local post_data = io.stdin:read"*a"
io.stdout:write (string.format ("post_data = {%s}", post_data))
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test.html000066400000000000000000000042561211610345200234010ustar00rootroot00000000000000



  

     GET: 
  

  

    
      cgi
    
    
      fcgi
    
    
      modulo
    
  


  

     POST: 
  

  

    
      

        

          

            
              field 1: 

              field 2: 

            		
          

          

            
              cgi
            
            
              fcgi
            
            
              modulo
            
          

        

      

    		
  


  

     POST (with upload): 
  

  

    
      

        

          

            
              field 1: 

              file: 

            		
          

          

            
              cgi
            
            
              fcgi
            
            
              modulo
            
          

        

      

    		
  



$Id: test.html,v 1.2 2004/06/07 12:04:10 tomas Exp $

genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_conc.lua000066400000000000000000000013571211610345200242170ustar00rootroot00000000000000cgilua.htmlheader()
if ap then
	local pid, ppid = ap.pid ()
	if not ppid then
		ppid = "no parent pid"
	end
	cgilua.put ("pid = "..pid.." ("..ppid..")".."\n")
end

assert(type(stable.get) == "function")
assert(type(stable.set) == "function")

cgilua.put"stable.pairs = {
\n"
for i, v in stable.pairs () do
	cgilua.put (i.." = "..tostring(v).."
\n")
end
cgilua.put"}
\n"

local counter = stable.get"counter" or 0
stable.set ("counter", counter + 1)

local f = stable.get"f"
if not f then
	local d = os.date()
	stable.set ("f", function () return d end)
else
	cgilua.put ("f() = "..tostring (f ()))
end

cgilua.put"
\n"
for i = 1,800 do
	cgilua.put (i)
	for ii = 1,1000 do
		cgilua.put ("")
	end
	cgilua.put ("\n")
end
cgilua.put ("End")
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_cookies.lp000066400000000000000000000004721211610345200245600ustar00rootroot00000000000000


Testing Cookies library


<%= CL_COOKIE%> = <%= tostring(test)%>

Assigning current date to cookie!

Reload this script to check cookie's value!
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_cookies.lua000066400000000000000000000005301211610345200247210ustar00rootroot00000000000000local cookies = require"cgilua.cookies"
CL_COOKIE = "cgilua_cookie"

local test = cookies.get (CL_COOKIE)
cookies.set (CL_COOKIE, os.date())

cgilua.htmlheader ()
cgilua.put ([[

Testing Cookies library


]]..CL_COOKIE..'  = '..tostring(test)..[[

Assigning current date to cookie!

Reload this script to check cookie's value!
]])
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_err.lua000066400000000000000000000001351211610345200240560ustar00rootroot00000000000000cgilua.htmlheader()
cgilua.put"Oi!"
--io.write"something\n"
cgilua.errorlog ("eca", "emerg")
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_fs.lua000066400000000000000000000011461211610345200237010ustar00rootroot00000000000000function link_dir (dir, base)
	local path = base.."/"..dir
	local mode = lfs.attributes (path).mode
	if mode == "directory" then
		return string.format ('%s',
			cgilua.mkurlpath ("test_fs.lua", { dir = path }),
			dir)
	else
		return dir
	end
end

cgilua.htmlheader ()
cgilua.put ("
Testing Filesystem library
\n")
cgilua.put ("\n")
cgilua.put ("\n")
local i = 0
local dir = cgi.dir or "."
for file in lfs.dir (dir) do
	i = i+1
	cgilua.put ("\n")
end
cgilua.put ("
Testing dir
"..i..""..link_dir(file, dir).."
\n")
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_htk.lua000066400000000000000000000006231211610345200240560ustar00rootroot00000000000000require"htk"

local a_table = {}
for i = 1, 20 do
	local l = {}
	for j = 1, 20 do
		table.insert (l, HTK.TD { "cell "..i..","..j })
	end
	table.insert (a_table, HTK.TR (l))
end

cgilua.htmlheader()
cgilua.put (HTK.HTML {
	HTK.HEAD { HTK.TITLE { "Titulo da Pagina" } },
	HTK.BODY {
		bgcolor = "#FFFFFF",
		HTK.H1 { "Titulo da Pagina" },
		HTK.P {},
		"Uma pgina qualquer",
		HTK.TABLE (a_table),
	}
})
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_lib.lua000066400000000000000000000014341211610345200240370ustar00rootroot00000000000000local function getfield (t, f)
  for w in string.gfind(f, "[%w_]+") do
    if not t then return nil end
    t = t[w]
  end
  return t
end

function test_lib (libname)
	local ok, err = pcall (require, libname)
	if not ok then
		cgilua.put ("Library "..libname.." not found
\n"..
			err)
	else
		cgilua.put ("Library "..libname.."
\n")
		local t = getfield (_G, libname)
		if type(t) ~= "table" then
			cgilua.put (tostring(t))
		else
			for i, v in pairs (t) do
				cgilua.put ("  "..tostring(i).." = "..tostring(v).."
\n")
			end
		end
	end
	cgilua.put ("\n
\n")
end

cgilua.htmlheader ()
for _, lib in ipairs { "lfs", "socket", "luasql.postgres", "luasql", "lxp", "lxp.lom", "lualdap", "htk", "xmlrpc", "xmlrpc.http" } do
	test_lib (lib)
end
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_main.html000066400000000000000000000133261211610345200244030ustar00rootroot00000000000000
Test Page



  

     GET: 
  

  

    Lua script
    cgi
    fcgi
    module
  

  

    HTML template
    cgi
    fcgi
    module
  


  

     POST: 
  

  

    
      

        

          

            
              field 1: 

              field 2: 

              field 3:
                op 1
                op 2
                op 3
            		
          

          

            Lua script
            
              cgi
            
            
              fcgi
            
            
              module
            
          

          

            HTML template
            
              cgi
            
            
              fcgi
            
            
              module
            
          

        

      

    		
  


  

     POST (with upload): 
  

  

    
      

        

          

            
              field 1: 

              file (binary!): 

            		
          

          

            Lua script
            
              cgi
            
            
              fcgi
            
            
              module
            
          

          

            HTML template
            
              cgi
            
            
              fcgi
            
            
              module
            
          

        

      

    		
  

  

     Cookies: 
  

  

    Lua script
    cgi
    fcgi
    module
  

  

    HTML template
    cgi
    fcgi
    module
  

  

     Filesystem: 
  

  

    Lua script
    cgi
    fcgi
    module
  

  

     Session: 
  

  

    Lua script
    cgi
    fcgi
    module
  

  

     CGI Variables: 
  

  

    HTML template
    cgi
    fcgi
    module
  

  

     Library Overview: 
  

  

    HTML template
    cgi
    fcgi
    module
  

  

     Concurrency 
  

  

    Lua script
    cgi
    fcgi
    module
  



$Id: test_main.html,v 1.12 2004/11/25 10:52:58 tomas Exp $

genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_main.lp000066400000000000000000000011731211610345200240470ustar00rootroot00000000000000
Embeded Lua Test


cgi = {
\n", vv, a, tostring(b))
		end
		v = vv.."}"
	end
?>
<%= i %> = <%= tostring(v) %> 

<%
end
%>
}


Remote address: <%= cgilua.servervariable"REMOTE_ADDR" %>


Is persistent = <%= tostring (SAPI.Info.ispersistent) %>


ap =  

lfcgi = <% = tostring(lfcgi) %> 

<%= (ap and ap.handler()) or "" %> 



$Id: test_main.lp,v 1.5 2005/02/11 14:39:21 tomas Exp $

genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_main.lua000066400000000000000000000023661211610345200242220ustar00rootroot00000000000000-- $Id: test_main.lua,v 1.11 2006/01/06 16:33:57 tomas Exp $
cgilua.htmlheader()
cgilua.put[[

Script Lua Test


cgi = {
]]

for i,v in pairs (cgi) do
	if type(v) == "table" then
		local vv = "{"
		for a,b in pairs(v) do
			vv = string.format ("%s%s = %s
\n", vv, a, tostring(b))
		end
		v = vv.."}"
	end
	cgilua.put (string.format ("%s = %s
\n", i, tostring(v)))
end
cgilua.put "}
\n"
cgilua.put ("Remote address: "..cgilua.servervariable"REMOTE_ADDR")
cgilua.put "
\n"
cgilua.put ("Is persistent = "..tostring (SAPI.Info.ispersistent).."
\n")
cgilua.put ("ap="..tostring(ap).."
\n")
cgilua.put ("lfcgi="..tostring(lfcgi).."
\n")

-- Checking Virtual Environment
local my_output = cgilua.put
cgilua.put = nil
local status, err = pcall (function ()
	assert (cgilua.put == nil, "cannot change cgilua.put value")
end)
cgilua.put = my_output
assert (status == true, err)

-- Checking require
local status, err = pcall (function () require"unknown_module" end)
assert (status == false, "unknown_module loaded!")
assert (package == nil, "Access to package table allowed!")

cgilua.put[[



$Id: test_main.lua,v 1.11 2006/01/06 16:33:57 tomas Exp $

]]
cgilua = nil
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_session.lua000066400000000000000000000017551211610345200247620ustar00rootroot00000000000000cgilua.enablesession ()

function pt (tab)
	for i, v in pairs (tab) do
		local vv = v
		if type(v) == "table" then
			vv = ""
			for _i, _v in pairs (v) do
				vv = vv..string.format ("%s = %q, ", _i, _v)
			end
			vv = '{'..vv..'}'
		end
		cgilua.put (string.format ("%s = %s
\n", tostring (i), tostring (vv)))
	end
end


if cgi.field then
	if not cgilua.session.data.field then
		cgilua.session.data.field = {}
	end
	table.insert (cgilua.session.data.field, cgi.field)
end
cgilua.htmlheader()
if cgilua.session then
	cgilua.put "cgi = {
\n"
	pt (cgi)
	cgilua.put "}
\n"
	cgilua.put "cgilua.session.data = {
\n"
	pt (cgilua.session.data)
	cgilua.put "}
\n"

	cgilua.put [[

  field: 

  


]]
else
	cgilua.put "Sessions library is not available or not well configured"
end
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_sql.lua000066400000000000000000000006331211610345200240700ustar00rootroot00000000000000local s = require"luasql.postgres"

local env = assert (luasql.postgres ())
local conn = assert (env:connect ("luasql-test", "tomas"))
local cur = assert (conn:execute ("select count(*) from fetch_test"))

cgilua.htmlheader()
cgilua.put ("Total lines at table fetch_test is "..cur:fetch())
cgilua.put (string.format ("
\n%s == %s
\n", tostring(s), tostring(luasql)))

cur:close()
conn:close()
env:close()
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_sql2.lua000066400000000000000000000012121211610345200241440ustar00rootroot00000000000000require"postgres"

local env = assert (luasql.postgres ())
local conn = assert (env:connect ("luasql-test", "tomas"))
local cur = assert (conn:execute ("select count(*) from t1"))
local total = tonumber (cur:fetch())
cur:close()
local aleatorio = math.random(total)
local cur = assert (conn:execute ("select * from t1, t2 where b = d and a != "..2*aleatorio))

cgilua.htmlheader()
cgilua.put ("Aleatorio = "..aleatorio.."
\n")

local a,b,c,d = cur:fetch()
cgilua.put ("\n")
while a do
--	cgilua.put ("")
	a,b,c,d = cur:fetch()
end
cgilua.put ("
",a,"",b,"",c,"",d,"
\n")

cur:close()
conn:close()
env:close()
genometools-1.5.1/src/external/cgilua-5.1.3/tests/test_variables.lp000066400000000000000000000013071211610345200250720ustar00rootroot00000000000000
<% for _, var in pairs { "SERVER_SOFTWARE", "SERVER_NAME", "GATEWAY_INTERFACE", "SERVER_PROTOCOL", "SERVER_PORT", "REQUEST_METHOD", "PATH_INFO", "PATH_TRANSLATED", "SCRIPT_NAME", "QUERY_STRING", "REMOTE_HOST", "REMOTE_ADDR", "AUTH_TYPE", "REMOTE_USER", "REMOTE_IDENT", "CONTENT_TYPE", "CONTENT_LENGTH", "HTTP_REFERER", "HTTP_COOKIE", "SCRIPT_FILENAME", "DOCUMENT_ROOT", } do %>
  
<% end %>

<%= var %>="<%= cgilua.servervariable(var) or "not defined"%>"





<% for _, var in ipairs { "script_file", "script_path", "script_pdir", "script_vdir", "script_vpath", "urlpath", } do %>
  
<% end %>

<%= var %>="<%= cgilua[var] %>"




genometools-1.5.1/src/external/cgilua-5.1.3/tests/tfcgi1.lua000066400000000000000000000005501211610345200234050ustar00rootroot00000000000000-- $Id: tfcgi1.lua,v 1.1 2004/03/25 19:31:05 tomas Exp $
lfcgi.stdout:write"Content-type: text/html\n\n"

for i,v in pairs{"QUERY_STRING", } do
	lfcgi.stdout:write (string.format ("%s = %s", v, os.getenv(v) or ' '))
end
lfcgi.stdout:write "
\n"

local post_data = lfcgi.stdin:read"*a"
lfcgi.stdout:write (string.format ("post_data = {%s}", post_data))
genometools-1.5.1/src/external/cgilua-5.1.3/tests/tmod1.lua000066400000000000000000000010621211610345200232530ustar00rootroot00000000000000-- $Id: tmod1.lua,v 1.1 2004/03/25 19:31:05 tomas Exp $
ap.set_content_type"text/html"

ap.rputs "ap.args = {"
ap.rputs (ap.args() or '')
ap.rputs "}
\n"

assert (ap.setup_client_block ("REQUEST_CHUNKED_ERROR") == ap.OK)
if ap.should_client_block () ~= 0 then
	post_data = {}
	local block, err = ap.get_client_block ()
	while block do
		table.insert (post_data, block)
		block, err = ap.get_client_block ()
	end
	if err then
		error (err)
	end
	post_data = table.concat (post_data)
end

ap.rputs "post_data = {"
ap.rputs (tostring (post_data))
ap.rputs "}\n"
genometools-1.5.1/src/external/expat-2.0.1/000077500000000000000000000000001211610345200202325ustar00rootroot00000000000000genometools-1.5.1/src/external/expat-2.0.1/COPYING000077500000000000000000000022701211610345200212710ustar00rootroot00000000000000Copyright (c) 1998, 1999, 2000 Thai Open Source Software Center Ltd
                               and Clark Cooper
Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006 Expat maintainers.

Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
genometools-1.5.1/src/external/expat-2.0.1/Changes000077500000000000000000000217641211610345200215420ustar00rootroot00000000000000Release 2.0.1 Tue June 5 2007
        - Fixed bugs #1515266, 1515600: The character data handler's calling
          of XML_StopParser() was not handled properly; if the parser was
          stopped and the handler set to NULL, the parser would segfault.
        - Fixed bug #1690883: Expat failed on EBCDIC systems as it assumed
          some character constants to be ASCII encoded.
        - Minor cleanups of the test harness.
        - Fixed xmlwf bug #1513566: "out of memory" error on file size zero.
        - Fixed outline.c bug #1543233: missing a final XML_ParserFree() call.
        - Fixes and improvements for Windows platform:
          bugs #1409451, #1476160, 1548182, 1602769, 1717322.
        - Build fixes for various platforms:
          HP-UX, Tru64, Solaris 9: patch #1437840, bug #1196180.
          All Unix: #1554618 (refreshed config.sub/config.guess).
                    #1490371, #1613457: support both, DESTDIR and INSTALL_ROOT,
                    without relying on GNU-Make specific features.
          #1647805: Patched configure.in to work better with Intel compiler.
        - Fixes to Makefile.in to have make check work correctly:
          bugs #1408143, #1535603, #1536684.
        - Added Open Watcom support: patch #1523242.

Release 2.0.0 Wed Jan 11 2006
        - We no longer use the "check" library for C unit testing; we
          always use the (partial) internal implementation of the API.
        - Report XML_NS setting via XML_GetFeatureList().
        - Fixed headers for use from C++.
        - XML_GetCurrentLineNumber() and  XML_GetCurrentColumnNumber()
          now return unsigned integers.
        - Added XML_LARGE_SIZE switch to enable 64-bit integers for
          byte indexes and line/column numbers.
        - Updated to use libtool 1.5.22 (the most recent).
        - Added support for AmigaOS.
        - Some mostly minor bug fixes. SF issues include: 1006708,
          1021776, 1023646, 1114960, 1156398, 1221160, 1271642.

Release 1.95.8 Fri Jul 23 2004
        - Major new feature: suspend/resume.  Handlers can now request
          that a parse be suspended for later resumption or aborted
          altogether.  See "Temporarily Stopping Parsing" in the
          documentation for more details.
        - Some mostly minor bug fixes, but compilation should no
          longer generate warnings on most platforms.  SF issues
          include: 827319, 840173, 846309, 888329, 896188, 923913,
          928113, 961698, 985192.

Release 1.95.7 Mon Oct 20 2003
        - Fixed enum XML_Status issue (reported on SourceForge many
          times), so compilers that are properly picky will be happy.
        - Introduced an XMLCALL macro to control the calling
          convention used by the Expat API; this macro should be used
          to annotate prototypes and definitions of callback
          implementations in code compiled with a calling convention
          other than the default convention for the host platform.
        - Improved ability to build without the configure-generated
          expat_config.h header.  This is useful for applications
          which embed Expat rather than linking in the library.
        - Fixed a variety of bugs: see SF issues 458907, 609603,
          676844, 679754, 692878, 692964, 695401, 699323, 699487,
          820946.
        - Improved hash table lookups.
        - Added more regression tests and improved documentation.

Release 1.95.6 Tue Jan 28 2003
        - Added XML_FreeContentModel().
        - Added XML_MemMalloc(), XML_MemRealloc(), XML_MemFree().
        - Fixed a variety of bugs: see SF issues 615606, 616863,
          618199, 653180, 673791.
        - Enhanced the regression test suite.
        - Man page improvements: includes SF issue 632146.

Release 1.95.5 Fri Sep 6 2002
        - Added XML_UseForeignDTD() for improved SAX2 support.
        - Added XML_GetFeatureList().
        - Defined XML_Bool type and the values XML_TRUE and XML_FALSE.
        - Use an incomplete struct instead of a void* for the parser
          (may not retain).
        - Fixed UTF-8 decoding bug that caused legal UTF-8 to be rejected.
        - Finally fixed bug where default handler would report DTD
          events that were already handled by another handler.
          Initial patch contributed by Darryl Miles.
        - Removed unnecessary DllMain() function that caused static
          linking into a DLL to be difficult.
        - Added VC++ projects for building static libraries.
        - Reduced line-length for all source code and headers to be
          no longer than 80 characters, to help with AS/400 support.
        - Reduced memory copying during parsing (SF patch #600964).
        - Fixed a variety of bugs: see SF issues 580793, 434664,
          483514, 580503, 581069, 584041, 584183, 584832, 585537,
          596555, 596678, 598352, 598944, 599715, 600479, 600971.

Release 1.95.4 Fri Jul 12 2002
        - Added support for VMS, contributed by Craig Berry.  See
          vms/README.vms for more information.
        - Added Mac OS (classic) support, with a makefile for MPW,
          contributed by Thomas Wegner and Daryle Walker.
        - Added Borland C++ Builder 5 / BCC 5.5 support, contributed
          by Patrick McConnell (SF patch #538032).
        - Fixed a variety of bugs: see SF issues 441449, 563184,
          564342, 566334, 566901, 569461, 570263, 575168, 579196.
        - Made skippedEntityHandler conform to SAX2 (see source comment)
        - Re-implemented WFC: Entity Declared from XML 1.0 spec and
          added a new error "entity declared in parameter entity":
          see SF bug report 569461 and SF patch 578161
        - Re-implemented section 5.1 from XML 1.0 spec:
          see SF bug report 570263 and SF patch 578161

Release 1.95.3 Mon Jun 3 2002
        - Added a project to the MSVC workspace to create a wchar_t
          version of the library; the DLLs are named libexpatw.dll.
        - Changed the name of the Windows DLLs from expat.dll to
          libexpat.dll; this fixes SF bug #432456.
        - Added the XML_ParserReset() API function.
        - Fixed XML_SetReturnNSTriplet() to work for element names.
        - Made the XML_UNICODE builds usable (thanks, Karl!).
        - Allow xmlwf to read from standard input.
        - Install a man page for xmlwf on Unix systems.
        - Fixed many bugs; see SF bug reports 231864, 461380, 464837,
          466885, 469226, 477667, 484419, 487840, 494749, 496505,
          547350.  Other bugs which we can't test as easily may also
          have been fixed, especially in the area of build support.

Release 1.95.2 Fri Jul 27 2001
        - More changes to make MSVC happy with the build; add a single
          workspace to support both the library and xmlwf application.
        - Added a Windows installer for Windows users; includes
          xmlwf.exe.
        - Added compile-time constants that can be used to determine the
          Expat version
        - Removed a lot of GNU-specific dependencies to aide portability
          among the various Unix flavors.
        - Fix the UTF-8 BOM bug.
        - Cleaned up warning messages for several compilers.
        - Added the -Wall, -Wstrict-prototypes options for GCC.

Release 1.95.1 Sun Oct 22 15:11:36 EDT 2000
        - Changes to get expat to build under Microsoft compiler
        - Removed all aborts and instead return an UNEXPECTED_STATE error.
        - Fixed a bug where a stray '%' in an entity value would cause an
          abort.
        - Defined XML_SetEndNamespaceDeclHandler. Thanks to Darryl Miles for
          finding this oversight.
        - Changed default patterns in lib/Makefile.in to fit non-GNU makes
          Thanks to robin@unrated.net for reporting and providing an
          account to test on.
        - The reference had the wrong label for XML_SetStartNamespaceDecl.
          Reported by an anonymous user.

Release 1.95.0 Fri Sep 29 2000
        - XML_ParserCreate_MM
                Allows you to set a memory management suite to replace the
                standard malloc,realloc, and free.
        - XML_SetReturnNSTriplet
                If you turn this feature on when namespace processing is in
                effect, then qualified, prefixed element and attribute names
                are returned as "uri|name|prefix" where '|' is whatever
                separator character is used in namespace processing.
        - Merged in features from perl-expat
                o XML_SetElementDeclHandler
                o XML_SetAttlistDeclHandler
                o XML_SetXmlDeclHandler
                o XML_SetEntityDeclHandler
                o StartDoctypeDeclHandler takes 3 additional parameters:
                        sysid, pubid, has_internal_subset
                o Many paired handler setters (like XML_SetElementHandler)
                  now have corresponding individual handler setters
                o XML_GetInputContext for getting the input context of
                  the current parse position.
        - Added reference material
        - Packaged into a distribution that builds a sharable library
genometools-1.5.1/src/external/expat-2.0.1/MANIFEST000077500000000000000000000043671211610345200214000ustar00rootroot00000000000000amiga/stdlib.c
amiga/launch.c
amiga/expat_vectors.c
amiga/expat_lib.c
amiga/expat.xml
amiga/README.txt
amiga/Makefile
amiga/include/proto/expat.h
amiga/include/libraries/expat.h
amiga/include/interfaces/expat.h
amiga/include/inline4/expat.h
bcb5/README.txt
bcb5/all_projects.bpg
bcb5/elements.bpf
bcb5/elements.bpr
bcb5/elements.mak
bcb5/expat.bpf
bcb5/expat.bpr
bcb5/expat.mak
bcb5/expat_static.bpf
bcb5/expat_static.bpr
bcb5/expat_static.mak
bcb5/expatw.bpf
bcb5/expatw.bpr
bcb5/expatw.mak
bcb5/expatw_static.bpf
bcb5/expatw_static.bpr
bcb5/expatw_static.mak
bcb5/libexpat_mtd.def
bcb5/libexpatw_mtd.def
bcb5/makefile.mak
bcb5/outline.bpf
bcb5/outline.bpr
bcb5/outline.mak
bcb5/setup.bat
bcb5/xmlwf.bpf
bcb5/xmlwf.bpr
bcb5/xmlwf.mak
doc/expat.png
doc/reference.html
doc/style.css
doc/valid-xhtml10.png
doc/xmlwf.1
doc/xmlwf.sgml
COPYING
Changes
MANIFEST
Makefile.in
README
configure
configure.in
expat_config.h.in
expat.dsw
conftools/PrintPath
conftools/ac_c_bigendian_cross.m4
conftools/config.guess
conftools/config.sub
conftools/expat.m4
conftools/get-version.sh
conftools/install-sh
conftools/libtool.m4
conftools/ltmain.sh
conftools/mkinstalldirs
examples/elements.c
examples/elements.dsp
examples/outline.c
examples/outline.dsp
lib/Makefile.MPW
lib/amigaconfig.h
lib/ascii.h
lib/asciitab.h
lib/expat.dsp
lib/expat.h
lib/expat_external.h
lib/expat_static.dsp
lib/expatw.dsp
lib/expatw_static.dsp
lib/iasciitab.h
lib/internal.h
lib/latin1tab.h
lib/libexpat.def
lib/libexpatw.def
lib/macconfig.h
lib/nametab.h
lib/utf8tab.h
lib/winconfig.h
lib/xmlparse.c
lib/xmlrole.c
lib/xmlrole.h
lib/xmltok.c
lib/xmltok.h
lib/xmltok_impl.c
lib/xmltok_impl.h
lib/xmltok_ns.c
tests/benchmark/README.txt
tests/benchmark/benchmark.c
tests/benchmark/benchmark.dsp
tests/benchmark/benchmark.dsw
tests/README.txt
tests/chardata.c
tests/chardata.h
tests/minicheck.c
tests/minicheck.h
tests/runtests.c
tests/runtestspp.cpp
tests/xmltest.sh
vms/README.vms
vms/descrip.mms
vms/expat_config.h
win32/MANIFEST.txt
win32/README.txt
win32/expat.iss
xmlwf/codepage.c
xmlwf/codepage.h
xmlwf/ct.c
xmlwf/filemap.h
xmlwf/readfilemap.c
xmlwf/unixfilemap.c
xmlwf/win32filemap.c
xmlwf/xmlfile.c
xmlwf/xmlfile.h
xmlwf/xmlmime.c
xmlwf/xmlmime.h
xmlwf/xmltchar.h
xmlwf/xmlurl.h
xmlwf/xmlwf.c
xmlwf/xmlwf.dsp
xmlwf/xmlwin32url.cxx
genometools-1.5.1/src/external/expat-2.0.1/README000077500000000000000000000131051211610345200211150ustar00rootroot00000000000000
                        Expat, Release 2.0.1

This is Expat, a C library for parsing XML, written by James Clark.
Expat is a stream-oriented XML parser.  This means that you register
handlers with the parser before starting the parse.  These handlers
are called when the parser discovers the associated structures in the
document being parsed.  A start tag is an example of the kind of
structures for which you may register handlers.

Windows users should use the expat_win32bin package, which includes
both precompiled libraries and executables, and source code for
developers.

Expat is free software.  You may copy, distribute, and modify it under
the terms of the License contained in the file COPYING distributed
with this package.  This license is the same as the MIT/X Consortium
license.

Versions of Expat that have an odd minor version (the middle number in
the release above), are development releases and should be considered
as beta software.  Releases with even minor version numbers are
intended to be production grade software.

If you are building Expat from a check-out from the CVS repository,
you need to run a script that generates the configure script using the
GNU autoconf and libtool tools.  To do this, you need to have
autoconf 2.52 or newer and libtool 1.4 or newer (1.5 or newer preferred).
Run the script like this:

        ./buildconf.sh

Once this has been done, follow the same instructions as for building
from a source distribution.

To build Expat from a source distribution, you first run the
configuration shell script in the top level distribution directory:

        ./configure

There are many options which you may provide to configure (which you
can discover by running configure with the --help option).  But the
one of most interest is the one that sets the installation directory.
By default, the configure script will set things up to install
libexpat into /usr/local/lib, expat.h into /usr/local/include, and
xmlwf into /usr/local/bin.  If, for example, you'd prefer to install
into /home/me/mystuff/lib, /home/me/mystuff/include, and
/home/me/mystuff/bin, you can tell configure about that with:

        ./configure --prefix=/home/me/mystuff
        
Another interesting option is to enable 64-bit integer support for
line and column numbers and the over-all byte index:

        ./configure CPPFLAGS=-DXML_LARGE_SIZE
        
However, such a modification would be a breaking change to the ABI
and is therefore not recommended for general use - e.g. as part of
a Linux distribution - but rather for builds with special requirements.

After running the configure script, the "make" command will build
things and "make install" will install things into their proper
location.  Have a look at the "Makefile" to learn about additional
"make" options.  Note that you need to have write permission into
the directories into which things will be installed.

If you are interested in building Expat to provide document
information in UTF-16 rather than the default UTF-8, follow these
instructions (after having run "make distclean"):

        1. For UTF-16 output as unsigned short (and version/error
           strings as char), run:

               ./configure CPPFLAGS=-DXML_UNICODE

           For UTF-16 output as wchar_t (incl. version/error strings),
           run:

               ./configure CFLAGS="-g -O2 -fshort-wchar" \
                           CPPFLAGS=-DXML_UNICODE_WCHAR_T

        2. Edit the MakeFile, changing:

               LIBRARY = libexpat.la

           to:

               LIBRARY = libexpatw.la

           (Note the additional "w" in the library name.)

        3. Run "make buildlib" (which builds the library only).
           Or, to save step 2, run "make buildlib LIBRARY=libexpatw.la".

        4. Run "make installlib" (which installs the library only).
           Or, if step 2 was omitted, run "make installlib LIBRARY=libexpatw.la".
           
Using DESTDIR or INSTALL_ROOT is enabled, with INSTALL_ROOT being the default
value for DESTDIR, and the rest of the make file using only DESTDIR.
It works as follows:
   $ make install DESTDIR=/path/to/image
overrides the in-makefile set DESTDIR, while both
   $ INSTALL_ROOT=/path/to/image make install
   $ make install INSTALL_ROOT=/path/to/image
use DESTDIR=$(INSTALL_ROOT), even if DESTDIR eventually is defined in the
environment, because variable-setting priority is
1) commandline
2) in-makefile
3) environment           

Note for Solaris users:  The "ar" command is usually located in
"/usr/ccs/bin", which is not in the default PATH.  You will need to
add this to your path for the "make" command, and probably also switch
to GNU make (the "make" found in /usr/ccs/bin does not seem to work
properly -- appearantly it does not understand .PHONY directives).  If
you're using ksh or bash, use this command to build:

        PATH=/usr/ccs/bin:$PATH make

When using Expat with a project using autoconf for configuration, you
can use the probing macro in conftools/expat.m4 to determine how to
include Expat.  See the comments at the top of that file for more
information.

A reference manual is available in the file doc/reference.html in this
distribution.

The homepage for this project is http://www.libexpat.org/.  There
are links there to connect you to the bug reports page.  If you need
to report a bug when you don't have access to a browser, you may also
send a bug report by email to expat-bugs@mail.libexpat.org.

Discussion related to the direction of future expat development takes
place on expat-discuss@mail.libexpat.org.  Archives of this list and
other Expat-related lists may be found at:

        http://mail.libexpat.org/mailman/listinfo/
genometools-1.5.1/src/external/expat-2.0.1/examples/000077500000000000000000000000001211610345200220505ustar00rootroot00000000000000genometools-1.5.1/src/external/expat-2.0.1/examples/elements.c000077500000000000000000000031211211610345200240300ustar00rootroot00000000000000/* This is simple demonstration of how to use expat. This program
   reads an XML document from standard input and writes a line with
   the name of each element to standard output indenting child
   elements by one tab stop more than their parent element.
   It must be used with Expat compiled for UTF-8 output.
*/

#include 
#include "expat.h"

#if defined(__amigaos__) && defined(__USE_INLINE__)
#include 
#endif

#ifdef XML_LARGE_SIZE
#if defined(XML_USE_MSC_EXTENSIONS) && _MSC_VER < 1400
#define XML_FMT_INT_MOD "I64"
#else
#define XML_FMT_INT_MOD "ll"
#endif
#else
#define XML_FMT_INT_MOD "l"
#endif

static void XMLCALL
startElement(void *userData, const char *name, const char **atts)
{
  int i;
  int *depthPtr = (int *)userData;
  for (i = 0; i < *depthPtr; i++)
    putchar('\t');
  puts(name);
  *depthPtr += 1;
}

static void XMLCALL
endElement(void *userData, const char *name)
{
  int *depthPtr = (int *)userData;
  *depthPtr -= 1;
}

int
main(int argc, char *argv[])
{
  char buf[BUFSIZ];
  XML_Parser parser = XML_ParserCreate(NULL);
  int done;
  int depth = 0;
  XML_SetUserData(parser, &depth);
  XML_SetElementHandler(parser, startElement, endElement);
  do {
    int len = (int)fread(buf, 1, sizeof(buf), stdin);
    done = len < sizeof(buf);
    if (XML_Parse(parser, buf, len, done) == XML_STATUS_ERROR) {
      fprintf(stderr,
              "%s at line %" XML_FMT_INT_MOD "u\n",
              XML_ErrorString(XML_GetErrorCode(parser)),
              XML_GetCurrentLineNumber(parser));
      return 1;
    }
  } while (!done);
  XML_ParserFree(parser);
  return 0;
}
genometools-1.5.1/src/external/expat-2.0.1/examples/elements.dsp000077500000000000000000000103421211610345200243770ustar00rootroot00000000000000# Microsoft Developer Studio Project File - Name="elements" - Package Owner=<4>
# Microsoft Developer Studio Generated Build File, Format Version 6.00
# ** DO NOT EDIT **

# TARGTYPE "Win32 (x86) Console Application" 0x0103

CFG=elements - Win32 Debug
!MESSAGE This is not a valid makefile. To build this project using NMAKE,
!MESSAGE use the Export Makefile command and run
!MESSAGE 
!MESSAGE NMAKE /f "elements.mak".
!MESSAGE 
!MESSAGE You can specify a configuration when running NMAKE
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genometools-1.5.1/src/external/expat-2.0.1/examples/outline.c000077500000000000000000000045571211610345200237110ustar00rootroot00000000000000/*****************************************************************
 * outline.c
 *
 * Copyright 1999, Clark Cooper
 * All rights reserved.
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the license contained in the
 * COPYING file that comes with the expat distribution.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
 * IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
 * CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 * TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
 * SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 *
 * Read an XML document from standard input and print an element
 * outline on standard output.
 * Must be used with Expat compiled for UTF-8 output.
 */


#include 
#include 

#if defined(__amigaos__) && defined(__USE_INLINE__)
#include 
#endif

#ifdef XML_LARGE_SIZE
#if defined(XML_USE_MSC_EXTENSIONS) && _MSC_VER < 1400
#define XML_FMT_INT_MOD "I64"
#else
#define XML_FMT_INT_MOD "ll"
#endif
#else
#define XML_FMT_INT_MOD "l"
#endif

#define BUFFSIZE        8192

char Buff[BUFFSIZE];

int Depth;

static void XMLCALL
start(void *data, const char *el, const char **attr)
{
  int i;

  for (i = 0; i < Depth; i++)
    printf("  ");

  printf("%s", el);

  for (i = 0; attr[i]; i += 2) {
    printf(" %s='%s'", attr[i], attr[i + 1]);
  }

  printf("\n");
  Depth++;
}

static void XMLCALL
end(void *data, const char *el)
{
  Depth--;
}

int
main(int argc, char *argv[])
{
  XML_Parser p = XML_ParserCreate(NULL);
  if (! p) {
    fprintf(stderr, "Couldn't allocate memory for parser\n");
    exit(-1);
  }

  XML_SetElementHandler(p, start, end);

  for (;;) {
    int done;
    int len;

    len = (int)fread(Buff, 1, BUFFSIZE, stdin);
    if (ferror(stdin)) {
      fprintf(stderr, "Read error\n");
      exit(-1);
    }
    done = feof(stdin);

    if (XML_Parse(p, Buff, len, done) == XML_STATUS_ERROR) {
      fprintf(stderr, "Parse error at line %" XML_FMT_INT_MOD "u:\n%s\n",
              XML_GetCurrentLineNumber(p),
              XML_ErrorString(XML_GetErrorCode(p)));
      exit(-1);
    }

    if (done)
      break;
  }
  XML_ParserFree(p);
  return 0;
}
genometools-1.5.1/src/external/expat-2.0.1/examples/outline.dsp000077500000000000000000000105621211610345200242460ustar00rootroot00000000000000# Microsoft Developer Studio Project File - Name="outline" - Package Owner=<4>
# Microsoft Developer Studio Generated Build File, Format Version 6.00
# ** DO NOT EDIT **

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CFG=outline - Win32 Debug
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genometools-1.5.1/src/external/expat-2.0.1/lib/000077500000000000000000000000001211610345200210005ustar00rootroot00000000000000genometools-1.5.1/src/external/expat-2.0.1/lib/Makefile.MPW000077500000000000000000000107671211610345200231200ustar00rootroot00000000000000#   File:       Makefile.MPW
#   Targets:    All, Dynamic, Static (and Clean, Clean-All)
#   Created:    Tuesday, July 02, 2002
#
#   MPW Makefile for building expat under the "classic" (i.e. pre-X) Mac OS
#   Copyright  2002 Daryle Walker
#   Portions Copyright  2002 Thomas Wegner
#   See the COPYING file for distribution information
#
#   Description: 
#   This Makefile lets you build static, dynamic (i.e. shared) and stub 
#   versions of the expat library as well as the elements.c and outline.c 
#   examples (built as tools for MPW). This is for PPC only; it should be 
#   no problem to build a 68K version of the expat library, though.
#
# 	Usage: 
#			       Buildprogram All
#			 or    Buildprogram Dynamic
#			 or    Buildprogram Static
#
#   Note: You first have to rename this file to "Makefile", or the Buildprogram 
#         commando will not recognize it.
#

MAKEFILE        = Makefile
MondoBuild    = {MAKEFILE}  # Make blank to avoid rebuilds when makefile is modified

ObjDir          = :
SrcDir          = :
HdrDir          = :

ToolDir         = ::examples:

Includes        = -i {HdrDir}

Sym-PPC         = -sym off

Defines         = -d MACOS_CLASSIC

PPCCOptions     = {Includes} {Sym-PPC} -w 35 {Defines}

FragName        = libexpat


### Source Files ###

SrcFiles        =  
				  "{SrcDir}xmlparse.c" 
				  "{SrcDir}xmlrole.c" 
				  "{SrcDir}xmltok.c"

ToolSrcFiles    =  
				  "{ToolDir}elements.c" 
				  "{ToolDir}outline.c"


### Object Files ###

ObjFiles-PPC    =  
				  "{ObjDir}xmlparse.c.o" 
				  "{ObjDir}xmlrole.c.o" 
				  "{ObjDir}xmltok.c.o"

ElementToolObjFile   =  "{ObjDir}elements.c.o"

OutlineToolObjFile   =  "{ObjDir}outline.c.o"


### Libraries ###

StLibFiles-PPC    =  
				  "{PPCLibraries}StdCRuntime.o" 
				  "{PPCLibraries}PPCCRuntime.o" 
				  "{PPCLibraries}PPCToolLibs.o"

ShLibFiles-PPC    =  
				  "{SharedLibraries}InterfaceLib" 
				  "{SharedLibraries}StdCLib" 
				  "{SharedLibraries}MathLib"

LibFiles-PPC    =  
				  {StLibFiles-PPC} 
				  {ShLibFiles-PPC}


### Special Files ###

ExportFile      = "{ObjDir}{FragName}.exp"

StLibFile       = "{ObjDir}{FragName}.MrC.o"

ShLibFile       = "{ObjDir}{FragName}"

StubFile        = "{ObjDir}{FragName}.stub"

ElementsTool    = "{ToolDir}elements"

OutlineTool     = "{ToolDir}outline"


### Default Rules ###

.c.o    .c  {MondoBuild}
	{PPCC} {depDir}{default}.c -o {targDir}{default}.c.o {PPCCOptions}


### Build Rules ###

All    Dynamic {ElementsTool} {OutlineTool}

Static    {StLibFile}

Dynamic    Static {ShLibFile} {StubFile}

{StLibFile}    {ObjFiles-PPC} {StLibFiles-PPC} {MondoBuild}
	PPCLink 
		-o {Targ} 
		{ObjFiles-PPC} 
		{StLibFiles-PPC} 
		{Sym-PPC} 
		-mf -d 
		-t 'XCOF' 
		-c 'MPS ' 
		-xm l

{ShLibFile}    {StLibFile} {ShLibFiles-PPC} {ExportFile} {MondoBuild}
	PPCLink 
		-o {Targ} 
		{StLibFile} 
		{ShLibFiles-PPC} 
		{Sym-PPC} 
		-@export {ExportFile} 
		-fragname {FragName} 
		-mf -d 
		-t 'shlb' 
		-c '????' 
		-xm s

{StubFile}    {ShLibFile} {MondoBuild}
	shlb2stub -o {Targ} {ShLibFile}

{ElementsTool}    {ElementToolObjFile} {StubFile} {LibFiles-PPC} {MondoBuild}
	PPCLink 
		-o {Targ} 
		{ElementToolObjFile} 
		{StLibFile} 
		{LibFiles-PPC} 
		{Sym-PPC} 
		-mf -d 
		-t 'MPST' 
		-c 'MPS '

{OutlineTool}    {OutlineToolObjFile} {StubFile} {LibFiles-PPC} {MondoBuild}
	PPCLink 
		-o {Targ} 
		{OutlineToolObjFile} 
		{StLibFile} 
		{LibFiles-PPC} 
		{Sym-PPC} 
		-mf -d 
		-t 'MPST' 
		-c 'MPS '


### Special Rules ###

{ExportFile}    "{HdrDir}expat.h" {MondoBuild}
	StreamEdit -d 
		-e "/('XMLPARSEAPI('') ')0,1'XML_'([A-Za-z0-9_]+)1'('/ Print 'XML_' 1" 
		"{HdrDir}expat.h" > {Targ}


### Required Dependencies ###

"{ObjDir}xmlparse.c.o"    "{SrcDir}xmlparse.c"
"{ObjDir}xmlrole.c.o"    "{SrcDir}xmlrole.c"
"{ObjDir}xmltok.c.o"    "{SrcDir}xmltok.c"

"{ObjDir}elements.c.o"   "{ToolDir}elements.c"
"{ObjDir}outline.c.o"   "{ToolDir}outline.c"


### Optional Dependencies ###
### Build this target to clean out generated intermediate files. ###

Clean  
	Delete {ObjFiles-PPC} {ExportFile} {ElementToolObjFile} {OutlineToolObjFile}

### Build this target to clean out all generated files. ###

Clean-All    Clean
	Delete {StLibFile} {ShLibFile} {StubFile} {ElementsTool} {OutlineTool}

### Build this target to generate "include file" dependencies. ###

Dependencies    $OutOfDate
	MakeDepend 
		-append {MAKEFILE} 
		-ignore "{CIncludes}" 
		-objdir "{ObjDir}" 
		-objext .o 
		{Defines} 
		{Includes} 
		{SrcFiles}


genometools-1.5.1/src/external/expat-2.0.1/lib/amigaconfig.h000077500000000000000000000014351211610345200234230ustar00rootroot00000000000000#ifndef AMIGACONFIG_H
#define AMIGACONFIG_H

/* 1234 = LIL_ENDIAN, 4321 = BIGENDIAN */
#define BYTEORDER 4321

/* Define to 1 if you have the `bcopy' function. */
#define HAVE_BCOPY 1

/* Define to 1 if you have the  header file. */
#undef HAVE_CHECK_H

/* Define to 1 if you have the `memmove' function. */
#define HAVE_MEMMOVE 1

/* Define to 1 if you have the  header file. */
#define HAVE_UNISTD_H 1

/* whether byteorder is bigendian */
#define WORDS_BIGENDIAN

/* Define to specify how much context to retain around the current parse
   point. */
#define XML_CONTEXT_BYTES 1024

/* Define to make parameter entity parsing functionality available. */
#define XML_DTD

/* Define to make XML Namespaces functionality available. */
#define XML_NS

#endif  /* AMIGACONFIG_H */
genometools-1.5.1/src/external/expat-2.0.1/lib/ascii.h000077500000000000000000000037011211610345200222450ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

#define ASCII_A 0x41
#define ASCII_B 0x42
#define ASCII_C 0x43
#define ASCII_D 0x44
#define ASCII_E 0x45
#define ASCII_F 0x46
#define ASCII_G 0x47
#define ASCII_H 0x48
#define ASCII_I 0x49
#define ASCII_J 0x4A
#define ASCII_K 0x4B
#define ASCII_L 0x4C
#define ASCII_M 0x4D
#define ASCII_N 0x4E
#define ASCII_O 0x4F
#define ASCII_P 0x50
#define ASCII_Q 0x51
#define ASCII_R 0x52
#define ASCII_S 0x53
#define ASCII_T 0x54
#define ASCII_U 0x55
#define ASCII_V 0x56
#define ASCII_W 0x57
#define ASCII_X 0x58
#define ASCII_Y 0x59
#define ASCII_Z 0x5A

#define ASCII_a 0x61
#define ASCII_b 0x62
#define ASCII_c 0x63
#define ASCII_d 0x64
#define ASCII_e 0x65
#define ASCII_f 0x66
#define ASCII_g 0x67
#define ASCII_h 0x68
#define ASCII_i 0x69
#define ASCII_j 0x6A
#define ASCII_k 0x6B
#define ASCII_l 0x6C
#define ASCII_m 0x6D
#define ASCII_n 0x6E
#define ASCII_o 0x6F
#define ASCII_p 0x70
#define ASCII_q 0x71
#define ASCII_r 0x72
#define ASCII_s 0x73
#define ASCII_t 0x74
#define ASCII_u 0x75
#define ASCII_v 0x76
#define ASCII_w 0x77
#define ASCII_x 0x78
#define ASCII_y 0x79
#define ASCII_z 0x7A

#define ASCII_0 0x30
#define ASCII_1 0x31
#define ASCII_2 0x32
#define ASCII_3 0x33
#define ASCII_4 0x34
#define ASCII_5 0x35
#define ASCII_6 0x36
#define ASCII_7 0x37
#define ASCII_8 0x38
#define ASCII_9 0x39

#define ASCII_TAB 0x09
#define ASCII_SPACE 0x20
#define ASCII_EXCL 0x21
#define ASCII_QUOT 0x22
#define ASCII_AMP 0x26
#define ASCII_APOS 0x27
#define ASCII_MINUS 0x2D
#define ASCII_PERIOD 0x2E
#define ASCII_COLON 0x3A
#define ASCII_SEMI 0x3B
#define ASCII_LT 0x3C
#define ASCII_EQUALS 0x3D
#define ASCII_GT 0x3E
#define ASCII_LSQB 0x5B
#define ASCII_RSQB 0x5D
#define ASCII_UNDERSCORE 0x5F
#define ASCII_LPAREN 0x28
#define ASCII_RPAREN 0x29
#define ASCII_FF 0x0C
#define ASCII_SLASH 0x2F
#define ASCII_HASH 0x23
#define ASCII_PIPE 0x7C
#define ASCII_COMMA 0x2C
genometools-1.5.1/src/external/expat-2.0.1/lib/asciitab.h000077500000000000000000000033401211610345200227330ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

/* 0x00 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x04 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x08 */ BT_NONXML, BT_S, BT_LF, BT_NONXML,
/* 0x0C */ BT_NONXML, BT_CR, BT_NONXML, BT_NONXML,
/* 0x10 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x14 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x18 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x1C */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x20 */ BT_S, BT_EXCL, BT_QUOT, BT_NUM,
/* 0x24 */ BT_OTHER, BT_PERCNT, BT_AMP, BT_APOS,
/* 0x28 */ BT_LPAR, BT_RPAR, BT_AST, BT_PLUS,
/* 0x2C */ BT_COMMA, BT_MINUS, BT_NAME, BT_SOL,
/* 0x30 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT,
/* 0x34 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT,
/* 0x38 */ BT_DIGIT, BT_DIGIT, BT_COLON, BT_SEMI,
/* 0x3C */ BT_LT, BT_EQUALS, BT_GT, BT_QUEST,
/* 0x40 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX,
/* 0x44 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT,
/* 0x48 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x4C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x50 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x54 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x58 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_LSQB,
/* 0x5C */ BT_OTHER, BT_RSQB, BT_OTHER, BT_NMSTRT,
/* 0x60 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX,
/* 0x64 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT,
/* 0x68 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x6C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x70 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x74 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x78 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_OTHER,
/* 0x7C */ BT_VERBAR, BT_OTHER, BT_OTHER, BT_OTHER,
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genometools-1.5.1/src/external/expat-2.0.1/lib/expat.h000077500000000000000000001166231211610345200223060ustar00rootroot00000000000000/* Copyright (c) 1998, 1999, 2000 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

#ifndef Expat_INCLUDED
#define Expat_INCLUDED 1

#ifdef __VMS
/*      0        1         2         3      0        1         2         3
        1234567890123456789012345678901     1234567890123456789012345678901 */
#define XML_SetProcessingInstructionHandler XML_SetProcessingInstrHandler
#define XML_SetUnparsedEntityDeclHandler    XML_SetUnparsedEntDeclHandler
#define XML_SetStartNamespaceDeclHandler    XML_SetStartNamespcDeclHandler
#define XML_SetExternalEntityRefHandlerArg  XML_SetExternalEntRefHandlerArg
#endif

#include 
#include "expat_external.h"

#ifdef __cplusplus
extern "C" {
#endif

struct XML_ParserStruct;
typedef struct XML_ParserStruct *XML_Parser;

/* Should this be defined using stdbool.h when C99 is available? */
typedef unsigned char XML_Bool;
#define XML_TRUE   ((XML_Bool) 1)
#define XML_FALSE  ((XML_Bool) 0)

/* The XML_Status enum gives the possible return values for several
   API functions.  The preprocessor #defines are included so this
   stanza can be added to code that still needs to support older
   versions of Expat 1.95.x:

   #ifndef XML_STATUS_OK
   #define XML_STATUS_OK    1
   #define XML_STATUS_ERROR 0
   #endif

   Otherwise, the #define hackery is quite ugly and would have been
   dropped.
*/
enum XML_Status {
  XML_STATUS_ERROR = 0,
#define XML_STATUS_ERROR XML_STATUS_ERROR
  XML_STATUS_OK = 1,
#define XML_STATUS_OK XML_STATUS_OK
  XML_STATUS_SUSPENDED = 2
#define XML_STATUS_SUSPENDED XML_STATUS_SUSPENDED
};

enum XML_Error {
  XML_ERROR_NONE,
  XML_ERROR_NO_MEMORY,
  XML_ERROR_SYNTAX,
  XML_ERROR_NO_ELEMENTS,
  XML_ERROR_INVALID_TOKEN,
  XML_ERROR_UNCLOSED_TOKEN,
  XML_ERROR_PARTIAL_CHAR,
  XML_ERROR_TAG_MISMATCH,
  XML_ERROR_DUPLICATE_ATTRIBUTE,
  XML_ERROR_JUNK_AFTER_DOC_ELEMENT,
  XML_ERROR_PARAM_ENTITY_REF,
  XML_ERROR_UNDEFINED_ENTITY,
  XML_ERROR_RECURSIVE_ENTITY_REF,
  XML_ERROR_ASYNC_ENTITY,
  XML_ERROR_BAD_CHAR_REF,
  XML_ERROR_BINARY_ENTITY_REF,
  XML_ERROR_ATTRIBUTE_EXTERNAL_ENTITY_REF,
  XML_ERROR_MISPLACED_XML_PI,
  XML_ERROR_UNKNOWN_ENCODING,
  XML_ERROR_INCORRECT_ENCODING,
  XML_ERROR_UNCLOSED_CDATA_SECTION,
  XML_ERROR_EXTERNAL_ENTITY_HANDLING,
  XML_ERROR_NOT_STANDALONE,
  XML_ERROR_UNEXPECTED_STATE,
  XML_ERROR_ENTITY_DECLARED_IN_PE,
  XML_ERROR_FEATURE_REQUIRES_XML_DTD,
  XML_ERROR_CANT_CHANGE_FEATURE_ONCE_PARSING,
  /* Added in 1.95.7. */
  XML_ERROR_UNBOUND_PREFIX,
  /* Added in 1.95.8. */
  XML_ERROR_UNDECLARING_PREFIX,
  XML_ERROR_INCOMPLETE_PE,
  XML_ERROR_XML_DECL,
  XML_ERROR_TEXT_DECL,
  XML_ERROR_PUBLICID,
  XML_ERROR_SUSPENDED,
  XML_ERROR_NOT_SUSPENDED,
  XML_ERROR_ABORTED,
  XML_ERROR_FINISHED,
  XML_ERROR_SUSPEND_PE,
  /* Added in 2.0. */
  XML_ERROR_RESERVED_PREFIX_XML,
  XML_ERROR_RESERVED_PREFIX_XMLNS,
  XML_ERROR_RESERVED_NAMESPACE_URI
};

enum XML_Content_Type {
  XML_CTYPE_EMPTY = 1,
  XML_CTYPE_ANY,
  XML_CTYPE_MIXED,
  XML_CTYPE_NAME,
  XML_CTYPE_CHOICE,
  XML_CTYPE_SEQ
};

enum XML_Content_Quant {
  XML_CQUANT_NONE,
  XML_CQUANT_OPT,
  XML_CQUANT_REP,
  XML_CQUANT_PLUS
};

/* If type == XML_CTYPE_EMPTY or XML_CTYPE_ANY, then quant will be
   XML_CQUANT_NONE, and the other fields will be zero or NULL.
   If type == XML_CTYPE_MIXED, then quant will be NONE or REP and
   numchildren will contain number of elements that may be mixed in
   and children point to an array of XML_Content cells that will be
   all of XML_CTYPE_NAME type with no quantification.

   If type == XML_CTYPE_NAME, then the name points to the name, and
   the numchildren field will be zero and children will be NULL. The
   quant fields indicates any quantifiers placed on the name.

   CHOICE and SEQ will have name NULL, the number of children in
   numchildren and children will point, recursively, to an array
   of XML_Content cells.

   The EMPTY, ANY, and MIXED types will only occur at top level.
*/

typedef struct XML_cp XML_Content;

struct XML_cp {
  enum XML_Content_Type         type;
  enum XML_Content_Quant        quant;
  XML_Char *                    name;
  unsigned int                  numchildren;
  XML_Content *                 children;
};


/* This is called for an element declaration. See above for
   description of the model argument. It's the caller's responsibility
   to free model when finished with it.
*/
typedef void (XMLCALL *XML_ElementDeclHandler) (void *userData,
                                                const XML_Char *name,
                                                XML_Content *model);

XMLPARSEAPI(void)
XML_SetElementDeclHandler(XML_Parser parser,
                          XML_ElementDeclHandler eldecl);

/* The Attlist declaration handler is called for *each* attribute. So
   a single Attlist declaration with multiple attributes declared will
   generate multiple calls to this handler. The "default" parameter
   may be NULL in the case of the "#IMPLIED" or "#REQUIRED"
   keyword. The "isrequired" parameter will be true and the default
   value will be NULL in the case of "#REQUIRED". If "isrequired" is
   true and default is non-NULL, then this is a "#FIXED" default.
*/
typedef void (XMLCALL *XML_AttlistDeclHandler) (
                                    void            *userData,
                                    const XML_Char  *elname,
                                    const XML_Char  *attname,
                                    const XML_Char  *att_type,
                                    const XML_Char  *dflt,
                                    int              isrequired);

XMLPARSEAPI(void)
XML_SetAttlistDeclHandler(XML_Parser parser,
                          XML_AttlistDeclHandler attdecl);

/* The XML declaration handler is called for *both* XML declarations
   and text declarations. The way to distinguish is that the version
   parameter will be NULL for text declarations. The encoding
   parameter may be NULL for XML declarations. The standalone
   parameter will be -1, 0, or 1 indicating respectively that there
   was no standalone parameter in the declaration, that it was given
   as no, or that it was given as yes.
*/
typedef void (XMLCALL *XML_XmlDeclHandler) (void           *userData,
                                            const XML_Char *version,
                                            const XML_Char *encoding,
                                            int             standalone);

XMLPARSEAPI(void)
XML_SetXmlDeclHandler(XML_Parser parser,
                      XML_XmlDeclHandler xmldecl);


typedef struct {
  void *(*malloc_fcn)(size_t size);
  void *(*realloc_fcn)(void *ptr, size_t size);
  void (*free_fcn)(void *ptr);
} XML_Memory_Handling_Suite;

/* Constructs a new parser; encoding is the encoding specified by the
   external protocol or NULL if there is none specified.
*/
XMLPARSEAPI(XML_Parser)
XML_ParserCreate(const XML_Char *encoding);

/* Constructs a new parser and namespace processor.  Element type
   names and attribute names that belong to a namespace will be
   expanded; unprefixed attribute names are never expanded; unprefixed
   element type names are expanded only if there is a default
   namespace. The expanded name is the concatenation of the namespace
   URI, the namespace separator character, and the local part of the
   name.  If the namespace separator is '\0' then the namespace URI
   and the local part will be concatenated without any separator.
   It is a programming error to use the separator '\0' with namespace
   triplets (see XML_SetReturnNSTriplet).
*/
XMLPARSEAPI(XML_Parser)
XML_ParserCreateNS(const XML_Char *encoding, XML_Char namespaceSeparator);


/* Constructs a new parser using the memory management suite referred to
   by memsuite. If memsuite is NULL, then use the standard library memory
   suite. If namespaceSeparator is non-NULL it creates a parser with
   namespace processing as described above. The character pointed at
   will serve as the namespace separator.

   All further memory operations used for the created parser will come from
   the given suite.
*/
XMLPARSEAPI(XML_Parser)
XML_ParserCreate_MM(const XML_Char *encoding,
                    const XML_Memory_Handling_Suite *memsuite,
                    const XML_Char *namespaceSeparator);

/* Prepare a parser object to be re-used.  This is particularly
   valuable when memory allocation overhead is disproportionatly high,
   such as when a large number of small documnents need to be parsed.
   All handlers are cleared from the parser, except for the
   unknownEncodingHandler. The parser's external state is re-initialized
   except for the values of ns and ns_triplets.

   Added in Expat 1.95.3.
*/
XMLPARSEAPI(XML_Bool)
XML_ParserReset(XML_Parser parser, const XML_Char *encoding);

/* atts is array of name/value pairs, terminated by 0;
   names and values are 0 terminated.
*/
typedef void (XMLCALL *XML_StartElementHandler) (void *userData,
                                                 const XML_Char *name,
                                                 const XML_Char **atts);

typedef void (XMLCALL *XML_EndElementHandler) (void *userData,
                                               const XML_Char *name);


/* s is not 0 terminated. */
typedef void (XMLCALL *XML_CharacterDataHandler) (void *userData,
                                                  const XML_Char *s,
                                                  int len);

/* target and data are 0 terminated */
typedef void (XMLCALL *XML_ProcessingInstructionHandler) (
                                                void *userData,
                                                const XML_Char *target,
                                                const XML_Char *data);

/* data is 0 terminated */
typedef void (XMLCALL *XML_CommentHandler) (void *userData,
                                            const XML_Char *data);

typedef void (XMLCALL *XML_StartCdataSectionHandler) (void *userData);
typedef void (XMLCALL *XML_EndCdataSectionHandler) (void *userData);

/* This is called for any characters in the XML document for which
   there is no applicable handler.  This includes both characters that
   are part of markup which is of a kind that is not reported
   (comments, markup declarations), or characters that are part of a
   construct which could be reported but for which no handler has been
   supplied. The characters are passed exactly as they were in the XML
   document except that they will be encoded in UTF-8 or UTF-16.
   Line boundaries are not normalized. Note that a byte order mark
   character is not passed to the default handler. There are no
   guarantees about how characters are divided between calls to the
   default handler: for example, a comment might be split between
   multiple calls.
*/
typedef void (XMLCALL *XML_DefaultHandler) (void *userData,
                                            const XML_Char *s,
                                            int len);

/* This is called for the start of the DOCTYPE declaration, before
   any DTD or internal subset is parsed.
*/
typedef void (XMLCALL *XML_StartDoctypeDeclHandler) (
                                            void *userData,
                                            const XML_Char *doctypeName,
                                            const XML_Char *sysid,
                                            const XML_Char *pubid,
                                            int has_internal_subset);

/* This is called for the start of the DOCTYPE declaration when the
   closing > is encountered, but after processing any external
   subset.
*/
typedef void (XMLCALL *XML_EndDoctypeDeclHandler)(void *userData);

/* This is called for entity declarations. The is_parameter_entity
   argument will be non-zero if the entity is a parameter entity, zero
   otherwise.

   For internal entities (), value will
   be non-NULL and systemId, publicID, and notationName will be NULL.
   The value string is NOT nul-terminated; the length is provided in
   the value_length argument. Since it is legal to have zero-length
   values, do not use this argument to test for internal entities.

   For external entities, value will be NULL and systemId will be
   non-NULL. The publicId argument will be NULL unless a public
   identifier was provided. The notationName argument will have a
   non-NULL value only for unparsed entity declarations.

   Note that is_parameter_entity can't be changed to XML_Bool, since
   that would break binary compatibility.
*/
typedef void (XMLCALL *XML_EntityDeclHandler) (
                              void *userData,
                              const XML_Char *entityName,
                              int is_parameter_entity,
                              const XML_Char *value,
                              int value_length,
                              const XML_Char *base,
                              const XML_Char *systemId,
                              const XML_Char *publicId,
                              const XML_Char *notationName);

XMLPARSEAPI(void)
XML_SetEntityDeclHandler(XML_Parser parser,
                         XML_EntityDeclHandler handler);

/* OBSOLETE -- OBSOLETE -- OBSOLETE
   This handler has been superceded by the EntityDeclHandler above.
   It is provided here for backward compatibility.

   This is called for a declaration of an unparsed (NDATA) entity.
   The base argument is whatever was set by XML_SetBase. The
   entityName, systemId and notationName arguments will never be
   NULL. The other arguments may be.
*/
typedef void (XMLCALL *XML_UnparsedEntityDeclHandler) (
                                    void *userData,
                                    const XML_Char *entityName,
                                    const XML_Char *base,
                                    const XML_Char *systemId,
                                    const XML_Char *publicId,
                                    const XML_Char *notationName);

/* This is called for a declaration of notation.  The base argument is
   whatever was set by XML_SetBase. The notationName will never be
   NULL.  The other arguments can be.
*/
typedef void (XMLCALL *XML_NotationDeclHandler) (
                                    void *userData,
                                    const XML_Char *notationName,
                                    const XML_Char *base,
                                    const XML_Char *systemId,
                                    const XML_Char *publicId);

/* When namespace processing is enabled, these are called once for
   each namespace declaration. The call to the start and end element
   handlers occur between the calls to the start and end namespace
   declaration handlers. For an xmlns attribute, prefix will be
   NULL.  For an xmlns="" attribute, uri will be NULL.
*/
typedef void (XMLCALL *XML_StartNamespaceDeclHandler) (
                                    void *userData,
                                    const XML_Char *prefix,
                                    const XML_Char *uri);

typedef void (XMLCALL *XML_EndNamespaceDeclHandler) (
                                    void *userData,
                                    const XML_Char *prefix);

/* This is called if the document is not standalone, that is, it has an
   external subset or a reference to a parameter entity, but does not
   have standalone="yes". If this handler returns XML_STATUS_ERROR,
   then processing will not continue, and the parser will return a
   XML_ERROR_NOT_STANDALONE error.
   If parameter entity parsing is enabled, then in addition to the
   conditions above this handler will only be called if the referenced
   entity was actually read.
*/
typedef int (XMLCALL *XML_NotStandaloneHandler) (void *userData);

/* This is called for a reference to an external parsed general
   entity.  The referenced entity is not automatically parsed.  The
   application can parse it immediately or later using
   XML_ExternalEntityParserCreate.

   The parser argument is the parser parsing the entity containing the
   reference; it can be passed as the parser argument to
   XML_ExternalEntityParserCreate.  The systemId argument is the
   system identifier as specified in the entity declaration; it will
   not be NULL.

   The base argument is the system identifier that should be used as
   the base for resolving systemId if systemId was relative; this is
   set by XML_SetBase; it may be NULL.

   The publicId argument is the public identifier as specified in the
   entity declaration, or NULL if none was specified; the whitespace
   in the public identifier will have been normalized as required by
   the XML spec.

   The context argument specifies the parsing context in the format
   expected by the context argument to XML_ExternalEntityParserCreate;
   context is valid only until the handler returns, so if the
   referenced entity is to be parsed later, it must be copied.
   context is NULL only when the entity is a parameter entity.

   The handler should return XML_STATUS_ERROR if processing should not
   continue because of a fatal error in the handling of the external
   entity.  In this case the calling parser will return an
   XML_ERROR_EXTERNAL_ENTITY_HANDLING error.

   Note that unlike other handlers the first argument is the parser,
   not userData.
*/
typedef int (XMLCALL *XML_ExternalEntityRefHandler) (
                                    XML_Parser parser,
                                    const XML_Char *context,
                                    const XML_Char *base,
                                    const XML_Char *systemId,
                                    const XML_Char *publicId);

/* This is called in two situations:
   1) An entity reference is encountered for which no declaration
      has been read *and* this is not an error.
   2) An internal entity reference is read, but not expanded, because
      XML_SetDefaultHandler has been called.
   Note: skipped parameter entities in declarations and skipped general
         entities in attribute values cannot be reported, because
         the event would be out of sync with the reporting of the
         declarations or attribute values
*/
typedef void (XMLCALL *XML_SkippedEntityHandler) (
                                    void *userData,
                                    const XML_Char *entityName,
                                    int is_parameter_entity);

/* This structure is filled in by the XML_UnknownEncodingHandler to
   provide information to the parser about encodings that are unknown
   to the parser.

   The map[b] member gives information about byte sequences whose
   first byte is b.

   If map[b] is c where c is >= 0, then b by itself encodes the
   Unicode scalar value c.

   If map[b] is -1, then the byte sequence is malformed.

   If map[b] is -n, where n >= 2, then b is the first byte of an
   n-byte sequence that encodes a single Unicode scalar value.

   The data member will be passed as the first argument to the convert
   function.

   The convert function is used to convert multibyte sequences; s will
   point to a n-byte sequence where map[(unsigned char)*s] == -n.  The
   convert function must return the Unicode scalar value represented
   by this byte sequence or -1 if the byte sequence is malformed.

   The convert function may be NULL if the encoding is a single-byte
   encoding, that is if map[b] >= -1 for all bytes b.

   When the parser is finished with the encoding, then if release is
   not NULL, it will call release passing it the data member; once
   release has been called, the convert function will not be called
   again.

   Expat places certain restrictions on the encodings that are supported
   using this mechanism.

   1. Every ASCII character that can appear in a well-formed XML document,
      other than the characters

      $@\^`{}~

      must be represented by a single byte, and that byte must be the
      same byte that represents that character in ASCII.

   2. No character may require more than 4 bytes to encode.

   3. All characters encoded must have Unicode scalar values <=
      0xFFFF, (i.e., characters that would be encoded by surrogates in
      UTF-16 are  not allowed).  Note that this restriction doesn't
      apply to the built-in support for UTF-8 and UTF-16.

   4. No Unicode character may be encoded by more than one distinct
      sequence of bytes.
*/
typedef struct {
  int map[256];
  void *data;
  int (XMLCALL *convert)(void *data, const char *s);
  void (XMLCALL *release)(void *data);
} XML_Encoding;

/* This is called for an encoding that is unknown to the parser.

   The encodingHandlerData argument is that which was passed as the
   second argument to XML_SetUnknownEncodingHandler.

   The name argument gives the name of the encoding as specified in
   the encoding declaration.

   If the callback can provide information about the encoding, it must
   fill in the XML_Encoding structure, and return XML_STATUS_OK.
   Otherwise it must return XML_STATUS_ERROR.

   If info does not describe a suitable encoding, then the parser will
   return an XML_UNKNOWN_ENCODING error.
*/
typedef int (XMLCALL *XML_UnknownEncodingHandler) (
                                    void *encodingHandlerData,
                                    const XML_Char *name,
                                    XML_Encoding *info);

XMLPARSEAPI(void)
XML_SetElementHandler(XML_Parser parser,
                      XML_StartElementHandler start,
                      XML_EndElementHandler end);

XMLPARSEAPI(void)
XML_SetStartElementHandler(XML_Parser parser,
                           XML_StartElementHandler handler);

XMLPARSEAPI(void)
XML_SetEndElementHandler(XML_Parser parser,
                         XML_EndElementHandler handler);

XMLPARSEAPI(void)
XML_SetCharacterDataHandler(XML_Parser parser,
                            XML_CharacterDataHandler handler);

XMLPARSEAPI(void)
XML_SetProcessingInstructionHandler(XML_Parser parser,
                                    XML_ProcessingInstructionHandler handler);
XMLPARSEAPI(void)
XML_SetCommentHandler(XML_Parser parser,
                      XML_CommentHandler handler);

XMLPARSEAPI(void)
XML_SetCdataSectionHandler(XML_Parser parser,
                           XML_StartCdataSectionHandler start,
                           XML_EndCdataSectionHandler end);

XMLPARSEAPI(void)
XML_SetStartCdataSectionHandler(XML_Parser parser,
                                XML_StartCdataSectionHandler start);

XMLPARSEAPI(void)
XML_SetEndCdataSectionHandler(XML_Parser parser,
                              XML_EndCdataSectionHandler end);

/* This sets the default handler and also inhibits expansion of
   internal entities. These entity references will be passed to the
   default handler, or to the skipped entity handler, if one is set.
*/
XMLPARSEAPI(void)
XML_SetDefaultHandler(XML_Parser parser,
                      XML_DefaultHandler handler);

/* This sets the default handler but does not inhibit expansion of
   internal entities.  The entity reference will not be passed to the
   default handler.
*/
XMLPARSEAPI(void)
XML_SetDefaultHandlerExpand(XML_Parser parser,
                            XML_DefaultHandler handler);

XMLPARSEAPI(void)
XML_SetDoctypeDeclHandler(XML_Parser parser,
                          XML_StartDoctypeDeclHandler start,
                          XML_EndDoctypeDeclHandler end);

XMLPARSEAPI(void)
XML_SetStartDoctypeDeclHandler(XML_Parser parser,
                               XML_StartDoctypeDeclHandler start);

XMLPARSEAPI(void)
XML_SetEndDoctypeDeclHandler(XML_Parser parser,
                             XML_EndDoctypeDeclHandler end);

XMLPARSEAPI(void)
XML_SetUnparsedEntityDeclHandler(XML_Parser parser,
                                 XML_UnparsedEntityDeclHandler handler);

XMLPARSEAPI(void)
XML_SetNotationDeclHandler(XML_Parser parser,
                           XML_NotationDeclHandler handler);

XMLPARSEAPI(void)
XML_SetNamespaceDeclHandler(XML_Parser parser,
                            XML_StartNamespaceDeclHandler start,
                            XML_EndNamespaceDeclHandler end);

XMLPARSEAPI(void)
XML_SetStartNamespaceDeclHandler(XML_Parser parser,
                                 XML_StartNamespaceDeclHandler start);

XMLPARSEAPI(void)
XML_SetEndNamespaceDeclHandler(XML_Parser parser,
                               XML_EndNamespaceDeclHandler end);

XMLPARSEAPI(void)
XML_SetNotStandaloneHandler(XML_Parser parser,
                            XML_NotStandaloneHandler handler);

XMLPARSEAPI(void)
XML_SetExternalEntityRefHandler(XML_Parser parser,
                                XML_ExternalEntityRefHandler handler);

/* If a non-NULL value for arg is specified here, then it will be
   passed as the first argument to the external entity ref handler
   instead of the parser object.
*/
XMLPARSEAPI(void)
XML_SetExternalEntityRefHandlerArg(XML_Parser parser,
                                   void *arg);

XMLPARSEAPI(void)
XML_SetSkippedEntityHandler(XML_Parser parser,
                            XML_SkippedEntityHandler handler);

XMLPARSEAPI(void)
XML_SetUnknownEncodingHandler(XML_Parser parser,
                              XML_UnknownEncodingHandler handler,
                              void *encodingHandlerData);

/* This can be called within a handler for a start element, end
   element, processing instruction or character data.  It causes the
   corresponding markup to be passed to the default handler.
*/
XMLPARSEAPI(void)
XML_DefaultCurrent(XML_Parser parser);

/* If do_nst is non-zero, and namespace processing is in effect, and
   a name has a prefix (i.e. an explicit namespace qualifier) then
   that name is returned as a triplet in a single string separated by
   the separator character specified when the parser was created: URI
   + sep + local_name + sep + prefix.

   If do_nst is zero, then namespace information is returned in the
   default manner (URI + sep + local_name) whether or not the name
   has a prefix.

   Note: Calling XML_SetReturnNSTriplet after XML_Parse or
     XML_ParseBuffer has no effect.
*/

XMLPARSEAPI(void)
XML_SetReturnNSTriplet(XML_Parser parser, int do_nst);

/* This value is passed as the userData argument to callbacks. */
XMLPARSEAPI(void)
XML_SetUserData(XML_Parser parser, void *userData);

/* Returns the last value set by XML_SetUserData or NULL. */
#define XML_GetUserData(parser) (*(void **)(parser))

/* This is equivalent to supplying an encoding argument to
   XML_ParserCreate. On success XML_SetEncoding returns non-zero,
   zero otherwise.
   Note: Calling XML_SetEncoding after XML_Parse or XML_ParseBuffer
     has no effect and returns XML_STATUS_ERROR.
*/
XMLPARSEAPI(enum XML_Status)
XML_SetEncoding(XML_Parser parser, const XML_Char *encoding);

/* If this function is called, then the parser will be passed as the
   first argument to callbacks instead of userData.  The userData will
   still be accessible using XML_GetUserData.
*/
XMLPARSEAPI(void)
XML_UseParserAsHandlerArg(XML_Parser parser);

/* If useDTD == XML_TRUE is passed to this function, then the parser
   will assume that there is an external subset, even if none is
   specified in the document. In such a case the parser will call the
   externalEntityRefHandler with a value of NULL for the systemId
   argument (the publicId and context arguments will be NULL as well).
   Note: For the purpose of checking WFC: Entity Declared, passing
     useDTD == XML_TRUE will make the parser behave as if the document
     had a DTD with an external subset.
   Note: If this function is called, then this must be done before
     the first call to XML_Parse or XML_ParseBuffer, since it will
     have no effect after that.  Returns
     XML_ERROR_CANT_CHANGE_FEATURE_ONCE_PARSING.
   Note: If the document does not have a DOCTYPE declaration at all,
     then startDoctypeDeclHandler and endDoctypeDeclHandler will not
     be called, despite an external subset being parsed.
   Note: If XML_DTD is not defined when Expat is compiled, returns
     XML_ERROR_FEATURE_REQUIRES_XML_DTD.
*/
XMLPARSEAPI(enum XML_Error)
XML_UseForeignDTD(XML_Parser parser, XML_Bool useDTD);


/* Sets the base to be used for resolving relative URIs in system
   identifiers in declarations.  Resolving relative identifiers is
   left to the application: this value will be passed through as the
   base argument to the XML_ExternalEntityRefHandler,
   XML_NotationDeclHandler and XML_UnparsedEntityDeclHandler. The base
   argument will be copied.  Returns XML_STATUS_ERROR if out of memory,
   XML_STATUS_OK otherwise.
*/
XMLPARSEAPI(enum XML_Status)
XML_SetBase(XML_Parser parser, const XML_Char *base);

XMLPARSEAPI(const XML_Char *)
XML_GetBase(XML_Parser parser);

/* Returns the number of the attribute/value pairs passed in last call
   to the XML_StartElementHandler that were specified in the start-tag
   rather than defaulted. Each attribute/value pair counts as 2; thus
   this correspondds to an index into the atts array passed to the
   XML_StartElementHandler.
*/
XMLPARSEAPI(int)
XML_GetSpecifiedAttributeCount(XML_Parser parser);

/* Returns the index of the ID attribute passed in the last call to
   XML_StartElementHandler, or -1 if there is no ID attribute.  Each
   attribute/value pair counts as 2; thus this correspondds to an
   index into the atts array passed to the XML_StartElementHandler.
*/
XMLPARSEAPI(int)
XML_GetIdAttributeIndex(XML_Parser parser);

/* Parses some input. Returns XML_STATUS_ERROR if a fatal error is
   detected.  The last call to XML_Parse must have isFinal true; len
   may be zero for this call (or any other).

   Though the return values for these functions has always been
   described as a Boolean value, the implementation, at least for the
   1.95.x series, has always returned exactly one of the XML_Status
   values.
*/
XMLPARSEAPI(enum XML_Status)
XML_Parse(XML_Parser parser, const char *s, int len, int isFinal);

XMLPARSEAPI(void *)
XML_GetBuffer(XML_Parser parser, int len);

XMLPARSEAPI(enum XML_Status)
XML_ParseBuffer(XML_Parser parser, int len, int isFinal);

/* Stops parsing, causing XML_Parse() or XML_ParseBuffer() to return.
   Must be called from within a call-back handler, except when aborting
   (resumable = 0) an already suspended parser. Some call-backs may
   still follow because they would otherwise get lost. Examples:
   - endElementHandler() for empty elements when stopped in
     startElementHandler(), 
   - endNameSpaceDeclHandler() when stopped in endElementHandler(), 
   and possibly others.

   Can be called from most handlers, including DTD related call-backs,
   except when parsing an external parameter entity and resumable != 0.
   Returns XML_STATUS_OK when successful, XML_STATUS_ERROR otherwise.
   Possible error codes: 
   - XML_ERROR_SUSPENDED: when suspending an already suspended parser.
   - XML_ERROR_FINISHED: when the parser has already finished.
   - XML_ERROR_SUSPEND_PE: when suspending while parsing an external PE.

   When resumable != 0 (true) then parsing is suspended, that is, 
   XML_Parse() and XML_ParseBuffer() return XML_STATUS_SUSPENDED. 
   Otherwise, parsing is aborted, that is, XML_Parse() and XML_ParseBuffer()
   return XML_STATUS_ERROR with error code XML_ERROR_ABORTED.

   *Note*:
   This will be applied to the current parser instance only, that is, if
   there is a parent parser then it will continue parsing when the
   externalEntityRefHandler() returns. It is up to the implementation of
   the externalEntityRefHandler() to call XML_StopParser() on the parent
   parser (recursively), if one wants to stop parsing altogether.

   When suspended, parsing can be resumed by calling XML_ResumeParser(). 
*/
XMLPARSEAPI(enum XML_Status)
XML_StopParser(XML_Parser parser, XML_Bool resumable);

/* Resumes parsing after it has been suspended with XML_StopParser().
   Must not be called from within a handler call-back. Returns same
   status codes as XML_Parse() or XML_ParseBuffer().
   Additional error code XML_ERROR_NOT_SUSPENDED possible.   

   *Note*:
   This must be called on the most deeply nested child parser instance
   first, and on its parent parser only after the child parser has finished,
   to be applied recursively until the document entity's parser is restarted.
   That is, the parent parser will not resume by itself and it is up to the
   application to call XML_ResumeParser() on it at the appropriate moment.
*/
XMLPARSEAPI(enum XML_Status)
XML_ResumeParser(XML_Parser parser);

enum XML_Parsing {
  XML_INITIALIZED,
  XML_PARSING,
  XML_FINISHED,
  XML_SUSPENDED
};

typedef struct {
  enum XML_Parsing parsing;
  XML_Bool finalBuffer;
} XML_ParsingStatus;

/* Returns status of parser with respect to being initialized, parsing,
   finished, or suspended and processing the final buffer.
   XXX XML_Parse() and XML_ParseBuffer() should return XML_ParsingStatus,
   XXX with XML_FINISHED_OK or XML_FINISHED_ERROR replacing XML_FINISHED
*/
XMLPARSEAPI(void)
XML_GetParsingStatus(XML_Parser parser, XML_ParsingStatus *status);

/* Creates an XML_Parser object that can parse an external general
   entity; context is a '\0'-terminated string specifying the parse
   context; encoding is a '\0'-terminated string giving the name of
   the externally specified encoding, or NULL if there is no
   externally specified encoding.  The context string consists of a
   sequence of tokens separated by formfeeds (\f); a token consisting
   of a name specifies that the general entity of the name is open; a
   token of the form prefix=uri specifies the namespace for a
   particular prefix; a token of the form =uri specifies the default
   namespace.  This can be called at any point after the first call to
   an ExternalEntityRefHandler so longer as the parser has not yet
   been freed.  The new parser is completely independent and may
   safely be used in a separate thread.  The handlers and userData are
   initialized from the parser argument.  Returns NULL if out of memory.
   Otherwise returns a new XML_Parser object.
*/
XMLPARSEAPI(XML_Parser)
XML_ExternalEntityParserCreate(XML_Parser parser,
                               const XML_Char *context,
                               const XML_Char *encoding);

enum XML_ParamEntityParsing {
  XML_PARAM_ENTITY_PARSING_NEVER,
  XML_PARAM_ENTITY_PARSING_UNLESS_STANDALONE,
  XML_PARAM_ENTITY_PARSING_ALWAYS
};

/* Controls parsing of parameter entities (including the external DTD
   subset). If parsing of parameter entities is enabled, then
   references to external parameter entities (including the external
   DTD subset) will be passed to the handler set with
   XML_SetExternalEntityRefHandler.  The context passed will be 0.

   Unlike external general entities, external parameter entities can
   only be parsed synchronously.  If the external parameter entity is
   to be parsed, it must be parsed during the call to the external
   entity ref handler: the complete sequence of
   XML_ExternalEntityParserCreate, XML_Parse/XML_ParseBuffer and
   XML_ParserFree calls must be made during this call.  After
   XML_ExternalEntityParserCreate has been called to create the parser
   for the external parameter entity (context must be 0 for this
   call), it is illegal to make any calls on the old parser until
   XML_ParserFree has been called on the newly created parser.
   If the library has been compiled without support for parameter
   entity parsing (ie without XML_DTD being defined), then
   XML_SetParamEntityParsing will return 0 if parsing of parameter
   entities is requested; otherwise it will return non-zero.
   Note: If XML_SetParamEntityParsing is called after XML_Parse or
      XML_ParseBuffer, then it has no effect and will always return 0.
*/
XMLPARSEAPI(int)
XML_SetParamEntityParsing(XML_Parser parser,
                          enum XML_ParamEntityParsing parsing);

/* If XML_Parse or XML_ParseBuffer have returned XML_STATUS_ERROR, then
   XML_GetErrorCode returns information about the error.
*/
XMLPARSEAPI(enum XML_Error)
XML_GetErrorCode(XML_Parser parser);

/* These functions return information about the current parse
   location.  They may be called from any callback called to report
   some parse event; in this case the location is the location of the
   first of the sequence of characters that generated the event.  When
   called from callbacks generated by declarations in the document
   prologue, the location identified isn't as neatly defined, but will
   be within the relevant markup.  When called outside of the callback
   functions, the position indicated will be just past the last parse
   event (regardless of whether there was an associated callback).
   
   They may also be called after returning from a call to XML_Parse
   or XML_ParseBuffer.  If the return value is XML_STATUS_ERROR then
   the location is the location of the character at which the error
   was detected; otherwise the location is the location of the last
   parse event, as described above.
*/
XMLPARSEAPI(XML_Size) XML_GetCurrentLineNumber(XML_Parser parser);
XMLPARSEAPI(XML_Size) XML_GetCurrentColumnNumber(XML_Parser parser);
XMLPARSEAPI(XML_Index) XML_GetCurrentByteIndex(XML_Parser parser);

/* Return the number of bytes in the current event.
   Returns 0 if the event is in an internal entity.
*/
XMLPARSEAPI(int)
XML_GetCurrentByteCount(XML_Parser parser);

/* If XML_CONTEXT_BYTES is defined, returns the input buffer, sets
   the integer pointed to by offset to the offset within this buffer
   of the current parse position, and sets the integer pointed to by size
   to the size of this buffer (the number of input bytes). Otherwise
   returns a NULL pointer. Also returns a NULL pointer if a parse isn't
   active.

   NOTE: The character pointer returned should not be used outside
   the handler that makes the call.
*/
XMLPARSEAPI(const char *)
XML_GetInputContext(XML_Parser parser,
                    int *offset,
                    int *size);

/* For backwards compatibility with previous versions. */
#define XML_GetErrorLineNumber   XML_GetCurrentLineNumber
#define XML_GetErrorColumnNumber XML_GetCurrentColumnNumber
#define XML_GetErrorByteIndex    XML_GetCurrentByteIndex

/* Frees the content model passed to the element declaration handler */
XMLPARSEAPI(void)
XML_FreeContentModel(XML_Parser parser, XML_Content *model);

/* Exposing the memory handling functions used in Expat */
XMLPARSEAPI(void *)
XML_MemMalloc(XML_Parser parser, size_t size);

XMLPARSEAPI(void *)
XML_MemRealloc(XML_Parser parser, void *ptr, size_t size);

XMLPARSEAPI(void)
XML_MemFree(XML_Parser parser, void *ptr);

/* Frees memory used by the parser. */
XMLPARSEAPI(void)
XML_ParserFree(XML_Parser parser);

/* Returns a string describing the error. */
XMLPARSEAPI(const XML_LChar *)
XML_ErrorString(enum XML_Error code);

/* Return a string containing the version number of this expat */
XMLPARSEAPI(const XML_LChar *)
XML_ExpatVersion(void);

typedef struct {
  int major;
  int minor;
  int micro;
} XML_Expat_Version;

/* Return an XML_Expat_Version structure containing numeric version
   number information for this version of expat.
*/
XMLPARSEAPI(XML_Expat_Version)
XML_ExpatVersionInfo(void);

/* Added in Expat 1.95.5. */
enum XML_FeatureEnum {
  XML_FEATURE_END = 0,
  XML_FEATURE_UNICODE,
  XML_FEATURE_UNICODE_WCHAR_T,
  XML_FEATURE_DTD,
  XML_FEATURE_CONTEXT_BYTES,
  XML_FEATURE_MIN_SIZE,
  XML_FEATURE_SIZEOF_XML_CHAR,
  XML_FEATURE_SIZEOF_XML_LCHAR,
  XML_FEATURE_NS,
  XML_FEATURE_LARGE_SIZE
  /* Additional features must be added to the end of this enum. */
};

typedef struct {
  enum XML_FeatureEnum  feature;
  const XML_LChar       *name;
  long int              value;
} XML_Feature;

XMLPARSEAPI(const XML_Feature *)
XML_GetFeatureList(void);


/* Expat follows the GNU/Linux convention of odd number minor version for
   beta/development releases and even number minor version for stable
   releases. Micro is bumped with each release, and set to 0 with each
   change to major or minor version.
*/
#define XML_MAJOR_VERSION 2
#define XML_MINOR_VERSION 0
#define XML_MICRO_VERSION 1

#ifdef __cplusplus
}
#endif

#endif /* not Expat_INCLUDED */
genometools-1.5.1/src/external/expat-2.0.1/lib/expat_external.h000077500000000000000000000064441211610345200242070ustar00rootroot00000000000000/* Copyright (c) 1998, 1999, 2000 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

#ifndef Expat_External_INCLUDED
#define Expat_External_INCLUDED 1

/* External API definitions */

#if defined(_MSC_EXTENSIONS) && !defined(__BEOS__) && !defined(__CYGWIN__)
#define XML_USE_MSC_EXTENSIONS 1
#endif

/* Expat tries very hard to make the API boundary very specifically
   defined.  There are two macros defined to control this boundary;
   each of these can be defined before including this header to
   achieve some different behavior, but doing so it not recommended or
   tested frequently.

   XMLCALL    - The calling convention to use for all calls across the
                "library boundary."  This will default to cdecl, and
                try really hard to tell the compiler that's what we
                want.

   XMLIMPORT  - Whatever magic is needed to note that a function is
                to be imported from a dynamically loaded library
                (.dll, .so, or .sl, depending on your platform).

   The XMLCALL macro was added in Expat 1.95.7.  The only one which is
   expected to be directly useful in client code is XMLCALL.

   Note that on at least some Unix versions, the Expat library must be
   compiled with the cdecl calling convention as the default since
   system headers may assume the cdecl convention.
*/
#ifndef XMLCALL
#if defined(_MSC_VER)
#define XMLCALL __cdecl
#elif defined(__GNUC__) && defined(__i386) && !defined(__INTEL_COMPILER)
#define XMLCALL __attribute__((cdecl))
#else
/* For any platform which uses this definition and supports more than
   one calling convention, we need to extend this definition to
   declare the convention used on that platform, if it's possible to
   do so.

   If this is the case for your platform, please file a bug report
   with information on how to identify your platform via the C
   pre-processor and how to specify the same calling convention as the
   platform's malloc() implementation.
*/
#define XMLCALL
#endif
#endif  /* not defined XMLCALL */


#if !defined(XML_STATIC) && !defined(XMLIMPORT)
#ifndef XML_BUILDING_EXPAT
/* using Expat from an application */

#ifdef XML_USE_MSC_EXTENSIONS
#define XMLIMPORT __declspec(dllimport)
#endif

#endif
#endif  /* not defined XML_STATIC */


/* If we didn't define it above, define it away: */
#ifndef XMLIMPORT
#define XMLIMPORT
#endif


#define XMLPARSEAPI(type) XMLIMPORT type XMLCALL

#ifdef __cplusplus
extern "C" {
#endif

#ifdef XML_UNICODE_WCHAR_T
#define XML_UNICODE
#endif

#ifdef XML_UNICODE     /* Information is UTF-16 encoded. */
#ifdef XML_UNICODE_WCHAR_T
typedef wchar_t XML_Char;
typedef wchar_t XML_LChar;
#else
typedef unsigned short XML_Char;
typedef char XML_LChar;
#endif /* XML_UNICODE_WCHAR_T */
#else                  /* Information is UTF-8 encoded. */
typedef char XML_Char;
typedef char XML_LChar;
#endif /* XML_UNICODE */

#ifdef XML_LARGE_SIZE  /* Use large integers for file/stream positions. */
#if defined(XML_USE_MSC_EXTENSIONS) && _MSC_VER < 1400
typedef __int64 XML_Index; 
typedef unsigned __int64 XML_Size;
#else
typedef long long XML_Index;
typedef unsigned long long XML_Size;
#endif
#else
typedef long XML_Index;
typedef unsigned long XML_Size;
#endif /* XML_LARGE_SIZE */

#ifdef __cplusplus
}
#endif

#endif /* not Expat_External_INCLUDED */
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genometools-1.5.1/src/external/expat-2.0.1/lib/expatw_static.dsp000077500000000000000000000103451211610345200243750ustar00rootroot00000000000000# Microsoft Developer Studio Project File - Name="expatw_static" - Package Owner=<4>
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genometools-1.5.1/src/external/expat-2.0.1/lib/iasciitab.h000077500000000000000000000034461211610345200231130ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

/* Like asciitab.h, except that 0xD has code BT_S rather than BT_CR */
/* 0x00 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x04 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x08 */ BT_NONXML, BT_S, BT_LF, BT_NONXML,
/* 0x0C */ BT_NONXML, BT_S, BT_NONXML, BT_NONXML,
/* 0x10 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x14 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x18 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x1C */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0x20 */ BT_S, BT_EXCL, BT_QUOT, BT_NUM,
/* 0x24 */ BT_OTHER, BT_PERCNT, BT_AMP, BT_APOS,
/* 0x28 */ BT_LPAR, BT_RPAR, BT_AST, BT_PLUS,
/* 0x2C */ BT_COMMA, BT_MINUS, BT_NAME, BT_SOL,
/* 0x30 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT,
/* 0x34 */ BT_DIGIT, BT_DIGIT, BT_DIGIT, BT_DIGIT,
/* 0x38 */ BT_DIGIT, BT_DIGIT, BT_COLON, BT_SEMI,
/* 0x3C */ BT_LT, BT_EQUALS, BT_GT, BT_QUEST,
/* 0x40 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX,
/* 0x44 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT,
/* 0x48 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x4C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x50 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x54 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x58 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_LSQB,
/* 0x5C */ BT_OTHER, BT_RSQB, BT_OTHER, BT_NMSTRT,
/* 0x60 */ BT_OTHER, BT_HEX, BT_HEX, BT_HEX,
/* 0x64 */ BT_HEX, BT_HEX, BT_HEX, BT_NMSTRT,
/* 0x68 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x6C */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x70 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x74 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0x78 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_OTHER,
/* 0x7C */ BT_VERBAR, BT_OTHER, BT_OTHER, BT_OTHER,
genometools-1.5.1/src/external/expat-2.0.1/lib/internal.h000077500000000000000000000037541211610345200230010ustar00rootroot00000000000000/* internal.h

   Internal definitions used by Expat.  This is not needed to compile
   client code.

   The following calling convention macros are defined for frequently
   called functions:

   FASTCALL    - Used for those internal functions that have a simple
                 body and a low number of arguments and local variables.

   PTRCALL     - Used for functions called though function pointers.

   PTRFASTCALL - Like PTRCALL, but for low number of arguments.

   inline      - Used for selected internal functions for which inlining
                 may improve performance on some platforms.

   Note: Use of these macros is based on judgement, not hard rules,
         and therefore subject to change.
*/

#if defined(__GNUC__) && defined(__i386__) && !defined(__MINGW32__)
/* We'll use this version by default only where we know it helps.

   regparm() generates warnings on Solaris boxes.   See SF bug #692878.

   Instability reported with egcs on a RedHat Linux 7.3.
   Let's comment out:
   #define FASTCALL __attribute__((stdcall, regparm(3)))
   and let's try this:
*/
#define FASTCALL __attribute__((regparm(3)))
#define PTRFASTCALL __attribute__((regparm(3)))
#endif

/* Using __fastcall seems to have an unexpected negative effect under
   MS VC++, especially for function pointers, so we won't use it for
   now on that platform. It may be reconsidered for a future release
   if it can be made more effective.
   Likely reason: __fastcall on Windows is like stdcall, therefore
   the compiler cannot perform stack optimizations for call clusters.
*/

/* Make sure all of these are defined if they aren't already. */

#ifndef FASTCALL
#define FASTCALL
#endif

#ifndef PTRCALL
#define PTRCALL
#endif

#ifndef PTRFASTCALL
#define PTRFASTCALL
#endif

#ifndef XML_MIN_SIZE
#if !defined(__cplusplus) && !defined(inline)
#ifdef __GNUC__
#define inline __inline
#endif /* __GNUC__ */
#endif
#endif /* XML_MIN_SIZE */

#ifdef __cplusplus
#define inline inline
#else
#ifndef inline
#define inline
#endif
#endif
genometools-1.5.1/src/external/expat-2.0.1/lib/latin1tab.h000077500000000000000000000034251211610345200230370ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

/* 0x80 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0x84 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0x88 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0x8C */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0x90 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0x94 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0x98 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0x9C */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0xA0 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0xA4 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0xA8 */ BT_OTHER, BT_OTHER, BT_NMSTRT, BT_OTHER,
/* 0xAC */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0xB0 */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0xB4 */ BT_OTHER, BT_NMSTRT, BT_OTHER, BT_NAME,
/* 0xB8 */ BT_OTHER, BT_OTHER, BT_NMSTRT, BT_OTHER,
/* 0xBC */ BT_OTHER, BT_OTHER, BT_OTHER, BT_OTHER,
/* 0xC0 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xC4 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xC8 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xCC */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xD0 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xD4 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_OTHER,
/* 0xD8 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xDC */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xE0 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xE4 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xE8 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xEC */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xF0 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xF4 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_OTHER,
/* 0xF8 */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
/* 0xFC */ BT_NMSTRT, BT_NMSTRT, BT_NMSTRT, BT_NMSTRT,
genometools-1.5.1/src/external/expat-2.0.1/lib/libexpat.def000077500000000000000000000037541211610345200233040ustar00rootroot00000000000000; DEF file for MS VC++

LIBRARY
EXPORTS
  XML_DefaultCurrent @1
  XML_ErrorString @2
  XML_ExpatVersion @3
  XML_ExpatVersionInfo @4
  XML_ExternalEntityParserCreate @5
  XML_GetBase @6
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  XML_GetCurrentByteCount @8
  XML_GetCurrentByteIndex @9
  XML_GetCurrentColumnNumber @10
  XML_GetCurrentLineNumber @11
  XML_GetErrorCode @12
  XML_GetIdAttributeIndex @13
  XML_GetInputContext @14
  XML_GetSpecifiedAttributeCount @15
  XML_Parse @16
  XML_ParseBuffer @17
  XML_ParserCreate @18
  XML_ParserCreateNS @19
  XML_ParserCreate_MM @20
  XML_ParserFree @21
  XML_SetAttlistDeclHandler @22
  XML_SetBase @23
  XML_SetCdataSectionHandler @24
  XML_SetCharacterDataHandler @25
  XML_SetCommentHandler @26
  XML_SetDefaultHandler @27
  XML_SetDefaultHandlerExpand @28
  XML_SetDoctypeDeclHandler @29
  XML_SetElementDeclHandler @30
  XML_SetElementHandler @31
  XML_SetEncoding @32
  XML_SetEndCdataSectionHandler @33
  XML_SetEndDoctypeDeclHandler @34
  XML_SetEndElementHandler @35
  XML_SetEndNamespaceDeclHandler @36
  XML_SetEntityDeclHandler @37
  XML_SetExternalEntityRefHandler @38
  XML_SetExternalEntityRefHandlerArg @39
  XML_SetNamespaceDeclHandler @40
  XML_SetNotStandaloneHandler @41
  XML_SetNotationDeclHandler @42
  XML_SetParamEntityParsing @43
  XML_SetProcessingInstructionHandler @44
  XML_SetReturnNSTriplet @45
  XML_SetStartCdataSectionHandler @46
  XML_SetStartDoctypeDeclHandler @47
  XML_SetStartElementHandler @48
  XML_SetStartNamespaceDeclHandler @49
  XML_SetUnknownEncodingHandler @50
  XML_SetUnparsedEntityDeclHandler @51
  XML_SetUserData @52
  XML_SetXmlDeclHandler @53
  XML_UseParserAsHandlerArg @54
; added with version 1.95.3
  XML_ParserReset @55
  XML_SetSkippedEntityHandler @56
; added with version 1.95.5
  XML_GetFeatureList @57
  XML_UseForeignDTD @58
; added with version 1.95.6
  XML_FreeContentModel @59
  XML_MemMalloc @60
  XML_MemRealloc @61
  XML_MemFree @62
; added with version 1.95.8
  XML_StopParser @63
  XML_ResumeParser @64
  XML_GetParsingStatus @65
genometools-1.5.1/src/external/expat-2.0.1/lib/libexpatw.def000077500000000000000000000037541211610345200234730ustar00rootroot00000000000000; DEF file for MS VC++

LIBRARY
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  XML_ErrorString @2
  XML_ExpatVersion @3
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  XML_ExternalEntityParserCreate @5
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  XML_GetCurrentByteCount @8
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  XML_GetCurrentColumnNumber @10
  XML_GetCurrentLineNumber @11
  XML_GetErrorCode @12
  XML_GetIdAttributeIndex @13
  XML_GetInputContext @14
  XML_GetSpecifiedAttributeCount @15
  XML_Parse @16
  XML_ParseBuffer @17
  XML_ParserCreate @18
  XML_ParserCreateNS @19
  XML_ParserCreate_MM @20
  XML_ParserFree @21
  XML_SetAttlistDeclHandler @22
  XML_SetBase @23
  XML_SetCdataSectionHandler @24
  XML_SetCharacterDataHandler @25
  XML_SetCommentHandler @26
  XML_SetDefaultHandler @27
  XML_SetDefaultHandlerExpand @28
  XML_SetDoctypeDeclHandler @29
  XML_SetElementDeclHandler @30
  XML_SetElementHandler @31
  XML_SetEncoding @32
  XML_SetEndCdataSectionHandler @33
  XML_SetEndDoctypeDeclHandler @34
  XML_SetEndElementHandler @35
  XML_SetEndNamespaceDeclHandler @36
  XML_SetEntityDeclHandler @37
  XML_SetExternalEntityRefHandler @38
  XML_SetExternalEntityRefHandlerArg @39
  XML_SetNamespaceDeclHandler @40
  XML_SetNotStandaloneHandler @41
  XML_SetNotationDeclHandler @42
  XML_SetParamEntityParsing @43
  XML_SetProcessingInstructionHandler @44
  XML_SetReturnNSTriplet @45
  XML_SetStartCdataSectionHandler @46
  XML_SetStartDoctypeDeclHandler @47
  XML_SetStartElementHandler @48
  XML_SetStartNamespaceDeclHandler @49
  XML_SetUnknownEncodingHandler @50
  XML_SetUnparsedEntityDeclHandler @51
  XML_SetUserData @52
  XML_SetXmlDeclHandler @53
  XML_UseParserAsHandlerArg @54
; added with version 1.95.3
  XML_ParserReset @55
  XML_SetSkippedEntityHandler @56
; added with version 1.95.5
  XML_GetFeatureList @57
  XML_UseForeignDTD @58
; added with version 1.95.6
  XML_FreeContentModel @59
  XML_MemMalloc @60
  XML_MemRealloc @61
  XML_MemFree @62
; added with version 1.95.8
  XML_StopParser @63
  XML_ResumeParser @64
  XML_GetParsingStatus @65
genometools-1.5.1/src/external/expat-2.0.1/lib/macconfig.h000077500000000000000000000024551211610345200231100ustar00rootroot00000000000000/*================================================================
** Copyright 2000, Clark Cooper
** All rights reserved.
**
** This is free software. You are permitted to copy, distribute, or modify
** it under the terms of the MIT/X license (contained in the COPYING file
** with this distribution.)
**
*/

#ifndef MACCONFIG_H
#define MACCONFIG_H


/* 1234 = LIL_ENDIAN, 4321 = BIGENDIAN */
#define BYTEORDER  4321

/* Define to 1 if you have the `bcopy' function. */
#undef HAVE_BCOPY

/* Define to 1 if you have the `memmove' function. */
#define HAVE_MEMMOVE

/* Define to 1 if you have a working `mmap' system call. */
#undef HAVE_MMAP

/* Define to 1 if you have the  header file. */
#undef HAVE_UNISTD_H

/* whether byteorder is bigendian */
#define WORDS_BIGENDIAN

/* Define to specify how much context to retain around the current parse
   point. */
#undef XML_CONTEXT_BYTES

/* Define to make parameter entity parsing functionality available. */
#define XML_DTD

/* Define to make XML Namespaces functionality available. */
#define XML_NS

/* Define to empty if `const' does not conform to ANSI C. */
#undef const

/* Define to `long' if  does not define. */
#define off_t  long

/* Define to `unsigned' if  does not define. */
#undef size_t


#endif /* ifndef MACCONFIG_H */
genometools-1.5.1/src/external/expat-2.0.1/lib/nametab.h000077500000000000000000000156121211610345200225700ustar00rootroot00000000000000static const unsigned namingBitmap[] = {
0x00000000, 0x00000000, 0x00000000, 0x00000000,
0x00000000, 0x00000000, 0x00000000, 0x00000000,
0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF,
0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF,
0x00000000, 0x04000000, 0x87FFFFFE, 0x07FFFFFE,
0x00000000, 0x00000000, 0xFF7FFFFF, 0xFF7FFFFF,
0xFFFFFFFF, 0x7FF3FFFF, 0xFFFFFDFE, 0x7FFFFFFF,
0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFE00F, 0xFC31FFFF,
0x00FFFFFF, 0x00000000, 0xFFFF0000, 0xFFFFFFFF,
0xFFFFFFFF, 0xF80001FF, 0x00000003, 0x00000000,
0x00000000, 0x00000000, 0x00000000, 0x00000000,
0xFFFFD740, 0xFFFFFFFB, 0x547F7FFF, 0x000FFFFD,
0xFFFFDFFE, 0xFFFFFFFF, 0xDFFEFFFF, 0xFFFFFFFF,
0xFFFF0003, 0xFFFFFFFF, 0xFFFF199F, 0x033FCFFF,
0x00000000, 0xFFFE0000, 0x027FFFFF, 0xFFFFFFFE,
0x0000007F, 0x00000000, 0xFFFF0000, 0x000707FF,
0x00000000, 0x07FFFFFE, 0x000007FE, 0xFFFE0000,
0xFFFFFFFF, 0x7CFFFFFF, 0x002F7FFF, 0x00000060,
0xFFFFFFE0, 0x23FFFFFF, 0xFF000000, 0x00000003,
0xFFF99FE0, 0x03C5FDFF, 0xB0000000, 0x00030003,
0xFFF987E0, 0x036DFDFF, 0x5E000000, 0x001C0000,
0xFFFBAFE0, 0x23EDFDFF, 0x00000000, 0x00000001,
0xFFF99FE0, 0x23CDFDFF, 0xB0000000, 0x00000003,
0xD63DC7E0, 0x03BFC718, 0x00000000, 0x00000000,
0xFFFDDFE0, 0x03EFFDFF, 0x00000000, 0x00000003,
0xFFFDDFE0, 0x03EFFDFF, 0x40000000, 0x00000003,
0xFFFDDFE0, 0x03FFFDFF, 0x00000000, 0x00000003,
0x00000000, 0x00000000, 0x00000000, 0x00000000,
0xFFFFFFFE, 0x000D7FFF, 0x0000003F, 0x00000000,
0xFEF02596, 0x200D6CAE, 0x0000001F, 0x00000000,
0x00000000, 0x00000000, 0xFFFFFEFF, 0x000003FF,
0x00000000, 0x00000000, 0x00000000, 0x00000000,
0x00000000, 0x00000000, 0x00000000, 0x00000000,
0x00000000, 0xFFFFFFFF, 0xFFFF003F, 0x007FFFFF,
0x0007DAED, 0x50000000, 0x82315001, 0x002C62AB,
0x40000000, 0xF580C900, 0x00000007, 0x02010800,
0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF,
0x0FFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0x03FFFFFF,
0x3F3FFFFF, 0xFFFFFFFF, 0xAAFF3F3F, 0x3FFFFFFF,
0xFFFFFFFF, 0x5FDFFFFF, 0x0FCF1FDC, 0x1FDC1FFF,
0x00000000, 0x00004C40, 0x00000000, 0x00000000,
0x00000007, 0x00000000, 0x00000000, 0x00000000,
0x00000080, 0x000003FE, 0xFFFFFFFE, 0xFFFFFFFF,
0x001FFFFF, 0xFFFFFFFE, 0xFFFFFFFF, 0x07FFFFFF,
0xFFFFFFE0, 0x00001FFF, 0x00000000, 0x00000000,
0x00000000, 0x00000000, 0x00000000, 0x00000000,
0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF,
0xFFFFFFFF, 0x0000003F, 0x00000000, 0x00000000,
0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF,
0xFFFFFFFF, 0x0000000F, 0x00000000, 0x00000000,
0x00000000, 0x07FF6000, 0x87FFFFFE, 0x07FFFFFE,
0x00000000, 0x00800000, 0xFF7FFFFF, 0xFF7FFFFF,
0x00FFFFFF, 0x00000000, 0xFFFF0000, 0xFFFFFFFF,
0xFFFFFFFF, 0xF80001FF, 0x00030003, 0x00000000,
0xFFFFFFFF, 0xFFFFFFFF, 0x0000003F, 0x00000003,
0xFFFFD7C0, 0xFFFFFFFB, 0x547F7FFF, 0x000FFFFD,
0xFFFFDFFE, 0xFFFFFFFF, 0xDFFEFFFF, 0xFFFFFFFF,
0xFFFF007B, 0xFFFFFFFF, 0xFFFF199F, 0x033FCFFF,
0x00000000, 0xFFFE0000, 0x027FFFFF, 0xFFFFFFFE,
0xFFFE007F, 0xBBFFFFFB, 0xFFFF0016, 0x000707FF,
0x00000000, 0x07FFFFFE, 0x0007FFFF, 0xFFFF03FF,
0xFFFFFFFF, 0x7CFFFFFF, 0xFFEF7FFF, 0x03FF3DFF,
0xFFFFFFEE, 0xF3FFFFFF, 0xFF1E3FFF, 0x0000FFCF,
0xFFF99FEE, 0xD3C5FDFF, 0xB080399F, 0x0003FFCF,
0xFFF987E4, 0xD36DFDFF, 0x5E003987, 0x001FFFC0,
0xFFFBAFEE, 0xF3EDFDFF, 0x00003BBF, 0x0000FFC1,
0xFFF99FEE, 0xF3CDFDFF, 0xB0C0398F, 0x0000FFC3,
0xD63DC7EC, 0xC3BFC718, 0x00803DC7, 0x0000FF80,
0xFFFDDFEE, 0xC3EFFDFF, 0x00603DDF, 0x0000FFC3,
0xFFFDDFEC, 0xC3EFFDFF, 0x40603DDF, 0x0000FFC3,
0xFFFDDFEC, 0xC3FFFDFF, 0x00803DCF, 0x0000FFC3,
0x00000000, 0x00000000, 0x00000000, 0x00000000,
0xFFFFFFFE, 0x07FF7FFF, 0x03FF7FFF, 0x00000000,
0xFEF02596, 0x3BFF6CAE, 0x03FF3F5F, 0x00000000,
0x03000000, 0xC2A003FF, 0xFFFFFEFF, 0xFFFE03FF,
0xFEBF0FDF, 0x02FE3FFF, 0x00000000, 0x00000000,
0x00000000, 0x00000000, 0x00000000, 0x00000000,
0x00000000, 0x00000000, 0x1FFF0000, 0x00000002,
0x000000A0, 0x003EFFFE, 0xFFFFFFFE, 0xFFFFFFFF,
0x661FFFFF, 0xFFFFFFFE, 0xFFFFFFFF, 0x77FFFFFF,
};
static const unsigned char nmstrtPages[] = {
0x02, 0x03, 0x04, 0x05, 0x06, 0x07, 0x08, 0x00,
0x00, 0x09, 0x0A, 0x0B, 0x0C, 0x0D, 0x0E, 0x0F,
0x10, 0x11, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x12, 0x13,
0x00, 0x14, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x15, 0x16, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x17,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
};
static const unsigned char namePages[] = {
0x19, 0x03, 0x1A, 0x1B, 0x1C, 0x1D, 0x1E, 0x00,
0x00, 0x1F, 0x20, 0x21, 0x22, 0x23, 0x24, 0x25,
0x10, 0x11, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x12, 0x13,
0x26, 0x14, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x27, 0x16, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x17,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01,
0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x01, 0x18,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
};
genometools-1.5.1/src/external/expat-2.0.1/lib/utf8tab.h000077500000000000000000000033431211610345200225340ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/


/* 0x80 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0x84 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0x88 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0x8C */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0x90 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0x94 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0x98 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0x9C */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0xA0 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0xA4 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0xA8 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0xAC */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0xB0 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0xB4 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0xB8 */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0xBC */ BT_TRAIL, BT_TRAIL, BT_TRAIL, BT_TRAIL,
/* 0xC0 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2,
/* 0xC4 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2,
/* 0xC8 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2,
/* 0xCC */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2,
/* 0xD0 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2,
/* 0xD4 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2,
/* 0xD8 */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2,
/* 0xDC */ BT_LEAD2, BT_LEAD2, BT_LEAD2, BT_LEAD2,
/* 0xE0 */ BT_LEAD3, BT_LEAD3, BT_LEAD3, BT_LEAD3,
/* 0xE4 */ BT_LEAD3, BT_LEAD3, BT_LEAD3, BT_LEAD3,
/* 0xE8 */ BT_LEAD3, BT_LEAD3, BT_LEAD3, BT_LEAD3,
/* 0xEC */ BT_LEAD3, BT_LEAD3, BT_LEAD3, BT_LEAD3,
/* 0xF0 */ BT_LEAD4, BT_LEAD4, BT_LEAD4, BT_LEAD4,
/* 0xF4 */ BT_LEAD4, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0xF8 */ BT_NONXML, BT_NONXML, BT_NONXML, BT_NONXML,
/* 0xFC */ BT_NONXML, BT_NONXML, BT_MALFORM, BT_MALFORM,
genometools-1.5.1/src/external/expat-2.0.1/lib/winconfig.h000077500000000000000000000013051211610345200231360ustar00rootroot00000000000000/*================================================================
** Copyright 2000, Clark Cooper
** All rights reserved.
**
** This is free software. You are permitted to copy, distribute, or modify
** it under the terms of the MIT/X license (contained in the COPYING file
** with this distribution.)
*/

#ifndef WINCONFIG_H
#define WINCONFIG_H

#define WIN32_LEAN_AND_MEAN
#include 
#undef WIN32_LEAN_AND_MEAN

#include 
#include 

#define XML_NS 1
#define XML_DTD 1
#define XML_CONTEXT_BYTES 1024

/* we will assume all Windows platforms are little endian */
#define BYTEORDER 1234

/* Windows has memmove() available. */
#define HAVE_MEMMOVE

#endif /* ndef WINCONFIG_H */
genometools-1.5.1/src/external/expat-2.0.1/lib/xmlparse.c000077500000000000000000005733511211610345200230200ustar00rootroot00000000000000/* Copyright (c) 1998, 1999, 2000 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

#include 
#include                      /* memset(), memcpy() */
#include 

#define XML_BUILDING_EXPAT 1

#ifdef COMPILED_FROM_DSP
#include "winconfig.h"
#elif defined(MACOS_CLASSIC)
#include "macconfig.h"
#elif defined(__amigaos4__)
#include "amigaconfig.h"
#elif defined(__WATCOMC__)
#include "watcomconfig.h"
#elif defined(HAVE_EXPAT_CONFIG_H)
#include 
#endif /* ndef COMPILED_FROM_DSP */

#include "ascii.h"
#include "expat.h"

#ifdef XML_UNICODE
#define XML_ENCODE_MAX XML_UTF16_ENCODE_MAX
#define XmlConvert XmlUtf16Convert
#define XmlGetInternalEncoding XmlGetUtf16InternalEncoding
#define XmlGetInternalEncodingNS XmlGetUtf16InternalEncodingNS
#define XmlEncode XmlUtf16Encode
/* Using pointer subtraction to convert to integer type. */
#define MUST_CONVERT(enc, s) (!(enc)->isUtf16 || (((char *)(s) - (char *)NULL) & 1))
typedef unsigned short ICHAR;
#else
#define XML_ENCODE_MAX XML_UTF8_ENCODE_MAX
#define XmlConvert XmlUtf8Convert
#define XmlGetInternalEncoding XmlGetUtf8InternalEncoding
#define XmlGetInternalEncodingNS XmlGetUtf8InternalEncodingNS
#define XmlEncode XmlUtf8Encode
#define MUST_CONVERT(enc, s) (!(enc)->isUtf8)
typedef char ICHAR;
#endif


#ifndef XML_NS

#define XmlInitEncodingNS XmlInitEncoding
#define XmlInitUnknownEncodingNS XmlInitUnknownEncoding
#undef XmlGetInternalEncodingNS
#define XmlGetInternalEncodingNS XmlGetInternalEncoding
#define XmlParseXmlDeclNS XmlParseXmlDecl

#endif

#ifdef XML_UNICODE

#ifdef XML_UNICODE_WCHAR_T
#define XML_T(x) (const wchar_t)x
#define XML_L(x) L ## x
#else
#define XML_T(x) (const unsigned short)x
#define XML_L(x) x
#endif

#else

#define XML_T(x) x
#define XML_L(x) x

#endif

/* Round up n to be a multiple of sz, where sz is a power of 2. */
#define ROUND_UP(n, sz) (((n) + ((sz) - 1)) & ~((sz) - 1))

/* Handle the case where memmove() doesn't exist. */
#ifndef HAVE_MEMMOVE
#ifdef HAVE_BCOPY
#define memmove(d,s,l) bcopy((s),(d),(l))
#else
#error memmove does not exist on this platform, nor is a substitute available
#endif /* HAVE_BCOPY */
#endif /* HAVE_MEMMOVE */

#include "internal.h"
#include "xmltok.h"
#include "xmlrole.h"

typedef const XML_Char *KEY;

typedef struct {
  KEY name;
} NAMED;

typedef struct {
  NAMED **v;
  unsigned char power;
  size_t size;
  size_t used;
  const XML_Memory_Handling_Suite *mem;
} HASH_TABLE;

/* Basic character hash algorithm, taken from Python's string hash:
   h = h * 1000003 ^ character, the constant being a prime number.

*/
#ifdef XML_UNICODE
#define CHAR_HASH(h, c) \
  (((h) * 0xF4243) ^ (unsigned short)(c))
#else
#define CHAR_HASH(h, c) \
  (((h) * 0xF4243) ^ (unsigned char)(c))
#endif

/* For probing (after a collision) we need a step size relative prime
   to the hash table size, which is a power of 2. We use double-hashing,
   since we can calculate a second hash value cheaply by taking those bits
   of the first hash value that were discarded (masked out) when the table
   index was calculated: index = hash & mask, where mask = table->size - 1.
   We limit the maximum step size to table->size / 4 (mask >> 2) and make
   it odd, since odd numbers are always relative prime to a power of 2.
*/
#define SECOND_HASH(hash, mask, power) \
  ((((hash) & ~(mask)) >> ((power) - 1)) & ((mask) >> 2))
#define PROBE_STEP(hash, mask, power) \
  ((unsigned char)((SECOND_HASH(hash, mask, power)) | 1))

typedef struct {
  NAMED **p;
  NAMED **end;
} HASH_TABLE_ITER;

#define INIT_TAG_BUF_SIZE 32  /* must be a multiple of sizeof(XML_Char) */
#define INIT_DATA_BUF_SIZE 1024
#define INIT_ATTS_SIZE 16
#define INIT_ATTS_VERSION 0xFFFFFFFF
#define INIT_BLOCK_SIZE 1024
#define INIT_BUFFER_SIZE 1024

#define EXPAND_SPARE 24

typedef struct binding {
  struct prefix *prefix;
  struct binding *nextTagBinding;
  struct binding *prevPrefixBinding;
  const struct attribute_id *attId;
  XML_Char *uri;
  int uriLen;
  int uriAlloc;
} BINDING;

typedef struct prefix {
  const XML_Char *name;
  BINDING *binding;
} PREFIX;

typedef struct {
  const XML_Char *str;
  const XML_Char *localPart;
  const XML_Char *prefix;
  int strLen;
  int uriLen;
  int prefixLen;
} TAG_NAME;

/* TAG represents an open element.
   The name of the element is stored in both the document and API
   encodings.  The memory buffer 'buf' is a separately-allocated
   memory area which stores the name.  During the XML_Parse()/
   XMLParseBuffer() when the element is open, the memory for the 'raw'
   version of the name (in the document encoding) is shared with the
   document buffer.  If the element is open across calls to
   XML_Parse()/XML_ParseBuffer(), the buffer is re-allocated to
   contain the 'raw' name as well.

   A parser re-uses these structures, maintaining a list of allocated
   TAG objects in a free list.
*/
typedef struct tag {
  struct tag *parent;           /* parent of this element */
  const char *rawName;          /* tagName in the original encoding */
  int rawNameLength;
  TAG_NAME name;                /* tagName in the API encoding */
  char *buf;                    /* buffer for name components */
  char *bufEnd;                 /* end of the buffer */
  BINDING *bindings;
} TAG;

typedef struct {
  const XML_Char *name;
  const XML_Char *textPtr;
  int textLen;                  /* length in XML_Chars */
  int processed;                /* # of processed bytes - when suspended */
  const XML_Char *systemId;
  const XML_Char *base;
  const XML_Char *publicId;
  const XML_Char *notation;
  XML_Bool open;
  XML_Bool is_param;
  XML_Bool is_internal; /* true if declared in internal subset outside PE */
} ENTITY;

typedef struct {
  enum XML_Content_Type         type;
  enum XML_Content_Quant        quant;
  const XML_Char *              name;
  int                           firstchild;
  int                           lastchild;
  int                           childcnt;
  int                           nextsib;
} CONTENT_SCAFFOLD;

#define INIT_SCAFFOLD_ELEMENTS 32

typedef struct block {
  struct block *next;
  int size;
  XML_Char s[1];
} BLOCK;

typedef struct {
  BLOCK *blocks;
  BLOCK *freeBlocks;
  const XML_Char *end;
  XML_Char *ptr;
  XML_Char *start;
  const XML_Memory_Handling_Suite *mem;
} STRING_POOL;

/* The XML_Char before the name is used to determine whether
   an attribute has been specified. */
typedef struct attribute_id {
  XML_Char *name;
  PREFIX *prefix;
  XML_Bool maybeTokenized;
  XML_Bool xmlns;
} ATTRIBUTE_ID;

typedef struct {
  const ATTRIBUTE_ID *id;
  XML_Bool isCdata;
  const XML_Char *value;
} DEFAULT_ATTRIBUTE;

typedef struct {
  unsigned long version;
  unsigned long hash;
  const XML_Char *uriName;
} NS_ATT;

typedef struct {
  const XML_Char *name;
  PREFIX *prefix;
  const ATTRIBUTE_ID *idAtt;
  int nDefaultAtts;
  int allocDefaultAtts;
  DEFAULT_ATTRIBUTE *defaultAtts;
} ELEMENT_TYPE;

typedef struct {
  HASH_TABLE generalEntities;
  HASH_TABLE elementTypes;
  HASH_TABLE attributeIds;
  HASH_TABLE prefixes;
  STRING_POOL pool;
  STRING_POOL entityValuePool;
  /* false once a parameter entity reference has been skipped */
  XML_Bool keepProcessing;
  /* true once an internal or external PE reference has been encountered;
     this includes the reference to an external subset */
  XML_Bool hasParamEntityRefs;
  XML_Bool standalone;
#ifdef XML_DTD
  /* indicates if external PE has been read */
  XML_Bool paramEntityRead;
  HASH_TABLE paramEntities;
#endif /* XML_DTD */
  PREFIX defaultPrefix;
  /* === scaffolding for building content model === */
  XML_Bool in_eldecl;
  CONTENT_SCAFFOLD *scaffold;
  unsigned contentStringLen;
  unsigned scaffSize;
  unsigned scaffCount;
  int scaffLevel;
  int *scaffIndex;
} DTD;

typedef struct open_internal_entity {
  const char *internalEventPtr;
  const char *internalEventEndPtr;
  struct open_internal_entity *next;
  ENTITY *entity;
  int startTagLevel;
  XML_Bool betweenDecl; /* WFC: PE Between Declarations */
} OPEN_INTERNAL_ENTITY;

typedef enum XML_Error PTRCALL Processor(XML_Parser parser,
                                         const char *start,
                                         const char *end,
                                         const char **endPtr);

static Processor prologProcessor;
static Processor prologInitProcessor;
static Processor contentProcessor;
static Processor cdataSectionProcessor;
#ifdef XML_DTD
static Processor ignoreSectionProcessor;
static Processor externalParEntProcessor;
static Processor externalParEntInitProcessor;
static Processor entityValueProcessor;
static Processor entityValueInitProcessor;
#endif /* XML_DTD */
static Processor epilogProcessor;
static Processor errorProcessor;
static Processor externalEntityInitProcessor;
static Processor externalEntityInitProcessor2;
static Processor externalEntityInitProcessor3;
static Processor externalEntityContentProcessor;
static Processor internalEntityProcessor;

static enum XML_Error
handleUnknownEncoding(XML_Parser parser, const XML_Char *encodingName);
static enum XML_Error
processXmlDecl(XML_Parser parser, int isGeneralTextEntity,
               const char *s, const char *next);
static enum XML_Error
initializeEncoding(XML_Parser parser);
static enum XML_Error
doProlog(XML_Parser parser, const ENCODING *enc, const char *s, 
         const char *end, int tok, const char *next, const char **nextPtr, 
         XML_Bool haveMore);
static enum XML_Error
processInternalEntity(XML_Parser parser, ENTITY *entity, 
                      XML_Bool betweenDecl);
static enum XML_Error
doContent(XML_Parser parser, int startTagLevel, const ENCODING *enc,
          const char *start, const char *end, const char **endPtr, 
          XML_Bool haveMore);
static enum XML_Error
doCdataSection(XML_Parser parser, const ENCODING *, const char **startPtr,
               const char *end, const char **nextPtr, XML_Bool haveMore);
#ifdef XML_DTD
static enum XML_Error
doIgnoreSection(XML_Parser parser, const ENCODING *, const char **startPtr,
                const char *end, const char **nextPtr, XML_Bool haveMore);
#endif /* XML_DTD */

static enum XML_Error
storeAtts(XML_Parser parser, const ENCODING *, const char *s,
          TAG_NAME *tagNamePtr, BINDING **bindingsPtr);
static enum XML_Error
addBinding(XML_Parser parser, PREFIX *prefix, const ATTRIBUTE_ID *attId,
           const XML_Char *uri, BINDING **bindingsPtr);
static int
defineAttribute(ELEMENT_TYPE *type, ATTRIBUTE_ID *, XML_Bool isCdata, 
                XML_Bool isId, const XML_Char *dfltValue, XML_Parser parser);
static enum XML_Error
storeAttributeValue(XML_Parser parser, const ENCODING *, XML_Bool isCdata,
                    const char *, const char *, STRING_POOL *);
static enum XML_Error
appendAttributeValue(XML_Parser parser, const ENCODING *, XML_Bool isCdata,
                     const char *, const char *, STRING_POOL *);
static ATTRIBUTE_ID *
getAttributeId(XML_Parser parser, const ENCODING *enc, const char *start,
               const char *end);
static int
setElementTypePrefix(XML_Parser parser, ELEMENT_TYPE *);
static enum XML_Error
storeEntityValue(XML_Parser parser, const ENCODING *enc, const char *start,
                 const char *end);
static int
reportProcessingInstruction(XML_Parser parser, const ENCODING *enc,
                            const char *start, const char *end);
static int
reportComment(XML_Parser parser, const ENCODING *enc, const char *start,
              const char *end);
static void
reportDefault(XML_Parser parser, const ENCODING *enc, const char *start,
              const char *end);

static const XML_Char * getContext(XML_Parser parser);
static XML_Bool
setContext(XML_Parser parser, const XML_Char *context);

static void FASTCALL normalizePublicId(XML_Char *s);

static DTD * dtdCreate(const XML_Memory_Handling_Suite *ms);
/* do not call if parentParser != NULL */
static void dtdReset(DTD *p, const XML_Memory_Handling_Suite *ms);
static void
dtdDestroy(DTD *p, XML_Bool isDocEntity, const XML_Memory_Handling_Suite *ms);
static int
dtdCopy(DTD *newDtd, const DTD *oldDtd, const XML_Memory_Handling_Suite *ms);
static int
copyEntityTable(HASH_TABLE *, STRING_POOL *, const HASH_TABLE *);

static NAMED *
lookup(HASH_TABLE *table, KEY name, size_t createSize);
static void FASTCALL
hashTableInit(HASH_TABLE *, const XML_Memory_Handling_Suite *ms);
static void FASTCALL hashTableClear(HASH_TABLE *);
static void FASTCALL hashTableDestroy(HASH_TABLE *);
static void FASTCALL
hashTableIterInit(HASH_TABLE_ITER *, const HASH_TABLE *);
static NAMED * FASTCALL hashTableIterNext(HASH_TABLE_ITER *);

static void FASTCALL
poolInit(STRING_POOL *, const XML_Memory_Handling_Suite *ms);
static void FASTCALL poolClear(STRING_POOL *);
static void FASTCALL poolDestroy(STRING_POOL *);
static XML_Char *
poolAppend(STRING_POOL *pool, const ENCODING *enc,
           const char *ptr, const char *end);
static XML_Char *
poolStoreString(STRING_POOL *pool, const ENCODING *enc,
                const char *ptr, const char *end);
static XML_Bool FASTCALL poolGrow(STRING_POOL *pool);
static const XML_Char * FASTCALL
poolCopyString(STRING_POOL *pool, const XML_Char *s);
static const XML_Char *
poolCopyStringN(STRING_POOL *pool, const XML_Char *s, int n);
static const XML_Char * FASTCALL
poolAppendString(STRING_POOL *pool, const XML_Char *s);

static int FASTCALL nextScaffoldPart(XML_Parser parser);
static XML_Content * build_model(XML_Parser parser);
static ELEMENT_TYPE *
getElementType(XML_Parser parser, const ENCODING *enc,
               const char *ptr, const char *end);

static XML_Parser
parserCreate(const XML_Char *encodingName,
             const XML_Memory_Handling_Suite *memsuite,
             const XML_Char *nameSep,
             DTD *dtd);
static void
parserInit(XML_Parser parser, const XML_Char *encodingName);

#define poolStart(pool) ((pool)->start)
#define poolEnd(pool) ((pool)->ptr)
#define poolLength(pool) ((pool)->ptr - (pool)->start)
#define poolChop(pool) ((void)--(pool->ptr))
#define poolLastChar(pool) (((pool)->ptr)[-1])
#define poolDiscard(pool) ((pool)->ptr = (pool)->start)
#define poolFinish(pool) ((pool)->start = (pool)->ptr)
#define poolAppendChar(pool, c) \
  (((pool)->ptr == (pool)->end && !poolGrow(pool)) \
   ? 0 \
   : ((*((pool)->ptr)++ = c), 1))

struct XML_ParserStruct {
  /* The first member must be userData so that the XML_GetUserData
     macro works. */
  void *m_userData;
  void *m_handlerArg;
  char *m_buffer;
  const XML_Memory_Handling_Suite m_mem;
  /* first character to be parsed */
  const char *m_bufferPtr;
  /* past last character to be parsed */
  char *m_bufferEnd;
  /* allocated end of buffer */
  const char *m_bufferLim;
  XML_Index m_parseEndByteIndex;
  const char *m_parseEndPtr;
  XML_Char *m_dataBuf;
  XML_Char *m_dataBufEnd;
  XML_StartElementHandler m_startElementHandler;
  XML_EndElementHandler m_endElementHandler;
  XML_CharacterDataHandler m_characterDataHandler;
  XML_ProcessingInstructionHandler m_processingInstructionHandler;
  XML_CommentHandler m_commentHandler;
  XML_StartCdataSectionHandler m_startCdataSectionHandler;
  XML_EndCdataSectionHandler m_endCdataSectionHandler;
  XML_DefaultHandler m_defaultHandler;
  XML_StartDoctypeDeclHandler m_startDoctypeDeclHandler;
  XML_EndDoctypeDeclHandler m_endDoctypeDeclHandler;
  XML_UnparsedEntityDeclHandler m_unparsedEntityDeclHandler;
  XML_NotationDeclHandler m_notationDeclHandler;
  XML_StartNamespaceDeclHandler m_startNamespaceDeclHandler;
  XML_EndNamespaceDeclHandler m_endNamespaceDeclHandler;
  XML_NotStandaloneHandler m_notStandaloneHandler;
  XML_ExternalEntityRefHandler m_externalEntityRefHandler;
  XML_Parser m_externalEntityRefHandlerArg;
  XML_SkippedEntityHandler m_skippedEntityHandler;
  XML_UnknownEncodingHandler m_unknownEncodingHandler;
  XML_ElementDeclHandler m_elementDeclHandler;
  XML_AttlistDeclHandler m_attlistDeclHandler;
  XML_EntityDeclHandler m_entityDeclHandler;
  XML_XmlDeclHandler m_xmlDeclHandler;
  const ENCODING *m_encoding;
  INIT_ENCODING m_initEncoding;
  const ENCODING *m_internalEncoding;
  const XML_Char *m_protocolEncodingName;
  XML_Bool m_ns;
  XML_Bool m_ns_triplets;
  void *m_unknownEncodingMem;
  void *m_unknownEncodingData;
  void *m_unknownEncodingHandlerData;
  void (XMLCALL *m_unknownEncodingRelease)(void *);
  PROLOG_STATE m_prologState;
  Processor *m_processor;
  enum XML_Error m_errorCode;
  const char *m_eventPtr;
  const char *m_eventEndPtr;
  const char *m_positionPtr;
  OPEN_INTERNAL_ENTITY *m_openInternalEntities;
  OPEN_INTERNAL_ENTITY *m_freeInternalEntities;
  XML_Bool m_defaultExpandInternalEntities;
  int m_tagLevel;
  ENTITY *m_declEntity;
  const XML_Char *m_doctypeName;
  const XML_Char *m_doctypeSysid;
  const XML_Char *m_doctypePubid;
  const XML_Char *m_declAttributeType;
  const XML_Char *m_declNotationName;
  const XML_Char *m_declNotationPublicId;
  ELEMENT_TYPE *m_declElementType;
  ATTRIBUTE_ID *m_declAttributeId;
  XML_Bool m_declAttributeIsCdata;
  XML_Bool m_declAttributeIsId;
  DTD *m_dtd;
  const XML_Char *m_curBase;
  TAG *m_tagStack;
  TAG *m_freeTagList;
  BINDING *m_inheritedBindings;
  BINDING *m_freeBindingList;
  int m_attsSize;
  int m_nSpecifiedAtts;
  int m_idAttIndex;
  ATTRIBUTE *m_atts;
  NS_ATT *m_nsAtts;
  unsigned long m_nsAttsVersion;
  unsigned char m_nsAttsPower;
  POSITION m_position;
  STRING_POOL m_tempPool;
  STRING_POOL m_temp2Pool;
  char *m_groupConnector;
  unsigned int m_groupSize;
  XML_Char m_namespaceSeparator;
  XML_Parser m_parentParser;
  XML_ParsingStatus m_parsingStatus;
#ifdef XML_DTD
  XML_Bool m_isParamEntity;
  XML_Bool m_useForeignDTD;
  enum XML_ParamEntityParsing m_paramEntityParsing;
#endif
};

#define MALLOC(s) (parser->m_mem.malloc_fcn((s)))
#define REALLOC(p,s) (parser->m_mem.realloc_fcn((p),(s)))
#define FREE(p) (parser->m_mem.free_fcn((p)))

#define userData (parser->m_userData)
#define handlerArg (parser->m_handlerArg)
#define startElementHandler (parser->m_startElementHandler)
#define endElementHandler (parser->m_endElementHandler)
#define characterDataHandler (parser->m_characterDataHandler)
#define processingInstructionHandler \
        (parser->m_processingInstructionHandler)
#define commentHandler (parser->m_commentHandler)
#define startCdataSectionHandler \
        (parser->m_startCdataSectionHandler)
#define endCdataSectionHandler (parser->m_endCdataSectionHandler)
#define defaultHandler (parser->m_defaultHandler)
#define startDoctypeDeclHandler (parser->m_startDoctypeDeclHandler)
#define endDoctypeDeclHandler (parser->m_endDoctypeDeclHandler)
#define unparsedEntityDeclHandler \
        (parser->m_unparsedEntityDeclHandler)
#define notationDeclHandler (parser->m_notationDeclHandler)
#define startNamespaceDeclHandler \
        (parser->m_startNamespaceDeclHandler)
#define endNamespaceDeclHandler (parser->m_endNamespaceDeclHandler)
#define notStandaloneHandler (parser->m_notStandaloneHandler)
#define externalEntityRefHandler \
        (parser->m_externalEntityRefHandler)
#define externalEntityRefHandlerArg \
        (parser->m_externalEntityRefHandlerArg)
#define internalEntityRefHandler \
        (parser->m_internalEntityRefHandler)
#define skippedEntityHandler (parser->m_skippedEntityHandler)
#define unknownEncodingHandler (parser->m_unknownEncodingHandler)
#define elementDeclHandler (parser->m_elementDeclHandler)
#define attlistDeclHandler (parser->m_attlistDeclHandler)
#define entityDeclHandler (parser->m_entityDeclHandler)
#define xmlDeclHandler (parser->m_xmlDeclHandler)
#define encoding (parser->m_encoding)
#define initEncoding (parser->m_initEncoding)
#define internalEncoding (parser->m_internalEncoding)
#define unknownEncodingMem (parser->m_unknownEncodingMem)
#define unknownEncodingData (parser->m_unknownEncodingData)
#define unknownEncodingHandlerData \
  (parser->m_unknownEncodingHandlerData)
#define unknownEncodingRelease (parser->m_unknownEncodingRelease)
#define protocolEncodingName (parser->m_protocolEncodingName)
#define ns (parser->m_ns)
#define ns_triplets (parser->m_ns_triplets)
#define prologState (parser->m_prologState)
#define processor (parser->m_processor)
#define errorCode (parser->m_errorCode)
#define eventPtr (parser->m_eventPtr)
#define eventEndPtr (parser->m_eventEndPtr)
#define positionPtr (parser->m_positionPtr)
#define position (parser->m_position)
#define openInternalEntities (parser->m_openInternalEntities)
#define freeInternalEntities (parser->m_freeInternalEntities)
#define defaultExpandInternalEntities \
        (parser->m_defaultExpandInternalEntities)
#define tagLevel (parser->m_tagLevel)
#define buffer (parser->m_buffer)
#define bufferPtr (parser->m_bufferPtr)
#define bufferEnd (parser->m_bufferEnd)
#define parseEndByteIndex (parser->m_parseEndByteIndex)
#define parseEndPtr (parser->m_parseEndPtr)
#define bufferLim (parser->m_bufferLim)
#define dataBuf (parser->m_dataBuf)
#define dataBufEnd (parser->m_dataBufEnd)
#define _dtd (parser->m_dtd)
#define curBase (parser->m_curBase)
#define declEntity (parser->m_declEntity)
#define doctypeName (parser->m_doctypeName)
#define doctypeSysid (parser->m_doctypeSysid)
#define doctypePubid (parser->m_doctypePubid)
#define declAttributeType (parser->m_declAttributeType)
#define declNotationName (parser->m_declNotationName)
#define declNotationPublicId (parser->m_declNotationPublicId)
#define declElementType (parser->m_declElementType)
#define declAttributeId (parser->m_declAttributeId)
#define declAttributeIsCdata (parser->m_declAttributeIsCdata)
#define declAttributeIsId (parser->m_declAttributeIsId)
#define freeTagList (parser->m_freeTagList)
#define freeBindingList (parser->m_freeBindingList)
#define inheritedBindings (parser->m_inheritedBindings)
#define tagStack (parser->m_tagStack)
#define atts (parser->m_atts)
#define attsSize (parser->m_attsSize)
#define nSpecifiedAtts (parser->m_nSpecifiedAtts)
#define idAttIndex (parser->m_idAttIndex)
#define nsAtts (parser->m_nsAtts)
#define nsAttsVersion (parser->m_nsAttsVersion)
#define nsAttsPower (parser->m_nsAttsPower)
#define tempPool (parser->m_tempPool)
#define temp2Pool (parser->m_temp2Pool)
#define groupConnector (parser->m_groupConnector)
#define groupSize (parser->m_groupSize)
#define namespaceSeparator (parser->m_namespaceSeparator)
#define parentParser (parser->m_parentParser)
#define ps_parsing (parser->m_parsingStatus.parsing)
#define ps_finalBuffer (parser->m_parsingStatus.finalBuffer)
#ifdef XML_DTD
#define isParamEntity (parser->m_isParamEntity)
#define useForeignDTD (parser->m_useForeignDTD)
#define paramEntityParsing (parser->m_paramEntityParsing)
#endif /* XML_DTD */

XML_Parser XMLCALL
XML_ParserCreate(const XML_Char *encodingName)
{
  return XML_ParserCreate_MM(encodingName, NULL, NULL);
}

XML_Parser XMLCALL
XML_ParserCreateNS(const XML_Char *encodingName, XML_Char nsSep)
{
  XML_Char tmp[2];
  *tmp = nsSep;
  return XML_ParserCreate_MM(encodingName, NULL, tmp);
}

static const XML_Char implicitContext[] = {
  ASCII_x, ASCII_m, ASCII_l, ASCII_EQUALS, ASCII_h, ASCII_t, ASCII_t, ASCII_p,
  ASCII_COLON, ASCII_SLASH, ASCII_SLASH, ASCII_w, ASCII_w, ASCII_w, 
  ASCII_PERIOD, ASCII_w, ASCII_3, ASCII_PERIOD, ASCII_o, ASCII_r, ASCII_g,
  ASCII_SLASH, ASCII_X, ASCII_M, ASCII_L, ASCII_SLASH, ASCII_1, ASCII_9,
  ASCII_9, ASCII_8, ASCII_SLASH, ASCII_n, ASCII_a, ASCII_m, ASCII_e,
  ASCII_s, ASCII_p, ASCII_a, ASCII_c, ASCII_e, '\0'
};

XML_Parser XMLCALL
XML_ParserCreate_MM(const XML_Char *encodingName,
                    const XML_Memory_Handling_Suite *memsuite,
                    const XML_Char *nameSep)
{
  XML_Parser parser = parserCreate(encodingName, memsuite, nameSep, NULL);
  if (parser != NULL && ns) {
    /* implicit context only set for root parser, since child
       parsers (i.e. external entity parsers) will inherit it
    */
    if (!setContext(parser, implicitContext)) {
      XML_ParserFree(parser);
      return NULL;
    }
  }
  return parser;
}

static XML_Parser
parserCreate(const XML_Char *encodingName,
             const XML_Memory_Handling_Suite *memsuite,
             const XML_Char *nameSep,
             DTD *dtd)
{
  XML_Parser parser;

  if (memsuite) {
    XML_Memory_Handling_Suite *mtemp;
    parser = (XML_Parser)
      memsuite->malloc_fcn(sizeof(struct XML_ParserStruct));
    if (parser != NULL) {
      mtemp = (XML_Memory_Handling_Suite *)&(parser->m_mem);
      mtemp->malloc_fcn = memsuite->malloc_fcn;
      mtemp->realloc_fcn = memsuite->realloc_fcn;
      mtemp->free_fcn = memsuite->free_fcn;
    }
  }
  else {
    XML_Memory_Handling_Suite *mtemp;
    parser = (XML_Parser)malloc(sizeof(struct XML_ParserStruct));
    if (parser != NULL) {
      mtemp = (XML_Memory_Handling_Suite *)&(parser->m_mem);
      mtemp->malloc_fcn = malloc;
      mtemp->realloc_fcn = realloc;
      mtemp->free_fcn = free;
    }
  }

  if (!parser)
    return parser;

  buffer = NULL;
  bufferLim = NULL;

  attsSize = INIT_ATTS_SIZE;
  atts = (ATTRIBUTE *)MALLOC(attsSize * sizeof(ATTRIBUTE));
  if (atts == NULL) {
    FREE(parser);
    return NULL;
  }
  dataBuf = (XML_Char *)MALLOC(INIT_DATA_BUF_SIZE * sizeof(XML_Char));
  if (dataBuf == NULL) {
    FREE(atts);
    FREE(parser);
    return NULL;
  }
  dataBufEnd = dataBuf + INIT_DATA_BUF_SIZE;

  if (dtd)
    _dtd = dtd;
  else {
    _dtd = dtdCreate(&parser->m_mem);
    if (_dtd == NULL) {
      FREE(dataBuf);
      FREE(atts);
      FREE(parser);
      return NULL;
    }
  }

  freeBindingList = NULL;
  freeTagList = NULL;
  freeInternalEntities = NULL;

  groupSize = 0;
  groupConnector = NULL;

  unknownEncodingHandler = NULL;
  unknownEncodingHandlerData = NULL;

  namespaceSeparator = ASCII_EXCL;
  ns = XML_FALSE;
  ns_triplets = XML_FALSE;

  nsAtts = NULL;
  nsAttsVersion = 0;
  nsAttsPower = 0;

  poolInit(&tempPool, &(parser->m_mem));
  poolInit(&temp2Pool, &(parser->m_mem));
  parserInit(parser, encodingName);

  if (encodingName && !protocolEncodingName) {
    XML_ParserFree(parser);
    return NULL;
  }

  if (nameSep) {
    ns = XML_TRUE;
    internalEncoding = XmlGetInternalEncodingNS();
    namespaceSeparator = *nameSep;
  }
  else {
    internalEncoding = XmlGetInternalEncoding();
  }

  return parser;
}

static void
parserInit(XML_Parser parser, const XML_Char *encodingName)
{
  processor = prologInitProcessor;
  XmlPrologStateInit(&prologState);
  protocolEncodingName = (encodingName != NULL
                          ? poolCopyString(&tempPool, encodingName)
                          : NULL);
  curBase = NULL;
  XmlInitEncoding(&initEncoding, &encoding, 0);
  userData = NULL;
  handlerArg = NULL;
  startElementHandler = NULL;
  endElementHandler = NULL;
  characterDataHandler = NULL;
  processingInstructionHandler = NULL;
  commentHandler = NULL;
  startCdataSectionHandler = NULL;
  endCdataSectionHandler = NULL;
  defaultHandler = NULL;
  startDoctypeDeclHandler = NULL;
  endDoctypeDeclHandler = NULL;
  unparsedEntityDeclHandler = NULL;
  notationDeclHandler = NULL;
  startNamespaceDeclHandler = NULL;
  endNamespaceDeclHandler = NULL;
  notStandaloneHandler = NULL;
  externalEntityRefHandler = NULL;
  externalEntityRefHandlerArg = parser;
  skippedEntityHandler = NULL;
  elementDeclHandler = NULL;
  attlistDeclHandler = NULL;
  entityDeclHandler = NULL;
  xmlDeclHandler = NULL;
  bufferPtr = buffer;
  bufferEnd = buffer;
  parseEndByteIndex = 0;
  parseEndPtr = NULL;
  declElementType = NULL;
  declAttributeId = NULL;
  declEntity = NULL;
  doctypeName = NULL;
  doctypeSysid = NULL;
  doctypePubid = NULL;
  declAttributeType = NULL;
  declNotationName = NULL;
  declNotationPublicId = NULL;
  declAttributeIsCdata = XML_FALSE;
  declAttributeIsId = XML_FALSE;
  memset(&position, 0, sizeof(POSITION));
  errorCode = XML_ERROR_NONE;
  eventPtr = NULL;
  eventEndPtr = NULL;
  positionPtr = NULL;
  openInternalEntities = NULL;
  defaultExpandInternalEntities = XML_TRUE;
  tagLevel = 0;
  tagStack = NULL;
  inheritedBindings = NULL;
  nSpecifiedAtts = 0;
  unknownEncodingMem = NULL;
  unknownEncodingRelease = NULL;
  unknownEncodingData = NULL;
  parentParser = NULL;
  ps_parsing = XML_INITIALIZED;
#ifdef XML_DTD
  isParamEntity = XML_FALSE;
  useForeignDTD = XML_FALSE;
  paramEntityParsing = XML_PARAM_ENTITY_PARSING_NEVER;
#endif
}

/* moves list of bindings to freeBindingList */
static void FASTCALL
moveToFreeBindingList(XML_Parser parser, BINDING *bindings)
{
  while (bindings) {
    BINDING *b = bindings;
    bindings = bindings->nextTagBinding;
    b->nextTagBinding = freeBindingList;
    freeBindingList = b;
  }
}

XML_Bool XMLCALL
XML_ParserReset(XML_Parser parser, const XML_Char *encodingName)
{
  TAG *tStk;
  OPEN_INTERNAL_ENTITY *openEntityList;
  if (parentParser)
    return XML_FALSE;
  /* move tagStack to freeTagList */
  tStk = tagStack;
  while (tStk) {
    TAG *tag = tStk;
    tStk = tStk->parent;
    tag->parent = freeTagList;
    moveToFreeBindingList(parser, tag->bindings);
    tag->bindings = NULL;
    freeTagList = tag;
  }
  /* move openInternalEntities to freeInternalEntities */
  openEntityList = openInternalEntities;
  while (openEntityList) {
    OPEN_INTERNAL_ENTITY *openEntity = openEntityList;
    openEntityList = openEntity->next;
    openEntity->next = freeInternalEntities;
    freeInternalEntities = openEntity;
  }
  moveToFreeBindingList(parser, inheritedBindings);
  FREE(unknownEncodingMem);
  if (unknownEncodingRelease)
    unknownEncodingRelease(unknownEncodingData);
  poolClear(&tempPool);
  poolClear(&temp2Pool);
  parserInit(parser, encodingName);
  dtdReset(_dtd, &parser->m_mem);
  return setContext(parser, implicitContext);
}

enum XML_Status XMLCALL
XML_SetEncoding(XML_Parser parser, const XML_Char *encodingName)
{
  /* Block after XML_Parse()/XML_ParseBuffer() has been called.
     XXX There's no way for the caller to determine which of the
     XXX possible error cases caused the XML_STATUS_ERROR return.
  */
  if (ps_parsing == XML_PARSING || ps_parsing == XML_SUSPENDED)
    return XML_STATUS_ERROR;
  if (encodingName == NULL)
    protocolEncodingName = NULL;
  else {
    protocolEncodingName = poolCopyString(&tempPool, encodingName);
    if (!protocolEncodingName)
      return XML_STATUS_ERROR;
  }
  return XML_STATUS_OK;
}

XML_Parser XMLCALL
XML_ExternalEntityParserCreate(XML_Parser oldParser,
                               const XML_Char *context,
                               const XML_Char *encodingName)
{
  XML_Parser parser = oldParser;
  DTD *newDtd = NULL;
  DTD *oldDtd = _dtd;
  XML_StartElementHandler oldStartElementHandler = startElementHandler;
  XML_EndElementHandler oldEndElementHandler = endElementHandler;
  XML_CharacterDataHandler oldCharacterDataHandler = characterDataHandler;
  XML_ProcessingInstructionHandler oldProcessingInstructionHandler
      = processingInstructionHandler;
  XML_CommentHandler oldCommentHandler = commentHandler;
  XML_StartCdataSectionHandler oldStartCdataSectionHandler
      = startCdataSectionHandler;
  XML_EndCdataSectionHandler oldEndCdataSectionHandler
      = endCdataSectionHandler;
  XML_DefaultHandler oldDefaultHandler = defaultHandler;
  XML_UnparsedEntityDeclHandler oldUnparsedEntityDeclHandler
      = unparsedEntityDeclHandler;
  XML_NotationDeclHandler oldNotationDeclHandler = notationDeclHandler;
  XML_StartNamespaceDeclHandler oldStartNamespaceDeclHandler
      = startNamespaceDeclHandler;
  XML_EndNamespaceDeclHandler oldEndNamespaceDeclHandler
      = endNamespaceDeclHandler;
  XML_NotStandaloneHandler oldNotStandaloneHandler = notStandaloneHandler;
  XML_ExternalEntityRefHandler oldExternalEntityRefHandler
      = externalEntityRefHandler;
  XML_SkippedEntityHandler oldSkippedEntityHandler = skippedEntityHandler;
  XML_UnknownEncodingHandler oldUnknownEncodingHandler
      = unknownEncodingHandler;
  XML_ElementDeclHandler oldElementDeclHandler = elementDeclHandler;
  XML_AttlistDeclHandler oldAttlistDeclHandler = attlistDeclHandler;
  XML_EntityDeclHandler oldEntityDeclHandler = entityDeclHandler;
  XML_XmlDeclHandler oldXmlDeclHandler = xmlDeclHandler;
  ELEMENT_TYPE * oldDeclElementType = declElementType;

  void *oldUserData = userData;
  void *oldHandlerArg = handlerArg;
  XML_Bool oldDefaultExpandInternalEntities = defaultExpandInternalEntities;
  XML_Parser oldExternalEntityRefHandlerArg = externalEntityRefHandlerArg;
#ifdef XML_DTD
  enum XML_ParamEntityParsing oldParamEntityParsing = paramEntityParsing;
  int oldInEntityValue = prologState.inEntityValue;
#endif
  XML_Bool oldns_triplets = ns_triplets;

#ifdef XML_DTD
  if (!context)
    newDtd = oldDtd;
#endif /* XML_DTD */

  /* Note that the magical uses of the pre-processor to make field
     access look more like C++ require that `parser' be overwritten
     here.  This makes this function more painful to follow than it
     would be otherwise.
  */
  if (ns) {
    XML_Char tmp[2];
    *tmp = namespaceSeparator;
    parser = parserCreate(encodingName, &parser->m_mem, tmp, newDtd);
  }
  else {
    parser = parserCreate(encodingName, &parser->m_mem, NULL, newDtd);
  }

  if (!parser)
    return NULL;

  startElementHandler = oldStartElementHandler;
  endElementHandler = oldEndElementHandler;
  characterDataHandler = oldCharacterDataHandler;
  processingInstructionHandler = oldProcessingInstructionHandler;
  commentHandler = oldCommentHandler;
  startCdataSectionHandler = oldStartCdataSectionHandler;
  endCdataSectionHandler = oldEndCdataSectionHandler;
  defaultHandler = oldDefaultHandler;
  unparsedEntityDeclHandler = oldUnparsedEntityDeclHandler;
  notationDeclHandler = oldNotationDeclHandler;
  startNamespaceDeclHandler = oldStartNamespaceDeclHandler;
  endNamespaceDeclHandler = oldEndNamespaceDeclHandler;
  notStandaloneHandler = oldNotStandaloneHandler;
  externalEntityRefHandler = oldExternalEntityRefHandler;
  skippedEntityHandler = oldSkippedEntityHandler;
  unknownEncodingHandler = oldUnknownEncodingHandler;
  elementDeclHandler = oldElementDeclHandler;
  attlistDeclHandler = oldAttlistDeclHandler;
  entityDeclHandler = oldEntityDeclHandler;
  xmlDeclHandler = oldXmlDeclHandler;
  declElementType = oldDeclElementType;
  userData = oldUserData;
  if (oldUserData == oldHandlerArg)
    handlerArg = userData;
  else
    handlerArg = parser;
  if (oldExternalEntityRefHandlerArg != oldParser)
    externalEntityRefHandlerArg = oldExternalEntityRefHandlerArg;
  defaultExpandInternalEntities = oldDefaultExpandInternalEntities;
  ns_triplets = oldns_triplets;
  parentParser = oldParser;
#ifdef XML_DTD
  paramEntityParsing = oldParamEntityParsing;
  prologState.inEntityValue = oldInEntityValue;
  if (context) {
#endif /* XML_DTD */
    if (!dtdCopy(_dtd, oldDtd, &parser->m_mem)
      || !setContext(parser, context)) {
      XML_ParserFree(parser);
      return NULL;
    }
    processor = externalEntityInitProcessor;
#ifdef XML_DTD
  }
  else {
    /* The DTD instance referenced by _dtd is shared between the document's
       root parser and external PE parsers, therefore one does not need to
       call setContext. In addition, one also *must* not call setContext,
       because this would overwrite existing prefix->binding pointers in
       _dtd with ones that get destroyed with the external PE parser.
       This would leave those prefixes with dangling pointers.
    */
    isParamEntity = XML_TRUE;
    XmlPrologStateInitExternalEntity(&prologState);
    processor = externalParEntInitProcessor;
  }
#endif /* XML_DTD */
  return parser;
}

static void FASTCALL
destroyBindings(BINDING *bindings, XML_Parser parser)
{
  for (;;) {
    BINDING *b = bindings;
    if (!b)
      break;
    bindings = b->nextTagBinding;
    FREE(b->uri);
    FREE(b);
  }
}

void XMLCALL
XML_ParserFree(XML_Parser parser)
{
  TAG *tagList;
  OPEN_INTERNAL_ENTITY *entityList;
  if (parser == NULL)
    return;
  /* free tagStack and freeTagList */
  tagList = tagStack;
  for (;;) {
    TAG *p;
    if (tagList == NULL) {
      if (freeTagList == NULL)
        break;
      tagList = freeTagList;
      freeTagList = NULL;
    }
    p = tagList;
    tagList = tagList->parent;
    FREE(p->buf);
    destroyBindings(p->bindings, parser);
    FREE(p);
  }
  /* free openInternalEntities and freeInternalEntities */
  entityList = openInternalEntities;
  for (;;) {
    OPEN_INTERNAL_ENTITY *openEntity;
    if (entityList == NULL) {
      if (freeInternalEntities == NULL)
        break;
      entityList = freeInternalEntities;
      freeInternalEntities = NULL;
    }
    openEntity = entityList;
    entityList = entityList->next;
    FREE(openEntity);
  }

  destroyBindings(freeBindingList, parser);
  destroyBindings(inheritedBindings, parser);
  poolDestroy(&tempPool);
  poolDestroy(&temp2Pool);
#ifdef XML_DTD
  /* external parameter entity parsers share the DTD structure
     parser->m_dtd with the root parser, so we must not destroy it
  */
  if (!isParamEntity && _dtd)
#else
  if (_dtd)
#endif /* XML_DTD */
    dtdDestroy(_dtd, (XML_Bool)!parentParser, &parser->m_mem);
  FREE((void *)atts);
  FREE(groupConnector);
  FREE(buffer);
  FREE(dataBuf);
  FREE(nsAtts);
  FREE(unknownEncodingMem);
  if (unknownEncodingRelease)
    unknownEncodingRelease(unknownEncodingData);
  FREE(parser);
}

void XMLCALL
XML_UseParserAsHandlerArg(XML_Parser parser)
{
  handlerArg = parser;
}

enum XML_Error XMLCALL
XML_UseForeignDTD(__attribute__ ((unused)) XML_Parser parser,
                  __attribute__ ((unused)) XML_Bool useDTD)
{
#ifdef XML_DTD
  /* block after XML_Parse()/XML_ParseBuffer() has been called */
  if (ps_parsing == XML_PARSING || ps_parsing == XML_SUSPENDED)
    return XML_ERROR_CANT_CHANGE_FEATURE_ONCE_PARSING;
  useForeignDTD = useDTD;
  return XML_ERROR_NONE;
#else
  return XML_ERROR_FEATURE_REQUIRES_XML_DTD;
#endif
}

void XMLCALL
XML_SetReturnNSTriplet(XML_Parser parser, int do_nst)
{
  /* block after XML_Parse()/XML_ParseBuffer() has been called */
  if (ps_parsing == XML_PARSING || ps_parsing == XML_SUSPENDED)
    return;
  ns_triplets = do_nst ? XML_TRUE : XML_FALSE;
}

void XMLCALL
XML_SetUserData(XML_Parser parser, void *p)
{
  if (handlerArg == userData)
    handlerArg = userData = p;
  else
    userData = p;
}

enum XML_Status XMLCALL
XML_SetBase(XML_Parser parser, const XML_Char *p)
{
  if (p) {
    p = poolCopyString(&_dtd->pool, p);
    if (!p)
      return XML_STATUS_ERROR;
    curBase = p;
  }
  else
    curBase = NULL;
  return XML_STATUS_OK;
}

const XML_Char * XMLCALL
XML_GetBase(XML_Parser parser)
{
  return curBase;
}

int XMLCALL
XML_GetSpecifiedAttributeCount(XML_Parser parser)
{
  return nSpecifiedAtts;
}

int XMLCALL
XML_GetIdAttributeIndex(XML_Parser parser)
{
  return idAttIndex;
}

void XMLCALL
XML_SetElementHandler(XML_Parser parser,
                      XML_StartElementHandler start,
                      XML_EndElementHandler end)
{
  startElementHandler = start;
  endElementHandler = end;
}

void XMLCALL
XML_SetStartElementHandler(XML_Parser parser,
                           XML_StartElementHandler start) {
  startElementHandler = start;
}

void XMLCALL
XML_SetEndElementHandler(XML_Parser parser,
                         XML_EndElementHandler end) {
  endElementHandler = end;
}

void XMLCALL
XML_SetCharacterDataHandler(XML_Parser parser,
                            XML_CharacterDataHandler handler)
{
  characterDataHandler = handler;
}

void XMLCALL
XML_SetProcessingInstructionHandler(XML_Parser parser,
                                    XML_ProcessingInstructionHandler handler)
{
  processingInstructionHandler = handler;
}

void XMLCALL
XML_SetCommentHandler(XML_Parser parser,
                      XML_CommentHandler handler)
{
  commentHandler = handler;
}

void XMLCALL
XML_SetCdataSectionHandler(XML_Parser parser,
                           XML_StartCdataSectionHandler start,
                           XML_EndCdataSectionHandler end)
{
  startCdataSectionHandler = start;
  endCdataSectionHandler = end;
}

void XMLCALL
XML_SetStartCdataSectionHandler(XML_Parser parser,
                                XML_StartCdataSectionHandler start) {
  startCdataSectionHandler = start;
}

void XMLCALL
XML_SetEndCdataSectionHandler(XML_Parser parser,
                              XML_EndCdataSectionHandler end) {
  endCdataSectionHandler = end;
}

void XMLCALL
XML_SetDefaultHandler(XML_Parser parser,
                      XML_DefaultHandler handler)
{
  defaultHandler = handler;
  defaultExpandInternalEntities = XML_FALSE;
}

void XMLCALL
XML_SetDefaultHandlerExpand(XML_Parser parser,
                            XML_DefaultHandler handler)
{
  defaultHandler = handler;
  defaultExpandInternalEntities = XML_TRUE;
}

void XMLCALL
XML_SetDoctypeDeclHandler(XML_Parser parser,
                          XML_StartDoctypeDeclHandler start,
                          XML_EndDoctypeDeclHandler end)
{
  startDoctypeDeclHandler = start;
  endDoctypeDeclHandler = end;
}

void XMLCALL
XML_SetStartDoctypeDeclHandler(XML_Parser parser,
                               XML_StartDoctypeDeclHandler start) {
  startDoctypeDeclHandler = start;
}

void XMLCALL
XML_SetEndDoctypeDeclHandler(XML_Parser parser,
                             XML_EndDoctypeDeclHandler end) {
  endDoctypeDeclHandler = end;
}

void XMLCALL
XML_SetUnparsedEntityDeclHandler(XML_Parser parser,
                                 XML_UnparsedEntityDeclHandler handler)
{
  unparsedEntityDeclHandler = handler;
}

void XMLCALL
XML_SetNotationDeclHandler(XML_Parser parser,
                           XML_NotationDeclHandler handler)
{
  notationDeclHandler = handler;
}

void XMLCALL
XML_SetNamespaceDeclHandler(XML_Parser parser,
                            XML_StartNamespaceDeclHandler start,
                            XML_EndNamespaceDeclHandler end)
{
  startNamespaceDeclHandler = start;
  endNamespaceDeclHandler = end;
}

void XMLCALL
XML_SetStartNamespaceDeclHandler(XML_Parser parser,
                                 XML_StartNamespaceDeclHandler start) {
  startNamespaceDeclHandler = start;
}

void XMLCALL
XML_SetEndNamespaceDeclHandler(XML_Parser parser,
                               XML_EndNamespaceDeclHandler end) {
  endNamespaceDeclHandler = end;
}

void XMLCALL
XML_SetNotStandaloneHandler(XML_Parser parser,
                            XML_NotStandaloneHandler handler)
{
  notStandaloneHandler = handler;
}

void XMLCALL
XML_SetExternalEntityRefHandler(XML_Parser parser,
                                XML_ExternalEntityRefHandler handler)
{
  externalEntityRefHandler = handler;
}

void XMLCALL
XML_SetExternalEntityRefHandlerArg(XML_Parser parser, void *arg)
{
  if (arg)
    externalEntityRefHandlerArg = (XML_Parser)arg;
  else
    externalEntityRefHandlerArg = parser;
}

void XMLCALL
XML_SetSkippedEntityHandler(XML_Parser parser,
                            XML_SkippedEntityHandler handler)
{
  skippedEntityHandler = handler;
}

void XMLCALL
XML_SetUnknownEncodingHandler(XML_Parser parser,
                              XML_UnknownEncodingHandler handler,
                              void *data)
{
  unknownEncodingHandler = handler;
  unknownEncodingHandlerData = data;
}

void XMLCALL
XML_SetElementDeclHandler(XML_Parser parser,
                          XML_ElementDeclHandler eldecl)
{
  elementDeclHandler = eldecl;
}

void XMLCALL
XML_SetAttlistDeclHandler(XML_Parser parser,
                          XML_AttlistDeclHandler attdecl)
{
  attlistDeclHandler = attdecl;
}

void XMLCALL
XML_SetEntityDeclHandler(XML_Parser parser,
                         XML_EntityDeclHandler handler)
{
  entityDeclHandler = handler;
}

void XMLCALL
XML_SetXmlDeclHandler(XML_Parser parser,
                      XML_XmlDeclHandler handler) {
  xmlDeclHandler = handler;
}

int XMLCALL
XML_SetParamEntityParsing(XML_Parser parser,
                          enum XML_ParamEntityParsing peParsing)
{
  /* block after XML_Parse()/XML_ParseBuffer() has been called */
  if (ps_parsing == XML_PARSING || ps_parsing == XML_SUSPENDED)
    return 0;
#ifdef XML_DTD
  paramEntityParsing = peParsing;
  return 1;
#else
  return peParsing == XML_PARAM_ENTITY_PARSING_NEVER;
#endif
}

enum XML_Status XMLCALL
XML_Parse(XML_Parser parser, const char *s, int len, int isFinal)
{
  switch (ps_parsing) {
  case XML_SUSPENDED:
    errorCode = XML_ERROR_SUSPENDED;
    return XML_STATUS_ERROR;
  case XML_FINISHED:
    errorCode = XML_ERROR_FINISHED;
    return XML_STATUS_ERROR;
  default:
    ps_parsing = XML_PARSING;
  }

  if (len == 0) {
    ps_finalBuffer = (XML_Bool)isFinal;
    if (!isFinal)
      return XML_STATUS_OK;
    positionPtr = bufferPtr;
    parseEndPtr = bufferEnd;

    /* If data are left over from last buffer, and we now know that these
       data are the final chunk of input, then we have to check them again
       to detect errors based on that fact.
    */
    errorCode = processor(parser, bufferPtr, parseEndPtr, &bufferPtr);

    if (errorCode == XML_ERROR_NONE) {
      switch (ps_parsing) {
      case XML_SUSPENDED:
        XmlUpdatePosition(encoding, positionPtr, bufferPtr, &position);
        positionPtr = bufferPtr;
        return XML_STATUS_SUSPENDED;
      case XML_INITIALIZED: 
      case XML_PARSING:
        ps_parsing = XML_FINISHED;
        /* fall through */
      default:
        return XML_STATUS_OK;
      }
    }
    eventEndPtr = eventPtr;
    processor = errorProcessor;
    return XML_STATUS_ERROR;
  }
#ifndef XML_CONTEXT_BYTES
  else if (bufferPtr == bufferEnd) {
    const char *end;
    int nLeftOver;
    enum XML_Status result = 0;
    parseEndByteIndex += len;
    positionPtr = s;
    ps_finalBuffer = (XML_Bool)isFinal;

    errorCode = processor(parser, s, parseEndPtr = s + len, &end);

    if (errorCode != XML_ERROR_NONE) {
      eventEndPtr = eventPtr;
      processor = errorProcessor;
      return XML_STATUS_ERROR;
    }
    else {
      switch (ps_parsing) {
      case XML_SUSPENDED:
        result = XML_STATUS_SUSPENDED;
        break;
      case XML_INITIALIZED:
      case XML_PARSING:
        result = XML_STATUS_OK;
        if (isFinal) {
          ps_parsing = XML_FINISHED;
          return result;
        }
      case XML_FINISHED:
        break;
      }
    }

    XmlUpdatePosition(encoding, positionPtr, end, &position);
    nLeftOver = s + len - end;
    if (nLeftOver) {
      if (buffer == NULL || nLeftOver > bufferLim - buffer) {
        /* FIXME avoid integer overflow */
        char *temp;
        temp = (buffer == NULL
                ? (char *)MALLOC(len * 2)
                : (char *)REALLOC(buffer, len * 2));
        if (temp == NULL) {
          errorCode = XML_ERROR_NO_MEMORY;
          return XML_STATUS_ERROR;
        }
        buffer = temp;
        if (!buffer) {
          errorCode = XML_ERROR_NO_MEMORY;
          eventPtr = eventEndPtr = NULL;
          processor = errorProcessor;
          return XML_STATUS_ERROR;
        }
        bufferLim = buffer + len * 2;
      }
      memcpy(buffer, end, nLeftOver);
    }
    bufferPtr = buffer;
    bufferEnd = buffer + nLeftOver;
    positionPtr = bufferPtr;
    parseEndPtr = bufferEnd;
    eventPtr = bufferPtr;
    eventEndPtr = bufferPtr;
    return result;
  }
#endif  /* not defined XML_CONTEXT_BYTES */
  else {
    void *buff = XML_GetBuffer(parser, len);
    if (buff == NULL)
      return XML_STATUS_ERROR;
    else {
      memcpy(buff, s, len);
      return XML_ParseBuffer(parser, len, isFinal);
    }
  }
}

enum XML_Status XMLCALL
XML_ParseBuffer(XML_Parser parser, int len, int isFinal)
{
  const char *start;
  enum XML_Status result = XML_STATUS_OK;

  switch (ps_parsing) {
  case XML_SUSPENDED:
    errorCode = XML_ERROR_SUSPENDED;
    return XML_STATUS_ERROR;
  case XML_FINISHED:
    errorCode = XML_ERROR_FINISHED;
    return XML_STATUS_ERROR;
  default:
    ps_parsing = XML_PARSING;
  }

  start = bufferPtr;
  positionPtr = start;
  bufferEnd += len;
  parseEndPtr = bufferEnd;
  parseEndByteIndex += len;
  ps_finalBuffer = (XML_Bool)isFinal;

  errorCode = processor(parser, start, parseEndPtr, &bufferPtr);

  if (errorCode != XML_ERROR_NONE) {
    eventEndPtr = eventPtr;
    processor = errorProcessor;
    return XML_STATUS_ERROR;
  }
  else {
    switch (ps_parsing) {
    case XML_SUSPENDED:
      result = XML_STATUS_SUSPENDED;
      break;
    case XML_INITIALIZED: 
    case XML_PARSING:
      if (isFinal) {
        ps_parsing = XML_FINISHED;
        return result;
      }
    default: ;  /* should not happen */
    }
  }

  XmlUpdatePosition(encoding, positionPtr, bufferPtr, &position);
  positionPtr = bufferPtr;
  return result;
}

void * XMLCALL
XML_GetBuffer(XML_Parser parser, int len)
{
  switch (ps_parsing) {
  case XML_SUSPENDED:
    errorCode = XML_ERROR_SUSPENDED;
    return NULL;
  case XML_FINISHED:
    errorCode = XML_ERROR_FINISHED;
    return NULL;
  default: ;
  }

  if (len > bufferLim - bufferEnd) {
    /* FIXME avoid integer overflow */
    int neededSize = len + (int)(bufferEnd - bufferPtr);
#ifdef XML_CONTEXT_BYTES
    int keep = (int)(bufferPtr - buffer);

    if (keep > XML_CONTEXT_BYTES)
      keep = XML_CONTEXT_BYTES;
    neededSize += keep;
#endif  /* defined XML_CONTEXT_BYTES */
    if (neededSize  <= bufferLim - buffer) {
#ifdef XML_CONTEXT_BYTES
      if (keep < bufferPtr - buffer) {
        int offset = (int)(bufferPtr - buffer) - keep;
        memmove(buffer, &buffer[offset], bufferEnd - bufferPtr + keep);
        bufferEnd -= offset;
        bufferPtr -= offset;
      }
#else
      memmove(buffer, bufferPtr, bufferEnd - bufferPtr);
      bufferEnd = buffer + (bufferEnd - bufferPtr);
      bufferPtr = buffer;
#endif  /* not defined XML_CONTEXT_BYTES */
    }
    else {
      char *newBuf;
      int bufferSize = (int)(bufferLim - bufferPtr);
      if (bufferSize == 0)
        bufferSize = INIT_BUFFER_SIZE;
      do {
        bufferSize *= 2;
      } while (bufferSize < neededSize);
      newBuf = (char *)MALLOC(bufferSize);
      if (newBuf == 0) {
        errorCode = XML_ERROR_NO_MEMORY;
        return NULL;
      }
      bufferLim = newBuf + bufferSize;
#ifdef XML_CONTEXT_BYTES
      if (bufferPtr) {
        int keep = (int)(bufferPtr - buffer);
        if (keep > XML_CONTEXT_BYTES)
          keep = XML_CONTEXT_BYTES;
        memcpy(newBuf, &bufferPtr[-keep], bufferEnd - bufferPtr + keep);
        FREE(buffer);
        buffer = newBuf;
        bufferEnd = buffer + (bufferEnd - bufferPtr) + keep;
        bufferPtr = buffer + keep;
      }
      else {
        bufferEnd = newBuf + (bufferEnd - bufferPtr);
        bufferPtr = buffer = newBuf;
      }
#else
      if (bufferPtr) {
        memcpy(newBuf, bufferPtr, bufferEnd - bufferPtr);
        FREE(buffer);
      }
      bufferEnd = newBuf + (bufferEnd - bufferPtr);
      bufferPtr = buffer = newBuf;
#endif  /* not defined XML_CONTEXT_BYTES */
    }
  }
  return bufferEnd;
}

enum XML_Status XMLCALL
XML_StopParser(XML_Parser parser, XML_Bool resumable)
{
  switch (ps_parsing) {
  case XML_SUSPENDED:
    if (resumable) {
      errorCode = XML_ERROR_SUSPENDED;
      return XML_STATUS_ERROR;
    }
    ps_parsing = XML_FINISHED;
    break;
  case XML_FINISHED:
    errorCode = XML_ERROR_FINISHED;
    return XML_STATUS_ERROR;
  default:
    if (resumable) {
#ifdef XML_DTD
      if (isParamEntity) {
        errorCode = XML_ERROR_SUSPEND_PE;
        return XML_STATUS_ERROR;
      }
#endif
      ps_parsing = XML_SUSPENDED;
    }
    else
      ps_parsing = XML_FINISHED;
  }
  return XML_STATUS_OK;
}

enum XML_Status XMLCALL
XML_ResumeParser(XML_Parser parser)
{
  enum XML_Status result = XML_STATUS_OK;

  if (ps_parsing != XML_SUSPENDED) {
    errorCode = XML_ERROR_NOT_SUSPENDED;
    return XML_STATUS_ERROR;
  }
  ps_parsing = XML_PARSING;

  errorCode = processor(parser, bufferPtr, parseEndPtr, &bufferPtr);

  if (errorCode != XML_ERROR_NONE) {
    eventEndPtr = eventPtr;
    processor = errorProcessor;
    return XML_STATUS_ERROR;
  }
  else {
    switch (ps_parsing) {
    case XML_SUSPENDED:
      result = XML_STATUS_SUSPENDED;
      break;
    case XML_INITIALIZED: 
    case XML_PARSING:
      if (ps_finalBuffer) {
        ps_parsing = XML_FINISHED;
        return result;
      }
    default: ;
    }
  }

  XmlUpdatePosition(encoding, positionPtr, bufferPtr, &position);
  positionPtr = bufferPtr;
  return result;
}

void XMLCALL
XML_GetParsingStatus(XML_Parser parser, XML_ParsingStatus *status)
{
  assert(status != NULL);
  *status = parser->m_parsingStatus;
}

enum XML_Error XMLCALL
XML_GetErrorCode(XML_Parser parser)
{
  return errorCode;
}

XML_Index XMLCALL
XML_GetCurrentByteIndex(XML_Parser parser)
{
  if (eventPtr)
    return parseEndByteIndex - (parseEndPtr - eventPtr);
  return -1;
}

int XMLCALL
XML_GetCurrentByteCount(XML_Parser parser)
{
  if (eventEndPtr && eventPtr)
    return (int)(eventEndPtr - eventPtr);
  return 0;
}

const char * XMLCALL
XML_GetInputContext(__attribute__ ((unused)) XML_Parser parser,
                    __attribute__ ((unused)) int *offset,
                    __attribute__ ((unused)) int *size)
{
#ifdef XML_CONTEXT_BYTES
  if (eventPtr && buffer) {
    *offset = (int)(eventPtr - buffer);
    *size   = (int)(bufferEnd - buffer);
    return buffer;
  }
#endif /* defined XML_CONTEXT_BYTES */
  return (char *) 0;
}

XML_Size XMLCALL
XML_GetCurrentLineNumber(XML_Parser parser)
{
  if (eventPtr && eventPtr >= positionPtr) {
    XmlUpdatePosition(encoding, positionPtr, eventPtr, &position);
    positionPtr = eventPtr;
  }
  return position.lineNumber + 1;
}

XML_Size XMLCALL
XML_GetCurrentColumnNumber(XML_Parser parser)
{
  if (eventPtr && eventPtr >= positionPtr) {
    XmlUpdatePosition(encoding, positionPtr, eventPtr, &position);
    positionPtr = eventPtr;
  }
  return position.columnNumber;
}

void XMLCALL
XML_FreeContentModel(XML_Parser parser, XML_Content *model)
{
  FREE(model);
}

void * XMLCALL
XML_MemMalloc(XML_Parser parser, size_t size)
{
  return MALLOC(size);
}

void * XMLCALL
XML_MemRealloc(XML_Parser parser, void *ptr, size_t size)
{
  return REALLOC(ptr, size);
}

void XMLCALL
XML_MemFree(XML_Parser parser, void *ptr)
{
  FREE(ptr);
}

void XMLCALL
XML_DefaultCurrent(XML_Parser parser)
{
  if (defaultHandler) {
    if (openInternalEntities)
      reportDefault(parser,
                    internalEncoding,
                    openInternalEntities->internalEventPtr,
                    openInternalEntities->internalEventEndPtr);
    else
      reportDefault(parser, encoding, eventPtr, eventEndPtr);
  }
}

const XML_LChar * XMLCALL
XML_ErrorString(enum XML_Error code)
{
  static const XML_LChar* const message[] = {
    0,
    XML_L("out of memory"),
    XML_L("syntax error"),
    XML_L("no element found"),
    XML_L("not well-formed (invalid token)"),
    XML_L("unclosed token"),
    XML_L("partial character"),
    XML_L("mismatched tag"),
    XML_L("duplicate attribute"),
    XML_L("junk after document element"),
    XML_L("illegal parameter entity reference"),
    XML_L("undefined entity"),
    XML_L("recursive entity reference"),
    XML_L("asynchronous entity"),
    XML_L("reference to invalid character number"),
    XML_L("reference to binary entity"),
    XML_L("reference to external entity in attribute"),
    XML_L("XML or text declaration not at start of entity"),
    XML_L("unknown encoding"),
    XML_L("encoding specified in XML declaration is incorrect"),
    XML_L("unclosed CDATA section"),
    XML_L("error in processing external entity reference"),
    XML_L("document is not standalone"),
    XML_L("unexpected parser state - please send a bug report"),
    XML_L("entity declared in parameter entity"),
    XML_L("requested feature requires XML_DTD support in Expat"),
    XML_L("cannot change setting once parsing has begun"),
    XML_L("unbound prefix"),
    XML_L("must not undeclare prefix"),
    XML_L("incomplete markup in parameter entity"),
    XML_L("XML declaration not well-formed"),
    XML_L("text declaration not well-formed"),
    XML_L("illegal character(s) in public id"),
    XML_L("parser suspended"),
    XML_L("parser not suspended"),
    XML_L("parsing aborted"),
    XML_L("parsing finished"),
    XML_L("cannot suspend in external parameter entity"),
    XML_L("reserved prefix (xml) must not be undeclared or bound to another namespace name"),
    XML_L("reserved prefix (xmlns) must not be declared or undeclared"),
    XML_L("prefix must not be bound to one of the reserved namespace names")
  };
  if (code > 0 && code < sizeof(message)/sizeof(message[0]))
    return message[code];
  return NULL;
}

const XML_LChar * XMLCALL
XML_ExpatVersion(void) {

  /* V1 is used to string-ize the version number. However, it would
     string-ize the actual version macro *names* unless we get them
     substituted before being passed to V1. CPP is defined to expand
     a macro, then rescan for more expansions. Thus, we use V2 to expand
     the version macros, then CPP will expand the resulting V1() macro
     with the correct numerals. */
  /* ### I'm assuming cpp is portable in this respect... */

#define V1(a,b,c) XML_L(#a)XML_L(".")XML_L(#b)XML_L(".")XML_L(#c)
#define V2(a,b,c) XML_L("expat_")V1(a,b,c)

  return V2(XML_MAJOR_VERSION, XML_MINOR_VERSION, XML_MICRO_VERSION);

#undef V1
#undef V2
}

XML_Expat_Version XMLCALL
XML_ExpatVersionInfo(void)
{
  XML_Expat_Version version;

  version.major = XML_MAJOR_VERSION;
  version.minor = XML_MINOR_VERSION;
  version.micro = XML_MICRO_VERSION;

  return version;
}

const XML_Feature * XMLCALL
XML_GetFeatureList(void)
{
  static const XML_Feature features[] = {
    {XML_FEATURE_SIZEOF_XML_CHAR,  XML_L("sizeof(XML_Char)"),
     sizeof(XML_Char)},
    {XML_FEATURE_SIZEOF_XML_LCHAR, XML_L("sizeof(XML_LChar)"),
     sizeof(XML_LChar)},
#ifdef XML_UNICODE
    {XML_FEATURE_UNICODE,          XML_L("XML_UNICODE"), 0},
#endif
#ifdef XML_UNICODE_WCHAR_T
    {XML_FEATURE_UNICODE_WCHAR_T,  XML_L("XML_UNICODE_WCHAR_T"), 0},
#endif
#ifdef XML_DTD
    {XML_FEATURE_DTD,              XML_L("XML_DTD"), 0},
#endif
#ifdef XML_CONTEXT_BYTES
    {XML_FEATURE_CONTEXT_BYTES,    XML_L("XML_CONTEXT_BYTES"),
     XML_CONTEXT_BYTES},
#endif
#ifdef XML_MIN_SIZE
    {XML_FEATURE_MIN_SIZE,         XML_L("XML_MIN_SIZE"), 0},
#endif
#ifdef XML_NS
    {XML_FEATURE_NS,               XML_L("XML_NS"), 0},
#endif
#ifdef XML_LARGE_SIZE
    {XML_FEATURE_LARGE_SIZE,       XML_L("XML_LARGE_SIZE"), 0},
#endif    
    {XML_FEATURE_END,              NULL, 0}
  };

  return features;
}

/* Initially tag->rawName always points into the parse buffer;
   for those TAG instances opened while the current parse buffer was
   processed, and not yet closed, we need to store tag->rawName in a more
   permanent location, since the parse buffer is about to be discarded.
*/
static XML_Bool
storeRawNames(XML_Parser parser)
{
  TAG *tag = tagStack;
  while (tag) {
    int bufSize;
    int nameLen = sizeof(XML_Char) * (tag->name.strLen + 1);
    char *rawNameBuf = tag->buf + nameLen;
    /* Stop if already stored.  Since tagStack is a stack, we can stop
       at the first entry that has already been copied; everything
       below it in the stack is already been accounted for in a
       previous call to this function.
    */
    if (tag->rawName == rawNameBuf)
      break;
    /* For re-use purposes we need to ensure that the
       size of tag->buf is a multiple of sizeof(XML_Char).
    */
    bufSize = nameLen + ROUND_UP(tag->rawNameLength, sizeof(XML_Char));
    if (bufSize > tag->bufEnd - tag->buf) {
      char *temp = (char *)REALLOC(tag->buf, bufSize);
      if (temp == NULL)
        return XML_FALSE;
      /* if tag->name.str points to tag->buf (only when namespace
         processing is off) then we have to update it
      */
      if (tag->name.str == (XML_Char *)tag->buf)
        tag->name.str = (XML_Char *)temp;
      /* if tag->name.localPart is set (when namespace processing is on)
         then update it as well, since it will always point into tag->buf
      */
      if (tag->name.localPart)
        tag->name.localPart = (XML_Char *)temp + (tag->name.localPart -
                                                  (XML_Char *)tag->buf);
      tag->buf = temp;
      tag->bufEnd = temp + bufSize;
      rawNameBuf = temp + nameLen;
    }
    memcpy(rawNameBuf, tag->rawName, tag->rawNameLength);
    tag->rawName = rawNameBuf;
    tag = tag->parent;
  }
  return XML_TRUE;
}

static enum XML_Error PTRCALL
contentProcessor(XML_Parser parser,
                 const char *start,
                 const char *end,
                 const char **endPtr)
{
  enum XML_Error result = doContent(parser, 0, encoding, start, end, 
                                    endPtr, (XML_Bool)!ps_finalBuffer);
  if (result == XML_ERROR_NONE) {
    if (!storeRawNames(parser))
      return XML_ERROR_NO_MEMORY;
  }
  return result;
}

static enum XML_Error PTRCALL
externalEntityInitProcessor(XML_Parser parser,
                            const char *start,
                            const char *end,
                            const char **endPtr)
{
  enum XML_Error result = initializeEncoding(parser);
  if (result != XML_ERROR_NONE)
    return result;
  processor = externalEntityInitProcessor2;
  return externalEntityInitProcessor2(parser, start, end, endPtr);
}

static enum XML_Error PTRCALL
externalEntityInitProcessor2(XML_Parser parser,
                             const char *start,
                             const char *end,
                             const char **endPtr)
{
  const char *next = start; /* XmlContentTok doesn't always set the last arg */
  int tok = XmlContentTok(encoding, start, end, &next);
  switch (tok) {
  case XML_TOK_BOM:
    /* If we are at the end of the buffer, this would cause the next stage,
       i.e. externalEntityInitProcessor3, to pass control directly to
       doContent (by detecting XML_TOK_NONE) without processing any xml text
       declaration - causing the error XML_ERROR_MISPLACED_XML_PI in doContent.
    */
    if (next == end && !ps_finalBuffer) {
      *endPtr = next;
      return XML_ERROR_NONE;
    }
    start = next;
    break;
  case XML_TOK_PARTIAL:
    if (!ps_finalBuffer) {
      *endPtr = start;
      return XML_ERROR_NONE;
    }
    eventPtr = start;
    return XML_ERROR_UNCLOSED_TOKEN;
  case XML_TOK_PARTIAL_CHAR:
    if (!ps_finalBuffer) {
      *endPtr = start;
      return XML_ERROR_NONE;
    }
    eventPtr = start;
    return XML_ERROR_PARTIAL_CHAR;
  }
  processor = externalEntityInitProcessor3;
  return externalEntityInitProcessor3(parser, start, end, endPtr);
}

static enum XML_Error PTRCALL
externalEntityInitProcessor3(XML_Parser parser,
                             const char *start,
                             const char *end,
                             const char **endPtr)
{
  int tok;
  const char *next = start; /* XmlContentTok doesn't always set the last arg */
  eventPtr = start;
  tok = XmlContentTok(encoding, start, end, &next);
  eventEndPtr = next;

  switch (tok) {
  case XML_TOK_XML_DECL:
    {
      enum XML_Error result;
      result = processXmlDecl(parser, 1, start, next);
      if (result != XML_ERROR_NONE)
        return result;
      switch (ps_parsing) {
      case XML_SUSPENDED: 
        *endPtr = next;
        return XML_ERROR_NONE;
      case XML_FINISHED:
        return XML_ERROR_ABORTED;
      default:
        start = next;
      }
    }
    break;
  case XML_TOK_PARTIAL:
    if (!ps_finalBuffer) {
      *endPtr = start;
      return XML_ERROR_NONE;
    }
    return XML_ERROR_UNCLOSED_TOKEN;
  case XML_TOK_PARTIAL_CHAR:
    if (!ps_finalBuffer) {
      *endPtr = start;
      return XML_ERROR_NONE;
    }
    return XML_ERROR_PARTIAL_CHAR;
  }
  processor = externalEntityContentProcessor;
  tagLevel = 1;
  return externalEntityContentProcessor(parser, start, end, endPtr);
}

static enum XML_Error PTRCALL
externalEntityContentProcessor(XML_Parser parser,
                               const char *start,
                               const char *end,
                               const char **endPtr)
{
  enum XML_Error result = doContent(parser, 1, encoding, start, end, 
                                    endPtr, (XML_Bool)!ps_finalBuffer);
  if (result == XML_ERROR_NONE) {
    if (!storeRawNames(parser))
      return XML_ERROR_NO_MEMORY;
  }
  return result;
}

static enum XML_Error
doContent(XML_Parser parser,
          int startTagLevel,
          const ENCODING *enc,
          const char *s,
          const char *end,
          const char **nextPtr,
          XML_Bool haveMore)
{
  /* save one level of indirection */
  DTD * const dtd = _dtd;  

  const char **eventPP;
  const char **eventEndPP;
  if (enc == encoding) {
    eventPP = &eventPtr;
    eventEndPP = &eventEndPtr;
  }
  else {
    eventPP = &(openInternalEntities->internalEventPtr);
    eventEndPP = &(openInternalEntities->internalEventEndPtr);
  }
  *eventPP = s;

  for (;;) {
    const char *next = s; /* XmlContentTok doesn't always set the last arg */
    int tok = XmlContentTok(enc, s, end, &next);
    *eventEndPP = next;
    switch (tok) {
    case XML_TOK_TRAILING_CR:
      if (haveMore) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      *eventEndPP = end;
      if (characterDataHandler) {
        XML_Char c = 0xA;
        characterDataHandler(handlerArg, &c, 1);
      }
      else if (defaultHandler)
        reportDefault(parser, enc, s, end);
      /* We are at the end of the final buffer, should we check for 
         XML_SUSPENDED, XML_FINISHED? 
      */
      if (startTagLevel == 0)
        return XML_ERROR_NO_ELEMENTS;
      if (tagLevel != startTagLevel)
        return XML_ERROR_ASYNC_ENTITY;
      *nextPtr = end;
      return XML_ERROR_NONE;
    case XML_TOK_NONE:
      if (haveMore) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      if (startTagLevel > 0) {
        if (tagLevel != startTagLevel)
          return XML_ERROR_ASYNC_ENTITY;
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      return XML_ERROR_NO_ELEMENTS;
    case XML_TOK_INVALID:
      *eventPP = next;
      return XML_ERROR_INVALID_TOKEN;
    case XML_TOK_PARTIAL:
      if (haveMore) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      return XML_ERROR_UNCLOSED_TOKEN;
    case XML_TOK_PARTIAL_CHAR:
      if (haveMore) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      return XML_ERROR_PARTIAL_CHAR;
    case XML_TOK_ENTITY_REF:
      {
        const XML_Char *name;
        ENTITY *entity;
        XML_Char ch = (XML_Char) XmlPredefinedEntityName(enc,
                                              s + enc->minBytesPerChar,
                                              next - enc->minBytesPerChar);
        if (ch) {
          if (characterDataHandler)
            characterDataHandler(handlerArg, &ch, 1);
          else if (defaultHandler)
            reportDefault(parser, enc, s, next);
          break;
        }
        name = poolStoreString(&dtd->pool, enc,
                                s + enc->minBytesPerChar,
                                next - enc->minBytesPerChar);
        if (!name)
          return XML_ERROR_NO_MEMORY;
        entity = (ENTITY *)lookup(&dtd->generalEntities, name, 0);
        poolDiscard(&dtd->pool);
        /* First, determine if a check for an existing declaration is needed;
           if yes, check that the entity exists, and that it is internal,
           otherwise call the skipped entity or default handler.
        */
        if (!dtd->hasParamEntityRefs || dtd->standalone) {
          if (!entity)
            return XML_ERROR_UNDEFINED_ENTITY;
          else if (!entity->is_internal)
            return XML_ERROR_ENTITY_DECLARED_IN_PE;
        }
        else if (!entity) {
          if (skippedEntityHandler)
            skippedEntityHandler(handlerArg, name, 0);
          else if (defaultHandler)
            reportDefault(parser, enc, s, next);
          break;
        }
        if (entity->open)
          return XML_ERROR_RECURSIVE_ENTITY_REF;
        if (entity->notation)
          return XML_ERROR_BINARY_ENTITY_REF;
        if (entity->textPtr) {
          enum XML_Error result;
          if (!defaultExpandInternalEntities) {
            if (skippedEntityHandler)
              skippedEntityHandler(handlerArg, entity->name, 0);
            else if (defaultHandler)
              reportDefault(parser, enc, s, next);
            break;
          }
          result = processInternalEntity(parser, entity, XML_FALSE);
          if (result != XML_ERROR_NONE)
            return result;
        }
        else if (externalEntityRefHandler) {
          const XML_Char *context;
          entity->open = XML_TRUE;
          context = getContext(parser);
          entity->open = XML_FALSE;
          if (!context)
            return XML_ERROR_NO_MEMORY;
          if (!externalEntityRefHandler(externalEntityRefHandlerArg,
                                        context,
                                        entity->base,
                                        entity->systemId,
                                        entity->publicId))
            return XML_ERROR_EXTERNAL_ENTITY_HANDLING;
          poolDiscard(&tempPool);
        }
        else if (defaultHandler)
          reportDefault(parser, enc, s, next);
        break;
      }
    case XML_TOK_START_TAG_NO_ATTS:
      /* fall through */
    case XML_TOK_START_TAG_WITH_ATTS:
      {
        TAG *tag;
        enum XML_Error result;
        XML_Char *toPtr;
        if (freeTagList) {
          tag = freeTagList;
          freeTagList = freeTagList->parent;
        }
        else {
          tag = (TAG *)MALLOC(sizeof(TAG));
          if (!tag)
            return XML_ERROR_NO_MEMORY;
          tag->buf = (char *)MALLOC(INIT_TAG_BUF_SIZE);
          if (!tag->buf) {
            FREE(tag);
            return XML_ERROR_NO_MEMORY;
          }
          tag->bufEnd = tag->buf + INIT_TAG_BUF_SIZE;
        }
        tag->bindings = NULL;
        tag->parent = tagStack;
        tagStack = tag;
        tag->name.localPart = NULL;
        tag->name.prefix = NULL;
        tag->rawName = s + enc->minBytesPerChar;
        tag->rawNameLength = XmlNameLength(enc, tag->rawName);
        ++tagLevel;
        {
          const char *rawNameEnd = tag->rawName + tag->rawNameLength;
          const char *fromPtr = tag->rawName;
          toPtr = (XML_Char *)tag->buf;
          for (;;) {
            int bufSize;
            int convLen;
            XmlConvert(enc,
                       &fromPtr, rawNameEnd,
                       (ICHAR **)&toPtr, (ICHAR *)tag->bufEnd - 1);
            convLen = (int)(toPtr - (XML_Char *)tag->buf);
            if (fromPtr == rawNameEnd) {
              tag->name.strLen = convLen;
              break;
            }
            bufSize = (int)(tag->bufEnd - tag->buf) << 1;
            {
              char *temp = (char *)REALLOC(tag->buf, bufSize);
              if (temp == NULL)
                return XML_ERROR_NO_MEMORY;
              tag->buf = temp;
              tag->bufEnd = temp + bufSize;
              toPtr = (XML_Char *)temp + convLen;
            }
          }
        }
        tag->name.str = (XML_Char *)tag->buf;
        *toPtr = XML_T('\0');
        result = storeAtts(parser, enc, s, &(tag->name), &(tag->bindings));
        if (result)
          return result;
        if (startElementHandler)
          startElementHandler(handlerArg, tag->name.str,
                              (const XML_Char **)atts);
        else if (defaultHandler)
          reportDefault(parser, enc, s, next);
        poolClear(&tempPool);
        break;
      }
    case XML_TOK_EMPTY_ELEMENT_NO_ATTS:
      /* fall through */
    case XML_TOK_EMPTY_ELEMENT_WITH_ATTS:
      {
        const char *rawName = s + enc->minBytesPerChar;
        enum XML_Error result;
        BINDING *bindings = NULL;
        XML_Bool noElmHandlers = XML_TRUE;
        TAG_NAME name;
        name.str = poolStoreString(&tempPool, enc, rawName,
                                   rawName + XmlNameLength(enc, rawName));
        if (!name.str)
          return XML_ERROR_NO_MEMORY;
        poolFinish(&tempPool);
        result = storeAtts(parser, enc, s, &name, &bindings);
        if (result)
          return result;
        poolFinish(&tempPool);
        if (startElementHandler) {
          startElementHandler(handlerArg, name.str, (const XML_Char **)atts);
          noElmHandlers = XML_FALSE;
        }
        if (endElementHandler) {
          if (startElementHandler)
            *eventPP = *eventEndPP;
          endElementHandler(handlerArg, name.str);
          noElmHandlers = XML_FALSE;
        }
        if (noElmHandlers && defaultHandler)
          reportDefault(parser, enc, s, next);
        poolClear(&tempPool);
        while (bindings) {
          BINDING *b = bindings;
          if (endNamespaceDeclHandler)
            endNamespaceDeclHandler(handlerArg, b->prefix->name);
          bindings = bindings->nextTagBinding;
          b->nextTagBinding = freeBindingList;
          freeBindingList = b;
          b->prefix->binding = b->prevPrefixBinding;
        }
      }
      if (tagLevel == 0)
        return epilogProcessor(parser, next, end, nextPtr);
      break;
    case XML_TOK_END_TAG:
      if (tagLevel == startTagLevel)
        return XML_ERROR_ASYNC_ENTITY;
      else {
        int len;
        const char *rawName;
        TAG *tag = tagStack;
        tagStack = tag->parent;
        tag->parent = freeTagList;
        freeTagList = tag;
        rawName = s + enc->minBytesPerChar*2;
        len = XmlNameLength(enc, rawName);
        if (len != tag->rawNameLength
            || memcmp(tag->rawName, rawName, len) != 0) {
          *eventPP = rawName;
          return XML_ERROR_TAG_MISMATCH;
        }
        --tagLevel;
        if (endElementHandler) {
          const XML_Char *localPart;
          const XML_Char *prefix;
          XML_Char *uri;
          localPart = tag->name.localPart;
          if (ns && localPart) {
            /* localPart and prefix may have been overwritten in
               tag->name.str, since this points to the binding->uri
               buffer which gets re-used; so we have to add them again
            */
            uri = (XML_Char *)tag->name.str + tag->name.uriLen;
            /* don't need to check for space - already done in storeAtts() */
            while (*localPart) *uri++ = *localPart++;
            prefix = (XML_Char *)tag->name.prefix;
            if (ns_triplets && prefix) {
              *uri++ = namespaceSeparator;
              while (*prefix) *uri++ = *prefix++;
             }
            *uri = XML_T('\0');
          }
          endElementHandler(handlerArg, tag->name.str);
        }
        else if (defaultHandler)
          reportDefault(parser, enc, s, next);
        while (tag->bindings) {
          BINDING *b = tag->bindings;
          if (endNamespaceDeclHandler)
            endNamespaceDeclHandler(handlerArg, b->prefix->name);
          tag->bindings = tag->bindings->nextTagBinding;
          b->nextTagBinding = freeBindingList;
          freeBindingList = b;
          b->prefix->binding = b->prevPrefixBinding;
        }
        if (tagLevel == 0)
          return epilogProcessor(parser, next, end, nextPtr);
      }
      break;
    case XML_TOK_CHAR_REF:
      {
        int n = XmlCharRefNumber(enc, s);
        if (n < 0)
          return XML_ERROR_BAD_CHAR_REF;
        if (characterDataHandler) {
          XML_Char buf[XML_ENCODE_MAX];
          characterDataHandler(handlerArg, buf, XmlEncode(n, (ICHAR *)buf));
        }
        else if (defaultHandler)
          reportDefault(parser, enc, s, next);
      }
      break;
    case XML_TOK_XML_DECL:
      return XML_ERROR_MISPLACED_XML_PI;
    case XML_TOK_DATA_NEWLINE:
      if (characterDataHandler) {
        XML_Char c = 0xA;
        characterDataHandler(handlerArg, &c, 1);
      }
      else if (defaultHandler)
        reportDefault(parser, enc, s, next);
      break;
    case XML_TOK_CDATA_SECT_OPEN:
      {
        enum XML_Error result;
        if (startCdataSectionHandler)
          startCdataSectionHandler(handlerArg);
#if 0
        /* Suppose you doing a transformation on a document that involves
           changing only the character data.  You set up a defaultHandler
           and a characterDataHandler.  The defaultHandler simply copies
           characters through.  The characterDataHandler does the
           transformation and writes the characters out escaping them as
           necessary.  This case will fail to work if we leave out the
           following two lines (because & and < inside CDATA sections will
           be incorrectly escaped).

           However, now we have a start/endCdataSectionHandler, so it seems
           easier to let the user deal with this.
        */
        else if (characterDataHandler)
          characterDataHandler(handlerArg, dataBuf, 0);
#endif
        else if (defaultHandler)
          reportDefault(parser, enc, s, next);
        result = doCdataSection(parser, enc, &next, end, nextPtr, haveMore);
        if (result != XML_ERROR_NONE)
          return result;
        else if (!next) {
          processor = cdataSectionProcessor;
          return result;
        }
      }
      break;
    case XML_TOK_TRAILING_RSQB:
      if (haveMore) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      if (characterDataHandler) {
        if (MUST_CONVERT(enc, s)) {
          ICHAR *dataPtr = (ICHAR *)dataBuf;
          XmlConvert(enc, &s, end, &dataPtr, (ICHAR *)dataBufEnd);
          characterDataHandler(handlerArg, dataBuf,
                               (int)(dataPtr - (ICHAR *)dataBuf));
        }
        else
          characterDataHandler(handlerArg,
                               (XML_Char *)s,
                               (int)((XML_Char *)end - (XML_Char *)s));
      }
      else if (defaultHandler)
        reportDefault(parser, enc, s, end);
      /* We are at the end of the final buffer, should we check for 
         XML_SUSPENDED, XML_FINISHED? 
      */
      if (startTagLevel == 0) {
        *eventPP = end;
        return XML_ERROR_NO_ELEMENTS;
      }
      if (tagLevel != startTagLevel) {
        *eventPP = end;
        return XML_ERROR_ASYNC_ENTITY;
      }
      *nextPtr = end;
      return XML_ERROR_NONE;
    case XML_TOK_DATA_CHARS: 
      {
        XML_CharacterDataHandler charDataHandler = characterDataHandler;
        if (charDataHandler) {
          if (MUST_CONVERT(enc, s)) {
            for (;;) {
              ICHAR *dataPtr = (ICHAR *)dataBuf;
              XmlConvert(enc, &s, next, &dataPtr, (ICHAR *)dataBufEnd);
              *eventEndPP = s;
              charDataHandler(handlerArg, dataBuf,
                              (int)(dataPtr - (ICHAR *)dataBuf));
              if (s == next)
                break;
              *eventPP = s;
            }
          }
          else
            charDataHandler(handlerArg,
                            (XML_Char *)s,
                            (int)((XML_Char *)next - (XML_Char *)s));
        }
        else if (defaultHandler)
          reportDefault(parser, enc, s, next);
      }
      break;
    case XML_TOK_PI:
      if (!reportProcessingInstruction(parser, enc, s, next))
        return XML_ERROR_NO_MEMORY;
      break;
    case XML_TOK_COMMENT:
      if (!reportComment(parser, enc, s, next))
        return XML_ERROR_NO_MEMORY;
      break;
    default:
      if (defaultHandler)
        reportDefault(parser, enc, s, next);
      break;
    }
    *eventPP = s = next;
    switch (ps_parsing) {
    case XML_SUSPENDED: 
      *nextPtr = next;
      return XML_ERROR_NONE;
    case XML_FINISHED:
      return XML_ERROR_ABORTED;
    default: ;
    }
  }
  /* not reached */
}

/* Precondition: all arguments must be non-NULL;
   Purpose:
   - normalize attributes
   - check attributes for well-formedness
   - generate namespace aware attribute names (URI, prefix)
   - build list of attributes for startElementHandler
   - default attributes
   - process namespace declarations (check and report them)
   - generate namespace aware element name (URI, prefix)
*/
static enum XML_Error
storeAtts(XML_Parser parser, const ENCODING *enc,
          const char *attStr, TAG_NAME *tagNamePtr,
          BINDING **bindingsPtr)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  ELEMENT_TYPE *elementType;
  int nDefaultAtts;
  const XML_Char **appAtts;   /* the attribute list for the application */
  int attIndex = 0;
  int prefixLen;
  int i;
  int n;
  XML_Char *uri;
  int nPrefixes = 0;
  BINDING *binding;
  const XML_Char *localPart;

  /* lookup the element type name */
  elementType = (ELEMENT_TYPE *)lookup(&dtd->elementTypes, tagNamePtr->str,0);
  if (!elementType) {
    const XML_Char *name = poolCopyString(&dtd->pool, tagNamePtr->str);
    if (!name)
      return XML_ERROR_NO_MEMORY;
    elementType = (ELEMENT_TYPE *)lookup(&dtd->elementTypes, name,
                                         sizeof(ELEMENT_TYPE));
    if (!elementType)
      return XML_ERROR_NO_MEMORY;
    if (ns && !setElementTypePrefix(parser, elementType))
      return XML_ERROR_NO_MEMORY;
  }
  nDefaultAtts = elementType->nDefaultAtts;

  /* get the attributes from the tokenizer */
  n = XmlGetAttributes(enc, attStr, attsSize, atts);
  if (n + nDefaultAtts > attsSize) {
    int oldAttsSize = attsSize;
    ATTRIBUTE *temp;
    attsSize = n + nDefaultAtts + INIT_ATTS_SIZE;
    temp = (ATTRIBUTE *)REALLOC((void *)atts, attsSize * sizeof(ATTRIBUTE));
    if (temp == NULL)
      return XML_ERROR_NO_MEMORY;
    atts = temp;
    if (n > oldAttsSize)
      XmlGetAttributes(enc, attStr, n, atts);
  }

  appAtts = (const XML_Char **)atts;
  for (i = 0; i < n; i++) {
    /* add the name and value to the attribute list */
    ATTRIBUTE_ID *attId = getAttributeId(parser, enc, atts[i].name,
                                         atts[i].name
                                         + XmlNameLength(enc, atts[i].name));
    if (!attId)
      return XML_ERROR_NO_MEMORY;
    /* Detect duplicate attributes by their QNames. This does not work when
       namespace processing is turned on and different prefixes for the same
       namespace are used. For this case we have a check further down.
    */
    if ((attId->name)[-1]) {
      if (enc == encoding)
        eventPtr = atts[i].name;
      return XML_ERROR_DUPLICATE_ATTRIBUTE;
    }
    (attId->name)[-1] = 1;
    appAtts[attIndex++] = attId->name;
    if (!atts[i].normalized) {
      enum XML_Error result;
      XML_Bool isCdata = XML_TRUE;

      /* figure out whether declared as other than CDATA */
      if (attId->maybeTokenized) {
        int j;
        for (j = 0; j < nDefaultAtts; j++) {
          if (attId == elementType->defaultAtts[j].id) {
            isCdata = elementType->defaultAtts[j].isCdata;
            break;
          }
        }
      }

      /* normalize the attribute value */
      result = storeAttributeValue(parser, enc, isCdata,
                                   atts[i].valuePtr, atts[i].valueEnd,
                                   &tempPool);
      if (result)
        return result;
      appAtts[attIndex] = poolStart(&tempPool);
      poolFinish(&tempPool);
    }
    else {
      /* the value did not need normalizing */
      appAtts[attIndex] = poolStoreString(&tempPool, enc, atts[i].valuePtr,
                                          atts[i].valueEnd);
      if (appAtts[attIndex] == 0)
        return XML_ERROR_NO_MEMORY;
      poolFinish(&tempPool);
    }
    /* handle prefixed attribute names */
    if (attId->prefix) {
      if (attId->xmlns) {
        /* deal with namespace declarations here */
        enum XML_Error result = addBinding(parser, attId->prefix, attId,
                                           appAtts[attIndex], bindingsPtr);
        if (result)
          return result;
        --attIndex;
      }
      else {
        /* deal with other prefixed names later */
        attIndex++;
        nPrefixes++;
        (attId->name)[-1] = 2;
      }
    }
    else
      attIndex++;
  }

  /* set-up for XML_GetSpecifiedAttributeCount and XML_GetIdAttributeIndex */
  nSpecifiedAtts = attIndex;
  if (elementType->idAtt && (elementType->idAtt->name)[-1]) {
    for (i = 0; i < attIndex; i += 2)
      if (appAtts[i] == elementType->idAtt->name) {
        idAttIndex = i;
        break;
      }
  }
  else
    idAttIndex = -1;

  /* do attribute defaulting */
  for (i = 0; i < nDefaultAtts; i++) {
    const DEFAULT_ATTRIBUTE *da = elementType->defaultAtts + i;
    if (!(da->id->name)[-1] && da->value) {
      if (da->id->prefix) {
        if (da->id->xmlns) {
          enum XML_Error result = addBinding(parser, da->id->prefix, da->id,
                                             da->value, bindingsPtr);
          if (result)
            return result;
        }
        else {
          (da->id->name)[-1] = 2;
          nPrefixes++;
          appAtts[attIndex++] = da->id->name;
          appAtts[attIndex++] = da->value;
        }
      }
      else {
        (da->id->name)[-1] = 1;
        appAtts[attIndex++] = da->id->name;
        appAtts[attIndex++] = da->value;
      }
    }
  }
  appAtts[attIndex] = 0;

  /* expand prefixed attribute names, check for duplicates,
     and clear flags that say whether attributes were specified */
  i = 0;
  if (nPrefixes) {
    int j;  /* hash table index */
    unsigned long version = nsAttsVersion;
    int nsAttsSize = (int)1 << nsAttsPower;
    /* size of hash table must be at least 2 * (# of prefixed attributes) */
    if ((nPrefixes << 1) >> nsAttsPower) {  /* true for nsAttsPower = 0 */
      NS_ATT *temp;
      /* hash table size must also be a power of 2 and >= 8 */
      while (nPrefixes >> nsAttsPower++);
      if (nsAttsPower < 3)
        nsAttsPower = 3;
      nsAttsSize = (int)1 << nsAttsPower;
      temp = (NS_ATT *)REALLOC(nsAtts, nsAttsSize * sizeof(NS_ATT));
      if (!temp)
        return XML_ERROR_NO_MEMORY;
      nsAtts = temp;
      version = 0;  /* force re-initialization of nsAtts hash table */
    }
    /* using a version flag saves us from initializing nsAtts every time */
    if (!version) {  /* initialize version flags when version wraps around */
      version = INIT_ATTS_VERSION;
      for (j = nsAttsSize; j != 0; )
        nsAtts[--j].version = version;
    }
    nsAttsVersion = --version;

    /* expand prefixed names and check for duplicates */
    for (; i < attIndex; i += 2) {
      const XML_Char *s = appAtts[i];
      if (s[-1] == 2) {  /* prefixed */
        ATTRIBUTE_ID *id;
        const BINDING *b;
        unsigned long uriHash = 0;
        ((XML_Char *)s)[-1] = 0;  /* clear flag */
        id = (ATTRIBUTE_ID *)lookup(&dtd->attributeIds, s, 0);
        b = id->prefix->binding;
        if (!b)
          return XML_ERROR_UNBOUND_PREFIX;

        /* as we expand the name we also calculate its hash value */
        for (j = 0; j < b->uriLen; j++) {
          const XML_Char c = b->uri[j];
          if (!poolAppendChar(&tempPool, c))
            return XML_ERROR_NO_MEMORY;
          uriHash = CHAR_HASH(uriHash, c);
        }
        while (*s++ != XML_T(ASCII_COLON))
          ;
        do {  /* copies null terminator */
          const XML_Char c = *s;
          if (!poolAppendChar(&tempPool, *s))
            return XML_ERROR_NO_MEMORY;
          uriHash = CHAR_HASH(uriHash, c);
        } while (*s++);

        { /* Check hash table for duplicate of expanded name (uriName).
             Derived from code in lookup(HASH_TABLE *table, ...).
          */
          unsigned char step = 0;
          unsigned long mask = nsAttsSize - 1;
          j = uriHash & mask;  /* index into hash table */
          while (nsAtts[j].version == version) {
            /* for speed we compare stored hash values first */
            if (uriHash == nsAtts[j].hash) {
              const XML_Char *s1 = poolStart(&tempPool);
              const XML_Char *s2 = nsAtts[j].uriName;
              /* s1 is null terminated, but not s2 */
              for (; *s1 == *s2 && *s1 != 0; s1++, s2++);
              if (*s1 == 0)
                return XML_ERROR_DUPLICATE_ATTRIBUTE;
            }
            if (!step)
              step = PROBE_STEP(uriHash, mask, nsAttsPower);
            j < step ? (j += nsAttsSize - step) : (j -= step);
          }
        }

        if (ns_triplets) {  /* append namespace separator and prefix */
          tempPool.ptr[-1] = namespaceSeparator;
          s = b->prefix->name;
          do {
            if (!poolAppendChar(&tempPool, *s))
              return XML_ERROR_NO_MEMORY;
          } while (*s++);
        }

        /* store expanded name in attribute list */
        s = poolStart(&tempPool);
        poolFinish(&tempPool);
        appAtts[i] = s;

        /* fill empty slot with new version, uriName and hash value */
        nsAtts[j].version = version;
        nsAtts[j].hash = uriHash;
        nsAtts[j].uriName = s;

        if (!--nPrefixes) {
          i += 2;
          break;
        }
      }
      else  /* not prefixed */
        ((XML_Char *)s)[-1] = 0;  /* clear flag */
    }
  }
  /* clear flags for the remaining attributes */
  for (; i < attIndex; i += 2)
    ((XML_Char *)(appAtts[i]))[-1] = 0;
  for (binding = *bindingsPtr; binding; binding = binding->nextTagBinding)
    binding->attId->name[-1] = 0;

  if (!ns)
    return XML_ERROR_NONE;

  /* expand the element type name */
  if (elementType->prefix) {
    binding = elementType->prefix->binding;
    if (!binding)
      return XML_ERROR_UNBOUND_PREFIX;
    localPart = tagNamePtr->str;
    while (*localPart++ != XML_T(ASCII_COLON))
      ;
  }
  else if (dtd->defaultPrefix.binding) {
    binding = dtd->defaultPrefix.binding;
    localPart = tagNamePtr->str;
  }
  else
    return XML_ERROR_NONE;
  prefixLen = 0;
  if (ns_triplets && binding->prefix->name) {
    for (; binding->prefix->name[prefixLen++];)
      ;  /* prefixLen includes null terminator */
  }
  tagNamePtr->localPart = localPart;
  tagNamePtr->uriLen = binding->uriLen;
  tagNamePtr->prefix = binding->prefix->name;
  tagNamePtr->prefixLen = prefixLen;
  for (i = 0; localPart[i++];)
    ;  /* i includes null terminator */
  n = i + binding->uriLen + prefixLen;
  if (n > binding->uriAlloc) {
    TAG *p;
    uri = (XML_Char *)MALLOC((n + EXPAND_SPARE) * sizeof(XML_Char));
    if (!uri)
      return XML_ERROR_NO_MEMORY;
    binding->uriAlloc = n + EXPAND_SPARE;
    memcpy(uri, binding->uri, binding->uriLen * sizeof(XML_Char));
    for (p = tagStack; p; p = p->parent)
      if (p->name.str == binding->uri)
        p->name.str = uri;
    FREE(binding->uri);
    binding->uri = uri;
  }
  /* if namespaceSeparator != '\0' then uri includes it already */
  uri = binding->uri + binding->uriLen;
  memcpy(uri, localPart, i * sizeof(XML_Char));
  /* we always have a namespace separator between localPart and prefix */
  if (prefixLen) {
    uri += i - 1;
    *uri = namespaceSeparator;  /* replace null terminator */
    memcpy(uri + 1, binding->prefix->name, prefixLen * sizeof(XML_Char));
  }
  tagNamePtr->str = binding->uri;
  return XML_ERROR_NONE;
}

/* addBinding() overwrites the value of prefix->binding without checking.
   Therefore one must keep track of the old value outside of addBinding().
*/
static enum XML_Error
addBinding(XML_Parser parser, PREFIX *prefix, const ATTRIBUTE_ID *attId,
           const XML_Char *uri, BINDING **bindingsPtr)
{
  static const XML_Char xmlNamespace[] = {
    ASCII_h, ASCII_t, ASCII_t, ASCII_p, ASCII_COLON, ASCII_SLASH, ASCII_SLASH,
    ASCII_w, ASCII_w, ASCII_w, ASCII_PERIOD, ASCII_w, ASCII_3, ASCII_PERIOD,
    ASCII_o, ASCII_r, ASCII_g, ASCII_SLASH, ASCII_X, ASCII_M, ASCII_L, 
    ASCII_SLASH, ASCII_1, ASCII_9, ASCII_9, ASCII_8, ASCII_SLASH,
    ASCII_n, ASCII_a, ASCII_m, ASCII_e, ASCII_s, ASCII_p, ASCII_a, ASCII_c,
    ASCII_e, '\0'
  };
  static const int xmlLen = 
    (int)sizeof(xmlNamespace)/sizeof(XML_Char) - 1;
  static const XML_Char xmlnsNamespace[] = {
    ASCII_h, ASCII_t, ASCII_t, ASCII_p, ASCII_COLON, ASCII_SLASH, ASCII_SLASH,
    ASCII_w, ASCII_w, ASCII_w, ASCII_PERIOD, ASCII_w, ASCII_3, ASCII_PERIOD,
    ASCII_o, ASCII_r, ASCII_g, ASCII_SLASH, ASCII_2, ASCII_0, ASCII_0, 
    ASCII_0, ASCII_SLASH, ASCII_x, ASCII_m, ASCII_l, ASCII_n, ASCII_s, 
    ASCII_SLASH, '\0'
  };
  static const int xmlnsLen = 
    (int)sizeof(xmlnsNamespace)/sizeof(XML_Char) - 1;

  XML_Bool mustBeXML = XML_FALSE;
  XML_Bool isXML = XML_TRUE;
  XML_Bool isXMLNS = XML_TRUE;
  
  BINDING *b;
  int len;

  /* empty URI is only valid for default namespace per XML NS 1.0 (not 1.1) */
  if (*uri == XML_T('\0') && prefix->name)
    return XML_ERROR_UNDECLARING_PREFIX;

  if (prefix->name
      && prefix->name[0] == XML_T(ASCII_x)
      && prefix->name[1] == XML_T(ASCII_m)
      && prefix->name[2] == XML_T(ASCII_l)) {

    /* Not allowed to bind xmlns */
    if (prefix->name[3] == XML_T(ASCII_n)
        && prefix->name[4] == XML_T(ASCII_s)
        && prefix->name[5] == XML_T('\0'))
      return XML_ERROR_RESERVED_PREFIX_XMLNS;

    if (prefix->name[3] == XML_T('\0'))
      mustBeXML = XML_TRUE;
  }

  for (len = 0; uri[len]; len++) {
    if (isXML && (len > xmlLen || uri[len] != xmlNamespace[len]))
      isXML = XML_FALSE;

    if (!mustBeXML && isXMLNS 
        && (len > xmlnsLen || uri[len] != xmlnsNamespace[len]))
      isXMLNS = XML_FALSE;
  }
  isXML = isXML && len == xmlLen;
  isXMLNS = isXMLNS && len == xmlnsLen;

  if (mustBeXML != isXML)
    return mustBeXML ? XML_ERROR_RESERVED_PREFIX_XML
                     : XML_ERROR_RESERVED_NAMESPACE_URI;

  if (isXMLNS)
    return XML_ERROR_RESERVED_NAMESPACE_URI;

  if (namespaceSeparator)
    len++;
  if (freeBindingList) {
    b = freeBindingList;
    if (len > b->uriAlloc) {
      XML_Char *temp = (XML_Char *)REALLOC(b->uri,
                          sizeof(XML_Char) * (len + EXPAND_SPARE));
      if (temp == NULL)
        return XML_ERROR_NO_MEMORY;
      b->uri = temp;
      b->uriAlloc = len + EXPAND_SPARE;
    }
    freeBindingList = b->nextTagBinding;
  }
  else {
    b = (BINDING *)MALLOC(sizeof(BINDING));
    if (!b)
      return XML_ERROR_NO_MEMORY;
    b->uri = (XML_Char *)MALLOC(sizeof(XML_Char) * (len + EXPAND_SPARE));
    if (!b->uri) {
      FREE(b);
      return XML_ERROR_NO_MEMORY;
    }
    b->uriAlloc = len + EXPAND_SPARE;
  }
  b->uriLen = len;
  memcpy(b->uri, uri, len * sizeof(XML_Char));
  if (namespaceSeparator)
    b->uri[len - 1] = namespaceSeparator;
  b->prefix = prefix;
  b->attId = attId;
  b->prevPrefixBinding = prefix->binding;
  /* NULL binding when default namespace undeclared */
  if (*uri == XML_T('\0') && prefix == &_dtd->defaultPrefix)
    prefix->binding = NULL;
  else
    prefix->binding = b;
  b->nextTagBinding = *bindingsPtr;
  *bindingsPtr = b;
  /* if attId == NULL then we are not starting a namespace scope */
  if (attId && startNamespaceDeclHandler)
    startNamespaceDeclHandler(handlerArg, prefix->name,
                              prefix->binding ? uri : 0);
  return XML_ERROR_NONE;
}

/* The idea here is to avoid using stack for each CDATA section when
   the whole file is parsed with one call.
*/
static enum XML_Error PTRCALL
cdataSectionProcessor(XML_Parser parser,
                      const char *start,
                      const char *end,
                      const char **endPtr)
{
  enum XML_Error result = doCdataSection(parser, encoding, &start, end,
                                         endPtr, (XML_Bool)!ps_finalBuffer);
  if (result != XML_ERROR_NONE)
    return result;
  if (start) {
    if (parentParser) {  /* we are parsing an external entity */
      processor = externalEntityContentProcessor;
      return externalEntityContentProcessor(parser, start, end, endPtr);
    }
    else {
      processor = contentProcessor;
      return contentProcessor(parser, start, end, endPtr);
    }
  }
  return result;
}

/* startPtr gets set to non-null if the section is closed, and to null if
   the section is not yet closed.
*/
static enum XML_Error
doCdataSection(XML_Parser parser,
               const ENCODING *enc,
               const char **startPtr,
               const char *end,
               const char **nextPtr,
               XML_Bool haveMore)
{
  const char *s = *startPtr;
  const char **eventPP;
  const char **eventEndPP;
  if (enc == encoding) {
    eventPP = &eventPtr;
    *eventPP = s;
    eventEndPP = &eventEndPtr;
  }
  else {
    eventPP = &(openInternalEntities->internalEventPtr);
    eventEndPP = &(openInternalEntities->internalEventEndPtr);
  }
  *eventPP = s;
  *startPtr = NULL;

  for (;;) {
    const char *next;
    int tok = XmlCdataSectionTok(enc, s, end, &next);
    *eventEndPP = next;
    switch (tok) {
    case XML_TOK_CDATA_SECT_CLOSE:
      if (endCdataSectionHandler)
        endCdataSectionHandler(handlerArg);
#if 0
      /* see comment under XML_TOK_CDATA_SECT_OPEN */
      else if (characterDataHandler)
        characterDataHandler(handlerArg, dataBuf, 0);
#endif
      else if (defaultHandler)
        reportDefault(parser, enc, s, next);
      *startPtr = next;
      *nextPtr = next;
      if (ps_parsing == XML_FINISHED)
        return XML_ERROR_ABORTED;
      else
        return XML_ERROR_NONE;
    case XML_TOK_DATA_NEWLINE:
      if (characterDataHandler) {
        XML_Char c = 0xA;
        characterDataHandler(handlerArg, &c, 1);
      }
      else if (defaultHandler)
        reportDefault(parser, enc, s, next);
      break;
    case XML_TOK_DATA_CHARS:
      {
        XML_CharacterDataHandler charDataHandler = characterDataHandler;
        if (charDataHandler) {
          if (MUST_CONVERT(enc, s)) {
            for (;;) {
              ICHAR *dataPtr = (ICHAR *)dataBuf;
              XmlConvert(enc, &s, next, &dataPtr, (ICHAR *)dataBufEnd);
              *eventEndPP = next;
              charDataHandler(handlerArg, dataBuf,
                              (int)(dataPtr - (ICHAR *)dataBuf));
              if (s == next)
                break;
              *eventPP = s;
            }
          }
          else
            charDataHandler(handlerArg,
                            (XML_Char *)s,
                            (int)((XML_Char *)next - (XML_Char *)s));
        }
        else if (defaultHandler)
          reportDefault(parser, enc, s, next);
      }
      break;
    case XML_TOK_INVALID:
      *eventPP = next;
      return XML_ERROR_INVALID_TOKEN;
    case XML_TOK_PARTIAL_CHAR:
      if (haveMore) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      return XML_ERROR_PARTIAL_CHAR;
    case XML_TOK_PARTIAL:
    case XML_TOK_NONE:
      if (haveMore) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      return XML_ERROR_UNCLOSED_CDATA_SECTION;
    default:
      *eventPP = next;
      return XML_ERROR_UNEXPECTED_STATE;
    }

    *eventPP = s = next;
    switch (ps_parsing) {
    case XML_SUSPENDED:
      *nextPtr = next;
      return XML_ERROR_NONE;
    case XML_FINISHED:
      return XML_ERROR_ABORTED;
    default: ;
    }
  }
  /* not reached */
}

#ifdef XML_DTD

/* The idea here is to avoid using stack for each IGNORE section when
   the whole file is parsed with one call.
*/
static enum XML_Error PTRCALL
ignoreSectionProcessor(XML_Parser parser,
                       const char *start,
                       const char *end,
                       const char **endPtr)
{
  enum XML_Error result = doIgnoreSection(parser, encoding, &start, end, 
                                          endPtr, (XML_Bool)!ps_finalBuffer);
  if (result != XML_ERROR_NONE)
    return result;
  if (start) {
    processor = prologProcessor;
    return prologProcessor(parser, start, end, endPtr);
  }
  return result;
}

/* startPtr gets set to non-null is the section is closed, and to null
   if the section is not yet closed.
*/
static enum XML_Error
doIgnoreSection(XML_Parser parser,
                const ENCODING *enc,
                const char **startPtr,
                const char *end,
                const char **nextPtr,
                XML_Bool haveMore)
{
  const char *next;
  int tok;
  const char *s = *startPtr;
  const char **eventPP;
  const char **eventEndPP;
  if (enc == encoding) {
    eventPP = &eventPtr;
    *eventPP = s;
    eventEndPP = &eventEndPtr;
  }
  else {
    eventPP = &(openInternalEntities->internalEventPtr);
    eventEndPP = &(openInternalEntities->internalEventEndPtr);
  }
  *eventPP = s;
  *startPtr = NULL;
  tok = XmlIgnoreSectionTok(enc, s, end, &next);
  *eventEndPP = next;
  switch (tok) {
  case XML_TOK_IGNORE_SECT:
    if (defaultHandler)
      reportDefault(parser, enc, s, next);
    *startPtr = next;
    *nextPtr = next;
    if (ps_parsing == XML_FINISHED)
      return XML_ERROR_ABORTED;
    else
      return XML_ERROR_NONE;
  case XML_TOK_INVALID:
    *eventPP = next;
    return XML_ERROR_INVALID_TOKEN;
  case XML_TOK_PARTIAL_CHAR:
    if (haveMore) {
      *nextPtr = s;
      return XML_ERROR_NONE;
    }
    return XML_ERROR_PARTIAL_CHAR;
  case XML_TOK_PARTIAL:
  case XML_TOK_NONE:
    if (haveMore) {
      *nextPtr = s;
      return XML_ERROR_NONE;
    }
    return XML_ERROR_SYNTAX; /* XML_ERROR_UNCLOSED_IGNORE_SECTION */
  default:
    *eventPP = next;
    return XML_ERROR_UNEXPECTED_STATE;
  }
  /* not reached */
}

#endif /* XML_DTD */

static enum XML_Error
initializeEncoding(XML_Parser parser)
{
  const char *s;
#ifdef XML_UNICODE
  char encodingBuf[128];
  if (!protocolEncodingName)
    s = NULL;
  else {
    int i;
    for (i = 0; protocolEncodingName[i]; i++) {
      if (i == sizeof(encodingBuf) - 1
          || (protocolEncodingName[i] & ~0x7f) != 0) {
        encodingBuf[0] = '\0';
        break;
      }
      encodingBuf[i] = (char)protocolEncodingName[i];
    }
    encodingBuf[i] = '\0';
    s = encodingBuf;
  }
#else
  s = protocolEncodingName;
#endif
  if ((ns ? XmlInitEncodingNS : XmlInitEncoding)(&initEncoding, &encoding, s))
    return XML_ERROR_NONE;
  return handleUnknownEncoding(parser, protocolEncodingName);
}

static enum XML_Error
processXmlDecl(XML_Parser parser, int isGeneralTextEntity,
               const char *s, const char *next)
{
  const char *encodingName = NULL;
  const XML_Char *storedEncName = NULL;
  const ENCODING *newEncoding = NULL;
  const char *version = NULL;
  const char *versionend;
  const XML_Char *storedversion = NULL;
  int standalone = -1;
  if (!(ns
        ? XmlParseXmlDeclNS
        : XmlParseXmlDecl)(isGeneralTextEntity,
                           encoding,
                           s,
                           next,
                           &eventPtr,
                           &version,
                           &versionend,
                           &encodingName,
                           &newEncoding,
                           &standalone)) {
    if (isGeneralTextEntity)
      return XML_ERROR_TEXT_DECL;
    else
      return XML_ERROR_XML_DECL;
  }
  if (!isGeneralTextEntity && standalone == 1) {
    _dtd->standalone = XML_TRUE;
#ifdef XML_DTD
    if (paramEntityParsing == XML_PARAM_ENTITY_PARSING_UNLESS_STANDALONE)
      paramEntityParsing = XML_PARAM_ENTITY_PARSING_NEVER;
#endif /* XML_DTD */
  }
  if (xmlDeclHandler) {
    if (encodingName != NULL) {
      storedEncName = poolStoreString(&temp2Pool,
                                      encoding,
                                      encodingName,
                                      encodingName
                                      + XmlNameLength(encoding, encodingName));
      if (!storedEncName)
              return XML_ERROR_NO_MEMORY;
      poolFinish(&temp2Pool);
    }
    if (version) {
      storedversion = poolStoreString(&temp2Pool,
                                      encoding,
                                      version,
                                      versionend - encoding->minBytesPerChar);
      if (!storedversion)
        return XML_ERROR_NO_MEMORY;
    }
    xmlDeclHandler(handlerArg, storedversion, storedEncName, standalone);
  }
  else if (defaultHandler)
    reportDefault(parser, encoding, s, next);
  if (protocolEncodingName == NULL) {
    if (newEncoding) {
      if (newEncoding->minBytesPerChar != encoding->minBytesPerChar) {
        eventPtr = encodingName;
        return XML_ERROR_INCORRECT_ENCODING;
      }
      encoding = newEncoding;
    }
    else if (encodingName) {
      enum XML_Error result;
      if (!storedEncName) {
        storedEncName = poolStoreString(
          &temp2Pool, encoding, encodingName,
          encodingName + XmlNameLength(encoding, encodingName));
        if (!storedEncName)
          return XML_ERROR_NO_MEMORY;
      }
      result = handleUnknownEncoding(parser, storedEncName);
      poolClear(&temp2Pool);
      if (result == XML_ERROR_UNKNOWN_ENCODING)
        eventPtr = encodingName;
      return result;
    }
  }

  if (storedEncName || storedversion)
    poolClear(&temp2Pool);

  return XML_ERROR_NONE;
}

static enum XML_Error
handleUnknownEncoding(XML_Parser parser, const XML_Char *encodingName)
{
  if (unknownEncodingHandler) {
    XML_Encoding info;
    int i;
    for (i = 0; i < 256; i++)
      info.map[i] = -1;
    info.convert = NULL;
    info.data = NULL;
    info.release = NULL;
    if (unknownEncodingHandler(unknownEncodingHandlerData, encodingName,
                               &info)) {
      ENCODING *enc;
      unknownEncodingMem = MALLOC(XmlSizeOfUnknownEncoding());
      if (!unknownEncodingMem) {
        if (info.release)
          info.release(info.data);
        return XML_ERROR_NO_MEMORY;
      }
      enc = (ns
             ? XmlInitUnknownEncodingNS
             : XmlInitUnknownEncoding)(unknownEncodingMem,
                                       info.map,
                                       info.convert,
                                       info.data);
      if (enc) {
        unknownEncodingData = info.data;
        unknownEncodingRelease = info.release;
        encoding = enc;
        return XML_ERROR_NONE;
      }
    }
    if (info.release != NULL)
      info.release(info.data);
  }
  return XML_ERROR_UNKNOWN_ENCODING;
}

static enum XML_Error PTRCALL
prologInitProcessor(XML_Parser parser,
                    const char *s,
                    const char *end,
                    const char **nextPtr)
{
  enum XML_Error result = initializeEncoding(parser);
  if (result != XML_ERROR_NONE)
    return result;
  processor = prologProcessor;
  return prologProcessor(parser, s, end, nextPtr);
}

#ifdef XML_DTD

static enum XML_Error PTRCALL
externalParEntInitProcessor(XML_Parser parser,
                            const char *s,
                            const char *end,
                            const char **nextPtr)
{
  enum XML_Error result = initializeEncoding(parser);
  if (result != XML_ERROR_NONE)
    return result;

  /* we know now that XML_Parse(Buffer) has been called,
     so we consider the external parameter entity read */
  _dtd->paramEntityRead = XML_TRUE;

  if (prologState.inEntityValue) {
    processor = entityValueInitProcessor;
    return entityValueInitProcessor(parser, s, end, nextPtr);
  }
  else {
    processor = externalParEntProcessor;
    return externalParEntProcessor(parser, s, end, nextPtr);
  }
}

static enum XML_Error PTRCALL
entityValueInitProcessor(XML_Parser parser,
                         const char *s,
                         const char *end,
                         const char **nextPtr)
{
  int tok;
  const char *start = s;
  const char *next = start;
  eventPtr = start;

  for (;;) {  
    tok = XmlPrologTok(encoding, start, end, &next);
    eventEndPtr = next;
    if (tok <= 0) {
      if (!ps_finalBuffer && tok != XML_TOK_INVALID) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      switch (tok) {
      case XML_TOK_INVALID:
        return XML_ERROR_INVALID_TOKEN;
      case XML_TOK_PARTIAL:
        return XML_ERROR_UNCLOSED_TOKEN;
      case XML_TOK_PARTIAL_CHAR:
        return XML_ERROR_PARTIAL_CHAR;
      case XML_TOK_NONE:   /* start == end */
      default:
        break;
      }
      /* found end of entity value - can store it now */
      return storeEntityValue(parser, encoding, s, end);
    }
    else if (tok == XML_TOK_XML_DECL) {
      enum XML_Error result;
      result = processXmlDecl(parser, 0, start, next);
      if (result != XML_ERROR_NONE)
        return result;
      switch (ps_parsing) {
      case XML_SUSPENDED: 
        *nextPtr = next;
        return XML_ERROR_NONE;
      case XML_FINISHED:
        return XML_ERROR_ABORTED;
      default:
        *nextPtr = next;
      }
      /* stop scanning for text declaration - we found one */
      processor = entityValueProcessor;
      return entityValueProcessor(parser, next, end, nextPtr);
    }
    /* If we are at the end of the buffer, this would cause XmlPrologTok to
       return XML_TOK_NONE on the next call, which would then cause the
       function to exit with *nextPtr set to s - that is what we want for other
       tokens, but not for the BOM - we would rather like to skip it;
       then, when this routine is entered the next time, XmlPrologTok will
       return XML_TOK_INVALID, since the BOM is still in the buffer
    */
    else if (tok == XML_TOK_BOM && next == end && !ps_finalBuffer) {
      *nextPtr = next;
      return XML_ERROR_NONE;
    }
    start = next;
    eventPtr = start;
  }
}

static enum XML_Error PTRCALL
externalParEntProcessor(XML_Parser parser,
                        const char *s,
                        const char *end,
                        const char **nextPtr)
{
  const char *next = s;
  int tok;

  tok = XmlPrologTok(encoding, s, end, &next);
  if (tok <= 0) {
    if (!ps_finalBuffer && tok != XML_TOK_INVALID) {
      *nextPtr = s;
      return XML_ERROR_NONE;
    }
    switch (tok) {
    case XML_TOK_INVALID:
      return XML_ERROR_INVALID_TOKEN;
    case XML_TOK_PARTIAL:
      return XML_ERROR_UNCLOSED_TOKEN;
    case XML_TOK_PARTIAL_CHAR:
      return XML_ERROR_PARTIAL_CHAR;
    case XML_TOK_NONE:   /* start == end */
    default:
      break;
    }
  }
  /* This would cause the next stage, i.e. doProlog to be passed XML_TOK_BOM.
     However, when parsing an external subset, doProlog will not accept a BOM
     as valid, and report a syntax error, so we have to skip the BOM
  */
  else if (tok == XML_TOK_BOM) {
    s = next;
    tok = XmlPrologTok(encoding, s, end, &next);
  }

  processor = prologProcessor;
  return doProlog(parser, encoding, s, end, tok, next, 
                  nextPtr, (XML_Bool)!ps_finalBuffer);
}

static enum XML_Error PTRCALL
entityValueProcessor(XML_Parser parser,
                     const char *s,
                     const char *end,
                     const char **nextPtr)
{
  const char *start = s;
  const char *next = s;
  const ENCODING *enc = encoding;
  int tok;

  for (;;) {
    tok = XmlPrologTok(enc, start, end, &next);
    if (tok <= 0) {
      if (!ps_finalBuffer && tok != XML_TOK_INVALID) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      switch (tok) {
      case XML_TOK_INVALID:
        return XML_ERROR_INVALID_TOKEN;
      case XML_TOK_PARTIAL:
        return XML_ERROR_UNCLOSED_TOKEN;
      case XML_TOK_PARTIAL_CHAR:
        return XML_ERROR_PARTIAL_CHAR;
      case XML_TOK_NONE:   /* start == end */
      default:
        break;
      }
      /* found end of entity value - can store it now */
      return storeEntityValue(parser, enc, s, end);
    }
    start = next;
  }
}

#endif /* XML_DTD */

static enum XML_Error PTRCALL
prologProcessor(XML_Parser parser,
                const char *s,
                const char *end,
                const char **nextPtr)
{
  const char *next = s;
  int tok = XmlPrologTok(encoding, s, end, &next);
  return doProlog(parser, encoding, s, end, tok, next, 
                  nextPtr, (XML_Bool)!ps_finalBuffer);
}

static enum XML_Error
doProlog(XML_Parser parser,
         const ENCODING *enc,
         const char *s,
         const char *end,
         int tok,
         const char *next,
         const char **nextPtr,
         XML_Bool haveMore)
{
#ifdef XML_DTD
  static const XML_Char externalSubsetName[] = { ASCII_HASH , '\0' };
#endif /* XML_DTD */
  static const XML_Char atypeCDATA[] = 
      { ASCII_C, ASCII_D, ASCII_A, ASCII_T, ASCII_A, '\0' };
  static const XML_Char atypeID[] = { ASCII_I, ASCII_D, '\0' };
  static const XML_Char atypeIDREF[] =
      { ASCII_I, ASCII_D, ASCII_R, ASCII_E, ASCII_F, '\0' };
  static const XML_Char atypeIDREFS[] =
      { ASCII_I, ASCII_D, ASCII_R, ASCII_E, ASCII_F, ASCII_S, '\0' };
  static const XML_Char atypeENTITY[] =
      { ASCII_E, ASCII_N, ASCII_T, ASCII_I, ASCII_T, ASCII_Y, '\0' };
  static const XML_Char atypeENTITIES[] = { ASCII_E, ASCII_N,
      ASCII_T, ASCII_I, ASCII_T, ASCII_I, ASCII_E, ASCII_S, '\0' };
  static const XML_Char atypeNMTOKEN[] = {
      ASCII_N, ASCII_M, ASCII_T, ASCII_O, ASCII_K, ASCII_E, ASCII_N, '\0' };
  static const XML_Char atypeNMTOKENS[] = { ASCII_N, ASCII_M, ASCII_T,
      ASCII_O, ASCII_K, ASCII_E, ASCII_N, ASCII_S, '\0' };
  static const XML_Char notationPrefix[] = { ASCII_N, ASCII_O, ASCII_T,
      ASCII_A, ASCII_T, ASCII_I, ASCII_O, ASCII_N, ASCII_LPAREN, '\0' };
  static const XML_Char enumValueSep[] = { ASCII_PIPE, '\0' };
  static const XML_Char enumValueStart[] = { ASCII_LPAREN, '\0' };

  /* save one level of indirection */
  DTD * const dtd = _dtd; 

  const char **eventPP;
  const char **eventEndPP;
  enum XML_Content_Quant quant;

  if (enc == encoding) {
    eventPP = &eventPtr;
    eventEndPP = &eventEndPtr;
  }
  else {
    eventPP = &(openInternalEntities->internalEventPtr);
    eventEndPP = &(openInternalEntities->internalEventEndPtr);
  }

  for (;;) {
    int role;
    XML_Bool handleDefault = XML_TRUE;
    *eventPP = s;
    *eventEndPP = next;
    if (tok <= 0) {
      if (haveMore && tok != XML_TOK_INVALID) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      switch (tok) {
      case XML_TOK_INVALID:
        *eventPP = next;
        return XML_ERROR_INVALID_TOKEN;
      case XML_TOK_PARTIAL:
        return XML_ERROR_UNCLOSED_TOKEN;
      case XML_TOK_PARTIAL_CHAR:
        return XML_ERROR_PARTIAL_CHAR;
      case XML_TOK_NONE:
#ifdef XML_DTD
        /* for internal PE NOT referenced between declarations */
        if (enc != encoding && !openInternalEntities->betweenDecl) {
          *nextPtr = s;
          return XML_ERROR_NONE;
        }
        /* WFC: PE Between Declarations - must check that PE contains
           complete markup, not only for external PEs, but also for
           internal PEs if the reference occurs between declarations.
        */
        if (isParamEntity || enc != encoding) {
          if (XmlTokenRole(&prologState, XML_TOK_NONE, end, end, enc)
              == XML_ROLE_ERROR)
            return XML_ERROR_INCOMPLETE_PE;
          *nextPtr = s;
          return XML_ERROR_NONE;
        }
#endif /* XML_DTD */
        return XML_ERROR_NO_ELEMENTS;
      default:
        tok = -tok;
        next = end;
        break;
      }
    }
    role = XmlTokenRole(&prologState, tok, s, next, enc);
    switch (role) {
    case XML_ROLE_XML_DECL:
      {
        enum XML_Error result = processXmlDecl(parser, 0, s, next);
        if (result != XML_ERROR_NONE)
          return result;
        enc = encoding;
        handleDefault = XML_FALSE;
      }
      break;
    case XML_ROLE_DOCTYPE_NAME:
      if (startDoctypeDeclHandler) {
        doctypeName = poolStoreString(&tempPool, enc, s, next);
        if (!doctypeName)
          return XML_ERROR_NO_MEMORY;
        poolFinish(&tempPool);
        doctypePubid = NULL;
        handleDefault = XML_FALSE;
      }
      doctypeSysid = NULL; /* always initialize to NULL */
      break;
    case XML_ROLE_DOCTYPE_INTERNAL_SUBSET:
      if (startDoctypeDeclHandler) {
        startDoctypeDeclHandler(handlerArg, doctypeName, doctypeSysid,
                                doctypePubid, 1);
        doctypeName = NULL;
        poolClear(&tempPool);
        handleDefault = XML_FALSE;
      }
      break;
#ifdef XML_DTD
    case XML_ROLE_TEXT_DECL:
      {
        enum XML_Error result = processXmlDecl(parser, 1, s, next);
        if (result != XML_ERROR_NONE)
          return result;
        enc = encoding;
        handleDefault = XML_FALSE;
      }
      break;
#endif /* XML_DTD */
    case XML_ROLE_DOCTYPE_PUBLIC_ID:
#ifdef XML_DTD
      useForeignDTD = XML_FALSE;
      declEntity = (ENTITY *)lookup(&dtd->paramEntities,
                                    externalSubsetName,
                                    sizeof(ENTITY));
      if (!declEntity)
        return XML_ERROR_NO_MEMORY;
#endif /* XML_DTD */
      dtd->hasParamEntityRefs = XML_TRUE;
      if (startDoctypeDeclHandler) {
        if (!XmlIsPublicId(enc, s, next, eventPP))
          return XML_ERROR_PUBLICID;
        {
          XML_Char *p;
          doctypePubid = p = poolStoreString(&tempPool, enc,
                                             s + enc->minBytesPerChar,
                                             next - enc->minBytesPerChar);
          if (!doctypePubid)
            return XML_ERROR_NO_MEMORY;
          normalizePublicId(p);
        }
        poolFinish(&tempPool);
        handleDefault = XML_FALSE;
        goto alreadyChecked;
      }
      /* fall through */
    case XML_ROLE_ENTITY_PUBLIC_ID:
      if (!XmlIsPublicId(enc, s, next, eventPP))
        return XML_ERROR_PUBLICID;
    alreadyChecked:
      if (dtd->keepProcessing && declEntity) {
        XML_Char *tem = poolStoreString(&dtd->pool,
                                        enc,
                                        s + enc->minBytesPerChar,
                                        next - enc->minBytesPerChar);
        if (!tem)
          return XML_ERROR_NO_MEMORY;
        normalizePublicId(tem);
        declEntity->publicId = tem;
        poolFinish(&dtd->pool);
        if (entityDeclHandler)
          handleDefault = XML_FALSE;
      }
      break;
    case XML_ROLE_DOCTYPE_CLOSE:
      if (doctypeName) {
        startDoctypeDeclHandler(handlerArg, doctypeName,
                                doctypeSysid, doctypePubid, 0);
        poolClear(&tempPool);
        handleDefault = XML_FALSE;
      }
      /* doctypeSysid will be non-NULL in the case of a previous
         XML_ROLE_DOCTYPE_SYSTEM_ID, even if startDoctypeDeclHandler
         was not set, indicating an external subset
      */
#ifdef XML_DTD
      if (doctypeSysid || useForeignDTD) {
        XML_Bool hadParamEntityRefs = dtd->hasParamEntityRefs;
        dtd->hasParamEntityRefs = XML_TRUE;
        if (paramEntityParsing && externalEntityRefHandler) {
          ENTITY *entity = (ENTITY *)lookup(&dtd->paramEntities,
                                            externalSubsetName,
                                            sizeof(ENTITY));
          if (!entity)
            return XML_ERROR_NO_MEMORY;
          if (useForeignDTD)
            entity->base = curBase;
          dtd->paramEntityRead = XML_FALSE;
          if (!externalEntityRefHandler(externalEntityRefHandlerArg,
                                        0,
                                        entity->base,
                                        entity->systemId,
                                        entity->publicId))
            return XML_ERROR_EXTERNAL_ENTITY_HANDLING;
          if (dtd->paramEntityRead) {
            if (!dtd->standalone && 
                notStandaloneHandler && 
                !notStandaloneHandler(handlerArg))
              return XML_ERROR_NOT_STANDALONE;
          }
          /* if we didn't read the foreign DTD then this means that there
             is no external subset and we must reset dtd->hasParamEntityRefs
          */
          else if (!doctypeSysid)
            dtd->hasParamEntityRefs = hadParamEntityRefs;
          /* end of DTD - no need to update dtd->keepProcessing */
        }
        useForeignDTD = XML_FALSE;
      }
#endif /* XML_DTD */
      if (endDoctypeDeclHandler) {
        endDoctypeDeclHandler(handlerArg);
        handleDefault = XML_FALSE;
      }
      break;
    case XML_ROLE_INSTANCE_START:
#ifdef XML_DTD
      /* if there is no DOCTYPE declaration then now is the
         last chance to read the foreign DTD
      */
      if (useForeignDTD) {
        XML_Bool hadParamEntityRefs = dtd->hasParamEntityRefs;
        dtd->hasParamEntityRefs = XML_TRUE;
        if (paramEntityParsing && externalEntityRefHandler) {
          ENTITY *entity = (ENTITY *)lookup(&dtd->paramEntities,
                                            externalSubsetName,
                                            sizeof(ENTITY));
          if (!entity)
            return XML_ERROR_NO_MEMORY;
          entity->base = curBase;
          dtd->paramEntityRead = XML_FALSE;
          if (!externalEntityRefHandler(externalEntityRefHandlerArg,
                                        0,
                                        entity->base,
                                        entity->systemId,
                                        entity->publicId))
            return XML_ERROR_EXTERNAL_ENTITY_HANDLING;
          if (dtd->paramEntityRead) {
            if (!dtd->standalone &&
                notStandaloneHandler &&
                !notStandaloneHandler(handlerArg))
              return XML_ERROR_NOT_STANDALONE;
          }
          /* if we didn't read the foreign DTD then this means that there
             is no external subset and we must reset dtd->hasParamEntityRefs
          */
          else
            dtd->hasParamEntityRefs = hadParamEntityRefs;
          /* end of DTD - no need to update dtd->keepProcessing */
        }
      }
#endif /* XML_DTD */
      processor = contentProcessor;
      return contentProcessor(parser, s, end, nextPtr);
    case XML_ROLE_ATTLIST_ELEMENT_NAME:
      declElementType = getElementType(parser, enc, s, next);
      if (!declElementType)
        return XML_ERROR_NO_MEMORY;
      goto checkAttListDeclHandler;
    case XML_ROLE_ATTRIBUTE_NAME:
      declAttributeId = getAttributeId(parser, enc, s, next);
      if (!declAttributeId)
        return XML_ERROR_NO_MEMORY;
      declAttributeIsCdata = XML_FALSE;
      declAttributeType = NULL;
      declAttributeIsId = XML_FALSE;
      goto checkAttListDeclHandler;
    case XML_ROLE_ATTRIBUTE_TYPE_CDATA:
      declAttributeIsCdata = XML_TRUE;
      declAttributeType = atypeCDATA;
      goto checkAttListDeclHandler;
    case XML_ROLE_ATTRIBUTE_TYPE_ID:
      declAttributeIsId = XML_TRUE;
      declAttributeType = atypeID;
      goto checkAttListDeclHandler;
    case XML_ROLE_ATTRIBUTE_TYPE_IDREF:
      declAttributeType = atypeIDREF;
      goto checkAttListDeclHandler;
    case XML_ROLE_ATTRIBUTE_TYPE_IDREFS:
      declAttributeType = atypeIDREFS;
      goto checkAttListDeclHandler;
    case XML_ROLE_ATTRIBUTE_TYPE_ENTITY:
      declAttributeType = atypeENTITY;
      goto checkAttListDeclHandler;
    case XML_ROLE_ATTRIBUTE_TYPE_ENTITIES:
      declAttributeType = atypeENTITIES;
      goto checkAttListDeclHandler;
    case XML_ROLE_ATTRIBUTE_TYPE_NMTOKEN:
      declAttributeType = atypeNMTOKEN;
      goto checkAttListDeclHandler;
    case XML_ROLE_ATTRIBUTE_TYPE_NMTOKENS:
      declAttributeType = atypeNMTOKENS;
    checkAttListDeclHandler:
      if (dtd->keepProcessing && attlistDeclHandler)
        handleDefault = XML_FALSE;
      break;
    case XML_ROLE_ATTRIBUTE_ENUM_VALUE:
    case XML_ROLE_ATTRIBUTE_NOTATION_VALUE:
      if (dtd->keepProcessing && attlistDeclHandler) {
        const XML_Char *prefix;
        if (declAttributeType) {
          prefix = enumValueSep;
        }
        else {
          prefix = (role == XML_ROLE_ATTRIBUTE_NOTATION_VALUE
                    ? notationPrefix
                    : enumValueStart);
        }
        if (!poolAppendString(&tempPool, prefix))
          return XML_ERROR_NO_MEMORY;
        if (!poolAppend(&tempPool, enc, s, next))
          return XML_ERROR_NO_MEMORY;
        declAttributeType = tempPool.start;
        handleDefault = XML_FALSE;
      }
      break;
    case XML_ROLE_IMPLIED_ATTRIBUTE_VALUE:
    case XML_ROLE_REQUIRED_ATTRIBUTE_VALUE:
      if (dtd->keepProcessing) {
        if (!defineAttribute(declElementType, declAttributeId,
                             declAttributeIsCdata, declAttributeIsId,
                             0, parser))
          return XML_ERROR_NO_MEMORY;
        if (attlistDeclHandler && declAttributeType) {
          if (*declAttributeType == XML_T(ASCII_LPAREN)
              || (*declAttributeType == XML_T(ASCII_N)
                  && declAttributeType[1] == XML_T(ASCII_O))) {
            /* Enumerated or Notation type */
            if (!poolAppendChar(&tempPool, XML_T(ASCII_RPAREN))
                || !poolAppendChar(&tempPool, XML_T('\0')))
              return XML_ERROR_NO_MEMORY;
            declAttributeType = tempPool.start;
            poolFinish(&tempPool);
          }
          *eventEndPP = s;
          attlistDeclHandler(handlerArg, declElementType->name,
                             declAttributeId->name, declAttributeType,
                             0, role == XML_ROLE_REQUIRED_ATTRIBUTE_VALUE);
          poolClear(&tempPool);
          handleDefault = XML_FALSE;
        }
      }
      break;
    case XML_ROLE_DEFAULT_ATTRIBUTE_VALUE:
    case XML_ROLE_FIXED_ATTRIBUTE_VALUE:
      if (dtd->keepProcessing) {
        const XML_Char *attVal;
        enum XML_Error result =
          storeAttributeValue(parser, enc, declAttributeIsCdata,
                              s + enc->minBytesPerChar,
                              next - enc->minBytesPerChar,
                              &dtd->pool);
        if (result)
          return result;
        attVal = poolStart(&dtd->pool);
        poolFinish(&dtd->pool);
        /* ID attributes aren't allowed to have a default */
        if (!defineAttribute(declElementType, declAttributeId,
                             declAttributeIsCdata, XML_FALSE, attVal, parser))
          return XML_ERROR_NO_MEMORY;
        if (attlistDeclHandler && declAttributeType) {
          if (*declAttributeType == XML_T(ASCII_LPAREN)
              || (*declAttributeType == XML_T(ASCII_N)
                  && declAttributeType[1] == XML_T(ASCII_O))) {
            /* Enumerated or Notation type */
            if (!poolAppendChar(&tempPool, XML_T(ASCII_RPAREN))
                || !poolAppendChar(&tempPool, XML_T('\0')))
              return XML_ERROR_NO_MEMORY;
            declAttributeType = tempPool.start;
            poolFinish(&tempPool);
          }
          *eventEndPP = s;
          attlistDeclHandler(handlerArg, declElementType->name,
                             declAttributeId->name, declAttributeType,
                             attVal,
                             role == XML_ROLE_FIXED_ATTRIBUTE_VALUE);
          poolClear(&tempPool);
          handleDefault = XML_FALSE;
        }
      }
      break;
    case XML_ROLE_ENTITY_VALUE:
      if (dtd->keepProcessing) {
        enum XML_Error result = storeEntityValue(parser, enc,
                                            s + enc->minBytesPerChar,
                                            next - enc->minBytesPerChar);
        if (declEntity) {
          declEntity->textPtr = poolStart(&dtd->entityValuePool);
          declEntity->textLen = (int)(poolLength(&dtd->entityValuePool));
          poolFinish(&dtd->entityValuePool);
          if (entityDeclHandler) {
            *eventEndPP = s;
            entityDeclHandler(handlerArg,
                              declEntity->name,
                              declEntity->is_param,
                              declEntity->textPtr,
                              declEntity->textLen,
                              curBase, 0, 0, 0);
            handleDefault = XML_FALSE;
          }
        }
        else
          poolDiscard(&dtd->entityValuePool);
        if (result != XML_ERROR_NONE)
          return result;
      }
      break;
    case XML_ROLE_DOCTYPE_SYSTEM_ID:
#ifdef XML_DTD
      useForeignDTD = XML_FALSE;
#endif /* XML_DTD */
      dtd->hasParamEntityRefs = XML_TRUE;
      if (startDoctypeDeclHandler) {
        doctypeSysid = poolStoreString(&tempPool, enc,
                                       s + enc->minBytesPerChar,
                                       next - enc->minBytesPerChar);
        if (doctypeSysid == NULL)
          return XML_ERROR_NO_MEMORY;
        poolFinish(&tempPool);
        handleDefault = XML_FALSE;
      }
#ifdef XML_DTD
      else
        /* use externalSubsetName to make doctypeSysid non-NULL
           for the case where no startDoctypeDeclHandler is set */
        doctypeSysid = externalSubsetName;
#endif /* XML_DTD */
      if (!dtd->standalone
#ifdef XML_DTD
          && !paramEntityParsing
#endif /* XML_DTD */
          && notStandaloneHandler
          && !notStandaloneHandler(handlerArg))
        return XML_ERROR_NOT_STANDALONE;
#ifndef XML_DTD
      break;
#else /* XML_DTD */
      if (!declEntity) {
        declEntity = (ENTITY *)lookup(&dtd->paramEntities,
                                      externalSubsetName,
                                      sizeof(ENTITY));
        if (!declEntity)
          return XML_ERROR_NO_MEMORY;
        declEntity->publicId = NULL;
      }
      /* fall through */
#endif /* XML_DTD */
    case XML_ROLE_ENTITY_SYSTEM_ID:
      if (dtd->keepProcessing && declEntity) {
        declEntity->systemId = poolStoreString(&dtd->pool, enc,
                                               s + enc->minBytesPerChar,
                                               next - enc->minBytesPerChar);
        if (!declEntity->systemId)
          return XML_ERROR_NO_MEMORY;
        declEntity->base = curBase;
        poolFinish(&dtd->pool);
        if (entityDeclHandler)
          handleDefault = XML_FALSE;
      }
      break;
    case XML_ROLE_ENTITY_COMPLETE:
      if (dtd->keepProcessing && declEntity && entityDeclHandler) {
        *eventEndPP = s;
        entityDeclHandler(handlerArg,
                          declEntity->name,
                          declEntity->is_param,
                          0,0,
                          declEntity->base,
                          declEntity->systemId,
                          declEntity->publicId,
                          0);
        handleDefault = XML_FALSE;
      }
      break;
    case XML_ROLE_ENTITY_NOTATION_NAME:
      if (dtd->keepProcessing && declEntity) {
        declEntity->notation = poolStoreString(&dtd->pool, enc, s, next);
        if (!declEntity->notation)
          return XML_ERROR_NO_MEMORY;
        poolFinish(&dtd->pool);
        if (unparsedEntityDeclHandler) {
          *eventEndPP = s;
          unparsedEntityDeclHandler(handlerArg,
                                    declEntity->name,
                                    declEntity->base,
                                    declEntity->systemId,
                                    declEntity->publicId,
                                    declEntity->notation);
          handleDefault = XML_FALSE;
        }
        else if (entityDeclHandler) {
          *eventEndPP = s;
          entityDeclHandler(handlerArg,
                            declEntity->name,
                            0,0,0,
                            declEntity->base,
                            declEntity->systemId,
                            declEntity->publicId,
                            declEntity->notation);
          handleDefault = XML_FALSE;
        }
      }
      break;
    case XML_ROLE_GENERAL_ENTITY_NAME:
      {
        if (XmlPredefinedEntityName(enc, s, next)) {
          declEntity = NULL;
          break;
        }
        if (dtd->keepProcessing) {
          const XML_Char *name = poolStoreString(&dtd->pool, enc, s, next);
          if (!name)
            return XML_ERROR_NO_MEMORY;
          declEntity = (ENTITY *)lookup(&dtd->generalEntities, name,
                                        sizeof(ENTITY));
          if (!declEntity)
            return XML_ERROR_NO_MEMORY;
          if (declEntity->name != name) {
            poolDiscard(&dtd->pool);
            declEntity = NULL;
          }
          else {
            poolFinish(&dtd->pool);
            declEntity->publicId = NULL;
            declEntity->is_param = XML_FALSE;
            /* if we have a parent parser or are reading an internal parameter
               entity, then the entity declaration is not considered "internal"
            */
            declEntity->is_internal = !(parentParser || openInternalEntities);
            if (entityDeclHandler)
              handleDefault = XML_FALSE;
          }
        }
        else {
          poolDiscard(&dtd->pool);
          declEntity = NULL;
        }
      }
      break;
    case XML_ROLE_PARAM_ENTITY_NAME:
#ifdef XML_DTD
      if (dtd->keepProcessing) {
        const XML_Char *name = poolStoreString(&dtd->pool, enc, s, next);
        if (!name)
          return XML_ERROR_NO_MEMORY;
        declEntity = (ENTITY *)lookup(&dtd->paramEntities,
                                           name, sizeof(ENTITY));
        if (!declEntity)
          return XML_ERROR_NO_MEMORY;
        if (declEntity->name != name) {
          poolDiscard(&dtd->pool);
          declEntity = NULL;
        }
        else {
          poolFinish(&dtd->pool);
          declEntity->publicId = NULL;
          declEntity->is_param = XML_TRUE;
          /* if we have a parent parser or are reading an internal parameter
             entity, then the entity declaration is not considered "internal"
          */
          declEntity->is_internal = !(parentParser || openInternalEntities);
          if (entityDeclHandler)
            handleDefault = XML_FALSE;
        }
      }
      else {
        poolDiscard(&dtd->pool);
        declEntity = NULL;
      }
#else /* not XML_DTD */
      declEntity = NULL;
#endif /* XML_DTD */
      break;
    case XML_ROLE_NOTATION_NAME:
      declNotationPublicId = NULL;
      declNotationName = NULL;
      if (notationDeclHandler) {
        declNotationName = poolStoreString(&tempPool, enc, s, next);
        if (!declNotationName)
          return XML_ERROR_NO_MEMORY;
        poolFinish(&tempPool);
        handleDefault = XML_FALSE;
      }
      break;
    case XML_ROLE_NOTATION_PUBLIC_ID:
      if (!XmlIsPublicId(enc, s, next, eventPP))
        return XML_ERROR_PUBLICID;
      if (declNotationName) {  /* means notationDeclHandler != NULL */
        XML_Char *tem = poolStoreString(&tempPool,
                                        enc,
                                        s + enc->minBytesPerChar,
                                        next - enc->minBytesPerChar);
        if (!tem)
          return XML_ERROR_NO_MEMORY;
        normalizePublicId(tem);
        declNotationPublicId = tem;
        poolFinish(&tempPool);
        handleDefault = XML_FALSE;
      }
      break;
    case XML_ROLE_NOTATION_SYSTEM_ID:
      if (declNotationName && notationDeclHandler) {
        const XML_Char *systemId
          = poolStoreString(&tempPool, enc,
                            s + enc->minBytesPerChar,
                            next - enc->minBytesPerChar);
        if (!systemId)
          return XML_ERROR_NO_MEMORY;
        *eventEndPP = s;
        notationDeclHandler(handlerArg,
                            declNotationName,
                            curBase,
                            systemId,
                            declNotationPublicId);
        handleDefault = XML_FALSE;
      }
      poolClear(&tempPool);
      break;
    case XML_ROLE_NOTATION_NO_SYSTEM_ID:
      if (declNotationPublicId && notationDeclHandler) {
        *eventEndPP = s;
        notationDeclHandler(handlerArg,
                            declNotationName,
                            curBase,
                            0,
                            declNotationPublicId);
        handleDefault = XML_FALSE;
      }
      poolClear(&tempPool);
      break;
    case XML_ROLE_ERROR:
      switch (tok) {
      case XML_TOK_PARAM_ENTITY_REF:
        /* PE references in internal subset are
           not allowed within declarations. */  
        return XML_ERROR_PARAM_ENTITY_REF;
      case XML_TOK_XML_DECL:
        return XML_ERROR_MISPLACED_XML_PI;
      default:
        return XML_ERROR_SYNTAX;
      }
#ifdef XML_DTD
    case XML_ROLE_IGNORE_SECT:
      {
        enum XML_Error result;
        if (defaultHandler)
          reportDefault(parser, enc, s, next);
        handleDefault = XML_FALSE;
        result = doIgnoreSection(parser, enc, &next, end, nextPtr, haveMore);
        if (result != XML_ERROR_NONE)
          return result;
        else if (!next) {
          processor = ignoreSectionProcessor;
          return result;
        }
      }
      break;
#endif /* XML_DTD */
    case XML_ROLE_GROUP_OPEN:
      if (prologState.level >= groupSize) {
        if (groupSize) {
          char *temp = (char *)REALLOC(groupConnector, groupSize *= 2);
          if (temp == NULL)
            return XML_ERROR_NO_MEMORY;
          groupConnector = temp;
          if (dtd->scaffIndex) {
            int *temp = (int *)REALLOC(dtd->scaffIndex,
                          groupSize * sizeof(int));
            if (temp == NULL)
              return XML_ERROR_NO_MEMORY;
            dtd->scaffIndex = temp;
          }
        }
        else {
          groupConnector = (char *)MALLOC(groupSize = 32);
          if (!groupConnector)
            return XML_ERROR_NO_MEMORY;
        }
      }
      groupConnector[prologState.level] = 0;
      if (dtd->in_eldecl) {
        int myindex = nextScaffoldPart(parser);
        if (myindex < 0)
          return XML_ERROR_NO_MEMORY;
        dtd->scaffIndex[dtd->scaffLevel] = myindex;
        dtd->scaffLevel++;
        dtd->scaffold[myindex].type = XML_CTYPE_SEQ;
        if (elementDeclHandler)
          handleDefault = XML_FALSE;
      }
      break;
    case XML_ROLE_GROUP_SEQUENCE:
      if (groupConnector[prologState.level] == ASCII_PIPE)
        return XML_ERROR_SYNTAX;
      groupConnector[prologState.level] = ASCII_COMMA;
      if (dtd->in_eldecl && elementDeclHandler)
        handleDefault = XML_FALSE;
      break;
    case XML_ROLE_GROUP_CHOICE:
      if (groupConnector[prologState.level] == ASCII_COMMA)
        return XML_ERROR_SYNTAX;
      if (dtd->in_eldecl
          && !groupConnector[prologState.level]
          && (dtd->scaffold[dtd->scaffIndex[dtd->scaffLevel - 1]].type
              != XML_CTYPE_MIXED)
          ) {
        dtd->scaffold[dtd->scaffIndex[dtd->scaffLevel - 1]].type
            = XML_CTYPE_CHOICE;
        if (elementDeclHandler)
          handleDefault = XML_FALSE;
      }
      groupConnector[prologState.level] = ASCII_PIPE;
      break;
    case XML_ROLE_PARAM_ENTITY_REF:
#ifdef XML_DTD
    case XML_ROLE_INNER_PARAM_ENTITY_REF:
      dtd->hasParamEntityRefs = XML_TRUE;
      if (!paramEntityParsing)
        dtd->keepProcessing = dtd->standalone;
      else {
        const XML_Char *name;
        ENTITY *entity;
        name = poolStoreString(&dtd->pool, enc,
                                s + enc->minBytesPerChar,
                                next - enc->minBytesPerChar);
        if (!name)
          return XML_ERROR_NO_MEMORY;
        entity = (ENTITY *)lookup(&dtd->paramEntities, name, 0);
        poolDiscard(&dtd->pool);
        /* first, determine if a check for an existing declaration is needed;
           if yes, check that the entity exists, and that it is internal,
           otherwise call the skipped entity handler
        */
        if (prologState.documentEntity &&
            (dtd->standalone
             ? !openInternalEntities
             : !dtd->hasParamEntityRefs)) {
          if (!entity)
            return XML_ERROR_UNDEFINED_ENTITY;
          else if (!entity->is_internal)
            return XML_ERROR_ENTITY_DECLARED_IN_PE;
        }
        else if (!entity) {
          dtd->keepProcessing = dtd->standalone;
          /* cannot report skipped entities in declarations */
          if ((role == XML_ROLE_PARAM_ENTITY_REF) && skippedEntityHandler) {
            skippedEntityHandler(handlerArg, name, 1);
            handleDefault = XML_FALSE;
          }
          break;
        }
        if (entity->open)
          return XML_ERROR_RECURSIVE_ENTITY_REF;
        if (entity->textPtr) {
          enum XML_Error result;
          XML_Bool betweenDecl = 
            (role == XML_ROLE_PARAM_ENTITY_REF ? XML_TRUE : XML_FALSE);
          result = processInternalEntity(parser, entity, betweenDecl);
          if (result != XML_ERROR_NONE)
            return result;
          handleDefault = XML_FALSE;
          break;
        }
        if (externalEntityRefHandler) {
          dtd->paramEntityRead = XML_FALSE;
          entity->open = XML_TRUE;
          if (!externalEntityRefHandler(externalEntityRefHandlerArg,
                                        0,
                                        entity->base,
                                        entity->systemId,
                                        entity->publicId)) {
            entity->open = XML_FALSE;
            return XML_ERROR_EXTERNAL_ENTITY_HANDLING;
          }
          entity->open = XML_FALSE;
          handleDefault = XML_FALSE;
          if (!dtd->paramEntityRead) {
            dtd->keepProcessing = dtd->standalone;
            break;
          }
        }
        else {
          dtd->keepProcessing = dtd->standalone;
          break;
        }
      }
#endif /* XML_DTD */
      if (!dtd->standalone &&
          notStandaloneHandler &&
          !notStandaloneHandler(handlerArg))
        return XML_ERROR_NOT_STANDALONE;
      break;

    /* Element declaration stuff */

    case XML_ROLE_ELEMENT_NAME:
      if (elementDeclHandler) {
        declElementType = getElementType(parser, enc, s, next);
        if (!declElementType)
          return XML_ERROR_NO_MEMORY;
        dtd->scaffLevel = 0;
        dtd->scaffCount = 0;
        dtd->in_eldecl = XML_TRUE;
        handleDefault = XML_FALSE;
      }
      break;

    case XML_ROLE_CONTENT_ANY:
    case XML_ROLE_CONTENT_EMPTY:
      if (dtd->in_eldecl) {
        if (elementDeclHandler) {
          XML_Content * content = (XML_Content *) MALLOC(sizeof(XML_Content));
          if (!content)
            return XML_ERROR_NO_MEMORY;
          content->quant = XML_CQUANT_NONE;
          content->name = NULL;
          content->numchildren = 0;
          content->children = NULL;
          content->type = ((role == XML_ROLE_CONTENT_ANY) ?
                           XML_CTYPE_ANY :
                           XML_CTYPE_EMPTY);
          *eventEndPP = s;
          elementDeclHandler(handlerArg, declElementType->name, content);
          handleDefault = XML_FALSE;
        }
        dtd->in_eldecl = XML_FALSE;
      }
      break;

    case XML_ROLE_CONTENT_PCDATA:
      if (dtd->in_eldecl) {
        dtd->scaffold[dtd->scaffIndex[dtd->scaffLevel - 1]].type
            = XML_CTYPE_MIXED;
        if (elementDeclHandler)
          handleDefault = XML_FALSE;
      }
      break;

    case XML_ROLE_CONTENT_ELEMENT:
      quant = XML_CQUANT_NONE;
      goto elementContent;
    case XML_ROLE_CONTENT_ELEMENT_OPT:
      quant = XML_CQUANT_OPT;
      goto elementContent;
    case XML_ROLE_CONTENT_ELEMENT_REP:
      quant = XML_CQUANT_REP;
      goto elementContent;
    case XML_ROLE_CONTENT_ELEMENT_PLUS:
      quant = XML_CQUANT_PLUS;
    elementContent:
      if (dtd->in_eldecl) {
        ELEMENT_TYPE *el;
        const XML_Char *name;
        int nameLen;
        const char *nxt = (quant == XML_CQUANT_NONE
                           ? next
                           : next - enc->minBytesPerChar);
        int myindex = nextScaffoldPart(parser);
        if (myindex < 0)
          return XML_ERROR_NO_MEMORY;
        dtd->scaffold[myindex].type = XML_CTYPE_NAME;
        dtd->scaffold[myindex].quant = quant;
        el = getElementType(parser, enc, s, nxt);
        if (!el)
          return XML_ERROR_NO_MEMORY;
        name = el->name;
        dtd->scaffold[myindex].name = name;
        nameLen = 0;
        for (; name[nameLen++]; );
        dtd->contentStringLen +=  nameLen;
        if (elementDeclHandler)
          handleDefault = XML_FALSE;
      }
      break;

    case XML_ROLE_GROUP_CLOSE:
      quant = XML_CQUANT_NONE;
      goto closeGroup;
    case XML_ROLE_GROUP_CLOSE_OPT:
      quant = XML_CQUANT_OPT;
      goto closeGroup;
    case XML_ROLE_GROUP_CLOSE_REP:
      quant = XML_CQUANT_REP;
      goto closeGroup;
    case XML_ROLE_GROUP_CLOSE_PLUS:
      quant = XML_CQUANT_PLUS;
    closeGroup:
      if (dtd->in_eldecl) {
        if (elementDeclHandler)
          handleDefault = XML_FALSE;
        dtd->scaffLevel--;
        dtd->scaffold[dtd->scaffIndex[dtd->scaffLevel]].quant = quant;
        if (dtd->scaffLevel == 0) {
          if (!handleDefault) {
            XML_Content *model = build_model(parser);
            if (!model)
              return XML_ERROR_NO_MEMORY;
            *eventEndPP = s;
            elementDeclHandler(handlerArg, declElementType->name, model);
          }
          dtd->in_eldecl = XML_FALSE;
          dtd->contentStringLen = 0;
        }
      }
      break;
      /* End element declaration stuff */

    case XML_ROLE_PI:
      if (!reportProcessingInstruction(parser, enc, s, next))
        return XML_ERROR_NO_MEMORY;
      handleDefault = XML_FALSE;
      break;
    case XML_ROLE_COMMENT:
      if (!reportComment(parser, enc, s, next))
        return XML_ERROR_NO_MEMORY;
      handleDefault = XML_FALSE;
      break;
    case XML_ROLE_NONE:
      switch (tok) {
      case XML_TOK_BOM:
        handleDefault = XML_FALSE;
        break;
      }
      break;
    case XML_ROLE_DOCTYPE_NONE:
      if (startDoctypeDeclHandler)
        handleDefault = XML_FALSE;
      break;
    case XML_ROLE_ENTITY_NONE:
      if (dtd->keepProcessing && entityDeclHandler)
        handleDefault = XML_FALSE;
      break;
    case XML_ROLE_NOTATION_NONE:
      if (notationDeclHandler)
        handleDefault = XML_FALSE;
      break;
    case XML_ROLE_ATTLIST_NONE:
      if (dtd->keepProcessing && attlistDeclHandler)
        handleDefault = XML_FALSE;
      break;
    case XML_ROLE_ELEMENT_NONE:
      if (elementDeclHandler)
        handleDefault = XML_FALSE;
      break;
    } /* end of big switch */

    if (handleDefault && defaultHandler)
      reportDefault(parser, enc, s, next);

    switch (ps_parsing) {
    case XML_SUSPENDED: 
      *nextPtr = next;
      return XML_ERROR_NONE;
    case XML_FINISHED:
      return XML_ERROR_ABORTED;
    default:
      s = next;
      tok = XmlPrologTok(enc, s, end, &next);
    }
  }
  /* not reached */
}

static enum XML_Error PTRCALL
epilogProcessor(XML_Parser parser,
                const char *s,
                const char *end,
                const char **nextPtr)
{
  processor = epilogProcessor;
  eventPtr = s;
  for (;;) {
    const char *next = NULL;
    int tok = XmlPrologTok(encoding, s, end, &next);
    eventEndPtr = next;
    switch (tok) {
    /* report partial linebreak - it might be the last token */
    case -XML_TOK_PROLOG_S:
      if (defaultHandler) {
        reportDefault(parser, encoding, s, next);
        if (ps_parsing == XML_FINISHED)
          return XML_ERROR_ABORTED;
      }
      *nextPtr = next;
      return XML_ERROR_NONE;
    case XML_TOK_NONE:
      *nextPtr = s;
      return XML_ERROR_NONE;
    case XML_TOK_PROLOG_S:
      if (defaultHandler)
        reportDefault(parser, encoding, s, next);
      break;
    case XML_TOK_PI:
      if (!reportProcessingInstruction(parser, encoding, s, next))
        return XML_ERROR_NO_MEMORY;
      break;
    case XML_TOK_COMMENT:
      if (!reportComment(parser, encoding, s, next))
        return XML_ERROR_NO_MEMORY;
      break;
    case XML_TOK_INVALID:
      eventPtr = next;
      return XML_ERROR_INVALID_TOKEN;
    case XML_TOK_PARTIAL:
      if (!ps_finalBuffer) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      return XML_ERROR_UNCLOSED_TOKEN;
    case XML_TOK_PARTIAL_CHAR:
      if (!ps_finalBuffer) {
        *nextPtr = s;
        return XML_ERROR_NONE;
      }
      return XML_ERROR_PARTIAL_CHAR;
    default:
      return XML_ERROR_JUNK_AFTER_DOC_ELEMENT;
    }
    eventPtr = s = next;
    switch (ps_parsing) {
    case XML_SUSPENDED: 
      *nextPtr = next;
      return XML_ERROR_NONE;
    case XML_FINISHED:
      return XML_ERROR_ABORTED;
    default: ;
    }
  }
}

static enum XML_Error
processInternalEntity(XML_Parser parser, ENTITY *entity,
                      XML_Bool betweenDecl)
{
  const char *textStart, *textEnd;
  const char *next;
  enum XML_Error result;
  OPEN_INTERNAL_ENTITY *openEntity;

  if (freeInternalEntities) {
    openEntity = freeInternalEntities;
    freeInternalEntities = openEntity->next;
  }
  else {
    openEntity = (OPEN_INTERNAL_ENTITY *)MALLOC(sizeof(OPEN_INTERNAL_ENTITY));
    if (!openEntity)
      return XML_ERROR_NO_MEMORY;
  }
  entity->open = XML_TRUE;
  entity->processed = 0;
  openEntity->next = openInternalEntities;
  openInternalEntities = openEntity;
  openEntity->entity = entity;
  openEntity->startTagLevel = tagLevel;
  openEntity->betweenDecl = betweenDecl;
  openEntity->internalEventPtr = NULL;
  openEntity->internalEventEndPtr = NULL;
  textStart = (char *)entity->textPtr;
  textEnd = (char *)(entity->textPtr + entity->textLen);

#ifdef XML_DTD
  if (entity->is_param) {
    int tok = XmlPrologTok(internalEncoding, textStart, textEnd, &next);
    result = doProlog(parser, internalEncoding, textStart, textEnd, tok, 
                      next, &next, XML_FALSE);
  }
  else 
#endif /* XML_DTD */
    result = doContent(parser, tagLevel, internalEncoding, textStart, 
                       textEnd, &next, XML_FALSE);

  if (result == XML_ERROR_NONE) {
    if (textEnd != next && ps_parsing == XML_SUSPENDED) {
      entity->processed = (int)(next - textStart);
      processor = internalEntityProcessor;
    }
    else {
      entity->open = XML_FALSE;
      openInternalEntities = openEntity->next;
      /* put openEntity back in list of free instances */
      openEntity->next = freeInternalEntities;
      freeInternalEntities = openEntity;
    }
  }
  return result;
}

static enum XML_Error PTRCALL
internalEntityProcessor(XML_Parser parser,
                        const char *s,
                        const char *end,
                        const char **nextPtr)
{
  ENTITY *entity;
  const char *textStart, *textEnd;
  const char *next;
  enum XML_Error result;
  OPEN_INTERNAL_ENTITY *openEntity = openInternalEntities;
  if (!openEntity)
    return XML_ERROR_UNEXPECTED_STATE;

  entity = openEntity->entity;
  textStart = ((char *)entity->textPtr) + entity->processed;
  textEnd = (char *)(entity->textPtr + entity->textLen);

#ifdef XML_DTD
  if (entity->is_param) {
    int tok = XmlPrologTok(internalEncoding, textStart, textEnd, &next);
    result = doProlog(parser, internalEncoding, textStart, textEnd, tok, 
                      next, &next, XML_FALSE);
  }
  else
#endif /* XML_DTD */
    result = doContent(parser, openEntity->startTagLevel, internalEncoding, 
                       textStart, textEnd, &next, XML_FALSE);  

  if (result != XML_ERROR_NONE)
    return result;
  else if (textEnd != next && ps_parsing == XML_SUSPENDED) {
    entity->processed = (int)(next - (char *)entity->textPtr);
    return result;
  }
  else {
    entity->open = XML_FALSE;
    openInternalEntities = openEntity->next;
    /* put openEntity back in list of free instances */
    openEntity->next = freeInternalEntities;
    freeInternalEntities = openEntity;
  }

#ifdef XML_DTD
  if (entity->is_param) {
    int tok;
    processor = prologProcessor;
    tok = XmlPrologTok(encoding, s, end, &next);
    return doProlog(parser, encoding, s, end, tok, next, nextPtr, 
                    (XML_Bool)!ps_finalBuffer);
  }
  else
#endif /* XML_DTD */
  {
    processor = contentProcessor;
    /* see externalEntityContentProcessor vs contentProcessor */
    return doContent(parser, parentParser ? 1 : 0, encoding, s, end,
                     nextPtr, (XML_Bool)!ps_finalBuffer); 
  }  
}

static enum XML_Error PTRCALL
errorProcessor(XML_Parser parser,
               __attribute__ ((unused)) const char *s,
               __attribute__ ((unused)) const char *end,
               __attribute__ ((unused)) const char **nextPtr)
{
  return errorCode;
}

static enum XML_Error
storeAttributeValue(XML_Parser parser, const ENCODING *enc, XML_Bool isCdata,
                    const char *ptr, const char *end,
                    STRING_POOL *pool)
{
  enum XML_Error result = appendAttributeValue(parser, enc, isCdata, ptr,
                                               end, pool);
  if (result)
    return result;
  if (!isCdata && poolLength(pool) && poolLastChar(pool) == 0x20)
    poolChop(pool);
  if (!poolAppendChar(pool, XML_T('\0')))
    return XML_ERROR_NO_MEMORY;
  return XML_ERROR_NONE;
}

static enum XML_Error
appendAttributeValue(XML_Parser parser, const ENCODING *enc, XML_Bool isCdata,
                     const char *ptr, const char *end,
                     STRING_POOL *pool)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  for (;;) {
    const char *next;
    int tok = XmlAttributeValueTok(enc, ptr, end, &next);
    switch (tok) {
    case XML_TOK_NONE:
      return XML_ERROR_NONE;
    case XML_TOK_INVALID:
      if (enc == encoding)
        eventPtr = next;
      return XML_ERROR_INVALID_TOKEN;
    case XML_TOK_PARTIAL:
      if (enc == encoding)
        eventPtr = ptr;
      return XML_ERROR_INVALID_TOKEN;
    case XML_TOK_CHAR_REF:
      {
        XML_Char buf[XML_ENCODE_MAX];
        int i;
        int n = XmlCharRefNumber(enc, ptr);
        if (n < 0) {
          if (enc == encoding)
            eventPtr = ptr;
          return XML_ERROR_BAD_CHAR_REF;
        }
        if (!isCdata
            && n == 0x20 /* space */
            && (poolLength(pool) == 0 || poolLastChar(pool) == 0x20))
          break;
        n = XmlEncode(n, (ICHAR *)buf);
        if (!n) {
          if (enc == encoding)
            eventPtr = ptr;
          return XML_ERROR_BAD_CHAR_REF;
        }
        for (i = 0; i < n; i++) {
          if (!poolAppendChar(pool, buf[i]))
            return XML_ERROR_NO_MEMORY;
        }
      }
      break;
    case XML_TOK_DATA_CHARS:
      if (!poolAppend(pool, enc, ptr, next))
        return XML_ERROR_NO_MEMORY;
      break;
    case XML_TOK_TRAILING_CR:
      next = ptr + enc->minBytesPerChar;
      /* fall through */
    case XML_TOK_ATTRIBUTE_VALUE_S:
    case XML_TOK_DATA_NEWLINE:
      if (!isCdata && (poolLength(pool) == 0 || poolLastChar(pool) == 0x20))
        break;
      if (!poolAppendChar(pool, 0x20))
        return XML_ERROR_NO_MEMORY;
      break;
    case XML_TOK_ENTITY_REF:
      {
        const XML_Char *name;
        ENTITY *entity;
        char checkEntityDecl;
        XML_Char ch = (XML_Char) XmlPredefinedEntityName(enc,
                                              ptr + enc->minBytesPerChar,
                                              next - enc->minBytesPerChar);
        if (ch) {
          if (!poolAppendChar(pool, ch))
                return XML_ERROR_NO_MEMORY;
          break;
        }
        name = poolStoreString(&temp2Pool, enc,
                               ptr + enc->minBytesPerChar,
                               next - enc->minBytesPerChar);
        if (!name)
          return XML_ERROR_NO_MEMORY;
        entity = (ENTITY *)lookup(&dtd->generalEntities, name, 0);
        poolDiscard(&temp2Pool);
        /* First, determine if a check for an existing declaration is needed;
           if yes, check that the entity exists, and that it is internal.
        */
        if (pool == &dtd->pool)  /* are we called from prolog? */
          checkEntityDecl =
#ifdef XML_DTD
              prologState.documentEntity &&
#endif /* XML_DTD */
              (dtd->standalone
               ? !openInternalEntities
               : !dtd->hasParamEntityRefs);
        else /* if (pool == &tempPool): we are called from content */
          checkEntityDecl = !dtd->hasParamEntityRefs || dtd->standalone;
        if (checkEntityDecl) {
          if (!entity)
            return XML_ERROR_UNDEFINED_ENTITY;
          else if (!entity->is_internal)
            return XML_ERROR_ENTITY_DECLARED_IN_PE;
        }
        else if (!entity) {
          /* Cannot report skipped entity here - see comments on
             skippedEntityHandler.
          if (skippedEntityHandler)
            skippedEntityHandler(handlerArg, name, 0);
          */
          /* Cannot call the default handler because this would be
             out of sync with the call to the startElementHandler.
          if ((pool == &tempPool) && defaultHandler)
            reportDefault(parser, enc, ptr, next);
          */
          break;
        }
        if (entity->open) {
          if (enc == encoding)
            eventPtr = ptr;
          return XML_ERROR_RECURSIVE_ENTITY_REF;
        }
        if (entity->notation) {
          if (enc == encoding)
            eventPtr = ptr;
          return XML_ERROR_BINARY_ENTITY_REF;
        }
        if (!entity->textPtr) {
          if (enc == encoding)
            eventPtr = ptr;
              return XML_ERROR_ATTRIBUTE_EXTERNAL_ENTITY_REF;
        }
        else {
          enum XML_Error result;
          const XML_Char *textEnd = entity->textPtr + entity->textLen;
          entity->open = XML_TRUE;
          result = appendAttributeValue(parser, internalEncoding, isCdata,
                                        (char *)entity->textPtr,
                                        (char *)textEnd, pool);
          entity->open = XML_FALSE;
          if (result)
            return result;
        }
      }
      break;
    default:
      if (enc == encoding)
        eventPtr = ptr;
      return XML_ERROR_UNEXPECTED_STATE;
    }
    ptr = next;
  }
  /* not reached */
}

static enum XML_Error
storeEntityValue(XML_Parser parser,
                 const ENCODING *enc,
                 const char *entityTextPtr,
                 const char *entityTextEnd)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  STRING_POOL *pool = &(dtd->entityValuePool);
  enum XML_Error result = XML_ERROR_NONE;
#ifdef XML_DTD
  int oldInEntityValue = prologState.inEntityValue;
  prologState.inEntityValue = 1;
#endif /* XML_DTD */
  /* never return Null for the value argument in EntityDeclHandler,
     since this would indicate an external entity; therefore we
     have to make sure that entityValuePool.start is not null */
  if (!pool->blocks) {
    if (!poolGrow(pool))
      return XML_ERROR_NO_MEMORY;
  }

  for (;;) {
    const char *next;
    int tok = XmlEntityValueTok(enc, entityTextPtr, entityTextEnd, &next);
    switch (tok) {
    case XML_TOK_PARAM_ENTITY_REF:
#ifdef XML_DTD
      if (isParamEntity || enc != encoding) {
        const XML_Char *name;
        ENTITY *entity;
        name = poolStoreString(&tempPool, enc,
                               entityTextPtr + enc->minBytesPerChar,
                               next - enc->minBytesPerChar);
        if (!name) {
          result = XML_ERROR_NO_MEMORY;
          goto endEntityValue;
        }
        entity = (ENTITY *)lookup(&dtd->paramEntities, name, 0);
        poolDiscard(&tempPool);
        if (!entity) {
          /* not a well-formedness error - see XML 1.0: WFC Entity Declared */
          /* cannot report skipped entity here - see comments on
             skippedEntityHandler
          if (skippedEntityHandler)
            skippedEntityHandler(handlerArg, name, 0);
          */
          dtd->keepProcessing = dtd->standalone;
          goto endEntityValue;
        }
        if (entity->open) {
          if (enc == encoding)
            eventPtr = entityTextPtr;
          result = XML_ERROR_RECURSIVE_ENTITY_REF;
          goto endEntityValue;
        }
        if (entity->systemId) {
          if (externalEntityRefHandler) {
            dtd->paramEntityRead = XML_FALSE;
            entity->open = XML_TRUE;
            if (!externalEntityRefHandler(externalEntityRefHandlerArg,
                                          0,
                                          entity->base,
                                          entity->systemId,
                                          entity->publicId)) {
              entity->open = XML_FALSE;
              result = XML_ERROR_EXTERNAL_ENTITY_HANDLING;
              goto endEntityValue;
            }
            entity->open = XML_FALSE;
            if (!dtd->paramEntityRead)
              dtd->keepProcessing = dtd->standalone;
          }
          else
            dtd->keepProcessing = dtd->standalone;
        }
        else {
          entity->open = XML_TRUE;
          result = storeEntityValue(parser,
                                    internalEncoding,
                                    (char *)entity->textPtr,
                                    (char *)(entity->textPtr
                                             + entity->textLen));
          entity->open = XML_FALSE;
          if (result)
            goto endEntityValue;
        }
        break;
      }
#endif /* XML_DTD */
      /* In the internal subset, PE references are not legal
         within markup declarations, e.g entity values in this case. */
      eventPtr = entityTextPtr;
      result = XML_ERROR_PARAM_ENTITY_REF;
      goto endEntityValue;
    case XML_TOK_NONE:
      result = XML_ERROR_NONE;
      goto endEntityValue;
    case XML_TOK_ENTITY_REF:
    case XML_TOK_DATA_CHARS:
      if (!poolAppend(pool, enc, entityTextPtr, next)) {
        result = XML_ERROR_NO_MEMORY;
        goto endEntityValue;
      }
      break;
    case XML_TOK_TRAILING_CR:
      next = entityTextPtr + enc->minBytesPerChar;
      /* fall through */
    case XML_TOK_DATA_NEWLINE:
      if (pool->end == pool->ptr && !poolGrow(pool)) {
              result = XML_ERROR_NO_MEMORY;
        goto endEntityValue;
      }
      *(pool->ptr)++ = 0xA;
      break;
    case XML_TOK_CHAR_REF:
      {
        XML_Char buf[XML_ENCODE_MAX];
        int i;
        int n = XmlCharRefNumber(enc, entityTextPtr);
        if (n < 0) {
          if (enc == encoding)
            eventPtr = entityTextPtr;
          result = XML_ERROR_BAD_CHAR_REF;
          goto endEntityValue;
        }
        n = XmlEncode(n, (ICHAR *)buf);
        if (!n) {
          if (enc == encoding)
            eventPtr = entityTextPtr;
          result = XML_ERROR_BAD_CHAR_REF;
          goto endEntityValue;
        }
        for (i = 0; i < n; i++) {
          if (pool->end == pool->ptr && !poolGrow(pool)) {
            result = XML_ERROR_NO_MEMORY;
            goto endEntityValue;
          }
          *(pool->ptr)++ = buf[i];
        }
      }
      break;
    case XML_TOK_PARTIAL:
      if (enc == encoding)
        eventPtr = entityTextPtr;
      result = XML_ERROR_INVALID_TOKEN;
      goto endEntityValue;
    case XML_TOK_INVALID:
      if (enc == encoding)
        eventPtr = next;
      result = XML_ERROR_INVALID_TOKEN;
      goto endEntityValue;
    default:
      if (enc == encoding)
        eventPtr = entityTextPtr;
      result = XML_ERROR_UNEXPECTED_STATE;
      goto endEntityValue;
    }
    entityTextPtr = next;
  }
endEntityValue:
#ifdef XML_DTD
  prologState.inEntityValue = oldInEntityValue;
#endif /* XML_DTD */
  return result;
}

static void FASTCALL
normalizeLines(XML_Char *s)
{
  XML_Char *p;
  for (;; s++) {
    if (*s == XML_T('\0'))
      return;
    if (*s == 0xD)
      break;
  }
  p = s;
  do {
    if (*s == 0xD) {
      *p++ = 0xA;
      if (*++s == 0xA)
        s++;
    }
    else
      *p++ = *s++;
  } while (*s);
  *p = XML_T('\0');
}

static int
reportProcessingInstruction(XML_Parser parser, const ENCODING *enc,
                            const char *start, const char *end)
{
  const XML_Char *target;
  XML_Char *data;
  const char *tem;
  if (!processingInstructionHandler) {
    if (defaultHandler)
      reportDefault(parser, enc, start, end);
    return 1;
  }
  start += enc->minBytesPerChar * 2;
  tem = start + XmlNameLength(enc, start);
  target = poolStoreString(&tempPool, enc, start, tem);
  if (!target)
    return 0;
  poolFinish(&tempPool);
  data = poolStoreString(&tempPool, enc,
                        XmlSkipS(enc, tem),
                        end - enc->minBytesPerChar*2);
  if (!data)
    return 0;
  normalizeLines(data);
  processingInstructionHandler(handlerArg, target, data);
  poolClear(&tempPool);
  return 1;
}

static int
reportComment(XML_Parser parser, const ENCODING *enc,
              const char *start, const char *end)
{
  XML_Char *data;
  if (!commentHandler) {
    if (defaultHandler)
      reportDefault(parser, enc, start, end);
    return 1;
  }
  data = poolStoreString(&tempPool,
                         enc,
                         start + enc->minBytesPerChar * 4,
                         end - enc->minBytesPerChar * 3);
  if (!data)
    return 0;
  normalizeLines(data);
  commentHandler(handlerArg, data);
  poolClear(&tempPool);
  return 1;
}

static void
reportDefault(XML_Parser parser, const ENCODING *enc,
              const char *s, const char *end)
{
  if (MUST_CONVERT(enc, s)) {
    const char **eventPP;
    const char **eventEndPP;
    if (enc == encoding) {
      eventPP = &eventPtr;
      eventEndPP = &eventEndPtr;
    }
    else {
      eventPP = &(openInternalEntities->internalEventPtr);
      eventEndPP = &(openInternalEntities->internalEventEndPtr);
    }
    do {
      ICHAR *dataPtr = (ICHAR *)dataBuf;
      XmlConvert(enc, &s, end, &dataPtr, (ICHAR *)dataBufEnd);
      *eventEndPP = s;
      defaultHandler(handlerArg, dataBuf, (int)(dataPtr - (ICHAR *)dataBuf));
      *eventPP = s;
    } while (s != end);
  }
  else
    defaultHandler(handlerArg, (XML_Char *)s, (int)((XML_Char *)end - (XML_Char *)s));
}


static int
defineAttribute(ELEMENT_TYPE *type, ATTRIBUTE_ID *attId, XML_Bool isCdata,
                XML_Bool isId, const XML_Char *value, XML_Parser parser)
{
  DEFAULT_ATTRIBUTE *att;
  if (value || isId) {
    /* The handling of default attributes gets messed up if we have
       a default which duplicates a non-default. */
    int i;
    for (i = 0; i < type->nDefaultAtts; i++)
      if (attId == type->defaultAtts[i].id)
        return 1;
    if (isId && !type->idAtt && !attId->xmlns)
      type->idAtt = attId;
  }
  if (type->nDefaultAtts == type->allocDefaultAtts) {
    if (type->allocDefaultAtts == 0) {
      type->allocDefaultAtts = 8;
      type->defaultAtts = (DEFAULT_ATTRIBUTE *)MALLOC(type->allocDefaultAtts
                            * sizeof(DEFAULT_ATTRIBUTE));
      if (!type->defaultAtts)
        return 0;
    }
    else {
      DEFAULT_ATTRIBUTE *temp;
      int count = type->allocDefaultAtts * 2;
      temp = (DEFAULT_ATTRIBUTE *)
        REALLOC(type->defaultAtts, (count * sizeof(DEFAULT_ATTRIBUTE)));
      if (temp == NULL)
        return 0;
      type->allocDefaultAtts = count;
      type->defaultAtts = temp;
    }
  }
  att = type->defaultAtts + type->nDefaultAtts;
  att->id = attId;
  att->value = value;
  att->isCdata = isCdata;
  if (!isCdata)
    attId->maybeTokenized = XML_TRUE;
  type->nDefaultAtts += 1;
  return 1;
}

static int
setElementTypePrefix(XML_Parser parser, ELEMENT_TYPE *elementType)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  const XML_Char *name;
  for (name = elementType->name; *name; name++) {
    if (*name == XML_T(ASCII_COLON)) {
      PREFIX *prefix;
      const XML_Char *s;
      for (s = elementType->name; s != name; s++) {
        if (!poolAppendChar(&dtd->pool, *s))
          return 0;
      }
      if (!poolAppendChar(&dtd->pool, XML_T('\0')))
        return 0;
      prefix = (PREFIX *)lookup(&dtd->prefixes, poolStart(&dtd->pool),
                                sizeof(PREFIX));
      if (!prefix)
        return 0;
      if (prefix->name == poolStart(&dtd->pool))
        poolFinish(&dtd->pool);
      else
        poolDiscard(&dtd->pool);
      elementType->prefix = prefix;

    }
  }
  return 1;
}

static ATTRIBUTE_ID *
getAttributeId(XML_Parser parser, const ENCODING *enc,
               const char *start, const char *end)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  ATTRIBUTE_ID *id;
  const XML_Char *name;
  if (!poolAppendChar(&dtd->pool, XML_T('\0')))
    return NULL;
  name = poolStoreString(&dtd->pool, enc, start, end);
  if (!name)
    return NULL;
  /* skip quotation mark - its storage will be re-used (like in name[-1]) */
  ++name;
  id = (ATTRIBUTE_ID *)lookup(&dtd->attributeIds, name, sizeof(ATTRIBUTE_ID));
  if (!id)
    return NULL;
  if (id->name != name)
    poolDiscard(&dtd->pool);
  else {
    poolFinish(&dtd->pool);
    if (!ns)
      ;
    else if (name[0] == XML_T(ASCII_x)
        && name[1] == XML_T(ASCII_m)
        && name[2] == XML_T(ASCII_l)
        && name[3] == XML_T(ASCII_n)
        && name[4] == XML_T(ASCII_s)
        && (name[5] == XML_T('\0') || name[5] == XML_T(ASCII_COLON))) {
      if (name[5] == XML_T('\0'))
        id->prefix = &dtd->defaultPrefix;
      else
        id->prefix = (PREFIX *)lookup(&dtd->prefixes, name + 6, sizeof(PREFIX));
      id->xmlns = XML_TRUE;
    }
    else {
      int i;
      for (i = 0; name[i]; i++) {
        /* attributes without prefix are *not* in the default namespace */
        if (name[i] == XML_T(ASCII_COLON)) {
          int j;
          for (j = 0; j < i; j++) {
            if (!poolAppendChar(&dtd->pool, name[j]))
              return NULL;
          }
          if (!poolAppendChar(&dtd->pool, XML_T('\0')))
            return NULL;
          id->prefix = (PREFIX *)lookup(&dtd->prefixes, poolStart(&dtd->pool),
                                        sizeof(PREFIX));
          if (id->prefix->name == poolStart(&dtd->pool))
            poolFinish(&dtd->pool);
          else
            poolDiscard(&dtd->pool);
          break;
        }
      }
    }
  }
  return id;
}

#define CONTEXT_SEP XML_T(ASCII_FF)

static const XML_Char *
getContext(XML_Parser parser)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  HASH_TABLE_ITER iter;
  XML_Bool needSep = XML_FALSE;

  if (dtd->defaultPrefix.binding) {
    int i;
    int len;
    if (!poolAppendChar(&tempPool, XML_T(ASCII_EQUALS)))
      return NULL;
    len = dtd->defaultPrefix.binding->uriLen;
    if (namespaceSeparator)
      len--;
    for (i = 0; i < len; i++)
      if (!poolAppendChar(&tempPool, dtd->defaultPrefix.binding->uri[i]))
        return NULL;
    needSep = XML_TRUE;
  }

  hashTableIterInit(&iter, &(dtd->prefixes));
  for (;;) {
    int i;
    int len;
    const XML_Char *s;
    PREFIX *prefix = (PREFIX *)hashTableIterNext(&iter);
    if (!prefix)
      break;
    if (!prefix->binding)
      continue;
    if (needSep && !poolAppendChar(&tempPool, CONTEXT_SEP))
      return NULL;
    for (s = prefix->name; *s; s++)
      if (!poolAppendChar(&tempPool, *s))
        return NULL;
    if (!poolAppendChar(&tempPool, XML_T(ASCII_EQUALS)))
      return NULL;
    len = prefix->binding->uriLen;
    if (namespaceSeparator)
      len--;
    for (i = 0; i < len; i++)
      if (!poolAppendChar(&tempPool, prefix->binding->uri[i]))
        return NULL;
    needSep = XML_TRUE;
  }


  hashTableIterInit(&iter, &(dtd->generalEntities));
  for (;;) {
    const XML_Char *s;
    ENTITY *e = (ENTITY *)hashTableIterNext(&iter);
    if (!e)
      break;
    if (!e->open)
      continue;
    if (needSep && !poolAppendChar(&tempPool, CONTEXT_SEP))
      return NULL;
    for (s = e->name; *s; s++)
      if (!poolAppendChar(&tempPool, *s))
        return 0;
    needSep = XML_TRUE;
  }

  if (!poolAppendChar(&tempPool, XML_T('\0')))
    return NULL;
  return tempPool.start;
}

static XML_Bool
setContext(XML_Parser parser, const XML_Char *context)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  const XML_Char *s = context;

  while (*context != XML_T('\0')) {
    if (*s == CONTEXT_SEP || *s == XML_T('\0')) {
      ENTITY *e;
      if (!poolAppendChar(&tempPool, XML_T('\0')))
        return XML_FALSE;
      e = (ENTITY *)lookup(&dtd->generalEntities, poolStart(&tempPool), 0);
      if (e)
        e->open = XML_TRUE;
      if (*s != XML_T('\0'))
        s++;
      context = s;
      poolDiscard(&tempPool);
    }
    else if (*s == XML_T(ASCII_EQUALS)) {
      PREFIX *prefix;
      if (poolLength(&tempPool) == 0)
        prefix = &dtd->defaultPrefix;
      else {
        if (!poolAppendChar(&tempPool, XML_T('\0')))
          return XML_FALSE;
        prefix = (PREFIX *)lookup(&dtd->prefixes, poolStart(&tempPool),
                                  sizeof(PREFIX));
        if (!prefix)
          return XML_FALSE;
        if (prefix->name == poolStart(&tempPool)) {
          prefix->name = poolCopyString(&dtd->pool, prefix->name);
          if (!prefix->name)
            return XML_FALSE;
        }
        poolDiscard(&tempPool);
      }
      for (context = s + 1;
           *context != CONTEXT_SEP && *context != XML_T('\0');
           context++)
        if (!poolAppendChar(&tempPool, *context))
          return XML_FALSE;
      if (!poolAppendChar(&tempPool, XML_T('\0')))
        return XML_FALSE;
      if (addBinding(parser, prefix, NULL, poolStart(&tempPool),
                     &inheritedBindings) != XML_ERROR_NONE)
        return XML_FALSE;
      poolDiscard(&tempPool);
      if (*context != XML_T('\0'))
        ++context;
      s = context;
    }
    else {
      if (!poolAppendChar(&tempPool, *s))
        return XML_FALSE;
      s++;
    }
  }
  return XML_TRUE;
}

static void FASTCALL
normalizePublicId(XML_Char *publicId)
{
  XML_Char *p = publicId;
  XML_Char *s;
  for (s = publicId; *s; s++) {
    switch (*s) {
    case 0x20:
    case 0xD:
    case 0xA:
      if (p != publicId && p[-1] != 0x20)
        *p++ = 0x20;
      break;
    default:
      *p++ = *s;
    }
  }
  if (p != publicId && p[-1] == 0x20)
    --p;
  *p = XML_T('\0');
}

static DTD *
dtdCreate(const XML_Memory_Handling_Suite *ms)
{
  DTD *p = (DTD *)ms->malloc_fcn(sizeof(DTD));
  if (p == NULL)
    return p;
  poolInit(&(p->pool), ms);
  poolInit(&(p->entityValuePool), ms);
  hashTableInit(&(p->generalEntities), ms);
  hashTableInit(&(p->elementTypes), ms);
  hashTableInit(&(p->attributeIds), ms);
  hashTableInit(&(p->prefixes), ms);
#ifdef XML_DTD
  p->paramEntityRead = XML_FALSE;
  hashTableInit(&(p->paramEntities), ms);
#endif /* XML_DTD */
  p->defaultPrefix.name = NULL;
  p->defaultPrefix.binding = NULL;

  p->in_eldecl = XML_FALSE;
  p->scaffIndex = NULL;
  p->scaffold = NULL;
  p->scaffLevel = 0;
  p->scaffSize = 0;
  p->scaffCount = 0;
  p->contentStringLen = 0;

  p->keepProcessing = XML_TRUE;
  p->hasParamEntityRefs = XML_FALSE;
  p->standalone = XML_FALSE;
  return p;
}

static void
dtdReset(DTD *p, const XML_Memory_Handling_Suite *ms)
{
  HASH_TABLE_ITER iter;
  hashTableIterInit(&iter, &(p->elementTypes));
  for (;;) {
    ELEMENT_TYPE *e = (ELEMENT_TYPE *)hashTableIterNext(&iter);
    if (!e)
      break;
    if (e->allocDefaultAtts != 0)
      ms->free_fcn(e->defaultAtts);
  }
  hashTableClear(&(p->generalEntities));
#ifdef XML_DTD
  p->paramEntityRead = XML_FALSE;
  hashTableClear(&(p->paramEntities));
#endif /* XML_DTD */
  hashTableClear(&(p->elementTypes));
  hashTableClear(&(p->attributeIds));
  hashTableClear(&(p->prefixes));
  poolClear(&(p->pool));
  poolClear(&(p->entityValuePool));
  p->defaultPrefix.name = NULL;
  p->defaultPrefix.binding = NULL;

  p->in_eldecl = XML_FALSE;

  ms->free_fcn(p->scaffIndex);
  p->scaffIndex = NULL;
  ms->free_fcn(p->scaffold);
  p->scaffold = NULL;

  p->scaffLevel = 0;
  p->scaffSize = 0;
  p->scaffCount = 0;
  p->contentStringLen = 0;

  p->keepProcessing = XML_TRUE;
  p->hasParamEntityRefs = XML_FALSE;
  p->standalone = XML_FALSE;
}

static void
dtdDestroy(DTD *p, XML_Bool isDocEntity, const XML_Memory_Handling_Suite *ms)
{
  HASH_TABLE_ITER iter;
  hashTableIterInit(&iter, &(p->elementTypes));
  for (;;) {
    ELEMENT_TYPE *e = (ELEMENT_TYPE *)hashTableIterNext(&iter);
    if (!e)
      break;
    if (e->allocDefaultAtts != 0)
      ms->free_fcn(e->defaultAtts);
  }
  hashTableDestroy(&(p->generalEntities));
#ifdef XML_DTD
  hashTableDestroy(&(p->paramEntities));
#endif /* XML_DTD */
  hashTableDestroy(&(p->elementTypes));
  hashTableDestroy(&(p->attributeIds));
  hashTableDestroy(&(p->prefixes));
  poolDestroy(&(p->pool));
  poolDestroy(&(p->entityValuePool));
  if (isDocEntity) {
    ms->free_fcn(p->scaffIndex);
    ms->free_fcn(p->scaffold);
  }
  ms->free_fcn(p);
}

/* Do a deep copy of the DTD. Return 0 for out of memory, non-zero otherwise.
   The new DTD has already been initialized.
*/
static int
dtdCopy(DTD *newDtd, const DTD *oldDtd, const XML_Memory_Handling_Suite *ms)
{
  HASH_TABLE_ITER iter;

  /* Copy the prefix table. */

  hashTableIterInit(&iter, &(oldDtd->prefixes));
  for (;;) {
    const XML_Char *name;
    const PREFIX *oldP = (PREFIX *)hashTableIterNext(&iter);
    if (!oldP)
      break;
    name = poolCopyString(&(newDtd->pool), oldP->name);
    if (!name)
      return 0;
    if (!lookup(&(newDtd->prefixes), name, sizeof(PREFIX)))
      return 0;
  }

  hashTableIterInit(&iter, &(oldDtd->attributeIds));

  /* Copy the attribute id table. */

  for (;;) {
    ATTRIBUTE_ID *newA;
    const XML_Char *name;
    const ATTRIBUTE_ID *oldA = (ATTRIBUTE_ID *)hashTableIterNext(&iter);

    if (!oldA)
      break;
    /* Remember to allocate the scratch byte before the name. */
    if (!poolAppendChar(&(newDtd->pool), XML_T('\0')))
      return 0;
    name = poolCopyString(&(newDtd->pool), oldA->name);
    if (!name)
      return 0;
    ++name;
    newA = (ATTRIBUTE_ID *)lookup(&(newDtd->attributeIds), name,
                                  sizeof(ATTRIBUTE_ID));
    if (!newA)
      return 0;
    newA->maybeTokenized = oldA->maybeTokenized;
    if (oldA->prefix) {
      newA->xmlns = oldA->xmlns;
      if (oldA->prefix == &oldDtd->defaultPrefix)
        newA->prefix = &newDtd->defaultPrefix;
      else
        newA->prefix = (PREFIX *)lookup(&(newDtd->prefixes),
                                        oldA->prefix->name, 0);
    }
  }

  /* Copy the element type table. */

  hashTableIterInit(&iter, &(oldDtd->elementTypes));

  for (;;) {
    int i;
    ELEMENT_TYPE *newE;
    const XML_Char *name;
    const ELEMENT_TYPE *oldE = (ELEMENT_TYPE *)hashTableIterNext(&iter);
    if (!oldE)
      break;
    name = poolCopyString(&(newDtd->pool), oldE->name);
    if (!name)
      return 0;
    newE = (ELEMENT_TYPE *)lookup(&(newDtd->elementTypes), name,
                                  sizeof(ELEMENT_TYPE));
    if (!newE)
      return 0;
    if (oldE->nDefaultAtts) {
      newE->defaultAtts = (DEFAULT_ATTRIBUTE *)
          ms->malloc_fcn(oldE->nDefaultAtts * sizeof(DEFAULT_ATTRIBUTE));
      if (!newE->defaultAtts) {
        ms->free_fcn(newE);
        return 0;
      }
    }
    if (oldE->idAtt)
      newE->idAtt = (ATTRIBUTE_ID *)
          lookup(&(newDtd->attributeIds), oldE->idAtt->name, 0);
    newE->allocDefaultAtts = newE->nDefaultAtts = oldE->nDefaultAtts;
    if (oldE->prefix)
      newE->prefix = (PREFIX *)lookup(&(newDtd->prefixes),
                                      oldE->prefix->name, 0);
    for (i = 0; i < newE->nDefaultAtts; i++) {
      newE->defaultAtts[i].id = (ATTRIBUTE_ID *)
          lookup(&(newDtd->attributeIds), oldE->defaultAtts[i].id->name, 0);
      newE->defaultAtts[i].isCdata = oldE->defaultAtts[i].isCdata;
      if (oldE->defaultAtts[i].value) {
        newE->defaultAtts[i].value
            = poolCopyString(&(newDtd->pool), oldE->defaultAtts[i].value);
        if (!newE->defaultAtts[i].value)
          return 0;
      }
      else
        newE->defaultAtts[i].value = NULL;
    }
  }

  /* Copy the entity tables. */
  if (!copyEntityTable(&(newDtd->generalEntities),
                       &(newDtd->pool),
                       &(oldDtd->generalEntities)))
      return 0;

#ifdef XML_DTD
  if (!copyEntityTable(&(newDtd->paramEntities),
                       &(newDtd->pool),
                       &(oldDtd->paramEntities)))
      return 0;
  newDtd->paramEntityRead = oldDtd->paramEntityRead;
#endif /* XML_DTD */

  newDtd->keepProcessing = oldDtd->keepProcessing;
  newDtd->hasParamEntityRefs = oldDtd->hasParamEntityRefs;
  newDtd->standalone = oldDtd->standalone;

  /* Don't want deep copying for scaffolding */
  newDtd->in_eldecl = oldDtd->in_eldecl;
  newDtd->scaffold = oldDtd->scaffold;
  newDtd->contentStringLen = oldDtd->contentStringLen;
  newDtd->scaffSize = oldDtd->scaffSize;
  newDtd->scaffLevel = oldDtd->scaffLevel;
  newDtd->scaffIndex = oldDtd->scaffIndex;

  return 1;
}  /* End dtdCopy */

static int
copyEntityTable(HASH_TABLE *newTable,
                STRING_POOL *newPool,
                const HASH_TABLE *oldTable)
{
  HASH_TABLE_ITER iter;
  const XML_Char *cachedOldBase = NULL;
  const XML_Char *cachedNewBase = NULL;

  hashTableIterInit(&iter, oldTable);

  for (;;) {
    ENTITY *newE;
    const XML_Char *name;
    const ENTITY *oldE = (ENTITY *)hashTableIterNext(&iter);
    if (!oldE)
      break;
    name = poolCopyString(newPool, oldE->name);
    if (!name)
      return 0;
    newE = (ENTITY *)lookup(newTable, name, sizeof(ENTITY));
    if (!newE)
      return 0;
    if (oldE->systemId) {
      const XML_Char *tem = poolCopyString(newPool, oldE->systemId);
      if (!tem)
        return 0;
      newE->systemId = tem;
      if (oldE->base) {
        if (oldE->base == cachedOldBase)
          newE->base = cachedNewBase;
        else {
          cachedOldBase = oldE->base;
          tem = poolCopyString(newPool, cachedOldBase);
          if (!tem)
            return 0;
          cachedNewBase = newE->base = tem;
        }
      }
      if (oldE->publicId) {
        tem = poolCopyString(newPool, oldE->publicId);
        if (!tem)
          return 0;
        newE->publicId = tem;
      }
    }
    else {
      const XML_Char *tem = poolCopyStringN(newPool, oldE->textPtr,
                                            oldE->textLen);
      if (!tem)
        return 0;
      newE->textPtr = tem;
      newE->textLen = oldE->textLen;
    }
    if (oldE->notation) {
      const XML_Char *tem = poolCopyString(newPool, oldE->notation);
      if (!tem)
        return 0;
      newE->notation = tem;
    }
    newE->is_param = oldE->is_param;
    newE->is_internal = oldE->is_internal;
  }
  return 1;
}

#define INIT_POWER 6

static XML_Bool FASTCALL
keyeq(KEY s1, KEY s2)
{
  for (; *s1 == *s2; s1++, s2++)
    if (*s1 == 0)
      return XML_TRUE;
  return XML_FALSE;
}

static unsigned long FASTCALL
hash(KEY s)
{
  unsigned long h = 0;
  while (*s)
    h = CHAR_HASH(h, *s++);
  return h;
}

static NAMED *
lookup(HASH_TABLE *table, KEY name, size_t createSize)
{
  size_t i;
  if (table->size == 0) {
    size_t tsize;
    if (!createSize)
      return NULL;
    table->power = INIT_POWER;
    /* table->size is a power of 2 */
    table->size = (size_t)1 << INIT_POWER;
    tsize = table->size * sizeof(NAMED *);
    table->v = (NAMED **)table->mem->malloc_fcn(tsize);
    if (!table->v) {
      table->size = 0;
      return NULL;
    }
    memset(table->v, 0, tsize);
    i = hash(name) & ((unsigned long)table->size - 1);
  }
  else {
    unsigned long h = hash(name);
    unsigned long mask = (unsigned long)table->size - 1;
    unsigned char step = 0;
    i = h & mask;
    while (table->v[i]) {
      if (keyeq(name, table->v[i]->name))
        return table->v[i];
      if (!step)
        step = PROBE_STEP(h, mask, table->power);
      i < step ? (i += table->size - step) : (i -= step);
    }
    if (!createSize)
      return NULL;

    /* check for overflow (table is half full) */
    if (table->used >> (table->power - 1)) {
      unsigned char newPower = table->power + 1;
      size_t newSize = (size_t)1 << newPower;
      unsigned long newMask = (unsigned long)newSize - 1;
      size_t tsize = newSize * sizeof(NAMED *);
      NAMED **newV = (NAMED **)table->mem->malloc_fcn(tsize);
      if (!newV)
        return NULL;
      memset(newV, 0, tsize);
      for (i = 0; i < table->size; i++)
        if (table->v[i]) {
          unsigned long newHash = hash(table->v[i]->name);
          size_t j = newHash & newMask;
          step = 0;
          while (newV[j]) {
            if (!step)
              step = PROBE_STEP(newHash, newMask, newPower);
            j < step ? (j += newSize - step) : (j -= step);
          }
          newV[j] = table->v[i];
        }
      table->mem->free_fcn(table->v);
      table->v = newV;
      table->power = newPower;
      table->size = newSize;
      i = h & newMask;
      step = 0;
      while (table->v[i]) {
        if (!step)
          step = PROBE_STEP(h, newMask, newPower);
        i < step ? (i += newSize - step) : (i -= step);
      }
    }
  }
  table->v[i] = (NAMED *)table->mem->malloc_fcn(createSize);
  if (!table->v[i])
    return NULL;
  memset(table->v[i], 0, createSize);
  table->v[i]->name = name;
  (table->used)++;
  return table->v[i];
}

static void FASTCALL
hashTableClear(HASH_TABLE *table)
{
  size_t i;
  for (i = 0; i < table->size; i++) {
    table->mem->free_fcn(table->v[i]);
    table->v[i] = NULL;
  }
  table->used = 0;
}

static void FASTCALL
hashTableDestroy(HASH_TABLE *table)
{
  size_t i;
  for (i = 0; i < table->size; i++)
    table->mem->free_fcn(table->v[i]);
  table->mem->free_fcn(table->v);
}

static void FASTCALL
hashTableInit(HASH_TABLE *p, const XML_Memory_Handling_Suite *ms)
{
  p->power = 0;
  p->size = 0;
  p->used = 0;
  p->v = NULL;
  p->mem = ms;
}

static void FASTCALL
hashTableIterInit(HASH_TABLE_ITER *iter, const HASH_TABLE *table)
{
  iter->p = table->v;
  iter->end = iter->p + table->size;
}

static NAMED * FASTCALL
hashTableIterNext(HASH_TABLE_ITER *iter)
{
  while (iter->p != iter->end) {
    NAMED *tem = *(iter->p)++;
    if (tem)
      return tem;
  }
  return NULL;
}

static void FASTCALL
poolInit(STRING_POOL *pool, const XML_Memory_Handling_Suite *ms)
{
  pool->blocks = NULL;
  pool->freeBlocks = NULL;
  pool->start = NULL;
  pool->ptr = NULL;
  pool->end = NULL;
  pool->mem = ms;
}

static void FASTCALL
poolClear(STRING_POOL *pool)
{
  if (!pool->freeBlocks)
    pool->freeBlocks = pool->blocks;
  else {
    BLOCK *p = pool->blocks;
    while (p) {
      BLOCK *tem = p->next;
      p->next = pool->freeBlocks;
      pool->freeBlocks = p;
      p = tem;
    }
  }
  pool->blocks = NULL;
  pool->start = NULL;
  pool->ptr = NULL;
  pool->end = NULL;
}

static void FASTCALL
poolDestroy(STRING_POOL *pool)
{
  BLOCK *p = pool->blocks;
  while (p) {
    BLOCK *tem = p->next;
    pool->mem->free_fcn(p);
    p = tem;
  }
  p = pool->freeBlocks;
  while (p) {
    BLOCK *tem = p->next;
    pool->mem->free_fcn(p);
    p = tem;
  }
}

static XML_Char *
poolAppend(STRING_POOL *pool, const ENCODING *enc,
           const char *ptr, const char *end)
{
  if (!pool->ptr && !poolGrow(pool))
    return NULL;
  for (;;) {
    XmlConvert(enc, &ptr, end, (ICHAR **)&(pool->ptr), (ICHAR *)pool->end);
    if (ptr == end)
      break;
    if (!poolGrow(pool))
      return NULL;
  }
  return pool->start;
}

static const XML_Char * FASTCALL
poolCopyString(STRING_POOL *pool, const XML_Char *s)
{
  do {
    if (!poolAppendChar(pool, *s))
      return NULL;
  } while (*s++);
  s = pool->start;
  poolFinish(pool);
  return s;
}

static const XML_Char *
poolCopyStringN(STRING_POOL *pool, const XML_Char *s, int n)
{
  if (!pool->ptr && !poolGrow(pool))
    return NULL;
  for (; n > 0; --n, s++) {
    if (!poolAppendChar(pool, *s))
      return NULL;
  }
  s = pool->start;
  poolFinish(pool);
  return s;
}

static const XML_Char * FASTCALL
poolAppendString(STRING_POOL *pool, const XML_Char *s)
{
  while (*s) {
    if (!poolAppendChar(pool, *s))
      return NULL;
    s++;
  }
  return pool->start;
}

static XML_Char *
poolStoreString(STRING_POOL *pool, const ENCODING *enc,
                const char *ptr, const char *end)
{
  if (!poolAppend(pool, enc, ptr, end))
    return NULL;
  if (pool->ptr == pool->end && !poolGrow(pool))
    return NULL;
  *(pool->ptr)++ = 0;
  return pool->start;
}

static XML_Bool FASTCALL
poolGrow(STRING_POOL *pool)
{
  if (pool->freeBlocks) {
    if (pool->start == 0) {
      pool->blocks = pool->freeBlocks;
      pool->freeBlocks = pool->freeBlocks->next;
      pool->blocks->next = NULL;
      pool->start = pool->blocks->s;
      pool->end = pool->start + pool->blocks->size;
      pool->ptr = pool->start;
      return XML_TRUE;
    }
    if (pool->end - pool->start < pool->freeBlocks->size) {
      BLOCK *tem = pool->freeBlocks->next;
      pool->freeBlocks->next = pool->blocks;
      pool->blocks = pool->freeBlocks;
      pool->freeBlocks = tem;
      memcpy(pool->blocks->s, pool->start,
             (pool->end - pool->start) * sizeof(XML_Char));
      pool->ptr = pool->blocks->s + (pool->ptr - pool->start);
      pool->start = pool->blocks->s;
      pool->end = pool->start + pool->blocks->size;
      return XML_TRUE;
    }
  }
  if (pool->blocks && pool->start == pool->blocks->s) {
    int blockSize = (int)(pool->end - pool->start)*2;
    pool->blocks = (BLOCK *)
      pool->mem->realloc_fcn(pool->blocks,
                             (offsetof(BLOCK, s)
                              + blockSize * sizeof(XML_Char)));
    if (pool->blocks == NULL)
      return XML_FALSE;
    pool->blocks->size = blockSize;
    pool->ptr = pool->blocks->s + (pool->ptr - pool->start);
    pool->start = pool->blocks->s;
    pool->end = pool->start + blockSize;
  }
  else {
    BLOCK *tem;
    int blockSize = (int)(pool->end - pool->start);
    if (blockSize < INIT_BLOCK_SIZE)
      blockSize = INIT_BLOCK_SIZE;
    else
      blockSize *= 2;
    tem = (BLOCK *)pool->mem->malloc_fcn(offsetof(BLOCK, s)
                                        + blockSize * sizeof(XML_Char));
    if (!tem)
      return XML_FALSE;
    tem->size = blockSize;
    tem->next = pool->blocks;
    pool->blocks = tem;
    if (pool->ptr != pool->start)
      memcpy(tem->s, pool->start,
             (pool->ptr - pool->start) * sizeof(XML_Char));
    pool->ptr = tem->s + (pool->ptr - pool->start);
    pool->start = tem->s;
    pool->end = tem->s + blockSize;
  }
  return XML_TRUE;
}

static int FASTCALL
nextScaffoldPart(XML_Parser parser)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  CONTENT_SCAFFOLD * me;
  int next;

  if (!dtd->scaffIndex) {
    dtd->scaffIndex = (int *)MALLOC(groupSize * sizeof(int));
    if (!dtd->scaffIndex)
      return -1;
    dtd->scaffIndex[0] = 0;
  }

  if (dtd->scaffCount >= dtd->scaffSize) {
    CONTENT_SCAFFOLD *temp;
    if (dtd->scaffold) {
      temp = (CONTENT_SCAFFOLD *)
        REALLOC(dtd->scaffold, dtd->scaffSize * 2 * sizeof(CONTENT_SCAFFOLD));
      if (temp == NULL)
        return -1;
      dtd->scaffSize *= 2;
    }
    else {
      temp = (CONTENT_SCAFFOLD *)MALLOC(INIT_SCAFFOLD_ELEMENTS
                                        * sizeof(CONTENT_SCAFFOLD));
      if (temp == NULL)
        return -1;
      dtd->scaffSize = INIT_SCAFFOLD_ELEMENTS;
    }
    dtd->scaffold = temp;
  }
  next = dtd->scaffCount++;
  me = &dtd->scaffold[next];
  if (dtd->scaffLevel) {
    CONTENT_SCAFFOLD *parent = &dtd->scaffold[dtd->scaffIndex[dtd->scaffLevel-1]];
    if (parent->lastchild) {
      dtd->scaffold[parent->lastchild].nextsib = next;
    }
    if (!parent->childcnt)
      parent->firstchild = next;
    parent->lastchild = next;
    parent->childcnt++;
  }
  me->firstchild = me->lastchild = me->childcnt = me->nextsib = 0;
  return next;
}

static void
build_node(XML_Parser parser,
           int src_node,
           XML_Content *dest,
           XML_Content **contpos,
           XML_Char **strpos)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  dest->type = dtd->scaffold[src_node].type;
  dest->quant = dtd->scaffold[src_node].quant;
  if (dest->type == XML_CTYPE_NAME) {
    const XML_Char *src;
    dest->name = *strpos;
    src = dtd->scaffold[src_node].name;
    for (;;) {
      *(*strpos)++ = *src;
      if (!*src)
        break;
      src++;
    }
    dest->numchildren = 0;
    dest->children = NULL;
  }
  else {
    unsigned int i;
    int cn;
    dest->numchildren = dtd->scaffold[src_node].childcnt;
    dest->children = *contpos;
    *contpos += dest->numchildren;
    for (i = 0, cn = dtd->scaffold[src_node].firstchild;
         i < dest->numchildren;
         i++, cn = dtd->scaffold[cn].nextsib) {
      build_node(parser, cn, &(dest->children[i]), contpos, strpos);
    }
    dest->name = NULL;
  }
}

static XML_Content *
build_model (XML_Parser parser)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  XML_Content *ret;
  XML_Content *cpos;
  XML_Char * str;
  int allocsize = (dtd->scaffCount * sizeof(XML_Content)
                   + (dtd->contentStringLen * sizeof(XML_Char)));

  ret = (XML_Content *)MALLOC(allocsize);
  if (!ret)
    return NULL;

  str =  (XML_Char *) (&ret[dtd->scaffCount]);
  cpos = &ret[1];

  build_node(parser, 0, ret, &cpos, &str);
  return ret;
}

static ELEMENT_TYPE *
getElementType(XML_Parser parser,
               const ENCODING *enc,
               const char *ptr,
               const char *end)
{
  DTD * const dtd = _dtd;  /* save one level of indirection */
  const XML_Char *name = poolStoreString(&dtd->pool, enc, ptr, end);
  ELEMENT_TYPE *ret;

  if (!name)
    return NULL;
  ret = (ELEMENT_TYPE *) lookup(&dtd->elementTypes, name, sizeof(ELEMENT_TYPE));
  if (!ret)
    return NULL;
  if (ret->name != name)
    poolDiscard(&dtd->pool);
  else {
    poolFinish(&dtd->pool);
    if (!setElementTypePrefix(parser, ret))
      return NULL;
  }
  return ret;
}
genometools-1.5.1/src/external/expat-2.0.1/lib/xmlrole.c000077500000000000000000001045501211610345200226360ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

#include 

#ifdef COMPILED_FROM_DSP
#include "winconfig.h"
#elif defined(MACOS_CLASSIC)
#include "macconfig.h"
#elif defined(__amigaos4__)
#include "amigaconfig.h"
#elif defined(__WATCOMC__)
#include "watcomconfig.h"
#else
#ifdef HAVE_EXPAT_CONFIG_H
#include 
#endif
#endif /* ndef COMPILED_FROM_DSP */

#include "expat_external.h"
#include "internal.h"
#include "xmlrole.h"
#include "ascii.h"

/* Doesn't check:

 that ,| are not mixed in a model group
 content of literals

*/

static const char KW_ANY[] = {
    ASCII_A, ASCII_N, ASCII_Y, '\0' };
static const char KW_ATTLIST[] = {
    ASCII_A, ASCII_T, ASCII_T, ASCII_L, ASCII_I, ASCII_S, ASCII_T, '\0' };
static const char KW_CDATA[] = {
    ASCII_C, ASCII_D, ASCII_A, ASCII_T, ASCII_A, '\0' };
static const char KW_DOCTYPE[] = {
    ASCII_D, ASCII_O, ASCII_C, ASCII_T, ASCII_Y, ASCII_P, ASCII_E, '\0' };
static const char KW_ELEMENT[] = {
    ASCII_E, ASCII_L, ASCII_E, ASCII_M, ASCII_E, ASCII_N, ASCII_T, '\0' };
static const char KW_EMPTY[] = {
    ASCII_E, ASCII_M, ASCII_P, ASCII_T, ASCII_Y, '\0' };
static const char KW_ENTITIES[] = {
    ASCII_E, ASCII_N, ASCII_T, ASCII_I, ASCII_T, ASCII_I, ASCII_E, ASCII_S,
    '\0' };
static const char KW_ENTITY[] = {
    ASCII_E, ASCII_N, ASCII_T, ASCII_I, ASCII_T, ASCII_Y, '\0' };
static const char KW_FIXED[] = {
    ASCII_F, ASCII_I, ASCII_X, ASCII_E, ASCII_D, '\0' };
static const char KW_ID[] = {
    ASCII_I, ASCII_D, '\0' };
static const char KW_IDREF[] = {
    ASCII_I, ASCII_D, ASCII_R, ASCII_E, ASCII_F, '\0' };
static const char KW_IDREFS[] = {
    ASCII_I, ASCII_D, ASCII_R, ASCII_E, ASCII_F, ASCII_S, '\0' };
#ifdef XML_DTD
static const char KW_IGNORE[] = {
    ASCII_I, ASCII_G, ASCII_N, ASCII_O, ASCII_R, ASCII_E, '\0' };
#endif
static const char KW_IMPLIED[] = {
    ASCII_I, ASCII_M, ASCII_P, ASCII_L, ASCII_I, ASCII_E, ASCII_D, '\0' };
#ifdef XML_DTD
static const char KW_INCLUDE[] = {
    ASCII_I, ASCII_N, ASCII_C, ASCII_L, ASCII_U, ASCII_D, ASCII_E, '\0' };
#endif
static const char KW_NDATA[] = {
    ASCII_N, ASCII_D, ASCII_A, ASCII_T, ASCII_A, '\0' };
static const char KW_NMTOKEN[] = {
    ASCII_N, ASCII_M, ASCII_T, ASCII_O, ASCII_K, ASCII_E, ASCII_N, '\0' };
static const char KW_NMTOKENS[] = {
    ASCII_N, ASCII_M, ASCII_T, ASCII_O, ASCII_K, ASCII_E, ASCII_N, ASCII_S,
    '\0' };
static const char KW_NOTATION[] =
    { ASCII_N, ASCII_O, ASCII_T, ASCII_A, ASCII_T, ASCII_I, ASCII_O, ASCII_N,
      '\0' };
static const char KW_PCDATA[] = {
    ASCII_P, ASCII_C, ASCII_D, ASCII_A, ASCII_T, ASCII_A, '\0' };
static const char KW_PUBLIC[] = {
    ASCII_P, ASCII_U, ASCII_B, ASCII_L, ASCII_I, ASCII_C, '\0' };
static const char KW_REQUIRED[] = {
    ASCII_R, ASCII_E, ASCII_Q, ASCII_U, ASCII_I, ASCII_R, ASCII_E, ASCII_D,
    '\0' };
static const char KW_SYSTEM[] = {
    ASCII_S, ASCII_Y, ASCII_S, ASCII_T, ASCII_E, ASCII_M, '\0' };

#ifndef MIN_BYTES_PER_CHAR
#define MIN_BYTES_PER_CHAR(enc) ((enc)->minBytesPerChar)
#endif

#ifdef XML_DTD
#define setTopLevel(state) \
  ((state)->handler = ((state)->documentEntity \
                       ? internalSubset \
                       : externalSubset1))
#else /* not XML_DTD */
#define setTopLevel(state) ((state)->handler = internalSubset)
#endif /* not XML_DTD */

typedef int PTRCALL PROLOG_HANDLER(PROLOG_STATE *state,
                                   int tok,
                                   const char *ptr,
                                   const char *end,
                                   const ENCODING *enc);

static PROLOG_HANDLER
  prolog0, prolog1, prolog2,
  doctype0, doctype1, doctype2, doctype3, doctype4, doctype5,
  internalSubset,
  entity0, entity1, entity2, entity3, entity4, entity5, entity6,
  entity7, entity8, entity9, entity10,
  notation0, notation1, notation2, notation3, notation4,
  attlist0, attlist1, attlist2, attlist3, attlist4, attlist5, attlist6,
  attlist7, attlist8, attlist9,
  element0, element1, element2, element3, element4, element5, element6,
  element7,
#ifdef XML_DTD
  externalSubset0, externalSubset1,
  condSect0, condSect1, condSect2,
#endif /* XML_DTD */
  declClose,
  error;

static int FASTCALL common(PROLOG_STATE *state, int tok);

static int PTRCALL
prolog0(PROLOG_STATE *state,
        int tok,
        const char *ptr,
        const char *end,
        const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    state->handler = prolog1;
    return XML_ROLE_NONE;
  case XML_TOK_XML_DECL:
    state->handler = prolog1;
    return XML_ROLE_XML_DECL;
  case XML_TOK_PI:
    state->handler = prolog1;
    return XML_ROLE_PI;
  case XML_TOK_COMMENT:
    state->handler = prolog1;
    return XML_ROLE_COMMENT;
  case XML_TOK_BOM:
    return XML_ROLE_NONE;
  case XML_TOK_DECL_OPEN:
    if (!XmlNameMatchesAscii(enc,
                             ptr + 2 * MIN_BYTES_PER_CHAR(enc),
                             end,
                             KW_DOCTYPE))
      break;
    state->handler = doctype0;
    return XML_ROLE_DOCTYPE_NONE;
  case XML_TOK_INSTANCE_START:
    state->handler = error;
    return XML_ROLE_INSTANCE_START;
  }
  return common(state, tok);
}

static int PTRCALL
prolog1(PROLOG_STATE *state,
        int tok,
        const char *ptr,
        const char *end,
        const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NONE;
  case XML_TOK_PI:
    return XML_ROLE_PI;
  case XML_TOK_COMMENT:
    return XML_ROLE_COMMENT;
  case XML_TOK_BOM:
    return XML_ROLE_NONE;
  case XML_TOK_DECL_OPEN:
    if (!XmlNameMatchesAscii(enc,
                             ptr + 2 * MIN_BYTES_PER_CHAR(enc),
                             end,
                             KW_DOCTYPE))
      break;
    state->handler = doctype0;
    return XML_ROLE_DOCTYPE_NONE;
  case XML_TOK_INSTANCE_START:
    state->handler = error;
    return XML_ROLE_INSTANCE_START;
  }
  return common(state, tok);
}

static int PTRCALL
prolog2(PROLOG_STATE *state,
        int tok,
        __attribute__ ((unused)) const char *ptr,
        __attribute__ ((unused)) const char *end,
        __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NONE;
  case XML_TOK_PI:
    return XML_ROLE_PI;
  case XML_TOK_COMMENT:
    return XML_ROLE_COMMENT;
  case XML_TOK_INSTANCE_START:
    state->handler = error;
    return XML_ROLE_INSTANCE_START;
  }
  return common(state, tok);
}

static int PTRCALL
doctype0(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_DOCTYPE_NONE;
  case XML_TOK_NAME:
  case XML_TOK_PREFIXED_NAME:
    state->handler = doctype1;
    return XML_ROLE_DOCTYPE_NAME;
  }
  return common(state, tok);
}

static int PTRCALL
doctype1(PROLOG_STATE *state,
         int tok,
         const char *ptr,
         const char *end,
         const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_DOCTYPE_NONE;
  case XML_TOK_OPEN_BRACKET:
    state->handler = internalSubset;
    return XML_ROLE_DOCTYPE_INTERNAL_SUBSET;
  case XML_TOK_DECL_CLOSE:
    state->handler = prolog2;
    return XML_ROLE_DOCTYPE_CLOSE;
  case XML_TOK_NAME:
    if (XmlNameMatchesAscii(enc, ptr, end, KW_SYSTEM)) {
      state->handler = doctype3;
      return XML_ROLE_DOCTYPE_NONE;
    }
    if (XmlNameMatchesAscii(enc, ptr, end, KW_PUBLIC)) {
      state->handler = doctype2;
      return XML_ROLE_DOCTYPE_NONE;
    }
    break;
  }
  return common(state, tok);
}

static int PTRCALL
doctype2(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_DOCTYPE_NONE;
  case XML_TOK_LITERAL:
    state->handler = doctype3;
    return XML_ROLE_DOCTYPE_PUBLIC_ID;
  }
  return common(state, tok);
}

static int PTRCALL
doctype3(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_DOCTYPE_NONE;
  case XML_TOK_LITERAL:
    state->handler = doctype4;
    return XML_ROLE_DOCTYPE_SYSTEM_ID;
  }
  return common(state, tok);
}

static int PTRCALL
doctype4(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_DOCTYPE_NONE;
  case XML_TOK_OPEN_BRACKET:
    state->handler = internalSubset;
    return XML_ROLE_DOCTYPE_INTERNAL_SUBSET;
  case XML_TOK_DECL_CLOSE:
    state->handler = prolog2;
    return XML_ROLE_DOCTYPE_CLOSE;
  }
  return common(state, tok);
}

static int PTRCALL
doctype5(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_DOCTYPE_NONE;
  case XML_TOK_DECL_CLOSE:
    state->handler = prolog2;
    return XML_ROLE_DOCTYPE_CLOSE;
  }
  return common(state, tok);
}

static int PTRCALL
internalSubset(PROLOG_STATE *state,
               int tok,
               const char *ptr,
               const char *end,
               const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NONE;
  case XML_TOK_DECL_OPEN:
    if (XmlNameMatchesAscii(enc,
                            ptr + 2 * MIN_BYTES_PER_CHAR(enc),
                            end,
                            KW_ENTITY)) {
      state->handler = entity0;
      return XML_ROLE_ENTITY_NONE;
    }
    if (XmlNameMatchesAscii(enc,
                            ptr + 2 * MIN_BYTES_PER_CHAR(enc),
                            end,
                            KW_ATTLIST)) {
      state->handler = attlist0;
      return XML_ROLE_ATTLIST_NONE;
    }
    if (XmlNameMatchesAscii(enc,
                            ptr + 2 * MIN_BYTES_PER_CHAR(enc),
                            end,
                            KW_ELEMENT)) {
      state->handler = element0;
      return XML_ROLE_ELEMENT_NONE;
    }
    if (XmlNameMatchesAscii(enc,
                            ptr + 2 * MIN_BYTES_PER_CHAR(enc),
                            end,
                            KW_NOTATION)) {
      state->handler = notation0;
      return XML_ROLE_NOTATION_NONE;
    }
    break;
  case XML_TOK_PI:
    return XML_ROLE_PI;
  case XML_TOK_COMMENT:
    return XML_ROLE_COMMENT;
  case XML_TOK_PARAM_ENTITY_REF:
    return XML_ROLE_PARAM_ENTITY_REF;
  case XML_TOK_CLOSE_BRACKET:
    state->handler = doctype5;
    return XML_ROLE_DOCTYPE_NONE;
  case XML_TOK_NONE:
    return XML_ROLE_NONE;
  }
  return common(state, tok);
}

#ifdef XML_DTD

static int PTRCALL
externalSubset0(PROLOG_STATE *state,
                int tok,
                const char *ptr,
                const char *end,
                const ENCODING *enc)
{
  state->handler = externalSubset1;
  if (tok == XML_TOK_XML_DECL)
    return XML_ROLE_TEXT_DECL;
  return externalSubset1(state, tok, ptr, end, enc);
}

static int PTRCALL
externalSubset1(PROLOG_STATE *state,
                int tok,
                const char *ptr,
                const char *end,
                const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_COND_SECT_OPEN:
    state->handler = condSect0;
    return XML_ROLE_NONE;
  case XML_TOK_COND_SECT_CLOSE:
    if (state->includeLevel == 0)
      break;
    state->includeLevel -= 1;
    return XML_ROLE_NONE;
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NONE;
  case XML_TOK_CLOSE_BRACKET:
    break;
  case XML_TOK_NONE:
    if (state->includeLevel)
      break;
    return XML_ROLE_NONE;
  default:
    return internalSubset(state, tok, ptr, end, enc);
  }
  return common(state, tok);
}

#endif /* XML_DTD */

static int PTRCALL
entity0(PROLOG_STATE *state,
        int tok,
        __attribute__ ((unused)) const char *ptr,
        __attribute__ ((unused)) const char *end,
        __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_PERCENT:
    state->handler = entity1;
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_NAME:
    state->handler = entity2;
    return XML_ROLE_GENERAL_ENTITY_NAME;
  }
  return common(state, tok);
}

static int PTRCALL
entity1(PROLOG_STATE *state,
        int tok,
        __attribute__ ((unused)) const char *ptr,
        __attribute__ ((unused)) const char *end,
        __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_NAME:
    state->handler = entity7;
    return XML_ROLE_PARAM_ENTITY_NAME;
  }
  return common(state, tok);
}

static int PTRCALL
entity2(PROLOG_STATE *state,
        int tok,
        const char *ptr,
        const char *end,
        const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_NAME:
    if (XmlNameMatchesAscii(enc, ptr, end, KW_SYSTEM)) {
      state->handler = entity4;
      return XML_ROLE_ENTITY_NONE;
    }
    if (XmlNameMatchesAscii(enc, ptr, end, KW_PUBLIC)) {
      state->handler = entity3;
      return XML_ROLE_ENTITY_NONE;
    }
    break;
  case XML_TOK_LITERAL:
    state->handler = declClose;
    state->role_none = XML_ROLE_ENTITY_NONE;
    return XML_ROLE_ENTITY_VALUE;
  }
  return common(state, tok);
}

static int PTRCALL
entity3(PROLOG_STATE *state,
        int tok,
        __attribute__ ((unused)) const char *ptr,
        __attribute__ ((unused)) const char *end,
        __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_LITERAL:
    state->handler = entity4;
    return XML_ROLE_ENTITY_PUBLIC_ID;
  }
  return common(state, tok);
}

static int PTRCALL
entity4(PROLOG_STATE *state,
        int tok,
        __attribute__ ((unused)) const char *ptr,
        __attribute__ ((unused)) const char *end,
        __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_LITERAL:
    state->handler = entity5;
    return XML_ROLE_ENTITY_SYSTEM_ID;
  }
  return common(state, tok);
}

static int PTRCALL
entity5(PROLOG_STATE *state,
        int tok,
        const char *ptr,
        const char *end,
        const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_DECL_CLOSE:
    setTopLevel(state);
    return XML_ROLE_ENTITY_COMPLETE;
  case XML_TOK_NAME:
    if (XmlNameMatchesAscii(enc, ptr, end, KW_NDATA)) {
      state->handler = entity6;
      return XML_ROLE_ENTITY_NONE;
    }
    break;
  }
  return common(state, tok);
}

static int PTRCALL
entity6(PROLOG_STATE *state,
        int tok,
        __attribute__ ((unused)) const char *ptr,
        __attribute__ ((unused)) const char *end,
        __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_NAME:
    state->handler = declClose;
    state->role_none = XML_ROLE_ENTITY_NONE;
    return XML_ROLE_ENTITY_NOTATION_NAME;
  }
  return common(state, tok);
}

static int PTRCALL
entity7(PROLOG_STATE *state,
        int tok,
        const char *ptr,
        const char *end,
        const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_NAME:
    if (XmlNameMatchesAscii(enc, ptr, end, KW_SYSTEM)) {
      state->handler = entity9;
      return XML_ROLE_ENTITY_NONE;
    }
    if (XmlNameMatchesAscii(enc, ptr, end, KW_PUBLIC)) {
      state->handler = entity8;
      return XML_ROLE_ENTITY_NONE;
    }
    break;
  case XML_TOK_LITERAL:
    state->handler = declClose;
    state->role_none = XML_ROLE_ENTITY_NONE;
    return XML_ROLE_ENTITY_VALUE;
  }
  return common(state, tok);
}

static int PTRCALL
entity8(PROLOG_STATE *state,
        int tok,
        __attribute__ ((unused)) const char *ptr,
        __attribute__ ((unused)) const char *end,
        __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_LITERAL:
    state->handler = entity9;
    return XML_ROLE_ENTITY_PUBLIC_ID;
  }
  return common(state, tok);
}

static int PTRCALL
entity9(PROLOG_STATE *state,
        int tok,
        __attribute__ ((unused)) const char *ptr,
        __attribute__ ((unused)) const char *end,
        __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_LITERAL:
    state->handler = entity10;
    return XML_ROLE_ENTITY_SYSTEM_ID;
  }
  return common(state, tok);
}

static int PTRCALL
entity10(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ENTITY_NONE;
  case XML_TOK_DECL_CLOSE:
    setTopLevel(state);
    return XML_ROLE_ENTITY_COMPLETE;
  }
  return common(state, tok);
}

static int PTRCALL
notation0(PROLOG_STATE *state,
          int tok,
          __attribute__ ((unused)) const char *ptr,
          __attribute__ ((unused)) const char *end,
          __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NOTATION_NONE;
  case XML_TOK_NAME:
    state->handler = notation1;
    return XML_ROLE_NOTATION_NAME;
  }
  return common(state, tok);
}

static int PTRCALL
notation1(PROLOG_STATE *state,
          int tok,
          const char *ptr,
          const char *end,
          const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NOTATION_NONE;
  case XML_TOK_NAME:
    if (XmlNameMatchesAscii(enc, ptr, end, KW_SYSTEM)) {
      state->handler = notation3;
      return XML_ROLE_NOTATION_NONE;
    }
    if (XmlNameMatchesAscii(enc, ptr, end, KW_PUBLIC)) {
      state->handler = notation2;
      return XML_ROLE_NOTATION_NONE;
    }
    break;
  }
  return common(state, tok);
}

static int PTRCALL
notation2(PROLOG_STATE *state,
          int tok,
          __attribute__ ((unused)) const char *ptr,
          __attribute__ ((unused)) const char *end,
          __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NOTATION_NONE;
  case XML_TOK_LITERAL:
    state->handler = notation4;
    return XML_ROLE_NOTATION_PUBLIC_ID;
  }
  return common(state, tok);
}

static int PTRCALL
notation3(PROLOG_STATE *state,
          int tok,
          __attribute__ ((unused)) const char *ptr,
          __attribute__ ((unused)) const char *end,
          __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NOTATION_NONE;
  case XML_TOK_LITERAL:
    state->handler = declClose;
    state->role_none = XML_ROLE_NOTATION_NONE;
    return XML_ROLE_NOTATION_SYSTEM_ID;
  }
  return common(state, tok);
}

static int PTRCALL
notation4(PROLOG_STATE *state,
          int tok,
          __attribute__ ((unused)) const char *ptr,
          __attribute__ ((unused)) const char *end,
          __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NOTATION_NONE;
  case XML_TOK_LITERAL:
    state->handler = declClose;
    state->role_none = XML_ROLE_NOTATION_NONE;
    return XML_ROLE_NOTATION_SYSTEM_ID;
  case XML_TOK_DECL_CLOSE:
    setTopLevel(state);
    return XML_ROLE_NOTATION_NO_SYSTEM_ID;
  }
  return common(state, tok);
}

static int PTRCALL
attlist0(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_NAME:
  case XML_TOK_PREFIXED_NAME:
    state->handler = attlist1;
    return XML_ROLE_ATTLIST_ELEMENT_NAME;
  }
  return common(state, tok);
}

static int PTRCALL
attlist1(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_DECL_CLOSE:
    setTopLevel(state);
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_NAME:
  case XML_TOK_PREFIXED_NAME:
    state->handler = attlist2;
    return XML_ROLE_ATTRIBUTE_NAME;
  }
  return common(state, tok);
}

static int PTRCALL
attlist2(PROLOG_STATE *state,
         int tok,
         const char *ptr,
         const char *end,
         const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_NAME:
    {
      static const char * const types[] = {
        KW_CDATA,
        KW_ID,
        KW_IDREF,
        KW_IDREFS,
        KW_ENTITY,
        KW_ENTITIES,
        KW_NMTOKEN,
        KW_NMTOKENS,
      };
      int i;
      for (i = 0; i < (int)(sizeof(types)/sizeof(types[0])); i++)
        if (XmlNameMatchesAscii(enc, ptr, end, types[i])) {
          state->handler = attlist8;
          return XML_ROLE_ATTRIBUTE_TYPE_CDATA + i;
        }
    }
    if (XmlNameMatchesAscii(enc, ptr, end, KW_NOTATION)) {
      state->handler = attlist5;
      return XML_ROLE_ATTLIST_NONE;
    }
    break;
  case XML_TOK_OPEN_PAREN:
    state->handler = attlist3;
    return XML_ROLE_ATTLIST_NONE;
  }
  return common(state, tok);
}

static int PTRCALL
attlist3(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_NMTOKEN:
  case XML_TOK_NAME:
  case XML_TOK_PREFIXED_NAME:
    state->handler = attlist4;
    return XML_ROLE_ATTRIBUTE_ENUM_VALUE;
  }
  return common(state, tok);
}

static int PTRCALL
attlist4(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_CLOSE_PAREN:
    state->handler = attlist8;
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_OR:
    state->handler = attlist3;
    return XML_ROLE_ATTLIST_NONE;
  }
  return common(state, tok);
}

static int PTRCALL
attlist5(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_OPEN_PAREN:
    state->handler = attlist6;
    return XML_ROLE_ATTLIST_NONE;
  }
  return common(state, tok);
}

static int PTRCALL
attlist6(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_NAME:
    state->handler = attlist7;
    return XML_ROLE_ATTRIBUTE_NOTATION_VALUE;
  }
  return common(state, tok);
}

static int PTRCALL
attlist7(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_CLOSE_PAREN:
    state->handler = attlist8;
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_OR:
    state->handler = attlist6;
    return XML_ROLE_ATTLIST_NONE;
  }
  return common(state, tok);
}

/* default value */
static int PTRCALL
attlist8(PROLOG_STATE *state,
         int tok,
         const char *ptr,
         const char *end,
         const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_POUND_NAME:
    if (XmlNameMatchesAscii(enc,
                            ptr + MIN_BYTES_PER_CHAR(enc),
                            end,
                            KW_IMPLIED)) {
      state->handler = attlist1;
      return XML_ROLE_IMPLIED_ATTRIBUTE_VALUE;
    }
    if (XmlNameMatchesAscii(enc,
                            ptr + MIN_BYTES_PER_CHAR(enc),
                            end,
                            KW_REQUIRED)) {
      state->handler = attlist1;
      return XML_ROLE_REQUIRED_ATTRIBUTE_VALUE;
    }
    if (XmlNameMatchesAscii(enc,
                            ptr + MIN_BYTES_PER_CHAR(enc),
                            end,
                            KW_FIXED)) {
      state->handler = attlist9;
      return XML_ROLE_ATTLIST_NONE;
    }
    break;
  case XML_TOK_LITERAL:
    state->handler = attlist1;
    return XML_ROLE_DEFAULT_ATTRIBUTE_VALUE;
  }
  return common(state, tok);
}

static int PTRCALL
attlist9(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ATTLIST_NONE;
  case XML_TOK_LITERAL:
    state->handler = attlist1;
    return XML_ROLE_FIXED_ATTRIBUTE_VALUE;
  }
  return common(state, tok);
}

static int PTRCALL
element0(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ELEMENT_NONE;
  case XML_TOK_NAME:
  case XML_TOK_PREFIXED_NAME:
    state->handler = element1;
    return XML_ROLE_ELEMENT_NAME;
  }
  return common(state, tok);
}

static int PTRCALL
element1(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ELEMENT_NONE;
  case XML_TOK_NAME:
    if (XmlNameMatchesAscii(enc, ptr, end, KW_EMPTY)) {
      state->handler = declClose;
      state->role_none = XML_ROLE_ELEMENT_NONE;
      return XML_ROLE_CONTENT_EMPTY;
    }
    if (XmlNameMatchesAscii(enc, ptr, end, KW_ANY)) {
      state->handler = declClose;
      state->role_none = XML_ROLE_ELEMENT_NONE;
      return XML_ROLE_CONTENT_ANY;
    }
    break;
  case XML_TOK_OPEN_PAREN:
    state->handler = element2;
    state->level = 1;
    return XML_ROLE_GROUP_OPEN;
  }
  return common(state, tok);
}

static int PTRCALL
element2(PROLOG_STATE *state,
         int tok,
         const char *ptr,
         const char *end,
         const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ELEMENT_NONE;
  case XML_TOK_POUND_NAME:
    if (XmlNameMatchesAscii(enc,
                            ptr + MIN_BYTES_PER_CHAR(enc),
                            end,
                            KW_PCDATA)) {
      state->handler = element3;
      return XML_ROLE_CONTENT_PCDATA;
    }
    break;
  case XML_TOK_OPEN_PAREN:
    state->level = 2;
    state->handler = element6;
    return XML_ROLE_GROUP_OPEN;
  case XML_TOK_NAME:
  case XML_TOK_PREFIXED_NAME:
    state->handler = element7;
    return XML_ROLE_CONTENT_ELEMENT;
  case XML_TOK_NAME_QUESTION:
    state->handler = element7;
    return XML_ROLE_CONTENT_ELEMENT_OPT;
  case XML_TOK_NAME_ASTERISK:
    state->handler = element7;
    return XML_ROLE_CONTENT_ELEMENT_REP;
  case XML_TOK_NAME_PLUS:
    state->handler = element7;
    return XML_ROLE_CONTENT_ELEMENT_PLUS;
  }
  return common(state, tok);
}

static int PTRCALL
element3(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ELEMENT_NONE;
  case XML_TOK_CLOSE_PAREN:
    state->handler = declClose;
    state->role_none = XML_ROLE_ELEMENT_NONE;
    return XML_ROLE_GROUP_CLOSE;
  case XML_TOK_CLOSE_PAREN_ASTERISK:
    state->handler = declClose;
    state->role_none = XML_ROLE_ELEMENT_NONE;
    return XML_ROLE_GROUP_CLOSE_REP;
  case XML_TOK_OR:
    state->handler = element4;
    return XML_ROLE_ELEMENT_NONE;
  }
  return common(state, tok);
}

static int PTRCALL
element4(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ELEMENT_NONE;
  case XML_TOK_NAME:
  case XML_TOK_PREFIXED_NAME:
    state->handler = element5;
    return XML_ROLE_CONTENT_ELEMENT;
  }
  return common(state, tok);
}

static int PTRCALL
element5(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ELEMENT_NONE;
  case XML_TOK_CLOSE_PAREN_ASTERISK:
    state->handler = declClose;
    state->role_none = XML_ROLE_ELEMENT_NONE;
    return XML_ROLE_GROUP_CLOSE_REP;
  case XML_TOK_OR:
    state->handler = element4;
    return XML_ROLE_ELEMENT_NONE;
  }
  return common(state, tok);
}

static int PTRCALL
element6(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ELEMENT_NONE;
  case XML_TOK_OPEN_PAREN:
    state->level += 1;
    return XML_ROLE_GROUP_OPEN;
  case XML_TOK_NAME:
  case XML_TOK_PREFIXED_NAME:
    state->handler = element7;
    return XML_ROLE_CONTENT_ELEMENT;
  case XML_TOK_NAME_QUESTION:
    state->handler = element7;
    return XML_ROLE_CONTENT_ELEMENT_OPT;
  case XML_TOK_NAME_ASTERISK:
    state->handler = element7;
    return XML_ROLE_CONTENT_ELEMENT_REP;
  case XML_TOK_NAME_PLUS:
    state->handler = element7;
    return XML_ROLE_CONTENT_ELEMENT_PLUS;
  }
  return common(state, tok);
}

static int PTRCALL
element7(PROLOG_STATE *state,
         int tok,
         __attribute__ ((unused)) const char *ptr,
         __attribute__ ((unused)) const char *end,
         __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_ELEMENT_NONE;
  case XML_TOK_CLOSE_PAREN:
    state->level -= 1;
    if (state->level == 0) {
      state->handler = declClose;
      state->role_none = XML_ROLE_ELEMENT_NONE;
    }
    return XML_ROLE_GROUP_CLOSE;
  case XML_TOK_CLOSE_PAREN_ASTERISK:
    state->level -= 1;
    if (state->level == 0) {
      state->handler = declClose;
      state->role_none = XML_ROLE_ELEMENT_NONE;
    }
    return XML_ROLE_GROUP_CLOSE_REP;
  case XML_TOK_CLOSE_PAREN_QUESTION:
    state->level -= 1;
    if (state->level == 0) {
      state->handler = declClose;
      state->role_none = XML_ROLE_ELEMENT_NONE;
    }
    return XML_ROLE_GROUP_CLOSE_OPT;
  case XML_TOK_CLOSE_PAREN_PLUS:
    state->level -= 1;
    if (state->level == 0) {
      state->handler = declClose;
      state->role_none = XML_ROLE_ELEMENT_NONE;
    }
    return XML_ROLE_GROUP_CLOSE_PLUS;
  case XML_TOK_COMMA:
    state->handler = element6;
    return XML_ROLE_GROUP_SEQUENCE;
  case XML_TOK_OR:
    state->handler = element6;
    return XML_ROLE_GROUP_CHOICE;
  }
  return common(state, tok);
}

#ifdef XML_DTD

static int PTRCALL
condSect0(PROLOG_STATE *state,
          int tok,
          const char *ptr,
          const char *end,
          const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NONE;
  case XML_TOK_NAME:
    if (XmlNameMatchesAscii(enc, ptr, end, KW_INCLUDE)) {
      state->handler = condSect1;
      return XML_ROLE_NONE;
    }
    if (XmlNameMatchesAscii(enc, ptr, end, KW_IGNORE)) {
      state->handler = condSect2;
      return XML_ROLE_NONE;
    }
    break;
  }
  return common(state, tok);
}

static int PTRCALL
condSect1(PROLOG_STATE *state,
          int tok,
          const char *ptr,
          const char *end,
          const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NONE;
  case XML_TOK_OPEN_BRACKET:
    state->handler = externalSubset1;
    state->includeLevel += 1;
    return XML_ROLE_NONE;
  }
  return common(state, tok);
}

static int PTRCALL
condSect2(PROLOG_STATE *state,
          int tok,
          const char *ptr,
          const char *end,
          const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return XML_ROLE_NONE;
  case XML_TOK_OPEN_BRACKET:
    state->handler = externalSubset1;
    return XML_ROLE_IGNORE_SECT;
  }
  return common(state, tok);
}

#endif /* XML_DTD */

static int PTRCALL
declClose(PROLOG_STATE *state,
          int tok,
          __attribute__ ((unused)) const char *ptr,
          __attribute__ ((unused)) const char *end,
          __attribute__ ((unused)) const ENCODING *enc)
{
  switch (tok) {
  case XML_TOK_PROLOG_S:
    return state->role_none;
  case XML_TOK_DECL_CLOSE:
    setTopLevel(state);
    return state->role_none;
  }
  return common(state, tok);
}

static int PTRCALL
error(__attribute__ ((unused)) PROLOG_STATE *state,
      __attribute__ ((unused)) int tok,
      __attribute__ ((unused)) const char *ptr,
      __attribute__ ((unused)) const char *end,
      __attribute__ ((unused)) const ENCODING *enc)
{
  return XML_ROLE_NONE;
}

static int FASTCALL
common(PROLOG_STATE *state, __attribute__ ((unused)) int tok)
{
#ifdef XML_DTD
  if (!state->documentEntity && tok == XML_TOK_PARAM_ENTITY_REF)
    return XML_ROLE_INNER_PARAM_ENTITY_REF;
#endif
  state->handler = error;
  return XML_ROLE_ERROR;
}

void
XmlPrologStateInit(PROLOG_STATE *state)
{
  state->handler = prolog0;
#ifdef XML_DTD
  state->documentEntity = 1;
  state->includeLevel = 0;
  state->inEntityValue = 0;
#endif /* XML_DTD */
}

#ifdef XML_DTD

void
XmlPrologStateInitExternalEntity(PROLOG_STATE *state)
{
  state->handler = externalSubset0;
  state->documentEntity = 0;
  state->includeLevel = 0;
}

#endif /* XML_DTD */
genometools-1.5.1/src/external/expat-2.0.1/lib/xmlrole.h000077500000000000000000000057171211610345200226500ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

#ifndef XmlRole_INCLUDED
#define XmlRole_INCLUDED 1

#ifdef __VMS
/*      0        1         2         3      0        1         2         3
        1234567890123456789012345678901     1234567890123456789012345678901 */
#define XmlPrologStateInitExternalEntity    XmlPrologStateInitExternalEnt
#endif

#include "xmltok.h"

#ifdef __cplusplus
extern "C" {
#endif

enum {
  XML_ROLE_ERROR = -1,
  XML_ROLE_NONE = 0,
  XML_ROLE_XML_DECL,
  XML_ROLE_INSTANCE_START,
  XML_ROLE_DOCTYPE_NONE,
  XML_ROLE_DOCTYPE_NAME,
  XML_ROLE_DOCTYPE_SYSTEM_ID,
  XML_ROLE_DOCTYPE_PUBLIC_ID,
  XML_ROLE_DOCTYPE_INTERNAL_SUBSET,
  XML_ROLE_DOCTYPE_CLOSE,
  XML_ROLE_GENERAL_ENTITY_NAME,
  XML_ROLE_PARAM_ENTITY_NAME,
  XML_ROLE_ENTITY_NONE,
  XML_ROLE_ENTITY_VALUE,
  XML_ROLE_ENTITY_SYSTEM_ID,
  XML_ROLE_ENTITY_PUBLIC_ID,
  XML_ROLE_ENTITY_COMPLETE,
  XML_ROLE_ENTITY_NOTATION_NAME,
  XML_ROLE_NOTATION_NONE,
  XML_ROLE_NOTATION_NAME,
  XML_ROLE_NOTATION_SYSTEM_ID,
  XML_ROLE_NOTATION_NO_SYSTEM_ID,
  XML_ROLE_NOTATION_PUBLIC_ID,
  XML_ROLE_ATTRIBUTE_NAME,
  XML_ROLE_ATTRIBUTE_TYPE_CDATA,
  XML_ROLE_ATTRIBUTE_TYPE_ID,
  XML_ROLE_ATTRIBUTE_TYPE_IDREF,
  XML_ROLE_ATTRIBUTE_TYPE_IDREFS,
  XML_ROLE_ATTRIBUTE_TYPE_ENTITY,
  XML_ROLE_ATTRIBUTE_TYPE_ENTITIES,
  XML_ROLE_ATTRIBUTE_TYPE_NMTOKEN,
  XML_ROLE_ATTRIBUTE_TYPE_NMTOKENS,
  XML_ROLE_ATTRIBUTE_ENUM_VALUE,
  XML_ROLE_ATTRIBUTE_NOTATION_VALUE,
  XML_ROLE_ATTLIST_NONE,
  XML_ROLE_ATTLIST_ELEMENT_NAME,
  XML_ROLE_IMPLIED_ATTRIBUTE_VALUE,
  XML_ROLE_REQUIRED_ATTRIBUTE_VALUE,
  XML_ROLE_DEFAULT_ATTRIBUTE_VALUE,
  XML_ROLE_FIXED_ATTRIBUTE_VALUE,
  XML_ROLE_ELEMENT_NONE,
  XML_ROLE_ELEMENT_NAME,
  XML_ROLE_CONTENT_ANY,
  XML_ROLE_CONTENT_EMPTY,
  XML_ROLE_CONTENT_PCDATA,
  XML_ROLE_GROUP_OPEN,
  XML_ROLE_GROUP_CLOSE,
  XML_ROLE_GROUP_CLOSE_REP,
  XML_ROLE_GROUP_CLOSE_OPT,
  XML_ROLE_GROUP_CLOSE_PLUS,
  XML_ROLE_GROUP_CHOICE,
  XML_ROLE_GROUP_SEQUENCE,
  XML_ROLE_CONTENT_ELEMENT,
  XML_ROLE_CONTENT_ELEMENT_REP,
  XML_ROLE_CONTENT_ELEMENT_OPT,
  XML_ROLE_CONTENT_ELEMENT_PLUS,
  XML_ROLE_PI,
  XML_ROLE_COMMENT,
#ifdef XML_DTD
  XML_ROLE_TEXT_DECL,
  XML_ROLE_IGNORE_SECT,
  XML_ROLE_INNER_PARAM_ENTITY_REF,
#endif /* XML_DTD */
  XML_ROLE_PARAM_ENTITY_REF
};

typedef struct prolog_state {
  int (PTRCALL *handler) (struct prolog_state *state,
                          int tok,
                          const char *ptr,
                          const char *end,
                          const ENCODING *enc);
  unsigned level;
  int role_none;
#ifdef XML_DTD
  unsigned includeLevel;
  int documentEntity;
  int inEntityValue;
#endif /* XML_DTD */
} PROLOG_STATE;

void XmlPrologStateInit(PROLOG_STATE *);
#ifdef XML_DTD
void XmlPrologStateInitExternalEntity(PROLOG_STATE *);
#endif /* XML_DTD */

#define XmlTokenRole(state, tok, ptr, end, enc) \
 (((state)->handler)(state, tok, ptr, end, enc))

#ifdef __cplusplus
}
#endif

#endif /* not XmlRole_INCLUDED */
genometools-1.5.1/src/external/expat-2.0.1/lib/xmltok.c000077500000000000000000001215301211610345200224670ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

#include 

#ifdef COMPILED_FROM_DSP
#include "winconfig.h"
#elif defined(MACOS_CLASSIC)
#include "macconfig.h"
#elif defined(__amigaos4__)
#include "amigaconfig.h"
#elif defined(__WATCOMC__)
#include "watcomconfig.h"
#else
#ifdef HAVE_EXPAT_CONFIG_H
#include 
#endif
#endif /* ndef COMPILED_FROM_DSP */

#include "expat_external.h"
#include "internal.h"
#include "xmltok.h"
#include "nametab.h"

#ifdef XML_DTD
#define IGNORE_SECTION_TOK_VTABLE , PREFIX(ignoreSectionTok)
#else
#define IGNORE_SECTION_TOK_VTABLE /* as nothing */
#endif

#define VTABLE1 \
  { PREFIX(prologTok), PREFIX(contentTok), \
    PREFIX(cdataSectionTok) IGNORE_SECTION_TOK_VTABLE }, \
  { PREFIX(attributeValueTok), PREFIX(entityValueTok) }, \
  PREFIX(sameName), \
  PREFIX(nameMatchesAscii), \
  PREFIX(nameLength), \
  PREFIX(skipS), \
  PREFIX(getAtts), \
  PREFIX(charRefNumber), \
  PREFIX(predefinedEntityName), \
  PREFIX(updatePosition), \
  PREFIX(isPublicId)

#define VTABLE VTABLE1, PREFIX(toUtf8), PREFIX(toUtf16)

#define UCS2_GET_NAMING(pages, hi, lo) \
   (namingBitmap[(pages[hi] << 3) + ((lo) >> 5)] & (1 << ((lo) & 0x1F)))

/* A 2 byte UTF-8 representation splits the characters 11 bits between
   the bottom 5 and 6 bits of the bytes.  We need 8 bits to index into
   pages, 3 bits to add to that index and 5 bits to generate the mask.
*/
#define UTF8_GET_NAMING2(pages, byte) \
    (namingBitmap[((pages)[(((byte)[0]) >> 2) & 7] << 3) \
                      + ((((byte)[0]) & 3) << 1) \
                      + ((((byte)[1]) >> 5) & 1)] \
         & (1 << (((byte)[1]) & 0x1F)))

/* A 3 byte UTF-8 representation splits the characters 16 bits between
   the bottom 4, 6 and 6 bits of the bytes.  We need 8 bits to index
   into pages, 3 bits to add to that index and 5 bits to generate the
   mask.
*/
#define UTF8_GET_NAMING3(pages, byte) \
  (namingBitmap[((pages)[((((byte)[0]) & 0xF) << 4) \
                             + ((((byte)[1]) >> 2) & 0xF)] \
                       << 3) \
                      + ((((byte)[1]) & 3) << 1) \
                      + ((((byte)[2]) >> 5) & 1)] \
         & (1 << (((byte)[2]) & 0x1F)))

#define UTF8_GET_NAMING(pages, p, n) \
  ((n) == 2 \
  ? UTF8_GET_NAMING2(pages, (const unsigned char *)(p)) \
  : ((n) == 3 \
     ? UTF8_GET_NAMING3(pages, (const unsigned char *)(p)) \
     : 0))

/* Detection of invalid UTF-8 sequences is based on Table 3.1B
   of Unicode 3.2: http://www.unicode.org/unicode/reports/tr28/
   with the additional restriction of not allowing the Unicode
   code points 0xFFFF and 0xFFFE (sequences EF,BF,BF and EF,BF,BE).
   Implementation details:
     (A & 0x80) == 0     means A < 0x80
   and
     (A & 0xC0) == 0xC0  means A > 0xBF
*/

#define UTF8_INVALID2(p) \
  ((*p) < 0xC2 || ((p)[1] & 0x80) == 0 || ((p)[1] & 0xC0) == 0xC0)

#define UTF8_INVALID3(p) \
  (((p)[2] & 0x80) == 0 \
  || \
  ((*p) == 0xEF && (p)[1] == 0xBF \
    ? \
    (p)[2] > 0xBD \
    : \
    ((p)[2] & 0xC0) == 0xC0) \
  || \
  ((*p) == 0xE0 \
    ? \
    (p)[1] < 0xA0 || ((p)[1] & 0xC0) == 0xC0 \
    : \
    ((p)[1] & 0x80) == 0 \
    || \
    ((*p) == 0xED ? (p)[1] > 0x9F : ((p)[1] & 0xC0) == 0xC0)))

#define UTF8_INVALID4(p) \
  (((p)[3] & 0x80) == 0 || ((p)[3] & 0xC0) == 0xC0 \
  || \
  ((p)[2] & 0x80) == 0 || ((p)[2] & 0xC0) == 0xC0 \
  || \
  ((*p) == 0xF0 \
    ? \
    (p)[1] < 0x90 || ((p)[1] & 0xC0) == 0xC0 \
    : \
    ((p)[1] & 0x80) == 0 \
    || \
    ((*p) == 0xF4 ? (p)[1] > 0x8F : ((p)[1] & 0xC0) == 0xC0)))

static int PTRFASTCALL
isNever(__attribute__ ((unused)) const ENCODING *enc,
        __attribute__ ((unused)) const char *p)
{
  return 0;
}

static int PTRFASTCALL
utf8_isName2(__attribute__ ((unused)) const ENCODING *enc, const char *p)
{
  return UTF8_GET_NAMING2(namePages, (const unsigned char *)p);
}

static int PTRFASTCALL
utf8_isName3(__attribute__ ((unused)) const ENCODING *enc, const char *p)
{
  return UTF8_GET_NAMING3(namePages, (const unsigned char *)p);
}

#define utf8_isName4 isNever

static int PTRFASTCALL
utf8_isNmstrt2(__attribute__ ((unused)) const ENCODING *enc, const char *p)
{
  return UTF8_GET_NAMING2(nmstrtPages, (const unsigned char *)p);
}

static int PTRFASTCALL
utf8_isNmstrt3(__attribute__ ((unused)) const ENCODING *enc, const char *p)
{
  return UTF8_GET_NAMING3(nmstrtPages, (const unsigned char *)p);
}

#define utf8_isNmstrt4 isNever

static int PTRFASTCALL
utf8_isInvalid2(__attribute__ ((unused)) const ENCODING *enc, const char *p)
{
  return UTF8_INVALID2((const unsigned char *)p);
}

static int PTRFASTCALL
utf8_isInvalid3(__attribute__ ((unused)) const ENCODING *enc, const char *p)
{
  return UTF8_INVALID3((const unsigned char *)p);
}

static int PTRFASTCALL
utf8_isInvalid4(__attribute__ ((unused)) const ENCODING *enc, const char *p)
{
  return UTF8_INVALID4((const unsigned char *)p);
}

struct normal_encoding {
  ENCODING enc;
  unsigned char type[256];
#ifdef XML_MIN_SIZE
  int (PTRFASTCALL *byteType)(const ENCODING *, const char *);
  int (PTRFASTCALL *isNameMin)(const ENCODING *, const char *);
  int (PTRFASTCALL *isNmstrtMin)(const ENCODING *, const char *);
  int (PTRFASTCALL *byteToAscii)(const ENCODING *, const char *);
  int (PTRCALL *charMatches)(const ENCODING *, const char *, int);
#endif /* XML_MIN_SIZE */
  int (PTRFASTCALL *isName2)(const ENCODING *, const char *);
  int (PTRFASTCALL *isName3)(const ENCODING *, const char *);
  int (PTRFASTCALL *isName4)(const ENCODING *, const char *);
  int (PTRFASTCALL *isNmstrt2)(const ENCODING *, const char *);
  int (PTRFASTCALL *isNmstrt3)(const ENCODING *, const char *);
  int (PTRFASTCALL *isNmstrt4)(const ENCODING *, const char *);
  int (PTRFASTCALL *isInvalid2)(const ENCODING *, const char *);
  int (PTRFASTCALL *isInvalid3)(const ENCODING *, const char *);
  int (PTRFASTCALL *isInvalid4)(const ENCODING *, const char *);
};

#define AS_NORMAL_ENCODING(enc)   ((const struct normal_encoding *) (enc))

#ifdef XML_MIN_SIZE

#define STANDARD_VTABLE(E) \
 E ## byteType, \
 E ## isNameMin, \
 E ## isNmstrtMin, \
 E ## byteToAscii, \
 E ## charMatches,

#else

#define STANDARD_VTABLE(E) /* as nothing */

#endif

#define NORMAL_VTABLE(E) \
 E ## isName2, \
 E ## isName3, \
 E ## isName4, \
 E ## isNmstrt2, \
 E ## isNmstrt3, \
 E ## isNmstrt4, \
 E ## isInvalid2, \
 E ## isInvalid3, \
 E ## isInvalid4

static int FASTCALL checkCharRefNumber(int);

#include "xmltok_impl.h"
#include "ascii.h"

#ifdef XML_MIN_SIZE
#define sb_isNameMin isNever
#define sb_isNmstrtMin isNever
#endif

#ifdef XML_MIN_SIZE
#define MINBPC(enc) ((enc)->minBytesPerChar)
#else
/* minimum bytes per character */
#define MINBPC(enc) 1
#endif

#define SB_BYTE_TYPE(enc, p) \
  (((struct normal_encoding *)(enc))->type[(unsigned char)*(p)])

#ifdef XML_MIN_SIZE
static int PTRFASTCALL
sb_byteType(const ENCODING *enc, const char *p)
{
  return SB_BYTE_TYPE(enc, p);
}
#define BYTE_TYPE(enc, p) \
 (AS_NORMAL_ENCODING(enc)->byteType(enc, p))
#else
#define BYTE_TYPE(enc, p) SB_BYTE_TYPE(enc, p)
#endif

#ifdef XML_MIN_SIZE
#define BYTE_TO_ASCII(enc, p) \
 (AS_NORMAL_ENCODING(enc)->byteToAscii(enc, p))
static int PTRFASTCALL
sb_byteToAscii(const ENCODING *enc, const char *p)
{
  return *p;
}
#else
#define BYTE_TO_ASCII(enc, p) (*(p))
#endif

#define IS_NAME_CHAR(enc, p, n) \
 (AS_NORMAL_ENCODING(enc)->isName ## n(enc, p))
#define IS_NMSTRT_CHAR(enc, p, n) \
 (AS_NORMAL_ENCODING(enc)->isNmstrt ## n(enc, p))
#define IS_INVALID_CHAR(enc, p, n) \
 (AS_NORMAL_ENCODING(enc)->isInvalid ## n(enc, p))

#ifdef XML_MIN_SIZE
#define IS_NAME_CHAR_MINBPC(enc, p) \
 (AS_NORMAL_ENCODING(enc)->isNameMin(enc, p))
#define IS_NMSTRT_CHAR_MINBPC(enc, p) \
 (AS_NORMAL_ENCODING(enc)->isNmstrtMin(enc, p))
#else
#define IS_NAME_CHAR_MINBPC(enc, p) (0)
#define IS_NMSTRT_CHAR_MINBPC(enc, p) (0)
#endif

#ifdef XML_MIN_SIZE
#define CHAR_MATCHES(enc, p, c) \
 (AS_NORMAL_ENCODING(enc)->charMatches(enc, p, c))
static int PTRCALL
sb_charMatches(const ENCODING *enc, const char *p, int c)
{
  return *p == c;
}
#else
/* c is an ASCII character */
#define CHAR_MATCHES(enc, p, c) (*(p) == c)
#endif

#define PREFIX(ident) normal_ ## ident
#define XML_TOK_IMPL_C
#include "xmltok_impl.c"
#undef XML_TOK_IMPL_C

#undef MINBPC
#undef BYTE_TYPE
#undef BYTE_TO_ASCII
#undef CHAR_MATCHES
#undef IS_NAME_CHAR
#undef IS_NAME_CHAR_MINBPC
#undef IS_NMSTRT_CHAR
#undef IS_NMSTRT_CHAR_MINBPC
#undef IS_INVALID_CHAR

enum {  /* UTF8_cvalN is value of masked first byte of N byte sequence */
  UTF8_cval1 = 0x00,
  UTF8_cval2 = 0xc0,
  UTF8_cval3 = 0xe0,
  UTF8_cval4 = 0xf0
};

static void PTRCALL
utf8_toUtf8(__attribute__ ((unused)) const ENCODING *enc,
            const char **fromP, const char *fromLim,
            char **toP, const char *toLim)
{
  char *to;
  const char *from;
  if (fromLim - *fromP > toLim - *toP) {
    /* Avoid copying partial characters. */
    for (fromLim = *fromP + (toLim - *toP); fromLim > *fromP; fromLim--)
      if (((unsigned char)fromLim[-1] & 0xc0) != 0x80)
        break;
  }
  for (to = *toP, from = *fromP; from != fromLim; from++, to++)
    *to = *from;
  *fromP = from;
  *toP = to;
}

static void PTRCALL
utf8_toUtf16(const ENCODING *enc,
             const char **fromP, const char *fromLim,
             unsigned short **toP, const unsigned short *toLim)
{
  unsigned short *to = *toP;
  const char *from = *fromP;
  while (from != fromLim && to != toLim) {
    switch (((struct normal_encoding *)enc)->type[(unsigned char)*from]) {
    case BT_LEAD2:
      *to++ = (unsigned short)(((from[0] & 0x1f) << 6) | (from[1] & 0x3f));
      from += 2;
      break;
    case BT_LEAD3:
      *to++ = (unsigned short)(((from[0] & 0xf) << 12)
                               | ((from[1] & 0x3f) << 6) | (from[2] & 0x3f));
      from += 3;
      break;
    case BT_LEAD4:
      {
        unsigned long n;
        if (to + 1 == toLim)
          goto after;
        n = ((from[0] & 0x7) << 18) | ((from[1] & 0x3f) << 12)
            | ((from[2] & 0x3f) << 6) | (from[3] & 0x3f);
        n -= 0x10000;
        to[0] = (unsigned short)((n >> 10) | 0xD800);
        to[1] = (unsigned short)((n & 0x3FF) | 0xDC00);
        to += 2;
        from += 4;
      }
      break;
    default:
      *to++ = *from++;
      break;
    }
  }
after:
  *fromP = from;
  *toP = to;
}

#ifdef XML_NS
static const struct normal_encoding utf8_encoding_ns = {
  { VTABLE1, utf8_toUtf8, utf8_toUtf16, 1, 1, 0 },
  {
#include "asciitab.h"
#include "utf8tab.h"
  },
  STANDARD_VTABLE(sb_) NORMAL_VTABLE(utf8_)
};
#endif

static const struct normal_encoding utf8_encoding = {
  { VTABLE1, utf8_toUtf8, utf8_toUtf16, 1, 1, 0 },
  {
#define BT_COLON BT_NMSTRT
#include "asciitab.h"
#undef BT_COLON
#include "utf8tab.h"
  },
  STANDARD_VTABLE(sb_) NORMAL_VTABLE(utf8_)
};

#ifdef XML_NS

static const struct normal_encoding internal_utf8_encoding_ns = {
  { VTABLE1, utf8_toUtf8, utf8_toUtf16, 1, 1, 0 },
  {
#include "iasciitab.h"
#include "utf8tab.h"
  },
  STANDARD_VTABLE(sb_) NORMAL_VTABLE(utf8_)
};

#endif

static const struct normal_encoding internal_utf8_encoding = {
  { VTABLE1, utf8_toUtf8, utf8_toUtf16, 1, 1, 0 },
  {
#define BT_COLON BT_NMSTRT
#include "iasciitab.h"
#undef BT_COLON
#include "utf8tab.h"
  },
  STANDARD_VTABLE(sb_) NORMAL_VTABLE(utf8_)
};

static void PTRCALL
latin1_toUtf8(__attribute__ ((unused)) const ENCODING *enc,
              const char **fromP, const char *fromLim,
              char **toP, const char *toLim)
{
  for (;;) {
    unsigned char c;
    if (*fromP == fromLim)
      break;
    c = (unsigned char)**fromP;
    if (c & 0x80) {
      if (toLim - *toP < 2)
        break;
      *(*toP)++ = (char)((c >> 6) | UTF8_cval2);
      *(*toP)++ = (char)((c & 0x3f) | 0x80);
      (*fromP)++;
    }
    else {
      if (*toP == toLim)
        break;
      *(*toP)++ = *(*fromP)++;
    }
  }
}

static void PTRCALL
latin1_toUtf16(__attribute__ ((unused)) const ENCODING *enc,
               const char **fromP, const char *fromLim,
               unsigned short **toP, const unsigned short *toLim)
{
  while (*fromP != fromLim && *toP != toLim)
    *(*toP)++ = (unsigned char)*(*fromP)++;
}

#ifdef XML_NS

static const struct normal_encoding latin1_encoding_ns = {
  { VTABLE1, latin1_toUtf8, latin1_toUtf16, 1, 0, 0 },
  {
#include "asciitab.h"
#include "latin1tab.h"
  },
  STANDARD_VTABLE(sb_)
};

#endif

static const struct normal_encoding latin1_encoding = {
  { VTABLE1, latin1_toUtf8, latin1_toUtf16, 1, 0, 0 },
  {
#define BT_COLON BT_NMSTRT
#include "asciitab.h"
#undef BT_COLON
#include "latin1tab.h"
  },
  STANDARD_VTABLE(sb_)
};

static void PTRCALL
ascii_toUtf8(__attribute__ ((unused)) const ENCODING *enc,
             const char **fromP, const char *fromLim,
             char **toP, const char *toLim)
{
  while (*fromP != fromLim && *toP != toLim)
    *(*toP)++ = *(*fromP)++;
}

#ifdef XML_NS

static const struct normal_encoding ascii_encoding_ns = {
  { VTABLE1, ascii_toUtf8, latin1_toUtf16, 1, 1, 0 },
  {
#include "asciitab.h"
/* BT_NONXML == 0 */
  },
  STANDARD_VTABLE(sb_)
};

#endif

static const struct normal_encoding ascii_encoding = {
  { VTABLE1, ascii_toUtf8, latin1_toUtf16, 1, 1, 0 },
  {
#define BT_COLON BT_NMSTRT
#include "asciitab.h"
#undef BT_COLON
/* BT_NONXML == 0 */
  },
  STANDARD_VTABLE(sb_)
};

static int PTRFASTCALL
unicode_byte_type(char hi, char lo)
{
  switch ((unsigned char)hi) {
  case 0xD8: case 0xD9: case 0xDA: case 0xDB:
    return BT_LEAD4;
  case 0xDC: case 0xDD: case 0xDE: case 0xDF:
    return BT_TRAIL;
  case 0xFF:
    switch ((unsigned char)lo) {
    case 0xFF:
    case 0xFE:
      return BT_NONXML;
    }
    break;
  }
  return BT_NONASCII;
}

#define DEFINE_UTF16_TO_UTF8(E) \
static void  PTRCALL \
E ## toUtf8(__attribute__ ((unused)) const ENCODING *enc, \
            const char **fromP, const char *fromLim, \
            char **toP, const char *toLim) \
{ \
  const char *from; \
  for (from = *fromP; from != fromLim; from += 2) { \
    int plane; \
    unsigned char lo2; \
    unsigned char lo = GET_LO(from); \
    unsigned char hi = GET_HI(from); \
    switch (hi) { \
    case 0: \
      if (lo < 0x80) { \
        if (*toP == toLim) { \
          *fromP = from; \
          return; \
        } \
        *(*toP)++ = lo; \
        break; \
      } \
      /* fall through */ \
    case 0x1: case 0x2: case 0x3: \
    case 0x4: case 0x5: case 0x6: case 0x7: \
      if (toLim -  *toP < 2) { \
        *fromP = from; \
        return; \
      } \
      *(*toP)++ = ((lo >> 6) | (hi << 2) |  UTF8_cval2); \
      *(*toP)++ = ((lo & 0x3f) | 0x80); \
      break; \
    default: \
      if (toLim -  *toP < 3)  { \
        *fromP = from; \
        return; \
      } \
      /* 16 bits divided 4, 6, 6 amongst 3 bytes */ \
      *(*toP)++ = ((hi >> 4) | UTF8_cval3); \
      *(*toP)++ = (((hi & 0xf) << 2) | (lo >> 6) | 0x80); \
      *(*toP)++ = ((lo & 0x3f) | 0x80); \
      break; \
    case 0xD8: case 0xD9: case 0xDA: case 0xDB: \
      if (toLim -  *toP < 4) { \
        *fromP = from; \
        return; \
      } \
      plane = (((hi & 0x3) << 2) | ((lo >> 6) & 0x3)) + 1; \
      *(*toP)++ = ((plane >> 2) | UTF8_cval4); \
      *(*toP)++ = (((lo >> 2) & 0xF) | ((plane & 0x3) << 4) | 0x80); \
      from += 2; \
      lo2 = GET_LO(from); \
      *(*toP)++ = (((lo & 0x3) << 4) \
                   | ((GET_HI(from) & 0x3) << 2) \
                   | (lo2 >> 6) \
                   | 0x80); \
      *(*toP)++ = ((lo2 & 0x3f) | 0x80); \
      break; \
    } \
  } \
  *fromP = from; \
}

#define DEFINE_UTF16_TO_UTF16(E) \
static void  PTRCALL \
E ## toUtf16(__attribute__ ((unused)) const ENCODING *enc, \
             const char **fromP, const char *fromLim, \
             unsigned short **toP, const unsigned short *toLim) \
{ \
  /* Avoid copying first half only of surrogate */ \
  if (fromLim - *fromP > ((toLim - *toP) << 1) \
      && (GET_HI(fromLim - 2) & 0xF8) == 0xD8) \
    fromLim -= 2; \
  for (; *fromP != fromLim && *toP != toLim; *fromP += 2) \
    *(*toP)++ = (GET_HI(*fromP) << 8) | GET_LO(*fromP); \
}

#define SET2(ptr, ch) \
  (((ptr)[0] = ((ch) & 0xff)), ((ptr)[1] = ((ch) >> 8)))
#define GET_LO(ptr) ((unsigned char)(ptr)[0])
#define GET_HI(ptr) ((unsigned char)(ptr)[1])

DEFINE_UTF16_TO_UTF8(little2_)
DEFINE_UTF16_TO_UTF16(little2_)

#undef SET2
#undef GET_LO
#undef GET_HI

#define SET2(ptr, ch) \
  (((ptr)[0] = ((ch) >> 8)), ((ptr)[1] = ((ch) & 0xFF)))
#define GET_LO(ptr) ((unsigned char)(ptr)[1])
#define GET_HI(ptr) ((unsigned char)(ptr)[0])

DEFINE_UTF16_TO_UTF8(big2_)
DEFINE_UTF16_TO_UTF16(big2_)

#undef SET2
#undef GET_LO
#undef GET_HI

#define LITTLE2_BYTE_TYPE(enc, p) \
 ((p)[1] == 0 \
  ? ((struct normal_encoding *)(enc))->type[(unsigned char)*(p)] \
  : unicode_byte_type((p)[1], (p)[0]))
#define LITTLE2_BYTE_TO_ASCII(enc, p) ((p)[1] == 0 ? (p)[0] : -1)
#define LITTLE2_CHAR_MATCHES(enc, p, c) ((p)[1] == 0 && (p)[0] == c)
#define LITTLE2_IS_NAME_CHAR_MINBPC(enc, p) \
  UCS2_GET_NAMING(namePages, (unsigned char)p[1], (unsigned char)p[0])
#define LITTLE2_IS_NMSTRT_CHAR_MINBPC(enc, p) \
  UCS2_GET_NAMING(nmstrtPages, (unsigned char)p[1], (unsigned char)p[0])

#ifdef XML_MIN_SIZE

static int PTRFASTCALL
little2_byteType(const ENCODING *enc, const char *p)
{
  return LITTLE2_BYTE_TYPE(enc, p);
}

static int PTRFASTCALL
little2_byteToAscii(const ENCODING *enc, const char *p)
{
  return LITTLE2_BYTE_TO_ASCII(enc, p);
}

static int PTRCALL
little2_charMatches(const ENCODING *enc, const char *p, int c)
{
  return LITTLE2_CHAR_MATCHES(enc, p, c);
}

static int PTRFASTCALL
little2_isNameMin(const ENCODING *enc, const char *p)
{
  return LITTLE2_IS_NAME_CHAR_MINBPC(enc, p);
}

static int PTRFASTCALL
little2_isNmstrtMin(const ENCODING *enc, const char *p)
{
  return LITTLE2_IS_NMSTRT_CHAR_MINBPC(enc, p);
}

#undef VTABLE
#define VTABLE VTABLE1, little2_toUtf8, little2_toUtf16

#else /* not XML_MIN_SIZE */

#undef PREFIX
#define PREFIX(ident) little2_ ## ident
#define MINBPC(enc) 2
/* CHAR_MATCHES is guaranteed to have MINBPC bytes available. */
#define BYTE_TYPE(enc, p) LITTLE2_BYTE_TYPE(enc, p)
#define BYTE_TO_ASCII(enc, p) LITTLE2_BYTE_TO_ASCII(enc, p)
#define CHAR_MATCHES(enc, p, c) LITTLE2_CHAR_MATCHES(enc, p, c)
#define IS_NAME_CHAR(enc, p, n) 0
#define IS_NAME_CHAR_MINBPC(enc, p) LITTLE2_IS_NAME_CHAR_MINBPC(enc, p)
#define IS_NMSTRT_CHAR(enc, p, n) (0)
#define IS_NMSTRT_CHAR_MINBPC(enc, p) LITTLE2_IS_NMSTRT_CHAR_MINBPC(enc, p)

#define XML_TOK_IMPL_C
#include "xmltok_impl.c"
#undef XML_TOK_IMPL_C

#undef MINBPC
#undef BYTE_TYPE
#undef BYTE_TO_ASCII
#undef CHAR_MATCHES
#undef IS_NAME_CHAR
#undef IS_NAME_CHAR_MINBPC
#undef IS_NMSTRT_CHAR
#undef IS_NMSTRT_CHAR_MINBPC
#undef IS_INVALID_CHAR

#endif /* not XML_MIN_SIZE */

#ifdef XML_NS

static const struct normal_encoding little2_encoding_ns = {
  { VTABLE, 2, 0,
#if BYTEORDER == 1234
    1
#else
    0
#endif
  },
  {
#include "asciitab.h"
#include "latin1tab.h"
  },
  STANDARD_VTABLE(little2_)
};

#endif

static const struct normal_encoding little2_encoding = {
  { VTABLE, 2, 0,
#if BYTEORDER == 1234
    1
#else
    0
#endif
  },
  {
#define BT_COLON BT_NMSTRT
#include "asciitab.h"
#undef BT_COLON
#include "latin1tab.h"
  },
  STANDARD_VTABLE(little2_)
};

#if BYTEORDER != 4321

#ifdef XML_NS

static const struct normal_encoding internal_little2_encoding_ns = {
  { VTABLE, 2, 0, 1 },
  {
#include "iasciitab.h"
#include "latin1tab.h"
  },
  STANDARD_VTABLE(little2_)
};

#endif

static const struct normal_encoding internal_little2_encoding = {
  { VTABLE, 2, 0, 1 },
  {
#define BT_COLON BT_NMSTRT
#include "iasciitab.h"
#undef BT_COLON
#include "latin1tab.h"
  },
  STANDARD_VTABLE(little2_)
};

#endif


#define BIG2_BYTE_TYPE(enc, p) \
 ((p)[0] == 0 \
  ? ((struct normal_encoding *)(enc))->type[(unsigned char)(p)[1]] \
  : unicode_byte_type((p)[0], (p)[1]))
#define BIG2_BYTE_TO_ASCII(enc, p) ((p)[0] == 0 ? (p)[1] : -1)
#define BIG2_CHAR_MATCHES(enc, p, c) ((p)[0] == 0 && (p)[1] == c)
#define BIG2_IS_NAME_CHAR_MINBPC(enc, p) \
  UCS2_GET_NAMING(namePages, (unsigned char)p[0], (unsigned char)p[1])
#define BIG2_IS_NMSTRT_CHAR_MINBPC(enc, p) \
  UCS2_GET_NAMING(nmstrtPages, (unsigned char)p[0], (unsigned char)p[1])

#ifdef XML_MIN_SIZE

static int PTRFASTCALL
big2_byteType(const ENCODING *enc, const char *p)
{
  return BIG2_BYTE_TYPE(enc, p);
}

static int PTRFASTCALL
big2_byteToAscii(const ENCODING *enc, const char *p)
{
  return BIG2_BYTE_TO_ASCII(enc, p);
}

static int PTRCALL
big2_charMatches(const ENCODING *enc, const char *p, int c)
{
  return BIG2_CHAR_MATCHES(enc, p, c);
}

static int PTRFASTCALL
big2_isNameMin(const ENCODING *enc, const char *p)
{
  return BIG2_IS_NAME_CHAR_MINBPC(enc, p);
}

static int PTRFASTCALL
big2_isNmstrtMin(const ENCODING *enc, const char *p)
{
  return BIG2_IS_NMSTRT_CHAR_MINBPC(enc, p);
}

#undef VTABLE
#define VTABLE VTABLE1, big2_toUtf8, big2_toUtf16

#else /* not XML_MIN_SIZE */

#undef PREFIX
#define PREFIX(ident) big2_ ## ident
#define MINBPC(enc) 2
/* CHAR_MATCHES is guaranteed to have MINBPC bytes available. */
#define BYTE_TYPE(enc, p) BIG2_BYTE_TYPE(enc, p)
#define BYTE_TO_ASCII(enc, p) BIG2_BYTE_TO_ASCII(enc, p)
#define CHAR_MATCHES(enc, p, c) BIG2_CHAR_MATCHES(enc, p, c)
#define IS_NAME_CHAR(enc, p, n) 0
#define IS_NAME_CHAR_MINBPC(enc, p) BIG2_IS_NAME_CHAR_MINBPC(enc, p)
#define IS_NMSTRT_CHAR(enc, p, n) (0)
#define IS_NMSTRT_CHAR_MINBPC(enc, p) BIG2_IS_NMSTRT_CHAR_MINBPC(enc, p)

#define XML_TOK_IMPL_C
#include "xmltok_impl.c"
#undef XML_TOK_IMPL_C

#undef MINBPC
#undef BYTE_TYPE
#undef BYTE_TO_ASCII
#undef CHAR_MATCHES
#undef IS_NAME_CHAR
#undef IS_NAME_CHAR_MINBPC
#undef IS_NMSTRT_CHAR
#undef IS_NMSTRT_CHAR_MINBPC
#undef IS_INVALID_CHAR

#endif /* not XML_MIN_SIZE */

#ifdef XML_NS

static const struct normal_encoding big2_encoding_ns = {
  { VTABLE, 2, 0,
#if BYTEORDER == 4321
  1
#else
  0
#endif
  },
  {
#include "asciitab.h"
#include "latin1tab.h"
  },
  STANDARD_VTABLE(big2_)
};

#endif

static const struct normal_encoding big2_encoding = {
  { VTABLE, 2, 0,
#if BYTEORDER == 4321
  1
#else
  0
#endif
  },
  {
#define BT_COLON BT_NMSTRT
#include "asciitab.h"
#undef BT_COLON
#include "latin1tab.h"
  },
  STANDARD_VTABLE(big2_)
};

#if BYTEORDER != 1234

#ifdef XML_NS

static const struct normal_encoding internal_big2_encoding_ns = {
  { VTABLE, 2, 0, 1 },
  {
#include "iasciitab.h"
#include "latin1tab.h"
  },
  STANDARD_VTABLE(big2_)
};

#endif

static const struct normal_encoding internal_big2_encoding = {
  { VTABLE, 2, 0, 1 },
  {
#define BT_COLON BT_NMSTRT
#include "iasciitab.h"
#undef BT_COLON
#include "latin1tab.h"
  },
  STANDARD_VTABLE(big2_)
};

#endif

#undef PREFIX

static int FASTCALL
streqci(const char *s1, const char *s2)
{
  for (;;) {
    char c1 = *s1++;
    char c2 = *s2++;
    if (ASCII_a <= c1 && c1 <= ASCII_z)
      c1 += ASCII_A - ASCII_a;
    if (ASCII_a <= c2 && c2 <= ASCII_z)
      c2 += ASCII_A - ASCII_a;
    if (c1 != c2)
      return 0;
    if (!c1)
      break;
  }
  return 1;
}

static void PTRCALL
initUpdatePosition(__attribute__ ((unused)) const ENCODING *enc, const char *ptr,
                   const char *end, POSITION *pos)
{
  normal_updatePosition(&utf8_encoding.enc, ptr, end, pos);
}

static int
toAscii(const ENCODING *enc, const char *ptr, const char *end)
{
  char buf[1];
  char *p = buf;
  XmlUtf8Convert(enc, &ptr, end, &p, p + 1);
  if (p == buf)
    return -1;
  else
    return buf[0];
}

static int FASTCALL
isSpace(int c)
{
  switch (c) {
  case 0x20:
  case 0xD:
  case 0xA:
  case 0x9:
    return 1;
  }
  return 0;
}

/* Return 1 if there's just optional white space or there's an S
   followed by name=val.
*/
static int
parsePseudoAttribute(const ENCODING *enc,
                     const char *ptr,
                     const char *end,
                     const char **namePtr,
                     const char **nameEndPtr,
                     const char **valPtr,
                     const char **nextTokPtr)
{
  int c;
  char open;
  if (ptr == end) {
    *namePtr = NULL;
    return 1;
  }
  if (!isSpace(toAscii(enc, ptr, end))) {
    *nextTokPtr = ptr;
    return 0;
  }
  do {
    ptr += enc->minBytesPerChar;
  } while (isSpace(toAscii(enc, ptr, end)));
  if (ptr == end) {
    *namePtr = NULL;
    return 1;
  }
  *namePtr = ptr;
  for (;;) {
    c = toAscii(enc, ptr, end);
    if (c == -1) {
      *nextTokPtr = ptr;
      return 0;
    }
    if (c == ASCII_EQUALS) {
      *nameEndPtr = ptr;
      break;
    }
    if (isSpace(c)) {
      *nameEndPtr = ptr;
      do {
        ptr += enc->minBytesPerChar;
      } while (isSpace(c = toAscii(enc, ptr, end)));
      if (c != ASCII_EQUALS) {
        *nextTokPtr = ptr;
        return 0;
      }
      break;
    }
    ptr += enc->minBytesPerChar;
  }
  if (ptr == *namePtr) {
    *nextTokPtr = ptr;
    return 0;
  }
  ptr += enc->minBytesPerChar;
  c = toAscii(enc, ptr, end);
  while (isSpace(c)) {
    ptr += enc->minBytesPerChar;
    c = toAscii(enc, ptr, end);
  }
  if (c != ASCII_QUOT && c != ASCII_APOS) {
    *nextTokPtr = ptr;
    return 0;
  }
  open = (char)c;
  ptr += enc->minBytesPerChar;
  *valPtr = ptr;
  for (;; ptr += enc->minBytesPerChar) {
    c = toAscii(enc, ptr, end);
    if (c == open)
      break;
    if (!(ASCII_a <= c && c <= ASCII_z)
        && !(ASCII_A <= c && c <= ASCII_Z)
        && !(ASCII_0 <= c && c <= ASCII_9)
        && c != ASCII_PERIOD
        && c != ASCII_MINUS
        && c != ASCII_UNDERSCORE) {
      *nextTokPtr = ptr;
      return 0;
    }
  }
  *nextTokPtr = ptr + enc->minBytesPerChar;
  return 1;
}

static const char KW_version[] = {
  ASCII_v, ASCII_e, ASCII_r, ASCII_s, ASCII_i, ASCII_o, ASCII_n, '\0'
};

static const char KW_encoding[] = {
  ASCII_e, ASCII_n, ASCII_c, ASCII_o, ASCII_d, ASCII_i, ASCII_n, ASCII_g, '\0'
};

static const char KW_standalone[] = {
  ASCII_s, ASCII_t, ASCII_a, ASCII_n, ASCII_d, ASCII_a, ASCII_l, ASCII_o,
  ASCII_n, ASCII_e, '\0'
};

static const char KW_yes[] = {
  ASCII_y, ASCII_e, ASCII_s,  '\0'
};

static const char KW_no[] = {
  ASCII_n, ASCII_o,  '\0'
};

static int
doParseXmlDecl(const ENCODING *(*encodingFinder)(const ENCODING *,
                                                 const char *,
                                                 const char *),
               int isGeneralTextEntity,
               const ENCODING *enc,
               const char *ptr,
               const char *end,
               const char **badPtr,
               const char **versionPtr,
               const char **versionEndPtr,
               const char **encodingName,
               const ENCODING **encoding,
               int *standalone)
{
  const char *val = NULL;
  const char *name = NULL;
  const char *nameEnd = NULL;
  ptr += 5 * enc->minBytesPerChar;
  end -= 2 * enc->minBytesPerChar;
  if (!parsePseudoAttribute(enc, ptr, end, &name, &nameEnd, &val, &ptr)
      || !name) {
    *badPtr = ptr;
    return 0;
  }
  if (!XmlNameMatchesAscii(enc, name, nameEnd, KW_version)) {
    if (!isGeneralTextEntity) {
      *badPtr = name;
      return 0;
    }
  }
  else {
    if (versionPtr)
      *versionPtr = val;
    if (versionEndPtr)
      *versionEndPtr = ptr;
    if (!parsePseudoAttribute(enc, ptr, end, &name, &nameEnd, &val, &ptr)) {
      *badPtr = ptr;
      return 0;
    }
    if (!name) {
      if (isGeneralTextEntity) {
        /* a TextDecl must have an EncodingDecl */
        *badPtr = ptr;
        return 0;
      }
      return 1;
    }
  }
  if (XmlNameMatchesAscii(enc, name, nameEnd, KW_encoding)) {
    int c = toAscii(enc, val, end);
    if (!(ASCII_a <= c && c <= ASCII_z) && !(ASCII_A <= c && c <= ASCII_Z)) {
      *badPtr = val;
      return 0;
    }
    if (encodingName)
      *encodingName = val;
    if (encoding)
      *encoding = encodingFinder(enc, val, ptr - enc->minBytesPerChar);
    if (!parsePseudoAttribute(enc, ptr, end, &name, &nameEnd, &val, &ptr)) {
      *badPtr = ptr;
      return 0;
    }
    if (!name)
      return 1;
  }
  if (!XmlNameMatchesAscii(enc, name, nameEnd, KW_standalone)
      || isGeneralTextEntity) {
    *badPtr = name;
    return 0;
  }
  if (XmlNameMatchesAscii(enc, val, ptr - enc->minBytesPerChar, KW_yes)) {
    if (standalone)
      *standalone = 1;
  }
  else if (XmlNameMatchesAscii(enc, val, ptr - enc->minBytesPerChar, KW_no)) {
    if (standalone)
      *standalone = 0;
  }
  else {
    *badPtr = val;
    return 0;
  }
  while (isSpace(toAscii(enc, ptr, end)))
    ptr += enc->minBytesPerChar;
  if (ptr != end) {
    *badPtr = ptr;
    return 0;
  }
  return 1;
}

static int FASTCALL
checkCharRefNumber(int result)
{
  switch (result >> 8) {
  case 0xD8: case 0xD9: case 0xDA: case 0xDB:
  case 0xDC: case 0xDD: case 0xDE: case 0xDF:
    return -1;
  case 0:
    if (latin1_encoding.type[result] == BT_NONXML)
      return -1;
    break;
  case 0xFF:
    if (result == 0xFFFE || result == 0xFFFF)
      return -1;
    break;
  }
  return result;
}

int FASTCALL
XmlUtf8Encode(int c, char *buf)
{
  enum {
    /* minN is minimum legal resulting value for N byte sequence */
    min2 = 0x80,
    min3 = 0x800,
    min4 = 0x10000
  };

  if (c < 0)
    return 0;
  if (c < min2) {
    buf[0] = (char)(c | UTF8_cval1);
    return 1;
  }
  if (c < min3) {
    buf[0] = (char)((c >> 6) | UTF8_cval2);
    buf[1] = (char)((c & 0x3f) | 0x80);
    return 2;
  }
  if (c < min4) {
    buf[0] = (char)((c >> 12) | UTF8_cval3);
    buf[1] = (char)(((c >> 6) & 0x3f) | 0x80);
    buf[2] = (char)((c & 0x3f) | 0x80);
    return 3;
  }
  if (c < 0x110000) {
    buf[0] = (char)((c >> 18) | UTF8_cval4);
    buf[1] = (char)(((c >> 12) & 0x3f) | 0x80);
    buf[2] = (char)(((c >> 6) & 0x3f) | 0x80);
    buf[3] = (char)((c & 0x3f) | 0x80);
    return 4;
  }
  return 0;
}

int FASTCALL
XmlUtf16Encode(int charNum, unsigned short *buf)
{
  if (charNum < 0)
    return 0;
  if (charNum < 0x10000) {
    buf[0] = (unsigned short)charNum;
    return 1;
  }
  if (charNum < 0x110000) {
    charNum -= 0x10000;
    buf[0] = (unsigned short)((charNum >> 10) + 0xD800);
    buf[1] = (unsigned short)((charNum & 0x3FF) + 0xDC00);
    return 2;
  }
  return 0;
}

struct unknown_encoding {
  struct normal_encoding normal;
  CONVERTER convert;
  void *userData;
  unsigned short utf16[256];
  char utf8[256][4];
};

#define AS_UNKNOWN_ENCODING(enc)  ((const struct unknown_encoding *) (enc))

int
XmlSizeOfUnknownEncoding(void)
{
  return sizeof(struct unknown_encoding);
}

static int PTRFASTCALL
unknown_isName(const ENCODING *enc, const char *p)
{
  const struct unknown_encoding *uenc = AS_UNKNOWN_ENCODING(enc);
  int c = uenc->convert(uenc->userData, p);
  if (c & ~0xFFFF)
    return 0;
  return UCS2_GET_NAMING(namePages, c >> 8, c & 0xFF);
}

static int PTRFASTCALL
unknown_isNmstrt(const ENCODING *enc, const char *p)
{
  const struct unknown_encoding *uenc = AS_UNKNOWN_ENCODING(enc);
  int c = uenc->convert(uenc->userData, p);
  if (c & ~0xFFFF)
    return 0;
  return UCS2_GET_NAMING(nmstrtPages, c >> 8, c & 0xFF);
}

static int PTRFASTCALL
unknown_isInvalid(const ENCODING *enc, const char *p)
{
  const struct unknown_encoding *uenc = AS_UNKNOWN_ENCODING(enc);
  int c = uenc->convert(uenc->userData, p);
  return (c & ~0xFFFF) || checkCharRefNumber(c) < 0;
}

static void PTRCALL
unknown_toUtf8(const ENCODING *enc,
               const char **fromP, const char *fromLim,
               char **toP, const char *toLim)
{
  const struct unknown_encoding *uenc = AS_UNKNOWN_ENCODING(enc);
  char buf[XML_UTF8_ENCODE_MAX];
  for (;;) {
    const char *utf8;
    int n;
    if (*fromP == fromLim)
      break;
    utf8 = uenc->utf8[(unsigned char)**fromP];
    n = *utf8++;
    if (n == 0) {
      int c = uenc->convert(uenc->userData, *fromP);
      n = XmlUtf8Encode(c, buf);
      if (n > toLim - *toP)
        break;
      utf8 = buf;
      *fromP += (AS_NORMAL_ENCODING(enc)->type[(unsigned char)**fromP]
                 - (BT_LEAD2 - 2));
    }
    else {
      if (n > toLim - *toP)
        break;
      (*fromP)++;
    }
    do {
      *(*toP)++ = *utf8++;
    } while (--n != 0);
  }
}

static void PTRCALL
unknown_toUtf16(const ENCODING *enc,
                const char **fromP, const char *fromLim,
                unsigned short **toP, const unsigned short *toLim)
{
  const struct unknown_encoding *uenc = AS_UNKNOWN_ENCODING(enc);
  while (*fromP != fromLim && *toP != toLim) {
    unsigned short c = uenc->utf16[(unsigned char)**fromP];
    if (c == 0) {
      c = (unsigned short)
          uenc->convert(uenc->userData, *fromP);
      *fromP += (AS_NORMAL_ENCODING(enc)->type[(unsigned char)**fromP]
                 - (BT_LEAD2 - 2));
    }
    else
      (*fromP)++;
    *(*toP)++ = c;
  }
}

ENCODING *
XmlInitUnknownEncoding(void *mem,
                       int *table,
                       CONVERTER convert, 
                       void *userData)
{
  int i;
  struct unknown_encoding *e = (struct unknown_encoding *)mem;
  for (i = 0; i < (int)sizeof(struct normal_encoding); i++)
    ((char *)mem)[i] = ((char *)&latin1_encoding)[i];
  for (i = 0; i < 128; i++)
    if (latin1_encoding.type[i] != BT_OTHER
        && latin1_encoding.type[i] != BT_NONXML
        && table[i] != i)
      return 0;
  for (i = 0; i < 256; i++) {
    int c = table[i];
    if (c == -1) {
      e->normal.type[i] = BT_MALFORM;
      /* This shouldn't really get used. */
      e->utf16[i] = 0xFFFF;
      e->utf8[i][0] = 1;
      e->utf8[i][1] = 0;
    }
    else if (c < 0) {
      if (c < -4)
        return 0;
      e->normal.type[i] = (unsigned char)(BT_LEAD2 - (c + 2));
      e->utf8[i][0] = 0;
      e->utf16[i] = 0;
    }
    else if (c < 0x80) {
      if (latin1_encoding.type[c] != BT_OTHER
          && latin1_encoding.type[c] != BT_NONXML
          && c != i)
        return 0;
      e->normal.type[i] = latin1_encoding.type[c];
      e->utf8[i][0] = 1;
      e->utf8[i][1] = (char)c;
      e->utf16[i] = (unsigned short)(c == 0 ? 0xFFFF : c);
    }
    else if (checkCharRefNumber(c) < 0) {
      e->normal.type[i] = BT_NONXML;
      /* This shouldn't really get used. */
      e->utf16[i] = 0xFFFF;
      e->utf8[i][0] = 1;
      e->utf8[i][1] = 0;
    }
    else {
      if (c > 0xFFFF)
        return 0;
      if (UCS2_GET_NAMING(nmstrtPages, c >> 8, c & 0xff))
        e->normal.type[i] = BT_NMSTRT;
      else if (UCS2_GET_NAMING(namePages, c >> 8, c & 0xff))
        e->normal.type[i] = BT_NAME;
      else
        e->normal.type[i] = BT_OTHER;
      e->utf8[i][0] = (char)XmlUtf8Encode(c, e->utf8[i] + 1);
      e->utf16[i] = (unsigned short)c;
    }
  }
  e->userData = userData;
  e->convert = convert;
  if (convert) {
    e->normal.isName2 = unknown_isName;
    e->normal.isName3 = unknown_isName;
    e->normal.isName4 = unknown_isName;
    e->normal.isNmstrt2 = unknown_isNmstrt;
    e->normal.isNmstrt3 = unknown_isNmstrt;
    e->normal.isNmstrt4 = unknown_isNmstrt;
    e->normal.isInvalid2 = unknown_isInvalid;
    e->normal.isInvalid3 = unknown_isInvalid;
    e->normal.isInvalid4 = unknown_isInvalid;
  }
  e->normal.enc.utf8Convert = unknown_toUtf8;
  e->normal.enc.utf16Convert = unknown_toUtf16;
  return &(e->normal.enc);
}

/* If this enumeration is changed, getEncodingIndex and encodings
must also be changed. */
enum {
  UNKNOWN_ENC = -1,
  ISO_8859_1_ENC = 0,
  US_ASCII_ENC,
  UTF_8_ENC,
  UTF_16_ENC,
  UTF_16BE_ENC,
  UTF_16LE_ENC,
  /* must match encodingNames up to here */
  NO_ENC
};

static const char KW_ISO_8859_1[] = {
  ASCII_I, ASCII_S, ASCII_O, ASCII_MINUS, ASCII_8, ASCII_8, ASCII_5, ASCII_9,
  ASCII_MINUS, ASCII_1, '\0'
};
static const char KW_US_ASCII[] = {
  ASCII_U, ASCII_S, ASCII_MINUS, ASCII_A, ASCII_S, ASCII_C, ASCII_I, ASCII_I,
  '\0'
};
static const char KW_UTF_8[] =  {
  ASCII_U, ASCII_T, ASCII_F, ASCII_MINUS, ASCII_8, '\0'
};
static const char KW_UTF_16[] = {
  ASCII_U, ASCII_T, ASCII_F, ASCII_MINUS, ASCII_1, ASCII_6, '\0'
};
static const char KW_UTF_16BE[] = {
  ASCII_U, ASCII_T, ASCII_F, ASCII_MINUS, ASCII_1, ASCII_6, ASCII_B, ASCII_E,
  '\0'
};
static const char KW_UTF_16LE[] = {
  ASCII_U, ASCII_T, ASCII_F, ASCII_MINUS, ASCII_1, ASCII_6, ASCII_L, ASCII_E,
  '\0'
};

static int FASTCALL
getEncodingIndex(const char *name)
{
  static const char * const encodingNames[] = {
    KW_ISO_8859_1,
    KW_US_ASCII,
    KW_UTF_8,
    KW_UTF_16,
    KW_UTF_16BE,
    KW_UTF_16LE,
  };
  int i;
  if (name == NULL)
    return NO_ENC;
  for (i = 0; i < (int)(sizeof(encodingNames)/sizeof(encodingNames[0])); i++)
    if (streqci(name, encodingNames[i]))
      return i;
  return UNKNOWN_ENC;
}

/* For binary compatibility, we store the index of the encoding
   specified at initialization in the isUtf16 member.
*/

#define INIT_ENC_INDEX(enc) ((int)(enc)->initEnc.isUtf16)
#define SET_INIT_ENC_INDEX(enc, i) ((enc)->initEnc.isUtf16 = (char)i)

/* This is what detects the encoding.  encodingTable maps from
   encoding indices to encodings; INIT_ENC_INDEX(enc) is the index of
   the external (protocol) specified encoding; state is
   XML_CONTENT_STATE if we're parsing an external text entity, and
   XML_PROLOG_STATE otherwise.
*/


static int
initScan(const ENCODING * const *encodingTable,
         const INIT_ENCODING *enc,
         int state,
         const char *ptr,
         const char *end,
         const char **nextTokPtr)
{
  const ENCODING **encPtr;

  if (ptr == end)
    return XML_TOK_NONE;
  encPtr = enc->encPtr;
  if (ptr + 1 == end) {
    /* only a single byte available for auto-detection */
#ifndef XML_DTD /* FIXME */
    /* a well-formed document entity must have more than one byte */
    if (state != XML_CONTENT_STATE)
      return XML_TOK_PARTIAL;
#endif
    /* so we're parsing an external text entity... */
    /* if UTF-16 was externally specified, then we need at least 2 bytes */
    switch (INIT_ENC_INDEX(enc)) {
    case UTF_16_ENC:
    case UTF_16LE_ENC:
    case UTF_16BE_ENC:
      return XML_TOK_PARTIAL;
    }
    switch ((unsigned char)*ptr) {
    case 0xFE:
    case 0xFF:
    case 0xEF: /* possibly first byte of UTF-8 BOM */
      if (INIT_ENC_INDEX(enc) == ISO_8859_1_ENC
          && state == XML_CONTENT_STATE)
        break;
      /* fall through */
    case 0x00:
    case 0x3C:
      return XML_TOK_PARTIAL;
    }
  }
  else {
    switch (((unsigned char)ptr[0] << 8) | (unsigned char)ptr[1]) {
    case 0xFEFF:
      if (INIT_ENC_INDEX(enc) == ISO_8859_1_ENC
          && state == XML_CONTENT_STATE)
        break;
      *nextTokPtr = ptr + 2;
      *encPtr = encodingTable[UTF_16BE_ENC];
      return XML_TOK_BOM;
    /* 00 3C is handled in the default case */
    case 0x3C00:
      if ((INIT_ENC_INDEX(enc) == UTF_16BE_ENC
           || INIT_ENC_INDEX(enc) == UTF_16_ENC)
          && state == XML_CONTENT_STATE)
        break;
      *encPtr = encodingTable[UTF_16LE_ENC];
      return XmlTok(*encPtr, state, ptr, end, nextTokPtr);
    case 0xFFFE:
      if (INIT_ENC_INDEX(enc) == ISO_8859_1_ENC
          && state == XML_CONTENT_STATE)
        break;
      *nextTokPtr = ptr + 2;
      *encPtr = encodingTable[UTF_16LE_ENC];
      return XML_TOK_BOM;
    case 0xEFBB:
      /* Maybe a UTF-8 BOM (EF BB BF) */
      /* If there's an explicitly specified (external) encoding
         of ISO-8859-1 or some flavour of UTF-16
         and this is an external text entity,
         don't look for the BOM,
         because it might be a legal data.
      */
      if (state == XML_CONTENT_STATE) {
        int e = INIT_ENC_INDEX(enc);
        if (e == ISO_8859_1_ENC || e == UTF_16BE_ENC
            || e == UTF_16LE_ENC || e == UTF_16_ENC)
          break;
      }
      if (ptr + 2 == end)
        return XML_TOK_PARTIAL;
      if ((unsigned char)ptr[2] == 0xBF) {
        *nextTokPtr = ptr + 3;
        *encPtr = encodingTable[UTF_8_ENC];
        return XML_TOK_BOM;
      }
      break;
    default:
      if (ptr[0] == '\0') {
        /* 0 isn't a legal data character. Furthermore a document
           entity can only start with ASCII characters.  So the only
           way this can fail to be big-endian UTF-16 if it it's an
           external parsed general entity that's labelled as
           UTF-16LE.
        */
        if (state == XML_CONTENT_STATE && INIT_ENC_INDEX(enc) == UTF_16LE_ENC)
          break;
        *encPtr = encodingTable[UTF_16BE_ENC];
        return XmlTok(*encPtr, state, ptr, end, nextTokPtr);
      }
      else if (ptr[1] == '\0') {
        /* We could recover here in the case:
            - parsing an external entity
            - second byte is 0
            - no externally specified encoding
            - no encoding declaration
           by assuming UTF-16LE.  But we don't, because this would mean when
           presented just with a single byte, we couldn't reliably determine
           whether we needed further bytes.
        */
        if (state == XML_CONTENT_STATE)
          break;
        *encPtr = encodingTable[UTF_16LE_ENC];
        return XmlTok(*encPtr, state, ptr, end, nextTokPtr);
      }
      break;
    }
  }
  *encPtr = encodingTable[INIT_ENC_INDEX(enc)];
  return XmlTok(*encPtr, state, ptr, end, nextTokPtr);
}


#define NS(x) x
#define ns(x) x
#define XML_TOK_NS_C
#include "xmltok_ns.c"
#undef XML_TOK_NS_C
#undef NS
#undef ns

#ifdef XML_NS

#define NS(x) x ## NS
#define ns(x) x ## _ns

#define XML_TOK_NS_C
#include "xmltok_ns.c"
#undef XML_TOK_NS_C

#undef NS
#undef ns

ENCODING *
XmlInitUnknownEncodingNS(void *mem,
                         int *table,
                         CONVERTER convert, 
                         void *userData)
{
  ENCODING *enc = XmlInitUnknownEncoding(mem, table, convert, userData);
  if (enc)
    ((struct normal_encoding *)enc)->type[ASCII_COLON] = BT_COLON;
  return enc;
}

#endif /* XML_NS */
genometools-1.5.1/src/external/expat-2.0.1/lib/xmltok.h000077500000000000000000000256601211610345200225030ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

#ifndef XmlTok_INCLUDED
#define XmlTok_INCLUDED 1

#ifdef __cplusplus
extern "C" {
#endif

/* The following token may be returned by XmlContentTok */
#define XML_TOK_TRAILING_RSQB -5 /* ] or ]] at the end of the scan; might be
                                    start of illegal ]]> sequence */
/* The following tokens may be returned by both XmlPrologTok and
   XmlContentTok.
*/
#define XML_TOK_NONE -4          /* The string to be scanned is empty */
#define XML_TOK_TRAILING_CR -3   /* A CR at the end of the scan;
                                    might be part of CRLF sequence */
#define XML_TOK_PARTIAL_CHAR -2  /* only part of a multibyte sequence */
#define XML_TOK_PARTIAL -1       /* only part of a token */
#define XML_TOK_INVALID 0

/* The following tokens are returned by XmlContentTok; some are also
   returned by XmlAttributeValueTok, XmlEntityTok, XmlCdataSectionTok.
*/
#define XML_TOK_START_TAG_WITH_ATTS 1
#define XML_TOK_START_TAG_NO_ATTS 2
#define XML_TOK_EMPTY_ELEMENT_WITH_ATTS 3 /* empty element tag  */
#define XML_TOK_EMPTY_ELEMENT_NO_ATTS 4
#define XML_TOK_END_TAG 5
#define XML_TOK_DATA_CHARS 6
#define XML_TOK_DATA_NEWLINE 7
#define XML_TOK_CDATA_SECT_OPEN 8
#define XML_TOK_ENTITY_REF 9
#define XML_TOK_CHAR_REF 10               /* numeric character reference */

/* The following tokens may be returned by both XmlPrologTok and
   XmlContentTok.
*/
#define XML_TOK_PI 11                     /* processing instruction */
#define XML_TOK_XML_DECL 12               /* XML decl or text decl */
#define XML_TOK_COMMENT 13
#define XML_TOK_BOM 14                    /* Byte order mark */

/* The following tokens are returned only by XmlPrologTok */
#define XML_TOK_PROLOG_S 15
#define XML_TOK_DECL_OPEN 16              /*  */
#define XML_TOK_NAME 18
#define XML_TOK_NMTOKEN 19
#define XML_TOK_POUND_NAME 20             /* #name */
#define XML_TOK_OR 21                     /* | */
#define XML_TOK_PERCENT 22
#define XML_TOK_OPEN_PAREN 23
#define XML_TOK_CLOSE_PAREN 24
#define XML_TOK_OPEN_BRACKET 25
#define XML_TOK_CLOSE_BRACKET 26
#define XML_TOK_LITERAL 27
#define XML_TOK_PARAM_ENTITY_REF 28
#define XML_TOK_INSTANCE_START 29

/* The following occur only in element type declarations */
#define XML_TOK_NAME_QUESTION 30          /* name? */
#define XML_TOK_NAME_ASTERISK 31          /* name* */
#define XML_TOK_NAME_PLUS 32              /* name+ */
#define XML_TOK_COND_SECT_OPEN 33         /*  */
#define XML_TOK_CLOSE_PAREN_QUESTION 35   /* )? */
#define XML_TOK_CLOSE_PAREN_ASTERISK 36   /* )* */
#define XML_TOK_CLOSE_PAREN_PLUS 37       /* )+ */
#define XML_TOK_COMMA 38

/* The following token is returned only by XmlAttributeValueTok */
#define XML_TOK_ATTRIBUTE_VALUE_S 39

/* The following token is returned only by XmlCdataSectionTok */
#define XML_TOK_CDATA_SECT_CLOSE 40

/* With namespace processing this is returned by XmlPrologTok for a
   name with a colon.
*/
#define XML_TOK_PREFIXED_NAME 41

#ifdef XML_DTD
#define XML_TOK_IGNORE_SECT 42
#endif /* XML_DTD */

#ifdef XML_DTD
#define XML_N_STATES 4
#else /* not XML_DTD */
#define XML_N_STATES 3
#endif /* not XML_DTD */

#define XML_PROLOG_STATE 0
#define XML_CONTENT_STATE 1
#define XML_CDATA_SECTION_STATE 2
#ifdef XML_DTD
#define XML_IGNORE_SECTION_STATE 3
#endif /* XML_DTD */

#define XML_N_LITERAL_TYPES 2
#define XML_ATTRIBUTE_VALUE_LITERAL 0
#define XML_ENTITY_VALUE_LITERAL 1

/* The size of the buffer passed to XmlUtf8Encode must be at least this. */
#define XML_UTF8_ENCODE_MAX 4
/* The size of the buffer passed to XmlUtf16Encode must be at least this. */
#define XML_UTF16_ENCODE_MAX 2

typedef struct position {
  /* first line and first column are 0 not 1 */
  XML_Size lineNumber;
  XML_Size columnNumber;
} POSITION;

typedef struct {
  const char *name;
  const char *valuePtr;
  const char *valueEnd;
  char normalized;
} ATTRIBUTE;

struct encoding;
typedef struct encoding ENCODING;

typedef int (PTRCALL *SCANNER)(const ENCODING *,
                               const char *,
                               const char *,
                               const char **);

struct encoding {
  SCANNER scanners[XML_N_STATES];
  SCANNER literalScanners[XML_N_LITERAL_TYPES];
  int (PTRCALL *sameName)(const ENCODING *,
                          const char *,
                          const char *);
  int (PTRCALL *nameMatchesAscii)(const ENCODING *,
                                  const char *,
                                  const char *,
                                  const char *);
  int (PTRFASTCALL *nameLength)(const ENCODING *, const char *);
  const char *(PTRFASTCALL *skipS)(const ENCODING *, const char *);
  int (PTRCALL *getAtts)(const ENCODING *enc,
                         const char *ptr,
                         int attsMax,
                         ATTRIBUTE *atts);
  int (PTRFASTCALL *charRefNumber)(const ENCODING *enc, const char *ptr);
  int (PTRCALL *predefinedEntityName)(const ENCODING *,
                                      const char *,
                                      const char *);
  void (PTRCALL *updatePosition)(const ENCODING *,
                                 const char *ptr,
                                 const char *end,
                                 POSITION *);
  int (PTRCALL *isPublicId)(const ENCODING *enc,
                            const char *ptr,
                            const char *end,
                            const char **badPtr);
  void (PTRCALL *utf8Convert)(const ENCODING *enc,
                              const char **fromP,
                              const char *fromLim,
                              char **toP,
                              const char *toLim);
  void (PTRCALL *utf16Convert)(const ENCODING *enc,
                               const char **fromP,
                               const char *fromLim,
                               unsigned short **toP,
                               const unsigned short *toLim);
  int minBytesPerChar;
  char isUtf8;
  char isUtf16;
};

/* Scan the string starting at ptr until the end of the next complete
   token, but do not scan past eptr.  Return an integer giving the
   type of token.

   Return XML_TOK_NONE when ptr == eptr; nextTokPtr will not be set.

   Return XML_TOK_PARTIAL when the string does not contain a complete
   token; nextTokPtr will not be set.

   Return XML_TOK_INVALID when the string does not start a valid
   token; nextTokPtr will be set to point to the character which made
   the token invalid.

   Otherwise the string starts with a valid token; nextTokPtr will be
   set to point to the character following the end of that token.

   Each data character counts as a single token, but adjacent data
   characters may be returned together.  Similarly for characters in
   the prolog outside literals, comments and processing instructions.
*/


#define XmlTok(enc, state, ptr, end, nextTokPtr) \
  (((enc)->scanners[state])(enc, ptr, end, nextTokPtr))

#define XmlPrologTok(enc, ptr, end, nextTokPtr) \
   XmlTok(enc, XML_PROLOG_STATE, ptr, end, nextTokPtr)

#define XmlContentTok(enc, ptr, end, nextTokPtr) \
   XmlTok(enc, XML_CONTENT_STATE, ptr, end, nextTokPtr)

#define XmlCdataSectionTok(enc, ptr, end, nextTokPtr) \
   XmlTok(enc, XML_CDATA_SECTION_STATE, ptr, end, nextTokPtr)

#ifdef XML_DTD

#define XmlIgnoreSectionTok(enc, ptr, end, nextTokPtr) \
   XmlTok(enc, XML_IGNORE_SECTION_STATE, ptr, end, nextTokPtr)

#endif /* XML_DTD */

/* This is used for performing a 2nd-level tokenization on the content
   of a literal that has already been returned by XmlTok.
*/
#define XmlLiteralTok(enc, literalType, ptr, end, nextTokPtr) \
  (((enc)->literalScanners[literalType])(enc, ptr, end, nextTokPtr))

#define XmlAttributeValueTok(enc, ptr, end, nextTokPtr) \
   XmlLiteralTok(enc, XML_ATTRIBUTE_VALUE_LITERAL, ptr, end, nextTokPtr)

#define XmlEntityValueTok(enc, ptr, end, nextTokPtr) \
   XmlLiteralTok(enc, XML_ENTITY_VALUE_LITERAL, ptr, end, nextTokPtr)

#define XmlSameName(enc, ptr1, ptr2) (((enc)->sameName)(enc, ptr1, ptr2))

#define XmlNameMatchesAscii(enc, ptr1, end1, ptr2) \
  (((enc)->nameMatchesAscii)(enc, ptr1, end1, ptr2))

#define XmlNameLength(enc, ptr) \
  (((enc)->nameLength)(enc, ptr))

#define XmlSkipS(enc, ptr) \
  (((enc)->skipS)(enc, ptr))

#define XmlGetAttributes(enc, ptr, attsMax, atts) \
  (((enc)->getAtts)(enc, ptr, attsMax, atts))

#define XmlCharRefNumber(enc, ptr) \
  (((enc)->charRefNumber)(enc, ptr))

#define XmlPredefinedEntityName(enc, ptr, end) \
  (((enc)->predefinedEntityName)(enc, ptr, end))

#define XmlUpdatePosition(enc, ptr, end, pos) \
  (((enc)->updatePosition)(enc, ptr, end, pos))

#define XmlIsPublicId(enc, ptr, end, badPtr) \
  (((enc)->isPublicId)(enc, ptr, end, badPtr))

#define XmlUtf8Convert(enc, fromP, fromLim, toP, toLim) \
  (((enc)->utf8Convert)(enc, fromP, fromLim, toP, toLim))

#define XmlUtf16Convert(enc, fromP, fromLim, toP, toLim) \
  (((enc)->utf16Convert)(enc, fromP, fromLim, toP, toLim))

typedef struct {
  ENCODING initEnc;
  const ENCODING **encPtr;
} INIT_ENCODING;

int XmlParseXmlDecl(int isGeneralTextEntity,
                    const ENCODING *enc,
                    const char *ptr,
                    const char *end,
                    const char **badPtr,
                    const char **versionPtr,
                    const char **versionEndPtr,
                    const char **encodingNamePtr,
                    const ENCODING **namedEncodingPtr,
                    int *standalonePtr);

int XmlInitEncoding(INIT_ENCODING *, const ENCODING **, const char *name);
const ENCODING *XmlGetUtf8InternalEncoding(void);
const ENCODING *XmlGetUtf16InternalEncoding(void);
int FASTCALL XmlUtf8Encode(int charNumber, char *buf);
int FASTCALL XmlUtf16Encode(int charNumber, unsigned short *buf);
int XmlSizeOfUnknownEncoding(void);


typedef int (XMLCALL *CONVERTER) (void *userData, const char *p);

ENCODING *
XmlInitUnknownEncoding(void *mem,
                       int *table,
                       CONVERTER convert,
                       void *userData);

int XmlParseXmlDeclNS(int isGeneralTextEntity,
                      const ENCODING *enc,
                      const char *ptr,
                      const char *end,
                      const char **badPtr,
                      const char **versionPtr,
                      const char **versionEndPtr,
                      const char **encodingNamePtr,
                      const ENCODING **namedEncodingPtr,
                      int *standalonePtr);

int XmlInitEncodingNS(INIT_ENCODING *, const ENCODING **, const char *name);
const ENCODING *XmlGetUtf8InternalEncodingNS(void);
const ENCODING *XmlGetUtf16InternalEncodingNS(void);
ENCODING *
XmlInitUnknownEncodingNS(void *mem,
                         int *table,
                         CONVERTER convert,
                         void *userData);
#ifdef __cplusplus
}
#endif

#endif /* not XmlTok_INCLUDED */
genometools-1.5.1/src/external/expat-2.0.1/lib/xmltok_impl.c000077500000000000000000001272111211610345200235120ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

/* This file is included! */
#ifdef XML_TOK_IMPL_C

#ifndef IS_INVALID_CHAR
#define IS_INVALID_CHAR(enc, ptr, n) (0)
#endif

#define INVALID_LEAD_CASE(n, ptr, nextTokPtr) \
    case BT_LEAD ## n: \
      if (end - ptr < n) \
        return XML_TOK_PARTIAL_CHAR; \
      if (IS_INVALID_CHAR(enc, ptr, n)) { \
        *(nextTokPtr) = (ptr); \
        return XML_TOK_INVALID; \
      } \
      ptr += n; \
      break;

#define INVALID_CASES(ptr, nextTokPtr) \
  INVALID_LEAD_CASE(2, ptr, nextTokPtr) \
  INVALID_LEAD_CASE(3, ptr, nextTokPtr) \
  INVALID_LEAD_CASE(4, ptr, nextTokPtr) \
  case BT_NONXML: \
  case BT_MALFORM: \
  case BT_TRAIL: \
    *(nextTokPtr) = (ptr); \
    return XML_TOK_INVALID;

#define CHECK_NAME_CASE(n, enc, ptr, end, nextTokPtr) \
   case BT_LEAD ## n: \
     if (end - ptr < n) \
       return XML_TOK_PARTIAL_CHAR; \
     if (!IS_NAME_CHAR(enc, ptr, n)) { \
       *nextTokPtr = ptr; \
       return XML_TOK_INVALID; \
     } \
     ptr += n; \
     break;

#define CHECK_NAME_CASES(enc, ptr, end, nextTokPtr) \
  case BT_NONASCII: \
    if (!IS_NAME_CHAR_MINBPC(enc, ptr)) { \
      *nextTokPtr = ptr; \
      return XML_TOK_INVALID; \
    } \
  case BT_NMSTRT: \
  case BT_HEX: \
  case BT_DIGIT: \
  case BT_NAME: \
  case BT_MINUS: \
    ptr += MINBPC(enc); \
    break; \
  CHECK_NAME_CASE(2, enc, ptr, end, nextTokPtr) \
  CHECK_NAME_CASE(3, enc, ptr, end, nextTokPtr) \
  CHECK_NAME_CASE(4, enc, ptr, end, nextTokPtr)

#define CHECK_NMSTRT_CASE(n, enc, ptr, end, nextTokPtr) \
   case BT_LEAD ## n: \
     if (end - ptr < n) \
       return XML_TOK_PARTIAL_CHAR; \
     if (!IS_NMSTRT_CHAR(enc, ptr, n)) { \
       *nextTokPtr = ptr; \
       return XML_TOK_INVALID; \
     } \
     ptr += n; \
     break;

#define CHECK_NMSTRT_CASES(enc, ptr, end, nextTokPtr) \
  case BT_NONASCII: \
    if (!IS_NMSTRT_CHAR_MINBPC(enc, ptr)) { \
      *nextTokPtr = ptr; \
      return XML_TOK_INVALID; \
    } \
  case BT_NMSTRT: \
  case BT_HEX: \
    ptr += MINBPC(enc); \
    break; \
  CHECK_NMSTRT_CASE(2, enc, ptr, end, nextTokPtr) \
  CHECK_NMSTRT_CASE(3, enc, ptr, end, nextTokPtr) \
  CHECK_NMSTRT_CASE(4, enc, ptr, end, nextTokPtr)

#ifndef PREFIX
#define PREFIX(ident) ident
#endif

/* ptr points to character following " */
      switch (BYTE_TYPE(enc, ptr + MINBPC(enc))) {
      case BT_S: case BT_CR: case BT_LF: case BT_PERCNT:
        *nextTokPtr = ptr;
        return XML_TOK_INVALID;
      }
      /* fall through */
    case BT_S: case BT_CR: case BT_LF:
      *nextTokPtr = ptr;
      return XML_TOK_DECL_OPEN;
    case BT_NMSTRT:
    case BT_HEX:
      ptr += MINBPC(enc);
      break;
    default:
      *nextTokPtr = ptr;
      return XML_TOK_INVALID;
    }
  }
  return XML_TOK_PARTIAL;
}

static int PTRCALL
PREFIX(checkPiTarget)(__attribute__ ((unused)) const ENCODING *enc, const char *ptr,
                      const char *end, int *tokPtr)
{
  int upper = 0;
  *tokPtr = XML_TOK_PI;
  if (end - ptr != MINBPC(enc)*3)
    return 1;
  switch (BYTE_TO_ASCII(enc, ptr)) {
  case ASCII_x:
    break;
  case ASCII_X:
    upper = 1;
    break;
  default:
    return 1;
  }
  ptr += MINBPC(enc);
  switch (BYTE_TO_ASCII(enc, ptr)) {
  case ASCII_m:
    break;
  case ASCII_M:
    upper = 1;
    break;
  default:
    return 1;
  }
  ptr += MINBPC(enc);
  switch (BYTE_TO_ASCII(enc, ptr)) {
  case ASCII_l:
    break;
  case ASCII_L:
    upper = 1;
    break;
  default:
    return 1;
  }
  if (upper)
    return 0;
  *tokPtr = XML_TOK_XML_DECL;
  return 1;
}

/* ptr points to character following " 1) {
    size_t n = end - ptr;
    if (n & (MINBPC(enc) - 1)) {
      n &= ~(MINBPC(enc) - 1);
      if (n == 0)
        return XML_TOK_PARTIAL;
      end = ptr + n;
    }
  }
  switch (BYTE_TYPE(enc, ptr)) {
  case BT_RSQB:
    ptr += MINBPC(enc);
    if (ptr == end)
      return XML_TOK_PARTIAL;
    if (!CHAR_MATCHES(enc, ptr, ASCII_RSQB))
      break;
    ptr += MINBPC(enc);
    if (ptr == end)
      return XML_TOK_PARTIAL;
    if (!CHAR_MATCHES(enc, ptr, ASCII_GT)) {
      ptr -= MINBPC(enc);
      break;
    }
    *nextTokPtr = ptr + MINBPC(enc);
    return XML_TOK_CDATA_SECT_CLOSE;
  case BT_CR:
    ptr += MINBPC(enc);
    if (ptr == end)
      return XML_TOK_PARTIAL;
    if (BYTE_TYPE(enc, ptr) == BT_LF)
      ptr += MINBPC(enc);
    *nextTokPtr = ptr;
    return XML_TOK_DATA_NEWLINE;
  case BT_LF:
    *nextTokPtr = ptr + MINBPC(enc);
    return XML_TOK_DATA_NEWLINE;
  INVALID_CASES(ptr, nextTokPtr)
  default:
    ptr += MINBPC(enc);
    break;
  }
  while (ptr != end) {
    switch (BYTE_TYPE(enc, ptr)) {
#define LEAD_CASE(n) \
    case BT_LEAD ## n: \
      if (end - ptr < n || IS_INVALID_CHAR(enc, ptr, n)) { \
        *nextTokPtr = ptr; \
        return XML_TOK_DATA_CHARS; \
      } \
      ptr += n; \
      break;
    LEAD_CASE(2) LEAD_CASE(3) LEAD_CASE(4)
#undef LEAD_CASE
    case BT_NONXML:
    case BT_MALFORM:
    case BT_TRAIL:
    case BT_CR:
    case BT_LF:
    case BT_RSQB:
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    default:
      ptr += MINBPC(enc);
      break;
    }
  }
  *nextTokPtr = ptr;
  return XML_TOK_DATA_CHARS;
}

/* ptr points to character following " 1) {
    size_t n = end - ptr;
    if (n & (MINBPC(enc) - 1)) {
      n &= ~(MINBPC(enc) - 1);
      if (n == 0)
        return XML_TOK_PARTIAL;
      end = ptr + n;
    }
  }
  switch (BYTE_TYPE(enc, ptr)) {
  case BT_LT:
    return PREFIX(scanLt)(enc, ptr + MINBPC(enc), end, nextTokPtr);
  case BT_AMP:
    return PREFIX(scanRef)(enc, ptr + MINBPC(enc), end, nextTokPtr);
  case BT_CR:
    ptr += MINBPC(enc);
    if (ptr == end)
      return XML_TOK_TRAILING_CR;
    if (BYTE_TYPE(enc, ptr) == BT_LF)
      ptr += MINBPC(enc);
    *nextTokPtr = ptr;
    return XML_TOK_DATA_NEWLINE;
  case BT_LF:
    *nextTokPtr = ptr + MINBPC(enc);
    return XML_TOK_DATA_NEWLINE;
  case BT_RSQB:
    ptr += MINBPC(enc);
    if (ptr == end)
      return XML_TOK_TRAILING_RSQB;
    if (!CHAR_MATCHES(enc, ptr, ASCII_RSQB))
      break;
    ptr += MINBPC(enc);
    if (ptr == end)
      return XML_TOK_TRAILING_RSQB;
    if (!CHAR_MATCHES(enc, ptr, ASCII_GT)) {
      ptr -= MINBPC(enc);
      break;
    }
    *nextTokPtr = ptr;
    return XML_TOK_INVALID;
  INVALID_CASES(ptr, nextTokPtr)
  default:
    ptr += MINBPC(enc);
    break;
  }
  while (ptr != end) {
    switch (BYTE_TYPE(enc, ptr)) {
#define LEAD_CASE(n) \
    case BT_LEAD ## n: \
      if (end - ptr < n || IS_INVALID_CHAR(enc, ptr, n)) { \
        *nextTokPtr = ptr; \
        return XML_TOK_DATA_CHARS; \
      } \
      ptr += n; \
      break;
    LEAD_CASE(2) LEAD_CASE(3) LEAD_CASE(4)
#undef LEAD_CASE
    case BT_RSQB:
      if (ptr + MINBPC(enc) != end) {
         if (!CHAR_MATCHES(enc, ptr + MINBPC(enc), ASCII_RSQB)) {
           ptr += MINBPC(enc);
           break;
         }
         if (ptr + 2*MINBPC(enc) != end) {
           if (!CHAR_MATCHES(enc, ptr + 2*MINBPC(enc), ASCII_GT)) {
             ptr += MINBPC(enc);
             break;
           }
           *nextTokPtr = ptr + 2*MINBPC(enc);
           return XML_TOK_INVALID;
         }
      }
      /* fall through */
    case BT_AMP:
    case BT_LT:
    case BT_NONXML:
    case BT_MALFORM:
    case BT_TRAIL:
    case BT_CR:
    case BT_LF:
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    default:
      ptr += MINBPC(enc);
      break;
    }
  }
  *nextTokPtr = ptr;
  return XML_TOK_DATA_CHARS;
}

/* ptr points to character following "%" */

static int PTRCALL
PREFIX(scanPercent)(const ENCODING *enc, const char *ptr, const char *end,
                    const char **nextTokPtr)
{
  if (ptr == end)
    return -XML_TOK_PERCENT;
  switch (BYTE_TYPE(enc, ptr)) {
  CHECK_NMSTRT_CASES(enc, ptr, end, nextTokPtr)
  case BT_S: case BT_LF: case BT_CR: case BT_PERCNT:
    *nextTokPtr = ptr;
    return XML_TOK_PERCENT;
  default:
    *nextTokPtr = ptr;
    return XML_TOK_INVALID;
  }
  while (ptr != end) {
    switch (BYTE_TYPE(enc, ptr)) {
    CHECK_NAME_CASES(enc, ptr, end, nextTokPtr)
    case BT_SEMI:
      *nextTokPtr = ptr + MINBPC(enc);
      return XML_TOK_PARAM_ENTITY_REF;
    default:
      *nextTokPtr = ptr;
      return XML_TOK_INVALID;
    }
  }
  return XML_TOK_PARTIAL;
}

static int PTRCALL
PREFIX(scanPoundName)(const ENCODING *enc, const char *ptr, const char *end,
                      const char **nextTokPtr)
{
  if (ptr == end)
    return XML_TOK_PARTIAL;
  switch (BYTE_TYPE(enc, ptr)) {
  CHECK_NMSTRT_CASES(enc, ptr, end, nextTokPtr)
  default:
    *nextTokPtr = ptr;
    return XML_TOK_INVALID;
  }
  while (ptr != end) {
    switch (BYTE_TYPE(enc, ptr)) {
    CHECK_NAME_CASES(enc, ptr, end, nextTokPtr)
    case BT_CR: case BT_LF: case BT_S:
    case BT_RPAR: case BT_GT: case BT_PERCNT: case BT_VERBAR:
      *nextTokPtr = ptr;
      return XML_TOK_POUND_NAME;
    default:
      *nextTokPtr = ptr;
      return XML_TOK_INVALID;
    }
  }
  return -XML_TOK_POUND_NAME;
}

static int PTRCALL
PREFIX(scanLit)(int open, const ENCODING *enc,
                const char *ptr, const char *end,
                const char **nextTokPtr)
{
  while (ptr != end) {
    int t = BYTE_TYPE(enc, ptr);
    switch (t) {
    INVALID_CASES(ptr, nextTokPtr)
    case BT_QUOT:
    case BT_APOS:
      ptr += MINBPC(enc);
      if (t != open)
        break;
      if (ptr == end)
        return -XML_TOK_LITERAL;
      *nextTokPtr = ptr;
      switch (BYTE_TYPE(enc, ptr)) {
      case BT_S: case BT_CR: case BT_LF:
      case BT_GT: case BT_PERCNT: case BT_LSQB:
        return XML_TOK_LITERAL;
      default:
        return XML_TOK_INVALID;
      }
    default:
      ptr += MINBPC(enc);
      break;
    }
  }
  return XML_TOK_PARTIAL;
}

static int PTRCALL
PREFIX(prologTok)(const ENCODING *enc, const char *ptr, const char *end,
                  const char **nextTokPtr)
{
  int tok;
  if (ptr == end)
    return XML_TOK_NONE;
  if (MINBPC(enc) > 1) {
    size_t n = end - ptr;
    if (n & (MINBPC(enc) - 1)) {
      n &= ~(MINBPC(enc) - 1);
      if (n == 0)
        return XML_TOK_PARTIAL;
      end = ptr + n;
    }
  }
  switch (BYTE_TYPE(enc, ptr)) {
  case BT_QUOT:
    return PREFIX(scanLit)(BT_QUOT, enc, ptr + MINBPC(enc), end, nextTokPtr);
  case BT_APOS:
    return PREFIX(scanLit)(BT_APOS, enc, ptr + MINBPC(enc), end, nextTokPtr);
  case BT_LT:
    {
      ptr += MINBPC(enc);
      if (ptr == end)
        return XML_TOK_PARTIAL;
      switch (BYTE_TYPE(enc, ptr)) {
      case BT_EXCL:
        return PREFIX(scanDecl)(enc, ptr + MINBPC(enc), end, nextTokPtr);
      case BT_QUEST:
        return PREFIX(scanPi)(enc, ptr + MINBPC(enc), end, nextTokPtr);
      case BT_NMSTRT:
      case BT_HEX:
      case BT_NONASCII:
      case BT_LEAD2:
      case BT_LEAD3:
      case BT_LEAD4:
        *nextTokPtr = ptr - MINBPC(enc);
        return XML_TOK_INSTANCE_START;
      }
      *nextTokPtr = ptr;
      return XML_TOK_INVALID;
    }
  case BT_CR:
    if (ptr + MINBPC(enc) == end) {
      *nextTokPtr = end;
      /* indicate that this might be part of a CR/LF pair */
      return -XML_TOK_PROLOG_S;
    }
    /* fall through */
  case BT_S: case BT_LF:
    for (;;) {
      ptr += MINBPC(enc);
      if (ptr == end)
        break;
      switch (BYTE_TYPE(enc, ptr)) {
      case BT_S: case BT_LF:
        break;
      case BT_CR:
        /* don't split CR/LF pair */
        if (ptr + MINBPC(enc) != end)
          break;
        /* fall through */
      default:
        *nextTokPtr = ptr;
        return XML_TOK_PROLOG_S;
      }
    }
    *nextTokPtr = ptr;
    return XML_TOK_PROLOG_S;
  case BT_PERCNT:
    return PREFIX(scanPercent)(enc, ptr + MINBPC(enc), end, nextTokPtr);
  case BT_COMMA:
    *nextTokPtr = ptr + MINBPC(enc);
    return XML_TOK_COMMA;
  case BT_LSQB:
    *nextTokPtr = ptr + MINBPC(enc);
    return XML_TOK_OPEN_BRACKET;
  case BT_RSQB:
    ptr += MINBPC(enc);
    if (ptr == end)
      return -XML_TOK_CLOSE_BRACKET;
    if (CHAR_MATCHES(enc, ptr, ASCII_RSQB)) {
      if (ptr + MINBPC(enc) == end)
        return XML_TOK_PARTIAL;
      if (CHAR_MATCHES(enc, ptr + MINBPC(enc), ASCII_GT)) {
        *nextTokPtr = ptr + 2*MINBPC(enc);
        return XML_TOK_COND_SECT_CLOSE;
      }
    }
    *nextTokPtr = ptr;
    return XML_TOK_CLOSE_BRACKET;
  case BT_LPAR:
    *nextTokPtr = ptr + MINBPC(enc);
    return XML_TOK_OPEN_PAREN;
  case BT_RPAR:
    ptr += MINBPC(enc);
    if (ptr == end)
      return -XML_TOK_CLOSE_PAREN;
    switch (BYTE_TYPE(enc, ptr)) {
    case BT_AST:
      *nextTokPtr = ptr + MINBPC(enc);
      return XML_TOK_CLOSE_PAREN_ASTERISK;
    case BT_QUEST:
      *nextTokPtr = ptr + MINBPC(enc);
      return XML_TOK_CLOSE_PAREN_QUESTION;
    case BT_PLUS:
      *nextTokPtr = ptr + MINBPC(enc);
      return XML_TOK_CLOSE_PAREN_PLUS;
    case BT_CR: case BT_LF: case BT_S:
    case BT_GT: case BT_COMMA: case BT_VERBAR:
    case BT_RPAR:
      *nextTokPtr = ptr;
      return XML_TOK_CLOSE_PAREN;
    }
    *nextTokPtr = ptr;
    return XML_TOK_INVALID;
  case BT_VERBAR:
    *nextTokPtr = ptr + MINBPC(enc);
    return XML_TOK_OR;
  case BT_GT:
    *nextTokPtr = ptr + MINBPC(enc);
    return XML_TOK_DECL_CLOSE;
  case BT_NUM:
    return PREFIX(scanPoundName)(enc, ptr + MINBPC(enc), end, nextTokPtr);
#define LEAD_CASE(n) \
  case BT_LEAD ## n: \
    if (end - ptr < n) \
      return XML_TOK_PARTIAL_CHAR; \
    if (IS_NMSTRT_CHAR(enc, ptr, n)) { \
      ptr += n; \
      tok = XML_TOK_NAME; \
      break; \
    } \
    if (IS_NAME_CHAR(enc, ptr, n)) { \
      ptr += n; \
      tok = XML_TOK_NMTOKEN; \
      break; \
    } \
    *nextTokPtr = ptr; \
    return XML_TOK_INVALID;
    LEAD_CASE(2) LEAD_CASE(3) LEAD_CASE(4)
#undef LEAD_CASE
  case BT_NMSTRT:
  case BT_HEX:
    tok = XML_TOK_NAME;
    ptr += MINBPC(enc);
    break;
  case BT_DIGIT:
  case BT_NAME:
  case BT_MINUS:
#ifdef XML_NS
  case BT_COLON:
#endif
    tok = XML_TOK_NMTOKEN;
    ptr += MINBPC(enc);
    break;
  case BT_NONASCII:
    if (IS_NMSTRT_CHAR_MINBPC(enc, ptr)) {
      ptr += MINBPC(enc);
      tok = XML_TOK_NAME;
      break;
    }
    if (IS_NAME_CHAR_MINBPC(enc, ptr)) {
      ptr += MINBPC(enc);
      tok = XML_TOK_NMTOKEN;
      break;
    }
    /* fall through */
  default:
    *nextTokPtr = ptr;
    return XML_TOK_INVALID;
  }
  while (ptr != end) {
    switch (BYTE_TYPE(enc, ptr)) {
    CHECK_NAME_CASES(enc, ptr, end, nextTokPtr)
    case BT_GT: case BT_RPAR: case BT_COMMA:
    case BT_VERBAR: case BT_LSQB: case BT_PERCNT:
    case BT_S: case BT_CR: case BT_LF:
      *nextTokPtr = ptr;
      return tok;
#ifdef XML_NS
    case BT_COLON:
      ptr += MINBPC(enc);
      switch (tok) {
      case XML_TOK_NAME:
        if (ptr == end)
          return XML_TOK_PARTIAL;
        tok = XML_TOK_PREFIXED_NAME;
        switch (BYTE_TYPE(enc, ptr)) {
        CHECK_NAME_CASES(enc, ptr, end, nextTokPtr)
        default:
          tok = XML_TOK_NMTOKEN;
          break;
        }
        break;
      case XML_TOK_PREFIXED_NAME:
        tok = XML_TOK_NMTOKEN;
        break;
      }
      break;
#endif
    case BT_PLUS:
      if (tok == XML_TOK_NMTOKEN)  {
        *nextTokPtr = ptr;
        return XML_TOK_INVALID;
      }
      *nextTokPtr = ptr + MINBPC(enc);
      return XML_TOK_NAME_PLUS;
    case BT_AST:
      if (tok == XML_TOK_NMTOKEN)  {
        *nextTokPtr = ptr;
        return XML_TOK_INVALID;
      }
      *nextTokPtr = ptr + MINBPC(enc);
      return XML_TOK_NAME_ASTERISK;
    case BT_QUEST:
      if (tok == XML_TOK_NMTOKEN)  {
        *nextTokPtr = ptr;
        return XML_TOK_INVALID;
      }
      *nextTokPtr = ptr + MINBPC(enc);
      return XML_TOK_NAME_QUESTION;
    default:
      *nextTokPtr = ptr;
      return XML_TOK_INVALID;
    }
  }
  return -tok;
}

static int PTRCALL
PREFIX(attributeValueTok)(const ENCODING *enc, const char *ptr,
                          const char *end, const char **nextTokPtr)
{
  const char *start;
  if (ptr == end)
    return XML_TOK_NONE;
  start = ptr;
  while (ptr != end) {
    switch (BYTE_TYPE(enc, ptr)) {
#define LEAD_CASE(n) \
    case BT_LEAD ## n: ptr += n; break;
    LEAD_CASE(2) LEAD_CASE(3) LEAD_CASE(4)
#undef LEAD_CASE
    case BT_AMP:
      if (ptr == start)
        return PREFIX(scanRef)(enc, ptr + MINBPC(enc), end, nextTokPtr);
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    case BT_LT:
      /* this is for inside entity references */
      *nextTokPtr = ptr;
      return XML_TOK_INVALID;
    case BT_LF:
      if (ptr == start) {
        *nextTokPtr = ptr + MINBPC(enc);
        return XML_TOK_DATA_NEWLINE;
      }
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    case BT_CR:
      if (ptr == start) {
        ptr += MINBPC(enc);
        if (ptr == end)
          return XML_TOK_TRAILING_CR;
        if (BYTE_TYPE(enc, ptr) == BT_LF)
          ptr += MINBPC(enc);
        *nextTokPtr = ptr;
        return XML_TOK_DATA_NEWLINE;
      }
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    case BT_S:
      if (ptr == start) {
        *nextTokPtr = ptr + MINBPC(enc);
        return XML_TOK_ATTRIBUTE_VALUE_S;
      }
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    default:
      ptr += MINBPC(enc);
      break;
    }
  }
  *nextTokPtr = ptr;
  return XML_TOK_DATA_CHARS;
}

static int PTRCALL
PREFIX(entityValueTok)(const ENCODING *enc, const char *ptr,
                       const char *end, const char **nextTokPtr)
{
  const char *start;
  if (ptr == end)
    return XML_TOK_NONE;
  start = ptr;
  while (ptr != end) {
    switch (BYTE_TYPE(enc, ptr)) {
#define LEAD_CASE(n) \
    case BT_LEAD ## n: ptr += n; break;
    LEAD_CASE(2) LEAD_CASE(3) LEAD_CASE(4)
#undef LEAD_CASE
    case BT_AMP:
      if (ptr == start)
        return PREFIX(scanRef)(enc, ptr + MINBPC(enc), end, nextTokPtr);
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    case BT_PERCNT:
      if (ptr == start) {
        int tok =  PREFIX(scanPercent)(enc, ptr + MINBPC(enc),
                                       end, nextTokPtr);
        return (tok == XML_TOK_PERCENT) ? XML_TOK_INVALID : tok;
      }
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    case BT_LF:
      if (ptr == start) {
        *nextTokPtr = ptr + MINBPC(enc);
        return XML_TOK_DATA_NEWLINE;
      }
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    case BT_CR:
      if (ptr == start) {
        ptr += MINBPC(enc);
        if (ptr == end)
          return XML_TOK_TRAILING_CR;
        if (BYTE_TYPE(enc, ptr) == BT_LF)
          ptr += MINBPC(enc);
        *nextTokPtr = ptr;
        return XML_TOK_DATA_NEWLINE;
      }
      *nextTokPtr = ptr;
      return XML_TOK_DATA_CHARS;
    default:
      ptr += MINBPC(enc);
      break;
    }
  }
  *nextTokPtr = ptr;
  return XML_TOK_DATA_CHARS;
}

#ifdef XML_DTD

static int PTRCALL
PREFIX(ignoreSectionTok)(const ENCODING *enc, const char *ptr,
                         const char *end, const char **nextTokPtr)
{
  int level = 0;
  if (MINBPC(enc) > 1) {
    size_t n = end - ptr;
    if (n & (MINBPC(enc) - 1)) {
      n &= ~(MINBPC(enc) - 1);
      end = ptr + n;
    }
  }
  while (ptr != end) {
    switch (BYTE_TYPE(enc, ptr)) {
    INVALID_CASES(ptr, nextTokPtr)
    case BT_LT:
      if ((ptr += MINBPC(enc)) == end)
        return XML_TOK_PARTIAL;
      if (CHAR_MATCHES(enc, ptr, ASCII_EXCL)) {
        if ((ptr += MINBPC(enc)) == end)
          return XML_TOK_PARTIAL;
        if (CHAR_MATCHES(enc, ptr, ASCII_LSQB)) {
          ++level;
          ptr += MINBPC(enc);
        }
      }
      break;
    case BT_RSQB:
      if ((ptr += MINBPC(enc)) == end)
        return XML_TOK_PARTIAL;
      if (CHAR_MATCHES(enc, ptr, ASCII_RSQB)) {
        if ((ptr += MINBPC(enc)) == end)
          return XML_TOK_PARTIAL;
        if (CHAR_MATCHES(enc, ptr, ASCII_GT)) {
          ptr += MINBPC(enc);
          if (level == 0) {
            *nextTokPtr = ptr;
            return XML_TOK_IGNORE_SECT;
          }
          --level;
        }
      }
      break;
    default:
      ptr += MINBPC(enc);
      break;
    }
  }
  return XML_TOK_PARTIAL;
}

#endif /* XML_DTD */

static int PTRCALL
PREFIX(isPublicId)(const ENCODING *enc, const char *ptr, const char *end,
                   const char **badPtr)
{
  ptr += MINBPC(enc);
  end -= MINBPC(enc);
  for (; ptr != end; ptr += MINBPC(enc)) {
    switch (BYTE_TYPE(enc, ptr)) {
    case BT_DIGIT:
    case BT_HEX:
    case BT_MINUS:
    case BT_APOS:
    case BT_LPAR:
    case BT_RPAR:
    case BT_PLUS:
    case BT_COMMA:
    case BT_SOL:
    case BT_EQUALS:
    case BT_QUEST:
    case BT_CR:
    case BT_LF:
    case BT_SEMI:
    case BT_EXCL:
    case BT_AST:
    case BT_PERCNT:
    case BT_NUM:
#ifdef XML_NS
    case BT_COLON:
#endif
      break;
    case BT_S:
      if (CHAR_MATCHES(enc, ptr, ASCII_TAB)) {
        *badPtr = ptr;
        return 0;
      }
      break;
    case BT_NAME:
    case BT_NMSTRT:
      if (!(BYTE_TO_ASCII(enc, ptr) & ~0x7f))
        break;
    default:
      switch (BYTE_TO_ASCII(enc, ptr)) {
      case 0x24: /* $ */
      case 0x40: /* @ */
        break;
      default:
        *badPtr = ptr;
        return 0;
      }
      break;
    }
  }
  return 1;
}

/* This must only be called for a well-formed start-tag or empty
   element tag.  Returns the number of attributes.  Pointers to the
   first attsMax attributes are stored in atts.
*/

static int PTRCALL
PREFIX(getAtts)(const ENCODING *enc, const char *ptr,
                int attsMax, ATTRIBUTE *atts)
{
  enum { other, inName, inValue } state = inName;
  int nAtts = 0;
  int open = 0; /* defined when state == inValue;
                   initialization just to shut up compilers */

  for (ptr += MINBPC(enc);; ptr += MINBPC(enc)) {
    switch (BYTE_TYPE(enc, ptr)) {
#define START_NAME \
      if (state == other) { \
        if (nAtts < attsMax) { \
          atts[nAtts].name = ptr; \
          atts[nAtts].normalized = 1; \
        } \
        state = inName; \
      }
#define LEAD_CASE(n) \
    case BT_LEAD ## n: START_NAME ptr += (n - MINBPC(enc)); break;
    LEAD_CASE(2) LEAD_CASE(3) LEAD_CASE(4)
#undef LEAD_CASE
    case BT_NONASCII:
    case BT_NMSTRT:
    case BT_HEX:
      START_NAME
      break;
#undef START_NAME
    case BT_QUOT:
      if (state != inValue) {
        if (nAtts < attsMax)
          atts[nAtts].valuePtr = ptr + MINBPC(enc);
        state = inValue;
        open = BT_QUOT;
      }
      else if (open == BT_QUOT) {
        state = other;
        if (nAtts < attsMax)
          atts[nAtts].valueEnd = ptr;
        nAtts++;
      }
      break;
    case BT_APOS:
      if (state != inValue) {
        if (nAtts < attsMax)
          atts[nAtts].valuePtr = ptr + MINBPC(enc);
        state = inValue;
        open = BT_APOS;
      }
      else if (open == BT_APOS) {
        state = other;
        if (nAtts < attsMax)
          atts[nAtts].valueEnd = ptr;
        nAtts++;
      }
      break;
    case BT_AMP:
      if (nAtts < attsMax)
        atts[nAtts].normalized = 0;
      break;
    case BT_S:
      if (state == inName)
        state = other;
      else if (state == inValue
               && nAtts < attsMax
               && atts[nAtts].normalized
               && (ptr == atts[nAtts].valuePtr
                   || BYTE_TO_ASCII(enc, ptr) != ASCII_SPACE
                   || BYTE_TO_ASCII(enc, ptr + MINBPC(enc)) == ASCII_SPACE
                   || BYTE_TYPE(enc, ptr + MINBPC(enc)) == open))
        atts[nAtts].normalized = 0;
      break;
    case BT_CR: case BT_LF:
      /* This case ensures that the first attribute name is counted
         Apart from that we could just change state on the quote. */
      if (state == inName)
        state = other;
      else if (state == inValue && nAtts < attsMax)
        atts[nAtts].normalized = 0;
      break;
    case BT_GT:
    case BT_SOL:
      if (state != inValue)
        return nAtts;
      break;
    default:
      break;
    }
  }
  /* not reached */
}

static int PTRFASTCALL
PREFIX(charRefNumber)(__attribute__ ((unused)) const ENCODING *enc, const char *ptr)
{
  int result = 0;
  /* skip &# */
  ptr += 2*MINBPC(enc);
  if (CHAR_MATCHES(enc, ptr, ASCII_x)) {
    for (ptr += MINBPC(enc);
         !CHAR_MATCHES(enc, ptr, ASCII_SEMI);
         ptr += MINBPC(enc)) {
      int c = BYTE_TO_ASCII(enc, ptr);
      switch (c) {
      case ASCII_0: case ASCII_1: case ASCII_2: case ASCII_3: case ASCII_4:
      case ASCII_5: case ASCII_6: case ASCII_7: case ASCII_8: case ASCII_9:
        result <<= 4;
        result |= (c - ASCII_0);
        break;
      case ASCII_A: case ASCII_B: case ASCII_C:
      case ASCII_D: case ASCII_E: case ASCII_F:
        result <<= 4;
        result += 10 + (c - ASCII_A);
        break;
      case ASCII_a: case ASCII_b: case ASCII_c:
      case ASCII_d: case ASCII_e: case ASCII_f:
        result <<= 4;
        result += 10 + (c - ASCII_a);
        break;
      }
      if (result >= 0x110000)
        return -1;
    }
  }
  else {
    for (; !CHAR_MATCHES(enc, ptr, ASCII_SEMI); ptr += MINBPC(enc)) {
      int c = BYTE_TO_ASCII(enc, ptr);
      result *= 10;
      result += (c - ASCII_0);
      if (result >= 0x110000)
        return -1;
    }
  }
  return checkCharRefNumber(result);
}

static int PTRCALL
PREFIX(predefinedEntityName)(__attribute__ ((unused)) const ENCODING *enc, const char *ptr,
                             const char *end)
{
  switch ((end - ptr)/MINBPC(enc)) {
  case 2:
    if (CHAR_MATCHES(enc, ptr + MINBPC(enc), ASCII_t)) {
      switch (BYTE_TO_ASCII(enc, ptr)) {
      case ASCII_l:
        return ASCII_LT;
      case ASCII_g:
        return ASCII_GT;
      }
    }
    break;
  case 3:
    if (CHAR_MATCHES(enc, ptr, ASCII_a)) {
      ptr += MINBPC(enc);
      if (CHAR_MATCHES(enc, ptr, ASCII_m)) {
        ptr += MINBPC(enc);
        if (CHAR_MATCHES(enc, ptr, ASCII_p))
          return ASCII_AMP;
      }
    }
    break;
  case 4:
    switch (BYTE_TO_ASCII(enc, ptr)) {
    case ASCII_q:
      ptr += MINBPC(enc);
      if (CHAR_MATCHES(enc, ptr, ASCII_u)) {
        ptr += MINBPC(enc);
        if (CHAR_MATCHES(enc, ptr, ASCII_o)) {
          ptr += MINBPC(enc);
          if (CHAR_MATCHES(enc, ptr, ASCII_t))
            return ASCII_QUOT;
        }
      }
      break;
    case ASCII_a:
      ptr += MINBPC(enc);
      if (CHAR_MATCHES(enc, ptr, ASCII_p)) {
        ptr += MINBPC(enc);
        if (CHAR_MATCHES(enc, ptr, ASCII_o)) {
          ptr += MINBPC(enc);
          if (CHAR_MATCHES(enc, ptr, ASCII_s))
            return ASCII_APOS;
        }
      }
      break;
    }
  }
  return 0;
}

static int PTRCALL
PREFIX(sameName)(const ENCODING *enc, const char *ptr1, const char *ptr2)
{
  for (;;) {
    switch (BYTE_TYPE(enc, ptr1)) {
#define LEAD_CASE(n) \
    case BT_LEAD ## n: \
      if (*ptr1++ != *ptr2++) \
        return 0;
    LEAD_CASE(4) LEAD_CASE(3) LEAD_CASE(2)
#undef LEAD_CASE
      /* fall through */
      if (*ptr1++ != *ptr2++)
        return 0;
      break;
    case BT_NONASCII:
    case BT_NMSTRT:
#ifdef XML_NS
    case BT_COLON:
#endif
    case BT_HEX:
    case BT_DIGIT:
    case BT_NAME:
    case BT_MINUS:
      if (*ptr2++ != *ptr1++)
        return 0;
      if (MINBPC(enc) > 1) {
        if (*ptr2++ != *ptr1++)
          return 0;
        if (MINBPC(enc) > 2) {
          if (*ptr2++ != *ptr1++)
            return 0;
          if (MINBPC(enc) > 3) {
            if (*ptr2++ != *ptr1++)
              return 0;
          }
        }
      }
      break;
    default:
      if (MINBPC(enc) == 1 && *ptr1 == *ptr2)
        return 1;
      switch (BYTE_TYPE(enc, ptr2)) {
      case BT_LEAD2:
      case BT_LEAD3:
      case BT_LEAD4:
      case BT_NONASCII:
      case BT_NMSTRT:
#ifdef XML_NS
      case BT_COLON:
#endif
      case BT_HEX:
      case BT_DIGIT:
      case BT_NAME:
      case BT_MINUS:
        return 0;
      default:
        return 1;
      }
    }
  }
  /* not reached */
}

static int PTRCALL
PREFIX(nameMatchesAscii)(__attribute__ ((unused)) const ENCODING *enc, const char *ptr1,
                         const char *end1, const char *ptr2)
{
  for (; *ptr2; ptr1 += MINBPC(enc), ptr2++) {
    if (ptr1 == end1)
      return 0;
    if (!CHAR_MATCHES(enc, ptr1, *ptr2))
      return 0;
  }
  return ptr1 == end1;
}

static int PTRFASTCALL
PREFIX(nameLength)(const ENCODING *enc, const char *ptr)
{
  const char *start = ptr;
  for (;;) {
    switch (BYTE_TYPE(enc, ptr)) {
#define LEAD_CASE(n) \
    case BT_LEAD ## n: ptr += n; break;
    LEAD_CASE(2) LEAD_CASE(3) LEAD_CASE(4)
#undef LEAD_CASE
    case BT_NONASCII:
    case BT_NMSTRT:
#ifdef XML_NS
    case BT_COLON:
#endif
    case BT_HEX:
    case BT_DIGIT:
    case BT_NAME:
    case BT_MINUS:
      ptr += MINBPC(enc);
      break;
    default:
      return (int)(ptr - start);
    }
  }
}

static const char * PTRFASTCALL
PREFIX(skipS)(const ENCODING *enc, const char *ptr)
{
  for (;;) {
    switch (BYTE_TYPE(enc, ptr)) {
    case BT_LF:
    case BT_CR:
    case BT_S:
      ptr += MINBPC(enc);
      break;
    default:
      return ptr;
    }
  }
}

static void PTRCALL
PREFIX(updatePosition)(const ENCODING *enc,
                       const char *ptr,
                       const char *end,
                       POSITION *pos)
{
  while (ptr != end) {
    switch (BYTE_TYPE(enc, ptr)) {
#define LEAD_CASE(n) \
    case BT_LEAD ## n: \
      ptr += n; \
      break;
    LEAD_CASE(2) LEAD_CASE(3) LEAD_CASE(4)
#undef LEAD_CASE
    case BT_LF:
      pos->columnNumber = (XML_Size)-1;
      pos->lineNumber++;
      ptr += MINBPC(enc);
      break;
    case BT_CR:
      pos->lineNumber++;
      ptr += MINBPC(enc);
      if (ptr != end && BYTE_TYPE(enc, ptr) == BT_LF)
        ptr += MINBPC(enc);
      pos->columnNumber = (XML_Size)-1;
      break;
    default:
      ptr += MINBPC(enc);
      break;
    }
    pos->columnNumber++;
  }
}

#undef DO_LEAD_CASE
#undef MULTIBYTE_CASES
#undef INVALID_CASES
#undef CHECK_NAME_CASE
#undef CHECK_NAME_CASES
#undef CHECK_NMSTRT_CASE
#undef CHECK_NMSTRT_CASES

#endif /* XML_TOK_IMPL_C */
genometools-1.5.1/src/external/expat-2.0.1/lib/xmltok_impl.h000077500000000000000000000012251211610345200235130ustar00rootroot00000000000000/*
Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
See the file COPYING for copying permission.
*/

enum {
  BT_NONXML,
  BT_MALFORM,
  BT_LT,
  BT_AMP,
  BT_RSQB,
  BT_LEAD2,
  BT_LEAD3,
  BT_LEAD4,
  BT_TRAIL,
  BT_CR,
  BT_LF,
  BT_GT,
  BT_QUOT,
  BT_APOS,
  BT_EQUALS,
  BT_QUEST,
  BT_EXCL,
  BT_SOL,
  BT_SEMI,
  BT_NUM,
  BT_LSQB,
  BT_S,
  BT_NMSTRT,
  BT_COLON,
  BT_HEX,
  BT_DIGIT,
  BT_NAME,
  BT_MINUS,
  BT_OTHER, /* known not to be a name or name start character */
  BT_NONASCII, /* might be a name or name start character */
  BT_PERCNT,
  BT_LPAR,
  BT_RPAR,
  BT_AST,
  BT_PLUS,
  BT_COMMA,
  BT_VERBAR
};

#include 
genometools-1.5.1/src/external/expat-2.0.1/lib/xmltok_ns.c000077500000000000000000000061101211610345200231630ustar00rootroot00000000000000/* Copyright (c) 1998, 1999 Thai Open Source Software Center Ltd
   See the file COPYING for copying permission.
*/

/* This file is included! */
#ifdef XML_TOK_NS_C

const ENCODING *
NS(XmlGetUtf8InternalEncoding)(void)
{
  return &ns(internal_utf8_encoding).enc;
}

const ENCODING *
NS(XmlGetUtf16InternalEncoding)(void)
{
#if BYTEORDER == 1234
  return &ns(internal_little2_encoding).enc;
#elif BYTEORDER == 4321
  return &ns(internal_big2_encoding).enc;
#else
  const short n = 1;
  return (*(const char *)&n
          ? &ns(internal_little2_encoding).enc
          : &ns(internal_big2_encoding).enc);
#endif
}

static const ENCODING * const NS(encodings)[] = {
  &ns(latin1_encoding).enc,
  &ns(ascii_encoding).enc,
  &ns(utf8_encoding).enc,
  &ns(big2_encoding).enc,
  &ns(big2_encoding).enc,
  &ns(little2_encoding).enc,
  &ns(utf8_encoding).enc /* NO_ENC */
};

static int PTRCALL
NS(initScanProlog)(const ENCODING *enc, const char *ptr, const char *end,
                   const char **nextTokPtr)
{
  return initScan(NS(encodings), (const INIT_ENCODING *)enc,
                  XML_PROLOG_STATE, ptr, end, nextTokPtr);
}

static int PTRCALL
NS(initScanContent)(const ENCODING *enc, const char *ptr, const char *end,
                    const char **nextTokPtr)
{
  return initScan(NS(encodings), (const INIT_ENCODING *)enc,
                  XML_CONTENT_STATE, ptr, end, nextTokPtr);
}

int
NS(XmlInitEncoding)(INIT_ENCODING *p, const ENCODING **encPtr,
                    const char *name)
{
  int i = getEncodingIndex(name);
  if (i == UNKNOWN_ENC)
    return 0;
  SET_INIT_ENC_INDEX(p, i);
  p->initEnc.scanners[XML_PROLOG_STATE] = NS(initScanProlog);
  p->initEnc.scanners[XML_CONTENT_STATE] = NS(initScanContent);
  p->initEnc.updatePosition = initUpdatePosition;
  p->encPtr = encPtr;
  *encPtr = &(p->initEnc);
  return 1;
}

static const ENCODING *
NS(findEncoding)(const ENCODING *enc, const char *ptr, const char *end)
{
#define ENCODING_MAX 128
  char buf[ENCODING_MAX];
  char *p = buf;
  int i;
  XmlUtf8Convert(enc, &ptr, end, &p, p + ENCODING_MAX - 1);
  if (ptr != end)
    return 0;
  *p = 0;
  if (streqci(buf, KW_UTF_16) && enc->minBytesPerChar == 2)
    return enc;
  i = getEncodingIndex(buf);
  if (i == UNKNOWN_ENC)
    return 0;
  return NS(encodings)[i];
}

int
NS(XmlParseXmlDecl)(int isGeneralTextEntity,
                    const ENCODING *enc,
                    const char *ptr,
                    const char *end,
                    const char **badPtr,
                    const char **versionPtr,
                    const char **versionEndPtr,
                    const char **encodingName,
                    const ENCODING **encoding,
                    int *standalone)
{
  return doParseXmlDecl(NS(findEncoding),
                        isGeneralTextEntity,
                        enc,
                        ptr,
                        end,
                        badPtr,
                        versionPtr,
                        versionEndPtr,
                        encodingName,
                        encoding,
                        standalone);
}

#endif /* XML_TOK_NS_C */
genometools-1.5.1/src/external/libtecla-1.6.1/000077500000000000000000000000001211610345200206755ustar00rootroot00000000000000genometools-1.5.1/src/external/libtecla-1.6.1/LICENSE.TERMS000066400000000000000000000027551211610345200226040ustar00rootroot00000000000000Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.

All rights reserved.

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, and/or sell copies of the Software, and to permit persons
to whom the Software is furnished to do so, provided that the above
copyright notice(s) and this permission notice appear in all copies of
the Software and that both the above copyright notice(s) and this
permission notice appear in supporting documentation.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

Except as contained in this notice, the name of a copyright holder
shall not be used in advertising or otherwise to promote the sale, use
or other dealings in this Software without prior written authorization
of the copyright holder.
genometools-1.5.1/src/external/libtecla-1.6.1/README000066400000000000000000000051671211610345200215660ustar00rootroot00000000000000This is version 1.6.1 of the tecla command-line editing library.

For the current official release, please direct your browser to:

  http://www.astro.caltech.edu/~mcs/tecla/index.html

The tecla library provides UNIX and LINUX programs with interactive
command line editing facilities, similar to those of the unix tcsh
shell. In addition to simple command-line editing, it supports recall
of previously entered command lines, TAB completion of file names, and
in-line wild-card expansion of filenames.  The internal functions
which perform file-name completion and wild-card expansion are also
available externally for optional use by programs, along with a module
for tab-completion and lookup of filenames in a list of directories.

Note that special care has been taken to allow the use of this library
in threaded programs. The option to enable this is discussed in the
Makefile, and specific discussions of thread safety are presented in
the included man pages.

For instructions on how to compile and install the library, please see
the INSTALL file, which should be in the same directory as this file.

Copyright and Disclaimer
------------------------
Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.

All rights reserved.

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, and/or sell copies of the Software, and to permit persons
to whom the Software is furnished to do so, provided that the above
copyright notice(s) and this permission notice appear in all copies of
the Software and that both the above copyright notice(s) and this
permission notice appear in supporting documentation.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

Except as contained in this notice, the name of a copyright holder
shall not be used in advertising or otherwise to promote the sale, use
or other dealings in this Software without prior written authorization
of the copyright holder.
genometools-1.5.1/src/external/libtecla-1.6.1/RELEASE.NOTES000066400000000000000000000702031211610345200225710ustar00rootroot00000000000000This file lists major changes which accompany each new release.

Version 1.6.1:

  This is primarily a minor bug-fix release.

  One added feature is the ability to call gl_normal_io() from
  callbacks registered by gl_watch_fd() and
  gl_inactivity_timeout(). This allows these callbacks to cleanly
  suspend line editing before either reading from the terminal, or
  writing to the terminal; and then subsequently causes the input line
  to be automatically redisplayed, and line-editing to be resumed by
  gl_get_line(), as soon as the callback returns.

  Another minor change is that if the terminal type specified in the
  TERM environment variable is set to "dumb", gl_get_line() now treats
  the terminal as though it were a non-interactive stream, rather than
  treating it as a VT100-compatible terminal. This means that it
  doesn't either prompt for input, or perform any command-line
  editing, even when it really is interacting with a terminal. This is
  aimed at the rare situation where a third-pary program that connects
  to libtecla through an embedded pseudo-terminal, needs to be forced
  to behave as though it weren't talking to a terminal, in order that
  it be useable in non-interactive scripts.

  Note that in the previous release, the optional configuration
  function, gl_tty_signals(), was incorrectly swapping the suspend and
  terminal signal handlers before installing them.

  A configuration problem that prevented select() from being used
  under MacOS X, has been fixed.

  Although not documented in the man page, it was meant to be possible
  to take the input line that one call to gl_get_line() returned, and
  ask the next call to gl_get_line() to present it back to the user
  for re-editing, simply by passing the pointer returned by one call
  to gl_get_line() as the start_line argument of the next call to
  gl_get_line(). This feature unfortunately stopped working in 1.6.0,
  so this release restores it, and officially documents it in the man
  page documentation of gl_get_line().

  In the previous version of the library, calling gl_terminal_size()
  on a system without SIGWINCH support, would crash the
  application. This has been fixed.

  Libtecla now apparently compiles cleanly under IRIX.

Version 1.6.0:

  This release is primarily a bug-fix release. However there are also
  four new functions, so the minor version number has been
  incremented to reflect this.

  Two of the new functions are gl_automatic_history() and
  gl_append_history(). The former of these functions allows the
  application to tell gl_get_line() not to automatically archive
  entered lines in the history list. The second of these functions
  allows the application to explicitly append a line to the history
  list. Thus together, these two functions allow the calling
  application to take over control of what is placed in the history
  list.

  The third new function is gl_query_char(), which prompts the user
  for a single character reply, which the user can then type without
  having to hit return to enter it. Unless echoing is disabled, the
  character that is entered is then displayed after the prompt,
  and a newline is started.

  Finally, the 4th new function is gl_read_char(), which also reads
  a single character from the user, but doesn't prompt the user, write
  anything to the terminal, or disturb any partially entered input
  line. It is thus safe to call this function not only from between
  calls to gl_get_line(), but also from application callback
  functions, even if gl_normal_io() hasn't been called.

  When using the history-search-backwards or history-search-forwards
  actions, if the search prefix that the user typed, contains any of
  the *,? or [ globbing characters, it is now treated as a glob
  pattern to be matched against historical lines, instead of a simple
  prefix.

  I have added a --without-file-system option to the configure
  script. This is intended for use in embedded systems that either
  don't have filesystems, or where the file-system code in libtecla is
  seen as unwanted bloat. See the INSTALL document for details.

  Similarly, I also added a --without-file-actions option to the
  configure script. This allows the application author/installer to
  prevent users of gl_get_line() from accessing the filesystem with
  the builtin actions of gl_get_line(). It does this by removing a
  number of action functions, such as expand-filename, and list-glob,
  and by changing the default behavior of other actions, such as
  complete-word and list-or-eof, to show no completions.

  Now to the bugs that have been fixed. Version 1.5.0 had a lot of big
  internal changes, so there are a number of bugs that needed to be
  fixed.  There was a bug which caused a crash if gl_load_history()
  was called multiple times. There was another bug which caused a
  prompt not to be displayed on the next line after switching from
  reading input from a file to reading from the terminal. Also, in
  tecla configuration files, backslash escaped characters within
  key-binding key-sequences weren't being escaped. Thus ^\\ got
  interpretted as a control-\ followed by a \ character instead of as
  a control-\. There was a bug in the history recall mechanism which
  caused the search prefix to be forgotten in certain complicated
  usage scenarios. There was a minor memory leak in the
  gl_configure_getline() function. Finally, if gl_get_line() was
  aborted by a signal, or any other abnormal event, the value of errno
  which originally indicated what had happened, got zeroed by the
  code that restored the terminal to a usable state. Thus the
  application couldn't figure out what had caused the error, apart
  from by looking at gl_return_status(). All of these bugs have been
  fixed.

  In the Makefile, there were a number of places where install-sh was
  invoked without a path prefix. This has now been remedied.

  A fully functional workaround for a bug in Solaris' terminal I/O
  code has also been implemented. This bug, which only manifested
  itself in libtecla's uncommonly used non-blocking server I/O mode,
  caused characters entered while in normal I/O mode, between calls to
  gl_get_line() to be invisible to the next call to gl_get_line(),
  until the user typed at least one more key after raw terminal mode
  was restored.

  The Gnu autoconf config.guess and config.sub scripts have been
  updated to their latest versions. Apparently the old versions that I
  was previously using were too old to know about certain BSD ports.
  
Version 1.5.0:

  This release includes several major new features for those using
  gl_get_line(), shared library support in Darwin, better cross
  compilation support, and various minor bug fixes.

  The biggest new feature is the option of a non-blocking I/O mode, in
  which gl_get_line() can safely be called from an application's
  external event-loop to incrementally read input lines from the user.
  This feature is documented in the gl_io_mode(3) man page.

  In addition, there is now support for the definition of additional
  word-completion action functions, which can then be bound to
  different keys. See the documentation of the gl_completion_action()
  function in the gl_get_line(3) man page.

  Externally defined action functions can also be defined, although
  presently they don't have write access to the input line, so they
  are restricted to operations that display information text to the
  terminal, or modify the environment of the calling application in
  some way. See the documentation of the gl_register_action() function
  in the gl_get_line(3) man page.

  Some of the non-blocking I/O support functions can also be used for
  improved signal handling in the normal blocking mode. In particular,
  the gl_list_signals() and gl_catch_blocked() functions make it
  easier to write reliable signal handling around gl_get_line(). The
  new "RELIABLE SIGNAL HANDLING" section of the gl_get_line(3) man
  page is intended as an introduction to this subject.

  Programs can now clear the terminal between calls to gl_get_line(),
  by calling the new gl_erase_terminal() function.

  The gl_display_text() function, now used in the demos to display
  introductory banners, is provided for formatting text according to
  the width of the terminal.

  It is now possible to install inactivity timeout callbacks in
  gl_get_line(), using the new gl_inactivity_timeout() function.

  The new gl_set_term_size() function allows the application to
  explicitly set the terminal size, for cases, such as when one is
  using a terminal at the end of a serial lineq, where the terminal
  driver doesn't send the process a SIGWINCH when the terminal size
  changes.

  The new gl_bind_keyseq() function provides a convenient
  alternative to gl_configure_getline(), for binding or unbinding
  one key-sequence at a time.

  gl_get_line()s signal handling, file-descriptor event-handling,
  inactivity-timeout handling and server-mode non-blocking I/O
  features now not only work when input is coming from a terminal, but
  now also work when input is coming from non-interactive streams,
  such as files and pipes.

  The history implementation has been re-written to make it more
  efficient and easier to modify. The biggest user-level change is
  that when recalling history lines using a search prefix, the same
  line is no longer returned more than once in a row.  Previously this
  duplicate elimination only worked when one was recalling a line
  without specifying a search prefix, and this was naively performed
  by preventing neighboring duplicates from existing in the history
  list, rather than by skipping duplicates at search time.

  In previous versions of the library, when gl_get_line() and its
  associated public functions detected invalid arguments, or couldn't
  allocate memory, etc, error messages were written to stderr. This
  isn't appropriate for library functions, so instead of writing such
  messages to stderr, these messages are now recorded in buffers
  within the affected GetLine object. The latest error message can
  then subsequently be queried by calling gl_error_message(). The use
  of errno has also been expanded, and a new function called
  gl_return_status() has been provided to expand on the cause of the
  last return from gl_get_line().

  User level usage and configuration information has now been split
  out of the gl_get_line(3) man page into a separate tecla(7) man
  page. The enhance(3) man page has also been renamed to enhance(1).

  When expanding "~/", gl_get_line() now checks for, and returns the
  value of the HOME environment variable, if it exists, in preference
  to looking up the directory of the current user in the password
  file.

  When the terminal was resized to a narrower width, previous versions
  of gl_get_line() would redraw the line higher up the terminal. This
  bug has been fixed. A bug in history recall has also been fixed, in
  which an error message was being generated if one attempted to
  recall a line while the cursor was at the end of the longest
  possible input line. A more serious bug, in which callbacks
  registered by gl_watch_fd() weren't being called for write-events,
  has also been fixed. Finally, a few minor fixes have been made to
  improve support under QNX and Mac OS X.

  Beware that in this release, much of the underlying code has
  undergone some radical re-work, so although backwards compatibility
  of all documented features has been preserved, there may be some
  lingering bugs that could break existing programs.  So, if you plan
  to use this version in production code, please test it as far as
  possible within your application before releasing it to your
  clients, and as always, please report any unexpected behavior.

Version 1.4.1:

  This is a maintenance release. It includes minor changes to support
  Mac OS X (Darwin), the QNX real-time operating system, and Cygwin
  under Windows. It also fixes an oversight that was preventing the
  tab key from inserting tab characters when users unbound the
  complete-word action from it.

Version 1.4.0:

  The contents of the history list can now be saved and restored with
  the new gl_save_history() and gl_load_history() functions.

  Event handlers can now be registered to watch for and respond to I/O
  on arbitrary file descriptors while gl_get_line() is waiting for
  terminal input from the user. See the gl_get_line(3) man page
  for details on gl_watch_fd().

  As an optional alternative to getting configuration information only
  from ~/.teclarc, the new gl_configure_getline() function allows
  configuration commands to be taken from any of, a string, a
  specified application-specific file, and/or a specified
  user-specific file. See the gl_get_line(3) man page for details.

  The version number of the library can now be queried using the
  libtecla_version() function. See the libtecla(3) man page.

  The new gl_group_history() function allows applications to group
  different types of input line in the history buffer, and arrange for
  only members of the appropriate group to be recalled on a given call
  to gl_get_line(). See the gl_get_line(3) man page.

  The new gl_show_history() function displays the current history list
  to a given stdio output stream. See the gl_get_line(3) man page.

  new_GetLine() now allows you to specify a history buffer size of
  zero, thus requesting that no history buffer be allocated. You can
  subsequently resize or delete the history buffer at any time, by
  calling gl_resize_history(), limit the number of lines that are
  allowed in the buffer by calling gl_limit_history(), clear either
  all history lines from the history list, or just the history lines
  that are associated with the current history group, by calling
  gl_clear_history, and toggle the history mechanism on and off by
  calling gl_toggle_history().

  The new gl_terminal_size() function can be used to query the
  current terminal size. It can also be used to supply a default
  terminal size on systems where no mechanism is available for
  looking up the size.

  The contents and configuration of the history list can now be
  obtained by the calling application, by calling the new
  gl_lookup_history(), gl_state_of_history(), gl_range_of_history()
  and gl_size_of_history() functions. See the gl_get_line(3) man page.

  Echoing of the input line as it is typed, can now be turned on and
  off via the new gl_echo_mode() function. While echoing is disabled,
  newly entered input lines are omitted from the history list.  See
  the gl_get_line(3) man page.

  While the default remains to display the prompt string literally,
  the new gl_prompt_style() function can be used to enable text
  attribute formatting directives in prompt strings, such as
  underlining, bold font, and highlighting directives.

  Signal handling in gl_get_line() is now customizable. The default
  signal handling behavior remains essentially the same, except that
  the SIGTSTP, SIGTTIN and SIGTTOU are now forwarded to the
  corresponding signal handler of the calling program, instead of
  causing a SIGSTOP to be sent to the application.  It is now possible
  to remove signals from the list that are trapped by gl_get_line(),
  as well as add new signals to this list. The signal and terminal
  environments in which the signal handler of the calling program is
  invoked, and what gl_get_line() does after the signal handler
  returns, is now customizable on a per signal basis. You can now also
  query the last signal that was caught by gl_get_line(). This is
  useful when gl_get_line() aborts with errno=EINTR, and you need to
  know which signal caused it to abort.

  Key-sequences bound to action functions can now start with printable
  characters. Previously only keysequences starting with control or
  meta characters were permitted.

  gl_get_line() is now 8-bit clean. If the calling program has
  correctly called setlocale(LC_CTYPE,""), then the user can select an
  alternate locale by setting the standard LC_CTYPE, LC_ALL, or LANG
  environment variables, and international characters can then be
  entered directly, either by using a non-US keyboard, or by using a
  compose key on a standard US keyboard. Note that in locales in which
  meta characters become printable, meta characters no longer match
  M-c bindings, which then have to be entered using their escape-c
  equivalents.  Fortunately most modern terminal emulators either
  output the escape-c version by default when the meta key is used, or
  can be configured to do so (see the gl_get_line(3) man page), so in
  most cases you can continue to use the meta key.

  Completion callback functions can now tell gl_get_line() to return
  the input line immediately after a successful tab completion, simply
  by setting the last character of the optional continuation suffix to
  a newline character (ie. in the call to cpl_add_completion()).

  It is now safe to create and use multiple GetLine objects, albeit
  still only from a single thread. In conjunction with the new
  gl_configure_getline() function, this optionally allows multiple
  GetLine objects with different bindings to be used to implement
  different input modes.

  The edit-mode configuration command now accepts the argument,
  none. This tells gl_get_line() to revert to using just the native
  line editing facilities provided by the terminal driver. This could
  be used if the termcap or terminfo entry of the host terminal were
  badly corrupted.

  Application callback functions invoked by gl_get_line() can now
  change the displayed prompt using the gl_replace_prompt() function.

  Their is now an optional program distributed with the library. This
  is a beta release of a program which adds tecla command-line editing
  to virtually any third party application without the application
  needing to be linked to the library. See the enhance(3) man page for
  further details. Although built and installed by default, the
  INSTALL document explains how to prevent this.

  The INSTALL document now explains how you can stop the demo programs
  from being built and installed.

  NetBSD/termcap fixes. Mike MacFaden reported two problems that he
  saw when compiling libtecla under NetBSD. Both cases were related to
  the use of termcap.  Most systems use terminfo, so this problem has
  gone unnoticed until now, and won't have affected the grand majority
  of users.  The configure script had a bug which prevented the check
  for CPP working properly, and getline.c wouldn't compile due to an
  undeclared variable when USE_TERMCAP was defined. Both problems have
  now been fixed. Note that if you successfully compiled version
  1.3.3, this problem didn't affect you.

  An unfortunate and undocumented binding of the key-sequence M-O was
  shadowing the arrow-key bindings on systems that use ^[OA etc. I
  have removed this binding (the documented lower case M-o binding
  remains bound). Under the KDE konsole terminal this was causing the
  arrow keys to do something other than expected.

  There was a bug in the history list code which could result in
  strange entries appearing at the start of the history list once
  enough history lines had been added to the list to cause the
  circular history buffer to wrap. This is now fixed.
 
Version 1.3.3:

  Signal handling has been re-written, and documentation of its
  behaviour has been added to the gl_get_line(3) man page. In addition
  to eliminating race conditions, and appropriately setting errno for
  those signals that abort gl_get_line(), many more signals are now
  intercepted, making it less likely that the terminal will be left in
  raw mode by a signal that isn't trapped by gl_get_line().

  A bug was also fixed that was leaving the terminal in raw mode if
  the editing mode was changed interactively between vi and emacs.
  This was only noticeable when running programs from old shells that
  don't reset terminal modes.

Version 1.3.2:

  Tim Eliseo contributed a number of improvements to vi mode,
  including a fuller set of vi key-bindings, implementation of the vi
  constraint that the cursor can't backup past the point at which
  input mode was entered, and restoration of overwritten characters
  when backspacing in overwrite mode. There are also now new bindings
  to allow users to toggle between vi and emacs modes interactively.
  The terminal bell is now used in some circumstances, such as when an
  unrecognized key sequence is entered. This can be turned off by the
  new nobeep option in the tecla configuration file.

  Unrelated to the above, a problem under Linux which prevented ^Q
  from being used to resume terminal output after the user had pressed
  ^S, has been fixed.

Version 1.3.1:

  In vi mode a bug was preventing the history-search-backward and
  history-search-forward actions from doing anything when invoked on
  empty lines. On empty lines they now act like up-history and
  down-history respectively, as in emacs mode.

  When creating shared libraries under Linux, the -soname directive
  was being used incorrectly. The result is that Linux binaries linked
  with the 1.2.3, 1.2.4 and 1.3.0 versions of the tecla shared
  libraries, will refuse to see other versions of the shared library
  until relinked with version 1.3.1 or higher.

  The configure script can now handle the fact that under Solaris-2.6
  and earlier, the only curses library is a static one that hides in
  /usr/ccs/lib. Under Linux it now also caters for old versions of GNU
  ld which don't accept version scripts.

  The demos are now linked against the shared version of the library
  if possible. Previously they were always linked with the static
  version.

Version 1.3.0:

  The major change in this release is the addition of an optional vi
  command-line editing mode in gl_get_line(), along with lots of new
  action functions to support its bindings. To enable this, first
  create a ~/.teclarc file if you don't already have one, then add the
  following line to it.

   edit-mode vi

  The default vi bindings, which are designed to mimic those of the vi
  editor as closely as possible, are described in the gl_get_line(3)
  man page.

  A new convenience function called ef_list_expansions() has been
  added for listing filename expansions. See the ef_list_expansions(3)
  man page for details. This is used in a new list-glob binding, bound
  to ^Xg in emacs mode, and ^G in vi input mode.

  A bug has been fixed in the key-binding table expansion code. This
  bug would have caused problems to anybody who defined more than
  about 18 personalized key-bindings in their ~/.teclarc file.

Version 1.2.4:

  Buffered I/O is now used for writing to terminals, and where
  supported, cursor motion is done with move-n-positions terminfo
  capabilities instead of doing lots of move-1-position requests. This
  greatly improves how the library feels over slow links.

  You can now optionally compile different architectures in different
  directories, without having to make multiple copies of the
  distribution. This is documented in the INSTALL file.

  The ksh ~+ directive is now supported.

  Thanks to Markus Gyger for the above improvements.

  Documentation has been added to the INSTALL file describing features
  designed to facilitate configuration and installation of the library
  as part of larger packages. These features are intended to remove
  the need to modify the tecla distribution's configuration and build
  procedures when embedding the libtecla distribution in other package
  distributions.

  A previous fix to stop the cursor from warping when the last
  character of the input line was in the last column of the terminal,
  was only being used for the first terminal line of the input line.
  It is now used for all subsequent lines as well, as originally
  intended.
  
Version 1.2.3:

  The installation procedure has been better automated with the
  addition of an autoconf configure script. This means that installers
  can now compile and install the library by typing:

    ./configure
    make
    make install

  On all systems this makes at least the normal static version of the
  tecla library. It also makes the reentrant version if reentrant
  POSIX functions are detected.  Under Solaris, Linux and HP-UX the
  configuration script arranges for shared libraries to be compiled in
  addition to the static libraries.  It is hoped that installers will
  return information about how to compile shared libraries on other
  systems, for inclusion in future releases, and to this end, a new
  PORTING guide has been provided.

  The versioning number scheme has been changed. This release would
  have been 1.2c, but instead will be refered to as 1.2.3. The
  versioning scheme, based on conventions used by Sun Microsystems, is
  described in configure.in.

  The library was also tested under HP-UX, and this revealed two
  serious bugs, both of which have now been fixed.
  
  The first bug prevented the library from writing control codes to
  terminals on big-endian machines, with the exception of those
  running under Solaris. This was due to an int variable being used
  where a char was needed.

  The second bug had the symptom that on systems that don't use the
  newline character as the control code for moving the cursor down a
  line, a newline wasn't started when the user hit enter.

Version 1.2b:

  Two more minor bug fixes:

  Many terminals don't wrap the cursor to the next line when a
  character is written to the rightmost terminal column. Instead, they
  delay starting a new line until one more character is written, at
  which point they move the cursor two positions.  gl_get_line()
  wasn't aware of this, so cursor repositionings just after writing
  the last character of a column, caused it to erroneously go up a
  line. This has now been remedied, using a method that should work
  regardless of whether a terminal exhibits this behavior or not.

  Some systems dynamically record the current terminal dimensions in
  environment variables called LINES and COLUMNS. On such systems,
  during the initial terminal setup, these values should override the
  static values read from the terminal information databases, and now
  do.  Previously they were only used if the dimensions returned by
  terminfo/termcap looked bogus.

Version 1.2a:

  This minor release fixes the following two bugs:

  The initial terminal size and subsequent changes thereto, weren't
  being noticed by gl_get_line(). This was because the test for the
  existence of TIOCWINSZ was erroneously placed before the inclusion
  of termios.h. One of the results was that on input lines that
  spanned more than one terminal line, the cursor occasionally jumped
  unexpectedly to the previous terminal line.

  On entering a line that wrapped over multiple terminal lines,
  gl_get_line() simply output a carriage-return line-feed at the point
  at which the user pressed return. Thus if one typed in such a line,
  then moved back onto one of the earlier terminal lines before
  hitting return, the cursor was left on a line containing part of the
  line that had just been entered. This didn't do any harm, but it
  looked a mess.

Version 1.2:

  A new facility for looking up and completing filenames in UNIX-style
  paths has now been added (eg. you can search for, or complete
  commands using the UNIX PATH environment variable). See the
  pca_lookup_file(3) man page.

  The already existing filename completion callback can now be made
  selective in what types of files it lists. See the
  cpl_complete_word(3) man page.

  Due to its potential to break applications when changed, the use of
  the publically defined CplFileArgs structure to configure the
  cpl_file_completions() callback is now deprecated.  The definition
  of this structure has been frozen, and its documentation has been
  removed from the man pages.  It will remain supported, but if you
  have used it, you are recommended to switch to the new method, which
  involves a new opaque configuration object, allocated via a provided
  constructor function, configured via accessor functions, and
  eventually deleted with a provided destructor function. The
  cpl_file_completions() callback distinguishes which structure type
  it has been sent by virtue of a code placed at the start of the new
  structure by the constructor.  It is assumed that no existing
  applications set the boolean 'escaped' member of the CplFileArgs
  structure to 4568.  The new method is documented in the
  cpl_complete_word(3) man page.

Version 1.1j

  This was the initial public release on freshmeat.org.
genometools-1.5.1/src/external/libtecla-1.6.1/chrqueue.c000066400000000000000000000332711211610345200226700ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */
#include 
#include 
#include 
#include 

#include "ioutil.h"
#include "chrqueue.h"
#include "freelist.h"
#include "errmsg.h"

/*
 * Set the number of bytes allocated to each node of the list of
 * character buffers. This facility is designed principally as
 * an expandible I/O output buffer, so use the stdio buffer size
 * where available.
 */
#ifdef BUFSIZ
#define GL_CQ_SIZE BUFSIZ
#else
#define GL_CQ_SIZE 512
#endif

/*
 * The queue is contained in a list of fixed sized buffers. New nodes
 * are appended to this list as needed to accomodate newly added bytes.
 * Old nodes at the head of the list are removed as they are emptied.
 */
typedef struct CqCharBuff CqCharBuff;
struct CqCharBuff {
  CqCharBuff *next;          /* The next node in the list of buffers */
  char bytes[GL_CQ_SIZE];    /* The fixed size buffer of this node */
};

/*
 * Define the structure that is used to contain a list of character
 * buffers.
 */
struct GlCharQueue {
  ErrMsg *err;          /* A buffer in which to record error messages */
  FreeList *bufmem;     /* A free-list of CqCharBuff structures */
  struct {
    CqCharBuff *head;   /* The head of the list of output buffers */
    CqCharBuff *tail;   /* The tail of the list of output buffers */
  } buffers;
  int nflush;           /* The total number of characters that have been */
                        /*  flushed from the start of the queue since */
                        /*  _glq_empty_queue() was last called. */
  int ntotal;           /* The total number of characters that have been */
                        /*  appended to the queue since _glq_empty_queue() */
                        /*  was last called. */
};

/*.......................................................................
 * Create a new GlCharQueue object.
 *
 * Output:
 *  return  GlCharQueue *  The new object, or NULL on error.
 */
GlCharQueue *_new_GlCharQueue(void)
{
  GlCharQueue *cq;  /* The object to be returned */
/*
 * Allocate the container.
 */
  cq = malloc(sizeof(GlCharQueue));
  if(!cq) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_GlCharQueue().
 */
  cq->err = NULL;
  cq->bufmem = NULL;
  cq->buffers.head = NULL;
  cq->buffers.tail = NULL;
  cq->nflush = cq->ntotal = 0;
/*
 * Allocate a place to record error messages.
 */
  cq->err = _new_ErrMsg();
  if(!cq->err)
    return _del_GlCharQueue(cq);
/*
 * Allocate the freelist of CqCharBuff structures.
 */
  cq->bufmem = _new_FreeList(sizeof(CqCharBuff), 1);
  if(!cq->bufmem)
    return _del_GlCharQueue(cq);
  return cq;
}

/*.......................................................................
 * Delete a GlCharQueue object.
 *
 * Input:
 *  cq     GlCharQueue *  The object to be deleted.
 * Output:
 *  return GlCharQueue *  The deleted object (always NULL).
 */
GlCharQueue *_del_GlCharQueue(GlCharQueue *cq)
{
  if(cq) {
    cq->err = _del_ErrMsg(cq->err);
    cq->bufmem = _del_FreeList(cq->bufmem, 1);
    free(cq);
  };
  return NULL;
}

/*.......................................................................
 * Append an array of n characters to a character queue.
 *
 * Input:
 *  cq        GlCharQueue *  The queue to append to.
 *  chars      const char *  The array of n characters to be appended.
 *  n                 int    The number of characters in chars[].
 *  write_fn  GL_WRITE_FN *  The function to call to output characters,
 *                           or 0 to simply discard the contents of the
 *                           queue. This will be called whenever the
 *                           buffer becomes full. If it fails to release
 *                           any space, the buffer will be extended.
 *  data             void *  Anonymous data to pass to write_fn().
 * Output:
 *  return        int    The number of characters successfully
 *                       appended. This will only be < n on error.
 */
int _glq_append_chars(GlCharQueue *cq, const char *chars, int n,
		      GlWriteFn *write_fn, void *data)
{
  int ndone = 0;  /* The number of characters appended so far */
/*
 * Check the arguments.
 */
  if(!cq || !chars) {
    errno = EINVAL;
    return 0;
  };
/*
 * The appended characters may have to be split between multiple
 * buffers, so loop for each buffer.
 */
  while(ndone < n) {
    int ntodo;     /* The number of characters remaining to be appended */
    int nleft;     /* The amount of space remaining in cq->buffers.tail */
    int nnew;      /* The number of characters to append to cq->buffers.tail */
/*
 * Compute the offset at which the next character should be written
 * into the tail buffer segment.
 */
    int boff = cq->ntotal % GL_CQ_SIZE;
/*
 * Since we don't allocate a new buffer until we have at least one
 * character to write into it, if boff is 0 at this point, it means
 * that we hit the end of the tail buffer segment on the last append,
 * so we need to allocate a new one.
 *
 * If allocating this new node will require a call to malloc(), as
 * opposed to using a currently unused node in the freelist, first try
 * flushing the current contents of the buffer to the terminal. When
 * write_fn() uses blocking I/O, this stops the buffer size ever getting
 * bigger than a single buffer node. When it is non-blocking, it helps
 * to keep the amount of memory, but it isn't gauranteed to do so.
 */
    if(boff == 0 && _idle_FreeListNodes(cq->bufmem) == 0) {
      switch(_glq_flush_queue(cq, write_fn, data)) {
      case GLQ_FLUSH_DONE:
	break;
      case GLQ_FLUSH_AGAIN:
	errno = 0;          /* Don't confuse the caller */
	break;
      default:
	return ndone;       /* Error */
      };
      boff = cq->ntotal % GL_CQ_SIZE;
    };
/*
 * Since we don't allocate a new buffer until we have at least one
 * character to write into it, if boff is 0 at this point, it means
 * that we hit the end of the tail buffer segment on the last append,
 * so we need to allocate a new one.
 */
    if(boff == 0) {
/*
 * Allocate the new node.
 */
      CqCharBuff *node = (CqCharBuff *) _new_FreeListNode(cq->bufmem);
      if(!node) {
	_err_record_msg(cq->err, "Insufficient memory to buffer output.",
			END_ERR_MSG);
	return ndone;
      };
/*
 * Initialize the node.
 */
      node->next = NULL;
/*
 * Append the new node to the tail of the list.
 */
      if(cq->buffers.tail)
	cq->buffers.tail->next = node;
      else
	cq->buffers.head = node;
      cq->buffers.tail = node;
    };
/*
 * How much room is there for new characters in the current tail node?
 */
    nleft = GL_CQ_SIZE - boff;
/*
 * How many characters remain to be appended?
 */
    ntodo = n - ndone;
/*
 * How many characters should we append to the current tail node?
 */
    nnew = nleft < ntodo ? nleft : ntodo;
/*
 * Append the latest prefix of nnew characters.
 */
    memcpy(cq->buffers.tail->bytes + boff, chars + ndone, nnew);
    cq->ntotal += nnew;
    ndone += nnew;
  };
/*
 * Return the count of the number of characters successfully appended.
 */
  return ndone;
}

/*.......................................................................
 * Discard the contents of a queue of characters.
 *
 * Input:
 *  cq    GlCharQueue *  The queue to clear.
 */
void _glq_empty_queue(GlCharQueue *cq)
{
  if(cq) {
/*
 * Return all list nodes to their respective free-lists.
 */
    _rst_FreeList(cq->bufmem);
/*
 * Mark the lists as empty.
 */
    cq->buffers.head = cq->buffers.tail = NULL;
    cq->nflush = cq->ntotal = 0;
  };
}

/*.......................................................................
 * Return a count of the number of characters currently in the queue.
 *
 * Input:
 *  cq    GlCharQueue *  The queue of interest.
 * Output:
 *  return        int    The number of characters in the queue.
 */
int _glq_char_count(GlCharQueue *cq)
{
  return (cq && cq->buffers.head) ? (cq->ntotal - cq->nflush) : 0;
}

/*.......................................................................
 * Write as many characters as possible from the start of a character
 * queue via a given output callback function, removing those written
 * from the queue.
 *
 * Input:
 *  cq        GlCharQueue *  The queue to write characters from.
 *  write_fn  GL_WRITE_FN *  The function to call to output characters,
 *                           or 0 to simply discard the contents of the
 *                           queue.
 *  data             void *  Anonymous data to pass to write_fn().
 * Output:
 *  return   GlFlushState    The status of the flush operation:
 *                             GLQ_FLUSH_DONE  -  The flush operation
 *                                                completed successfully.
 *                             GLQ_FLUSH_AGAIN -  The flush operation
 *                                                couldn't be completed
 *                                                on this call. Call this
 *                                                function again when the
 *                                                output channel can accept
 *                                                further output.
 *                             GLQ_FLUSH_ERROR    Unrecoverable error.
 */
GlqFlushState _glq_flush_queue(GlCharQueue *cq, GlWriteFn *write_fn,
			       void *data)
{
/*
 * Check the arguments.
 */
  if(!cq) {
    errno = EINVAL;
    return GLQ_FLUSH_ERROR;
  };
/*
 * If possible keep writing until all of the chained buffers have been
 * emptied and removed from the list.
 */
  while(cq->buffers.head) {
/*
 * Are we looking at the only node in the list?
 */
    int is_tail = cq->buffers.head == cq->buffers.tail;
/*
 * How many characters more than an exact multiple of the buffer-segment
 * size have been added to the buffer so far?
 */
    int nmodulo = cq->ntotal % GL_CQ_SIZE;
/*
 * How many characters of the buffer segment at the head of the list
 * have been used? Note that this includes any characters that have
 * already been flushed. Also note that if nmodulo==0, this means that
 * the tail buffer segment is full. The reason for this is that we
 * don't allocate new tail buffer segments until there is at least one
 * character to be added to them.
 */
    int nhead = (!is_tail || nmodulo == 0) ? GL_CQ_SIZE : nmodulo;
/*
 * How many characters remain to be flushed from the buffer
 * at the head of the list?
 */
    int nbuff = nhead - (cq->nflush % GL_CQ_SIZE);
/*
 * Attempt to write this number.
 */
    int nnew = write_fn(data, cq->buffers.head->bytes +
			cq->nflush % GL_CQ_SIZE, nbuff);
/*
 * Was anything written?
 */
    if(nnew > 0) {
/*
 * Increment the count of the number of characters that have
 * been flushed from the head of the queue.
 */
      cq->nflush += nnew;
/*
 * If we succeded in writing all of the contents of the current
 * buffer segment, remove it from the queue.
 */
      if(nnew == nbuff) {
/*
 * If we just emptied the last node left in the list, then the queue is
 * now empty and should be reset.
 */
	if(is_tail) {
	  _glq_empty_queue(cq);
	} else {
/*
 * Get the node to be removed from the head of the list.
 */
	  CqCharBuff *node = cq->buffers.head;
/*
 * Make the node that follows it the new head of the queue.
 */
	  cq->buffers.head = node->next;
/*
 * Return it to the freelist.
 */
	  node = (CqCharBuff *) _del_FreeListNode(cq->bufmem, node);
	};
      };
/*
 * If the write blocked, request that this function be called again
 * when space to write next becomes available.
 */
    } else if(nnew==0) {
      return GLQ_FLUSH_AGAIN;
/*
 * I/O error.
 */
    } else {
      _err_record_msg(cq->err, "Error writing to terminal", END_ERR_MSG);
      return GLQ_FLUSH_ERROR;
    };
  };
/*
 * To get here the queue must now be empty.
 */
  return GLQ_FLUSH_DONE;
}

/*.......................................................................
 * Return extra information (ie. in addition to that provided by errno)
 * about the last error to occur in any of the public functions of this
 * module.
 *
 * Input:
 *  cq     GlCharQueue *  The container of the history list.
 * Output:
 *  return  const char *  A pointer to the internal buffer in which
 *                        the error message is temporarily stored.
 */
const char *_glq_last_error(GlCharQueue *cq)
{
  return cq ? _err_get_msg(cq->err) : "NULL GlCharQueue argument";
}
genometools-1.5.1/src/external/libtecla-1.6.1/chrqueue.h000066400000000000000000000074371211610345200227020ustar00rootroot00000000000000#ifndef chrqueue_h
#define chrqueue_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*-----------------------------------------------------------------------
 * This module implements a queue of characters to be processed in some
 * way. It is used by gl_get_line() to maintain a queue of characters
 * to be sent to a remote terminal. Characters are recorded in a
 * dynamically extensible list of fixed sized buffers.
 */

typedef struct GlCharQueue GlCharQueue;

/*
 * Create a new character queue.
 */
GlCharQueue *_new_GlCharQueue(void);

/*
 * Delete a redundant character queue.
 */
GlCharQueue *_del_GlCharQueue(GlCharQueue *cq);

/*
 * Append an array of n characters to a character queue.
 */
int _glq_append_chars(GlCharQueue *cq, const char *chars, int n,
		      GlWriteFn *write_fn, void *data);

/*
 * Clear a character queue.
 */
void _glq_empty_queue(GlCharQueue *cq);

/*
 * Return a count of the number of characters in the queue.
 */
int _glq_char_count(GlCharQueue *cq);

/*
 * A structure of the following type is used by _glq_peek_chars() to
 * return characters at the start of the queue.
 */
typedef struct {
  const char *buff;  /* A pointer to the first undeleted byte in the */
                     /*  first buffer of the queue. */
  int nbuff;         /* The number of characters in buff[] */
} GlCharQueueBuff;

/*
 * Enumerator values of the following type are returned by
 * _glq_flush_queue() to indicate the status of the flush operation.
 */
typedef enum {
  GLQ_FLUSH_DONE,   /* The flush operation completed successfully */
  GLQ_FLUSH_AGAIN,  /* The flush operation couldn't be completed on this */
                    /*  call. Call this function again when the output */
                    /*  channel can accept further output. */
  GLQ_FLUSH_ERROR   /* Unrecoverable error. */
} GlqFlushState;

/*
 * Transfer as much of the contents of a character queue to an output
 * channel as possible, returning before the queue is empty if the
 * write_fn() callback says that it can't currently write anymore.
 */
GlqFlushState _glq_flush_queue(GlCharQueue *cq, GlWriteFn *write_fn,
			       void *data);

/*
 * Provide information about the last error that occurred while calling
 * any of the above functions.
 */
const char *_glq_last_error(GlCharQueue *cq);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/cplfile.c000066400000000000000000000702671211610345200224730ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * If file-system access is to be excluded, this module has no function,
 * so all of its code should be excluded.
 */
#ifndef WITHOUT_FILE_SYSTEM

/*
 * Standard includes.
 */
#include 
#include 
#include 
#include 
#include 
#include 

/*
 * Local includes.
 */
#include "libtecla.h"
#include "direader.h"
#include "homedir.h"
#include "pathutil.h"
#include "cplfile.h"
#include "errmsg.h"

/*
 * Set the maximum length allowed for usernames.
 * names.
 */
#define USR_LEN 100

/*
 * Set the maximum length allowed for environment variable names.
 */
#define ENV_LEN 100

/*
 * The resources needed to complete a filename are maintained in objects
 * of the following type.
 */
struct CompleteFile {
  ErrMsg *err;                 /* The error reporting buffer */
  DirReader *dr;               /* A directory reader */
  HomeDir *home;               /* A home directory expander */
  PathName *path;              /* The buffer in which to accumulate the path */
  PathName *buff;              /* A pathname work buffer */
  char usrnam[USR_LEN+1];      /* The buffer used when reading the names of */
                               /*  users. */
  char envnam[ENV_LEN+1];      /* The buffer used when reading the names of */
                               /*  environment variables. */
};

static int cf_expand_home_dir(CompleteFile *cf, const char *user);
static int cf_complete_username(CompleteFile *cf, WordCompletion *cpl,
				const char *prefix, const char *line,
				int word_start, int word_end, int escaped);
static HOME_DIR_FN(cf_homedir_callback);
static int cf_complete_entry(CompleteFile *cf, WordCompletion *cpl,
			     const char *line, int word_start, int word_end,
			     int escaped, CplCheckFn *check_fn,
			     void *check_data);
static char *cf_read_name(CompleteFile *cf, const char *type,
			  const char *string, int slen,
			  char *nambuf, int nammax);
static int cf_prepare_suffix(CompleteFile *cf, const char *suffix,
			     int add_escapes);

/*
 * A stack based object of the following type is used to pass data to the
 * cf_homedir_callback() function.
 */
typedef struct {
  CompleteFile *cf;    /* The file-completion resource object */
  WordCompletion *cpl; /* The string-completion rsource object */
  size_t prefix_len;   /* The length of the prefix being completed */
  const char *line;    /* The line from which the prefix was extracted */
  int word_start;      /* The index in line[] of the start of the username */
  int word_end;        /* The index in line[] following the end of the prefix */
  int escaped;         /* If true, add escapes to the completion suffixes */
} CfHomeArgs;

/*.......................................................................
 * Create a new file-completion object.
 *
 * Output:
 *  return  CompleteFile *  The new object, or NULL on error.
 */
CompleteFile *_new_CompleteFile(void)
{
  CompleteFile *cf;  /* The object to be returned */
/*
 * Allocate the container.
 */
  cf = (CompleteFile *) malloc(sizeof(CompleteFile));
  if(!cf) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to _del_CompleteFile().
 */
  cf->err = NULL;
  cf->dr = NULL;
  cf->home = NULL;
  cf->path = NULL;
  cf->buff = NULL;
  cf->usrnam[0] = '\0';
  cf->envnam[0] = '\0';
/*
 * Allocate a place to record error messages.
 */
  cf->err = _new_ErrMsg();
  if(!cf->err)
    return _del_CompleteFile(cf);
/*
 * Create the object that is used for reading directories.
 */
  cf->dr = _new_DirReader();
  if(!cf->dr)
    return _del_CompleteFile(cf);
/*
 * Create the object that is used to lookup home directories.
 */
  cf->home = _new_HomeDir();
  if(!cf->home)
    return _del_CompleteFile(cf);
/*
 * Create the buffer in which the completed pathname is accumulated.
 */
  cf->path = _new_PathName();
  if(!cf->path)
    return _del_CompleteFile(cf);
/*
 * Create a pathname work buffer.
 */
  cf->buff = _new_PathName();
  if(!cf->buff)
    return _del_CompleteFile(cf);
  return cf;
}

/*.......................................................................
 * Delete a file-completion object.
 *
 * Input:
 *  cf     CompleteFile *  The object to be deleted.
 * Output:
 *  return CompleteFile *  The deleted object (always NULL).
 */
CompleteFile *_del_CompleteFile(CompleteFile *cf)
{
  if(cf) {
    cf->err = _del_ErrMsg(cf->err);
    cf->dr = _del_DirReader(cf->dr);
    cf->home = _del_HomeDir(cf->home);
    cf->path = _del_PathName(cf->path);
    cf->buff = _del_PathName(cf->buff);
    free(cf);
  };
  return NULL;
}

/*.......................................................................
 * Look up the possible completions of the incomplete filename that
 * lies between specified indexes of a given command-line string.
 *
 * Input:
 *  cpl   WordCompletion *  The object in which to record the completions.
 *  cf      CompleteFile *  The filename-completion resource object.
 *  line      const char *  The string containing the incomplete filename.
 *  word_start       int    The index of the first character in line[]
 *                          of the incomplete filename.
 *  word_end         int    The index of the character in line[] that
 *                          follows the last character of the incomplete
 *                          filename.
 *  escaped          int    If true, backslashes in line[] are
 *                          interpreted as escaping the characters
 *                          that follow them, and any spaces, tabs,
 *                          backslashes, or wildcard characters in the
 *                          returned suffixes will be similarly escaped.
 *                          If false, backslashes will be interpreted as
 *                          literal parts of the file name, and no
 *                          backslashes will be added to the returned
 *                          suffixes.
 *  check_fn  CplCheckFn *  If not zero, this argument specifies a
 *                          function to call to ask whether a given
 *                          file should be included in the list
 *                          of completions.
 *  check_data      void *  Anonymous data to be passed to check_fn().
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error. A description of the error can be
 *                                     acquired by calling _cf_last_error(cf).
 */
int _cf_complete_file(WordCompletion *cpl, CompleteFile *cf,
		     const char *line, int word_start, int word_end,
		     int escaped, CplCheckFn *check_fn, void *check_data)
{
  const char *lptr; /* A pointer into line[] */
  int nleft;        /* The number of characters still to be processed */
                    /*  in line[]. */
/*
 * Check the arguments.
 */
  if(!cpl || !cf || !line || word_end < word_start) {
    if(cf) {
      _err_record_msg(cf->err, "_cf_complete_file: Invalid arguments",
		      END_ERR_MSG);
    };
    return 1;
  };
/*
 * Clear the buffer in which the filename will be constructed.
 */
  _pn_clear_path(cf->path);
/*
 * How many characters are to be processed?
 */
  nleft = word_end - word_start;
/*
 * Get a pointer to the start of the incomplete filename.
 */
  lptr = line + word_start;
/*
 * If the first character is a tilde, then perform home-directory
 * interpolation.
 */
  if(nleft > 0 && *lptr == '~') {
    int slen;
    if(!cf_read_name(cf, "User", ++lptr, --nleft, cf->usrnam, USR_LEN))
      return 1;
/*
 * Advance over the username in the input line.
 */
    slen = strlen(cf->usrnam);
    lptr += slen;
    nleft -= slen;
/*
 * If we haven't hit the end of the input string then we have a complete
 * username to translate to the corresponding home directory.
 */
    if(nleft > 0) {
      if(cf_expand_home_dir(cf, cf->usrnam))
	return 1;
/*
 * ~user and ~ are usually followed by a directory separator to
 * separate them from the file contained in the home directory.
 * If the home directory is the root directory, then we don't want
 * to follow the home directory by a directory separator, so we should
 * skip over it so that it doesn't get copied into the filename.
 */
      if(strcmp(cf->path->name, FS_ROOT_DIR) == 0 &&
	 strncmp(lptr, FS_DIR_SEP, FS_DIR_SEP_LEN) == 0) {
	lptr += FS_DIR_SEP_LEN;
	nleft -= FS_DIR_SEP_LEN;
      };
/*
 * If we have reached the end of the input string, then the username
 * may be incomplete, and we should attempt to complete it.
 */
    } else {
/*
 * Look up the possible completions of the username.
 */
      return cf_complete_username(cf, cpl, cf->usrnam, line, word_start+1,
				  word_end, escaped);
    };
  };
/*
 * Copy the rest of the path, stopping to expand $envvar expressions
 * where encountered.
 */
  while(nleft > 0) {
    int seglen;   /* The length of the next segment to be copied */
/*
 * Find the length of the next segment to be copied, stopping if an
 * unescaped '$' is seen, or the end of the path is reached.
 */
    for(seglen=0; seglen < nleft; seglen++) {
      int c = lptr[seglen];
      if(escaped && c == '\\')
	seglen++;
      else if(c == '$')
	break;
/*
 * We will be completing the last component of the file name,
 * so whenever a directory separator is seen, assume that it
 * might be the start of the last component, and mark the character
 * that follows it as the start of the name that is to be completed.
 */
      if(nleft >= FS_DIR_SEP_LEN &&
	 strncmp(lptr + seglen, FS_DIR_SEP, FS_DIR_SEP_LEN)==0) {
	word_start = (lptr + seglen) - line + FS_DIR_SEP_LEN;
      };
    };
/*
 * We have reached either the end of the filename or the start of
 * $environment_variable expression. Record the newly checked
 * segment of the filename in the output filename, removing
 * backslash-escapes where needed.
 */
    if(_pn_append_to_path(cf->path, lptr, seglen, escaped) == NULL) {
      _err_record_msg(cf->err, "Insufficient memory to complete filename",
		      END_ERR_MSG);
      return 1;
    };
    lptr += seglen;
    nleft -= seglen;
/*
 * If the above loop finished before we hit the end of the filename,
 * then this was because an unescaped $ was seen. In this case, interpolate
 * the value of the environment variable that follows it into the output
 * filename.
 */
    if(nleft > 0) {
      char *value;    /* The value of the environment variable */
      int vlen;       /* The length of the value string */
      int nlen;       /* The length of the environment variable name */
/*
 * Read the name of the environment variable.
 */
      if(!cf_read_name(cf, "Environment", ++lptr, --nleft, cf->envnam, ENV_LEN))
	return 1;
/*
 * Advance over the environment variable name in the input line.
 */
      nlen = strlen(cf->envnam);
      lptr += nlen;
      nleft -= nlen;
/*
 * Get the value of the environment variable.
 */
      value = getenv(cf->envnam);
      if(!value) {
	_err_record_msg(cf->err, "Unknown environment variable: ", cf->envnam,
			END_ERR_MSG);
	return 1;
      };
      vlen = strlen(value);
/*
 * If we are at the start of the filename and the first character of the
 * environment variable value is a '~', attempt home-directory
 * interpolation.
 */
      if(cf->path->name[0] == '\0' && value[0] == '~') {
	if(!cf_read_name(cf, "User", value+1, vlen-1, cf->usrnam, USR_LEN) ||
	   cf_expand_home_dir(cf, cf->usrnam))
	  return 1;
/*
 * If the home directory is the root directory, and the ~usrname expression
 * was followed by a directory separator, prevent the directory separator
 * from being appended to the root directory by skipping it in the
 * input line.
 */
	if(strcmp(cf->path->name, FS_ROOT_DIR) == 0 &&
	   strncmp(lptr, FS_DIR_SEP, FS_DIR_SEP_LEN) == 0) {
	  lptr += FS_DIR_SEP_LEN;
	  nleft -= FS_DIR_SEP_LEN;
	};
      } else {
/*
 * Append the value of the environment variable to the output path.
 */
	if(_pn_append_to_path(cf->path, value, strlen(value), escaped)==NULL) {
	  _err_record_msg(cf->err, "Insufficient memory to complete filename",
			  END_ERR_MSG);
	  return 1;
	};
/*
 * Prevent extra directory separators from being added.
 */
	if(nleft >= FS_DIR_SEP_LEN &&
	   strcmp(cf->path->name, FS_ROOT_DIR) == 0 &&
	   strncmp(lptr, FS_DIR_SEP, FS_DIR_SEP_LEN) == 0) {
	  lptr += FS_DIR_SEP_LEN;
	  nleft -= FS_DIR_SEP_LEN;
	} else if(vlen > FS_DIR_SEP_LEN &&
		  strcmp(value + vlen - FS_DIR_SEP_LEN, FS_DIR_SEP)==0) {
	  cf->path->name[vlen-FS_DIR_SEP_LEN] = '\0';
	};
      };
/*
 * If adding the environment variable didn't form a valid directory,
 * we can't complete the line, since there is no way to separate append
 * a partial filename to an environment variable reference without
 * that appended part of the name being seen later as part of the
 * environment variable name. Thus if the currently constructed path
 * isn't a directory, quite now with no completions having been
 * registered.
 */
      if(!_pu_path_is_dir(cf->path->name))
	return 0;
/*
 * For the reasons given above, if we have reached the end of the filename
 * with the expansion of an environment variable, the only allowed
 * completion involves the addition of a directory separator.
 */
      if(nleft == 0) {
	if(cpl_add_completion(cpl, line, lptr-line, word_end, FS_DIR_SEP,
			      "", "")) {
	  _err_record_msg(cf->err, cpl_last_error(cpl), END_ERR_MSG);
	  return 1;
	};
	return 0;
      };
    };
  };
/*
 * Complete the filename if possible.
 */
  return cf_complete_entry(cf, cpl, line, word_start, word_end, escaped,
			   check_fn, check_data);
}

/*.......................................................................
 * Return a description of the last path-completion error that occurred.
 *
 * Input:
 *  cf    CompleteFile *  The path-completion resource object.
 * Output:
 *  return  const char *  The description of the last error.
 */
const char *_cf_last_error(CompleteFile *cf)
{
  return cf ? _err_get_msg(cf->err) : "NULL CompleteFile argument";
}

/*.......................................................................
 * Lookup the home directory of the specified user, or the current user
 * if no name is specified, appending it to output pathname.
 *
 * Input:
 *  cf  CompleteFile *  The pathname completion resource object.
 *  user  const char *  The username to lookup, or "" to lookup the
 *                      current user.
 * Output:
 *  return        int    0 - OK.
 *                       1 - Error.
 */
static int cf_expand_home_dir(CompleteFile *cf, const char *user)
{
/*
 * Attempt to lookup the home directory.
 */
  const char *home_dir = _hd_lookup_home_dir(cf->home, user);
/*
 * Failed?
 */
  if(!home_dir) {
    _err_record_msg(cf->err, _hd_last_home_dir_error(cf->home), END_ERR_MSG);
    return 1;
  };
/*
 * Append the home directory to the pathname string.
 */
  if(_pn_append_to_path(cf->path, home_dir, -1, 0) == NULL) {
    _err_record_msg(cf->err, "Insufficient memory for home directory expansion",
		    END_ERR_MSG);
    return 1;
  };
  return 0;
}

/*.......................................................................
 * Lookup and report all completions of a given username prefix.
 *
 * Input:
 *  cf     CompleteFile *  The filename-completion resource object.
 *  cpl  WordCompletion *  The object in which to record the completions.
 *  prefix   const char *  The prefix of the usernames to lookup.
 *  line     const char *  The command-line in which the username appears.
 *  word_start      int    The index within line[] of the start of the
 *                         username that is being completed.
 *  word_end        int    The index within line[] of the character which
 *                         follows the incomplete username.
 *  escaped         int    True if the completions need to have special
 *                         characters escaped.
 * Output:
 *  return          int    0 - OK.
 *                         1 - Error.
 */
static int cf_complete_username(CompleteFile *cf, WordCompletion *cpl,
				const char *prefix, const char *line,
				int word_start, int word_end, int escaped)
{
/*
 * Set up a container of anonymous arguments to be sent to the
 * username-lookup iterator.
 */
  CfHomeArgs args;
  args.cf = cf;
  args.cpl = cpl;
  args.prefix_len = strlen(prefix);
  args.line = line;
  args.word_start = word_start;
  args.word_end = word_end;
  args.escaped = escaped;
/*
 * Iterate through the list of users, recording those which start
 * with the specified prefix.
 */
  if(_hd_scan_user_home_dirs(cf->home, prefix, &args, cf_homedir_callback)) {
    _err_record_msg(cf->err, _hd_last_home_dir_error(cf->home), END_ERR_MSG);
    return 1;
  };
  return 0;
}

/*.......................................................................
 * The user/home-directory scanner callback function (see homedir.h)
 * used by cf_complete_username().
 */
static HOME_DIR_FN(cf_homedir_callback)
{
/*
 * Get the file-completion resources from the anonymous data argument.
 */
  CfHomeArgs *args = (CfHomeArgs *) data;
  WordCompletion *cpl = args->cpl;
  CompleteFile *cf = args->cf;
/*
 * Copy the username into the pathname work buffer, adding backslash
 * escapes where needed.
 */
  if(cf_prepare_suffix(cf, usrnam+args->prefix_len, args->escaped)) {
    strncpy(errmsg, _err_get_msg(cf->err), maxerr);
    errmsg[maxerr] = '\0';
    return 1;
  };
/*
 * Report the completion suffix that was copied above.
 */
  if(cpl_add_completion(cpl, args->line, args->word_start, args->word_end,
			cf->buff->name, FS_DIR_SEP, FS_DIR_SEP)) {
    strncpy(errmsg, cpl_last_error(cpl), maxerr);
    errmsg[maxerr] = '\0';
    return 1;
  };
  return 0;
}

/*.......................................................................
 * Report possible completions of the filename in cf->path->name[].
 *
 * Input:
 *  cf      CompleteFile *  The file-completion resource object.
 *  cpl   WordCompletion *  The object in which to record the completions.
 *  line      const char *  The input line, as received by the callback
 *                          function.
 *  word_start       int    The index within line[] of the start of the
 *                          last component of the filename that is being
 *                          completed.
 *  word_end         int    The index within line[] of the character which
 *                          follows the incomplete filename.
 *  escaped          int    If true, escape special characters in the
 *                          completion suffixes.
 *  check_fn  CplCheckFn *  If not zero, this argument specifies a
 *                          function to call to ask whether a given
 *                          file should be included in the list
 *                          of completions.
 *  check_data      void *  Anonymous data to be passed to check_fn().
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error.
 */
static int cf_complete_entry(CompleteFile *cf, WordCompletion *cpl,
			     const char *line, int word_start, int word_end,
			     int escaped, CplCheckFn *check_fn,
			     void *check_data)
{
  const char *dirpath;   /* The name of the parent directory */
  int start;             /* The index of the start of the last filename */
                         /*  component in the transcribed filename. */
  const char *prefix;    /* The filename prefix to be completed */
  int prefix_len;        /* The length of the filename prefix */
  const char *file_name; /* The lastest filename being compared */
  int waserr = 0;        /* True after errors */
  int terminated=0;      /* True if the directory part had to be terminated */
/*
 * Get the pathname string and its current length.
 */
  char *pathname = cf->path->name;
  int pathlen = strlen(pathname);
/*
 * Locate the start of the final component of the pathname.
 */
  for(start=pathlen - 1; start >= 0 &&
      strncmp(pathname + start, FS_DIR_SEP, FS_DIR_SEP_LEN) != 0; start--)
    ;
/*
 * Is the parent directory the root directory?
 */
  if(start==0 ||
     (start < 0 && strncmp(pathname, FS_ROOT_DIR, FS_ROOT_DIR_LEN) == 0)) {
    dirpath = FS_ROOT_DIR;
    start += FS_ROOT_DIR_LEN;
/*
 * If we found a directory separator then the part which precedes the
 * last component is the name of the directory to be opened.
 */
  } else if(start > 0) {
/*
 * The _dr_open_dir() function requires the directory name to be '\0'
 * terminated, so temporarily do this by overwriting the first character
 * of the directory separator.
 */
    pathname[start] = '\0';
    dirpath = pathname;
    terminated = 1;
/*
 * We reached the start of the pathname before finding a directory
 * separator, so arrange to open the current working directory.
 */
  } else {
    start = 0;
    dirpath = FS_PWD;
  };
/*
 * Attempt to open the directory.
 */
  if(_dr_open_dir(cf->dr, dirpath, NULL)) {
    _err_record_msg(cf->err, "Can't open directory: ", dirpath, END_ERR_MSG);
    return 1;
  };
/*
 * If removed above, restore the directory separator and skip over it
 * to the start of the filename.
 */
  if(terminated) {
    memcpy(pathname + start, FS_DIR_SEP, FS_DIR_SEP_LEN);
    start += FS_DIR_SEP_LEN;
  };
/*
 * Get the filename prefix and its length.
 */
  prefix = pathname + start;
  prefix_len = strlen(prefix);
/*
 * Traverse the directory, looking for files who's prefixes match the
 * last component of the pathname.
 */
  while((file_name = _dr_next_file(cf->dr)) != NULL && !waserr) {
    int name_len = strlen(file_name);
/*
 * Is the latest filename a possible completion of the filename prefix?
 */
    if(name_len >= prefix_len && strncmp(prefix, file_name, prefix_len)==0) {
/*
 * When listing all files in a directory, don't list files that start
 * with '.'. This is how hidden files are denoted in UNIX.
 */
      if(prefix_len > 0 || file_name[0] != '.') {
/*
 * Copy the completion suffix into the work pathname cf->buff->name,
 * adding backslash escapes if needed.
 */
	if(cf_prepare_suffix(cf, file_name + prefix_len, escaped)) {
	  waserr = 1;
	} else {
/*
 * We want directories to be displayed with directory suffixes,
 * and other fully completed filenames to be followed by spaces.
 * To check the type of the file, append the current suffix
 * to the path being completed, check the filetype, then restore
 * the path to its original form.
 */
	  const char *cont_suffix = "";  /* The suffix to add if fully */
                                         /*  completed. */
	  const char *type_suffix = "";  /* The suffix to add when listing */
	  if(_pn_append_to_path(cf->path, file_name + prefix_len,
				-1, escaped) == NULL) {
	    _err_record_msg(cf->err,
			    "Insufficient memory to complete filename.",
			    END_ERR_MSG);
	    return 1;
	  };
/*
 * Specify suffixes according to the file type.
 */
	  if(_pu_path_is_dir(cf->path->name)) {
	    cont_suffix = FS_DIR_SEP;
	    type_suffix = FS_DIR_SEP;
	  } else if(!check_fn || check_fn(check_data, cf->path->name)) {
	    cont_suffix = " ";
	  } else {
	    cf->path->name[pathlen] = '\0';
	    continue;
	  };
/*
 * Remove the temporarily added suffix.
 */
	  cf->path->name[pathlen] = '\0';
/*
 * Record the latest completion.
 */
	  if(cpl_add_completion(cpl, line, word_start, word_end, cf->buff->name,
				type_suffix, cont_suffix))
	    waserr = 1;
	};
      };
    };
  };
/*
 * Close the directory.
 */
  _dr_close_dir(cf->dr);
  return waserr;
}

/*.......................................................................
 * Read a username or environment variable name, stopping when a directory
 * separator is seen, when the end of the string is reached, or the
 * output buffer overflows.
 *
 * Input:
 *  cf   CompleteFile *  The file-completion resource object.
 *  type         char *  The capitalized name of the type of name being read.
 *  string       char *  The string who's prefix contains the name.
 *  slen          int    The number of characters in string[].
 *  nambuf       char *  The output name buffer.
 *  nammax        int    The longest string that will fit in nambuf[], excluding
 *                       the '\0' terminator.
 * Output:
 *  return       char *  A pointer to nambuf on success. On error NULL is
 *                       returned and a description of the error is recorded
 *                       in cf->err.
 */
static char *cf_read_name(CompleteFile *cf, const char *type,
			  const char *string, int slen,
			  char *nambuf, int nammax)
{
  int namlen;         /* The number of characters in nambuf[] */
  const char *sptr;   /* A pointer into string[] */
/*
 * Work out the max number of characters that should be copied.
 */
  int nmax = nammax < slen ? nammax : slen;
/*
 * Get the environment variable name that follows the dollar.
 */
  for(sptr=string,namlen=0;
      namlen < nmax && (slen-namlen < FS_DIR_SEP_LEN ||
			strncmp(sptr, FS_DIR_SEP, FS_DIR_SEP_LEN) != 0);
      namlen++) {
    nambuf[namlen] = *sptr++;
  };
/*
 * Did the name overflow the buffer?
 */
  if(namlen >= nammax) {
    _err_record_msg(cf->err, type, " name too long", END_ERR_MSG);
    return NULL;
  };
/*
 * Terminate the string.
 */
  nambuf[namlen] = '\0';
  return nambuf;
}

/*.......................................................................
 * Using the work buffer cf->buff, make a suitably escaped copy of a
 * given completion suffix, ready to be passed to cpl_add_completion().
 *
 * Input:
 *  cf   CompleteFile *  The file-completion resource object.
 *  suffix       char *  The suffix to be copied.
 *  add_escapes   int    If true, escape special characters.
 * Output:
 *  return        int    0 - OK.
 *                       1 - Error.
 */
static int cf_prepare_suffix(CompleteFile *cf, const char *suffix,
			     int add_escapes)
{
  const char *sptr; /* A pointer into suffix[] */
  int nbsl;         /* The number of backslashes to add to the suffix */
  int i;
/*
 * How long is the suffix?
 */
  int suffix_len = strlen(suffix);
/*
 * Clear the work buffer.
 */
  _pn_clear_path(cf->buff);
/*
 * Count the number of backslashes that will have to be added to
 * escape spaces, tabs, backslashes and wildcard characters.
 */
  nbsl = 0;
  if(add_escapes) {
    for(sptr = suffix; *sptr; sptr++) {
      switch(*sptr) {
      case ' ': case '\t': case '\\': case '*': case '?': case '[':
	nbsl++;
	break;
      };
    };
  };
/*
 * Arrange for the output path buffer to have sufficient room for the
 * both the suffix and any backslashes that have to be inserted.
 */
  if(_pn_resize_path(cf->buff, suffix_len + nbsl) == NULL) {
    _err_record_msg(cf->err, "Insufficient memory to complete filename",
		    END_ERR_MSG);
    return 1;
  };
/*
 * If the suffix doesn't need any escapes, copy it directly into the
 * work buffer.
 */
  if(nbsl==0) {
    strcpy(cf->buff->name, suffix);
  } else {
/*
 * Make a copy with special characters escaped?
 */
    if(nbsl > 0) {
      const char *src = suffix;
      char *dst = cf->buff->name;
      for(i=0; i
#include 
#include 
#include 

/*
 * Local includes.
 */
#include "libtecla.h"
#include "ioutil.h"
#include "stringrp.h"
#include "pathutil.h"
#include "cplfile.h"
#include "cplmatch.h"
#include "errmsg.h"

/*
 * Specify the number of strings to allocate when the string free-list
 * is exhausted. This also sets the number of elements to expand the
 * matches[] array by whenever it is found to be too small.
 */
#define STR_BLK_FACT 100

/*
 * Set the default number of spaces place between columns when listing
 * a set of completions.
 */
#define CPL_COL_SEP 2

/*
 * Completion matches are recorded in containers of the following
 * type.
 */
struct WordCompletion {
  ErrMsg *err;            /* The error reporting buffer */
  StringGroup *sg;        /* Memory for a group of strings */
  int matches_dim;        /* The allocated size of result.matches[] */
  CplMatches result;      /* Completions to be returned to the caller */
#ifndef WITHOUT_FILE_SYSTEM
  CompleteFile *cf;       /* The resources used for filename completion */
#endif
};

static void cpl_sort_matches(WordCompletion *cpl);
static void cpl_zap_duplicates(WordCompletion *cpl);
static void cpl_clear_completions(WordCompletion *cpl);
static int cpl_cmp_matches(const void *v1, const void *v2);
static int cpl_cmp_suffixes(const void *v1, const void *v2);

/*
 * The new_CplFileConf() constructor sets the integer first member of
 * the returned object to the following magic number. On seeing this,
 * cpl_file_completions() knows when it is passed a valid CplFileConf
 * object.
 */
#define CFC_ID_CODE 4568

#ifndef WITHOUT_FILE_SYSTEM
/*
 * A pointer to a structure of the following type can be passed to
 * the builtin file-completion callback function to modify its behavior.
 */
struct CplFileConf {
  int id;             /* new_CplFileConf() sets this to CFC_ID_CODE */
  int escaped;        /* If none-zero, backslashes in the input line are */
                      /*  interpreted as escaping special characters and */
                      /*  spaces, and any special characters and spaces in */
                      /*  the listed completions will also be escaped with */
                      /*  added backslashes. This is the default behaviour. */
                      /* If zero, backslashes are interpreted as being */
                      /*  literal parts of the filename, and none are added */
                      /*  to the completion suffixes. */
  int file_start;     /* The index in the input line of the first character */
                      /*  of the filename. If you specify -1 here, */
                      /*  cpl_file_completions() identifies the */
                      /*  the start of the filename by looking backwards for */
                      /*  an unescaped space, or the beginning of the line. */
  CplCheckFn *chk_fn; /* If not zero, this argument specifies a */
                      /*  function to call to ask whether a given */
                      /*  file should be included in the list */
                      /*  of completions. */
  void *chk_data;     /* Anonymous data to be passed to check_fn(). */
};

static void cpl_init_FileConf(CplFileConf *cfc);

/*
 * When file-system access is being excluded, define a dummy structure
 * to satisfy the typedef in libtecla.h.
 */
#else
struct CplFileConf {int dummy;};
#endif

/*
 * Encapsulate the formatting information needed to layout a
 * multi-column listing of completions.
 */
typedef struct {
  int term_width;     /* The width of the terminal (characters) */
  int column_width;   /* The number of characters within in each column. */
  int ncol;           /* The number of columns needed */
  int nline;          /* The number of lines needed */
} CplListFormat;

/*
 * Given the current terminal width, and a list of completions, determine
 * how to best use the terminal width to display a multi-column listing
 * of completions.
 */
static void cpl_plan_listing(CplMatches *result, int term_width,
			     CplListFormat *fmt);

/*
 * Display a given line of a multi-column list of completions.
 */
static int cpl_format_line(CplMatches *result, CplListFormat *fmt, int lnum,
			   GlWriteFn *write_fn, void *data);

/*.......................................................................
 * Create a new string-completion object.
 *
 * Output:
 *  return    WordCompletion *  The new object, or NULL on error.
 */
WordCompletion *new_WordCompletion(void)
{
  WordCompletion *cpl;  /* The object to be returned */
/*
 * Allocate the container.
 */
  cpl = (WordCompletion *) malloc(sizeof(WordCompletion));
  if(!cpl) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_WordCompletion().
 */
  cpl->err = NULL;
  cpl->sg = NULL;
  cpl->matches_dim = 0;
  cpl->result.suffix = NULL;
  cpl->result.cont_suffix = NULL;
  cpl->result.matches = NULL;
  cpl->result.nmatch = 0;
#ifndef WITHOUT_FILE_SYSTEM
  cpl->cf = NULL;
#endif
/*
 * Allocate a place to record error messages.
 */
  cpl->err = _new_ErrMsg();
  if(!cpl->err)
    return del_WordCompletion(cpl);
/*
 * Allocate an object that allows a group of strings to be allocated
 * efficiently by placing many of them in contiguous string segments.
 */
#ifdef WITHOUT_FILE_SYSTEM
  cpl->sg = _new_StringGroup(MAX_PATHLEN_FALLBACK);
#else
  cpl->sg = _new_StringGroup(_pu_pathname_dim());
#endif
  if(!cpl->sg)
    return del_WordCompletion(cpl);
/*
 * Allocate an array for matching completions. This will be extended later
 * if needed.
 */
  cpl->matches_dim = STR_BLK_FACT;
  cpl->result.matches = (CplMatch *) malloc(sizeof(cpl->result.matches[0]) *
					    cpl->matches_dim);
  if(!cpl->result.matches) {
    errno = ENOMEM;
    return del_WordCompletion(cpl);
  };
/*
 * Allocate a filename-completion resource object.
 */
#ifndef WITHOUT_FILE_SYSTEM
  cpl->cf = _new_CompleteFile();
  if(!cpl->cf)
    return del_WordCompletion(cpl);
#endif
  return cpl;
}

/*.......................................................................
 * Delete a string-completion object.
 *
 * Input:
 *  cpl    WordCompletion *  The object to be deleted.
 * Output:
 *  return WordCompletion *  The deleted object (always NULL).
 */
WordCompletion *del_WordCompletion(WordCompletion *cpl)
{
  if(cpl) {
    cpl->err = _del_ErrMsg(cpl->err);
    cpl->sg = _del_StringGroup(cpl->sg);
    if(cpl->result.matches) {
      free(cpl->result.matches);
      cpl->result.matches = NULL;
#ifndef WITHOUT_FILE_SYSTEM
      cpl->cf = _del_CompleteFile(cpl->cf);
#endif
    };
    free(cpl);
  };
  return NULL;
}

/*.......................................................................
 * This function is designed to be called by CplMatchFn callback
 * functions. It adds one possible completion of the token that is being
 * completed to an array of completions. If the completion needs any
 * special quoting to be valid when displayed in the input line, this
 * quoting must be included in the string.
 *
 * Input:
 *  cpl     WordCompletion *  The argument of the same name that was passed
 *                            to the calling CplMatchFn callback function.
 *  line        const char *  The input line, as received by the callback
 *                            function.
 *  word_start         int    The index within line[] of the start of the
 *                            word that is being completed.
 *  word_end           int    The index within line[] of the character which
 *                            follows the incomplete word, as received by the
 *                            calling callback function.
 *  suffix      const char *  The appropriately quoted string that could
 *                            be appended to the incomplete token to complete
 *                            it. A copy of this string will be allocated
 *                            internally.
 *  type_suffix const char *  When listing multiple completions, gl_get_line()
 *                            appends this string to the completion to indicate
 *                            its type to the user. If not pertinent pass "".
 *                            Otherwise pass a literal or static string.
 *  cont_suffix const char *  If this turns out to be the only completion,
 *                            gl_get_line() will append this string as
 *                            a continuation. For example, the builtin
 *                            file-completion callback registers a directory
 *                            separator here for directory matches, and a
 *                            space otherwise. If the match were a function
 *                            name you might want to append an open
 *                            parenthesis, etc.. If not relevant pass "".
 *                            Otherwise pass a literal or static string.
 * Output:
 *  return             int    0 - OK.
 *                            1 - Error.
 */
int cpl_add_completion(WordCompletion *cpl, const char *line,
		       int word_start, int word_end, const char *suffix,
		       const char *type_suffix, const char *cont_suffix)
{
  CplMatch *match; /* The container of the new match */
  char *string;    /* A newly allocated copy of the completion string */
/*
 * Check the arguments.
 */
  if(!cpl)
    return 1;
  if(!suffix)
    return 0;
  if(!type_suffix)
    type_suffix = "";
  if(!cont_suffix)
    cont_suffix = "";
/*
 * Do we need to extend the array of matches[]?
 */
  if(cpl->result.nmatch+1 > cpl->matches_dim) {
    int needed = cpl->matches_dim + STR_BLK_FACT;
    CplMatch *matches = (CplMatch *) realloc(cpl->result.matches,
			    sizeof(cpl->result.matches[0]) * needed);
    if(!matches) {
      _err_record_msg(cpl->err,
		      "Insufficient memory to extend array of matches.",
		      END_ERR_MSG);
      return 1;
    };
    cpl->result.matches = matches;
    cpl->matches_dim = needed;
  };
/*
 * Allocate memory to store the combined completion prefix and the
 * new suffix.
 */
  string = _sg_alloc_string(cpl->sg, word_end-word_start + strlen(suffix));
  if(!string) {
    _err_record_msg(cpl->err, "Insufficient memory to extend array of matches.",
		    END_ERR_MSG);
    return 1;
  };
/*
 * Compose the string.
 */
  strncpy(string, line + word_start, word_end - word_start);
  strcpy(string + word_end - word_start, suffix);
/*
 * Record the new match.
 */
  match = cpl->result.matches + cpl->result.nmatch++;
  match->completion = string;
  match->suffix = string + word_end - word_start;
  match->type_suffix = type_suffix;
/*
 * Record the continuation suffix.
 */
  cpl->result.cont_suffix = cont_suffix;
  return 0;
}

/*.......................................................................
 * Sort the array of matches.
 *
 * Input:
 *  cpl   WordCompletion *  The completion resource object.
 */
static void cpl_sort_matches(WordCompletion *cpl)
{
  qsort(cpl->result.matches, cpl->result.nmatch,
	sizeof(cpl->result.matches[0]), cpl_cmp_matches);
}

/*.......................................................................
 * This is a qsort() comparison function used to sort matches.
 *
 * Input:
 *  v1, v2   void *  Pointers to the two matches to be compared.
 * Output:
 *  return    int    -1 -> v1 < v2.
 *                    0 -> v1 == v2
 *                    1 -> v1 > v2
 */
static int cpl_cmp_matches(const void *v1, const void *v2)
{
  const CplMatch *m1 = (const CplMatch *) v1;
  const CplMatch *m2 = (const CplMatch *) v2;
  return strcmp(m1->completion, m2->completion);
}

/*.......................................................................
 * Sort the array of matches in order of their suffixes.
 *
 * Input:
 *  cpl   WordCompletion *  The completion resource object.
 */
static void cpl_sort_suffixes(WordCompletion *cpl)
{
  qsort(cpl->result.matches, cpl->result.nmatch,
	sizeof(cpl->result.matches[0]), cpl_cmp_suffixes);
}

/*.......................................................................
 * This is a qsort() comparison function used to sort matches in order of
 * their suffixes.
 *
 * Input:
 *  v1, v2   void *  Pointers to the two matches to be compared.
 * Output:
 *  return    int    -1 -> v1 < v2.
 *                    0 -> v1 == v2
 *                    1 -> v1 > v2
 */
static int cpl_cmp_suffixes(const void *v1, const void *v2)
{
  const CplMatch *m1 = (const CplMatch *) v1;
  const CplMatch *m2 = (const CplMatch *) v2;
  return strcmp(m1->suffix, m2->suffix);
}

/*.......................................................................
 * Find the common prefix of all of the matching completion matches,
 * and record a pointer to it in cpl->result.suffix. Note that this has
 * the side effect of sorting the matches into suffix order.
 *
 * Input:
 *  cpl   WordCompletion *  The completion resource object.
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error.
 */
static int cpl_common_suffix(WordCompletion *cpl)
{
  CplMatches *result;       /* The result container */
  const char *first, *last; /* The first and last matching suffixes */
  int length;               /* The length of the common suffix */
/*
 * Get the container of the array of matching files.
 */
  result = &cpl->result;
/*
 * No matching completions?
 */
  if(result->nmatch < 1)
    return 0;
/*
 * Sort th matches into suffix order.
 */
  cpl_sort_suffixes(cpl);
/*
 * Given that the array of matches is sorted, the first and last
 * suffixes are those that differ most in their prefixes, so the common
 * prefix of these strings is the longest common prefix of all of the
 * suffixes.
 */
  first = result->matches[0].suffix;
  last = result->matches[result->nmatch - 1].suffix;
/*
 * Find the point at which the first and last matching strings
 * first difffer.
 */
  while(*first && *first == *last) {
    first++;
    last++;
  };
/*
 * How long is the common suffix?
 */
  length = first - result->matches[0].suffix;
/*
 * Allocate memory to record the common suffix.
 */
  result->suffix = _sg_alloc_string(cpl->sg, length);
  if(!result->suffix) {
    _err_record_msg(cpl->err,
		    "Insufficient memory to record common completion suffix.",
		    END_ERR_MSG);
    return 1;
  };
/*
 * Record the common suffix.
 */
  strncpy(result->suffix, result->matches[0].suffix, length);
  result->suffix[length] = '\0'; 
  return 0;
}

/*.......................................................................
 * Discard the contents of the array of possible completion matches.
 *
 * Input:
 *  cpl   WordCompletion *  The word-completion resource object.
 */
static void cpl_clear_completions(WordCompletion *cpl)
{
/*
 * Discard all of the strings.
 */
  _clr_StringGroup(cpl->sg);
/*
 * Record the fact that the array is now empty.
 */
  cpl->result.nmatch = 0;
  cpl->result.suffix = NULL;
  cpl->result.cont_suffix = "";
/*
 * Also clear the error message.
 */
  _err_clear_msg(cpl->err);
  return;
}

/*.......................................................................
 * Given an input line and the point at which it completion is to be
 * attempted, return an array of possible completions.
 *
 * Input:
 *  cpl    WordCompletion *  The completion resource object.
 *  line             char *  The current input line.
 *  word_end          int    The index of the character in line[] which
 *                           follows the end of the token that is being
 *                           completed.
 *  data             void *  Anonymous 'data' to be passed to match_fn().
 *  match_fn   CplMatchFn *  The function that will identify the prefix
 *                           to be completed from the input line, and
 *                           record completion matches.
 * Output:
 *  return     CplMatches *  The container of the array of possible
 *                           completions. The returned pointer refers
 *                           to a container owned by the parent WordCompletion
 *                           object, and its contents thus potentially
 *                           change on every call to cpl_matches().
 *                           On error, NULL is returned, and a description
 *                           of the error can be acquired by calling
 *                           cpl_last_error(cpl).
 */
CplMatches *cpl_complete_word(WordCompletion *cpl, const char *line,
			      int word_end, void *data, 
			      CplMatchFn *match_fn)
{
  int line_len;   /* The total length of the input line */
/*
 * How long is the input line?
 */
  line_len = strlen(line);
/*
 * Check the arguments.
 */
  if(!cpl || !line || !match_fn || word_end < 0 || word_end > line_len) {
    if(cpl) {
      _err_record_msg(cpl->err, "cpl_complete_word: Invalid arguments.",
		      END_ERR_MSG);
    };
    return NULL;
  };
/*
 * Clear the return container.
 */
  cpl_clear_completions(cpl);
/*
 * Have the matching function record possible completion matches in
 * cpl->result.matches.
 */
  if(match_fn(cpl, data, line, word_end)) {
    if(_err_get_msg(cpl->err)[0] == '\0')
      _err_record_msg(cpl->err, "Error completing word.", END_ERR_MSG);
    return NULL;
  };
/*
 * Record a copy of the common initial part of all of the prefixes
 * in cpl->result.common.
 */
  if(cpl_common_suffix(cpl))
    return NULL;
/*
 * Sort the matches into lexicographic order.
 */
  cpl_sort_matches(cpl);
/*
 * Discard any duplicate matches.
 */
  cpl_zap_duplicates(cpl);
/*
 * If there is more than one match, discard the continuation suffix.
 */
  if(cpl->result.nmatch > 1)
    cpl->result.cont_suffix = "";
/*
 * Return the array of matches.
 */
  return &cpl->result;
}

/*.......................................................................
 * Recall the return value of the last call to cpl_complete_word().
 *
 * Input:
 *  cpl    WordCompletion *  The completion resource object.
 * Output:
 *  return     CplMatches *  The container of the array of possible
 *                           completions, as returned by the last call to
 *                           cpl_complete_word(). The returned pointer refers
 *                           to a container owned by the parent WordCompletion
 *                           object, and its contents thus potentially
 *                           change on every call to cpl_complete_word().
 *                           On error, either in the execution of this
 *                           function, or in the last call to
 *                           cpl_complete_word(), NULL is returned, and a
 *                           description of the error can be acquired by
 *                           calling cpl_last_error(cpl).
 */
CplMatches *cpl_recall_matches(WordCompletion *cpl)
{
  return (!cpl || *_err_get_msg(cpl->err)!='\0') ? NULL : &cpl->result;
}

/*.......................................................................
 * Print out an array of matching completions.
 *
 * Input:
 *  result  CplMatches *   The container of the sorted array of
 *                         completions.
 *  fp            FILE *   The output stream to write to.
 *  term_width     int     The width of the terminal.
 * Output:
 *  return         int     0 - OK.
 *                         1 - Error.
 */
int cpl_list_completions(CplMatches *result, FILE *fp, int term_width)
{
  return _cpl_output_completions(result, _io_write_stdio, fp, term_width);
}

/*.......................................................................
 * Print an array of matching completions via a callback function.
 *
 * Input:
 *  result   CplMatches *  The container of the sorted array of
 *                         completions.
 *  write_fn  GlWriteFn *  The function to call to write the completions,
 *                         or 0 to discard the output.
 *  data           void *  Anonymous data to pass to write_fn().
 *  term_width      int    The width of the terminal.
 * Output:
 *  return          int     0 - OK.
 *                          1 - Error.
 */
int _cpl_output_completions(CplMatches *result, GlWriteFn *write_fn, void *data,
			    int term_width)
{
  CplListFormat fmt; /* List formatting information */
  int lnum;          /* The sequential number of the line to print next */
/*
 * Not enough space to list anything?
 */
  if(term_width < 1)
    return 0;
/*
 * Do we have a callback to write via, and any completions to be listed?
 */
  if(write_fn && result && result->nmatch>0) {
/*
 * Work out how to arrange the listing into fixed sized columns.
 */
    cpl_plan_listing(result, term_width, &fmt);
/*
 * Print the listing via the specified callback.
 */
    for(lnum=0; lnum < fmt.nline; lnum++) {
      if(cpl_format_line(result, &fmt, lnum, write_fn, data))
	return 1;
    };
  };
  return 0;
}

/*.......................................................................
 * Return a description of the string-completion error that occurred.
 *
 * Input:
 *  cpl   WordCompletion *  The string-completion resource object.
 * Output:
 *  return    const char *  The description of the last error.
 */
const char *cpl_last_error(WordCompletion *cpl)
{
  return cpl ? _err_get_msg(cpl->err) : "NULL WordCompletion argument";
}

/*.......................................................................
 * When an error occurs while performing a completion, you registerf a
 * terse description of the error by calling cpl_record_error(). This
 * message will then be returned on the next call to cpl_last_error().
 *
 * Input:
 *  cpl   WordCompletion *  The string-completion resource object that was
 *                          originally passed to the callback.
 *  errmsg    const char *  The description of the error.
 */
void cpl_record_error(WordCompletion *cpl, const char *errmsg)
{
  if(cpl && errmsg)
    _err_record_msg(cpl->err, errmsg, END_ERR_MSG);
}

/*.......................................................................
 * This is the builtin completion callback function which performs file
 * completion.
 *
 * Input:
 *  cpl  WordCompletion *  An opaque pointer to the object that will
 *                         contain the matches. This should be filled
 *                         via zero or more calls to cpl_add_completion().
 *  data           void *  Either NULL to request the default
 *                         file-completion behavior, or a pointer to a
 *                         CplFileConf structure, whose members specify
 *                         a different behavior.
 *  line           char *  The current input line.
 *  word_end        int    The index of the character in line[] which
 *                         follows the end of the token that is being
 *                         completed.
 * Output
 *  return          int    0 - OK.
 *                         1 - Error.
 */
CPL_MATCH_FN(cpl_file_completions)
{
#ifdef WITHOUT_FILE_SYSTEM
  return 0;
#else
  const char *start_path;  /* The pointer to the start of the pathname */
                           /*  in line[]. */
  CplFileConf *conf;       /* The new-style configuration object. */
/*
 * The following configuration object will be used if the caller didn't
 * provide one.
 */
  CplFileConf default_conf;
/*
 * This function can be called externally, so check its arguments.
 */
  if(!cpl)
    return 1;
  if(!line || word_end < 0) {
    _err_record_msg(cpl->err, "cpl_file_completions: Invalid arguments.",
		    END_ERR_MSG);
    return 1;
  };
/*
 * The 'data' argument is either a CplFileConf pointer, identifiable
 * by having an integer id code as its first member, or the deprecated
 * CplFileArgs pointer, or can be NULL to request the default
 * configuration.
 */
  if(data && *(int *)data == CFC_ID_CODE) {
    conf = (CplFileConf *) data;
  } else {
/*
 * Select the defaults.
 */
    conf = &default_conf;
    cpl_init_FileConf(&default_conf);
/*
 * If we have been passed an instance of the deprecated CplFileArgs
 * structure, copy its configuration parameters over the defaults.
 */
    if(data) {
      CplFileArgs *args = (CplFileArgs *) data;
      conf->escaped = args->escaped;
      conf->file_start = args->file_start;
    };
  };
/*
 * Get the start of the filename. If not specified by the caller
 * identify it by searching backwards in the input line for an
 * unescaped space or the start of the line.
 */
  if(conf->file_start < 0) {
    start_path = _pu_start_of_path(line, word_end);
    if(!start_path) {
      _err_record_msg(cpl->err, "Unable to find the start of the filename.",
		      END_ERR_MSG);
      return 1;
    };
  } else {
    start_path = line + conf->file_start;
  };
/*
 * Perform the completion.
 */
  if(_cf_complete_file(cpl, cpl->cf, line, start_path - line, word_end,
		      conf->escaped, conf->chk_fn, conf->chk_data)) {
    cpl_record_error(cpl, _cf_last_error(cpl->cf));
    return 1;
  };
  return 0;
#endif
}

/*.......................................................................
 * Initialize a CplFileArgs structure with default configuration
 * parameters. Note that the CplFileArgs configuration type is
 * deprecated. The opaque CplFileConf object should be used in future
 * applications.
 *
 * Input:
 *  cfa  CplFileArgs *  The configuration object of the
 *                      cpl_file_completions() callback.
 */
void cpl_init_FileArgs(CplFileArgs *cfa)
{
  if(cfa) {
    cfa->escaped = 1;
    cfa->file_start = -1;
  };
}

#ifndef WITHOUT_FILE_SYSTEM
/*.......................................................................
 * Initialize a CplFileConf structure with default configuration
 * parameters.
 *
 * Input:
 *  cfc  CplFileConf *  The configuration object of the
 *                      cpl_file_completions() callback.
 */
static void cpl_init_FileConf(CplFileConf *cfc)
{
  if(cfc) {
    cfc->id = CFC_ID_CODE;
    cfc->escaped = 1;
    cfc->file_start = -1;
    cfc->chk_fn = 0;
    cfc->chk_data = NULL;
  };
}
#endif

/*.......................................................................
 * Create a new CplFileConf object and initialize it with defaults.
 *
 * Output:
 *  return  CplFileConf *  The new object, or NULL on error.
 */
CplFileConf *new_CplFileConf(void)
{
#ifdef WITHOUT_FILE_SYSTEM
  errno = EINVAL;
  return NULL;
#else
  CplFileConf *cfc;  /* The object to be returned */
/*
 * Allocate the container.
 */
  cfc = (CplFileConf *)malloc(sizeof(CplFileConf));
  if(!cfc)
    return NULL;
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_CplFileConf().
 */
  cpl_init_FileConf(cfc);
  return cfc;
#endif
}

/*.......................................................................
 * Delete a CplFileConf object.
 *
 * Input:
 *  cfc    CplFileConf *  The object to be deleted.
 * Output:
 *  return CplFileConf *  The deleted object (always NULL).
 */
CplFileConf *del_CplFileConf(CplFileConf *cfc)
{
#ifndef WITHOUT_FILE_SYSTEM
  if(cfc) {
/*
 * Delete the container.
 */
    free(cfc);
  };
#endif
  return NULL;
}

/*.......................................................................
 * If backslashes in the filename should be treated as literal
 * characters, call the following function with literal=1. Otherwise
 * the default is to treat them as escape characters, used for escaping
 * spaces etc..
 *
 * Input:
 *  cfc    CplFileConf *  The cpl_file_completions() configuration object
 *                        to be configured.
 *  literal        int    Pass non-zero here to enable literal interpretation
 *                        of backslashes. Pass 0 to turn off literal
 *                        interpretation.
 */
void cfc_literal_escapes(CplFileConf *cfc, int literal)
{
#ifndef WITHOUT_FILE_SYSTEM
  if(cfc)
    cfc->escaped = !literal;
#endif
}

/*.......................................................................
 * Call this function if you know where the index at which the
 * filename prefix starts in the input line. Otherwise by default,
 * or if you specify start_index to be -1, the filename is taken
 * to start after the first unescaped space preceding the cursor,
 * or the start of the line, which ever comes first.
 *
 * Input:
 *  cfc    CplFileConf *  The cpl_file_completions() configuration object
 *                        to be configured.
 *  start_index    int    The index of the start of the filename in
 *                        the input line, or -1 to select the default.
 */
void cfc_file_start(CplFileConf *cfc, int start_index)
{
#ifndef WITHOUT_FILE_SYSTEM
  if(cfc)
    cfc->file_start = start_index;
#endif
}

/*.......................................................................
 * If you only want certain types of files to be included in the
 * list of completions, you use the following function to specify a
 * callback function which will be called to ask whether a given file
 * should be included.
 *
 * Input:
 *  cfc    CplFileConf *  The cpl_file_completions() configuration object
 *                        to be configured.
 *  chk_fn  CplCheckFn *  Zero to disable filtering, or a pointer to a
 *                        function that returns 1 if a given file should
 *                        be included in the list of completions.
 *  chk_data      void *  Anonymous data to be passed to chk_fn()
 *                        every time that it is called.
 */
void cfc_set_check_fn(CplFileConf *cfc, CplCheckFn *chk_fn, void *chk_data)
{
#ifndef WITHOUT_FILE_SYSTEM
  if(cfc) {
    cfc->chk_fn = chk_fn;
    cfc->chk_data = chk_data;
  };
#endif
}

/*.......................................................................
 * The following CplCheckFn callback returns non-zero if the specified
 * filename is that of an executable.
 */
CPL_CHECK_FN(cpl_check_exe)
{
#ifdef WITHOUT_FILE_SYSTEM
  return 0;
#else
  return _pu_path_is_exe(pathname);
#endif
}

/*.......................................................................
 * Remove duplicates from a sorted array of matches.
 *
 * Input:
 *  cpl   WordCompletion *  The completion resource object.
 */
static void cpl_zap_duplicates(WordCompletion *cpl)
{
  CplMatch *matches;       /* The array of matches */
  int nmatch;              /* The number of elements in matches[] */
  const char *completion;  /* The completion string of the last unique match */
  const char *type_suffix; /* The type of the last unique match */
  int src;                 /* The index of the match being considered */
  int dst;                 /* The index at which to record the next */
                           /*  unique match. */
/*
 * Get the array of matches and the number of matches that it
 * contains.
 */
  matches = cpl->result.matches;
  nmatch = cpl->result.nmatch;
/*
 * No matches?
 */
  if(nmatch < 1)
    return;
/*
 * Initialize the comparison strings with the first match.
 */
  completion = matches[0].completion;
  type_suffix = matches[0].type_suffix;
/*
 * Go through the array of matches, copying each new unrecorded
 * match at the head of the array, while discarding duplicates.
 */
  for(src=dst=1; srccompletion) != 0 ||
       strcmp(type_suffix, match->type_suffix) != 0) {
      if(src != dst)
	matches[dst] = *match;
      dst++;
      completion = match->completion;
      type_suffix = match->type_suffix;
    };
  };
/*
 * Record the number of unique matches that remain.
 */
  cpl->result.nmatch = dst;
  return;
}

/*.......................................................................
 * Work out how to arrange a given array of completions into a listing
 * of one or more fixed size columns.
 *
 * Input:
 *  result   CplMatches *   The set of completions to be listed.
 *  term_width      int     The width of the terminal. A lower limit of
 *                          zero is quietly enforced.
 * Input/Output:
 *  fmt   CplListFormat *   The formatting information will be assigned
 *                          to the members of *fmt.
 */
static void cpl_plan_listing(CplMatches *result, int term_width,
			     CplListFormat *fmt)
{
  int maxlen;    /* The length of the longest matching string */
  int i;
/*
 * Ensure that term_width >= 0.
 */
  if(term_width < 0)
    term_width = 0;
/*
 * Start by assuming the worst case, that either nothing will fit
 * on the screen, or that there are no matches to be listed.
 */
  fmt->term_width = term_width;
  fmt->column_width = 0;
  fmt->nline = fmt->ncol = 0;
/*
 * Work out the maximum length of the matching strings.
 */
  maxlen = 0;
  for(i=0; inmatch; i++) {
    CplMatch *match = result->matches + i;
    int len = strlen(match->completion) + strlen(match->type_suffix);
    if(len > maxlen)
      maxlen = len;
  };
/*
 * Nothing to list?
 */
  if(maxlen == 0)
    return;
/*
 * Split the available terminal width into columns of
 * maxlen + CPL_COL_SEP characters.
 */
  fmt->column_width = maxlen;
  fmt->ncol = fmt->term_width / (fmt->column_width + CPL_COL_SEP);
/*
 * If the column width is greater than the terminal width, zero columns
 * will have been selected. Set a lower limit of one column. Leave it
 * up to the caller how to deal with completions who's widths exceed
 * the available terminal width.
 */
  if(fmt->ncol < 1)
    fmt->ncol = 1;
/*
 * How many lines of output will be needed?
 */
  fmt->nline = (result->nmatch + fmt->ncol - 1) / fmt->ncol;
  return;
}

/*.......................................................................
 * Render one line of a multi-column listing of completions, using a
 * callback function to pass the output to an arbitrary destination.
 *
 * Input:
 *  result      CplMatches *  The container of the sorted array of
 *                            completions.
 *  fmt      CplListFormat *  Formatting information.
 *  lnum               int    The index of the line to print, starting
 *                            from 0, and incrementing until the return
 *                            value indicates that there is nothing more
 *                            to be printed.
 *  write_fn     GlWriteFn *  The function to call to write the line, or
 *                            0 to discard the output.
 *  data              void *  Anonymous data to pass to write_fn().
 * Output:
 *  return             int    0 - Line printed ok.
 *                            1 - Nothing to print.
 */
static int cpl_format_line(CplMatches *result, CplListFormat *fmt, int lnum,
			   GlWriteFn *write_fn, void *data)
{
  int col;             /* The index of the list column being output */
/*
 * If the line index is out of bounds, there is nothing to be written.
 */
  if(lnum < 0 || lnum >= fmt->nline)
    return 1;
/*
 * If no output function has been provided, return as though the
 * line had been printed.
 */
  if(!write_fn)
    return 0;
/*
 * Print the matches in 'ncol' columns, sorted in line order within each
 * column.
 */
  for(col=0; col < fmt->ncol; col++) {
    int m = col*fmt->nline + lnum;
/*
 * Is there another match to be written? Note that in general
 * the last line of a listing will have fewer filled columns
 * than the initial lines.
 */
    if(m < result->nmatch) {
      CplMatch *match = result->matches + m;
/*
 * How long are the completion and type-suffix strings?
 */
      int clen = strlen(match->completion);
      int tlen = strlen(match->type_suffix);
/*
 * Write the completion string.
 */
      if(write_fn(data, match->completion, clen) != clen)
	return 1;
/*
 * Write the type suffix, if any.
 */
      if(tlen > 0 && write_fn(data, match->type_suffix, tlen) != tlen)
	return 1;
/*
 * If another column follows the current one, pad to its start with spaces.
 */
      if(col+1 < fmt->ncol) {
/*
 * The following constant string of spaces is used to pad the output.
 */
	static const char spaces[] = "                    ";
	static const int nspace = sizeof(spaces) - 1;
/*
 * Pad to the next column, using as few sub-strings of the spaces[]
 * array as possible.
 */
	int npad = fmt->column_width + CPL_COL_SEP - clen - tlen;
	while(npad>0) {
	  int n = npad > nspace ? nspace : npad;
	  if(write_fn(data, spaces + nspace - n, n) != n)
	    return 1;
	  npad -= n;
	};
      };
    };
  };
/*
 * Start a new line.
 */
  {
    char s[] = "\r\n";
    int n = strlen(s);
    if(write_fn(data, s, n) != n)
      return 1;
  };
  return 0;
}
genometools-1.5.1/src/external/libtecla-1.6.1/cplmatch.h000066400000000000000000000037361211610345200226520ustar00rootroot00000000000000#ifndef cplmatch_h
#define cplmatch_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * This header is not for use by external applicatons. It contains
 * internal immplementation features of the libtecla library, which
 * may change incompatibly between releases.
 */

/*
 * Display a list of completions via a callback function.
 */
int _cpl_output_completions(CplMatches *result, GlWriteFn *write_fn, void *data,
			    int term_width);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/demo.c000066400000000000000000000125571211610345200217770ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include 
#include 
#include 
#include 
#include 
#include 

#include 
#include 

#include "libtecla.h"

/* The function which displays the introductory text of the demo */

static void show_demo_introduction(GetLine *gl);

/*.......................................................................
 * This program demonstrates how to use gl_get_line() as a line editor to
 * to enable users to enter input. It takes no arguments.
 */
int main(int argc, char *argv[])
{
  char *line;             /* A line of input */
  GetLine *gl;            /* The line editor */
  int major,minor,micro;  /* The version number of the library */
/*
 * Create the line editor, specifying a max line length of 500 bytes,
 * and 10000 bytes to allocate to storage of historical input lines.
 */
  gl = new_GetLine(500, 5000);
  if(!gl)
    return 1;
/*
 * If the user has the LC_CTYPE or LC_ALL environment variables set,
 * enable display of characters corresponding to the specified locale.
 */
  (void) setlocale(LC_CTYPE, "");
/*
 * Lookup and display the version number of the library.
 */
  libtecla_version(&major, &minor, µ);
  printf("\n Welcome to the main demo program of libtecla version %d.%d.%d\n",
	 major, minor, micro);
/*
 * Display an introductory banner.
 */
  show_demo_introduction(gl);
/*
 * Load history.
 */
#ifndef WITHOUT_FILE_SYSTEM
  (void) gl_load_history(gl, "~/.demo_history", "#");
#endif
/*
 * Read lines of input from the user and print them to stdout.
 */
  do {
/*
 * Get a new line from the user.
 */
    line = gl_get_line(gl, "$ ", NULL, 0);
    if(!line)
      break;
/*
 * Display what was entered.
 */
    if(printf("You entered: %s", line) < 0 || fflush(stdout))
      break;
/*
 * If the user types "exit", quit the program.
 */
    if(strcmp(line, "exit\n")==0)
      break;
    else if(strcmp(line, "history\n")==0)
      gl_show_history(gl, stdout, "%N  %T   %H\n", 0, -1);
    else if(strcmp(line, "size\n")==0) {
      GlTerminalSize size = gl_terminal_size(gl, 80, 24);
      printf("Terminal size = %d columns x %d lines.\n", size.ncolumn,
	     size.nline);
    } else if(strcmp(line, "clear\n")==0) {
      if(gl_erase_terminal(gl))
	return 1;
    };
  } while(1);
/*
 * Save historical command lines.
 */
#ifndef WITHOUT_FILE_SYSTEM
  (void) gl_save_history(gl, "~/.demo_history", "#", -1);
#endif
/*
 * Clean up.
 */
  gl = del_GetLine(gl);
  return 0;
}

/*.......................................................................
 * Display introductory text to the user, formatted according to the
 * current terminal width and enclosed in a box of asterixes.
 *
 * Input:
 *  gl      GetLine *   The resource object of gl_get_line().
 */
static void show_demo_introduction(GetLine *gl)
{
  int start;     /* The column in which gl_display_text() left the cursor */
  int i;
/*
 * Break the indtroductory text into an array of strings, so as to
 * avoid overflowing any compiler string limits.
 */
  const char *doc[] = {
    "This program is a simple shell with which you can experiment with the ",
    "line editing and tab completion facilities provided by the gl_get_line() ",
    "function. The file demo.c also serves as a fully commented example ",
    "of how to use gl_get_line().\n"
  };
/*
 * Form the top line of the documentation box by filling the area of
 * the line between a " *" prefix and a "* " suffix with asterixes.
 */
  printf("\n");
  gl_display_text(gl, 0, " *", "* ", '*', 80, 0, "\n");
/*
 * Justify the documentation text within margins of asterixes.
 */
  for(start=0,i=0; i= 0; i++)
    start = gl_display_text(gl, 0, " * ", " * ", ' ', 80, start,doc[i]);
/*
 * Draw the bottom line of the documentation box.
 */
  gl_display_text(gl, 0, " *", "* ", '*', 80, 0, "\n");
  printf("\n");
}
genometools-1.5.1/src/external/libtecla-1.6.1/demo2.c000066400000000000000000000330601211610345200220510ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include 
#include 
#include 
#include 
#include 
#include 

#include 
#include 

#include "libtecla.h"

/*
 * If the library is being built with file-system access excluded, this
 * demo program won't have anything to demonstrate.
 */
#ifdef WITHOUT_FILE_SYSTEM
int main(int argc, char *argv[])
{
  fprintf(stderr, "\n"
	  "  This program normally demonstrates tecla's path-lookup\n"
	  "  facility. However libtecla has been installed with\n"
	  "  file-system facilities explicitly excluded, so there is\n"
          "  nothing to demonstrate.\n\n");
  return 1;
}
#else
/*
 * Encapsulate the resources needed by this demo.
 */
typedef struct {
  GetLine *gl;      /* The line editor */
  PathCache *pc;    /* A cache of executables in the user's path */
  PcaPathConf *ppc; /* The configuration argument of pca_path_completions() */
} DemoRes;

/*
 * The following functions allocate and free instances of the above
 * structure.
 */
static DemoRes *new_DemoRes(void);
static DemoRes *del_DemoRes(DemoRes *res);

/*
 * Search backwards for the start of a pathname.
 */
static char *start_of_path(const char *string, int back_from);

/*
 * Find the array indexes of the first character of the first
 * space-delimited word in the specified string, and of the character
 * that follows it.
 */
static int get_word_limits(const char *string, int *wa, int *wb);

/*
 * This is the demonstration completion callback function (defined below).
 */
static CPL_MATCH_FN(demo_cpl_fn);

/* The function which displays the introductory text of the demo */

static void show_demo_introduction(GetLine *gl);

/*.......................................................................
 * This demo takes no arguments. It reads lines of input until the
 * word 'exit' is entered, or C-d is pressed. It replaces the default
 * tab-completion callback with one which when invoked at the start of
 * a line, looks up completions of commands in the user's execution
 * path, and when invoked in other parts of the line, reverts to
 * normal filename completion. Whenever a new line is entered, it
 * extracts the first word on the line, looks it up in the user's
 * execution path to see if it corresponds to a known executable file,
 * and if so, displays the full pathname of the file, along with the
 * remaining arguments.
 */
int main(int argc, char *argv[])
{
  char *line;             /* A line of input */
  DemoRes *res;           /* The resources of the demo */
  int wa,wb;              /* The delimiting indexes of a word in line[] */
  int major,minor,micro;  /* The version number of the library */
/*
 * Allocate the resources needed by this demo.
 */
  res = new_DemoRes();
  if(!res)
    return 1;
/*
 * If the user has the LC_CTYPE or LC_ALL environment variables set,
 * enable display of characters corresponding to the specified locale.
 */
  (void) setlocale(LC_CTYPE, "");
/*
 * Lookup and display the version number of the library.
 */
  libtecla_version(&major, &minor, µ);
  printf("\n Welcome to the path-search demo of libtecla version %d.%d.%d\n",
	 major, minor, micro);
/*
 * Display some introductory text, left-justifying it within the current
 * width of the terminal and enclosing it in a box of asterixes.
 */
  show_demo_introduction(res->gl);
/*
 * Read lines of input from the user and print them to stdout.
 */
  do {
/*
 * Get a new line from the user.
 */
    line = gl_get_line(res->gl, "$ ", NULL, 0);
    if(!line)
      break;
/*
 * Work out the extent of the first word in the input line, and
 * try to identify this as a command in the path, displaying the
 * full pathname of the match if found.
 */
    if(get_word_limits(line, &wa, &wb) == 0) {
      char *cmd = pca_lookup_file(res->pc, line + wa, wb-wa, 0);
      if(cmd) {
	printf("Command=%s\n", cmd);
	printf("Arguments=%s", line+wb);
      } else {
	printf("Command not found\n");
      };
    };
/*
 * If the user types "exit", quit the program.
 */
    if(strcmp(line, "exit\n")==0)
      break;
  } while(1);
/*
 * Clean up.
 */
  res = del_DemoRes(res);
  return 0;
}

/*.......................................................................
 * This completion callback searches for completions of executables in
 * the user's path when invoked on a word at the start of the path, and
 * performs normal filename completion elsewhere.
 */
static CPL_MATCH_FN(demo_cpl_fn)
{
/*
 * Get the resource object that was passed to gl_customize_completion().
 */
  DemoRes *res = (DemoRes *) data;
/*
 * Find the start of the filename prefix to be completed, searching
 * backwards for the first unescaped space, or the start of the line.
 */
  char *start = start_of_path(line, word_end);
/*
 * Skip spaces preceding the start of the prefix.
 */
  while(start > line && isspace((int)(unsigned char) start[-1]))
    start--;
/*
 * If the filename prefix is at the start of the line, attempt
 * to complete the filename as a command in the path. Otherwise
 * perform normal filename completion.
 */
  return (start == line) ?
    pca_path_completions(cpl, res->ppc, line, word_end) :
    cpl_file_completions(cpl, NULL, line, word_end);
}

/*.......................................................................
 * Search backwards for the potential start of a filename. This
 * looks backwards from the specified index in a given string,
 * stopping at the first unescaped space or the start of the line.
 *
 * Input:
 *  string  const char *  The string to search backwards in.
 *  back_from      int    The index of the first character in string[]
 *                        that follows the pathname.
 * Output:
 *  return        char *  The pointer to the first character of
 *                        the potential pathname, or NULL on error.
 */
static char *start_of_path(const char *string, int back_from)
{
  int i, j;
/*
 * Search backwards from the specified index.
 */
  for(i=back_from-1; i>=0; i--) {
    int c = string[i];
/*
 * Stop on unescaped spaces.
 */
    if(isspace((int)(unsigned char)c)) {
/*
 * The space can't be escaped if we are at the start of the line.
 */
      if(i==0)
        break;
/*
 * Find the extent of the escape characters which precedes the space.
 */
      for(j=i-1; j>=0 && string[j]=='\\'; j--)
	;
/*
 * If there isn't an odd number of escape characters before the space,
 * then the space isn't escaped.
 */
      if((i - 1 - j) % 2 == 0)
	break;
    };
  };
  return (char *)string + i + 1;
}

/*.......................................................................
 * Create a new DemoRes object containing the resources needed by the
 * demo.
 *
 * Output:
 *  return  DemoRes *  The new object, or NULL on error.
 */
static DemoRes *new_DemoRes(void)
{
  DemoRes *res;  /* The object to be returned */
/*
 * Allocate the container.
 */
  res = (DemoRes *)malloc(sizeof(DemoRes));
  if(!res) {
    fprintf(stderr, "new_DemoRes: Insufficient memory.\n");
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_DemoRes().
 */
  res->gl = NULL;
  res->pc = NULL;
  res->ppc = NULL;
/*
 * Create the line editor, specifying a max line length of 500 bytes,
 * and 10000 bytes to allocate to storage of historical input lines.
 */
  res->gl = new_GetLine(500, 10000);
  if(!res->gl)
    return del_DemoRes(res);
/*
 * Enable text attribute formatting directives in prompt strings.
 */
  gl_prompt_style(res->gl, GL_FORMAT_PROMPT);
/*
 * Allocate a cache of the executable files found in the user's path.
 */
  res->pc = new_PathCache();
  if(!res->pc)
    return del_DemoRes(res);
/*
 * Populate the cache with the contents of the user's path.
 */
  if(pca_scan_path(res->pc, getenv("PATH")))
    return del_DemoRes(res);
/*
 * Arrange for susequent calls to pca_lookup_file() and pca_path_completions()
 * to only report files that are executable by the user.
 */
  pca_set_check_fn(res->pc, cpl_check_exe, NULL);
/*
 * Allocate a configuration object for use with pca_path_completions().
 */
  res->ppc = new_PcaPathConf(res->pc);
  if(!res->ppc)
    return del_DemoRes(res);
/*
 * Replace the builtin filename completion callback with one which
 * searches for completions of executables in the user's path when
 * invoked on a word at the start of the path, and completes files
 * elsewhere.
 */
  if(gl_customize_completion(res->gl, res, demo_cpl_fn))
    return del_DemoRes(res);
  return res;
}

/*.......................................................................
 * Delete a DemoRes object.
 *
 * Input:
 *  res     DemoRes *  The object to be deleted.
 * Output:
 *  return  DemoRes *  The deleted object (always NULL).
 */
static DemoRes *del_DemoRes(DemoRes *res)
{
  if(res) {
    res->gl = del_GetLine(res->gl);
    res->pc = del_PathCache(res->pc);
    res->ppc = del_PcaPathConf(res->ppc);
    free(res);
  };
  return NULL;
}

/*.......................................................................
 * Return the limits of the word at the start of a given string, ignoring
 * leading white-space, and interpretting the first unescaped space, tab or
 * the end of the line, as the end of the word.
 *
 * Input:
 *  string   const char *  The string to tokenize.
 * Input/Output:
 *  wa,wb           int *  The indexes of the first character of the word,
 *                         and the character which follows the last
 *                         character of the word, will be assigned to
 *                         *wa and *wb, respectively.
 * Output:
 *  return          int    0 - A word was found.
 *                         1 - No word was found before the end of the
 *                             string.
 */
static int get_word_limits(const char *string, int *wa, int *wb)
{
  int escaped = 0;  /* True if the next character is escaped */
/*
 * Skip leading white-space.
 */
  for(*wa=0; isspace((int)(unsigned char)string[*wa]); (*wa)++)
    ;
/*
 * Find the first unescaped space, stopping early if the end of the
 * string is reached.
 */
  for(*wb = *wa; ; (*wb)++) {
    int c = string[*wb];
    if(c=='\\')
      escaped = !escaped;
    else if((!escaped && isspace((int)(unsigned char)c)) || c=='\0')
      break;
  };
  return *wa == *wb;
}

/*.......................................................................
 * Display introductory text to the user, formatted according to the
 * current terminal width and enclosed in a box of asterixes.
 *
 * Input:
 *  gl      GetLine *   The resource object of gl_get_line().
 */
static void show_demo_introduction(GetLine *gl)
{
  int start;     /* The column in which gl_display_text() left the cursor */
  int i;
/*
 * Break the indtroductory text into an array of strings, so as to
 * avoid overflowing any compiler string limits.
 */
  const char *doc[] = {
    "This program demonstrates the use of the pca_lookup_file() function ",
    "for finding executables in the UNIX PATH. It also demonstrates ",
    "tab completion of the names of executables found in the path. For ",
    "example, if you type:\n\n ta\n\nthen hit the tab key, you will be ",
    "presented with a list of executables such as tar and tail whose names ",
    "start with the string \"ta\". If you decide to add an \"r\" to select ",
    "the tar command, then you type return, the full pathname of the tar ",
    "program will be printed.\n\nThe file demo2.c contains the code ",
    "of this program, and is fully commented to enable its use as ",
    "a working example of how to use the facilities documented in the ",
    "pca_lookup_file man page.\n"};
/*
 * Form the top line of the documentation box by filling the area of
 * the line between a " *" prefix and a "* " suffix with asterixes.
 */
  printf("\n");
  gl_display_text(gl, 0, " *", "* ", '*', 80, 0, "\n");
/*
 * Justify the documentation text within margins of asterixes.
 */
  for(start=0,i=0; i= 0; i++)
    start = gl_display_text(gl, 0, " * ", " * ", ' ', 80, start,doc[i]);
/*
 * Draw the bottom line of the documentation box.
 */
  gl_display_text(gl, 0, " *", "* ", '*', 80, 0, "\n");
  printf("\n");
}

#endif  /* ifndef WITHOUT_FILE_SYSTEM */
genometools-1.5.1/src/external/libtecla-1.6.1/demo3.c000066400000000000000000000633051211610345200220570ustar00rootroot00000000000000/*
 * Copyright (c) 2002, 2003, 2004 by Martin C. Shepherd
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include 
#include 
#include 
#include 
#include 
#include 
#include 

#ifdef HAVE_SELECT
#ifdef HAVE_SYS_SELECT_H
#include 
#endif
#endif

#include 
#include 
#include     
#include 
#include 

#include "libtecla.h"

/*
 * The SignalActions object provides a way to temporarily install
 * a signal handler to a given set of signals, and later restore all
 * of the signal handlers that this displaced.
 */
typedef struct {
  int nsignal;               /* The number of signals on the host OS */
  sigset_t mask;             /* The set of signals who's signal handlers */
                             /*  are stored in the following actions[] */
                             /*  array. */
  struct sigaction *actions; /* An array of nsignal actions */
} SignalActions;

static SignalActions *new_SignalActions(void);
static SignalActions *del_SignalActions(SignalActions *si);
static int displace_signal_handlers(SignalActions *si, sigset_t *mask,
				    void (*handler)(int));
static int reinstate_signal_handlers(SignalActions *si);

/* Return resources, restore the terminal to a usable state and exit */

static void cleanup_and_exit(GetLine *gl, SignalActions *si, int status);

/* The function which displays the introductory text of the demo */

static void show_demo_introduction(GetLine *gl);

/* A signal-aware version of select() */

static int demo_sigselect(int n, fd_set *readfds, fd_set *writefds,
			  fd_set *exceptfds, struct timeval *timeout,
			  sigset_t *mask, SignalActions *si);

/*
 * The following variables are accessed from signal handlers.  Note
 * that these variables don't need to be either volatile or
 * sig_atomic_t because:
 *
 * 1. Outside of signal handlers we only access them when signal
 *    delivery is blocked, so we know that no signal handlers can
 *    be accessing them at that time.
 *
 * 2. When the signal handlers that set these variables are installed,
 *    the sa_mask member of the sigaction structure is used to ensure
 *    that only one instance of these signal handlers can be running
 *    at a time, so we also know that there can't be simultaneous
 *    accesses to them by multiple signal handlers.
 */
static GetLine *demo_gl;                /* The line editor object */
static sigjmp_buf demo_setjmp_buffer;   /* The sigsetjmp() buffer */
static int demo_setjmp_signo = -1;      /* The signal that was caught */

/* Signal handlers */

static void demo_signal_handler(int signo);
static void demo_setjmp_handler(int signo);

/*
 * Set the amount of time that gl_get_line() should wait for I/O before
 * returning to let the external event loop continue.
 */
#define DEMO_IO_TIMEOUT 100000000 /* ns => 100ms */

/* The timeout handler */

static GL_TIMEOUT_FN(demo_timeout_fn);

/*.......................................................................
 * This program demonstrates the use of gl_get_line() from an external
 * event loop. It takes no arguments.
 */
int main(int argc, char *argv[])
{
  int major,minor,micro;      /* The version number of the library */
  GetLine *gl=NULL;           /* The resource object of gl_get_line() */
  SignalActions *si=NULL;     /* Temporary storage of displaced signal */
                              /*  handlers. */
  sigset_t all_signal_mask;   /* The set of signals known by gl_get_line() */
/*
 * This program requires select().
 */
#if !defined(HAVE_SELECT)
  fprintf(stderr, "The select() system call isn't available - aborting.\n");
  exit(1);
#else
/*
 * Create the line editor, specifying a maximum line length of 500 bytes,
 * and 10000 bytes to allocate to storage of historical input lines.
 */
  gl = demo_gl = new_GetLine(500, 5000);
  if(!gl)
    cleanup_and_exit(gl, si, 1);

/*
 * Allocate an object in which to temporarily record displaced
 * signal handlers.
 */
  si = new_SignalActions();
  if(!si)
    cleanup_and_exit(gl, si, 1);
/*
 * If the user has the LC_CTYPE or LC_ALL environment variables set,
 * enable display of characters corresponding to the specified locale.
 */
  (void) setlocale(LC_CTYPE, "");
/*
 * Lookup and display the version number of the library.
 */
  libtecla_version(&major, &minor, µ);
  printf(
    "\n Welcome to the server-mode demo program of libtecla version %d.%d.%d\n",
      major, minor, micro);
/*
 * Display some introductory text, left-justifying it within the current
 * width of the terminal and enclosing it in a box of asterixes.
 */
  show_demo_introduction(gl);
/*
 * Load history.
 */
#ifndef WITHOUT_FILE_SYSTEM
  (void) gl_load_history(gl, "~/.demo_history", "#");
#endif
/*
 * In this demo, rather than having gl_get_line() return immediately
 * when it would otherwise have to wait for I/O, we register a timeout
 * callback which causes gl_get_line() to give up waiting after a short
 * interval.
 */
  gl_inactivity_timeout(gl, demo_timeout_fn, NULL, 0, DEMO_IO_TIMEOUT);
/*
 * Install our signal handlers for process termination, suspension and
 * terminal resize signals. Ignore process continuation signals.
 */
  gl_tty_signals(demo_signal_handler, demo_signal_handler, SIG_DFL,
		 demo_signal_handler);
/*
 * Get a list of all of the signals that gl_get_line() currently catches.
 */
  gl_list_signals(gl, &all_signal_mask);
/*
 * Switch gl_get_line() to non-blocking server mode.
 */
  if(gl_io_mode(gl, GL_SERVER_MODE))
    cleanup_and_exit(gl, si, 1);
/*
 * Instruct gl_get_line() to unblock any signals that it catches
 * while waiting for input. Note that in non-blocking server mode,
 * this is only necessary when using gl_inactivity_timeout() to make
 * gl_get_line() block for a non-zero amount of time.
 */
  gl_catch_blocked(gl);
/*
 * Enter the event loop.
 */
  while(1) {
    int nready;        /* The number of file-descriptors that are */
                       /*  ready for I/O */
    fd_set rfds;       /* The set of file descriptors to watch for */
                       /*  readability */
    fd_set wfds;       /* The set of file descriptors to watch for */
                       /*  writability */
/*
 * Construct the sets of file descriptors to be watched by select(),
 * starting from empty sets.
 */
    FD_ZERO(&rfds);
    FD_ZERO(&wfds);
/*
 * To ensure that no signals are received whos handlers might change
 * the requirements for the contents of the above signal sets, block
 * all of the signals that we are handling.
 */
    sigprocmask(SIG_BLOCK, &all_signal_mask, NULL);
/*
 * Depending on which direction of I/O gl_get_line()s is currently
 * waiting for, add the terminal file descriptor to either the set
 * of file descriptors to watch for readability, or those to watch
 * for writability. Note that at the start of a new line, such as
 * after an error, or the return of a completed line, we need to
 * wait for writability, so that a prompt can be written.
 */
    switch(gl_pending_io(gl)) {
    case GLP_READ:
      FD_SET(STDIN_FILENO, &rfds);
      break;
    default:
      FD_SET(STDIN_FILENO, &wfds);
      break;
    };
/*
 * Wait for I/O to become possible on the selected file descriptors.
 * The following is a signal-aware wrapper around the select() system
 * call. This wrapper guarantees that if any of the signals marked in
 * all_signal_mask arrive after the statement above where we blocked
 * these signals, it will detect this and abort with nready=-1 and
 * errno=EINTR. If instead, we just unblocked the above signals just
 * before calling a normal call to select(), there would be a small
 * window of time between those two statements in which a signal could
 * arrive without aborting select(). This would be a problem, since
 * the functions called by our signal handler may change the type
 * of I/O that gl_get_line() wants us to wait for in select().
 */
    nready = demo_sigselect(STDIN_FILENO + 1, &rfds, &wfds, NULL, NULL,
			    &all_signal_mask, si);
/*
 * We can now unblock our signals again.
 */
    sigprocmask(SIG_UNBLOCK, &all_signal_mask, NULL);
/*
 * Did an I/O error occur?
 */
    if(nready < 0 && errno != EINTR)
      cleanup_and_exit(gl, si, 1);
/*
 * If the terminal file descriptor is now ready for I/O, call
 * gl_get_line() to continue editing the current input line.
 */
    if(FD_ISSET(STDIN_FILENO, &rfds) || FD_ISSET(STDIN_FILENO, &wfds)) {
/*
 * Start or continue editing an input line.
 */
      char *line = gl_get_line(gl, "$ ", NULL, 0);
/*
 * Did the user finish entering a new line?
 */
      if(line) {
/*
 * Before writing messages to the terminal, start a new line and
 * switch back to normal terminal I/O.
 */
	gl_normal_io(gl);
/*
 * Display what was entered.
 */
	if(printf("You entered: %s", line) < 0 || fflush(stdout))
	  break;
/*
 * Implement a few simple commands.
 */
	if(strcmp(line, "exit\n")==0)
	  cleanup_and_exit(gl, si, 0);
	else if(strcmp(line, "history\n")==0)
	  gl_show_history(gl, stdout, "%N  %T   %H\n", 0, -1);
	else if(strcmp(line, "size\n")==0) {
	  GlTerminalSize size = gl_terminal_size(gl, 80, 24);
	  printf("Terminal size = %d columns x %d lines.\n", size.ncolumn,
		 size.nline);
	} else if(strcmp(line, "clear\n")==0) {
	  if(gl_erase_terminal(gl))
	    return 1;
	};
/*
 * To resume command-line editing, return the terminal to raw,
 * non-blocking I/O mode.
 */
	gl_raw_io(gl);
/*
 * If gl_get_line() returned NULL because of an error or end-of-file,
 * abort the program.
 */
      } else if(gl_return_status(gl) == GLR_ERROR ||
		gl_return_status(gl) == GLR_EOF) {
	cleanup_and_exit(gl, si, 1);
      };
    };
  };
#endif
  return 0;
}

/*.......................................................................
 * This function is called to return resources to the system and restore
 * the terminal to its original state before exiting the process.
 *
 * Input:
 *  gl        GetLine *   The line editor.
 *  si  SignalActions *   The repository for displaced signal handlers.
 *  status        int     The exit code of the process.
 */
static void cleanup_and_exit(GetLine *gl, SignalActions *si, int status)
{
/*
 * Restore the terminal to its original state before exiting the program.
 */
  gl_normal_io(gl);
/*
 * Save historical command lines.
 */
#ifndef WITHOUT_FILE_SYSTEM
  (void) gl_save_history(gl, "~/.demo_history", "#", -1);
#endif
/*
 * Clean up.
 */
  gl = del_GetLine(gl);
  si = del_SignalActions(si);
/*
 * Exit the process.
 */
  exit(status);
}

/*.......................................................................
 * This is a signal-aware wrapper around the select() system call. It
 * is designed to facilitate reliable signal handling of a given set
 * of signals, without the race conditions that would usually surround
 * the use of select(). See the "RELIABLE SIGNAL HANDLING" section of
 * the gl_get_line(3) man page for further details.
 *
 * Provided that the calling function has blocked the specified set of
 * signals before calling this function, this function guarantees that
 * select() will be aborted by any signal that arrives between the
 * time that the caller blocked the specified signals and this
 * function returns. On return these signals will again be blocked to
 * prevent any signals that arrive after select() returns, from being
 * missed by the caller.
 *
 * Note that this function is written not to be specific to this
 * program, and is thus suitable for use in other programs, whether or
 * not they use gl_get_line().
 *
 * Also note that this function depends on the NSIG preprocessor
 * constant being >= the maximum number of signals available on the
 * host operating system. Under BSD and SysV, this macro is set
 * appropriately in signal.h. On other systems, a reasonably large
 * guess should be substituted. Although nothing terrible will happen
 * if a value that is too small is chosen, signal numbers that exceed
 * the specified value of NSIG will be ignored by this function. A
 * more robust method than depending on nsig would be to use the
 * POSIX sigismember() function to count valid signals, and use this
 * to allocate the array of sigaction structures used to preserve
 * 
 *
 * Input:
 *  n                   int    The number of file descriptors to pay
 *                             attention to at the start of each of the
 *                             following sets of file descriptors.
 *  readfds          fd_set *  The set of file descriptors to check for
 *                             readability, or NULL if not pertinent.
 *  wwritefds        fd_set *  The set of file descriptors to check for
 *                             writability, or NULL if not pertinent.
 *  exceptfds        fd_set *  The set of file descriptors to check for
 *                             the arrival of urgent data, or NULL if
 *                             not pertinent.
 *  timeout  struct timeval *  The maximum time that select() should
 *                             wait, or NULL to wait forever.
 *  mask           sigset_t *  The set of signals to catch.
 *  si       SignalHandlers *  An object in which to preserve temporary
 *                             copies signal handlers.
 * Output:
 *  return              int    > 0  The number of entries in all of the
 *                                  sets of descriptors that are ready
 *                                  for I/O.
 *                               0  Select() timed out.
 *                              -1  Error (see errno).
 */
static int demo_sigselect(int n, fd_set *readfds, fd_set *writefds,
			  fd_set *exceptfds, struct timeval *timeout,
			  sigset_t *mask, SignalActions *si)
{
/*
 * The reason that the the following variables are marked as volatile
 * is to prevent the compiler from placing their values in registers
 * that might not be saved and restored by sigsetjmp().
 */
  volatile sigset_t old_mask;  /* The displaced process signal mask */
  volatile int status;         /* The return value of select() */
/*
 * Make sure that all of the specified signals are blocked. This is
 * redundant if the caller has already blocked signals.
 */
  if(sigprocmask(SIG_BLOCK, mask, (sigset_t *) &old_mask) < 0)
    return -1;
/*
 * Record the fact that no signal has been caught yet.
 */
  demo_setjmp_signo = -1;
/*
 * Now set up the point where our temporary signal handlers will return
 * control if a signal is received.
 */
  if(sigsetjmp(demo_setjmp_buffer, 1) == 0) {
/*
 * Now install the temporary signal handlers that cause the above
 * sigsetjmp() to return non-zero when a signal is detected.
 */
    if(displace_signal_handlers(si, mask, demo_setjmp_handler)) {
      reinstate_signal_handlers(si);
      return 1;
    };
/*
 * Now that we are ready to catch the signals, unblock them.
 */
    sigprocmask(SIG_UNBLOCK, mask, NULL);
/*
 * At last, call select().
 */
    status = select(n, readfds, writefds, exceptfds, timeout);
/*
 * Block the specified signals again.
 */
    sigprocmask(SIG_BLOCK, mask, NULL);
/*
 * Record the fact that no signal was caught.
 */
    demo_setjmp_signo = -1;
  };
/*
 * We can get to this point in one of two ways. Either no signals were
 * caught, and the above block ran to completion (with demo_setjmp_signo=-1),
 * or a signal was caught that caused the above block to be aborted,
 * in which case demo_setjmp_signo will now equal the number of the signal that
 * was caught, and sigsetjmp() will have restored the process signal
 * mask to how it was before it was called (ie. all of the specified
 * signals blocked).
 *
 * First restore the signal handlers to how they were on entry to
 * this function.
 */
  reinstate_signal_handlers(si);
/*
 * Was a signal caught?
 */
  if(demo_setjmp_signo > 0) {
    sigset_t new_mask;
/*
 * Send the signal again, then unblock its delivery, so that the application's
 * signal handler gets invoked.
 */
    raise(demo_setjmp_signo);
    sigemptyset(&new_mask);
    sigaddset(&new_mask, demo_setjmp_signo);
    sigprocmask(SIG_UNBLOCK, &new_mask, NULL);
/*
 * Set the return status to show that a signal was caught.
 */
    errno = EINTR;
    status = -1;
  };
/*
 * Now restore the process signal mask to how it was on entry to this
 * function.
 */
  sigprocmask(SIG_SETMASK, (sigset_t *) &old_mask, NULL);
  return status;
}

/*.......................................................................
 * This is the main signal handler of this demonstration program. If a
 * SIGINT is received by the process, it arranges that the next call
 * to gl_get_line() will abort entry of the current line and start
 * entering a new one. Otherwise it calls the library function which
 * handles terminal resize signals and process suspension and process
 * termination signals. Both of the functions called by this signal
 * handler are designed to be async-signal safe, provided that the
 * rules laid out in the gl_io_mode(3) man page are followed.
 */
static void demo_signal_handler(int signo)
{
  if(signo==SIGINT)
    gl_abandon_line(demo_gl);
  else
    gl_handle_signal(signo, demo_gl, 1);
}

/*.......................................................................
 * The following signal handler is installed while select() is being
 * called from within a block of code protected by sigsetjmp(). It
 * simply records the signal that was caught in setjmp_signo, then
 * causes the sigsetjmp() to return non-zero.
 */
static void demo_setjmp_handler(int signo)
{
  demo_setjmp_signo = signo;
  siglongjmp(demo_setjmp_buffer, 1);
}

/*.......................................................................
 * This optional inactivity timeout function is used in this
 * demonstration to cause gl_get_line() to wait for a small amount of
 * time for I/O, before returning and allowing the event loop to
 * continue. This isn't needed if you want gl_get_line() to return
 * immediately, rather than blocking.
 */
static GL_TIMEOUT_FN(demo_timeout_fn)
{
  return GLTO_CONTINUE;
}

/*.......................................................................
 * Display introductory text to the user, formatted according to the
 * current terminal width and enclosed in a box of asterixes.
 *
 * Input:
 *  gl      GetLine *   The resource object of gl_get_line().
 */
static void show_demo_introduction(GetLine *gl)
{
  int start;     /* The column in which gl_display_text() left the cursor */
  int i;
/*
 * Break the indtroductory text into an array of strings, so as to
 * avoid overflowing any compiler string limits.
 */
  const char *doc[] = {
    "To the user this program appears to act identically to the main ",
    "demo program. However whereas the code underlying the main demo ",
    "program uses gl_get_line() in its default configuration, where each ",
    "call blocks the caller until the user has entered a complete input ",
    "line, demo3 uses gl_get_line() in its non-blocking server mode, ",
    "where it must be called repeatedly from an external ",
    "event loop to incrementally accept entry of the input ",
    "line, as and when terminal I/O becomes possible. The well commented ",
    "source code of demo3, which can be found in demo3.c, thus provides ",
    "a working example of how to use gl_get_line() in a manner that ",
    "doesn't block the caller. Documentation of this mode can be found ",
    "in the gl_io_mode(3) man page.\n"
  };
/*
 * Form the top line of the documentation box by filling the area of
 * the line between a " *" prefix and a "* " suffix with asterixes.
 */
  printf("\n");
  gl_display_text(gl, 0, " *", "* ", '*', 80, 0, "\n");
/*
 * Justify the documentation text within margins of asterixes.
 */
  for(start=0,i=0; i= 0; i++)
    start = gl_display_text(gl, 0, " * ", " * ", ' ', 80, start,doc[i]);
/*
 * Draw the bottom line of the documentation box.
 */
  gl_display_text(gl, 0, " *", "* ", '*', 80, 0, "\n");
  printf("\n");
}


/*.......................................................................
 * This is a constructor function for an object who's role is to allow
 * a signal handler to be assigned to potentially all available signals,
 * while preserving a copy of the original signal handlers, for later
 * restration.
 *
 * Output:
 *  return  SignalActions *  The new object, or NULL on error.
 */
static SignalActions *new_SignalActions(void)
{
  SignalActions *si;  /* The object to be returned */
/*
 * Allocate the container.
 */
  si = malloc(sizeof(SignalActions));
  if(!si) {
    fprintf(stderr, "new_SignalActions: Insufficient memory.\n");
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_SignalActions().
 */
  si->nsignal = 0;
  sigemptyset(&si->mask);
  si->actions = NULL;
/*
 * Count the number of signals that are available of the host
 * platform. Note that si->mask has no members set, and that
 * sigismember() is defined to return -1 if the signal number
 * isn't valid.
 */
  for(si->nsignal=1; sigismember(&si->mask, si->nsignal) == 0; si->nsignal++)
    ;
/*
 * Allocate the array of sigaction structures to use to keep a record
 * of displaced signal handlers.
 */
  si->actions = (struct sigaction *) malloc(sizeof(*si->actions) * si->nsignal);
  if(!si->actions) {
    fprintf(stderr, "Insufficient memory for %d sigaction structures.\n",
	    si->nsignal);
    return del_SignalActions(si);
  };
  return si;
}

/*.......................................................................
 * Delete a SignalActions object.
 *
 * Input:
 *  si     SignalActions *  The object to be deleted.
 * Output:
 *  return SignalActions *  The deleted object (always NULL).
 */
static SignalActions *del_SignalActions(SignalActions *si)
{
  if(si) {
    if(si->actions)
      free(si->actions);
    free(si);
  };
  return NULL;
}

/*.......................................................................
 * Replace the signal handlers of all of the signals in 'mask' with
 * the signal handler 'handler'.
 *
 * Input:
 *  si       SignalActions *     The object in which to record the displaced
 *                               signal handlers.
 *  mask          sigset_t *     The set of signals who's signal handlers
 *                               should be displaced.
 *  handler void (*handler)(int) The new signal handler to assign to each
 *                               of the signals marked in 'mask'.
 * Output:
 *  return             int       0 - OK.
 *                               1 - Error.
 */
static int displace_signal_handlers(SignalActions *si, sigset_t *mask,
				    void (*handler)(int))
{
  int signo;                /* A signal number */
  struct sigaction action;  /* The new signal handler */
/*
 * Mark the fact that so far we haven't displaced any signal handlers.
 */
  sigemptyset(&si->mask);
/*
 * Set up the description of the new signal handler. Note that
 * we make sa_mask=mask. This ensures that only one instance of the
 * signal handler will ever be running at one time.
 */
  action.sa_handler = handler;
  memcpy(&action.sa_mask, mask, sizeof(*mask));
  action.sa_flags = 0;
/*
 * Check each of the available signals to see if it is specified in 'mask'.
 * If so, install the new signal handler, record the displaced one in
 * the corresponding element of si->actions[], and make a record in
 * si->mask that this signal handler has been displaced.
 */
  for(signo=1; signo < si->nsignal; signo++) {
    if(sigismember(mask, signo)) {
      if(sigaction(signo, &action, &si->actions[signo]) < 0) {
	fprintf(stderr, "sigaction error (%s)\n", strerror(errno));
	return 1;
      };
      sigaddset(&si->mask, signo);
    };
  };
  return 0;
}

/*.......................................................................
 * Reinstate any signal handlers displaced by displace_signal_handlers().
 *
 * Input:
 *  sig   SignalActions *  The object containing the displaced signal
 *                         handlers.
 * Output:
 *  return          int    0 - OK.
 *                         1 - Error.
 */
static int reinstate_signal_handlers(SignalActions *si)
{
  int signo;                /* A signal number */
/*
 * Check each of the available signals to see if it is specified in
 * si->mask. If so, reinstate the displaced recorded in the
 * corresponding element of si->actions[], and make a record in
 * si->mask that this signal handler has been reinstated.
 */
  for(signo=1; signo < si->nsignal; signo++) {
    if(sigismember(&si->mask, signo)) {
      if(sigaction(signo, &si->actions[signo], NULL) < 0) {
	fprintf(stderr, "sigaction error (%s)\n", strerror(errno));
	return 1;
      };
      sigdelset(&si->mask, signo);
    };
  };
  return 0;
}
genometools-1.5.1/src/external/libtecla-1.6.1/direader.c000066400000000000000000000201141211610345200226160ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * If file-system access is to be excluded, this module has no function,
 * so all of its code should be excluded.
 */
#ifndef WITHOUT_FILE_SYSTEM

/*
 * Standard includes.
 */
#include 
#include 
#include 
#include 

/*
 * Operating system includes.
 */
#include 
#include 
#include 
#include 

#include "direader.h"
#include "errmsg.h"

/*
 * Use the reentrant POSIX threads version of readdir()?
 */
#if defined(PREFER_REENTRANT) && defined(_POSIX_C_SOURCE) && _POSIX_C_SOURCE >= 199506L
#define USE_READDIR_R 1
#endif

/*
 * Objects of the following type are used to maintain the resources
 * needed to read directories.
 */
struct DirReader {
  ErrMsg *err;             /* The error reporting buffer */
  DIR *dir;                /* The directory stream (if open, NULL otherwise) */
  struct dirent *file;     /* The latest directory entry */
#ifdef USE_READDIR_R
  struct dirent *buffer;   /* A buffer used by the threaded version of */
                           /*  readdir() */
  int buffer_dim;          /* The allocated size of buffer[] */
#endif
};

static int _dr_path_is_dir(const char *pathname);

/*.......................................................................
 * Create a new DirReader object.
 *
 * Output:
 *  return  DirReader *  The new object, or NULL on error.
 */
DirReader *_new_DirReader(void)
{
  DirReader *dr;  /* The object to be returned */
/*
 * Allocate the container.
 */
  dr = (DirReader *) malloc(sizeof(DirReader));
  if(!dr) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to _del_DirReader().
 */
  dr->err = NULL;
  dr->dir = NULL;
  dr->file = NULL;
#ifdef USE_READDIR_R
  dr->buffer = NULL;
  dr->buffer_dim = 0;
#endif
/*
 * Allocate a place to record error messages.
 */
  dr->err = _new_ErrMsg();
  if(!dr->err)
    return _del_DirReader(dr);
  return dr;
}

/*.......................................................................
 * Delete a DirReader object.
 *
 * Input:
 *  dr     DirReader *  The object to be deleted.
 * Output:
 *  return DirReader *  The deleted object (always NULL).
 */
DirReader *_del_DirReader(DirReader *dr)
{
  if(dr) {
    _dr_close_dir(dr);
#ifdef USE_READDIR_R
    free(dr->buffer);
#endif
    dr->err = _del_ErrMsg(dr->err);
    free(dr);
  };
  return NULL;
}

/*.......................................................................
 * Open a new directory.
 *
 * Input:
 *  dr      DirReader *   The directory reader resource object.
 *  path   const char *   The directory to be opened.
 * Input/Output:
 *  errmsg       char **  If an error occurs and errmsg isn't NULL, a
 *                        pointer to an error description will be assigned
 *                        to *errmsg.
 * Output:
 *  return        int     0 - OK.
 *                        1 - Error (see *errmsg for a description).
 */
int _dr_open_dir(DirReader *dr, const char *path, char **errmsg)
{
  DIR *dir = NULL;   /* The directory stream */
/*
 * If a directory is already open, close it first.
 */
  (void) _dr_close_dir(dr);
/*
 * Is the path a directory?
 */
  if(!_dr_path_is_dir(path)) {
    if(errmsg) {
      _err_record_msg(dr->err, "Can't open directory: ", path, END_ERR_MSG);
      *errmsg = _err_get_msg(dr->err);
    };
    return 1;
  };
/*
 * Attempt to open the directory.
 */
  dir = opendir(path);
  if(!dir) {
    if(errmsg) {
      _err_record_msg(dr->err, "Can't open directory: ", path, END_ERR_MSG);
      *errmsg = _err_get_msg(dr->err);
    };
    return 1;
  };
/*
 * If using POSIX threads, allocate a buffer for readdir_r().
 */
#ifdef USE_READDIR_R
  {
    size_t size;
    int name_max = pathconf(path, _PC_NAME_MAX);
#ifdef NAME_MAX
    if(name_max < 0)
      name_max = NAME_MAX;
#endif
    if(name_max < 0) {
      if(errmsg) {
	_err_record_msg(dr->err, "Unable to deduce readdir() buffer size.",
			END_ERR_MSG);
	*errmsg = _err_get_msg(dr->err);
      };
      closedir(dir);
      return 1;
    };
/*
 * How big a buffer do we need to allocate?
 */
    size = sizeof(struct dirent) + name_max;
/*
 * Extend the buffer?
 */
    if(size > dr->buffer_dim || !dr->buffer) {
      struct dirent *buffer = (struct dirent *) (dr->buffer ?
						 realloc(dr->buffer, size) :
						 malloc(size));
      if(!buffer) {
	if(errmsg) {
	  _err_record_msg(dr->err, "Insufficient memory for readdir() buffer.",
			  END_ERR_MSG);
	  *errmsg = _err_get_msg(dr->err);
	};
	closedir(dir);
	errno = ENOMEM;
	return 1;
      };
      dr->buffer = buffer;
      dr->buffer_dim = size;
    };
  };
#endif
/*
 * Record the successfully opened directory.
 */
  dr->dir = dir;
  return 0;
}

/*.......................................................................
 * If the DirReader object is currently contains an open directory,
 * close it.
 *
 * Input:
 *  dr    DirReader *   The directory reader resource object.
 */
void _dr_close_dir(DirReader *dr)
{
  if(dr && dr->dir) {
    closedir(dr->dir);
    dr->dir = NULL;
    dr->file = NULL;
    _err_clear_msg(dr->err);
  };
}

/*.......................................................................
 * Read the next file from the directory opened with _dr_open_dir().
 *
 * Input:
 *  dr    DirReader *  The directory reader resource object.
 * Output:
 *  return     char *  The name of the new file, or NULL if we reached
 *                     the end of the directory.
 */
char *_dr_next_file(DirReader *dr)
{
/*
 * Are we currently reading a directory?
 */
  if(dr->dir) {
/*
 * Read the next directory entry.
 */
#ifdef USE_READDIR_R 
    if(readdir_r(dr->dir, dr->buffer, &dr->file) == 0 && dr->file)
      return dr->file->d_name;
#else
    dr->file = readdir(dr->dir);
    if(dr->file)
      return dr->file->d_name;
#endif
  };
/*
 * When the end of a directory is reached, close it.
 */
  _dr_close_dir(dr);
  return NULL;
}

/*.......................................................................
 * Return 1 if the specified pathname refers to a directory.
 *
 * Input:
 *  pathname  const char *  The path to test.
 * Output:
 *  return           int    0 - Not a directory.
 *                          1 - pathname[] refers to a directory.
 */
static int _dr_path_is_dir(const char *pathname)
{
  struct stat statbuf;    /* The file-statistics return buffer */
/*
 * Look up the file attributes.
 */
  if(stat(pathname, &statbuf) < 0)
    return 0;
/*
 * Is the file a directory?
 */
  return S_ISDIR(statbuf.st_mode) != 0;
}

#endif  /* ifndef WITHOUT_FILE_SYSTEM */
genometools-1.5.1/src/external/libtecla-1.6.1/direader.h000066400000000000000000000035701211610345200226320ustar00rootroot00000000000000#ifndef dirreader_h
#define dirreader_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

typedef struct DirReader DirReader;

DirReader *_new_DirReader(void);
DirReader *_del_DirReader(DirReader *dr);

int _dr_open_dir(DirReader *dr, const char *pathname, char **errmsg);
char *_dr_next_file(DirReader *dr);
void _dr_close_dir(DirReader *dr);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/enhance.c000066400000000000000000000520141211610345200224440ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include 

#include 
#include 

#ifdef HAVE_SELECT
#ifdef HAVE_SYS_SELECT_H
#include 
#endif
#endif

#include 
#include 
#include 
#include 
#include 

#if HAVE_SYSV_PTY
#include     /* System-V stream I/O */
char *ptsname(int fd);
int grantpt(int fd);
int unlockpt(int fd);
#endif

#include "libtecla.h"

/*
 * Pseudo-terminal devices are found in the following directory.
 */
#define PTY_DEV_DIR "/dev/"

/*
 * Pseudo-terminal controller device file names start with the following
 * prefix.
 */
#define PTY_CNTRL "pty"

/*
 * Pseudo-terminal slave device file names start with the following
 * prefix.
 */
#define PTY_SLAVE "tty"

/*
 * Specify the maximum suffix length for the control and slave device
 * names.
 */
#define PTY_MAX_SUFFIX 10

/*
 * Set the maximum length of the master and slave terminal device filenames,
 * including space for a terminating '\0'.
 */
#define PTY_MAX_NAME (sizeof(PTY_DEV_DIR)-1 + \
		      (sizeof(PTY_SLAVE) > sizeof(PTY_CNTRL) ? \
		       sizeof(PTY_SLAVE) : sizeof(PTY_CNTRL))-1 \
		      + PTY_MAX_SUFFIX + 1)
/*
 * Set the maximum length of an input line.
 */
#define PTY_MAX_LINE 4096

/*
 * Set the size of the buffer used for accumulating bytes written by the
 * user's terminal to its stdout.
 */
#define PTY_MAX_READ 1000

/*
 * Set the amount of memory used to record history.
 */
#define PTY_HIST_SIZE 10000

/*
 * Set the timeout delay used to check for quickly arriving
 * sequential output from the application.
 */
#define PTY_READ_TIMEOUT 100000    /* micro-seconds */

static int pty_open_master(const char *prog, int *cntrl, char *slave_name);
static int pty_open_slave(const char *prog, char *slave_name);
static int pty_child(const char *prog, int slave, char *argv[]);
static int pty_parent(const char *prog, int cntrl);
static int pty_stop_parent(int waserr, int cntrl, GetLine *gl, char *rbuff);
static GL_FD_EVENT_FN(pty_read_from_program);
static int pty_write_to_fd(int fd, const char *string, int n);
static void pty_child_exited(int sig);
static int pty_master_readable(int fd, long usec);

/*.......................................................................
 * Run a program with enhanced terminal editing facilities.
 *
 * Usage:
 *  enhance program [args...]
 */
int main(int argc, char *argv[])
{
  int cntrl = -1;  /* The fd of the pseudo-terminal controller device */
  int slave = -1;  /* The fd of the pseudo-terminal slave device */
  pid_t pid;       /* The return value of fork() */
  int status;      /* The return statuses of the parent and child functions */
  char slave_name[PTY_MAX_NAME]; /* The filename of the slave end of the */
                                 /*  pseudo-terminal. */
  char *prog;      /* The name of the program (ie. argv[0]) */
/*
 * Check the arguments.
 */
  if(argc < 2) {
    fprintf(stderr, "Usage: %s  [arguments...]\n", argv[0]);
    return 1;
  };
/*
 * Get the name of the program.
 */
  prog = argv[0];
/*
 * If the user has the LC_CTYPE or LC_ALL environment variables set,
 * enable display of characters corresponding to the specified locale.
 */
  (void) setlocale(LC_CTYPE, "");
/*
 * If the program is taking its input from a pipe or a file, or
 * sending its output to something other than a terminal, run the
 * program without tecla.
 */
  if(!isatty(STDIN_FILENO) || !isatty(STDOUT_FILENO)) {
    if(execvp(argv[1], argv + 1) < 0) {
      fprintf(stderr, "%s: Unable to execute %s (%s).\n", prog, argv[1],
	      strerror(errno));
      fflush(stderr);
      _exit(1);
    };
  };
/*
 * Open the master side of a pseudo-terminal pair, and return
 * the corresponding file descriptor and the filename of the
 * slave end of the pseudo-terminal.
 */
  if(pty_open_master(prog, &cntrl, slave_name))
    return 1;
/*
 * Set up a signal handler to watch for the child process exiting.
 */
  signal(SIGCHLD, pty_child_exited);
/*
 * The above signal handler sends the parent process a SIGINT signal.
 * This signal is caught by gl_get_line(), which resets the terminal
 * settings, and if the application signal handler for this signal
 * doesn't abort the process, gl_get_line() returns NULL with errno
 * set to EINTR. Arrange to ignore the signal, so that gl_get_line()
 * returns and we have a chance to cleanup.
 */
  signal(SIGINT, SIG_IGN);
/*
 * We will read user input in one process, and run the user's program
 * in a child process.
 */
  pid = fork();
  if(pid < 0) {
    fprintf(stderr, "%s: Unable to fork child process (%s).\n", prog,
	    strerror(errno));
    return 1;
  };
/*
 * Are we the parent?
 */
  if(pid!=0) {
    status = pty_parent(prog, cntrl);
    close(cntrl);
  } else {
    close(cntrl); /* The child doesn't use the slave device */
    signal(SIGCHLD, pty_child_exited);
    if((slave = pty_open_slave(prog, slave_name)) >= 0) {
      status = pty_child(prog, slave, argv + 1);
      close(slave);
    } else {
      status = 1;
    };
  };
  return status;
}

/*.......................................................................
 * Open the master side of a pseudo-terminal pair, and return
 * the corresponding file descriptor and the filename of the
 * slave end of the pseudo-terminal.
 *
 * Input/Output:
 *  prog  const char *  The name of this program.
 *  cntrl        int *  The file descriptor of the pseudo-terminal
 *                      controller device will be assigned tp *cntrl.
 *  slave_name  char *  The file-name of the pseudo-terminal slave device
 *                      will be recorded in slave_name[], which must have
 *                      at least PTY_MAX_NAME elements.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 */
static int pty_open_master(const char *prog, int *cntrl, char *slave_name)
{
  char master_name[PTY_MAX_NAME]; /* The filename of the master device */
  DIR *dir;                       /* The directory iterator */
  struct dirent *file;            /* A file in "/dev" */
/*
 * Mark the controller device as not opened yet.
 */
  *cntrl = -1;
/*
 * On systems with the Sys-V pseudo-terminal interface, we don't
 * have to search for a free master terminal. We just open /dev/ptmx,
 * and if there is a free master terminal device, we are given a file
 * descriptor connected to it.
 */
#if HAVE_SYSV_PTY
  *cntrl = open("/dev/ptmx", O_RDWR);
  if(*cntrl >= 0) {
/*
 * Get the filename of the slave side of the pseudo-terminal.
 */
    char *name = ptsname(*cntrl);
    if(name) {
      if(strlen(name)+1 > PTY_MAX_NAME) {
	fprintf(stderr, "%s: Slave pty filename too long.\n", prog);
	return 1;
      };
      strcpy(slave_name, name);
/*
 * If unable to get the slave name, discard the controller file descriptor,
 * ready to try a search instead.
 */
    } else {
      close(*cntrl);
      *cntrl = -1;
    };
  } else {
#endif
/*
 * On systems without /dev/ptmx, or if opening /dev/ptmx failed,
 * we open one master terminal after another, until one that isn't
 * in use by another program is found.
 *
 * Open the devices directory.
 */
    dir = opendir(PTY_DEV_DIR);
    if(!dir) {
      fprintf(stderr, "%s: Couldn't open %s (%s)\n", prog, PTY_DEV_DIR,
	      strerror(errno));
      return 1;
    };
/*
 * Look for pseudo-terminal controller device files in the devices
 * directory.
 */
    while(*cntrl < 0 && (file = readdir(dir))) {
      if(strncmp(file->d_name, PTY_CNTRL, sizeof(PTY_CNTRL)-1) == 0) {
/*
 * Get the common extension of the control and slave filenames.
 */
	const char *ext = file->d_name + sizeof(PTY_CNTRL)-1;
	if(strlen(ext) > PTY_MAX_SUFFIX)
	  continue;
/*
 * Attempt to open the control file.
 */
	strcpy(master_name, PTY_DEV_DIR);
	strcat(master_name, PTY_CNTRL);
	strcat(master_name, ext);
	*cntrl = open(master_name, O_RDWR);
	if(*cntrl < 0)
	  continue;
/*
 * Attempt to open the matching slave file.
 */
	strcpy(slave_name, PTY_DEV_DIR);
	strcat(slave_name, PTY_SLAVE);
	strcat(slave_name, ext);
      };
    };
    closedir(dir);
#if HAVE_SYSV_PTY
  };
#endif
/*
 * Did we fail to find a pseudo-terminal pair that we could open?
 */
  if(*cntrl < 0) {
    fprintf(stderr, "%s: Unable to find a free pseudo-terminal.\n", prog);
    return 1;
  };
/*
 * System V systems require the program that opens the master to
 * grant access to the slave side of the pseudo-terminal.
 */
#ifdef HAVE_SYSV_PTY
  if(grantpt(*cntrl) < 0 ||
     unlockpt(*cntrl) < 0) {
    fprintf(stderr, "%s: Unable to unlock terminal (%s).\n", prog,
	    strerror(errno));
    return 1;
  };
#endif
/*
 * Success.
 */
  return 0;
}

/*.......................................................................
 * Open the slave end of a pseudo-terminal.
 *
 * Input:
 *  prog   const char *  The name of this program.
 *  slave_name   char *  The filename of the slave device.
 * Output:
 *  return        int    The file descriptor of the successfully opened
 *                       slave device, or < 0 on error.
 */
static int pty_open_slave(const char *prog, char *slave_name)
{
  int fd;  /* The file descriptor of the slave device */
/*
 * Place the process in its own process group. In system-V based
 * OS's, this ensures that when the pseudo-terminal is opened, it
 * becomes the controlling terminal of the process.
 */
  if(setsid() < 0) {
    fprintf(stderr, "%s: Unable to form new process group (%s).\n", prog,
	    strerror(errno));
    return -1;
  };
/*
 * Attempt to open the specified device.
 */
  fd = open(slave_name, O_RDWR);
  if(fd < 0) {
    fprintf(stderr, "%s: Unable to open pseudo-terminal slave device (%s).\n",
	    prog, strerror(errno));
    return -1;
  };
/*
 * On system-V streams based systems, we need to push the stream modules
 * that implement pseudo-terminal and termio interfaces. At least on
 * Solaris, which pushes these automatically when a slave is opened,
 * this is redundant, so ignore errors when pushing the modules.
 */
#if HAVE_SYSV_PTY
  (void) ioctl(fd, I_PUSH, "ptem");
  (void) ioctl(fd, I_PUSH, "ldterm");
/*
 * On BSD based systems other than SunOS 4.x, the following makes the
 * pseudo-terminal the controlling terminal of the child process.
 * According to the pseudo-terminal example code in Steven's
 * Advanced programming in the unix environment, the !defined(CIBAUD)
 * part of the clause prevents this from being used under SunOS. Since
 * I only have his code with me, and won't have access to the book,
 * I don't know why this is necessary.
 */
#elif defined(TIOCSCTTY) && !defined(CIBAUD)
  if(ioctl(fd, TIOCSCTTY, (char *) 0) < 0) {
    fprintf(stderr, "%s: Unable to establish controlling terminal (%s).\n",
	    prog, strerror(errno));
    close(fd);
    return -1;
  };
#endif
  return fd;
}

/*.......................................................................
 * Read input from the controlling terminal of the program, using
 * gl_get_line(), and feed it to the user's program running in a child
 * process, via the controller side of the pseudo-terminal. Also pass
 * data received from the user's program via the conroller end of
 * the pseudo-terminal, to stdout.
 *
 * Input:
 *  prog  const char *  The name of this program.
 *  cntrl        int    The file descriptor of the controller end of the
 *                      pseudo-terminal.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 */
static int pty_parent(const char *prog, int cntrl)
{
  GetLine *gl = NULL;  /* The gl_get_line() resource object */
  char *line;          /* An input line read from the user */
  char *rbuff=NULL;    /* A buffer for reading from the pseudo terminal */
/*
 * Allocate the gl_get_line() resource object.
 */
  gl = new_GetLine(PTY_MAX_LINE, PTY_HIST_SIZE);
  if(!gl)
    return pty_stop_parent(1, cntrl, gl, rbuff);
/*
 * Allocate a buffer to use to accumulate bytes read from the
 * pseudo-terminal.
 */
  rbuff = (char *) malloc(PTY_MAX_READ+1);
  if(!rbuff)
    return pty_stop_parent(1, cntrl, gl, rbuff);
  rbuff[0] = '\0';
/*
 * Register an event handler to watch for data appearing from the
 * user's program on the controller end of the pseudo terminal.
 */
  if(gl_watch_fd(gl, cntrl, GLFD_READ, pty_read_from_program, rbuff))
    return pty_stop_parent(1, cntrl, gl, rbuff);
/*
 * Read input lines from the user and pass them on to the user's program,
 * by writing to the controller end of the pseudo-terminal.
 */
  while((line=gl_get_line(gl, rbuff, NULL, 0))) {
    if(pty_write_to_fd(cntrl, line, strlen(line)))
       return pty_stop_parent(1, cntrl, gl, rbuff);
    rbuff[0] = '\0';
  };
  return pty_stop_parent(0, cntrl, gl, rbuff);
}

/*.......................................................................
 * This is a private return function of pty_parent(), used to release
 * dynamically allocated resources, close the controller end of the
 * pseudo-terminal, and wait for the child to exit. It returns the
 * exit status of the child process, unless the caller reports an
 * error itself, in which case the caller's error status is returned.
 *
 * Input:
 *  waserr   int    True if the caller is calling this function because
 *                  an error occured.
 *  cntrl    int    The file descriptor of the controller end of the
 *                  pseudo-terminal.
 *  gl   GetLine *  The resource object of gl_get_line().
 *  rbuff   char *  The buffer used to accumulate bytes read from
 *                  the pseudo-terminal.
 * Output:
 *  return  int    The desired exit status of the program.
 */
static int pty_stop_parent(int waserr, int cntrl, GetLine *gl, char *rbuff)
{
  int status;  /* The return status of the child process */
/*
 * Close the controller end of the terminal.
 */
  close(cntrl);
/*
 * Delete the resource object.
 */
  gl = del_GetLine(gl);
/*
 * Delete the read buffer.
 */
  if(rbuff)
    free(rbuff);
/*
 * Wait for the user's program to end.
 */
  (void) wait(&status);
/*
 * Return either our error status, or the return status of the child
 * program.
 */
  return waserr ? 1 : status;
}

/*.......................................................................
 * Run the user's program, with its stdin and stdout connected to the
 * slave end of the psuedo-terminal.
 *
 * Input:
 *  prog  const char *   The name of this program.
 *  slave        int     The file descriptor of the slave end of the
 *                       pseudo terminal.
 *  argv        char *[] The argument vector to pass to the user's program,
 *                       where argv[0] is the name of the user's program,
 *                       and the last argument is followed by a pointer
 *                       to NULL.
 * Output:
 *  return   int         If this function returns at all, an error must
 *                       have occured when trying to overlay the process
 *                       with the user's program. In this case 1 is
 *                       returned.
 */
static int pty_child(const char *prog, int slave, char *argv[])
{
  struct termios attr; /* The terminal attributes */
/*
 * We need to stop the pseudo-terminal from echoing everything that we send it.
 */
  if(tcgetattr(slave, &attr)) {
    fprintf(stderr, "%s: Can't get pseudo-terminal attributes (%s).\n", prog,
	    strerror(errno));
    return 1;
  };
  attr.c_lflag &= ~(ECHO);
  while(tcsetattr(slave, TCSADRAIN, &attr)) {
    if(errno != EINTR) {
      fprintf(stderr, "%s: tcsetattr error: %s\n", prog, strerror(errno));
      return 1;
    };
  };
/*
 * Arrange for stdin, stdout and stderr to be connected to the slave device,
 * ignoring errors that imply that either stdin or stdout is closed.
 */
  while(dup2(slave, STDIN_FILENO) < 0 && errno==EINTR)
    ;
  while(dup2(slave, STDOUT_FILENO) < 0 && errno==EINTR)
    ;
  while(dup2(slave, STDERR_FILENO) < 0 && errno==EINTR)
    ;
/*
 * Run the user's program.
 */
  if(execvp(argv[0], argv) < 0) {
    fprintf(stderr, "%s: Unable to execute %s (%s).\n", prog, argv[0],
	    strerror(errno));
    fflush(stderr);
    _exit(1);
  };
  return 0;  /* This should never be reached */
}

/*.......................................................................
 * This is the event-handler that is called by gl_get_line() whenever
 * there is tet waiting to be read from the user's program, via the
 * controller end of the pseudo-terminal. See libtecla.h for details
 * about its arguments.
 */
static GL_FD_EVENT_FN(pty_read_from_program)
{
  char *nlptr;   /* A pointer to the last newline in the accumulated string */
  char *crptr;   /* A pointer to the last '\r' in the accumulated string */
  char *nextp;   /* A pointer to the next unprocessed character */
/*
 * Get the read buffer in which we are accumulating a line to be
 * forwarded to stdout.
 */
  char *rbuff = (char *) data;
/*
 * New data may arrive while we are processing the current read, and
 * it is more efficient to display this here than to keep returning to
 * gl_get_line() and have it display the latest prefix as a prompt,
 * followed by the current input line, so we loop, delaying a bit at
 * the end of each iteration to check for more data arriving from
 * the application, before finally returning to gl_get_line() when
 * no more input is available.
 */
  do {
/*
 * Get the current length of the output string.
 */
    int len = strlen(rbuff);
/*
 * Read the text from the program.
 */
    int nnew = read(fd, rbuff + len, PTY_MAX_READ - len);
    if(nnew < 0)
      return GLFD_ABORT;
    len += nnew;
/*
 * Nul terminate the accumulated string.
 */
    rbuff[len] = '\0';
/*
 * Find the last newline and last carriage return in the buffer, if any.
 */
    nlptr = strrchr(rbuff, '\n');
    crptr = strrchr(rbuff, '\r');
/*
 * We want to output up to just before the last newline or carriage
 * return. If there are no newlines of carriage returns in the line,
 * and the buffer is full, then we should output the whole line. In
 * all cases a new output line will be started after the latest text
 * has been output. The intention is to leave any incomplete line
 * in the buffer, for (perhaps temporary) use as the current prompt.
 */
    if(nlptr) {
      nextp = crptr && crptr < nlptr ? crptr : nlptr;
    } else if(crptr) {
      nextp = crptr;
    } else if(len >= PTY_MAX_READ) {
      nextp = rbuff + len;
    } else {
      nextp = NULL;
    };
/*
 * Do we have any text to output yet?
 */
    if(nextp) {
/*
 * If there was already some text in rbuff before this function
 * was called, then it will have been used as a prompt. Arrange
 * to rewrite this prefix, plus the new suffix, by moving back to
 * the start of the line.
 */
      if(len > 0)
	(void) pty_write_to_fd(STDOUT_FILENO, "\r", 1);
/*
 * Write everything up to the last newline to stdout.
 */
      (void) pty_write_to_fd(STDOUT_FILENO, rbuff, nextp - rbuff);
/*
 * Start a new line.
 */
      (void) pty_write_to_fd(STDOUT_FILENO, "\r\n", 2);
/*
 * Skip trailing carriage returns and newlines.
 */
      while(*nextp=='\n' || *nextp=='\r')
	nextp++;
/*
 * Move any unwritten text following the newline, to the start of the
 * buffer.
 */
      memmove(rbuff, nextp, len - (nextp - rbuff) + 1);
    };
  } while(pty_master_readable(fd, PTY_READ_TIMEOUT));
/*
 * Make the incomplete line in the output buffer the current prompt.
 */
  gl_replace_prompt(gl, rbuff);
  return GLFD_REFRESH;
}

/*.......................................................................
 * Write a given string to a specified file descriptor.
 *
 * Input:
 *  fd             int     The file descriptor to write to.
 *  string  const char *   The string to write (of at least 'n' characters).
 *  n              int     The number of characters to write.
 * Output:
 *  return         int     0 - OK.
 *                         1 - Error.
 */
static int pty_write_to_fd(int fd, const char *string, int n)
{
  int ndone = 0;  /* The number of characters written so far */
/*
 * Do as many writes as are needed to write the whole string.
 */
  while(ndone < n) {
    int nnew = write(fd, string + ndone, n - ndone);
    if(nnew > 0)
      ndone += nnew;
    else if(errno != EINTR)
      return 1;
  };
  return 0;
}

/*.......................................................................
 * This is the signal handler that is called when the child process
 * that is running the user's program exits for any reason. It closes
 * the slave end of the terminal, so that gl_get_line() in the parent
 * process sees an end of file.
 */
static void pty_child_exited(int sig)
{
  raise(SIGINT);
}

/*.......................................................................
 * Return non-zero after a given amount of time if there is data waiting
 * to be read from a given file descriptor.
 *
 * Input:
 *  fd        int  The descriptor to watch.
 *  usec     long  The number of micro-seconds to wait for input to
 *                 arrive before giving up.
 * Output:
 *  return    int  0 - No data is waiting to be read (or select isn't
 *                     available).
 *                 1 - Data is waiting to be read.
 */
static int pty_master_readable(int fd, long usec)
{
#if HAVE_SELECT
  fd_set rfds;             /* The set of file descriptors to check */
  struct timeval timeout;  /* The timeout */
  FD_ZERO(&rfds);
  FD_SET(fd, &rfds);
  timeout.tv_sec = 0;
  timeout.tv_usec = usec;
  return select(fd+1, &rfds, NULL, NULL, &timeout) == 1;
#else
  return 0;
#endif
}
genometools-1.5.1/src/external/libtecla-1.6.1/errmsg.c000066400000000000000000000114471211610345200223470ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include 
#include 
#include 
#include 

#include "errmsg.h"

/*
 * Encapsulate the error reporting buffer in an opaque object.
 */
struct ErrMsg {
  char msg[ERR_MSG_LEN+1];  /* An error message */
};

/*.......................................................................
 * Create a new error-message object.
 *
 * Output:
 *  return  ErrMsg *  The new object, or NULL on error.
 */
ErrMsg *_new_ErrMsg(void)
{
  ErrMsg *err;  /* The object to be returned */
/*
 * Allocate the container.
 */
  err = malloc(sizeof(ErrMsg));
  if(!err) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_ErrMsg().
 */
  err->msg[0] = '\0';
  return err;
}

/*.......................................................................
 * Delete an error-message object.
 *
 * Input:
 *  err     ErrMsg *  The object to be deleted.
 * Output:
 *  return  ErrMsg *  The deleted object (always NULL).
 */
ErrMsg *_del_ErrMsg(ErrMsg *err)
{
  if(err) {
    free(err);
  };
  return NULL;
}

/*.......................................................................
 * Record the concatenation of a list of string arguments in an error
 * message object. The last argument must be END_ERR_MSG to terminate
 * the argument list.
 *
 * Input:
 *  err      ErrMsg *   The error-message container.
 *  ...  const char *   Zero or more strings to be concatenated in buff[].
 *  ...  const char *   The last argument must always be END_ERR_MSG to
 *                      terminate the argument list.
 */
void _err_record_msg(ErrMsg *err, ...)
{
  va_list ap;         /* The variable argument list */
  const char *s;      /* The string being printed */
  size_t msglen = 0;  /* The total length of the message */
/*
 * Nowhere to record the result?
 */
  if(!err) {
    errno = EINVAL;
    return;
  };
/*
 * Concatenate the list of argument strings in err->msg[].
 */
  va_start(ap, err);
  while((s = va_arg(ap, const char *)) != END_ERR_MSG) {
/*
 * How much room is left in the output buffer (note that the output
 * buffer has ERR_MSG_LEN+1 elements).
 */
    int nleft = ERR_MSG_LEN - msglen;
/*
 * How long is the next string to be appended?
 */
    size_t slen = strlen(s);
/*
 * If there is any room left, append as much of the string
 * as will fit.
 */
    if(nleft > 0) {
      int nnew = slen < nleft ? slen : nleft;
      strncpy(err->msg + msglen, s, nnew);
      msglen += nnew;
    };
  };
  va_end(ap);
/*
 * Terminate the message.
 */
  err->msg[msglen] = '\0';
  return;
}

/*.......................................................................
 * Return a pointer to the error message buffer.
 *
 * Input:
 *  err     ErrMsg *  The container of the error message buffer.
 * Output:
 *  return    char *  The current error message, or NULL if err==NULL.
 */
char *_err_get_msg(ErrMsg *err)
{
  return err ? err->msg : NULL;
}

/*.......................................................................
 * Replace the current error message with an empty string.
 *
 * Input:
 *  err     ErrMsg *  The container of the error message buffer.
 */
void _err_clear_msg(ErrMsg *err)
{
  if(err)
    err->msg[0] = '\0';
}

genometools-1.5.1/src/external/libtecla-1.6.1/errmsg.h000066400000000000000000000056241211610345200223540ustar00rootroot00000000000000#ifndef errmsg_h
#define errmsg_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * Set the longest expected length of an error message (excluding its
 * '\0' terminator. Since any message over a nominal terminal width of
 * 80 characters is going to look a mess, it makes no sense to support
 * huge lengths. Note that many uses of strings declared with this
 * macro assume that it will be at least 81, so don't reduce it below
 * this limit.
 */
#define ERR_MSG_LEN 128

/*
 * Provide an opaque typedef to the error-message object.
 */
typedef struct ErrMsg ErrMsg;

/*
 * The following token is used to terminate the argument lists of calls
 * to _err_record_msg().
 */
#define END_ERR_MSG ((const char *)0)

/*
 * Allocate a new error-message buffer.
 */
ErrMsg *_new_ErrMsg(void);

/*
 * Delete an error message buffer.
 */
ErrMsg *_del_ErrMsg(ErrMsg *err);

/*
 * Concatenate a list of string arguments into the specified buffer, buff[],
 * which has an allocated size of buffdim characters.
 * The last argument must be END_ERR_MSG to terminate the argument list.
 */
void _err_record_msg(ErrMsg *err, ...);

/*
 * Replace the current error message with an empty string.
 */
void _err_clear_msg(ErrMsg *err);

/*
 * Return a pointer to the error message buffer. This is
 * a '\0' terminated character array containing ERR_MSG_LEN+1
 * elements.
 */
char *_err_get_msg(ErrMsg *err);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/expand.c000066400000000000000000001302401211610345200223200ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * If file-system access is to be excluded, this module has no function,
 * so all of its code should be excluded.
 */
#ifndef WITHOUT_FILE_SYSTEM

#include 
#include 
#include 
#include 

#include "freelist.h"
#include "direader.h"
#include "pathutil.h"
#include "homedir.h"
#include "stringrp.h"
#include "libtecla.h"
#include "ioutil.h"
#include "expand.h"
#include "errmsg.h"

/*
 * Specify the number of elements to extend the files[] array by
 * when it proves to be too small. This also sets the initial size
 * of the array.
 */
#define MATCH_BLK_FACT 256

/*
 * A list of directory iterators is maintained using nodes of the
 * following form.
 */
typedef struct DirNode DirNode;
struct DirNode {
  DirNode *next;       /* The next directory in the list */
  DirNode *prev;       /* The node that precedes this node in the list */
  DirReader *dr;       /* The directory reader object */
};

typedef struct {
  FreeList *mem;       /* Memory for DirNode list nodes */
  DirNode *head;       /* The head of the list of used and unused cache nodes */
  DirNode *next;       /* The next unused node between head and tail */
  DirNode *tail;       /* The tail of the list of unused cache nodes */
} DirCache;

/*
 * Specify how many directory cache nodes to allocate at a time.
 */
#define DIR_CACHE_BLK 20

/*
 * Set the maximum length allowed for usernames.
 */
#define USR_LEN 100

/*
 * Set the maximum length allowed for environment variable names.
 */
#define ENV_LEN 100

/*
 * Set the default number of spaces place between columns when listing
 * a set of expansions.
 */
#define EF_COL_SEP 2

struct ExpandFile {
  ErrMsg *err;            /* The error reporting buffer */
  StringGroup *sg;        /* A list of string segments in which */
                          /*  matching filenames are stored. */
  DirCache cache;         /* The cache of directory reader objects */
  PathName *path;         /* The pathname being matched */
  HomeDir *home;          /* Home-directory lookup object */
  int files_dim;          /* The allocated dimension of result.files[] */
  char usrnam[USR_LEN+1]; /* A user name */
  char envnam[ENV_LEN+1]; /* An environment variable name */
  FileExpansion result;   /* The container used to return the results of */
                          /*  expanding a path. */
};

static int ef_record_pathname(ExpandFile *ef, const char *pathname,
			      int remove_escapes);
static char *ef_cache_pathname(ExpandFile *ef, const char *pathname,
			       int remove_escapes);
static void ef_clear_files(ExpandFile *ef);

static DirNode *ef_open_dir(ExpandFile *ef, const char *pathname);
static DirNode *ef_close_dir(ExpandFile *ef, DirNode *node);
static char *ef_expand_special(ExpandFile *ef, const char *path, int pathlen);
static int ef_match_relative_pathname(ExpandFile *ef, DirReader *dr,
				      const char *pattern, int separate);
static int ef_matches_range(int c, const char *pattern, const char **endp);
static int ef_string_matches_pattern(const char *file, const char *pattern,
				      int xplicit, const char *nextp);
static int ef_cmp_strings(const void *v1, const void *v2);

/*
 * Encapsulate the formatting information needed to layout a
 * multi-column listing of expansions.
 */
typedef struct {
  int term_width;     /* The width of the terminal (characters) */
  int column_width;   /* The number of characters within in each column. */
  int ncol;           /* The number of columns needed */
  int nline;          /* The number of lines needed */
} EfListFormat;

/*
 * Given the current terminal width, and a list of file expansions,
 * determine how to best use the terminal width to display a multi-column
 * listing of expansions.
 */
static void ef_plan_listing(FileExpansion *result, int term_width,
			    EfListFormat *fmt);

/*
 * Display a given line of a multi-column list of file-expansions.
 */
static int ef_format_line(FileExpansion *result, EfListFormat *fmt, int lnum,
			  GlWriteFn *write_fn, void *data);

/*.......................................................................
 * Create the resources needed to expand filenames.
 *
 * Output:
 *  return  ExpandFile *  The new object, or NULL on error.
 */
ExpandFile *new_ExpandFile(void)
{
  ExpandFile *ef;  /* The object to be returned */
/*
 * Allocate the container.
 */
  ef = (ExpandFile *) malloc(sizeof(ExpandFile));
  if(!ef) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_ExpandFile().
 */
  ef->err = NULL;
  ef->sg = NULL;
  ef->cache.mem = NULL;
  ef->cache.head = NULL;
  ef->cache.next = NULL;
  ef->cache.tail = NULL;
  ef->path = NULL;
  ef->home = NULL;
  ef->result.files = NULL;
  ef->result.nfile = 0;
  ef->usrnam[0] = '\0';
  ef->envnam[0] = '\0';
/*
 * Allocate a place to record error messages.
 */
  ef->err = _new_ErrMsg();
  if(!ef->err)
    return del_ExpandFile(ef);
/*
 * Allocate a list of string segments for storing filenames.
 */
  ef->sg = _new_StringGroup(_pu_pathname_dim());
  if(!ef->sg)
    return del_ExpandFile(ef);
/*
 * Allocate a freelist for allocating directory cache nodes.
 */
  ef->cache.mem = _new_FreeList(sizeof(DirNode), DIR_CACHE_BLK);
  if(!ef->cache.mem)
    return del_ExpandFile(ef);
/*
 * Allocate a pathname buffer.
 */
  ef->path = _new_PathName();
  if(!ef->path)
    return del_ExpandFile(ef);
/*
 * Allocate an object for looking up home-directories.
 */
  ef->home = _new_HomeDir();
  if(!ef->home)
    return del_ExpandFile(ef);
/*
 * Allocate an array for files. This will be extended later if needed.
 */
  ef->files_dim = MATCH_BLK_FACT;
  ef->result.files = (char **) malloc(sizeof(ef->result.files[0]) *
				      ef->files_dim);
  if(!ef->result.files) {
    errno = ENOMEM;
    return del_ExpandFile(ef);
  };
  return ef;
}

/*.......................................................................
 * Delete a ExpandFile object.
 *
 * Input:
 *  ef     ExpandFile *  The object to be deleted.
 * Output:
 *  return ExpandFile *  The deleted object (always NULL).
 */
ExpandFile *del_ExpandFile(ExpandFile *ef)
{
  if(ef) {
    DirNode *dnode;
/*
 * Delete the string segments.
 */
    ef->sg = _del_StringGroup(ef->sg);
/*
 * Delete the cached directory readers.
 */
    for(dnode=ef->cache.head; dnode; dnode=dnode->next)
      dnode->dr = _del_DirReader(dnode->dr);
/*
 * Delete the memory from which the DirNode list was allocated, thus
 * deleting the list at the same time.
 */
    ef->cache.mem = _del_FreeList(ef->cache.mem, 1);
    ef->cache.head = ef->cache.tail = ef->cache.next = NULL;
/*
 * Delete the pathname buffer.
 */
    ef->path = _del_PathName(ef->path);
/*
 * Delete the home-directory lookup object.
 */
    ef->home = _del_HomeDir(ef->home);
/*
 * Delete the array of pointers to files.
 */
    if(ef->result.files) {
      free(ef->result.files);
      ef->result.files = NULL;
    };
/*
 * Delete the error report buffer.
 */
    ef->err = _del_ErrMsg(ef->err);
/*
 * Delete the container.
 */
    free(ef);
  };
  return NULL;
}

/*.......................................................................
 * Expand a pathname, converting ~user/ and ~/ patterns at the start
 * of the pathname to the corresponding home directories, replacing
 * $envvar with the value of the corresponding environment variable,
 * and then, if there are any wildcards, matching these against existing
 * filenames.
 *
 * If no errors occur, a container is returned containing the array of
 * files that resulted from the expansion. If there were no wildcards
 * in the input pathname, this will contain just the original pathname
 * after expansion of ~ and $ expressions. If there were any wildcards,
 * then the array will contain the files that matched them. Note that
 * if there were any wildcards but no existing files match them, this
 * is counted as an error and NULL is returned.
 *
 * The supported wildcards and their meanings are:
 *  *        -  Match any sequence of zero or more characters.
 *  ?        -  Match any single character.
 *  [chars]  -  Match any single character that appears in 'chars'.
 *              If 'chars' contains an expression of the form a-b,
 *              then any character between a and b, including a and b,
 *              matches. The '-' character looses its special meaning
 *              as a range specifier when it appears at the start
 *              of the sequence of characters.
 *  [^chars] -  The same as [chars] except that it matches any single
 *              character that doesn't appear in 'chars'.
 *
 * Wildcard expressions are applied to individual filename components.
 * They don't match across directory separators. A '.' character at
 * the beginning of a filename component must also be matched
 * explicitly by a '.' character in the input pathname, since these
 * are UNIX's hidden files.
 *
 * Input:
 *  ef         ExpandFile *  The pathname expansion resource object.
 *  path             char *  The path name to be expanded.
 *  pathlen           int    The length of the suffix of path[] that
 *                           constitutes the filename to be expanded,
 *                           or -1 to specify that the whole of the
 *                           path string should be used. Note that
 *                           regardless of the value of this argument,
 *                           path[] must contain a '\0' terminated
 *                           string, since this function checks that
 *                           pathlen isn't mistakenly too long.
 * Output:
 *  return  FileExpansion *  A pointer to a container within the given
 *                           ExpandFile object. This contains an array
 *                           of the pathnames that resulted from expanding
 *                           ~ and $ expressions and from matching any
 *                           wildcards, sorted into lexical order.
 *                           This container and its contents will be
 *                           recycled on subsequent calls, so if you need
 *                           to keep the results of two successive runs,
 *                           you will either have to allocate a private
 *                           copy of the array, or use two ExpandFile
 *                           objects.
 *
 *                           On error NULL is returned. A description
 *                           of the error can be acquired by calling the
 *                           ef_last_error() function.
 */
FileExpansion *ef_expand_file(ExpandFile *ef, const char *path, int pathlen)
{
  DirNode *dnode;       /* A directory-reader cache node */
  const char *dirname;  /* The name of the top level directory of the search */
  const char *pptr;     /* A pointer into path[] */
  int wild;             /* True if the path contains any wildcards */
/*
 * Check the arguments.
 */
  if(!ef || !path) {
    if(ef) {
      _err_record_msg(ef->err, "ef_expand_file: NULL path argument",
		      END_ERR_MSG);
    };
    errno = EINVAL;
    return NULL;
  };
/*
 * If the caller specified that the whole of path[] be matched,
 * work out the corresponding length.
 */
  if(pathlen < 0 || pathlen > strlen(path))
    pathlen = strlen(path);
/*
 * Discard previous expansion results.
 */
  ef_clear_files(ef);
/*
 * Preprocess the path, expanding ~/, ~user/ and $envvar references,
 * using ef->path as a work directory and returning a pointer to
 * a copy of the resulting pattern in the cache.
 */
  path = ef_expand_special(ef, path, pathlen);
  if(!path)
    return NULL;
/*
 * Clear the pathname buffer.
 */
  _pn_clear_path(ef->path);
/*
 * Does the pathname contain any wildcards?
 */
  for(wild=0,pptr=path; !wild && *pptr; pptr++) {
    switch(*pptr) {
    case '\\':                      /* Skip escaped characters */
      if(pptr[1])
	pptr++;
      break; 
    case '*': case '?': case '[':   /* A wildcard character? */
      wild = 1;
      break;
    };
  };
/*
 * If there are no wildcards to match, copy the current expanded
 * path into the output array, removing backslash escapes while doing so.
 */
  if(!wild) {
    if(ef_record_pathname(ef, path, 1))
      return NULL;
/*
 * Does the filename exist?
 */
    ef->result.exists = _pu_file_exists(ef->result.files[0]);
/*
 * Match wildcards against existing files.
 */
  } else {
/*
 * Only existing files that match the pattern will be returned in the
 * cache.
 */
    ef->result.exists = 1;
/*
 * Treat matching of the root-directory as a special case since it
 * isn't contained in a directory.
 */
    if(strcmp(path, FS_ROOT_DIR) == 0) {
      if(ef_record_pathname(ef, FS_ROOT_DIR, 0))
	return NULL;
    } else {
/*
 * What should the top level directory of the search be?
 */
      if(strncmp(path, FS_ROOT_DIR, FS_ROOT_DIR_LEN) == 0) {
	dirname = FS_ROOT_DIR;
	if(!_pn_append_to_path(ef->path, FS_ROOT_DIR, -1, 0)) {
	  _err_record_msg(ef->err, "Insufficient memory to record path",
			  END_ERR_MSG);
	  return NULL;
	};
	path += FS_ROOT_DIR_LEN;
      } else {
	dirname = FS_PWD;
      };
/*
 * Open the top-level directory of the search.
 */
      dnode = ef_open_dir(ef, dirname);
      if(!dnode)
	return NULL;
/*
 * Recursively match successive directory components of the path.
 */
      if(ef_match_relative_pathname(ef, dnode->dr, path, 0)) {
	dnode = ef_close_dir(ef, dnode);
	return NULL;
      };
/*
 * Cleanup.
 */
      dnode = ef_close_dir(ef, dnode);
    };
/*
 * No files matched?
 */
    if(ef->result.nfile < 1) {
      _err_record_msg(ef->err, "No files match", END_ERR_MSG);
      return NULL;
    };
/*
 * Sort the pathnames that matched.
 */
    qsort(ef->result.files, ef->result.nfile, sizeof(ef->result.files[0]),
	  ef_cmp_strings);
  };
/*
 * Return the result container.
 */
  return &ef->result;
}

/*.......................................................................
 * Attempt to recursively match the given pattern with the contents of
 * the current directory, descending sub-directories as needed.
 *
 * Input:
 *  ef      ExpandFile *  The pathname expansion resource object.
 *  dr       DirReader *  The directory reader object of the directory
 *                        to be searched.
 *  pattern const char *  The pattern to match with files in the current
 *                        directory.
 *  separate       int    When appending a filename from the specified
 *                        directory to ef->pathname, insert a directory
 *                        separator between the existing pathname and
 *                        the filename, unless separate is zero.
 * Output:
 *  return         int    0 - OK.
 *                        1 - Error.
 */
static int ef_match_relative_pathname(ExpandFile *ef, DirReader *dr,
				       const char *pattern, int separate)
{
  const char *nextp;  /* The pointer to the character that follows the part */
                      /*  of the pattern that is to be matched with files */
                      /*  in the current directory. */
  char *file;         /* The name of the file being matched */
  int pathlen;        /* The length of ef->pathname[] on entry to this */
                      /*  function */
/*
 * Record the current length of the pathname string recorded in
 * ef->pathname[].
 */
  pathlen = strlen(ef->path->name);
/*
 * Get a pointer to the character that follows the end of the part of
 * the pattern that should be matched to files within the current directory.
 * This will either point to a directory separator, or to the '\0' terminator
 * of the pattern string.
 */
  for(nextp=pattern; *nextp && strncmp(nextp, FS_DIR_SEP, FS_DIR_SEP_LEN) != 0;
      nextp++)
    ;
/*
 * Read each file from the directory, attempting to match it to the
 * current pattern.
 */
  while((file=_dr_next_file(dr)) != NULL) {
/*
 * Does the latest file match the pattern up to nextp?
 */
    if(ef_string_matches_pattern(file, pattern, file[0]=='.', nextp)) {
/*
 * Append the new directory entry to the current matching pathname.
 */
      if((separate && _pn_append_to_path(ef->path, FS_DIR_SEP, -1, 0)==NULL) ||
	 _pn_append_to_path(ef->path, file, -1, 0)==NULL) {
	_err_record_msg(ef->err, "Insufficient memory to record path",
			END_ERR_MSG);
	return 1;
      };
/*
 * If we have reached the end of the pattern, record the accumulated
 * pathname in the list of matching files.
 */
      if(*nextp == '\0') {
	if(ef_record_pathname(ef, ef->path->name, 0))
	  return 1;
/*
 * If the matching directory entry is a subdirectory, and the
 * next character of the pattern is a directory separator,
 * recursively call the current function to scan the sub-directory
 * for matches.
 */
      } else if(_pu_path_is_dir(ef->path->name) &&
		strncmp(nextp, FS_DIR_SEP, FS_DIR_SEP_LEN) == 0) {
/*
 * If the pattern finishes with the directory separator, then
 * record the pathame as matching.
 */
	if(nextp[FS_DIR_SEP_LEN] == '\0') {
	  if(ef_record_pathname(ef, ef->path->name, 0))
	    return 1;
/*
 * Match files within the directory.
 */
	} else {
	  DirNode *subdnode = ef_open_dir(ef, ef->path->name);
	  if(subdnode) {
	    if(ef_match_relative_pathname(ef, subdnode->dr,
					   nextp+FS_DIR_SEP_LEN, 1)) {
	      subdnode = ef_close_dir(ef, subdnode);
	      return 1;
	    };
	    subdnode = ef_close_dir(ef, subdnode);
	  };
	};
      };
/*
 * Remove the latest filename from the pathname string, so that
 * another matching file can be appended.
 */
      ef->path->name[pathlen] = '\0';
    };
  };
  return 0;
}

/*.......................................................................
 * Record a new matching filename.
 *
 * Input:
 *  ef        ExpandFile *  The filename-match resource object.
 *  pathname  const char *  The pathname to record.
 *  remove_escapes   int    If true, remove backslash escapes in the
 *                          recorded copy of the pathname.
 * Output:
 *  return           int     0 - OK.
 *                           1 - Error (ef->err will contain a
 *                                      description of the error).
 */
static int ef_record_pathname(ExpandFile *ef, const char *pathname,
			      int remove_escapes)
{
  char *copy;          /* The recorded copy of pathname[] */
/*
 * Attempt to make a copy of the pathname in the cache.
 */
  copy = ef_cache_pathname(ef, pathname, remove_escapes);
  if(!copy)
    return 1;
/*
 * If there isn't room to record a pointer to the recorded pathname in the
 * array of files, attempt to extend the array.
 */
  if(ef->result.nfile + 1 > ef->files_dim) {
    int files_dim = ef->files_dim + MATCH_BLK_FACT;
    char **files = (char **) realloc(ef->result.files,
				     files_dim * sizeof(files[0]));
    if(!files) {
      _err_record_msg(ef->err,
	     "Insufficient memory to record all of the matching filenames",
	     END_ERR_MSG);
      errno = ENOMEM;
      return 1;
    };
    ef->result.files = files;
    ef->files_dim = files_dim;
  };
/*
 * Record a pointer to the new match.
 */
  ef->result.files[ef->result.nfile++] = copy;
  return 0;
}

/*.......................................................................
 * Record a pathname in the cache.
 *
 * Input:
 *  ef       ExpandFile *  The filename-match resource object.
 *  pathname       char *  The pathname to record.
 *  remove_escapes  int    If true, remove backslash escapes in the
 *                         copy of the pathname.
 * Output:
 *  return         char *  The pointer to the copy of the pathname.
 *                         On error NULL is returned and a description
 *                         of the error is left in ef->err.
 */
static char *ef_cache_pathname(ExpandFile *ef, const char *pathname,
			       int remove_escapes)
{
  char *copy = _sg_store_string(ef->sg, pathname, remove_escapes);
  if(!copy)
    _err_record_msg(ef->err, "Insufficient memory to store pathname",
		    END_ERR_MSG);
  return copy;
}

/*.......................................................................
 * Clear the results of the previous expansion operation, ready for the
 * next.
 *
 * Input:
 *  ef    ExpandFile *  The pathname expansion resource object.
 */
static void ef_clear_files(ExpandFile *ef)
{
  _clr_StringGroup(ef->sg);
  _pn_clear_path(ef->path);
  ef->result.exists = 0;
  ef->result.nfile = 0;
  _err_clear_msg(ef->err);
  return;
}

/*.......................................................................
 * Get a new directory reader object from the cache.
 *
 * Input:
 *  ef        ExpandFile *  The pathname expansion resource object.
 *  pathname  const char *  The pathname of the directory.
 * Output:
 *  return       DirNode *  The cache entry of the new directory reader,
 *                          or NULL on error. On error, ef->err will
 *                          contain a description of the error.
 */
static DirNode *ef_open_dir(ExpandFile *ef, const char *pathname)
{
  char *errmsg = NULL;  /* An error message from a called function */
  DirNode *node;        /* The cache node used */
/*
 * Get the directory reader cache.
 */
  DirCache *cache = &ef->cache;
/*
 * Extend the cache if there are no free cache nodes.
 */
  if(!cache->next) {
    node = (DirNode *) _new_FreeListNode(cache->mem);
    if(!node) {
      _err_record_msg(ef->err, "Insufficient memory to open a new directory",
		      END_ERR_MSG);
      return NULL;
    };
/*
 * Initialize the cache node.
 */
    node->next = NULL;
    node->prev = NULL;
    node->dr = NULL;
/*
 * Allocate a directory reader object.
 */
    node->dr = _new_DirReader();
    if(!node->dr) {
      _err_record_msg(ef->err, "Insufficient memory to open a new directory",
		      END_ERR_MSG);
      node = (DirNode *) _del_FreeListNode(cache->mem, node);
      return NULL;
    };
/*
 * Append the node to the cache list.
 */
    node->prev = cache->tail;
    if(cache->tail)
      cache->tail->next = node;
    else
      cache->head = node;
    cache->next = cache->tail = node;
  };
/*
 * Get the first unused node, but don't remove it from the list yet.
 */
  node = cache->next;
/*
 * Attempt to open the specified directory.
 */
  if(_dr_open_dir(node->dr, pathname, &errmsg)) {
    _err_record_msg(ef->err, errmsg, END_ERR_MSG);
    return NULL;
  };
/*
 * Now that we have successfully opened the specified directory,
 * remove the cache node from the list, and relink the list around it.
 */
  cache->next = node->next;
  if(node->prev)
    node->prev->next = node->next;
  else
    cache->head = node->next;
  if(node->next)
    node->next->prev = node->prev;
  else
    cache->tail = node->prev;
  node->next = node->prev = NULL;
/*
 * Return the successfully initialized cache node to the caller.
 */
  return node;
}

/*.......................................................................
 * Return a directory reader object to the cache, after first closing
 * the directory that it was managing.
 *
 * Input:
 *  ef    ExpandFile *  The pathname expansion resource object.
 *  node     DirNode *  The cache entry of the directory reader, as returned
 *                      by ef_open_dir().
 * Output:
 *  return   DirNode *  The deleted DirNode (ie. allways NULL).
 */
static DirNode *ef_close_dir(ExpandFile *ef, DirNode *node)
{
/*
 * Get the directory reader cache.
 */
  DirCache *cache = &ef->cache;
/*
 * Close the directory.
 */
  _dr_close_dir(node->dr);
/*
 * Return the node to the tail of the cache list.
 */
  node->next = NULL;
  node->prev = cache->tail;
  if(cache->tail)
    cache->tail->next = node;
  else
    cache->head = cache->tail = node;
  if(!cache->next)
    cache->next = node;
  return NULL;
}

/*.......................................................................
 * Return non-zero if the specified file name matches a given glob
 * pattern.
 *
 * Input:
 *  file     const char *  The file-name component to be matched to the pattern.
 *  pattern  const char *  The start of the pattern to match against file[].
 *  xplicit         int    If non-zero, the first character must be matched
 *                         explicitly (ie. not with a wildcard).
 *  nextp    const char *  The pointer to the the character following the
 *                         end of the pattern in pattern[].
 * Output:
 *  return    int          0 - Doesn't match.
 *                         1 - The file-name string matches the pattern.
 */
static int ef_string_matches_pattern(const char *file, const char *pattern,
				      int xplicit, const char *nextp)
{
  const char *pptr = pattern; /* The pointer used to scan the pattern */
  const char *fptr = file;    /* The pointer used to scan the filename string */
/*
 * Match each character of the pattern in turn.
 */
  while(pptr < nextp) {
/*
 * Handle the next character of the pattern.
 */
    switch(*pptr) {
/*
 * A match zero-or-more characters wildcard operator.
 */
    case '*':
/*
 * Skip the '*' character in the pattern.
 */
      pptr++;
/*
 * If wildcards aren't allowed, the pattern doesn't match.
 */
      if(xplicit)
	return 0;
/*
 * If the pattern ends with a the '*' wildcard, then the
 * rest of the filename matches this.
 */
      if(pptr >= nextp)
	return 1;
/*
 * Using the wildcard to match successively longer sections of
 * the remaining characters of the filename, attempt to match
 * the tail of the filename against the tail of the pattern.
 */
      for( ; *fptr; fptr++) {
	if(ef_string_matches_pattern(fptr, pptr, 0, nextp))
	  return 1;
      };
      return 0; /* The pattern following the '*' didn't match */
      break;
/*
 * A match-one-character wildcard operator.
 */
    case '?':
/*
 * If there is a character to be matched, skip it and advance the
 * pattern pointer.
 */
      if(!xplicit && *fptr) {
        fptr++;
        pptr++;
/*
 * If we hit the end of the filename string, there is no character
 * matching the operator, so the string doesn't match.
 */
      } else {
        return 0;
      };
      break;
/*
 * A character range operator, with the character ranges enclosed
 * in matching square brackets.
 */
    case '[':
      if(xplicit || !ef_matches_range(*fptr++, ++pptr, &pptr))
        return 0;
      break;
/*
 * A backslash in the pattern prevents the following character as
 * being seen as a special character.
 */
    case '\\':
      pptr++;
      /* Note fallthrough to default */
/*
 * A normal character to be matched explicitly.
 */
    default:
      if(*fptr == *pptr) {
        fptr++;
        pptr++;
      } else {
        return 0;
      };
      break;
    };
/*
 * After passing the first character, turn off the explicit match
 * requirement.
 */
    xplicit = 0;
  };
/*
 * To get here the pattern must have been exhausted. If the filename
 * string matched, then the filename string must also have been
 * exhausted.
 */
  return *fptr == '\0';
}

/*.......................................................................
 * Match a character range expression terminated by an unescaped close
 * square bracket.
 *
 * Input:
 *  c               int     The character to be matched with the range
 *                          pattern.
 *  pattern  const char *   The range pattern to be matched (ie. after the
 *                          initiating '[' character).
 *  endp     const char **  On output a pointer to the character following the
 *                          range expression will be assigned to *endp.
 * Output:
 *  return          int     0 - Doesn't match.
 *                          1 - The character matched.
 */
static int ef_matches_range(int c, const char *pattern, const char **endp)
{
  const char *pptr = pattern;  /* The pointer used to scan the pattern */
  int invert = 0;              /* True to invert the sense of the match */
  int matched = 0;             /* True if the character matched the pattern */
/*
 * If the first character is a caret, the sense of the match is
 * inverted and only if the character isn't one of those in the
 * range, do we say that it matches.
 */
  if(*pptr == '^') {
    pptr++;
    invert = 1;
  };
/*
 * The hyphen is only a special character when it follows the first
 * character of the range (not including the caret).
 */
  if(*pptr == '-') {
    pptr++;
    if(c == '-') {
      *endp = pptr;
      matched = 1;
    };
/*
 * Skip other leading '-' characters since they make no sense.
 */
    while(*pptr == '-')
      pptr++;
  };
/*
 * The hyphen is only a special character when it follows the first
 * character of the range (not including the caret or a hyphen).
 */
  if(*pptr == ']') {
    pptr++;
    if(c == ']') {
      *endp = pptr;
      matched = 1;
    };
  };
/*
 * Having dealt with the characters that have special meanings at
 * the beginning of a character range expression, see if the
 * character matches any of the remaining characters of the range,
 * up until a terminating ']' character is seen.
 */
  while(!matched && *pptr && *pptr != ']') {
/*
 * Is this a range of characters signaled by the two end characters
 * separated by a hyphen?
 */
    if(*pptr == '-') {
      if(pptr[1] != ']') {
        if(c >= pptr[-1] && c <= pptr[1])
	  matched = 1;
	pptr += 2;
      };
/*
 * A normal character to be compared directly.
 */
    } else if(*pptr++ == c) {
      matched = 1;
    };
  };
/*
 * Find the terminating ']'.
 */
  while(*pptr && *pptr != ']')
    pptr++;
/*
 * Did we find a terminating ']'?
 */
  if(*pptr == ']') {
    *endp = pptr + 1;
    return matched ? !invert : invert;
  };
/*
 * If the pattern didn't end with a ']' then it doesn't match, regardless
 * of the value of the required sense of the match.
 */
  *endp = pptr;
  return 0;
}

/*.......................................................................
 * This is a qsort() comparison function used to sort strings.
 *
 * Input:
 *  v1, v2   void *  Pointers to the two strings to be compared.
 * Output:
 *  return    int    -1 -> v1 < v2.
 *                    0 -> v1 == v2
 *                    1 -> v1 > v2
 */
static int ef_cmp_strings(const void *v1, const void *v2)
{
  char * const *s1 = (char * const *) v1;
  char * const *s2 = (char * const *) v2;
  return strcmp(*s1, *s2);
}

/*.......................................................................
 * Preprocess a path, expanding ~/, ~user/ and $envvar references, using
 * ef->path as a work buffer, then copy the result into a cache entry,
 * and return a pointer to this copy.
 *
 * Input:
 *  ef    ExpandFile *  The resource object of the file matcher.
 *  pathlen      int    The length of the prefix of path[] to be expanded.
 * Output:
 *  return      char *  A pointer to a copy of the output path in the
 *                      cache. On error NULL is returned, and a description
 *                      of the error is left in ef->err.
 */
static char *ef_expand_special(ExpandFile *ef, const char *path, int pathlen)
{
  int spos;      /* The index of the start of the path segment that needs */
                 /*  to be copied from path[] to the output pathname. */
  int ppos;      /* The index of a character in path[] */
  char *pptr;    /* A pointer into the output path */
  int escaped;   /* True if the previous character was a '\' */
  int i;
/*
 * Clear the pathname buffer.
 */
  _pn_clear_path(ef->path);
/*
 * We need to perform two passes, one to expand environment variables
 * and a second to do tilde expansion. This caters for the case
 * where an initial dollar expansion yields a tilde expression.
 */
  escaped = 0;
  for(spos=ppos=0; ppos < pathlen; ppos++) {
    int c = path[ppos];
    if(escaped) {
      escaped = 0;
    } else if(c == '\\') {
      escaped = 1;
    } else if(c == '$') {
      int envlen;   /* The length of the environment variable */
      char *value;  /* The value of the environment variable */
/*
 * Record the preceding unrecorded part of the pathname.
 */
      if(spos < ppos && _pn_append_to_path(ef->path, path + spos, ppos-spos, 0)
	 == NULL) {
	_err_record_msg(ef->err, "Insufficient memory to expand path",
			END_ERR_MSG);
	return NULL;
      };
/*
 * Skip the dollar.
 */
      ppos++;
/*
 * Copy the environment variable name that follows the dollar into
 * ef->envnam[], stopping if a directory separator or end of string
 * is seen.
 */
      for(envlen=0; envlenenvnam[envlen] = path[ppos++];
/*
 * If the username overflowed the buffer, treat it as invalid (note that
 * on most unix systems only 8 characters are allowed in a username,
 * whereas our ENV_LEN is much bigger than that.
 */
      if(envlen >= ENV_LEN) {
	_err_record_msg(ef->err, "Environment variable name too long",
			END_ERR_MSG);
	return NULL;
      };
/*
 * Terminate the environment variable name.
 */
      ef->envnam[envlen] = '\0';
/*
 * Lookup the value of the environment variable.
 */
      value = getenv(ef->envnam);
      if(!value) {
	_err_record_msg(ef->err, "No expansion found for: $", ef->envnam,
			END_ERR_MSG);
	return NULL;
      };
/*
 * Copy the value of the environment variable into the output pathname.
 */
      if(_pn_append_to_path(ef->path, value, -1, 0) == NULL) {
	_err_record_msg(ef->err, "Insufficient memory to expand path",
			END_ERR_MSG);
	return NULL;
      };
/*
 * Record the start of the uncopied tail of the input pathname.
 */
      spos = ppos;
    };
  };
/*
 * Record the uncopied tail of the pathname.
 */
  if(spos < ppos && _pn_append_to_path(ef->path, path + spos, ppos-spos, 0)
     == NULL) {
    _err_record_msg(ef->err, "Insufficient memory to expand path", END_ERR_MSG);
    return NULL;
  };
/*
 * If the first character of the resulting pathname is a tilde,
 * then attempt to substitute the home directory of the specified user.
 */
  pptr = ef->path->name;
  if(*pptr == '~' && path[0] != '\\') {
    int usrlen;           /* The length of the username following the tilde */
    const char *homedir;  /* The home directory of the user */
    int homelen;          /* The length of the home directory string */
    int plen;             /* The current length of the path */
    int skip=0;           /* The number of characters to skip after the ~user */
/*
 * Get the current length of the output path.
 */
    plen = strlen(ef->path->name);
/*
 * Skip the tilde.
 */
    pptr++;
/*
 * Copy the optional username that follows the tilde into ef->usrnam[].
 */
    for(usrlen=0; usrlenusrnam[usrlen] = *pptr++;
/*
 * If the username overflowed the buffer, treat it as invalid (note that
 * on most unix systems only 8 characters are allowed in a username,
 * whereas our USR_LEN is much bigger than that.
 */
    if(usrlen >= USR_LEN) {
      _err_record_msg(ef->err, "Username too long", END_ERR_MSG);
      return NULL;
    };
/*
 * Terminate the username string.
 */
    ef->usrnam[usrlen] = '\0';
/*
 * Lookup the home directory of the user.
 */
    homedir = _hd_lookup_home_dir(ef->home, ef->usrnam);
    if(!homedir) {
      _err_record_msg(ef->err, _hd_last_home_dir_error(ef->home), END_ERR_MSG);
      return NULL;
    };
    homelen = strlen(homedir);
/*
 * ~user and ~ are usually followed by a directory separator to
 * separate them from the file contained in the home directory.
 * If the home directory is the root directory, then we don't want
 * to follow the home directory by a directory separator, so we must
 * erase it.
 */
    if(strcmp(homedir, FS_ROOT_DIR) == 0 &&
       strncmp(pptr, FS_DIR_SEP, FS_DIR_SEP_LEN) == 0) {
      skip = FS_DIR_SEP_LEN;
    };
/*
 * If needed, increase the size of the pathname buffer to allow it
 * to accomodate the home directory instead of the tilde expression.
 * Note that pptr may not be valid after this call.
 */
    if(_pn_resize_path(ef->path, plen - usrlen - 1 - skip + homelen)==NULL) {
      _err_record_msg(ef->err, "Insufficient memory to expand filename",
		      END_ERR_MSG);
      return NULL;
    };
/*
 * Move the part of the pathname that follows the tilde expression to
 * the end of where the home directory will need to be inserted.
 */
    memmove(ef->path->name + homelen,
	    ef->path->name + 1 + usrlen + skip, plen - usrlen - 1 - skip+1);
/*
 * Write the home directory at the beginning of the string.
 */
    for(i=0; ipath->name[i] = homedir[i];
  };
/*
 * Copy the result into the cache, and return a pointer to the copy.
 */
  return ef_cache_pathname(ef, ef->path->name, 0);
}

/*.......................................................................
 * Return a description of the last path-expansion error that occurred.
 *
 * Input:
 *  ef     ExpandFile *   The path-expansion resource object.
 * Output:
 *  return       char *   The description of the last error.
 */
const char *ef_last_error(ExpandFile *ef)
{
  return ef ? _err_get_msg(ef->err) : "NULL ExpandFile argument";
}

/*.......................................................................
 * Print out an array of matching files.
 *
 * Input:
 *  result  FileExpansion *   The container of the sorted array of
 *                            expansions.
 *  fp               FILE *   The output stream to write to.
 *  term_width        int     The width of the terminal.
 * Output:
 *  return            int     0 - OK.
 *                            1 - Error.
 */
int ef_list_expansions(FileExpansion *result, FILE *fp, int term_width)
{
  return _ef_output_expansions(result, _io_write_stdio, fp, term_width);
}

/*.......................................................................
 * Print out an array of matching files via a callback.
 *
 * Input:
 *  result  FileExpansion *  The container of the sorted array of
 *                           expansions.
 *  write_fn    GlWriteFn *  The function to call to write the
 *                           expansions or 0 to discard the output.
 *  data             void *  Anonymous data to pass to write_fn().
 *  term_width        int    The width of the terminal.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int _ef_output_expansions(FileExpansion *result, GlWriteFn *write_fn,
			  void *data, int term_width)
{
  EfListFormat fmt; /* List formatting information */
  int lnum;          /* The sequential number of the line to print next */
/*
 * Not enough space to list anything?
 */
  if(term_width < 1)
    return 0;
/*
 * Do we have a callback to write via, and any expansions to be listed?
 */
  if(write_fn && result && result->nfile>0) {
/*
 * Work out how to arrange the listing into fixed sized columns.
 */
    ef_plan_listing(result, term_width, &fmt);
/*
 * Print the listing to the specified stream.
 */
    for(lnum=0; lnum < fmt.nline; lnum++) {
      if(ef_format_line(result, &fmt, lnum, write_fn, data))
	return 1;
    };
  };
  return 0;
}

/*.......................................................................
 * Work out how to arrange a given array of completions into a listing
 * of one or more fixed size columns.
 *
 * Input:
 *  result   FileExpansion *   The set of completions to be listed.
 *  term_width         int     The width of the terminal. A lower limit of
 *                             zero is quietly enforced.
 * Input/Output:
 *  fmt       EfListFormat *   The formatting information will be assigned
 *                             to the members of *fmt.
 */
static void ef_plan_listing(FileExpansion *result, int term_width,
			    EfListFormat *fmt)
{
  int maxlen;    /* The length of the longest matching string */
  int i;
/*
 * Ensure that term_width >= 0.
 */
  if(term_width < 0)
    term_width = 0;
/*
 * Start by assuming the worst case, that either nothing will fit
 * on the screen, or that there are no matches to be listed.
 */
  fmt->term_width = term_width;
  fmt->column_width = 0;
  fmt->nline = fmt->ncol = 0;
/*
 * Work out the maximum length of the matching strings.
 */
  maxlen = 0;
  for(i=0; infile; i++) {
    int len = strlen(result->files[i]);
    if(len > maxlen)
      maxlen = len;
  };
/*
 * Nothing to list?
 */
  if(maxlen == 0)
    return;
/*
 * Split the available terminal width into columns of
 * maxlen + EF_COL_SEP characters.
 */
  fmt->column_width = maxlen;
  fmt->ncol = fmt->term_width / (fmt->column_width + EF_COL_SEP);
/*
 * If the column width is greater than the terminal width, zero columns
 * will have been selected. Set a lower limit of one column. Leave it
 * up to the caller how to deal with completions who's widths exceed
 * the available terminal width.
 */
  if(fmt->ncol < 1)
    fmt->ncol = 1;
/*
 * How many lines of output will be needed?
 */
  fmt->nline = (result->nfile + fmt->ncol - 1) / fmt->ncol;
  return;
}

/*.......................................................................
 * Render one line of a multi-column listing of completions, using a
 * callback function to pass the output to an arbitrary destination.
 *
 * Input:
 *  result   FileExpansion *  The container of the sorted array of
 *                            completions.
 *  fmt       EfListFormat *  Formatting information.
 *  lnum               int    The index of the line to print, starting
 *                            from 0, and incrementing until the return
 *                            value indicates that there is nothing more
 *                            to be printed.
 *  write_fn     GlWriteFn *  The function to call to write the line, or
 *                            0 to discard the output.
 *  data              void *  Anonymous data to pass to write_fn().
 * Output:
 *  return             int    0 - Line printed ok.
 *                            1 - Nothing to print.
 */
static int ef_format_line(FileExpansion *result, EfListFormat *fmt, int lnum,
			  GlWriteFn *write_fn, void *data)
{
  int col;             /* The index of the list column being output */
/*
 * If the line index is out of bounds, there is nothing to be written.
 */
  if(lnum < 0 || lnum >= fmt->nline)
    return 1;
/*
 * If no output function has been provided, return as though the line
 * had been printed.
 */
  if(!write_fn)
    return 0;
/*
 * Print the matches in 'ncol' columns, sorted in line order within each
 * column.
 */
  for(col=0; col < fmt->ncol; col++) {
    int m = col*fmt->nline + lnum;
/*
 * Is there another match to be written? Note that in general
 * the last line of a listing will have fewer filled columns
 * than the initial lines.
 */
    if(m < result->nfile) {
      char *file = result->files[m];
/*
 * How long are the completion and type-suffix strings?
 */
      int flen = strlen(file);
/*
 * Write the completion string.
 */
      if(write_fn(data, file, flen) != flen)
	return 1;
/*
 * If another column follows the current one, pad to its start with spaces.
 */
      if(col+1 < fmt->ncol) {
/*
 * The following constant string of spaces is used to pad the output.
 */
	static const char spaces[] = "                    ";
	static const int nspace = sizeof(spaces) - 1;
/*
 * Pad to the next column, using as few sub-strings of the spaces[]
 * array as possible.
 */
	int npad = fmt->column_width + EF_COL_SEP - flen;
	while(npad>0) {
	  int n = npad > nspace ? nspace : npad;
	  if(write_fn(data, spaces + nspace - n, n) != n)
	    return 1;
	  npad -= n;
	};
      };
    };
  };
/*
 * Start a new line.
 */
  {
    char s[] = "\r\n";
    int n = strlen(s);
    if(write_fn(data, s, n) != n)
      return 1;
  };
  return 0;
}

#endif  /* ifndef WITHOUT_FILE_SYSTEM */
genometools-1.5.1/src/external/libtecla-1.6.1/expand.h000066400000000000000000000037271211610345200223360ustar00rootroot00000000000000#ifndef expand_h
#define expand_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * This header is not for use by external applicatons. It contains
 * internal immplementation features of the libtecla library, which
 * may change incompatibly between releases.
 */

/*
 * Print a list of expansions via a callback function.
 */
int _ef_output_expansions(FileExpansion *result, GlWriteFn *write_fn,
			  void *data, int term_width);


#endif
genometools-1.5.1/src/external/libtecla-1.6.1/freelist.c000066400000000000000000000275231211610345200226670ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include 
#include 
#include 

#include "freelist.h"

typedef struct FreeListBlock FreeListBlock;
struct FreeListBlock {
  FreeListBlock *next;   /* The next block in the list */
  char *nodes;           /* The array of free-list nodes */
};

struct FreeList {
  size_t node_size;         /* The size of a free-list node */
  unsigned blocking_factor; /* The number of nodes per block */
  long nbusy;               /* The number of nodes that are in use */
  long ntotal;              /* The total number of nodes in the free list */
  FreeListBlock *block;     /* The head of the list of free-list blocks */
  void *free_list;          /* The free-list of nodes */
};

static FreeListBlock *_new_FreeListBlock(FreeList *fl);
static FreeListBlock *_del_FreeListBlock(FreeListBlock *fl);
static void _thread_FreeListBlock(FreeList *fl, FreeListBlock *block);

/*.......................................................................
 * Allocate a new free-list from blocks of 'blocking_factor' objects of size
 * node_size.
 *
 * Input:
 *  node_size         size_t    The size of the free-list nodes to be returned
 *                              by _new_FreeListNode(). Use sizeof() to
 *                              determine this.
 *  blocking_factor unsigned    The number of objects of size 'object_size'
 *                              to allocate per block.
 * Output:
 *  return          FreeList *  The new freelist, or NULL on error.
 */
FreeList *_new_FreeList(size_t node_size, unsigned blocking_factor)
{
  FreeList *fl;  /* The new free-list container */
/*
 * When a free-list node is on the free-list, it is used as a (void *)
 * link field. Roundup node_size to a mulitple of the size of a void
 * pointer. This, plus the fact that the array of nodes is obtained via
 * malloc, which returns memory suitably aligned for any object, will
 * ensure that the first sizeof(void *) bytes of each node will be
 * suitably aligned to use as a (void *) link pointer.
 */
  node_size = sizeof(void *) *
    ((node_size + sizeof(void *) - 1) / sizeof(void *));
/*
 * Enfore a minimum block size.
 */
  if(blocking_factor < 1)
    blocking_factor = 1;
/*
 * Allocate the container of the free list.
 */
  fl = (FreeList *) malloc(sizeof(FreeList));
  if(!fl) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to _del_FreeList().
 */
  fl->node_size = node_size;
  fl->blocking_factor = blocking_factor;
  fl->nbusy = 0;
  fl->ntotal = 0;
  fl->block = NULL;
  fl->free_list = NULL;
/*
 * Allocate the first block of memory.
 */
  fl->block = _new_FreeListBlock(fl);
  if(!fl->block) {
    errno = ENOMEM;
    return _del_FreeList(fl, 1);
  };
/*
 * Add the new list of nodes to the free-list.
 */
  fl->free_list = fl->block->nodes;
/*
 * Return the free-list for use.
 */
  return fl;
}

/*.......................................................................
 * Re-thread a freelist to reclaim all allocated nodes.
 * This function should not be called unless if it is known that none
 * of the currently allocated nodes are still being used.
 *
 * Input:
 *  fl          FreeList *  The free-list to be reset, or NULL.
 */
void _rst_FreeList(FreeList *fl)
{
  if(fl) {
    FreeListBlock *block;
/*
 * Re-thread the nodes of each block into individual free-lists.
 */
    for(block=fl->block; block; block=block->next)
      _thread_FreeListBlock(fl, block);
/*
 * Link all of the block freelists into one large freelist.
 */
    fl->free_list = NULL;
    for(block=fl->block; block; block=block->next) {
/*
 * Locate the last node of the current block.
 */
      char *last_node = block->nodes + fl->node_size *
	(fl->blocking_factor - 1);
/*
 * Make the link-field of the last node point to the first
 * node of the current freelist, then make the first node of the
 * new block the start of the freelist. 
 */
      *(void **)last_node = fl->free_list;
      fl->free_list = block->nodes;
    };
/*
 * All allocated nodes have now been returned to the freelist.
 */
    fl->nbusy = 0;
  };
}

/*.......................................................................
 * Delete a free-list.
 *
 * Input:
 *  fl          FreeList *  The free-list to be deleted, or NULL.
 *  force            int    If force==0 then _del_FreeList() will complain
 *                           and refuse to delete the free-list if any
 *                           of nodes have not been returned to the free-list.
 *                          If force!=0 then _del_FreeList() will not check
 *                           whether any nodes are still in use and will
 *                           always delete the list.
 * Output:
 *  return      FreeList *  Always NULL (even if the list couldn't be
 *                          deleted).
 */
FreeList *_del_FreeList(FreeList *fl, int force)
{
  if(fl) {
/*
 * Check whether any nodes are in use.
 */
    if(!force && _busy_FreeListNodes(fl) != 0) {
      errno = EBUSY;
      return NULL;
    };
/*
 * Delete the list blocks.
 */
    {
      FreeListBlock *next = fl->block;
      while(next) {
	FreeListBlock *block = next;
	next = block->next;
	block = _del_FreeListBlock(block);
      };
    };
    fl->block = NULL;
    fl->free_list = NULL;
/*
 * Discard the container.
 */
    free(fl);
  };
  return NULL;
}

/*.......................................................................
 * Allocate a new object from a free-list.
 *
 * Input:
 *  fl        FreeList *  The free-list to return an object from.
 * Output:
 *  return        void *  A new object of the size that was specified via
 *                        the node_size argument of _new_FreeList() when
 *                        the free-list was created, or NULL if there
 *                        is insufficient memory, or 'fl' is NULL.
 */
void *_new_FreeListNode(FreeList *fl)
{
  void *node;  /* The node to be returned */
/*
 * Check arguments.
 */
  if(!fl)
    return NULL;
/*
 * If the free-list has been exhausted extend it by allocating
 * another block of nodes.
 */
  if(!fl->free_list) {
    FreeListBlock *block = _new_FreeListBlock(fl);
    if(!block)
      return NULL;
/*
 * Prepend the new block to the list of free-list blocks.
 */
    block->next = fl->block;
    fl->block = block;
/*
 * Add the new list of nodes to the free-list.
 */
    fl->free_list = fl->block->nodes;
  };
/*
 * Remove and return a node from the front of the free list.
 */
  node = fl->free_list;
  fl->free_list = *(void **)node;
/*
 * Record the loss of a node from the free-list.
 */
  fl->nbusy++;
/*
 * Return the node.
 */
  return node;
}

/*.......................................................................
 * Return an object to the free-list that it was allocated from.
 *
 * Input:
 *  fl        FreeList *  The free-list from which the object was taken.
 *  object        void *  The node to be returned.
 * Output:
 *  return        void *  Always NULL.
 */
void *_del_FreeListNode(FreeList *fl, void *object)
{
/*
 * Check arguments.
 */
  if(!fl)
    return NULL;
/*
 * Return the node to the head of the free list.
 */
  if(object) {
    *(void **)object = fl->free_list;
    fl->free_list = object;
/*
 * Record the return of the node to the free-list.
 */
    fl->nbusy--;
  };
  return NULL;
}

/*.......................................................................
 * Return a count of the number of nodes that are currently allocated.
 *
 * Input:
 *  fl      FreeList *  The list to count wrt, or NULL.
 * Output:
 *  return      long    The number of nodes (or 0 if fl==NULL).
 */
long _busy_FreeListNodes(FreeList *fl)
{
  return fl ? fl->nbusy : 0;
}

/*.......................................................................
 * Query the number of allocated nodes in the freelist which are
 * currently unused.
 *
 * Input:
 *  fl      FreeList *  The list to count wrt, or NULL.
 * Output:
 *  return      long    The number of unused nodes (or 0 if fl==NULL).
 */
long _idle_FreeListNodes(FreeList *fl)
{
  return fl ? (fl->ntotal - fl->nbusy) : 0;
}

/*.......................................................................
 * Allocate a new list of free-list nodes. On return the nodes will
 * be linked together as a list starting with the node at the lowest
 * address and ending with a NULL next pointer.
 *
 * Input:
 *  fl          FreeList *  The free-list to allocate the list for.
 * Output:
 *  return FreeListBlock *  The new linked block of free-list nodes,
 *                          or NULL on error.
 */
static FreeListBlock *_new_FreeListBlock(FreeList *fl)
{
  FreeListBlock *block;  /* The new block to be returned */
/*
 * Allocate the container.
 */
  block = (FreeListBlock *) malloc(sizeof(FreeListBlock));
  if(!block)
    return NULL;
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to _del_FreeListBlock().
 */
  block->next = NULL;
  block->nodes = NULL;
/*
 * Allocate the block of nodes.
 */
  block->nodes = (char *) malloc(fl->node_size * fl->blocking_factor);
  if(!block->nodes)
    return _del_FreeListBlock(block);
/*
 * Initialize the block as a linked list of FreeListNode's.
 */
  _thread_FreeListBlock(fl, block);
/*
 * Update the record of the number of nodes in the freelist.
 */
  fl->ntotal += fl->blocking_factor;
  return block;
}

/*.......................................................................
 * Link each node of a freelist block to the node that follows it.
 *
 * Input:
 *  fl         FreeList *   The freelist that contains the block.
 *  block FreeListBlock *   The block to be threaded.
 */
static void _thread_FreeListBlock(FreeList *fl, FreeListBlock *block)
{
  char *mem = block->nodes;
  int i;
  for(i=0; iblocking_factor - 1; i++, mem += fl->node_size)
    *(void **)mem = mem + fl->node_size;  /* Link to the next node */
  *(void **)mem = NULL;                   /* Terminate the list */
}

/*.......................................................................
 * Delete a free-list block.
 *
 * Input:
 *  fl      FreeListBlock *  The block to be deleted, or NULL.
 * Output:
 *  return  FreeListBlock *  Always NULL.
 */
static FreeListBlock *_del_FreeListBlock(FreeListBlock *fl)
{
  if(fl) {
    fl->next = NULL;
    if(fl->nodes)
      free(fl->nodes);
    fl->nodes = NULL;
    free(fl);
  };
  return NULL;
}
genometools-1.5.1/src/external/libtecla-1.6.1/freelist.h000066400000000000000000000062011211610345200226620ustar00rootroot00000000000000#ifndef freelist_h
#define freelist_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * This module provides a memory allocation scheme that helps to
 * prevent memory fragmentation by allocating large blocks of
 * fixed sized objects and forming them into a free-list for
 * subsequent allocations. The free-list is expanded as needed.
 */
typedef struct FreeList FreeList;

/*
 * Allocate a new free-list from blocks of 'blocking_factor' objects of size
 * node_size. The node_size argument should be determined by applying
 * the sizeof() operator to the object type that you intend to allocate from
 * the freelist.
 */
FreeList *_new_FreeList(size_t node_size, unsigned blocking_factor);

/*
 * If it is known that none of the nodes currently allocated from
 * a freelist are still in use, the following function can be called
 * to return all nodes to the freelist without the overhead of
 * having to call del_FreeListNode() for every allocated node. The
 * nodes of the freelist can then be reused by future callers to
 * new_FreeListNode().
 */
void _rst_FreeList(FreeList *fl);

/*
 * Delete a free-list.
 */
FreeList *_del_FreeList(FreeList *fl, int force);

/*
 * Determine the number of nodes that are currently in use.
 */
long _busy_FreeListNodes(FreeList *fl);

/*
 * Query the number of allocated nodes in the freelist which are
 * currently unused.
 */
long _idle_FreeListNodes(FreeList *fl);

/*
 * Allocate a new object from a free-list.
 */
void *_new_FreeListNode(FreeList *fl);

/*
 * Return an object to the free-list that it was allocated from.
 */
void *_del_FreeListNode(FreeList *fl, void *object);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/getline.c000066400000000000000000014164431211610345200225050ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * Standard headers.
 */
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

/*
 * UNIX headers.
 */
#include 
#ifdef HAVE_SELECT
#ifdef HAVE_SYS_SELECT_H
#include 
#endif
#include 
#include 
#endif

/*
 * Handle the different sources of terminal control string and size
 * information. Note that if no terminal information database is available,
 * ANSI VT100 control sequences are used.
 */
#if defined(USE_TERMINFO) || defined(USE_TERMCAP)
/*
 * Include curses.h or ncurses/curses.h depending on which is available.
 */
#ifdef HAVE_CURSES_H
#include 
#elif defined(HAVE_NCURSES_CURSES_H)
#include 
#endif
/*
 * Include term.h where available.
 */
#if defined(HAVE_TERM_H)
#include 
#elif defined(HAVE_NCURSES_TERM_H)
#include 
#endif
/*
 * When using termcap, include termcap.h on systems that have it.
 * Otherwise assume that all prototypes are provided by curses.h.
 */
#if defined(USE_TERMCAP) && defined(HAVE_TERMCAP_H)
#include 
#endif

/*
 * Under Solaris default Curses the output function that tputs takes is
 * declared to have a char argument. On all other systems and on Solaris
 * X/Open Curses (Issue 4, Version 2) it expects an int argument (using
 * c89 or options -I /usr/xpg4/include -L /usr/xpg4/lib -R /usr/xpg4/lib
 * selects XPG4v2 Curses on Solaris 2.6 and later).
 *
 * Similarly, under Mac OS X, the return value of the tputs output
 * function is declared as void, whereas it is declared as int on
 * other systems.
 */
#if defined __sun && defined __SVR4 && !defined _XOPEN_CURSES
typedef int TputsRetType;
typedef char TputsArgType;              /* int tputs(char c, FILE *fp) */
#define TPUTS_RETURNS_VALUE 1
#else
typedef int TputsRetType;
typedef int TputsArgType;               /* int tputs(int c, FILE *fp) */
#define TPUTS_RETURNS_VALUE 1
#endif

/*
 * Use the above specifications to prototype our tputs callback function.
 */
static TputsRetType gl_tputs_putchar(TputsArgType c);

#endif  /* defined(USE_TERMINFO) || defined(USE_TERMCAP) */

/*
 * If the library is being compiled without filesystem access facilities,
 * ensure that none of the action functions that normally do access the
 * filesystem are bound by default, and that it they do get bound, that
 * they don't do anything.
 */
#if WITHOUT_FILE_SYSTEM
#define HIDE_FILE_SYSTEM
#endif

/*
 * POSIX headers.
 */
#include 
#include 
#include 

/*
 * Provide typedefs for standard POSIX structures.
 */
typedef struct sigaction SigAction;
typedef struct termios Termios;

/*
 * Which flag is used to select non-blocking I/O with fcntl()?
 */
#undef NON_BLOCKING_FLAG
#if defined(O_NONBLOCK)
#define NON_BLOCKING_FLAG (O_NONBLOCK)
#elif defined(O_NDELAY)
#define NON_BLOCKING_FLAG (O_NDELAY)
#endif

/*
 * What value should we give errno if I/O blocks when it shouldn't.
 */
#undef BLOCKED_ERRNO
#if defined(EAGAIN)
#define BLOCKED_ERRNO (EAGAIN)
#elif defined(EWOULDBLOCK)
#define BLOCKED_ERRNO (EWOULDBLOCK)
#elif defined(EIO)
#define BLOCKED_ERRNO (EIO)
#else
#define BLOCKED_ERRNO 0
#endif

/*
 * Local headers.
 */
#ifndef WITHOUT_FILE_SYSTEM
#include "pathutil.h"
#endif
#include "libtecla.h"
#include "keytab.h"
#include "getline.h"
#include "ioutil.h"
#include "history.h"
#include "freelist.h"
#include "stringrp.h"
#include "chrqueue.h"
#include "cplmatch.h"
#ifndef WITHOUT_FILE_SYSTEM
#include "expand.h"
#endif
#include "errmsg.h"

/*
 * Enumerate the available editing styles.
 */
typedef enum {
  GL_EMACS_MODE,   /* Emacs style editing */
  GL_VI_MODE,      /* Vi style editing */
  GL_NO_EDITOR     /* Fall back to the basic OS-provided editing */
} GlEditor;

/*
 * Set the largest key-sequence that can be handled.
 */
#define GL_KEY_MAX 64

/*
 * In vi mode, the following datatype is used to implement the
 * undo command. It records a copy of the input line from before
 * the command-mode action which edited the input line.
 */
typedef struct {
  char *line;        /* A historical copy of the input line */
  int buff_curpos;   /* The historical location of the cursor in */
                     /*  line[] when the line was modified. */
  int ntotal;        /* The number of characters in line[] */
  int saved;         /* True once a line has been saved after the */
                     /*  last call to gl_interpret_char(). */
} ViUndo;

/*
 * In vi mode, the following datatype is used to record information
 * needed by the vi-repeat-change command.
 */
typedef struct {
  KtAction action;           /* The last action function that made a */
                             /*  change to the line. */
  int count;                 /* The repeat count that was passed to the */
                             /*  above command. */  
  int input_curpos;          /* Whenever vi command mode is entered, the */
                             /*  the position at which it was first left */
                             /*  is recorded here. */
  int command_curpos;        /* Whenever vi command mode is entered, the */
                             /*  the location of the cursor is recorded */
                             /*  here. */
  char input_char;           /* Commands that call gl_read_terminal() */
                             /*  record the character here, so that it can */
                             /*  used on repeating the function. */
  int saved;                 /* True if a function has been saved since the */
                             /*  last call to gl_interpret_char(). */
  int active;                /* True while a function is being repeated. */
} ViRepeat;

/*
 * The following datatype is used to encapsulate information specific
 * to vi mode.
 */
typedef struct {
  ViUndo undo;               /* Information needed to implement the vi */
                             /*  undo command. */
  ViRepeat repeat;           /* Information needed to implement the vi */
                             /*  repeat command. */
  int command;               /* True in vi command-mode */
  int find_forward;          /* True if the last character search was in the */
                             /*  forward direction. */
  int find_onto;             /* True if the last character search left the */
                             /*  on top of the located character, as opposed */
                             /*  to just before or after it. */
  char find_char;            /* The last character sought, or '\0' if no */
                             /*  searches have been performed yet. */
} ViMode;

#ifdef HAVE_SELECT
/*
 * Define a type for recording a file-descriptor callback and its associated
 * data.
 */
typedef struct {
  GlFdEventFn *fn;   /* The callback function */
  void *data;        /* Anonymous data to pass to the callback function */
} GlFdHandler;

/*
 * A list of nodes of the following type is used to record file-activity
 * event handlers, but only on systems that have the select() system call.
 */
typedef struct GlFdNode GlFdNode;
struct GlFdNode {
  GlFdNode *next;    /* The next in the list of nodes */
  int fd;            /* The file descriptor being watched */
  GlFdHandler rd;    /* The callback to call when fd is readable */
  GlFdHandler wr;    /* The callback to call when fd is writable */
  GlFdHandler ur;    /* The callback to call when fd has urgent data */
};

/*
 * Set the number of the above structures to allocate every time that
 * the freelist of GlFdNode's becomes exhausted.
 */
#define GLFD_FREELIST_BLOCKING 10


static int gl_call_fd_handler(GetLine *gl, GlFdHandler *gfh, int fd,
			      GlFdEvent event);

static int gl_call_timeout_handler(GetLine *gl);

#endif

/*
 * Each signal that gl_get_line() traps is described by a list node
 * of the following type.
 */
typedef struct GlSignalNode GlSignalNode;
struct GlSignalNode {
  GlSignalNode *next;  /* The next signal in the list */
  int signo;           /* The number of the signal */
  sigset_t proc_mask;  /* A process mask which only includes signo */
  SigAction original;  /* The signal disposition of the calling program */
                       /*  for this signal. */
  unsigned flags;      /* A bitwise union of GlSignalFlags enumerators */
  GlAfterSignal after; /* What to do after the signal has been handled */
  int errno_value;     /* What to set errno to */
};

/*
 * Set the number of the above structures to allocate every time that
 * the freelist of GlSignalNode's becomes exhausted.
 */
#define GLS_FREELIST_BLOCKING 30

/*
 * Completion handlers and their callback data are recorded in
 * nodes of the following type.
 */
typedef struct GlCplCallback GlCplCallback;
struct GlCplCallback {
  CplMatchFn *fn;            /* The completion callback function */
  void *data;                /* Arbitrary callback data */
};

/*
 * The following function is used as the default completion handler when
 * the filesystem is to be hidden. It simply reports no completions.
 */
#ifdef HIDE_FILE_SYSTEM
static CPL_MATCH_FN(gl_no_completions);
#endif

/*
 * Specify how many GlCplCallback nodes are added to the GlCplCallback freelist
 * whenever it becomes exhausted.
 */
#define GL_CPL_FREELIST_BLOCKING 10

/*
 * External action functions and their callback data are recorded in
 * nodes of the following type.
 */
typedef struct GlExternalAction GlExternalAction;
struct GlExternalAction {
  GlActionFn *fn;          /* The function which implements the action */
  void *data;              /* Arbitrary callback data */
};

/*
 * Specify how many GlExternalAction nodes are added to the
 * GlExternalAction freelist whenever it becomes exhausted.
 */
#define GL_EXT_ACT_FREELIST_BLOCKING 10

/*
 * Define the contents of the GetLine object.
 * Note that the typedef for this object can be found in libtecla.h.
 */
struct GetLine {
  ErrMsg *err;               /* The error-reporting buffer */
  GlHistory *glh;            /* The line-history buffer */
  WordCompletion *cpl;       /* String completion resource object */
  GlCplCallback cplfn;       /* The completion callback */
#ifndef WITHOUT_FILE_SYSTEM
  ExpandFile *ef;            /* ~user/, $envvar and wildcard expansion */
                             /*  resource object. */
#endif
  StringGroup *capmem;       /* Memory for recording terminal capability */
                             /*  strings. */
  GlCharQueue *cq;           /* The terminal output character queue */
  int input_fd;              /* The file descriptor to read on */
  int output_fd;             /* The file descriptor to write to */
  FILE *input_fp;            /* A stream wrapper around input_fd */
  FILE *output_fp;           /* A stream wrapper around output_fd */
  FILE *file_fp;             /* When input is being temporarily taken from */
                             /*  a file, this is its file-pointer. Otherwise */
                             /*  it is NULL. */
  char *term;                /* The terminal type specified on the last call */
                             /*  to gl_change_terminal(). */
  int is_term;               /* True if stdin is a terminal */
  GlWriteFn *flush_fn;       /* The function to call to write to the terminal */
  GlIOMode io_mode;          /* The I/O mode established by gl_io_mode() */
  int raw_mode;              /* True while the terminal is in raw mode */
  GlPendingIO pending_io;    /* The type of I/O that is currently pending */
  GlReturnStatus rtn_status; /* The reason why gl_get_line() returned */
  int rtn_errno;             /* THe value of errno associated with rtn_status */
  size_t linelen;            /* The max number of characters per line */
  char *line;                /* A line-input buffer of allocated size */
                             /*  linelen+2. The extra 2 characters are */
                             /*  reserved for "\n\0". */
  char *cutbuf;              /* A cut-buffer of the same size as line[] */
  char *prompt;              /* The current prompt string */
  int prompt_len;            /* The length of the prompt string */
  int prompt_changed;        /* True after a callback changes the prompt */
  int prompt_style;          /* How the prompt string is displayed */
  FreeList *cpl_mem;         /* Memory for GlCplCallback objects */
  FreeList *ext_act_mem;     /* Memory for GlExternalAction objects */
  FreeList *sig_mem;         /* Memory for nodes of the signal list */
  GlSignalNode *sigs;        /* The head of the list of signals */
  int signals_masked;        /* True between calls to gl_mask_signals() and */
                             /*  gl_unmask_signals() */
  int signals_overriden;     /* True between calls to gl_override_signals() */
                             /*  and gl_restore_signals() */
  sigset_t all_signal_set;   /* The set of all signals that we are trapping */
  sigset_t old_signal_set;   /* The set of blocked signals on entry to */
                             /*  gl_get_line(). */
  sigset_t use_signal_set;   /* The subset of all_signal_set to unblock */
                             /*  while waiting for key-strokes */
  Termios oldattr;           /* Saved terminal attributes. */
  KeyTab *bindings;          /* A table of key-bindings */
  int ntotal;                /* The number of characters in gl->line[] */
  int buff_curpos;           /* The cursor position within gl->line[] */
  int term_curpos;           /* The cursor position on the terminal */
  int term_len;              /* The number of terminal characters used to */
                             /*  display the current input line. */
  int buff_mark;             /* A marker location in the buffer */
  int insert_curpos;         /* The cursor position at start of insert */
  int insert;                /* True in insert mode */ 
  int number;                /* If >= 0, a numeric argument is being read */
  int endline;               /* True to tell gl_get_input_line() to return */
                             /*  the current contents of gl->line[] */
  int displayed;             /* True if an input line is currently displayed */
  int redisplay;             /* If true, the input line will be redrawn */
                             /*  either after the current action function */
                             /*  returns, or when gl_get_input_line() */
                             /*  is next called. */
  int postpone;              /* _gl_normal_io() sets this flag, to */
                             /*  postpone any redisplays until */
                             /*  is next called, to resume line editing. */
  char keybuf[GL_KEY_MAX+1]; /* A buffer of currently unprocessed key presses */
  int nbuf;                  /* The number of characters in keybuf[] */
  int nread;                 /* The number of characters read from keybuf[] */
  KtAction current_action;   /* The action function that is being invoked */
  int current_count;         /* The repeat count passed to */
                             /*  current_acction.fn() */
  GlhLineID preload_id;      /* When not zero, this should be the ID of a */
                             /*  line in the history buffer for potential */
                             /*  recall. */
  int preload_history;       /* If true, preload the above history line when */
                             /*  gl_get_input_line() is next called. */
  long keyseq_count;         /* The number of key sequences entered by the */
                             /*  the user since new_GetLine() was called. */
  long last_search;          /* The value of keyseq_count during the last */
                             /*  history search operation. */
  GlEditor editor;           /* The style of editing, (eg. vi or emacs) */
  int silence_bell;          /* True if gl_ring_bell() should do nothing. */
  int automatic_history;     /* True to automatically archive entered lines */
                             /*  in the history list. */
  ViMode vi;                 /* Parameters used when editing in vi mode */
  const char *left;          /* The string that moves the cursor 1 character */
                             /*  left. */
  const char *right;         /* The string that moves the cursor 1 character */
                             /*  right. */
  const char *up;            /* The string that moves the cursor 1 character */
                             /*  up. */
  const char *down;          /* The string that moves the cursor 1 character */
                             /*  down. */
  const char *home;          /* The string that moves the cursor home */
  const char *bol;           /* Move cursor to beginning of line */
  const char *clear_eol;     /* The string that clears from the cursor to */
                             /*  the end of the line. */
  const char *clear_eod;     /* The string that clears from the cursor to */
                             /*  the end of the display. */
  const char *u_arrow;       /* The string returned by the up-arrow key */
  const char *d_arrow;       /* The string returned by the down-arrow key */
  const char *l_arrow;       /* The string returned by the left-arrow key */
  const char *r_arrow;       /* The string returned by the right-arrow key */
  const char *sound_bell;    /* The string needed to ring the terminal bell */
  const char *bold;          /* Switch to the bold font */
  const char *underline;     /* Underline subsequent characters */
  const char *standout;      /* Turn on standout mode */
  const char *dim;           /* Switch to a dim font */
  const char *reverse;       /* Turn on reverse video */
  const char *blink;         /* Switch to a blinking font */
  const char *text_attr_off; /* Turn off all text attributes */
  int nline;                 /* The height of the terminal in lines */
  int ncolumn;               /* The width of the terminal in columns */
#ifdef USE_TERMCAP
  char *tgetent_buf;         /* The buffer that is used by tgetent() to */
                             /*  store a terminal description. */
  char *tgetstr_buf;         /* The buffer that is used by tgetstr() to */
                             /*  store terminal capabilities. */
#endif
#ifdef USE_TERMINFO
  const char *left_n;        /* The parameter string that moves the cursor */
                             /*  n characters left. */
  const char *right_n;       /* The parameter string that moves the cursor */
                             /*  n characters right. */
#endif
  char *app_file;            /* The pathname of the application-specific */
                             /*  .teclarc configuration file, or NULL. */
  char *user_file;           /* The pathname of the user-specific */
                             /*  .teclarc configuration file, or NULL. */
  int configured;            /* True as soon as any teclarc configuration */
                             /*  file has been read. */
  int echo;                  /* True to display the line as it is being */
                             /*  entered. If 0, only the prompt will be */
                             /*  displayed, and the line will not be */
                             /*  archived in the history list. */
  int last_signal;           /* The last signal that was caught by */
                             /*  the last call to gl_get_line(), or -1 */
                             /*  if no signal has been caught yet. */
#ifdef HAVE_SELECT
  FreeList *fd_node_mem;     /* A freelist of GlFdNode structures */
  GlFdNode *fd_nodes;        /* The list of fd event descriptions */
  fd_set rfds;               /* The set of fds to watch for readability */
  fd_set wfds;               /* The set of fds to watch for writability */
  fd_set ufds;               /* The set of fds to watch for urgent data */
  int max_fd;                /* The maximum file-descriptor being watched */
  struct {                   /* Inactivity timeout related data */
    struct timeval dt;       /* The inactivity timeout when timer.fn() */
                             /*  isn't 0 */
    GlTimeoutFn *fn;         /* The application callback to call when */
                             /*  the inactivity timer expires, or 0 if */
                             /*  timeouts are not required. */
    void *data;              /* Application provided data to be passed to */
                             /*  timer.fn(). */
  } timer;
#endif
};

/*
 * Define the max amount of space needed to store a termcap terminal
 * description. Unfortunately this has to be done by guesswork, so
 * there is the potential for buffer overflows if we guess too small.
 * Fortunately termcap has been replaced by terminfo on most
 * platforms, and with terminfo this isn't an issue. The value that I
 * am using here is the conventional value, as recommended by certain
 * web references.
 */
#ifdef USE_TERMCAP
#define TERMCAP_BUF_SIZE 2048
#endif

/*
 * Set the size of the string segments used to store terminal capability
 * strings.
 */
#define CAPMEM_SEGMENT_SIZE 512

/*
 * If no terminal size information is available, substitute the
 * following vt100 default sizes.
 */
#define GL_DEF_NLINE 24
#define GL_DEF_NCOLUMN 80

/*
 * Enumerate the attributes needed to classify different types of
 * signals. These attributes reflect the standard default
 * characteristics of these signals (according to Richard Steven's
 * Advanced Programming in the UNIX Environment). Note that these values
 * are all powers of 2, so that they can be combined in a bitwise union.
 */
typedef enum {
  GLSA_TERM=1,   /* A signal that terminates processes */
  GLSA_SUSP=2,   /* A signal that suspends processes */
  GLSA_CONT=4,   /* A signal that is sent when suspended processes resume */
  GLSA_IGN=8,    /* A signal that is ignored */
  GLSA_CORE=16,  /* A signal that generates a core dump */
  GLSA_HARD=32,  /* A signal generated by a hardware exception */
  GLSA_SIZE=64   /* A signal indicating terminal size changes */
} GlSigAttr;

/*
 * List the signals that we need to catch. In general these are
 * those that by default terminate or suspend the process, since
 * in such cases we need to restore terminal settings.
 */
static const struct GlDefSignal {
  int signo;            /* The number of the signal */
  unsigned flags;       /* A bitwise union of GlSignalFlags enumerators */
  GlAfterSignal after;  /* What to do after the signal has been delivered */
  int attr;             /* The default attributes of this signal, expressed */
                        /* as a bitwise union of GlSigAttr enumerators */
  int errno_value;      /* What to set errno to */
} gl_signal_list[] = {
  {SIGABRT,   GLS_SUSPEND_INPUT,    GLS_ABORT, GLSA_TERM|GLSA_CORE, EINTR},
  {SIGALRM,   GLS_RESTORE_ENV,   GLS_CONTINUE, GLSA_TERM,           0},
  {SIGCONT,   GLS_RESTORE_ENV,   GLS_CONTINUE, GLSA_CONT|GLSA_IGN,  0},
#if defined(SIGHUP)
#ifdef ENOTTY
  {SIGHUP,    GLS_SUSPEND_INPUT,    GLS_ABORT, GLSA_TERM,           ENOTTY},
#else
  {SIGHUP,    GLS_SUSPEND_INPUT,    GLS_ABORT, GLSA_TERM,           EINTR},
#endif
#endif
  {SIGINT,    GLS_SUSPEND_INPUT,    GLS_ABORT, GLSA_TERM,           EINTR},
#if defined(SIGPIPE)
#ifdef EPIPE
  {SIGPIPE,   GLS_SUSPEND_INPUT,    GLS_ABORT, GLSA_TERM,           EPIPE},
#else
  {SIGPIPE,   GLS_SUSPEND_INPUT,    GLS_ABORT, GLSA_TERM,           EINTR},
#endif
#endif
#ifdef SIGPOLL
  {SIGPOLL,   GLS_SUSPEND_INPUT,    GLS_ABORT, GLSA_TERM,           EINTR},
#endif
#ifdef SIGPWR
  {SIGPWR,    GLS_RESTORE_ENV,   GLS_CONTINUE, GLSA_IGN,            0},
#endif
#ifdef SIGQUIT
  {SIGQUIT,   GLS_SUSPEND_INPUT,    GLS_ABORT, GLSA_TERM|GLSA_CORE, EINTR},
#endif
  {SIGTERM,   GLS_SUSPEND_INPUT,    GLS_ABORT, GLSA_TERM,           EINTR},
#ifdef SIGTSTP
  {SIGTSTP,   GLS_SUSPEND_INPUT, GLS_CONTINUE, GLSA_SUSP,           0},
#endif
#ifdef SIGTTIN
  {SIGTTIN,   GLS_SUSPEND_INPUT, GLS_CONTINUE, GLSA_SUSP,           0},
#endif
#ifdef SIGTTOU
  {SIGTTOU,   GLS_SUSPEND_INPUT, GLS_CONTINUE, GLSA_SUSP,           0},
#endif
#ifdef SIGUSR1
  {SIGUSR1,   GLS_RESTORE_ENV,   GLS_CONTINUE, GLSA_TERM,           0},
#endif
#ifdef SIGUSR2
  {SIGUSR2,   GLS_RESTORE_ENV,   GLS_CONTINUE, GLSA_TERM,           0},
#endif
#ifdef SIGVTALRM
  {SIGVTALRM, GLS_RESTORE_ENV,   GLS_CONTINUE, GLSA_TERM,           0},
#endif
#ifdef SIGWINCH
  {SIGWINCH,  GLS_RESTORE_ENV,   GLS_CONTINUE, GLSA_SIZE|GLSA_IGN,  0},
#endif
#ifdef SIGXCPU
  {SIGXCPU,   GLS_RESTORE_ENV,   GLS_CONTINUE, GLSA_TERM|GLSA_CORE, 0},
#endif
#ifdef SIGXFSZ
  {SIGXFSZ,   GLS_RESTORE_ENV,   GLS_CONTINUE, GLSA_TERM|GLSA_CORE, 0},
#endif
};

/*
 * Define file-scope variables for use in signal handlers.
 */
static volatile sig_atomic_t gl_pending_signal = -1;
static sigjmp_buf gl_setjmp_buffer;

static void gl_signal_handler(int signo);

static int gl_check_caught_signal(GetLine *gl);

/*
 * Respond to an externally caught process suspension or
 * termination signal.
 */
static void gl_suspend_process(int signo, GetLine *gl, int ngl);

/* Return the default attributes of a given signal */

static int gl_classify_signal(int signo);

/*
 * Unfortunately both terminfo and termcap require one to use the tputs()
 * function to output terminal control characters, and this function
 * doesn't allow one to specify a file stream. As a result, the following
 * file-scope variable is used to pass the current output file stream.
 * This is bad, but there doesn't seem to be any alternative.
 */
#if defined(USE_TERMINFO) || defined(USE_TERMCAP)
static GetLine *tputs_gl = NULL;
#endif

/*
 * Define a tab to be a string of 8 spaces.
 */
#define TAB_WIDTH 8

/*
 * Lookup the current size of the terminal.
 */
static void gl_query_size(GetLine *gl, int *ncolumn, int *nline);

/*
 * Getline calls this to temporarily override certain signal handlers
 * of the calling program.
 */
static int gl_override_signal_handlers(GetLine *gl);

/*
 * Getline calls this to restore the signal handlers of the calling
 * program.
 */
static int gl_restore_signal_handlers(GetLine *gl);

/*
 * Temporarily block the delivery of all signals that gl_get_line()
 * is currently configured to trap.
 */
static int gl_mask_signals(GetLine *gl, sigset_t *oldset);

/*
 * Restore the process signal mask that was overriden by a previous
 * call to gl_mask_signals().
 */
static int gl_unmask_signals(GetLine *gl, sigset_t *oldset);

/*
 * Unblock the signals that gl_get_line() has been configured to catch.
 */
static int gl_catch_signals(GetLine *gl);

/*
 * Return the set of all trappable signals.
 */
static void gl_list_trappable_signals(sigset_t *signals);

/*
 * Put the terminal into raw input mode, after saving the original
 * terminal attributes in gl->oldattr.
 */
static int gl_raw_terminal_mode(GetLine *gl);

/*
 * Restore the terminal attributes from gl->oldattr.
 */
static int gl_restore_terminal_attributes(GetLine *gl);

/*
 * Switch to non-blocking I/O if possible.
 */
static int gl_nonblocking_io(GetLine *gl, int fd);

/*
 * Switch to blocking I/O if possible.
 */
static int gl_blocking_io(GetLine *gl, int fd);

/*
 * Read a line from the user in raw mode.
 */
static int gl_get_input_line(GetLine *gl, const char *prompt,
			     const char *start_line, int start_pos);

/*
 * Query the user for a single character.
 */
static int gl_get_query_char(GetLine *gl, const char *prompt, int defchar);

/*
 * Read input from a non-interactive input stream.
 */
static int gl_read_stream_line(GetLine *gl);

/*
 * Read a single character from a non-interactive input stream.
 */
static int gl_read_stream_char(GetLine *gl);

/*
 * Prepare to edit a new line.
 */
static int gl_present_line(GetLine *gl, const char *prompt,
			   const char *start_line, int start_pos);

/*
 * Reset all line-editing parameters for a new input line.
 */
static void gl_reset_editor(GetLine *gl);

/*
 * Handle the receipt of the potential start of a new key-sequence from
 * the user.
 */
static int gl_interpret_char(GetLine *gl, char c);

/*
 * Bind a single control or meta character to an action.
 */
static int gl_bind_control_char(GetLine *gl, KtBinder binder,
				char c, const char *action);

/*
 * Set up terminal-specific key bindings.
 */
static int gl_bind_terminal_keys(GetLine *gl);

/*
 * Lookup terminal control string and size information.
 */
static int gl_control_strings(GetLine *gl, const char *term);

/*
 * Wrappers around the terminfo and termcap functions that lookup
 * strings in the terminal information databases.
 */
#ifdef USE_TERMINFO
static const char *gl_tigetstr(GetLine *gl, const char *name);
#elif defined(USE_TERMCAP)
static const char *gl_tgetstr(GetLine *gl, const char *name, char **bufptr);
#endif

/*
 * Output a binary string directly to the terminal.
 */
static int gl_print_raw_string(GetLine *gl, int buffered,
			       const char *string, int n);

/*
 * Print an informational message, starting and finishing on new lines.
 * After the list of strings to be printed, the last argument MUST be
 * GL_END_INFO.
 */
static int gl_print_info(GetLine *gl, ...);
#define GL_END_INFO ((const char *)0)

/*
 * Start a newline and place the cursor at its start.
 */
static int gl_start_newline(GetLine *gl, int buffered);

/*
 * Output a terminal control sequence.
 */
static int gl_print_control_sequence(GetLine *gl, int nline,
				     const char *string);

/*
 * Output a character or string to the terminal after converting tabs
 * to spaces and control characters to a caret followed by the modified
 * character.
 */
static int gl_print_char(GetLine *gl, char c, char pad);
static int gl_print_string(GetLine *gl, const char *string, char pad);

/*
 * Delete nc characters starting from the one under the cursor.
 * Optionally copy the deleted characters to the cut buffer.
 */
static int gl_delete_chars(GetLine *gl, int nc, int cut);

/*
 * Add a character to the line buffer at the current cursor position,
 * inserting or overwriting according the current mode.
 */
static int gl_add_char_to_line(GetLine *gl, char c);

/*
 * Insert/append a string to the line buffer and terminal at the current
 * cursor position.
 */
static int gl_add_string_to_line(GetLine *gl, const char *s);

/*
 * Record a new character in the input-line buffer.
 */
static int gl_buffer_char(GetLine *gl, char c, int bufpos);

/*
 * Record a string in the input-line buffer.
 */
static int gl_buffer_string(GetLine *gl, const char *s, int n, int bufpos);

/*
 * Make way to insert a string in the input-line buffer.
 */
static int gl_make_gap_in_buffer(GetLine *gl, int start, int n);

/*
 * Remove characters from the input-line buffer, and move any characters
 * that followed them to the start of the vacated space.
 */
static void gl_remove_from_buffer(GetLine *gl, int start, int n);

/*
 * Terminate the input-line buffer after a specified number of characters.
 */
static int gl_truncate_buffer(GetLine *gl, int n);

/*
 * Delete the displayed part of the input line that follows the current
 * terminal cursor position.
 */
static int gl_truncate_display(GetLine *gl);

/*
 * Accomodate changes to the contents of the input line buffer
 * that weren't made by the above gl_*buffer functions.
 */
static void gl_update_buffer(GetLine *gl);

/*
 * Read a single character from the terminal.
 */
static int gl_read_terminal(GetLine *gl, int keep, char *c);

/*
 * Discard processed characters from the key-press lookahead buffer.
 */
static void gl_discard_chars(GetLine *gl, int nused);

/*
 * Move the terminal cursor n positions to the left or right.
 */
static int gl_terminal_move_cursor(GetLine *gl, int n);

/*
 * Move the terminal cursor to a given position.
 */
static int gl_set_term_curpos(GetLine *gl, int term_curpos);

/*
 * Set the position of the cursor both in the line input buffer and on the
 * terminal.
 */
static int gl_place_cursor(GetLine *gl, int buff_curpos);

/*
 * How many characters are needed to write a number as an octal string?
 */
static int gl_octal_width(unsigned num);

/*
 * Return the number of spaces needed to display a tab character at
 * a given location of the terminal.
 */
static int gl_displayed_tab_width(GetLine *gl, int term_curpos);

/*
 * Return the number of terminal characters needed to display a
 * given raw character.
 */
static int gl_displayed_char_width(GetLine *gl, char c, int term_curpos);

/*
 * Return the number of terminal characters needed to display a
 * given substring.
 */
static int gl_displayed_string_width(GetLine *gl, const char *string, int nc,
				     int term_curpos);

/*
 * Return non-zero if 'c' is to be considered part of a word.
 */
static int gl_is_word_char(int c);

/*
 * Read a tecla configuration file.
 */
static int _gl_read_config_file(GetLine *gl, const char *filename, KtBinder who);

/*
 * Read a tecla configuration string.
 */
static int _gl_read_config_string(GetLine *gl, const char *buffer, KtBinder who);

/*
 * Define the callback function used by _gl_parse_config_line() to
 * read the next character of a configuration stream.
 */
#define GLC_GETC_FN(fn) int (fn)(void *stream)
typedef GLC_GETC_FN(GlcGetcFn);

static GLC_GETC_FN(glc_file_getc);  /* Read from a file */
static GLC_GETC_FN(glc_buff_getc);  /* Read from a string */

/*
 * Parse a single configuration command line.
 */
static int _gl_parse_config_line(GetLine *gl, void *stream, GlcGetcFn *getc_fn,
				 const char *origin, KtBinder who, int *lineno);
static int gl_report_config_error(GetLine *gl, const char *origin, int lineno,
				  const char *errmsg);

/*
 * Bind the actual arrow key bindings to match those of the symbolic
 * arrow-key bindings.
 */
static int _gl_bind_arrow_keys(GetLine *gl);

/*
 * Copy the binding of the specified symbolic arrow-key binding to
 * the terminal specific, and default arrow-key key-sequences. 
 */
static int _gl_rebind_arrow_key(GetLine *gl, const char *name,
				const char *term_seq,
				const char *def_seq1,
				const char *def_seq2);

/*
 * After the gl_read_from_file() action has been used to tell gl_get_line()
 * to temporarily read input from a file, gl_revert_input() arranges
 * for input to be reverted to the input stream last registered with
 * gl_change_terminal().
 */
static void gl_revert_input(GetLine *gl);

/*
 * Flush unwritten characters to the terminal.
 */
static int gl_flush_output(GetLine *gl);

/*
 * The callback through which all terminal output is routed.
 * This simply appends characters to a queue buffer, which is
 * subsequently flushed to the output channel by gl_flush_output().
 */
static GL_WRITE_FN(gl_write_fn);

/*
 * The callback function which the output character queue object
 * calls to transfer characters to the output channel.
 */
static GL_WRITE_FN(gl_flush_terminal);

/*
 * Enumerate the possible return statuses of gl_read_input().
 */
typedef enum {
  GL_READ_OK,      /* A character was read successfully */
  GL_READ_ERROR,   /* A read-error occurred */
  GL_READ_BLOCKED, /* The read would have blocked the caller */
  GL_READ_EOF      /* The end of the current input file was reached */
} GlReadStatus;

static GlReadStatus gl_read_input(GetLine *gl, char *c);
/*
 * Private functions of gl_read_input().
 */
static int gl_event_handler(GetLine *gl, int fd);
static GlReadStatus gl_read_unmasked(GetLine *gl, int fd, char *c);


/*
 * A private function of gl_tty_signals().
 */
static int gl_set_tty_signal(int signo, void (*handler)(int));

/*
 * Change the editor style being emulated.
 */
static int gl_change_editor(GetLine *gl, GlEditor editor);

/*
 * Searching in a given direction, return the index of a given (or
 * read) character in the input line, or the character that precedes
 * it in the specified search direction. Return -1 if not found.
 */
static int gl_find_char(GetLine *gl, int count, int forward, int onto, char c);

/*
 * Return the buffer index of the nth word ending after the cursor.
 */
static int gl_nth_word_end_forward(GetLine *gl, int n);

/*
 * Return the buffer index of the nth word start after the cursor.
 */
static int gl_nth_word_start_forward(GetLine *gl, int n);

/*
 * Return the buffer index of the nth word start before the cursor.
 */
static int gl_nth_word_start_backward(GetLine *gl, int n);

/*
 * When called when vi command mode is enabled, this function saves the
 * current line and cursor position for potential restoration later
 * by the vi undo command.
 */
static void gl_save_for_undo(GetLine *gl);

/*
 * If in vi mode, switch to vi command mode.
 */
static void gl_vi_command_mode(GetLine *gl);

/*
 * In vi mode this is used to delete up to or onto a given or read
 * character in the input line. Also switch to insert mode if requested
 * after the deletion.
 */
static int gl_delete_find(GetLine *gl, int count, char c, int forward,
			  int onto, int change);

/*
 * Copy the characters between the cursor and the count'th instance of
 * a specified (or read) character in the input line, into the cut buffer.
 */
static int gl_copy_find(GetLine *gl, int count, char c, int forward, int onto);

/*
 * Return the line index of the parenthesis that either matches the one under
 * the cursor, or not over a parenthesis character, the index of the next
 * close parenthesis. Return -1 if not found.
 */
static int gl_index_of_matching_paren(GetLine *gl);

/*
 * Replace a malloc'd string (or NULL), with another malloc'd copy of
 * a string (or NULL).
 */
static int gl_record_string(char **sptr, const char *string);

/*
 * Enumerate text display attributes as powers of two, suitable for
 * use in a bit-mask.
 */
typedef enum {
  GL_TXT_STANDOUT=1,   /* Display text highlighted */
  GL_TXT_UNDERLINE=2,  /* Display text underlined */
  GL_TXT_REVERSE=4,    /* Display text with reverse video */
  GL_TXT_BLINK=8,      /* Display blinking text */
  GL_TXT_DIM=16,       /* Display text in a dim font */
  GL_TXT_BOLD=32       /* Display text using a bold font */
} GlTextAttr;

/*
 * Display the prompt regardless of the current visibility mode.
 */
static int gl_display_prompt(GetLine *gl);

/*
 * Return the number of characters used by the prompt on the terminal.
 */
static int gl_displayed_prompt_width(GetLine *gl);

/*
 * Prepare to return the current input line to the caller of gl_get_line().
 */
static int gl_line_ended(GetLine *gl, int newline_char);

/*
 * Arrange for the input line to be redisplayed when the current contents
 * of the output queue have been flushed.
 */
static void gl_queue_redisplay(GetLine *gl);

/*
 * Erase the displayed representation of the input line, without
 * touching the buffered copy.
 */
static int gl_erase_line(GetLine *gl);

/*
 * This function is called whenever the input line has been erased.
 */
static void gl_line_erased(GetLine *gl);

/*
 * Arrange for the current input line to be discarded.
 */
void _gl_abandon_line(GetLine *gl);

/*
 * The following are private internally callable versions of pertinent
 * public functions. Unlike their public wrapper functions, they don't
 * block signals while running, and assume that their arguments are valid.
 * They are designed to be called from places where signals are already
 * blocked, and where simple sanity checks have already been applied to
 * their arguments.
 */
static char *_gl_get_line(GetLine *gl, const char *prompt,
			  const char *start_line, int start_pos);
static int _gl_query_char(GetLine *gl, const char *prompt, char defchar);
static int _gl_read_char(GetLine *gl);
static int _gl_update_size(GetLine *gl);
/*
 * Redraw the current input line to account for a change in the terminal
 * size. Also install the new size in gl.
 */
static int gl_handle_tty_resize(GetLine *gl, int ncolumn, int nline);

static int _gl_change_terminal(GetLine *gl, FILE *input_fp, FILE *output_fp,
			       const char *term);
static int _gl_configure_getline(GetLine *gl, const char *app_string,
				 const char *app_file, const char *user_file);
static int _gl_save_history(GetLine *gl, const char *filename,
			    const char *comment, int max_lines);
static int _gl_load_history(GetLine *gl, const char *filename,
			    const char *comment);
static int _gl_watch_fd(GetLine *gl, int fd, GlFdEvent event,
			GlFdEventFn *callback, void *data);
static void _gl_terminal_size(GetLine *gl, int def_ncolumn, int def_nline,
			      GlTerminalSize *size);
static void _gl_replace_prompt(GetLine *gl, const char *prompt);
static int _gl_trap_signal(GetLine *gl, int signo, unsigned flags,
			   GlAfterSignal after, int errno_value);
static int _gl_raw_io(GetLine *gl, int redisplay);
static int _gl_normal_io(GetLine *gl);
static int _gl_completion_action(GetLine *gl, void *data, CplMatchFn *match_fn,
				 int list_only, const char *name,
				 const char *keyseq);
static int _gl_register_action(GetLine *gl, void *data, GlActionFn *fn,
			       const char *name, const char *keyseq);
static int _gl_io_mode(GetLine *gl, GlIOMode mode);
static int _gl_set_term_size(GetLine *gl, int ncolumn, int nline);
static int _gl_append_history(GetLine *gl, const char *line);

/*
 * Reset the completion status and associated errno value in
 * gl->rtn_status and gl->rtn_errno.
 */
static void gl_clear_status(GetLine *gl);

/*
 * Record a completion status, unless a previous abnormal completion
 * status has already been recorded for the current call.
 */
static void gl_record_status(GetLine *gl, GlReturnStatus rtn_status,
			     int rtn_errno);

/*
 * Set the maximum length of a line in a user's tecla configuration
 * file (not counting comments).
 */
#define GL_CONF_BUFLEN 100

/*
 * Set the maximum number of arguments supported by individual commands
 * in tecla configuration files.
 */
#define GL_CONF_MAXARG 10

/*
 * Prototype the available action functions.
 */
static KT_KEY_FN(gl_user_interrupt);
static KT_KEY_FN(gl_abort);
static KT_KEY_FN(gl_suspend);
static KT_KEY_FN(gl_stop_output);
static KT_KEY_FN(gl_start_output);
static KT_KEY_FN(gl_literal_next);
static KT_KEY_FN(gl_cursor_left);
static KT_KEY_FN(gl_cursor_right);
static KT_KEY_FN(gl_insert_mode);
static KT_KEY_FN(gl_beginning_of_line);
static KT_KEY_FN(gl_end_of_line);
static KT_KEY_FN(gl_delete_line);
static KT_KEY_FN(gl_kill_line);
static KT_KEY_FN(gl_forward_word);
static KT_KEY_FN(gl_backward_word);
static KT_KEY_FN(gl_forward_delete_char);
static KT_KEY_FN(gl_backward_delete_char);
static KT_KEY_FN(gl_forward_delete_word);
static KT_KEY_FN(gl_backward_delete_word);
static KT_KEY_FN(gl_delete_refind);
static KT_KEY_FN(gl_delete_invert_refind);
static KT_KEY_FN(gl_delete_to_column);
static KT_KEY_FN(gl_delete_to_parenthesis);
static KT_KEY_FN(gl_forward_delete_find);
static KT_KEY_FN(gl_backward_delete_find);
static KT_KEY_FN(gl_forward_delete_to);
static KT_KEY_FN(gl_backward_delete_to);
static KT_KEY_FN(gl_upcase_word);
static KT_KEY_FN(gl_downcase_word);
static KT_KEY_FN(gl_capitalize_word);
static KT_KEY_FN(gl_redisplay);
static KT_KEY_FN(gl_clear_screen);
static KT_KEY_FN(gl_transpose_chars);
static KT_KEY_FN(gl_set_mark);
static KT_KEY_FN(gl_exchange_point_and_mark);
static KT_KEY_FN(gl_kill_region);
static KT_KEY_FN(gl_copy_region_as_kill);
static KT_KEY_FN(gl_yank);
static KT_KEY_FN(gl_up_history);
static KT_KEY_FN(gl_down_history);
static KT_KEY_FN(gl_history_search_backward);
static KT_KEY_FN(gl_history_re_search_backward);
static KT_KEY_FN(gl_history_search_forward);
static KT_KEY_FN(gl_history_re_search_forward);
static KT_KEY_FN(gl_complete_word);
#ifndef HIDE_FILE_SYSTEM
static KT_KEY_FN(gl_expand_filename);
static KT_KEY_FN(gl_read_from_file);
static KT_KEY_FN(gl_read_init_files);
static KT_KEY_FN(gl_list_glob);
#endif
static KT_KEY_FN(gl_del_char_or_list_or_eof);
static KT_KEY_FN(gl_list_or_eof);
static KT_KEY_FN(gl_beginning_of_history);
static KT_KEY_FN(gl_end_of_history);
static KT_KEY_FN(gl_digit_argument);
static KT_KEY_FN(gl_newline);
static KT_KEY_FN(gl_repeat_history);
static KT_KEY_FN(gl_vi_insert);
static KT_KEY_FN(gl_vi_overwrite);
static KT_KEY_FN(gl_change_case);
static KT_KEY_FN(gl_vi_insert_at_bol);
static KT_KEY_FN(gl_vi_append_at_eol);
static KT_KEY_FN(gl_vi_append);
static KT_KEY_FN(gl_backward_kill_line);
static KT_KEY_FN(gl_goto_column);
static KT_KEY_FN(gl_forward_to_word);
static KT_KEY_FN(gl_vi_replace_char);
static KT_KEY_FN(gl_vi_change_rest_of_line);
static KT_KEY_FN(gl_vi_change_line);
static KT_KEY_FN(gl_vi_change_to_bol);
static KT_KEY_FN(gl_vi_change_refind);
static KT_KEY_FN(gl_vi_change_invert_refind);
static KT_KEY_FN(gl_vi_change_to_column);
static KT_KEY_FN(gl_vi_change_to_parenthesis);
static KT_KEY_FN(gl_vi_forward_change_word);
static KT_KEY_FN(gl_vi_backward_change_word);
static KT_KEY_FN(gl_vi_forward_change_find);
static KT_KEY_FN(gl_vi_backward_change_find);
static KT_KEY_FN(gl_vi_forward_change_to);
static KT_KEY_FN(gl_vi_backward_change_to);
static KT_KEY_FN(gl_vi_forward_change_char);
static KT_KEY_FN(gl_vi_backward_change_char);
static KT_KEY_FN(gl_forward_copy_char);
static KT_KEY_FN(gl_backward_copy_char);
static KT_KEY_FN(gl_forward_find_char);
static KT_KEY_FN(gl_backward_find_char);
static KT_KEY_FN(gl_forward_to_char);
static KT_KEY_FN(gl_backward_to_char);
static KT_KEY_FN(gl_repeat_find_char);
static KT_KEY_FN(gl_invert_refind_char);
static KT_KEY_FN(gl_append_yank);
static KT_KEY_FN(gl_backward_copy_word);
static KT_KEY_FN(gl_forward_copy_word);
static KT_KEY_FN(gl_copy_to_bol);
static KT_KEY_FN(gl_copy_refind);
static KT_KEY_FN(gl_copy_invert_refind);
static KT_KEY_FN(gl_copy_to_column);
static KT_KEY_FN(gl_copy_to_parenthesis);
static KT_KEY_FN(gl_copy_rest_of_line);
static KT_KEY_FN(gl_copy_line);
static KT_KEY_FN(gl_backward_copy_find);
static KT_KEY_FN(gl_forward_copy_find);
static KT_KEY_FN(gl_backward_copy_to);
static KT_KEY_FN(gl_forward_copy_to);
static KT_KEY_FN(gl_vi_undo);
static KT_KEY_FN(gl_emacs_editing_mode);
static KT_KEY_FN(gl_vi_editing_mode);
static KT_KEY_FN(gl_ring_bell);
static KT_KEY_FN(gl_vi_repeat_change);
static KT_KEY_FN(gl_find_parenthesis);
static KT_KEY_FN(gl_list_history);
static KT_KEY_FN(gl_list_completions);
static KT_KEY_FN(gl_run_external_action);

/*
 * Name the available action functions.
 */
static const struct {const char *name; KT_KEY_FN(*fn);} gl_actions[] = {
  {"user-interrupt",             gl_user_interrupt},
  {"abort",                      gl_abort},
  {"suspend",                    gl_suspend},
  {"stop-output",                gl_stop_output},
  {"start-output",               gl_start_output},
  {"literal-next",               gl_literal_next},
  {"cursor-right",               gl_cursor_right},
  {"cursor-left",                gl_cursor_left},
  {"insert-mode",                gl_insert_mode},
  {"beginning-of-line",          gl_beginning_of_line},
  {"end-of-line",                gl_end_of_line},
  {"delete-line",                gl_delete_line},
  {"kill-line",                  gl_kill_line},
  {"forward-word",               gl_forward_word},
  {"backward-word",              gl_backward_word},
  {"forward-delete-char",        gl_forward_delete_char},
  {"backward-delete-char",       gl_backward_delete_char},
  {"forward-delete-word",        gl_forward_delete_word},
  {"backward-delete-word",       gl_backward_delete_word},
  {"delete-refind",              gl_delete_refind},
  {"delete-invert-refind",       gl_delete_invert_refind},
  {"delete-to-column",           gl_delete_to_column},
  {"delete-to-parenthesis",      gl_delete_to_parenthesis},
  {"forward-delete-find",        gl_forward_delete_find},
  {"backward-delete-find",       gl_backward_delete_find},
  {"forward-delete-to",          gl_forward_delete_to},
  {"backward-delete-to",         gl_backward_delete_to},
  {"upcase-word",                gl_upcase_word},
  {"downcase-word",              gl_downcase_word},
  {"capitalize-word",            gl_capitalize_word},
  {"redisplay",                  gl_redisplay},
  {"clear-screen",               gl_clear_screen},
  {"transpose-chars",            gl_transpose_chars},
  {"set-mark",                   gl_set_mark},
  {"exchange-point-and-mark",    gl_exchange_point_and_mark},
  {"kill-region",                gl_kill_region},
  {"copy-region-as-kill",        gl_copy_region_as_kill},
  {"yank",                       gl_yank},
  {"up-history",                 gl_up_history},
  {"down-history",               gl_down_history},
  {"history-search-backward",    gl_history_search_backward},
  {"history-re-search-backward", gl_history_re_search_backward},
  {"history-search-forward",     gl_history_search_forward},
  {"history-re-search-forward",  gl_history_re_search_forward},
  {"complete-word",              gl_complete_word},
#ifndef HIDE_FILE_SYSTEM
  {"expand-filename",            gl_expand_filename},
  {"read-from-file",             gl_read_from_file},
  {"read-init-files",            gl_read_init_files},
  {"list-glob",                  gl_list_glob},
#endif
  {"del-char-or-list-or-eof",    gl_del_char_or_list_or_eof},
  {"beginning-of-history",       gl_beginning_of_history},
  {"end-of-history",             gl_end_of_history},
  {"digit-argument",             gl_digit_argument},
  {"newline",                    gl_newline},
  {"repeat-history",             gl_repeat_history},
  {"vi-insert",                  gl_vi_insert},
  {"vi-overwrite",               gl_vi_overwrite},
  {"vi-insert-at-bol",           gl_vi_insert_at_bol},
  {"vi-append-at-eol",           gl_vi_append_at_eol},
  {"vi-append",                  gl_vi_append},
  {"change-case",                gl_change_case},
  {"backward-kill-line",         gl_backward_kill_line},
  {"goto-column",                gl_goto_column},
  {"forward-to-word",            gl_forward_to_word},
  {"vi-replace-char",            gl_vi_replace_char},
  {"vi-change-rest-of-line",     gl_vi_change_rest_of_line},
  {"vi-change-line",             gl_vi_change_line},
  {"vi-change-to-bol",           gl_vi_change_to_bol},
  {"vi-change-refind",           gl_vi_change_refind},
  {"vi-change-invert-refind",    gl_vi_change_invert_refind},
  {"vi-change-to-column",        gl_vi_change_to_column},
  {"vi-change-to-parenthesis",   gl_vi_change_to_parenthesis},
  {"forward-copy-char",          gl_forward_copy_char},
  {"backward-copy-char",         gl_backward_copy_char},
  {"forward-find-char",          gl_forward_find_char},
  {"backward-find-char",         gl_backward_find_char},
  {"forward-to-char",            gl_forward_to_char},
  {"backward-to-char",           gl_backward_to_char},
  {"repeat-find-char",           gl_repeat_find_char},
  {"invert-refind-char",         gl_invert_refind_char},
  {"append-yank",                gl_append_yank},
  {"backward-copy-word",         gl_backward_copy_word},
  {"forward-copy-word",          gl_forward_copy_word},
  {"copy-to-bol",                gl_copy_to_bol},
  {"copy-refind",                gl_copy_refind},
  {"copy-invert-refind",         gl_copy_invert_refind},
  {"copy-to-column",             gl_copy_to_column},
  {"copy-to-parenthesis",        gl_copy_to_parenthesis},
  {"copy-rest-of-line",          gl_copy_rest_of_line},
  {"copy-line",                  gl_copy_line},
  {"backward-copy-find",         gl_backward_copy_find},
  {"forward-copy-find",          gl_forward_copy_find},
  {"backward-copy-to",           gl_backward_copy_to},
  {"forward-copy-to",            gl_forward_copy_to},
  {"list-or-eof",                gl_list_or_eof},
  {"vi-undo",                    gl_vi_undo},
  {"vi-backward-change-word",    gl_vi_backward_change_word},
  {"vi-forward-change-word",     gl_vi_forward_change_word},
  {"vi-backward-change-find",    gl_vi_backward_change_find},
  {"vi-forward-change-find",     gl_vi_forward_change_find},
  {"vi-backward-change-to",      gl_vi_backward_change_to},
  {"vi-forward-change-to",       gl_vi_forward_change_to},
  {"vi-backward-change-char",    gl_vi_backward_change_char},
  {"vi-forward-change-char",     gl_vi_forward_change_char},
  {"emacs-mode",                 gl_emacs_editing_mode},
  {"vi-mode",                    gl_vi_editing_mode},
  {"ring-bell",                  gl_ring_bell},
  {"vi-repeat-change",           gl_vi_repeat_change},
  {"find-parenthesis",           gl_find_parenthesis},
  {"list-history",               gl_list_history},
};

/*
 * Define the default key-bindings in emacs mode.
 */
static const KtKeyBinding gl_emacs_bindings[] = {
  {"right",        "cursor-right"},
  {"^F",           "cursor-right"},
  {"left",         "cursor-left"},
  {"^B",           "cursor-left"},
  {"M-i",          "insert-mode"},
  {"M-I",          "insert-mode"},
  {"^A",           "beginning-of-line"},
  {"^E",           "end-of-line"},
  {"^U",           "delete-line"},
  {"^K",           "kill-line"},
  {"M-f",          "forward-word"},
  {"M-F",          "forward-word"},
  {"M-b",          "backward-word"},
  {"M-B",          "backward-word"},
  {"^D",           "del-char-or-list-or-eof"},
  {"^H",           "backward-delete-char"},
  {"^?",           "backward-delete-char"},
  {"M-d",          "forward-delete-word"},
  {"M-D",          "forward-delete-word"},
  {"M-^H",         "backward-delete-word"},
  {"M-^?",         "backward-delete-word"},
  {"M-u",          "upcase-word"},
  {"M-U",          "upcase-word"},
  {"M-l",          "downcase-word"},
  {"M-L",          "downcase-word"},
  {"M-c",          "capitalize-word"},
  {"M-C",          "capitalize-word"},
  {"^R",           "redisplay"},
  {"^L",           "clear-screen"},
  {"^T",           "transpose-chars"},
  {"^@",           "set-mark"},
  {"^X^X",         "exchange-point-and-mark"},
  {"^W",           "kill-region"},
  {"M-w",          "copy-region-as-kill"},
  {"M-W",          "copy-region-as-kill"},
  {"^Y",           "yank"},
  {"^P",           "up-history"},
  {"up",           "up-history"},
  {"^N",           "down-history"},
  {"down",         "down-history"},
  {"M-p",          "history-search-backward"},
  {"M-P",          "history-search-backward"},
  {"M-n",          "history-search-forward"},
  {"M-N",          "history-search-forward"},
  {"\t",           "complete-word"},
#ifndef HIDE_FILE_SYSTEM
  {"^X*",          "expand-filename"},
  {"^X^F",         "read-from-file"},
  {"^X^R",         "read-init-files"},
  {"^Xg",          "list-glob"},
  {"^XG",          "list-glob"},
#endif
  {"^Xh",          "list-history"},
  {"^XH",          "list-history"},
  {"M-<",          "beginning-of-history"},
  {"M->",          "end-of-history"},
  {"M-0",          "digit-argument"},
  {"M-1",          "digit-argument"},
  {"M-2",          "digit-argument"},
  {"M-3",          "digit-argument"},
  {"M-4",          "digit-argument"},
  {"M-5",          "digit-argument"},
  {"M-6",          "digit-argument"},
  {"M-7",          "digit-argument"},
  {"M-8",          "digit-argument"},
  {"M-9",          "digit-argument"},
  {"\r",           "newline"},
  {"\n",           "newline"},
  {"M-o",          "repeat-history"},
  {"M-C-v",        "vi-mode"},
};

/*
 * Define the default key-bindings in vi mode. Note that in vi-mode
 * meta-key bindings are command-mode bindings. For example M-i first
 * switches to command mode if not already in that mode, then moves
 * the cursor one position right, as in vi.
 */
static const KtKeyBinding gl_vi_bindings[] = {
  {"^D",           "list-or-eof"},
#ifndef HIDE_FILE_SYSTEM
  {"^G",           "list-glob"},
#endif
  {"^H",           "backward-delete-char"},
  {"\t",           "complete-word"},
  {"\r",           "newline"},
  {"\n",           "newline"},
  {"^L",           "clear-screen"},
  {"^N",           "down-history"},
  {"^P",           "up-history"},
  {"^R",           "redisplay"},
  {"^U",           "backward-kill-line"},
  {"^W",           "backward-delete-word"},
#ifndef HIDE_FILE_SYSTEM
  {"^X^F",         "read-from-file"},
  {"^X^R",         "read-init-files"},
  {"^X*",          "expand-filename"},
#endif
  {"^?",           "backward-delete-char"},
  {"M- ",          "cursor-right"},
  {"M-$",          "end-of-line"},
#ifndef HIDE_FILE_SYSTEM
  {"M-*",          "expand-filename"},
#endif
  {"M-+",          "down-history"},
  {"M--",          "up-history"},
  {"M-<",          "beginning-of-history"},
  {"M->",          "end-of-history"},
  {"M-^",          "beginning-of-line"},
  {"M-;",          "repeat-find-char"},
  {"M-,",          "invert-refind-char"},
  {"M-|",          "goto-column"},
  {"M-~",          "change-case"},
  {"M-.",          "vi-repeat-change"},
  {"M-%",          "find-parenthesis"},
  {"M-0",          "digit-argument"},
  {"M-1",          "digit-argument"},
  {"M-2",          "digit-argument"},
  {"M-3",          "digit-argument"},
  {"M-4",          "digit-argument"},
  {"M-5",          "digit-argument"},
  {"M-6",          "digit-argument"},
  {"M-7",          "digit-argument"},
  {"M-8",          "digit-argument"},
  {"M-9",          "digit-argument"},
  {"M-a",          "vi-append"},
  {"M-A",          "vi-append-at-eol"},
  {"M-b",          "backward-word"},
  {"M-B",          "backward-word"},
  {"M-C",          "vi-change-rest-of-line"},
  {"M-cb",         "vi-backward-change-word"},
  {"M-cB",         "vi-backward-change-word"},
  {"M-cc",         "vi-change-line"},
  {"M-ce",         "vi-forward-change-word"},
  {"M-cE",         "vi-forward-change-word"},
  {"M-cw",         "vi-forward-change-word"},
  {"M-cW",         "vi-forward-change-word"},
  {"M-cF",         "vi-backward-change-find"},
  {"M-cf",         "vi-forward-change-find"},
  {"M-cT",         "vi-backward-change-to"},
  {"M-ct",         "vi-forward-change-to"},
  {"M-c;",         "vi-change-refind"},
  {"M-c,",         "vi-change-invert-refind"},
  {"M-ch",         "vi-backward-change-char"},
  {"M-c^H",        "vi-backward-change-char"},
  {"M-c^?",        "vi-backward-change-char"},
  {"M-cl",         "vi-forward-change-char"},
  {"M-c ",         "vi-forward-change-char"},
  {"M-c^",         "vi-change-to-bol"},
  {"M-c0",         "vi-change-to-bol"},
  {"M-c$",         "vi-change-rest-of-line"},
  {"M-c|",         "vi-change-to-column"},
  {"M-c%",         "vi-change-to-parenthesis"},
  {"M-dh",         "backward-delete-char"},
  {"M-d^H",        "backward-delete-char"},
  {"M-d^?",        "backward-delete-char"},
  {"M-dl",         "forward-delete-char"},
  {"M-d ",         "forward-delete-char"},
  {"M-dd",         "delete-line"},
  {"M-db",         "backward-delete-word"},
  {"M-dB",         "backward-delete-word"},
  {"M-de",         "forward-delete-word"},
  {"M-dE",         "forward-delete-word"},
  {"M-dw",         "forward-delete-word"},
  {"M-dW",         "forward-delete-word"},
  {"M-dF",         "backward-delete-find"},
  {"M-df",         "forward-delete-find"},
  {"M-dT",         "backward-delete-to"},
  {"M-dt",         "forward-delete-to"},
  {"M-d;",         "delete-refind"},
  {"M-d,",         "delete-invert-refind"},
  {"M-d^",         "backward-kill-line"},
  {"M-d0",         "backward-kill-line"},
  {"M-d$",         "kill-line"},
  {"M-D",          "kill-line"},
  {"M-d|",         "delete-to-column"},
  {"M-d%",         "delete-to-parenthesis"},
  {"M-e",          "forward-word"},
  {"M-E",          "forward-word"},
  {"M-f",          "forward-find-char"},
  {"M-F",          "backward-find-char"},
  {"M--",          "up-history"},
  {"M-h",          "cursor-left"},
  {"M-H",          "beginning-of-history"},
  {"M-i",          "vi-insert"},
  {"M-I",          "vi-insert-at-bol"},
  {"M-j",          "down-history"},
  {"M-J",          "history-search-forward"},
  {"M-k",          "up-history"},
  {"M-K",          "history-search-backward"},
  {"M-l",          "cursor-right"},
  {"M-L",          "end-of-history"},
  {"M-n",          "history-re-search-forward"},
  {"M-N",          "history-re-search-backward"},
  {"M-p",          "append-yank"},
  {"M-P",          "yank"},
  {"M-r",          "vi-replace-char"},
  {"M-R",          "vi-overwrite"},
  {"M-s",          "vi-forward-change-char"},
  {"M-S",          "vi-change-line"},
  {"M-t",          "forward-to-char"},
  {"M-T",          "backward-to-char"},
  {"M-u",          "vi-undo"},
  {"M-w",          "forward-to-word"},
  {"M-W",          "forward-to-word"},
  {"M-x",          "forward-delete-char"},
  {"M-X",          "backward-delete-char"},
  {"M-yh",         "backward-copy-char"},
  {"M-y^H",        "backward-copy-char"},
  {"M-y^?",        "backward-copy-char"},
  {"M-yl",         "forward-copy-char"},
  {"M-y ",         "forward-copy-char"},
  {"M-ye",         "forward-copy-word"},
  {"M-yE",         "forward-copy-word"},
  {"M-yw",         "forward-copy-word"},
  {"M-yW",         "forward-copy-word"},
  {"M-yb",         "backward-copy-word"},
  {"M-yB",         "backward-copy-word"},
  {"M-yf",         "forward-copy-find"},
  {"M-yF",         "backward-copy-find"},
  {"M-yt",         "forward-copy-to"},
  {"M-yT",         "backward-copy-to"},
  {"M-y;",         "copy-refind"},
  {"M-y,",         "copy-invert-refind"},
  {"M-y^",         "copy-to-bol"},
  {"M-y0",         "copy-to-bol"},
  {"M-y$",         "copy-rest-of-line"},
  {"M-yy",         "copy-line"},
  {"M-Y",          "copy-line"},
  {"M-y|",         "copy-to-column"},
  {"M-y%",         "copy-to-parenthesis"},
  {"M-^E",         "emacs-mode"},
  {"M-^H",         "cursor-left"},
  {"M-^?",         "cursor-left"},
  {"M-^L",         "clear-screen"},
  {"M-^N",         "down-history"},
  {"M-^P",         "up-history"},
  {"M-^R",         "redisplay"},
  {"M-^D",         "list-or-eof"},
  {"M-\r",         "newline"},
  {"M-\t",         "complete-word"},
  {"M-\n",         "newline"},
#ifndef HIDE_FILE_SYSTEM
  {"M-^X^R",       "read-init-files"},
#endif
  {"M-^Xh",        "list-history"},
  {"M-^XH",        "list-history"},
  {"down",         "down-history"},
  {"up",           "up-history"},
  {"left",         "cursor-left"},
  {"right",        "cursor-right"},
};

/*.......................................................................
 * Create a new GetLine object.
 *
 * Input:
 *  linelen  size_t    The maximum line length to allow for.
 *  histlen  size_t    The number of bytes to allocate for recording
 *                     a circular buffer of history lines.
 * Output:
 *  return  GetLine *  The new object, or NULL on error.
 */
GetLine *new_GetLine(size_t linelen, size_t histlen)
{
  GetLine *gl;  /* The object to be returned */
  int i;
/*
 * Check the arguments.
 */
  if(linelen < 10) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Allocate the container.
 */
  gl = (GetLine *) malloc(sizeof(GetLine));
  if(!gl) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_GetLine().
 */
  gl->err = NULL;
  gl->glh = NULL;
  gl->cpl = NULL;
#ifndef HIDE_FILE_SYSTEM
  gl->cplfn.fn = cpl_file_completions;
#else
  gl->cplfn.fn = gl_no_completions;
#endif
  gl->cplfn.data = NULL;
#ifndef WITHOUT_FILE_SYSTEM
  gl->ef = NULL;
#endif
  gl->capmem = NULL;
  gl->cq = NULL;
  gl->input_fd = -1;
  gl->output_fd = -1;
  gl->input_fp = NULL;
  gl->output_fp = NULL;
  gl->file_fp = NULL;
  gl->term = NULL;
  gl->is_term = 0;
  gl->flush_fn = gl_flush_terminal;
  gl->io_mode = GL_NORMAL_MODE;
  gl->raw_mode = 0;
  gl->pending_io = GLP_WRITE;  /* We will start by writing the prompt */
  gl_clear_status(gl);
  gl->linelen = linelen;
  gl->line = NULL;
  gl->cutbuf = NULL;
  gl->prompt = NULL;
  gl->prompt_len = 0;
  gl->prompt_changed = 0;
  gl->prompt_style = GL_LITERAL_PROMPT;
  gl->cpl_mem = NULL;
  gl->ext_act_mem = NULL;
  gl->sig_mem = NULL;
  gl->sigs = NULL;
  gl->signals_masked = 0;
  gl->signals_overriden = 0;
  sigemptyset(&gl->all_signal_set);
  sigemptyset(&gl->old_signal_set);
  sigemptyset(&gl->use_signal_set);
  gl->bindings = NULL;
  gl->ntotal = 0;
  gl->buff_curpos = 0;
  gl->term_curpos = 0;
  gl->term_len = 0;
  gl->buff_mark = 0;
  gl->insert_curpos = 0;
  gl->insert = 1;
  gl->number = -1;
  gl->endline = 1;
  gl->displayed = 0;
  gl->redisplay = 0;
  gl->postpone = 0;
  gl->keybuf[0]='\0';
  gl->nbuf = 0;
  gl->nread = 0;
  gl->current_action.fn = 0;
  gl->current_action.data = NULL;
  gl->current_count = 0;
  gl->preload_id = 0;
  gl->preload_history = 0;
  gl->keyseq_count = 0;
  gl->last_search = -1;
  gl->editor = GL_EMACS_MODE;
  gl->silence_bell = 0;
  gl->automatic_history = 1;
  gl->vi.undo.line = NULL;
  gl->vi.undo.buff_curpos = 0;
  gl->vi.undo.ntotal = 0;
  gl->vi.undo.saved = 0;
  gl->vi.repeat.action.fn = 0;
  gl->vi.repeat.action.data = 0;
  gl->vi.repeat.count = 0;
  gl->vi.repeat.input_curpos = 0;
  gl->vi.repeat.command_curpos = 0;
  gl->vi.repeat.input_char = '\0';
  gl->vi.repeat.saved = 0;
  gl->vi.repeat.active = 0;
  gl->vi.command = 0;
  gl->vi.find_forward = 0;
  gl->vi.find_onto = 0;
  gl->vi.find_char = '\0';
  gl->left = NULL;
  gl->right = NULL;
  gl->up = NULL;
  gl->down = NULL;
  gl->home = NULL;
  gl->bol = 0;
  gl->clear_eol = NULL;
  gl->clear_eod = NULL;
  gl->u_arrow = NULL;
  gl->d_arrow = NULL;
  gl->l_arrow = NULL;
  gl->r_arrow = NULL;
  gl->sound_bell = NULL;
  gl->bold = NULL;
  gl->underline = NULL;
  gl->standout = NULL;
  gl->dim = NULL;
  gl->reverse = NULL;
  gl->blink = NULL;
  gl->text_attr_off = NULL;
  gl->nline = 0;
  gl->ncolumn = 0;
#ifdef USE_TERMINFO
  gl->left_n = NULL;
  gl->right_n = NULL;
#elif defined(USE_TERMCAP)
  gl->tgetent_buf = NULL;
  gl->tgetstr_buf = NULL;
#endif
  gl->app_file = NULL;
  gl->user_file = NULL;
  gl->configured = 0;
  gl->echo = 1;
  gl->last_signal = -1;
#ifdef HAVE_SELECT
  gl->fd_node_mem = NULL;
  gl->fd_nodes = NULL;
  FD_ZERO(&gl->rfds);
  FD_ZERO(&gl->wfds);
  FD_ZERO(&gl->ufds);
  gl->max_fd = 0;
  gl->timer.dt.tv_sec = 0;
  gl->timer.dt.tv_usec = 0;
  gl->timer.fn = 0;
  gl->timer.data = NULL;
#endif
/*
 * Allocate an error reporting buffer.
 */
  gl->err = _new_ErrMsg();
  if(!gl->err)
    return del_GetLine(gl);
/*
 * Allocate the history buffer.
 */
  gl->glh = _new_GlHistory(histlen);
  if(!gl->glh)
    return del_GetLine(gl);
/*
 * Allocate the resource object for file-completion.
 */
  gl->cpl = new_WordCompletion();
  if(!gl->cpl)
    return del_GetLine(gl);
/*
 * Allocate the resource object for file-completion.
 */
#ifndef WITHOUT_FILE_SYSTEM
  gl->ef = new_ExpandFile();
  if(!gl->ef)
    return del_GetLine(gl);
#endif
/*
 * Allocate a string-segment memory allocator for use in storing terminal
 * capablity strings.
 */
  gl->capmem = _new_StringGroup(CAPMEM_SEGMENT_SIZE);
  if(!gl->capmem)
    return del_GetLine(gl);
/*
 * Allocate the character queue that is used to buffer terminal output.
 */
  gl->cq = _new_GlCharQueue();
  if(!gl->cq)
    return del_GetLine(gl);
/*
 * Allocate a line buffer, leaving 2 extra characters for the terminating
 * '\n' and '\0' characters
 */
  gl->line = (char *) malloc(linelen + 2);
  if(!gl->line) {
    errno = ENOMEM;
    return del_GetLine(gl);
  };
/*
 * Start with an empty input line.
 */
  gl_truncate_buffer(gl, 0);
/*
 * Allocate a cut buffer.
 */
  gl->cutbuf = (char *) malloc(linelen + 2);
  if(!gl->cutbuf) {
    errno = ENOMEM;
    return del_GetLine(gl);
  };
  gl->cutbuf[0] = '\0';
/*
 * Allocate an initial empty prompt.
 */
  _gl_replace_prompt(gl, NULL);
  if(!gl->prompt) {
    errno = ENOMEM;
    return del_GetLine(gl);
  };
/*
 * Allocate a vi undo buffer.
 */
  gl->vi.undo.line = (char *) malloc(linelen + 2);
  if(!gl->vi.undo.line) {
    errno = ENOMEM;
    return del_GetLine(gl);
  };
  gl->vi.undo.line[0] = '\0';
/*
 * Allocate a freelist from which to allocate nodes for the list
 * of completion functions.
 */
  gl->cpl_mem = _new_FreeList(sizeof(GlCplCallback), GL_CPL_FREELIST_BLOCKING);
  if(!gl->cpl_mem)
    return del_GetLine(gl);
/*
 * Allocate a freelist from which to allocate nodes for the list
 * of external action functions.
 */
  gl->ext_act_mem = _new_FreeList(sizeof(GlExternalAction),
				  GL_EXT_ACT_FREELIST_BLOCKING);
  if(!gl->ext_act_mem)
    return del_GetLine(gl);
/*
 * Allocate a freelist from which to allocate nodes for the list
 * of signals.
 */
  gl->sig_mem = _new_FreeList(sizeof(GlSignalNode), GLS_FREELIST_BLOCKING);
  if(!gl->sig_mem)
    return del_GetLine(gl);
/*
 * Install initial dispositions for the default list of signals that
 * gl_get_line() traps.
 */
  for(i=0; isigno, sig->flags, sig->after,
		       sig->errno_value))
      return del_GetLine(gl);
  };
/*
 * Allocate an empty table of key bindings.
 */
  gl->bindings = _new_KeyTab();
  if(!gl->bindings)
    return del_GetLine(gl);
/*
 * Define the available actions that can be bound to key sequences.
 */
  for(i=0; ibindings, gl_actions[i].name, gl_actions[i].fn, NULL))
      return del_GetLine(gl);
  };
/*
 * Set up the default bindings.
 */
  if(gl_change_editor(gl, gl->editor))
    return del_GetLine(gl);
/*
 * Allocate termcap buffers.
 */
#ifdef USE_TERMCAP
  gl->tgetent_buf = (char *) malloc(TERMCAP_BUF_SIZE);
  gl->tgetstr_buf = (char *) malloc(TERMCAP_BUF_SIZE);
  if(!gl->tgetent_buf || !gl->tgetstr_buf) {
    errno = ENOMEM;
    return del_GetLine(gl);
  };
#endif
/*
 * Set up for I/O assuming stdin and stdout.
 */
  if(_gl_change_terminal(gl, stdin, stdout, getenv("TERM")))
    return del_GetLine(gl);
/*
 * Create a freelist for use in allocating GlFdNode list nodes.
 */
#ifdef HAVE_SELECT
  gl->fd_node_mem = _new_FreeList(sizeof(GlFdNode), GLFD_FREELIST_BLOCKING);
  if(!gl->fd_node_mem)
    return del_GetLine(gl);
#endif
/*
 * We are done for now.
 */
  return gl;
}

/*.......................................................................
 * Delete a GetLine object.
 *
 * Input:
 *  gl     GetLine *  The object to be deleted.
 * Output:
 *  return GetLine *  The deleted object (always NULL).
 */
GetLine *del_GetLine(GetLine *gl)
{
  if(gl) {
/*
 * If the terminal is in raw server mode, reset it.
 */
    _gl_normal_io(gl);
/*
 * Deallocate all objects contained by gl.
 */
    gl->err = _del_ErrMsg(gl->err);
    gl->glh = _del_GlHistory(gl->glh);
    gl->cpl = del_WordCompletion(gl->cpl);
#ifndef WITHOUT_FILE_SYSTEM
    gl->ef = del_ExpandFile(gl->ef);
#endif
    gl->capmem = _del_StringGroup(gl->capmem);
    gl->cq = _del_GlCharQueue(gl->cq);
    if(gl->file_fp)
      fclose(gl->file_fp);
    if(gl->term)
      free(gl->term);
    if(gl->line)
      free(gl->line);
    if(gl->cutbuf)
      free(gl->cutbuf);
    if(gl->prompt)
      free(gl->prompt);
    gl->cpl_mem = _del_FreeList(gl->cpl_mem, 1);
    gl->ext_act_mem = _del_FreeList(gl->ext_act_mem, 1);
    gl->sig_mem = _del_FreeList(gl->sig_mem, 1);
    gl->sigs = NULL;       /* Already freed by freeing sig_mem */
    gl->bindings = _del_KeyTab(gl->bindings);
    if(gl->vi.undo.line)
      free(gl->vi.undo.line);
#ifdef USE_TERMCAP
    if(gl->tgetent_buf)
      free(gl->tgetent_buf);
    if(gl->tgetstr_buf)
      free(gl->tgetstr_buf);
#endif
    if(gl->app_file)
      free(gl->app_file);
    if(gl->user_file)
      free(gl->user_file);
#ifdef HAVE_SELECT
    gl->fd_node_mem = _del_FreeList(gl->fd_node_mem, 1);
    gl->fd_nodes = NULL;  /* Already freed by freeing gl->fd_node_mem */
#endif
/*
 * Delete the now empty container.
 */
    free(gl);
  };
  return NULL;
}

/*.......................................................................
 * Bind a control or meta character to an action.
 *
 * Input:
 *  gl         GetLine *  The resource object of this program.
 *  binder    KtBinder    The source of the binding.
 *  c             char    The control or meta character.
 *                        If this is '\0', the call is ignored.
 *  action  const char *  The action name to bind the key to.
 * Output:
 *  return         int    0 - OK.
 *                        1 - Error.
 */
static int gl_bind_control_char(GetLine *gl, KtBinder binder, char c,
				const char *action)
{
  char keyseq[2];
/*
 * Quietly reject binding to the NUL control character, since this
 * is an ambiguous prefix of all bindings.
 */
  if(c == '\0')
    return 0;
/*
 * Making sure not to bind characters which aren't either control or
 * meta characters.
 */
  if(IS_CTRL_CHAR(c) || IS_META_CHAR(c)) {
    keyseq[0] = c;
    keyseq[1] = '\0';
  } else {
    return 0;
  };
/*
 * Install the binding.
 */
  if(_kt_set_keybinding(gl->bindings, binder, keyseq, action)) {
    _err_record_msg(gl->err, _kt_last_error(gl->bindings), END_ERR_MSG);
    return 1;
  };
  return 0;
}

/*.......................................................................
 * Read a line from the user.
 *
 * Input:
 *  gl       GetLine *  A resource object returned by new_GetLine().
 *  prompt      char *  The prompt to prefix the line with.
 *  start_line  char *  The initial contents of the input line, or NULL
 *                      if it should start out empty.
 *  start_pos    int    If start_line isn't NULL, this specifies the
 *                      index of the character over which the cursor
 *                      should initially be positioned within the line.
 *                      If you just want it to follow the last character
 *                      of the line, send -1.
 * Output:
 *  return      char *  An internal buffer containing the input line, or
 *                      NULL at the end of input. If the line fitted in
 *                      the buffer there will be a '\n' newline character
 *                      before the terminating '\0'. If it was truncated
 *                      there will be no newline character, and the remains
 *                      of the line should be retrieved via further calls
 *                      to this function.
 */
char *gl_get_line(GetLine *gl, const char *prompt,
		  const char *start_line, int start_pos)
{
  char *retval;   /* The return value of _gl_get_line() */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Temporarily block all of the signals that we have been asked to trap.
 */
  if(gl_mask_signals(gl, &gl->old_signal_set))
    return NULL;
/*
 * Perform the command-line editing task.
 */
  retval = _gl_get_line(gl, prompt, start_line, start_pos);
/*
 * Restore the process signal mask to how it was when this function was
 * first called.
 */
  gl_unmask_signals(gl, &gl->old_signal_set);
  return retval;
}


/*.......................................................................
 * This is the main body of the public function gl_get_line().
 */
static char *_gl_get_line(GetLine *gl, const char *prompt,
			  const char *start_line, int start_pos)
{
  int waserr = 0;    /* True if an error occurs */
/*
 * Assume that this call will successfully complete the input
 * line until proven otherwise.
 */
  gl_clear_status(gl);
/*
 * If this is the first call to this function since new_GetLine(),
 * complete any postponed configuration.
 */
  if(!gl->configured) {
    (void) _gl_configure_getline(gl, NULL, NULL, TECLA_CONFIG_FILE);
    gl->configured = 1;
  };
/*
 * Before installing our signal handler functions, record the fact
 * that there are no pending signals.
 */
  gl_pending_signal = -1;
/*
 * Temporarily override the signal handlers of the calling program,
 * so that we can intercept signals that would leave the terminal
 * in a bad state.
 */
  waserr = gl_override_signal_handlers(gl);
/*
 * After recording the current terminal settings, switch the terminal
 * into raw input mode.
 */
  waserr = waserr || _gl_raw_io(gl, 1);
/*
 * Attempt to read the line. This will require more than one attempt if
 * either a current temporary input file is opened by gl_get_input_line()
 * or the end of a temporary input file is reached by gl_read_stream_line().
 */
  while(!waserr) {
/*
 * Read a line from a non-interactive stream?
 */
    if(gl->file_fp || !gl->is_term) {
      if(gl_read_stream_line(gl)==0) {
	break;
      } else if(gl->file_fp) {
	gl_revert_input(gl);
	gl_record_status(gl, GLR_NEWLINE, 0);
      } else {
	waserr = 1;
	break;
      };
    };
/*
 * Read from the terminal? Note that the above if() block may have
 * changed gl->file_fp, so it is necessary to retest it here, rather
 * than using an else statement.
 */
    if(!gl->file_fp && gl->is_term) {
      if(gl_get_input_line(gl, prompt, start_line, start_pos))
	waserr = 1;
      else
	break;
    };
  };
/*
 * If an error occurred, but gl->rtn_status is still set to
 * GLR_NEWLINE, change the status to GLR_ERROR. Otherwise
 * leave it at whatever specific value was assigned by the function
 * that aborted input. This means that only functions that trap
 * non-generic errors have to remember to update gl->rtn_status
 * themselves.
 */
  if(waserr && gl->rtn_status == GLR_NEWLINE)
    gl_record_status(gl, GLR_ERROR, errno);
/*
 * Restore terminal settings.
 */
  if(gl->io_mode != GL_SERVER_MODE)
    _gl_normal_io(gl);
/*
 * Restore the signal handlers.
 */
  gl_restore_signal_handlers(gl);
/*
 * If gl_get_line() gets aborted early, the errno value associated
 * with the event that caused this to happen is recorded in
 * gl->rtn_errno. Since errno may have been overwritten by cleanup
 * functions after this, restore its value to the value that it had
 * when the error condition occured, so that the caller can examine it
 * to find out what happened.
 */
  errno = gl->rtn_errno;
/*
 * Check the completion status to see how to return.
 */
  switch(gl->rtn_status) {
  case GLR_NEWLINE:    /* Success */
    return gl->line;
  case GLR_BLOCKED:    /* These events abort the current input line, */
  case GLR_SIGNAL:     /*  when in normal blocking I/O mode, but only */
  case GLR_TIMEOUT:    /*  temporarily pause line editing when in */
  case GLR_FDABORT:    /*  non-blocking server I/O mode. */
    if(gl->io_mode != GL_SERVER_MODE)
      _gl_abandon_line(gl);
    return NULL;
  case GLR_ERROR:      /* Unrecoverable errors abort the input line, */
  case GLR_EOF:        /*  regardless of the I/O mode. */
  default:
    _gl_abandon_line(gl);
    return NULL;
  };
}

/*.......................................................................
 * Read a single character from the user.
 *
 * Input:
 *  gl       GetLine *  A resource object returned by new_GetLine().
 *  prompt      char *  The prompt to prefix the line with, or NULL if
 *                      no prompt is required.
 *  defchar     char    The character to substitute if the
 *                      user simply hits return, or '\n' if you don't
 *                      need to substitute anything.
 * Output:
 *  return       int    The character that was read, or EOF if the read
 *                      had to be aborted (in which case you can call
 *                      gl_return_status() to find out why).
 */
int gl_query_char(GetLine *gl, const char *prompt, char defchar)
{
  int retval;   /* The return value of _gl_query_char() */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return EOF;
  };
/*
 * Temporarily block all of the signals that we have been asked to trap.
 */
  if(gl_mask_signals(gl, &gl->old_signal_set))
    return EOF;
/*
 * Perform the character reading task.
 */
  retval = _gl_query_char(gl, prompt, defchar);
/*
 * Restore the process signal mask to how it was when this function was
 * first called.
 */
  gl_unmask_signals(gl, &gl->old_signal_set);
  return retval;
}

/*.......................................................................
 * This is the main body of the public function gl_query_char().
 */
static int _gl_query_char(GetLine *gl, const char *prompt, char defchar)
{
  int c = EOF;       /* The character to be returned */
  int waserr = 0;    /* True if an error occurs */
/*
 * Assume that this call will successfully complete the input operation
 * until proven otherwise.
 */
  gl_clear_status(gl);
/*
 * If this is the first call to this function or gl_get_line(),
 * since new_GetLine(), complete any postponed configuration.
 */
  if(!gl->configured) {
    (void) _gl_configure_getline(gl, NULL, NULL, TECLA_CONFIG_FILE);
    gl->configured = 1;
  };
/*
 * Before installing our signal handler functions, record the fact
 * that there are no pending signals.
 */
  gl_pending_signal = -1;
/*
 * Temporarily override the signal handlers of the calling program,
 * so that we can intercept signals that would leave the terminal
 * in a bad state.
 */
  waserr = gl_override_signal_handlers(gl);
/*
 * After recording the current terminal settings, switch the terminal
 * into raw input mode without redisplaying any partially entered
 * input line.
 */
  waserr = waserr || _gl_raw_io(gl, 0);
/*
 * Attempt to read the line. This will require more than one attempt if
 * either a current temporary input file is opened by gl_get_input_line()
 * or the end of a temporary input file is reached by gl_read_stream_line().
 */
  while(!waserr) {
/*
 * Read a line from a non-interactive stream?
 */
    if(gl->file_fp || !gl->is_term) {
      c = gl_read_stream_char(gl);
      if(c != EOF) {            /* Success? */
	if(c=='\n') c = defchar;
	break;
      } else if(gl->file_fp) {  /* End of temporary input file? */
	gl_revert_input(gl);
	gl_record_status(gl, GLR_NEWLINE, 0);
      } else {                  /* An error? */
	waserr = 1;
	break;
      };
    };
/*
 * Read from the terminal? Note that the above if() block may have
 * changed gl->file_fp, so it is necessary to retest it here, rather
 * than using an else statement.
 */
    if(!gl->file_fp && gl->is_term) {
      c = gl_get_query_char(gl, prompt, defchar);
      if(c==EOF)
	waserr = 1;
      else
	break;
    };
  };
/*
 * If an error occurred, but gl->rtn_status is still set to
 * GLR_NEWLINE, change the status to GLR_ERROR. Otherwise
 * leave it at whatever specific value was assigned by the function
 * that aborted input. This means that only functions that trap
 * non-generic errors have to remember to update gl->rtn_status
 * themselves.
 */
  if(waserr && gl->rtn_status == GLR_NEWLINE)
    gl_record_status(gl, GLR_ERROR, errno);
/*
 * Restore terminal settings.
 */
  if(gl->io_mode != GL_SERVER_MODE)
    _gl_normal_io(gl);
/*
 * Restore the signal handlers.
 */
  gl_restore_signal_handlers(gl);
/*
 * If this function gets aborted early, the errno value associated
 * with the event that caused this to happen is recorded in
 * gl->rtn_errno. Since errno may have been overwritten by cleanup
 * functions after this, restore its value to the value that it had
 * when the error condition occured, so that the caller can examine it
 * to find out what happened.
 */
  errno = gl->rtn_errno;
/*
 * Error conditions are signalled to the caller, by setting the returned
 * character to EOF.
 */
  if(gl->rtn_status != GLR_NEWLINE)
    c = EOF;
/*
 * In this mode, every character that is read is a completed
 * transaction, just like reading a completed input line, so prepare
 * for the next input line or character.
 */
  _gl_abandon_line(gl);
/*
 * Return the acquired character.
 */
  return c;
}

/*.......................................................................
 * Record of the signal handlers of the calling program, so that they
 * can be restored later.
 *
 * Input:
 *  gl    GetLine *   The resource object of this library.
 * Output:
 *  return    int     0 - OK.
 *                    1 - Error.
 */
static int gl_override_signal_handlers(GetLine *gl)
{
  GlSignalNode *sig;   /* A node in the list of signals to be caught */
/*
 * Set up our signal handler.
 */
  SigAction act;
  act.sa_handler = gl_signal_handler;
  memcpy(&act.sa_mask, &gl->all_signal_set, sizeof(sigset_t));
  act.sa_flags = 0;
/*
 * Get the subset of the signals that we are supposed to trap that
 * should actually be trapped.
 */
  sigemptyset(&gl->use_signal_set);
  for(sig=gl->sigs; sig; sig=sig->next) {
/*
 * Trap this signal? If it is blocked by the calling program and we
 * haven't been told to unblock it, don't arrange to trap this signal.
 */
    if(sig->flags & GLS_UNBLOCK_SIG ||
       !sigismember(&gl->old_signal_set, sig->signo)) {
      if(sigaddset(&gl->use_signal_set, sig->signo) == -1) {
	_err_record_msg(gl->err, "sigaddset error", END_ERR_MSG);
	return 1;
      };
    };
  };
/*
 * Override the actions of the signals that we are trapping.
 */
  for(sig=gl->sigs; sig; sig=sig->next) {
    if(sigismember(&gl->use_signal_set, sig->signo)) {
      sigdelset(&act.sa_mask, sig->signo);
      if(sigaction(sig->signo, &act, &sig->original)) {
	_err_record_msg(gl->err, "sigaction error", END_ERR_MSG);
	return 1;
      };
      sigaddset(&act.sa_mask, sig->signo);
    };
  };
/*
 * Record the fact that the application's signal handlers have now
 * been overriden.
 */
  gl->signals_overriden = 1;
/*
 * Just in case a SIGWINCH signal was sent to the process while our
 * SIGWINCH signal handler wasn't in place, check to see if the terminal
 * size needs updating.
 */
  if(_gl_update_size(gl))
    return 1;
  return 0;
}

/*.......................................................................
 * Restore the signal handlers of the calling program.
 *
 * Input:
 *  gl     GetLine *  The resource object of this library.
 * Output:
 *  return     int    0 - OK.
 *                    1 - Error.
 */
static int gl_restore_signal_handlers(GetLine *gl)
{
  GlSignalNode *sig;   /* A node in the list of signals to be caught */
/*
 * Restore application signal handlers that were overriden
 * by gl_override_signal_handlers().
 */
  for(sig=gl->sigs; sig; sig=sig->next) {
    if(sigismember(&gl->use_signal_set, sig->signo) &&
       sigaction(sig->signo, &sig->original, NULL)) {
      _err_record_msg(gl->err, "sigaction error", END_ERR_MSG);
      return 1;
    };
  };
/*
 * Record the fact that the application's signal handlers have now
 * been restored.
 */
  gl->signals_overriden = 0;
  return 0;
}

/*.......................................................................
 * This signal handler simply records the fact that a given signal was
 * caught in the file-scope gl_pending_signal variable.
 */
static void gl_signal_handler(int signo)
{
  gl_pending_signal = signo;
  siglongjmp(gl_setjmp_buffer, 1);
}

/*.......................................................................
 * Switch the terminal into raw mode after storing the previous terminal
 * settings in gl->attributes.
 *
 * Input:
 *  gl     GetLine *   The resource object of this program.
 * Output:
 *  return     int     0 - OK.
 *                     1 - Error.
 */
static int gl_raw_terminal_mode(GetLine *gl)
{
  Termios newattr;   /* The new terminal attributes */
/*
 * If the terminal is already in raw mode, do nothing.
 */
  if(gl->raw_mode)
    return 0;
/*
 * Record the current terminal attributes.
 */
  if(tcgetattr(gl->input_fd, &gl->oldattr)) {
    _err_record_msg(gl->err, "tcgetattr error", END_ERR_MSG);
    return 1;
  };
/*
 * This function shouldn't do anything but record the current terminal
 * attritubes if editing has been disabled.
 */
  if(gl->editor == GL_NO_EDITOR)
    return 0;
/*
 * Modify the existing attributes.
 */
  newattr = gl->oldattr;
/*
 * Turn off local echo, canonical input mode and extended input processing.
 */
  newattr.c_lflag &= ~(ECHO | ICANON | IEXTEN);
/*
 * Don't translate carriage return to newline, turn off input parity
 * checking, don't strip off 8th bit, turn off output flow control.
 */
  newattr.c_iflag &= ~(ICRNL | INPCK | ISTRIP);
/*
 * Clear size bits, turn off parity checking, and allow 8-bit characters.
 */
  newattr.c_cflag &= ~(CSIZE | PARENB);
  newattr.c_cflag |= CS8;
/*
 * Turn off output processing.
 */
  newattr.c_oflag &= ~(OPOST);
/*
 * Request one byte at a time, without waiting.
 */
  newattr.c_cc[VMIN] = gl->io_mode==GL_SERVER_MODE ? 0:1;
  newattr.c_cc[VTIME] = 0;
/*
 * Install the new terminal modes.
 */
  while(tcsetattr(gl->input_fd, TCSADRAIN, &newattr)) {
    if(errno != EINTR) {
      _err_record_msg(gl->err, "tcsetattr error", END_ERR_MSG);
      return 1;
    };
  };
/*
 * Record the new terminal mode.
 */
  gl->raw_mode = 1;
  return 0;
}

/*.......................................................................
 * Restore the terminal attributes recorded in gl->oldattr.
 *
 * Input:
 *  gl     GetLine *   The resource object of this library.
 * Output:
 *  return     int     0 - OK.
 *                     1 - Error.
 */
static int gl_restore_terminal_attributes(GetLine *gl)
{
  int waserr = 0;
/*
 * If not in raw mode, do nothing.
 */
  if(!gl->raw_mode)
    return 0;
/*
 * Before changing the terminal attributes, make sure that all output
 * has been passed to the terminal.
 */
  if(gl_flush_output(gl))
    waserr = 1;
/*
 * Reset the terminal attributes to the values that they had on
 * entry to gl_get_line().
 */
  while(tcsetattr(gl->input_fd, TCSADRAIN, &gl->oldattr)) {
    if(errno != EINTR) {
      _err_record_msg(gl->err, "tcsetattr error", END_ERR_MSG);
      waserr = 1;
      break;
    };
  };
/*
 * Record the new terminal mode.
 */
  gl->raw_mode = 0;
  return waserr;
}

/*.......................................................................
 * Switch the terminal file descriptor to use non-blocking I/O.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  fd             int    The file descriptor to make non-blocking.
 */
static int gl_nonblocking_io(GetLine *gl, int fd)
{
  int fcntl_flags;   /* The new file-descriptor control flags */
/*
 * Is non-blocking I/O supported on this system?  Note that even
 * without non-blocking I/O, the terminal will probably still act as
 * though it was non-blocking, because we also set the terminal
 * attributes to return immediately if no input is available and we
 * use select() to wait to be able to write. If select() also isn't
 * available, then input will probably remain fine, but output could
 * block, depending on the behaviour of the terminal driver.
 */
#if defined(NON_BLOCKING_FLAG)
/*
 * Query the current file-control flags, and add the
 * non-blocking I/O flag.
 */
  fcntl_flags = fcntl(fd, F_GETFL) | NON_BLOCKING_FLAG;
/*
 * Install the new control flags.
 */
  if(fcntl(fd, F_SETFL, fcntl_flags) == -1) {
    _err_record_msg(gl->err, "fcntl error", END_ERR_MSG);
    return 1;
  };
#endif
  return 0;
}

/*.......................................................................
 * Switch to blocking terminal I/O.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  fd             int    The file descriptor to make blocking.
 */
static int gl_blocking_io(GetLine *gl, int fd)
{
  int fcntl_flags;   /* The new file-descriptor control flags */
/*
 * Is non-blocking I/O implemented on this system?
 */
#if defined(NON_BLOCKING_FLAG)
/*
 * Query the current file control flags and remove the non-blocking
 * I/O flag.
 */
  fcntl_flags = fcntl(fd, F_GETFL) & ~NON_BLOCKING_FLAG;
/*
 * Install the modified control flags.
 */
  if(fcntl(fd, F_SETFL, fcntl_flags) == -1) {
    _err_record_msg(gl->err, "fcntl error", END_ERR_MSG);
    return 1;
  };
#endif
  return 0;
}

/*.......................................................................
 * Read a new input line from the user.
 *
 * Input:
 *  gl         GetLine *  The resource object of this library.
 *  prompt        char *  The prompt to prefix the line with, or NULL to
 *                        use the same prompt that was used by the previous
 *                        line.
 *  start_line    char *  The initial contents of the input line, or NULL
 *                        if it should start out empty.
 *  start_pos      int    If start_line isn't NULL, this specifies the
 *                        index of the character over which the cursor
 *                        should initially be positioned within the line.
 *                        If you just want it to follow the last character
 *                        of the line, send -1.
 * Output:
 *  return    int    0 - OK.
 *                   1 - Error.
 */
static int gl_get_input_line(GetLine *gl, const char *prompt,
			     const char *start_line, int start_pos)
{
  char c;               /* The character being read */
/*
 * Flush any pending output to the terminal.
 */
  if(_glq_char_count(gl->cq) > 0 && gl_flush_output(gl))
    return 1;
/*
 * Are we starting a new line?
 */
  if(gl->endline) {
/*
 * Delete any incompletely enterred line.
 */
    if(gl_erase_line(gl))
      return 1;
/*
 * Display the new line to be edited.
 */
    if(gl_present_line(gl, prompt, start_line, start_pos))
      return 1;
  };
/*
 * Read one character at a time.
 */
  while(gl_read_terminal(gl, 1, &c) == 0) {
/*
 * Increment the count of the number of key sequences entered.
 */
    gl->keyseq_count++;
/*
 * Interpret the character either as the start of a new key-sequence,
 * as a continuation of a repeat count, or as a printable character
 * to be added to the line.
 */
    if(gl_interpret_char(gl, c))
      break;
/*
 * If we just ran an action function which temporarily asked for
 * input to be taken from a file, abort this call.
 */
    if(gl->file_fp)
      return 0;
/*
 * Has the line been completed?
 */
    if(gl->endline)
      return gl_line_ended(gl, c);
  };
/*
 * To get here, gl_read_terminal() must have returned non-zero. See
 * whether a signal was caught that requested that the current line
 * be returned.
 */
  if(gl->endline)
    return gl_line_ended(gl, '\n');
/*
 * If I/O blocked while attempting to get the latest character
 * of the key sequence, rewind the key buffer to allow interpretation of
 * the current key sequence to be restarted on the next call to this
 * function.
 */
  if(gl->rtn_status == GLR_BLOCKED && gl->pending_io == GLP_READ)
    gl->nread = 0;
  return 1;
}

/*.......................................................................
 * This is the private function of gl_query_char() that handles
 * prompting the user, reading a character from the terminal, and
 * displaying what the user entered.
 *
 * Input:
 *  gl         GetLine *  The resource object of this library.
 *  prompt        char *  The prompt to prefix the line with.
 *  defchar       char    The character to substitute if the
 *                        user simply hits return, or '\n' if you don't
 *                        need to substitute anything.
 * Output:
 *  return         int    The character that was read, or EOF if something
 *                        prevented a character from being read.
 */
static int gl_get_query_char(GetLine *gl, const char *prompt, int defchar)
{
  char c;               /* The character being read */
  int retval;           /* The return value of this function */
/*
 * Flush any pending output to the terminal.
 */
  if(_glq_char_count(gl->cq) > 0 && gl_flush_output(gl))
    return EOF;
/*
 * Delete any incompletely entered line.
 */
  if(gl_erase_line(gl))
    return EOF;
/*
 * Reset the line input parameters and display the prompt, if any.
 */
  if(gl_present_line(gl, prompt, NULL, 0))
    return EOF;
/*
 * Read one character.
 */
  if(gl_read_terminal(gl, 1, &c) == 0) {
/*
 * In this mode, count each character as being a new key-sequence.
 */
    gl->keyseq_count++;
/*
 * Delete the character that was read, from the key-press buffer.
 */
    gl_discard_chars(gl, gl->nread);
/*
 * Convert carriage returns to newlines.
 */
    if(c == '\r')
      c = '\n';
/*
 * If the user just hit return, subsitute the default character.
 */
    if(c == '\n')
      c = defchar;
/*
 * Display the entered character to the right of the prompt.
 */
    if(c!='\n') {
      if(gl_end_of_line(gl, 1, NULL)==0)
	gl_print_char(gl, c, ' ');
    };
/*
 * Record the return character, and mark the call as successful.
 */
    retval = c;
    gl_record_status(gl, GLR_NEWLINE, 0);
/*
 * Was a signal caught whose disposition is to cause the current input
 * line to be returned? If so return a newline character.
 */
  } else if(gl->endline) {
    retval = '\n';
    gl_record_status(gl, GLR_NEWLINE, 0);
  } else {
    retval = EOF;
  };
/*
 * Start a new line.
 */
  if(gl_start_newline(gl, 1))
    return EOF;
/*
 * Attempt to flush any pending output.
 */
  (void) gl_flush_output(gl);
/*
 * Return either the character that was read, or EOF if an error occurred.
 */
  return retval;
}

/*.......................................................................
 * Add a character to the line buffer at the current cursor position,
 * inserting or overwriting according the current mode.
 *
 * Input:
 *  gl   GetLine *   The resource object of this library.
 *  c       char     The character to be added.
 * Output:
 *  return   int     0 - OK.
 *                   1 - Insufficient room.
 */
static int gl_add_char_to_line(GetLine *gl, char c)
{
/*
 * Keep a record of the current cursor position.
 */
  int buff_curpos = gl->buff_curpos;
  int term_curpos = gl->term_curpos;
/*
 * Work out the displayed width of the new character.
 */
  int width = gl_displayed_char_width(gl, c, term_curpos);
/*
 * If we are in insert mode, or at the end of the line,
 * check that we can accomodate a new character in the buffer.
 * If not, simply return, leaving it up to the calling program
 * to check for the absence of a newline character.
 */
  if((gl->insert || buff_curpos >= gl->ntotal) && gl->ntotal >= gl->linelen)
    return 0;
/*
 * Are we adding characters to the line (ie. inserting or appending)?
 */
  if(gl->insert || buff_curpos >= gl->ntotal) {
/*
 * If inserting, make room for the new character.
 */
    if(buff_curpos < gl->ntotal)
      gl_make_gap_in_buffer(gl, buff_curpos, 1);
/*
 * Copy the character into the buffer.
 */
    gl_buffer_char(gl, c, buff_curpos);
    gl->buff_curpos++;
/*
 * Redraw the line from the cursor position to the end of the line,
 * and move the cursor to just after the added character.
 */
    if(gl_print_string(gl, gl->line + buff_curpos, '\0') ||
       gl_set_term_curpos(gl, term_curpos + width))
      return 1;
/*
 * Are we overwriting an existing character?
 */
  } else {
/*
 * Get the width of the character being overwritten.
 */
    int old_width = gl_displayed_char_width(gl, gl->line[buff_curpos],
					    term_curpos);
/*
 * Overwrite the character in the buffer.
 */
    gl_buffer_char(gl, c, buff_curpos);
/*
 * If we are replacing with a narrower character, we need to
 * redraw the terminal string to the end of the line, then
 * overwrite the trailing old_width - width characters
 * with spaces.
 */
    if(old_width > width) {
      if(gl_print_string(gl, gl->line + buff_curpos, '\0'))
	return 1;
/*
 * Clear to the end of the terminal.
 */
      if(gl_truncate_display(gl))
	return 1;
/*
 * Move the cursor to the end of the new character.
 */
      if(gl_set_term_curpos(gl, term_curpos + width))
	return 1;
      gl->buff_curpos++;
/*
 * If we are replacing with a wider character, then we will be
 * inserting new characters, and thus extending the line.
 */
    } else if(width > old_width) {
/*
 * Redraw the line from the cursor position to the end of the line,
 * and move the cursor to just after the added character.
 */
      if(gl_print_string(gl, gl->line + buff_curpos, '\0') ||
	 gl_set_term_curpos(gl, term_curpos + width))
	return 1;
      gl->buff_curpos++;
/*
 * The original and replacement characters have the same width,
 * so simply overwrite.
 */
    } else {
/*
 * Copy the character into the buffer.
 */
      gl_buffer_char(gl, c, buff_curpos);
      gl->buff_curpos++;
/*
 * Overwrite the original character.
 */
      if(gl_print_char(gl, c, gl->line[gl->buff_curpos]))
	return 1;
    };
  };
  return 0;
}

/*.......................................................................
 * Insert/append a string to the line buffer and terminal at the current
 * cursor position.
 *
 * Input:
 *  gl   GetLine *   The resource object of this library.
 *  s       char *   The string to be added.
 * Output:
 *  return   int     0 - OK.
 *                   1 - Insufficient room.
 */
static int gl_add_string_to_line(GetLine *gl, const char *s)
{
  int buff_slen;   /* The length of the string being added to line[] */
  int term_slen;   /* The length of the string being written to the terminal */
  int buff_curpos; /* The original value of gl->buff_curpos */
  int term_curpos; /* The original value of gl->term_curpos */
/*
 * Keep a record of the current cursor position.
 */
  buff_curpos = gl->buff_curpos;
  term_curpos = gl->term_curpos;
/*
 * How long is the string to be added?
 */
  buff_slen = strlen(s);
  term_slen = gl_displayed_string_width(gl, s, buff_slen, term_curpos);
/*
 * Check that we can accomodate the string in the buffer.
 * If not, simply return, leaving it up to the calling program
 * to check for the absence of a newline character.
 */
  if(gl->ntotal + buff_slen > gl->linelen)
    return 0;
/*
 * Move the characters that follow the cursor in the buffer by
 * buff_slen characters to the right.
 */
  if(gl->ntotal > gl->buff_curpos)
    gl_make_gap_in_buffer(gl, gl->buff_curpos, buff_slen);
/*
 * Copy the string into the buffer.
 */
  gl_buffer_string(gl, s, buff_slen, gl->buff_curpos);
  gl->buff_curpos += buff_slen;
/*
 * Write the modified part of the line to the terminal, then move
 * the terminal cursor to the end of the displayed input string.
 */
  if(gl_print_string(gl, gl->line + buff_curpos, '\0') ||
     gl_set_term_curpos(gl, term_curpos + term_slen))
    return 1;
  return 0;
}

/*.......................................................................
 * Read a single character from the terminal.
 *
 * Input:
 *  gl    GetLine *   The resource object of this library.
 *  keep      int     If true, the returned character will be kept in
 *                    the input buffer, for potential replays. It should
 *                    subsequently be removed from the buffer when the
 *                    key sequence that it belongs to has been fully
 *                    processed, by calling gl_discard_chars().
 * Input/Output:
 *  c        char *   The character that is read, is assigned to *c.
 * Output:
 *  return    int     0 - OK.
 *                    1 - Either an I/O error occurred, or a signal was
 *                        caught who's disposition is to abort gl_get_line()
 *                        or to have gl_get_line() return the current line
 *                        as though the user had pressed return. In the
 *                        latter case gl->endline will be non-zero.
 */
static int gl_read_terminal(GetLine *gl, int keep, char *c)
{
/*
 * Before waiting for a new character to be input, flush unwritten
 * characters to the terminal.
 */
  if(gl_flush_output(gl))
    return 1;
/*
 * Record the fact that we are about to read from the terminal.
 */
  gl->pending_io = GLP_READ;
/*
 * If there is already an unread character in the buffer,
 * return it.
 */
  if(gl->nread < gl->nbuf) {
    *c = gl->keybuf[gl->nread];
/*
 * Retain the character in the key buffer, but mark it as having been read?
 */
    if(keep) {
      gl->nread++;
/*
 * Completely remove the character from the key buffer?
 */
    } else {
      memmove(gl->keybuf + gl->nread, gl->keybuf + gl->nread + 1,
	      gl->nbuf - gl->nread - 1);
    };
    return 0;
  };
/*
 * Make sure that there is space in the key buffer for one more character.
 * This should always be true if gl_interpret_char() is called for each
 * new character added, since it will clear the buffer once it has recognized
 * or rejected a key sequence.
 */
  if(gl->nbuf + 1 > GL_KEY_MAX) {
    gl_print_info(gl, "gl_read_terminal: Buffer overflow avoided.",
		  GL_END_INFO);
    errno = EIO;
    return 1;
  };
/*
 * Read one character from the terminal.
 */
  switch(gl_read_input(gl, c)) {
  case GL_READ_OK:
    break;
  case GL_READ_BLOCKED:
    gl_record_status(gl, GLR_BLOCKED, BLOCKED_ERRNO);
    return 1;
    break;
  default:
    return 1;
    break;
  };
/*
 * Append the character to the key buffer?
 */
  if(keep) {
    gl->keybuf[gl->nbuf] = *c;
    gl->nread = ++gl->nbuf;
  };
  return 0;
}

/*.......................................................................
 * Read one or more keypresses from the terminal of an input stream.
 * 
 * Input:
 *  gl           GetLine *  The resource object of this module.
 *  c               char *  The character that was read is assigned to *c.
 * Output:
 *  return  GlReadStatus    The completion status of the read operation.
 */
static GlReadStatus gl_read_input(GetLine *gl, char *c)
{
/*
 * We may have to repeat the read if window change signals are received.
 */
  for(;;) {
/*
 * Which file descriptor should we read from? Mark this volatile, so
 * that siglongjmp() can't clobber it.
 */
    volatile int fd = gl->file_fp ? fileno(gl->file_fp) : gl->input_fd;
/*
 * If the endline flag becomes set, don't wait for another character.
 */
    if(gl->endline)
      return GL_READ_ERROR;
/*
 * Since the code in this function can block, trap signals.
 */
    if(sigsetjmp(gl_setjmp_buffer, 1)==0) {
/*
 * Handle the different I/O modes.
 */
      switch(gl->io_mode) {
/*
 * In normal I/O mode, we call the event handler before attempting
 * to read, since read() blocks.
 */
      case GL_NORMAL_MODE:
	if(gl_event_handler(gl, fd))
	  return GL_READ_ERROR;
	return gl_read_unmasked(gl, fd, c);  /* Read one character */
	break;
/*
 * In non-blocking server I/O mode, we attempt to read a character,
 * and only if this fails, call the event handler to wait for a any
 * user-configured timeout and any other user-configured events.  In
 * addition, we turn off the fcntl() non-blocking flag when reading
 * from the terminal, to work around a bug in Solaris. We can do this
 * without causing the read() to block, because when in non-blocking
 * server-I/O mode, gl_raw_io() sets the VMIN terminal attribute to 0,
 * which tells the terminal driver to return immediately if no
 * characters are available to be read.
 */
      case GL_SERVER_MODE:
	{
	  GlReadStatus status;        /* The return status */
	  if(isatty(fd))              /* If we reading from a terminal, */
	     gl_blocking_io(gl, fd);  /* switch to blocking I/O */
	  status = gl_read_unmasked(gl, fd, c); /* Try reading */
	  if(status == GL_READ_BLOCKED) {       /* Nothing readable yet */
	    if(gl_event_handler(gl, fd))        /* Wait for input */
	      status = GL_READ_ERROR;
	    else
	      status = gl_read_unmasked(gl, fd, c); /* Try reading again */
	  };
	  gl_nonblocking_io(gl, fd); /* Restore non-blocking I/O */
	  return status;
	};
	break;
      };
    };
/*
 * To get here, one of the signals that we are trapping must have
 * been received. Note that by using sigsetjmp() instead of setjmp()
 * the signal mask that was blocking these signals will have been
 * reinstated, so we can be sure that no more of these signals will
 * be received until we explicitly unblock them again.
 *
 * First, if non-blocking I/O was temporarily disabled, reinstate it.
 */
    if(gl->io_mode == GL_SERVER_MODE)
      gl_nonblocking_io(gl, fd);
/*
 * Now respond to the signal that was caught.
 */      
    if(gl_check_caught_signal(gl))
      return GL_READ_ERROR;
  };
}

/*.......................................................................
 * This is a private function of gl_read_input(), which unblocks signals
 * temporarily while it reads a single character from the specified file
 * descriptor.
 *
 * Input:
 *  gl          GetLine *  The resource object of this module.
 *  fd              int    The file descriptor to read from.
 *  c              char *  The character that was read is assigned to *c.
 * Output:
 *  return GlReadStatus    The completion status of the read.
 */
static GlReadStatus gl_read_unmasked(GetLine *gl, int fd, char *c)
{
  int nread;  /* The return value of read() */
/*
 * Unblock the signals that we are trapping, while waiting for I/O.
 */
  gl_catch_signals(gl);
/*
 * Attempt to read one character from the terminal, restarting the read
 * if any signals that we aren't trapping, are received.
 */
  do {
    errno = 0;
    nread = read(fd, c, 1);
  } while(nread < 0 && errno==EINTR);
/*
 * Block all of the signals that we are trapping.
 */
  gl_mask_signals(gl, NULL);
/*
 * Check the completion status of the read.
 */
  switch(nread) {
  case 1:
    return GL_READ_OK;
  case 0:
    return (isatty(fd) || errno != 0) ? GL_READ_BLOCKED : GL_READ_EOF;
  default:
    return GL_READ_ERROR;
  };
}

/*.......................................................................
 * Remove a specified number of characters from the start of the 
 * key-press lookahead buffer, gl->keybuf[], and arrange for the next
 * read to start from the character at the start of the shifted buffer.
 *
 * Input:
 *  gl      GetLine *  The resource object of this module.
 *  nused       int    The number of characters to discard from the start
 *                     of the buffer.
 */
static void gl_discard_chars(GetLine *gl, int nused)
{
  int nkeep = gl->nbuf - nused;
  if(nkeep > 0) {
    memmove(gl->keybuf, gl->keybuf + nused, nkeep);
    gl->nbuf = nkeep;
    gl->nread = 0;
  } else {
    gl->nbuf = gl->nread = 0;
  };
}

/*.......................................................................
 * This function is called to handle signals caught between calls to
 * sigsetjmp() and siglongjmp().
 *
 * Input:
 *  gl      GetLine *   The resource object of this library.
 * Output:
 *  return      int     0 - Signal handled internally.
 *                      1 - Signal requires gl_get_line() to abort.
 */
static int gl_check_caught_signal(GetLine *gl)
{
  GlSignalNode *sig;      /* The signal disposition */
  SigAction keep_action;  /* The signal disposition of tecla signal handlers */
  unsigned flags;         /* The signal processing flags to use */
  int signo;              /* The signal to be handled */
/*
 * Was no signal caught?
 */
  if(gl_pending_signal == -1)
    return 0;
/*
 * Get the signal to be handled.
 */
  signo = gl_pending_signal;
/*
 * Mark the signal as handled. Note that at this point, all of
 * the signals that we are trapping are blocked from delivery.
 */
  gl_pending_signal = -1;
/*
 * Record the signal that was caught, so that the user can query it later.
 */
  gl->last_signal = signo;
/*
 * In non-blocking server mode, the application is responsible for
 * responding to terminal signals, and we don't want gl_get_line()s
 * normal signal handling to clash with this, so whenever a signal
 * is caught, we arrange for gl_get_line() to abort and requeue the
 * signal while signals are still blocked. If the application
 * had the signal unblocked when gl_get_line() was called, the signal
 * will be delivered again as soon as gl_get_line() restores the
 * process signal mask, just before returning to the application.
 * Note that the caller of this function should set gl->pending_io
 * to the appropriate choice of GLP_READ and GLP_WRITE, before returning.
 */
  if(gl->io_mode==GL_SERVER_MODE) {
    gl_record_status(gl, GLR_SIGNAL, EINTR);
    raise(signo);
    return 1;
  };
/*
 * Lookup the requested disposition of this signal.
 */
  for(sig=gl->sigs; sig && sig->signo != signo; sig=sig->next)
    ;
  if(!sig)
    return 0;
/*
 * Get the signal response flags for this signal.
 */
  flags = sig->flags;
/*
 * Only perform terminal-specific actions if the session is interactive.
 */
  if(gl->is_term) {
/*
 * Did we receive a terminal size signal?
 */
#ifdef SIGWINCH
    if(signo == SIGWINCH && _gl_update_size(gl))
      return 1;
#endif
/*
 * Start a fresh line?
 */
    if(flags & GLS_RESTORE_LINE) {
      if(gl_start_newline(gl, 0))
	return 1;
    };
/*
 * Restore terminal settings to how they were before gl_get_line() was
 * called?
 */
    if(flags & GLS_RESTORE_TTY)
      gl_restore_terminal_attributes(gl);
  };
/*
 * Restore signal handlers to how they were before gl_get_line() was
 * called? If this hasn't been requested, only reinstate the signal
 * handler of the signal that we are handling.
 */
  if(flags & GLS_RESTORE_SIG) {
    gl_restore_signal_handlers(gl);
    gl_unmask_signals(gl, &gl->old_signal_set);
  } else {
    (void) sigaction(sig->signo, &sig->original, &keep_action);
    (void) sigprocmask(SIG_UNBLOCK, &sig->proc_mask, NULL);
  };
/*
 * Forward the signal to the application's signal handler.
 */
  if(!(flags & GLS_DONT_FORWARD))
    raise(signo);
/*
 * Reinstate our signal handlers.
 */
  if(flags & GLS_RESTORE_SIG) {
    gl_mask_signals(gl, NULL);
    gl_override_signal_handlers(gl);
  } else {
    (void) sigaction(sig->signo, &keep_action, NULL);
    (void) sigprocmask(SIG_BLOCK, &sig->proc_mask, NULL);
  };
/*
 * Prepare the terminal for continued editing, if this is an interactive
 * session.
 */
  if(gl->is_term) {
/*
 * Do we need to reinstate our terminal settings?
 */
    if(flags & GLS_RESTORE_TTY)
      gl_raw_terminal_mode(gl);
/*
 * Redraw the line?
 */
    if(flags & GLS_REDRAW_LINE)
      gl_queue_redisplay(gl);
  };
/*
 * What next?
 */
  switch(sig->after) {
  case GLS_RETURN:
    gl_newline(gl, 1, NULL);
    return gl->is_term && gl_flush_output(gl);
    break;
  case GLS_ABORT:
    gl_record_status(gl, GLR_SIGNAL, sig->errno_value);
    return 1;
    break;
  case GLS_CONTINUE:
    return gl->is_term && gl_flush_output(gl);
    break;
  };
  return 0;
}

/*.......................................................................
 * Get pertinent terminal control strings and the initial terminal size.
 *
 * Input:
 *  gl     GetLine *  The resource object of this library.
 *  term      char *  The type of the terminal.
 * Output:
 *  return     int    0 - OK.
 *                    1 - Error.
 */
static int gl_control_strings(GetLine *gl, const char *term)
{
  int bad_term = 0;   /* True if term is unusable */
/*
 * Discard any existing control strings from a previous terminal.
 */
  gl->left = NULL;
  gl->right = NULL;
  gl->up = NULL;
  gl->down = NULL;
  gl->home = NULL;
  gl->bol = 0;
  gl->clear_eol = NULL;
  gl->clear_eod = NULL;
  gl->u_arrow = NULL;
  gl->d_arrow = NULL;
  gl->l_arrow = NULL;
  gl->r_arrow = NULL;
  gl->sound_bell = NULL;
  gl->bold = NULL;
  gl->underline = NULL;
  gl->standout = NULL;
  gl->dim = NULL;
  gl->reverse = NULL;
  gl->blink = NULL;
  gl->text_attr_off = NULL;
  gl->nline = 0;
  gl->ncolumn = 0;
#ifdef USE_TERMINFO
  gl->left_n = NULL;
  gl->right_n = NULL;
#endif
/*
 * If possible lookup the information in a terminal information
 * database.
 */
#ifdef USE_TERMINFO
  {
    int errret;
    if(!term || setupterm((char *)term, gl->input_fd, &errret) == ERR) {
      bad_term = 1;
    } else {
      _clr_StringGroup(gl->capmem);
      gl->left = gl_tigetstr(gl, "cub1");
      gl->right = gl_tigetstr(gl, "cuf1");
      gl->up = gl_tigetstr(gl, "cuu1");
      gl->down = gl_tigetstr(gl, "cud1");
      gl->home = gl_tigetstr(gl, "home");
      gl->clear_eol = gl_tigetstr(gl, "el");
      gl->clear_eod = gl_tigetstr(gl, "ed");
      gl->u_arrow = gl_tigetstr(gl, "kcuu1");
      gl->d_arrow = gl_tigetstr(gl, "kcud1");
      gl->l_arrow = gl_tigetstr(gl, "kcub1");
      gl->r_arrow = gl_tigetstr(gl, "kcuf1");
      gl->left_n = gl_tigetstr(gl, "cub");
      gl->right_n = gl_tigetstr(gl, "cuf");
      gl->sound_bell = gl_tigetstr(gl, "bel");
      gl->bold = gl_tigetstr(gl, "bold");
      gl->underline = gl_tigetstr(gl, "smul");
      gl->standout = gl_tigetstr(gl, "smso");
      gl->dim = gl_tigetstr(gl, "dim");
      gl->reverse = gl_tigetstr(gl, "rev");
      gl->blink = gl_tigetstr(gl, "blink");
      gl->text_attr_off = gl_tigetstr(gl, "sgr0");
    };
  };
#elif defined(USE_TERMCAP)
  if(!term || tgetent(gl->tgetent_buf, (char *)term) < 0) {
    bad_term = 1;
  } else {
    char *tgetstr_buf_ptr = gl->tgetstr_buf;
    _clr_StringGroup(gl->capmem);
    gl->left = gl_tgetstr(gl, "le", &tgetstr_buf_ptr);
    gl->right = gl_tgetstr(gl, "nd", &tgetstr_buf_ptr);
    gl->up = gl_tgetstr(gl, "up", &tgetstr_buf_ptr);
    gl->down = gl_tgetstr(gl, "do", &tgetstr_buf_ptr);
    gl->home = gl_tgetstr(gl, "ho", &tgetstr_buf_ptr);
    gl->clear_eol = gl_tgetstr(gl, "ce", &tgetstr_buf_ptr);
    gl->clear_eod = gl_tgetstr(gl, "cd", &tgetstr_buf_ptr);
    gl->u_arrow = gl_tgetstr(gl, "ku", &tgetstr_buf_ptr);
    gl->d_arrow = gl_tgetstr(gl, "kd", &tgetstr_buf_ptr);
    gl->l_arrow = gl_tgetstr(gl, "kl", &tgetstr_buf_ptr);
    gl->r_arrow = gl_tgetstr(gl, "kr", &tgetstr_buf_ptr);
    gl->sound_bell = gl_tgetstr(gl, "bl", &tgetstr_buf_ptr);
    gl->bold = gl_tgetstr(gl, "md", &tgetstr_buf_ptr);
    gl->underline = gl_tgetstr(gl, "us", &tgetstr_buf_ptr);
    gl->standout = gl_tgetstr(gl, "so", &tgetstr_buf_ptr);
    gl->dim = gl_tgetstr(gl, "mh", &tgetstr_buf_ptr);
    gl->reverse = gl_tgetstr(gl, "mr", &tgetstr_buf_ptr);
    gl->blink = gl_tgetstr(gl, "mb", &tgetstr_buf_ptr);
    gl->text_attr_off = gl_tgetstr(gl, "me", &tgetstr_buf_ptr);
  };
#endif
/*
 * Report term being unusable.
 */
  if(bad_term) {
    gl_print_info(gl, "Bad terminal type: \"", term ? term : "(null)",
		  "\". Will assume vt100.", GL_END_INFO);
  };
/*
 * Fill in missing information with ANSI VT100 strings.
 */
  if(!gl->left)
    gl->left = "\b";    /* ^H */
  if(!gl->right)
    gl->right = GL_ESC_STR "[C";
  if(!gl->up)
    gl->up = GL_ESC_STR "[A";
  if(!gl->down)
    gl->down = "\n";
  if(!gl->home)
    gl->home = GL_ESC_STR "[H";
  if(!gl->bol)
    gl->bol = "\r";
  if(!gl->clear_eol)
    gl->clear_eol = GL_ESC_STR "[K";
  if(!gl->clear_eod)
    gl->clear_eod = GL_ESC_STR "[J";
  if(!gl->u_arrow)
    gl->u_arrow = GL_ESC_STR "[A";
  if(!gl->d_arrow)
    gl->d_arrow = GL_ESC_STR "[B";
  if(!gl->l_arrow)
    gl->l_arrow = GL_ESC_STR "[D";
  if(!gl->r_arrow)
    gl->r_arrow = GL_ESC_STR "[C";
  if(!gl->sound_bell)
    gl->sound_bell = "\a";
  if(!gl->bold)
    gl->bold = GL_ESC_STR "[1m";
  if(!gl->underline)
    gl->underline = GL_ESC_STR "[4m";
  if(!gl->standout)
    gl->standout = GL_ESC_STR "[1;7m";
  if(!gl->dim)
    gl->dim = "";  /* Not available */
  if(!gl->reverse)
    gl->reverse = GL_ESC_STR "[7m";
  if(!gl->blink)
    gl->blink = GL_ESC_STR "[5m";
  if(!gl->text_attr_off)
    gl->text_attr_off = GL_ESC_STR "[m";
/*
 * Find out the current terminal size.
 */
  (void) _gl_terminal_size(gl, GL_DEF_NCOLUMN, GL_DEF_NLINE, NULL);
  return 0;
}

#ifdef USE_TERMINFO
/*.......................................................................
 * This is a private function of gl_control_strings() used to look up
 * a termninal capability string from the terminfo database and make
 * a private copy of it.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  name    const char *  The name of the terminfo string to look up.
 * Output:
 *  return  const char *  The local copy of the capability, or NULL
 *                        if not available.
 */
static const char *gl_tigetstr(GetLine *gl, const char *name)
{
  const char *value = tigetstr((char *)name);
  if(!value || value == (char *) -1)
    return NULL;
  return _sg_store_string(gl->capmem, value, 0);
}
#elif defined(USE_TERMCAP)
/*.......................................................................
 * This is a private function of gl_control_strings() used to look up
 * a termninal capability string from the termcap database and make
 * a private copy of it. Note that some emulations of tgetstr(), such
 * as that used by Solaris, ignores the buffer pointer that is past to
 * it, so we can't assume that a private copy has been made that won't
 * be trashed by another call to gl_control_strings() by another
 * GetLine object. So we make what may be a redundant private copy
 * of the string in gl->capmem.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  name    const char *  The name of the terminfo string to look up.
 * Input/Output:
 *  bufptr        char ** On input *bufptr points to the location in
 *                        gl->tgetstr_buf at which to record the
 *                        capability string. On output *bufptr is
 *                        incremented over the stored string.
 * Output:
 *  return  const char *  The local copy of the capability, or NULL
 *                        on error.
 */
static const char *gl_tgetstr(GetLine *gl, const char *name, char **bufptr)
{
  const char *value = tgetstr((char *)name, bufptr);
  if(!value || value == (char *) -1)
    return NULL;
  return _sg_store_string(gl->capmem, value, 0);
}
#endif

/*.......................................................................
 * This is an action function that implements a user interrupt (eg. ^C).
 */
static KT_KEY_FN(gl_user_interrupt)
{
  raise(SIGINT);
  return 1;
}

/*.......................................................................
 * This is an action function that implements the abort signal.
 */
static KT_KEY_FN(gl_abort)
{
  raise(SIGABRT);
  return 1;
}

/*.......................................................................
 * This is an action function that sends a suspend signal (eg. ^Z) to the
 * the parent process.
 */
static KT_KEY_FN(gl_suspend)
{
  raise(SIGTSTP);
  return 0;
}

/*.......................................................................
 * This is an action function that halts output to the terminal.
 */
static KT_KEY_FN(gl_stop_output)
{
  tcflow(gl->output_fd, TCOOFF);
  return 0;
}

/*.......................................................................
 * This is an action function that resumes halted terminal output.
 */
static KT_KEY_FN(gl_start_output)
{
  tcflow(gl->output_fd, TCOON);
  return 0;
}

/*.......................................................................
 * This is an action function that allows the next character to be accepted
 * without any interpretation as a special character.
 */
static KT_KEY_FN(gl_literal_next)
{
  char c;   /* The character to be added to the line */
  int i;
/*
 * Get the character to be inserted literally.
 */
  if(gl_read_terminal(gl, 1, &c))
    return 1;
/*
 * Add the character to the line 'count' times.
 */
  for(i=0; incolumn) % TAB_WIDTH);
}

/*.......................................................................
 * Return the number of characters needed to display a given character
 * on the screen. Tab characters require eight spaces, and control
 * characters are represented by a caret followed by the modified
 * character.
 *
 * Input:
 *  gl       GetLine *  The resource object of this library.
 *  c           char    The character to be displayed.
 *  term_curpos  int    The destination terminal location of the character.
 *                      This is needed because the width of tab characters
 *                      depends on where they are, relative to the
 *                      preceding tab stops.
 * Output:
 *  return       int    The number of terminal charaters needed.
 */
static int gl_displayed_char_width(GetLine *gl, char c, int term_curpos)
{
  if(c=='\t')
    return gl_displayed_tab_width(gl, term_curpos);
  if(IS_CTRL_CHAR(c))
    return 2;
  if(!isprint((int)(unsigned char) c))
    return gl_octal_width((int)(unsigned char)c) + 1;
  return 1;
}


/*.......................................................................
 * Work out the length of given string of characters on the terminal.
 *
 * Input:
 *  gl       GetLine *  The resource object of this library.
 *  string      char *  The string to be measured.
 *  nc           int    The number of characters to be measured, or -1
 *                      to measure the whole string.
 *  term_curpos  int    The destination terminal location of the character.
 *                      This is needed because the width of tab characters
 *                      depends on where they are, relative to the
 *                      preceding tab stops.
 * Output:
 *  return       int    The number of displayed characters.
 */
static int gl_displayed_string_width(GetLine *gl, const char *string, int nc,
				     int term_curpos)
{
  int slen = 0;   /* The displayed number of characters */
  int i;
/*
 * How many characters are to be measured?
 */
  if(nc < 0)
    nc = strlen(string);
/*
 * Add up the length of the displayed string.
 */
  for(i=0; iflush_fn;
/*
 * Only display output when echoing is turned on.
 */
  if(gl->echo) {
    int ndone = 0;   /* The number of characters written so far */
/*
 * When using un-buffered I/O, flush pending output first.
 */
    if(!buffered) {
      if(gl_flush_output(gl))
	return 1;
    };
/*
 * If no length has been provided, measure the length of the string.
 */
    if(n < 0)
      n = strlen(string);
/*
 * Write the string.
 */
    if(write_fn(gl, string + ndone, n-ndone) != n)
      return 1;
  };
  return 0;
}

/*.......................................................................
 * Output a terminal control sequence. When using terminfo,
 * this must be a sequence returned by tgetstr() or tigetstr()
 * respectively.
 *
 * Input:
 *  gl     GetLine *   The resource object of this library.
 *  nline      int     The number of lines affected by the operation,
 *                     or 1 if not relevant.
 *  string    char *   The control sequence to be sent.
 * Output:
 *  return     int     0 - OK.
 *                     1 - Error.
 */
static int gl_print_control_sequence(GetLine *gl, int nline, const char *string)
{
  int waserr = 0;   /* True if an error occurs */
/*
 * Only write characters to the terminal when echoing is enabled.
 */
  if(gl->echo) {
#if defined(USE_TERMINFO) || defined(USE_TERMCAP)
    tputs_gl = gl;
    errno = 0;
    tputs((char *)string, nline, gl_tputs_putchar);
    waserr = errno != 0;
#else
    waserr = gl_print_raw_string(gl, 1, string, -1);
#endif
  };
  return waserr;
}

#if defined(USE_TERMINFO) || defined(USE_TERMCAP)
/*.......................................................................
 * The following callback function is called by tputs() to output a raw
 * control character to the terminal.
 */
static TputsRetType gl_tputs_putchar(TputsArgType c)
{
  char ch = c;
#if TPUTS_RETURNS_VALUE
  return gl_print_raw_string(tputs_gl, 1, &ch, 1);
#else
  (void) gl_print_raw_string(tputs_gl, 1, &ch, 1);
#endif
}
#endif

/*.......................................................................
 * Move the terminal cursor n characters to the left or right.
 *
 * Input:
 *  gl     GetLine *   The resource object of this program.
 *  n          int     number of positions to the right (> 0) or left (< 0).
 * Output:
 *  return     int     0 - OK.
 *                     1 - Error.
 */
static int gl_terminal_move_cursor(GetLine *gl, int n)
{
  int cur_row, cur_col; /* The current terminal row and column index of */
                        /*  the cursor wrt the start of the input line. */
  int new_row, new_col; /* The target terminal row and column index of */
                        /*  the cursor wrt the start of the input line. */
/*
 * Do nothing if the input line isn't currently displayed. In this
 * case, the cursor will be moved to the right place when the line
 * is next redisplayed.
 */
  if(!gl->displayed)
    return 0;
/*
 * How far can we move left?
 */
  if(gl->term_curpos + n < 0)
    n = gl->term_curpos;
/*
 * Break down the current and target cursor locations into rows and columns.
 */
  cur_row = gl->term_curpos / gl->ncolumn;
  cur_col = gl->term_curpos % gl->ncolumn;
  new_row = (gl->term_curpos + n) / gl->ncolumn;
  new_col = (gl->term_curpos + n) % gl->ncolumn;
/*
 * Move down to the next line.
 */
  for(; cur_row < new_row; cur_row++) {
    if(gl_print_control_sequence(gl, 1, gl->down))
      return 1;
  };
/*
 * Move up to the previous line.
 */
  for(; cur_row > new_row; cur_row--) {
    if(gl_print_control_sequence(gl, 1, gl->up))
      return 1;
  };
/*
 * Move to the right within the target line?
 */
  if(cur_col < new_col) {
#ifdef USE_TERMINFO
/*
 * Use a parameterized control sequence if it generates less control
 * characters (guess based on ANSI terminal termcap entry).
 */
    if(gl->right_n != NULL && new_col - cur_col > 1) {
      if(gl_print_control_sequence(gl, 1, tparm((char *)gl->right_n,
           (long)(new_col - cur_col), 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l)))
	return 1;
    } else
#endif
    {
      for(; cur_col < new_col; cur_col++) {
        if(gl_print_control_sequence(gl, 1, gl->right))
          return 1;
      };
    };
/*
 * Move to the left within the target line?
 */
  } else if(cur_col > new_col) {
#ifdef USE_TERMINFO
/*
 * Use a parameterized control sequence if it generates less control
 * characters (guess based on ANSI terminal termcap entry).
 */
    if(gl->left_n != NULL && cur_col - new_col > 3) {
      if(gl_print_control_sequence(gl, 1, tparm((char *)gl->left_n,
           (long)(cur_col - new_col), 0l, 0l, 0l, 0l, 0l, 0l, 0l, 0l)))
	return 1;
    } else
#endif
    {
      for(; cur_col > new_col; cur_col--) {
        if(gl_print_control_sequence(gl, 1, gl->left))
          return 1;
      };
    };
  }
/*
 * Update the recorded position of the terminal cursor.
 */
  gl->term_curpos += n;
  return 0;
}

/*.......................................................................
 * Write a character to the terminal after expanding tabs and control
 * characters to their multi-character representations.
 *
 * Input:
 *  gl    GetLine *   The resource object of this program.
 *  c        char     The character to be output.
 *  pad      char     Many terminals have the irritating feature that
 *                    when one writes a character in the last column of
 *                    of the terminal, the cursor isn't wrapped to the
 *                    start of the next line until one more character
 *                    is written. Some terminals don't do this, so
 *                    after such a write, we don't know where the
 *                    terminal is unless we output an extra character.
 *                    This argument specifies the character to write.
 *                    If at the end of the input line send '\0' or a
 *                    space, and a space will be written. Otherwise,
 *                    pass the next character in the input line
 *                    following the one being written.
 * Output:
 *  return    int     0 - OK.
 */ 
static int gl_print_char(GetLine *gl, char c, char pad)
{
  char string[TAB_WIDTH + 4]; /* A work area for composing compound strings */
  int nchar;                  /* The number of terminal characters */
  int i;
/*
 * Check for special characters.
 */
  if(c == '\t') {
/*
 * How many spaces do we need to represent a tab at the current terminal
 * column?
 */
    nchar = gl_displayed_tab_width(gl, gl->term_curpos);
/*
 * Compose the tab string.
 */
    for(i=0; iterm_curpos += nchar;
/*
 * Keep a record of the number of characters in the terminal version
 * of the input line.
 */
  if(gl->term_curpos > gl->term_len)
    gl->term_len = gl->term_curpos;
/*
 * If the new character ended exactly at the end of a line,
 * most terminals won't move the cursor onto the next line until we
 * have written a character on the next line, so append an extra
 * space then move the cursor back.
 */
  if(gl->term_curpos % gl->ncolumn == 0) {
    int term_curpos = gl->term_curpos;
    if(gl_print_char(gl, pad ? pad : ' ', ' ') ||
       gl_set_term_curpos(gl, term_curpos))
      return 1;
  };
  return 0;
}

/*.......................................................................
 * Write a string to the terminal after expanding tabs and control
 * characters to their multi-character representations.
 *
 * Input:
 *  gl    GetLine *   The resource object of this program.
 *  string   char *   The string to be output.
 *  pad      char     Many terminals have the irritating feature that
 *                    when one writes a character in the last column of
 *                    of the terminal, the cursor isn't wrapped to the
 *                    start of the next line until one more character
 *                    is written. Some terminals don't do this, so
 *                    after such a write, we don't know where the
 *                    terminal is unless we output an extra character.
 *                    This argument specifies the character to write.
 *                    If at the end of the input line send '\0' or a
 *                    space, and a space will be written. Otherwise,
 *                    pass the next character in the input line
 *                    following the one being written.
 * Output:
 *  return    int     0 - OK.
 */
static int gl_print_string(GetLine *gl, const char *string, char pad)
{
  const char *cptr;   /* A pointer into string[] */
  for(cptr=string; *cptr; cptr++) {
    char nextc = cptr[1];
    if(gl_print_char(gl, *cptr, nextc ? nextc : pad))
      return 1;
  };
  return 0;
}

/*.......................................................................
 * Move the terminal cursor position.
 *
 * Input:
 *  gl      GetLine *  The resource object of this library.
 *  term_curpos int    The destination terminal cursor position.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
static int gl_set_term_curpos(GetLine *gl, int term_curpos)
{
  return gl_terminal_move_cursor(gl, term_curpos - gl->term_curpos);
}

/*.......................................................................
 * This is an action function that moves the buffer cursor one character
 * left, and updates the terminal cursor to match.
 */
static KT_KEY_FN(gl_cursor_left)
{
  return gl_place_cursor(gl, gl->buff_curpos - count);
}

/*.......................................................................
 * This is an action function that moves the buffer cursor one character
 * right, and updates the terminal cursor to match.
 */
static KT_KEY_FN(gl_cursor_right)
{
  return gl_place_cursor(gl, gl->buff_curpos + count);
}

/*.......................................................................
 * This is an action function that toggles between overwrite and insert
 * mode.
 */
static KT_KEY_FN(gl_insert_mode)
{
  gl->insert = !gl->insert;
  return 0;
}

/*.......................................................................
 * This is an action function which moves the cursor to the beginning of
 * the line.
 */
static KT_KEY_FN(gl_beginning_of_line)
{
  return gl_place_cursor(gl, 0);
}

/*.......................................................................
 * This is an action function which moves the cursor to the end of
 * the line.
 */
static KT_KEY_FN(gl_end_of_line)
{
  return gl_place_cursor(gl, gl->ntotal);
}

/*.......................................................................
 * This is an action function which deletes the entire contents of the
 * current line.
 */
static KT_KEY_FN(gl_delete_line)
{
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Copy the contents of the line to the cut buffer.
 */
  strcpy(gl->cutbuf, gl->line);
/*
 * Clear the buffer.
 */
  gl_truncate_buffer(gl, 0);
/*
 * Move the terminal cursor to just after the prompt.
 */
  if(gl_place_cursor(gl, 0))
    return 1;
/*
 * Clear from the end of the prompt to the end of the terminal.
 */
  if(gl_truncate_display(gl))
    return 1;
  return 0;
}

/*.......................................................................
 * This is an action function which deletes all characters between the
 * current cursor position and the end of the line.
 */
static KT_KEY_FN(gl_kill_line)
{
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Copy the part of the line that is about to be deleted to the cut buffer.
 */
  strcpy(gl->cutbuf, gl->line + gl->buff_curpos);
/*
 * Terminate the buffered line at the current cursor position.
 */
  gl_truncate_buffer(gl, gl->buff_curpos);
/*
 * Clear the part of the line that follows the cursor.
 */
  if(gl_truncate_display(gl))
    return 1;
/*
 * Explicitly reset the cursor position to allow vi command mode
 * constraints on its position to be set.
 */
  return gl_place_cursor(gl, gl->buff_curpos);
}

/*.......................................................................
 * This is an action function which deletes all characters between the
 * start of the line and the current cursor position.
 */
static KT_KEY_FN(gl_backward_kill_line)
{
/*
 * How many characters are to be deleted from before the cursor?
 */
  int nc = gl->buff_curpos - gl->insert_curpos;
  if (!nc)
    return 0;
/*
 * Move the cursor to the start of the line, or in vi input mode,
 * the start of the sub-line at which insertion started, and delete
 * up to the old cursor position.
 */
  return gl_place_cursor(gl, gl->insert_curpos) ||
         gl_delete_chars(gl, nc, gl->editor == GL_EMACS_MODE || gl->vi.command);
}

/*.......................................................................
 * This is an action function which moves the cursor forward by a word.
 */
static KT_KEY_FN(gl_forward_word)
{
  return gl_place_cursor(gl, gl_nth_word_end_forward(gl, count) +
			 (gl->editor==GL_EMACS_MODE));
}

/*.......................................................................
 * This is an action function which moves the cursor forward to the start
 * of the next word.
 */
static KT_KEY_FN(gl_forward_to_word)
{
  return gl_place_cursor(gl, gl_nth_word_start_forward(gl, count));
}

/*.......................................................................
 * This is an action function which moves the cursor backward by a word.
 */
static KT_KEY_FN(gl_backward_word)
{
  return gl_place_cursor(gl, gl_nth_word_start_backward(gl, count));
}

/*.......................................................................
 * Delete one or more characters, starting with the one under the cursor.
 *
 * Input:
 *  gl     GetLine *  The resource object of this library.
 *  nc         int    The number of characters to delete.
 *  cut        int    If true, copy the characters to the cut buffer.
 * Output:
 *  return     int    0 - OK.
 *                    1 - Error.
 */
static int gl_delete_chars(GetLine *gl, int nc, int cut)
{
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * If there are fewer than nc characters following the cursor, limit
 * nc to the number available.
 */
  if(gl->buff_curpos + nc > gl->ntotal)
    nc = gl->ntotal - gl->buff_curpos;
/*
 * Copy the about to be deleted region to the cut buffer.
 */
  if(cut) {
    memcpy(gl->cutbuf, gl->line + gl->buff_curpos, nc);
    gl->cutbuf[nc] = '\0';
  }
/*
 * Nothing to delete?
 */
  if(nc <= 0)
    return 0;
/*
 * In vi overwrite mode, restore any previously overwritten characters
 * from the undo buffer.
 */
  if(gl->editor == GL_VI_MODE && !gl->vi.command && !gl->insert) {
/*
 * How many of the characters being deleted can be restored from the
 * undo buffer?
 */
    int nrestore = gl->buff_curpos + nc <= gl->vi.undo.ntotal ?
      nc : gl->vi.undo.ntotal - gl->buff_curpos;
/*
 * Restore any available characters.
 */
    if(nrestore > 0) {
      gl_buffer_string(gl, gl->vi.undo.line + gl->buff_curpos, nrestore,
		       gl->buff_curpos);
    };
/*
 * If their were insufficient characters in the undo buffer, then this
 * implies that we are deleting from the end of the line, so we need
 * to terminate the line either where the undo buffer ran out, or if
 * we are deleting from beyond the end of the undo buffer, at the current
 * cursor position.
 */
    if(nc != nrestore) {
      gl_truncate_buffer(gl, (gl->vi.undo.ntotal > gl->buff_curpos) ?
			 gl->vi.undo.ntotal : gl->buff_curpos);
    };
  } else {
/*
 * Copy the remaining part of the line back over the deleted characters.
 */
    gl_remove_from_buffer(gl, gl->buff_curpos, nc);
  };
/*
 * Redraw the remaining characters following the cursor.
 */
  if(gl_print_string(gl, gl->line + gl->buff_curpos, '\0'))
    return 1;
/*
 * Clear to the end of the terminal.
 */
  if(gl_truncate_display(gl))
    return 1;
/*
 * Place the cursor at the start of where the deletion was performed.
 */
  return gl_place_cursor(gl, gl->buff_curpos);
}

/*.......................................................................
 * This is an action function which deletes character(s) under the
 * cursor without moving the cursor.
 */
static KT_KEY_FN(gl_forward_delete_char)
{
/*
 * Delete 'count' characters.
 */
  return gl_delete_chars(gl, count, gl->vi.command);
}

/*.......................................................................
 * This is an action function which deletes character(s) under the
 * cursor and moves the cursor back one character.
 */
static KT_KEY_FN(gl_backward_delete_char)
{
/*
 * Restrict the deletion count to the number of characters that
 * precede the insertion point.
 */
  if(count > gl->buff_curpos - gl->insert_curpos)
    count = gl->buff_curpos - gl->insert_curpos;
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
  return gl_cursor_left(gl, count, NULL) ||
    gl_delete_chars(gl, count, gl->vi.command);
}

/*.......................................................................
 * Starting from the cursor position delete to the specified column.
 */
static KT_KEY_FN(gl_delete_to_column)
{
  if (--count >= gl->buff_curpos)
    return gl_forward_delete_char(gl, count - gl->buff_curpos, NULL);
  else
    return gl_backward_delete_char(gl, gl->buff_curpos - count, NULL);
}

/*.......................................................................
 * Starting from the cursor position delete characters to a matching
 * parenthesis.
 */
static KT_KEY_FN(gl_delete_to_parenthesis)
{
  int curpos = gl_index_of_matching_paren(gl);
  if(curpos >= 0) {
    gl_save_for_undo(gl);
    if(curpos >= gl->buff_curpos)
      return gl_forward_delete_char(gl, curpos - gl->buff_curpos + 1, NULL);
    else
      return gl_backward_delete_char(gl, ++gl->buff_curpos - curpos + 1, NULL);
  };
  return 0;
}

/*.......................................................................
 * This is an action function which deletes from the cursor to the end
 * of the word that the cursor is either in or precedes.
 */
static KT_KEY_FN(gl_forward_delete_word)
{
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * In emacs mode delete to the end of the word. In vi mode delete to the
 * start of the net word.
 */
  if(gl->editor == GL_EMACS_MODE) {
    return gl_delete_chars(gl,
		gl_nth_word_end_forward(gl,count) - gl->buff_curpos + 1, 1);
  } else {
    return gl_delete_chars(gl,
		gl_nth_word_start_forward(gl,count) - gl->buff_curpos,
		gl->vi.command);
  };
}

/*.......................................................................
 * This is an action function which deletes the word that precedes the
 * cursor.
 */
static KT_KEY_FN(gl_backward_delete_word)
{
/*
 * Keep a record of the current cursor position.
 */
  int buff_curpos = gl->buff_curpos;
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Move back 'count' words.
 */
  if(gl_backward_word(gl, count, NULL))
    return 1;
/*
 * Delete from the new cursor position to the original one.
 */
  return gl_delete_chars(gl, buff_curpos - gl->buff_curpos,
  			 gl->editor == GL_EMACS_MODE || gl->vi.command);
}

/*.......................................................................
 * Searching in a given direction, delete to the count'th
 * instance of a specified or queried character, in the input line.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 *  count        int    The number of times to search.
 *  c           char    The character to be searched for, or '\0' if
 *                      the character should be read from the user.
 *  forward      int    True if searching forward.
 *  onto         int    True if the search should end on top of the
 *                      character, false if the search should stop
 *                      one character before the character in the
 *                      specified search direction.
 *  change       int    If true, this function is being called upon
 *                      to do a vi change command, in which case the
 *                      user will be left in insert mode after the
 *                      deletion.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 */
static int gl_delete_find(GetLine *gl, int count, char c, int forward,
			  int onto, int change)
{
/*
 * Search for the character, and abort the deletion if not found.
 */
  int pos = gl_find_char(gl, count, forward, onto, c);
  if(pos < 0)
    return 0;
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Allow the cursor to be at the end of the line if this is a change
 * command.
 */
  if(change)
    gl->vi.command = 0;
/*
 * Delete the appropriate span of characters.
 */
  if(forward) {
    if(gl_delete_chars(gl, pos - gl->buff_curpos + 1, 1))
      return 1;
  } else {
    int buff_curpos = gl->buff_curpos;
    if(gl_place_cursor(gl, pos) ||
       gl_delete_chars(gl, buff_curpos - gl->buff_curpos, 1))
      return 1;
  };
/*
 * If this is a change operation, switch the insert mode.
 */
  if(change && gl_vi_insert(gl, 0, NULL))
    return 1;
  return 0;
}

/*.......................................................................
 * This is an action function which deletes forward from the cursor up to and
 * including a specified character.
 */
static KT_KEY_FN(gl_forward_delete_find)
{
  return gl_delete_find(gl, count, '\0', 1, 1, 0);
}

/*.......................................................................
 * This is an action function which deletes backward from the cursor back to
 * and including a specified character.
 */
static KT_KEY_FN(gl_backward_delete_find)
{
  return gl_delete_find(gl, count, '\0', 0, 1, 0);
}

/*.......................................................................
 * This is an action function which deletes forward from the cursor up to but
 * not including a specified character.
 */
static KT_KEY_FN(gl_forward_delete_to)
{
  return gl_delete_find(gl, count, '\0', 1, 0, 0);
}

/*.......................................................................
 * This is an action function which deletes backward from the cursor back to
 * but not including a specified character.
 */
static KT_KEY_FN(gl_backward_delete_to)
{
  return gl_delete_find(gl, count, '\0', 0, 0, 0);
}

/*.......................................................................
 * This is an action function which deletes to a character specified by a
 * previous search.
 */
static KT_KEY_FN(gl_delete_refind)
{
  return gl_delete_find(gl, count, gl->vi.find_char, gl->vi.find_forward,
			gl->vi.find_onto, 0);
}

/*.......................................................................
 * This is an action function which deletes to a character specified by a
 * previous search, but in the opposite direction.
 */
static KT_KEY_FN(gl_delete_invert_refind)
{
  return gl_delete_find(gl, count, gl->vi.find_char,
			!gl->vi.find_forward, gl->vi.find_onto, 0);
}

/*.......................................................................
 * This is an action function which converts the characters in the word
 * following the cursor to upper case.
 */
static KT_KEY_FN(gl_upcase_word)
{
/*
 * Locate the count'th word ending after the cursor.
 */
  int last = gl_nth_word_end_forward(gl, count);
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Upcase characters from the current cursor position to 'last'.
 */
  while(gl->buff_curpos <= last) {
    char *cptr = gl->line + gl->buff_curpos;
/*
 * Convert the character to upper case?
 */
    if(islower((int)(unsigned char) *cptr))
      gl_buffer_char(gl, toupper((int) *cptr), gl->buff_curpos);
    gl->buff_curpos++;
/*
 * Write the possibly modified character back. Note that for non-modified
 * characters we want to do this as well, so as to advance the cursor.
 */
    if(gl_print_char(gl, *cptr, cptr[1]))
      return 1;
  };
  return gl_place_cursor(gl, gl->buff_curpos);	/* bounds check */
}

/*.......................................................................
 * This is an action function which converts the characters in the word
 * following the cursor to lower case.
 */
static KT_KEY_FN(gl_downcase_word)
{
/*
 * Locate the count'th word ending after the cursor.
 */
  int last = gl_nth_word_end_forward(gl, count);
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Upcase characters from the current cursor position to 'last'.
 */
  while(gl->buff_curpos <= last) {
    char *cptr = gl->line + gl->buff_curpos;
/*
 * Convert the character to upper case?
 */
    if(isupper((int)(unsigned char) *cptr))
      gl_buffer_char(gl, tolower((int) *cptr), gl->buff_curpos);
    gl->buff_curpos++;
/*
 * Write the possibly modified character back. Note that for non-modified
 * characters we want to do this as well, so as to advance the cursor.
 */
    if(gl_print_char(gl, *cptr, cptr[1]))
      return 1;
  };
  return gl_place_cursor(gl, gl->buff_curpos);	/* bounds check */
}

/*.......................................................................
 * This is an action function which converts the first character of the
 * following word to upper case, in order to capitalize the word, and
 * leaves the cursor at the end of the word.
 */
static KT_KEY_FN(gl_capitalize_word)
{
  char *cptr;   /* &gl->line[gl->buff_curpos] */
  int first;    /* True for the first letter of the word */
  int i;
/*
 * Keep a record of the current insert mode and the cursor position.
 */
  int insert = gl->insert;
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * We want to overwrite the modified word.
 */
  gl->insert = 0;
/*
 * Capitalize 'count' words.
 */
  for(i=0; ibuff_curpos < gl->ntotal; i++) {
    int pos = gl->buff_curpos;
/*
 * If we are not already within a word, skip to the start of the word.
 */
    for(cptr = gl->line + pos ; posntotal && !gl_is_word_char((int) *cptr);
	pos++, cptr++)
      ;
/*
 * Move the cursor to the new position.
 */
    if(gl_place_cursor(gl, pos))
      return 1;
/*
 * While searching for the end of the word, change lower case letters
 * to upper case.
 */
    for(first=1; gl->buff_curposntotal && gl_is_word_char((int) *cptr);
	gl->buff_curpos++, cptr++) {
/*
 * Convert the character to upper case?
 */
      if(first) {
	if(islower((int)(unsigned char) *cptr))
	  gl_buffer_char(gl, toupper((int) *cptr), cptr - gl->line);
      } else {
	if(isupper((int)(unsigned char) *cptr))
	  gl_buffer_char(gl, tolower((int) *cptr), cptr - gl->line);
      };
      first = 0;
/*
 * Write the possibly modified character back. Note that for non-modified
 * characters we want to do this as well, so as to advance the cursor.
 */
      if(gl_print_char(gl, *cptr, cptr[1]))
	return 1;
    };
  };
/*
 * Restore the insertion mode.
 */
  gl->insert = insert;
  return gl_place_cursor(gl, gl->buff_curpos);	/* bounds check */
}

/*.......................................................................
 * This is an action function which redraws the current line.
 */
static KT_KEY_FN(gl_redisplay)
{
/*
 * Keep a record of the current cursor position.
 */
  int buff_curpos = gl->buff_curpos;
/*
 * Do nothing if there is no line to be redisplayed.
 */
  if(gl->endline)
    return 0;
/*
 * Erase the current input line.
 */
  if(gl_erase_line(gl))
    return 1;
/*
 * Display the current prompt.
 */
  if(gl_display_prompt(gl))
    return 1;
/*
 * Render the part of the line that the user has typed in so far.
 */
  if(gl_print_string(gl, gl->line, '\0'))
    return 1;
/*
 * Restore the cursor position.
 */
  if(gl_place_cursor(gl, buff_curpos))
    return 1;
/*
 * Mark the redisplay operation as having been completed.
 */
  gl->redisplay = 0;
/*
 * Flush the redisplayed line to the terminal.
 */
  return gl_flush_output(gl);
}

/*.......................................................................
 * This is an action function which clears the display and redraws the
 * input line from the home position.
 */
static KT_KEY_FN(gl_clear_screen)
{
/*
 * Home the cursor and clear from there to the end of the display.
 */
  if(gl_print_control_sequence(gl, gl->nline, gl->home) ||
     gl_print_control_sequence(gl, gl->nline, gl->clear_eod))
    return 1;
/*
 * The input line is no longer displayed.
 */
  gl_line_erased(gl);
/*
 * Arrange for the input line to be redisplayed.
 */
  gl_queue_redisplay(gl);
  return 0;
}

/*.......................................................................
 * This is an action function which swaps the character under the cursor
 * with the character to the left of the cursor.
 */
static KT_KEY_FN(gl_transpose_chars)
{
  char from[3];     /* The original string of 2 characters */
  char swap[3];     /* The swapped string of two characters */
/*
 * If we are at the beginning or end of the line, there aren't two
 * characters to swap.
 */
  if(gl->buff_curpos < 1 || gl->buff_curpos >= gl->ntotal)
    return 0;
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Get the original and swapped strings of the two characters.
 */
  from[0] = gl->line[gl->buff_curpos - 1];
  from[1] = gl->line[gl->buff_curpos];
  from[2] = '\0';
  swap[0] = gl->line[gl->buff_curpos];
  swap[1] = gl->line[gl->buff_curpos - 1];
  swap[2] = '\0';
/*
 * Move the cursor to the start of the two characters.
 */
  if(gl_place_cursor(gl, gl->buff_curpos-1))
    return 1;
/*
 * Swap the two characters in the buffer.
 */
  gl_buffer_char(gl, swap[0], gl->buff_curpos);
  gl_buffer_char(gl, swap[1], gl->buff_curpos+1);
/*
 * If the sum of the displayed width of the two characters
 * in their current and final positions is the same, swapping can
 * be done by just overwriting with the two swapped characters.
 */
  if(gl_displayed_string_width(gl, from, -1, gl->term_curpos) ==
     gl_displayed_string_width(gl, swap, -1, gl->term_curpos)) {
    int insert = gl->insert;
    gl->insert = 0;
    if(gl_print_char(gl, swap[0], swap[1]) ||
       gl_print_char(gl, swap[1], gl->line[gl->buff_curpos+2]))
      return 1;
    gl->insert = insert;
/*
 * If the swapped substring has a different displayed size, we need to
 * redraw everything after the first of the characters.
 */
  } else {
    if(gl_print_string(gl, gl->line + gl->buff_curpos, '\0') ||
       gl_truncate_display(gl))
      return 1;
  };
/*
 * Advance the cursor to the character after the swapped pair.
 */
  return gl_place_cursor(gl, gl->buff_curpos + 2);
}

/*.......................................................................
 * This is an action function which sets a mark at the current cursor
 * location.
 */
static KT_KEY_FN(gl_set_mark)
{
  gl->buff_mark = gl->buff_curpos;
  return 0;
}

/*.......................................................................
 * This is an action function which swaps the mark location for the
 * cursor location.
 */
static KT_KEY_FN(gl_exchange_point_and_mark)
{
/*
 * Get the old mark position, and limit to the extent of the input
 * line.
 */
  int old_mark = gl->buff_mark <= gl->ntotal ? gl->buff_mark : gl->ntotal;
/*
 * Make the current cursor position the new mark.
 */
  gl->buff_mark = gl->buff_curpos;
/*
 * Move the cursor to the old mark position.
 */
  return gl_place_cursor(gl, old_mark);
}

/*.......................................................................
 * This is an action function which deletes the characters between the
 * mark and the cursor, recording them in gl->cutbuf for later pasting.
 */
static KT_KEY_FN(gl_kill_region)
{
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Limit the mark to be within the line.
 */
  if(gl->buff_mark > gl->ntotal)
    gl->buff_mark = gl->ntotal;
/*
 * If there are no characters between the cursor and the mark, simply clear
 * the cut buffer.
 */
  if(gl->buff_mark == gl->buff_curpos) {
    gl->cutbuf[0] = '\0';
    return 0;
  };
/*
 * If the mark is before the cursor, swap the cursor and the mark.
 */
  if(gl->buff_mark < gl->buff_curpos && gl_exchange_point_and_mark(gl,1,NULL))
    return 1;
/*
 * Delete the characters.
 */
  if(gl_delete_chars(gl, gl->buff_mark - gl->buff_curpos, 1))
    return 1;
/*
 * Make the mark the same as the cursor position.
 */
  gl->buff_mark = gl->buff_curpos;
  return 0;
}

/*.......................................................................
 * This is an action function which records the characters between the
 * mark and the cursor, in gl->cutbuf for later pasting.
 */
static KT_KEY_FN(gl_copy_region_as_kill)
{
  int ca, cb;  /* The indexes of the first and last characters in the region */
  int mark;    /* The position of the mark */
/*
 * Get the position of the mark, limiting it to lie within the line.
 */
  mark = gl->buff_mark > gl->ntotal ? gl->ntotal : gl->buff_mark;
/*
 * If there are no characters between the cursor and the mark, clear
 * the cut buffer.
 */
  if(mark == gl->buff_curpos) {
    gl->cutbuf[0] = '\0';
    return 0;
  };
/*
 * Get the line indexes of the first and last characters in the region.
 */
  if(mark < gl->buff_curpos) {
    ca = mark;
    cb = gl->buff_curpos - 1;
  } else {
    ca = gl->buff_curpos;
    cb = mark - 1;
  };
/*
 * Copy the region to the cut buffer.
 */
  memcpy(gl->cutbuf, gl->line + ca, cb + 1 - ca);
  gl->cutbuf[cb + 1 - ca] = '\0';
  return 0;
}

/*.......................................................................
 * This is an action function which inserts the contents of the cut
 * buffer at the current cursor location.
 */
static KT_KEY_FN(gl_yank)
{
  int i;
/*
 * Set the mark at the current location.
 */
  gl->buff_mark = gl->buff_curpos;
/*
 * Do nothing else if the cut buffer is empty.
 */
  if(gl->cutbuf[0] == '\0')
    return gl_ring_bell(gl, 1, NULL);
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Insert the string count times.
 */
  for(i=0; icutbuf))
      return 1;
  };
/*
 * gl_add_string_to_line() leaves the cursor after the last character that
 * was pasted, whereas vi leaves the cursor over the last character pasted.
 */
  if(gl->editor == GL_VI_MODE && gl_cursor_left(gl, 1, NULL))
    return 1;
  return 0;
}

/*.......................................................................
 * This is an action function which inserts the contents of the cut
 * buffer one character beyond the current cursor location.
 */
static KT_KEY_FN(gl_append_yank)
{
  int was_command = gl->vi.command;
  int i;
/*
 * If the cut buffer is empty, ring the terminal bell.
 */
  if(gl->cutbuf[0] == '\0')
    return gl_ring_bell(gl, 1, NULL);
/*
 * Set the mark at the current location + 1.
 */
  gl->buff_mark = gl->buff_curpos + 1;
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Arrange to paste the text in insert mode after the current character.
 */
  if(gl_vi_append(gl, 0, NULL))
    return 1;
/*
 * Insert the string count times.
 */
  for(i=0; icutbuf))
      return 1;
  };
/*
 * Switch back to command mode if necessary.
 */
  if(was_command)
    gl_vi_command_mode(gl);
  return 0;
}

/*.......................................................................
 * Attempt to ask the terminal for its current size. On systems that
 * don't support the TIOCWINSZ ioctl() for querying the terminal size,
 * the current values of gl->ncolumn and gl->nrow are returned.
 *
 * Input:
 *  gl     GetLine *  The resource object of gl_get_line().
 * Input/Output:
 *  ncolumn    int *  The number of columns will be assigned to *ncolumn.
 *  nline      int *  The number of lines will be assigned to *nline.
 */
static void gl_query_size(GetLine *gl, int *ncolumn, int *nline)
{
#ifdef TIOCGWINSZ
/*
 * Query the new terminal window size. Ignore invalid responses.
 */
  struct winsize size;
  if(ioctl(gl->output_fd, TIOCGWINSZ, &size) == 0 &&
     size.ws_row > 0 && size.ws_col > 0) {
    *ncolumn = size.ws_col;
    *nline = size.ws_row;
    return;
  };
#endif
/*
 * Return the existing values.
 */
  *ncolumn = gl->ncolumn;
  *nline = gl->nline;
  return;
}

/*.......................................................................
 * Query the size of the terminal, and if it has changed, redraw the
 * current input line accordingly.
 *
 * Input:
 *  gl     GetLine *  The resource object of gl_get_line().
 * Output:
 *  return     int    0 - OK.
 *                    1 - Error.
 */
static int _gl_update_size(GetLine *gl)
{
  int ncolumn, nline;    /* The new size of the terminal */
/*
 * Query the new terminal window size.
 */
  gl_query_size(gl, &ncolumn, &nline);
/*
 * Update gl and the displayed line to fit the new dimensions.
 */
  return gl_handle_tty_resize(gl, ncolumn, nline);
}

/*.......................................................................
 * Redraw the current input line to account for a change in the terminal
 * size. Also install the new size in gl.
 *
 * Input:
 *  gl     GetLine *  The resource object of gl_get_line().
 *  ncolumn    int    The new number of columns.
 *  nline      int    The new number of lines.
 * Output:
 *  return     int    0 - OK.
 *                    1 - Error.
 */
static int gl_handle_tty_resize(GetLine *gl, int ncolumn, int nline)
{
/*
 * If the input device isn't a terminal, just record the new size.
 */
  if(!gl->is_term) {
    gl->nline = nline;
    gl->ncolumn = ncolumn;
/*
 * Has the size actually changed?
 */
  } else if(ncolumn != gl->ncolumn || nline != gl->nline) {
/*
 * If we are currently editing a line, erase it.
 */
    if(gl_erase_line(gl))
      return 1;
/*
 * Update the recorded window size.
 */
    gl->nline = nline;
    gl->ncolumn = ncolumn;
/*
 * Arrange for the input line to be redrawn before the next character
 * is read from the terminal.
 */
    gl_queue_redisplay(gl);
  };
  return 0;
}

/*.......................................................................
 * This is the action function that recalls the previous line in the
 * history buffer.
 */
static KT_KEY_FN(gl_up_history)
{
/*
 * In vi mode, switch to command mode, since the user is very
 * likely to want to move around newly recalled lines.
 */
  gl_vi_command_mode(gl);
/*
 * Forget any previous recall session.
 */
  gl->preload_id = 0;
/*
 * Record the key sequence number of this search action.
 */
  gl->last_search = gl->keyseq_count;
/*
 * We don't want a search prefix for this function.
 */
  if(_glh_search_prefix(gl->glh, gl->line, 0)) {
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
    return 1;
  };
/*
 * Recall the count'th next older line in the history list. If the first one
 * fails we can return since nothing has changed, otherwise we must continue
 * and update the line state.
 */
  if(_glh_find_backwards(gl->glh, gl->line, gl->linelen+1) == NULL)
    return 0;
  while(--count && _glh_find_backwards(gl->glh, gl->line, gl->linelen+1))
    ;
/*
 * Accomodate the new contents of gl->line[].
 */
  gl_update_buffer(gl);
/*
 * Arrange to have the cursor placed at the end of the new line.
 */
  gl->buff_curpos = gl->ntotal;
/*
 * Erase and display the new line.
 */
  gl_queue_redisplay(gl);
  return 0;
}

/*.......................................................................
 * This is the action function that recalls the next line in the
 * history buffer.
 */
static KT_KEY_FN(gl_down_history)
{
/*
 * In vi mode, switch to command mode, since the user is very
 * likely to want to move around newly recalled lines.
 */
  gl_vi_command_mode(gl);
/*
 * Record the key sequence number of this search action.
 */
  gl->last_search = gl->keyseq_count;
/*
 * If no search is currently in progress continue a previous recall
 * session from a previous entered line if possible.
 */
  if(_glh_line_id(gl->glh, 0) == 0 && gl->preload_id) {
    _glh_recall_line(gl->glh, gl->preload_id, gl->line, gl->linelen+1);
    gl->preload_id = 0;
  } else {
/*
 * We don't want a search prefix for this function.
 */
    if(_glh_search_prefix(gl->glh, gl->line, 0)) {
      _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
      return 1;
    };
/*
 * Recall the count'th next newer line in the history list. If the first one
 * fails we can return since nothing has changed otherwise we must continue
 * and update the line state.
 */
    if(_glh_find_forwards(gl->glh, gl->line, gl->linelen+1) == NULL)
      return 0;
    while(--count && _glh_find_forwards(gl->glh, gl->line, gl->linelen+1))
      ;
  };
/*
 * Accomodate the new contents of gl->line[].
 */
  gl_update_buffer(gl);
/*
 * Arrange to have the cursor placed at the end of the new line.
 */
  gl->buff_curpos = gl->ntotal;
/*
 * Erase and display the new line.
 */
  gl_queue_redisplay(gl);
  return 0;
}

/*.......................................................................
 * This is the action function that recalls the previous line in the
 * history buffer whos prefix matches the characters that currently
 * precede the cursor. By setting count=-1, this can be used internally
 * to force searching for the prefix used in the last search.
 */
static KT_KEY_FN(gl_history_search_backward)
{
/*
 * In vi mode, switch to command mode, since the user is very
 * likely to want to move around newly recalled lines.
 */
  gl_vi_command_mode(gl);
/*
 * Forget any previous recall session.
 */
  gl->preload_id = 0;
/*
 * Record the key sequence number of this search action.
 */
  gl->last_search = gl->keyseq_count;
/*
 * If a prefix search isn't already in progress, replace the search
 * prefix to the string that precedes the cursor. In vi command mode
 * include the character that is under the cursor in the string.  If
 * count<0 keep the previous search prefix regardless, so as to force
 * a repeat search even if the last command wasn't a history command.
 */
  if(count >= 0 && !_glh_search_active(gl->glh) &&
     _glh_search_prefix(gl->glh, gl->line, gl->buff_curpos +
			(gl->editor==GL_VI_MODE && gl->ntotal>0))) {
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
    return 1;
  };
/*
 * Search backwards for a match to the part of the line which precedes the
 * cursor.
 */
  if(_glh_find_backwards(gl->glh, gl->line, gl->linelen+1) == NULL)
    return 0;
/*
 * Accomodate the new contents of gl->line[].
 */
  gl_update_buffer(gl);
/*
 * Arrange to have the cursor placed at the end of the new line.
 */
  gl->buff_curpos = gl->ntotal;
/*
 * Erase and display the new line.
 */
  gl_queue_redisplay(gl);
  return 0;
}

/*.......................................................................
 * This is the action function that recalls the previous line in the
 * history buffer who's prefix matches that specified in an earlier call
 * to gl_history_search_backward() or gl_history_search_forward().
 */
static KT_KEY_FN(gl_history_re_search_backward)
{
  return gl_history_search_backward(gl, -1, NULL);
}

/*.......................................................................
 * This is the action function that recalls the next line in the
 * history buffer who's prefix matches that specified in the earlier call
 * to gl_history_search_backward) which started the history search.
 * By setting count=-1, this can be used internally to force searching
 * for the prefix used in the last search.
 */
static KT_KEY_FN(gl_history_search_forward)
{
/*
 * In vi mode, switch to command mode, since the user is very
 * likely to want to move around newly recalled lines.
 */
  gl_vi_command_mode(gl);
/*
 * Record the key sequence number of this search action.
 */
  gl->last_search = gl->keyseq_count;
/*
 * If a prefix search isn't already in progress, replace the search
 * prefix to the string that precedes the cursor. In vi command mode
 * include the character that is under the cursor in the string.  If
 * count<0 keep the previous search prefix regardless, so as to force
 * a repeat search even if the last command wasn't a history command.
 */
  if(count >= 0 && !_glh_search_active(gl->glh) &&
     _glh_search_prefix(gl->glh, gl->line, gl->buff_curpos +
			(gl->editor==GL_VI_MODE && gl->ntotal>0))) {
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
    return 1;
  };
/*
 * Search forwards for the next matching line.
 */
  if(_glh_find_forwards(gl->glh, gl->line, gl->linelen+1) == NULL)
    return 0;
/*
 * Accomodate the new contents of gl->line[].
 */
  gl_update_buffer(gl);
/*
 * Arrange for the cursor to be placed at the end of the new line.
 */
  gl->buff_curpos = gl->ntotal;
/*
 * Erase and display the new line.
 */
  gl_queue_redisplay(gl);
  return 0;
}

/*.......................................................................
 * This is the action function that recalls the next line in the
 * history buffer who's prefix matches that specified in an earlier call
 * to gl_history_search_backward() or gl_history_search_forward().
 */
static KT_KEY_FN(gl_history_re_search_forward)
{
  return gl_history_search_forward(gl, -1, NULL);
}

#ifdef HIDE_FILE_SYSTEM
/*.......................................................................
 * The following function is used as the default completion handler when
 * the filesystem is to be hidden. It simply reports no completions.
 */
static CPL_MATCH_FN(gl_no_completions)
{
  return 0;
}
#endif

/*.......................................................................
 * This is the tab completion function that completes the filename that
 * precedes the cursor position. Its callback data argument must be a
 * pointer to a GlCplCallback containing the completion callback function
 * and its callback data, or NULL to use the builtin filename completer.
 */
static KT_KEY_FN(gl_complete_word)
{
  CplMatches *matches;    /* The possible completions */
  int suffix_len;         /* The length of the completion extension */
  int cont_len;           /* The length of any continuation suffix */
  int nextra;             /* The number of characters being added to the */
                          /*  total length of the line. */
  int buff_pos;           /* The buffer index at which the completion is */
                          /*  to be inserted. */
  int waserr = 0;         /* True after errors */
/*
 * Get the container of the completion callback and its callback data.
 */
  GlCplCallback *cb = data ? (GlCplCallback *) data : &gl->cplfn;
/*
 * In vi command mode, switch to append mode so that the character under
 * the cursor is included in the completion (otherwise people can't
 * complete at the end of the line).
 */
  if(gl->vi.command && gl_vi_append(gl, 0, NULL))
    return 1;
/*
 * Get the cursor position at which the completion is to be inserted.
 */
  buff_pos = gl->buff_curpos;
/*
 * Perform the completion.
 */
  matches = cpl_complete_word(gl->cpl, gl->line, gl->buff_curpos, cb->data,
			      cb->fn);
/*
 * No matching completions?
 */
  if(!matches) {
    waserr = gl_print_info(gl, cpl_last_error(gl->cpl), GL_END_INFO);
/*
 * Are there any completions?
 */
  } else if(matches->nmatch >= 1) {
/*
 * If there any ambiguous matches, report them, starting on a new line.
 */
    if(matches->nmatch > 1 && gl->echo) {
      if(_gl_normal_io(gl) ||
	 _cpl_output_completions(matches, gl_write_fn, gl, gl->ncolumn))
	waserr = 1;
    };
/*
 * Get the length of the suffix and any continuation suffix to add to it.
 */
    suffix_len = strlen(matches->suffix);
    cont_len = strlen(matches->cont_suffix);
/*
 * If there is an unambiguous match, and the continuation suffix ends in
 * a newline, strip that newline and arrange to have getline return
 * after this action function returns.
 */
    if(matches->nmatch==1 && cont_len > 0 &&
       matches->cont_suffix[cont_len - 1] == '\n') {
      cont_len--;
      if(gl_newline(gl, 1, NULL))
	waserr = 1;
    };
/*
 * Work out the number of characters that are to be added.
 */
    nextra = suffix_len + cont_len;
/*
 * Is there anything to be added?
 */
    if(!waserr && nextra) {
/*
 * Will there be space for the expansion in the line buffer?
 */
      if(gl->ntotal + nextra < gl->linelen) {
/*
 * Make room to insert the filename extension.
 */
	gl_make_gap_in_buffer(gl, gl->buff_curpos, nextra);
/*
 * Insert the filename extension.
 */
	gl_buffer_string(gl, matches->suffix, suffix_len, gl->buff_curpos);
/*
 * Add the terminating characters.
 */
	gl_buffer_string(gl, matches->cont_suffix, cont_len,
			 gl->buff_curpos + suffix_len);
/*
 * Place the cursor position at the end of the completion.
 */
	gl->buff_curpos += nextra;
/*
 * If we don't have to redisplay the whole line, redisplay the part
 * of the line which follows the original cursor position, and place
 * the cursor at the end of the completion.
 */
	if(gl->displayed) {
	  if(gl_truncate_display(gl) ||
	     gl_print_string(gl, gl->line + buff_pos, '\0') ||
	     gl_place_cursor(gl, gl->buff_curpos))
	    waserr = 1;
	};
      } else {
	(void) gl_print_info(gl,
			     "Insufficient room in line for file completion.",
			     GL_END_INFO);
	waserr = 1;
      };
    };
  };
/*
 * If any output had to be written to the terminal, then editing will
 * have been suspended, make sure that we are back in raw line editing
 * mode before returning.
 */
  if(_gl_raw_io(gl, 1))
    waserr = 1;
  return 0;
}

#ifndef HIDE_FILE_SYSTEM
/*.......................................................................
 * This is the function that expands the filename that precedes the
 * cursor position. It expands ~user/ expressions, $envvar expressions,
 * and wildcards.
 */
static KT_KEY_FN(gl_expand_filename)
{
  char *start_path;      /* The pointer to the start of the pathname in */
                         /*  gl->line[]. */
  FileExpansion *result; /* The results of the filename expansion */
  int pathlen;           /* The length of the pathname being expanded */
  int length;            /* The number of characters needed to display the */
                         /*  expanded files. */
  int nextra;            /* The number of characters to be added */
  int i,j;
/*
 * In vi command mode, switch to append mode so that the character under
 * the cursor is included in the completion (otherwise people can't
 * complete at the end of the line).
 */
  if(gl->vi.command && gl_vi_append(gl, 0, NULL))
    return 1;
/*
 * Locate the start of the filename that precedes the cursor position.
 */
  start_path = _pu_start_of_path(gl->line, gl->buff_curpos);
  if(!start_path)
    return 1;
/*
 * Get the length of the string that is to be expanded.
 */
  pathlen = gl->buff_curpos - (start_path - gl->line);
/*
 * Attempt to expand it.
 */
  result = ef_expand_file(gl->ef, start_path, pathlen);
/*
 * If there was an error, report the error on a new line.
 */
  if(!result)
    return gl_print_info(gl, ef_last_error(gl->ef), GL_END_INFO);
/*
 * If no files matched, report this as well.
 */
  if(result->nfile == 0 || !result->exists)
    return gl_print_info(gl, "No files match.", GL_END_INFO);
/*
 * If in vi command mode, preserve the current line for potential use by
 * vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Work out how much space we will need to display all of the matching
 * filenames, taking account of the space that we need to place between
 * them, and the number of additional '\' characters needed to escape
 * spaces, tabs and backslash characters in the individual filenames.
 */
  length = 0;
  for(i=0; infile; i++) {
    char *file = result->files[i];
    while(*file) {
      int c = *file++;
      switch(c) {
      case ' ': case '\t': case '\\': case '*': case '?': case '[':
	length++;  /* Count extra backslash characters */
      };
      length++;    /* Count the character itself */
    };
    length++;      /* Count the space that follows each filename */
  };
/*
 * Work out the number of characters that are to be added.
 */
  nextra = length - pathlen;
/*
 * Will there be space for the expansion in the line buffer?
 */
  if(gl->ntotal + nextra >= gl->linelen) {
    return gl_print_info(gl, "Insufficient room in line for file expansion.",
			 GL_END_INFO);
  } else {
/*
 * Do we need to move the part of the line that followed the unexpanded
 * filename?
 */
    if(nextra > 0) {
      gl_make_gap_in_buffer(gl, gl->buff_curpos, nextra);
    } else if(nextra < 0) {
      gl->buff_curpos += nextra;
      gl_remove_from_buffer(gl, gl->buff_curpos, -nextra);
    };
/*
 * Insert the filenames, separated by spaces, and with internal spaces,
 * tabs and backslashes escaped with backslashes.
 */
    for(i=0,j=start_path - gl->line; infile; i++) {
      char *file = result->files[i];
      while(*file) {
	int c = *file++;
	switch(c) {
	case ' ': case '\t': case '\\': case '*': case '?': case '[':
	  gl_buffer_char(gl, '\\', j++);
	};
	gl_buffer_char(gl, c, j++);
      };
      gl_buffer_char(gl, ' ', j++);
    };
  };
/*
 * Redisplay the part of the line which follows the start of
 * the original filename.
 */
  if(gl_place_cursor(gl, start_path - gl->line) ||
     gl_truncate_display(gl) ||
     gl_print_string(gl, start_path, start_path[length]))
    return 1;
/*
 * Move the cursor to the end of the expansion.
 */
  return gl_place_cursor(gl, (start_path - gl->line) + length);
}
#endif

#ifndef HIDE_FILE_SYSTEM
/*.......................................................................
 * This is the action function that lists glob expansions of the
 * filename that precedes the cursor position. It expands ~user/
 * expressions, $envvar expressions, and wildcards.
 */
static KT_KEY_FN(gl_list_glob)
{
  char *start_path;      /* The pointer to the start of the pathname in */
                         /*  gl->line[]. */
  FileExpansion *result; /* The results of the filename expansion */
  int pathlen;           /* The length of the pathname being expanded */
/*
 * Locate the start of the filename that precedes the cursor position.
 */
  start_path = _pu_start_of_path(gl->line, gl->buff_curpos);
  if(!start_path)
    return 1;
/*
 * Get the length of the string that is to be expanded.
 */
  pathlen = gl->buff_curpos - (start_path - gl->line);
/*
 * Attempt to expand it.
 */
  result = ef_expand_file(gl->ef, start_path, pathlen);
/*
 * If there was an error, report it.
 */
  if(!result) {
    return gl_print_info(gl,  ef_last_error(gl->ef), GL_END_INFO);
/*
 * If no files matched, report this as well.
 */
  } else if(result->nfile == 0 || !result->exists) {
    return gl_print_info(gl, "No files match.", GL_END_INFO);
/*
 * List the matching expansions.
 */
  } else if(gl->echo) {
    if(gl_start_newline(gl, 1) ||
       _ef_output_expansions(result, gl_write_fn, gl, gl->ncolumn))
      return 1;
    gl_queue_redisplay(gl);
  };
  return 0;
}
#endif

/*.......................................................................
 * Return non-zero if a character should be considered a part of a word.
 *
 * Input:
 *  c       int  The character to be tested.
 * Output:
 *  return  int  True if the character should be considered part of a word.
 */
static int gl_is_word_char(int c)
{
  return isalnum((int)(unsigned char)c) || strchr(GL_WORD_CHARS, c) != NULL;
}

/*.......................................................................
 * Override the builtin file-completion callback that is bound to the
 * "complete_word" action function.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  data             void *  This is passed to match_fn() whenever it is
 *                           called. It could, for example, point to a
 *                           symbol table where match_fn() could look
 *                           for possible completions.
 *  match_fn   CplMatchFn *  The function that will identify the prefix
 *                           to be completed from the input line, and
 *                           report matching symbols.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_customize_completion(GetLine *gl, void *data, CplMatchFn *match_fn)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
/*
 * Check the arguments.
 */
  if(!gl || !match_fn) {
    if(gl)
      _err_record_msg(gl->err, "NULL argument", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Temporarily block all signals.
 */
  gl_mask_signals(gl, &oldset);
/*
 * Record the new completion function and its callback data.
 */
  gl->cplfn.fn = match_fn;
  gl->cplfn.data = data;
/*
 * Restore the process signal mask before returning.
 */
  gl_unmask_signals(gl, &oldset);
  return 0;
}

/*.......................................................................
 * Change the terminal (or stream) that getline interacts with.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  input_fp         FILE *  The stdio stream to read from.
 *  output_fp        FILE *  The stdio stream to write to.
 *  term             char *  The terminal type. This can be NULL if
 *                           either or both of input_fp and output_fp don't
 *                           refer to a terminal. Otherwise it should refer
 *                           to an entry in the terminal information database.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_change_terminal(GetLine *gl, FILE *input_fp, FILE *output_fp,
		       const char *term)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_change_terminal() */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Execute the private body of the function while signals are blocked.
 */
  status = _gl_change_terminal(gl, input_fp, output_fp, term);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the gl_change_terminal() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_change_terminal(GetLine *gl, FILE *input_fp, FILE *output_fp,
			       const char *term)
{
  int is_term = 0;   /* True if both input_fd and output_fd are associated */
                     /*  with a terminal. */
/*
 * Require that input_fp and output_fp both be valid.
 */
  if(!input_fp || !output_fp) {
    gl_print_info(gl, "Can't change terminal. Bad input/output stream(s).",
		  GL_END_INFO);
    return 1;
  };
/*
 * Are we displacing an existing terminal (as opposed to setting the
 * initial terminal)?
 */
  if(gl->input_fd >= 0) {
/*
 * Make sure to leave the previous terminal in a usable state.
 */
    if(_gl_normal_io(gl))
      return 1;
/*
 * Remove the displaced terminal from the list of fds to watch.
 */
#ifdef HAVE_SELECT
    FD_CLR(gl->input_fd, &gl->rfds);
#endif
  };
/*
 * Record the file descriptors and streams.
 */
  gl->input_fp = input_fp;
  gl->input_fd = fileno(input_fp);
  gl->output_fp = output_fp;
  gl->output_fd = fileno(output_fp);
/*
 * If needed, expand the record of the maximum file-descriptor that might
 * need to be monitored with select().
 */
#ifdef HAVE_SELECT
  if(gl->input_fd > gl->max_fd)
    gl->max_fd = gl->input_fd;
#endif
/*
 * Disable terminal interaction until we have enough info to interact
 * with the terminal.
 */
  gl->is_term = 0;
/*
 * For terminal editing, we need both output_fd and input_fd to refer to
 * a terminal. While we can't verify that they both point to the same
 * terminal, we can verify that they point to terminals. If the user
 * sets the TERM environment variable to "dumb", treat a terminal as
 * a non-interactive I/O stream.
 */
  is_term = (isatty(gl->input_fd) && isatty(gl->output_fd)) &&
    !(term && strcmp(term, "dumb")==0);
/*
 * If we are interacting with a terminal and no terminal type has been
 * specified, treat it as a generic ANSI terminal.
 */
  if(is_term && !term)
    term = "ansi";
/*
 * Make a copy of the terminal type string.
 */
  if(term != gl->term) {
/*
 * Delete any old terminal type string.
 */
    if(gl->term) {
      free(gl->term);
      gl->term = NULL;
    };
/*
 * Make a copy of the new terminal-type string, if any.
 */
    if(term) {
      gl->term = (char *) malloc(strlen(term)+1);
      if(gl->term)
	strcpy(gl->term, term);
    };
  };
/*
 * Clear any terminal-specific key bindings that were taken from the
 * settings of the last terminal.
 */
  _kt_clear_bindings(gl->bindings, KTB_TERM);
/*
 * If we have a terminal install new bindings for it.
 */
  if(is_term) {
/*
 * Get the current settings of the terminal.
 */
    if(tcgetattr(gl->input_fd, &gl->oldattr)) {
      _err_record_msg(gl->err, "tcgetattr error", END_ERR_MSG);
      return 1;
    };
/*
 * If we don't set this now, gl_control_strings() won't know
 * that it is talking to a terminal.
 */
    gl->is_term = 1;
/*
 * Lookup the terminal control string and size information.
 */
    if(gl_control_strings(gl, term)) {
      gl->is_term = 0;
      return 1;
    };
/*
 * Bind terminal-specific keys.
 */
    if(gl_bind_terminal_keys(gl))
      return 1;
  };
/*
 * Assume that the caller has given us a terminal in a sane state.
 */
  gl->io_mode = GL_NORMAL_MODE;
/*
 * Switch into the currently configured I/O mode.
 */
  if(_gl_io_mode(gl, gl->io_mode))
    return 1;
  return 0;
}

/*.......................................................................
 * Set up terminal-specific key bindings.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
static int gl_bind_terminal_keys(GetLine *gl)
{
/*
 * Install key-bindings for the special terminal characters.
 */
  if(gl_bind_control_char(gl, KTB_TERM, gl->oldattr.c_cc[VINTR],
			  "user-interrupt") ||
     gl_bind_control_char(gl, KTB_TERM, gl->oldattr.c_cc[VQUIT], "abort") ||
     gl_bind_control_char(gl, KTB_TERM, gl->oldattr.c_cc[VSUSP], "suspend"))
    return 1;
/*
 * In vi-mode, arrange for the above characters to be seen in command
 * mode.
 */
  if(gl->editor == GL_VI_MODE) {
    if(gl_bind_control_char(gl, KTB_TERM, MAKE_META(gl->oldattr.c_cc[VINTR]),
			    "user-interrupt") ||
       gl_bind_control_char(gl, KTB_TERM, MAKE_META(gl->oldattr.c_cc[VQUIT]),
			    "abort") ||
       gl_bind_control_char(gl, KTB_TERM, MAKE_META(gl->oldattr.c_cc[VSUSP]),
			    "suspend"))
      return 1;
  };
/*
 * Non-universal special keys.
 */
#ifdef VLNEXT
  if(gl_bind_control_char(gl, KTB_TERM, gl->oldattr.c_cc[VLNEXT],
			  "literal-next"))
    return 1;
#else
  if(_kt_set_keybinding(gl->bindings, KTB_TERM, "^V", "literal-next")) {
    _err_record_msg(gl->err, _kt_last_error(gl->bindings), END_ERR_MSG);
    return 1;
  };
#endif
/*
 * Bind action functions to the terminal-specific arrow keys
 * looked up by gl_control_strings().
 */
  if(_gl_bind_arrow_keys(gl))
    return 1;
  return 0;
}

/*.......................................................................
 * This function is normally bound to control-D. When it is invoked within
 * a line it deletes the character which follows the cursor. When invoked
 * at the end of the line it lists possible file completions, and when
 * invoked on an empty line it causes gl_get_line() to return EOF. This
 * function emulates the one that is normally bound to control-D by tcsh.
 */
static KT_KEY_FN(gl_del_char_or_list_or_eof)
{
/*
 * If we have an empty line arrange to return EOF.
 */
  if(gl->ntotal < 1) {
    gl_record_status(gl, GLR_EOF, 0);
    return 1;
/*
 * If we are at the end of the line list possible completions.
 */
  } else if(gl->buff_curpos >= gl->ntotal) {
    return gl_list_completions(gl, 1, NULL);
/*
 * Within the line delete the character that follows the cursor.
 */
  } else {
/*
 * If in vi command mode, first preserve the current line for potential use
 * by vi-undo.
 */
    gl_save_for_undo(gl);
/*
 * Delete 'count' characters.
 */
    return gl_forward_delete_char(gl, count, NULL);
  };
}

/*.......................................................................
 * This function is normally bound to control-D in vi mode. When it is
 * invoked within a line it lists possible file completions, and when
 * invoked on an empty line it causes gl_get_line() to return EOF. This
 * function emulates the one that is normally bound to control-D by tcsh.
 */
static KT_KEY_FN(gl_list_or_eof)
{
/*
 * If we have an empty line arrange to return EOF.
 */
  if(gl->ntotal < 1) {
    gl_record_status(gl, GLR_EOF, 0);
    return 1;
/*
 * Otherwise list possible completions.
 */
  } else {
    return gl_list_completions(gl, 1, NULL);
  };
}

/*.......................................................................
 * List possible completions of the word that precedes the cursor. The
 * callback data argument must either be NULL to select the default
 * file completion callback, or be a GlCplCallback object containing the
 * completion callback function to call.
 */
static KT_KEY_FN(gl_list_completions)
{
  int waserr = 0;   /* True after errors */
/*
 * Get the container of the completion callback and its callback data.
 */
  GlCplCallback *cb = data ? (GlCplCallback *) data : &gl->cplfn;
/*
 * Get the list of possible completions.
 */
  CplMatches *matches = cpl_complete_word(gl->cpl, gl->line, gl->buff_curpos,
					  cb->data, cb->fn);
/*
 * No matching completions?
 */
  if(!matches) {
    waserr = gl_print_info(gl, cpl_last_error(gl->cpl), GL_END_INFO);
/*
 * List the matches.
 */
  } else if(matches->nmatch > 0 && gl->echo) {
    if(_gl_normal_io(gl) ||
       _cpl_output_completions(matches, gl_write_fn, gl, gl->ncolumn))
      waserr = 1;
  };
/*
 * If any output had to be written to the terminal, then editing will
 * have been suspended, make sure that we are back in raw line editing
 * mode before returning.
 */
  if(_gl_raw_io(gl, 1))
    waserr = 1;
  return waserr;
}

/*.......................................................................
 * Where the user has used the symbolic arrow-key names to specify
 * arrow key bindings, bind the specified action functions to the default
 * and terminal specific arrow key sequences.
 *
 * Input:
 *  gl     GetLine *   The getline resource object.
 * Output:
 *  return     int     0 - OK.
 *                     1 - Error.
 */
static int _gl_bind_arrow_keys(GetLine *gl)
{
/*
 * Process each of the arrow keys.
 */
  if(_gl_rebind_arrow_key(gl, "up", gl->u_arrow, "^[[A", "^[OA") ||
     _gl_rebind_arrow_key(gl, "down", gl->d_arrow, "^[[B", "^[OB") ||
     _gl_rebind_arrow_key(gl, "left", gl->l_arrow, "^[[D", "^[OD") ||
     _gl_rebind_arrow_key(gl, "right", gl->r_arrow, "^[[C", "^[OC"))
    return 1;
  return 0;
}

/*.......................................................................
 * Lookup the action function of a symbolic arrow-key binding, and bind
 * it to the terminal-specific and default arrow-key sequences. Note that
 * we don't trust the terminal-specified key sequences to be correct.
 * The main reason for this is that on some machines the xterm terminfo
 * entry is for hardware X-terminals, rather than xterm terminal emulators
 * and the two terminal types emit different character sequences when the
 * their cursor keys are pressed. As a result we also supply a couple
 * of default key sequences.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 *  name           char *   The symbolic name of the arrow key.
 *  term_seq       char *   The terminal-specific arrow-key sequence.
 *  def_seq1       char *   The first default arrow-key sequence.
 *  def_seq2       char *   The second arrow-key sequence.
 * Output:
 *  return          int     0 - OK.
 *                          1 - Error.
 */
static int _gl_rebind_arrow_key(GetLine *gl, const char *name,
				const char *term_seq, const char *def_seq1,
				const char *def_seq2)
{
  KeySym *keysym;  /* The binding-table entry matching the arrow-key name */
  int nsym;        /* The number of ambiguous matches */
/*
 * Lookup the key binding for the symbolic name of the arrow key. This
 * will either be the default action, or a user provided one.
 */
  if(_kt_lookup_keybinding(gl->bindings, name, strlen(name), &keysym, &nsym)
     == KT_EXACT_MATCH) {
/*
 * Get the action function.
 */
    KtAction *action = keysym->actions + keysym->binder;
    KtKeyFn *fn = action->fn;
    void *data = action->data;
/*
 * Bind this to each of the specified key sequences.
 */
    if((term_seq &&
	_kt_set_keyfn(gl->bindings, KTB_TERM, term_seq, fn, data)) ||
       (def_seq1 &&
	_kt_set_keyfn(gl->bindings, KTB_NORM, def_seq1, fn, data)) ||
       (def_seq2 &&
	_kt_set_keyfn(gl->bindings, KTB_NORM, def_seq2, fn, data))) {
      _err_record_msg(gl->err, _kt_last_error(gl->bindings), END_ERR_MSG);
      return 1;
    };
  };
  return 0;
}

/*.......................................................................
 * Read getline configuration information from a given file.
 *
 * Input:
 *  gl           GetLine *  The getline resource object.
 *  filename  const char *  The name of the file to read configuration
 *                          information from. The contents of this file
 *                          are as described in the gl_get_line(3) man
 *                          page for the default ~/.teclarc configuration
 *                          file.
 *  who         KtBinder    Who bindings are to be installed for.
 * Output:
 *  return           int    0 - OK.
 *                          1 - Irrecoverable error.
 */
static int _gl_read_config_file(GetLine *gl, const char *filename, KtBinder who)
{
/*
 * If filesystem access is to be excluded, configuration files can't
 * be read.
 */
#ifdef WITHOUT_FILE_SYSTEM
  _err_record_msg(gl->err,
		  "Can't read configuration files without filesystem access",
		  END_ERR_MSG);
  errno = EINVAL;
  return 1;
#else
  FileExpansion *expansion; /* The expansion of the filename */
  FILE *fp;                 /* The opened file */
  int waserr = 0;           /* True if an error occurred while reading */
  int lineno = 1;           /* The line number being processed */
/*
 * Check the arguments.
 */
  if(!gl || !filename) {
    if(gl)
      _err_record_msg(gl->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Expand the filename.
 */
  expansion = ef_expand_file(gl->ef, filename, -1);
  if(!expansion) {
    gl_print_info(gl, "Unable to expand ", filename, " (",
		  ef_last_error(gl->ef), ").", GL_END_INFO);
    return 1;
  };
/*
 * Attempt to open the file.
 */
  fp = fopen(expansion->files[0], "r");
/*
 * It isn't an error for there to be no configuration file.
 */
  if(!fp)
    return 0;
/*
 * Parse the contents of the file.
 */
  while(!waserr && !feof(fp))
    waserr = _gl_parse_config_line(gl, fp, glc_file_getc, filename, who,
				   &lineno);
/*
 * Bind action functions to the terminal-specific arrow keys.
 */
  if(_gl_bind_arrow_keys(gl))
    return 1;
/*
 * Clean up.
 */
  (void) fclose(fp);
  return waserr;
#endif
}

/*.......................................................................
 * Read GetLine configuration information from a string. The contents of
 * the string are the same as those described in the gl_get_line(3)
 * man page for the contents of the ~/.teclarc configuration file.
 */
static int _gl_read_config_string(GetLine *gl, const char *buffer, KtBinder who)
{
  const char *bptr;         /* A pointer into buffer[] */
  int waserr = 0;           /* True if an error occurred while reading */
  int lineno = 1;           /* The line number being processed */
/*
 * Check the arguments.
 */
  if(!gl || !buffer) {
    if(gl)
      _err_record_msg(gl->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Get a pointer to the start of the buffer.
 */
  bptr = buffer;
/*
 * Parse the contents of the buffer.
 */
  while(!waserr && *bptr)
    waserr = _gl_parse_config_line(gl, &bptr, glc_buff_getc, "", who, &lineno);
/*
 * Bind action functions to the terminal-specific arrow keys.
 */
  if(_gl_bind_arrow_keys(gl))
    return 1;
  return waserr;
}

/*.......................................................................
 * Parse the next line of a getline configuration file.
 *
 * Input:
 *  gl         GetLine *  The getline resource object.
 *  stream        void *  The pointer representing the stream to be read
 *                        by getc_fn().
 *  getc_fn  GlcGetcFn *  A callback function which when called with
 *                       'stream' as its argument, returns the next
 *                        unread character from the stream.
 *  origin  const char *  The name of the entity being read (eg. a
 *                        file name).
 *  who       KtBinder    Who bindings are to be installed for.
 * Input/Output:
 *  lineno         int *  The line number being processed is to be
 *                        maintained in *lineno.
 * Output:
 *  return         int    0 - OK.
 *                        1 - Irrecoverable error.
 */
static int _gl_parse_config_line(GetLine *gl, void *stream, GlcGetcFn *getc_fn,
				 const char *origin, KtBinder who, int *lineno)
{
  char buffer[GL_CONF_BUFLEN+1];  /* The input line buffer */
  char *argv[GL_CONF_MAXARG];     /* The argument list */
  int argc = 0;                   /* The number of arguments in argv[] */
  int c;                          /* A character from the file */
  int escaped = 0;                /* True if the next character is escaped */
  int i;
/*
 * Skip spaces and tabs.
 */
  do c = getc_fn(stream); while(c==' ' || c=='\t');
/*
 * Comments extend to the end of the line.
 */
  if(c=='#')
    do c = getc_fn(stream); while(c != '\n' && c != EOF);
/*
 * Ignore empty lines.
 */
  if(c=='\n' || c==EOF) {
    (*lineno)++;
    return 0;
  };
/*
 * Record the buffer location of the start of the first argument.
 */
  argv[argc] = buffer;
/*
 * Read the rest of the line, stopping early if a comment is seen, or
 * the buffer overflows, and replacing sequences of spaces with a
 * '\0', and recording the thus terminated string as an argument.
 */
  i = 0;
  while(i= GL_CONF_MAXARG) {
	gl_report_config_error(gl, origin, *lineno, "Too many arguments.");
	do c = getc_fn(stream); while(c!='\n' && c!=EOF);  /* Skip past eol */
	return 0;
      };
      argv[argc] = buffer + i;
/*
 * The next character was preceded by spaces, so it isn't escaped.
 */
      escaped = 0;
    } else {
/*
 * If we hit an unescaped backslash, this means that we should arrange
 * to treat the next character like a simple alphabetical character.
 */
      if(c=='\\' && !escaped) {
	escaped = 1;
/*
 * Splice lines where the newline is escaped.
 */
      } else if(c=='\n' && escaped) {
	(*lineno)++;
/*
 * Record a normal character, preserving any preceding backslash.
 */
      } else {
	if(escaped)
	  buffer[i++] = '\\';
	if(i>=GL_CONF_BUFLEN)
	  break;
	escaped = 0;
	buffer[i++] = c;
      };
/*
 * Get the next character.
 */
      c = getc_fn(stream);
    };
  };
/*
 * Did the buffer overflow?
 */
  if(i>=GL_CONF_BUFLEN) {
    gl_report_config_error(gl, origin, *lineno, "Line too long.");
    return 0;
  };
/*
 * The first argument should be a command name.
 */
  if(strcmp(argv[0], "bind") == 0) {
    const char *action = NULL; /* A NULL action removes a keybinding */
    const char *keyseq = NULL;
    switch(argc) {
    case 3:
      action = argv[2];
    case 2:              /* Note the intentional fallthrough */
      keyseq = argv[1];
/*
 * Attempt to record the new keybinding.
 */
      if(_kt_set_keybinding(gl->bindings, who, keyseq, action)) {
	gl_report_config_error(gl, origin, *lineno,
			       _kt_last_error(gl->bindings));
      };
      break;
    default:
      gl_report_config_error(gl, origin, *lineno, "Wrong number of arguments.");
    };
  } else if(strcmp(argv[0], "edit-mode") == 0) {
    if(argc == 2 && strcmp(argv[1], "emacs") == 0) {
      gl_change_editor(gl, GL_EMACS_MODE);
    } else if(argc == 2 && strcmp(argv[1], "vi") == 0) {
      gl_change_editor(gl, GL_VI_MODE);
    } else if(argc == 2 && strcmp(argv[1], "none") == 0) {
      gl_change_editor(gl, GL_NO_EDITOR);
    } else {
      gl_report_config_error(gl, origin, *lineno,
			     "The argument of editor should be vi or emacs.");
    };
  } else if(strcmp(argv[0], "nobeep") == 0) {
    gl->silence_bell = 1;
  } else {
    gl_report_config_error(gl, origin, *lineno, "Unknown command name.");
  };
/*
 * Skip any trailing comment.
 */
  while(c != '\n' && c != EOF)
    c = getc_fn(stream);
  (*lineno)++;
  return 0;
}

/*.......................................................................
 * This is a private function of _gl_parse_config_line() which prints
 * out an error message about the contents of the line, prefixed by the
 * name of the origin of the line and its line number.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  origin  const char *  The name of the entity being read (eg. a
 *                        file name).
 *  lineno         int    The line number at which the error occurred.
 *  errmsg  const char *  The error message.
 * Output:
 *  return         int    0 - OK.
 *                        1 - Error.
 */
static int gl_report_config_error(GetLine *gl, const char *origin, int lineno,
				  const char *errmsg)
{
  char lnum[20];   /* A buffer in which to render a single integer */
/*
 * Convert the line number into a string.
 */
  sprintf(lnum, "%d", lineno);
/*
 * Have the string printed on the terminal.
 */
  return gl_print_info(gl, origin, ":", lnum, ": ", errmsg, GL_END_INFO);
}

/*.......................................................................
 * This is the _gl_parse_config_line() callback function which reads the
 * next character from a configuration file.
 */
static GLC_GETC_FN(glc_file_getc)
{
  return fgetc((FILE *) stream);
}

/*.......................................................................
 * This is the _gl_parse_config_line() callback function which reads the
 * next character from a buffer. Its stream argument is a pointer to a
 * variable which is, in turn, a pointer into the buffer being read from.
 */
static GLC_GETC_FN(glc_buff_getc)
{
  const char **lptr = (char const **) stream;
  return **lptr ? *(*lptr)++ : EOF;
}

#ifndef HIDE_FILE_SYSTEM
/*.......................................................................
 * When this action is triggered, it arranges to temporarily read command
 * lines from the regular file whos name precedes the cursor.
 * The current line is first discarded.
 */
static KT_KEY_FN(gl_read_from_file)
{
  char *start_path;       /* The pointer to the start of the pathname in */
                          /*  gl->line[]. */
  FileExpansion *result;  /* The results of the filename expansion */
  int pathlen;            /* The length of the pathname being expanded */
/*
 * Locate the start of the filename that precedes the cursor position.
 */
  start_path = _pu_start_of_path(gl->line, gl->buff_curpos);
  if(!start_path)
    return 1;
/*
 * Get the length of the pathname string.
 */
  pathlen = gl->buff_curpos - (start_path - gl->line);
/*
 * Attempt to expand the pathname.
 */
  result = ef_expand_file(gl->ef, start_path, pathlen);
/*
 * If there was an error, report the error on a new line.
 */
  if(!result) {
    return gl_print_info(gl, ef_last_error(gl->ef), GL_END_INFO);
/*
 * If no files matched, report this as well.
 */
  } else if(result->nfile == 0 || !result->exists) {
    return gl_print_info(gl, "No files match.", GL_END_INFO);
/*
 * Complain if more than one file matches.
 */
  } else if(result->nfile > 1) {
    return gl_print_info(gl, "More than one file matches.", GL_END_INFO);
/*
 * Disallow input from anything but normal files. In principle we could
 * also support input from named pipes. Terminal files would be a problem
 * since we wouldn't know the terminal type, and other types of files
 * might cause the library to lock up.
 */
  } else if(!_pu_path_is_file(result->files[0])) {
    return gl_print_info(gl, "Not a normal file.", GL_END_INFO);
  } else {
/*
 * Attempt to open and install the specified file for reading.
 */
    gl->file_fp = fopen(result->files[0], "r");
    if(!gl->file_fp) {
      return gl_print_info(gl, "Unable to open: ", result->files[0],
			   GL_END_INFO);
    };
/*
 * If needed, expand the record of the maximum file-descriptor that might
 * need to be monitored with select().
 */
#ifdef HAVE_SELECT
    if(fileno(gl->file_fp) > gl->max_fd)
      gl->max_fd = fileno(gl->file_fp);
#endif
/*
 * Is non-blocking I/O needed?
 */
    if(gl->raw_mode && gl->io_mode==GL_SERVER_MODE &&
       gl_nonblocking_io(gl, fileno(gl->file_fp))) {
      gl_revert_input(gl);
      return gl_print_info(gl, "Can't read file %s with non-blocking I/O",
			   result->files[0]);
    };
/*
 * Inform the user what is happening.
 */
    if(gl_print_info(gl, "files[0], ">",
		     GL_END_INFO))
      return 1;
  };
  return 0;
}
#endif

/*.......................................................................
 * Close any temporary file that is being used for input.
 *
 * Input:
 *  gl     GetLine *  The getline resource object.
 */
static void gl_revert_input(GetLine *gl)
{
  if(gl->file_fp)
    fclose(gl->file_fp);
  gl->file_fp = NULL;
  gl->endline = 1;
}

/*.......................................................................
 * This is the action function that recalls the oldest line in the
 * history buffer.
 */
static KT_KEY_FN(gl_beginning_of_history)
{
/*
 * In vi mode, switch to command mode, since the user is very
 * likely to want to move around newly recalled lines.
 */
  gl_vi_command_mode(gl);
/*
 * Forget any previous recall session.
 */
  gl->preload_id = 0;
/*
 * Record the key sequence number of this search action.
 */
  gl->last_search = gl->keyseq_count;
/*
 * Recall the next oldest line in the history list.
 */
  if(_glh_oldest_line(gl->glh, gl->line, gl->linelen+1) == NULL)
    return 0;
/*
 * Accomodate the new contents of gl->line[].
 */
  gl_update_buffer(gl);
/*
 * Arrange to have the cursor placed at the end of the new line.
 */
  gl->buff_curpos = gl->ntotal;
/*
 * Erase and display the new line.
 */
  gl_queue_redisplay(gl);
  return 0;
}

/*.......................................................................
 * If a history session is currently in progress, this action function
 * recalls the line that was being edited when the session started. If
 * no history session is in progress, it does nothing.
 */
static KT_KEY_FN(gl_end_of_history)
{
/*
 * In vi mode, switch to command mode, since the user is very
 * likely to want to move around newly recalled lines.
 */
  gl_vi_command_mode(gl);
/*
 * Forget any previous recall session.
 */
  gl->preload_id = 0;
/*
 * Record the key sequence number of this search action.
 */
  gl->last_search = gl->keyseq_count;
/*
 * Recall the next oldest line in the history list.
 */
  if(_glh_current_line(gl->glh, gl->line, gl->linelen+1) == NULL)
    return 0;
/*
 * Accomodate the new contents of gl->line[].
 */
  gl_update_buffer(gl);
/*
 * Arrange to have the cursor placed at the end of the new line.
 */
  gl->buff_curpos = gl->ntotal;
/*
 * Erase and display the new line.
 */
  gl_queue_redisplay(gl);
  return 0;
}

/*.......................................................................
 * This action function is treated specially, in that its count argument
 * is set to the end keystroke of the keysequence that activated it.
 * It accumulates a numeric argument, adding one digit on each call in
 * which the last keystroke was a numeric digit.
 */
static KT_KEY_FN(gl_digit_argument)
{
/*
 * Was the last keystroke a digit?
 */
  int is_digit = isdigit((int)(unsigned char) count);
/*
 * In vi command mode, a lone '0' means goto-start-of-line.
 */
  if(gl->vi.command && gl->number < 0 && count == '0')
    return gl_beginning_of_line(gl, count, NULL);
/*
 * Are we starting to accumulate a new number?
 */
  if(gl->number < 0 || !is_digit)
    gl->number = 0;
/*
 * Was the last keystroke a digit?
 */
  if(is_digit) {
/*
 * Read the numeric value of the digit, without assuming ASCII.
 */
    int n;
    char s[2]; s[0] = count; s[1] = '\0';
    n = atoi(s);
/*
 * Append the new digit.
 */
    gl->number = gl->number * 10 + n;
  };
  return 0;
}

/*.......................................................................
 * The newline action function sets gl->endline to tell
 * gl_get_input_line() that the line is now complete.
 */
static KT_KEY_FN(gl_newline)
{
  GlhLineID id;    /* The last history line recalled while entering this line */
/*
 * Flag the line as ended.
 */
  gl->endline = 1;
/*
 * Record the next position in the history buffer, for potential
 * recall by an action function on the next call to gl_get_line().
 */
  id = _glh_line_id(gl->glh, 1);
  if(id)
    gl->preload_id = id;
  return 0;
}

/*.......................................................................
 * The 'repeat' action function sets gl->endline to tell
 * gl_get_input_line() that the line is now complete, and records the
 * ID of the next history line in gl->preload_id so that the next call
 * to gl_get_input_line() will preload the line with that history line.
 */
static KT_KEY_FN(gl_repeat_history)
{
  gl->endline = 1;
  gl->preload_id = _glh_line_id(gl->glh, 1);
  gl->preload_history = 1;
  return 0;
}

/*.......................................................................
 * Flush unwritten characters to the terminal.
 *
 * Input:
 *  gl     GetLine *  The getline resource object.
 * Output:
 *  return     int    0 - OK.
 *                    1 - Either an error occured, or the output
 *                        blocked and non-blocking I/O is being used.
 *                        See gl->rtn_status for details.
 */
static int gl_flush_output(GetLine *gl)
{
/*
 * Record the fact that we are about to write to the terminal.
 */
  gl->pending_io = GLP_WRITE;
/*
 * Attempt to flush the output to the terminal.
 */
  errno = 0;
  switch(_glq_flush_queue(gl->cq, gl->flush_fn, gl)) {
  case GLQ_FLUSH_DONE:
    return gl->redisplay && !gl->postpone && gl_redisplay(gl, 1, NULL);
    break;
  case GLQ_FLUSH_AGAIN:      /* Output blocked */
    gl_record_status(gl, GLR_BLOCKED, BLOCKED_ERRNO);
    return 1;
    break;
  default:                   /* Abort the line if an error occurs */
    gl_record_status(gl, errno==EINTR ? GLR_SIGNAL : GLR_ERROR, errno);
    return 1;
    break;
  };
}

/*.......................................................................
 * This is the callback which _glq_flush_queue() uses to write buffered
 * characters to the terminal.
 */
static GL_WRITE_FN(gl_flush_terminal)
{
  int ndone = 0;    /* The number of characters written so far */
/*
 * Get the line-editor resource object.
 */
  GetLine *gl = (GetLine *) data;
/*
 * Transfer the latest array of characters to stdio.
 */
  while(ndone < n) {
    int nnew = write(gl->output_fd, s, n-ndone);
/*
 * If the write was successful, add to the recorded number of bytes
 * that have now been written.
 */
    if(nnew > 0) {
      ndone += nnew;
/*
 * If a signal interrupted the call, restart the write(), since all of
 * the signals that gl_get_line() has been told to watch for are
 * currently blocked.
 */
    } else if(errno == EINTR) {
      continue;
/*
 * If we managed to write something before an I/O error occurred, or
 * output blocked before anything was written, report the number of
 * bytes that were successfully written before this happened.
 */
    } else if(ndone > 0
#if defined(EAGAIN)
	      || errno==EAGAIN
#endif
#if defined(EWOULDBLOCK)
	      || errno==EWOULDBLOCK
#endif
	      ) {
      return ndone;

/*
 * To get here, an error must have occurred before anything new could
 * be written.
 */
    } else {
      return -1;
    };
  };
/*
 * To get here, we must have successfully written the number of
 * bytes that was specified.
 */
  return n;
}

/*.......................................................................
 * Change the style of editing to emulate a given editor.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 *  editor  GlEditor    The type of editor to emulate.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 */
static int gl_change_editor(GetLine *gl, GlEditor editor)
{
/*
 * Install the default key-bindings of the requested editor.
 */
  switch(editor) {
  case GL_EMACS_MODE:
    _kt_clear_bindings(gl->bindings, KTB_NORM);
    _kt_clear_bindings(gl->bindings, KTB_TERM);
    (void) _kt_add_bindings(gl->bindings, KTB_NORM, gl_emacs_bindings,
		   sizeof(gl_emacs_bindings)/sizeof(gl_emacs_bindings[0]));
    break;
  case GL_VI_MODE:
    _kt_clear_bindings(gl->bindings, KTB_NORM);
    _kt_clear_bindings(gl->bindings, KTB_TERM);
    (void) _kt_add_bindings(gl->bindings, KTB_NORM, gl_vi_bindings,
			    sizeof(gl_vi_bindings)/sizeof(gl_vi_bindings[0]));
    break;
  case GL_NO_EDITOR:
    break;
  default:
    _err_record_msg(gl->err, "Unknown editor", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Record the new editing mode.
 */
  gl->editor = editor;
  gl->vi.command = 0;     /* Start in input mode */
  gl->insert_curpos = 0;
/*
 * Reinstate terminal-specific bindings.
 */
  if(gl->editor != GL_NO_EDITOR && gl->input_fp)
    (void) gl_bind_terminal_keys(gl);
  return 0;
}

/*.......................................................................
 * This is an action function that switches to editing using emacs bindings
 */
static KT_KEY_FN(gl_emacs_editing_mode)
{
  return gl_change_editor(gl, GL_EMACS_MODE);
}

/*.......................................................................
 * This is an action function that switches to editing using vi bindings
 */
static KT_KEY_FN(gl_vi_editing_mode)
{
  return gl_change_editor(gl, GL_VI_MODE);
}

/*.......................................................................
 * This is the action function that switches to insert mode.
 */
static KT_KEY_FN(gl_vi_insert)
{
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Switch to vi insert mode.
 */
  gl->insert = 1;
  gl->vi.command = 0;
  gl->insert_curpos = gl->buff_curpos;
  return 0;
}

/*.......................................................................
 * This is an action function that switches to overwrite mode.
 */
static KT_KEY_FN(gl_vi_overwrite)
{
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * Switch to vi overwrite mode.
 */
  gl->insert = 0;
  gl->vi.command = 0;
  gl->insert_curpos = gl->buff_curpos;
  return 0;
}

/*.......................................................................
 * This action function toggles the case of the character under the
 * cursor.
 */
static KT_KEY_FN(gl_change_case)
{
  int i;
/*
 * Keep a record of the current insert mode and the cursor position.
 */
  int insert = gl->insert;
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
  gl_save_for_undo(gl);
/*
 * We want to overwrite the modified word.
 */
  gl->insert = 0;
/*
 * Toggle the case of 'count' characters.
 */
  for(i=0; ibuff_curpos < gl->ntotal; i++) {
    char *cptr = gl->line + gl->buff_curpos++;
/*
 * Convert the character to upper case?
 */
    if(islower((int)(unsigned char) *cptr))
      gl_buffer_char(gl, toupper((int) *cptr), cptr - gl->line);
    else if(isupper((int)(unsigned char) *cptr))
      gl_buffer_char(gl, tolower((int) *cptr), cptr - gl->line);
/*
 * Write the possibly modified character back. Note that for non-modified
 * characters we want to do this as well, so as to advance the cursor.
 */
      if(gl_print_char(gl, *cptr, cptr[1]))
	return 1;
  };
/*
 * Restore the insertion mode.
 */
  gl->insert = insert;
  return gl_place_cursor(gl, gl->buff_curpos);	/* bounds check */
}

/*.......................................................................
 * This is the action function which implements the vi-style action which
 * moves the cursor to the start of the line, then switches to insert mode.
 */
static KT_KEY_FN(gl_vi_insert_at_bol)
{
  gl_save_for_undo(gl);
  return gl_beginning_of_line(gl, 0, NULL) ||
         gl_vi_insert(gl, 0, NULL);
         
}

/*.......................................................................
 * This is the action function which implements the vi-style action which
 * moves the cursor to the end of the line, then switches to insert mode
 * to allow text to be appended to the line.
 */
static KT_KEY_FN(gl_vi_append_at_eol)
{
  gl_save_for_undo(gl);
  gl->vi.command = 0;	/* Allow cursor at EOL */
  return gl_end_of_line(gl, 0, NULL) ||
         gl_vi_insert(gl, 0, NULL);
}

/*.......................................................................
 * This is the action function which implements the vi-style action which
 * moves the cursor to right one then switches to insert mode, thus
 * allowing text to be appended after the next character.
 */
static KT_KEY_FN(gl_vi_append)
{
  gl_save_for_undo(gl);
  gl->vi.command = 0;	/* Allow cursor at EOL */
  return gl_cursor_right(gl, 1, NULL) ||
         gl_vi_insert(gl, 0, NULL);
}

/*.......................................................................
 * This action function moves the cursor to the column specified by the
 * numeric argument. Column indexes start at 1.
 */
static KT_KEY_FN(gl_goto_column)
{
  return gl_place_cursor(gl, count - 1);
}

/*.......................................................................
 * Starting with the character under the cursor, replace 'count'
 * characters with the next character that the user types.
 */
static KT_KEY_FN(gl_vi_replace_char)
{
  char c;  /* The replacement character */
  int i;
/*
 * Keep a record of the current insert mode.
 */
  int insert = gl->insert;
/*
 * Get the replacement character.
 */
  if(gl->vi.repeat.active) {
    c = gl->vi.repeat.input_char;
  } else {
    if(gl_read_terminal(gl, 1, &c))
      return 1;
    gl->vi.repeat.input_char = c;
  };
/*
 * Are there 'count' characters to be replaced?
 */
  if(gl->ntotal - gl->buff_curpos >= count) {
/*
 * If in vi command mode, preserve the current line for potential
 * use by vi-undo.
 */
    gl_save_for_undo(gl);
/*
 * Temporarily switch to overwrite mode.
 */
    gl->insert = 0;
/*
 * Overwrite the current character plus count-1 subsequent characters
 * with the replacement character.
 */
    for(i=0; iinsert = insert;
  };
  return gl_place_cursor(gl, gl->buff_curpos);	/* bounds check */
}

/*.......................................................................
 * This is an action function which changes all characters between the
 * current cursor position and the end of the line.
 */
static KT_KEY_FN(gl_vi_change_rest_of_line)
{
  gl_save_for_undo(gl);
  gl->vi.command = 0;	/* Allow cursor at EOL */
  return gl_kill_line(gl, count, NULL) || gl_vi_insert(gl, 0, NULL);
}

/*.......................................................................
 * This is an action function which changes all characters between the
 * start of the line and the current cursor position.
 */
static KT_KEY_FN(gl_vi_change_to_bol)
{
  return gl_backward_kill_line(gl,count,NULL) || gl_vi_insert(gl,0,NULL);
}

/*.......................................................................
 * This is an action function which deletes the entire contents of the
 * current line and switches to insert mode.
 */
static KT_KEY_FN(gl_vi_change_line)
{
  return gl_delete_line(gl,count,NULL) || gl_vi_insert(gl,0,NULL);
}

/*.......................................................................
 * Starting from the cursor position and looking towards the end of the
 * line, copy 'count' characters to the cut buffer.
 */
static KT_KEY_FN(gl_forward_copy_char)
{
/*
 * Limit the count to the number of characters available.
 */
  if(gl->buff_curpos + count >= gl->ntotal)
    count = gl->ntotal - gl->buff_curpos;
  if(count < 0)
    count = 0;
/*
 * Copy the characters to the cut buffer.
 */
  memcpy(gl->cutbuf, gl->line + gl->buff_curpos, count);
  gl->cutbuf[count] = '\0';
  return 0;
}

/*.......................................................................
 * Starting from the character before the cursor position and looking
 * backwards towards the start of the line, copy 'count' characters to
 * the cut buffer.
 */
static KT_KEY_FN(gl_backward_copy_char)
{
/*
 * Limit the count to the number of characters available.
 */
  if(count > gl->buff_curpos)
    count = gl->buff_curpos;
  if(count < 0)
    count = 0;
  gl_place_cursor(gl, gl->buff_curpos - count);
/*
 * Copy the characters to the cut buffer.
 */
  memcpy(gl->cutbuf, gl->line + gl->buff_curpos, count);
  gl->cutbuf[count] = '\0';
  return 0;
}

/*.......................................................................
 * Starting from the cursor position copy to the specified column into the
 * cut buffer.
 */
static KT_KEY_FN(gl_copy_to_column)
{
  if (--count >= gl->buff_curpos)
    return gl_forward_copy_char(gl, count - gl->buff_curpos, NULL);
  else
    return gl_backward_copy_char(gl, gl->buff_curpos - count, NULL);
}

/*.......................................................................
 * Starting from the cursor position copy characters up to a matching
 * parenthesis into the cut buffer.
 */
static KT_KEY_FN(gl_copy_to_parenthesis)
{
  int curpos = gl_index_of_matching_paren(gl);
  if(curpos >= 0) {
    gl_save_for_undo(gl);
    if(curpos >= gl->buff_curpos)
      return gl_forward_copy_char(gl, curpos - gl->buff_curpos + 1, NULL);
    else
      return gl_backward_copy_char(gl, ++gl->buff_curpos - curpos + 1, NULL);
  };
  return 0;
}

/*.......................................................................
 * Starting from the cursor position copy the rest of the line into the
 * cut buffer.
 */
static KT_KEY_FN(gl_copy_rest_of_line)
{
/*
 * Copy the characters to the cut buffer.
 */
  memcpy(gl->cutbuf, gl->line + gl->buff_curpos, gl->ntotal - gl->buff_curpos);
  gl->cutbuf[gl->ntotal - gl->buff_curpos] = '\0';
  return 0;
}

/*.......................................................................
 * Copy from the beginning of the line to the cursor position into the
 * cut buffer.
 */
static KT_KEY_FN(gl_copy_to_bol)
{
/*
 * Copy the characters to the cut buffer.
 */
  memcpy(gl->cutbuf, gl->line, gl->buff_curpos);
  gl->cutbuf[gl->buff_curpos] = '\0';
  gl_place_cursor(gl, 0);
  return 0;
}

/*.......................................................................
 * Copy the entire line into the cut buffer.
 */
static KT_KEY_FN(gl_copy_line)
{
/*
 * Copy the characters to the cut buffer.
 */
  memcpy(gl->cutbuf, gl->line, gl->ntotal);
  gl->cutbuf[gl->ntotal] = '\0';
  return 0;
}

/*.......................................................................
 * Search forwards for the next character that the user enters.
 */
static KT_KEY_FN(gl_forward_find_char)
{
  int pos = gl_find_char(gl, count, 1, 1, '\0');
  return pos >= 0 && gl_place_cursor(gl, pos);
}

/*.......................................................................
 * Search backwards for the next character that the user enters.
 */
static KT_KEY_FN(gl_backward_find_char)
{
  int pos = gl_find_char(gl, count, 0, 1, '\0');
  return pos >= 0 && gl_place_cursor(gl, pos);
}

/*.......................................................................
 * Search forwards for the next character that the user enters. Move up to,
 * but not onto, the found character.
 */
static KT_KEY_FN(gl_forward_to_char)
{
  int pos = gl_find_char(gl, count, 1, 0, '\0');
  return pos >= 0 && gl_place_cursor(gl, pos);
}

/*.......................................................................
 * Search backwards for the next character that the user enters. Move back to,
 * but not onto, the found character.
 */
static KT_KEY_FN(gl_backward_to_char)
{
  int pos = gl_find_char(gl, count, 0, 0, '\0');
  return pos >= 0 && gl_place_cursor(gl, pos);
}

/*.......................................................................
 * Searching in a given direction, return the index of a given (or
 * read) character in the input line, or the character that precedes
 * it in the specified search direction. Return -1 if not found.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 *  count        int    The number of times to search.
 *  forward      int    True if searching forward.
 *  onto         int    True if the search should end on top of the
 *                      character, false if the search should stop
 *                      one character before the character in the
 *                      specified search direction.
 *  c           char    The character to be sought, or '\0' if the
 *                      character should be read from the user.
 * Output:
 *  return       int    The index of the character in gl->line[], or
 *                      -1 if not found.
 */
static int gl_find_char(GetLine *gl, int count, int forward, int onto, char c)
{
  int pos;     /* The index reached in searching the input line */
  int i;
/*
 * Get a character from the user?
 */
  if(!c) {
/*
 * If we are in the process of repeating a previous change command, substitute
 * the last find character.
 */
    if(gl->vi.repeat.active) {
      c = gl->vi.find_char;
    } else {
      if(gl_read_terminal(gl, 1, &c))
	return -1;
/*
 * Record the details of the new search, for use by repeat finds.
 */
      gl->vi.find_forward = forward;
      gl->vi.find_onto = onto;
      gl->vi.find_char = c;
    };
  };
/*
 * Which direction should we search?
 */
  if(forward) {
/*
 * Search forwards 'count' times for the character, starting with the
 * character that follows the cursor.
 */
    for(i=0, pos=gl->buff_curpos; intotal; i++) {
/*
 * Advance past the last match (or past the current cursor position
 * on the first search).
 */
      pos++;
/*
 * Search for the next instance of c.
 */
      for( ; posntotal && c!=gl->line[pos]; pos++)
	;
    };
/*
 * If the character was found and we have been requested to return the
 * position of the character that precedes the desired character, then
 * we have gone one character too far.
 */
    if(!onto && posntotal)
      pos--;
  } else {
/*
 * Search backwards 'count' times for the character, starting with the
 * character that precedes the cursor.
 */
    for(i=0, pos=gl->buff_curpos; i= gl->insert_curpos; i++) {
/*
 * Step back one from the last match (or from the current cursor
 * position on the first search).
 */
      pos--;
/*
 * Search for the next instance of c.
 */
      for( ; pos>=gl->insert_curpos && c!=gl->line[pos]; pos--)
	;
    };
/*
 * If the character was found and we have been requested to return the
 * position of the character that precedes the desired character, then
 * we have gone one character too far.
 */
    if(!onto && pos>=gl->insert_curpos)
      pos++;
  };
/*
 * If found, return the cursor position of the count'th match.
 * Otherwise ring the terminal bell.
 */
  if(pos >= gl->insert_curpos && pos < gl->ntotal) {
    return pos;
  } else {
    (void) gl_ring_bell(gl, 1, NULL);
    return -1;
  }
}

/*.......................................................................
 * Repeat the last character search in the same direction as the last
 * search.
 */
static KT_KEY_FN(gl_repeat_find_char)
{
  int pos = gl->vi.find_char ?
    gl_find_char(gl, count, gl->vi.find_forward, gl->vi.find_onto,
		 gl->vi.find_char) : -1;
  return pos >= 0 && gl_place_cursor(gl, pos);
}

/*.......................................................................
 * Repeat the last character search in the opposite direction as the last
 * search.
 */
static KT_KEY_FN(gl_invert_refind_char)
{
  int pos = gl->vi.find_char ?
    gl_find_char(gl, count, !gl->vi.find_forward, gl->vi.find_onto,
		 gl->vi.find_char) : -1;
  return pos >= 0 && gl_place_cursor(gl, pos);
}

/*.......................................................................
 * Search forward from the current position of the cursor for 'count'
 * word endings, returning the index of the last one found, or the end of
 * the line if there were less than 'count' words.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 *  n            int    The number of word boundaries to search for.
 * Output:
 *  return       int    The buffer index of the located position.
 */
static int gl_nth_word_end_forward(GetLine *gl, int n)
{
  int bufpos;   /* The buffer index being checked. */
  int i;
/*
 * In order to guarantee forward motion to the next word ending,
 * we need to start from one position to the right of the cursor
 * position, since this may already be at the end of a word.
 */
  bufpos = gl->buff_curpos + 1;
/*
 * If we are at the end of the line, return the index of the last
 * real character on the line. Note that this will be -1 if the line
 * is empty.
 */
  if(bufpos >= gl->ntotal)
    return gl->ntotal - 1;
/*
 * Search 'n' times, unless the end of the input line is reached first.
 */
  for(i=0; intotal; i++) {
/*
 * If we are not already within a word, skip to the start of the next word.
 */
    for( ; bufposntotal && !gl_is_word_char((int)gl->line[bufpos]);
	bufpos++)
      ;
/*
 * Find the end of the next word.
 */
    for( ; bufposntotal && gl_is_word_char((int)gl->line[bufpos]);
	bufpos++)
      ;
  };
/*
 * We will have overshot.
 */
  return bufpos > 0 ? bufpos-1 : bufpos;
}

/*.......................................................................
 * Search forward from the current position of the cursor for 'count'
 * word starts, returning the index of the last one found, or the end of
 * the line if there were less than 'count' words.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 *  n            int    The number of word boundaries to search for.
 * Output:
 *  return       int    The buffer index of the located position.
 */
static int gl_nth_word_start_forward(GetLine *gl, int n)
{
  int bufpos;   /* The buffer index being checked. */
  int i;
/*
 * Get the current cursor position.
 */
  bufpos = gl->buff_curpos;
/*
 * Search 'n' times, unless the end of the input line is reached first.
 */
  for(i=0; intotal; i++) {
/*
 * Find the end of the current word.
 */
    for( ; bufposntotal && gl_is_word_char((int)gl->line[bufpos]);
	bufpos++)
      ;
/*
 * Skip to the start of the next word.
 */
    for( ; bufposntotal && !gl_is_word_char((int)gl->line[bufpos]);
	bufpos++)
      ;
  };
  return bufpos;
}

/*.......................................................................
 * Search backward from the current position of the cursor for 'count'
 * word starts, returning the index of the last one found, or the start
 * of the line if there were less than 'count' words.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 *  n            int    The number of word boundaries to search for.
 * Output:
 *  return       int    The buffer index of the located position.
 */
static int gl_nth_word_start_backward(GetLine *gl, int n)
{
  int bufpos;   /* The buffer index being checked. */
  int i;
/*
 * Get the current cursor position.
 */
  bufpos = gl->buff_curpos;
/*
 * Search 'n' times, unless the beginning of the input line (or vi insertion
 * point) is reached first.
 */
  for(i=0; i gl->insert_curpos; i++) {
/*
 * Starting one character back from the last search, so as not to keep
 * settling on the same word-start, search backwards until finding a
 * word character.
 */
    while(--bufpos >= gl->insert_curpos &&
          !gl_is_word_char((int)gl->line[bufpos]))
      ;
/*
 * Find the start of the word.
 */
    while(--bufpos >= gl->insert_curpos &&
          gl_is_word_char((int)gl->line[bufpos]))
      ;
/*
 * We will have gone one character too far.
 */
    bufpos++;
  };
  return bufpos >= gl->insert_curpos ? bufpos : gl->insert_curpos;
}

/*.......................................................................
 * Copy one or more words into the cut buffer without moving the cursor
 * or deleting text.
 */
static KT_KEY_FN(gl_forward_copy_word)
{
/*
 * Find the location of the count'th start or end of a word
 * after the cursor, depending on whether in emacs or vi mode.
 */
  int next = gl->editor == GL_EMACS_MODE ?
    gl_nth_word_end_forward(gl, count) :
    gl_nth_word_start_forward(gl, count);
/*
 * How many characters are to be copied into the cut buffer?
 */
  int n = next - gl->buff_curpos;
/*
 * Copy the specified segment and terminate the string.
 */
  memcpy(gl->cutbuf, gl->line + gl->buff_curpos, n);
  gl->cutbuf[n] = '\0';
  return 0;
}

/*.......................................................................
 * Copy one or more words preceding the cursor into the cut buffer,
 * without moving the cursor or deleting text.
 */
static KT_KEY_FN(gl_backward_copy_word)
{
/*
 * Find the location of the count'th start of word before the cursor.
 */
  int next = gl_nth_word_start_backward(gl, count);
/*
 * How many characters are to be copied into the cut buffer?
 */
  int n = gl->buff_curpos - next;
  gl_place_cursor(gl, next);
/*
 * Copy the specified segment and terminate the string.
 */
  memcpy(gl->cutbuf, gl->line + next, n);
  gl->cutbuf[n] = '\0';
  return 0;
}

/*.......................................................................
 * Copy the characters between the cursor and the count'th instance of
 * a specified character in the input line, into the cut buffer.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 *  count        int    The number of times to search.
 *  c           char    The character to be searched for, or '\0' if
 *                      the character should be read from the user.
 *  forward      int    True if searching forward.
 *  onto         int    True if the search should end on top of the
 *                      character, false if the search should stop
 *                      one character before the character in the
 *                      specified search direction.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 *
 */
static int gl_copy_find(GetLine *gl, int count, char c, int forward, int onto)
{
  int n;  /* The number of characters in the cut buffer */
/*
 * Search for the character, and abort the operation if not found.
 */
  int pos = gl_find_char(gl, count, forward, onto, c);
  if(pos < 0)
    return 0;
/*
 * Copy the specified segment.
 */
  if(forward) {
    n = pos + 1 - gl->buff_curpos;
    memcpy(gl->cutbuf, gl->line + gl->buff_curpos, n);
  } else {
    n = gl->buff_curpos - pos;
    memcpy(gl->cutbuf, gl->line + pos, n);
    if(gl->editor == GL_VI_MODE)
      gl_place_cursor(gl, pos);
  }
/*
 * Terminate the copy.
 */
  gl->cutbuf[n] = '\0';
  return 0;
}

/*.......................................................................
 * Copy a section up to and including a specified character into the cut
 * buffer without moving the cursor or deleting text.
 */
static KT_KEY_FN(gl_forward_copy_find)
{
  return gl_copy_find(gl, count, '\0', 1, 1);
}

/*.......................................................................
 * Copy a section back to and including a specified character into the cut
 * buffer without moving the cursor or deleting text.
 */
static KT_KEY_FN(gl_backward_copy_find)
{
  return gl_copy_find(gl, count, '\0', 0, 1);
}

/*.......................................................................
 * Copy a section up to and not including a specified character into the cut
 * buffer without moving the cursor or deleting text.
 */
static KT_KEY_FN(gl_forward_copy_to)
{
  return gl_copy_find(gl, count, '\0', 1, 0);
}

/*.......................................................................
 * Copy a section back to and not including a specified character into the cut
 * buffer without moving the cursor or deleting text.
 */
static KT_KEY_FN(gl_backward_copy_to)
{
  return gl_copy_find(gl, count, '\0', 0, 0);
}

/*.......................................................................
 * Copy to a character specified in a previous search into the cut
 * buffer without moving the cursor or deleting text.
 */
static KT_KEY_FN(gl_copy_refind)
{
  return gl_copy_find(gl, count, gl->vi.find_char, gl->vi.find_forward,
		      gl->vi.find_onto);
}

/*.......................................................................
 * Copy to a character specified in a previous search, but in the opposite
 * direction, into the cut buffer without moving the cursor or deleting text.
 */
static KT_KEY_FN(gl_copy_invert_refind)
{
  return gl_copy_find(gl, count, gl->vi.find_char, !gl->vi.find_forward,
		      gl->vi.find_onto);
}

/*.......................................................................
 * Set the position of the cursor in the line input buffer and the
 * terminal.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 *  buff_curpos  int    The new buffer cursor position.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 */
static int gl_place_cursor(GetLine *gl, int buff_curpos)
{
/*
 * Don't allow the cursor position to go out of the bounds of the input
 * line.
 */
  if(buff_curpos >= gl->ntotal)
    buff_curpos = gl->vi.command ? gl->ntotal-1 : gl->ntotal;
  if(buff_curpos < 0)
    buff_curpos = 0;
/*
 * Record the new buffer position.
 */
  gl->buff_curpos = buff_curpos;
/*
 * Move the terminal cursor to the corresponding character.
 */
  return gl_set_term_curpos(gl, gl->prompt_len +
    gl_displayed_string_width(gl, gl->line, buff_curpos, gl->prompt_len));
}

/*.......................................................................
 * In vi command mode, this function saves the current line to the
 * historical buffer needed by the undo command. In emacs mode it does
 * nothing. In order to allow action functions to call other action
 * functions, gl_interpret_char() sets gl->vi.undo.saved to 0 before
 * invoking an action, and thereafter once any call to this function
 * has set it to 1, further calls are ignored.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 */
static void gl_save_for_undo(GetLine *gl)
{
  if(gl->vi.command && !gl->vi.undo.saved) {
    strcpy(gl->vi.undo.line, gl->line);
    gl->vi.undo.buff_curpos = gl->buff_curpos;
    gl->vi.undo.ntotal = gl->ntotal;
    gl->vi.undo.saved = 1;
  };
  if(gl->vi.command && !gl->vi.repeat.saved &&
     gl->current_action.fn != gl_vi_repeat_change) {
    gl->vi.repeat.action = gl->current_action;
    gl->vi.repeat.count = gl->current_count;
    gl->vi.repeat.saved = 1;
  };
  return;
}

/*.......................................................................
 * In vi mode, restore the line to the way it was before the last command
 * mode operation, storing the current line in the buffer so that the
 * undo operation itself can subsequently be undone.
 */
static KT_KEY_FN(gl_vi_undo)
{
/*
 * Get pointers into the two lines.
 */
  char *undo_ptr = gl->vi.undo.line;
  char *line_ptr = gl->line;
/*
 * Swap the characters of the two buffers up to the length of the shortest
 * line.
 */
  while(*undo_ptr && *line_ptr) {
    char c = *undo_ptr;
    *undo_ptr++ = *line_ptr;
    *line_ptr++ = c;
  };
/*
 * Copy the rest directly.
 */
  if(gl->ntotal > gl->vi.undo.ntotal) {
    strcpy(undo_ptr, line_ptr);
    *line_ptr = '\0';
  } else {
    strcpy(line_ptr, undo_ptr);
    *undo_ptr = '\0';
  };
/*
 * Record the length of the stored string.
 */
  gl->vi.undo.ntotal = gl->ntotal;
/*
 * Accomodate the new contents of gl->line[].
 */
  gl_update_buffer(gl);
/*
 * Set both cursor positions to the leftmost of the saved and current
 * cursor positions to emulate what vi does.
 */
  if(gl->buff_curpos < gl->vi.undo.buff_curpos)
    gl->vi.undo.buff_curpos = gl->buff_curpos;
  else
    gl->buff_curpos = gl->vi.undo.buff_curpos;
/*
 * Since we have bipassed calling gl_save_for_undo(), record repeat
 * information inline.
 */
  gl->vi.repeat.action.fn = gl_vi_undo;
  gl->vi.repeat.action.data = NULL;
  gl->vi.repeat.count = 1;
/*
 * Display the restored line.
 */
  gl_queue_redisplay(gl);
  return 0;
}

/*.......................................................................
 * Delete the following word and leave the user in vi insert mode.
 */
static KT_KEY_FN(gl_vi_forward_change_word)
{
  gl_save_for_undo(gl);
  gl->vi.command = 0;	/* Allow cursor at EOL */
  return gl_forward_delete_word(gl, count, NULL) || gl_vi_insert(gl, 0, NULL);
}

/*.......................................................................
 * Delete the preceding word and leave the user in vi insert mode.
 */
static KT_KEY_FN(gl_vi_backward_change_word)
{
  return gl_backward_delete_word(gl, count, NULL) || gl_vi_insert(gl, 0, NULL);
}

/*.......................................................................
 * Delete the following section and leave the user in vi insert mode.
 */
static KT_KEY_FN(gl_vi_forward_change_find)
{
  return gl_delete_find(gl, count, '\0', 1, 1, 1);
}

/*.......................................................................
 * Delete the preceding section and leave the user in vi insert mode.
 */
static KT_KEY_FN(gl_vi_backward_change_find)
{
  return gl_delete_find(gl, count, '\0', 0, 1, 1);
}

/*.......................................................................
 * Delete the following section and leave the user in vi insert mode.
 */
static KT_KEY_FN(gl_vi_forward_change_to)
{
  return gl_delete_find(gl, count, '\0', 1, 0, 1);
}

/*.......................................................................
 * Delete the preceding section and leave the user in vi insert mode.
 */
static KT_KEY_FN(gl_vi_backward_change_to)
{
  return gl_delete_find(gl, count, '\0', 0, 0, 1);
}

/*.......................................................................
 * Delete to a character specified by a previous search and leave the user
 * in vi insert mode.
 */
static KT_KEY_FN(gl_vi_change_refind)
{
  return gl_delete_find(gl, count, gl->vi.find_char, gl->vi.find_forward,
			gl->vi.find_onto, 1);
}

/*.......................................................................
 * Delete to a character specified by a previous search, but in the opposite
 * direction, and leave the user in vi insert mode.
 */
static KT_KEY_FN(gl_vi_change_invert_refind)
{
  return gl_delete_find(gl, count, gl->vi.find_char, !gl->vi.find_forward,
			gl->vi.find_onto, 1);
}

/*.......................................................................
 * Delete the following character and leave the user in vi insert mode.
 */
static KT_KEY_FN(gl_vi_forward_change_char)
{
  gl_save_for_undo(gl);
  gl->vi.command = 0;	/* Allow cursor at EOL */
  return gl_delete_chars(gl, count, 1) || gl_vi_insert(gl, 0, NULL);
}

/*.......................................................................
 * Delete the preceding character and leave the user in vi insert mode.
 */
static KT_KEY_FN(gl_vi_backward_change_char)
{
  return gl_backward_delete_char(gl, count, NULL) || gl_vi_insert(gl, 0, NULL);
}

/*.......................................................................
 * Starting from the cursor position change characters to the specified column.
 */
static KT_KEY_FN(gl_vi_change_to_column)
{
  if (--count >= gl->buff_curpos)
    return gl_vi_forward_change_char(gl, count - gl->buff_curpos, NULL);
  else
    return gl_vi_backward_change_char(gl, gl->buff_curpos - count, NULL);
}

/*.......................................................................
 * Starting from the cursor position change characters to a matching
 * parenthesis.
 */
static KT_KEY_FN(gl_vi_change_to_parenthesis)
{
  int curpos = gl_index_of_matching_paren(gl);
  if(curpos >= 0) {
    gl_save_for_undo(gl);
    if(curpos >= gl->buff_curpos)
      return gl_vi_forward_change_char(gl, curpos - gl->buff_curpos + 1, NULL);
    else
      return gl_vi_backward_change_char(gl, ++gl->buff_curpos - curpos + 1,
					NULL);
  };
  return 0;
}

/*.......................................................................
 * If in vi mode, switch to vi command mode.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 */
static void gl_vi_command_mode(GetLine *gl)
{
  if(gl->editor == GL_VI_MODE && !gl->vi.command) {
    gl->insert = 1;
    gl->vi.command = 1;
    gl->vi.repeat.input_curpos = gl->insert_curpos;
    gl->vi.repeat.command_curpos = gl->buff_curpos;
    gl->insert_curpos = 0;	 /* unrestrict left motion boundary */
    gl_cursor_left(gl, 1, NULL); /* Vi moves 1 left on entering command mode */
  };
}

/*.......................................................................
 * This is an action function which rings the terminal bell.
 */
static KT_KEY_FN(gl_ring_bell)
{
  return gl->silence_bell ? 0 :
    gl_print_control_sequence(gl, 1, gl->sound_bell);
}

/*.......................................................................
 * This is the action function which implements the vi-repeat-change
 * action.
 */
static KT_KEY_FN(gl_vi_repeat_change)
{
  int status;   /* The return status of the repeated action function */
  int i;
/*
 * Nothing to repeat?
 */
  if(!gl->vi.repeat.action.fn)
    return gl_ring_bell(gl, 1, NULL);
/*
 * Provide a way for action functions to know whether they are being
 * called by us.
 */
  gl->vi.repeat.active = 1;
/*
 * Re-run the recorded function.
 */
  status = gl->vi.repeat.action.fn(gl, gl->vi.repeat.count,
				   gl->vi.repeat.action.data);
/*
 * Mark the repeat as completed.
 */
  gl->vi.repeat.active = 0;
/*
 * Is we are repeating a function that has just switched to input
 * mode to allow the user to type, re-enter the text that the user
 * previously entered.
 */
  if(status==0 && !gl->vi.command) {
/*
 * Make sure that the current line has been saved.
 */
    gl_save_for_undo(gl);
/*
 * Repeat a previous insertion or overwrite?
 */
    if(gl->vi.repeat.input_curpos >= 0 &&
       gl->vi.repeat.input_curpos <= gl->vi.repeat.command_curpos &&
       gl->vi.repeat.command_curpos <= gl->vi.undo.ntotal) {
/*
 * Using the current line which is saved in the undo buffer, plus
 * the range of characters therein, as recorded by gl_vi_command_mode(),
 * add the characters that the user previously entered, to the input
 * line.
 */
      for(i=gl->vi.repeat.input_curpos; ivi.repeat.command_curpos; i++) {
	if(gl_add_char_to_line(gl, gl->vi.undo.line[i]))
	  return 1;
      };
    };
/*
 * Switch back to command mode, now that the insertion has been repeated.
 */
    gl_vi_command_mode(gl);
  };
  return status;
}

/*.......................................................................
 * If the cursor is currently over a parenthesis character, return the
 * index of its matching parenthesis. If not currently over a parenthesis
 * character, return the next close parenthesis character to the right of
 * the cursor. If the respective parenthesis character isn't found,
 * ring the terminal bell and return -1.
 *
 * Input:
 *  gl       GetLine *  The getline resource object.
 * Output:
 *  return       int    Either the index of the matching parenthesis,
 *                      or -1 if not found.
 */
static int gl_index_of_matching_paren(GetLine *gl)
{
  int i;
/*
 * List the recognized parentheses, and their matches.
 */
  const char *o_paren = "([{";
  const char *c_paren = ")]}";
  const char *cptr;
/*
 * Get the character that is currently under the cursor.
 */
  char c = gl->line[gl->buff_curpos];
/*
 * If the character under the cursor is an open parenthesis, look forward
 * for the matching close parenthesis.
 */
  if((cptr=strchr(o_paren, c))) {
    char match = c_paren[cptr - o_paren];
    int matches_needed = 1;
    for(i=gl->buff_curpos+1; intotal; i++) {
      if(gl->line[i] == c)
	matches_needed++;
      else if(gl->line[i] == match && --matches_needed==0)
	return i;
    };
/*
 * If the character under the cursor is an close parenthesis, look forward
 * for the matching open parenthesis.
 */
  } else if((cptr=strchr(c_paren, c))) {
    char match = o_paren[cptr - c_paren];
    int matches_needed = 1;
    for(i=gl->buff_curpos-1; i>=0; i--) {
      if(gl->line[i] == c)
	matches_needed++;
      else if(gl->line[i] == match && --matches_needed==0)
	return i;
    };
/*
 * If not currently over a parenthesis character, search forwards for
 * the first close parenthesis (this is what the vi % binding does).
 */
  } else {
    for(i=gl->buff_curpos+1; intotal; i++)
      if(strchr(c_paren, gl->line[i]) != NULL)
	return i;
  };
/*
 * Not found.
 */
  (void) gl_ring_bell(gl, 1, NULL);
  return -1;
}

/*.......................................................................
 * If the cursor is currently over a parenthesis character, this action
 * function moves the cursor to its matching parenthesis.
 */
static KT_KEY_FN(gl_find_parenthesis)
{
  int curpos = gl_index_of_matching_paren(gl);
  if(curpos >= 0)
    return gl_place_cursor(gl, curpos);
  return 0;
}

/*.......................................................................
 * Handle the receipt of the potential start of a new key-sequence from
 * the user.
 *
 * Input:
 *  gl      GetLine *   The resource object of this library.
 *  first_char char     The first character of the sequence.
 * Output:
 *  return      int     0 - OK.
 *                      1 - Error.
 */
static int gl_interpret_char(GetLine *gl, char first_char)
{
  char keyseq[GL_KEY_MAX+1]; /* A special key sequence being read */
  int nkey=0;                /* The number of characters in the key sequence */
  int count;                 /* The repeat count of an action function */
  int ret;                   /* The return value of an action function */
  int i;
/*
 * Get the first character.
 */
  char c = first_char;
/*
 * If editing is disabled, just add newly entered characters to the
 * input line buffer, and watch for the end of the line.
 */
  if(gl->editor == GL_NO_EDITOR) {
    gl_discard_chars(gl, 1);
    if(gl->ntotal >= gl->linelen)
      return 0;
    if(c == '\n' || c == '\r')
      return gl_newline(gl, 1, NULL);
    gl_buffer_char(gl, c, gl->ntotal);
    return 0;
  };
/*
 * If the user is in the process of specifying a repeat count and the
 * new character is a digit, increment the repeat count accordingly.
 */
  if(gl->number >= 0 && isdigit((int)(unsigned char) c)) {
    gl_discard_chars(gl, 1);
    return gl_digit_argument(gl, c, NULL);
/*
 * In vi command mode, all key-sequences entered need to be
 * either implicitly or explicitly prefixed with an escape character.
 */
  } else if(gl->vi.command && c != GL_ESC_CHAR) {
    keyseq[nkey++] = GL_ESC_CHAR;
/*
 * If the first character of the sequence is a printable character,
 * then to avoid confusion with the special "up", "down", "left"
 * or "right" cursor key bindings, we need to prefix the
 * printable character with a backslash escape before looking it up.
 */
  } else if(!IS_META_CHAR(c) && !IS_CTRL_CHAR(c)) {
    keyseq[nkey++] = '\\';
  };
/*
 * Compose a potentially multiple key-sequence in gl->keyseq.
 */
  while(nkey < GL_KEY_MAX) {
    KtAction *action; /* An action function */
    KeySym *keysym;   /* The symbol-table entry of a key-sequence */
    int nsym;         /* The number of ambiguously matching key-sequences */
/*
 * If the character is an unprintable meta character, split it
 * into two characters, an escape character and the character
 * that was modified by the meta key.
 */
    if(IS_META_CHAR(c)) {
      keyseq[nkey++] = GL_ESC_CHAR;
      c = META_TO_CHAR(c);
      continue;
    };
/*
 * Append the latest character to the key sequence.
 */
    keyseq[nkey++] = c;
/*
 * When doing vi-style editing, an escape at the beginning of any binding
 * switches to command mode.
 */
    if(keyseq[0] == GL_ESC_CHAR && !gl->vi.command)
      gl_vi_command_mode(gl);
/*
 * Lookup the key sequence.
 */
    switch(_kt_lookup_keybinding(gl->bindings, keyseq, nkey, &keysym, &nsym)) {
    case KT_EXACT_MATCH:
/*
 * Get the matching action function.
 */
      action = keysym->actions + keysym->binder;
/*
 * Get the repeat count, passing the last keystroke if executing the
 * digit-argument action.
 */
      if(action->fn == gl_digit_argument) {
	count = c;
      } else {
	count = gl->number >= 0 ? gl->number : 1;
      };
/*
 * Record the function that is being invoked.
 */
      gl->current_action = *action;
      gl->current_count = count;
/*
 * Mark the current line as not yet preserved for use by the vi undo command.
 */
      gl->vi.undo.saved = 0;
      gl->vi.repeat.saved = 0;
/*
 * Execute the action function. Note the action function can tell
 * whether the provided repeat count was defaulted or specified
 * explicitly by looking at whether gl->number is -1 or not. If
 * it is negative, then no repeat count was specified by the user.
 */
      ret = action->fn(gl, count, action->data);
/*
 * In server mode, the action will return immediately if it tries to
 * read input from the terminal, and no input is currently available.
 * If this happens, abort. Note that gl_get_input_line() will rewind
 * the read-ahead buffer to allow the next call to redo the function
 * from scratch.
 */
      if(gl->rtn_status == GLR_BLOCKED && gl->pending_io==GLP_READ)
	return 1;
/*
 * Discard the now processed characters from the key sequence buffer.
 */
      gl_discard_chars(gl, gl->nread);
/*
 * If the latest action function wasn't a history action, cancel any
 * current history search.
 */
      if(gl->last_search != gl->keyseq_count)
	_glh_cancel_search(gl->glh);
/*
 * Reset the repeat count after running action functions.
 */
      if(action->fn != gl_digit_argument)
	gl->number = -1;
      return ret ? 1 : 0;
      break;
    case KT_AMBIG_MATCH:    /* Ambiguous match - so read the next character */
      if(gl_read_terminal(gl, 1, &c))
	return 1;
      break;
    case KT_NO_MATCH:
/*
 * If the first character looked like it might be a prefix of a key-sequence
 * but it turned out not to be, ring the bell to tell the user that it
 * wasn't recognised.
 */
      if(keyseq[0] != '\\' && keyseq[0] != '\t') {
	gl_ring_bell(gl, 1, NULL);
      } else {
/*
 * The user typed a single printable character that doesn't match
 * the start of any keysequence, so add it to the line in accordance
 * with the current repeat count.
 */
	count = gl->number >= 0 ? gl->number : 1;
	for(i=0; inumber = -1;
      };
      gl_discard_chars(gl, 1);
      _glh_cancel_search(gl->glh);
      return 0;
      break;
    case KT_BAD_MATCH:
      gl_ring_bell(gl, 1, NULL);
      gl_discard_chars(gl, gl->nread);
      _glh_cancel_search(gl->glh);
      return 1;
      break;
    };
  };
/*
 * If the key sequence was too long to match, ring the bell, then
 * discard the first character, so that the next attempt to match a
 * key-sequence continues with the next key press. In practice this
 * shouldn't happen, since one isn't allowed to bind action functions
 * to keysequences that are longer than GL_KEY_MAX.
 */
  gl_ring_bell(gl, 1, NULL);
  gl_discard_chars(gl, 1);
  return 0;
}

/*.......................................................................
 * Configure the application and/or user-specific behavior of
 * gl_get_line().
 *
 * Note that calling this function between calling new_GetLine() and
 * the first call to gl_get_line(), disables the otherwise automatic
 * reading of ~/.teclarc on the first call to gl_get_line().
 *
 * Input:
 *  gl             GetLine *  The resource object of this library.
 *  app_string  const char *  Either NULL, or a string containing one
 *                            or more .teclarc command lines, separated
 *                            by newline characters. This can be used to
 *                            establish an application-specific
 *                            configuration, without the need for an external
 *                            file. This is particularly useful in embedded
 *                            environments where there is no filesystem.
 *  app_file    const char *  Either NULL, or the pathname of an
 *                            application-specific .teclarc file. The
 *                            contents of this file, if provided, are
 *                            read after the contents of app_string[].
 *  user_file   const char *  Either NULL, or the pathname of a
 *                            user-specific .teclarc file. Except in
 *                            embedded applications, this should
 *                            usually be "~/.teclarc".
 * Output:
 *  return             int    0 - OK.
 *                            1 - Bad argument(s).
 */
int gl_configure_getline(GetLine *gl, const char *app_string,
			 const char *app_file, const char *user_file)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_configure_getline() */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Execute the private body of the function while signals are blocked.
 */
  status = _gl_configure_getline(gl, app_string, app_file, user_file);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the gl_configure_getline() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_configure_getline(GetLine *gl, const char *app_string,
				 const char *app_file, const char *user_file)
{
/*
 * Mark getline as having been explicitly configured.
 */
  gl->configured = 1;
/*
 * Start by parsing the configuration string, if provided.
 */
  if(app_string)
    (void) _gl_read_config_string(gl, app_string, KTB_NORM);
/*
 * Now parse the application-specific configuration file, if provided.
 */
  if(app_file)
    (void) _gl_read_config_file(gl, app_file, KTB_NORM);
/*
 * Finally, parse the user-specific configuration file, if provided.
 */
  if(user_file)
    (void) _gl_read_config_file(gl, user_file, KTB_USER);
/*
 * Record the names of the configuration files to allow them to
 * be re-read if requested at a later time.
 */
  if(gl_record_string(&gl->app_file, app_file) ||
     gl_record_string(&gl->user_file, user_file)) {
    errno = ENOMEM;
    _err_record_msg(gl->err,
	   "Insufficient memory to record tecla configuration file names",
	   END_ERR_MSG);
    return 1;
  };
  return 0;
}

/*.......................................................................
 * Replace a malloc'd string (or NULL), with another malloc'd copy of
 * a string (or NULL).
 *
 * Input:
 *  sptr          char **  On input if *sptr!=NULL, *sptr will be
 *                         free'd and *sptr will be set to NULL. Then,
 *                         on output, if string!=NULL a malloc'd copy
 *                         of this string will be assigned to *sptr.
 *  string  const char *   The string to be copied, or NULL to simply
 *                         discard any existing string.
 * Output:
 *  return         int     0 - OK.
 *                         1 - Malloc failure (no error message is generated).
 */
static int gl_record_string(char **sptr, const char *string)
{
/*
 * If the original string is the same string, don't do anything.
 */
  if(*sptr == string || (*sptr && string && strcmp(*sptr, string)==0))
    return 0;
/*
 * Discard any existing cached string.
 */
  if(*sptr) {
    free(*sptr);
    *sptr = NULL;
  };
/*
 * Allocate memory for a copy of the specified string.
 */
  if(string) {
    *sptr = (char *) malloc(strlen(string) + 1);
    if(!*sptr)
      return 1;
/*
 * Copy the string.
 */
    strcpy(*sptr, string);
  };
  return 0;
}

#ifndef HIDE_FILE_SYSTEM
/*.......................................................................
 * Re-read any application-specific and user-specific files previously
 * specified via the gl_configure_getline() function.
 */
static KT_KEY_FN(gl_read_init_files)
{
  return _gl_configure_getline(gl, NULL, gl->app_file, gl->user_file);
}
#endif

/*.......................................................................
 * Save the contents of the history buffer to a given new file.
 *
 * Input:
 *  gl             GetLine *  The resource object of this library.
 *  filename    const char *  The name of the new file to write to.
 *  comment     const char *  Extra information such as timestamps will
 *                            be recorded on a line started with this
 *                            string, the idea being that the file can
 *                            double as a command file. Specify "" if
 *                            you don't care.
 *  max_lines          int    The maximum number of lines to save, or -1
 *                            to save all of the lines in the history
 *                            list.
 * Output:
 *  return             int     0 - OK.
 *                             1 - Error.
 */
int gl_save_history(GetLine *gl, const char *filename, const char *comment,
		    int max_lines)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_save_history() */
/*
 * Check the arguments.
 */
  if(!gl || !filename || !comment) {
    if(gl)
      _err_record_msg(gl->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Execute the private body of the function while signals are blocked.
 */
  status = _gl_save_history(gl, filename, comment, max_lines);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the gl_save_history() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_save_history(GetLine *gl, const char *filename,
			    const char *comment, int max_lines)
{
/*
 * If filesystem access is to be excluded, then history files can't
 * be written.
 */
#ifdef WITHOUT_FILE_SYSTEM
  _err_record_msg(gl->err, "Can't save history without filesystem access",
		  END_ERR_MSG);
  errno = EINVAL;
  return 1;
#else
  FileExpansion *expansion; /* The expansion of the filename */
/*
 * Expand the filename.
 */
  expansion = ef_expand_file(gl->ef, filename, -1);
  if(!expansion) {
    gl_print_info(gl, "Unable to expand ", filename, " (",
		  ef_last_error(gl->ef), ").", GL_END_INFO);
    return 1;
  };
/*
 * Attempt to save to the specified file.
 */
  if(_glh_save_history(gl->glh, expansion->files[0], comment, max_lines)) {
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
    return 1;
  };
  return 0;
#endif
}

/*.......................................................................
 * Restore the contents of the history buffer from a given new file.
 *
 * Input:
 *  gl             GetLine *  The resource object of this library.
 *  filename    const char *  The name of the new file to write to.
 *  comment     const char *  This must be the same string that was
 *                            passed to gl_save_history() when the file
 *                            was written.
 * Output:
 *  return             int     0 - OK.
 *                             1 - Error.
 */
int gl_load_history(GetLine *gl, const char *filename, const char *comment)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_load_history() */
/*
 * Check the arguments.
 */
  if(!gl || !filename || !comment) {
    if(gl)
      _err_record_msg(gl->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Execute the private body of the function while signals are blocked.
 */
  status = _gl_load_history(gl, filename, comment);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the gl_load_history() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_load_history(GetLine *gl, const char *filename,
			    const char *comment)
{
/*
 * If filesystem access is to be excluded, then history files can't
 * be read.
 */
#ifdef WITHOUT_FILE_SYSTEM
  _err_record_msg(gl->err, "Can't load history without filesystem access",
		  END_ERR_MSG);
  errno = EINVAL;
  return 1;
#else
  FileExpansion *expansion; /* The expansion of the filename */
/*
 * Expand the filename.
 */
  expansion = ef_expand_file(gl->ef, filename, -1);
  if(!expansion) {
    gl_print_info(gl, "Unable to expand ", filename, " (",
		  ef_last_error(gl->ef), ").", GL_END_INFO);
    return 1;
  };
/*
 * Attempt to load from the specified file.
 */
  if(_glh_load_history(gl->glh, expansion->files[0], comment,
		       gl->cutbuf, gl->linelen+1)) {
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
    gl->cutbuf[0] = '\0';
    return 1;
  };
  gl->cutbuf[0] = '\0';
  return 0;
#endif
}

/*.......................................................................
 * Where possible, register a function and associated data to be called
 * whenever a specified event is seen on a file descriptor.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  fd                int    The file descriptor to watch.
 *  event       GlFdEvent    The type of activity to watch for.
 *  callback  GlFdEventFn *  The function to call when the specified
 *                           event occurs. Setting this to 0 removes
 *                           any existing callback.
 *  data             void *  A pointer to arbitrary data to pass to the
 *                           callback function.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Either gl==NULL, or this facility isn't
 *                               available on the the host system
 *                               (ie. select() isn't available). No
 *                               error message is generated in the latter
 *                               case.
 */
int gl_watch_fd(GetLine *gl, int fd, GlFdEvent event,
		GlFdEventFn *callback, void *data)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_watch_fd() */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
  if(fd < 0) {
    _err_record_msg(gl->err, "Error: fd < 0", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Execute the private body of the function while signals are blocked.
 */
  status = _gl_watch_fd(gl, fd, event, callback, data);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the gl_watch_fd() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_watch_fd(__attribute__ ((unused)) GetLine *gl,
                        __attribute__ ((unused)) int fd,
                        __attribute__ ((unused)) GlFdEvent event,
			__attribute__ ((unused)) GlFdEventFn *callback,
                        __attribute__ ((unused)) void *data)
#if !defined(HAVE_SELECT)
{return 1;}               /* The facility isn't supported on this system */
#else
{
  GlFdNode *prev;  /* The node that precedes 'node' in gl->fd_nodes */
  GlFdNode *node;  /* The file-descriptor node being checked */
/*
 * Search the list of already registered fd activity nodes for the specified
 * file descriptor.
 */
  for(prev=NULL,node=gl->fd_nodes; node && node->fd != fd;
      prev=node, node=node->next)
    ;
/*
 * Hasn't a node been allocated for this fd yet?
 */
  if(!node) {
/*
 * If there is no callback to record, just ignore the call.
 */
    if(!callback)
      return 0;
/*
 * Allocate the new node.
 */
    node = (GlFdNode *) _new_FreeListNode(gl->fd_node_mem);
    if(!node) {
      errno = ENOMEM;
      _err_record_msg(gl->err, "Insufficient memory", END_ERR_MSG);
      return 1;
    };
/*
 * Prepend the node to the list.
 */
    node->next = gl->fd_nodes;
    gl->fd_nodes = node;
/*
 * Initialize the node.
 */
    node->fd = fd;
    node->rd.fn = 0;
    node->rd.data = NULL;
    node->ur = node->wr = node->rd;
  };
/*
 * Record the new callback.
 */
  switch(event) {
  case GLFD_READ:
    node->rd.fn = callback;
    node->rd.data = data;
    if(callback)
      FD_SET(fd, &gl->rfds);
    else
      FD_CLR(fd, &gl->rfds);
    break;
  case GLFD_WRITE:
    node->wr.fn = callback;
    node->wr.data = data;
    if(callback)
      FD_SET(fd, &gl->wfds);
    else
      FD_CLR(fd, &gl->wfds);
    break;
  case GLFD_URGENT:
    node->ur.fn = callback;
    node->ur.data = data;
    if(callback)
      FD_SET(fd, &gl->ufds);
    else
      FD_CLR(fd, &gl->ufds);
    break;
  };
/*
 * Keep a record of the largest file descriptor being watched.
 */
  if(fd > gl->max_fd)
    gl->max_fd = fd;
/*
 * If we are deleting an existing callback, also delete the parent
 * activity node if no callbacks are registered to the fd anymore.
 */
  if(!callback) {
    if(!node->rd.fn && !node->wr.fn && !node->ur.fn) {
      if(prev)
	prev->next = node->next;
      else
	gl->fd_nodes = node->next;
      node = (GlFdNode *) _del_FreeListNode(gl->fd_node_mem, node);
    };
  };
  return 0;
}
#endif

/*.......................................................................
 * On systems with the select() system call, the gl_inactivity_timeout()
 * function provides the option of setting (or cancelling) an
 * inactivity timeout. Inactivity, in this case, refers both to
 * terminal input received from the user, and to I/O on any file
 * descriptors registered by calls to gl_watch_fd(). If at any time,
 * no activity is seen for the requested time period, the specified
 * timeout callback function is called. On returning, this callback
 * returns a code which tells gl_get_line() what to do next. Note that
 * each call to gl_inactivity_timeout() replaces any previously installed
 * timeout callback, and that specifying a callback of 0, turns off
 * inactivity timing. 
 *
 * Beware that although the timeout argument includes a nano-second
 * component, few computer clocks presently have resolutions finer
 * than a few milliseconds, so asking for less than a few milliseconds
 * is equivalent to zero on a lot of systems.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  callback  GlTimeoutFn *  The function to call when the inactivity
 *                           timeout is exceeded. To turn off
 *                           inactivity timeouts altogether, send 0.
 *  data             void *  A pointer to arbitrary data to pass to the
 *                           callback function.
 *  sec     unsigned long    The number of whole seconds in the timeout.
 *  nsec    unsigned long    The fractional number of seconds in the
 *                           timeout, expressed in nano-seconds (see
 *                           the caveat above).
 * Output:
 *  return            int    0 - OK.
 *                           1 - Either gl==NULL, or this facility isn't
 *                               available on the the host system
 *                               (ie. select() isn't available). No
 *                               error message is generated in the latter
 *                               case.
 */
int gl_inactivity_timeout(__attribute__ ((unused)) GetLine *gl,
                          __attribute__ ((unused)) GlTimeoutFn *timeout_fn,
                          __attribute__ ((unused)) void *data,
		          __attribute__ ((unused)) unsigned long sec,
                          __attribute__ ((unused)) unsigned long nsec)
#if !defined(HAVE_SELECT)
{return 1;}               /* The facility isn't supported on this system */
#else
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Install a new timeout?
 */
  if(timeout_fn) {
    gl->timer.dt.tv_sec = sec;
    gl->timer.dt.tv_usec = nsec / 1000;
    gl->timer.fn = timeout_fn;
    gl->timer.data = data;
  } else {
    gl->timer.fn = 0;
    gl->timer.data = NULL;
  };
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return 0;
}
#endif

/*.......................................................................
 * When select() is available, this is a private function of
 * gl_read_input() which responds to file-descriptor events registered by
 * the caller. Note that it assumes that it is being called from within
 * gl_read_input()'s sigsetjump() clause.
 *
 * Input:
 *  gl    GetLine *  The resource object of this module.
 *  fd        int    The file descriptor to be watched for user input.
 * Output:
 *  return    int    0 - OK.
 *                   1 - An error occurred.
 */
static int gl_event_handler(__attribute__ ((unused)) GetLine *gl,
                            __attribute__ ((unused)) int fd)
#if !defined(HAVE_SELECT)
{return 0;}
#else
{
/*
 * Set up a zero-second timeout.
 */
  struct timeval zero;
  zero.tv_sec = zero.tv_usec = 0;
/*
 * If at any time no external callbacks remain, quit the loop return,
 * so that we can simply wait in read(). This is designed as an
 * optimization for when no callbacks have been registered on entry to
 * this function, but since callbacks can delete themselves, it can
 * also help later.
 */
  while(gl->fd_nodes || gl->timer.fn) {
    int nready;   /* The number of file descriptors that are ready for I/O */
/*
 * Get the set of descriptors to be watched.
 */
    fd_set rfds = gl->rfds;
    fd_set wfds = gl->wfds;
    fd_set ufds = gl->ufds;
/*
 * Get the appropriate timeout.
 */
    struct timeval dt = gl->timer.fn ? gl->timer.dt : zero;
/*
 * Add the specified user-input file descriptor tot he set that is to
 * be watched.
 */
    FD_SET(fd, &rfds);
/*
 * Unblock the signals that we are watching, while select is blocked
 * waiting for I/O.
 */
    gl_catch_signals(gl);
/*
 * Wait for activity on any of the file descriptors.
 */
    nready = select(gl->max_fd+1, &rfds, &wfds, &ufds,
	    (gl->timer.fn || gl->io_mode==GL_SERVER_MODE) ? &dt : NULL);
/*
 * We don't want to do a longjmp in the middle of a callback that
 * might be modifying global or heap data, so block all the signals
 * that we are trapping before executing callback functions. Note that
 * the caller will unblock them again when it needs to, so there is
 * no need to undo this before returning.
 */
    gl_mask_signals(gl, NULL);
/*
 * If select() returns but none of the file descriptors are reported
 * to have activity, then select() timed out.
 */
    if(nready == 0) {
/*
 * Note that in non-blocking server mode, the inactivity timer is used
 * to allow I/O to block for a specified amount of time, so in this
 * mode we return the postponed blocked status when an abort is
 * requested.
 */
      if(gl_call_timeout_handler(gl)) {
	return 1;
      } else if(gl->io_mode == GL_SERVER_MODE) {
	gl_record_status(gl, GLR_BLOCKED, BLOCKED_ERRNO);
	return 1;
      };
/*
 * If nready < 0, this means an error occurred.
 */
    } else if(nready < 0) {
      if(errno != EINTR) {
	gl_record_status(gl, GLR_ERROR, errno);
	return 1;
      };
/*
 * If the user-input file descriptor has data available, return.
 */
    } else if(FD_ISSET(fd, &rfds)) {
      return 0;
/*
 * Check for activity on any of the file descriptors registered by the
 * calling application, and call the associated callback functions.
 */
    } else {
      GlFdNode *node;   /* The fd event node being checked */
/*
 * Search the list for the file descriptor that caused select() to return.
 */
      for(node=gl->fd_nodes; node; node=node->next) {
/*
 * Is there urgent out of band data waiting to be read on fd?
 */
	if(node->ur.fn && FD_ISSET(node->fd, &ufds)) {
	  if(gl_call_fd_handler(gl, &node->ur, node->fd, GLFD_URGENT))
	    return 1;
	  break;  /* The callback may have changed the list of nodes */
/*
 * Is the fd readable?
 */
	} else if(node->rd.fn && FD_ISSET(node->fd, &rfds)) {
	  if(gl_call_fd_handler(gl, &node->rd, node->fd, GLFD_READ))
	    return 1;
	  break;  /* The callback may have changed the list of nodes */
/*
 * Is the fd writable?
 */
	} else if(node->wr.fn && FD_ISSET(node->fd, &wfds)) {
	  if(gl_call_fd_handler(gl, &node->wr, node->fd, GLFD_WRITE))
	    return 1;
	  break;  /* The callback may have changed the list of nodes */
	};
      };
    };
/*
 * Just in case the above event handlers asked for the input line to
 * be redrawn, flush any pending output.
 */
    if(gl_flush_output(gl))
      return 1;
  };
  return 0;
}
#endif

#if defined(HAVE_SELECT)
/*.......................................................................
 * This is a private function of gl_event_handler(), used to call a
 * file-descriptor callback.
 *
 * Input:
 *  gl       GetLine *  The resource object of gl_get_line().
 *  gfh  GlFdHandler *  The I/O handler.
 *  fd           int    The file-descriptor being reported.
 *  event  GlFdEvent    The I/O event being reported.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 */
static int gl_call_fd_handler(GetLine *gl, GlFdHandler *gfh, int fd,
			      GlFdEvent event)
{
  Termios attr;       /* The terminal attributes */
  int waserr = 0;     /* True after any error */
/*
 * Re-enable conversion of newline characters to carriage-return/linefeed,
 * so that the callback can write to the terminal without having to do
 * anything special.
 */
  if(tcgetattr(gl->input_fd, &attr)) {
    _err_record_msg(gl->err, "tcgetattr error", END_ERR_MSG);
    return 1;
  };
  attr.c_oflag |= OPOST;
  while(tcsetattr(gl->input_fd, TCSADRAIN, &attr)) {
    if(errno != EINTR) {
      _err_record_msg(gl->err, "tcsetattr error", END_ERR_MSG);
      return 1;
    };
  };
/*
 * Invoke the application's callback function.
 */
  switch(gfh->fn(gl, gfh->data, fd, event)) {
  default:
  case GLFD_ABORT:
    gl_record_status(gl, GLR_FDABORT, 0);
    waserr = 1;
    break;
  case GLFD_REFRESH:
    gl_queue_redisplay(gl);
    break;
  case GLFD_CONTINUE:
    break;
  };
/*
 * If the callback function called gl_normal_io(), restore raw mode,
 * and queue a redisplay of the input line.
 */
  if(!gl->raw_mode)
    waserr = waserr || _gl_raw_io(gl, 1);
/*
 * Disable conversion of newline characters to carriage-return/linefeed.
 */
  attr.c_oflag &= ~(OPOST);
  while(tcsetattr(gl->input_fd, TCSADRAIN, &attr)) {
    if(errno != EINTR) {
      _err_record_msg(gl->err, "tcsetattr error", END_ERR_MSG);
      return 1;
    };
  };
  return waserr;
}

/*.......................................................................
 * This is a private function of gl_event_handler(), used to call a
 * inactivity timer callbacks.
 *
 * Input:
 *  gl       GetLine *  The resource object of gl_get_line().
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 */
static int gl_call_timeout_handler(GetLine *gl)
{
  Termios attr;       /* The terminal attributes */
  int waserr = 0;     /* True after any error */
/*
 * Make sure that there is an inactivity timeout callback.
 */
  if(!gl->timer.fn)
    return 0;
/*
 * Re-enable conversion of newline characters to carriage-return/linefeed,
 * so that the callback can write to the terminal without having to do
 * anything special.
 */
  if(tcgetattr(gl->input_fd, &attr)) {
    _err_record_msg(gl->err, "tcgetattr error", END_ERR_MSG);
    return 1;
  };
  attr.c_oflag |= OPOST;
  while(tcsetattr(gl->input_fd, TCSADRAIN, &attr)) {
    if(errno != EINTR) {
      _err_record_msg(gl->err, "tcsetattr error", END_ERR_MSG);
      return 1;
    };
  };
/*
 * Invoke the application's callback function.
 */
  switch(gl->timer.fn(gl, gl->timer.data)) {
  default:
  case GLTO_ABORT:
    gl_record_status(gl, GLR_TIMEOUT, 0);
    waserr = 1;
    break;
  case GLTO_REFRESH:
    gl_queue_redisplay(gl);
    break;
  case GLTO_CONTINUE:
    break;
  };
/*
 * If the callback function called gl_normal_io(), restore raw mode,
 * and queue a redisplay of the input line.
 */
  if(!gl->raw_mode)
    waserr = waserr || _gl_raw_io(gl, 1);
/*
 * Disable conversion of newline characters to carriage-return/linefeed.
 */
  attr.c_oflag &= ~(OPOST);
  while(tcsetattr(gl->input_fd, TCSADRAIN, &attr)) {
    if(errno != EINTR) {
      _err_record_msg(gl->err, "tcsetattr error", END_ERR_MSG);
      return 1;
    };
  };
  return waserr;
}
#endif  /* HAVE_SELECT */

/*.......................................................................
 * Switch history groups. History groups represent separate history
 * lists recorded within a single history buffer. Different groups
 * are distinguished by integer identifiers chosen by the calling
 * appplicaton. Initially new_GetLine() sets the group identifier to
 * 0. Whenever a new line is appended to the history list, the current
 * group identifier is recorded with it, and history lookups only
 * consider lines marked with the current group identifier.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  id     unsigned    The new history group identifier.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
int gl_group_history(GetLine *gl, unsigned id)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of this function */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals while we install the new configuration.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * If the group isn't being changed, do nothing.
 */
  if(_glh_get_group(gl->glh) == id) {
    status = 0;
/*
 * Establish the new group.
 */
  } else if(_glh_set_group(gl->glh, id)) {
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
    status = 1;
/*
 * Prevent history information from the previous group being
 * inappropriately used by the next call to gl_get_line().
 */
  } else {
    gl->preload_history = 0;
    gl->last_search = -1;
    status = 0;
  };
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * Display the contents of the history list.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  fp         FILE *  The stdio output stream to write to.
 *  fmt  const char *  A format string. This containing characters to be
 *                     written verbatim, plus any of the following
 *                     format directives:
 *                       %D  -  The date, formatted like 2001-11-20
 *                       %T  -  The time of day, formatted like 23:59:59
 *                       %N  -  The sequential entry number of the
 *                              line in the history buffer.
 *                       %G  -  The number of the history group that
 *                              the line belongs to.
 *                       %%  -  A literal % character.
 *                       %H  -  The history line itself.
 *                     Note that a '\n' newline character is not
 *                     appended by default.
 *  all_groups  int    If true, display history lines from all
 *                     history groups. Otherwise only display
 *                     those of the current history group.
 *  max_lines   int    If max_lines is < 0, all available lines
 *                     are displayed. Otherwise only the most
 *                     recent max_lines lines will be displayed.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
int gl_show_history(GetLine *gl, FILE *fp, const char *fmt, int all_groups,
		    int max_lines)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of this function */
/*
 * Check the arguments.
 */
  if(!gl || !fp || !fmt) {
    if(gl)
      _err_record_msg(gl->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Display the specified history group(s) while signals are blocked.
 */
  status = _glh_show_history(gl->glh, _io_write_stdio, fp, fmt, all_groups, 
			     max_lines) || fflush(fp)==EOF;
  if(!status)
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * Update if necessary, and return the current size of the terminal.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 *  def_ncolumn       int    If the number of columns in the terminal
 *                           can't be determined, substitute this number.
 *  def_nline         int    If the number of lines in the terminal can't
 *                           be determined, substitute this number.
 * Output:
 *  return GlTerminalSize    The current terminal size.
 */
GlTerminalSize gl_terminal_size(GetLine *gl, int def_ncolumn, int def_nline)
{
  GlTerminalSize size;  /* The object to be returned */
  sigset_t oldset;      /* The signals that were blocked on entry */
                        /*  to this function */
/*
 * Block all signals while accessing gl.
 */
  gl_mask_signals(gl, &oldset);
/*
 * Lookup/configure the terminal size.
 */
  _gl_terminal_size(gl, def_ncolumn, def_nline, &size);
/*
 * Restore the process signal mask before returning.
 */
  gl_unmask_signals(gl, &oldset);
  return size;
}

/*.......................................................................
 * This is the private body of the gl_terminal_size() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static void _gl_terminal_size(GetLine *gl, int def_ncolumn, int def_nline,
			      GlTerminalSize *size)
{
  const char *env;      /* The value of an environment variable */
  int n;                /* A number read from env[] */
/*
 * Set the number of lines and columns to non-sensical values so that
 * we know later if they have been set.
 */
  gl->nline = 0;
  gl->ncolumn = 0;
/*
 * Are we reading from a terminal?
 */
  if(gl->is_term) {
/*
 * Ask the terminal directly if possible.
 */
    gl_query_size(gl, &gl->ncolumn, &gl->nline);
/*
 * If gl_query_size() couldn't ask the terminal, it will have
 * left gl->nrow and gl->ncolumn unchanged. If these values haven't
 * been changed from their initial values of zero, we need to find
 * a different method to get the terminal size.
 *
 * If the number of lines isn't known yet, first see if the
 * LINES environment ariable exists and specifies a believable number.
 * If this doesn't work, look up the default size in the terminal
 * information database.
 */
    if(gl->nline < 1) {
      if((env = getenv("LINES")) && (n=atoi(env)) > 0)
	gl->nline = n;
#ifdef USE_TERMINFO
      else
	gl->nline = tigetnum((char *)"lines");
#elif defined(USE_TERMCAP)
      else
        gl->nline = tgetnum("li");
#endif
    };
/*
 * If the number of lines isn't known yet, first see if the COLUMNS
 * environment ariable exists and specifies a believable number.  If
 * this doesn't work, look up the default size in the terminal
 * information database.
 */
    if(gl->ncolumn < 1) {
      if((env = getenv("COLUMNS")) && (n=atoi(env)) > 0)
	gl->ncolumn = n;
#ifdef USE_TERMINFO
      else
	gl->ncolumn = tigetnum((char *)"cols");
#elif defined(USE_TERMCAP)
      else
	gl->ncolumn = tgetnum("co");
#endif
    };
  };
/*
 * If we still haven't been able to acquire reasonable values, substitute
 * the default values specified by the caller.
 */
  if(gl->nline <= 0)
    gl->nline = def_nline;
  if(gl->ncolumn <= 0)
    gl->ncolumn = def_ncolumn;
/*
 * Copy the new size into the return value.
 */
  if(size) {
    size->nline = gl->nline;
    size->ncolumn = gl->ncolumn;
  };
  return;
}

/*.......................................................................
 * Resize or delete the history buffer.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  bufsize  size_t    The number of bytes in the history buffer, or 0
 *                     to delete the buffer completely.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Insufficient memory (the previous buffer
 *                         will have been retained). No error message
 *                         will be displayed.
 */
int gl_resize_history(GetLine *gl, size_t bufsize)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of this function */
/*
 * Check the arguments.
 */
  if(!gl)
    return 1;
/*
 * Block all signals while modifying the contents of gl.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Perform the resize while signals are blocked.
 */
  status = _glh_resize_history(gl->glh, bufsize);
  if(status)
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
/*
 * Restore the process signal mask before returning.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * Set an upper limit to the number of lines that can be recorded in the
 * history list, or remove a previously specified limit.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  max_lines   int    The maximum number of lines to allow, or -1 to
 *                     cancel a previous limit and allow as many lines
 *                     as will fit in the current history buffer size.
 */
void gl_limit_history(GetLine *gl, int max_lines)
{
  if(gl) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Apply the limit while signals are blocked.
 */
    _glh_limit_history(gl->glh, max_lines);
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
}

/*.......................................................................
 * Discard either all historical lines, or just those associated with the
 * current history group.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  all_groups  int    If true, clear all of the history. If false,
 *                     clear only the stored lines associated with the
 *                     currently selected history group.
 */
void gl_clear_history(GetLine *gl, int all_groups)
{
  if(gl) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Clear the history buffer while signals are blocked.
 */
    _glh_clear_history(gl->glh, all_groups);
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
}

/*.......................................................................
 * Temporarily enable or disable the gl_get_line() history mechanism.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  enable      int    If true, turn on the history mechanism. If
 *                     false, disable it.
 */
void gl_toggle_history(GetLine *gl, int enable)
{
  if(gl) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Change the history recording mode while signals are blocked.
 */
    _glh_toggle_history(gl->glh, enable);
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
}

/*.......................................................................
 * Lookup a history line by its sequential number of entry in the
 * history buffer.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 *  id      unsigned long    The identification number of the line to
 *                           be returned, where 0 denotes the first line
 *                           that was entered in the history list, and
 *                           each subsequently added line has a number
 *                           one greater than the previous one. For
 *                           the range of lines currently in the list,
 *                           see the gl_range_of_history() function.
 * Input/Output:
 *  line    GlHistoryLine *  A pointer to the variable in which to
 *                           return the details of the line.
 * Output:
 *  return            int    0 - The line is no longer in the history
 *                               list, and *line has not been changed.
 *                           1 - The requested line can be found in
 *                               *line. Note that line->line is part
 *                               of the history buffer, so a
 *                               private copy should be made if you
 *                               wish to use it after subsequent calls
 *                               to any functions that take *gl as an
 *                               argument.
 */
int gl_lookup_history(GetLine *gl, unsigned long id, GlHistoryLine *line)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of this function */
/*
 * Check the arguments.
 */
  if(!gl)
    return 0;
/*
 * Block all signals while modifying the contents of gl.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Perform the lookup while signals are blocked.
 */
  status = _glh_lookup_history(gl->glh, (GlhLineID) id, &line->line,
			       &line->group, &line->timestamp);
  if(status)
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
/*
 * Restore the process signal mask before returning.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * Query the state of the history list. Note that any of the input/output
 * pointers can be specified as NULL.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 * Input/Output:
 *  state  GlHistoryState *  A pointer to the variable in which to record
 *                           the return values.
 */
void gl_state_of_history(GetLine *gl, GlHistoryState *state)
{
  if(gl && state) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Lookup the status while signals are blocked.
 */
    _glh_state_of_history(gl->glh, &state->enabled, &state->group,
			  &state->max_lines);
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
}

/*.......................................................................
 * Query the number and range of lines in the history buffer.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 *  range  GlHistoryRange *  A pointer to the variable in which to record
 *                           the return values. If range->nline=0, the
 *                           range of lines will be given as 0-0.
 */
void gl_range_of_history(GetLine *gl, GlHistoryRange *range)
{
  if(gl && range) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Lookup the information while signals are blocked.
 */
    _glh_range_of_history(gl->glh, &range->oldest, &range->newest,
			  &range->nlines);
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
}

/*.......................................................................
 * Return the size of the history buffer and the amount of the
 * buffer that is currently in use.
 *
 * Input:
 *  gl         GetLine *  The gl_get_line() resource object.
 * Input/Output:
 *  GlHistorySize size *  A pointer to the variable in which to return
 *                        the results.
 */
void gl_size_of_history(GetLine *gl, GlHistorySize *size)
{
  if(gl && size) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Lookup the information while signals are blocked.
 */
    _glh_size_of_history(gl->glh, &size->size, &size->used);
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
}

/*.......................................................................
 * This is the action function that lists the contents of the history
 * list.
 */
static KT_KEY_FN(gl_list_history)
{
/*
 * Start a new line.
 */
  if(gl_start_newline(gl, 1))
    return 1;
/*
 * List history lines that belong to the current group.
 */
  _glh_show_history(gl->glh, gl_write_fn, gl, "%N  %T   %H\r\n", 0,
		    count<=1 ? -1 : count);
/*
 * Arrange for the input line to be redisplayed.
 */
  gl_queue_redisplay(gl);
  return 0;
}

/*.......................................................................
 * Specify whether text that users type should be displayed or hidden.
 * In the latter case, only the prompt is displayed, and the final
 * input line is not archived in the history list.
 *
 * Input:
 *  gl         GetLine *  The gl_get_line() resource object.
 *  enable         int     0 - Disable echoing.
 *                         1 - Enable echoing.
 *                        -1 - Just query the mode without changing it.
 * Output:
 *  return         int    The echoing disposition that was in effect
 *                        before this function was called:
 *                         0 - Echoing was disabled.
 *                         1 - Echoing was enabled.
 */
int gl_echo_mode(GetLine *gl, int enable)
{
  if(gl) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
    int was_echoing; /* The echoing disposition on entry to this function */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Install the new disposition while signals are blocked.
 */
    was_echoing = gl->echo;
    if(enable >= 0)
      gl->echo = enable;
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
/*
 * Return the original echoing disposition.
 */
    return was_echoing;
  };
  return 1;
}

/*.......................................................................
 * Display the prompt.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 * Output:
 *  return         int    0 - OK.
 *                        1 - Error.
 */
static int gl_display_prompt(GetLine *gl)
{
  const char *pptr;       /* A pointer into gl->prompt[] */
  unsigned old_attr=0;    /* The current text display attributes */
  unsigned new_attr=0;    /* The requested text display attributes */
/*
 * Temporarily switch to echoing output characters.
 */
  int kept_echo = gl->echo;
  gl->echo = 1;
/*
 * In case the screen got messed up, send a carriage return to
 * put the cursor at the beginning of the current terminal line.
 */
  if(gl_print_control_sequence(gl, 1, gl->bol))
    return 1;
/*
 * Mark the line as partially displayed.
 */
  gl->displayed = 1;
/*
 * Write the prompt, using the currently selected prompt style.
 */
  switch(gl->prompt_style) {
  case GL_LITERAL_PROMPT:
    if(gl_print_string(gl, gl->prompt, '\0'))
      return 1;
    break;
  case GL_FORMAT_PROMPT:
    for(pptr=gl->prompt; *pptr; pptr++) {
/*
 * Does the latest character appear to be the start of a directive?
 */
      if(*pptr == '%') {
/*
 * Check for and act on attribute changing directives.
 */
	switch(pptr[1]) {
/*
 * Add or remove a text attribute from the new set of attributes.
 */ 
	case 'B': case 'U': case 'S': case 'P': case 'F': case 'V':
	case 'b': case 'u': case 's': case 'p': case 'f': case 'v':
	  switch(*++pptr) {
	  case 'B':           /* Switch to a bold font */
	    new_attr |= GL_TXT_BOLD;
	    break;
	  case 'b':           /* Switch to a non-bold font */
	    new_attr &= ~GL_TXT_BOLD;
	    break;
	  case 'U':           /* Start underlining */
	    new_attr |= GL_TXT_UNDERLINE;
	    break;
	  case 'u':           /* Stop underlining */
	    new_attr &= ~GL_TXT_UNDERLINE;
	    break;
	  case 'S':           /* Start highlighting */
	    new_attr |= GL_TXT_STANDOUT;
	    break;
	  case 's':           /* Stop highlighting */
	    new_attr &= ~GL_TXT_STANDOUT;
	    break;
	  case 'P':           /* Switch to a pale font */
	    new_attr |= GL_TXT_DIM;
	    break;
	  case 'p':           /* Switch to a non-pale font */
	    new_attr &= ~GL_TXT_DIM;
	    break;
	  case 'F':           /* Switch to a flashing font */
	    new_attr |= GL_TXT_BLINK;
	    break;
	  case 'f':           /* Switch to a steady font */
	    new_attr &= ~GL_TXT_BLINK;
	    break;
	  case 'V':           /* Switch to reverse video */
	    new_attr |= GL_TXT_REVERSE;
	    break;
	  case 'v':           /* Switch out of reverse video */
	    new_attr &= ~GL_TXT_REVERSE;
	    break;
	  };
	  continue;
/*
 * A literal % is represented by %%. Skip the leading %.
 */
	case '%':
	  pptr++;
	  break;
	};
      };
/*
 * Many terminals, when asked to turn off a single text attribute, turn
 * them all off, so the portable way to turn one off individually is to
 * explicitly turn them all off, then specify those that we want from
 * scratch.
 */
      if(old_attr & ~new_attr) {
	if(gl_print_control_sequence(gl, 1, gl->text_attr_off))
	  return 1;
	old_attr = 0;
      };
/*
 * Install new text attributes?
 */
      if(new_attr != old_attr) {
	if(new_attr & GL_TXT_BOLD && !(old_attr & GL_TXT_BOLD) &&
	   gl_print_control_sequence(gl, 1, gl->bold))
	  return 1;
	if(new_attr & GL_TXT_UNDERLINE && !(old_attr & GL_TXT_UNDERLINE) &&
	   gl_print_control_sequence(gl, 1, gl->underline))
	  return 1;
	if(new_attr & GL_TXT_STANDOUT && !(old_attr & GL_TXT_STANDOUT) &&
	   gl_print_control_sequence(gl, 1, gl->standout))
	  return 1;
	if(new_attr & GL_TXT_DIM && !(old_attr & GL_TXT_DIM) &&
	   gl_print_control_sequence(gl, 1, gl->dim))
	  return 1;
	if(new_attr & GL_TXT_REVERSE && !(old_attr & GL_TXT_REVERSE) &&
	   gl_print_control_sequence(gl, 1, gl->reverse))
	  return 1;
	if(new_attr & GL_TXT_BLINK && !(old_attr & GL_TXT_BLINK) &&
	   gl_print_control_sequence(gl, 1, gl->blink))
	  return 1;
	old_attr = new_attr;
      };
/*
 * Display the latest character.
 */
      if(gl_print_char(gl, *pptr, pptr[1]))
	return 1;
    };
/*
 * Turn off all text attributes now that we have finished drawing
 * the prompt.
 */
    if(gl_print_control_sequence(gl, 1, gl->text_attr_off))
      return 1;
    break;
  };
/*
 * Restore the original echo mode.
 */
  gl->echo = kept_echo;
/*
 * The prompt has now been displayed at least once.
 */
  gl->prompt_changed = 0;
  return 0;
}

/*.......................................................................
 * This function can be called from gl_get_line() callbacks to have
 * the prompt changed when they return. It has no effect if gl_get_line()
 * is not currently being invoked.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  prompt  const char *  The new prompt.
 */
void gl_replace_prompt(GetLine *gl, const char *prompt)
{
  if(gl) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Replace the prompt.
 */
    _gl_replace_prompt(gl, prompt);
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
}

/*.......................................................................
 * This is the private body of the gl_replace_prompt() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static void _gl_replace_prompt(GetLine *gl, const char *prompt)
{
/*
 * Substitute an empty prompt?
 */
  if(!prompt)
    prompt = "";
/*
 * Gaurd against aliasing between prompt and gl->prompt.
 */
  if(gl->prompt != prompt) {
/*
 * Get the length of the new prompt string.
 */
    size_t slen = strlen(prompt);
/*
 * If needed, allocate a new buffer for the prompt string.
 */
    if(!gl->prompt || slen > strlen(gl->prompt)) {
      size_t size = sizeof(char) * (slen + 1);
      char *new_prompt = gl->prompt ? realloc(gl->prompt, size) : malloc(size);
      if(!new_prompt)
	return;
      gl->prompt = new_prompt;
    };
/*
 * Make a copy of the new prompt.
 */
    strcpy(gl->prompt, prompt);
  };
/*
 * Record the statistics of the new prompt.
 */
  gl->prompt_len = gl_displayed_prompt_width(gl);
  gl->prompt_changed = 1;
  gl_queue_redisplay(gl);
  return;
}

/*.......................................................................
 * Work out the length of the current prompt on the terminal, according
 * to the current prompt formatting style.
 *
 * Input:
 *  gl       GetLine *  The resource object of this library.
 * Output:
 *  return       int    The number of displayed characters.
 */
static int gl_displayed_prompt_width(GetLine *gl)
{
  int slen=0;         /* The displayed number of characters */
  const char *pptr;   /* A pointer into prompt[] */
/*
 * The length differs according to the prompt display style.
 */
  switch(gl->prompt_style) {
  case GL_LITERAL_PROMPT:
    return gl_displayed_string_width(gl, gl->prompt, -1, 0);
    break;
  case GL_FORMAT_PROMPT:
/*
 * Add up the length of the displayed string, while filtering out
 * attribute directives.
 */
    for(pptr=gl->prompt; *pptr; pptr++) {
/*
 * Does the latest character appear to be the start of a directive?
 */
      if(*pptr == '%') {
/*
 * Check for and skip attribute changing directives.
 */
	switch(pptr[1]) {
	case 'B': case 'b': case 'U': case 'u': case 'S': case 's':
	  pptr++;
	  continue;
/*
 * A literal % is represented by %%. Skip the leading %.
 */
	case '%':
	  pptr++;
	  break;
	};
      };
      slen += gl_displayed_char_width(gl, *pptr, slen);
    };
    break;
  };
  return slen;
}

/*.......................................................................
 * Specify whether to heed text attribute directives within prompt
 * strings.
 *
 * Input:
 *  gl           GetLine *  The resource object of gl_get_line().
 *  style  GlPromptStyle    The style of prompt (see the definition of
 *                          GlPromptStyle in libtecla.h for details).
 */
void gl_prompt_style(GetLine *gl, GlPromptStyle style)
{
  if(gl) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Install the new style in gl while signals are blocked.
 */
    if(style != gl->prompt_style) {
      gl->prompt_style = style;
      gl->prompt_len = gl_displayed_prompt_width(gl);
      gl->prompt_changed = 1;
      gl_queue_redisplay(gl);
    };
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
}

/*.......................................................................
 * Tell gl_get_line() how to respond to a given signal. This can be used
 * both to override the default responses to signals that gl_get_line()
 * normally catches and to add new signals to the list that are to be
 * caught.
 *
 * Input:
 *  gl           GetLine *  The resource object of gl_get_line().
 *  signo            int    The number of the signal to be caught.
 *  flags       unsigned    A bitwise union of GlSignalFlags enumerators.
 *  after  GlAfterSignal    What to do after the application's signal
 *                          handler has been called.
 *  errno_value      int    The value to set errno to.
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error.
 */
int gl_trap_signal(GetLine *gl, int signo, unsigned flags,
		   GlAfterSignal after, int errno_value)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of this function */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals while modifying the contents of gl.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Perform the modification while signals are blocked.
 */
  status = _gl_trap_signal(gl, signo, flags, after, errno_value);
/*
 * Restore the process signal mask before returning.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the gl_trap_signal() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_trap_signal(GetLine *gl, int signo, unsigned flags,
			   GlAfterSignal after, int errno_value)
{
  GlSignalNode *sig;
/*
 * Complain if an attempt is made to trap untrappable signals.
 * These would otherwise cause errors later in gl_mask_signals().
 */
  if(0
#ifdef SIGKILL
     || signo==SIGKILL
#endif
#ifdef SIGBLOCK
     || signo==SIGBLOCK
#endif
     ) {
    return 1;
  };
/*
 * See if the signal has already been registered.
 */
  for(sig=gl->sigs; sig && sig->signo != signo; sig = sig->next)
    ;
/*
 * If the signal hasn't already been registered, allocate a node for
 * it.
 */
  if(!sig) {
    sig = (GlSignalNode *) _new_FreeListNode(gl->sig_mem);
    if(!sig)
      return 1;
/*
 * Add the new node to the head of the list.
 */
    sig->next = gl->sigs;
    gl->sigs = sig;
/*
 * Record the signal number.
 */
    sig->signo = signo;
/*
 * Create a signal set that includes just this signal.
 */
    sigemptyset(&sig->proc_mask);
    if(sigaddset(&sig->proc_mask, signo) == -1) {
      _err_record_msg(gl->err, "sigaddset error", END_ERR_MSG);
      sig = (GlSignalNode *) _del_FreeListNode(gl->sig_mem, sig);
      return 1;
    };
/*
 * Add the signal to the bit-mask of signals being trapped.
 */
    sigaddset(&gl->all_signal_set, signo);
  };
/*
 * Record the new signal attributes.
 */
  sig->flags = flags;
  sig->after = after;
  sig->errno_value = errno_value;
  return 0;
}

/*.......................................................................
 * Remove a signal from the list of signals that gl_get_line() traps.
 *
 * Input:
 *  gl           GetLine *  The resource object of gl_get_line().
 *  signo            int    The number of the signal to be ignored.
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error.
 */
int gl_ignore_signal(GetLine *gl, int signo)
{
  GlSignalNode *sig;  /* The gl->sigs list node of the specified signal */
  GlSignalNode *prev; /* The node that precedes sig in the list */
  sigset_t oldset;    /* The signals that were blocked on entry to this */
                      /*  function. */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals while modifying the contents of gl.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Find the node of the gl->sigs list which records the disposition
 * of the specified signal.
 */
  for(prev=NULL,sig=gl->sigs; sig && sig->signo != signo;
      prev=sig,sig=sig->next)
    ;
  if(sig) {
/*
 * Remove the node from the list.
 */
    if(prev)
      prev->next = sig->next;
    else
      gl->sigs = sig->next;
/*
 * Return the node to the freelist.
 */
    sig = (GlSignalNode *) _del_FreeListNode(gl->sig_mem, sig);
/*
 * Remove the signal from the bit-mask union of signals being trapped.
 */
    sigdelset(&gl->all_signal_set, signo);
  };
/*
 * Restore the process signal mask before returning.
 */
  gl_unmask_signals(gl, &oldset);
  return 0;
}

/*.......................................................................
 * This function is called when an input line has been completed. It
 * appends the specified newline character, terminates the line,
 * records the line in the history buffer if appropriate, and positions
 * the terminal cursor at the start of the next line.
 *
 * Input:
 *  gl           GetLine *  The resource object of gl_get_line().
 *  newline_char     int    The newline character to add to the end
 *                          of the line.
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error.
 */
static int gl_line_ended(GetLine *gl, int newline_char)
{
/*
 * If the newline character is printable, display it at the end of
 * the line, and add it to the input line buffer.
 */
  if(isprint((int)(unsigned char) newline_char)) {
    if(gl_end_of_line(gl, 1, NULL) || gl_add_char_to_line(gl, newline_char))
      return 1;
  } else {
/*
 * Otherwise just append a newline character to the input line buffer.
 */
    newline_char = '\n';
    gl_buffer_char(gl, newline_char, gl->ntotal);
  };
/*
 * Add the line to the history buffer if it was entered with a
 * newline character.
 */
  if(gl->echo && gl->automatic_history && newline_char=='\n')
    (void) _gl_append_history(gl, gl->line);
/*
 * Except when depending on the system-provided line editing, start a new
 * line after the end of the line that has just been entered.
 */
  if(gl->editor != GL_NO_EDITOR && gl_start_newline(gl, 1))
    return 1;
/*
 * Record the successful return status.
 */
  gl_record_status(gl, GLR_NEWLINE, 0);
/*
 * Attempt to flush any pending output.
 */
  (void) gl_flush_output(gl);
/*
 * The next call to gl_get_line() will write the prompt for a new line
 * (or continue the above flush if incomplete), so if we manage to
 * flush the terminal now, report that we are waiting to write to the
 * terminal.
 */
  gl->pending_io = GLP_WRITE;
  return 0;
}

/*.......................................................................
 * Return the last signal that was caught by the most recent call to
 * gl_get_line(), or -1 if no signals were caught. This is useful if
 * gl_get_line() returns errno=EINTR and you need to find out what signal
 * caused it to abort.
 *
 * Input:
 *  gl           GetLine *  The resource object of gl_get_line().
 * Output:
 *  return           int    The last signal caught by the most recent
 *                          call to gl_get_line(), or -1 if no signals
 *                          were caught.
 */
int gl_last_signal(GetLine *gl)
{
  int signo = -1;   /* The requested signal number */
  if(gl) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Access gl now that signals are blocked.
 */    
    signo = gl->last_signal;
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
  return signo;
}

/*.......................................................................
 * Prepare to edit a new line.
 *
 * Input:
 *  gl         GetLine *  The resource object of this library.
 *  prompt        char *  The prompt to prefix the line with, or NULL to
 *                        use the same prompt that was used by the previous
 *                        line.
 *  start_line    char *  The initial contents of the input line, or NULL
 *                        if it should start out empty.
 *  start_pos      int    If start_line isn't NULL, this specifies the
 *                        index of the character over which the cursor
 *                        should initially be positioned within the line.
 *                        If you just want it to follow the last character
 *                        of the line, send -1.
 * Output:
 *  return    int    0 - OK.
 *                   1 - Error.
 */
static int gl_present_line(GetLine *gl, const char *prompt,
			   const char *start_line, int start_pos)
{
/*
 * Prepare the line-editing properties for a new editing session.
 */
  gl_reset_editor(gl);
/*
 * Record the new prompt and its displayed width.
 */
  if(prompt)
    _gl_replace_prompt(gl, prompt);
/*
 * Reset the history search pointers.
 */
  if(_glh_cancel_search(gl->glh)) {
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
    return 1;
  };
/*
 * If the previous line was entered via the repeat-history action,
 * preload the specified history line.
 */
  if(gl->preload_history) {
    gl->preload_history = 0;
    if(_glh_recall_line(gl->glh, gl->preload_id, gl->line, gl->linelen+1)) {
      gl_update_buffer(gl);          /* Compute gl->ntotal etc.. */
      gl->buff_curpos = gl->ntotal;
    } else {
      gl_truncate_buffer(gl, 0);
    };
    gl->preload_id = 0;
/*
 * Present a specified initial line?
 */
  } else if(start_line) {
    char *cptr;      /* A pointer into gl->line[] */
/*
 * Measure the length of the starting line.
 */
    int start_len = strlen(start_line);
/*
 * If the length of the line is greater than the available space,
 * truncate it.
 */
    if(start_len > gl->linelen)
      start_len = gl->linelen;
/*
 * Load the line into the buffer.
 */
    if(start_line != gl->line)
      gl_buffer_string(gl, start_line, start_len, 0);
/*
 * Strip off any trailing newline and carriage return characters.
 */
    for(cptr=gl->line + gl->ntotal - 1; cptr >= gl->line &&
	(*cptr=='\n' || *cptr=='\r'); cptr--,gl->ntotal--)
      ;
    gl_truncate_buffer(gl, gl->ntotal < 0 ? 0 : gl->ntotal);
/*
 * Where should the cursor be placed within the line?
 */
    if(start_pos < 0 || start_pos > gl->ntotal) {
      if(gl_place_cursor(gl, gl->ntotal))
	return 1;
    } else {
      if(gl_place_cursor(gl, start_pos))
	return 1;
    };
/*
 * Clear the input line?
 */
  } else {
    gl_truncate_buffer(gl, 0);
  };
/*
 * Arrange for the line to be displayed by gl_flush_output().
 */
  gl_queue_redisplay(gl);
/*
 * Update the display.
 */
  return gl_flush_output(gl);
}

/*.......................................................................
 * Reset all line-editing parameters for a new editing session. Note
 * that this does not empty the input line, since that would prevent a
 * gl_get_line() caller from specifying the returned line buffer as
 * the start_line argument of the next call to gl_get_line().
 *
 * Input:
 *  gl      GetLine *  The line editor resource object.
 */
static void gl_reset_editor(GetLine *gl)
{
/*
 * Warning: Don't clear gl->line[] and gl->ntotal here (see above).
 */
  gl->buff_curpos = 0;
  gl->term_curpos = 0;
  gl->term_len = 0;
  gl->insert_curpos = 0;
  gl->number = -1;
  gl->displayed = 0;
  gl->endline = 0;
  gl->redisplay = 0;
  gl->postpone = 0;
  gl->nbuf = 0;
  gl->nread = 0;
  gl->vi.command = 0;
  gl->vi.undo.line[0] = '\0';
  gl->vi.undo.ntotal = 0;
  gl->vi.undo.buff_curpos = 0;
  gl->vi.repeat.action.fn = 0;
  gl->vi.repeat.action.data = 0;
  gl->last_signal = -1;
}

/*.......................................................................
 * Print an informational message to the terminal, after starting a new
 * line.
 *
 * Input:
 *  gl      GetLine *  The line editor resource object.
 *  ...  const char *  Zero or more strings to be printed.
 *  ...        void *  The last argument must always be GL_END_INFO.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
static int gl_print_info(GetLine *gl, ...)
{
  va_list ap;     /* The variable argument list */
  const char *s;  /* The string being printed */
  int waserr = 0; /* True after an error */
/*
 * Only display output when echoing is on.
 */
  if(gl->echo) {
/*
 * Skip to the start of the next empty line before displaying the message.
 */
    if(gl_start_newline(gl, 1))
      return 1;
/*
 * Display the list of provided messages.
 */
    va_start(ap, gl);
    while(!waserr && (s = va_arg(ap, const char *)) != GL_END_INFO)
      waserr = gl_print_raw_string(gl, 1, s, -1);
    va_end(ap);
/*
 * Start a newline.
 */
    waserr = waserr || gl_print_raw_string(gl, 1, "\n\r", -1);
/*
 * Arrange for the input line to be redrawn.
 */
    gl_queue_redisplay(gl);
  };
  return waserr;
}

/*.......................................................................
 * Go to the start of the next empty line, ready to output miscellaneous
 * text to the screen.
 *
 * Note that when async-signal safety is required, the 'buffered'
 * argument must be 0.
 *
 * Input:
 *  gl          GetLine *  The line editor resource object.
 *  buffered        int    If true, used buffered I/O when writing to
 *                         the terminal. Otherwise use async-signal-safe
 *                         unbuffered I/O.
 * Output:
 *  return          int    0 - OK.
 *                         1 - Error.
 */
static int gl_start_newline(GetLine *gl, int buffered)
{
  int waserr = 0;  /* True after any I/O error */
/*
 * Move the cursor to the start of the terminal line that follows the
 * last line of the partially enterred line. In order that this
 * function remain async-signal safe when write_fn is signal safe, we
 * can't call our normal output functions, since they call tputs(),
 * who's signal saftey isn't defined. Fortunately, we can simply use
 * \r and \n to move the cursor to the right place.
 */
  if(gl->displayed) {   /* Is an input line currently displayed? */
/*
 * On which terminal lines are the cursor and the last character of the
 * input line?
 */
    int curs_line = gl->term_curpos / gl->ncolumn;
    int last_line = gl->term_len / gl->ncolumn;
/*
 * Move the cursor to the start of the line that follows the last
 * terminal line that is occupied by the input line.
 */
    for( ; curs_line < last_line + 1; curs_line++)
      waserr = waserr || gl_print_raw_string(gl, buffered, "\n", 1);
    waserr = waserr || gl_print_raw_string(gl, buffered, "\r", 1);
/*
 * Mark the line as no longer displayed.
 */
    gl_line_erased(gl);
  };
  return waserr;
}

/*.......................................................................
 * The callback through which all terminal output is routed.
 * This simply appends characters to a queue buffer, which is
 * subsequently flushed to the output channel by gl_flush_output().
 *
 * Input:
 *  data     void *  The pointer to a GetLine line editor resource object
 *                   cast to (void *).
 *  s  const char *  The string to be written.
 *  n         int    The number of characters to write from s[].
 * Output:
 *  return    int    The number of characters written. This will always
 *                   be equal to 'n' unless an error occurs.
 */
static GL_WRITE_FN(gl_write_fn)
{
  GetLine *gl = (GetLine *) data;
  int ndone = _glq_append_chars(gl->cq, s, n, gl->flush_fn, gl);
  if(ndone != n)
    _err_record_msg(gl->err, _glq_last_error(gl->cq), END_ERR_MSG);
  return ndone;
}

/*.......................................................................
 * Ask gl_get_line() what caused it to return.
 *
 * Input:
 *  gl             GetLine *  The line editor resource object.
 * Output:
 *  return  GlReturnStatus    The return status of the last call to
 *                            gl_get_line().
 */
GlReturnStatus gl_return_status(GetLine *gl)
{
  GlReturnStatus rtn_status = GLR_ERROR;   /* The requested status */
  if(gl) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Access gl while signals are blocked.
 */    
    rtn_status = gl->rtn_status;
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
  return rtn_status;
}

/*.......................................................................
 * In non-blocking server-I/O mode, this function should be called
 * from the application's external event loop to see what type of
 * terminal I/O is being waited for by gl_get_line(), and thus what
 * direction of I/O to wait for with select() or poll().
 *
 * Input:
 *  gl          GetLine *  The resource object of gl_get_line().
 * Output:
 *  return  GlPendingIO    The type of pending I/O being waited for.
 */
GlPendingIO gl_pending_io(GetLine *gl)
{
  GlPendingIO pending_io = GLP_WRITE;   /* The requested information */
  if(gl) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Access gl while signals are blocked.
 */    
    pending_io = gl->pending_io;
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  };
  return pending_io;
}

/*.......................................................................
 * In server mode, this function configures the terminal for non-blocking
 * raw terminal I/O. In normal I/O mode it does nothing.
 *
 * Callers of this function must be careful to trap all signals that
 * terminate or suspend the program, and call gl_normal_io()
 * from the corresponding signal handlers in order to restore the
 * terminal to its original settings before the program is terminated
 * or suspended. They should also trap the SIGCONT signal to detect
 * when the program resumes, and ensure that its signal handler
 * call gl_raw_io() to redisplay the line and resume editing.
 *
 * This function is async signal safe.
 * 
 * Input:
 *  gl      GetLine *  The line editor resource object.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
int gl_raw_io(GetLine *gl)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_raw_io() */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Don't allow applications to switch into raw mode unless in server mode.
 */
  if(gl->io_mode != GL_SERVER_MODE) {
    _err_record_msg(gl->err, "Can't switch to raw I/O unless in server mode",
		    END_ERR_MSG);
    errno = EPERM;
    status = 1;
  } else {
/*
 * Execute the private body of the function while signals are blocked.
 */
    status = _gl_raw_io(gl, 1);
  };
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the public function, gl_raw_io().
 * It assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 *
 * This function is async signal safe.
 */
static int _gl_raw_io(GetLine *gl, int redisplay)
{
/*
 * If we are already in the correct mode, do nothing.
 */
  if(gl->raw_mode)
    return 0;
/*
 * Switch the terminal to raw mode.
 */
  if(gl->is_term && gl_raw_terminal_mode(gl))
    return 1;
/*
 * Switch to non-blocking I/O mode?
 */
  if(gl->io_mode==GL_SERVER_MODE && 
     (gl_nonblocking_io(gl, gl->input_fd) ||
      gl_nonblocking_io(gl, gl->output_fd) ||
      (gl->file_fp && gl_nonblocking_io(gl, fileno(gl->file_fp))))) {
    if(gl->is_term)
      gl_restore_terminal_attributes(gl);
    return 1;
  };
/*
 * If an input line is being entered, arrange for it to be
 * displayed.
 */
  if(redisplay) {
    gl->postpone = 0;
    gl_queue_redisplay(gl);
  };
  return 0;
}

/*.......................................................................
 * Restore the terminal to the state that it had when
 * gl_raw_io() was last called. After calling
 * gl_raw_io(), this function must be called before
 * terminating or suspending the program, and before attempting other
 * uses of the terminal from within the program. See gl_raw_io()
 * for more details.
 *
 * Input:
 *  gl      GetLine *  The line editor resource object.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
int gl_normal_io(GetLine *gl)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_normal_io() */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Execute the private body of the function while signals are blocked.
 */
  status = _gl_normal_io(gl);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the public function, gl_normal_io().
 * It assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_normal_io(GetLine *gl)
{
/*
 * If we are already in normal mode, do nothing.
 */
  if(!gl->raw_mode)
    return 0;
/*
 * Postpone subsequent redisplays until after _gl_raw_io(gl, 1)
 * is next called.
 */
  gl->postpone = 1;
/*
 * Switch back to blocking I/O. Note that this is essential to do
 * here, because when using non-blocking I/O, the terminal output
 * buffering code can't always make room for new output without calling
 * malloc(), and a call to malloc() would mean that this function
 * couldn't safely be called from signal handlers.
 */
  if(gl->io_mode==GL_SERVER_MODE &&
     (gl_blocking_io(gl, gl->input_fd) ||
      gl_blocking_io(gl, gl->output_fd) ||
      (gl->file_fp && gl_blocking_io(gl, fileno(gl->file_fp)))))
    return 1;
/*
 * Move the cursor to the next empty terminal line. Note that
 * unbuffered I/O is requested, to ensure that gl_start_newline() be
 * async-signal-safe.
 */
  if(gl->is_term && gl_start_newline(gl, 0))
    return 1;
/*
 * Switch the terminal to normal mode.
 */
  if(gl->is_term && gl_restore_terminal_attributes(gl)) {
/*
 * On error, revert to non-blocking I/O if needed, so that on failure
 * we remain in raw mode.
 */
    if(gl->io_mode==GL_SERVER_MODE) {
      gl_nonblocking_io(gl, gl->input_fd);
      gl_nonblocking_io(gl, gl->output_fd);
      if(gl->file_fp)
	gl_nonblocking_io(gl, fileno(gl->file_fp));
    };
    return 1;
  };
  return 0;
}

/*.......................................................................
 * This function allows you to install an additional completion
 * action, or to change the completion function of an existing
 * one. This should be called before the first call to gl_get_line()
 * so that the name of the action be defined before the user's
 * configuration file is read.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  data             void *  This is passed to match_fn() whenever it is
 *                           called. It could, for example, point to a
 *                           symbol table that match_fn() would look up
 *                           matches in.
 *  match_fn   CplMatchFn *  The function that will identify the prefix
 *                           to be completed from the input line, and
 *                           report matching symbols.
 *  list_only         int    If non-zero, install an action that only lists
 *                           possible completions, rather than attempting
 *                           to perform the completion.
 *  name       const char *  The name with which users can refer to the
 *                           binding in tecla configuration files.
 *  keyseq     const char *  Either NULL, or a key sequence with which
 *                           to invoke the binding. This should be
 *                           specified in the same manner as key-sequences
 *                           in tecla configuration files (eg. "M-^I").
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_completion_action(GetLine *gl, void *data, CplMatchFn *match_fn,
			 int list_only, const char *name, const char *keyseq)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_completion_action() */
/*
 * Check the arguments.
 */
  if(!gl || !name || !match_fn) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Install the new action while signals are blocked.
 */
  status = _gl_completion_action(gl, data, match_fn, list_only, name, keyseq);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the public function, gl_completion_action().
 * It assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_completion_action(GetLine *gl, void *data, CplMatchFn *match_fn,
				 int list_only, const char *name,
				 const char *keyseq)
{
  KtKeyFn *current_fn;      /* An existing action function */
  void *current_data;       /* The action-function callback data */
/*
 * Which action function is desired?
 */
  KtKeyFn *action_fn = list_only ? gl_list_completions : gl_complete_word;
/*
 * Is there already an action of the specified name?
 */
  if(_kt_lookup_action(gl->bindings, name, ¤t_fn, ¤t_data) == 0) {
/*
 * If the action has the same type as the one being requested,
 * simply change the contents of its GlCplCallback callback data.
 */
    if(current_fn == action_fn) {
      GlCplCallback *cb = (GlCplCallback *) current_data;
      cb->fn = match_fn;
      cb->data = data;
    } else {
      errno = EINVAL;
      _err_record_msg(gl->err,
        "Illegal attempt to change the type of an existing completion action",
        END_ERR_MSG);
      return 1;
    };
/*
 * No existing action has the specified name.
 */
  } else {
/*
 * Allocate a new GlCplCallback callback object.
 */
    GlCplCallback *cb = (GlCplCallback *) _new_FreeListNode(gl->cpl_mem);
    if(!cb) {
      errno = ENOMEM;
      _err_record_msg(gl->err, "Insufficient memory to add completion action",
		      END_ERR_MSG);
      return 1;
    };
/*
 * Record the completion callback data.
 */
    cb->fn = match_fn;
    cb->data = data;
/*
 * Attempt to register the new action.
 */
    if(_kt_set_action(gl->bindings, name, action_fn, cb)) {
      _err_record_msg(gl->err, _kt_last_error(gl->bindings), END_ERR_MSG);
      _del_FreeListNode(gl->cpl_mem, (void *) cb);
      return 1;
    };
  };
/*
 * Bind the action to a given key-sequence?
 */
  if(keyseq && _kt_set_keybinding(gl->bindings, KTB_NORM, keyseq, name)) {
    _err_record_msg(gl->err, _kt_last_error(gl->bindings), END_ERR_MSG);
    return 1;
  };
  return 0;
}

/*.......................................................................
 * Register an application-provided function as an action function.
 * This should preferably be called before the first call to gl_get_line()
 * so that the name of the action becomes defined before the user's
 * configuration file is read.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  data             void *  Arbitrary application-specific callback
 *                           data to be passed to the callback
 *                           function, fn().
 *  fn         GlActionFn *  The application-specific function that
 *                           implements the action. This will be invoked
 *                           whenever the user presses any
 *                           key-sequence which is bound to this action.
 *  name       const char *  The name with which users can refer to the
 *                           binding in tecla configuration files.
 *  keyseq     const char *  The key sequence with which to invoke
 *                           the binding. This should be specified in the
 *                           same manner as key-sequences in tecla
 *                           configuration files (eg. "M-^I").
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_register_action(GetLine *gl, void *data, GlActionFn *fn,
                       const char *name, const char *keyseq)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_register_action() */
/*
 * Check the arguments.
 */
  if(!gl || !name || !fn) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Install the new action while signals are blocked.
 */
  status = _gl_register_action(gl, data, fn, name, keyseq);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the public function, gl_register_action().
 * It assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_register_action(GetLine *gl, void *data, GlActionFn *fn,
			       const char *name, const char *keyseq)
{
  KtKeyFn *current_fn;      /* An existing action function */
  void *current_data;       /* The action-function callback data */
/*
 * Get the action function which actually runs the application-provided
 * function.
 */
  KtKeyFn *action_fn = gl_run_external_action;
/*
 * Is there already an action of the specified name?
 */
  if(_kt_lookup_action(gl->bindings, name, ¤t_fn, ¤t_data) == 0) {
/*
 * If the action has the same type as the one being requested,
 * simply change the contents of its GlCplCallback callback data.
 */
    if(current_fn == action_fn) {
      GlExternalAction *a = (GlExternalAction *) current_data;
      a->fn = fn;
      a->data = data;
    } else {
      errno = EINVAL;
      _err_record_msg(gl->err,
        "Illegal attempt to change the type of an existing action",
		      END_ERR_MSG);
      return 1;
    };
/*
 * No existing action has the specified name.
 */
  } else {
/*
 * Allocate a new GlCplCallback callback object.
 */
    GlExternalAction *a =
      (GlExternalAction *) _new_FreeListNode(gl->ext_act_mem);
    if(!a) {
      errno = ENOMEM;
      _err_record_msg(gl->err, "Insufficient memory to add completion action",
		      END_ERR_MSG);
      return 1;
    };
/*
 * Record the completion callback data.
 */
    a->fn = fn;
    a->data = data;
/*
 * Attempt to register the new action.
 */
    if(_kt_set_action(gl->bindings, name, action_fn, a)) {
      _err_record_msg(gl->err, _kt_last_error(gl->bindings), END_ERR_MSG);
      _del_FreeListNode(gl->cpl_mem, (void *) a);
      return 1;
    };
  };
/*
 * Bind the action to a given key-sequence?
 */
  if(keyseq && _kt_set_keybinding(gl->bindings, KTB_NORM, keyseq, name)) {
    _err_record_msg(gl->err, _kt_last_error(gl->bindings), END_ERR_MSG);
    return 1;
  };
  return 0;
}

/*.......................................................................
 * Invoke an action function previously registered by a call to
 * gl_register_action().
 */
static KT_KEY_FN(gl_run_external_action)
{
  GlAfterAction status;  /* The return value of the action function */
/*
 * Get the container of the action function and associated callback data.
 */
  GlExternalAction *a = (GlExternalAction *) data;
/*
 * Invoke the action function.
 */
  status = a->fn(gl, a->data, count, gl->buff_curpos, gl->line);
/*
 * If the callback took us out of raw (possibly non-blocking) input
 * mode, restore this mode, and queue a redisplay of the input line.
 */
  if(_gl_raw_io(gl, 1))
    return 1;
/*
 * Finally, check to see what the action function wants us to do next.
 */
  switch(status) {
  default:
  case GLA_ABORT:
    gl_record_status(gl, GLR_ERROR, errno);
    return 1;
    break;
  case GLA_RETURN:
    return gl_newline(gl, 1, NULL);
    break;
  case GLA_CONTINUE:
    break;
  };
  return 0;
}

/*.......................................................................
 * In server-I/O mode the terminal is left in raw mode between calls
 * to gl_get_line(), so it is necessary for the application to install
 * terminal restoring signal handlers for signals that could terminate
 * or suspend the process, plus a terminal reconfiguration handler to
 * be called when a process resumption signal is received, and finally
 * a handler to be called when a terminal-resize signal is received.
 *
 * Since there are many signals that by default terminate or suspend
 * processes, and different systems support different sub-sets of
 * these signals, this function provides a convenient wrapper around
 * sigaction() for assigning the specified handlers to all appropriate
 * signals. It also arranges that when any one of these signals is
 * being handled, all other catchable signals are blocked. This is
 * necessary so that the specified signal handlers can safely call
 * gl_raw_io(), gl_normal_io() and gl_update_size() without
 * reentrancy issues.
 *
 * Input:
 *  term_handler  void (*)(int)  The signal handler to invoke when
 *                               a process-terminating signal is
 *                               received.
 *  susp_handler  void (*)(int)  The signal handler to invoke when
 *                               a process-suspending signal is
 *                               received.
 *  cont_handler  void (*)(int)  The signal handler to invoke when
 *                               a process-resumption signal is
 *                               received (ie. SIGCONT).
 *  size_handler  void (*)(int)  The signal handler to invoke when
 *                               a terminal-resize signal (ie. SIGWINCH)
 *                               is received.
 * Output:
 *  return                  int  0 - OK.
 *                               1 - Error.
 */
int gl_tty_signals(void (*term_handler)(int), void (*susp_handler)(int),
		   void (*cont_handler)(int), void (*size_handler)(int))
{
  int i;
/*
 * Search for signals of the specified classes, and assign the
 * associated signal handler to them.
 */
  for(i=0; iattr & GLSA_SUSP) {
      if(gl_set_tty_signal(sig->signo, susp_handler))
	return 1;
    } else if(sig->attr & GLSA_TERM) {
      if(gl_set_tty_signal(sig->signo, term_handler))
	return 1;
    } else if(sig->attr & GLSA_CONT) {
      if(gl_set_tty_signal(sig->signo, cont_handler))
	return 1;
    } else if(sig->attr & GLSA_SIZE) {
      if(gl_set_tty_signal(sig->signo, size_handler))
	return 1;
    };      
  };
  return 0;
}

/*.......................................................................
 * This is a private function of gl_tty_signals(). It installs a given
 * signal handler, and arranges that when that signal handler is being
 * invoked other signals are blocked. The latter is important to allow
 * functions like gl_normal_io(), gl_raw_io() and gl_update_size()
 * to be called from signal handlers.
 *
 * Input:
 *  signo     int           The signal to be trapped.
 *  handler  void (*)(int)  The signal handler to assign to the signal.
 */
static int gl_set_tty_signal(int signo, void (*handler)(int))
{
  SigAction act;   /* The signal handler configuation */
/*
 * Arrange to block all trappable signals except the one that is being
 * assigned (the trapped signal will be blocked automatically by the
 * system).
 */
  gl_list_trappable_signals(&act.sa_mask);
  sigdelset(&act.sa_mask, signo);
/*
 * Assign the signal handler.
 */
  act.sa_handler = handler;
/*
 * There is only one portable signal handling flag, and it isn't
 * relevant to us, so don't specify any flags.
 */
  act.sa_flags = 0;
/*
 * Register the signal handler.
 */
  if(sigaction(signo, &act, NULL))
    return 1;
  return 0;
}

/*.......................................................................
 * Display a left-justified string over multiple terminal lines,
 * taking account of the current width of the terminal. Optional
 * indentation and an optional prefix string can be specified to be
 * displayed at the start of each new terminal line used. Similarly,
 * an optional suffix can be specified to be displayed at the end of
 * each terminal line.  If needed, a single paragraph can be broken
 * across multiple calls.  Note that literal newlines in the input
 * string can be used to force a newline at any point and that you
 * should use this feature to explicitly end all paragraphs, including
 * at the end of the last string that you write. Note that when a new
 * line is started between two words that are separated by spaces,
 * those spaces are not output, whereas when a new line is started
 * because a newline character was found in the string, only the
 * spaces before the newline character are discarded.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  indentation    int    The number of spaces of indentation to write
 *                        at the beginning of each new terminal line.
 *  prefix  const char *  An optional prefix string to write after the
 *                        indentation margin at the start of each new
 *                        terminal line. You can specify NULL if no
 *                        prefix is required.
 *  suffix  const char *  An optional suffix string to draw at the end
 *                        of the terminal line. Spaces will be added
 *                        where necessary to ensure that the suffix ends
 *                        in the last column of the terminal line. If
 *                        no suffix is desired, specify NULL.
 *  fill_char      int    The padding character to use when indenting
 *                        the line or padding up to the suffix.
 *  def_width      int    If the terminal width isn't known, such as when
 *                        writing to a pipe or redirecting to a file,
 *                        this number specifies what width to assume.
 *  start          int    The number of characters already written to
 *                        the start of the current terminal line. This
 *                        is primarily used to allow individual
 *                        paragraphs to be written over multiple calls
 *                        to this function, but can also be used to
 *                        allow you to start the first line of a
 *                        paragraph with a different prefix or
 *                        indentation than those specified above.
 *  string  const char *  The string to be written.
 * Output:
 *  return         int    On error -1 is returned. Otherwise the
 *                        return value is the terminal column index at
 *                        which the cursor was left after writing the
 *                        final word in the string. Successful return
 *                        values can thus be passed verbatim to the
 *                        'start' arguments of subsequent calls to
 *                        gl_display_text() to allow the printing of a
 *                        paragraph to be broken across multiple calls
 *                        to gl_display_text().
 */
int gl_display_text(GetLine *gl, int indentation, const char *prefix,
		    const char *suffix, int fill_char,
		    int def_width, int start, const char *string)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_completion_action() */
/*
 * Check the arguments?
 */
  if(!gl || !string) {
    errno = EINVAL;
    return -1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return -1;
/*
 * Display the text while signals are blocked.
 */
  status = _io_display_text(_io_write_stdio, gl->output_fp, indentation,
			    prefix, suffix, fill_char,
			    gl->ncolumn > 0 ? gl->ncolumn : def_width,
			    start, string);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * Block all of the signals that we are currently trapping.
 *
 * Input:
 *  gl       GetLine *   The resource object of gl_get_line().
 * Input/Output:
 *  oldset   sigset_t *   The superseded process signal mask
 *                        will be return in *oldset unless oldset is
 *                        NULL.
 * Output:
 *  return        int     0 - OK.
 *                        1 - Error.
 */
static int gl_mask_signals(GetLine *gl, sigset_t *oldset)
{
/*
 * Block all signals in all_signal_set, along with any others that are
 * already blocked by the application.
 */
  if(sigprocmask(SIG_BLOCK, &gl->all_signal_set, oldset) >= 0) {
    gl->signals_masked = 1;
    return 0;
  };
/*
 * On error attempt to query the current process signal mask, so
 * that oldset be the correct process signal mask to restore later
 * if the caller of this function ignores the error return value.
 */
  if(oldset)
    (void) sigprocmask(SIG_SETMASK, NULL, oldset);
  gl->signals_masked = 0;
  return 1;
}

/*.......................................................................
 * Restore a process signal mask that was previously returned via the
 * oldset argument of gl_mask_signals().
 *
 * Input:
 *  gl        GetLine *   The resource object of gl_get_line().
 * Input/Output:
 *  oldset   sigset_t *   The process signal mask to be restored.
 * Output:
 *  return        int     0 - OK.
 *                        1 - Error.
 */
static int gl_unmask_signals(GetLine *gl, sigset_t *oldset)
{
  gl->signals_masked = 0;
  return sigprocmask(SIG_SETMASK, oldset, NULL) < 0;
}

/*.......................................................................
 * Arrange to temporarily catch the signals marked in gl->use_signal_set.
 *
 * Input:
 *  gl        GetLine *   The resource object of gl_get_line().
 * Output:
 *  return        int     0 - OK.
 *                        1 - Error.
 */
static int gl_catch_signals(GetLine *gl)
{
  return sigprocmask(SIG_UNBLOCK, &gl->use_signal_set, NULL) < 0;
}

/*.......................................................................
 * Select the I/O mode to be used by gl_get_line().
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  mode      GlIOMode    The I/O mode to establish.
 * Output:
 *  return         int    0 - OK.
 *                        1 - Error.
 */
int gl_io_mode(GetLine *gl, GlIOMode mode)
{
  sigset_t oldset; /* The signals that were blocked on entry to this function */
  int status;      /* The return status of _gl_io_mode() */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Check that the requested mode is known.
 */
  switch(mode) {
  case GL_NORMAL_MODE:
  case GL_SERVER_MODE:
    break;
  default:
    errno = EINVAL;
    _err_record_msg(gl->err, "Unknown gl_get_line() I/O mode requested.",
		    END_ERR_MSG);
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Invoke the private body of this function.
 */
  status = _gl_io_mode(gl, mode);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the public function, gl_io_mode().
 * It assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_io_mode(GetLine *gl, GlIOMode mode)
{
/*
 * Are we already in the specified mode?
 */
  if(mode == gl->io_mode)
    return 0;
/*
 * First revert to normal I/O in the current I/O mode.
 */
  _gl_normal_io(gl);
/*
 * Record the new mode.
 */
  gl->io_mode = mode;
/*
 * Perform any actions needed by the new mode.
 */
  if(mode==GL_SERVER_MODE) {
    if(_gl_raw_io(gl, 1))
      return 1;
  };
  return 0;
}

/*.......................................................................
 * Return extra information (ie. in addition to that provided by errno)
 * about the last error to occur in either gl_get_line() or its
 * associated public functions.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 * Input/Output:
 *  buff          char *  An optional output buffer. Note that if the
 *                        calling application calls any gl_*()
 *                        functions from signal handlers, it should
 *                        provide a buffer here, so that a copy of
 *                        the latest error message can safely be made
 *                        while signals are blocked.
 *  n           size_t    The allocated size of buff[].
 * Output:
 *  return  const char *  A pointer to the error message. This will
 *                        be the buff argument, unless buff==NULL, in
 *                        which case it will be a pointer to an
 *                        internal error buffer. In the latter case,
 *                        note that the contents of the returned buffer
 *                        will change on subsequent calls to any gl_*()
 *                        functions.
 */
const char *gl_error_message(GetLine *gl, char *buff, size_t n)
{
  if(!gl) {
    static const char *msg = "NULL GetLine argument";
    if(buff) {
      strncpy(buff, msg, n);
      buff[n-1] = '\0';
    } else {
      return msg;
    };
  } else if(buff) {
    sigset_t oldset; /* The signals that were blocked on entry to this block */
/*
 * Temporarily block all signals.
 */
    gl_mask_signals(gl, &oldset);
/*
 * Copy the error message into the specified buffer.
 */
    if(buff && n > 0) {
      strncpy(buff, _err_get_msg(gl->err), n);
      buff[n-1] = '\0';
    };
/*
 * Restore the process signal mask before returning.
 */
    gl_unmask_signals(gl, &oldset);
  } else {
    return _err_get_msg(gl->err);
  };
  return buff;
}

/*.......................................................................
 * Return the signal mask used by gl_get_line(). This is the set of
 * signals that gl_get_line() is currently configured to trap.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 * Input/Output:
 *  set       sigset_t *  The set of signals will be returned in *set,
 *                        in the form of a signal process mask, as
 *                        used by sigaction(), sigprocmask(),
 *                        sigpending(), sigsuspend(), sigsetjmp() and
 *                        other standard POSIX signal-aware
 *                        functions.
 * Output:
 *  return         int    0 - OK.
 *                        1 - Error (examine errno for reason).
 */
int gl_list_signals(GetLine *gl, sigset_t *set)
{
/*
 * Check the arguments.
 */
  if(!gl || !set) {
    if(gl)
      _err_record_msg(gl->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Copy the signal mask into *set.
 */
  memcpy(set, &gl->all_signal_set, sizeof(*set));
  return 0;
}

/*.......................................................................
 * By default, gl_get_line() doesn't trap signals that are blocked
 * when it is called. This default can be changed either on a
 * per-signal basis by calling gl_trap_signal(), or on a global basis
 * by calling this function. What this function does is add the
 * GLS_UNBLOCK_SIG flag to all signals that are currently configured
 * to be trapped by gl_get_line(), such that when subsequent calls to
 * gl_get_line() wait for I/O, these signals are temporarily
 * unblocked. This behavior is useful in non-blocking server-I/O mode,
 * where it is used to avoid race conditions related to handling these
 * signals externally to gl_get_line(). See the demonstration code in
 * demo3.c, or the gl_handle_signal() man page for further
 * information.
 *
 * Input:
 *  gl         GetLine *   The resource object of gl_get_line().
 */
void gl_catch_blocked(GetLine *gl)
{
  sigset_t oldset;    /* The process signal mask to restore */
  GlSignalNode *sig;  /* A signal node in gl->sigs */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return;
  };
/*
 * Temporarily block all signals while we modify the contents of gl.
 */
  gl_mask_signals(gl, &oldset);
/*
 * Add the GLS_UNBLOCK_SIG flag to all configured signals.
 */
  for(sig=gl->sigs; sig; sig=sig->next)
    sig->flags |= GLS_UNBLOCK_SIG;
/*
 * Restore the process signal mask that was superseded by the call
 * to gl_mask_signals().
 */
  gl_unmask_signals(gl, &oldset);
  return;
}

/*.......................................................................
 * Respond to signals who's default effects have important
 * consequences to gl_get_line(). This is intended for use in
 * non-blocking server mode, where the external event loop is
 * responsible for catching signals. Signals that are handled include
 * those that by default terminate or suspend the process, and the
 * signal that indicates that the terminal size has changed. Note that
 * this function is not signal safe and should thus not be called from
 * a signal handler itself. See the gl_io_mode() man page for how it
 * should be used.
 *
 * In the case of signals that by default terminate or suspend
 * processes, command-line editing will be suspended, the terminal
 * returned to a usable state, then the default disposition of the
 * signal restored and the signal resent, in order to suspend or
 * terminate the process.  If the process subsequently resumes,
 * command-line editing is resumed.
 *
 * In the case of signals that indicate that the terminal has been
 * resized, the new size will be queried, and any input line that is
 * being edited will be redrawn to fit the new dimensions of the
 * terminal.
 *
 * Input:
 *  signo    int    The number of the signal to respond to.
 *  gl   GetLine *  The first element of an array of 'ngl' GetLine
 *                  objects.
 *  ngl      int    The number of elements in the gl[] array. Normally
 *                  this will be one.
 */
void gl_handle_signal(int signo, GetLine *gl, int ngl)
{
  int attr;             /* The attributes of the specified signal */
  sigset_t all_signals; /* The set of trappable signals */
  sigset_t oldset;      /* The process signal mask to restore */
  int i;
/*
 * NULL operation?
 */
  if(ngl < 1 || !gl)
    return;
/*
 * Look up the default attributes of the specified signal.
 */
  attr = gl_classify_signal(signo);
/*
 * If the signal isn't known, we are done.
 */
  if(!attr)
    return;
/*
 * Temporarily block all signals while we modify the gl objects.
 */
  gl_list_trappable_signals(&all_signals);
  sigprocmask(SIG_BLOCK, &all_signals, &oldset);
/*
 * Suspend or terminate the process?
 */
  if(attr & (GLSA_SUSP | GLSA_TERM)) {
    gl_suspend_process(signo, gl, ngl);
/*
 * Resize the terminal? Note that ioctl() isn't defined as being
 * signal safe, so we can't call gl_update_size() here. However,
 * gl_get_line() checks for resizes on each call, so simply arrange
 * for the application's event loop to call gl_get_line() as soon as
 * it becomes possible to write to the terminal. Note that if the
 * caller is calling select() or poll when this happens, these functions
 * get interrupted, since a signal has been caught.
 */
  } else if(attr & GLSA_SIZE) {
    for(i=0; iraw_mode) {
      _gl_normal_io(obj);
      if(!obj->raw_mode)        /* Check that gl_normal_io() succeded */
	obj->raw_mode = -1;     /* Flag raw mode as needing to be restored */
    };
  };
/*
 * Restore the system default disposition of the signal that we
 * caught.  Note that this signal is currently blocked. Note that we
 * don't use memcpy() to copy signal sets here, because the signal safety
 * of memcpy() is undefined.
 */
  def_action.sa_handler = SIG_DFL;
  {
    char *orig = (char *) &all_signals;
    char *dest = (char *) &def_action.sa_mask;
    for(i=0; iraw_mode == -1) { /* Did we flag the need to restore raw mode? */
      obj->raw_mode = 0;      /* gl_raw_io() does nothing unless raw_mode==0 */
      _gl_raw_io(obj, 1);
    };
  };
/*
 * Restore the process signal mask to the way it was when this function
 * was called.
 */
  sigprocmask(SIG_SETMASK, &oldset, NULL);
  return;
}

/*.......................................................................
 * Return the information about the default attributes of a given signal.
 * The attributes that are returned are as defined by the standards that
 * created them, including POSIX, SVR4 and 4.3+BSD, and are taken from a
 * table in Richard Steven's book, "Advanced programming in the UNIX
 * environment".
 *
 * Input:
 *  signo        int   The signal to be characterized.
 * Output:
 *  return       int   A bitwise union of GlSigAttr enumerators, or 0
 *                     if the signal isn't known.
 */
static int gl_classify_signal(int signo)
{
  int i;
/*
 * Search for the specified signal in the gl_signal_list[] table.
 */
  for(i=0; isigno == signo)
      return sig->attr;
  };
/*
 * Signal not known.
 */
  return 0;
}

/*.......................................................................
 * When in non-blocking server mode, this function can be used to abandon
 * the current incompletely entered input line, and prepare to start 
 * editing a new line on the next call to gl_get_line().
 *
 * Input:
 *  gl      GetLine *  The line editor resource object.
 */
void gl_abandon_line(GetLine *gl)
{
  sigset_t oldset;    /* The process signal mask to restore */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return;
  };
/*
 * Temporarily block all signals while we modify the contents of gl.
 */
  gl_mask_signals(gl, &oldset);
/*
 * Mark the input line as discarded.
 */
  _gl_abandon_line(gl);
/*
 * Restore the process signal mask that was superseded by the call
 * to gl_mask_signals().
 */
  gl_unmask_signals(gl, &oldset);
  return;
}

/*.......................................................................
 * This is the private body of the gl_abandon_line() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
void _gl_abandon_line(GetLine *gl)
{
  gl->endline = 1;
  gl->pending_io = GLP_WRITE;
}

/*.......................................................................
 * How many characters are needed to write a number as an octal string?
 *
 * Input:
 *  num   unsigned   The to be measured.
 * Output:
 *  return     int   The number of characters needed.
 */
static int gl_octal_width(unsigned num)
{
  int n;    /* The number of characters needed to render the number */
  for(n=1; num /= 8; n++)
    ;
  return n;
}

/*.......................................................................
 * Tell gl_get_line() the current terminal size. Note that this is only
 * necessary on systems where changes in terminal size aren't reported
 * via SIGWINCH.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 *  ncolumn           int    The number of columns in the terminal.
 *  nline             int    The number of lines in the terminal.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_set_term_size(GetLine *gl, int ncolumn, int nline)
{
  sigset_t oldset;      /* The signals that were blocked on entry */
                        /*  to this function */
  int status;           /* The return status */
/*
 * Block all signals while accessing gl.
 */
  gl_mask_signals(gl, &oldset);
/*
 * Install the new terminal size.
 */
  status = _gl_set_term_size(gl, ncolumn, nline);
/*
 * Restore the process signal mask before returning.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the gl_set_term_size() function. It
 * assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_set_term_size(GetLine *gl, int ncolumn, int nline)
{
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Reject non-sensical dimensions.
 */
  if(ncolumn <= 0 || nline <= 0) {
    _err_record_msg(gl->err, "Invalid terminal size", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Install the new dimensions in the terminal driver if possible, so
 * that future calls to gl_query_size() get the new value.
 */
#ifdef TIOCSWINSZ
  if(gl->is_term) {
    struct winsize size;
    size.ws_row = nline;
    size.ws_col = ncolumn;
    size.ws_xpixel = 0;
    size.ws_ypixel = 0;
    if(ioctl(gl->output_fd, TIOCSWINSZ, &size) == -1) {
      _err_record_msg(gl->err, "Can't change terminal size", END_ERR_MSG);
      return 1;
    };
  };
#endif
/*
 * If an input line is in the process of being edited, redisplay it to
 * accomodate the new dimensions, and record the new dimensions in
 * gl->nline and gl->ncolumn.
 */
  return gl_handle_tty_resize(gl, ncolumn, nline);
}

/*.......................................................................
 * Record a character in the input line buffer at a given position.
 *
 * Input:
 *  gl    GetLine *   The resource object of gl_get_line().
 *  c        char     The character to be recorded.
 *  bufpos    int     The index in the buffer at which to record the
 *                    character.
 * Output:
 *  return    int     0 - OK.
 *                    1 - Insufficient room.
 */
static int gl_buffer_char(GetLine *gl, char c, int bufpos)
{
/*
 * Guard against buffer overruns.
 */
  if(bufpos >= gl->linelen)
    return 1;
/*
 * Record the new character.
 */
  gl->line[bufpos] = c;
/*
 * If the new character was placed beyond the end of the current input
 * line, update gl->ntotal to reflect the increased number of characters
 * that are in gl->line, and terminate the string.
 */
  if(bufpos >= gl->ntotal) {
    gl->ntotal = bufpos+1;
    gl->line[gl->ntotal] = '\0';
  };
  return 0;
}

/*.......................................................................
 * Copy a given string into the input buffer, overwriting the current
 * contents.
 *
 * Input:
 *  gl    GetLine *   The resource object of gl_get_line().
 *  s  const char *   The string to be recorded.
 *  n         int     The number of characters to be copied from the
 *                    string.
 *  bufpos    int     The index in the buffer at which to place the
 *                    the first character of the string.
 * Output:
 *  return    int     0 - OK.
 *                    1 - String truncated to fit.
 */
static int gl_buffer_string(GetLine *gl, const char *s, int n, int bufpos)
{
  int nnew;  /* The number of characters actually recorded */
  int i;
/*
 * How many of the characters will fit within the buffer?
 */
  nnew = bufpos + n <= gl->linelen ? n : (gl->linelen - bufpos);
/*
 * Record the first nnew characters of s[] in the buffer.
 */
  for(i=0; intotal + n > gl->linelen)
    return 1;
/*
 * Move everything including and beyond the character at 'start'
 * towards the end of the string.
 */
  memmove(gl->line + start + n, gl->line + start, gl->ntotal - start + 1);
/*
 * Update the recorded size of the line.
 */
  gl->ntotal += n;
  return 1;
}

/*.......................................................................
 * Remove a given number of characters from the input buffer. This
 * involves moving the characters that follow the removed characters to
 * where the removed sub-string started in the input buffer.
 *
 * Input:
 *  gl    GetLine *   The resource object of gl_get_line().
 *  start     int     The first character to be removed.
 *  n         int     The number of characters to remove.
 */
static void gl_remove_from_buffer(GetLine *gl, int start, int n)
{
  memmove(gl->line + start, gl->line + start + n, gl->ntotal - start - n + 1);
/*
 * Update the recorded size of the line.
 */
  gl->ntotal -= n;
}

/*.......................................................................
 * Truncate the string in the input line buffer after a given number of
 * characters.
 *
 * Input:
 *  gl       GetLine *   The resource object of gl_get_line().
 *  n            int     The new length of the line.
 * Output:
 *  return       int     0 - OK.
 *                       1 - n > gl->linelen.
 */
static int gl_truncate_buffer(GetLine *gl, int n)
{
  if(n > gl->linelen)
    return 1;
  gl->line[n] = '\0';
  gl->ntotal = n;
  return 0;
}

/*.......................................................................
 * When the contents of gl->line[] are changed without calling any of the
 * gl_ buffer manipulation functions, this function must be called to
 * compute the length of this string, and ancillary information.
 *
 * Input:
 *  gl      GetLine *   The resource object of gl_get_line().
 */
static void gl_update_buffer(GetLine *gl)
{
  int len;  /* The length of the line */
/*
 * Measure the length of the input line.
 */
  for(len=0; len <= gl->linelen && gl->line[len]; len++)
    ;
/*
 * Just in case the string wasn't correctly terminated, do so here.
 */
  gl->line[len] = '\0';
/*
 * Record the number of characters that are now in gl->line[].
 */
  gl->ntotal = len;
/*
 * Ensure that the cursor stays within the bounds of the modified
 * input line.
 */
  if(gl->buff_curpos > gl->ntotal)
    gl->buff_curpos = gl->ntotal;
/*
 * Arrange for the input line to be redrawn.
 */
  gl_queue_redisplay(gl);
  return;
}

/*.......................................................................
 * Erase the displayed input line, including its prompt, and leave the
 * cursor where the erased line started. Note that to allow this
 * function to be used when responding to a terminal resize, this
 * function is designed to work even if the horizontal cursor position
 * doesn't match the internally recorded position.
 *
 * Input:
 *  gl      GetLine *   The resource object of gl_get_line().
 * Output:
 *  return      int     0 - OK.
 *                      1 - Error.
 */
static int gl_erase_line(GetLine *gl)
{
/*
 * Is a line currently displayed?
 */
  if(gl->displayed) {
/*
 * Relative the the start of the input line, which terminal line of
 * the current input line is the cursor currently on?
 */
    int cursor_line = gl->term_curpos / gl->ncolumn;
/*
 * Move the cursor to the start of the line.
 */
    for( ; cursor_line > 0; cursor_line--) {
      if(gl_print_control_sequence(gl, 1, gl->up))
	return 1;
    };
    if(gl_print_control_sequence(gl, 1, gl->bol))
      return 1;
/*
 * Clear from the start of the line to the end of the terminal.
 */
    if(gl_print_control_sequence(gl, gl->nline, gl->clear_eod))
      return 1;
/*
 * Mark the line as no longer displayed.
 */
    gl_line_erased(gl);
  };
  return 0;
}

/*.......................................................................
 * Arrange for the input line to be redisplayed by gl_flush_output(),
 * as soon as the output queue becomes empty.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 */
static void gl_queue_redisplay(GetLine *gl)
{
  gl->redisplay = 1;
  gl->pending_io = GLP_WRITE;
}

/*.......................................................................
 * Truncate the displayed input line starting from the current
 * terminal cursor position, and leave the cursor at the end of the
 * truncated line. The input-line buffer is not affected.
 *
 * Input:
 *  gl     GetLine *   The resource object of gl_get_line().
 * Output:
 *  return     int     0 - OK.
 *                     1 - Error.
 */
static int gl_truncate_display(GetLine *gl)
{
/*
 * Keep a record of the current terminal cursor position.
 */
  int term_curpos = gl->term_curpos;
/*
 * First clear from the cursor to the end of the current input line.
 */
  if(gl_print_control_sequence(gl, 1, gl->clear_eol))
    return 1;
/*
 * If there is more than one line displayed, go to the start of the
 * next line and clear from there to the end of the display. Note that
 * we can't use clear_eod to do the whole job of clearing from the
 * current cursor position to the end of the terminal because
 * clear_eod is only defined when used at the start of a terminal line
 * (eg. with gnome terminals, clear_eod clears from the start of the
 * current terminal line, rather than from the current cursor
 * position).
 */
  if(gl->term_len / gl->ncolumn > gl->term_curpos / gl->ncolumn) {
    if(gl_print_control_sequence(gl, 1, gl->down) ||
       gl_print_control_sequence(gl, 1, gl->bol) ||
       gl_print_control_sequence(gl, gl->nline, gl->clear_eod))
      return 1;
/*
 * Where is the cursor now?
 */
    gl->term_curpos = gl->ncolumn * (term_curpos / gl->ncolumn + 1);
/*
 * Restore the cursor position.
 */
    gl_set_term_curpos(gl, term_curpos);
  };
/*
 * Update the recorded position of the final character.
 */
  gl->term_len = gl->term_curpos;
  return 0;
}

/*.......................................................................
 * Return the set of all trappable signals.
 *
 * Input:
 *  signals   sigset_t *  The set of signals will be recorded in
 *                        *signals.
 */
static void gl_list_trappable_signals(sigset_t *signals)
{
/*
 * Start with the set of all signals.
 */
  sigfillset(signals);
/*
 * Remove un-trappable signals from this set.
 */
#ifdef SIGKILL
  sigdelset(signals, SIGKILL);
#endif
#ifdef SIGSTOP
  sigdelset(signals, SIGSTOP);
#endif
}

/*.......................................................................
 * Read an input line from a non-interactive input stream.
 *
 * Input:
 *  gl     GetLine *   The resource object of gl_get_line().
 * Output:
 *  return     int     0 - OK
 *                     1 - Error.
 */
static int gl_read_stream_line(GetLine *gl)
{
  char c = '\0'; /* The latest character read from fp */
/*
 * Record the fact that we are about to read input.
 */
  gl->pending_io = GLP_READ;
/*
 * If we are starting a new line, reset the line-editing parameters,
 * and discard the previous input line.
 */
  if(gl->endline) {
    gl_reset_editor(gl);
    gl_truncate_buffer(gl, 0);
  };
/*
 * Read one character at a time.
 */
  while(gl->ntotal < gl->linelen && c != '\n') {
/*
 * Attempt to read one more character.
 */
    switch(gl_read_input(gl, &c)) {
    case GL_READ_OK:
      break;
    case GL_READ_EOF:        /* Reached end-of-file? */
/*
 * If any characters were read before the end-of-file condition,
 * interpolate a newline character, so that the caller sees a
 * properly terminated line. Otherwise return an end-of-file
 * condition.
 */
      if(gl->ntotal > 0) {
	c = '\n';
      } else {
	gl_record_status(gl, GLR_EOF, 0);
	return 1;
      };
      break;
    case GL_READ_BLOCKED:    /* Input blocked? */
      gl_record_status(gl, GLR_BLOCKED, BLOCKED_ERRNO);
      return 1;
      break;
    case GL_READ_ERROR:     /* I/O error? */
      return 1;
      break;
    };
/*
 * Append the character to the line buffer.
 */
    if(gl_buffer_char(gl, c, gl->ntotal))
      return 1;
  };
/*
 * Was the end of the input line reached before running out of buffer space?
 */
  gl->endline = (c == '\n');
  return 0;
}

/*.......................................................................
 * Read a single character from a non-interactive input stream.
 *
 * Input:
 *  gl     GetLine *   The resource object of gl_get_line().
 * Output:
 *  return     int     The character, or EOF on error.
 */
static int gl_read_stream_char(GetLine *gl)
{
  char c = '\0';    /* The latest character read from fp */
  int retval = EOF; /* The return value of this function */
/*
 * Arrange to discard any incomplete input line.
 */
  _gl_abandon_line(gl);
/*
 * Record the fact that we are about to read input.
 */
  gl->pending_io = GLP_READ;
/*
 * Attempt to read one more character.
 */
  switch(gl_read_input(gl, &c)) {
  case GL_READ_OK:      /* Success */
    retval = c;
    break;
  case GL_READ_BLOCKED: /* The read blocked */
    gl_record_status(gl, GLR_BLOCKED, BLOCKED_ERRNO);
    retval = EOF;  /* Failure */
    break;
  case GL_READ_EOF:     /* End of file reached */
    gl_record_status(gl, GLR_EOF, 0);
    retval = EOF;  /* Failure */
    break;
  case GL_READ_ERROR:
    retval = EOF;  /* Failure */
    break;
  };
  return retval;
}

/*.......................................................................
 * Bind a key sequence to a given action.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 *  origin  GlKeyOrigin     The originator of the key binding.
 *  key      const char *   The key-sequence to be bound (or unbound).
 *  action   const char *   The name of the action to bind the key to,
 *                          or either NULL or "" to unbind the
 *                          key-sequence.
 * Output:
 *  return          int     0 - OK
 *                          1 - Error.
 */
int gl_bind_keyseq(GetLine *gl, GlKeyOrigin origin, const char *keyseq, 
		   const char *action)
{
  KtBinder binder;  /* The private internal equivalent of 'origin' */
/*
 * Check the arguments.
 */
  if(!gl || !keyseq) {
    errno = EINVAL;
    if(gl)
      _err_record_msg(gl->err, "NULL argument(s)", END_ERR_MSG);
    return 1;
  };
/*
 * An empty action string requests that the key-sequence be unbound.
 * This is indicated to _kt_set_keybinding() by passing a NULL action
 * string, so convert an empty string to a NULL action pointer.
 */
  if(action && *action=='\0')
    action = NULL;
/*
 * Translate the public originator enumeration to the private equivalent.
 */
  binder = origin==GL_USER_KEY ? KTB_USER : KTB_NORM;
/*
 * Bind the action to a given key-sequence?
 */
  if(keyseq && _kt_set_keybinding(gl->bindings, binder, keyseq, action)) {
    _err_record_msg(gl->err, _kt_last_error(gl->bindings), END_ERR_MSG);
    return 1;
  };
  return 0;
}

/*.......................................................................
 * This is the public wrapper around the gl_clear_termina() function.
 * It clears the terminal and leaves the cursor at the home position.
 * In server I/O mode, the next call to gl_get_line() will also
 * redisplay the current input line.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 * Output:
 *  return          int     0 - OK.
 *                          1 - Error.
 */
int gl_erase_terminal(GetLine *gl)
{
  sigset_t oldset;      /* The signals that were blocked on entry */
                        /*  to this function */
  int status;           /* The return status */
/*
 * Block all signals while accessing gl.
 */
  gl_mask_signals(gl, &oldset);
/*
 * Clear the terminal.
 */
  status = gl_clear_screen(gl, 1, NULL);
/*
 * Attempt to flush the clear-screen control codes to the terminal.
 * If this doesn't complete the job, the next call to gl_get_line()
 * will.
 */
  (void) gl_flush_output(gl);
/*
 * Restore the process signal mask before returning.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This function must be called by any function that erases the input
 * line.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 */
static void gl_line_erased(GetLine *gl)
{
  gl->displayed = 0;
  gl->term_curpos = 0;
  gl->term_len = 0;
}

/*.......................................................................
 * Append a specified line to the history list.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 *  line     const char *   The line to be added.
 * Output:
 *  return          int     0 - OK.
 *                          1 - Error.
 */
int gl_append_history(GetLine *gl, const char *line)
{
  sigset_t oldset;      /* The signals that were blocked on entry */
                        /*  to this function */
  int status;           /* The return status */
/*
 * Check the arguments.
 */
  if(!gl || !line) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Execute the private body of the function while signals are blocked.
 */
  status = _gl_append_history(gl, line);
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return status;
}

/*.......................................................................
 * This is the private body of the public function, gl_append_history().
 * It assumes that the caller has checked its arguments and blocked the
 * delivery of signals.
 */
static int _gl_append_history(GetLine *gl, const char *line)
{
  int status =_glh_add_history(gl->glh, line, 0);
  if(status)
    _err_record_msg(gl->err, _glh_last_error(gl->glh), END_ERR_MSG);
  return status;
}

/*.......................................................................
 * Enable or disable the automatic addition of newly entered lines to the
 * history list.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 *  enable          int     If true, subsequently entered lines will
 *                          automatically be added to the history list
 *                          before they are returned to the caller of
 *                          gl_get_line(). If 0, the choice of how and
 *                          when to archive lines in the history list,
 *                          is left up to the calling application, which
 *                          can do so via calls to gl_append_history().
 * Output:
 *  return          int     0 - OK.
 *                          1 - Error.
 */
int gl_automatic_history(GetLine *gl, int enable)
{
  sigset_t oldset;      /* The signals that were blocked on entry */
                        /*  to this function */
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return 1;
  };
/*
 * Block all signals.
 */
  if(gl_mask_signals(gl, &oldset))
    return 1;
/*
 * Execute the private body of the function while signals are blocked.
 */
  gl->automatic_history = enable;
/*
 * Restore the process signal mask.
 */
  gl_unmask_signals(gl, &oldset);
  return 0;
}

/*.......................................................................
 * This is a public function that reads a single uninterpretted
 * character from the user, without displaying anything.
 *
 * Input:
 *  gl     GetLine *  A resource object previously returned by
 *                    new_GetLine().
 * Output:
 *  return     int    The character that was read, or EOF if the read
 *                    had to be aborted (in which case you can call
 *                    gl_return_status() to find out why).
 */
int gl_read_char(GetLine *gl)
{
  int retval;   /* The return value of _gl_read_char() */
/*
 * This function can be called from application callback functions,
 * so check whether signals have already been masked, so that we don't
 * do it again, and overwrite gl->old_signal_set.
 */
  int was_masked = gl->signals_masked;
/*
 * Check the arguments.
 */
  if(!gl) {
    errno = EINVAL;
    return EOF;
  };
/*
 * Temporarily block all of the signals that we have been asked to trap.
 */
  if(!was_masked && gl_mask_signals(gl, &gl->old_signal_set))
    return EOF;
/*
 * Perform the character reading task.
 */
  retval = _gl_read_char(gl);
/*
 * Restore the process signal mask to how it was when this function was
 * first called.
 */
  if(!was_masked)
    gl_unmask_signals(gl, &gl->old_signal_set);
  return retval;
}

/*.......................................................................
 * This is the main body of the public function gl_read_char().
 */
static int _gl_read_char(GetLine *gl)
{
  int retval = EOF;  /* The return value */
  int waserr = 0;    /* True if an error occurs */
  char c;            /* The character read */
/*
 * This function can be called from application callback functions,
 * so check whether signals have already been overriden, so that we don't
 * overwrite the preserved signal handlers with gl_get_line()s. Also
 * record whether we are currently in raw I/O mode or not, so that this
 * can be left in the same state on leaving this function.
 */
  int was_overriden = gl->signals_overriden;
  int was_raw = gl->raw_mode;
/*
 * Also keep a record of the direction of any I/O that gl_get_line()
 * is awaiting, so that we can restore this status on return.
 */
  GlPendingIO old_pending_io = gl->pending_io;
/*
 * Assume that this call will successfully complete the input operation
 * until proven otherwise.
 */
  gl_clear_status(gl);
/*
 * If this is the first call to this function or gl_get_line(),
 * since new_GetLine(), complete any postponed configuration.
 */
  if(!gl->configured) {
    (void) _gl_configure_getline(gl, NULL, NULL, TECLA_CONFIG_FILE);
    gl->configured = 1;
  };
/*
 * Before installing our signal handler functions, record the fact
 * that there are no pending signals.
 */
  gl_pending_signal = -1;
/*
 * Temporarily override the signal handlers of the calling program,
 * so that we can intercept signals that would leave the terminal
 * in a bad state.
 */
  if(!was_overriden)
    waserr = gl_override_signal_handlers(gl);
/*
 * After recording the current terminal settings, switch the terminal
 * into raw input mode, without redisplaying any partially entered input
 * line.
 */
  if(!was_raw)
    waserr = waserr || _gl_raw_io(gl, 0);
/*
 * Attempt to read the line. This will require more than one attempt if
 * either a current temporary input file is opened by gl_get_input_line()
 * or the end of a temporary input file is reached by gl_read_stream_line().
 */
  while(!waserr) {
/*
 * Read a line from a non-interactive stream?
 */
    if(gl->file_fp || !gl->is_term) {
      retval = gl_read_stream_char(gl);
      if(retval != EOF) {            /* Success? */
	break;
      } else if(gl->file_fp) {  /* End of temporary input file? */
	gl_revert_input(gl);
	gl_record_status(gl, GLR_NEWLINE, 0);
      } else {                  /* An error? */
	waserr = 1;
	break;
      };
    };
/*
 * Read from the terminal? Note that the above if() block may have
 * changed gl->file_fp, so it is necessary to retest it here, rather
 * than using an else statement.
 */
    if(!gl->file_fp && gl->is_term) {
/*
 * Flush any pending output to the terminal before waiting
 * for the user to type a character.
 */
      if(_glq_char_count(gl->cq) > 0 && gl_flush_output(gl)) {
	retval = EOF;
/*
 * Read one character. Don't append it to the key buffer, since
 * this would subseuqnely appear as bogus input to the line editor.
 */
      } else if(gl_read_terminal(gl, 0, &c) == 0) {
/*
 * Record the character for return.
 */
	retval = c;
/*
 * In this mode, count each character as being a new key-sequence.
 */
	gl->keyseq_count++;
/*
 * Delete the character that was read, from the key-press buffer.
 */
	gl_discard_chars(gl, 1);
      };
      if(retval==EOF)
	waserr = 1;
      else
	break;
    };
  };
/*
 * If an error occurred, but gl->rtn_status is still set to
 * GLR_NEWLINE, change the status to GLR_ERROR. Otherwise
 * leave it at whatever specific value was assigned by the function
 * that aborted input. This means that only functions that trap
 * non-generic errors have to remember to update gl->rtn_status
 * themselves.
 */
  if(waserr && gl->rtn_status == GLR_NEWLINE)
    gl_record_status(gl, GLR_ERROR, errno);
/*
 * Restore terminal settings, if they were changed by this function.
 */
  if(!was_raw && gl->io_mode != GL_SERVER_MODE)
    _gl_normal_io(gl);
/*
 * Restore the signal handlers, if they were overriden by this function.
 */
  if(!was_overriden)
    gl_restore_signal_handlers(gl);
/*
 * If this function gets aborted early, the errno value associated
 * with the event that caused this to happen is recorded in
 * gl->rtn_errno. Since errno may have been overwritten by cleanup
 * functions after this, restore its value to the value that it had
 * when the error condition occured, so that the caller can examine it
 * to find out what happened.
 */
  errno = gl->rtn_errno;
/*
 * Error conditions are signalled to the caller, by setting the returned
 * character to EOF.
 */
  if(gl->rtn_status != GLR_NEWLINE)
    retval = EOF;
/*
 * Restore the indication of what direction of I/O gl_get_line()
 * was awaiting before this call.
 */
  gl->pending_io = old_pending_io;
/*
 * Return the acquired character.
 */
  return retval;
}

/*.......................................................................
 * Reset the GetLine completion status. This function should be called
 * at the start of gl_get_line(), gl_read_char() and gl_query_char()
 * to discard the completion status and non-zero errno value of any
 * preceding calls to these functions.
 *
 * Input:
 *  gl       GetLine *  The resource object of this module.
 */
static void gl_clear_status(GetLine *gl)
{
  gl_record_status(gl, GLR_NEWLINE, 0);
}

/*.......................................................................
 * When an error or other event causes gl_get_line() to return, this
 * function should be called to record information about what
 * happened, including the value of errno and the value that
 * gl_return_status() should return.
 *
 * Input:
 *  gl                GetLine *  The resource object of this module.
 *  rtn_status GlReturnStatus    The completion status. To clear a
 *                               previous abnormal completion status,
 *                               specify GLR_NEWLINE (this is what
 *                               gl_clear_status() does).
 *  rtn_errno             int    The associated value of errno.
 */
static void gl_record_status(GetLine *gl, GlReturnStatus rtn_status,
			     int rtn_errno)
{
/*
 * If rtn_status==GLR_NEWLINE, then this resets the completion status, so we
 * should always heed this. Otherwise, only record the first abnormal
 * condition that occurs after such a reset.
 */
  if(rtn_status == GLR_NEWLINE || gl->rtn_status == GLR_NEWLINE) {
    gl->rtn_status = rtn_status;
    gl->rtn_errno = rtn_errno;
  };
}

genometools-1.5.1/src/external/libtecla-1.6.1/getline.h000066400000000000000000000060221211610345200224750ustar00rootroot00000000000000#ifndef getline_h
#define getline_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * Set the name of the getline configuration file.
 */
#define TECLA_CONFIG_FILE "~/.teclarc"

/*
 * The following macro returns non-zero if a character is
 * a control character.
 */
#define IS_CTRL_CHAR(c) ((unsigned char)(c) < ' ' || (unsigned char)(c)=='\177')

/*
 * The following macro returns non-zero if a character is
 * a meta character.
 */
#define IS_META_CHAR(c) (((unsigned char)(c) & 0x80) && !isprint((int)(unsigned char)(c)))

/*
 * Return the character that would be produced by pressing the
 * specified key plus the control key.
 */
#define MAKE_CTRL(c) ((c)=='?' ? '\177' : ((unsigned char)toupper(c) & ~0x40))

/*
 * Return the character that would be produced by pressing the
 * specified key plus the meta key.
 */
#define MAKE_META(c) ((unsigned char)(c) | 0x80)

/*
 * Given a binary control character, return the character that
 * had to be pressed at the same time as the control key.
 */
#define CTRL_TO_CHAR(c) (toupper((unsigned char)(c) | 0x40))

/*
 * Given a meta character, return the character that was pressed
 * at the same time as the meta key.
 */
#define META_TO_CHAR(c) ((unsigned char)(c) & ~0x80)

/*
 * Specify the string of characters other than the alphanumeric characters,
 * that are to be considered parts of words.
 */
#define GL_WORD_CHARS "_*\?\\[]"

/*
 * Define the escape character, both as a string and as a character.
 */
#define GL_ESC_STR "\033"
#define GL_ESC_CHAR '\033'

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/hash.c000066400000000000000000000576101211610345200217750ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include 
#include 
#include 
#include 
#include 

#include "hash.h"
#include "strngmem.h"
#include "freelist.h"

/*
 * The following container object contains free-lists to be used
 * for allocation of HashTable containers and nodes.
 */
struct HashMemory {
  FreeList *hash_memory;    /* HashTable free-list */
  FreeList *node_memory;    /* HashNode free-list */
  StringMem *string_memory; /* Memory used to allocate hash strings */
};

/*
 * Define a hash symbol-table entry.
 * See symbol.h for the definition of the Symbol container type.
 */
typedef struct HashNode HashNode;
struct HashNode {
  Symbol symbol;       /* The symbol stored in the hash-entry */
  HashNode *next;      /* The next hash-table entry in a bucket list */
};

/*
 * Each hash-table bucket contains a linked list of entries that
 * hash to the same bucket.
 */
typedef struct {
  HashNode *head;   /* The head of the bucket hash-node list */
  int count;        /* The number of entries in the list */
} HashBucket;

/*
 * A hash-table consists of 'size' hash buckets.
 * Note that the HashTable typedef for this struct is contained in hash.h.
 */
struct HashTable {
  HashMemory *mem;         /* HashTable free-list */
  int internal_mem;        /* True if 'mem' was allocated by _new_HashTable() */
  int case_sensitive;      /* True if case is significant in lookup keys */
  int size;                /* The number of hash buckets */
  HashBucket *bucket;      /* An array of 'size' hash buckets */
  int (*keycmp)(const char *, const char *); /* Key comparison function */
  void *app_data;          /* Application-provided data */
  HASH_DEL_FN(*del_fn);    /* Application-provided 'app_data' destructor */
};

static HashNode *_del_HashNode(HashTable *hash, HashNode *node);
static HashNode *_new_HashNode(HashTable *hash, const char *name, int code,
		      void (*fn)(void), void *data, SYM_DEL_FN(*del_fn));
static HashNode *_find_HashNode(HashTable *hash, HashBucket *bucket,
				const char *name, HashNode **prev);
static HashBucket *_find_HashBucket(HashTable *hash, const char *name);
static int _ht_lower_strcmp(const char *node_key, const char *look_key);
static int _ht_strcmp(const char *node_key, const char *look_key);

/*.......................................................................
 * Allocate a free-list for use in allocating hash tables and their nodes.
 *
 * Input:
 *  list_count    int    The number of HashTable containers per free-list
 *                       block.
 *  node_count    int    The number of HashTable nodes per free-list block.
 * Output:
 *  return HashMemory *  The new free-list for use in allocating hash tables
 *                       and their nodes.
 */
HashMemory *_new_HashMemory(int hash_count, int node_count)
{
  HashMemory *mem;
/*
 * Allocate the free-list container.
 */
  mem = (HashMemory *) malloc(sizeof(HashMemory));
  if(!mem) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Initialize the container at least up to the point at which it can
 * safely be passed to _del_HashMemory().
 */
  mem->hash_memory = NULL;
  mem->node_memory = NULL;
  mem->string_memory = NULL;
/*
 * Allocate the two free-lists.
 */
  mem->hash_memory = _new_FreeList(sizeof(HashTable), hash_count);
  if(!mem->hash_memory)
    return _del_HashMemory(mem, 1);
  mem->node_memory = _new_FreeList(sizeof(HashNode), node_count);
  if(!mem->node_memory)
    return _del_HashMemory(mem, 1);
  mem->string_memory = _new_StringMem(64);
  if(!mem->string_memory)
    return _del_HashMemory(mem, 1);
/*
 * Return the free-list container.
 */
  return mem;
}

/*.......................................................................
 * Delete a HashTable free-list. An error will be displayed if the list is
 * still in use and the deletion will be aborted.
 *
 * Input:
 *  mem    HashMemory *  The free-list container to be deleted.
 *  force         int    If force==0 then _del_HashMemory() will complain
 *                        and refuse to delete the free-list if any
 *                        of nodes have not been returned to the free-list.
 *                       If force!=0 then _del_HashMemory() will not check
 *                        whether any nodes are still in use and will
 *                        always delete the list.
 * Output:
 *  return HashMemory *  Always NULL (even if the memory could not be
 *                       deleted).
 */
HashMemory *_del_HashMemory(HashMemory *mem, int force)
{
  if(mem) {
    if(!force && (_busy_FreeListNodes(mem->hash_memory) > 0 ||
		  _busy_FreeListNodes(mem->node_memory) > 0)) {
      errno = EBUSY;
      return NULL;
    };
    mem->hash_memory = _del_FreeList(mem->hash_memory, force);
    mem->node_memory = _del_FreeList(mem->node_memory, force);
    mem->string_memory = _del_StringMem(mem->string_memory, force);
    free(mem);
  };
  return NULL;
}

/*.......................................................................
 * Create a new hash table.
 *
 * Input:
 *  mem       HashMemory *  An optional free-list for use in allocating
 *                          HashTable containers and nodes. See explanation
 *                          in hash.h. If you are going to allocate more
 *                          than one hash table, then it will be more
 *                          efficient to allocate a single free-list for
 *                          all of them than to force each hash table
 *                          to allocate its own private free-list.
 *  size             int    The size of the hash table. Best performance
 *                          will be acheived if this is a prime number.
 *  hcase       HashCase    Specify how symbol case is considered when
 *                          looking up symbols, from:
 *                           IGNORE_CASE - Upper and lower case versions
 *                                         of a letter are treated as
 *                                         being identical.
 *                           HONOUR_CASE - Upper and lower case versions
 *                                         of a letter are treated as
 *                                         being distinct.
 *                          characters in a lookup name is significant.
 *  app_data        void *  Optional application data to be registered
 *                          to the table. This is presented to user
 *                          provided SYM_DEL_FN() symbol destructors along
 *                          with the symbol data.
 *  del_fn() HASH_DEL_FN(*) If you want app_data to be free'd when the
 *                          hash-table is destroyed, register a suitable
 *                          destructor function here.
 * Output:
 *  return HashTable *  The new hash table, or NULL on error.
 */
HashTable *_new_HashTable(HashMemory *mem, int size, HashCase hcase,
			 void *app_data, HASH_DEL_FN(*del_fn))
{
  HashTable *hash;         /* The table to be returned */
  int allocate_mem = !mem; /* True if mem should be internally allocated */
  int i;
/*
 * Check arguments.
 */
  if(size <= 0) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Allocate an internal free-list?
 */
  if(allocate_mem) {
    mem = _new_HashMemory(1, 100);
    if(!mem)
      return NULL;
  };
/*
 * Allocate the container.
 */
  hash = (HashTable *) _new_FreeListNode(mem->hash_memory);
  if(!hash) {
    errno = ENOMEM;
    if(allocate_mem)
      mem = _del_HashMemory(mem, 1);
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize
 * the container at least up to the point at which it can safely
 * be passed to _del_HashTable().
 */
  hash->mem = mem;
  hash->internal_mem = allocate_mem;
  hash->case_sensitive = hcase==HONOUR_CASE;
  hash->size = size;
  hash->bucket = NULL;
  hash->keycmp = hash->case_sensitive ? _ht_strcmp : _ht_lower_strcmp;
  hash->app_data = app_data;
  hash->del_fn = del_fn;
/*
 * Allocate the array of 'size' hash buckets.
 */
  hash->bucket = (HashBucket *) malloc(sizeof(HashBucket) * size);
  if(!hash->bucket) {
    errno = ENOMEM;
    return _del_HashTable(hash);
  };
/*
 * Initialize the bucket array.
 */
  for(i=0; ibucket + i;
    b->head = NULL;
    b->count = 0;
  };
/*
 * The table is ready for use - albeit currently empty.
 */
  return hash;
}

/*.......................................................................
 * Delete a hash-table.
 *
 * Input:
 *  hash   HashTable *  The hash table to be deleted.
 * Output:
 *  return HashTable *  The deleted hash table (always NULL).
 */
HashTable *_del_HashTable(HashTable *hash)
{
  if(hash) {
/*
 * Clear and delete the bucket array.
 */
    if(hash->bucket) {
      _clear_HashTable(hash);
      free(hash->bucket);
      hash->bucket = NULL;
    };
/*
 * Delete application data.
 */
    if(hash->del_fn)
      hash->del_fn(hash->app_data);
/*
 * If the hash table was allocated from an internal free-list, delete
 * it and the hash table by deleting the free-list. Otherwise just
 * return the hash-table to the external free-list.
 */
    if(hash->internal_mem)
      _del_HashMemory(hash->mem, 1);
    else
      hash = (HashTable *) _del_FreeListNode(hash->mem->hash_memory, hash);
  };
  return NULL;
}

/*.......................................................................
 * Create and install a new entry in a hash table. If an entry with the
 * same name already exists, replace its contents with the new data.
 *
 * Input:
 *  hash   HashTable *  The hash table to insert the symbol into.
 *  name  const char *  The name to tag the entry with.
 *  code         int    An application-specific code to be stored in
 *                      the entry.
 *  fn  void (*)(void)  An application-specific function to be stored
 *                      in the entry.
 *  data        void *  An application-specific pointer to data to be
 *                      associated with the entry, or NULL if not
 *                      relevant.
 *  del_fn SYM_DEL_FN(*) An optional destructor function. When the
 *                      symbol is deleted this function will be called
 *                      with the 'code' and 'data' arguments given
 *                      above. Any application data that was registered
 *                      to the table via the app_data argument of
 *                      _new_HashTable() will also be passed.
 * Output:
 *  return  HashNode *  The new entry, or NULL if there was insufficient
 *                      memory or the arguments were invalid.
 */
Symbol *_new_HashSymbol(HashTable *hash, const char *name, int code,
			void (*fn)(void), void *data, SYM_DEL_FN(*del_fn))
{
  HashBucket *bucket;  /* The hash-bucket associated with the name */
  HashNode *node;      /* The new node */
/*
 * Check arguments.
 */
  if(!hash || !name) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Get the hash bucket of the specified name.
 */
  bucket = _find_HashBucket(hash, name);
/*
 * See if a node with the same name already exists.
 */
  node = _find_HashNode(hash, bucket, name, NULL);
/*
 * If found, delete its contents by calling the user-supplied
 * destructor function, if provided.
 */
  if(node) {
    if(node->symbol.data && node->symbol.del_fn) {
      node->symbol.data = node->symbol.del_fn(hash->app_data, node->symbol.code,
					      node->symbol.data);
    };
/*
 * Allocate a new node if necessary.
 */
  } else {
    node = _new_HashNode(hash, name, code, fn, data, del_fn);
    if(!node)
      return NULL;
  };
/*
 * Install the node at the head of the hash-bucket list.
 */
  node->next = bucket->head;
  bucket->head = node;
  bucket->count++;
  return &node->symbol;
}

/*.......................................................................
 * Remove and delete a given hash-table entry.
 *
 * Input:
 *  hash   HashTable *  The hash table to find the symbol in.
 *  name  const char *  The name of the entry.
 * Output:
 *  return  HashNode *  The deleted hash node (always NULL).
 */
Symbol *_del_HashSymbol(HashTable *hash, const char *name)
{
  if(hash && name) {
    HashBucket *bucket = _find_HashBucket(hash, name);
    HashNode *prev;   /* The node preceding the located node */
    HashNode *node = _find_HashNode(hash, bucket, name, &prev);
/*
 * Node found?
 */
    if(node) {
/*
 * Remove the node from the bucket list.
 */
      if(prev) {
	prev->next = node->next;
      } else {
	bucket->head = node->next;
      };
/*
 * Record the loss of a node.
 */
      bucket->count--;
/*
 * Delete the node.
 */
      (void) _del_HashNode(hash, node);
    };
  };
  return NULL;
}

/*.......................................................................
 * Look up a symbol in the hash table.
 *
 * Input:
 *  hash   HashTable *   The table to look up the string in.
 *  name  const char *   The name of the symbol to look up.
 * Output:
 *  return    Symbol *   The located hash-table symbol, or NULL if not
 *                       found.
 */
Symbol *_find_HashSymbol(HashTable *hash, const char *name)
{
  HashBucket *bucket;  /* The hash-table bucket associated with name[] */
  HashNode *node;      /* The hash-table node of the requested symbol */
/*
 * Check arguments.
 */
  if(!hash)
    return NULL;
/*
 * Nothing to lookup?
 */
  if(!name)
    return NULL;
/*
 * Hash the name to a hash-table bucket.
 */
  bucket = _find_HashBucket(hash, name);
/*
 * Find the bucket entry that exactly matches the name.
 */
  node = _find_HashNode(hash, bucket, name, NULL);
  if(!node)
    return NULL;
  return &node->symbol;
}

/*.......................................................................
 * Private function used to allocate a hash-table node.
 * The caller is responsible for checking that the specified symbol
 * is unique and for installing the returned entry in the table.
 *
 * Input:
 *  hash     HashTable *  The table to allocate the node for.
 *  name    const char *  The name of the new entry.
 *  code           int    A user-supplied context code.
 *  fn  void (*)(void)    A user-supplied function pointer.
 *  data          void *  A user-supplied data pointer.
 *  del_fn  SYM_DEL_FN(*) An optional 'data' destructor function.
 * Output:
 *  return    HashNode *  The new node, or NULL on error.
 */
static HashNode *_new_HashNode(HashTable *hash, const char *name, int code,
			      void (*fn)(void), void *data, SYM_DEL_FN(*del_fn))
{
  HashNode *node;  /* The new node */
/*
 * Allocate the new node from the free list.
 */
  node = (HashNode *) _new_FreeListNode(hash->mem->node_memory);
  if(!node)
    return NULL;
/*
 * Before attempting any operation that might fail, initialize the
 * contents of 'node' at least up to the point at which it can be
 * safely passed to _del_HashNode().
 */
  node->symbol.name = NULL;
  node->symbol.code = code;
  node->symbol.fn = fn;
  node->symbol.data = data;
  node->symbol.del_fn = del_fn;
  node->next = NULL;
/*
 * Allocate a copy of 'name'.
 */
  node->symbol.name = _new_StringMemString(hash->mem->string_memory,
					  strlen(name) + 1);
  if(!node->symbol.name)
    return _del_HashNode(hash, node);
/*
 * If character-case is insignificant in the current table, convert the
 * name to lower case while copying it.
 */
  if(hash->case_sensitive) {
    strcpy(node->symbol.name, name);
  } else {
    const char *src = name;
    char *dst = node->symbol.name;
    for( ; *src; src++,dst++)
      *dst = tolower(*src);
    *dst = '\0';
  };
  return node;
}

/*.......................................................................
 * Private function used to delete a hash-table node.
 * The node must have been removed from its list before calling this
 * function.
 *
 * Input:
 *  hash   HashTable *  The table for which the node was originally
 *                      allocated.
 *  node    HashNode *  The node to be deleted.
 * Output:
 *  return  HashNode *  The deleted node (always NULL).
 */
static HashNode *_del_HashNode(HashTable *hash, HashNode *node)
{
  if(node) {
    node->symbol.name = _del_StringMemString(hash->mem->string_memory,
					    node->symbol.name);
/*
 * Call the user-supplied data-destructor if provided.
 */
    if(node->symbol.data && node->symbol.del_fn)
      node->symbol.data = node->symbol.del_fn(hash->app_data,
					      node->symbol.code,
					      node->symbol.data);
/*
 * Return the node to the free-list.
 */
    node->next = NULL;
    node = (HashNode *) _del_FreeListNode(hash->mem->node_memory, node);
  };
  return NULL;
}

/*.......................................................................
 * Private function to locate the hash bucket associated with a given
 * name.
 *
 * This uses a hash-function described in the dragon-book
 * ("Compilers - Principles, Techniques and Tools", by Aho, Sethi and
 *  Ullman; pub. Adison Wesley) page 435.
 *
 * Input:
 *  hash    HashTable *   The table to look up the string in.
 *  name   const char *   The name of the symbol to look up.
 * Output:
 *  return HashBucket *   The located hash-bucket.
 */
static HashBucket *_find_HashBucket(HashTable *hash, const char *name)
{
  unsigned const char *kp;
  unsigned long h = 0L;
  if(hash->case_sensitive) {
    for(kp=(unsigned const char *) name; *kp; kp++)
      h = 65599UL * h + *kp;  /* 65599 is a prime close to 2^16 */
  } else {
    for(kp=(unsigned const char *) name; *kp; kp++)
      h = 65599UL * h + tolower((int)*kp);  /* 65599 is a prime close to 2^16 */
  };
  return hash->bucket + (h % hash->size);
}

/*.......................................................................
 * Search for a given name in the entries of a given bucket.
 *
 * Input:
 *  hash     HashTable *  The hash-table being searched.
 *  bucket  HashBucket *  The bucket to search (use _find_HashBucket()).
 *  name    const char *  The name to search for.
 * Output:
 *  prev      HashNode ** If prev!=NULL then the pointer to the node
 *                        preceding the located node in the list will
 *                        be recorded in *prev. This will be NULL either
 *                        if the name is not found or the located node is
 *                        at the head of the list of entries.
 * return     HashNode *  The located hash-table node, or NULL if not
 *                        found.
 */
static HashNode *_find_HashNode(HashTable *hash, HashBucket *bucket,
			       const char *name, HashNode **prev)
{
  HashNode *last;  /* The previously searched node */
  HashNode *node;  /* The node that is being searched */
/*
 * Search the list for a node containing the specified name.
 */
  for(last=NULL, node=bucket->head;
      node && hash->keycmp(node->symbol.name, name)!=0;
      last = node, node=node->next)
    ;
  if(prev)
    *prev = node ? last : NULL;
  return node;
}

/*.......................................................................
 * When hash->case_sensitive is zero this function is called
 * in place of strcmp(). In such cases the hash-table names are stored
 * as lower-case versions of the original strings so this function
 * performs the comparison against lower-case copies of the characters
 * of the string being compared.
 *
 * Input:
 *  node_key   const char *  The lower-case hash-node key being compared
 *                           against.
 *  look_key   const char *  The lookup key.
 * Output:
 *  return            int    <0 if node_key < look_key.
 *                            0 if node_key == look_key.
 *                           >0 if node_key > look_key.
 */
static int _ht_lower_strcmp(const char *node_key, const char *look_key)
{
  int cn;  /* The latest character from node_key[] */
  int cl;  /* The latest character from look_key[] */
  do {
    cn = *node_key++;
    cl = *look_key++;
  } while(cn && cn==tolower(cl));
  return cn - tolower(cl);
}

/*.......................................................................
 * This is a wrapper around strcmp for comparing hash-keys in a case
 * sensitive manner. The reason for having this wrapper, instead of using
 * strcmp() directly, is to make some C++ compilers happy. The problem
 * is that when the library is compiled with a C++ compiler, the
 * declaration of the comparison function is a C++ declaration, whereas
 * strcmp() is a pure C function and thus although it appears to have the
 * same declaration, the compiler disagrees.
 *
 * Input:
 *  node_key   char *  The lower-case hash-node key being compared against.
 *  look_key   char *  The lookup key.
 * Output:
 *  return      int    <0 if node_key < look_key.
 *                      0 if node_key == look_key.
 *                     >0 if node_key > look_key.
 */
static int _ht_strcmp(const char *node_key, const char *look_key)
{
  return strcmp(node_key, look_key);
}

/*.......................................................................
 * Empty a hash-table by deleting all of its entries.
 *
 * Input:
 *  hash    HashTable *  The hash table to clear.
 * Output:
 *  return        int    0 - OK.
 *                       1 - Invalid arguments.
 */
int _clear_HashTable(HashTable *hash)
{
  int i;
/*
 * Check the arguments.
 */
  if(!hash)
    return 1;
/*
 * Clear the contents of the bucket array.
 */
  for(i=0; isize; i++) {
    HashBucket *bucket = hash->bucket + i;
/*
 * Delete the list of active hash nodes from the bucket.
 */
    HashNode *node = bucket->head;
    while(node) {
      HashNode *next = node->next;
      (void) _del_HashNode(hash, node);
      node = next;
    };
/*
 * Mark the bucket as empty.
 */
    bucket->head = NULL;
    bucket->count = 0;
  };
  return 0;
}

/*.......................................................................
 * Execute a given function on each entry of a hash table, returning
 * before completion if the the specified function returns non-zero.
 *
 * Input:
 *  hash       HashTable *    The table to traverse.
 *  scan_fn HASH_SCAN_FN(*)   The function to call.
 *  context         void *    Optional caller-specific context data
 *                            to be passed to scan_fn().
 * Output:
 *  return           int      0 - OK.
 *                            1 - Either the arguments were invalid, or
 *                                scan_fn() returned non-zero at some
 *                                point.
 */
int _scan_HashTable(HashTable *hash, HASH_SCAN_FN(*scan_fn), void *context)
{
  int i;
/*
 * Check the arguments.
 */
  if(!hash || !scan_fn)
    return 1;
/*
 * Iterate through the buckets of the table.
 */
  for(i=0; isize; i++) {
    HashBucket *bucket = hash->bucket + i;
    HashNode *node;
/*
 * Iterate through the list of symbols that fall into bucket i,
 * passing each one to the caller-specified function.
 */
    for(node=bucket->head; node; node=node->next) {
      if(scan_fn(&node->symbol, context))
	return 1;
    };
  };
  return 0;
}
genometools-1.5.1/src/external/libtecla-1.6.1/hash.h000066400000000000000000000134641211610345200220010ustar00rootroot00000000000000#ifndef hash_h
#define hash_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * The following macro can be used to prototype or define a
 * function that deletes the data of a symbol-table entry.
 *
 * Input:
 *  app_data void *  The _new_HashTable() app_data argument.
 *  code      int    The Symbol::code argument.
 *  sym_data void *  The Symbol::data argument to be deleted.
 * Output:
 *  return  void * The deleted data (always return NULL).
 */
#define SYM_DEL_FN(fn) void *(fn)(void *app_data, int code, void *sym_data)

/*
 * The following macro can be used to prototype or define a
 * function that deletes the application-data of a hash-table.
 *
 * Input:
 *  data    void * The _new_HashTable() 'app_data' argument to be
 *                 deleted.
 * Output:
 *  return  void * The deleted data (always return NULL).
 */
#define HASH_DEL_FN(fn) void *(fn)(void *app_data)

/*
 * The following is a container for recording the context
 * of a symbol in a manner that is independant of the particular
 * symbol-table implementation. Each hash-table entry contains
 * the following user supplied parameters:
 *
 * 1. An optional integral parameter 'code'. This is useful for
 *    enumerating a symbol or for describing what type of data
 *    or function is stored in the symbol.
 *
 * 2. An optional generic function pointer. This is useful for
 *    associating functions with names. The user is responsible
 *    for casting between the generic function type and the
 *    actual function type. The code field could be used to
 *    enumerate what type of function to cast to.
 *
 * 3. An optional generic pointer to a static or heap-allocated
 *    object. It is up to the user to cast this back to the
 *    appropriate object type. Again, the code field could be used
 *    to describe what type of object is stored there.
 *    If the object is dynamically allocated and should be discarded
 *    when the symbol is deleted from the symbol table, send a
 *    destructor function to have it deleted automatically.
 */
typedef struct {
  char *name;           /* The name of the symbol */
  int code;             /* Application supplied integral code */
  void (*fn)(void);     /* Application supplied generic function */
  void *data;           /* Application supplied context data */
  SYM_DEL_FN(*del_fn);  /* Data destructor function */
} Symbol;

/*
 * HashNode's and HashTable's are small objects. Separately allocating
 * many such objects would normally cause memory fragmentation. To
 * counter this, HashMemory objects are used. These contain
 * dedicated free-lists formed from large dynamically allocated arrays
 * of objects. One HashMemory object can be shared between multiple hash
 * tables (within a single thread).
 */
typedef struct HashMemory HashMemory;

  /* Create a free-list for allocation of hash tables and their nodes */

HashMemory *_new_HashMemory(int hash_count, int node_count);

  /* Delete a redundant free-list if not being used */

HashMemory *_del_HashMemory(HashMemory *mem, int force);

/*
 * Declare an alias for the private HashTable structure defined in
 * hash.c.
 */
typedef struct HashTable HashTable;

/*
 * Enumerate case-sensitivity options.
 */
typedef enum {
  IGNORE_CASE,     /* Ignore case when looking up symbols */
  HONOUR_CASE      /* Honor case when looking up symbols */
} HashCase;

  /* Create a new hash-table */

HashTable *_new_HashTable(HashMemory *mem, int size, HashCase hcase,
			  void *app_data, HASH_DEL_FN(*del_fn));

  /* Delete a reference to a hash-table */

HashTable *_del_HashTable(HashTable *hash);

  /* Add an entry to a hash table */

Symbol *_new_HashSymbol(HashTable *hash, const char *key, int code,
			void (*fn)(void), void *data, SYM_DEL_FN(*del_fn));

  /* Remove and delete all the entries in a given hash table */

int _clear_HashTable(HashTable *hash);

  /* Remove and delete a given hash-table entry */

Symbol *_del_HashSymbol(HashTable *hash, const char *key);

  /* Lookup a given hash-table entry */

Symbol *_find_HashSymbol(HashTable *hash, const char *key);

  /* Execute a given function on each entry of a hash table, returning */
  /*  before completion if the specified function returns non-zero. */

#define HASH_SCAN_FN(fn)  int (fn)(Symbol *sym, void *context)

int _scan_HashTable(HashTable *hash, HASH_SCAN_FN(*scan_fn), void *context);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/history.c000066400000000000000000002462041211610345200225520ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include 
#include 
#include 
#include 
#include 
#include 

#include "ioutil.h"
#include "history.h"
#include "freelist.h"
#include "errmsg.h"

/*
 * History lines are split into sub-strings of GLH_SEG_SIZE
 * characters.  To avoid wasting space in the GlhLineSeg structure,
 * this should be a multiple of the size of a pointer.
 */
#define GLH_SEG_SIZE 16

/*
 * GlhLineSeg structures contain fixed sized segments of a larger
 * string. These are linked into lists to record strings, with all but
 * the last segment having GLH_SEG_SIZE characters. The last segment
 * of a string is terminated within the GLH_SEG_SIZE characters with a
 * '\0'.
 */
typedef struct GlhLineSeg GlhLineSeg;
struct GlhLineSeg {
  GlhLineSeg *next;     /* The next sub-string of the history line */
  char s[GLH_SEG_SIZE]; /* The sub-string. Beware that only the final */
                        /*  substring of a line, as indicated by 'next' */
                        /*  being NULL, is '\0' terminated. */
};

/*
 * History lines are recorded in a hash table, such that repeated
 * lines are stored just once.
 *
 * Start by defining the size of the hash table. This should be a
 * prime number.
 */
#define GLH_HASH_SIZE 113

typedef struct GlhHashBucket GlhHashBucket;

/*
 * Each history line will be represented in the hash table by a
 * structure of the following type.
 */
typedef struct GlhHashNode GlhHashNode;
struct GlhHashNode {
  GlhHashBucket *bucket; /* The parent hash-table bucket of this node */
  GlhHashNode *next;     /* The next in the list of nodes within the */
                         /*  parent hash-table bucket. */
  GlhLineSeg *head;      /* The list of sub-strings which make up a line */
  int len;               /* The length of the line, excluding any '\0' */
  int used;              /* The number of times this string is pointed to by */
                         /*  the time-ordered list of history lines. */
  int reported;          /* A flag that is used when searching to ensure that */
                         /*  a line isn't reported redundantly. */
};

/*
 * How many new GlhHashNode elements should be allocated at a time?
 */
#define GLH_HASH_INCR 50

static int _glh_is_line(GlhHashNode *hash, const char *line, size_t n);
static int _glh_line_matches_prefix(GlhHashNode *line, GlhHashNode *prefix);
static void _glh_return_line(GlhHashNode *hash, char *line, size_t dim);

/*
 * All history lines which hash to a given bucket in the hash table, are
 * recorded in a structure of the following type.
 */
struct GlhHashBucket {
  GlhHashNode *lines;  /* The list of history lines which fall in this bucket */
};

static GlhHashBucket *glh_find_bucket(GlHistory *glh, const char *line,
				      size_t n);
static GlhHashNode *glh_find_hash_node(GlhHashBucket *bucket, const char *line,
				       size_t n);

typedef struct {
  FreeList *node_mem;  /* A free-list of GlhHashNode structures */
  GlhHashBucket bucket[GLH_HASH_SIZE]; /* The buckets of the hash table */
} GlhLineHash;

/*
 * GlhLineNode's are used to record history lines in time order.
 */
typedef struct GlhLineNode GlhLineNode;
struct GlhLineNode {
  long id;             /* The unique identifier of this history line */
  time_t timestamp;    /* The time at which the line was archived */
  unsigned group;      /* The identifier of the history group to which the */
                       /*  the line belongs. */
  GlhLineNode *next;   /* The next youngest line in the list */
  GlhLineNode *prev;   /* The next oldest line in the list */
  GlhHashNode *line;   /* The hash-table entry of the history line */
};

/*
 * The number of GlhLineNode elements per freelist block.
 */
#define GLH_LINE_INCR 100

/*
 * Encapsulate the time-ordered list of historical lines.
 */
typedef struct {
  FreeList *node_mem;  /* A freelist of GlhLineNode objects */ 
  GlhLineNode *head;   /* The oldest line in the list */
  GlhLineNode *tail;   /* The newest line in the list */
} GlhLineList;

/*
 * The _glh_lookup_history() returns copies of history lines in a
 * dynamically allocated array. This array is initially allocated
 * GLH_LOOKUP_SIZE bytes. If subsequently this size turns out to be
 * too small, realloc() is used to increase its size to the required
 * size plus GLH_LOOKUP_MARGIN. The idea of the later parameter is to
 * reduce the number of realloc() operations needed.
 */
#define GLH_LBUF_SIZE 300
#define GLH_LBUF_MARGIN 100

/*
 * Encapsulate all of the resources needed to store historical input lines.
 */
struct GlHistory {
  ErrMsg *err;         /* The error-reporting buffer */
  GlhLineSeg *buffer;  /* An array of sub-line nodes to be partitioned */
                       /* into lists of sub-strings recording input lines. */
  int nbuff;           /* The allocated dimension of buffer[] */
  GlhLineSeg *unused;  /* The list of free nodes in buffer[] */
  GlhLineList list;    /* A time ordered list of history lines */
  GlhLineNode *recall; /* The last line recalled, or NULL if no recall */
                       /*  session is currently active. */
  GlhLineNode *id_node;/* The node at which the last ID search terminated */
  GlhLineHash hash;    /* A hash-table of reference-counted history lines */
  GlhHashNode *prefix; /* A pointer to a line containing the prefix that */
                       /*  is being searched for. Note that if prefix==NULL */
                       /*  and prefix_len>0, this means that no line in */
                       /*  the buffer starts with the requested prefix. */
  int prefix_len;      /* The length of the prefix being searched for. */
  char *lbuf;          /* The array in which _glh_lookup_history() returns */
                       /*  history lines */
  int lbuf_dim;        /* The allocated size of lbuf[] */
  int nbusy;           /* The number of line segments in buffer[] that are */
                       /*  currently being used to record sub-lines */
  int nfree;           /* The number of line segments in buffer that are */
                       /*  not currently being used to record sub-lines */
  unsigned long seq;   /* The next ID to assign to a line node */
  unsigned group;      /* The identifier of the current history group */
  int nline;           /* The number of lines currently in the history list */
  int max_lines;       /* Either -1 or a ceiling on the number of lines */
  int enable;          /* If false, ignore history additions and lookups */
};

#ifndef WITHOUT_FILE_SYSTEM
static int _glh_cant_load_history(GlHistory *glh, const char *filename,
				  int lineno, const char *message, FILE *fp);
static int _glh_cant_save_history(GlHistory *glh, const char *message,
				  const char *filename, FILE *fp);
static int _glh_write_timestamp(FILE *fp, time_t timestamp);
static int _glh_decode_timestamp(char *string, char **endp, time_t *timestamp);
#endif
static void _glh_discard_line(GlHistory *glh, GlhLineNode *node);
static GlhLineNode *_glh_find_id(GlHistory *glh, GlhLineID id);
static GlhHashNode *_glh_acquire_copy(GlHistory *glh, const char *line,
				      size_t n);
static GlhHashNode *_glh_discard_copy(GlHistory *glh, GlhHashNode *hnode);
static int _glh_prepare_for_recall(GlHistory *glh, char *line);

/*
 * The following structure and functions are used to iterate through
 * the characters of a segmented history line.
 */
typedef struct {
  GlhLineSeg *seg;  /* The line segment that the next character will */
                    /*  be returned from. */
  int posn;         /* The index in the above line segment, containing */
                    /*  the next unread character. */
  char c;           /* The current character in the input line */
} GlhLineStream;
static void glh_init_stream(GlhLineStream *str, GlhHashNode *line);
static void glh_step_stream(GlhLineStream *str);

/*
 * See if search prefix contains any globbing characters.
 */
static int glh_contains_glob(GlhHashNode *prefix);
/*
 * Match a line against a search pattern.
 */
static int glh_line_matches_glob(GlhLineStream *lstr, GlhLineStream *pstr);
static int glh_matches_range(char c, GlhLineStream *pstr);

/*.......................................................................
 * Create a line history maintenance object.
 *
 * Input:
 *  buflen     size_t    The number of bytes to allocate to the
 *                       buffer that is used to record all of the
 *                       most recent lines of user input that will fit.
 *                       If buflen==0, no buffer will be allocated.
 * Output:
 *  return  GlHistory *  The new object, or NULL on error.
 */
GlHistory *_new_GlHistory(size_t buflen)
{
  GlHistory *glh;  /* The object to be returned */
  int i;
/*
 * Allocate the container.
 */
  glh = (GlHistory *) malloc(sizeof(GlHistory));
  if(!glh) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to _del_GlHistory().
 */
  glh->err = NULL;
  glh->buffer = NULL;
  glh->nbuff = (buflen+GLH_SEG_SIZE-1) / GLH_SEG_SIZE;
  glh->unused = NULL;
  glh->list.node_mem = NULL;
  glh->list.head = glh->list.tail = NULL;
  glh->recall = NULL;
  glh->id_node = NULL;
  glh->hash.node_mem = NULL;
  for(i=0; ihash.bucket[i].lines = NULL;
  glh->prefix = NULL;
  glh->lbuf = NULL;
  glh->lbuf_dim = 0;
  glh->nbusy = 0;
  glh->nfree = glh->nbuff;
  glh->seq = 0;
  glh->group = 0;
  glh->nline = 0;
  glh->max_lines = -1;
  glh->enable = 1;
/*
 * Allocate a place to record error messages.
 */
  glh->err = _new_ErrMsg();
  if(!glh->err)
    return _del_GlHistory(glh);
/*
 * Allocate the buffer, if required.
 */
  if(glh->nbuff > 0) {
    glh->nbuff = glh->nfree;
    glh->buffer = (GlhLineSeg *) malloc(sizeof(GlhLineSeg) * glh->nbuff);
    if(!glh->buffer) {
      errno = ENOMEM;
      return _del_GlHistory(glh);
    };
/*
 * All nodes of the buffer are currently unused, so link them all into
 * a list and make glh->unused point to the head of this list.
 */
    glh->unused = glh->buffer;
    for(i=0; inbuff-1; i++) {
      GlhLineSeg *seg = glh->unused + i;
      seg->next = seg + 1;
    };
    glh->unused[i].next = NULL;
  };
/*
 * Allocate the GlhLineNode freelist.
 */
  glh->list.node_mem = _new_FreeList(sizeof(GlhLineNode), GLH_LINE_INCR);
  if(!glh->list.node_mem)
    return _del_GlHistory(glh);
/*
 * Allocate the GlhHashNode freelist.
 */
  glh->hash.node_mem = _new_FreeList(sizeof(GlhLineNode), GLH_HASH_INCR);
  if(!glh->hash.node_mem)
    return _del_GlHistory(glh);
/*
 * Allocate the array that _glh_lookup_history() uses to return a
 * copy of a given history line. This will be resized when necessary.
 */
  glh->lbuf_dim = GLH_LBUF_SIZE;
  glh->lbuf = (char *) malloc(glh->lbuf_dim);
  if(!glh->lbuf) {
    errno = ENOMEM;
    return _del_GlHistory(glh);
  };
  return glh;
}

/*.......................................................................
 * Delete a GlHistory object.
 *
 * Input:
 *  glh    GlHistory *  The object to be deleted.
 * Output:
 *  return GlHistory *  The deleted object (always NULL).
 */
GlHistory *_del_GlHistory(GlHistory *glh)
{
  if(glh) {
/*
 * Delete the error-message buffer.
 */
    glh->err = _del_ErrMsg(glh->err);
/*
 * Delete the buffer.
 */
    if(glh->buffer) {
      free(glh->buffer);
      glh->buffer = NULL;
      glh->unused = NULL;
    };
/*
 * Delete the freelist of GlhLineNode's.
 */
    glh->list.node_mem = _del_FreeList(glh->list.node_mem, 1);
/*
 * The contents of the list were deleted by deleting the freelist.
 */
    glh->list.head = NULL;
    glh->list.tail = NULL;
/*
 * Delete the freelist of GlhHashNode's.
 */
    glh->hash.node_mem = _del_FreeList(glh->hash.node_mem, 1);
/*
 * Delete the lookup buffer.
 */
    if(glh->lbuf)
      free(glh->lbuf);
/*
 * Delete the container.
 */
    free(glh);
  };
  return NULL;
}

/*.......................................................................
 * Append a new line to the history list, deleting old lines to make
 * room, if needed.
 *
 * Input:
 *  glh  GlHistory *  The input-line history maintenance object.
 *  line      char *  The line to be archived.
 *  force      int    Unless this flag is non-zero, empty lines aren't
 *                    archived. This flag requests that the line be
 *                    archived regardless.
 * Output:
 *  return     int    0 - OK.
 *                    1 - Error.
 */
int _glh_add_history(GlHistory *glh, const char *line, int force)
{
  int slen;         /* The length of the line to be recorded (minus the '\0') */
  int empty;          /* True if the string is empty */
  const char *nlptr;  /* A pointer to a newline character in line[] */
  GlhHashNode *hnode; /* The hash-table node of the line */
  GlhLineNode *lnode; /* A node in the time-ordered list of lines */
  int i;
/*
 * Check the arguments.
 */
  if(!glh || !line) {
    errno = EINVAL;
    return 1;
  };
/*
 * Is history enabled?
 */
  if(!glh->enable || !glh->buffer || glh->max_lines == 0)
    return 0;
/*
 * Cancel any ongoing search.
 */
  if(_glh_cancel_search(glh))
    return 1;
/*
 * How long is the string to be recorded, being careful not to include
 * any terminating '\n' character.
 */
  nlptr = strchr(line, '\n');
  if(nlptr)
    slen = (nlptr - line);
  else
    slen = strlen(line);
/*
 * Is the line empty?
 */
  empty = 1;
  for(i=0; imax_lines >= 0) {
/*
 * If necessary, remove old lines until there is room to add one new
 * line without exceeding the specified line limit.
 */
    while(glh->nline > 0 && glh->nline >= glh->max_lines)
      _glh_discard_line(glh, glh->list.head);
/*
 * We can't archive the line if the maximum number of lines allowed is
 * zero.
 */
    if(glh->max_lines == 0)
      return 0;
  };
/*
 * Unless already stored, store a copy of the line in the history buffer,
 * then return a reference-counted hash-node pointer to this copy.
 */
  hnode = _glh_acquire_copy(glh, line, slen);
  if(!hnode) {
    _err_record_msg(glh->err, "No room to store history line", END_ERR_MSG);
    errno = ENOMEM;
    return 1;
  };
/*
 * Allocate a new node in the time-ordered list of lines.
 */
  lnode = (GlhLineNode *) _new_FreeListNode(glh->list.node_mem);
/*
 * If a new line-node couldn't be allocated, discard our copy of the
 * stored line before reporting the error.
 */
  if(!lnode) {
    hnode = _glh_discard_copy(glh, hnode);
    _err_record_msg(glh->err, "No room to store history line", END_ERR_MSG);
    errno = ENOMEM;
    return 1;
  };
/*
 * Record a pointer to the hash-table record of the line in the new
 * list node.
 */
  lnode->id = glh->seq++;
  lnode->timestamp = time(NULL);
  lnode->group = glh->group;
  lnode->line = hnode;
/*
 * Append the new node to the end of the time-ordered list.
 */
  if(glh->list.head)
    glh->list.tail->next = lnode;
  else
    glh->list.head = lnode;
  lnode->next = NULL;
  lnode->prev = glh->list.tail;
  glh->list.tail = lnode;
/*
 * Record the addition of a line to the list.
 */
  glh->nline++;
  return 0;
}

/*.......................................................................
 * Recall the next oldest line that has the search prefix last recorded
 * by _glh_search_prefix().
 *
 * Input:
 *  glh  GlHistory *  The input-line history maintenance object.
 *  line      char *  The input line buffer. On input this should contain
 *                    the current input line, and on output, if anything
 *                    was found, its contents will have been replaced
 *                    with the matching line.
 *  dim     size_t    The allocated dimension of the line buffer.
 * Output:
 *  return    char *  A pointer to line[0], or NULL if not found.
 */
char *_glh_find_backwards(GlHistory *glh, char *line, size_t dim)
{
  GlhLineNode *node;     /* The line location node being checked */
  GlhHashNode *old_line; /* The previous recalled line */
/*
 * Check the arguments.
 */
  if(!glh || !line) {
    if(glh)
      _err_record_msg(glh->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return NULL;
  };
/*
 * Is history enabled?
 */
  if(!glh->enable || !glh->buffer || glh->max_lines == 0)
    return NULL;
/*
 * Check the line dimensions.
 */
  if(dim < strlen(line) + 1) {
    _err_record_msg(glh->err, "'dim' argument inconsistent with strlen(line)",
		    END_ERR_MSG);
    errno = EINVAL;
    return NULL;
  };
/*
 * Preserve the input line if needed.
 */
  if(_glh_prepare_for_recall(glh, line))
    return NULL;
/*
 * From where should we start the search?
 */
  if(glh->recall) {
    node = glh->recall->prev;
    old_line = glh->recall->line;
  } else {
    node = glh->list.tail;
    old_line = NULL;
  };
/*
 * Search backwards through the list for the first match with the
 * prefix string that differs from the last line that was recalled.
 */
  while(node && (node->group != glh->group || node->line == old_line ||
	  !_glh_line_matches_prefix(node->line, glh->prefix)))
    node = node->prev;
/*
 * Was a matching line found?
 */
  if(node) {
/*
 * Recall the found node as the starting point for subsequent
 * searches.
 */
    glh->recall = node;
/*
 * Copy the matching line into the provided line buffer.
 */
    _glh_return_line(node->line, line, dim);
/*
 * Return it.
 */
    return line;
  };
/*
 * No match was found.
 */
  return NULL;
}

/*.......................................................................
 * Recall the next newest line that has the search prefix last recorded
 * by _glh_search_prefix().
 *
 * Input:
 *  glh  GlHistory *  The input-line history maintenance object.
 *  line      char *  The input line buffer. On input this should contain
 *                    the current input line, and on output, if anything
 *                    was found, its contents will have been replaced
 *                    with the matching line.
 *  dim     size_t    The allocated dimensions of the line buffer.
 * Output:
 *  return    char *  The line requested, or NULL if no matching line
 *                    was found.
 */
char *_glh_find_forwards(GlHistory *glh, char *line, size_t dim)
{
  GlhLineNode *node;     /* The line location node being checked */
  GlhHashNode *old_line; /* The previous recalled line */
/*
 * Check the arguments.
 */
  if(!glh || !line) {
    if(glh)
      _err_record_msg(glh->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return NULL;
  };
/*
 * Is history enabled?
 */
  if(!glh->enable || !glh->buffer || glh->max_lines == 0)
    return NULL;
/*
 * Check the line dimensions.
 */
  if(dim < strlen(line) + 1) {
    _err_record_msg(glh->err, "'dim' argument inconsistent with strlen(line)",
		    END_ERR_MSG);
    errno = EINVAL;
    return NULL;
  };
/*
 * From where should we start the search?
 */
  if(glh->recall) {
    node = glh->recall->next;
    old_line = glh->recall->line;
  } else {
    return NULL;
  };
/*
 * Search forwards through the list for the first match with the
 * prefix string.
 */
  while(node && (node->group != glh->group || node->line == old_line ||
	  !_glh_line_matches_prefix(node->line, glh->prefix)))
    node = node->next;
/*
 * Was a matching line found?
 */
  if(node) {
/*
 * Copy the matching line into the provided line buffer.
 */
    _glh_return_line(node->line, line, dim);
/*
 * Record the starting point of the next search.
 */
    glh->recall = node;
/*
 * If we just returned the line that was being entered when the search
 * session first started, cancel the search.
 */
    if(node == glh->list.tail)
      _glh_cancel_search(glh);
/*
 * Return the matching line to the user.
 */
    return line;
  };
/*
 * No match was found.
 */
  return NULL;
}

/*.......................................................................
 * If a search is in progress, cancel it.
 *
 * This involves discarding the line that was temporarily saved by
 * _glh_find_backwards() when the search was originally started,
 * and reseting the search iteration pointer to NULL.
 *
 * Input:
 *  glh  GlHistory *  The input-line history maintenance object.
 * Output:
 *  return     int    0 - OK.
 *                    1 - Error.
 */
int _glh_cancel_search(GlHistory *glh)
{
/*
 * Check the arguments.
 */
  if(!glh) {
    errno = EINVAL;
    return 1;
  };
/*
 * If there wasn't a search in progress, do nothing.
 */
  if(!glh->recall)
    return 0;
/*
 * Reset the search pointers. Note that it is essential to set
 * glh->recall to NULL before calling _glh_discard_line(), to avoid an
 * infinite recursion.
 */
  glh->recall = NULL;
/*
 * Delete the node of the preserved line.
 */
  _glh_discard_line(glh, glh->list.tail);
  return 0;
}

/*.......................................................................
 * Set the prefix of subsequent history searches.
 *
 * Input:
 *  glh    GlHistory *  The input-line history maintenance object.
 *  line  const char *  The command line who's prefix is to be used.
 *  prefix_len   int    The length of the prefix.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 */
int _glh_search_prefix(GlHistory *glh, const char *line, int prefix_len)
{
/*
 * Check the arguments.
 */
  if(!glh) {
    errno = EINVAL;
    return 1;
  };
/*
 * Is history enabled?
 */
  if(!glh->enable || !glh->buffer || glh->max_lines == 0)
    return 0;
/*
 * Discard any existing prefix.
 */
  glh->prefix = _glh_discard_copy(glh, glh->prefix);
/*
 * Only store a copy of the prefix string if it isn't a zero-length string.
 */
  if(prefix_len > 0) {
/*
 * Get a reference-counted copy of the prefix from the history cache buffer.
 */
    glh->prefix = _glh_acquire_copy(glh, line, prefix_len);
/*
 * Was there insufficient buffer space?
 */
    if(!glh->prefix) {
      _err_record_msg(glh->err, "The search prefix is too long to store",
		      END_ERR_MSG);
      errno = ENOMEM;
      return 1;
    };
  };
  return 0;
}

/*.......................................................................
 * Recall the oldest recorded line.
 *
 * Input:
 *  glh  GlHistory *  The input-line history maintenance object.
 *  line      char *  The input line buffer. On input this should contain
 *                    the current input line, and on output, its contents
 *                    will have been replaced with the oldest line.
 *  dim     size_t    The allocated dimensions of the line buffer.
 * Output:
 *  return    char *  A pointer to line[0], or NULL if not found.
 */
char *_glh_oldest_line(GlHistory *glh, char *line, size_t dim)
{
  GlhLineNode *node; /* The line location node being checked */
/*
 * Check the arguments.
 */
  if(!glh || !line) {
    if(glh)
      _err_record_msg(glh->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return NULL;
  };
/*
 * Is history enabled?
 */
  if(!glh->enable || !glh->buffer || glh->max_lines == 0)
    return NULL;
/*
 * Check the line dimensions.
 */
  if(dim < strlen(line) + 1) {
    _err_record_msg(glh->err, "'dim' argument inconsistent with strlen(line)",
		    END_ERR_MSG);
    errno = EINVAL;
    return NULL;
  };
/*
 * Preserve the input line if needed.
 */
  if(_glh_prepare_for_recall(glh, line))
    return NULL;
/*
 * Locate the oldest line that belongs to the current group.
 */
  for(node=glh->list.head; node && node->group != glh->group; 
      node = node->next)
    ;
/*
 * No line found?
 */
  if(!node)
    return NULL;
/*
 * Record the above node as the starting point for subsequent
 * searches.
 */
  glh->recall = node;
/*
 * Copy the recalled line into the provided line buffer.
 */
  _glh_return_line(node->line, line, dim);
/*
 * If we just returned the line that was being entered when the search
 * session first started, cancel the search.
 */
  if(node == glh->list.tail)
    _glh_cancel_search(glh);
  return line;
}

/*.......................................................................
 * Recall the line that was being entered when the search started.
 *
 * Input:
 *  glh  GlHistory *  The input-line history maintenance object.
 *  line      char *  The input line buffer. On input this should contain
 *                    the current input line, and on output, its contents
 *                    will have been replaced with the line that was
 *                    being entered when the search was started.
 *  dim     size_t    The allocated dimensions of the line buffer.
 * Output:
 *  return    char *  A pointer to line[0], or NULL if not found.
 */
char *_glh_current_line(GlHistory *glh, char *line, size_t dim)
{
/*
 * Check the arguments.
 */
  if(!glh || !line) {
    if(glh)
      _err_record_msg(glh->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return NULL;
  };
/*
 * If history isn't enabled, or no history search has yet been started,
 * ignore the call.
 */
  if(!glh->enable || !glh->buffer || glh->max_lines == 0 || !glh->recall)
    return NULL;
/*
 * Check the line dimensions.
 */
  if(dim < strlen(line) + 1) {
    _err_record_msg(glh->err, "'dim' argument inconsistent with strlen(line)",
		    END_ERR_MSG);
    errno = EINVAL;
    return NULL;
  };
/*
 * Copy the recalled line into the provided line buffer.
 */
  _glh_return_line(glh->list.tail->line, line, dim);
/*
 * Since we have returned to the starting point of the search, cancel it.
 */
  _glh_cancel_search(glh);
  return line;
}

/*.......................................................................
 * Query the id of a history line offset by a given number of lines from
 * the one that is currently being recalled. If a recall session isn't
 * in progress, or the offset points outside the history list, 0 is
 * returned.
 *
 * Input:
 *  glh    GlHistory *  The input-line history maintenance object.
 *  offset       int    The line offset (0 for the current line, < 0
 *                      for an older line, > 0 for a newer line.
 * Output:
 *  return GlhLineID    The identifier of the line that is currently
 *                      being recalled, or 0 if no recall session is
 *                      currently in progress.
 */
GlhLineID _glh_line_id(GlHistory *glh, int offset)
{
  GlhLineNode *node; /* The line location node being checked */
/*
 * Is history enabled?
 */
  if(!glh->enable || !glh->buffer || glh->max_lines == 0)
    return 0;
/*
 * Search forward 'offset' lines to find the required line.
 */
  if(offset >= 0) {
    for(node=glh->recall; node && offset != 0; node=node->next) {
      if(node->group == glh->group)
	offset--;
    };
  } else {
    for(node=glh->recall; node && offset != 0; node=node->prev) {
      if(node->group == glh->group)
	offset++;
    };
  };
  return node ? node->id : 0;
}

/*.......................................................................
 * Recall a line by its history buffer ID. If the line is no longer
 * in the buffer, or the id is zero, NULL is returned.
 *
 * Input:
 *  glh  GlHistory *  The input-line history maintenance object.
 *  id   GlhLineID    The ID of the line to be returned.
 *  line      char *  The input line buffer. On input this should contain
 *                    the current input line, and on output, its contents
 *                    will have been replaced with the saved line.
 *  dim     size_t    The allocated dimensions of the line buffer.
 * Output:
 *  return    char *  A pointer to line[0], or NULL if not found.
 */
char *_glh_recall_line(GlHistory *glh, GlhLineID id, char *line, size_t dim)
{
  GlhLineNode *node; /* The line location node being checked */
/*
 * Is history enabled?
 */
  if(!glh->enable || !glh->buffer || glh->max_lines == 0)
    return NULL;
/*
 * Preserve the input line if needed.
 */
  if(_glh_prepare_for_recall(glh, line))
    return NULL;
/*
 * Search for the specified line.
 */
  node = _glh_find_id(glh, id);
/*
 * Not found?
 */
  if(!node || node->group != glh->group)
    return NULL;
/*
 * Record the node of the matching line as the starting point
 * for subsequent searches.
 */
  glh->recall = node;
/*
 * Copy the recalled line into the provided line buffer.
 */
  _glh_return_line(node->line, line, dim);
  return line;
}

/*.......................................................................
 * Save the current history in a specified file.
 *
 * Input:
 *  glh        GlHistory *  The input-line history maintenance object.
 *  filename  const char *  The name of the new file to record the
 *                          history in.
 *  comment   const char *  Extra information such as timestamps will
 *                          be recorded on a line started with this
 *                          string, the idea being that the file can
 *                          double as a command file. Specify "" if
 *                          you don't care.
 *  max_lines        int    The maximum number of lines to save, or -1
 *                          to save all of the lines in the history
 *                          list.
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error.
 */
int _glh_save_history(GlHistory *glh, const char *filename, const char *comment,
		      int max_lines)
{
#ifdef WITHOUT_FILE_SYSTEM
  _err_record_msg(glh->err, "Can't save history without filesystem access",
		  END_ERR_MSG);
  errno = EINVAL;
  return 1;
#else
  FILE *fp;          /* The output file */
  GlhLineNode *node; /* The line being saved */
  GlhLineNode *head; /* The head of the list of lines to be saved */
  GlhLineSeg *seg;   /* One segment of a line being saved */
/*
 * Check the arguments.
 */
  if(!glh || !filename || !comment) {
    if(glh)
      _err_record_msg(glh->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Attempt to open the specified file.
 */
  fp = fopen(filename, "w");
  if(!fp)
    return _glh_cant_save_history(glh, "Can't open", filename, NULL);
/*
 * If a ceiling on the number of lines to save was specified, count
 * that number of lines backwards, to find the first line to be saved.
 */
  head = NULL;
  if(max_lines >= 0) {
    for(head=glh->list.tail; head && --max_lines > 0; head=head->prev)
      ;
  };
  if(!head)
    head = glh->list.head;
/*
 * Write the contents of the history buffer to the history file, writing
 * associated data such as timestamps, to a line starting with the
 * specified comment string.
 */
  for(node=head; node; node=node->next) {
/*
 * Write peripheral information associated with the line, as a comment.
 */
    if(fprintf(fp, "%s ", comment) < 0 ||
       _glh_write_timestamp(fp, node->timestamp) ||
       fprintf(fp, " %u\n", node->group) < 0) {
      return _glh_cant_save_history(glh, "Error writing", filename, fp);
    };
/*
 * Write the history line.
 */
    for(seg=node->line->head; seg; seg=seg->next) {
      size_t slen = seg->next ? GLH_SEG_SIZE : strlen(seg->s);
      if(fwrite(seg->s, sizeof(char), slen, fp) != slen)
	return _glh_cant_save_history(glh, "Error writing", filename, fp);
    };
    fputc('\n', fp);
  };
/*
 * Close the history file.
 */
  if(fclose(fp) == EOF)
    return _glh_cant_save_history(glh, "Error writing", filename, NULL);
  return 0;
#endif
}

#ifndef WITHOUT_FILE_SYSTEM
/*.......................................................................
 * This is a private error return function of _glh_save_history(). It
 * composes an error report in the error buffer, composed using
 * sprintf("%s %s (%s)", message, filename, strerror(errno)). It then
 * closes fp and returns the error return code of _glh_save_history().
 *
 * Input:
 *  glh        GlHistory *  The input-line history maintenance object.
 *  message   const char *  A message to be followed by the filename.
 *  filename  const char *  The name of the offending output file.
 *  fp              FILE *  The stream to be closed (send NULL if not
 *                          open).
 * Output:
 *  return           int    Always 1.
 */
static int _glh_cant_save_history(GlHistory *glh, const char *message,
				  const char *filename, FILE *fp)
{
  _err_record_msg(glh->err, message, filename, " (",
		     strerror(errno), ")", END_ERR_MSG);
  if(fp)
    (void) fclose(fp);
  return 1;
}

/*.......................................................................
 * Write a timestamp to a given stdio stream, in the format
 * yyyymmddhhmmss
 *
 * Input:
 *  fp             FILE *  The stream to write to.
 *  timestamp    time_t    The timestamp to be written.
 * Output:
 *  return          int    0 - OK.
 *                         1 - Error.
 */
static int _glh_write_timestamp(FILE *fp, time_t timestamp)
{
  struct tm *t;  /* THe broken-down calendar time */
/*
 * Get the calendar components corresponding to the given timestamp.
 */
  if(timestamp < 0 || (t = localtime(×tamp)) == NULL) {
    if(fprintf(fp, "?") < 0)
      return 1;
    return 0;
  };
/*
 * Write the calendar time as yyyymmddhhmmss.
 */
  if(fprintf(fp, "%04d%02d%02d%02d%02d%02d", t->tm_year + 1900, t->tm_mon + 1,
	     t->tm_mday, t->tm_hour, t->tm_min, t->tm_sec) < 0)
    return 1;
  return 0;
}

#endif

/*.......................................................................
 * Restore previous history lines from a given file.
 *
 * Input:
 *  glh        GlHistory *  The input-line history maintenance object.
 *  filename  const char *  The name of the file to read from.
 *  comment   const char *  The same comment string that was passed to
 *                          _glh_save_history() when this file was
 *                          written.
 *  line            char *  A buffer into which lines can be read.
 *  dim            size_t   The allocated dimension of line[].
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error.
 */
int _glh_load_history(GlHistory *glh, const char *filename, const char *comment,
		      char *line, size_t dim)
{
#ifdef WITHOUT_FILE_SYSTEM
  _err_record_msg(glh->err, "Can't load history without filesystem access",
		  END_ERR_MSG);
  errno = EINVAL;
  return 1;
#else
  FILE *fp;            /* The output file */
  size_t comment_len;  /* The length of the comment string */
  time_t timestamp;    /* The timestamp of the history line */
  unsigned group;      /* The identifier of the history group to which */
                       /*  the line belongs. */
  int lineno;          /* The line number being read */
/*
 * Check the arguments.
 */
  if(!glh || !filename || !comment || !line) {
    if(glh)
      _err_record_msg(glh->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Measure the length of the comment string.
 */
  comment_len = strlen(comment);
/*
 * Clear the history list.
 */
  _glh_clear_history(glh, 1);
/*
 * Attempt to open the specified file. Don't treat it as an error
 * if the file doesn't exist.
 */
  fp = fopen(filename, "r");
  if(!fp)
    return 0;
/*
 * Attempt to read each line and preceding peripheral info, and add these
 * to the history list.
 */
  for(lineno=1; fgets(line, dim, fp) != NULL; lineno++) {
    char *lptr;          /* A pointer into the input line */
/*
 * Check that the line starts with the comment string.
 */
    if(strncmp(line, comment, comment_len) != 0) {
      return _glh_cant_load_history(glh, filename, lineno,
				    "Corrupt history parameter line", fp);
    };
/*
 * Skip spaces and tabs after the comment.
 */
    for(lptr=line+comment_len; *lptr && (*lptr==' ' || *lptr=='\t'); lptr++)
      ;
/*
 * The next word must be a timestamp.
 */
    if(_glh_decode_timestamp(lptr, &lptr, ×tamp)) {
      return _glh_cant_load_history(glh, filename, lineno,
				    "Corrupt timestamp", fp);
    };
/*
 * Skip spaces and tabs.
 */
    while(*lptr==' ' || *lptr=='\t')
      lptr++;
/*
 * The next word must be an unsigned integer group number.
 */
    group = (int) strtoul(lptr, &lptr, 10);
    if(*lptr != ' ' && *lptr != '\n') {
      return _glh_cant_load_history(glh, filename, lineno,
				    "Corrupt group id", fp);
    };
/*
 * Skip spaces and tabs.
 */
    while(*lptr==' ' || *lptr=='\t')
      lptr++;
/*
 * There shouldn't be anything left on the line.
 */
    if(*lptr != '\n') {
      return _glh_cant_load_history(glh, filename, lineno,
				    "Corrupt parameter line", fp);
    };
/*
 * Now read the history line itself.
 */
    lineno++;
    if(fgets(line, dim, fp) == NULL)
      return _glh_cant_load_history(glh, filename, lineno, "Read error", fp);
/*
 * Append the line to the history buffer.
 */
    if(_glh_add_history(glh, line, 1)) {
      return _glh_cant_load_history(glh, filename, lineno,
				    "Insufficient memory to record line", fp);
    };
/*
 * Record the group and timestamp information along with the line.
 */
    if(glh->list.tail) {
      glh->list.tail->timestamp = timestamp;
      glh->list.tail->group = group;
    };
  };
/*
 * Close the file.
 */
  (void) fclose(fp);
  return 0;
#endif
}

#ifndef WITHOUT_FILE_SYSTEM
/*.......................................................................
 * This is a private error return function of _glh_load_history().
 */
static int _glh_cant_load_history(GlHistory *glh, const char *filename,
				  int lineno, const char *message, FILE *fp)
{
  char lnum[20];
/*
 * Convert the line number to a string.
 */
  sprintf(lnum, "%d", lineno);
/*
 * Render an error message.
 */
  _err_record_msg(glh->err, filename, ":", lnum, ":", message, END_ERR_MSG);
/*
 * Close the file.
 */
  if(fp)
    (void) fclose(fp);
  return 1;
}

/*.......................................................................
 * Read a timestamp from a string.
 *
 * Input:
 *  string    char *  The string to read from.
 * Input/Output:
 *  endp        char ** On output *endp will point to the next unprocessed
 *                      character in string[].
 *  timestamp time_t *  The timestamp will be assigned to *t.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Error.
 */
static int _glh_decode_timestamp(char *string, char **endp, time_t *timestamp)
{
  unsigned year,month,day,hour,min,sec;  /* Calendar time components */
  struct tm t;
/*
 * There are 14 characters in the date format yyyymmddhhmmss.
 */
  enum {TSLEN=14};                    
  char timestr[TSLEN+1];   /* The timestamp part of the string */
/*
 * If the time wasn't available at the time that the line was recorded
 * it will have been written as "?". Check for this before trying
 * to read the timestamp.
 */
  if(string[0] == '\?') {
    *endp = string+1;
    *timestamp = -1;
    return 0;
  };
/*
 * The timestamp is expected to be written in the form yyyymmddhhmmss.
 */
  if(strlen(string) < TSLEN) {
    *endp = string;
    return 1;
  };
/*
 * Copy the timestamp out of the string.
 */
  strncpy(timestr, string, TSLEN);
  timestr[TSLEN] = '\0';
/*
 * Decode the timestamp.
 */
  if(sscanf(timestr, "%4u%2u%2u%2u%2u%2u", &year, &month, &day, &hour, &min,
	    &sec) != 6) {
    *endp = string;
    return 1;
  };
/*
 * Advance the string pointer over the successfully read timestamp.
 */
  *endp = string + TSLEN;
/*
 * Copy the read values into a struct tm.
 */
  t.tm_sec = sec;
  t.tm_min = min;
  t.tm_hour = hour;
  t.tm_mday = day;
  t.tm_wday = 0;
  t.tm_yday = 0;
  t.tm_mon = month - 1;
  t.tm_year = year - 1900;
  t.tm_isdst = -1;
/*
 * Convert the contents of the struct tm to a time_t.
 */
  *timestamp = mktime(&t);
  return 0;
}
#endif

/*.......................................................................
 * Switch history groups.
 *
 * Input:
 *  glh        GlHistory *  The input-line history maintenance object.
 *  group       unsigned    The new group identifier. This will be recorded
 *                          with subsequent history lines, and subsequent
 *                          history searches will only return lines with
 *                          this group identifier. This allows multiple
 *                          separate history lists to exist within
 *                          a single GlHistory object. Note that the
 *                          default group identifier is 0.
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error.
 */
int _glh_set_group(GlHistory *glh, unsigned group)
{
/*
 * Check the arguments.
 */
  if(!glh) {
    if(glh)
      _err_record_msg(glh->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Is the group being changed?
 */
  if(group != glh->group) {
/*
 * Cancel any ongoing search.
 */
    if(_glh_cancel_search(glh))
      return 1;
/*
 * Record the new group.
 */
    glh->group = group;
  };
  return 0;
}

/*.......................................................................
 * Query the current history group.
 *
 * Input:
 *  glh        GlHistory *  The input-line history maintenance object.
 * Output:
 *  return      unsigned    The group identifier.    
 */
int _glh_get_group(GlHistory *glh)
{
  return glh ? glh->group : 0;
}

/*.......................................................................
 * Display the contents of the history list.
 *
 * Input:
 *  glh       GlHistory *  The input-line history maintenance object.
 *  write_fn  GlWriteFn *  The function to call to write the line, or
 *                         0 to discard the output.
 *  data           void *  Anonymous data to pass to write_fn().
 *  fmt      const char *  A format string. This can contain arbitrary
 *                         characters, which are written verbatim, plus
 *                         any of the following format directives:
 *                          %D  -  The date, like 2001-11-20
 *                          %T  -  The time of day, like 23:59:59
 *                          %N  -  The sequential entry number of the
 *                                 line in the history buffer.
 *                          %G  -  The history group number of the line.
 *                          %%  -  A literal % character.
 *                          %H  -  The history line.
 *  all_groups      int    If true, display history lines from all
 *                         history groups. Otherwise only display
 *                         those of the current history group.
 *  max_lines       int    If max_lines is < 0, all available lines
 *                         are displayed. Otherwise only the most
 *                         recent max_lines lines will be displayed.
 * Output:
 *  return          int    0 - OK.
 *                         1 - Error.
 */
int _glh_show_history(GlHistory *glh, GlWriteFn *write_fn, void *data,
		      const char *fmt, int all_groups, int max_lines)
{
  GlhLineNode *node;     /* The line being displayed */
  GlhLineNode *oldest;   /* The oldest line to display */
  GlhLineSeg *seg;       /* One segment of a line being displayed */
  enum {TSMAX=32};       /* The maximum length of the date and time string */
  char buffer[TSMAX+1];  /* The buffer in which to write the date and time */
  int idlen;             /* The length of displayed ID strings */
  unsigned grpmax;       /* The maximum group number in the buffer */
  int grplen;            /* The number of characters needed to print grpmax */
  int len;               /* The length of a string to be written */
/*
 * Check the arguments.
 */
  if(!glh || !write_fn || !fmt) {
    if(glh)
      _err_record_msg(glh->err, "NULL argument(s)", END_ERR_MSG);
    errno = EINVAL;
    return 1;
  };
/*
 * Is history enabled?
 */
  if(!glh->enable || !glh->list.head)
    return 0;
/*
 * Work out the length to display ID numbers, choosing the length of
 * the biggest number in the buffer. Smaller numbers will be padded 
 * with leading zeroes if needed.
 */
  sprintf(buffer, "%lu", (unsigned long) glh->list.tail->id);
  idlen = strlen(buffer);
/*
 * Find the largest group number.
 */
  grpmax = 0;
  for(node=glh->list.head; node; node=node->next) {
    if(node->group > grpmax)
      grpmax = node->group;
  };
/*
 * Find out how many characters are needed to display the group number.
 */
  sprintf(buffer, "%u", (unsigned) grpmax);
  grplen = strlen(buffer);
/*
 * Find the node that follows the oldest line to be displayed.
 */
  if(max_lines < 0) {
    oldest = glh->list.head;
  } else if(max_lines==0) {
    return 0;
  } else {
    for(oldest=glh->list.tail; oldest; oldest=oldest->prev) {
      if((all_groups || oldest->group == glh->group) && --max_lines <= 0)
	break;
    };
/*
 * If the number of lines in the buffer doesn't exceed the specified
 * maximum, start from the oldest line in the buffer.
 */
    if(!oldest)
      oldest = glh->list.head;
  };
/*
 * List the history lines in increasing time order.
 */
  for(node=oldest; node; node=node->next) {
/*
 * Only display lines from the current history group, unless
 * told otherwise.
 */
    if(all_groups || node->group == glh->group) {
      const char *fptr;      /* A pointer into the format string */
      struct tm *t = NULL;   /* The broken time version of the timestamp */
/*
 * Work out the calendar representation of the node timestamp.
 */
      if(node->timestamp != (time_t) -1)
	t = localtime(&node->timestamp);
/*
 * Parse the format string.
 */
      fptr = fmt;
      while(*fptr) {
/*
 * Search for the start of the next format directive or the end of the string.
 */
	const char *start = fptr;
	while(*fptr && *fptr != '%')
	  fptr++;
/*
 * Display any literal characters that precede the located directive.
 */
	if(fptr > start) {
	  len = (int) (fptr - start);
	  if(write_fn(data, start, len) != len)
	    return 1;
	};
/*
 * Did we hit a new directive before the end of the line?
 */
	if(*fptr) {
/*
 * Obey the directive. Ignore unknown directives.
 */
	  switch(*++fptr) {
	  case 'D':          /* Display the date */
	    if(t && strftime(buffer, TSMAX, "%Y-%m-%d", t) != 0) {
	      len = strlen(buffer);
	      if(write_fn(data, buffer, len) != len)
		return 1;
	    };
	    break;
	  case 'T':          /* Display the time of day */
	    if(t && strftime(buffer, TSMAX, "%H:%M:%S", t) != 0) {
	      len = strlen(buffer);
	      if(write_fn(data, buffer, len) != len)
		return 1;
	    };
	    break;
	  case 'N':          /* Display the sequential entry number */
	    sprintf(buffer, "%*lu", idlen, (unsigned long) node->id);
	    len = strlen(buffer);
	    if(write_fn(data, buffer, len) != len)
	      return 1;
	    break;
	  case 'G':
	    sprintf(buffer, "%*u", grplen, (unsigned) node->group);
	    len = strlen(buffer);
	    if(write_fn(data, buffer, len) != len)
	      return 1;
	    break;
	  case 'H':          /* Display the history line */
	    for(seg=node->line->head; seg; seg=seg->next) {
	      len = seg->next ? GLH_SEG_SIZE : strlen(seg->s);
	      if(write_fn(data, seg->s, len) != len)
		return 1;
	    };
	    break;
	  case '%':          /* A literal % symbol */
	    if(write_fn(data, "%", 1) != 1)
	      return 1;
	    break;
	  };
/*
 * Skip the directive.
 */
	  if(*fptr)
	    fptr++;
	};
      };
    };
  };
  return 0;
}

/*.......................................................................
 * Change the size of the history buffer.
 *
 * Input:
 *  glh    GlHistory *  The input-line history maintenance object.
 *  bufsize   size_t    The number of bytes in the history buffer, or 0
 *                      to delete the buffer completely.
 * Output:
 *  return       int    0 - OK.
 *                      1 - Insufficient memory (the previous buffer
 *                          will have been retained). No error message
 *                          will be displayed.
 */
int _glh_resize_history(GlHistory *glh, size_t bufsize)
{
  int nbuff;     /* The number of segments in the new buffer */
  int i;
/*
 * Check the arguments.
 */
  if(!glh) {
    errno = EINVAL;
    return 1;
  };
/*
 * How many buffer segments does the requested buffer size correspond
 * to?
 */
  nbuff = (bufsize+GLH_SEG_SIZE-1) / GLH_SEG_SIZE;
/*
 * Has a different size than the current size been requested?
 */
  if(glh->nbuff != nbuff) {
/*
 * Cancel any ongoing search.
 */
    (void) _glh_cancel_search(glh);
/*
 * Create a wholly new buffer?
 */
    if(glh->nbuff == 0 && nbuff>0) {
      glh->buffer = (GlhLineSeg *) malloc(sizeof(GlhLineSeg) * nbuff);
      if(!glh->buffer)
	return 1;
      glh->nbuff = nbuff;
      glh->nfree = glh->nbuff;
      glh->nbusy = 0;
      glh->nline = 0;
/*
 * Link the currently unused nodes of the buffer into a list.
 */
      glh->unused = glh->buffer;
      for(i=0; inbuff-1; i++) {
	GlhLineSeg *seg = glh->unused + i;
	seg->next = seg + 1;
      };
      glh->unused[i].next = NULL;
/*
 * Delete an existing buffer?
 */
    } else if(nbuff == 0) {
      _glh_clear_history(glh, 1);
      free(glh->buffer);
      glh->buffer = NULL;
      glh->unused = NULL;
      glh->nbuff = 0;
      glh->nfree = 0;
      glh->nbusy = 0;
      glh->nline = 0;
/*
 * Change from one finite buffer size to another?
 */
    } else {
      GlhLineSeg *buffer; /* The resized buffer */
      int nbusy;      /* The number of used line segments in the new buffer */
/*
 * Starting from the oldest line in the buffer, discard lines until
 * the buffer contains at most 'nbuff' used line segments.
 */
      while(glh->list.head && glh->nbusy > nbuff)
	_glh_discard_line(glh, glh->list.head);
/*
 * Attempt to allocate a new buffer.
 */
      buffer = (GlhLineSeg *) malloc(nbuff * sizeof(GlhLineSeg));
      if(!buffer) {
	errno = ENOMEM;
	return 1;
      };
/*
 * Copy the used segments of the old buffer to the start of the new buffer.
 */
      nbusy = 0;
      for(i=0; ihash.bucket + i;
	GlhHashNode *hnode;
	for(hnode=b->lines; hnode; hnode=hnode->next) {
	  GlhLineSeg *seg = hnode->head;
	  hnode->head = buffer + nbusy;
	  for( ; seg; seg=seg->next) {
	    buffer[nbusy] = *seg;
	    buffer[nbusy].next = seg->next ? &buffer[nbusy+1] : NULL;
	    nbusy++;
	  };
	};
      };
/*
 * Make a list of the new buffer's unused segments.
 */
      for(i=nbusy; ibuffer);
/*
 * Install the new buffer.
 */
      glh->buffer = buffer;
      glh->nbuff = nbuff;
      glh->nbusy = nbusy;
      glh->nfree = nbuff - nbusy;
      glh->unused = glh->nfree > 0 ? (buffer + nbusy) : NULL;
    };
  };
  return 0;
}

/*.......................................................................
 * Set an upper limit to the number of lines that can be recorded in the
 * history list, or remove a previously specified limit.
 *
 * Input:
 *  glh    GlHistory *  The input-line history maintenance object.
 *  max_lines    int    The maximum number of lines to allow, or -1 to
 *                      cancel a previous limit and allow as many lines
 *                      as will fit in the current history buffer size.
 */
void _glh_limit_history(GlHistory *glh, int max_lines)
{
  if(!glh)
    return;
/*
 * Apply a new limit?
 */
  if(max_lines >= 0 && max_lines != glh->max_lines) {
/*
 * Count successively older lines until we reach the start of the
 * list, or until we have seen max_lines lines (at which point 'node'
 * will be line number max_lines+1).
 */
    int nline = 0;
    GlhLineNode *node;
    for(node=glh->list.tail; node && ++nline <= max_lines; node=node->prev)
      ;
/*
 * Discard any lines that exceed the limit.
 */
    if(node) {
      GlhLineNode *oldest = node->next;  /* The oldest line to be kept */
/*
 * Delete nodes from the head of the list until we reach the node that
 * is to be kept.
 */
      while(glh->list.head && glh->list.head != oldest)
	_glh_discard_line(glh, glh->list.head);
    };
  };
/*
 * Record the new limit.
 */
  glh->max_lines = max_lines;
  return;
}

/*.......................................................................
 * Discard either all history, or the history associated with the current
 * history group.
 *
 * Input:
 *  glh    GlHistory *  The input-line history maintenance object.
 *  all_groups   int    If true, clear all of the history. If false,
 *                      clear only the stored lines associated with the
 *                      currently selected history group.
 */
void _glh_clear_history(GlHistory *glh, int all_groups)
{
  int i;
/*
 * Check the arguments.
 */
  if(!glh)
    return;
/*
 * Cancel any ongoing search.
 */
  (void) _glh_cancel_search(glh);
/*
 * Delete all history lines regardless of group?
 */
  if(all_groups) {
/*
 * Claer the time-ordered list of lines.
 */
    _rst_FreeList(glh->list.node_mem);
    glh->list.head = glh->list.tail = NULL;
    glh->nline = 0;
    glh->id_node = NULL;
/*
 * Clear the hash table.
 */
    for(i=0; ihash.bucket[i].lines = NULL;
    _rst_FreeList(glh->hash.node_mem);
/*
 * Move all line segment nodes back onto the list of unused segments.
 */
    if(glh->buffer) {
      glh->unused = glh->buffer;
      for(i=0; inbuff-1; i++) {
	GlhLineSeg *seg = glh->unused + i;
	seg->next = seg + 1;
      };
      glh->unused[i].next = NULL;
      glh->nfree = glh->nbuff;
      glh->nbusy = 0;
    } else {
      glh->unused = NULL;
      glh->nbusy = glh->nfree = 0;
    };
/*
 * Just delete lines of the current group?
 */
  } else {
    GlhLineNode *node;  /* The line node being checked */
    GlhLineNode *next;  /* The line node that follows 'node' */
/*
 * Search out and delete the line nodes of the current group.
 */
    for(node=glh->list.head; node; node=next) {
/*
 * Keep a record of the following node before we delete the current
 * node.
 */
      next = node->next;
/*
 * Discard this node?
 */
      if(node->group == glh->group)
	_glh_discard_line(glh, node);
    };
  };
  return;
}

/*.......................................................................
 * Temporarily enable or disable the history list.
 *
 * Input:
 *  glh    GlHistory *  The input-line history maintenance object.
 *  enable       int    If true, turn on the history mechanism. If
 *                      false, disable it.
 */
void _glh_toggle_history(GlHistory *glh, int enable)
{
  if(glh)
    glh->enable = enable;
}

/*.......................................................................
 * Discard a given archived input line.
 *
 * Input:
 *  glh      GlHistory *  The history container object.
 *  node   GlhLineNode *  The line to be discarded, specified via its
 *                        entry in the time-ordered list of historical
 *                        input lines.
 */
static void _glh_discard_line(GlHistory *glh, GlhLineNode *node)
{
/*
 * Remove the node from the linked list.
 */
  if(node->prev)
    node->prev->next = node->next;
  else
    glh->list.head = node->next;
  if(node->next)
    node->next->prev = node->prev;
  else
    glh->list.tail = node->prev;
/*
 * If we are deleting the node that is marked as the start point of the
 * last ID search, remove the cached starting point.
 */
  if(node == glh->id_node)
    glh->id_node = NULL;
/*
 * If we are deleting the node that is marked as the start point of the
 * next prefix search, cancel the search.
 */
  if(node == glh->recall)
    _glh_cancel_search(glh);
/*
 * Delete our copy of the line.
 */
  node->line = _glh_discard_copy(glh, node->line);
/*
 * Return the node to the freelist.
 */
  (void) _del_FreeListNode(glh->list.node_mem, node);
/*
 * Record the removal of a line from the list.
 */
  glh->nline--;
  return;
}

/*.......................................................................
 * Lookup the details of a given history line, given its id.
 *
 * Input:
 *  glh      GlHistory *  The input-line history maintenance object.
 *  id        GlLineID    The sequential number of the line.
 * Input/Output:
 *  line    const char ** A pointer to a copy of the history line will be
 *                        assigned to *line. Beware that this pointer may
 *                        be invalidated by the next call to any public
 *                        history function.
 *  group     unsigned *  The group membership of the line will be assigned
 *                        to *group.
 *  timestamp   time_t *  The timestamp of the line will be assigned to
 *                        *timestamp.
 * Output:
 *  return         int    0 - The requested line wasn't found.
 *                        1 - The line was found.
 */
int _glh_lookup_history(GlHistory *glh, GlhLineID id, const char **line,
			unsigned *group, time_t *timestamp)
{
  GlhLineNode *node; /* The located line location node */
/*
 * Check the arguments.
 */
  if(!glh)
    return 0;
/*
 * Search for the line that has the specified ID.
 */
  node = _glh_find_id(glh, id);
/*
 * Not found?
 */
  if(!node)
    return 0;
/*
 * Has the history line been requested?
 */
  if(line) {
/*
 * If necessary, reallocate the lookup buffer to accomodate the size of
 * a copy of the located line.
 */
    if(node->line->len + 1 > glh->lbuf_dim) {
      int lbuf_dim = node->line->len + 1;
      char *lbuf = realloc(glh->lbuf, lbuf_dim);
      if(!lbuf) {
	errno = ENOMEM;
	return 0;
      };
      glh->lbuf_dim = lbuf_dim;
      glh->lbuf = lbuf;
    };
/*
 * Copy the history line into the lookup buffer.
 */
    _glh_return_line(node->line, glh->lbuf, glh->lbuf_dim);
/*
 * Assign the lookup buffer as the returned line pointer.
 */
    *line = glh->lbuf;
  };    
/*
 * Does the caller want to know the group of the line?
 */
  if(group)
    *group = node->group;
/*
 * Does the caller want to know the timestamp of the line?
 */
  if(timestamp)
    *timestamp = node->timestamp;
  return 1;
}

/*.......................................................................
 * Lookup a node in the history list by its ID.
 *
 * Input:
 *  glh       GlHistory *  The input-line history maintenance object.
 *  id        GlhLineID    The ID of the line to be returned.
 * Output:
 *  return  GlhLIneNode *  The located node, or NULL if not found.
 */
static GlhLineNode *_glh_find_id(GlHistory *glh, GlhLineID id)
{
  GlhLineNode *node;  /* The node being checked */
/*
 * Is history enabled?
 */
  if(!glh->enable || !glh->list.head)
    return NULL;
/*
 * If possible, start at the end point of the last ID search.
 * Otherwise start from the head of the list.
 */
  node = glh->id_node;
  if(!node)
    node = glh->list.head;
/*
 * Search forwards from 'node'?
 */
  if(node->id < id) {
    while(node && node->id != id)
      node = node->next;
    glh->id_node = node ? node : glh->list.tail;
/*
 * Search backwards from 'node'?
 */
  } else {
    while(node && node->id != id)
      node = node->prev;
    glh->id_node = node ? node : glh->list.head;
  };
/*
 * Return the located node (this will be NULL if the ID wasn't found).
 */
  return node;
}

/*.......................................................................
 * Query the state of the history list. Note that any of the input/output
 * pointers can be specified as NULL.
 *
 * Input:
 *  glh         GlHistory *  The input-line history maintenance object.
 * Input/Output:
 *  enabled           int *  If history is enabled, *enabled will be
 *                           set to 1. Otherwise it will be assigned 0.
 *  group        unsigned *  The current history group ID will be assigned
 *                           to *group.
 *  max_lines         int *  The currently requested limit on the number
 *                           of history lines in the list, or -1 if
 *                           unlimited.
 */
void _glh_state_of_history(GlHistory *glh, int *enabled, unsigned *group,
			   int *max_lines)
{
  if(glh) {
    if(enabled)
     *enabled = glh->enable;
    if(group)
     *group = glh->group;
    if(max_lines)
     *max_lines = glh->max_lines;
  };
}

/*.......................................................................
 * Get the range of lines in the history buffer.
 *
 * Input:
 *  glh         GlHistory *  The input-line history maintenance object.
 * Input/Output:
 *  oldest  unsigned long *  The sequential entry number of the oldest
 *                           line in the history list will be assigned
 *                           to *oldest, unless there are no lines, in
 *                           which case 0 will be assigned.
 *  newest  unsigned long *  The sequential entry number of the newest
 *                           line in the history list will be assigned
 *                           to *newest, unless there are no lines, in
 *                           which case 0 will be assigned.
 *  nlines            int *  The number of lines currently in the history
 *                           list.
 */
void _glh_range_of_history(GlHistory *glh, unsigned long *oldest,
			   unsigned long *newest, int *nlines)
{
  if(glh) {
    if(oldest)
      *oldest = glh->list.head ? glh->list.head->id : 0;
    if(newest)
      *newest = glh->list.tail ? glh->list.tail->id : 0;
    if(nlines)
      *nlines = glh->nline;
  };
}

/*.......................................................................
 * Return the size of the history buffer and the amount of the
 * buffer that is currently in use.
 *
 * Input:
 *  glh      GlHistory *  The input-line history maintenance object.
 * Input/Output:
 *  buff_size   size_t *  The size of the history buffer (bytes).
 *  buff_used   size_t *  The amount of the history buffer that
 *                        is currently occupied (bytes).
 */
void _glh_size_of_history(GlHistory *glh, size_t *buff_size, size_t *buff_used)
{
  if(glh) {
    if(buff_size)
      *buff_size = (glh->nbusy + glh->nfree) * GLH_SEG_SIZE;
/*
 * Determine the amount of buffer space that is currently occupied.
 */
    if(buff_used)
      *buff_used = glh->nbusy * GLH_SEG_SIZE;
  };
}

/*.......................................................................
 * Return extra information (ie. in addition to that provided by errno)
 * about the last error to occur in any of the public functions of this
 * module.
 *
 * Input:
 *  glh      GlHistory *  The container of the history list.
 * Output:
 *  return  const char *  A pointer to the internal buffer in which
 *                        the error message is temporarily stored.
 */
const char *_glh_last_error(GlHistory *glh)
{
  return glh ? _err_get_msg(glh->err) : "NULL GlHistory argument";
}

/*.......................................................................
 * Unless already stored, store a copy of the line in the history buffer,
 * then return a reference-counted hash-node pointer to this copy.
 *
 * Input:
 *  glh       GlHistory *   The history maintenance buffer.
 *  line     const char *   The history line to be recorded.
 *  n            size_t     The length of the string, excluding any '\0'
 *                          terminator.
 * Output:
 *  return  GlhHashNode *   The hash-node containing the stored line, or
 *                          NULL on error.
 */
static GlhHashNode *_glh_acquire_copy(GlHistory *glh, const char *line,
				      size_t n)
{
  GlhHashBucket *bucket;   /* The hash-table bucket of the line */
  GlhHashNode *hnode;      /* The hash-table node of the line */
  int i;
/*
 * In which bucket should the line be recorded?
 */
  bucket = glh_find_bucket(glh, line, n);
/*
 * Is the line already recorded there?
 */
  hnode = glh_find_hash_node(bucket, line, n);
/*
 * If the line isn't recorded in the buffer yet, make room for it.
 */
  if(!hnode) {
    GlhLineSeg *seg;   /* A line segment */
    int offset;        /* An offset into line[] */
/*
 * How many string segments will be needed to record the new line,
 * including space for a '\0' terminator?
 */
    int nseg = ((n+1) + GLH_SEG_SIZE-1) /  GLH_SEG_SIZE;
/*
 * Discard the oldest history lines in the buffer until at least
 * 'nseg' segments have been freed up, or until we run out of buffer
 * space.
 */
    while(glh->nfree < nseg && glh->nbusy > 0)
      _glh_discard_line(glh, glh->list.head);
/*
 * If the buffer is smaller than the new line, don't attempt to truncate
 * it to fit. Simply don't archive it.
 */
    if(glh->nfree < nseg)
      return NULL;
/*
 * Record the line in the first 'nseg' segments of the list of unused segments.
 */
    offset = 0;
    for(i=0,seg=glh->unused; inext, offset+=GLH_SEG_SIZE)
      memcpy(seg->s, line + offset, GLH_SEG_SIZE);
    memcpy(seg->s, line + offset, n-offset);
    seg->s[n-offset] = '\0';
/*
 * Create a new hash-node for the line.
 */
    hnode = (GlhHashNode *) _new_FreeListNode(glh->hash.node_mem);
    if(!hnode)
      return NULL;
/*
 * Move the copy of the line from the list of unused segments to
 * the hash node.
 */
    hnode->head = glh->unused;
    glh->unused = seg->next;
    seg->next = NULL;
    glh->nbusy += nseg;
    glh->nfree -= nseg;
/*
 * Prepend the new hash node to the list within the associated bucket.
 */
    hnode->next = bucket->lines;
    bucket->lines = hnode;
/*
 * Initialize the rest of the members of the hash node.
 */
    hnode->len = n;
    hnode->reported = 0;
    hnode->used = 0;
    hnode->bucket = bucket;
  };
/*
 * Increment the reference count of the line.
 */
  hnode->used++;
  return hnode;
}

/*.......................................................................
 * Decrement the reference count of the history line of a given hash-node,
 * and if the count reaches zero, delete both the hash-node and the
 * buffered copy of the line.
 *
 * Input:
 *  glh      GlHistory *  The history container object.
 *  hnode  GlhHashNode *  The node to be removed.
 * Output:
 *  return GlhHashNode *  The deleted hash-node (ie. NULL).
 */
static GlhHashNode *_glh_discard_copy(GlHistory *glh, GlhHashNode *hnode)
{
  if(hnode) {
    GlhHashBucket *bucket = hnode->bucket;
/*
 * If decrementing the reference count of the hash-node doesn't reduce
 * the reference count to zero, then the line is still in use in another
 * object, so don't delete it yet. Return NULL to indicate that the caller's
 * access to the hash-node copy has been deleted.
 */
    if(--hnode->used >= 1)
      return NULL;
/*
 * Remove the hash-node from the list in its parent bucket.
 */
    if(bucket->lines == hnode) {
      bucket->lines = hnode->next;
    } else {
      GlhHashNode *prev;    /* The node which precedes hnode in the bucket */
      for(prev=bucket->lines; prev && prev->next != hnode; prev=prev->next)
	;
      if(prev)
	prev->next = hnode->next;
    };
    hnode->next = NULL;
/*
 * Return the line segments of the hash-node to the list of unused segments.
 */
    if(hnode->head) {
      GlhLineSeg *tail; /* The last node in the list of line segments */
      int nseg;         /* The number of segments being discarded */
/*
 * Get the last node of the list of line segments referenced in the hash-node,
 * while counting the number of line segments used.
 */
      for(nseg=1,tail=hnode->head; tail->next; nseg++,tail=tail->next)
	;
/*
 * Prepend the list of line segments used by the hash node to the
 * list of unused line segments.
 */
      tail->next = glh->unused;
      glh->unused = hnode->head;
      glh->nbusy -= nseg;
      glh->nfree += nseg;
    };
/*
 * Return the container of the hash-node to the freelist.
 */
    hnode = (GlhHashNode *) _del_FreeListNode(glh->hash.node_mem, hnode);
  };
  return NULL;
}

/*.......................................................................
 * Private function to locate the hash bucket associated with a given
 * history line.
 *
 * This uses a hash-function described in the dragon-book
 * ("Compilers - Principles, Techniques and Tools", by Aho, Sethi and
 *  Ullman; pub. Adison Wesley) page 435.
 *
 * Input:
 *  glh        GlHistory *   The history container object.
 *  line      const char *   The historical line to look up.
 *  n             size_t     The length of the line in line[], excluding
 *                           any '\0' terminator.
 * Output:
 *  return GlhHashBucket *   The located hash-bucket.
 */
static GlhHashBucket *glh_find_bucket(GlHistory *glh, const char *line,
				      size_t n)
{
  unsigned long h = 0L;
  int i;
  for(i=0; ihash.bucket + (h % GLH_HASH_SIZE);
}

/*.......................................................................
 * Find a given history line within a given hash-table bucket.
 *
 * Input:
 *  bucket  GlhHashBucket *  The hash-table bucket in which to search.
 *  line       const char *  The historical line to lookup.
 *  n             size_t     The length of the line in line[], excluding
 *                           any '\0' terminator.
 * Output:
 *  return    GlhHashNode *  The hash-table entry of the line, or NULL
 *                           if not found.
 */
static GlhHashNode *glh_find_hash_node(GlhHashBucket *bucket, const char *line,
				       size_t n)
{
  GlhHashNode *node;  /* A node in the list of lines in the bucket */
/*
 * Compare each of the lines in the list of lines, against 'line'.
 */
  for(node=bucket->lines; node; node=node->next) {
    if(_glh_is_line(node, line, n))
      return node;
  };
  return NULL;
}

/*.......................................................................
 * Return non-zero if a given string is equal to a given segmented line
 * node.
 *
 * Input:
 *  hash   GlhHashNode *   The hash-table entry of the line.
 *  line    const char *   The string to be compared to the segmented
 *                         line.
 *  n           size_t     The length of the line in line[], excluding
 *                         any '\0' terminator.
 * Output:
 *  return         int     0 - The lines differ.
 *                         1 - The lines are the same.
 */
static int _glh_is_line(GlhHashNode *hash, const char *line, size_t n)
{
  GlhLineSeg *seg;   /* A node in the list of line segments */
  int i;
/*
 * Do the two lines have the same length?
 */
  if(n != hash->len)
    return 0;
/*
 * Compare the characters of the segmented and unsegmented versions
 * of the line.
 */
  for(seg=hash->head; n>0 && seg; seg=seg->next) {
    const char *s = seg->s;
    for(i=0; n>0 && ilen > line->len)
    return 0;
/*
 * Compare the line to the prefix.
 */
  while(pstr.c != '\0' && pstr.c == lstr.c) {
    glh_step_stream(&lstr);
    glh_step_stream(&pstr);
  };
/*
 * Did we reach the end of the prefix string before finding
 * any differences?
 */
  return pstr.c == '\0';
}

/*.......................................................................
 * Copy a given history line into a specified output string.
 *
 * Input:
 *  hash  GlhHashNode    The hash-table entry of the history line to
 *                       be copied.
 *  line         char *  A copy of the history line.
 *  dim        size_t    The allocated dimension of the line buffer.
 */
static void _glh_return_line(GlhHashNode *hash, char *line, size_t dim)
{
  GlhLineSeg *seg;   /* A node in the list of line segments */
  int i;
  for(seg=hash->head; dim>0 && seg; seg=seg->next) {
    const char *s = seg->s;
    for(i=0; dim>0 && irecall && glh->recall == glh->list.tail &&
     !_glh_is_line(glh->recall->line, line, strlen(line))) {
    _glh_cancel_search(glh);
  };
/*
 * If this is the first line recall of a new recall session, save the
 * current line for potential recall later, and mark it as the last
 * line recalled.
 */
  if(!glh->recall) {
    if(_glh_add_history(glh, line, 1))
      return 1;
    glh->recall = glh->list.tail;
/*
 * The above call to _glh_add_history() will have incremented the line
 * sequence number, after adding the line. Since we only want this to
 * to be incremented for permanently entered lines, decrement it again.
 */
    glh->seq--;
  };
  return 0;
}

/*.......................................................................
 * Return non-zero if a history search session is currently in progress.
 *
 * Input:
 *  glh  GlHistory *  The input-line history maintenance object.
 * Output:
 *  return     int    0 - No search is currently in progress.
 *                    1 - A search is in progress.
 */
int _glh_search_active(GlHistory *glh)
{
  return glh && glh->recall;
}

/*.......................................................................
 * Initialize a character iterator object to point to the start of a
 * given history line. The first character of the line will be placed
 * in str->c, and subsequent characters can be placed there by calling
 * glh_strep_stream().
 *
 * Input:
 *  str  GlhLineStream *  The iterator object to be initialized.
 *  line   GlhHashNode *  The history line to be iterated over (a
 *                        NULL value here, is interpretted as an
 *                        empty string by glh_step_stream()).
 */
static void glh_init_stream(GlhLineStream *str, GlhHashNode *line)
{
  str->seg = line ? line->head : NULL;
  str->posn = 0;
  str->c = str->seg ? str->seg->s[0] : '\0';
}

/*.......................................................................
 * Copy the next unread character in the line being iterated, in str->c.
 * Once the end of the history line has been reached, all futher calls
 * set str->c to '\0'.
 *
 * Input:
 *  str   GlhLineStream *  The history-line iterator to read from.
 */
static void glh_step_stream(GlhLineStream *str)
{
/*
 * Get the character from the current iterator position within the line.
 */
  str->c = str->seg ? str->seg->s[str->posn] : '\0';
/*
 * Unless we have reached the end of the string, move the iterator
 * to the position of the next character in the line.
 */
  if(str->c != '\0' && ++str->posn >= GLH_SEG_SIZE) {
    str->posn = 0;
    str->seg = str->seg->next;
  };
}

/*.......................................................................
 * Return non-zero if the specified search prefix contains any glob
 * wildcard characters.
 *
 * Input:
 *  prefix   GlhHashNode *  The search prefix.
 * Output:
 *  return           int    0 - The prefix doesn't contain any globbing
 *                              characters.
 *                          1 - The prefix contains at least one
 *                              globbing character.
 */
static int glh_contains_glob(GlhHashNode *prefix)
{
  GlhLineStream pstr; /* The stream that is used to traverse 'prefix' */
/*
 * Wrap a stream iterator around the prefix, so that we can traverse it
 * without worrying about line-segmentation.
 */
  glh_init_stream(&pstr, prefix);
/*
 * Search for unescaped wildcard characters.
 */
  while(pstr.c != '\0') {
    switch(pstr.c) {
    case '\\':                      /* Skip escaped characters */
      glh_step_stream(&pstr);
      break; 
    case '*': case '?': case '[':   /* A wildcard character? */
      return 1;
      break;
    };
    glh_step_stream(&pstr);
  };
/*
 * No wildcard characters were found.
 */
  return 0;
}

/*.......................................................................
 * Return non-zero if the history line matches a search prefix containing
 * a glob pattern.
 *
 * Input:
 *  lstr  GlhLineStream *  The iterator stream being used to traverse
 *                         the history line that is being matched.
 *  pstr  GlhLineStream *  The iterator stream being used to traverse
 *                         the pattern.
 * Output:
 *  return    int          0 - Doesn't match.
 *                         1 - The line matches the pattern.
 */
static int glh_line_matches_glob(GlhLineStream *lstr, GlhLineStream *pstr)
{
/*
 * Match each character of the pattern until we reach the end of the
 * pattern.
 */
  while(pstr->c != '\0') {
/*
 * Handle the next character of the pattern.
 */
    switch(pstr->c) {
/*
 * A match zero-or-more characters wildcard operator.
 */
    case '*':
/*
 * Skip the '*' character in the pattern.
 */
      glh_step_stream(pstr);
/*
 * If the pattern ends with the '*' wildcard, then the
 * rest of the line matches this.
 */
      if(pstr->c == '\0')
	return 1;
/*
 * Using the wildcard to match successively longer sections of
 * the remaining characters of the line, attempt to match
 * the tail of the line against the tail of the pattern.
 */
      while(lstr->c) {
	GlhLineStream old_lstr = *lstr;
	GlhLineStream old_pstr = *pstr;
	if(glh_line_matches_glob(lstr, pstr))
	  return 1;
/*
 * Restore the line and pattern iterators for a new try.
 */
	*lstr = old_lstr;
	*pstr = old_pstr;
/*
 * Prepare to try again, one character further into the line.
 */
	glh_step_stream(lstr);
      };
      return 0; /* The pattern following the '*' didn't match */
      break;
/*
 * A match-one-character wildcard operator.
 */
    case '?':
/*
 * If there is a character to be matched, skip it and advance the
 * pattern pointer.
 */
      if(lstr->c) {
	glh_step_stream(lstr);
	glh_step_stream(pstr);
/*
 * If we hit the end of the line, there is no character
 * matching the operator, so the pattern doesn't match.
 */
      } else {
        return 0;
      };
      break;
/*
 * A character range operator, with the character ranges enclosed
 * in matching square brackets.
 */
    case '[':
      glh_step_stream(pstr);  /* Skip the '[' character */
      if(!lstr->c || !glh_matches_range(lstr->c, pstr))
        return 0;
      glh_step_stream(lstr);  /* Skip the character that matched */
      break;
/*
 * A backslash in the pattern prevents the following character as
 * being seen as a special character.
 */
    case '\\':
      glh_step_stream(pstr);  /* Skip the backslash */
      /* Note fallthrough to default */
/*
 * A normal character to be matched explicitly.
 */
    default:
      if(lstr->c == pstr->c) {
	glh_step_stream(lstr);
	glh_step_stream(pstr);
      } else {
        return 0;
      };
      break;
    };
  };
/*
 * To get here, pattern must have been exhausted. The line only
 * matches the pattern if the line as also been exhausted.
 */
  return pstr->c == '\0' && lstr->c == '\0';
}

/*.......................................................................
 * Match a character range expression terminated by an unescaped close
 * square bracket.
 *
 * Input:
 *  c              char    The character to be matched with the range
 *                         pattern.
 *  pstr  GlhLineStream *  The iterator stream being used to traverse
 *                         the pattern.
 * Output:
 *  return          int    0 - Doesn't match.
 *                         1 - The character matched.
 */
static int glh_matches_range(char c, GlhLineStream *pstr)
{
  int invert = 0;              /* True to invert the sense of the match */
  int matched = 0;             /* True if the character matched the pattern */
  char lastc = '\0';           /* The previous character in the pattern */
/*
 * If the first character is a caret, the sense of the match is
 * inverted and only if the character isn't one of those in the
 * range, do we say that it matches.
 */
  if(pstr->c == '^') {
    glh_step_stream(pstr);
    invert = 1;
  };
/*
 * The hyphen is only a special character when it follows the first
 * character of the range (not including the caret).
 */
  if(pstr->c == '-') {
    glh_step_stream(pstr);
    if(c == '-')
      matched = 1;
/*
 * Skip other leading '-' characters since they make no sense.
 */
    while(pstr->c == '-')
      glh_step_stream(pstr);
  };
/*
 * The hyphen is only a special character when it follows the first
 * character of the range (not including the caret or a hyphen).
 */
  if(pstr->c == ']') {
    glh_step_stream(pstr);
    if(c == ']')
      matched = 1;
  };
/*
 * Having dealt with the characters that have special meanings at
 * the beginning of a character range expression, see if the
 * character matches any of the remaining characters of the range,
 * up until a terminating ']' character is seen.
 */
  while(!matched && pstr->c && pstr->c != ']') {
/*
 * Is this a range of characters signaled by the two end characters
 * separated by a hyphen?
 */
    if(pstr->c == '-') {
      glh_step_stream(pstr);  /* Skip the hyphen */
      if(pstr->c != ']') {
        if(c >= lastc && c <= pstr->c)
	  matched = 1;
      };
/*
 * A normal character to be compared directly.
 */
    } else if(pstr->c == c) {
      matched = 1;
    };
/*
 * Record and skip the character that we just processed.
 */
    lastc = pstr->c;
    if(pstr->c != ']')
      glh_step_stream(pstr);
  };
/*
 * Find the terminating ']'.
 */
  while(pstr->c && pstr->c != ']')
    glh_step_stream(pstr);
/*
 * Did we find a terminating ']'?
 */
  if(pstr->c == ']') {
/*
 * Skip the terminating ']'.
 */
    glh_step_stream(pstr);
/*
 * If the pattern started with a caret, invert the sense of the match.
 */
    if(invert)
      matched = !matched;
/*
 * If the pattern didn't end with a ']', then it doesn't match,
 * regardless of the value of the required sense of the match.
 */
  } else {
    matched = 0;
  };
  return matched;
}

genometools-1.5.1/src/external/libtecla-1.6.1/history.h000066400000000000000000000126601211610345200225540ustar00rootroot00000000000000#ifndef history_h
#define history_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include     /* FILE * */

/*-----------------------------------------------------------------------
 * This module is used to record and traverse historical lines of user input.
 */

typedef struct GlHistory GlHistory;

/*
 * Create a new history maintenance object.
 */
GlHistory *_new_GlHistory(size_t buflen);

/*
 * Delete a history maintenance object.
 */
GlHistory *_del_GlHistory(GlHistory *glh);

int _glh_add_history(GlHistory *glh, const char *line, int force);

int _glh_search_prefix(GlHistory *glh, const char *line, int prefix_len);

char *_glh_find_backwards(GlHistory *glh, char *line, size_t dim);
char *_glh_find_forwards(GlHistory *glh, char *line, size_t dim);

int _glh_cancel_search(GlHistory *glh);

char *_glh_oldest_line(GlHistory *glh, char *line, size_t dim);
char *_glh_current_line(GlHistory *glh, char *line, size_t dim);

/*
 * Whenever a new line is added to the history buffer, it is given
 * a unique ID, recorded in an object of the following type.
 */
typedef unsigned long GlhLineID;

/*
 * Query the id of a history line offset by a given number of lines from
 * the one that is currently being recalled. If a recall session isn't
 * in progress, or the offset points outside the history list, 0 is
 * returned.
 */
GlhLineID _glh_line_id(GlHistory *glh, int offset);

/*
 * Recall a line by its history buffer ID. If the line is no longer
 * in the buffer, or the specified id is zero, NULL is returned.
 */
char *_glh_recall_line(GlHistory *glh, GlhLineID id, char *line, size_t dim);

/*
 * Write the contents of the history buffer to a given file. Note that
 * ~ and $ expansion are not performed on the filename.
 */
int _glh_save_history(GlHistory *glh, const char *filename,
		      const char *comment, int max_lines);

/*
 * Restore the contents of the history buffer from a given file.
 * Note that ~ and $ expansion are not performed on the filename.
 */
int _glh_load_history(GlHistory *glh, const char *filename, const char *comment,
		      char *line, size_t dim);

/*
 * Set and query the current history group.
 */
int _glh_set_group(GlHistory *glh, unsigned group);
int _glh_get_group(GlHistory *glh);

/*
 * Display the contents of the history list to the specified stdio
 * output group.
 */
int _glh_show_history(GlHistory *glh, GlWriteFn *write_fn, void *data,
		      const char *fmt, int all_groups, int max_lines);

/*
 * Change the size of the history buffer.
 */
int _glh_resize_history(GlHistory *glh, size_t bufsize);

/*
 * Set an upper limit to the number of lines that can be recorded in the
 * history list, or remove a previously specified limit.
 */
void _glh_limit_history(GlHistory *glh, int max_lines);

/*
 * Discard either all history, or the history associated with the current
 * history group.
 */
void _glh_clear_history(GlHistory *glh, int all_groups);

/*
 * Temporarily enable or disable the history facility.
 */
void _glh_toggle_history(GlHistory *glh, int enable);

/*
 * Lookup a history line by its sequential number of entry in the
 * history buffer.
 */
int _glh_lookup_history(GlHistory *glh, GlhLineID id, const char **line,
			unsigned *group, time_t *timestamp);

/*
 * Query the state of the history list.
 */
void _glh_state_of_history(GlHistory *glh, int *enabled, unsigned *group,
			   int *max_lines);

/*
 * Get the range of lines in the history buffer.
 */
void _glh_range_of_history(GlHistory *glh, unsigned long *oldest,
			   unsigned long *newest, int *nlines);

/*
 * Return the size of the history buffer and the amount of the
 * buffer that is currently in use.
 */
void _glh_size_of_history(GlHistory *glh, size_t *buff_size, size_t *buff_used);

/*
 * Get information about the last error in this module.
 */
const char *_glh_last_error(GlHistory *glh);

/*
 * Return non-zero if a history search session is currently in progress.
 */
int _glh_search_active(GlHistory *glh);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/homedir.c000066400000000000000000000354441211610345200225020ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * If file-system access is to be excluded, this module has no function,
 * so all of its code should be excluded.
 */
#ifndef WITHOUT_FILE_SYSTEM

#include 
#include 
#include 
#include 

#include 
#include 
#include 
#include 

#include "pathutil.h"
#include "homedir.h"
#include "errmsg.h"

/*
 * Use the reentrant POSIX threads versions of the password lookup functions?
 */
#if defined(PREFER_REENTRANT) && defined(_POSIX_C_SOURCE) && _POSIX_C_SOURCE >= 199506L
#define THREAD_COMPATIBLE 1
/*
 * Under Solaris we can use thr_main() to determine whether
 * threads are actually running, and thus when it is necessary
 * to avoid non-reentrant features.
 */
#if defined __sun && defined __SVR4
#include                       /* Solaris thr_main() */
#endif
#endif

/*
 * Provide a password buffer size fallback in case the max size reported
 * by sysconf() is said to be indeterminate.
 */
#define DEF_GETPW_R_SIZE_MAX 1024

/*
 * The resources needed to lookup and record a home directory are
 * maintained in objects of the following type.
 */
struct HomeDir {
  ErrMsg *err;             /* The error message report buffer */
  char *buffer;            /* A buffer for reading password entries and */
                           /*  directory paths. */
  int buflen;              /* The allocated size of buffer[] */
#ifdef THREAD_COMPATIBLE
  struct passwd pwd;       /* The password entry of a user */
#endif
};

static const char *hd_getpwd(HomeDir *home);

/*.......................................................................
 * Create a new HomeDir object.
 *
 * Output:
 *  return  HomeDir *  The new object, or NULL on error.
 */
HomeDir *_new_HomeDir(void)
{
  HomeDir *home;  /* The object to be returned */
  size_t pathlen; /* The estimated maximum size of a pathname */
/*
 * Allocate the container.
 */
  home = (HomeDir *) malloc(sizeof(HomeDir));
  if(!home) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to _del_HomeDir().
 */
  home->err = NULL;
  home->buffer = NULL;
  home->buflen = 0;
/*
 * Allocate a place to record error messages.
 */
  home->err = _new_ErrMsg();
  if(!home->err)
    return _del_HomeDir(home);
/*
 * Allocate the buffer that is used by the reentrant POSIX password-entry
 * lookup functions.
 */
#ifdef THREAD_COMPATIBLE
/*
 * Get the length of the buffer needed by the reentrant version
 * of getpwnam().
 */
#ifndef _SC_GETPW_R_SIZE_MAX
  home->buflen = DEF_GETPW_R_SIZE_MAX;
#else
  errno = 0;
  home->buflen = sysconf(_SC_GETPW_R_SIZE_MAX);
/*
 * If the limit isn't available, substitute a suitably large fallback value.
 */
  if(home->buflen < 0 || errno)
    home->buflen = DEF_GETPW_R_SIZE_MAX;
#endif
#endif
/*
 * If the existing buffer length requirement is too restrictive to record
 * a pathname, increase its length.
 */
  pathlen = _pu_pathname_dim();
  if(pathlen > home->buflen)
    home->buflen = pathlen;
/*
 * Allocate a work buffer.
 */
  home->buffer = (char *) malloc(home->buflen);
  if(!home->buffer) {
    errno = ENOMEM;
    return _del_HomeDir(home);
  };
  return home;
}

/*.......................................................................
 * Delete a HomeDir object.
 *
 * Input:
 *  home   HomeDir *  The object to be deleted.
 * Output:
 *  return HomeDir *  The deleted object (always NULL).
 */
HomeDir *_del_HomeDir(HomeDir *home)
{
  if(home) {
    home->err = _del_ErrMsg(home->err);
    if(home->buffer)
      free(home->buffer);
    free(home);
  };
  return NULL;
}

/*.......................................................................
 * Lookup the home directory of a given user in the password file.
 *
 * Input:
 *  home      HomeDir *   The resources needed to lookup the home directory.
 *  user   const char *   The name of the user to lookup, or "" to lookup
 *                        the home directory of the person running the
 *                        program.
 * Output:
 *  return const char *   The home directory. If the library was compiled
 *                        with threads, this string is part of the HomeDir
 *                        object and will change on subsequent calls. If
 *                        the library wasn't compiled to be reentrant,
 *                        then the string is a pointer into a static string
 *                        in the C library and will change not only on
 *                        subsequent calls to this function, but also if
 *                        any calls are made to the C library password
 *                        file lookup functions. Thus to be safe, you should
 *                        make a copy of this string before calling any
 *                        other function that might do a password file
 *                        lookup.
 *
 *                        On error, NULL is returned and a description
 *                        of the error can be acquired by calling
 *                        _hd_last_home_dir_error().
 */
const char *_hd_lookup_home_dir(HomeDir *home, const char *user)
{
  const char *home_dir;   /* A pointer to the home directory of the user */
/*
 * If no username has been specified, arrange to lookup the current
 * user.
 */
  int login_user = !user || *user=='\0';
/*
 * Check the arguments.
 */
  if(!home) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Handle the ksh "~+". This expands to the absolute path of the
 * current working directory.
 */
  if(!login_user && strcmp(user, "+") == 0) {
    home_dir = hd_getpwd(home);
    if(!home_dir) {
      _err_record_msg(home->err, "Can't determine current directory",
		      END_ERR_MSG);
      return NULL;
    }
    return home_dir;
  };
/*
 * When looking up the home directory of the current user, see if the
 * HOME environment variable is set, and if so, return its value.
 */
  if(login_user) {
    home_dir = getenv("HOME");
    if(home_dir)
      return home_dir;
  };
/*
 * Look up the password entry of the user.
 * First the POSIX threads version - this is painful!
 */
#ifdef THREAD_COMPATIBLE
  {
    struct passwd *ret; /* The returned pointer to pwd */
    int status;         /* The return value of getpwnam_r() */
/*
 * Look up the password entry of the specified user.
 */
    if(login_user)
      status = getpwuid_r(geteuid(), &home->pwd, home->buffer, home->buflen,
			  &ret);
    else
      status = getpwnam_r(user, &home->pwd, home->buffer, home->buflen, &ret);
    if(status || !ret) {
      _err_record_msg(home->err, "User '", user, "' doesn't exist.",
		      END_ERR_MSG);
      return NULL;
    };
/*
 * Get a pointer to the string that holds the home directory.
 */
    home_dir = home->pwd.pw_dir;
  };
/*
 * Now the classic unix version.
 */
#else
  {
    struct passwd *pwd = login_user ? getpwuid(geteuid()) : getpwnam(user);
    if(!pwd) {
      _err_record_msg(home->err, "User '", user, "' doesn't exist.",
		      END_ERR_MSG);
      return NULL;
    };
/*
 * Get a pointer to the home directory.
 */
    home_dir = pwd->pw_dir;
  };
#endif
  return home_dir;
}

/*.......................................................................
 * Return a description of the last error that caused _hd_lookup_home_dir()
 * to return NULL.
 *
 * Input:
 *  home   HomeDir *  The resources needed to record the home directory.
 * Output:
 *  return    char *  The description of the last error.
 */
const char *_hd_last_home_dir_error(HomeDir *home)
{
  return home ? _err_get_msg(home->err) : "NULL HomeDir argument";
}

/*.......................................................................
 * The _hd_scan_user_home_dirs() function calls a user-provided function
 * for each username known by the system, passing the function both
 * the name and the home directory of the user.
 *
 * Input:
 *  home             HomeDir *  The resource object for reading home
 *                              directories.
 *  prefix        const char *  Only information for usernames that
 *                              start with this prefix will be
 *                              returned. Note that the empty
 &                              string "", matches all usernames.
 *  data                void *  Anonymous data to be passed to the
 *                              callback function.
 *  callback_fn  HOME_DIR_FN(*) The function to call for each user.
 * Output:
 *  return               int    0 - Successful completion.
 *                              1 - An error occurred. A description
 *                                  of the error can be obtained by
 *                                  calling _hd_last_home_dir_error().
 */
int _hd_scan_user_home_dirs(HomeDir *home, const char *prefix,
			    void *data, HOME_DIR_FN(*callback_fn))
{
  int waserr = 0;       /* True after errors */
  int prefix_len;       /* The length of prefix[] */
/*
 * Check the arguments.
 */
  if(!home || !prefix || !callback_fn) {
    if(home) {
      _err_record_msg(home->err,
		      "_hd_scan_user_home_dirs: Missing callback function",
		      END_ERR_MSG);
    };
    return 1;
  };
/*
 * Get the length of the username prefix.
 */
  prefix_len = strlen(prefix);
/*
 * There are no reentrant versions of getpwent() etc for scanning
 * the password file, so disable username completion when the
 * library is compiled to be reentrant.
 */
#if defined(PREFER_REENTRANT) && defined(_POSIX_C_SOURCE) && _POSIX_C_SOURCE >= 199506L
#if defined __sun && defined __SVR4
  if(thr_main() >= 0) /* thread library is linked in */
#else
  if(1)
#endif
  {
    struct passwd pwd_buffer;  /* A returned password entry */
    struct passwd *pwd;        /* A pointer to pwd_buffer */
    char buffer[512];          /* The buffer in which the string members of */
                               /* pwd_buffer are stored. */
/*
 * See if the prefix that is being completed is a complete username.
 */
    if(!waserr && getpwnam_r(prefix, &pwd_buffer, buffer, sizeof(buffer),
			     &pwd) == 0 && pwd != NULL) {
      waserr = callback_fn(data, pwd->pw_name, pwd->pw_dir,
			   _err_get_msg(home->err), ERR_MSG_LEN);
    };
/*
 * See if the username of the current user minimally matches the prefix.
 */
    if(!waserr && getpwuid_r(getuid(), &pwd_buffer, buffer, sizeof(buffer),
			     &pwd) == 0 && pwd != NULL &&
                             strncmp(prefix, pwd->pw_name, prefix_len)==0) {
      waserr = callback_fn(data, pwd->pw_name, pwd->pw_dir,
			   _err_get_msg(home->err), ERR_MSG_LEN);
    };
/*
 * Reentrancy not required?
 */
  } else
#endif
  {
    struct passwd *pwd;   /* The pointer to the latest password entry */
/*
 * Open the password file.
 */
    setpwent();
/*
 * Read the contents of the password file, looking for usernames
 * that start with the specified prefix, and adding them to the
 * list of matches.
 */
    while((pwd = getpwent()) != NULL && !waserr) {
      if(strncmp(prefix, pwd->pw_name, prefix_len) == 0) {
	waserr = callback_fn(data, pwd->pw_name, pwd->pw_dir,
			     _err_get_msg(home->err), ERR_MSG_LEN);
      };
    };
/*
 * Close the password file.
 */
    endpwent();
  };
/*
 * Under ksh ~+ stands for the absolute pathname of the current working
 * directory.
 */
  if(!waserr && strncmp(prefix, "+", prefix_len) == 0) {
    const char *pwd = hd_getpwd(home);
    if(pwd) {
      waserr = callback_fn(data, "+", pwd, _err_get_msg(home->err),ERR_MSG_LEN);
    } else {
      waserr = 1;
      _err_record_msg(home->err, "Can't determine current directory.",
		      END_ERR_MSG);
    };
  };
  return waserr;
}

/*.......................................................................
 * Return the value of getenv("PWD") if this points to the current
 * directory, or the return value of getcwd() otherwise. The reason for
 * prefering PWD over getcwd() is that the former preserves the history
 * of symbolic links that have been traversed to reach the current
 * directory. This function is designed to provide the equivalent
 * expansion of the ksh ~+ directive, which normally returns its value
 * of PWD.
 *
 * Input:
 *  home      HomeDir *  The resource object for reading home directories.
 * Output:
 *  return const char *  A pointer to either home->buffer, where the
 *                       pathname is recorded, the string returned by
 *                       getenv("PWD"), or NULL on error.
 */
static const char *hd_getpwd(HomeDir *home)
{
/*
 * Get the absolute path of the current working directory.
 */
  char *cwd = getcwd(home->buffer, home->buflen);
/*
 * Some shells set PWD with the path of the current working directory.
 * This will differ from cwd in that it won't have had symbolic links
 * expanded.
 */
  const char *pwd = getenv("PWD");
/*
 * If PWD was set, and it points to the same directory as cwd, return
 * its value. Note that it won't be the same if the current shell or
 * the current program has changed directories, after inheriting PWD
 * from a parent shell.
 */
  struct stat cwdstat, pwdstat;
  if(pwd && cwd && stat(cwd, &cwdstat)==0 && stat(pwd, &pwdstat)==0 &&
     cwdstat.st_dev == pwdstat.st_dev && cwdstat.st_ino == pwdstat.st_ino)
    return pwd;
/*
 * Also return pwd if getcwd() failed, since it represents the best
 * information that we have access to.
 */
  if(!cwd)
    return pwd;
/*
 * In the absence of a valid PWD, return cwd.
 */
  return cwd;
}

#endif  /* ifndef WITHOUT_FILE_SYSTEM */
genometools-1.5.1/src/external/libtecla-1.6.1/homedir.h000066400000000000000000000070151211610345200225000ustar00rootroot00000000000000#ifndef homedir_h
#define homedir_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

typedef struct HomeDir HomeDir;

/*
 * The following constructor and destructor functions create and
 * delete the resources needed to look up home directories.
 */
HomeDir *_new_HomeDir(void);
HomeDir *_del_HomeDir(HomeDir *home);

/*
 * Return the home directory of a specified user, or NULL if unknown.
 */
const char *_hd_lookup_home_dir(HomeDir *home, const char *user);

/*
 * Get the description of the that occured when _hd_lookup_home_dir() was
 * last called.
 */
const char *_hd_last_home_dir_error(HomeDir *home);

/*
 * The _hd_scan_user_home_dirs() function calls a user-provided function
 * for each username known by the system, passing the function both
 * the name and the home directory of the user.
 *
 * The following macro can be used to declare both pointers and
 * prototypes for the callback functions. The 'data' argument is
 * a copy of the 'data' argument passed to _hd_scan_user_home_dirs()
 * and is intended for the user of _hd_scan_user_home_dirs() to use
 * to pass anonymous context data to the callback function.
 * The username and home directories are passed to the callback function
 * in the *usrnam and *homedir arguments respectively.
 * To abort the scan, and have _hd_scan_user_home_dirs() return 1, the
 * callback function can return 1. A description of up to maxerr
 * characters before the terminating '\0', can be written to errmsg[].
 * This can then be examined by calling _hd_last_home_dir_error().
 * To indicate success and continue the scan, the callback function
 * should return 0. _hd_scan_user_home_dirs() returns 0 on successful
 * completion of the scan, or 1 if an error occurred or a call to the
 * callback function returned 1.
 */
#define HOME_DIR_FN(fn) int (fn)(void *data, const char *usrnam, __attribute__ ((unused)) const char *homedir, char *errmsg, int maxerr)

int _hd_scan_user_home_dirs(HomeDir *home, const char *prefix, void *data,
			    HOME_DIR_FN(*callback_fn));

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/html/000077500000000000000000000000001211610345200216415ustar00rootroot00000000000000genometools-1.5.1/src/external/libtecla-1.6.1/html/changes.html000066400000000000000000004246211211610345200241500ustar00rootroot00000000000000The tecla library change log

In the following log, modification dates are listed using the European
convention in which the day comes before the month (ie. DD/MM/YYYY).
The most recent modifications are listed first.

31/10/2004 mcs@astro.caltech.edu (problem reported by Godfrey van der Linden) 
           getline.c
             The gl_event_handler() function had the endif of a
             conditional compilation clause in the wrong place. This
             only upset the compiler on unusual systems that don't
             have select(). The problem was seen under Mac OS X, due
             to the configuration problem in 1.6.0 that caused the
             configure script to mistakenly report that select wasn't
             available.

31/10/2004 mcs@astro.caltech.edu (info provided by Ivan Rayner)
           configure.in configure Makefile.in
             Ivan reported that under IRIX 6.5 it is necessary to add
             -D_XOPEN_SOURCE=500 to the compiler flags, when compiling
             the reentrant version of the library. Thus, whereas
             previously I hardwired the value of DEFINES_R in
             Makefile.in, I have now made this a variable in the
             configure script, which is augmented with the above
             addition, within an IRIX-specific switch clause.

             Also apparently configure leaves the RANLIB variable
             blank, instead of setting it to ":", so I have now
             explicitly set this to ":", within the new IRIX clause of
             the configure script.

31/10/2004 mcs@astro.caltech.edu (info provided by Ivan Rayner)
           getline.c
             Under IRIX, the compiler warned that gl_read_unmasked()
             was returning an int, which was then being assigned to an
             enumeration type. This is techically fine, but it
             highlighted the fact that I had meant to declare
             gl_read_unmasked() to directly return the enumerated
             type. I have now done so.

26/09/2004 mcs@astro.caltech.edu
           getline.c
             Users can now turn off interactive command-line editing
             by setting the TERM environment variable to the word "dumb".

18/07/2004 mcs@astro.caltech.edu (problem noted by Michael MacFaden)
           getline.c
             Calling gl_terminal_size() on a system without support
             for SIGWINCH caused a divide-by-zero error in an unintended
             call to gl_erase_line(), because gl_update_size() was
             incorrectly being called to query the terminal size,
             instead of gl_query_size().

18/07/2004 Padraig Brady  (documented here by mcs@astro.caltech.edu)
           getline.c
             The suspend and termination signal-handlers installed by
             gl_tty_signals(), were being installed swapped.

03/06/2004 Mike Meaney  (documented here by mcs@astro.caltech.edu)
           getline.c
             Mike pointed out the fact that the curses setupterm()
             function is actually documented to exit the application
             if an error occurs while its optional errret argument is
             NULL. I hadn't noticed this, and because I didn't need
             the extra information returned in the errret argument, I
             was passing it a NULL. As suggested by Mike, I now pass
             this argument a pointer to a dummy errret variable.

23/05/2004 mcs@astro.caltech.edu (problem noted by John Beck)
           man/func/cpl_complete_word.in
             Some of the prototypes of functions and types documented
             by the cpl_complete_word man page, weren't listed in the
             Synopsis section of this man page. They are now listed
             there.
            
23/05/2004 mcs@astro.caltech.edu
           getline.c man/func/gl_get_line.in
             I have now added support for calling gl_normal_io() from
             any callback functions that the application installs by
             calling either gl_inactivity_timeout(), or gl_watch_fd().
             Previously, if one of these callback functions called
             gl_normal_io(), then after returning to gl_get_line(),
             gl_get_line() would incorrectly assume that the terminal
             was still in raw I/O mode. Now, gl_get_line() checks to
             see if gl_normal_io() was called by the callback, and
             if so, calls _gl_raw_io() to reinstate raw I/O mode.

21/05/2004 mcs@astro.caltech.edu
           configure.in configure
             On Mac OS X the code that the configure script used to
             check for select() failed due to missing symbols in
             sys/select.h. Moving the inclusion of sys/select.h to
             after the inclusion of sys/time.h, sys/types.h and
             sys/unistd.h fixed this.

11/05/2004 mcs@astro.caltech.edu
           getline.c man/func/gl_get_line.in
             If the line buffer returned by one call to gl_get_line()
             was passed as the start_line argument of the next call to
             gl_get_line(), then instead of the just-entered line
             being presented back to the user for further editing, the
             start_line argument was effectively ignored, because the
             line buffer whose pointer was being passed back, was
             being cleared before the start_line pointer was examined.
             This appears to have been a case of me incorrectly
             thinking that I had forgotten to initialize gl->line[]
             and gl->ntotal in the gl_reset_input_line() function, and
             then "fixing" this supposed omission. Removing this
             erroneous fix, restored things to how they were meant to
             be. To make it unlikely that I will make the same mistake
             again, I have renamed the function from
             gl_reset_input_line() to gl_reset_editor(), to stop it
             looking as though it is meant to reset the contents of
             the input line (that is what gl_truncate_buffer() is
             for), explicitly stated that it doesn't clear the input
             line, in the header comments of the function, and added a
             prominent warning comment in the body of the function.

             Also, since support for passing back the returned line
             pointer via the start_line argument of the next call to
             gl_get_line(), wasn't documented in the man page, but was
             meant to be supported, and definitely used to work, I
             have now amended the man page documentation of
             gl_get_line() to explicitly state that this feature is
             officially supported.

2?/04/2004 Released 1.6.0

22/04/2004 mcs@astro.caltech.edu  (Fixed a bug reported by John Beck)
           getline.c
             When an error, signal, or other abnormal event aborted
             gl_get_line(), the cleanup code that restored the
             terminal to a sane state, also overwrote the value of
             errno that was associated with the aborting event. An
             I/O error occurring in the cleanup code would have also
             overwritten the value to be returned by
             gl_return_status(), and thus remove any possibility of
             the caller finding out what really caused gl_get_line()
             to abort. I have now written a new internal function
             called, gl_record_status(), which records the completion
             status to be returned by gl_return_status(), and the
             value to assign to errno just before gl_get_line()
             returns. This is called wherever code detects conditions
             that require gl_get_line() to return early. The function
             ensures that once an abnormal completion status has been
             recorded for return, subsequent completions statuses
             aren't recorded. This ensures that the caller sees the
             original cause of the abnormal return, rather than any
             error that occurs during cleaning up from this before
             return.

17/04/2004 mcs@astro.caltech.edu
           getline.c
             If an application's callback called gl_read_char() after
             calling gl_normal_io(), it would inappropriately
             redisplay the input line, when it called _gl_raw_io() to
             temporarily switch the terminal back into raw mode.

             To fix this, _gl_raw_io() now takes a new 'redisplay'
             argument, which specifies whether or not to queue a
             redisplay of the input line. I also created a new
             gl->postpone flag, which is set by gl_normal_io(), and
             cleared by _gl_raw_io() (when its redisplay argument is
             true). When this flag is set, gl_flush_output() ignores
             queued redisplays, as it generally should between calls
             to gl_normal_io() and gl_raw_io(). Thus its effect is to
             postpone redisplays while line editing is suspended.

11/04/2004 mcs@astro.caltech.edu
           history.c man/misc/tecla.in
             History searches can now include the globbing operators
             *, ?, []. When a search prefix is found to have at least
             one of these characters, then only history lines that
             completely match that pattern are returned.

11/04/2004 mcs@astro.caltech.edu  (issue raised by Mark Coiley)
           getline.c ioutil.c
             There appears to be a bug in Solaris's terminal I/O.
             When the terminal file descriptor is placed in
             non-blocking I/O mode, and the terminal is switched from
             canonical to raw mode, characters that were previously
             entered in canonical I/O mode don't become available to
             be read until the user types one character more. Select()
             incorrectly says that there are no characters available,
             and read() returns EAGAIN. This is only a problem for
             gl_get_line() when gl_get_line() is in non-blocking
             server I/O mode, so most users won't have experienced any
             problems with this.

             The only way that I have found to get read() to return
             the characters, without the user first having to type
             another character, is to turn off non-blocking I/O before
             calling read(). Select() still claims that there are no
             characters available to be read, but read happily returns
             them anyway. Fortunately, one can perform non-blocking
             terminal reads without setting the non-blocking I/O flag
             of the file descriptor, simply by setting the VTIME
             terminal attribute to zero (which I already was
             doing). Thus, when in non-blocking server I/O, I now turn
             off the non-blocking I/O flag, attempt to read one
             character and only if this fails, do I then call the
             select() based event handler to implement any configured
             non-zero timeout, before attempting the read again. Of
             course the non-blocking I/O flag is still needed for
             writing, so I only turn it off temporarily while reading.

25/03/2004 mcs@astro.caltech.edu  (bug reported by Gregory Harris)
           Makefile.in
             It appears that when in February, I patched Makefile.in
             to add abolute paths to the install-sh shell-script,
             I accidentally replaced install-sh with install.sh. I
             corrected the name in the Makefile.

25/03/2004 Gregory Harris  (documented here by mcs)
           configure.in configure
             Greg added the configuration parameters needed to build
             the shared version of the libtecla library under FreeBSD.

25/03/2004 mcs@astro.caltech.edu
           getline.c libtecla.h libtecla.map man/func/gl_get_line.in
           man/func/gl_read_char.in
             I wrote a public function called gl_read_char(). Unlike
             gl_query_char(), this function neither prompts the user
             for input, nor displays the character that was entered.
             In fact it doesn't write anything to the terminal, and
             takes pains not to disturb any incompletely entered
             input line, and can safely be called from application
             callback functions.

21/03/2004 mcs@astro.caltech.edu
           getline.c libtecla.h libtecla.map man/func/gl_get_line.in
           man/func/gl_query_char.in
             I wrote a public function called gl_query_char(), which
             prompts the user and awaits a single-character reply,
             without the user having to hit return.

23/02/2004 mcs@astro.caltech.edu (bug reported by Gregory Harris)
           configure.in configure getline.c enhance.c demo3.c
             The configure script now checks for the sys/select.h
             header file, and arranges for a C macro called
             HAVE_SYS_SELECT_H to be set if it exists. Thus the files
             that use select() now use this macro to conditionally
             include sys/select.h where available. Apparently this
             header is required under FreeBSD 5.1.

23/02/2004 mcs@astro.caltech.edu
           getline.c libtecla.h man/func/gl_get_line.in
             I wrote two new public functions, gl_append_history() and
             gl_automatic_history(). Together these allow the
             application to take over the responsibility of adding
             lines to the history list from gl_get_line(). I then
             documented their functionality in the gl_get_line man
             page.
           Version 1.6.0
             I incremented the minor version number of the library, to
             comply with the requirement to do so when additions are
             made to the public interface. See libtecla.map for
             details.
           libtecla.map
             I added a new 1.6.0 group for the new minor version, and
             added the above pair of functions to it.

15/02/2004 mcs@astro.caltech.edu (fixes a bug reported by Satya Sahoo)
           history.c
             Calling gl_load_history() multiple times, eventually led
             to a segmentation fault. This was due to the head of the
             list of unused history string segments not getting
             reset when the history buffer was cleared. While
             debugging this problem I also noticed that the history
             resizing function was way too complicated to verify, so
             after fixing the above bug, I heavily simplified the
             history resizing function, trading off a small reduction
             in memory efficiency, for greatly improved clarity, and
             thus made it much more verifiable and maintainable.

14/02/2004 mcs@astro.caltech.edu (fixes a bug reported by Tim Burress).
           getline.c
             If gl_change_terminal() was first used to tell
             gl_get_line to read input from a file, then called later
             to tell it to read subsequent input from a terminal, no
             prompt would be displayed for the first line of
             interactive input. The problem was that on reaching the
             end of the input file, gl_get_line() should have called
             gl_abandon_line(), to tell the next call to gl_get_line()
             to start inputting a new line from scratch. I have added
             this now.

14/02/2004 Krister Walfridsson (documented here by mcs@astro.caltech.edu)
           Makefile.in
             Krister noticed that I had failed to put $(srcdir)/ in front
             of some invokations of install.sh. I have remedied this.
           config.guess config.sub
             I hadn't updated these for a long time, so apparently they
             didn't recognise the BSD system that Krister was using.
             I have now updated them to the versions that come with
             autoconf-2.59. 

22/01/2004 mcs@astro.caltech.edu
           keytab.c
             When parsing key-binding specifications, backslash escaped
             characters following ^ characters were not being expanded.
             Thus ^\\ got interpretted as a control-\ character followed
             by a \ character, rather than simply as a control-\
             character.

12/01/2004 mcs@astro.caltech.edu
           cplfile.c cplmatch.c demo2.c demo3.c demo.c direader.c
           expand.c getline.c history.c homedir.c pathutil.c pcache.c
           configure.in configure INSTALL
             The configuration script now takes a
             "--without-file-system" argument. This is primarily for
             intended for embedded systems that either don't have
             filesystems, or where the file-system code in libtecla is
             unwanted bloat. It sets the WITHOUT_FILE_SYSTEM
             macro. This removes all code related to filesystem
             access, including the entire public file-expansion,
             file-completion and path-lookup facilities. Note that the
             general word completion facility is still included, but
             without the normally bundled file completion
             callback. Actually the callback is still there, but it
             reports no completions, regardless of what string you ask
             it to complete.

             This option is described in the INSTALL document.

12/01/2004 mcs@astro.caltech.edu
           getline.c configure.in configure INSTALL
             The configuration script now takes a
             "--without-file-actions" argument. This allows an
             application author/installer to prevent users of
             gl_get_line() from accessing the filesystem from the
             builtin actions of gl_get_line(). It defines a macro
             called HIDE_FILE_SYSTEM. This causes the
             "expand-filename", "read-from-file", "read-init-files",
             and "list-glob" action functions to be completely
             removed. It also changes the default behavior of actions
             such as "complete-word" and "list-or-eof" to show no
             completions, instead of the normal default of showing
             filename completions.

             This option is described in the INSTALL document.

11/01/2004 mcs@astro.caltech.edu
           getline.c man/func/gl_get_line.in
             In case an application's customized completion handler
             needs to write to the terminal for some unforseen reason,
             there needs to be a way for the it to cleanly suspend raw
             line editing, before writing to the terminal, and the
             caller then needs to be aware that it may need to
             resurrect the input line when the callback returns. I
             have now arranged that the completion callback functions
             can call the gl_normal_io() function for this purpose,
             and documented this in the gl_get_line() man page.

11/01/2004 mcs@astro.caltech.edu  (In response to a bug report by Satya Sahoo)
           getline.c
             The gl_configure_getline() function makes a malloc'd copy
             of the names of the configuration files that it is asked
             to read. Before the bug fix, if the application made one
             or more calls to this function, the memory allocated by
             the final call that it made before calling del_GetLine(),
             wasn't being freed. Note that memory allocated in all but
             the final call was being correctly freed, so the maximum
             extent of the memory leak was the length of the file
             name(s) passed in the final call to
             gl_configure_getline(), and an application that didn't
             call gl_configure_getline() didn't suffer any leak.

20/12/2003 mcs@astro.caltech.edu
           history.c
             Ellen tested the history fix that I reported below, and
             pointed out that it still had a problem. This turned out
             to be because getline.c was making some incorrect
             assumptions about the new behavior of history.c. This
             problem and the previous one both revolved around how
             search prefixes were stored and discarded, so I have now
             re-written this part of the code. Previously the search
             prefix was retained by looking for a line with that
             prefix, and keeping a pointer to that line. This saved
             memory, compared to storing a separate copy of the
             prefix, but it led to all kinds of hairy
             interdependencies, so I have now changed the code to keep
             a separate copy of search prefixes. To keep the memory
             requirements constant, the search prefix is stored in the
             history buffer, like normal history lines, but not
             referenced by the time-ordered history list. The prefix
             can now be kept around indefinitely, until a new search
             prefix is specified, regardless of changes to the
             archived lines in the history buffer. This is actually
             necessary to make the vi-mode re-search actions work
             correctly. In particular, I no longer discard the search
             prefix whenever a history search session ends. Also,
             rather than have getline.c keep its own record of when a
             history session is in progress, it now consults
             history.c, so that failed assumptions can't cause the
             kind of discrepancy that occurred before. For this to
             work, getline.c now explicitly tells history.c to cancel
             search sessions whenever it executes any non-history
             action.

14/12/2003 mcs@astro.caltech.edu (bug reported by Ellen Oschmann)
           history.c
             If one searched backwards for a prefix, then returned to
             the original line, changed that line, then started
             another backwards prefix search, getline incorrectly
             discarded the new search prefix in the process of
             throwing away its cached copy of the previous pre-search
             input line. In other words getline was belatedly
             cancelling a previous search, after a new search had
             already partially begun, and thus messed up the new
             search. The obvious fix was to arrange for the current
             search to be cancelled whenever the history pointer
             returns to its starting point, rather than waiting for
             the next search to begin from there.

14/12/2003 mcs@astro.caltech.edu
           history.c
             _glh_recall_line() was returning the last line in the
             history buffer instead of the line requested by the
             caller. This only affected the obscure "repeat-history"
             action-function, which probably isn't used by anybody.

09/12/2003 Version 1.5.0 released.

28/09/2003 mcs@astro.caltech.edu
           homedir.c
             When the home directory of the login user is requested,
             see if the HOME environment variable exists, and if so
             return its value, rather than looking up the user's home
             directory in the password file. This seems to be the
             convention adopted by other unix programs that perform
             tilde expansion, and it works around a strange problem,
             where a third-party libtecla program, statically compiled
             under an old version of RedHat, unexpectedly complained
             that getpwd() returned an error when the program was run
             under RedHat 9.

01/09/2003 mcs@astro.caltech.edu
           getline.c libtecla.h libtecla.map man/func/gl_get_line.in
           man/func/gl_register_action.in.
             It is now possible for an application to register
             external functions as action functions. These actions are
             initially bound to specified key-sequences, but if they
             are registered before the user's configuration file is
             loaded, they can also be re-bound by the user to
             different key-sequences. The function used to register a
             new action, is called gl_register_action().  Action
             functions are passed a readonly copy of the input line
             and the cursor position. They can display text to the
             terminal, or perform other operations on the application
             environment. Currently, they can't edit the input line or
             move the cursor. This will require the future addition of
             functions to queue the invokation of the built-in action
             functions.

26/08/2003 mcs@astro.caltech.edu
           getline.c
             I modified gl_update_buffer() to ensure that the cursor
             stays within the input line after external line
             modifications, and to queue a redisplay of the
             potentially modified input line.

21/07/2003 mcs@astro.caltech.edu
           configure.in configure Makefile.in Makefile.stub INSTALL
             By specifying --without-man-pages or --with-man-pages=no
             as command-line arguments to the configure script, it is
             now possible to have the configure script skip the
             man-page preprocessing step, and arrange for the man-page
             installation targets in the Makefile to do nothing. This
             option is designed for people who embed libtecla within
             other packages. It is also used by Makefile.stub when
             the distclean target is specified.

21/07/2003 mcs@astro.caltech.edu
           configure.in configure
             The previous workaround for recent versions of gcc
             placing /usr/local/include at the start of the system
             inlcude-file search path, broke something else.  The fix
             placed /usr/include before gcc's include area, which
             meant that gcc's modified version of stdarg.h was being
             ignored in deference to the version in /usr/include. I
             have changed the fix to have gcc report the search path,
             then have awk add options to CFLAGS to reorder this path,
             plaing /usr/local/include at the end.

             Also, under Solaris 9, including term.h without first
             including curses.h results in complaints about undefined
             symbols, such as bool. As a result the configure script's
             test for term.h was failing. I have now modified it to
             include curses.h in the test code that it uses to check
             for term.h. In the process I also improved the tests for
             curses.h and term.h to prevent an ncurses version of
             term.h from being used with the system-default version of
             curses.h.

29/06/2003 mcs@astro.caltech.edu
           Makefile.in direader.c homedir.c
             On some systems (eg. linux) the _POSIX_C_SOURCE
             feature-test macro is set by system headers, rather than
             being an option set by a project's Makefile at
             compilation time.  In software, such as tecla, where the
             definition of this macro is used as an indication of
             whether to use the non-reentrant or reentrant versions of
             system functions, this means that the reentrant functions
             are always used, regardless of whether this macro is set
             or not by the project Makefile. Thus, on such systems the
             reentrant and non-reentrant versions of the tecla library
             are essentially identical. This has a couple of
             drawbacks.  First, since thread-safe functions for
             traversing the password file don't exist, the supposedly
             non-reentrant version of the tecla library can't support
             ambiguous tab-completion of usernames in ~username/
             constructions. Secondly, on some systems the use of
             reentrant system functions dictates the use of a shared
             library that isn't needed for the non-reentrant
             functions, thus making it more difficult to distribute
             binary versions of the library.

             To remedy this situation I have modified the DEFINES_R
             variable in Makefile.in to arrange for the compiler to
             define a C macro called PREFER_REENTRANT when it is
             compiling the reentrant version of the tecla library.
             This macro is now used in the source code to determine
             when to require reentrant code. Whithin the source code,
             wherever a potentially non-reentrant interface is used,
             the existance of both this macro and a suitably valued
             _POSIX_C_SOURCE macro, are tested for to see if a
             reentrant alternative to the problem code should be used.

22/06/2003 mcs@astro.caltech.edu
           getline.c
             I changed the way that redisplays are requested and
             performed.  Redisplays are now queued by calling
             gl_queue_redisplay(), and subsequently performed by
             gl_flush_output(), when the queue of already pending
             output has been completely dispatched. This was necessary
             to prevent event handlers from filling up the output
             queue with redisplays, and it also simplifies a number of
             things. In the process I removed the gl_queue_display()
             function. I also wrote a gl_line_erased() function, which
             is now called by all functions that erase the input
             line. I also split the gl_abandon_line() function into
             public and private callable parts, and used the private
             version internally to arrange to discard the input line
             after errors.

             The raw_mode flag was not being initialized by new_GetLine().
             It is now initialized to zero.

             I removed the zapline flag, since using the endline flag to
             communicate the desire to terminate the line, did the same
             thing.

             gl_terminal_move_cursor() now does nothing when the input
             line isn't displayed.

18/03/2003 mcs@astro.caltech.edu
           getline.c
             Fixed bug which was causing newlines not to be output
             at the end of each newly entered line. I was
             interpreting the gl->endline flag in conflicting ways in
             two places. To fix this I have created a gl->displayed
             flag. This flags whether an input line is currently
             displayed.

17/03/2003 mcs@astro.caltech.edu
           getline.c libtecla.h man/func/gl_get_line.in
           man/func/gl_erase_terminal.in libtecla.map
             I added a new function that programs can call to clear
             the terminal between calls to gl_get_line().

11/03/2003 mcs@astro.caltech.edu
           configure.in configure
             Under linux when _POSIX_C_SOURCE is defined, getpwent()
             and associated functions become undefined, because
             _SVID_SOURCE and _BSD_SOURCE become undefined. Adding
             these feature macros back to CFLAGS resolves this.

06/03/2003 mcs@astro.caltech.edu
           getline.c libtecla.map man/func/gl_get_line.in
             Following the lead of Edward Chien, I wrote a function
             called gl_bind_keyseq(), which binds a specified
             key-sequence to a given action, or unbinds the
             key-sequence.

24/02/2003 mcs@astro.caltech.edu
           getline.c libtecla.map man/func/cpl_complete_word.in
             I implemented a simple function called
             cpl_recall_matches().  This recalls the return value of
             the last call to cpl_complete_word().

19/01/2003 mcs@astro.caltech.edu
           getline.c
             The documented signal handling, fd event-handling,
             inactivity timeout handling, and server-mode non-blocking
             I/O features are now implemented for non-interactive
             input streams, such as pipes and files.

19/01/2003 mcs@astro.caltech.edu
           getline.c libtecla.h man/func/gl_get_line.in demo3.c
             I added a new return status enumerator to report
             when an end-of-file condition causes gl_get_line()
             to return NULL.

13/01/2003 mcs@astro.caltech.edu
           history.c
             I rewrote the history facility. The previous
             circular buffer implementation was a nightmare to change,
             and it couldn't efficiently support certain newly
             requested features. The new implementation stores history
             lines in linked lists of fixed sized string segments,
             taken from the buffer, with each line being reference
             counted and recorded in a hash table. If the user enters
             a line multiple times, only one copy of the line is now
             stored. Not only does this make better use of the
             available buffer space, but it also makes it easy to
             ensure that a line whose prefix matches the current
             search prefix, isn't returned more than once in sequence,
             since we can simply see if the latest search result has
             the same hash-table pointer as the previous one, rather
             than having to compare strings. Another plus is that due
             to the use of linked lists of nodes of fixed size line
             segments, there is no longer any need to continually
             shuffle the contents of the buffer in order to defragment
             it. As far as the user is concerned, the visible
             differences are as follows:

             1. If the user enters a given line multiple times in a
                row, each one will be recorded in the history list,
                and will thus be listed by gl_show_history(), and
                saved in the history file. Previously only one line
                was recorded when consecutive duplicates were entered.
                This was a kludge to prevent history recall from
                recalling the same line multiple times in a row. This
                only achieved the desired result when not recalling by
                prefix.

             2. Not only simple recall, but prefix-based history line
                recalls now don't return the same line multiple times
                in a row. As mentioned in (1) above, previously this
                only worked when performing a simple recall, without a
                search prefix.

28/12/2002 mcs@astro.caltech.edu
           getline.c
             The one-line function, gl_buff_curpos_to_term_curpos()
             was only being used by gl_place_cursor(), so I inlined it
             in that function, and removed it.

28/12/2002 mcs@astro.caltech.edu
           getline.c
             gl_suspend_process() was calling the application-level
             gl_normal_io() and gl_raw_io() functions, where it should
             have been calling the internal versions _gl_normal_io()
             and _gl_raw_io().
             Also gl_handle_signal() was masking and unmasking just
             the signals of the first element of the gl[] array
             argument. It now masks and unmasks all trappable signals.

28/12/2002 mcs@astro.caltech.edu
           getline.c
             Now that the number of terminal characters used to
             display the current input line, is recorded, the relative
             line on which the last character of the input line
             resides can be determined without having to call
             gl_buff_curpos_to_term_curpos(). This is now used by
             gl_normal_io() via gl_start_newline(), so there is now no
             need for gl_buff_curpos_to_term_curpos() to be
             async-signal safe. I have thus removed the annoying
             gl->cwidth[] array, and gl_buff_curpos_to_term_curpos()
             now calls gl_width_of_char() directly again. There is
             also now no need for the gl_line_of_char_start() and
             gl_line_of_char_end() functions, so I have removed them.

28/12/2002 mcs@astro.caltech.edu
           getline.c
             Unfortunately it turns out that the terminfo/termcap
             control sequence which is defined to delete everything
             from the current position to the end of the terminal, is
             only defined to work when at the start of a terminal
             line. In gnome terminals in RedHat 8.0, if it is used
             within a terminal line, it erases the whole terminal
             line, rather than just what follows the cursor. Thus to
             portably truncate the displayed input line it is
             necessary to first use the control sequence which deletes
             from the cursor position to the end of the line, then if
             there are more terminal lines, move to the start of the
             next line, and use the delete to end-of-terminal control
             sequence, then restore the cursor position. This requires
             that one know how many physical terminal lines are used
             by the current input line, so I now keep a record of the
             number of characters so far displayed to the terminal
             following the start of the prompt, and the new
             gl_truncate_display() function uses this information to
             truncate the displayed input line from the current cursor
             position.

28/12/2002 mcs@astro.caltech.edu
           getline.c
             gl_start_newline() now moves to an empty line following
             the input line, rather than just to the next line. It
             also arranges for the input line to be redisplayed before
             editing resumes. A major user of this is gl_print_info(),
             which now need not be followed by an explicit call to
             gl_redisplay(), since the terminal input loop in
             gl_get_input_line() ensures that gl_redisplay() is called
             after any action function that asserts gl->redisplay.
             Also, all functions that erase the displayed input line
             can now call the gl_erase_line() function, which is
             designed to work correctly even when a terminal resize
             invalidates the horizontal cursor position.  Finally, the
             new gl_queue_display() function is now used by functions
             that need to arrange for the input line to be displayed
             from scratch after the displayed line has been erased or
             invalidated by other text being written to the terminal.
             All of these changes are aimed at reducing the number of
             places that directly modify gl->term_curpos and
             gl->redisplay.

22/12/2002 Markus Gyger   (logged here by mcs)
           Makefile.in update_html
	     In places where echo and sed were being used to extract
	     the base names of files, Markus substituted the basename
	     command. He also replaced explicit cp and chmod commands
	     with invokations of the install-sh script.
           configure.in
             Use $target_os and $target_cpu, where appropriate,
	     instead of $target.
           configure.in
             The Solaris man function and library man pages should
	     be in sections 3lib and 3tecla respectively, only in
	     Solaris version 2.8 and above.
           configure.in
             Markus provided values for the man page configuration
             variables for HPUX.
           man/*/*.in
             I had missed parameterizing man page section numbers in
	     the man page titles, Markus corrected this.
           man/func/libtecla_version.in
             Fixed incorrect section number in the link to the
             libtecla man page.
           homedir.c
             When compiled to be reentrant, although one can't use the
	     non-reentrant getpwent() function to scan the password
	     file for username completions, one can at least see if
	     the prefix being completed is a valid username, and if
	     the username of the current user minimally matches the
	     prefix, and if so list them. I simplified Markus'
	     modification by adding a prefix argument to the
             _hd_scan_user_home_dirs() function, and redefining the
	     function description accordingly, such that now it
	     reports only those password file entries who's usernames
	     minimally match the specified prefix. Without this, it
	     would have been necessary to peak inside the private data
	     argument passed in by cf_complete_username().
             Markus also provided code which under Solaris uses the
             non-reentrant interfaces if the reentrant version of the
             library isn't linked with the threads library.

19/12/2002 mcs@astro.caltech.edu
           Makefile.in
             Markus pointed out that LDFLAGS was being picked up by
             the configure script, but not then being interpolated
             into te Makefile. I have thus added the necessary
             assignment to Makefile.in and arranged for the value of
             LDFLAGS to be passed on to recursive make's. I also did
             the same for CPPFLAGS, which had also been omitted.

18/12/2002 mcs@astro.caltech.edu
           man/* man/*/* configure.in configure Makefile.in
           update_html
             It turns out that the assignment of man page sections to
             topics differs somewhat from system to system, so this is
             another thing that needs to be configured by the main
             configuration script, rather than being hardwired. All
             man pages have now been moved into suitably named
             topic-specific sub-directories of the top-level man
             directory, and instead of having a numeric suffix, now
             have the .in suffix, since they are now preprocessed by
             the configure script, in the same fashion as Makefile.in.
             Whithin these *.in versions of the man pages, and within
             Makefile.in, the installation subdirectory (eg. man1) and
             the file-name suffix (eg. 1), are written using
             configuration macros, so that they get expanded to the
             appropriate tokens when the configure script is run. In
             principle, the man pages could also take advantage of
             other configuration macros, such as the one which expands
             to the library installation directory, to include full
             path names to installed files in the documentation, so in
             the future this feature could have more uses than just
             that of parameterizing man page sections.

18/12/2002 mcs@astro.caltech.edu
           man3 man3/* Makefile.in html/index.html update_html
             Markus suggested splitting the gl_get_line(3) man page
             into user and developer sections, and also pointed out
             that the enhance man page should be in section 1, not
             section 3. I have thus created a top-level man
             directory in which to place the various sections, and
             moved the man3 directory into it. The enhance.3 man page
             is now in man/man1/enhance.1. I have extracted all
             user-oriented sections from the gl_get_line(3) man page
             and placed them in a new man7/tecla.7 man page.

18/12/2002 mcs@astro.caltech.edu
           getline.c
             Terminal resizing was broken in normal mode, due to
             me forcing the terminal cursor position to zero in the
             wrong place in gl_check_caught_signal().

14/12/2002 Markus Gyger  (logged here by mcs)
           configure.in configure
             Under Solaris, recent versions of gcc search
             /usr/local/include for header files before the system
             directories. This caused a problem if ncurses was
             installed under Solaris, since the termcap.h include file
             in /usr/local/include ended up being used at compile
             time, whereas the system default version of the curses
             library was used at link time. Since the two libraries
             declare tputs() differently, this evoked a complaint from
             gcc. Markus came up with a way to force Gnu cpp to move
             /usr/local/include to the end of the system-include-file
             search path, where it belongs.

13/12/2002 mcs@astro.caltech.edu
           man3/gl_io_mode.3
             I rewrote the man page which documents the new non-blocking
             server I/O mode.

12/12/2002 mcs@astro.caltech.edu
           demo3.c
             I wrote a new version of demo3.c, using signal handlers
             that call gl_handle_signal() and gl_abandon_line(), where
             previously in this demo, these functions were called from
             the application code.

05/12/2002 mcs@astro.caltech.edu
           getline.c
             gl_normal_io(), gl_raw_io() and gl_handle_signal() and
             gl_abandon_line() are now signal safe, provided that
             signal handlers that call them are installed with sa_mask's
             that block all other signals who's handlers call them.
             This is the case if gl_tty_signals() is used to install
             signal handlers that call any of these functions.

             A major stumbling block that had to be overcome was that
             gl_displayed_char_width() calls isprint(), which can't
             safely be called from a signal handler (eg. under linux,
             the is*() functions all use thread-specific data
             facilities to support per-thread locales, and the
             thread-specific data facilities aren't signal safe). To
             work around this, all functions that modify the
             input-line buffer, now do so via accessor functions which
             also maintain a parallel array of character widths, for
             use by gl_buff_curpos_to_term_curpos() in place of
             gl_displayed_char_width(). Other minor problems were the
             need to avoid tputs(), who's signal safety isn't defined.

05/12/2002 Eric Norum        (logged here by mcs@astro.caltech.edu)
           configure.in
             Eric provided the configuration information needed
             to build shared libraries under Darwin (Max OS X).

05/12/2002 Richard Mlynarik  (logged here by mcs@astro.caltech.edu)
           configure.in
             AC_PROG_RANLIB gets the wrong version of ranlib when
             cross compiling, so has now been replaced by an
             invokation of AC_CHECK_TOOL. In addition, AC_CHECK_TOOL
             is also now used to find an appropriate version of LD.

05/12/2002 mcs@astro.caltech.edu (based on patch by Pankaj Rathore)
           getline.c libtecla.h libtecla.map man3/gl_get_line.3
             The new gl_set_term_size() function provides a way
             to tell gl_get_line() about changes in the size of
             the terminal in cases where the values returned by
             ioctl(TIOCGWINSZ) isn't correct.

05/12/2002 mcs@astro.caltech.edu
           getline.c
             Rather than calling sprintf() to see how much space would
             be needed to print a given number in octal, I wrote a
             gl_octal_width() function, for use by
             gl_displayed_char_width().  This makes the latter
             function async signal safe.

05/12/2002 mcs@astro.caltech.edu
           chrqueue.c
             Whenever the buffer is exhausted, and getting a new
             buffer node would require a call to malloc(), attempt
             to flush the buffer to the terminal. In blocking I/O
             mode this means that the buffer never grows. In
             non-blocking I/O mode, it just helps keep the buffer
             size down.

05/12/2002 mcs@astro.caltech.edu
           freelist.h freelist.c
             The new _idle_FreeListNodes() function queries the
             number of nodes in the freelist which aren't currently
             in use.

05/12/2002 mcs@astro.caltech.edu
           Makefile.stub
             This now accepts all of the targets that the configured
             makefile does, and after configuring the latter makefile,
             it invokes it with the same options.

03/12/2002 mcs@astro.caltech.edu
           mans3/gl_io_mode.3
             I completed the man page for all of the new functions
             related to non-blocking I/O.

01/12/2002 mcs@astro.caltech.edu
           man3/gl_get_line.3
             I wrote a long section on reliable signal handling,
             explaining how gl_get_line() does this, how to make
             use of this in a program, and how to handle signals
             reliably when faced with other blocking functions.
             This basically documents what I have learnt about
             signal handling while working on this library.

01/12/2002 mcs@astro.caltech.edu
           getline.c man3/gl_get_line.3
             In non-blocking server mode, the gl_replace_prompt()
             function can now be used between calls to gl_get_line()
             if the application wants to change the prompt of the
             line that is being edited.

01/12/2002 mcs@astro.caltech.edu
           man3/gl_get_line.3
             I documented the new gl_return_status() and
             gl_error_message() functions.

01/12/2002 mcs@astro.caltech.edu
           getline.c man3/gl_get_line.3
             Added SIGPOLL and SIGXFSZ to the list of signals that
             are trapped by default. These are process termination
             signals, so the terminal needs to be restored to a
             usable state before they terminate the process.

27/11/2002 mcs@astro.caltech.edu
           getline.c libtecla.h
             Completed the essential changes needed to support
             non-blocking server-I/O mode.

             The new gl_io_mode() function allows one to switch to
             and from non-blocking server-I/O mode.

             The new gl_raw_io() function is used in non-blocking
             server-I/O mode to switch the terminal into non-blocking
             raw I/O mode.

             The new gl_normal_io() function is used in non-blocking
             server-I/O mode to switch the restore the terminal to
             a normal, blocking state. This is used to suspend line
             input before suspending the process or writing messages
             to the terminal.

             The new gl_tty_signals() function installs specified
             signals handlers for all signals that suspend, terminate
             or resume processes, and also for signals that indicate
             that the terminal has been resized. This not only saves
             the application from having to keep its own ifdef'd list
             of such signals, of which there are many, but it also
             makes sure that these signal handlers are registered
             correctly. This includes using the sa_mask member of each
             sigaction structure to ensure that only one of these
             handlers runs at a time. This is essential to avoid the
             signal handlers all trying to simultaneously modify
             shared global data.

             The new gl_handle_signal() function is provided for
             responding (from application level) to signals caught by
             the application. It handles process suspension, process
             termination and terminal resize signals.

             The new gl_pending_io() function tells the application
             what direction of I/O gl_get_line() is currently waiting
             for.

             In non-blocking server I/O mode, the new
             gl_abandon_line() function can be called between calls to
             gl_get_line() to discard an input line and force the next
             call to gl_get_line() to start the input of a new line.

             Also, in non-blocking server-I/O gl_get_line() doesn't
             attempt to do anything but return when one of the signals
             that it is configured to catch is caught. This is
             necessary because when in this mode, the application is
             required to handle these signals when gl_get_line() is
             running, and the default configuration of most of these
             signals in gl_get_line() is to restore the terminal then
             call the application signal handlers. This would be a
             case of too many cooks spoiling the broth, so in this
             mode, gl_get_line() always defers to the application's
             signal handlers.
             
26/11/2002 mcs@astro.caltech.edu
           getline.c libtecla.h
             I implemented a couple of new functions to support
             reliable signal handling, as now documented
             (see above) in the gl_get_line(3) man page.

             The new gl_catch_blocked() function tells gl_get_line()
             to unblock all configured signals around calls to
             long-running functions, not only those that aren't
             blocked when gl_get_line() is called. This allows
             the caller to implement reliable signal handling,
             since the unblocking is only done from within code
             protected by sigsetjmp(), which avoids race conditions.

             The new gl_list_signals() function fills a provided
             sigset_t with the set of signals that gl_get_line() is
             currently configured to catch. This allows callers to
             block said signals, such that they are only unblocked by
             gl_get_line() when it is waiting for I/O. When used in
             conjunction with the gl_catch_blocked() function, this
             removes the potential for race conditions.

             Also, when gl_get_line() installs its signal handler,
             it uses the sa_mask member of the sigaction structure
             to ensure that only one instance of this signal handler
             will ever be executing at a time.

25/11/2002 mcs@astro.caltech.edu (bug reported by Pankaj Rathore)
           getline.c
             When any history recall action was invoked when the
             input line buffer was full, an error message would be
             displayed complaining about the length of the string
             in the line input buffer being inconsistent with the
             specified allocated size. This was because instead of
             sending the allocated size of the input line, I was
             sending the length excluding the element that is
             reserved for the '\0' terminator. Sending it the
             correct size corrected the problem.

24/11/2002 mcs@astro.caltech.edu
           getline.c
             All public functions which take GetLine objects as
             arguments now block signals on entry and restore the
             signal mask on return. This was an attempt to make it
             safe to call getline functions from signal handlers, but
             the fact is that the functions that I really wanted this
             to apply to, potentially call malloc(), so this currently
             isn't the case.

23/11/2002 mcs@astro.caltech.edu
           getline.c libtecla.h
             The new gl_return_status() function returns an enumerated
             return status which can be used to query what caused
             gl_get_line() to return.

22/11/2002 mcs@astro.caltech.edu
           Most existing .c and .h files, plus errmsg.c errmsg.h
           Makefile.rules
             Until now, many library functions would report error
             messages to stderr. This isn't appropriate for library
             functions, so in place of this behavior, error messages
             are now recorded in internal ErrMsg objects, and passed
             between modules via new module-specific error querying
             functions. In addition, errno is now set appropriately.
             Thus when gl_get_line() and related functions return an
             error, strerror() can be used to look up system errors,
             and gl_error_message() can be used to recover a higher level
             error message. Note that error messages that are
             responses to user actions continue to be reported to the
             terminal, as before.

21/11/2002 mcs@astro.caltech.edu
           getline.c keytab.h keytab.c Makefile.rules
             I wrote a new version of _kt_lookup_binding() that didn't
             require the caller to have access to the innards of a
             KeyTab object. This then enabled me to move the definition
             of KeyTab objects into keytab.c and make the typedef in
             keytab.h opaque. Many nested includes were also moved from
             keytab.h into keytab.c.

05/11/2002 mcs@astro.caltech.edu
           getline.c libtecla.map libtecla.h demo3.c
             I split the old gl_resize_terminal() function into
             two parts, gl_query_size() and gl_update_size(), with
             the latter calling the former to get the new terminal
             size.

05/11/2002 mcs@astro.caltech.edu
           getline.c
             I fixed a long time bug in the terminal resizing code.
             When the cursor wasn't on the last terminal line of the
             input line, the resizing code would redisplay the
             the line one or more lines above where it should be
             restored. This was due to an error in the calculation of
             the number of lines above the cursor position.

04/11/2002 mcs@astro.caltech.edu
           demo.c demo2.c demo3.c
             I used the new gl_display_text() function to display
             introductory text at the startup of each of the demo
             programs. The text is enclosed within a box of asterixes,
             drawn dynamically to fit within the confines of the
             available terminal width.

04/11/2002 mcs@astro.caltech.edu
           libtecla.h getline.c ioutil.c ioutil.h Makefile.rules
           libtecla.map man3/gl_get_line.3 man3/gl_display_text.3
             Needing a way to display introductory text intelligently
             in the demo programs, I wrote and documented the
             gl_display_text() function. This justifies arbitrary
             length text within the bounds of the terminal width,
             with or without optional indentation, prefixes and
             suffixes.

03/11/2002 mcs@astro.caltech.edu
           demo3.c Makefile.rules
             I wrote a new demonstration program. This program acts
             exactly like the main demonstration program, except that
             it uses an external event loop instead of using the
             gl_get_line() internal event loop. This is thus an example
             of the new non-blocking server I/O facility.

02/11/2002 mcs@astro.caltech.edu
           getline.c keytab.c keytab.h libtecla.h man3/gl_get_line.3
           man3/gl_completion_action.3
             I added the ability to register additional word
             completion actions via the new function
             gl_completion_action().  All action functions now take a
             new (void *data) argument, which is stored with the
             function in the symbol table of actions. The new
             gl_completion_action() function uses this feature to
             record dynamically allocated objects containing the
             specified completion function and callback data along
             with either the gl_complete_word() action function, or
             the gl_list_completions() action function.  These two
             actions continue to use the builtin completion functions
             when their data pointer is NULL.

20/10/2002 mcs@astro.caltech.edu
           The following are changes merged from the non-blocking
           gl_get_line() development branch.

           getline.c
             I wrote a gl_start_newline() function, to replace all of
             the explicit calls to output \r\n to stdout.

             Informational messages are now written to the terminal
             using a new variadic function called gl_print_info().
             This starts a newline, writes string arguments until a
             special argument, GL_END_INFO, is seen, then starts
             another newline.

             Changed _output_ to _print_ in the following function
             names gl_output_control_sequence(), gl_output_char(),
             gl_output_string() and gl_output_raw_string().

             gl_print_raw_string() now has a length argument, so that
             strings that aren't terminated with '\0' can be printed.

             The display of the initial contents of a new line to be
             edited has been moved into a new function called
             gl_present_line().

             The gl_get_input_line() function now takes the prompt
             string as an argument so that gl_replace_prompt() can be
             called from within this function instead of from
             gl_get_line().

             Keyboard input is now buffered in a persistent buffer in
             the parent GetLine object. gl_read_character() checks
             this for unprocessed characters in preference to calling
             gl_read_terminal() to append characters to it.  A new
             function, gl_discard_chars(), removes processed
             characters from this buffer. This change is in
             preparation for a non-blocking version of gl_get_line(),
             where partially input key-sequences must be stored
             between calls to gl_get_line().

           getline.c getline.h history.c history.h cplmatch.c \
           cplmatch.h expand.c expand.h
             All terminal output from gl_get_line() is now routed
             through a GL_WRITE_FN() callback function called
             gl_write_fn. Internal functions in cplmatch.c,
             expand.c and history.c have been created which take
             such callbacks to write output. These are used both
             by functions in getline.c, to display file completions,
             expansions, history etc, and as the internals of existing
             public functions in these files that print to stdio
             streams. In the latter case an internal stdio
             GL_WRITE_FN() callback is substituted, so that the
             functions behave as before.

           getline.c chrqueue.c chrqueue.h
             The gl_write_fn() callback used by gl_get_line() now
             writes to a queue, implemented in chrqueue.c. This queue
             is implemented as a list of blocks of buffer segments,
             the number of which shrink and grow as
             needed. The contents of the queue are flushed to the
             terminal via another GL_WRITE_FN() callback passed to the
             queue object. Currently gl_get_line() passes an internal
             function assigned to gl->flush_fn, called
             gl_flush_terminal(), which writes the contents of the
             queue to the terminal, and knows how to handle both
             blocking and non-blocking I/O. The output queue is
             designed to be flushed to the terminal incrementally, and
             thereby also facilitates non-blocking I/O.

           getline.c getline.h
             gl_get_line() now reads all input via the GL_READ_FN()
             callback, assigned to gl->read_fn. Currently this is
             set to an internal function called gl_read_terminal(),
             which knows how to handle both blocking and
             non-blocking I/O.

           getline.c libtecla.h
             The new gl_set_nonblocking() function can be used to
             enable or disable non-blocking I/O. The default is still
             blocking I/O. In non-blocking mode, the terminal is told
             not to wait when either reading or writing would block.
             gl_get_line() then returns, with a return value of NULL,
             but with the terminal left in raw mode, so that the
             caller's event loop can detect key presses. The caller
             should call gl_return_status() to check whether the NULL
             return value was due to an error, lack of input, or
             inability to write to the terminal without waiting. If
             either reading or writing was said to have blocked, the
             user then should check for I/O readiness in the specified
             direction before calling gl_get_line() again to
             incrementally build up the input line.

05/08/2002 mcs@astro.caltech.edu
           man3/gl_get_line.3 man3/gl_inactivity_timeout.3
             I documented the new gl_inactivity_timeout() function.

08/07/2002 mcs@astro.caltech.edu
           libtecla.h getline.c libtecla.map
             I added a new gl_inactivity_timeout() function. On
             systems that have the select system call, this provides
             the option of registering a function that is then called
             whenever no I/O activity has been seen for more than a
             specified period of time. Like the gl_watch_fd()
             facility, timeout callbacks return a code which tells
             gl_get_line() how to proceed after the timeout has been
             handled.
             
04/07/2002 mcs@astro.caltech.edu  (based on a bug report from Michael MacFaden)
           getline.c
             The internal event handler wasn't responding to write
             events on client file descriptors, due to a typo which
             resulted in read events being checked for twice, and
             writes not checked for at all.
           pathutil.c
             The amount of space to allocate for pathnames is supposed
             to come from PATH_MAX in limits.h, but I had neglected to
             include limits.h. This went unnoticed because on most
             systems the equivalent number is deduced by calling
             pathconf(). Apparently under NetBSD this function doesn't
             work correctly over NFS mounts.

30/05/2002 Version 1.4.1 released.

25/05/2002 mcs@astro.caltech.edu  (based on suggestions by Paul Smith)
           pathutil.c
             Apparently, under QNX pathconf("/",_PC_PATH_MAX) returns
             EINVAL. At Paul's suggestion I have modified the code to
             silently substitute the existing MAX_PATHLEN_FALLBACK
             value if pathconf() returns an error of any kind.
           homedir.c
             Under QNX, sysconf(_SC_GETPW_R_SIZE_MAX) also apparently
             returns EINVAL, so as with pathconf() I modified the code
             to substitute a fallback default, rather than
             complaining and failing.
           enhance.c
             Paul told me that the inclusion of sys/termios.h was
             causing compilation of enhance.c to fail under QNX. This
             line is a bug.  The correct thing to do is include
             termios.h without a sub-directory prefix, as I was
             already doing futher up in the file, so I have just
             removed the errant include line.

07/05/2002 mcs@astro.caltech.edu  (async development branch only)
           getline.c
             gl_read_character() now caches and reads unprocessed
             characters from a key-press lookahead buffer. Whenever
             gl_intepret_char() receives a new character which makes
             an initially promising key-sequence no longer match the
             prefix of any binding, it now simply discards the first
             character from the key-press buffer and resets the buffer
             pointer so that the next call to gl_read_character()
             returns the character that followed it, from the buffer.
           getline.c
             The part of gl_get_input_line() which preloads, displays
             and prepares to edit a new input line, has now been moved
             into a function called gl_present_line().

12/02/2002 mcs@astro.caltech.edu
           getline.c configure.in configure
             Mac OS X doesn't have a term.h or termcap.h, but it does
             define prototypes for tputs() and setupterm(), so the
             default prototypes that I was including if no headers
             where available, upset it. I've removed these prototypes.
             I also now conditionally include whichever is found of
             curses.h and ncurses/curses.h for both termcap and
             terminfo (before I wasn't including curses.h when
             termcap was selected).

12/02/2002 mcs@astro.caltech.edu
           Updated version number to 1.4.1, ready for a micro
           release.

12/02/2002 mcs@astro.caltech.edu
           html/index.html
             Added Mac OS X and Cygwin to the list of systems that
             can compile libtecla.

12/02/2002 mcs@astro.caltech.edu
           getline.c
             Under Mac OS X, the tputs() callback function returns
             void, instead of the int return value used by other
             systems. This declaration is now used if both __MACH__
             and __APPLE__ are defined. Hopefully these are the
             correct system macros to check. Thanks for Stephan
             Fiedler for providing information on Mac OS X.

11/02/2002 mcs@astro.caltech.edu
           configure.in configure getline.c
             Some systems don't have term.h, and others have it hidden
             in an ncurses sub-directory of the standard system include
             directory. If term.h can't be found, simply don't include
             it. If it is in an ncurses sub-directory, include
             ncurses/term.h instead of term.h.

04/02/2002 mcs@astro.caltech.edu
           configure.in configure Makefile.in Makefile.rules
             Use ranlib on systems that need it (Mac OS X).  Also,
             make all components of the installation directories where
             needed, instead of assuming that they exist.

04/02/2002 mcs@astro.caltech.edu
           getline.c
             When the tab completion binding was unbound from the tab
             key, hitting the tab key caused gl_get_line() to ring the
             bell instead of inserting a tab character. This is
             problematic when using the 'enhance' program with
             Jython, since tabs are important in Python. I have
             corrected this.

10/12/2001 Version 1.4.0 released.

10/12/2001 mcs@astro.caltech.edu
           getline.c
             If the TIOCGWINSZ ioctl doesn't work, as is the case when
             running in an emacs shell, leave the size unchanged, rather
             than returning a fatal error.

07/12/2001 mcs@astro.caltech.edu
           configure.in configure
             Now that the configure version of CFLAGS is included in
             the makefile, I noticed that the optimization flags -g
             and -O2 had been added. It turns out that if CFLAGS isn't
             already set, the autoconf AC_PROG_CC macro initializes it
             with these two optimization flags. Since this would break
             backwards compatibility in embedded distributions that
             already use the OPT= makefile argument, and because
             turning debugging on needlessly bloats the library, I now
             make sure that CFLAGS is set before calling this macro.

07/12/2001 mcs@astro.caltech.edu
           enhance.c
             Use argv[0] in error reports instead of using a
             hardcoded macro.

07/12/2001 mcs@astro.caltech.edu
           getline.c
             The cut buffer wasn't being cleared after being
             used as a work buffer by gl_load_history().

06/12/2001 mcs@astro.caltech.edu
           configure.in configure
             I removed my now redundant definition of SUN_TPUTS from
             CFLAGS. I also added "-I/usr/include" to CFLAGS under
             Solaris to prevent gcc from seeing conflicting versions
             of system header files in /usr/local/include.

06/12/2001 Markus Gyger (logged here by mcs)
           Lots of files.
             Lots of corrections to misspellings and typos in the
             comments.
           getline.c
             Markus reverted a supposed fix that I added a day or two
             ago. I had incorrectly thought that in Solaris 8, Sun had
             finally brought their declaration of the callback
             function of tputs() into line with other systems, but it
             turned out that gcc was pulling in a GNU version of
             term.h from /usr/local/include, and this was what
             confused me.

05/12/2001 mcs@astro.caltech.edu
           Makefile.in
             I added @CFLAGS@ to the CFLAGS assignment, so that
             if CFLAGS is set as an environment variable when
             configure is run, the corresponding make variable
             includes its values in the output makefile.

05/12/2001 mcs@astro.caltech.edu
           getline.c libtecla.h libtecla.map man3/gl_get_line.3
           man3/gl_last_signal.3
             I added a function that programs can use to find out
             which signal caused gl_get_line() to return EINTR.

05/12/2001 mcs@astro.caltech.edu
           getline.c
             When the newline action was triggered by a printable
             character, it failed to display that character. It now
             does. Also, extra control codes that I had added, to
             clear to the end of the display after the carriage return,
             but before displaying the prompt, were confusing expect
             scripts, so I have removed them. This step is now done
             instead in gl_redisplay() after displaying the full input
             line.

05/12/2001 mcs@astro.caltech.edu
           getline.c man3/gl_get_line.3
             A user convinced me that continuing to invoke meta
             keybindings for meta characters that are printable is a
             bad idea, as is allowing users to ask to have setlocale()
             called behind the application's back. I have thus changed
             this. The setlocale configuration option has gone, and
             gl_get_line() is now completely 8-bit clean, by default.
             This means that if a meta character is printable, it is
             treated as a literal character, rather than a potential
             M-c binding.  Meta bindings can still be invoked via
             their Esc-c equivalents, and indeed most terminal
             emulators either output such escape pairs by default when
             the meta character is pressed, or can be configured to do
             so. I have documented how to configure xterm to do this,
             in the man page.

03/12/2001 mcs@astro.caltech.edu
           getline.c man3/gl_get_line.3
             gl_get_line() by default now prints any 8-bit printable
             characters that don't match keybindings. Previously
             characters > 127 were only printed if preceded by the
             literal-next action.  Alternatively, by placing the
             command literal_if_printable in the tecla configuration
             file, all printable characters are treated as literal
             characters, even if they are bound to action functions.

             For international users of programs written by
             programmers that weren't aware of the need to call
             setlocale() to support alternate character sets, the
             configuration file can now also contain the single-word
             command "setlocale", which tells gl_get_line() to remedy
             this.

27/11/2001 mcs@astro.caltech.edu
           demo.c demo2.c enhance man3/gl_get_line.3
             All demos and programs now call setlocale(LC_CTYPE,"").
             This makes them support character sets of different
             locales, where specified with the LC_CTYPE, LC_ALL, or
             LANG environment variables. I also added this to the demo
             in the man page, and documented its effect.

27/11/2001 mcs@astro.caltech.edu
           getline.c
             When displaying unsigned characters with values over
             127 literally, previously it was assumed that they would
             all be displayable. Now isprint() is consulted, and if it
             says that a character isn't printable, the character code
             is displayed in octal like \307. In non-C locales, some
             characters with values > 127 are displayable, and
             isprint() tells gl_get_line() which are and which aren't.

27/11/2001 mcs@astro.caltech.edu
           getline.c pathutil.c history.c enhance.c demo2.c
             All arguments of the ctype.h character class functions
             are now cast to (int)(unsigned char). Previously they
             were cast to (int), which doesn't correctly conform to
             the requirements of the C standard, and could cause
             problems for characters with values > 127 on systems
             with signed char's.

26/11/2001 mcs@astro.caltech.edu
           man3/enhance.3 man3/libtecla.3
             I started writing a man page for the enhance program.

26/11/2001 mcs@astro.caltech.edu
           Makefile.in Makefile.rules INSTALL
             It is now possible to specify whether the demos and other
             programs are to be built, by overriding the default
             values of the DEMOS, PROGRAMS and PROGRAMS_R variables.
             I have also documented the BINDIR variable and the
             install_bin makefile target.

22/11/2001 mcs@astro.caltech.edu
           getline.c libtecla.h libtecla.map man3/gl_get_line.3
           man3/gl_ignore_signal.3 man3/gl_trap_signal.3
             Signal handling has now been modified to be customizable.
             Signals that are trapped by default can be removed from
             the list of trapped signals, and signals that aren't
             currently trapped, can be added to the list. Applications
             can also specify the signal and terminal environments in
             which an application's signal handler is invoked, and
             what gl_get_line() does after the signal handler returns.

13/11/2001 mcs@astro.caltech.edu
           getline.c man3/gl_get_line.3
             Added half-bright, reverse-video and blinking text to the
             available prompt formatting options.
           getline.c
             Removed ^O from the default VT100 sgr0 capability
             string.  Apparently it can cause problems with some
             terminal emulators, and we don't need it, since it turns
             off the alternative character set mode, which we don't
             use.
           getline.c
             gl_tigetstr() and gl_tgetstr() didn't guard against the
             error returns of tigetstr() and tgetstr() respectively.
             They now do.

11/11/2001 mcs@astro.caltech.edu
           getline.c libtecla.h libtecla.map man3/gl_get_line.3
           man3/gl_prompt_style.3
             Although the default remains to display the prompt string
             literally, the new gl_prompt_style() function can be used
             to enable text attribute formatting directives in prompt
             strings, such as underlining, bold font, and highlighting
             directives.

09/11/2001 mcs@astro.caltech.edu
           enhance.c Makefile.rules configure.in configure
             I added a new program to the distribution that allows one
             to run most third party programs with the tecla library
             providing command-line editing.

08/11/2001 mcs@astro.caltech.edu
           libtecla.h getline.c man3/gl_get_line.3 history.c history.h
             I added a max_lines argument to gl_show_history() and
             _glh_show_history(). This can optionally be used to
             set a limit on the number of history lines displayed.
           libtecla.h getline.c man3/gl_get_line.3
             I added a new function called gl_replace_prompt(). This
             can be used by gl_get_line() callback functions to
             request that a new prompt be use when they return.

06/11/2001 mcs@astro.caltech.edu
           getline.c man3/gl_get_line.3
             I implemented, bound and documented the list-history
             action, used for listing historical lines of the current
             history group.
           getline.c man3/gl_get_line.3 man3/gl_echo_mode.3
             I wrote functions to specify and query whether subsequent
             lines will be visible as they are being typed.

28/10/2001 mcs@astro.caltech.edu
           getline.c man3/gl_get_line.3
             For those cases where a terminal provides its own
             high-level terminal editing facilities, you can now
             specify an edit-mode argument of 'none'. This disables
             all tecla key bindings, and by using canonical terminal
             input mode instead of raw input mode, editing is left up
             to the terminal driver.

21/10/2001 mcs@astro.caltech.edu
           libtecla.h getline.c history.c history.h
           man3/gl_get_line.3 man3/gl_history_info.3
             I added the new gl_state_of_history(),
             gl_range_of_history() and gl_size_of_history()
             functions for querying information about the
             history list.
           history.c
             While testing the new gl_size_of_history()
             function, I noticed that when the history buffer
             wrapped, any location nodes of old lines between
             the most recent line and the end of the buffer
             weren't being removed. This could result in bogus
             entries appearing at the start of the history list.
             Now fixed.

20/10/2001 mcs@astro.caltech.edu

           libtecla.h getline.c history.c history.h
           man3/gl_get_line.3 man3/gl_lookup_history.3
             I added a function called gl_lookup_history(), that
             the application can use to lookup lines in the history
             list.
           libtecla.h getline.c history.c history.h man3/gl_get_line.3
             gl_show_history() now takes a format string argument
             to control how the line is displayed, and with what
             information. It also now provides the option of either
             displaying all history lines or just those of the
             current history group.
           getline.c man3/gl_get_line.3
             gl_get_line() only archives lines in the history buffer
             if the newline action was invoked by a newline or
             carriage return character.

16/10/2001 mcs@astro.caltech.edu

           history.c history.h getline.c libtecla.h libtecla.map
           man3/gl_get_line.3 man3/gl_resize_history.3
           man3/gl_limit_history.3 man3/gl_clear_history.3
           man3/gl_toggle_history.3
	     I added a number of miscellaneous history configuration
	     functions. You can now resize or delete the history
	     buffer, limit the number of lines that are allowed in the
	     buffer, clear either all history or just the history of
	     the current history group, and temporarily enable and
	     disable the history mechanism.

13/10/2001 mcs@astro.caltech.edu

           getline.c
             tputs_fp is now only declared if using termcap or
             terminfo.
           getline.c libtecla.map man3/gl_get_line.3
           man3/gl_terminal_size.3
             I added a public gl_terminal_size() function for
             updating and querying the current size of the terminal.
           update_version configure.in libtecla.h
             A user noted that on systems where the configure script
             couldn't be used, it was inconvenient to have the version
             number macros set by the configure script, so they are
             now specified in libtecla.h. To reduce the likelihood
             that the various files where the version number now
             appears might get out of sync, I have written the
             update_version script, which changes the version number
             in all of these files to a given value.

01/10/2001 mcs@astro.caltech.edu

           getline.c history.c history.h man3/gl_get_line.3
             I added a max_lines argument to gl_save_history(), to
             allow people to optionally place a ceiling on the number
             of history lines saved. Specifying this as -1 sets the
             ceiling to infinity.

01/10/2001 mcs@astro.caltech.edu

           configure.in configure
             Under digital unix, getline wouldn't compile with
             _POSIX_C_SOURCE set, due to type definitions needed by
             select being excluded by this flag. Defining the
             _OSF_SOURCE macro as well on this system, resolved this.

30/09/2001 mcs@astro.caltech.edu

           getline.c libtecla.h history.c history.h man3/gl_get_line.3
           man3/gl_group_history.3
             I implemented history streams. History streams
             effectively allow multiple history lists to be stored in
             a single history buffer. Lines in the buffer are tagged
             with the current stream identification number, and
             lookups only consider lines that are marked with the
             current stream identifier.
           getline.c libtecla.h history.c history.h man3/gl_get_line.3
           man3/gl_show_history.3
             The new gl_show_history function displays the current
             history to a given stdio output stream.

29/09/2001 mcs@astro.caltech.edu

           getline.c
             Previously new_GetLine() installed a persistent signal
             handler to be sure to catch the SIGWINCH (terminal size
             change) signal between calls to gl_get_line(). This had
             the drawback that if multiple GetLine objects were
             created, only the first GetLine object used after the
             signal was received, would see the signal and adapt to
             the new terminal size. Instead of this, a signal handler
             for sigwinch is only installed while gl_get_line() is
             running, and just after installing this handler,
             gl_get_line() checks for terminal size changes that
             might have occurred while the signal handler wasn't
             installed.
           getline.c
             Dynamically allocated copies of capability strings looked
             up in the terminfo or termcap databases are now made, so
             that calls to setupterm() etc for one GetLine object
             don't get trashed when another GetLine object calls
             setupterm() etc. It is now safe to allocate and use
             multiple GetLine objects, albeit only within a single
             thread.
           
28/09/2001 mcs@astro.caltech.edu

           version.c Makefile.rules
             I added a function for querying the version number of
             the library.

26/09/2001 mcs@astro.caltech.edu

           getline.c man3/gl_get_line.3
             I added the new gl_watch_fd() function, which allows
             applications to register callback functions to be invoked
             when activity is seen on arbitrary file descriptors while
             gl_get_line() is awaiting keyboard input from the user.

           keytab.c
             If a request is received to delete a non-existent
             binding, which happens to be an ambiguous prefix of other
             bindings no complaint is now generated about it being
             ambiguous.

23/09/2001 mcs@astro.caltech.edu

           getline.c history.c history.h man3/gl_get_line.3
           libtecla.map demo.c
             I added new public functions for saving and restoring the
             contents of the history list. The demo program now uses
             these functions to load and save history in ~/.demo_history.

23/09/2001 mcs@astro.caltech.edu

           getline.c
             On trying the demo for the first time on a KDE konsole
             terminal, I discovered that the default M-O binding
             to repeat history was hiding the arrow keys, which are
             M-OA etc. I have removed this binding. The M-o (ie the
             lower case version of this), is still bound.

18/09/2001 mcs@astro.caltech.edu

           getline.c man3/gl_get_line.3 libtecla.map
             Automatic reading of ~/.teclarc is now postponed until
             the first call to gl_get_line(), to give the application
             the chance to specify alternative configuration sources
             with the new function gl_configure_getline(). The latter
             function allows configuration to be done with a string, a
             specified application-specific file, and/or a specified
             user-specific file. I also added a read-init-files action
             function, for re-reading the configuration files, if any.
             This is by default bound to ^X^R. This is all documented
             in gl_get_line.3.

08/09/2001 mcs@astro.caltech.edu

           getline.c man3/gl_get_line.3
             It is now possible to bind actions to key-sequences
             that start with printable characters. Previously
             keysequences were required to start with meta or control
             characters. This is documented in gl_get_line.3.

           getline.c man3/gl_get_line.3
             A customized completion function can now arrange for
             gl_get_line() to return the current input line whenever a
             successful completion has been made. This is signalled by
             setting the last character of the optional continuation
             suffix to a newline character. This is documented in
             gl_get_line.3.

05/07/2001 Bug reported by Mike MacFaden, fixed by mcs

           configure.in
             There was a bug in the configure script that only
             revealed itself on systems without termcap but not
             terminfo (eg. NetBSD). I traced the bug back to a lack of
             sufficient quoting of multi-line m4 macro arguments in
             configure.in, and have now fixed this and recreated the
             configure script.

05/07/2001 Bug reported and patched by Mike MacFaden (patch modified
           by mcs to match original intentions).

           getline.c
             getline.c wouldn't compile when termcap was selected as
             the terminal information database. setupterm() was being
             passed a non-existent variable, in place of the term[]
             argument of gl_control_strings(). Also if
             gl_change_terminal() is called with term==NULL, "ansi"
             is now substituted.

02/07/2001 Version 1.3.3 released.

27/06/2001 mcs@astro.caltech.edu

           getline.c expand.c cplmatch.c
             Added checks to fprintf() statements that write to the
             terminal.
           getline.c
             Move the cursor to the end of the line before suspending,
             so that the cursor doesn't get left in the middle of the
             input line.
           Makefile.in
             On systems that don't support shared libraries, the
             distclean target of make deleted libtecla.h. This has
             now been fixed.
           getline.c
             gl_change_terminal() was being called by gl_change_editor(),
             with the unwanted side effect that raw terminal modes were
             stored as those to be restored later, if called by an
             action function. gl_change_terminal() was being called in
             this case to re-establish terminal-specific key bindings,
             so I have just split this part of the function out into
             a separate function for both gl_change_editor() and
             gl_change_terminal() to call.

12/06/2001 mcs@astro.caltech.edu

           getline.c
             Signal handling has been improved. Many more signals are
             now trapped, and instead of using a simple flag set by a
             signal handler, race conditions are avoided by blocking
             signals during most of the gl_get_line() code, and
             unblocking them via calls to sigsetjmp(), just before
             attempting to read each new character from the user.
             The matching use of siglongjmp() in the signal
             handlers ensures that signals are reblocked correctly
             before they are handled. In most cases, signals cause
             gl_get_line() to restore the terminal modes and signal
             handlers of the calling application, then resend the
             signal to the application. In the case of SIGINT, SIGHUP,
             SIGPIPE, and SIGQUIT, if the process still exists after
             the signals are resent, gl_get_line() immediately returns
             with appropriate values assigned to errno. If SIGTSTP,
             SIGTTIN or SIGTTOU signals are received, the process is
             suspended. If any other signal is received, and the
             process continues to exist after the signal is resent to
             the calling application, line input is resumed after the
             terminal is put back into raw mode, the gl_get_line()
             signal handling is restored, and the input line redrawn.
           man/gl_get_line(3)
             I added a SIGNAL HANDLING section to the gl_get_line()
             man page, describing the new signal handling features.

21/05/2001 Version 1.3.2 released.

21/05/2001 mcs@astro.caltech.edu

           getline.c
             When vi-replace-char was used to replace the character at
             the end of the line, it left the cursor one character to
             its right instead of on top of it. Now rememdied.
           getline.c
             When undoing, to properly emulate vi, the cursor is now
             left at the leftmost of the saved and current cursor
             positions.
           getline.c man3/gl_get_line.3
             Implemented find-parenthesis (%), delete-to-paren (M-d%),
             vi-change-to-paren (M-c%), copy-to-paren (M-y%).
           cplfile.c pcache.c
             In three places I was comparing the last argument of
             strncmp() to zero instead of the return value of
             strncmp().

20/05/2001 mcs@astro.caltech.edu

           getline.c man3/gl_get_line.3
             Implemented and documented the vi-repeat-change action,
             bound to the period key. This repeats the last action
             that modified the input line.

19/05/2001 mcs@astro.caltech.edu

           man3/gl_get_line.3
             I documented the new action functions and bindings
             provided by Tim Eliseo, plus the ring-bell action and
             the new "nobeep" configuration option.
           getline.c
             I modified gl_change_editor() to remove and reinstate the
             terminal settings as well as the default bindings, since
             these have editor-specific differences. I also modified
             it to not abort if a key-sequence can't be bound for some
             reason. This allows the new vi-mode and emacs-mode
             bindings to be used safely.
           getline.c
             When the line was re-displayed on receipt of a SIGWINCH
             signal, the result wasn't visible until the next
             character was typed, since a call to fflush() was needed.
             gl_redisplay_line() now calls gl_flush_output() to remedy
             this.

17/05/2001 mcs@astro.catlech.edu

           getline.c
             Under Linux, calling fflush(gl->output_fd) hangs if
             terminal output has been suspended with ^S. With the
             tecla library taking responsability for reading the stop
             and start characters this was a problem, because once
             hung in fflush(), the keyboard input loop wasn't entered,
             so the user couldn't type the start character to resume
             output.  To remedy this, I now have the terminal process
             these characters, rather than the library.

12/05/2001 mcs@astro.caltech.edu

           getline.c
             The literal-next action is now implemented as a single
             function which reads the next character itself.
             Previously it just set a flag which effected the
             interpretation of the next character read by the input
             loop.
           getline.c
             Added a ring-bell action function. This is currently
             unbound to any key by default, but it is used internally,
             and can be used by users that want to disable any of the
             default key-bindings.

12/05/2001 Tim Eliseo    (logged here by mcs)

           getline.c
             Don't reset gl->number until after calling an action
             function. By looking at whether gl->number is <0 or
             not, action functions can then tell whether the count
             that they were passed was explicitly specified by the
             user, as opposed to being defaulted to 1.
           getline.c
             In vi, the position at which input mode is entered
             acts as a barrier to backward motion for the few
             backward moving actions that are enabled in input mode.
             Tim added this barrier to getline.
           getline.c
             In gl_get_line() after reading an input line, or
             having the read aborted by a signal, the sig_atomic_t
             gl_pending_signal was being compared to zero instead
             of -1 to see if no signals had been received.
             gl_get_line() will thus have been calling raise(-1),
             which luckily didn't seem to do anything. Tim also
             arranged for errno to be set to EINTR when a signal
             aborts gl_get_line().
           getline.c
             The test in gl_add_char_to_line() for detecting
             when overwriting a character with a wider character,
             had a < where it needed a >. Overwriting with a wider
             character thus overwrote trailing characters. Tim also
             removed a redundant copy of the character into the
             line buffer.
           getline.c
             gl_cursor_left() and gl->cursor_right() were executing
             a lot of redundant code, when the existing call to the
             recently added gl_place_cursor() function, does all that
             is necessary.
           getline.c
             Remove redundant code from backward_kill_line() by
             re-implimenting in terms of gl_place_cursor() and
             gl_delete_chars().
           getline.c
             gl_forward_delete_char() now records characters in cut
             buffer when in vi command mode.
           getline.c
             In vi mode gl_backward_delete_char() now only deletes
             up to the point at which input mode was entered. Also
             gl_delete_chars() restores from the undo buffer when
             deleting in vi insert mode.
           getline.c
             Added action functions, vi-delete-goto-column,
             vi-change-to-bol, vi-change-line, emacs-mode, vi-mode,
             vi-forward-change-find, vi-backward-change-find,
             vi-forward-change-to, vi-backward-change-to,
             vi-change-goto-col, forward-delete-find, backward-delete-find,
             forward-delete-to, backward-delete-to,
             delete-refind, delete-invert-refind, forward-copy-find,
             backward-copy-find, forward-copy-to, backward-copy-to
             copy-goto-column, copy-rest-of-line, copy-to-bol, copy-line,
             history-re-search-forward, history-re-search-backward.

06/05/2001 Version 1.3.1 released.

03/05/2001 mcs@astro.caltech.edu

           configure.in
             Old versions of GNU ld don't accept version scripts.
             Under Linux I thus added a test to try out ld with
             the --version-script argument to see if it works.
             If not, version scripts aren't used.
           configure.in
             My test for versions of Solaris earlier than 7
             failed when confronted by a three figure version
             number (2.5.1). Fixed.

30/04/2001 mcs@astro.caltech.edu

           getline.c
             In vi mode, history-search-backward and
             history-search-forward weren't doing anything when
             invoked at the start of an empty line, whereas
             they should have acted like up-history and down-history.
           Makefile.in Makefile.rules
             When shared libraries are being created, the build
             procedure now arranges for any alternate library
             links to be created as well, before linking the
             demos. Without this the demos always linked to the
             static libraries (which was perfectly ok, but wasn't a
             good example).
           Makefile.in Makefile.rules
             On systems on which shared libraries were being created,
             if there were no alternate list of names, make would
             abort due to a Bourne shell 'for' statement that didn't
             have any arguments. Currently there are no systems who's
             shared library configurations would trigger this
             problem.
           Makefile.rules
             The demos now relink to take account of changes to the
             library.
           configure.in configure
             When determining whether the reentrant version of the
             library should be compiled by default, the configure
             script now attempts to compile a dummy program that
             includes all of the appropriate system headers and
             defines _POSIX_C_SOURCE. This should now be a robust test
             on systems which use C macros to alias these function
             names to other internal functions.
           configure.in
             Under Solaris 2.6 and earlier, the curses library is in
             /usr/ccs/lib. Gcc wasn't finding this. In addition to
             remedying this, I had to remove "-z text" from
             LINK_SHARED under Solaris to get it to successfully
             compile the shared library against the static curses
             library.
           configure.in
             Under Linux the -soname directive was being used
             incorrectly, citing the fully qualified name of the
             library instead of its major version alias. This will
             unfortunately mean that binaries linked with the 1.2.3
             and 1.2.4 versions of the shared library won't use
             later versions of the library unless relinked.

30/04/2001 mcs@astro.caltech.edu

           getline.c
             In gl_get_input_line(), don't redundantly copy the
             start_line if start_line == gl->line.

30/04/2001 Version 1.3.0 released.

28/04/2001 mcs@astro.caltech.edu

           configure.in
             I removed the --no-undefined directive from the Linux
             LINK_SHARED command. After recent patches to our RedHat
             7.0 systems ld started reporting some internal symbols of
             libc as being undefined.  Using nm on libc indicated that
             the offending symbols are indeed defined, albeit as
             "common" symbols, so there appears to be a bug in
             RedHat's ld. Removing this flag allows the tecla shared
             library to compile, and programs appear to function fine.
           man3/gl_get_line.3
             The default key-sequence used to invoke the
             read-from-file action was incorrectly cited as ^Xi
             instead of ^X^F.

26/04/2001 mcs@astro.caltech.edu

           getline.c man3/gl_get_line.3
             A new vi-style editing mode was added. This involved
             adding many new action functions, adding support for
             specifying editing modes in users' ~/.teclarc files,
             writing a higher level cursor motion function to support
             the different line-end bounds required in vi command
             mode, and a few small changes to support the fact that vi
             has two modes, input mode and command mode with different
             bindings.

             When vi editing mode is enabled, any binding that starts
             with an escape or a meta character, is interpreted as a
             command-mode binding, and switches the library to vi
             command mode if not already in that mode. Once in command
             mode the first character of all keysequences entered
             until input mode is re-enabled, are quietly coerced to
             meta characters before being looked up in the key-binding
             table. So, for example, in the key-binding table, the
             standard vi command-mode 'w' key, which moves the cursor
             one word to the right, is represented by M-w. This
             emulates vi's dual sets of bindings in a natural way
             without needing large changes to the library, or new
             binding syntaxes. Since cursor keys normally emit
             keysequences which start with escape, it also does
             something sensible when a cursor key is pressed during
             input mode (unlike true vi, which gets upset).

             I also added a ^Xg binding for the new list-glob action
             to both the emacs and vi key-binding tables. This lists
             the files that match the wild-card expression that
             precedes it on the command line.

             The function that reads in ~/.teclarc used to tell
             new_GetLine() to abort if it encountered anything that it
             didn't understand in this file. It now just reports an
             error and continues onto the next line.
           Makefile.in:
             When passing LIBS=$(LIBS) to recursive invokations of
             make, quotes weren't included around the $(LIBS) part.
             This would cause problems if LIBS ever contained more
             than one word (with the supplied configure script this
             doesn't happen currently). I added these quotes.
           expand.c man3/ef_expand_file.3:
             I wrote a new public function called ef_list_expansions(),
             to list the matching filenames returned by
             ef_expand_file().

             I also fixed the example in the man page, which cited
             exp->file instead of exp->files, and changed the
             dangerous name 'exp' with 'expn'.
           keytab.c:
             Key-binding tables start with 100 elements, and are
             supposedly incremented in size by 100 elements whenever
             the a table runs out of space. The realloc arguments to
             do this were wrong. This would have caused problems if
             anybody added a lot of personal bindings in their
             ~/.teclarc file. I only noticed it because the number of
             key bindings needed by the new vi mode exceeded this
             number.
           libtecla.map
             ef_expand_file() is now reported as having been added in
             the upcoming 1.3.0 release.

25/03/2001 Markus Gyger  (logged here by mcs)

           Makefile.in:
             Make symbolic links to alternative shared library names
             relative instead of absolute.
           Makefile.rules:
             The HP-UX libtecla.map.opt file should be made in the
             compilation directory, to allow the source code directory
             to be on a readonly filesystem.
           cplmatch.c demo2.c history.c pcache.c
             To allow the library to be compiled with a C++ compiler,
             without generating warnings, a few casts were added where
             void* return values were being assigned directly to
             none void* pointer variables.

25/03/2001 mcs@astro.caltech.edu

           libtecla.map:
             Added comment header to explain the purpose of the file.
             Also added cpl_init_FileArgs to the list of exported
             symbols. This symbol is deprecated, and no longer
             documented, but for backwards compatibility, it should
             still be exported.
           configure:
             I had forgotten to run autoconf before releasing version
             1.2.4, so I have just belatedly done so.  This enables
             Markus' changes to "configure.in" documented previously,
             (see 17/03/2001).

20/03/2001 John Levon   (logged here by mcs)

           libtecla.h
             A couple of the function prototypes in libtecla.h have
             (FILE *) argument declarations, which means that stdio.h
             needs to be included. The header file should be self
             contained, so libtecla.h now includes stdio.h.

18/03/2001 Version 1.2.4 released.

           README html/index.html configure.in
             Incremented minor version from 3 to 4.

18/03/2001 mcs@astro.caltech.edu

           getline.c
             The fix for the end-of-line problem that I released a
             couple of weeks ago, only worked for the first line,
             because I was handling this case when the cursor position
             was equal to the last column, rather than when the cursor
             position modulo ncolumn was zero.
           Makefile.in Makefile.rules
             The demos are now made by default, their rules now being
             int Makefile.rules instead of Makefile.in.
           INSTALL
             I documented how to compile the library in a different
             directory than the distribution directory.
             I also documented features designed to facilitate
             configuring and building the library as part of another
             package.

17/03/2001 Markus Gyger (logged here by mcs)

           getline.c
             Until now cursor motions were done one at a time. Markus
             has added code to make use the of the terminfo capability
             that moves the cursor by more than one position at a
             time. This greatly improves performance when editing near
             the start of long lines.
           getline.c
             To further improve performance, Markus switched from
             writing one character at a time to the terminal, using
             the write() system call, to using C buffered output
             streams. The output buffer is only flushed when
             necessary.
           Makefile.rules Makefile.in configure.in
             Added support for compiling for different architectures
             in different directories. Simply create another directory
             and run the configure script located in the original
             directory.
           Makefile.in configure.in libtecla.map
             Under Solaris, Linux and HP-UX, symbols that are to be
             exported by tecla shared libraries are explicitly specified
             via symbol map files. Only publicly documented functions
             are thus visible to applications.
           configure.in
             When linking shared libraries under Solaris SPARC,
             registers that are reserved for applications are marked
             as off limits to the library, using -xregs=no%appl when
             compiling with Sun cc, or -mno-app-regs when compiling
             with gcc. Also removed -z redlocsym for Solaris, which
             caused problems under some releases of ld.
           homedir.c  (after minor changes by mcs)
             Under ksh, ~+ expands to the current value of the ksh
             PWD environment variable, which contains the path of
             the current working directory, including any symbolic
             links that were traversed to get there. The special
             username "+" is now treated equally by tecla, except
             that it substitutes the return value of getcwd() if PWD
             either isn't set, or if it points at a different
             directory than that reported by getcwd().

08/03/2001 Version 1.2.3 released.

08/03/2001 mcs@astro.caltech.edu

           getline.c
             On compiling the library under HP-UX for the first time
             I encountered and fixed a couple of bugs:

             1. On all systems except Solaris, the callback function
                required by tputs() takes an int argument for the
                character that is to be printed. Under Solaris it
                takes a char argument. The callback function was
                passing this argument, regardless of type, to write(),
                which wrote the first byte of the argument.  This was
                fine under Solaris and under little-endian systems,
                because the first byte contained the character to be
                written, but on big-endian systems, it always wrote
                the zero byte at the other end of the word. As a
                result, no control characters were being written to
                the terminal.
             2. While attempting to start a newline after the user hit
                enter, the library was outputting the control sequence
                for moving the cursor down, instead of the newline
                character. On many systems the control sequence for
                moving the cursor down happends to be a newline
                character, but under HP-UX it isn't. The result was
                that no new line was being started under HP-UX.

04/03/2001 mcs@astro.caltech.edu

           configure.in Makefile.in Makefile.stub configure config.guess
           config.sub Makefile.rules install-sh PORTING README INSTALL
             Configuration and compilation of the library is now
             performed with the help of an autoconf configure
             script. In addition to relieving the user of the need to
             edit the Makefile, this also allows automatic compilation
             of the reentrant version of the library on platforms that
             can handle it, along with the creation of shared
             libraries where configured. On systems that aren't known
             to the configure script, just the static tecla library is
             compiled. This is currently the case on all systems
             except Linux, Solaris and HP-UX. In the hope that
             installers will provide specific conigurations for other
             systems, the configure.in script is heavily commented,
             and instructions on how to use are included in a new
             PORTING file.

24/02/2001 Version 1.2b released.

22/02/2001 mcs@astro.caltech.edu

           getline.c
             It turns out that most terminals, but not all, on writing
             a character in the rightmost column, don't wrap the
             cursor onto the next line until the next character is
             output. This library wasn't aware of this and thus if one
             tried to reposition the cursor from the last column,
             gl_get_line() thought that it was moving relative to a
             point on the next line, and thus moved the cursor up a
             line. The fix was to write one extra character when in
             the last column to force the cursor onto the next line,
             then backup the cursor to the start of the new line.
           getline.c
             On terminal initialization, the dynamic LINES and COLUMNS
             environment variables were ignored unless
             terminfo/termcap didn't return sensible dimensions. In
             practice, when present they should override the static
             versions in the terminfo/termcap databases. This is the
             new behavior. In reality this probably won't have caused
             many problems, because a SIGWINCH signal which informs of
             terminal size changes is sent when the terminal is
             opened, so the dimensions established during
             initialization quickly get updated on most systems.

18/02/2001 Version 1.2a released.

18/02/2001 mcs@astro.caltech.edu

           getline.c
             Three months ago I moved the point at which termios.h
             was included in getline.c. Unfortunately, I didn't notice
             that this moved it to after the test for TIOCGWINSZ being
             defined. This resulted in SIGWINCH signals not being
             trapped for, and thus terminal size changes went
             unnoticed. I have now moved the test to after the 
             inclusion of termios.h.

12/02/2001 Markus Gyger     (described here by mcs)

           man3/pca_lookup_file.3 man3/gl_get_line.3
           man3/ef_expand_file.3 man3/cpl_complete_word.3
             In the 1.2 release of the library, all functions in the
             library were given man pages. Most of these simply
             include one of the above 4 man pages, which describe the
             functions while describing the modules that they are in.
             Markus added all of these function names to the lists in
             the "NAME" headers of the respective man pages.
             Previously only the primary function of each module was
             named there.

11/02/2001 mcs@astro.caltech.edu

           getline.c
             On entering a line that wrapped over two or more
             terminal, if the user pressed enter when the cursor
             wasn't on the last of the wrapped lines, the text of the
             wrapped lines that followed it got mixed up with the next
             line written by the application, or the next input
             line. Somehow this slipped through the cracks and wasn't
             noticed until now. Anyway, it is fixed now.

09/02/2001 Version 1.2 released.

04/02/2001 mcs@astro.caltech.edu

           pcache.c libtecla.h
             With all filesystems local, demo2 was very fast to start
             up, but on a Sun system with one of the target
             directories being on a remote nfs mounted filesystem, the
             startup time was many seconds. This was due to the
             executable selection callback being applied to all files
             in the path at startup. To avoid this, all files are now
             included in the cache, and the application specified
             file-selection callback is only called on files as they
             are matched. Whether the callback rejected or accepted
             them is then cached so that the next time an already
             checked file is looked at, the callback doesn't have to
             be called. As a result, startup is now fast on all
             systems, and since usually there are only a few matching
             file completions at a time, the delay during completion
             is also usually small. The only exception is if the user
             tries to complete an empty string, at which point all
             files have to be checked. Having done this once, however,
             doing it again is fast.
           man3/pca_lookup_file.3
             I added a man page documenting the new PathCache module.
           man3/<many-new-files>.3
             I have added man pages for all of the functions in each
             of the modules. These 1-line pages use the .so directive
             to redirect nroff to the man page of the parent module.
           man Makefile update_html
             I renamed man to man3 to make it easier to test man page
             rediction, and updated Makefile and update_html
             accordingly. I also instructed update_html to ignore
             1-line man pages when making html equivalents of the man
             pages.
           cplmatch.c
             In cpl_list_completions() the size_t return value of
             strlen() was being used as the length argument of a "%*s"
             printf directive. This ought to be an int, so the return
             value of strlen() is now cast to int. This would have
             caused problems on architectures where the size of a
             size_t is not equal to the size of an int.

02/02/2001 mcs@astro.caltech.edu

           getline.c
             Under UNIX, certain terminal bindings are set using the
             stty command. This, for example, specifies which control
             key generates a user-interrupt (usually ^C or ^Y). What I
             hadn't realized was that ASCII NUL is used as the way to
             specify that one of these bindings is unset. I have now
             modified the code to skip unset bindings, leaving the
             corresponding action bound to the built-in default, or a
             user provided binding.

28/01/2001 mcs@astro.caltech.edu

           pcache.c libtecla.h
             A new module was added which supports searching for files
             in any colon separated list of directories, such as the
             unix execution PATH environment variable. Files in these
             directories, after being individually okayed for
             inclusion via an application provided callback, are
             cached in a PathCache object. You can then look up the
             full pathname of a given filename, or you can use the
             provided completion callback to list possible completions
             in the path-list. The contents of relative directories,
             such as ".", obviously can't be cached, so these
             directories are read on the fly during lookups and
             completions. The obvious application of this facility is
             to provide Tab-completion of commands, and thus a
             callback to place executable files in the cache, is
             provided.
           demo2.c
             This new program demonstrates the new PathCache
             module. It reads and processes lines of input until the
             word 'exit' is entered, or C-d is pressed. The default
             tab-completion callback is replaced with one which at the
             start of a line, looks up completions of commands in the
             user's execution path, and when invoked in other parts of
             the line, reverts to normal filename completion. Whenever
             a new line is entered, it extracts the first word on the
             line, looks it up in the user's execution path to see if
             it corresponds to a known command file, and if so,
             displays the full pathname of the file, along with the
             remaining arguments.
           cplfile.c
             I added an optional pair of callback function/data
             members to the new cpl_file_completions() configuration
             structure. Where provided, this callback is asked
             on a file-by-file basis, which files should be included
             in the list of file completions. For example, a callback
             is provided for listing only completions of executable
             files.
           cplmatch.c
             When listing completions, the length of the type suffix
             of each completion wasn't being taken into account
             correctly when computing the column widths. Thus the
             listing appeared ragged sometimes. This is now fixed.
           pathutil.c
             I added a function for prepending a string to a path,
             and another for testing whether a pathname referred to
             an executable file.

28/01/2001 mcs@astro.caltech.edu

           libtecla.h cplmatch.c man/cpl_complete_word.3
             The use of a publically defined structure to configure
             the cpl_file_completions() callback was flawed, so a new
             approach has been designed, and the old method, albeit
             still supported, is no longer documented in the man
             pages. The definition of the CplFileArgs structure in
             libtecla.h is now accompanied by comments warning people
             not to modify it, since modifications could break
             applications linked to shared versions of the tecla
             library. The new method involves an opaque CplFileConf
             object, instances of which are returned by a provided
             constructor function, configured with provided accessor
             functions, and when no longer needed, deleted with a
             provided destructor function. This is documented in the
             cpl_complete_word man page. The cpl_file_completions()
             callback distinguishes what type of configuration
             structure it has been sent by virtue of a code placed at
             the beginning of the CplFileConf argument by its
             constructor.

04/01/2001 mcs@astro.caltech.edu (Release of version 1.1j)

           getline.c
             I added upper-case bindings for the default meta-letter
             keysequences such as M-b. They thus continue to work
             when the user has caps-lock on.
           Makefile
             I re-implemented the "install" target in terms of new
             install_lib, install_inc and install_man targets. When
             distributing the library with other packages, these new
             targets allows for finer grained control of the
             installation process.

30/12/2000 mcs@astro.caltech.edu

           getline.c man/gl_get_line.3
             I realized that the recall-history action that I
             implemented wasn't what Markus had asked me for. What he
             actually wanted was for down-history to continue going
             forwards through a previous history recall session if no
             history recall session had been started while entering
             the current line. I have thus removed the recall-history
             action and modified the down-history action function
             accordingly.

24/12/2000 mcs@astro.caltech.edu

           getline.c
             I modified gl_get_line() to allow the previously returned
             line to be passed in the start_line argument.
           getline.c man/gl_get_line.3
             I added a recall-history action function, bound to M^P.
             This recalls the last recalled history line, regardless
             of whether it was from the current or previous line.

13/12/2000 mcs@astro.caltech.edu (Release of version 1.1i)

           getline.c history.h history.c man/gl_get_line.3
             I implemented the equivalent of the ksh Operate action. I
             have named the tecla equivalent "repeat-history". This
             causes the line that is to be edited to returned, and
             arranges for the next most recent history line to be
             preloaded on the next call to gl_get_line(). Repeated
             invocations of this action thus result in successive
             history lines being repeated - hence the
             name. Implementing the ksh Operate action was suggested
             by Markus Gyger. In ksh it is bound to ^O, but since ^O
             is traditionally bound by the default terminal settings,
             to stop-output, I have bound the tecla equivalent to M-o.

01/12/2000 mcs@astro.caltech.edu (Release of version 1.1h)

           getline.c keytab.c keytab.h man/gl_get_line.3
             I added a digit-argument action, to allow repeat
             counts for actions to be entered. As in both tcsh
             and readline, this is bound by default to each of
             M-0, M-1 through to M-9, the number being appended
             to the current repeat count. Once one of these has been
             pressed, the subsequent digits of the repeat count can be
             typed with or without the meta key pressed. It is also
             possible to bind digit-argument to other keys, with or
             without a numeric final keystroke. See man page for
             details.

           getline.c man/gl_get_line.3
             Markus noted that my choice of M-< for the default
             binding of read-from-file, could be confusing, since
             readline binds this to beginning-of-history. I have
             thus rebound it to ^X^F (ie. like find-file in emacs).

           getline.c history.c history.h man/gl_get_line.3
             I have now implemented equivalents of the readline
             beginning-of-history and end-of-history actions.
             These are bound to M-< and M-> respectively.

           history.c history.h
             I Moved the definition of the GlHistory type, and
             its subordinate types from history.h to history.c.
             There is no good reason for any other module to
             have access to the innards of this structure.

27/11/2000 mcs@astro.caltech.edu (Release of version 1.1g)

           getline.c man/gl_get_line.3
             I added a "read-from-file" action function and bound it
             by default to M-<. This causes gl_get_line() to
             temporarily return input from the file who's name
             precedes the cursor.
             
26/11/2000 mcs@astro.caltech.edu

           getline.c keytab.c keytab.h man/gl_get_line.3
             I have reworked some of the keybinding code again.

             Now, within key binding strings, in addition to the
             previously existing notation, you can now use M-a to
             denote meta-a, and C-a to denote control-a. For example,
             a key binding which triggers when the user presses the
             meta key, the control key and the letter [
             simultaneously, can now be denoted by M-C-[, or M-^[ or
             \EC-[ or \E^[.

             I also updated the man page to use M- instead of \E in
             the list of default bindings, since this looks cleaner.

           getline.c man/gl_get_line.3
             I added a copy-region-as-kill action function and
             gave it a default binding to M-w.

22/11/2000 mcs@astro.caltech.edu

           *.c
             Markus Gyger sent me a copy of a previous version of
             the library, with const qualifiers added in appropriate
             places. I have done the same for the latest version.
             Among other things, this gets rid of the warnings
             that are generated if one tells the compiler to
             const qualify literal strings.

           getline.c getline.h glconf.c
             I have moved the contents of glconf.c and the declaration
             of the GetLine structure into getline.c. This is cleaner,
             since now only functions in getline.c can mess with the
             innards of GetLine objects. It also clears up some problems
             with system header inclusion order under Solaris, and also
             the possibility that this might result in inconsistent
             system macro definitions, which in turn could cause different
             declarations of the structure to be seen in different files.

           hash.c
             I wrote a wrapper function to go around strcmp(), such that
             when hash.c is compiled with a C++ compiler, the pointer
             to the wrapper function is a C++ function pointer.
             This makes it compatible with comparison function pointer
             recorded in the hash table.

           cplmatch.c getline.c libtecla.h
             Markus noted that the Sun C++ compiler wasn't able to
             match up the declaration of cpl_complete_word() in
             libtecla.h, where it is surrounded by a extern "C" {}
             wrapper, with the definition of this function in
             cplmatch.c. My suspicion is that the compiler looks not
             only at the function name, but also at the function
             arguments to see if two functions match, and that the
             match_fn() argument, being a fully blown function pointer
             declaration, got interpetted as that of a C function in
             one case, and a C++ function in the other, thus
             preventing a match.

             To fix this I now define a CplMatchFn typedef in libtecla.h,
             and use this to declare the match_fn callback.

20/11/2000 (Changes suggested by Markus Gyger to support C++ compilers):
           expand.c
             Renamed a variable called "explicit" to "xplicit", to
             avoid conflicts when compiling with C++ compilers.
           *.c
             Added explicit casts when converting from (void *) to
             other pointer types. This isn't needed in C but it is
             in C++.
           getline.c
             tputs() has a strange declaration under Solaris. I was
             enabling this declaration when the SPARC feature-test
             macro was set. Markus changed the test to hinge on the
             __sun and __SVR4 macros.
           direader.c glconf.c stringrp.c
             I had omitted to include string.h in these two files.

           Markus also suggested some other changes, which are still
           under discussion. With the just above changes however, the
           library compiles without complaint using g++.

19/11/2000 mcs@astro.caltech.edu
           getline.h getline.c keytab.c keytab.h glconf.c
           man/gl_get_line.3
             I added support for backslash escapes (include \e
             for the keyboard escape key) and literal binary
             characters to the characters allowed within key sequences
             of key bindings.

           getline.h getline.c keytab.c keytab.h glconf.c
           man/gl_get_line.3
             I introduced symbolic names for the arrow keys, and
             modified the library to use the cursor key sequences
             reported by terminfo/termcap in addition to the default
             ANSI ones. Anything bound to the symbolically named arrow
             keys also gets bound to the default and terminfo/termcap
             cursor key sequences. Note that under Solaris
             terminfo/termcap report the properties of hardware X
             terminals when TERM is xterm instead of the terminal
             emulator properties, and the cursor keys on these two
             systems generate different key sequences. This is an
             example of why extra default sequences are needed.

           getline.h getline.c keytab.c
             For some reason I was using \e to represent the escape
             character. This is supported by gcc, which thus doesn't
             emit a warning except with the -pedantic flag, but isn't
             part of standard C. I now use a macro to define escape
             as \033 in getline.h, and this is now used wherever the
             escape character is needed.

17/11/2000 mcs@astro.caltech.edu (Release of version 1.1d)

           getline.c, man/gl_get_line(3), html/gl_get_line.html
             In tcsh ^D is bound to a function which does different
             things depending on where the cursor is within the input
             line. I have implemented its equivalent in the tecla
             library. When invoked at the end of the line this action
             function displays possible completions. When invoked on
             an empty line it causes gl_get_line() to return NULL,
             thus signalling end of input. When invoked within a line
             it invokes forward-delete-char, as before. The new action
             function is called del-char-or-list-or-eof.

           getline.c, man/gl_get_line(3), html/gl_get_line.html
             I found that the complete-word and expand-file actions
             had underscores in their names instead of hyphens. This
             made them different from all other action functions, so I
             have changed the underscores to hyphens.

           homedir.c
             On SCO UnixWare while getpwuid_r() is available, the
             associated _SC_GETPW_R_SIZE_MAX macro used by sysconf()
             to find out how big to make the buffer to pass to this
             function to cater for any password entry, doesn't
             exist. I also hadn't catered for the case where sysconf()
             reports that this limit is indeterminate. I have thus
             change the code to substitute a default limit of 1024 if
             either the above macro isn't defined or if sysconf() says
             that the associated limit is indeterminate.
           
17/11/2000 mcs@astro.caltech.edu (Release of version 1.1c)

           getline.c, getline.h, history.c, history.h
             I have modified the way that the history recall functions
             operate, to make them better emulate the behavior of
             tcsh. Previously the history search bindings always
             searched for the prefix that preceded the cursor, then
             left the cursor at the same point in the line, so that a
             following search would search using the same prefix. This
             isn't how tcsh operates. On finding a matching line, tcsh
             puts the cursor at the end of the line, but arranges for
             the followup search to continue with the same prefix,
             unless the user does any cursor motion or character
             insertion operations in between, in which case it changes
             the search prefix to the new set of characters that are
             before the cursor. There are other complications as well,
             which I have attempted to emulate. As far as I can
             tell, the tecla history recall facilities now fully
             emulate those of tcsh.

16/11/2000 mcs@astro.caltech.edu (Release of version 1.1b)

           demo.c:
             One can now quit from the demo by typing exit.

           keytab.c:
             The first entry of the table was getting deleted
             by _kt_clear_bindings() regardless of the source
             of the binding. This deleted the up-arrow binding.
             Symptoms noted by gazelle@yin.interaccess.com.

           getline.h:
             Depending on which system include files were include
             before the inclusion of getline.h, SIGWINCH and
             TIOCGWINSZ might or might not be defined. This resulted
             in different definitions of the GetLine object in
             different files, and thus some very strange bugs! I have
             now added #includes for the necessary system header files
             in getline.h itself. The symptom was that on creating a
             ~/.teclarc file, the demo program complained of a NULL
             argument to kt_set_keybinding() for the first line of the
             file.

15/11/2000 mcs@astro.caltech.edu (Release of version 1.1a)

           demo.c:
             I had neglected to check the return value of
             new_GetLine() in the demo program. Oops.

           getline.c libtecla.h:
             I wrote gl_change_terminal(). This allows one to change to
             a different terminal or I/O stream, by specifying the
             stdio streams to use for input and output, along with the
             type of terminal that they are connected to.

           getline.c libtecla.h:
             Renamed GetLine::isterm to GetLine::is_term. Standard
             C reserves names that start with "is" followed by
             alphanumeric characters, so this avoids potential
             clashes in the future.

           keytab.c keytab.h
             Each key-sequence can now have different binding
             functions from different sources, with the user provided
             binding having the highest precedence, followed by the
             default binding, followed by any terminal specific
             binding. This allows gl_change_terminal() to redefine the
             terminal-specific bindings each time that
             gl_change_terminal() is called, without overwriting the
             user specified or default bindings. In the future, it will
             also allow for reconfiguration of user specified
             bindings after the call to new_GetLine(). Ie. deleting a
             user specified binding should reinstate any default or
             terminal specific binding.

           man/cpl_complete_word.3 html/cpl_complete_word.html
           man/ef_expand_file.3    html/ef_expand_file.html
           man/gl_get_line.3       html/gl_get_line.html
             I added sections on thread safety to the man pages of the
             individual modules.

           man/gl_get_line.3       html/gl_get_line.html
             I documented the new gl_change_terminal() function.

           man/gl_get_line.3       html/gl_get_line.html
             In the description of the ~/.teclarc configuration file,
             I had omitted the 'bind' command word in the example
             entry. I have now remedied this.


genometools-1.5.1/src/external/libtecla-1.6.1/html/cpl_complete_word.html000066400000000000000000000460601211610345200262360ustar00rootroot00000000000000
Manual Page



cpl_complete_word              cpl_complete_word




NAME
       cpl_complete_word,         cfc_file_start,         cfc_literal_escapes,
       cfc_set_check_fn,       cpl_add_completion,       cpl_file_completions,
       cpl_last_error,        cpl_list_completions,        cpl_recall_matches,
       cpl_record_error, del_CplFileConf, del_WordCompletion, new_CplFileConf,
       new_WordCompletion - lookup possible completions for a word


SYNOPSIS
       #include <stdio.h>
       #include <libtecla.h>

       WordCompletion *new_WordCompletion(void);

       WordCompletion *del_WordCompletion(WordCompletion *cpl);


       #define CPL_MATCH_FN(fn) int (fn)(WordCompletion *cpl, \
                                         void *data, \
                                         const char *line, \
                                         int word_end)
       typedef CPL_MATCH_FN(CplMatchFn);

       CPL_MATCH_FN(cpl_file_completions);


       CplMatches *cpl_complete_word(WordCompletion *cpl,
                                     const char *line,
                                     int word_end, void *data,
                                     CplMatchFn *match_fn);

       CplMatches *cpl_recall_matches(WordCompletion *cpl);

       int cpl_list_completions(CplMatches *result, FILE *fp,
                                int term_width);

       int cpl_add_completion(WordCompletion *cpl,
                              const char *line, int word_start,
                              int word_end, const char *suffix,
                              const char *type_suffix,
                              const char *cont_suffix);

       void cpl_record_error(WordCompletion *cpl,
                             const char *errmsg);

       const char *cpl_last_error(WordCompletion *cpl);


       #define CPL_CHECK_FN(fn) int (fn)(void *data, \
                                         const char *pathname)

       typedef CPL_CHECK_FN(CplCheckFn);

       CPL_CHECK_FN(cpl_check_exe);

       CplFileConf *new_CplFileConf(void);

       CplFileConf *del_CplFileConf(CplFileConf *cfc);

       void cfc_literal_escapes(CplFileConf *cfc, int literal);

       void cfc_file_start(CplFileConf *cfc, int start_index);

       void cfc_set_check_fn(CplFileConf *cfc, CplCheckFn *chk_fn,
                             void *chk_data);




DESCRIPTION
       The  cpl_complete_word() function is part of the tecla library (see the
       libtecla man page). It  is  usually  called  behind  the
       scenes  by  gl_get_line,  but  can  also be called sepa-
       rately.

       Given an input line containing an incomplete word to be  completed,  it
       calls  a  user-provided callback function (or the provided file-comple-
       tion callback function) to look up all possible completion suffixes for
       that  word.  The  callback function is expected to look backward in the
       line, starting from the specified cursor position, to find the start of
       the  word  to be completed, then to look up all possible completions of
       that word and record them, one at a  time  by  calling  cpl_add_comple-
       tion().


       Descriptions of the functions of this module are as follows:

         WordCompletion *new_WordCompletion(void)

       This  function  creates  the  resources used by the cpl_complete_word()
       function. In particular, it maintains the memory that is used to return
       the results of calling cpl_complete_word().

         WordCompletion *del_WordCompletion(WordCompletion *cpl)

       This  function  deletes  the resources that were returned by a previous
       call to new_WordCompletion(). It always returns  NULL  (ie.  a  deleted
       object). It does nothing if the cpl argument is NULL.

       The  callback  functions  which  lookup  possible completions should be
       defined with the following macro (which is defined in libtecla.h).

         #define CPL_MATCH_FN(fn) int (fn)(WordCompletion *cpl, \
                                           void *data, \
                                           const char *line, \
                                           int word_end)

       Functions of this type are called by cpl_complete_word(),  and  all  of
       the  arguments of the callback are those that were passed to said func-
       tion. In particular, the line argument contains the input line contain-
       ing  the word to be completed, and word_end is the index of the charac-
       ter that follows the last character of the incomplete word within  this
       string.  The  callback  is expected to look backwards from word_end for
       the start of the incomplete word. What constitutes the start of a  word
       clearly  depends on the application, so it makes sense for the callback
       to take on this responsibility. For example, the builtin filename  com-
       pletion  function  looks backwards until it hits an unescaped space, or
       the start of the line.  Having found the start of the word,  the  call-
       back  should  then  lookup  all  possible completions of this word, and
       record each completion via separate calls to  cpl_add_completion().  If
       the  callback  needs access to an application-specific symbol table, it
       can pass it and any other data that it needs, via  the  data  argument.
       This removes any need for globals.

       The callback function should return 0 if no errors occur. On failure it
       should return 1, and register a terse description of the error by call-
       ing cpl_record_error().

         void cpl_record_error(WordCompletion *cpl,
                               const char *errmsg);

       The last error message recorded by calling cpl_record_error(), can sub-
       sequently be queried by calling cpl_last_error(), as described later.

         int cpl_add_completion(WordCompletion *cpl,
                                const char *line, int word_start,
                                int word_end, const char *suffix,
                                const char *type_suffix,
                                const char *cont_suffix);

       The cpl_add_completion() function is called zero or more times  by  the
       completion  callback function to record each possible completion in the
       specified WordCompletion object.  These  completions  are  subsequently
       returned by cpl_complete_word(), as described later. The cpl, line, and
       word_end arguments should be those that were  passed  to  the  callback
       function.  The word_start argument should be the index within the input
       line string of the start of the word  that  is  being  completed.  This
       should  equal  word_end if a zero-length string is being completed. The
       suffix argument is the string that would have to  be  appended  to  the
       incomplete  word  to  complete  it.  If this needs any quoting (eg. the
       addition of backslashes before special charaters) to  be  valid  within
       the displayed input line, this should be included. A copy of the suffix
       string is allocated internally, so there is no need  to  maintain  your
       copy of the string after cpl_add_completion() returns.

       Note  that  in  the  array  of  possible completions which the cpl_com-
       plete_word() function returns, the suffix recorded  by  cpl_add_comple-
       tion()  is listed along with the concatentation of this suffix with the
       word that lies between word_start and word_end in the input line.

       The type_suffix argument specifies an optional string to be appended to
       the  completion  if it is displayed as part of a list of completions by
       cpl_list_completions(). The intention is that this indicate to the user
       the  type of each completion. For example, the file completion function
       places a directory separator after completions that are directories, to
       indicate  their  nature to the user. Similary, if the completion were a
       function, you could indicate this to the user by setting type_suffix to
       "()". Note that the type_suffix string isn't copied, so if the argument
       isn't a literal string between speech marks, be sure  that  the  string
       remains  valid  for  at  least  as  long  as  the  results  of cpl_com-
       plete_word() are needed.

       The cont_suffix is a continuation suffix to  append  to  the  completed
       word  in  the  input line if this is the only completion. This is some-
       thing that isn't part of the completion itself, but that gives the user
       an  indication  about how they might continue to extend the token.  For
       example, the file-completion callback function adds a directory separa-
       tor  if the completed word is a directory. If the completed word were a
       function name, you could similarly aid the user  by  arranging  for  an
       open parenthesis to be appended.

         CplMatches *cpl_complete_word(WordCompletion *cpl,
                                       const char *line,
                                       int word_end, void *data,
                                       CplMatchFn *match_fn);

       The  cpl_complete_word()  is  normally  called  behind  the  scenes  by
       gl_get_line, but can also be called  separately  if  you
       separately  allocate  a WordCompletion object. It performs word comple-
       tion, as described at the beginning of this section. Its first argument
       is  a resource object previously returned by new_WordCompletion().  The
       line argument is the input line string, containing the word to be  com-
       pleted.  The  word_end  argument contains the index of the character in
       the input line, that just follows the last character of the word to  be
       completed.  When  called  by  gl_get_line(), this is the character over
       which the user pressed TAB.  The  match_fn  argument  is  the  function
       pointer of the callback function which will lookup possible completions
       of the word, as described above, and the data argument provides  a  way
       for the application to pass arbitrary data to the callback function.

       If  no errors occur, the cpl_complete_word() function returns a pointer
       to a CplMatches container, as defined below. This  container  is  allo-
       cated as part of the cpl object that was passed to cpl_complete_word(),
       and will thus change on each call which uses the same cpl argument.

         typedef struct {
           char *completion;        /* A matching completion */
                                    /*  string */
           char *suffix;            /* The part of the */
                                    /*  completion string which */
                                    /*  would have to be */
                                    /*  appended to complete the */
                                    /*  original word. */
           const char *type_suffix; /* A suffix to be added when */
                                    /*  listing completions, to */
                                    /*  indicate the type of the */
                                    /*  completion. */
         } CplMatch;

         typedef struct {
           char *suffix;            /* The common initial part */
                                    /*  of all of the completion */
                                    /*  suffixes. */
           const char *cont_suffix; /* Optional continuation */
                                    /*  string to be appended to */
                                    /*  the sole completion when */
                                    /*  nmatch==1. */
           CplMatch *matches;       /* The array of possible */
                                    /*  completion strings, */
                                    /*  sorted into lexical */
                                    /*  order. */
           int nmatch;              /* The number of elements in */
                                    /*  the above matches[] */
                                    /*  array. */
         } CplMatches;

       If an error occurs during completion, cpl_complete_word() returns NULL.
       A   description   of   the   error  can  be  acquired  by  calling  the
       cpl_last_error() function.

         const char *cpl_last_error(WordCompletion *cpl);

       The cpl_last_error() function returns a terse description of the  error
       which  occurred on the last call to cpl_complete_word() or cpl_add_com-
       pletion().

         CplMatches *cpl_recall_matches(WordCompletion *cpl);

       As a convenience, the  return  value  of  the  last  call  to  cpl_com-
       plete_word()   can   be   recalled   at   a   later   time  by  calling
       cpl_recall_matches(). If cpl_complete_word()  returned  NULL,  so  will
       cpl_recall_matches().

         int cpl_list_completions(CplMatches *result, FILE *fp,
                                  int terminal_width);

       When the cpl_complete_word() function returns multiple possible comple-
       tions, the cpl_list_completions() function can be called upon  to  list
       them,  suitably arranged across the available width of the terminal. It
       arranges for the displayed columns of completions to all have the  same
       width,  set  by the longest completion. It also appends the type_suffix
       strings that were recorded with each completion, thus indicating  their
       types to the user.



THE BUILT-IN FILENAME-COMPLETION CALLBACK
       By  default the gl_get_line function, passes the follow-
       ing completion callback function to cpl_complete_word(). This  function
       can  also  be  used  separately,  either  by  sending  it  to  cpl_com-
       plete_word(), or by calling it directly from your own completion  call-
       back function.

         CPL_MATCH_FN(cpl_file_completions);

       Certain aspects of the behavior of this callback can be changed via its
       data argument. If you are happy with its default behavior you can  pass
       NULL  in  this argument. Otherwise it should be a pointer to a CplFile-
       Conf object, previously allocated by calling new_CplFileConf().

         CplFileConf *new_CplFileConf(void);

       CplFileConf  objects  encapsulate  the  configuration   parameters   of
       cpl_file_completions().  These parameters, which start out with default
       values, can be changed by  calling  the  accessor  functions  described
       below.

       By default, the cpl_file_completions() callback function searches back-
       wards for the start of the filename being completed,  looking  for  the
       first  un-escaped  space or the start of the input line. If you wish to
       specify a different location, call cfc_file_start() with the  index  at
       which the filename starts in the input line. Passing start_index=-1 re-
       enables the default behavior.

         void cfc_file_start(CplFileConf *cfc, int start_index);

       By default, when cpl_file_completions() looks  at  a  filename  in  the
       input  line,  each  lone  backslash in the input line is interpreted as
       being a special character which removes any special significance of the
       character  which  follows  it, such as a space which should be taken as
       part of the filename rather than delimiting the start of the  filename.
       These  backslashes  are thus ignored while looking for completions, and
       subsequently added before spaces, tabs and literal backslashes  in  the
       list  of  completions.  To have unescaped backslashes treated as normal
       characters, call cfc_literal_escapes() with a  non-zero  value  in  its
       literal argument.

         void cfc_literal_escapes(CplFileConf *cfc, int literal);

       By  default, cpl_file_completions() reports all files who's names start
       with the prefix that is being completed. If you only  want  a  selected
       subset  of  these  files to be reported in the list of completions, you
       can arrange this by providing a callback function which takes the  full
       pathname  of  a file, and returns 0 if the file should be ignored, or 1
       if the file should be included in the list of completions. To  register
       such    a    function   for   use   by   cpl_file_completions(),   call
       cfc_set_check_fn(), and pass it a pointer  to  the  function,  together
       with  a pointer to any data that you would like passed to this callback
       whenever it is called. Your callback can make its  decisions  based  on
       any property of the file, such as the filename itself, whether the file
       is readable, writable or executable, or even based  on  what  the  file
       contains.

         #define CPL_CHECK_FN(fn) int (fn)(void *data, \
                                           const char *pathname)
         typedef CPL_CHECK_FN(CplCheckFn);

         void cfc_set_check_fn(CplFileConf *cfc,
                               CplCheckFn *chk_fn, void *chk_data);

       The  cpl_check_exe() function is a provided callback of the above type,
       for use with cpl_file_completions(). It returns non-zero if  the  file-
       name  that  it is given represents a normal file that the user has exe-
       cute permission to. You could use this to  have  cpl_file_completions()
       only list completions of executable files.

       When  you have finished with a CplFileConf variable, you can pass it to
       the del_CplFileConf() destructor function to reclaim its memory.

         CplFileConf *del_CplFileConf(CplFileConf *cfc);




THREAD SAFETY
       In multi-threaded programs, you should use the libtecla_r.a version  of
       the library. This uses POSIX reentrant functions where available (hence
       the _r suffix), and disables features that rely on non-reentrant system
       functions.  In  the  case  of this module, the only disabled feature is
       username completion  in  ~username/  expressions,  in  cpl_file_comple-
       tions().

       Using  the  libtecla_r.a  version of the library, it is safe to use the
       facilities of this module  in  multiple  threads,  provided  that  each
       thread  uses  a  separately  allocated  WordCompletion object. In other
       words, if two threads want to do word completion, they should each call
       new_WordCompletion() to allocate their own completion objects.



FILES
       libtecla.a    -    The tecla library
       libtecla.h    -    The tecla header file.



SEE ALSO
       libtecla, gl_get_line, ef_expand_file,
       pca_lookup_file



AUTHOR
       Martin Shepherd  (mcs@astro.caltech.edu)



                                              cpl_complete_word



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ef_expand_file                    ef_expand_file




NAME
       ef_expand_file,   del_ExpandFile,   ef_last_error,  ef_list_expansions,
       new_ExpandFile - expand filenames containing ~user/$envvar and wildcard
       expressions


SYNOPSIS
       #include <libtecla.h>

       ExpandFile *new_ExpandFile(void);

       ExpandFile *del_ExpandFile(ExpandFile *ef);

       FileExpansion *ef_expand_file(ExpandFile *ef,
                                     const char *path,
                                     int pathlen);

       int ef_list_expansions(FileExpansion *result, FILE *fp,
                              int term_width);

       const char *ef_last_error(ExpandFile *ef);



DESCRIPTION
       The  ef_expand_file()  function  is  part of the tecla library (see the
       libtecla man page). It  expands  a  specified  filename,
       converting  ~user/  and  ~/ expressions at the start of the filename to
       the corresponding home directories, replacing $envvar with the value of
       the  corresponding  environment  variable,  and  then, if there are any
       wildcards, matching these against existing  filenames.  Backslashes  in
       the  input filename are interpreted as escaping any special meanings of
       the characters that follow them.  Only backslahes that  are  themselves
       preceded by backslashes are preserved in the expanded filename.

       In  the  presence  of  wildcards,  the  returned list of filenames only
       includes the names of existing files which match the wildcards.  Other-
       wise,  the  original  filename is returned after expansion of tilde and
       dollar expressions, and the result  is  not  checked  against  existing
       files. This mimics the file-globbing behavior of the unix tcsh shell.

       The supported wildcards and their meanings are:
         *        -  Match any sequence of zero or more characters.
         ?        -  Match any single character.
         [chars]  -  Match any single character that appears in
                     'chars'.  If 'chars' contains an expression of
                     the form a-b, then any character between a and
                     b, including a and b, matches. The '-'
                     character looses its special meaning as a
                     range specifier when it appears at the start
                     of the sequence of characters. The ']'
                     character also looses its significance as the
                     terminator of the range expression if it
                     appears immediately after the opening '[', at
                     which point it is treated one of the
                     characters of the range. If you want both '-'
                     and ']' to be part of the range, the '-'
                     should come first and the ']' second.

         [^chars] -  The same as [chars] except that it matches any
                     single character that doesn't appear in
                     'chars'.

       Note that wildcards never match the initial dot in filenames that start
       with '.'. The initial '.' must be explicitly specified in the filename.
       This  again  mimics  the globbing behavior of most unix shells, and its
       rational is based in the fact that in unix, files with names that start
       with  '.'  are usually hidden configuration files, which are not listed
       by default by the ls command.

       The following is a complete example of how to use  the  file  expansion
       function.

         #include <stdio.h>
         #include <libtecla.h>

         int main(int argc, char *argv[])
         {
           ExpandFile *ef;      /* The expansion resource object */
           char *filename;      /* The filename being expanded */
           FileExpansion *expn; /* The results of the expansion */
           int i;

           ef = new_ExpandFile();
           if(!ef)
             return 1;

           for(arg = *(argv++); arg; arg = *(argv++)) {
             if((expn = ef_expand_file(ef, arg, -1)) == NULL) {
               fprintf(stderr, "Error expanding %s (%s).\n", arg,
                                ef_last_error(ef));
             } else {
               printf("%s matches the following files:\n", arg);
               for(i=0; i<expn->nfile; i++)
                 printf(" %s\n", expn->files[i]);
             }
           }

           ef = del_ExpandFile(ef);
           return 0;
         }

       Descriptions of the functions used above are as follows:

         ExpandFile *new_ExpandFile(void)

       This  function creates the resources used by the ef_expand_file() func-
       tion. In particular, it maintains the memory that is used to record the
       array  of matching filenames that is returned by ef_expand_file(). This
       array is expanded as needed, so there is no built in limit to the  num-
       ber of files that can be matched.

         ExpandFile *del_ExpandFile(ExpandFile *ef)

       This  function  deletes  the resources that were returned by a previous
       call to new_ExpandFile(). It always returns NULL (ie a deleted object).
       It does nothing if the ef argument is NULL.

       A container of the following type is returned by ef_expand_file().

         typedef struct {
           int exists;   /* True if the files in files[] exist */
           int nfile;    /* The number of files in files[] */
           char **files; /* An array of 'nfile' filenames. */
         } FileExpansion;

         FileExpansion *ef_expand_file(ExpandFile *ef,
                                       const char *path,
                                       int pathlen)

       The  ef_expand_file()  function  performs  filename expansion, as docu-
       mented at the start of this section. Its first argument is  a  resource
       object  returned  by  new_ExpandFile().  A  pointer to the start of the
       filename to be matched is passed via the path argument. This must be  a
       normal  NUL  terminated  string, but unless a length of -1 is passed in
       pathlen, only the first pathlen characters will be used in the filename
       expansion.   If  the length is specified as -1, the whole of the string
       will be expanded.

       The function returns a pointer to a container who's  contents  are  the
       results  of  the expansion. If there were no wildcards in the filename,
       the nfile member will be 1, and the exists member should be queried  if
       it  is  important to know if the expanded file currently exists or not.
       If there were wildcards, then the contained files[] array will  contain
       the names of the nfile existing files that matched the wildcarded file-
       name, and the exists member will  have  the  value  1.  Note  that  the
       returned container belongs to the specified ef object, and its contents
       will change on each call, so if you need to retain the results of  more
       than  one  call  to  ef_expand_file(), you should either make a private
       copy  of  the  returned  results,  or  create  multiple  file-expansion
       resource objects via multiple calls to new_ExpandFile().

       On  error,  NULL  is  returned,  and an explanation of the error can be
       determined by calling ef_last_error(ef).

         const char *ef_last_error(ExpandFile *ef)

       This function returns  the  message  which  describes  the  error  that
       occurred  on  the last call to ef_expand_file(), for the given (Expand-
       File *ef) resource object.

         int ef_list_expansions(FileExpansion *result, FILE *fp,
                                int terminal_width);

       The ef_list_expansions() function provides a convenient way to list the
       filename expansions returned by ef_expand_file(). Like the unix ls com-
       mand, it arranges the filenames into equal width columns,  each  column
       having  the  width  of  the largest file. The number of columns used is
       thus determined by the length of the longest filename, and  the  speci-
       fied  terminal  width.  Beware  that filenames that are longer than the
       specified terminal width are printed without being truncated, so output
       longer than the specified terminal width can occur. The list is written
       to the stdio stream specified by the fp argument.



THREAD SAFETY
       In multi-threaded programs, you should use the libtecla_r.a version  of
       the library. This uses POSIX reentrant functions where available (hence
       the _r suffix), and disables features that rely on non-reentrant system
       functions. Currently there are no features disabled in this module.

       Using  the  libtecla_r.a  version of the library, it is safe to use the
       facilities of this module  in  multiple  threads,  provided  that  each
       thread  uses  a separately allocated ExpandFile object. In other words,
       if two threads want  to  do  file  expansion,  they  should  each  call
       new_ExpandFile() to allocate their own file-expansion objects.



FILES
       libtecla.a    -    The tecla library
       libtecla.h    -    The tecla header file.



SEE ALSO
       libtecla, gl_get_line, cpl_complete_word,
       pca_lookup_file



AUTHOR
       Martin Shepherd  (mcs@astro.caltech.edu)



                                                 ef_expand_file



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enhance                                  enhance




NAME
       enhance  - A program that adds command-line editing to third party pro-
       grams.


SYNOPSIS
       enhance command [ argument ... ]



DESCRIPTION
       The enhance program provides enhanced command-line  editing  facilities
       to  users  of  third  party applications, to which one doesn't have any
       source code. It does this by  placing  a  pseudo-terminal  between  the
       application and the real terminal. It uses the tecla command-line edit-
       ing library to read input from the real terminal,  then  forwards  each
       just  completed  input line to the application via the pseudo-terminal.
       All output from the application is forwarded back unchanged to the real
       terminal.

       Whenever  the application stops generating output for more than a tenth
       of a second, the enhance program treats the  latest  incomplete  output
       line  as the prompt, and redisplays any incompleted input line that the
       user has typed after it. Note that the small delay, which is  impercep-
       tible  to  the  user, isn't necessary for correct operation of the pro-
       gram. It is just an optimization, designed to stop the input line  from
       being redisplayed so often that it slows down output.

       Note  that  the  user-level command-line editing facilities provided by
       the Tecla library are documented in the tecla man page



DEFICIENCIES
       The one major problem that hasn't been solved yet, is how to deal  with
       applications  that  change  whether typed input is echo'd by their con-
       trolling terminal. For example, programs that ask for a password,  such
       as  ftp  and telnet, temporarily tell their controlling terminal not to
       echo what the user types. Since this request goes  to  the  application
       side  of the psuedo terminal, the enhance program has no way of knowing
       that this has happened, and continues to echo typed input to  its  con-
       trolling terminal, while the user types their password.

       Furthermore, before executing the host application, the enhance program
       initially sets the pseudo terminal to noecho mode, so  that  everything
       that  it sends to the program doesn't get redundantly echoed. If a pro-
       gram that switches to noecho mode explicitly  restores  echoing  after-
       wards, rather than restoring the terminal modes that were previously in
       force, then subsequently, every time that you enter a new input line, a
       duplicate copy will be displayed on the next line.



FILES
       libtecla.a    -   The tecla library.
       ~/.teclarc    -   The tecla personal customization file.



SEE ALSO
       tecla, libtecla



AUTHOR
       Martin Shepherd  (mcs@astro.caltech.edu)



                                                        enhance



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gl_get_line                          gl_get_line




NAME
       gl_get_line,    new_GetLine,    del_GetLine,   gl_customize_completion,
       gl_change_terminal, gl_configure_getline, gl_load_history, gl_save_his-
       tory,   gl_group_history,   gl_show_history,  gl_watch_fd,  gl_inactiv-
       ity_timeout,  gl_terminal_size,  gl_set_term_size,   gl_resize_history,
       gl_limit_history,  gl_clear_history,  gl_toggle_history, gl_lookup_his-
       tory,  gl_state_of_history,  gl_range_of_history,   gl_size_of_history,
       gl_echo_mode,   gl_replace_prompt,  gl_prompt_style,  gl_ignore_signal,
       gl_trap_signal, gl_last_signal, gl_completion_action,  gl_display_text,
       gl_return_status,  gl_error_message, gl_catch_blocked, gl_list_signals,
       gl_bind_keyseq, gl_erase_terminal, gl_automatic_history, gl_append_his-
       tory,  gl_query_char, gl_read_char - allow the user to compose an input
       line


SYNOPSIS
       #include <stdio.h>
       #include <libtecla.h>

       GetLine *new_GetLine(size_t linelen, size_t histlen);

       GetLine *del_GetLine(GetLine *gl);

       char *gl_get_line(GetLine *gl, const char *prompt,
                         const char *start_line, int start_pos);

       int gl_query_char(GetLine *gl, const char *prompt,
                         char defchar);

       int gl_read_char(GetLine *gl);

       int gl_customize_completion(GetLine *gl, void *data,
                                   CplMatchFn *match_fn);

       int gl_change_terminal(GetLine *gl, FILE *input_fp,
                              FILE *output_fp, const char *term);

       int gl_configure_getline(GetLine *gl,
                                const char *app_string,
                                const char *app_file,
                                const char *user_file);

       int gl_bind_keyseq(GetLine *gl, GlKeyOrigin origin,
                          const char *keyseq, const char *action);

       int gl_save_history(GetLine *gl, const char *filename,
                           const char *comment, int max_lines);

       int gl_load_history(GetLine *gl, const char *filename,
                           const char *comment);

       int gl_watch_fd(GetLine *gl, int fd, GlFdEvent event,
                       GlFdEventFn *callback, void *data);

       int gl_inactivity_timeout(GetLine *gl, GlTimeoutFn *callback,
                          void *data, unsigned long sec,
                          unsigned long nsec);

       int gl_group_history(GetLine *gl, unsigned stream);

       int gl_show_history(GetLine *gl, FILE *fp,
                           const char *fmt, int all_groups,
                           int max_lines);

       int gl_resize_history(GetLine *gl, size_t bufsize);

       void gl_limit_history(GetLine *gl, int max_lines);

       void gl_clear_history(GetLine *gl, int all_groups);

       void gl_toggle_history(GetLine *gl, int enable);

       GlTerminalSize gl_terminal_size(GetLine *gl,
                                       int def_ncolumn,
                                       int def_nline);

       int gl_set_term_size(GetLine *gl, int ncolumn, int nline);

       int gl_lookup_history(GetLine *gl, unsigned long id,
                             GlHistoryLine *hline);

       void gl_state_of_history(GetLine *gl,
                                GlHistoryState *state);

       void gl_range_of_history(GetLine *gl,
                                GlHistoryRange *range);

       void gl_size_of_history(GetLine *gl, GlHistorySize *size);

       void gl_echo_mode(GetLine *gl, int enable);

       void gl_replace_prompt(GetLine *gl, const char *prompt);

       void gl_prompt_style(GetLine *gl, GlPromptStyle style);

       int gl_ignore_signal(GetLine *gl, int signo);

       int gl_trap_signal(GetLine *gl, int signo, unsigned flags,
                          GlAfterSignal after, int errno_value);

       int gl_last_signal(GetLine *gl);

       int gl_completion_action(GetLine *gl,
                                void *data, CplMatchFn *match_fn,
                                int list_only, const char *name,
                                const char *keyseq);

       int gl_register_action(GetLine *gl, void *data,
                              GlActionFn *fn, const char *name,
                              const char *keyseq);

       int gl_display_text(GetLine *gl, int indentation,
                           const char *prefix,
                           const char *suffix, int fill_char,
                           int def_width, int start,
                           const char *string);

       GlReturnStatus gl_return_status(GetLine *gl);

       const char *gl_error_message(GetLine *gl, char *buff,
                                    size_t n);

       void gl_catch_blocked(GetLine *gl);

       int gl_list_signals(GetLine *gl, sigset_t *set);

       int gl_append_history(GetLine *gl, const char *line);

       int gl_automatic_history(GetLine *gl, int enable);




DESCRIPTION
       The gl_get_line() function is part of the tecla library (see the libte-
       cla(@LIBR_MANEXT@) man page). If the user is typing at a terminal, each
       call prompts them for an line of input, then provides interactive edit-
       ing facilities, similar to those of the unix tcsh shell. In addition to
       simple command-line editing, it supports recall of  previously  entered
       command  lines,  TAB  completion  of  file names, and in-line wild-card
       expansion of filenames. Documentation of both the  user-level  command-
       line  editing features and all user configuration options, can be found
       in the tecla man page. This  man  page  concerns  itself
       with  documentation for programmers interested in using this library in
       their application.



AN EXAMPLE
       The following shows a complete example of how to use the  gl_get_line()
       function to get input from the user:

         #include <stdio.h>
         #include <locale.h>
         #include <libtecla.h>

         int main(int argc, char *argv[])
         {
           char *line;    /* The line that the user typed */
           GetLine *gl;   /* The gl_get_line() resource object */

           setlocale(LC_CTYPE, ""); /* Adopt the user's choice */
                                    /* of character set. */

           gl = new_GetLine(1024, 2048);
           if(!gl)
             return 1;

           while((line=gl_get_line(gl, "$ ", NULL, -1)) != NULL &&
                  strcmp(line, "exit\n") != 0)
             printf("You typed: %s\n", line);

           gl = del_GetLine(gl);
           return 0;
         }

       In  the  example, first the resources needed by the gl_get_line() func-
       tion are created by calling new_GetLine(). This  allocates  the  memory
       used  in  subsequent calls to the gl_get_line() function, including the
       history buffer for recording previously entered lines. Then one or more
       lines are read from the user, until either an error occurs, or the user
       types exit. Then finally the resources that were allocated by  new_Get-
       Line(),  are  returned to the system by calling del_GetLine(). Note the
       use of the NULL return value of del_GetLine() to make gl NULL. This  is
       a safety precaution. If the program subsequently attempts to pass gl to
       gl_get_line(), said  function  will  complain,  and  return  an  error,
       instead of attempting to use the deleted resource object.




THE FUNCTIONS USED IN THE EXAMPLE
       The descriptions of the functions used in the example are as follows:

         GetLine *new_GetLine(size_t linelen, size_t histlen)

       This  function creates the resources used by the gl_get_line() function
       and returns an opaque pointer to the object that  contains  them.   The
       maximum  length of an input line is specified via the linelen argument,
       and the number of bytes to allocate for storing history lines is set by
       the histlen argument. History lines are stored back-to-back in a single
       buffer of this size. Note that this means that the  number  of  history
       lines  that  can be stored at any given time, depends on the lengths of
       the individual lines.  If you want to place an upper limit on the  num-
       ber  of  lines  that can be stored, see the gl_limit_history() function
       described later. If you don't want history at all, specify  histlen  as
       zero, and no history buffer will be allocated.

       On error, a message is printed to stderr and NULL is returned.

         GetLine *del_GetLine(GetLine *gl)

       This  function  deletes  the resources that were returned by a previous
       call to new_GetLine(). It always returns NULL (ie a deleted object). It
       does nothing if the gl argument is NULL.

         char *gl_get_line(GetLine *gl, const char *prompt,
                          const char *start_line, int start_pos);

       The  gl_get_line()  function  can be called any number of times to read
       input from the user. The gl argument must have been previously returned
       by  a call to new_GetLine(). The prompt argument should be a normal NUL
       terminated string, specifying the prompt to present the user  with.  By
       default  prompts  are  displayed  literally,  but  if  enabled with the
       gl_prompt_style() function (see later), prompts can contain  directives
       to  do underlining, switch to and from bold fonts, or turn highlighting
       on and off.

       If you want to specify the initial contents of the line, for  the  user
       to  edit,  pass the desired string via the start_line argument. You can
       then specify which character of this line the cursor is initially posi-
       tioned  over,  using  the  start_pos argument. This should be -1 if you
       want the cursor to follow the last character of the start line. If  you
       don't want to preload the line in this manner, send start_line as NULL,
       and set start_pos to -1. Note that the line  pointer  returned  by  one
       call  to  gl_get_line()  can  be  passed  back  to  the  next  call  to
       gl_get_line() via the start_line. This allows the application  to  take
       the  last entered line, and if it contains an error, to then present it
       back to the user for re-editing, with the cursor  initially  positioned
       where the error was encountered.

       The gl_get_line() function returns a pointer to the line entered by the
       user, or NULL on error or at the end of the input. The returned pointer
       is  part  of  the  specified gl resource object, and thus should not be
       free'd by the caller, or assumed to be unchanging from one call to  the
       next.  When  reading  from a user at a terminal, there will always be a
       newline character at the end of the returned line.  When standard input
       is being taken from a pipe or a file, there will similarly be a newline
       unless the input line was too long to store in the internal buffer.  In
       the latter case you should call gl_get_line() again to read the rest of
       the line. Note  that  this  behavior  makes  gl_get_line()  similar  to
       fgets().    In   fact   when   stdin   isn't   connected  to  a  termi-
       nal,gl_get_line() just calls fgets().



THE RETURN STATUS OF GL_GET_LINE
       As described above, the gl_get_line() function has two possible  return
       values;  a pointer to the completed input line, or NULL. Extra informa-
       tion about what caused gl_get_line() to return  is  available  both  by
       inspecting errno, and by calling the gl_return_status() function.


         GlReturnStatus gl_return_status(GetLine *gl);


       The  following  are  the  possible enumerated values that this function
       returns.


         GLR_NEWLINE     -  The last call to gl_get_line()
                            successfully returned a completed
                            input line.

         GLR_BLOCKED     -  gl_get_line() was in non-blocking
                            server mode, and returned early to
                            avoid blocking the process while
                            waiting for terminal I/O. The
                            gl_pending_io() function can be
                            used to see what type of I/O
                            gl_get_line() was waiting for.
                            (see the gl_io_mode man page
                            for details).

         GLR_SIGNAL      -  A signal was caught by
                            gl_get_line() that had an
                            after-signal disposition of
                            GLS_ABORT (See gl_trap_signal()).

         GLR_TIMEOUT     -  The inactivity timer expired while
                            gl_get_line() was waiting for
                            input, and the timeout callback
                            function returned GLTO_ABORT.
                            See gl_inactivity_timeout() for
                            information about timeouts.

         GLR_FDABORT     -  An application I/O callack returned
                            GLFD_ABORT (see gl_watch_fd()).

         GLR_EOF         -  End of file reached. This can happen
                            when input is coming from a file or a
                            pipe, instead of the terminal. It also
                            occurs if the user invokes the
                            list-or-eof or del-char-or-list-or-eof
                            actions at the start of a new line.

         GLR_ERROR       -  An unexpected error caused
                            gl_get_line() to abort (consult
                            errno and/or
                            gl_error_message() for details.


       When gl_return_status() returns GLR_ERROR, and the value of errno isn't
       sufficient to explain what happened, you can use the gl_error_message()
       function to request a description of the last error that occurred.


         const char *gl_error_message(GetLine *gl, char *buff,
                                      size_t n);


       The return value is a pointer to the message that occurred. If the buff
       argument  is  NULL, this will be a pointer to a buffer within gl, who's
       value will probably change on the next call to any function  associated
       with gl_get_line(). Otherwise, if a non-NULL buff argument is provided,
       the error message, including a '\0' terminator, will be written  within
       the  first  n  elements  of this buffer, and the return value will be a
       pointer to the first element of this buffer. If the message  won't  fit
       in the provided buffer, it will be truncated to fit.



OPTIONAL PROMPT FORMATTING
       Whereas by default the prompt string that you specify is displayed lit-
       erally, without any special interpretation of the characters within it,
       the  gl_prompt_style()  function can be used to enable optional format-
       ting directives within the prompt.

         void gl_prompt_style(GetLine *gl, GlPromptStyle style);

       The style argument, which specifies the formatting style, can take  any
       of the following values:

         GL_FORMAT_PROMPT   -  In this style, the formatting
                               directives described below, when
                               included in prompt strings, are
                               interpreted as follows:

                                 %B  -  Display subsequent
                                        characters with a bold
                                        font.
                                 %b  -  Stop displaying characters
                                        with the bold font.
                                 %F  -  Make subsequent characters
                                        flash.
                                 %f  -  Turn off flashing
                                        characters.
                                 %U  -  Underline subsequent
                                        characters.
                                 %u  -  Stop underlining
                                        characters.
                                 %P  -  Switch to a pale (half
                                        brightness) font.
                                 %p  -  Stop using the pale font.
                                 %S  -  Highlight subsequent
                                        characters (also known as
                                        standout mode).
                                 %s  -  Stop highlighting
                                        characters.
                                 %V  -  Turn on reverse video.
                                 %v  -  Turn off reverse video.
                                 %%  -  Display a single %
                                        character.

                               For example, in this mode, a prompt
                               string like "%UOK%u$ " would
                               display the prompt "OK$ ",
                               but with the OK part
                               underlined.

                               Note that although a pair of
                               characters that starts with a %
                               character, but doesn't match any of
                               the above directives is displayed
                               literally, if a new directive is
                               subsequently introduced which does
                               match, the displayed prompt will
                               change, so it is better to always
                               use %% to display a literal %.

                               Also note that not all terminals
                               support all of these text
                               attributes, and that some substitute
                               a different attribute for missing
                               ones.

         GL_LITERAL_PROMPT  -  In this style, the prompt string is
                               printed literally. This is the
                               default style.



ALTERNATE CONFIGURATION SOURCES
       As mentioned above, by default users have the option of configuring the
       behavior of gl_get_line() via a configuration file called  .teclarc  in
       their  home directories. The fact that all applications share this same
       configuration file is both an advantage and a  disadvantage.   In  most
       cases it is an advantage, since it encourages uniformity, and frees the
       user from having to configure each  application  separately.   In  some
       applications, however, this single means of configuration is a problem.
       This is particularly  true  of  embedded  software,  where  there's  no
       filesystem  to read a configuration file from, and also in applications
       where a radically different choice of keybindings is needed to  emulate
       a  legacy  keyboard  interface.  To cater for such cases, the following
       function allows the application to control where configuration informa-
       tion is read from.


         int gl_configure_getline(GetLine *gl,
                                  const char *app_string,
                                  const char *app_file,
                                  const char *user_file);


       It allows the configuration commands that would normally be read from a
       user's ~/.teclarc file, to be read from any or none of,  a  string,  an
       application specific configuration file, and/or a user-specific config-
       uration file. If this function is  called  before  the  first  call  to
       gl_get_line(),  the default behavior of reading ~/.teclarc on the first
       call to  gl_get_line()  is  disabled,  so  all  configuration  must  be
       achieved  using the configuration sources specified with this function.

       If app_string != NULL, then it is interpreted as  a  string  containing
       one  or  more  configuration commands, separated from each other in the
       string by embedded newline characters. If app_file != NULL then  it  is
       interpreted  as the full pathname of an application-specific configura-
       tion file. If user_file != NULL then it  is  interpreted  as  the  full
       pathname of a user-specific configuration file, such as ~/.teclarc. For
       example, in the following call,


         gl_configure_getline(gl, "edit-mode vi \n nobeep",
                                  "/usr/share/myapp/teclarc",
                                  "~/.teclarc");


       the app_string argument causes the calling application to start  in  vi
       edit-mode,  instead of the default emacs mode, and turns off the use of
       the terminal bell by the library. It then attempts to read  system-wide
       configuration     commands     from    an    optional    file    called
       /usr/share/myapp/teclarc, then finally reads  user-specific  configura-
       tion  commands from an optional .teclarc file in the user's home direc-
       tory. Note that the arguments are listed in ascending order  of  prior-
       ity,  with  the  contents  of app_string being potentially overriden by
       commands in app_file, and commands in app_file potentially being  over-
       riden by commands in user_file.

       You  can  call this function as many times as needed, the results being
       cumulative, but note that copies of any  filenames  specified  via  the
       app_file and user_file arguments are recorded internally for subsequent
       use by the read-init-files key-binding function, so if you plan to call
       this  function multiple times, be sure that the last call specifies the
       filenames that you want re-read when the user requests that the config-
       uration files be re-read.

       Individual  key  sequences  can  also  be  bound  and unbound using the
       gl_bind_keyseq() function.


         int gl_bind_keyseq(GetLine *gl, GlKeyOrigin origin,
                            const char *keyseq,
                            const char *action);


       The origin argument specifies the priority of the binding, according to
       who  it  is being established for, and must be one of the following two
       values.

         GL_USER_KEY   -   The user requested this key-binding.
         GL_APP_KEY    -   This is a default binding set by the
                           application.

       When both user and application bindings for a given  key-sequence  have
       been  specified,  the  user binding takes precedence. The application's
       binding is subsequently reinstated  if  the  user's  binding  is  later
       unbound  via  either  another to this function, or a call to gl_config-
       ure_getline().

       The keyseq argument specifies the key-sequence to be bound or  unbound,
       and is expressed in the same way as in a ~/.teclarc configuration file.
       The action argument must either be a string containing the name of  the
       action  to bind the key-sequence to, or it must be NULL or "" to unbind
       the key-sequence.



CUSTOMIZED WORD COMPLETION
       If in your application, you would like to have TAB completion  complete
       other  things  in  addition to or instead of filenames, you can arrange
       this by registering an alternate completion callback  function,  via  a
       call to the gl_customize_completion() function.

         int gl_customize_completion(GetLine *gl, void *data,
                                     CplMatchFn *match_fn);

       The  data  argument  provides  a way for your application to pass arbi-
       trary, application-specific information to the callback function.  This
       is  passed  to  the callback every time that it is called. It might for
       example, point to the symbol table from which possible completions  are
       to  be sought. The match_fn argument specifies the callback function to
       be called. The CplMatchFn function type is defined in libtecla.h, as is
       a  CPL_MATCH_FN() macro that you can use to declare and prototype call-
       back functions. The declaration and responsibilities of callback  func-
       tions  are  described  in depth in the cpl_complete_word
       man page.

       In brief, the callback function is responsible for looking backwards in
       the  input  line, back from the point at which the user pressed TAB, to
       find the start of the word being completed. It then must lookup  possi-
       ble  completions  of this word, and record them one by one in the Word-
       Completion object that is passed to it as an argument, by  calling  the
       cpl_add_completion()  function. If the callback function wishes to pro-
       vide filename completion in addition to its own  specific  completions,
       it  has  the  option of itself calling the builtin file-name completion
       callback.    This    also,    is    documented    in    the    cpl_com-
       plete_word(@FUNC_MANEXT@) man page.

       Note  that  if you would like gl_get_line() to return the current input
       line when a successful completion is been made, you  can  arrange  this
       when you call cpl_add_completion(), by making the last character of the
       continuation suffix a newline character. If you do this, the input line
       will   be   updated  to  display  the  completion,  together  with  any
       contiuation suffix up to the newline character, then gl_get_line() will
       return this input line.


       If, for some reason, your callback function needs to write something to
       the terminal, it must call gl_normal_io() before doing  so.  This  will
       start  a  new line after the input line that is currently being edited,
       reinstate normal terminal I/O, and tell gl_get_line()  that  the  input
       line will need to be redrawn when the callback returns.



ADDING COMPLETION ACTIONS
       In  the  previous  section the ability to customize the behavior of the
       only default completion action, complete-word, was described.  In  this
       section  the  ability  to  install additional action functions, so that
       different types of word completion  can  be  bound  to  different  key-
       sequences,  is  described.  This  is  achieved  by using the gl_comple-
       tion_action() function.


         int gl_completion_action(GetLine *gl,
                                  void *data, CplMatchFn *match_fn,
                                  int list_only, const char *name,
                                  const char *keyseq);


       The data and match_fn  arguments  are  as  described  in  the  cpl_com-
       plete_word  man  page, and specify the callback function that should be
       invoked to  identify  possible  completions.   The  list_only  argument
       determines  whether  the action that is being defined should attempt to
       complete the word as far as possible in the input line before  display-
       ing  any  possible  ambiguous  completions, or whether it should simply
       display the list of possible completions  without  touching  the  input
       line. The former option is selected by specifying a value of 0, and the
       latter by specifying a value of 1. The name argument specifies the name
       by  which  configuration  files and future invokations of this function
       should refer to the action. This must either be the name of an existing
       completion  action  to  be  changed,  or be a new unused name for a new
       action. Finally, the keyseq argument specifies the default key-sequence
       to  bind  the  action  to.  If this is NULL, no new keysequence will be
       bound to the action.

       Beware that in order for the user to be able to change the key-sequence
       that  is  bound  to actions that are installed in this manner, when you
       call gl_completion_action() to install a given  action  for  the  first
       time,  you  should  do this between calling new_GetLine() and the first
       call to gl_get_line().  Otherwise, when the user's  configuration  file
       is  read on the first call to gl_get_line(), the name of the your addi-
       tional action won't be known, and any reference to it in the configura-
       tion file will generate an error.

       As  discussed for gl_customize_completion(), if your callback function,
       for some reason, needs to write anything to the terminal, it must  call
       gl_normal_io() before doing so.



DEFINING CUSTOM ACTIONS
       Although  the built-in key-binding actions are sufficient for the needs
       of most applications, occasionally a specialized application  may  need
       to  define  one  or  more custom actions, bound to application-specific
       key-sequences. For example, a sales application would benefit from hav-
       ing  a key-sequence that displayed the part name that corresponded to a
       part number preceding the cursor. Such a feature is clearly beyond  the
       scope  of the built-in action functions. So for such special cases, the
       gl_register_action() function is provided.


         int gl_register_action(GetLine *gl, void *data,
                       GlActionFn *fn, const char *name,
                       const char *keyseq);


       This function lets the application register an external  function,  fn,
       that  will  thereafter  be  called  whenever  either the specified key-
       sequence, keyseq, is entered by the user, or the user enters any  other
       key-sequence  that  the user subsequently binds to the specified action
       name, name, in their configuration file. The data  argument  can  be  a
       pointer  to  anything that the application wishes to have passed to the
       action function, fn, whenever that function is invoked.

       The action function, fn, should be declared using the following  macro,
       which is defined in libtecla.h.


         #define GL_ACTION_FN(fn) GlAfterAction (fn)(GetLine *gl, \
                     void *data, int count, size_t curpos, \
                     const char *line)


       The  gl  and  data  arguments  are those that were previously passed to
       gl_register_action() when the action function was registered. The count
       argument  is a numeric argument which the user has the option of enter-
       ing using the digit-argument action, before invoking the action. If the
       user doesn't enter a number, then the count argument is set to 1. Nomi-
       nally this argument is interpreted as a repeat count, meaning that  the
       action  should  be  repeated  that many times. In practice however, for
       some actions a repeat count makes little sense. In such cases,  actions
       can  either  simply  ignore  the count argument, or use its value for a
       different purpose.

       A copy of the current input line is passed in the read-only line  argu-
       ment.  The  current  cursor position within this string is given by the
       index contained in the curpos argument. Note that  direct  manipulation
       of  the  input  line  and the cursor position is not permitted. This is
       because the rules dicated by various modes,  such  as  vi  mode  versus
       emacs  mode,  no-echo mode, and insert mode versus overstrike mode etc,
       make it too complex for an application writer  to  write  a  conforming
       editing action, as well as constrain future changes to the internals of
       gl_get_line(). A potential solution to this dilema would  be  to  allow
       the  action  function  to  edit  the  line  using  the existing editing
       actions. This is currently under consideration.

       If the action function wishes to write text to  the  terminal,  without
       this  getting  mixed  up  with the displayed text of the input line, or
       read from the terminal without having to handle raw terminal I/O,  then
       before  doing  either  of these operations, it must temporarily suspend
       line editing by calling  the  gl_normal_io()  function.  This  function
       flushes  any  pending  output  to the terminal, moves the cursor to the
       start of the line that follows the last  terminal  line  of  the  input
       line,  then  restores  the terminal to a state that is suitable for use
       with the C stdio facilities. The latter includes such things as restor-
       ing the normal mapping of \n to \r\n, and, when in server mode, restor-
       ing the normal blocking form of terminal I/O. Having called this  func-
       tion, the action function can read from and write to the terminal with-
       out the fear of creating a mess.  It isn't  necessary  for  the  action
       function to restore the original editing environment before it returns.
       This is done automatically by gl_get_line() after the  action  function
       returns.  The following is a simple example of an action function which
       writes the sentence "Hello world" on a new terminal line after the line
       being  edited. When this function returns, the input line is redrawn on
       the line that follows the "Hello world" line, and line editing resumes.


         static GL_ACTION_FN(say_hello_fn)
         {
           if(gl_normal_io(gl))   /* Temporarily suspend editing */
             return GLA_ABORT;
           printf("Hello world\n");
           return GLA_CONTINUE;
         }


       Action  functions  must  return  one  of  the following values, to tell
       gl_get_line() how to procede.


         GLA_ABORT     -   Cause gl_get_line() to return NULL.
         GLA_RETURN    -   Cause gl_get_line() to return the
                           completed input line.
         GLA_CONTINUE  -   Resume command-line editing.


       Note that the name argument of gl_register_action() specifies the  name
       by  which  a  user can refer to the action in their configuration file.
       This allows them to re-bind the action to an alternate key-seqeunce. In
       order  for  this  to work, it is necessary to call gl_register_action()
       between calling new_GetLine() and the first call to gl_get_line().



HISTORY FILES
       To save the contents of the history buffer before quitting your  appli-
       cation,  and subsequently restore them when you next start the applica-
       tion, the following functions are provided.


        int gl_save_history(GetLine *gl, const char *filename,
                            const char *comment, int max_lines);
        int gl_load_history(GetLine *gl, const char *filename,
                            const char *comment);


       The filename argument specifies the name to give the history file  when
       saving, or the name of an existing history file, when loading. This may
       contain home-directory and environment variable  expressions,  such  as
       "~/.myapp_history" or "$HOME/.myapp_history".

       Along  with each history line, extra information about it, such as when
       it was entered by the user, and what its nesting level is, is  recorded
       as  a comment preceding the line in the history file. Writing this as a
       comment allows the history file to double as a command  file,  just  in
       case  you  wish  to replay a whole session using it. Since comment pre-
       fixes differ in different languages, the comment argument  is  provided
       for  specifying  the  comment  prefix. For example, if your application
       were a unix shell, such as the bourne  shell,  you  would  specify  "#"
       here.  Whatever  you choose for the comment character, you must specify
       the same prefix to gl_load_history() that  you  used  when  you  called
       gl_save_history() to write the history file.

       The  max_lines  must be either -1 to specify that all lines in the his-
       tory list be saved, or a positive number specifying a  ceiling  on  how
       many of the most recent lines should be saved.

       Both  fuctions return non-zero on error, after writing an error message
       to stderr. Note that gl_load_history() does not consider the  non-exis-
       tence of a file to be an error.



MULTIPLE HISTORY LISTS
       If your application uses a single GetLine object for entering many dif-
       ferent types of input lines, you may wish gl_get_line() to  distinguish
       the different types of lines in the history list, and only recall lines
       that match the current type  of  line.  To  support  this  requirement,
       gl_get_line()  marks  lines  being recorded in the history list with an
       integer identifier chosen by the application.  Initially  this  identi-
       fier  is  set to 0 by new_GetLine(), but it can be changed subsequently
       by calling gl_group_history().


         int gl_group_history(GetLine *gl, unsigned id);


       The integer identifier id can be any number chosen by the  application,
       but  note  that  gl_save_history()  and  gl_load_history() preserve the
       association between identifiers and historical input lines between pro-
       gram  invokations,  so you should choose fixed identifiers for the dif-
       ferent types of input line used by your application.

       Whenever gl_get_line() appends a new input line to  the  history  list,
       the  current  history  identifier  is  recorded with it, and when it is
       asked to recall a historical input line, it only recalls lines that are
       marked with the current identifier.



DISPLAYING HISTORY
       The history list can be displayed by calling gl_show_history().


         int gl_show_history(GetLine *gl, FILE *fp,
                             const char *fmt,
                             int all_groups,
                             int max_lines);


       This  displays  the  current  contents of the history list to the stdio
       output stream fp. If the max_lines argument is greater than or equal to
       zero,  then  no  more than this number of the most recent lines will be
       displayed. If the all_groups argument is non-zero, lines from all  his-
       tory  groups  are  displayed.  Otherwise  just  those  of the currently
       selected history group are displayed. The format string argument,  fmt,
       determines  how the line is displayed. This can contain arbitrary char-
       acters which are written verbatim, interleaved with any of the  follow-
       ing format directives:

         %D  -  The date on which the line was originally
                entered, formatted like 2001-11-20.
         %T  -  The time of day when the line was entered,
                formatted like 23:59:59.
         %N  -  The sequential entry number of the line in
                the history buffer.
         %G  -  The number of the history group which the
                line belongs to.
         %%  -  A literal % character.
         %H  -  The history line itself.

       Thus a format string like "%D %T  %H0 would output something like:

         2001-11-20 10:23:34  Hello world

       Note  the  inclusion  of  an  explicit  newline character in the format
       string.



LOOKING UP HISTORY
       The gl_lookup_history() function allows the calling application to look
       up lines in the history list.


         typedef struct {
           const char *line;    /* The requested historical */
                                /*  line. */
           unsigned group;      /* The history group to which */
                                /*  the line belongs. */
           time_t timestamp;    /* The date and time at which */
                                /*  the line was originally */
                                /*  entered. */
         } GlHistoryLine;

         int gl_lookup_history(GetLine *gl, unsigned long id,
                               GlHistoryLine *hline);


       The  id  argument indicates which line to look up, where the first line
       that was entered in the history list after new_GetLine() was called, is
       denoted  by  0, and subsequently entered lines are denoted with succes-
       sively higher numbers. Note that the range of lines currently preserved
       in the history list can be queried by calling the gl_range_of_history()
       function, described later. If the requested  line  is  in  the  history
       list,  the  details of the line are recorded in the variable pointed to
       by the hline argument, and 1 is returned. Otherwise 0 is returned,  and
       the variable pointed to by hline is left unchanged.

       Beware  that  the string returned in hline->line is part of the history
       buffer, so it must not be modified by the caller, and will be  recycled
       on  the next call to any function that takes gl as its argument. There-
       fore you should make a private copy of this string if you need to  keep
       it around.



MANUAL HISTORY ARCHIVAL
       By default, whenever a line is entered by the user, it is automatically
       appended to the history list, just  before  gl_get_line()  returns  the
       line  to  the  caller.  This is convenient for the majority of applica-
       tions, but there are also applications that need finer grained  control
       over  what gets added to the history list. In such cases, the automatic
       addition of entered lines to the history list  can  be  turned  off  by
       calling the gl_automatic_history() function.


         int gl_automatic_history(GetLine *gl, int enable);


       If  this  function  is  called  with  its  enable  argument  set  to 0,
       gl_get_line() won't automatically archive subsequently  entered  lines.
       Automatic  archiving  can be reenabled at a later time, by calling this
       function again, with its enable argument set  to  1.   While  automatic
       history  archiving  is  disabled,  the  calling application can use the
       gl_append_history() to append lines to the history list as needed.


         int gl_append_history(GetLine *gl, const char *line);


       The line argument specifies the line to be added to the  history  list.
       This  must  be  a normal ' ' terminated string. If this string contains
       any newline characters, the line that gets archived in the history list
       will  be  terminated by the first of these. Otherwise it will be termi-
       nated by the ' ' terminator.  If the line is longer  than  the  maximum
       input  line  length,  that was specified when new_GetLine() was called,
       when the line  is  recalled,  it  will  get  truncated  to  the  actual
       gl_get_line() line length.

       If successful, gl_append_history() returns 0. Otherwise it returns non-
       zero, and sets errno to one of the following values.


          EINVAL  -  One of the arguments passed to
                     gl_append_history() was NULL.
          ENOMEM  -  The specified line was longer than the allocated
                     size of the history buffer (as specified when
                     new_GetLine() was called), so it couldn't be
                     archived.


       A textual description of the error can optionally be obtained by  call-
       ing gl_error_message(). Note that after such an error, the history list
       remains in a valid state to receive new history lines, so there is lit-
       tle harm in simply ignoring the return status of gl_append_history().



MISCELLANEOUS HISTORY CONFIGURATION
       If  you  wish  to change the size of the history buffer that was origi-
       nally specified in the call to new_GetLine(), you can do  so  with  the
       gl_resize_history() function.


         int gl_resize_history(GetLine *gl, size_t histlen);


       The  histlen argument specifies the new size in bytes, and if you spec-
       ify this as 0, the buffer will be deleted.

       As mentioned in the discussion of new_GetLine(), the  number  of  lines
       that can be stored in the history buffer, depends on the lengths of the
       individual lines. For example, a 1000 byte buffer could  equally  store
       10  lines  of average length 100 bytes, or 2 lines of average length 50
       bytes. Although the buffer is never expanded when new lines are  added,
       a  list  of  pointers  into the buffer does get expanded when needed to
       accomodate the number of lines currently stored in the buffer. To place
       an upper limit on the number of lines in the buffer, and thus a ceiling
       on  the  amount  of  memory  used  in  this  list,  you  can  call  the
       gl_limit_history() function.


         void gl_limit_history(GetLine *gl, int max_lines);


       The  max_lines  should  either be a positive number >= 0, specifying an
       upper limit on the number of lines in the buffer, or be  -1  to  cancel
       any  previously  specified  limit.  When a limit is in effect, only the
       max_lines most recently appended lines are kept in  the  buffer.  Older
       lines are discarded.

       To  discard  lines  from the history buffer, use the gl_clear_history()
       function.

         void gl_clear_history(GetLine *gl, int all_groups);

       The all_groups argument tells the function whether to delete  just  the
       lines  associated  with  the  current  history group (see gl_group_his-
       tory()), or all historical lines in the buffer.

       The gl_toggle_history() function allows you to toggle  history  on  and
       off without losing the current contents of the history list.


         void gl_toggle_history(GetLine *gl, int enable);


       Setting  the  enable argument to 0 turns off the history mechanism, and
       setting it to 1 turns it back on. When history is turned  off,  no  new
       lines  will  be added to the history list, and history lookup key-bind-
       ings will act as though there is nothing in the history buffer.



QUERYING HISTORY INFORMATION
       The configured state of the  history  list  can  be  queried  with  the
       gl_history_state() function.


         typedef struct {
           int enabled;     /* True if history is enabled */
           unsigned group;  /* The current history group */
           int max_lines;   /* The current upper limit on the */
                            /*  number of lines in the history */
                            /*  list, or -1 if unlimited. */
         } GlHistoryState;

         void gl_state_of_history(GetLine *gl,
                                  GlHistoryState *state);

       On  return,  the status information is recorded in the variable pointed
       to by the state argument.

       The gl_range_of_history() function returns  the  number  and  range  of
       lines in the history list.


       typedef struct {
         unsigned long oldest;  /* The sequential entry number */
                                /*  of the oldest line in the */
                                /*  history list. */
         unsigned long newest;  /* The sequential entry number */
                                /*  of the newest line in the */
                                /*  history list. */
         int nlines;            /* The number of lines in the */
                                /*  history list. */
       } GlHistoryRange;

       void gl_range_of_history(GetLine *gl, GlHistoryRange *range);

       The  return values are recorded in the variable pointed to by the range
       argument. If the nlines member of this structure is greater than  zero,
       then  the  oldest  and  newest members report the range of lines in the
       list, and newest=oldest+nlines-1.  Otherwise they are both zero.

       The gl_size_of_history() function returns the total size of the history
       buffer and the amount of the buffer that is currently occupied.

         typedef struct {
           size_t size;      /* The size of the history buffer */
                             /*  (bytes). */
           size_t used;      /* The number of bytes of the */
                             /*  history buffer that are */
                             /*  currently occupied. */
         } GlHistorySize;

         void gl_size_of_history(GetLine *gl, GlHistorySize *size);

       On  return, the size information is recorded in the variable pointed to
       by the size argument.



CHANGING TERMINALS
       The new_GetLine() constructor function assumes that input is to be read
       from stdin, and output written to stdout. The following function allows
       you to switch to different input and output streams.

         int gl_change_terminal(GetLine *gl, FILE *input_fp,
                                FILE *output_fp, const char *term);

       The gl argument is the object that was returned by new_GetLine().   The
       input_fp  argument  specifies  the  stream  to read from, and output_fp
       specifies the stream to be written to. Only if both of these refer to a
       terminal,  will  interactive  terminal  input  be  enabled.   Otherwise
       gl_get_line() will simply call fgets() to read command input.  If  both
       streams refer to a terminal, then they must refer to the same terminal,
       and the type of this terminal must be specified via the term  argument.
       The value of the term argument is looked up in the terminal information
       database (terminfo or termcap), in order  to  determine  which  special
       control  sequences  are needed to control various aspects of the termi-
       nal.  new_GetLine()  for  example,   passes   the   return   value   of
       getenv("TERM")  in  this argument. Note that if one or both of input_fp
       and output_fp don't refer to a terminal, then it is legal to pass  NULL
       instead of a terminal type.

       Note that if you want to pass file descriptors to gl_change_terminal(),
       you can do this by creating  stdio  stream  wrappers  using  the  POSIX
       fdopen() function.



EXTERNAL EVENT HANDLING
       By  default, gl_get_line() doesn't return until either a complete input
       line has been entered by the user, or an error occurs. In programs that
       need  to  watch for I/O from other sources than the terminal, there are
       two options.


         1. Use the functions described in the
            gl_io_mode man page to switch
            gl_get_line() into non-blocking server mode. In this mode,
            gl_get_line() becomes a non-blocking, incremental
            line-editing function that can safely be called from
            an external event loop. Although this is a very
            versatile method, it involves taking on some
            responsibilities that are normally performed behind
            the scenes by gl_get_line().

         2. While gl_get_line() is waiting for keyboard
            input from the user, you can ask it to also watch for
            activity on arbitrary file descriptors, such as
            network sockets, pipes etc, and have it call functions
            of your choosing when activity is seen. This works on
            any system that has the select() system call,
            which is most, if not all flavors of unix.


       Registering a file descriptor to be watched by  gl_get_line()  involves
       calling the gl_watch_fd() function.


         int gl_watch_fd(GetLine *gl, int fd, GlFdEvent event,
                         GlFdEventFn *callback, void *data);


       If  this returns non-zero, then it means that either your arguments are
       invalid, or that this facility isn't supported on the host system.

       The fd argument is the file descriptor to be watched. The  event  argu-
       ment  specifies  what  type of activity is of interest, chosen from the
       following enumerated values:


         GLFD_READ   -  Watch for the arrival of data to be read.
         GLFD_WRITE  -  Watch for the ability to write to the file
                        descriptor without blocking.
         GLFD_URGENT -  Watch for the arrival of urgent
                        out-of-band data on the file descriptor.


       The callback argument  is  the  function  to  call  when  the  selected
       activity  is seen. It should be defined with the following macro, which
       is defined in libtecla.h.


         #define GL_FD_EVENT_FN(fn) GlFdStatus (fn)(GetLine *gl, \
                                             void *data, int fd, \
                                             GlFdEvent event)

       The data argument of the gl_watch_fd() function is passed to the  call-
       back  function  for  its  own  use, and can point to anything you like,
       including NULL. The file descriptor and the  event  argument  are  also
       passed  to  the callback function, and this potentially allows the same
       callback function to be registered to  more  than  one  type  of  event
       and/or  more than one file descriptor. The return value of the callback
       function should be one of the following values.


         GLFD_ABORT    -  Tell gl_get_line() to abort. When this
                          happens, gl_get_line() returns
                          NULL, and a following call to
                          gl_return_status() will return
                          GLR_FDABORT. Note that if the
                          application needs errno always to
                          have a meaningful value when
                          gl_get_line() returns NULL,
                          the callback function should set
                          errno appropriately.
         GLFD_REFRESH  -  Redraw the input line then continue
                          waiting for input. Return this if
                          your callback wrote to the terminal.
         GLFD_CONTINUE -  Continue to wait for input, without
                          redrawing the line.

       Note that before calling the callback, gl_get_line() blocks  most  sig-
       nals,  and  leaves its own signal handlers installed, so if you need to
       catch a particular signal you will need  to  both  temporarily  install
       your  own  signal  handler, and unblock the signal. Be sure to re-block
       the signal (if it was originally blocked) and  reinstate  the  original
       signal handler, if any, before returning.



       If  the  callback  function  needs to read or write to the terminal, it
       should ideally first call gl_normal_io(gl) to temporarily suspend  line
       editing.  This  will  restore  the terminal to canonical, blocking-I/O,
       mode, and move the cursor to the start of a new terminal  line.  Later,
       when  the  callback  returns,  gl_get_line()  will  notice that gl_nor-
       mal_io() was called, redisplay the input line and resume editing.  Note
       that in this case the return values, GLFD_REFRESH and GLFD_CONTINUE are
       equivalent.



       To support cases where the callback function calls a third-party  func-
       tion  which  occasionally and u0prisicre-enabledesbeforee themicallback
       automatic conversion of "0 to "
       function  is called. If the callack knows that the third-party function
       wrote to the terminal, it should then return  the  GLFD_REFRESH  return
       value, to tell gl_get_line() to redisplay the input line.



       To  remove  a  callback  function  that you previously registered for a
       given file descriptor and event, simply  call  gl_watch_fd()  with  the
       same  file descriptor and event arguments, but with a callback argument
       of 0. The data argument is ignored in this case.



SETTING AN INACTIVITY TIMEOUT
       On systems with the select() system call,  the  gl_inactivity_timeout()
       function can be used to set or cancel an inactivity timeout. Inactivity
       in this case refers both to keyboard input, and  to  I/O  on  any  file
       descriptors  registered by prior and subsequent calls to gl_watch_fd().
       On oddball systems that don't have select(), this call has no effect.


         int gl_inactivity_timeout(GetLine *gl, GlTimeoutFn *callback,
                            void *data, unsigned long sec,
                            unsigned long nsec);


       The timeout is specified in the form of an integral number  of  seconds
       and  an  integral number of nanoseconds, via the sec and nsec arguments
       respectively. Subsequently, whenever no activity is seen for this  time
       period, the function specified via the callback argument is called. The
       data argument of gl_inactivity_timeout() is  passed  verbatim  to  this
       callback  function whenever it is invoked, and can thus be used to pass
       arbitrary application-specific information to the callback. The follow-
       ing  macro is provided in libtecla.h for applications to use to declare
       and prototype timeout callback functions.


         #define GL_TIMEOUT_FN(fn) \
                      GlAfterTimeout (fn)(GetLine *gl, void *data)


       On returning, the application's callback is expected to return  one  of
       the  following  enumerators  to tell gl_get_line() how to procede after
       the timeout has been handled by the callback.


         GLTO_ABORT    -  Tell gl_get_line() to abort. When
                          this happens, gl_get_line() will
                          return NULL, and a following call
                          to gl_return_status() will return
                          GLR_TIMEOUT. Note that if the
                          application needs errno always to
                          have a meaningful value when
                          gl_get_line() returns NULL,
                          the callback function should set
                          errno appropriately.
         GLTO_REFRESH  -  Redraw the input line, then continue
                          waiting for input. You should return
                          this value if your callback wrote to the
                          terminal without having first called
                          gl_normal_io(gl).
         GLTO_CONTINUE -  In normal blocking-I/O mode, continue to
                          wait for input, without redrawing the
                          user's input line.
                          In non-blocking server I/O mode (see
                          gl_io_mode), cause gl_get_line()
                          to act as though I/O blocked. This means
                          that gl_get_line() will immediately
                          return NULL, and a following call
                          to gl_return_status() will return
                          GLR_BLOCKED.


       Note that before calling the callback, gl_get_line() blocks  most  sig-
       nals,  and  leaves its own signal handlers installed, so if you need to
       catch a particular signal you will need  to  both  temporarily  install
       your  own  signal  handler, and unblock the signal. Be sure to re-block
       the signal (if it was originally blocked) and  reinstate  the  original
       signal handler, if any, before returning.



       If  the  callback  function  needs to read or write to the terminal, it
       should ideally first call gl_normal_io(gl) to temporarily suspend  line
       editing.  This  will  restore  the terminal to canonical, blocking-I/O,
       mode, and move the cursor to the start of a new terminal  line.  Later,
       when  the  callback  returns,  gl_get_line()  will  notice that gl_nor-
       mal_io() was called, redisplay the input line and resume editing.  Note
       that in this case the return values, GLTO_REFRESH and GLTO_CONTINUE are
       equivalent.



       To support cases where the callback function calls a third-party  func-
       tion  which  occasionally and u0prisicre-enabledesbeforee themicallback
       automatic conversion of "0 to "
       function  is called. If the callack knows that the third-party function
       wrote to the terminal, it should then return  the  GLTO_REFRESH  return
       value, to tell gl_get_line() to redisplay the input line.



       Note  that  although the timeout argument includes a nano-second compo-
       nent, few computer clocks presently have  resolutions  that  are  finer
       than  a few milliseconds, so asking for less than a few milliseconds is
       equivalent to requesting zero seconds on a  lot  of  systems.  If  this
       would  be  a  problem,  you  should  base your timeout selection on the
       actual   resolution   of   the   host    clock    (eg.    by    calling
       sysconf(_SC_CLK_TCK)).



       To  turn off timeouts, simply call gl_inactivity_timeout() with a call-
       back argument of 0. The data argument is ignored in this case.



SIGNAL HANDLING DEFAULTS
       By default, the gl_get_line() function intercepts a number of  signals.
       This  is particularly important for signals which would by default ter-
       minate the process, since the terminal needs to be restored to a usable
       state  before  this  happens.  In  this  section,  the signals that are
       trapped  by  default,  and  how  gl_get_line()  responds  to  them,  is
       described.  Changing  these defaults is the topic of the following sec-
       tion.

       When the following subset of signals are  caught,  gl_get_line()  first
       restores  the  terminal  settings  and signal handling to how they were
       before gl_get_line() was called, resends the signal, to allow the call-
       ing  application's  signal  handlers  to handle it, then if the process
       still exists, gl_get_line() returns NULL and sets  errno  as  specified
       below.


        SIGINT  -  This signal is generated both by the keyboard
                   interrupt key (usually ^C), and the keyboard
                   break key.

                   errno=EINTR

        SIGHUP  -  This signal is generated when the controlling
                   terminal exits.

                   errno=ENOTTY

        SIGPIPE -  This signal is generated when a program attempts
                   to write to a pipe who's remote end isn't being
                   read by any process. This can happen for example
                   if you have called gl_change_terminal() to
                   redirect output to a pipe hidden under a pseudo
                   terminal.

                   errno=EPIPE

        SIGQUIT -  This signal is generated by the keyboard quit
                   key (usually ^\).

                   errno=EINTR

        SIGABRT -  This signal is generated by the standard C,
                   abort() function. By default it both
                   terminates the process and generates a core
                   dump.

                   errno=EINTR

        SIGTERM -  This is the default signal that the UN*X
                   kill command sends to processes.

                   errno=EINTR

       Note  that in the case of all of the above signals, POSIX mandates that
       by default the process is terminated, with the addition of a core  dump
       in  the  case  of  the  SIGQUIT  signal. In other words, if the calling
       application doesn't override the default handler by supplying  its  own
       signal  handler, receipt of the corresponding signal will terminate the
       application before gl_get_line() returns.

       If gl_get_line() aborts with errno set to EINTR, you can find out  what
       signal caused it to abort, by calling the following function.

         int gl_last_signal(const GetLine *gl);

       This  returns the numeric code (eg. SIGINT) of the last signal that was
       received during the most recent call to gl_get_line(), or -1 if no sig-
       nals were received.

       On  systems  that support it, when a SIGWINCH (window change) signal is
       received, gl_get_line() queries the terminal to find out its new  size,
       redraws the current input line to accomodate the new size, then returns
       to waiting for keyboard input from the user. Unlike other signals, this
       signal isn't resent to the application.

       Finally, the following signals cause gl_get_line() to first restore the
       terminal  and  signal  environment  to  that  which  prevailed   before
       gl_get_line() was called, then resend the signal to the application. If
       the process still exists after the  signal  has  been  delivered,  then
       gl_get_line() then re-establishes its own signal handlers, switches the
       terminal back to raw mode, redisplays the input line, and goes back  to
       awaiting terminal input from the user.

        SIGCONT    -  This signal is generated when a suspended
                      process is resumed.

        SIGPOLL    -  On SVR4 systems, this signal notifies the
                      process of an asynchronous I/O event. Note
                      that under 4.3+BSD, SIGIO and SIGPOLL are
                      the same. On other systems, SIGIO is ignored
                      by default, so gl_get_line() doesn't
                      trap it by default.

        SIGPWR     -  This signal is generated when a power failure
                      occurs (presumably when the system is on a
                      UPS).

        SIGALRM    -  This signal is generated when a timer
                      expires.

        SIGUSR1    -  An application specific signal.

        SIGUSR2    -  Another application specific signal.

        SIGVTALRM  -  This signal is generated when a virtual
                      timer expires (see man setitimer(2)).

        SIGXCPU    -  This signal is generated when a process
                      exceeds its soft CPU time limit.

        SIGXFSZ    -  This signal is generated when a process
                      exceeds its soft file-size limit.

        SIGTSTP    -  This signal is generated by the terminal
                      suspend key, which is usually ^Z, or the
                      delayed terminal suspend key, which is
                      usually ^Y.

        SIGTTIN    -  This signal is generated if the program
                      attempts to read from the terminal while the
                      program is running in the background.

        SIGTTOU    -  This signal is generated if the program
                      attempts to write to the terminal while the
                      program is running in the background.


       Obviously not all of the above signals are supported on all systems, so
       code to support them is conditionally compiled into the tecla  library.

       Note  that  if SIGKILL or SIGPOLL, which by definition can't be caught,
       or any of the hardware generated exception signals,  such  as  SIGSEGV,
       SIGBUS  and  SIGFPE, are received and unhandled while gl_get_line() has
       the terminal in raw mode, the program will be  terminated  without  the
       terminal  having been restored to a usable state. In practice, job-con-
       trol shells usually reset the terminal settings when a  process  relin-
       quishes  the controlling terminal, so this is only a problem with older
       shells.



CUSTOMIZED SIGNAL HANDLING
       The previous section listed the signals  that  gl_get_line()  traps  by
       default,  and described how it responds to them. This section describes
       how to both add and remove signals from the list  of  trapped  signals,
       and  how to specify how gl_get_line() should respond to a given signal.

       If you don't need gl_get_line() to do anything in response to a  signal
       that  it  normally  traps, you can tell to gl_get_line() to ignore that
       signal by calling gl_ignore_signal().

         int gl_ignore_signal(GetLine *gl, int signo);

       The signo argument is the number of the signal (eg.  SIGINT)  that  you
       want  to  have  ignored. If the specified signal isn't currently one of
       those being trapped, this function does nothing.

       The gl_trap_signal() function allows you to either add a new signal  to
       the  list that gl_get_line() traps, or modify how it responds to a sig-
       nal that it already traps.

         int gl_trap_signal(GetLine *gl, int signo, unsigned flags,
                            GlAfterSignal after, int errno_value);

       The signo argument is the number of the signal that you  wish  to  have
       trapped. The flags argument is a set of flags which determine the envi-
       ronment in which the application's signal handler is invoked, the after
       argument  tells gl_get_line() what to do after the application's signal
       handler returns, and errno_value tells gl_get_line() what to set  errno
       to if told to abort.

       The  flags  argument  is  a bitwise OR of zero or more of the following
       enumerators:

         GLS_RESTORE_SIG  -  Restore the caller's signal
                             environment while handling the
                             signal.

         GLS_RESTORE_TTY  -  Restore the caller's terminal settings
                             while handling the signal.

         GLS_RESTORE_LINE -  Move the cursor to the start of the
                             line following the input line before
                             invoking the application's signal
                             handler.

         GLS_REDRAW_LINE  -  Redraw the input line when the
                             application's signal handler returns.

         GLS_UNBLOCK_SIG  -  Normally, if the calling program has
                             a signal blocked (man sigprocmask),
                             gl_get_line() does not trap that
                             signal. This flag tells gl_get_line()
                             to trap the signal and unblock it for
                             the duration of the call to
                             gl_get_line().

         GLS_DONT_FORWARD -  If this flag is included, the signal
                             will not be forwarded to the signal
                             handler of the calling program.

       Two commonly useful flag combinations are also enumerated as follows:

         GLS_RESTORE_ENV   = GLS_RESTORE_SIG | GLS_RESTORE_TTY |
                             GLS_REDRAW_LINE

         GLS_SUSPEND_INPUT = GLS_RESTORE_ENV | GLS_RESTORE_LINE


       If your signal handler, or the default system signal handler  for  this
       signal, if you haven't overridden it, never either writes to the termi-
       nal, nor suspends or terminates  the  calling  program,  then  you  can
       safely set the flags argument to 0.

       If your signal handler always writes to the terminal, reads from it, or
       suspends or terminates the program, you should specify the flags  argu-
       ment as GL_SUSPEND_INPUT, so that:

       1. The cursor doesn't get left in the middle of the input
          line.
       2. So that the user can type in input and have it echoed.
       3. So that you don't need to end each output line with
          \r\n, instead of just \n.

       The  GL_RESTORE_ENV combination is the same as GL_SUSPEND_INPUT, except
       that it doesn't move the cursor, and if  your  signal  handler  doesn't
       read  or write anything to the terminal, the user won't see any visible
       indication that a signal was caught. This can be useful if you  have  a
       signal  handler  that  only  occasionally writes to the terminal, where
       using GL_SUSPEND_LINE would cause the input line  to  be  unnecessarily
       duplicated  when nothing had been written to the terminal.  Such a sig-
       nal handler, when it does write to the  terminal,  should  be  sure  to
       start a new line at the start of its first write, by writing a new line
       before returning. If the signal arrives while the user  is  entering  a
       line  that only occupies a signal terminal line, or if the cursor is on
       the last terminal line of a longer input line, this will have the  same
       effect  as  GL_SUSPEND_INPUT. Otherwise it will start writing on a line
       that already contains part of the displayed input line.   This  doesn't
       do any harm, but it looks a bit ugly, which is why the GL_SUSPEND_INPUT
       combination is better if you know that you are always going to be writ-
       ting to the terminal.

       The  after argument, which determines what gl_get_line() does after the
       application's signal handler returns (if it returns), can take any  one
       of the following values:

         GLS_RETURN   - Return the completed input line, just as
                        though the user had pressed the return
                        key.

         GLS_ABORT    - Cause gl_get_line() to abort. When
                        this happens, gl_get_line() returns
                        NULL, and a following call to
                        gl_return_status() will return
                        GLR_SIGNAL. Note that if the
                        application needs errno always to
                        have a meaningful value when
                        gl_get_line() returns NULL,
                        the callback function should set
                        errno appropriately.
         GLS_CONTINUE - Resume command line editing.

       The  errno_value argument is intended to be combined with the GLS_ABORT
       option, telling gl_get_line() what to set the standard  errno  variable
       to  before returning NULL to the calling program. It can also, however,
       be used with the GL_RETURN option, in case you wish to have  a  way  to
       distinguish  between  an  input  line that was entered using the return
       key, and one that was entered by the receipt of a signal.



RELIABLE SIGNAL HANDLING
       Signal handling is suprisingly hard to do reliably without race  condi-
       tions.  In gl_get_line() a lot of care has been taken to allow applica-
       tions to perform reliable signal handling  around  gl_get_line().  This
       section explains how to make use of this.

       As  an  example of the problems that can arise if the application isn't
       written correctly, imagine that one's application has a  SIGINT  signal
       handler that sets a global flag. Now suppose that the application tests
       this flag just before invoking gl_get_line(). If a SIGINT  signal  hap-
       pens  to  be received in the small window of time between the statement
       that tests the value  of  this  flag,  and  the  statement  that  calls
       gl_get_line(), then gl_get_line() will not see the signal, and will not
       be interrupted. As a result, the application won't be able  to  respond
       to  the  signal  until  the  user gets around to finishing entering the
       input line and gl_get_line() returns.  Depending  on  the  application,
       this  might  or might not be a disaster, but at the very least it would
       puzzle the user.

       The way to avoid such problems is to do the following.

       1. If needed, use the gl_trap_signal() function to
          configure gl_get_line() to abort when important
          signals are caught.

       2. Configure gl_get_line() such that if any of the
          signals that it catches are blocked when
          gl_get_line() is called, they will be unblocked
          automatically during times when gl_get_line() is
          waiting for I/O. This can be done either
          on a per signal basis, by calling the
          gl_trap_signal() function, and specifying the
          GLS_UNBLOCK attribute of the signal, or globally by
          calling the gl_catch_blocked() function.


            void gl_catch_blocked(GetLine *gl);


          This function simply adds the GLS_UNBLOCK attribute
          to all of the signals that it is currently configured to
          trap.

       3. Just before calling gl_get_line(), block delivery
          of all of the signals that gl_get_line() is
          configured to trap. This can be done using the POSIX
          sigprocmask() function in conjunction with the
          gl_list_signals() function.


             int gl_list_signals(GetLine *gl, sigset_t *set);


          This function returns the set of signals that it is
          currently configured to catch in the set argument,
          which is in the form required by sigprocmask().

       4. In the example, one would now test the global flag that
          the signal handler sets, knowing that there is now no
          danger of this flag being set again until
          gl_get_line() unblocks its signals while performing
          I/O.

       5. Eventually gl_get_line() returns, either because
          a signal was caught, an error occurred, or the user
          finished entering their input line.

       6. Now one would check the global signal flag again, and if
          it is set, respond to it, and zero the flag.

       7. Use sigprocmask() to unblock the signals that were
          blocked in step 3.

       The same technique can be used around certain POSIX signal-aware  func-
       tions,  such  as  sigsetjmp()  and sigsuspend(), and in particular, the
       former of these two functions can be  used  in  conjunction  with  sig-
       longjmp() to implement race-condition free signal handling around other
       long-running system calls. The way to do this, is  explained  next,  by
       showing how gl_get_line() manages to reliably trap signals around calls
       to functions like read() and select() without race conditions.

       The first thing that gl_get_line() does, whenever it is called,  is  to
       use  the  POSIX  sigprocmask() function to block the delivery of all of
       the signals that it is currently configured to catch. This is redundant
       if  the  application  has already blocked them, but it does no harm. It
       undoes this step just before returning.

       Whenever gl_get_line() needs to call read() or  select()  to  wait  for
       input  from  the  user,  it first calls the POSIX sigsetjmp() function,
       being sure to specify a non-zero value for its savesigs argument.   The
       reason for the latter argument will become clear shortly.

       If sigsetjmp() returns zero, gl_get_line() then does the following.


       a. It uses the POSIX sigaction() function to register
          a temporary signal handler to all of the signals that it
          is configured to catch. This signal handler does two
          things.

          1. It records the number of the signal that was received
             in a file-scope variable.

          2. It then calls the POSIX siglongjmp()
             function using the buffer that was passed to
             sigsetjmp() for its first argument, and
             a non-zero value for its second argument.

          When this signal handler is registered, the sa_mask
          member of the struct sigaction act argument of the
          call to sigaction() is configured to contain all of
          the signals that gl_get_line() is catching. This
          ensures that only one signal will be caught at once by
          our signal handler, which in turn ensures that multiple
          instances of our signal handler don't tread on each
          other's toes.

       b. Now that the signal handler has been set up,
          gl_get_line() unblocks all of the signals that it
          is configured to catch.

       c. It then calls the read() or select() system
          calls to wait for keyboard input.

       d. If this system call returns (ie. no signal is received),
          gl_get_line() blocks delivery of the signals of
          interest again.

       e. It then reinstates the signal handlers that were
          displaced by the one that was just installed.


       Alternatively,  if sigsetjmp() returns non-zero, this means that one of
       the signals being trapped was caught while the above steps were execut-
       ing. When this happens, gl_get_line() does the following.

       First,  note  that  when  a  call to siglongjmp() causes sigsetjmp() to
       return, provided that the savesigs argument  of  sigsetjmp()  was  non-
       zero, as specified above, the signal process mask is restored to how it
       was when sigsetjmp() was  called.  This  is  the  important  difference
       between  sigsetjmp()  and  the  older  problematic setjmp(), and is the
       essential ingredient that makes it possible to  avoid  signal  handling
       race  conditions.   Because  of  this we are guaranteed that all of the
       signals that we blocked before calling sigsetjmp() are blocked again as
       soon  as any signal is caught. The following statements, which are then
       executed, are thus guaranteed to be executed without any  further  sig-
       nals being caught.

       1. If so instructed by the gl_get_line() configuration
          attributes of the signal that was caught,
          gl_get_line() restores the terminal attributes to
          the state that they had when gl_get_line() was
          called. This is particularly important for signals that
          suspend or terminate the process, since otherwise the
          terminal would be left in an unusable state.

       2. It then reinstates the application's signal handlers.

       3. Then it uses the C standard-library raise()
          function to re-send the application the signal that
          was caught.

       3. Next it unblocks delivery of the signal that we just
          sent. This results in the signal that was just sent
          via raise(), being caught by the application's
          original signal handler, which can now handle it as it
          sees fit.

       4. If the signal handler returns (ie. it doesn't terminate
          the process), gl_get_line() blocks delivery of the
          above signal again.

       5. It then undoes any actions performed in the first of the
          above steps, and redisplays the line, if the signal
          configuration calls for this.

       6. gl_get_line() then either resumes trying to
          read a character, or aborts, depending on the
          configuration of the signal that was caught.

       What  the above steps do in essence is to take asynchronously delivered
       signals and handle them synchronously, one at a time, at a point in the
       code where gl_get_line() has complete control over its environment.



THE TERMINAL SIZE
       On  most  systems  the combination of the TIOCGWINSZ ioctl and the SIG-
       WINCH signal is used to maintain an accurate idea of the terminal size.
       The  terminal  size  is  newly queried every time that gl_get_line() is
       called and whenever a SIGWINCH signal is received.

       On the few systems where this mechanism  isn't  available,  at  startup
       new_GetLine()  first  looks for the LINES and COLUMNS environment vari-
       ables.  If these aren't found, or they contain unusable values, then if
       a  terminal information database like terminfo or termcap is available,
       the default size of the terminal is looked up in this database. If this
       too fails to provide the terminal size, a default size of 80 columns by
       24 lines is used.

       Even on systems that do support ioctl(TIOCGWINSZ), if the  terminal  is
       on the other end of a serial line, the terminal driver generally has no
       way of detecting when a resize occurs or of querying what  the  current
       size  is.  In  such  cases  no SIGWINCH is sent to the process, and the
       dimensions returned by ioctl(TIOCGWINSZ) aren't correct. The  only  way
       to  handle  such  instances is to provide a way for the user to enter a
       command that tells the remote system what the new size is. This command
       would  then  call the gl_set_term_size() function to tell gl_get_line()
       about the change in size.


         int gl_set_term_size(GetLine *gl, int ncolumn, int nline);


       The ncolumn and nline arguments are used to specify the new  dimensions
       of  the  terminal, and must not be less than 1. On systems that do sup-
       port ioctl(TIOCGWINSZ), this function first calls ioctl(TIOCSWINSZ)  to
       tell  the  terminal  driver  about  the change in size. In non-blocking
       server-I/O mode, if a line is currently being input, the input line  is
       then redrawn to accomodate the changed size. Finally the new values are
       recorded in gl for future use by gl_get_line().

       The gl_terminal_size() function allows you to query the current size of
       the  terminal,  and  install an alternate fallback size for cases where
       the size isn't available.  Beware  that  the  terminal  size  won't  be
       available  if  reading from a pipe or a file, so the default values can
       be important even on systems that do support ways of  finding  out  the
       terminal size.

         typedef struct {
           int nline;        /* The terminal has nline lines */
           int ncolumn;      /* The terminal has ncolumn columns */
         } GlTerminalSize;

         GlTerminalSize gl_terminal_size(GetLine *gl,
                                         int def_ncolumn,
                                         int def_nline);

       This  function  first  updates gl_get_line()'s fallback terminal dimen-
       sions, then records its findings in the return value.

       The def_ncolumn and def_nline specify the default  number  of  terminal
       columns  and  lines to use if the terminal size can't be determined via
       ioctl(TIOCGWINSZ) or environment variables.



HIDING WHAT YOU TYPE
       When entering sensitive information, such as passwords, it is best  not
       to  have  the  text that you are entering echoed on the terminal.  Fur-
       thermore, such text should not be recorded in the history  list,  since
       somebody  finding  your  terminal  unattended  could then recall it, or
       somebody snooping through your directories could see it in your history
       file. With this in mind, the gl_echo_mode() function allows you to tog-
       gle on and off the display and archival of  any  text  that  is  subse-
       quently entered in calls to gl_get_line().


         int gl_echo_mode(GetLine *gl, int enable);


       The enable argument specifies whether entered text should be visible or
       not. If it is 0, then subsequently entered lines will not be visible on
       the terminal, and will not be recorded in the history list. If it is 1,
       then subsequent input lines will be displayed as they are entered,  and
       provided  that  history  hasn't  been  turned off via a call to gl_tog-
       gle_history(), then they will also be archived  in  the  history  list.
       Finally,  if  the  enable argument is -1, then the echoing mode is left
       unchanged, which allows you to non-destructively query the current set-
       ting  via the return value. In all cases, the return value of the func-
       tion is 0 if echoing was disabled before the function was called, and 1
       if it was enabled.

       When  echoing  is  turned  off,  note that although tab completion will
       invisibly complete your prefix as far as  possible,  ambiguous  comple-
       tions will not be displayed.



SINGLE CHARACTER QUERIES
       Using  gl_get_line() to query the user for a single character reply, is
       inconvenient for the user, since they must hit the enter or return  key
       before  the  character that they typed is returned to the program. Thus
       the gl_query_char() function has been  provided  for  single  character
       queries like this.


         int gl_query_char(GetLine *gl, const char *prompt,
                           char defchar);


       This function displays the specified prompt at the start of a new line,
       and waits for the user to type a character. When the user types a char-
       acter, gl_query_char() displays it to the right of the prompt, starts a
       newline, then returns the character to the calling program. The  return
       value  of the function is the character that was typed. If the read had
       to be aborted for some reason, EOF is returned instead. In  the  latter
       case, the application can call the previously documented gl_return_sta-
       tus(), to find out what went wrong. This could, for example, have  been
       the  reception of a signal, or the optional inactivity timer going off.

       If the user simply hits enter, the value of  the  defchar  argument  is
       substituted.  This  means  that  when  the  user hits either newline or
       return, the character specified in  defchar,  is  displayed  after  the
       prompt,  as  though the user had typed it, as well as being returned to
       the calling application. If such a replacement is not important, simply
       pass '0 as the value of defchar.

       If  the  entered character is an unprintable character, it is displayed
       symbolically. For example, control-A is displayed as ^A, and characters
       beyond 127 are displayed in octal, preceded by a backslash.

       As with gl_get_line(), echoing of the entered character can be disabled
       using the gl_echo_mode() function.

       If the calling process is suspended while waiting for the user to  type
       their  response,  the  cursor is moved to the line following the prompt
       line, then when the process resumes, the  prompt  is  redisplayed,  and
       gl_query_char() resumes waiting for the user to type a character.

       Note that in non-blocking server mode, (see gl_io_mode),
       if an incomplete input line is  in  the  process  of  being  read  when
       gl_query_char()  is  called,  the  partial input line is discarded, and
       erased from the terminal, before the new prompt is displayed. The  next
       call to gl_get_line() will thus start editing a new line.



READING RAW CHARACTERS
       Whereas  the  gl_query_char()  function  visibly prompts the user for a
       character, and displays what they typed,  the  gl_read_char()  function
       reads a signal character from the user, without writing anything to the
       terminal, or perturbing any incompletely entered input line. This means
       that it can be called not only from between calls to gl_get_line(), but
       also from callback functions that the application has registered to  be
       called by gl_get_line().


         int gl_read_char(GetLine *gl);


       On  success,  the  return value of gl_read_char() is the character that
       was read. On failure, EOF is returned, and the gl_return_status() func-
       tion  can  be called to find out what went wrong. Possibilities include
       the optional inactivity timer going off, the receipt of a  signal  that
       is configured to abort gl_get_line(), or terminal I/O blocking, when in
       non-blocking server-I/O mode.

       Beware that certain keyboard keys, such as function  keys,  and  cursor
       keys,  usually generate at least 3 characters each, so a single call to
       gl_read_char() won't be enough to identify such keystrokes.



CLEARING THE TERMINAL
       The calling program can clear the terminal by  calling  gl_erase_termi-
       nal(). In non-blocking server-I/O mode, this function also arranges for
       the current input line to be redrawn from scratch when gl_get_line() is
       next called.


         int gl_erase_terminal(GetLine *gl);




DISPLAYING TEXT DYNAMICALLY
       Between calls to gl_get_line(), the gl_display_text() function provides
       a convenient way to display  paragraphs  of  text,  left-justified  and
       split  over  one or more terminal lines according to the constraints of
       the current width of the terminal. Examples of the use of this function
       may  be  found in the demo programs, where it is used to display intro-
       ductions. In those examples the advanced use of optional prefixes, suf-
       fixes  and  filled  lines  to draw a box around the text is also illus-
       trated.


         int gl_display_text(GetLine *gl, int indentation,
                             const char *prefix,
                             const char *suffix, int fill_char,
                             int def_width, int start,
                             const char *string);

       If gl isn't currently connected to a terminal, for example if the  out-
       put of a program that uses gl_get_line() is being piped to another pro-
       gram or redirected to a file, then the value of the def_width parameter
       is used as the terminal width.

       The  indentation  argument specifies the number of characters to use to
       indent each line of ouput. The fill_char argument specifies the charac-
       ter that will be used to perform this indentation.

       The  prefix argument can either be NULL, or be a string to place at the
       beginning of each new line (after  any  indentation).   Similarly,  the
       suffix  argument can either be NULL, or be a string to place at the end
       of each line. The suffix is placed flush against the right edge of  the
       terminal,  and  any space between its first character and the last word
       on that line is filled with the character specified via  the  fill_char
       argument.  Normally the fill-character is a space.

       The  start  argument  tells  gl_display_text() how many characters have
       already been written to the current terminal line, and  thus  tells  it
       the  starting  column  index  of the cursor.  Since the return value of
       gl_display_text() is the ending column index of the cursor, by  passing
       the  return value of one call to the start argument of the next call, a
       paragraph that is broken between more than one string can  be  composed
       by  calling  gl_display_text() for each successive portion of the para-
       graph. Note that literal newline characters are necessary at the end of
       each paragraph to force a new line to be started.

       On error, gl_display_text() returns -1.



CALLBACK FUNCTION FACILITIES
       Unless  otherwise  stated,  callback  functions, such as tab completion
       callbacks and event callbacks should not call  any  functions  in  this
       module.  The following functions, however, are designed specifically to
       be used by callback functions.

       Calling  the  gl_replace_prompt()  function  from  a   callback   tells
       gl_get_line()  to display a different prompt when the callback returns.
       Except in non-blocking server mode, it has no effect  if  used  between
       calls   to   gl_get_line().   In  non-blocking  server  mode  (see  the
       gl_io_mode man page, when  used  between  two  calls  to
       gl_get_line()  that  are  operating on the same input line, the current
       input line will be re-drawn with the new prompt on the  following  call
       to gl_get_line().


         void gl_replace_prompt(GetLine *gl, const char *prompt);




INTERNATIONAL CHARACTER SETS
       Since  libtecla version 1.4.0, gl_get_line() has been 8-bit clean. This
       means that all 8-bit characters that are printable in the  user's  cur-
       rent  locale  are  now  displayed verbatim and included in the returned
       input line.  Assuming that the calling  program  correctly  contains  a
       call like the following,

         setlocale(LC_CTYPE, "");

       then  the  current locale is determined by the first of the environment
       variables LC_CTYPE, LC_ALL, and LANG, that is found to contain a  valid
       locale  name.  If  none  of these variables are defined, or the program
       neglects to call setlocale, then the default C locale is used, which is
       US  7-bit  ASCII.  On  most  unix-like platforms, you can get a list of
       valid locales by typing the command:

         locale -a

       at the shell prompt. Further documentation on how the user can make use
       of  this  to  enter  international  characters  can  be  found  in  the
       tecla man page.



THREAD SAFETY
       In a multi-threaded program, you should use the libtecla_r.a version of
       the  library.  This  uses reentrant versions of system functions, where
       available. Unfortunately neither terminfo nor termcap were designed  to
       be reentrant, so you can't safely use the functions of the getline mod-
       ule in multiple threads (you can use the  separate  file-expansion  and
       word-completion  modules in multiple threads, see the corresponding man
       pages for details). However due to the use of POSIX reentrant functions
       for looking up home directories etc, it is safe to use this module from
       a single thread of a multi-threaded program, provided that  your  other
       threads don't use any termcap or terminfo functions.



FILES
       libtecla.a      -    The tecla library
       libtecla.h      -    The tecla header file.
       ~/.teclarc      -    The personal tecla customization file.



SEE ALSO
       libtecla, gl_io_mode, tecla, ef_expand_file,
       cpl_complete_word, pca_lookup_file



AUTHOR
       Martin Shepherd  (mcs@astro.caltech.edu)



                                                    gl_get_line



genometools-1.5.1/src/external/libtecla-1.6.1/html/gl_io_mode.html000066400000000000000000000614751211610345200246410ustar00rootroot00000000000000
Manual Page



gl_io_mode                            gl_io_mode




NAME
        gl_io_mode, gl_raw_io, gl_normal_io, gl_tty_signals, gl_abandon_line,
        gl_handle_signal,  gl_pending_io  -  How  to use gl_get_line() from an
       external event loop.


SYNOPSIS
       #include <libtecla.h>

       int gl_io_mode(GetLine *gl, GlIOMode mode);

       int gl_raw_io(GetLine *gl);

       int gl_normal_io(GetLine *gl);

       int gl_tty_signals(void (*term_handler)(int),
                          void (*susp_handler)(int),
                          void (*cont_handler)(int),
                          void (*size_handler)(int));

       void gl_abandon_line(GetLine *gl);

       void gl_handle_signal(int signo, GetLine *gl, int ngl);

       GlPendingIO gl_pending_io(GetLine *gl);




DESCRIPTION
       The gl_get_line() function,  which  is  documented  separately  in  the
       gl_get_line  man page, supports two different I/O modes.
       These are selected by calling the gl_io_mode() function.


         int gl_io_mode(GetLine *gl, GlIOMode mode);


       The mode argument of this function specifies the new I/O mode, and must
       be one of the following.


         GL_NORMAL_MODE   -  Select the normal blocking-I/O mode.
                             In this mode gl_get_line()
                             doesn't return until either an error
                             occurs of the user finishes entering a
                             new line. This mode is the focus of
                             the gl_get_line man page.

         GL_SERVER_MODE   -  Select non-blocking server I/O mode.
                             In this mode, since non-blocking
                             terminal I/O is used, the entry of
                             each new input line typically requires
                             many calls to gl_get_line() from
                             an external I/O-driven event loop.
                             This mode is the focus of this man
                             page.


       Newly created GetLine objects start in normal I/O mode, so to switch to
       non-blocking server mode requires an initial call to gl_io_mode().



SERVER I/O MODE
       In non-blocking server I/O mode, the application is required to have an
       event  loop  which  calls  gl_get_line()  whenever  the  terminal  file
       descriptor can do the type I/O that gl_get_line() is  waiting  for.  To
       determine  which type of I/O gl_get_line() is waiting for, the applica-
       tion calls the gl_pending_io() function.


         GlPendingIO gl_pending_io(GetLine *gl);


       The return value of this function is one of the following  two  enumer-
       ated values.


         GLP_READ    -  gl_get_line() is waiting to write a
                        character to the terminal.

         GLP_WRITE   -  gl_get_line() is waiting to read a
                        character from the keyboad.


       If  the application is using either the select() or poll() system calls
       to watch for I/O on a group of file descriptors, then  it  should  call
       the gl_pending_io() function before each call to these functions to see
       which direction of I/O it should tell them to watch for, and  configure
       their  arguments  accordingly. In the case of the select() system call,
       this means using the FD_SET() macro to add the terminal file descriptor
       either to the set of file descriptors to be watched for readability, or
       the set to be watched for writability.

       As in normal I/O mode, the return value of gl_get_line()  is  either  a
       pointer  to a completed input line, or NULL. However, whereas in normal
       I/O mode a NULL return value always means that an  error  occurred,  in
       non-blocking  server  mode,  NULL  is  also returned when gl_get_line()
       can't read or write to the terminal  without  blocking.  Thus  in  non-
       blocking  server  mode,  in order to determine when a NULL return value
       signifies that an error occurred or not, it is necessary  to  call  the
       gl_return_status()  function.  If  this function returns the enumerated
       value, GLR_BLOCKED, as documented in the gl_get_line man
       page,  this  means  that gl_get_line() is waiting for I/O, and no error
       has occurred.

       When gl_get_line() returns NULL and gl_return_status()  indicates  that
       this  is  due  to  blocked  terminal  I/O,  the application should call
       gl_get_line() again when the type of I/O  reported  by  gl_pending_io()
       becomes  possible.  The  prompt,  start_line and start_pos arguments of
       gl_get_line() will be ignored on these calls.  If you  need  to  change
       the  prompt  of  the  line that is currently being edited, then you can
       call   the   gl_replace_prompt()   function    (documented    in    the
       gl_get_line man page) between calls to gl_get_line().



GIVING UP THE TERMINAL
       A  complication  that  is unique to non-blocking server mode is that it
       requires that the terminal  be  left  in  raw  mode  between  calls  to
       gl_get_line().  If  this  weren't  the  case,  the  external event loop
       wouldn't be able to detect individual key-presses, and the  basic  line
       editing implemented by the terminal driver would clash with the editing
       provided by gl_get_line(). What this means is that any  time  that  the
       terminal  needs  to  be used for other things than entering a new input
       line with gl_get_line(), it needs to be restored to a usable state.  In
       particular, whenever the process is suspended or terminated, the termi-
       nal must be returned to a  normal  state.  If  this  isn't  done,  then
       depending  on  the characteristics of the shell that was used to invoke
       the program, the user may end up with a hung terminal. To this end, the
       gl_normal_io()  function is provided for switching the terminal back to
       the state that it was in when raw mode was last established.


         int gl_normal_io(GetLine *gl);


       What this function does is first flush any pending output to the termi-
       nal,  then move the cursor to the start of the terminal line which fol-
       lows the end of the incompletely entered input line. At this  point  it
       is  safe  to  suspend  or terminate the process, and it is safe for the
       application to read and write to the terminal. To resume entry  of  the
       input line, the application should call the gl_raw_io() function.


         int gl_raw_io(GetLine *gl);


       This  function  starts  a  new line, redisplays the partially completed
       input line (if any), restores the cursor position within this  line  to
       where it was when gl_normal_io() was called, then switches back to raw,
       non-blocking terminal mode ready to continue entry of  the  input  line
       when gl_get_line() is next called.

       Note that in non-blocking server mode, if gl_get_line() is called after
       a call to gl_normal_io(), without an intervening call  to  gl_raw_io(),
       gl_get_line()  will  call  gl_raw_mode()  itself, and the terminal will
       remain in this mode when gl_get_line() returns.



SIGNAL HANDLING
       In the previous section it was pointed out that in non-blocking  server
       mode,  the  terminal must be restored to a sane state whenever a signal
       is received that either suspends or terminates the process.  In  normal
       I/O  mode,  this  is done for you by gl_get_line(), but in non-blocking
       server mode, since the terminal is left in raw mode  between  calls  to
       gl_get_line(),  this signal handling has to be done by the application.
       Since there are many signals that can suspend or terminate  a  process,
       as  well  as other signals that are important to gl_get_line(), such as
       the SIGWINCH signal, which tells it when the terminal size has changed,
       the  gl_tty_signals()  function  is provided for installing signal han-
       dlers for all pertinent signals.


         int gl_tty_signals(void (*term_handler)(int),
                            void (*susp_handler)(int),
                            void (*cont_handler)(int),
                            void (*size_handler)(int));


       What this does is use  gl_get_line()'s  internal  list  of  signals  to
       assign specified signal handlers to groups of signals. The arguments of
       this function are as follows.


         term_handler  -  This is the signal handler that is to be
                          used to trap signals that by default
                          terminate any process that receives
                          them (eg. SIGINT or SIGTERM).

         susp_handler  -  This is the signal handler that is to be
                          used to trap signals that by default
                          suspend any process that receives them,
                          (eg. SIGTSTP or SIGTTOU).

         cont_handler  -  This is the signal handler that is to be
                          used to trap signals that are usually
                          sent when a process resumes after being
                          suspended (usually SIGCONT). Beware that there is
                          nothing to stop a user from sending one of these
                          signals at other times.

         size_handler  -  This signal handler is used to trap
                          signals that are sent to processes when
                          their controlling terminals are resized
                          by the user (eg. SIGWINCH).


       These arguments can all be the same, if so desired, and you can specify
       SIG_IGN  (ignore  this  signal)  or  SIG_DFL  (use  the system-provided
       default signal handler) instead of a function where pertinent. In  par-
       ticular, it is rarely useful to trap SIGCONT, so the cont_handler argu-
       ment will usually be SIG_DFL or SIG_IGN.

       The gl_tty_signals() function uses the POSIX  sigaction()  function  to
       install  these  signal  handlers,  and it is careful to use the sa_mask
       member of each sigaction structure to ensure that  only  one  of  these
       signals  is  ever  delivered  at  a time. This guards against different
       instances of these signal handlers from simultaneously trying to  write
       to common global data, such as a shared sigsetjmp() buffer or a signal-
       received flag.

       The signal handlers that are installed by this  function,  should  call
       the gl_handle_signal().


         void gl_handle_signal(int signo, GetLine *gl, int ngl);


       The  signo  argument tells this function which signal it is being asked
       to respond to, and the gl argument should be a  pointer  to  the  first
       element  of  an  array of ngl GetLine objects. If your application only
       has one of these objects, just pass its pointer as the gl argument  and
       specify ngl as 1.

       Depending  on the signal that is being handled, this function does dif-
       ferent things.


   Terminal resize signals (SIGWINCH)
       If the signal indicates that the terminal was resized, then it arranges
       for the next call to gl_get_line() to ask the terminal for its new size
       and redraw the input line accordingly. In order that  gl_get_line()  be
       called as soon as possible to do this, gl_handle_signal() also arranges
       that the next call to gl_pending_io() will return  GLP_WRITE.  Thus  if
       the  application waits for I/O in select() or poll(), then the applica-
       tion needs to ensure that these functions will be reliably aborted when
       a  signal is caught and handled by the application. More on this below.



Process termination signals.
       If the signal that was caught is one of those that  by  default  termi-
       nates  any  process  that receives it, then gl_handle_signal() does the
       following steps.

       1. First it blocks the delivery of all signals that can be
          blocked (ie. SIGKILL and SIGSTOP can't be blocked)

       2. Next it calls gl_normal_io() for each of the ngl
          GetLine objects. Note that this does nothing to any of the
          GetLine objects that aren't currently in raw mode.

       3. Next it sets the signal handler of the signal to its default,
          process-termination disposition.

       4. Next it re-sends the process the signal that was caught.

       5. Finally it unblocks delivery of this signal, which
          results in the process being terminated.



Process suspension signals.
       If the default disposition of the signal is to suspend the process, the
       same steps are executed as for process termination signals, except that
       when the process is later resumed,  gl_handle_signal()  continues,  and
       does the following steps.

       6. It re-blocks delivery of the signal.

       7. It reinstates the signal handler of the signal to the one
          that was displaced when its default disposition was substituted.

       8. For any of the GetLine objects that were in raw mode when
          gl_handle_signal() was called, gl_handle_signal() then
          calls gl_raw_io(), to resume entry of the input lines on
          those terminals.

       9. Finally, it restores the signal process mask to how it
          was when gl_handle_signal() was called.

       Note  that  the  process  is suspended or terminated using the original
       signal that was caught, rather than using the uncatchable  SIGSTOP  and
       SIGKILL signals. This is important, because when a process is suspended
       or terminated, the parent of the process may wish  to  use  the  status
       value returned by the wait() system call to figure out which signal was
       responsible. In particular, most shells use this information to print a
       corresponding  message to the terminal. Users would be rightly confused
       if when their process received a SIGPIPE signal, the program  responded
       by  sending itself a SIGKILL signal, and the shell then printed out the
       provocative statement, "Killed!".



INTERRUPTING THE EVENT LOOP
       If a signal is caught and handled when the application's event loop  is
       waiting  in  select()  or  poll(), these functions will be aborted with
       errno set to EINTR. When  this  happens  the  event  loop  should  call
       gl_pending_io(),  before  calling  select()  or poll() again. It should
       then arrange for select() or poll() to wait for the type  of  I/O  that
       this reports. This is necessary, because any signal handler which calls
       gl_handle_signal(),  will  frequently  change  the  type  of  I/O  that
       gl_get_line() is waiting for.

       Unfortunately, if a signal arrives between the statements which config-
       ure the arguments of select() or poll() and the calls  to  these  func-
       tions,  then the signal will not be seen by these functions, which will
       then not be aborted. If these functions are waiting for keyboard  input
       from  the  user  when  the  signal  is received, and the signal handler
       arranges to redraw the input line to accomodate a  terminal  resize  or
       the resumption of the process, then this redisplay will be end up being
       delayed until the user hits the next key. Apart from puzzling the user,
       this  clearly  isn't  a serious problem. However there is a way, albeit
       complicated, to completely avoid this  race  condition.  The  following
       steps illustrate this.

       1. Block all of the signals that gl_get_line() catches,
          by passing the signal set returned by gl_list_signals() to
          sigprocmask().

       2. Call gl_pending_io() and set up the arguments of
          select() or poll() accordingly.

       3. Call sigsetjmp() with a non-zero savesigs argument.

       4. Initially this sigsetjmp() statement will return zero,
          indicating that control isn't resuming there after a matching
          call to siglongjmp().

       5. Replace all of the handlers of the signals that gl_get_line()
          is configured to catch, with a signal handler that first records
          the number of the signal that was caught, in a file-scope variable,
          then calls siglongjmp() with a non-zero value argument, to
          return execution to the above sigsetjmp()
          statement.  Registering these signal handlers can conveniently be
          done using the gl_tty_signals() function.

       6. Set the file-scope variable that the above signal handler uses to
          record any signal that is caught to -1, so that we can check
          whether a signal was caught by seeing if it contains a valid signal
          number.

       7. Now unblock the signals that were blocked in step 1. Any signal
          that was received by the process in between step 1 and now will
          now be delivered, and trigger our signal handler, as will any
          signal that is received until we block these signals again.

       8. Now call select() or poll().

       9. When select() returns, again block the signals that were
          unblocked in step 7.

       If a signal is arrived any time during the above steps, our signal han-
       dler will be triggered and cause control to return to  the  sigsetjmp()
       statement,  where this time, sigsetjmp() will return non-zero, indicat-
       ing that a signal was caught. When this  happens  we  simply  skip  the
       above  block of statements, and continue with the following statements,
       which are executed regardless of whether or not  a  signal  is  caught.
       Note  that when sigsetjmp() returns, regardless of why it returned, the
       process signal mask is returned to how  it  was  when  sigsetjmp()  was
       called.  Thus  the following statements are always executed with all of
       our signals blocked.

       9. Reinstate the signal handlers that were displaced in step 5.

       10. Check wether a signal was caught, by checking the file-scope
           variable that the signal handler records signal numbers in.

       11. If a signal was caught, send this signal to the application
           again, and unblock just this signal, so that it invokes the
           signal handler which we just reinstated in step 10.

       12. Unblock all of the signals that were blocked in step 7.

       Since this is complicated, note that demo3.c includes a working example
       of  how to do this. The method used there however, is more general than
       the above. What it provides is a wrapper function around select() which
       encompasses   steps   3  to  11.  In  this  wrapper,  rather  than  use
       gl_list_signals()  to  figure  out  the  signals  to  block,  and   and
       gl_tty_signals() to assign and revert signal handlers, one of its argu-
       ments is a sigset_t which specifies which signals to block  and  assign
       signal  handlers to. This function thus doesn't depend on gl_get_line()
       and can thus be used in other situations where race-condition-free sig-
       nal handling is required.



SIGNALS CAUGHT BY GL_GET_LINE
       Since  the  application  is  expected to handle signals in non-blocking
       server mode, gl_get_line() doesn't attempt to duplicate this when it is
       being  called.  If one of the signals that it is configured to catch is
       sent  to  the  application  while  gl_get_line()   is   being   called,
       gl_get_line() reinstates the caller's signal handlers, then just before
       returning, re-sends the signal to the process to let the  application's
       signal  handler handle it. If the process isn't terminated by this sig-
       nal, gl_get_line() returns NULL, and a following call to gl_return_sta-
       tus() returns the enumerated value GLR_SIGNAL.



ABORTING LINE INPUT
       Often,  rather  than  letting  it  terminate  the process, applications
       respond to the SIGINT user-interrupt signal  by  aborting  the  current
       input  line.  The  way to do this in non-blocking server-I/O mode is to
       not call gl_handle_signal() when this signal is caught, but instead  to
       call the gl_abandon_line().


         void gl_abandon_line(GetLine *gl);


       This function arranges that when gl_get_line() is next called, it first
       flushes any pending output to the terminal, then discardes the  current
       input  line,  outputs a new prompt on the next line, and finally starts
       accepting input of a new input line from the user.



SIGNAL SAFE FUNCTIONS
       Provided that certain rules are followed, the following  functions  can
       have  been  written  to  be safely callable from signal handlers. Other
       functions in this library should not be called from signal handlers.


         gl_normal_io()
         gl_raw_io()
         gl_handle_signal()
         gl_abandon_line()


       In order for this to be true, all signal handlers that call these func-
       tions  must  be  registered in such a way that only one instance of any
       one of them can be running at one time. The way to do this  is  to  use
       the  POSIX  sigaction()  function  to register all signal handlers, and
       when doing this, use the sa_mask member of the corresponding  sigaction
       structure,  to  indicate  that all of the signals who's handlers invoke
       the above functions, should be blocked when the current signal is being
       handled.  This prevents two signal handlers from operating on a GetLine
       object at the same time.

       To prevent signal  handlers  from  accessing  a  GetLine  object  while
       gl_get_line()  or  any of its associated public functions are operating
       on it, all public functions associated  with  gl_get_line(),  including
       gl_get_line()  itself,  temporarily  block the delivery of signals when
       they are accessing GetLine objects. Beware that the only  signals  that
       they  block  are the signals that gl_get_line() is currently configured
       to catch, so be sure that if you call any of the above  functions  from
       signal  handlers,  that the signals that these handlers are assigned to
       are configured to be caught by gl_get_line() (see gl_trap_signal()).



USING TIMEOUTS TO POLL
       If instead of using select() or poll() to wait for I/O,  your  applica-
       tion  just needs to get out of gl_get_line() periodically to briefly do
       something else before returning to accept input from the user, this can
       be  done  in  non-blocking server mode by using the gl_inactivity_time-
       out() function (see  gl_get_line),  to  specify  that  a
       callback  function that returns GLTO_CONTINUE should be called whenever
       gl_get_line() has been waiting for I/O for more than a specified amount
       of time.

       When  this callback is triggered, gl_get_line() will return NULL, and a
       following call to gl_return_status() will return GLR_BLOCKED.

       Beware that gl_get_line() won't return until the user  hasn't  typed  a
       key  for  the  specified  interval, so if the interval is long, and the
       user keeps typing, gl_get_line() may not return for a while.  In  other
       words  there is no guarantee that it will return in the time specified.



THE SERVER DEMO PROGRAM
       The demo3 program that is distributed  with  the  library,  provides  a
       working  example  of  how to use non-blocking server I/O mode in a real
       program. As far  as  the  user  is  concerned,  this  program  operates
       identically to the main demo program (called demo), except that whereas
       the main demo program uses the normal blocking I/O  mode,  demo3  using
       non-blocking  I/O  and  an  external event loop. The source code can be
       found in demo3.c, and the comments therein explain the various steps.



FILES
       libtecla.a      -    The tecla library
       libtecla.h      -    The tecla header file.



SEE ALSO
       libtecla, gl_get_line, tecla, ef_expand_file,
       cpl_complete_word, pca_lookup_file



AUTHOR
       Martin Shepherd  (mcs@astro.caltech.edu)



                                                     gl_io_mode



genometools-1.5.1/src/external/libtecla-1.6.1/html/index.html000066400000000000000000000113011211610345200236320ustar00rootroot00000000000000The tecla command-line editing library.


The Tecla command-line editing library.


The tecla library provides UNIX and LINUX programs with interactive
command line editing facilities, similar to those of the UNIX tcsh
shell. In addition to simple command-line editing, it supports recall
of previously entered command lines, TAB completion of file names or
other tokens, and in-line wild-card expansion of filenames.  The
internal functions which perform file-name completion and wild-card
expansion are also available externally for optional use by programs.


In addition, the library includes a path-searching module.  This
allows an application to provide completion and lookup of files
located in UNIX style paths. Although not built into the line editor
by default, it can easily be called from custom tab-completion
callback functions. This was originally conceived for completing the
names of executables and providing a way to look up their locations in
the user's PATH environment variable, but it can easily be asked to
look up and complete other types of files in any list of directories.



Note that special care has been taken to allow the use of this library
in threaded programs. The option to enable this is discussed in the
Makefile, and specific discussions of thread safety are presented in
the included man pages.


The current version is version 1.6.1. This may be obtained from:


  http://www.astro.caltech.edu/~mcs/tecla/libtecla-1.6.1.tar.gz



For the sake of automated scripts, the following URL always points to
the latest version. Note that the version number can be found in the
README file.



  http://www.astro.caltech.edu/~mcs/tecla/libtecla.tar.gz



The library is distributed under a permissive non-copyleft
free software license (the X11 license with
the name of the copyright holder changed). This is compatible with,
but not as restrictive as the GNU GPL.


Release notes


The list of major changes that accompany each new release can be found
here.


Modifications


The gory details of changes in the latest and previous versions of the
library can be found here.


Library documentation


The following are html versions of the libtecla man pages:


    

  •   tecla            -   Documentation for users of programs which use gl_get_line().

  •   libtecla           -  A programmers introduction to the tecla library.

  •   gl_get_line        -  The interactive line-input function.

  •   gl_io_mode        -  Using gl_get_line() in a non-blocking fashion.

  •   cpl_complete_word  -  The word (eg. filename) completion function.

  •   ef_expand_file     -  The filename expansion function.

  •   pca_lookup_file     -  A directory-list based filename lookup and completion module.

  •   enhance     -  A  program that adds command-line editing to third party programs.




Portability


In principle, the standard version of the library should compile
without any problems on any UNIX or UNIX like system. So far it has
been reported to work on the following systems:


  Sun Solaris 2.5,2.6,7,8,9 with any of gcc, Sun C, or g++.
  Mandrake Linux 7.1 etc.., gcc
  Red Hat Linux 7 etc.., gcc
  Fedora Core 1, gcc
  Suse Linux 6.4, gcc
  IBM AIX 4.3.3, gcc
  HP-UX 10.20, HP-UX 11, gcc, c89
  FreeBSD, gcc
  Alpha OSF1, cc, gcc
  Mac OS X
  Cygwin (running under Windows)
  QNX
  NetBSD 1.6, 386, gcc
  SGI IRIX 6.5



There haven't been many reports concerning the POSIX reentrant
version, so the absence of any of the above from the following list of
systems on which the reentrant version is known to work, shouldn't be
taken as an indication that the reentrant version doesn't work.


  Sun Solaris 2.5,2.6,7,8,9 with any of gcc, Sun C, or g++.
  Mandrake Linux, gcc
  RedHat Linux, gcc
  Fedora Core, gcc
  SuSE Linux, gcc
  HP-UX 11, gcc
  IBM AIX 4.3.3, gcc
  Alpha OSF1, cc
  SGI IRIX 6.5



The only system that is known to have issues with the reentrant
version of the library is SCO UnixWare 7.1.1. The problem is in the
system provided signal.h, which breaks when POSIX_C_SOURCE is
defined. It has been reported that this can be "fixed" by editing
signal.h.



If you compile the library on a system that isn't mentioned above,
please send E-mail to mcs@astro.caltech.edu.


Martin Shepherd (31-Oct-2004)

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Manual Page



libtecla                                libtecla




NAME
       libtecla - An interactive command-line input library.


SYNOPSIS
       @CC@ ... -ltecla -lcurses



DESCRIPTION
       The tecla library provides programs with interactive command line edit-
       ing facilities, similar to those of the unix tcsh shell. In addition to
       simple  command-line  editing, it supports recall of previously entered
       command lines, TAB completion of file names or other  tokens,  and  in-
       line  wild-card  expansion  of  filenames. The internal functions which
       perform file-name completion and wild-card expansion are also available
       externally for optional use by the calling program.

       The  various  parts  of the library are documented in the following man
       pages:

         tecla              -  Use level documentation of the
                               command-line editing facilities
                               provided by gl_get_line().
         gl_get_line        -  The interactive line-input module.
         gl_io_mode         -  How to use gl_get_line() in an
                               incremental, non-blocking fashion.
         cpl_complete_word  -  The word completion module.
         ef_expand_file     -  The filename expansion module.
         pca_lookup_file    -  A directory-list based filename
                               lookup and completion module.

       In addition there is one  optional  application  distributed  with  the
       library:

         enhance            -  Add command-line editing to third
                                  party applications.



THREAD SAFETY
       If  the  library  is compiled with -D_POSIX_C_SOURCE=199506L, reentrant
       versions of as many functions as possible are used. This includes using
       getpwuid_r() and getpwnam_r() instead of getpwuid() and getpwnam() when
       looking up the home directories of specific users in the password  file
       (for  ~user/ expansion), and readdir_r() instead of readdir() for read-
       ing directory entries when doing  filename  completion.  The  reentrant
       version of the library is usually called libtecla_r.a instead of libte-
       cla.a, so if only the latter is available, it probably isn't  the  cor-
       rect version to link with threaded programs.

       Reentrant  functions  for  iterating  through  the password file aren't
       available, so when the library is compiled to be reentrant, TAB comple-
       tion  of  incomplete  usernames  in ~username/ expressions is disabled.
       This doesn't disable expansion of complete ~username expressions, which
       can  be  done  reentrantly, or expansion of the parts of filenames that
       follow them, so this doesn't remove much functionality.

       The terminfo functions setupterm(), tigetstr(), tigetnum() and  tputs()
       also aren't reentrant, but very few programs will want to interact with
       multiple terminals, so this shouldn't prevent this library  from  being
       used in threaded programs.



LIBRARY VERSION NUMBER
       The  version  number  of the library can be queried using the following
       function.

        void libtecla_version(int *major, int *minor, int *micro);


       On return, this function records the three components of  the  libtecla
       version  number  in  *major,  *minor, *micro. The formal meaning of the
       three components is as follows.


        major - Incrementing this number implies that a change has
                been made to the library's public interface, which
                makes it binary incompatible  with programs that
                were linked with previous shared versions of the
                tecla library.

        minor - This number is incremented by one whenever
                additional functionality, such as new functions or
                modules, are added to the library.

        micro - This is incremented whenever modifications to the
                library are made which make no changes to the
                public interface, but which fix bugs and/or improve
                the behind-the-scenes implementation.




TRIVIA
       In Spanish, a "tecla" is the key of a keyboard. Since this library cen-
       ters  on  keyboard  input,  and  given that I wrote much of the library
       while working in Chile, this seemed like a suitable name.



FILES
       libtecla.a    -   The tecla library.
       libtecla.h    -   The tecla header file.
       ~/.teclarc    -   The tecla personal customization file.



SEE ALSO
       gl_get_line, tecla, gl_io_mode, ef_expand_file,
       cpl_complete_word, pca_lookup_file, enhance



AUTHOR
       Martin Shepherd  (mcs@astro.caltech.edu)



ACKNOWLEDGMENTS
       Markus Gyger  - Lots of assistance, including help with
                       shared libraries, configuration information,
                       particularly for Solaris; modifications to
                       support C++ compilers, improvements for ksh
                       users, faster cursor motion, output
                       buffering, and changes to make gl_get_line()
                       8-bit clean.
       Mike MacFaden - Suggestions, feedback and testing that led
                       to many of the major new functions that were
                       added in version 1.4.0.
       Tim Eliseo    - Many vi-mode bindings and fixes.



                                                       libtecla



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Manual Page



pca_lookup_file                  pca_lookup_file




NAME
       pca_lookup_file,    del_PathCache,    del_PcaPathConf,   new_PathCache,
       new_PcaPathConf, pca_last_error,  pca_path_completions,  pca_scan_path,
       pca_set_check_fn,  ppc_file_start,  ppc_literal_escapes - lookup a file
       in a list of directories


SYNOPSIS
       #include <libtecla.h>

       PathCache *new_PathCache(void);

       PathCache *del_PathCache(PathCache *pc);

       int pca_scan_path(PathCache *pc, const char *path);

       void pca_set_check_fn(PathCache *pc, CplCheckFn *check_fn,
                             void *data);

       char *pca_lookup_file(PathCache *pc, const char *name,
                             int name_len, int literal);

       const char *pca_last_error(PathCache *pc);

       CPL_MATCH_FN(pca_path_completions);




DESCRIPTION
       The PathCache object is part of  the  tecla  library  (see  the  libte-
       cla(@LIBR_MANEXT@) man page).

       PathCache objects allow an application to search for files in any colon
       separated list of directories, such as the unix execution PATH environ-
       ment  variable. Files in absolute directories are cached in a PathCache
       object, whereas relative directories are scanned  as  needed.  Using  a
       PathCache  object,  you can look up the full pathname of a simple file-
       name, or you can obtain a list of the possible completions of  a  given
       filename  prefix.  By  default all files in the list of directories are
       targets for lookup and completion, but a versatile  mechanism  is  pro-
       vided  for only selecting specific types of files. The obvious applica-
       tion of this facility is to provide Tab-completion and lookup  of  exe-
       cutable  commands  in  the  unix  PATH,  so  an optional callback which
       rejects all but executable files, is provided.



AN EXAMPLE
       Under UNIX, the following example program looks  up  and  displays  the
       full pathnames of each of the command names on the command line.

         #include <stdio.h>
         #include <stdlib.h>
         #include <libtecla.h>

         int main(int argc, char *argv[])
         {
           int i;
         /*
          * Create a cache for executable files.
          */
           PathCache *pc = new_PathCache();
           if(!pc)
             exit(1);
         /*
          * Scan the user's PATH for executables.
          */
           if(pca_scan_path(pc, getenv("PATH"))) {
             fprintf(stderr, "%s\n", pca_last_error(pc));
             exit(1);
           }
         /*
          * Arrange to only report executable files.
          */
          pca_set_check_fn(pc, cpl_check_exe, NULL);
         /*
          * Lookup and display the full pathname of each of the
          * commands listed on the command line.
          */
           for(i=1; i<argc; i++) {
             char *cmd = pca_lookup_file(pc, argv[i], -1, 0);
             printf("The full pathname of '%s' is %s\n", argv[i],
                    cmd ? cmd : "unknown");
           }
           pc = del_PathCache(pc);  /* Clean up */
           return 0;
         }

       The following is an example of what this does on my laptop under linux:

         $ ./example less more blob
         The full pathname of 'less' is /usr/bin/less
         The full pathname of 'more' is /bin/more
         The full pathname of 'blob' is unknown
         $



FUNCTION DESCRIPTIONS
       In order to use the facilities of this module, you must first  allocate
       a PathCache object by calling the new_PathCache() constructor function.

         PathCache *new_PathCache(void)

       This function creates the resources needed to cache and lookup files in
       a list of directories. It returns NULL on error.



POPULATING THE CACHE
       Once you have created a cache, it needs to be populated with files.  To
       do this, call the pca_scan_path() function.

         int pca_scan_path(PathCache *pc, const char *path);

       Whenever this function is called, it discards the current  contents  of
       the  cache,  then  scans  the list of directories specified in its path
       argument for files. The path argument must be  a  string  containing  a
       colon-separated       list       of      directories,      such      as
       "/usr/bin:/home/mcs/bin:.". This can include directories  specified  by
       absolute pathnames such as "/usr/bin", as well as sub-directories spec-
       ified by relative pathnames such as "." or "bin". Files in the absolute
       directories  are  immediately cached in the specified PathCache object,
       whereas sub-directories, whose identities obviously change whenever the
       current  working  directory is changed, are marked to be scanned on the
       fly whenever a file is looked up.

       On success this function return  0.  On  error  it  returns  1,  and  a
       description of the error can be obtained by calling pca_last_error(pc).



LOOKING UP FILES
       Once the cache has been populated with files, you can look up the  full
       pathname   of   a   file,   simply   by   specifying  its  filename  to
       pca_lookup_file().

         char *pca_lookup_file(PathCache *pc, const char *name,
                               int name_len, int literal);

       To make it possible to pass this function a filename which is  actually
       part  of  a longer string, the name_len argument can be used to specify
       the length of the filename at the start of the name[] argument. If  you
       pass  -1  for  this length, the length of the string will be determined
       with strlen(). If the name[]  string  might  contain  backslashes  that
       escape  the  special  meanings  of spaces and tabs within the filename,
       give the literal argument,  the  value  0.  Otherwise,  if  backslashes
       should  be  treated  as  normal characters, pass 1 for the value of the
       literal argument.



FILENAME COMPLETION
       Looking up the potential completions of a filename-prefix in the  file-
       name  cache, is achieved by passing the provided pca_path_completions()
       callback function to the cpl_complete_word() function (see the cpl_com-
       plete_word(@FUNC_MANEXT@) man page).

         CPL_MATCH_FN(pca_path_completions);

       This  callback  requires that its data argument be a pointer to a PcaP-
       athConf object. Configuration objects of this  type  are  allocated  by
       calling new_PcaPathConf().

         PcaPathConf *new_PcaPathConf(PathCache *pc);

       This  function returns an object initialized with default configuration
       parameters, which determine  how  the  cpl_path_completions()  callback
       function  behaves. The functions which allow you to individually change
       these parameters are discussed below.

       By default, the pca_path_completions() callback function searches back-
       wards  for  the  start of the filename being completed, looking for the
       first un-escaped space or the start of the input line. If you  wish  to
       specify  a  different location, call ppc_file_start() with the index at
       which the filename starts in the input line. Passing start_index=-1 re-
       enables the default behavior.

         void ppc_file_start(PcaPathConf *ppc, int start_index);

       By  default,  when  pca_path_completions()  looks  at a filename in the
       input line, each lone backslash in the input  line  is  interpreted  as
       being a special character which removes any special significance of the
       character which follows it, such as a space which should  be  taken  as
       part  of the filename rather than delimiting the start of the filename.
       These backslashes are thus ignored while looking for  completions,  and
       subsequently  added  before spaces, tabs and literal backslashes in the
       list of completions. To have unescaped backslashes  treated  as  normal
       characters,  call  ppc_literal_escapes()  with  a non-zero value in its
       literal argument.

         void ppc_literal_escapes(PcaPathConf *ppc, int literal);

       When you have finished with a PcaPathConf variable, you can pass it  to
       the del_PcaPathConf() destructor function to reclaim its memory.

         PcaPathConf *del_PcaPathConf(PcaPathConf *ppc);




BEING SELECTIVE
       If  you  are  only  interested  in certain types or files, such as, for
       example, executable files, or files whose names  end  in  a  particular
       suffix, you can arrange for the file completion and lookup functions to
       be selective in the filenames that they return.  This is done by regis-
       tering  a  callback  function  with  your PathCache object. Thereafter,
       whenever a filename is found which  either  matches  a  filename  being
       looked  up, or matches a prefix which is being completed, your callback
       function will be called with the full pathname of the  file,  plus  any
       application-specific data that you provide, and if the callback returns
       1 the filename will be reported as a match, and if  it  returns  0,  it
       will  be  ignored.   Suitable  callback  functions and their prototypes
       should be declared with the following macro. The CplCheckFn typedef  is
       also provided in case you wish to declare pointers to such functions.

         #define CPL_CHECK_FN(fn) int (fn)(void *data, \
                                           const char *pathname)
         typedef CPL_CHECK_FN(CplCheckFn);

       Registering    one    of   these   functions   involves   calling   the
       pca_set_check_fn() function. In  addition  to  the  callback  function,
       passed  via  the  check_fn argument, you can pass a pointer to anything
       via the data argument. This pointer will be passed on to your  callback
       function,  via  its  own  data argument, whenever it is called, so this
       provides a way to pass appplication specific data to your callback.

         void pca_set_check_fn(PathCache *pc, CplCheckFn *check_fn,
                               void *data);

       Note that these callbacks are passed the full pathname of each matching
       file,  so the decision about whether a file is of interest can be based
       on any property of the file, not just its filename. As an example,  the
       provided cpl_check_exe() callback function looks at the executable per-
       missions of the file and the permissions of its parent directories, and
       only  returns  1  if  the user has execute permission to the file. This
       callback function can thus be used to lookup or complete command  names
       found  in  the  directories listed in the user's PATH environment vari-
       able. The example program given earlier in this  man  page  provides  a
       demonstration of this.

       Beware  that  if somebody tries to complete an empty string, your call-
       back will get called once for every file in the cache, which could num-
       ber  in  the  thousands. If your callback does anything time consuming,
       this could result in an unacceptable delay for the user,  so  callbacks
       should be kept short.

       To  improve performance, whenever one of these callbacks is called, the
       choice that it makes is cached, and the  next  time  the  corresponding
       file  is  looked  up, instead of calling the callback again, the cached
       record of whether it was accepted or rejected is used. Thus if somebody
       tries  to  complete  an  empty  string, and hits tab a second time when
       nothing appears to happen, there will only be one long delay, since the
       second  pass  will operate entirely from the cached dispositions of the
       files. These cached dipositions are discarded whenever  pca_scan_path()
       is called, and whenever pca_set_check_fn() is called with changed call-
       back function or data arguments.



ERROR HANDLING
       If pca_scan_path() reports that an error occurred by returning  1,  you
       can   obtain   a   terse   description   of   the   error   by  calling
       pca_last_error(pc). This returns an internal string containing an error
       message.

         const char *pca_last_error(PathCache *pc);




CLEANING UP
       Once  you  have  finished using a PathCache object, you can reclaim its
       resources by passing it to  the  del_PathCache()  destructor  function.
       This  takes a pointer to one of these objects, and always returns NULL.

         PathCache *del_PathCache(PathCache *pc);



THREAD SAFETY
       In multi-threaded programs, you should use the libtecla_r.a version  of
       the library. This uses POSIX reentrant functions where available (hence
       the _r suffix), and disables features that rely on non-reentrant system
       functions.  In  the  case  of this module, the only disabled feature is
       username completion  in  ~username/  expressions,  in  cpl_path_comple-
       tions().

       Using  the  libtecla_r.a  version of the library, it is safe to use the
       facilities of this module  in  multiple  threads,  provided  that  each
       thread uses a separately allocated PathCache object. In other words, if
       two threads want to do path searching, they should each call  new_Path-
       Cache() to allocate their own caches.



FILES
       libtecla.a    -    The tecla library
       libtecla.h    -    The tecla header file.



SEE ALSO
       libtecla, gl_get_line, ef_expand_file,
       cpl_complete_word



AUTHOR
       Martin Shepherd  (mcs@astro.caltech.edu)



                                                pca_lookup_file



genometools-1.5.1/src/external/libtecla-1.6.1/html/release.html000066400000000000000000000703701211610345200241560ustar00rootroot00000000000000The tecla library release notes

This file lists major changes which accompany each new release.

Version 1.6.1:

  This is primarily a minor bug-fix release.

  One added feature is the ability to call gl_normal_io() from
  callbacks registered by gl_watch_fd() and
  gl_inactivity_timeout(). This allows these callbacks to cleanly
  suspend line editing before either reading from the terminal, or
  writing to the terminal; and then subsequently causes the input line
  to be automatically redisplayed, and line-editing to be resumed by
  gl_get_line(), as soon as the callback returns.

  Another minor change is that if the terminal type specified in the
  TERM environment variable is set to "dumb", gl_get_line() now treats
  the terminal as though it were a non-interactive stream, rather than
  treating it as a VT100-compatible terminal. This means that it
  doesn't either prompt for input, or perform any command-line
  editing, even when it really is interacting with a terminal. This is
  aimed at the rare situation where a third-pary program that connects
  to libtecla through an embedded pseudo-terminal, needs to be forced
  to behave as though it weren't talking to a terminal, in order that
  it be useable in non-interactive scripts.

  Note that in the previous release, the optional configuration
  function, gl_tty_signals(), was incorrectly swapping the suspend and
  terminal signal handlers before installing them.

  A configuration problem that prevented select() from being used
  under MacOS X, has been fixed.

  Although not documented in the man page, it was meant to be possible
  to take the input line that one call to gl_get_line() returned, and
  ask the next call to gl_get_line() to present it back to the user
  for re-editing, simply by passing the pointer returned by one call
  to gl_get_line() as the start_line argument of the next call to
  gl_get_line(). This feature unfortunately stopped working in 1.6.0,
  so this release restores it, and officially documents it in the man
  page documentation of gl_get_line().

  In the previous version of the library, calling gl_terminal_size()
  on a system without SIGWINCH support, would crash the
  application. This has been fixed.

  Libtecla now apparently compiles cleanly under IRIX.

Version 1.6.0:

  This release is primarily a bug-fix release. However there are also
  four new functions, so the minor version number has been
  incremented to reflect this.

  Two of the new functions are gl_automatic_history() and
  gl_append_history(). The former of these functions allows the
  application to tell gl_get_line() not to automatically archive
  entered lines in the history list. The second of these functions
  allows the application to explicitly append a line to the history
  list. Thus together, these two functions allow the calling
  application to take over control of what is placed in the history
  list.

  The third new function is gl_query_char(), which prompts the user
  for a single character reply, which the user can then type without
  having to hit return to enter it. Unless echoing is disabled, the
  character that is entered is then displayed after the prompt,
  and a newline is started.

  Finally, the 4th new function is gl_read_char(), which also reads
  a single character from the user, but doesn't prompt the user, write
  anything to the terminal, or disturb any partially entered input
  line. It is thus safe to call this function not only from between
  calls to gl_get_line(), but also from application callback
  functions, even if gl_normal_io() hasn't been called.

  When using the history-search-backwards or history-search-forwards
  actions, if the search prefix that the user typed, contains any of
  the *,? or [ globbing characters, it is now treated as a glob
  pattern to be matched against historical lines, instead of a simple
  prefix.

  I have added a --without-file-system option to the configure
  script. This is intended for use in embedded systems that either
  don't have filesystems, or where the file-system code in libtecla is
  seen as unwanted bloat. See the INSTALL document for details.

  Similarly, I also added a --without-file-actions option to the
  configure script. This allows the application author/installer to
  prevent users of gl_get_line() from accessing the filesystem with
  the builtin actions of gl_get_line(). It does this by removing a
  number of action functions, such as expand-filename, and list-glob,
  and by changing the default behavior of other actions, such as
  complete-word and list-or-eof, to show no completions.

  Now to the bugs that have been fixed. Version 1.5.0 had a lot of big
  internal changes, so there are a number of bugs that needed to be
  fixed.  There was a bug which caused a crash if gl_load_history()
  was called multiple times. There was another bug which caused a
  prompt not to be displayed on the next line after switching from
  reading input from a file to reading from the terminal. Also, in
  tecla configuration files, backslash escaped characters within
  key-binding key-sequences weren't being escaped. Thus ^\\ got
  interpretted as a control-\ followed by a \ character instead of as
  a control-\. There was a bug in the history recall mechanism which
  caused the search prefix to be forgotten in certain complicated
  usage scenarios. There was a minor memory leak in the
  gl_configure_getline() function. Finally, if gl_get_line() was
  aborted by a signal, or any other abnormal event, the value of errno
  which originally indicated what had happened, got zeroed by the
  code that restored the terminal to a usable state. Thus the
  application couldn't figure out what had caused the error, apart
  from by looking at gl_return_status(). All of these bugs have been
  fixed.

  In the Makefile, there were a number of places where install-sh was
  invoked without a path prefix. This has now been remedied.

  A fully functional workaround for a bug in Solaris' terminal I/O
  code has also been implemented. This bug, which only manifested
  itself in libtecla's uncommonly used non-blocking server I/O mode,
  caused characters entered while in normal I/O mode, between calls to
  gl_get_line() to be invisible to the next call to gl_get_line(),
  until the user typed at least one more key after raw terminal mode
  was restored.

  The Gnu autoconf config.guess and config.sub scripts have been
  updated to their latest versions. Apparently the old versions that I
  was previously using were too old to know about certain BSD ports.
  
Version 1.5.0:

  This release includes several major new features for those using
  gl_get_line(), shared library support in Darwin, better cross
  compilation support, and various minor bug fixes.

  The biggest new feature is the option of a non-blocking I/O mode, in
  which gl_get_line() can safely be called from an application's
  external event-loop to incrementally read input lines from the user.
  This feature is documented in the gl_io_mode(3) man page.

  In addition, there is now support for the definition of additional
  word-completion action functions, which can then be bound to
  different keys. See the documentation of the gl_completion_action()
  function in the gl_get_line(3) man page.

  Externally defined action functions can also be defined, although
  presently they don't have write access to the input line, so they
  are restricted to operations that display information text to the
  terminal, or modify the environment of the calling application in
  some way. See the documentation of the gl_register_action() function
  in the gl_get_line(3) man page.

  Some of the non-blocking I/O support functions can also be used for
  improved signal handling in the normal blocking mode. In particular,
  the gl_list_signals() and gl_catch_blocked() functions make it
  easier to write reliable signal handling around gl_get_line(). The
  new "RELIABLE SIGNAL HANDLING" section of the gl_get_line(3) man
  page is intended as an introduction to this subject.

  Programs can now clear the terminal between calls to gl_get_line(),
  by calling the new gl_erase_terminal() function.

  The gl_display_text() function, now used in the demos to display
  introductory banners, is provided for formatting text according to
  the width of the terminal.

  It is now possible to install inactivity timeout callbacks in
  gl_get_line(), using the new gl_inactivity_timeout() function.

  The new gl_set_term_size() function allows the application to
  explicitly set the terminal size, for cases, such as when one is
  using a terminal at the end of a serial lineq, where the terminal
  driver doesn't send the process a SIGWINCH when the terminal size
  changes.

  The new gl_bind_keyseq() function provides a convenient
  alternative to gl_configure_getline(), for binding or unbinding
  one key-sequence at a time.

  gl_get_line()s signal handling, file-descriptor event-handling,
  inactivity-timeout handling and server-mode non-blocking I/O
  features now not only work when input is coming from a terminal, but
  now also work when input is coming from non-interactive streams,
  such as files and pipes.

  The history implementation has been re-written to make it more
  efficient and easier to modify. The biggest user-level change is
  that when recalling history lines using a search prefix, the same
  line is no longer returned more than once in a row.  Previously this
  duplicate elimination only worked when one was recalling a line
  without specifying a search prefix, and this was naively performed
  by preventing neighboring duplicates from existing in the history
  list, rather than by skipping duplicates at search time.

  In previous versions of the library, when gl_get_line() and its
  associated public functions detected invalid arguments, or couldn't
  allocate memory, etc, error messages were written to stderr. This
  isn't appropriate for library functions, so instead of writing such
  messages to stderr, these messages are now recorded in buffers
  within the affected GetLine object. The latest error message can
  then subsequently be queried by calling gl_error_message(). The use
  of errno has also been expanded, and a new function called
  gl_return_status() has been provided to expand on the cause of the
  last return from gl_get_line().

  User level usage and configuration information has now been split
  out of the gl_get_line(3) man page into a separate tecla(7) man
  page. The enhance(3) man page has also been renamed to enhance(1).

  When expanding "~/", gl_get_line() now checks for, and returns the
  value of the HOME environment variable, if it exists, in preference
  to looking up the directory of the current user in the password
  file.

  When the terminal was resized to a narrower width, previous versions
  of gl_get_line() would redraw the line higher up the terminal. This
  bug has been fixed. A bug in history recall has also been fixed, in
  which an error message was being generated if one attempted to
  recall a line while the cursor was at the end of the longest
  possible input line. A more serious bug, in which callbacks
  registered by gl_watch_fd() weren't being called for write-events,
  has also been fixed. Finally, a few minor fixes have been made to
  improve support under QNX and Mac OS X.

  Beware that in this release, much of the underlying code has
  undergone some radical re-work, so although backwards compatibility
  of all documented features has been preserved, there may be some
  lingering bugs that could break existing programs.  So, if you plan
  to use this version in production code, please test it as far as
  possible within your application before releasing it to your
  clients, and as always, please report any unexpected behavior.

Version 1.4.1:

  This is a maintenance release. It includes minor changes to support
  Mac OS X (Darwin), the QNX real-time operating system, and Cygwin
  under Windows. It also fixes an oversight that was preventing the
  tab key from inserting tab characters when users unbound the
  complete-word action from it.

Version 1.4.0:

  The contents of the history list can now be saved and restored with
  the new gl_save_history() and gl_load_history() functions.

  Event handlers can now be registered to watch for and respond to I/O
  on arbitrary file descriptors while gl_get_line() is waiting for
  terminal input from the user. See the gl_get_line(3) man page
  for details on gl_watch_fd().

  As an optional alternative to getting configuration information only
  from ~/.teclarc, the new gl_configure_getline() function allows
  configuration commands to be taken from any of, a string, a
  specified application-specific file, and/or a specified
  user-specific file. See the gl_get_line(3) man page for details.

  The version number of the library can now be queried using the
  libtecla_version() function. See the libtecla(3) man page.

  The new gl_group_history() function allows applications to group
  different types of input line in the history buffer, and arrange for
  only members of the appropriate group to be recalled on a given call
  to gl_get_line(). See the gl_get_line(3) man page.

  The new gl_show_history() function displays the current history list
  to a given stdio output stream. See the gl_get_line(3) man page.

  new_GetLine() now allows you to specify a history buffer size of
  zero, thus requesting that no history buffer be allocated. You can
  subsequently resize or delete the history buffer at any time, by
  calling gl_resize_history(), limit the number of lines that are
  allowed in the buffer by calling gl_limit_history(), clear either
  all history lines from the history list, or just the history lines
  that are associated with the current history group, by calling
  gl_clear_history, and toggle the history mechanism on and off by
  calling gl_toggle_history().

  The new gl_terminal_size() function can be used to query the
  current terminal size. It can also be used to supply a default
  terminal size on systems where no mechanism is available for
  looking up the size.

  The contents and configuration of the history list can now be
  obtained by the calling application, by calling the new
  gl_lookup_history(), gl_state_of_history(), gl_range_of_history()
  and gl_size_of_history() functions. See the gl_get_line(3) man page.

  Echoing of the input line as it is typed, can now be turned on and
  off via the new gl_echo_mode() function. While echoing is disabled,
  newly entered input lines are omitted from the history list.  See
  the gl_get_line(3) man page.

  While the default remains to display the prompt string literally,
  the new gl_prompt_style() function can be used to enable text
  attribute formatting directives in prompt strings, such as
  underlining, bold font, and highlighting directives.

  Signal handling in gl_get_line() is now customizable. The default
  signal handling behavior remains essentially the same, except that
  the SIGTSTP, SIGTTIN and SIGTTOU are now forwarded to the
  corresponding signal handler of the calling program, instead of
  causing a SIGSTOP to be sent to the application.  It is now possible
  to remove signals from the list that are trapped by gl_get_line(),
  as well as add new signals to this list. The signal and terminal
  environments in which the signal handler of the calling program is
  invoked, and what gl_get_line() does after the signal handler
  returns, is now customizable on a per signal basis. You can now also
  query the last signal that was caught by gl_get_line(). This is
  useful when gl_get_line() aborts with errno=EINTR, and you need to
  know which signal caused it to abort.

  Key-sequences bound to action functions can now start with printable
  characters. Previously only keysequences starting with control or
  meta characters were permitted.

  gl_get_line() is now 8-bit clean. If the calling program has
  correctly called setlocale(LC_CTYPE,""), then the user can select an
  alternate locale by setting the standard LC_CTYPE, LC_ALL, or LANG
  environment variables, and international characters can then be
  entered directly, either by using a non-US keyboard, or by using a
  compose key on a standard US keyboard. Note that in locales in which
  meta characters become printable, meta characters no longer match
  M-c bindings, which then have to be entered using their escape-c
  equivalents.  Fortunately most modern terminal emulators either
  output the escape-c version by default when the meta key is used, or
  can be configured to do so (see the gl_get_line(3) man page), so in
  most cases you can continue to use the meta key.

  Completion callback functions can now tell gl_get_line() to return
  the input line immediately after a successful tab completion, simply
  by setting the last character of the optional continuation suffix to
  a newline character (ie. in the call to cpl_add_completion()).

  It is now safe to create and use multiple GetLine objects, albeit
  still only from a single thread. In conjunction with the new
  gl_configure_getline() function, this optionally allows multiple
  GetLine objects with different bindings to be used to implement
  different input modes.

  The edit-mode configuration command now accepts the argument,
  none. This tells gl_get_line() to revert to using just the native
  line editing facilities provided by the terminal driver. This could
  be used if the termcap or terminfo entry of the host terminal were
  badly corrupted.

  Application callback functions invoked by gl_get_line() can now
  change the displayed prompt using the gl_replace_prompt() function.

  Their is now an optional program distributed with the library. This
  is a beta release of a program which adds tecla command-line editing
  to virtually any third party application without the application
  needing to be linked to the library. See the enhance(3) man page for
  further details. Although built and installed by default, the
  INSTALL document explains how to prevent this.

  The INSTALL document now explains how you can stop the demo programs
  from being built and installed.

  NetBSD/termcap fixes. Mike MacFaden reported two problems that he
  saw when compiling libtecla under NetBSD. Both cases were related to
  the use of termcap.  Most systems use terminfo, so this problem has
  gone unnoticed until now, and won't have affected the grand majority
  of users.  The configure script had a bug which prevented the check
  for CPP working properly, and getline.c wouldn't compile due to an
  undeclared variable when USE_TERMCAP was defined. Both problems have
  now been fixed. Note that if you successfully compiled version
  1.3.3, this problem didn't affect you.

  An unfortunate and undocumented binding of the key-sequence M-O was
  shadowing the arrow-key bindings on systems that use ^[OA etc. I
  have removed this binding (the documented lower case M-o binding
  remains bound). Under the KDE konsole terminal this was causing the
  arrow keys to do something other than expected.

  There was a bug in the history list code which could result in
  strange entries appearing at the start of the history list once
  enough history lines had been added to the list to cause the
  circular history buffer to wrap. This is now fixed.
 
Version 1.3.3:

  Signal handling has been re-written, and documentation of its
  behaviour has been added to the gl_get_line(3) man page. In addition
  to eliminating race conditions, and appropriately setting errno for
  those signals that abort gl_get_line(), many more signals are now
  intercepted, making it less likely that the terminal will be left in
  raw mode by a signal that isn't trapped by gl_get_line().

  A bug was also fixed that was leaving the terminal in raw mode if
  the editing mode was changed interactively between vi and emacs.
  This was only noticeable when running programs from old shells that
  don't reset terminal modes.

Version 1.3.2:

  Tim Eliseo contributed a number of improvements to vi mode,
  including a fuller set of vi key-bindings, implementation of the vi
  constraint that the cursor can't backup past the point at which
  input mode was entered, and restoration of overwritten characters
  when backspacing in overwrite mode. There are also now new bindings
  to allow users to toggle between vi and emacs modes interactively.
  The terminal bell is now used in some circumstances, such as when an
  unrecognized key sequence is entered. This can be turned off by the
  new nobeep option in the tecla configuration file.

  Unrelated to the above, a problem under Linux which prevented ^Q
  from being used to resume terminal output after the user had pressed
  ^S, has been fixed.

Version 1.3.1:

  In vi mode a bug was preventing the history-search-backward and
  history-search-forward actions from doing anything when invoked on
  empty lines. On empty lines they now act like up-history and
  down-history respectively, as in emacs mode.

  When creating shared libraries under Linux, the -soname directive
  was being used incorrectly. The result is that Linux binaries linked
  with the 1.2.3, 1.2.4 and 1.3.0 versions of the tecla shared
  libraries, will refuse to see other versions of the shared library
  until relinked with version 1.3.1 or higher.

  The configure script can now handle the fact that under Solaris-2.6
  and earlier, the only curses library is a static one that hides in
  /usr/ccs/lib. Under Linux it now also caters for old versions of GNU
  ld which don't accept version scripts.

  The demos are now linked against the shared version of the library
  if possible. Previously they were always linked with the static
  version.

Version 1.3.0:

  The major change in this release is the addition of an optional vi
  command-line editing mode in gl_get_line(), along with lots of new
  action functions to support its bindings. To enable this, first
  create a ~/.teclarc file if you don't already have one, then add the
  following line to it.

   edit-mode vi

  The default vi bindings, which are designed to mimic those of the vi
  editor as closely as possible, are described in the gl_get_line(3)
  man page.

  A new convenience function called ef_list_expansions() has been
  added for listing filename expansions. See the ef_list_expansions(3)
  man page for details. This is used in a new list-glob binding, bound
  to ^Xg in emacs mode, and ^G in vi input mode.

  A bug has been fixed in the key-binding table expansion code. This
  bug would have caused problems to anybody who defined more than
  about 18 personalized key-bindings in their ~/.teclarc file.

Version 1.2.4:

  Buffered I/O is now used for writing to terminals, and where
  supported, cursor motion is done with move-n-positions terminfo
  capabilities instead of doing lots of move-1-position requests. This
  greatly improves how the library feels over slow links.

  You can now optionally compile different architectures in different
  directories, without having to make multiple copies of the
  distribution. This is documented in the INSTALL file.

  The ksh ~+ directive is now supported.

  Thanks to Markus Gyger for the above improvements.

  Documentation has been added to the INSTALL file describing features
  designed to facilitate configuration and installation of the library
  as part of larger packages. These features are intended to remove
  the need to modify the tecla distribution's configuration and build
  procedures when embedding the libtecla distribution in other package
  distributions.

  A previous fix to stop the cursor from warping when the last
  character of the input line was in the last column of the terminal,
  was only being used for the first terminal line of the input line.
  It is now used for all subsequent lines as well, as originally
  intended.
  
Version 1.2.3:

  The installation procedure has been better automated with the
  addition of an autoconf configure script. This means that installers
  can now compile and install the library by typing:

    ./configure
    make
    make install

  On all systems this makes at least the normal static version of the
  tecla library. It also makes the reentrant version if reentrant
  POSIX functions are detected.  Under Solaris, Linux and HP-UX the
  configuration script arranges for shared libraries to be compiled in
  addition to the static libraries.  It is hoped that installers will
  return information about how to compile shared libraries on other
  systems, for inclusion in future releases, and to this end, a new
  PORTING guide has been provided.

  The versioning number scheme has been changed. This release would
  have been 1.2c, but instead will be refered to as 1.2.3. The
  versioning scheme, based on conventions used by Sun Microsystems, is
  described in configure.in.

  The library was also tested under HP-UX, and this revealed two
  serious bugs, both of which have now been fixed.
  
  The first bug prevented the library from writing control codes to
  terminals on big-endian machines, with the exception of those
  running under Solaris. This was due to an int variable being used
  where a char was needed.

  The second bug had the symptom that on systems that don't use the
  newline character as the control code for moving the cursor down a
  line, a newline wasn't started when the user hit enter.

Version 1.2b:

  Two more minor bug fixes:

  Many terminals don't wrap the cursor to the next line when a
  character is written to the rightmost terminal column. Instead, they
  delay starting a new line until one more character is written, at
  which point they move the cursor two positions.  gl_get_line()
  wasn't aware of this, so cursor repositionings just after writing
  the last character of a column, caused it to erroneously go up a
  line. This has now been remedied, using a method that should work
  regardless of whether a terminal exhibits this behavior or not.

  Some systems dynamically record the current terminal dimensions in
  environment variables called LINES and COLUMNS. On such systems,
  during the initial terminal setup, these values should override the
  static values read from the terminal information databases, and now
  do.  Previously they were only used if the dimensions returned by
  terminfo/termcap looked bogus.

Version 1.2a:

  This minor release fixes the following two bugs:

  The initial terminal size and subsequent changes thereto, weren't
  being noticed by gl_get_line(). This was because the test for the
  existence of TIOCWINSZ was erroneously placed before the inclusion
  of termios.h. One of the results was that on input lines that
  spanned more than one terminal line, the cursor occasionally jumped
  unexpectedly to the previous terminal line.

  On entering a line that wrapped over multiple terminal lines,
  gl_get_line() simply output a carriage-return line-feed at the point
  at which the user pressed return. Thus if one typed in such a line,
  then moved back onto one of the earlier terminal lines before
  hitting return, the cursor was left on a line containing part of the
  line that had just been entered. This didn't do any harm, but it
  looked a mess.

Version 1.2:

  A new facility for looking up and completing filenames in UNIX-style
  paths has now been added (eg. you can search for, or complete
  commands using the UNIX PATH environment variable). See the
  pca_lookup_file(3) man page.

  The already existing filename completion callback can now be made
  selective in what types of files it lists. See the
  cpl_complete_word(3) man page.

  Due to its potential to break applications when changed, the use of
  the publically defined CplFileArgs structure to configure the
  cpl_file_completions() callback is now deprecated.  The definition
  of this structure has been frozen, and its documentation has been
  removed from the man pages.  It will remain supported, but if you
  have used it, you are recommended to switch to the new method, which
  involves a new opaque configuration object, allocated via a provided
  constructor function, configured via accessor functions, and
  eventually deleted with a provided destructor function. The
  cpl_file_completions() callback distinguishes which structure type
  it has been sent by virtue of a code placed at the start of the new
  structure by the constructor.  It is assumed that no existing
  applications set the boolean 'escaped' member of the CplFileArgs
  structure to 4568.  The new method is documented in the
  cpl_complete_word(3) man page.

Version 1.1j

  This was the initial public release on freshmeat.org.


genometools-1.5.1/src/external/libtecla-1.6.1/html/tecla.html000066400000000000000000001624741211610345200236350ustar00rootroot00000000000000
Manual Page



tecla                                      tecla




NAME
       tecla, teclarc - The user interface provided by the Tecla library.


DESCRIPTION
       This  man  page  describes  the  command-line editing features that are
       available to users of programs that read keyboard input via  the  Tecla
       library.  Users  of  the  tcsh shell will find the default key-bindings
       very familiar. Users of the bash shell will also find it  quite  famil-
       iar,  but with a few minor differences, most notably in how forward and
       backward searches through the list  of  historical  commands  are  per-
       formed.  There  are  two  major editing modes, one with emacs-like key-
       bindings and another with vi-like key-bindings. By default  emacs  mode
       is  enabled,  but  vi mode can alternatively be selected via the user's
       configuration file. This file can also be used to change  the  bindings
       of individual keys to suit the user's preferences. By default, tab com-
       pletion is provided. If the application  hasn't  reconfigured  this  to
       complete  other  types  of symbols, then tab completion completes file-
       names.



KEY SEQUENCE NOTATION
       In the rest of this man page,  and  also  in  all  Tecla  configuration
       files, key-sequences are expressed as follows.


       ^A  or  C-a
           This is a control-A, entered by pressing the control key at
           the same time as the A key.

       \E    or   M-
           In key-sequences, both of these notations can be entered
           either by pressing the escape key, then the following key, or by
           pressing the Meta key at the same time as the following key. Thus
           the key sequence M-p can be typed in two ways, by pressing
           the escape key, followed by pressing p, or by pressing the
           Meta key at the same time as p.

       up
           This refers to the up-arrow key.

       down
           This refers to the down-arrow key.

       left
           This refers to the left-arrow key.

       right
           This refers to the right-arrow key.

       a
           This is just a normal A key.




THE TECLA CONFIGURATION FILE
       By  default, Tecla looks for a file called .teclarc in your home direc-
       tory (ie. ~/.teclarc).  If it finds this file, it reads it,  interpret-
       ing each line as defining a new key binding or an editing configuration
       option. Since the emacs keybindings are installed by  default,  if  you
       want to use the non-default vi editing mode, the most important item to
       go in this file is the following line:

         edit-mode vi

       This will re-configure the default bindings for vi-mode.  The  complete
       set of arguments that this command accepts are:

         vi     -  Install key-bindings like those of the vi
                   editor.
         emacs  -  Install key-bindings like those of the emacs
                   editor. This is the default.
         none   -  Use just the native line editing facilities
                   provided by the terminal driver.

       To  prevent the terminal bell from being rung, such as when an unrecog-
       nized control-sequence is typed, place the following line in  the  con-
       figuration file:

         nobeep

       An  example of a key binding line in the configuration file is the fol-
       lowing.

         bind M-[2~ insert-mode

       On many keyboards, the above key sequence is generated when one presses
       the  insert  key,  so  with this keybinding, one can toggle between the
       emacs-mode insert and overwrite modes by hitting  one  key.  One  could
       also  do  it by typing out the above sequence of characters one by one.
       As explained above, the M- part of this sequence can be typed either by
       pressing  the  escape  key before the following key, or by pressing the
       Meta key at the same time as the following key. Thus if you had set the
       above  key binding, and the insert key on your keyboard didn't generate
       the above key sequence, you could still type it in either of  the  fol-
       lowing 2 ways.

         1. Hit the escape key momentarily, then press '[', then '2', then
            finally '~'.

         2. Press the meta key at the same time as pressing the '[' key,
            then press '2', then '~'.

       If  you  set a keybinding for a key-sequence that is already bound to a
       function, the new binding overrides the old one. If in the new  binding
       you  omit the name of the new function to bind to the key-sequence, the
       original binding becomes undefined.

       Starting with versions of libtecla later than 1.3.3 it is now  possible
       to  bind keysequences that begin with a printable character. Previously
       key-sequences were required to start with a control or meta  character.

       Note  that  the special keywords "up", "down", "left" and "right" refer
       to the arrow keys, and are thus not treated as  keysequences.  So,  for
       example, to rebind the up and down arrow keys to use the history search
       mechanism instead of the simple history recall method, you could  place
       the following in your configuration file:

         bind up history-search-backwards
         bind down history-search-backwards

       To unbind an existing binding, you can do this with the bind command by
       omitting to name any action to rebind the key sequence to.   For  exam-
       ple,  by  not  specifying  an  action  function,  the following command
       unbinds the default beginning-of-line action from the ^A key sequence:

         bind ^A

       If you create a ~/.teclarc configuration file, but it appears  to  have
       no effect on the program, check the documentation of the program to see
       if the author chose a different name for this file.



FILENAME AND TILDE COMPLETION
       With the default key bindings, pressing the TAB key (aka.  ^I)  results
       in  Tecla  attempting to complete the incomplete filename that precedes
       the cursor. Tecla searches backwards from the cursor, looking  for  the
       start  of  the  filename,  stopping  when it hits either a space or the
       start of the line. If more than one file has the specified prefix, then
       Tecla  completes  the  filename  up to the point at which the ambiguous
       matches start to differ, then lists the possible matches.

       In addition to literally written filenames, Tecla  can  complete  files
       that  start  with  ~/  and  ~user/ expressions and that contain $envvar
       expressions. In particular, if you hit TAB within an incomplete  ~user,
       expression,  Tecla  will  attempt to complete the username, listing any
       ambiguous matches.

       The completion binding is implemented using the  cpl_word_completions()
       function,  which is also available separately to users of this library.
       See the cpl_word_completions(@LIBR_MANEXT@) man page for more  details.



FILENAME EXPANSION
       With  the default key bindings, pressing ^X* causes Tecla to expand the
       filename that precedes the cursor, replacing ~/ and ~user/  expressions
       with  the corresponding home directories, and replacing $envvar expres-
       sions with the value of the specified  environment  variable,  then  if
       there  are any wildcards, replacing the so far expanded filename with a
       space-separated list of the files which match the wild cards.

       The expansion binding is implemented using the  ef_expand_file()  func-
       tion.  See the ef_expand_file man page for more details.



RECALLING PREVIOUSLY TYPED LINES
       Every time that a new line is entered by the user, it is appended to  a
       list  of  historical input lines maintained within the GetLine resource
       object. You can traverse up and down this list using the  up  and  down
       arrow  keys.  Alternatively,  you  can  do the same with the ^P, and ^N
       keys, and in vi command mode you can alternatively  use  the  k  and  j
       characters.  Thus  pressing  up-arrow  once, replaces the current input
       line  with  the  previously  entered  line.  Pressing  up-arrow  again,
       replaces  this  with  the line that was entered before it, etc.. Having
       gone back one or more lines into the history list, one  can  return  to
       newer  lines  by  pressing down-arrow one or more times. If you do this
       sufficient times, you will return to the original line  that  you  were
       entering when you first hit up-arrow.

       Note  that  in  vi mode, all of the history recall functions switch the
       library into command mode.

       In emacs mode the M-p and M-n keys work just like the ^P and  ^N  keys,
       except  that  they  skip all but those historical lines which share the
       prefix that precedes the cursor. In vi command mode the  upper  case  K
       and  J  characters  do the same thing, except that the string that they
       search for includes the character under the cursor as well as what pre-
       cedes it.

       Thus for example, suppose that you were in emacs mode, and you had just
       entered the following list of commands in the order shown:

         ls ~/tecla/
         cd ~/tecla
         ls -l getline.c
         emacs ~/tecla/getline.c

       If you next typed:

         ls

       and then hit M-p, then rather than returning the previously typed emacs
       line, which doesn't start with "ls", Tecla would recall the "ls -l get-
       line.c" line. Pressing M-p again would recall the "ls ~/tecla/" line.

       Note that if the string that you are searching for, contains any of the
       special  characters, *, ?, or '[', then it is interpretted as a pattern
       to be matched. Thus, cotinuing with the above example, after typing  in
       the list of commands shown, if you then typed:

         *tecla*

       and  hit M-p, then the "emacs ~/tecla/getline.c" line would be recalled
       first, since it contains the word tecla somewhere in  the  line,  Simi-
       larly, hitting M-p again, would recall the "ls ~/tecla/" line, and hit-
       ting it once more would recall the "ls ~/tecla/" line. The pattern syn-
       tax  is  the  same  as  that  described  for filename expansion, in the
       ef_expand_file(@LIBR_MANEXT@ man page.



HISTORY FILES
       Authors of programs that use the Tecla library have the option of  sav-
       ing historical command-lines in a file before exiting, and subsequently
       reading them back in from this file when the program is  next  started.
       There  is no standard name for this file, since it makes sense for each
       application to use its own history file, so that commands from  differ-
       ent applications don't get mixed up.



INTERNATIONAL CHARACTER SETS
       Since  libtecla  version  1.4.0, Tecla has been 8-bit clean. This means
       that all 8-bit characters that are  printable  in  the  user's  current
       locale  are  now  displayed verbatim and included in the returned input
       line.  Assuming that the calling program correctly contains a call like
       the following,

         setlocale(LC_CTYPE, "");

       then  the  current locale is determined by the first of the environment
       variables LC_CTYPE, LC_ALL, and LANG, that is found to contain a  valid
       locale  name.  If  none  of these variables are defined, or the program
       neglects to call setlocale, then the default C locale is used, which is
       US  7-bit  ASCII.  On  most  unix-like platforms, you can get a list of
       valid locales by typing the command:

         locale -a

       at the shell prompt.


   Meta keys and locales
       Beware that in most locales other than the default C locale, meta char-
       acters  become  printable,  and  they  are then no longer considered to
       match M-c style key bindings. This allows international  characters  to
       be  entered  with  the compose key without unexpectedly triggering meta
       key bindings. You can still invoke meta bindings, since there are actu-
       ally  two  ways  to  do  this.  For example the binding M-c can also be
       invoked by pressing the escape key momentarily,  then  pressing  the  c
       key,  and  this  will  work regardless of locale. Moreover, many modern
       terminal emulators, such as gnome's gnome-terminal's and KDE's  konsole
       terminals,  already  generate  escape  pairs like this when you use the
       meta key, rather than a real meta character, and other  emulators  usu-
       ally  have  a  way to request this behavior, so you can continue to use
       the meta key on most systems.

       For example, although xterm terminal emulators generate real 8-bit meta
       characters by default when you use the meta key, they can be configured
       to output the equivalent escape pair by setting their  EightBitInput  X
       resource  to  False.  You can either do this by placing a line like the
       following in your ~/.Xdefaults file,

         XTerm*EightBitInput: False

       or by starting an xterm with an -xrm '*EightBitInput:  False'  command-
       line  argument. In recent versions of xterm you can toggle this feature
       on and off with the "Meta Sends Escape" option in the menu that is dis-
       played  when you press the left mouse button and the control key within
       an xterm window. In CDE, dtterms can be similarly coerced  to  generate
       escape pairs in place of meta characters, by setting the Dtterm*KshMode
       resource to True.


   Entering international characters
       If you don't have a keyboard that generates all  of  the  international
       characters  that  you  need,  there  is usually a compose key that will
       allow you to enter special characters, or a  way  to  create  one.  For
       example, under X windows on unix-like systems, if your keyboard doesn't
       have a compose key, you can designate a redundant  key  to  serve  this
       purpose  with  the  xmodmap  command. For example, on many PC keyboards
       there is a microsoft-windows key,  which  is  otherwise  useless  under
       Linux. On my laptop the xev program reports that pressing this key gen-
       erates keycode 115, so to turn this key into a compose key,  I  do  the
       following:

         xmodmap -e 'keycode 115 = Multi_key'

       I  can  then  enter an i with a umlaut over it by typing this key, fol-
       lowed by ", followed by i.



THE AVAILABLE KEY BINDING FUNCTIONS
       The following is a list of the editing functions provided by the  Tecla
       library.  The  names  in the leftmost column of the list can be used in
       configuration files to specify which function a given key  or  combina-
       tion of keys should invoke. They are also used in the next two sections
       to list the default key-bindings in emacs and vi modes.

         user-interrupt           -  Send a SIGINT signal to the
                                     parent process.
         abort                    -  Send a SIGABRT signal to the
                                     parent process.
         suspend                  -  Suspend the parent process.
         stop-output              -  Pause terminal output.
         start-output             -  Resume paused terminal output.
         literal-next             -  Arrange for the next character
                                     to be treated as a normal
                                     character. This allows control
                                     characters to be entered.
         cursor-right             -  Move the cursor one character
                                     right.
         cursor-left              -  Move the cursor one character
                                     left.
         insert-mode              -  Toggle between insert mode and
                                     overwrite mode.
         beginning-of-line        -  Move the cursor to the
                                     beginning of the line.
         end-of-line              -  Move the cursor to the end of
                                     the line.
         delete-line              -  Delete the contents of the
                                     current line.
         kill-line                -  Delete everything that follows
                                     the cursor.
         backward-kill-line       -  Delete all characters between
                                     the cursor and the start of the
                                     line.
         forward-word             -  Move to the end of the word
                                     which follows the cursor.
         forward-to-word          -  Move the cursor to the start of
                                     the word that follows the
                                     cursor.
         backward-word            -  Move to the start of the word
                                     which precedes the cursor.
         goto-column              -  Move the cursor to the
                                     1-relative column in the line
                                     specified by any preceding
                                     digit-argument sequences (see
                                     ENTERING REPEAT COUNTS below).
         find-parenthesis         -  If the cursor is currently
                                     over a parenthesis character,
                                     move it to the matching
                                     parenthesis character. If not
                                     over a parenthesis character
                                     move right to the next close
                                     parenthesis.
         forward-delete-char      -  Delete the character under the
                                     cursor.
         backward-delete-char     -  Delete the character which
                                     precedes the cursor.
         list-or-eof              -  This is intended for binding
                                     to ^D. When invoked when the
                                     cursor is within the line it
                                     displays all possible
                                     completions then redisplays
                                     the line unchanged. When
                                     invoked on an empty line, it
                                     signals end-of-input (EOF) to
                                     the caller of gl_get_line().
         del-char-or-list-or-eof  -  This is intended for binding
                                     to ^D. When invoked when the
                                     cursor is within the line it
                                     invokes forward-delete-char.
                                     When invoked at the end of the
                                     line it displays all possible
                                     completions then redisplays
                                     the line unchanged. When
                                     invoked on an empty line, it
                                     signals end-of-input (EOF) to
                                     the caller of gl_get_line().
         forward-delete-word      -  Delete the word which follows
                                     the cursor.
         backward-delete-word     -  Delete the word which precedes
                                     the cursor.
         upcase-word              -  Convert all of the characters
                                     of the word which follows the
                                     cursor, to upper case.
         downcase-word            -  Convert all of the characters
                                     of the word which follows the
                                     cursor, to lower case.
         capitalize-word          -  Capitalize the word which
                                     follows the cursor.
         change-case              -  If the next character is upper
                                     case, toggle it to lower case
                                     and vice versa.
         redisplay                -  Redisplay the line.
         clear-screen             -  Clear the terminal, then
                                     redisplay the current line.
         transpose-chars          -  Swap the character under the
                                     cursor with the character just
                                     before the cursor.
         set-mark                 -  Set a mark at the position of
                                     the cursor.
         exchange-point-and-mark  -  Move the cursor to the last
                                     mark that was set, and move
                                     the mark to where the cursor
                                     used to be.
         kill-region              -  Delete the characters that lie
                                     between the last mark that was
                                     set, and the cursor.
         copy-region-as-kill      -  Copy the text between the mark
                                     and the cursor to the cut
                                     buffer, without deleting the
                                     original text.
         yank                     -  Insert the text that was last
                                     deleted, just before the
                                     current position of the cursor.
         append-yank              -  Paste the current contents of
                                     the cut buffer, after the
                                     cursor.
         up-history               -  Recall the next oldest line
                                     that was entered. Note that
                                     in vi mode you are left in
                                     command mode.
         down-history             -  Recall the next most recent
                                     line that was entered. If no
                                     history recall session is
                                     currently active, the next
                                     line from a previous recall
                                     session is recalled. Note that
                                     in vi mode you are left in
                                     command mode.
         history-search-backward  -  Recall the next oldest line
                                     who's prefix matches the string
                                     which currently precedes the
                                     cursor (in vi command-mode the
                                     character under the cursor is
                                     also included in the search
                                     string).  Note that in vi mode
                                     you are left in command mode.
         history-search-forward   -  Recall the next newest line
                                     who's prefix matches the string
                                     which currently precedes the
                                     cursor (in vi command-mode the
                                     character under the cursor is
                                     also included in the search
                                     string).  Note that in vi mode
                                     you are left in command mode.
         history-re-search-backward -Recall the next oldest line
                                     who's prefix matches that
                                     established by the last
                                     invocation of either
                                     history-search-forward or
                                     history-search-backward.
         history-re-search-forward - Recall the next newest line
                                     who's prefix matches that
                                     established by the last
                                     invocation of either
                                     history-search-forward or
                                     history-search-backward.
         complete-word            -  Attempt to complete the
                                     incomplete word which
                                     precedes the cursor. Unless
                                     the host program has customized
                                     word completion, filename
                                     completion is attempted. In vi
                                     commmand mode the character
                                     under the cursor is also
                                     included in the word being
                                     completed, and you are left in
                                     vi insert mode.
         expand-filename          -  Within the command line, expand
                                     wild cards, tilde expressions
                                     and dollar expressions in the
                                     filename which immediately
                                     precedes the cursor. In vi
                                     commmand mode the character
                                     under the cursor is also
                                     included in the filename being
                                     expanded, and you are left in
                                     vi insert mode.
         list-glob                -  List any filenames which match
                                     the wild-card, tilde and dollar
                                     expressions in the filename
                                     which immediately precedes the
                                     cursor, then redraw the input
                                     line unchanged.
         list-history             -  Display the contents of the
                                     history list for the current
                                     history group. If a repeat
                                     count of > 1 is specified,
                                     only that many of the most
                                     recent lines are displayed.
                                     See the "ENTERING REPEAT
                                     COUNTS" section.
         read-from-file           -  Temporarily switch to reading
                                     input from the file who's
                                     name precedes the cursor.
         read-init-files          -  Re-read teclarc configuration
                                     files.
         beginning-of-history     -  Move to the oldest line in the
                                     history list. Note that in vi
                                     mode you are left in command
                                     mode.
         end-of-history           -  Move to the newest line in the
                                     history list (ie. the current
                                     line). Note that in vi mode
                                     this leaves you in command
                                     mode.
         digit-argument           -  Enter a repeat count for the
                                     next key-binding function.
                                     For details, see the ENTERING
                                     REPEAT COUNTS section.
         newline                  -  Terminate and return the
                                     current contents of the
                                     line, after appending a
                                     newline character. The newline
                                     character is normally '\n',
                                     but will be the first
                                     character of the key-sequence
                                     that invoked the newline
                                     action, if this happens to be
                                     a printable character. If the
                                     action was invoked by the
                                     '\n' newline character or the
                                     '\r' carriage return
                                     character, the line is
                                     appended to the history
                                     buffer.
         repeat-history           -  Return the line that is being
                                     edited, then arrange for the
                                     next most recent entry in the
                                     history buffer to be recalled
                                     when Tecla is next called.
                                     Repeatedly invoking this
                                     action causes successive
                                     historical input lines to be
                                     re-executed. Note that this
                                     action is equivalent to the
                                     'Operate' action in ksh.
         ring-bell                -  Ring the terminal bell, unless
                                     the bell has been silenced via
                                     the nobeep configuration
                                     option (see the THE TECLA
                                     CONFIGURATION FILE section).
         forward-copy-char        -  Copy the next character into
                                     the cut buffer (NB. use repeat
                                     counts to copy more than one).
         backward-copy-char       -  Copy the previous character
                                     into the cut buffer.
         forward-copy-word        -  Copy the next word into the cut
                                     buffer.
         backward-copy-word       -  Copy the previous word into the
                                     cut buffer.
         forward-find-char        -  Move the cursor to the next
                                     occurrence of the next
                                     character that you type.
         backward-find-char       -  Move the cursor to the last
                                     occurrence of the next
                                     character that you type.
         forward-to-char          -  Move the cursor to the
                                     character just before the next
                                     occurrence of the next
                                     character that the user types.
         backward-to-char         -  Move the cursor to the
                                     character just after the last
                                     occurrence before the cursor
                                     of the next character that the
                                     user types.
         repeat-find-char         -  Repeat the last
                                     backward-find-char,
                                     forward-find-char,
                                     backward-to-char or
                                     forward-to-char.
         invert-refind-char       -  Repeat the last
                                     backward-find-char,
                                     forward-find-char,
                                     backward-to-char, or
                                     forward-to-char in the
                                     opposite direction.
         delete-to-column         -  Delete the characters from the
                                     cursor up to the column that
                                     is specified by the repeat
                                     count.
         delete-to-parenthesis    -  Delete the characters from the
                                     cursor up to and including
                                     the matching parenthesis, or
                                     next close parenthesis.
         forward-delete-find      -  Delete the characters from the
                                     cursor up to and including the
                                     following occurence of the
                                     next character typed.
         backward-delete-find     -  Delete the characters from the
                                     cursor up to and including the
                                     preceding occurence of the
                                     next character typed.
         forward-delete-to        -  Delete the characters from the
                                     cursor up to, but not
                                     including, the following
                                     occurence of the next
                                     character typed.
         backward-delete-to       -  Delete the characters from the
                                     cursor up to, but not
                                     including, the preceding
                                     occurence of the next
                                     character typed.
         delete-refind            -  Repeat the last *-delete-find
                                     or *-delete-to action.
         delete-invert-refind     -  Repeat the last *-delete-find
                                     or *-delete-to action, in the
                                     opposite direction.
         copy-to-column           -  Copy the characters from the
                                     cursor up to the column that
                                     is specified by the repeat
                                     count, into the cut buffer.
         copy-to-parenthesis      -  Copy the characters from the
                                     cursor up to and including
                                     the matching parenthesis, or
                                     next close parenthesis, into
                                     the cut buffer.
         forward-copy-find        -  Copy the characters from the
                                     cursor up to and including the
                                     following occurence of the
                                     next character typed, into the
                                     cut buffer.
         backward-copy-find       -  Copy the characters from the
                                     cursor up to and including the
                                     preceding occurence of the
                                     next character typed, into the
                                     cut buffer.
         forward-copy-to          -  Copy the characters from the
                                     cursor up to, but not
                                     including, the following
                                     occurence of the next
                                     character typed, into the cut
                                     buffer.
         backward-copy-to         -  Copy the characters from the
                                     cursor up to, but not
                                     including, the preceding
                                     occurence of the next
                                     character typed, into the cut
                                     buffer.
         copy-refind              -  Repeat the last *-copy-find
                                     or *-copy-to action.
         copy-invert-refind       -  Repeat the last *-copy-find
                                     or *-copy-to action, in the
                                     opposite direction.
         vi-mode                  -  Switch to vi mode from emacs
                                     mode.
         emacs-mode               -  Switch to emacs mode from vi
                                     mode.
         vi-insert                -  From vi command mode, switch to
                                     insert mode.
         vi-overwrite             -  From vi command mode, switch to
                                     overwrite mode.
         vi-insert-at-bol         -  From vi command mode, move the
                                     cursor to the start of the line
                                     and switch to insert mode.
         vi-append-at-eol         -  From vi command mode, move the
                                     cursor to the end of the line
                                     and switch to append mode.
         vi-append                -  From vi command mode, move the
                                     cursor one position right, and
                                     switch to insert mode.
         vi-replace-char          -  From vi command mode, replace
                                     the character under the cursor
                                     with the the next character
                                     entered.
         vi-forward-change-char   -  From vi command mode, delete
                                     the next character then enter
                                     insert mode.
         vi-backward-change-char  -  From vi command mode, delete
                                     the preceding character then
                                     enter insert mode.
         vi-forward-change-word   -  From vi command mode, delete
                                     the next word then enter
                                     insert mode.
         vi-backward-change-word  -  From vi command mode, delete
                                     the preceding word then
                                     enter insert mode.
         vi-change-rest-of-line   -  From vi command mode, delete
                                     from the cursor to the end of
                                     the line, then enter insert
                                     mode.
         vi-change-line           -  From vi command mode, delete
                                     the current line, then enter
                                     insert mode.
         vi-change-to-bol         -  From vi command mode, delete
                                     all characters between the
                                     cursor and the beginning of
                                     the line, then enter insert
                                     mode.
         vi-change-to-column      -  From vi command mode, delete
                                     the characters from the cursor
                                     up to the column that is
                                     specified by the repeat count,
                                     then enter insert mode.
         vi-change-to-parenthesis -  Delete the characters from the
                                     cursor up to and including
                                     the matching parenthesis, or
                                     next close parenthesis, then
                                     enter vi insert mode.
         vi-forward-change-find   -  From vi command mode, delete
                                     the characters from the
                                     cursor up to and including the
                                     following occurence of the
                                     next character typed, then
                                     enter insert mode.
         vi-backward-change-find  -  From vi command mode, delete
                                     the characters from the
                                     cursor up to and including the
                                     preceding occurence of the
                                     next character typed, then
                                     enter insert mode.
         vi-forward-change-to     -  From vi command mode, delete
                                     the characters from the
                                     cursor up to, but not
                                     including, the following
                                     occurence of the next
                                     character typed, then enter
                                     insert mode.
         vi-backward-change-to    -  From vi command mode, delete
                                     the characters from the
                                     cursor up to, but not
                                     including, the preceding
                                     occurence of the next
                                     character typed, then enter
                                     insert mode.
         vi-change-refind         -  Repeat the last
                                     vi-*-change-find or
                                     vi-*-change-to action.
         vi-change-invert-refind  -  Repeat the last
                                     vi-*-change-find or
                                     vi-*-change-to action, in the
                                     opposite direction.
         vi-undo                  -  In vi mode, undo the last
                                     editing operation.
         vi-repeat-change         -  In vi command mode, repeat the
                                     last command that modified the
                                     line.



DEFAULT KEY BINDINGS IN EMACS MODE
       The following default key bindings, which can be overriden by the Tecla
       configuration  file,  are designed to mimic most of the bindings of the
       unix tcsh shell, when it is in emacs editing mode.

       This is the default editing mode of the Tecla library.

       Under UNIX the terminal driver sets a number of special keys  for  cer-
       tain  functions. The tecla library attempts to use the same keybindings
       to maintain consistency. The key sequences shown for  the  following  6
       bindings  are  thus just examples of what they will probably be set to.
       If you have used the stty  command  to  change  these  keys,  then  the
       default bindings should match.

         ^C     ->   user-interrupt
         ^\     ->   abort
         ^Z     ->   suspend
         ^Q     ->   start-output
         ^S     ->   stop-output
         ^V     ->   literal-next

       The  cursor  keys are refered to by name, as follows. This is necessary
       because different types of terminals generate different  key  sequences
       when their cursor keys are pressed.

         right  ->   cursor-right
         left   ->   cursor-left
         up     ->   up-history
         down   ->   down-history

       The remaining bindings don't depend on the terminal setttings.

         ^F     ->   cursor-right
         ^B     ->   cursor-left
         M-i    ->   insert-mode
         ^A     ->   beginning-of-line
         ^E     ->   end-of-line
         ^U     ->   delete-line
         ^K     ->   kill-line
         M-f    ->   forward-word
         M-b    ->   backward-word
         ^D     ->   del-char-or-list-or-eof
         ^H     ->   backward-delete-char
         ^?     ->   backward-delete-char
         M-d    ->   forward-delete-word
         M-^H   ->   backward-delete-word
         M-^?   ->   backward-delete-word
         M-u    ->   upcase-word
         M-l    ->   downcase-word
         M-c    ->   capitalize-word
         ^R     ->   redisplay
         ^L     ->   clear-screen
         ^T     ->   transpose-chars
         ^@     ->   set-mark
         ^X^X   ->   exchange-point-and-mark
         ^W     ->   kill-region
         M-w    ->   copy-region-as-kill
         ^Y     ->   yank
         ^P     ->   up-history
         ^N     ->   down-history
         M-p    ->   history-search-backward
         M-n    ->   history-search-forward
         ^I     ->   complete-word
         ^X*    ->   expand-filename
         ^X^F   ->   read-from-file
         ^X^R   ->   read-init-files
         ^Xg    ->   list-glob
         ^Xh    ->   list-history
         M-<    ->   beginning-of-history
         M->    ->   end-of-history
         \n     ->   newline
         \r     ->   newline
         M-o    ->   repeat-history
         M-^V   ->   vi-mode

         M-0, M-1, ... M-9  ->  digit-argument  (see below)

       Note  that  ^I is what the TAB key generates, and that ^@ can be gener-
       ated not only by pressing the control key and the @ key simultaneously,
       but  also  by  pressing  the  control key and the space bar at the same
       time.



DEFAULT KEY BINDINGS IN VI MODE
       The following default key bindings are designed to mimic the  vi  style
       of  editing  as  closely  as possible. This means that very few editing
       functions are provided in the initial  character  input  mode,  editing
       functions  instead  being  provided  by the vi command mode. Vi command
       mode is entered whenever the escape character is pressed, or whenever a
       key-sequence  that starts with a meta character is entered. In addition
       to mimicing vi, libtecla provides bindings for  tab  completion,  wild-
       card expansion of file names, and historical line recall.

       To  learn  how  to tell the Tecla library to use vi mode instead of the
       default emacs editing mode, see the earlier section entitled THE  TECLA
       CONFIGURATION FILE.

       Under  UNIX  the terminal driver sets a number of special keys for cer-
       tain functions. The Tecla library attempts to use the same  keybindings
       to maintain consistency, binding them both in input mode and in command
       mode. The key sequences shown for the following  6  bindings  are  thus
       just  examples  of  what they will probably be set to. If you have used
       the stty command to change these keys, then the default bindings should
       match.

         ^C     ->   user-interrupt
         ^\     ->   abort
         ^Z     ->   suspend
         ^Q     ->   start-output
         ^S     ->   stop-output
         ^V     ->   literal-next
         M-^C   ->   user-interrupt
         M-^\   ->   abort
         M-^Z   ->   suspend
         M-^Q   ->   start-output
         M-^S   ->   stop-output

       Note  that above, most of the bindings are defined twice, once as a raw
       control code like ^C and then a second time as a  meta  character  like
       M-^C.  The  former is the binding for vi input mode, whereas the latter
       is the binding for vi command mode.  Once  in  command  mode  all  key-
       sequences  that the user types that they don't explicitly start with an
       escape or a meta key, have their first key secretly converted to a meta
       character  before  the key sequence is looked up in the key binding ta-
       ble. Thus, once in command mode, when you type the letter i, for  exam-
       ple, the Tecla library actually looks up the binding for M-i.

       The  cursor  keys are refered to by name, as follows. This is necessary
       because different types of terminals generate different  key  sequences
       when their cursor keys are pressed.

         right  ->   cursor-right
         left   ->   cursor-left
         up     ->   up-history
         down   ->   down-history

       The  cursor  keys  normally  generate  a keysequence that start with an
       escape character, so beware that using the arrow keys will put you into
       command mode (if you aren't already in command mode).

       The  following  are  the terminal-independent key bindings for vi input
       mode.

         ^D     ->   list-or-eof
         ^G     ->   list-glob
         ^H     ->   backward-delete-char
         ^I     ->   complete-word
         \r     ->   newline
         \n     ->   newline
         ^L     ->   clear-screen
         ^N     ->   down-history
         ^P     ->   up-history
         ^R     ->   redisplay
         ^U     ->   backward-kill-line
         ^W     ->   backward-delete-word
         ^X*    ->   expand-filename
         ^X^F   ->   read-from-file
         ^X^R   ->   read-init-files
         ^?     ->   backward-delete-char

       The following are the key bindings that are defined in vi command mode,
       this  being  specified  by  them all starting with a meta character. As
       mentioned above, once in command mode the  initial  meta  character  is
       optional.  For example, you might enter command mode by typing Esc, and
       then press h twice to move the cursor two positions to the left. Both h
       characters  get  quietly  converted to M-h before being compared to the
       key-binding table, the first one because Escape followed by a character
       is  always  converted  to the equivalent meta character, and the second
       because command mode was already active.

         M-\     ->   cursor-right     (Meta-space)
         M-$     ->   end-of-line
         M-*     ->   expand-filename
         M-+     ->   down-history
         M--     ->   up-history
         M-<     ->   beginning-of-history
         M->     ->   end-of-history
         M-^     ->   beginning-of-line
         M-;     ->   repeat-find-char
         M-,     ->   invert-refind-char
         M-|     ->   goto-column
         M-~     ->   change-case
         M-.     ->   vi-repeat-change
         M-%     ->   find-parenthesis
         M-a     ->   vi-append
         M-A     ->   vi-append-at-eol
         M-b     ->   backward-word
         M-B     ->   backward-word
         M-C     ->   vi-change-rest-of-line
         M-cb    ->   vi-backward-change-word
         M-cB    ->   vi-backward-change-word
         M-cc    ->   vi-change-line
         M-ce    ->   vi-forward-change-word
         M-cE    ->   vi-forward-change-word
         M-cw    ->   vi-forward-change-word
         M-cW    ->   vi-forward-change-word
         M-cF    ->   vi-backward-change-find
         M-cf    ->   vi-forward-change-find
         M-cT    ->   vi-backward-change-to
         M-ct    ->   vi-forward-change-to
         M-c;    ->   vi-change-refind
         M-c,    ->   vi-change-invert-refind
         M-ch    ->   vi-backward-change-char
         M-c^H   ->   vi-backward-change-char
         M-c^?   ->   vi-backward-change-char
         M-cl    ->   vi-forward-change-char
         M-c\    ->   vi-forward-change-char  (Meta-c-space)
         M-c^    ->   vi-change-to-bol
         M-c0    ->   vi-change-to-bol
         M-c$    ->   vi-change-rest-of-line
         M-c|    ->   vi-change-to-column
         M-c%    ->   vi-change-to-parenthesis
         M-dh    ->   backward-delete-char
         M-d^H   ->   backward-delete-char
         M-d^?   ->   backward-delete-char
         M-dl    ->   forward-delete-char
         M-d     ->   forward-delete-char    (Meta-d-space)
         M-dd    ->   delete-line
         M-db    ->   backward-delete-word
         M-dB    ->   backward-delete-word
         M-de    ->   forward-delete-word
         M-dE    ->   forward-delete-word
         M-dw    ->   forward-delete-word
         M-dW    ->   forward-delete-word
         M-dF    ->   backward-delete-find
         M-df    ->   forward-delete-find
         M-dT    ->   backward-delete-to
         M-dt    ->   forward-delete-to
         M-d;    ->   delete-refind
         M-d,    ->   delete-invert-refind
         M-d^    ->   backward-kill-line
         M-d0    ->   backward-kill-line
         M-d$    ->   kill-line
         M-D     ->   kill-line
         M-d|    ->   delete-to-column
         M-d%    ->   delete-to-parenthesis
         M-e     ->   forward-word
         M-E     ->   forward-word
         M-f     ->   forward-find-char
         M-F     ->   backward-find-char
         M--     ->   up-history
         M-h     ->   cursor-left
         M-H     ->   beginning-of-history
         M-i     ->   vi-insert
         M-I     ->   vi-insert-at-bol
         M-j     ->   down-history
         M-J     ->   history-search-forward
         M-k     ->   up-history
         M-K     ->   history-search-backward
         M-l     ->   cursor-right
         M-L     ->   end-of-history
         M-n     ->   history-re-search-forward
         M-N     ->   history-re-search-backward
         M-p     ->   append-yank
         M-P     ->   yank
         M-r     ->   vi-replace-char
         M-R     ->   vi-overwrite
         M-s     ->   vi-forward-change-char
         M-S     ->   vi-change-line
         M-t     ->   forward-to-char
         M-T     ->   backward-to-char
         M-u     ->   vi-undo
         M-w     ->   forward-to-word
         M-W     ->   forward-to-word
         M-x     ->   forward-delete-char
         M-X     ->   backward-delete-char
         M-yh    ->   backward-copy-char
         M-y^H   ->   backward-copy-char
         M-y^?   ->   backward-copy-char
         M-yl    ->   forward-copy-char
         M-y\    ->   forward-copy-char  (Meta-y-space)
         M-ye    ->   forward-copy-word
         M-yE    ->   forward-copy-word
         M-yw    ->   forward-copy-word
         M-yW    ->   forward-copy-word
         M-yb    ->   backward-copy-word
         M-yB    ->   backward-copy-word
         M-yf    ->   forward-copy-find
         M-yF    ->   backward-copy-find
         M-yt    ->   forward-copy-to
         M-yT    ->   backward-copy-to
         M-y;    ->   copy-refind
         M-y,    ->   copy-invert-refind
         M-y^    ->   copy-to-bol
         M-y0    ->   copy-to-bol
         M-y$    ->   copy-rest-of-line
         M-yy    ->   copy-line
         M-Y     ->   copy-line
         M-y|    ->   copy-to-column
         M-y%    ->   copy-to-parenthesis
         M-^E    ->   emacs-mode
         M-^H    ->   cursor-left
         M-^?    ->   cursor-left
         M-^L    ->   clear-screen
         M-^N    ->   down-history
         M-^P    ->   up-history
         M-^R    ->   redisplay
         M-^D    ->   list-or-eof
         M-^I    ->   complete-word
         M-\r    ->   newline
         M-\n    ->   newline
         M-^X^R  ->   read-init-files
         M-^Xh   ->   list-history

         M-0, M-1, ... M-9  ->  digit-argument  (see below)

       Note that ^I is what the TAB key generates.



ENTERING REPEAT COUNTS
       Many of  the  key  binding  functions  described  previously,  take  an
       optional count, typed in before the target keysequence.  This is inter-
       preted as a repeat count by most bindings. A notable exception  is  the
       goto-column binding, which interprets the count as a column number.

       By default you can specify this count argument by pressing the meta key
       while typing in the numeric count. This relies  on  the  digit-argument
       action  being bound to Meta-0, Meta-1 etc.  Once any one of these bind-
       ings has been activated, you can optionally take your  finger  off  the
       meta  key  to type in the rest of the number, since every numeric digit
       thereafter is treated as part of the number, unless it is  preceded  by
       the  literal-next binding. As soon as a non-digit, or literal digit key
       is pressed the repeat count is terminated and either  causes  the  just
       typed  character to be added to the line that many times, or causes the
       next key-binding function to be given that argument.

       For example, in emacs mode, typing:

         M-12a

       causes the letter 'a' to be added to the line 12 times, whereas

         M-4M-c

       Capitalizes the next 4 words.

       In vi command mode the Meta modifier  is  automatically  added  to  all
       characters  typed  in,  so  to  enter  a count in vi command-mode, just
       involves typing in the number, just as it does in the vi editor itself.
       So for example, in vi command mode, typing:

         4w2x

       moves  the cursor four words to the right, then deletes two characters.

       You can also bind digit-argument to other key sequences. If  these  end
       in  a  numeric  digit,  that  digit gets appended to the current repeat
       count. If it doesn't end in a numeric digit,  a  new  repeat  count  is
       started  with  a  value  of zero, and can be completed by typing in the
       number, after letting go of the key which triggered the  digit-argument
       action.



FILES
       libtecla.a      -    The Tecla library
       libtecla.h      -    The Tecla header file.
       ~/.teclarc      -    The personal Tecla customization file.



SEE ALSO
       libtecla, gl_get_line, gl_io_mode, ef_expand_file,
       cpl_complete_word, pca_lookup_file



AUTHOR
       Martin Shepherd  (mcs@astro.caltech.edu)



                                                          tecla



genometools-1.5.1/src/external/libtecla-1.6.1/install-sh000077500000000000000000000127361211610345200227120ustar00rootroot00000000000000#!/bin/sh
#
# install - install a program, script, or datafile
# This comes from X11R5 (mit/util/scripts/install.sh).
#
# Copyright 1991 by the Massachusetts Institute of Technology
#
# Permission to use, copy, modify, distribute, and sell this software and its
# documentation for any purpose is hereby granted without fee, provided that
# the above copyright notice appear in all copies and that both that
# copyright notice and this permission notice appear in supporting
# documentation, and that the name of M.I.T. not be used in advertising or
# publicity pertaining to distribution of the software without specific,
# written prior permission.  M.I.T. makes no representations about the
# suitability of this software for any purpose.  It is provided "as is"
# without express or implied warranty.
#
# Calling this script install-sh is preferred over install.sh, to prevent
# `make' implicit rules from creating a file called install from it
# when there is no Makefile.
#
# This script is compatible with the BSD install script, but was written
# from scratch.  It can only install one file at a time, a restriction
# shared with many OS's install programs.


# set DOITPROG to echo to test this script

# Don't use :- since 4.3BSD and earlier shells don't like it.
doit="${DOITPROG-}"


# put in absolute paths if you don't have them in your path; or use env. vars.

mvprog="${MVPROG-mv}"
cpprog="${CPPROG-cp}"
chmodprog="${CHMODPROG-chmod}"
chownprog="${CHOWNPROG-chown}"
chgrpprog="${CHGRPPROG-chgrp}"
stripprog="${STRIPPROG-strip}"
rmprog="${RMPROG-rm}"
mkdirprog="${MKDIRPROG-mkdir}"

transformbasename=""
transform_arg=""
instcmd="$mvprog"
chmodcmd="$chmodprog 0755"
chowncmd=""
chgrpcmd=""
stripcmd=""
rmcmd="$rmprog -f"
mvcmd="$mvprog"
src=""
dst=""
dir_arg=""

while [ x"$1" != x ]; do
    case $1 in
	-c) instcmd="$cpprog"
	    shift
	    continue;;

	-d) dir_arg=true
	    shift
	    continue;;

	-m) chmodcmd="$chmodprog $2"
	    shift
	    shift
	    continue;;

	-o) chowncmd="$chownprog $2"
	    shift
	    shift
	    continue;;

	-g) chgrpcmd="$chgrpprog $2"
	    shift
	    shift
	    continue;;

	-s) stripcmd="$stripprog"
	    shift
	    continue;;

	-t=*) transformarg=`echo $1 | sed 's/-t=//'`
	    shift
	    continue;;

	-b=*) transformbasename=`echo $1 | sed 's/-b=//'`
	    shift
	    continue;;

	*)  if [ x"$src" = x ]
	    then
		src=$1
	    else
		# this colon is to work around a 386BSD /bin/sh bug
		:
		dst=$1
	    fi
	    shift
	    continue;;
    esac
done

if [ x"$src" = x ]
then
	echo "install:	no input file specified"
	exit 1
else
	true
fi

if [ x"$dir_arg" != x ]; then
	dst=$src
	src=""
	
	if [ -d $dst ]; then
		instcmd=:
		chmodcmd=""
	else
		instcmd=mkdir
	fi
else

# Waiting for this to be detected by the "$instcmd $src $dsttmp" command
# might cause directories to be created, which would be especially bad 
# if $src (and thus $dsttmp) contains '*'.

	if [ -f $src -o -d $src ]
	then
		true
	else
		echo "install:  $src does not exist"
		exit 1
	fi
	
	if [ x"$dst" = x ]
	then
		echo "install:	no destination specified"
		exit 1
	else
		true
	fi

# If destination is a directory, append the input filename; if your system
# does not like double slashes in filenames, you may need to add some logic

	if [ -d $dst ]
	then
		dst="$dst"/`basename $src`
	else
		true
	fi
fi

## this sed command emulates the dirname command
dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`

# Make sure that the destination directory exists.
#  this part is taken from Noah Friedman's mkinstalldirs script

# Skip lots of stat calls in the usual case.
if [ ! -d "$dstdir" ]; then
defaultIFS='	
'
IFS="${IFS-${defaultIFS}}"

oIFS="${IFS}"
# Some sh's can't handle IFS=/ for some reason.
IFS='%'
set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'`
IFS="${oIFS}"

pathcomp=''

while [ $# -ne 0 ] ; do
	pathcomp="${pathcomp}${1}"
	shift

	if [ ! -d "${pathcomp}" ] ;
        then
		$mkdirprog "${pathcomp}"
	else
		true
	fi

	pathcomp="${pathcomp}/"
done
fi

if [ x"$dir_arg" != x ]
then
	$doit $instcmd $dst &&

	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else true ; fi &&
	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else true ; fi &&
	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else true ; fi &&
	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else true ; fi
else

# If we're going to rename the final executable, determine the name now.

	if [ x"$transformarg" = x ] 
	then
		dstfile=`basename $dst`
	else
		dstfile=`basename $dst $transformbasename | 
			sed $transformarg`$transformbasename
	fi

# don't allow the sed command to completely eliminate the filename

	if [ x"$dstfile" = x ] 
	then
		dstfile=`basename $dst`
	else
		true
	fi

# Make a temp file name in the proper directory.

	dsttmp=$dstdir/#inst.$$#

# Move or copy the file name to the temp name

	$doit $instcmd $src $dsttmp &&

	trap "rm -f ${dsttmp}" 0 &&

# and set any options; do chmod last to preserve setuid bits

# If any of these fail, we abort the whole thing.  If we want to
# ignore errors from any of these, just make sure not to ignore
# errors from the above "$doit $instcmd $src $dsttmp" command.

	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else true;fi &&
	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else true;fi &&
	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else true;fi &&
	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else true;fi &&

# Now rename the file to the real destination.

	$doit $rmcmd -f $dstdir/$dstfile &&
	$doit $mvcmd $dsttmp $dstdir/$dstfile 

fi &&


exit 0
genometools-1.5.1/src/external/libtecla-1.6.1/ioutil.c000066400000000000000000000302601211610345200223470ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include 
#include 
#include 
#include 
#include 

#include "ioutil.h"

static int _io_pad_line(GlWriteFn *write_fn, void *data, int c, int n);

/*.......................................................................
 * Display a left-justified string over multiple terminal lines,
 * taking account of the specified width of the terminal. Optional
 * indentation and an option prefix string can be specified to be
 * displayed at the start of each new terminal line used, and if
 * needed, a single paragraph can be broken across multiple calls.
 * Note that literal newlines in the input string can be used to force
 * a newline at any point, and that in order to allow individual
 * paragraphs to be written using multiple calls to this function,
 * unless an explicit newline character is specified at the end of the
 * string, a newline will not be started at the end of the last word
 * in the string. Note that when a new line is started between two
 * words that are separated by spaces, those spaces are not output,
 * whereas when a new line is started because a newline character was
 * found in the string, only the spaces before the newline character
 * are discarded.
 *
 * Input:
 *  write_fn  GlWriteFn *  The callback function to use to write the
 *                         output.
 *  data           void *  A pointer to arbitrary data to be passed to
 *                         write_fn() whenever it is called.
 *  fp             FILE *  The stdio stream to write to.
 *  indentation     int    The number of fill characters to use to
 *                        indent the start of each new terminal line.
 *  prefix   const char *  An optional prefix string to write after the
 *                         indentation margin at the start of each new
 *                         terminal line. You can specify NULL if no
 *                         prefix is required.
 *  suffix   const char *  An optional suffix string to draw at the end
 *                         of the terminal line. The line will be padded
 *                         where necessary to ensure that the suffix ends
 *                         in the last column of the terminal line. If
 *                         no suffix is desired, specify NULL.
 *  fill_char       int    The padding character to use when indenting
 *                         and filling up to the suffix.
 *  term_width      int    The width of the terminal being written to.
 *  start           int    The number of characters already written to
 *                         the start of the current terminal line. This
 *                         is primarily used to allow individual
 *                         paragraphs to be written over multiple calls
 *                         to this function, but can also be used to
 *                         allow you to start the first line of a
 *                         paragraph with a different prefix or
 *                         indentation than those specified above.
 *  string   const char *  The string to be written.
 * Output:
 *  return          int    On error -1 is returned. Otherwise the
 *                         return value is the terminal column index at
 *                         which the cursor was left after writing the
 *                         final word in the string. Successful return
 *                         values can thus be passed verbatim to the
 *                         'start' arguments of subsequent calls to
 *                         _io_display_text() to allow the printing of a
 *                         paragraph to be broken across multiple calls
 *                         to _io_display_text().
 */
int _io_display_text(GlWriteFn *write_fn, void *data, int indentation,
		     const char *prefix, const char *suffix, int fill_char,
		     int term_width, int start, const char *string)
{
  int ndone;        /* The number of characters written from string[] */
  int nnew;         /* The number of characters to be displayed next */
  int was_space;    /* True if the previous character was a space or tab */
  int last = start; /* The column number of the last character written */
  int prefix_len;   /* The length of the optional line prefix string */
  int suffix_len;   /* The length of the optional line prefix string */
  int margin_width; /* The total number of columns used by the indentation */
                    /*  margin and the prefix string. */
  int i;
/*
 * Check the arguments?
 */
  if(!string || !write_fn) {
    errno = EINVAL;
    return -1;
  };
/*
 * Enforce sensible values on the arguments.
 */
  if(term_width < 0)
    term_width = 0;
  if(indentation > term_width)
    indentation = term_width;
  else if(indentation < 0)
    indentation = 0;
  if(start > term_width)
    start = term_width;
  else if(start < 0)
    start = 0;
/*
 * Get the length of the prefix string.
 */
  prefix_len = prefix ? strlen(prefix) : 0;
/*
 * Get the length of the suffix string.
 */
  suffix_len = suffix ? strlen(suffix) : 0;
/*
 * How many characters are devoted to indenting and prefixing each line?
 */
  margin_width = indentation + prefix_len;
/*
 * Write as many terminal lines as are needed to display the whole string.
 */
  for(ndone=0; string[ndone]; start=0) {
    last = start;
/*
 * Write spaces from the current position in the terminal line to the
 * width of the requested indentation margin.
 */
    if(indentation > 0 && last < indentation) {
      if(_io_pad_line(write_fn, data, fill_char, indentation - last))
	return -1;
      last = indentation;
    };
/*
 * If a prefix string has been specified, display it unless we have
 * passed where it should end in the terminal output line.
 */
    if(prefix_len > 0 && last < margin_width) {
      int pstart = last - indentation;
      int plen = prefix_len - pstart;
      if(write_fn(data, prefix+pstart, plen) != plen)
	return -1;
      last = margin_width;
    };
/*
 * Locate the end of the last complete word in the string before
 * (term_width - start) characters have been seen. To handle the case
 * where a single word is wider than the available space after the
 * indentation and prefix margins, always make sure that at least one
 * word is printed after the margin, regardless of whether it won't
 * fit on the line. The two exceptions to this rule are if an embedded
 * newline is found in the string or the end of the string is reached
 * before any word has been seen.
 */
    nnew = 0;
    was_space = 0;
    for(i=ndone; string[i] && (last+i-ndone < term_width - suffix_len ||
			   (nnew==0 && last==margin_width)); i++) {
      if(string[i] == '\n') {
	if(!was_space)
	  nnew = i-ndone;
	break;
      } else if(isspace((int) string[i])) {
	if(!was_space) {
	  nnew = i-ndone+1;
	  was_space = 1;
	};
      } else {
	was_space = 0;
      };
    };
/*
 * Does the end of the string delimit the last word that will fit on the
 * output line?
 */
    if(nnew==0 && string[i] == '\0')
      nnew = i-ndone;
/*
 * Write the new line.
 */
    if(write_fn(data, string+ndone, nnew) != nnew)
      return -1;
    ndone += nnew;
    last += nnew;
/*
 * Start a newline unless we have reached the end of the input string.
 * In the latter case, in order to give the caller the chance to
 * concatenate multiple calls to _io_display_text(), omit the newline,
 * leaving it up to the caller to write this.
 */
    if(string[ndone] != '\0') {
/*
 * If a suffix has been provided, pad out the end of the line with spaces
 * such that the suffix will end in the right-most terminal column.
 */
      if(suffix_len > 0) {
	int npad = term_width - suffix_len - last;
	if(npad > 0 && _io_pad_line(write_fn, data, fill_char, npad))
	  return -1;
	last += npad;
	if(write_fn(data, suffix, suffix_len) != suffix_len)
	  return -1;
	last += suffix_len;
      };
/*
 * Start a new line.
 */
      if(write_fn(data, "\n",  1) != 1)
	return -1;
/*
 * Skip any spaces and tabs that follow the last word that was written.
 */
      while(string[ndone] && isspace((int)string[ndone]) &&
	    string[ndone] != '\n')
	ndone++;
/*
 * If the terminating character was a literal newline character,
 * skip it in the input string, since we just wrote it.
 */
      if(string[ndone] == '\n')
	ndone++;
      last = 0;
    };
  };
/*
 * Return the column number of the last character printed.
 */
  return last;
}

/*.......................................................................
 * Write a given number of spaces to the specified stdio output string.
 *
 * Input:
 *  write_fn  GlWriteFn *  The callback function to use to write the
 *                         output.
 *  data           void *  A pointer to arbitrary data to be passed to
 *                         write_fn() whenever it is called.
 *  c               int    The padding character.
 *  n               int    The number of spaces to be written.
 * Output:
 *  return          int    0 - OK.
 *                         1 - Error.
 */
static int _io_pad_line(GlWriteFn *write_fn, void *data, int c, int n)
{
  enum {FILL_SIZE=20};
  char fill[FILL_SIZE+1];
/*
 * Fill the buffer with the specified padding character.
 */
  memset(fill, c, FILL_SIZE);
  fill[FILL_SIZE] = '\0';
/*
 * Write the spaces using the above literal string of spaces as
 * many times as needed to output the requested number of spaces.
 */
  while(n > 0) {
    int nnew = n <= FILL_SIZE ? n : FILL_SIZE;
    if(write_fn(data, fill, nnew) != nnew)
      return 1;
    n -= nnew;
  };
  return 0;
}

/*.......................................................................
 * The following is an output callback function which uses fwrite()
 * to write to the stdio stream specified via its callback data argument.
 *
 * Input:
 *  data     void *  The stdio stream to write to, specified via a
 *                   (FILE *) pointer cast to (void *).
 *  s  const char *  The string to be written.
 *  n         int    The length of the prefix of s[] to attempt to
 *                   write.
 * Output:
 *  return    int    The number of characters written from s[]. This
 *                   should normally be a number in the range 0 to n.
 *                   To signal that an I/O error occurred, return -1.
 */
GL_WRITE_FN(_io_write_stdio)
{
  int ndone;   /* The total number of characters written */
  int nnew;    /* The number of characters written in the latest write */
/*
 * The callback data is the stdio stream to write to.
 */
  FILE *fp = (FILE *) data;
/*
 * Because of signals we may need to do more than one write to output
 * the whole string.
 */
  for(ndone=0; ndone
#include 
#include 
#include 
#include 

#include "keytab.h"
#include "strngmem.h"
#include "getline.h"
#include "errmsg.h"
#include "hash.h"

/*
 * When allocating or reallocating the key-binding table, how
 * many entries should be added?
 */
#define KT_TABLE_INC 100

/*
 * Define the size of the hash table that is used to associate action
 * names with action functions. This should be a prime number.
 */
#define KT_HASH_SIZE 113

/*
 * Define a binary-symbol-table object.
 */
struct KeyTab {
  ErrMsg *err;            /* Information about the last error */
  int size;               /* The allocated dimension of table[] */
  int nkey;               /* The current number of members in the table */
  KeySym *table;          /* The table of lexically sorted key sequences */
  HashTable *actions;     /* The hash table of actions */
  StringMem *smem;        /* Memory for allocating strings */
};

static int _kt_extend_table(KeyTab *kt);
static int _kt_parse_keybinding_string(const char *keyseq,
				       char *binary, int *nc);
static int _kt_compare_strings(const char *s1, int n1, const char *s2, int n2);
static void _kt_assign_action(KeySym *sym, KtBinder binder, KtKeyFn *keyfn,
			      void *data);
static char _kt_backslash_escape(const char *string, const char **endp);
static int _kt_is_emacs_meta(const char *string);
static int _kt_is_emacs_ctrl(const char *string);
static KtKeyMatch _kt_locate_keybinding(KeyTab *kt, const char *binary_keyseq,
					int nc, int *first, int *last);

/*.......................................................................
 * Create a new key-binding symbol table.
 *
 * Output:
 *  return  KeyTab *  The new object, or NULL on error.
 */
KeyTab *_new_KeyTab(void)
{
  KeyTab *kt;  /* The object to be returned */
/*
 * Allocate the container.
 */
  kt = (KeyTab *) malloc(sizeof(KeyTab));
  if(!kt) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_KeyTab().
 */
  kt->err = NULL;
  kt->size = KT_TABLE_INC;
  kt->nkey = 0;
  kt->table = NULL;
  kt->actions = NULL;
  kt->smem = NULL;
/*
 * Allocate a place to record error messages.
 */
  kt->err = _new_ErrMsg();
  if(!kt->err)
    return _del_KeyTab(kt);
/*
 * Allocate the table.
 */
  kt->table = (KeySym *) malloc(sizeof(kt->table[0]) * kt->size);
  if(!kt->table) {
    errno = ENOMEM;
    return _del_KeyTab(kt);
  };
/*
 * Allocate a hash table of actions.
 */
  kt->actions = _new_HashTable(NULL, KT_HASH_SIZE, IGNORE_CASE, NULL, 0);
  if(!kt->actions)
    return _del_KeyTab(kt);
/*
 * Allocate a string allocation object. This allows allocation of
 * small strings without fragmenting the heap.
 */
  kt->smem = _new_StringMem(KT_TABLE_INC);
  if(!kt->smem)
    return _del_KeyTab(kt);
  return kt;
}

/*.......................................................................
 * Delete a KeyTab object.
 *
 * Input:
 *  kt   KeyTab *  The object to be deleted.
 * Output:
 *  return KeyTab *  The deleted object (always NULL).
 */
KeyTab *_del_KeyTab(KeyTab *kt)
{
  if(kt) {
    if(kt->table)
      free(kt->table);
    kt->actions = _del_HashTable(kt->actions);
    kt->smem = _del_StringMem(kt->smem, 1);
    kt->err = _del_ErrMsg(kt->err);
    free(kt);
  };
  return NULL;
}

/*.......................................................................
 * Increase the size of the table to accomodate more keys.
 *
 * Input:
 *  kt       KeyTab *  The table to be extended.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
static int _kt_extend_table(KeyTab *kt)
{
/*
 * Attempt to increase the size of the table.
 */
  KeySym *newtab = (KeySym *) realloc(kt->table, sizeof(kt->table[0]) *
				      (kt->size + KT_TABLE_INC));
/*
 * Failed?
 */
  if(!newtab) {
    _err_record_msg(kt->err, "Can't extend keybinding table", END_ERR_MSG);
    errno = ENOMEM;
    return 1;
  };
/*
 * Install the resized table.
 */
  kt->table = newtab;
  kt->size += KT_TABLE_INC;
  return 0;
}

/*.......................................................................
 * Add, update or remove a keybinding to the table.
 *
 * Input:
 *  kt           KeyTab *  The table to add the binding to.
 *  binder     KtBinder    The source of the binding.
 *  keyseq   const char *  The key-sequence to bind.
 *  action         char *  The action to associate with the key sequence, or
 *                         NULL to remove the action associated with the
 *                         key sequence.
 * Output:
 *  return          int    0 - OK.
 *                         1 - Error.
 */
int _kt_set_keybinding(KeyTab *kt, KtBinder binder, const char *keyseq,
		       const char *action)
{
  KtKeyFn *keyfn; /* The action function */
  void *data;     /* The callback data of the action function */
/*
 * Check arguments.
 */
  if(kt==NULL || !keyseq) {
    errno = EINVAL;
    if(kt)
      _err_record_msg(kt->err, "NULL argument(s)", END_ERR_MSG);
    return 1;
  };
/*
 * Lookup the function that implements the specified action.
 */
  if(!action) {
    keyfn = 0;
    data = NULL;
  } else {
    Symbol *sym = _find_HashSymbol(kt->actions, action);
    if(!sym) {
      _err_record_msg(kt->err, "Unknown key-binding action: ", action,
		      END_ERR_MSG);
      errno = EINVAL;
      return 1;
    };
    keyfn = (KtKeyFn *) sym->fn;
    data = sym->data;
  };
/*
 * Record the action in the table.
 */
  return _kt_set_keyfn(kt, binder, keyseq, keyfn, data);
}

/*.......................................................................
 * Add, update or remove a keybinding to the table, specifying an action
 * function directly.
 *
 * Input:
 *  kt       KeyTab *  The table to add the binding to.
 *  binder KtBinder    The source of the binding.
 *  keyseq     char *  The key-sequence to bind.
 *  keyfn   KtKeyFn *  The action function, or NULL to remove any existing
 *                     action function.
 *  data       void *  A pointer to anonymous data to be passed to keyfn
 *                     whenever it is called.
 * Output:
 *  return     int    0 - OK.
 *                    1 - Error.
 */
int _kt_set_keyfn(KeyTab *kt, KtBinder binder, const char *keyseq,
		  KtKeyFn *keyfn, void *data)
{
  const char *kptr;  /* A pointer into keyseq[] */
  char *binary;      /* The binary version of keyseq[] */
  int nc;            /* The number of characters in binary[] */
  int first,last;    /* The first and last entries in the table which */
                     /*  minimally match. */
  int size;          /* The size to allocate for the binary string */
  int i;
/*
 * Check arguments.
 */
  if(kt==NULL || !keyseq) {
    errno = EINVAL;
    if(kt)
      _err_record_msg(kt->err, "NULL argument(s)", END_ERR_MSG);
    return 1;
  };
/*
 * Work out a pessimistic estimate of how much space will be needed
 * for the binary copy of the string, noting that binary meta characters
 * embedded in the input string get split into two characters.
 */
  for(size=0,kptr = keyseq; *kptr; kptr++)
    size += IS_META_CHAR(*kptr) ? 2 : 1;
/*
 * Allocate a string that has the length of keyseq[].
 */
  binary = _new_StringMemString(kt->smem, size + 1);
  if(!binary) {
    errno = ENOMEM;
    _err_record_msg(kt->err, "Insufficient memory to record key sequence",
		    END_ERR_MSG);
    return 1;
  };
/*
 * Convert control and octal character specifications to binary characters.
 */
  if(_kt_parse_keybinding_string(keyseq, binary, &nc)) {
    binary = _del_StringMemString(kt->smem, binary);
    return 1;
  };
/*
 * Lookup the position in the table at which to insert the binding.
 */
  switch(_kt_locate_keybinding(kt, binary, nc, &first, &last)) {
/*
 * If an exact match for the key-sequence is already in the table,
 * simply replace its binding function (or delete the entry if
 * the new binding is 0).
 */
  case KT_EXACT_MATCH:
    if(keyfn) {
      _kt_assign_action(kt->table + first, binder, keyfn, data);
    } else {
      _del_StringMemString(kt->smem, kt->table[first].keyseq);
      memmove(kt->table + first, kt->table + first + 1,
	      (kt->nkey - first - 1) * sizeof(kt->table[0]));
      kt->nkey--;
    };
    binary = _del_StringMemString(kt->smem, binary);
    break;
/*
 * If an ambiguous match has been found and we are installing a
 * callback, then our new key-sequence would hide all of the ambiguous
 * matches, so we shouldn't allow it.
 */
  case KT_AMBIG_MATCH:
    if(keyfn) {
      _err_record_msg(kt->err, "Can't bind \"", keyseq,
		      "\", because it is a prefix of another binding",
		      END_ERR_MSG);
      binary = _del_StringMemString(kt->smem, binary);
      errno = EPERM;
      return 1;
    };
    break;
/*
 * If the entry doesn't exist, create it.
 */
  case KT_NO_MATCH:
/*
 * Add a new binding?
 */
    if(keyfn) {
      KeySym *sym;
/*
 * We will need a new entry, extend the table if needed.
 */
      if(kt->nkey + 1 > kt->size) {
	if(_kt_extend_table(kt)) {
	  binary = _del_StringMemString(kt->smem, binary);
	  return 1;
	};
      };
/*
 * Make space to insert the new key-sequence before 'last'.
 */
      if(last < kt->nkey) {
	memmove(kt->table + last + 1, kt->table + last,
		(kt->nkey - last) * sizeof(kt->table[0]));
      };
/*
 * Insert the new binding in the vacated position.
 */
      sym = kt->table + last;
      sym->keyseq = binary;
      sym->nc = nc;
      for(i=0; iactions + i;
	action->fn = 0;
	action->data = NULL;
      };
      sym->binder = -1;
      _kt_assign_action(sym, binder, keyfn, data);
      kt->nkey++;
    };
    break;
  case KT_BAD_MATCH:
    binary = _del_StringMemString(kt->smem, binary);
    return 1;
    break;
  };
  return 0;
}

/*.......................................................................
 * Perform a min-match lookup of a key-binding.
 *
 * Input:
 *  kt          KeyTab *   The keybinding table to lookup in.
 *  binary_keyseq char *   The binary key-sequence to lookup.
 *  nc             int     the number of characters in keyseq[].
 * Input/Output:
 *  first,last     int *   If there is an ambiguous or exact match, the indexes
 *                         of the first and last symbols that minimally match
 *                         will be assigned to *first and *last respectively.
 *                         If there is no match, then first and last will
 *                         bracket the location where the symbol should be
 *                         inserted.
 * Output:
 *  return  KtKeyMatch     One of the following enumerators:
 *                          KT_EXACT_MATCH - An exact match was found.
 *                          KT_AMBIG_MATCH - An ambiguous match was found.
 *                          KT_NO_MATCH    - No match was found.
 *                          KT_BAD_MATCH   - An error occurred while searching.
 */
static KtKeyMatch _kt_locate_keybinding(KeyTab *kt, const char *binary_keyseq,
					int nc, int *first, int *last)
{
  int mid;     /* The index at which to bisect the table */
  int bot;     /* The lowest index of the table not searched yet */
  int top;     /* The highest index of the table not searched yet */
  int test;    /* The return value of strcmp() */
/*
 * Perform a binary search for the key-sequence.
 */
  bot = 0;
  top = kt->nkey - 1;
  while(top >= bot) {
    mid = (top + bot)/2;
    test = _kt_compare_strings(kt->table[mid].keyseq, kt->table[mid].nc,
			   binary_keyseq, nc);
    if(test > 0)
      top = mid - 1;
    else if(test < 0)
      bot = mid + 1;
    else {
      *first = *last = mid;
      return KT_EXACT_MATCH;
    };
  };
/*
 * An exact match wasn't found, but top is the index just below the
 * index where a match would be found, and bot is the index just above
 * where the match ought to be found.
 */
  *first = top;
  *last = bot;
/*
 * See if any ambiguous matches exist, and if so make *first and *last
 * refer to the first and last matches.
 */
  if(*last < kt->nkey && kt->table[*last].nc > nc &&
     _kt_compare_strings(kt->table[*last].keyseq, nc, binary_keyseq, nc)==0) {
    *first = *last;
    while(*last+1 < kt->nkey && kt->table[*last+1].nc > nc &&
	  _kt_compare_strings(kt->table[*last+1].keyseq, nc, binary_keyseq, nc)==0)
      (*last)++;
    return KT_AMBIG_MATCH;
  };
/*
 * No match.
 */
  return KT_NO_MATCH;
}

/*.......................................................................
 * Lookup the sub-array of key-bindings who's key-sequences minimally
 * match a given key-sequence.
 *
 * Input:
 *  kt          KeyTab *   The keybinding table to lookup in.
 *  binary_keyseq char *   The binary key-sequence to lookup.
 *  nc             int     the number of characters in keyseq[].
 * Input/Output:
 *  matches     KeySym **  The array of minimally matching symbols
 *                         can be found in (*matches)[0..nmatch-1], unless
 *                         no match was found, in which case *matches will
 *                         be set to NULL.
 *  nmatch         int     The number of ambiguously matching symbols. This
 *                         will be 0 if there is no match, 1 for an exact
 *                         match, and a number greater than 1 for an ambiguous
 *                         match.
 * Output:
 *  return  KtKeyMatch     One of the following enumerators:
 *                          KT_EXACT_MATCH - An exact match was found.
 *                          KT_AMBIG_MATCH - An ambiguous match was found.
 *                          KT_NO_MATCH    - No match was found.
 *                          KT_BAD_MATCH   - An error occurred while searching.
 */
KtKeyMatch _kt_lookup_keybinding(KeyTab *kt, const char *binary_keyseq,
				 int nc, KeySym **matches, int *nmatch)
{
  KtKeyMatch status;  /* The return status */
  int first,last;     /* The indexes of the first and last matching entry */
                      /* in the symbol table. */
/*
 * Check the arguments.
 */
  if(!kt || !binary_keyseq || !matches || !nmatch || nc < 0) {
    errno = EINVAL;
    if(kt)
      _err_record_msg(kt->err, "NULL argument(s)", END_ERR_MSG);
    return KT_BAD_MATCH;
  };
/*
 * Lookup the indexes of the binding-table entries that bracket the
 * target key-sequence.
 */
  status = _kt_locate_keybinding(kt, binary_keyseq, nc, &first, &last);
/*
 * Translate the indexes into the corresponding subarray of matching
 * table entries.
 */
  switch(status) {
  case KT_EXACT_MATCH:
  case KT_AMBIG_MATCH:
    *matches = kt->table + first;
    *nmatch = last - first + 1;
    break;
  default:
    *matches = NULL;
    *nmatch = 0;
    break;
  };
  return status;
}

/*.......................................................................
 * Convert a keybinding string into a uniq binary representation.
 *
 * Control characters can be given directly in their binary form,
 * expressed as either ^ or C-, followed by the character, expressed in
 * octal, like \129 or via C-style backslash escapes, with the addition
 * of '\E' to denote the escape key. Similarly, meta characters can be
 * given directly in binary or expressed as M- followed by the character.
 * Meta characters are recorded as two characters in the binary output
 * string, the first being the escape key, and the second being the key
 * that was modified by the meta key. This means that binding to
 * \EA or ^[A or M-A are all equivalent.
 *
 * Input:
 *  keyseq   char *  The key sequence being added.
 * Input/Output:
 *  binary   char *  The binary version of the key sequence will be
 *                   assigned to binary[], which must have at least
 *                   as many characters as keyseq[] plus the number
 *                   of embedded binary meta characters.
 *  nc        int *  The number of characters assigned to binary[]
 *                   will be recorded in *nc.
 * Output:
 *  return    int    0 - OK.
 *                   1 - Error.
 */
static int _kt_parse_keybinding_string(const char *keyseq, char *binary,
				       int *nc)
{
  const char *iptr = keyseq;   /* Pointer into keyseq[] */
  char *optr = binary;         /* Pointer into binary[] */
  char c;                      /* An intermediate character */
/*
 * Parse the input characters until they are exhausted or the
 * output string becomes full.
 */
  while(*iptr) {
/*
 * Check for special characters.
 */
    switch(*iptr) {
    case '^':        /* A control character specification */
/*
 * Convert the caret expression into the corresponding control
 * character unless no character follows the caret, in which case
 * record a literal caret.
 */
      if(iptr[1]) {
/*
 * Get the next, possibly escaped, character.
 */
	if(iptr[1] == '\\') {
	  c = _kt_backslash_escape(iptr+2, &iptr);
	} else {
	  c = iptr[1];
	  iptr += 2;
	};
/*
 * Convert the character to a control character.
 */
	*optr++ = MAKE_CTRL(c);
      } else {
	*optr++ = *iptr++;
      };
      break;
/*
 * A backslash-escaped character?
 */
    case '\\':
/*
 * Convert the escape sequence to a binary character.
 */
      *optr++ = _kt_backslash_escape(iptr+1, &iptr);
      break;
/*
 * Possibly an emacs-style meta character?
 */
    case 'M':
      if(_kt_is_emacs_meta(iptr)) {
	*optr++ = GL_ESC_CHAR;
	iptr += 2;
      } else {
	*optr++ = *iptr++;
      };
      break;
/*
 * Possibly an emacs-style control character specification?
 */
    case 'C':
      if(_kt_is_emacs_ctrl(iptr)) {
	*optr++ = MAKE_CTRL(iptr[2]);
	iptr += 3;
      } else {
	*optr++ = *iptr++;
      };
      break;
    default:

/*
 * Convert embedded meta characters into an escape character followed
 * by the meta-unmodified character.
 */
      if(IS_META_CHAR(*iptr)) {
	*optr++ = GL_ESC_CHAR;
	*optr++ = META_TO_CHAR(*iptr);
	iptr++;
/*
 * To allow keysequences that start with printable characters to
 * be distinguished from the cursor-key keywords, prepend a backslash
 * to the former. This same operation is performed in gl_interpret_char()
 * before looking up a keysequence that starts with a printable character.
 */
      } else if(iptr==keyseq && !IS_CTRL_CHAR(*iptr) &&
		strcmp(keyseq, "up") != 0 && strcmp(keyseq, "down") != 0 &&
		strcmp(keyseq, "left") != 0 && strcmp(keyseq, "right") != 0) {
	*optr++ = '\\';
	*optr++ = *iptr++;
      } else {
	*optr++ = *iptr++;
      };
    };
  };
/*
 * How many characters were placed in the output array?
 */
  *nc = optr - binary;
  return 0;
}

/*.......................................................................
 * Add, remove or modify an action.
 *
 * Input:
 *  kt     KeyTab *  The key-binding table.
 *  action   char *  The name of the action.
 *  fn    KtKeyFn *  The function that implements the action, or NULL
 *                   to remove an existing action.
 *  data     void *  A pointer to arbitrary callback data to pass to the
 *                   action function whenever it is called.
 * Output:
 *  return    int    0 - OK.
 *                   1 - Error.
 */
int _kt_set_action(KeyTab *kt, const char *action, KtKeyFn *fn, void *data)
{
  Symbol *sym;   /* The symbol table entry of the action */
/*
 * Check the arguments.
 */
  if(!kt || !action) {
    errno = EINVAL;
    if(kt)
      _err_record_msg(kt->err, "NULL argument(s)", END_ERR_MSG);
    return 1;
  };
/*
 * If no function was provided, delete an existing action.
 */
  if(!fn) {
    sym = _del_HashSymbol(kt->actions, action);
    return 0;
  };
/*
 * If the action already exists, replace its action function.
 */
  sym = _find_HashSymbol(kt->actions, action);
  if(sym) {
    sym->fn = (void (*)(void))fn;
    sym->data = data;
    return 0;
  };
/*
 * Add a new action.
 */
  if(!_new_HashSymbol(kt->actions, action, 0, (void (*)(void))fn, data, 0)) {
    _err_record_msg(kt->err, "Insufficient memory to record key-binding action",
		    END_ERR_MSG);
    return 1;
  };
  return 0;
}

/*.......................................................................
 * Compare two strings of specified length which may contain embedded
 * ascii NUL's.
 *
 * Input:
 *  s1       char *  The first of the strings to be compared.
 *  n1        int    The length of the string in s1.
 *  s2       char *  The second of the strings to be compared.
 *  n2        int    The length of the string in s2.
 * Output:
 *  return    int    < 0 if(s1 < s2)
 *                     0 if(s1 == s2)
 *                   > 0 if(s1 > s2)
 */
static int _kt_compare_strings(const char *s1, int n1, const char *s2, int n2)
{
  int i;
/*
 * Find the first character where the two strings differ.
 */
  for(i=0; i= KTB_NBIND)
    return;
/*
 * Record the action according to its source.
 */
  action = sym->actions + binder;
  action->fn = keyfn;
  action->data = data;
/*
 * Find the highest priority binding source that has supplied an
 * action. Note that the actions[] array is ordered in order of
 * descreasing priority, so the first entry that contains a function
 * is the one to use.
 */
  for(i=0; iactions[i].fn; i++)
    ;
/*
 * Record the index of this action for use during lookups.
 */
  sym->binder = i < KTB_NBIND ? i : -1;
  return;
}

/*.......................................................................
 * Remove all key bindings that came from a specified source.
 *
 * Input:
 *  kt        KeyTab *  The table of key bindings.
 *  binder  KtBinder    The source of the bindings to be cleared.
 */
void _kt_clear_bindings(KeyTab *kt, KtBinder binder)
{
  int oldkey;   /* The index of a key in the original binding table */
  int newkey;   /* The index of a key in the updated binding table */
/*
 * If there is no table, then no bindings exist to be deleted.
 */
  if(!kt)
    return;
/*
 * Clear bindings of the given source.
 */
  for(oldkey=0; oldkeynkey; oldkey++)
    _kt_assign_action(kt->table + oldkey, binder, 0, NULL);
/*
 * Delete entries that now don't have a binding from any source.
 */
  newkey = 0;
  for(oldkey=0; oldkeynkey; oldkey++) {
    KeySym *sym = kt->table + oldkey;
    if(sym->binder < 0) {
      _del_StringMemString(kt->smem, sym->keyseq);
    } else {
      if(oldkey != newkey)
	kt->table[newkey] = *sym;
      newkey++;
    };
  };
/*
 * Record the number of keys that were kept.
 */
  kt->nkey = newkey;
  return;
}

/*.......................................................................
 * Translate a backslash escape sequence to a binary character.
 *
 * Input:
 *  string  const char *   The characters that follow the backslash.
 * Input/Output:
 *  endp    const char **  If endp!=NULL, on return *endp will be made to
 *                         point to the character in string[] which follows
 *                         the escape sequence.
 * Output:
 *  return        char     The binary character.
 */
static char _kt_backslash_escape(const char *string, const char **endp)
{
  char c;  /* The output character */
/*
 * Is the backslash followed by one or more octal digits?
 */
  switch(*string) {
  case '0': case '1': case '2': case '3':
  case '4': case '5': case '6': case '7':
    c = strtol(string, (char **)&string, 8);
    break;
  case 'a':
    c = '\a';
    string++;
    break;
  case 'b':
    c = '\b';
    string++;
    break;
  case 'e': case 'E': /* Escape */
    c = GL_ESC_CHAR;
    string++;
    break;
  case 'f':
    c = '\f';
    string++;
    break;
  case 'n':
    c = '\n';
    string++;
    break;
  case 'r':
    c = '\r';
    string++;
    break;
  case 't':
    c = '\t';
    string++;
    break;
  case 'v':
    c = '\v';
    string++;
    break;
  case '\0':
    c = '\\';
    break;
  default:
    c = *string++;
    break;
  };
/*
 * Report the character which follows the escape sequence.
 */
  if(endp)
    *endp = string;
  return c;
}

/*.......................................................................
 * Return non-zero if the next two characters are M- and a third character
 * follows. Otherwise return 0.
 *
 * Input:
 *  string   const char *  The sub-string to scan.
 * Output:
 *  return          int    1 - The next two characters are M- and these
 *                             are followed by at least one character.
 *                         0 - The next two characters aren't M- or no
 *                             character follows a M- pair.
 */
static int _kt_is_emacs_meta(const char *string)
{
  return *string++ == 'M' && *string++ == '-' && *string;
}

/*.......................................................................
 * Return non-zero if the next two characters are C- and a third character
 * follows. Otherwise return 0.
 *
 * Input:
 *  string   const char *  The sub-string to scan.
 * Output:
 *  return          int    1 - The next two characters are C- and these
 *                             are followed by at least one character.
 *                         0 - The next two characters aren't C- or no
 *                             character follows a C- pair.
 */
static int _kt_is_emacs_ctrl(const char *string)
{
  return *string++ == 'C' && *string++ == '-' && *string;
}

/*.......................................................................
 * Merge an array of bindings with existing bindings.
 *
 * Input:
 *  kt                    KeyTab *  The table of key bindings.
 *  binder              KtBinder    The source of the bindings.
 *  bindings  const KtKeyBinding *  The array of bindings.
 *  n                        int    The number of bindings in bindings[].
 * Output:
 *  return                   int    0 - OK.
 *                                  1 - Error.
 */
int _kt_add_bindings(KeyTab *kt, KtBinder binder, const KtKeyBinding *bindings,
		     unsigned n)
{
  int i;
/*
 * Check the arguments.
 */
  if(!kt || !bindings) {
    errno = EINVAL;
    if(kt)
      _err_record_msg(kt->err, "NULL argument(s)", END_ERR_MSG);
    return 1;
  };
/*
 * Install the array of bindings.
 */
  for(i=0; ierr, "NULL argument(s)", END_ERR_MSG);
    return 1;
  };
/*
 * Lookup the symbol table entry of the action.
 */
  sym = _find_HashSymbol(kt->actions, action);
  if(!sym)
    return 1;
/*
 * Return the function and ccallback data associated with the action.
 */
  if(fn)
    *fn = (KtKeyFn *) sym->fn;
  if(data)
    *data = sym->data;
  return 0;
}

/*.......................................................................
 * Return extra information (ie. in addition to that provided by errno)
 * about the last error to occur in any of the public functions of this
 * module.
 *
 * Input:
 *  kt          KeyTab *  The table of key bindings.
 * Output:
 *  return  const char *  A pointer to the internal buffer in which
 *                        the error message is temporarily stored.
 */
const char *_kt_last_error(KeyTab *kt)
{
  return kt ? _err_get_msg(kt->err) : "NULL KeyTab argument";
}
genometools-1.5.1/src/external/libtecla-1.6.1/keytab.h000066400000000000000000000127601211610345200223330ustar00rootroot00000000000000#ifndef keytab_h
#define keytab_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include "libtecla.h"

/*-----------------------------------------------------------------------*
 * This module defines a binary-search symbol table of key-bindings.     *
 *-----------------------------------------------------------------------*/

/*
 * All key-binding functions are defined as follows.
 *
 * Input:
 *  gl    GetLine *  The resource object of this library.
 *  count     int    A positive repeat count specified by the user,
 *                   or 1. Action functions should ignore this if
 *                   repeating the action multiple times isn't
 *                   appropriate.
 *  data     void *  A pointer to action-specific data,
 *                   cast to (void *).
 * Output:
 *  return    int    0 - OK.
 *                   1 - Error.
 */
#define KT_KEY_FN(fn) int (fn)(__attribute__ ((unused)) GetLine *gl, __attribute__ ((unused)) int count, __attribute__ ((unused)) void *data)

typedef KT_KEY_FN(KtKeyFn);

/*
 * Allow the association of arbitrary callback data with each action
 * function.
 */
typedef struct {
  KtKeyFn *fn;          /* The acion function */
  void *data;           /* A pointer to arbitrary data to be passed to */
                        /*  fn() whenever it is called. */
} KtAction;

/*
 * Enumerate the possible sources of key-bindings in order of decreasing
 * priority.
 */
typedef enum {
  KTB_USER,         /* This is a binding being set by the user */
  KTB_NORM,         /* This is the default binding set by the library */
  KTB_TERM,         /* This is a binding taken from the terminal settings */
/* The following entry must always be last */
  KTB_NBIND         /* The number of binding sources listed above */
} KtBinder;

/*
 * Define an entry of a key-binding binary symbol table.
 */
typedef struct {
  char *keyseq;                /* The key sequence that triggers the macro */
  int nc;                      /* The number of characters in keyseq[] */
  KtAction actions[KTB_NBIND]; /* Bindings from different sources */
  int binder;                  /* The index of the highest priority element */
                               /*  of actions[] that has been assigned an */
                               /*  action function, or -1 if none have. */
} KeySym;

/*
 * Provide an opaque type alias to the symbol table container.
 */
typedef struct KeyTab KeyTab;

/*
 * Create a new symbol table.
 */
KeyTab *_new_KeyTab(void);

/*
 * Delete the symbol table.
 */
KeyTab *_del_KeyTab(KeyTab *kt);

int _kt_set_keybinding(KeyTab *kt, KtBinder binder,
		       const char *keyseq, const char *action);
int _kt_set_keyfn(KeyTab *kt, KtBinder binder, const char *keyseq,
		  KtKeyFn *fn, void *data);

int _kt_set_action(KeyTab *kt, const char *action, KtKeyFn *fn, void *data);

/*
 * Lookup the function that implements a given action.
 */
int _kt_lookup_action(KeyTab *kt, const char *action,
		      KtKeyFn **fn, void **data);

typedef enum {
  KT_EXACT_MATCH,   /* An exact match was found */
  KT_AMBIG_MATCH,   /* An ambiguous match was found */
  KT_NO_MATCH,      /* No match was found */
  KT_BAD_MATCH      /* An error occurred while searching */
} KtKeyMatch;

KtKeyMatch _kt_lookup_keybinding(KeyTab *kt, const char *binary_keyseq,
				 int nc, KeySym **matches, int *nmatch);

/*
 * Remove all key bindings that came from a specified source.
 */
void _kt_clear_bindings(KeyTab *kt, KtBinder binder);

/*
 * When installing an array of keybings each binding is defined by
 * an element of the following type:
 */
typedef struct {
  const char *keyseq;   /* The sequence of keys that trigger this binding */
  const char *action;   /* The name of the action function that is triggered */
} KtKeyBinding;

/*
 * Merge an array of bindings with existing bindings.
 */
int _kt_add_bindings(KeyTab *kt, KtBinder binder, const KtKeyBinding *bindings,
		     unsigned n);

/*
 * Get information about the last error in this module.
 */
const char *_kt_last_error(KeyTab *kt);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/libtecla.h000066400000000000000000002436351211610345200226420ustar00rootroot00000000000000#ifndef libtecla_h
#define libtecla_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#ifdef __cplusplus
extern "C" {
#endif

#include    /* FILE * */
#include   /* size_t */
#include     /* time_t */
#include   /* struct sigaction */

/*
 * The following are the three components of the libtecla version number.
 * Note that it is better to use the libtecla_version() function than these
 * macros since the macros only tell you which version of the library your
 * code was compiled against, whereas the libtecla_version() function
 * tells you which version of the shared tecla library your program is
 * actually linked to.
 */
#define TECLA_MAJOR_VER 1
#define TECLA_MINOR_VER 6
#define TECLA_MICRO_VER 1

/*.......................................................................
 * Query the version number of the tecla library.
 *
 * Input:
 *  major    int *   The major version number of the library
 *                   will be assigned to *major. This number is
 *                   only incremented when a change to the library is
 *                   made that breaks binary (shared library) and/or
 *                   compilation backwards compatibility.
 *  minor    int *   The minor version number of the library
 *                   will be assigned to *minor. This number is
 *                   incremented whenever new functions are added to
 *                   the public API.
 *  micro    int *   The micro version number of the library will be
 *                   assigned to *micro. This number is incremented
 *                   whenever internal changes are made that don't
 *                   change the public API, such as bug fixes and
 *                   performance enhancements.
 */
void libtecla_version(int *major, int *minor, int *micro);

/*-----------------------------------------------------------------------
 * The getline module provides interactive command-line input, recall
 * and editing by users at terminals. See the gl_getline(3) man page for
 * more details.
 *-----------------------------------------------------------------------*/

/*
 * Provide an opaque handle for the resource object that is defined in
 * getline.h.
 */
typedef struct GetLine GetLine;

/*
 * The following two functions are used to create and delete the
 * resource objects that are used by the gl_getline() function.
 */
GetLine *new_GetLine(size_t linelen, size_t histlen);
GetLine *del_GetLine(GetLine *gl);

/*
 * Read a line into an internal buffer of gl.
 */
char *gl_get_line(GetLine *gl, const char *prompt, const char *start_line,
		  int start_pos);

/*.......................................................................
 * Prompt the user for a single-character reply.
 *
 * Input:
 *  gl       GetLine *  A resource object returned by new_GetLine().
 *  prompt      char *  The prompt to prefix the query with, or NULL
 *                      to reuse the previous prompt.
 *  defchar     char    The character to substitute if the
 *                      user simply hits return, or '\n' if you don't
 *                      need to substitute anything.
 * Output:
 *  return       int    The character that was read, or EOF if the read
 *                      had to be aborted (in which case you can call
 *                      gl_return_status() to find out why).
 */
int gl_query_char(GetLine *gl, const char *prompt, char defchar);

/*.......................................................................
 * Read a single uninterpretted character from the user, without
 * displaying anything.
 *
 * Input:
 *  gl     GetLine *  A resource object previously returned by
 *                    new_GetLine().
 * Output:
 *  return     int    The character that was read, or EOF if the read
 *                    had to be aborted (in which case you can call
 *                    gl_return_status() to find out why).
 */
int gl_read_char(GetLine *gl);

/*
 * Configure the application specific and/or user-specific behavior of
 * gl_get_line().
 */
int gl_configure_getline(GetLine *gl, const char *app_string,
			 const char *app_file, const char *user_file);

/*
 * The following enumerators specify the origin of a key binding, and
 * are listed in order of decreasing priority, such that user-specified
 * key-bindings take precedence over application default bindings.
 */
typedef enum {
  GL_USER_KEY,  /* A key-binding specified by the user */
  GL_APP_KEY    /* A key-binding specified by the application */
} GlKeyOrigin;

/*
 * Bind a key sequence to a given action. If action==NULL, unbind the
 * key-sequence.
 */
int gl_bind_keyseq(GetLine *gl, GlKeyOrigin origin, const char *keyseq,
		   const char *action);

/*-----------------------------------------------------------------------
 * The file-expansion module provides facilities for expanding ~user/ and
 * $envvar expressions, and for expanding glob-style wildcards.
 * See the ef_expand_file(3) man page for more details.
 *-----------------------------------------------------------------------*/

/*
 * ExpandFile objects contain the resources needed to expand pathnames.
 */
typedef struct ExpandFile ExpandFile;

/*
 * The following functions are used to create and delete the resource
 * objects that are used by the ef_expand_file() function.
 */
ExpandFile *new_ExpandFile(void);
ExpandFile *del_ExpandFile(ExpandFile *ef);

/*
 * A container of the following type is returned by ef_expand_file().
 */
typedef struct {
  int exists;       /* True if the files in files[] currently exist. */
                    /*  This only time that this may not be true is if */
                    /*  the input filename didn't contain any wildcards */
                    /*  and thus wasn't matched against existing files. */
                    /*  In this case the single entry in 'nfile' may not */
                    /*  refer to an existing file. */
  int nfile;        /* The number of files in files[] */
  char **files;     /* An array of 'nfile' filenames. */
} FileExpansion;

/* 
 * The ef_expand_file() function expands a specified pathname, converting
 * ~user/ and ~/ patterns at the start of the pathname to the
 * corresponding home directories, replacing $envvar with the value of
 * the corresponding environment variable, and then, if there are any
 * wildcards, matching these against existing filenames.
 *
 * If no errors occur, a container is returned containing the array of
 * files that resulted from the expansion. If there were no wildcards
 * in the input pathname, this will contain just the original pathname
 * after expansion of ~ and $ expressions. If there were any wildcards,
 * then the array will contain the files that matched them. Note that
 * if there were any wildcards but no existing files match them, this
 * is counted as an error and NULL is returned.
 *
 * The supported wildcards and their meanings are:
 *  *        -  Match any sequence of zero or more characters.
 *  ?        -  Match any single character.
 *  [chars]  -  Match any single character that appears in 'chars'.
 *              If 'chars' contains an expression of the form a-b,
 *              then any character between a and b, including a and b,
 *              matches. The '-' character looses its special meaning
 *              as a range specifier when it appears at the start
 *              of the sequence of characters.
 *  [^chars] -  The same as [chars] except that it matches any single
 *              character that doesn't appear in 'chars'.
 *
 * Wildcard expressions are applied to individual filename components.
 * They don't match across directory separators. A '.' character at
 * the beginning of a filename component must also be matched
 * explicitly by a '.' character in the input pathname, since these
 * are UNIX's hidden files.
 *
 * Input:
 *  fe         ExpandFile *  The pathname expansion resource object.
 *  path       const char *  The path name to be expanded.
 *  pathlen           int    The length of the suffix of path[] that
 *                           constitutes the filename to be expanded,
 *                           or -1 to specify that the whole of the
 *                           path string should be used.
 * Output:
 *  return  FileExpansion *  A pointer to a results container within the
 *                           given ExpandFile object. This contains an
 *                           array of the pathnames that resulted from
 *                           expanding ~ and $ expressions and from
 *                           matching any wildcards, sorted into lexical
 *                           order.
 *
 *                           This container and its contents will be
 *                           recycled on subsequent calls, so if you need
 *                           to keep the results of two successive runs,
 *                           you will either have to allocate a private
 *                           copy of the array, or use two ExpandFile
 *                           objects.
 *
 *                           On error, NULL is returned. A description
 *                           of the error can be acquired by calling the
 *                           ef_last_error() function.
 */
FileExpansion *ef_expand_file(ExpandFile *ef, const char *path, int pathlen);

/*.......................................................................
 * Print out an array of matching files.
 *
 * Input:
 *  result  FileExpansion *   The container of the sorted array of
 *                            expansions.
 *  fp               FILE *   The output stream to write to.
 *  term_width        int     The width of the terminal.
 * Output:
 *  return            int     0 - OK.
 *                            1 - Error.
 */
int ef_list_expansions(FileExpansion *result, FILE *fp, int term_width);

/*
 * The ef_last_error() function returns a description of the last error
 * that occurred in a call ef_expand_file(). Note that this message is
 * contained in an array which is allocated as part of *ef, and its
 * contents thus potentially change on every call to ef_expand_file().
 */
const char *ef_last_error(ExpandFile *ef);

/*-----------------------------------------------------------------------
 * The WordCompletion module is used for completing incomplete words, such
 * as filenames. Programs can use functions within this module to register
 * their own customized completion functions.
 *-----------------------------------------------------------------------*/

/*
 * Ambiguous completion matches are recorded in objects of the
 * following type.
 */
typedef struct WordCompletion WordCompletion;

/*
 * Create a new completion object.
 */
WordCompletion *new_WordCompletion(void);

/*
 * Delete a redundant completion object.
 */
WordCompletion *del_WordCompletion(WordCompletion *cpl);

/*.......................................................................
 * Callback functions declared and prototyped using the following macro
 * are called upon to return an array of possible completion suffixes
 * for the token that precedes a specified location in the given
 * input line. It is up to this function to figure out where the token
 * starts, and to call cpl_add_completion() to register each possible
 * completion before returning.
 *
 * Input:
 *  cpl  WordCompletion *  An opaque pointer to the object that will
 *                         contain the matches. This should be filled
 *                         via zero or more calls to cpl_add_completion().
 *  data           void *  The anonymous 'data' argument that was
 *                         passed to cpl_complete_word() or
 *                         gl_customize_completion()).
 *  line     const char *  The current input line.
 *  word_end        int    The index of the character in line[] which
 *                         follows the end of the token that is being
 *                         completed.
 * Output
 *  return          int    0 - OK.
 *                         1 - Error.
 */
#define CPL_MATCH_FN(fn) int (fn)(WordCompletion *cpl, void *data, \
                                  const char *line, int word_end)
typedef CPL_MATCH_FN(CplMatchFn);

/*.......................................................................
 * Optional callback functions declared and prototyped using the
 * following macro are called upon to return non-zero if a given
 * file, specified by its pathname, is to be included in a list of
 * completions.
 *
 * Input:
 *  data            void *  The application specified pointer which
 *                          was specified when this callback function
 *                          was registered. This can be used to have
 *                          anything you like passed to your callback.
 *  pathname  const char *  The pathname of the file to be checked to
 *                          see if it should be included in the list
 *                          of completions.
 * Output
 *  return           int    0 - Ignore this file.
 *                          1 - Do include this file in the list
 *                              of completions.
 */
#define CPL_CHECK_FN(fn) int (fn)(__attribute__ ((unused)) void *data, const char *pathname)
typedef CPL_CHECK_FN(CplCheckFn);

/*
 * You can use the following CplCheckFn callback function to only
 * have executables included in a list of completions.
 */
CPL_CHECK_FN(cpl_check_exe);

/*
 * cpl_file_completions() is the builtin filename completion callback
 * function. This can also be called by your own custom CPL_MATCH_FN()
 * callback functions. To do this pass on all of the arguments of your
 * custom callback function to cpl_file_completions(), with the exception
 * of the (void *data) argument. The data argument should either be passed
 * NULL to request the default behaviour of the file-completion function,
 * or be passed a pointer to a CplFileConf structure (see below). In the
 * latter case the contents of the structure modify the behavior of the
 * file-completer.
 */
CPL_MATCH_FN(cpl_file_completions);

/*
 * Objects of the following type can be used to change the default
 * behavior of the cpl_file_completions() callback function.
 */
typedef struct CplFileConf CplFileConf;

/*
 * If you want to change the behavior of the cpl_file_completions()
 * callback function, call the following function to allocate a
 * configuration object, then call one or more of the subsequent
 * functions to change any of the default configuration parameters
 * that you don't want. This function returns NULL when there is
 * insufficient memory.
 */
CplFileConf *new_CplFileConf(void);

/*
 * If backslashes in the prefix being passed to cpl_file_completions()
 * should be treated as literal characters, call the following function
 * with literal=1. Otherwise the default is to treat them as escape
 * characters which remove the special meanings of spaces etc..
 */
void cfc_literal_escapes(CplFileConf *cfc, int literal);

/*
 * Before calling cpl_file_completions(), call this function if you
 * know the index at which the filename prefix starts in the input line.
 * Otherwise by default, or if you specify start_index to be -1, the
 * filename is taken to start after the first unescaped space preceding
 * the cursor, or the start of the line, which ever comes first.
 */
void cfc_file_start(CplFileConf *cfc, int start_index);

/*
 * If you only want certain types of files to be included in the
 * list of completions, use the following function to specify a
 * callback function which will be called to ask whether a given file
 * should be included. The chk_data argument is will be passed to the
 * callback function whenever it is called and can be anything you want.
 */
void cfc_set_check_fn(CplFileConf *cfc, CplCheckFn *chk_fn, void *chk_data);

/*
 * The following function deletes a CplFileConf objects previously
 * returned by new_CplFileConf(). It always returns NULL.
 */
CplFileConf *del_CplFileConf(CplFileConf *cfc);

/*
 * The following configuration structure is deprecated. Do not change
 * its contents, since this will break any programs that still use it,
 * and don't use it in new programs. Instead use opaque CplFileConf
 * objects as described above. cpl_file_completions() figures out
 * what type of structure you pass it, by virtue of a magic int code
 * placed at the start of CplFileConf object by new_CplFileConf().
 */
typedef struct {
  int escaped;     /* Opposite to the argument of cfc_literal_escapes() */
  int file_start;  /* Equivalent to the argument of cfc_file_start() */
} CplFileArgs;
/*
 * This initializes the deprecated CplFileArgs structures.
 */
void cpl_init_FileArgs(CplFileArgs *cfa);

/*.......................................................................
 * When an error occurs while performing a completion, custom completion
 * callback functions should register a terse description of the error
 * by calling cpl_record_error(). This message will then be returned on
 * the next call to cpl_last_error() and used by getline to display an
 * error message to the user.
 *
 * Input:
 *  cpl  WordCompletion *  The string-completion resource object that was
 *                         originally passed to the callback.
 *  errmsg   const char *  The description of the error.
 */
void cpl_record_error(WordCompletion *cpl, const char *errmsg);

/*.......................................................................
 * This function can be used to replace the builtin filename-completion
 * function with one of the user's choice. The user's completion function
 * has the option of calling the builtin filename-completion function
 * if it believes that the token that it has been presented with is a
 * filename (see cpl_file_completions() above).
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  data             void *  This is passed to match_fn() whenever it is
 *                           called. It could, for example, point to a
 *                           symbol table that match_fn() would look up
 *                           matches in.
 *  match_fn   CplMatchFn *  The function that will identify the prefix
 *                           to be completed from the input line, and
 *                           report matching symbols.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_customize_completion(GetLine *gl, void *data, CplMatchFn *match_fn);

/*.......................................................................
 * This function allows you to install alternate completion action
 * functions or completion listing functions, or to change the
 * completion function of an existing action of the same type. This
 * should preferably be called before the first call to gl_get_line()
 * so that the name of the action becomes defined before the user's
 * configuration file is read.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  data             void *  This is passed to match_fn() whenever it is
 *                           called. It could, for example, point to a
 *                           symbol table that match_fn() would look up
 *                           matches in.
 *  match_fn   CplMatchFn *  The function that will identify the prefix
 *                           to be completed from the input line, and
 *                           report matching symbols.
 *  list_only         int    If non-zero, install an action that only lists
 *                           possible completions, rather than attempting
 *                           to perform the completion.
 *  name       const char *  The name with which users can refer to the
 *                           binding in tecla configuration files.
 *  keyseq     const char *  The key sequence with which to invoke
 *                           the binding. This should be specified in the
 *                           same manner as key-sequences in tecla
 *                           configuration files (eg. "M-^I").
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_completion_action(GetLine *gl, void *data, CplMatchFn *match_fn,
			 int list_only, const char *name, const char *keyseq);

/*.......................................................................
 * Change the terminal (or stream) that getline interacts with.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  input_fp         FILE *  The stdio stream to read from.
 *  output_fp        FILE *  The stdio stream to write to.
 *  term       const char *  The terminal type. This can be NULL if
 *                           either or both of input_fp and output_fp don't
 *                           refer to a terminal. Otherwise it should refer
 *                           to an entry in the terminal information database.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_change_terminal(GetLine *gl, FILE *input_fp, FILE *output_fp,
		       const char *term);

/*.......................................................................
 * The following functions can be used to save and restore the contents
 * of the history buffer.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  filename   const char *  The name of the new file to write to.
 *  comment    const char *  Extra information such as timestamps will
 *                           be recorded on a line started with this
 *                           string, the idea being that the file can
 *                           double as a command file. Specify "" if
 *                           you don't care. Be sure to specify the
 *                           same string to both functions.
 *  max_lines         int    The maximum number of lines to save, or -1
 *                           to save all of the lines in the history
 *                           list.
 * Output:
 *  return            int     0 - OK.
 *                            1 - Error.
 */
int gl_save_history(GetLine *gl, const char *filename, const char *comment,
		    int max_lines);
int gl_load_history(GetLine *gl, const char *filename, const char *comment);

/*
 * Enumerate file-descriptor events that can be waited for.
 */
typedef enum {
  GLFD_READ,   /* Watch for data waiting to be read from a file descriptor */
  GLFD_WRITE,  /* Watch for ability to write to a file descriptor */
  GLFD_URGENT  /* Watch for urgent out-of-band data on the file descriptor */
} GlFdEvent;

/*
 * The following enumeration is used for the return status of file
 * descriptor event callbacks.
 */
typedef enum {
  GLFD_ABORT,    /* Cause gl_get_line() to abort with an error */
  GLFD_REFRESH,  /* Redraw the input line and continue waiting for input */
  GLFD_CONTINUE  /* Continue to wait for input, without redrawing the line */
} GlFdStatus;

/*.......................................................................
 * On systems that have the select() system call, while gl_get_line()
 * is waiting for terminal input, it can also be asked to listen for
 * activity on arbitrary file descriptors.  Callback functions of the
 * following type can be registered to be called when activity is
 * seen. If your callback needs to write to the terminal or use
 * signals, please see the gl_get_line(3) man page.
 *
 * Input:
 *  gl       GetLine *  The gl_get_line() resource object. You can use
 *                      this safely to call gl_watch_fd() or
 *                      gl_inactivity_timeout(). The effect of calling other
 *                      functions that take a gl argument is undefined,
 *                      and must be avoided.
 *  data        void *  A pointer to arbitrary callback data, as originally
 *                      registered with gl_watch_fd().
 *  fd           int    The file descriptor that has activity.
 *  event  GlFdEvent    The activity seen on the file descriptor. The
 *                      inclusion of this argument allows the same
 *                      callback to be registered for multiple events.
 * Output:
 *  return GlFdStatus   GLFD_ABORT    - Cause gl_get_line() to abort with
 *                                      an error (set errno if you need it).
 *                      GLFD_REFRESH  - Redraw the input line and continue
 *                                      waiting for input. Use this if you
 *                                      wrote something to the terminal.
 *                      GLFD_CONTINUE - Continue to wait for input, without
 *                                      redrawing the line.
 */
#define GL_FD_EVENT_FN(fn) GlFdStatus (fn)(GetLine *gl, void *data, int fd, \
					   GlFdEvent event)
typedef GL_FD_EVENT_FN(GlFdEventFn);

/*.......................................................................
 * Where possible, register a function and associated data to be called
 * whenever a specified event is seen on a file descriptor.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  fd                int    The file descriptor to watch.
 *  event       GlFdEvent    The type of activity to watch for.
 *  callback  GlFdEventFn *  The function to call when the specified
 *                           event occurs. Setting this to 0 removes
 *                           any existing callback.
 *  data             void *  A pointer to arbitrary data to pass to the
 *                           callback function.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Either gl==NULL, or this facility isn't
 *                               available on the the host system
 *                               (ie. select() isn't available). No
 *                               error message is generated in the latter
 *                               case.
 */
int gl_watch_fd(GetLine *gl, int fd, GlFdEvent event,
		GlFdEventFn *callback, void *data);

/*
 * Enumerators from the following list are returned by activity
 * timeout callbacks registered by gl_inactivity_timeout(). They tell
 * gl_get_line() whether and how to procede.
 */
typedef enum {
  GLTO_ABORT,    /* Cause gl_get_line() to abort with an error */
  GLTO_REFRESH,  /* Redraw the input line and continue waiting for input */
  GLTO_CONTINUE  /* Continue to wait for input, without redrawing the line */
} GlAfterTimeout;

/*.......................................................................
 * On systems that have the select() system call, the application has
 * the option of providing a callback function of the following type,
 * which is called whenever no terminal input or other I/O activity is
 * seen for the timeout duration specified in the last call to
 * gl_inactivity_timeout().
 *
 * Input:
 *  gl            GetLine *  The gl_get_line() resource object. You can use
 *                           this safely to call gl_watch_fd() or
 *                           gl_inactivity_timeout(). The effect of calling other
 *                           functions that take a gl argument is undefined,
 *                           and must be avoided.
 *  data             void *  A pointer to arbitrary callback data, as
 *                           originally registered with gl_inactivity_timeout().
 * Output:
 *  return GlAfterTimeout    GLTO_ABORT    - Cause gl_get_line() to
 *                                           abort with an error (set
 *                                           errno if you need it).
 *                           GLTO_REFRESH  - Redraw the input line and
 *                                           continue waiting for
 *                                           input. Use this if you
 *                                           wrote something to the
 *                                           terminal.
 *                           GLTO_CONTINUE - Continue to wait for
 *                                           input, without redrawing
 *                                           the line.
 */
#define GL_TIMEOUT_FN(fn) GlAfterTimeout (fn)(GetLine *gl, void *data)
typedef GL_TIMEOUT_FN(GlTimeoutFn);

/*.......................................................................
 * On systems with the select() system call, the gl_inactivity_timeout()
 * function provides the option of setting (or cancelling) an
 * inactivity timeout. Inactivity, in this case, refers both to
 * terminal input received from the user, and to I/O on any file
 * descriptors registered by calls to gl_watch_fd(). If at any time,
 * no activity is seen for the requested time period, the specified
 * timeout callback function is called. On returning, this callback
 * returns a code which tells gl_get_line() what to do next. Note that
 * each call to gl_inactivity_timeout() replaces any previously installed
 * timeout callback, and that specifying a callback of 0, turns off
 * inactivity timing. 
 *
 * Beware that although the timeout argument includes a nano-second
 * component, few computer clocks presently have resolutions finer
 * than a few milliseconds, so asking for less than a few milliseconds
 * is equivalent to zero on a lot of systems.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  callback  GlTimeoutFn *  The function to call when the inactivity
 *                           timeout is exceeded. To turn off
 *                           inactivity timeouts altogether, send 0.
 *  data             void *  A pointer to arbitrary data to pass to the
 *                           callback function.
 *  sec     unsigned long    The number of whole seconds in the timeout.
 *  nsec    unsigned long    The fractional number of seconds in the
 *                           timeout, expressed in nano-seconds (see
 *                           the caveat above).
 * Output:
 *  return            int    0 - OK.
 *                           1 - Either gl==NULL, or this facility isn't
 *                               available on the the host system
 *                               (ie. select() isn't available). No
 *                               error message is generated in the latter
 *                               case.
 */
int gl_inactivity_timeout(GetLine *gl, GlTimeoutFn *timeout_fn, void *data,
		   unsigned long sec, unsigned long nsec);

/*.......................................................................
 * Switch history streams. History streams represent separate history
 * lists recorded within a single history buffer. Different streams
 * are distinguished by integer identifiers chosen by the calling
 * appplicaton. Initially new_GetLine() sets the stream identifier to
 * 0. Whenever a new line is appended to the history list, the current
 * stream identifier is recorded with it, and history lookups only
 * consider lines marked with the current stream identifier.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  id     unsigned    The new history stream identifier.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
int gl_group_history(GetLine *gl, unsigned id);

/*.......................................................................
 * Display the contents of the history list.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  fp         FILE *  The stdio output stream to write to.
 *  fmt  const char *  A format string. This containing characters to be
 *                     written verbatim, plus any of the following
 *                     format directives:
 *                       %D  -  The date, formatted like 2001-11-20
 *                       %T  -  The time of day, formatted like 23:59:59
 *                       %N  -  The sequential entry number of the
 *                              line in the history buffer.
 *                       %G  -  The number of the history group that
 *                              the line belongs to.
 *                       %%  -  A literal % character.
 *                       %H  -  The history line itself.
 *                     Note that a '\n' newline character is not
 *                     appended by default.
 *  all_groups  int    If true, display history lines from all
 *                     history groups. Otherwise only display
 *                     those of the current history group.
 *  max_lines   int    If max_lines is < 0, all available lines
 *                     are displayed. Otherwise only the most
 *                     recent max_lines lines will be displayed.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
int gl_show_history(GetLine *gl, FILE *fp, const char *fmt, int all_groups,
		    int max_lines);

/*.......................................................................
 * Resize or delete the history buffer.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  bufsize  size_t    The number of bytes in the history buffer, or 0
 *                     to delete the buffer completely.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Insufficient memory (the previous buffer
 *                         will have been retained). No error message
 *                         will be displayed.
 */
int gl_resize_history(GetLine *gl, size_t bufsize);

/*.......................................................................
 * Set an upper limit to the number of lines that can be recorded in the
 * history list, or remove a previously specified limit.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  max_lines   int    The maximum number of lines to allow, or -1 to
 *                     cancel a previous limit and allow as many lines
 *                     as will fit in the current history buffer size.
 */
void gl_limit_history(GetLine *gl, int max_lines);

/*.......................................................................
 * Discard either all historical lines, or just those associated with the
 * current history group.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  all_groups  int    If true, clear all of the history. If false,
 *                     clear only the stored lines associated with the
 *                     currently selected history group.
 */
void gl_clear_history(GetLine *gl, int all_groups);

/*.......................................................................
 * Temporarily enable or disable the gl_get_line() history mechanism.
 *
 * Input:
 *  gl      GetLine *  The resource object of gl_get_line().
 *  enable      int    If true, turn on the history mechanism. If
 *                     false, disable it.
 */
void gl_toggle_history(GetLine *gl, int enable);

/*
 * Objects of the following type are returned by gl_terminal_size().
 */
typedef struct {
  int nline;        /* The terminal has nline lines */
  int ncolumn;      /* The terminal has ncolumn columns */
} GlTerminalSize;

/*.......................................................................
 * Update if necessary, and return the current size of the terminal.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 *  def_ncolumn       int    If the number of columns in the terminal
 *                           can't be determined, substitute this number.
 *  def_nline         int    If the number of lines in the terminal can't
 *                           be determined, substitute this number.
 * Output:
 *  return GlTerminalSize    The current terminal size.
 */
GlTerminalSize gl_terminal_size(GetLine *gl, int def_ncolumn, int def_nline);

/*.......................................................................
 * Tell gl_get_line() the current terminal size. Note that this is only
 * necessary on systems where changes in terminal size aren't reported
 * via SIGWINCH.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 *  ncolumn           int    The number of columns in the terminal.
 *  nline             int    The number of rows in the terminal.
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_set_term_size(GetLine *gl, int ncolumn, int nline);

/*
 * The gl_lookup_history() function returns information in an
 * argument of the following type.
 */
typedef struct {
  const char *line;    /* The requested history line */
  unsigned group;      /* The history group to which the */
                       /*  line belongs. */
  time_t timestamp;    /* The date and time at which the */
                       /*  line was originally entered. */
} GlHistoryLine;

/*.......................................................................
 * Lookup a history line by its sequential number of entry in the
 * history buffer.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 *  id      unsigned long    The identification number of the line to
 *                           be returned, where 0 denotes the first line
 *                           that was entered in the history list, and
 *                           each subsequently added line has a number
 *                           one greater than the previous one. For
 *                           the range of lines currently in the list,
 *                           see the gl_range_of_history() function.
 * Input/Output:
 *  line    GlHistoryLine *  A pointer to the variable in which to
 *                           return the details of the line.
 * Output:
 *  return            int    0 - The line is no longer in the history
 *                               list, and *line has not been changed.
 *                           1 - The requested line can be found in
 *                               *line. Note that the string in
 *                               line->line is part of the history
 *                               buffer and will change, so a private
 *                               copy should be made if you wish to
 *                               use it after subsequent calls to any
 *                               functions that take gl as an argument.
 */
int gl_lookup_history(GetLine *gl, unsigned long id, GlHistoryLine *line);

/*
 * The gl_state_of_history() function returns information in an argument
 * of the following type.
 */
typedef struct {
  int enabled;     /* True if history is enabled */
  unsigned group;  /* The current history group */
  int max_lines;   /* The current upper limit on the number of lines */
                   /*  in the history list, or -1 if unlimited. */
} GlHistoryState;

/*.......................................................................
 * Query the state of the history list. Note that any of the input/output
 * pointers can be specified as NULL.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 * Input/Output:
 *  state  GlHistoryState *  A pointer to the variable in which to record
 *                           the return values.
 */
void gl_state_of_history(GetLine *gl, GlHistoryState *state);

/*
 * The gl_range_of_history() function returns information in an argument
 * of the following type.
 */
typedef struct {
  unsigned long oldest;  /* The sequential entry number of the oldest */
                         /*  line in the history list. */
  unsigned long newest;  /* The sequential entry number of the newest */
                         /*  line in the history list. */
  int nlines;            /* The number of lines in the history list */
} GlHistoryRange;

/*.......................................................................
 * Query the number and range of lines in the history buffer.
 *
 * Input:
 *  gl            GetLine *  The resource object of gl_get_line().
 *  range  GlHistoryRange *  A pointer to the variable in which to record
 *                           the return values. If range->nline=0, the
 *                           range of lines will be given as 0-0.
 */
void gl_range_of_history(GetLine *gl, GlHistoryRange *range);

/*
 * The gl_size_of_history() function returns information in an argument
 * of the following type.
 */
typedef struct {
  size_t size;      /* The size of the history buffer (bytes) */
  size_t used;      /* The number of bytes of the history buffer */
                    /*  that are currently occupied. */
} GlHistorySize;

/*.......................................................................
 * Return the size of the history buffer and the amount of the
 * buffer that is currently in use.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 * Input/Output:
 *  GlHistorySize size *  A pointer to the variable in which to return
 *                        the results.
 */
void gl_size_of_history(GetLine *gl, GlHistorySize *size);

/*.......................................................................
 * Enable or disable the automatic addition of newly entered lines to the
 * history list.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 *  enable          int     If true, subsequently entered lines will
 *                          automatically be added to the history list
 *                          before they are returned to the caller of
 *                          gl_get_line(). If 0, the choice of how and
 *                          when to archive lines in the history list,
 *                          is left up to the calling application, which
 *                          can do so via calls to gl_append_history().
 * Output:
 *  return          int     0 - OK.
 *                          1 - Error.
 */
int gl_automatic_history(GetLine *gl, int enable);

/*.......................................................................
 * Append a specified line to the history list.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 *  line     const char *   The line to be added.
 * Output:
 *  return          int     0 - OK.
 *                          1 - Error.
 */
int gl_append_history(GetLine *gl, const char *line);

/*.......................................................................
 * Specify whether text that users type should be displayed or hidden.
 * In the latter case, only the prompt is displayed, and the final
 * input line is not archived in the history list.
 *
 * Input:
 *  gl         GetLine *  The input-line history maintenance object.
 *  enable         int     0 - Disable echoing.
 *                         1 - Enable echoing.
 *                        -1 - Just query the mode without changing it.
 * Output:
 *  return         int    The echoing disposition that was in effect
 *                        before this function was called:
 *                         0 - Echoing was disabled.
 *                         1 - Echoing was enabled.
 */
int gl_echo_mode(GetLine *gl, int enable);

/*.......................................................................
 * This function can be called from gl_get_line() callbacks to have
 * the prompt changed when they return. It has no effect if gl_get_line()
 * is not currently being invoked.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  prompt  const char *  The new prompt.
 */
void gl_replace_prompt(GetLine *gl, const char *prompt);

/*
 * Enumerate the available prompt formatting styles.
 */
typedef enum {
  GL_LITERAL_PROMPT,   /* Display the prompt string literally */
  GL_FORMAT_PROMPT     /* The prompt string can contain any of the */
                       /* following formatting directives: */
                       /*   %B  -  Display subsequent characters */
                       /*          with a bold font. */
                       /*   %b  -  Stop displaying characters */
                       /*          with the bold font. */
                       /*   %U  -  Underline subsequent characters. */
                       /*   %u  -  Stop underlining characters. */
                       /*   %S  -  Highlight subsequent characters */
                       /*          (also known as standout mode). */
                       /*   %s  -  Stop highlighting characters */
                       /*   %%  -  Display a single % character. */
} GlPromptStyle;

/*.......................................................................
 * Specify whether to heed text attribute directives within prompt
 * strings.
 *
 * Input:
 *  gl           GetLine *  The resource object of gl_get_line().
 *  style  GlPromptStyle    The style of prompt (see the definition of
 *                          GlPromptStyle in libtecla.h for details).
 */
void gl_prompt_style(GetLine *gl, GlPromptStyle style);

/*.......................................................................
 * Remove a signal from the list of signals that gl_get_line() traps.
 *
 * Input:
 *  gl           GetLine *  The resource object of gl_get_line().
 *  signo            int    The number of the signal to be ignored.
 * Output:
 *  return           int    0 - OK.
 *                          1 - Error.
 */
int gl_ignore_signal(GetLine *gl, int signo);

/*
 * A bitwise union of the following enumerators is passed to
 * gl_trap_signal() to specify the environment in which the
 * application's signal handler is to be called.
 */
typedef enum {
  GLS_RESTORE_SIG=1,  /* Restore the caller's signal environment */
                      /* while handling the signal. */
  GLS_RESTORE_TTY=2,  /* Restore the caller's terminal settings */
                      /* while handling the signal. */
  GLS_RESTORE_LINE=4, /* Move the cursor to the start of the next line */
  GLS_REDRAW_LINE=8,  /* Redraw the input line when the signal handler */
                      /*  returns. */
  GLS_UNBLOCK_SIG=16, /* Normally a signal who's delivery is found to */
                      /*  be blocked by the calling application is not */
                      /*  trapped by gl_get_line(). Including this flag */
                      /*  causes it to be temporarily unblocked and */
                      /*  trapped while gl_get_line() is executing. */
  GLS_DONT_FORWARD=32,/* Don't forward the signal to the signal handler */
                      /*  of the calling program. */
  GLS_RESTORE_ENV = GLS_RESTORE_SIG | GLS_RESTORE_TTY | GLS_REDRAW_LINE,
  GLS_SUSPEND_INPUT = GLS_RESTORE_ENV | GLS_RESTORE_LINE
} GlSignalFlags;

/*
 * The following enumerators are passed to gl_trap_signal() to tell
 * it what to do after the application's signal handler has been called.
 */
typedef enum {
  GLS_RETURN,      /* Return the line as though the user had pressed the */
                   /*  return key. */
  GLS_ABORT,       /* Cause gl_get_line() to return NULL */
  GLS_CONTINUE     /* After handling the signal, resume command line editing */
} GlAfterSignal;

/*.......................................................................
 * Tell gl_get_line() how to respond to a given signal. This can be used
 * both to override the default responses to signals that gl_get_line()
 * normally catches and to add new signals to the list that are to be
 * caught.
 *
 * Input:
 *  gl           GetLine *  The resource object of gl_get_line().
 *  signo            int    The number of the signal to be caught.
 *  flags       unsigned    A bitwise union of GlSignalFlags enumerators.
 *  after  GlAfterSignal    What to do after the application's signal
 *                          handler has been called.
 *  errno_value      int    The value to set errno to.
 * Output:
 *  return           int    0 - OK.
 *                          1 - Insufficient memory to record the
 *                              new signal disposition.
 */
int gl_trap_signal(GetLine *gl, int signo, unsigned flags,
		   GlAfterSignal after, int errno_value);

/*.......................................................................
 * By default, gl_get_line() doesn't trap signals that are blocked
 * when it is called. This default can be changed either on a
 * per-signal basis by calling gl_trap_signal(), or on a global basis
 * by calling this function. What this function does is add the
 * GLS_UNBLOCK_SIG flag to all signals that are currently configured
 * to be trapped by gl_get_line(), such that when subsequent calls to
 * gl_get_line() wait for I/O, these signals are temporarily
 * unblocked. This behavior is useful in non-blocking server-I/O mode,
 * where it is used to avoid race conditions related to handling these
 * signals externally to gl_get_line(). See the demonstration code in
 * demo3.c, or the gl_handle_signal() man page for further
 * information.
 *
 * Input:
 *  gl         GetLine *   The resource object of gl_get_line().
 */
void gl_catch_blocked(GetLine *gl);

/*.......................................................................
 * In server-I/O mode the terminal is left in raw mode between calls
 * to gl_get_line(), so it is necessary for the application to install
 * terminal restoring signal handlers for signals that could terminate
 * or suspend the process, plus a terminal reconfiguration handler to
 * be called when a process resumption signal is received, and finally
 * a handler to be called when a terminal-resize signal is received.
 *
 * Since there are many signals that by default terminate or suspend
 * processes, and different systems support different sub-sets of
 * these signals, this function provides a convenient wrapper around
 * sigaction() for assigning the specified handlers to all appropriate
 * signals. It also arranges that when any one of these signals is
 * being handled, all other catchable signals are blocked. This is
 * necessary so that the specified signal handlers can safely call
 * gl_raw_io(), gl_normal_io() and gl_update_size() without reentrancy
 * issues.
 *
 * Input:
 *  term_handler  void (*)(int)  The signal handler to invoke when
 *                               a process terminating signal is
 *                               received.
 *  susp_handler  void (*)(int)  The signal handler to invoke when
 *                               a process suspending signal is
 *                               received.
 *  cont_handler  void (*)(int)  The signal handler to invoke when
 *                               a process resumption signal is
 *                               received (ie. SIGCONT).
 *  size_handler  void (*)(int)  The signal handler to invoke when
 *                               a terminal-resize signal (ie. SIGWINCH)
 *                               is received.
 * Output:
 *  return                  int  0 - OK.
 *                               1 - Error.
 */
int gl_tty_signals(void (*term_handler)(int), void (*susp_handler)(int),
		   void (*cont_handler)(int), void (*size_handler)(int));

/*.......................................................................
 * Return the last signal that was caught by the most recent call to
 * gl_get_line(), or -1 if no signals were caught. This is useful if
 * gl_get_line() returns errno=EINTR and you need to find out what signal
 * caused it to abort.
 *
 * Input:
 *  gl           GetLine *  The resource object of gl_get_line().
 * Output:
 *  return           int    The last signal caught by the most recent
 *                          call to gl_get_line(), or -1 if no signals
 *                          were caught.
 */
int gl_last_signal(GetLine *gl);

/*.......................................................................
 * Return the signal mask used by gl_get_line(). This is the set of
 * signals that gl_get_line() is currently configured to trap.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 * Input/Output:
 *  set       sigset_t *  The set of signals will be returned in *set,
 *                        in the form of a signal process mask, as
 *                        used by sigaction(), sigprocmask(),
 *                        sigpending(), sigsuspend(), sigsetjmp() and
 *                        other standard POSIX signal-aware
 *                        functions.
 * Output:
 *  return         int    0 - OK.
 *                        1 - Error (examine errno for reason).
 */
int gl_list_signals(GetLine *gl, sigset_t *set);

/*.......................................................................
 * Respond to signals who's default effects have important
 * consequences to gl_get_line(). This is intended for use in
 * non-blocking server mode, where the external event loop is
 * responsible for catching signals. Signals that are handled include
 * those that by default terminate or suspend the process, and the
 * signal that indicates that the terminal size has changed. Note that
 * this function is not signal safe and should thus not be called from
 * a signal handler itself. See the gl_io_mode() man page for how it
 * should be used.
 *
 * In the case of signals that by default terminate or suspend
 * processes, command-line editing will be suspended, the terminal
 * returned to a usable state, then the default disposition of the
 * signal restored and the signal resent, in order to suspend or
 * terminate the process.  If the process subsequently resumes,
 * command-line editing is resumed.
 *
 * In the case of signals that indicate that the terminal has been
 * resized, the new size will be queried, and any input line that is
 * being edited will be redrawn to fit the new dimensions of the
 * terminal.
 *
 * Input:
 *  signo    int    The number of the signal to respond to.
 *  gl   GetLine *  The first element of an array of 'ngl' GetLine
 *                  objects.
 *  ngl      int    The number of elements in the gl[] array. Normally
 *                  this will be one.
 */
void gl_handle_signal(int signo, GetLine *gl, int ngl);

/*.......................................................................
 * Return extra information (ie. in addition to that provided by errno)
 * about the last error to occur in either gl_get_line() or its
 * associated public functions.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 * Input/Output:
 *  buff          char *  An optional output buffer. Note that if the
 *                        calling application calls any gl_*()
 *                        functions from signal handlers, it should
 *                        provide a buffer here, so that a copy of
 *                        the latest error message can safely be made
 *                        while signals are blocked.
 *  n           size_t    The allocated size of buff[].
 * Output:
 *  return  const char *  A pointer to the error message. This will
 *                        be the buff argument, unless buff==NULL, in
 *                        which case it will be a pointer to an
 *                        internal error buffer. In the latter case,
 *                        note that the contents of the returned buffer
 *                        will change on subsequent calls to any gl_*()
 *                        functions.
 */
const char *gl_error_message(GetLine *gl, char *buff, size_t n);

/*.......................................................................
 * Clear the terminal and leave the cursor at the home position.  In
 * server I/O mode, arrange for the input line to be redrawn from scratch
 * when gl_get_line() is next called.
 *
 * Input:
 *  gl          GetLine *   The resource object of gl_get_line().
 * Output:
 *  return          int     0 - OK.
 *                          1 - Error.
 */
int gl_erase_terminal(GetLine *gl);

/*.......................................................................
 * Display a left-justified string over multiple terminal lines,
 * taking account of the current width of the terminal. Optional
 * indentation and an optional prefix string can be specified to be
 * displayed at the start of each new terminal line used. Similarly,
 * an optional suffix can be specified to be displayed at the end of
 * each terminal line.  If needed, a single paragraph can be broken
 * across multiple calls.  Note that literal newlines in the input
 * string can be used to force a newline at any point and that you
 * should use this feature to explicitly end all paragraphs, including
 * at the end of the last string that you write. Note that when a new
 * line is started between two words that are separated by spaces,
 * those spaces are not output, whereas when a new line is started
 * because a newline character was found in the string, only the
 * spaces before the newline character are discarded.
 *
 * Input:
 *  gl         GetLine *  The resource object of gl_get_line().
 *  indentation    int    The number of spaces of indentation to write
 *                        at the beginning of each new terminal line.
 *  prefix  const char *  An optional prefix string to write after the
 *                        indentation margin at the start of each new
 *                        terminal line. You can specify NULL if no
 *                        prefix is required.
 *  suffix  const char *  An optional suffix string to draw at the end
 *                        of the terminal line. Spaces will be added
 *                        where necessary to ensure that the suffix ends
 *                        in the last column of the terminal line. If
 *                        no suffix is desired, specify NULL.
 *  fill_char      int    The padding character to use when indenting
 *                        the line or padding up to the suffix.
 *  def_width      int    If the terminal width isn't known, such as when
 *                        writing to a pipe or redirecting to a file,
 *                        this number specifies what width to assume.
 *  start          int    The number of characters already written to
 *                        the start of the current terminal line. This
 *                        is primarily used to allow individual
 *                        paragraphs to be written over multiple calls
 *                        to this function, but can also be used to
 *                        allow you to start the first line of a
 *                        paragraph with a different prefix or
 *                        indentation than those specified above.
 *  string  const char *  The string to be written.
 * Output:
 *  return         int    On error -1 is returned. Otherwise the
 *                        return value is the terminal column index at
 *                        which the cursor was left after writing the
 *                        final word in the string. Successful return
 *                        values can thus be passed verbatim to the
 *                        'start' arguments of subsequent calls to
 *                        gl_display_text() to allow the printing of a
 *                        paragraph to be broken across multiple calls
 *                        to gl_display_text().
 */
int gl_display_text(GetLine *gl, int indentation, const char *prefix,
		    const char *suffix, int fill_char, int def_width,
		    int start, const char *string);


/*
 * Enumerate the I/O modes supported by gl_get_line().
 */
typedef enum {
  GL_NORMAL_MODE,    /* Normal line-at-a-time mode using gl_get_line()'s */
                     /*  internal event loop. */
  GL_SERVER_MODE     /* Non-blocking server mode, driven by an external */
                     /*  event loop. */
} GlIOMode;

/*.......................................................................
 * Select the I/O mode to be used by gl_get_line().
 *
 * Input:
 *  gl         GetLine *         The resource object of gl_get_line().
 *  mode      GlIOMode           The I/O mode to establish. Note that
 *                               when server mode, the terminal is placed
 *                               in raw mode, as though gl_raw_io() had
 *                               been called.
 * Output:
 *  return                  int  0 - OK.
 *                               1 - Error.
 */
int gl_io_mode(GetLine *gl, GlIOMode mode);

/*.......................................................................
 * In server mode, this function configures the terminal for non-blocking
 * raw terminal I/O. In normal I/O mode it does nothing.
 *
 * Callers of this function must be careful to trap all signals that
 * terminate or suspend the program, and call gl_normal_io()
 * from the corresponding signal handlers in order to restore the
 * terminal to its original settings before the program is terminated
 * or suspended. They should also trap the SIGCONT signal to detect
 * when the program resumes, and ensure that its signal handler
 * call gl_raw_io() to redisplay the line and resume editing.
 *
 * Input:
 *  gl      GetLine *  The line editor resource object.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
int gl_raw_io(GetLine *gl);

/*.......................................................................
 * Restore the terminal to the state that it had when gl_raw_io() was
 * last called. After calling gl_raw_io(), this function must be called
 * before terminating or suspending the program, and before attempting
 * other uses of the terminal from within the program. See gl_raw_io()
 * for more details.
 *
 * Input:
 *  gl      GetLine *  The line editor resource object.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
int gl_normal_io(GetLine *gl);

/*.......................................................................
 * When in non-blocking server mode, this function can be used to abandon
 * the current incompletely entered input line, and prepare to start 
 * editing a new line on the next call to gl_get_line().
 *
 * Input:
 *  gl      GetLine *  The line editor resource object.
 * Output:
 *  return      int    0 - OK.
 *                     1 - Error.
 */
void gl_abandon_line(GetLine *gl);

/*
 * Enumerators of the following type are used to report why
 * gl_get_line() returned. This is most useful in non-blocking
 * server mode, since in that mode a NULL return value can mean
 * either that an error occurred, or that I/O blocked.
 */
typedef enum {
  GLR_NEWLINE,  /* A new input line was returned */
  GLR_BLOCKED,  /* The terminal was in non-blocking mode, and input */
                /* or output would have blocked. */
  GLR_SIGNAL,   /* A signal caused gl_get_line() to return. */
  GLR_TIMEOUT,  /* An application timeout callback returned GLTO_ABORT */
  GLR_FDABORT,  /* An application I/O callack returned GLFD_ABORT */
  GLR_EOF,      /* End of file reached */
  GLR_ERROR     /* An unexpected error caused gl_get_line() to abort */
} GlReturnStatus;

/*.......................................................................
 * Ask gl_get_line() what caused it to return.
 *
 * Input:
 *  gl             GetLine *  The line editor resource object.
 * Output:
 *  return  GlReturnStatus    The return status of the last call to
 *                            gl_get_line().
 */
GlReturnStatus gl_return_status(GetLine *gl);

/*
 * Enumerate the types of I/O that gl_get_line() can be waiting for
 * in non-blocking sedrver I/O mode.
 */
typedef enum {
  GLP_READ,   /* gl_get_line() is waiting to write to the terminal */
  GLP_WRITE   /* gl_get_line() is waiting to read from the terminal */
} GlPendingIO;

/*.......................................................................
 * In non-blocking server-I/O mode, this function should be called
 * from the application's external event loop to see what type of
 * terminal I/O is being waited for by gl_get_line(), and thus what
 * direction of I/O to wait for with select() or poll().
 *
 * Input:
 *  gl          GetLine *  The resource object of gl_get_line().
 * Output:
 *  return  GlPendingIO    The type of pending I/O being waited for.
 */
GlPendingIO gl_pending_io(GetLine *gl);

/*
 * The following enumerators are returned by externally defined action
 * functions to tell gl_get_line() how to procede after the action
 * function returns.
 */
typedef enum {
  GLA_ABORT,     /* Cause gl_get_line() to return NULL */
  GLA_RETURN,    /* Return the line as though the user had pressed the */
                 /*  return key. */
  GLA_CONTINUE   /* Resume command-line editing */
} GlAfterAction;

/*.......................................................................
 * Functions of the following form implement external
 * application-specific action functions, which can then be bound to
 * sequences of terminal keys.
 * 
 * Input:
 *  gl            GetLine *  The line editor resource object.
 *  data             void *  The anonymous 'data' argument that was
 *                           passed to gl_external_action() when the
 *                           callback function was registered.
 *  count             int    A positive repeat count specified by the user,
 *                           or 1 if not specified. Action functions should
 *                           ignore this if repeating the action multiple
 *                           times isn't appropriate. Alternatively they
 *                           can interpret it as a general numeric
 *                           argument.
 *  curpos         size_t    The position of the cursor within the input
 *                           line, expressed as the index of the
 *                           corresponding character within the line[]
 *                           array.
 *  line       const char *  A read-only copy of the current input line.
 * Output
 *  return  GlAfterAction    What should gl_get_line() do when the action
 *                           function returns?
 *                            GLA_ABORT    - Cause gl_get_line() to
 *                                           abort with an error (set
 *                                           errno if you need it).
 *                            GLA_RETURN   - Return the input line as
 *                                           though the user had typed
 *                                           the return key.
 *                            GLA_CONTINUE - Resume waiting for keyboard
 *                                           input.
 */
#define GL_ACTION_FN(fn) GlAfterAction (fn)(GetLine *gl, void *data, \
	      int count, size_t curpos, const char *line)

typedef GL_ACTION_FN(GlActionFn);

/*.......................................................................
 * Register an application-provided function as an action function.
 * This should preferably be called before the first call to gl_get_line()
 * so that the name of the action becomes defined before the user's
 * configuration file is read.
 *
 * Input:
 *  gl            GetLine *  The resource object of the command-line input
 *                           module.
 *  data             void *  Arbitrary application-specific callback
 *                           data to be passed to the callback
 *                           function, fn().
 *  fn         GlActionFn *  The application-specific function that
 *                           implements the action. This will be invoked
 *                           whenever the user presses any
 *                           key-sequence which is bound to this action.
 *  name       const char *  The name with which users can refer to the
 *                           binding in tecla configuration files.
 *  keyseq     const char *  The key sequence with which to invoke
 *                           the binding. This should be specified in the
 *                           same manner as key-sequences in tecla
 *                           configuration files (eg. "M-^I").
 * Output:
 *  return            int    0 - OK.
 *                           1 - Error.
 */
int gl_register_action(GetLine *gl, void *data, GlActionFn *fn,
                       const char *name, const char *keyseq);

/*.......................................................................
 * This function is designed to be called by CPL_MATCH_FN() callback
 * functions. It adds one possible completion of the token that is being
 * completed to an array of completions. If the completion needs any
 * special quoting to be valid when displayed in the input line, this
 * quoting must be included in the string.
 *
 * Input:
 *  cpl      WordCompletion *  The argument of the same name that was passed
 *                             to the calling CPL_MATCH_FN() callback function.
 *  line         const char *  The input line, as received by the callback
 *                             function.
 *  word_start          int    The index within line[] of the start of the
 *                             word that is being completed. If an empty
 *                             string is being completed, set this to be
 *                             the same as word_end.
 *  word_end            int    The index within line[] of the character which
 *                             follows the incomplete word, as received by the
 *                             callback function.
 *  suffix       const char *  The appropriately quoted string that could
 *                             be appended to the incomplete token to complete
 *                             it. A copy of this string will be allocated
 *                             internally.
 *  type_suffix  const char *  When listing multiple completions, gl_get_line()
 *                             appends this string to the completion to indicate
 *                             its type to the user. If not pertinent pass "".
 *                             Otherwise pass a literal or static string.
 *  cont_suffix  const char *  If this turns out to be the only completion,
 *                             gl_get_line() will append this string as
 *                             a continuation. For example, the builtin
 *                             file-completion callback registers a directory
 *                             separator here for directory matches, and a
 *                             space otherwise. If the match were a function
 *                             name you might want to append an open
 *                             parenthesis, etc.. If not relevant pass "".
 *                             Otherwise pass a literal or static string.
 * Output:
 *  return              int    0 - OK.
 *                             1 - Error.
 */
int cpl_add_completion(WordCompletion *cpl, const char *line,
		       int word_start, int word_end, const char *suffix,
		       const char *type_suffix, const char *cont_suffix);

/*
 * Each possible completion string is recorded in an array element of
 * the following type.
 */
typedef struct {
  char *completion;        /* The matching completion string */
  char *suffix;            /* The pointer into completion[] at which the */
                           /*  string was extended. */
  const char *type_suffix; /* A suffix to be added when listing completions */
                           /*  to indicate the type of the completion. */
} CplMatch;

/*
 * Completions are returned in a container of the following form.
 */
typedef struct {
  char *suffix;            /* The common initial part of all of the */
                           /*  completion suffixes. */
  const char *cont_suffix; /* Optional continuation string to be appended to */
                           /*  the sole completion when nmatch==1. */
  CplMatch *matches;       /* The array of possible completion strings, */
                           /*  sorted into lexical order. */
  int nmatch;              /* The number of elements in matches[] */
} CplMatches;

/*.......................................................................
 * Given an input line and the point at which completion is to be
 * attempted, return an array of possible completions.
 *
 * Input:
 *  cpl    WordCompletion *  The word-completion resource object.
 *  line       const char *  The current input line.
 *  word_end          int    The index of the character in line[] which
 *                           follows the end of the token that is being
 *                           completed.
 *  data             void *  Anonymous 'data' to be passed to match_fn().
 *  match_fn   CplMatchFn *  The function that will identify the prefix
 *                           to be completed from the input line, and
 *                           record completion suffixes.
 * Output:
 *  return     CplMatches *  The container of the array of possible
 *                           completions. The returned pointer refers
 *                           to a container owned by the parent Completion
 *                           object, and its contents thus potentially
 *                           change on every call to cpl_complete_word().
 */
CplMatches *cpl_complete_word(WordCompletion *cpl, const char *line,
			      int word_end, void *data, 
			      CplMatchFn *match_fn);

/*.......................................................................
 * Recall the return value of the last call to cpl_complete_word().
 *
 * Input:
 *  cpl    WordCompletion *  The completion resource object.
 * Output:
 *  return     CplMatches *  The container of the array of possible
 *                           completions, as returned by the last call to
 *                           cpl_complete_word(). The returned pointer refers
 *                           to a container owned by the parent WordCompletion
 *                           object, and its contents thus potentially
 *                           change on every call to cpl_complete_word().
 *                           On error, either in the execution of this
 *                           function, or in the last call to
 *                           cpl_complete_word(), NULL is returned, and a
 *                           description of the error can be acquired by
 *                           calling cpl_last_error(cpl).
 */
CplMatches *cpl_recall_matches(WordCompletion *cpl);

/*.......................................................................
 * Print out an array of matching completions.
 *
 * Input:
 *  result  CplMatches *   The container of the sorted array of
 *                         completions.
 *  fp            FILE *   The output stream to write to.
 *  term_width     int     The width of the terminal.
 * Output:
 *  return         int     0 - OK.
 *                         1 - Error.
 */
int cpl_list_completions(CplMatches *result, FILE *fp, int term_width);

/*.......................................................................
 * Return a description of the error that occurred on the last call to
 * cpl_complete_word() or cpl_add_completion().
 *
 * Input:
 *  cpl   WordCompletion *  The string-completion resource object.
 * Output:
 *  return    const char *  The description of the last error.
 */
const char *cpl_last_error(WordCompletion *cpl);

/*
 * PathCache objects encapsulate the resources needed to record
 * files of interest from comma-separated lists of directories.
 */
typedef struct PathCache PathCache;

/*.......................................................................
 * Create an object who's function is to maintain a cache of filenames
 * found within a list of directories, and provide quick lookup and
 * completion of selected files in this cache.
 *
 * Output:
 *  return     PathCache *  The new, initially empty cache, or NULL
 *                          on error.
 */
PathCache *new_PathCache(void);

/*.......................................................................
 * Delete a given cache of files, returning the resources that it
 * was using to the system.
 *
 * Input:
 *  pc      PathCache *  The cache to be deleted (can be NULL).
 * Output:
 *  return  PathCache *  The deleted object (ie. allways NULL).
 */
PathCache *del_PathCache(PathCache *pc);

/*.......................................................................
 * Return a description of the last path-caching error that occurred.
 *
 * Input:
 *  pc     PathCache *   The filename cache that suffered the error.
 * Output:
 *  return      char *   The description of the last error.
 */
const char *pca_last_error(PathCache *pc);

/*.......................................................................
 * Build the list of files of interest contained in a given
 * colon-separated list of directories.
 *
 * Input:
 *  pc         PathCache *  The cache in which to store the names of
 *                          the files that are found in the list of
 *                          directories.
 *  path      const char *  A colon-separated list of directory
 *                          paths. Under UNIX, when searching for
 *                          executables, this should be the return
 *                          value of getenv("PATH").
 * Output:
 *  return           int    0 - OK.
 *                          1 - An error occurred.
 */
int pca_scan_path(PathCache *pc, const char *path);

/*.......................................................................
 * If you want subsequent calls to pca_lookup_file() and
 * pca_path_completions() to only return the filenames of certain
 * types of files, for example executables, or filenames ending in
 * ".ps", call this function to register a file-selection callback
 * function. This callback function takes the full pathname of a file,
 * plus application-specific data, and returns 1 if the file is of
 * interest, and zero otherwise.
 *
 * Input:
 *  pc         PathCache *  The filename cache.
 *  check_fn  CplCheckFn *  The function to call to see if the name of
 *                          a given file should be included in the
 *                          cache. This determines what type of files
 *                          will reside in the cache. To revert to
 *                          selecting all files, regardless of type,
 *                          pass 0 here.
 *  data            void *  You can pass a pointer to anything you
 *                          like here, including NULL. It will be
 *                          passed to your check_fn() callback
 *                          function, for its private use.
 */
void pca_set_check_fn(PathCache *pc, CplCheckFn *check_fn, void *data);

/*.......................................................................
 * Given the simple name of a file, search the cached list of files
 * in the order in which they where found in the list of directories
 * previously presented to pca_scan_path(), and return the pathname
 * of the first file which has this name.
 *
 * Input:
 *  pc     PathCache *  The cached list of files.
 *  name  const char *  The name of the file to lookup.
 *  name_len     int    The length of the filename substring at the
 *                      beginning of name[], or -1 to assume that the
 *                      filename occupies the whole of the string.
 *  literal      int    If this argument is zero, lone backslashes
 *                      in name[] are ignored during comparison
 *                      with filenames in the cache, under the
 *                      assumption that they were in the input line
 *                      soley to escape the special significance of
 *                      characters like spaces. To have them treated
 *                      as normal characters, give this argument a
 *                      non-zero value, such as 1.
 * Output:
 *  return      char *  The pathname of the first matching file,
 *                      or NULL if not found. Note that the returned
 *                      pointer points to memory owned by *pc, and
 *                      will become invalid on the next call.
 */
char *pca_lookup_file(PathCache *pc, const char *name, int name_len,
		      int literal);

/*
 * Objects of the following type can be used to change the default
 * behavior of the pca_path_completions() callback function.
 */
typedef struct PcaPathConf PcaPathConf;

/*
 * pca_path_completions() is a completion callback function for use directly
 * with cpl_complete_word() or gl_customize_completions(), or indirectly
 * from your own completion callback function. It requires that a PcaPathConf
 * object be passed via its 'void *data' argument (see below).
 */
CPL_MATCH_FN(pca_path_completions);

/*.......................................................................
 * Allocate and initialize a pca_path_completions() configuration object.
 *
 * Input:
 *  pc         PathCache *  The filename cache in which to look for
 *                          file name completions.
 * Output:
 *  return   PcaPathConf *  The new configuration structure, or NULL
 *                          on error.
 */
PcaPathConf *new_PcaPathConf(PathCache *pc);

/*.......................................................................
 * Deallocate memory, previously allocated by new_PcaPathConf().
 *
 * Input:
 *  ppc     PcaPathConf *  Any pointer previously returned by
 *                         new_PcaPathConf() [NULL is allowed].
 * Output:
 *  return  PcaPathConf *  The deleted structure (always NULL).
 */
PcaPathConf *del_PcaPathConf(PcaPathConf *ppc);

/*
 * If backslashes in the prefix being passed to pca_path_completions()
 * should be treated as literal characters, call the following function
 * with literal=1. Otherwise the default is to treat them as escape
 * characters which remove the special meanings of spaces etc..
 */
void ppc_literal_escapes(PcaPathConf *ppc, int literal);

/*
 * Before calling pca_path_completions, call this function if you know
 * the index at which the filename prefix starts in the input line.
 * Otherwise by default, or if you specify start_index to be -1, the
 * filename is taken to start after the first unescaped space preceding
 * the cursor, or the start of the line, whichever comes first.
 */
void ppc_file_start(PcaPathConf *ppc, int start_index);

#ifdef __cplusplus
}
#endif

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/libtecla.map000066400000000000000000000101121211610345200231460ustar00rootroot00000000000000# This mapfile (or version script) lists the public symbols that are
# publically exported by each version of the tecla library. This file
# has the format required by the Sun and Linux linkers, and also acts
# as a template from which map files for other systems can be derived
# with awk or sed.
#
# Under Solaris and Linux, this map file is used by ld during shared
# library creation. It has two purposes:
#
# 1. It specifies which symbols in the library are to be made visible
#    to applications. This has the dual benefits of reducing namespace
#    polution, and of preventing applications from using private
#    internal library functions that might change or disappear in
#    future releases.
#
# 2. The information listed in this file is recorded in the shared
#    library, such that when an application is linked against it, the
#    linker can record a dependency in the application which says
#    which is the earliest library version which included all of the
#    symbols that the application needs. This means that if the
#    application is copied to another system that has an earlier
#    version of the library, the linker can quickly determine whether
#    the earlier version contains all of the symbols that it needs.
#
# Under Linux, mapfiles can also be used to allow multiple
# incompatible versions of a given function to exist in a library,
# thus supporting applications that were compiled against different
# incompatible versions of the library. Since this feature (and the
# inclusion of .symver directives) isn't supported by Solaris, it
# can't be included in this file. Non backwards compatibility in the
# ABI must instead be handled in the more traditional way, by
# incrementing the major version number.
#
# When a new minor release is made, a new tecla_1.x specification
# should be added which inherits the symbols of the previous release
# and lists newly added functions. For example, below you will find
# the following clause:
#
# tecla_1.3 {
#    global:
#	ef_list_expansions;
# } tecla_1.2;
#
# This says that ef_list_expansions is the name of a public function
# that was added in the 1.3 release, and that the symbols defined in
# the previous tecla_1.2 clause have been inherited by tecla_1.3.
#
# For more details see the following URL:
#
# http://www.usenix.org/publications/library/proceedings/als2000/browndavid.html
#-------------------------------------------------------------------------------

tecla_1.2 {
    global:
	cfc_file_start;
	cfc_literal_escapes;
	cfc_set_check_fn;
	cpl_add_completion;
	cpl_check_exe;
	cpl_complete_word;
	cpl_file_completions;
	cpl_init_FileArgs;
	cpl_last_error;
	cpl_list_completions;
	cpl_record_error;
	del_CplFileConf;
	del_ExpandFile;
	del_GetLine;
	del_PathCache;
	del_PcaPathConf;
	del_WordCompletion;
	ef_expand_file;
	ef_last_error;
	gl_change_terminal;
	gl_customize_completion;
	gl_get_line;
	new_CplFileConf;
	new_ExpandFile;
	new_GetLine;
	new_PathCache;
	new_PcaPathConf;
	new_WordCompletion;
	pca_last_error;
	pca_lookup_file;
	pca_path_completions;
	pca_scan_path;
	pca_set_check_fn;
	ppc_file_start;
	ppc_literal_escapes;

    local:
	*;
};

tecla_1.3 {
    global:
	ef_list_expansions;
} tecla_1.2;

tecla_1.4 {
    global:
	gl_configure_getline;
	gl_save_history;
	gl_load_history;
	gl_group_history;
	gl_show_history;
	gl_resize_history;
	gl_limit_history;
	gl_clear_history;
	gl_toggle_history;
	gl_watch_fd;
	libtecla_version;
	gl_terminal_size;
	gl_state_of_history;
	gl_range_of_history;
	gl_size_of_history;
	gl_lookup_history;
	gl_echo_mode;
	gl_replace_prompt;
	gl_prompt_style;
	gl_ignore_signal;
	gl_trap_signal;
	gl_last_signal;
} tecla_1.3;

tecla_l.5 {
   global:
	gl_inactivity_timeout;
	gl_completion_action;
	gl_register_action;
	gl_display_text;
	gl_error_message;
	gl_return_status;
	gl_set_term_size;
        gl_list_signals;
	gl_catch_blocked;
	gl_io_mode;
	gl_raw_io;
	gl_normal_io;
	gl_tty_signals;
	gl_abandon_line;
	gl_handle_signal;
	gl_pending_io;
	gl_bind_keyseq;
	cpl_recall_matches;
	gl_erase_terminal;
} tecla_1.4;

tecla_1.6 {
   global:
	gl_append_history;
	gl_automatic_history;
	gl_query_char;
	gl_read_char;
} tecla_l.5;
genometools-1.5.1/src/external/libtecla-1.6.1/pathutil.c000066400000000000000000000363301211610345200227000ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * If file-system access is to be excluded, this module has no function,
 * so all of its code should be excluded.
 */
#ifndef WITHOUT_FILE_SYSTEM

#include 
#include 
#include 
#include 
#include 
#include 

#include 
#include 
#include 

#include "pathutil.h"

/*.......................................................................
 * Create a new PathName object.
 *
 * Output:
 *  return  PathName *  The new object, or NULL on error.
 */
PathName *_new_PathName(void)
{
  PathName *path;  /* The object to be returned */
/*
 * Allocate the container.
 */
  path = (PathName *) malloc(sizeof(PathName));
  if(!path) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to _del_PathName().
 */
  path->name = NULL;
  path->dim = 0;
/*
 * Figure out the maximum length of an expanded pathname.
 */
  path->dim = _pu_pathname_dim();
  if(path->dim == 0)
    return _del_PathName(path);
/*
 * Allocate the pathname buffer.
 */
  path->name = (char *)malloc(path->dim * sizeof(char));
  if(!path->name) {
    errno = ENOMEM;
    return _del_PathName(path);
  };
  return path;
}

/*.......................................................................
 * Delete a PathName object.
 *
 * Input:
 *  path   PathName *  The object to be deleted.
 * Output:
 *  return PathName *  The deleted object (always NULL).
 */
PathName *_del_PathName(PathName *path)
{
  if(path) {
    if(path->name)
      free(path->name);
    free(path);
  };
  return NULL;
}

/*.......................................................................
 * Return the pathname to a zero-length string.
 *
 * Input:
 *  path     PathName *  The pathname container.
 * Output:
 *  return       char *  The cleared pathname buffer, or NULL on error.
 */
char *_pn_clear_path(PathName *path)
{
/*
 * Check the arguments.
 */
  if(!path) {
    errno = EINVAL;
    return NULL;
  };
  path->name[0] = '\0';
  return path->name;
}

/*.......................................................................
 * Append a string to a pathname, increasing the size of the pathname
 * buffer if needed.
 *
 * Input:
 *  path        PathName *  The pathname container.
 *  string    const char *  The string to be appended to the pathname.
 *                          Note that regardless of the slen argument,
 *                          this should be a '\0' terminated string.
 *  slen             int    The maximum number of characters to append
 *                          from string[], or -1 to append the whole
 *                          string.
 *  remove_escapes   int    If true, remove the backslashes that escape
 *                          spaces, tabs, backslashes etc..
 * Output:
 *  return          char *  The pathname string path->name[], which may
 *                          have been reallocated, or NULL if there was
 *                          insufficient memory to extend the pathname.
 */
char *_pn_append_to_path(PathName *path, const char *string, int slen,
			int remove_escapes)
{
  int pathlen;     /* The length of the pathname */
  int i;
/*
 * Check the arguments.
 */
  if(!path || !string) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Get the current length of the pathname.
 */
  pathlen = strlen(path->name);
/*
 * How many characters should be appended?
 */
  if(slen < 0 || slen > strlen(string))
    slen = strlen(string);
/*
 * Resize the pathname if needed.
 */
  if(!_pn_resize_path(path, pathlen + slen))
    return NULL;
/*
 * Append the string to the output pathname, removing any escape
 * characters found therein.
 */
  if(remove_escapes) {
    int is_escape = 0;
    for(i=0; iname[pathlen++] = string[i];
    };
/*
 * Terminate the string.
 */
    path->name[pathlen] = '\0';
  } else {
/*
 * Append the string directly to the pathname.
 */
    memcpy(path->name + pathlen, string, slen);
    path->name[pathlen + slen] = '\0';
  };
  return path->name;
}

/*.......................................................................
 * Prepend a string to a pathname, increasing the size of the pathname
 * buffer if needed.
 *
 * Input:
 *  path        PathName *  The pathname container.
 *  string    const char *  The string to be prepended to the pathname.
 *                          Note that regardless of the slen argument,
 *                          this should be a '\0' terminated string.
 *  slen             int    The maximum number of characters to prepend
 *                          from string[], or -1 to append the whole
 *                          string.
 *  remove_escapes   int    If true, remove the backslashes that escape
 *                          spaces, tabs, backslashes etc..
 * Output:
 *  return          char *  The pathname string path->name[], which may
 *                          have been reallocated, or NULL if there was
 *                          insufficient memory to extend the pathname.
 */
char *_pn_prepend_to_path(PathName *path, const char *string, int slen,
			  int remove_escapes)
{
  int pathlen;     /* The length of the pathname */
  int shift;       /* The number of characters to shift the suffix by */
  int i,j;
/*
 * Check the arguments.
 */
  if(!path || !string) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Get the current length of the pathname.
 */
  pathlen = strlen(path->name);
/*
 * How many characters should be appended?
 */
  if(slen < 0 || slen > strlen(string))
    slen = strlen(string);
/*
 * Work out how far we need to shift the original path string to make
 * way for the new prefix. When removing escape characters, we need
 * final length of the new prefix, after unescaped backslashes have
 * been removed.
 */
  if(remove_escapes) {
    int is_escape = 0;
    for(shift=0,i=0; iname + shift, path->name, pathlen+1);
/*
 * Copy the new prefix into the vacated space at the beginning of the
 * output pathname, removing any escape characters if needed.
 */
  if(remove_escapes) {
    int is_escape = 0;
    for(i=j=0; iname[j++] = string[i];
    };
  } else {
    memcpy(path->name, string, slen);
  };
  return path->name;
}

/*.......................................................................
 * If needed reallocate a given pathname buffer to allow a string of
 * a given length to be stored in it.
 *
 * Input:
 *  path     PathName *  The pathname container object.
 *  length     size_t    The required length of the pathname buffer,
 *                       not including the terminating '\0'.
 * Output:
 *  return       char *  The pathname buffer, or NULL if there was
 *                       insufficient memory.
 */
char *_pn_resize_path(PathName *path, size_t length)
{
/*
 * Check the arguments.
 */
  if(!path) {
    errno = EINVAL;
    return NULL;
  };
/*
 * If the pathname buffer isn't large enough to accomodate a string
 * of the specified length, attempt to reallocate it with the new
 * size, plus space for a terminating '\0'. Also add a bit of
 * head room to prevent too many reallocations if the initial length
 * turned out to be very optimistic.
 */
  if(length + 1 > path->dim) {
    size_t dim =  length + 1 + PN_PATHNAME_INC;
    char *name = (char *) realloc(path->name, dim);
    if(!name)
      return NULL;
    path->name = name;
    path->dim = dim;
  };
  return path->name;
}

/*.......................................................................
 * Estimate the largest amount of space needed to store a pathname.
 *
 * Output:
 *  return size_t   The number of bytes needed, including space for the
 *                  terminating '\0'.
 */
size_t _pu_pathname_dim(void)
{
  int maxlen;   /* The return value excluding space for the '\0' */
/*
 * If the POSIX PATH_MAX macro is defined in limits.h, use it.
 */
#ifdef PATH_MAX
  maxlen = PATH_MAX;
/*
 * If we have pathconf, use it.
 */
#elif defined(_PC_PATH_MAX)
  errno = 0;
  maxlen = pathconf(FS_ROOT_DIR, _PC_PATH_MAX);
  if(maxlen <= 0 || errno)
    maxlen = MAX_PATHLEN_FALLBACK;
/*
 * None of the above approaches worked, so substitute our fallback
 * guess.
 */
#else
    maxlen = MAX_PATHLEN_FALLBACK;
#endif
/*
 * Return the amount of space needed to accomodate a pathname plus
 * a terminating '\0'.
 */
  return maxlen + 1;
}

/*.......................................................................
 * Return non-zero if the specified path name refers to a directory.
 *
 * Input:
 *  pathname  const char *  The path to test.
 * Output:
 *  return           int    0 - Not a directory.
 *                          1 - pathname[] refers to a directory.
 */
int _pu_path_is_dir(const char *pathname)
{
  struct stat statbuf;    /* The file-statistics return buffer */
/*
 * Look up the file attributes.
 */
  if(stat(pathname, &statbuf) < 0)
    return 0;
/*
 * Is the file a directory?
 */
  return S_ISDIR(statbuf.st_mode) != 0;
}

/*.......................................................................
 * Return non-zero if the specified path name refers to a regular file.
 *
 * Input:
 *  pathname  const char *  The path to test.
 * Output:
 *  return           int    0 - Not a regular file.
 *                          1 - pathname[] refers to a regular file.
 */
int _pu_path_is_file(const char *pathname)
{
  struct stat statbuf;    /* The file-statistics return buffer */
/*
 * Look up the file attributes.
 */
  if(stat(pathname, &statbuf) < 0)
    return 0;
/*
 * Is the file a regular file?
 */
  return S_ISREG(statbuf.st_mode) != 0;
}

/*.......................................................................
 * Return non-zero if the specified path name refers to an executable.
 *
 * Input:
 *  pathname  const char *  The path to test.
 * Output:
 *  return           int    0 - Not an executable file.
 *                          1 - pathname[] refers to an executable file.
 */
int _pu_path_is_exe(const char *pathname)
{
  struct stat statbuf;    /* The file-statistics return buffer */
/*
 * Look up the file attributes.
 */
  if(stat(pathname, &statbuf) < 0)
    return 0;
/*
 * Is the file a regular file which is executable by the current user.
 */
  return S_ISREG(statbuf.st_mode) != 0 &&
    (statbuf.st_mode & (S_IXOTH | S_IXGRP | S_IXUSR)) &&
    access(pathname, X_OK) == 0;
}

/*.......................................................................
 * Search backwards for the potential start of a filename. This
 * looks backwards from the specified index in a given string,
 * stopping at the first unescaped space or the start of the line.
 *
 * Input:
 *  string  const char *  The string to search backwards in.
 *  back_from      int    The index of the first character in string[]
 *                        that follows the pathname.
 * Output:
 *  return        char *  The pointer to the first character of
 *                        the potential pathname, or NULL on error.
 */
char *_pu_start_of_path(const char *string, int back_from)
{
  int i, j;
/*
 * Check the arguments.
 */
  if(!string || back_from < 0) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Search backwards from the specified index.
 */
  for(i=back_from-1; i>=0; i--) {
    int c = string[i];
/*
 * Stop on unescaped spaces.
 */
    if(isspace((int)(unsigned char)c)) {
/*
 * The space can't be escaped if we are at the start of the line.
 */
      if(i==0)
        break;
/*
 * Find the extent of the escape characters which precedes the space.
 */
      for(j=i-1; j>=0 && string[j]=='\\'; j--)
	;
/*
 * If there isn't an odd number of escape characters before the space,
 * then the space isn't escaped.
 */
      if((i - 1 - j) % 2 == 0)
	break;
    };
  };
  return (char *)string + i + 1;
}

/*.......................................................................
 * Find the length of a potential filename starting from a given
 * point. This looks forwards from the specified index in a given string,
 * stopping at the first unescaped space or the end of the line.
 *
 * Input:
 *  string   const char *  The string to search backwards in.
 *  start_from      int    The index of the first character of the pathname
 *                         in string[].
 * Output:
 *  return         char *  The pointer to the character that follows
 *                         the potential pathname, or NULL on error.
 */
char *_pu_end_of_path(const char *string, int start_from)
{
  int c;             /* The character being examined */
  int escaped = 0;   /* True when the next character is escaped */
  int i;
/*
 * Check the arguments.
 */
  if(!string || start_from < 0) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Search forwards from the specified index.
 */
  for(i=start_from; (c=string[i]) != '\0'; i++) {
    if(escaped) {
      escaped = 0;
    } else if(isspace(c)) {
      break;
    } else if(c == '\\') {
      escaped = 1;
    };
  };
  return (char *)string + i;
}

/*.......................................................................
 * Return non-zero if the specified path name refers to an existing file.
 *
 * Input:
 *  pathname   const char *  The path to test.
 * Output:
 *  return            int    0 - The file doesn't exist.
 *                           1 - The file does exist.
 */
int _pu_file_exists(const char *pathname)
{
  struct stat statbuf;
  return stat(pathname, &statbuf) == 0;
}

#endif  /* ifndef WITHOUT_FILE_SYSTEM */
genometools-1.5.1/src/external/libtecla-1.6.1/pathutil.h000066400000000000000000000105631211610345200227050ustar00rootroot00000000000000#ifndef pathutil_h
#define pathutil_h

/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * The following object encapsulates a buffer designed to be used to
 * store pathnames. The pathname member of the object is initially
 * allocated with the size that _pu_pathname_dim() returns, and then
 * if this turns out to be pessimistic, the pathname can be reallocated
 * via calls to pb_append_to_path() and/or pb_resize_path().
 */
typedef struct {
  char *name;         /* The path buffer */
  size_t dim;         /* The current allocated size of buffer[] */
} PathName;

PathName *_new_PathName(void);
PathName *_del_PathName(PathName *path);

char *_pn_clear_path(PathName *path);
char *_pn_append_to_path(PathName *path, const char *string, int slen,
			int remove_escapes);
char *_pn_prepend_to_path(PathName *path, const char *string, int slen,
			  int remove_escapes);
char *_pn_resize_path(PathName *path, size_t length);

/*
 * Search backwards for the potential start of a filename. This
 * looks backwards from the specified index in a given string,
 * stopping at the first unescaped space or the start of the line.
 */
char *_pu_start_of_path(const char *string, int back_from);

/*
 * Find the end of a potential filename, starting from a given index
 * in the string. This looks forwards from the specified index in a
 * given string, stopping at the first unescaped space or the end
 * of the line.
 */
char *_pu_end_of_path(const char *string, int start_from);


/*
 * Return an estimate of the the length of the longest pathname
 * on the local system.
 */
size_t _pu_pathname_dim(void);

/*
 * Return non-zero if the specified path name refers to a directory.
 */
int _pu_path_is_dir(const char *pathname);

/*
 * Return non-zero if the specified path name refers to a regular file.
 */
int _pu_path_is_file(const char *pathname);

/*
 * Return non-zero if the specified path name refers to an executable.
 */
int _pu_path_is_exe(const char *pathname);

/*
 * Return non-zero if a file exists with the specified pathname.
 */
int _pu_file_exists(const char *pathname);

/*
 * If neither the POSIX PATH_MAX macro nor the pathconf() function
 * can be used to find out the maximum pathlength on the target
 * system, the following fallback maximum length is used.
 */
#define MAX_PATHLEN_FALLBACK 1024

/*
 * If the pathname buffer turns out to be too small, it will be extended
 * in chunks of the following amount (plus whatever is needed at the time).
 */
#define PN_PATHNAME_INC 100

/*
 * Define the special character-sequences of the filesystem.
 */
#define FS_ROOT_DIR "/"     /* The root directory */
#define FS_ROOT_DIR_LEN (sizeof(FS_ROOT_DIR) - 1)
#define FS_PWD "."          /* The current working directory */
#define FS_PWD_LEN (sizeof(FS_PWD_LEN) - 1)
#define FS_DIR_SEP "/"      /* The directory separator string */
#define FS_DIR_SEP_LEN (sizeof(FS_DIR_SEP) - 1)

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/pcache.c000066400000000000000000001521771211610345200223010ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * If file-system access is to be excluded, this module has no function,
 * so all of its code should be excluded.
 */
#ifndef WITHOUT_FILE_SYSTEM

#include 
#include 
#include 
#include 

#include "libtecla.h"
#include "pathutil.h"
#include "homedir.h"
#include "freelist.h"
#include "direader.h"
#include "stringrp.h"
#include "errmsg.h"

/*
 * The new_PcaPathConf() constructor sets the integer first member of
 * the returned object to the following magic number. This is then
 * checked for by pca_path_completions() as a sanity check.
 */
#define PPC_ID_CODE 4567

/*
 * A pointer to a structure of the following type can be passed to
 * the builtin path-completion callback function to modify its behavior.
 */
struct PcaPathConf {
  int id;          /* This is set to PPC_ID_CODE by new_PcaPathConf() */
  PathCache *pc;   /* The path-list cache in which to look up the executables */
  int escaped;     /* If non-zero, backslashes in the input line are */
                   /*  interpreted as escaping special characters and */
                   /*  spaces, and any special characters and spaces in */
                   /*  the listed completions will also be escaped with */
                   /*  added backslashes. This is the default behaviour. */
                   /* If zero, backslashes are interpreted as being */
                   /*  literal parts of the file name, and none are added */
                   /*  to the completion suffixes. */
  int file_start;  /* The index in the input line of the first character */
                   /*  of the file name. If you specify -1 here, */
                   /*  pca_path_completions() identifies the */
                   /*  the start of the file by looking backwards for */
                   /*  an unescaped space, or the beginning of the line. */
};

/*
 * Prepended to each chached filename is a character which contains
 * one of the following status codes. When a given filename (minus
 * this byte) is passed to the application's check_fn(), the result
 * is recorded in this byte, such that the next time it is looked
 * up, we don't have to call check_fn() again. These codes are cleared
 * whenever the path is scanned and whenever the check_fn() callback
 * is changed.
 */
typedef enum {
  PCA_F_ENIGMA='?', /* The file remains to be checked */
  PCA_F_WANTED='+', /* The file has been selected by the caller's callback */
  PCA_F_IGNORE='-'  /* The file has been rejected by the caller's callback */
} PcaFileStatus;

/*
 * Encapsulate the memory management objects which supply memoy for
 * the arrays of filenames.
 */
typedef struct {
  StringGroup *sg;       /* The memory used to record the names of files */
  size_t files_dim;      /* The allocated size of files[] */
  char **files;          /* Memory for 'files_dim' pointers to files */
  size_t nfiles;         /* The number of filenames currently in files[] */
} CacheMem;

static CacheMem *new_CacheMem(void);
static CacheMem *del_CacheMem(CacheMem *cm);
static void rst_CacheMem(CacheMem *cm);

/*
 * Lists of nodes of the following type are used to record the
 * names and contents of individual directories.
 */
typedef struct PathNode PathNode;
struct PathNode {
  PathNode *next;   /* The next directory in the path */
  int relative;     /* True if the directory is a relative pathname */
  CacheMem *mem;    /* The memory used to store dir[] and files[] */
  char *dir;        /* The directory pathname (stored in pc->sg) */
  int nfile;        /* The number of filenames stored in 'files' */
  char **files;     /* Files of interest in the current directory, */
                    /*  or NULL if dir[] is a relative pathname */
                    /*  who's contents can't be cached. This array */
                    /*  and its contents are taken from pc->abs_mem */
                    /*  or pc->rel_mem */
};

/*
 * Append a new node to the list of directories in the path.
 */
static int add_PathNode(PathCache *pc, const char *dirname);

/*
 * Set the maximum length allowed for usernames.
 * names.
 */
#define USR_LEN 100

/*
 * PathCache objects encapsulate the resources needed to record
 * files of interest from comma-separated lists of directories.
 */
struct PathCache {
  ErrMsg *err;           /* The error reporting buffer */
  FreeList *node_mem;    /* A free-list of PathNode objects */
  CacheMem *abs_mem;     /* Memory for the filenames of absolute paths */
  CacheMem *rel_mem;     /* Memory for the filenames of relative paths */
  PathNode *head;        /* The head of the list of directories in the */
                         /*  path, or NULL if no path has been scanned yet. */
  PathNode *tail;        /* The tail of the list of directories in the */
                         /*  path, or NULL if no path has been scanned yet. */
  PathName *path;        /* The fully qualified name of a file */
  HomeDir *home;         /* Home-directory lookup object */
  DirReader *dr;         /* A portable directory reader */
  CplFileConf *cfc;      /* Configuration parameters to pass to */
                         /*  cpl_file_completions() */
  CplCheckFn *check_fn;  /* The callback used to determine if a given */
                         /*  filename should be recorded in the cache. */
  void *data;            /* Annonymous data to be passed to pc->check_fn() */
  char usrnam[USR_LEN+1];/* The buffer used when reading the names of */
                         /*  users. */
};

/*
 * Empty the cache.
 */
static void pca_clear_cache(PathCache *pc);

/*
 * Read a username from string[] and record it in pc->usrnam[].
 */
static int pca_read_username(PathCache *pc, const char *string, int slen,
			     int literal, const char **nextp);

/*
 * Extract the next component of a colon separated list of directory
 * paths.
 */
static int pca_extract_dir(PathCache *pc, const char *path,
			   const char **nextp);

/*
 * Scan absolute directories for files of interest, recording their names
 * in mem->sg and recording pointers to these names in mem->files[].
 */
static int pca_scan_dir(PathCache *pc, const char *dirname, CacheMem *mem);

/*
 * A qsort() comparison function for comparing the cached filename
 * strings pointed to by two (char **) array elements. Note that
 * this ignores the initial cache-status byte of each filename.
 */
static int pca_cmp_matches(const void *v1, const void *v2);

/*
 * A qsort() comparison function for comparing a filename
 * against an element of an array of pointers to filename cache
 * entries.
 */
static int pca_cmp_file(const void *v1, const void *v2);

/*
 * Initialize a PcaPathConf configuration objects with the default
 * options.
 */
static int pca_init_PcaPathConf(PcaPathConf *ppc, PathCache *pc);

/*
 * Make a copy of a completion suffix, suitable for passing to
 * cpl_add_completion().
 */
static int pca_prepare_suffix(PathCache *pc, const char *suffix,
			      int add_escapes);

/*
 * Return non-zero if the specified string appears to start with a pathname.
 */
static int cpa_cmd_contains_path(const char *prefix, int prefix_len);

/*
 * Return a given prefix with escapes optionally removed.
 */
static const char *pca_prepare_prefix(PathCache *pc, const char *prefix,
				      size_t prefix_len, int escaped);

/*
 * If there is a tilde expression at the beginning of the specified path,
 * place the corresponding home directory into pc->path. Otherwise
 * just clear pc->path.
 */
static int pca_expand_tilde(PathCache *pc, const char *path, int pathlen,
			    int literal, const char **endp);

/*
 * Clear the filename status codes that are recorded before each filename
 * in the cache.
 */
static void pca_remove_marks(PathCache *pc);

/*
 * Specify how many PathNode's to allocate at a time.
 */
#define PATH_NODE_BLK 30

/*
 * Specify the amount by which the files[] arrays are to be extended
 * whenever they are found to be too small.
 */
#define FILES_BLK_FACT 256

/*.......................................................................
 * Create a new object who's function is to maintain a cache of
 * filenames found within a list of directories, and provide quick
 * lookup and completion of selected files in this cache.
 *
 * Output:
 *  return     PathCache *  The new, initially empty cache, or NULL
 *                          on error.
 */
PathCache *new_PathCache(void)
{
  PathCache *pc;  /* The object to be returned */
/*
 * Allocate the container.
 */
  pc = (PathCache *)malloc(sizeof(PathCache));
  if(!pc) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_PathCache().
 */
  pc->err = NULL;
  pc->node_mem = NULL;
  pc->abs_mem = NULL;
  pc->rel_mem = NULL;
  pc->head = NULL;
  pc->tail = NULL;
  pc->path = NULL;
  pc->home = NULL;
  pc->dr = NULL;
  pc->cfc = NULL;
  pc->check_fn = 0;
  pc->data = NULL;
  pc->usrnam[0] = '\0';
/*
 * Allocate a place to record error messages.
 */
  pc->err = _new_ErrMsg();
  if(!pc->err)
    return del_PathCache(pc);
/*
 * Allocate the freelist of directory list nodes.
 */
  pc->node_mem = _new_FreeList(sizeof(PathNode), PATH_NODE_BLK);
  if(!pc->node_mem)
    return del_PathCache(pc);
/*
 * Allocate memory for recording names of files in absolute paths.
 */
  pc->abs_mem = new_CacheMem();
  if(!pc->abs_mem)
    return del_PathCache(pc);
/*
 * Allocate memory for recording names of files in relative paths.
 */
  pc->rel_mem = new_CacheMem();
  if(!pc->rel_mem)
    return del_PathCache(pc);
/*
 * Allocate a pathname buffer.
 */
  pc->path = _new_PathName();
  if(!pc->path)
    return del_PathCache(pc);
/*
 * Allocate an object for looking up home-directories.
 */
  pc->home = _new_HomeDir();
  if(!pc->home)
    return del_PathCache(pc);
/*
 * Allocate an object for reading directories.
 */
  pc->dr = _new_DirReader();
  if(!pc->dr)
    return del_PathCache(pc);
/*
 * Allocate a cpl_file_completions() configuration object.
 */
  pc->cfc = new_CplFileConf();
  if(!pc->cfc)
    return del_PathCache(pc);
/*
 * Configure cpl_file_completions() to use check_fn() to select
 * files of interest.
 */
  cfc_set_check_fn(pc->cfc, pc->check_fn, pc->data);
/*
 * Return the cache, ready for use.
 */
  return pc;
}

/*.......................................................................
 * Delete a given cache of files, returning the resources that it
 * was using to the system.
 *
 * Input:
 *  pc      PathCache *  The cache to be deleted (can be NULL).
 * Output:
 *  return  PathCache *  The deleted object (ie. allways NULL).
 */
PathCache *del_PathCache(PathCache *pc)
{
  if(pc) {
/*
 * Delete the error message buffer.
 */
    pc->err = _del_ErrMsg(pc->err);
/*
 * Delete the memory of the list of path nodes.
 */
    pc->node_mem = _del_FreeList(pc->node_mem, 1);
/*
 * Delete the memory used to record filenames.
 */
    pc->abs_mem = del_CacheMem(pc->abs_mem);
    pc->rel_mem = del_CacheMem(pc->rel_mem);
/*
 * The list of PathNode's was already deleted when node_mem was
 * deleted.
 */
    pc->head = NULL;
    pc->tail = NULL;
/*
 * Delete the pathname buffer.
 */
    pc->path = _del_PathName(pc->path);
/*
 * Delete the home-directory lookup object.
 */
    pc->home = _del_HomeDir(pc->home);
/*
 * Delete the directory reader.
 */
    pc->dr = _del_DirReader(pc->dr);
/*
 * Delete the cpl_file_completions() config object.
 */
    pc->cfc = del_CplFileConf(pc->cfc);
/*
 * Delete the container.
 */
    free(pc);
  };
  return NULL;
}

/*.......................................................................
 * If you want subsequent calls to pca_lookup_file() and
 * pca_path_completions() to only return the filenames of certain
 * types of files, for example executables, or filenames ending in
 * ".ps", call this function to register a file-selection callback
 * function. This callback function takes the full pathname of a file,
 * plus application-specific data, and returns 1 if the file is of
 * interest, and zero otherwise.
 *
 * Input:
 *  pc         PathCache *  The filename cache.
 *  check_fn  CplCheckFn *  The function to call to see if the name of
 *                          a given file should be included in the
 *                          cache. This determines what type of files
 *                          will reside in the cache. To revert to
 *                          selecting all files, regardless of type,
 *                          pass 0 here.
 *  data            void *  You can pass a pointer to anything you
 *                          like here, including NULL. It will be
 *                          passed to your check_fn() callback
 *                          function, for its private use.
 */
void pca_set_check_fn(PathCache *pc, CplCheckFn *check_fn, void *data)
{
  if(pc) {
/*
 * If the callback or its data pointer have changed, clear the cached
 * statuses of files that were accepted or rejected by the previous
 * calback.
 */
    if(check_fn != pc->check_fn || data != pc->data)
      pca_remove_marks(pc);
/*
 * Record the new callback locally.
 */
    pc->check_fn = check_fn;
    pc->data = data;
/*
 * Configure cpl_file_completions() to use the same callback to
 * select files of interest.
 */
    cfc_set_check_fn(pc->cfc, check_fn, data);
  };
  return;
}

/*.......................................................................
 * Return a description of the last path-caching error that occurred.
 *
 * Input:
 *  pc     PathCache *   The filename cache that suffered the error.
 * Output:
 *  return      char *   The description of the last error.
 */
const char *pca_last_error(PathCache *pc)
{
  return pc ? _err_get_msg(pc->err) : "NULL PathCache argument";
}

/*.......................................................................
 * Discard all cached filenames.
 *
 * Input:
 *  pc   PathCache *  The cache to be cleared.
 */
static void pca_clear_cache(PathCache *pc)
{
  if(pc) {
/*
 * Return all path-nodes to the freelist.
 */
    _rst_FreeList(pc->node_mem);
    pc->head = pc->tail = NULL;
/*
 * Delete all filename strings.
 */
    rst_CacheMem(pc->abs_mem);
    rst_CacheMem(pc->rel_mem);
  };
  return;
}

/*.......................................................................
 * Build the list of files of interest contained in a given
 * colon-separated list of directories.
 *
 * Input:
 *  pc         PathCache *  The cache in which to store the names of
 *                          the files that are found in the list of
 *                          directories.
 *  path      const char *  A colon-separated list of directory
 *                          paths. Under UNIX, when searching for
 *                          executables, this should be the return
 *                          value of getenv("PATH").
 * Output:
 *  return           int    0 - OK.
 *                          1 - An error occurred. A description of
 *                              the error can be acquired by calling
 *                              pca_last_error(pc).
 */
int pca_scan_path(PathCache *pc, const char *path)
{
  const char *pptr; /* A pointer to the next unprocessed character in path[] */
  PathNode *node;   /* A node in the list of directory paths */
  char **fptr;      /* A pointer into pc->abs_mem->files[] */
/*
 * Check the arguments.
 */
  if(!pc)
    return 1;
/*
 * Clear the outdated contents of the cache.
 */
  pca_clear_cache(pc);
/*
 * If no path list was provided, there is nothing to be added to the
 * cache.
 */
  if(!path)
    return 0;
/*
 * Extract directories from the path list, expanding tilde expressions
 * on the fly into pc->pathname, then add them to the list of path
 * nodes, along with a sorted list of the filenames of interest that
 * the directories hold.
 */
  pptr = path;
  while(*pptr) {
/*
 * Extract the next pathname component into pc->path->name.
 */
    if(pca_extract_dir(pc, pptr, &pptr))
      return 1;
/*
 * Add a new node to the list of paths, containing both the
 * directory name and, if not a relative pathname, the list of
 * files of interest in the directory.
 */
    if(add_PathNode(pc, pc->path->name))
      return 1;
  };
/*
 * The file arrays in each absolute directory node are sections of
 * pc->abs_mem->files[]. Record pointers to the starts of each
 * of these sections in each directory node. Note that this couldn't
 * be done in add_PathNode(), because pc->abs_mem->files[] may
 * get reallocated in subsequent calls to add_PathNode(), thus
 * invalidating any pointers to it.
 */
  fptr = pc->abs_mem->files;
  for(node=pc->head; node; node=node->next) {
    node->files = fptr;
    fptr += node->nfile;
  };
  return 0;
}

/*.......................................................................
 * Extract the next directory path from a colon-separated list of
 * directories, expanding tilde home-directory expressions where needed.
 *
 * Input:
 *  pc      PathCache *   The cache of filenames.
 *  path   const char *   A pointer to the start of the next component
 *                        in the path list.
 * Input/Output:
 *  nextp  const char **  A pointer to the next unprocessed character
 *                        in path[] will be assigned to *nextp.
 * Output:
 *  return        int     0 - OK. The extracted path is in pc->path->name.
 *                        1 - Error. A description of the error will
 *                            have been left in pc->err.
 */
static int pca_extract_dir(PathCache *pc, const char *path, const char **nextp)
{
  const char *pptr;         /* A pointer into path[] */
  const char *sptr;         /* The path following tilde expansion */
  int escaped = 0;          /* True if the last character was a backslash */
/*
 * If there is a tilde expression at the beginning of the specified path,
 * place the corresponding home directory into pc->path. Otherwise
 * just clear pc->path.
 */
  if(pca_expand_tilde(pc, path, strlen(path), 0, &pptr))
    return 1;
/*
 * Keep a record of the current location in the path.
 */
  sptr = pptr;
/*
 * Locate the end of the directory name in the pathname string, stopping
 * when either the end of the string is reached, or an un-escaped colon
 * separator is seen.
 */
  while(*pptr && (escaped || *pptr != ':'))
    escaped = !escaped && *pptr++ == '\\';
/*
 * Append the rest of the directory path to the pathname buffer.
 */
  if(_pn_append_to_path(pc->path, sptr, pptr - sptr, 1) == NULL) {
    _err_record_msg(pc->err, "Insufficient memory to record directory name",
		    END_ERR_MSG);
    return 1;
  };
/*
 * To facilitate subsequently appending filenames to the directory
 * path name, make sure that the recorded directory name ends in a
 * directory separator.
 */
  {
    int dirlen = strlen(pc->path->name);
    if(dirlen < FS_DIR_SEP_LEN ||
       strncmp(pc->path->name + dirlen - FS_DIR_SEP_LEN, FS_DIR_SEP,
	       FS_DIR_SEP_LEN) != 0) {
      if(_pn_append_to_path(pc->path, FS_DIR_SEP, FS_DIR_SEP_LEN, 0) == NULL) {
	_err_record_msg(pc->err, "Insufficient memory to record directory name",
			END_ERR_MSG);
	return 1;
      };
    };
  };
/*
 * Skip the separator unless we have reached the end of the path.
 */
  if(*pptr==':')
    pptr++;
/*
 * Return the unprocessed tail of the path-list string.
 */
  *nextp = pptr;
  return 0;
}

/*.......................................................................
 * Read a username, stopping when a directory separator is seen, a colon
 * separator is seen, the end of the string is reached, or the username
 * buffer overflows.
 *
 * Input:
 *  pc   PathCache *   The cache of filenames.
 *  string    char *   The string who's prefix contains the name.
 *  slen       int     The max number of characters to read from string[].
 *  literal    int     If true, treat backslashes as literal characters
 *                     instead of escapes.
 * Input/Output:
 *  nextp     char **  A pointer to the next unprocessed character
 *                     in string[] will be assigned to *nextp.
 * Output:
 *  return     int     0 - OK. The username can be found in pc->usrnam.
 *                     1 - Error. A description of the error message
 *                         can be found in pc->err.
 */
static int pca_read_username(PathCache *pc, const char *string, int slen,
			     int literal, const char **nextp)
{
  int usrlen;         /* The number of characters in pc->usrnam[] */
  const char *sptr;   /* A pointer into string[] */
  int escaped = 0;    /* True if the last character was a backslash */
/*
 * Extract the username.
 */
  for(sptr=string,usrlen=0; usrlen < USR_LEN && (sptr-string) < slen; sptr++) {
/*
 * Stop if the end of the string is reached, or a directory separator
 * or un-escaped colon separator is seen.
 */
    if(!*sptr || strncmp(sptr, FS_DIR_SEP, FS_DIR_SEP_LEN)==0 ||
       (!escaped && *sptr == ':'))
      break;
/*
 * Escape the next character?
 */
    if(!literal && !escaped && *sptr == '\\') {
      escaped = 1;
    } else {
      escaped = 0;
      pc->usrnam[usrlen++] = *sptr;
    };
  };
/*
 * Did the username overflow the buffer?
 */
  if(usrlen >= USR_LEN) {
    _err_record_msg(pc->err, "Username too long", END_ERR_MSG);
    return 1;
  };
/*
 * Terminate the string.
 */
  pc->usrnam[usrlen] = '\0';
/*
 * Indicate where processing of the input string should continue.
 */
  *nextp = sptr;
  return 0;
}


/*.......................................................................
 * Create a new CacheMem object.
 *
 * Output:
 *  return  CacheMem *  The new object, or NULL on error.
 */
static CacheMem *new_CacheMem(void)
{
  CacheMem *cm;  /* The object to be returned */
/*
 * Allocate the container.
 */
  cm = (CacheMem *)malloc(sizeof(CacheMem));
  if(!cm) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_CacheMem().
 */
  cm->sg = NULL;
  cm->files_dim = 0;
  cm->files = NULL;
  cm->nfiles = 0;
/*
 * Allocate a list of string segments for storing filenames.
 */
  cm->sg = _new_StringGroup(_pu_pathname_dim());
  if(!cm->sg)
    return del_CacheMem(cm);
/*
 * Allocate an array of pointers to filenames.
 * This will be extended later if needed.
 */
  cm->files_dim = FILES_BLK_FACT;
  cm->files = (char **) malloc(sizeof(*cm->files) * cm->files_dim);
  if(!cm->files) {
    errno = ENOMEM;
    return del_CacheMem(cm);
  };
  return cm;
}

/*.......................................................................
 * Delete a CacheMem object.
 *
 * Input:
 *  cm   CacheMem *  The object to be deleted.
 * Output:
 *  return CacheMem *  The deleted object (always NULL).
 */
static CacheMem *del_CacheMem(CacheMem *cm)
{
  if(cm) {
/*
 * Delete the memory that was used to record filename strings.
 */
    cm->sg = _del_StringGroup(cm->sg);
/*
 * Delete the array of pointers to filenames.
 */
    cm->files_dim = 0;
    if(cm->files) {
      free(cm->files);
      cm->files = NULL;
    };
/*
 * Delete the container.
 */
    free(cm);
  };
  return NULL;
}

/*.......................................................................
 * Re-initialize the memory used to allocate filename strings.
 *
 * Input:
 *  cm     CacheMem *  The memory cache to be cleared.
 */
static void rst_CacheMem(CacheMem *cm)
{
  _clr_StringGroup(cm->sg);
  cm->nfiles = 0;
  return;
}

/*.......................................................................
 * Append a new directory node to the list of directories read from the
 * path.
 *
 * Input:
 *  pc        PathCache *  The filename cache.
 *  dirname  const char *  The name of the new directory.
 * Output:
 *  return          int    0 - OK.
 *                         1 - Error.
 */
static int add_PathNode(PathCache *pc, const char *dirname)
{
  PathNode *node;  /* The new directory list node */
  int relative;    /* True if dirname[] is a relative pathname */
/*
 * Have we been passed a relative pathname or an absolute pathname?
 */
  relative = strncmp(dirname, FS_ROOT_DIR, FS_ROOT_DIR_LEN) != 0;
/*
 * If it's an absolute pathname, ignore it if the corresponding
 * directory doesn't exist.
 */
  if(!relative && !_pu_path_is_dir(dirname))
    return 0;
/*
 * Allocate a new list node to record the specifics of the new directory.
 */
  node = (PathNode *) _new_FreeListNode(pc->node_mem);
  if(!node) {
    _err_record_msg(pc->err, "Insufficient memory to cache new directory.",
		    END_ERR_MSG);
    return 1;
  };
/*
 * Initialize the node.
 */
  node->next = NULL;
  node->relative = relative;
  node->mem = relative ? pc->rel_mem : pc->abs_mem;
  node->dir = NULL;
  node->nfile = 0;
  node->files = NULL;
/*
 * Make a copy of the directory pathname.
 */
  node->dir = _sg_store_string(pc->abs_mem->sg, dirname, 0);
  if(!node->dir) {
    _err_record_msg(pc->err, "Insufficient memory to store directory name.",
		    END_ERR_MSG);
    return 1;
  };
/*
 * Scan absolute directories for files of interest, recording their names
 * in node->mem->sg and appending pointers to these names to the
 * node->mem->files[] array.
 */
  if(!node->relative) {
    int nfile = node->nfile = pca_scan_dir(pc, node->dir, node->mem);
    if(nfile < 1) {  /* No files matched or an error occurred */
      node = (PathNode *) _del_FreeListNode(pc->node_mem, node);
      return nfile < 0;
    };
  };
/*
 * Append the new node to the list.
 */
  if(pc->head) {
    pc->tail->next = node;
    pc->tail = node;
  } else {
    pc->head = pc->tail = node;
  };
  return 0;
}

/*.......................................................................
 * Scan a given directory for files of interest, record their names
 * in mem->sg and append pointers to them to the mem->files[] array.
 *
 * Input:
 *  pc        PathCache *  The filename cache.
 *  dirname  const char *  The pathname of the directory to be scanned.
 *  mem        CacheMem *  The memory in which to store filenames of
 *                         interest.
 * Output:
 *  return          int    The number of files recorded, or -1 if a
 *                         memory error occurs. Note that the
 *                         inability to read the contents of the
 *                         directory is not counted as an error.
 */
static int pca_scan_dir(PathCache *pc, const char *dirname, CacheMem *mem)
{
  int nfile = 0;        /* The number of filenames recorded */
  const char *filename; /* The name of the file being looked at */
/*
 * Attempt to open the directory. If the directory can't be read then
 * there are no accessible files of interest in the directory.
 */
  if(_dr_open_dir(pc->dr, dirname, NULL))
    return 0;
/*
 * Record the names of all files in the directory in the cache.
 */
  while((filename = _dr_next_file(pc->dr))) {
    char *copy;        /* A copy of the filename */
/*
 * Make a temporary copy of the filename with an extra byte prepended.
 */
    _pn_clear_path(pc->path);
    if(_pn_append_to_path(pc->path, " ", 1, 0) == NULL ||
       _pn_append_to_path(pc->path, filename, -1, 1) == NULL) {
      _err_record_msg(pc->err, "Insufficient memory to record filename",
		      END_ERR_MSG);
      return -1;
    };
/*
 * Store the filename.
 */
    copy = _sg_store_string(mem->sg, pc->path->name, 0);
    if(!copy) {
      _err_record_msg(pc->err, "Insufficient memory to cache file name.",
		      END_ERR_MSG);
      return -1;
    };
/*
 * Mark the filename as unchecked.
 */
    copy[0] = PCA_F_ENIGMA;
/*
 * Make room to store a pointer to the copy in mem->files[].
 */
    if(mem->nfiles + 1 > mem->files_dim) {
      int needed = mem->files_dim + FILES_BLK_FACT;
      char **files = (char **) realloc(mem->files, sizeof(*mem->files)*needed);
      if(!files) {
	_err_record_msg(pc->err,
			"Insufficient memory to extend filename cache.",
			END_ERR_MSG);
	return 1;
      };
      mem->files = files;
      mem->files_dim = needed;
    };
/*
 * Record a pointer to the copy of the filename at the end of the files[]
 * array.
 */
    mem->files[mem->nfiles++] = copy;
/*
 * Keep a record of the number of files matched so far.
 */
    nfile++;
  };
/*
 * Sort the list of files into lexical order.
 */
  qsort(mem->files + mem->nfiles - nfile, nfile, sizeof(*mem->files),
	pca_cmp_matches);
/*
 * Return the number of files recorded in mem->files[].
 */
  return nfile;
}

/*.......................................................................
 * A qsort() comparison function for comparing the cached filename
 * strings pointed to by two (char **) array elements. Note that
 * this ignores the initial cache-status byte of each filename.
 *
 * Input:
 *  v1, v2   void *  Pointers to the pointers of two strings to be compared.
 * Output:
 *  return    int    -1 -> v1 < v2.
 *                    0 -> v1 == v2
 *                    1 -> v1 > v2
 */
static int pca_cmp_matches(const void *v1, const void *v2)
{
  const char **s1 = (const char **) v1;
  const char **s2 = (const char **) v2;
  return strcmp(*s1+1, *s2+1);
}

/*.......................................................................
 * Given the simple name of a file, search the cached list of files
 * in the order in which they where found in the list of directories
 * previously presented to pca_scan_path(), and return the pathname
 * of the first file which has this name. If a pathname to a file is
 * given instead of a simple filename, this is returned without being
 * looked up in the cache, but with any initial ~username expression
 * expanded, and optionally, unescaped backslashes removed.
 *
 * Input:
 *  pc     PathCache *  The cached list of files.
 *  name  const char *  The name of the file to lookup.
 *  name_len     int    The length of the filename string at the
 *                      beginning of name[], or -1 to indicate that
 *                      the filename occupies the whole of the
 *                      string.
 *  literal      int    If this argument is zero, lone backslashes
 *                      in name[] are ignored during comparison
 *                      with filenames in the cache, under the
 *                      assumption that they were in the input line
 *                      soley to escape the special significance of
 *                      characters like spaces. To have them treated
 *                      as normal characters, give this argument a
 *                      non-zero value, such as 1.
 * Output:
 *  return      char *  The pathname of the first matching file,
 *                      or NULL if not found. Note that the returned
 *                      pointer points to memory owned by *pc, and
 *                      will become invalid on the next call to any
 *                      function in the PathCache module.
 */
char *pca_lookup_file(PathCache *pc, const char *name, int name_len,
		      int literal)
{
  PathNode *node;   /* A node in the list of directories in the path */
  char **match;     /* A pointer to a matching filename string in the cache */
/*
 * Check the arguments.
 */
  if(!pc || !name || name_len==0)
    return NULL;
/*
 * If no length was specified, determine the length of the string to
 * be looked up.
 */
  if(name_len < 0)
    name_len = strlen(name);
/*
 * If the word starts with a ~username expression, the root directory,
 * of it contains any directory separators, then treat it isn't a simple
 * filename that can be looked up in the cache, but rather appears to
 * be the pathname of a file. If so, return a copy of this pathname with
 * escapes removed, if requested, and any initial ~username expression
 * expanded.
 */
  if(cpa_cmd_contains_path(name, name_len)) {
    const char *nptr;
    if(pca_expand_tilde(pc, name, name_len, literal, &nptr) || 
       _pn_append_to_path(pc->path, nptr, name_len - (nptr-name),
			  !literal) == NULL)
      return NULL;
    return pc->path->name;
  };
/*
 * Look up the specified filename in each of the directories of the path,
 * in the same order that they were listed in the path, and stop as soon
 * as an instance of the file is found.
 */
  for(node=pc->head; node; node=node->next) {
/*
 * If the directory of the latest node is a relative pathname,
 * scan it for files of interest.
 */
    if(node->relative) {
      rst_CacheMem(node->mem);
      if(pca_scan_dir(pc, node->dir, node->mem) < 1)
	continue;
      node->files = node->mem->files;
      node->nfile = node->mem->nfiles;
    };
/*
 * Copy the filename into a temporary buffer, while interpretting
 * escape characters if needed.
 */
    _pn_clear_path(pc->path);
    if(_pn_append_to_path(pc->path, name, name_len, !literal) == NULL)
      return NULL;
/*
 * Perform a binary search for the requested filename.
 */
    match = (char **)bsearch(pc->path->name, node->files, node->nfile,
		             sizeof(*node->files), pca_cmp_file);
    if(match) {
/*
 * Prepend the pathname in which the directory was found, which we have
 * guaranteed to end in a directory separator, to the located filename.
 */
      if(_pn_prepend_to_path(pc->path, node->dir, -1, 0) == NULL)
	return NULL;
/*
 * Return the matching pathname unless it is rejected by the application.
 */
      if(!pc->check_fn || (*match)[0] == PCA_F_WANTED ||
	 ((*match)[0]==PCA_F_ENIGMA && pc->check_fn(pc->data, pc->path->name))){
	(*match)[0] = PCA_F_WANTED;
	return pc->path->name;
      } else {
	*(match)[0] = PCA_F_IGNORE;
      };
    };
  };
/*
 * File not found.
 */
  return NULL;
}

/*.......................................................................
 * A qsort() comparison function for comparing a filename string to
 * a cached filename string pointed to by a (char **) array element.
 * This ignores the initial code byte at the start of the cached filename
 * string.
 *
 * Input:
 *  v1, v2   void *  Pointers to the pointers of two strings to be compared.
 * Output:
 *  return    int    -1 -> v1 < v2.
 *                    0 -> v1 == v2
 *                    1 -> v1 > v2
 */
static int pca_cmp_file(const void *v1, const void *v2)
{
  const char *file_name = (const char *) v1;
  const char **cache_name = (const char **) v2;
  return strcmp(file_name, *cache_name + 1);
}

/*.......................................................................
 * The PcaPathConf structure may have options added to it in the future.
 * To allow your application to be linked against a shared version of the
 * tecla library, without these additions causing your application to
 * crash, you should use new_PcaPathConf() to allocate such structures.
 * This will set all of the configuration options to their default values,
 * which you can then change before passing the structure to
 * pca_path_completions().
 *
 * Input:
 *  pc         PathCache *  The filename cache in which to look for
 *                          file name completions.
 * Output:
 *  return   PcaPathConf *  The new configuration structure, or NULL
 *                          on error. A descripition of the error
 *                          can be found by calling pca_last_error(pc).
 */
PcaPathConf *new_PcaPathConf(PathCache *pc)
{
  PcaPathConf *ppc;  /* The object to be returned */
/*
 * Check the arguments.
 */
  if(!pc)
    return NULL;
/*
 * Allocate the container.
 */
  ppc = (PcaPathConf *)malloc(sizeof(PcaPathConf));
  if(!ppc) {
    _err_record_msg(pc->err, "Insufficient memory.", END_ERR_MSG);
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to del_PcaPathConf().
 */
  if(pca_init_PcaPathConf(ppc, pc))
    return del_PcaPathConf(ppc);
  return ppc;
}

/*.......................................................................
 * Initialize a PcaPathConf configuration structure with defaults.
 *
 * Input:
 *  ppc   PcaPathConf *  The structre to be initialized.
 *  pc      PathCache *  The cache in which completions will be looked up.
 * Output:
 *  return        int    0 - OK.
 *                       1 - Error. A description of the error can be
 *                           obtained by calling pca_last_error(pc).
 */
static int pca_init_PcaPathConf(PcaPathConf *ppc, PathCache *pc)
{
/*
 * Check the arguments.
 */
  if(!pc)
    return 1;
/*
 * Set the default options.
 */
  ppc->id = PPC_ID_CODE;
  ppc->pc = pc;
  ppc->escaped = 1;
  ppc->file_start = -1;
  return 0;
}

/*.......................................................................
 * Delete a PcaPathConf object.
 *
 * Input:
 *  ppc    PcaPathConf *  The object to be deleted.
 * Output:
 *  return PcaPathConf *  The deleted object (always NULL).
 */
PcaPathConf *del_PcaPathConf(PcaPathConf *ppc)
{
  if(ppc) {
    ppc->pc = NULL;  /* It is up to the caller to delete the cache */
/*
 * Delete the container.
 */
    free(ppc);
  };
  return NULL;
}

/*.......................................................................
 * pca_path_completions() is a completion callback function for use
 * directly with cpl_complete_word() or gl_customize_completions(), or
 * indirectly from your own completion callback function. It requires
 * that a CpaPathArgs object be passed via its 'void *data' argument.
 */
CPL_MATCH_FN(pca_path_completions)
{
  PcaPathConf *ppc;       /* The configuration arguments */
  PathCache *pc;          /* The cache in which to look for completions */
  PathNode *node;         /* A node in the list of directories in the path */
  const char *filename;   /* The name of the file being looked at */
  const char *start_path; /* The pointer to the start of the pathname */
                          /*  in line[]. */
  int word_start;         /* The index in line[] corresponding to start_path */
  const char *prefix;     /* The file-name prefix being searched for */
  size_t prefix_len;      /* The length of the prefix being completed */
  int bot;                /* The lowest index of the array not searched yet */
  int top;                /* The highest index of the array not searched yet */
/*
 * Check the arguments.
 */
  if(!cpl)
    return 1;
  if(!line || word_end < 0 || !data) {
    cpl_record_error(cpl, "pca_path_completions: Invalid arguments.");
    return 1;
  };
/*
 * Get the configuration arguments.
 */
  ppc = (PcaPathConf *) data;
/*
 * Check that the callback data is a PcaPathConf structure returned
 * by new_PcaPathConf().
 */
  if(ppc->id != PPC_ID_CODE) {
    cpl_record_error(cpl,
		     "Invalid callback data passed to pca_path_completions()");
    return 1;
  };
/*
 * Get the filename cache.
 */
  pc = ppc->pc;
/*
 * Get the start of the file name. If not specified by the caller,
 * identify it by searching backwards in the input line for an
 * unescaped space or the start of the line.
 */
  if(ppc->file_start < 0) {
    start_path = _pu_start_of_path(line, word_end);
    if(!start_path) {
      cpl_record_error(cpl, "Unable to find the start of the file name.");
      return 1;
    };
  } else {
    start_path = line + ppc->file_start;
  };
/*
 * Get the index of the start of the word being completed.
 */
  word_start = start_path - line;
/*
 * Work out the length of the prefix that is bein completed.
 */
  prefix_len = word_end - word_start;
/*
 * If the word starts with a ~username expression or the root directory,
 * of it contains any directory separators, then completion must be
 * delegated to cpl_file_completions().
 */
  if(cpa_cmd_contains_path(start_path, prefix_len)) {
    cfc_file_start(pc->cfc, word_start);
    return cpl_file_completions(cpl, pc->cfc, line, word_end);
  };
/*
 * Look up the specified file name in each of the directories of the path,
 * in the same order that they were listed in the path, and stop as soon
 * as an instance of the file is found.
 */
  for(node=pc->head; node; node=node->next) {
/*
 * If the directory of the latest node is a relative pathname,
 * scan it for files of interest.
 */
    if(node->relative) {
      rst_CacheMem(node->mem);
      if(pca_scan_dir(pc, node->dir, node->mem) < 1)
	continue;
      node->files = node->mem->files;
      node->nfile = node->mem->nfiles;
    };
/*
 * If needed, make a copy of the file-name being matched, with
 * escapes removed. Note that we need to do this anew every loop
 * iteration, because the above call to pca_scan_dir() uses
 * pc->path.
 */
    prefix = pca_prepare_prefix(pc, start_path, prefix_len, ppc->escaped);
    if(!prefix)
      return 1;
/*
 * The directory entries are sorted, so we can perform a binary
 * search for an instance of the prefix being searched for.
 */
    bot = 0;
    top = node->nfile - 1;
    while(top >= bot) {
      int mid = (top + bot)/2;
      int test = strncmp(node->files[mid]+1, prefix, prefix_len);
      if(test > 0)
	top = mid - 1;
      else if(test < 0)
	bot = mid + 1;
      else {
	top = bot = mid;
	break;
      };
    };
/*
 * If we found a match, look to see if any of its neigbors also match.
 */
    if(top == bot) {
      while(--bot >= 0 && strncmp(node->files[bot]+1, prefix, prefix_len) == 0)
	;
      while(++top < node->nfile &&
	    strncmp(node->files[top]+1, prefix, prefix_len) == 0)
	;
/*
 * We will have gone one too far in each direction.
 */
      bot++;
      top--;
/*
 * Add the completions to the list after checking them against the
 * callers requirements.
 */
      for( ; bot<=top; bot++) {
	char *match = node->files[bot];
/*
 * Form the full pathname of the file.
 */
	_pn_clear_path(pc->path);
	if(_pn_append_to_path(pc->path, node->dir, -1, 0) == NULL ||
	   _pn_append_to_path(pc->path, match+1, -1, 0) == NULL) {
	  _err_record_msg(pc->err, "Insufficient memory to complete file name",
			  END_ERR_MSG);
	  return 1;
	};
/*
 * Should the file be included in the list of completions?
 */
	if(!pc->check_fn || match[0] == PCA_F_WANTED ||
	   (match[0]==PCA_F_ENIGMA && pc->check_fn(pc->data, pc->path->name))) {
	  match[0] = PCA_F_WANTED;
/*
 * Copy the completion suffix into the work pathname pc->path->name,
 * adding backslash escapes if needed.
 */
	  if(pca_prepare_suffix(pc, match + 1 + prefix_len,
				ppc->escaped))
	    return 1;
/*
 * Record the completion.
 */
	  if(cpl_add_completion(cpl, line, word_start, word_end, pc->path->name,
				"", " "))
	    return 1;
/*
 * The file was rejected by the application.
 */
	} else {
	  match[0] = PCA_F_IGNORE;
	};
      };
    };
  };
/*
 * We now need to search for subdirectories of the current directory which
 * have matching prefixes. First, if needed, make a copy of the word being
 * matched, with escapes removed.
 */
  prefix = pca_prepare_prefix(pc, start_path, prefix_len, ppc->escaped);
  if(!prefix)
    return 1;
/*
 * Now open the current directory.
 */
  if(_dr_open_dir(pc->dr, FS_PWD, NULL))
    return 0;
/*
 * Scan the current directory for sub-directories whos names start with
 * the prefix that we are completing.
 */
  while((filename = _dr_next_file(pc->dr))) {
/*
 * Does the latest filename match the prefix, and is it a directory?
 */
    if(strncmp(filename, prefix, prefix_len) == 0 && _pu_path_is_dir(filename)){
/*
 * Record the completion.
 */
      if(pca_prepare_suffix(pc, filename + prefix_len, ppc->escaped) ||
	 cpl_add_completion(cpl, line, word_start, word_end, pc->path->name,
			    FS_DIR_SEP, FS_DIR_SEP))
	return 1;
/*
 * The prefix in pc->path->name will have been overwritten by
 * pca_prepare_suffix(). Restore it here.
 */
      prefix = pca_prepare_prefix(pc, start_path, prefix_len, ppc->escaped);
      if(!prefix)
	return 1;
    };
  };
  _dr_close_dir(pc->dr);
  return 0;
}

/*.......................................................................
 * Using the work buffer pc->path, make a suitably escaped copy of a
 * given completion suffix, ready to be passed to cpl_add_completion().
 *
 * Input:
 *  pc      PathCache *  The filename cache resource object.
 *  suffix       char *  The suffix to be copied.
 *  add_escapes   int    If true, escape special characters.
 * Output:
 *  return        int    0 - OK.
 *                       1 - Error.
 */
static int pca_prepare_suffix(PathCache *pc, const char *suffix,
			      int add_escapes)
{
  const char *sptr; /* A pointer into suffix[] */
  int nbsl;         /* The number of backslashes to add to the suffix */
  int i;
/*
 * How long is the suffix?
 */
  int suffix_len = strlen(suffix);
/*
 * Clear the work buffer.
 */
  _pn_clear_path(pc->path);
/*
 * Count the number of backslashes that will have to be added to
 * escape spaces, tabs, backslashes and wildcard characters.
 */
  nbsl = 0;
  if(add_escapes) {
    for(sptr = suffix; *sptr; sptr++) {
      switch(*sptr) {
      case ' ': case '\t': case '\\': case '*': case '?': case '[':
	nbsl++;
	break;
      };
    };
  };
/*
 * Arrange for the output path buffer to have sufficient room for the
 * both the suffix and any backslashes that have to be inserted.
 */
  if(_pn_resize_path(pc->path, suffix_len + nbsl) == NULL) {
    _err_record_msg(pc->err, "Insufficient memory to complete file name",
		    END_ERR_MSG);
    return 1;
  };
/*
 * If the suffix doesn't need any escapes, copy it directly into the
 * work buffer.
 */
  if(nbsl==0) {
    strcpy(pc->path->name, suffix);
  } else {
/*
 * Make a copy with special characters escaped?
 */
    if(nbsl > 0) {
      const char *src = suffix;
      char *dst = pc->path->name;
      for(i=0; i= FS_ROOT_DIR_LEN && 
     strncmp(prefix, FS_ROOT_DIR, FS_ROOT_DIR_LEN) == 0)
    return 1;
/*
 * Search the prefix for directory separators, returning as soon as
 * any are found, since their presence indicates that the filename
 * starts with a pathname specification (valid or otherwise).
 */
  for(i=0; i= FS_DIR_SEP_LEN &&
       strncmp(prefix + i, FS_DIR_SEP, FS_DIR_SEP_LEN) == 0)
      return 1;
  };
/*
 * The file name doesn't appear to start with a pathname specification.
 */
  return 0;
}

/*.......................................................................
 * If needed make a new copy of the prefix being matched, in pc->path->name,
 * but with escapes removed. If no escapes are to be removed, simply return
 * the original prefix string.
 *
 * Input:
 *  pc      PathCache *   The cache being searched.
 *  prefix const char *   The prefix to be processed.
 *  prefix_len size_t     The length of the prefix.
 *  escaped       int     If true, return a copy with escapes removed.
 * Output:
 *  return const char *   The prepared prefix, or NULL on error, in
 *                        which case an error message will have been
 *                        left in pc->err.
 */
static const char *pca_prepare_prefix(PathCache *pc, const char *prefix,
				      size_t prefix_len, int escaped)
{
/*
 * Make a copy with escapes removed?
 */
  if(escaped) {
    _pn_clear_path(pc->path);
    if(_pn_append_to_path(pc->path, prefix, prefix_len, 1) == NULL) {
      _err_record_msg(pc->err, "Insufficient memory to complete filename",
		      END_ERR_MSG);
      return NULL;
    };
    return pc->path->name;
  };
  return prefix;
}

/*.......................................................................
 * If backslashes in the filename should be treated as literal
 * characters, call the following function with literal=1. Otherwise
 * the default is to treat them as escape characters, used for escaping
 * spaces etc..
 *
 * Input:
 *  ppc    PcaPathConf *  The pca_path_completions() configuration object
 *                        to be configured.
 *  literal        int    Pass non-zero here to enable literal interpretation
 *                        of backslashes. Pass 0 to turn off literal
 *                        interpretation.
 */
void ppc_literal_escapes(PcaPathConf *ppc, int literal)
{
  if(ppc)
    ppc->escaped = !literal;
}

/*.......................................................................
 * Call this function if you know where the index at which the
 * filename prefix starts in the input line. Otherwise by default,
 * or if you specify start_index to be -1, the filename is taken
 * to start after the first unescaped space preceding the cursor,
 * or the start of the line, which ever comes first.
 *
 * Input:
 *  ppc    PcaPathConf *  The pca_path_completions() configuration object
 *                        to be configured.
 *  start_index    int    The index of the start of the filename in
 *                        the input line, or -1 to select the default.
 */
void ppc_file_start(PcaPathConf *ppc, int start_index)
{
  if(ppc)
    ppc->file_start = start_index;
}

/*.......................................................................
 * Expand any ~user expression found at the start of a path, leaving
 * either an empty string in pc->path if there is no ~user expression,
 * or the corresponding home directory.
 *
 * Input:
 *  pc     PathCache *  The filename cache.
 *  path  const char *  The path to expand.
 *  pathlen      int    The max number of characters to look at in path[].
 *  literal      int    If true, treat backslashes as literal characters
 *                      instead of escapes.
 * Input/Output:
 *  endp  const char *  A pointer to the next unprocessed character in
 *                      path[] will be assigned to *endp.
 * Output:
 *  return       int    0 - OK
 *                      1 - Error (a description will have been placed
 *                                 in pc->err).
 */
static int pca_expand_tilde(PathCache *pc, const char *path, int pathlen,
			    int literal, const char **endp)
{
  const char *pptr = path;  /* A pointer into path[] */
  const char *homedir=NULL; /* A home directory */
/*
 * Clear the pathname buffer.
 */
  _pn_clear_path(pc->path);
/*
 * If the first character is a tilde, then perform home-directory
 * interpolation.
 */
  if(*pptr == '~') {
/*
 * Skip the tilde character and attempt to read the username that follows
 * it, into pc->usrnam[].
 */
    if(pca_read_username(pc, ++pptr, pathlen-1, literal, &pptr))
      return 1;
/*
 * Attempt to lookup the home directory of the user.
 */
    homedir = _hd_lookup_home_dir(pc->home, pc->usrnam);
    if(!homedir) {
      _err_record_msg(pc->err, _hd_last_home_dir_error(pc->home), END_ERR_MSG);
      return 1;
    };
/*
 * Append the home directory to the pathname string.
 */
    if(_pn_append_to_path(pc->path, homedir, -1, 0) == NULL) {
      _err_record_msg(pc->err,
		      "Insufficient memory for home directory expansion",
		      END_ERR_MSG);
      return 1;
    };
  };
/*
 * ~user and ~ are usually followed by a directory separator to
 * separate them from the file contained in the home directory.
 * If the home directory is the root directory, then we don't want
 * to follow the home directory by a directory separator, so we should
 * skip over it so that it doesn't get copied into the output pathname
 */
  if(homedir && strcmp(homedir, FS_ROOT_DIR) == 0 &&
     (pptr-path) + FS_DIR_SEP_LEN < pathlen &&
     strncmp(pptr, FS_DIR_SEP, FS_DIR_SEP_LEN) == 0) {
    pptr += FS_DIR_SEP_LEN;
  };
/*
 * Return a pointer to the next unprocessed character.
 */
  *endp = pptr;
  return 0;
}

/*.......................................................................
 * Clear the filename status codes that are recorded before each filename
 * in the cache.
 *
 * Input:
 *  pc     PathCache *  The filename cache.
 */
static void pca_remove_marks(PathCache *pc)
{
  PathNode *node;         /* A node in the list of directories in the path */
  int i;
/*
 * Traverse the absolute directories of the path, clearing the
 * filename status marks that precede each filename.
 */
  for(node=pc->head; node; node=node->next) {
    if(!node->relative) {
      for(i=0; infile; i++)
	*node->files[i] = PCA_F_ENIGMA;
    };
  };
  return;
}

#endif  /* ifndef WITHOUT_FILE_SYSTEM */
genometools-1.5.1/src/external/libtecla-1.6.1/stringrp.c000066400000000000000000000211301211610345200227060ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */
#include 
#include 
#include 
#include 

#include "freelist.h"
#include "stringrp.h"

/*
 * StringSegment objects store lots of small strings in larger
 * character arrays. Since the total length of all of the strings can't
 * be known in advance, an extensible list of large character arrays,
 * called string-segments are used.
 */
typedef struct StringSegment StringSegment;
struct StringSegment {
  StringSegment *next; /* A pointer to the next segment in the list */
  char *block;         /* An array of characters to be shared between strings */
  int unused;          /* The amount of unused space at the end of block[] */
};

/*
 * StringGroup is typedef'd in stringrp.h.
 */
struct StringGroup {
  FreeList *node_mem;  /* The StringSegment free-list */
  int block_size;      /* The dimension of each character array block */
  StringSegment *head; /* The list of character arrays */
};

/*
 * Specify how many StringSegment's to allocate at a time.
 */
#define STR_SEG_BLK 20

/*.......................................................................
 * Create a new StringGroup object.
 *
 * Input:
 *  segment_size    int    The length of each of the large character
 *                         arrays in which multiple strings will be
 *                         stored. This sets the length of longest
 *                         string that can be stored, and for efficiency
 *                         should be at least 10 times as large as
 *                         the average string that will be stored.
 * Output:
 *  return  StringGroup *  The new object, or NULL on error.
 */
StringGroup *_new_StringGroup(int segment_size)
{
  StringGroup *sg;    /* The object to be returned */
/*
 * Check the arguments.
 */
  if(segment_size < 1) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Allocate the container.
 */
  sg = (StringGroup *) malloc(sizeof(StringGroup));
  if(!sg) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize the
 * container at least up to the point at which it can safely be passed
 * to _del_StringGroup().
 */
  sg->node_mem = NULL;
  sg->head = NULL;
  sg->block_size = segment_size;
/*
 * Allocate the free list that is used to allocate list nodes.
 */
  sg->node_mem = _new_FreeList(sizeof(StringSegment), STR_SEG_BLK);
  if(!sg->node_mem)
    return _del_StringGroup(sg);
  return sg;
}

/*.......................................................................
 * Delete a StringGroup object.
 *
 * Input:
 *  sg     StringGroup *  The object to be deleted.
 * Output:
 *  return StringGroup *  The deleted object (always NULL).
 */
StringGroup *_del_StringGroup(StringGroup *sg)
{
  if(sg) {
    StringSegment *node;
/*
 * Delete the character arrays.
 */
    for(node=sg->head; node; node=node->next) {
      if(node->block)
	free(node->block);
      node->block = NULL;
    };
/*
 * Delete the list nodes that contained the string segments.
 */
    sg->node_mem = _del_FreeList(sg->node_mem, 1);
    sg->head = NULL; /* Already deleted by deleting sg->node_mem */
/*
 * Delete the container.
 */
    free(sg);
  };
  return NULL;
}

/*.......................................................................
 * Make a copy of a string in the specified string group, and return
 * a pointer to the copy. 
 *
 * Input:
 *  sg      StringGroup *  The group to store the string in.
 *  string   const char *  The string to be recorded.
 *  remove_escapes  int    If true, omit backslashes which escape
 *                         other characters when making the copy.
 * Output:
 *  return         char *  The pointer to the copy of the string,
 *                         or NULL if there was insufficient memory.
 */
char *_sg_store_string(StringGroup *sg, const char *string, int remove_escapes)
{
  char *copy;           /* The recorded copy of string[] */
/*
 * Check the arguments.
 */
  if(!sg || !string)
    return NULL;
/*
 * Get memory for the string.
 */
  copy = _sg_alloc_string(sg, strlen(string));
  if(copy) {
/*
 * If needed, remove backslash escapes while copying the input string
 * into the cache string.
 */
    if(remove_escapes) {
      int escaped = 0;             /* True if the next character should be */
                                   /*  escaped. */
      const char *src = string;    /* A pointer into the input string */
      char *dst = copy;            /* A pointer into the cached copy of the */
                                   /*  string. */
      while(*src) {
	if(!escaped && *src == '\\') {
	  escaped = 1;
	  src++;
	} else {
	  escaped = 0;
	  *dst++ = *src++;
	};
      };
      *dst = '\0';
/*
 * If escapes have already been removed, copy the input string directly
 * into the cache.
 */
    } else {
      strcpy(copy, string);
    };
  };
/*
 * Return a pointer to the copy of the string (or NULL if the allocation
 * failed).
 */
  return copy;
}

/*.......................................................................
 * Allocate memory for a string of a given length.
 *
 * Input:
 *  sg      StringGroup *  The group to store the string in.
 *  length          int    The required length of the string.
 * Output:
 *  return         char *  The pointer to the copy of the string,
 *                         or NULL if there was insufficient memory.
 */
char *_sg_alloc_string(StringGroup *sg, int length)
{
  StringSegment *node;  /* A node of the list of string segments */
  char *copy;           /* The allocated string */
/*
 * If the string is longer than block_size, then we can't record it.
 */
  if(length > sg->block_size || length < 0)
    return NULL;
/*
 * See if there is room to record the string in one of the existing
 * string segments. Do this by advancing the node pointer until we find
 * a node with length+1 bytes unused, or we get to the end of the list.
 */
  for(node=sg->head; node && node->unused <= length; node=node->next)
    ;
/*
 * If there wasn't room, allocate a new string segment.
 */
  if(!node) {
    node = (StringSegment *) _new_FreeListNode(sg->node_mem);
    if(!node)
      return NULL;
/*
 * Initialize the segment.
 */
    node->next = NULL;
    node->block = NULL;
    node->unused = sg->block_size;
/*
 * Attempt to allocate the string segment character array.
 */
    node->block = (char *) malloc(sg->block_size);
    if(!node->block)
      return NULL;
/*
 * Prepend the node to the list.
 */
    node->next = sg->head;
    sg->head = node;
  };
/*
 * Get memory for the string.
 */
  copy = node->block + sg->block_size - node->unused;
  node->unused -= length + 1;
/*
 * Return a pointer to the string memory.
 */
  return copy;
}

/*.......................................................................
 * Delete all of the strings that are currently stored by a specified
 * StringGroup object.
 *
 * Input:
 *  sg   StringGroup *   The group of strings to clear.
 */
void _clr_StringGroup(StringGroup *sg)
{
  StringSegment *node;   /* A node in the list of string segments */
/*
 * Mark all of the string segments as unoccupied.
 */
  for(node=sg->head; node; node=node->next)
    node->unused = sg->block_size;
  return;
}
genometools-1.5.1/src/external/libtecla-1.6.1/stringrp.h000066400000000000000000000067361211610345200227320ustar00rootroot00000000000000#ifndef stringrp_h
#define stringrp_h
/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

/*
 * StringGroup objects provide memory for modules that need to
 * allocate lots of small strings without needing to free any of them
 * individually, but rather is happy to free them all at the same
 * time. Taking advantage of these properties, StringGroup objects
 * avoid the heap fragmentation that tends to occur when lots of small
 * strings are allocated directly from the heap and later free'd. They
 * do this by allocating a list of large character arrays in each of
 * which multiple strings are stored. Thus instead of allocating lots
 * of small strings, a few large character arrays are allocated. When
 * the strings are free'd on mass, this list of character arrays is
 * maintained, ready for subsequent use in recording another set of
 * strings.
 */
typedef struct StringGroup StringGroup;

/*
 * The following constructor allocates a string-allocation object.
 * The segment_size argument specifies how long each string segment
 * array should be. This should be at least 10 times the length of
 * the average string to be recorded in the string group, and
 * sets the length of the longest string that can be stored.
 */
StringGroup *_new_StringGroup(int segment_size);

/*
 * Delete all of the strings that are currently stored by a specified
 * StringGroup object.
 */
void _clr_StringGroup(StringGroup *sg);

/*
 * Make a copy of the specified string, returning a pointer to
 * the copy, or NULL if there was insufficient memory. If the
 * remove_escapes argument is non-zero, backslashes that escape
 * other characters will be removed.
 */
char *_sg_store_string(StringGroup *sg, const char *string, int remove_escapes);

/*
 * Allocate memory for a string of a given length.
 */
char *_sg_alloc_string(StringGroup *sg, int length);

/*
 * Delete a StringGroup object (and all of the strings that it
 * contains).
 */
StringGroup *_del_StringGroup(StringGroup *sg);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/strngmem.c000066400000000000000000000152521211610345200227020ustar00rootroot00000000000000/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

#include 
#include 
#include 

#include "strngmem.h"
#include "freelist.h"

struct StringMem {
  unsigned long nmalloc;  /* The number of strings allocated with malloc */
  FreeList *fl;           /* The free-list */
};

/*.......................................................................
 * Create a string free-list container and the first block of its free-list.
 *
 * Input:
 *  blocking_factor   int    The blocking_factor argument specifies how
 *                           many strings of length SM_STRLEN
 *                           bytes (see stringmem.h) are allocated in each
 *                           free-list block.
 *                           For example if blocking_factor=64 and
 *                           SM_STRLEN=16, then each new
 *                           free-list block will take 1K of memory.
 * Output:
 *  return      StringMem *  The new free-list container, or NULL on
 *                           error.
 */
StringMem *_new_StringMem(unsigned blocking_factor)
{
  StringMem *sm;    /* The container to be returned. */
/*
 * Check arguments.
 */
  if(blocking_factor < 1) {
    errno = EINVAL;
    return NULL;
  };
/*
 * Allocate the container.
 */
  sm = (StringMem *) malloc(sizeof(StringMem));
  if(!sm) {
    errno = ENOMEM;
    return NULL;
  };
/*
 * Before attempting any operation that might fail, initialize
 * the container at least up to the point at which it can safely
 * be passed to _del_StringMem().
 */
  sm->nmalloc = 0;
  sm->fl = NULL;
/*
 * Allocate the free-list.
 */
  sm->fl = _new_FreeList(SM_STRLEN, blocking_factor);
  if(!sm->fl)
    return _del_StringMem(sm, 1);
/*
 * Return the free-list container.
 */
  return sm;
}

/*.......................................................................
 * Delete a string free-list.
 *
 * Input:
 *  sm       StringMem *  The string free-list to be deleted, or NULL.
 *  force          int    If force==0 then _del_StringMem() will complain
 *                         and refuse to delete the free-list if any
 *                         of nodes have not been returned to the free-list.
 *                        If force!=0 then _del_StringMem() will not check
 *                         whether any nodes are still in use and will
 *                         always delete the list.
 * Output:
 *  return   StringMem *  Always NULL (even if the list couldn't be
 *                        deleted).
 */
StringMem *_del_StringMem(StringMem *sm, int force)
{
  if(sm) {
/*
 * Check whether any strings have not been returned to the free-list.
 */
    if(!force && (sm->nmalloc > 0 || _busy_FreeListNodes(sm->fl) > 0)) {
      errno = EBUSY;
      return NULL;
    };
/*
 * Delete the free-list.
 */
    sm->fl = _del_FreeList(sm->fl, force);
/*
 * Delete the container.
 */
    free(sm);
  };
  return NULL;
}

/*.......................................................................
 * Allocate an array of 'length' chars.
 *
 * Input:
 *  sm      StringMem *  The string free-list to allocate from.
 *  length     size_t    The length of the new string (including '\0').
 * Output:
 *  return       char *  The new string or NULL on error.
 */
char *_new_StringMemString(StringMem *sm, size_t length)
{
  char *string;   /* The string to be returned */
  int was_malloc; /* True if malloc was used to allocate the string */
/*
 * Check arguments.
 */
  if(!sm)
    return NULL;
  if(length < 1)
    length = 1;
/*
 * Allocate the new node from the free list if possible.
 */
  if(length < SM_STRLEN) {
    string = (char *)_new_FreeListNode(sm->fl);
    if(!string)
      return NULL;
    was_malloc = 0;
  } else {
    string = (char *) malloc(length+1); /* Leave room for the flag byte */
    if(!string)
      return NULL;
/*
 * Count malloc allocations.
 */
    was_malloc = 1;
    sm->nmalloc++;
  };
/*
 * Use the first byte of the string to record whether the string was
 * allocated with malloc or from the free-list. Then return the rest
 * of the string for use by the user.
 */
  string[0] = (char) was_malloc;
  return string + 1;
}

/*.......................................................................
 * Free a string that was previously returned by _new_StringMemString().
 *
 * Input:
 *  sm      StringMem *  The free-list from which the string was originally
 *                       allocated.
 *  s            char *  The string to be returned to the free-list, or NULL.
 * Output:
 *  return       char *  Always NULL.
 */
char *_del_StringMemString(StringMem *sm, char *s)
{
  int was_malloc;  /* True if the string originally came from malloc() */
/*
 * Is there anything to be deleted?
 */
  if(s && sm) {
/*
 * Retrieve the true string pointer. This is one less than the one
 * returned by _new_StringMemString() because the first byte of the
 * allocated memory is reserved by _new_StringMemString as a flag byte
 * to say whether the memory was allocated from the free-list or directly
 * from malloc().
 */
    s--;
/*
 * Get the origination flag.
 */
    was_malloc = s[0];
    if(was_malloc) {
      free(s);
      s = NULL;
      sm->nmalloc--;
    } else {
      s = (char *) _del_FreeListNode(sm->fl, s);
    };
  };
  return NULL;
}
genometools-1.5.1/src/external/libtecla-1.6.1/strngmem.h000066400000000000000000000062671211610345200227150ustar00rootroot00000000000000#ifndef stringmem_h
#define stringmem_h
/*
 * Copyright (c) 2000, 2001, 2002, 2003, 2004 by Martin C. Shepherd.
 * 
 * All rights reserved.
 * 
 * Permission is hereby granted, free of charge, to any person obtaining a
 * copy of this software and associated documentation files (the
 * "Software"), to deal in the Software without restriction, including
 * without limitation the rights to use, copy, modify, merge, publish,
 * distribute, and/or sell copies of the Software, and to permit persons
 * to whom the Software is furnished to do so, provided that the above
 * copyright notice(s) and this permission notice appear in all copies of
 * the Software and that both the above copyright notice(s) and this
 * permission notice appear in supporting documentation.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
 * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
 * OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
 * HOLDERS INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL
 * INDIRECT OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING
 * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 * WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 * 
 * Except as contained in this notice, the name of a copyright holder
 * shall not be used in advertising or otherwise to promote the sale, use
 * or other dealings in this Software without prior written authorization
 * of the copyright holder.
 */

typedef struct StringMem StringMem;

/*
 * Applications that dynamically allocate lots of small strings
 * run the risk of significantly fragmenting the heap. This module
 * aims to reduce this risk by allocating large arrays of small fixed
 * length strings, arranging them as a free-list and allowing
 * callers to allocate from the list. Strings that are too long
 * to be allocated from the free-list are allocated from the heap.
 * Since typical implementations of malloc() eat up a minimum of
 * 16 bytes per call to malloc() [because of alignment and space
 * management constraints] it makes sense to set the free-list
 * string size to 16 bytes. Note that unlike malloc() which typically
 * keeps 8 bytes per allocation for its own use, our allocator will
 * return all but one of the 16 bytes for use. One hidden byte of overhead
 * is reserved for flagging whether the string was allocated directly
 * from malloc or from the free-list.
 */

/*
 * Set the length of each free-list string. The longest string that
 * will be returned without calling malloc() will be one less than
 * this number.
 */
#define SM_STRLEN 16

/*
 * Create a string free-list container and the first block of its free-list.
 */
StringMem *_new_StringMem(unsigned blocking_factor);

/*
 * Delete a string free-list.
 */
StringMem *_del_StringMem(StringMem *sm, int force);

/*
 * Allocate an array of 'length' chars.
 */
char *_new_StringMemString(StringMem *sm, size_t size);

/*
 * Free a string that was previously returned by _new_StringMemString().
 */
char *_del_StringMemString(StringMem *sm, char *s);

#endif
genometools-1.5.1/src/external/libtecla-1.6.1/update_html000077500000000000000000000021721211610345200231330ustar00rootroot00000000000000#!/bin/sh

# Convert man pages to html files.

for dir in man/prog man/libr man/func man/misc man/file; do
  for template in $dir/*.in;do
    page=`basename "$template" .in`
    if [ `wc -l < $template` -gt 1 ]; then
      html="html/$page.html"
      man2html $template > $html
      for ref in libtecla cpl_complete_word ef_expand_file gl_get_line pca_lookup_file enhance gl_io_mode tecla; do
	link="$ref.html"
	ed -s $html << EOF
	  %s|$ref[(][^)][^) ]*[)]|$ref|g
	  w
	  q
EOF
      done
    fi
  done
done

# Convert the change log into a web page.

cd html
echo 'The tecla library change log' > changes.html
echo '
' >> changes.html
sed 's/&/&/g; s//\>/g' ../CHANGES >> changes.html
echo '
' >> changes.html

# Do the same to the release-notes file.

cd ../html
echo 'The tecla library release notes' > release.html
echo '
' >> release.html
sed 's/&/&/g; s/> release.html
echo '
' >> release.html
genometools-1.5.1/src/external/libtecla-1.6.1/version.c000066400000000000000000000023071211610345200225300ustar00rootroot00000000000000#include "libtecla.h"

/*.......................................................................
 * Return the version number of the tecla library.
 *
 * Input:
 *  major    int *   The major version number of the library
 *                   will be assigned to *major. This number is
 *                   only incremented when a change to the library is
 *                   made that breaks binary (shared library) and/or
 *                   compilation backwards compatibility.
 *  minor    int *   The minor version number of the library
 *                   will be assigned to *minor. This number is
 *                   incremented whenever new functions are added to
 *                   the public API.
 *  micro    int *   The micro version number of the library will be
 *                   assigned to *micro. This number is incremented
 *                   whenever internal changes are made that don't
 *                   change the public API, such as bug fixes and
 *                   performance enhancements.
 */
void libtecla_version(int *major, int *minor, int *micro)
{
  if(major)
    *major = TECLA_MAJOR_VER;
  if(minor)
    *minor = TECLA_MINOR_VER;
  if(micro)
    *micro = TECLA_MICRO_VER;
}
genometools-1.5.1/src/external/lpeg-0.10.2/000077500000000000000000000000001211610345200201205ustar00rootroot00000000000000genometools-1.5.1/src/external/lpeg-0.10.2/HISTORY000066400000000000000000000050521211610345200212060ustar00rootroot00000000000000HISTORY for LPeg 0.10

* Changes from version 0.9 to 0.10
  -------------------------------  
  + backtrack stack has configurable size
  + better error messages
  + Notation for non-terminals in 're' back to A instead o 
  + experimental look-behind pattern
  + support for external extensions
  + works with Lua 5.2
  + consumes less C stack

  - "and" predicates do not keep captures

* Changes from version 0.8 to 0.9
  -------------------------------  
  + The accumulator capture was replaced by a fold capture;
    programs that used the old 'lpeg.Ca' will need small changes.
  + Some support for character classes from old C locales.
  + A new named-group capture.

* Changes from version 0.7 to 0.8
  -------------------------------  
  + New "match-time" capture.
  + New "argument capture" that allows passing arguments into the pattern.
  + Better documentation for 're'.
  + Several small improvements for 're'.
  + The 're' module has an incompatibility with previous versions: 
    now, any use of a non-terminal must be enclosed in angle brackets 
    (like ).

* Changes from version 0.6 to 0.7
  -------------------------------  
  + Several improvements in module 're':
    - better documentation;
    - support for most captures (all but accumulator);
    - limited repetitions p{n,m}.
  + Small improvements in efficiency.
  + Several small bugs corrected (special thanks to Hans Hagen 
    and Taco Hoekwater).

* Changes from version 0.5 to 0.6
  -------------------------------  
  + Support for non-numeric indices in grammars.
  + Some bug fixes (thanks to the luatex team).
  + Some new optimizations; (thanks to Mike Pall).
  + A new page layout (thanks to Andre Carregal).
  + Minimal documentation for module 're'.

* Changes from version 0.4 to 0.5
  -------------------------------  
  + Several optimizations.
  + lpeg.P now accepts booleans.
  + Some new examples.
  + A proper license.
  + Several small improvements.

* Changes from version 0.3 to 0.4
  -------------------------------  
  + Static check for loops in repetitions and grammars.
  + Removed label option in captures.
  + The implementation of captures uses less memory.

* Changes from version 0.2 to 0.3
  -------------------------------  
  + User-defined patterns in Lua.
  + Several new captures.

* Changes from version 0.1 to 0.2
  -------------------------------  
  + Several small corrections.
  + Handles embedded zeros like any other character.
  + Capture "name" can be any Lua value.
  + Unlimited number of captures.
  + Match gets an optional initial position.

(end of HISTORY)
genometools-1.5.1/src/external/lpeg-0.10.2/lpeg-128.gif000066400000000000000000000114731211610345200220540ustar00rootroot00000000000000GIF89a	
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0nzv{Ȃ<Ȅ\Ȇ|ȈȊȌ;genometools-1.5.1/src/external/lpeg-0.10.2/lpeg.c000066400000000000000000001763011211610345200212230ustar00rootroot00000000000000/*
** $Id: lpeg.c,v 1.114 2011/02/16 15:02:20 roberto Exp $
** LPeg - PEG pattern matching for Lua
** Copyright 2007, Lua.org & PUC-Rio  (see 'lpeg.html' for license)
** written by Roberto Ierusalimschy
*/


#include 
#include 
#include 
#include 
#include 

#include "lua.h"
#include "lauxlib.h"

#include "lpeg.h"


#define VERSION		"0.10"
#define PATTERN_T	"lpeg-pattern"
#define MAXSTACKIDX	"lpeg-maxstack"


/*
** compatibility with Lua 5.2
*/
#if (LUA_VERSION_NUM == 502)

#undef lua_equal
#define lua_equal(L,idx1,idx2)  lua_compare(L,(idx1),(idx2),LUA_OPEQ)

#undef lua_getfenv
#define lua_getfenv	lua_getuservalue
#undef lua_setfenv
#define lua_setfenv	lua_setuservalue

#undef lua_objlen
#define lua_objlen	lua_rawlen

#undef luaL_register
#define luaL_register(L,n,f) \
	{ if ((n) == NULL) luaL_setfuncs(L,f,0); else luaL_newlib(L,f); }

#endif



/* initial size for call/backtrack stack */
#define INITBACK	100

/* default maximum size for call/backtrack stack */
#define MAXBACK		INITBACK

/* size for call/backtrack stack for verifier */
#define MAXBACKVER	200

/* initial size for capture's list */
#define INITCAPSIZE	32


/* index, on Lua stack, for subject */
#define SUBJIDX		2

/* number of fixed arguments to 'match' (before capture arguments) */
#define FIXEDARGS	3

/* index, on Lua stack, for substitution value cache */
#define subscache(cs)	((cs)->ptop + 1)

/* index, on Lua stack, for capture list */
#define caplistidx(ptop)	((ptop) + 2)

/* index, on Lua stack, for pattern's fenv */
#define penvidx(ptop)	((ptop) + 3)

/* index, on Lua stack, for backtracking stack */
#define stackidx(ptop)	((ptop) + 4)



typedef unsigned char byte;


#define CHARSETSIZE		((UCHAR_MAX/CHAR_BIT) + 1)


typedef byte Charset[CHARSETSIZE];


/* Virtual Machine's instructions */
typedef enum Opcode {
  IAny, IChar, ISet, ISpan,
  IBack,
  IRet, IEnd,
  IChoice, IJmp, ICall, IOpenCall,
  ICommit, IPartialCommit, IBackCommit, IFailTwice, IFail, IGiveup,
  IFunc,
  IFullCapture, IEmptyCapture, IEmptyCaptureIdx,
  IOpenCapture, ICloseCapture, ICloseRunTime
} Opcode;


#define ISJMP		0x1
#define ISCHECK		0x2
#define ISFIXCHECK	0x4
#define ISNOFAIL	0x8
#define ISCAPTURE	0x10
#define ISMOVABLE	0x20
#define ISFENVOFF	0x40

static const int opproperties[] = {
  /* IAny */		ISCHECK | ISFIXCHECK | ISJMP,
  /* IChar */		ISCHECK | ISFIXCHECK | ISJMP,
  /* ISet */		ISCHECK | ISFIXCHECK | ISJMP,
  /* ISpan */		ISNOFAIL,
  /* IBack */		0,
  /* IRet */		0,
  /* IEnd */		0,
  /* IChoice */		ISJMP,
  /* IJmp */		ISJMP | ISNOFAIL,
  /* ICall */		ISJMP,
  /* IOpenCall */	ISFENVOFF,
  /* ICommit */		ISJMP,
  /* IPartialCommit */	ISJMP,
  /* IBackCommit */	ISJMP,
  /* IFailTwice */	0,
  /* IFail */		0,
  /* IGiveup */		0,
  /* IFunc */		ISCHECK | ISJMP,
  /* IFullCapture */	ISCAPTURE | ISNOFAIL | ISFENVOFF,
  /* IEmptyCapture */	ISCAPTURE | ISNOFAIL | ISMOVABLE,
  /* IEmptyCaptureIdx */ISCAPTURE | ISNOFAIL | ISMOVABLE | ISFENVOFF,
  /* IOpenCapture */	ISCAPTURE | ISNOFAIL | ISMOVABLE | ISFENVOFF,
  /* ICloseCapture */	ISCAPTURE | ISNOFAIL | ISMOVABLE | ISFENVOFF,
  /* ICloseRunTime */	ISCAPTURE | ISFENVOFF
};


typedef union Instruction {
  struct Inst {
    byte code;
    byte aux;
    short offset;
  } i;
  PattFunc f;
  int iv;
  byte buff[1];
} Instruction;

static const Instruction giveup = {{IGiveup, 0, 0}};

#define getkind(op)	((op)->i.aux & 0xF)
#define getoff(op)	(((op)->i.aux >> 4) & 0xF)

#define dest(p,x)	((x) + ((p)+(x))->i.offset)

#define MAXOFF		0xF
#define MAXAUX		0xFF

/* maximum size (in elements) for a pattern */
#define MAXPATTSIZE	(SHRT_MAX - 10)


#define isprop(op,p)	(opproperties[(op)->i.code] & (p))
#define isjmp(op)	(isprop(op, ISJMP) && (op)->i.offset != 0)
#define iscapture(op) 	isprop(op, ISCAPTURE)
#define ischeck(op)	(isprop(op, ISCHECK) && (op)->i.offset == 0)
#define isfixcheck(op)	(isprop(op, ISFIXCHECK) && (op)->i.offset == 0)
#define istest(op)	(isprop(op, ISCHECK) && (op)->i.offset != 0)
#define isnofail(op)	isprop(op, ISNOFAIL)
#define ismovable(op)	isprop(op, ISMOVABLE)
#define isfenvoff(op)	isprop(op, ISFENVOFF)


/* kinds of captures */
typedef enum CapKind {
  Cclose, Cposition, Cconst, Cbackref, Carg, Csimple, Ctable, Cfunction,
  Cquery, Cstring, Csubst, Cfold, Cruntime, Cgroup
} CapKind;

#define iscapnosize(k)	((k) == Cposition || (k) == Cconst)


typedef struct Capture {
  const char *s;  /* position */
  short idx;
  byte kind;
  byte siz;
} Capture;


/* size (in elements) for an instruction plus extra l bytes */
#define instsize(l)  (((l) + sizeof(Instruction) - 1)/sizeof(Instruction) + 1)


/* size (in elements) for a ISet instruction */
#define CHARSETINSTSIZE		instsize(CHARSETSIZE)

/* size (in elements) for a IFunc instruction */
#define funcinstsize(p)		((p)->i.aux + 2)


#define loopset(v,b)	{ int v; for (v = 0; v < CHARSETSIZE; v++) b; }


#define testchar(st,c)	(((int)(st)[((c) >> 3)] & (1 << ((c) & 7))))
#define setchar(st,c)	((st)[(c) >> 3] |= (1 << ((c) & 7)))


static int target (Instruction *p, int i);


static int sizei (const Instruction *i) {
  switch((Opcode)i->i.code) {
    case ISet: case ISpan: return CHARSETINSTSIZE;
    case IFunc: return funcinstsize(i);
    default: return 1;
  }
}


static const char *val2str (lua_State *L, int idx) {
  const char *k = lua_tostring(L, idx);
  if (k != NULL)
    return lua_pushfstring(L, "rule '%s'", k);
  else
    return lua_pushfstring(L, "rule ", luaL_typename(L, idx));
}


static int getposition (lua_State *L, int t, int i) {
  int res;
  lua_getfenv(L, -1);
  lua_rawgeti(L, -1, i);  /* get key from pattern's environment */
  lua_gettable(L, t);  /* get position from positions table */
  res = lua_tointeger(L, -1);
  if (res == 0) {  /* key has no registered position? */
    lua_rawgeti(L, -2, i);  /* get key again */
    return luaL_error(L, "%s is not defined in given grammar", val2str(L, -1));
  }
  lua_pop(L, 2);  /* remove environment and position */
  return res;
}


/*
** {======================================================
** Printing patterns (for debugging)
** =======================================================
*/


static void printcharset (const Charset st) {
  int i;
  printf("[");
  for (i = 0; i <= UCHAR_MAX; i++) {
    int first = i;
    while (testchar(st, i) && i <= UCHAR_MAX) i++;
    if (i - 1 == first)  /* unary range? */
      printf("(%02x)", first);
    else if (i - 1 > first)  /* non-empty range? */
      printf("(%02x-%02x)", first, i - 1);
  }
  printf("]");
}


static void printcapkind (int kind) {
  const char *const modes[] = {
    "close", "position", "constant", "backref",
    "argument", "simple", "table", "function",
    "query", "string", "substitution", "fold",
    "runtime", "group"};
  printf("%s", modes[kind]);
}


static void printjmp (const Instruction *op, const Instruction *p) {
  printf("-> ");
  if (p->i.offset == 0) printf("FAIL");
  else printf("%d", (int)(dest(0, p) - op));
}


static void printinst (const Instruction *op, const Instruction *p) {
  const char *const names[] = {
    "any", "char", "set", "span", "back",
    "ret", "end",
    "choice", "jmp", "call", "open_call",
    "commit", "partial_commit", "back_commit", "failtwice", "fail", "giveup",
     "func",
     "fullcapture", "emptycapture", "emptycaptureidx", "opencapture",
     "closecapture", "closeruntime"
  };
  printf("%02ld: %s ", (long)(p - op), names[p->i.code]);
  switch ((Opcode)p->i.code) {
    case IChar: {
      printf("'%c'", p->i.aux);
      printjmp(op, p);
      break;
    }
    case IAny: {
      printf("* %d", p->i.aux);
      printjmp(op, p);
      break;
    }
    case IFullCapture: case IOpenCapture:
    case IEmptyCapture: case IEmptyCaptureIdx:
    case ICloseCapture: case ICloseRunTime: {
      printcapkind(getkind(p));
      printf("(n = %d)  (off = %d)", getoff(p), p->i.offset);
      break;
    }
    case ISet: {
      printcharset((p+1)->buff);
      printjmp(op, p);
      break;
    }
    case ISpan: {
      printcharset((p+1)->buff);
      break;
    }
    case IOpenCall: {
      printf("-> %d", p->i.offset);
      break;
    }
    case IChoice: {
      printjmp(op, p);
      printf(" (%d)", p->i.aux);
      break;
    }
    case IJmp: case ICall: case ICommit:
    case IPartialCommit: case IBackCommit: {
      printjmp(op, p);
      break;
    }
    default: break;
  }
  printf("\n");
}


static void printpatt (Instruction *p) {
  Instruction *op = p;
  for (;;) {
    printinst(op, p);
    if ((Opcode)p->i.code == IEnd) break;
    p += sizei(p);
  }
}


#if 0
static void printcap (Capture *cap) {
  printcapkind(cap->kind);
  printf(" (idx: %d - size: %d) -> %p\n", cap->idx, cap->siz, cap->s);
}


static void printcaplist (Capture *cap) {
  for (; cap->s; cap++) printcap(cap);
}
#endif

/* }====================================================== */


/*
** {======================================================
** Virtual Machine
** =======================================================
*/


typedef struct Stack {
  const char *s;
  const Instruction *p;
  int caplevel;
} Stack;


#define getstackbase(L, ptop)	((Stack *)lua_touserdata(L, stackidx(ptop)))


static int runtimecap (lua_State *L, Capture *close, Capture *ocap,
                       const char *o, const char *s, int ptop);


static Capture *doublecap (lua_State *L, Capture *cap, int captop, int ptop) {
  Capture *newc;
  if (captop >= INT_MAX/((int)sizeof(Capture) * 2))
    luaL_error(L, "too many captures");
  newc = (Capture *)lua_newuserdata(L, captop * 2 * sizeof(Capture));
  memcpy(newc, cap, captop * sizeof(Capture));
  lua_replace(L, caplistidx(ptop));
  return newc;
}


static Stack *doublestack (lua_State *L, Stack **stacklimit, int ptop) {
  Stack *stack = getstackbase(L, ptop);
  Stack *newstack;
  int n = *stacklimit - stack;
  int max, newn;
  lua_getfield(L, LUA_REGISTRYINDEX, MAXSTACKIDX);
  max = lua_tointeger(L, -1);
  lua_pop(L, 1);
  if (n >= max)
    luaL_error(L, "too many pending calls/choices");
  newn = 2*n; if (newn > max) newn = max;
  newstack = (Stack *)lua_newuserdata(L, newn * sizeof(Stack));
  memcpy(newstack, stack, n * sizeof(Stack));
  lua_replace(L, stackidx(ptop));
  *stacklimit = newstack + newn;
  return newstack + n;

}


static void adddyncaptures (const char *s, Capture *base, int n, int fd) {
  int i;
  assert(base[0].kind == Cruntime && base[0].siz == 0);
  base[0].idx = fd;  /* first returned capture */
  for (i = 1; i < n; i++) {  /* add extra captures */
    base[i].siz = 1;  /* mark it as closed */
    base[i].s = s;
    base[i].kind = Cruntime;
    base[i].idx = fd + i;  /* stack index */
  }
  base[n].kind = Cclose;  /* add closing entry */
  base[n].siz = 1;
  base[n].s = s;
}


#define condfailed(p)	{ int f = p->i.offset; if (f) p+=f; else goto fail; }

static const char *match (lua_State *L,
                          const char *o, const char *s, const char *e,
                          Instruction *op, Capture *capture, int ptop) {
  Stack stackbase[INITBACK];
  Stack *stacklimit = stackbase + INITBACK;
  Stack *stack = stackbase;  /* point to first empty slot in stack */
  int capsize = INITCAPSIZE;
  int captop = 0;  /* point to first empty slot in captures */
  const Instruction *p = op;
  stack->p = &giveup; stack->s = s; stack->caplevel = 0; stack++;
  lua_pushlightuserdata(L, stackbase);
  for (;;) {
#if defined(DEBUG)
      printf("s: |%s| stck: %d c: %d  ",
             s, stack - getstackbase(L, ptop), captop);
      printinst(op, p);
#endif
    switch ((Opcode)p->i.code) {
      case IEnd: {
        assert(stack == getstackbase(L, ptop) + 1);
        capture[captop].kind = Cclose;
        capture[captop].s = NULL;
        return s;
      }
      case IGiveup: {
        assert(stack == getstackbase(L, ptop));
        return NULL;
      }
      case IRet: {
        assert(stack > getstackbase(L, ptop) && (stack - 1)->s == NULL);
        p = (--stack)->p;
        continue;
      }
      case IAny: {
        int n = p->i.aux;
        if (n <= e - s) { p++; s += n; }
        else condfailed(p);
        continue;
      }
      case IChar: {
        if ((byte)*s == p->i.aux && s < e) { p++; s++; }
        else condfailed(p);
        continue;
      }
      case ISet: {
        int c = (byte)*s;
        if (testchar((p+1)->buff, c) && s < e)
          { p += CHARSETINSTSIZE; s++; }
        else condfailed(p);
        continue;
      }
      case IBack: {
        int n = p->i.aux;
        if (n > s - o) goto fail;
        s -= n; p++;
        continue;
      }
      case ISpan: {
        for (; s < e; s++) {
          int c = (byte)*s;
          if (!testchar((p+1)->buff, c)) break;
        }
        p += CHARSETINSTSIZE;
        continue;
      }
      case IFunc: {
        const char *r = (p+1)->f(s, e, o, (p+2)->buff);
        if (r != NULL) { s = r; p += funcinstsize(p); }
        else condfailed(p);
        continue;
      }
      case IJmp: {
        p += p->i.offset;
        continue;
      }
      case IChoice: {
        if (stack == stacklimit)
          stack = doublestack(L, &stacklimit, ptop);
        stack->p = dest(0, p);
        stack->s = s - p->i.aux;
        stack->caplevel = captop;
        stack++;
        p++;
        continue;
      }
      case ICall: {
        if (stack == stacklimit)
          stack = doublestack(L, &stacklimit, ptop);
        stack->s = NULL;
        stack->p = p + 1;  /* save return address */
        stack++;
        p += p->i.offset;
        continue;
      }
      case ICommit: {
        assert(stack > getstackbase(L, ptop) && (stack - 1)->s != NULL);
        stack--;
        p += p->i.offset;
        continue;
      }
      case IPartialCommit: {
        assert(stack > getstackbase(L, ptop) && (stack - 1)->s != NULL);
        (stack - 1)->s = s;
        (stack - 1)->caplevel = captop;
        p += p->i.offset;
        continue;
      }
      case IBackCommit: {
        assert(stack > getstackbase(L, ptop) && (stack - 1)->s != NULL);
        s = (--stack)->s;
        captop = stack->caplevel;
        p += p->i.offset;
        continue;
      }
      case IFailTwice:
        assert(stack > getstackbase(L, ptop));
        stack--;
        /* go through */
      case IFail:
      fail: { /* pattern failed: try to backtrack */
        do {  /* remove pending calls */
          assert(stack > getstackbase(L, ptop));
          s = (--stack)->s;
        } while (s == NULL);
        captop = stack->caplevel;
        p = stack->p;
        continue;
      }
      case ICloseRunTime: {
        int fr = lua_gettop(L) + 1;  /* stack index of first result */
        int ncap = runtimecap(L, capture + captop, capture, o, s, ptop);
        lua_Integer res = lua_tointeger(L, fr) - 1;  /* offset */
        int n = lua_gettop(L) - fr;  /* number of new captures */
        if (res == -1) {  /* may not be a number */
          if (!lua_toboolean(L, fr)) {  /* false value? */
            lua_settop(L, fr - 1);  /* remove results */
            goto fail;  /* and fail */
          }
          else if (lua_isboolean(L, fr))  /* true? */
            res = s - o;  /* keep current position */
        }
        if (res < s - o || res > e - o)
          luaL_error(L, "invalid position returned by match-time capture");
        s = o + res;  /* update current position */
        captop -= ncap;  /* remove nested captures */
        lua_remove(L, fr);  /* remove first result (offset) */
        if (n > 0) {  /* captures? */
          if ((captop += n + 1) >= capsize) {
            capture = doublecap(L, capture, captop, ptop);
            capsize = 2 * captop;
          }
          adddyncaptures(s, capture + captop - n - 1, n, fr);
        }
        p++;
        continue;
      }
      case ICloseCapture: {
        const char *s1 = s - getoff(p);
        assert(captop > 0);
        if (capture[captop - 1].siz == 0 &&
            s1 - capture[captop - 1].s < UCHAR_MAX) {
          capture[captop - 1].siz = s1 - capture[captop - 1].s + 1;
          p++;
          continue;
        }
        else {
          capture[captop].siz = 1;  /* mark entry as closed */
          goto capture;
        }
      }
      case IEmptyCapture: case IEmptyCaptureIdx:
        capture[captop].siz = 1;  /* mark entry as closed */
        goto capture;
      case IOpenCapture:
        capture[captop].siz = 0;  /* mark entry as open */
        goto capture;
      case IFullCapture:
        capture[captop].siz = getoff(p) + 1;  /* save capture size */
      capture: {
        capture[captop].s = s - getoff(p);
        capture[captop].idx = p->i.offset;
        capture[captop].kind = getkind(p);
        if (++captop >= capsize) {
          capture = doublecap(L, capture, captop, ptop);
          capsize = 2 * captop;
        }
        p++;
        continue;
      }
      case IOpenCall: {
        lua_rawgeti(L, penvidx(ptop), p->i.offset);
        luaL_error(L, "reference to %s outside a grammar", val2str(L, -1));
      }
      default: assert(0); return NULL;
    }
  }
}

/* }====================================================== */


/*
** {======================================================
** Verifier
** =======================================================
*/


/*
** check whether pattern may go from 'p' to 'e' without consuming any
** input. Raises an error if it detects a left recursion. 'op' points
** the beginning of the pattern.  If pattern belongs to a grammar,
** 'rule' is the stack index where is its corresponding key (only for
** error messages) and 'posttable' is the stack index with a table
** mapping rule keys to the position of their code in the pattern.
*/
static int verify (lua_State *L, Instruction *op, const Instruction *p,
                   Instruction *e, int postable, int rule) {
  static const char dummy[] = "";
  Stack back[MAXBACKVER];
  int backtop = 0;  /* point to first empty slot in back */
  while (p != e) {
    switch ((Opcode)p->i.code) {
      case IRet: {
        p = back[--backtop].p;
        continue;
      }
      case IChoice: {
        if (backtop >= MAXBACKVER)
          return luaL_error(L, "too many pending calls/choices");
        back[backtop].p = dest(0, p);
        back[backtop++].s = dummy;
        p++;
        continue;
      }
      case ICall: {
        assert((p + 1)->i.code != IRet);  /* no tail call */
        if (backtop >= MAXBACKVER)
          return luaL_error(L, "too many pending calls/choices");
        back[backtop].s = NULL;
        back[backtop++].p = p + 1;
        goto dojmp;
      }
      case IOpenCall: {
        int i;
        if (postable == 0)  /* grammar still not fixed? */
          goto fail;  /* to be verified later */
        for (i = 0; i < backtop; i++) {
          if (back[i].s == NULL && back[i].p == p + 1)
            return luaL_error(L, "%s is left recursive", val2str(L, rule));
        }
        if (backtop >= MAXBACKVER)
          return luaL_error(L, "too many pending calls/choices");
        back[backtop].s = NULL;
        back[backtop++].p = p + 1;
        p = op + getposition(L, postable, p->i.offset);
        continue;
      }
      case IBackCommit:
      case ICommit: {
        assert(backtop > 0 && p->i.offset > 0);
        backtop--;
        goto dojmp;
      }
      case IPartialCommit: {
        assert(backtop > 0);
        if (p->i.offset > 0) goto dojmp;  /* forward jump */
        else {  /* loop will be detected when checking corresponding rule */
          assert(postable != 0);
          backtop--;
          p++;  /* just go on now */
          continue;
        }
      }
      case IBack: {
        if (p->i.aux == 1 && isfixcheck(p + 1)) {  /* char test? */
          p++;  /* skip back instruction */
          p += sizei(p);  /* skip char test */
        }
        else {  /* standard lookbehind code */
          assert((Opcode)(p - 1)->i.code == IChoice);  /* look behind */
          backtop--;
          p += (p - 1)->i.offset;
          assert((Opcode)(p - 1)->i.code == IFail);  /* look behind */
        }
        continue;
      }
      case IAny:
      case IChar:
      case ISet: {
        const Instruction *next = p + sizei(p);
        if ((Opcode)next->i.code == IBack)
          p = next + 1;  /* continue after the back instruction */
        else if (p->i.offset == 0) goto fail;
        else  /* jump */
          p += p->i.offset;
        continue;
      }
      case IJmp:
      dojmp: {
        p += p->i.offset;
        continue;
      }
      case IFailTwice:  /* 'not' predicate */
        goto fail;  /* body could have failed; try to backtrack it */
      case IFail: {
        if (p > op && (p - 1)->i.code == IBackCommit) {  /* 'and' predicate? */
          p++;  /* pretend it succeeded and go ahead */
          continue;
        }
        /* else failed: go through */
      }
      fail: { /* pattern failed: try to backtrack */
        do {
          if (backtop-- == 0)
            return 1;  /* no more backtracking */
        } while (back[backtop].s == NULL);
        p = back[backtop].p;
        continue;
      }
      case ISpan:
      case IOpenCapture: case ICloseCapture:
      case IEmptyCapture: case IEmptyCaptureIdx:
      case IFullCapture: {
        p += sizei(p);
        continue;
      }
      case ICloseRunTime: {
        goto fail;  /* be liberal in this case */
      }
      case IFunc: {
        const char *r = (p+1)->f(dummy, dummy, dummy, (p+2)->buff);
        if (r != NULL) { p += funcinstsize(p); }
        else condfailed(p);
        continue;
      }
      case IEnd:  /* cannot happen (should stop before it) */
      default: assert(0); return 0;
    }
  }
  assert(backtop == 0);
  return 0;
}


static void checkrule (lua_State *L, Instruction *op, int from, int to,
                       int postable, int rule) {
  int i;
  int lastopen = 0;  /* more recent OpenCall seen in the code */
  for (i = from; i < to; i += sizei(op + i)) {
    if (op[i].i.code == IPartialCommit && op[i].i.offset < 0) {  /* loop? */
      int start = dest(op, i);
      assert(op[start - 1].i.code == IChoice &&
             dest(op, start - 1) == target(op, i + 1));
      if (start <= lastopen) {  /* loop does contain an open call? */
        if (!verify(L, op, op + start, op + i, postable, rule)) /* check body */
          luaL_error(L, "possible infinite loop in %s", val2str(L, rule));
      }
    }
    else if (op[i].i.code == IOpenCall)
      lastopen = i;
  }
  assert(op[i - 1].i.code == IRet);
  verify(L, op, op + from, op + to - 1, postable, rule);
}




/* }====================================================== */


/*
** {======================================================
** Building Patterns
** =======================================================
*/

enum charsetanswer { NOINFO, ISCHARSET, VALIDSTARTS };

typedef struct CharsetTag {
  enum charsetanswer tag;
  Charset cs;
} CharsetTag;


static Instruction *getpatt (lua_State *L, int idx, int *size);


static void check2test (Instruction *p, int n) {
  assert(ischeck(p) && n != 0);
  p->i.offset = n;
}


/*
** invert array slice p[0]-p[e] (both inclusive)
*/
static void invert (Instruction *p, int e) {
  int i;
  for (i = 0; i < e; i++, e--) {
    Instruction temp = p[i];
    p[i] = p[e];
    p[e] = temp;
  }
}


/*
** rotate array slice p[0]-p[e] (both inclusive) 'n' steps
** to the 'left'
*/
static void rotate (Instruction *p, int e, int n) {
  invert(p, n - 1);
  invert(p + n, e - n);
  invert(p, e);
}


#define op_step(p)	((p)->i.code == IAny ? (p)->i.aux : 1)


static int skipchecks (Instruction *p, int up, int *pn) {
  int i, n = 0;
  for (i = 0; isfixcheck(p + i); i += sizei(p + i)) {
    int st = op_step(p + i);
    if (n + st > MAXOFF - up) break;
    n += st;
  }
  *pn = n;
  return i;
}


#define ismovablecap(op)	(ismovable(op) && getoff(op) < MAXOFF)

static void optimizecaptures (Instruction *p) {
  int i;
  int limit = 0;
  for (i = 0; p[i].i.code != IEnd; i += sizei(p + i)) {
    if (isjmp(p + i) && dest(p, i) >= limit)
      limit = dest(p, i) + 1;  /* do not optimize jump targets */
    else if (i >= limit && ismovablecap(p + i) && isfixcheck(p + i + 1)) {
      int end, n, j;  /* found a border capture|check */
      int maxoff = getoff(p + i);
      int start = i;
      /* find first capture in the group */
      while (start > limit && ismovablecap(p + start - 1)) {
        start--;
        if (getoff(p + start) > maxoff) maxoff = getoff(p + start);
      }
      end = skipchecks(p + i + 1, maxoff, &n) + i;  /* find last check */
      if (n == 0) continue;  /* first check is too big to move across */
      assert(n <= MAXOFF && start <= i && i < end);
      for (j = start; j <= i; j++)
        p[j].i.aux += (n << 4);  /* correct offset of captures to be moved */
      rotate(p + start, end - start, i - start + 1);  /* move them up */
      i = end;
      assert(isfixcheck(p + start) && iscapture(p + i));
    }
  }
}


static int target (Instruction *p, int i) {
  while (p[i].i.code == IJmp)  i += p[i].i.offset;
  return i;
}


static void optimizejumps (Instruction *p) {
  int i;
  for (i = 0; p[i].i.code != IEnd; i += sizei(p + i)) {
    if (isjmp(p + i))
      p[i].i.offset = target(p, dest(p, i)) - i;
  }
}


static void optimizechoice (Instruction *p) {
  assert(p->i.code == IChoice);
  if (isfixcheck(p + 1)) {
    int lc = sizei(p + 1);
    rotate(p, lc, 1);
    assert(isfixcheck(p) && (p + lc)->i.code == IChoice);
    (p + lc)->i.aux = op_step(p);
    check2test(p, (p + lc)->i.offset);
    (p + lc)->i.offset -= lc;
  }
}


/*
** A 'headfail' pattern is a pattern that can only fails in its first
** instruction, which must be a check.
*/
static int isheadfail (Instruction *p) {
  if (!ischeck(p)) return 0;
  /* check that other operations cannot fail */
  for (p += sizei(p); p->i.code != IEnd; p += sizei(p))
    if (!isnofail(p)) return 0;
  return 1;
}


#define checkpattern(L, idx) ((Instruction *)luaL_checkudata(L, idx, PATTERN_T))


/*
** Return the number of elements in the ktable of a pattern.
** in Lua 5.2, default "environment" for patterns is nil, not
** a table. Treat it as an empty table.
*/
static int ktablelen (lua_State *L, int idx) {
  if (!lua_istable(L, idx)) return 0;
  else return lua_objlen(L, idx);
}


/*
** join the elements of the ktable from pattern 'p1' into the ktable of
** the pattern at the top of the stack ('p').  If 'p1' has no elements,
** 'p' keeps its original ktable.  If 'p' has no elements, it shares
** 'p1' ktable.  Otherwise, this function creates a new ktable for 'p'.
** Return the offset of original 'p' elements in the new ktable.
*/ 
static int jointable (lua_State *L, int p1) {
  int n, n1, i;
  lua_getfenv(L, p1);
  n1 = ktablelen(L, -1);  /* number of elements in p1's env */
  lua_getfenv(L, -2);
  if (n1 == 0 || lua_equal(L, -2, -1)) {
    lua_pop(L, 2);
    return 0;  /* no need to change anything */
  }
  n = ktablelen(L, -1);  /* number of elements in p's env */
  if (n == 0) {
    lua_pop(L, 1);  /* removes p env */
    lua_setfenv(L, -2);  /* p now shares p1's env */
    return 0;  /* no need to correct anything */
  }
  lua_createtable(L, n + n1, 0);
  /* stack: p; p1 env; p env; new p env */
  for (i = 1; i <= n; i++) {
    lua_rawgeti(L, -2, i);
    lua_rawseti(L, -2, i);
  }
  for (i = 1; i <= n1; i++) {
    lua_rawgeti(L, -3, i);
    lua_rawseti(L, -2, n + i);
  }
  lua_setfenv(L, -4);  /* new table becomes p env */
  lua_pop(L, 2);  /* remove p1 env and old p env */
  return n;
}


#define copypatt(p1,p2,sz)	memcpy(p1, p2, (sz) * sizeof(Instruction));

#define pattsize(L,idx)		(lua_objlen(L, idx)/sizeof(Instruction) - 1)


static int addpatt (lua_State *L, Instruction *p, int p1idx) {
  Instruction *p1 = (Instruction *)lua_touserdata(L, p1idx);
  int sz = pattsize(L, p1idx);
  int corr = jointable(L, p1idx);
  copypatt(p, p1, sz + 1);
  if (corr != 0) {
    Instruction *px;
    for (px = p; px < p + sz; px += sizei(px)) {
      if (isfenvoff(px) && px->i.offset != 0)
        px->i.offset += corr;
    }
  }
  return sz;
}


static void setinstaux (Instruction *i, Opcode op, int offset, int aux) {
  assert(aux <= MAXAUX);
  i->i.code = op;
  i->i.offset = offset;
  i->i.aux = aux;
}

#define setinst(i,op,off)	setinstaux(i,op,off,0)

#define setinstcap(i,op,idx,k,n)  setinstaux(i,op,idx,((k) | ((n) << 4)))


/*
** create a new ktable for pattern at the stack top, mapping
** '1' to the value at stack position 'vidx'.
*/
static int value2fenv (lua_State *L, int vidx) {
  lua_createtable(L, 1, 0);
  lua_pushvalue(L, vidx);
  lua_rawseti(L, -2, 1);
  lua_setfenv(L, -2);
  return 1;
}


static Instruction *newpatt (lua_State *L, size_t n) {
  Instruction *p;
  if (n >= MAXPATTSIZE - 1)
    luaL_error(L, "pattern too big");
  p = (Instruction *)lua_newuserdata(L, (n + 1) * sizeof(Instruction));
  luaL_getmetatable(L, PATTERN_T);
  lua_setmetatable(L, -2);
  setinst(p + n, IEnd, 0);
  return p;
}


static void fillcharset (Instruction *p, Charset cs) {
  switch (p[0].i.code) {
    case ISet: {
      loopset(i, cs[i] = p[1].buff[i]);
      break;
    }
    case IChar: {
      loopset(i, cs[i] = 0);
      setchar(cs, p[0].i.aux);
      break;
    }
    default: {  /* any char may start unhandled instructions */
      loopset(i, cs[i] = 0xff);
      break;
    }
  }
}


/*
** Function 'tocharset' gets information about which chars may be a
** valid start for a pattern.
*/

static enum charsetanswer tocharset (Instruction *p, CharsetTag *c) {
  if (isfixcheck(p)) {
    fillcharset(p, c->cs);
    if ((p + sizei(p))->i.code == IEnd && op_step(p) == 1)
      c->tag = ISCHARSET;
    else
      c->tag = VALIDSTARTS;
  }
  else
    c->tag = NOINFO;
  return c->tag;
}


static int exclusiveset (Charset c1, Charset c2) {
  /* non-empty intersection? */
  loopset(i, {if ((c1[i] & c2[i]) != 0) return 0;});
  return 1;  /* no intersection */
}


static int exclusive (CharsetTag *c1, CharsetTag *c2) {
  if (c1->tag == NOINFO || c2->tag == NOINFO)
    return 0;  /* one of them is not filled */
  else return exclusiveset(c1->cs, c2->cs);
}


static Instruction *newcharset (lua_State *L) {
  Instruction *p = newpatt(L, CHARSETINSTSIZE);
  p[0].i.code = ISet;
  p[0].i.offset = 0;
  loopset(i, p[1].buff[i] = 0);
  return p;
}


static int set_l (lua_State *L) {
  size_t l;
  const char *s = luaL_checklstring(L, 1, &l);
  if (l == 1)
    getpatt(L, 1, NULL);  /* a unit set is equivalent to a literal */
  else {
    Instruction *p = newcharset(L);
    while (l--) {
      setchar(p[1].buff, (byte)(*s));
      s++;
    }
  }
  return 1;
}


static int range_l (lua_State *L) {
  int arg;
  int top = lua_gettop(L);
  Instruction *p = newcharset(L);
  for (arg = 1; arg <= top; arg++) {
    int c;
    size_t l;
    const char *r = luaL_checklstring(L, arg, &l);
    luaL_argcheck(L, l == 2, arg, "range must have two characters");
    for (c = (byte)r[0]; c <= (byte)r[1]; c++)
      setchar(p[1].buff, c);
  }
  return 1;
}


static int nter_l (lua_State *L) {
  Instruction *p;
  luaL_argcheck(L, !lua_isnoneornil(L, 1), 1, "non-nil value expected");
  p = newpatt(L, 1);
  setinst(p, IOpenCall, value2fenv(L, 1));
  return 1;
}



static int testpattern (lua_State *L, int idx) {
  if (lua_touserdata(L, idx)) {  /* value is a userdata? */
    if (lua_getmetatable(L, idx)) {  /* does it have a metatable? */
      luaL_getmetatable(L, PATTERN_T);
      if (lua_rawequal(L, -1, -2)) {  /* does it have the correct mt? */
        lua_pop(L, 2);  /* remove both metatables */
        return 1;
      }
    }
  }
  return 0;
}


static Instruction *fix_l (lua_State *L, int t) {
  Instruction *p;
  int i;
  int totalsize = 2;  /* include initial call and jump */
  int n = 0;  /* number of rules */
  int base = lua_gettop(L);
  lua_newtable(L);  /* to store relative positions of each rule */
  lua_pushinteger(L, 1);  /* default initial rule */
  /* collect patterns and compute sizes */
  lua_pushnil(L);
  while (lua_next(L, t) != 0) {
    int l;
    if (lua_tonumber(L, -2) == 1 && lua_isstring(L, -1)) {
      lua_replace(L, base + 2);  /* use this value as initial rule */
      continue;
    }
    if (!testpattern(L, -1))
      luaL_error(L, "%s is not a pattern", val2str(L, -2));
    l = pattsize(L, -1) + 1;  /* space for pattern + ret */
    if (totalsize >= MAXPATTSIZE - l)
      luaL_error(L, "grammar too large");
    luaL_checkstack(L, LUA_MINSTACK, "grammar has too many rules");
    lua_insert(L, -2);  /* put key on top */
    lua_pushvalue(L, -1);  /* duplicate key (for lua_next) */
    lua_pushvalue(L, -1);  /* duplicate key (to index positions table)) */
    lua_pushinteger(L, totalsize);  /* position for this rule */
    lua_settable(L, base + 1);  /* store key=>position in positions table */
    totalsize += l;
    n++;
  }
  luaL_argcheck(L, n > 0, t, "empty grammar");
  p = newpatt(L, totalsize);  /* create new pattern */
  p++;  /* save space for call */
  setinst(p++, IJmp, totalsize - 1);  /* after call, jumps to the end */
  for (i = 1; i <= n; i++) {  /* copy all rules into new pattern */
    p += addpatt(L, p, base + 1 + i*2);
    setinst(p++, IRet, 0);
  }
  p -= totalsize;  /* back to first position */
  totalsize = 2;  /* go through each rule's position */
  for (i = 1; i <= n; i++) {  /* check all rules */
    int l = pattsize(L, base + 1 + i*2) + 1;
    checkrule(L, p, totalsize, totalsize + l, base + 1, base + 2 + i*2);
    totalsize += l;
  }
  lua_pushvalue(L, base + 2);  /* get initial rule */
  lua_gettable(L, base + 1);  /* get its position in postions table */
  i = lua_tonumber(L, -1);  /* convert to number */
  lua_pop(L, 1);
  if (i == 0)  /* is it defined? */
    luaL_error(L, "initial rule not defined in given grammar");
  setinst(p, ICall, i);  /* first instruction calls initial rule */
  /* correct calls */
  for (i = 0; i < totalsize; i += sizei(p + i)) {
    if (p[i].i.code == IOpenCall) {
      int pos = getposition(L, base + 1, p[i].i.offset);
      p[i].i.code = (p[target(p, i + 1)].i.code == IRet) ? IJmp : ICall;
      p[i].i.offset = pos - i;
    }
  }
  optimizejumps(p);
  lua_replace(L, t);  /* put new pattern in old's position */
  lua_settop(L, base);  /* remove rules and positions table */
  return p;
}


static Instruction *any (lua_State *L, int n, int extra, int *offsetp) {
  int offset = offsetp ? *offsetp : 0;
  Instruction *p = newpatt(L, (n - 1)/UCHAR_MAX + extra + 1);
  Instruction *p1 = p + offset;
  for (; n > UCHAR_MAX; n -= UCHAR_MAX)
    setinstaux(p1++, IAny, 0, UCHAR_MAX);
  setinstaux(p1++, IAny, 0, n);
  if (offsetp) *offsetp = p1 - p;
  return p;
}


static Instruction *getpatt (lua_State *L, int idx, int *size) {
  Instruction *p;
  switch (lua_type(L, idx)) {
    case LUA_TSTRING: {
      size_t i, len;
      const char *s = lua_tolstring(L, idx, &len);
      p = newpatt(L, len);
      for (i = 0; i < len; i++)
        setinstaux(p + i, IChar, 0, (byte)s[i]);
      lua_replace(L, idx);
      break;
    }
    case LUA_TNUMBER: {
      int n = lua_tointeger(L, idx);
      if (n == 0)  /* empty pattern? */
        p = newpatt(L, 0);
      else if (n > 0)
        p = any(L, n, 0, NULL);
      else if (-n <= UCHAR_MAX) {
        p = newpatt(L, 2);
        setinstaux(p, IAny, 2, -n);
        setinst(p + 1, IFail, 0);
      }
      else {
        int offset = 2;  /* space for ITestAny & IChoice */
        p = any(L, -n - UCHAR_MAX, 3, &offset);
        setinstaux(p, IAny, offset + 1, UCHAR_MAX);
        setinstaux(p + 1, IChoice, offset, UCHAR_MAX);
        setinst(p + offset, IFailTwice, 0);
      }
      lua_replace(L, idx);
      break;
    }
    case LUA_TBOOLEAN: {
      if (lua_toboolean(L, idx))  /* true? */
        p = newpatt(L, 0);  /* empty pattern (always succeeds) */
      else {
        p = newpatt(L, 1);
        setinst(p, IFail, 0);
      }
      lua_replace(L, idx);
      break;
    }
    case LUA_TTABLE: {
      p = fix_l(L, idx);
      break;
    }
    case LUA_TFUNCTION: {
      p = newpatt(L, 2);
      setinstcap(p, IOpenCapture, value2fenv(L, idx), Cruntime, 0);
      setinstcap(p + 1, ICloseRunTime, 0, Cclose, 0);
      lua_replace(L, idx);
      break;
    }
    default: {
      p = checkpattern(L, idx);
      break;
    }
  }
  if (size) *size = pattsize(L, idx);
  return p;
}


static int getpattl (lua_State *L, int idx) {
  int size;
  getpatt(L, idx, &size);
  return size;
}


static int pattern_l (lua_State *L) {
  lua_settop(L, 1);
  getpatt(L, 1, NULL);
  return 1;
}


#define isany(p)	((p)->i.code == IAny && ((p) + 1)->i.code == IEnd)
#define isfail(p)	((p)->i.code == IFail)
#define issucc(p)	((p)->i.code == IEnd)

static int concat_l (lua_State *L) {
  /* p1; p2; */
  int l1, l2;
  Instruction *p1 = getpatt(L, 1, &l1);
  Instruction *p2 = getpatt(L, 2, &l2);
  if (isfail(p1) || issucc(p2))
    lua_pushvalue(L, 1);  /* fail * x == fail; x * true == x */
  else if (isfail(p2) || issucc(p1))
    lua_pushvalue(L, 2);  /* x * fail == fail; true * x == x */
  else if (isany(p1) && isany(p2))
    any(L, p1->i.aux + p2->i.aux, 0, NULL);
  else {
    Instruction *op = newpatt(L, l1 + l2);
    Instruction *p = op + addpatt(L, op, 1);
    addpatt(L, p, 2);
    optimizecaptures(op);
  }
  return 1;
}


static int diff_l (lua_State *L) {
  int l1, l2;
  Instruction *p1 = getpatt(L, 1, &l1);
  Instruction *p2 = getpatt(L, 2, &l2);
  CharsetTag st1, st2;
  if (tocharset(p1, &st1) == ISCHARSET && tocharset(p2, &st2) == ISCHARSET) {
    Instruction *p = newcharset(L);
    loopset(i, p[1].buff[i] = st1.cs[i] & ~st2.cs[i]);
  }
  else if (isheadfail(p2)) {
    Instruction *p = newpatt(L, l2 + 1 + l1);
    p += addpatt(L, p, 2);
    check2test(p - l2, l2 + 1);
    setinst(p++, IFail, 0);
    addpatt(L, p, 1);
  }
  else {  /* !e2 . e1 */
    /* !e -> choice L1; e; failtwice; L1: ... */
    Instruction *p = newpatt(L, 1 + l2 + 1 + l1);
    Instruction *pi = p;
    setinst(p++, IChoice, 1 + l2 + 1);
    p += addpatt(L, p, 2);
    setinst(p++, IFailTwice, 0);
    addpatt(L, p, 1);
    optimizechoice(pi);
  }
  return 1;
}


static int unm_l (lua_State *L) {
  Instruction *p = getpatt(L, 1, NULL);
  if (isfail(p)) {  /* -false? */
    newpatt(L, 0);  /* true */
    return 1;
  }
  else if (issucc(p)) {  /* -true? */
    Instruction *p1 = newpatt(L, 1);  /* false */
    setinst(p1, IFail, 0);
    return 1;
  }
  else {  /* -A == '' - A */
    lua_pushliteral(L, "");
    lua_insert(L, 1);
    return diff_l(L);
  }
}


static int pattand_l (lua_State *L) {
  int l1;
  CharsetTag st1;
  Instruction *p1 = getpatt(L, 1, &l1);
  if (isfail(p1) || issucc(p1))
    lua_pushvalue(L, 1);  /* &fail == fail; &true == true */
  else if (tocharset(p1, &st1) == ISCHARSET) {
    Instruction *p = newpatt(L, l1 + 1);
    copypatt(p, p1, l1); p += l1;
    setinstaux(p, IBack, 0, 1);
  }
  else {  /* Choice L1; p1; BackCommit L2; L1: Fail; L2: */
    Instruction *p = newpatt(L, 1 + l1 + 2);
    setinst(p++, IChoice, 1 + l1 + 1);
    p += addpatt(L, p, 1);
    setinst(p++, IBackCommit, 2);
    setinst(p, IFail, 0);
  }
  return 1;
}


static int nocalls (const Instruction *p) {
  for (; (Opcode)p->i.code != IEnd; p += sizei(p))
    if ((Opcode)p->i.code == IOpenCall) return 0;
  return 1;
}


static int pattbehind (lua_State *L) {
  int l1;
  CharsetTag st1;
  Instruction *p1 = getpatt(L, 1, &l1);
  int n = luaL_optint(L, 2, 1);
  luaL_argcheck(L, n <= MAXAUX, 2, "lookbehind delta too large");
  if (!nocalls(p1))
    luaL_error(L, "lookbehind pattern cannot contain non terminals");
  if (isfail(p1) || issucc(p1))
    lua_pushvalue(L, 1);  /* tag == NOINFO) return 1;
  assert(p1->i.offset != 0);
  switch (p1->i.code) {
    case IChar: return testchar(st2->cs, p1->i.aux);
    case ISet: return !exclusiveset(st2->cs, (p1 + 1)->buff);
    default: assert(p1->i.code == IAny); return 1;
  }
}


static Instruction *basicUnion (lua_State *L, Instruction *p1, int l1,
                                int l2, int *size, CharsetTag *st2) {
  Instruction *op;
  CharsetTag st1;
  tocharset(p1, &st1);
  if (st1.tag == ISCHARSET && st2->tag == ISCHARSET) {
    Instruction *p = auxnew(L, &op, size, CHARSETINSTSIZE);
    setinst(p, ISet, 0);
    loopset(i, p[1].buff[i] = st1.cs[i] | st2->cs[i]);
  }
  else if (exclusive(&st1, st2) || isheadfail(p1)) {
    Instruction *p = auxnew(L, &op, size, l1 + 1 + l2);
    copypatt(p, p1, l1);
    check2test(p, l1 + 1);
    p += l1;
    setinst(p++, IJmp, l2 + 1);
    addpatt(L, p, 2);
  }
  else {
    /* choice L1; e1; commit L2; L1: e2; L2: ... */
    Instruction *p = auxnew(L, &op, size, 1 + l1 + 1 + l2);
    setinst(p++, IChoice, 1 + l1 + 1);
    copypatt(p, p1, l1); p += l1;
    setinst(p++, ICommit, 1 + l2);
    addpatt(L, p, 2);
    optimizechoice(p - (1 + l1 + 1));
  }
  return op;
}


static Instruction *separateparts (lua_State *L, Instruction *p1, int l1,
                                   int l2, int *size, CharsetTag *st2) {
  int sp = firstpart(p1, l1);
  if (sp == 0)  /* first part is entire p1? */
    return basicUnion(L, p1, l1, l2, size, st2);
  else if ((p1 + sp - 1)->i.code == ICommit || !interfere(p1, sp, st2)) {
    Instruction *p;
    int init = *size;
    int end = init + sp;
    *size = end;
    p = separateparts(L, p1 + sp, l1 - sp, l2, size, st2);
    copypatt(p + init, p1, sp);
    (p + end - 1)->i.offset = *size - (end - 1);
    return p;
  }
  else {  /* must change back to non-optimized choice */
    Instruction *p;
    int init = *size;
    int end = init + sp + 1;  /* needs one extra instruction (choice) */
    int sizefirst = sizei(p1);  /* size of p1's first instruction (the test) */
    *size = end;
    p = separateparts(L, p1 + sp, l1 - sp, l2, size, st2);
    copypatt(p + init, p1, sizefirst);  /* copy the test */
    (p + init)->i.offset++;  /* correct jump (because of new instruction) */
    init += sizefirst;
    setinstaux(p + init, IChoice, sp - sizefirst + 1, 1); init++;
    copypatt(p + init, p1 + sizefirst, sp - sizefirst - 1);
    init += sp - sizefirst - 1;
    setinst(p + init, ICommit, *size - (end - 1));
    return p;
  }
}


static int union_l (lua_State *L) {
  int l1, l2;
  int size = 0;
  Instruction *p1 = getpatt(L, 1, &l1);
  Instruction *p2 = getpatt(L, 2, &l2);
  CharsetTag st2;
  if (isfail(p1))  /* check for simple identities */
    lua_pushvalue(L, 2);  /* fail / a == a */
  else if (isfail(p2) || issucc(p1))
    lua_pushvalue(L, 1);  /* a / fail == a; true / a == true */
  else {
    tocharset(p2, &st2);
    separateparts(L, p1, l1, l2, &size, &st2);
  }
  return 1;
}


static int repeatcharset (lua_State *L, Charset cs, int l1, int n) {
  /* e; ...; e; span; */
  int i;
  Instruction *p = newpatt(L, n*l1 + CHARSETINSTSIZE);
  for (i = 0; i < n; i++) {
    p += addpatt(L, p, 1);
  }
  setinst(p, ISpan, 0);
  loopset(k, p[1].buff[k] = cs[k]);
  return 1;
}


static Instruction *repeatheadfail (lua_State *L, int l1, int n) {
  /* e; ...; e; L2: e'(L1); jump L2; L1: ... */
  int i;
  Instruction *p = newpatt(L, (n + 1)*l1 + 1);
  Instruction *op = p;
  for (i = 0; i < n; i++) {
    p += addpatt(L, p, 1);
  }
  p += addpatt(L, p, 1);
  check2test(p - l1, l1 + 1);
  setinst(p, IJmp, -l1);
  return op;
}


static Instruction *repeats (lua_State *L, Instruction *p1, int l1, int n) {
  /* e; ...; e; choice L1; L2: e; partialcommit L2; L1: ... */
  int i;
  Instruction *op = newpatt(L, (n + 1)*l1 + 2);
  Instruction *p = op;
  if (!verify(L, p1, p1, p1 + l1, 0, 0))
    luaL_error(L, "loop body may accept empty string");
  for (i = 0; i < n; i++) {
    p += addpatt(L, p, 1);
  }
  setinst(p++, IChoice, 1 + l1 + 1);
  p += addpatt(L, p, 1);
  setinst(p, IPartialCommit, -l1);
  return op;
}


static void optionalheadfail (lua_State *L, int l1, int n) {
  Instruction *op = newpatt(L, n * l1);
  Instruction *p = op;
  int i;
  for (i = 0; i < n; i++) {
    p += addpatt(L, p, 1);
    check2test(p - l1, (n - i)*l1);
  }
}


static void optionals (lua_State *L, int l1, int n) {
  /* choice L1; e; partialcommit L2; L2: ... e; L1: commit L3; L3: ... */
  int i;
  Instruction *op = newpatt(L, n*(l1 + 1) + 1);
  Instruction *p = op;
  setinst(p++, IChoice, 1 + n*(l1 + 1));
  for (i = 0; i < n; i++) {
    p += addpatt(L, p, 1);
    setinst(p++, IPartialCommit, 1);
  }
  setinst(p - 1, ICommit, 1);  /* correct last commit */
  optimizechoice(op);
}


static int star_l (lua_State *L) {
  int l1;
  int n = luaL_checkint(L, 2);
  Instruction *p1 = getpatt(L, 1, &l1);
  if (n >= 0) {
    CharsetTag st;
    Instruction *op;
    if (tocharset(p1, &st) == ISCHARSET)
      return repeatcharset(L, st.cs, l1, n);
    if (isheadfail(p1))
      op = repeatheadfail(L, l1, n);
    else
      op = repeats(L, p1, l1, n);
    optimizecaptures(op);
    optimizejumps(op);
  }
  else {
    if (isheadfail(p1))
      optionalheadfail(L, l1, -n);
    else
      optionals(L, l1, -n);
  }
  return 1;
}


static int getlabel (lua_State *L, int labelidx) {
  if (labelidx == 0) return 0;
  else return value2fenv(L, labelidx);
}


static int capture_aux (lua_State *L, int kind, int labelidx) {
  int l1, n;
  Instruction *p1 = getpatt(L, 1, &l1);
  int lc = skipchecks(p1, 0, &n);
  if (lc == l1) {  /* got whole pattern? */
    /* may use a IFullCapture instruction at its end */
    Instruction *p = newpatt(L, l1 + 1);
    int label = getlabel(L, labelidx);
    p += addpatt(L, p, 1);
    setinstcap(p, IFullCapture, label, kind, n);
  }
  else {  /* must use open-close pair */
    Instruction *op = newpatt(L, 1 + l1 + 1);
    Instruction *p = op;
    setinstcap(p++, IOpenCapture, getlabel(L, labelidx), kind, 0);
    p += addpatt(L, p, 1);
    setinstcap(p, ICloseCapture, 0, Cclose, 0);
    optimizecaptures(op);
  }
  return 1;
}


static int capture_l (lua_State *L) { return capture_aux(L, Csimple, 0); }
static int tcapture_l (lua_State *L) { return capture_aux(L, Ctable, 0); }
static int capsubst_l (lua_State *L) { return capture_aux(L, Csubst, 0); }

static int rcapture_l (lua_State *L) {
  switch (lua_type(L, 2)) {
    case LUA_TFUNCTION: return capture_aux(L, Cfunction, 2);
    case LUA_TTABLE: return capture_aux(L, Cquery, 2);
    case LUA_TSTRING: return capture_aux(L, Cstring, 2);
    default: return luaL_argerror(L, 2, "invalid replacement value");
  }
}


static int fold_l (lua_State *L) {
  luaL_checktype(L, 2, LUA_TFUNCTION);
  return capture_aux(L, Cfold, 2);
}


static int group_l (lua_State *L) {
  if (lua_isnoneornil(L, 2))
    return capture_aux(L, Cgroup, 0);
  else {
    luaL_checkstring(L, 2);
    return capture_aux(L, Cgroup, 2);
  }
}


static int position_l (lua_State *L) {
  Instruction *p = newpatt(L, 1);
  setinstcap(p, IEmptyCapture, 0, Cposition, 0);
  return 1;
}


static int backref_l (lua_State *L) {
  Instruction *p = newpatt(L, 1);
  int n = getlabel(L, 1);
  setinstcap(p, IEmptyCaptureIdx, n, Cbackref, 0);
  return 1;
}


static int argcap_l (lua_State *L) {
  int n = luaL_checkint(L, 1);
  Instruction *p = newpatt(L, 1);
  luaL_argcheck(L, 0 < n && n <= SHRT_MAX, 1, "invalid argument index");
  setinstcap(p, IEmptyCapture, n, Carg, 0);
  return 1;
}


static int matchtime_l (lua_State *L) {
  int l1 = getpattl(L, 1);
  Instruction *op = newpatt(L, 1 + l1 + 1);
  Instruction *p = op;
  luaL_checktype(L, 2, LUA_TFUNCTION);
  setinstcap(p++, IOpenCapture, value2fenv(L, 2), Cruntime, 0);
  p += addpatt(L, p, 1);
  setinstcap(p, ICloseRunTime, 0, Cclose, 0);
  optimizecaptures(op);
  return 1;
}


static int capconst_l (lua_State *L) {
  int i, j;
  int n = lua_gettop(L);
  Instruction *p = newpatt(L, n > 1 ? n + 2 : n);
  lua_createtable(L, n, 0);  /* new environment for the new pattern */
  if (n > 1) setinstcap(p++, IOpenCapture, 0, Cgroup, 0);
  for (i = j = 1; i <= n; i++) {
    if (lua_isnil(L, i))
      setinstcap(p++, IEmptyCaptureIdx, 0, Cconst, 0);
    else {
      setinstcap(p++, IEmptyCaptureIdx, j, Cconst, 0);
      lua_pushvalue(L, i);
      lua_rawseti(L, -2, j++);
    }
  }
  if (n > 1) setinstcap(p++, ICloseCapture, 0, Cclose, 0);
  lua_setfenv(L, -2);   /* set environment */
  return 1;
}


/* }====================================================== */


/*
** {======================================================
** User-Defined Patterns
** =======================================================
*/

static void l_newpf (lua_State *L, PattFunc f, const void *ud, size_t l) {
  int n = instsize(l) + 1;
  Instruction *p = newpatt(L, n);
  if (n > MAXAUX) luaL_error(L, "pattern data too long");
  p[0].i.code = IFunc;
  p[0].i.aux = n - 2;
  p[0].i.offset = 0;
  p[1].f = f;
  memcpy(p[2].buff, ud, l);
}

/* }====================================================== */


/*
** {======================================================
** Captures
** =======================================================
*/


typedef struct CapState {
  Capture *cap;  /* current capture */
  Capture *ocap;  /* (original) capture list */
  lua_State *L;
  int ptop;  /* index of last argument to 'match' */
  const char *s;  /* original string */
  int valuecached;  /* value stored in cache slot */
} CapState;


#define captype(cap)	((cap)->kind)

#define isclosecap(cap)	(captype(cap) == Cclose)

#define closeaddr(c)	((c)->s + (c)->siz - 1)

#define isfullcap(cap)	((cap)->siz != 0)

#define getfromenv(cs,v)	lua_rawgeti((cs)->L, penvidx((cs)->ptop), v)
#define pushluaval(cs)		getfromenv(cs, (cs)->cap->idx)

#define pushsubject(cs, c) lua_pushlstring((cs)->L, (c)->s, (c)->siz - 1)


#define updatecache(cs,v) { if ((v) != (cs)->valuecached) updatecache_(cs,v); }


static void updatecache_ (CapState *cs, int v) {
  getfromenv(cs, v);
  lua_replace(cs->L, subscache(cs));
  cs->valuecached = v;
}


static int pushcapture (CapState *cs);


static Capture *findopen (Capture *cap) {
  int n = 0;
  for (;;) {
    cap--;
    if (isclosecap(cap)) n++;
    else if (!isfullcap(cap))
      if (n-- == 0) return cap;
  }
}


static Capture *nextcap (Capture *cap) {
  if (isfullcap(cap)) return cap + 1;
  else {
    int n = 0;
    for (;;) {
      cap++;
      if (isclosecap(cap)) {
        if (n-- == 0) return cap + 1;
      }
      else if (!isfullcap(cap)) n++;
    }
  }
}


static int pushallvalues (CapState *cs, int addextra) {
  Capture *co = cs->cap;
  int n = 0;
  if (isfullcap(cs->cap++)) {
    pushsubject(cs, co);  /* push whole match */
    return 1;
  }
  while (!isclosecap(cs->cap))
    n += pushcapture(cs);
  if (addextra || n == 0) {  /* need extra? */
    lua_pushlstring(cs->L, co->s, cs->cap->s - co->s);  /* push whole match */
    n++;
  }
  cs->cap++;  /* skip close entry */
  return n;
}


static Capture *findback (CapState *cs, Capture *cap) {
  lua_State *L = cs->L;
  for (;;) {
    if (cap == cs->ocap) {  /* not found */
      const char *s = lua_tostring(L, -1);
      if (s == NULL) s = lua_pushfstring(L, "(a %s)", luaL_typename(L, -1));
      luaL_error(L, "back reference '%s' not found", s);
    }
    cap--;
    if (isclosecap(cap))
      cap = findopen(cap);
    else if (!isfullcap(cap))
      continue; /* opening an enclosing capture: skip and get previous */
    if (captype(cap) == Cgroup) {
      getfromenv(cs, cap->idx);  /* get group name */
      if (lua_equal(L, -2, -1)) {  /* right group? */
        lua_pop(L, 2);  /* remove reference name and group name */
        return cap;
      }
      else lua_pop(L, 1);  /* remove group name */
    }
  }
}


static int backrefcap (CapState *cs) {
  int n;
  Capture *curr = cs->cap;
  pushluaval(cs);  /* reference name */
  cs->cap = findback(cs, curr);
  n = pushallvalues(cs, 0);
  cs->cap = curr + 1;
  return n;
}


static int tablecap (CapState *cs) {
  lua_State *L = cs->L;
  int n = 0;
  lua_newtable(L);
  if (isfullcap(cs->cap++))
    return 1;  /* table is empty */
  while (!isclosecap(cs->cap)) {
    if (captype(cs->cap) == Cgroup && cs->cap->idx != 0) {  /* named group? */
      int k;
      pushluaval(cs);  /* push group name */
      k = pushallvalues(cs, 0);
      if (k == 0) {  /* no value? */
        lua_pop(L, 1);  /* remove group name */
        continue;  /* and go on */
      }
      else if (k > 1)
        lua_pop(L, k - 1);  /* keep just one value */
      lua_settable(L, -3);
    }
    else {
      int i;
      int k = pushcapture(cs);
      for (i = k; i > 0; i--)
        lua_rawseti(L, -(i + 1), n + i);
      n += k;
    }
  }
  cs->cap++;  /* skip close entry */
  return 1;
}


static int querycap (CapState *cs) {
  int idx = cs->cap->idx;
  int n = pushallvalues(cs, 0);
  if (n > 1)  /* extra captures? */
    lua_pop(cs->L, n - 1);  /* throw them away */
  updatecache(cs, idx);
  lua_gettable(cs->L, subscache(cs));
  if (!lua_isnil(cs->L, -1))
    return 1;
  else {
    lua_pop(cs->L, 1);  /* remove value */
    return 0;
  }
}


static int foldcap (CapState *cs) {
  int n;
  lua_State *L = cs->L;
  int idx = cs->cap->idx;
  if (isfullcap(cs->cap++) || isclosecap(cs->cap) || (n = pushcapture(cs)) == 0)
    return luaL_error(L, "no initial value for fold capture");
  if (n > 1)
    lua_pop(L, n - 1);  /* leave only one result */
  while (!isclosecap(cs->cap)) {
    updatecache(cs, idx);
    lua_pushvalue(L, subscache(cs));  /* get folding function */
    lua_insert(L, -2);  /* put it before accumulator */
    n = pushcapture(cs);  /* get other captures */
    lua_call(L, n + 1, 1);  /* call folding function */
  }
  cs->cap++;  /* skip close entry */
  return 1;
}


static int functioncap (CapState *cs) {
  int n;
  int top = lua_gettop(cs->L);
  pushluaval(cs);
  n = pushallvalues(cs, 0);
  lua_call(cs->L, n, LUA_MULTRET);
  return lua_gettop(cs->L) - top;
}


static int runtimecap (lua_State *L, Capture *close, Capture *ocap,
                       const char *o, const char *s, int ptop) {
  CapState cs;
  int n;
  Capture *open = findopen(close);
  assert(captype(open) == Cruntime);
  close->kind = Cclose;
  close->s = s;
  cs.ocap = ocap; cs.cap = open; cs.L = L;
  cs.s = o; cs.valuecached = 0; cs.ptop = ptop;
  luaL_checkstack(L, 4, "too many runtime captures");
  pushluaval(&cs);
  lua_pushvalue(L, SUBJIDX);  /* push original subject */
  lua_pushinteger(L, s - o + 1);  /* current position */
  n = pushallvalues(&cs, 0);
  lua_call(L, n + 2, LUA_MULTRET);
  return close - open;
}



typedef struct StrAux {
  int isstring;
  union {
    Capture *cp;
    struct {
      const char *s;
      const char *e;
    } s;
  } u;
} StrAux;

#define MAXSTRCAPS	10

static int getstrcaps (CapState *cs, StrAux *cps, int n) {
  int k = n++;
  cps[k].isstring = 1;
  cps[k].u.s.s = cs->cap->s;
  if (!isfullcap(cs->cap++)) {
    while (!isclosecap(cs->cap)) {
      if (n >= MAXSTRCAPS)  /* too many captures? */
        cs->cap = nextcap(cs->cap);  /* skip it */
      else if (captype(cs->cap) == Csimple)
        n = getstrcaps(cs, cps, n);
      else {
        cps[n].isstring = 0;
        cps[n].u.cp = cs->cap;
        cs->cap = nextcap(cs->cap);
        n++;
      }
    }
    cs->cap++;  /* skip close */
  }
  cps[k].u.s.e = closeaddr(cs->cap - 1);
  return n;
}


/*
** add next capture (which should be a string) to buffer
*/
static int addonestring (luaL_Buffer *b, CapState *cs, const char *what);


static void stringcap (luaL_Buffer *b, CapState *cs) {
  StrAux cps[MAXSTRCAPS];
  int n;
  size_t len, i;
  const char *c;
  updatecache(cs, cs->cap->idx);
  c = lua_tolstring(cs->L, subscache(cs), &len);
  n = getstrcaps(cs, cps, 0) - 1;
  for (i = 0; i < len; i++) {
    if (c[i] != '%' || c[++i] < '0' || c[i] > '9')
      luaL_addchar(b, c[i]);
    else {
      int l = c[i] - '0';
      if (l > n)
        luaL_error(cs->L, "invalid capture index (%d)", l);
      else if (cps[l].isstring)
        luaL_addlstring(b, cps[l].u.s.s, cps[l].u.s.e - cps[l].u.s.s);
      else {
        Capture *curr = cs->cap;
        cs->cap = cps[l].u.cp;
        if (addonestring(b, cs, "capture") == 0)
          luaL_error(cs->L, "no values in capture index %d", l);
        cs->cap = curr;
      }
    }
  }
}


static void substcap (luaL_Buffer *b, CapState *cs) {
  const char *curr = cs->cap->s;
  if (isfullcap(cs->cap))  /* no nested captures? */
    luaL_addlstring(b, curr, cs->cap->siz - 1);  /* keep original text */
  else {
    cs->cap++;
    while (!isclosecap(cs->cap)) {
      const char *next = cs->cap->s;
      luaL_addlstring(b, curr, next - curr);  /* add text up to capture */
      if (addonestring(b, cs, "replacement") == 0)  /* no capture value? */
        curr = next;  /* keep original text in final result */
      else
        curr = closeaddr(cs->cap - 1);  /* continue after match */
    }
    luaL_addlstring(b, curr, cs->cap->s - curr);  /* add last piece of text */
  }
  cs->cap++;  /* go to next capture */
}


static int addonestring (luaL_Buffer *b, CapState *cs, const char *what) {
  switch (captype(cs->cap)) {
    case Cstring:
      stringcap(b, cs);  /* add capture directly to buffer */
      return 1;
    case Csubst:
      substcap(b, cs);  /* add capture directly to buffer */
      return 1;
    default: {
      lua_State *L = cs->L;
      int n = pushcapture(cs);
      if (n > 0) {
        if (n > 1) lua_pop(L, n - 1);  /* only one result */
        if (!lua_isstring(L, -1))
          luaL_error(L, "invalid %s value (a %s)", what, luaL_typename(L, -1));
        luaL_addvalue(b);
      }
      return n;
    }
  }
}


static int pushcapture (CapState *cs) {
  luaL_checkstack(cs->L, 4, "too many captures");
  switch (captype(cs->cap)) {
    case Cposition: {
      lua_pushinteger(cs->L, cs->cap->s - cs->s + 1);
      cs->cap++;
      return 1;
    }
    case Cconst: {
      pushluaval(cs);
      cs->cap++;
      return 1;
    }
    case Carg: {
      int arg = (cs->cap++)->idx;
      if (arg + FIXEDARGS > cs->ptop)
        return luaL_error(cs->L, "reference to absent argument #%d", arg);
      lua_pushvalue(cs->L, arg + FIXEDARGS);
      return 1;
    }
    case Csimple: {
      int k = pushallvalues(cs, 1);
      if (k > 1)
        lua_insert(cs->L, -k);  /* whole match is first result */
      return k;
    }
    case Cruntime: {
      int n = 0;
      while (!isclosecap(cs->cap++)) {
        luaL_checkstack(cs->L, 4, "too many captures");
        lua_pushvalue(cs->L, (cs->cap - 1)->idx);
        n++;
      }
      return n;
    }
    case Cstring: {
      luaL_Buffer b;
      luaL_buffinit(cs->L, &b);
      stringcap(&b, cs);
      luaL_pushresult(&b);
      return 1;
    }
    case Csubst: {
      luaL_Buffer b;
      luaL_buffinit(cs->L, &b);
      substcap(&b, cs);
      luaL_pushresult(&b);
      return 1;
    }
    case Cgroup: {
      if (cs->cap->idx == 0)  /* anonymous group? */
        return pushallvalues(cs, 0);  /* add all nested values */
      else {  /* named group: add no values */
        cs->cap = nextcap(cs->cap);  /* skip capture */
        return 0;
      }
    }
    case Cbackref: return backrefcap(cs);
    case Ctable: return tablecap(cs);
    case Cfunction: return functioncap(cs);
    case Cquery: return querycap(cs);
    case Cfold: return foldcap(cs);
    default: assert(0); return 0;
  }
}


static int getcaptures (lua_State *L, const char *s, const char *r, int ptop) {
  Capture *capture = (Capture *)lua_touserdata(L, caplistidx(ptop));
  int n = 0;
  if (!isclosecap(capture)) {  /* is there any capture? */
    CapState cs;
    cs.ocap = cs.cap = capture; cs.L = L;
    cs.s = s; cs.valuecached = 0; cs.ptop = ptop;
    do {  /* collect their values */
      n += pushcapture(&cs);
    } while (!isclosecap(cs.cap));
  }
  if (n == 0) {  /* no capture values? */
    lua_pushinteger(L, r - s + 1);  /* return only end position */
    n = 1;
  }
  return n;
}

/* }====================================================== */


static int version_l (lua_State *L) {
  lua_pushstring(L, VERSION);
  return 1;
}


static int type_l (lua_State *L) {
  if (testpattern(L, 1))
    lua_pushliteral(L, "pattern");
  else
    lua_pushnil(L);
  return 1;
}


static void createcat (lua_State *L, const char *catname, int (catf) (int)) {
  Instruction *p = newcharset(L);
  int i;
  for (i = 0; i < CHAR_MAX; i++)
    if (catf(i)) setchar(p[1].buff, i);
  lua_setfield(L, -2, catname);
}


static int locale_l (lua_State *L) {
  if (lua_isnoneornil(L, 1)) {
    lua_settop(L, 0);
    lua_createtable(L, 0, 12);
  }
  else {
    luaL_checktype(L, 1, LUA_TTABLE);
    lua_settop(L, 1);
  }
  createcat(L, "alnum", isalnum);
  createcat(L, "alpha", isalpha);
  createcat(L, "cntrl", iscntrl);
  createcat(L, "digit", isdigit);
  createcat(L, "graph", isgraph);
  createcat(L, "lower", islower);
  createcat(L, "print", isprint);
  createcat(L, "punct", ispunct);
  createcat(L, "space", isspace);
  createcat(L, "upper", isupper);
  createcat(L, "xdigit", isxdigit);
  return 1;
}


static int setmax (lua_State *L) {
  luaL_optinteger(L, 1, -1);
  lua_settop(L, 1);
  lua_setfield(L, LUA_REGISTRYINDEX, MAXSTACKIDX);
  return 0;
}


static int printpat_l (lua_State *L) {
  Instruction *p = getpatt(L, 1, NULL);
  int n, i;
  lua_getfenv(L, 1);
  n = ktablelen(L, -1);
  printf("[");
  for (i = 1; i <= n; i++) {
    printf("%d = ", i);
    lua_rawgeti(L, -1, i);
    if (lua_isstring(L, -1))
      printf("%s  ", lua_tostring(L, -1));
    else
      printf("%s  ", lua_typename(L, lua_type(L, -1)));
    lua_pop(L, 1);
  }
  printf("]\n");
  printpatt(p);
  return 0;
}


static int matchl (lua_State *L) {
  Capture capture[INITCAPSIZE];
  const char *r;
  size_t l;
  Instruction *p = getpatt(L, 1, NULL);
  const char *s = luaL_checklstring(L, SUBJIDX, &l);
  int ptop = lua_gettop(L);
  lua_Integer ii = luaL_optinteger(L, 3, 1);
  size_t i = (ii > 0) ?
             (((size_t)ii <= l) ? (size_t)ii - 1 : l) :
             (((size_t)-ii <= l) ? l - ((size_t)-ii) : 0);
  lua_pushnil(L);  /* subscache */
  lua_pushlightuserdata(L, capture);  /* caplistidx */
  lua_getfenv(L, 1);  /* penvidx */
  r = match(L, s, s + i, s + l, p, capture, ptop);
  if (r == NULL) {
    lua_pushnil(L);
    return 1;
  }
  return getcaptures(L, s, r, ptop);
}


static struct luaL_Reg pattreg[] = {
  {"match", matchl},
  {"print", printpat_l},
  {"locale", locale_l},
  {"setmaxstack", setmax},
  {"B", pattbehind},
  {"C", capture_l},
  {"Cf", fold_l},
  {"Cc", capconst_l},
  {"Cg", group_l},
  {"Cp", position_l},
  {"Cb", backref_l},
  {"Carg", argcap_l},
  {"Cmt", matchtime_l},
  {"Cs", capsubst_l},
  {"Ct", tcapture_l},
  {"P", pattern_l},
  {"R", range_l},
  {"S", set_l},
  {"V", nter_l},
  {"type", type_l},
  {"version", version_l},
  {NULL, NULL}
};


static struct luaL_Reg metapattreg[] = {
  {"__add", union_l},
  {"__pow", star_l},
  {"__sub", diff_l},
  {"__mul", concat_l},
  {"__div", rcapture_l},
  {"__unm", unm_l},
  {"__len", pattand_l},
  {NULL, NULL}
};


int luaopen_lpeg (lua_State *L);
int luaopen_lpeg (lua_State *L) {
  lua_pushcfunction(L, (lua_CFunction)&l_newpf);  /* new-pattern function */
  lua_setfield(L, LUA_REGISTRYINDEX, KEYNEWPATT);  /* register it */
  luaL_newmetatable(L, PATTERN_T);
  lua_pushnumber(L, MAXBACK);
  lua_setfield(L, LUA_REGISTRYINDEX, MAXSTACKIDX);
  luaL_register(L, NULL, metapattreg);
  luaL_register(L, "lpeg", pattreg);
  lua_pushliteral(L, "__index");
  lua_pushvalue(L, -2);
  lua_settable(L, -4);
  return 1;
}

genometools-1.5.1/src/external/lpeg-0.10.2/lpeg.h000066400000000000000000000023761211610345200212300ustar00rootroot00000000000000/*
** $Id: lpeg.h,v 1.1 2009/12/23 16:15:36 roberto Exp $
** LPeg - PEG pattern matching for Lua
** Copyright 2009, Lua.org & PUC-Rio  (see 'lpeg.html' for license)
** written by Roberto Ierusalimschy
*/

#ifndef lpeg_h
#define lpeg_h

#include "lua.h"

int luaopen_lpeg (lua_State *L);

#define KEYNEWPATT	"lpeg.newpf"


/*
** type of extension functions that define new "patterns" for LPEG
** It should return the new current position or NULL if match fails
*/
typedef const char *(*PattFunc) (const char *s,  /* current position */
                                 const char *e,  /* string end */
                                 const char *o,  /* string start */
                                 const void *ud);  /* user data */

/*
** function to create new patterns based on 'PattFunc' functions.
** This function is available at *registry[KEYNEWPATT]. (Notice
** the extra indirection; the userdata at the registry points to
** a variable that points to the function. In ANSI C a void* cannot
** point to a function.)
*/
typedef void (*Newpf) (lua_State *L,
                       PattFunc f,  /* pattern */
                       const void *ud,  /* (user) data to be passed to 'f' */
                       size_t l);  /* size of data to be passed to 'f' */

#endif
genometools-1.5.1/src/external/lpeg-0.10.2/lpeg.html000066400000000000000000001233541211610345200217450ustar00rootroot00000000000000


    LPeg - Parsing Expression Grammars For Lua
    
	







	


  
  
LPeg

  

     Parsing Expression Grammars For Lua, version 0.10
  


 



	
 






Introduction




LPeg is a new pattern-matching library for Lua,
based on

Parsing Expression Grammars (PEGs).
This text is a reference manual for the library.
For a more formal treatment of LPeg,
as well as some discussion about its implementation,
see

A Text Pattern-Matching Tool based on Parsing Expression Grammars.
(You may also be interested in my
talk about LPeg
given at the III Lua Workshop.)





Following the Snobol tradition,
LPeg defines patterns as first-class objects.
That is, patterns are regular Lua values
(represented by userdata).
The library offers several functions to create
and compose patterns.
With the use of metamethods,
several of these functions are provided as infix or prefix
operators.
On the one hand,
the result is usually much more verbose than the typical
encoding of patterns using the so called
regular expressions
(which typically are not regular expressions in the formal sense).
On the other hand,
first-class patterns allow much better documentation
(as it is easy to comment the code,
to break complex definitions in smaller parts, etc.)
and are extensible,
as we can define new functions to create and compose patterns.





For a quick glance of the library,
the following table summarizes its basic operations
for creating patterns:





OperatorDescription


lpeg.P(string)
  Matches string literally


lpeg.P(n)
  Matches exactly n characters


lpeg.S(string)
  Matches any character in string (Set)


lpeg.R("xy")
  Matches any character between x and y (Range)


patt^n
  Matches at least n repetitions of patt


patt^-n
  Matches at most n repetitions of patt


patt1 * patt2
  Matches patt1 followed by patt2


patt1 + patt2
  Matches patt1 or patt2
      (ordered choice)


patt1 - patt2
  Matches patt1 if patt2 does not match


-patt
  Equivalent to ("" - patt)


#patt
  Matches patt but consumes no input


lpeg.B(patt, n)
  Matches patt n characters behind
      the current position, consuming no input





As a very simple example,
lpeg.R("09")^1 creates a pattern that
matches a non-empty sequence of digits.
As a not so simple example,
-lpeg.P(1)
(which can be written as lpeg.P(-1)
or simply -1 for operations expecting a pattern)
matches an empty string only if it cannot match a single character;
so, it succeeds only at the subject's end.





LPeg also offers the re module,
which implements patterns following a regular-expression style
(e.g., [09]+).
(This module is 250 lines of Lua code,
and of course uses LPeg to parse regular expressions and
translate them to regular LPeg patterns.)





Functions




lpeg.match (pattern, subject [, init])



The matching function.
It attempts to match the given pattern against the subject string.
If the match succeeds,
returns the index in the subject of the first character after the match,
or the captured values
(if the pattern captured any value).





An optional numeric argument init makes the match
starts at that position in the subject string.
As usual in Lua libraries,
a negative value counts from the end.





Unlike typical pattern-matching functions,
match works only in anchored mode;
that is, it tries to match the pattern with a prefix of
the given subject string (at position init),
not with an arbitrary substring of the subject.
So, if we want to find a pattern anywhere in a string,
we must either write a loop in Lua or write a pattern that
matches anywhere.
This second approach is easy and quite efficient;
see examples.




lpeg.type (value)



If the given value is a pattern,
returns the string "pattern".
Otherwise returns nil.




lpeg.version ()



Returns a string with the running version of LPeg.




lpeg.setmaxstack (max)



Sets the maximum size for the backtrack stack used by LPeg to
track calls and choices.
Most well-written patterns need little backtrack levels and
therefore you seldom need to change this maximum;
but a few useful patterns may need more space.
Before changing this maximum you should try to rewrite your
pattern to avoid the need for extra space.





Basic Constructions




The following operations build patterns.
All operations that expect a pattern as an argument
may receive also strings, tables, numbers, booleans, or functions,
which are translated to patterns according to
the rules of function lpeg.P.






lpeg.P (value)



Converts the given value into a proper pattern,
according to the following rules:



    


  • 
If the argument is a pattern,
it is returned unmodified.

    • 


  • 
If the argument is a string,
it is translated to a pattern that matches literally the string.

    • 


  • 
If the argument is a non-negative number n,
the result is a pattern that matches exactly n characters.

    • 


  • 
If the argument is a negative number -n,
the result is a pattern that
succeeds only if the input string does not have n characters:
lpeg.P(-n)
is equivalent to -lpeg.P(n)
(see the  unary minus operation).

    • 


  • 
If the argument is a boolean,
the result is a pattern that always succeeds or always fails
(according to the boolean value),
without consuming any input.

    • 


  • 
If the argument is a table,
it is interpreted as a grammar
(see Grammars).

    • 


  • 
If the argument is a function,
returns a pattern equivalent to a
match-time capture over the empty string.

    • 






lpeg.B(patt [, n])



Returns a pattern that
matches only if the input string matches patt
starting n positions behind the current position.
(The default value for n is 1.)
If the current position is less than or equal to n,
this pattern fails.





Like the and predicate,
this pattern never consumes any input,
independently of success or failure,
and it never produces any capture.





The pattern patt cannot contain any open reference
to grammar rules (see grammars).





(This is an experimental feature.
There is a good chance it will change in future versions.)





lpeg.R ({range})



Returns a pattern that matches any single character
belonging to one of the given ranges.
Each range is a string xy of length 2,
representing all characters with code
between the codes of x and y
(both inclusive).





As an example, the pattern
lpeg.R("09") matches any digit,
and lpeg.R("az", "AZ") matches any ASCII letter.





lpeg.S (string)



Returns a pattern that matches any single character that
appears in the given string.
(The S stands for Set.)





As an example, the pattern
lpeg.S("+-*/") matches any arithmetic operator.





Note that, if s is a character
(that is, a string of length 1),
then lpeg.P(s) is equivalent to lpeg.S(s)
which is equivalent to lpeg.R(s..s).
Note also that both lpeg.S("") and lpeg.R()
are patterns that always fail.





lpeg.V (v)



This operation creates a non-terminal (a variable)
for a grammar.
The created non-terminal refers to the rule indexed by v
in the enclosing grammar.
(See Grammars for details.)





lpeg.locale ([table])



Returns a table with patterns for matching some character classes
according to the current locale.
The table has fields named
alnum,
alpha,
cntrl,
digit,
graph,
lower,
print,
punct,
space,
upper, and
xdigit,
each one containing a correspondent pattern.
Each pattern matches any single character that belongs to its class.





If called with an argument table,
then it creates those fields inside the given table and
returns that table. 





#patt



Returns a pattern that
matches only if the input string matches patt,
but without consuming any input,
independently of success or failure.
(This pattern is called an and predicate
and it is equivalent to
&patt in the original PEG notation.)






This pattern never produces any capture.

.



-patt



Returns a pattern that
matches only if the input string does not match patt.
It does not consume any input,
independently of success or failure.
(This pattern is equivalent to
!patt in the original PEG notation.)





As an example, the pattern
-lpeg.P(1) matches only the end of string.





This pattern never produces any captures,
because either patt fails
or -patt fails.
(A failing pattern never produces captures.)





patt1 + patt2



Returns a pattern equivalent to an ordered choice
of patt1 and patt2.
(This is denoted by patt1 / patt2 in the original PEG notation,
not to be confused with the / operation in LPeg.)
It matches either patt1 or patt2,
with no backtracking once one of them succeeds.
The identity element for this operation is the pattern
lpeg.P(false),
which always fails.





If both patt1 and patt2 are
character sets,
this operation is equivalent to set union.



lower = lpeg.R("az")
upper = lpeg.R("AZ")
letter = lower + upper





patt1 - patt2



Returns a pattern equivalent to !patt2 patt1.
This pattern asserts that the input does not match
patt2 and then matches patt1.





When succeeded,
this pattern produces all captures from patt1.
It never produces any capture from patt2
(as either patt2 fails or
patt1 - patt2 fails).





If both patt1 and patt2 are
character sets,
this operation is equivalent to set difference.
Note that -patt is equivalent to "" - patt
(or 0 - patt).
If patt is a character set,
1 - patt is its complement.





patt1 * patt2



Returns a pattern that matches patt1
and then matches patt2,
starting where patt1 finished.
The identity element for this operation is the
pattern lpeg.P(true),
which always succeeds.





(LPeg uses the * operator
[instead of the more obvious ..]
both because it has
the right priority and because in formal languages it is
common to use a dot for denoting concatenation.)





patt^n



If n is nonnegative,
this pattern is
equivalent to pattn patt*.
It matches at least n occurrences of patt.





Otherwise, when n is negative,
this pattern is equivalent to (patt?)-n.
That is, it matches at most |n|
occurrences of patt.





In particular, patt^0 is equivalent to patt*,
patt^1 is equivalent to patt+,
and patt^-1 is equivalent to patt?
in the original PEG notation.





In all cases,
the resulting pattern is greedy with no backtracking
(also called a possessive repetition).
That is, it matches only the longest possible sequence
of matches for patt.






Grammars




With the use of Lua variables,
it is possible to define patterns incrementally,
with each new pattern using previously defined ones.
However, this technique does not allow the definition of
recursive patterns.
For recursive patterns,
we need real grammars.





LPeg represents grammars with tables,
where each entry is a rule.





The call lpeg.V(v)
creates a pattern that represents the nonterminal
(or variable) with index v in a grammar.
Because the grammar still does not exist when
this function is evaluated,
the result is an open reference to the respective rule.





A table is fixed when it is converted to a pattern
(either by calling lpeg.P or by using it wherein a
pattern is expected).
Then every open reference created by lpeg.V(v)
is corrected to refer to the rule indexed by v in the table.





When a table is fixed,
the result is a pattern that matches its initial rule.
The entry with index 1 in the table defines its initial rule.
If that entry is a string,
it is assumed to be the name of the initial rule.
Otherwise, LPeg assumes that the entry 1 itself is the initial rule.





As an example,
the following grammar matches strings of a's and b's that
have the same number of a's and b's:



equalcount = lpeg.P{
  "S";   -- initial rule name
  S = "a" * lpeg.V"B" + "b" * lpeg.V"A" + "",
  A = "a" * lpeg.V"S" + "b" * lpeg.V"A" * lpeg.V"A",
  B = "b" * lpeg.V"S" + "a" * lpeg.V"B" * lpeg.V"B",
} * -1




It is equivalent to the following grammar in standard PEG notation:



  S <- 'a' B / 'b' A / ''
  A <- 'a' S / 'b' A A
  B <- 'b' S / 'a' B B





Captures




A capture is a pattern that creates values
(the so called semantic information) when it matches.
LPeg offers several kinds of captures,
which produces values based on matches and combine these values to
produce new values.
Each capture may produce zero or more values.





The following table summarizes the basic captures:





OperationWhat it Produces


lpeg.C(patt)
  the match for patt plus all captures
      made by patt


lpeg.Carg(n)
    the value of the nth extra argument to
        lpeg.match (matches the empty string)


lpeg.Cb(name)
    the values produced by the previous
        group capture named name
        (matches the empty string)


lpeg.Cc(values)
    the given values (matches the empty string)


lpeg.Cf(patt, func)
  a folding of the captures from patt


lpeg.Cg(patt [, name])
    the values produced by patt,
        optionally tagged with name


lpeg.Cp()
    the current position (matches the empty string)


lpeg.Cs(patt)
  the match for patt
      with the values from nested captures replacing their matches


lpeg.Ct(patt)
  a table with all captures from patt


patt / string
  string, with some marks replaced by captures
      of patt


patt / table
  table[c], where c is the (first)
      capture of patt


patt / function
  the returns of function applied to the captures
      of patt


lpeg.Cmt(patt, function)
  the returns of function applied to the captures
      of patt; the application is done at match time






A capture pattern produces its values every time it succeeds.
For instance,
a capture inside a loop produces as many values as matched by the loop.
A capture produces a value only when it succeeds.
For instance,
the pattern lpeg.C(lpeg.P"a"^-1)
produces the empty string when there is no "a"
(because the pattern "a"? succeeds),
while the pattern lpeg.C("a")^-1
does not produce any value when there is no "a"
(because the pattern "a" fails).





Usually,
LPeg evaluates all captures only after (and if) the entire match succeeds.
During the match time it only gathers enough information
to produce the capture values later.
As a particularly important consequence,
most captures cannot affect the way a pattern matches a subject.
The only exception to this rule is the
so-called match-time capture.
When a match-time capture matches,
it forces the immediate evaluation of all its nested captures
and then calls its corresponding function,
which tells whether the match succeeds and also
what values are produced.




lpeg.C (patt)



Creates a simple capture,
which captures the substring of the subject that matches patt.
The captured value is a string.
If patt has other captures,
their values are returned after this one.





lpeg.Carg (n)



Creates an argument capture.
This pattern matches the empty string and
produces the value given as the nth extra
argument given in the call to lpeg.match.





lpeg.Cb (name)



Creates a back capture.
This pattern matches the empty string and
produces the values produced by the most recent
group capture named name.





Most recent means the last
complete
outermost
group capture with the given name.
A Complete capture means that the entire pattern
corresponding to the capture has matched.
An Outermost capture means that the capture is not inside
another complete capture.





lpeg.Cc ([value, ...])



Creates a constant capture.
This pattern matches the empty string and
produces all given values as its captured values.





lpeg.Cf (patt, func)



Creates a fold capture.
If patt produces a list of captures
C1 C2 ... Cn,
this capture will produce the value
func(...func(func(C1, C2), C3)...,
         Cn),
that is, it will fold
(or accumulate, or reduce)
the captures from patt using function func.





This capture assumes that patt should produce
at least one capture with at least one value (of any type),
which becomes the initial value of an accumulator.
(If you need a specific initial value,
you may prefix a constant capture to patt.)
For each subsequent capture
LPeg calls func
with this accumulator as the first argument and all values produced
by the capture as extra arguments;
the value returned by this call
becomes the new value for the accumulator.
The final value of the accumulator becomes the captured value.





As an example,
the following pattern matches a list of numbers separated
by commas and returns their addition:



-- matches a numeral and captures its value
number = lpeg.R"09"^1 / tonumber

-- matches a list of numbers, captures their values
list = number * ("," * number)^0

-- auxiliary function to add two numbers
function add (acc, newvalue) return acc + newvalue end

-- folds the list of numbers adding them
sum = lpeg.Cf(list, add)

-- example of use
print(sum:match("10,30,43"))   --> 83





lpeg.Cg (patt [, name])



Creates a group capture.
It groups all values returned by patt
into a single capture.
The group may be anonymous (if no name is given)
or named with the given name.





An anonymous group serves to join values from several captures into
a single capture.
A named group has a different behavior.
In most situations, a named group returns no values at all.
Its values are only relevant for a following
back capture or when used
inside a table capture.





lpeg.Cp ()



Creates a position capture.
It matches the empty string and
captures the position in the subject where the match occurs.
The captured value is a number.





lpeg.Cs (patt)



Creates a substitution capture,
which captures the substring of the subject that matches patt,
with substitutions.
For any capture inside patt with a value,
the substring that matched the capture is replaced by the capture value
(which should be a string).
The final captured value is the string resulting from
all replacements.





lpeg.Ct (patt)



Creates a table capture.
This capture creates a table and puts all values from all anonymous captures
made by patt inside this table in successive integer keys,
starting at 1.
Moreover,
for each named capture group created by patt,
the first value of the group is put into the table
with the group name as its key.
The captured value is only the table.





patt / string



Creates a string capture.
It creates a capture string based on string.
The captured value is a copy of string,
except that the character % works as an escape character:
any sequence in string of the form %n,
with n between 1 and 9,
stands for the match of the n-th capture in patt.
The sequence %0 stands for the whole match.
The sequence %% stands for a single %.



patt / table



Creates a query capture.
It indexes the given table using as key the first value captured by
patt,
or the whole match if patt produced no value.
The value at that index is the final value of the capture.
If the table does not have that key,
there is no captured value.





patt / function



Creates a function capture.
It calls the given function passing all captures made by
patt as arguments,
or the whole match if patt made no capture.
The values returned by the function
are the final values of the capture.
In particular,
if function returns no value,
there is no captured value.





lpeg.Cmt(patt, function)



Creates a match-time capture.
Unlike all other captures,
this one is evaluated immediately when a match occurs.
It forces the immediate evaluation of all its nested captures
and then calls function.





The given function gets as arguments the entire subject,
the current position (after the match of patt),
plus any capture values produced by patt.





The first value returned by function
defines how the match happens.
If the call returns a number,
the match succeeds
and the returned number becomes the new current position.
(Assuming a subject s and current position i,
the returned number must be in the range [i, len(s) + 1].)
If the call returns true,
the match succeeds without consuming any input.
(So, to return true is equivalent to return i.)
If the call returns false, nil, or no value,
the match fails.





Any extra values returned by the function become the
values produced by the capture.







Some Examples



Using a Pattern



This example shows a very simple but complete program
that builds and uses a pattern:



local lpeg = require "lpeg"

-- matches a word followed by end-of-string
p = lpeg.R"az"^1 * -1

print(p:match("hello"))        --> 6
print(lpeg.match(p, "hello"))  --> 6
print(p:match("1 hello"))      --> nil




The pattern is simply a sequence of one or more lower-case letters
followed by the end of string (-1).
The program calls match both as a method
and as a function.
In both sucessful cases,
the match returns 
the index of the first character after the match,
which is the string length plus one.





Name-value lists



This example parses a list of name-value pairs and returns a table
with those pairs:



lpeg.locale(lpeg)   -- adds locale entries into 'lpeg' table

local space = lpeg.space^0
local name = lpeg.C(lpeg.alpha^1) * space
local sep = lpeg.S(",;") * space
local pair = lpeg.Cg(name * "=" * space * name) * sep^-1
local list = lpeg.Cf(lpeg.Ct("") * pair^0, rawset)
t = list:match("a=b, c = hi; next = pi")  --> { a = "b", c = "hi", next = "pi" }




Each pair has the format name = name followed by
an optional separator (a comma or a semicolon).
The pair pattern encloses the pair in a group pattern,
so that the names become the values of a single capture.
The list pattern then folds these captures.
It starts with an empty table,
created by a table capture matching an empty string;
then for each capture (a pair of names) it applies rawset
over the accumulator (the table) and the capture values (the pair of names).
rawset returns the table itself,
so the accumulator is always the table.




Splitting a string



The following code builds a pattern that
splits a string using a given pattern
sep as a separator:



function split (s, sep)
  sep = lpeg.P(sep)
  local elem = lpeg.C((1 - sep)^0)
  local p = elem * (sep * elem)^0
  return lpeg.match(p, s)
end




First the function ensures that sep is a proper pattern.
The pattern elem is a repetition of zero of more
arbitrary characters as long as there is not a match against
the separator. It also captures its result.
The pattern p matches a list of elements separated
by sep.





If the split results in too many values,
it may overflow the maximum number of values
that can be returned by a Lua function.
In this case,
we should collect these values in a table:



function split (s, sep)
  sep = lpeg.P(sep)
  local elem = lpeg.C((1 - sep)^0)
  local p = lpeg.Ct(elem * (sep * elem)^0)   -- make a table capture
  return lpeg.match(p, s)
end





Searching for a pattern



The primitive match works only in anchored mode.
If we want to find a pattern anywhere in a string,
we must write a pattern that matches anywhere.





Because patterns are composable,
we can write a function that,
given any arbitrary pattern p,
returns a new pattern that searches for p
anywhere in a string.
There are several ways to do the search.
One way is like this:



function anywhere (p)
  return lpeg.P{ p + 1 * lpeg.V(1) }
end




This grammar has a straight reading:
it matches p or skips one character and tries again.





If we want to know where the pattern is in the string
(instead of knowing only that it is there somewhere),
we can add position captures to the pattern:



local I = lpeg.Cp()
function anywhere (p)
  return lpeg.P{ I * p * I + 1 * lpeg.V(1) }
end





Another option for the search is like this:



local I = lpeg.Cp()
function anywhere (p)
  return (1 - lpeg.P(p))^0 * I * p * I
end




Again the pattern has a straight reading:
it skips as many characters as possible while not matching p,
and then matches p (plus appropriate captures).





If we want to look for a pattern only at word boundaries,
we can use the following transformer:




local t = lpeg.locale()

function atwordboundary (p)
  return lpeg.P{
    [1] = p + t.alpha^0 * (1 - t.alpha)^1 * lpeg.V(1)
  }
end





Balanced parentheses



The following pattern matches only strings with balanced parentheses:



b = lpeg.P{ "(" * ((1 - lpeg.S"()") + lpeg.V(1))^0 * ")" }




Reading the first (and only) rule of the given grammar,
we have that a balanced string is
an open parenthesis,
followed by zero or more repetitions of either
a non-parenthesis character or
a balanced string (lpeg.V(1)),
followed by a closing parenthesis.





Global substitution



The next example does a job somewhat similar to string.gsub.
It receives a pattern and a replacement value,
and substitutes the replacement value for all occurrences of the pattern
in a given string:



function gsub (s, patt, repl)
  patt = lpeg.P(patt)
  patt = lpeg.Cs((patt / repl + 1)^0)
  return lpeg.match(patt, s)
end




As in string.gsub,
the replacement value can be a string,
a function, or a table.





Comma-Separated Values (CSV)



This example breaks a string into comma-separated values,
returning all fields:



local field = '"' * lpeg.Cs(((lpeg.P(1) - '"') + lpeg.P'""' / '"')^0) * '"' +
                    lpeg.C((1 - lpeg.S',\n"')^0)

local record = field * (',' * field)^0 * (lpeg.P'\n' + -1)

function csv (s)
  return lpeg.match(record, s)
end




A field is either a quoted field
(which may contain any character except an individual quote,
which may be written as two quotes that are replaced by one)
or an unquoted field
(which cannot contain commas, newlines, or quotes).
A record is a list of fields separated by commas,
ending with a newline or the string end (-1).





As it is,
the previous pattern returns each field as a separated result.
If we add a table capture in the definition of record,
the pattern will return instead a single table
containing all fields:



local record = lpeg.Ct(field * (',' * field)^0) * (lpeg.P'\n' + -1)





UTF-8 and Latin 1



It is not difficult to use LPeg to convert a string from
UTF-8 encoding to Latin 1 (ISO 8859-1):




-- convert a two-byte UTF-8 sequence to a Latin 1 character
local function f2 (s)
  local c1, c2 = string.byte(s, 1, 2)
  return string.char(c1 * 64 + c2 - 12416)
end

local utf8 = lpeg.R("\0\127")
           + lpeg.R("\194\195") * lpeg.R("\128\191") / f2

local decode_pattern = lpeg.Cs(utf8^0) * -1




In this code,
the definition of UTF-8 is already restricted to the
Latin 1 range (from 0 to 255).
Any encoding outside this range (as well as any invalid encoding)
will not match that pattern.





As the definition of decode_pattern demands that
the pattern matches the whole input (because of the -1 at its end),
any invalid string will simply fail to match,
without any useful information about the problem.
We can improve this situation redefining decode_pattern
as follows:



local function er (_, i) error("invalid encoding at position " .. i) end

local decode_pattern = lpeg.Cs(utf8^0) * (-1 + lpeg.P(er))




Now, if the pattern utf8^0 stops
before the end of the string,
an appropriate error function is called.





UTF-8 and Unicode



We can extend the previous patterns to handle all Unicode code points.
Of course,
we cannot translate them to Latin 1 or any other one-byte encoding.
Instead, our translation results in a array with the code points
represented as numbers.
The full code is here:



-- decode a two-byte UTF-8 sequence
local function f2 (s)
  local c1, c2 = string.byte(s, 1, 2)
  return c1 * 64 + c2 - 12416
end

-- decode a three-byte UTF-8 sequence
local function f3 (s)
  local c1, c2, c3 = string.byte(s, 1, 3)
  return (c1 * 64 + c2) * 64 + c3 - 925824
end

-- decode a four-byte UTF-8 sequence
local function f4 (s)
  local c1, c2, c3, c4 = string.byte(s, 1, 4)
  return ((c1 * 64 + c2) * 64 + c3) * 64 + c4 - 63447168
end

local cont = lpeg.R("\128\191")   -- continuation byte

local utf8 = lpeg.R("\0\127") / string.byte
           + lpeg.R("\194\223") * cont / f2
           + lpeg.R("\224\239") * cont * cont / f3
           + lpeg.R("\240\244") * cont * cont * cont / f4

local decode_pattern = lpeg.Ct(utf8^0) * -1





Lua's long strings



A long string in Lua starts with the pattern [=*[
and ends at the first occurrence of ]=*] with
exactly the same number of equal signs.
If the opening brackets are followed by a newline,
this newline is discharged
(that is, it is not part of the string).





To match a long string in Lua,
the pattern must capture the first repetition of equal signs and then,
whenever it finds a candidate for closing the string,
check whether it has the same number of equal signs.




equals = lpeg.P"="^0
open = "[" * lpeg.Cg(equals, "init") * "[" * lpeg.P"\n"^-1
close = "]" * lpeg.C(equals) * "]"
closeeq = lpeg.Cmt(close * lpeg.Cb("init"), function (s, i, a, b) return a == b end)
string = open * lpeg.C((lpeg.P(1) - closeeq)^0) * close /
  function (s, o) return s end





The open pattern matches [=*[,
capturing the repetitions of equal signs in a group named init;
it also discharges an optional newline, if present.
The close pattern matches ]=*],
also capturing the repetitions of equal signs.
The closeeq pattern first matches close;
then it uses a back capture to recover the capture made
by the previous open,
which is named init;
finally it uses a match-time capture to check
whether both captures are equal.
The string pattern starts with an open,
then it goes as far as possible until matching closeeq,
and then matches the final close.
The final function capture simply discards
the capture made by close.





Arithmetic expressions



This example is a complete parser and evaluator for simple
arithmetic expressions.
We write it in two styles.
The first approach first builds a syntax tree and then
traverses this tree to compute the expression value:



-- Lexical Elements
local Space = lpeg.S(" \n\t")^0
local Number = lpeg.C(lpeg.P"-"^-1 * lpeg.R("09")^1) * Space
local FactorOp = lpeg.C(lpeg.S("+-")) * Space
local TermOp = lpeg.C(lpeg.S("*/")) * Space
local Open = "(" * Space
local Close = ")" * Space

-- Grammar
local Exp, Term, Factor = lpeg.V"Exp", lpeg.V"Term", lpeg.V"Factor"
G = lpeg.P{ Exp,
  Exp = lpeg.Ct(Factor * (FactorOp * Factor)^0);
  Factor = lpeg.Ct(Term * (TermOp * Term)^0);
  Term = Number + Open * Exp * Close;
}

G = Space * G * -1

-- Evaluator
function eval (x)
  if type(x) == "string" then
    return tonumber(x)
  else
    local op1 = eval(x[1])
    for i = 2, #x, 2 do
      local op = x[i]
      local op2 = eval(x[i + 1])
      if (op == "+") then op1 = op1 + op2
      elseif (op == "-") then op1 = op1 - op2
      elseif (op == "*") then op1 = op1 * op2
      elseif (op == "/") then op1 = op1 / op2
      end
    end
    return op1
  end
end

-- Parser/Evaluator
function evalExp (s)
  local t = lpeg.match(G, s)
  if not t then error("syntax error", 2) end
  return eval(t)
end

-- small example
print(evalExp"3 + 5*9 / (1+1) - 12")   --> 13.5





The second style computes the expression value on the fly,
without building the syntax tree.
The following grammar takes this approach.
(It assumes the same lexical elements as before.)



-- Auxiliary function
function eval (v1, op, v2)
  if (op == "+") then return v1 + v2
  elseif (op == "-") then return v1 - v2
  elseif (op == "*") then return v1 * v2
  elseif (op == "/") then return v1 / v2
  end
end

-- Grammar
local V = lpeg.V
G = lpeg.P{ "Exp",
  Exp = lpeg.Cf(V"Factor" * lpeg.Cg(FactorOp * V"Factor")^0, eval);
  Factor = lpeg.Cf(V"Term" * lpeg.Cg(TermOp * V"Term")^0, eval);
  Term = Number / tonumber + Open * V"Exp" * Close;
}

-- small example
print(lpeg.match(G, "3 + 5*9 / (1+1) - 12"))   --> 13.5




Note the use of the fold (accumulator) capture.
To compute the value of an expression,
the accumulator starts with the value of the first factor,
and then applies eval over
the accumulator, the operator,
and the new factor for each repetition.






Download



LPeg 
source code.




License




Copyright © 2008 Lua.org, PUC-Rio.




Permission is hereby granted, free of charge,
to any person obtaining a copy of this software and
associated documentation files (the "Software"),
to deal in the Software without restriction,
including without limitation the rights to use,
copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software,
and to permit persons to whom the Software is
furnished to do so,
subject to the following conditions:





The above copyright notice and this permission notice
shall be included in all copies or substantial portions of the Software.





THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.




 


 





$Id: lpeg.html,v 1.64 2011/02/16 15:01:58 roberto Exp $



 


 


 
genometools-1.5.1/src/external/lpeg-0.10.2/makefile000066400000000000000000000014451211610345200216240ustar00rootroot00000000000000LIBNAME = lpeg
LUADIR = /usr/include/lua5.1/

COPT = -O2 -DNDEBUG

CWARNS = -Wall -Wextra -pedantic \
        -Waggregate-return \
	-Wbad-function-cast \
        -Wcast-align \
        -Wcast-qual \
	-Wdeclaration-after-statement \
	-Wdisabled-optimization \
        -Wmissing-prototypes \
        -Wnested-externs \
        -Wpointer-arith \
        -Wshadow \
	-Wsign-compare \
	-Wstrict-prototypes \
	-Wundef \
        -Wwrite-strings \
	#  -Wunreachable-code \


CFLAGS = $(CWARNS) $(COPT) -ansi -I$(LUADIR)
CC = gcc

# For Linux
DLLFLAGS = -shared -fpic
ENV = 

# For Mac OS
# ENV = MACOSX_DEPLOYMENT_TARGET=10.4
# DLLFLAGS = -bundle -undefined dynamic_lookup

lpeg.so: lpeg.o
	env $(ENV) $(CC) $(DLLFLAGS) lpeg.o -o lpeg.so

lpeg.o:		makefile lpeg.c lpeg.h

test: test.lua re.lua lpeg.so
	test.lua

genometools-1.5.1/src/external/lpeg-0.10.2/re.html000066400000000000000000000343261211610345200214240ustar00rootroot00000000000000


    LPeg.re - Regex syntax for LPEG
    
	







	


  
  
LPeg.re

  

     Regex syntax for LPEG
  


 



	
 





The re Module




The re module
(provided by file re.lua in the distribution)
supports a somewhat conventional regex syntax
for pattern usage within LPeg.





The next table summarizes re's syntax.
A p represents an arbitrary pattern;
num represents a number ([0-9]+);
name represents an identifier
([a-zA-Z][a-zA-Z0-9_]*).
Constructions are listed in order of decreasing precedence.



SyntaxDescription


( p ) grouping


'string' literal string


"string" literal string


[class] character class


. any character


%name
  pattern defs[name] or a pre-defined pattern


namenon terminal


<name>non terminal


{} position capture


{ p } simple capture


{: p :} anonymous group capture


{:name: p :} named group capture


{~ p ~} substitution capture


=name back reference



p ? optional match


p * zero or more repetitions


p + one or more repetitions


p^num exactly n repetitions


p^+num
      at least n repetitions


p^-num
      at most n repetitions


p -> 'string' string capture


p -> "string" string capture


p -> {} table capture


p -> name function/query/string capture
equivalent to p / defs[name]


p => name match-time capture
equivalent to lpeg.Cmt(p, defs[name])


& p and predicate


! p not predicate


p1 p2 concatenation


p1 / p2 ordered choice


(name <- p)+ grammar





Any space appearing in a syntax description can be
replaced by zero or more space characters and Lua-style comments
(-- until end of line).





Character classes define sets of characters.
An initial ^ complements the resulting set.
A range x-y includes in the set
all characters with codes between the codes of x and y.
A pre-defined class %name includes all
characters of that class.
A simple character includes itself in the set.
The only special characters inside a class are ^
(special only if it is the first character);
]
(can be included in the set as the first character,
after the optional ^);
% (special only if followed by a letter);
and -
(can be included in the set as the first or the last character).





Currently the pre-defined classes are similar to those from the
Lua's string library
(%a for letters,
%A for non letters, etc.).
There is also a class %nl
containing only the newline character,
which is particularly handy for grammars written inside long strings,
as long strings do not interpret escape sequences like \n.





Functions



re.compile (string, [, defs])



Compiles the given string and
returns an equivalent LPeg pattern.
The given string may define either an expression or a grammar.
The optional defs table provides extra Lua values
to be used by the pattern.




re.find (subject, pattern [, init])



Searches the given pattern in the given subject.
If it finds a match,
returns the index where this occurrence starts,
plus the captures made by the pattern (if any).
Otherwise, returns nil.





An optional numeric argument init makes the search
starts at that position in the subject string.
As usual in Lua libraries,
a negative value counts from the end.




re.match (subject, pattern)



Matches the given pattern against the given subject.




re.updatelocale ()



Updates the pre-defined character classes to the current locale.





Some Examples



A complete simple program



The next code shows a simple complete Lua program using
the re module:



local re = require"re"

-- find the position of the first number in a string
print(re.find("the number 423 is odd", "[0-9]+"))  --> 12

-- similar, but also captures (and returns) the number
print(re.find("the number 423 is odd", "{[0-9]+}"))  --> 12    423

-- returns all words in a string
print(re.match("the number 423 is odd", "({%a+} / .)*"))
--> the    number    is    odd





Balanced parentheses



The following call will produce the same pattern produced by the
Lua expression in the
balanced parentheses example:



b = re.compile[[  balanced <- "(" ([^()] / balanced)* ")"  ]]




String reversal



The next example reverses a string:



rev = re.compile[[ R <- (!.) -> '' / ({.} R) -> '%2%1']]
print(rev:match"0123456789")   --> 9876543210




CSV decoder



The next example replicates the CSV decoder:



record = re.compile[[
  record <- ( field (',' field)* ) -> {} (%nl / !.)
  field <- escaped / nonescaped
  nonescaped <- { [^,"%nl]* }
  escaped <- '"' {~ ([^"] / '""' -> '"')* ~} '"'
]]




Lua's long strings



The next example matches Lua long strings:



c = re.compile([[
  longstring <- ('[' {:eq: '='* :} '[' close) -> void
  close <- ']' =eq ']' / . close
]], {void = function () end})

print(c:match'[==[]]===]]]]==]===[]')   --> 17




Abstract Syntax Trees



This example shows a simple way to build an
abstract syntax tree (AST) for a given grammar.
To keep our example simple,
let us consider the following grammar
for lists of names:



p = re.compile[[
      listname <- (name s)*
      name <- [a-z][a-z]*
      s <- %s*
]]




Now, we will add captures to build a corresponding AST.
As a first step, the pattern will build a table to
represent each non terminal;
terminals will be represented by their corresponding strings:



c = re.compile[[
      listname <- (name s)* -> {}
      name <- {[a-z][a-z]*} -> {}
      s <- %s*
]]




Now, a match against "hi hello bye"
results in the table
{{"hi"}, {"hello"}, {"bye"}}.




For such a simple grammar,
this AST is more than enough;
actually, the tables around each single name
are already overkilling.
More complex grammars,
however, may need some more structure.
Specifically,
it would be useful if each table had
a tag field telling what non terminal
that table represents.
We can add such a tag using
named group captures:



x = re.compile[[
      listname <- ({:tag: '' -> 'list':} (name s)*) -> {}
      name <- ({:tag: '' -> 'id':} {[a-z][a-z]*}) -> {}
      s <- ' '*
]]




With these group captures,
a match against "hi hello bye"
results in the following table:



{tag="list",
  {tag="id", "hi"},
  {tag="id", "hello"},
  {tag="id", "bye"}
}





Indented blocks



This example breaks indented blocks into tables,
respecting the indentation:



p = re.compile[[
  block <- ({:ident:' '*:} line
           ((=ident !' ' line) / &(=ident ' ') block)*) -> {}
  line <- {[^%nl]*} %nl
]]




As an example,
consider the following text:



t = p:match[[
first line
  subline 1
  subline 2
second line
third line
  subline 3.1
    subline 3.1.1
  subline 3.2
]]




The resulting table t will be like this:



   {'first line'; {'subline 1'; 'subline 2'; ident = '  '};
    'second line';
    'third line'; { 'subline 3.1'; {'subline 3.1.1'; ident = '    '};
                    'subline 3.2'; ident = '  '};
    ident = ''}




Macro expander



This example implements a simple macro expander.
Macros must be defined as part of the pattern,
following some simple rules:



p = re.compile[[
      text <- {~ item* ~}
      item <- macro / [^()] / '(' item* ')'
      arg <- ' '* {~ (!',' item)* ~}
      args <- '(' arg (',' arg)* ')'
      -- now we define some macros
      macro <- ('apply' args) -> '%1(%2)'
             / ('add' args) -> '%1 + %2'
             / ('mul' args) -> '%1 * %2'
]]

print(p:match"add(mul(a,b), apply(f,x))")   --> a * b + f(x)




A text is a sequence of items,
wherein we apply a substitution capture to expand any macros.
An item is either a macro,
any character different from parentheses,
or a parenthesized expression.
A macro argument (arg) is a sequence
of items different from a comma.
(Note that a comma may appear inside an item,
e.g., inside a parenthesized expression.)
Again we do a substitution capture to expand any macro
in the argument before expanding the outer macro.
args is a list of arguments separated by commas.
Finally we define the macros.
Each macro is a string substitution;
it replaces the macro name and its arguments by its corresponding string,
with each %n replaced by the n-th argument.




Patterns



This example shows the complete syntax
of patterns accepted by re.



p = [=[

pattern         <- exp !.
exp             <- S (alternative / grammar)

alternative     <- seq ('/' S seq)*
seq             <- prefix*
prefix          <- '&' S prefix / '!' S prefix / suffix
suffix          <- primary S (([+*?]
                            / '^' [+-]? num
                            / '->' S (string / '{}' / name)
                            / '=>' S name) S)*

primary         <- '(' exp ')' / string / class / defined
                 / '{:' (name ':')? exp ':}'
                 / '=' name
                 / '{}'
                 / '{~' exp '~}'
                 / '{' exp '}'
                 / '.'
                 / name S !arrow
                 / '<' name '>'          -- old-style non terminals

grammar         <- definition+
definition      <- name S arrow exp

class           <- '[' '^'? item (!']' item)* ']'
item            <- defined / range / .
range           <- . '-' [^]]

S               <- (%s / '--' [^%nl]*)*   -- spaces and comments
name            <- [A-Za-z][A-Za-z0-9_]*
arrow           <- '<-'
num             <- [0-9]+
string          <- '"' [^"]* '"' / "'" [^']* "'"
defined         <- '%' name

]=]

print(re.match(p, p))   -- a self description must match itself






License




Copyright © 2008-2010 Lua.org, PUC-Rio.




Permission is hereby granted, free of charge,
to any person obtaining a copy of this software and
associated documentation files (the "Software"),
to deal in the Software without restriction,
including without limitation the rights to use,
copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software,
and to permit persons to whom the Software is
furnished to do so,
subject to the following conditions:





The above copyright notice and this permission notice
shall be included in all copies or substantial portions of the Software.





THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.




 


 





$Id: re.html,v 1.17 2011/01/10 15:08:06 roberto Exp $



 


 


 
genometools-1.5.1/src/external/lpeg-0.10.2/re.lua000066400000000000000000000136151211610345200212370ustar00rootroot00000000000000-- $Id: re.lua,v 1.39 2010/11/04 19:44:18 roberto Exp $

-- imported functions and modules
local tonumber, type, print, error = tonumber, type, print, error
local setmetatable = setmetatable
local m = require"lpeg"

-- 'm' will be used to parse expressions, and 'mm' will be used to
-- create expressions; that is, 're' runs on 'm', creating patterns
-- on 'mm'
local mm = m

-- pattern's metatable 
local mt = getmetatable(mm.P(0))



-- No more global accesses after this point
local version = _VERSION
if version == "Lua 5.2" then _ENV = nil end


local any = m.P(1)


-- Pre-defined names
local Predef = { nl = m.P"\n" }


local mem
local fmem
local gmem


local function updatelocale ()
  mm.locale(Predef)
  Predef.a = Predef.alpha
  Predef.c = Predef.cntrl
  Predef.d = Predef.digit
  Predef.g = Predef.graph
  Predef.l = Predef.lower
  Predef.p = Predef.punct
  Predef.s = Predef.space
  Predef.u = Predef.upper
  Predef.w = Predef.alnum
  Predef.x = Predef.xdigit
  Predef.A = any - Predef.a
  Predef.C = any - Predef.c
  Predef.D = any - Predef.d
  Predef.G = any - Predef.g
  Predef.L = any - Predef.l
  Predef.P = any - Predef.p
  Predef.S = any - Predef.s
  Predef.U = any - Predef.u
  Predef.W = any - Predef.w
  Predef.X = any - Predef.x
  mem = {}    -- restart memoization
  fmem = {}
  gmem = {}
  local mt = {__mode = "v"}
  setmetatable(mem, mt)
  setmetatable(fmem, mt)
  setmetatable(gmem, mt)
end


updatelocale()



local I = m.P(function (s,i) print(i, s:sub(1, i-1)); return i end)


local function getdef (id, Defs)
  local c = Defs and Defs[id]
  if not c then error("undefined name: " .. id) end
  return c
end


local function patt_error (s, i)
  local msg = (#s < i + 20) and s:sub(i)
                             or s:sub(i,i+20) .. "..."
  msg = ("pattern error near '%s'"):format(msg)
  error(msg, 2)
end

local function mult (p, n)
  local np = mm.P(true)
  while n >= 1 do
    if n%2 >= 1 then np = np * p end
    p = p * p
    n = n/2
  end
  return np
end

local function equalcap (s, i, c)
  if type(c) ~= "string" then return nil end
  local e = #c + i
  if s:sub(i, e - 1) == c then return e else return nil end
end


local S = (m.S(" \f\n\r\t\v") + "--" * (any - Predef.nl)^0)^0

local name = m.R("AZ", "az") * m.R("AZ", "az", "__", "09")^0

local arrow = S * "<-"

local exp_follow = m.P"/" + ")" + "}" + ":}" + "~}" + (name * arrow) + -1

name = m.C(name)


-- identifiers only have meaning in a given environment
local Identifier = name * m.Carg(1)

local num = m.C(m.R"09"^1) * S / tonumber

local String = "'" * m.C((any - "'")^0) * "'" +
               '"' * m.C((any - '"')^0) * '"'


local defined = "%" * Identifier / function (c,Defs)
  local cat =  Defs and Defs[c] or Predef[c]
  if not cat then error ("name '" .. c .. "' undefined") end
  return cat
end

local Range = m.Cs(any * (m.P"-"/"") * (any - "]")) / mm.R

local item = defined + Range + m.C(any)

local Class =
    "["
  * (m.C(m.P"^"^-1))    -- optional complement symbol
  * m.Cf(item * (item - "]")^0, mt.__add) /
                          function (c, p) return c == "^" and any - p or p end
  * "]"

local function adddef (t, k, Defs, exp)
  if t[k] then
    error("'"..k.."' already defined as a rule")
  else
    t[k] = exp
  end
  return t
end

local function firstdef (n, Defs, r) return adddef({n}, n, Defs, r) end



local exp = m.P{ "Exp",
  Exp = S * ( m.V"Grammar"
            + m.Cf(m.V"Seq" * ("/" * S * m.V"Seq")^0, mt.__add) );
  Seq = m.Cf(m.Cc(m.P"") * m.V"Prefix"^0 , mt.__mul)
        * (#exp_follow + patt_error);
  Prefix = "&" * S * m.V"Prefix" / mt.__len
         + "!" * S * m.V"Prefix" / mt.__unm
         + m.V"Suffix";
  Suffix = m.Cf(m.V"Primary" * S *
          ( ( m.P"+" * m.Cc(1, mt.__pow)
            + m.P"*" * m.Cc(0, mt.__pow)
            + m.P"?" * m.Cc(-1, mt.__pow)
            + "^" * ( m.Cg(num * m.Cc(mult))
                    + m.Cg(m.C(m.S"+-" * m.R"09"^1) * m.Cc(mt.__pow))
                    )
            + "->" * S * ( m.Cg(String * m.Cc(mt.__div))
                         + m.P"{}" * m.Cc(nil, m.Ct)
                         + m.Cg(Identifier / getdef * m.Cc(mt.__div))
                         )
            + "=>" * S * m.Cg(Identifier / getdef * m.Cc(m.Cmt))
            ) * S
          )^0, function (a,b,f) return f(a,b) end );
  Primary = "(" * m.V"Exp" * ")"
            + String / mm.P
            + Class
            + defined
            + "{:" * (name * ":" + m.Cc(nil)) * m.V"Exp" * ":}" /
                     function (n, p) return mm.Cg(p, n) end
            + "=" * name / function (n) return mm.Cmt(mm.Cb(n), equalcap) end
            + m.P"{}" / mm.Cp
            + "{~" * m.V"Exp" * "~}" / mm.Cs
            + "{" * m.V"Exp" * "}" / mm.C
            + m.P"." * m.Cc(any)
            + name * -arrow / mm.V
            + "<" * name * ">" / mm.V;
  Definition = Identifier * arrow * m.V"Exp";
  Grammar = m.Cf(m.V"Definition" / firstdef * m.Cg(m.V"Definition")^0, adddef) /
                mm.P
}

local pattern = S * exp / mm.P * (-any + patt_error)


local function compile (p, defs)
  if mm.type(p) == "pattern" then return p end   -- already compiled
  local cp = pattern:match(p, 1, defs)
  if not cp then error("incorrect pattern", 3) end
  return cp
end

local function match (s, p, i)
  local cp = mem[p]
  if not cp then
    cp = compile(p)
    mem[p] = cp
  end
  return cp:match(s, i or 1)
end

local function find (s, p, i)
  local cp = fmem[p]
  if not cp then
    cp = compile(p)
    cp = mm.P{ mm.Cp() * cp + 1 * mm.V(1) }
    fmem[p] = cp
  end
  return cp:match(s, i or 1)
end

local function gsub (s, p, rep)
  local g = gmem[p] or {}   -- ensure gmem[p] is not collected while here
  gmem[p] = g
  local cp = g[rep]
  if not cp then
    cp = compile(p)
    cp = mm.Cs((cp / rep + 1)^0)
    g[rep] = cp
  end
  return cp:match(s)
end


-- exported names
local re = {
  compile = compile,
  match = match,
  find = find,
  gsub = gsub,
  updatelocale = updatelocale,
}

if version == "Lua 5.1" then _G.re = re end

return re
genometools-1.5.1/src/external/lpeg-0.10.2/test.lua000077500000000000000000001063151211610345200216130ustar00rootroot00000000000000#!/usr/bin/env lua5.1

-- $Id: test.lua,v 1.82 2010/12/03 14:49:54 roberto Exp $

--require"strict"    -- just to be pedantic

local m = require"lpeg"

local debug = require"debug"


-- compatibility with Lua 5.2
local unpack = table.unpack or unpack


-- most tests here do not need much stack space
m.setmaxstack(5)

any = m.P(1)
space = m.S" \t\n"^0

local function checkeq (x, y, p)
if p then print(x,y) end
  if type(x) ~= "table" then assert(x == y)
  else
    for k,v in pairs(x) do checkeq(v, y[k], p) end
    for k,v in pairs(y) do checkeq(v, x[k], p) end
  end
end


mt = getmetatable(m.P(1))


local allchar = {}
for i=0,255 do allchar[i + 1] = i end
allchar = string.char(unpack(allchar))
assert(#allchar == 256)

local function cs2str (c)
  return m.match(m.Cs((c + m.P(1)/"")^0), allchar)
end

local function eqcharset (c1, c2)
  assert(cs2str(c1) == cs2str(c2))
end


print"General tests for LPeg library"

assert(type(m.version()) == "string")
print("version " .. m.version())
assert(m.type("alo") ~= "pattern")
assert(m.type(io.input) ~= "pattern")
assert(m.type(m.P"alo") == "pattern")

-- tests for some basic optimizations
assert(m.match(m.P(false) + "a", "a") == 2)
assert(m.match(m.P(true) + "a", "a") == 1)
assert(m.match("a" + m.P(false), "b") == nil)
assert(m.match("a" + m.P(true), "b") == 1)

assert(m.match(m.P(false) * "a", "a") == nil)
assert(m.match(m.P(true) * "a", "a") == 2)
assert(m.match("a" * m.P(false), "a") == nil)
assert(m.match("a" * m.P(true), "a") == 2)

assert(m.match(#m.P(false) * "a", "a") == nil)
assert(m.match(#m.P(true) * "a", "a") == 2)
assert(m.match("a" * #m.P(false), "a") == nil)
assert(m.match("a" * #m.P(true), "a") == 2)


-- tests for locale
do
  assert(m.locale(m) == m)
  local t = {}
  assert(m.locale(t, m) == t)
  local x = m.locale()
  for n,v in pairs(x) do
    assert(type(n) == "string")
    eqcharset(v, m[n])
  end
end



assert(m.match(3, "aaaa"))
assert(m.match(4, "aaaa"))
assert(not m.match(5, "aaaa"))
assert(m.match(-3, "aa"))
assert(not m.match(-3, "aaa"))
assert(not m.match(-3, "aaaa"))
assert(not m.match(-4, "aaaa"))
assert(m.P(-5):match"aaaa")

assert(m.match("a", "alo") == 2)
assert(m.match("al", "alo") == 3)
assert(not m.match("alu", "alo"))
assert(m.match(true, "") == 1)

digit = m.S"0123456789"
upper = m.S"ABCDEFGHIJKLMNOPQRSTUVWXYZ"
lower = m.S"abcdefghijklmnopqrstuvwxyz"
letter = m.S"" + upper + lower
alpha = letter + digit + m.R()

eqcharset(m.S"", m.P(false))
eqcharset(upper, m.R("AZ"))
eqcharset(lower, m.R("az"))
eqcharset(upper + lower, m.R("AZ", "az"))
eqcharset(upper + lower, m.R("AZ", "cz", "aa", "bb", "90"))
eqcharset(digit, m.S"01234567" + "8" + "9")
eqcharset(upper, letter - lower)
eqcharset(m.S(""), m.R())
assert(cs2str(m.S("")) == "")

eqcharset(m.S"\0", "\0")
eqcharset(m.S"\1\0\2", m.R"\0\2")
eqcharset(m.S"\1\0\2", m.R"\1\2" + "\0")
eqcharset(m.S"\1\0\2" - "\0", m.R"\1\2")

word = alpha^1 * (1 - alpha)^0

assert((word^0 * -1):match"alo alo")
assert(m.match(word^1 * -1, "alo alo"))
assert(m.match(word^2 * -1, "alo alo"))
assert(not m.match(word^3 * -1, "alo alo"))

assert(not m.match(word^-1 * -1, "alo alo"))
assert(m.match(word^-2 * -1, "alo alo"))
assert(m.match(word^-3 * -1, "alo alo"))

eos = m.P(-1)

assert(m.match(digit^0 * letter * digit * eos, "1298a1"))
assert(not m.match(digit^0 * letter * eos, "1257a1"))

b = {
  [1] = "(" * (((1 - m.S"()") + #m.P"(" * m.V(1))^0) * ")"
}

assert(m.match(b, "(al())()"))
assert(not m.match(b * eos, "(al())()"))
assert(m.match(b * eos, "((al())()(é))"))
assert(not m.match(b, "(al()()"))

assert(not m.match(letter^1 - "for", "foreach"))
assert(m.match(letter^1 - ("for" * eos), "foreach"))
assert(not m.match(letter^1 - ("for" * eos), "for"))

function basiclookfor (p)
  return m.P {
    [1] = p + (1 * m.V(1))
  }
end

function caplookfor (p)
  return basiclookfor(p:C())
end

assert(m.match(caplookfor(letter^1), "   4achou123...") == "achou")
a = {m.match(caplookfor(letter^1)^0, " two words, one more  ")}
checkeq(a, {"two", "words", "one", "more"})

assert(m.match( basiclookfor((#m.P(b) * 1) * m.Cp()), "  (  (a)") == 7)

a = {m.match(m.C(digit^1 * m.Cc"d") + m.C(letter^1 * m.Cc"l"), "123")}
checkeq(a, {"123", "d"})

a = {m.match(m.C(digit^1) * "d" * -1 + m.C(letter^1 * m.Cc"l"), "123d")}
checkeq(a, {"123"})

a = {m.match(m.C(digit^1 * m.Cc"d") + m.C(letter^1 * m.Cc"l"), "abcd")}
checkeq(a, {"abcd", "l"})

a = {m.match(m.Cc(10,20,30) * 'a' * m.Cp(), 'aaa')}
checkeq(a, {10,20,30,2})
a = {m.match(m.Cp() * m.Cc(10,20,30) * 'a' * m.Cp(), 'aaa')}
checkeq(a, {1,10,20,30,2})
a = m.match(m.Ct(m.Cp() * m.Cc(10,20,30) * 'a' * m.Cp()), 'aaa')
checkeq(a, {1,10,20,30,2})
a = m.match(m.Ct(m.Cp() * m.Cc(7,8) * m.Cc(10,20,30) * 'a' * m.Cp()), 'aaa')
checkeq(a, {1,7,8,10,20,30,2})
a = {m.match(m.Cc() * m.Cc() * m.Cc(1) * m.Cc(2,3,4) * m.Cc() * 'a', 'aaa')}
checkeq(a, {1,2,3,4})

a = {m.match(m.Cp() * letter^1 * m.Cp(), "abcd")}
checkeq(a, {1, 5})


t = {m.match({[1] = m.C(m.C(1) * m.V(1) + -1)}, "abc")}
checkeq(t, {"abc", "a", "bc", "b", "c", "c", ""})


-- test for small capture boundary
for i = 250,260 do
  assert(#m.match(m.C(i), string.rep('a', i)) == i)
  assert(#m.match(m.C(m.C(i)), string.rep('a', i)) == i)
end


-- tests for any*n
for n = 1, 550 do
  local x_1 = string.rep('x', n - 1)
  local x = x_1 .. 'a'
  assert(not m.P(n):match(x_1))
  assert(m.P(n):match(x) == n + 1)
  assert(n < 4 or m.match(m.P(n) + "xxx", x_1) == 4)
  assert(m.C(n):match(x) == x)
  assert(m.C(m.C(n)):match(x) == x)
  assert(m.P(-n):match(x_1) == 1)
  assert(not m.P(-n):match(x))
  assert(n < 13 or m.match(m.Cc(20) * ((n - 13) * m.P(10)) * 3, x) == 20)
  local n3 = math.floor(n/3)
  assert(m.match(n3 * m.Cp() * n3 * n3, x) == n3 + 1)
end

assert(m.P(0):match("x") == 1)
assert(m.P(0):match("") == 1)
assert(m.C(0):match("x") == "")
assert(m.match(m.Cc(0) * m.P(10) + m.Cc(1) * "xuxu", "xuxu") == 1)
assert(m.match(m.Cc(0) * m.P(10) + m.Cc(1) * "xuxu", "xuxuxuxuxu") == 0)
assert(m.match(m.C(m.P(2)^1), "abcde") == "abcd")
p = m.Cc(0) * 1 + m.Cc(1) * 2 + m.Cc(2) * 3 + m.Cc(3) * 4


-- test for alternation optimization
assert(m.match(m.P"a"^1 + "ab" + m.P"x"^0, "ab") == 2)
assert(m.match((m.P"a"^1 + "ab" + m.P"x"^0 * 1)^0, "ab") == 3)
assert(m.match(m.P"ab" + "cd" + "" + "cy" + "ak", "98") == 1)
assert(m.match(m.P"ab" + "cd" + "ax" + "cy", "ax") == 3)
assert(m.match("a" * m.P"b"^0 * "c"  + "cd" + "ax" + "cy", "ax") == 3)
assert(m.match((m.P"ab" + "cd" + "ax" + "cy")^0, "ax") == 3)
assert(m.match(m.P(1) * "x" + m.S"" * "xu" + "ay", "ay") == 3)
assert(m.match(m.P"abc" + "cde" + "aka", "aka") == 4)
assert(m.match(m.S"abc" * "x" + "cde" + "aka", "ax") == 3)
assert(m.match(m.S"abc" * "x" + "cde" + "aka", "aka") == 4)
assert(m.match(m.S"abc" * "x" + "cde" + "aka", "cde") == 4)
assert(m.match(m.S"abc" * "x" + "ide" + m.S"ab" * "ka", "aka") == 4)
assert(m.match("ab" + m.S"abc" * m.P"y"^0 * "x" + "cde" + "aka", "ax") == 3)
assert(m.match("ab" + m.S"abc" * m.P"y"^0 * "x" + "cde" + "aka", "aka") == 4)
assert(m.match("ab" + m.S"abc" * m.P"y"^0 * "x" + "cde" + "aka", "cde") == 4)
assert(m.match("ab" + m.S"abc" * m.P"y"^0 * "x" + "ide" + m.S"ab" * "ka", "aka") == 4)
assert(m.match("ab" + m.S"abc" * m.P"y"^0 * "x" + "ide" + m.S"ab" * "ka", "ax") == 3)
assert(m.match(m.P(1) * "x" + "cde" + m.S"ab" * "ka", "aka") == 4)
assert(m.match(m.P(1) * "x" + "cde" + m.P(1) * "ka", "aka") == 4)
assert(m.match(m.P(1) * "x" + "cde" + m.P(1) * "ka", "cde") == 4)
assert(m.match(m.P"eb" + "cd" + m.P"e"^0 + "x", "ee") == 3)
assert(m.match(m.P"ab" + "cd" + m.P"e"^0 + "x", "abcd") == 3)
assert(m.match(m.P"ab" + "cd" + m.P"e"^0 + "x", "eeex") == 4)
assert(m.match(m.P"ab" + "cd" + m.P"e"^0 + "x", "cd") == 3)
assert(m.match(m.P"ab" + "cd" + m.P"e"^0 + "x", "x") == 1)
assert(m.match(m.P"ab" + "cd" + m.P"e"^0 + "x" + "", "zee") == 1)
assert(m.match(m.P"ab" + "cd" + m.P"e"^1 + "x", "abcd") == 3)
assert(m.match(m.P"ab" + "cd" + m.P"e"^1 + "x", "eeex") == 4)
assert(m.match(m.P"ab" + "cd" + m.P"e"^1 + "x", "cd") == 3)
assert(m.match(m.P"ab" + "cd" + m.P"e"^1 + "x", "x") == 2)
assert(m.match(m.P"ab" + "cd" + m.P"e"^1 + "x" + "", "zee") == 1)

pi = "3.14159 26535 89793 23846 26433 83279 50288 41971 69399 37510"
assert(m.match(m.Cs((m.P"1" / "a" + m.P"5" / "b" + m.P"9" / "c" + 1)^0), pi) ==
  m.match(m.Cs((m.P(1) / {["1"] = "a", ["5"] = "b", ["9"] = "c"})^0), pi))
print"+"


-- tests for capture optimizations
assert(m.match((m.P(3) +  4 * m.Cp()) * "a", "abca") == 5)
t = {m.match(((m.P"a" + m.Cp()) * m.P"x")^0, "axxaxx")}
checkeq(t, {3, 6})

-- test for table captures
t = m.match(m.Ct(letter^1), "alo")
checkeq(t, {})

t, n = m.match(m.Ct(m.C(letter)^1) * m.Cc"t", "alo")
assert(n == "t" and table.concat(t) == "alo")

t = m.match(m.Ct(m.C(m.C(letter)^1)), "alo")
assert(table.concat(t, ";") == "alo;a;l;o")

t = m.match(m.Ct(m.C(m.C(letter)^1)), "alo")
assert(table.concat(t, ";") == "alo;a;l;o")

t = m.match(m.Ct(m.Ct((m.Cp() * letter * m.Cp())^1)), "alo")
assert(table.concat(t[1], ";") == "1;2;2;3;3;4")

t = m.match(m.Ct(m.C(m.C(1) * 1 * m.C(1))), "alo")
checkeq(t, {"alo", "a", "o"})


-- tests for groups
p = m.Cg(1)   -- no capture
assert(p:match('x') == 'x')
p = m.Cg(m.P(true)/function () end * 1)   -- no value
assert(p:match('x') == 'x')
p = m.Cg(m.Cg(m.Cg(m.C(1))))
assert(p:match('x') == 'x')
p = m.Cg(m.Cg(m.Cg(m.C(1))^0) * m.Cg(m.Cc(1) * m.Cc(2)))
t = {p:match'abc'}
checkeq(t, {'a', 'b', 'c', 1, 2})

-- test for non-pattern as arguments to pattern functions

p = { ('a' * m.V(1))^-1 } * m.P'b' * { 'a' * m.V(2); m.V(1)^-1 }
assert(m.match(p, "aaabaac") == 7)

-- a large table capture
t = m.match(m.Ct(m.C('a')^0), string.rep("a", 10000))
assert(#t == 10000 and t[1] == 'a' and t[#t] == 'a')


-- test for errors
local function checkerr (msg, ...)
  assert(m.match({ m.P(msg) + 1 * m.V(1) }, select(2, pcall(...))))
end

-- checkerr("rule '1' is left recursive", m.match, { m.V(1) * 'a' }, "a")
checkerr("rule '1' outside a grammar", m.match, m.V(1), "")
checkerr("rule 'hiii' outside a grammar", m.match, m.V('hiii'), "")
checkerr("rule 'hiii' is not defined", m.match, { m.V('hiii') }, "")
checkerr("rule  is not defined", m.match, { m.V{} }, "")

checkerr("rule 'A' is not a pattern", m.P, { A = {} })
checkerr("rule  is not a pattern", m.P, { [print] = {} })

-- test for non-pattern as arguments to pattern functions

p = { ('a' * m.V(1))^-1 } * m.P'b' * { 'a' * m.V(2); m.V(1)^-1 }
assert(m.match(p, "aaabaac") == 7)

-- a large table capture
t = m.match(m.Ct(m.C('a')^0), string.rep("a", 10000))
assert(#t == 10000 and t[1] == 'a' and t[#t] == 'a')


-- test for errors
local function checkerr (msg, ...)
  assert(m.match({ m.P(msg) + 1 * m.V(1) }, select(2, pcall(...))))
end

checkerr("rule '1' is left recursive", m.match, { m.V(1) * 'a' }, "a")
checkerr("rule '1' outside a grammar", m.match, m.V(1), "")
checkerr("rule 'hiii' outside a grammar", m.match, m.V('hiii'), "")
checkerr("rule 'hiii' is not defined", m.match, { m.V('hiii') }, "")
checkerr("rule  is not defined", m.match, { m.V({}) }, "")

print('+')


-- bug in 0.10 (rechecking a grammar, after tail-call optimization)
m.P{ m.P { (m.P(3) + "xuxu")^0 * m.V"xuxu", xuxu = m.P(1) } }

local V = m.V

local Space = m.S(" \n\t")^0
local Number = m.C(m.R("09")^1) * Space
local FactorOp = m.C(m.S("+-")) * Space
local TermOp = m.C(m.S("*/")) * Space
local Open = "(" * Space
local Close = ")" * Space


local function f_factor (v1, op, v2, d)
  assert(d == nil)
  if op == "+" then return v1 + v2
  else return v1 - v2
  end
end


local function f_term (v1, op, v2, d)
  assert(d == nil)
  if op == "*" then return v1 * v2
  else return v1 / v2
  end
end

G = m.P{ "Exp",
  Exp = m.Cf(V"Factor" * m.Cg(FactorOp * V"Factor")^0, f_factor);
  Factor = m.Cf(V"Term" * m.Cg(TermOp * V"Term")^0, f_term);
  Term = Number / tonumber  +  Open * V"Exp" * Close;
}

G = Space * G * -1

for _, s in ipairs{" 3 + 5*9 / (1+1) ", "3+4/2", "3+3-3- 9*2+3*9/1-  8"} do
  assert(m.match(G, s) == loadstring("return "..s)())
end


-- test for grammars (errors deep in calling non-terminals)
g = m.P{
  [1] = m.V(2) + "a",
  [2] = "a" * m.V(3) * "x",
  [3] = "b" * m.V(3) + "c"
}

assert(m.match(g, "abbbcx") == 7)
assert(m.match(g, "abbbbx") == 2)


-- tests for \0
assert(m.match(m.R("\0\1")^1, "\0\1\0") == 4)
assert(m.match(m.S("\0\1ab")^1, "\0\1\0a") == 5)
assert(m.match(m.P(1)^3, "\0\1\0a") == 5)
assert(not m.match(-4, "\0\1\0a"))
assert(m.match("\0\1\0a", "\0\1\0a") == 5)
assert(m.match("\0\0\0", "\0\0\0") == 4)
assert(not m.match("\0\0\0", "\0\0"))


-- tests for predicates
assert(not m.match(-m.P("a") * 2, "alo"))
assert(m.match(- -m.P("a") * 2, "alo") == 3)
assert(m.match(#m.P("a") * 2, "alo") == 3)
assert(m.match(##m.P("a") * 2, "alo") == 3)
assert(not m.match(##m.P("c") * 2, "alo"))
assert(m.match(m.Cs((##m.P("a") * 1 + m.P(1)/".")^0), "aloal") == "a..a.")
assert(m.match(m.Cs((#((#m.P"a")/"") * 1 + m.P(1)/".")^0), "aloal") == "a..a.")
assert(m.match(m.Cs((- -m.P("a") * 1 + m.P(1)/".")^0), "aloal") == "a..a.")
assert(m.match(m.Cs((-((-m.P"a")/"") * 1 + m.P(1)/".")^0), "aloal") == "a..a.")


-- look-behind predicate
assert(not m.match(m.B'a', 'a'))
assert(m.match(1 * m.B'a', 'a') == 2)
assert(not m.match(m.B(1), 'a'))
assert(m.match(1 * m.B(1), 'a') == 2)
assert(m.match(-m.B(1), 'a') == 1)

B = #letter * -m.B(letter) + -letter * m.B(letter)
x = m.Ct({ (B * m.Cp())^-1 * (1 * m.V(1) + m.P(true)) })
checkeq(m.match(x, 'ar cal  c'), {1,3,4,7,9,10})
checkeq(m.match(x, ' ar cal  '), {2,4,5,8})
checkeq(m.match(x, '   '), {})
checkeq(m.match(x, 'aloalo'), {1,7})

assert(m.match(B, "a") == 1)
assert(m.match(1 * B, "a") == 2)
assert(not m.B(-letter):match(""))
assert((-m.B(letter)):match("") == 1)

assert((4 * m.B(letter, 4)):match("aaaaaaaa") == 5)
assert(not (4 * m.B(letter, 5)):match("aaaaaaaa"))
assert((4 * -m.B(letter, 5)):match("aaaaaaaa") == 5)

assert((3 * m.B(m.C(1))):match("12345") == 4)


-- bug in 0.9
assert(m.match(('a' * #m.P'b'), "ab") == 2)
assert(not m.match(('a' * #m.P'b'), "a"))

assert(not m.match(#m.S'567', ""))
assert(m.match(#m.S'567' * 1, "6") == 2)


-- tests for Tail Calls

-- create a grammar for a simple DFA for even number of 0s and 1s
-- finished in '$':
--
--  ->1 <---0---> 2
--    ^           ^
--    |           |
--    1           1
--    |           |
--    V           V
--    3 <---0---> 4
--
-- this grammar should keep no backtracking information

p = m.P{
  [1] = '0' * m.V(2) + '1' * m.V(3) + '$',
  [2] = '0' * m.V(1) + '1' * m.V(4),
  [3] = '0' * m.V(4) + '1' * m.V(1),
  [4] = '0' * m.V(3) + '1' * m.V(2),
}

assert(p:match(string.rep("00", 10000) .. "$"))
assert(p:match(string.rep("01", 10000) .. "$"))
assert(p:match(string.rep("011", 10000) .. "$"))
assert(not p:match(string.rep("011", 10001) .. "$"))


-- this grammar does need backtracking info.
local lim = 10000
p = m.P{ '0' * m.V(1) + '0' }
assert(not pcall(m.match, p, string.rep("0", lim)))
m.setmaxstack(2*lim)
assert(not pcall(m.match, p, string.rep("0", lim)))
m.setmaxstack(2*lim + 2)
assert(pcall(m.match, p, string.rep("0", lim)))

-- tests for optional start position
assert(m.match("a", "abc", 1))
assert(m.match("b", "abc", 2))
assert(m.match("c", "abc", 3))
assert(not m.match(1, "abc", 4))
assert(m.match("a", "abc", -3))
assert(m.match("b", "abc", -2))
assert(m.match("c", "abc", -1))
assert(m.match("abc", "abc", -4))   -- truncate to position 1

assert(m.match("", "abc", 10))   -- empty string is everywhere!
assert(m.match("", "", 10))
assert(not m.match(1, "", 1))
assert(not m.match(1, "", -1))
assert(not m.match(1, "", 0))

print("+")


-- tests for argument captures
assert(not pcall(m.Carg, 0))
assert(not pcall(m.Carg, -1))
assert(not pcall(m.Carg, 2^18))
assert(not pcall(m.match, m.Carg(1), 'a', 1))
assert(m.match(m.Carg(1), 'a', 1, print) == print)
x = {m.match(m.Carg(1) * m.Carg(2), '', 1, 10, 20)}
checkeq(x, {10, 20})

assert(m.match(m.Cmt(m.Cg(m.Carg(3), "a") *
                     m.Cmt(m.Cb("a"), function (s,i,x)
                                        assert(s == "a" and i == 1);
                                        return i, x+1
                                      end) *
                     m.Carg(2), function (s,i,a,b,c)
                                  assert(s == "a" and i == 1 and c == nil);
				  return i, 2*a + 3*b
                                end) * "a",
               "a", 1, false, 100, 1000) == 2*1001 + 3*100)


-- tests for Lua functions

t = {}
s = ""
p = function (s1, i) assert(s == s1); t[#t + 1] = i; return nil end
s = "hi, this is a test"
assert(m.match(((p - m.P(-1)) + 2)^0, s) == string.len(s) + 1)
assert(#t == string.len(s)/2 and t[1] == 1 and t[2] == 3)

assert(not m.match(p, s))

p = mt.__add(function (s, i) return i end, function (s, i) return nil end)
assert(m.match(p, "alo"))

p = mt.__mul(function (s, i) return i end, function (s, i) return nil end)
assert(not m.match(p, "alo"))


t = {}
p = function (s1, i) assert(s == s1); t[#t + 1] = i; return i end
s = "hi, this is a test"
assert(m.match((m.P(1) * p)^0, s) == string.len(s) + 1)
assert(#t == string.len(s) and t[1] == 2 and t[2] == 3)

t = {}
p = m.P(function (s1, i) assert(s == s1); t[#t + 1] = i;
                         return i <= s1:len() and i + 1 end)
s = "hi, this is a test"
assert(m.match(p^0, s) == string.len(s) + 1)
assert(#t == string.len(s) + 1 and t[1] == 1 and t[2] == 2)

p = function (s1, i) return m.match(m.P"a"^1, s1, i) end
assert(m.match(p, "aaaa") == 5)
assert(m.match(p, "abaa") == 2)
assert(not m.match(p, "baaa"))

assert(not pcall(m.match, function () return 2^20 end, s))
assert(not pcall(m.match, function () return 0 end, s))
assert(not pcall(m.match, function (s, i) return i - 1 end, s))
assert(not pcall(m.match, m.P(1)^0 * function (_, i) return i - 1 end, s))
assert(m.match(m.P(1)^0 * function (_, i) return i end * -1, s))
assert(not pcall(m.match, m.P(1)^0 * function (_, i) return i + 1 end, s))
assert(m.match(m.P(function (s, i) return s:len() + 1 end) * -1, s))
assert(not pcall(m.match, m.P(function (s, i) return s:len() + 2 end) * -1, s))
assert(not m.match(m.P(function (s, i) return s:len() end) * -1, s))
assert(m.match(m.P(1)^0 * function (_, i) return true end, s) ==
       string.len(s) + 1)
for i = 1, string.len(s) + 1 do
  assert(m.match(function (_, _) return i end, s) == i)
end

p = (m.P(function (s, i) return i%2 == 0 and i + 1 end)
  +  m.P(function (s, i) return i%2 ~= 0 and i + 2 <= s:len() and i + 3 end))^0
  * -1
assert(p:match(string.rep('a', 14000)))

-- tests for Function Replacements
f = function (a, ...) if a ~= "x" then return {a, ...} end end

t = m.match(m.C(1)^0/f, "abc")
checkeq(t, {"a", "b", "c"})

t = m.match(m.C(1)^0/f/f, "abc")
checkeq(t, {{"a", "b", "c"}})

t = m.match(m.P(1)^0/f/f, "abc")   -- no capture
checkeq(t, {{"abc"}})

t = m.match((m.P(1)^0/f * m.Cp())/f, "abc")
checkeq(t, {{"abc"}, 4})

t = m.match((m.C(1)^0/f * m.Cp())/f, "abc")
checkeq(t, {{"a", "b", "c"}, 4})

t = m.match((m.C(1)^0/f * m.Cp())/f, "xbc")
checkeq(t, {4})

t = m.match(m.C(m.C(1)^0)/f, "abc")
checkeq(t, {"abc", "a", "b", "c"})

g = function (...) return 1, ... end
t = {m.match(m.C(1)^0/g/g, "abc")}
checkeq(t, {1, 1, "a", "b", "c"})

t = {m.match(m.Cc(nil,nil,4) * m.Cc(nil,3) * m.Cc(nil, nil) / g / g, "")}
t1 = {1,1,nil,nil,4,nil,3,nil,nil}
for i=1,10 do assert(t[i] == t1[i]) end

t = {m.match((m.C(1) / function (x) return x, x.."x" end)^0, "abc")}
checkeq(t, {"a", "ax", "b", "bx", "c", "cx"})

t = m.match(m.Ct((m.C(1) / function (x,y) return y, x end * m.Cc(1))^0), "abc")
checkeq(t, {nil, "a", 1, nil, "b", 1, nil, "c", 1})

-- tests for Query Replacements

assert(m.match(m.C(m.C(1)^0)/{abc = 10}, "abc") == 10)
assert(m.match(m.C(1)^0/{a = 10}, "abc") == 10)
assert(m.match(m.S("ba")^0/{ab = 40}, "abc") == 40)
t = m.match(m.Ct((m.S("ba")/{a = 40})^0), "abc")
checkeq(t, {40})

assert(m.match(m.Cs((m.C(1)/{a=".", d=".."})^0), "abcdde") == ".bc....e")
assert(m.match(m.Cs((m.C(1)/{f="."})^0), "abcdde") == "abcdde")
assert(m.match(m.Cs((m.C(1)/{d="."})^0), "abcdde") == "abc..e")
assert(m.match(m.Cs((m.C(1)/{e="."})^0), "abcdde") == "abcdd.")
assert(m.match(m.Cs((m.C(1)/{e=".", f="+"})^0), "eefef") == "..+.+")
assert(m.match(m.Cs((m.C(1))^0), "abcdde") == "abcdde")
assert(m.match(m.Cs(m.C(m.C(1)^0)), "abcdde") == "abcdde")
assert(m.match(1 * m.Cs(m.P(1)^0), "abcdde") == "bcdde")
assert(m.match(m.Cs((m.C('0')/'x' + 1)^0), "abcdde") == "abcdde")
assert(m.match(m.Cs((m.C('0')/'x' + 1)^0), "0ab0b0") == "xabxbx")
assert(m.match(m.Cs((m.C('0')/'x' + m.P(1)/{b=3})^0), "b0a0b") == "3xax3")
assert(m.match(m.P(1)/'%0%0'/{aa = -3} * 'x', 'ax') == -3)
assert(m.match(m.C(1)/'%0%1'/{aa = 'z'}/{z = -3} * 'x', 'ax') == -3)

assert(m.match(m.Cs(m.Cc(0) * (m.P(1)/"")), "4321") == "0")

assert(m.match(m.Cs((m.P(1) / "%0")^0), "abcd") == "abcd")
assert(m.match(m.Cs((m.P(1) / "%0.%0")^0), "abcd") == "a.ab.bc.cd.d")
assert(m.match(m.Cs((m.P("a") / "%0.%0" + 1)^0), "abcad") == "a.abca.ad")
assert(m.match(m.C("a") / "%1%%%0", "a") == "a%a")
assert(m.match(m.Cs((m.P(1) / ".xx")^0), "abcd") == ".xx.xx.xx.xx")
assert(m.match(m.Cp() * m.P(3) * m.Cp()/"%2%1%1 - %0 ", "abcde") ==
   "411 - abc ")

assert(pcall(m.match, m.P(1)/"%0", "abc"))
assert(not pcall(m.match, m.P(1)/"%1", "abc"))   -- out of range
assert(not pcall(m.match, m.P(1)/"%9", "abc"))   -- out of range

p = m.C(1)
p = p * p; p = p * p; p = p * p * m.C(1) / "%9 - %1"
assert(p:match("1234567890") == "9 - 1")

assert(m.match(m.Cc(print), "") == print)

-- too many captures (just ignore extra ones)
p = m.C(1)^0 / "%2-%9-%0-%9"
assert(p:match"01234567890123456789" == "1-8-01234567890123456789-8")
s = string.rep("12345678901234567890", 20)
assert(m.match(m.C(1)^0 / "%9-%1-%0-%3", s) == "9-1-" .. s .. "-3")

-- string captures with non-string subcaptures
p = m.Cc('alo') * m.C(1) / "%1 - %2 - %1"
assert(p:match'x' == 'alo - x - alo')

assert(not pcall(m.match, m.Cc(true) / "%1", "a"))

-- long strings for string capture
l = 10000
s = string.rep('a', l) .. string.rep('b', l) .. string.rep('c', l)

p = (m.C(m.P'a'^1) * m.C(m.P'b'^1) * m.C(m.P'c'^1)) / '%3%2%1'

assert(p:match(s) == string.rep('c', l) ..
                     string.rep('b', l) .. 
                     string.rep('a', l))

print"+"

-- accumulator capture
function f (x) return x + 1 end
assert(m.match(m.Cf(m.Cc(0) * m.C(1)^0, f), "alo alo") == 7)

t = {m.match(m.Cf(m.Cc(1,2,3), error), "")}
checkeq(t, {1})
p = m.Cf(m.Ct(true) * m.Cg(m.C(m.R"az"^1) * "=" * m.C(m.R"az"^1) * ";")^0,
         rawset)
t = p:match("a=b;c=du;xux=yuy;")
checkeq(t, {a="b", c="du", xux="yuy"})
 

-- tests for loop checker

local function haveloop (p)
  assert(not pcall(function (p) return p^0 end, m.P(p)))
end

haveloop(m.P("x")^-4)
assert(m.match(((m.P(0) + 1) * m.S"al")^0, "alo") == 3)
assert(m.match((("x" + #m.P(1))^-4 * m.S"al")^0, "alo") == 3)
haveloop("")
haveloop(m.P("x")^0)
haveloop(m.P("x")^-1)
haveloop(m.P("x") + 1 + 2 + m.P("a")^-1)
haveloop(-m.P("ab"))
haveloop(- -m.P("ab"))
haveloop(# #(m.P("ab") + "xy"))
haveloop(- #m.P("ab")^0)
haveloop(# -m.P("ab")^1)
haveloop(#m.V(3))
haveloop(m.V(3) + m.V(1) + m.P('a')^-1)
haveloop({[1] = m.V(2) * m.V(3), [2] = m.V(3), [3] = m.P(0)})
assert(m.match(m.P{[1] = m.V(2) * m.V(3), [2] = m.V(3), [3] = m.P(1)}^0, "abc")
       == 3)
assert(m.match(m.P""^-3, "a") == 1)

local function find (p, s)
  return m.match(basiclookfor(p), s)
end


local function badgrammar (g, exp)
  local err, msg = pcall(m.P, g)
  assert(not err)
  if exp then assert(find(exp, msg)) end
end

badgrammar({[1] = m.V(1)}, "rule '1'")
badgrammar({[1] = m.V(2)}, "rule '2'")   -- invalid non-terminal
badgrammar({[1] = m.V"x"}, "rule 'x'")   -- invalid non-terminal
badgrammar({[1] = m.V{}}, "rule ")   -- invalid non-terminal
badgrammar({[1] = #m.P("a") * m.V(1)}, "rule '1'")
badgrammar({[1] = -m.P("a") * m.V(1)}, "rule '1'")
badgrammar({[1] = -1 * m.V(1)}, "rule '1'")
badgrammar({[1] = 1 * m.V(2), [2] = m.V(2)}, "rule '2'")
badgrammar({[1] = m.P(0), [2] = 1 * m.V(1)^0}, "loop in rule '2'")
badgrammar({ m.V(2), m.V(3)^0, m.P"" }, "rule '2'")
badgrammar({ m.V(2) * m.V(3)^0, m.V(3)^0, m.P"" }, "rule '1'")
badgrammar({ #(m.V(1) * 'a') }, "rule '1'")
badgrammar({ -(m.V(1) * 'a') }, "rule '1'")

assert(m.match({'a' * -m.V(1)}, "aaa") == 2)
assert(m.match({'a' * -m.V(1)}, "aaaa") == nil)


-- simple tests for maximum sizes:
local p = m.P"a"
for i=1,14 do p = p * p end

p = {}
for i=1,100 do p[i] = m.P"a" end
p = m.P(p)


-- strange values for rule labels

p = m.P{ "print",
     print = m.V(print),
     [print] = m.V(_G),
     [_G] = m.P"a",
   }

assert(p:match("a"))

-- initial rule
g = {}
for i = 1, 10 do g["i"..i] =  "a" * m.V("i"..i+1) end
g.i11 = m.P""
for i = 1, 10 do
  g[1] = "i"..i
  local p = m.P(g)
  assert(p:match("aaaaaaaaaaa") == 11 - i + 1)
end

print"+"


-- tests for back references
assert(not pcall(m.match, m.Cb('x'), ''))
assert(not pcall(m.match, m.Cg(1, 'a') * m.Cb('b'), 'a'))

p = m.Cg(m.C(1) * m.C(1), "k") * m.Ct(m.Cb("k"))
t = p:match("ab")
checkeq(t, {"a", "b"})


t = {}
function foo (p) t[#t + 1] = p; return p .. "x" end

p = m.Cg(m.C(2)    / foo, "x") * m.Cb"x" *
    m.Cg(m.Cb('x') / foo, "x") * m.Cb"x" *
    m.Cg(m.Cb('x') / foo, "x") * m.Cb"x" *
    m.Cg(m.Cb('x') / foo, "x") * m.Cb"x"
x = {p:match'ab'}
checkeq(x, {'abx', 'abxx', 'abxxx', 'abxxxx'})
checkeq(t, {'ab',
            'ab', 'abx',
            'ab', 'abx', 'abxx',
            'ab', 'abx', 'abxx', 'abxxx'})



-- tests for match-time captures

local function id (s, i, ...)
  return true, ...
end

assert(m.Cmt(m.Cs((m.Cmt(m.S'abc' / { a = 'x', c = 'y' }, id) +
              m.R'09'^1 /  string.char +
              m.P(1))^0), id):match"acb98+68c" == "xyb\98+\68y")

p = m.P{'S',
  S = m.V'atom' * space
    + m.Cmt(m.Ct("(" * space * (m.Cmt(m.V'S'^1, id) + m.P(true)) * ")" * space), id),
  atom = m.Cmt(m.C(m.R("AZ", "az", "09")^1), id)
}
x = p:match"(a g () ((b) c) (d (e)))"
checkeq(x, {'a', 'g', {}, {{'b'}, 'c'}, {'d', {'e'}}});

x = {(m.Cmt(1, id)^0):match(string.rep('a', 500))}
assert(#x == 500)

local function id(s, i, x)
  if x == 'a' then return i + 1, 1, 3, 7
  else return nil, 2, 4, 6, 8
  end   
end     

p = ((m.P(id) + m.Cmt(2, id)  + m.Cmt(1, id)))^0
assert(table.concat{p:match('abababab')} == string.rep('137', 4))

local function ref (s, i, x)
  return m.match(x, s, i - x:len())
end

assert(m.Cmt(m.P(1)^0, ref):match('alo') == 4)
assert((m.P(1) * m.Cmt(m.P(1)^0, ref)):match('alo') == 4)
assert(not (m.P(1) * m.Cmt(m.C(1)^0, ref)):match('alo'))

ref = function (s,i,x) return i == tonumber(x) and i, 'xuxu' end

assert(m.Cmt(1, ref):match'2')
assert(not m.Cmt(1, ref):match'1')
assert(m.Cmt(m.P(1)^0, ref):match'03')

function ref (s, i, a, b)
  if a == b then return i, a:upper() end
end

p = m.Cmt(m.C(m.R"az"^1) * "-" * m.C(m.R"az"^1), ref)
p = (any - p)^0 * p * any^0 * -1

assert(p:match'abbbc-bc ddaa' == 'BC')


c = '[' * m.Cg(m.P'='^0, "init") * '[' *
    { m.Cmt(']' * m.C(m.P'='^0) * ']' * m.Cb("init"), function (_, _, s1, s2)
                                               return s1 == s2 end)
       + 1 * m.V(1) } / function () end

assert(c:match'[==[]]====]]]]==]===[]' == 18)
assert(c:match'[[]=]====]=]]]==]===[]' == 14)
assert(not c:match'[[]=]====]=]=]==]===[]')



-------------------------------------------------------------------
-- Tests for 're' module
-------------------------------------------------------------------

local re = require "re"

local match, compile = re.match, re.compile



assert(match("a", ".") == 2)
assert(match("a", "''") == 1)
assert(match("", " ! . ") == 1)
assert(not match("a", " ! . "))
assert(match("abcde", "  ( . . ) * ") == 5)
assert(match("abbcde", " [a-c] +") == 5)
assert(match("0abbc1de", "'0' [a-c]+ '1'") == 7)
assert(match("0zz1dda", "'0' [^a-c]+ 'a'") == 8)
assert(match("abbc--", " [a-c] + +") == 5)
assert(match("abbc--", " [ac-] +") == 2)
assert(match("abbc--", " [-acb] + ") == 7)
assert(not match("abbcde", " [b-z] + "))
assert(match("abb\"de", '"abb"["]"de"') == 7)
assert(match("abceeef", "'ac' ? 'ab' * 'c' { 'e' * } / 'abceeef' ") == "eee")
assert(match("abceeef", "'ac'? 'ab'* 'c' { 'f'+ } / 'abceeef' ") == 8)
local t = {match("abceefe", "( ( & 'e' {} ) ? . ) * ")}
checkeq(t, {4, 5, 7})
local t = {match("abceefe", "((&&'e' {})? .)*")}
checkeq(t, {4, 5, 7})
local t = {match("abceefe", "( ( ! ! 'e' {} ) ? . ) *")}
checkeq(t, {4, 5, 7})
local t = {match("abceefe", "(( & ! & ! 'e' {})? .)*")}
checkeq(t, {4, 5, 7})

assert(match("cccx" , "'ab'? ('ccc' / ('cde' / 'cd'*)? / 'ccc') 'x'+") == 5)
assert(match("cdx" , "'ab'? ('ccc' / ('cde' / 'cd'*)? / 'ccc') 'x'+") == 4)
assert(match("abcdcdx" , "'ab'? ('ccc' / ('cde' / 'cd'*)? / 'ccc') 'x'+") == 8)

assert(match("abc", "a <- (. a)?") == 4)
b = "balanced <- '(' ([^()] / balanced)* ')'"
assert(match("(abc)", b))
assert(match("(a(b)((c) (d)))", b))
assert(not match("(a(b ((c) (d)))", b))

b = compile[[  balanced <- "(" ([^()] / balanced)* ")" ]]
assert(b == m.P(b))
assert(b:match"((((a))(b)))")

local g = [[
  S <- "0" B / "1" A / ""   -- balanced strings
  A <- "0" S / "1" A A      -- one more 0
  B <- "1" S / "0" B B      -- one more 1
]]
assert(match("00011011", g) == 9)

local g = [[
  S <- ("0" B / "1" A)*
  A <- "0" / "1" A A
  B <- "1" / "0" B B
]]
assert(match("00011011", g) == 9)
assert(match("000110110", g) == 9)
assert(match("011110110", g) == 3)
assert(match("000110010", g) == 1)

s = "aaaaaaaaaaaaaaaaaaaaaaaa"
assert(match(s, "'a'^3") == 4)
assert(match(s, "'a'^0") == 1)
assert(match(s, "'a'^+3") == s:len() + 1)
assert(not match(s, "'a'^+30"))
assert(match(s, "'a'^-30") == s:len() + 1)
assert(match(s, "'a'^-5") == 6)
for i = 1, s:len() do
  assert(match(s, string.format("'a'^+%d", i)) >= i + 1)
  assert(match(s, string.format("'a'^-%d", i)) <= i + 1)
  assert(match(s, string.format("'a'^%d", i)) == i + 1)
end
assert(match("01234567890123456789", "[0-9]^3+") == 19)


assert(match("01234567890123456789", "({....}{...}) -> '%2%1'") == "4560123")
t = match("0123456789", "{.}*->{}")
checkeq(t, {"0", "1", "2", "3", "4", "5", "6", "7", "8", "9"})
assert(match("012345", "( (..) -> '%0%0' ) -> {}")[1] == "0101")

eqcharset(compile"[]]", "]")
eqcharset(compile"[][]", m.S"[]")
eqcharset(compile"[]-]", m.S"-]")
eqcharset(compile"[-]", m.S"-")
eqcharset(compile"[az-]", m.S"a-z")
eqcharset(compile"[-az]", m.S"a-z")
eqcharset(compile"[a-z]", m.R"az")
eqcharset(compile"[]['\"]", m.S[[]['"]])

eqcharset(compile"[^]]", any - "]")
eqcharset(compile"[^][]", any - m.S"[]")
eqcharset(compile"[^]-]", any - m.S"-]")
eqcharset(compile"[^]-]", any - m.S"-]")
eqcharset(compile"[^-]", any - m.S"-")
eqcharset(compile"[^az-]", any - m.S"a-z")
eqcharset(compile"[^-az]", any - m.S"a-z")
eqcharset(compile"[^a-z]", any - m.R"az")
eqcharset(compile"[^]['\"]", any - m.S[[]['"]])

-- tests for comments in 're'
e = compile[[
A <- B   -- \t	\n %nl .<> <- -> --
B <- 'x'  --]]
assert(e:match'xy' == 2)

-- tests for 're' with pre-definitions
defs = {digits = m.R"09", letters = m.R"az"}
e = compile("%letters (%letters / %digits)*", defs)
assert(e:match"x123" == 5)

e = compile([[
  S <- A+
  A <- %letters+ B
  B <- %digits+
]], defs)

e = compile("{[0-9]+'.'?[0-9]*} -> sin", math)
assert(e:match("2.34") == math.sin(2.34))


function eq (_, _, a, b) return a == b end

c = re.compile([[
  longstring <- '[' {:init: '='* :} '[' close
  close <- ']' =init ']' / . close
]])

assert(c:match'[==[]]===]]]]==]===[]' == 17)
assert(c:match'[[]=]====]=]]]==]===[]' == 14)
assert(not c:match'[[]=]====]=]=]==]===[]')

c = re.compile" '[' {:init: '='* :} '[' (!(']' =init ']') .)* ']' =init ']' !. "

assert(c:match'[==[]]===]]]]==]')
assert(c:match'[[]=]====]=][]==]===[]]')
assert(not c:match'[[]=]====]=]=]==]===[]')

assert(re.find("hi alalo", "{:x:..:} =x") == 4)
assert(re.find("hi alalo", "{:x:..:} =x", 4) == 4)
assert(not re.find("hi alalo", "{:x:..:} =x", 5))
assert(re.find("hi alalo", "'al'", 5) == 6)
assert(re.find("hi aloalolo", "{:x:..:} =x") == 8)
assert(re.find("alo alohi x x", "{:word:%w+:}%W*(=word)!%w") == 11)

assert(re.gsub("alo alo", "[abc]", "x") == "xlo xlo")
assert(re.gsub("alo alo", "%w+", ".") == ". .")
assert(re.gsub("hi, how are you", "[aeiou]", string.upper) ==
               "hI, hOw ArE yOU")

s = 'hi [[a comment[=]=] ending here]] and [=[another]]=]]'
c = re.compile" '[' {:i: '='* :} '[' (!(']' =i ']') .)* ']' { =i } ']' "
assert(re.gsub(s, c, "%2") == 'hi  and =]')
assert(re.gsub(s, c, "%0") == s)
assert(re.gsub('[=[hi]=]', c, "%2") == '=')

assert(re.find("", "!.") == 1)
assert(re.find("alo", "!.") == 4)

function addtag (s, i, t, tag) t.tag = tag; return i, t end

c = re.compile([[
  doc <- block !.
  block <- (start (block / { [^<]+ })* -> {} end?) => addtag
  start <- '<' {:tag: [a-z]+ :} '>'
  end <- ''
]], {addtag = addtag})

x = c:match[[
hihellobuttotheend]]
checkeq(x, {tag='x', 'hi', {tag = 'b', 'hello'}, 'but',
                     {'totheend'}})

assert(not pcall(compile, "x <- 'a'  x <- 'b'"))
assert(not pcall(compile, "'x' -> x", {x = 3}))


-- tests for look-ahead captures
x = {re.match("alo", "&(&{.}) !{'b'} {&(...)} &{..} {...} {!.}")}
checkeq(x, {"", "alo", ""})

assert(re.match("aloalo",
   "{~ (((&'al' {.}) -> 'A%1' / (&%l {.}) -> '%1%1') / .)* ~}")
       == "AallooAalloo")

-- bug in 0.9 (and older versions), due to captures in look-aheads
x = re.compile[[   {~ (&(. ([a-z]* -> '*')) ([a-z]+ -> '+') ' '*)* ~}  ]]
assert(x:match"alo alo" == "+ +")

-- valid capture in look-ahead (used inside the look-ahead itself)
x = re.compile[[
      S <- &({:two: .. :} . =two) {[a-z]+} / . S
]]
assert(x:match("hello aloaLo aloalo xuxu") == "aloalo")


p = re.compile[[
  block <- ({:ident:' '*:} line
           ((=ident !' ' line) / &(=ident ' ') block)*) -> {}
  line <- {[^%nl]*} %nl
]]

t= p:match[[
1
  1.1
  1.2
    1.2.1
    
2
  2.1
]]
checkeq(t, {"1", {"1.1", "1.2", {"1.2.1", "", ident = "    "}, ident = "  "},
            "2", {"2.1", ident = "  "}, ident = ""})


-- nested grammars
p = re.compile[[
       s <- a b !.
       b <- ( x <- ('b' x)? )
       a <- ( x <- 'a' x? )
]]

assert(p:match'aaabbb')
assert(p:match'aaa')
assert(not p:match'bbb')
assert(not p:match'aaabbba')

-- testing groups
t = {re.match("abc", "{:S <- {:.:} {S} / '':}")}
checkeq(t, {"a", "bc", "b", "c", "c", ""})

t = re.match("1234", "({:a:.:} {:b:.:} {:c:.{.}:}) -> {}")
checkeq(t, {a="1", b="2", c="4"})
t = re.match("1234", "({:a:.:} {:b:{.}{.}:} {:c:{.}:}) -> {}")
checkeq(t, {a="1", b="2", c="4"})
t = re.match("12345", "({:.:} {:b:{.}{.}:} {:{.}{.}:}) -> {}")
checkeq(t, {"1", b="2", "4", "5"})
t = re.match("12345", "({:.:} {:{:b:{.}{.}:}:} {:{.}{.}:}) -> {}")
checkeq(t, {"1", "23", "4", "5"})
t = re.match("12345", "({:.:} {{:b:{.}{.}:}} {:{.}{.}:}) -> {}")
checkeq(t, {"1", "23", "4", "5"})


-- testing pre-defined names
assert(os.setlocale("C") == "C")

function eqlpeggsub (p1, p2)
  local s1 = cs2str(re.compile(p1))
  local s2 = string.gsub(allchar, "[^" .. p2 .. "]", "")
if s1 ~= s2 then print(s1,s2) end
  assert(s1 == s2)
end


eqlpeggsub("%w", "%w")
eqlpeggsub("%a", "%a")
eqlpeggsub("%l", "%l")
eqlpeggsub("%u", "%u")
eqlpeggsub("%p", "%p")
eqlpeggsub("%d", "%d")
eqlpeggsub("%x", "%x")
eqlpeggsub("%s", "%s")

eqlpeggsub("%W", "%W")
eqlpeggsub("%A", "%A")
eqlpeggsub("%L", "%L")
eqlpeggsub("%U", "%U")
eqlpeggsub("%P", "%P")
eqlpeggsub("%D", "%D")
eqlpeggsub("%X", "%X")
eqlpeggsub("%S", "%S")

eqlpeggsub("[%w]", "%w")
eqlpeggsub("[_%w]", "_%w")
eqlpeggsub("[^%w]", "%W")
eqlpeggsub("[%W%S]", "%W%S")

re.updatelocale()


-- testing nested substitutions x string captures

p = re.compile[[
      text <- {~ item* ~}
      item <- macro / [^()] / '(' item* ')'
      arg <- ' '* {~ (!',' item)* ~}
      args <- '(' arg (',' arg)* ')'
      macro <- ('apply' args) -> '%1(%2)'
             / ('add' args) -> '%1 + %2'
             / ('mul' args) -> '%1 * %2'
]]

assert(p:match"add(mul(a,b), apply(f,x))" == "a * b + f(x)")

rev = re.compile[[ R <- (!.) -> '' / ({.} R) -> '%2%1']]

assert(rev:match"0123456789" == "9876543210")

print"OK"


genometools-1.5.1/src/external/lua-5.1.5/000077500000000000000000000000001211610345200177025ustar00rootroot00000000000000genometools-1.5.1/src/external/lua-5.1.5/COPYRIGHT000066400000000000000000000027701211610345200212030ustar00rootroot00000000000000Lua License
-----------

Lua is licensed under the terms of the MIT license reproduced below.
This means that Lua is free software and can be used for both academic
and commercial purposes at absolutely no cost.

For details and rationale, see http://www.lua.org/license.html .

===============================================================================

Copyright (C) 1994-2012 Lua.org, PUC-Rio.

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

===============================================================================

(end of COPYRIGHT)
genometools-1.5.1/src/external/lua-5.1.5/HISTORY000066400000000000000000000173431211610345200207760ustar00rootroot00000000000000HISTORY for Lua 5.1

* Changes from version 5.0 to 5.1
  -------------------------------
  Language:
  + new module system.
  + new semantics for control variables of fors.
  + new semantics for setn/getn.
  + new syntax/semantics for varargs.
  + new long strings and comments.
  + new `mod' operator (`%')
  + new length operator #t
  + metatables for all types
  API:
  + new functions: lua_createtable, lua_get(set)field, lua_push(to)integer.
  + user supplies memory allocator (lua_open becomes lua_newstate).
  + luaopen_* functions must be called through Lua.
  Implementation:
  + new configuration scheme via luaconf.h.
  + incremental garbage collection.
  + better handling of end-of-line in the lexer.
  + fully reentrant parser (new Lua function `load')
  + better support for 64-bit machines.
  + native loadlib support for Mac OS X.
  + standard distribution in only one library (lualib.a merged into lua.a)

* Changes from version 4.0 to 5.0
  -------------------------------
  Language:
  + lexical scoping.
  + Lua coroutines.
  + standard libraries now packaged in tables.
  + tags replaced by metatables and tag methods replaced by metamethods,
    stored in metatables.
  + proper tail calls.
  + each function can have its own global table, which can be shared.
  + new __newindex metamethod, called when we insert a new key into a table.
  + new block comments: --[[ ... ]].
  + new generic for.
  + new weak tables.
  + new boolean type.
  + new syntax "local function".
  + (f()) returns the first value returned by f.
  + {f()} fills a table with all values returned by f.
  + \n ignored in [[\n .
  + fixed and-or priorities.
  + more general syntax for function definition (e.g. function a.x.y:f()...end).
  + more general syntax for function calls (e.g. (print or write)(9)).
  + new functions (time/date, tmpfile, unpack, require, load*, etc.).
  API:
  + chunks are loaded by using lua_load; new luaL_loadfile and luaL_loadbuffer.
  + introduced lightweight userdata, a simple "void*" without a metatable.
  + new error handling protocol: the core no longer prints error messages;
    all errors are reported to the caller on the stack.
  + new lua_atpanic for host cleanup.
  + new, signal-safe, hook scheme.
  Implementation:
  + new license: MIT.
  + new, faster, register-based virtual machine.
  + support for external multithreading and coroutines.
  + new and consistent error message format.
  + the core no longer needs "stdio.h" for anything (except for a single
    use of sprintf to convert numbers to strings).
  + lua.c now runs the environment variable LUA_INIT, if present. It can
    be "@filename", to run a file, or the chunk itself.
  + support for user extensions in lua.c.
    sample implementation given for command line editing.
  + new dynamic loading library, active by default on several platforms.
  + safe garbage-collector metamethods.
  + precompiled bytecodes checked for integrity (secure binary dostring).
  + strings are fully aligned.
  + position capture in string.find.
  + read('*l') can read lines with embedded zeros.

* Changes from version 3.2 to 4.0
  -------------------------------
  Language:
  + new "break" and "for" statements (both numerical and for tables).
  + uniform treatment of globals: globals are now stored in a Lua table.
  + improved error messages.
  + no more '$debug': full speed *and* full debug information.
  + new read form: read(N) for next N bytes.
  + general read patterns now deprecated.
    (still available with -DCOMPAT_READPATTERNS.)
  + all return values are passed as arguments for the last function
    (old semantics still available with -DLUA_COMPAT_ARGRET)
  + garbage collection tag methods for tables now deprecated.
  + there is now only one tag method for order.
  API:
  + New API: fully re-entrant, simpler, and more efficient.
  + New debug API.
  Implementation:
  + faster than ever: cleaner virtual machine and new hashing algorithm.
  + non-recursive garbage-collector algorithm.
  + reduced memory usage for programs with many strings.
  + improved treatment for memory allocation errors.
  + improved support for 16-bit machines (we hope).
  + code now compiles unmodified as both ANSI C and C++.
  + numbers in bases other than 10 are converted using strtoul.
  + new -f option in Lua to support #! scripts.
  + luac can now combine text and binaries.

* Changes from version 3.1 to 3.2
  -------------------------------
  + redirected all output in Lua's core to _ERRORMESSAGE and _ALERT.
  + increased limit on the number of constants and globals per function
    (from 2^16 to 2^24).
  + debugging info (lua_debug and hooks) moved into lua_state and new API
    functions provided to get and set this info.
  + new debug lib gives full debugging access within Lua.
  + new table functions "foreachi", "sort", "tinsert", "tremove", "getn".
  + new io functions "flush", "seek".

* Changes from version 3.0 to 3.1
  -------------------------------
  + NEW FEATURE: anonymous functions with closures (via "upvalues").
  + new syntax:
    - local variables in chunks.
    - better scope control with DO block END.
    - constructors can now be also written: { record-part; list-part }.
    - more general syntax for function calls and lvalues, e.g.:
      f(x).y=1
      o:f(x,y):g(z)
      f"string" is sugar for f("string")
  + strings may now contain arbitrary binary data (e.g., embedded zeros).
  + major code re-organization and clean-up; reduced module interdependecies.
  + no arbitrary limits on the total number of constants and globals.
  + support for multiple global contexts.
  + better syntax error messages.
  + new traversal functions "foreach" and "foreachvar".
  + the default for numbers is now double.
    changing it to use floats or longs is easy.
  + complete debug information stored in pre-compiled chunks.
  + sample interpreter now prompts user when run interactively, and also
    handles control-C interruptions gracefully.

* Changes from version 2.5 to 3.0
  -------------------------------
  + NEW CONCEPT: "tag methods".
    Tag methods replace fallbacks as the meta-mechanism for extending the
    semantics of Lua. Whereas fallbacks had a global nature, tag methods
    work on objects having the same tag (e.g., groups of tables).
    Existing code that uses fallbacks should work without change.
  + new, general syntax for constructors {[exp] = exp, ... }.
  + support for handling variable number of arguments in functions (varargs).
  + support for conditional compilation ($if ... $else ... $end).
  + cleaner semantics in API simplifies host code.
  + better support for writing libraries (auxlib.h).
  + better type checking and error messages in the standard library.
  + luac can now also undump.

* Changes from version 2.4 to 2.5
  -------------------------------
  + io and string libraries are now based on pattern matching;
    the old libraries are still available for compatibility
  + dofile and dostring can now return values (via return statement)
  + better support for 16- and 64-bit machines
  + expanded documentation, with more examples

* Changes from version 2.2 to 2.4
  -------------------------------
  + external compiler creates portable binary files that can be loaded faster
  + interface for debugging and profiling
  + new "getglobal" fallback
  + new functions for handling references to Lua objects
  + new functions in standard lib
  + only one copy of each string is stored
  + expanded documentation, with more examples

* Changes from version 2.1 to 2.2
  -------------------------------
  + functions now may be declared with any "lvalue" as a name
  + garbage collection of functions
  + support for pipes

* Changes from version 1.1 to 2.1
  -------------------------------
  + object-oriented support
  + fallbacks
  + simplified syntax for tables
  + many internal improvements

(end of HISTORY)
genometools-1.5.1/src/external/lua-5.1.5/INSTALL000066400000000000000000000074341211610345200207430ustar00rootroot00000000000000INSTALL for Lua 5.1

* Building Lua
  ------------
  Lua is built in the src directory, but the build process can be
  controlled from the top-level Makefile.

  Building Lua on Unix systems should be very easy. First do "make" and
  see if your platform is listed. If so, just do "make xxx", where xxx
  is your platform name. The platforms currently supported are:
    aix ansi bsd freebsd generic linux macosx mingw posix solaris

  If your platform is not listed, try the closest one or posix, generic,
  ansi, in this order.

  See below for customization instructions and for instructions on how
  to build with other Windows compilers.

  If you want to check that Lua has been built correctly, do "make test"
  after building Lua. Also, have a look at the example programs in test.

* Installing Lua
  --------------
  Once you have built Lua, you may want to install it in an official
  place in your system. In this case, do "make install". The official
  place and the way to install files are defined in Makefile. You must
  have the right permissions to install files.

  If you want to build and install Lua in one step, do "make xxx install",
  where xxx is your platform name.

  If you want to install Lua locally, then do "make local". This will
  create directories bin, include, lib, man, and install Lua there as
  follows:

    bin:	lua luac
    include:	lua.h luaconf.h lualib.h lauxlib.h lua.hpp
    lib:	liblua.a
    man/man1:	lua.1 luac.1

  These are the only directories you need for development.

  There are man pages for lua and luac, in both nroff and html, and a
  reference manual in html in doc, some sample code in test, and some
  useful stuff in etc. You don't need these directories for development.

  If you want to install Lua locally, but in some other directory, do
  "make install INSTALL_TOP=xxx", where xxx is your chosen directory.

  See below for instructions for Windows and other systems.

* Customization
  -------------
  Three things can be customized by editing a file:
    - Where and how to install Lua -- edit Makefile.
    - How to build Lua -- edit src/Makefile.
    - Lua features -- edit src/luaconf.h.

  You don't actually need to edit the Makefiles because you may set the
  relevant variables when invoking make.

  On the other hand, if you need to select some Lua features, you'll need
  to edit src/luaconf.h. The edited file will be the one installed, and
  it will be used by any Lua clients that you build, to ensure consistency.

  We strongly recommend that you enable dynamic loading. This is done
  automatically for all platforms listed above that have this feature
  (and also Windows). See src/luaconf.h and also src/Makefile.

* Building Lua on Windows and other systems
  -----------------------------------------
  If you're not using the usual Unix tools, then the instructions for
  building Lua depend on the compiler you use. You'll need to create
  projects (or whatever your compiler uses) for building the library,
  the interpreter, and the compiler, as follows:

  library:	lapi.c lcode.c ldebug.c ldo.c ldump.c lfunc.c lgc.c llex.c
		lmem.c lobject.c lopcodes.c lparser.c lstate.c lstring.c
		ltable.c ltm.c lundump.c lvm.c lzio.c
		lauxlib.c lbaselib.c ldblib.c liolib.c lmathlib.c loslib.c
		ltablib.c lstrlib.c loadlib.c linit.c

  interpreter:	library, lua.c

  compiler:	library, luac.c print.c

  If you use Visual Studio .NET, you can use etc/luavs.bat in its
  "Command Prompt".

  If all you want is to build the Lua interpreter, you may put all .c files
  in a single project, except for luac.c and print.c. Or just use etc/all.c.

  To use Lua as a library in your own programs, you'll need to know how to
  create and use libraries with your compiler.

  As mentioned above, you may edit luaconf.h to select some features before
  building Lua.

(end of INSTALL)
genometools-1.5.1/src/external/lua-5.1.5/Makefile000066400000000000000000000071571211610345200213540ustar00rootroot00000000000000# makefile for installing Lua
# see INSTALL for installation instructions
# see src/Makefile and src/luaconf.h for further customization

# == CHANGE THE SETTINGS BELOW TO SUIT YOUR ENVIRONMENT =======================

# Your platform. See PLATS for possible values.
PLAT= none

# Where to install. The installation starts in the src and doc directories,
# so take care if INSTALL_TOP is not an absolute path.
INSTALL_TOP= /usr/local
INSTALL_BIN= $(INSTALL_TOP)/bin
INSTALL_INC= $(INSTALL_TOP)/include
INSTALL_LIB= $(INSTALL_TOP)/lib
INSTALL_MAN= $(INSTALL_TOP)/man/man1
#
# You probably want to make INSTALL_LMOD and INSTALL_CMOD consistent with
# LUA_ROOT, LUA_LDIR, and LUA_CDIR in luaconf.h (and also with etc/lua.pc).
INSTALL_LMOD= $(INSTALL_TOP)/share/lua/$V
INSTALL_CMOD= $(INSTALL_TOP)/lib/lua/$V

# How to install. If your install program does not support "-p", then you
# may have to run ranlib on the installed liblua.a (do "make ranlib").
INSTALL= install -p
INSTALL_EXEC= $(INSTALL) -m 0755
INSTALL_DATA= $(INSTALL) -m 0644
#
# If you don't have install you can use cp instead.
# INSTALL= cp -p
# INSTALL_EXEC= $(INSTALL)
# INSTALL_DATA= $(INSTALL)

# Utilities.
MKDIR= mkdir -p
RANLIB= ranlib

# == END OF USER SETTINGS. NO NEED TO CHANGE ANYTHING BELOW THIS LINE =========

# Convenience platforms targets.
PLATS= aix ansi bsd freebsd generic linux macosx mingw posix solaris

# What to install.
TO_BIN= lua luac
TO_INC= lua.h luaconf.h lualib.h lauxlib.h ../etc/lua.hpp
TO_LIB= liblua.a
TO_MAN= lua.1 luac.1

# Lua version and release.
V= 5.1
R= 5.1.5

all:	$(PLAT)

$(PLATS) clean:
	cd src && $(MAKE) $@

test:	dummy
	src/lua test/hello.lua

install: dummy
	cd src && $(MKDIR) $(INSTALL_BIN) $(INSTALL_INC) $(INSTALL_LIB) $(INSTALL_MAN) $(INSTALL_LMOD) $(INSTALL_CMOD)
	cd src && $(INSTALL_EXEC) $(TO_BIN) $(INSTALL_BIN)
	cd src && $(INSTALL_DATA) $(TO_INC) $(INSTALL_INC)
	cd src && $(INSTALL_DATA) $(TO_LIB) $(INSTALL_LIB)
	cd doc && $(INSTALL_DATA) $(TO_MAN) $(INSTALL_MAN)

ranlib:
	cd src && cd $(INSTALL_LIB) && $(RANLIB) $(TO_LIB)

local:
	$(MAKE) install INSTALL_TOP=..

none:
	@echo "Please do"
	@echo "   make PLATFORM"
	@echo "where PLATFORM is one of these:"
	@echo "   $(PLATS)"
	@echo "See INSTALL for complete instructions."

# make may get confused with test/ and INSTALL in a case-insensitive OS
dummy:

# echo config parameters
echo:
	@echo ""
	@echo "These are the parameters currently set in src/Makefile to build Lua $R:"
	@echo ""
	@cd src && $(MAKE) -s echo
	@echo ""
	@echo "These are the parameters currently set in Makefile to install Lua $R:"
	@echo ""
	@echo "PLAT = $(PLAT)"
	@echo "INSTALL_TOP = $(INSTALL_TOP)"
	@echo "INSTALL_BIN = $(INSTALL_BIN)"
	@echo "INSTALL_INC = $(INSTALL_INC)"
	@echo "INSTALL_LIB = $(INSTALL_LIB)"
	@echo "INSTALL_MAN = $(INSTALL_MAN)"
	@echo "INSTALL_LMOD = $(INSTALL_LMOD)"
	@echo "INSTALL_CMOD = $(INSTALL_CMOD)"
	@echo "INSTALL_EXEC = $(INSTALL_EXEC)"
	@echo "INSTALL_DATA = $(INSTALL_DATA)"
	@echo ""
	@echo "See also src/luaconf.h ."
	@echo ""

# echo private config parameters
pecho:
	@echo "V = $(V)"
	@echo "R = $(R)"
	@echo "TO_BIN = $(TO_BIN)"
	@echo "TO_INC = $(TO_INC)"
	@echo "TO_LIB = $(TO_LIB)"
	@echo "TO_MAN = $(TO_MAN)"

# echo config parameters as Lua code
# uncomment the last sed expression if you want nil instead of empty strings
lecho:
	@echo "-- installation parameters for Lua $R"
	@echo "VERSION = '$V'"
	@echo "RELEASE = '$R'"
	@$(MAKE) echo | grep = | sed -e 's/= /= "/' -e 's/$$/"/' #-e 's/""/nil/'
	@echo "-- EOF"

# list targets that do not create files (but not all makes understand .PHONY)
.PHONY: all $(PLATS) clean test install local none dummy echo pecho lecho

# (end of Makefile)
genometools-1.5.1/src/external/lua-5.1.5/README000066400000000000000000000025421211610345200205650ustar00rootroot00000000000000README for Lua 5.1

See INSTALL for installation instructions.
See HISTORY for a summary of changes since the last released version.

* What is Lua?
  ------------
  Lua is a powerful, light-weight programming language designed for extending
  applications. Lua is also frequently used as a general-purpose, stand-alone
  language. Lua is free software.

  For complete information, visit Lua's web site at http://www.lua.org/ .
  For an executive summary, see http://www.lua.org/about.html .

  Lua has been used in many different projects around the world.
  For a short list, see http://www.lua.org/uses.html .

* Availability
  ------------
  Lua is freely available for both academic and commercial purposes.
  See COPYRIGHT and http://www.lua.org/license.html for details.
  Lua can be downloaded at http://www.lua.org/download.html .

* Installation
  ------------
  Lua is implemented in pure ANSI C, and compiles unmodified in all known
  platforms that have an ANSI C compiler. In most Unix-like platforms, simply
  do "make" with a suitable target. See INSTALL for detailed instructions.

* Origin
  ------
  Lua is developed at Lua.org, a laboratory of the Department of Computer
  Science of PUC-Rio (the Pontifical Catholic University of Rio de Janeiro
  in Brazil).
  For more information about the authors, see http://www.lua.org/authors.html .

(end of README)
genometools-1.5.1/src/external/lua-5.1.5/doc/000077500000000000000000000000001211610345200204475ustar00rootroot00000000000000genometools-1.5.1/src/external/lua-5.1.5/doc/contents.html000066400000000000000000000537221211610345200232030ustar00rootroot00000000000000


Lua 5.1 Reference Manual - contents












Lua 5.1 Reference Manual





The reference manual is the official definition of the Lua language.
For a complete introduction to Lua programming, see the book
Programming in Lua.



This manual is also available as a book:





Lua 5.1 Reference Manual

by R. Ierusalimschy, L. H. de Figueiredo, W. Celes

Lua.org, August 2006

ISBN 85-903798-3-3







Buy a copy
of this book and
help to support
the Lua project.



start
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Copyright © 2006–2012 Lua.org, PUC-Rio.
Freely available under the terms of the
Lua license.



Contents




Index







Lua functions

_G

_VERSION




assert

collectgarbage

dofile

error

getfenv

getmetatable

ipairs

load

loadfile

loadstring

module

next

pairs

pcall

print

rawequal

rawget

rawset

require

select

setfenv

setmetatable

tonumber

tostring

type

unpack

xpcall




coroutine.create

coroutine.resume

coroutine.running

coroutine.status

coroutine.wrap

coroutine.yield




debug.debug

debug.getfenv

debug.gethook

debug.getinfo

debug.getlocal

debug.getmetatable

debug.getregistry

debug.getupvalue

debug.setfenv

debug.sethook

debug.setlocal

debug.setmetatable

debug.setupvalue

debug.traceback






 

file:close

file:flush

file:lines

file:read

file:seek

file:setvbuf

file:write




io.close

io.flush

io.input

io.lines

io.open

io.output

io.popen

io.read

io.stderr

io.stdin

io.stdout

io.tmpfile

io.type

io.write




math.abs

math.acos

math.asin

math.atan

math.atan2

math.ceil

math.cos

math.cosh

math.deg

math.exp

math.floor

math.fmod

math.frexp

math.huge

math.ldexp

math.log

math.log10

math.max

math.min

math.modf

math.pi

math.pow

math.rad

math.random

math.randomseed

math.sin

math.sinh

math.sqrt

math.tan

math.tanh




os.clock

os.date

os.difftime

os.execute

os.exit

os.getenv

os.remove

os.rename

os.setlocale

os.time

os.tmpname




package.cpath

package.loaded

package.loaders

package.loadlib

package.path

package.preload

package.seeall




string.byte

string.char

string.dump

string.find

string.format

string.gmatch

string.gsub

string.len

string.lower

string.match

string.rep

string.reverse

string.sub

string.upper




table.concat

table.insert

table.maxn

table.remove

table.sort






C API

lua_Alloc

lua_CFunction

lua_Debug

lua_Hook

lua_Integer

lua_Number

lua_Reader

lua_State

lua_Writer




lua_atpanic

lua_call

lua_checkstack

lua_close

lua_concat

lua_cpcall

lua_createtable

lua_dump

lua_equal

lua_error

lua_gc

lua_getallocf

lua_getfenv

lua_getfield

lua_getglobal

lua_gethook

lua_gethookcount

lua_gethookmask

lua_getinfo

lua_getlocal

lua_getmetatable

lua_getstack

lua_gettable

lua_gettop

lua_getupvalue

lua_insert

lua_isboolean

lua_iscfunction

lua_isfunction

lua_islightuserdata

lua_isnil

lua_isnone

lua_isnoneornil

lua_isnumber

lua_isstring

lua_istable

lua_isthread

lua_isuserdata

lua_lessthan

lua_load

lua_newstate

lua_newtable

lua_newthread

lua_newuserdata

lua_next

lua_objlen

lua_pcall

lua_pop

lua_pushboolean

lua_pushcclosure

lua_pushcfunction

lua_pushfstring

lua_pushinteger

lua_pushlightuserdata

lua_pushliteral

lua_pushlstring

lua_pushnil

lua_pushnumber

lua_pushstring

lua_pushthread

lua_pushvalue

lua_pushvfstring

lua_rawequal

lua_rawget

lua_rawgeti

lua_rawset

lua_rawseti

lua_register

lua_remove

lua_replace

lua_resume

lua_setallocf

lua_setfenv

lua_setfield

lua_setglobal

lua_sethook

lua_setlocal

lua_setmetatable

lua_settable

lua_settop

lua_setupvalue

lua_status

lua_toboolean

lua_tocfunction

lua_tointeger

lua_tolstring

lua_tonumber

lua_topointer

lua_tostring

lua_tothread

lua_touserdata

lua_type

lua_typename

lua_upvalueindex

lua_xmove

lua_yield






auxiliary library

luaL_Buffer

luaL_Reg




luaL_addchar

luaL_addlstring

luaL_addsize

luaL_addstring

luaL_addvalue

luaL_argcheck

luaL_argerror

luaL_buffinit

luaL_callmeta

luaL_checkany

luaL_checkint

luaL_checkinteger

luaL_checklong

luaL_checklstring

luaL_checknumber

luaL_checkoption

luaL_checkstack

luaL_checkstring

luaL_checktype

luaL_checkudata

luaL_dofile

luaL_dostring

luaL_error

luaL_getmetafield

luaL_getmetatable

luaL_gsub

luaL_loadbuffer

luaL_loadfile

luaL_loadstring

luaL_newmetatable

luaL_newstate

luaL_openlibs

luaL_optint

luaL_optinteger

luaL_optlong

luaL_optlstring

luaL_optnumber

luaL_optstring

luaL_prepbuffer

luaL_pushresult

luaL_ref

luaL_register

luaL_typename

luaL_typerror

luaL_unref

luaL_where














Last update:
Mon Feb 13 18:53:32 BRST 2012





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1{:LSPU@QzRʪ#4PG`Nڬ;genometools-1.5.1/src/external/lua-5.1.5/doc/lua.1000066400000000000000000000070431211610345200213160ustar00rootroot00000000000000.\" $Id: lua.man,v 1.11 2006/01/06 16:03:34 lhf Exp $
.TH LUA 1 "$Date: 2006/01/06 16:03:34 $"
.SH NAME
lua \- Lua interpreter
.SH SYNOPSIS
.B lua
[
.I options
]
[
.I script
[
.I args
]
]
.SH DESCRIPTION
.B lua
is the stand-alone Lua interpreter.
It loads and executes Lua programs,
either in textual source form or
in precompiled binary form.
(Precompiled binaries are output by
.BR luac ,
the Lua compiler.)
.B lua
can be used as a batch interpreter and also interactively.
.LP
The given
.I options
(see below)
are executed and then
the Lua program in file
.I script
is loaded and executed.
The given
.I args
are available to
.I script
as strings in a global table named
.BR arg .
If these arguments contain spaces or other characters special to the shell,
then they should be quoted
(but note that the quotes will be removed by the shell).
The arguments in
.B arg
start at 0,
which contains the string
.RI ' script '.
The index of the last argument is stored in
.BR arg.n .
The arguments given in the command line before
.IR script ,
including the name of the interpreter,
are available in negative indices in
.BR arg .
.LP
At the very start,
before even handling the command line,
.B lua
executes the contents of the environment variable
.BR LUA_INIT ,
if it is defined.
If the value of
.B LUA_INIT
is of the form
.RI '@ filename ',
then
.I filename
is executed.
Otherwise, the string is assumed to be a Lua statement and is executed.
.LP
Options start with
.B '\-'
and are described below.
You can use
.B "'\--'"
to signal the end of options.
.LP
If no arguments are given,
then
.B "\-v \-i"
is assumed when the standard input is a terminal;
otherwise,
.B "\-"
is assumed.
.LP
In interactive mode,
.B lua
prompts the user,
reads lines from the standard input,
and executes them as they are read.
If a line does not contain a complete statement,
then a secondary prompt is displayed and
lines are read until a complete statement is formed or
a syntax error is found.
So, one way to interrupt the reading of an incomplete statement is
to force a syntax error:
adding a
.B ';' 
in the middle of a statement is a sure way of forcing a syntax error
(except inside multiline strings and comments; these must be closed explicitly).
If a line starts with
.BR '=' ,
then
.B lua
displays the values of all the expressions in the remainder of the
line. The expressions must be separated by commas.
The primary prompt is the value of the global variable
.BR _PROMPT ,
if this value is a string;
otherwise, the default prompt is used.
Similarly, the secondary prompt is the value of the global variable
.BR _PROMPT2 .
So,
to change the prompts,
set the corresponding variable to a string of your choice.
You can do that after calling the interpreter
or on the command line
(but in this case you have to be careful with quotes
if the prompt string contains a space; otherwise you may confuse the shell.)
The default prompts are "> " and ">> ".
.SH OPTIONS
.TP
.B \-
load and execute the standard input as a file,
that is,
not interactively,
even when the standard input is a terminal.
.TP
.BI \-e " stat"
execute statement
.IR stat .
You need to quote
.I stat 
if it contains spaces, quotes,
or other characters special to the shell.
.TP
.B \-i
enter interactive mode after
.I script
is executed.
.TP
.BI \-l " name"
call
.BI require(' name ')
before executing
.IR script .
Typically used to load libraries.
.TP
.B \-v
show version information.
.SH "SEE ALSO"
.BR luac (1)
.br
http://www.lua.org/
.SH DIAGNOSTICS
Error messages should be self explanatory.
.SH AUTHORS
R. Ierusalimschy,
L. H. de Figueiredo,
and
W. Celes
.\" EOF
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genometools-1.5.1/src/external/lua-5.1.5/doc/lua.html000066400000000000000000000075571211610345200221340ustar00rootroot00000000000000


LUA man page






NAME

lua - Lua interpreter

SYNOPSIS

lua
[
options
]
[
script
[
args
]
]

DESCRIPTION

lua
is the stand-alone Lua interpreter.
It loads and executes Lua programs,
either in textual source form or
in precompiled binary form.
(Precompiled binaries are output by
luac,
the Lua compiler.)
lua
can be used as a batch interpreter and also interactively.


The given
options
(see below)
are executed and then
the Lua program in file
script
is loaded and executed.
The given
args
are available to
script
as strings in a global table named
arg.
If these arguments contain spaces or other characters special to the shell,
then they should be quoted
(but note that the quotes will be removed by the shell).
The arguments in
arg
start at 0,
which contains the string
'script'.
The index of the last argument is stored in
arg.n.
The arguments given in the command line before
script,
including the name of the interpreter,
are available in negative indices in
arg.


At the very start,
before even handling the command line,
lua
executes the contents of the environment variable
LUA_INIT,
if it is defined.
If the value of
LUA_INIT
is of the form
'@filename',
then
filename
is executed.
Otherwise, the string is assumed to be a Lua statement and is executed.


Options start with
'-'
and are described below.
You can use
'--'
to signal the end of options.


If no arguments are given,
then
"-v -i"
is assumed when the standard input is a terminal;
otherwise,
"-"
is assumed.


In interactive mode,
lua
prompts the user,
reads lines from the standard input,
and executes them as they are read.
If a line does not contain a complete statement,
then a secondary prompt is displayed and
lines are read until a complete statement is formed or
a syntax error is found.
So, one way to interrupt the reading of an incomplete statement is
to force a syntax error:
adding a
';'
in the middle of a statement is a sure way of forcing a syntax error
(except inside multiline strings and comments; these must be closed explicitly).
If a line starts with
'=',
then
lua
displays the values of all the expressions in the remainder of the
line. The expressions must be separated by commas.
The primary prompt is the value of the global variable
_PROMPT,
if this value is a string;
otherwise, the default prompt is used.
Similarly, the secondary prompt is the value of the global variable
_PROMPT2.
So,
to change the prompts,
set the corresponding variable to a string of your choice.
You can do that after calling the interpreter
or on the command line
(but in this case you have to be careful with quotes
if the prompt string contains a space; otherwise you may confuse the shell.)
The default prompts are "> " and ">> ".

OPTIONS



-
load and execute the standard input as a file,
that is,
not interactively,
even when the standard input is a terminal.


-e stat
execute statement
stat.
You need to quote
stat 
if it contains spaces, quotes,
or other characters special to the shell.


-i
enter interactive mode after
script
is executed.


-l name
call
require('name')
before executing
script.
Typically used to load libraries.


-v
show version information.

SEE ALSO

luac(1)


http://www.lua.org/

DIAGNOSTICS

Error messages should be self explanatory.

AUTHORS

R. Ierusalimschy,
L. H. de Figueiredo,
and
W. Celes



genometools-1.5.1/src/external/lua-5.1.5/doc/luac.1000066400000000000000000000070411211610345200214570ustar00rootroot00000000000000.\" $Id: luac.man,v 1.28 2006/01/06 16:03:34 lhf Exp $
.TH LUAC 1 "$Date: 2006/01/06 16:03:34 $"
.SH NAME
luac \- Lua compiler
.SH SYNOPSIS
.B luac
[
.I options
] [
.I filenames
]
.SH DESCRIPTION
.B luac
is the Lua compiler.
It translates programs written in the Lua programming language
into binary files that can be later loaded and executed.
.LP
The main advantages of precompiling chunks are:
faster loading,
protecting source code from accidental user changes,
and
off-line syntax checking.
.LP
Pre-compiling does not imply faster execution
because in Lua chunks are always compiled into bytecodes before being executed.
.B luac
simply allows those bytecodes to be saved in a file for later execution.
.LP
Pre-compiled chunks are not necessarily smaller than the corresponding source.
The main goal in pre-compiling is faster loading.
.LP
The binary files created by
.B luac
are portable only among architectures with the same word size and byte order.
.LP
.B luac
produces a single output file containing the bytecodes
for all source files given.
By default,
the output file is named
.BR luac.out ,
but you can change this with the
.B \-o
option.
.LP
In the command line,
you can mix
text files containing Lua source and
binary files containing precompiled chunks.
This is useful to combine several precompiled chunks,
even from different (but compatible) platforms,
into a single precompiled chunk.
.LP
You can use
.B "'\-'"
to indicate the standard input as a source file
and
.B "'\--'"
to signal the end of options
(that is,
all remaining arguments will be treated as files even if they start with
.BR "'\-'" ).
.LP
The internal format of the binary files produced by
.B luac
is likely to change when a new version of Lua is released.
So,
save the source files of all Lua programs that you precompile.
.LP
.SH OPTIONS
Options must be separate.
.TP
.B \-l
produce a listing of the compiled bytecode for Lua's virtual machine.
Listing bytecodes is useful to learn about Lua's virtual machine.
If no files are given, then
.B luac
loads
.B luac.out
and lists its contents.
.TP
.BI \-o " file"
output to
.IR file ,
instead of the default
.BR luac.out .
(You can use
.B "'\-'"
for standard output,
but not on platforms that open standard output in text mode.)
The output file may be a source file because
all files are loaded before the output file is written.
Be careful not to overwrite precious files.
.TP
.B \-p
load files but do not generate any output file.
Used mainly for syntax checking and for testing precompiled chunks:
corrupted files will probably generate errors when loaded.
Lua always performs a thorough integrity test on precompiled chunks.
Bytecode that passes this test is completely safe,
in the sense that it will not break the interpreter.
However,
there is no guarantee that such code does anything sensible.
(None can be given, because the halting problem is unsolvable.)
If no files are given, then
.B luac
loads
.B luac.out
and tests its contents.
No messages are displayed if the file passes the integrity test.
.TP
.B \-s
strip debug information before writing the output file.
This saves some space in very large chunks,
but if errors occur when running a stripped chunk,
then the error messages may not contain the full information they usually do.
For instance,
line numbers and names of local variables are lost.
.TP
.B \-v
show version information.
.SH FILES
.TP 15
.B luac.out
default output file
.SH "SEE ALSO"
.BR lua (1)
.br
http://www.lua.org/
.SH DIAGNOSTICS
Error messages should be self explanatory.
.SH AUTHORS
L. H. de Figueiredo,
R. Ierusalimschy and
W. Celes
.\" EOF
genometools-1.5.1/src/external/lua-5.1.5/doc/luac.html000066400000000000000000000074701211610345200222710ustar00rootroot00000000000000


LUAC man page






NAME

luac - Lua compiler

SYNOPSIS

luac
[
options
] [
filenames
]

DESCRIPTION

luac
is the Lua compiler.
It translates programs written in the Lua programming language
into binary files that can be later loaded and executed.


The main advantages of precompiling chunks are:
faster loading,
protecting source code from accidental user changes,
and
off-line syntax checking.


Precompiling does not imply faster execution
because in Lua chunks are always compiled into bytecodes before being executed.
luac
simply allows those bytecodes to be saved in a file for later execution.


Precompiled chunks are not necessarily smaller than the corresponding source.
The main goal in precompiling is faster loading.


The binary files created by
luac
are portable only among architectures with the same word size and byte order.


luac
produces a single output file containing the bytecodes
for all source files given.
By default,
the output file is named
luac.out,
but you can change this with the
-o
option.


In the command line,
you can mix
text files containing Lua source and
binary files containing precompiled chunks.
This is useful because several precompiled chunks,
even from different (but compatible) platforms,
can be combined into a single precompiled chunk.


You can use
'-'
to indicate the standard input as a source file
and
'--'
to signal the end of options
(that is,
all remaining arguments will be treated as files even if they start with
'-').


The internal format of the binary files produced by
luac
is likely to change when a new version of Lua is released.
So,
save the source files of all Lua programs that you precompile.



OPTIONS

Options must be separate.


-l
produce a listing of the compiled bytecode for Lua's virtual machine.
Listing bytecodes is useful to learn about Lua's virtual machine.
If no files are given, then
luac
loads
luac.out
and lists its contents.


-o file
output to
file,
instead of the default
luac.out.
(You can use
'-'
for standard output,
but not on platforms that open standard output in text mode.)
The output file may be a source file because
all files are loaded before the output file is written.
Be careful not to overwrite precious files.


-p
load files but do not generate any output file.
Used mainly for syntax checking and for testing precompiled chunks:
corrupted files will probably generate errors when loaded.
Lua always performs a thorough integrity test on precompiled chunks.
Bytecode that passes this test is completely safe,
in the sense that it will not break the interpreter.
However,
there is no guarantee that such code does anything sensible.
(None can be given, because the halting problem is unsolvable.)
If no files are given, then
luac
loads
luac.out
and tests its contents.
No messages are displayed if the file passes the integrity test.


-s
strip debug information before writing the output file.
This saves some space in very large chunks,
but if errors occur when running a stripped chunk,
then the error messages may not contain the full information they usually do.
For instance,
line numbers and names of local variables are lost.


-v
show version information.

FILES



luac.out
default output file

SEE ALSO

lua(1)


http://www.lua.org/

DIAGNOSTICS

Error messages should be self explanatory.

AUTHORS

L. H. de Figueiredo,
R. Ierusalimschy and
W. Celes



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genometools-1.5.1/src/external/lua-5.1.5/doc/manual.html000066400000000000000000007614311211610345200226260ustar00rootroot00000000000000



Lua 5.1 Reference Manual












Lua 5.1 Reference Manual



by Roberto Ierusalimschy, Luiz Henrique de Figueiredo, Waldemar Celes



Copyright © 2006–2012 Lua.org, PUC-Rio.
Freely available under the terms of the
Lua license.






contents
·
index
·
other versions











1 - Introduction




Lua is an extension programming language designed to support
general procedural programming with data description
facilities.
It also offers good support for object-oriented programming,
functional programming, and data-driven programming.
Lua is intended to be used as a powerful, light-weight
scripting language for any program that needs one.
Lua is implemented as a library, written in clean C
(that is, in the common subset of ANSI C and C++).




Being an extension language, Lua has no notion of a "main" program:
it only works embedded in a host client,
called the embedding program or simply the host.
This host program can invoke functions to execute a piece of Lua code,
can write and read Lua variables,
and can register C functions to be called by Lua code.
Through the use of C functions, Lua can be augmented to cope with
a wide range of different domains,
thus creating customized programming languages sharing a syntactical framework.
The Lua distribution includes a sample host program called lua,
which uses the Lua library to offer a complete, stand-alone Lua interpreter.




Lua is free software,
and is provided as usual with no guarantees,
as stated in its license.
The implementation described in this manual is available
at Lua's official web site, www.lua.org.




Like any other reference manual,
this document is dry in places.
For a discussion of the decisions behind the design of Lua,
see the technical papers available at Lua's web site.
For a detailed introduction to programming in Lua,
see Roberto's book, Programming in Lua (Second Edition).




2 - The Language




This section describes the lexis, the syntax, and the semantics of Lua.
In other words,
this section describes
which tokens are valid,
how they can be combined,
and what their combinations mean.




The language constructs will be explained using the usual extended BNF notation,
in which
{a} means 0 or more a's, and
[a] means an optional a.
Non-terminals are shown like non-terminal,
keywords are shown like kword,
and other terminal symbols are shown like `=´.
The complete syntax of Lua can be found in §8
at the end of this manual.




2.1 - Lexical Conventions




Names
(also called identifiers)
in Lua can be any string of letters,
digits, and underscores,
not beginning with a digit.
This coincides with the definition of names in most languages.
(The definition of letter depends on the current locale:
any character considered alphabetic by the current locale
can be used in an identifier.)
Identifiers are used to name variables and table fields.




The following keywords are reserved
and cannot be used as names:



     and       break     do        else      elseif
     end       false     for       function  if
     in        local     nil       not       or
     repeat    return    then      true      until     while





Lua is a case-sensitive language:
and is a reserved word, but And and AND
are two different, valid names.
As a convention, names starting with an underscore followed by
uppercase letters (such as _VERSION)
are reserved for internal global variables used by Lua.




The following strings denote other tokens:


     +     -     *     /     %     ^     #
     ==    ~=    <=    >=    <     >     =
     (     )     {     }     [     ]
     ;     :     ,     .     ..    ...





Literal strings
can be delimited by matching single or double quotes,
and can contain the following C-like escape sequences:
'\a' (bell),
'\b' (backspace),
'\f' (form feed),
'\n' (newline),
'\r' (carriage return),
'\t' (horizontal tab),
'\v' (vertical tab),
'\\' (backslash),
'\"' (quotation mark [double quote]),
and '\'' (apostrophe [single quote]).
Moreover, a backslash followed by a real newline
results in a newline in the string.
A character in a string can also be specified by its numerical value
using the escape sequence \ddd,
where ddd is a sequence of up to three decimal digits.
(Note that if a numerical escape is to be followed by a digit,
it must be expressed using exactly three digits.)
Strings in Lua can contain any 8-bit value, including embedded zeros,
which can be specified as '\0'.




Literal strings can also be defined using a long format
enclosed by long brackets.
We define an opening long bracket of level n as an opening
square bracket followed by n equal signs followed by another
opening square bracket.
So, an opening long bracket of level 0 is written as [[,
an opening long bracket of level 1 is written as [=[,
and so on.
A closing long bracket is defined similarly;
for instance, a closing long bracket of level 4 is written as ]====].
A long string starts with an opening long bracket of any level and
ends at the first closing long bracket of the same level.
Literals in this bracketed form can run for several lines,
do not interpret any escape sequences,
and ignore long brackets of any other level.
They can contain anything except a closing bracket of the proper level.




For convenience,
when the opening long bracket is immediately followed by a newline,
the newline is not included in the string.
As an example, in a system using ASCII
(in which 'a' is coded as 97,
newline is coded as 10, and '1' is coded as 49),
the five literal strings below denote the same string:


     a = 'alo\n123"'
     a = "alo\n123\""
     a = '\97lo\10\04923"'
     a = [[alo
     123"]]
     a = [==[
     alo
     123"]==]





A numerical constant can be written with an optional decimal part
and an optional decimal exponent.
Lua also accepts integer hexadecimal constants,
by prefixing them with 0x.
Examples of valid numerical constants are


     3   3.0   3.1416   314.16e-2   0.31416E1   0xff   0x56





A comment starts with a double hyphen (--)
anywhere outside a string.
If the text immediately after -- is not an opening long bracket,
the comment is a short comment,
which runs until the end of the line.
Otherwise, it is a long comment,
which runs until the corresponding closing long bracket.
Long comments are frequently used to disable code temporarily.






2.2 - Values and Types




Lua is a dynamically typed language.
This means that
variables do not have types; only values do.
There are no type definitions in the language.
All values carry their own type.




All values in Lua are first-class values.
This means that all values can be stored in variables,
passed as arguments to other functions, and returned as results.




There are eight basic types in Lua:
nil, boolean, number,
string, function, userdata,
thread, and table.
Nil is the type of the value nil,
whose main property is to be different from any other value;
it usually represents the absence of a useful value.
Boolean is the type of the values false and true.
Both nil and false make a condition false;
any other value makes it true.
Number represents real (double-precision floating-point) numbers.
(It is easy to build Lua interpreters that use other
internal representations for numbers,
such as single-precision float or long integers;
see file luaconf.h.)
String represents arrays of characters.

Lua is 8-bit clean:
strings can contain any 8-bit character,
including embedded zeros ('\0') (see §2.1).




Lua can call (and manipulate) functions written in Lua and
functions written in C
(see §2.5.8).




The type userdata is provided to allow arbitrary C data to
be stored in Lua variables.
This type corresponds to a block of raw memory
and has no pre-defined operations in Lua,
except assignment and identity test.
However, by using metatables,
the programmer can define operations for userdata values
(see §2.8).
Userdata values cannot be created or modified in Lua,
only through the C API.
This guarantees the integrity of data owned by the host program.




The type thread represents independent threads of execution
and it is used to implement coroutines (see §2.11).
Do not confuse Lua threads with operating-system threads.
Lua supports coroutines on all systems,
even those that do not support threads.




The type table implements associative arrays,
that is, arrays that can be indexed not only with numbers,
but with any value (except nil).
Tables can be heterogeneous;
that is, they can contain values of all types (except nil).
Tables are the sole data structuring mechanism in Lua;
they can be used to represent ordinary arrays,
symbol tables, sets, records, graphs, trees, etc.
To represent records, Lua uses the field name as an index.
The language supports this representation by
providing a.name as syntactic sugar for a["name"].
There are several convenient ways to create tables in Lua
(see §2.5.7).




Like indices,
the value of a table field can be of any type (except nil).
In particular,
because functions are first-class values,
table fields can contain functions.
Thus tables can also carry methods (see §2.5.9).




Tables, functions, threads, and (full) userdata values are objects:
variables do not actually contain these values,
only references to them.
Assignment, parameter passing, and function returns
always manipulate references to such values;
these operations do not imply any kind of copy.




The library function type returns a string describing the type
of a given value.




2.2.1 - Coercion




Lua provides automatic conversion between
string and number values at run time.
Any arithmetic operation applied to a string tries to convert
this string to a number, following the usual conversion rules.
Conversely, whenever a number is used where a string is expected,
the number is converted to a string, in a reasonable format.
For complete control over how numbers are converted to strings,
use the format function from the string library
(see string.format).








2.3 - Variables




Variables are places that store values.

There are three kinds of variables in Lua:
global variables, local variables, and table fields.




A single name can denote a global variable or a local variable
(or a function's formal parameter,
which is a particular kind of local variable):


	var ::= Name


Name denotes identifiers, as defined in §2.1.




Any variable is assumed to be global unless explicitly declared
as a local (see §2.4.7).
Local variables are lexically scoped:
local variables can be freely accessed by functions
defined inside their scope (see §2.6).




Before the first assignment to a variable, its value is nil.




Square brackets are used to index a table:


	var ::= prefixexp `[´ exp `]´


The meaning of accesses to global variables 
and table fields can be changed via metatables.
An access to an indexed variable t[i] is equivalent to
a call gettable_event(t,i).
(See §2.8 for a complete description of the
gettable_event function.
This function is not defined or callable in Lua.
We use it here only for explanatory purposes.)




The syntax var.Name is just syntactic sugar for
var["Name"]:


	var ::= prefixexp `.´ Name





All global variables live as fields in ordinary Lua tables,
called environment tables or simply
environments (see §2.9).
Each function has its own reference to an environment,
so that all global variables in this function
will refer to this environment table.
When a function is created,
it inherits the environment from the function that created it.
To get the environment table of a Lua function,
you call getfenv.
To replace it,
you call setfenv.
(You can only manipulate the environment of C functions
through the debug library; (see §5.9).)




An access to a global variable x
is equivalent to _env.x,
which in turn is equivalent to


     gettable_event(_env, "x")


where _env is the environment of the running function.
(See §2.8 for a complete description of the
gettable_event function.
This function is not defined or callable in Lua.
Similarly, the _env variable is not defined in Lua.
We use them here only for explanatory purposes.)






2.4 - Statements




Lua supports an almost conventional set of statements,
similar to those in Pascal or C.
This set includes
assignments, control structures, function calls,
and variable declarations.




2.4.1 - Chunks




The unit of execution of Lua is called a chunk.
A chunk is simply a sequence of statements,
which are executed sequentially.
Each statement can be optionally followed by a semicolon:


	chunk ::= {stat [`;´]}


There are no empty statements and thus ';;' is not legal.




Lua handles a chunk as the body of an anonymous function 
with a variable number of arguments
(see §2.5.9).
As such, chunks can define local variables,
receive arguments, and return values.




A chunk can be stored in a file or in a string inside the host program.
To execute a chunk,
Lua first pre-compiles the chunk into instructions for a virtual machine,
and then it executes the compiled code
with an interpreter for the virtual machine.




Chunks can also be pre-compiled into binary form;
see program luac for details.
Programs in source and compiled forms are interchangeable;
Lua automatically detects the file type and acts accordingly.







2.4.2 - Blocks

A block is a list of statements;
syntactically, a block is the same as a chunk:


	block ::= chunk





A block can be explicitly delimited to produce a single statement:


	stat ::= do block end


Explicit blocks are useful
to control the scope of variable declarations.
Explicit blocks are also sometimes used to
add a return or break statement in the middle
of another block (see §2.4.4).






2.4.3 - Assignment




Lua allows multiple assignments.
Therefore, the syntax for assignment
defines a list of variables on the left side
and a list of expressions on the right side.
The elements in both lists are separated by commas:


	stat ::= varlist `=´ explist
	varlist ::= var {`,´ var}
	explist ::= exp {`,´ exp}


Expressions are discussed in §2.5.




Before the assignment,
the list of values is adjusted to the length of
the list of variables.
If there are more values than needed,
the excess values are thrown away.
If there are fewer values than needed,
the list is extended with as many  nil's as needed.
If the list of expressions ends with a function call,
then all values returned by that call enter the list of values,
before the adjustment
(except when the call is enclosed in parentheses; see §2.5).




The assignment statement first evaluates all its expressions
and only then are the assignments performed.
Thus the code


     i = 3
     i, a[i] = i+1, 20


sets a[3] to 20, without affecting a[4]
because the i in a[i] is evaluated (to 3)
before it is assigned 4.
Similarly, the line


     x, y = y, x


exchanges the values of x and y,
and


     x, y, z = y, z, x


cyclically permutes the values of x, y, and z.




The meaning of assignments to global variables
and table fields can be changed via metatables.
An assignment to an indexed variable t[i] = val is equivalent to
settable_event(t,i,val).
(See §2.8 for a complete description of the
settable_event function.
This function is not defined or callable in Lua.
We use it here only for explanatory purposes.)




An assignment to a global variable x = val
is equivalent to the assignment
_env.x = val,
which in turn is equivalent to


     settable_event(_env, "x", val)


where _env is the environment of the running function.
(The _env variable is not defined in Lua.
We use it here only for explanatory purposes.)






2.4.4 - Control Structures

The control structures
if, while, and repeat have the usual meaning and
familiar syntax:





	stat ::= while exp do block end
	stat ::= repeat block until exp
	stat ::= if exp then block {elseif exp then block} [else block] end


Lua also has a for statement, in two flavors (see §2.4.5).




The condition expression of a
control structure can return any value.
Both false and nil are considered false.
All values different from nil and false are considered true
(in particular, the number 0 and the empty string are also true).




In the repeat–until loop,
the inner block does not end at the until keyword,
but only after the condition.
So, the condition can refer to local variables
declared inside the loop block.




The return statement is used to return values
from a function or a chunk (which is just a function).

Functions and chunks can return more than one value,
and so the syntax for the return statement is


	stat ::= return [explist]





The break statement is used to terminate the execution of a
while, repeat, or for loop,
skipping to the next statement after the loop:



	stat ::= break


A break ends the innermost enclosing loop.




The return and break
statements can only be written as the last statement of a block.
If it is really necessary to return or break in the
middle of a block,
then an explicit inner block can be used,
as in the idioms
do return end and do break end,
because now return and break are the last statements in
their (inner) blocks.






2.4.5 - For Statement





The for statement has two forms:
one numeric and one generic.




The numeric for loop repeats a block of code while a
control variable runs through an arithmetic progression.
It has the following syntax:


	stat ::= for Name `=´ exp `,´ exp [`,´ exp] do block end


The block is repeated for name starting at the value of
the first exp, until it passes the second exp by steps of the
third exp.
More precisely, a for statement like


     for v = e1, e2, e3 do block end


is equivalent to the code:


     do
       local var, limit, step = tonumber(e1), tonumber(e2), tonumber(e3)
       if not (var and limit and step) then error() end
       while (step > 0 and var <= limit) or (step <= 0 and var >= limit) do
         local v = var
         block
         var = var + step
       end
     end


Note the following:


    


  • 
All three control expressions are evaluated only once,
before the loop starts.
They must all result in numbers.

    • 


  • 
var, limit, and step are invisible variables.
The names shown here are for explanatory purposes only.

    • 


  • 
If the third expression (the step) is absent,
then a step of 1 is used.

    • 


  • 
You can use break to exit a for loop.

    • 


  • 
The loop variable v is local to the loop;
you cannot use its value after the for ends or is broken.
If you need this value,
assign it to another variable before breaking or exiting the loop.

    • 






The generic for statement works over functions,
called iterators.
On each iteration, the iterator function is called to produce a new value,
stopping when this new value is nil.
The generic for loop has the following syntax:


	stat ::= for namelist in explist do block end
	namelist ::= Name {`,´ Name}


A for statement like


     for var_1, ···, var_n in explist do block end


is equivalent to the code:


     do
       local f, s, var = explist
       while true do
         local var_1, ···, var_n = f(s, var)
         var = var_1
         if var == nil then break end
         block
       end
     end


Note the following:


    


  • 
explist is evaluated only once.
Its results are an iterator function,
a state,
and an initial value for the first iterator variable.

    • 


  • 
f, s, and var are invisible variables.
The names are here for explanatory purposes only.

    • 


  • 
You can use break to exit a for loop.

    • 


  • 
The loop variables var_i are local to the loop;
you cannot use their values after the for ends.
If you need these values,
then assign them to other variables before breaking or exiting the loop.

    • 








2.4.6 - Function Calls as Statements

To allow possible side-effects,
function calls can be executed as statements:


	stat ::= functioncall


In this case, all returned values are thrown away.
Function calls are explained in §2.5.8.






2.4.7 - Local Declarations

Local variables can be declared anywhere inside a block.
The declaration can include an initial assignment:


	stat ::= local namelist [`=´ explist]


If present, an initial assignment has the same semantics
of a multiple assignment (see §2.4.3).
Otherwise, all variables are initialized with nil.




A chunk is also a block (see §2.4.1),
and so local variables can be declared in a chunk outside any explicit block.
The scope of such local variables extends until the end of the chunk.




The visibility rules for local variables are explained in §2.6.








2.5 - Expressions




The basic expressions in Lua are the following:


	exp ::= prefixexp
	exp ::= nil | false | true
	exp ::= Number
	exp ::= String
	exp ::= function
	exp ::= tableconstructor
	exp ::= `...´
	exp ::= exp binop exp
	exp ::= unop exp
	prefixexp ::= var | functioncall | `(´ exp `)´





Numbers and literal strings are explained in §2.1;
variables are explained in §2.3;
function definitions are explained in §2.5.9;
function calls are explained in §2.5.8;
table constructors are explained in §2.5.7.
Vararg expressions,
denoted by three dots ('...'), can only be used when
directly inside a vararg function;
they are explained in §2.5.9.




Binary operators comprise arithmetic operators (see §2.5.1),
relational operators (see §2.5.2), logical operators (see §2.5.3),
and the concatenation operator (see §2.5.4).
Unary operators comprise the unary minus (see §2.5.1),
the unary not (see §2.5.3),
and the unary length operator (see §2.5.5).




Both function calls and vararg expressions can result in multiple values.
If an expression is used as a statement
(only possible for function calls (see §2.4.6)),
then its return list is adjusted to zero elements,
thus discarding all returned values.
If an expression is used as the last (or the only) element
of a list of expressions,
then no adjustment is made
(unless the call is enclosed in parentheses).
In all other contexts,
Lua adjusts the result list to one element,
discarding all values except the first one.




Here are some examples:


     f()                -- adjusted to 0 results
     g(f(), x)          -- f() is adjusted to 1 result
     g(x, f())          -- g gets x plus all results from f()
     a,b,c = f(), x     -- f() is adjusted to 1 result (c gets nil)
     a,b = ...          -- a gets the first vararg parameter, b gets
                        -- the second (both a and b can get nil if there
                        -- is no corresponding vararg parameter)
     
     a,b,c = x, f()     -- f() is adjusted to 2 results
     a,b,c = f()        -- f() is adjusted to 3 results
     return f()         -- returns all results from f()
     return ...         -- returns all received vararg parameters
     return x,y,f()     -- returns x, y, and all results from f()
     {f()}              -- creates a list with all results from f()
     {...}              -- creates a list with all vararg parameters
     {f(), nil}         -- f() is adjusted to 1 result





Any expression enclosed in parentheses always results in only one value.
Thus,
(f(x,y,z)) is always a single value,
even if f returns several values.
(The value of (f(x,y,z)) is the first value returned by f
or nil if f does not return any values.)




2.5.1 - Arithmetic Operators

Lua supports the usual arithmetic operators:
the binary + (addition),
- (subtraction), * (multiplication),
/ (division), % (modulo), and ^ (exponentiation);
and unary - (negation).
If the operands are numbers, or strings that can be converted to
numbers (see §2.2.1),
then all operations have the usual meaning.
Exponentiation works for any exponent.
For instance, x^(-0.5) computes the inverse of the square root of x.
Modulo is defined as


     a % b == a - math.floor(a/b)*b


That is, it is the remainder of a division that rounds
the quotient towards minus infinity.






2.5.2 - Relational Operators

The relational operators in Lua are


     ==    ~=    <     >     <=    >=


These operators always result in false or true.




Equality (==) first compares the type of its operands.
If the types are different, then the result is false.
Otherwise, the values of the operands are compared.
Numbers and strings are compared in the usual way.
Objects (tables, userdata, threads, and functions)
are compared by reference:
two objects are considered equal only if they are the same object.
Every time you create a new object
(a table, userdata, thread, or function),
this new object is different from any previously existing object.




You can change the way that Lua compares tables and userdata 
by using the "eq" metamethod (see §2.8).




The conversion rules of §2.2.1
do not apply to equality comparisons.
Thus, "0"==0 evaluates to false,
and t[0] and t["0"] denote different
entries in a table.




The operator ~= is exactly the negation of equality (==).




The order operators work as follows.
If both arguments are numbers, then they are compared as such.
Otherwise, if both arguments are strings,
then their values are compared according to the current locale.
Otherwise, Lua tries to call the "lt" or the "le"
metamethod (see §2.8).
A comparison a > b is translated to b < a
and a >= b is translated to b <= a.






2.5.3 - Logical Operators

The logical operators in Lua are
and, or, and not.
Like the control structures (see §2.4.4),
all logical operators consider both false and nil as false
and anything else as true.




The negation operator not always returns false or true.
The conjunction operator and returns its first argument
if this value is false or nil;
otherwise, and returns its second argument.
The disjunction operator or returns its first argument
if this value is different from nil and false;
otherwise, or returns its second argument.
Both and and or use short-cut evaluation;
that is,
the second operand is evaluated only if necessary.
Here are some examples:


     10 or 20            --> 10
     10 or error()       --> 10
     nil or "a"          --> "a"
     nil and 10          --> nil
     false and error()   --> false
     false and nil       --> false
     false or nil        --> nil
     10 and 20           --> 20


(In this manual,
--> indicates the result of the preceding expression.)






2.5.4 - Concatenation

The string concatenation operator in Lua is
denoted by two dots ('..').
If both operands are strings or numbers, then they are converted to
strings according to the rules mentioned in §2.2.1.
Otherwise, the "concat" metamethod is called (see §2.8).






2.5.5 - The Length Operator




The length operator is denoted by the unary operator #.
The length of a string is its number of bytes
(that is, the usual meaning of string length when each
character is one byte).




The length of a table t is defined to be any
integer index n
such that t[n] is not nil and t[n+1] is nil;
moreover, if t[1] is nil, n can be zero.
For a regular array, with non-nil values from 1 to a given n,
its length is exactly that n,
the index of its last value.
If the array has "holes"
(that is, nil values between other non-nil values),
then #t can be any of the indices that
directly precedes a nil value
(that is, it may consider any such nil value as the end of
the array). 






2.5.6 - Precedence

Operator precedence in Lua follows the table below,
from lower to higher priority:


     or
     and
     <     >     <=    >=    ~=    ==
     ..
     +     -
     *     /     %
     not   #     - (unary)
     ^


As usual,
you can use parentheses to change the precedences of an expression.
The concatenation ('..') and exponentiation ('^')
operators are right associative.
All other binary operators are left associative.






2.5.7 - Table Constructors

Table constructors are expressions that create tables.
Every time a constructor is evaluated, a new table is created.
A constructor can be used to create an empty table
or to create a table and initialize some of its fields.
The general syntax for constructors is


	tableconstructor ::= `{´ [fieldlist] `}´
	fieldlist ::= field {fieldsep field} [fieldsep]
	field ::= `[´ exp `]´ `=´ exp | Name `=´ exp | exp
	fieldsep ::= `,´ | `;´





Each field of the form [exp1] = exp2 adds to the new table an entry
with key exp1 and value exp2.
A field of the form name = exp is equivalent to
["name"] = exp.
Finally, fields of the form exp are equivalent to
[i] = exp, where i are consecutive numerical integers,
starting with 1.
Fields in the other formats do not affect this counting.
For example,


     a = { [f(1)] = g; "x", "y"; x = 1, f(x), [30] = 23; 45 }


is equivalent to


     do
       local t = {}
       t[f(1)] = g
       t[1] = "x"         -- 1st exp
       t[2] = "y"         -- 2nd exp
       t.x = 1            -- t["x"] = 1
       t[3] = f(x)        -- 3rd exp
       t[30] = 23
       t[4] = 45          -- 4th exp
       a = t
     end





If the last field in the list has the form exp
and the expression is a function call or a vararg expression,
then all values returned by this expression enter the list consecutively
(see §2.5.8).
To avoid this,
enclose the function call or the vararg expression
in parentheses (see §2.5).




The field list can have an optional trailing separator,
as a convenience for machine-generated code.






2.5.8 - Function Calls

A function call in Lua has the following syntax:


	functioncall ::= prefixexp args


In a function call,
first prefixexp and args are evaluated.
If the value of prefixexp has type function,
then this function is called
with the given arguments.
Otherwise, the prefixexp "call" metamethod is called,
having as first parameter the value of prefixexp,
followed by the original call arguments
(see §2.8).




The form


	functioncall ::= prefixexp `:´ Name args


can be used to call "methods".
A call v:name(args)
is syntactic sugar for v.name(v,args),
except that v is evaluated only once.




Arguments have the following syntax:


	args ::= `(´ [explist] `)´
	args ::= tableconstructor
	args ::= String


All argument expressions are evaluated before the call.
A call of the form f{fields} is
syntactic sugar for f({fields});
that is, the argument list is a single new table.
A call of the form f'string'
(or f"string" or f[[string]])
is syntactic sugar for f('string');
that is, the argument list is a single literal string.




As an exception to the free-format syntax of Lua,
you cannot put a line break before the '(' in a function call.
This restriction avoids some ambiguities in the language.
If you write


     a = f
     (g).x(a)


Lua would see that as a single statement, a = f(g).x(a).
So, if you want two statements, you must add a semi-colon between them.
If you actually want to call f,
you must remove the line break before (g).




A call of the form return functioncall is called
a tail call.
Lua implements proper tail calls
(or proper tail recursion):
in a tail call,
the called function reuses the stack entry of the calling function.
Therefore, there is no limit on the number of nested tail calls that
a program can execute.
However, a tail call erases any debug information about the
calling function.
Note that a tail call only happens with a particular syntax,
where the return has one single function call as argument;
this syntax makes the calling function return exactly
the returns of the called function.
So, none of the following examples are tail calls:


     return (f(x))        -- results adjusted to 1
     return 2 * f(x)
     return x, f(x)       -- additional results
     f(x); return         -- results discarded
     return x or f(x)     -- results adjusted to 1







2.5.9 - Function Definitions




The syntax for function definition is


	function ::= function funcbody
	funcbody ::= `(´ [parlist] `)´ block end





The following syntactic sugar simplifies function definitions:


	stat ::= function funcname funcbody
	stat ::= local function Name funcbody
	funcname ::= Name {`.´ Name} [`:´ Name]


The statement


     function f () body end


translates to


     f = function () body end


The statement


     function t.a.b.c.f () body end


translates to


     t.a.b.c.f = function () body end


The statement


     local function f () body end


translates to


     local f; f = function () body end


not to


     local f = function () body end


(This only makes a difference when the body of the function
contains references to f.)




A function definition is an executable expression,
whose value has type function.
When Lua pre-compiles a chunk,
all its function bodies are pre-compiled too.
Then, whenever Lua executes the function definition,
the function is instantiated (or closed).
This function instance (or closure)
is the final value of the expression.
Different instances of the same function
can refer to different  external local variables
and can have different environment tables.




Parameters act as local variables that are
initialized with the argument values:


	parlist ::= namelist [`,´ `...´] | `...´


When a function is called,
the list of arguments is adjusted to
the length of the list of parameters,
unless the function is a variadic or vararg function,
which is
indicated by three dots ('...') at the end of its parameter list.
A vararg function does not adjust its argument list;
instead, it collects all extra arguments and supplies them
to the function through a vararg expression,
which is also written as three dots.
The value of this expression is a list of all actual extra arguments,
similar to a function with multiple results.
If a vararg expression is used inside another expression
or in the middle of a list of expressions,
then its return list is adjusted to one element.
If the expression is used as the last element of a list of expressions,
then no adjustment is made
(unless that last expression is enclosed in parentheses).




As an example, consider the following definitions:


     function f(a, b) end
     function g(a, b, ...) end
     function r() return 1,2,3 end


Then, we have the following mapping from arguments to parameters and
to the vararg expression:


     CALL            PARAMETERS
     
     f(3)             a=3, b=nil
     f(3, 4)          a=3, b=4
     f(3, 4, 5)       a=3, b=4
     f(r(), 10)       a=1, b=10
     f(r())           a=1, b=2
     
     g(3)             a=3, b=nil, ... -->  (nothing)
     g(3, 4)          a=3, b=4,   ... -->  (nothing)
     g(3, 4, 5, 8)    a=3, b=4,   ... -->  5  8
     g(5, r())        a=5, b=1,   ... -->  2  3





Results are returned using the return statement (see §2.4.4).
If control reaches the end of a function
without encountering a return statement,
then the function returns with no results.




The colon syntax
is used for defining methods,
that is, functions that have an implicit extra parameter self.
Thus, the statement


     function t.a.b.c:f (params) body end


is syntactic sugar for


     t.a.b.c.f = function (self, params) body end









2.6 - Visibility Rules





Lua is a lexically scoped language.
The scope of variables begins at the first statement after
their declaration and lasts until the end of the innermost block that
includes the declaration.
Consider the following example:


     x = 10                -- global variable
     do                    -- new block
       local x = x         -- new 'x', with value 10
       print(x)            --> 10
       x = x+1
       do                  -- another block
         local x = x+1     -- another 'x'
         print(x)          --> 12
       end
       print(x)            --> 11
     end
     print(x)              --> 10  (the global one)





Notice that, in a declaration like local x = x,
the new x being declared is not in scope yet,
and so the second x refers to the outside variable.




Because of the lexical scoping rules,
local variables can be freely accessed by functions
defined inside their scope.
A local variable used by an inner function is called
an upvalue, or external local variable,
inside the inner function.




Notice that each execution of a local statement
defines new local variables.
Consider the following example:


     a = {}
     local x = 20
     for i=1,10 do
       local y = 0
       a[i] = function () y=y+1; return x+y end
     end


The loop creates ten closures
(that is, ten instances of the anonymous function).
Each of these closures uses a different y variable,
while all of them share the same x.






2.7 - Error Handling




Because Lua is an embedded extension language,
all Lua actions start from C code in the host program
calling a function from the Lua library (see lua_pcall).
Whenever an error occurs during Lua compilation or execution,
control returns to C,
which can take appropriate measures
(such as printing an error message).




Lua code can explicitly generate an error by calling the
error function.
If you need to catch errors in Lua,
you can use the pcall function.






2.8 - Metatables




Every value in Lua can have a metatable.
This metatable is an ordinary Lua table
that defines the behavior of the original value
under certain special operations.
You can change several aspects of the behavior
of operations over a value by setting specific fields in its metatable.
For instance, when a non-numeric value is the operand of an addition,
Lua checks for a function in the field "__add" in its metatable.
If it finds one,
Lua calls this function to perform the addition.




We call the keys in a metatable events
and the values metamethods.
In the previous example, the event is "add" 
and the metamethod is the function that performs the addition.




You can query the metatable of any value
through the getmetatable function.




You can replace the metatable of tables
through the setmetatable
function.
You cannot change the metatable of other types from Lua
(except by using the debug library);
you must use the C API for that.




Tables and full userdata have individual metatables
(although multiple tables and userdata can share their metatables).
Values of all other types share one single metatable per type;
that is, there is one single metatable for all numbers,
one for all strings, etc.




A metatable controls how an object behaves in arithmetic operations,
order comparisons, concatenation, length operation, and indexing.
A metatable also can define a function to be called when a userdata
is garbage collected.
For each of these operations Lua associates a specific key
called an event.
When Lua performs one of these operations over a value,
it checks whether this value has a metatable with the corresponding event.
If so, the value associated with that key (the metamethod)
controls how Lua will perform the operation.




Metatables control the operations listed next.
Each operation is identified by its corresponding name.
The key for each operation is a string with its name prefixed by
two underscores, '__';
for instance, the key for operation "add" is the
string "__add".
The semantics of these operations is better explained by a Lua function
describing how the interpreter executes the operation.




The code shown here in Lua is only illustrative;
the real behavior is hard coded in the interpreter
and it is much more efficient than this simulation.
All functions used in these descriptions
(rawget, tonumber, etc.)
are described in §5.1.
In particular, to retrieve the metamethod of a given object,
we use the expression


     metatable(obj)[event]


This should be read as


     rawget(getmetatable(obj) or {}, event)



That is, the access to a metamethod does not invoke other metamethods,
and the access to objects with no metatables does not fail
(it simply results in nil).




    


  • "add":
the + operation.




    
The function getbinhandler below defines how Lua chooses a handler
for a binary operation.
First, Lua tries the first operand.
If its type does not define a handler for the operation,
then Lua tries the second operand.


         function getbinhandler (op1, op2, event)
       return metatable(op1)[event] or metatable(op2)[event]
     end

    
By using this function,
the behavior of the op1 + op2 is


         function add_event (op1, op2)
       local o1, o2 = tonumber(op1), tonumber(op2)
       if o1 and o2 then  -- both operands are numeric?
         return o1 + o2   -- '+' here is the primitive 'add'
       else  -- at least one of the operands is not numeric
         local h = getbinhandler(op1, op2, "__add")
         if h then
           -- call the handler with both operands
           return (h(op1, op2))
         else  -- no handler available: default behavior
           error(···)
         end
       end
     end

    

    • 


  • "sub":
the - operation.

Behavior similar to the "add" operation.

    • 


  • "mul":
the * operation.

Behavior similar to the "add" operation.

    • 


  • "div":
the / operation.

Behavior similar to the "add" operation.

    • 


  • "mod":
the % operation.

Behavior similar to the "add" operation,
with the operation
o1 - floor(o1/o2)*o2 as the primitive operation.

    • 


  • "pow":
the ^ (exponentiation) operation.

Behavior similar to the "add" operation,
with the function pow (from the C math library)
as the primitive operation.

    • 


  • "unm":
the unary - operation.



         function unm_event (op)
       local o = tonumber(op)
       if o then  -- operand is numeric?
         return -o  -- '-' here is the primitive 'unm'
       else  -- the operand is not numeric.
         -- Try to get a handler from the operand
         local h = metatable(op).__unm
         if h then
           -- call the handler with the operand
           return (h(op))
         else  -- no handler available: default behavior
           error(···)
         end
       end
     end

    

    • 


  • "concat":
the .. (concatenation) operation.



         function concat_event (op1, op2)
       if (type(op1) == "string" or type(op1) == "number") and
          (type(op2) == "string" or type(op2) == "number") then
         return op1 .. op2  -- primitive string concatenation
       else
         local h = getbinhandler(op1, op2, "__concat")
         if h then
           return (h(op1, op2))
         else
           error(···)
         end
       end
     end

    

    • 


  • "len":
the # operation.



         function len_event (op)
       if type(op) == "string" then
         return strlen(op)         -- primitive string length
       elseif type(op) == "table" then
         return #op                -- primitive table length
       else
         local h = metatable(op).__len
         if h then
           -- call the handler with the operand
           return (h(op))
         else  -- no handler available: default behavior
           error(···)
         end
       end
     end

    
See §2.5.5 for a description of the length of a table.

    • 


  • "eq":
the == operation.

The function getcomphandler defines how Lua chooses a metamethod
for comparison operators.
A metamethod only is selected when both objects
being compared have the same type
and the same metamethod for the selected operation.


         function getcomphandler (op1, op2, event)
       if type(op1) ~= type(op2) then return nil end
       local mm1 = metatable(op1)[event]
       local mm2 = metatable(op2)[event]
       if mm1 == mm2 then return mm1 else return nil end
     end

    
The "eq" event is defined as follows:


         function eq_event (op1, op2)
       if type(op1) ~= type(op2) then  -- different types?
         return false   -- different objects
       end
       if op1 == op2 then   -- primitive equal?
         return true   -- objects are equal
       end
       -- try metamethod
       local h = getcomphandler(op1, op2, "__eq")
       if h then
         return (h(op1, op2))
       else
         return false
       end
     end

    
a ~= b is equivalent to not (a == b).

    • 


  • "lt":
the < operation.



         function lt_event (op1, op2)
       if type(op1) == "number" and type(op2) == "number" then
         return op1 < op2   -- numeric comparison
       elseif type(op1) == "string" and type(op2) == "string" then
         return op1 < op2   -- lexicographic comparison
       else
         local h = getcomphandler(op1, op2, "__lt")
         if h then
           return (h(op1, op2))
         else
           error(···)
         end
       end
     end

    
a > b is equivalent to b < a.

    • 


  • "le":
the <= operation.



         function le_event (op1, op2)
       if type(op1) == "number" and type(op2) == "number" then
         return op1 <= op2   -- numeric comparison
       elseif type(op1) == "string" and type(op2) == "string" then
         return op1 <= op2   -- lexicographic comparison
       else
         local h = getcomphandler(op1, op2, "__le")
         if h then
           return (h(op1, op2))
         else
           h = getcomphandler(op1, op2, "__lt")
           if h then
             return not h(op2, op1)
           else
             error(···)
           end
         end
       end
     end

    
a >= b is equivalent to b <= a.
Note that, in the absence of a "le" metamethod,
Lua tries the "lt", assuming that a <= b is
equivalent to not (b < a).

    • 


  • "index":
The indexing access table[key].



         function gettable_event (table, key)
       local h
       if type(table) == "table" then
         local v = rawget(table, key)
         if v ~= nil then return v end
         h = metatable(table).__index
         if h == nil then return nil end
       else
         h = metatable(table).__index
         if h == nil then
           error(···)
         end
       end
       if type(h) == "function" then
         return (h(table, key))     -- call the handler
       else return h[key]           -- or repeat operation on it
       end
     end

    

    • 


  • "newindex":
The indexing assignment table[key] = value.



         function settable_event (table, key, value)
       local h
       if type(table) == "table" then
         local v = rawget(table, key)
         if v ~= nil then rawset(table, key, value); return end
         h = metatable(table).__newindex
         if h == nil then rawset(table, key, value); return end
       else
         h = metatable(table).__newindex
         if h == nil then
           error(···)
         end
       end
       if type(h) == "function" then
         h(table, key,value)           -- call the handler
       else h[key] = value             -- or repeat operation on it
       end
     end

    

    • 


  • "call":
called when Lua calls a value.



         function function_event (func, ...)
       if type(func) == "function" then
         return func(...)   -- primitive call
       else
         local h = metatable(func).__call
         if h then
           return h(func, ...)
         else
           error(···)
         end
       end
     end

    

    • 








2.9 - Environments




Besides metatables,
objects of types thread, function, and userdata
have another table associated with them,
called their environment.
Like metatables, environments are regular tables and
multiple objects can share the same environment.




Threads are created sharing the environment of the creating thread.
Userdata and C functions are created sharing the environment
of the creating C function.
Non-nested Lua functions
(created by loadfile, loadstring or load)
are created sharing the environment of the creating thread.
Nested Lua functions are created sharing the environment of
the creating Lua function.




Environments associated with userdata have no meaning for Lua.
It is only a convenience feature for programmers to associate a table to
a userdata.




Environments associated with threads are called
global environments.
They are used as the default environment for threads and
non-nested Lua functions created by the thread
and can be directly accessed by C code (see §3.3).




The environment associated with a C function can be directly
accessed by C code (see §3.3).
It is used as the default environment for other C functions
and userdata created by the function.




Environments associated with Lua functions are used to resolve
all accesses to global variables within the function (see §2.3).
They are used as the default environment for nested Lua functions
created by the function.




You can change the environment of a Lua function or the
running thread by calling setfenv.
You can get the environment of a Lua function or the running thread
by calling getfenv.
To manipulate the environment of other objects
(userdata, C functions, other threads) you must
use the C API.






2.10 - Garbage Collection




Lua performs automatic memory management.
This means that
you have to worry neither about allocating memory for new objects
nor about freeing it when the objects are no longer needed.
Lua manages memory automatically by running
a garbage collector from time to time
to collect all dead objects
(that is, objects that are no longer accessible from Lua).
All memory used by Lua is subject to automatic management:
tables, userdata, functions, threads, strings, etc.




Lua implements an incremental mark-and-sweep collector.
It uses two numbers to control its garbage-collection cycles:
the garbage-collector pause and
the garbage-collector step multiplier.
Both use percentage points as units
(so that a value of 100 means an internal value of 1).




The garbage-collector pause
controls how long the collector waits before starting a new cycle.
Larger values make the collector less aggressive.
Values smaller than 100 mean the collector will not wait to
start a new cycle.
A value of 200 means that the collector waits for the total memory in use
to double before starting a new cycle.




The step multiplier
controls the relative speed of the collector relative to
memory allocation.
Larger values make the collector more aggressive but also increase
the size of each incremental step.
Values smaller than 100 make the collector too slow and
can result in the collector never finishing a cycle.
The default, 200, means that the collector runs at "twice"
the speed of memory allocation.




You can change these numbers by calling lua_gc in C
or collectgarbage in Lua.
With these functions you can also control 
the collector directly (e.g., stop and restart it).




2.10.1 - Garbage-Collection Metamethods




Using the C API,
you can set garbage-collector metamethods for userdata (see §2.8).
These metamethods are also called finalizers.
Finalizers allow you to coordinate Lua's garbage collection
with external resource management
(such as closing files, network or database connections,
or freeing your own memory).




Garbage userdata with a field __gc in their metatables are not
collected immediately by the garbage collector.
Instead, Lua puts them in a list.
After the collection,
Lua does the equivalent of the following function
for each userdata in that list:


     function gc_event (udata)
       local h = metatable(udata).__gc
       if h then
         h(udata)
       end
     end





At the end of each garbage-collection cycle,
the finalizers for userdata are called in reverse
order of their creation,
among those collected in that cycle.
That is, the first finalizer to be called is the one associated
with the userdata created last in the program.
The userdata itself is freed only in the next garbage-collection cycle.






2.10.2 - Weak Tables




A weak table is a table whose elements are
weak references.
A weak reference is ignored by the garbage collector.
In other words,
if the only references to an object are weak references,
then the garbage collector will collect this object.




A weak table can have weak keys, weak values, or both.
A table with weak keys allows the collection of its keys,
but prevents the collection of its values.
A table with both weak keys and weak values allows the collection of
both keys and values.
In any case, if either the key or the value is collected,
the whole pair is removed from the table.
The weakness of a table is controlled by the
__mode field of its metatable.
If the __mode field is a string containing the character 'k',
the keys in the table are weak.
If __mode contains 'v',
the values in the table are weak.




After you use a table as a metatable,
you should not change the value of its __mode field.
Otherwise, the weak behavior of the tables controlled by this
metatable is undefined.








2.11 - Coroutines




Lua supports coroutines,
also called collaborative multithreading.
A coroutine in Lua represents an independent thread of execution.
Unlike threads in multithread systems, however,
a coroutine only suspends its execution by explicitly calling
a yield function.




You create a coroutine with a call to coroutine.create.
Its sole argument is a function
that is the main function of the coroutine.
The create function only creates a new coroutine and
returns a handle to it (an object of type thread);
it does not start the coroutine execution.




When you first call coroutine.resume,
passing as its first argument
a thread returned by coroutine.create,
the coroutine starts its execution,
at the first line of its main function.
Extra arguments passed to coroutine.resume are passed on
to the coroutine main function.
After the coroutine starts running,
it runs until it terminates or yields.




A coroutine can terminate its execution in two ways:
normally, when its main function returns
(explicitly or implicitly, after the last instruction);
and abnormally, if there is an unprotected error.
In the first case, coroutine.resume returns true,
plus any values returned by the coroutine main function.
In case of errors, coroutine.resume returns false
plus an error message.




A coroutine yields by calling coroutine.yield.
When a coroutine yields,
the corresponding coroutine.resume returns immediately,
even if the yield happens inside nested function calls
(that is, not in the main function,
but in a function directly or indirectly called by the main function).
In the case of a yield, coroutine.resume also returns true,
plus any values passed to coroutine.yield.
The next time you resume the same coroutine,
it continues its execution from the point where it yielded,
with the call to coroutine.yield returning any extra
arguments passed to coroutine.resume.




Like coroutine.create,
the coroutine.wrap function also creates a coroutine,
but instead of returning the coroutine itself,
it returns a function that, when called, resumes the coroutine.
Any arguments passed to this function
go as extra arguments to coroutine.resume.
coroutine.wrap returns all the values returned by coroutine.resume,
except the first one (the boolean error code).
Unlike coroutine.resume,
coroutine.wrap does not catch errors;
any error is propagated to the caller.




As an example,
consider the following code:


     function foo (a)
       print("foo", a)
       return coroutine.yield(2*a)
     end
     
     co = coroutine.create(function (a,b)
           print("co-body", a, b)
           local r = foo(a+1)
           print("co-body", r)
           local r, s = coroutine.yield(a+b, a-b)
           print("co-body", r, s)
           return b, "end"
     end)
            
     print("main", coroutine.resume(co, 1, 10))
     print("main", coroutine.resume(co, "r"))
     print("main", coroutine.resume(co, "x", "y"))
     print("main", coroutine.resume(co, "x", "y"))


When you run it, it produces the following output:


     co-body 1       10
     foo     2
     
     main    true    4
     co-body r
     main    true    11      -9
     co-body x       y
     main    true    10      end
     main    false   cannot resume dead coroutine







3 - The Application Program Interface





This section describes the C API for Lua, that is,
the set of C functions available to the host program to communicate
with Lua.
All API functions and related types and constants
are declared in the header file lua.h.




Even when we use the term "function",
any facility in the API may be provided as a macro instead.
All such macros use each of their arguments exactly once
(except for the first argument, which is always a Lua state),
and so do not generate any hidden side-effects.




As in most C libraries,
the Lua API functions do not check their arguments for validity or consistency.
However, you can change this behavior by compiling Lua
with a proper definition for the macro luai_apicheck,
in file luaconf.h.




3.1 - The Stack




Lua uses a virtual stack to pass values to and from C.
Each element in this stack represents a Lua value
(nil, number, string, etc.).




Whenever Lua calls C, the called function gets a new stack,
which is independent of previous stacks and of stacks of
C functions that are still active.
This stack initially contains any arguments to the C function
and it is where the C function pushes its results
to be returned to the caller (see lua_CFunction).




For convenience,
most query operations in the API do not follow a strict stack discipline.
Instead, they can refer to any element in the stack
by using an index:
A positive index represents an absolute stack position
(starting at 1);
a negative index represents an offset relative to the top of the stack.
More specifically, if the stack has n elements,
then index 1 represents the first element
(that is, the element that was pushed onto the stack first)
and
index n represents the last element;
index -1 also represents the last element
(that is, the element at the top)
and index -n represents the first element.
We say that an index is valid
if it lies between 1 and the stack top
(that is, if 1 ≤ abs(index) ≤ top).
 






3.2 - Stack Size




When you interact with Lua API,
you are responsible for ensuring consistency.
In particular,
you are responsible for controlling stack overflow.
You can use the function lua_checkstack
to grow the stack size.




Whenever Lua calls C,
it ensures that at least LUA_MINSTACK stack positions are available.
LUA_MINSTACK is defined as 20,
so that usually you do not have to worry about stack space
unless your code has loops pushing elements onto the stack.




Most query functions accept as indices any value inside the
available stack space, that is, indices up to the maximum stack size
you have set through lua_checkstack.
Such indices are called acceptable indices.
More formally, we define an acceptable index
as follows:


     (index < 0 && abs(index) <= top) ||
     (index > 0 && index <= stackspace)


Note that 0 is never an acceptable index.






3.3 - Pseudo-Indices




Unless otherwise noted,
any function that accepts valid indices can also be called with
pseudo-indices,
which represent some Lua values that are accessible to C code
but which are not in the stack.
Pseudo-indices are used to access the thread environment,
the function environment,
the registry,
and the upvalues of a C function (see §3.4).




The thread environment (where global variables live) is
always at pseudo-index LUA_GLOBALSINDEX.
The environment of the running C function is always
at pseudo-index LUA_ENVIRONINDEX.




To access and change the value of global variables,
you can use regular table operations over an environment table.
For instance, to access the value of a global variable, do


     lua_getfield(L, LUA_GLOBALSINDEX, varname);







3.4 - C Closures




When a C function is created,
it is possible to associate some values with it,
thus creating a C closure;
these values are called upvalues and are
accessible to the function whenever it is called
(see lua_pushcclosure).




Whenever a C function is called,
its upvalues are located at specific pseudo-indices.
These pseudo-indices are produced by the macro
lua_upvalueindex.
The first value associated with a function is at position
lua_upvalueindex(1), and so on.
Any access to lua_upvalueindex(n),
where n is greater than the number of upvalues of the
current function (but not greater than 256),
produces an acceptable (but invalid) index.






3.5 - Registry




Lua provides a registry,
a pre-defined table that can be used by any C code to
store whatever Lua value it needs to store.
This table is always located at pseudo-index
LUA_REGISTRYINDEX.
Any C library can store data into this table,
but it should take care to choose keys different from those used
by other libraries, to avoid collisions.
Typically, you should use as key a string containing your library name
or a light userdata with the address of a C object in your code.




The integer keys in the registry are used by the reference mechanism,
implemented by the auxiliary library,
and therefore should not be used for other purposes.






3.6 - Error Handling in C




Internally, Lua uses the C longjmp facility to handle errors.
(You can also choose to use exceptions if you use C++;
see file luaconf.h.)
When Lua faces any error
(such as memory allocation errors, type errors, syntax errors,
and runtime errors)
it raises an error;
that is, it does a long jump.
A protected environment uses setjmp
to set a recover point;
any error jumps to the most recent active recover point.




Most functions in the API can throw an error,
for instance due to a memory allocation error.
The documentation for each function indicates whether
it can throw errors.




Inside a C function you can throw an error by calling lua_error.






3.7 - Functions and Types




Here we list all functions and types from the C API in
alphabetical order.
Each function has an indicator like this:
[-o, +p, x]




The first field, o,
is how many elements the function pops from the stack.
The second field, p,
is how many elements the function pushes onto the stack.
(Any function always pushes its results after popping its arguments.)
A field in the form x|y means the function can push (or pop)
x or y elements,
depending on the situation;
an interrogation mark '?' means that
we cannot know how many elements the function pops/pushes
by looking only at its arguments
(e.g., they may depend on what is on the stack).
The third field, x,
tells whether the function may throw errors:
'-' means the function never throws any error;
'm' means the function may throw an error
only due to not enough memory;
'e' means the function may throw other kinds of errors;
'v' means the function may throw an error on purpose.




lua_Alloc


typedef void * (*lua_Alloc) (void *ud,
                             void *ptr,
                             size_t osize,
                             size_t nsize);




The type of the memory-allocation function used by Lua states.
The allocator function must provide a
functionality similar to realloc,
but not exactly the same.
Its arguments are
ud, an opaque pointer passed to lua_newstate;
ptr, a pointer to the block being allocated/reallocated/freed;
osize, the original size of the block;
nsize, the new size of the block.
ptr is NULL if and only if osize is zero.
When nsize is zero, the allocator must return NULL;
if osize is not zero,
it should free the block pointed to by ptr.
When nsize is not zero, the allocator returns NULL
if and only if it cannot fill the request.
When nsize is not zero and osize is zero,
the allocator should behave like malloc.
When nsize and osize are not zero,
the allocator behaves like realloc.
Lua assumes that the allocator never fails when
osize >= nsize.




Here is a simple implementation for the allocator function.
It is used in the auxiliary library by luaL_newstate.


     static void *l_alloc (void *ud, void *ptr, size_t osize,
                                                size_t nsize) {
       (void)ud;  (void)osize;  /* not used */
       if (nsize == 0) {
         free(ptr);
         return NULL;
       }
       else
         return realloc(ptr, nsize);
     }


This code assumes
that free(NULL) has no effect and that
realloc(NULL, size) is equivalent to malloc(size).
ANSI C ensures both behaviors.






lua_atpanic

[-0, +0, -]

lua_CFunction lua_atpanic (lua_State *L, lua_CFunction panicf);




Sets a new panic function and returns the old one.




If an error happens outside any protected environment,
Lua calls a panic function
and then calls exit(EXIT_FAILURE),
thus exiting the host application.
Your panic function can avoid this exit by
never returning (e.g., doing a long jump).




The panic function can access the error message at the top of the stack.






lua_call

[-(nargs + 1), +nresults, e]

void lua_call (lua_State *L, int nargs, int nresults);




Calls a function.




To call a function you must use the following protocol:
first, the function to be called is pushed onto the stack;
then, the arguments to the function are pushed
in direct order;
that is, the first argument is pushed first.
Finally you call lua_call;
nargs is the number of arguments that you pushed onto the stack.
All arguments and the function value are popped from the stack
when the function is called.
The function results are pushed onto the stack when the function returns.
The number of results is adjusted to nresults,
unless nresults is LUA_MULTRET.
In this case, all results from the function are pushed.
Lua takes care that the returned values fit into the stack space.
The function results are pushed onto the stack in direct order
(the first result is pushed first),
so that after the call the last result is on the top of the stack.




Any error inside the called function is propagated upwards
(with a longjmp).




The following example shows how the host program can do the
equivalent to this Lua code:


     a = f("how", t.x, 14)


Here it is in C:


     lua_getfield(L, LUA_GLOBALSINDEX, "f"); /* function to be called */
     lua_pushstring(L, "how");                        /* 1st argument */
     lua_getfield(L, LUA_GLOBALSINDEX, "t");   /* table to be indexed */
     lua_getfield(L, -1, "x");        /* push result of t.x (2nd arg) */
     lua_remove(L, -2);                  /* remove 't' from the stack */
     lua_pushinteger(L, 14);                          /* 3rd argument */
     lua_call(L, 3, 1);     /* call 'f' with 3 arguments and 1 result */
     lua_setfield(L, LUA_GLOBALSINDEX, "a");        /* set global 'a' */


Note that the code above is "balanced":
at its end, the stack is back to its original configuration.
This is considered good programming practice.






lua_CFunction


typedef int (*lua_CFunction) (lua_State *L);




Type for C functions.




In order to communicate properly with Lua,
a C function must use the following protocol,
which defines the way parameters and results are passed:
a C function receives its arguments from Lua in its stack
in direct order (the first argument is pushed first).
So, when the function starts,
lua_gettop(L) returns the number of arguments received by the function.
The first argument (if any) is at index 1
and its last argument is at index lua_gettop(L).
To return values to Lua, a C function just pushes them onto the stack,
in direct order (the first result is pushed first),
and returns the number of results.
Any other value in the stack below the results will be properly
discarded by Lua.
Like a Lua function, a C function called by Lua can also return
many results.




As an example, the following function receives a variable number
of numerical arguments and returns their average and sum:


     static int foo (lua_State *L) {
       int n = lua_gettop(L);    /* number of arguments */
       lua_Number sum = 0;
       int i;
       for (i = 1; i <= n; i++) {
         if (!lua_isnumber(L, i)) {
           lua_pushstring(L, "incorrect argument");
           lua_error(L);
         }
         sum += lua_tonumber(L, i);
       }
       lua_pushnumber(L, sum/n);        /* first result */
       lua_pushnumber(L, sum);         /* second result */
       return 2;                   /* number of results */
     }







lua_checkstack

[-0, +0, m]

int lua_checkstack (lua_State *L, int extra);




Ensures that there are at least extra free stack slots in the stack.
It returns false if it cannot grow the stack to that size.
This function never shrinks the stack;
if the stack is already larger than the new size,
it is left unchanged.






lua_close

[-0, +0, -]

void lua_close (lua_State *L);




Destroys all objects in the given Lua state
(calling the corresponding garbage-collection metamethods, if any)
and frees all dynamic memory used by this state.
On several platforms, you may not need to call this function,
because all resources are naturally released when the host program ends.
On the other hand, long-running programs,
such as a daemon or a web server,
might need to release states as soon as they are not needed,
to avoid growing too large.






lua_concat

[-n, +1, e]

void lua_concat (lua_State *L, int n);




Concatenates the n values at the top of the stack,
pops them, and leaves the result at the top.
If n is 1, the result is the single value on the stack
(that is, the function does nothing);
if n is 0, the result is the empty string.
Concatenation is performed following the usual semantics of Lua
(see §2.5.4).






lua_cpcall

[-0, +(0|1), -]

int lua_cpcall (lua_State *L, lua_CFunction func, void *ud);




Calls the C function func in protected mode.
func starts with only one element in its stack,
a light userdata containing ud.
In case of errors,
lua_cpcall returns the same error codes as lua_pcall,
plus the error object on the top of the stack;
otherwise, it returns zero, and does not change the stack.
All values returned by func are discarded.






lua_createtable

[-0, +1, m]

void lua_createtable (lua_State *L, int narr, int nrec);




Creates a new empty table and pushes it onto the stack.
The new table has space pre-allocated
for narr array elements and nrec non-array elements.
This pre-allocation is useful when you know exactly how many elements
the table will have.
Otherwise you can use the function lua_newtable.






lua_dump

[-0, +0, m]

int lua_dump (lua_State *L, lua_Writer writer, void *data);




Dumps a function as a binary chunk.
Receives a Lua function on the top of the stack
and produces a binary chunk that,
if loaded again,
results in a function equivalent to the one dumped.
As it produces parts of the chunk,
lua_dump calls function writer (see lua_Writer)
with the given data
to write them.




The value returned is the error code returned by the last
call to the writer;
0 means no errors.




This function does not pop the Lua function from the stack.






lua_equal

[-0, +0, e]

int lua_equal (lua_State *L, int index1, int index2);




Returns 1 if the two values in acceptable indices index1 and
index2 are equal,
following the semantics of the Lua == operator
(that is, may call metamethods).
Otherwise returns 0.
Also returns 0 if any of the indices is non valid.






lua_error

[-1, +0, v]

int lua_error (lua_State *L);




Generates a Lua error.
The error message (which can actually be a Lua value of any type)
must be on the stack top.
This function does a long jump,
and therefore never returns.
(see luaL_error).






lua_gc

[-0, +0, e]

int lua_gc (lua_State *L, int what, int data);




Controls the garbage collector.




This function performs several tasks,
according to the value of the parameter what:


    


  • LUA_GCSTOP:
stops the garbage collector.

    • 


  • LUA_GCRESTART:
restarts the garbage collector.

    • 


  • LUA_GCCOLLECT:
performs a full garbage-collection cycle.

    • 


  • LUA_GCCOUNT:
returns the current amount of memory (in Kbytes) in use by Lua.

    • 


  • LUA_GCCOUNTB:
returns the remainder of dividing the current amount of bytes of
memory in use by Lua by 1024.

    • 


  • LUA_GCSTEP:
performs an incremental step of garbage collection.
The step "size" is controlled by data
(larger values mean more steps) in a non-specified way.
If you want to control the step size
you must experimentally tune the value of data.
The function returns 1 if the step finished a
garbage-collection cycle.

    • 


  • LUA_GCSETPAUSE:
sets data as the new value
for the pause of the collector (see §2.10).
The function returns the previous value of the pause.

    • 


  • LUA_GCSETSTEPMUL:
sets data as the new value for the step multiplier of
the collector (see §2.10).
The function returns the previous value of the step multiplier.

    • 








lua_getallocf

[-0, +0, -]

lua_Alloc lua_getallocf (lua_State *L, void **ud);




Returns the memory-allocation function of a given state.
If ud is not NULL, Lua stores in *ud the
opaque pointer passed to lua_newstate.






lua_getfenv

[-0, +1, -]

void lua_getfenv (lua_State *L, int index);




Pushes onto the stack the environment table of
the value at the given index.






lua_getfield

[-0, +1, e]

void lua_getfield (lua_State *L, int index, const char *k);




Pushes onto the stack the value t[k],
where t is the value at the given valid index.
As in Lua, this function may trigger a metamethod
for the "index" event (see §2.8).






lua_getglobal

[-0, +1, e]

void lua_getglobal (lua_State *L, const char *name);




Pushes onto the stack the value of the global name.
It is defined as a macro:


     #define lua_getglobal(L,s)  lua_getfield(L, LUA_GLOBALSINDEX, s)







lua_getmetatable

[-0, +(0|1), -]

int lua_getmetatable (lua_State *L, int index);




Pushes onto the stack the metatable of the value at the given
acceptable index.
If the index is not valid,
or if the value does not have a metatable,
the function returns 0 and pushes nothing on the stack.






lua_gettable

[-1, +1, e]

void lua_gettable (lua_State *L, int index);




Pushes onto the stack the value t[k],
where t is the value at the given valid index
and k is the value at the top of the stack.




This function pops the key from the stack
(putting the resulting value in its place).
As in Lua, this function may trigger a metamethod
for the "index" event (see §2.8).






lua_gettop

[-0, +0, -]

int lua_gettop (lua_State *L);




Returns the index of the top element in the stack.
Because indices start at 1,
this result is equal to the number of elements in the stack
(and so 0 means an empty stack).






lua_insert

[-1, +1, -]

void lua_insert (lua_State *L, int index);




Moves the top element into the given valid index,
shifting up the elements above this index to open space.
Cannot be called with a pseudo-index,
because a pseudo-index is not an actual stack position.






lua_Integer


typedef ptrdiff_t lua_Integer;




The type used by the Lua API to represent integral values.




By default it is a ptrdiff_t,
which is usually the largest signed integral type the machine handles
"comfortably".






lua_isboolean

[-0, +0, -]

int lua_isboolean (lua_State *L, int index);




Returns 1 if the value at the given acceptable index has type boolean,
and 0 otherwise.






lua_iscfunction

[-0, +0, -]

int lua_iscfunction (lua_State *L, int index);




Returns 1 if the value at the given acceptable index is a C function,
and 0 otherwise.






lua_isfunction

[-0, +0, -]

int lua_isfunction (lua_State *L, int index);




Returns 1 if the value at the given acceptable index is a function
(either C or Lua), and 0 otherwise.






lua_islightuserdata

[-0, +0, -]

int lua_islightuserdata (lua_State *L, int index);




Returns 1 if the value at the given acceptable index is a light userdata,
and 0 otherwise.






lua_isnil

[-0, +0, -]

int lua_isnil (lua_State *L, int index);




Returns 1 if the value at the given acceptable index is nil,
and 0 otherwise.






lua_isnone

[-0, +0, -]

int lua_isnone (lua_State *L, int index);




Returns 1 if the given acceptable index is not valid
(that is, it refers to an element outside the current stack),
and 0 otherwise.






lua_isnoneornil

[-0, +0, -]

int lua_isnoneornil (lua_State *L, int index);




Returns 1 if the given acceptable index is not valid
(that is, it refers to an element outside the current stack)
or if the value at this index is nil,
and 0 otherwise.






lua_isnumber

[-0, +0, -]

int lua_isnumber (lua_State *L, int index);




Returns 1 if the value at the given acceptable index is a number
or a string convertible to a number,
and 0 otherwise.






lua_isstring

[-0, +0, -]

int lua_isstring (lua_State *L, int index);




Returns 1 if the value at the given acceptable index is a string
or a number (which is always convertible to a string),
and 0 otherwise.






lua_istable

[-0, +0, -]

int lua_istable (lua_State *L, int index);




Returns 1 if the value at the given acceptable index is a table,
and 0 otherwise.






lua_isthread

[-0, +0, -]

int lua_isthread (lua_State *L, int index);




Returns 1 if the value at the given acceptable index is a thread,
and 0 otherwise.






lua_isuserdata

[-0, +0, -]

int lua_isuserdata (lua_State *L, int index);




Returns 1 if the value at the given acceptable index is a userdata
(either full or light), and 0 otherwise.






lua_lessthan

[-0, +0, e]

int lua_lessthan (lua_State *L, int index1, int index2);




Returns 1 if the value at acceptable index index1 is smaller
than the value at acceptable index index2,
following the semantics of the Lua < operator
(that is, may call metamethods).
Otherwise returns 0.
Also returns 0 if any of the indices is non valid.






lua_load

[-0, +1, -]

int lua_load (lua_State *L,
              lua_Reader reader,
              void *data,
              const char *chunkname);




Loads a Lua chunk.
If there are no errors,
lua_load pushes the compiled chunk as a Lua
function on top of the stack.
Otherwise, it pushes an error message.
The return values of lua_load are:






This function only loads a chunk;
it does not run it.




lua_load automatically detects whether the chunk is text or binary,
and loads it accordingly (see program luac).




The lua_load function uses a user-supplied reader function
to read the chunk (see lua_Reader).
The data argument is an opaque value passed to the reader function.




The chunkname argument gives a name to the chunk,
which is used for error messages and in debug information (see §3.8).






lua_newstate

[-0, +0, -]

lua_State *lua_newstate (lua_Alloc f, void *ud);




Creates a new, independent state.
Returns NULL if cannot create the state
(due to lack of memory).
The argument f is the allocator function;
Lua does all memory allocation for this state through this function.
The second argument, ud, is an opaque pointer that Lua
simply passes to the allocator in every call.






lua_newtable

[-0, +1, m]

void lua_newtable (lua_State *L);




Creates a new empty table and pushes it onto the stack.
It is equivalent to lua_createtable(L, 0, 0).






lua_newthread

[-0, +1, m]

lua_State *lua_newthread (lua_State *L);




Creates a new thread, pushes it on the stack,
and returns a pointer to a lua_State that represents this new thread.
The new state returned by this function shares with the original state
all global objects (such as tables),
but has an independent execution stack.




There is no explicit function to close or to destroy a thread.
Threads are subject to garbage collection,
like any Lua object.






lua_newuserdata

[-0, +1, m]

void *lua_newuserdata (lua_State *L, size_t size);




This function allocates a new block of memory with the given size,
pushes onto the stack a new full userdata with the block address,
and returns this address.




Userdata represent C values in Lua.
A full userdata represents a block of memory.
It is an object (like a table):
you must create it, it can have its own metatable,
and you can detect when it is being collected.
A full userdata is only equal to itself (under raw equality).




When Lua collects a full userdata with a gc metamethod,
Lua calls the metamethod and marks the userdata as finalized.
When this userdata is collected again then
Lua frees its corresponding memory.






lua_next

[-1, +(2|0), e]

int lua_next (lua_State *L, int index);




Pops a key from the stack,
and pushes a key-value pair from the table at the given index
(the "next" pair after the given key).
If there are no more elements in the table,
then lua_next returns 0 (and pushes nothing).




A typical traversal looks like this:


     /* table is in the stack at index 't' */
     lua_pushnil(L);  /* first key */
     while (lua_next(L, t) != 0) {
       /* uses 'key' (at index -2) and 'value' (at index -1) */
       printf("%s - %s\n",
              lua_typename(L, lua_type(L, -2)),
              lua_typename(L, lua_type(L, -1)));
       /* removes 'value'; keeps 'key' for next iteration */
       lua_pop(L, 1);
     }





While traversing a table,
do not call lua_tolstring directly on a key,
unless you know that the key is actually a string.
Recall that lua_tolstring changes
the value at the given index;
this confuses the next call to lua_next.






lua_Number


typedef double lua_Number;




The type of numbers in Lua.
By default, it is double, but that can be changed in luaconf.h.




Through the configuration file you can change
Lua to operate with another type for numbers (e.g., float or long).






lua_objlen

[-0, +0, -]

size_t lua_objlen (lua_State *L, int index);




Returns the "length" of the value at the given acceptable index:
for strings, this is the string length;
for tables, this is the result of the length operator ('#');
for userdata, this is the size of the block of memory allocated
for the userdata;
for other values, it is 0.






lua_pcall

[-(nargs + 1), +(nresults|1), -]

int lua_pcall (lua_State *L, int nargs, int nresults, int errfunc);




Calls a function in protected mode.




Both nargs and nresults have the same meaning as
in lua_call.
If there are no errors during the call,
lua_pcall behaves exactly like lua_call.
However, if there is any error,
lua_pcall catches it,
pushes a single value on the stack (the error message),
and returns an error code.
Like lua_call,
lua_pcall always removes the function
and its arguments from the stack.




If errfunc is 0,
then the error message returned on the stack
is exactly the original error message.
Otherwise, errfunc is the stack index of an
error handler function.
(In the current implementation, this index cannot be a pseudo-index.)
In case of runtime errors,
this function will be called with the error message
and its return value will be the message returned on the stack by lua_pcall.




Typically, the error handler function is used to add more debug
information to the error message, such as a stack traceback.
Such information cannot be gathered after the return of lua_pcall,
since by then the stack has unwound.




The lua_pcall function returns 0 in case of success
or one of the following error codes
(defined in lua.h):


    


  • LUA_ERRRUN:
a runtime error.

    • 


  • LUA_ERRMEM:
memory allocation error.
For such errors, Lua does not call the error handler function.

    • 


  • LUA_ERRERR:
error while running the error handler function.

    • 








lua_pop

[-n, +0, -]

void lua_pop (lua_State *L, int n);




Pops n elements from the stack.






lua_pushboolean

[-0, +1, -]

void lua_pushboolean (lua_State *L, int b);




Pushes a boolean value with value b onto the stack.






lua_pushcclosure

[-n, +1, m]

void lua_pushcclosure (lua_State *L, lua_CFunction fn, int n);




Pushes a new C closure onto the stack.




When a C function is created,
it is possible to associate some values with it,
thus creating a C closure (see §3.4);
these values are then accessible to the function whenever it is called.
To associate values with a C function,
first these values should be pushed onto the stack
(when there are multiple values, the first value is pushed first).
Then lua_pushcclosure
is called to create and push the C function onto the stack,
with the argument n telling how many values should be
associated with the function.
lua_pushcclosure also pops these values from the stack.




The maximum value for n is 255.






lua_pushcfunction

[-0, +1, m]

void lua_pushcfunction (lua_State *L, lua_CFunction f);




Pushes a C function onto the stack.
This function receives a pointer to a C function
and pushes onto the stack a Lua value of type function that,
when called, invokes the corresponding C function.




Any function to be registered in Lua must
follow the correct protocol to receive its parameters
and return its results (see lua_CFunction).




lua_pushcfunction is defined as a macro:


     #define lua_pushcfunction(L,f)  lua_pushcclosure(L,f,0)







lua_pushfstring

[-0, +1, m]

const char *lua_pushfstring (lua_State *L, const char *fmt, ...);




Pushes onto the stack a formatted string
and returns a pointer to this string.
It is similar to the C function sprintf,
but has some important differences:


    


  • 
You do not have to allocate space for the result:
the result is a Lua string and Lua takes care of memory allocation
(and deallocation, through garbage collection).

    • 


  • 
The conversion specifiers are quite restricted.
There are no flags, widths, or precisions.
The conversion specifiers can only be
'%%' (inserts a '%' in the string),
'%s' (inserts a zero-terminated string, with no size restrictions),
'%f' (inserts a lua_Number),
'%p' (inserts a pointer as a hexadecimal numeral),
'%d' (inserts an int), and
'%c' (inserts an int as a character).

    • 








lua_pushinteger

[-0, +1, -]

void lua_pushinteger (lua_State *L, lua_Integer n);




Pushes a number with value n onto the stack.






lua_pushlightuserdata

[-0, +1, -]

void lua_pushlightuserdata (lua_State *L, void *p);




Pushes a light userdata onto the stack.




Userdata represent C values in Lua.
A light userdata represents a pointer.
It is a value (like a number):
you do not create it, it has no individual metatable,
and it is not collected (as it was never created).
A light userdata is equal to "any"
light userdata with the same C address.






lua_pushliteral

[-0, +1, m]

void lua_pushliteral (lua_State *L, const char *s);




This macro is equivalent to lua_pushlstring,
but can be used only when s is a literal string.
In these cases, it automatically provides the string length.






lua_pushlstring

[-0, +1, m]

void lua_pushlstring (lua_State *L, const char *s, size_t len);




Pushes the string pointed to by s with size len
onto the stack.
Lua makes (or reuses) an internal copy of the given string,
so the memory at s can be freed or reused immediately after
the function returns.
The string can contain embedded zeros.






lua_pushnil

[-0, +1, -]

void lua_pushnil (lua_State *L);




Pushes a nil value onto the stack.






lua_pushnumber

[-0, +1, -]

void lua_pushnumber (lua_State *L, lua_Number n);




Pushes a number with value n onto the stack.






lua_pushstring

[-0, +1, m]

void lua_pushstring (lua_State *L, const char *s);




Pushes the zero-terminated string pointed to by s
onto the stack.
Lua makes (or reuses) an internal copy of the given string,
so the memory at s can be freed or reused immediately after
the function returns.
The string cannot contain embedded zeros;
it is assumed to end at the first zero.






lua_pushthread

[-0, +1, -]

int lua_pushthread (lua_State *L);




Pushes the thread represented by L onto the stack.
Returns 1 if this thread is the main thread of its state.






lua_pushvalue

[-0, +1, -]

void lua_pushvalue (lua_State *L, int index);




Pushes a copy of the element at the given valid index
onto the stack.






lua_pushvfstring

[-0, +1, m]

const char *lua_pushvfstring (lua_State *L,
                              const char *fmt,
                              va_list argp);




Equivalent to lua_pushfstring, except that it receives a va_list
instead of a variable number of arguments.






lua_rawequal

[-0, +0, -]

int lua_rawequal (lua_State *L, int index1, int index2);




Returns 1 if the two values in acceptable indices index1 and
index2 are primitively equal
(that is, without calling metamethods).
Otherwise returns 0.
Also returns 0 if any of the indices are non valid.






lua_rawget

[-1, +1, -]

void lua_rawget (lua_State *L, int index);




Similar to lua_gettable, but does a raw access
(i.e., without metamethods).






lua_rawgeti

[-0, +1, -]

void lua_rawgeti (lua_State *L, int index, int n);




Pushes onto the stack the value t[n],
where t is the value at the given valid index.
The access is raw;
that is, it does not invoke metamethods.






lua_rawset

[-2, +0, m]

void lua_rawset (lua_State *L, int index);




Similar to lua_settable, but does a raw assignment
(i.e., without metamethods).






lua_rawseti

[-1, +0, m]

void lua_rawseti (lua_State *L, int index, int n);




Does the equivalent of t[n] = v,
where t is the value at the given valid index
and v is the value at the top of the stack.




This function pops the value from the stack.
The assignment is raw;
that is, it does not invoke metamethods.






lua_Reader


typedef const char * (*lua_Reader) (lua_State *L,
                                    void *data,
                                    size_t *size);




The reader function used by lua_load.
Every time it needs another piece of the chunk,
lua_load calls the reader,
passing along its data parameter.
The reader must return a pointer to a block of memory
with a new piece of the chunk
and set size to the block size.
The block must exist until the reader function is called again.
To signal the end of the chunk,
the reader must return NULL or set size to zero.
The reader function may return pieces of any size greater than zero.






lua_register

[-0, +0, e]

void lua_register (lua_State *L,
                   const char *name,
                   lua_CFunction f);




Sets the C function f as the new value of global name.
It is defined as a macro:


     #define lua_register(L,n,f) \
            (lua_pushcfunction(L, f), lua_setglobal(L, n))







lua_remove

[-1, +0, -]

void lua_remove (lua_State *L, int index);




Removes the element at the given valid index,
shifting down the elements above this index to fill the gap.
Cannot be called with a pseudo-index,
because a pseudo-index is not an actual stack position.






lua_replace

[-1, +0, -]

void lua_replace (lua_State *L, int index);




Moves the top element into the given position (and pops it),
without shifting any element
(therefore replacing the value at the given position).






lua_resume

[-?, +?, -]

int lua_resume (lua_State *L, int narg);




Starts and resumes a coroutine in a given thread.




To start a coroutine, you first create a new thread
(see lua_newthread);
then you push onto its stack the main function plus any arguments;
then you call lua_resume,
with narg being the number of arguments.
This call returns when the coroutine suspends or finishes its execution.
When it returns, the stack contains all values passed to lua_yield,
or all values returned by the body function.
lua_resume returns
LUA_YIELD if the coroutine yields,
0 if the coroutine finishes its execution
without errors,
or an error code in case of errors (see lua_pcall).
In case of errors,
the stack is not unwound,
so you can use the debug API over it.
The error message is on the top of the stack.
To restart a coroutine, you put on its stack only the values to
be passed as results from yield,
and then call lua_resume.






lua_setallocf

[-0, +0, -]

void lua_setallocf (lua_State *L, lua_Alloc f, void *ud);




Changes the allocator function of a given state to f
with user data ud.






lua_setfenv

[-1, +0, -]

int lua_setfenv (lua_State *L, int index);




Pops a table from the stack and sets it as
the new environment for the value at the given index.
If the value at the given index is
neither a function nor a thread nor a userdata,
lua_setfenv returns 0.
Otherwise it returns 1.






lua_setfield

[-1, +0, e]

void lua_setfield (lua_State *L, int index, const char *k);




Does the equivalent to t[k] = v,
where t is the value at the given valid index
and v is the value at the top of the stack.




This function pops the value from the stack.
As in Lua, this function may trigger a metamethod
for the "newindex" event (see §2.8).






lua_setglobal

[-1, +0, e]

void lua_setglobal (lua_State *L, const char *name);




Pops a value from the stack and
sets it as the new value of global name.
It is defined as a macro:


     #define lua_setglobal(L,s)   lua_setfield(L, LUA_GLOBALSINDEX, s)







lua_setmetatable

[-1, +0, -]

int lua_setmetatable (lua_State *L, int index);




Pops a table from the stack and
sets it as the new metatable for the value at the given
acceptable index.






lua_settable

[-2, +0, e]

void lua_settable (lua_State *L, int index);




Does the equivalent to t[k] = v,
where t is the value at the given valid index,
v is the value at the top of the stack,
and k is the value just below the top.




This function pops both the key and the value from the stack.
As in Lua, this function may trigger a metamethod
for the "newindex" event (see §2.8).






lua_settop

[-?, +?, -]

void lua_settop (lua_State *L, int index);




Accepts any acceptable index, or 0,
and sets the stack top to this index.
If the new top is larger than the old one,
then the new elements are filled with nil.
If index is 0, then all stack elements are removed.






lua_State


typedef struct lua_State lua_State;




Opaque structure that keeps the whole state of a Lua interpreter.
The Lua library is fully reentrant:
it has no global variables.
All information about a state is kept in this structure.




A pointer to this state must be passed as the first argument to
every function in the library, except to lua_newstate,
which creates a Lua state from scratch.






lua_status

[-0, +0, -]

int lua_status (lua_State *L);




Returns the status of the thread L.




The status can be 0 for a normal thread,
an error code if the thread finished its execution with an error,
or LUA_YIELD if the thread is suspended.






lua_toboolean

[-0, +0, -]

int lua_toboolean (lua_State *L, int index);




Converts the Lua value at the given acceptable index to a C boolean
value (0 or 1).
Like all tests in Lua,
lua_toboolean returns 1 for any Lua value
different from false and nil;
otherwise it returns 0.
It also returns 0 when called with a non-valid index.
(If you want to accept only actual boolean values,
use lua_isboolean to test the value's type.)






lua_tocfunction

[-0, +0, -]

lua_CFunction lua_tocfunction (lua_State *L, int index);




Converts a value at the given acceptable index to a C function.
That value must be a C function;
otherwise, returns NULL.






lua_tointeger

[-0, +0, -]

lua_Integer lua_tointeger (lua_State *L, int index);




Converts the Lua value at the given acceptable index
to the signed integral type lua_Integer.
The Lua value must be a number or a string convertible to a number
(see §2.2.1);
otherwise, lua_tointeger returns 0.




If the number is not an integer,
it is truncated in some non-specified way.






lua_tolstring

[-0, +0, m]

const char *lua_tolstring (lua_State *L, int index, size_t *len);




Converts the Lua value at the given acceptable index to a C string.
If len is not NULL,
it also sets *len with the string length.
The Lua value must be a string or a number;
otherwise, the function returns NULL.
If the value is a number,
then lua_tolstring also
changes the actual value in the stack to a string.
(This change confuses lua_next
when lua_tolstring is applied to keys during a table traversal.)




lua_tolstring returns a fully aligned pointer
to a string inside the Lua state.
This string always has a zero ('\0')
after its last character (as in C),
but can contain other zeros in its body.
Because Lua has garbage collection,
there is no guarantee that the pointer returned by lua_tolstring
will be valid after the corresponding value is removed from the stack.






lua_tonumber

[-0, +0, -]

lua_Number lua_tonumber (lua_State *L, int index);




Converts the Lua value at the given acceptable index
to the C type lua_Number (see lua_Number).
The Lua value must be a number or a string convertible to a number
(see §2.2.1);
otherwise, lua_tonumber returns 0.






lua_topointer

[-0, +0, -]

const void *lua_topointer (lua_State *L, int index);




Converts the value at the given acceptable index to a generic
C pointer (void*).
The value can be a userdata, a table, a thread, or a function;
otherwise, lua_topointer returns NULL.
Different objects will give different pointers.
There is no way to convert the pointer back to its original value.




Typically this function is used only for debug information.






lua_tostring

[-0, +0, m]

const char *lua_tostring (lua_State *L, int index);




Equivalent to lua_tolstring with len equal to NULL.






lua_tothread

[-0, +0, -]

lua_State *lua_tothread (lua_State *L, int index);




Converts the value at the given acceptable index to a Lua thread
(represented as lua_State*).
This value must be a thread;
otherwise, the function returns NULL.






lua_touserdata

[-0, +0, -]

void *lua_touserdata (lua_State *L, int index);




If the value at the given acceptable index is a full userdata,
returns its block address.
If the value is a light userdata,
returns its pointer.
Otherwise, returns NULL.






lua_type

[-0, +0, -]

int lua_type (lua_State *L, int index);




Returns the type of the value in the given acceptable index,
or LUA_TNONE for a non-valid index
(that is, an index to an "empty" stack position).
The types returned by lua_type are coded by the following constants
defined in lua.h:
LUA_TNIL,
LUA_TNUMBER,
LUA_TBOOLEAN,
LUA_TSTRING,
LUA_TTABLE,
LUA_TFUNCTION,
LUA_TUSERDATA,
LUA_TTHREAD,
and
LUA_TLIGHTUSERDATA.






lua_typename

[-0, +0, -]

const char *lua_typename  (lua_State *L, int tp);




Returns the name of the type encoded by the value tp,
which must be one the values returned by lua_type.






lua_Writer


typedef int (*lua_Writer) (lua_State *L,
                           const void* p,
                           size_t sz,
                           void* ud);




The type of the writer function used by lua_dump.
Every time it produces another piece of chunk,
lua_dump calls the writer,
passing along the buffer to be written (p),
its size (sz),
and the data parameter supplied to lua_dump.




The writer returns an error code:
0 means no errors;
any other value means an error and stops lua_dump from
calling the writer again.






lua_xmove

[-?, +?, -]

void lua_xmove (lua_State *from, lua_State *to, int n);




Exchange values between different threads of the same global state.




This function pops n values from the stack from,
and pushes them onto the stack to.






lua_yield

[-?, +?, -]

int lua_yield  (lua_State *L, int nresults);




Yields a coroutine.




This function should only be called as the
return expression of a C function, as follows:


     return lua_yield (L, nresults);


When a C function calls lua_yield in that way,
the running coroutine suspends its execution,
and the call to lua_resume that started this coroutine returns.
The parameter nresults is the number of values from the stack
that are passed as results to lua_resume.








3.8 - The Debug Interface




Lua has no built-in debugging facilities.
Instead, it offers a special interface
by means of functions and hooks.
This interface allows the construction of different
kinds of debuggers, profilers, and other tools
that need "inside information" from the interpreter.




lua_Debug


typedef struct lua_Debug {
  int event;
  const char *name;           /* (n) */
  const char *namewhat;       /* (n) */
  const char *what;           /* (S) */
  const char *source;         /* (S) */
  int currentline;            /* (l) */
  int nups;                   /* (u) number of upvalues */
  int linedefined;            /* (S) */
  int lastlinedefined;        /* (S) */
  char short_src[LUA_IDSIZE]; /* (S) */
  /* private part */
  other fields
} lua_Debug;




A structure used to carry different pieces of
information about an active function.
lua_getstack fills only the private part
of this structure, for later use.
To fill the other fields of lua_Debug with useful information,
call lua_getinfo.




The fields of lua_Debug have the following meaning:


    


  • source:
If the function was defined in a string,
then source is that string.
If the function was defined in a file,
then source starts with a '@' followed by the file name.

    • 


  • short_src:
a "printable" version of source, to be used in error messages.

    • 


  • linedefined:
the line number where the definition of the function starts.

    • 


  • lastlinedefined:
the line number where the definition of the function ends.

    • 


  • what:
the string "Lua" if the function is a Lua function,
"C" if it is a C function,
"main" if it is the main part of a chunk,
and "tail" if it was a function that did a tail call.
In the latter case,
Lua has no other information about the function.

    • 


  • currentline:
the current line where the given function is executing.
When no line information is available,
currentline is set to -1.

    • 


  • name:
a reasonable name for the given function.
Because functions in Lua are first-class values,
they do not have a fixed name:
some functions can be the value of multiple global variables,
while others can be stored only in a table field.
The lua_getinfo function checks how the function was
called to find a suitable name.
If it cannot find a name,
then name is set to NULL.

    • 


  • namewhat:
explains the name field.
The value of namewhat can be
"global", "local", "method",
"field", "upvalue", or "" (the empty string),
according to how the function was called.
(Lua uses the empty string when no other option seems to apply.)

    • 


  • nups:
the number of upvalues of the function.

    • 








lua_gethook

[-0, +0, -]

lua_Hook lua_gethook (lua_State *L);




Returns the current hook function.






lua_gethookcount

[-0, +0, -]

int lua_gethookcount (lua_State *L);




Returns the current hook count.






lua_gethookmask

[-0, +0, -]

int lua_gethookmask (lua_State *L);




Returns the current hook mask.






lua_getinfo

[-(0|1), +(0|1|2), m]

int lua_getinfo (lua_State *L, const char *what, lua_Debug *ar);




Returns information about a specific function or function invocation.




To get information about a function invocation,
the parameter ar must be a valid activation record that was
filled by a previous call to lua_getstack or
given as argument to a hook (see lua_Hook).




To get information about a function you push it onto the stack
and start the what string with the character '>'.
(In that case,
lua_getinfo pops the function in the top of the stack.)
For instance, to know in which line a function f was defined,
you can write the following code:


     lua_Debug ar;
     lua_getfield(L, LUA_GLOBALSINDEX, "f");  /* get global 'f' */
     lua_getinfo(L, ">S", &ar);
     printf("%d\n", ar.linedefined);





Each character in the string what
selects some fields of the structure ar to be filled or
a value to be pushed on the stack:


    


  • 'n': fills in the field name and namewhat;

    • 


  • 'S':
fills in the fields source, short_src,
linedefined, lastlinedefined, and what;

    • 


  • 'l': fills in the field currentline;

    • 


  • 'u': fills in the field nups;

    • 


  • 'f':
pushes onto the stack the function that is
running at the given level;

    • 


  • 'L':
pushes onto the stack a table whose indices are the
numbers of the lines that are valid on the function.
(A valid line is a line with some associated code,
that is, a line where you can put a break point.
Non-valid lines include empty lines and comments.)

    • 






This function returns 0 on error
(for instance, an invalid option in what).






lua_getlocal

[-0, +(0|1), -]

const char *lua_getlocal (lua_State *L, lua_Debug *ar, int n);




Gets information about a local variable of a given activation record.
The parameter ar must be a valid activation record that was
filled by a previous call to lua_getstack or
given as argument to a hook (see lua_Hook).
The index n selects which local variable to inspect
(1 is the first parameter or active local variable, and so on,
until the last active local variable).
lua_getlocal pushes the variable's value onto the stack
and returns its name.




Variable names starting with '(' (open parentheses)
represent internal variables
(loop control variables, temporaries, and C function locals).




Returns NULL (and pushes nothing)
when the index is greater than
the number of active local variables.






lua_getstack

[-0, +0, -]

int lua_getstack (lua_State *L, int level, lua_Debug *ar);




Get information about the interpreter runtime stack.




This function fills parts of a lua_Debug structure with
an identification of the activation record
of the function executing at a given level.
Level 0 is the current running function,
whereas level n+1 is the function that has called level n.
When there are no errors, lua_getstack returns 1;
when called with a level greater than the stack depth,
it returns 0.






lua_getupvalue

[-0, +(0|1), -]

const char *lua_getupvalue (lua_State *L, int funcindex, int n);




Gets information about a closure's upvalue.
(For Lua functions,
upvalues are the external local variables that the function uses,
and that are consequently included in its closure.)
lua_getupvalue gets the index n of an upvalue,
pushes the upvalue's value onto the stack,
and returns its name.
funcindex points to the closure in the stack.
(Upvalues have no particular order,
as they are active through the whole function.
So, they are numbered in an arbitrary order.)




Returns NULL (and pushes nothing)
when the index is greater than the number of upvalues.
For C functions, this function uses the empty string ""
as a name for all upvalues.






lua_Hook


typedef void (*lua_Hook) (lua_State *L, lua_Debug *ar);




Type for debugging hook functions.




Whenever a hook is called, its ar argument has its field
event set to the specific event that triggered the hook.
Lua identifies these events with the following constants:
LUA_HOOKCALL, LUA_HOOKRET,
LUA_HOOKTAILRET, LUA_HOOKLINE,
and LUA_HOOKCOUNT.
Moreover, for line events, the field currentline is also set.
To get the value of any other field in ar,
the hook must call lua_getinfo.
For return events, event can be LUA_HOOKRET,
the normal value, or LUA_HOOKTAILRET.
In the latter case, Lua is simulating a return from
a function that did a tail call;
in this case, it is useless to call lua_getinfo.




While Lua is running a hook, it disables other calls to hooks.
Therefore, if a hook calls back Lua to execute a function or a chunk,
this execution occurs without any calls to hooks.






lua_sethook

[-0, +0, -]

int lua_sethook (lua_State *L, lua_Hook f, int mask, int count);




Sets the debugging hook function.




Argument f is the hook function.
mask specifies on which events the hook will be called:
it is formed by a bitwise or of the constants
LUA_MASKCALL,
LUA_MASKRET,
LUA_MASKLINE,
and LUA_MASKCOUNT.
The count argument is only meaningful when the mask
includes LUA_MASKCOUNT.
For each event, the hook is called as explained below:


    


  • The call hook: is called when the interpreter calls a function.
The hook is called just after Lua enters the new function,
before the function gets its arguments.

    • 


  • The return hook: is called when the interpreter returns from a function.
The hook is called just before Lua leaves the function.
You have no access to the values to be returned by the function.

    • 


  • The line hook: is called when the interpreter is about to
start the execution of a new line of code,
or when it jumps back in the code (even to the same line).
(This event only happens while Lua is executing a Lua function.)

    • 


  • The count hook: is called after the interpreter executes every
count instructions.
(This event only happens while Lua is executing a Lua function.)

    • 






A hook is disabled by setting mask to zero.






lua_setlocal

[-(0|1), +0, -]

const char *lua_setlocal (lua_State *L, lua_Debug *ar, int n);




Sets the value of a local variable of a given activation record.
Parameters ar and n are as in lua_getlocal
(see lua_getlocal).
lua_setlocal assigns the value at the top of the stack
to the variable and returns its name.
It also pops the value from the stack.




Returns NULL (and pops nothing)
when the index is greater than
the number of active local variables.






lua_setupvalue

[-(0|1), +0, -]

const char *lua_setupvalue (lua_State *L, int funcindex, int n);




Sets the value of a closure's upvalue.
It assigns the value at the top of the stack
to the upvalue and returns its name.
It also pops the value from the stack.
Parameters funcindex and n are as in the lua_getupvalue
(see lua_getupvalue).




Returns NULL (and pops nothing)
when the index is greater than the number of upvalues.








4 - The Auxiliary Library





The auxiliary library provides several convenient functions
to interface C with Lua.
While the basic API provides the primitive functions for all 
interactions between C and Lua,
the auxiliary library provides higher-level functions for some
common tasks.




All functions from the auxiliary library
are defined in header file lauxlib.h and
have a prefix luaL_.




All functions in the auxiliary library are built on
top of the basic API,
and so they provide nothing that cannot be done with this API.




Several functions in the auxiliary library are used to
check C function arguments.
Their names are always luaL_check* or luaL_opt*.
All of these functions throw an error if the check is not satisfied.
Because the error message is formatted for arguments
(e.g., "bad argument #1"),
you should not use these functions for other stack values.




4.1 - Functions and Types




Here we list all functions and types from the auxiliary library
in alphabetical order.




luaL_addchar

[-0, +0, m]

void luaL_addchar (luaL_Buffer *B, char c);




Adds the character c to the buffer B
(see luaL_Buffer).






luaL_addlstring

[-0, +0, m]

void luaL_addlstring (luaL_Buffer *B, const char *s, size_t l);




Adds the string pointed to by s with length l to
the buffer B
(see luaL_Buffer).
The string may contain embedded zeros.






luaL_addsize

[-0, +0, m]

void luaL_addsize (luaL_Buffer *B, size_t n);




Adds to the buffer B (see luaL_Buffer)
a string of length n previously copied to the
buffer area (see luaL_prepbuffer).






luaL_addstring

[-0, +0, m]

void luaL_addstring (luaL_Buffer *B, const char *s);




Adds the zero-terminated string pointed to by s
to the buffer B
(see luaL_Buffer).
The string may not contain embedded zeros.






luaL_addvalue

[-1, +0, m]

void luaL_addvalue (luaL_Buffer *B);




Adds the value at the top of the stack
to the buffer B
(see luaL_Buffer).
Pops the value.




This is the only function on string buffers that can (and must)
be called with an extra element on the stack,
which is the value to be added to the buffer.






luaL_argcheck

[-0, +0, v]

void luaL_argcheck (lua_State *L,
                    int cond,
                    int narg,
                    const char *extramsg);




Checks whether cond is true.
If not, raises an error with the following message,
where func is retrieved from the call stack:


     bad argument #<narg> to <func> (<extramsg>)







luaL_argerror

[-0, +0, v]

int luaL_argerror (lua_State *L, int narg, const char *extramsg);




Raises an error with the following message,
where func is retrieved from the call stack:


     bad argument #<narg> to <func> (<extramsg>)





This function never returns,
but it is an idiom to use it in C functions
as return luaL_argerror(args).






luaL_Buffer


typedef struct luaL_Buffer luaL_Buffer;




Type for a string buffer.




A string buffer allows C code to build Lua strings piecemeal.
Its pattern of use is as follows:


    


  • First you declare a variable b of type luaL_Buffer.
    • 


  • Then you initialize it with a call luaL_buffinit(L, &b).
    • 


  • 
Then you add string pieces to the buffer calling any of
the luaL_add* functions.

    • 


  • 
You finish by calling luaL_pushresult(&b).
This call leaves the final string on the top of the stack.

    • 






During its normal operation,
a string buffer uses a variable number of stack slots.
So, while using a buffer, you cannot assume that you know where
the top of the stack is.
You can use the stack between successive calls to buffer operations
as long as that use is balanced;
that is,
when you call a buffer operation,
the stack is at the same level
it was immediately after the previous buffer operation.
(The only exception to this rule is luaL_addvalue.)
After calling luaL_pushresult the stack is back to its
level when the buffer was initialized,
plus the final string on its top.






luaL_buffinit

[-0, +0, -]

void luaL_buffinit (lua_State *L, luaL_Buffer *B);




Initializes a buffer B.
This function does not allocate any space;
the buffer must be declared as a variable
(see luaL_Buffer).






luaL_callmeta

[-0, +(0|1), e]

int luaL_callmeta (lua_State *L, int obj, const char *e);




Calls a metamethod.




If the object at index obj has a metatable and this
metatable has a field e,
this function calls this field and passes the object as its only argument.
In this case this function returns 1 and pushes onto the
stack the value returned by the call.
If there is no metatable or no metamethod,
this function returns 0 (without pushing any value on the stack).






luaL_checkany

[-0, +0, v]

void luaL_checkany (lua_State *L, int narg);




Checks whether the function has an argument
of any type (including nil) at position narg.






luaL_checkint

[-0, +0, v]

int luaL_checkint (lua_State *L, int narg);




Checks whether the function argument narg is a number
and returns this number cast to an int.






luaL_checkinteger

[-0, +0, v]

lua_Integer luaL_checkinteger (lua_State *L, int narg);




Checks whether the function argument narg is a number
and returns this number cast to a lua_Integer.






luaL_checklong

[-0, +0, v]

long luaL_checklong (lua_State *L, int narg);




Checks whether the function argument narg is a number
and returns this number cast to a long.






luaL_checklstring

[-0, +0, v]

const char *luaL_checklstring (lua_State *L, int narg, size_t *l);




Checks whether the function argument narg is a string
and returns this string;
if l is not NULL fills *l
with the string's length.




This function uses lua_tolstring to get its result,
so all conversions and caveats of that function apply here.






luaL_checknumber

[-0, +0, v]

lua_Number luaL_checknumber (lua_State *L, int narg);




Checks whether the function argument narg is a number
and returns this number.






luaL_checkoption

[-0, +0, v]

int luaL_checkoption (lua_State *L,
                      int narg,
                      const char *def,
                      const char *const lst[]);




Checks whether the function argument narg is a string and
searches for this string in the array lst
(which must be NULL-terminated).
Returns the index in the array where the string was found.
Raises an error if the argument is not a string or
if the string cannot be found.




If def is not NULL,
the function uses def as a default value when
there is no argument narg or if this argument is nil.




This is a useful function for mapping strings to C enums.
(The usual convention in Lua libraries is
to use strings instead of numbers to select options.)






luaL_checkstack

[-0, +0, v]

void luaL_checkstack (lua_State *L, int sz, const char *msg);




Grows the stack size to top + sz elements,
raising an error if the stack cannot grow to that size.
msg is an additional text to go into the error message.






luaL_checkstring

[-0, +0, v]

const char *luaL_checkstring (lua_State *L, int narg);




Checks whether the function argument narg is a string
and returns this string.




This function uses lua_tolstring to get its result,
so all conversions and caveats of that function apply here.






luaL_checktype

[-0, +0, v]

void luaL_checktype (lua_State *L, int narg, int t);




Checks whether the function argument narg has type t.
See lua_type for the encoding of types for t.






luaL_checkudata

[-0, +0, v]

void *luaL_checkudata (lua_State *L, int narg, const char *tname);




Checks whether the function argument narg is a userdata
of the type tname (see luaL_newmetatable).






luaL_dofile

[-0, +?, m]

int luaL_dofile (lua_State *L, const char *filename);




Loads and runs the given file.
It is defined as the following macro:


     (luaL_loadfile(L, filename) || lua_pcall(L, 0, LUA_MULTRET, 0))


It returns 0 if there are no errors
or 1 in case of errors.






luaL_dostring

[-0, +?, m]

int luaL_dostring (lua_State *L, const char *str);




Loads and runs the given string.
It is defined as the following macro:


     (luaL_loadstring(L, str) || lua_pcall(L, 0, LUA_MULTRET, 0))


It returns 0 if there are no errors
or 1 in case of errors.






luaL_error

[-0, +0, v]

int luaL_error (lua_State *L, const char *fmt, ...);




Raises an error.
The error message format is given by fmt
plus any extra arguments,
following the same rules of lua_pushfstring.
It also adds at the beginning of the message the file name and
the line number where the error occurred,
if this information is available.




This function never returns,
but it is an idiom to use it in C functions
as return luaL_error(args).






luaL_getmetafield

[-0, +(0|1), m]

int luaL_getmetafield (lua_State *L, int obj, const char *e);




Pushes onto the stack the field e from the metatable
of the object at index obj.
If the object does not have a metatable,
or if the metatable does not have this field,
returns 0 and pushes nothing.






luaL_getmetatable

[-0, +1, -]

void luaL_getmetatable (lua_State *L, const char *tname);




Pushes onto the stack the metatable associated with name tname
in the registry (see luaL_newmetatable).






luaL_gsub

[-0, +1, m]

const char *luaL_gsub (lua_State *L,
                       const char *s,
                       const char *p,
                       const char *r);




Creates a copy of string s by replacing
any occurrence of the string p
with the string r.
Pushes the resulting string on the stack and returns it.






luaL_loadbuffer

[-0, +1, m]

int luaL_loadbuffer (lua_State *L,
                     const char *buff,
                     size_t sz,
                     const char *name);




Loads a buffer as a Lua chunk.
This function uses lua_load to load the chunk in the
buffer pointed to by buff with size sz.




This function returns the same results as lua_load.
name is the chunk name,
used for debug information and error messages.






luaL_loadfile

[-0, +1, m]

int luaL_loadfile (lua_State *L, const char *filename);




Loads a file as a Lua chunk.
This function uses lua_load to load the chunk in the file
named filename.
If filename is NULL,
then it loads from the standard input.
The first line in the file is ignored if it starts with a #.




This function returns the same results as lua_load,
but it has an extra error code LUA_ERRFILE
if it cannot open/read the file.




As lua_load, this function only loads the chunk;
it does not run it.






luaL_loadstring

[-0, +1, m]

int luaL_loadstring (lua_State *L, const char *s);




Loads a string as a Lua chunk.
This function uses lua_load to load the chunk in
the zero-terminated string s.




This function returns the same results as lua_load.




Also as lua_load, this function only loads the chunk;
it does not run it.






luaL_newmetatable

[-0, +1, m]

int luaL_newmetatable (lua_State *L, const char *tname);




If the registry already has the key tname,
returns 0.
Otherwise,
creates a new table to be used as a metatable for userdata,
adds it to the registry with key tname,
and returns 1.




In both cases pushes onto the stack the final value associated
with tname in the registry.






luaL_newstate

[-0, +0, -]

lua_State *luaL_newstate (void);




Creates a new Lua state.
It calls lua_newstate with an
allocator based on the standard C realloc function
and then sets a panic function (see lua_atpanic) that prints
an error message to the standard error output in case of fatal
errors.




Returns the new state,
or NULL if there is a memory allocation error.






luaL_openlibs

[-0, +0, m]

void luaL_openlibs (lua_State *L);




Opens all standard Lua libraries into the given state.






luaL_optint

[-0, +0, v]

int luaL_optint (lua_State *L, int narg, int d);




If the function argument narg is a number,
returns this number cast to an int.
If this argument is absent or is nil,
returns d.
Otherwise, raises an error.






luaL_optinteger

[-0, +0, v]

lua_Integer luaL_optinteger (lua_State *L,
                             int narg,
                             lua_Integer d);




If the function argument narg is a number,
returns this number cast to a lua_Integer.
If this argument is absent or is nil,
returns d.
Otherwise, raises an error.






luaL_optlong

[-0, +0, v]

long luaL_optlong (lua_State *L, int narg, long d);




If the function argument narg is a number,
returns this number cast to a long.
If this argument is absent or is nil,
returns d.
Otherwise, raises an error.






luaL_optlstring

[-0, +0, v]

const char *luaL_optlstring (lua_State *L,
                             int narg,
                             const char *d,
                             size_t *l);




If the function argument narg is a string,
returns this string.
If this argument is absent or is nil,
returns d.
Otherwise, raises an error.




If l is not NULL,
fills the position *l with the results's length.






luaL_optnumber

[-0, +0, v]

lua_Number luaL_optnumber (lua_State *L, int narg, lua_Number d);




If the function argument narg is a number,
returns this number.
If this argument is absent or is nil,
returns d.
Otherwise, raises an error.






luaL_optstring

[-0, +0, v]

const char *luaL_optstring (lua_State *L,
                            int narg,
                            const char *d);




If the function argument narg is a string,
returns this string.
If this argument is absent or is nil,
returns d.
Otherwise, raises an error.






luaL_prepbuffer

[-0, +0, -]

char *luaL_prepbuffer (luaL_Buffer *B);




Returns an address to a space of size LUAL_BUFFERSIZE
where you can copy a string to be added to buffer B
(see luaL_Buffer).
After copying the string into this space you must call
luaL_addsize with the size of the string to actually add 
it to the buffer.






luaL_pushresult

[-?, +1, m]

void luaL_pushresult (luaL_Buffer *B);




Finishes the use of buffer B leaving the final string on
the top of the stack.






luaL_ref

[-1, +0, m]

int luaL_ref (lua_State *L, int t);




Creates and returns a reference,
in the table at index t,
for the object at the top of the stack (and pops the object).




A reference is a unique integer key.
As long as you do not manually add integer keys into table t,
luaL_ref ensures the uniqueness of the key it returns.
You can retrieve an object referred by reference r
by calling lua_rawgeti(L, t, r).
Function luaL_unref frees a reference and its associated object.




If the object at the top of the stack is nil,
luaL_ref returns the constant LUA_REFNIL.
The constant LUA_NOREF is guaranteed to be different
from any reference returned by luaL_ref.






luaL_Reg


typedef struct luaL_Reg {
  const char *name;
  lua_CFunction func;
} luaL_Reg;




Type for arrays of functions to be registered by
luaL_register.
name is the function name and func is a pointer to
the function.
Any array of luaL_Reg must end with an sentinel entry
in which both name and func are NULL.






luaL_register

[-(0|1), +1, m]

void luaL_register (lua_State *L,
                    const char *libname,
                    const luaL_Reg *l);




Opens a library.




When called with libname equal to NULL,
it simply registers all functions in the list l
(see luaL_Reg) into the table on the top of the stack.




When called with a non-null libname,
luaL_register creates a new table t,
sets it as the value of the global variable libname,
sets it as the value of package.loaded[libname],
and registers on it all functions in the list l.
If there is a table in package.loaded[libname] or in
variable libname,
reuses this table instead of creating a new one.




In any case the function leaves the table
on the top of the stack.






luaL_typename

[-0, +0, -]

const char *luaL_typename (lua_State *L, int index);




Returns the name of the type of the value at the given index.






luaL_typerror

[-0, +0, v]

int luaL_typerror (lua_State *L, int narg, const char *tname);




Generates an error with a message like the following:


     location: bad argument narg to 'func' (tname expected, got rt)


where location is produced by luaL_where,
func is the name of the current function,
and rt is the type name of the actual argument.






luaL_unref

[-0, +0, -]

void luaL_unref (lua_State *L, int t, int ref);




Releases reference ref from the table at index t
(see luaL_ref).
The entry is removed from the table,
so that the referred object can be collected.
The reference ref is also freed to be used again.




If ref is LUA_NOREF or LUA_REFNIL,
luaL_unref does nothing.






luaL_where

[-0, +1, m]

void luaL_where (lua_State *L, int lvl);




Pushes onto the stack a string identifying the current position
of the control at level lvl in the call stack.
Typically this string has the following format:


     chunkname:currentline:


Level 0 is the running function,
level 1 is the function that called the running function,
etc.




This function is used to build a prefix for error messages.








5 - Standard Libraries




The standard Lua libraries provide useful functions
that are implemented directly through the C API.
Some of these functions provide essential services to the language
(e.g., type and getmetatable);
others provide access to "outside" services (e.g., I/O);
and others could be implemented in Lua itself,
but are quite useful or have critical performance requirements that
deserve an implementation in C (e.g., table.sort).




All libraries are implemented through the official C API
and are provided as separate C modules.
Currently, Lua has the following standard libraries:


    


  • basic library, which includes the coroutine sub-library;
    • 


  • package library;
    • 


  • string manipulation;
    • 


  • table manipulation;
    • 


  • mathematical functions (sin, log, etc.);
    • 


  • input and output;
    • 


  • operating system facilities;
    • 


  • debug facilities.
    • 



Except for the basic and package libraries,
each library provides all its functions as fields of a global table
or as methods of its objects.




To have access to these libraries,
the C host program should call the luaL_openlibs function,
which opens all standard libraries.
Alternatively,
it can open them individually by calling
luaopen_base (for the basic library),
luaopen_package (for the package library),
luaopen_string (for the string library),
luaopen_table (for the table library),
luaopen_math (for the mathematical library),
luaopen_io (for the I/O library),
luaopen_os (for the Operating System library),
and luaopen_debug (for the debug library).
These functions are declared in lualib.h
and should not be called directly:
you must call them like any other Lua C function,
e.g., by using lua_call.




5.1 - Basic Functions




The basic library provides some core functions to Lua.
If you do not include this library in your application,
you should check carefully whether you need to provide 
implementations for some of its facilities.





assert (v [, message])

Issues an  error when
the value of its argument v is false (i.e., nil or false);
otherwise, returns all its arguments.
message is an error message;
when absent, it defaults to "assertion failed!"







collectgarbage ([opt [, arg]])





This function is a generic interface to the garbage collector.
It performs different functions according to its first argument, opt:


    


  • "collect":
performs a full garbage-collection cycle.
This is the default option.

    • 


  • "stop":
stops the garbage collector.

    • 


  • "restart":
restarts the garbage collector.

    • 


  • "count":
returns the total memory in use by Lua (in Kbytes).

    • 


  • "step":
performs a garbage-collection step.
The step "size" is controlled by arg
(larger values mean more steps) in a non-specified way.
If you want to control the step size
you must experimentally tune the value of arg.
Returns true if the step finished a collection cycle.

    • 


  • "setpause":
sets arg as the new value for the pause of
the collector (see §2.10).
Returns the previous value for pause.

    • 


  • "setstepmul":
sets arg as the new value for the step multiplier of
the collector (see §2.10).
Returns the previous value for step.

    • 









dofile ([filename])

Opens the named file and executes its contents as a Lua chunk.
When called without arguments,
dofile executes the contents of the standard input (stdin).
Returns all values returned by the chunk.
In case of errors, dofile propagates the error
to its caller (that is, dofile does not run in protected mode).







error (message [, level])

Terminates the last protected function called
and returns message as the error message.
Function error never returns.




Usually, error adds some information about the error position
at the beginning of the message.
The level argument specifies how to get the error position.
With level 1 (the default), the error position is where the
error function was called.
Level 2 points the error to where the function
that called error was called; and so on.
Passing a level 0 avoids the addition of error position information
to the message.







_G

A global variable (not a function) that
holds the global environment (that is, _G._G = _G).
Lua itself does not use this variable;
changing its value does not affect any environment,
nor vice-versa.
(Use setfenv to change environments.)







getfenv ([f])

Returns the current environment in use by the function.
f can be a Lua function or a number
that specifies the function at that stack level:
Level 1 is the function calling getfenv.
If the given function is not a Lua function,
or if f is 0,
getfenv returns the global environment.
The default for f is 1.







getmetatable (object)





If object does not have a metatable, returns nil.
Otherwise,
if the object's metatable has a "__metatable" field,
returns the associated value.
Otherwise, returns the metatable of the given object.







ipairs (t)





Returns three values: an iterator function, the table t, and 0,
so that the construction


     for i,v in ipairs(t) do body end


will iterate over the pairs (1,t[1]), (2,t[2]), ···,
up to the first integer key absent from the table.







load (func [, chunkname])





Loads a chunk using function func to get its pieces.
Each call to func must return a string that concatenates
with previous results.
A return of an empty string, nil, or no value signals the end of the chunk.




If there are no errors, 
returns the compiled chunk as a function;
otherwise, returns nil plus the error message.
The environment of the returned function is the global environment.




chunkname is used as the chunk name for error messages
and debug information.
When absent,
it defaults to "=(load)".







loadfile ([filename])





Similar to load,
but gets the chunk from file filename
or from the standard input,
if no file name is given.







loadstring (string [, chunkname])





Similar to load,
but gets the chunk from the given string.




To load and run a given string, use the idiom


     assert(loadstring(s))()





When absent,
chunkname defaults to the given string.







next (table [, index])





Allows a program to traverse all fields of a table.
Its first argument is a table and its second argument
is an index in this table.
next returns the next index of the table
and its associated value.
When called with nil as its second argument,
next returns an initial index
and its associated value.
When called with the last index,
or with nil in an empty table,
next returns nil.
If the second argument is absent, then it is interpreted as nil.
In particular,
you can use next(t) to check whether a table is empty.




The order in which the indices are enumerated is not specified,
even for numeric indices.
(To traverse a table in numeric order,
use a numerical for or the ipairs function.)




The behavior of next is undefined if,
during the traversal,
you assign any value to a non-existent field in the table.
You may however modify existing fields.
In particular, you may clear existing fields.







pairs (t)





Returns three values: the next function, the table t, and nil,
so that the construction


     for k,v in pairs(t) do body end


will iterate over all key–value pairs of table t.




See function next for the caveats of modifying
the table during its traversal.







pcall (f, arg1, ···)





Calls function f with
the given arguments in protected mode.
This means that any error inside f is not propagated;
instead, pcall catches the error
and returns a status code.
Its first result is the status code (a boolean),
which is true if the call succeeds without errors.
In such case, pcall also returns all results from the call,
after this first result.
In case of any error, pcall returns false plus the error message.







print (···)

Receives any number of arguments,
and prints their values to stdout,
using the tostring function to convert them to strings.
print is not intended for formatted output,
but only as a quick way to show a value,
typically for debugging.
For formatted output, use string.format.







rawequal (v1, v2)

Checks whether v1 is equal to v2,
without invoking any metamethod.
Returns a boolean.







rawget (table, index)

Gets the real value of table[index],
without invoking any metamethod.
table must be a table;
index may be any value.







rawset (table, index, value)

Sets the real value of table[index] to value,
without invoking any metamethod.
table must be a table,
index any value different from nil,
and value any Lua value.




This function returns table.







select (index, ···)





If index is a number,
returns all arguments after argument number index.
Otherwise, index must be the string "#",
and select returns the total number of extra arguments it received.







setfenv (f, table)





Sets the environment to be used by the given function.
f can be a Lua function or a number
that specifies the function at that stack level:
Level 1 is the function calling setfenv.
setfenv returns the given function.




As a special case, when f is 0 setfenv changes
the environment of the running thread.
In this case, setfenv returns no values.







setmetatable (table, metatable)





Sets the metatable for the given table.
(You cannot change the metatable of other types from Lua, only from C.)
If metatable is nil,
removes the metatable of the given table.
If the original metatable has a "__metatable" field,
raises an error.




This function returns table.







tonumber (e [, base])

Tries to convert its argument to a number.
If the argument is already a number or a string convertible
to a number, then tonumber returns this number;
otherwise, it returns nil.




An optional argument specifies the base to interpret the numeral.
The base may be any integer between 2 and 36, inclusive.
In bases above 10, the letter 'A' (in either upper or lower case)
represents 10, 'B' represents 11, and so forth,
with 'Z' representing 35.
In base 10 (the default), the number can have a decimal part,
as well as an optional exponent part (see §2.1).
In other bases, only unsigned integers are accepted.







tostring (e)

Receives an argument of any type and
converts it to a string in a reasonable format.
For complete control of how numbers are converted,
use string.format.




If the metatable of e has a "__tostring" field,
then tostring calls the corresponding value
with e as argument,
and uses the result of the call as its result.







type (v)

Returns the type of its only argument, coded as a string.
The possible results of this function are
"nil" (a string, not the value nil),
"number",
"string",
"boolean",
"table",
"function",
"thread",
and "userdata".







unpack (list [, i [, j]])

Returns the elements from the given table.
This function is equivalent to


     return list[i], list[i+1], ···, list[j]


except that the above code can be written only for a fixed number
of elements.
By default, i is 1 and j is the length of the list,
as defined by the length operator (see §2.5.5).







_VERSION

A global variable (not a function) that
holds a string containing the current interpreter version.
The current contents of this variable is "Lua 5.1".







xpcall (f, err)





This function is similar to pcall,
except that you can set a new error handler.




xpcall calls function f in protected mode,
using err as the error handler.
Any error inside f is not propagated;
instead, xpcall catches the error,
calls the err function with the original error object,
and returns a status code.
Its first result is the status code (a boolean),
which is true if the call succeeds without errors.
In this case, xpcall also returns all results from the call,
after this first result.
In case of any error,
xpcall returns false plus the result from err.








5.2 - Coroutine Manipulation




The operations related to coroutines comprise a sub-library of
the basic library and come inside the table coroutine.
See §2.11 for a general description of coroutines.





coroutine.create (f)





Creates a new coroutine, with body f.
f must be a Lua function.
Returns this new coroutine,
an object with type "thread".







coroutine.resume (co [, val1, ···])





Starts or continues the execution of coroutine co.
The first time you resume a coroutine,
it starts running its body.
The values val1, ··· are passed
as the arguments to the body function.
If the coroutine has yielded,
resume restarts it;
the values val1, ··· are passed
as the results from the yield.




If the coroutine runs without any errors,
resume returns true plus any values passed to yield
(if the coroutine yields) or any values returned by the body function
(if the coroutine terminates).
If there is any error,
resume returns false plus the error message.







coroutine.running ()





Returns the running coroutine,
or nil when called by the main thread.







coroutine.status (co)





Returns the status of coroutine co, as a string:
"running",
if the coroutine is running (that is, it called status);
"suspended", if the coroutine is suspended in a call to yield,
or if it has not started running yet;
"normal" if the coroutine is active but not running
(that is, it has resumed another coroutine);
and "dead" if the coroutine has finished its body function,
or if it has stopped with an error.







coroutine.wrap (f)





Creates a new coroutine, with body f.
f must be a Lua function.
Returns a function that resumes the coroutine each time it is called.
Any arguments passed to the function behave as the
extra arguments to resume.
Returns the same values returned by resume,
except the first boolean.
In case of error, propagates the error.







coroutine.yield (···)





Suspends the execution of the calling coroutine.
The coroutine cannot be running a C function,
a metamethod, or an iterator.
Any arguments to yield are passed as extra results to resume.








5.3 - Modules




The package library provides basic
facilities for loading and building modules in Lua.
It exports two of its functions directly in the global environment:
require and module.
Everything else is exported in a table package.





module (name [, ···])





Creates a module.
If there is a table in package.loaded[name],
this table is the module.
Otherwise, if there is a global table t with the given name,
this table is the module.
Otherwise creates a new table t and
sets it as the value of the global name and
the value of package.loaded[name].
This function also initializes t._NAME with the given name,
t._M with the module (t itself),
and t._PACKAGE with the package name
(the full module name minus last component; see below).
Finally, module sets t as the new environment
of the current function and the new value of package.loaded[name],
so that require returns t.




If name is a compound name
(that is, one with components separated by dots),
module creates (or reuses, if they already exist)
tables for each component.
For instance, if name is a.b.c,
then module stores the module table in field c of
field b of global a.




This function can receive optional options after
the module name,
where each option is a function to be applied over the module.







require (modname)





Loads the given module.
The function starts by looking into the package.loaded table
to determine whether modname is already loaded.
If it is, then require returns the value stored
at package.loaded[modname].
Otherwise, it tries to find a loader for the module.




To find a loader,
require is guided by the package.loaders array.
By changing this array,
we can change how require looks for a module.
The following explanation is based on the default configuration
for package.loaders.




First require queries package.preload[modname].
If it has a value,
this value (which should be a function) is the loader.
Otherwise require searches for a Lua loader using the
path stored in package.path.
If that also fails, it searches for a C loader using the
path stored in package.cpath.
If that also fails,
it tries an all-in-one loader (see package.loaders).




Once a loader is found,
require calls the loader with a single argument, modname.
If the loader returns any value,
require assigns the returned value to package.loaded[modname].
If the loader returns no value and
has not assigned any value to package.loaded[modname],
then require assigns true to this entry.
In any case, require returns the
final value of package.loaded[modname].




If there is any error loading or running the module,
or if it cannot find any loader for the module,
then require signals an error. 







package.cpath





The path used by require to search for a C loader.




Lua initializes the C path package.cpath in the same way
it initializes the Lua path package.path,
using the environment variable LUA_CPATH
or a default path defined in luaconf.h.








package.loaded





A table used by require to control which
modules are already loaded.
When you require a module modname and
package.loaded[modname] is not false,
require simply returns the value stored there.







package.loaders





A table used by require to control how to load modules.




Each entry in this table is a searcher function.
When looking for a module,
require calls each of these searchers in ascending order,
with the module name (the argument given to require) as its
sole parameter.
The function can return another function (the module loader)
or a string explaining why it did not find that module
(or nil if it has nothing to say).
Lua initializes this table with four functions.




The first searcher simply looks for a loader in the
package.preload table.




The second searcher looks for a loader as a Lua library,
using the path stored at package.path.
A path is a sequence of templates separated by semicolons.
For each template,
the searcher will change each interrogation
mark in the template by filename,
which is the module name with each dot replaced by a
"directory separator" (such as "/" in Unix);
then it will try to open the resulting file name.
So, for instance, if the Lua path is the string


     "./?.lua;./?.lc;/usr/local/?/init.lua"


the search for a Lua file for module foo
will try to open the files
./foo.lua, ./foo.lc, and
/usr/local/foo/init.lua, in that order.




The third searcher looks for a loader as a C library,
using the path given by the variable package.cpath.
For instance,
if the C path is the string


     "./?.so;./?.dll;/usr/local/?/init.so"


the searcher for module foo
will try to open the files ./foo.so, ./foo.dll,
and /usr/local/foo/init.so, in that order.
Once it finds a C library,
this searcher first uses a dynamic link facility to link the
application with the library.
Then it tries to find a C function inside the library to
be used as the loader.
The name of this C function is the string "luaopen_"
concatenated with a copy of the module name where each dot
is replaced by an underscore.
Moreover, if the module name has a hyphen,
its prefix up to (and including) the first hyphen is removed.
For instance, if the module name is a.v1-b.c,
the function name will be luaopen_b_c.




The fourth searcher tries an all-in-one loader.
It searches the C path for a library for
the root name of the given module.
For instance, when requiring a.b.c,
it will search for a C library for a.
If found, it looks into it for an open function for
the submodule;
in our example, that would be luaopen_a_b_c.
With this facility, a package can pack several C submodules
into one single library,
with each submodule keeping its original open function.







package.loadlib (libname, funcname)





Dynamically links the host program with the C library libname.
Inside this library, looks for a function funcname
and returns this function as a C function.
(So, funcname must follow the protocol (see lua_CFunction)).




This is a low-level function.
It completely bypasses the package and module system.
Unlike require,
it does not perform any path searching and
does not automatically adds extensions.
libname must be the complete file name of the C library,
including if necessary a path and extension.
funcname must be the exact name exported by the C library
(which may depend on the C compiler and linker used).




This function is not supported by ANSI C.
As such, it is only available on some platforms
(Windows, Linux, Mac OS X, Solaris, BSD,
plus other Unix systems that support the dlfcn standard).







package.path





The path used by require to search for a Lua loader.




At start-up, Lua initializes this variable with
the value of the environment variable LUA_PATH or
with a default path defined in luaconf.h,
if the environment variable is not defined.
Any ";;" in the value of the environment variable
is replaced by the default path.







package.preload





A table to store loaders for specific modules
(see require).







package.seeall (module)





Sets a metatable for module with
its __index field referring to the global environment,
so that this module inherits values
from the global environment.
To be used as an option to function module.








5.4 - String Manipulation




This library provides generic functions for string manipulation,
such as finding and extracting substrings, and pattern matching.
When indexing a string in Lua, the first character is at position 1
(not at 0, as in C).
Indices are allowed to be negative and are interpreted as indexing backwards,
from the end of the string.
Thus, the last character is at position -1, and so on.




The string library provides all its functions inside the table
string.
It also sets a metatable for strings
where the __index field points to the string table.
Therefore, you can use the string functions in object-oriented style.
For instance, string.byte(s, i)
can be written as s:byte(i).




The string library assumes one-byte character encodings.





string.byte (s [, i [, j]])

Returns the internal numerical codes of the characters s[i],
s[i+1], ···, s[j].
The default value for i is 1;
the default value for j is i.




Note that numerical codes are not necessarily portable across platforms.







string.char (···)

Receives zero or more integers.
Returns a string with length equal to the number of arguments,
in which each character has the internal numerical code equal
to its corresponding argument.




Note that numerical codes are not necessarily portable across platforms.







string.dump (function)





Returns a string containing a binary representation of the given function,
so that a later loadstring on this string returns
a copy of the function.
function must be a Lua function without upvalues.







string.find (s, pattern [, init [, plain]])

Looks for the first match of
pattern in the string s.
If it finds a match, then find returns the indices of s
where this occurrence starts and ends;
otherwise, it returns nil.
A third, optional numerical argument init specifies
where to start the search;
its default value is 1 and can be negative.
A value of true as a fourth, optional argument plain
turns off the pattern matching facilities,
so the function does a plain "find substring" operation,
with no characters in pattern being considered "magic".
Note that if plain is given, then init must be given as well.




If the pattern has captures,
then in a successful match
the captured values are also returned,
after the two indices.







string.format (formatstring, ···)

Returns a formatted version of its variable number of arguments
following the description given in its first argument (which must be a string).
The format string follows the same rules as the printf family of
standard C functions.
The only differences are that the options/modifiers
*, l, L, n, p,
and h are not supported
and that there is an extra option, q.
The q option formats a string in a form suitable to be safely read
back by the Lua interpreter:
the string is written between double quotes,
and all double quotes, newlines, embedded zeros,
and backslashes in the string
are correctly escaped when written.
For instance, the call


     string.format('%q', 'a string with "quotes" and \n new line')


will produce the string:


     "a string with \"quotes\" and \
      new line"





The options c, d, E, e, f,
g, G, i, o, u, X, and x all
expect a number as argument,
whereas q and s expect a string.




This function does not accept string values
containing embedded zeros,
except as arguments to the q option.







string.gmatch (s, pattern)

Returns an iterator function that,
each time it is called,
returns the next captures from pattern over string s.
If pattern specifies no captures,
then the whole match is produced in each call.




As an example, the following loop


     s = "hello world from Lua"
     for w in string.gmatch(s, "%a+") do
       print(w)
     end


will iterate over all the words from string s,
printing one per line.
The next example collects all pairs key=value from the
given string into a table:


     t = {}
     s = "from=world, to=Lua"
     for k, v in string.gmatch(s, "(%w+)=(%w+)") do
       t[k] = v
     end





For this function, a '^' at the start of a pattern does not
work as an anchor, as this would prevent the iteration.







string.gsub (s, pattern, repl [, n])

Returns a copy of s
in which all (or the first n, if given)
occurrences of the pattern have been
replaced by a replacement string specified by repl,
which can be a string, a table, or a function.
gsub also returns, as its second value,
the total number of matches that occurred.




If repl is a string, then its value is used for replacement.
The character % works as an escape character:
any sequence in repl of the form %n,
with n between 1 and 9,
stands for the value of the n-th captured substring (see below).
The sequence %0 stands for the whole match.
The sequence %% stands for a single %.




If repl is a table, then the table is queried for every match,
using the first capture as the key;
if the pattern specifies no captures,
then the whole match is used as the key.




If repl is a function, then this function is called every time a
match occurs, with all captured substrings passed as arguments,
in order;
if the pattern specifies no captures,
then the whole match is passed as a sole argument.




If the value returned by the table query or by the function call
is a string or a number,
then it is used as the replacement string;
otherwise, if it is false or nil,
then there is no replacement
(that is, the original match is kept in the string).




Here are some examples:


     x = string.gsub("hello world", "(%w+)", "%1 %1")
     --> x="hello hello world world"
     
     x = string.gsub("hello world", "%w+", "%0 %0", 1)
     --> x="hello hello world"
     
     x = string.gsub("hello world from Lua", "(%w+)%s*(%w+)", "%2 %1")
     --> x="world hello Lua from"
     
     x = string.gsub("home = $HOME, user = $USER", "%$(%w+)", os.getenv)
     --> x="home = /home/roberto, user = roberto"
     
     x = string.gsub("4+5 = $return 4+5$", "%$(.-)%$", function (s)
           return loadstring(s)()
         end)
     --> x="4+5 = 9"
     
     local t = {name="lua", version="5.1"}
     x = string.gsub("$name-$version.tar.gz", "%$(%w+)", t)
     --> x="lua-5.1.tar.gz"








string.len (s)

Receives a string and returns its length.
The empty string "" has length 0.
Embedded zeros are counted,
so "a\000bc\000" has length 5.







string.lower (s)

Receives a string and returns a copy of this string with all
uppercase letters changed to lowercase.
All other characters are left unchanged.
The definition of what an uppercase letter is depends on the current locale.







string.match (s, pattern [, init])

Looks for the first match of
pattern in the string s.
If it finds one, then match returns
the captures from the pattern;
otherwise it returns nil.
If pattern specifies no captures,
then the whole match is returned.
A third, optional numerical argument init specifies
where to start the search;
its default value is 1 and can be negative.







string.rep (s, n)

Returns a string that is the concatenation of n copies of
the string s.







string.reverse (s)

Returns a string that is the string s reversed.







string.sub (s, i [, j])

Returns the substring of s that
starts at i  and continues until j;
i and j can be negative.
If j is absent, then it is assumed to be equal to -1
(which is the same as the string length).
In particular,
the call string.sub(s,1,j) returns a prefix of s
with length j,
and string.sub(s, -i) returns a suffix of s
with length i.







string.upper (s)

Receives a string and returns a copy of this string with all
lowercase letters changed to uppercase.
All other characters are left unchanged.
The definition of what a lowercase letter is depends on the current locale.




5.4.1 - Patterns




Character Class:

A character class is used to represent a set of characters.
The following combinations are allowed in describing a character class:


    


  • x:
(where x is not one of the magic characters
^$()%.[]*+-?)
represents the character x itself.

    • 


  • .: (a dot) represents all characters.
    • 


  • %a: represents all letters.
    • 


  • %c: represents all control characters.
    • 


  • %d: represents all digits.
    • 


  • %l: represents all lowercase letters.
    • 


  • %p: represents all punctuation characters.
    • 


  • %s: represents all space characters.
    • 


  • %u: represents all uppercase letters.
    • 


  • %w: represents all alphanumeric characters.
    • 


  • %x: represents all hexadecimal digits.
    • 


  • %z: represents the character with representation 0.
    • 


  • %x: (where x is any non-alphanumeric character)
represents the character x.
This is the standard way to escape the magic characters.
Any punctuation character (even the non magic)
can be preceded by a '%'
when used to represent itself in a pattern.

    • 


  • [set]:
represents the class which is the union of all
characters in set.
A range of characters can be specified by
separating the end characters of the range with a '-'.
All classes %x described above can also be used as
components in set.
All other characters in set represent themselves.
For example, [%w_] (or [_%w])
represents all alphanumeric characters plus the underscore,
[0-7] represents the octal digits,
and [0-7%l%-] represents the octal digits plus
the lowercase letters plus the '-' character.



    
The interaction between ranges and classes is not defined.
Therefore, patterns like [%a-z] or [a-%%]
have no meaning.

    • 


  • [^set]:
represents the complement of set,
where set is interpreted as above.

    • 



For all classes represented by single letters (%a, %c, etc.),
the corresponding uppercase letter represents the complement of the class.
For instance, %S represents all non-space characters.




The definitions of letter, space, and other character groups
depend on the current locale.
In particular, the class [a-z] may not be equivalent to %l.






Pattern Item:

A pattern item can be


    


  • 
a single character class,
which matches any single character in the class;

    • 


  • 
a single character class followed by '*',
which matches 0 or more repetitions of characters in the class.
These repetition items will always match the longest possible sequence;

    • 


  • 
a single character class followed by '+',
which matches 1 or more repetitions of characters in the class.
These repetition items will always match the longest possible sequence;

    • 


  • 
a single character class followed by '-',
which also matches 0 or more repetitions of characters in the class.
Unlike '*',
these repetition items will always match the shortest possible sequence;

    • 


  • 
a single character class followed by '?',
which matches 0 or 1 occurrence of a character in the class;

    • 


  • 
%n, for n between 1 and 9;
such item matches a substring equal to the n-th captured string
(see below);

    • 


  • 
%bxy, where x and y are two distinct characters;
such item matches strings that start with x, end with y,
and where the x and y are balanced.
This means that, if one reads the string from left to right,
counting +1 for an x and -1 for a y,
the ending y is the first y where the count reaches 0.
For instance, the item %b() matches expressions with
balanced parentheses.

    • 








Pattern:

A pattern is a sequence of pattern items.
A '^' at the beginning of a pattern anchors the match at the
beginning of the subject string.
A '$' at the end of a pattern anchors the match at the
end of the subject string.
At other positions,
'^' and '$' have no special meaning and represent themselves.






Captures:

A pattern can contain sub-patterns enclosed in parentheses;
they describe captures.
When a match succeeds, the substrings of the subject string
that match captures are stored (captured) for future use.
Captures are numbered according to their left parentheses.
For instance, in the pattern "(a*(.)%w(%s*))",
the part of the string matching "a*(.)%w(%s*)" is
stored as the first capture (and therefore has number 1);
the character matching "." is captured with number 2,
and the part matching "%s*" has number 3.




As a special case, the empty capture () captures
the current string position (a number).
For instance, if we apply the pattern "()aa()" on the
string "flaaap", there will be two captures: 3 and 5.




A pattern cannot contain embedded zeros.  Use %z instead.












5.5 - Table Manipulation

This library provides generic functions for table manipulation.
It provides all its functions inside the table table.




Most functions in the table library assume that the table
represents an array or a list.
For these functions, when we talk about the "length" of a table
we mean the result of the length operator.





table.concat (table [, sep [, i [, j]]])

Given an array where all elements are strings or numbers,
returns table[i]..sep..table[i+1] ··· sep..table[j].
The default value for sep is the empty string,
the default for i is 1,
and the default for j is the length of the table.
If i is greater than j, returns the empty string.







table.insert (table, [pos,] value)





Inserts element value at position pos in table,
shifting up other elements to open space, if necessary.
The default value for pos is n+1,
where n is the length of the table (see §2.5.5),
so that a call table.insert(t,x) inserts x at the end
of table t.







table.maxn (table)





Returns the largest positive numerical index of the given table,
or zero if the table has no positive numerical indices.
(To do its job this function does a linear traversal of
the whole table.) 







table.remove (table [, pos])





Removes from table the element at position pos,
shifting down other elements to close the space, if necessary.
Returns the value of the removed element.
The default value for pos is n,
where n is the length of the table,
so that a call table.remove(t) removes the last element
of table t.







table.sort (table [, comp])

Sorts table elements in a given order, in-place,
from table[1] to table[n],
where n is the length of the table.
If comp is given,
then it must be a function that receives two table elements,
and returns true
when the first is less than the second
(so that not comp(a[i+1],a[i]) will be true after the sort).
If comp is not given,
then the standard Lua operator < is used instead.




The sort algorithm is not stable;
that is, elements considered equal by the given order
may have their relative positions changed by the sort.








5.6 - Mathematical Functions




This library is an interface to the standard C math library.
It provides all its functions inside the table math.





math.abs (x)





Returns the absolute value of x.







math.acos (x)





Returns the arc cosine of x (in radians).







math.asin (x)





Returns the arc sine of x (in radians).







math.atan (x)





Returns the arc tangent of x (in radians).







math.atan2 (y, x)





Returns the arc tangent of y/x (in radians),
but uses the signs of both parameters to find the
quadrant of the result.
(It also handles correctly the case of x being zero.)







math.ceil (x)





Returns the smallest integer larger than or equal to x.







math.cos (x)





Returns the cosine of x (assumed to be in radians).







math.cosh (x)





Returns the hyperbolic cosine of x.







math.deg (x)





Returns the angle x (given in radians) in degrees.







math.exp (x)





Returns the value ex.







math.floor (x)





Returns the largest integer smaller than or equal to x.







math.fmod (x, y)





Returns the remainder of the division of x by y
that rounds the quotient towards zero.







math.frexp (x)





Returns m and e such that x = m2e,
e is an integer and the absolute value of m is
in the range [0.5, 1)
(or zero when x is zero).







math.huge





The value HUGE_VAL,
a value larger than or equal to any other numerical value.







math.ldexp (m, e)





Returns m2e (e should be an integer).







math.log (x)





Returns the natural logarithm of x.







math.log10 (x)





Returns the base-10 logarithm of x.







math.max (x, ···)





Returns the maximum value among its arguments.







math.min (x, ···)





Returns the minimum value among its arguments.







math.modf (x)





Returns two numbers,
the integral part of x and the fractional part of x.







math.pi





The value of pi.







math.pow (x, y)





Returns xy.
(You can also use the expression x^y to compute this value.)







math.rad (x)





Returns the angle x (given in degrees) in radians.







math.random ([m [, n]])





This function is an interface to the simple
pseudo-random generator function rand provided by ANSI C.
(No guarantees can be given for its statistical properties.)




When called without arguments,
returns a uniform pseudo-random real number
in the range [0,1).  
When called with an integer number m,
math.random returns
a uniform pseudo-random integer in the range [1, m].
When called with two integer numbers m and n,
math.random returns a uniform pseudo-random
integer in the range [m, n].







math.randomseed (x)





Sets x as the "seed"
for the pseudo-random generator:
equal seeds produce equal sequences of numbers.







math.sin (x)





Returns the sine of x (assumed to be in radians).







math.sinh (x)





Returns the hyperbolic sine of x.







math.sqrt (x)





Returns the square root of x.
(You can also use the expression x^0.5 to compute this value.)







math.tan (x)





Returns the tangent of x (assumed to be in radians).







math.tanh (x)





Returns the hyperbolic tangent of x.








5.7 - Input and Output Facilities




The I/O library provides two different styles for file manipulation.
The first one uses implicit file descriptors;
that is, there are operations to set a default input file and a
default output file,
and all input/output operations are over these default files.
The second style uses explicit file descriptors.




When using implicit file descriptors,
all operations are supplied by table io.
When using explicit file descriptors,
the operation io.open returns a file descriptor
and then all operations are supplied as methods of the file descriptor.




The table io also provides
three predefined file descriptors with their usual meanings from C:
io.stdin, io.stdout, and io.stderr.
The I/O library never closes these files.




Unless otherwise stated,
all I/O functions return nil on failure
(plus an error message as a second result and
a system-dependent error code as a third result)
and some value different from nil on success.





io.close ([file])





Equivalent to file:close().
Without a file, closes the default output file.







io.flush ()





Equivalent to file:flush over the default output file.







io.input ([file])





When called with a file name, it opens the named file (in text mode),
and sets its handle as the default input file.
When called with a file handle,
it simply sets this file handle as the default input file.
When called without parameters,
it returns the current default input file.




In case of errors this function raises the error,
instead of returning an error code.







io.lines ([filename])





Opens the given file name in read mode
and returns an iterator function that,
each time it is called,
returns a new line from the file.
Therefore, the construction


     for line in io.lines(filename) do body end


will iterate over all lines of the file.
When the iterator function detects the end of file,
it returns nil (to finish the loop) and automatically closes the file.




The call io.lines() (with no file name) is equivalent
to io.input():lines();
that is, it iterates over the lines of the default input file.
In this case it does not close the file when the loop ends.







io.open (filename [, mode])





This function opens a file,
in the mode specified in the string mode.
It returns a new file handle,
or, in case of errors, nil plus an error message.




The mode string can be any of the following:


    

  • "r": read mode (the default);
    • 

  • "w": write mode;
    • 

  • "a": append mode;
    • 

  • "r+": update mode, all previous data is preserved;
    • 

  • "w+": update mode, all previous data is erased;
    • 

  • "a+": append update mode, previous data is preserved,
  writing is only allowed at the end of file.
    • 


The mode string can also have a 'b' at the end,
which is needed in some systems to open the file in binary mode.
This string is exactly what is used in the
standard C function fopen.







io.output ([file])





Similar to io.input, but operates over the default output file.







io.popen (prog [, mode])





Starts program prog in a separated process and returns
a file handle that you can use to read data from this program
(if mode is "r", the default)
or to write data to this program
(if mode is "w").




This function is system dependent and is not available
on all platforms.







io.read (···)





Equivalent to io.input():read.







io.tmpfile ()





Returns a handle for a temporary file.
This file is opened in update mode
and it is automatically removed when the program ends.







io.type (obj)





Checks whether obj is a valid file handle.
Returns the string "file" if obj is an open file handle,
"closed file" if obj is a closed file handle,
or nil if obj is not a file handle.







io.write (···)





Equivalent to io.output():write.







file:close ()





Closes file.
Note that files are automatically closed when
their handles are garbage collected,
but that takes an unpredictable amount of time to happen.







file:flush ()





Saves any written data to file.







file:lines ()





Returns an iterator function that,
each time it is called,
returns a new line from the file.
Therefore, the construction


     for line in file:lines() do body end


will iterate over all lines of the file.
(Unlike io.lines, this function does not close the file
when the loop ends.)







file:read (···)





Reads the file file,
according to the given formats, which specify what to read.
For each format,
the function returns a string (or a number) with the characters read,
or nil if it cannot read data with the specified format.
When called without formats,
it uses a default format that reads the entire next line
(see below).




The available formats are


    


  • "*n":
reads a number;
this is the only format that returns a number instead of a string.

    • 


  • "*a":
reads the whole file, starting at the current position.
On end of file, it returns the empty string.

    • 


  • "*l":
reads the next line (skipping the end of line),
returning nil on end of file.
This is the default format.

    • 


  • number:
reads a string with up to this number of characters,
returning nil on end of file.
If number is zero,
it reads nothing and returns an empty string,
or nil on end of file.

    • 









file:seek ([whence] [, offset])





Sets and gets the file position,
measured from the beginning of the file,
to the position given by offset plus a base
specified by the string whence, as follows:


    

  • "set": base is position 0 (beginning of the file);
    • 

  • "cur": base is current position;
    • 

  • "end": base is end of file;
    • 


In case of success, function seek returns the final file position,
measured in bytes from the beginning of the file.
If this function fails, it returns nil,
plus a string describing the error.




The default value for whence is "cur",
and for offset is 0.
Therefore, the call file:seek() returns the current
file position, without changing it;
the call file:seek("set") sets the position to the
beginning of the file (and returns 0);
and the call file:seek("end") sets the position to the
end of the file, and returns its size.







file:setvbuf (mode [, size])





Sets the buffering mode for an output file.
There are three available modes:


    


  • "no":
no buffering; the result of any output operation appears immediately.

    • 


  • "full":
full buffering; output operation is performed only
when the buffer is full (or when you explicitly flush the file
(see io.flush)).

    • 


  • "line":
line buffering; output is buffered until a newline is output
or there is any input from some special files
(such as a terminal device).

    • 



For the last two cases, size
specifies the size of the buffer, in bytes.
The default is an appropriate size.







file:write (···)





Writes the value of each of its arguments to
the file.
The arguments must be strings or numbers.
To write other values,
use tostring or string.format before write.








5.8 - Operating System Facilities




This library is implemented through table os.





os.clock ()





Returns an approximation of the amount in seconds of CPU time
used by the program.







os.date ([format [, time]])





Returns a string or a table containing date and time,
formatted according to the given string format.




If the time argument is present,
this is the time to be formatted
(see the os.time function for a description of this value).
Otherwise, date formats the current time.




If format starts with '!',
then the date is formatted in Coordinated Universal Time.
After this optional character,
if format is the string "*t",
then date returns a table with the following fields:
year (four digits), month (1--12), day (1--31),
hour (0--23), min (0--59), sec (0--61),
wday (weekday, Sunday is 1),
yday (day of the year),
and isdst (daylight saving flag, a boolean).




If format is not "*t",
then date returns the date as a string,
formatted according to the same rules as the C function strftime.




When called without arguments,
date returns a reasonable date and time representation that depends on
the host system and on the current locale
(that is, os.date() is equivalent to os.date("%c")).







os.difftime (t2, t1)





Returns the number of seconds from time t1 to time t2.
In POSIX, Windows, and some other systems,
this value is exactly t2-t1.







os.execute ([command])





This function is equivalent to the C function system.
It passes command to be executed by an operating system shell.
It returns a status code, which is system-dependent.
If command is absent, then it returns nonzero if a shell is available
and zero otherwise.







os.exit ([code])





Calls the C function exit,
with an optional code,
to terminate the host program.
The default value for code is the success code.







os.getenv (varname)





Returns the value of the process environment variable varname,
or nil if the variable is not defined.







os.remove (filename)





Deletes the file or directory with the given name.
Directories must be empty to be removed.
If this function fails, it returns nil,
plus a string describing the error.







os.rename (oldname, newname)





Renames file or directory named oldname to newname.
If this function fails, it returns nil,
plus a string describing the error.







os.setlocale (locale [, category])





Sets the current locale of the program.
locale is a string specifying a locale;
category is an optional string describing which category to change:
"all", "collate", "ctype",
"monetary", "numeric", or "time";
the default category is "all".
The function returns the name of the new locale,
or nil if the request cannot be honored.




If locale is the empty string,
the current locale is set to an implementation-defined native locale.
If locale is the string "C",
the current locale is set to the standard C locale.




When called with nil as the first argument,
this function only returns the name of the current locale
for the given category.







os.time ([table])





Returns the current time when called without arguments,
or a time representing the date and time specified by the given table.
This table must have fields year, month, and day,
and may have fields hour, min, sec, and isdst
(for a description of these fields, see the os.date function).




The returned value is a number, whose meaning depends on your system.
In POSIX, Windows, and some other systems, this number counts the number
of seconds since some given start time (the "epoch").
In other systems, the meaning is not specified,
and the number returned by time can be used only as an argument to
date and difftime.







os.tmpname ()





Returns a string with a file name that can
be used for a temporary file.
The file must be explicitly opened before its use
and explicitly removed when no longer needed.




On some systems (POSIX),
this function also creates a file with that name,
to avoid security risks.
(Someone else might create the file with wrong permissions
in the time between getting the name and creating the file.)
You still have to open the file to use it
and to remove it (even if you do not use it).




When possible,
you may prefer to use io.tmpfile,
which automatically removes the file when the program ends.








5.9 - The Debug Library




This library provides
the functionality of the debug interface to Lua programs.
You should exert care when using this library.
The functions provided here should be used exclusively for debugging
and similar tasks, such as profiling.
Please resist the temptation to use them as a
usual programming tool:
they can be very slow.
Moreover, several of these functions
violate some assumptions about Lua code
(e.g., that variables local to a function
cannot be accessed from outside or
that userdata metatables cannot be changed by Lua code)
and therefore can compromise otherwise secure code.




All functions in this library are provided
inside the debug table.
All functions that operate over a thread
have an optional first argument which is the
thread to operate over.
The default is always the current thread.





debug.debug ()





Enters an interactive mode with the user,
running each string that the user enters.
Using simple commands and other debug facilities,
the user can inspect global and local variables,
change their values, evaluate expressions, and so on.
A line containing only the word cont finishes this function,
so that the caller continues its execution.




Note that commands for debug.debug are not lexically nested
within any function, and so have no direct access to local variables.







debug.getfenv (o)

Returns the environment of object o.







debug.gethook ([thread])





Returns the current hook settings of the thread, as three values:
the current hook function, the current hook mask,
and the current hook count
(as set by the debug.sethook function).







debug.getinfo ([thread,] function [, what])





Returns a table with information about a function.
You can give the function directly,
or you can give a number as the value of function,
which means the function running at level function of the call stack
of the given thread:
level 0 is the current function (getinfo itself);
level 1 is the function that called getinfo;
and so on.
If function is a number larger than the number of active functions,
then getinfo returns nil.




The returned table can contain all the fields returned by lua_getinfo,
with the string what describing which fields to fill in.
The default for what is to get all information available,
except the table of valid lines.
If present,
the option 'f'
adds a field named func with the function itself.
If present,
the option 'L'
adds a field named activelines with the table of
valid lines.




For instance, the expression debug.getinfo(1,"n").name returns
a table with a name for the current function,
if a reasonable name can be found,
and the expression debug.getinfo(print)
returns a table with all available information
about the print function.







debug.getlocal ([thread,] level, local)





This function returns the name and the value of the local variable
with index local of the function at level level of the stack.
(The first parameter or local variable has index 1, and so on,
until the last active local variable.)
The function returns nil if there is no local
variable with the given index,
and raises an error when called with a level out of range.
(You can call debug.getinfo to check whether the level is valid.)




Variable names starting with '(' (open parentheses)
represent internal variables
(loop control variables, temporaries, and C function locals).







debug.getmetatable (object)





Returns the metatable of the given object
or nil if it does not have a metatable.







debug.getregistry ()





Returns the registry table (see §3.5).







debug.getupvalue (func, up)





This function returns the name and the value of the upvalue
with index up of the function func.
The function returns nil if there is no upvalue with the given index.







debug.setfenv (object, table)





Sets the environment of the given object to the given table.
Returns object.







debug.sethook ([thread,] hook, mask [, count])





Sets the given function as a hook.
The string mask and the number count describe
when the hook will be called.
The string mask may have the following characters,
with the given meaning:


    

  • "c": the hook is called every time Lua calls a function;
    • 

  • "r": the hook is called every time Lua returns from a function;
    • 

  • "l": the hook is called every time Lua enters a new line of code.
    • 


With a count different from zero,
the hook is called after every count instructions.




When called without arguments,
debug.sethook turns off the hook.




When the hook is called, its first parameter is a string
describing the event that has triggered its call:
"call", "return" (or "tail return",
when simulating a return from a tail call),
"line", and "count".
For line events,
the hook also gets the new line number as its second parameter.
Inside a hook,
you can call getinfo with level 2 to get more information about
the running function
(level 0 is the getinfo function,
and level 1 is the hook function),
unless the event is "tail return".
In this case, Lua is only simulating the return,
and a call to getinfo will return invalid data.







debug.setlocal ([thread,] level, local, value)





This function assigns the value value to the local variable
with index local of the function at level level of the stack.
The function returns nil if there is no local
variable with the given index,
and raises an error when called with a level out of range.
(You can call getinfo to check whether the level is valid.)
Otherwise, it returns the name of the local variable.







debug.setmetatable (object, table)





Sets the metatable for the given object to the given table
(which can be nil).







debug.setupvalue (func, up, value)





This function assigns the value value to the upvalue
with index up of the function func.
The function returns nil if there is no upvalue
with the given index.
Otherwise, it returns the name of the upvalue.







debug.traceback ([thread,] [message [, level]])





Returns a string with a traceback of the call stack.
An optional message string is appended
at the beginning of the traceback.
An optional level number tells at which level
to start the traceback
(default is 1, the function calling traceback).








6 - Lua Stand-alone




Although Lua has been designed as an extension language,
to be embedded in a host C program,
it is also frequently used as a stand-alone language.
An interpreter for Lua as a stand-alone language,
called simply lua,
is provided with the standard distribution.
The stand-alone interpreter includes
all standard libraries, including the debug library.
Its usage is:


     lua [options] [script [args]]


The options are:


    

  • -e stat: executes string stat;
    • 

  • -l mod: "requires" mod;
    • 

  • -i: enters interactive mode after running script;
    • 

  • -v: prints version information;
    • 

  • --: stops handling options;
    • 

  • -: executes stdin as a file and stops handling options.
    • 


After handling its options, lua runs the given script,
passing to it the given args as string arguments.
When called without arguments,
lua behaves as lua -v -i
when the standard input (stdin) is a terminal,
and as lua - otherwise.




Before running any argument,
the interpreter checks for an environment variable LUA_INIT.
If its format is @filename,
then lua executes the file.
Otherwise, lua executes the string itself.




All options are handled in order, except -i.
For instance, an invocation like


     $ lua -e'a=1' -e 'print(a)' script.lua


will first set a to 1, then print the value of a (which is '1'),
and finally run the file script.lua with no arguments.
(Here $ is the shell prompt. Your prompt may be different.)




Before starting to run the script,
lua collects all arguments in the command line
in a global table called arg.
The script name is stored at index 0,
the first argument after the script name goes to index 1,
and so on.
Any arguments before the script name
(that is, the interpreter name plus the options)
go to negative indices.
For instance, in the call


     $ lua -la b.lua t1 t2


the interpreter first runs the file a.lua,
then creates a table


     arg = { [-2] = "lua", [-1] = "-la",
             [0] = "b.lua",
             [1] = "t1", [2] = "t2" }


and finally runs the file b.lua.
The script is called with arg[1], arg[2], ···
as arguments;
it can also access these arguments with the vararg expression '...'.




In interactive mode,
if you write an incomplete statement,
the interpreter waits for its completion
by issuing a different prompt.




If the global variable _PROMPT contains a string,
then its value is used as the prompt.
Similarly, if the global variable _PROMPT2 contains a string,
its value is used as the secondary prompt
(issued during incomplete statements).
Therefore, both prompts can be changed directly on the command line
or in any Lua programs by assigning to _PROMPT.
See the next example:


     $ lua -e"_PROMPT='myprompt> '" -i


(The outer pair of quotes is for the shell,
the inner pair is for Lua.)
Note the use of -i to enter interactive mode;
otherwise,
the program would just end silently
right after the assignment to _PROMPT.




To allow the use of Lua as a
script interpreter in Unix systems,
the stand-alone interpreter skips
the first line of a chunk if it starts with #.
Therefore, Lua scripts can be made into executable programs
by using chmod +x and the #! form,
as in


     #!/usr/local/bin/lua


(Of course,
the location of the Lua interpreter may be different in your machine.
If lua is in your PATH,
then 


     #!/usr/bin/env lua


is a more portable solution.) 




7 - Incompatibilities with the Previous Version




Here we list the incompatibilities that you may find when moving a program
from Lua 5.0 to Lua 5.1.
You can avoid most of the incompatibilities compiling Lua with
appropriate options (see file luaconf.h).
However,
all these compatibility options will be removed in the next version of Lua.




7.1 - Changes in the Language


    


  • 
The vararg system changed from the pseudo-argument arg with a
table with the extra arguments to the vararg expression.
(See compile-time option LUA_COMPAT_VARARG in luaconf.h.)

    • 


  • 
There was a subtle change in the scope of the implicit
variables of the for statement and for the repeat statement.

    • 


  • 
The long string/long comment syntax ([[string]])
does not allow nesting.
You can use the new syntax ([=[string]=]) in these cases.
(See compile-time option LUA_COMPAT_LSTR in luaconf.h.)

    • 








7.2 - Changes in the Libraries


    


  • 
Function string.gfind was renamed string.gmatch.
(See compile-time option LUA_COMPAT_GFIND in luaconf.h.)

    • 


  • 
When string.gsub is called with a function as its
third argument,
whenever this function returns nil or false the
replacement string is the whole match,
instead of the empty string.

    • 


  • 
Function table.setn was deprecated.
Function table.getn corresponds
to the new length operator (#);
use the operator instead of the function.
(See compile-time option LUA_COMPAT_GETN in luaconf.h.)

    • 


  • 
Function loadlib was renamed package.loadlib.
(See compile-time option LUA_COMPAT_LOADLIB in luaconf.h.)

    • 


  • 
Function math.mod was renamed math.fmod.
(See compile-time option LUA_COMPAT_MOD in luaconf.h.)

    • 


  • 
Functions table.foreach and table.foreachi are deprecated.
You can use a for loop with pairs or ipairs instead.

    • 


  • 
There were substantial changes in function require due to
the new module system.
However, the new behavior is mostly compatible with the old,
but require gets the path from package.path instead
of from LUA_PATH.

    • 


  • 
Function collectgarbage has different arguments.
Function gcinfo is deprecated;
use collectgarbage("count") instead.

    • 








7.3 - Changes in the API


    


  • 
The luaopen_* functions (to open libraries)
cannot be called directly,
like a regular C function.
They must be called through Lua,
like a Lua function.

    • 


  • 
Function lua_open was replaced by lua_newstate to
allow the user to set a memory-allocation function.
You can use luaL_newstate from the standard library to
create a state with a standard allocation function
(based on realloc).

    • 


  • 
Functions luaL_getn and luaL_setn
(from the auxiliary library) are deprecated.
Use lua_objlen instead of luaL_getn
and nothing instead of luaL_setn.

    • 


  • 
Function luaL_openlib was replaced by luaL_register.

    • 


  • 
Function luaL_checkudata now throws an error when the given value
is not a userdata of the expected type.
(In Lua 5.0 it returned NULL.)

    • 








8 - The Complete Syntax of Lua




Here is the complete syntax of Lua in extended BNF.
(It does not describe operator precedences.)






	chunk ::= {stat [`;´]} [laststat [`;´]]

	block ::= chunk

	stat ::=  varlist `=´ explist | 
		 functioncall | 
		 do block end | 
		 while exp do block end | 
		 repeat block until exp | 
		 if exp then block {elseif exp then block} [else block] end | 
		 for Name `=´ exp `,´ exp [`,´ exp] do block end | 
		 for namelist in explist do block end | 
		 function funcname funcbody | 
		 local function Name funcbody | 
		 local namelist [`=´ explist] 

	laststat ::= return [explist] | break

	funcname ::= Name {`.´ Name} [`:´ Name]

	varlist ::= var {`,´ var}

	var ::=  Name | prefixexp `[´ exp `]´ | prefixexp `.´ Name 

	namelist ::= Name {`,´ Name}

	explist ::= {exp `,´} exp

	exp ::=  nil | false | true | Number | String | `...´ | function | 
		 prefixexp | tableconstructor | exp binop exp | unop exp 

	prefixexp ::= var | functioncall | `(´ exp `)´

	functioncall ::=  prefixexp args | prefixexp `:´ Name args 

	args ::=  `(´ [explist] `)´ | tableconstructor | String 

	function ::= function funcbody

	funcbody ::= `(´ [parlist] `)´ block end

	parlist ::= namelist [`,´ `...´] | `...´

	tableconstructor ::= `{´ [fieldlist] `}´

	fieldlist ::= field {fieldsep field} [fieldsep]

	field ::= `[´ exp `]´ `=´ exp | Name `=´ exp | exp

	fieldsep ::= `,´ | `;´

	binop ::= `+´ | `-´ | `*´ | `/´ | `^´ | `%´ | `..´ | 
		 `<´ | `<=´ | `>´ | `>=´ | `==´ | `~=´ | 
		 and | or

	unop ::= `-´ | not | `#´
















Last update:
Mon Feb 13 18:54:19 BRST 2012





genometools-1.5.1/src/external/lua-5.1.5/doc/readme.html000066400000000000000000000015021211610345200225700ustar00rootroot00000000000000

Lua documentation









Lua
Documentation



This is the documentation included in the source distribution of Lua 5.1.5.



Lua's
official web site
contains updated documentation,
especially the
reference manual.






Last update:
Fri Feb  3 09:44:42 BRST 2012




genometools-1.5.1/src/external/lua-5.1.5/etc/000077500000000000000000000000001211610345200204555ustar00rootroot00000000000000genometools-1.5.1/src/external/lua-5.1.5/etc/Makefile000066400000000000000000000016201211610345200221140ustar00rootroot00000000000000# makefile for Lua etc

TOP= ..
LIB= $(TOP)/src
INC= $(TOP)/src
BIN= $(TOP)/src
SRC= $(TOP)/src
TST= $(TOP)/test

CC= gcc
CFLAGS= -O2 -Wall -I$(INC) $(MYCFLAGS)
MYCFLAGS= 
MYLDFLAGS= -Wl,-E
MYLIBS= -lm
#MYLIBS= -lm -Wl,-E -ldl -lreadline -lhistory -lncurses
RM= rm -f

default:
	@echo 'Please choose a target: min noparser one strict clean'

min:	min.c
	$(CC) $(CFLAGS) $@.c -L$(LIB) -llua $(MYLIBS)
	echo 'print"Hello there!"' | ./a.out

noparser: noparser.o
	$(CC) noparser.o $(SRC)/lua.o -L$(LIB) -llua $(MYLIBS)
	$(BIN)/luac $(TST)/hello.lua
	-./a.out luac.out
	-./a.out -e'a=1'

one:
	$(CC) $(CFLAGS) all.c $(MYLIBS)
	./a.out $(TST)/hello.lua

strict:
	-$(BIN)/lua -e 'print(a);b=2'
	-$(BIN)/lua -lstrict -e 'print(a)'
	-$(BIN)/lua -e 'function f() b=2 end f()'
	-$(BIN)/lua -lstrict -e 'function f() b=2 end f()'

clean:
	$(RM) a.out core core.* *.o luac.out

.PHONY:	default min noparser one strict clean
genometools-1.5.1/src/external/lua-5.1.5/etc/README000066400000000000000000000017141211610345200213400ustar00rootroot00000000000000This directory contains some useful files and code.
Unlike the code in ../src, everything here is in the public domain.

If any of the makes fail, you're probably not using the same libraries
used to build Lua. Set MYLIBS in Makefile accordingly.

all.c
	Full Lua interpreter in a single file.
	Do "make one" for a demo.

lua.hpp
	Lua header files for C++ using 'extern "C"'.

lua.ico
	A Lua icon for Windows (and web sites: save as favicon.ico).
	Drawn by hand by Markus Gritsch .

lua.pc
	pkg-config data for Lua

luavs.bat
	Script to build Lua under "Visual Studio .NET Command Prompt".
	Run it from the toplevel as etc\luavs.bat.

min.c
	A minimal Lua interpreter.
	Good for learning and for starting your own.
	Do "make min" for a demo.

noparser.c
	Linking with noparser.o avoids loading the parsing modules in lualib.a.
	Do "make noparser" for a demo.

strict.lua
	Traps uses of undeclared global variables.
	Do "make strict" for a demo.

genometools-1.5.1/src/external/lua-5.1.5/etc/all.c000066400000000000000000000012461211610345200213740ustar00rootroot00000000000000/*
* all.c -- Lua core, libraries and interpreter in a single file
*/

#define luaall_c

#include "lapi.c"
#include "lcode.c"
#include "ldebug.c"
#include "ldo.c"
#include "ldump.c"
#include "lfunc.c"
#include "lgc.c"
#include "llex.c"
#include "lmem.c"
#include "lobject.c"
#include "lopcodes.c"
#include "lparser.c"
#include "lstate.c"
#include "lstring.c"
#include "ltable.c"
#include "ltm.c"
#include "lundump.c"
#include "lvm.c"
#include "lzio.c"

#include "lauxlib.c"
#include "lbaselib.c"
#include "ldblib.c"
#include "liolib.c"
#include "linit.c"
#include "lmathlib.c"
#include "loadlib.c"
#include "loslib.c"
#include "lstrlib.c"
#include "ltablib.c"

#include "lua.c"
genometools-1.5.1/src/external/lua-5.1.5/etc/lua.hpp000066400000000000000000000002771211610345200217550ustar00rootroot00000000000000// lua.hpp
// Lua header files for C++
// <> not supplied automatically because Lua also compiles as C++

extern "C" {
#include "lua.h"
#include "lualib.h"
#include "lauxlib.h"
}
genometools-1.5.1/src/external/lua-5.1.5/etc/lua.ico000066400000000000000000000020661211610345200217360ustar00rootroot00000000000000  &(( @DDHDDDDDDDDDDDDDDpDDDDDDDDHDDDDDDDDDDtDDDDDDDDDDGDDDDDDDDDDDDDHDDOxD@DDDOODDHDDDOOODHDDDDOODHDDDDDDOODDDDDDOOtDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDtDHDDDDDDHDHDDDDDDHD@DDDDDDHDDDDDDDDtDtDDDDDDGDDDDDDDDwpDDDDDDDDHxDHpDDDDDDDDpDDDDDDDDDDDGDDHDDDGDDDGDDxDHpwp????G( DHDDDHDDDDDDDDDD@DDDDDHDDDDDDDDDDDDDDDDDDDDDDDDDDDDDHDDD@DDDDDDHtGDHDDDDtG?DDDDDDDDDHDDDH0genometools-1.5.1/src/external/lua-5.1.5/etc/lua.pc000066400000000000000000000012221211610345200215570ustar00rootroot00000000000000# lua.pc -- pkg-config data for Lua

# vars from install Makefile

# grep '^V=' ../Makefile
V= 5.1
# grep '^R=' ../Makefile
R= 5.1.5

# grep '^INSTALL_.*=' ../Makefile | sed 's/INSTALL_TOP/prefix/'
prefix= /usr/local
INSTALL_BIN= ${prefix}/bin
INSTALL_INC= ${prefix}/include
INSTALL_LIB= ${prefix}/lib
INSTALL_MAN= ${prefix}/man/man1
INSTALL_LMOD= ${prefix}/share/lua/${V}
INSTALL_CMOD= ${prefix}/lib/lua/${V}

# canonical vars
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include

Name: Lua
Description: An Extensible Extension Language
Version: ${R}
Requires: 
Libs: -L${libdir} -llua -lm
Cflags: -I${includedir}

# (end of lua.pc)
genometools-1.5.1/src/external/lua-5.1.5/etc/luavs.bat000066400000000000000000000020561211610345200223020ustar00rootroot00000000000000@rem Script to build Lua under "Visual Studio .NET Command Prompt".
@rem Do not run from this directory; run it from the toplevel: etc\luavs.bat .
@rem It creates lua51.dll, lua51.lib, lua.exe, and luac.exe in src.
@rem (contributed by David Manura and Mike Pall)

@setlocal
@set MYCOMPILE=cl /nologo /MD /O2 /W3 /c /D_CRT_SECURE_NO_DEPRECATE
@set MYLINK=link /nologo
@set MYMT=mt /nologo

cd src
%MYCOMPILE% /DLUA_BUILD_AS_DLL l*.c
del lua.obj luac.obj
%MYLINK% /DLL /out:lua51.dll l*.obj
if exist lua51.dll.manifest^
  %MYMT% -manifest lua51.dll.manifest -outputresource:lua51.dll;2
%MYCOMPILE% /DLUA_BUILD_AS_DLL lua.c
%MYLINK% /out:lua.exe lua.obj lua51.lib
if exist lua.exe.manifest^
  %MYMT% -manifest lua.exe.manifest -outputresource:lua.exe
%MYCOMPILE% l*.c print.c
del lua.obj linit.obj lbaselib.obj ldblib.obj liolib.obj lmathlib.obj^
    loslib.obj ltablib.obj lstrlib.obj loadlib.obj
%MYLINK% /out:luac.exe *.obj
if exist luac.exe.manifest^
  %MYMT% -manifest luac.exe.manifest -outputresource:luac.exe
del *.obj *.manifest
cd ..
genometools-1.5.1/src/external/lua-5.1.5/etc/min.c000066400000000000000000000014401211610345200214030ustar00rootroot00000000000000/*
* min.c -- a minimal Lua interpreter
* loads stdin only with minimal error handling.
* no interaction, and no standard library, only a "print" function.
*/

#include 

#include "lua.h"
#include "lauxlib.h"

static int print(lua_State *L)
{
 int n=lua_gettop(L);
 int i;
 for (i=1; i<=n; i++)
 {
  if (i>1) printf("\t");
  if (lua_isstring(L,i))
   printf("%s",lua_tostring(L,i));
  else if (lua_isnil(L,i))
   printf("%s","nil");
  else if (lua_isboolean(L,i))
   printf("%s",lua_toboolean(L,i) ? "true" : "false");
  else
   printf("%s:%p",luaL_typename(L,i),lua_topointer(L,i));
 }
 printf("\n");
 return 0;
}

int main(void)
{
 lua_State *L=lua_open();
 lua_register(L,"print",print);
 if (luaL_dofile(L,NULL)!=0) fprintf(stderr,"%s\n",lua_tostring(L,-1));
 lua_close(L);
 return 0;
}
genometools-1.5.1/src/external/lua-5.1.5/etc/noparser.c000066400000000000000000000023451211610345200224560ustar00rootroot00000000000000/*
* The code below can be used to make a Lua core that does not contain the
* parsing modules (lcode, llex, lparser), which represent 35% of the total core.
* You'll only be able to load binary files and strings, precompiled with luac.
* (Of course, you'll have to build luac with the original parsing modules!)
*
* To use this module, simply compile it ("make noparser" does that) and list
* its object file before the Lua libraries. The linker should then not load
* the parsing modules. To try it, do "make luab".
*
* If you also want to avoid the dump module (ldump.o), define NODUMP.
* #define NODUMP
*/

#define LUA_CORE

#include "llex.h"
#include "lparser.h"
#include "lzio.h"

LUAI_FUNC void luaX_init (lua_State *L) {
  UNUSED(L);
}

LUAI_FUNC Proto *luaY_parser (lua_State *L, ZIO *z, Mbuffer *buff, const char *name) {
  UNUSED(z);
  UNUSED(buff);
  UNUSED(name);
  lua_pushliteral(L,"parser not loaded");
  lua_error(L);
  return NULL;
}

#ifdef NODUMP
#include "lundump.h"

LUAI_FUNC int luaU_dump (lua_State* L, const Proto* f, lua_Writer w, void* data, int strip) {
  UNUSED(f);
  UNUSED(w);
  UNUSED(data);
  UNUSED(strip);
#if 1
  UNUSED(L);
  return 0;
#else
  lua_pushliteral(L,"dumper not loaded");
  lua_error(L);
#endif
}
#endif
genometools-1.5.1/src/external/lua-5.1.5/etc/strict.lua000066400000000000000000000016401211610345200224710ustar00rootroot00000000000000--
-- strict.lua
-- checks uses of undeclared global variables
-- All global variables must be 'declared' through a regular assignment
-- (even assigning nil will do) in a main chunk before being used
-- anywhere or assigned to inside a function.
--

local getinfo, error, rawset, rawget = debug.getinfo, error, rawset, rawget

local mt = getmetatable(_G)
if mt == nil then
  mt = {}
  setmetatable(_G, mt)
end

mt.__declared = {}

local function what ()
  local d = getinfo(3, "S")
  return d and d.what or "C"
end

mt.__newindex = function (t, n, v)
  if not mt.__declared[n] then
    local w = what()
    if w ~= "main" and w ~= "C" then
      error("assign to undeclared variable '"..n.."'", 2)
    end
    mt.__declared[n] = true
  end
  rawset(t, n, v)
end
  
mt.__index = function (t, n)
  if not mt.__declared[n] and what() ~= "C" then
    error("variable '"..n.."' is not declared", 2)
  end
  return rawget(t, n)
end

genometools-1.5.1/src/external/lua-5.1.5/src/000077500000000000000000000000001211610345200204715ustar00rootroot00000000000000genometools-1.5.1/src/external/lua-5.1.5/src/Makefile000066400000000000000000000137651211610345200221450ustar00rootroot00000000000000# makefile for building Lua
# see ../INSTALL for installation instructions
# see ../Makefile and luaconf.h for further customization

# == CHANGE THE SETTINGS BELOW TO SUIT YOUR ENVIRONMENT =======================

# Your platform. See PLATS for possible values.
PLAT= none

CC= gcc
CFLAGS= -O2 -Wall $(MYCFLAGS)
AR= ar rcu
RANLIB= ranlib
RM= rm -f
LIBS= -lm $(MYLIBS)

MYCFLAGS=
MYLDFLAGS=
MYLIBS=

# == END OF USER SETTINGS. NO NEED TO CHANGE ANYTHING BELOW THIS LINE =========

PLATS= aix ansi bsd freebsd generic linux macosx mingw posix solaris

LUA_A=	liblua.a
CORE_O=	lapi.o lcode.o ldebug.o ldo.o ldump.o lfunc.o lgc.o llex.o lmem.o \
	lobject.o lopcodes.o lparser.o lstate.o lstring.o ltable.o ltm.o  \
	lundump.o lvm.o lzio.o
LIB_O=	lauxlib.o lbaselib.o ldblib.o liolib.o lmathlib.o loslib.o ltablib.o \
	lstrlib.o loadlib.o linit.o

LUA_T=	lua
LUA_O=	lua.o

LUAC_T=	luac
LUAC_O=	luac.o print.o

ALL_O= $(CORE_O) $(LIB_O) $(LUA_O) $(LUAC_O)
ALL_T= $(LUA_A) $(LUA_T) $(LUAC_T)
ALL_A= $(LUA_A)

default: $(PLAT)

all:	$(ALL_T)

o:	$(ALL_O)

a:	$(ALL_A)

$(LUA_A): $(CORE_O) $(LIB_O)
	$(AR) $@ $(CORE_O) $(LIB_O)	# DLL needs all object files
	$(RANLIB) $@

$(LUA_T): $(LUA_O) $(LUA_A)
	$(CC) -o $@ $(MYLDFLAGS) $(LUA_O) $(LUA_A) $(LIBS)

$(LUAC_T): $(LUAC_O) $(LUA_A)
	$(CC) -o $@ $(MYLDFLAGS) $(LUAC_O) $(LUA_A) $(LIBS)

clean:
	$(RM) $(ALL_T) $(ALL_O)

depend:
	@$(CC) $(CFLAGS) -MM l*.c print.c

echo:
	@echo "PLAT = $(PLAT)"
	@echo "CC = $(CC)"
	@echo "CFLAGS = $(CFLAGS)"
	@echo "AR = $(AR)"
	@echo "RANLIB = $(RANLIB)"
	@echo "RM = $(RM)"
	@echo "MYCFLAGS = $(MYCFLAGS)"
	@echo "MYLDFLAGS = $(MYLDFLAGS)"
	@echo "MYLIBS = $(MYLIBS)"

# convenience targets for popular platforms

none:
	@echo "Please choose a platform:"
	@echo "   $(PLATS)"

aix:
	$(MAKE) all CC="xlc" CFLAGS="-O2 -DLUA_USE_POSIX -DLUA_USE_DLOPEN" MYLIBS="-ldl" MYLDFLAGS="-brtl -bexpall"

ansi:
	$(MAKE) all MYCFLAGS=-DLUA_ANSI

bsd:
	$(MAKE) all MYCFLAGS="-DLUA_USE_POSIX -DLUA_USE_DLOPEN" MYLIBS="-Wl,-E"

freebsd:
	$(MAKE) all MYCFLAGS="-DLUA_USE_LINUX" MYLIBS="-Wl,-E -lreadline"

generic:
	$(MAKE) all MYCFLAGS=

linux:
	$(MAKE) all MYCFLAGS=-DLUA_USE_LINUX MYLIBS="-Wl,-E -ldl -lreadline -lhistory -lncurses"

macosx:
	$(MAKE) all MYCFLAGS=-DLUA_USE_LINUX MYLIBS="-lreadline"
# use this on Mac OS X 10.3-
#	$(MAKE) all MYCFLAGS=-DLUA_USE_MACOSX

mingw:
	$(MAKE) "LUA_A=lua51.dll" "LUA_T=lua.exe" \
	"AR=$(CC) -shared -o" "RANLIB=strip --strip-unneeded" \
	"MYCFLAGS=-DLUA_BUILD_AS_DLL" "MYLIBS=" "MYLDFLAGS=-s" lua.exe
	$(MAKE) "LUAC_T=luac.exe" luac.exe

posix:
	$(MAKE) all MYCFLAGS=-DLUA_USE_POSIX

solaris:
	$(MAKE) all MYCFLAGS="-DLUA_USE_POSIX -DLUA_USE_DLOPEN" MYLIBS="-ldl"

# list targets that do not create files (but not all makes understand .PHONY)
.PHONY: all $(PLATS) default o a clean depend echo none

# DO NOT DELETE

lapi.o: lapi.c lua.h luaconf.h lapi.h lobject.h llimits.h ldebug.h \
  lstate.h ltm.h lzio.h lmem.h ldo.h lfunc.h lgc.h lstring.h ltable.h \
  lundump.h lvm.h
lauxlib.o: lauxlib.c lua.h luaconf.h lauxlib.h
lbaselib.o: lbaselib.c lua.h luaconf.h lauxlib.h lualib.h
lcode.o: lcode.c lua.h luaconf.h lcode.h llex.h lobject.h llimits.h \
  lzio.h lmem.h lopcodes.h lparser.h ldebug.h lstate.h ltm.h ldo.h lgc.h \
  ltable.h
ldblib.o: ldblib.c lua.h luaconf.h lauxlib.h lualib.h
ldebug.o: ldebug.c lua.h luaconf.h lapi.h lobject.h llimits.h lcode.h \
  llex.h lzio.h lmem.h lopcodes.h lparser.h ldebug.h lstate.h ltm.h ldo.h \
  lfunc.h lstring.h lgc.h ltable.h lvm.h
ldo.o: ldo.c lua.h luaconf.h ldebug.h lstate.h lobject.h llimits.h ltm.h \
  lzio.h lmem.h ldo.h lfunc.h lgc.h lopcodes.h lparser.h lstring.h \
  ltable.h lundump.h lvm.h
ldump.o: ldump.c lua.h luaconf.h lobject.h llimits.h lstate.h ltm.h \
  lzio.h lmem.h lundump.h
lfunc.o: lfunc.c lua.h luaconf.h lfunc.h lobject.h llimits.h lgc.h lmem.h \
  lstate.h ltm.h lzio.h
lgc.o: lgc.c lua.h luaconf.h ldebug.h lstate.h lobject.h llimits.h ltm.h \
  lzio.h lmem.h ldo.h lfunc.h lgc.h lstring.h ltable.h
linit.o: linit.c lua.h luaconf.h lualib.h lauxlib.h
liolib.o: liolib.c lua.h luaconf.h lauxlib.h lualib.h
llex.o: llex.c lua.h luaconf.h ldo.h lobject.h llimits.h lstate.h ltm.h \
  lzio.h lmem.h llex.h lparser.h lstring.h lgc.h ltable.h
lmathlib.o: lmathlib.c lua.h luaconf.h lauxlib.h lualib.h
lmem.o: lmem.c lua.h luaconf.h ldebug.h lstate.h lobject.h llimits.h \
  ltm.h lzio.h lmem.h ldo.h
loadlib.o: loadlib.c lua.h luaconf.h lauxlib.h lualib.h
lobject.o: lobject.c lua.h luaconf.h ldo.h lobject.h llimits.h lstate.h \
  ltm.h lzio.h lmem.h lstring.h lgc.h lvm.h
lopcodes.o: lopcodes.c lopcodes.h llimits.h lua.h luaconf.h
loslib.o: loslib.c lua.h luaconf.h lauxlib.h lualib.h
lparser.o: lparser.c lua.h luaconf.h lcode.h llex.h lobject.h llimits.h \
  lzio.h lmem.h lopcodes.h lparser.h ldebug.h lstate.h ltm.h ldo.h \
  lfunc.h lstring.h lgc.h ltable.h
lstate.o: lstate.c lua.h luaconf.h ldebug.h lstate.h lobject.h llimits.h \
  ltm.h lzio.h lmem.h ldo.h lfunc.h lgc.h llex.h lstring.h ltable.h
lstring.o: lstring.c lua.h luaconf.h lmem.h llimits.h lobject.h lstate.h \
  ltm.h lzio.h lstring.h lgc.h
lstrlib.o: lstrlib.c lua.h luaconf.h lauxlib.h lualib.h
ltable.o: ltable.c lua.h luaconf.h ldebug.h lstate.h lobject.h llimits.h \
  ltm.h lzio.h lmem.h ldo.h lgc.h ltable.h
ltablib.o: ltablib.c lua.h luaconf.h lauxlib.h lualib.h
ltm.o: ltm.c lua.h luaconf.h lobject.h llimits.h lstate.h ltm.h lzio.h \
  lmem.h lstring.h lgc.h ltable.h
lua.o: lua.c lua.h luaconf.h lauxlib.h lualib.h
luac.o: luac.c lua.h luaconf.h lauxlib.h ldo.h lobject.h llimits.h \
  lstate.h ltm.h lzio.h lmem.h lfunc.h lopcodes.h lstring.h lgc.h \
  lundump.h
lundump.o: lundump.c lua.h luaconf.h ldebug.h lstate.h lobject.h \
  llimits.h ltm.h lzio.h lmem.h ldo.h lfunc.h lstring.h lgc.h lundump.h
lvm.o: lvm.c lua.h luaconf.h ldebug.h lstate.h lobject.h llimits.h ltm.h \
  lzio.h lmem.h ldo.h lfunc.h lgc.h lopcodes.h lstring.h ltable.h lvm.h
lzio.o: lzio.c lua.h luaconf.h llimits.h lmem.h lstate.h lobject.h ltm.h \
  lzio.h
print.o: print.c ldebug.h lstate.h lua.h luaconf.h lobject.h llimits.h \
  ltm.h lzio.h lmem.h lopcodes.h lundump.h

# (end of Makefile)
genometools-1.5.1/src/external/lua-5.1.5/src/lapi.c000066400000000000000000000542641211610345200215750ustar00rootroot00000000000000/*
** $Id: lapi.c,v 2.55.1.5 2008/07/04 18:41:18 roberto Exp $
** Lua API
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 
#include 

#define lapi_c
#define LUA_CORE

#include "lua.h"

#include "lapi.h"
#include "ldebug.h"
#include "ldo.h"
#include "lfunc.h"
#include "lgc.h"
#include "lmem.h"
#include "lobject.h"
#include "lstate.h"
#include "lstring.h"
#include "ltable.h"
#include "ltm.h"
#include "lundump.h"
#include "lvm.h"



const char lua_ident[] =
  "$Lua: " LUA_RELEASE " " LUA_COPYRIGHT " $\n"
  "$Authors: " LUA_AUTHORS " $\n"
  "$URL: www.lua.org $\n";



#define api_checknelems(L, n)	api_check(L, (n) <= (L->top - L->base))

#define api_checkvalidindex(L, i)	api_check(L, (i) != luaO_nilobject)

#define api_incr_top(L)   {api_check(L, L->top < L->ci->top); L->top++;}



static TValue *index2adr (lua_State *L, int idx) {
  if (idx > 0) {
    TValue *o = L->base + (idx - 1);
    api_check(L, idx <= L->ci->top - L->base);
    if (o >= L->top) return cast(TValue *, luaO_nilobject);
    else return o;
  }
  else if (idx > LUA_REGISTRYINDEX) {
    api_check(L, idx != 0 && -idx <= L->top - L->base);
    return L->top + idx;
  }
  else switch (idx) {  /* pseudo-indices */
    case LUA_REGISTRYINDEX: return registry(L);
    case LUA_ENVIRONINDEX: {
      Closure *func = curr_func(L);
      sethvalue(L, &L->env, func->c.env);
      return &L->env;
    }
    case LUA_GLOBALSINDEX: return gt(L);
    default: {
      Closure *func = curr_func(L);
      idx = LUA_GLOBALSINDEX - idx;
      return (idx <= func->c.nupvalues)
                ? &func->c.upvalue[idx-1]
                : cast(TValue *, luaO_nilobject);
    }
  }
}


static Table *getcurrenv (lua_State *L) {
  if (L->ci == L->base_ci)  /* no enclosing function? */
    return hvalue(gt(L));  /* use global table as environment */
  else {
    Closure *func = curr_func(L);
    return func->c.env;
  }
}


void luaA_pushobject (lua_State *L, const TValue *o) {
  setobj2s(L, L->top, o);
  api_incr_top(L);
}


LUA_API int lua_checkstack (lua_State *L, int size) {
  int res = 1;
  lua_lock(L);
  if (size > LUAI_MAXCSTACK || (L->top - L->base + size) > LUAI_MAXCSTACK)
    res = 0;  /* stack overflow */
  else if (size > 0) {
    luaD_checkstack(L, size);
    if (L->ci->top < L->top + size)
      L->ci->top = L->top + size;
  }
  lua_unlock(L);
  return res;
}


LUA_API void lua_xmove (lua_State *from, lua_State *to, int n) {
  int i;
  if (from == to) return;
  lua_lock(to);
  api_checknelems(from, n);
  api_check(from, G(from) == G(to));
  api_check(from, to->ci->top - to->top >= n);
  from->top -= n;
  for (i = 0; i < n; i++) {
    setobj2s(to, to->top++, from->top + i);
  }
  lua_unlock(to);
}


LUA_API void lua_setlevel (lua_State *from, lua_State *to) {
  to->nCcalls = from->nCcalls;
}


LUA_API lua_CFunction lua_atpanic (lua_State *L, lua_CFunction panicf) {
  lua_CFunction old;
  lua_lock(L);
  old = G(L)->panic;
  G(L)->panic = panicf;
  lua_unlock(L);
  return old;
}


LUA_API lua_State *lua_newthread (lua_State *L) {
  lua_State *L1;
  lua_lock(L);
  luaC_checkGC(L);
  L1 = luaE_newthread(L);
  setthvalue(L, L->top, L1);
  api_incr_top(L);
  lua_unlock(L);
  luai_userstatethread(L, L1);
  return L1;
}



/*
** basic stack manipulation
*/


LUA_API int lua_gettop (lua_State *L) {
  return cast_int(L->top - L->base);
}


LUA_API void lua_settop (lua_State *L, int idx) {
  lua_lock(L);
  if (idx >= 0) {
    api_check(L, idx <= L->stack_last - L->base);
    while (L->top < L->base + idx)
      setnilvalue(L->top++);
    L->top = L->base + idx;
  }
  else {
    api_check(L, -(idx+1) <= (L->top - L->base));
    L->top += idx+1;  /* `subtract' index (index is negative) */
  }
  lua_unlock(L);
}


LUA_API void lua_remove (lua_State *L, int idx) {
  StkId p;
  lua_lock(L);
  p = index2adr(L, idx);
  api_checkvalidindex(L, p);
  while (++p < L->top) setobjs2s(L, p-1, p);
  L->top--;
  lua_unlock(L);
}


LUA_API void lua_insert (lua_State *L, int idx) {
  StkId p;
  StkId q;
  lua_lock(L);
  p = index2adr(L, idx);
  api_checkvalidindex(L, p);
  for (q = L->top; q>p; q--) setobjs2s(L, q, q-1);
  setobjs2s(L, p, L->top);
  lua_unlock(L);
}


LUA_API void lua_replace (lua_State *L, int idx) {
  StkId o;
  lua_lock(L);
  /* explicit test for incompatible code */
  if (idx == LUA_ENVIRONINDEX && L->ci == L->base_ci)
    luaG_runerror(L, "no calling environment");
  api_checknelems(L, 1);
  o = index2adr(L, idx);
  api_checkvalidindex(L, o);
  if (idx == LUA_ENVIRONINDEX) {
    Closure *func = curr_func(L);
    api_check(L, ttistable(L->top - 1)); 
    func->c.env = hvalue(L->top - 1);
    luaC_barrier(L, func, L->top - 1);
  }
  else {
    setobj(L, o, L->top - 1);
    if (idx < LUA_GLOBALSINDEX)  /* function upvalue? */
      luaC_barrier(L, curr_func(L), L->top - 1);
  }
  L->top--;
  lua_unlock(L);
}


LUA_API void lua_pushvalue (lua_State *L, int idx) {
  lua_lock(L);
  setobj2s(L, L->top, index2adr(L, idx));
  api_incr_top(L);
  lua_unlock(L);
}



/*
** access functions (stack -> C)
*/


LUA_API int lua_type (lua_State *L, int idx) {
  StkId o = index2adr(L, idx);
  return (o == luaO_nilobject) ? LUA_TNONE : ttype(o);
}


LUA_API const char *lua_typename (lua_State *L, int t) {
  UNUSED(L);
  return (t == LUA_TNONE) ? "no value" : luaT_typenames[t];
}


LUA_API int lua_iscfunction (lua_State *L, int idx) {
  StkId o = index2adr(L, idx);
  return iscfunction(o);
}


LUA_API int lua_isnumber (lua_State *L, int idx) {
  TValue n;
  const TValue *o = index2adr(L, idx);
  return tonumber(o, &n);
}


LUA_API int lua_isstring (lua_State *L, int idx) {
  int t = lua_type(L, idx);
  return (t == LUA_TSTRING || t == LUA_TNUMBER);
}


LUA_API int lua_isuserdata (lua_State *L, int idx) {
  const TValue *o = index2adr(L, idx);
  return (ttisuserdata(o) || ttislightuserdata(o));
}


LUA_API int lua_rawequal (lua_State *L, int index1, int index2) {
  StkId o1 = index2adr(L, index1);
  StkId o2 = index2adr(L, index2);
  return (o1 == luaO_nilobject || o2 == luaO_nilobject) ? 0
         : luaO_rawequalObj(o1, o2);
}


LUA_API int lua_equal (lua_State *L, int index1, int index2) {
  StkId o1, o2;
  int i;
  lua_lock(L);  /* may call tag method */
  o1 = index2adr(L, index1);
  o2 = index2adr(L, index2);
  i = (o1 == luaO_nilobject || o2 == luaO_nilobject) ? 0 : equalobj(L, o1, o2);
  lua_unlock(L);
  return i;
}


LUA_API int lua_lessthan (lua_State *L, int index1, int index2) {
  StkId o1, o2;
  int i;
  lua_lock(L);  /* may call tag method */
  o1 = index2adr(L, index1);
  o2 = index2adr(L, index2);
  i = (o1 == luaO_nilobject || o2 == luaO_nilobject) ? 0
       : luaV_lessthan(L, o1, o2);
  lua_unlock(L);
  return i;
}



LUA_API lua_Number lua_tonumber (lua_State *L, int idx) {
  TValue n;
  const TValue *o = index2adr(L, idx);
  if (tonumber(o, &n))
    return nvalue(o);
  else
    return 0;
}


LUA_API lua_Integer lua_tointeger (lua_State *L, int idx) {
  TValue n;
  const TValue *o = index2adr(L, idx);
  if (tonumber(o, &n)) {
    lua_Integer res;
    lua_Number num = nvalue(o);
    lua_number2integer(res, num);
    return res;
  }
  else
    return 0;
}


LUA_API int lua_toboolean (lua_State *L, int idx) {
  const TValue *o = index2adr(L, idx);
  return !l_isfalse(o);
}


LUA_API const char *lua_tolstring (lua_State *L, int idx, size_t *len) {
  StkId o = index2adr(L, idx);
  if (!ttisstring(o)) {
    lua_lock(L);  /* `luaV_tostring' may create a new string */
    if (!luaV_tostring(L, o)) {  /* conversion failed? */
      if (len != NULL) *len = 0;
      lua_unlock(L);
      return NULL;
    }
    luaC_checkGC(L);
    o = index2adr(L, idx);  /* previous call may reallocate the stack */
    lua_unlock(L);
  }
  if (len != NULL) *len = tsvalue(o)->len;
  return svalue(o);
}


LUA_API size_t lua_objlen (lua_State *L, int idx) {
  StkId o = index2adr(L, idx);
  switch (ttype(o)) {
    case LUA_TSTRING: return tsvalue(o)->len;
    case LUA_TUSERDATA: return uvalue(o)->len;
    case LUA_TTABLE: return luaH_getn(hvalue(o));
    case LUA_TNUMBER: {
      size_t l;
      lua_lock(L);  /* `luaV_tostring' may create a new string */
      l = (luaV_tostring(L, o) ? tsvalue(o)->len : 0);
      lua_unlock(L);
      return l;
    }
    default: return 0;
  }
}


LUA_API lua_CFunction lua_tocfunction (lua_State *L, int idx) {
  StkId o = index2adr(L, idx);
  return (!iscfunction(o)) ? NULL : clvalue(o)->c.f;
}


LUA_API void *lua_touserdata (lua_State *L, int idx) {
  StkId o = index2adr(L, idx);
  switch (ttype(o)) {
    case LUA_TUSERDATA: return (rawuvalue(o) + 1);
    case LUA_TLIGHTUSERDATA: return pvalue(o);
    default: return NULL;
  }
}


LUA_API lua_State *lua_tothread (lua_State *L, int idx) {
  StkId o = index2adr(L, idx);
  return (!ttisthread(o)) ? NULL : thvalue(o);
}


LUA_API const void *lua_topointer (lua_State *L, int idx) {
  StkId o = index2adr(L, idx);
  switch (ttype(o)) {
    case LUA_TTABLE: return hvalue(o);
    case LUA_TFUNCTION: return clvalue(o);
    case LUA_TTHREAD: return thvalue(o);
    case LUA_TUSERDATA:
    case LUA_TLIGHTUSERDATA:
      return lua_touserdata(L, idx);
    default: return NULL;
  }
}



/*
** push functions (C -> stack)
*/


LUA_API void lua_pushnil (lua_State *L) {
  lua_lock(L);
  setnilvalue(L->top);
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API void lua_pushnumber (lua_State *L, lua_Number n) {
  lua_lock(L);
  setnvalue(L->top, n);
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API void lua_pushinteger (lua_State *L, lua_Integer n) {
  lua_lock(L);
  setnvalue(L->top, cast_num(n));
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API void lua_pushlstring (lua_State *L, const char *s, size_t len) {
  lua_lock(L);
  luaC_checkGC(L);
  setsvalue2s(L, L->top, luaS_newlstr(L, s, len));
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API void lua_pushstring (lua_State *L, const char *s) {
  if (s == NULL)
    lua_pushnil(L);
  else
    lua_pushlstring(L, s, strlen(s));
}


LUA_API const char *lua_pushvfstring (lua_State *L, const char *fmt,
                                      va_list argp) {
  const char *ret;
  lua_lock(L);
  luaC_checkGC(L);
  ret = luaO_pushvfstring(L, fmt, argp);
  lua_unlock(L);
  return ret;
}


LUA_API const char *lua_pushfstring (lua_State *L, const char *fmt, ...) {
  const char *ret;
  va_list argp;
  lua_lock(L);
  luaC_checkGC(L);
  va_start(argp, fmt);
  ret = luaO_pushvfstring(L, fmt, argp);
  va_end(argp);
  lua_unlock(L);
  return ret;
}


LUA_API void lua_pushcclosure (lua_State *L, lua_CFunction fn, int n) {
  Closure *cl;
  lua_lock(L);
  luaC_checkGC(L);
  api_checknelems(L, n);
  cl = luaF_newCclosure(L, n, getcurrenv(L));
  cl->c.f = fn;
  L->top -= n;
  while (n--)
    setobj2n(L, &cl->c.upvalue[n], L->top+n);
  setclvalue(L, L->top, cl);
  lua_assert(iswhite(obj2gco(cl)));
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API void lua_pushboolean (lua_State *L, int b) {
  lua_lock(L);
  setbvalue(L->top, (b != 0));  /* ensure that true is 1 */
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API void lua_pushlightuserdata (lua_State *L, void *p) {
  lua_lock(L);
  setpvalue(L->top, p);
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API int lua_pushthread (lua_State *L) {
  lua_lock(L);
  setthvalue(L, L->top, L);
  api_incr_top(L);
  lua_unlock(L);
  return (G(L)->mainthread == L);
}



/*
** get functions (Lua -> stack)
*/


LUA_API void lua_gettable (lua_State *L, int idx) {
  StkId t;
  lua_lock(L);
  t = index2adr(L, idx);
  api_checkvalidindex(L, t);
  luaV_gettable(L, t, L->top - 1, L->top - 1);
  lua_unlock(L);
}


LUA_API void lua_getfield (lua_State *L, int idx, const char *k) {
  StkId t;
  TValue key;
  lua_lock(L);
  t = index2adr(L, idx);
  api_checkvalidindex(L, t);
  setsvalue(L, &key, luaS_new(L, k));
  luaV_gettable(L, t, &key, L->top);
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API void lua_rawget (lua_State *L, int idx) {
  StkId t;
  lua_lock(L);
  t = index2adr(L, idx);
  api_check(L, ttistable(t));
  setobj2s(L, L->top - 1, luaH_get(hvalue(t), L->top - 1));
  lua_unlock(L);
}


LUA_API void lua_rawgeti (lua_State *L, int idx, int n) {
  StkId o;
  lua_lock(L);
  o = index2adr(L, idx);
  api_check(L, ttistable(o));
  setobj2s(L, L->top, luaH_getnum(hvalue(o), n));
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API void lua_createtable (lua_State *L, int narray, int nrec) {
  lua_lock(L);
  luaC_checkGC(L);
  sethvalue(L, L->top, luaH_new(L, narray, nrec));
  api_incr_top(L);
  lua_unlock(L);
}


LUA_API int lua_getmetatable (lua_State *L, int objindex) {
  const TValue *obj;
  Table *mt = NULL;
  int res;
  lua_lock(L);
  obj = index2adr(L, objindex);
  switch (ttype(obj)) {
    case LUA_TTABLE:
      mt = hvalue(obj)->metatable;
      break;
    case LUA_TUSERDATA:
      mt = uvalue(obj)->metatable;
      break;
    default:
      mt = G(L)->mt[ttype(obj)];
      break;
  }
  if (mt == NULL)
    res = 0;
  else {
    sethvalue(L, L->top, mt);
    api_incr_top(L);
    res = 1;
  }
  lua_unlock(L);
  return res;
}


LUA_API void lua_getfenv (lua_State *L, int idx) {
  StkId o;
  lua_lock(L);
  o = index2adr(L, idx);
  api_checkvalidindex(L, o);
  switch (ttype(o)) {
    case LUA_TFUNCTION:
      sethvalue(L, L->top, clvalue(o)->c.env);
      break;
    case LUA_TUSERDATA:
      sethvalue(L, L->top, uvalue(o)->env);
      break;
    case LUA_TTHREAD:
      setobj2s(L, L->top,  gt(thvalue(o)));
      break;
    default:
      setnilvalue(L->top);
      break;
  }
  api_incr_top(L);
  lua_unlock(L);
}


/*
** set functions (stack -> Lua)
*/


LUA_API void lua_settable (lua_State *L, int idx) {
  StkId t;
  lua_lock(L);
  api_checknelems(L, 2);
  t = index2adr(L, idx);
  api_checkvalidindex(L, t);
  luaV_settable(L, t, L->top - 2, L->top - 1);
  L->top -= 2;  /* pop index and value */
  lua_unlock(L);
}


LUA_API void lua_setfield (lua_State *L, int idx, const char *k) {
  StkId t;
  TValue key;
  lua_lock(L);
  api_checknelems(L, 1);
  t = index2adr(L, idx);
  api_checkvalidindex(L, t);
  setsvalue(L, &key, luaS_new(L, k));
  luaV_settable(L, t, &key, L->top - 1);
  L->top--;  /* pop value */
  lua_unlock(L);
}


LUA_API void lua_rawset (lua_State *L, int idx) {
  StkId t;
  lua_lock(L);
  api_checknelems(L, 2);
  t = index2adr(L, idx);
  api_check(L, ttistable(t));
  setobj2t(L, luaH_set(L, hvalue(t), L->top-2), L->top-1);
  luaC_barriert(L, hvalue(t), L->top-1);
  L->top -= 2;
  lua_unlock(L);
}


LUA_API void lua_rawseti (lua_State *L, int idx, int n) {
  StkId o;
  lua_lock(L);
  api_checknelems(L, 1);
  o = index2adr(L, idx);
  api_check(L, ttistable(o));
  setobj2t(L, luaH_setnum(L, hvalue(o), n), L->top-1);
  luaC_barriert(L, hvalue(o), L->top-1);
  L->top--;
  lua_unlock(L);
}


LUA_API int lua_setmetatable (lua_State *L, int objindex) {
  TValue *obj;
  Table *mt;
  lua_lock(L);
  api_checknelems(L, 1);
  obj = index2adr(L, objindex);
  api_checkvalidindex(L, obj);
  if (ttisnil(L->top - 1))
    mt = NULL;
  else {
    api_check(L, ttistable(L->top - 1));
    mt = hvalue(L->top - 1);
  }
  switch (ttype(obj)) {
    case LUA_TTABLE: {
      hvalue(obj)->metatable = mt;
      if (mt)
        luaC_objbarriert(L, hvalue(obj), mt);
      break;
    }
    case LUA_TUSERDATA: {
      uvalue(obj)->metatable = mt;
      if (mt)
        luaC_objbarrier(L, rawuvalue(obj), mt);
      break;
    }
    default: {
      G(L)->mt[ttype(obj)] = mt;
      break;
    }
  }
  L->top--;
  lua_unlock(L);
  return 1;
}


LUA_API int lua_setfenv (lua_State *L, int idx) {
  StkId o;
  int res = 1;
  lua_lock(L);
  api_checknelems(L, 1);
  o = index2adr(L, idx);
  api_checkvalidindex(L, o);
  api_check(L, ttistable(L->top - 1));
  switch (ttype(o)) {
    case LUA_TFUNCTION:
      clvalue(o)->c.env = hvalue(L->top - 1);
      break;
    case LUA_TUSERDATA:
      uvalue(o)->env = hvalue(L->top - 1);
      break;
    case LUA_TTHREAD:
      sethvalue(L, gt(thvalue(o)), hvalue(L->top - 1));
      break;
    default:
      res = 0;
      break;
  }
  if (res) luaC_objbarrier(L, gcvalue(o), hvalue(L->top - 1));
  L->top--;
  lua_unlock(L);
  return res;
}


/*
** `load' and `call' functions (run Lua code)
*/


#define adjustresults(L,nres) \
    { if (nres == LUA_MULTRET && L->top >= L->ci->top) L->ci->top = L->top; }


#define checkresults(L,na,nr) \
     api_check(L, (nr) == LUA_MULTRET || (L->ci->top - L->top >= (nr) - (na)))
	

LUA_API void lua_call (lua_State *L, int nargs, int nresults) {
  StkId func;
  lua_lock(L);
  api_checknelems(L, nargs+1);
  checkresults(L, nargs, nresults);
  func = L->top - (nargs+1);
  luaD_call(L, func, nresults);
  adjustresults(L, nresults);
  lua_unlock(L);
}



/*
** Execute a protected call.
*/
struct CallS {  /* data to `f_call' */
  StkId func;
  int nresults;
};


static void f_call (lua_State *L, void *ud) {
  struct CallS *c = cast(struct CallS *, ud);
  luaD_call(L, c->func, c->nresults);
}



LUA_API int lua_pcall (lua_State *L, int nargs, int nresults, int errfunc) {
  struct CallS c;
  int status;
  ptrdiff_t func;
  lua_lock(L);
  api_checknelems(L, nargs+1);
  checkresults(L, nargs, nresults);
  if (errfunc == 0)
    func = 0;
  else {
    StkId o = index2adr(L, errfunc);
    api_checkvalidindex(L, o);
    func = savestack(L, o);
  }
  c.func = L->top - (nargs+1);  /* function to be called */
  c.nresults = nresults;
  status = luaD_pcall(L, f_call, &c, savestack(L, c.func), func);
  adjustresults(L, nresults);
  lua_unlock(L);
  return status;
}


/*
** Execute a protected C call.
*/
struct CCallS {  /* data to `f_Ccall' */
  lua_CFunction func;
  void *ud;
};


static void f_Ccall (lua_State *L, void *ud) {
  struct CCallS *c = cast(struct CCallS *, ud);
  Closure *cl;
  cl = luaF_newCclosure(L, 0, getcurrenv(L));
  cl->c.f = c->func;
  setclvalue(L, L->top, cl);  /* push function */
  api_incr_top(L);
  setpvalue(L->top, c->ud);  /* push only argument */
  api_incr_top(L);
  luaD_call(L, L->top - 2, 0);
}


LUA_API int lua_cpcall (lua_State *L, lua_CFunction func, void *ud) {
  struct CCallS c;
  int status;
  lua_lock(L);
  c.func = func;
  c.ud = ud;
  status = luaD_pcall(L, f_Ccall, &c, savestack(L, L->top), 0);
  lua_unlock(L);
  return status;
}


LUA_API int lua_load (lua_State *L, lua_Reader reader, void *data,
                      const char *chunkname) {
  ZIO z;
  int status;
  lua_lock(L);
  if (!chunkname) chunkname = "?";
  luaZ_init(L, &z, reader, data);
  status = luaD_protectedparser(L, &z, chunkname);
  lua_unlock(L);
  return status;
}


LUA_API int lua_dump (lua_State *L, lua_Writer writer, void *data) {
  int status;
  TValue *o;
  lua_lock(L);
  api_checknelems(L, 1);
  o = L->top - 1;
  if (isLfunction(o))
    status = luaU_dump(L, clvalue(o)->l.p, writer, data, 0);
  else
    status = 1;
  lua_unlock(L);
  return status;
}


LUA_API int  lua_status (lua_State *L) {
  return L->status;
}


/*
** Garbage-collection function
*/

LUA_API int lua_gc (lua_State *L, int what, int data) {
  int res = 0;
  global_State *g;
  lua_lock(L);
  g = G(L);
  switch (what) {
    case LUA_GCSTOP: {
      g->GCthreshold = MAX_LUMEM;
      break;
    }
    case LUA_GCRESTART: {
      g->GCthreshold = g->totalbytes;
      break;
    }
    case LUA_GCCOLLECT: {
      luaC_fullgc(L);
      break;
    }
    case LUA_GCCOUNT: {
      /* GC values are expressed in Kbytes: #bytes/2^10 */
      res = cast_int(g->totalbytes >> 10);
      break;
    }
    case LUA_GCCOUNTB: {
      res = cast_int(g->totalbytes & 0x3ff);
      break;
    }
    case LUA_GCSTEP: {
      lu_mem a = (cast(lu_mem, data) << 10);
      if (a <= g->totalbytes)
        g->GCthreshold = g->totalbytes - a;
      else
        g->GCthreshold = 0;
      while (g->GCthreshold <= g->totalbytes) {
        luaC_step(L);
        if (g->gcstate == GCSpause) {  /* end of cycle? */
          res = 1;  /* signal it */
          break;
        }
      }
      break;
    }
    case LUA_GCSETPAUSE: {
      res = g->gcpause;
      g->gcpause = data;
      break;
    }
    case LUA_GCSETSTEPMUL: {
      res = g->gcstepmul;
      g->gcstepmul = data;
      break;
    }
    default: res = -1;  /* invalid option */
  }
  lua_unlock(L);
  return res;
}



/*
** miscellaneous functions
*/


LUA_API int lua_error (lua_State *L) {
  lua_lock(L);
  api_checknelems(L, 1);
  luaG_errormsg(L);
  lua_unlock(L);
  return 0;  /* to avoid warnings */
}


LUA_API int lua_next (lua_State *L, int idx) {
  StkId t;
  int more;
  lua_lock(L);
  t = index2adr(L, idx);
  api_check(L, ttistable(t));
  more = luaH_next(L, hvalue(t), L->top - 1);
  if (more) {
    api_incr_top(L);
  }
  else  /* no more elements */
    L->top -= 1;  /* remove key */
  lua_unlock(L);
  return more;
}


LUA_API void lua_concat (lua_State *L, int n) {
  lua_lock(L);
  api_checknelems(L, n);
  if (n >= 2) {
    luaC_checkGC(L);
    luaV_concat(L, n, cast_int(L->top - L->base) - 1);
    L->top -= (n-1);
  }
  else if (n == 0) {  /* push empty string */
    setsvalue2s(L, L->top, luaS_newlstr(L, "", 0));
    api_incr_top(L);
  }
  /* else n == 1; nothing to do */
  lua_unlock(L);
}


LUA_API lua_Alloc lua_getallocf (lua_State *L, void **ud) {
  lua_Alloc f;
  lua_lock(L);
  if (ud) *ud = G(L)->ud;
  f = G(L)->frealloc;
  lua_unlock(L);
  return f;
}


LUA_API void lua_setallocf (lua_State *L, lua_Alloc f, void *ud) {
  lua_lock(L);
  G(L)->ud = ud;
  G(L)->frealloc = f;
  lua_unlock(L);
}


LUA_API void *lua_newuserdata (lua_State *L, size_t size) {
  Udata *u;
  lua_lock(L);
  luaC_checkGC(L);
  u = luaS_newudata(L, size, getcurrenv(L));
  setuvalue(L, L->top, u);
  api_incr_top(L);
  lua_unlock(L);
  return u + 1;
}




static const char *aux_upvalue (StkId fi, int n, TValue **val) {
  Closure *f;
  if (!ttisfunction(fi)) return NULL;
  f = clvalue(fi);
  if (f->c.isC) {
    if (!(1 <= n && n <= f->c.nupvalues)) return NULL;
    *val = &f->c.upvalue[n-1];
    return "";
  }
  else {
    Proto *p = f->l.p;
    if (!(1 <= n && n <= p->sizeupvalues)) return NULL;
    *val = f->l.upvals[n-1]->v;
    return getstr(p->upvalues[n-1]);
  }
}


LUA_API const char *lua_getupvalue (lua_State *L, int funcindex, int n) {
  const char *name;
  TValue *val;
  lua_lock(L);
  name = aux_upvalue(index2adr(L, funcindex), n, &val);
  if (name) {
    setobj2s(L, L->top, val);
    api_incr_top(L);
  }
  lua_unlock(L);
  return name;
}


LUA_API const char *lua_setupvalue (lua_State *L, int funcindex, int n) {
  const char *name;
  TValue *val;
  StkId fi;
  lua_lock(L);
  fi = index2adr(L, funcindex);
  api_checknelems(L, 1);
  name = aux_upvalue(fi, n, &val);
  if (name) {
    L->top--;
    setobj(L, val, L->top);
    luaC_barrier(L, clvalue(fi), L->top);
  }
  lua_unlock(L);
  return name;
}

genometools-1.5.1/src/external/lua-5.1.5/src/lapi.h000066400000000000000000000004061211610345200215670ustar00rootroot00000000000000/*
** $Id: lapi.h,v 2.2.1.1 2007/12/27 13:02:25 roberto Exp $
** Auxiliary functions from Lua API
** See Copyright Notice in lua.h
*/

#ifndef lapi_h
#define lapi_h


#include "lobject.h"


LUAI_FUNC void luaA_pushobject (lua_State *L, const TValue *o);

#endif
genometools-1.5.1/src/external/lua-5.1.5/src/lauxlib.c000066400000000000000000000420111211610345200222730ustar00rootroot00000000000000/*
** $Id: lauxlib.c,v 1.159.1.3 2008/01/21 13:20:51 roberto Exp $
** Auxiliary functions for building Lua libraries
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 
#include 
#include 
#include 


/* This file uses only the official API of Lua.
** Any function declared here could be written as an application function.
*/

#define lauxlib_c
#define LUA_LIB

#include "lua.h"

#include "lauxlib.h"


#define FREELIST_REF	0	/* free list of references */


/* convert a stack index to positive */
#define abs_index(L, i)		((i) > 0 || (i) <= LUA_REGISTRYINDEX ? (i) : \
					lua_gettop(L) + (i) + 1)


/*
** {======================================================
** Error-report functions
** =======================================================
*/


LUALIB_API int luaL_argerror (lua_State *L, int narg, const char *extramsg) {
  lua_Debug ar;
  if (!lua_getstack(L, 0, &ar))  /* no stack frame? */
    return luaL_error(L, "bad argument #%d (%s)", narg, extramsg);
  lua_getinfo(L, "n", &ar);
  if (strcmp(ar.namewhat, "method") == 0) {
    narg--;  /* do not count `self' */
    if (narg == 0)  /* error is in the self argument itself? */
      return luaL_error(L, "calling " LUA_QS " on bad self (%s)",
                           ar.name, extramsg);
  }
  if (ar.name == NULL)
    ar.name = "?";
  return luaL_error(L, "bad argument #%d to " LUA_QS " (%s)",
                        narg, ar.name, extramsg);
}


LUALIB_API int luaL_typerror (lua_State *L, int narg, const char *tname) {
  const char *msg = lua_pushfstring(L, "%s expected, got %s",
                                    tname, luaL_typename(L, narg));
  return luaL_argerror(L, narg, msg);
}


static void tag_error (lua_State *L, int narg, int tag) {
  luaL_typerror(L, narg, lua_typename(L, tag));
}


LUALIB_API void luaL_where (lua_State *L, int level) {
  lua_Debug ar;
  if (lua_getstack(L, level, &ar)) {  /* check function at level */
    lua_getinfo(L, "Sl", &ar);  /* get info about it */
    if (ar.currentline > 0) {  /* is there info? */
      lua_pushfstring(L, "%s:%d: ", ar.short_src, ar.currentline);
      return;
    }
  }
  lua_pushliteral(L, "");  /* else, no information available... */
}


LUALIB_API int luaL_error (lua_State *L, const char *fmt, ...) {
  va_list argp;
  va_start(argp, fmt);
  luaL_where(L, 1);
  lua_pushvfstring(L, fmt, argp);
  va_end(argp);
  lua_concat(L, 2);
  return lua_error(L);
}

/* }====================================================== */


LUALIB_API int luaL_checkoption (lua_State *L, int narg, const char *def,
                                 const char *const lst[]) {
  const char *name = (def) ? luaL_optstring(L, narg, def) :
                             luaL_checkstring(L, narg);
  int i;
  for (i=0; lst[i]; i++)
    if (strcmp(lst[i], name) == 0)
      return i;
  return luaL_argerror(L, narg,
                       lua_pushfstring(L, "invalid option " LUA_QS, name));
}


LUALIB_API int luaL_newmetatable (lua_State *L, const char *tname) {
  lua_getfield(L, LUA_REGISTRYINDEX, tname);  /* get registry.name */
  if (!lua_isnil(L, -1))  /* name already in use? */
    return 0;  /* leave previous value on top, but return 0 */
  lua_pop(L, 1);
  lua_newtable(L);  /* create metatable */
  lua_pushvalue(L, -1);
  lua_setfield(L, LUA_REGISTRYINDEX, tname);  /* registry.name = metatable */
  return 1;
}


LUALIB_API void *luaL_checkudata (lua_State *L, int ud, const char *tname) {
  void *p = lua_touserdata(L, ud);
  if (p != NULL) {  /* value is a userdata? */
    if (lua_getmetatable(L, ud)) {  /* does it have a metatable? */
      lua_getfield(L, LUA_REGISTRYINDEX, tname);  /* get correct metatable */
      if (lua_rawequal(L, -1, -2)) {  /* does it have the correct mt? */
        lua_pop(L, 2);  /* remove both metatables */
        return p;
      }
    }
  }
  luaL_typerror(L, ud, tname);  /* else error */
  return NULL;  /* to avoid warnings */
}


LUALIB_API void luaL_checkstack (lua_State *L, int space, const char *mes) {
  if (!lua_checkstack(L, space))
    luaL_error(L, "stack overflow (%s)", mes);
}


LUALIB_API void luaL_checktype (lua_State *L, int narg, int t) {
  if (lua_type(L, narg) != t)
    tag_error(L, narg, t);
}


LUALIB_API void luaL_checkany (lua_State *L, int narg) {
  if (lua_type(L, narg) == LUA_TNONE)
    luaL_argerror(L, narg, "value expected");
}


LUALIB_API const char *luaL_checklstring (lua_State *L, int narg, size_t *len) {
  const char *s = lua_tolstring(L, narg, len);
  if (!s) tag_error(L, narg, LUA_TSTRING);
  return s;
}


LUALIB_API const char *luaL_optlstring (lua_State *L, int narg,
                                        const char *def, size_t *len) {
  if (lua_isnoneornil(L, narg)) {
    if (len)
      *len = (def ? strlen(def) : 0);
    return def;
  }
  else return luaL_checklstring(L, narg, len);
}


LUALIB_API lua_Number luaL_checknumber (lua_State *L, int narg) {
  lua_Number d = lua_tonumber(L, narg);
  if (d == 0 && !lua_isnumber(L, narg))  /* avoid extra test when d is not 0 */
    tag_error(L, narg, LUA_TNUMBER);
  return d;
}


LUALIB_API lua_Number luaL_optnumber (lua_State *L, int narg, lua_Number def) {
  return luaL_opt(L, luaL_checknumber, narg, def);
}


LUALIB_API lua_Integer luaL_checkinteger (lua_State *L, int narg) {
  lua_Integer d = lua_tointeger(L, narg);
  if (d == 0 && !lua_isnumber(L, narg))  /* avoid extra test when d is not 0 */
    tag_error(L, narg, LUA_TNUMBER);
  return d;
}


LUALIB_API lua_Integer luaL_optinteger (lua_State *L, int narg,
                                                      lua_Integer def) {
  return luaL_opt(L, luaL_checkinteger, narg, def);
}


LUALIB_API int luaL_getmetafield (lua_State *L, int obj, const char *event) {
  if (!lua_getmetatable(L, obj))  /* no metatable? */
    return 0;
  lua_pushstring(L, event);
  lua_rawget(L, -2);
  if (lua_isnil(L, -1)) {
    lua_pop(L, 2);  /* remove metatable and metafield */
    return 0;
  }
  else {
    lua_remove(L, -2);  /* remove only metatable */
    return 1;
  }
}


LUALIB_API int luaL_callmeta (lua_State *L, int obj, const char *event) {
  obj = abs_index(L, obj);
  if (!luaL_getmetafield(L, obj, event))  /* no metafield? */
    return 0;
  lua_pushvalue(L, obj);
  lua_call(L, 1, 1);
  return 1;
}


LUALIB_API void (luaL_register) (lua_State *L, const char *libname,
                                const luaL_Reg *l) {
  luaI_openlib(L, libname, l, 0);
}


static int libsize (const luaL_Reg *l) {
  int size = 0;
  for (; l->name; l++) size++;
  return size;
}


LUALIB_API void luaI_openlib (lua_State *L, const char *libname,
                              const luaL_Reg *l, int nup) {
  if (libname) {
    int size = libsize(l);
    /* check whether lib already exists */
    luaL_findtable(L, LUA_REGISTRYINDEX, "_LOADED", 1);
    lua_getfield(L, -1, libname);  /* get _LOADED[libname] */
    if (!lua_istable(L, -1)) {  /* not found? */
      lua_pop(L, 1);  /* remove previous result */
      /* try global variable (and create one if it does not exist) */
      if (luaL_findtable(L, LUA_GLOBALSINDEX, libname, size) != NULL)
        luaL_error(L, "name conflict for module " LUA_QS, libname);
      lua_pushvalue(L, -1);
      lua_setfield(L, -3, libname);  /* _LOADED[libname] = new table */
    }
    lua_remove(L, -2);  /* remove _LOADED table */
    lua_insert(L, -(nup+1));  /* move library table to below upvalues */
  }
  for (; l->name; l++) {
    int i;
    for (i=0; ifunc, nup);
    lua_setfield(L, -(nup+2), l->name);
  }
  lua_pop(L, nup);  /* remove upvalues */
}



/*
** {======================================================
** getn-setn: size for arrays
** =======================================================
*/

#if defined(LUA_COMPAT_GETN)

static int checkint (lua_State *L, int topop) {
  int n = (lua_type(L, -1) == LUA_TNUMBER) ? lua_tointeger(L, -1) : -1;
  lua_pop(L, topop);
  return n;
}


static void getsizes (lua_State *L) {
  lua_getfield(L, LUA_REGISTRYINDEX, "LUA_SIZES");
  if (lua_isnil(L, -1)) {  /* no `size' table? */
    lua_pop(L, 1);  /* remove nil */
    lua_newtable(L);  /* create it */
    lua_pushvalue(L, -1);  /* `size' will be its own metatable */
    lua_setmetatable(L, -2);
    lua_pushliteral(L, "kv");
    lua_setfield(L, -2, "__mode");  /* metatable(N).__mode = "kv" */
    lua_pushvalue(L, -1);
    lua_setfield(L, LUA_REGISTRYINDEX, "LUA_SIZES");  /* store in register */
  }
}


LUALIB_API void luaL_setn (lua_State *L, int t, int n) {
  t = abs_index(L, t);
  lua_pushliteral(L, "n");
  lua_rawget(L, t);
  if (checkint(L, 1) >= 0) {  /* is there a numeric field `n'? */
    lua_pushliteral(L, "n");  /* use it */
    lua_pushinteger(L, n);
    lua_rawset(L, t);
  }
  else {  /* use `sizes' */
    getsizes(L);
    lua_pushvalue(L, t);
    lua_pushinteger(L, n);
    lua_rawset(L, -3);  /* sizes[t] = n */
    lua_pop(L, 1);  /* remove `sizes' */
  }
}


LUALIB_API int luaL_getn (lua_State *L, int t) {
  int n;
  t = abs_index(L, t);
  lua_pushliteral(L, "n");  /* try t.n */
  lua_rawget(L, t);
  if ((n = checkint(L, 1)) >= 0) return n;
  getsizes(L);  /* else try sizes[t] */
  lua_pushvalue(L, t);
  lua_rawget(L, -2);
  if ((n = checkint(L, 2)) >= 0) return n;
  return (int)lua_objlen(L, t);
}

#endif

/* }====================================================== */



LUALIB_API const char *luaL_gsub (lua_State *L, const char *s, const char *p,
                                                               const char *r) {
  const char *wild;
  size_t l = strlen(p);
  luaL_Buffer b;
  luaL_buffinit(L, &b);
  while ((wild = strstr(s, p)) != NULL) {
    luaL_addlstring(&b, s, wild - s);  /* push prefix */
    luaL_addstring(&b, r);  /* push replacement in place of pattern */
    s = wild + l;  /* continue after `p' */
  }
  luaL_addstring(&b, s);  /* push last suffix */
  luaL_pushresult(&b);
  return lua_tostring(L, -1);
}


LUALIB_API const char *luaL_findtable (lua_State *L, int idx,
                                       const char *fname, int szhint) {
  const char *e;
  lua_pushvalue(L, idx);
  do {
    e = strchr(fname, '.');
    if (e == NULL) e = fname + strlen(fname);
    lua_pushlstring(L, fname, e - fname);
    lua_rawget(L, -2);
    if (lua_isnil(L, -1)) {  /* no such field? */
      lua_pop(L, 1);  /* remove this nil */
      lua_createtable(L, 0, (*e == '.' ? 1 : szhint)); /* new table for field */
      lua_pushlstring(L, fname, e - fname);
      lua_pushvalue(L, -2);
      lua_settable(L, -4);  /* set new table into field */
    }
    else if (!lua_istable(L, -1)) {  /* field has a non-table value? */
      lua_pop(L, 2);  /* remove table and value */
      return fname;  /* return problematic part of the name */
    }
    lua_remove(L, -2);  /* remove previous table */
    fname = e + 1;
  } while (*e == '.');
  return NULL;
}



/*
** {======================================================
** Generic Buffer manipulation
** =======================================================
*/


#define bufflen(B)	((B)->p - (B)->buffer)
#define bufffree(B)	((size_t)(LUAL_BUFFERSIZE - bufflen(B)))

#define LIMIT	(LUA_MINSTACK/2)


static int emptybuffer (luaL_Buffer *B) {
  size_t l = bufflen(B);
  if (l == 0) return 0;  /* put nothing on stack */
  else {
    lua_pushlstring(B->L, B->buffer, l);
    B->p = B->buffer;
    B->lvl++;
    return 1;
  }
}


static void adjuststack (luaL_Buffer *B) {
  if (B->lvl > 1) {
    lua_State *L = B->L;
    int toget = 1;  /* number of levels to concat */
    size_t toplen = lua_strlen(L, -1);
    do {
      size_t l = lua_strlen(L, -(toget+1));
      if (B->lvl - toget + 1 >= LIMIT || toplen > l) {
        toplen += l;
        toget++;
      }
      else break;
    } while (toget < B->lvl);
    lua_concat(L, toget);
    B->lvl = B->lvl - toget + 1;
  }
}


LUALIB_API char *luaL_prepbuffer (luaL_Buffer *B) {
  if (emptybuffer(B))
    adjuststack(B);
  return B->buffer;
}


LUALIB_API void luaL_addlstring (luaL_Buffer *B, const char *s, size_t l) {
  while (l--)
    luaL_addchar(B, *s++);
}


LUALIB_API void luaL_addstring (luaL_Buffer *B, const char *s) {
  luaL_addlstring(B, s, strlen(s));
}


LUALIB_API void luaL_pushresult (luaL_Buffer *B) {
  emptybuffer(B);
  lua_concat(B->L, B->lvl);
  B->lvl = 1;
}


LUALIB_API void luaL_addvalue (luaL_Buffer *B) {
  lua_State *L = B->L;
  size_t vl;
  const char *s = lua_tolstring(L, -1, &vl);
  if (vl <= bufffree(B)) {  /* fit into buffer? */
    memcpy(B->p, s, vl);  /* put it there */
    B->p += vl;
    lua_pop(L, 1);  /* remove from stack */
  }
  else {
    if (emptybuffer(B))
      lua_insert(L, -2);  /* put buffer before new value */
    B->lvl++;  /* add new value into B stack */
    adjuststack(B);
  }
}


LUALIB_API void luaL_buffinit (lua_State *L, luaL_Buffer *B) {
  B->L = L;
  B->p = B->buffer;
  B->lvl = 0;
}

/* }====================================================== */


LUALIB_API int luaL_ref (lua_State *L, int t) {
  int ref;
  t = abs_index(L, t);
  if (lua_isnil(L, -1)) {
    lua_pop(L, 1);  /* remove from stack */
    return LUA_REFNIL;  /* `nil' has a unique fixed reference */
  }
  lua_rawgeti(L, t, FREELIST_REF);  /* get first free element */
  ref = (int)lua_tointeger(L, -1);  /* ref = t[FREELIST_REF] */
  lua_pop(L, 1);  /* remove it from stack */
  if (ref != 0) {  /* any free element? */
    lua_rawgeti(L, t, ref);  /* remove it from list */
    lua_rawseti(L, t, FREELIST_REF);  /* (t[FREELIST_REF] = t[ref]) */
  }
  else {  /* no free elements */
    ref = (int)lua_objlen(L, t);
    ref++;  /* create new reference */
  }
  lua_rawseti(L, t, ref);
  return ref;
}


LUALIB_API void luaL_unref (lua_State *L, int t, int ref) {
  if (ref >= 0) {
    t = abs_index(L, t);
    lua_rawgeti(L, t, FREELIST_REF);
    lua_rawseti(L, t, ref);  /* t[ref] = t[FREELIST_REF] */
    lua_pushinteger(L, ref);
    lua_rawseti(L, t, FREELIST_REF);  /* t[FREELIST_REF] = ref */
  }
}



/*
** {======================================================
** Load functions
** =======================================================
*/

typedef struct LoadF {
  int extraline;
  FILE *f;
  char buff[LUAL_BUFFERSIZE];
} LoadF;


static const char *getF (lua_State *L, void *ud, size_t *size) {
  LoadF *lf = (LoadF *)ud;
  (void)L;
  if (lf->extraline) {
    lf->extraline = 0;
    *size = 1;
    return "\n";
  }
  if (feof(lf->f)) return NULL;
  *size = fread(lf->buff, 1, sizeof(lf->buff), lf->f);
  return (*size > 0) ? lf->buff : NULL;
}


static int errfile (lua_State *L, const char *what, int fnameindex) {
  const char *serr = strerror(errno);
  const char *filename = lua_tostring(L, fnameindex) + 1;
  lua_pushfstring(L, "cannot %s %s: %s", what, filename, serr);
  lua_remove(L, fnameindex);
  return LUA_ERRFILE;
}


LUALIB_API int luaL_loadfile (lua_State *L, const char *filename) {
  LoadF lf;
  int status, readstatus;
  int c;
  int fnameindex = lua_gettop(L) + 1;  /* index of filename on the stack */
  lf.extraline = 0;
  if (filename == NULL) {
    lua_pushliteral(L, "=stdin");
    lf.f = stdin;
  }
  else {
    lua_pushfstring(L, "@%s", filename);
    lf.f = fopen(filename, "r");
    if (lf.f == NULL) return errfile(L, "open", fnameindex);
  }
  c = getc(lf.f);
  if (c == '#') {  /* Unix exec. file? */
    lf.extraline = 1;
    while ((c = getc(lf.f)) != EOF && c != '\n') ;  /* skip first line */
    if (c == '\n') c = getc(lf.f);
  }
  if (c == LUA_SIGNATURE[0] && filename) {  /* binary file? */
    lf.f = freopen(filename, "rb", lf.f);  /* reopen in binary mode */
    if (lf.f == NULL) return errfile(L, "reopen", fnameindex);
    /* skip eventual `#!...' */
   while ((c = getc(lf.f)) != EOF && c != LUA_SIGNATURE[0]) ;
    lf.extraline = 0;
  }
  ungetc(c, lf.f);
  status = lua_load(L, getF, &lf, lua_tostring(L, -1));
  readstatus = ferror(lf.f);
  if (filename) fclose(lf.f);  /* close file (even in case of errors) */
  if (readstatus) {
    lua_settop(L, fnameindex);  /* ignore results from `lua_load' */
    return errfile(L, "read", fnameindex);
  }
  lua_remove(L, fnameindex);
  return status;
}


typedef struct LoadS {
  const char *s;
  size_t size;
} LoadS;


static const char *getS (lua_State *L, void *ud, size_t *size) {
  LoadS *ls = (LoadS *)ud;
  (void)L;
  if (ls->size == 0) return NULL;
  *size = ls->size;
  ls->size = 0;
  return ls->s;
}


LUALIB_API int luaL_loadbuffer (lua_State *L, const char *buff, size_t size,
                                const char *name) {
  LoadS ls;
  ls.s = buff;
  ls.size = size;
  return lua_load(L, getS, &ls, name);
}


LUALIB_API int (luaL_loadstring) (lua_State *L, const char *s) {
  return luaL_loadbuffer(L, s, strlen(s), s);
}



/* }====================================================== */


static void *l_alloc (void *ud, void *ptr, size_t osize, size_t nsize) {
  (void)ud;
  (void)osize;
  if (nsize == 0) {
    free(ptr);
    return NULL;
  }
  else
    return realloc(ptr, nsize);
}


static int panic (lua_State *L) {
  (void)L;  /* to avoid warnings */
  fprintf(stderr, "PANIC: unprotected error in call to Lua API (%s)\n",
                   lua_tostring(L, -1));
  return 0;
}


LUALIB_API lua_State *luaL_newstate (void) {
  lua_State *L = lua_newstate(l_alloc, NULL);
  if (L) lua_atpanic(L, &panic);
  return L;
}

genometools-1.5.1/src/external/lua-5.1.5/src/lauxlib.h000066400000000000000000000132211211610345200223010ustar00rootroot00000000000000/*
** $Id: lauxlib.h,v 1.88.1.1 2007/12/27 13:02:25 roberto Exp $
** Auxiliary functions for building Lua libraries
** See Copyright Notice in lua.h
*/


#ifndef lauxlib_h
#define lauxlib_h


#include 
#include 

#include "lua.h"


#if defined(LUA_COMPAT_GETN)
LUALIB_API int (luaL_getn) (lua_State *L, int t);
LUALIB_API void (luaL_setn) (lua_State *L, int t, int n);
#else
#define luaL_getn(L,i)          ((int)lua_objlen(L, i))
#define luaL_setn(L,i,j)        ((void)0)  /* no op! */
#endif

#if defined(LUA_COMPAT_OPENLIB)
#define luaI_openlib	luaL_openlib
#endif


/* extra error code for `luaL_load' */
#define LUA_ERRFILE     (LUA_ERRERR+1)


typedef struct luaL_Reg {
  const char *name;
  lua_CFunction func;
} luaL_Reg;



LUALIB_API void (luaI_openlib) (lua_State *L, const char *libname,
                                const luaL_Reg *l, int nup);
LUALIB_API void (luaL_register) (lua_State *L, const char *libname,
                                const luaL_Reg *l);
LUALIB_API int (luaL_getmetafield) (lua_State *L, int obj, const char *e);
LUALIB_API int (luaL_callmeta) (lua_State *L, int obj, const char *e);
LUALIB_API int (luaL_typerror) (lua_State *L, int narg, const char *tname);
LUALIB_API int (luaL_argerror) (lua_State *L, int numarg, const char *extramsg);
LUALIB_API const char *(luaL_checklstring) (lua_State *L, int numArg,
                                                          size_t *l);
LUALIB_API const char *(luaL_optlstring) (lua_State *L, int numArg,
                                          const char *def, size_t *l);
LUALIB_API lua_Number (luaL_checknumber) (lua_State *L, int numArg);
LUALIB_API lua_Number (luaL_optnumber) (lua_State *L, int nArg, lua_Number def);

LUALIB_API lua_Integer (luaL_checkinteger) (lua_State *L, int numArg);
LUALIB_API lua_Integer (luaL_optinteger) (lua_State *L, int nArg,
                                          lua_Integer def);

LUALIB_API void (luaL_checkstack) (lua_State *L, int sz, const char *msg);
LUALIB_API void (luaL_checktype) (lua_State *L, int narg, int t);
LUALIB_API void (luaL_checkany) (lua_State *L, int narg);

LUALIB_API int   (luaL_newmetatable) (lua_State *L, const char *tname);
LUALIB_API void *(luaL_checkudata) (lua_State *L, int ud, const char *tname);

LUALIB_API void (luaL_where) (lua_State *L, int lvl);
LUALIB_API int (luaL_error) (lua_State *L, const char *fmt, ...);

LUALIB_API int (luaL_checkoption) (lua_State *L, int narg, const char *def,
                                   const char *const lst[]);

LUALIB_API int (luaL_ref) (lua_State *L, int t);
LUALIB_API void (luaL_unref) (lua_State *L, int t, int ref);

LUALIB_API int (luaL_loadfile) (lua_State *L, const char *filename);
LUALIB_API int (luaL_loadbuffer) (lua_State *L, const char *buff, size_t sz,
                                  const char *name);
LUALIB_API int (luaL_loadstring) (lua_State *L, const char *s);

LUALIB_API lua_State *(luaL_newstate) (void);


LUALIB_API const char *(luaL_gsub) (lua_State *L, const char *s, const char *p,
                                                  const char *r);

LUALIB_API const char *(luaL_findtable) (lua_State *L, int idx,
                                         const char *fname, int szhint);




/*
** ===============================================================
** some useful macros
** ===============================================================
*/

#define luaL_argcheck(L, cond,numarg,extramsg)	\
		((void)((cond) || luaL_argerror(L, (numarg), (extramsg))))
#define luaL_checkstring(L,n)	(luaL_checklstring(L, (n), NULL))
#define luaL_optstring(L,n,d)	(luaL_optlstring(L, (n), (d), NULL))
#define luaL_checkint(L,n)	((int)luaL_checkinteger(L, (n)))
#define luaL_optint(L,n,d)	((int)luaL_optinteger(L, (n), (d)))
#define luaL_checklong(L,n)	((long)luaL_checkinteger(L, (n)))
#define luaL_optlong(L,n,d)	((long)luaL_optinteger(L, (n), (d)))

#define luaL_typename(L,i)	lua_typename(L, lua_type(L,(i)))

#define luaL_dofile(L, fn) \
	(luaL_loadfile(L, fn) || lua_pcall(L, 0, LUA_MULTRET, 0))

#define luaL_dostring(L, s) \
	(luaL_loadstring(L, s) || lua_pcall(L, 0, LUA_MULTRET, 0))

#define luaL_getmetatable(L,n)	(lua_getfield(L, LUA_REGISTRYINDEX, (n)))

#define luaL_opt(L,f,n,d)	(lua_isnoneornil(L,(n)) ? (d) : f(L,(n)))

/*
** {======================================================
** Generic Buffer manipulation
** =======================================================
*/



typedef struct luaL_Buffer {
  char *p;			/* current position in buffer */
  int lvl;  /* number of strings in the stack (level) */
  lua_State *L;
  char buffer[LUAL_BUFFERSIZE];
} luaL_Buffer;

#define luaL_addchar(B,c) \
  ((void)((B)->p < ((B)->buffer+LUAL_BUFFERSIZE) || luaL_prepbuffer(B)), \
   (*(B)->p++ = (char)(c)))

/* compatibility only */
#define luaL_putchar(B,c)	luaL_addchar(B,c)

#define luaL_addsize(B,n)	((B)->p += (n))

LUALIB_API void (luaL_buffinit) (lua_State *L, luaL_Buffer *B);
LUALIB_API char *(luaL_prepbuffer) (luaL_Buffer *B);
LUALIB_API void (luaL_addlstring) (luaL_Buffer *B, const char *s, size_t l);
LUALIB_API void (luaL_addstring) (luaL_Buffer *B, const char *s);
LUALIB_API void (luaL_addvalue) (luaL_Buffer *B);
LUALIB_API void (luaL_pushresult) (luaL_Buffer *B);


/* }====================================================== */


/* compatibility with ref system */

/* pre-defined references */
#define LUA_NOREF       (-2)
#define LUA_REFNIL      (-1)

#define lua_ref(L,lock) ((lock) ? luaL_ref(L, LUA_REGISTRYINDEX) : \
      (lua_pushstring(L, "unlocked references are obsolete"), lua_error(L), 0))

#define lua_unref(L,ref)        luaL_unref(L, LUA_REGISTRYINDEX, (ref))

#define lua_getref(L,ref)       lua_rawgeti(L, LUA_REGISTRYINDEX, (ref))


#define luaL_reg	luaL_Reg

#endif


genometools-1.5.1/src/external/lua-5.1.5/src/lbaselib.c000066400000000000000000000412251211610345200224160ustar00rootroot00000000000000/*
** $Id: lbaselib.c,v 1.191.1.6 2008/02/14 16:46:22 roberto Exp $
** Basic library
** See Copyright Notice in lua.h
*/



#include 
#include 
#include 
#include 

#define lbaselib_c
#define LUA_LIB

#include "lua.h"

#include "lauxlib.h"
#include "lualib.h"




/*
** If your system does not support `stdout', you can just remove this function.
** If you need, you can define your own `print' function, following this
** model but changing `fputs' to put the strings at a proper place
** (a console window or a log file, for instance).
*/
static int luaB_print (lua_State *L) {
  int n = lua_gettop(L);  /* number of arguments */
  int i;
  lua_getglobal(L, "tostring");
  for (i=1; i<=n; i++) {
    const char *s;
    lua_pushvalue(L, -1);  /* function to be called */
    lua_pushvalue(L, i);   /* value to print */
    lua_call(L, 1, 1);
    s = lua_tostring(L, -1);  /* get result */
    if (s == NULL)
      return luaL_error(L, LUA_QL("tostring") " must return a string to "
                           LUA_QL("print"));
    if (i>1) fputs("\t", stdout);
    fputs(s, stdout);
    lua_pop(L, 1);  /* pop result */
  }
  fputs("\n", stdout);
  return 0;
}


static int luaB_tonumber (lua_State *L) {
  int base = luaL_optint(L, 2, 10);
  if (base == 10) {  /* standard conversion */
    luaL_checkany(L, 1);
    if (lua_isnumber(L, 1)) {
      lua_pushnumber(L, lua_tonumber(L, 1));
      return 1;
    }
  }
  else {
    const char *s1 = luaL_checkstring(L, 1);
    char *s2;
    unsigned long n;
    luaL_argcheck(L, 2 <= base && base <= 36, 2, "base out of range");
    n = strtoul(s1, &s2, base);
    if (s1 != s2) {  /* at least one valid digit? */
      while (isspace((unsigned char)(*s2))) s2++;  /* skip trailing spaces */
      if (*s2 == '\0') {  /* no invalid trailing characters? */
        lua_pushnumber(L, (lua_Number)n);
        return 1;
      }
    }
  }
  lua_pushnil(L);  /* else not a number */
  return 1;
}


static int luaB_error (lua_State *L) {
  int level = luaL_optint(L, 2, 1);
  lua_settop(L, 1);
  if (lua_isstring(L, 1) && level > 0) {  /* add extra information? */
    luaL_where(L, level);
    lua_pushvalue(L, 1);
    lua_concat(L, 2);
  }
  return lua_error(L);
}


static int luaB_getmetatable (lua_State *L) {
  luaL_checkany(L, 1);
  if (!lua_getmetatable(L, 1)) {
    lua_pushnil(L);
    return 1;  /* no metatable */
  }
  luaL_getmetafield(L, 1, "__metatable");
  return 1;  /* returns either __metatable field (if present) or metatable */
}


static int luaB_setmetatable (lua_State *L) {
  int t = lua_type(L, 2);
  luaL_checktype(L, 1, LUA_TTABLE);
  luaL_argcheck(L, t == LUA_TNIL || t == LUA_TTABLE, 2,
                    "nil or table expected");
  if (luaL_getmetafield(L, 1, "__metatable"))
    luaL_error(L, "cannot change a protected metatable");
  lua_settop(L, 2);
  lua_setmetatable(L, 1);
  return 1;
}


static void getfunc (lua_State *L, int opt) {
  if (lua_isfunction(L, 1)) lua_pushvalue(L, 1);
  else {
    lua_Debug ar;
    int level = opt ? luaL_optint(L, 1, 1) : luaL_checkint(L, 1);
    luaL_argcheck(L, level >= 0, 1, "level must be non-negative");
    if (lua_getstack(L, level, &ar) == 0)
      luaL_argerror(L, 1, "invalid level");
    lua_getinfo(L, "f", &ar);
    if (lua_isnil(L, -1))
      luaL_error(L, "no function environment for tail call at level %d",
                    level);
  }
}


static int luaB_getfenv (lua_State *L) {
  getfunc(L, 1);
  if (lua_iscfunction(L, -1))  /* is a C function? */
    lua_pushvalue(L, LUA_GLOBALSINDEX);  /* return the thread's global env. */
  else
    lua_getfenv(L, -1);
  return 1;
}


static int luaB_setfenv (lua_State *L) {
  luaL_checktype(L, 2, LUA_TTABLE);
  getfunc(L, 0);
  lua_pushvalue(L, 2);
  if (lua_isnumber(L, 1) && lua_tonumber(L, 1) == 0) {
    /* change environment of current thread */
    lua_pushthread(L);
    lua_insert(L, -2);
    lua_setfenv(L, -2);
    return 0;
  }
  else if (lua_iscfunction(L, -2) || lua_setfenv(L, -2) == 0)
    luaL_error(L,
          LUA_QL("setfenv") " cannot change environment of given object");
  return 1;
}


static int luaB_rawequal (lua_State *L) {
  luaL_checkany(L, 1);
  luaL_checkany(L, 2);
  lua_pushboolean(L, lua_rawequal(L, 1, 2));
  return 1;
}


static int luaB_rawget (lua_State *L) {
  luaL_checktype(L, 1, LUA_TTABLE);
  luaL_checkany(L, 2);
  lua_settop(L, 2);
  lua_rawget(L, 1);
  return 1;
}

static int luaB_rawset (lua_State *L) {
  luaL_checktype(L, 1, LUA_TTABLE);
  luaL_checkany(L, 2);
  luaL_checkany(L, 3);
  lua_settop(L, 3);
  lua_rawset(L, 1);
  return 1;
}


static int luaB_gcinfo (lua_State *L) {
  lua_pushinteger(L, lua_getgccount(L));
  return 1;
}


static int luaB_collectgarbage (lua_State *L) {
  static const char *const opts[] = {"stop", "restart", "collect",
    "count", "step", "setpause", "setstepmul", NULL};
  static const int optsnum[] = {LUA_GCSTOP, LUA_GCRESTART, LUA_GCCOLLECT,
    LUA_GCCOUNT, LUA_GCSTEP, LUA_GCSETPAUSE, LUA_GCSETSTEPMUL};
  int o = luaL_checkoption(L, 1, "collect", opts);
  int ex = luaL_optint(L, 2, 0);
  int res = lua_gc(L, optsnum[o], ex);
  switch (optsnum[o]) {
    case LUA_GCCOUNT: {
      int b = lua_gc(L, LUA_GCCOUNTB, 0);
      lua_pushnumber(L, res + ((lua_Number)b/1024));
      return 1;
    }
    case LUA_GCSTEP: {
      lua_pushboolean(L, res);
      return 1;
    }
    default: {
      lua_pushnumber(L, res);
      return 1;
    }
  }
}


static int luaB_type (lua_State *L) {
  luaL_checkany(L, 1);
  lua_pushstring(L, luaL_typename(L, 1));
  return 1;
}


static int luaB_next (lua_State *L) {
  luaL_checktype(L, 1, LUA_TTABLE);
  lua_settop(L, 2);  /* create a 2nd argument if there isn't one */
  if (lua_next(L, 1))
    return 2;
  else {
    lua_pushnil(L);
    return 1;
  }
}


static int luaB_pairs (lua_State *L) {
  luaL_checktype(L, 1, LUA_TTABLE);
  lua_pushvalue(L, lua_upvalueindex(1));  /* return generator, */
  lua_pushvalue(L, 1);  /* state, */
  lua_pushnil(L);  /* and initial value */
  return 3;
}


static int ipairsaux (lua_State *L) {
  int i = luaL_checkint(L, 2);
  luaL_checktype(L, 1, LUA_TTABLE);
  i++;  /* next value */
  lua_pushinteger(L, i);
  lua_rawgeti(L, 1, i);
  return (lua_isnil(L, -1)) ? 0 : 2;
}


static int luaB_ipairs (lua_State *L) {
  luaL_checktype(L, 1, LUA_TTABLE);
  lua_pushvalue(L, lua_upvalueindex(1));  /* return generator, */
  lua_pushvalue(L, 1);  /* state, */
  lua_pushinteger(L, 0);  /* and initial value */
  return 3;
}


static int load_aux (lua_State *L, int status) {
  if (status == 0)  /* OK? */
    return 1;
  else {
    lua_pushnil(L);
    lua_insert(L, -2);  /* put before error message */
    return 2;  /* return nil plus error message */
  }
}


static int luaB_loadstring (lua_State *L) {
  size_t l;
  const char *s = luaL_checklstring(L, 1, &l);
  const char *chunkname = luaL_optstring(L, 2, s);
  return load_aux(L, luaL_loadbuffer(L, s, l, chunkname));
}


static int luaB_loadfile (lua_State *L) {
  const char *fname = luaL_optstring(L, 1, NULL);
  return load_aux(L, luaL_loadfile(L, fname));
}


/*
** Reader for generic `load' function: `lua_load' uses the
** stack for internal stuff, so the reader cannot change the
** stack top. Instead, it keeps its resulting string in a
** reserved slot inside the stack.
*/
static const char *generic_reader (lua_State *L, void *ud, size_t *size) {
  (void)ud;  /* to avoid warnings */
  luaL_checkstack(L, 2, "too many nested functions");
  lua_pushvalue(L, 1);  /* get function */
  lua_call(L, 0, 1);  /* call it */
  if (lua_isnil(L, -1)) {
    *size = 0;
    return NULL;
  }
  else if (lua_isstring(L, -1)) {
    lua_replace(L, 3);  /* save string in a reserved stack slot */
    return lua_tolstring(L, 3, size);
  }
  else luaL_error(L, "reader function must return a string");
  return NULL;  /* to avoid warnings */
}


static int luaB_load (lua_State *L) {
  int status;
  const char *cname = luaL_optstring(L, 2, "=(load)");
  luaL_checktype(L, 1, LUA_TFUNCTION);
  lua_settop(L, 3);  /* function, eventual name, plus one reserved slot */
  status = lua_load(L, generic_reader, NULL, cname);
  return load_aux(L, status);
}


static int luaB_dofile (lua_State *L) {
  const char *fname = luaL_optstring(L, 1, NULL);
  int n = lua_gettop(L);
  if (luaL_loadfile(L, fname) != 0) lua_error(L);
  lua_call(L, 0, LUA_MULTRET);
  return lua_gettop(L) - n;
}


static int luaB_assert (lua_State *L) {
  luaL_checkany(L, 1);
  if (!lua_toboolean(L, 1))
    return luaL_error(L, "%s", luaL_optstring(L, 2, "assertion failed!"));
  return lua_gettop(L);
}


static int luaB_unpack (lua_State *L) {
  int i, e, n;
  luaL_checktype(L, 1, LUA_TTABLE);
  i = luaL_optint(L, 2, 1);
  e = luaL_opt(L, luaL_checkint, 3, luaL_getn(L, 1));
  if (i > e) return 0;  /* empty range */
  n = e - i + 1;  /* number of elements */
  if (n <= 0 || !lua_checkstack(L, n))  /* n <= 0 means arith. overflow */
    return luaL_error(L, "too many results to unpack");
  lua_rawgeti(L, 1, i);  /* push arg[i] (avoiding overflow problems) */
  while (i++ < e)  /* push arg[i + 1...e] */
    lua_rawgeti(L, 1, i);
  return n;
}


static int luaB_select (lua_State *L) {
  int n = lua_gettop(L);
  if (lua_type(L, 1) == LUA_TSTRING && *lua_tostring(L, 1) == '#') {
    lua_pushinteger(L, n-1);
    return 1;
  }
  else {
    int i = luaL_checkint(L, 1);
    if (i < 0) i = n + i;
    else if (i > n) i = n;
    luaL_argcheck(L, 1 <= i, 1, "index out of range");
    return n - i;
  }
}


static int luaB_pcall (lua_State *L) {
  int status;
  luaL_checkany(L, 1);
  status = lua_pcall(L, lua_gettop(L) - 1, LUA_MULTRET, 0);
  lua_pushboolean(L, (status == 0));
  lua_insert(L, 1);
  return lua_gettop(L);  /* return status + all results */
}


static int luaB_xpcall (lua_State *L) {
  int status;
  luaL_checkany(L, 2);
  lua_settop(L, 2);
  lua_insert(L, 1);  /* put error function under function to be called */
  status = lua_pcall(L, 0, LUA_MULTRET, 1);
  lua_pushboolean(L, (status == 0));
  lua_replace(L, 1);
  return lua_gettop(L);  /* return status + all results */
}


static int luaB_tostring (lua_State *L) {
  luaL_checkany(L, 1);
  if (luaL_callmeta(L, 1, "__tostring"))  /* is there a metafield? */
    return 1;  /* use its value */
  switch (lua_type(L, 1)) {
    case LUA_TNUMBER:
      lua_pushstring(L, lua_tostring(L, 1));
      break;
    case LUA_TSTRING:
      lua_pushvalue(L, 1);
      break;
    case LUA_TBOOLEAN:
      lua_pushstring(L, (lua_toboolean(L, 1) ? "true" : "false"));
      break;
    case LUA_TNIL:
      lua_pushliteral(L, "nil");
      break;
    default:
      lua_pushfstring(L, "%s: %p", luaL_typename(L, 1), lua_topointer(L, 1));
      break;
  }
  return 1;
}


static int luaB_newproxy (lua_State *L) {
  lua_settop(L, 1);
  lua_newuserdata(L, 0);  /* create proxy */
  if (lua_toboolean(L, 1) == 0)
    return 1;  /* no metatable */
  else if (lua_isboolean(L, 1)) {
    lua_newtable(L);  /* create a new metatable `m' ... */
    lua_pushvalue(L, -1);  /* ... and mark `m' as a valid metatable */
    lua_pushboolean(L, 1);
    lua_rawset(L, lua_upvalueindex(1));  /* weaktable[m] = true */
  }
  else {
    int validproxy = 0;  /* to check if weaktable[metatable(u)] == true */
    if (lua_getmetatable(L, 1)) {
      lua_rawget(L, lua_upvalueindex(1));
      validproxy = lua_toboolean(L, -1);
      lua_pop(L, 1);  /* remove value */
    }
    luaL_argcheck(L, validproxy, 1, "boolean or proxy expected");
    lua_getmetatable(L, 1);  /* metatable is valid; get it */
  }
  lua_setmetatable(L, 2);
  return 1;
}


static const luaL_Reg base_funcs[] = {
  {"assert", luaB_assert},
  {"collectgarbage", luaB_collectgarbage},
  {"dofile", luaB_dofile},
  {"error", luaB_error},
  {"gcinfo", luaB_gcinfo},
  {"getfenv", luaB_getfenv},
  {"getmetatable", luaB_getmetatable},
  {"loadfile", luaB_loadfile},
  {"load", luaB_load},
  {"loadstring", luaB_loadstring},
  {"next", luaB_next},
  {"pcall", luaB_pcall},
  {"print", luaB_print},
  {"rawequal", luaB_rawequal},
  {"rawget", luaB_rawget},
  {"rawset", luaB_rawset},
  {"select", luaB_select},
  {"setfenv", luaB_setfenv},
  {"setmetatable", luaB_setmetatable},
  {"tonumber", luaB_tonumber},
  {"tostring", luaB_tostring},
  {"type", luaB_type},
  {"unpack", luaB_unpack},
  {"xpcall", luaB_xpcall},
  {NULL, NULL}
};


/*
** {======================================================
** Coroutine library
** =======================================================
*/

#define CO_RUN	0	/* running */
#define CO_SUS	1	/* suspended */
#define CO_NOR	2	/* 'normal' (it resumed another coroutine) */
#define CO_DEAD	3

static const char *const statnames[] =
    {"running", "suspended", "normal", "dead"};

static int costatus (lua_State *L, lua_State *co) {
  if (L == co) return CO_RUN;
  switch (lua_status(co)) {
    case LUA_YIELD:
      return CO_SUS;
    case 0: {
      lua_Debug ar;
      if (lua_getstack(co, 0, &ar) > 0)  /* does it have frames? */
        return CO_NOR;  /* it is running */
      else if (lua_gettop(co) == 0)
          return CO_DEAD;
      else
        return CO_SUS;  /* initial state */
    }
    default:  /* some error occured */
      return CO_DEAD;
  }
}


static int luaB_costatus (lua_State *L) {
  lua_State *co = lua_tothread(L, 1);
  luaL_argcheck(L, co, 1, "coroutine expected");
  lua_pushstring(L, statnames[costatus(L, co)]);
  return 1;
}


static int auxresume (lua_State *L, lua_State *co, int narg) {
  int status = costatus(L, co);
  if (!lua_checkstack(co, narg))
    luaL_error(L, "too many arguments to resume");
  if (status != CO_SUS) {
    lua_pushfstring(L, "cannot resume %s coroutine", statnames[status]);
    return -1;  /* error flag */
  }
  lua_xmove(L, co, narg);
  lua_setlevel(L, co);
  status = lua_resume(co, narg);
  if (status == 0 || status == LUA_YIELD) {
    int nres = lua_gettop(co);
    if (!lua_checkstack(L, nres + 1))
      luaL_error(L, "too many results to resume");
    lua_xmove(co, L, nres);  /* move yielded values */
    return nres;
  }
  else {
    lua_xmove(co, L, 1);  /* move error message */
    return -1;  /* error flag */
  }
}


static int luaB_coresume (lua_State *L) {
  lua_State *co = lua_tothread(L, 1);
  int r;
  luaL_argcheck(L, co, 1, "coroutine expected");
  r = auxresume(L, co, lua_gettop(L) - 1);
  if (r < 0) {
    lua_pushboolean(L, 0);
    lua_insert(L, -2);
    return 2;  /* return false + error message */
  }
  else {
    lua_pushboolean(L, 1);
    lua_insert(L, -(r + 1));
    return r + 1;  /* return true + `resume' returns */
  }
}


static int luaB_auxwrap (lua_State *L) {
  lua_State *co = lua_tothread(L, lua_upvalueindex(1));
  int r = auxresume(L, co, lua_gettop(L));
  if (r < 0) {
    if (lua_isstring(L, -1)) {  /* error object is a string? */
      luaL_where(L, 1);  /* add extra info */
      lua_insert(L, -2);
      lua_concat(L, 2);
    }
    lua_error(L);  /* propagate error */
  }
  return r;
}


static int luaB_cocreate (lua_State *L) {
  lua_State *NL = lua_newthread(L);
  luaL_argcheck(L, lua_isfunction(L, 1) && !lua_iscfunction(L, 1), 1,
    "Lua function expected");
  lua_pushvalue(L, 1);  /* move function to top */
  lua_xmove(L, NL, 1);  /* move function from L to NL */
  return 1;
}


static int luaB_cowrap (lua_State *L) {
  luaB_cocreate(L);
  lua_pushcclosure(L, luaB_auxwrap, 1);
  return 1;
}


static int luaB_yield (lua_State *L) {
  return lua_yield(L, lua_gettop(L));
}


static int luaB_corunning (lua_State *L) {
  if (lua_pushthread(L))
    lua_pushnil(L);  /* main thread is not a coroutine */
  return 1;
}


static const luaL_Reg co_funcs[] = {
  {"create", luaB_cocreate},
  {"resume", luaB_coresume},
  {"running", luaB_corunning},
  {"status", luaB_costatus},
  {"wrap", luaB_cowrap},
  {"yield", luaB_yield},
  {NULL, NULL}
};

/* }====================================================== */


static void auxopen (lua_State *L, const char *name,
                     lua_CFunction f, lua_CFunction u) {
  lua_pushcfunction(L, u);
  lua_pushcclosure(L, f, 1);
  lua_setfield(L, -2, name);
}


static void base_open (lua_State *L) {
  /* set global _G */
  lua_pushvalue(L, LUA_GLOBALSINDEX);
  lua_setglobal(L, "_G");
  /* open lib into global table */
  luaL_register(L, "_G", base_funcs);
  lua_pushliteral(L, LUA_VERSION);
  lua_setglobal(L, "_VERSION");  /* set global _VERSION */
  /* `ipairs' and `pairs' need auxiliary functions as upvalues */
  auxopen(L, "ipairs", luaB_ipairs, ipairsaux);
  auxopen(L, "pairs", luaB_pairs, luaB_next);
  /* `newproxy' needs a weaktable as upvalue */
  lua_createtable(L, 0, 1);  /* new table `w' */
  lua_pushvalue(L, -1);  /* `w' will be its own metatable */
  lua_setmetatable(L, -2);
  lua_pushliteral(L, "kv");
  lua_setfield(L, -2, "__mode");  /* metatable(w).__mode = "kv" */
  lua_pushcclosure(L, luaB_newproxy, 1);
  lua_setglobal(L, "newproxy");  /* set global `newproxy' */
}


LUALIB_API int luaopen_base (lua_State *L) {
  base_open(L);
  luaL_register(L, LUA_COLIBNAME, co_funcs);
  return 2;
}

genometools-1.5.1/src/external/lua-5.1.5/src/lcode.c000066400000000000000000000512621211610345200217310ustar00rootroot00000000000000/*
** $Id: lcode.c,v 2.25.1.5 2011/01/31 14:53:16 roberto Exp $
** Code generator for Lua
** See Copyright Notice in lua.h
*/


#include 

#define lcode_c
#define LUA_CORE

#include "lua.h"

#include "lcode.h"
#include "ldebug.h"
#include "ldo.h"
#include "lgc.h"
#include "llex.h"
#include "lmem.h"
#include "lobject.h"
#include "lopcodes.h"
#include "lparser.h"
#include "ltable.h"


#define hasjumps(e)	((e)->t != (e)->f)


static int isnumeral(expdesc *e) {
  return (e->k == VKNUM && e->t == NO_JUMP && e->f == NO_JUMP);
}


void luaK_nil (FuncState *fs, int from, int n) {
  Instruction *previous;
  if (fs->pc > fs->lasttarget) {  /* no jumps to current position? */
    if (fs->pc == 0) {  /* function start? */
      if (from >= fs->nactvar)
        return;  /* positions are already clean */
    }
    else {
      previous = &fs->f->code[fs->pc-1];
      if (GET_OPCODE(*previous) == OP_LOADNIL) {
        int pfrom = GETARG_A(*previous);
        int pto = GETARG_B(*previous);
        if (pfrom <= from && from <= pto+1) {  /* can connect both? */
          if (from+n-1 > pto)
            SETARG_B(*previous, from+n-1);
          return;
        }
      }
    }
  }
  luaK_codeABC(fs, OP_LOADNIL, from, from+n-1, 0);  /* else no optimization */
}


int luaK_jump (FuncState *fs) {
  int jpc = fs->jpc;  /* save list of jumps to here */
  int j;
  fs->jpc = NO_JUMP;
  j = luaK_codeAsBx(fs, OP_JMP, 0, NO_JUMP);
  luaK_concat(fs, &j, jpc);  /* keep them on hold */
  return j;
}


void luaK_ret (FuncState *fs, int first, int nret) {
  luaK_codeABC(fs, OP_RETURN, first, nret+1, 0);
}


static int condjump (FuncState *fs, OpCode op, int A, int B, int C) {
  luaK_codeABC(fs, op, A, B, C);
  return luaK_jump(fs);
}


static void fixjump (FuncState *fs, int pc, int dest) {
  Instruction *jmp = &fs->f->code[pc];
  int offset = dest-(pc+1);
  lua_assert(dest != NO_JUMP);
  if (abs(offset) > MAXARG_sBx)
    luaX_syntaxerror(fs->ls, "control structure too long");
  SETARG_sBx(*jmp, offset);
}


/*
** returns current `pc' and marks it as a jump target (to avoid wrong
** optimizations with consecutive instructions not in the same basic block).
*/
int luaK_getlabel (FuncState *fs) {
  fs->lasttarget = fs->pc;
  return fs->pc;
}


static int getjump (FuncState *fs, int pc) {
  int offset = GETARG_sBx(fs->f->code[pc]);
  if (offset == NO_JUMP)  /* point to itself represents end of list */
    return NO_JUMP;  /* end of list */
  else
    return (pc+1)+offset;  /* turn offset into absolute position */
}


static Instruction *getjumpcontrol (FuncState *fs, int pc) {
  Instruction *pi = &fs->f->code[pc];
  if (pc >= 1 && testTMode(GET_OPCODE(*(pi-1))))
    return pi-1;
  else
    return pi;
}


/*
** check whether list has any jump that do not produce a value
** (or produce an inverted value)
*/
static int need_value (FuncState *fs, int list) {
  for (; list != NO_JUMP; list = getjump(fs, list)) {
    Instruction i = *getjumpcontrol(fs, list);
    if (GET_OPCODE(i) != OP_TESTSET) return 1;
  }
  return 0;  /* not found */
}


static int patchtestreg (FuncState *fs, int node, int reg) {
  Instruction *i = getjumpcontrol(fs, node);
  if (GET_OPCODE(*i) != OP_TESTSET)
    return 0;  /* cannot patch other instructions */
  if (reg != NO_REG && reg != GETARG_B(*i))
    SETARG_A(*i, reg);
  else  /* no register to put value or register already has the value */
    *i = CREATE_ABC(OP_TEST, GETARG_B(*i), 0, GETARG_C(*i));

  return 1;
}


static void removevalues (FuncState *fs, int list) {
  for (; list != NO_JUMP; list = getjump(fs, list))
      patchtestreg(fs, list, NO_REG);
}


static void patchlistaux (FuncState *fs, int list, int vtarget, int reg,
                          int dtarget) {
  while (list != NO_JUMP) {
    int next = getjump(fs, list);
    if (patchtestreg(fs, list, reg))
      fixjump(fs, list, vtarget);
    else
      fixjump(fs, list, dtarget);  /* jump to default target */
    list = next;
  }
}


static void dischargejpc (FuncState *fs) {
  patchlistaux(fs, fs->jpc, fs->pc, NO_REG, fs->pc);
  fs->jpc = NO_JUMP;
}


void luaK_patchlist (FuncState *fs, int list, int target) {
  if (target == fs->pc)
    luaK_patchtohere(fs, list);
  else {
    lua_assert(target < fs->pc);
    patchlistaux(fs, list, target, NO_REG, target);
  }
}


void luaK_patchtohere (FuncState *fs, int list) {
  luaK_getlabel(fs);
  luaK_concat(fs, &fs->jpc, list);
}


void luaK_concat (FuncState *fs, int *l1, int l2) {
  if (l2 == NO_JUMP) return;
  else if (*l1 == NO_JUMP)
    *l1 = l2;
  else {
    int list = *l1;
    int next;
    while ((next = getjump(fs, list)) != NO_JUMP)  /* find last element */
      list = next;
    fixjump(fs, list, l2);
  }
}


void luaK_checkstack (FuncState *fs, int n) {
  int newstack = fs->freereg + n;
  if (newstack > fs->f->maxstacksize) {
    if (newstack >= MAXSTACK)
      luaX_syntaxerror(fs->ls, "function or expression too complex");
    fs->f->maxstacksize = cast_byte(newstack);
  }
}


void luaK_reserveregs (FuncState *fs, int n) {
  luaK_checkstack(fs, n);
  fs->freereg += n;
}


static void freereg (FuncState *fs, int reg) {
  if (!ISK(reg) && reg >= fs->nactvar) {
    fs->freereg--;
    lua_assert(reg == fs->freereg);
  }
}


static void freeexp (FuncState *fs, expdesc *e) {
  if (e->k == VNONRELOC)
    freereg(fs, e->u.s.info);
}


static int addk (FuncState *fs, TValue *k, TValue *v) {
  lua_State *L = fs->L;
  TValue *idx = luaH_set(L, fs->h, k);
  Proto *f = fs->f;
  int oldsize = f->sizek;
  if (ttisnumber(idx)) {
    lua_assert(luaO_rawequalObj(&fs->f->k[cast_int(nvalue(idx))], v));
    return cast_int(nvalue(idx));
  }
  else {  /* constant not found; create a new entry */
    setnvalue(idx, cast_num(fs->nk));
    luaM_growvector(L, f->k, fs->nk, f->sizek, TValue,
                    MAXARG_Bx, "constant table overflow");
    while (oldsize < f->sizek) setnilvalue(&f->k[oldsize++]);
    setobj(L, &f->k[fs->nk], v);
    luaC_barrier(L, f, v);
    return fs->nk++;
  }
}


int luaK_stringK (FuncState *fs, TString *s) {
  TValue o;
  setsvalue(fs->L, &o, s);
  return addk(fs, &o, &o);
}


int luaK_numberK (FuncState *fs, lua_Number r) {
  TValue o;
  setnvalue(&o, r);
  return addk(fs, &o, &o);
}


static int boolK (FuncState *fs, int b) {
  TValue o;
  setbvalue(&o, b);
  return addk(fs, &o, &o);
}


static int nilK (FuncState *fs) {
  TValue k, v;
  setnilvalue(&v);
  /* cannot use nil as key; instead use table itself to represent nil */
  sethvalue(fs->L, &k, fs->h);
  return addk(fs, &k, &v);
}


void luaK_setreturns (FuncState *fs, expdesc *e, int nresults) {
  if (e->k == VCALL) {  /* expression is an open function call? */
    SETARG_C(getcode(fs, e), nresults+1);
  }
  else if (e->k == VVARARG) {
    SETARG_B(getcode(fs, e), nresults+1);
    SETARG_A(getcode(fs, e), fs->freereg);
    luaK_reserveregs(fs, 1);
  }
}


void luaK_setoneret (FuncState *fs, expdesc *e) {
  if (e->k == VCALL) {  /* expression is an open function call? */
    e->k = VNONRELOC;
    e->u.s.info = GETARG_A(getcode(fs, e));
  }
  else if (e->k == VVARARG) {
    SETARG_B(getcode(fs, e), 2);
    e->k = VRELOCABLE;  /* can relocate its simple result */
  }
}


void luaK_dischargevars (FuncState *fs, expdesc *e) {
  switch (e->k) {
    case VLOCAL: {
      e->k = VNONRELOC;
      break;
    }
    case VUPVAL: {
      e->u.s.info = luaK_codeABC(fs, OP_GETUPVAL, 0, e->u.s.info, 0);
      e->k = VRELOCABLE;
      break;
    }
    case VGLOBAL: {
      e->u.s.info = luaK_codeABx(fs, OP_GETGLOBAL, 0, e->u.s.info);
      e->k = VRELOCABLE;
      break;
    }
    case VINDEXED: {
      freereg(fs, e->u.s.aux);
      freereg(fs, e->u.s.info);
      e->u.s.info = luaK_codeABC(fs, OP_GETTABLE, 0, e->u.s.info, e->u.s.aux);
      e->k = VRELOCABLE;
      break;
    }
    case VVARARG:
    case VCALL: {
      luaK_setoneret(fs, e);
      break;
    }
    default: break;  /* there is one value available (somewhere) */
  }
}


static int code_label (FuncState *fs, int A, int b, int jump) {
  luaK_getlabel(fs);  /* those instructions may be jump targets */
  return luaK_codeABC(fs, OP_LOADBOOL, A, b, jump);
}


static void discharge2reg (FuncState *fs, expdesc *e, int reg) {
  luaK_dischargevars(fs, e);
  switch (e->k) {
    case VNIL: {
      luaK_nil(fs, reg, 1);
      break;
    }
    case VFALSE:  case VTRUE: {
      luaK_codeABC(fs, OP_LOADBOOL, reg, e->k == VTRUE, 0);
      break;
    }
    case VK: {
      luaK_codeABx(fs, OP_LOADK, reg, e->u.s.info);
      break;
    }
    case VKNUM: {
      luaK_codeABx(fs, OP_LOADK, reg, luaK_numberK(fs, e->u.nval));
      break;
    }
    case VRELOCABLE: {
      Instruction *pc = &getcode(fs, e);
      SETARG_A(*pc, reg);
      break;
    }
    case VNONRELOC: {
      if (reg != e->u.s.info)
        luaK_codeABC(fs, OP_MOVE, reg, e->u.s.info, 0);
      break;
    }
    default: {
      lua_assert(e->k == VVOID || e->k == VJMP);
      return;  /* nothing to do... */
    }
  }
  e->u.s.info = reg;
  e->k = VNONRELOC;
}


static void discharge2anyreg (FuncState *fs, expdesc *e) {
  if (e->k != VNONRELOC) {
    luaK_reserveregs(fs, 1);
    discharge2reg(fs, e, fs->freereg-1);
  }
}


static void exp2reg (FuncState *fs, expdesc *e, int reg) {
  discharge2reg(fs, e, reg);
  if (e->k == VJMP)
    luaK_concat(fs, &e->t, e->u.s.info);  /* put this jump in `t' list */
  if (hasjumps(e)) {
    int final;  /* position after whole expression */
    int p_f = NO_JUMP;  /* position of an eventual LOAD false */
    int p_t = NO_JUMP;  /* position of an eventual LOAD true */
    if (need_value(fs, e->t) || need_value(fs, e->f)) {
      int fj = (e->k == VJMP) ? NO_JUMP : luaK_jump(fs);
      p_f = code_label(fs, reg, 0, 1);
      p_t = code_label(fs, reg, 1, 0);
      luaK_patchtohere(fs, fj);
    }
    final = luaK_getlabel(fs);
    patchlistaux(fs, e->f, final, reg, p_f);
    patchlistaux(fs, e->t, final, reg, p_t);
  }
  e->f = e->t = NO_JUMP;
  e->u.s.info = reg;
  e->k = VNONRELOC;
}


void luaK_exp2nextreg (FuncState *fs, expdesc *e) {
  luaK_dischargevars(fs, e);
  freeexp(fs, e);
  luaK_reserveregs(fs, 1);
  exp2reg(fs, e, fs->freereg - 1);
}


int luaK_exp2anyreg (FuncState *fs, expdesc *e) {
  luaK_dischargevars(fs, e);
  if (e->k == VNONRELOC) {
    if (!hasjumps(e)) return e->u.s.info;  /* exp is already in a register */
    if (e->u.s.info >= fs->nactvar) {  /* reg. is not a local? */
      exp2reg(fs, e, e->u.s.info);  /* put value on it */
      return e->u.s.info;
    }
  }
  luaK_exp2nextreg(fs, e);  /* default */
  return e->u.s.info;
}


void luaK_exp2val (FuncState *fs, expdesc *e) {
  if (hasjumps(e))
    luaK_exp2anyreg(fs, e);
  else
    luaK_dischargevars(fs, e);
}


int luaK_exp2RK (FuncState *fs, expdesc *e) {
  luaK_exp2val(fs, e);
  switch (e->k) {
    case VKNUM:
    case VTRUE:
    case VFALSE:
    case VNIL: {
      if (fs->nk <= MAXINDEXRK) {  /* constant fit in RK operand? */
        e->u.s.info = (e->k == VNIL)  ? nilK(fs) :
                      (e->k == VKNUM) ? luaK_numberK(fs, e->u.nval) :
                                        boolK(fs, (e->k == VTRUE));
        e->k = VK;
        return RKASK(e->u.s.info);
      }
      else break;
    }
    case VK: {
      if (e->u.s.info <= MAXINDEXRK)  /* constant fit in argC? */
        return RKASK(e->u.s.info);
      else break;
    }
    default: break;
  }
  /* not a constant in the right range: put it in a register */
  return luaK_exp2anyreg(fs, e);
}


void luaK_storevar (FuncState *fs, expdesc *var, expdesc *ex) {
  switch (var->k) {
    case VLOCAL: {
      freeexp(fs, ex);
      exp2reg(fs, ex, var->u.s.info);
      return;
    }
    case VUPVAL: {
      int e = luaK_exp2anyreg(fs, ex);
      luaK_codeABC(fs, OP_SETUPVAL, e, var->u.s.info, 0);
      break;
    }
    case VGLOBAL: {
      int e = luaK_exp2anyreg(fs, ex);
      luaK_codeABx(fs, OP_SETGLOBAL, e, var->u.s.info);
      break;
    }
    case VINDEXED: {
      int e = luaK_exp2RK(fs, ex);
      luaK_codeABC(fs, OP_SETTABLE, var->u.s.info, var->u.s.aux, e);
      break;
    }
    default: {
      lua_assert(0);  /* invalid var kind to store */
      break;
    }
  }
  freeexp(fs, ex);
}


void luaK_self (FuncState *fs, expdesc *e, expdesc *key) {
  int func;
  luaK_exp2anyreg(fs, e);
  freeexp(fs, e);
  func = fs->freereg;
  luaK_reserveregs(fs, 2);
  luaK_codeABC(fs, OP_SELF, func, e->u.s.info, luaK_exp2RK(fs, key));
  freeexp(fs, key);
  e->u.s.info = func;
  e->k = VNONRELOC;
}


static void invertjump (FuncState *fs, expdesc *e) {
  Instruction *pc = getjumpcontrol(fs, e->u.s.info);
  lua_assert(testTMode(GET_OPCODE(*pc)) && GET_OPCODE(*pc) != OP_TESTSET &&
                                           GET_OPCODE(*pc) != OP_TEST);
  SETARG_A(*pc, !(GETARG_A(*pc)));
}


static int jumponcond (FuncState *fs, expdesc *e, int cond) {
  if (e->k == VRELOCABLE) {
    Instruction ie = getcode(fs, e);
    if (GET_OPCODE(ie) == OP_NOT) {
      fs->pc--;  /* remove previous OP_NOT */
      return condjump(fs, OP_TEST, GETARG_B(ie), 0, !cond);
    }
    /* else go through */
  }
  discharge2anyreg(fs, e);
  freeexp(fs, e);
  return condjump(fs, OP_TESTSET, NO_REG, e->u.s.info, cond);
}


void luaK_goiftrue (FuncState *fs, expdesc *e) {
  int pc;  /* pc of last jump */
  luaK_dischargevars(fs, e);
  switch (e->k) {
    case VK: case VKNUM: case VTRUE: {
      pc = NO_JUMP;  /* always true; do nothing */
      break;
    }
    case VJMP: {
      invertjump(fs, e);
      pc = e->u.s.info;
      break;
    }
    default: {
      pc = jumponcond(fs, e, 0);
      break;
    }
  }
  luaK_concat(fs, &e->f, pc);  /* insert last jump in `f' list */
  luaK_patchtohere(fs, e->t);
  e->t = NO_JUMP;
}


static void luaK_goiffalse (FuncState *fs, expdesc *e) {
  int pc;  /* pc of last jump */
  luaK_dischargevars(fs, e);
  switch (e->k) {
    case VNIL: case VFALSE: {
      pc = NO_JUMP;  /* always false; do nothing */
      break;
    }
    case VJMP: {
      pc = e->u.s.info;
      break;
    }
    default: {
      pc = jumponcond(fs, e, 1);
      break;
    }
  }
  luaK_concat(fs, &e->t, pc);  /* insert last jump in `t' list */
  luaK_patchtohere(fs, e->f);
  e->f = NO_JUMP;
}


static void codenot (FuncState *fs, expdesc *e) {
  luaK_dischargevars(fs, e);
  switch (e->k) {
    case VNIL: case VFALSE: {
      e->k = VTRUE;
      break;
    }
    case VK: case VKNUM: case VTRUE: {
      e->k = VFALSE;
      break;
    }
    case VJMP: {
      invertjump(fs, e);
      break;
    }
    case VRELOCABLE:
    case VNONRELOC: {
      discharge2anyreg(fs, e);
      freeexp(fs, e);
      e->u.s.info = luaK_codeABC(fs, OP_NOT, 0, e->u.s.info, 0);
      e->k = VRELOCABLE;
      break;
    }
    default: {
      lua_assert(0);  /* cannot happen */
      break;
    }
  }
  /* interchange true and false lists */
  { int temp = e->f; e->f = e->t; e->t = temp; }
  removevalues(fs, e->f);
  removevalues(fs, e->t);
}


void luaK_indexed (FuncState *fs, expdesc *t, expdesc *k) {
  t->u.s.aux = luaK_exp2RK(fs, k);
  t->k = VINDEXED;
}


static int constfolding (OpCode op, expdesc *e1, expdesc *e2) {
  lua_Number v1, v2, r;
  if (!isnumeral(e1) || !isnumeral(e2)) return 0;
  v1 = e1->u.nval;
  v2 = e2->u.nval;
  switch (op) {
    case OP_ADD: r = luai_numadd(v1, v2); break;
    case OP_SUB: r = luai_numsub(v1, v2); break;
    case OP_MUL: r = luai_nummul(v1, v2); break;
    case OP_DIV:
      if (v2 == 0) return 0;  /* do not attempt to divide by 0 */
      r = luai_numdiv(v1, v2); break;
    case OP_MOD:
      if (v2 == 0) return 0;  /* do not attempt to divide by 0 */
      r = luai_nummod(v1, v2); break;
    case OP_POW: r = luai_numpow(v1, v2); break;
    case OP_UNM: r = luai_numunm(v1); break;
    case OP_LEN: return 0;  /* no constant folding for 'len' */
    default: lua_assert(0); r = 0; break;
  }
  if (luai_numisnan(r)) return 0;  /* do not attempt to produce NaN */
  e1->u.nval = r;
  return 1;
}


static void codearith (FuncState *fs, OpCode op, expdesc *e1, expdesc *e2) {
  if (constfolding(op, e1, e2))
    return;
  else {
    int o2 = (op != OP_UNM && op != OP_LEN) ? luaK_exp2RK(fs, e2) : 0;
    int o1 = luaK_exp2RK(fs, e1);
    if (o1 > o2) {
      freeexp(fs, e1);
      freeexp(fs, e2);
    }
    else {
      freeexp(fs, e2);
      freeexp(fs, e1);
    }
    e1->u.s.info = luaK_codeABC(fs, op, 0, o1, o2);
    e1->k = VRELOCABLE;
  }
}


static void codecomp (FuncState *fs, OpCode op, int cond, expdesc *e1,
                                                          expdesc *e2) {
  int o1 = luaK_exp2RK(fs, e1);
  int o2 = luaK_exp2RK(fs, e2);
  freeexp(fs, e2);
  freeexp(fs, e1);
  if (cond == 0 && op != OP_EQ) {
    int temp;  /* exchange args to replace by `<' or `<=' */
    temp = o1; o1 = o2; o2 = temp;  /* o1 <==> o2 */
    cond = 1;
  }
  e1->u.s.info = condjump(fs, op, cond, o1, o2);
  e1->k = VJMP;
}


void luaK_prefix (FuncState *fs, UnOpr op, expdesc *e) {
  expdesc e2;
  e2.t = e2.f = NO_JUMP; e2.k = VKNUM; e2.u.nval = 0;
  switch (op) {
    case OPR_MINUS: {
      if (!isnumeral(e))
        luaK_exp2anyreg(fs, e);  /* cannot operate on non-numeric constants */
      codearith(fs, OP_UNM, e, &e2);
      break;
    }
    case OPR_NOT: codenot(fs, e); break;
    case OPR_LEN: {
      luaK_exp2anyreg(fs, e);  /* cannot operate on constants */
      codearith(fs, OP_LEN, e, &e2);
      break;
    }
    default: lua_assert(0);
  }
}


void luaK_infix (FuncState *fs, BinOpr op, expdesc *v) {
  switch (op) {
    case OPR_AND: {
      luaK_goiftrue(fs, v);
      break;
    }
    case OPR_OR: {
      luaK_goiffalse(fs, v);
      break;
    }
    case OPR_CONCAT: {
      luaK_exp2nextreg(fs, v);  /* operand must be on the `stack' */
      break;
    }
    case OPR_ADD: case OPR_SUB: case OPR_MUL: case OPR_DIV:
    case OPR_MOD: case OPR_POW: {
      if (!isnumeral(v)) luaK_exp2RK(fs, v);
      break;
    }
    default: {
      luaK_exp2RK(fs, v);
      break;
    }
  }
}


void luaK_posfix (FuncState *fs, BinOpr op, expdesc *e1, expdesc *e2) {
  switch (op) {
    case OPR_AND: {
      lua_assert(e1->t == NO_JUMP);  /* list must be closed */
      luaK_dischargevars(fs, e2);
      luaK_concat(fs, &e2->f, e1->f);
      *e1 = *e2;
      break;
    }
    case OPR_OR: {
      lua_assert(e1->f == NO_JUMP);  /* list must be closed */
      luaK_dischargevars(fs, e2);
      luaK_concat(fs, &e2->t, e1->t);
      *e1 = *e2;
      break;
    }
    case OPR_CONCAT: {
      luaK_exp2val(fs, e2);
      if (e2->k == VRELOCABLE && GET_OPCODE(getcode(fs, e2)) == OP_CONCAT) {
        lua_assert(e1->u.s.info == GETARG_B(getcode(fs, e2))-1);
        freeexp(fs, e1);
        SETARG_B(getcode(fs, e2), e1->u.s.info);
        e1->k = VRELOCABLE; e1->u.s.info = e2->u.s.info;
      }
      else {
        luaK_exp2nextreg(fs, e2);  /* operand must be on the 'stack' */
        codearith(fs, OP_CONCAT, e1, e2);
      }
      break;
    }
    case OPR_ADD: codearith(fs, OP_ADD, e1, e2); break;
    case OPR_SUB: codearith(fs, OP_SUB, e1, e2); break;
    case OPR_MUL: codearith(fs, OP_MUL, e1, e2); break;
    case OPR_DIV: codearith(fs, OP_DIV, e1, e2); break;
    case OPR_MOD: codearith(fs, OP_MOD, e1, e2); break;
    case OPR_POW: codearith(fs, OP_POW, e1, e2); break;
    case OPR_EQ: codecomp(fs, OP_EQ, 1, e1, e2); break;
    case OPR_NE: codecomp(fs, OP_EQ, 0, e1, e2); break;
    case OPR_LT: codecomp(fs, OP_LT, 1, e1, e2); break;
    case OPR_LE: codecomp(fs, OP_LE, 1, e1, e2); break;
    case OPR_GT: codecomp(fs, OP_LT, 0, e1, e2); break;
    case OPR_GE: codecomp(fs, OP_LE, 0, e1, e2); break;
    default: lua_assert(0);
  }
}


void luaK_fixline (FuncState *fs, int line) {
  fs->f->lineinfo[fs->pc - 1] = line;
}


static int luaK_code (FuncState *fs, Instruction i, int line) {
  Proto *f = fs->f;
  dischargejpc(fs);  /* `pc' will change */
  /* put new instruction in code array */
  luaM_growvector(fs->L, f->code, fs->pc, f->sizecode, Instruction,
                  MAX_INT, "code size overflow");
  f->code[fs->pc] = i;
  /* save corresponding line information */
  luaM_growvector(fs->L, f->lineinfo, fs->pc, f->sizelineinfo, int,
                  MAX_INT, "code size overflow");
  f->lineinfo[fs->pc] = line;
  return fs->pc++;
}


int luaK_codeABC (FuncState *fs, OpCode o, int a, int b, int c) {
  lua_assert(getOpMode(o) == iABC);
  lua_assert(getBMode(o) != OpArgN || b == 0);
  lua_assert(getCMode(o) != OpArgN || c == 0);
  return luaK_code(fs, CREATE_ABC(o, a, b, c), fs->ls->lastline);
}


int luaK_codeABx (FuncState *fs, OpCode o, int a, unsigned int bc) {
  lua_assert(getOpMode(o) == iABx || getOpMode(o) == iAsBx);
  lua_assert(getCMode(o) == OpArgN);
  return luaK_code(fs, CREATE_ABx(o, a, bc), fs->ls->lastline);
}


void luaK_setlist (FuncState *fs, int base, int nelems, int tostore) {
  int c =  (nelems - 1)/LFIELDS_PER_FLUSH + 1;
  int b = (tostore == LUA_MULTRET) ? 0 : tostore;
  lua_assert(tostore != 0);
  if (c <= MAXARG_C)
    luaK_codeABC(fs, OP_SETLIST, base, b, c);
  else {
    luaK_codeABC(fs, OP_SETLIST, base, b, 0);
    luaK_code(fs, cast(Instruction, c), fs->ls->lastline);
  }
  fs->freereg = base + 1;  /* free registers with list values */
}

genometools-1.5.1/src/external/lua-5.1.5/src/lcode.h000066400000000000000000000052761211610345200217420ustar00rootroot00000000000000/*
** $Id: lcode.h,v 1.48.1.1 2007/12/27 13:02:25 roberto Exp $
** Code generator for Lua
** See Copyright Notice in lua.h
*/

#ifndef lcode_h
#define lcode_h

#include "llex.h"
#include "lobject.h"
#include "lopcodes.h"
#include "lparser.h"


/*
** Marks the end of a patch list. It is an invalid value both as an absolute
** address, and as a list link (would link an element to itself).
*/
#define NO_JUMP (-1)


/*
** grep "ORDER OPR" if you change these enums
*/
typedef enum BinOpr {
  OPR_ADD, OPR_SUB, OPR_MUL, OPR_DIV, OPR_MOD, OPR_POW,
  OPR_CONCAT,
  OPR_NE, OPR_EQ,
  OPR_LT, OPR_LE, OPR_GT, OPR_GE,
  OPR_AND, OPR_OR,
  OPR_NOBINOPR
} BinOpr;


typedef enum UnOpr { OPR_MINUS, OPR_NOT, OPR_LEN, OPR_NOUNOPR } UnOpr;


#define getcode(fs,e)	((fs)->f->code[(e)->u.s.info])

#define luaK_codeAsBx(fs,o,A,sBx)	luaK_codeABx(fs,o,A,(sBx)+MAXARG_sBx)

#define luaK_setmultret(fs,e)	luaK_setreturns(fs, e, LUA_MULTRET)

LUAI_FUNC int luaK_codeABx (FuncState *fs, OpCode o, int A, unsigned int Bx);
LUAI_FUNC int luaK_codeABC (FuncState *fs, OpCode o, int A, int B, int C);
LUAI_FUNC void luaK_fixline (FuncState *fs, int line);
LUAI_FUNC void luaK_nil (FuncState *fs, int from, int n);
LUAI_FUNC void luaK_reserveregs (FuncState *fs, int n);
LUAI_FUNC void luaK_checkstack (FuncState *fs, int n);
LUAI_FUNC int luaK_stringK (FuncState *fs, TString *s);
LUAI_FUNC int luaK_numberK (FuncState *fs, lua_Number r);
LUAI_FUNC void luaK_dischargevars (FuncState *fs, expdesc *e);
LUAI_FUNC int luaK_exp2anyreg (FuncState *fs, expdesc *e);
LUAI_FUNC void luaK_exp2nextreg (FuncState *fs, expdesc *e);
LUAI_FUNC void luaK_exp2val (FuncState *fs, expdesc *e);
LUAI_FUNC int luaK_exp2RK (FuncState *fs, expdesc *e);
LUAI_FUNC void luaK_self (FuncState *fs, expdesc *e, expdesc *key);
LUAI_FUNC void luaK_indexed (FuncState *fs, expdesc *t, expdesc *k);
LUAI_FUNC void luaK_goiftrue (FuncState *fs, expdesc *e);
LUAI_FUNC void luaK_storevar (FuncState *fs, expdesc *var, expdesc *e);
LUAI_FUNC void luaK_setreturns (FuncState *fs, expdesc *e, int nresults);
LUAI_FUNC void luaK_setoneret (FuncState *fs, expdesc *e);
LUAI_FUNC int luaK_jump (FuncState *fs);
LUAI_FUNC void luaK_ret (FuncState *fs, int first, int nret);
LUAI_FUNC void luaK_patchlist (FuncState *fs, int list, int target);
LUAI_FUNC void luaK_patchtohere (FuncState *fs, int list);
LUAI_FUNC void luaK_concat (FuncState *fs, int *l1, int l2);
LUAI_FUNC int luaK_getlabel (FuncState *fs);
LUAI_FUNC void luaK_prefix (FuncState *fs, UnOpr op, expdesc *v);
LUAI_FUNC void luaK_infix (FuncState *fs, BinOpr op, expdesc *v);
LUAI_FUNC void luaK_posfix (FuncState *fs, BinOpr op, expdesc *v1, expdesc *v2);
LUAI_FUNC void luaK_setlist (FuncState *fs, int base, int nelems, int tostore);


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/ldblib.c000066400000000000000000000235541211610345200220760ustar00rootroot00000000000000/*
** $Id: ldblib.c,v 1.104.1.4 2009/08/04 18:50:18 roberto Exp $
** Interface from Lua to its debug API
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 

#define ldblib_c
#define LUA_LIB

#include "lua.h"

#include "lauxlib.h"
#include "lualib.h"



static int db_getregistry (lua_State *L) {
  lua_pushvalue(L, LUA_REGISTRYINDEX);
  return 1;
}


static int db_getmetatable (lua_State *L) {
  luaL_checkany(L, 1);
  if (!lua_getmetatable(L, 1)) {
    lua_pushnil(L);  /* no metatable */
  }
  return 1;
}


static int db_setmetatable (lua_State *L) {
  int t = lua_type(L, 2);
  luaL_argcheck(L, t == LUA_TNIL || t == LUA_TTABLE, 2,
                    "nil or table expected");
  lua_settop(L, 2);
  lua_pushboolean(L, lua_setmetatable(L, 1));
  return 1;
}


static int db_getfenv (lua_State *L) {
  luaL_checkany(L, 1);
  lua_getfenv(L, 1);
  return 1;
}


static int db_setfenv (lua_State *L) {
  luaL_checktype(L, 2, LUA_TTABLE);
  lua_settop(L, 2);
  if (lua_setfenv(L, 1) == 0)
    luaL_error(L, LUA_QL("setfenv")
                  " cannot change environment of given object");
  return 1;
}


static void settabss (lua_State *L, const char *i, const char *v) {
  lua_pushstring(L, v);
  lua_setfield(L, -2, i);
}


static void settabsi (lua_State *L, const char *i, int v) {
  lua_pushinteger(L, v);
  lua_setfield(L, -2, i);
}


static lua_State *getthread (lua_State *L, int *arg) {
  if (lua_isthread(L, 1)) {
    *arg = 1;
    return lua_tothread(L, 1);
  }
  else {
    *arg = 0;
    return L;
  }
}


static void treatstackoption (lua_State *L, lua_State *L1, const char *fname) {
  if (L == L1) {
    lua_pushvalue(L, -2);
    lua_remove(L, -3);
  }
  else
    lua_xmove(L1, L, 1);
  lua_setfield(L, -2, fname);
}


static int db_getinfo (lua_State *L) {
  lua_Debug ar;
  int arg;
  lua_State *L1 = getthread(L, &arg);
  const char *options = luaL_optstring(L, arg+2, "flnSu");
  if (lua_isnumber(L, arg+1)) {
    if (!lua_getstack(L1, (int)lua_tointeger(L, arg+1), &ar)) {
      lua_pushnil(L);  /* level out of range */
      return 1;
    }
  }
  else if (lua_isfunction(L, arg+1)) {
    lua_pushfstring(L, ">%s", options);
    options = lua_tostring(L, -1);
    lua_pushvalue(L, arg+1);
    lua_xmove(L, L1, 1);
  }
  else
    return luaL_argerror(L, arg+1, "function or level expected");
  if (!lua_getinfo(L1, options, &ar))
    return luaL_argerror(L, arg+2, "invalid option");
  lua_createtable(L, 0, 2);
  if (strchr(options, 'S')) {
    settabss(L, "source", ar.source);
    settabss(L, "short_src", ar.short_src);
    settabsi(L, "linedefined", ar.linedefined);
    settabsi(L, "lastlinedefined", ar.lastlinedefined);
    settabss(L, "what", ar.what);
  }
  if (strchr(options, 'l'))
    settabsi(L, "currentline", ar.currentline);
  if (strchr(options, 'u'))
    settabsi(L, "nups", ar.nups);
  if (strchr(options, 'n')) {
    settabss(L, "name", ar.name);
    settabss(L, "namewhat", ar.namewhat);
  }
  if (strchr(options, 'L'))
    treatstackoption(L, L1, "activelines");
  if (strchr(options, 'f'))
    treatstackoption(L, L1, "func");
  return 1;  /* return table */
}
    

static int db_getlocal (lua_State *L) {
  int arg;
  lua_State *L1 = getthread(L, &arg);
  lua_Debug ar;
  const char *name;
  if (!lua_getstack(L1, luaL_checkint(L, arg+1), &ar))  /* out of range? */
    return luaL_argerror(L, arg+1, "level out of range");
  name = lua_getlocal(L1, &ar, luaL_checkint(L, arg+2));
  if (name) {
    lua_xmove(L1, L, 1);
    lua_pushstring(L, name);
    lua_pushvalue(L, -2);
    return 2;
  }
  else {
    lua_pushnil(L);
    return 1;
  }
}


static int db_setlocal (lua_State *L) {
  int arg;
  lua_State *L1 = getthread(L, &arg);
  lua_Debug ar;
  if (!lua_getstack(L1, luaL_checkint(L, arg+1), &ar))  /* out of range? */
    return luaL_argerror(L, arg+1, "level out of range");
  luaL_checkany(L, arg+3);
  lua_settop(L, arg+3);
  lua_xmove(L, L1, 1);
  lua_pushstring(L, lua_setlocal(L1, &ar, luaL_checkint(L, arg+2)));
  return 1;
}


static int auxupvalue (lua_State *L, int get) {
  const char *name;
  int n = luaL_checkint(L, 2);
  luaL_checktype(L, 1, LUA_TFUNCTION);
  if (lua_iscfunction(L, 1)) return 0;  /* cannot touch C upvalues from Lua */
  name = get ? lua_getupvalue(L, 1, n) : lua_setupvalue(L, 1, n);
  if (name == NULL) return 0;
  lua_pushstring(L, name);
  lua_insert(L, -(get+1));
  return get + 1;
}


static int db_getupvalue (lua_State *L) {
  return auxupvalue(L, 1);
}


static int db_setupvalue (lua_State *L) {
  luaL_checkany(L, 3);
  return auxupvalue(L, 0);
}



static const char KEY_HOOK = 'h';


static void hookf (lua_State *L, lua_Debug *ar) {
  static const char *const hooknames[] =
    {"call", "return", "line", "count", "tail return"};
  lua_pushlightuserdata(L, (void *)&KEY_HOOK);
  lua_rawget(L, LUA_REGISTRYINDEX);
  lua_pushlightuserdata(L, L);
  lua_rawget(L, -2);
  if (lua_isfunction(L, -1)) {
    lua_pushstring(L, hooknames[(int)ar->event]);
    if (ar->currentline >= 0)
      lua_pushinteger(L, ar->currentline);
    else lua_pushnil(L);
    lua_assert(lua_getinfo(L, "lS", ar));
    lua_call(L, 2, 0);
  }
}


static int makemask (const char *smask, int count) {
  int mask = 0;
  if (strchr(smask, 'c')) mask |= LUA_MASKCALL;
  if (strchr(smask, 'r')) mask |= LUA_MASKRET;
  if (strchr(smask, 'l')) mask |= LUA_MASKLINE;
  if (count > 0) mask |= LUA_MASKCOUNT;
  return mask;
}


static char *unmakemask (int mask, char *smask) {
  int i = 0;
  if (mask & LUA_MASKCALL) smask[i++] = 'c';
  if (mask & LUA_MASKRET) smask[i++] = 'r';
  if (mask & LUA_MASKLINE) smask[i++] = 'l';
  smask[i] = '\0';
  return smask;
}


static void gethooktable (lua_State *L) {
  lua_pushlightuserdata(L, (void *)&KEY_HOOK);
  lua_rawget(L, LUA_REGISTRYINDEX);
  if (!lua_istable(L, -1)) {
    lua_pop(L, 1);
    lua_createtable(L, 0, 1);
    lua_pushlightuserdata(L, (void *)&KEY_HOOK);
    lua_pushvalue(L, -2);
    lua_rawset(L, LUA_REGISTRYINDEX);
  }
}


static int db_sethook (lua_State *L) {
  int arg, mask, count;
  lua_Hook func;
  lua_State *L1 = getthread(L, &arg);
  if (lua_isnoneornil(L, arg+1)) {
    lua_settop(L, arg+1);
    func = NULL; mask = 0; count = 0;  /* turn off hooks */
  }
  else {
    const char *smask = luaL_checkstring(L, arg+2);
    luaL_checktype(L, arg+1, LUA_TFUNCTION);
    count = luaL_optint(L, arg+3, 0);
    func = hookf; mask = makemask(smask, count);
  }
  gethooktable(L);
  lua_pushlightuserdata(L, L1);
  lua_pushvalue(L, arg+1);
  lua_rawset(L, -3);  /* set new hook */
  lua_pop(L, 1);  /* remove hook table */
  lua_sethook(L1, func, mask, count);  /* set hooks */
  return 0;
}


static int db_gethook (lua_State *L) {
  int arg;
  lua_State *L1 = getthread(L, &arg);
  char buff[5];
  int mask = lua_gethookmask(L1);
  lua_Hook hook = lua_gethook(L1);
  if (hook != NULL && hook != hookf)  /* external hook? */
    lua_pushliteral(L, "external hook");
  else {
    gethooktable(L);
    lua_pushlightuserdata(L, L1);
    lua_rawget(L, -2);   /* get hook */
    lua_remove(L, -2);  /* remove hook table */
  }
  lua_pushstring(L, unmakemask(mask, buff));
  lua_pushinteger(L, lua_gethookcount(L1));
  return 3;
}


static int db_debug (lua_State *L) {
  for (;;) {
    char buffer[250];
    fputs("lua_debug> ", stderr);
    if (fgets(buffer, sizeof(buffer), stdin) == 0 ||
        strcmp(buffer, "cont\n") == 0)
      return 0;
    if (luaL_loadbuffer(L, buffer, strlen(buffer), "=(debug command)") ||
        lua_pcall(L, 0, 0, 0)) {
      fputs(lua_tostring(L, -1), stderr);
      fputs("\n", stderr);
    }
    lua_settop(L, 0);  /* remove eventual returns */
  }
}


#define LEVELS1	12	/* size of the first part of the stack */
#define LEVELS2	10	/* size of the second part of the stack */

static int db_errorfb (lua_State *L) {
  int level;
  int firstpart = 1;  /* still before eventual `...' */
  int arg;
  lua_State *L1 = getthread(L, &arg);
  lua_Debug ar;
  if (lua_isnumber(L, arg+2)) {
    level = (int)lua_tointeger(L, arg+2);
    lua_pop(L, 1);
  }
  else
    level = (L == L1) ? 1 : 0;  /* level 0 may be this own function */
  if (lua_gettop(L) == arg)
    lua_pushliteral(L, "");
  else if (!lua_isstring(L, arg+1)) return 1;  /* message is not a string */
  else lua_pushliteral(L, "\n");
  lua_pushliteral(L, "stack traceback:");
  while (lua_getstack(L1, level++, &ar)) {
    if (level > LEVELS1 && firstpart) {
      /* no more than `LEVELS2' more levels? */
      if (!lua_getstack(L1, level+LEVELS2, &ar))
        level--;  /* keep going */
      else {
        lua_pushliteral(L, "\n\t...");  /* too many levels */
        while (lua_getstack(L1, level+LEVELS2, &ar))  /* find last levels */
          level++;
      }
      firstpart = 0;
      continue;
    }
    lua_pushliteral(L, "\n\t");
    lua_getinfo(L1, "Snl", &ar);
    lua_pushfstring(L, "%s:", ar.short_src);
    if (ar.currentline > 0)
      lua_pushfstring(L, "%d:", ar.currentline);
    if (*ar.namewhat != '\0')  /* is there a name? */
        lua_pushfstring(L, " in function " LUA_QS, ar.name);
    else {
      if (*ar.what == 'm')  /* main? */
        lua_pushfstring(L, " in main chunk");
      else if (*ar.what == 'C' || *ar.what == 't')
        lua_pushliteral(L, " ?");  /* C function or tail call */
      else
        lua_pushfstring(L, " in function <%s:%d>",
                           ar.short_src, ar.linedefined);
    }
    lua_concat(L, lua_gettop(L) - arg);
  }
  lua_concat(L, lua_gettop(L) - arg);
  return 1;
}


static const luaL_Reg dblib[] = {
  {"debug", db_debug},
  {"getfenv", db_getfenv},
  {"gethook", db_gethook},
  {"getinfo", db_getinfo},
  {"getlocal", db_getlocal},
  {"getregistry", db_getregistry},
  {"getmetatable", db_getmetatable},
  {"getupvalue", db_getupvalue},
  {"setfenv", db_setfenv},
  {"sethook", db_sethook},
  {"setlocal", db_setlocal},
  {"setmetatable", db_setmetatable},
  {"setupvalue", db_setupvalue},
  {"traceback", db_errorfb},
  {NULL, NULL}
};


LUALIB_API int luaopen_debug (lua_State *L) {
  luaL_register(L, LUA_DBLIBNAME, dblib);
  return 1;
}

genometools-1.5.1/src/external/lua-5.1.5/src/ldebug.c000066400000000000000000000407111211610345200221020ustar00rootroot00000000000000/*
** $Id: ldebug.c,v 2.29.1.6 2008/05/08 16:56:26 roberto Exp $
** Debug Interface
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 


#define ldebug_c
#define LUA_CORE

#include "lua.h"

#include "lapi.h"
#include "lcode.h"
#include "ldebug.h"
#include "ldo.h"
#include "lfunc.h"
#include "lobject.h"
#include "lopcodes.h"
#include "lstate.h"
#include "lstring.h"
#include "ltable.h"
#include "ltm.h"
#include "lvm.h"



static const char *getfuncname (lua_State *L, CallInfo *ci, const char **name);


static int currentpc (lua_State *L, CallInfo *ci) {
  if (!isLua(ci)) return -1;  /* function is not a Lua function? */
  if (ci == L->ci)
    ci->savedpc = L->savedpc;
  return pcRel(ci->savedpc, ci_func(ci)->l.p);
}


static int currentline (lua_State *L, CallInfo *ci) {
  int pc = currentpc(L, ci);
  if (pc < 0)
    return -1;  /* only active lua functions have current-line information */
  else
    return lgetline(ci_func(ci)->l.p, pc);
}


/*
** this function can be called asynchronous (e.g. during a signal)
*/
LUA_API int lua_sethook (lua_State *L, lua_Hook func, int mask, int count) {
  if (func == NULL || mask == 0) {  /* turn off hooks? */
    mask = 0;
    func = NULL;
  }
  L->hook = func;
  L->basehookcount = count;
  resethookcount(L);
  L->hookmask = cast_byte(mask);
  return 1;
}


LUA_API lua_Hook lua_gethook (lua_State *L) {
  return L->hook;
}


LUA_API int lua_gethookmask (lua_State *L) {
  return L->hookmask;
}


LUA_API int lua_gethookcount (lua_State *L) {
  return L->basehookcount;
}


LUA_API int lua_getstack (lua_State *L, int level, lua_Debug *ar) {
  int status;
  CallInfo *ci;
  lua_lock(L);
  for (ci = L->ci; level > 0 && ci > L->base_ci; ci--) {
    level--;
    if (f_isLua(ci))  /* Lua function? */
      level -= ci->tailcalls;  /* skip lost tail calls */
  }
  if (level == 0 && ci > L->base_ci) {  /* level found? */
    status = 1;
    ar->i_ci = cast_int(ci - L->base_ci);
  }
  else if (level < 0) {  /* level is of a lost tail call? */
    status = 1;
    ar->i_ci = 0;
  }
  else status = 0;  /* no such level */
  lua_unlock(L);
  return status;
}


static Proto *getluaproto (CallInfo *ci) {
  return (isLua(ci) ? ci_func(ci)->l.p : NULL);
}


static const char *findlocal (lua_State *L, CallInfo *ci, int n) {
  const char *name;
  Proto *fp = getluaproto(ci);
  if (fp && (name = luaF_getlocalname(fp, n, currentpc(L, ci))) != NULL)
    return name;  /* is a local variable in a Lua function */
  else {
    StkId limit = (ci == L->ci) ? L->top : (ci+1)->func;
    if (limit - ci->base >= n && n > 0)  /* is 'n' inside 'ci' stack? */
      return "(*temporary)";
    else
      return NULL;
  }
}


LUA_API const char *lua_getlocal (lua_State *L, const lua_Debug *ar, int n) {
  CallInfo *ci = L->base_ci + ar->i_ci;
  const char *name = findlocal(L, ci, n);
  lua_lock(L);
  if (name)
      luaA_pushobject(L, ci->base + (n - 1));
  lua_unlock(L);
  return name;
}


LUA_API const char *lua_setlocal (lua_State *L, const lua_Debug *ar, int n) {
  CallInfo *ci = L->base_ci + ar->i_ci;
  const char *name = findlocal(L, ci, n);
  lua_lock(L);
  if (name)
      setobjs2s(L, ci->base + (n - 1), L->top - 1);
  L->top--;  /* pop value */
  lua_unlock(L);
  return name;
}


static void funcinfo (lua_Debug *ar, Closure *cl) {
  if (cl->c.isC) {
    ar->source = "=[C]";
    ar->linedefined = -1;
    ar->lastlinedefined = -1;
    ar->what = "C";
  }
  else {
    ar->source = getstr(cl->l.p->source);
    ar->linedefined = cl->l.p->linedefined;
    ar->lastlinedefined = cl->l.p->lastlinedefined;
    ar->what = (ar->linedefined == 0) ? "main" : "Lua";
  }
  luaO_chunkid(ar->short_src, ar->source, LUA_IDSIZE);
}


static void info_tailcall (lua_Debug *ar) {
  ar->name = ar->namewhat = "";
  ar->what = "tail";
  ar->lastlinedefined = ar->linedefined = ar->currentline = -1;
  ar->source = "=(tail call)";
  luaO_chunkid(ar->short_src, ar->source, LUA_IDSIZE);
  ar->nups = 0;
}


static void collectvalidlines (lua_State *L, Closure *f) {
  if (f == NULL || f->c.isC) {
    setnilvalue(L->top);
  }
  else {
    Table *t = luaH_new(L, 0, 0);
    int *lineinfo = f->l.p->lineinfo;
    int i;
    for (i=0; il.p->sizelineinfo; i++)
      setbvalue(luaH_setnum(L, t, lineinfo[i]), 1);
    sethvalue(L, L->top, t); 
  }
  incr_top(L);
}


static int auxgetinfo (lua_State *L, const char *what, lua_Debug *ar,
                    Closure *f, CallInfo *ci) {
  int status = 1;
  if (f == NULL) {
    info_tailcall(ar);
    return status;
  }
  for (; *what; what++) {
    switch (*what) {
      case 'S': {
        funcinfo(ar, f);
        break;
      }
      case 'l': {
        ar->currentline = (ci) ? currentline(L, ci) : -1;
        break;
      }
      case 'u': {
        ar->nups = f->c.nupvalues;
        break;
      }
      case 'n': {
        ar->namewhat = (ci) ? getfuncname(L, ci, &ar->name) : NULL;
        if (ar->namewhat == NULL) {
          ar->namewhat = "";  /* not found */
          ar->name = NULL;
        }
        break;
      }
      case 'L':
      case 'f':  /* handled by lua_getinfo */
        break;
      default: status = 0;  /* invalid option */
    }
  }
  return status;
}


LUA_API int lua_getinfo (lua_State *L, const char *what, lua_Debug *ar) {
  int status;
  Closure *f = NULL;
  CallInfo *ci = NULL;
  lua_lock(L);
  if (*what == '>') {
    StkId func = L->top - 1;
    luai_apicheck(L, ttisfunction(func));
    what++;  /* skip the '>' */
    f = clvalue(func);
    L->top--;  /* pop function */
  }
  else if (ar->i_ci != 0) {  /* no tail call? */
    ci = L->base_ci + ar->i_ci;
    lua_assert(ttisfunction(ci->func));
    f = clvalue(ci->func);
  }
  status = auxgetinfo(L, what, ar, f, ci);
  if (strchr(what, 'f')) {
    if (f == NULL) setnilvalue(L->top);
    else setclvalue(L, L->top, f);
    incr_top(L);
  }
  if (strchr(what, 'L'))
    collectvalidlines(L, f);
  lua_unlock(L);
  return status;
}


/*
** {======================================================
** Symbolic Execution and code checker
** =======================================================
*/

#define check(x)		if (!(x)) return 0;

#define checkjump(pt,pc)	check(0 <= pc && pc < pt->sizecode)

#define checkreg(pt,reg)	check((reg) < (pt)->maxstacksize)



static int precheck (const Proto *pt) {
  check(pt->maxstacksize <= MAXSTACK);
  check(pt->numparams+(pt->is_vararg & VARARG_HASARG) <= pt->maxstacksize);
  check(!(pt->is_vararg & VARARG_NEEDSARG) ||
              (pt->is_vararg & VARARG_HASARG));
  check(pt->sizeupvalues <= pt->nups);
  check(pt->sizelineinfo == pt->sizecode || pt->sizelineinfo == 0);
  check(pt->sizecode > 0 && GET_OPCODE(pt->code[pt->sizecode-1]) == OP_RETURN);
  return 1;
}


#define checkopenop(pt,pc)	luaG_checkopenop((pt)->code[(pc)+1])

int luaG_checkopenop (Instruction i) {
  switch (GET_OPCODE(i)) {
    case OP_CALL:
    case OP_TAILCALL:
    case OP_RETURN:
    case OP_SETLIST: {
      check(GETARG_B(i) == 0);
      return 1;
    }
    default: return 0;  /* invalid instruction after an open call */
  }
}


static int checkArgMode (const Proto *pt, int r, enum OpArgMask mode) {
  switch (mode) {
    case OpArgN: check(r == 0); break;
    case OpArgU: break;
    case OpArgR: checkreg(pt, r); break;
    case OpArgK:
      check(ISK(r) ? INDEXK(r) < pt->sizek : r < pt->maxstacksize);
      break;
  }
  return 1;
}


static Instruction symbexec (const Proto *pt, int lastpc, int reg) {
  int pc;
  int last;  /* stores position of last instruction that changed `reg' */
  last = pt->sizecode-1;  /* points to final return (a `neutral' instruction) */
  check(precheck(pt));
  for (pc = 0; pc < lastpc; pc++) {
    Instruction i = pt->code[pc];
    OpCode op = GET_OPCODE(i);
    int a = GETARG_A(i);
    int b = 0;
    int c = 0;
    check(op < NUM_OPCODES);
    checkreg(pt, a);
    switch (getOpMode(op)) {
      case iABC: {
        b = GETARG_B(i);
        c = GETARG_C(i);
        check(checkArgMode(pt, b, getBMode(op)));
        check(checkArgMode(pt, c, getCMode(op)));
        break;
      }
      case iABx: {
        b = GETARG_Bx(i);
        if (getBMode(op) == OpArgK) check(b < pt->sizek);
        break;
      }
      case iAsBx: {
        b = GETARG_sBx(i);
        if (getBMode(op) == OpArgR) {
          int dest = pc+1+b;
          check(0 <= dest && dest < pt->sizecode);
          if (dest > 0) {
            int j;
            /* check that it does not jump to a setlist count; this
               is tricky, because the count from a previous setlist may
               have the same value of an invalid setlist; so, we must
               go all the way back to the first of them (if any) */
            for (j = 0; j < dest; j++) {
              Instruction d = pt->code[dest-1-j];
              if (!(GET_OPCODE(d) == OP_SETLIST && GETARG_C(d) == 0)) break;
            }
            /* if 'j' is even, previous value is not a setlist (even if
               it looks like one) */
            check((j&1) == 0);
          }
        }
        break;
      }
    }
    if (testAMode(op)) {
      if (a == reg) last = pc;  /* change register `a' */
    }
    if (testTMode(op)) {
      check(pc+2 < pt->sizecode);  /* check skip */
      check(GET_OPCODE(pt->code[pc+1]) == OP_JMP);
    }
    switch (op) {
      case OP_LOADBOOL: {
        if (c == 1) {  /* does it jump? */
          check(pc+2 < pt->sizecode);  /* check its jump */
          check(GET_OPCODE(pt->code[pc+1]) != OP_SETLIST ||
                GETARG_C(pt->code[pc+1]) != 0);
        }
        break;
      }
      case OP_LOADNIL: {
        if (a <= reg && reg <= b)
          last = pc;  /* set registers from `a' to `b' */
        break;
      }
      case OP_GETUPVAL:
      case OP_SETUPVAL: {
        check(b < pt->nups);
        break;
      }
      case OP_GETGLOBAL:
      case OP_SETGLOBAL: {
        check(ttisstring(&pt->k[b]));
        break;
      }
      case OP_SELF: {
        checkreg(pt, a+1);
        if (reg == a+1) last = pc;
        break;
      }
      case OP_CONCAT: {
        check(b < c);  /* at least two operands */
        break;
      }
      case OP_TFORLOOP: {
        check(c >= 1);  /* at least one result (control variable) */
        checkreg(pt, a+2+c);  /* space for results */
        if (reg >= a+2) last = pc;  /* affect all regs above its base */
        break;
      }
      case OP_FORLOOP:
      case OP_FORPREP:
        checkreg(pt, a+3);
        /* go through */
      case OP_JMP: {
        int dest = pc+1+b;
        /* not full check and jump is forward and do not skip `lastpc'? */
        if (reg != NO_REG && pc < dest && dest <= lastpc)
          pc += b;  /* do the jump */
        break;
      }
      case OP_CALL:
      case OP_TAILCALL: {
        if (b != 0) {
          checkreg(pt, a+b-1);
        }
        c--;  /* c = num. returns */
        if (c == LUA_MULTRET) {
          check(checkopenop(pt, pc));
        }
        else if (c != 0)
          checkreg(pt, a+c-1);
        if (reg >= a) last = pc;  /* affect all registers above base */
        break;
      }
      case OP_RETURN: {
        b--;  /* b = num. returns */
        if (b > 0) checkreg(pt, a+b-1);
        break;
      }
      case OP_SETLIST: {
        if (b > 0) checkreg(pt, a + b);
        if (c == 0) {
          pc++;
          check(pc < pt->sizecode - 1);
        }
        break;
      }
      case OP_CLOSURE: {
        int nup, j;
        check(b < pt->sizep);
        nup = pt->p[b]->nups;
        check(pc + nup < pt->sizecode);
        for (j = 1; j <= nup; j++) {
          OpCode op1 = GET_OPCODE(pt->code[pc + j]);
          check(op1 == OP_GETUPVAL || op1 == OP_MOVE);
        }
        if (reg != NO_REG)  /* tracing? */
          pc += nup;  /* do not 'execute' these pseudo-instructions */
        break;
      }
      case OP_VARARG: {
        check((pt->is_vararg & VARARG_ISVARARG) &&
             !(pt->is_vararg & VARARG_NEEDSARG));
        b--;
        if (b == LUA_MULTRET) check(checkopenop(pt, pc));
        checkreg(pt, a+b-1);
        break;
      }
      default: break;
    }
  }
  return pt->code[last];
}

#undef check
#undef checkjump
#undef checkreg

/* }====================================================== */


int luaG_checkcode (const Proto *pt) {
  return (symbexec(pt, pt->sizecode, NO_REG) != 0);
}


static const char *kname (Proto *p, int c) {
  if (ISK(c) && ttisstring(&p->k[INDEXK(c)]))
    return svalue(&p->k[INDEXK(c)]);
  else
    return "?";
}


static const char *getobjname (lua_State *L, CallInfo *ci, int stackpos,
                               const char **name) {
  if (isLua(ci)) {  /* a Lua function? */
    Proto *p = ci_func(ci)->l.p;
    int pc = currentpc(L, ci);
    Instruction i;
    *name = luaF_getlocalname(p, stackpos+1, pc);
    if (*name)  /* is a local? */
      return "local";
    i = symbexec(p, pc, stackpos);  /* try symbolic execution */
    lua_assert(pc != -1);
    switch (GET_OPCODE(i)) {
      case OP_GETGLOBAL: {
        int g = GETARG_Bx(i);  /* global index */
        lua_assert(ttisstring(&p->k[g]));
        *name = svalue(&p->k[g]);
        return "global";
      }
      case OP_MOVE: {
        int a = GETARG_A(i);
        int b = GETARG_B(i);  /* move from `b' to `a' */
        if (b < a)
          return getobjname(L, ci, b, name);  /* get name for `b' */
        break;
      }
      case OP_GETTABLE: {
        int k = GETARG_C(i);  /* key index */
        *name = kname(p, k);
        return "field";
      }
      case OP_GETUPVAL: {
        int u = GETARG_B(i);  /* upvalue index */
        *name = p->upvalues ? getstr(p->upvalues[u]) : "?";
        return "upvalue";
      }
      case OP_SELF: {
        int k = GETARG_C(i);  /* key index */
        *name = kname(p, k);
        return "method";
      }
      default: break;
    }
  }
  return NULL;  /* no useful name found */
}


static const char *getfuncname (lua_State *L, CallInfo *ci, const char **name) {
  Instruction i;
  if ((isLua(ci) && ci->tailcalls > 0) || !isLua(ci - 1))
    return NULL;  /* calling function is not Lua (or is unknown) */
  ci--;  /* calling function */
  i = ci_func(ci)->l.p->code[currentpc(L, ci)];
  if (GET_OPCODE(i) == OP_CALL || GET_OPCODE(i) == OP_TAILCALL ||
      GET_OPCODE(i) == OP_TFORLOOP)
    return getobjname(L, ci, GETARG_A(i), name);
  else
    return NULL;  /* no useful name can be found */
}


/* only ANSI way to check whether a pointer points to an array */
static int isinstack (CallInfo *ci, const TValue *o) {
  StkId p;
  for (p = ci->base; p < ci->top; p++)
    if (o == p) return 1;
  return 0;
}


void luaG_typeerror (lua_State *L, const TValue *o, const char *op) {
  const char *name = NULL;
  const char *t = luaT_typenames[ttype(o)];
  const char *kind = (isinstack(L->ci, o)) ?
                         getobjname(L, L->ci, cast_int(o - L->base), &name) :
                         NULL;
  if (kind)
    luaG_runerror(L, "attempt to %s %s " LUA_QS " (a %s value)",
                op, kind, name, t);
  else
    luaG_runerror(L, "attempt to %s a %s value", op, t);
}


void luaG_concaterror (lua_State *L, StkId p1, StkId p2) {
  if (ttisstring(p1) || ttisnumber(p1)) p1 = p2;
  lua_assert(!ttisstring(p1) && !ttisnumber(p1));
  luaG_typeerror(L, p1, "concatenate");
}


void luaG_aritherror (lua_State *L, const TValue *p1, const TValue *p2) {
  TValue temp;
  if (luaV_tonumber(p1, &temp) == NULL)
    p2 = p1;  /* first operand is wrong */
  luaG_typeerror(L, p2, "perform arithmetic on");
}


int luaG_ordererror (lua_State *L, const TValue *p1, const TValue *p2) {
  const char *t1 = luaT_typenames[ttype(p1)];
  const char *t2 = luaT_typenames[ttype(p2)];
  if (t1[2] == t2[2])
    luaG_runerror(L, "attempt to compare two %s values", t1);
  else
    luaG_runerror(L, "attempt to compare %s with %s", t1, t2);
  return 0;
}


static void addinfo (lua_State *L, const char *msg) {
  CallInfo *ci = L->ci;
  if (isLua(ci)) {  /* is Lua code? */
    char buff[LUA_IDSIZE];  /* add file:line information */
    int line = currentline(L, ci);
    luaO_chunkid(buff, getstr(getluaproto(ci)->source), LUA_IDSIZE);
    luaO_pushfstring(L, "%s:%d: %s", buff, line, msg);
  }
}


void luaG_errormsg (lua_State *L) {
  if (L->errfunc != 0) {  /* is there an error handling function? */
    StkId errfunc = restorestack(L, L->errfunc);
    if (!ttisfunction(errfunc)) luaD_throw(L, LUA_ERRERR);
    setobjs2s(L, L->top, L->top - 1);  /* move argument */
    setobjs2s(L, L->top - 1, errfunc);  /* push function */
    incr_top(L);
    luaD_call(L, L->top - 2, 1);  /* call it */
  }
  luaD_throw(L, LUA_ERRRUN);
}


void luaG_runerror (lua_State *L, const char *fmt, ...) {
  va_list argp;
  va_start(argp, fmt);
  addinfo(L, luaO_pushvfstring(L, fmt, argp));
  va_end(argp);
  luaG_errormsg(L);
}

genometools-1.5.1/src/external/lua-5.1.5/src/ldebug.h000066400000000000000000000020461211610345200221060ustar00rootroot00000000000000/*
** $Id: ldebug.h,v 2.3.1.1 2007/12/27 13:02:25 roberto Exp $
** Auxiliary functions from Debug Interface module
** See Copyright Notice in lua.h
*/

#ifndef ldebug_h
#define ldebug_h


#include "lstate.h"


#define pcRel(pc, p)	(cast(int, (pc) - (p)->code) - 1)

#define lgetline(f,pc)	(((f)->lineinfo) ? (f)->lineinfo[pc] : 0)

#define resethookcount(L)	(L->hookcount = L->basehookcount)


LUAI_FUNC void luaG_typeerror (lua_State *L, const TValue *o,
                                             const char *opname);
LUAI_FUNC void luaG_concaterror (lua_State *L, StkId p1, StkId p2);
LUAI_FUNC void luaG_aritherror (lua_State *L, const TValue *p1,
                                              const TValue *p2);
LUAI_FUNC int luaG_ordererror (lua_State *L, const TValue *p1,
                                             const TValue *p2);
LUAI_FUNC void luaG_runerror (lua_State *L, const char *fmt, ...);
LUAI_FUNC void luaG_errormsg (lua_State *L);
LUAI_FUNC int luaG_checkcode (const Proto *pt);
LUAI_FUNC int luaG_checkopenop (Instruction i);

#endif
genometools-1.5.1/src/external/lua-5.1.5/src/ldo.c000066400000000000000000000350541211610345200214220ustar00rootroot00000000000000/*
** $Id: ldo.c,v 2.38.1.4 2012/01/18 02:27:10 roberto Exp $
** Stack and Call structure of Lua
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 

#define ldo_c
#define LUA_CORE

#include "lua.h"

#include "ldebug.h"
#include "ldo.h"
#include "lfunc.h"
#include "lgc.h"
#include "lmem.h"
#include "lobject.h"
#include "lopcodes.h"
#include "lparser.h"
#include "lstate.h"
#include "lstring.h"
#include "ltable.h"
#include "ltm.h"
#include "lundump.h"
#include "lvm.h"
#include "lzio.h"




/*
** {======================================================
** Error-recovery functions
** =======================================================
*/


/* chain list of long jump buffers */
struct lua_longjmp {
  struct lua_longjmp *previous;
  luai_jmpbuf b;
  volatile int status;  /* error code */
};


void luaD_seterrorobj (lua_State *L, int errcode, StkId oldtop) {
  switch (errcode) {
    case LUA_ERRMEM: {
      setsvalue2s(L, oldtop, luaS_newliteral(L, MEMERRMSG));
      break;
    }
    case LUA_ERRERR: {
      setsvalue2s(L, oldtop, luaS_newliteral(L, "error in error handling"));
      break;
    }
    case LUA_ERRSYNTAX:
    case LUA_ERRRUN: {
      setobjs2s(L, oldtop, L->top - 1);  /* error message on current top */
      break;
    }
  }
  L->top = oldtop + 1;
}


static void restore_stack_limit (lua_State *L) {
  lua_assert(L->stack_last - L->stack == L->stacksize - EXTRA_STACK - 1);
  if (L->size_ci > LUAI_MAXCALLS) {  /* there was an overflow? */
    int inuse = cast_int(L->ci - L->base_ci);
    if (inuse + 1 < LUAI_MAXCALLS)  /* can `undo' overflow? */
      luaD_reallocCI(L, LUAI_MAXCALLS);
  }
}


static void resetstack (lua_State *L, int status) {
  L->ci = L->base_ci;
  L->base = L->ci->base;
  luaF_close(L, L->base);  /* close eventual pending closures */
  luaD_seterrorobj(L, status, L->base);
  L->nCcalls = L->baseCcalls;
  L->allowhook = 1;
  restore_stack_limit(L);
  L->errfunc = 0;
  L->errorJmp = NULL;
}


void luaD_throw (lua_State *L, int errcode) {
  if (L->errorJmp) {
    L->errorJmp->status = errcode;
    LUAI_THROW(L, L->errorJmp);
  }
  else {
    L->status = cast_byte(errcode);
    if (G(L)->panic) {
      resetstack(L, errcode);
      lua_unlock(L);
      G(L)->panic(L);
    }
    exit(EXIT_FAILURE);
  }
}


int luaD_rawrunprotected (lua_State *L, Pfunc f, void *ud) {
  struct lua_longjmp lj;
  lj.status = 0;
  lj.previous = L->errorJmp;  /* chain new error handler */
  L->errorJmp = &lj;
  LUAI_TRY(L, &lj,
    (*f)(L, ud);
  );
  L->errorJmp = lj.previous;  /* restore old error handler */
  return lj.status;
}

/* }====================================================== */


static void correctstack (lua_State *L, TValue *oldstack) {
  CallInfo *ci;
  GCObject *up;
  L->top = (L->top - oldstack) + L->stack;
  for (up = L->openupval; up != NULL; up = up->gch.next)
    gco2uv(up)->v = (gco2uv(up)->v - oldstack) + L->stack;
  for (ci = L->base_ci; ci <= L->ci; ci++) {
    ci->top = (ci->top - oldstack) + L->stack;
    ci->base = (ci->base - oldstack) + L->stack;
    ci->func = (ci->func - oldstack) + L->stack;
  }
  L->base = (L->base - oldstack) + L->stack;
}


void luaD_reallocstack (lua_State *L, int newsize) {
  TValue *oldstack = L->stack;
  int realsize = newsize + 1 + EXTRA_STACK;
  lua_assert(L->stack_last - L->stack == L->stacksize - EXTRA_STACK - 1);
  luaM_reallocvector(L, L->stack, L->stacksize, realsize, TValue);
  L->stacksize = realsize;
  L->stack_last = L->stack+newsize;
  correctstack(L, oldstack);
}


void luaD_reallocCI (lua_State *L, int newsize) {
  CallInfo *oldci = L->base_ci;
  luaM_reallocvector(L, L->base_ci, L->size_ci, newsize, CallInfo);
  L->size_ci = newsize;
  L->ci = (L->ci - oldci) + L->base_ci;
  L->end_ci = L->base_ci + L->size_ci - 1;
}


void luaD_growstack (lua_State *L, int n) {
  if (n <= L->stacksize)  /* double size is enough? */
    luaD_reallocstack(L, 2*L->stacksize);
  else
    luaD_reallocstack(L, L->stacksize + n);
}


static CallInfo *growCI (lua_State *L) {
  if (L->size_ci > LUAI_MAXCALLS)  /* overflow while handling overflow? */
    luaD_throw(L, LUA_ERRERR);
  else {
    luaD_reallocCI(L, 2*L->size_ci);
    if (L->size_ci > LUAI_MAXCALLS)
      luaG_runerror(L, "stack overflow");
  }
  return ++L->ci;
}


void luaD_callhook (lua_State *L, int event, int line) {
  lua_Hook hook = L->hook;
  if (hook && L->allowhook) {
    ptrdiff_t top = savestack(L, L->top);
    ptrdiff_t ci_top = savestack(L, L->ci->top);
    lua_Debug ar;
    ar.event = event;
    ar.currentline = line;
    if (event == LUA_HOOKTAILRET)
      ar.i_ci = 0;  /* tail call; no debug information about it */
    else
      ar.i_ci = cast_int(L->ci - L->base_ci);
    luaD_checkstack(L, LUA_MINSTACK);  /* ensure minimum stack size */
    L->ci->top = L->top + LUA_MINSTACK;
    lua_assert(L->ci->top <= L->stack_last);
    L->allowhook = 0;  /* cannot call hooks inside a hook */
    lua_unlock(L);
    (*hook)(L, &ar);
    lua_lock(L);
    lua_assert(!L->allowhook);
    L->allowhook = 1;
    L->ci->top = restorestack(L, ci_top);
    L->top = restorestack(L, top);
  }
}


static StkId adjust_varargs (lua_State *L, Proto *p, int actual) {
  int i;
  int nfixargs = p->numparams;
  Table *htab = NULL;
  StkId base, fixed;
  for (; actual < nfixargs; ++actual)
    setnilvalue(L->top++);
#if defined(LUA_COMPAT_VARARG)
  if (p->is_vararg & VARARG_NEEDSARG) { /* compat. with old-style vararg? */
    int nvar = actual - nfixargs;  /* number of extra arguments */
    lua_assert(p->is_vararg & VARARG_HASARG);
    luaC_checkGC(L);
    luaD_checkstack(L, p->maxstacksize);
    htab = luaH_new(L, nvar, 1);  /* create `arg' table */
    for (i=0; itop - nvar + i);
    /* store counter in field `n' */
    setnvalue(luaH_setstr(L, htab, luaS_newliteral(L, "n")), cast_num(nvar));
  }
#endif
  /* move fixed parameters to final position */
  fixed = L->top - actual;  /* first fixed argument */
  base = L->top;  /* final position of first argument */
  for (i=0; itop++, fixed+i);
    setnilvalue(fixed+i);
  }
  /* add `arg' parameter */
  if (htab) {
    sethvalue(L, L->top++, htab);
    lua_assert(iswhite(obj2gco(htab)));
  }
  return base;
}


static StkId tryfuncTM (lua_State *L, StkId func) {
  const TValue *tm = luaT_gettmbyobj(L, func, TM_CALL);
  StkId p;
  ptrdiff_t funcr = savestack(L, func);
  if (!ttisfunction(tm))
    luaG_typeerror(L, func, "call");
  /* Open a hole inside the stack at `func' */
  for (p = L->top; p > func; p--) setobjs2s(L, p, p-1);
  incr_top(L);
  func = restorestack(L, funcr);  /* previous call may change stack */
  setobj2s(L, func, tm);  /* tag method is the new function to be called */
  return func;
}



#define inc_ci(L) \
  ((L->ci == L->end_ci) ? growCI(L) : \
   (condhardstacktests(luaD_reallocCI(L, L->size_ci)), ++L->ci))


int luaD_precall (lua_State *L, StkId func, int nresults) {
  LClosure *cl;
  ptrdiff_t funcr;
  if (!ttisfunction(func)) /* `func' is not a function? */
    func = tryfuncTM(L, func);  /* check the `function' tag method */
  funcr = savestack(L, func);
  cl = &clvalue(func)->l;
  L->ci->savedpc = L->savedpc;
  if (!cl->isC) {  /* Lua function? prepare its call */
    CallInfo *ci;
    StkId st, base;
    Proto *p = cl->p;
    luaD_checkstack(L, p->maxstacksize);
    func = restorestack(L, funcr);
    if (!p->is_vararg) {  /* no varargs? */
      base = func + 1;
      if (L->top > base + p->numparams)
        L->top = base + p->numparams;
    }
    else {  /* vararg function */
      int nargs = cast_int(L->top - func) - 1;
      base = adjust_varargs(L, p, nargs);
      func = restorestack(L, funcr);  /* previous call may change the stack */
    }
    ci = inc_ci(L);  /* now `enter' new function */
    ci->func = func;
    L->base = ci->base = base;
    ci->top = L->base + p->maxstacksize;
    lua_assert(ci->top <= L->stack_last);
    L->savedpc = p->code;  /* starting point */
    ci->tailcalls = 0;
    ci->nresults = nresults;
    for (st = L->top; st < ci->top; st++)
      setnilvalue(st);
    L->top = ci->top;
    if (L->hookmask & LUA_MASKCALL) {
      L->savedpc++;  /* hooks assume 'pc' is already incremented */
      luaD_callhook(L, LUA_HOOKCALL, -1);
      L->savedpc--;  /* correct 'pc' */
    }
    return PCRLUA;
  }
  else {  /* if is a C function, call it */
    CallInfo *ci;
    int n;
    luaD_checkstack(L, LUA_MINSTACK);  /* ensure minimum stack size */
    ci = inc_ci(L);  /* now `enter' new function */
    ci->func = restorestack(L, funcr);
    L->base = ci->base = ci->func + 1;
    ci->top = L->top + LUA_MINSTACK;
    lua_assert(ci->top <= L->stack_last);
    ci->nresults = nresults;
    if (L->hookmask & LUA_MASKCALL)
      luaD_callhook(L, LUA_HOOKCALL, -1);
    lua_unlock(L);
    n = (*curr_func(L)->c.f)(L);  /* do the actual call */
    lua_lock(L);
    if (n < 0)  /* yielding? */
      return PCRYIELD;
    else {
      luaD_poscall(L, L->top - n);
      return PCRC;
    }
  }
}


static StkId callrethooks (lua_State *L, StkId firstResult) {
  ptrdiff_t fr = savestack(L, firstResult);  /* next call may change stack */
  luaD_callhook(L, LUA_HOOKRET, -1);
  if (f_isLua(L->ci)) {  /* Lua function? */
    while ((L->hookmask & LUA_MASKRET) && L->ci->tailcalls--) /* tail calls */
      luaD_callhook(L, LUA_HOOKTAILRET, -1);
  }
  return restorestack(L, fr);
}


int luaD_poscall (lua_State *L, StkId firstResult) {
  StkId res;
  int wanted, i;
  CallInfo *ci;
  if (L->hookmask & LUA_MASKRET)
    firstResult = callrethooks(L, firstResult);
  ci = L->ci--;
  res = ci->func;  /* res == final position of 1st result */
  wanted = ci->nresults;
  L->base = (ci - 1)->base;  /* restore base */
  L->savedpc = (ci - 1)->savedpc;  /* restore savedpc */
  /* move results to correct place */
  for (i = wanted; i != 0 && firstResult < L->top; i--)
    setobjs2s(L, res++, firstResult++);
  while (i-- > 0)
    setnilvalue(res++);
  L->top = res;
  return (wanted - LUA_MULTRET);  /* 0 iff wanted == LUA_MULTRET */
}


/*
** Call a function (C or Lua). The function to be called is at *func.
** The arguments are on the stack, right after the function.
** When returns, all the results are on the stack, starting at the original
** function position.
*/ 
void luaD_call (lua_State *L, StkId func, int nResults) {
  if (++L->nCcalls >= LUAI_MAXCCALLS) {
    if (L->nCcalls == LUAI_MAXCCALLS)
      luaG_runerror(L, "C stack overflow");
    else if (L->nCcalls >= (LUAI_MAXCCALLS + (LUAI_MAXCCALLS>>3)))
      luaD_throw(L, LUA_ERRERR);  /* error while handing stack error */
  }
  if (luaD_precall(L, func, nResults) == PCRLUA)  /* is a Lua function? */
    luaV_execute(L, 1);  /* call it */
  L->nCcalls--;
  luaC_checkGC(L);
}


static void resume (lua_State *L, void *ud) {
  StkId firstArg = cast(StkId, ud);
  CallInfo *ci = L->ci;
  if (L->status == 0) {  /* start coroutine? */
    lua_assert(ci == L->base_ci && firstArg > L->base);
    if (luaD_precall(L, firstArg - 1, LUA_MULTRET) != PCRLUA)
      return;
  }
  else {  /* resuming from previous yield */
    lua_assert(L->status == LUA_YIELD);
    L->status = 0;
    if (!f_isLua(ci)) {  /* `common' yield? */
      /* finish interrupted execution of `OP_CALL' */
      lua_assert(GET_OPCODE(*((ci-1)->savedpc - 1)) == OP_CALL ||
                 GET_OPCODE(*((ci-1)->savedpc - 1)) == OP_TAILCALL);
      if (luaD_poscall(L, firstArg))  /* complete it... */
        L->top = L->ci->top;  /* and correct top if not multiple results */
    }
    else  /* yielded inside a hook: just continue its execution */
      L->base = L->ci->base;
  }
  luaV_execute(L, cast_int(L->ci - L->base_ci));
}


static int resume_error (lua_State *L, const char *msg) {
  L->top = L->ci->base;
  setsvalue2s(L, L->top, luaS_new(L, msg));
  incr_top(L);
  lua_unlock(L);
  return LUA_ERRRUN;
}


LUA_API int lua_resume (lua_State *L, int nargs) {
  int status;
  lua_lock(L);
  if (L->status != LUA_YIELD && (L->status != 0 || L->ci != L->base_ci))
      return resume_error(L, "cannot resume non-suspended coroutine");
  if (L->nCcalls >= LUAI_MAXCCALLS)
    return resume_error(L, "C stack overflow");
  luai_userstateresume(L, nargs);
  lua_assert(L->errfunc == 0);
  L->baseCcalls = ++L->nCcalls;
  status = luaD_rawrunprotected(L, resume, L->top - nargs);
  if (status != 0) {  /* error? */
    L->status = cast_byte(status);  /* mark thread as `dead' */
    luaD_seterrorobj(L, status, L->top);
    L->ci->top = L->top;
  }
  else {
    lua_assert(L->nCcalls == L->baseCcalls);
    status = L->status;
  }
  --L->nCcalls;
  lua_unlock(L);
  return status;
}


LUA_API int lua_yield (lua_State *L, int nresults) {
  luai_userstateyield(L, nresults);
  lua_lock(L);
  if (L->nCcalls > L->baseCcalls)
    luaG_runerror(L, "attempt to yield across metamethod/C-call boundary");
  L->base = L->top - nresults;  /* protect stack slots below */
  L->status = LUA_YIELD;
  lua_unlock(L);
  return -1;
}


int luaD_pcall (lua_State *L, Pfunc func, void *u,
                ptrdiff_t old_top, ptrdiff_t ef) {
  int status;
  unsigned short oldnCcalls = L->nCcalls;
  ptrdiff_t old_ci = saveci(L, L->ci);
  lu_byte old_allowhooks = L->allowhook;
  ptrdiff_t old_errfunc = L->errfunc;
  L->errfunc = ef;
  status = luaD_rawrunprotected(L, func, u);
  if (status != 0) {  /* an error occurred? */
    StkId oldtop = restorestack(L, old_top);
    luaF_close(L, oldtop);  /* close eventual pending closures */
    luaD_seterrorobj(L, status, oldtop);
    L->nCcalls = oldnCcalls;
    L->ci = restoreci(L, old_ci);
    L->base = L->ci->base;
    L->savedpc = L->ci->savedpc;
    L->allowhook = old_allowhooks;
    restore_stack_limit(L);
  }
  L->errfunc = old_errfunc;
  return status;
}



/*
** Execute a protected parser.
*/
struct SParser {  /* data to `f_parser' */
  ZIO *z;
  Mbuffer buff;  /* buffer to be used by the scanner */
  const char *name;
};

static void f_parser (lua_State *L, void *ud) {
  int i;
  Proto *tf;
  Closure *cl;
  struct SParser *p = cast(struct SParser *, ud);
  int c = luaZ_lookahead(p->z);
  luaC_checkGC(L);
  tf = ((c == LUA_SIGNATURE[0]) ? luaU_undump : luaY_parser)(L, p->z,
                                                             &p->buff, p->name);
  cl = luaF_newLclosure(L, tf->nups, hvalue(gt(L)));
  cl->l.p = tf;
  for (i = 0; i < tf->nups; i++)  /* initialize eventual upvalues */
    cl->l.upvals[i] = luaF_newupval(L);
  setclvalue(L, L->top, cl);
  incr_top(L);
}


int luaD_protectedparser (lua_State *L, ZIO *z, const char *name) {
  struct SParser p;
  int status;
  p.z = z; p.name = name;
  luaZ_initbuffer(L, &p.buff);
  status = luaD_pcall(L, f_parser, &p, savestack(L, L->top), L->errfunc);
  luaZ_freebuffer(L, &p.buff);
  return status;
}


genometools-1.5.1/src/external/lua-5.1.5/src/ldo.h000066400000000000000000000035511211610345200214240ustar00rootroot00000000000000/*
** $Id: ldo.h,v 2.7.1.1 2007/12/27 13:02:25 roberto Exp $
** Stack and Call structure of Lua
** See Copyright Notice in lua.h
*/

#ifndef ldo_h
#define ldo_h


#include "lobject.h"
#include "lstate.h"
#include "lzio.h"


#define luaD_checkstack(L,n)	\
  if ((char *)L->stack_last - (char *)L->top <= (n)*(int)sizeof(TValue)) \
    luaD_growstack(L, n); \
  else condhardstacktests(luaD_reallocstack(L, L->stacksize - EXTRA_STACK - 1));


#define incr_top(L) {luaD_checkstack(L,1); L->top++;}

#define savestack(L,p)		((char *)(p) - (char *)L->stack)
#define restorestack(L,n)	((TValue *)((char *)L->stack + (n)))

#define saveci(L,p)		((char *)(p) - (char *)L->base_ci)
#define restoreci(L,n)		((CallInfo *)((char *)L->base_ci + (n)))


/* results from luaD_precall */
#define PCRLUA		0	/* initiated a call to a Lua function */
#define PCRC		1	/* did a call to a C function */
#define PCRYIELD	2	/* C funtion yielded */


/* type of protected functions, to be ran by `runprotected' */
typedef void (*Pfunc) (lua_State *L, void *ud);

LUAI_FUNC int luaD_protectedparser (lua_State *L, ZIO *z, const char *name);
LUAI_FUNC void luaD_callhook (lua_State *L, int event, int line);
LUAI_FUNC int luaD_precall (lua_State *L, StkId func, int nresults);
LUAI_FUNC void luaD_call (lua_State *L, StkId func, int nResults);
LUAI_FUNC int luaD_pcall (lua_State *L, Pfunc func, void *u,
                                        ptrdiff_t oldtop, ptrdiff_t ef);
LUAI_FUNC int luaD_poscall (lua_State *L, StkId firstResult);
LUAI_FUNC void luaD_reallocCI (lua_State *L, int newsize);
LUAI_FUNC void luaD_reallocstack (lua_State *L, int newsize);
LUAI_FUNC void luaD_growstack (lua_State *L, int n);

LUAI_FUNC void luaD_throw (lua_State *L, int errcode);
LUAI_FUNC int luaD_rawrunprotected (lua_State *L, Pfunc f, void *ud);

LUAI_FUNC void luaD_seterrorobj (lua_State *L, int errcode, StkId oldtop);

#endif

genometools-1.5.1/src/external/lua-5.1.5/src/ldump.c000066400000000000000000000060521211610345200217610ustar00rootroot00000000000000/*
** $Id: ldump.c,v 2.8.1.1 2007/12/27 13:02:25 roberto Exp $
** save precompiled Lua chunks
** See Copyright Notice in lua.h
*/

#include 

#define ldump_c
#define LUA_CORE

#include "lua.h"

#include "lobject.h"
#include "lstate.h"
#include "lundump.h"

typedef struct {
 lua_State* L;
 lua_Writer writer;
 void* data;
 int strip;
 int status;
} DumpState;

#define DumpMem(b,n,size,D)	DumpBlock(b,(n)*(size),D)
#define DumpVar(x,D)	 	DumpMem(&x,1,sizeof(x),D)

static void DumpBlock(const void* b, size_t size, DumpState* D)
{
 if (D->status==0)
 {
  lua_unlock(D->L);
  D->status=(*D->writer)(D->L,b,size,D->data);
  lua_lock(D->L);
 }
}

static void DumpChar(int y, DumpState* D)
{
 char x=(char)y;
 DumpVar(x,D);
}

static void DumpInt(int x, DumpState* D)
{
 DumpVar(x,D);
}

static void DumpNumber(lua_Number x, DumpState* D)
{
 DumpVar(x,D);
}

static void DumpVector(const void* b, int n, size_t size, DumpState* D)
{
 DumpInt(n,D);
 DumpMem(b,n,size,D);
}

static void DumpString(const TString* s, DumpState* D)
{
 if (s==NULL || getstr(s)==NULL)
 {
  size_t size=0;
  DumpVar(size,D);
 }
 else
 {
  size_t size=s->tsv.len+1;		/* include trailing '\0' */
  DumpVar(size,D);
  DumpBlock(getstr(s),size,D);
 }
}

#define DumpCode(f,D)	 DumpVector(f->code,f->sizecode,sizeof(Instruction),D)

static void DumpFunction(const Proto* f, const TString* p, DumpState* D);

static void DumpConstants(const Proto* f, DumpState* D)
{
 int i,n=f->sizek;
 DumpInt(n,D);
 for (i=0; ik[i];
  DumpChar(ttype(o),D);
  switch (ttype(o))
  {
   case LUA_TNIL:
	break;
   case LUA_TBOOLEAN:
	DumpChar(bvalue(o),D);
	break;
   case LUA_TNUMBER:
	DumpNumber(nvalue(o),D);
	break;
   case LUA_TSTRING:
	DumpString(rawtsvalue(o),D);
	break;
   default:
	lua_assert(0);			/* cannot happen */
	break;
  }
 }
 n=f->sizep;
 DumpInt(n,D);
 for (i=0; ip[i],f->source,D);
}

static void DumpDebug(const Proto* f, DumpState* D)
{
 int i,n;
 n= (D->strip) ? 0 : f->sizelineinfo;
 DumpVector(f->lineinfo,n,sizeof(int),D);
 n= (D->strip) ? 0 : f->sizelocvars;
 DumpInt(n,D);
 for (i=0; ilocvars[i].varname,D);
  DumpInt(f->locvars[i].startpc,D);
  DumpInt(f->locvars[i].endpc,D);
 }
 n= (D->strip) ? 0 : f->sizeupvalues;
 DumpInt(n,D);
 for (i=0; iupvalues[i],D);
}

static void DumpFunction(const Proto* f, const TString* p, DumpState* D)
{
 DumpString((f->source==p || D->strip) ? NULL : f->source,D);
 DumpInt(f->linedefined,D);
 DumpInt(f->lastlinedefined,D);
 DumpChar(f->nups,D);
 DumpChar(f->numparams,D);
 DumpChar(f->is_vararg,D);
 DumpChar(f->maxstacksize,D);
 DumpCode(f,D);
 DumpConstants(f,D);
 DumpDebug(f,D);
}

static void DumpHeader(DumpState* D)
{
 char h[LUAC_HEADERSIZE];
 luaU_header(h);
 DumpBlock(h,LUAC_HEADERSIZE,D);
}

/*
** dump Lua function as precompiled chunk
*/
int luaU_dump (lua_State* L, const Proto* f, lua_Writer w, void* data, int strip)
{
 DumpState D;
 D.L=L;
 D.writer=w;
 D.data=data;
 D.strip=strip;
 D.status=0;
 DumpHeader(&D);
 DumpFunction(f,NULL,&D);
 return D.status;
}
genometools-1.5.1/src/external/lua-5.1.5/src/lfunc.c000066400000000000000000000110121211610345200217370ustar00rootroot00000000000000/*
** $Id: lfunc.c,v 2.12.1.2 2007/12/28 14:58:43 roberto Exp $
** Auxiliary functions to manipulate prototypes and closures
** See Copyright Notice in lua.h
*/


#include 

#define lfunc_c
#define LUA_CORE

#include "lua.h"

#include "lfunc.h"
#include "lgc.h"
#include "lmem.h"
#include "lobject.h"
#include "lstate.h"



Closure *luaF_newCclosure (lua_State *L, int nelems, Table *e) {
  Closure *c = cast(Closure *, luaM_malloc(L, sizeCclosure(nelems)));
  luaC_link(L, obj2gco(c), LUA_TFUNCTION);
  c->c.isC = 1;
  c->c.env = e;
  c->c.nupvalues = cast_byte(nelems);
  return c;
}


Closure *luaF_newLclosure (lua_State *L, int nelems, Table *e) {
  Closure *c = cast(Closure *, luaM_malloc(L, sizeLclosure(nelems)));
  luaC_link(L, obj2gco(c), LUA_TFUNCTION);
  c->l.isC = 0;
  c->l.env = e;
  c->l.nupvalues = cast_byte(nelems);
  while (nelems--) c->l.upvals[nelems] = NULL;
  return c;
}


UpVal *luaF_newupval (lua_State *L) {
  UpVal *uv = luaM_new(L, UpVal);
  luaC_link(L, obj2gco(uv), LUA_TUPVAL);
  uv->v = &uv->u.value;
  setnilvalue(uv->v);
  return uv;
}


UpVal *luaF_findupval (lua_State *L, StkId level) {
  global_State *g = G(L);
  GCObject **pp = &L->openupval;
  UpVal *p;
  UpVal *uv;
  while (*pp != NULL && (p = ngcotouv(*pp))->v >= level) {
    lua_assert(p->v != &p->u.value);
    if (p->v == level) {  /* found a corresponding upvalue? */
      if (isdead(g, obj2gco(p)))  /* is it dead? */
        changewhite(obj2gco(p));  /* ressurect it */
      return p;
    }
    pp = &p->next;
  }
  uv = luaM_new(L, UpVal);  /* not found: create a new one */
  uv->tt = LUA_TUPVAL;
  uv->marked = luaC_white(g);
  uv->v = level;  /* current value lives in the stack */
  uv->next = *pp;  /* chain it in the proper position */
  *pp = obj2gco(uv);
  uv->u.l.prev = &g->uvhead;  /* double link it in `uvhead' list */
  uv->u.l.next = g->uvhead.u.l.next;
  uv->u.l.next->u.l.prev = uv;
  g->uvhead.u.l.next = uv;
  lua_assert(uv->u.l.next->u.l.prev == uv && uv->u.l.prev->u.l.next == uv);
  return uv;
}


static void unlinkupval (UpVal *uv) {
  lua_assert(uv->u.l.next->u.l.prev == uv && uv->u.l.prev->u.l.next == uv);
  uv->u.l.next->u.l.prev = uv->u.l.prev;  /* remove from `uvhead' list */
  uv->u.l.prev->u.l.next = uv->u.l.next;
}


void luaF_freeupval (lua_State *L, UpVal *uv) {
  if (uv->v != &uv->u.value)  /* is it open? */
    unlinkupval(uv);  /* remove from open list */
  luaM_free(L, uv);  /* free upvalue */
}


void luaF_close (lua_State *L, StkId level) {
  UpVal *uv;
  global_State *g = G(L);
  while (L->openupval != NULL && (uv = ngcotouv(L->openupval))->v >= level) {
    GCObject *o = obj2gco(uv);
    lua_assert(!isblack(o) && uv->v != &uv->u.value);
    L->openupval = uv->next;  /* remove from `open' list */
    if (isdead(g, o))
      luaF_freeupval(L, uv);  /* free upvalue */
    else {
      unlinkupval(uv);
      setobj(L, &uv->u.value, uv->v);
      uv->v = &uv->u.value;  /* now current value lives here */
      luaC_linkupval(L, uv);  /* link upvalue into `gcroot' list */
    }
  }
}


Proto *luaF_newproto (lua_State *L) {
  Proto *f = luaM_new(L, Proto);
  luaC_link(L, obj2gco(f), LUA_TPROTO);
  f->k = NULL;
  f->sizek = 0;
  f->p = NULL;
  f->sizep = 0;
  f->code = NULL;
  f->sizecode = 0;
  f->sizelineinfo = 0;
  f->sizeupvalues = 0;
  f->nups = 0;
  f->upvalues = NULL;
  f->numparams = 0;
  f->is_vararg = 0;
  f->maxstacksize = 0;
  f->lineinfo = NULL;
  f->sizelocvars = 0;
  f->locvars = NULL;
  f->linedefined = 0;
  f->lastlinedefined = 0;
  f->source = NULL;
  return f;
}


void luaF_freeproto (lua_State *L, Proto *f) {
  luaM_freearray(L, f->code, f->sizecode, Instruction);
  luaM_freearray(L, f->p, f->sizep, Proto *);
  luaM_freearray(L, f->k, f->sizek, TValue);
  luaM_freearray(L, f->lineinfo, f->sizelineinfo, int);
  luaM_freearray(L, f->locvars, f->sizelocvars, struct LocVar);
  luaM_freearray(L, f->upvalues, f->sizeupvalues, TString *);
  luaM_free(L, f);
}


void luaF_freeclosure (lua_State *L, Closure *c) {
  int size = (c->c.isC) ? sizeCclosure(c->c.nupvalues) :
                          sizeLclosure(c->l.nupvalues);
  luaM_freemem(L, c, size);
}


/*
** Look for n-th local variable at line `line' in function `func'.
** Returns NULL if not found.
*/
const char *luaF_getlocalname (const Proto *f, int local_number, int pc) {
  int i;
  for (i = 0; isizelocvars && f->locvars[i].startpc <= pc; i++) {
    if (pc < f->locvars[i].endpc) {  /* is variable active? */
      local_number--;
      if (local_number == 0)
        return getstr(f->locvars[i].varname);
    }
  }
  return NULL;  /* not found */
}

genometools-1.5.1/src/external/lua-5.1.5/src/lfunc.h000066400000000000000000000021451211610345200217530ustar00rootroot00000000000000/*
** $Id: lfunc.h,v 2.4.1.1 2007/12/27 13:02:25 roberto Exp $
** Auxiliary functions to manipulate prototypes and closures
** See Copyright Notice in lua.h
*/

#ifndef lfunc_h
#define lfunc_h


#include "lobject.h"


#define sizeCclosure(n)	(cast(int, sizeof(CClosure)) + \
                         cast(int, sizeof(TValue)*((n)-1)))

#define sizeLclosure(n)	(cast(int, sizeof(LClosure)) + \
                         cast(int, sizeof(TValue *)*((n)-1)))


LUAI_FUNC Proto *luaF_newproto (lua_State *L);
LUAI_FUNC Closure *luaF_newCclosure (lua_State *L, int nelems, Table *e);
LUAI_FUNC Closure *luaF_newLclosure (lua_State *L, int nelems, Table *e);
LUAI_FUNC UpVal *luaF_newupval (lua_State *L);
LUAI_FUNC UpVal *luaF_findupval (lua_State *L, StkId level);
LUAI_FUNC void luaF_close (lua_State *L, StkId level);
LUAI_FUNC void luaF_freeproto (lua_State *L, Proto *f);
LUAI_FUNC void luaF_freeclosure (lua_State *L, Closure *c);
LUAI_FUNC void luaF_freeupval (lua_State *L, UpVal *uv);
LUAI_FUNC const char *luaF_getlocalname (const Proto *func, int local_number,
                                         int pc);


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/lgc.c000066400000000000000000000471251211610345200214130ustar00rootroot00000000000000/*
** $Id: lgc.c,v 2.38.1.2 2011/03/18 18:05:38 roberto Exp $
** Garbage Collector
** See Copyright Notice in lua.h
*/

#include 

#define lgc_c
#define LUA_CORE

#include "lua.h"

#include "ldebug.h"
#include "ldo.h"
#include "lfunc.h"
#include "lgc.h"
#include "lmem.h"
#include "lobject.h"
#include "lstate.h"
#include "lstring.h"
#include "ltable.h"
#include "ltm.h"


#define GCSTEPSIZE	1024u
#define GCSWEEPMAX	40
#define GCSWEEPCOST	10
#define GCFINALIZECOST	100


#define maskmarks	cast_byte(~(bitmask(BLACKBIT)|WHITEBITS))

#define makewhite(g,x)	\
   ((x)->gch.marked = cast_byte(((x)->gch.marked & maskmarks) | luaC_white(g)))

#define white2gray(x)	reset2bits((x)->gch.marked, WHITE0BIT, WHITE1BIT)
#define black2gray(x)	resetbit((x)->gch.marked, BLACKBIT)

#define stringmark(s)	reset2bits((s)->tsv.marked, WHITE0BIT, WHITE1BIT)


#define isfinalized(u)		testbit((u)->marked, FINALIZEDBIT)
#define markfinalized(u)	l_setbit((u)->marked, FINALIZEDBIT)


#define KEYWEAK         bitmask(KEYWEAKBIT)
#define VALUEWEAK       bitmask(VALUEWEAKBIT)



#define markvalue(g,o) { checkconsistency(o); \
  if (iscollectable(o) && iswhite(gcvalue(o))) reallymarkobject(g,gcvalue(o)); }

#define markobject(g,t) { if (iswhite(obj2gco(t))) \
		reallymarkobject(g, obj2gco(t)); }


#define setthreshold(g)  (g->GCthreshold = (g->estimate/100) * g->gcpause)


static void removeentry (Node *n) {
  lua_assert(ttisnil(gval(n)));
  if (iscollectable(gkey(n)))
    setttype(gkey(n), LUA_TDEADKEY);  /* dead key; remove it */
}


static void reallymarkobject (global_State *g, GCObject *o) {
  lua_assert(iswhite(o) && !isdead(g, o));
  white2gray(o);
  switch (o->gch.tt) {
    case LUA_TSTRING: {
      return;
    }
    case LUA_TUSERDATA: {
      Table *mt = gco2u(o)->metatable;
      gray2black(o);  /* udata are never gray */
      if (mt) markobject(g, mt);
      markobject(g, gco2u(o)->env);
      return;
    }
    case LUA_TUPVAL: {
      UpVal *uv = gco2uv(o);
      markvalue(g, uv->v);
      if (uv->v == &uv->u.value)  /* closed? */
        gray2black(o);  /* open upvalues are never black */
      return;
    }
    case LUA_TFUNCTION: {
      gco2cl(o)->c.gclist = g->gray;
      g->gray = o;
      break;
    }
    case LUA_TTABLE: {
      gco2h(o)->gclist = g->gray;
      g->gray = o;
      break;
    }
    case LUA_TTHREAD: {
      gco2th(o)->gclist = g->gray;
      g->gray = o;
      break;
    }
    case LUA_TPROTO: {
      gco2p(o)->gclist = g->gray;
      g->gray = o;
      break;
    }
    default: lua_assert(0);
  }
}


static void marktmu (global_State *g) {
  GCObject *u = g->tmudata;
  if (u) {
    do {
      u = u->gch.next;
      makewhite(g, u);  /* may be marked, if left from previous GC */
      reallymarkobject(g, u);
    } while (u != g->tmudata);
  }
}


/* move `dead' udata that need finalization to list `tmudata' */
size_t luaC_separateudata (lua_State *L, int all) {
  global_State *g = G(L);
  size_t deadmem = 0;
  GCObject **p = &g->mainthread->next;
  GCObject *curr;
  while ((curr = *p) != NULL) {
    if (!(iswhite(curr) || all) || isfinalized(gco2u(curr)))
      p = &curr->gch.next;  /* don't bother with them */
    else if (fasttm(L, gco2u(curr)->metatable, TM_GC) == NULL) {
      markfinalized(gco2u(curr));  /* don't need finalization */
      p = &curr->gch.next;
    }
    else {  /* must call its gc method */
      deadmem += sizeudata(gco2u(curr));
      markfinalized(gco2u(curr));
      *p = curr->gch.next;
      /* link `curr' at the end of `tmudata' list */
      if (g->tmudata == NULL)  /* list is empty? */
        g->tmudata = curr->gch.next = curr;  /* creates a circular list */
      else {
        curr->gch.next = g->tmudata->gch.next;
        g->tmudata->gch.next = curr;
        g->tmudata = curr;
      }
    }
  }
  return deadmem;
}


static int traversetable (global_State *g, Table *h) {
  int i;
  int weakkey = 0;
  int weakvalue = 0;
  const TValue *mode;
  if (h->metatable)
    markobject(g, h->metatable);
  mode = gfasttm(g, h->metatable, TM_MODE);
  if (mode && ttisstring(mode)) {  /* is there a weak mode? */
    weakkey = (strchr(svalue(mode), 'k') != NULL);
    weakvalue = (strchr(svalue(mode), 'v') != NULL);
    if (weakkey || weakvalue) {  /* is really weak? */
      h->marked &= ~(KEYWEAK | VALUEWEAK);  /* clear bits */
      h->marked |= cast_byte((weakkey << KEYWEAKBIT) |
                             (weakvalue << VALUEWEAKBIT));
      h->gclist = g->weak;  /* must be cleared after GC, ... */
      g->weak = obj2gco(h);  /* ... so put in the appropriate list */
    }
  }
  if (weakkey && weakvalue) return 1;
  if (!weakvalue) {
    i = h->sizearray;
    while (i--)
      markvalue(g, &h->array[i]);
  }
  i = sizenode(h);
  while (i--) {
    Node *n = gnode(h, i);
    lua_assert(ttype(gkey(n)) != LUA_TDEADKEY || ttisnil(gval(n)));
    if (ttisnil(gval(n)))
      removeentry(n);  /* remove empty entries */
    else {
      lua_assert(!ttisnil(gkey(n)));
      if (!weakkey) markvalue(g, gkey(n));
      if (!weakvalue) markvalue(g, gval(n));
    }
  }
  return weakkey || weakvalue;
}


/*
** All marks are conditional because a GC may happen while the
** prototype is still being created
*/
static void traverseproto (global_State *g, Proto *f) {
  int i;
  if (f->source) stringmark(f->source);
  for (i=0; isizek; i++)  /* mark literals */
    markvalue(g, &f->k[i]);
  for (i=0; isizeupvalues; i++) {  /* mark upvalue names */
    if (f->upvalues[i])
      stringmark(f->upvalues[i]);
  }
  for (i=0; isizep; i++) {  /* mark nested protos */
    if (f->p[i])
      markobject(g, f->p[i]);
  }
  for (i=0; isizelocvars; i++) {  /* mark local-variable names */
    if (f->locvars[i].varname)
      stringmark(f->locvars[i].varname);
  }
}



static void traverseclosure (global_State *g, Closure *cl) {
  markobject(g, cl->c.env);
  if (cl->c.isC) {
    int i;
    for (i=0; ic.nupvalues; i++)  /* mark its upvalues */
      markvalue(g, &cl->c.upvalue[i]);
  }
  else {
    int i;
    lua_assert(cl->l.nupvalues == cl->l.p->nups);
    markobject(g, cl->l.p);
    for (i=0; il.nupvalues; i++)  /* mark its upvalues */
      markobject(g, cl->l.upvals[i]);
  }
}


static void checkstacksizes (lua_State *L, StkId max) {
  int ci_used = cast_int(L->ci - L->base_ci);  /* number of `ci' in use */
  int s_used = cast_int(max - L->stack);  /* part of stack in use */
  if (L->size_ci > LUAI_MAXCALLS)  /* handling overflow? */
    return;  /* do not touch the stacks */
  if (4*ci_used < L->size_ci && 2*BASIC_CI_SIZE < L->size_ci)
    luaD_reallocCI(L, L->size_ci/2);  /* still big enough... */
  condhardstacktests(luaD_reallocCI(L, ci_used + 1));
  if (4*s_used < L->stacksize &&
      2*(BASIC_STACK_SIZE+EXTRA_STACK) < L->stacksize)
    luaD_reallocstack(L, L->stacksize/2);  /* still big enough... */
  condhardstacktests(luaD_reallocstack(L, s_used));
}


static void traversestack (global_State *g, lua_State *l) {
  StkId o, lim;
  CallInfo *ci;
  markvalue(g, gt(l));
  lim = l->top;
  for (ci = l->base_ci; ci <= l->ci; ci++) {
    lua_assert(ci->top <= l->stack_last);
    if (lim < ci->top) lim = ci->top;
  }
  for (o = l->stack; o < l->top; o++)
    markvalue(g, o);
  for (; o <= lim; o++)
    setnilvalue(o);
  checkstacksizes(l, lim);
}


/*
** traverse one gray object, turning it to black.
** Returns `quantity' traversed.
*/
static l_mem propagatemark (global_State *g) {
  GCObject *o = g->gray;
  lua_assert(isgray(o));
  gray2black(o);
  switch (o->gch.tt) {
    case LUA_TTABLE: {
      Table *h = gco2h(o);
      g->gray = h->gclist;
      if (traversetable(g, h))  /* table is weak? */
        black2gray(o);  /* keep it gray */
      return sizeof(Table) + sizeof(TValue) * h->sizearray +
                             sizeof(Node) * sizenode(h);
    }
    case LUA_TFUNCTION: {
      Closure *cl = gco2cl(o);
      g->gray = cl->c.gclist;
      traverseclosure(g, cl);
      return (cl->c.isC) ? sizeCclosure(cl->c.nupvalues) :
                           sizeLclosure(cl->l.nupvalues);
    }
    case LUA_TTHREAD: {
      lua_State *th = gco2th(o);
      g->gray = th->gclist;
      th->gclist = g->grayagain;
      g->grayagain = o;
      black2gray(o);
      traversestack(g, th);
      return sizeof(lua_State) + sizeof(TValue) * th->stacksize +
                                 sizeof(CallInfo) * th->size_ci;
    }
    case LUA_TPROTO: {
      Proto *p = gco2p(o);
      g->gray = p->gclist;
      traverseproto(g, p);
      return sizeof(Proto) + sizeof(Instruction) * p->sizecode +
                             sizeof(Proto *) * p->sizep +
                             sizeof(TValue) * p->sizek + 
                             sizeof(int) * p->sizelineinfo +
                             sizeof(LocVar) * p->sizelocvars +
                             sizeof(TString *) * p->sizeupvalues;
    }
    default: lua_assert(0); return 0;
  }
}


static size_t propagateall (global_State *g) {
  size_t m = 0;
  while (g->gray) m += propagatemark(g);
  return m;
}


/*
** The next function tells whether a key or value can be cleared from
** a weak table. Non-collectable objects are never removed from weak
** tables. Strings behave as `values', so are never removed too. for
** other objects: if really collected, cannot keep them; for userdata
** being finalized, keep them in keys, but not in values
*/
static int iscleared (const TValue *o, int iskey) {
  if (!iscollectable(o)) return 0;
  if (ttisstring(o)) {
    stringmark(rawtsvalue(o));  /* strings are `values', so are never weak */
    return 0;
  }
  return iswhite(gcvalue(o)) ||
    (ttisuserdata(o) && (!iskey && isfinalized(uvalue(o))));
}


/*
** clear collected entries from weaktables
*/
static void cleartable (GCObject *l) {
  while (l) {
    Table *h = gco2h(l);
    int i = h->sizearray;
    lua_assert(testbit(h->marked, VALUEWEAKBIT) ||
               testbit(h->marked, KEYWEAKBIT));
    if (testbit(h->marked, VALUEWEAKBIT)) {
      while (i--) {
        TValue *o = &h->array[i];
        if (iscleared(o, 0))  /* value was collected? */
          setnilvalue(o);  /* remove value */
      }
    }
    i = sizenode(h);
    while (i--) {
      Node *n = gnode(h, i);
      if (!ttisnil(gval(n)) &&  /* non-empty entry? */
          (iscleared(key2tval(n), 1) || iscleared(gval(n), 0))) {
        setnilvalue(gval(n));  /* remove value ... */
        removeentry(n);  /* remove entry from table */
      }
    }
    l = h->gclist;
  }
}


static void freeobj (lua_State *L, GCObject *o) {
  switch (o->gch.tt) {
    case LUA_TPROTO: luaF_freeproto(L, gco2p(o)); break;
    case LUA_TFUNCTION: luaF_freeclosure(L, gco2cl(o)); break;
    case LUA_TUPVAL: luaF_freeupval(L, gco2uv(o)); break;
    case LUA_TTABLE: luaH_free(L, gco2h(o)); break;
    case LUA_TTHREAD: {
      lua_assert(gco2th(o) != L && gco2th(o) != G(L)->mainthread);
      luaE_freethread(L, gco2th(o));
      break;
    }
    case LUA_TSTRING: {
      G(L)->strt.nuse--;
      luaM_freemem(L, o, sizestring(gco2ts(o)));
      break;
    }
    case LUA_TUSERDATA: {
      luaM_freemem(L, o, sizeudata(gco2u(o)));
      break;
    }
    default: lua_assert(0);
  }
}



#define sweepwholelist(L,p)	sweeplist(L,p,MAX_LUMEM)


static GCObject **sweeplist (lua_State *L, GCObject **p, lu_mem count) {
  GCObject *curr;
  global_State *g = G(L);
  int deadmask = otherwhite(g);
  while ((curr = *p) != NULL && count-- > 0) {
    if (curr->gch.tt == LUA_TTHREAD)  /* sweep open upvalues of each thread */
      sweepwholelist(L, &gco2th(curr)->openupval);
    if ((curr->gch.marked ^ WHITEBITS) & deadmask) {  /* not dead? */
      lua_assert(!isdead(g, curr) || testbit(curr->gch.marked, FIXEDBIT));
      makewhite(g, curr);  /* make it white (for next cycle) */
      p = &curr->gch.next;
    }
    else {  /* must erase `curr' */
      lua_assert(isdead(g, curr) || deadmask == bitmask(SFIXEDBIT));
      *p = curr->gch.next;
      if (curr == g->rootgc)  /* is the first element of the list? */
        g->rootgc = curr->gch.next;  /* adjust first */
      freeobj(L, curr);
    }
  }
  return p;
}


static void checkSizes (lua_State *L) {
  global_State *g = G(L);
  /* check size of string hash */
  if (g->strt.nuse < cast(lu_int32, g->strt.size/4) &&
      g->strt.size > MINSTRTABSIZE*2)
    luaS_resize(L, g->strt.size/2);  /* table is too big */
  /* check size of buffer */
  if (luaZ_sizebuffer(&g->buff) > LUA_MINBUFFER*2) {  /* buffer too big? */
    size_t newsize = luaZ_sizebuffer(&g->buff) / 2;
    luaZ_resizebuffer(L, &g->buff, newsize);
  }
}


static void GCTM (lua_State *L) {
  global_State *g = G(L);
  GCObject *o = g->tmudata->gch.next;  /* get first element */
  Udata *udata = rawgco2u(o);
  const TValue *tm;
  /* remove udata from `tmudata' */
  if (o == g->tmudata)  /* last element? */
    g->tmudata = NULL;
  else
    g->tmudata->gch.next = udata->uv.next;
  udata->uv.next = g->mainthread->next;  /* return it to `root' list */
  g->mainthread->next = o;
  makewhite(g, o);
  tm = fasttm(L, udata->uv.metatable, TM_GC);
  if (tm != NULL) {
    lu_byte oldah = L->allowhook;
    lu_mem oldt = g->GCthreshold;
    L->allowhook = 0;  /* stop debug hooks during GC tag method */
    g->GCthreshold = 2*g->totalbytes;  /* avoid GC steps */
    setobj2s(L, L->top, tm);
    setuvalue(L, L->top+1, udata);
    L->top += 2;
    luaD_call(L, L->top - 2, 0);
    L->allowhook = oldah;  /* restore hooks */
    g->GCthreshold = oldt;  /* restore threshold */
  }
}


/*
** Call all GC tag methods
*/
void luaC_callGCTM (lua_State *L) {
  while (G(L)->tmudata)
    GCTM(L);
}


void luaC_freeall (lua_State *L) {
  global_State *g = G(L);
  int i;
  g->currentwhite = WHITEBITS | bitmask(SFIXEDBIT);  /* mask to collect all elements */
  sweepwholelist(L, &g->rootgc);
  for (i = 0; i < g->strt.size; i++)  /* free all string lists */
    sweepwholelist(L, &g->strt.hash[i]);
}


static void markmt (global_State *g) {
  int i;
  for (i=0; imt[i]) markobject(g, g->mt[i]);
}


/* mark root set */
static void markroot (lua_State *L) {
  global_State *g = G(L);
  g->gray = NULL;
  g->grayagain = NULL;
  g->weak = NULL;
  markobject(g, g->mainthread);
  /* make global table be traversed before main stack */
  markvalue(g, gt(g->mainthread));
  markvalue(g, registry(L));
  markmt(g);
  g->gcstate = GCSpropagate;
}


static void remarkupvals (global_State *g) {
  UpVal *uv;
  for (uv = g->uvhead.u.l.next; uv != &g->uvhead; uv = uv->u.l.next) {
    lua_assert(uv->u.l.next->u.l.prev == uv && uv->u.l.prev->u.l.next == uv);
    if (isgray(obj2gco(uv)))
      markvalue(g, uv->v);
  }
}


static void atomic (lua_State *L) {
  global_State *g = G(L);
  size_t udsize;  /* total size of userdata to be finalized */
  /* remark occasional upvalues of (maybe) dead threads */
  remarkupvals(g);
  /* traverse objects cautch by write barrier and by 'remarkupvals' */
  propagateall(g);
  /* remark weak tables */
  g->gray = g->weak;
  g->weak = NULL;
  lua_assert(!iswhite(obj2gco(g->mainthread)));
  markobject(g, L);  /* mark running thread */
  markmt(g);  /* mark basic metatables (again) */
  propagateall(g);
  /* remark gray again */
  g->gray = g->grayagain;
  g->grayagain = NULL;
  propagateall(g);
  udsize = luaC_separateudata(L, 0);  /* separate userdata to be finalized */
  marktmu(g);  /* mark `preserved' userdata */
  udsize += propagateall(g);  /* remark, to propagate `preserveness' */
  cleartable(g->weak);  /* remove collected objects from weak tables */
  /* flip current white */
  g->currentwhite = cast_byte(otherwhite(g));
  g->sweepstrgc = 0;
  g->sweepgc = &g->rootgc;
  g->gcstate = GCSsweepstring;
  g->estimate = g->totalbytes - udsize;  /* first estimate */
}


static l_mem singlestep (lua_State *L) {
  global_State *g = G(L);
  /*lua_checkmemory(L);*/
  switch (g->gcstate) {
    case GCSpause: {
      markroot(L);  /* start a new collection */
      return 0;
    }
    case GCSpropagate: {
      if (g->gray)
        return propagatemark(g);
      else {  /* no more `gray' objects */
        atomic(L);  /* finish mark phase */
        return 0;
      }
    }
    case GCSsweepstring: {
      lu_mem old = g->totalbytes;
      sweepwholelist(L, &g->strt.hash[g->sweepstrgc++]);
      if (g->sweepstrgc >= g->strt.size)  /* nothing more to sweep? */
        g->gcstate = GCSsweep;  /* end sweep-string phase */
      lua_assert(old >= g->totalbytes);
      g->estimate -= old - g->totalbytes;
      return GCSWEEPCOST;
    }
    case GCSsweep: {
      lu_mem old = g->totalbytes;
      g->sweepgc = sweeplist(L, g->sweepgc, GCSWEEPMAX);
      if (*g->sweepgc == NULL) {  /* nothing more to sweep? */
        checkSizes(L);
        g->gcstate = GCSfinalize;  /* end sweep phase */
      }
      lua_assert(old >= g->totalbytes);
      g->estimate -= old - g->totalbytes;
      return GCSWEEPMAX*GCSWEEPCOST;
    }
    case GCSfinalize: {
      if (g->tmudata) {
        GCTM(L);
        if (g->estimate > GCFINALIZECOST)
          g->estimate -= GCFINALIZECOST;
        return GCFINALIZECOST;
      }
      else {
        g->gcstate = GCSpause;  /* end collection */
        g->gcdept = 0;
        return 0;
      }
    }
    default: lua_assert(0); return 0;
  }
}


void luaC_step (lua_State *L) {
  global_State *g = G(L);
  l_mem lim = (GCSTEPSIZE/100) * g->gcstepmul;
  if (lim == 0)
    lim = (MAX_LUMEM-1)/2;  /* no limit */
  g->gcdept += g->totalbytes - g->GCthreshold;
  do {
    lim -= singlestep(L);
    if (g->gcstate == GCSpause)
      break;
  } while (lim > 0);
  if (g->gcstate != GCSpause) {
    if (g->gcdept < GCSTEPSIZE)
      g->GCthreshold = g->totalbytes + GCSTEPSIZE;  /* - lim/g->gcstepmul;*/
    else {
      g->gcdept -= GCSTEPSIZE;
      g->GCthreshold = g->totalbytes;
    }
  }
  else {
    setthreshold(g);
  }
}


void luaC_fullgc (lua_State *L) {
  global_State *g = G(L);
  if (g->gcstate <= GCSpropagate) {
    /* reset sweep marks to sweep all elements (returning them to white) */
    g->sweepstrgc = 0;
    g->sweepgc = &g->rootgc;
    /* reset other collector lists */
    g->gray = NULL;
    g->grayagain = NULL;
    g->weak = NULL;
    g->gcstate = GCSsweepstring;
  }
  lua_assert(g->gcstate != GCSpause && g->gcstate != GCSpropagate);
  /* finish any pending sweep phase */
  while (g->gcstate != GCSfinalize) {
    lua_assert(g->gcstate == GCSsweepstring || g->gcstate == GCSsweep);
    singlestep(L);
  }
  markroot(L);
  while (g->gcstate != GCSpause) {
    singlestep(L);
  }
  setthreshold(g);
}


void luaC_barrierf (lua_State *L, GCObject *o, GCObject *v) {
  global_State *g = G(L);
  lua_assert(isblack(o) && iswhite(v) && !isdead(g, v) && !isdead(g, o));
  lua_assert(g->gcstate != GCSfinalize && g->gcstate != GCSpause);
  lua_assert(ttype(&o->gch) != LUA_TTABLE);
  /* must keep invariant? */
  if (g->gcstate == GCSpropagate)
    reallymarkobject(g, v);  /* restore invariant */
  else  /* don't mind */
    makewhite(g, o);  /* mark as white just to avoid other barriers */
}


void luaC_barrierback (lua_State *L, Table *t) {
  global_State *g = G(L);
  GCObject *o = obj2gco(t);
  lua_assert(isblack(o) && !isdead(g, o));
  lua_assert(g->gcstate != GCSfinalize && g->gcstate != GCSpause);
  black2gray(o);  /* make table gray (again) */
  t->gclist = g->grayagain;
  g->grayagain = o;
}


void luaC_link (lua_State *L, GCObject *o, lu_byte tt) {
  global_State *g = G(L);
  o->gch.next = g->rootgc;
  g->rootgc = o;
  o->gch.marked = luaC_white(g);
  o->gch.tt = tt;
}


void luaC_linkupval (lua_State *L, UpVal *uv) {
  global_State *g = G(L);
  GCObject *o = obj2gco(uv);
  o->gch.next = g->rootgc;  /* link upvalue into `rootgc' list */
  g->rootgc = o;
  if (isgray(o)) { 
    if (g->gcstate == GCSpropagate) {
      gray2black(o);  /* closed upvalues need barrier */
      luaC_barrier(L, uv, uv->v);
    }
    else {  /* sweep phase: sweep it (turning it into white) */
      makewhite(g, o);
      lua_assert(g->gcstate != GCSfinalize && g->gcstate != GCSpause);
    }
  }
}

genometools-1.5.1/src/external/lua-5.1.5/src/lgc.h000066400000000000000000000061271211610345200214150ustar00rootroot00000000000000/*
** $Id: lgc.h,v 2.15.1.1 2007/12/27 13:02:25 roberto Exp $
** Garbage Collector
** See Copyright Notice in lua.h
*/

#ifndef lgc_h
#define lgc_h


#include "lobject.h"


/*
** Possible states of the Garbage Collector
*/
#define GCSpause	0
#define GCSpropagate	1
#define GCSsweepstring	2
#define GCSsweep	3
#define GCSfinalize	4


/*
** some userful bit tricks
*/
#define resetbits(x,m)	((x) &= cast(lu_byte, ~(m)))
#define setbits(x,m)	((x) |= (m))
#define testbits(x,m)	((x) & (m))
#define bitmask(b)	(1<<(b))
#define bit2mask(b1,b2)	(bitmask(b1) | bitmask(b2))
#define l_setbit(x,b)	setbits(x, bitmask(b))
#define resetbit(x,b)	resetbits(x, bitmask(b))
#define testbit(x,b)	testbits(x, bitmask(b))
#define set2bits(x,b1,b2)	setbits(x, (bit2mask(b1, b2)))
#define reset2bits(x,b1,b2)	resetbits(x, (bit2mask(b1, b2)))
#define test2bits(x,b1,b2)	testbits(x, (bit2mask(b1, b2)))



/*
** Layout for bit use in `marked' field:
** bit 0 - object is white (type 0)
** bit 1 - object is white (type 1)
** bit 2 - object is black
** bit 3 - for userdata: has been finalized
** bit 3 - for tables: has weak keys
** bit 4 - for tables: has weak values
** bit 5 - object is fixed (should not be collected)
** bit 6 - object is "super" fixed (only the main thread)
*/


#define WHITE0BIT	0
#define WHITE1BIT	1
#define BLACKBIT	2
#define FINALIZEDBIT	3
#define KEYWEAKBIT	3
#define VALUEWEAKBIT	4
#define FIXEDBIT	5
#define SFIXEDBIT	6
#define WHITEBITS	bit2mask(WHITE0BIT, WHITE1BIT)


#define iswhite(x)      test2bits((x)->gch.marked, WHITE0BIT, WHITE1BIT)
#define isblack(x)      testbit((x)->gch.marked, BLACKBIT)
#define isgray(x)	(!isblack(x) && !iswhite(x))

#define otherwhite(g)	(g->currentwhite ^ WHITEBITS)
#define isdead(g,v)	((v)->gch.marked & otherwhite(g) & WHITEBITS)

#define changewhite(x)	((x)->gch.marked ^= WHITEBITS)
#define gray2black(x)	l_setbit((x)->gch.marked, BLACKBIT)

#define valiswhite(x)	(iscollectable(x) && iswhite(gcvalue(x)))

#define luaC_white(g)	cast(lu_byte, (g)->currentwhite & WHITEBITS)


#define luaC_checkGC(L) { \
  condhardstacktests(luaD_reallocstack(L, L->stacksize - EXTRA_STACK - 1)); \
  if (G(L)->totalbytes >= G(L)->GCthreshold) \
	luaC_step(L); }


#define luaC_barrier(L,p,v) { if (valiswhite(v) && isblack(obj2gco(p)))  \
	luaC_barrierf(L,obj2gco(p),gcvalue(v)); }

#define luaC_barriert(L,t,v) { if (valiswhite(v) && isblack(obj2gco(t)))  \
	luaC_barrierback(L,t); }

#define luaC_objbarrier(L,p,o)  \
	{ if (iswhite(obj2gco(o)) && isblack(obj2gco(p))) \
		luaC_barrierf(L,obj2gco(p),obj2gco(o)); }

#define luaC_objbarriert(L,t,o)  \
   { if (iswhite(obj2gco(o)) && isblack(obj2gco(t))) luaC_barrierback(L,t); }

LUAI_FUNC size_t luaC_separateudata (lua_State *L, int all);
LUAI_FUNC void luaC_callGCTM (lua_State *L);
LUAI_FUNC void luaC_freeall (lua_State *L);
LUAI_FUNC void luaC_step (lua_State *L);
LUAI_FUNC void luaC_fullgc (lua_State *L);
LUAI_FUNC void luaC_link (lua_State *L, GCObject *o, lu_byte tt);
LUAI_FUNC void luaC_linkupval (lua_State *L, UpVal *uv);
LUAI_FUNC void luaC_barrierf (lua_State *L, GCObject *o, GCObject *v);
LUAI_FUNC void luaC_barrierback (lua_State *L, Table *t);


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/linit.c000066400000000000000000000013751211610345200217620ustar00rootroot00000000000000/*
** $Id: linit.c,v 1.14.1.1 2007/12/27 13:02:25 roberto Exp $
** Initialization of libraries for lua.c
** See Copyright Notice in lua.h
*/


#define linit_c
#define LUA_LIB

#include "lua.h"

#include "lualib.h"
#include "lauxlib.h"


static const luaL_Reg lualibs[] = {
  {"", luaopen_base},
  {LUA_LOADLIBNAME, luaopen_package},
  {LUA_TABLIBNAME, luaopen_table},
  {LUA_IOLIBNAME, luaopen_io},
  {LUA_OSLIBNAME, luaopen_os},
  {LUA_STRLIBNAME, luaopen_string},
  {LUA_MATHLIBNAME, luaopen_math},
  {LUA_DBLIBNAME, luaopen_debug},
  {NULL, NULL}
};


LUALIB_API void luaL_openlibs (lua_State *L) {
  const luaL_Reg *lib = lualibs;
  for (; lib->func; lib++) {
    lua_pushcfunction(L, lib->func);
    lua_pushstring(L, lib->name);
    lua_call(L, 1, 0);
  }
}

genometools-1.5.1/src/external/lua-5.1.5/src/liolib.c000066400000000000000000000322321211610345200221110ustar00rootroot00000000000000/*
** $Id: liolib.c,v 2.73.1.4 2010/05/14 15:33:51 roberto Exp $
** Standard I/O (and system) library
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 
#include 

#define liolib_c
#define LUA_LIB

#include "lua.h"

#include "lauxlib.h"
#include "lualib.h"



#define IO_INPUT	1
#define IO_OUTPUT	2


static const char *const fnames[] = {"input", "output"};


static int pushresult (lua_State *L, int i, const char *filename) {
  int en = errno;  /* calls to Lua API may change this value */
  if (i) {
    lua_pushboolean(L, 1);
    return 1;
  }
  else {
    lua_pushnil(L);
    if (filename)
      lua_pushfstring(L, "%s: %s", filename, strerror(en));
    else
      lua_pushfstring(L, "%s", strerror(en));
    lua_pushinteger(L, en);
    return 3;
  }
}


static void fileerror (lua_State *L, int arg, const char *filename) {
  lua_pushfstring(L, "%s: %s", filename, strerror(errno));
  luaL_argerror(L, arg, lua_tostring(L, -1));
}


#define tofilep(L)	((FILE **)luaL_checkudata(L, 1, LUA_FILEHANDLE))


static int io_type (lua_State *L) {
  void *ud;
  luaL_checkany(L, 1);
  ud = lua_touserdata(L, 1);
  lua_getfield(L, LUA_REGISTRYINDEX, LUA_FILEHANDLE);
  if (ud == NULL || !lua_getmetatable(L, 1) || !lua_rawequal(L, -2, -1))
    lua_pushnil(L);  /* not a file */
  else if (*((FILE **)ud) == NULL)
    lua_pushliteral(L, "closed file");
  else
    lua_pushliteral(L, "file");
  return 1;
}


static FILE *tofile (lua_State *L) {
  FILE **f = tofilep(L);
  if (*f == NULL)
    luaL_error(L, "attempt to use a closed file");
  return *f;
}



/*
** When creating file handles, always creates a `closed' file handle
** before opening the actual file; so, if there is a memory error, the
** file is not left opened.
*/
static FILE **newfile (lua_State *L) {
  FILE **pf = (FILE **)lua_newuserdata(L, sizeof(FILE *));
  *pf = NULL;  /* file handle is currently `closed' */
  luaL_getmetatable(L, LUA_FILEHANDLE);
  lua_setmetatable(L, -2);
  return pf;
}


/*
** function to (not) close the standard files stdin, stdout, and stderr
*/
static int io_noclose (lua_State *L) {
  lua_pushnil(L);
  lua_pushliteral(L, "cannot close standard file");
  return 2;
}


/*
** function to close 'popen' files
*/
static int io_pclose (lua_State *L) {
  FILE **p = tofilep(L);
  int ok = lua_pclose(L, *p);
  *p = NULL;
  return pushresult(L, ok, NULL);
}


/*
** function to close regular files
*/
static int io_fclose (lua_State *L) {
  FILE **p = tofilep(L);
  int ok = (fclose(*p) == 0);
  *p = NULL;
  return pushresult(L, ok, NULL);
}


static int aux_close (lua_State *L) {
  lua_getfenv(L, 1);
  lua_getfield(L, -1, "__close");
  return (lua_tocfunction(L, -1))(L);
}


static int io_close (lua_State *L) {
  if (lua_isnone(L, 1))
    lua_rawgeti(L, LUA_ENVIRONINDEX, IO_OUTPUT);
  tofile(L);  /* make sure argument is a file */
  return aux_close(L);
}


static int io_gc (lua_State *L) {
  FILE *f = *tofilep(L);
  /* ignore closed files */
  if (f != NULL)
    aux_close(L);
  return 0;
}


static int io_tostring (lua_State *L) {
  FILE *f = *tofilep(L);
  if (f == NULL)
    lua_pushliteral(L, "file (closed)");
  else
    lua_pushfstring(L, "file (%p)", f);
  return 1;
}


static int io_open (lua_State *L) {
  const char *filename = luaL_checkstring(L, 1);
  const char *mode = luaL_optstring(L, 2, "r");
  FILE **pf = newfile(L);
  *pf = fopen(filename, mode);
  return (*pf == NULL) ? pushresult(L, 0, filename) : 1;
}


/*
** this function has a separated environment, which defines the
** correct __close for 'popen' files
*/
static int io_popen (lua_State *L) {
  const char *filename = luaL_checkstring(L, 1);
  const char *mode = luaL_optstring(L, 2, "r");
  FILE **pf = newfile(L);
  *pf = lua_popen(L, filename, mode);
  return (*pf == NULL) ? pushresult(L, 0, filename) : 1;
}


static int io_tmpfile (lua_State *L) {
  FILE **pf = newfile(L);
  *pf = tmpfile();
  return (*pf == NULL) ? pushresult(L, 0, NULL) : 1;
}


static FILE *getiofile (lua_State *L, int findex) {
  FILE *f;
  lua_rawgeti(L, LUA_ENVIRONINDEX, findex);
  f = *(FILE **)lua_touserdata(L, -1);
  if (f == NULL)
    luaL_error(L, "standard %s file is closed", fnames[findex - 1]);
  return f;
}


static int g_iofile (lua_State *L, int f, const char *mode) {
  if (!lua_isnoneornil(L, 1)) {
    const char *filename = lua_tostring(L, 1);
    if (filename) {
      FILE **pf = newfile(L);
      *pf = fopen(filename, mode);
      if (*pf == NULL)
        fileerror(L, 1, filename);
    }
    else {
      tofile(L);  /* check that it's a valid file handle */
      lua_pushvalue(L, 1);
    }
    lua_rawseti(L, LUA_ENVIRONINDEX, f);
  }
  /* return current value */
  lua_rawgeti(L, LUA_ENVIRONINDEX, f);
  return 1;
}


static int io_input (lua_State *L) {
  return g_iofile(L, IO_INPUT, "r");
}


static int io_output (lua_State *L) {
  return g_iofile(L, IO_OUTPUT, "w");
}


static int io_readline (lua_State *L);


static void aux_lines (lua_State *L, int idx, int toclose) {
  lua_pushvalue(L, idx);
  lua_pushboolean(L, toclose);  /* close/not close file when finished */
  lua_pushcclosure(L, io_readline, 2);
}


static int f_lines (lua_State *L) {
  tofile(L);  /* check that it's a valid file handle */
  aux_lines(L, 1, 0);
  return 1;
}


static int io_lines (lua_State *L) {
  if (lua_isnoneornil(L, 1)) {  /* no arguments? */
    /* will iterate over default input */
    lua_rawgeti(L, LUA_ENVIRONINDEX, IO_INPUT);
    return f_lines(L);
  }
  else {
    const char *filename = luaL_checkstring(L, 1);
    FILE **pf = newfile(L);
    *pf = fopen(filename, "r");
    if (*pf == NULL)
      fileerror(L, 1, filename);
    aux_lines(L, lua_gettop(L), 1);
    return 1;
  }
}


/*
** {======================================================
** READ
** =======================================================
*/


static int read_number (lua_State *L, FILE *f) {
  lua_Number d;
  if (fscanf(f, LUA_NUMBER_SCAN, &d) == 1) {
    lua_pushnumber(L, d);
    return 1;
  }
  else {
    lua_pushnil(L);  /* "result" to be removed */
    return 0;  /* read fails */
  }
}


static int test_eof (lua_State *L, FILE *f) {
  int c = getc(f);
  ungetc(c, f);
  lua_pushlstring(L, NULL, 0);
  return (c != EOF);
}


static int read_line (lua_State *L, FILE *f) {
  luaL_Buffer b;
  luaL_buffinit(L, &b);
  for (;;) {
    size_t l;
    char *p = luaL_prepbuffer(&b);
    if (fgets(p, LUAL_BUFFERSIZE, f) == NULL) {  /* eof? */
      luaL_pushresult(&b);  /* close buffer */
      return (lua_objlen(L, -1) > 0);  /* check whether read something */
    }
    l = strlen(p);
    if (l == 0 || p[l-1] != '\n')
      luaL_addsize(&b, l);
    else {
      luaL_addsize(&b, l - 1);  /* do not include `eol' */
      luaL_pushresult(&b);  /* close buffer */
      return 1;  /* read at least an `eol' */
    }
  }
}


static int read_chars (lua_State *L, FILE *f, size_t n) {
  size_t rlen;  /* how much to read */
  size_t nr;  /* number of chars actually read */
  luaL_Buffer b;
  luaL_buffinit(L, &b);
  rlen = LUAL_BUFFERSIZE;  /* try to read that much each time */
  do {
    char *p = luaL_prepbuffer(&b);
    if (rlen > n) rlen = n;  /* cannot read more than asked */
    nr = fread(p, sizeof(char), rlen, f);
    luaL_addsize(&b, nr);
    n -= nr;  /* still have to read `n' chars */
  } while (n > 0 && nr == rlen);  /* until end of count or eof */
  luaL_pushresult(&b);  /* close buffer */
  return (n == 0 || lua_objlen(L, -1) > 0);
}


static int g_read (lua_State *L, FILE *f, int first) {
  int nargs = lua_gettop(L) - 1;
  int success;
  int n;
  clearerr(f);
  if (nargs == 0) {  /* no arguments? */
    success = read_line(L, f);
    n = first+1;  /* to return 1 result */
  }
  else {  /* ensure stack space for all results and for auxlib's buffer */
    luaL_checkstack(L, nargs+LUA_MINSTACK, "too many arguments");
    success = 1;
    for (n = first; nargs-- && success; n++) {
      if (lua_type(L, n) == LUA_TNUMBER) {
        size_t l = (size_t)lua_tointeger(L, n);
        success = (l == 0) ? test_eof(L, f) : read_chars(L, f, l);
      }
      else {
        const char *p = lua_tostring(L, n);
        luaL_argcheck(L, p && p[0] == '*', n, "invalid option");
        switch (p[1]) {
          case 'n':  /* number */
            success = read_number(L, f);
            break;
          case 'l':  /* line */
            success = read_line(L, f);
            break;
          case 'a':  /* file */
            read_chars(L, f, ~((size_t)0));  /* read MAX_SIZE_T chars */
            success = 1; /* always success */
            break;
          default:
            return luaL_argerror(L, n, "invalid format");
        }
      }
    }
  }
  if (ferror(f))
    return pushresult(L, 0, NULL);
  if (!success) {
    lua_pop(L, 1);  /* remove last result */
    lua_pushnil(L);  /* push nil instead */
  }
  return n - first;
}


static int io_read (lua_State *L) {
  return g_read(L, getiofile(L, IO_INPUT), 1);
}


static int f_read (lua_State *L) {
  return g_read(L, tofile(L), 2);
}


static int io_readline (lua_State *L) {
  FILE *f = *(FILE **)lua_touserdata(L, lua_upvalueindex(1));
  int sucess;
  if (f == NULL)  /* file is already closed? */
    luaL_error(L, "file is already closed");
  sucess = read_line(L, f);
  if (ferror(f))
    return luaL_error(L, "%s", strerror(errno));
  if (sucess) return 1;
  else {  /* EOF */
    if (lua_toboolean(L, lua_upvalueindex(2))) {  /* generator created file? */
      lua_settop(L, 0);
      lua_pushvalue(L, lua_upvalueindex(1));
      aux_close(L);  /* close it */
    }
    return 0;
  }
}

/* }====================================================== */


static int g_write (lua_State *L, FILE *f, int arg) {
  int nargs = lua_gettop(L) - 1;
  int status = 1;
  for (; nargs--; arg++) {
    if (lua_type(L, arg) == LUA_TNUMBER) {
      /* optimization: could be done exactly as for strings */
      status = status &&
          fprintf(f, LUA_NUMBER_FMT, lua_tonumber(L, arg)) > 0;
    }
    else {
      size_t l;
      const char *s = luaL_checklstring(L, arg, &l);
      status = status && (fwrite(s, sizeof(char), l, f) == l);
    }
  }
  return pushresult(L, status, NULL);
}


static int io_write (lua_State *L) {
  return g_write(L, getiofile(L, IO_OUTPUT), 1);
}


static int f_write (lua_State *L) {
  return g_write(L, tofile(L), 2);
}


static int f_seek (lua_State *L) {
  static const int mode[] = {SEEK_SET, SEEK_CUR, SEEK_END};
  static const char *const modenames[] = {"set", "cur", "end", NULL};
  FILE *f = tofile(L);
  int op = luaL_checkoption(L, 2, "cur", modenames);
  long offset = luaL_optlong(L, 3, 0);
  op = fseek(f, offset, mode[op]);
  if (op)
    return pushresult(L, 0, NULL);  /* error */
  else {
    lua_pushinteger(L, ftell(f));
    return 1;
  }
}


static int f_setvbuf (lua_State *L) {
  static const int mode[] = {_IONBF, _IOFBF, _IOLBF};
  static const char *const modenames[] = {"no", "full", "line", NULL};
  FILE *f = tofile(L);
  int op = luaL_checkoption(L, 2, NULL, modenames);
  lua_Integer sz = luaL_optinteger(L, 3, LUAL_BUFFERSIZE);
  int res = setvbuf(f, NULL, mode[op], sz);
  return pushresult(L, res == 0, NULL);
}



static int io_flush (lua_State *L) {
  return pushresult(L, fflush(getiofile(L, IO_OUTPUT)) == 0, NULL);
}


static int f_flush (lua_State *L) {
  return pushresult(L, fflush(tofile(L)) == 0, NULL);
}


static const luaL_Reg iolib[] = {
  {"close", io_close},
  {"flush", io_flush},
  {"input", io_input},
  {"lines", io_lines},
  {"open", io_open},
  {"output", io_output},
  {"popen", io_popen},
  {"read", io_read},
  {"tmpfile", io_tmpfile},
  {"type", io_type},
  {"write", io_write},
  {NULL, NULL}
};


static const luaL_Reg flib[] = {
  {"close", io_close},
  {"flush", f_flush},
  {"lines", f_lines},
  {"read", f_read},
  {"seek", f_seek},
  {"setvbuf", f_setvbuf},
  {"write", f_write},
  {"__gc", io_gc},
  {"__tostring", io_tostring},
  {NULL, NULL}
};


static void createmeta (lua_State *L) {
  luaL_newmetatable(L, LUA_FILEHANDLE);  /* create metatable for file handles */
  lua_pushvalue(L, -1);  /* push metatable */
  lua_setfield(L, -2, "__index");  /* metatable.__index = metatable */
  luaL_register(L, NULL, flib);  /* file methods */
}


static void createstdfile (lua_State *L, FILE *f, int k, const char *fname) {
  *newfile(L) = f;
  if (k > 0) {
    lua_pushvalue(L, -1);
    lua_rawseti(L, LUA_ENVIRONINDEX, k);
  }
  lua_pushvalue(L, -2);  /* copy environment */
  lua_setfenv(L, -2);  /* set it */
  lua_setfield(L, -3, fname);
}


static void newfenv (lua_State *L, lua_CFunction cls) {
  lua_createtable(L, 0, 1);
  lua_pushcfunction(L, cls);
  lua_setfield(L, -2, "__close");
}


LUALIB_API int luaopen_io (lua_State *L) {
  createmeta(L);
  /* create (private) environment (with fields IO_INPUT, IO_OUTPUT, __close) */
  newfenv(L, io_fclose);
  lua_replace(L, LUA_ENVIRONINDEX);
  /* open library */
  luaL_register(L, LUA_IOLIBNAME, iolib);
  /* create (and set) default files */
  newfenv(L, io_noclose);  /* close function for default files */
  createstdfile(L, stdin, IO_INPUT, "stdin");
  createstdfile(L, stdout, IO_OUTPUT, "stdout");
  createstdfile(L, stderr, 0, "stderr");
  lua_pop(L, 1);  /* pop environment for default files */
  lua_getfield(L, -1, "popen");
  newfenv(L, io_pclose);  /* create environment for 'popen' */
  lua_setfenv(L, -2);  /* set fenv for 'popen' */
  lua_pop(L, 1);  /* pop 'popen' */
  return 1;
}

genometools-1.5.1/src/external/lua-5.1.5/src/llex.c000066400000000000000000000303251211610345200216040ustar00rootroot00000000000000/*
** $Id: llex.c,v 2.20.1.2 2009/11/23 14:58:22 roberto Exp $
** Lexical Analyzer
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 

#define llex_c
#define LUA_CORE

#include "lua.h"

#include "ldo.h"
#include "llex.h"
#include "lobject.h"
#include "lparser.h"
#include "lstate.h"
#include "lstring.h"
#include "ltable.h"
#include "lzio.h"



#define next(ls) (ls->current = zgetc(ls->z))




#define currIsNewline(ls)	(ls->current == '\n' || ls->current == '\r')


/* ORDER RESERVED */
const char *const luaX_tokens [] = {
    "and", "break", "do", "else", "elseif",
    "end", "false", "for", "function", "if",
    "in", "local", "nil", "not", "or", "repeat",
    "return", "then", "true", "until", "while",
    "..", "...", "==", ">=", "<=", "~=",
    "", "", "", "",
    NULL
};


#define save_and_next(ls) (save(ls, ls->current), next(ls))


static void save (LexState *ls, int c) {
  Mbuffer *b = ls->buff;
  if (b->n + 1 > b->buffsize) {
    size_t newsize;
    if (b->buffsize >= MAX_SIZET/2)
      luaX_lexerror(ls, "lexical element too long", 0);
    newsize = b->buffsize * 2;
    luaZ_resizebuffer(ls->L, b, newsize);
  }
  b->buffer[b->n++] = cast(char, c);
}


void luaX_init (lua_State *L) {
  int i;
  for (i=0; itsv.reserved = cast_byte(i+1);  /* reserved word */
  }
}


#define MAXSRC          80


const char *luaX_token2str (LexState *ls, int token) {
  if (token < FIRST_RESERVED) {
    lua_assert(token == cast(unsigned char, token));
    return (iscntrl(token)) ? luaO_pushfstring(ls->L, "char(%d)", token) :
                              luaO_pushfstring(ls->L, "%c", token);
  }
  else
    return luaX_tokens[token-FIRST_RESERVED];
}


static const char *txtToken (LexState *ls, int token) {
  switch (token) {
    case TK_NAME:
    case TK_STRING:
    case TK_NUMBER:
      save(ls, '\0');
      return luaZ_buffer(ls->buff);
    default:
      return luaX_token2str(ls, token);
  }
}


void luaX_lexerror (LexState *ls, const char *msg, int token) {
  char buff[MAXSRC];
  luaO_chunkid(buff, getstr(ls->source), MAXSRC);
  msg = luaO_pushfstring(ls->L, "%s:%d: %s", buff, ls->linenumber, msg);
  if (token)
    luaO_pushfstring(ls->L, "%s near " LUA_QS, msg, txtToken(ls, token));
  luaD_throw(ls->L, LUA_ERRSYNTAX);
}


void luaX_syntaxerror (LexState *ls, const char *msg) {
  luaX_lexerror(ls, msg, ls->t.token);
}


TString *luaX_newstring (LexState *ls, const char *str, size_t l) {
  lua_State *L = ls->L;
  TString *ts = luaS_newlstr(L, str, l);
  TValue *o = luaH_setstr(L, ls->fs->h, ts);  /* entry for `str' */
  if (ttisnil(o)) {
    setbvalue(o, 1);  /* make sure `str' will not be collected */
    luaC_checkGC(L);
  }
  return ts;
}


static void inclinenumber (LexState *ls) {
  int old = ls->current;
  lua_assert(currIsNewline(ls));
  next(ls);  /* skip `\n' or `\r' */
  if (currIsNewline(ls) && ls->current != old)
    next(ls);  /* skip `\n\r' or `\r\n' */
  if (++ls->linenumber >= MAX_INT)
    luaX_syntaxerror(ls, "chunk has too many lines");
}


void luaX_setinput (lua_State *L, LexState *ls, ZIO *z, TString *source) {
  ls->decpoint = '.';
  ls->L = L;
  ls->lookahead.token = TK_EOS;  /* no look-ahead token */
  ls->z = z;
  ls->fs = NULL;
  ls->linenumber = 1;
  ls->lastline = 1;
  ls->source = source;
  luaZ_resizebuffer(ls->L, ls->buff, LUA_MINBUFFER);  /* initialize buffer */
  next(ls);  /* read first char */
}



/*
** =======================================================
** LEXICAL ANALYZER
** =======================================================
*/



static int check_next (LexState *ls, const char *set) {
  if (!strchr(set, ls->current))
    return 0;
  save_and_next(ls);
  return 1;
}


static void buffreplace (LexState *ls, char from, char to) {
  size_t n = luaZ_bufflen(ls->buff);
  char *p = luaZ_buffer(ls->buff);
  while (n--)
    if (p[n] == from) p[n] = to;
}


static void trydecpoint (LexState *ls, SemInfo *seminfo) {
  /* format error: try to update decimal point separator */
  struct lconv *cv = localeconv();
  char old = ls->decpoint;
  ls->decpoint = (cv ? cv->decimal_point[0] : '.');
  buffreplace(ls, old, ls->decpoint);  /* try updated decimal separator */
  if (!luaO_str2d(luaZ_buffer(ls->buff), &seminfo->r)) {
    /* format error with correct decimal point: no more options */
    buffreplace(ls, ls->decpoint, '.');  /* undo change (for error message) */
    luaX_lexerror(ls, "malformed number", TK_NUMBER);
  }
}


/* LUA_NUMBER */
static void read_numeral (LexState *ls, SemInfo *seminfo) {
  lua_assert(isdigit(ls->current));
  do {
    save_and_next(ls);
  } while (isdigit(ls->current) || ls->current == '.');
  if (check_next(ls, "Ee"))  /* `E'? */
    check_next(ls, "+-");  /* optional exponent sign */
  while (isalnum(ls->current) || ls->current == '_')
    save_and_next(ls);
  save(ls, '\0');
  buffreplace(ls, '.', ls->decpoint);  /* follow locale for decimal point */
  if (!luaO_str2d(luaZ_buffer(ls->buff), &seminfo->r))  /* format error? */
    trydecpoint(ls, seminfo); /* try to update decimal point separator */
}


static int skip_sep (LexState *ls) {
  int count = 0;
  int s = ls->current;
  lua_assert(s == '[' || s == ']');
  save_and_next(ls);
  while (ls->current == '=') {
    save_and_next(ls);
    count++;
  }
  return (ls->current == s) ? count : (-count) - 1;
}


static void read_long_string (LexState *ls, SemInfo *seminfo, int sep) {
  int cont = 0;
  (void)(cont);  /* avoid warnings when `cont' is not used */
  save_and_next(ls);  /* skip 2nd `[' */
  if (currIsNewline(ls))  /* string starts with a newline? */
    inclinenumber(ls);  /* skip it */
  for (;;) {
    switch (ls->current) {
      case EOZ:
        luaX_lexerror(ls, (seminfo) ? "unfinished long string" :
                                   "unfinished long comment", TK_EOS);
        break;  /* to avoid warnings */
#if defined(LUA_COMPAT_LSTR)
      case '[': {
        if (skip_sep(ls) == sep) {
          save_and_next(ls);  /* skip 2nd `[' */
          cont++;
#if LUA_COMPAT_LSTR == 1
          if (sep == 0)
            luaX_lexerror(ls, "nesting of [[...]] is deprecated", '[');
#endif
        }
        break;
      }
#endif
      case ']': {
        if (skip_sep(ls) == sep) {
          save_and_next(ls);  /* skip 2nd `]' */
#if defined(LUA_COMPAT_LSTR) && LUA_COMPAT_LSTR == 2
          cont--;
          if (sep == 0 && cont >= 0) break;
#endif
          goto endloop;
        }
        break;
      }
      case '\n':
      case '\r': {
        save(ls, '\n');
        inclinenumber(ls);
        if (!seminfo) luaZ_resetbuffer(ls->buff);  /* avoid wasting space */
        break;
      }
      default: {
        if (seminfo) save_and_next(ls);
        else next(ls);
      }
    }
  } endloop:
  if (seminfo)
    seminfo->ts = luaX_newstring(ls, luaZ_buffer(ls->buff) + (2 + sep),
                                     luaZ_bufflen(ls->buff) - 2*(2 + sep));
}


static void read_string (LexState *ls, int del, SemInfo *seminfo) {
  save_and_next(ls);
  while (ls->current != del) {
    switch (ls->current) {
      case EOZ:
        luaX_lexerror(ls, "unfinished string", TK_EOS);
        continue;  /* to avoid warnings */
      case '\n':
      case '\r':
        luaX_lexerror(ls, "unfinished string", TK_STRING);
        continue;  /* to avoid warnings */
      case '\\': {
        int c;
        next(ls);  /* do not save the `\' */
        switch (ls->current) {
          case 'a': c = '\a'; break;
          case 'b': c = '\b'; break;
          case 'f': c = '\f'; break;
          case 'n': c = '\n'; break;
          case 'r': c = '\r'; break;
          case 't': c = '\t'; break;
          case 'v': c = '\v'; break;
          case '\n':  /* go through */
          case '\r': save(ls, '\n'); inclinenumber(ls); continue;
          case EOZ: continue;  /* will raise an error next loop */
          default: {
            if (!isdigit(ls->current))
              save_and_next(ls);  /* handles \\, \", \', and \? */
            else {  /* \xxx */
              int i = 0;
              c = 0;
              do {
                c = 10*c + (ls->current-'0');
                next(ls);
              } while (++i<3 && isdigit(ls->current));
              if (c > UCHAR_MAX)
                luaX_lexerror(ls, "escape sequence too large", TK_STRING);
              save(ls, c);
            }
            continue;
          }
        }
        save(ls, c);
        next(ls);
        continue;
      }
      default:
        save_and_next(ls);
    }
  }
  save_and_next(ls);  /* skip delimiter */
  seminfo->ts = luaX_newstring(ls, luaZ_buffer(ls->buff) + 1,
                                   luaZ_bufflen(ls->buff) - 2);
}


static int llex (LexState *ls, SemInfo *seminfo) {
  luaZ_resetbuffer(ls->buff);
  for (;;) {
    switch (ls->current) {
      case '\n':
      case '\r': {
        inclinenumber(ls);
        continue;
      }
      case '-': {
        next(ls);
        if (ls->current != '-') return '-';
        /* else is a comment */
        next(ls);
        if (ls->current == '[') {
          int sep = skip_sep(ls);
          luaZ_resetbuffer(ls->buff);  /* `skip_sep' may dirty the buffer */
          if (sep >= 0) {
            read_long_string(ls, NULL, sep);  /* long comment */
            luaZ_resetbuffer(ls->buff);
            continue;
          }
        }
        /* else short comment */
        while (!currIsNewline(ls) && ls->current != EOZ)
          next(ls);
        continue;
      }
      case '[': {
        int sep = skip_sep(ls);
        if (sep >= 0) {
          read_long_string(ls, seminfo, sep);
          return TK_STRING;
        }
        else if (sep == -1) return '[';
        else luaX_lexerror(ls, "invalid long string delimiter", TK_STRING);
      }
      case '=': {
        next(ls);
        if (ls->current != '=') return '=';
        else { next(ls); return TK_EQ; }
      }
      case '<': {
        next(ls);
        if (ls->current != '=') return '<';
        else { next(ls); return TK_LE; }
      }
      case '>': {
        next(ls);
        if (ls->current != '=') return '>';
        else { next(ls); return TK_GE; }
      }
      case '~': {
        next(ls);
        if (ls->current != '=') return '~';
        else { next(ls); return TK_NE; }
      }
      case '"':
      case '\'': {
        read_string(ls, ls->current, seminfo);
        return TK_STRING;
      }
      case '.': {
        save_and_next(ls);
        if (check_next(ls, ".")) {
          if (check_next(ls, "."))
            return TK_DOTS;   /* ... */
          else return TK_CONCAT;   /* .. */
        }
        else if (!isdigit(ls->current)) return '.';
        else {
          read_numeral(ls, seminfo);
          return TK_NUMBER;
        }
      }
      case EOZ: {
        return TK_EOS;
      }
      default: {
        if (isspace(ls->current)) {
          lua_assert(!currIsNewline(ls));
          next(ls);
          continue;
        }
        else if (isdigit(ls->current)) {
          read_numeral(ls, seminfo);
          return TK_NUMBER;
        }
        else if (isalpha(ls->current) || ls->current == '_') {
          /* identifier or reserved word */
          TString *ts;
          do {
            save_and_next(ls);
          } while (isalnum(ls->current) || ls->current == '_');
          ts = luaX_newstring(ls, luaZ_buffer(ls->buff),
                                  luaZ_bufflen(ls->buff));
          if (ts->tsv.reserved > 0)  /* reserved word? */
            return ts->tsv.reserved - 1 + FIRST_RESERVED;
          else {
            seminfo->ts = ts;
            return TK_NAME;
          }
        }
        else {
          int c = ls->current;
          next(ls);
          return c;  /* single-char tokens (+ - / ...) */
        }
      }
    }
  }
}


void luaX_next (LexState *ls) {
  ls->lastline = ls->linenumber;
  if (ls->lookahead.token != TK_EOS) {  /* is there a look-ahead token? */
    ls->t = ls->lookahead;  /* use this one */
    ls->lookahead.token = TK_EOS;  /* and discharge it */
  }
  else
    ls->t.token = llex(ls, &ls->t.seminfo);  /* read next token */
}


void luaX_lookahead (LexState *ls) {
  lua_assert(ls->lookahead.token == TK_EOS);
  ls->lookahead.token = llex(ls, &ls->lookahead.seminfo);
}

genometools-1.5.1/src/external/lua-5.1.5/src/llex.h000066400000000000000000000042011211610345200216030ustar00rootroot00000000000000/*
** $Id: llex.h,v 1.58.1.1 2007/12/27 13:02:25 roberto Exp $
** Lexical Analyzer
** See Copyright Notice in lua.h
*/

#ifndef llex_h
#define llex_h

#include "lobject.h"
#include "lzio.h"


#define FIRST_RESERVED	257

/* maximum length of a reserved word */
#define TOKEN_LEN	(sizeof("function")/sizeof(char))


/*
* WARNING: if you change the order of this enumeration,
* grep "ORDER RESERVED"
*/
enum RESERVED {
  /* terminal symbols denoted by reserved words */
  TK_AND = FIRST_RESERVED, TK_BREAK,
  TK_DO, TK_ELSE, TK_ELSEIF, TK_END, TK_FALSE, TK_FOR, TK_FUNCTION,
  TK_IF, TK_IN, TK_LOCAL, TK_NIL, TK_NOT, TK_OR, TK_REPEAT,
  TK_RETURN, TK_THEN, TK_TRUE, TK_UNTIL, TK_WHILE,
  /* other terminal symbols */
  TK_CONCAT, TK_DOTS, TK_EQ, TK_GE, TK_LE, TK_NE, TK_NUMBER,
  TK_NAME, TK_STRING, TK_EOS
};

/* number of reserved words */
#define NUM_RESERVED	(cast(int, TK_WHILE-FIRST_RESERVED+1))


/* array with token `names' */
LUAI_DATA const char *const luaX_tokens [];


typedef union {
  lua_Number r;
  TString *ts;
} SemInfo;  /* semantics information */


typedef struct Token {
  int token;
  SemInfo seminfo;
} Token;


typedef struct LexState {
  int current;  /* current character (charint) */
  int linenumber;  /* input line counter */
  int lastline;  /* line of last token `consumed' */
  Token t;  /* current token */
  Token lookahead;  /* look ahead token */
  struct FuncState *fs;  /* `FuncState' is private to the parser */
  struct lua_State *L;
  ZIO *z;  /* input stream */
  Mbuffer *buff;  /* buffer for tokens */
  TString *source;  /* current source name */
  char decpoint;  /* locale decimal point */
} LexState;


LUAI_FUNC void luaX_init (lua_State *L);
LUAI_FUNC void luaX_setinput (lua_State *L, LexState *ls, ZIO *z,
                              TString *source);
LUAI_FUNC TString *luaX_newstring (LexState *ls, const char *str, size_t l);
LUAI_FUNC void luaX_next (LexState *ls);
LUAI_FUNC void luaX_lookahead (LexState *ls);
LUAI_FUNC void luaX_lexerror (LexState *ls, const char *msg, int token);
LUAI_FUNC void luaX_syntaxerror (LexState *ls, const char *s);
LUAI_FUNC const char *luaX_token2str (LexState *ls, int token);


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/llimits.h000066400000000000000000000044551211610345200223270ustar00rootroot00000000000000/*
** $Id: llimits.h,v 1.69.1.1 2007/12/27 13:02:25 roberto Exp $
** Limits, basic types, and some other `installation-dependent' definitions
** See Copyright Notice in lua.h
*/

#ifndef llimits_h
#define llimits_h


#include 
#include 


#include "lua.h"


typedef LUAI_UINT32 lu_int32;

typedef LUAI_UMEM lu_mem;

typedef LUAI_MEM l_mem;



/* chars used as small naturals (so that `char' is reserved for characters) */
typedef unsigned char lu_byte;


#define MAX_SIZET	((size_t)(~(size_t)0)-2)

#define MAX_LUMEM	((lu_mem)(~(lu_mem)0)-2)


#define MAX_INT (INT_MAX-2)  /* maximum value of an int (-2 for safety) */

/*
** conversion of pointer to integer
** this is for hashing only; there is no problem if the integer
** cannot hold the whole pointer value
*/
#define IntPoint(p)  ((unsigned int)(lu_mem)(p))



/* type to ensure maximum alignment */
typedef LUAI_USER_ALIGNMENT_T L_Umaxalign;


/* result of a `usual argument conversion' over lua_Number */
typedef LUAI_UACNUMBER l_uacNumber;


/* internal assertions for in-house debugging */
#ifdef lua_assert

#define check_exp(c,e)		(lua_assert(c), (e))
#define api_check(l,e)		lua_assert(e)

#else

#define lua_assert(c)		((void)0)
#define check_exp(c,e)		(e)
#define api_check		luai_apicheck

#endif


#ifndef UNUSED
#define UNUSED(x)	((void)(x))	/* to avoid warnings */
#endif


#ifndef cast
#define cast(t, exp)	((t)(exp))
#endif

#define cast_byte(i)	cast(lu_byte, (i))
#define cast_num(i)	cast(lua_Number, (i))
#define cast_int(i)	cast(int, (i))



/*
** type for virtual-machine instructions
** must be an unsigned with (at least) 4 bytes (see details in lopcodes.h)
*/
typedef lu_int32 Instruction;



/* maximum stack for a Lua function */
#define MAXSTACK	250



/* minimum size for the string table (must be power of 2) */
#ifndef MINSTRTABSIZE
#define MINSTRTABSIZE	32
#endif


/* minimum size for string buffer */
#ifndef LUA_MINBUFFER
#define LUA_MINBUFFER	32
#endif


#ifndef lua_lock
#define lua_lock(L)     ((void) 0) 
#define lua_unlock(L)   ((void) 0)
#endif

#ifndef luai_threadyield
#define luai_threadyield(L)     {lua_unlock(L); lua_lock(L);}
#endif


/*
** macro to control inclusion of some hard tests on stack reallocation
*/ 
#ifndef HARDSTACKTESTS
#define condhardstacktests(x)	((void)0)
#else
#define condhardstacktests(x)	x
#endif

#endif
genometools-1.5.1/src/external/lua-5.1.5/src/lmathlib.c000066400000000000000000000133071211610345200224350ustar00rootroot00000000000000/*
** $Id: lmathlib.c,v 1.67.1.1 2007/12/27 13:02:25 roberto Exp $
** Standard mathematical library
** See Copyright Notice in lua.h
*/


#include 
#include 

#define lmathlib_c
#define LUA_LIB

#include "lua.h"

#include "lauxlib.h"
#include "lualib.h"


#undef PI
#define PI (3.14159265358979323846)
#define RADIANS_PER_DEGREE (PI/180.0)



static int math_abs (lua_State *L) {
  lua_pushnumber(L, fabs(luaL_checknumber(L, 1)));
  return 1;
}

static int math_sin (lua_State *L) {
  lua_pushnumber(L, sin(luaL_checknumber(L, 1)));
  return 1;
}

static int math_sinh (lua_State *L) {
  lua_pushnumber(L, sinh(luaL_checknumber(L, 1)));
  return 1;
}

static int math_cos (lua_State *L) {
  lua_pushnumber(L, cos(luaL_checknumber(L, 1)));
  return 1;
}

static int math_cosh (lua_State *L) {
  lua_pushnumber(L, cosh(luaL_checknumber(L, 1)));
  return 1;
}

static int math_tan (lua_State *L) {
  lua_pushnumber(L, tan(luaL_checknumber(L, 1)));
  return 1;
}

static int math_tanh (lua_State *L) {
  lua_pushnumber(L, tanh(luaL_checknumber(L, 1)));
  return 1;
}

static int math_asin (lua_State *L) {
  lua_pushnumber(L, asin(luaL_checknumber(L, 1)));
  return 1;
}

static int math_acos (lua_State *L) {
  lua_pushnumber(L, acos(luaL_checknumber(L, 1)));
  return 1;
}

static int math_atan (lua_State *L) {
  lua_pushnumber(L, atan(luaL_checknumber(L, 1)));
  return 1;
}

static int math_atan2 (lua_State *L) {
  lua_pushnumber(L, atan2(luaL_checknumber(L, 1), luaL_checknumber(L, 2)));
  return 1;
}

static int math_ceil (lua_State *L) {
  lua_pushnumber(L, ceil(luaL_checknumber(L, 1)));
  return 1;
}

static int math_floor (lua_State *L) {
  lua_pushnumber(L, floor(luaL_checknumber(L, 1)));
  return 1;
}

static int math_fmod (lua_State *L) {
  lua_pushnumber(L, fmod(luaL_checknumber(L, 1), luaL_checknumber(L, 2)));
  return 1;
}

static int math_modf (lua_State *L) {
  double ip;
  double fp = modf(luaL_checknumber(L, 1), &ip);
  lua_pushnumber(L, ip);
  lua_pushnumber(L, fp);
  return 2;
}

static int math_sqrt (lua_State *L) {
  lua_pushnumber(L, sqrt(luaL_checknumber(L, 1)));
  return 1;
}

static int math_pow (lua_State *L) {
  lua_pushnumber(L, pow(luaL_checknumber(L, 1), luaL_checknumber(L, 2)));
  return 1;
}

static int math_log (lua_State *L) {
  lua_pushnumber(L, log(luaL_checknumber(L, 1)));
  return 1;
}

static int math_log10 (lua_State *L) {
  lua_pushnumber(L, log10(luaL_checknumber(L, 1)));
  return 1;
}

static int math_exp (lua_State *L) {
  lua_pushnumber(L, exp(luaL_checknumber(L, 1)));
  return 1;
}

static int math_deg (lua_State *L) {
  lua_pushnumber(L, luaL_checknumber(L, 1)/RADIANS_PER_DEGREE);
  return 1;
}

static int math_rad (lua_State *L) {
  lua_pushnumber(L, luaL_checknumber(L, 1)*RADIANS_PER_DEGREE);
  return 1;
}

static int math_frexp (lua_State *L) {
  int e;
  lua_pushnumber(L, frexp(luaL_checknumber(L, 1), &e));
  lua_pushinteger(L, e);
  return 2;
}

static int math_ldexp (lua_State *L) {
  lua_pushnumber(L, ldexp(luaL_checknumber(L, 1), luaL_checkint(L, 2)));
  return 1;
}



static int math_min (lua_State *L) {
  int n = lua_gettop(L);  /* number of arguments */
  lua_Number dmin = luaL_checknumber(L, 1);
  int i;
  for (i=2; i<=n; i++) {
    lua_Number d = luaL_checknumber(L, i);
    if (d < dmin)
      dmin = d;
  }
  lua_pushnumber(L, dmin);
  return 1;
}


static int math_max (lua_State *L) {
  int n = lua_gettop(L);  /* number of arguments */
  lua_Number dmax = luaL_checknumber(L, 1);
  int i;
  for (i=2; i<=n; i++) {
    lua_Number d = luaL_checknumber(L, i);
    if (d > dmax)
      dmax = d;
  }
  lua_pushnumber(L, dmax);
  return 1;
}


static int math_random (lua_State *L) {
  /* the `%' avoids the (rare) case of r==1, and is needed also because on
     some systems (SunOS!) `rand()' may return a value larger than RAND_MAX */
  lua_Number r = (lua_Number)(rand()%RAND_MAX) / (lua_Number)RAND_MAX;
  switch (lua_gettop(L)) {  /* check number of arguments */
    case 0: {  /* no arguments */
      lua_pushnumber(L, r);  /* Number between 0 and 1 */
      break;
    }
    case 1: {  /* only upper limit */
      int u = luaL_checkint(L, 1);
      luaL_argcheck(L, 1<=u, 1, "interval is empty");
      lua_pushnumber(L, floor(r*u)+1);  /* int between 1 and `u' */
      break;
    }
    case 2: {  /* lower and upper limits */
      int l = luaL_checkint(L, 1);
      int u = luaL_checkint(L, 2);
      luaL_argcheck(L, l<=u, 2, "interval is empty");
      lua_pushnumber(L, floor(r*(u-l+1))+l);  /* int between `l' and `u' */
      break;
    }
    default: return luaL_error(L, "wrong number of arguments");
  }
  return 1;
}


static int math_randomseed (lua_State *L) {
  srand(luaL_checkint(L, 1));
  return 0;
}


static const luaL_Reg mathlib[] = {
  {"abs",   math_abs},
  {"acos",  math_acos},
  {"asin",  math_asin},
  {"atan2", math_atan2},
  {"atan",  math_atan},
  {"ceil",  math_ceil},
  {"cosh",   math_cosh},
  {"cos",   math_cos},
  {"deg",   math_deg},
  {"exp",   math_exp},
  {"floor", math_floor},
  {"fmod",   math_fmod},
  {"frexp", math_frexp},
  {"ldexp", math_ldexp},
  {"log10", math_log10},
  {"log",   math_log},
  {"max",   math_max},
  {"min",   math_min},
  {"modf",   math_modf},
  {"pow",   math_pow},
  {"rad",   math_rad},
  {"random",     math_random},
  {"randomseed", math_randomseed},
  {"sinh",   math_sinh},
  {"sin",   math_sin},
  {"sqrt",  math_sqrt},
  {"tanh",   math_tanh},
  {"tan",   math_tan},
  {NULL, NULL}
};


/*
** Open math library
*/
LUALIB_API int luaopen_math (lua_State *L) {
  luaL_register(L, LUA_MATHLIBNAME, mathlib);
  lua_pushnumber(L, PI);
  lua_setfield(L, -2, "pi");
  lua_pushnumber(L, HUGE_VAL);
  lua_setfield(L, -2, "huge");
#if defined(LUA_COMPAT_MOD)
  lua_getfield(L, -1, "fmod");
  lua_setfield(L, -2, "mod");
#endif
  return 1;
}

genometools-1.5.1/src/external/lua-5.1.5/src/lmem.c000066400000000000000000000041741211610345200215750ustar00rootroot00000000000000/*
** $Id: lmem.c,v 1.70.1.1 2007/12/27 13:02:25 roberto Exp $
** Interface to Memory Manager
** See Copyright Notice in lua.h
*/


#include 

#define lmem_c
#define LUA_CORE

#include "lua.h"

#include "ldebug.h"
#include "ldo.h"
#include "lmem.h"
#include "lobject.h"
#include "lstate.h"



/*
** About the realloc function:
** void * frealloc (void *ud, void *ptr, size_t osize, size_t nsize);
** (`osize' is the old size, `nsize' is the new size)
**
** Lua ensures that (ptr == NULL) iff (osize == 0).
**
** * frealloc(ud, NULL, 0, x) creates a new block of size `x'
**
** * frealloc(ud, p, x, 0) frees the block `p'
** (in this specific case, frealloc must return NULL).
** particularly, frealloc(ud, NULL, 0, 0) does nothing
** (which is equivalent to free(NULL) in ANSI C)
**
** frealloc returns NULL if it cannot create or reallocate the area
** (any reallocation to an equal or smaller size cannot fail!)
*/



#define MINSIZEARRAY	4


void *luaM_growaux_ (lua_State *L, void *block, int *size, size_t size_elems,
                     int limit, const char *errormsg) {
  void *newblock;
  int newsize;
  if (*size >= limit/2) {  /* cannot double it? */
    if (*size >= limit)  /* cannot grow even a little? */
      luaG_runerror(L, errormsg);
    newsize = limit;  /* still have at least one free place */
  }
  else {
    newsize = (*size)*2;
    if (newsize < MINSIZEARRAY)
      newsize = MINSIZEARRAY;  /* minimum size */
  }
  newblock = luaM_reallocv(L, block, *size, newsize, size_elems);
  *size = newsize;  /* update only when everything else is OK */
  return newblock;
}


void *luaM_toobig (lua_State *L) {
  luaG_runerror(L, "memory allocation error: block too big");
  return NULL;  /* to avoid warnings */
}



/*
** generic allocation routine.
*/
void *luaM_realloc_ (lua_State *L, void *block, size_t osize, size_t nsize) {
  global_State *g = G(L);
  lua_assert((osize == 0) == (block == NULL));
  block = (*g->frealloc)(g->ud, block, osize, nsize);
  if (block == NULL && nsize > 0)
    luaD_throw(L, LUA_ERRMEM);
  lua_assert((nsize == 0) == (block == NULL));
  g->totalbytes = (g->totalbytes - osize) + nsize;
  return block;
}

genometools-1.5.1/src/external/lua-5.1.5/src/lmem.h000066400000000000000000000027261211610345200216030ustar00rootroot00000000000000/*
** $Id: lmem.h,v 1.31.1.1 2007/12/27 13:02:25 roberto Exp $
** Interface to Memory Manager
** See Copyright Notice in lua.h
*/

#ifndef lmem_h
#define lmem_h


#include 

#include "llimits.h"
#include "lua.h"

#define MEMERRMSG	"not enough memory"


#define luaM_reallocv(L,b,on,n,e) \
	((cast(size_t, (n)+1) <= MAX_SIZET/(e)) ?  /* +1 to avoid warnings */ \
		luaM_realloc_(L, (b), (on)*(e), (n)*(e)) : \
		luaM_toobig(L))

#define luaM_freemem(L, b, s)	luaM_realloc_(L, (b), (s), 0)
#define luaM_free(L, b)		luaM_realloc_(L, (b), sizeof(*(b)), 0)
#define luaM_freearray(L, b, n, t)   luaM_reallocv(L, (b), n, 0, sizeof(t))

#define luaM_malloc(L,t)	luaM_realloc_(L, NULL, 0, (t))
#define luaM_new(L,t)		cast(t *, luaM_malloc(L, sizeof(t)))
#define luaM_newvector(L,n,t) \
		cast(t *, luaM_reallocv(L, NULL, 0, n, sizeof(t)))

#define luaM_growvector(L,v,nelems,size,t,limit,e) \
          if ((nelems)+1 > (size)) \
            ((v)=cast(t *, luaM_growaux_(L,v,&(size),sizeof(t),limit,e)))

#define luaM_reallocvector(L, v,oldn,n,t) \
   ((v)=cast(t *, luaM_reallocv(L, v, oldn, n, sizeof(t))))


LUAI_FUNC void *luaM_realloc_ (lua_State *L, void *block, size_t oldsize,
                                                          size_t size);
LUAI_FUNC void *luaM_toobig (lua_State *L);
LUAI_FUNC void *luaM_growaux_ (lua_State *L, void *block, int *size,
                               size_t size_elem, int limit,
                               const char *errormsg);

#endif

genometools-1.5.1/src/external/lua-5.1.5/src/loadlib.c000066400000000000000000000454201211610345200222500ustar00rootroot00000000000000/*
** $Id: loadlib.c,v 1.52.1.4 2009/09/09 13:17:16 roberto Exp $
** Dynamic library loader for Lua
** See Copyright Notice in lua.h
**
** This module contains an implementation of loadlib for Unix systems
** that have dlfcn, an implementation for Darwin (Mac OS X), an
** implementation for Windows, and a stub for other systems.
*/


#include 
#include 


#define loadlib_c
#define LUA_LIB

#include "lua.h"

#include "lauxlib.h"
#include "lualib.h"


/* prefix for open functions in C libraries */
#define LUA_POF		"luaopen_"

/* separator for open functions in C libraries */
#define LUA_OFSEP	"_"


#define LIBPREFIX	"LOADLIB: "

#define POF		LUA_POF
#define LIB_FAIL	"open"


/* error codes for ll_loadfunc */
#define ERRLIB		1
#define ERRFUNC		2

#define setprogdir(L)		((void)0)


static void ll_unloadlib (void *lib);
static void *ll_load (lua_State *L, const char *path);
static lua_CFunction ll_sym (lua_State *L, void *lib, const char *sym);



#if defined(LUA_DL_DLOPEN)
/*
** {========================================================================
** This is an implementation of loadlib based on the dlfcn interface.
** The dlfcn interface is available in Linux, SunOS, Solaris, IRIX, FreeBSD,
** NetBSD, AIX 4.2, HPUX 11, and  probably most other Unix flavors, at least
** as an emulation layer on top of native functions.
** =========================================================================
*/

#include 

static void ll_unloadlib (void *lib) {
  dlclose(lib);
}


static void *ll_load (lua_State *L, const char *path) {
  void *lib = dlopen(path, RTLD_NOW);
  if (lib == NULL) lua_pushstring(L, dlerror());
  return lib;
}


static lua_CFunction ll_sym (lua_State *L, void *lib, const char *sym) {
  lua_CFunction f = (lua_CFunction)dlsym(lib, sym);
  if (f == NULL) lua_pushstring(L, dlerror());
  return f;
}

/* }====================================================== */



#elif defined(LUA_DL_DLL)
/*
** {======================================================================
** This is an implementation of loadlib for Windows using native functions.
** =======================================================================
*/

#include 


#undef setprogdir

static void setprogdir (lua_State *L) {
  char buff[MAX_PATH + 1];
  char *lb;
  DWORD nsize = sizeof(buff)/sizeof(char);
  DWORD n = GetModuleFileNameA(NULL, buff, nsize);
  if (n == 0 || n == nsize || (lb = strrchr(buff, '\\')) == NULL)
    luaL_error(L, "unable to get ModuleFileName");
  else {
    *lb = '\0';
    luaL_gsub(L, lua_tostring(L, -1), LUA_EXECDIR, buff);
    lua_remove(L, -2);  /* remove original string */
  }
}


static void pusherror (lua_State *L) {
  int error = GetLastError();
  char buffer[128];
  if (FormatMessageA(FORMAT_MESSAGE_IGNORE_INSERTS | FORMAT_MESSAGE_FROM_SYSTEM,
      NULL, error, 0, buffer, sizeof(buffer), NULL))
    lua_pushstring(L, buffer);
  else
    lua_pushfstring(L, "system error %d\n", error);
}

static void ll_unloadlib (void *lib) {
  FreeLibrary((HINSTANCE)lib);
}


static void *ll_load (lua_State *L, const char *path) {
  HINSTANCE lib = LoadLibraryA(path);
  if (lib == NULL) pusherror(L);
  return lib;
}


static lua_CFunction ll_sym (lua_State *L, void *lib, const char *sym) {
  lua_CFunction f = (lua_CFunction)GetProcAddress((HINSTANCE)lib, sym);
  if (f == NULL) pusherror(L);
  return f;
}

/* }====================================================== */



#elif defined(LUA_DL_DYLD)
/*
** {======================================================================
** Native Mac OS X / Darwin Implementation
** =======================================================================
*/

#include 


/* Mac appends a `_' before C function names */
#undef POF
#define POF	"_" LUA_POF


static void pusherror (lua_State *L) {
  const char *err_str;
  const char *err_file;
  NSLinkEditErrors err;
  int err_num;
  NSLinkEditError(&err, &err_num, &err_file, &err_str);
  lua_pushstring(L, err_str);
}


static const char *errorfromcode (NSObjectFileImageReturnCode ret) {
  switch (ret) {
    case NSObjectFileImageInappropriateFile:
      return "file is not a bundle";
    case NSObjectFileImageArch:
      return "library is for wrong CPU type";
    case NSObjectFileImageFormat:
      return "bad format";
    case NSObjectFileImageAccess:
      return "cannot access file";
    case NSObjectFileImageFailure:
    default:
      return "unable to load library";
  }
}


static void ll_unloadlib (void *lib) {
  NSUnLinkModule((NSModule)lib, NSUNLINKMODULE_OPTION_RESET_LAZY_REFERENCES);
}


static void *ll_load (lua_State *L, const char *path) {
  NSObjectFileImage img;
  NSObjectFileImageReturnCode ret;
  /* this would be a rare case, but prevents crashing if it happens */
  if(!_dyld_present()) {
    lua_pushliteral(L, "dyld not present");
    return NULL;
  }
  ret = NSCreateObjectFileImageFromFile(path, &img);
  if (ret == NSObjectFileImageSuccess) {
    NSModule mod = NSLinkModule(img, path, NSLINKMODULE_OPTION_PRIVATE |
                       NSLINKMODULE_OPTION_RETURN_ON_ERROR);
    NSDestroyObjectFileImage(img);
    if (mod == NULL) pusherror(L);
    return mod;
  }
  lua_pushstring(L, errorfromcode(ret));
  return NULL;
}


static lua_CFunction ll_sym (lua_State *L, void *lib, const char *sym) {
  NSSymbol nss = NSLookupSymbolInModule((NSModule)lib, sym);
  if (nss == NULL) {
    lua_pushfstring(L, "symbol " LUA_QS " not found", sym);
    return NULL;
  }
  return (lua_CFunction)NSAddressOfSymbol(nss);
}

/* }====================================================== */



#else
/*
** {======================================================
** Fallback for other systems
** =======================================================
*/

#undef LIB_FAIL
#define LIB_FAIL	"absent"


#define DLMSG	"dynamic libraries not enabled; check your Lua installation"


static void ll_unloadlib (void *lib) {
  (void)lib;  /* to avoid warnings */
}


static void *ll_load (lua_State *L, const char *path) {
  (void)path;  /* to avoid warnings */
  lua_pushliteral(L, DLMSG);
  return NULL;
}


static lua_CFunction ll_sym (lua_State *L, void *lib, const char *sym) {
  (void)lib; (void)sym;  /* to avoid warnings */
  lua_pushliteral(L, DLMSG);
  return NULL;
}

/* }====================================================== */
#endif



static void **ll_register (lua_State *L, const char *path) {
  void **plib;
  lua_pushfstring(L, "%s%s", LIBPREFIX, path);
  lua_gettable(L, LUA_REGISTRYINDEX);  /* check library in registry? */
  if (!lua_isnil(L, -1))  /* is there an entry? */
    plib = (void **)lua_touserdata(L, -1);
  else {  /* no entry yet; create one */
    lua_pop(L, 1);
    plib = (void **)lua_newuserdata(L, sizeof(const void *));
    *plib = NULL;
    luaL_getmetatable(L, "_LOADLIB");
    lua_setmetatable(L, -2);
    lua_pushfstring(L, "%s%s", LIBPREFIX, path);
    lua_pushvalue(L, -2);
    lua_settable(L, LUA_REGISTRYINDEX);
  }
  return plib;
}


/*
** __gc tag method: calls library's `ll_unloadlib' function with the lib
** handle
*/
static int gctm (lua_State *L) {
  void **lib = (void **)luaL_checkudata(L, 1, "_LOADLIB");
  if (*lib) ll_unloadlib(*lib);
  *lib = NULL;  /* mark library as closed */
  return 0;
}


static int ll_loadfunc (lua_State *L, const char *path, const char *sym) {
  void **reg = ll_register(L, path);
  if (*reg == NULL) *reg = ll_load(L, path);
  if (*reg == NULL)
    return ERRLIB;  /* unable to load library */
  else {
    lua_CFunction f = ll_sym(L, *reg, sym);
    if (f == NULL)
      return ERRFUNC;  /* unable to find function */
    lua_pushcfunction(L, f);
    return 0;  /* return function */
  }
}


static int ll_loadlib (lua_State *L) {
  const char *path = luaL_checkstring(L, 1);
  const char *init = luaL_checkstring(L, 2);
  int stat = ll_loadfunc(L, path, init);
  if (stat == 0)  /* no errors? */
    return 1;  /* return the loaded function */
  else {  /* error; error message is on stack top */
    lua_pushnil(L);
    lua_insert(L, -2);
    lua_pushstring(L, (stat == ERRLIB) ?  LIB_FAIL : "init");
    return 3;  /* return nil, error message, and where */
  }
}



/*
** {======================================================
** 'require' function
** =======================================================
*/


static int readable (const char *filename) {
  FILE *f = fopen(filename, "r");  /* try to open file */
  if (f == NULL) return 0;  /* open failed */
  fclose(f);
  return 1;
}


static const char *pushnexttemplate (lua_State *L, const char *path) {
  const char *l;
  while (*path == *LUA_PATHSEP) path++;  /* skip separators */
  if (*path == '\0') return NULL;  /* no more templates */
  l = strchr(path, *LUA_PATHSEP);  /* find next separator */
  if (l == NULL) l = path + strlen(path);
  lua_pushlstring(L, path, l - path);  /* template */
  return l;
}


static const char *findfile (lua_State *L, const char *name,
                                           const char *pname) {
  const char *path;
  name = luaL_gsub(L, name, ".", LUA_DIRSEP);
  lua_getfield(L, LUA_ENVIRONINDEX, pname);
  path = lua_tostring(L, -1);
  if (path == NULL)
    luaL_error(L, LUA_QL("package.%s") " must be a string", pname);
  lua_pushliteral(L, "");  /* error accumulator */
  while ((path = pushnexttemplate(L, path)) != NULL) {
    const char *filename;
    filename = luaL_gsub(L, lua_tostring(L, -1), LUA_PATH_MARK, name);
    lua_remove(L, -2);  /* remove path template */
    if (readable(filename))  /* does file exist and is readable? */
      return filename;  /* return that file name */
    lua_pushfstring(L, "\n\tno file " LUA_QS, filename);
    lua_remove(L, -2);  /* remove file name */
    lua_concat(L, 2);  /* add entry to possible error message */
  }
  return NULL;  /* not found */
}


static void loaderror (lua_State *L, const char *filename) {
  luaL_error(L, "error loading module " LUA_QS " from file " LUA_QS ":\n\t%s",
                lua_tostring(L, 1), filename, lua_tostring(L, -1));
}


static int loader_Lua (lua_State *L) {
  const char *filename;
  const char *name = luaL_checkstring(L, 1);
  filename = findfile(L, name, "path");
  if (filename == NULL) return 1;  /* library not found in this path */
  if (luaL_loadfile(L, filename) != 0)
    loaderror(L, filename);
  return 1;  /* library loaded successfully */
}


static const char *mkfuncname (lua_State *L, const char *modname) {
  const char *funcname;
  const char *mark = strchr(modname, *LUA_IGMARK);
  if (mark) modname = mark + 1;
  funcname = luaL_gsub(L, modname, ".", LUA_OFSEP);
  funcname = lua_pushfstring(L, POF"%s", funcname);
  lua_remove(L, -2);  /* remove 'gsub' result */
  return funcname;
}


static int loader_C (lua_State *L) {
  const char *funcname;
  const char *name = luaL_checkstring(L, 1);
  const char *filename = findfile(L, name, "cpath");
  if (filename == NULL) return 1;  /* library not found in this path */
  funcname = mkfuncname(L, name);
  if (ll_loadfunc(L, filename, funcname) != 0)
    loaderror(L, filename);
  return 1;  /* library loaded successfully */
}


static int loader_Croot (lua_State *L) {
  const char *funcname;
  const char *filename;
  const char *name = luaL_checkstring(L, 1);
  const char *p = strchr(name, '.');
  int stat;
  if (p == NULL) return 0;  /* is root */
  lua_pushlstring(L, name, p - name);
  filename = findfile(L, lua_tostring(L, -1), "cpath");
  if (filename == NULL) return 1;  /* root not found */
  funcname = mkfuncname(L, name);
  if ((stat = ll_loadfunc(L, filename, funcname)) != 0) {
    if (stat != ERRFUNC) loaderror(L, filename);  /* real error */
    lua_pushfstring(L, "\n\tno module " LUA_QS " in file " LUA_QS,
                       name, filename);
    return 1;  /* function not found */
  }
  return 1;
}


static int loader_preload (lua_State *L) {
  const char *name = luaL_checkstring(L, 1);
  lua_getfield(L, LUA_ENVIRONINDEX, "preload");
  if (!lua_istable(L, -1))
    luaL_error(L, LUA_QL("package.preload") " must be a table");
  lua_getfield(L, -1, name);
  if (lua_isnil(L, -1))  /* not found? */
    lua_pushfstring(L, "\n\tno field package.preload['%s']", name);
  return 1;
}


static const int sentinel_ = 0;
#define sentinel	((void *)&sentinel_)


static int ll_require (lua_State *L) {
  const char *name = luaL_checkstring(L, 1);
  int i;
  lua_settop(L, 1);  /* _LOADED table will be at index 2 */
  lua_getfield(L, LUA_REGISTRYINDEX, "_LOADED");
  lua_getfield(L, 2, name);
  if (lua_toboolean(L, -1)) {  /* is it there? */
    if (lua_touserdata(L, -1) == sentinel)  /* check loops */
      luaL_error(L, "loop or previous error loading module " LUA_QS, name);
    return 1;  /* package is already loaded */
  }
  /* else must load it; iterate over available loaders */
  lua_getfield(L, LUA_ENVIRONINDEX, "loaders");
  if (!lua_istable(L, -1))
    luaL_error(L, LUA_QL("package.loaders") " must be a table");
  lua_pushliteral(L, "");  /* error message accumulator */
  for (i=1; ; i++) {
    lua_rawgeti(L, -2, i);  /* get a loader */
    if (lua_isnil(L, -1))
      luaL_error(L, "module " LUA_QS " not found:%s",
                    name, lua_tostring(L, -2));
    lua_pushstring(L, name);
    lua_call(L, 1, 1);  /* call it */
    if (lua_isfunction(L, -1))  /* did it find module? */
      break;  /* module loaded successfully */
    else if (lua_isstring(L, -1))  /* loader returned error message? */
      lua_concat(L, 2);  /* accumulate it */
    else
      lua_pop(L, 1);
  }
  lua_pushlightuserdata(L, sentinel);
  lua_setfield(L, 2, name);  /* _LOADED[name] = sentinel */
  lua_pushstring(L, name);  /* pass name as argument to module */
  lua_call(L, 1, 1);  /* run loaded module */
  if (!lua_isnil(L, -1))  /* non-nil return? */
    lua_setfield(L, 2, name);  /* _LOADED[name] = returned value */
  lua_getfield(L, 2, name);
  if (lua_touserdata(L, -1) == sentinel) {   /* module did not set a value? */
    lua_pushboolean(L, 1);  /* use true as result */
    lua_pushvalue(L, -1);  /* extra copy to be returned */
    lua_setfield(L, 2, name);  /* _LOADED[name] = true */
  }
  return 1;
}

/* }====================================================== */



/*
** {======================================================
** 'module' function
** =======================================================
*/
  

static void setfenv (lua_State *L) {
  lua_Debug ar;
  if (lua_getstack(L, 1, &ar) == 0 ||
      lua_getinfo(L, "f", &ar) == 0 ||  /* get calling function */
      lua_iscfunction(L, -1))
    luaL_error(L, LUA_QL("module") " not called from a Lua function");
  lua_pushvalue(L, -2);
  lua_setfenv(L, -2);
  lua_pop(L, 1);
}


static void dooptions (lua_State *L, int n) {
  int i;
  for (i = 2; i <= n; i++) {
    lua_pushvalue(L, i);  /* get option (a function) */
    lua_pushvalue(L, -2);  /* module */
    lua_call(L, 1, 0);
  }
}


static void modinit (lua_State *L, const char *modname) {
  const char *dot;
  lua_pushvalue(L, -1);
  lua_setfield(L, -2, "_M");  /* module._M = module */
  lua_pushstring(L, modname);
  lua_setfield(L, -2, "_NAME");
  dot = strrchr(modname, '.');  /* look for last dot in module name */
  if (dot == NULL) dot = modname;
  else dot++;
  /* set _PACKAGE as package name (full module name minus last part) */
  lua_pushlstring(L, modname, dot - modname);
  lua_setfield(L, -2, "_PACKAGE");
}


static int ll_module (lua_State *L) {
  const char *modname = luaL_checkstring(L, 1);
  int loaded = lua_gettop(L) + 1;  /* index of _LOADED table */
  lua_getfield(L, LUA_REGISTRYINDEX, "_LOADED");
  lua_getfield(L, loaded, modname);  /* get _LOADED[modname] */
  if (!lua_istable(L, -1)) {  /* not found? */
    lua_pop(L, 1);  /* remove previous result */
    /* try global variable (and create one if it does not exist) */
    if (luaL_findtable(L, LUA_GLOBALSINDEX, modname, 1) != NULL)
      return luaL_error(L, "name conflict for module " LUA_QS, modname);
    lua_pushvalue(L, -1);
    lua_setfield(L, loaded, modname);  /* _LOADED[modname] = new table */
  }
  /* check whether table already has a _NAME field */
  lua_getfield(L, -1, "_NAME");
  if (!lua_isnil(L, -1))  /* is table an initialized module? */
    lua_pop(L, 1);
  else {  /* no; initialize it */
    lua_pop(L, 1);
    modinit(L, modname);
  }
  lua_pushvalue(L, -1);
  setfenv(L);
  dooptions(L, loaded - 1);
  return 0;
}


static int ll_seeall (lua_State *L) {
  luaL_checktype(L, 1, LUA_TTABLE);
  if (!lua_getmetatable(L, 1)) {
    lua_createtable(L, 0, 1); /* create new metatable */
    lua_pushvalue(L, -1);
    lua_setmetatable(L, 1);
  }
  lua_pushvalue(L, LUA_GLOBALSINDEX);
  lua_setfield(L, -2, "__index");  /* mt.__index = _G */
  return 0;
}


/* }====================================================== */



/* auxiliary mark (for internal use) */
#define AUXMARK		"\1"

static void setpath (lua_State *L, const char *fieldname, const char *envname,
                                   const char *def) {
  const char *path = getenv(envname);
  if (path == NULL)  /* no environment variable? */
    lua_pushstring(L, def);  /* use default */
  else {
    /* replace ";;" by ";AUXMARK;" and then AUXMARK by default path */
    path = luaL_gsub(L, path, LUA_PATHSEP LUA_PATHSEP,
                              LUA_PATHSEP AUXMARK LUA_PATHSEP);
    luaL_gsub(L, path, AUXMARK, def);
    lua_remove(L, -2);
  }
  setprogdir(L);
  lua_setfield(L, -2, fieldname);
}


static const luaL_Reg pk_funcs[] = {
  {"loadlib", ll_loadlib},
  {"seeall", ll_seeall},
  {NULL, NULL}
};


static const luaL_Reg ll_funcs[] = {
  {"module", ll_module},
  {"require", ll_require},
  {NULL, NULL}
};


static const lua_CFunction loaders[] =
  {loader_preload, loader_Lua, loader_C, loader_Croot, NULL};


LUALIB_API int luaopen_package (lua_State *L) {
  int i;
  /* create new type _LOADLIB */
  luaL_newmetatable(L, "_LOADLIB");
  lua_pushcfunction(L, gctm);
  lua_setfield(L, -2, "__gc");
  /* create `package' table */
  luaL_register(L, LUA_LOADLIBNAME, pk_funcs);
#if defined(LUA_COMPAT_LOADLIB) 
  lua_getfield(L, -1, "loadlib");
  lua_setfield(L, LUA_GLOBALSINDEX, "loadlib");
#endif
  lua_pushvalue(L, -1);
  lua_replace(L, LUA_ENVIRONINDEX);
  /* create `loaders' table */
  lua_createtable(L, sizeof(loaders)/sizeof(loaders[0]) - 1, 0);
  /* fill it with pre-defined loaders */
  for (i=0; loaders[i] != NULL; i++) {
    lua_pushcfunction(L, loaders[i]);
    lua_rawseti(L, -2, i+1);
  }
  lua_setfield(L, -2, "loaders");  /* put it in field `loaders' */
  setpath(L, "path", LUA_PATH, LUA_PATH_DEFAULT);  /* set field `path' */
  setpath(L, "cpath", LUA_CPATH, LUA_CPATH_DEFAULT); /* set field `cpath' */
  /* store config information */
  lua_pushliteral(L, LUA_DIRSEP "\n" LUA_PATHSEP "\n" LUA_PATH_MARK "\n"
                     LUA_EXECDIR "\n" LUA_IGMARK);
  lua_setfield(L, -2, "config");
  /* set field `loaded' */
  luaL_findtable(L, LUA_REGISTRYINDEX, "_LOADED", 2);
  lua_setfield(L, -2, "loaded");
  /* set field `preload' */
  lua_newtable(L);
  lua_setfield(L, -2, "preload");
  lua_pushvalue(L, LUA_GLOBALSINDEX);
  luaL_register(L, NULL, ll_funcs);  /* open lib into global table */
  lua_pop(L, 1);
  return 1;  /* return 'package' table */
}

genometools-1.5.1/src/external/lua-5.1.5/src/lobject.c000066400000000000000000000125721211610345200222660ustar00rootroot00000000000000/*
** $Id: lobject.c,v 2.22.1.1 2007/12/27 13:02:25 roberto Exp $
** Some generic functions over Lua objects
** See Copyright Notice in lua.h
*/

#include 
#include 
#include 
#include 
#include 

#define lobject_c
#define LUA_CORE

#include "lua.h"

#include "ldo.h"
#include "lmem.h"
#include "lobject.h"
#include "lstate.h"
#include "lstring.h"
#include "lvm.h"



const TValue luaO_nilobject_ = {{NULL}, LUA_TNIL};


/*
** converts an integer to a "floating point byte", represented as
** (eeeeexxx), where the real value is (1xxx) * 2^(eeeee - 1) if
** eeeee != 0 and (xxx) otherwise.
*/
int luaO_int2fb (unsigned int x) {
  int e = 0;  /* expoent */
  while (x >= 16) {
    x = (x+1) >> 1;
    e++;
  }
  if (x < 8) return x;
  else return ((e+1) << 3) | (cast_int(x) - 8);
}


/* converts back */
int luaO_fb2int (int x) {
  int e = (x >> 3) & 31;
  if (e == 0) return x;
  else return ((x & 7)+8) << (e - 1);
}


int luaO_log2 (unsigned int x) {
  static const lu_byte log_2[256] = {
    0,1,2,2,3,3,3,3,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
    6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,
    7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
    7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,
    8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,
    8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,
    8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,
    8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8,8
  };
  int l = -1;
  while (x >= 256) { l += 8; x >>= 8; }
  return l + log_2[x];

}


int luaO_rawequalObj (const TValue *t1, const TValue *t2) {
  if (ttype(t1) != ttype(t2)) return 0;
  else switch (ttype(t1)) {
    case LUA_TNIL:
      return 1;
    case LUA_TNUMBER:
      return luai_numeq(nvalue(t1), nvalue(t2));
    case LUA_TBOOLEAN:
      return bvalue(t1) == bvalue(t2);  /* boolean true must be 1 !! */
    case LUA_TLIGHTUSERDATA:
      return pvalue(t1) == pvalue(t2);
    default:
      lua_assert(iscollectable(t1));
      return gcvalue(t1) == gcvalue(t2);
  }
}


int luaO_str2d (const char *s, lua_Number *result) {
  char *endptr;
  *result = lua_str2number(s, &endptr);
  if (endptr == s) return 0;  /* conversion failed */
  if (*endptr == 'x' || *endptr == 'X')  /* maybe an hexadecimal constant? */
    *result = cast_num(strtoul(s, &endptr, 16));
  if (*endptr == '\0') return 1;  /* most common case */
  while (isspace(cast(unsigned char, *endptr))) endptr++;
  if (*endptr != '\0') return 0;  /* invalid trailing characters? */
  return 1;
}



static void pushstr (lua_State *L, const char *str) {
  setsvalue2s(L, L->top, luaS_new(L, str));
  incr_top(L);
}


/* this function handles only `%d', `%c', %f, %p, and `%s' formats */
const char *luaO_pushvfstring (lua_State *L, const char *fmt, va_list argp) {
  int n = 1;
  pushstr(L, "");
  for (;;) {
    const char *e = strchr(fmt, '%');
    if (e == NULL) break;
    setsvalue2s(L, L->top, luaS_newlstr(L, fmt, e-fmt));
    incr_top(L);
    switch (*(e+1)) {
      case 's': {
        const char *s = va_arg(argp, char *);
        if (s == NULL) s = "(null)";
        pushstr(L, s);
        break;
      }
      case 'c': {
        char buff[2];
        buff[0] = cast(char, va_arg(argp, int));
        buff[1] = '\0';
        pushstr(L, buff);
        break;
      }
      case 'd': {
        setnvalue(L->top, cast_num(va_arg(argp, int)));
        incr_top(L);
        break;
      }
      case 'f': {
        setnvalue(L->top, cast_num(va_arg(argp, l_uacNumber)));
        incr_top(L);
        break;
      }
      case 'p': {
        char buff[4*sizeof(void *) + 8]; /* should be enough space for a `%p' */
        sprintf(buff, "%p", va_arg(argp, void *));
        pushstr(L, buff);
        break;
      }
      case '%': {
        pushstr(L, "%");
        break;
      }
      default: {
        char buff[3];
        buff[0] = '%';
        buff[1] = *(e+1);
        buff[2] = '\0';
        pushstr(L, buff);
        break;
      }
    }
    n += 2;
    fmt = e+2;
  }
  pushstr(L, fmt);
  luaV_concat(L, n+1, cast_int(L->top - L->base) - 1);
  L->top -= n;
  return svalue(L->top - 1);
}


const char *luaO_pushfstring (lua_State *L, const char *fmt, ...) {
  const char *msg;
  va_list argp;
  va_start(argp, fmt);
  msg = luaO_pushvfstring(L, fmt, argp);
  va_end(argp);
  return msg;
}


void luaO_chunkid (char *out, const char *source, size_t bufflen) {
  if (*source == '=') {
    strncpy(out, source+1, bufflen);  /* remove first char */
    out[bufflen-1] = '\0';  /* ensures null termination */
  }
  else {  /* out = "source", or "...source" */
    if (*source == '@') {
      size_t l;
      source++;  /* skip the `@' */
      bufflen -= sizeof(" '...' ");
      l = strlen(source);
      strcpy(out, "");
      if (l > bufflen) {
        source += (l-bufflen);  /* get last part of file name */
        strcat(out, "...");
      }
      strcat(out, source);
    }
    else {  /* out = [string "string"] */
      size_t len = strcspn(source, "\n\r");  /* stop at first newline */
      bufflen -= sizeof(" [string \"...\"] ");
      if (len > bufflen) len = bufflen;
      strcpy(out, "[string \"");
      if (source[len] != '\0') {  /* must truncate? */
        strncat(out, source, len);
        strcat(out, "...");
      }
      else
        strcat(out, source);
      strcat(out, "\"]");
    }
  }
}
genometools-1.5.1/src/external/lua-5.1.5/src/lobject.h000066400000000000000000000204661211610345200222740ustar00rootroot00000000000000/*
** $Id: lobject.h,v 2.20.1.2 2008/08/06 13:29:48 roberto Exp $
** Type definitions for Lua objects
** See Copyright Notice in lua.h
*/


#ifndef lobject_h
#define lobject_h


#include 


#include "llimits.h"
#include "lua.h"


/* tags for values visible from Lua */
#define LAST_TAG	LUA_TTHREAD

#define NUM_TAGS	(LAST_TAG+1)


/*
** Extra tags for non-values
*/
#define LUA_TPROTO	(LAST_TAG+1)
#define LUA_TUPVAL	(LAST_TAG+2)
#define LUA_TDEADKEY	(LAST_TAG+3)


/*
** Union of all collectable objects
*/
typedef union GCObject GCObject;


/*
** Common Header for all collectable objects (in macro form, to be
** included in other objects)
*/
#define CommonHeader	GCObject *next; lu_byte tt; lu_byte marked


/*
** Common header in struct form
*/
typedef struct GCheader {
  CommonHeader;
} GCheader;




/*
** Union of all Lua values
*/
typedef union {
  GCObject *gc;
  void *p;
  lua_Number n;
  int b;
} Value;


/*
** Tagged Values
*/

#define TValuefields	Value value; int tt

typedef struct lua_TValue {
  TValuefields;
} TValue;


/* Macros to test type */
#define ttisnil(o)	(ttype(o) == LUA_TNIL)
#define ttisnumber(o)	(ttype(o) == LUA_TNUMBER)
#define ttisstring(o)	(ttype(o) == LUA_TSTRING)
#define ttistable(o)	(ttype(o) == LUA_TTABLE)
#define ttisfunction(o)	(ttype(o) == LUA_TFUNCTION)
#define ttisboolean(o)	(ttype(o) == LUA_TBOOLEAN)
#define ttisuserdata(o)	(ttype(o) == LUA_TUSERDATA)
#define ttisthread(o)	(ttype(o) == LUA_TTHREAD)
#define ttislightuserdata(o)	(ttype(o) == LUA_TLIGHTUSERDATA)

/* Macros to access values */
#define ttype(o)	((o)->tt)
#define gcvalue(o)	check_exp(iscollectable(o), (o)->value.gc)
#define pvalue(o)	check_exp(ttislightuserdata(o), (o)->value.p)
#define nvalue(o)	check_exp(ttisnumber(o), (o)->value.n)
#define rawtsvalue(o)	check_exp(ttisstring(o), &(o)->value.gc->ts)
#define tsvalue(o)	(&rawtsvalue(o)->tsv)
#define rawuvalue(o)	check_exp(ttisuserdata(o), &(o)->value.gc->u)
#define uvalue(o)	(&rawuvalue(o)->uv)
#define clvalue(o)	check_exp(ttisfunction(o), &(o)->value.gc->cl)
#define hvalue(o)	check_exp(ttistable(o), &(o)->value.gc->h)
#define bvalue(o)	check_exp(ttisboolean(o), (o)->value.b)
#define thvalue(o)	check_exp(ttisthread(o), &(o)->value.gc->th)

#define l_isfalse(o)	(ttisnil(o) || (ttisboolean(o) && bvalue(o) == 0))

/*
** for internal debug only
*/
#define checkconsistency(obj) \
  lua_assert(!iscollectable(obj) || (ttype(obj) == (obj)->value.gc->gch.tt))

#define checkliveness(g,obj) \
  lua_assert(!iscollectable(obj) || \
  ((ttype(obj) == (obj)->value.gc->gch.tt) && !isdead(g, (obj)->value.gc)))


/* Macros to set values */
#define setnilvalue(obj) ((obj)->tt=LUA_TNIL)

#define setnvalue(obj,x) \
  { TValue *i_o=(obj); i_o->value.n=(x); i_o->tt=LUA_TNUMBER; }

#define setpvalue(obj,x) \
  { TValue *i_o=(obj); i_o->value.p=(x); i_o->tt=LUA_TLIGHTUSERDATA; }

#define setbvalue(obj,x) \
  { TValue *i_o=(obj); i_o->value.b=(x); i_o->tt=LUA_TBOOLEAN; }

#define setsvalue(L,obj,x) \
  { TValue *i_o=(obj); \
    i_o->value.gc=cast(GCObject *, (x)); i_o->tt=LUA_TSTRING; \
    checkliveness(G(L),i_o); }

#define setuvalue(L,obj,x) \
  { TValue *i_o=(obj); \
    i_o->value.gc=cast(GCObject *, (x)); i_o->tt=LUA_TUSERDATA; \
    checkliveness(G(L),i_o); }

#define setthvalue(L,obj,x) \
  { TValue *i_o=(obj); \
    i_o->value.gc=cast(GCObject *, (x)); i_o->tt=LUA_TTHREAD; \
    checkliveness(G(L),i_o); }

#define setclvalue(L,obj,x) \
  { TValue *i_o=(obj); \
    i_o->value.gc=cast(GCObject *, (x)); i_o->tt=LUA_TFUNCTION; \
    checkliveness(G(L),i_o); }

#define sethvalue(L,obj,x) \
  { TValue *i_o=(obj); \
    i_o->value.gc=cast(GCObject *, (x)); i_o->tt=LUA_TTABLE; \
    checkliveness(G(L),i_o); }

#define setptvalue(L,obj,x) \
  { TValue *i_o=(obj); \
    i_o->value.gc=cast(GCObject *, (x)); i_o->tt=LUA_TPROTO; \
    checkliveness(G(L),i_o); }




#define setobj(L,obj1,obj2) \
  { const TValue *o2=(obj2); TValue *o1=(obj1); \
    o1->value = o2->value; o1->tt=o2->tt; \
    checkliveness(G(L),o1); }


/*
** different types of sets, according to destination
*/

/* from stack to (same) stack */
#define setobjs2s	setobj
/* to stack (not from same stack) */
#define setobj2s	setobj
#define setsvalue2s	setsvalue
#define sethvalue2s	sethvalue
#define setptvalue2s	setptvalue
/* from table to same table */
#define setobjt2t	setobj
/* to table */
#define setobj2t	setobj
/* to new object */
#define setobj2n	setobj
#define setsvalue2n	setsvalue

#define setttype(obj, tt) (ttype(obj) = (tt))


#define iscollectable(o)	(ttype(o) >= LUA_TSTRING)



typedef TValue *StkId;  /* index to stack elements */


/*
** String headers for string table
*/
typedef union TString {
  L_Umaxalign dummy;  /* ensures maximum alignment for strings */
  struct {
    CommonHeader;
    lu_byte reserved;
    unsigned int hash;
    size_t len;
  } tsv;
} TString;


#define getstr(ts)	cast(const char *, (ts) + 1)
#define svalue(o)       getstr(rawtsvalue(o))



typedef union Udata {
  L_Umaxalign dummy;  /* ensures maximum alignment for `local' udata */
  struct {
    CommonHeader;
    struct Table *metatable;
    struct Table *env;
    size_t len;
  } uv;
} Udata;




/*
** Function Prototypes
*/
typedef struct Proto {
  CommonHeader;
  TValue *k;  /* constants used by the function */
  Instruction *code;
  struct Proto **p;  /* functions defined inside the function */
  int *lineinfo;  /* map from opcodes to source lines */
  struct LocVar *locvars;  /* information about local variables */
  TString **upvalues;  /* upvalue names */
  TString  *source;
  int sizeupvalues;
  int sizek;  /* size of `k' */
  int sizecode;
  int sizelineinfo;
  int sizep;  /* size of `p' */
  int sizelocvars;
  int linedefined;
  int lastlinedefined;
  GCObject *gclist;
  lu_byte nups;  /* number of upvalues */
  lu_byte numparams;
  lu_byte is_vararg;
  lu_byte maxstacksize;
} Proto;


/* masks for new-style vararg */
#define VARARG_HASARG		1
#define VARARG_ISVARARG		2
#define VARARG_NEEDSARG		4


typedef struct LocVar {
  TString *varname;
  int startpc;  /* first point where variable is active */
  int endpc;    /* first point where variable is dead */
} LocVar;



/*
** Upvalues
*/

typedef struct UpVal {
  CommonHeader;
  TValue *v;  /* points to stack or to its own value */
  union {
    TValue value;  /* the value (when closed) */
    struct {  /* double linked list (when open) */
      struct UpVal *prev;
      struct UpVal *next;
    } l;
  } u;
} UpVal;


/*
** Closures
*/

#define ClosureHeader \
	CommonHeader; lu_byte isC; lu_byte nupvalues; GCObject *gclist; \
	struct Table *env

typedef struct CClosure {
  ClosureHeader;
  lua_CFunction f;
  TValue upvalue[1];
} CClosure;


typedef struct LClosure {
  ClosureHeader;
  struct Proto *p;
  UpVal *upvals[1];
} LClosure;


typedef union Closure {
  CClosure c;
  LClosure l;
} Closure;


#define iscfunction(o)	(ttype(o) == LUA_TFUNCTION && clvalue(o)->c.isC)
#define isLfunction(o)	(ttype(o) == LUA_TFUNCTION && !clvalue(o)->c.isC)


/*
** Tables
*/

typedef union TKey {
  struct {
    TValuefields;
    struct Node *next;  /* for chaining */
  } nk;
  TValue tvk;
} TKey;


typedef struct Node {
  TValue i_val;
  TKey i_key;
} Node;


typedef struct Table {
  CommonHeader;
  lu_byte flags;  /* 1<
lsizenode))


#define luaO_nilobject		(&luaO_nilobject_)

LUAI_DATA const TValue luaO_nilobject_;

#define ceillog2(x)	(luaO_log2((x)-1) + 1)

LUAI_FUNC int luaO_log2 (unsigned int x);
LUAI_FUNC int luaO_int2fb (unsigned int x);
LUAI_FUNC int luaO_fb2int (int x);
LUAI_FUNC int luaO_rawequalObj (const TValue *t1, const TValue *t2);
LUAI_FUNC int luaO_str2d (const char *s, lua_Number *result);
LUAI_FUNC const char *luaO_pushvfstring (lua_State *L, const char *fmt,
                                                       va_list argp);
LUAI_FUNC const char *luaO_pushfstring (lua_State *L, const char *fmt, ...);
LUAI_FUNC void luaO_chunkid (char *out, const char *source, size_t len);


#endif

genometools-1.5.1/src/external/lua-5.1.5/src/lopcodes.c000066400000000000000000000055041211610345200224510ustar00rootroot00000000000000/*
** $Id: lopcodes.c,v 1.37.1.1 2007/12/27 13:02:25 roberto Exp $
** See Copyright Notice in lua.h
*/


#define lopcodes_c
#define LUA_CORE


#include "lopcodes.h"


/* ORDER OP */

const char *const luaP_opnames[NUM_OPCODES+1] = {
  "MOVE",
  "LOADK",
  "LOADBOOL",
  "LOADNIL",
  "GETUPVAL",
  "GETGLOBAL",
  "GETTABLE",
  "SETGLOBAL",
  "SETUPVAL",
  "SETTABLE",
  "NEWTABLE",
  "SELF",
  "ADD",
  "SUB",
  "MUL",
  "DIV",
  "MOD",
  "POW",
  "UNM",
  "NOT",
  "LEN",
  "CONCAT",
  "JMP",
  "EQ",
  "LT",
  "LE",
  "TEST",
  "TESTSET",
  "CALL",
  "TAILCALL",
  "RETURN",
  "FORLOOP",
  "FORPREP",
  "TFORLOOP",
  "SETLIST",
  "CLOSE",
  "CLOSURE",
  "VARARG",
  NULL
};


#define opmode(t,a,b,c,m) (((t)<<7) | ((a)<<6) | ((b)<<4) | ((c)<<2) | (m))

const lu_byte luaP_opmodes[NUM_OPCODES] = {
/*       T  A    B       C     mode		   opcode	*/
  opmode(0, 1, OpArgR, OpArgN, iABC) 		/* OP_MOVE */
 ,opmode(0, 1, OpArgK, OpArgN, iABx)		/* OP_LOADK */
 ,opmode(0, 1, OpArgU, OpArgU, iABC)		/* OP_LOADBOOL */
 ,opmode(0, 1, OpArgR, OpArgN, iABC)		/* OP_LOADNIL */
 ,opmode(0, 1, OpArgU, OpArgN, iABC)		/* OP_GETUPVAL */
 ,opmode(0, 1, OpArgK, OpArgN, iABx)		/* OP_GETGLOBAL */
 ,opmode(0, 1, OpArgR, OpArgK, iABC)		/* OP_GETTABLE */
 ,opmode(0, 0, OpArgK, OpArgN, iABx)		/* OP_SETGLOBAL */
 ,opmode(0, 0, OpArgU, OpArgN, iABC)		/* OP_SETUPVAL */
 ,opmode(0, 0, OpArgK, OpArgK, iABC)		/* OP_SETTABLE */
 ,opmode(0, 1, OpArgU, OpArgU, iABC)		/* OP_NEWTABLE */
 ,opmode(0, 1, OpArgR, OpArgK, iABC)		/* OP_SELF */
 ,opmode(0, 1, OpArgK, OpArgK, iABC)		/* OP_ADD */
 ,opmode(0, 1, OpArgK, OpArgK, iABC)		/* OP_SUB */
 ,opmode(0, 1, OpArgK, OpArgK, iABC)		/* OP_MUL */
 ,opmode(0, 1, OpArgK, OpArgK, iABC)		/* OP_DIV */
 ,opmode(0, 1, OpArgK, OpArgK, iABC)		/* OP_MOD */
 ,opmode(0, 1, OpArgK, OpArgK, iABC)		/* OP_POW */
 ,opmode(0, 1, OpArgR, OpArgN, iABC)		/* OP_UNM */
 ,opmode(0, 1, OpArgR, OpArgN, iABC)		/* OP_NOT */
 ,opmode(0, 1, OpArgR, OpArgN, iABC)		/* OP_LEN */
 ,opmode(0, 1, OpArgR, OpArgR, iABC)		/* OP_CONCAT */
 ,opmode(0, 0, OpArgR, OpArgN, iAsBx)		/* OP_JMP */
 ,opmode(1, 0, OpArgK, OpArgK, iABC)		/* OP_EQ */
 ,opmode(1, 0, OpArgK, OpArgK, iABC)		/* OP_LT */
 ,opmode(1, 0, OpArgK, OpArgK, iABC)		/* OP_LE */
 ,opmode(1, 1, OpArgR, OpArgU, iABC)		/* OP_TEST */
 ,opmode(1, 1, OpArgR, OpArgU, iABC)		/* OP_TESTSET */
 ,opmode(0, 1, OpArgU, OpArgU, iABC)		/* OP_CALL */
 ,opmode(0, 1, OpArgU, OpArgU, iABC)		/* OP_TAILCALL */
 ,opmode(0, 0, OpArgU, OpArgN, iABC)		/* OP_RETURN */
 ,opmode(0, 1, OpArgR, OpArgN, iAsBx)		/* OP_FORLOOP */
 ,opmode(0, 1, OpArgR, OpArgN, iAsBx)		/* OP_FORPREP */
 ,opmode(1, 0, OpArgN, OpArgU, iABC)		/* OP_TFORLOOP */
 ,opmode(0, 0, OpArgU, OpArgU, iABC)		/* OP_SETLIST */
 ,opmode(0, 0, OpArgN, OpArgN, iABC)		/* OP_CLOSE */
 ,opmode(0, 1, OpArgU, OpArgN, iABx)		/* OP_CLOSURE */
 ,opmode(0, 1, OpArgU, OpArgN, iABC)		/* OP_VARARG */
};

genometools-1.5.1/src/external/lua-5.1.5/src/lopcodes.h000066400000000000000000000176261211610345200224660ustar00rootroot00000000000000/*
** $Id: lopcodes.h,v 1.125.1.1 2007/12/27 13:02:25 roberto Exp $
** Opcodes for Lua virtual machine
** See Copyright Notice in lua.h
*/

#ifndef lopcodes_h
#define lopcodes_h

#include "llimits.h"


/*===========================================================================
  We assume that instructions are unsigned numbers.
  All instructions have an opcode in the first 6 bits.
  Instructions can have the following fields:
	`A' : 8 bits
	`B' : 9 bits
	`C' : 9 bits
	`Bx' : 18 bits (`B' and `C' together)
	`sBx' : signed Bx

  A signed argument is represented in excess K; that is, the number
  value is the unsigned value minus K. K is exactly the maximum value
  for that argument (so that -max is represented by 0, and +max is
  represented by 2*max), which is half the maximum for the corresponding
  unsigned argument.
===========================================================================*/


enum OpMode {iABC, iABx, iAsBx};  /* basic instruction format */


/*
** size and position of opcode arguments.
*/
#define SIZE_C		9
#define SIZE_B		9
#define SIZE_Bx		(SIZE_C + SIZE_B)
#define SIZE_A		8

#define SIZE_OP		6

#define POS_OP		0
#define POS_A		(POS_OP + SIZE_OP)
#define POS_C		(POS_A + SIZE_A)
#define POS_B		(POS_C + SIZE_C)
#define POS_Bx		POS_C


/*
** limits for opcode arguments.
** we use (signed) int to manipulate most arguments,
** so they must fit in LUAI_BITSINT-1 bits (-1 for sign)
*/
#if SIZE_Bx < LUAI_BITSINT-1
#define MAXARG_Bx        ((1<>1)         /* `sBx' is signed */
#else
#define MAXARG_Bx        MAX_INT
#define MAXARG_sBx        MAX_INT
#endif


#define MAXARG_A        ((1<>POS_OP) & MASK1(SIZE_OP,0)))
#define SET_OPCODE(i,o)	((i) = (((i)&MASK0(SIZE_OP,POS_OP)) | \
		((cast(Instruction, o)<>POS_A) & MASK1(SIZE_A,0)))
#define SETARG_A(i,u)	((i) = (((i)&MASK0(SIZE_A,POS_A)) | \
		((cast(Instruction, u)<>POS_B) & MASK1(SIZE_B,0)))
#define SETARG_B(i,b)	((i) = (((i)&MASK0(SIZE_B,POS_B)) | \
		((cast(Instruction, b)<>POS_C) & MASK1(SIZE_C,0)))
#define SETARG_C(i,b)	((i) = (((i)&MASK0(SIZE_C,POS_C)) | \
		((cast(Instruction, b)<>POS_Bx) & MASK1(SIZE_Bx,0)))
#define SETARG_Bx(i,b)	((i) = (((i)&MASK0(SIZE_Bx,POS_Bx)) | \
		((cast(Instruction, b)< C) then pc++			*/ 
OP_TESTSET,/*	A B C	if (R(B) <=> C) then R(A) := R(B) else pc++	*/ 

OP_CALL,/*	A B C	R(A), ... ,R(A+C-2) := R(A)(R(A+1), ... ,R(A+B-1)) */
OP_TAILCALL,/*	A B C	return R(A)(R(A+1), ... ,R(A+B-1))		*/
OP_RETURN,/*	A B	return R(A), ... ,R(A+B-2)	(see note)	*/

OP_FORLOOP,/*	A sBx	R(A)+=R(A+2);
			if R(A) =) R(A)*/
OP_CLOSURE,/*	A Bx	R(A) := closure(KPROTO[Bx], R(A), ... ,R(A+n))	*/

OP_VARARG/*	A B	R(A), R(A+1), ..., R(A+B-1) = vararg		*/
} OpCode;


#define NUM_OPCODES	(cast(int, OP_VARARG) + 1)



/*===========================================================================
  Notes:
  (*) In OP_CALL, if (B == 0) then B = top. C is the number of returns - 1,
      and can be 0: OP_CALL then sets `top' to last_result+1, so
      next open instruction (OP_CALL, OP_RETURN, OP_SETLIST) may use `top'.

  (*) In OP_VARARG, if (B == 0) then use actual number of varargs and
      set top (like in OP_CALL with C == 0).

  (*) In OP_RETURN, if (B == 0) then return up to `top'

  (*) In OP_SETLIST, if (B == 0) then B = `top';
      if (C == 0) then next `instruction' is real C

  (*) For comparisons, A specifies what condition the test should accept
      (true or false).

  (*) All `skips' (pc++) assume that next instruction is a jump
===========================================================================*/


/*
** masks for instruction properties. The format is:
** bits 0-1: op mode
** bits 2-3: C arg mode
** bits 4-5: B arg mode
** bit 6: instruction set register A
** bit 7: operator is a test
*/  

enum OpArgMask {
  OpArgN,  /* argument is not used */
  OpArgU,  /* argument is used */
  OpArgR,  /* argument is a register or a jump offset */
  OpArgK   /* argument is a constant or register/constant */
};

LUAI_DATA const lu_byte luaP_opmodes[NUM_OPCODES];

#define getOpMode(m)	(cast(enum OpMode, luaP_opmodes[m] & 3))
#define getBMode(m)	(cast(enum OpArgMask, (luaP_opmodes[m] >> 4) & 3))
#define getCMode(m)	(cast(enum OpArgMask, (luaP_opmodes[m] >> 2) & 3))
#define testAMode(m)	(luaP_opmodes[m] & (1 << 6))
#define testTMode(m)	(luaP_opmodes[m] & (1 << 7))


LUAI_DATA const char *const luaP_opnames[NUM_OPCODES+1];  /* opcode names */


/* number of list items to accumulate before a SETLIST instruction */
#define LFIELDS_PER_FLUSH	50


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/loslib.c000066400000000000000000000135501211610345200221250ustar00rootroot00000000000000/*
** $Id: loslib.c,v 1.19.1.3 2008/01/18 16:38:18 roberto Exp $
** Standard Operating System library
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 
#include 
#include 

#define loslib_c
#define LUA_LIB

#include "lua.h"

#include "lauxlib.h"
#include "lualib.h"


static int os_pushresult (lua_State *L, int i, const char *filename) {
  int en = errno;  /* calls to Lua API may change this value */
  if (i) {
    lua_pushboolean(L, 1);
    return 1;
  }
  else {
    lua_pushnil(L);
    lua_pushfstring(L, "%s: %s", filename, strerror(en));
    lua_pushinteger(L, en);
    return 3;
  }
}


static int os_execute (lua_State *L) {
  lua_pushinteger(L, system(luaL_optstring(L, 1, NULL)));
  return 1;
}


static int os_remove (lua_State *L) {
  const char *filename = luaL_checkstring(L, 1);
  return os_pushresult(L, remove(filename) == 0, filename);
}


static int os_rename (lua_State *L) {
  const char *fromname = luaL_checkstring(L, 1);
  const char *toname = luaL_checkstring(L, 2);
  return os_pushresult(L, rename(fromname, toname) == 0, fromname);
}


static int os_tmpname (lua_State *L) {
  char buff[LUA_TMPNAMBUFSIZE];
  int err;
  lua_tmpnam(buff, err);
  if (err)
    return luaL_error(L, "unable to generate a unique filename");
  lua_pushstring(L, buff);
  return 1;
}


static int os_getenv (lua_State *L) {
  lua_pushstring(L, getenv(luaL_checkstring(L, 1)));  /* if NULL push nil */
  return 1;
}


static int os_clock (lua_State *L) {
  lua_pushnumber(L, ((lua_Number)clock())/(lua_Number)CLOCKS_PER_SEC);
  return 1;
}


/*
** {======================================================
** Time/Date operations
** { year=%Y, month=%m, day=%d, hour=%H, min=%M, sec=%S,
**   wday=%w+1, yday=%j, isdst=? }
** =======================================================
*/

static void setfield (lua_State *L, const char *key, int value) {
  lua_pushinteger(L, value);
  lua_setfield(L, -2, key);
}

static void setboolfield (lua_State *L, const char *key, int value) {
  if (value < 0)  /* undefined? */
    return;  /* does not set field */
  lua_pushboolean(L, value);
  lua_setfield(L, -2, key);
}

static int getboolfield (lua_State *L, const char *key) {
  int res;
  lua_getfield(L, -1, key);
  res = lua_isnil(L, -1) ? -1 : lua_toboolean(L, -1);
  lua_pop(L, 1);
  return res;
}


static int getfield (lua_State *L, const char *key, int d) {
  int res;
  lua_getfield(L, -1, key);
  if (lua_isnumber(L, -1))
    res = (int)lua_tointeger(L, -1);
  else {
    if (d < 0)
      return luaL_error(L, "field " LUA_QS " missing in date table", key);
    res = d;
  }
  lua_pop(L, 1);
  return res;
}


static int os_date (lua_State *L) {
  const char *s = luaL_optstring(L, 1, "%c");
  time_t t = luaL_opt(L, (time_t)luaL_checknumber, 2, time(NULL));
  struct tm *stm;
  if (*s == '!') {  /* UTC? */
    stm = gmtime(&t);
    s++;  /* skip `!' */
  }
  else
    stm = localtime(&t);
  if (stm == NULL)  /* invalid date? */
    lua_pushnil(L);
  else if (strcmp(s, "*t") == 0) {
    lua_createtable(L, 0, 9);  /* 9 = number of fields */
    setfield(L, "sec", stm->tm_sec);
    setfield(L, "min", stm->tm_min);
    setfield(L, "hour", stm->tm_hour);
    setfield(L, "day", stm->tm_mday);
    setfield(L, "month", stm->tm_mon+1);
    setfield(L, "year", stm->tm_year+1900);
    setfield(L, "wday", stm->tm_wday+1);
    setfield(L, "yday", stm->tm_yday+1);
    setboolfield(L, "isdst", stm->tm_isdst);
  }
  else {
    char cc[3];
    luaL_Buffer b;
    cc[0] = '%'; cc[2] = '\0';
    luaL_buffinit(L, &b);
    for (; *s; s++) {
      if (*s != '%' || *(s + 1) == '\0')  /* no conversion specifier? */
        luaL_addchar(&b, *s);
      else {
        size_t reslen;
        char buff[200];  /* should be big enough for any conversion result */
        cc[1] = *(++s);
        reslen = strftime(buff, sizeof(buff), cc, stm);
        luaL_addlstring(&b, buff, reslen);
      }
    }
    luaL_pushresult(&b);
  }
  return 1;
}


static int os_time (lua_State *L) {
  time_t t;
  if (lua_isnoneornil(L, 1))  /* called without args? */
    t = time(NULL);  /* get current time */
  else {
    struct tm ts;
    luaL_checktype(L, 1, LUA_TTABLE);
    lua_settop(L, 1);  /* make sure table is at the top */
    ts.tm_sec = getfield(L, "sec", 0);
    ts.tm_min = getfield(L, "min", 0);
    ts.tm_hour = getfield(L, "hour", 12);
    ts.tm_mday = getfield(L, "day", -1);
    ts.tm_mon = getfield(L, "month", -1) - 1;
    ts.tm_year = getfield(L, "year", -1) - 1900;
    ts.tm_isdst = getboolfield(L, "isdst");
    t = mktime(&ts);
  }
  if (t == (time_t)(-1))
    lua_pushnil(L);
  else
    lua_pushnumber(L, (lua_Number)t);
  return 1;
}


static int os_difftime (lua_State *L) {
  lua_pushnumber(L, difftime((time_t)(luaL_checknumber(L, 1)),
                             (time_t)(luaL_optnumber(L, 2, 0))));
  return 1;
}

/* }====================================================== */


static int os_setlocale (lua_State *L) {
  static const int cat[] = {LC_ALL, LC_COLLATE, LC_CTYPE, LC_MONETARY,
                      LC_NUMERIC, LC_TIME};
  static const char *const catnames[] = {"all", "collate", "ctype", "monetary",
     "numeric", "time", NULL};
  const char *l = luaL_optstring(L, 1, NULL);
  int op = luaL_checkoption(L, 2, "all", catnames);
  lua_pushstring(L, setlocale(cat[op], l));
  return 1;
}


static int os_exit (lua_State *L) {
  exit(luaL_optint(L, 1, EXIT_SUCCESS));
}

static const luaL_Reg syslib[] = {
  {"clock",     os_clock},
  {"date",      os_date},
  {"difftime",  os_difftime},
  {"execute",   os_execute},
  {"exit",      os_exit},
  {"getenv",    os_getenv},
  {"remove",    os_remove},
  {"rename",    os_rename},
  {"setlocale", os_setlocale},
  {"time",      os_time},
  {"tmpname",   os_tmpname},
  {NULL, NULL}
};

/* }====================================================== */



LUALIB_API int luaopen_os (lua_State *L) {
  luaL_register(L, LUA_OSLIBNAME, syslib);
  return 1;
}

genometools-1.5.1/src/external/lua-5.1.5/src/lparser.c000066400000000000000000001075301211610345200223130ustar00rootroot00000000000000/*
** $Id: lparser.c,v 2.42.1.4 2011/10/21 19:31:42 roberto Exp $
** Lua Parser
** See Copyright Notice in lua.h
*/


#include 

#define lparser_c
#define LUA_CORE

#include "lua.h"

#include "lcode.h"
#include "ldebug.h"
#include "ldo.h"
#include "lfunc.h"
#include "llex.h"
#include "lmem.h"
#include "lobject.h"
#include "lopcodes.h"
#include "lparser.h"
#include "lstate.h"
#include "lstring.h"
#include "ltable.h"



#define hasmultret(k)		((k) == VCALL || (k) == VVARARG)

#define getlocvar(fs, i)	((fs)->f->locvars[(fs)->actvar[i]])

#define luaY_checklimit(fs,v,l,m)	if ((v)>(l)) errorlimit(fs,l,m)


/*
** nodes for block list (list of active blocks)
*/
typedef struct BlockCnt {
  struct BlockCnt *previous;  /* chain */
  int breaklist;  /* list of jumps out of this loop */
  lu_byte nactvar;  /* # active locals outside the breakable structure */
  lu_byte upval;  /* true if some variable in the block is an upvalue */
  lu_byte isbreakable;  /* true if `block' is a loop */
} BlockCnt;



/*
** prototypes for recursive non-terminal functions
*/
static void chunk (LexState *ls);
static void expr (LexState *ls, expdesc *v);


static void anchor_token (LexState *ls) {
  if (ls->t.token == TK_NAME || ls->t.token == TK_STRING) {
    TString *ts = ls->t.seminfo.ts;
    luaX_newstring(ls, getstr(ts), ts->tsv.len);
  }
}


static void error_expected (LexState *ls, int token) {
  luaX_syntaxerror(ls,
      luaO_pushfstring(ls->L, LUA_QS " expected", luaX_token2str(ls, token)));
}


static void errorlimit (FuncState *fs, int limit, const char *what) {
  const char *msg = (fs->f->linedefined == 0) ?
    luaO_pushfstring(fs->L, "main function has more than %d %s", limit, what) :
    luaO_pushfstring(fs->L, "function at line %d has more than %d %s",
                            fs->f->linedefined, limit, what);
  luaX_lexerror(fs->ls, msg, 0);
}


static int testnext (LexState *ls, int c) {
  if (ls->t.token == c) {
    luaX_next(ls);
    return 1;
  }
  else return 0;
}


static void check (LexState *ls, int c) {
  if (ls->t.token != c)
    error_expected(ls, c);
}

static void checknext (LexState *ls, int c) {
  check(ls, c);
  luaX_next(ls);
}


#define check_condition(ls,c,msg)	{ if (!(c)) luaX_syntaxerror(ls, msg); }



static void check_match (LexState *ls, int what, int who, int where) {
  if (!testnext(ls, what)) {
    if (where == ls->linenumber)
      error_expected(ls, what);
    else {
      luaX_syntaxerror(ls, luaO_pushfstring(ls->L,
             LUA_QS " expected (to close " LUA_QS " at line %d)",
              luaX_token2str(ls, what), luaX_token2str(ls, who), where));
    }
  }
}


static TString *str_checkname (LexState *ls) {
  TString *ts;
  check(ls, TK_NAME);
  ts = ls->t.seminfo.ts;
  luaX_next(ls);
  return ts;
}


static void init_exp (expdesc *e, expkind k, int i) {
  e->f = e->t = NO_JUMP;
  e->k = k;
  e->u.s.info = i;
}


static void codestring (LexState *ls, expdesc *e, TString *s) {
  init_exp(e, VK, luaK_stringK(ls->fs, s));
}


static void checkname(LexState *ls, expdesc *e) {
  codestring(ls, e, str_checkname(ls));
}


static int registerlocalvar (LexState *ls, TString *varname) {
  FuncState *fs = ls->fs;
  Proto *f = fs->f;
  int oldsize = f->sizelocvars;
  luaM_growvector(ls->L, f->locvars, fs->nlocvars, f->sizelocvars,
                  LocVar, SHRT_MAX, "too many local variables");
  while (oldsize < f->sizelocvars) f->locvars[oldsize++].varname = NULL;
  f->locvars[fs->nlocvars].varname = varname;
  luaC_objbarrier(ls->L, f, varname);
  return fs->nlocvars++;
}


#define new_localvarliteral(ls,v,n) \
  new_localvar(ls, luaX_newstring(ls, "" v, (sizeof(v)/sizeof(char))-1), n)


static void new_localvar (LexState *ls, TString *name, int n) {
  FuncState *fs = ls->fs;
  luaY_checklimit(fs, fs->nactvar+n+1, LUAI_MAXVARS, "local variables");
  fs->actvar[fs->nactvar+n] = cast(unsigned short, registerlocalvar(ls, name));
}


static void adjustlocalvars (LexState *ls, int nvars) {
  FuncState *fs = ls->fs;
  fs->nactvar = cast_byte(fs->nactvar + nvars);
  for (; nvars; nvars--) {
    getlocvar(fs, fs->nactvar - nvars).startpc = fs->pc;
  }
}


static void removevars (LexState *ls, int tolevel) {
  FuncState *fs = ls->fs;
  while (fs->nactvar > tolevel)
    getlocvar(fs, --fs->nactvar).endpc = fs->pc;
}


static int indexupvalue (FuncState *fs, TString *name, expdesc *v) {
  int i;
  Proto *f = fs->f;
  int oldsize = f->sizeupvalues;
  for (i=0; inups; i++) {
    if (fs->upvalues[i].k == v->k && fs->upvalues[i].info == v->u.s.info) {
      lua_assert(f->upvalues[i] == name);
      return i;
    }
  }
  /* new one */
  luaY_checklimit(fs, f->nups + 1, LUAI_MAXUPVALUES, "upvalues");
  luaM_growvector(fs->L, f->upvalues, f->nups, f->sizeupvalues,
                  TString *, MAX_INT, "");
  while (oldsize < f->sizeupvalues) f->upvalues[oldsize++] = NULL;
  f->upvalues[f->nups] = name;
  luaC_objbarrier(fs->L, f, name);
  lua_assert(v->k == VLOCAL || v->k == VUPVAL);
  fs->upvalues[f->nups].k = cast_byte(v->k);
  fs->upvalues[f->nups].info = cast_byte(v->u.s.info);
  return f->nups++;
}


static int searchvar (FuncState *fs, TString *n) {
  int i;
  for (i=fs->nactvar-1; i >= 0; i--) {
    if (n == getlocvar(fs, i).varname)
      return i;
  }
  return -1;  /* not found */
}


static void markupval (FuncState *fs, int level) {
  BlockCnt *bl = fs->bl;
  while (bl && bl->nactvar > level) bl = bl->previous;
  if (bl) bl->upval = 1;
}


static int singlevaraux (FuncState *fs, TString *n, expdesc *var, int base) {
  if (fs == NULL) {  /* no more levels? */
    init_exp(var, VGLOBAL, NO_REG);  /* default is global variable */
    return VGLOBAL;
  }
  else {
    int v = searchvar(fs, n);  /* look up at current level */
    if (v >= 0) {
      init_exp(var, VLOCAL, v);
      if (!base)
        markupval(fs, v);  /* local will be used as an upval */
      return VLOCAL;
    }
    else {  /* not found at current level; try upper one */
      if (singlevaraux(fs->prev, n, var, 0) == VGLOBAL)
        return VGLOBAL;
      var->u.s.info = indexupvalue(fs, n, var);  /* else was LOCAL or UPVAL */
      var->k = VUPVAL;  /* upvalue in this level */
      return VUPVAL;
    }
  }
}


static void singlevar (LexState *ls, expdesc *var) {
  TString *varname = str_checkname(ls);
  FuncState *fs = ls->fs;
  if (singlevaraux(fs, varname, var, 1) == VGLOBAL)
    var->u.s.info = luaK_stringK(fs, varname);  /* info points to global name */
}


static void adjust_assign (LexState *ls, int nvars, int nexps, expdesc *e) {
  FuncState *fs = ls->fs;
  int extra = nvars - nexps;
  if (hasmultret(e->k)) {
    extra++;  /* includes call itself */
    if (extra < 0) extra = 0;
    luaK_setreturns(fs, e, extra);  /* last exp. provides the difference */
    if (extra > 1) luaK_reserveregs(fs, extra-1);
  }
  else {
    if (e->k != VVOID) luaK_exp2nextreg(fs, e);  /* close last expression */
    if (extra > 0) {
      int reg = fs->freereg;
      luaK_reserveregs(fs, extra);
      luaK_nil(fs, reg, extra);
    }
  }
}


static void enterlevel (LexState *ls) {
  if (++ls->L->nCcalls > LUAI_MAXCCALLS)
	luaX_lexerror(ls, "chunk has too many syntax levels", 0);
}


#define leavelevel(ls)	((ls)->L->nCcalls--)


static void enterblock (FuncState *fs, BlockCnt *bl, lu_byte isbreakable) {
  bl->breaklist = NO_JUMP;
  bl->isbreakable = isbreakable;
  bl->nactvar = fs->nactvar;
  bl->upval = 0;
  bl->previous = fs->bl;
  fs->bl = bl;
  lua_assert(fs->freereg == fs->nactvar);
}


static void leaveblock (FuncState *fs) {
  BlockCnt *bl = fs->bl;
  fs->bl = bl->previous;
  removevars(fs->ls, bl->nactvar);
  if (bl->upval)
    luaK_codeABC(fs, OP_CLOSE, bl->nactvar, 0, 0);
  /* a block either controls scope or breaks (never both) */
  lua_assert(!bl->isbreakable || !bl->upval);
  lua_assert(bl->nactvar == fs->nactvar);
  fs->freereg = fs->nactvar;  /* free registers */
  luaK_patchtohere(fs, bl->breaklist);
}


static void pushclosure (LexState *ls, FuncState *func, expdesc *v) {
  FuncState *fs = ls->fs;
  Proto *f = fs->f;
  int oldsize = f->sizep;
  int i;
  luaM_growvector(ls->L, f->p, fs->np, f->sizep, Proto *,
                  MAXARG_Bx, "constant table overflow");
  while (oldsize < f->sizep) f->p[oldsize++] = NULL;
  f->p[fs->np++] = func->f;
  luaC_objbarrier(ls->L, f, func->f);
  init_exp(v, VRELOCABLE, luaK_codeABx(fs, OP_CLOSURE, 0, fs->np-1));
  for (i=0; if->nups; i++) {
    OpCode o = (func->upvalues[i].k == VLOCAL) ? OP_MOVE : OP_GETUPVAL;
    luaK_codeABC(fs, o, 0, func->upvalues[i].info, 0);
  }
}


static void open_func (LexState *ls, FuncState *fs) {
  lua_State *L = ls->L;
  Proto *f = luaF_newproto(L);
  fs->f = f;
  fs->prev = ls->fs;  /* linked list of funcstates */
  fs->ls = ls;
  fs->L = L;
  ls->fs = fs;
  fs->pc = 0;
  fs->lasttarget = -1;
  fs->jpc = NO_JUMP;
  fs->freereg = 0;
  fs->nk = 0;
  fs->np = 0;
  fs->nlocvars = 0;
  fs->nactvar = 0;
  fs->bl = NULL;
  f->source = ls->source;
  f->maxstacksize = 2;  /* registers 0/1 are always valid */
  fs->h = luaH_new(L, 0, 0);
  /* anchor table of constants and prototype (to avoid being collected) */
  sethvalue2s(L, L->top, fs->h);
  incr_top(L);
  setptvalue2s(L, L->top, f);
  incr_top(L);
}


static void close_func (LexState *ls) {
  lua_State *L = ls->L;
  FuncState *fs = ls->fs;
  Proto *f = fs->f;
  removevars(ls, 0);
  luaK_ret(fs, 0, 0);  /* final return */
  luaM_reallocvector(L, f->code, f->sizecode, fs->pc, Instruction);
  f->sizecode = fs->pc;
  luaM_reallocvector(L, f->lineinfo, f->sizelineinfo, fs->pc, int);
  f->sizelineinfo = fs->pc;
  luaM_reallocvector(L, f->k, f->sizek, fs->nk, TValue);
  f->sizek = fs->nk;
  luaM_reallocvector(L, f->p, f->sizep, fs->np, Proto *);
  f->sizep = fs->np;
  luaM_reallocvector(L, f->locvars, f->sizelocvars, fs->nlocvars, LocVar);
  f->sizelocvars = fs->nlocvars;
  luaM_reallocvector(L, f->upvalues, f->sizeupvalues, f->nups, TString *);
  f->sizeupvalues = f->nups;
  lua_assert(luaG_checkcode(f));
  lua_assert(fs->bl == NULL);
  ls->fs = fs->prev;
  /* last token read was anchored in defunct function; must reanchor it */
  if (fs) anchor_token(ls);
  L->top -= 2;  /* remove table and prototype from the stack */
}


Proto *luaY_parser (lua_State *L, ZIO *z, Mbuffer *buff, const char *name) {
  struct LexState lexstate;
  struct FuncState funcstate;
  lexstate.buff = buff;
  luaX_setinput(L, &lexstate, z, luaS_new(L, name));
  open_func(&lexstate, &funcstate);
  funcstate.f->is_vararg = VARARG_ISVARARG;  /* main func. is always vararg */
  luaX_next(&lexstate);  /* read first token */
  chunk(&lexstate);
  check(&lexstate, TK_EOS);
  close_func(&lexstate);
  lua_assert(funcstate.prev == NULL);
  lua_assert(funcstate.f->nups == 0);
  lua_assert(lexstate.fs == NULL);
  return funcstate.f;
}



/*============================================================*/
/* GRAMMAR RULES */
/*============================================================*/


static void field (LexState *ls, expdesc *v) {
  /* field -> ['.' | ':'] NAME */
  FuncState *fs = ls->fs;
  expdesc key;
  luaK_exp2anyreg(fs, v);
  luaX_next(ls);  /* skip the dot or colon */
  checkname(ls, &key);
  luaK_indexed(fs, v, &key);
}


static void yindex (LexState *ls, expdesc *v) {
  /* index -> '[' expr ']' */
  luaX_next(ls);  /* skip the '[' */
  expr(ls, v);
  luaK_exp2val(ls->fs, v);
  checknext(ls, ']');
}


/*
** {======================================================================
** Rules for Constructors
** =======================================================================
*/


struct ConsControl {
  expdesc v;  /* last list item read */
  expdesc *t;  /* table descriptor */
  int nh;  /* total number of `record' elements */
  int na;  /* total number of array elements */
  int tostore;  /* number of array elements pending to be stored */
};


static void recfield (LexState *ls, struct ConsControl *cc) {
  /* recfield -> (NAME | `['exp1`]') = exp1 */
  FuncState *fs = ls->fs;
  int reg = ls->fs->freereg;
  expdesc key, val;
  int rkkey;
  if (ls->t.token == TK_NAME) {
    luaY_checklimit(fs, cc->nh, MAX_INT, "items in a constructor");
    checkname(ls, &key);
  }
  else  /* ls->t.token == '[' */
    yindex(ls, &key);
  cc->nh++;
  checknext(ls, '=');
  rkkey = luaK_exp2RK(fs, &key);
  expr(ls, &val);
  luaK_codeABC(fs, OP_SETTABLE, cc->t->u.s.info, rkkey, luaK_exp2RK(fs, &val));
  fs->freereg = reg;  /* free registers */
}


static void closelistfield (FuncState *fs, struct ConsControl *cc) {
  if (cc->v.k == VVOID) return;  /* there is no list item */
  luaK_exp2nextreg(fs, &cc->v);
  cc->v.k = VVOID;
  if (cc->tostore == LFIELDS_PER_FLUSH) {
    luaK_setlist(fs, cc->t->u.s.info, cc->na, cc->tostore);  /* flush */
    cc->tostore = 0;  /* no more items pending */
  }
}


static void lastlistfield (FuncState *fs, struct ConsControl *cc) {
  if (cc->tostore == 0) return;
  if (hasmultret(cc->v.k)) {
    luaK_setmultret(fs, &cc->v);
    luaK_setlist(fs, cc->t->u.s.info, cc->na, LUA_MULTRET);
    cc->na--;  /* do not count last expression (unknown number of elements) */
  }
  else {
    if (cc->v.k != VVOID)
      luaK_exp2nextreg(fs, &cc->v);
    luaK_setlist(fs, cc->t->u.s.info, cc->na, cc->tostore);
  }
}


static void listfield (LexState *ls, struct ConsControl *cc) {
  expr(ls, &cc->v);
  luaY_checklimit(ls->fs, cc->na, MAX_INT, "items in a constructor");
  cc->na++;
  cc->tostore++;
}


static void constructor (LexState *ls, expdesc *t) {
  /* constructor -> ?? */
  FuncState *fs = ls->fs;
  int line = ls->linenumber;
  int pc = luaK_codeABC(fs, OP_NEWTABLE, 0, 0, 0);
  struct ConsControl cc;
  cc.na = cc.nh = cc.tostore = 0;
  cc.t = t;
  init_exp(t, VRELOCABLE, pc);
  init_exp(&cc.v, VVOID, 0);  /* no value (yet) */
  luaK_exp2nextreg(ls->fs, t);  /* fix it at stack top (for gc) */
  checknext(ls, '{');
  do {
    lua_assert(cc.v.k == VVOID || cc.tostore > 0);
    if (ls->t.token == '}') break;
    closelistfield(fs, &cc);
    switch(ls->t.token) {
      case TK_NAME: {  /* may be listfields or recfields */
        luaX_lookahead(ls);
        if (ls->lookahead.token != '=')  /* expression? */
          listfield(ls, &cc);
        else
          recfield(ls, &cc);
        break;
      }
      case '[': {  /* constructor_item -> recfield */
        recfield(ls, &cc);
        break;
      }
      default: {  /* constructor_part -> listfield */
        listfield(ls, &cc);
        break;
      }
    }
  } while (testnext(ls, ',') || testnext(ls, ';'));
  check_match(ls, '}', '{', line);
  lastlistfield(fs, &cc);
  SETARG_B(fs->f->code[pc], luaO_int2fb(cc.na)); /* set initial array size */
  SETARG_C(fs->f->code[pc], luaO_int2fb(cc.nh));  /* set initial table size */
}

/* }====================================================================== */



static void parlist (LexState *ls) {
  /* parlist -> [ param { `,' param } ] */
  FuncState *fs = ls->fs;
  Proto *f = fs->f;
  int nparams = 0;
  f->is_vararg = 0;
  if (ls->t.token != ')') {  /* is `parlist' not empty? */
    do {
      switch (ls->t.token) {
        case TK_NAME: {  /* param -> NAME */
          new_localvar(ls, str_checkname(ls), nparams++);
          break;
        }
        case TK_DOTS: {  /* param -> `...' */
          luaX_next(ls);
#if defined(LUA_COMPAT_VARARG)
          /* use `arg' as default name */
          new_localvarliteral(ls, "arg", nparams++);
          f->is_vararg = VARARG_HASARG | VARARG_NEEDSARG;
#endif
          f->is_vararg |= VARARG_ISVARARG;
          break;
        }
        default: luaX_syntaxerror(ls, " or " LUA_QL("...") " expected");
      }
    } while (!f->is_vararg && testnext(ls, ','));
  }
  adjustlocalvars(ls, nparams);
  f->numparams = cast_byte(fs->nactvar - (f->is_vararg & VARARG_HASARG));
  luaK_reserveregs(fs, fs->nactvar);  /* reserve register for parameters */
}


static void body (LexState *ls, expdesc *e, int needself, int line) {
  /* body ->  `(' parlist `)' chunk END */
  FuncState new_fs;
  open_func(ls, &new_fs);
  new_fs.f->linedefined = line;
  checknext(ls, '(');
  if (needself) {
    new_localvarliteral(ls, "self", 0);
    adjustlocalvars(ls, 1);
  }
  parlist(ls);
  checknext(ls, ')');
  chunk(ls);
  new_fs.f->lastlinedefined = ls->linenumber;
  check_match(ls, TK_END, TK_FUNCTION, line);
  close_func(ls);
  pushclosure(ls, &new_fs, e);
}


static int explist1 (LexState *ls, expdesc *v) {
  /* explist1 -> expr { `,' expr } */
  int n = 1;  /* at least one expression */
  expr(ls, v);
  while (testnext(ls, ',')) {
    luaK_exp2nextreg(ls->fs, v);
    expr(ls, v);
    n++;
  }
  return n;
}


static void funcargs (LexState *ls, expdesc *f) {
  FuncState *fs = ls->fs;
  expdesc args;
  int base, nparams;
  int line = ls->linenumber;
  switch (ls->t.token) {
    case '(': {  /* funcargs -> `(' [ explist1 ] `)' */
      if (line != ls->lastline)
        luaX_syntaxerror(ls,"ambiguous syntax (function call x new statement)");
      luaX_next(ls);
      if (ls->t.token == ')')  /* arg list is empty? */
        args.k = VVOID;
      else {
        explist1(ls, &args);
        luaK_setmultret(fs, &args);
      }
      check_match(ls, ')', '(', line);
      break;
    }
    case '{': {  /* funcargs -> constructor */
      constructor(ls, &args);
      break;
    }
    case TK_STRING: {  /* funcargs -> STRING */
      codestring(ls, &args, ls->t.seminfo.ts);
      luaX_next(ls);  /* must use `seminfo' before `next' */
      break;
    }
    default: {
      luaX_syntaxerror(ls, "function arguments expected");
      return;
    }
  }
  lua_assert(f->k == VNONRELOC);
  base = f->u.s.info;  /* base register for call */
  if (hasmultret(args.k))
    nparams = LUA_MULTRET;  /* open call */
  else {
    if (args.k != VVOID)
      luaK_exp2nextreg(fs, &args);  /* close last argument */
    nparams = fs->freereg - (base+1);
  }
  init_exp(f, VCALL, luaK_codeABC(fs, OP_CALL, base, nparams+1, 2));
  luaK_fixline(fs, line);
  fs->freereg = base+1;  /* call remove function and arguments and leaves
                            (unless changed) one result */
}




/*
** {======================================================================
** Expression parsing
** =======================================================================
*/


static void prefixexp (LexState *ls, expdesc *v) {
  /* prefixexp -> NAME | '(' expr ')' */
  switch (ls->t.token) {
    case '(': {
      int line = ls->linenumber;
      luaX_next(ls);
      expr(ls, v);
      check_match(ls, ')', '(', line);
      luaK_dischargevars(ls->fs, v);
      return;
    }
    case TK_NAME: {
      singlevar(ls, v);
      return;
    }
    default: {
      luaX_syntaxerror(ls, "unexpected symbol");
      return;
    }
  }
}


static void primaryexp (LexState *ls, expdesc *v) {
  /* primaryexp ->
        prefixexp { `.' NAME | `[' exp `]' | `:' NAME funcargs | funcargs } */
  FuncState *fs = ls->fs;
  prefixexp(ls, v);
  for (;;) {
    switch (ls->t.token) {
      case '.': {  /* field */
        field(ls, v);
        break;
      }
      case '[': {  /* `[' exp1 `]' */
        expdesc key;
        luaK_exp2anyreg(fs, v);
        yindex(ls, &key);
        luaK_indexed(fs, v, &key);
        break;
      }
      case ':': {  /* `:' NAME funcargs */
        expdesc key;
        luaX_next(ls);
        checkname(ls, &key);
        luaK_self(fs, v, &key);
        funcargs(ls, v);
        break;
      }
      case '(': case TK_STRING: case '{': {  /* funcargs */
        luaK_exp2nextreg(fs, v);
        funcargs(ls, v);
        break;
      }
      default: return;
    }
  }
}


static void simpleexp (LexState *ls, expdesc *v) {
  /* simpleexp -> NUMBER | STRING | NIL | true | false | ... |
                  constructor | FUNCTION body | primaryexp */
  switch (ls->t.token) {
    case TK_NUMBER: {
      init_exp(v, VKNUM, 0);
      v->u.nval = ls->t.seminfo.r;
      break;
    }
    case TK_STRING: {
      codestring(ls, v, ls->t.seminfo.ts);
      break;
    }
    case TK_NIL: {
      init_exp(v, VNIL, 0);
      break;
    }
    case TK_TRUE: {
      init_exp(v, VTRUE, 0);
      break;
    }
    case TK_FALSE: {
      init_exp(v, VFALSE, 0);
      break;
    }
    case TK_DOTS: {  /* vararg */
      FuncState *fs = ls->fs;
      check_condition(ls, fs->f->is_vararg,
                      "cannot use " LUA_QL("...") " outside a vararg function");
      fs->f->is_vararg &= ~VARARG_NEEDSARG;  /* don't need 'arg' */
      init_exp(v, VVARARG, luaK_codeABC(fs, OP_VARARG, 0, 1, 0));
      break;
    }
    case '{': {  /* constructor */
      constructor(ls, v);
      return;
    }
    case TK_FUNCTION: {
      luaX_next(ls);
      body(ls, v, 0, ls->linenumber);
      return;
    }
    default: {
      primaryexp(ls, v);
      return;
    }
  }
  luaX_next(ls);
}


static UnOpr getunopr (int op) {
  switch (op) {
    case TK_NOT: return OPR_NOT;
    case '-': return OPR_MINUS;
    case '#': return OPR_LEN;
    default: return OPR_NOUNOPR;
  }
}


static BinOpr getbinopr (int op) {
  switch (op) {
    case '+': return OPR_ADD;
    case '-': return OPR_SUB;
    case '*': return OPR_MUL;
    case '/': return OPR_DIV;
    case '%': return OPR_MOD;
    case '^': return OPR_POW;
    case TK_CONCAT: return OPR_CONCAT;
    case TK_NE: return OPR_NE;
    case TK_EQ: return OPR_EQ;
    case '<': return OPR_LT;
    case TK_LE: return OPR_LE;
    case '>': return OPR_GT;
    case TK_GE: return OPR_GE;
    case TK_AND: return OPR_AND;
    case TK_OR: return OPR_OR;
    default: return OPR_NOBINOPR;
  }
}


static const struct {
  lu_byte left;  /* left priority for each binary operator */
  lu_byte right; /* right priority */
} priority[] = {  /* ORDER OPR */
   {6, 6}, {6, 6}, {7, 7}, {7, 7}, {7, 7},  /* `+' `-' `/' `%' */
   {10, 9}, {5, 4},                 /* power and concat (right associative) */
   {3, 3}, {3, 3},                  /* equality and inequality */
   {3, 3}, {3, 3}, {3, 3}, {3, 3},  /* order */
   {2, 2}, {1, 1}                   /* logical (and/or) */
};

#define UNARY_PRIORITY	8  /* priority for unary operators */


/*
** subexpr -> (simpleexp | unop subexpr) { binop subexpr }
** where `binop' is any binary operator with a priority higher than `limit'
*/
static BinOpr subexpr (LexState *ls, expdesc *v, unsigned int limit) {
  BinOpr op;
  UnOpr uop;
  enterlevel(ls);
  uop = getunopr(ls->t.token);
  if (uop != OPR_NOUNOPR) {
    luaX_next(ls);
    subexpr(ls, v, UNARY_PRIORITY);
    luaK_prefix(ls->fs, uop, v);
  }
  else simpleexp(ls, v);
  /* expand while operators have priorities higher than `limit' */
  op = getbinopr(ls->t.token);
  while (op != OPR_NOBINOPR && priority[op].left > limit) {
    expdesc v2;
    BinOpr nextop;
    luaX_next(ls);
    luaK_infix(ls->fs, op, v);
    /* read sub-expression with higher priority */
    nextop = subexpr(ls, &v2, priority[op].right);
    luaK_posfix(ls->fs, op, v, &v2);
    op = nextop;
  }
  leavelevel(ls);
  return op;  /* return first untreated operator */
}


static void expr (LexState *ls, expdesc *v) {
  subexpr(ls, v, 0);
}

/* }==================================================================== */



/*
** {======================================================================
** Rules for Statements
** =======================================================================
*/


static int block_follow (int token) {
  switch (token) {
    case TK_ELSE: case TK_ELSEIF: case TK_END:
    case TK_UNTIL: case TK_EOS:
      return 1;
    default: return 0;
  }
}


static void block (LexState *ls) {
  /* block -> chunk */
  FuncState *fs = ls->fs;
  BlockCnt bl;
  enterblock(fs, &bl, 0);
  chunk(ls);
  lua_assert(bl.breaklist == NO_JUMP);
  leaveblock(fs);
}


/*
** structure to chain all variables in the left-hand side of an
** assignment
*/
struct LHS_assign {
  struct LHS_assign *prev;
  expdesc v;  /* variable (global, local, upvalue, or indexed) */
};


/*
** check whether, in an assignment to a local variable, the local variable
** is needed in a previous assignment (to a table). If so, save original
** local value in a safe place and use this safe copy in the previous
** assignment.
*/
static void check_conflict (LexState *ls, struct LHS_assign *lh, expdesc *v) {
  FuncState *fs = ls->fs;
  int extra = fs->freereg;  /* eventual position to save local variable */
  int conflict = 0;
  for (; lh; lh = lh->prev) {
    if (lh->v.k == VINDEXED) {
      if (lh->v.u.s.info == v->u.s.info) {  /* conflict? */
        conflict = 1;
        lh->v.u.s.info = extra;  /* previous assignment will use safe copy */
      }
      if (lh->v.u.s.aux == v->u.s.info) {  /* conflict? */
        conflict = 1;
        lh->v.u.s.aux = extra;  /* previous assignment will use safe copy */
      }
    }
  }
  if (conflict) {
    luaK_codeABC(fs, OP_MOVE, fs->freereg, v->u.s.info, 0);  /* make copy */
    luaK_reserveregs(fs, 1);
  }
}


static void assignment (LexState *ls, struct LHS_assign *lh, int nvars) {
  expdesc e;
  check_condition(ls, VLOCAL <= lh->v.k && lh->v.k <= VINDEXED,
                      "syntax error");
  if (testnext(ls, ',')) {  /* assignment -> `,' primaryexp assignment */
    struct LHS_assign nv;
    nv.prev = lh;
    primaryexp(ls, &nv.v);
    if (nv.v.k == VLOCAL)
      check_conflict(ls, lh, &nv.v);
    luaY_checklimit(ls->fs, nvars, LUAI_MAXCCALLS - ls->L->nCcalls,
                    "variables in assignment");
    assignment(ls, &nv, nvars+1);
  }
  else {  /* assignment -> `=' explist1 */
    int nexps;
    checknext(ls, '=');
    nexps = explist1(ls, &e);
    if (nexps != nvars) {
      adjust_assign(ls, nvars, nexps, &e);
      if (nexps > nvars)
        ls->fs->freereg -= nexps - nvars;  /* remove extra values */
    }
    else {
      luaK_setoneret(ls->fs, &e);  /* close last expression */
      luaK_storevar(ls->fs, &lh->v, &e);
      return;  /* avoid default */
    }
  }
  init_exp(&e, VNONRELOC, ls->fs->freereg-1);  /* default assignment */
  luaK_storevar(ls->fs, &lh->v, &e);
}


static int cond (LexState *ls) {
  /* cond -> exp */
  expdesc v;
  expr(ls, &v);  /* read condition */
  if (v.k == VNIL) v.k = VFALSE;  /* `falses' are all equal here */
  luaK_goiftrue(ls->fs, &v);
  return v.f;
}


static void breakstat (LexState *ls) {
  FuncState *fs = ls->fs;
  BlockCnt *bl = fs->bl;
  int upval = 0;
  while (bl && !bl->isbreakable) {
    upval |= bl->upval;
    bl = bl->previous;
  }
  if (!bl)
    luaX_syntaxerror(ls, "no loop to break");
  if (upval)
    luaK_codeABC(fs, OP_CLOSE, bl->nactvar, 0, 0);
  luaK_concat(fs, &bl->breaklist, luaK_jump(fs));
}


static void whilestat (LexState *ls, int line) {
  /* whilestat -> WHILE cond DO block END */
  FuncState *fs = ls->fs;
  int whileinit;
  int condexit;
  BlockCnt bl;
  luaX_next(ls);  /* skip WHILE */
  whileinit = luaK_getlabel(fs);
  condexit = cond(ls);
  enterblock(fs, &bl, 1);
  checknext(ls, TK_DO);
  block(ls);
  luaK_patchlist(fs, luaK_jump(fs), whileinit);
  check_match(ls, TK_END, TK_WHILE, line);
  leaveblock(fs);
  luaK_patchtohere(fs, condexit);  /* false conditions finish the loop */
}


static void repeatstat (LexState *ls, int line) {
  /* repeatstat -> REPEAT block UNTIL cond */
  int condexit;
  FuncState *fs = ls->fs;
  int repeat_init = luaK_getlabel(fs);
  BlockCnt bl1, bl2;
  enterblock(fs, &bl1, 1);  /* loop block */
  enterblock(fs, &bl2, 0);  /* scope block */
  luaX_next(ls);  /* skip REPEAT */
  chunk(ls);
  check_match(ls, TK_UNTIL, TK_REPEAT, line);
  condexit = cond(ls);  /* read condition (inside scope block) */
  if (!bl2.upval) {  /* no upvalues? */
    leaveblock(fs);  /* finish scope */
    luaK_patchlist(ls->fs, condexit, repeat_init);  /* close the loop */
  }
  else {  /* complete semantics when there are upvalues */
    breakstat(ls);  /* if condition then break */
    luaK_patchtohere(ls->fs, condexit);  /* else... */
    leaveblock(fs);  /* finish scope... */
    luaK_patchlist(ls->fs, luaK_jump(fs), repeat_init);  /* and repeat */
  }
  leaveblock(fs);  /* finish loop */
}


static int exp1 (LexState *ls) {
  expdesc e;
  int k;
  expr(ls, &e);
  k = e.k;
  luaK_exp2nextreg(ls->fs, &e);
  return k;
}


static void forbody (LexState *ls, int base, int line, int nvars, int isnum) {
  /* forbody -> DO block */
  BlockCnt bl;
  FuncState *fs = ls->fs;
  int prep, endfor;
  adjustlocalvars(ls, 3);  /* control variables */
  checknext(ls, TK_DO);
  prep = isnum ? luaK_codeAsBx(fs, OP_FORPREP, base, NO_JUMP) : luaK_jump(fs);
  enterblock(fs, &bl, 0);  /* scope for declared variables */
  adjustlocalvars(ls, nvars);
  luaK_reserveregs(fs, nvars);
  block(ls);
  leaveblock(fs);  /* end of scope for declared variables */
  luaK_patchtohere(fs, prep);
  endfor = (isnum) ? luaK_codeAsBx(fs, OP_FORLOOP, base, NO_JUMP) :
                     luaK_codeABC(fs, OP_TFORLOOP, base, 0, nvars);
  luaK_fixline(fs, line);  /* pretend that `OP_FOR' starts the loop */
  luaK_patchlist(fs, (isnum ? endfor : luaK_jump(fs)), prep + 1);
}


static void fornum (LexState *ls, TString *varname, int line) {
  /* fornum -> NAME = exp1,exp1[,exp1] forbody */
  FuncState *fs = ls->fs;
  int base = fs->freereg;
  new_localvarliteral(ls, "(for index)", 0);
  new_localvarliteral(ls, "(for limit)", 1);
  new_localvarliteral(ls, "(for step)", 2);
  new_localvar(ls, varname, 3);
  checknext(ls, '=');
  exp1(ls);  /* initial value */
  checknext(ls, ',');
  exp1(ls);  /* limit */
  if (testnext(ls, ','))
    exp1(ls);  /* optional step */
  else {  /* default step = 1 */
    luaK_codeABx(fs, OP_LOADK, fs->freereg, luaK_numberK(fs, 1));
    luaK_reserveregs(fs, 1);
  }
  forbody(ls, base, line, 1, 1);
}


static void forlist (LexState *ls, TString *indexname) {
  /* forlist -> NAME {,NAME} IN explist1 forbody */
  FuncState *fs = ls->fs;
  expdesc e;
  int nvars = 0;
  int line;
  int base = fs->freereg;
  /* create control variables */
  new_localvarliteral(ls, "(for generator)", nvars++);
  new_localvarliteral(ls, "(for state)", nvars++);
  new_localvarliteral(ls, "(for control)", nvars++);
  /* create declared variables */
  new_localvar(ls, indexname, nvars++);
  while (testnext(ls, ','))
    new_localvar(ls, str_checkname(ls), nvars++);
  checknext(ls, TK_IN);
  line = ls->linenumber;
  adjust_assign(ls, 3, explist1(ls, &e), &e);
  luaK_checkstack(fs, 3);  /* extra space to call generator */
  forbody(ls, base, line, nvars - 3, 0);
}


static void forstat (LexState *ls, int line) {
  /* forstat -> FOR (fornum | forlist) END */
  FuncState *fs = ls->fs;
  TString *varname;
  BlockCnt bl;
  enterblock(fs, &bl, 1);  /* scope for loop and control variables */
  luaX_next(ls);  /* skip `for' */
  varname = str_checkname(ls);  /* first variable name */
  switch (ls->t.token) {
    case '=': fornum(ls, varname, line); break;
    case ',': case TK_IN: forlist(ls, varname); break;
    default: luaX_syntaxerror(ls, LUA_QL("=") " or " LUA_QL("in") " expected");
  }
  check_match(ls, TK_END, TK_FOR, line);
  leaveblock(fs);  /* loop scope (`break' jumps to this point) */
}


static int test_then_block (LexState *ls) {
  /* test_then_block -> [IF | ELSEIF] cond THEN block */
  int condexit;
  luaX_next(ls);  /* skip IF or ELSEIF */
  condexit = cond(ls);
  checknext(ls, TK_THEN);
  block(ls);  /* `then' part */
  return condexit;
}


static void ifstat (LexState *ls, int line) {
  /* ifstat -> IF cond THEN block {ELSEIF cond THEN block} [ELSE block] END */
  FuncState *fs = ls->fs;
  int flist;
  int escapelist = NO_JUMP;
  flist = test_then_block(ls);  /* IF cond THEN block */
  while (ls->t.token == TK_ELSEIF) {
    luaK_concat(fs, &escapelist, luaK_jump(fs));
    luaK_patchtohere(fs, flist);
    flist = test_then_block(ls);  /* ELSEIF cond THEN block */
  }
  if (ls->t.token == TK_ELSE) {
    luaK_concat(fs, &escapelist, luaK_jump(fs));
    luaK_patchtohere(fs, flist);
    luaX_next(ls);  /* skip ELSE (after patch, for correct line info) */
    block(ls);  /* `else' part */
  }
  else
    luaK_concat(fs, &escapelist, flist);
  luaK_patchtohere(fs, escapelist);
  check_match(ls, TK_END, TK_IF, line);
}


static void localfunc (LexState *ls) {
  expdesc v, b;
  FuncState *fs = ls->fs;
  new_localvar(ls, str_checkname(ls), 0);
  init_exp(&v, VLOCAL, fs->freereg);
  luaK_reserveregs(fs, 1);
  adjustlocalvars(ls, 1);
  body(ls, &b, 0, ls->linenumber);
  luaK_storevar(fs, &v, &b);
  /* debug information will only see the variable after this point! */
  getlocvar(fs, fs->nactvar - 1).startpc = fs->pc;
}


static void localstat (LexState *ls) {
  /* stat -> LOCAL NAME {`,' NAME} [`=' explist1] */
  int nvars = 0;
  int nexps;
  expdesc e;
  do {
    new_localvar(ls, str_checkname(ls), nvars++);
  } while (testnext(ls, ','));
  if (testnext(ls, '='))
    nexps = explist1(ls, &e);
  else {
    e.k = VVOID;
    nexps = 0;
  }
  adjust_assign(ls, nvars, nexps, &e);
  adjustlocalvars(ls, nvars);
}


static int funcname (LexState *ls, expdesc *v) {
  /* funcname -> NAME {field} [`:' NAME] */
  int needself = 0;
  singlevar(ls, v);
  while (ls->t.token == '.')
    field(ls, v);
  if (ls->t.token == ':') {
    needself = 1;
    field(ls, v);
  }
  return needself;
}


static void funcstat (LexState *ls, int line) {
  /* funcstat -> FUNCTION funcname body */
  int needself;
  expdesc v, b;
  luaX_next(ls);  /* skip FUNCTION */
  needself = funcname(ls, &v);
  body(ls, &b, needself, line);
  luaK_storevar(ls->fs, &v, &b);
  luaK_fixline(ls->fs, line);  /* definition `happens' in the first line */
}


static void exprstat (LexState *ls) {
  /* stat -> func | assignment */
  FuncState *fs = ls->fs;
  struct LHS_assign v;
  primaryexp(ls, &v.v);
  if (v.v.k == VCALL)  /* stat -> func */
    SETARG_C(getcode(fs, &v.v), 1);  /* call statement uses no results */
  else {  /* stat -> assignment */
    v.prev = NULL;
    assignment(ls, &v, 1);
  }
}


static void retstat (LexState *ls) {
  /* stat -> RETURN explist */
  FuncState *fs = ls->fs;
  expdesc e;
  int first, nret;  /* registers with returned values */
  luaX_next(ls);  /* skip RETURN */
  if (block_follow(ls->t.token) || ls->t.token == ';')
    first = nret = 0;  /* return no values */
  else {
    nret = explist1(ls, &e);  /* optional return values */
    if (hasmultret(e.k)) {
      luaK_setmultret(fs, &e);
      if (e.k == VCALL && nret == 1) {  /* tail call? */
        SET_OPCODE(getcode(fs,&e), OP_TAILCALL);
        lua_assert(GETARG_A(getcode(fs,&e)) == fs->nactvar);
      }
      first = fs->nactvar;
      nret = LUA_MULTRET;  /* return all values */
    }
    else {
      if (nret == 1)  /* only one single value? */
        first = luaK_exp2anyreg(fs, &e);
      else {
        luaK_exp2nextreg(fs, &e);  /* values must go to the `stack' */
        first = fs->nactvar;  /* return all `active' values */
        lua_assert(nret == fs->freereg - first);
      }
    }
  }
  luaK_ret(fs, first, nret);
}


static int statement (LexState *ls) {
  int line = ls->linenumber;  /* may be needed for error messages */
  switch (ls->t.token) {
    case TK_IF: {  /* stat -> ifstat */
      ifstat(ls, line);
      return 0;
    }
    case TK_WHILE: {  /* stat -> whilestat */
      whilestat(ls, line);
      return 0;
    }
    case TK_DO: {  /* stat -> DO block END */
      luaX_next(ls);  /* skip DO */
      block(ls);
      check_match(ls, TK_END, TK_DO, line);
      return 0;
    }
    case TK_FOR: {  /* stat -> forstat */
      forstat(ls, line);
      return 0;
    }
    case TK_REPEAT: {  /* stat -> repeatstat */
      repeatstat(ls, line);
      return 0;
    }
    case TK_FUNCTION: {
      funcstat(ls, line);  /* stat -> funcstat */
      return 0;
    }
    case TK_LOCAL: {  /* stat -> localstat */
      luaX_next(ls);  /* skip LOCAL */
      if (testnext(ls, TK_FUNCTION))  /* local function? */
        localfunc(ls);
      else
        localstat(ls);
      return 0;
    }
    case TK_RETURN: {  /* stat -> retstat */
      retstat(ls);
      return 1;  /* must be last statement */
    }
    case TK_BREAK: {  /* stat -> breakstat */
      luaX_next(ls);  /* skip BREAK */
      breakstat(ls);
      return 1;  /* must be last statement */
    }
    default: {
      exprstat(ls);
      return 0;  /* to avoid warnings */
    }
  }
}


static void chunk (LexState *ls) {
  /* chunk -> { stat [`;'] } */
  int islast = 0;
  enterlevel(ls);
  while (!islast && !block_follow(ls->t.token)) {
    islast = statement(ls);
    testnext(ls, ';');
    lua_assert(ls->fs->f->maxstacksize >= ls->fs->freereg &&
               ls->fs->freereg >= ls->fs->nactvar);
    ls->fs->freereg = ls->fs->nactvar;  /* free registers */
  }
  leavelevel(ls);
}

/* }====================================================================== */
genometools-1.5.1/src/external/lua-5.1.5/src/lparser.h000066400000000000000000000043251211610345200223160ustar00rootroot00000000000000/*
** $Id: lparser.h,v 1.57.1.1 2007/12/27 13:02:25 roberto Exp $
** Lua Parser
** See Copyright Notice in lua.h
*/

#ifndef lparser_h
#define lparser_h

#include "llimits.h"
#include "lobject.h"
#include "lzio.h"


/*
** Expression descriptor
*/

typedef enum {
  VVOID,	/* no value */
  VNIL,
  VTRUE,
  VFALSE,
  VK,		/* info = index of constant in `k' */
  VKNUM,	/* nval = numerical value */
  VLOCAL,	/* info = local register */
  VUPVAL,       /* info = index of upvalue in `upvalues' */
  VGLOBAL,	/* info = index of table; aux = index of global name in `k' */
  VINDEXED,	/* info = table register; aux = index register (or `k') */
  VJMP,		/* info = instruction pc */
  VRELOCABLE,	/* info = instruction pc */
  VNONRELOC,	/* info = result register */
  VCALL,	/* info = instruction pc */
  VVARARG	/* info = instruction pc */
} expkind;

typedef struct expdesc {
  expkind k;
  union {
    struct { int info, aux; } s;
    lua_Number nval;
  } u;
  int t;  /* patch list of `exit when true' */
  int f;  /* patch list of `exit when false' */
} expdesc;


typedef struct upvaldesc {
  lu_byte k;
  lu_byte info;
} upvaldesc;


struct BlockCnt;  /* defined in lparser.c */


/* state needed to generate code for a given function */
typedef struct FuncState {
  Proto *f;  /* current function header */
  Table *h;  /* table to find (and reuse) elements in `k' */
  struct FuncState *prev;  /* enclosing function */
  struct LexState *ls;  /* lexical state */
  struct lua_State *L;  /* copy of the Lua state */
  struct BlockCnt *bl;  /* chain of current blocks */
  int pc;  /* next position to code (equivalent to `ncode') */
  int lasttarget;   /* `pc' of last `jump target' */
  int jpc;  /* list of pending jumps to `pc' */
  int freereg;  /* first free register */
  int nk;  /* number of elements in `k' */
  int np;  /* number of elements in `p' */
  short nlocvars;  /* number of elements in `locvars' */
  lu_byte nactvar;  /* number of active local variables */
  upvaldesc upvalues[LUAI_MAXUPVALUES];  /* upvalues */
  unsigned short actvar[LUAI_MAXVARS];  /* declared-variable stack */
} FuncState;


LUAI_FUNC Proto *luaY_parser (lua_State *L, ZIO *z, Mbuffer *buff,
                                            const char *name);


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/lstate.c000066400000000000000000000130521211610345200221320ustar00rootroot00000000000000/*
** $Id: lstate.c,v 2.36.1.2 2008/01/03 15:20:39 roberto Exp $
** Global State
** See Copyright Notice in lua.h
*/


#include 

#define lstate_c
#define LUA_CORE

#include "lua.h"

#include "ldebug.h"
#include "ldo.h"
#include "lfunc.h"
#include "lgc.h"
#include "llex.h"
#include "lmem.h"
#include "lstate.h"
#include "lstring.h"
#include "ltable.h"
#include "ltm.h"


#define state_size(x)	(sizeof(x) + LUAI_EXTRASPACE)
#define fromstate(l)	(cast(lu_byte *, (l)) - LUAI_EXTRASPACE)
#define tostate(l)   (cast(lua_State *, cast(lu_byte *, l) + LUAI_EXTRASPACE))


/*
** Main thread combines a thread state and the global state
*/
typedef struct LG {
  lua_State l;
  global_State g;
} LG;
  


static void stack_init (lua_State *L1, lua_State *L) {
  /* initialize CallInfo array */
  L1->base_ci = luaM_newvector(L, BASIC_CI_SIZE, CallInfo);
  L1->ci = L1->base_ci;
  L1->size_ci = BASIC_CI_SIZE;
  L1->end_ci = L1->base_ci + L1->size_ci - 1;
  /* initialize stack array */
  L1->stack = luaM_newvector(L, BASIC_STACK_SIZE + EXTRA_STACK, TValue);
  L1->stacksize = BASIC_STACK_SIZE + EXTRA_STACK;
  L1->top = L1->stack;
  L1->stack_last = L1->stack+(L1->stacksize - EXTRA_STACK)-1;
  /* initialize first ci */
  L1->ci->func = L1->top;
  setnilvalue(L1->top++);  /* `function' entry for this `ci' */
  L1->base = L1->ci->base = L1->top;
  L1->ci->top = L1->top + LUA_MINSTACK;
}


static void freestack (lua_State *L, lua_State *L1) {
  luaM_freearray(L, L1->base_ci, L1->size_ci, CallInfo);
  luaM_freearray(L, L1->stack, L1->stacksize, TValue);
}


/*
** open parts that may cause memory-allocation errors
*/
static void f_luaopen (lua_State *L, void *ud) {
  global_State *g = G(L);
  UNUSED(ud);
  stack_init(L, L);  /* init stack */
  sethvalue(L, gt(L), luaH_new(L, 0, 2));  /* table of globals */
  sethvalue(L, registry(L), luaH_new(L, 0, 2));  /* registry */
  luaS_resize(L, MINSTRTABSIZE);  /* initial size of string table */
  luaT_init(L);
  luaX_init(L);
  luaS_fix(luaS_newliteral(L, MEMERRMSG));
  g->GCthreshold = 4*g->totalbytes;
}


static void preinit_state (lua_State *L, global_State *g) {
  G(L) = g;
  L->stack = NULL;
  L->stacksize = 0;
  L->errorJmp = NULL;
  L->hook = NULL;
  L->hookmask = 0;
  L->basehookcount = 0;
  L->allowhook = 1;
  resethookcount(L);
  L->openupval = NULL;
  L->size_ci = 0;
  L->nCcalls = L->baseCcalls = 0;
  L->status = 0;
  L->base_ci = L->ci = NULL;
  L->savedpc = NULL;
  L->errfunc = 0;
  setnilvalue(gt(L));
}


static void close_state (lua_State *L) {
  global_State *g = G(L);
  luaF_close(L, L->stack);  /* close all upvalues for this thread */
  luaC_freeall(L);  /* collect all objects */
  lua_assert(g->rootgc == obj2gco(L));
  lua_assert(g->strt.nuse == 0);
  luaM_freearray(L, G(L)->strt.hash, G(L)->strt.size, TString *);
  luaZ_freebuffer(L, &g->buff);
  freestack(L, L);
  lua_assert(g->totalbytes == sizeof(LG));
  (*g->frealloc)(g->ud, fromstate(L), state_size(LG), 0);
}


lua_State *luaE_newthread (lua_State *L) {
  lua_State *L1 = tostate(luaM_malloc(L, state_size(lua_State)));
  luaC_link(L, obj2gco(L1), LUA_TTHREAD);
  preinit_state(L1, G(L));
  stack_init(L1, L);  /* init stack */
  setobj2n(L, gt(L1), gt(L));  /* share table of globals */
  L1->hookmask = L->hookmask;
  L1->basehookcount = L->basehookcount;
  L1->hook = L->hook;
  resethookcount(L1);
  lua_assert(iswhite(obj2gco(L1)));
  return L1;
}


void luaE_freethread (lua_State *L, lua_State *L1) {
  luaF_close(L1, L1->stack);  /* close all upvalues for this thread */
  lua_assert(L1->openupval == NULL);
  luai_userstatefree(L1);
  freestack(L, L1);
  luaM_freemem(L, fromstate(L1), state_size(lua_State));
}


LUA_API lua_State *lua_newstate (lua_Alloc f, void *ud) {
  int i;
  lua_State *L;
  global_State *g;
  void *l = (*f)(ud, NULL, 0, state_size(LG));
  if (l == NULL) return NULL;
  L = tostate(l);
  g = &((LG *)L)->g;
  L->next = NULL;
  L->tt = LUA_TTHREAD;
  g->currentwhite = bit2mask(WHITE0BIT, FIXEDBIT);
  L->marked = luaC_white(g);
  set2bits(L->marked, FIXEDBIT, SFIXEDBIT);
  preinit_state(L, g);
  g->frealloc = f;
  g->ud = ud;
  g->mainthread = L;
  g->uvhead.u.l.prev = &g->uvhead;
  g->uvhead.u.l.next = &g->uvhead;
  g->GCthreshold = 0;  /* mark it as unfinished state */
  g->strt.size = 0;
  g->strt.nuse = 0;
  g->strt.hash = NULL;
  setnilvalue(registry(L));
  luaZ_initbuffer(L, &g->buff);
  g->panic = NULL;
  g->gcstate = GCSpause;
  g->rootgc = obj2gco(L);
  g->sweepstrgc = 0;
  g->sweepgc = &g->rootgc;
  g->gray = NULL;
  g->grayagain = NULL;
  g->weak = NULL;
  g->tmudata = NULL;
  g->totalbytes = sizeof(LG);
  g->gcpause = LUAI_GCPAUSE;
  g->gcstepmul = LUAI_GCMUL;
  g->gcdept = 0;
  for (i=0; imt[i] = NULL;
  if (luaD_rawrunprotected(L, f_luaopen, NULL) != 0) {
    /* memory allocation error: free partial state */
    close_state(L);
    L = NULL;
  }
  else
    luai_userstateopen(L);
  return L;
}


static void callallgcTM (lua_State *L, void *ud) {
  UNUSED(ud);
  luaC_callGCTM(L);  /* call GC metamethods for all udata */
}


LUA_API void lua_close (lua_State *L) {
  L = G(L)->mainthread;  /* only the main thread can be closed */
  lua_lock(L);
  luaF_close(L, L->stack);  /* close all upvalues for this thread */
  luaC_separateudata(L, 1);  /* separate udata that have GC metamethods */
  L->errfunc = 0;  /* no error function during GC metamethods */
  do {  /* repeat until no more errors */
    L->ci = L->base_ci;
    L->base = L->top = L->ci->base;
    L->nCcalls = L->baseCcalls = 0;
  } while (luaD_rawrunprotected(L, callallgcTM, NULL) != 0);
  lua_assert(G(L)->tmudata == NULL);
  luai_userstateclose(L);
  close_state(L);
}

genometools-1.5.1/src/external/lua-5.1.5/src/lstate.h000066400000000000000000000116231211610345200221410ustar00rootroot00000000000000/*
** $Id: lstate.h,v 2.24.1.2 2008/01/03 15:20:39 roberto Exp $
** Global State
** See Copyright Notice in lua.h
*/

#ifndef lstate_h
#define lstate_h

#include "lua.h"

#include "lobject.h"
#include "ltm.h"
#include "lzio.h"



struct lua_longjmp;  /* defined in ldo.c */


/* table of globals */
#define gt(L)	(&L->l_gt)

/* registry */
#define registry(L)	(&G(L)->l_registry)


/* extra stack space to handle TM calls and some other extras */
#define EXTRA_STACK   5


#define BASIC_CI_SIZE           8

#define BASIC_STACK_SIZE        (2*LUA_MINSTACK)



typedef struct stringtable {
  GCObject **hash;
  lu_int32 nuse;  /* number of elements */
  int size;
} stringtable;


/*
** informations about a call
*/
typedef struct CallInfo {
  StkId base;  /* base for this function */
  StkId func;  /* function index in the stack */
  StkId	top;  /* top for this function */
  const Instruction *savedpc;
  int nresults;  /* expected number of results from this function */
  int tailcalls;  /* number of tail calls lost under this entry */
} CallInfo;



#define curr_func(L)	(clvalue(L->ci->func))
#define ci_func(ci)	(clvalue((ci)->func))
#define f_isLua(ci)	(!ci_func(ci)->c.isC)
#define isLua(ci)	(ttisfunction((ci)->func) && f_isLua(ci))


/*
** `global state', shared by all threads of this state
*/
typedef struct global_State {
  stringtable strt;  /* hash table for strings */
  lua_Alloc frealloc;  /* function to reallocate memory */
  void *ud;         /* auxiliary data to `frealloc' */
  lu_byte currentwhite;
  lu_byte gcstate;  /* state of garbage collector */
  int sweepstrgc;  /* position of sweep in `strt' */
  GCObject *rootgc;  /* list of all collectable objects */
  GCObject **sweepgc;  /* position of sweep in `rootgc' */
  GCObject *gray;  /* list of gray objects */
  GCObject *grayagain;  /* list of objects to be traversed atomically */
  GCObject *weak;  /* list of weak tables (to be cleared) */
  GCObject *tmudata;  /* last element of list of userdata to be GC */
  Mbuffer buff;  /* temporary buffer for string concatentation */
  lu_mem GCthreshold;
  lu_mem totalbytes;  /* number of bytes currently allocated */
  lu_mem estimate;  /* an estimate of number of bytes actually in use */
  lu_mem gcdept;  /* how much GC is `behind schedule' */
  int gcpause;  /* size of pause between successive GCs */
  int gcstepmul;  /* GC `granularity' */
  lua_CFunction panic;  /* to be called in unprotected errors */
  TValue l_registry;
  struct lua_State *mainthread;
  UpVal uvhead;  /* head of double-linked list of all open upvalues */
  struct Table *mt[NUM_TAGS];  /* metatables for basic types */
  TString *tmname[TM_N];  /* array with tag-method names */
} global_State;


/*
** `per thread' state
*/
struct lua_State {
  CommonHeader;
  lu_byte status;
  StkId top;  /* first free slot in the stack */
  StkId base;  /* base of current function */
  global_State *l_G;
  CallInfo *ci;  /* call info for current function */
  const Instruction *savedpc;  /* `savedpc' of current function */
  StkId stack_last;  /* last free slot in the stack */
  StkId stack;  /* stack base */
  CallInfo *end_ci;  /* points after end of ci array*/
  CallInfo *base_ci;  /* array of CallInfo's */
  int stacksize;
  int size_ci;  /* size of array `base_ci' */
  unsigned short nCcalls;  /* number of nested C calls */
  unsigned short baseCcalls;  /* nested C calls when resuming coroutine */
  lu_byte hookmask;
  lu_byte allowhook;
  int basehookcount;
  int hookcount;
  lua_Hook hook;
  TValue l_gt;  /* table of globals */
  TValue env;  /* temporary place for environments */
  GCObject *openupval;  /* list of open upvalues in this stack */
  GCObject *gclist;
  struct lua_longjmp *errorJmp;  /* current error recover point */
  ptrdiff_t errfunc;  /* current error handling function (stack index) */
};


#define G(L)	(L->l_G)


/*
** Union of all collectable objects
*/
union GCObject {
  GCheader gch;
  union TString ts;
  union Udata u;
  union Closure cl;
  struct Table h;
  struct Proto p;
  struct UpVal uv;
  struct lua_State th;  /* thread */
};


/* macros to convert a GCObject into a specific value */
#define rawgco2ts(o)	check_exp((o)->gch.tt == LUA_TSTRING, &((o)->ts))
#define gco2ts(o)	(&rawgco2ts(o)->tsv)
#define rawgco2u(o)	check_exp((o)->gch.tt == LUA_TUSERDATA, &((o)->u))
#define gco2u(o)	(&rawgco2u(o)->uv)
#define gco2cl(o)	check_exp((o)->gch.tt == LUA_TFUNCTION, &((o)->cl))
#define gco2h(o)	check_exp((o)->gch.tt == LUA_TTABLE, &((o)->h))
#define gco2p(o)	check_exp((o)->gch.tt == LUA_TPROTO, &((o)->p))
#define gco2uv(o)	check_exp((o)->gch.tt == LUA_TUPVAL, &((o)->uv))
#define ngcotouv(o) \
	check_exp((o) == NULL || (o)->gch.tt == LUA_TUPVAL, &((o)->uv))
#define gco2th(o)	check_exp((o)->gch.tt == LUA_TTHREAD, &((o)->th))

/* macro to convert any Lua object into a GCObject */
#define obj2gco(v)	(cast(GCObject *, (v)))


LUAI_FUNC lua_State *luaE_newthread (lua_State *L);
LUAI_FUNC void luaE_freethread (lua_State *L, lua_State *L1);

#endif

genometools-1.5.1/src/external/lua-5.1.5/src/lstring.c000066400000000000000000000060461211610345200223250ustar00rootroot00000000000000/*
** $Id: lstring.c,v 2.8.1.1 2007/12/27 13:02:25 roberto Exp $
** String table (keeps all strings handled by Lua)
** See Copyright Notice in lua.h
*/


#include 

#define lstring_c
#define LUA_CORE

#include "lua.h"

#include "lmem.h"
#include "lobject.h"
#include "lstate.h"
#include "lstring.h"



void luaS_resize (lua_State *L, int newsize) {
  GCObject **newhash;
  stringtable *tb;
  int i;
  if (G(L)->gcstate == GCSsweepstring)
    return;  /* cannot resize during GC traverse */
  newhash = luaM_newvector(L, newsize, GCObject *);
  tb = &G(L)->strt;
  for (i=0; isize; i++) {
    GCObject *p = tb->hash[i];
    while (p) {  /* for each node in the list */
      GCObject *next = p->gch.next;  /* save next */
      unsigned int h = gco2ts(p)->hash;
      int h1 = lmod(h, newsize);  /* new position */
      lua_assert(cast_int(h%newsize) == lmod(h, newsize));
      p->gch.next = newhash[h1];  /* chain it */
      newhash[h1] = p;
      p = next;
    }
  }
  luaM_freearray(L, tb->hash, tb->size, TString *);
  tb->size = newsize;
  tb->hash = newhash;
}


static TString *newlstr (lua_State *L, const char *str, size_t l,
                                       unsigned int h) {
  TString *ts;
  stringtable *tb;
  if (l+1 > (MAX_SIZET - sizeof(TString))/sizeof(char))
    luaM_toobig(L);
  ts = cast(TString *, luaM_malloc(L, (l+1)*sizeof(char)+sizeof(TString)));
  ts->tsv.len = l;
  ts->tsv.hash = h;
  ts->tsv.marked = luaC_white(G(L));
  ts->tsv.tt = LUA_TSTRING;
  ts->tsv.reserved = 0;
  memcpy(ts+1, str, l*sizeof(char));
  ((char *)(ts+1))[l] = '\0';  /* ending 0 */
  tb = &G(L)->strt;
  h = lmod(h, tb->size);
  ts->tsv.next = tb->hash[h];  /* chain new entry */
  tb->hash[h] = obj2gco(ts);
  tb->nuse++;
  if (tb->nuse > cast(lu_int32, tb->size) && tb->size <= MAX_INT/2)
    luaS_resize(L, tb->size*2);  /* too crowded */
  return ts;
}


TString *luaS_newlstr (lua_State *L, const char *str, size_t l) {
  GCObject *o;
  unsigned int h = cast(unsigned int, l);  /* seed */
  size_t step = (l>>5)+1;  /* if string is too long, don't hash all its chars */
  size_t l1;
  for (l1=l; l1>=step; l1-=step)  /* compute hash */
    h = h ^ ((h<<5)+(h>>2)+cast(unsigned char, str[l1-1]));
  for (o = G(L)->strt.hash[lmod(h, G(L)->strt.size)];
       o != NULL;
       o = o->gch.next) {
    TString *ts = rawgco2ts(o);
    if (ts->tsv.len == l && (memcmp(str, getstr(ts), l) == 0)) {
      /* string may be dead */
      if (isdead(G(L), o)) changewhite(o);
      return ts;
    }
  }
  return newlstr(L, str, l, h);  /* not found */
}


Udata *luaS_newudata (lua_State *L, size_t s, Table *e) {
  Udata *u;
  if (s > MAX_SIZET - sizeof(Udata))
    luaM_toobig(L);
  u = cast(Udata *, luaM_malloc(L, s + sizeof(Udata)));
  u->uv.marked = luaC_white(G(L));  /* is not finalized */
  u->uv.tt = LUA_TUSERDATA;
  u->uv.len = s;
  u->uv.metatable = NULL;
  u->uv.env = e;
  /* chain it on udata list (after main thread) */
  u->uv.next = G(L)->mainthread->next;
  G(L)->mainthread->next = obj2gco(u);
  return u;
}

genometools-1.5.1/src/external/lua-5.1.5/src/lstring.h000066400000000000000000000014561211610345200223320ustar00rootroot00000000000000/*
** $Id: lstring.h,v 1.43.1.1 2007/12/27 13:02:25 roberto Exp $
** String table (keep all strings handled by Lua)
** See Copyright Notice in lua.h
*/

#ifndef lstring_h
#define lstring_h


#include "lgc.h"
#include "lobject.h"
#include "lstate.h"


#define sizestring(s)	(sizeof(union TString)+((s)->len+1)*sizeof(char))

#define sizeudata(u)	(sizeof(union Udata)+(u)->len)

#define luaS_new(L, s)	(luaS_newlstr(L, s, strlen(s)))
#define luaS_newliteral(L, s)	(luaS_newlstr(L, "" s, \
                                 (sizeof(s)/sizeof(char))-1))

#define luaS_fix(s)	l_setbit((s)->tsv.marked, FIXEDBIT)

LUAI_FUNC void luaS_resize (lua_State *L, int newsize);
LUAI_FUNC Udata *luaS_newudata (lua_State *L, size_t s, Table *e);
LUAI_FUNC TString *luaS_newlstr (lua_State *L, const char *str, size_t l);


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/lstrlib.c000066400000000000000000000560111211610345200223130ustar00rootroot00000000000000/*
** $Id: lstrlib.c,v 1.132.1.5 2010/05/14 15:34:19 roberto Exp $
** Standard library for string operations and pattern-matching
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 
#include 
#include 

#define lstrlib_c
#define LUA_LIB

#include "lua.h"

#include "lauxlib.h"
#include "lualib.h"


/* macro to `unsign' a character */
#define uchar(c)        ((unsigned char)(c))



static int str_len (lua_State *L) {
  size_t l;
  luaL_checklstring(L, 1, &l);
  lua_pushinteger(L, l);
  return 1;
}


static ptrdiff_t posrelat (ptrdiff_t pos, size_t len) {
  /* relative string position: negative means back from end */
  if (pos < 0) pos += (ptrdiff_t)len + 1;
  return (pos >= 0) ? pos : 0;
}


static int str_sub (lua_State *L) {
  size_t l;
  const char *s = luaL_checklstring(L, 1, &l);
  ptrdiff_t start = posrelat(luaL_checkinteger(L, 2), l);
  ptrdiff_t end = posrelat(luaL_optinteger(L, 3, -1), l);
  if (start < 1) start = 1;
  if (end > (ptrdiff_t)l) end = (ptrdiff_t)l;
  if (start <= end)
    lua_pushlstring(L, s+start-1, end-start+1);
  else lua_pushliteral(L, "");
  return 1;
}


static int str_reverse (lua_State *L) {
  size_t l;
  luaL_Buffer b;
  const char *s = luaL_checklstring(L, 1, &l);
  luaL_buffinit(L, &b);
  while (l--) luaL_addchar(&b, s[l]);
  luaL_pushresult(&b);
  return 1;
}


static int str_lower (lua_State *L) {
  size_t l;
  size_t i;
  luaL_Buffer b;
  const char *s = luaL_checklstring(L, 1, &l);
  luaL_buffinit(L, &b);
  for (i=0; i 0)
    luaL_addlstring(&b, s, l);
  luaL_pushresult(&b);
  return 1;
}


static int str_byte (lua_State *L) {
  size_t l;
  const char *s = luaL_checklstring(L, 1, &l);
  ptrdiff_t posi = posrelat(luaL_optinteger(L, 2, 1), l);
  ptrdiff_t pose = posrelat(luaL_optinteger(L, 3, posi), l);
  int n, i;
  if (posi <= 0) posi = 1;
  if ((size_t)pose > l) pose = l;
  if (posi > pose) return 0;  /* empty interval; return no values */
  n = (int)(pose -  posi + 1);
  if (posi + n <= pose)  /* overflow? */
    luaL_error(L, "string slice too long");
  luaL_checkstack(L, n, "string slice too long");
  for (i=0; i= ms->level || ms->capture[l].len == CAP_UNFINISHED)
    return luaL_error(ms->L, "invalid capture index");
  return l;
}


static int capture_to_close (MatchState *ms) {
  int level = ms->level;
  for (level--; level>=0; level--)
    if (ms->capture[level].len == CAP_UNFINISHED) return level;
  return luaL_error(ms->L, "invalid pattern capture");
}


static const char *classend (MatchState *ms, const char *p) {
  switch (*p++) {
    case L_ESC: {
      if (*p == '\0')
        luaL_error(ms->L, "malformed pattern (ends with " LUA_QL("%%") ")");
      return p+1;
    }
    case '[': {
      if (*p == '^') p++;
      do {  /* look for a `]' */
        if (*p == '\0')
          luaL_error(ms->L, "malformed pattern (missing " LUA_QL("]") ")");
        if (*(p++) == L_ESC && *p != '\0')
          p++;  /* skip escapes (e.g. `%]') */
      } while (*p != ']');
      return p+1;
    }
    default: {
      return p;
    }
  }
}


static int match_class (int c, int cl) {
  int res;
  switch (tolower(cl)) {
    case 'a' : res = isalpha(c); break;
    case 'c' : res = iscntrl(c); break;
    case 'd' : res = isdigit(c); break;
    case 'l' : res = islower(c); break;
    case 'p' : res = ispunct(c); break;
    case 's' : res = isspace(c); break;
    case 'u' : res = isupper(c); break;
    case 'w' : res = isalnum(c); break;
    case 'x' : res = isxdigit(c); break;
    case 'z' : res = (c == 0); break;
    default: return (cl == c);
  }
  return (islower(cl) ? res : !res);
}


static int matchbracketclass (int c, const char *p, const char *ec) {
  int sig = 1;
  if (*(p+1) == '^') {
    sig = 0;
    p++;  /* skip the `^' */
  }
  while (++p < ec) {
    if (*p == L_ESC) {
      p++;
      if (match_class(c, uchar(*p)))
        return sig;
    }
    else if ((*(p+1) == '-') && (p+2 < ec)) {
      p+=2;
      if (uchar(*(p-2)) <= c && c <= uchar(*p))
        return sig;
    }
    else if (uchar(*p) == c) return sig;
  }
  return !sig;
}


static int singlematch (int c, const char *p, const char *ep) {
  switch (*p) {
    case '.': return 1;  /* matches any char */
    case L_ESC: return match_class(c, uchar(*(p+1)));
    case '[': return matchbracketclass(c, p, ep-1);
    default:  return (uchar(*p) == c);
  }
}


static const char *match (MatchState *ms, const char *s, const char *p);


static const char *matchbalance (MatchState *ms, const char *s,
                                   const char *p) {
  if (*p == 0 || *(p+1) == 0)
    luaL_error(ms->L, "unbalanced pattern");
  if (*s != *p) return NULL;
  else {
    int b = *p;
    int e = *(p+1);
    int cont = 1;
    while (++s < ms->src_end) {
      if (*s == e) {
        if (--cont == 0) return s+1;
      }
      else if (*s == b) cont++;
    }
  }
  return NULL;  /* string ends out of balance */
}


static const char *max_expand (MatchState *ms, const char *s,
                                 const char *p, const char *ep) {
  ptrdiff_t i = 0;  /* counts maximum expand for item */
  while ((s+i)src_end && singlematch(uchar(*(s+i)), p, ep))
    i++;
  /* keeps trying to match with the maximum repetitions */
  while (i>=0) {
    const char *res = match(ms, (s+i), ep+1);
    if (res) return res;
    i--;  /* else didn't match; reduce 1 repetition to try again */
  }
  return NULL;
}


static const char *min_expand (MatchState *ms, const char *s,
                                 const char *p, const char *ep) {
  for (;;) {
    const char *res = match(ms, s, ep+1);
    if (res != NULL)
      return res;
    else if (ssrc_end && singlematch(uchar(*s), p, ep))
      s++;  /* try with one more repetition */
    else return NULL;
  }
}


static const char *start_capture (MatchState *ms, const char *s,
                                    const char *p, int what) {
  const char *res;
  int level = ms->level;
  if (level >= LUA_MAXCAPTURES) luaL_error(ms->L, "too many captures");
  ms->capture[level].init = s;
  ms->capture[level].len = what;
  ms->level = level+1;
  if ((res=match(ms, s, p)) == NULL)  /* match failed? */
    ms->level--;  /* undo capture */
  return res;
}


static const char *end_capture (MatchState *ms, const char *s,
                                  const char *p) {
  int l = capture_to_close(ms);
  const char *res;
  ms->capture[l].len = s - ms->capture[l].init;  /* close capture */
  if ((res = match(ms, s, p)) == NULL)  /* match failed? */
    ms->capture[l].len = CAP_UNFINISHED;  /* undo capture */
  return res;
}


static const char *match_capture (MatchState *ms, const char *s, int l) {
  size_t len;
  l = check_capture(ms, l);
  len = ms->capture[l].len;
  if ((size_t)(ms->src_end-s) >= len &&
      memcmp(ms->capture[l].init, s, len) == 0)
    return s+len;
  else return NULL;
}


static const char *match (MatchState *ms, const char *s, const char *p) {
  init: /* using goto's to optimize tail recursion */
  switch (*p) {
    case '(': {  /* start capture */
      if (*(p+1) == ')')  /* position capture? */
        return start_capture(ms, s, p+2, CAP_POSITION);
      else
        return start_capture(ms, s, p+1, CAP_UNFINISHED);
    }
    case ')': {  /* end capture */
      return end_capture(ms, s, p+1);
    }
    case L_ESC: {
      switch (*(p+1)) {
        case 'b': {  /* balanced string? */
          s = matchbalance(ms, s, p+2);
          if (s == NULL) return NULL;
          p+=4; goto init;  /* else return match(ms, s, p+4); */
        }
        case 'f': {  /* frontier? */
          const char *ep; char previous;
          p += 2;
          if (*p != '[')
            luaL_error(ms->L, "missing " LUA_QL("[") " after "
                               LUA_QL("%%f") " in pattern");
          ep = classend(ms, p);  /* points to what is next */
          previous = (s == ms->src_init) ? '\0' : *(s-1);
          if (matchbracketclass(uchar(previous), p, ep-1) ||
             !matchbracketclass(uchar(*s), p, ep-1)) return NULL;
          p=ep; goto init;  /* else return match(ms, s, ep); */
        }
        default: {
          if (isdigit(uchar(*(p+1)))) {  /* capture results (%0-%9)? */
            s = match_capture(ms, s, uchar(*(p+1)));
            if (s == NULL) return NULL;
            p+=2; goto init;  /* else return match(ms, s, p+2) */
          }
          goto dflt;  /* case default */
        }
      }
    }
    case '\0': {  /* end of pattern */
      return s;  /* match succeeded */
    }
    case '$': {
      if (*(p+1) == '\0')  /* is the `$' the last char in pattern? */
        return (s == ms->src_end) ? s : NULL;  /* check end of string */
      else goto dflt;
    }
    default: dflt: {  /* it is a pattern item */
      const char *ep = classend(ms, p);  /* points to what is next */
      int m = ssrc_end && singlematch(uchar(*s), p, ep);
      switch (*ep) {
        case '?': {  /* optional */
          const char *res;
          if (m && ((res=match(ms, s+1, ep+1)) != NULL))
            return res;
          p=ep+1; goto init;  /* else return match(ms, s, ep+1); */
        }
        case '*': {  /* 0 or more repetitions */
          return max_expand(ms, s, p, ep);
        }
        case '+': {  /* 1 or more repetitions */
          return (m ? max_expand(ms, s+1, p, ep) : NULL);
        }
        case '-': {  /* 0 or more repetitions (minimum) */
          return min_expand(ms, s, p, ep);
        }
        default: {
          if (!m) return NULL;
          s++; p=ep; goto init;  /* else return match(ms, s+1, ep); */
        }
      }
    }
  }
}



static const char *lmemfind (const char *s1, size_t l1,
                               const char *s2, size_t l2) {
  if (l2 == 0) return s1;  /* empty strings are everywhere */
  else if (l2 > l1) return NULL;  /* avoids a negative `l1' */
  else {
    const char *init;  /* to search for a `*s2' inside `s1' */
    l2--;  /* 1st char will be checked by `memchr' */
    l1 = l1-l2;  /* `s2' cannot be found after that */
    while (l1 > 0 && (init = (const char *)memchr(s1, *s2, l1)) != NULL) {
      init++;   /* 1st char is already checked */
      if (memcmp(init, s2+1, l2) == 0)
        return init-1;
      else {  /* correct `l1' and `s1' to try again */
        l1 -= init-s1;
        s1 = init;
      }
    }
    return NULL;  /* not found */
  }
}


static void push_onecapture (MatchState *ms, int i, const char *s,
                                                    const char *e) {
  if (i >= ms->level) {
    if (i == 0)  /* ms->level == 0, too */
      lua_pushlstring(ms->L, s, e - s);  /* add whole match */
    else
      luaL_error(ms->L, "invalid capture index");
  }
  else {
    ptrdiff_t l = ms->capture[i].len;
    if (l == CAP_UNFINISHED) luaL_error(ms->L, "unfinished capture");
    if (l == CAP_POSITION)
      lua_pushinteger(ms->L, ms->capture[i].init - ms->src_init + 1);
    else
      lua_pushlstring(ms->L, ms->capture[i].init, l);
  }
}


static int push_captures (MatchState *ms, const char *s, const char *e) {
  int i;
  int nlevels = (ms->level == 0 && s) ? 1 : ms->level;
  luaL_checkstack(ms->L, nlevels, "too many captures");
  for (i = 0; i < nlevels; i++)
    push_onecapture(ms, i, s, e);
  return nlevels;  /* number of strings pushed */
}


static int str_find_aux (lua_State *L, int find) {
  size_t l1, l2;
  const char *s = luaL_checklstring(L, 1, &l1);
  const char *p = luaL_checklstring(L, 2, &l2);
  ptrdiff_t init = posrelat(luaL_optinteger(L, 3, 1), l1) - 1;
  if (init < 0) init = 0;
  else if ((size_t)(init) > l1) init = (ptrdiff_t)l1;
  if (find && (lua_toboolean(L, 4) ||  /* explicit request? */
      strpbrk(p, SPECIALS) == NULL)) {  /* or no special characters? */
    /* do a plain search */
    const char *s2 = lmemfind(s+init, l1-init, p, l2);
    if (s2) {
      lua_pushinteger(L, s2-s+1);
      lua_pushinteger(L, s2-s+l2);
      return 2;
    }
  }
  else {
    MatchState ms;
    int anchor = (*p == '^') ? (p++, 1) : 0;
    const char *s1=s+init;
    ms.L = L;
    ms.src_init = s;
    ms.src_end = s+l1;
    do {
      const char *res;
      ms.level = 0;
      if ((res=match(&ms, s1, p)) != NULL) {
        if (find) {
          lua_pushinteger(L, s1-s+1);  /* start */
          lua_pushinteger(L, res-s);   /* end */
          return push_captures(&ms, NULL, 0) + 2;
        }
        else
          return push_captures(&ms, s1, res);
      }
    } while (s1++ < ms.src_end && !anchor);
  }
  lua_pushnil(L);  /* not found */
  return 1;
}


static int str_find (lua_State *L) {
  return str_find_aux(L, 1);
}


static int str_match (lua_State *L) {
  return str_find_aux(L, 0);
}


static int gmatch_aux (lua_State *L) {
  MatchState ms;
  size_t ls;
  const char *s = lua_tolstring(L, lua_upvalueindex(1), &ls);
  const char *p = lua_tostring(L, lua_upvalueindex(2));
  const char *src;
  ms.L = L;
  ms.src_init = s;
  ms.src_end = s+ls;
  for (src = s + (size_t)lua_tointeger(L, lua_upvalueindex(3));
       src <= ms.src_end;
       src++) {
    const char *e;
    ms.level = 0;
    if ((e = match(&ms, src, p)) != NULL) {
      lua_Integer newstart = e-s;
      if (e == src) newstart++;  /* empty match? go at least one position */
      lua_pushinteger(L, newstart);
      lua_replace(L, lua_upvalueindex(3));
      return push_captures(&ms, src, e);
    }
  }
  return 0;  /* not found */
}


static int gmatch (lua_State *L) {
  luaL_checkstring(L, 1);
  luaL_checkstring(L, 2);
  lua_settop(L, 2);
  lua_pushinteger(L, 0);
  lua_pushcclosure(L, gmatch_aux, 3);
  return 1;
}


static int gfind_nodef (lua_State *L) {
  return luaL_error(L, LUA_QL("string.gfind") " was renamed to "
                       LUA_QL("string.gmatch"));
}


static void add_s (MatchState *ms, luaL_Buffer *b, const char *s,
                                                   const char *e) {
  size_t l, i;
  const char *news = lua_tolstring(ms->L, 3, &l);
  for (i = 0; i < l; i++) {
    if (news[i] != L_ESC)
      luaL_addchar(b, news[i]);
    else {
      i++;  /* skip ESC */
      if (!isdigit(uchar(news[i])))
        luaL_addchar(b, news[i]);
      else if (news[i] == '0')
          luaL_addlstring(b, s, e - s);
      else {
        push_onecapture(ms, news[i] - '1', s, e);
        luaL_addvalue(b);  /* add capture to accumulated result */
      }
    }
  }
}


static void add_value (MatchState *ms, luaL_Buffer *b, const char *s,
                                                       const char *e) {
  lua_State *L = ms->L;
  switch (lua_type(L, 3)) {
    case LUA_TNUMBER:
    case LUA_TSTRING: {
      add_s(ms, b, s, e);
      return;
    }
    case LUA_TFUNCTION: {
      int n;
      lua_pushvalue(L, 3);
      n = push_captures(ms, s, e);
      lua_call(L, n, 1);
      break;
    }
    case LUA_TTABLE: {
      push_onecapture(ms, 0, s, e);
      lua_gettable(L, 3);
      break;
    }
  }
  if (!lua_toboolean(L, -1)) {  /* nil or false? */
    lua_pop(L, 1);
    lua_pushlstring(L, s, e - s);  /* keep original text */
  }
  else if (!lua_isstring(L, -1))
    luaL_error(L, "invalid replacement value (a %s)", luaL_typename(L, -1)); 
  luaL_addvalue(b);  /* add result to accumulator */
}


static int str_gsub (lua_State *L) {
  size_t srcl;
  const char *src = luaL_checklstring(L, 1, &srcl);
  const char *p = luaL_checkstring(L, 2);
  int  tr = lua_type(L, 3);
  int max_s = luaL_optint(L, 4, srcl+1);
  int anchor = (*p == '^') ? (p++, 1) : 0;
  int n = 0;
  MatchState ms;
  luaL_Buffer b;
  luaL_argcheck(L, tr == LUA_TNUMBER || tr == LUA_TSTRING ||
                   tr == LUA_TFUNCTION || tr == LUA_TTABLE, 3,
                      "string/function/table expected");
  luaL_buffinit(L, &b);
  ms.L = L;
  ms.src_init = src;
  ms.src_end = src+srcl;
  while (n < max_s) {
    const char *e;
    ms.level = 0;
    e = match(&ms, src, p);
    if (e) {
      n++;
      add_value(&ms, &b, src, e);
    }
    if (e && e>src) /* non empty match? */
      src = e;  /* skip it */
    else if (src < ms.src_end)
      luaL_addchar(&b, *src++);
    else break;
    if (anchor) break;
  }
  luaL_addlstring(&b, src, ms.src_end-src);
  luaL_pushresult(&b);
  lua_pushinteger(L, n);  /* number of substitutions */
  return 2;
}

/* }====================================================== */


/* maximum size of each formatted item (> len(format('%99.99f', -1e308))) */
#define MAX_ITEM	512
/* valid flags in a format specification */
#define FLAGS	"-+ #0"
/*
** maximum size of each format specification (such as '%-099.99d')
** (+10 accounts for %99.99x plus margin of error)
*/
#define MAX_FORMAT	(sizeof(FLAGS) + sizeof(LUA_INTFRMLEN) + 10)


static void addquoted (lua_State *L, luaL_Buffer *b, int arg) {
  size_t l;
  const char *s = luaL_checklstring(L, arg, &l);
  luaL_addchar(b, '"');
  while (l--) {
    switch (*s) {
      case '"': case '\\': case '\n': {
        luaL_addchar(b, '\\');
        luaL_addchar(b, *s);
        break;
      }
      case '\r': {
        luaL_addlstring(b, "\\r", 2);
        break;
      }
      case '\0': {
        luaL_addlstring(b, "\\000", 4);
        break;
      }
      default: {
        luaL_addchar(b, *s);
        break;
      }
    }
    s++;
  }
  luaL_addchar(b, '"');
}

static const char *scanformat (lua_State *L, const char *strfrmt, char *form) {
  const char *p = strfrmt;
  while (*p != '\0' && strchr(FLAGS, *p) != NULL) p++;  /* skip flags */
  if ((size_t)(p - strfrmt) >= sizeof(FLAGS))
    luaL_error(L, "invalid format (repeated flags)");
  if (isdigit(uchar(*p))) p++;  /* skip width */
  if (isdigit(uchar(*p))) p++;  /* (2 digits at most) */
  if (*p == '.') {
    p++;
    if (isdigit(uchar(*p))) p++;  /* skip precision */
    if (isdigit(uchar(*p))) p++;  /* (2 digits at most) */
  }
  if (isdigit(uchar(*p)))
    luaL_error(L, "invalid format (width or precision too long)");
  *(form++) = '%';
  strncpy(form, strfrmt, p - strfrmt + 1);
  form += p - strfrmt + 1;
  *form = '\0';
  return p;
}


static void addintlen (char *form) {
  size_t l = strlen(form);
  char spec = form[l - 1];
  strcpy(form + l - 1, LUA_INTFRMLEN);
  form[l + sizeof(LUA_INTFRMLEN) - 2] = spec;
  form[l + sizeof(LUA_INTFRMLEN) - 1] = '\0';
}


static int str_format (lua_State *L) {
  int top = lua_gettop(L);
  int arg = 1;
  size_t sfl;
  const char *strfrmt = luaL_checklstring(L, arg, &sfl);
  const char *strfrmt_end = strfrmt+sfl;
  luaL_Buffer b;
  luaL_buffinit(L, &b);
  while (strfrmt < strfrmt_end) {
    if (*strfrmt != L_ESC)
      luaL_addchar(&b, *strfrmt++);
    else if (*++strfrmt == L_ESC)
      luaL_addchar(&b, *strfrmt++);  /* %% */
    else { /* format item */
      char form[MAX_FORMAT];  /* to store the format (`%...') */
      char buff[MAX_ITEM];  /* to store the formatted item */
      if (++arg > top)
        luaL_argerror(L, arg, "no value");
      strfrmt = scanformat(L, strfrmt, form);
      switch (*strfrmt++) {
        case 'c': {
          sprintf(buff, form, (int)luaL_checknumber(L, arg));
          break;
        }
        case 'd':  case 'i': {
          addintlen(form);
          sprintf(buff, form, (LUA_INTFRM_T)luaL_checknumber(L, arg));
          break;
        }
        case 'o':  case 'u':  case 'x':  case 'X': {
          addintlen(form);
          sprintf(buff, form, (unsigned LUA_INTFRM_T)luaL_checknumber(L, arg));
          break;
        }
        case 'e':  case 'E': case 'f':
        case 'g': case 'G': {
          sprintf(buff, form, (double)luaL_checknumber(L, arg));
          break;
        }
        case 'q': {
          addquoted(L, &b, arg);
          continue;  /* skip the 'addsize' at the end */
        }
        case 's': {
          size_t l;
          const char *s = luaL_checklstring(L, arg, &l);
          if (!strchr(form, '.') && l >= 100) {
            /* no precision and string is too long to be formatted;
               keep original string */
            lua_pushvalue(L, arg);
            luaL_addvalue(&b);
            continue;  /* skip the `addsize' at the end */
          }
          else {
            sprintf(buff, form, s);
            break;
          }
        }
        default: {  /* also treat cases `pnLlh' */
          return luaL_error(L, "invalid option " LUA_QL("%%%c") " to "
                               LUA_QL("format"), *(strfrmt - 1));
        }
      }
      luaL_addlstring(&b, buff, strlen(buff));
    }
  }
  luaL_pushresult(&b);
  return 1;
}


static const luaL_Reg strlib[] = {
  {"byte", str_byte},
  {"char", str_char},
  {"dump", str_dump},
  {"find", str_find},
  {"format", str_format},
  {"gfind", gfind_nodef},
  {"gmatch", gmatch},
  {"gsub", str_gsub},
  {"len", str_len},
  {"lower", str_lower},
  {"match", str_match},
  {"rep", str_rep},
  {"reverse", str_reverse},
  {"sub", str_sub},
  {"upper", str_upper},
  {NULL, NULL}
};


static void createmetatable (lua_State *L) {
  lua_createtable(L, 0, 1);  /* create metatable for strings */
  lua_pushliteral(L, "");  /* dummy string */
  lua_pushvalue(L, -2);
  lua_setmetatable(L, -2);  /* set string metatable */
  lua_pop(L, 1);  /* pop dummy string */
  lua_pushvalue(L, -2);  /* string library... */
  lua_setfield(L, -2, "__index");  /* ...is the __index metamethod */
  lua_pop(L, 1);  /* pop metatable */
}


/*
** Open string library
*/
LUALIB_API int luaopen_string (lua_State *L) {
  luaL_register(L, LUA_STRLIBNAME, strlib);
#if defined(LUA_COMPAT_GFIND)
  lua_getfield(L, -1, "gmatch");
  lua_setfield(L, -2, "gfind");
#endif
  createmetatable(L);
  return 1;
}

genometools-1.5.1/src/external/lua-5.1.5/src/ltable.c000066400000000000000000000376071211610345200221150ustar00rootroot00000000000000/*
** $Id: ltable.c,v 2.32.1.2 2007/12/28 15:32:23 roberto Exp $
** Lua tables (hash)
** See Copyright Notice in lua.h
*/


/*
** Implementation of tables (aka arrays, objects, or hash tables).
** Tables keep its elements in two parts: an array part and a hash part.
** Non-negative integer keys are all candidates to be kept in the array
** part. The actual size of the array is the largest `n' such that at
** least half the slots between 0 and n are in use.
** Hash uses a mix of chained scatter table with Brent's variation.
** A main invariant of these tables is that, if an element is not
** in its main position (i.e. the `original' position that its hash gives
** to it), then the colliding element is in its own main position.
** Hence even when the load factor reaches 100%, performance remains good.
*/

#include 
#include 

#define ltable_c
#define LUA_CORE

#include "lua.h"

#include "ldebug.h"
#include "ldo.h"
#include "lgc.h"
#include "lmem.h"
#include "lobject.h"
#include "lstate.h"
#include "ltable.h"


/*
** max size of array part is 2^MAXBITS
*/
#if LUAI_BITSINT > 26
#define MAXBITS		26
#else
#define MAXBITS		(LUAI_BITSINT-2)
#endif

#define MAXASIZE	(1 << MAXBITS)


#define hashpow2(t,n)      (gnode(t, lmod((n), sizenode(t))))
  
#define hashstr(t,str)  hashpow2(t, (str)->tsv.hash)
#define hashboolean(t,p)        hashpow2(t, p)


/*
** for some types, it is better to avoid modulus by power of 2, as
** they tend to have many 2 factors.
*/
#define hashmod(t,n)	(gnode(t, ((n) % ((sizenode(t)-1)|1))))


#define hashpointer(t,p)	hashmod(t, IntPoint(p))


/*
** number of ints inside a lua_Number
*/
#define numints		cast_int(sizeof(lua_Number)/sizeof(int))



#define dummynode		(&dummynode_)

static const Node dummynode_ = {
  {{NULL}, LUA_TNIL},  /* value */
  {{{NULL}, LUA_TNIL, NULL}}  /* key */
};


/*
** hash for lua_Numbers
*/
static Node *hashnum (const Table *t, lua_Number n) {
  unsigned int a[numints];
  int i;
  if (luai_numeq(n, 0))  /* avoid problems with -0 */
    return gnode(t, 0);
  memcpy(a, &n, sizeof(a));
  for (i = 1; i < numints; i++) a[0] += a[i];
  return hashmod(t, a[0]);
}



/*
** returns the `main' position of an element in a table (that is, the index
** of its hash value)
*/
static Node *mainposition (const Table *t, const TValue *key) {
  switch (ttype(key)) {
    case LUA_TNUMBER:
      return hashnum(t, nvalue(key));
    case LUA_TSTRING:
      return hashstr(t, rawtsvalue(key));
    case LUA_TBOOLEAN:
      return hashboolean(t, bvalue(key));
    case LUA_TLIGHTUSERDATA:
      return hashpointer(t, pvalue(key));
    default:
      return hashpointer(t, gcvalue(key));
  }
}


/*
** returns the index for `key' if `key' is an appropriate key to live in
** the array part of the table, -1 otherwise.
*/
static int arrayindex (const TValue *key) {
  if (ttisnumber(key)) {
    lua_Number n = nvalue(key);
    int k;
    lua_number2int(k, n);
    if (luai_numeq(cast_num(k), n))
      return k;
  }
  return -1;  /* `key' did not match some condition */
}


/*
** returns the index of a `key' for table traversals. First goes all
** elements in the array part, then elements in the hash part. The
** beginning of a traversal is signalled by -1.
*/
static int findindex (lua_State *L, Table *t, StkId key) {
  int i;
  if (ttisnil(key)) return -1;  /* first iteration */
  i = arrayindex(key);
  if (0 < i && i <= t->sizearray)  /* is `key' inside array part? */
    return i-1;  /* yes; that's the index (corrected to C) */
  else {
    Node *n = mainposition(t, key);
    do {  /* check whether `key' is somewhere in the chain */
      /* key may be dead already, but it is ok to use it in `next' */
      if (luaO_rawequalObj(key2tval(n), key) ||
            (ttype(gkey(n)) == LUA_TDEADKEY && iscollectable(key) &&
             gcvalue(gkey(n)) == gcvalue(key))) {
        i = cast_int(n - gnode(t, 0));  /* key index in hash table */
        /* hash elements are numbered after array ones */
        return i + t->sizearray;
      }
      else n = gnext(n);
    } while (n);
    luaG_runerror(L, "invalid key to " LUA_QL("next"));  /* key not found */
    return 0;  /* to avoid warnings */
  }
}


int luaH_next (lua_State *L, Table *t, StkId key) {
  int i = findindex(L, t, key);  /* find original element */
  for (i++; i < t->sizearray; i++) {  /* try first array part */
    if (!ttisnil(&t->array[i])) {  /* a non-nil value? */
      setnvalue(key, cast_num(i+1));
      setobj2s(L, key+1, &t->array[i]);
      return 1;
    }
  }
  for (i -= t->sizearray; i < sizenode(t); i++) {  /* then hash part */
    if (!ttisnil(gval(gnode(t, i)))) {  /* a non-nil value? */
      setobj2s(L, key, key2tval(gnode(t, i)));
      setobj2s(L, key+1, gval(gnode(t, i)));
      return 1;
    }
  }
  return 0;  /* no more elements */
}


/*
** {=============================================================
** Rehash
** ==============================================================
*/


static int computesizes (int nums[], int *narray) {
  int i;
  int twotoi;  /* 2^i */
  int a = 0;  /* number of elements smaller than 2^i */
  int na = 0;  /* number of elements to go to array part */
  int n = 0;  /* optimal size for array part */
  for (i = 0, twotoi = 1; twotoi/2 < *narray; i++, twotoi *= 2) {
    if (nums[i] > 0) {
      a += nums[i];
      if (a > twotoi/2) {  /* more than half elements present? */
        n = twotoi;  /* optimal size (till now) */
        na = a;  /* all elements smaller than n will go to array part */
      }
    }
    if (a == *narray) break;  /* all elements already counted */
  }
  *narray = n;
  lua_assert(*narray/2 <= na && na <= *narray);
  return na;
}


static int countint (const TValue *key, int *nums) {
  int k = arrayindex(key);
  if (0 < k && k <= MAXASIZE) {  /* is `key' an appropriate array index? */
    nums[ceillog2(k)]++;  /* count as such */
    return 1;
  }
  else
    return 0;
}


static int numusearray (const Table *t, int *nums) {
  int lg;
  int ttlg;  /* 2^lg */
  int ause = 0;  /* summation of `nums' */
  int i = 1;  /* count to traverse all array keys */
  for (lg=0, ttlg=1; lg<=MAXBITS; lg++, ttlg*=2) {  /* for each slice */
    int lc = 0;  /* counter */
    int lim = ttlg;
    if (lim > t->sizearray) {
      lim = t->sizearray;  /* adjust upper limit */
      if (i > lim)
        break;  /* no more elements to count */
    }
    /* count elements in range (2^(lg-1), 2^lg] */
    for (; i <= lim; i++) {
      if (!ttisnil(&t->array[i-1]))
        lc++;
    }
    nums[lg] += lc;
    ause += lc;
  }
  return ause;
}


static int numusehash (const Table *t, int *nums, int *pnasize) {
  int totaluse = 0;  /* total number of elements */
  int ause = 0;  /* summation of `nums' */
  int i = sizenode(t);
  while (i--) {
    Node *n = &t->node[i];
    if (!ttisnil(gval(n))) {
      ause += countint(key2tval(n), nums);
      totaluse++;
    }
  }
  *pnasize += ause;
  return totaluse;
}


static void setarrayvector (lua_State *L, Table *t, int size) {
  int i;
  luaM_reallocvector(L, t->array, t->sizearray, size, TValue);
  for (i=t->sizearray; iarray[i]);
  t->sizearray = size;
}


static void setnodevector (lua_State *L, Table *t, int size) {
  int lsize;
  if (size == 0) {  /* no elements to hash part? */
    t->node = cast(Node *, dummynode);  /* use common `dummynode' */
    lsize = 0;
  }
  else {
    int i;
    lsize = ceillog2(size);
    if (lsize > MAXBITS)
      luaG_runerror(L, "table overflow");
    size = twoto(lsize);
    t->node = luaM_newvector(L, size, Node);
    for (i=0; ilsizenode = cast_byte(lsize);
  t->lastfree = gnode(t, size);  /* all positions are free */
}


static void resize (lua_State *L, Table *t, int nasize, int nhsize) {
  int i;
  int oldasize = t->sizearray;
  int oldhsize = t->lsizenode;
  Node *nold = t->node;  /* save old hash ... */
  if (nasize > oldasize)  /* array part must grow? */
    setarrayvector(L, t, nasize);
  /* create new hash part with appropriate size */
  setnodevector(L, t, nhsize);  
  if (nasize < oldasize) {  /* array part must shrink? */
    t->sizearray = nasize;
    /* re-insert elements from vanishing slice */
    for (i=nasize; iarray[i]))
        setobjt2t(L, luaH_setnum(L, t, i+1), &t->array[i]);
    }
    /* shrink array */
    luaM_reallocvector(L, t->array, oldasize, nasize, TValue);
  }
  /* re-insert elements from hash part */
  for (i = twoto(oldhsize) - 1; i >= 0; i--) {
    Node *old = nold+i;
    if (!ttisnil(gval(old)))
      setobjt2t(L, luaH_set(L, t, key2tval(old)), gval(old));
  }
  if (nold != dummynode)
    luaM_freearray(L, nold, twoto(oldhsize), Node);  /* free old array */
}


void luaH_resizearray (lua_State *L, Table *t, int nasize) {
  int nsize = (t->node == dummynode) ? 0 : sizenode(t);
  resize(L, t, nasize, nsize);
}


static void rehash (lua_State *L, Table *t, const TValue *ek) {
  int nasize, na;
  int nums[MAXBITS+1];  /* nums[i] = number of keys between 2^(i-1) and 2^i */
  int i;
  int totaluse;
  for (i=0; i<=MAXBITS; i++) nums[i] = 0;  /* reset counts */
  nasize = numusearray(t, nums);  /* count keys in array part */
  totaluse = nasize;  /* all those keys are integer keys */
  totaluse += numusehash(t, nums, &nasize);  /* count keys in hash part */
  /* count extra key */
  nasize += countint(ek, nums);
  totaluse++;
  /* compute new size for array part */
  na = computesizes(nums, &nasize);
  /* resize the table to new computed sizes */
  resize(L, t, nasize, totaluse - na);
}



/*
** }=============================================================
*/


Table *luaH_new (lua_State *L, int narray, int nhash) {
  Table *t = luaM_new(L, Table);
  luaC_link(L, obj2gco(t), LUA_TTABLE);
  t->metatable = NULL;
  t->flags = cast_byte(~0);
  /* temporary values (kept only if some malloc fails) */
  t->array = NULL;
  t->sizearray = 0;
  t->lsizenode = 0;
  t->node = cast(Node *, dummynode);
  setarrayvector(L, t, narray);
  setnodevector(L, t, nhash);
  return t;
}


void luaH_free (lua_State *L, Table *t) {
  if (t->node != dummynode)
    luaM_freearray(L, t->node, sizenode(t), Node);
  luaM_freearray(L, t->array, t->sizearray, TValue);
  luaM_free(L, t);
}


static Node *getfreepos (Table *t) {
  while (t->lastfree-- > t->node) {
    if (ttisnil(gkey(t->lastfree)))
      return t->lastfree;
  }
  return NULL;  /* could not find a free place */
}



/*
** inserts a new key into a hash table; first, check whether key's main 
** position is free. If not, check whether colliding node is in its main 
** position or not: if it is not, move colliding node to an empty place and 
** put new key in its main position; otherwise (colliding node is in its main 
** position), new key goes to an empty position. 
*/
static TValue *newkey (lua_State *L, Table *t, const TValue *key) {
  Node *mp = mainposition(t, key);
  if (!ttisnil(gval(mp)) || mp == dummynode) {
    Node *othern;
    Node *n = getfreepos(t);  /* get a free place */
    if (n == NULL) {  /* cannot find a free place? */
      rehash(L, t, key);  /* grow table */
      return luaH_set(L, t, key);  /* re-insert key into grown table */
    }
    lua_assert(n != dummynode);
    othern = mainposition(t, key2tval(mp));
    if (othern != mp) {  /* is colliding node out of its main position? */
      /* yes; move colliding node into free position */
      while (gnext(othern) != mp) othern = gnext(othern);  /* find previous */
      gnext(othern) = n;  /* redo the chain with `n' in place of `mp' */
      *n = *mp;  /* copy colliding node into free pos. (mp->next also goes) */
      gnext(mp) = NULL;  /* now `mp' is free */
      setnilvalue(gval(mp));
    }
    else {  /* colliding node is in its own main position */
      /* new node will go into free position */
      gnext(n) = gnext(mp);  /* chain new position */
      gnext(mp) = n;
      mp = n;
    }
  }
  gkey(mp)->value = key->value; gkey(mp)->tt = key->tt;
  luaC_barriert(L, t, key);
  lua_assert(ttisnil(gval(mp)));
  return gval(mp);
}


/*
** search function for integers
*/
const TValue *luaH_getnum (Table *t, int key) {
  /* (1 <= key && key <= t->sizearray) */
  if (cast(unsigned int, key-1) < cast(unsigned int, t->sizearray))
    return &t->array[key-1];
  else {
    lua_Number nk = cast_num(key);
    Node *n = hashnum(t, nk);
    do {  /* check whether `key' is somewhere in the chain */
      if (ttisnumber(gkey(n)) && luai_numeq(nvalue(gkey(n)), nk))
        return gval(n);  /* that's it */
      else n = gnext(n);
    } while (n);
    return luaO_nilobject;
  }
}


/*
** search function for strings
*/
const TValue *luaH_getstr (Table *t, TString *key) {
  Node *n = hashstr(t, key);
  do {  /* check whether `key' is somewhere in the chain */
    if (ttisstring(gkey(n)) && rawtsvalue(gkey(n)) == key)
      return gval(n);  /* that's it */
    else n = gnext(n);
  } while (n);
  return luaO_nilobject;
}


/*
** main search function
*/
const TValue *luaH_get (Table *t, const TValue *key) {
  switch (ttype(key)) {
    case LUA_TNIL: return luaO_nilobject;
    case LUA_TSTRING: return luaH_getstr(t, rawtsvalue(key));
    case LUA_TNUMBER: {
      int k;
      lua_Number n = nvalue(key);
      lua_number2int(k, n);
      if (luai_numeq(cast_num(k), nvalue(key))) /* index is int? */
        return luaH_getnum(t, k);  /* use specialized version */
      /* else go through */
    }
    default: {
      Node *n = mainposition(t, key);
      do {  /* check whether `key' is somewhere in the chain */
        if (luaO_rawequalObj(key2tval(n), key))
          return gval(n);  /* that's it */
        else n = gnext(n);
      } while (n);
      return luaO_nilobject;
    }
  }
}


TValue *luaH_set (lua_State *L, Table *t, const TValue *key) {
  const TValue *p = luaH_get(t, key);
  t->flags = 0;
  if (p != luaO_nilobject)
    return cast(TValue *, p);
  else {
    if (ttisnil(key)) luaG_runerror(L, "table index is nil");
    else if (ttisnumber(key) && luai_numisnan(nvalue(key)))
      luaG_runerror(L, "table index is NaN");
    return newkey(L, t, key);
  }
}


TValue *luaH_setnum (lua_State *L, Table *t, int key) {
  const TValue *p = luaH_getnum(t, key);
  if (p != luaO_nilobject)
    return cast(TValue *, p);
  else {
    TValue k;
    setnvalue(&k, cast_num(key));
    return newkey(L, t, &k);
  }
}


TValue *luaH_setstr (lua_State *L, Table *t, TString *key) {
  const TValue *p = luaH_getstr(t, key);
  if (p != luaO_nilobject)
    return cast(TValue *, p);
  else {
    TValue k;
    setsvalue(L, &k, key);
    return newkey(L, t, &k);
  }
}


static int unbound_search (Table *t, unsigned int j) {
  unsigned int i = j;  /* i is zero or a present index */
  j++;
  /* find `i' and `j' such that i is present and j is not */
  while (!ttisnil(luaH_getnum(t, j))) {
    i = j;
    j *= 2;
    if (j > cast(unsigned int, MAX_INT)) {  /* overflow? */
      /* table was built with bad purposes: resort to linear search */
      i = 1;
      while (!ttisnil(luaH_getnum(t, i))) i++;
      return i - 1;
    }
  }
  /* now do a binary search between them */
  while (j - i > 1) {
    unsigned int m = (i+j)/2;
    if (ttisnil(luaH_getnum(t, m))) j = m;
    else i = m;
  }
  return i;
}


/*
** Try to find a boundary in table `t'. A `boundary' is an integer index
** such that t[i] is non-nil and t[i+1] is nil (and 0 if t[1] is nil).
*/
int luaH_getn (Table *t) {
  unsigned int j = t->sizearray;
  if (j > 0 && ttisnil(&t->array[j - 1])) {
    /* there is a boundary in the array part: (binary) search for it */
    unsigned int i = 0;
    while (j - i > 1) {
      unsigned int m = (i+j)/2;
      if (ttisnil(&t->array[m - 1])) j = m;
      else i = m;
    }
    return i;
  }
  /* else must find a boundary in hash part */
  else if (t->node == dummynode)  /* hash part is empty? */
    return j;  /* that is easy... */
  else return unbound_search(t, j);
}



#if defined(LUA_DEBUG)

Node *luaH_mainposition (const Table *t, const TValue *key) {
  return mainposition(t, key);
}

int luaH_isdummy (Node *n) { return n == dummynode; }

#endif
genometools-1.5.1/src/external/lua-5.1.5/src/ltable.h000066400000000000000000000022401211610345200221030ustar00rootroot00000000000000/*
** $Id: ltable.h,v 2.10.1.1 2007/12/27 13:02:25 roberto Exp $
** Lua tables (hash)
** See Copyright Notice in lua.h
*/

#ifndef ltable_h
#define ltable_h

#include "lobject.h"


#define gnode(t,i)	(&(t)->node[i])
#define gkey(n)		(&(n)->i_key.nk)
#define gval(n)		(&(n)->i_val)
#define gnext(n)	((n)->i_key.nk.next)

#define key2tval(n)	(&(n)->i_key.tvk)


LUAI_FUNC const TValue *luaH_getnum (Table *t, int key);
LUAI_FUNC TValue *luaH_setnum (lua_State *L, Table *t, int key);
LUAI_FUNC const TValue *luaH_getstr (Table *t, TString *key);
LUAI_FUNC TValue *luaH_setstr (lua_State *L, Table *t, TString *key);
LUAI_FUNC const TValue *luaH_get (Table *t, const TValue *key);
LUAI_FUNC TValue *luaH_set (lua_State *L, Table *t, const TValue *key);
LUAI_FUNC Table *luaH_new (lua_State *L, int narray, int lnhash);
LUAI_FUNC void luaH_resizearray (lua_State *L, Table *t, int nasize);
LUAI_FUNC void luaH_free (lua_State *L, Table *t);
LUAI_FUNC int luaH_next (lua_State *L, Table *t, StkId key);
LUAI_FUNC int luaH_getn (Table *t);


#if defined(LUA_DEBUG)
LUAI_FUNC Node *luaH_mainposition (const Table *t, const TValue *key);
LUAI_FUNC int luaH_isdummy (Node *n);
#endif


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/ltablib.c000066400000000000000000000162571211610345200222610ustar00rootroot00000000000000/*
** $Id: ltablib.c,v 1.38.1.3 2008/02/14 16:46:58 roberto Exp $
** Library for Table Manipulation
** See Copyright Notice in lua.h
*/


#include 

#define ltablib_c
#define LUA_LIB

#include "lua.h"

#include "lauxlib.h"
#include "lualib.h"


#define aux_getn(L,n)	(luaL_checktype(L, n, LUA_TTABLE), luaL_getn(L, n))


static int foreachi (lua_State *L) {
  int i;
  int n = aux_getn(L, 1);
  luaL_checktype(L, 2, LUA_TFUNCTION);
  for (i=1; i <= n; i++) {
    lua_pushvalue(L, 2);  /* function */
    lua_pushinteger(L, i);  /* 1st argument */
    lua_rawgeti(L, 1, i);  /* 2nd argument */
    lua_call(L, 2, 1);
    if (!lua_isnil(L, -1))
      return 1;
    lua_pop(L, 1);  /* remove nil result */
  }
  return 0;
}


static int foreach (lua_State *L) {
  luaL_checktype(L, 1, LUA_TTABLE);
  luaL_checktype(L, 2, LUA_TFUNCTION);
  lua_pushnil(L);  /* first key */
  while (lua_next(L, 1)) {
    lua_pushvalue(L, 2);  /* function */
    lua_pushvalue(L, -3);  /* key */
    lua_pushvalue(L, -3);  /* value */
    lua_call(L, 2, 1);
    if (!lua_isnil(L, -1))
      return 1;
    lua_pop(L, 2);  /* remove value and result */
  }
  return 0;
}


static int maxn (lua_State *L) {
  lua_Number max = 0;
  luaL_checktype(L, 1, LUA_TTABLE);
  lua_pushnil(L);  /* first key */
  while (lua_next(L, 1)) {
    lua_pop(L, 1);  /* remove value */
    if (lua_type(L, -1) == LUA_TNUMBER) {
      lua_Number v = lua_tonumber(L, -1);
      if (v > max) max = v;
    }
  }
  lua_pushnumber(L, max);
  return 1;
}


static int getn (lua_State *L) {
  lua_pushinteger(L, aux_getn(L, 1));
  return 1;
}


static int setn (lua_State *L) {
  luaL_checktype(L, 1, LUA_TTABLE);
#ifndef luaL_setn
  luaL_setn(L, 1, luaL_checkint(L, 2));
#else
  luaL_error(L, LUA_QL("setn") " is obsolete");
#endif
  lua_pushvalue(L, 1);
  return 1;
}


static int tinsert (lua_State *L) {
  int e = aux_getn(L, 1) + 1;  /* first empty element */
  int pos;  /* where to insert new element */
  switch (lua_gettop(L)) {
    case 2: {  /* called with only 2 arguments */
      pos = e;  /* insert new element at the end */
      break;
    }
    case 3: {
      int i;
      pos = luaL_checkint(L, 2);  /* 2nd argument is the position */
      if (pos > e) e = pos;  /* `grow' array if necessary */
      for (i = e; i > pos; i--) {  /* move up elements */
        lua_rawgeti(L, 1, i-1);
        lua_rawseti(L, 1, i);  /* t[i] = t[i-1] */
      }
      break;
    }
    default: {
      return luaL_error(L, "wrong number of arguments to " LUA_QL("insert"));
    }
  }
  luaL_setn(L, 1, e);  /* new size */
  lua_rawseti(L, 1, pos);  /* t[pos] = v */
  return 0;
}


static int tremove (lua_State *L) {
  int e = aux_getn(L, 1);
  int pos = luaL_optint(L, 2, e);
  if (!(1 <= pos && pos <= e))  /* position is outside bounds? */
   return 0;  /* nothing to remove */
  luaL_setn(L, 1, e - 1);  /* t.n = n-1 */
  lua_rawgeti(L, 1, pos);  /* result = t[pos] */
  for ( ;pos= P */
      while (lua_rawgeti(L, 1, ++i), sort_comp(L, -1, -2)) {
        if (i>u) luaL_error(L, "invalid order function for sorting");
        lua_pop(L, 1);  /* remove a[i] */
      }
      /* repeat --j until a[j] <= P */
      while (lua_rawgeti(L, 1, --j), sort_comp(L, -3, -1)) {
        if (j

#define ltm_c
#define LUA_CORE

#include "lua.h"

#include "lobject.h"
#include "lstate.h"
#include "lstring.h"
#include "ltable.h"
#include "ltm.h"



const char *const luaT_typenames[] = {
  "nil", "boolean", "userdata", "number",
  "string", "table", "function", "userdata", "thread",
  "proto", "upval"
};


void luaT_init (lua_State *L) {
  static const char *const luaT_eventname[] = {  /* ORDER TM */
    "__index", "__newindex",
    "__gc", "__mode", "__eq",
    "__add", "__sub", "__mul", "__div", "__mod",
    "__pow", "__unm", "__len", "__lt", "__le",
    "__concat", "__call"
  };
  int i;
  for (i=0; itmname[i] = luaS_new(L, luaT_eventname[i]);
    luaS_fix(G(L)->tmname[i]);  /* never collect these names */
  }
}


/*
** function to be used with macro "fasttm": optimized for absence of
** tag methods
*/
const TValue *luaT_gettm (Table *events, TMS event, TString *ename) {
  const TValue *tm = luaH_getstr(events, ename);
  lua_assert(event <= TM_EQ);
  if (ttisnil(tm)) {  /* no tag method? */
    events->flags |= cast_byte(1u<metatable;
      break;
    case LUA_TUSERDATA:
      mt = uvalue(o)->metatable;
      break;
    default:
      mt = G(L)->mt[ttype(o)];
  }
  return (mt ? luaH_getstr(mt, G(L)->tmname[event]) : luaO_nilobject);
}

genometools-1.5.1/src/external/lua-5.1.5/src/ltm.h000066400000000000000000000017721211610345200214450ustar00rootroot00000000000000/*
** $Id: ltm.h,v 2.6.1.1 2007/12/27 13:02:25 roberto Exp $
** Tag methods
** See Copyright Notice in lua.h
*/

#ifndef ltm_h
#define ltm_h


#include "lobject.h"


/*
* WARNING: if you change the order of this enumeration,
* grep "ORDER TM"
*/
typedef enum {
  TM_INDEX,
  TM_NEWINDEX,
  TM_GC,
  TM_MODE,
  TM_EQ,  /* last tag method with `fast' access */
  TM_ADD,
  TM_SUB,
  TM_MUL,
  TM_DIV,
  TM_MOD,
  TM_POW,
  TM_UNM,
  TM_LEN,
  TM_LT,
  TM_LE,
  TM_CONCAT,
  TM_CALL,
  TM_N		/* number of elements in the enum */
} TMS;



#define gfasttm(g,et,e) ((et) == NULL ? NULL : \
  ((et)->flags & (1u<<(e))) ? NULL : luaT_gettm(et, e, (g)->tmname[e]))

#define fasttm(l,et,e)	gfasttm(G(l), et, e)

LUAI_DATA const char *const luaT_typenames[];


LUAI_FUNC const TValue *luaT_gettm (Table *events, TMS event, TString *ename);
LUAI_FUNC const TValue *luaT_gettmbyobj (lua_State *L, const TValue *o,
                                                       TMS event);
LUAI_FUNC void luaT_init (lua_State *L);

#endif
genometools-1.5.1/src/external/lua-5.1.5/src/lua.c000066400000000000000000000236631211610345200214300ustar00rootroot00000000000000/*
** $Id: lua.c,v 1.160.1.2 2007/12/28 15:32:23 roberto Exp $
** Lua stand-alone interpreter
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 
#include 

#define lua_c

#include "lua.h"

#include "lauxlib.h"
#include "lualib.h"



static lua_State *globalL = NULL;

static const char *progname = LUA_PROGNAME;



static void lstop (lua_State *L, lua_Debug *ar) {
  (void)ar;  /* unused arg. */
  lua_sethook(L, NULL, 0, 0);
  luaL_error(L, "interrupted!");
}


static void laction (int i) {
  signal(i, SIG_DFL); /* if another SIGINT happens before lstop,
                              terminate process (default action) */
  lua_sethook(globalL, lstop, LUA_MASKCALL | LUA_MASKRET | LUA_MASKCOUNT, 1);
}


static void print_usage (void) {
  fprintf(stderr,
  "usage: %s [options] [script [args]].\n"
  "Available options are:\n"
  "  -e stat  execute string " LUA_QL("stat") "\n"
  "  -l name  require library " LUA_QL("name") "\n"
  "  -i       enter interactive mode after executing " LUA_QL("script") "\n"
  "  -v       show version information\n"
  "  --       stop handling options\n"
  "  -        execute stdin and stop handling options\n"
  ,
  progname);
  fflush(stderr);
}


static void l_message (const char *pname, const char *msg) {
  if (pname) fprintf(stderr, "%s: ", pname);
  fprintf(stderr, "%s\n", msg);
  fflush(stderr);
}


static int report (lua_State *L, int status) {
  if (status && !lua_isnil(L, -1)) {
    const char *msg = lua_tostring(L, -1);
    if (msg == NULL) msg = "(error object is not a string)";
    l_message(progname, msg);
    lua_pop(L, 1);
  }
  return status;
}


static int traceback (lua_State *L) {
  if (!lua_isstring(L, 1))  /* 'message' not a string? */
    return 1;  /* keep it intact */
  lua_getfield(L, LUA_GLOBALSINDEX, "debug");
  if (!lua_istable(L, -1)) {
    lua_pop(L, 1);
    return 1;
  }
  lua_getfield(L, -1, "traceback");
  if (!lua_isfunction(L, -1)) {
    lua_pop(L, 2);
    return 1;
  }
  lua_pushvalue(L, 1);  /* pass error message */
  lua_pushinteger(L, 2);  /* skip this function and traceback */
  lua_call(L, 2, 1);  /* call debug.traceback */
  return 1;
}


static int docall (lua_State *L, int narg, int clear) {
  int status;
  int base = lua_gettop(L) - narg;  /* function index */
  lua_pushcfunction(L, traceback);  /* push traceback function */
  lua_insert(L, base);  /* put it under chunk and args */
  signal(SIGINT, laction);
  status = lua_pcall(L, narg, (clear ? 0 : LUA_MULTRET), base);
  signal(SIGINT, SIG_DFL);
  lua_remove(L, base);  /* remove traceback function */
  /* force a complete garbage collection in case of errors */
  if (status != 0) lua_gc(L, LUA_GCCOLLECT, 0);
  return status;
}


static void print_version (void) {
  l_message(NULL, LUA_RELEASE "  " LUA_COPYRIGHT);
}


static int getargs (lua_State *L, char **argv, int n) {
  int narg;
  int i;
  int argc = 0;
  while (argv[argc]) argc++;  /* count total number of arguments */
  narg = argc - (n + 1);  /* number of arguments to the script */
  luaL_checkstack(L, narg + 3, "too many arguments to script");
  for (i=n+1; i < argc; i++)
    lua_pushstring(L, argv[i]);
  lua_createtable(L, narg, n + 1);
  for (i=0; i < argc; i++) {
    lua_pushstring(L, argv[i]);
    lua_rawseti(L, -2, i - n);
  }
  return narg;
}


static int dofile (lua_State *L, const char *name) {
  int status = luaL_loadfile(L, name) || docall(L, 0, 1);
  return report(L, status);
}


static int dostring (lua_State *L, const char *s, const char *name) {
  int status = luaL_loadbuffer(L, s, strlen(s), name) || docall(L, 0, 1);
  return report(L, status);
}


static int dolibrary (lua_State *L, const char *name) {
  lua_getglobal(L, "require");
  lua_pushstring(L, name);
  return report(L, docall(L, 1, 1));
}


static const char *get_prompt (lua_State *L, int firstline) {
  const char *p;
  lua_getfield(L, LUA_GLOBALSINDEX, firstline ? "_PROMPT" : "_PROMPT2");
  p = lua_tostring(L, -1);
  if (p == NULL) p = (firstline ? LUA_PROMPT : LUA_PROMPT2);
  lua_pop(L, 1);  /* remove global */
  return p;
}


static int incomplete (lua_State *L, int status) {
  if (status == LUA_ERRSYNTAX) {
    size_t lmsg;
    const char *msg = lua_tolstring(L, -1, &lmsg);
    const char *tp = msg + lmsg - (sizeof(LUA_QL("")) - 1);
    if (strstr(msg, LUA_QL("")) == tp) {
      lua_pop(L, 1);
      return 1;
    }
  }
  return 0;  /* else... */
}


static int pushline (lua_State *L, int firstline) {
  char buffer[LUA_MAXINPUT];
  char *b = buffer;
  size_t l;
  const char *prmt = get_prompt(L, firstline);
  if (lua_readline(L, b, prmt) == 0)
    return 0;  /* no input */
  l = strlen(b);
  if (l > 0 && b[l-1] == '\n')  /* line ends with newline? */
    b[l-1] = '\0';  /* remove it */
  if (firstline && b[0] == '=')  /* first line starts with `=' ? */
    lua_pushfstring(L, "return %s", b+1);  /* change it to `return' */
  else
    lua_pushstring(L, b);
  lua_freeline(L, b);
  return 1;
}


static int loadline (lua_State *L) {
  int status;
  lua_settop(L, 0);
  if (!pushline(L, 1))
    return -1;  /* no input */
  for (;;) {  /* repeat until gets a complete line */
    status = luaL_loadbuffer(L, lua_tostring(L, 1), lua_strlen(L, 1), "=stdin");
    if (!incomplete(L, status)) break;  /* cannot try to add lines? */
    if (!pushline(L, 0))  /* no more input? */
      return -1;
    lua_pushliteral(L, "\n");  /* add a new line... */
    lua_insert(L, -2);  /* ...between the two lines */
    lua_concat(L, 3);  /* join them */
  }
  lua_saveline(L, 1);
  lua_remove(L, 1);  /* remove line */
  return status;
}


static void dotty (lua_State *L) {
  int status;
  const char *oldprogname = progname;
  progname = NULL;
  while ((status = loadline(L)) != -1) {
    if (status == 0) status = docall(L, 0, 0);
    report(L, status);
    if (status == 0 && lua_gettop(L) > 0) {  /* any result to print? */
      lua_getglobal(L, "print");
      lua_insert(L, 1);
      if (lua_pcall(L, lua_gettop(L)-1, 0, 0) != 0)
        l_message(progname, lua_pushfstring(L,
                               "error calling " LUA_QL("print") " (%s)",
                               lua_tostring(L, -1)));
    }
  }
  lua_settop(L, 0);  /* clear stack */
  fputs("\n", stdout);
  fflush(stdout);
  progname = oldprogname;
}


static int handle_script (lua_State *L, char **argv, int n) {
  int status;
  const char *fname;
  int narg = getargs(L, argv, n);  /* collect arguments */
  lua_setglobal(L, "arg");
  fname = argv[n];
  if (strcmp(fname, "-") == 0 && strcmp(argv[n-1], "--") != 0) 
    fname = NULL;  /* stdin */
  status = luaL_loadfile(L, fname);
  lua_insert(L, -(narg+1));
  if (status == 0)
    status = docall(L, narg, 0);
  else
    lua_pop(L, narg);      
  return report(L, status);
}


/* check that argument has no extra characters at the end */
#define notail(x)	{if ((x)[2] != '\0') return -1;}


static int collectargs (char **argv, int *pi, int *pv, int *pe) {
  int i;
  for (i = 1; argv[i] != NULL; i++) {
    if (argv[i][0] != '-')  /* not an option? */
        return i;
    switch (argv[i][1]) {  /* option */
      case '-':
        notail(argv[i]);
        return (argv[i+1] != NULL ? i+1 : 0);
      case '\0':
        return i;
      case 'i':
        notail(argv[i]);
        *pi = 1;  /* go through */
      case 'v':
        notail(argv[i]);
        *pv = 1;
        break;
      case 'e':
        *pe = 1;  /* go through */
      case 'l':
        if (argv[i][2] == '\0') {
          i++;
          if (argv[i] == NULL) return -1;
        }
        break;
      default: return -1;  /* invalid option */
    }
  }
  return 0;
}


static int runargs (lua_State *L, char **argv, int n) {
  int i;
  for (i = 1; i < n; i++) {
    if (argv[i] == NULL) continue;
    lua_assert(argv[i][0] == '-');
    switch (argv[i][1]) {  /* option */
      case 'e': {
        const char *chunk = argv[i] + 2;
        if (*chunk == '\0') chunk = argv[++i];
        lua_assert(chunk != NULL);
        if (dostring(L, chunk, "=(command line)") != 0)
          return 1;
        break;
      }
      case 'l': {
        const char *filename = argv[i] + 2;
        if (*filename == '\0') filename = argv[++i];
        lua_assert(filename != NULL);
        if (dolibrary(L, filename))
          return 1;  /* stop if file fails */
        break;
      }
      default: break;
    }
  }
  return 0;
}


static int handle_luainit (lua_State *L) {
  const char *init = getenv(LUA_INIT);
  if (init == NULL) return 0;  /* status OK */
  else if (init[0] == '@')
    return dofile(L, init+1);
  else
    return dostring(L, init, "=" LUA_INIT);
}


struct Smain {
  int argc;
  char **argv;
  int status;
};


static int pmain (lua_State *L) {
  struct Smain *s = (struct Smain *)lua_touserdata(L, 1);
  char **argv = s->argv;
  int script;
  int has_i = 0, has_v = 0, has_e = 0;
  globalL = L;
  if (argv[0] && argv[0][0]) progname = argv[0];
  lua_gc(L, LUA_GCSTOP, 0);  /* stop collector during initialization */
  luaL_openlibs(L);  /* open libraries */
  lua_gc(L, LUA_GCRESTART, 0);
  s->status = handle_luainit(L);
  if (s->status != 0) return 0;
  script = collectargs(argv, &has_i, &has_v, &has_e);
  if (script < 0) {  /* invalid args? */
    print_usage();
    s->status = 1;
    return 0;
  }
  if (has_v) print_version();
  s->status = runargs(L, argv, (script > 0) ? script : s->argc);
  if (s->status != 0) return 0;
  if (script)
    s->status = handle_script(L, argv, script);
  if (s->status != 0) return 0;
  if (has_i)
    dotty(L);
  else if (script == 0 && !has_e && !has_v) {
    if (lua_stdin_is_tty()) {
      print_version();
      dotty(L);
    }
    else dofile(L, NULL);  /* executes stdin as a file */
  }
  return 0;
}


int main (int argc, char **argv) {
  int status;
  struct Smain s;
  lua_State *L = lua_open();  /* create state */
  if (L == NULL) {
    l_message(argv[0], "cannot create state: not enough memory");
    return EXIT_FAILURE;
  }
  s.argc = argc;
  s.argv = argv;
  status = lua_cpcall(L, &pmain, &s);
  report(L, status);
  lua_close(L);
  return (status || s.status) ? EXIT_FAILURE : EXIT_SUCCESS;
}

genometools-1.5.1/src/external/lua-5.1.5/src/lua.h000066400000000000000000000266501211610345200214340ustar00rootroot00000000000000/*
** $Id: lua.h,v 1.218.1.7 2012/01/13 20:36:20 roberto Exp $
** Lua - An Extensible Extension Language
** Lua.org, PUC-Rio, Brazil (http://www.lua.org)
** See Copyright Notice at the end of this file
*/


#ifndef lua_h
#define lua_h

#include 
#include 


#include "luaconf.h"


#define LUA_VERSION	"Lua 5.1"
#define LUA_RELEASE	"Lua 5.1.5"
#define LUA_VERSION_NUM	501
#define LUA_COPYRIGHT	"Copyright (C) 1994-2012 Lua.org, PUC-Rio"
#define LUA_AUTHORS 	"R. Ierusalimschy, L. H. de Figueiredo & W. Celes"


/* mark for precompiled code (`Lua') */
#define	LUA_SIGNATURE	"\033Lua"

/* option for multiple returns in `lua_pcall' and `lua_call' */
#define LUA_MULTRET	(-1)


/*
** pseudo-indices
*/
#define LUA_REGISTRYINDEX	(-10000)
#define LUA_ENVIRONINDEX	(-10001)
#define LUA_GLOBALSINDEX	(-10002)
#define lua_upvalueindex(i)	(LUA_GLOBALSINDEX-(i))


/* thread status; 0 is OK */
#define LUA_YIELD	1
#define LUA_ERRRUN	2
#define LUA_ERRSYNTAX	3
#define LUA_ERRMEM	4
#define LUA_ERRERR	5


typedef struct lua_State lua_State;

typedef int (*lua_CFunction) (lua_State *L);


/*
** functions that read/write blocks when loading/dumping Lua chunks
*/
typedef const char * (*lua_Reader) (lua_State *L, void *ud, size_t *sz);

typedef int (*lua_Writer) (lua_State *L, const void* p, size_t sz, void* ud);


/*
** prototype for memory-allocation functions
*/
typedef void * (*lua_Alloc) (void *ud, void *ptr, size_t osize, size_t nsize);


/*
** basic types
*/
#define LUA_TNONE		(-1)

#define LUA_TNIL		0
#define LUA_TBOOLEAN		1
#define LUA_TLIGHTUSERDATA	2
#define LUA_TNUMBER		3
#define LUA_TSTRING		4
#define LUA_TTABLE		5
#define LUA_TFUNCTION		6
#define LUA_TUSERDATA		7
#define LUA_TTHREAD		8



/* minimum Lua stack available to a C function */
#define LUA_MINSTACK	20


/*
** generic extra include file
*/
#if defined(LUA_USER_H)
#include LUA_USER_H
#endif


/* type of numbers in Lua */
typedef LUA_NUMBER lua_Number;


/* type for integer functions */
typedef LUA_INTEGER lua_Integer;



/*
** state manipulation
*/
LUA_API lua_State *(lua_newstate) (lua_Alloc f, void *ud);
LUA_API void       (lua_close) (lua_State *L);
LUA_API lua_State *(lua_newthread) (lua_State *L);

LUA_API lua_CFunction (lua_atpanic) (lua_State *L, lua_CFunction panicf);


/*
** basic stack manipulation
*/
LUA_API int   (lua_gettop) (lua_State *L);
LUA_API void  (lua_settop) (lua_State *L, int idx);
LUA_API void  (lua_pushvalue) (lua_State *L, int idx);
LUA_API void  (lua_remove) (lua_State *L, int idx);
LUA_API void  (lua_insert) (lua_State *L, int idx);
LUA_API void  (lua_replace) (lua_State *L, int idx);
LUA_API int   (lua_checkstack) (lua_State *L, int sz);

LUA_API void  (lua_xmove) (lua_State *from, lua_State *to, int n);


/*
** access functions (stack -> C)
*/

LUA_API int             (lua_isnumber) (lua_State *L, int idx);
LUA_API int             (lua_isstring) (lua_State *L, int idx);
LUA_API int             (lua_iscfunction) (lua_State *L, int idx);
LUA_API int             (lua_isuserdata) (lua_State *L, int idx);
LUA_API int             (lua_type) (lua_State *L, int idx);
LUA_API const char     *(lua_typename) (lua_State *L, int tp);

LUA_API int            (lua_equal) (lua_State *L, int idx1, int idx2);
LUA_API int            (lua_rawequal) (lua_State *L, int idx1, int idx2);
LUA_API int            (lua_lessthan) (lua_State *L, int idx1, int idx2);

LUA_API lua_Number      (lua_tonumber) (lua_State *L, int idx);
LUA_API lua_Integer     (lua_tointeger) (lua_State *L, int idx);
LUA_API int             (lua_toboolean) (lua_State *L, int idx);
LUA_API const char     *(lua_tolstring) (lua_State *L, int idx, size_t *len);
LUA_API size_t          (lua_objlen) (lua_State *L, int idx);
LUA_API lua_CFunction   (lua_tocfunction) (lua_State *L, int idx);
LUA_API void	       *(lua_touserdata) (lua_State *L, int idx);
LUA_API lua_State      *(lua_tothread) (lua_State *L, int idx);
LUA_API const void     *(lua_topointer) (lua_State *L, int idx);


/*
** push functions (C -> stack)
*/
LUA_API void  (lua_pushnil) (lua_State *L);
LUA_API void  (lua_pushnumber) (lua_State *L, lua_Number n);
LUA_API void  (lua_pushinteger) (lua_State *L, lua_Integer n);
LUA_API void  (lua_pushlstring) (lua_State *L, const char *s, size_t l);
LUA_API void  (lua_pushstring) (lua_State *L, const char *s);
LUA_API const char *(lua_pushvfstring) (lua_State *L, const char *fmt,
                                                      va_list argp);
LUA_API const char *(lua_pushfstring) (lua_State *L, const char *fmt, ...);
LUA_API void  (lua_pushcclosure) (lua_State *L, lua_CFunction fn, int n);
LUA_API void  (lua_pushboolean) (lua_State *L, int b);
LUA_API void  (lua_pushlightuserdata) (lua_State *L, void *p);
LUA_API int   (lua_pushthread) (lua_State *L);


/*
** get functions (Lua -> stack)
*/
LUA_API void  (lua_gettable) (lua_State *L, int idx);
LUA_API void  (lua_getfield) (lua_State *L, int idx, const char *k);
LUA_API void  (lua_rawget) (lua_State *L, int idx);
LUA_API void  (lua_rawgeti) (lua_State *L, int idx, int n);
LUA_API void  (lua_createtable) (lua_State *L, int narr, int nrec);
LUA_API void *(lua_newuserdata) (lua_State *L, size_t sz);
LUA_API int   (lua_getmetatable) (lua_State *L, int objindex);
LUA_API void  (lua_getfenv) (lua_State *L, int idx);


/*
** set functions (stack -> Lua)
*/
LUA_API void  (lua_settable) (lua_State *L, int idx);
LUA_API void  (lua_setfield) (lua_State *L, int idx, const char *k);
LUA_API void  (lua_rawset) (lua_State *L, int idx);
LUA_API void  (lua_rawseti) (lua_State *L, int idx, int n);
LUA_API int   (lua_setmetatable) (lua_State *L, int objindex);
LUA_API int   (lua_setfenv) (lua_State *L, int idx);


/*
** `load' and `call' functions (load and run Lua code)
*/
LUA_API void  (lua_call) (lua_State *L, int nargs, int nresults);
LUA_API int   (lua_pcall) (lua_State *L, int nargs, int nresults, int errfunc);
LUA_API int   (lua_cpcall) (lua_State *L, lua_CFunction func, void *ud);
LUA_API int   (lua_load) (lua_State *L, lua_Reader reader, void *dt,
                                        const char *chunkname);

LUA_API int (lua_dump) (lua_State *L, lua_Writer writer, void *data);


/*
** coroutine functions
*/
LUA_API int  (lua_yield) (lua_State *L, int nresults);
LUA_API int  (lua_resume) (lua_State *L, int narg);
LUA_API int  (lua_status) (lua_State *L);

/*
** garbage-collection function and options
*/

#define LUA_GCSTOP		0
#define LUA_GCRESTART		1
#define LUA_GCCOLLECT		2
#define LUA_GCCOUNT		3
#define LUA_GCCOUNTB		4
#define LUA_GCSTEP		5
#define LUA_GCSETPAUSE		6
#define LUA_GCSETSTEPMUL	7

LUA_API int (lua_gc) (lua_State *L, int what, int data);


/*
** miscellaneous functions
*/

LUA_API int   (lua_error) (lua_State *L);

LUA_API int   (lua_next) (lua_State *L, int idx);

LUA_API void  (lua_concat) (lua_State *L, int n);

LUA_API lua_Alloc (lua_getallocf) (lua_State *L, void **ud);
LUA_API void lua_setallocf (lua_State *L, lua_Alloc f, void *ud);



/* 
** ===============================================================
** some useful macros
** ===============================================================
*/

#define lua_pop(L,n)		lua_settop(L, -(n)-1)

#define lua_newtable(L)		lua_createtable(L, 0, 0)

#define lua_register(L,n,f) (lua_pushcfunction(L, (f)), lua_setglobal(L, (n)))

#define lua_pushcfunction(L,f)	lua_pushcclosure(L, (f), 0)

#define lua_strlen(L,i)		lua_objlen(L, (i))

#define lua_isfunction(L,n)	(lua_type(L, (n)) == LUA_TFUNCTION)
#define lua_istable(L,n)	(lua_type(L, (n)) == LUA_TTABLE)
#define lua_islightuserdata(L,n)	(lua_type(L, (n)) == LUA_TLIGHTUSERDATA)
#define lua_isnil(L,n)		(lua_type(L, (n)) == LUA_TNIL)
#define lua_isboolean(L,n)	(lua_type(L, (n)) == LUA_TBOOLEAN)
#define lua_isthread(L,n)	(lua_type(L, (n)) == LUA_TTHREAD)
#define lua_isnone(L,n)		(lua_type(L, (n)) == LUA_TNONE)
#define lua_isnoneornil(L, n)	(lua_type(L, (n)) <= 0)

#define lua_pushliteral(L, s)	\
	lua_pushlstring(L, "" s, (sizeof(s)/sizeof(char))-1)

#define lua_setglobal(L,s)	lua_setfield(L, LUA_GLOBALSINDEX, (s))
#define lua_getglobal(L,s)	lua_getfield(L, LUA_GLOBALSINDEX, (s))

#define lua_tostring(L,i)	lua_tolstring(L, (i), NULL)



/*
** compatibility macros and functions
*/

#define lua_open()	luaL_newstate()

#define lua_getregistry(L)	lua_pushvalue(L, LUA_REGISTRYINDEX)

#define lua_getgccount(L)	lua_gc(L, LUA_GCCOUNT, 0)

#define lua_Chunkreader		lua_Reader
#define lua_Chunkwriter		lua_Writer


/* hack */
LUA_API void lua_setlevel	(lua_State *from, lua_State *to);


/*
** {======================================================================
** Debug API
** =======================================================================
*/


/*
** Event codes
*/
#define LUA_HOOKCALL	0
#define LUA_HOOKRET	1
#define LUA_HOOKLINE	2
#define LUA_HOOKCOUNT	3
#define LUA_HOOKTAILRET 4


/*
** Event masks
*/
#define LUA_MASKCALL	(1 << LUA_HOOKCALL)
#define LUA_MASKRET	(1 << LUA_HOOKRET)
#define LUA_MASKLINE	(1 << LUA_HOOKLINE)
#define LUA_MASKCOUNT	(1 << LUA_HOOKCOUNT)

typedef struct lua_Debug lua_Debug;  /* activation record */


/* Functions to be called by the debuger in specific events */
typedef void (*lua_Hook) (lua_State *L, lua_Debug *ar);


LUA_API int lua_getstack (lua_State *L, int level, lua_Debug *ar);
LUA_API int lua_getinfo (lua_State *L, const char *what, lua_Debug *ar);
LUA_API const char *lua_getlocal (lua_State *L, const lua_Debug *ar, int n);
LUA_API const char *lua_setlocal (lua_State *L, const lua_Debug *ar, int n);
LUA_API const char *lua_getupvalue (lua_State *L, int funcindex, int n);
LUA_API const char *lua_setupvalue (lua_State *L, int funcindex, int n);

LUA_API int lua_sethook (lua_State *L, lua_Hook func, int mask, int count);
LUA_API lua_Hook lua_gethook (lua_State *L);
LUA_API int lua_gethookmask (lua_State *L);
LUA_API int lua_gethookcount (lua_State *L);


struct lua_Debug {
  int event;
  const char *name;	/* (n) */
  const char *namewhat;	/* (n) `global', `local', `field', `method' */
  const char *what;	/* (S) `Lua', `C', `main', `tail' */
  const char *source;	/* (S) */
  int currentline;	/* (l) */
  int nups;		/* (u) number of upvalues */
  int linedefined;	/* (S) */
  int lastlinedefined;	/* (S) */
  char short_src[LUA_IDSIZE]; /* (S) */
  /* private part */
  int i_ci;  /* active function */
};

/* }====================================================================== */


/******************************************************************************
* Copyright (C) 1994-2012 Lua.org, PUC-Rio.  All rights reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject to
* the following conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
* CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
* TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
* SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
******************************************************************************/


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/luac.c000066400000000000000000000110651211610345200215640ustar00rootroot00000000000000/*
** $Id: luac.c,v 1.54 2006/06/02 17:37:11 lhf Exp $
** Lua compiler (saves bytecodes to files; also list bytecodes)
** See Copyright Notice in lua.h
*/

#include 
#include 
#include 
#include 

#define luac_c
#define LUA_CORE

#include "lua.h"
#include "lauxlib.h"

#include "ldo.h"
#include "lfunc.h"
#include "lmem.h"
#include "lobject.h"
#include "lopcodes.h"
#include "lstring.h"
#include "lundump.h"

#define PROGNAME	"luac"		/* default program name */
#define	OUTPUT		PROGNAME ".out"	/* default output file */

static int listing=0;			/* list bytecodes? */
static int dumping=1;			/* dump bytecodes? */
static int stripping=0;			/* strip debug information? */
static char Output[]={ OUTPUT };	/* default output file name */
static const char* output=Output;	/* actual output file name */
static const char* progname=PROGNAME;	/* actual program name */

static void fatal(const char* message)
{
 fprintf(stderr,"%s: %s\n",progname,message);
 exit(EXIT_FAILURE);
}

static void cannot(const char* what)
{
 fprintf(stderr,"%s: cannot %s %s: %s\n",progname,what,output,strerror(errno));
 exit(EXIT_FAILURE);
}

static void usage(const char* message)
{
 if (*message=='-')
  fprintf(stderr,"%s: unrecognized option " LUA_QS "\n",progname,message);
 else
  fprintf(stderr,"%s: %s\n",progname,message);
 fprintf(stderr,
 "usage: %s [options] [filenames].\n"
 "Available options are:\n"
 "  -        process stdin\n"
 "  -l       list\n"
 "  -o name  output to file " LUA_QL("name") " (default is \"%s\")\n"
 "  -p       parse only\n"
 "  -s       strip debug information\n"
 "  -v       show version information\n"
 "  --       stop handling options\n",
 progname,Output);
 exit(EXIT_FAILURE);
}

#define	IS(s)	(strcmp(argv[i],s)==0)

static int doargs(int argc, char* argv[])
{
 int i;
 int version=0;
 if (argv[0]!=NULL && *argv[0]!=0) progname=argv[0];
 for (i=1; itop+(i))->l.p)

static const Proto* combine(lua_State* L, int n)
{
 if (n==1)
  return toproto(L,-1);
 else
 {
  int i,pc;
  Proto* f=luaF_newproto(L);
  setptvalue2s(L,L->top,f); incr_top(L);
  f->source=luaS_newliteral(L,"=(" PROGNAME ")");
  f->maxstacksize=1;
  pc=2*n+1;
  f->code=luaM_newvector(L,pc,Instruction);
  f->sizecode=pc;
  f->p=luaM_newvector(L,n,Proto*);
  f->sizep=n;
  pc=0;
  for (i=0; ip[i]=toproto(L,i-n-1);
   f->code[pc++]=CREATE_ABx(OP_CLOSURE,0,i);
   f->code[pc++]=CREATE_ABC(OP_CALL,0,1,1);
  }
  f->code[pc++]=CREATE_ABC(OP_RETURN,0,1,0);
  return f;
 }
}

static int writer(lua_State* L, const void* p, size_t size, void* u)
{
 UNUSED(L);
 return (fwrite(p,size,1,(FILE*)u)!=1) && (size!=0);
}

struct Smain {
 int argc;
 char** argv;
};

static int pmain(lua_State* L)
{
 struct Smain* s = (struct Smain*)lua_touserdata(L, 1);
 int argc=s->argc;
 char** argv=s->argv;
 const Proto* f;
 int i;
 if (!lua_checkstack(L,argc)) fatal("too many input files");
 for (i=0; i1);
 if (dumping)
 {
  FILE* D= (output==NULL) ? stdout : fopen(output,"wb");
  if (D==NULL) cannot("open");
  lua_lock(L);
  luaU_dump(L,f,writer,D,stripping);
  lua_unlock(L);
  if (ferror(D)) cannot("write");
  if (fclose(D)) cannot("close");
 }
 return 0;
}

int main(int argc, char* argv[])
{
 lua_State* L;
 struct Smain s;
 int i=doargs(argc,argv);
 argc-=i; argv+=i;
 if (argc<=0) usage("no input files given");
 L=lua_open();
 if (L==NULL) fatal("not enough memory for state");
 s.argc=argc;
 s.argv=argv;
 if (lua_cpcall(L,pmain,&s)!=0) fatal(lua_tostring(L,-1));
 lua_close(L);
 return EXIT_SUCCESS;
}
genometools-1.5.1/src/external/lua-5.1.5/src/luaconf.h000066400000000000000000000534331211610345200223010ustar00rootroot00000000000000/*
** $Id: luaconf.h,v 1.82.1.7 2008/02/11 16:25:08 roberto Exp $
** Configuration file for Lua
** See Copyright Notice in lua.h
*/


#ifndef lconfig_h
#define lconfig_h

#include 
#include 


/*
** ==================================================================
** Search for "@@" to find all configurable definitions.
** ===================================================================
*/


/*
@@ LUA_ANSI controls the use of non-ansi features.
** CHANGE it (define it) if you want Lua to avoid the use of any
** non-ansi feature or library.
*/
#if defined(__STRICT_ANSI__)
#define LUA_ANSI
#endif


#if !defined(LUA_ANSI) && defined(_WIN32)
#define LUA_WIN
#endif

#if defined(LUA_USE_LINUX)
#define LUA_USE_POSIX
#define LUA_USE_DLOPEN		/* needs an extra library: -ldl */
#define LUA_USE_READLINE	/* needs some extra libraries */
#endif

#if defined(LUA_USE_MACOSX)
#define LUA_USE_POSIX
#define LUA_DL_DYLD		/* does not need extra library */
#endif



/*
@@ LUA_USE_POSIX includes all functionallity listed as X/Open System
@* Interfaces Extension (XSI).
** CHANGE it (define it) if your system is XSI compatible.
*/
#if defined(LUA_USE_POSIX)
#define LUA_USE_MKSTEMP
#define LUA_USE_ISATTY
#define LUA_USE_POPEN
#define LUA_USE_ULONGJMP
#endif


/*
@@ LUA_PATH and LUA_CPATH are the names of the environment variables that
@* Lua check to set its paths.
@@ LUA_INIT is the name of the environment variable that Lua
@* checks for initialization code.
** CHANGE them if you want different names.
*/
#define LUA_PATH        "LUA_PATH"
#define LUA_CPATH       "LUA_CPATH"
#define LUA_INIT	"LUA_INIT"


/*
@@ LUA_PATH_DEFAULT is the default path that Lua uses to look for
@* Lua libraries.
@@ LUA_CPATH_DEFAULT is the default path that Lua uses to look for
@* C libraries.
** CHANGE them if your machine has a non-conventional directory
** hierarchy or if you want to install your libraries in
** non-conventional directories.
*/
#if defined(_WIN32)
/*
** In Windows, any exclamation mark ('!') in the path is replaced by the
** path of the directory of the executable file of the current process.
*/
#define LUA_LDIR	"!\\lua\\"
#define LUA_CDIR	"!\\"
#define LUA_PATH_DEFAULT  \
		".\\?.lua;"  LUA_LDIR"?.lua;"  LUA_LDIR"?\\init.lua;" \
		             LUA_CDIR"?.lua;"  LUA_CDIR"?\\init.lua"
#define LUA_CPATH_DEFAULT \
	".\\?.dll;"  LUA_CDIR"?.dll;" LUA_CDIR"loadall.dll"

#else
#define LUA_ROOT	"/usr/local/"
#define LUA_LDIR	LUA_ROOT "share/lua/5.1/"
#define LUA_CDIR	LUA_ROOT "lib/lua/5.1/"
#define LUA_PATH_DEFAULT  \
		"./?.lua;"  LUA_LDIR"?.lua;"  LUA_LDIR"?/init.lua;" \
		            LUA_CDIR"?.lua;"  LUA_CDIR"?/init.lua"
#define LUA_CPATH_DEFAULT \
	"./?.so;"  LUA_CDIR"?.so;" LUA_CDIR"loadall.so"
#endif


/*
@@ LUA_DIRSEP is the directory separator (for submodules).
** CHANGE it if your machine does not use "/" as the directory separator
** and is not Windows. (On Windows Lua automatically uses "\".)
*/
#if defined(_WIN32)
#define LUA_DIRSEP	"\\"
#else
#define LUA_DIRSEP	"/"
#endif


/*
@@ LUA_PATHSEP is the character that separates templates in a path.
@@ LUA_PATH_MARK is the string that marks the substitution points in a
@* template.
@@ LUA_EXECDIR in a Windows path is replaced by the executable's
@* directory.
@@ LUA_IGMARK is a mark to ignore all before it when bulding the
@* luaopen_ function name.
** CHANGE them if for some reason your system cannot use those
** characters. (E.g., if one of those characters is a common character
** in file/directory names.) Probably you do not need to change them.
*/
#define LUA_PATHSEP	";"
#define LUA_PATH_MARK	"?"
#define LUA_EXECDIR	"!"
#define LUA_IGMARK	"-"


/*
@@ LUA_INTEGER is the integral type used by lua_pushinteger/lua_tointeger.
** CHANGE that if ptrdiff_t is not adequate on your machine. (On most
** machines, ptrdiff_t gives a good choice between int or long.)
*/
#define LUA_INTEGER	ptrdiff_t


/*
@@ LUA_API is a mark for all core API functions.
@@ LUALIB_API is a mark for all standard library functions.
** CHANGE them if you need to define those functions in some special way.
** For instance, if you want to create one Windows DLL with the core and
** the libraries, you may want to use the following definition (define
** LUA_BUILD_AS_DLL to get it).
*/
#if defined(LUA_BUILD_AS_DLL)

#if defined(LUA_CORE) || defined(LUA_LIB)
#define LUA_API __declspec(dllexport)
#else
#define LUA_API __declspec(dllimport)
#endif

#else

#define LUA_API		extern

#endif

/* more often than not the libs go together with the core */
#define LUALIB_API	LUA_API


/*
@@ LUAI_FUNC is a mark for all extern functions that are not to be
@* exported to outside modules.
@@ LUAI_DATA is a mark for all extern (const) variables that are not to
@* be exported to outside modules.
** CHANGE them if you need to mark them in some special way. Elf/gcc
** (versions 3.2 and later) mark them as "hidden" to optimize access
** when Lua is compiled as a shared library.
*/
#if defined(luaall_c)
#define LUAI_FUNC	static
#define LUAI_DATA	/* empty */

#elif defined(__GNUC__) && ((__GNUC__*100 + __GNUC_MINOR__) >= 302) && \
      defined(__ELF__)
#define LUAI_FUNC	__attribute__((visibility("hidden"))) extern
#define LUAI_DATA	LUAI_FUNC

#else
#define LUAI_FUNC	extern
#define LUAI_DATA	extern
#endif



/*
@@ LUA_QL describes how error messages quote program elements.
** CHANGE it if you want a different appearance.
*/
#define LUA_QL(x)	"'" x "'"
#define LUA_QS		LUA_QL("%s")


/*
@@ LUA_IDSIZE gives the maximum size for the description of the source
@* of a function in debug information.
** CHANGE it if you want a different size.
*/
#define LUA_IDSIZE	60


/*
** {==================================================================
** Stand-alone configuration
** ===================================================================
*/

#if defined(lua_c) || defined(luaall_c)

/*
@@ lua_stdin_is_tty detects whether the standard input is a 'tty' (that
@* is, whether we're running lua interactively).
** CHANGE it if you have a better definition for non-POSIX/non-Windows
** systems.
*/
#if defined(LUA_USE_ISATTY)
#include 
#define lua_stdin_is_tty()	isatty(0)
#elif defined(LUA_WIN)
#include 
#include 
#define lua_stdin_is_tty()	_isatty(_fileno(stdin))
#else
#define lua_stdin_is_tty()	1  /* assume stdin is a tty */
#endif


/*
@@ LUA_PROMPT is the default prompt used by stand-alone Lua.
@@ LUA_PROMPT2 is the default continuation prompt used by stand-alone Lua.
** CHANGE them if you want different prompts. (You can also change the
** prompts dynamically, assigning to globals _PROMPT/_PROMPT2.)
*/
#define LUA_PROMPT		"> "
#define LUA_PROMPT2		">> "


/*
@@ LUA_PROGNAME is the default name for the stand-alone Lua program.
** CHANGE it if your stand-alone interpreter has a different name and
** your system is not able to detect that name automatically.
*/
#define LUA_PROGNAME		"lua"


/*
@@ LUA_MAXINPUT is the maximum length for an input line in the
@* stand-alone interpreter.
** CHANGE it if you need longer lines.
*/
#define LUA_MAXINPUT	512


/*
@@ lua_readline defines how to show a prompt and then read a line from
@* the standard input.
@@ lua_saveline defines how to "save" a read line in a "history".
@@ lua_freeline defines how to free a line read by lua_readline.
** CHANGE them if you want to improve this functionality (e.g., by using
** GNU readline and history facilities).
*/
#if defined(LUA_USE_READLINE)
#include 
#include 
#include 
#define lua_readline(L,b,p)	((void)L, ((b)=readline(p)) != NULL)
#define lua_saveline(L,idx) \
	if (lua_strlen(L,idx) > 0)  /* non-empty line? */ \
	  add_history(lua_tostring(L, idx));  /* add it to history */
#define lua_freeline(L,b)	((void)L, free(b))
#else
#define lua_readline(L,b,p)	\
	((void)L, fputs(p, stdout), fflush(stdout),  /* show prompt */ \
	fgets(b, LUA_MAXINPUT, stdin) != NULL)  /* get line */
#define lua_saveline(L,idx)	{ (void)L; (void)idx; }
#define lua_freeline(L,b)	{ (void)L; (void)b; }
#endif

#endif

/* }================================================================== */


/*
@@ LUAI_GCPAUSE defines the default pause between garbage-collector cycles
@* as a percentage.
** CHANGE it if you want the GC to run faster or slower (higher values
** mean larger pauses which mean slower collection.) You can also change
** this value dynamically.
*/
#define LUAI_GCPAUSE	200  /* 200% (wait memory to double before next GC) */


/*
@@ LUAI_GCMUL defines the default speed of garbage collection relative to
@* memory allocation as a percentage.
** CHANGE it if you want to change the granularity of the garbage
** collection. (Higher values mean coarser collections. 0 represents
** infinity, where each step performs a full collection.) You can also
** change this value dynamically.
*/
#define LUAI_GCMUL	200 /* GC runs 'twice the speed' of memory allocation */



/*
@@ LUA_COMPAT_GETN controls compatibility with old getn behavior.
** CHANGE it (define it) if you want exact compatibility with the
** behavior of setn/getn in Lua 5.0.
*/
#undef LUA_COMPAT_GETN

/*
@@ LUA_COMPAT_LOADLIB controls compatibility about global loadlib.
** CHANGE it to undefined as soon as you do not need a global 'loadlib'
** function (the function is still available as 'package.loadlib').
*/
#undef LUA_COMPAT_LOADLIB

/*
@@ LUA_COMPAT_VARARG controls compatibility with old vararg feature.
** CHANGE it to undefined as soon as your programs use only '...' to
** access vararg parameters (instead of the old 'arg' table).
*/
#define LUA_COMPAT_VARARG

/*
@@ LUA_COMPAT_MOD controls compatibility with old math.mod function.
** CHANGE it to undefined as soon as your programs use 'math.fmod' or
** the new '%' operator instead of 'math.mod'.
*/
#define LUA_COMPAT_MOD

/*
@@ LUA_COMPAT_LSTR controls compatibility with old long string nesting
@* facility.
** CHANGE it to 2 if you want the old behaviour, or undefine it to turn
** off the advisory error when nesting [[...]].
*/
#define LUA_COMPAT_LSTR		1

/*
@@ LUA_COMPAT_GFIND controls compatibility with old 'string.gfind' name.
** CHANGE it to undefined as soon as you rename 'string.gfind' to
** 'string.gmatch'.
*/
#define LUA_COMPAT_GFIND

/*
@@ LUA_COMPAT_OPENLIB controls compatibility with old 'luaL_openlib'
@* behavior.
** CHANGE it to undefined as soon as you replace to 'luaL_register'
** your uses of 'luaL_openlib'
*/
#define LUA_COMPAT_OPENLIB



/*
@@ luai_apicheck is the assert macro used by the Lua-C API.
** CHANGE luai_apicheck if you want Lua to perform some checks in the
** parameters it gets from API calls. This may slow down the interpreter
** a bit, but may be quite useful when debugging C code that interfaces
** with Lua. A useful redefinition is to use assert.h.
*/
#if defined(LUA_USE_APICHECK)
#include 
#define luai_apicheck(L,o)	{ (void)L; assert(o); }
#else
#define luai_apicheck(L,o)	{ (void)L; }
#endif


/*
@@ LUAI_BITSINT defines the number of bits in an int.
** CHANGE here if Lua cannot automatically detect the number of bits of
** your machine. Probably you do not need to change this.
*/
/* avoid overflows in comparison */
#if INT_MAX-20 < 32760
#define LUAI_BITSINT	16
#elif INT_MAX > 2147483640L
/* int has at least 32 bits */
#define LUAI_BITSINT	32
#else
#error "you must define LUA_BITSINT with number of bits in an integer"
#endif


/*
@@ LUAI_UINT32 is an unsigned integer with at least 32 bits.
@@ LUAI_INT32 is an signed integer with at least 32 bits.
@@ LUAI_UMEM is an unsigned integer big enough to count the total
@* memory used by Lua.
@@ LUAI_MEM is a signed integer big enough to count the total memory
@* used by Lua.
** CHANGE here if for some weird reason the default definitions are not
** good enough for your machine. (The definitions in the 'else'
** part always works, but may waste space on machines with 64-bit
** longs.) Probably you do not need to change this.
*/
#if LUAI_BITSINT >= 32
#define LUAI_UINT32	unsigned int
#define LUAI_INT32	int
#define LUAI_MAXINT32	INT_MAX
#define LUAI_UMEM	size_t
#define LUAI_MEM	ptrdiff_t
#else
/* 16-bit ints */
#define LUAI_UINT32	unsigned long
#define LUAI_INT32	long
#define LUAI_MAXINT32	LONG_MAX
#define LUAI_UMEM	unsigned long
#define LUAI_MEM	long
#endif


/*
@@ LUAI_MAXCALLS limits the number of nested calls.
** CHANGE it if you need really deep recursive calls. This limit is
** arbitrary; its only purpose is to stop infinite recursion before
** exhausting memory.
*/
#define LUAI_MAXCALLS	20000


/*
@@ LUAI_MAXCSTACK limits the number of Lua stack slots that a C function
@* can use.
** CHANGE it if you need lots of (Lua) stack space for your C
** functions. This limit is arbitrary; its only purpose is to stop C
** functions to consume unlimited stack space. (must be smaller than
** -LUA_REGISTRYINDEX)
*/
#define LUAI_MAXCSTACK	8000



/*
** {==================================================================
** CHANGE (to smaller values) the following definitions if your system
** has a small C stack. (Or you may want to change them to larger
** values if your system has a large C stack and these limits are
** too rigid for you.) Some of these constants control the size of
** stack-allocated arrays used by the compiler or the interpreter, while
** others limit the maximum number of recursive calls that the compiler
** or the interpreter can perform. Values too large may cause a C stack
** overflow for some forms of deep constructs.
** ===================================================================
*/


/*
@@ LUAI_MAXCCALLS is the maximum depth for nested C calls (short) and
@* syntactical nested non-terminals in a program.
*/
#define LUAI_MAXCCALLS		200


/*
@@ LUAI_MAXVARS is the maximum number of local variables per function
@* (must be smaller than 250).
*/
#define LUAI_MAXVARS		200


/*
@@ LUAI_MAXUPVALUES is the maximum number of upvalues per function
@* (must be smaller than 250).
*/
#define LUAI_MAXUPVALUES	60


/*
@@ LUAL_BUFFERSIZE is the buffer size used by the lauxlib buffer system.
*/
#define LUAL_BUFFERSIZE		BUFSIZ

/* }================================================================== */




/*
** {==================================================================
@@ LUA_NUMBER is the type of numbers in Lua.
** CHANGE the following definitions only if you want to build Lua
** with a number type different from double. You may also need to
** change lua_number2int & lua_number2integer.
** ===================================================================
*/

#define LUA_NUMBER_DOUBLE
#define LUA_NUMBER	double

/*
@@ LUAI_UACNUMBER is the result of an 'usual argument conversion'
@* over a number.
*/
#define LUAI_UACNUMBER	double


/*
@@ LUA_NUMBER_SCAN is the format for reading numbers.
@@ LUA_NUMBER_FMT is the format for writing numbers.
@@ lua_number2str converts a number to a string.
@@ LUAI_MAXNUMBER2STR is maximum size of previous conversion.
@@ lua_str2number converts a string to a number.
*/
#define LUA_NUMBER_SCAN		"%lf"
#define LUA_NUMBER_FMT		"%.14g"
#define lua_number2str(s,n)	sprintf((s), LUA_NUMBER_FMT, (n))
#define LUAI_MAXNUMBER2STR	32 /* 16 digits, sign, point, and \0 */
#define lua_str2number(s,p)	strtod((s), (p))


/*
@@ The luai_num* macros define the primitive operations over numbers.
*/
#if defined(LUA_CORE)
#include 
#define luai_numadd(a,b)	((a)+(b))
#define luai_numsub(a,b)	((a)-(b))
#define luai_nummul(a,b)	((a)*(b))
#define luai_numdiv(a,b)	((a)/(b))
#define luai_nummod(a,b)	((a) - floor((a)/(b))*(b))
#define luai_numpow(a,b)	(pow(a,b))
#define luai_numunm(a)		(-(a))
#define luai_numeq(a,b)		((a)==(b))
#define luai_numlt(a,b)		((a)<(b))
#define luai_numle(a,b)		((a)<=(b))
#define luai_numisnan(a)	(!luai_numeq((a), (a)))
#endif


/*
@@ lua_number2int is a macro to convert lua_Number to int.
@@ lua_number2integer is a macro to convert lua_Number to lua_Integer.
** CHANGE them if you know a faster way to convert a lua_Number to
** int (with any rounding method and without throwing errors) in your
** system. In Pentium machines, a naive typecast from double to int
** in C is extremely slow, so any alternative is worth trying.
*/

/* On a Pentium, resort to a trick */
#if defined(LUA_NUMBER_DOUBLE) && !defined(LUA_ANSI) && !defined(__SSE2__) && \
    (defined(__i386) || defined (_M_IX86) || defined(__i386__))

/* On a Microsoft compiler, use assembler */
#if defined(_MSC_VER)

#define lua_number2int(i,d)   __asm fld d   __asm fistp i
#define lua_number2integer(i,n)		lua_number2int(i, n)

/* the next trick should work on any Pentium, but sometimes clashes
   with a DirectX idiosyncrasy */
#else

union luai_Cast { double l_d; long l_l; };
#define lua_number2int(i,d) \
  { volatile union luai_Cast u; u.l_d = (d) + 6755399441055744.0; (i) = u.l_l; }
#define lua_number2integer(i,n)		lua_number2int(i, n)

#endif


/* this option always works, but may be slow */
#else
#define lua_number2int(i,d)	((i)=(int)(d))
#define lua_number2integer(i,d)	((i)=(lua_Integer)(d))

#endif

/* }================================================================== */


/*
@@ LUAI_USER_ALIGNMENT_T is a type that requires maximum alignment.
** CHANGE it if your system requires alignments larger than double. (For
** instance, if your system supports long doubles and they must be
** aligned in 16-byte boundaries, then you should add long double in the
** union.) Probably you do not need to change this.
*/
#define LUAI_USER_ALIGNMENT_T	union { double u; void *s; long l; }


/*
@@ LUAI_THROW/LUAI_TRY define how Lua does exception handling.
** CHANGE them if you prefer to use longjmp/setjmp even with C++
** or if want/don't to use _longjmp/_setjmp instead of regular
** longjmp/setjmp. By default, Lua handles errors with exceptions when
** compiling as C++ code, with _longjmp/_setjmp when asked to use them,
** and with longjmp/setjmp otherwise.
*/
#if defined(__cplusplus)
/* C++ exceptions */
#define LUAI_THROW(L,c)	throw(c)
#define LUAI_TRY(L,c,a)	try { a } catch(...) \
	{ if ((c)->status == 0) (c)->status = -1; }
#define luai_jmpbuf	int  /* dummy variable */

#elif defined(LUA_USE_ULONGJMP)
/* in Unix, try _longjmp/_setjmp (more efficient) */
#define LUAI_THROW(L,c)	_longjmp((c)->b, 1)
#define LUAI_TRY(L,c,a)	if (_setjmp((c)->b) == 0) { a }
#define luai_jmpbuf	jmp_buf

#else
/* default handling with long jumps */
#define LUAI_THROW(L,c)	longjmp((c)->b, 1)
#define LUAI_TRY(L,c,a)	if (setjmp((c)->b) == 0) { a }
#define luai_jmpbuf	jmp_buf

#endif


/*
@@ LUA_MAXCAPTURES is the maximum number of captures that a pattern
@* can do during pattern-matching.
** CHANGE it if you need more captures. This limit is arbitrary.
*/
#define LUA_MAXCAPTURES		32


/*
@@ lua_tmpnam is the function that the OS library uses to create a
@* temporary name.
@@ LUA_TMPNAMBUFSIZE is the maximum size of a name created by lua_tmpnam.
** CHANGE them if you have an alternative to tmpnam (which is considered
** insecure) or if you want the original tmpnam anyway.  By default, Lua
** uses tmpnam except when POSIX is available, where it uses mkstemp.
*/
#if defined(loslib_c) || defined(luaall_c)

#if defined(LUA_USE_MKSTEMP)
#include 
#define LUA_TMPNAMBUFSIZE	32
#define lua_tmpnam(b,e)	{ \
	strcpy(b, "/tmp/lua_XXXXXX"); \
	e = mkstemp(b); \
	if (e != -1) close(e); \
	e = (e == -1); }

#else
#define LUA_TMPNAMBUFSIZE	L_tmpnam
#define lua_tmpnam(b,e)		{ e = (tmpnam(b) == NULL); }
#endif

#endif


/*
@@ lua_popen spawns a new process connected to the current one through
@* the file streams.
** CHANGE it if you have a way to implement it in your system.
*/
#if defined(LUA_USE_POPEN)

#define lua_popen(L,c,m)	((void)L, fflush(NULL), popen(c,m))
#define lua_pclose(L,file)	((void)L, (pclose(file) != -1))

#elif defined(LUA_WIN)

#define lua_popen(L,c,m)	((void)L, _popen(c,m))
#define lua_pclose(L,file)	((void)L, (_pclose(file) != -1))

#else

#define lua_popen(L,c,m)	((void)((void)c, m),  \
		luaL_error(L, LUA_QL("popen") " not supported"), (FILE*)0)
#define lua_pclose(L,file)		((void)((void)L, file), 0)

#endif

/*
@@ LUA_DL_* define which dynamic-library system Lua should use.
** CHANGE here if Lua has problems choosing the appropriate
** dynamic-library system for your platform (either Windows' DLL, Mac's
** dyld, or Unix's dlopen). If your system is some kind of Unix, there
** is a good chance that it has dlopen, so LUA_DL_DLOPEN will work for
** it.  To use dlopen you also need to adapt the src/Makefile (probably
** adding -ldl to the linker options), so Lua does not select it
** automatically.  (When you change the makefile to add -ldl, you must
** also add -DLUA_USE_DLOPEN.)
** If you do not want any kind of dynamic library, undefine all these
** options.
** By default, _WIN32 gets LUA_DL_DLL and MAC OS X gets LUA_DL_DYLD.
*/
#if defined(LUA_USE_DLOPEN)
#define LUA_DL_DLOPEN
#endif

#if defined(LUA_WIN)
#define LUA_DL_DLL
#endif


/*
@@ LUAI_EXTRASPACE allows you to add user-specific data in a lua_State
@* (the data goes just *before* the lua_State pointer).
** CHANGE (define) this if you really need that. This value must be
** a multiple of the maximum alignment required for your machine.
*/
#define LUAI_EXTRASPACE		0


/*
@@ luai_userstate* allow user-specific actions on threads.
** CHANGE them if you defined LUAI_EXTRASPACE and need to do something
** extra when a thread is created/deleted/resumed/yielded.
*/
#define luai_userstateopen(L)		((void)L)
#define luai_userstateclose(L)		((void)L)
#define luai_userstatethread(L,L1)	((void)L)
#define luai_userstatefree(L)		((void)L)
#define luai_userstateresume(L,n)	((void)L)
#define luai_userstateyield(L,n)	((void)L)


/*
@@ LUA_INTFRMLEN is the length modifier for integer conversions
@* in 'string.format'.
@@ LUA_INTFRM_T is the integer type correspoding to the previous length
@* modifier.
** CHANGE them if your system supports long long or does not support long.
*/

#if defined(LUA_USELONGLONG)

#define LUA_INTFRMLEN		"ll"
#define LUA_INTFRM_T		long long

#else

#define LUA_INTFRMLEN		"l"
#define LUA_INTFRM_T		long

#endif



/* =================================================================== */

/*
** Local configuration. You can use this space to add your redefinitions
** without modifying the main part of the file.
*/



#endif

genometools-1.5.1/src/external/lua-5.1.5/src/lualib.h000066400000000000000000000020021211610345200221040ustar00rootroot00000000000000/*
** $Id: lualib.h,v 1.36.1.1 2007/12/27 13:02:25 roberto Exp $
** Lua standard libraries
** See Copyright Notice in lua.h
*/


#ifndef lualib_h
#define lualib_h

#include "lua.h"


/* Key to file-handle type */
#define LUA_FILEHANDLE		"FILE*"


#define LUA_COLIBNAME	"coroutine"
LUALIB_API int (luaopen_base) (lua_State *L);

#define LUA_TABLIBNAME	"table"
LUALIB_API int (luaopen_table) (lua_State *L);

#define LUA_IOLIBNAME	"io"
LUALIB_API int (luaopen_io) (lua_State *L);

#define LUA_OSLIBNAME	"os"
LUALIB_API int (luaopen_os) (lua_State *L);

#define LUA_STRLIBNAME	"string"
LUALIB_API int (luaopen_string) (lua_State *L);

#define LUA_MATHLIBNAME	"math"
LUALIB_API int (luaopen_math) (lua_State *L);

#define LUA_DBLIBNAME	"debug"
LUALIB_API int (luaopen_debug) (lua_State *L);

#define LUA_LOADLIBNAME	"package"
LUALIB_API int (luaopen_package) (lua_State *L);


/* open all previous libraries */
LUALIB_API void (luaL_openlibs) (lua_State *L); 



#ifndef lua_assert
#define lua_assert(x)	((void)0)
#endif


#endif
genometools-1.5.1/src/external/lua-5.1.5/src/lundump.c000066400000000000000000000110251211610345200223200ustar00rootroot00000000000000/*
** $Id: lundump.c,v 2.7.1.4 2008/04/04 19:51:41 roberto Exp $
** load precompiled Lua chunks
** See Copyright Notice in lua.h
*/

#include 

#define lundump_c
#define LUA_CORE

#include "lua.h"

#include "ldebug.h"
#include "ldo.h"
#include "lfunc.h"
#include "lmem.h"
#include "lobject.h"
#include "lstring.h"
#include "lundump.h"
#include "lzio.h"

typedef struct {
 lua_State* L;
 ZIO* Z;
 Mbuffer* b;
 const char* name;
} LoadState;

#ifdef LUAC_TRUST_BINARIES
#define IF(c,s)
#define error(S,s)
#else
#define IF(c,s)		if (c) error(S,s)

static void error(LoadState* S, const char* why)
{
 luaO_pushfstring(S->L,"%s: %s in precompiled chunk",S->name,why);
 luaD_throw(S->L,LUA_ERRSYNTAX);
}
#endif

#define LoadMem(S,b,n,size)	LoadBlock(S,b,(n)*(size))
#define	LoadByte(S)		(lu_byte)LoadChar(S)
#define LoadVar(S,x)		LoadMem(S,&x,1,sizeof(x))
#define LoadVector(S,b,n,size)	LoadMem(S,b,n,size)

static void LoadBlock(LoadState* S, void* b, size_t size)
{
 size_t r=luaZ_read(S->Z,b,size);
 IF (r!=0, "unexpected end");
}

static int LoadChar(LoadState* S)
{
 char x;
 LoadVar(S,x);
 return x;
}

static int LoadInt(LoadState* S)
{
 int x;
 LoadVar(S,x);
 IF (x<0, "bad integer");
 return x;
}

static lua_Number LoadNumber(LoadState* S)
{
 lua_Number x;
 LoadVar(S,x);
 return x;
}

static TString* LoadString(LoadState* S)
{
 size_t size;
 LoadVar(S,size);
 if (size==0)
  return NULL;
 else
 {
  char* s=luaZ_openspace(S->L,S->b,size);
  LoadBlock(S,s,size);
  return luaS_newlstr(S->L,s,size-1);		/* remove trailing '\0' */
 }
}

static void LoadCode(LoadState* S, Proto* f)
{
 int n=LoadInt(S);
 f->code=luaM_newvector(S->L,n,Instruction);
 f->sizecode=n;
 LoadVector(S,f->code,n,sizeof(Instruction));
}

static Proto* LoadFunction(LoadState* S, TString* p);

static void LoadConstants(LoadState* S, Proto* f)
{
 int i,n;
 n=LoadInt(S);
 f->k=luaM_newvector(S->L,n,TValue);
 f->sizek=n;
 for (i=0; ik[i]);
 for (i=0; ik[i];
  int t=LoadChar(S);
  switch (t)
  {
   case LUA_TNIL:
   	setnilvalue(o);
	break;
   case LUA_TBOOLEAN:
   	setbvalue(o,LoadChar(S)!=0);
	break;
   case LUA_TNUMBER:
	setnvalue(o,LoadNumber(S));
	break;
   case LUA_TSTRING:
	setsvalue2n(S->L,o,LoadString(S));
	break;
   default:
	error(S,"bad constant");
	break;
  }
 }
 n=LoadInt(S);
 f->p=luaM_newvector(S->L,n,Proto*);
 f->sizep=n;
 for (i=0; ip[i]=NULL;
 for (i=0; ip[i]=LoadFunction(S,f->source);
}

static void LoadDebug(LoadState* S, Proto* f)
{
 int i,n;
 n=LoadInt(S);
 f->lineinfo=luaM_newvector(S->L,n,int);
 f->sizelineinfo=n;
 LoadVector(S,f->lineinfo,n,sizeof(int));
 n=LoadInt(S);
 f->locvars=luaM_newvector(S->L,n,LocVar);
 f->sizelocvars=n;
 for (i=0; ilocvars[i].varname=NULL;
 for (i=0; ilocvars[i].varname=LoadString(S);
  f->locvars[i].startpc=LoadInt(S);
  f->locvars[i].endpc=LoadInt(S);
 }
 n=LoadInt(S);
 f->upvalues=luaM_newvector(S->L,n,TString*);
 f->sizeupvalues=n;
 for (i=0; iupvalues[i]=NULL;
 for (i=0; iupvalues[i]=LoadString(S);
}

static Proto* LoadFunction(LoadState* S, TString* p)
{
 Proto* f;
 if (++S->L->nCcalls > LUAI_MAXCCALLS) error(S,"code too deep");
 f=luaF_newproto(S->L);
 setptvalue2s(S->L,S->L->top,f); incr_top(S->L);
 f->source=LoadString(S); if (f->source==NULL) f->source=p;
 f->linedefined=LoadInt(S);
 f->lastlinedefined=LoadInt(S);
 f->nups=LoadByte(S);
 f->numparams=LoadByte(S);
 f->is_vararg=LoadByte(S);
 f->maxstacksize=LoadByte(S);
 LoadCode(S,f);
 LoadConstants(S,f);
 LoadDebug(S,f);
 IF (!luaG_checkcode(f), "bad code");
 S->L->top--;
 S->L->nCcalls--;
 return f;
}

static void LoadHeader(LoadState* S)
{
 char h[LUAC_HEADERSIZE];
 char s[LUAC_HEADERSIZE];
 luaU_header(h);
 LoadBlock(S,s,LUAC_HEADERSIZE);
 IF (memcmp(h,s,LUAC_HEADERSIZE)!=0, "bad header");
}

/*
** load precompiled chunk
*/
Proto* luaU_undump (lua_State* L, ZIO* Z, Mbuffer* buff, const char* name)
{
 LoadState S;
 if (*name=='@' || *name=='=')
  S.name=name+1;
 else if (*name==LUA_SIGNATURE[0])
  S.name="binary string";
 else
  S.name=name;
 S.L=L;
 S.Z=Z;
 S.b=buff;
 LoadHeader(&S);
 return LoadFunction(&S,luaS_newliteral(L,"=?"));
}

/*
* make header
*/
void luaU_header (char* h)
{
 int x=1;
 memcpy(h,LUA_SIGNATURE,sizeof(LUA_SIGNATURE)-1);
 h+=sizeof(LUA_SIGNATURE)-1;
 *h++=(char)LUAC_VERSION;
 *h++=(char)LUAC_FORMAT;
 *h++=(char)*(char*)&x;				/* endianness */
 *h++=(char)sizeof(int);
 *h++=(char)sizeof(size_t);
 *h++=(char)sizeof(Instruction);
 *h++=(char)sizeof(lua_Number);
 *h++=(char)(((lua_Number)0.5)==0);		/* is lua_Number integral? */
}
genometools-1.5.1/src/external/lua-5.1.5/src/lundump.h000066400000000000000000000015721211610345200223330ustar00rootroot00000000000000/*
** $Id: lundump.h,v 1.37.1.1 2007/12/27 13:02:25 roberto Exp $
** load precompiled Lua chunks
** See Copyright Notice in lua.h
*/

#ifndef lundump_h
#define lundump_h

#include "lobject.h"
#include "lzio.h"

/* load one chunk; from lundump.c */
LUAI_FUNC Proto* luaU_undump (lua_State* L, ZIO* Z, Mbuffer* buff, const char* name);

/* make header; from lundump.c */
LUAI_FUNC void luaU_header (char* h);

/* dump one chunk; from ldump.c */
LUAI_FUNC int luaU_dump (lua_State* L, const Proto* f, lua_Writer w, void* data, int strip);

#ifdef luac_c
/* print one chunk; from print.c */
LUAI_FUNC void luaU_print (const Proto* f, int full);
#endif

/* for header of binary files -- this is Lua 5.1 */
#define LUAC_VERSION		0x51

/* for header of binary files -- this is the official format */
#define LUAC_FORMAT		0

/* size of header of binary files */
#define LUAC_HEADERSIZE		12

#endif
genometools-1.5.1/src/external/lua-5.1.5/src/lvm.c000066400000000000000000000553141211610345200214430ustar00rootroot00000000000000/*
** $Id: lvm.c,v 2.63.1.5 2011/08/17 20:43:11 roberto Exp $
** Lua virtual machine
** See Copyright Notice in lua.h
*/


#include 
#include 
#include 

#define lvm_c
#define LUA_CORE

#include "lua.h"

#include "ldebug.h"
#include "ldo.h"
#include "lfunc.h"
#include "lgc.h"
#include "lobject.h"
#include "lopcodes.h"
#include "lstate.h"
#include "lstring.h"
#include "ltable.h"
#include "ltm.h"
#include "lvm.h"



/* limit for table tag-method chains (to avoid loops) */
#define MAXTAGLOOP	100


const TValue *luaV_tonumber (const TValue *obj, TValue *n) {
  lua_Number num;
  if (ttisnumber(obj)) return obj;
  if (ttisstring(obj) && luaO_str2d(svalue(obj), &num)) {
    setnvalue(n, num);
    return n;
  }
  else
    return NULL;
}


int luaV_tostring (lua_State *L, StkId obj) {
  if (!ttisnumber(obj))
    return 0;
  else {
    char s[LUAI_MAXNUMBER2STR];
    lua_Number n = nvalue(obj);
    lua_number2str(s, n);
    setsvalue2s(L, obj, luaS_new(L, s));
    return 1;
  }
}


static void traceexec (lua_State *L, const Instruction *pc) {
  lu_byte mask = L->hookmask;
  const Instruction *oldpc = L->savedpc;
  L->savedpc = pc;
  if ((mask & LUA_MASKCOUNT) && L->hookcount == 0) {
    resethookcount(L);
    luaD_callhook(L, LUA_HOOKCOUNT, -1);
  }
  if (mask & LUA_MASKLINE) {
    Proto *p = ci_func(L->ci)->l.p;
    int npc = pcRel(pc, p);
    int newline = lgetline(p, npc);
    /* call linehook when enter a new function, when jump back (loop),
       or when enter a new line */
    if (npc == 0 || pc <= oldpc || newline != lgetline(p, pcRel(oldpc, p)))
      luaD_callhook(L, LUA_HOOKLINE, newline);
  }
}


static void callTMres (lua_State *L, StkId res, const TValue *f,
                        const TValue *p1, const TValue *p2) {
  ptrdiff_t result = savestack(L, res);
  setobj2s(L, L->top, f);  /* push function */
  setobj2s(L, L->top+1, p1);  /* 1st argument */
  setobj2s(L, L->top+2, p2);  /* 2nd argument */
  luaD_checkstack(L, 3);
  L->top += 3;
  luaD_call(L, L->top - 3, 1);
  res = restorestack(L, result);
  L->top--;
  setobjs2s(L, res, L->top);
}



static void callTM (lua_State *L, const TValue *f, const TValue *p1,
                    const TValue *p2, const TValue *p3) {
  setobj2s(L, L->top, f);  /* push function */
  setobj2s(L, L->top+1, p1);  /* 1st argument */
  setobj2s(L, L->top+2, p2);  /* 2nd argument */
  setobj2s(L, L->top+3, p3);  /* 3th argument */
  luaD_checkstack(L, 4);
  L->top += 4;
  luaD_call(L, L->top - 4, 0);
}


void luaV_gettable (lua_State *L, const TValue *t, TValue *key, StkId val) {
  int loop;
  for (loop = 0; loop < MAXTAGLOOP; loop++) {
    const TValue *tm;
    if (ttistable(t)) {  /* `t' is a table? */
      Table *h = hvalue(t);
      const TValue *res = luaH_get(h, key); /* do a primitive get */
      if (!ttisnil(res) ||  /* result is no nil? */
          (tm = fasttm(L, h->metatable, TM_INDEX)) == NULL) { /* or no TM? */
        setobj2s(L, val, res);
        return;
      }
      /* else will try the tag method */
    }
    else if (ttisnil(tm = luaT_gettmbyobj(L, t, TM_INDEX)))
      luaG_typeerror(L, t, "index");
    if (ttisfunction(tm)) {
      callTMres(L, val, tm, t, key);
      return;
    }
    t = tm;  /* else repeat with `tm' */ 
  }
  luaG_runerror(L, "loop in gettable");
}


void luaV_settable (lua_State *L, const TValue *t, TValue *key, StkId val) {
  int loop;
  TValue temp;
  for (loop = 0; loop < MAXTAGLOOP; loop++) {
    const TValue *tm;
    if (ttistable(t)) {  /* `t' is a table? */
      Table *h = hvalue(t);
      TValue *oldval = luaH_set(L, h, key); /* do a primitive set */
      if (!ttisnil(oldval) ||  /* result is no nil? */
          (tm = fasttm(L, h->metatable, TM_NEWINDEX)) == NULL) { /* or no TM? */
        setobj2t(L, oldval, val);
        h->flags = 0;
        luaC_barriert(L, h, val);
        return;
      }
      /* else will try the tag method */
    }
    else if (ttisnil(tm = luaT_gettmbyobj(L, t, TM_NEWINDEX)))
      luaG_typeerror(L, t, "index");
    if (ttisfunction(tm)) {
      callTM(L, tm, t, key, val);
      return;
    }
    /* else repeat with `tm' */
    setobj(L, &temp, tm);  /* avoid pointing inside table (may rehash) */
    t = &temp;
  }
  luaG_runerror(L, "loop in settable");
}


static int call_binTM (lua_State *L, const TValue *p1, const TValue *p2,
                       StkId res, TMS event) {
  const TValue *tm = luaT_gettmbyobj(L, p1, event);  /* try first operand */
  if (ttisnil(tm))
    tm = luaT_gettmbyobj(L, p2, event);  /* try second operand */
  if (ttisnil(tm)) return 0;
  callTMres(L, res, tm, p1, p2);
  return 1;
}


static const TValue *get_compTM (lua_State *L, Table *mt1, Table *mt2,
                                  TMS event) {
  const TValue *tm1 = fasttm(L, mt1, event);
  const TValue *tm2;
  if (tm1 == NULL) return NULL;  /* no metamethod */
  if (mt1 == mt2) return tm1;  /* same metatables => same metamethods */
  tm2 = fasttm(L, mt2, event);
  if (tm2 == NULL) return NULL;  /* no metamethod */
  if (luaO_rawequalObj(tm1, tm2))  /* same metamethods? */
    return tm1;
  return NULL;
}


static int call_orderTM (lua_State *L, const TValue *p1, const TValue *p2,
                         TMS event) {
  const TValue *tm1 = luaT_gettmbyobj(L, p1, event);
  const TValue *tm2;
  if (ttisnil(tm1)) return -1;  /* no metamethod? */
  tm2 = luaT_gettmbyobj(L, p2, event);
  if (!luaO_rawequalObj(tm1, tm2))  /* different metamethods? */
    return -1;
  callTMres(L, L->top, tm1, p1, p2);
  return !l_isfalse(L->top);
}


static int l_strcmp (const TString *ls, const TString *rs) {
  const char *l = getstr(ls);
  size_t ll = ls->tsv.len;
  const char *r = getstr(rs);
  size_t lr = rs->tsv.len;
  for (;;) {
    int temp = strcoll(l, r);
    if (temp != 0) return temp;
    else {  /* strings are equal up to a `\0' */
      size_t len = strlen(l);  /* index of first `\0' in both strings */
      if (len == lr)  /* r is finished? */
        return (len == ll) ? 0 : 1;
      else if (len == ll)  /* l is finished? */
        return -1;  /* l is smaller than r (because r is not finished) */
      /* both strings longer than `len'; go on comparing (after the `\0') */
      len++;
      l += len; ll -= len; r += len; lr -= len;
    }
  }
}


int luaV_lessthan (lua_State *L, const TValue *l, const TValue *r) {
  int res;
  if (ttype(l) != ttype(r))
    return luaG_ordererror(L, l, r);
  else if (ttisnumber(l))
    return luai_numlt(nvalue(l), nvalue(r));
  else if (ttisstring(l))
    return l_strcmp(rawtsvalue(l), rawtsvalue(r)) < 0;
  else if ((res = call_orderTM(L, l, r, TM_LT)) != -1)
    return res;
  return luaG_ordererror(L, l, r);
}


static int lessequal (lua_State *L, const TValue *l, const TValue *r) {
  int res;
  if (ttype(l) != ttype(r))
    return luaG_ordererror(L, l, r);
  else if (ttisnumber(l))
    return luai_numle(nvalue(l), nvalue(r));
  else if (ttisstring(l))
    return l_strcmp(rawtsvalue(l), rawtsvalue(r)) <= 0;
  else if ((res = call_orderTM(L, l, r, TM_LE)) != -1)  /* first try `le' */
    return res;
  else if ((res = call_orderTM(L, r, l, TM_LT)) != -1)  /* else try `lt' */
    return !res;
  return luaG_ordererror(L, l, r);
}


int luaV_equalval (lua_State *L, const TValue *t1, const TValue *t2) {
  const TValue *tm;
  lua_assert(ttype(t1) == ttype(t2));
  switch (ttype(t1)) {
    case LUA_TNIL: return 1;
    case LUA_TNUMBER: return luai_numeq(nvalue(t1), nvalue(t2));
    case LUA_TBOOLEAN: return bvalue(t1) == bvalue(t2);  /* true must be 1 !! */
    case LUA_TLIGHTUSERDATA: return pvalue(t1) == pvalue(t2);
    case LUA_TUSERDATA: {
      if (uvalue(t1) == uvalue(t2)) return 1;
      tm = get_compTM(L, uvalue(t1)->metatable, uvalue(t2)->metatable,
                         TM_EQ);
      break;  /* will try TM */
    }
    case LUA_TTABLE: {
      if (hvalue(t1) == hvalue(t2)) return 1;
      tm = get_compTM(L, hvalue(t1)->metatable, hvalue(t2)->metatable, TM_EQ);
      break;  /* will try TM */
    }
    default: return gcvalue(t1) == gcvalue(t2);
  }
  if (tm == NULL) return 0;  /* no TM? */
  callTMres(L, L->top, tm, t1, t2);  /* call TM */
  return !l_isfalse(L->top);
}


void luaV_concat (lua_State *L, int total, int last) {
  do {
    StkId top = L->base + last + 1;
    int n = 2;  /* number of elements handled in this pass (at least 2) */
    if (!(ttisstring(top-2) || ttisnumber(top-2)) || !tostring(L, top-1)) {
      if (!call_binTM(L, top-2, top-1, top-2, TM_CONCAT))
        luaG_concaterror(L, top-2, top-1);
    } else if (tsvalue(top-1)->len == 0)  /* second op is empty? */
      (void)tostring(L, top - 2);  /* result is first op (as string) */
    else {
      /* at least two string values; get as many as possible */
      size_t tl = tsvalue(top-1)->len;
      char *buffer;
      int i;
      /* collect total length */
      for (n = 1; n < total && tostring(L, top-n-1); n++) {
        size_t l = tsvalue(top-n-1)->len;
        if (l >= MAX_SIZET - tl) luaG_runerror(L, "string length overflow");
        tl += l;
      }
      buffer = luaZ_openspace(L, &G(L)->buff, tl);
      tl = 0;
      for (i=n; i>0; i--) {  /* concat all strings */
        size_t l = tsvalue(top-i)->len;
        memcpy(buffer+tl, svalue(top-i), l);
        tl += l;
      }
      setsvalue2s(L, top-n, luaS_newlstr(L, buffer, tl));
    }
    total -= n-1;  /* got `n' strings to create 1 new */
    last -= n-1;
  } while (total > 1);  /* repeat until only 1 result left */
}


static void Arith (lua_State *L, StkId ra, const TValue *rb,
                   const TValue *rc, TMS op) {
  TValue tempb, tempc;
  const TValue *b, *c;
  if ((b = luaV_tonumber(rb, &tempb)) != NULL &&
      (c = luaV_tonumber(rc, &tempc)) != NULL) {
    lua_Number nb = nvalue(b), nc = nvalue(c);
    switch (op) {
      case TM_ADD: setnvalue(ra, luai_numadd(nb, nc)); break;
      case TM_SUB: setnvalue(ra, luai_numsub(nb, nc)); break;
      case TM_MUL: setnvalue(ra, luai_nummul(nb, nc)); break;
      case TM_DIV: setnvalue(ra, luai_numdiv(nb, nc)); break;
      case TM_MOD: setnvalue(ra, luai_nummod(nb, nc)); break;
      case TM_POW: setnvalue(ra, luai_numpow(nb, nc)); break;
      case TM_UNM: setnvalue(ra, luai_numunm(nb)); break;
      default: lua_assert(0); break;
    }
  }
  else if (!call_binTM(L, rb, rc, ra, op))
    luaG_aritherror(L, rb, rc);
}



/*
** some macros for common tasks in `luaV_execute'
*/

#define runtime_check(L, c)	{ if (!(c)) break; }

#define RA(i)	(base+GETARG_A(i))
/* to be used after possible stack reallocation */
#define RB(i)	check_exp(getBMode(GET_OPCODE(i)) == OpArgR, base+GETARG_B(i))
#define RC(i)	check_exp(getCMode(GET_OPCODE(i)) == OpArgR, base+GETARG_C(i))
#define RKB(i)	check_exp(getBMode(GET_OPCODE(i)) == OpArgK, \
	ISK(GETARG_B(i)) ? k+INDEXK(GETARG_B(i)) : base+GETARG_B(i))
#define RKC(i)	check_exp(getCMode(GET_OPCODE(i)) == OpArgK, \
	ISK(GETARG_C(i)) ? k+INDEXK(GETARG_C(i)) : base+GETARG_C(i))
#define KBx(i)	check_exp(getBMode(GET_OPCODE(i)) == OpArgK, k+GETARG_Bx(i))


#define dojump(L,pc,i)	{(pc) += (i); luai_threadyield(L);}


#define Protect(x)	{ L->savedpc = pc; {x;}; base = L->base; }


#define arith_op(op,tm) { \
        TValue *rb = RKB(i); \
        TValue *rc = RKC(i); \
        if (ttisnumber(rb) && ttisnumber(rc)) { \
          lua_Number nb = nvalue(rb), nc = nvalue(rc); \
          setnvalue(ra, op(nb, nc)); \
        } \
        else \
          Protect(Arith(L, ra, rb, rc, tm)); \
      }



void luaV_execute (lua_State *L, int nexeccalls) {
  LClosure *cl;
  StkId base;
  TValue *k;
  const Instruction *pc;
 reentry:  /* entry point */
  lua_assert(isLua(L->ci));
  pc = L->savedpc;
  cl = &clvalue(L->ci->func)->l;
  base = L->base;
  k = cl->p->k;
  /* main loop of interpreter */
  for (;;) {
    const Instruction i = *pc++;
    StkId ra;
    if ((L->hookmask & (LUA_MASKLINE | LUA_MASKCOUNT)) &&
        (--L->hookcount == 0 || L->hookmask & LUA_MASKLINE)) {
      traceexec(L, pc);
      if (L->status == LUA_YIELD) {  /* did hook yield? */
        L->savedpc = pc - 1;
        return;
      }
      base = L->base;
    }
    /* warning!! several calls may realloc the stack and invalidate `ra' */
    ra = RA(i);
    lua_assert(base == L->base && L->base == L->ci->base);
    lua_assert(base <= L->top && L->top <= L->stack + L->stacksize);
    lua_assert(L->top == L->ci->top || luaG_checkopenop(i));
    switch (GET_OPCODE(i)) {
      case OP_MOVE: {
        setobjs2s(L, ra, RB(i));
        continue;
      }
      case OP_LOADK: {
        setobj2s(L, ra, KBx(i));
        continue;
      }
      case OP_LOADBOOL: {
        setbvalue(ra, GETARG_B(i));
        if (GETARG_C(i)) pc++;  /* skip next instruction (if C) */
        continue;
      }
      case OP_LOADNIL: {
        TValue *rb = RB(i);
        do {
          setnilvalue(rb--);
        } while (rb >= ra);
        continue;
      }
      case OP_GETUPVAL: {
        int b = GETARG_B(i);
        setobj2s(L, ra, cl->upvals[b]->v);
        continue;
      }
      case OP_GETGLOBAL: {
        TValue g;
        TValue *rb = KBx(i);
        sethvalue(L, &g, cl->env);
        lua_assert(ttisstring(rb));
        Protect(luaV_gettable(L, &g, rb, ra));
        continue;
      }
      case OP_GETTABLE: {
        Protect(luaV_gettable(L, RB(i), RKC(i), ra));
        continue;
      }
      case OP_SETGLOBAL: {
        TValue g;
        sethvalue(L, &g, cl->env);
        lua_assert(ttisstring(KBx(i)));
        Protect(luaV_settable(L, &g, KBx(i), ra));
        continue;
      }
      case OP_SETUPVAL: {
        UpVal *uv = cl->upvals[GETARG_B(i)];
        setobj(L, uv->v, ra);
        luaC_barrier(L, uv, ra);
        continue;
      }
      case OP_SETTABLE: {
        Protect(luaV_settable(L, ra, RKB(i), RKC(i)));
        continue;
      }
      case OP_NEWTABLE: {
        int b = GETARG_B(i);
        int c = GETARG_C(i);
        sethvalue(L, ra, luaH_new(L, luaO_fb2int(b), luaO_fb2int(c)));
        Protect(luaC_checkGC(L));
        continue;
      }
      case OP_SELF: {
        StkId rb = RB(i);
        setobjs2s(L, ra+1, rb);
        Protect(luaV_gettable(L, rb, RKC(i), ra));
        continue;
      }
      case OP_ADD: {
        arith_op(luai_numadd, TM_ADD);
        continue;
      }
      case OP_SUB: {
        arith_op(luai_numsub, TM_SUB);
        continue;
      }
      case OP_MUL: {
        arith_op(luai_nummul, TM_MUL);
        continue;
      }
      case OP_DIV: {
        arith_op(luai_numdiv, TM_DIV);
        continue;
      }
      case OP_MOD: {
        arith_op(luai_nummod, TM_MOD);
        continue;
      }
      case OP_POW: {
        arith_op(luai_numpow, TM_POW);
        continue;
      }
      case OP_UNM: {
        TValue *rb = RB(i);
        if (ttisnumber(rb)) {
          lua_Number nb = nvalue(rb);
          setnvalue(ra, luai_numunm(nb));
        }
        else {
          Protect(Arith(L, ra, rb, rb, TM_UNM));
        }
        continue;
      }
      case OP_NOT: {
        int res = l_isfalse(RB(i));  /* next assignment may change this value */
        setbvalue(ra, res);
        continue;
      }
      case OP_LEN: {
        const TValue *rb = RB(i);
        switch (ttype(rb)) {
          case LUA_TTABLE: {
            setnvalue(ra, cast_num(luaH_getn(hvalue(rb))));
            break;
          }
          case LUA_TSTRING: {
            setnvalue(ra, cast_num(tsvalue(rb)->len));
            break;
          }
          default: {  /* try metamethod */
            Protect(
              if (!call_binTM(L, rb, luaO_nilobject, ra, TM_LEN))
                luaG_typeerror(L, rb, "get length of");
            )
          }
        }
        continue;
      }
      case OP_CONCAT: {
        int b = GETARG_B(i);
        int c = GETARG_C(i);
        Protect(luaV_concat(L, c-b+1, c); luaC_checkGC(L));
        setobjs2s(L, RA(i), base+b);
        continue;
      }
      case OP_JMP: {
        dojump(L, pc, GETARG_sBx(i));
        continue;
      }
      case OP_EQ: {
        TValue *rb = RKB(i);
        TValue *rc = RKC(i);
        Protect(
          if (equalobj(L, rb, rc) == GETARG_A(i))
            dojump(L, pc, GETARG_sBx(*pc));
        )
        pc++;
        continue;
      }
      case OP_LT: {
        Protect(
          if (luaV_lessthan(L, RKB(i), RKC(i)) == GETARG_A(i))
            dojump(L, pc, GETARG_sBx(*pc));
        )
        pc++;
        continue;
      }
      case OP_LE: {
        Protect(
          if (lessequal(L, RKB(i), RKC(i)) == GETARG_A(i))
            dojump(L, pc, GETARG_sBx(*pc));
        )
        pc++;
        continue;
      }
      case OP_TEST: {
        if (l_isfalse(ra) != GETARG_C(i))
          dojump(L, pc, GETARG_sBx(*pc));
        pc++;
        continue;
      }
      case OP_TESTSET: {
        TValue *rb = RB(i);
        if (l_isfalse(rb) != GETARG_C(i)) {
          setobjs2s(L, ra, rb);
          dojump(L, pc, GETARG_sBx(*pc));
        }
        pc++;
        continue;
      }
      case OP_CALL: {
        int b = GETARG_B(i);
        int nresults = GETARG_C(i) - 1;
        if (b != 0) L->top = ra+b;  /* else previous instruction set top */
        L->savedpc = pc;
        switch (luaD_precall(L, ra, nresults)) {
          case PCRLUA: {
            nexeccalls++;
            goto reentry;  /* restart luaV_execute over new Lua function */
          }
          case PCRC: {
            /* it was a C function (`precall' called it); adjust results */
            if (nresults >= 0) L->top = L->ci->top;
            base = L->base;
            continue;
          }
          default: {
            return;  /* yield */
          }
        }
      }
      case OP_TAILCALL: {
        int b = GETARG_B(i);
        if (b != 0) L->top = ra+b;  /* else previous instruction set top */
        L->savedpc = pc;
        lua_assert(GETARG_C(i) - 1 == LUA_MULTRET);
        switch (luaD_precall(L, ra, LUA_MULTRET)) {
          case PCRLUA: {
            /* tail call: put new frame in place of previous one */
            CallInfo *ci = L->ci - 1;  /* previous frame */
            int aux;
            StkId func = ci->func;
            StkId pfunc = (ci+1)->func;  /* previous function index */
            if (L->openupval) luaF_close(L, ci->base);
            L->base = ci->base = ci->func + ((ci+1)->base - pfunc);
            for (aux = 0; pfunc+aux < L->top; aux++)  /* move frame down */
              setobjs2s(L, func+aux, pfunc+aux);
            ci->top = L->top = func+aux;  /* correct top */
            lua_assert(L->top == L->base + clvalue(func)->l.p->maxstacksize);
            ci->savedpc = L->savedpc;
            ci->tailcalls++;  /* one more call lost */
            L->ci--;  /* remove new frame */
            goto reentry;
          }
          case PCRC: {  /* it was a C function (`precall' called it) */
            base = L->base;
            continue;
          }
          default: {
            return;  /* yield */
          }
        }
      }
      case OP_RETURN: {
        int b = GETARG_B(i);
        if (b != 0) L->top = ra+b-1;
        if (L->openupval) luaF_close(L, base);
        L->savedpc = pc;
        b = luaD_poscall(L, ra);
        if (--nexeccalls == 0)  /* was previous function running `here'? */
          return;  /* no: return */
        else {  /* yes: continue its execution */
          if (b) L->top = L->ci->top;
          lua_assert(isLua(L->ci));
          lua_assert(GET_OPCODE(*((L->ci)->savedpc - 1)) == OP_CALL);
          goto reentry;
        }
      }
      case OP_FORLOOP: {
        lua_Number step = nvalue(ra+2);
        lua_Number idx = luai_numadd(nvalue(ra), step); /* increment index */
        lua_Number limit = nvalue(ra+1);
        if (luai_numlt(0, step) ? luai_numle(idx, limit)
                                : luai_numle(limit, idx)) {
          dojump(L, pc, GETARG_sBx(i));  /* jump back */
          setnvalue(ra, idx);  /* update internal index... */
          setnvalue(ra+3, idx);  /* ...and external index */
        }
        continue;
      }
      case OP_FORPREP: {
        const TValue *init = ra;
        const TValue *plimit = ra+1;
        const TValue *pstep = ra+2;
        L->savedpc = pc;  /* next steps may throw errors */
        if (!tonumber(init, ra))
          luaG_runerror(L, LUA_QL("for") " initial value must be a number");
        else if (!tonumber(plimit, ra+1))
          luaG_runerror(L, LUA_QL("for") " limit must be a number");
        else if (!tonumber(pstep, ra+2))
          luaG_runerror(L, LUA_QL("for") " step must be a number");
        setnvalue(ra, luai_numsub(nvalue(ra), nvalue(pstep)));
        dojump(L, pc, GETARG_sBx(i));
        continue;
      }
      case OP_TFORLOOP: {
        StkId cb = ra + 3;  /* call base */
        setobjs2s(L, cb+2, ra+2);
        setobjs2s(L, cb+1, ra+1);
        setobjs2s(L, cb, ra);
        L->top = cb+3;  /* func. + 2 args (state and index) */
        Protect(luaD_call(L, cb, GETARG_C(i)));
        L->top = L->ci->top;
        cb = RA(i) + 3;  /* previous call may change the stack */
        if (!ttisnil(cb)) {  /* continue loop? */
          setobjs2s(L, cb-1, cb);  /* save control variable */
          dojump(L, pc, GETARG_sBx(*pc));  /* jump back */
        }
        pc++;
        continue;
      }
      case OP_SETLIST: {
        int n = GETARG_B(i);
        int c = GETARG_C(i);
        int last;
        Table *h;
        if (n == 0) {
          n = cast_int(L->top - ra) - 1;
          L->top = L->ci->top;
        }
        if (c == 0) c = cast_int(*pc++);
        runtime_check(L, ttistable(ra));
        h = hvalue(ra);
        last = ((c-1)*LFIELDS_PER_FLUSH) + n;
        if (last > h->sizearray)  /* needs more space? */
          luaH_resizearray(L, h, last);  /* pre-alloc it at once */
        for (; n > 0; n--) {
          TValue *val = ra+n;
          setobj2t(L, luaH_setnum(L, h, last--), val);
          luaC_barriert(L, h, val);
        }
        continue;
      }
      case OP_CLOSE: {
        luaF_close(L, ra);
        continue;
      }
      case OP_CLOSURE: {
        Proto *p;
        Closure *ncl;
        int nup, j;
        p = cl->p->p[GETARG_Bx(i)];
        nup = p->nups;
        ncl = luaF_newLclosure(L, nup, cl->env);
        ncl->l.p = p;
        for (j=0; jl.upvals[j] = cl->upvals[GETARG_B(*pc)];
          else {
            lua_assert(GET_OPCODE(*pc) == OP_MOVE);
            ncl->l.upvals[j] = luaF_findupval(L, base + GETARG_B(*pc));
          }
        }
        setclvalue(L, ra, ncl);
        Protect(luaC_checkGC(L));
        continue;
      }
      case OP_VARARG: {
        int b = GETARG_B(i) - 1;
        int j;
        CallInfo *ci = L->ci;
        int n = cast_int(ci->base - ci->func) - cl->p->numparams - 1;
        if (b == LUA_MULTRET) {
          Protect(luaD_checkstack(L, n));
          ra = RA(i);  /* previous call may change the stack */
          b = n;
          L->top = ra + n;
        }
        for (j = 0; j < b; j++) {
          if (j < n) {
            setobjs2s(L, ra + j, ci->base - n + j);
          }
          else {
            setnilvalue(ra + j);
          }
        }
        continue;
      }
    }
  }
}

genometools-1.5.1/src/external/lua-5.1.5/src/lvm.h000066400000000000000000000022071211610345200214410ustar00rootroot00000000000000/*
** $Id: lvm.h,v 2.5.1.1 2007/12/27 13:02:25 roberto Exp $
** Lua virtual machine
** See Copyright Notice in lua.h
*/

#ifndef lvm_h
#define lvm_h


#include "ldo.h"
#include "lobject.h"
#include "ltm.h"


#define tostring(L,o) ((ttype(o) == LUA_TSTRING) || (luaV_tostring(L, o)))

#define tonumber(o,n)	(ttype(o) == LUA_TNUMBER || \
                         (((o) = luaV_tonumber(o,n)) != NULL))

#define equalobj(L,o1,o2) \
	(ttype(o1) == ttype(o2) && luaV_equalval(L, o1, o2))


LUAI_FUNC int luaV_lessthan (lua_State *L, const TValue *l, const TValue *r);
LUAI_FUNC int luaV_equalval (lua_State *L, const TValue *t1, const TValue *t2);
LUAI_FUNC const TValue *luaV_tonumber (const TValue *obj, TValue *n);
LUAI_FUNC int luaV_tostring (lua_State *L, StkId obj);
LUAI_FUNC void luaV_gettable (lua_State *L, const TValue *t, TValue *key,
                                            StkId val);
LUAI_FUNC void luaV_settable (lua_State *L, const TValue *t, TValue *key,
                                            StkId val);
LUAI_FUNC void luaV_execute (lua_State *L, int nexeccalls);
LUAI_FUNC void luaV_concat (lua_State *L, int total, int last);

#endif
genometools-1.5.1/src/external/lua-5.1.5/src/lzio.c000066400000000000000000000031341211610345200216130ustar00rootroot00000000000000/*
** $Id: lzio.c,v 1.31.1.1 2007/12/27 13:02:25 roberto Exp $
** a generic input stream interface
** See Copyright Notice in lua.h
*/


#include 

#define lzio_c
#define LUA_CORE

#include "lua.h"

#include "llimits.h"
#include "lmem.h"
#include "lstate.h"
#include "lzio.h"


int luaZ_fill (ZIO *z) {
  size_t size;
  lua_State *L = z->L;
  const char *buff;
  lua_unlock(L);
  buff = z->reader(L, z->data, &size);
  lua_lock(L);
  if (buff == NULL || size == 0) return EOZ;
  z->n = size - 1;
  z->p = buff;
  return char2int(*(z->p++));
}


int luaZ_lookahead (ZIO *z) {
  if (z->n == 0) {
    if (luaZ_fill(z) == EOZ)
      return EOZ;
    else {
      z->n++;  /* luaZ_fill removed first byte; put back it */
      z->p--;
    }
  }
  return char2int(*z->p);
}


void luaZ_init (lua_State *L, ZIO *z, lua_Reader reader, void *data) {
  z->L = L;
  z->reader = reader;
  z->data = data;
  z->n = 0;
  z->p = NULL;
}


/* --------------------------------------------------------------- read --- */
size_t luaZ_read (ZIO *z, void *b, size_t n) {
  while (n) {
    size_t m;
    if (luaZ_lookahead(z) == EOZ)
      return n;  /* return number of missing bytes */
    m = (n <= z->n) ? n : z->n;  /* min. between n and z->n */
    memcpy(b, z->p, m);
    z->n -= m;
    z->p += m;
    b = (char *)b + m;
    n -= m;
  }
  return 0;
}

/* ------------------------------------------------------------------------ */
char *luaZ_openspace (lua_State *L, Mbuffer *buff, size_t n) {
  if (n > buff->buffsize) {
    if (n < LUA_MINBUFFER) n = LUA_MINBUFFER;
    luaZ_resizebuffer(L, buff, n);
  }
  return buff->buffer;
}


genometools-1.5.1/src/external/lua-5.1.5/src/lzio.h000066400000000000000000000030241211610345200216160ustar00rootroot00000000000000/*
** $Id: lzio.h,v 1.21.1.1 2007/12/27 13:02:25 roberto Exp $
** Buffered streams
** See Copyright Notice in lua.h
*/


#ifndef lzio_h
#define lzio_h

#include "lua.h"

#include "lmem.h"


#define EOZ	(-1)			/* end of stream */

typedef struct Zio ZIO;

#define char2int(c)	cast(int, cast(unsigned char, (c)))

#define zgetc(z)  (((z)->n--)>0 ?  char2int(*(z)->p++) : luaZ_fill(z))

typedef struct Mbuffer {
  char *buffer;
  size_t n;
  size_t buffsize;
} Mbuffer;

#define luaZ_initbuffer(L, buff) ((buff)->buffer = NULL, (buff)->buffsize = 0)

#define luaZ_buffer(buff)	((buff)->buffer)
#define luaZ_sizebuffer(buff)	((buff)->buffsize)
#define luaZ_bufflen(buff)	((buff)->n)

#define luaZ_resetbuffer(buff) ((buff)->n = 0)


#define luaZ_resizebuffer(L, buff, size) \
	(luaM_reallocvector(L, (buff)->buffer, (buff)->buffsize, size, char), \
	(buff)->buffsize = size)

#define luaZ_freebuffer(L, buff)	luaZ_resizebuffer(L, buff, 0)


LUAI_FUNC char *luaZ_openspace (lua_State *L, Mbuffer *buff, size_t n);
LUAI_FUNC void luaZ_init (lua_State *L, ZIO *z, lua_Reader reader,
                                        void *data);
LUAI_FUNC size_t luaZ_read (ZIO* z, void* b, size_t n);	/* read next n bytes */
LUAI_FUNC int luaZ_lookahead (ZIO *z);



/* --------- Private Part ------------------ */

struct Zio {
  size_t n;			/* bytes still unread */
  const char *p;		/* current position in buffer */
  lua_Reader reader;
  void* data;			/* additional data */
  lua_State *L;			/* Lua state (for reader) */
};


LUAI_FUNC int luaZ_fill (ZIO *z);

#endif
genometools-1.5.1/src/external/lua-5.1.5/src/print.c000066400000000000000000000115211211610345200217710ustar00rootroot00000000000000/*
** $Id: print.c,v 1.55a 2006/05/31 13:30:05 lhf Exp $
** print bytecodes
** See Copyright Notice in lua.h
*/

#include 
#include 

#define luac_c
#define LUA_CORE

#include "ldebug.h"
#include "lobject.h"
#include "lopcodes.h"
#include "lundump.h"

#define PrintFunction	luaU_print

#define Sizeof(x)	((int)sizeof(x))
#define VOID(p)		((const void*)(p))

static void PrintString(const TString* ts)
{
 const char* s=getstr(ts);
 size_t i,n=ts->tsv.len;
 putchar('"');
 for (i=0; ik[i];
 switch (ttype(o))
 {
  case LUA_TNIL:
	printf("nil");
	break;
  case LUA_TBOOLEAN:
	printf(bvalue(o) ? "true" : "false");
	break;
  case LUA_TNUMBER:
	printf(LUA_NUMBER_FMT,nvalue(o));
	break;
  case LUA_TSTRING:
	PrintString(rawtsvalue(o));
	break;
  default:				/* cannot happen */
	printf("? type=%d",ttype(o));
	break;
 }
}

static void PrintCode(const Proto* f)
{
 const Instruction* code=f->code;
 int pc,n=f->sizecode;
 for (pc=0; pc0) printf("[%d]\t",line); else printf("[-]\t");
  printf("%-9s\t",luaP_opnames[o]);
  switch (getOpMode(o))
  {
   case iABC:
    printf("%d",a);
    if (getBMode(o)!=OpArgN) printf(" %d",ISK(b) ? (-1-INDEXK(b)) : b);
    if (getCMode(o)!=OpArgN) printf(" %d",ISK(c) ? (-1-INDEXK(c)) : c);
    break;
   case iABx:
    if (getBMode(o)==OpArgK) printf("%d %d",a,-1-bx); else printf("%d %d",a,bx);
    break;
   case iAsBx:
    if (o==OP_JMP) printf("%d",sbx); else printf("%d %d",a,sbx);
    break;
  }
  switch (o)
  {
   case OP_LOADK:
    printf("\t; "); PrintConstant(f,bx);
    break;
   case OP_GETUPVAL:
   case OP_SETUPVAL:
    printf("\t; %s", (f->sizeupvalues>0) ? getstr(f->upvalues[b]) : "-");
    break;
   case OP_GETGLOBAL:
   case OP_SETGLOBAL:
    printf("\t; %s",svalue(&f->k[bx]));
    break;
   case OP_GETTABLE:
   case OP_SELF:
    if (ISK(c)) { printf("\t; "); PrintConstant(f,INDEXK(c)); }
    break;
   case OP_SETTABLE:
   case OP_ADD:
   case OP_SUB:
   case OP_MUL:
   case OP_DIV:
   case OP_POW:
   case OP_EQ:
   case OP_LT:
   case OP_LE:
    if (ISK(b) || ISK(c))
    {
     printf("\t; ");
     if (ISK(b)) PrintConstant(f,INDEXK(b)); else printf("-");
     printf(" ");
     if (ISK(c)) PrintConstant(f,INDEXK(c)); else printf("-");
    }
    break;
   case OP_JMP:
   case OP_FORLOOP:
   case OP_FORPREP:
    printf("\t; to %d",sbx+pc+2);
    break;
   case OP_CLOSURE:
    printf("\t; %p",VOID(f->p[bx]));
    break;
   case OP_SETLIST:
    if (c==0) printf("\t; %d",(int)code[++pc]);
    else printf("\t; %d",c);
    break;
   default:
    break;
  }
  printf("\n");
 }
}

#define SS(x)	(x==1)?"":"s"
#define S(x)	x,SS(x)

static void PrintHeader(const Proto* f)
{
 const char* s=getstr(f->source);
 if (*s=='@' || *s=='=')
  s++;
 else if (*s==LUA_SIGNATURE[0])
  s="(bstring)";
 else
  s="(string)";
 printf("\n%s <%s:%d,%d> (%d instruction%s, %d bytes at %p)\n",
 	(f->linedefined==0)?"main":"function",s,
	f->linedefined,f->lastlinedefined,
	S(f->sizecode),f->sizecode*Sizeof(Instruction),VOID(f));
 printf("%d%s param%s, %d slot%s, %d upvalue%s, ",
	f->numparams,f->is_vararg?"+":"",SS(f->numparams),
	S(f->maxstacksize),S(f->nups));
 printf("%d local%s, %d constant%s, %d function%s\n",
	S(f->sizelocvars),S(f->sizek),S(f->sizep));
}

static void PrintConstants(const Proto* f)
{
 int i,n=f->sizek;
 printf("constants (%d) for %p:\n",n,VOID(f));
 for (i=0; isizelocvars;
 printf("locals (%d) for %p:\n",n,VOID(f));
 for (i=0; ilocvars[i].varname),f->locvars[i].startpc+1,f->locvars[i].endpc+1);
 }
}

static void PrintUpvalues(const Proto* f)
{
 int i,n=f->sizeupvalues;
 printf("upvalues (%d) for %p:\n",n,VOID(f));
 if (f->upvalues==NULL) return;
 for (i=0; iupvalues[i]));
 }
}

void PrintFunction(const Proto* f, int full)
{
 int i,n=f->sizep;
 PrintHeader(f);
 PrintCode(f);
 if (full)
 {
  PrintConstants(f);
  PrintLocals(f);
  PrintUpvalues(f);
 }
 for (i=0; ip[i],full);
}
genometools-1.5.1/src/external/lua-5.1.5/test/000077500000000000000000000000001211610345200206615ustar00rootroot00000000000000genometools-1.5.1/src/external/lua-5.1.5/test/README000066400000000000000000000022311211610345200215370ustar00rootroot00000000000000These are simple tests for Lua.  Some of them contain useful code.
They are meant to be run to make sure Lua is built correctly and also
to be read, to see how Lua programs look.

Here is a one-line summary of each program:

   bisect.lua		bisection method for solving non-linear equations
   cf.lua		temperature conversion table (celsius to farenheit)
   echo.lua             echo command line arguments
   env.lua              environment variables as automatic global variables
   factorial.lua	factorial without recursion
   fib.lua		fibonacci function with cache
   fibfor.lua		fibonacci numbers with coroutines and generators
   globals.lua		report global variable usage
   hello.lua		the first program in every language
   life.lua		Conway's Game of Life
   luac.lua	 	bare-bones luac
   printf.lua		an implementation of printf
   readonly.lua		make global variables readonly
   sieve.lua		the sieve of of Eratosthenes programmed with coroutines
   sort.lua		two implementations of a sort function
   table.lua		make table, grouping all data for the same item
   trace-calls.lua	trace calls
   trace-globals.lua	trace assigments to global variables
   xd.lua		hex dump

genometools-1.5.1/src/external/lua-5.1.5/test/bisect.lua000066400000000000000000000012051211610345200226330ustar00rootroot00000000000000-- bisection method for solving non-linear equations

delta=1e-6	-- tolerance

function bisect(f,a,b,fa,fb)
 local c=(a+b)/2
 io.write(n," c=",c," a=",a," b=",b,"\n")
 if c==a or c==b or math.abs(a-b) posted to lua-l
-- modified to use ANSI terminal escape sequences
-- modified to use for instead of while

local write=io.write

ALIVE=""	DEAD=""
ALIVE="O"	DEAD="-"

function delay() -- NOTE: SYSTEM-DEPENDENT, adjust as necessary
  for i=1,10000 do end
  -- local i=os.clock()+1 while(os.clock() 0 do
    local xm1,x,xp1,xi=self.w-1,self.w,1,self.w
    while xi > 0 do
      local sum = self[ym1][xm1] + self[ym1][x] + self[ym1][xp1] +
                  self[y][xm1] + self[y][xp1] +
                  self[yp1][xm1] + self[yp1][x] + self[yp1][xp1]
      next[y][x] = ((sum==2) and self[y][x]) or ((sum==3) and 1) or 0
      xm1,x,xp1,xi = x,xp1,xp1+1,xi-1
    end
    ym1,y,yp1,yi = y,yp1,yp1+1,yi-1
  end
end

-- output the array to screen
function _CELLS:draw()
  local out="" -- accumulate to reduce flicker
  for y=1,self.h do
   for x=1,self.w do
      out=out..(((self[y][x]>0) and ALIVE) or DEAD)
    end
    out=out.."\n"
  end
  write(out)
end

-- constructor
function CELLS(w,h)
  local c = ARRAY2D(w,h)
  c.spawn = _CELLS.spawn
  c.evolve = _CELLS.evolve
  c.draw = _CELLS.draw
  return c
end

--
-- shapes suitable for use with spawn() above
--
HEART = { 1,0,1,1,0,1,1,1,1; w=3,h=3 }
GLIDER = { 0,0,1,1,0,1,0,1,1; w=3,h=3 }
EXPLODE = { 0,1,0,1,1,1,1,0,1,0,1,0; w=3,h=4 }
FISH = { 0,1,1,1,1,1,0,0,0,1,0,0,0,0,1,1,0,0,1,0; w=5,h=4 }
BUTTERFLY = { 1,0,0,0,1,0,1,1,1,0,1,0,0,0,1,1,0,1,0,1,1,0,0,0,1; w=5,h=5 }

-- the main routine
function LIFE(w,h)
  -- create two arrays
  local thisgen = CELLS(w,h)
  local nextgen = CELLS(w,h)

  -- create some life
  -- about 1000 generations of fun, then a glider steady-state
  thisgen:spawn(GLIDER,5,4)
  thisgen:spawn(EXPLODE,25,10)
  thisgen:spawn(FISH,4,12)

  -- run until break
  local gen=1
  write("\027[2J")	-- ANSI clear screen
  while 1 do
    thisgen:evolve(nextgen)
    thisgen,nextgen = nextgen,thisgen
    write("\027[H")	-- ANSI home cursor
    thisgen:draw()
    write("Life - generation ",gen,"\n")
    gen=gen+1
    if gen>2000 then break end
    --delay()		-- no delay
  end
end

LIFE(40,20)
genometools-1.5.1/src/external/lua-5.1.5/test/luac.lua000066400000000000000000000003521211610345200223100ustar00rootroot00000000000000-- bare-bones luac in Lua
-- usage: lua luac.lua file.lua

assert(arg[1]~=nil and arg[2]==nil,"usage: lua luac.lua file.lua")
f=assert(io.open("luac.out","wb"))
assert(f:write(string.dump(assert(loadfile(arg[1])))))
assert(f:close())
genometools-1.5.1/src/external/lua-5.1.5/test/printf.lua000066400000000000000000000002511211610345200226640ustar00rootroot00000000000000-- an implementation of printf

function printf(...)
 io.write(string.format(...))
end

printf("Hello %s from %s on %s\n",os.getenv"USER" or "there",_VERSION,os.date())
genometools-1.5.1/src/external/lua-5.1.5/test/readonly.lua000066400000000000000000000004041211610345200231770ustar00rootroot00000000000000-- make global variables readonly

local f=function (t,i) error("cannot redefine global variable `"..i.."'",2) end
local g={}
local G=getfenv()
setmetatable(g,{__index=G,__newindex=f})
setfenv(1,g)

-- an example
rawset(g,"x",3)
x=2
y=1	-- cannot redefine `y'
genometools-1.5.1/src/external/lua-5.1.5/test/sieve.lua000066400000000000000000000014061211610345200225000ustar00rootroot00000000000000-- the sieve of of Eratosthenes programmed with coroutines
-- typical usage: lua -e N=1000 sieve.lua | column

-- generate all the numbers from 2 to n
function gen (n)
  return coroutine.wrap(function ()
    for i=2,n do coroutine.yield(i) end
  end)
end

-- filter the numbers generated by `g', removing multiples of `p'
function filter (p, g)
  return coroutine.wrap(function ()
    while 1 do
      local n = g()
      if n == nil then return end
      if math.mod(n, p) ~= 0 then coroutine.yield(n) end
    end
  end)
end

N=N or 1000		-- from command line
x = gen(N)		-- generate primes up to N
while 1 do
  local n = x()		-- pick a number until done
  if n == nil then break end
  print(n)		-- must be a prime number
  x = filter(n, x)	-- now remove its multiples
end
genometools-1.5.1/src/external/lua-5.1.5/test/sort.lua000066400000000000000000000027261211610345200223620ustar00rootroot00000000000000-- two implementations of a sort function
-- this is an example only. Lua has now a built-in function "sort"

-- extracted from Programming Pearls, page 110
function qsort(x,l,u,f)
 if ly end)
 show("after reverse selection sort",x)
 qsort(x,1,n,function (x,y) return x>> ",string.rep(" ",level))
 if t~=nil and t.currentline>=0 then io.write(t.short_src,":",t.currentline," ") end
 t=debug.getinfo(2)
 if event=="call" then
  level=level+1
 else
  level=level-1 if level<0 then level=0 end
 end
 if t.what=="main" then
  if event=="call" then
   io.write("begin ",t.short_src)
  else
   io.write("end ",t.short_src)
  end
 elseif t.what=="Lua" then
-- table.foreach(t,print)
  io.write(event," ",t.name or "(Lua)"," <",t.linedefined,":",t.short_src,">")
 else
 io.write(event," ",t.name or "(C)"," [",t.what,"] ")
 end
 io.write("\n")
end

debug.sethook(hook,"cr")
level=0
genometools-1.5.1/src/external/lua-5.1.5/test/trace-globals.lua000066400000000000000000000013301211610345200241000ustar00rootroot00000000000000-- trace assigments to global variables

do
 -- a tostring that quotes strings. note the use of the original tostring.
 local _tostring=tostring
 local tostring=function(a)
  if type(a)=="string" then
   return string.format("%q",a)
  else
   return _tostring(a)
  end
 end

 local log=function (name,old,new)
  local t=debug.getinfo(3,"Sl")
  local line=t.currentline
  io.write(t.short_src)
  if line>=0 then io.write(":",line) end
  io.write(": ",name," is now ",tostring(new)," (was ",tostring(old),")","\n")
 end

 local g={}
 local set=function (t,name,value)
  log(name,g[name],value)
  g[name]=value
 end
 setmetatable(getfenv(),{__index=g,__newindex=set})
end

-- an example

a=1
b=2
a=10
b=20
b=nil
b=200
print(a,b,c)
genometools-1.5.1/src/external/lua-5.1.5/test/xd.lua000066400000000000000000000005541211610345200220030ustar00rootroot00000000000000-- hex dump
-- usage: lua xd.lua < file

local offset=0
while true do
 local s=io.read(16)
 if s==nil then return end
 io.write(string.format("%08X  ",offset))
 string.gsub(s,"(.)",
	function (c) io.write(string.format("%02X ",string.byte(c))) end)
 io.write(string.rep(" ",3*(16-string.len(s))))
 io.write(" ",string.gsub(s,"%c","."),"\n") 
 offset=offset+16
end
genometools-1.5.1/src/external/luafilesystem-1.5.0/000077500000000000000000000000001211610345200220025ustar00rootroot00000000000000genometools-1.5.1/src/external/luafilesystem-1.5.0/Makefile000066400000000000000000000006071211610345200234450ustar00rootroot00000000000000# $Id: Makefile,v 1.36 2009/09/21 17:02:44 mascarenhas Exp $

T= lfs

CONFIG= ./config

include $(CONFIG)

SRCS= src/$T.c
OBJS= src/$T.o

lib: src/lfs.so

src/lfs.so: $(OBJS)
	MACOSX_DEPLOYMENT_TARGET="10.3"; export MACOSX_DEPLOYMENT_TARGET; $(CC) $(CFLAGS) $(LIB_OPTION) -o src/lfs.so $(OBJS)

install:
	mkdir -p $(LUA_LIBDIR)
	cp src/lfs.so $(LUA_LIBDIR)

clean:
	rm -f src/lfs.so $(OBJS)
genometools-1.5.1/src/external/luafilesystem-1.5.0/Makefile.win000066400000000000000000000011031211610345200242310ustar00rootroot00000000000000# $Id: Makefile.win,v 1.11 2008/05/07 19:06:37 carregal Exp $

T= lfs

include config.win

SRCS= src\$T.c
OBJS= src\$T.obj

lib: src\lfs.dll

.c.obj:
	$(CC) /c /Fo$@ $(CFLAGS) $<

src\lfs.dll: $(OBJS)
	link /dll /def:src\$T.def /out:src\lfs.dll $(OBJS) "$(LUA_LIB)"
	IF EXIST src\lfs.dll.manifest mt -manifest src\lfs.dll.manifest -outputresource:src\lfs.dll;2

install: src\lfs.dll
	IF NOT EXIST "$(LUA_LIBDIR)" mkdir "$(LUA_LIBDIR)"
	copy src\lfs.dll "$(LUA_LIBDIR)"

clean:
	del src\lfs.dll $(OBJS) src\$T.lib src\$T.exp
	IF EXIST src\lfs.dll.manifest del src\lfs.dll.manifestgenometools-1.5.1/src/external/luafilesystem-1.5.0/README000066400000000000000000000040741211610345200226670ustar00rootroot00000000000000LuaFileSystem - File System Library for Lua
Copyright 2003 Kepler Project
http://www.keplerproject.org/luafilesystem

Description
-----------
LuaFileSystem is a Lua library developed to complement the set of functions
related to file systems offered by the standard Lua distribution.

LuaFileSystem offers a portable way to access the underlying directory structure and file attributes.
LuaFileSystem is free software and uses the same license as Lua 5.1

LuaRocks Installation
---------------------
luarocks install luafilesystem


Documentation
-------------
Please check the documentation at doc/us/ for more information.

History
-------

Version 1.5.0 [20/Oct/2009]
	* added explicit next and close methods to second return value of lfs.dir (the directory object), for explicit iteration or explicit closing.
	* added directory locking via lfs.lock_dir function (see the manual).

Version 1.4.2 [03/Feb/2009]

        * fixed bug [#13198] lfs.attributes(filename, 'size') overflow on files > 2 Gb again (bug report and patch by KUBO Takehiro).
        * fixed bug [#39794] Compile error on Solaris 10 (bug report and patch by Aaron B).
        * fixed compilation problems with Borland C.

Version 1.4.1 [07/May/2008]

        * documentation review
        * fixed Windows compilation issues
        * fixed bug in the Windows tests (patch by Shmuel Zeigerman)
        * fixed bug [#2185] lfs.attributes(filename, 'size') overflow on files > 2 Gb

Version 1.4.0 [13/Feb/2008]

        * added function lfs.setmode (works only in Windows systems).
        * lfs.attributes raises an error if attribute does not exist

Version 1.3.0 [26/Oct/2007]

        * added function lfs.symlinkattributes (works only in non Windows systems).

Version 1.2.1 [08/May/2007]

        * compatible only with Lua 5.1 (Lua 5.0 support was dropped)

Version 1.2 [15/Mar/2006]

        * added optional argument to lfs.attributes
        * added function lfs.rmdir
        * bug correction on lfs.dir

Version 1.1 [30/May/2005]

        * added function lfs.touch.

Version 1.0 [21/Jan/2005]
Version 1.0 Beta [10/Nov/2004]
genometools-1.5.1/src/external/luafilesystem-1.5.0/config000066400000000000000000000011601211610345200231700ustar00rootroot00000000000000# Installation directories

# Default installation prefix
PREFIX=/usr/local

# System's libraries directory (where binary libraries are installed)
LUA_LIBDIR= $(PREFIX)/lib/lua/5.1

# Lua includes directory
LUA_INC= $(PREFIX)/include

# OS dependent
LIB_OPTION= -shared #for Linux
#LIB_OPTION= -bundle -undefined dynamic_lookup #for MacOS X

LIBNAME= $T.so.$V

# Compilation directives
WARN= -O2 -Wall -fPIC -W -Waggregate-return -Wcast-align -Wmissing-prototypes -Wnested-externs -Wshadow -Wwrite-strings -pedantic
INCS= -I$(LUA_INC)
CFLAGS= $(WARN) $(INCS)
CC= gcc

# $Id: config,v 1.21 2007/10/27 22:42:32 carregal Exp $
genometools-1.5.1/src/external/luafilesystem-1.5.0/config.win000066400000000000000000000006111211610345200237640ustar00rootroot00000000000000# Installation directories
# System's libraries directory (where binary libraries are installed)
LUA_LIBDIR= "c:\lua5.1"

# Lua includes directory
LUA_INC= "c:\lua5.1\include"

# Lua library
LUA_LIB= "c:\lua5.1\lua5.1.lib"

LIBNAME= $T.dll

# Compilation directives
WARN= /O2
INCS= /I$(LUA_INC)
CFLAGS= /MD $(WARN) $(INCS)
CC= cl

# $Id: config.win,v 1.7 2008/03/25 17:39:29 mascarenhas Exp $
genometools-1.5.1/src/external/luafilesystem-1.5.0/doc/000077500000000000000000000000001211610345200225475ustar00rootroot00000000000000genometools-1.5.1/src/external/luafilesystem-1.5.0/doc/us/000077500000000000000000000000001211610345200231765ustar00rootroot00000000000000genometools-1.5.1/src/external/luafilesystem-1.5.0/doc/us/examples.html000066400000000000000000000057421211610345200257120ustar00rootroot00000000000000


	LuaFileSystem
    
	









	
	
LuaFileSystem

	
File System Library for the Lua Programming Language


 



	
 





Examples



Directory iterator



The following example iterates over a directory and recursively lists the
attributes for each file inside it.



require"lfs"

function attrdir (path)
    for file in lfs.dir(path) do
        if file ~= "." and file ~= ".." then
            local f = path..'/'..file
            print ("\t "..f)
            local attr = lfs.attributes (f)
            assert (type(attr) == "table")
            if attr.mode == "directory" then
                attrdir (f)
            else
                for name, value in pairs(attr) do
                    print (name, value)
                end
            end
        end
    end
end

attrdir (".")




 


 



	
Valid XHTML 1.0!

	
$Id: examples.html,v 1.8 2007/12/14 15:28:04 carregal Exp $


 


 



genometools-1.5.1/src/external/luafilesystem-1.5.0/doc/us/index.html000066400000000000000000000152721211610345200252020ustar00rootroot00000000000000


	LuaFileSystem
    
	









	
	
LuaFileSystem

	
File System Library for the Lua Programming Language


 



	
 





Overview



LuaFileSystem is a Lua library
developed to complement the set of functions related to file
systems offered by the standard Lua distribution.



LuaFileSystem offers a portable way to access
the underlying directory structure and file attributes.



LuaFileSystem is free software and uses the same
license as Lua 5.1.



Status



Current version is 1.5.0. It was developed for Lua 5.1.



Download



LuaFileSystem source can be downloaded from its
Github
page.



History




	
Version 1.5.0 [20/Oct/2009]

	
  • Added explicit next and close methods to second return value of lfs.dir 
(the directory object), for explicit iteration or explicit closing.
    • 
	
  • Added directory locking via lfs.lock_dir function (see the manual).
    • 
	
    Version 1.4.2 [03/Feb/2009]
    
	
    
		
      
			
    • fixed bug [#13198]
				lfs.attributes(filename, 'size') overflow on files > 2 Gb again  (bug report and patch by KUBO Takehiro).
      • 
			
    • fixed bug [#39794]
				Compile error on Solaris 10 (bug report and patch by Aaron B).
      • 
			
    • fixed compilation problems with Borland C.
      • 
		
    
	
    
	
    
    Version 1.4.1 [07/May/2008]
    
	
    
	
      
	
    • documentation review
      • 
	
    • fixed Windows compilation issues
      • 
	
    • fixed bug in the Windows tests (patch by Shmuel Zeigerman)
      • 
	
    • fixed bug [#2185]
		lfs.attributes(filename, 'size') overflow on files > 2 Gb
	
      • 
	
    
	
    
	
    
    Version 1.4.0 [13/Feb/2008]
    
    
    
    
    
    
    
    
    Version 1.3.0 [26/Oct/2007]
    
    
    
    
    
    

    
    Version 1.2.1 [08/May/2007]
    
    
    
    
      
        
    • compatible only with Lua 5.1 (Lua 5.0 support was dropped)
      • 
    
    
    
    

    
    Version 1.2 [15/Mar/2006]
    
    
    
    
    
    

    
    Version 1.1 [30/May/2005]
    
    
    
    
    
    

    
    Version 1.0 [21/Jan/2005]
    
    
    

    
    Version 1.0 Beta [10/Nov/2004]
    
    
    

    


    Credits
    


    LuaFileSystem was designed by Roberto Ierusalimschy,
André Carregal and Tomás Guisasola as part of the
Kepler Project,
which holds its copyright. LuaFileSystem is currently maintained by Fábio Mascarenhas.
    


    Contact us
    


    For more information please
contact us.
Comments are welcome!
    


    You can also reach other Kepler developers and users on the Kepler Project
mailing list.
    


     


     


    
	
    Valid XHTML 1.0!
    
	
    $Id: index.html,v 1.44 2009/02/04 21:21:33 carregal Exp $
    

     


     



genometools-1.5.1/src/external/luafilesystem-1.5.0/doc/us/license.html000066400000000000000000000105541211610345200255130ustar00rootroot00000000000000


	LuaFileSystem
    
	





    


    
	
	
    LuaFileSystem
    
	
    File System Library for the Lua Programming Language
    

     


    
	
 


    


    License
    


    
LuaFileSystem is free software: it can be used for both academic
and commercial purposes at absolutely no cost. There are no
royalties or GNU-like "copyleft" restrictions. LuaFileSystem
qualifies as
Open Source
software.
Its licenses are compatible with
GPL.
LuaFileSystem is not in the public domain and the
Kepler Project
keep its copyright.
The legal details are below. 

    


    The spirit of the license is that you are free to use
LuaFileSystem for any purpose at no cost without having to ask us.
The only requirement is that if you do use LuaFileSystem, then you
should give us credit by including the appropriate copyright notice
somewhere in your product or its documentation.
    


    The LuaFileSystem library is designed and implemented by Roberto
Ierusalimschy, André Carregal and Tomás Guisasola.
The implementation is not derived from licensed software.
    


    

    Copyright © 2003 Kepler Project.
    


    Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use, copy,
modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
    


    The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
    


    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
    


     


     


    
	
    Valid XHTML 1.0!
    
	
    $Id: license.html,v 1.13 2008/02/11 22:42:21 carregal Exp $
    

    


    



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`SS


	LuaFileSystem
    
	





    


    
	
	
    LuaFileSystem
    
	
    File System Library for the Lua Programming Language
    

     


    
	
 


    


    Introduction
    


    LuaFileSystem is a Lua library
developed to complement the set of functions related to file
systems offered by the standard Lua distribution.
    


    LuaFileSystem offers a portable way to access
the underlying directory structure and file attributes.
    


    Building
    


    
LuaFileSystem should be built with Lua 5.1 so the language library
and header files for the target version must be installed properly.

    


    
LuaFileSystem offers a Makefile and a separate configuration file,
config,
which should be edited to suit your installation before running
make.
The file has some definitions like paths to the external libraries,
compiler options and the like.

    


    On Windows, the C runtime used to compile LuaFileSystem must be the same
runtime that Lua uses, or some LuaFileSystem functions will not work.
    


    Installation
    


    The easiest way to install LuaFileSystem is to use LuaRocks:
    


    luarocks install luafilesystem

    


    If you prefer to install LuaFileSystem manually, the compiled binary should be copied to a directory in your
C path.
    


    Reference
    


    
LuaFileSystem offers the following functions:

    


    
    
    lfs.attributes (filepath [, aname])
    
    
    Returns a table with the file attributes corresponding to
    filepath (or nil followed by an error message
    in case of error).
    If the second optional argument is given, then only the value of the
    named attribute is returned (this use is equivalent to
    lfs.attributes(filepath).aname, but the table is not created
    and only one attribute is retrieved from the O.S.).
    The attributes are described as follows;
    attribute mode is a string, all the others are numbers,
    and the time related attributes use the same time reference of
    os.time: 
        
    
        
    dev
    
        
    on Unix systems, this represents the device that the inode resides on. On Windows systems,
        represents the drive number of the disk containing the file
    
        
        
    ino
    
        
    on Unix systems, this represents the inode number. On Windows systems this has no meaning
    
        
        
    mode
    
        
    string representing the associated protection mode (the values could be
        file, directory, link, socket,
        named pipe, char device, block device or
        other)
    
        
        
    nlink
    
		
    number of hard links to the file
    

        
    uid
    
		
    user-id of owner (Unix only, always 0 on Windows)
    

        
    gid
    
		
    group-id of owner (Unix only, always 0 on Windows)
    

        
    rdev
    
		
    on Unix systems, represents the device type, for special file inodes.
        On Windows systems represents the same as dev
    

        
    access
    
		
    time of last access
    

        
    modification
    
		
    time of last data modification
    

        
    change
    
		
    time of last file status change
    

        
    size
    
		
    file size, in bytes
    

        
    blocks
    
		
    block allocated for file; (Unix only)
    
        
        
    blksize
    
		
    optimal file system I/O blocksize; (Unix only)
    
	    
    
    This function uses stat internally thus if the given
    filepath is a symbolic link, it is followed (if it points to
    another link the chain is followed recursively) and the information
    is about the file it refers to.
    To obtain information about the link itself, see function
    lfs.symlinkattributes.
	
    

    
    lfs.chdir (path)
    
    
    Changes the current working directory to the given
    path.
    
    Returns true in case of success or nil plus an
    error string.
    

    
    lfs.lock_dir(path, [seconds_stale])
    
    
    Creates a lockfile (called lockfile.lfs) in path if it does not
  exist and returns the lock. If the lock already exists checks it
  it's stale, using the second parameter (default for the second
  parameter is INT_MAX, which in practice means the lock will never
  be stale. To free the the lock call lock:free(). 
    
   In case of any errors it returns nil and the error message. In
  particular, if the lock exists and is not stale it returns the
  "File exists" message.
    
        
    
    lfs.currentdir ()
    
    
    Returns a string with the current working directory or nil
    plus an error string.
    
    
    
    iter, dir_obj = lfs.dir (path)
    
    
    
    Lua iterator over the entries of a given directory.
    Each time the iterator is called with dir_obj it returns a directory entry's name as a string, or
    nil if there are no more entries. You can also iterate by calling dir_obj:next(), and
    explicitly close the directory before the iteration finished with dir_obj:close().
    Raises an error if path is not a directory.
    
    
    
    
    lfs.lock (filehandle, mode[, start[, length]])
    
    
    Locks a file or a part of it. This function works on open files; the
    file handle should be specified as the first argument.
    The string mode could be either
    r (for a read/shared lock) or w (for a
    write/exclusive lock). The optional arguments start
    and length can be used to specify a starting point and
    its length; both should be numbers.
    
    Returns true if the operation was successful; in
    case of error, it returns nil plus an error string.
    
    
    
    
    lfs.mkdir (dirname)
    
    
    Creates a new directory. The argument is the name of the new
    directory.
    
    Returns true if the operation was successful;
    in case of error, it returns nil plus an error string.
    
    
    
    
    lfs.rmdir (dirname)
    
    
    Removes an existing directory. The argument is the name of the directory.
    
    Returns true if the operation was successful;
    in case of error, it returns nil plus an error string.
    

    
    lfs.setmode (file, mode)
    
    
    Sets the writing mode for a file. The mode string can be either binary or text.
    Returns the previous mode string for the file. This function is only available in Windows, so you may want to make sure that
    lfs.setmode exists before using it.
    
    
    
    
    lfs.symlinkattributes (filepath [, aname])
    
    
    Identical to lfs.attributes except that
    it obtains information about the link itself (not the file it refers to).
    This function is not available in Windows so you may want to make sure that
    lfs.symlinkattributes exists before using it.
    
    

    
    lfs.touch (filepath [, atime [, mtime]])
    
    
    Set access and modification times of a file. This function is
    a bind to utime function. The first argument is the
    filename, the second argument (atime) is the access time,
    and the third argument (mtime) is the modification time.
    Both times are provided in seconds (which should be generated with
    Lua standard function os.time).
    If the modification time is omitted, the access time provided is used;
    if both times are omitted, the current time is used.
    
    Returns true if the operation was successful;
    in case of error, it returns nil plus an error string.
    
    
    
    
    lfs.unlock (filehandle[, start[, length]])
    
    
    Unlocks a file or a part of it. This function works on
    open files; the file handle should be specified as the first
    argument. The optional arguments start and
    length can be used to specify a starting point and its
    length; both should be numbers.
    
    Returns true if the operation was successful;
    in case of error, it returns nil plus an error string.
    
    

    


     


     


    
	
    Valid XHTML 1.0!
    
	
    $Id: manual.html,v 1.45 2009/06/03 20:53:55 mascarenhas Exp $
    

     


     



genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/000077500000000000000000000000001211610345200237765ustar00rootroot00000000000000genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.3.0-1.rockspec000066400000000000000000000013411211610345200312110ustar00rootroot00000000000000package = "LuaFileSystem"
version = "1.3.0-1"
source = {
   url = "http://luaforge.net/frs/download.php/2679/luafilesystem-1.3.0.tar.gz"
}
description = {
   summary = "File System Library for the Lua Programming Language",
   detailed = [[
      LuaFileSystem is a Lua library developed to complement the set of
      functions related to file systems offered by the standard Lua
      distribution. LuaFileSystem offers a portable way to access the
      underlying directory structure and file attributes.
   ]]
}
dependencies = {
   "lua >= 5.1"
}
build = {
   type = "make",
   build_variables = {
      LUA_INC = "$(LUA_INCDIR)",
      LIB_OPTION = "$(LIBFLAG)"
   },
   install_variables = {
      LUA_LIBDIR = "$(LIBDIR)"
   }
}
genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.0-1.rockspec000066400000000000000000000013411211610345200312120ustar00rootroot00000000000000package = "LuaFileSystem"
version = "1.4.0-1"
source = {
   url = "http://luaforge.net/frs/download.php/3158/luafilesystem-1.4.0.tar.gz"
}
description = {
   summary = "File System Library for the Lua Programming Language",
   detailed = [[
      LuaFileSystem is a Lua library developed to complement the set of
      functions related to file systems offered by the standard Lua
      distribution. LuaFileSystem offers a portable way to access the
      underlying directory structure and file attributes.
   ]]
}
dependencies = {
   "lua >= 5.1"
}
build = {
   type = "make",
   build_variables = {
      LUA_INC = "$(LUA_INCDIR)",
      LIB_OPTION = "$(LIBFLAG)"
   },
   install_variables = {
      LUA_LIBDIR = "$(LIBDIR)"
   }
}
genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.0-2.rockspec000066400000000000000000000021651211610345200312200ustar00rootroot00000000000000package = "LuaFileSystem"
version = "1.4.0-2"
source = {
   url = "http://luaforge.net/frs/download.php/3158/luafilesystem-1.4.0.tar.gz"
}
description = {
   summary = "File System Library for the Lua Programming Language",
   detailed = [[
      LuaFileSystem is a Lua library developed to complement the set of
      functions related to file systems offered by the standard Lua
      distribution. LuaFileSystem offers a portable way to access the
      underlying directory structure and file attributes.
   ]]
}
dependencies = {
   "lua >= 5.1"
}
build = {
   platforms = {
     unix = {
        type = "make",
       	build_variables = {
         LIB_OPTION = "$(LIBFLAG)",
         CFLAGS = "$(CFLAGS) -I$(LUA_INCDIR)",
       	},
       	install_variables = {
         LUA_LIBDIR = "$(LIBDIR)"
       	}
     },
     win32 = {
        type = "make",
       	build_variables = {
         LUA_LIB = "$(LUA_LIBDIR)\\lua5.1.lib",
         CFLAGS = "/MD $(CFLAGS) /I$(LUA_INCDIR)",
       	},
       	install_variables = {
         LUA_LIBDIR = "$(LIBDIR)",
         LUA_DIR = "$(LUADIR)",
	 	 BIN_DIR = "$(BINDIR)"
       	}
     }
  }
}genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.1-1.rockspec000066400000000000000000000022011211610345200312070ustar00rootroot00000000000000package = "LuaFileSystem"
version = "1.4.1-1"
source = {
   url = "http://luaforge.net/frs/download.php/3345/luafilesystem-1.4.1.tar.gz",
}
description = {
   summary = "File System Library for the Lua Programming Language",
   detailed = [[
      LuaFileSystem is a Lua library developed to complement the set of
      functions related to file systems offered by the standard Lua
      distribution. LuaFileSystem offers a portable way to access the
      underlying directory structure and file attributes.
   ]]
}
dependencies = {
   "lua >= 5.1"
}
build = {
   platforms = {
     unix = {
        type = "make",
       	build_variables = {
         LIB_OPTION = "$(LIBFLAG)",
         CFLAGS = "$(CFLAGS) -I$(LUA_INCDIR) $(STAT64)",
       	},
       	install_variables = {
         LUA_LIBDIR = "$(LIBDIR)"
       	}
     },
     win32 = {
        type = "make",
       	build_variables = {
         LUA_LIB = "$(LUA_LIBDIR)\\lua5.1.lib",
         CFLAGS = "/MD $(CFLAGS) /I$(LUA_INCDIR)",
       	},
       	install_variables = {
         LUA_LIBDIR = "$(LIBDIR)",
         LUA_DIR = "$(LUADIR)",
	 	 BIN_DIR = "$(BINDIR)"
       	}
     }
  }
}
genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.1rc1-1.rockspec000066400000000000000000000021771211610345200316310ustar00rootroot00000000000000package = "LuaFileSystem"
version = "1.4.1rc1-1"
source = {
   url = "http://luafilesystem.luaforge.net/luafilesystem-1.4.1rc1.tar.gz",
}
description = {
   summary = "File System Library for the Lua Programming Language",
   detailed = [[
      LuaFileSystem is a Lua library developed to complement the set of
      functions related to file systems offered by the standard Lua
      distribution. LuaFileSystem offers a portable way to access the
      underlying directory structure and file attributes.
   ]]
}
dependencies = {
   "lua >= 5.1"
}
build = {
   platforms = {
     unix = {
        type = "make",
       	build_variables = {
         LIB_OPTION = "$(LIBFLAG)",
         CFLAGS = "$(CFLAGS) -I$(LUA_INCDIR) $(STAT64)",
       	},
       	install_variables = {
         LUA_LIBDIR = "$(LIBDIR)"
       	}
     },
     win32 = {
        type = "make",
       	build_variables = {
         LUA_LIB = "$(LUA_LIBDIR)\\lua5.1.lib",
         CFLAGS = "/MD $(CFLAGS) /I$(LUA_INCDIR)",
       	},
       	install_variables = {
         LUA_LIBDIR = "$(LIBDIR)",
         LUA_DIR = "$(LUADIR)",
	 	 BIN_DIR = "$(BINDIR)"
       	}
     }
  }
}
genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.2-1.rockspec000066400000000000000000000011601211610345200312130ustar00rootroot00000000000000package = "LuaFileSystem"

version = "1.4.2-1"

source = {
   url = "http://luaforge.net/frs/download.php/3931/luafilesystem-1.4.2.tar.gz",
}

description = {
   summary = "File System Library for the Lua Programming Language",
   detailed = [[
      LuaFileSystem is a Lua library developed to complement the set of
      functions related to file systems offered by the standard Lua
      distribution. LuaFileSystem offers a portable way to access the
      underlying directory structure and file attributes.
   ]]
}

dependencies = {
   "lua >= 5.1"
}

build = {
   type = "module",
   modules = { lfs = "src/lfs.c" }
}genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.5.0-1.rockspec000066400000000000000000000012571211610345200312210ustar00rootroot00000000000000package = "LuaFileSystem"

version = "1.5.0-1"

source = {
   url = "http://cloud.github.com/downloads/keplerproject/luafilesystem/luafilesystem-1.5.0.tar.gz",
}

description = {
   summary = "File System Library for the Lua Programming Language",
   detailed = [[
      LuaFileSystem is a Lua library developed to complement the set of
      functions related to file systems offered by the standard Lua
      distribution. LuaFileSystem offers a portable way to access the
      underlying directory structure and file attributes.
   ]]
}

dependencies = {
   "lua >= 5.1"
}

build = {
   type = "module",
   modules = { lfs = "src/lfs.c" },
   copy_directories = { "doc", "tests" }
}
genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-cvs-1.rockspec000066400000000000000000000022001211610345200313400ustar00rootroot00000000000000package = "LuaFileSystem"
version = "cvs-1"
source = {
   url = "cvs://:pserver:anonymous:@cvs.luaforge.net:/cvsroot/luafilesystem",
   cvs_tag = "HEAD"
}
description = {
   summary = "File System Library for the Lua Programming Language",
   detailed = [[
      LuaFileSystem is a Lua library developed to complement the set of
      functions related to file systems offered by the standard Lua
      distribution. LuaFileSystem offers a portable way to access the
      underlying directory structure and file attributes.
   ]]
}
dependencies = {
   "lua >= 5.1"
}
build = {
   platforms = {
     unix = {
        type = "make",
       	build_variables = {
         LIB_OPTION = "$(LIBFLAG)",
         CFLAGS = "$(CFLAGS) -I$(LUA_INCDIR)",
       	},
       	install_variables = {
         LUA_LIBDIR = "$(LIBDIR)"
       	}
     },
     win32 = {
        type = "make",
       	build_variables = {
         LUA_LIB = "$(LUA_LIBDIR)\\lua5.1.lib",
         CFLAGS = "$(CFLAGS) /I$(LUA_INCDIR)",
       	},
       	install_variables = {
         LUA_LIBDIR = "$(LIBDIR)",
         LUA_DIR = "$(LUADIR)",
	 BIN_DIR = "$(BINDIR)"
       	}
     }
  }
}
genometools-1.5.1/src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-cvs-2.rockspec000066400000000000000000000011331211610345200313450ustar00rootroot00000000000000package = "LuaFileSystem"

version = "cvs-2"

source = {
   url = "git://github.com/keplerproject/luafilesystem.git",
}

description = {
   summary = "File System Library for the Lua Programming Language",
   detailed = [[
      LuaFileSystem is a Lua library developed to complement the set of
      functions related to file systems offered by the standard Lua
      distribution. LuaFileSystem offers a portable way to access the
      underlying directory structure and file attributes.
   ]]
}

dependencies = {
   "lua >= 5.1"
}

build = {
   type = "module",
   modules = { lfs = "src/lfs.c" }
}
genometools-1.5.1/src/external/luafilesystem-1.5.0/src/000077500000000000000000000000001211610345200225715ustar00rootroot00000000000000genometools-1.5.1/src/external/luafilesystem-1.5.0/src/lfs.c000066400000000000000000000465371211610345200235400ustar00rootroot00000000000000/*
** LuaFileSystem
** Copyright Kepler Project 2003 (http://www.keplerproject.org/luafilesystem)
**
** File system manipulation library.
** This library offers these functions:
**   lfs.attributes (filepath [, attributename])
**   lfs.chdir (path)
**   lfs.currentdir ()
**   lfs.dir (path)
**   lfs.lock (fh, mode)
**   lfs.lock_dir (path)
**   lfs.mkdir (path)
**   lfs.rmdir (path)
**   lfs.setmode (filepath, mode)
**   lfs.symlinkattributes (filepath [, attributename]) -- thanks to Sam Roberts
**   lfs.touch (filepath [, atime [, mtime]])
**   lfs.unlock (fh)
**
** $Id: lfs.c,v 1.61 2009/07/04 02:10:16 mascarenhas Exp $
*/

#ifndef _WIN32
#ifndef _AIX
#define _FILE_OFFSET_BITS 64 /* Linux, Solaris and HP-UX */
#else
#define _LARGE_FILES 1 /* AIX */
#endif
#endif

/* #define _LARGEFILE64_SOURCE */

#include 
#include 
#include 
#include 
#include 
#include 

#ifdef _WIN32
#include 
#include 
#include 
#include 
#ifdef __BORLANDC__
 #include 
#else
 #include 
#endif
#include 
#else
#include 
#include 
#include 
#include 
#include 
#endif

#include "lua.h"
#include "lauxlib.h"
#include "lualib.h"
#include "lfs.h"

/* Define 'strerror' for systems that do not implement it */
#ifdef NO_STRERROR
#define strerror(_)	"System unable to describe the error"
#endif

/* Define 'getcwd' for systems that do not implement it */
#ifdef NO_GETCWD
#define getcwd(p,s)	NULL
#define getcwd_error	"Function 'getcwd' not provided by system"
#else
#define getcwd_error	strerror(errno)
#endif

#define DIR_METATABLE "directory metatable"
#define MAX_DIR_LENGTH 1023
typedef struct dir_data {
	int  closed;
#ifdef _WIN32
	long hFile;
	char pattern[MAX_DIR_LENGTH+1];
#else
	DIR *dir;
#endif
} dir_data;

#define LOCK_METATABLE "lock metatable"

#ifdef _WIN32
 #ifdef __BORLANDC__
  #define lfs_setmode(L,file,m)   ((void)L, setmode(_fileno(file), m))
  #define STAT_STRUCT struct stati64
 #else
  #define lfs_setmode(L,file,m)   ((void)L, _setmode(_fileno(file), m))
  #define STAT_STRUCT struct _stati64
 #endif
#define STAT_FUNC _stati64
#else
#define _O_TEXT               0
#define _O_BINARY             0
#define lfs_setmode(L,file,m)   ((void)((void)file,m),  \
		 luaL_error(L, LUA_QL("setmode") " not supported on this platform"), -1)
#define STAT_STRUCT struct stat
#define STAT_FUNC stat
#define LSTAT_FUNC lstat
#endif

/*
** This function changes the working (current) directory
*/
static int change_dir (lua_State *L) {
	const char *path = luaL_checkstring(L, 1);
	if (chdir(path)) {
		lua_pushnil (L);
		lua_pushfstring (L,"Unable to change working directory to '%s'\n%s\n",
				path, chdir_error);
		return 2;
	} else {
		lua_pushboolean (L, 1);
		return 1;
	}
}

/*
** This function returns the current directory
** If unable to get the current directory, it returns nil
**  and a string describing the error
*/
static int get_dir (lua_State *L) {
  char *path;
  if ((path = getcwd(NULL, 0)) == NULL) {
    lua_pushnil(L);
    lua_pushstring(L, getcwd_error);
    return 2;
  }
  else {
    lua_pushstring(L, path);
    free(path);
    return 1;
  }
}

/*
** Check if the given element on the stack is a file and returns it.
*/
static FILE *check_file (lua_State *L, int idx, const char *funcname) {
	FILE **fh = (FILE **)luaL_checkudata (L, idx, "FILE*");
	if (fh == NULL) {
		luaL_error (L, "%s: not a file", funcname);
		return 0;
	} else if (*fh == NULL) {
		luaL_error (L, "%s: closed file", funcname);
		return 0;
	} else
		return *fh;
}


/*
**
*/
static int _file_lock (lua_State *L, FILE *fh, const char *mode, const long start, long len, const char *funcname) {
	int code;
#ifdef _WIN32
	/* lkmode valid values are:
	   LK_LOCK    Locks the specified bytes. If the bytes cannot be locked, the program immediately tries again after 1 second. If, after 10 attempts, the bytes cannot be locked, the constant returns an error.
	   LK_NBLCK   Locks the specified bytes. If the bytes cannot be locked, the constant returns an error.
	   LK_NBRLCK  Same as _LK_NBLCK.
	   LK_RLCK    Same as _LK_LOCK.
	   LK_UNLCK   Unlocks the specified bytes, which must have been previously locked.

	   Regions should be locked only briefly and should be unlocked before closing a file or exiting the program.

	   http://msdn.microsoft.com/library/default.asp?url=/library/en-us/vclib/html/_crt__locking.asp
	*/
	int lkmode;
	switch (*mode) {
		case 'r': lkmode = LK_NBLCK; break;
		case 'w': lkmode = LK_NBLCK; break;
		case 'u': lkmode = LK_UNLCK; break;
		default : return luaL_error (L, "%s: invalid mode", funcname);
	}
	if (!len) {
		fseek (fh, 0L, SEEK_END);
		len = ftell (fh);
	}
	fseek (fh, start, SEEK_SET);
#ifdef __BORLANDC__
	code = locking (fileno(fh), lkmode, len);
#else
	code = _locking (fileno(fh), lkmode, len);
#endif
#else
	struct flock f;
	switch (*mode) {
		case 'w': f.l_type = F_WRLCK; break;
		case 'r': f.l_type = F_RDLCK; break;
		case 'u': f.l_type = F_UNLCK; break;
		default : return luaL_error (L, "%s: invalid mode", funcname);
	}
	f.l_whence = SEEK_SET;
	f.l_start = (off_t)start;
	f.l_len = (off_t)len;
	code = fcntl (fileno(fh), F_SETLK, &f);
#endif
	return (code != -1);
}

#ifdef _WIN32
typedef struct lfs_Lock {
  HANDLE fd;
} lfs_Lock;
static int lfs_lock_dir(lua_State *L) {
  size_t pathl; HANDLE fd;
  lfs_Lock *lock;
  char *ln;
  const char *lockfile = "/lockfile.lfs";
  const char *path = luaL_checklstring(L, 1, &pathl);
  ln = (char*)malloc(pathl + strlen(lockfile) + 1);
  if(!ln) { 
    lua_pushnil(L); lua_pushstring(L, strerror(errno)); return 2;
  }
  strcpy(ln, path); strcat(ln, lockfile);
  if((fd = CreateFile(ln, GENERIC_WRITE, 0, NULL, CREATE_NEW, 
	  	FILE_ATTRIBUTE_NORMAL | FILE_FLAG_DELETE_ON_CLOSE, NULL)) == INVALID_HANDLE_VALUE) {
  	int en = GetLastError();
  	free(ln); lua_pushnil(L);
  	if(en == ERROR_FILE_EXISTS || en == ERROR_SHARING_VIOLATION)
  		lua_pushstring(L, "File exists");
  	else
		lua_pushstring(L, strerror(en));
	return 2;
  }
  free(ln);
  lock = (lfs_Lock*)lua_newuserdata(L, sizeof(lfs_Lock));
  lock->fd = fd;
  luaL_getmetatable (L, LOCK_METATABLE);
  lua_setmetatable (L, -2);
  return 1;
}
static int lfs_unlock_dir(lua_State *L) {
  lfs_Lock *lock = luaL_checkudata(L, 1, LOCK_METATABLE);
  CloseHandle(lock->fd);
  return 0;
}
#else
typedef struct lfs_Lock {
  char *ln;
} lfs_Lock;
static int lfs_lock_dir(lua_State *L) {
  lfs_Lock *lock;
  size_t pathl;
  char *ln;
  const char *lockfile = "/lockfile.lfs";
  const char *path = luaL_checklstring(L, 1, &pathl);
  lock = (lfs_Lock*)lua_newuserdata(L, sizeof(lfs_Lock));
  ln = (char*)malloc(pathl + strlen(lockfile) + 1);
  if(!ln) { 
    lua_pushnil(L); lua_pushstring(L, strerror(errno)); return 2;
  }
  strcpy(ln, path); strcat(ln, lockfile);
  if(symlink("lock", ln) == -1) {
    free(ln); lua_pushnil(L); 
    lua_pushstring(L, strerror(errno)); return 2;
  }
  lock->ln = ln;
  luaL_getmetatable (L, LOCK_METATABLE);
  lua_setmetatable (L, -2);
  return 1;
}
static int lfs_unlock_dir(lua_State *L) {
  lfs_Lock *lock = luaL_checkudata(L, 1, LOCK_METATABLE);
  if(lock->ln) {
    unlink(lock->ln);
    free(lock->ln);
    lock->ln = NULL;
  }
  return 0;
}
#endif

#ifdef _WIN32
static int lfs_g_setmode (lua_State *L, FILE *f, int arg) {
  static const int mode[] = {_O_TEXT, _O_BINARY};
  static const char *const modenames[] = {"text", "binary", NULL};
  int op = luaL_checkoption(L, arg, NULL, modenames);
  int res = lfs_setmode(L, f, mode[op]);
  if (res != -1) {
    int i;
    lua_pushboolean(L, 1);
    for (i = 0; modenames[i] != NULL; i++) {
      if (mode[i] == res) {
        lua_pushstring(L, modenames[i]);
        goto exit;
      }
    }
    lua_pushnil(L);
  exit:
    return 2;
  } else {
    int en = errno;
    lua_pushnil(L);
    lua_pushfstring(L, "%s", strerror(en));
    lua_pushinteger(L, en);
    return 3;
  }
}
#else
static int lfs_g_setmode (lua_State *L, __attribute__ ((unused)) FILE *f,
                          __attribute__ ((unused)) int arg) {
  lua_pushboolean(L, 0);
  lua_pushliteral(L, "setmode not supported on this platform");
  return 2;
}
#endif

static int lfs_f_setmode(lua_State *L) {
  return lfs_g_setmode(L, check_file(L, 1, "setmode"), 2);
}

/*
** Locks a file.
** @param #1 File handle.
** @param #2 String with lock mode ('w'rite, 'r'ead).
** @param #3 Number with start position (optional).
** @param #4 Number with length (optional).
*/
static int file_lock (lua_State *L) {
	FILE *fh = check_file (L, 1, "lock");
	const char *mode = luaL_checkstring (L, 2);
	const long start = luaL_optlong (L, 3, 0);
	long len = luaL_optlong (L, 4, 0);
	if (_file_lock (L, fh, mode, start, len, "lock")) {
		lua_pushboolean (L, 1);
		return 1;
	} else {
		lua_pushnil (L);
		lua_pushfstring (L, "%s", strerror(errno));
		return 2;
	}
}


/*
** Unlocks a file.
** @param #1 File handle.
** @param #2 Number with start position (optional).
** @param #3 Number with length (optional).
*/
static int file_unlock (lua_State *L) {
	FILE *fh = check_file (L, 1, "unlock");
	const long start = luaL_optlong (L, 2, 0);
	long len = luaL_optlong (L, 3, 0);
	if (_file_lock (L, fh, "u", start, len, "unlock")) {
		lua_pushboolean (L, 1);
		return 1;
	} else {
		lua_pushnil (L);
		lua_pushfstring (L, "%s", strerror(errno));
		return 2;
	}
}


static int make_dir (lua_State *L) {
	const char *path = luaL_checkstring (L, 1);
	int fail;
#ifdef _WIN32
	int oldmask = umask (0);
	fail = _mkdir (path);
#else
	mode_t oldmask = umask( (mode_t)0 );
	fail =  mkdir (path, S_IRUSR | S_IWUSR | S_IXUSR | S_IRGRP |
	                     S_IWGRP | S_IXGRP | S_IROTH | S_IXOTH );
#endif
	if (fail) {
		lua_pushnil (L);
        lua_pushfstring (L, "%s", strerror(errno));
		return 2;
	}
	umask (oldmask);
	lua_pushboolean (L, 1);
	return 1;
}

/*
** Removes a directory.
** @param #1 Directory path.
*/
static int remove_dir (lua_State *L) {
	const char *path = luaL_checkstring (L, 1);
	int fail;

	fail = rmdir (path);

	if (fail) {
		lua_pushnil (L);
		lua_pushfstring (L, "%s", strerror(errno));
		return 2;
	}
	lua_pushboolean (L, 1);
	return 1;
}

/*
** Directory iterator
*/
static int dir_iter (lua_State *L) {
#ifdef _WIN32
	struct _finddata_t c_file;
#else
	struct dirent *entry;
#endif
	dir_data *d = (dir_data *)luaL_checkudata (L, 1, DIR_METATABLE);
	luaL_argcheck (L, !d->closed, 1, "closed directory");
#ifdef _WIN32
	if (d->hFile == 0L) { /* first entry */
		if ((d->hFile = _findfirst (d->pattern, &c_file)) == -1L) {
			lua_pushnil (L);
			lua_pushstring (L, strerror (errno));
			return 2;
		} else {
			lua_pushstring (L, c_file.name);
			return 1;
		}
	} else { /* next entry */
		if (_findnext (d->hFile, &c_file) == -1L) {
			/* no more entries => close directory */
			_findclose (d->hFile);
			d->closed = 1;
			return 0;
		} else {
			lua_pushstring (L, c_file.name);
			return 1;
		}
	}
#else
	if ((entry = readdir (d->dir)) != NULL) {
		lua_pushstring (L, entry->d_name);
		return 1;
	} else {
		/* no more entries => close directory */
		closedir (d->dir);
		d->closed = 1;
		return 0;
	}
#endif
}


/*
** Closes directory iterators
*/
static int dir_close (lua_State *L) {
	dir_data *d = (dir_data *)lua_touserdata (L, 1);
#ifdef _WIN32
	if (!d->closed && d->hFile) {
		_findclose (d->hFile);
		d->closed = 1;
	}
#else
	if (!d->closed && d->dir) {
		closedir (d->dir);
		d->closed = 1;
	}
#endif
	return 0;
}


/*
** Factory of directory iterators
*/
static int dir_iter_factory (lua_State *L) {
	const char *path = luaL_checkstring (L, 1);
	dir_data *d;
	lua_pushcfunction (L, dir_iter);
	d = (dir_data *) lua_newuserdata (L, sizeof(dir_data));
	d->closed = 0;
#ifdef _WIN32
	d->hFile = 0L;
	luaL_getmetatable (L, DIR_METATABLE);
	lua_setmetatable (L, -2);
	if (strlen(path) > MAX_DIR_LENGTH)
		luaL_error (L, "path too long: %s", path);
	else
		sprintf (d->pattern, "%s/*", path);
#else
	luaL_getmetatable (L, DIR_METATABLE);
	lua_setmetatable (L, -2);
	d->dir = opendir (path);
	if (d->dir == NULL)
		luaL_error (L, "cannot open %s: %s", path, strerror (errno));
#endif
	return 2;
}


/*
** Creates directory metatable.
*/
static int dir_create_meta (lua_State *L) {
	luaL_newmetatable (L, DIR_METATABLE);
	/* set its __gc field */
	lua_pushstring (L, "__index");
	lua_newtable(L);
	lua_pushstring (L, "next");
	lua_pushcfunction (L, dir_iter);
	lua_settable(L, -3);
	lua_pushstring (L, "close");
	lua_pushcfunction (L, dir_close);
	lua_settable(L, -3);
	lua_settable (L, -3);
	lua_pushstring (L, "__gc");
	lua_pushcfunction (L, dir_close);
	lua_settable (L, -3);
	return 1;
}

/*
** Creates lock metatable.
*/
static int lock_create_meta (lua_State *L) {
	luaL_newmetatable (L, LOCK_METATABLE);
	/* set its __gc field */
	lua_newtable(L);
	lua_pushcfunction(L, lfs_unlock_dir);
	lua_setfield(L, -2, "free");
	lua_setfield(L, -2, "__index");
	lua_pushcfunction(L, lfs_unlock_dir);
	lua_setfield(L, -2, "__gc");
	return 1;
}


#ifdef _WIN32
 #ifndef S_ISDIR
   #define S_ISDIR(mode)  (mode&_S_IFDIR)
 #endif
 #ifndef S_ISREG
   #define S_ISREG(mode)  (mode&_S_IFREG)
 #endif
 #ifndef S_ISLNK
   #define S_ISLNK(mode)  (0)
 #endif
 #ifndef S_ISSOCK
   #define S_ISSOCK(mode)  (0)
 #endif
 #ifndef S_ISFIFO
   #define S_ISFIFO(mode)  (0)
 #endif
 #ifndef S_ISCHR
   #define S_ISCHR(mode)  (mode&_S_IFCHR)
 #endif
 #ifndef S_ISBLK
   #define S_ISBLK(mode)  (0)
 #endif
#endif
/*
** Convert the inode protection mode to a string.
*/
#ifdef _WIN32
static const char *mode2string (unsigned short mode) {
#else
static const char *mode2string (mode_t mode) {
#endif
  if ( S_ISREG(mode) )
    return "file";
  else if ( S_ISDIR(mode) )
    return "directory";
  else if ( S_ISLNK(mode) )
	return "link";
  else if ( S_ISSOCK(mode) )
    return "socket";
  else if ( S_ISFIFO(mode) )
	return "named pipe";
  else if ( S_ISCHR(mode) )
	return "char device";
  else if ( S_ISBLK(mode) )
	return "block device";
  else
	return "other";
}


/*
** Set access time and modification values for file
*/
static int file_utime (lua_State *L) {
	const char *file = luaL_checkstring (L, 1);
	struct utimbuf utb, *buf;

	if (lua_gettop (L) == 1) /* set to current date/time */
		buf = NULL;
	else {
		utb.actime = (time_t)luaL_optnumber (L, 2, 0);
		utb.modtime = (time_t)luaL_optnumber (L, 3, utb.actime);
		buf = &utb;
	}
	if (utime (file, buf)) {
		lua_pushnil (L);
		lua_pushfstring (L, "%s", strerror (errno));
		return 2;
	}
	lua_pushboolean (L, 1);
	return 1;
}


/* inode protection mode */
static void push_st_mode (lua_State *L, STAT_STRUCT *info) {
	lua_pushstring (L, mode2string (info->st_mode));
}
/* device inode resides on */
static void push_st_dev (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, (lua_Number)info->st_dev);
}
/* inode's number */
static void push_st_ino (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, (lua_Number)info->st_ino);
}
/* number of hard links to the file */
static void push_st_nlink (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, (lua_Number)info->st_nlink);
}
/* user-id of owner */
static void push_st_uid (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, (lua_Number)info->st_uid);
}
/* group-id of owner */
static void push_st_gid (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, (lua_Number)info->st_gid);
}
/* device type, for special file inode */
static void push_st_rdev (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, (lua_Number)info->st_rdev);
}
/* time of last access */
static void push_st_atime (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, info->st_atime);
}
/* time of last data modification */
static void push_st_mtime (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, info->st_mtime);
}
/* time of last file status change */
static void push_st_ctime (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, info->st_ctime);
}
/* file size, in bytes */
static void push_st_size (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, (lua_Number)info->st_size);
}
#ifndef _WIN32
/* blocks allocated for file */
static void push_st_blocks (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, (lua_Number)info->st_blocks);
}
/* optimal file system I/O blocksize */
static void push_st_blksize (lua_State *L, STAT_STRUCT *info) {
	lua_pushnumber (L, (lua_Number)info->st_blksize);
}
#endif
static void push_invalid (lua_State *L, STAT_STRUCT *info) {
  luaL_error(L, "invalid attribute name");
#ifndef _WIN32
  info->st_blksize = 0; /* never reached */
#endif
}

typedef void (*_push_function) (lua_State *L, STAT_STRUCT *info);

struct _stat_members {
	const char *name;
	_push_function push;
};

struct _stat_members members[] = {
	{ "mode",         push_st_mode },
	{ "dev",          push_st_dev },
	{ "ino",          push_st_ino },
	{ "nlink",        push_st_nlink },
	{ "uid",          push_st_uid },
	{ "gid",          push_st_gid },
	{ "rdev",         push_st_rdev },
	{ "access",       push_st_atime },
	{ "modification", push_st_mtime },
	{ "change",       push_st_ctime },
	{ "size",         push_st_size },
#ifndef _WIN32
	{ "blocks",       push_st_blocks },
	{ "blksize",      push_st_blksize },
#endif
	{ NULL, push_invalid }
};

/*
** Get file or symbolic link information
*/
static int _file_info_ (lua_State *L, int (*st)(const char*, STAT_STRUCT*)) {
	int i;
	STAT_STRUCT info;
	const char *file = luaL_checkstring (L, 1);

	if (st(file, &info)) {
		lua_pushnil (L);
		lua_pushfstring (L, "cannot obtain information from file `%s'", file);
		return 2;
	}
	if (lua_isstring (L, 2)) {
		int v;
		const char *member = lua_tostring (L, 2);
		if (strcmp (member, "mode") == 0) v = 0;
#ifndef _WIN32
		else if (strcmp (member, "blocks")  == 0) v = 11;
		else if (strcmp (member, "blksize") == 0) v = 12;
#endif
		else /* look for member */
			for (v = 1; members[v].name; v++)
				if (*members[v].name == *member)
					break;
		/* push member value and return */
		members[v].push (L, &info);
		return 1;
	} else if (!lua_istable (L, 2))
		/* creates a table if none is given */
		lua_newtable (L);
	/* stores all members in table on top of the stack */
	for (i = 0; members[i].name; i++) {
		lua_pushstring (L, members[i].name);
		members[i].push (L, &info);
		lua_rawset (L, -3);
	}
	return 1;
}


/*
** Get file information using stat.
*/
static int file_info (lua_State *L) {
	return _file_info_ (L, STAT_FUNC);
}


/*
** Get symbolic link information using lstat.
*/
#ifndef _WIN32
static int link_info (lua_State *L) {
	return _file_info_ (L, LSTAT_FUNC);
}
#else
static int link_info (lua_State *L) {
  lua_pushboolean(L, 0);
  lua_pushliteral(L, "symlinkattributes not supported on this platform");
  return 2;
}
#endif


/*
** Assumes the table is on top of the stack.
*/
static void set_info (lua_State *L) {
	lua_pushliteral (L, "_COPYRIGHT");
	lua_pushliteral (L, "Copyright (C) 2003-2009 Kepler Project");
	lua_settable (L, -3);
	lua_pushliteral (L, "_DESCRIPTION");
	lua_pushliteral (L, "LuaFileSystem is a Lua library developed to complement the set of functions related to file systems offered by the standard Lua distribution");
	lua_settable (L, -3);
	lua_pushliteral (L, "_VERSION");
	lua_pushliteral (L, "LuaFileSystem 1.5.0");
	lua_settable (L, -3);
}


static const struct luaL_reg fslib[] = {
	{"attributes", file_info},
	{"chdir", change_dir},
	{"currentdir", get_dir},
	{"dir", dir_iter_factory},
	{"lock", file_lock},
	{"mkdir", make_dir},
	{"rmdir", remove_dir},
	{"symlinkattributes", link_info},
	{"setmode", lfs_f_setmode},
	{"touch", file_utime},
	{"unlock", file_unlock},
	{"lock_dir", lfs_lock_dir},
	{NULL, NULL},
};

int luaopen_lfs (lua_State *L) {
	dir_create_meta (L);
	lock_create_meta (L);
	luaL_register (L, "lfs", fslib);
	set_info (L);
	return 1;
}
genometools-1.5.1/src/external/luafilesystem-1.5.0/src/lfs.def000066400000000000000000000001231211610345200240310ustar00rootroot00000000000000LIBRARY lfs.dll
DESCRIPTION "LuaFileSystem"
VERSION 1.4.2
EXPORTS
luaopen_lfs
genometools-1.5.1/src/external/luafilesystem-1.5.0/src/lfs.h000066400000000000000000000006241211610345200235300ustar00rootroot00000000000000/*
** LuaFileSystem
** Copyright Kepler Project 2003 (http://www.keplerproject.org/luafilesystem)
**
** $Id: lfs.h,v 1.5 2008/02/19 20:08:23 mascarenhas Exp $
*/

/* Define 'chdir' for systems that do not implement it */
#ifdef NO_CHDIR
#define chdir(p)	(-1)
#define chdir_error	"Function 'chdir' not provided by system"
#else
#define chdir_error	strerror(errno)
#endif


int luaopen_lfs (lua_State *L);
genometools-1.5.1/src/external/luafilesystem-1.5.0/tests/000077500000000000000000000000001211610345200231445ustar00rootroot00000000000000genometools-1.5.1/src/external/luafilesystem-1.5.0/tests/test.lua000066400000000000000000000110321211610345200246230ustar00rootroot00000000000000#!/usr/local/bin/lua5.1

local tmp = "/tmp"
local sep = "/"
local upper = ".."

require"lfs"
print (lfs._VERSION)

function attrdir (path)
	for file in lfs.dir(path) do
		if file ~= "." and file ~= ".." then
			local f = path..sep..file
			print ("\t=> "..f.." <=")
			local attr = lfs.attributes (f)
			assert (type(attr) == "table")
			if attr.mode == "directory" then
				attrdir (f)
			else
				for name, value in pairs(attr) do
					print (name, value)
				end
			end
		end
	end
end

-- Checking changing directories
local current = assert (lfs.currentdir())
local reldir = string.gsub (current, "^.*%"..sep.."([^"..sep.."])$", "%1")
assert (lfs.chdir (upper), "could not change to upper directory")
assert (lfs.chdir (reldir), "could not change back to current directory")
assert (lfs.currentdir() == current, "error trying to change directories")
assert (lfs.chdir ("this couldn't be an actual directory") == nil, "could change to a non-existent directory")

-- Changing creating and removing directories
local tmpdir = current..sep.."lfs_tmp_dir"
local tmpfile = tmpdir..sep.."tmp_file"
-- Test for existence of a previous lfs_tmp_dir
-- that may have resulted from an interrupted test execution and remove it
if lfs.chdir (tmpdir) then
    assert (lfs.chdir (upper), "could not change to upper directory")
    assert (os.remove (tmpfile), "could not remove file from previous test")    
    assert (lfs.rmdir (tmpdir), "could not remove directory from previous test")
end

-- tries to create a directory
assert (lfs.mkdir (tmpdir), "could not make a new directory")
local attrib, errmsg = lfs.attributes (tmpdir)
if not attrib then
	error ("could not get attributes of file `"..tmpdir.."':\n"..errmsg)
end
local f = io.open(tmpfile, "w")
f:close()

-- Change access time
local testdate = os.time({ year = 2007, day = 10, month = 2, hour=0})
assert (lfs.touch (tmpfile, testdate))
local new_att = assert (lfs.attributes (tmpfile))
assert (new_att.access == testdate, "could not set access time")
assert (new_att.modification == testdate, "could not set modification time")

-- Change access and modification time
local testdate1 = os.time({ year = 2007, day = 10, month = 2, hour=0})
local testdate2 = os.time({ year = 2007, day = 11, month = 2, hour=0})

assert (lfs.touch (tmpfile, testdate2, testdate1))
local new_att = assert (lfs.attributes (tmpfile))
assert (new_att.access == testdate2, "could not set access time")
assert (new_att.modification == testdate1, "could not set modification time")

local res, err = lfs.symlinkattributes(tmpfile)
if err ~= "symlinkattributes not supported on this platform" then
    -- Checking symbolic link information (does not work in Windows)
    assert (os.execute ("ln -s "..tmpfile.." _a_link_for_test_"))
    assert (lfs.attributes"_a_link_for_test_".mode == "file")
    assert (lfs.symlinkattributes"_a_link_for_test_".mode == "link")
    assert (os.remove"_a_link_for_test_")
end

if lfs.setmode then
    -- Checking text/binary modes (works only in Windows)
    local f = io.open(tmpfile, "w")
    local result, mode = lfs.setmode(f, "binary")
    assert((result and mode == "text") or (not result and mode == "setmode not supported on this platform"))
    result, mode = lfs.setmode(f, "text")
    assert((result and mode == "binary") or (not result and mode == "setmode not supported on this platform"))
    f:close()
end
    
-- Restore access time to current value
assert (lfs.touch (tmpfile, attrib.access, attrib.modification))
new_att = assert (lfs.attributes (tmpfile))
assert (new_att.access == attrib.access)
assert (new_att.modification == attrib.modification)

-- Remove new file and directory
assert (os.remove (tmpfile), "could not remove new file")
assert (lfs.rmdir (tmpdir), "could not remove new directory")
assert (lfs.mkdir (tmpdir..sep.."lfs_tmp_dir") == nil, "could create a directory inside a non-existent one")

-- Trying to get attributes of a non-existent file
assert (lfs.attributes ("this couldn't be an actual file") == nil, "could get attributes of a non-existent file")
assert (type(lfs.attributes (upper)) == "table", "couldn't get attributes of upper directory")

-- Stressing directory iterator
count = 0
for i = 1, 4000 do
	for file in lfs.dir (tmp) do
		count = count + 1
	end
end

-- Stressing directory iterator, explicit version
count = 0
for i = 1, 4000 do
  local iter, dir = lfs.dir(tmp)
  local file = dir:next()
  while file do
    count = count + 1
    file = dir:next()
  end
  assert(not pcall(dir.next, dir))
end

-- directory explicit close
local iter, dir = lfs.dir(tmp)
dir:close()
assert(not pcall(dir.next, dir))
print"Ok!"
genometools-1.5.1/src/external/luafilesystem-1.5.0/vc6/000077500000000000000000000000001211610345200225005ustar00rootroot00000000000000genometools-1.5.1/src/external/luafilesystem-1.5.0/vc6/lfs.def000066400000000000000000000001141211610345200237400ustar00rootroot00000000000000LIBRARY lfs.dll
DESCRIPTION "LuaFileSystem"
VERSION 1.2
EXPORTS
luaopen_lfs
genometools-1.5.1/src/external/luafilesystem-1.5.0/vc6/luafilesystem.dsw000066400000000000000000000011431211610345200261040ustar00rootroot00000000000000Microsoft Developer Studio Workspace File, Format Version 6.00
# WARNING: DO NOT EDIT OR DELETE THIS WORKSPACE FILE!

###############################################################################

Project: "luafilesystem_dll"=.\luafilesystem_dll.dsp - Package Owner=<4>

Package=<5>
{{{
    begin source code control
    luafilesystem
    ..
    end source code control
}}}

Package=<4>
{{{
}}}

###############################################################################

Global:

Package=<5>
{{{
}}}

Package=<3>
{{{
}}}

###############################################################################

genometools-1.5.1/src/external/luafilesystem-1.5.0/vc6/luafilesystem_dll.dsp000066400000000000000000000114431211610345200267340ustar00rootroot00000000000000# Microsoft Developer Studio Project File - Name="luafilesystem_dll" - Package Owner=<4>
# Microsoft Developer Studio Generated Build File, Format Version 6.00
# ** DO NOT EDIT **

# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102

CFG=luafilesystem_dll - Win32 Debug
!MESSAGE This is not a valid makefile. To build this project using NMAKE,
!MESSAGE use the Export Makefile command and run
!MESSAGE 
!MESSAGE NMAKE /f "luafilesystem_dll.mak".
!MESSAGE 
!MESSAGE You can specify a configuration when running NMAKE
!MESSAGE by defining the macro CFG on the command line. For example:
!MESSAGE 
!MESSAGE NMAKE /f "luafilesystem_dll.mak" CFG="luafilesystem_dll - Win32 Debug"
!MESSAGE 
!MESSAGE Possible choices for configuration are:
!MESSAGE 
!MESSAGE "luafilesystem_dll - Win32 Release" (based on "Win32 (x86) Dynamic-Link Library")
!MESSAGE "luafilesystem_dll - Win32 Debug" (based on "Win32 (x86) Dynamic-Link Library")
!MESSAGE 

# Begin Project
# PROP AllowPerConfigDependencies 0
# PROP Scc_ProjName "luafilesystem_dll"
# PROP Scc_LocalPath ".."
CPP=cl.exe
MTL=midl.exe
RSC=rc.exe

!IF  "$(CFG)" == "luafilesystem_dll - Win32 Release"

# PROP BASE Use_MFC 0
# PROP BASE Use_Debug_Libraries 0
# PROP BASE Output_Dir "Release"
# PROP BASE Intermediate_Dir "Release"
# PROP BASE Target_Dir ""
# PROP Use_MFC 0
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# PROP Output_Dir "../lib/vc6"
# PROP Intermediate_Dir "luafilesystem_dll/Release"
# PROP Ignore_Export_Lib 0
# PROP Target_Dir ""
# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "LUAFILESYSTEM_EXPORTS" /YX /FD /c
# ADD CPP /nologo /MD /W3 /GX /O2 /I "../../external-src/lua50/include" /I "../../compat/src" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "LUAFILESYSTEM_EXPORTS" /YX /FD /c
# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /win32
# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /win32
# ADD BASE RSC /l 0x416 /d "NDEBUG"
# ADD RSC /l 0x416 /d "NDEBUG"
BSC32=bscmake.exe
# ADD BASE BSC32 /nologo
# ADD BSC32 /nologo
LINK32=link.exe
# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /dll /machine:I386
# ADD LINK32 lua50.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /dll /machine:I386 /out:"../bin/vc6/lfs.dll" /libpath:"../../external-src/lua50/lib/dll"
# Begin Special Build Tool
SOURCE="$(InputPath)"
PostBuild_Cmds=cd ../bin/vc6	zip.exe luafilesystem-1.2-win32.zip lfs.dll
# End Special Build Tool

!ELSEIF  "$(CFG)" == "luafilesystem_dll - Win32 Debug"

# PROP BASE Use_MFC 0
# PROP BASE Use_Debug_Libraries 1
# PROP BASE Output_Dir "Debug"
# PROP BASE Intermediate_Dir "Debug"
# PROP BASE Target_Dir ""
# PROP Use_MFC 0
# PROP Use_Debug_Libraries 1
# PROP Output_Dir "../lib/vc6"
# PROP Intermediate_Dir "luafilesystem_dll/Debug"
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# ADD CPP /nologo /MDd /W3 /Gm /GX /ZI /Od /I "../../external-src/lua50/include" /I "../../compat/src" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "LUAFILESYSTEM_EXPORTS" /YX /FD /GZ /c
# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
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# ADD RSC /l 0x416 /d "_DEBUG"
BSC32=bscmake.exe
# ADD BASE BSC32 /nologo
# ADD BSC32 /nologo
LINK32=link.exe
# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /dll /debug /machine:I386 /pdbtype:sept
# ADD LINK32 lua50.lib kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib /nologo /dll /debug /machine:I386 /out:"../bin/vc6/lfsd.dll" /pdbtype:sept /libpath:"../../external-src/lua50/lib/dll"

!ENDIF 

# Begin Target

# Name "luafilesystem_dll - Win32 Release"
# Name "luafilesystem_dll - Win32 Debug"
# Begin Group "Source Files"

# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
# Begin Source File

SOURCE="..\..\compat\src\compat-5.1.c"
# End Source File
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SOURCE=..\src\lfs.c
# End Source File
# Begin Source File

SOURCE=.\lfs.def
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# PROP Default_Filter "h;hpp;hxx;hm;inl"
# Begin Source File

SOURCE="..\..\compat\src\compat-5.1.h"
# End Source File
# Begin Source File

SOURCE=..\src\lfs.h
# End Source File
# End Group
# Begin Group "Resource Files"

# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
# End Group
# End Target
# End Project
genometools-1.5.1/src/external/md5-1.1.2/000077500000000000000000000000001211610345200175775ustar00rootroot00000000000000genometools-1.5.1/src/external/md5-1.1.2/Makefile000066400000000000000000000020421211610345200212350ustar00rootroot00000000000000# $Id: Makefile,v 1.7 2007/10/11 00:02:56 carregal Exp $

CONFIG= ./config

include $(CONFIG)

ifeq "$(LUA_VERSION_NUM)" "500"
COMPAT_O= $(COMPAT_DIR)/compat-5.1.o
endif

MD5_OBJS= src/md5.o src/md5lib.o $(COMPAT_O)
MD5_LUAS= src/md5.lua
MD5_LIBNAME = core.so

DES56_OBJS= src/des56.o src/ldes56.o
DES56_LIBNAME= des56.so

all: src/$(MD5_LIBNAME) src/$(DES56_LIBNAME)

src/$(MD5_LIBNAME) : $(MD5_OBJS)
	export MACOSX_DEPLOYMENT_TARGET="10.3"; $(CC) $(CFLAGS) $(LIB_OPTION) -o src/$(MD5_LIBNAME) $(MD5_OBJS)

src/$(DES56_LIBNAME) : $(DES56_OBJS)
	export MACOSX_DEPLOYMENT_TARGET="10.3"; $(CC) $(CFLAGS) $(LIB_OPTION) -o src/$(DES56_LIBNAME) $(DES56_OBJS)

$(COMPAT_DIR)/compat-5.1.o: $(COMPAT_DIR)/compat-5.1.c
	$(CC) -c $(CFLAGS) -o $@ $(COMPAT_DIR)/compat-5.1.c

install: src/$(MD5_LIBNAME) src/$(DES56_LIBNAME)
	mkdir -p $(LUA_LIBDIR)/md5
	cp src/$(MD5_LIBNAME) $(LUA_LIBDIR)/md5/core.so
	mkdir -p $(LUA_DIR)
	cp $(MD5_LUAS) $(LUA_DIR)
	cp src/$(DES56_LIBNAME) $(LUA_LIBDIR)

clean:
	rm -f $(MD5_OBJS) src/$(MD5_LIBNAME) $(DES56_OBJS) src/$(DES56_LIBNAME)
genometools-1.5.1/src/external/md5-1.1.2/Makefile.win000066400000000000000000000023061211610345200220340ustar00rootroot00000000000000# $Id: Makefile.win,v 1.13 2008/05/12 17:49:05 carregal Exp $

include config.win

MD5_OBJS= src\md5.obj src\md5lib.obj 
MD5_LUAS= src\md5.lua
MD5_LIBNAME = core.dll

DES56_OBJS= src\des56.obj src\ldes56.obj
DES56_LIBNAME= des56.dll

all: src\$(MD5_LIBNAME) src\$(DES56_LIBNAME)

.c.obj:
	$(CC) /MD /c /Fo$@ $(CFLAGS) $<

src\$(MD5_LIBNAME) : $(MD5_OBJS)
	link /dll /def:src\md5.def /out:src\$(MD5_LIBNAME) $(MD5_OBJS) $(LUA_LIB)
	IF EXIST src\core.dll.manifest mt -manifest src\core.dll.manifest -outputresource:src\core.dll;2

src\$(DES56_LIBNAME) : $(DES56_OBJS)
	link /dll /def:src\des56.def /out:src\$(DES56_LIBNAME) $(DES56_OBJS) $(LUA_LIB)
	IF EXIST src\des56.dll.manifest mt -manifest src\des56.dll.manifest -outputresource:src\des56.dll;2

install: src\$(MD5_LIBNAME) src\$(DES56_LIBNAME)
	IF NOT EXIST "$(LUA_LIBDIR)\md5" mkdir "$(LUA_LIBDIR)\md5"
	copy "src\$(MD5_LIBNAME)" "$(LUA_LIBDIR)\md5\core.dll"
	IF NOT EXIST "$(LUA_DIR)" mkdir "$(LUA_DIR)"
	copy "$(MD5_LUAS)" "$(LUA_DIR)"
	copy "src\$(DES56_LIBNAME)" "$(LUA_LIBDIR)\"

clean:
	FOR %i in ($(MD5_OBJS)) DO del %i
	FOR %i in ($(DES56_OBJS)) DO del %i
	del "src\$(MD5_LIBNAME)" "src\$(DES56_LIBNAME)" src\core.lib src\core.exp src\des56.lib src\des56.exp
genometools-1.5.1/src/external/md5-1.1.2/README000066400000000000000000000015431211610345200204620ustar00rootroot00000000000000MD5 - Cryptographic Library for Lua
Copyright 2003 PUC-Rio
http://www.keplerproject.org/md5

MD5 offers basic cryptographic facilities for Lua 5.1: a hash (digest)
function, a pair crypt/decrypt based on MD5 and CFB, and a pair crypt/decrypt based
on DES with 56-bit keys.

MD5 current version is 1.1.2.

To install on Linux/OSX/BSD, please edit the config file and then call

make
make install

The last step may require root privileges.

If you are using LuaRocks you can also install MD5 with:

luarocks install md5

History

Version 1.1.2 [12/May/2008]
* Fixed bug in 64-bit systems
* Fixed the Windows makefile to accept longer directory names
  (patch by Alessandro Hecht and Ignacio Burgueño).


Please check the documentation at /doc/us/ for more information.

The DES 56 C library was implemented by Stuart Levy and uses a MIT license too (check the source)genometools-1.5.1/src/external/md5-1.1.2/config000066400000000000000000000016351211610345200207740ustar00rootroot00000000000000# Installation directories

# Default prefix
PREFIX = /usr/local

# System's libraries directory (where binary libraries are installed)
LUA_LIBDIR= $(PREFIX)/lib/lua/5.1

# System's lua directory (where Lua libraries are installed)
LUA_DIR= $(PREFIX)/share/lua/5.1

# Lua includes directory
LUA_INC= $(PREFIX)/include

# OS dependent
LIB_OPTION= -shared #for Linux
#LIB_OPTION= -bundle -undefined dynamic_lookup #for MacOS X

# Lua version number
# (according to Lua 5.1 definition:
# first version digit * 100 + second version digit
# e.g. Lua 5.0.2 => 500, Lua 5.1 => 501, Lua 5.1.1 => 501)
LUA_VERSION_NUM= 501
COMPAT_DIR= ../compat/src

# Compilation directives
WARN= -O2 -Wall -fPIC -W -Waggregate-return -Wcast-align -Wmissing-prototypes -Wnested-externs -Wshadow -Wwrite-strings -Wpointer-arith
INCS= -I$(LUA_INC) -I$(COMPAT_DIR)
CFLAGS= $(WARN) $(INCS)
CC= gcc

# $Id: config,v 1.6 2007/10/29 23:00:23 carregal Exp $
genometools-1.5.1/src/external/md5-1.1.2/config.win000066400000000000000000000012111211610345200215560ustar00rootroot00000000000000# Installation directories
# System's libraries directory (where binary libraries are installed)
LUA_LIBDIR= c:\lua5.1
# Lua directory (where Lua source libraries will be installed)
# This is the LUA_PATH
LUA_DIR= c:\lua5.1\lua
# Lua includes directory
LUA_INC= c:\lua5.1\include
LUA_LIB= c:\lua5.1\lua5.1.lib

# Lua version number
# (according to Lua 5.1 definition:
# first version digit * 100 + second version digit
# e.g. Lua 5.0.2 => 500, Lua 5.1 => 501, Lua 5.1.1 => 501)
LUA_VERSION_NUM= 501

# Compilation directives
WARN= /O2 
INCS= /I$(LUA_INC)
CFLAGS= $(WARN) $(INCS)
CC= cl

# $Id: config.win,v 1.5 2007/07/23 20:24:23 mascarenhas Exp $
genometools-1.5.1/src/external/md5-1.1.2/configure000077500000000000000000000010301211610345200215000ustar00rootroot00000000000000#!/bin/sh

if [ -f config.orig ]; then
  mv config.orig config
fi

echo "Trying to where you installed Lua..."

if which lua; then
  lua_bin=`which lua`
  lua_bin_dir=`dirname $lua_bin`
else
  lua_bin=`which lua51`
  lua_bin_dir=`dirname $lua_bin`
fi

lua_root=`dirname $lua_bin_dir`

if [ $lua_root != "" ]; then
  echo "Lua is in $lua_root"
  echo "Changing config"
  sed -i.orig -e "s|/usr/local|$lua_root|" config
  echo "Now run 'make' and 'make install'"
else
  echo "Lua not found, please install Lua (and put in your PATH)"
fi

genometools-1.5.1/src/external/md5-1.1.2/doc/000077500000000000000000000000001211610345200203445ustar00rootroot00000000000000genometools-1.5.1/src/external/md5-1.1.2/doc/us/000077500000000000000000000000001211610345200207735ustar00rootroot00000000000000genometools-1.5.1/src/external/md5-1.1.2/doc/us/index.html000066400000000000000000000124061211610345200227730ustar00rootroot00000000000000


    MD5: Cryptographic Library for Lua
    
	




    
	

    
	
	
    MD5
    
	
    Cryptographic Library for Lua
    

     


    
	
 


    


    Overview
    


    
MD5 offers basic cryptographic facilities for 
Lua 5.1:
a hash (digest) function, a pair crypt/decrypt based on MD5 and CFB,
and a pair crypt/decrypt based on DES with 56-bit keys.

    


    
MD5 is free software and uses the same license
as Lua.

    


    Status
    


    MD5 version 1.1.2 for Lua 5.1 is now available for
download.
    


    Download
    


    
MD5 can be downloaded in source code from its
LuaForge
page. If you are using LuaBinaries 5.1.x, a Windows
precompiled version of MD5 can also be found at the same LuaForge page.

    


    You can also install MD5 using LuaRocks:
    


    luarocks install md5

    


    History
    


    
    
    Version 1.1.2 [12/May/2008]
    
	
      
		
    • Fixed bug in 64-bit systems
      • 
		
    • Fixed the Windows makefile to accept longer directory names
		(patch by Alessandro Hecht and Ignacio Burgueño).
      •  
	
    
	
    
    Version 1.1.1 [28/Nov/2007]
    
    
    
    
      
        
    • Added DES56 tests (by Mauricio Bomfim)
      • 
        
    • Updated DES56 source to the latest release from Stuart Levy
      • 
    
    
    
    
    
    
    Version 1.1.0 [30/Oct/2007]
    
    
    
    Added DES56 crypt/decrypt functions.
    
    

    
    Version 1.0.2 [08/May/2007]
    
    
    
    
      
        
    • Added a nmake version for Lua 5.1
      • 
        
    • Windows binaries for Lua 5.1.2
      • 
    
    
    
    

    
    Version 1.0.1 [21/Aug/2006]
    
    
    
    
      
        
    • Adapted to work with both Lua 5.0 and Lua 5.1
      • 
        
    • Windows binaries for Lua 5.0.3
      • 
    
    
    
    

    
    Version 1.0.0
    
    
    
    
      
        
    • First public version
      • 
    
    
    
    

    


    Credits
    


    MD5 was designed and implemented by
Roberto Ierusalimschy and Marcela Ozório Suarez. The DES 56 C library was implemented by Stuart Levy
and uses a MIT license too.
The current distribution was packed by Tomás Guisasola and Fábio Mascarenhas
as part of the Kepler Project.
    


    Contact us
    


    For more information please
contact us.
Comments are welcome!
    


    You can also reach other Kepler developers and users on the Kepler Project
mailing list.
    


     


     


    
    
    Valid XHTML 1.0!
    
    
    $Id: index.html,v 1.20 2008/05/12 20:51:27 carregal Exp $
    

     


     


 
genometools-1.5.1/src/external/md5-1.1.2/doc/us/license.html000066400000000000000000000105541211610345200233100ustar00rootroot00000000000000


    MD5 License
    
	




    


    
	
	
    MD5
    
	
    Cryptographic Library for Lua
    

     


    

 


    


    License
    


    
MD5 is free software: it can be used for both academic and commercial
purposes at absolutely no cost. There are no royalties or GNU-like "copyleft"
restrictions. MD5 qualifies as
Open Source
software. 
Its licenses are compatible with
GPL.
MD5 is not in the public domain and PUC-Rio
keeps its copyright. The legal details are below.

    


    
The spirit of the license is that
you are free to use MD5 for any purpose at no cost without having to ask us.
The only requirement is that if you do use MD5,
then you should give us credit by including the appropriate copyright notice
somewhere in your product or its documentation.

    


    
MD5 was designed and implemented by Roberto Ierusalimschy and Marcela Ozório Suarez.
The implementation is not derived from licensed software. The DES 56 C library was implemented by Stuart Levy
and uses a MIT licence too.

    


    


    Copyright © 2003 PUC-Rio.  All rights reserved.
    


    Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
    


    The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
    


    
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
    


     

     


    
    
    Valid XHTML 1.0!
    
    
    $Id: license.html,v 1.9 2008/05/12 20:51:27 carregal Exp $
    

     


     


genometools-1.5.1/src/external/md5-1.1.2/doc/us/manual.html000066400000000000000000000203771211610345200231470ustar00rootroot00000000000000


    MD5: Cryptographic Library for Lua
    
	




    


    
	
	
    MD5
    
	
    Cryptographic Library for Lua
    

     



    

 


    


    Introduction
    


    
MD5 offers basic cryptographic facilities for Lua 5.1:
a hash (digest) function, a pair crypt/decrypt based on MD5 and CFB,
and a pair crypt/decrypt based on DES with 56-bit keys.

    


    
MD5 is free software and uses the same license
as Lua.

    


    Building
    


    
If you are using Unix MD5 offers a Makefile and a separate configuration file,
config, which should be edited to suit the particularities of the target platform
before running make.
The file has some definitions like paths to the external libraries,
compiler options and the like. One important definition is the Lua version,
which is not obtained from the installed software.

    


    
If you want to build MD5 on Windows MD5 offers the equivalent config.win
and Makefile.win files to be used with Microsoft Visual Studio 2005.

    


    Installation
    


    
The easiest way to install MD5 is to use LuaRocks:

    


    luarocks install md5

    


    
If you prefer to install the files manually and are using Unix, the build generates
two compiled binary files, core.so and des56.so.
The first should be copied to a directory called md5
in your C path.
Just copy the second to a directory in your Lua C path.

    


    
Windows users can use the binary version of MD5 available at
LuaForge.
    


    
In both Unix and Windows systems the file md5.lua should be copied to a directory in your
Lua path.

    


    Reference
    


    Lua API
    


    All MD5-based functions are registered inside a table md5.
    


    
    
    md5.sum (message)
    
    
    Computes the MD5 message-digest of the string message.
        This function takes as input a message of arbitrary length and content
        and returns as output a 128-bit "fingerprint" (or "message digest")
        of the input.
    
        The output is formated as a binary string with 16 characters.
        It is conjectured that it is computationally infeasible to produce
        two messages having the same message digest, or to produce any
        message having a given pre-specified target message digest.
        (see RFC 1321)
    
    

    
    md5.sumhexa (message)
    
    
    Similar to md5.sum, but returns its value as a
        string of 32 hexadecimal digits.
    
    

    
    md5.crypt (message, key [,seed])
    
    
    Encrypts a string, using MD5 in CFB (Cipher-feedback mode).
        message is an arbitrary binary string to be encrypted.
        key is an arbitrary binary string to be used as a key.
        seed is an arbitrary binary string to be used as a seed;
        Returns the cyphertext (as a binary string).
    
        
        If no seed is provided, the function uses the result of
        os.time() as a seed. It is recommended that you use
        different seeds for each message;  the seed itself is not private,
        and should contain no private data, because it goes plain in the
        beginning of the encrypted message.
    
        
        The length of the cyphertext is the length of the message plus the
        length of the seed plus one.
    
    

    
    md5.decrypt (message, key)
    
    
    Decrypts a string. The input message must be the result of
        a previous call to crypt. For any msg,
        key, and seed, we have that
        
    md5.decrypt(md5.crypt(msg, key, seed), key) == msg
    
    
    

    
    md5.exor (s1, s2)
    
    
    Does a bit-a-bit exclusive or of strings s1 and s2.
        Both strings must have the same length, which will be also the length of
        the resulting string.
    
    

    


    The DES-based functions are registered inside a table des56.
    


    
    
    des56.crypt (message, key)
    
    
    Encrypts a string, using DES with a 56-bit key.
        message is an arbitrary binary string to be encrypted.
        key is an 8-byte binary string to be used as a key.
        Returns the cyphertext (as a binary string).
    
    
    

    
    des56.decrypt (message, key)
    
    
    Decrypts a string. The input message must be the result of
        a previous call to des56.crypt. For any msg
        and key, we have that
        
    des56.decrypt(des56.crypt(msg, key), key) == msg
    
    
    


    


    C API
    


    The following functions are declared in md5.h
    


    
    
    int luaopen_md5_core (lua_State *L)
    
    
    Opens the library and registers the "md5" Lua functions in the given state.
    
    
    
    void md5 (const char *message, long len, char *output)
    
    
    Computes the MD5 message-digest of message.
        len is the length of message.
        output is a buffer that receives the result;
        it must have at least 16 bytes (128 bits).
    
    

    


    The following function is declared in ldes56.h
    
    

    
    
    int luaopen_des56 (lua_State *L)
    
    
    Opens the library and registers the "des56" Lua functions in the given state.
    

    




     


     


    
    
    Valid XHTML 1.0!
    
    
    $Id: manual.html,v 1.14 2008/05/12 20:51:27 carregal Exp $
    

     


     


 
genometools-1.5.1/src/external/md5-1.1.2/doc/us/md5.png000066400000000000000000000100311211610345200221610ustar00rootroot00000000000000PNG


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f'M 4CU)()455߄k,7zc3#({)32~ҩ6\H &.*ȳU+3ޝcsȦX9ӫ/a#^pp;]nwq+s uIENDB`genometools-1.5.1/src/external/md5-1.1.2/rockspec/000077500000000000000000000000001211610345200214105ustar00rootroot00000000000000genometools-1.5.1/src/external/md5-1.1.2/rockspec/md5-1.1.1-1.rockspec000066400000000000000000000013071211610345200244230ustar00rootroot00000000000000package = "MD5"
version = "1.1.1-1"
source = {
   url = "http://luaforge.net/frs/download.php/2746/md5-1.1.1.tar.gz"
}
description = {
   summary = "Basic cryptographic library",
   detailed = [[
      MD5 offers basic cryptographic facilities for Lua 5.1: a hash
      (digest) function, and a pair crypt/decrypt.
   ]],
   license = "MIT/X11",
   homepage = "http://www.keplerproject.org/md5/"
}
dependencies = {
   "lua >= 5.1"
}
build = {
   type = "make",
   variables = {
      LUA_VERSION_NUM="501",
   },
   build_variables = {
      LIB_OPTION = "$(LIBFLAG)",
      CFLAGS = "$(CFLAGS) -I$(LUA_INCDIR)",
   },
   install_variables = {
      LUA_LIBDIR = "$(LIBDIR)",
      LUA_DIR = "$(LUADIR)"
   }
}
genometools-1.5.1/src/external/md5-1.1.2/rockspec/md5-1.1.2-1.rockspec000066400000000000000000000015231211610345200244240ustar00rootroot00000000000000package = "MD5"
version = "1.1.2-1"
source = {
   url = ""
}
description = {
   summary = "Basic cryptographic library",
   detailed = [[
      MD5 offers basic cryptographic facilities for Lua 5.1:
      a hash (digest) function, a pair crypt/decrypt based on MD5 and CFB,
      and a pair crypt/decrypt based on DES with 56-bit keys.
   ]],
   license = "MIT/X11",
   homepage = "http://www.keplerproject.org/md5/"
}
dependencies = {
   "lua >= 5.1"
}
build = {
   type = "make",
   variables = {
      LUA_VERSION_NUM="501",
   },
   build_variables = {
     LIB_OPTION = "$(LIBFLAG)",
     CFLAGS = "$(CFLAGS) -I$(LUA_INCDIR)",
   },
   install_variables = {
      LUA_LIBDIR = "$(LIBDIR)",
      LUA_DIR = "$(LUADIR)"
   },
   platforms = {
     win32 = {
       build_variables = {
	 LUA_LIB = "$(LUA_LIBDIR)\\lua5.1.lib"
       }
     }
   }
}
genometools-1.5.1/src/external/md5-1.1.2/rockspec/md5-cvs-1.rockspec000066400000000000000000000015151211610345200245610ustar00rootroot00000000000000package = "MD5"
version = "cvs-1"
source = {
   cvs_tag = "HEAD",
   url = "cvs://:pserver:anonymous@cvs.luaforge.net:/cvsroot/md5"
}
description = {
   summary = "Basic cryptographic library",
   detailed = [[
      MD5 offers basic cryptographic facilities for Lua 5.1: a hash
      (digest) function, and a pair crypt/decrypt.
   ]],
   license = "MIT/X11",
   homepage = "http://www.keplerproject.org/md5/"
}
dependencies = {
   "lua >= 5.1"
}
build = {
   type = "make",
   variables = {
      LUA_VERSION_NUM="501",
   },
   build_variables = {
     LIB_OPTION = "$(LIBFLAG)",
     CFLAGS = "$(CFLAGS) -I$(LUA_INCDIR)",
   },
   install_variables = {
      LUA_LIBDIR = "$(LIBDIR)",
      LUA_DIR = "$(LUADIR)"
   },
   platforms = {
     win32 = {
       build_variables = {
	 LUA_LIB = "$(LUA_LIBDIR)\\lua5.1.lib"
       }
     }
   }
}
genometools-1.5.1/src/external/md5-1.1.2/src/000077500000000000000000000000001211610345200203665ustar00rootroot00000000000000genometools-1.5.1/src/external/md5-1.1.2/src/des56.c000066400000000000000000000357521211610345200214740ustar00rootroot00000000000000
/*
 * Fast implementation of the DES, as described in the Federal Register,
 * Vol. 40, No. 52, p. 12134, March 17, 1975.
 *
 * Stuart Levy, Minnesota Supercomputer Center, April 1988.
 * Currently (2007) slevy@ncsa.uiuc.edu
 * NCSA, University of Illinois Urbana-Champaign
 *
 * Calling sequence:
 *
 * typedef unsigned long keysched[32];
 *
 * fsetkey(key, keysched)	/ * Converts a DES key to a "key schedule" * /
 *	unsigned char	key[8];
 *	keysched	*ks;
 *
 * fencrypt(block, decrypt, keysched)	/ * En/decrypts one 64-bit block * /
 *	unsigned char	block[8];	/ * data, en/decrypted in place * /
 *	int		decrypt;	/ * 0=>encrypt, 1=>decrypt * /
 *	keysched	*ks;		/ * key schedule, as set by fsetkey * /
 *
 * Key and data block representation:
 * The 56-bit key (bits 1..64 including "parity" bits 8, 16, 24, ..., 64)
 * and the 64-bit data block (bits 1..64)
 * are each stored in arrays of 8 bytes.
 * Following the NBS numbering, the MSB has the bit number 1, so
 *  key[0] = 128*bit1 + 64*bit2 + ... + 1*bit8, ... through
 *  key[7] = 128*bit57 + 64*bit58 + ... + 1*bit64.
 * In the key, "parity" bits are not checked; their values are ignored.
 *
*/

/*
===============================================================================
License

des56.c is licensed under the terms of the MIT license reproduced below.
This means that des56.c is free software and can be used for both academic
and commercial purposes at absolutely no cost.
===============================================================================
Copyright (C) 1988 Stuart Levy

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
 */


#include "des56.h"


/*
 * Key schedule generation.
 * We begin by pointlessly permuting the 56 useful key bits into
 * two groups of 28 bits called C and D.
 * bK_C and bK_D are indexed by C and D bit numbers, respectively,
 * and give the key bit number (1..64) which should initialize that C/D bit.
 * This is the "permuted choice 1" table.
 */

static tiny bK_C[28] = {
	57, 49, 41, 33, 25, 17,  9,
	 1, 58, 50, 42, 34, 26, 18,
	10,  2, 59, 51, 43, 35, 27,
	19, 11,  3, 60, 52, 44, 36,
};
static tiny bK_D[28] = {
	63, 55, 47, 39, 31, 23, 15,
	 7, 62, 54, 46, 38, 30, 22,
	14,  6, 61, 53, 45, 37, 29,
	21, 13,  5, 28, 20, 12, 4,
};

/*
 * For speed, we invert these, building tables to map groups of
 * key bits into the corresponding C and D bits.
 * We represent C and D each as 28 contiguous bits right-justified in a
 * word, padded on the left with zeros.
 * If key byte `i' is said to contain bits Ki,0 (MSB) Ki,1 ... Ki,7 (LSB)
 * then
 *	wC_K4[i][Ki,0 Ki,1 Ki,2 Ki,3] gives the C bits for Ki,0..3,
 *	wD_K4[i][Ki,0 Ki,1 Ki,2 Ki,3] the corresponding D bits,
 *	wC_K3[i][Ki,4 Ki,5 Ki,6] the C bits for Ki,4..6,
 * and	wD_K3[i][Ki,4 Ki,5 Ki,6] the D bits for Ki,4..6.
 * Ki,7 is ignored since it is the nominal parity bit.
 * We could just use a single table for [i][Ki,0 .. Ki,6] but that
 * would take a lot of storage for such a rarely-used function.
 */

static	word32 wC_K4[8][16], wC_K3[8][8];
static	word32 wD_K4[8][16], wD_K3[8][8];

/*
 * Successive Ci and Di for the sixteen steps in the key schedule are
 * created by independent 28-bit left circular shifts on C and D.
 * The shift count varies with the step number.
 */
static tiny preshift[16] = {
	1, 1, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 1,
};

/*
 * Each step in the key schedule is generated by selecting 48 bits
 * (8 groups of 6 bits) from the appropriately shifted Ci and Di.
 * bCD_KS, indexed by the key schedule bit number, gives the bit number
 * in CD (CD1 = MSB of C, CD28 = LSB of C, CD29 = MSB of D, CD56 = LSB of D)
 * which determines that bit of the key schedule.
 * Note that only C bits (1..28) appear in the first (upper) 24 bits of
 * the key schedule, and D bits (29..56) in the second (lower) 24 bits.
 * This is the "permuted-choice-2" table.
 */

static tiny bCD_KS[48] = {
	14, 17, 11, 24,  1,  5,
	3,  28, 15,  6, 21, 10,
	23, 19, 12,  4, 26,  8,
	16,  7, 27, 20, 13,  2,
	41, 52, 31, 37, 47, 55,
	30, 40, 51, 45, 33, 48,
	44, 49, 39, 56, 34, 53,
	46, 42, 50, 36, 29, 32,
};

/*
 * We invert bCD_KS into a pair of tables which map groups of 4
 * C or D bits into corresponding key schedule bits.
 * We represent each step of the key schedule as 8 groups of 8 bits,
 * with the 6 real bits right-justified in each 8-bit group.
 * hKS_C4[i][C4i+1 .. C4i+4] gives the bits in the high order (first four)
 * key schedule "bytes" which correspond to C bits 4i+1 .. 4i+4.
 * lKS_D4[i][D4i+1 .. D4i+4] gives the appropriate bits in the latter (last 4)
 * key schedule bytes, from the corresponding D bits.
 */

static word32 hKS_C4[7][16];
static word32 lKS_D4[7][16];

/*
 * Encryption/decryption.
 * Before beginning, and after ending, we perform another useless permutation
 * on the bits in the data block.
 *
 * The initial permutation and its inverse, final permutation
 * are too simple to need a table for.	If we break the input I1 .. I64 into
 * 8-bit chunks I0,0 I0,1 ... I0,7 I1,0 I1,1 ... I7,7
 * then the initial permutation sets LR as follows:
 * L = I7,1 I6,1 I5,1 ... I0,1	I7,3 I6,3 ... I0,3  I7,5 ... I0,5  I7,7 ... I0,7
 * and
 * R = I7,0 I6,0 I5,0 ... I0,0	I7,2 I6,2 ... I0,2  I7,4 ... I0,4  I7,6 ... I0,6
 *
 * If we number the bits in the final LR similarly,
 * L = L0,0 L0,1 ... L3,7  R = R0,0 R0,1 ... R3,7
 * then the output is
 * O = R0,7 L0,7 R1,7 L1,7 ... R3,7 L3,7 R0,6 L0,6 ... L3,6 R0,5 ... R3,0 L3,0
 *
 * To speed I => LR shuffling we use an array of 32-bit values indexed by
 * 8-bit input bytes.
 * wL_I8[ 0 I0,1 0 I0,3 0 I0,5 0 I0,7 ] = the corresponding L bits.
 * Other R and L bits are derived from wL_I8 by shifting.
 *
 * To speed LR => O shuffling, an array of 32-bit values indexed by 4-bit lumps:
 * wO_L4[ L0,4 L0,5 L0,6 L0,7 ] = the corresponding high-order 32 O bits.
 */

static word32 wL_I8[0x55 + 1];
static word32 wO_L4[16];

/*
 * Core of encryption/decryption.
 * In each key schedule stage, we:
 *	take 8 overlapping groups of 6 bits each from R
 *	   (the NBS tabulates the bit selections in the E table,
 *	    but it's so simple we just use shifting to get the right bits)
 *	XOR each group with the corresponding bits from the key schedule
 *	Use the resulting 6 bits as an index into the appropriate S table
 *	   (there are 8 such tables, one per group of 6 bits)
 *	Each S entry yields 4 bits.
 *	The 8 groups of 4 bits are catenated into a 32-bit value.
 *	Those 32 bits are permuted according to the P table.
 *	Finally the permuted 32-bit value is XORed with L and becomes
 *	the R value for the next stage, while the previous R becomes the new L.
 *
 * Here, we merge the P permutation with the S tables by making the
 * S entries be 32-bit masks, already suitably permuted.
 * Also, the bits in each six-bit group must be permuted before use as
 * an index into the NBS-tabulated S tables.
 * We rearrange entries in wPS so that natural bit order can be used.
 */

static word32 wPS[8][64];

static tiny P[32] = {
	16,  7, 20, 21,
	29, 12, 28, 17,
	 1, 15, 23, 26,
	 5, 18, 31, 10,
	 2,  8, 24, 14,
	32, 27,  3,  9,
	19, 13, 30,  6,
	22, 11,  4, 25,
};

static tiny S[8][64] = {
     {
	14, 4,13, 1, 2,15,11, 8, 3,10, 6,12, 5, 9, 0, 7,
	 0,15, 7, 4,14, 2,13, 1,10, 6,12,11, 9, 5, 3, 8,
	 4, 1,14, 8,13, 6, 2,11,15,12, 9, 7, 3,10, 5, 0,
	15,12, 8, 2, 4, 9, 1, 7, 5,11, 3,14,10, 0, 6,13,
     },

     {
	15, 1, 8,14, 6,11, 3, 4, 9, 7, 2,13,12, 0, 5,10,
	 3,13, 4, 7,15, 2, 8,14,12, 0, 1,10, 6, 9,11, 5,
	 0,14, 7,11,10, 4,13, 1, 5, 8,12, 6, 9, 3, 2,15,
	13, 8,10, 1, 3,15, 4, 2,11, 6, 7,12, 0, 5,14, 9,
     },

     {
	10, 0, 9,14, 6, 3,15, 5, 1,13,12, 7,11, 4, 2, 8,
	13, 7, 0, 9, 3, 4, 6,10, 2, 8, 5,14,12,11,15, 1,
	13, 6, 4, 9, 8,15, 3, 0,11, 1, 2,12, 5,10,14, 7,
	 1,10,13, 0, 6, 9, 8, 7, 4,15,14, 3,11, 5, 2,12,
     },

     {
	 7,13,14, 3, 0, 6, 9,10, 1, 2, 8, 5,11,12, 4,15,
	13, 8,11, 5, 6,15, 0, 3, 4, 7, 2,12, 1,10,14, 9,
	10, 6, 9, 0,12,11, 7,13,15, 1, 3,14, 5, 2, 8, 4,
	 3,15, 0, 6,10, 1,13, 8, 9, 4, 5,11,12, 7, 2,14,
     },

     {
	 2,12, 4, 1, 7,10,11, 6, 8, 5, 3,15,13, 0,14, 9,
	14,11, 2,12, 4, 7,13, 1, 5, 0,15,10, 3, 9, 8, 6,
	 4, 2, 1,11,10,13, 7, 8,15, 9,12, 5, 6, 3, 0,14,
	11, 8,12, 7, 1,14, 2,13, 6,15, 0, 9,10, 4, 5, 3,
     },

     {
	12, 1,10,15, 9, 2, 6, 8, 0,13, 3, 4,14, 7, 5,11,
	10,15, 4, 2, 7,12, 9, 5, 6, 1,13,14, 0,11, 3, 8,
	 9,14,15, 5, 2, 8,12, 3, 7, 0, 4,10, 1,13,11, 6,
	 4, 3, 2,12, 9, 5,15,10,11,14, 1, 7, 6, 0, 8,13,
     },

     {
	 4,11, 2,14,15, 0, 8,13, 3,12, 9, 7, 5,10, 6, 1,
	13, 0,11, 7, 4, 9, 1,10,14, 3, 5,12, 2,15, 8, 6,
	 1, 4,11,13,12, 3, 7,14,10,15, 6, 8, 0, 5, 9, 2,
	 6,11,13, 8, 1, 4,10, 7, 9, 5, 0,15,14, 2, 3,12,
     },

     {
	13, 2, 8, 4, 6,15,11, 1,10, 9, 3,14, 5, 0,12, 7,
	 1,15,13, 8,10, 3, 7, 4,12, 5, 6,11, 0,14, 9, 2,
	 7,11, 4, 1, 9,12,14, 2, 0, 6,10,13,15, 3, 5, 8,
	 2, 1,14, 7, 4,10, 8,13,15,12, 9, 0, 3, 5, 6,11,
     },
};

static void buildtables( void )
{
	register int i, j;
	register word32 v;
	word32 wC_K[64], wD_K[64];
	word32 hKS_C[28], lKS_D[28];
	int Smap[64];
	word32 wP[32];

#if USG
#  define	ZERO(array)	memset((char *)(array), '\0', sizeof(array))
#else
# if BSD
#  define	ZERO(array)	bzero((char *)(array), sizeof(array))
# else 
#  define	ZERO(array)	{ register word32 *p = (word32 *)(array); \
				  i = sizeof(array) / sizeof(*p); \
				  do { *p++ = 0; } while(--i > 0); \
				}
# endif 
#endif 


	/* Invert permuted-choice-1 (key => C,D) */

	ZERO(wC_K);
	ZERO(wD_K);
	v = 1;
	for(j = 28; --j >= 0; ) {
		wC_K[ bK_C[j] - 1 ] = wD_K[ bK_D[j] - 1 ] = v;
		v += v; 	/* (i.e. v <<= 1) */
	}

	for(i = 0; i < 64; i++) {
	    int t = 8 >> (i & 3);
	    for(j = 0; j < 16; j++) {
		if(j & t) {
		    wC_K4[i >> 3][j] |= wC_K[i];
		    wD_K4[i >> 3][j] |= wD_K[i];
		    if(j < 8) {
			wC_K3[i >> 3][j] |= wC_K[i + 3];
			wD_K3[i >> 3][j] |= wD_K[i + 3];
		    }
		}
	    }
	    /* Generate the sequence 0,1,2,3, 8,9,10,11, ..., 56,57,58,59. */
	    if(t == 1) i += 4;
	}

	/* Invert permuted-choice-2 */

	ZERO(hKS_C);
	ZERO(lKS_D);
	v = 1;
	for(i = 24; (i -= 6) >= 0; ) {
	    j = i+5;
	    do {
		hKS_C[ bCD_KS[j] - 1 ] = lKS_D[ bCD_KS[j+24] - 28 - 1 ] = v;
		v += v; 	/* Like v <<= 1 but may be faster */
	    } while(--j >= i);
	    v <<= 2;		/* Keep byte aligned */
	}

	for(i = 0; i < 28; i++) {
	    v = 8 >> (i & 3);
	    for(j = 0; j < 16; j++) {
		if(j & v) {
		    hKS_C4[i >> 2][j] |= hKS_C[i];
		    lKS_D4[i >> 2][j] |= lKS_D[i];
		}
	    }
	}

	/* Initial permutation */

	for(i = 0; i <= 0x55; i++) {
	    v = 0;
	    if(i & 64) v =  (word32) 1 << 24;
	    if(i & 16) v |= (word32) 1 << 16;
	    if(i & 4)  v |= (word32) 1 << 8;
	    if(i & 1)  v |= 1;
	    wL_I8[i] = v;
	}

	/* Final permutation */

	for(i = 0; i < 16; i++) {
	    v = 0;
	    if(i & 1) v = (word32) 1 << 24;
	    if(i & 2) v |= (word32) 1 << 16;
	    if(i & 4) v |= (word32) 1 << 8;
	    if(i & 8) v |= (word32) 1;
	    wO_L4[i] = v;
	}

	/* Funny bit rearrangement on second index into S tables */

	for(i = 0; i < 64; i++) {
		Smap[i] = (i & 0x20) | (i & 1) << 4 | (i & 0x1e) >> 1;
	}

	/* Invert permutation P into mask indexed by R bit number */

	v = 1;
	for(i = 32; --i >= 0; ) {
		wP[ P[i] - 1 ] = v;
		v += v;
	}

	/* Build bit-mask versions of S tables, indexed in natural bit order */

	for(i = 0; i < 8; i++) {
	    for(j = 0; j < 64; j++) {
		int k, t;

		t = S[i][ Smap[j] ];
		for(k = 0; k < 4; k++) {
		    if(t & 8)
			wPS[i][j] |= wP[4*i + k];
		    t += t;
		}
	    }
	}
}


void fsetkey(char key[8], keysched *ks)
{
	register int i;
	register word32 C, D;
	static int built = 0;

	if(!built) {
		buildtables();
		built = 1;
	}

	C = D = 0;
	for(i = 0; i < 8; i++) {
		register int v;

		v = key[i] >> 1;	/* Discard "parity" bit */
		C |= wC_K4[i][(v>>3) & 15] | wC_K3[i][v & 7];
		D |= wD_K4[i][(v>>3) & 15] | wD_K3[i][v & 7];
	}

	/*
	 * C and D now hold the suitably right-justified
	 * 28 permuted key bits each.
	 */
	for(i = 0; i < 16; i++) {
#ifdef CRAY
#define choice2(x, v)  x[6][v&15] | x[5][(v>>4)&15] | x[4][(v>>8)&15] | \
		    x[3][(v>>12)&15] | x[2][(v>>16)&15] | x[1][(v>>20)&15] | \
		    x[0][(v>>24)&15]
#else
		register word32 *ap;

#  define choice2(x, v)  ( \
		    ap = &(x)[0][0], \
		    ap[16*6 + (v&15)] | \
		    ap[16*5 + ((v>>4)&15)]  | ap[16*4 + ((v>>8)&15)]  | \
		    ap[16*3 + ((v>>12)&15)] | ap[16*2 + ((v>>16)&15)] | \
		    ap[16*1 + ((v>>20)&15)] | ap[16*0 + ((v>>24)&15)] )
#endif 


		/* 28-bit left circular shift */
		C <<= preshift[i];
		C = ((C >> 28) & 3) | (C & (((word32)1<<28) - 1));
		ks->KS[i].h = choice2(hKS_C4, C);

		D <<= preshift[i];
		D = ((D >> 28) & 3) | (D & (((word32)1<<28) - 1));
		ks->KS[i].l = choice2(lKS_D4, D);
	}
}

void
fencrypt(char block[8], int decrypt, keysched *ks)
{
	int i;
	register word32 L, R;
	register struct keystage *ksp;
	register word32 *ap;

	/* Initial permutation */

	L = R = 0;
	i = 7;
	ap = wL_I8;
	do {
		register int v;

		v = block[i];	/* Could optimize according to ENDIAN */
		L = ap[v & 0x55] | (L << 1);
		R = ap[(v >> 1) & 0x55] | (R << 1);
	} while(--i >= 0);

	if(decrypt) {
		ksp = &ks->KS[15];
	} else {
		ksp = &ks->KS[0];
	}

#ifdef CRAY
#  define PS(i,j)	wPS[i][j]
#else 
#  define PS(i,j)	ap[64*(i) + (j)]
	ap = &wPS[0][0];
#endif 

	i = 16;
	do {
		register word32 k, tR;

		tR = (R >> 15) | (R << 17);

		k = ksp->h;
		L ^= PS(0, ((tR >> 12) ^ (k >> 24)) & 63)
		   | PS(1, ((tR >> 8) ^ (k >> 16)) & 63)
		   | PS(2, ((tR >> 4) ^ (k >> 8)) & 63)
		   | PS(3, (tR ^ k) & 63);

		k = ksp->l;
		L ^= PS(4, ((R >> 11) ^ (k >> 24)) & 63)
		   | PS(5, ((R >> 7) ^ (k >> 16)) & 63)
		   | PS(6, ((R >> 3) ^ (k >> 8)) & 63)
		   | PS(7, ((tR >> 16) ^ k) & 63);

		tR = L;
		L = R;
		R = tR;


		if(decrypt)
			ksp--;
		else
			ksp++;
	} while(--i > 0);
	{
		register word32 t;

#ifdef CRAY
# define FP(k)	(wO_L4[ (L >> (k)) & 15 ] << 1 | wO_L4[ (R >> (k)) & 15 ])
#else 
# define FP(k)	(ap[ (L >> (k)) & 15 ] << 1 | ap[ (R >> (k)) & 15 ])

		ap = wO_L4;
#endif 

		t = FP(0) | (FP(8) | (FP(16) | (FP(24) << 2)) << 2) << 2;
		R = FP(4) | (FP(12) | (FP(20) | (FP(28) << 2)) << 2) << 2;
		L = t;
	}
	{
		register word32 t;
		register char *bp;

		bp = &block[7];
		t = R;
		*bp = t & 255;
		*--bp = (t >>= 8) & 255;
		*--bp = (t >>= 8) & 255;
		*--bp = (t >> 8) & 255;
		t = L;
		*--bp = t & 255;
		*--bp = (t >>= 8) & 255;
		*--bp = (t >>= 8) & 255;
		*--bp = (t >> 8) & 255;
	}
}

genometools-1.5.1/src/external/md5-1.1.2/src/des56.def000066400000000000000000000001121211610345200217660ustar00rootroot00000000000000LIBRARY des56.dll
DESCRIPTION "DES56"
VERSION 1.1.2
EXPORTS
luaopen_des56
genometools-1.5.1/src/external/md5-1.1.2/src/des56.h000066400000000000000000000055201211610345200214670ustar00rootroot00000000000000#ifndef DES56_H
#define DES56_H 1
/*
 * Fast implementation of the DES, as described in the Federal Register,
 * Vol. 40, No. 52, p. 12134, March 17, 1975.
 *
 * Stuart Levy, Minnesota Supercomputer Center, April 1988.
 * Currently (2007) slevy@ncsa.uiuc.edu
 * NCSA, University of Illinois Urbana-Champaign
 *
 * Calling sequence:
 *
 * typedef unsigned long keysched[32];
 *
 * fsetkey(key, keysched)	/ * Converts a DES key to a "key schedule" * /
 *	unsigned char	key[8];
 *	keysched	*ks;
 *
 * fencrypt(block, decrypt, keysched)	/ * En/decrypts one 64-bit block * /
 *	unsigned char	block[8];	/ * data, en/decrypted in place * /
 *	int		decrypt;	/ * 0=>encrypt, 1=>decrypt * /
 *	keysched	*ks;		/ * key schedule, as set by fsetkey * /
 *
 * Key and data block representation:
 * The 56-bit key (bits 1..64 including "parity" bits 8, 16, 24, ..., 64)
 * and the 64-bit data block (bits 1..64)
 * are each stored in arrays of 8 bytes.
 * Following the NBS numbering, the MSB has the bit number 1, so
 *  key[0] = 128*bit1 + 64*bit2 + ... + 1*bit8, ... through
 *  key[7] = 128*bit57 + 64*bit58 + ... + 1*bit64.
 * In the key, "parity" bits are not checked; their values are ignored.
 *
*/

/*
===============================================================================
License

des56.c is licensed under the terms of the MIT license reproduced below.
This means that des56.c is free software and can be used for both academic
and commercial purposes at absolutely no cost.
===============================================================================
Copyright (C) 1988 Stuart Levy

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
 */

typedef unsigned long word32;
typedef unsigned char tiny;

typedef struct keysched {
	struct keystage {
		word32 h, l;
	} KS[16];
} keysched;

extern void fsetkey(char key[8], keysched *ks);

extern void fencrypt(char block[8], int decrypt, keysched *ks);

#endif /*DES56_H*/
genometools-1.5.1/src/external/md5-1.1.2/src/ldes56.c000066400000000000000000000063461211610345200216450ustar00rootroot00000000000000#include 
#include 

#include "des56.h"

#include "lua.h"
#include "lauxlib.h"

#include "ldes56.h"

static int des56_decrypt( lua_State *L )
{
  char* decypheredText;
  keysched KS;
  int rel_index, abs_index;
  size_t cypherlen;
  const char *cypheredText = 
    luaL_checklstring( L, 1, &cypherlen );
  const char *key = luaL_optstring( L, 2, NULL );
  int padinfo;

  padinfo = cypheredText[cypherlen-1];
  cypherlen--;

  /* Aloca array */
  decypheredText = 
    (char *) malloc( (cypherlen+1) * sizeof(char));
  if(decypheredText == NULL) {
    lua_pushstring(L, "Error decrypting file. Not enough memory.");
    lua_error(L);
  }

  /* Inicia decifragem */
  if (key && strlen(key) >= 8)
  {
    char k[8];
    int i;

    for (i=0; i<8; i++)
      k[i] = (unsigned char)key[i];
    fsetkey(k, &KS);
  } else {
    lua_pushstring(L, "Error decrypting file. Invalid key.");
    lua_error(L);
  }

  rel_index = 0;
  abs_index = 0;

  while (abs_index < (int) cypherlen)
  {
    decypheredText[abs_index] = cypheredText[abs_index];
    abs_index++;
    rel_index++;
    if( rel_index == 8 )
    {
      rel_index = 0;
      fencrypt(&(decypheredText[abs_index - 8]), 1, &KS);
    }
  }
  decypheredText[abs_index] = 0;

  lua_pushlstring(L, decypheredText, (abs_index-padinfo));
  free( decypheredText );
  return 1;
}

static int des56_crypt( lua_State *L )
{
  char *cypheredText;
  keysched KS;
  int rel_index, pad, abs_index;
  size_t plainlen;
  const char *plainText = luaL_checklstring( L, 1, &plainlen );
  const char *key = luaL_optstring( L, 2, NULL );

  cypheredText = (char *) malloc( (plainlen+8) * sizeof(char));
  if(cypheredText == NULL) {
    lua_pushstring(L, "Error encrypting file. Not enough memory."); 
    lua_error(L);
  }

  if (key && strlen(key) >= 8)
  {
    char k[8];
    int i;

    for (i=0; i<8; i++)
      k[i] = (unsigned char)key[i];
    fsetkey(k, &KS);
  } else {
    lua_pushstring(L, "Error encrypting file. Invalid key.");
    lua_error(L);
  }

  rel_index = 0;
  abs_index = 0;
  while (abs_index < (int) plainlen) {
    cypheredText[abs_index] = plainText[abs_index];
    abs_index++;
    rel_index++;
    if( rel_index == 8 ) {
      rel_index = 0;
      fencrypt(&(cypheredText[abs_index - 8]), 0, &KS);
    }
  }

  pad = 0;
  if(rel_index != 0) { /* Pads remaining bytes with zeroes */
    while(rel_index < 8)
    {
      pad++;
      cypheredText[abs_index++] = 0;
      rel_index++;
    }
    fencrypt(&(cypheredText[abs_index - 8]), 0, &KS);
  }
  cypheredText[abs_index] = pad;

  lua_pushlstring( L, cypheredText, abs_index+1 );
  free( cypheredText );
  return 1;
}

/*
** Assumes the table is on top of the stack.
*/
static void set_info (lua_State *L) {
	lua_pushliteral (L, "_COPYRIGHT");
	lua_pushliteral (L, "Copyright (C) 2007 PUC-Rio");
	lua_settable (L, -3);
	lua_pushliteral (L, "_DESCRIPTION");
	lua_pushliteral (L, "DES 56 cryptographic facilities for Lua");
	lua_settable (L, -3);
	lua_pushliteral (L, "_VERSION");
	lua_pushliteral (L, "DES56 1.1.2");
	lua_settable (L, -3);
}

static const struct luaL_reg des56lib[] = {
  {"crypt", des56_crypt},
  {"decrypt", des56_decrypt},
  {NULL, NULL},
};

int luaopen_des56 (lua_State *L) {
  luaL_openlib (L, "des56", des56lib, 0);
  set_info (L);
  return 1;
}


genometools-1.5.1/src/external/md5-1.1.2/src/ldes56.h000066400000000000000000000000421211610345200216350ustar00rootroot00000000000000int luaopen_des56 (lua_State *L);
genometools-1.5.1/src/external/md5-1.1.2/src/md5.c000066400000000000000000000144201211610345200212200ustar00rootroot00000000000000/**
*  $Id: md5.c,v 1.2 2008/03/24 20:59:12 mascarenhas Exp $
*  Hash function MD5
*  @author  Marcela Ozorio Suarez, Roberto I.
*/


#include 

#include "md5.h"


#define WORD 32
#define MASK 0xFFFFFFFF
#if __STDC_VERSION__ >= 199901L
#include 
typedef uint32_t WORD32;
#else
typedef unsigned int WORD32;
#endif


/**
*  md5 hash function.
*  @param message: aribtary string.
*  @param len: message length.
*  @param output: buffer to receive the hash value. Its size must be
*  (at least) HASHSIZE.
*/
void md5 (const char *message, long len, char *output);



/*
** Realiza a rotacao no sentido horario dos bits da variavel 'D' do tipo WORD32.
** Os bits sao deslocados de 'num' posicoes
*/
#define rotate(D, num)  (D<>(WORD-num))

/*Macros que definem operacoes relizadas pelo algoritmo  md5 */
#define F(x, y, z) (((x) & (y)) | ((~(x)) & (z)))
#define G(x, y, z) (((x) & (z)) | ((y) & (~(z))))
#define H(x, y, z) ((x) ^ (y) ^ (z))
#define I(x, y, z) ((y) ^ ((x) | (~(z))))


/*vetor de numeros utilizados pelo algoritmo md5 para embaralhar bits */
static const WORD32 T[64]={
                     0xd76aa478, 0xe8c7b756, 0x242070db, 0xc1bdceee,
                     0xf57c0faf, 0x4787c62a, 0xa8304613, 0xfd469501,
                     0x698098d8, 0x8b44f7af, 0xffff5bb1, 0x895cd7be,
                     0x6b901122, 0xfd987193, 0xa679438e, 0x49b40821,
                     0xf61e2562, 0xc040b340, 0x265e5a51, 0xe9b6c7aa,
                     0xd62f105d, 0x02441453, 0xd8a1e681, 0xe7d3fbc8,
                     0x21e1cde6, 0xc33707d6, 0xf4d50d87, 0x455a14ed,
                     0xa9e3e905, 0xfcefa3f8, 0x676f02d9, 0x8d2a4c8a,
                     0xfffa3942, 0x8771f681, 0x6d9d6122, 0xfde5380c,
                     0xa4beea44, 0x4bdecfa9, 0xf6bb4b60, 0xbebfbc70,
                     0x289b7ec6, 0xeaa127fa, 0xd4ef3085, 0x04881d05,
                     0xd9d4d039, 0xe6db99e5, 0x1fa27cf8, 0xc4ac5665,
                     0xf4292244, 0x432aff97, 0xab9423a7, 0xfc93a039,
                     0x655b59c3, 0x8f0ccc92, 0xffeff47d, 0x85845dd1,
                     0x6fa87e4f, 0xfe2ce6e0, 0xa3014314, 0x4e0811a1,
                     0xf7537e82, 0xbd3af235, 0x2ad7d2bb, 0xeb86d391
};


static void word32tobytes (const WORD32 *input, char *output) {
  int j = 0;
  while (j<4*4) {
    WORD32 v = *input++;
    output[j++] = (char)(v & 0xff); v >>= 8;
    output[j++] = (char)(v & 0xff); v >>= 8;
    output[j++] = (char)(v & 0xff); v >>= 8;
    output[j++] = (char)(v & 0xff);
  }
}


static void inic_digest(WORD32 *d) {
  d[0] = 0x67452301;
  d[1] = 0xEFCDAB89;
  d[2] = 0x98BADCFE;
  d[3] = 0x10325476;
}


/*funcao que implemeta os quatro passos principais do algoritmo MD5 */
static void digest(const WORD32 *m, WORD32 *d) {
  int j;
  /*MD5 PASSO1 */
  for (j=0; j<4*4; j+=4) {
    d[0] = d[0]+ F(d[1], d[2], d[3])+ m[j] + T[j];       d[0]=rotate(d[0], 7);
    d[0]+=d[1];
    d[3] = d[3]+ F(d[0], d[1], d[2])+ m[(j)+1] + T[j+1]; d[3]=rotate(d[3], 12);
    d[3]+=d[0];
    d[2] = d[2]+ F(d[3], d[0], d[1])+ m[(j)+2] + T[j+2]; d[2]=rotate(d[2], 17);
    d[2]+=d[3];
    d[1] = d[1]+ F(d[2], d[3], d[0])+ m[(j)+3] + T[j+3]; d[1]=rotate(d[1], 22);
    d[1]+=d[2];
  }
  /*MD5 PASSO2 */
  for (j=0; j<4*4; j+=4) {
    d[0] = d[0]+ G(d[1], d[2], d[3])+ m[(5*j+1)&0x0f] + T[(j-1)+17];
    d[0] = rotate(d[0],5);
    d[0]+=d[1];
    d[3] = d[3]+ G(d[0], d[1], d[2])+ m[((5*(j+1)+1)&0x0f)] + T[(j+0)+17];
    d[3] = rotate(d[3], 9);
    d[3]+=d[0];
    d[2] = d[2]+ G(d[3], d[0], d[1])+ m[((5*(j+2)+1)&0x0f)] + T[(j+1)+17];
    d[2] = rotate(d[2], 14);
    d[2]+=d[3];
    d[1] = d[1]+ G(d[2], d[3], d[0])+ m[((5*(j+3)+1)&0x0f)] + T[(j+2)+17];
    d[1] = rotate(d[1], 20);
    d[1]+=d[2];
  }
  /*MD5 PASSO3 */
  for (j=0; j<4*4; j+=4) {
    d[0] = d[0]+ H(d[1], d[2], d[3])+ m[(3*j+5)&0x0f] + T[(j-1)+33];
    d[0] = rotate(d[0], 4);
    d[0]+=d[1];
    d[3] = d[3]+ H(d[0], d[1], d[2])+ m[(3*(j+1)+5)&0x0f] + T[(j+0)+33];
    d[3] = rotate(d[3], 11);
    d[3]+=d[0];
    d[2] = d[2]+ H(d[3], d[0], d[1])+ m[(3*(j+2)+5)&0x0f] + T[(j+1)+33];
    d[2] = rotate(d[2], 16);
    d[2]+=d[3];
    d[1] = d[1]+ H(d[2], d[3], d[0])+ m[(3*(j+3)+5)&0x0f] + T[(j+2)+33];
    d[1] = rotate(d[1], 23);
    d[1]+=d[2];
  }
  /*MD5 PASSO4 */
  for (j=0; j<4*4; j+=4) {
    d[0] = d[0]+ I(d[1], d[2], d[3])+ m[(7*j)&0x0f] + T[(j-1)+49];
    d[0] = rotate(d[0], 6);
    d[0]+=d[1];
    d[3] = d[3]+ I(d[0], d[1], d[2])+ m[(7*(j+1))&0x0f] + T[(j+0)+49];
    d[3] = rotate(d[3], 10);
    d[3]+=d[0];
    d[2] = d[2]+ I(d[3], d[0], d[1])+ m[(7*(j+2))&0x0f] + T[(j+1)+49];
    d[2] = rotate(d[2], 15);
    d[2]+=d[3];
    d[1] = d[1]+ I(d[2], d[3], d[0])+ m[(7*(j+3))&0x0f] + T[(j+2)+49];
    d[1] = rotate(d[1], 21);
    d[1]+=d[2];
  }
}


static void bytestoword32 (WORD32 *x, const char *pt) {
  int i;
  for (i=0; i<16; i++) {
    int j=i*4;
    x[i] = (((WORD32)(unsigned char)pt[j+3] << 8 |
           (WORD32)(unsigned char)pt[j+2]) << 8 |
           (WORD32)(unsigned char)pt[j+1]) << 8 |
           (WORD32)(unsigned char)pt[j];
  }

}


static void put_length(WORD32 *x, long len) {
  /* in bits! */
  x[14] = (WORD32)((len<<3) & MASK);
  x[15] = (WORD32)(len>>(32-3) & 0x7);
}


/*
** returned status:
*  0 - normal message (full 64 bytes)
*  1 - enough room for 0x80, but not for message length (two 4-byte words)
*  2 - enough room for 0x80 plus message length (at least 9 bytes free)
*/
static int converte (WORD32 *x, const char *pt, int num, int old_status) {
  int new_status = 0;
  char buff[64];
  if (num<64) {
    memcpy(buff, pt, num);  /* to avoid changing original string */
    memset(buff+num, 0, 64-num);
    if (old_status == 0)
      buff[num] = '\200';
    new_status = 1;
    pt = buff;
  }
  bytestoword32(x, pt);
  if (num <= (64 - 9))
    new_status = 2;
  return new_status;
}



void md5 (const char *message, long len, char *output) {
  WORD32 d[4];
  int status = 0;
  long i = 0;
  inic_digest(d);
  while (status != 2) {
    WORD32 d_old[4];
    WORD32 wbuff[16];
    int numbytes = (len-i >= 64) ? 64 : len-i;
    /*salva os valores do vetor digest*/
    d_old[0]=d[0]; d_old[1]=d[1]; d_old[2]=d[2]; d_old[3]=d[3];
    status = converte(wbuff, message+i, numbytes, status);
    if (status == 2) put_length(wbuff, len);
    digest(wbuff, d);
    d[0]+=d_old[0]; d[1]+=d_old[1]; d[2]+=d_old[2]; d[3]+=d_old[3];
    i += numbytes;
  }
  word32tobytes(d, output);
}

genometools-1.5.1/src/external/md5-1.1.2/src/md5.def000066400000000000000000000001151211610345200215300ustar00rootroot00000000000000LIBRARY core.dll
DESCRIPTION "LuaMD5"
VERSION 1.1.2
EXPORTS
luaopen_md5_core
genometools-1.5.1/src/external/md5-1.1.2/src/md5.h000066400000000000000000000004611211610345200212250ustar00rootroot00000000000000/**
*  $Id: md5.h,v 1.2 2006/03/03 15:04:49 tomas Exp $
*  Cryptographic module for Lua.
*  @author  Roberto Ierusalimschy
*/


#ifndef md5_h
#define md5_h

#include 


#define HASHSIZE       16

void md5 (const char *message, long len, char *output);
int luaopen_md5_core (lua_State *L);


#endif
genometools-1.5.1/src/external/md5-1.1.2/src/md5lib.c000066400000000000000000000124161211610345200217120ustar00rootroot00000000000000/**
*  $Id: md5lib.c,v 1.10 2008/05/12 20:51:27 carregal Exp $
*  Cryptographic and Hash functions for Lua
*  @author  Roberto Ierusalimschy
*/


#include 
#include 
#include 

#include 
#include 

#if ! defined (LUA_VERSION_NUM) || LUA_VERSION_NUM < 501
#include "compat-5.1.h"
#endif

#include "md5.h"


/**
*  Hash function. Returns a hash for a given string.
*  @param message: arbitrary binary string.
*  @return  A 128-bit hash string.
*/
static int lmd5 (lua_State *L) {
  char buff[16];
  size_t l;
  const char *message = luaL_checklstring(L, 1, &l);
  md5(message, l, buff);
  lua_pushlstring(L, buff, 16L);
  return 1;
}


/**
*  X-Or. Does a bit-a-bit exclusive-or of two strings.
*  @param s1: arbitrary binary string.
*  @param s2: arbitrary binary string with same length as s1.
*  @return  a binary string with same length as s1 and s2,
*   where each bit is the exclusive-or of the corresponding bits in s1-s2.
*/
static int ex_or (lua_State *L) {
  size_t l1, l2;
  const char *s1 = luaL_checklstring(L, 1, &l1);
  const char *s2 = luaL_checklstring(L, 2, &l2);
  luaL_Buffer b;
  luaL_argcheck( L, l1 == l2, 2, "lengths must be equal" );
  luaL_buffinit(L, &b);
  while (l1--) luaL_putchar(&b, (*s1++)^(*s2++));
  luaL_pushresult(&b);
  return 1;
}


static void checkseed (lua_State *L) {
  if (lua_isnone(L, 3)) {  /* no seed? */
    time_t tm = time(NULL);  /* for `random' seed */
    lua_pushlstring(L, (char *)&tm, sizeof(tm));
  }
}


#define MAXKEY	256
#define BLOCKSIZE	16



static int initblock (lua_State *L, const char *seed, int lseed, char *block) {
  size_t lkey;
  const char *key = luaL_checklstring(L, 2, &lkey);
  if (lkey > MAXKEY)
    luaL_error(L, "key too long (> %d)", MAXKEY);
  memset(block, 0, BLOCKSIZE);
  memcpy(block, seed, lseed);
  memcpy(block+BLOCKSIZE, key, lkey);
  return (int)lkey+BLOCKSIZE;
}


static void codestream (lua_State *L, const char *msg, size_t lmsg,
                                      char *block, int lblock) {
  luaL_Buffer b;
  luaL_buffinit(L, &b);
  while (lmsg > 0) {
    char code[BLOCKSIZE];
    int i;
    md5(block, lblock, code);
    for (i=0; i 0; i++, lmsg--)
      code[i] ^= *msg++;
    luaL_addlstring(&b, code, i); 
    memcpy(block, code, i); /* update seed */
  }
  luaL_pushresult(&b);
}


static void decodestream (lua_State *L, const char *cypher, size_t lcypher,
                          char *block, int lblock) {
  luaL_Buffer b;
  luaL_buffinit(L, &b);
  while (lcypher > 0) {
    char code[BLOCKSIZE];
    int i;
    md5(block, lblock, code);  /* update seed */
    for (i=0; i 0; i++, lcypher--)
      code[i] ^= *cypher++;
    luaL_addlstring(&b, code, i); 
    memcpy(block, cypher-i, i);
  }
  luaL_pushresult(&b);
}


/**
*  Encrypts a string. Uses the hash function md5 in CFB (Cipher-feedback
*  mode).
*  @param message: arbitrary binary string to be encrypted.
*  @param key: arbitrary binary string to be used as a key.
*  @param [seed]: optional arbitrary binary string to be used as a seed.
*  if no seed is provided, the function uses the result of
*  time() as a seed.  
*  @return  The cyphertext (as a binary string).
*/
static int crypt (lua_State *L) {
  size_t lmsg;
  const char *msg = luaL_checklstring(L, 1, &lmsg);
  size_t lseed;
  const char *seed;
  int lblock;
  char block[BLOCKSIZE+MAXKEY];
  checkseed(L);
  seed = luaL_checklstring(L, 3, &lseed);
  if (lseed > BLOCKSIZE)
    luaL_error(L, "seed too long (> %d)", BLOCKSIZE);
  /* put seed and seed length at the beginning of result */
  block[0] = (char)lseed;
  memcpy(block+1, seed, lseed);
  lua_pushlstring(L, block, lseed+1);  /* to concat with result */
  lblock = initblock(L, seed, lseed, block);
  codestream(L, msg, lmsg, block, lblock);
  lua_concat(L, 2);
  return 1;
}


/**
*  Decrypts a string. For any message, key, and seed, we have that
*  decrypt(crypt(msg, key, seed), key) == msg.
*  @param cyphertext: message to be decrypted (this must be the result of
   a previous call to crypt.
*  @param key: arbitrary binary string to be used as a key.
*  @return  The plaintext.
*/
static int decrypt (lua_State *L) {
  size_t lcyphertext;
  const char *cyphertext = luaL_checklstring(L, 1, &lcyphertext);
  size_t lseed = cyphertext[0];
  const char *seed = cyphertext+1;
  int lblock;
  char block[BLOCKSIZE+MAXKEY];
  luaL_argcheck(L, lcyphertext >= lseed+1 && lseed <= BLOCKSIZE, 1,
                 "invalid cyphered string");
  cyphertext += lseed+1;
  lcyphertext -= lseed+1;
  lblock = initblock(L, seed, lseed, block);
  decodestream(L, cyphertext, lcyphertext, block, lblock);
  return 1;
}


/*
** Assumes the table is on top of the stack.
*/
static void set_info (lua_State *L) {
	lua_pushliteral (L, "_COPYRIGHT");
	lua_pushliteral (L, "Copyright (C) 2003 PUC-Rio");
	lua_settable (L, -3);
	lua_pushliteral (L, "_DESCRIPTION");
	lua_pushliteral (L, "Basic cryptographic facilities");
	lua_settable (L, -3);
	lua_pushliteral (L, "_VERSION");
	lua_pushliteral (L, "MD5 1.1.2");
	lua_settable (L, -3);
}


static struct luaL_reg md5lib[] = {
  {"sum", lmd5},
  {"exor", ex_or},
  {"crypt", crypt},
  {"decrypt", decrypt},
  {NULL, NULL}
};


int luaopen_md5_core (lua_State *L) {
  luaL_openlib(L, "md5.core", md5lib, 0);
  set_info (L);
  return 1;
}

genometools-1.5.1/src/external/md5-1.1.2/tests/000077500000000000000000000000001211610345200207415ustar00rootroot00000000000000genometools-1.5.1/src/external/md5-1.1.2/tests/DES56/000077500000000000000000000000001211610345200215275ustar00rootroot00000000000000genometools-1.5.1/src/external/md5-1.1.2/tests/DES56/Makefile000066400000000000000000000011071211610345200231660ustar00rootroot00000000000000
CFLAGS= -O6 -DUSG=0 -DBSD=0

FILES=	Makefile des56.h des56.c fdemo.c ftest.c

all:	demo test

# demo -- evaluate, test and time DES, works even on non-UNIX systems

demo:	fdemo
	./fdemo -demo -c 1000

fdemo:	fdemo.o des56.o
	${CC} -o $@ $@.o des56.o

# test -- evaluates DES, compares with UNIX crypt

test:	ftest
	./ftest 4869207468657265 a820105412de3991 77129bd8c052e7
	./ftest 1.21280ac -c 5000000 -k 1000000 -C 100000 -K 100000

ftest:	ftest.o des56.o
	${CC} -o $@ $@.o des56.o -lcrypt

dist:
	@tar cvf - ${FILES}

clean:
	rm -f clean core fdemo ftest fdemo.o ftest.o des56.o

genometools-1.5.1/src/external/md5-1.1.2/tests/DES56/fdemo.c000066400000000000000000000101441211610345200227650ustar00rootroot00000000000000
/*
 * Fast DES evaluation & benchmarking, not dependent on UNIX
 */
#include 
#include 
#include 

#include "des56.h"


typedef struct {
	char b[8];
} chunk;

char *wprint(chunk *v)
{
	static char s[18];
	register int i;
	register char *p;

	p = s;
	for(i = 0; i < 8; i++) {
		sprintf(p, "%02x", v->b[i] & 0xff);
		p += 2;
		if(i == 4-1) *p++ = '.';
	}
	return(s);
}

void getv(char *s, chunk *v)
{
	register int i, t;

	if(s[0] == '0' && s[1] == 'x')
		s += 2; /* Ignore C-style 0x prefix */
	for(i = 0; i < 8; i++) {
		t = 0;
		if(*s >= '0' && *s <= '9') t = *s++ - '0';
		else if(*s >= 'a' && *s <= 'f') t = *s++ - 'a' + 10;
		else if(*s >= 'A' && *s <= 'F') t = *s++ - 'A' + 10;
		t <<= 4;
		if(*s >= '0' && *s <= '9') t |= *s++ - '0';
		else if(*s >= 'a' && *s <= 'f') t |= *s++ - 'a' + 10;
		else if(*s >= 'A' && *s <= 'F') t |= *s++ - 'A' + 10;
		v->b[i] = t;
		if(*s == '.' && i == 3) {
			s++;
		}
	}
}

struct demo {
	int  decrypt;
	char *key, *data;
	char *expect;
};

struct demo demos[] = {
   { 0, "00000000.00000000", "00000000.00000000", "8ca64de9.c1b123a7" },
   { 0, "11111111.11111111", "00000000.00000000", "82e13665.b4624df5" },
   { 0, "12486248.62486248", "f0e1d2c3.b4a59687", "f4682865.376f93ea" },
   { 1, "12486248.62486248", "f0e1d2c3.b4a59687", "df597e0f.84fd994f" },
   { 0, "1bac8107.6a39042d", "812801da.cbe98103", "d8883b2c.4a7c61dd" },
   { 1, "1bac8107.6a39042d", "d8883b2c.4a7c61dd", "812801da.cbe98103" },
   { 1, "fedcba98.76543210", "a68cdca9.0c9021f9", "00000000.00000000" },
   { 0, "eca86420.13579bdf", "01234567.89abcdef", "a8418a54.ff97a505" },
};


void fdemo(void)
{
	keysched KS;
	register struct demo *dp;
	chunk key, data;
	char *got;

	printf("\
Op(	 Key,	    Data to En/Decrypt) =      Computed     ?=	  Expected\n");
	for(dp = demos; dp < &demos[sizeof(demos)/sizeof(*demos)]; dp++) {
		getv(dp->key, &key);
		fsetkey(key.b, &KS);
		getv(dp->data, &data);
		fencrypt(data.b, dp->decrypt, &KS);
		got = wprint(&data);
		printf("%c(%s, %s) = %s %c %s\n",
			"ED"[dp->decrypt], dp->key, dp->data,
			got,
			strcmp(got, dp->expect) ? '!' : '=',
			dp->expect);
	}
}

int main(int argc, char *argv[])
{
	register int i;
	chunk key, olddata, newdata;
	int decrypt = 0;
	int first = 1;
	keysched KS;

	if(argc <= 1) {

    usage:
		printf("\
Usage: fdemo  key  [ -demo ] [ -{ck} N ] [ [-{ed}] data ... ]\n\
Demonstrate and/or time fast DES routines.\n\
``key'' and ``data'' are left-justified, 0-padded hex values <= 16 digits\n\
	optionally with a `.' at the 32-bit point\n\
-demo	tries a batch of values, compares fencrypt() with precomputed result\n\
-c N	encrypt N times using fast DES\n\
-k N	set-key N times using fast DES\n\
-e	encrypt following data value(s) (default)\n\
-d	decrypt following data value(s)\n");
		return(1);
	}


	for(i = 1; i < argc; i++) {
	    if(argv[i][0] == '-') {
		int count, n;
		char c, *op;

		/* Should use getopt but it might not be there */
		c = argv[i][1];
		if(c == 'e' || c == 'd') {
		    if(strcmp(argv[i], "-demo") == 0) {
			fdemo();
		    } else {
			decrypt = (c == 'd');
		    }
		    continue;
		}

		fsetkey(key.b, &KS);	/* Make sure it's done at least once */
		op = &argv[i][2];
		if(*op == '\0')
			if((op = argv[++i]) == NULL)
				goto usage;
		count = atoi(op);
		if(count <= 0) count = 1;
		n = count;
		printf("Starting ...<\007");
		fflush(stdout);
		switch(c) {
		case 'c':
		    op = "fencrypt";
		    do fencrypt(newdata.b, 0, &KS); while(--n > 0); break;
		case 'k':
		    op = "fsetkey";
		    do fsetkey(key.b, &KS); while(--n > 0); break;
		default:
		    printf("Unknown option -%c\n", c);
		    goto usage;
		}
		printf("\007> completed %d %s's\n", count, op);
	    } else if(first) {
		getv(argv[1], &key);
		fsetkey(key.b, &KS);
		printf("key\t%s\n", wprint(&key));
		first = 0;
	    } else {
		getv(argv[i], &olddata);
		newdata = olddata;

		printf("%s %s => ",
		    decrypt ? "decrypt" : "encrypt",
		    wprint(&olddata));
		fencrypt(newdata.b, decrypt, &KS);
		printf("%s %s => ",
		    !decrypt ? "decrypt" : "encrypt",
		    wprint(&newdata));
		fencrypt(newdata.b, !decrypt, &KS);
		printf("%s\n", wprint(&newdata));
	    }
	}
	return(0);
}
genometools-1.5.1/src/external/md5-1.1.2/tests/DES56/ftest.c000066400000000000000000000107421211610345200230240ustar00rootroot00000000000000
/*
 * Fast DES evaluation & benchmarking for UNIX
 * Compares output of fencrypt()/fsetkey() with UNIX crypt()/encrypt()/setkey()
 * and measures speed using times().
 */

#include 
#include 
#if USG
#include 
#endif /*USG*/
#include 	/* for HZ */
#include 

#include 

#include "des56.h"

typedef struct {
	char b[8];
} chunk;

#ifdef CRAY
#  define  USG	1
#endif /*CRAY*/

#ifndef USG
#  define  USG	0
#endif	/*!USG*/

#if BSD >= 43 && defined(vax) && !defined(HZ)
#  define  HZ 100
#endif


char *
bprint(char b[64])
{
	static char s[17];
	register int i;

	for(i = 0; i < 64; i += 4)
	    sprintf(&s[i/4], "%1x", b[i]<<3 | b[i+1]<<2 | b[i+2]<<1 | b[i+3]);
	return(s);
}

char *
wprint(chunk *v)
{
	static char s[17];
	register int i;

	for(i = 0; i < 8; i++)
		sprintf(&s[2*i], "%02x", v->b[i] & 0xff);
	return(s);
}

void getv(char *s, chunk *v)
{
	register int i, t;

	if(s[0] == '0' && s[1] == 'x')
		s += 2;
	for(i = 0; i < 8; i++) {
		t = 0;
		if(*s >= '0' && *s <= '9') t = *s++ - '0';
		else if(*s >= 'a' && *s <= 'f') t = *s++ - 'a' + 10;
		else if(*s >= 'A' && *s <= 'F') t = *s++ - 'A' + 10;
		t <<= 4;
		if(*s >= '0' && *s <= '9') t |= *s++ - '0';
		else if(*s >= 'a' && *s <= 'f') t |= *s++ - 'a' + 10;
		else if(*s >= 'A' && *s <= 'F') t |= *s++ - 'A' + 10;
		v->b[i] = t;
		if(*s == '.') {
			s++;
			i = 4-1;
		}
	}
}

void expand(chunk *v, char bits[64])
{
	register unsigned int i;

	for(i = 0; i < 64; i++)
		bits[i] = (v->b[i/8] >> (7 - i%8)) & 1;
}


int
main(int argc, char *argv[])
{
	register int i;
	chunk key, olddata, newdata;
	char bkey[64], bdata[64];
	int decrypt = 0;
	keysched KS;

	if(argc < 2 || argv[1][0] == '-') {

    usage:
		printf("\
Usage: %s  key	[ -{ckCK} count ] [ data ... ]\n\
Demonstrate and/or time fast DES routines.\n\
``key'' and ``data'' are left-justified, 0-padded hex values <= 16 digits\n\
By default, encrypts & decrypts each 'data' block with both fastdes and\n\
crypt() library DES routines to show equality.\n\
-c N	encrypt N times using fast DES\n\
-k N	set-key N times using fast DES\n\
-C N	encrypt N times using library DES\n\
%s",
			argv[0],
			USG ? "" : "\
-K N	set-key N times using library DES\n");
		exit(1);
	}

	getv(argv[1], &key);
	fsetkey(key.b, &KS);
	expand(&key, bkey);
#if USG
	/* System V systems don't seem to have setkey, just crypt
	 * so we use that to set the key.
	 */
	for(i = 0; i < 8; i++)
		bdata[i] = (key.b[i] >> 1) | 0x80;
	bdata[8] = '\0';
	crypt((char *)bdata, "..");	/* Key, no salt */
#else /*!USG*/
	setkey(bkey);
#endif /*!USG*/
	printf("key\t%s\n", bprint(bkey));

	for(i = 2; i < argc; i++) {
	    if(argv[i][0] == '-') {
		int count, n;
		char c, *op;
		struct tms now, then;

		c = argv[i][1];
		op = &argv[i][2];
		if(*op == '\0')
			if((op = argv[++i]) == NULL)
				goto usage;
		count = atoi(op);
		if(count <= 0)
		    count = 1;
		n = count;
		expand(&olddata, bdata);
		times(&now);
		switch(c) {
		case 'c':
		    op = "fencrypt";
		    do fencrypt(newdata.b, 0, &KS); while(--n > 0); break;
		case 'k':
		    op = "fsetkey";
		    do fsetkey(key.b, &KS); while(--n > 0); break;

		case 'C':
		    op = "library encrypt";
		    do encrypt(bdata, decrypt); while(--n > 0); break;

		case 'K':
#if USG
		    printf("UNIX library has no setkey() function on this system\n");
		    continue;
#else /*!USG*/
		    op = "library setkey";
		    do setkey(bkey); while(--n > 0); break;
#endif /*!USG*/

		default:
		    printf("Unknown option -%c\n", c);
		    goto usage;
		}
		times(&then);
		n = then.tms_utime - now.tms_utime;
		printf("%d %s's in %0.2f seconds (%.2f us apiece)\n",
		    count, op, (float) n / HZ,
		    (1.0e6 * n / (HZ * count)));
	    } else {
		/* Demonstrate that it works for a particular data block.
		 * To compare with UNIX encrypt(), we must play its game.
		 * On BSD systems, encrypt(block, 1) is the inverse of (..., 0)
		 * but on USG systems the second parameter is ignored and
		 * encrypt(block, x) always encrypts.
		 */
		getv(argv[i], &olddata);
		newdata = olddata;

		printf("\tOriginal data\t\tEncrypted\t\t%s\n",
			USG ? "Encrypted again" : "Decrypted");

		printf("fastdes\t%s", wprint(&olddata));
		fencrypt(newdata.b, 0, &KS);
		printf("\t%s", wprint(&newdata));
		fencrypt(newdata.b, USG ? 0 : 1, &KS);
		printf("\t%s\n", wprint(&newdata));

		expand(&olddata, bdata);
		printf("UNIXdes\t%s", bprint(bdata));
		encrypt(bdata, 0);
		printf("\t%s", bprint(bdata));
		encrypt(bdata, USG ? 0 : 1);
		printf("\t%s\n", bprint(bdata));
	    }
	}
	exit(0);
}

genometools-1.5.1/src/external/md5-1.1.2/tests/test.lua000066400000000000000000000065751211610345200224400ustar00rootroot00000000000000#!/usr/local/bin/lua50

-- Testing MD5

require"md5"


assert(md5.exor('', '') == '')
assert(md5.exor('alo alo', '\0\0\0\0\0\0\0') == 'alo alo')

local function invert (s)
  return md5.exor(s, string.rep('\255', string.len(s)))
end

x = string.rep('0123456789', 1000)
assert(md5.exor(x,x) == string.rep('\0', 10000))
assert(md5.exor(x,invert(x)) == string.rep('\255', 10000))

assert(invert(invert('alo alo')) == 'alo alo')

assert(invert(invert(invert('alo\0\255alo'))) == invert('alo\0\255alo'))

-- test some known sums
assert(md5.sumhexa("") == "d41d8cd98f00b204e9800998ecf8427e")
assert(md5.sumhexa("a") == "0cc175b9c0f1b6a831c399e269772661")
assert(md5.sumhexa("abc") == "900150983cd24fb0d6963f7d28e17f72")
assert(md5.sumhexa("message digest") == "f96b697d7cb7938d525a2f31aaf161d0")
assert(md5.sumhexa("abcdefghijklmnopqrstuvwxyz") == "c3fcd3d76192e4007dfb496cca67e13b")
assert(md5.sumhexa("ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789")
 == "d174ab98d277d9f5a5611c2c9f419d9f")


-- test padding borders
assert(md5.sumhexa(string.rep('a',53)) == "e9e7e260dce84ffa6e0e7eb5fd9d37fc")
assert(md5.sumhexa(string.rep('a',54)) == "eced9e0b81ef2bba605cbc5e2e76a1d0")
assert(md5.sumhexa(string.rep('a',55)) == "ef1772b6dff9a122358552954ad0df65")
assert(md5.sumhexa(string.rep('a',56)) == "3b0c8ac703f828b04c6c197006d17218")
assert(md5.sumhexa(string.rep('a',57)) == "652b906d60af96844ebd21b674f35e93")
assert(md5.sumhexa(string.rep('a',63)) == "b06521f39153d618550606be297466d5")
assert(md5.sumhexa(string.rep('a',64)) == "014842d480b571495a4a0363793f7367")
assert(md5.sumhexa(string.rep('a',65)) == "c743a45e0d2e6a95cb859adae0248435")
assert(md5.sumhexa(string.rep('a',255)) == "46bc249a5a8fc5d622cf12c42c463ae0")
assert(md5.sumhexa(string.rep('a',256)) == "81109eec5aa1a284fb5327b10e9c16b9")

assert(md5.sumhexa(
"12345678901234567890123456789012345678901234567890123456789012345678901234567890")
   == "57edf4a22be3c955ac49da2e2107b67a")

print '+'



local tolerance = 1.12

local function contchars (s)
  local a = {}
  for i=0,255 do a[string.char(i)] = 0 end
  for c in string.gfind(s, '.') do
    a[c] = a[c] + 1
  end
  local av = string.len(s)/256
  for i=0,255 do
    local c = string.char(i)
    assert(a[c] < av*tolerance and a[c] > av/tolerance, i)
  end
end


local key = 'xuxu bacana'
assert(md5.decrypt(md5.crypt('', key), key) == '')
assert(md5.decrypt(md5.crypt('', key, '\0\0seed\0'), key) == '')
assert(md5.decrypt(md5.crypt('a', key), key) == 'a')
local msg = string.rep("1233456789\0\1\2\3\0\255", 10000)
local code = md5.crypt(msg, key, "seed")
assert(md5.decrypt(code, key) == msg)
contchars(code)

assert(md5.crypt('a', 'a') ~= md5.crypt('a', 'b'))

print"MD5 OK"


-- Testing DES 56
require 'des56'

local key = '&3g4&gs*&3'

assert(des56.decrypt(des56.crypt('', key), key) == '')
assert(des56.decrypt(des56.crypt('', key), key) == '')
assert(des56.decrypt(des56.crypt('a', key), key) == 'a')
assert(des56.decrypt(des56.crypt('1234567890', key), key) == '1234567890')

local msg = string.rep("1233456789\0\1\2\3\0\255", 10000)
local code = des56.crypt(msg, key)

assert(des56.decrypt(code, key) == msg)
assert(des56.crypt('a', '12345678') ~= des56.crypt('a', '87654321'))

local ascii = ""

for i = 0, 255 do
	ascii = ascii..string.char(i)
end

assert(des56.decrypt(des56.crypt(ascii, key), key) == ascii)
key = string.sub(ascii, 2)
assert(des56.decrypt(des56.crypt(ascii, key), key) == ascii)

print"DES56 OK"genometools-1.5.1/src/external/md5-1.1.2/vc6/000077500000000000000000000000001211610345200202755ustar00rootroot00000000000000genometools-1.5.1/src/external/md5-1.1.2/vc6/md5.def000066400000000000000000000001151211610345200214370ustar00rootroot00000000000000LIBRARY core.dll
DESCRIPTION "LuaMD5"
VERSION 1.0.1
EXPORTS
luaopen_md5_core
genometools-1.5.1/src/external/md5-1.1.2/vc6/md5.dsw000066400000000000000000000011051211610345200214760ustar00rootroot00000000000000Microsoft Developer Studio Workspace File, Format Version 6.00
# WARNING: DO NOT EDIT OR DELETE THIS WORKSPACE FILE!

###############################################################################

Project: "md5_dll"=.\md5_dll.dsp - Package Owner=<4>

Package=<5>
{{{
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    ..
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}}}

Package=<4>
{{{
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###############################################################################

Global:

Package=<5>
{{{
}}}

Package=<3>
{{{
}}}

###############################################################################

genometools-1.5.1/src/external/md5-1.1.2/vc6/md5_dll.dsp000066400000000000000000000112361211610345200223300ustar00rootroot00000000000000# Microsoft Developer Studio Project File - Name="md5_dll" - Package Owner=<4>
# Microsoft Developer Studio Generated Build File, Format Version 6.00
# ** DO NOT EDIT **

# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102

CFG=md5_dll - Win32 Debug
!MESSAGE This is not a valid makefile. To build this project using NMAKE,
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!MESSAGE You can specify a configuration when running NMAKE
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MTL=midl.exe
RSC=rc.exe

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# PROP Intermediate_Dir "md5_dll/Release"
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# Begin Special Build Tool
SOURCE="$(InputPath)"
# End Special Build Tool

!ELSEIF  "$(CFG)" == "md5_dll - Win32 Debug"

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BSC32=bscmake.exe
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LINK32=link.exe
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!ENDIF 

# Begin Target

# Name "md5_dll - Win32 Release"
# Name "md5_dll - Win32 Debug"
# Begin Group "Source Files"

# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
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genometools-1.5.1/src/external/samtools-0.1.18/000077500000000000000000000000001211610345200210415ustar00rootroot00000000000000genometools-1.5.1/src/external/samtools-0.1.18/AUTHORS000066400000000000000000000016241211610345200221140ustar00rootroot00000000000000Heng Li from the Sanger Institute wrote most of the initial source codes
of SAMtools and various converters.

Bob Handsaker from the Broad Institute is a major contributor to the
SAM/BAM specification. He designed and implemented the BGZF format, the
underlying indexable compression format for the BAM format. BGZF does
not support arithmetic between file offsets.

Jue Ruan for the Beijing Genome Institute designed and implemented the
RAZF format, an alternative indexable compression format. RAZF supports
arithmetic between file offsets, at the cost of increased index file
size and the full compatibility with gzip. RAZF is optional and only
used in `faidx' for indexing RAZF compressed fasta files.

Colin Hercus updated novo2sam.pl to support gapped alignment by
novoalign.

Petr Danecek contributed the header parsing library sam_header.c and 
sam2vcf.pl script and added knet support to the RAZF library.

genometools-1.5.1/src/external/samtools-0.1.18/COPYING000066400000000000000000000020751211610345200221000ustar00rootroot00000000000000The MIT License

Copyright (c) 2008-2009 Genome Research Ltd.

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.genometools-1.5.1/src/external/samtools-0.1.18/ChangeLog000066400000000000000000006211161211610345200226220ustar00rootroot00000000000000------------------------------------------------------------------------
r925 | lh3lh3 | 2011-02-28 15:45:17 -0500 (Mon, 28 Feb 2011) | 2 lines
Changed paths:
   M /trunk/samtools/phase.c

minor changes to a heuristic rule

------------------------------------------------------------------------
r924 | lh3lh3 | 2011-02-28 15:24:04 -0500 (Mon, 28 Feb 2011) | 4 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bcftools/vcfutils.pl
   M /trunk/samtools/phase.c

 * 0.1.12-r924:126
 * fixed a bug in phase (due to recent changes)
 * fixed a bug in vcf2fq

------------------------------------------------------------------------
r923 | lh3lh3 | 2011-02-28 12:57:39 -0500 (Mon, 28 Feb 2011) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/phase.c

 * put version number in bam.h
 * write version to BCF
 * in phase, change the default -q to 37
 * output a little more information during phasing

------------------------------------------------------------------------
r922 | lh3lh3 | 2011-02-25 16:40:09 -0500 (Fri, 25 Feb 2011) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.tex
   M /trunk/samtools/bcftools/bcf2qcall.c
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/ld.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/vcf.c
   M /trunk/samtools/cut_target.c

 * change the order of PL/GL according to the latest VCF spec
 * change the type of SP to int32_t

------------------------------------------------------------------------
r921 | lh3lh3 | 2011-02-25 14:40:56 -0500 (Fri, 25 Feb 2011) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.tex

update the BCF spec

------------------------------------------------------------------------
r920 | lh3lh3 | 2011-02-25 00:59:27 -0500 (Fri, 25 Feb 2011) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/cut_target.c
   M /trunk/samtools/errmod.h
   M /trunk/samtools/faidx.c
   M /trunk/samtools/khash.h
   M /trunk/samtools/kstring.c
   M /trunk/samtools/kstring.h
   A /trunk/samtools/phase.c
   M /trunk/samtools/samtools.1

added the phase command

------------------------------------------------------------------------
r918 | lh3lh3 | 2011-02-24 10:05:54 -0500 (Thu, 24 Feb 2011) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h

added "const" to bcf_p1_cal()

------------------------------------------------------------------------
r917 | lh3lh3 | 2011-02-24 09:36:30 -0500 (Thu, 24 Feb 2011) | 2 lines
Changed paths:
   M /trunk/samtools/bam.c

more meaningful BAM truncation message

------------------------------------------------------------------------
r916 | lh3lh3 | 2011-02-24 09:35:06 -0500 (Thu, 24 Feb 2011) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/vcf.c

 * automatically fix errors in GL
 * output unrecognized FORMAT as "."

------------------------------------------------------------------------
r913 | lh3lh3 | 2011-02-10 22:59:47 -0500 (Thu, 10 Feb 2011) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/vcf.c

finished VCF->BCF conversion

------------------------------------------------------------------------
r910 | petulda | 2011-02-03 03:13:48 -0500 (Thu, 03 Feb 2011) | 1 line
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

Prevent division by zero
------------------------------------------------------------------------
r909 | lh3lh3 | 2011-02-02 11:29:20 -0500 (Wed, 02 Feb 2011) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c

fixed a typo in the VCF header

------------------------------------------------------------------------
r908 | lh3lh3 | 2011-02-02 11:28:24 -0500 (Wed, 02 Feb 2011) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam_index.c

 * fixed an out-of-boundary bug
 * improved sorting order checking in index

------------------------------------------------------------------------
r907 | lh3lh3 | 2011-01-29 22:59:20 -0500 (Sat, 29 Jan 2011) | 4 lines
Changed paths:
   M /trunk/samtools/INSTALL
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/knetfile.c

 * avoid a segfault when network connect fails
 * update INSTALL
 * fixed a bug in tview on big-endian by Nathan Weeks

------------------------------------------------------------------------
r903 | lh3lh3 | 2011-01-27 14:50:02 -0500 (Thu, 27 Jan 2011) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_md.c

 * fixed a rare memory issue in bam_md.c
 * fixed a bug in indel calling related to unmapped and refskip reads

------------------------------------------------------------------------
r902 | lh3lh3 | 2011-01-23 21:46:18 -0500 (Sun, 23 Jan 2011) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/fet.c

fixed two minor bugs in Fisher's exact test

------------------------------------------------------------------------
r899 | petulda | 2011-01-19 09:28:02 -0500 (Wed, 19 Jan 2011) | 1 line
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

Skip sites with unknown ref
------------------------------------------------------------------------
r898 | lh3lh3 | 2011-01-15 12:56:05 -0500 (Sat, 15 Jan 2011) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_md.c

move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c

------------------------------------------------------------------------
r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/call1.c

 * samtools-0.1.12-10 (r896)
 * allow to exclude read groups in mpileup

------------------------------------------------------------------------
r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.tex

sorry. It is SP not ST

------------------------------------------------------------------------
r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.tex

added ST

------------------------------------------------------------------------
r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line
Changed paths:
   M /trunk/samtools/bcftools/call1.c

Fixed a typo in read_samples
------------------------------------------------------------------------
r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bcftools/Makefile
   M /trunk/samtools/examples/Makefile

System libraries go *after* user libraries in link commands, because
the user libraries may themselves have dependencies that are satisfied
by the system libraries.  It's not rocket science!

This makes a difference with some linkers; or with -static or --as-needed.

The examples/Makefile fix is from Charles Plessy.
See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004

------------------------------------------------------------------------
r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/call1.c

 * samtools-0.1.12-9 (r891)
 * allow to call SNPs from a subset of samples

------------------------------------------------------------------------
r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.12-12 (r889)
 * set mapQ as 20 if it equals 255

------------------------------------------------------------------------
r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

When -B is applied to mpileup, still use paired reads only unless -A is flagged.

------------------------------------------------------------------------
r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.12-6 (r887)
 * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.

------------------------------------------------------------------------
r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c

(Arguably) improved the indel caller a tiny bit for lowCov data.

------------------------------------------------------------------------
r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line
Changed paths:
   M /trunk/samtools/bcftools/call1.c

Fixed the VCF header to pass validation
------------------------------------------------------------------------
r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/vcfutils.pl

 * samtools-0.1.12-4 (r884)
 * fixed a long-existing flaw in the INDEL calling model

------------------------------------------------------------------------
r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/vcfutils.pl

compute max SP and max GQ from sample genotypes

------------------------------------------------------------------------
r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines
Changed paths:
   D /trunk/samtools/bcftools/bcf-fix.pl

drop bcf-fix.pl as it is redundant by the latest changes

------------------------------------------------------------------------
r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/vcf.c

 * fixed a minor issue in printing VCFs
 * write bcftools specific INFO and FORMAT in the header

------------------------------------------------------------------------
r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/call1.c

Make sure that the GT genotype field is the first

------------------------------------------------------------------------
r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.12-2 (r877)

 * allow to fine control the selection of indel candidates. The current
   setting is okay for lowCov and highCov with ~100 samples, but it
   skips too many indels for highCov with >250 samples.


------------------------------------------------------------------------
r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c

a spelling error..

------------------------------------------------------------------------
r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.12-1 (r873)
 * added a switch to allow anomalous read pairs in calling

------------------------------------------------------------------------
r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

fixed a bug in vcf2fq

------------------------------------------------------------------------
r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c

added a warning for the Windows version

------------------------------------------------------------------------
r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c

In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
According to the manual page, this change is valid. However, MinGW seems
to interpret "%lf" as "%Lf".

------------------------------------------------------------------------
r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.mingw
   M /trunk/samtools/bam_aux.c

bring back the windows support

------------------------------------------------------------------------
r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_reheader.c
   M /trunk/samtools/bcftools/vcfutils.pl

Fixed a compiling error when knetfile is not used.

------------------------------------------------------------------------
r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

vcf->fastq

------------------------------------------------------------------------
r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h

 * remove "-f". Instead always compute consensus quality
 * increase the upper limit of quality

------------------------------------------------------------------------
r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c

more informative error message

------------------------------------------------------------------------
r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c

Release samtools-0.1.12a

------------------------------------------------------------------------
r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c

a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect

------------------------------------------------------------------------
r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines
Changed paths:
   M /trunk/samtools/NEWS
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

Release samtools-0.1.12

------------------------------------------------------------------------
r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/bcf.c

 * samtools-0.1.11-1 (r858)
 * fixed a bug in mpileup which causes segfaults
 * bcftools: do not segfault when BCF contains errors

------------------------------------------------------------------------
r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_index.c

fixed a memory leak in bam_fetch()

------------------------------------------------------------------------
r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bcftools/vcfutils.pl

 * fixed a memory violation
 * added splitchr to vcfutils.pl

------------------------------------------------------------------------
r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/ld.c

fixed a typo/bug in r^2 computation

------------------------------------------------------------------------
r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c

forget to change the version information

------------------------------------------------------------------------
r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bcftools/bcftools.1
   M /trunk/samtools/samtools.1

Release samtools-0.1.11

------------------------------------------------------------------------
r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h

 * samtools-0.1.10-9 (r844)
 * added the "folded" or reference-free mode for variant calling

------------------------------------------------------------------------
r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/NEWS
   M /trunk/samtools/bam_sort.c

In merging, if -R is specified, do not abort if the sequence dictionary is different.

------------------------------------------------------------------------
r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
Changed paths:
   M /trunk/samtools/bam_sort.c

When merging BAM headers, compare the list of target reference sequences
strictly (and fail/abort if there is a mismatch), but allow one list to be a
prefix of the other.  (i.e., check that the lists are identical up until the
shorter runs out, and add the excess targets from the longer to the output.)

------------------------------------------------------------------------
r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.10 (r841)
 * fixed a bug in pileup when the first CIGAR operation is D
 * fixed a bug in view with range query

------------------------------------------------------------------------
r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.10-4 (r840)

 * drop the MNP caller. It is slow while does not diliver too much
   benefit. Possibly I will work on it in future given more time.

 * there is a segfault in pileup 

 * someone has reported segfault from view/index/sort


------------------------------------------------------------------------
r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
Changed paths:
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.10-6 (r839)

 * call MNPs without realignment because it seems to me that it is not
   worthwhile to significantly slow down SNP calling.

 * the result looks quite different from the previous version. I have
   work to do...


------------------------------------------------------------------------
r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c

Apply a patch by Rob Davis, which improves fault detection.

------------------------------------------------------------------------
r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c

 * samtools-r836
 * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)

------------------------------------------------------------------------
r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

 * modify the filtering rule: also filter SNPs around filtered indels
 * added MNP filter

------------------------------------------------------------------------
r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.10-4 (r834)
 * fixed a silly bug in printing MNP
 * restrict to at most 1 alternative allele

------------------------------------------------------------------------
r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bamtk.c

fixed a bug in printing MNPs

------------------------------------------------------------------------
r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c

minor change to how seqQ is applied

------------------------------------------------------------------------
r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.10 (r831)
 * initial MNP caller

------------------------------------------------------------------------
r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c

Release samtools-0.1.10 (r829)

------------------------------------------------------------------------
r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c

update version information: samtools-0.1.9-20 (r828)

------------------------------------------------------------------------
r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c

bcftools: allow to skip indels

------------------------------------------------------------------------
r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_md.c

remove ZQ if both BQ and ZQ are present

------------------------------------------------------------------------
r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.9-18 (r825)
 * change the behaviour of calmd such that by default it does not change the base quality

------------------------------------------------------------------------
r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.9-17 (r824)
 * added command line options to change the default parameters in indel calling
 * update the manual

------------------------------------------------------------------------
r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-r823
 * the BQ tag is now 64 shifted, not 33 shifted

------------------------------------------------------------------------
r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/vcfutils.pl
   M /trunk/samtools/misc/samtools.pl

 * samtools-0.1.9-16 (r822)
 * keep the raw depth because in indel calling, DP4 may be way off the true depth

------------------------------------------------------------------------
r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-15 (r821)
 * calmd: write BQ
 * skip realignment if BQ is present

------------------------------------------------------------------------
r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-14 (r820)
 * penalize reads with excessive differences in indel calling

------------------------------------------------------------------------
r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-13 (r819)
 * fixed a bug in pileup given refskip

------------------------------------------------------------------------
r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c

 * samtools-r818
 * for indel calling, do two rounds of probabilistic realignments

------------------------------------------------------------------------
r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/vcfutils.pl

 * samtools-0.1.19-11 (r817)
 * only initiate indel calling when 0.2% of reads contain a gap

------------------------------------------------------------------------
r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-10 (r816)

 * I know why the forward method fails. it is because of zero base
   qualities. when that is fixed, the forward method seems to give
   better results than Viterbi, as it should be. I am tired...


------------------------------------------------------------------------
r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam2bcf_indel.c

effectively revert to the viterbi version. The forward realignment gives too many false positives.

------------------------------------------------------------------------
r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-9 (r810)
 * use forward, instead of viterbi, for realignment
 * realignment is now quality aware

------------------------------------------------------------------------
r813 | lh3lh3 | 2010-11-10 22:45:24 -0500 (Wed, 10 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/kprobaln.c
   M /trunk/samtools/kprobaln.h

 * prepare to replace kaln with kprobaln in realignment

------------------------------------------------------------------------
r812 | lh3lh3 | 2010-11-10 17:28:50 -0500 (Wed, 10 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c

fixed a typo

------------------------------------------------------------------------
r811 | lh3lh3 | 2010-11-10 16:54:46 -0500 (Wed, 10 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h

use zlib for direct reading when BCF_LITE is in use

------------------------------------------------------------------------
r810 | lh3lh3 | 2010-11-10 16:32:13 -0500 (Wed, 10 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c

 * do not use reads containing too many mismatches for indel calling
 * fixed a trivial bug in case of multi-allelic indels

------------------------------------------------------------------------
r809 | lh3lh3 | 2010-11-10 13:23:02 -0500 (Wed, 10 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-8 (r809)
 * fixed a bug in the indel caller

------------------------------------------------------------------------
r808 | lh3lh3 | 2010-11-10 12:24:10 -0500 (Wed, 10 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile

minor change to makefile

------------------------------------------------------------------------
r807 | lh3lh3 | 2010-11-10 12:10:21 -0500 (Wed, 10 Nov 2010) | 4 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/vcfutils.pl

 * samtools-0.1.9-8 (r807)
 * collect indel candidates only from specified platforms (@RG-PL)
 * merge varFilter and filter4vcf in vcfutils.pl 

------------------------------------------------------------------------
r806 | lh3lh3 | 2010-11-09 22:05:46 -0500 (Tue, 09 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h

bcftools: compute equal-tail (Bayesian) credible interval

------------------------------------------------------------------------
r805 | lh3lh3 | 2010-11-09 16:28:39 -0500 (Tue, 09 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

added a double-hit filter to avoid overestimated indel likelihood

------------------------------------------------------------------------
r804 | lh3lh3 | 2010-11-09 14:12:06 -0500 (Tue, 09 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-7 (r804)
 * fixed a bug in the gap caller

------------------------------------------------------------------------
r803 | lh3lh3 | 2010-11-09 10:45:33 -0500 (Tue, 09 Nov 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/prob1.c

 * samtools-0.1.9-6 (r803)
 * mpileup: apply homopolymer correction when calculating GL, instead of before
 * bcftools: apply a different prior to indels

------------------------------------------------------------------------
r802 | lh3lh3 | 2010-11-08 23:53:15 -0500 (Mon, 08 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-5 (r802)
 * relax tandem penalty. this will be made a command-line option in future.

------------------------------------------------------------------------
r801 | lh3lh3 | 2010-11-08 23:35:52 -0500 (Mon, 08 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-4 (r801)
 * fixed a minor issue in printing indel VCF

------------------------------------------------------------------------
r800 | lh3lh3 | 2010-11-08 15:28:14 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bcftools/vcfutils.pl

fixed another silly bug in mpileup's indel caller

------------------------------------------------------------------------
r799 | lh3lh3 | 2010-11-08 14:28:27 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c

fixed a silly bug in the indel caller

------------------------------------------------------------------------
r798 | lh3lh3 | 2010-11-08 14:07:33 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/sam_view.c
   M /trunk/samtools/samtools.1

Incorporate patches by Marcel Martin for read counting.

------------------------------------------------------------------------
r797 | lh3lh3 | 2010-11-08 13:39:52 -0500 (Mon, 08 Nov 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-2 (r797)
 * mpileup: indel calling seems to be working

------------------------------------------------------------------------
r796 | lh3lh3 | 2010-11-08 10:54:46 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/kaln.c

indel calling is apparently working, but more information needs to be collected

------------------------------------------------------------------------
r795 | lh3lh3 | 2010-11-08 00:39:18 -0500 (Mon, 08 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf_indel.c

fixed a few bugs in the indel caller. Probably there are more.

------------------------------------------------------------------------
r794 | lh3lh3 | 2010-11-07 22:23:16 -0500 (Sun, 07 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   A /trunk/samtools/bam2bcf_indel.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/kaln.c
   M /trunk/samtools/kaln.h

prepare for the indel caller. It is not ready yet.

------------------------------------------------------------------------
r793 | lh3lh3 | 2010-11-05 11:28:23 -0400 (Fri, 05 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam_plcmd.c

Revert to r790. The recent changes are not good...

------------------------------------------------------------------------
r792 | lh3lh3 | 2010-11-05 00:19:14 -0400 (Fri, 05 Nov 2010) | 6 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam_plcmd.c

 * this revision is UNSTABLE

 * indel caller seems working, but it is very insensitive and has
   several things I do not quite understand.


------------------------------------------------------------------------
r791 | lh3lh3 | 2010-11-04 22:58:43 -0400 (Thu, 04 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam_plcmd.c

for backup. no effective changes

------------------------------------------------------------------------
r790 | lh3lh3 | 2010-11-03 15:51:24 -0400 (Wed, 03 Nov 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl
   M /trunk/samtools/kprobaln.c

fixed a minor problem in the example coming with kprobaln.c

------------------------------------------------------------------------
r789 | lh3lh3 | 2010-11-02 15:41:27 -0400 (Tue, 02 Nov 2010) | 4 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/kaln.c
   M /trunk/samtools/kaln.h
   A /trunk/samtools/kprobaln.c
   A /trunk/samtools/kprobaln.h

Separate kaln and kprobaln as I am preparing further changes. At
present, the results should be identical to the previous.


------------------------------------------------------------------------
r788 | petulda | 2010-11-02 12:19:04 -0400 (Tue, 02 Nov 2010) | 1 line
Changed paths:
   M /trunk/samtools/bam_plcmd.c

Added -b option: read file names from a file
------------------------------------------------------------------------
r787 | lh3lh3 | 2010-10-29 23:17:22 -0400 (Fri, 29 Oct 2010) | 7 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.9-2 (r787)

 * Allow to set a maximum per-sample depth to reduce memory. However,
   BAQ computation is still applied to every read. The speed is not
   improved.


------------------------------------------------------------------------
r786 | lh3lh3 | 2010-10-29 12:10:40 -0400 (Fri, 29 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/vcf.c

 * samtools-0.1.9-1 (r786)
 * samtools: optionally perform exact test for each sample

------------------------------------------------------------------------
r785 | lh3lh3 | 2010-10-29 09:42:25 -0400 (Fri, 29 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bcftools/bcf.c

Optionally output "DP", the individual read depth

------------------------------------------------------------------------
r784 | lh3lh3 | 2010-10-27 23:10:27 -0400 (Wed, 27 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/samtools.1

acknowledge Petr and John who have greatly contributed to the project.

------------------------------------------------------------------------
r783 | lh3lh3 | 2010-10-27 22:47:47 -0400 (Wed, 27 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

Release samtools-0.1.9 (r783)

------------------------------------------------------------------------
r782 | lh3lh3 | 2010-10-27 19:58:54 -0400 (Wed, 27 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c

fixed a silly bug in pileup

------------------------------------------------------------------------
r781 | lh3lh3 | 2010-10-27 14:39:48 -0400 (Wed, 27 Oct 2010) | 5 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.8-22 (r781)
 * made BAQ the default behavior of mpileup
 * updated manual
 * in merge, force to exit given inconsistent header when "-R" is not in use.

------------------------------------------------------------------------
r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-21 (r780)
 * minor speedup to pileup

------------------------------------------------------------------------
r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/examples/toy.sam

improve pileup a little bit

------------------------------------------------------------------------
r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-20 (r778)
 * speed up pileup, although I do not know how much is the improvement

------------------------------------------------------------------------
r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/examples/Makefile

 * samtools-0.1.8-19 (r777)
 * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior

------------------------------------------------------------------------
r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_md.c

remove local realignment (probabilistic realignment is still there)

------------------------------------------------------------------------
r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/sam_view.c

Add the relevant filename or region to error messages, and cause a failure
exit status where appropriate.  Based on a patch provided by Marcel Martin.

------------------------------------------------------------------------
r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/examples/toy.sam
   M /trunk/samtools/kaln.c

 * Minor code changes. No real effect.
 * change quality to 30 in toy.sam

------------------------------------------------------------------------
r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/examples/toy.fa
   M /trunk/samtools/examples/toy.sam

added another toy example

------------------------------------------------------------------------
r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/ld.c
   M /trunk/samtools/bcftools/vcfutils.pl

improve the LD statistics

------------------------------------------------------------------------
r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/vcfutils.pl

 * a minor fix to the -L option
 * add ldstats to vcfutils.pl

------------------------------------------------------------------------
r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c

a minor change

------------------------------------------------------------------------
r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   A /trunk/samtools/bcftools/ld.c

forget to add the key file

------------------------------------------------------------------------
r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/vcfutils.pl

 * vcfutils.pl: fixed a typo in help message
 * added APIs: bcf_append_info() and bcf_cpy()
 * calculate adjacent LD

------------------------------------------------------------------------
r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

added filter for samtools/bcftools genetated VCFs

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r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl
   M /trunk/samtools/kaln.c

 * removed a comment line in kaln.c
 * vcfutils.pl fillac works when GT is not the first field

------------------------------------------------------------------------
r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
Changed paths:
   A /trunk/samtools/bcftools/bcf-fix.pl

Convert VCF output of "bcftools view -bgcv" to a valid VCF file
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r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/bcftools/bcftools.1
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.8-18 (r763)
 * added bcftools manual page
 * minor fix to mpileup and view command lines

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r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/vcfutils.pl

 * vcfutils.pl qstats: calculate marginal ts/tv
 * allow to call genotypes at variant sites

------------------------------------------------------------------------
r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
Changed paths:
   M /trunk/samtools/kaln.c
   M /trunk/samtools/misc/HmmGlocal.java

I am changing the gap open probability back to 0.001. It seems that
being conservative here is a good thing...

------------------------------------------------------------------------
r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kaln.c
   A /trunk/samtools/misc/HmmGlocal.java

 * samtools-0.1.8-17 (r760)
 * the default gap open penalty is too small (a typo)
 * added comments on hmm_realn
 * Java implementation

------------------------------------------------------------------------
r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c

mark samtools-0.1.8-16 (r759)

------------------------------------------------------------------------
r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c

round to the nearest integer

------------------------------------------------------------------------
r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
Changed paths:
   M /trunk/samtools/kaln.c

I was trying to accelerate ka_prob_glocal() as this will be the
bottleneck. After an hour, the only gain is to change division to
multiplication. OK. I will stop.

------------------------------------------------------------------------
r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c

this is interesting. multiplication is much faster than division, at least on my Mac

------------------------------------------------------------------------
r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c

minor changes

------------------------------------------------------------------------
r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/kaln.c

prob_realn() seems working!

------------------------------------------------------------------------
r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c

minor

------------------------------------------------------------------------
r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c
   M /trunk/samtools/kaln.h

Convert phredQ to probabilities

------------------------------------------------------------------------
r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c
   M /trunk/samtools/kaln.h

Implement the glocal HMM; discard the extention HMM

------------------------------------------------------------------------
r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c

improve numerical stability

------------------------------------------------------------------------
r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c

more comments

------------------------------------------------------------------------
r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c

fixed a bug in banded DP

------------------------------------------------------------------------
r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
Changed paths:
   M /trunk/samtools/kaln.c

 * fixed that weird issue.
 * the banded version is NOT working

------------------------------------------------------------------------
r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/kaln.c

More comments. This version seems working, but something is a little weird...

------------------------------------------------------------------------
r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
Changed paths:
   M /trunk/samtools/kaln.c

A little code cleanup. Now the forward and backback algorithms give
nearly identical P(x), which means both are close to the correct
forms. However, I have only tested on toy examples. Minor errors in
the implementation may not be obvious.


------------------------------------------------------------------------
r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/kaln.c
   M /trunk/samtools/kaln.h

...

------------------------------------------------------------------------
r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
Changed paths:
   M /trunk/samtools/bam_sort.c

Abort if merge -h's INH.SAM cannot be opened, just as we abort
if any of the IN#.BAM input files cannot be opened.

Also propagate any error indication returned by bam_merge_core()
to samtools merge's exit status.

------------------------------------------------------------------------
r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
Changed paths:
   M /trunk/samtools/bam_index.c

Use bam_validate1() to detect garbage records in the event of a corrupt
BAI index file that causes a bam_seek() to an invalid position.  At most
one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
call, so the cost is insignificant in the normal case.

------------------------------------------------------------------------
r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h

Add bam_validate1().

------------------------------------------------------------------------
r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-15 (r379)
 * allow to change capQ parameter in calmd

------------------------------------------------------------------------
r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/sam_view.c

When bam_read1() returns an error (return value <= -2), propagate that error
to bam_iter_read()'s own return value.  Similarly, also propagate it up to
bam_fetch()'s return value.  Previously bam_fetch() always returned 0, and
callers ignored its return value anyway.  With this change, 0 continues to
indicate success, while <= -2 (which can be written as < 0, as -1 is never
returned) indicates corrupted input.

bam_iter_read() ought also to propagate errors returned by bam_seek().

main_samview() can now print an error message and fail when bam_fetch()
detects that a .bai index file is corrupted or otherwise does not correspond
to the .bam file it is being used with.

------------------------------------------------------------------------
r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c

0 is a successful return value from bam_read1().  (In practice, it never
returns 0 anyway; but all the other callers treat 0 as successful.)

------------------------------------------------------------------------
r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_sort.c

 * merge files region-by-region. work on small examples but more tests are needed.

------------------------------------------------------------------------
r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

improve qstats by checking the alleles as well

------------------------------------------------------------------------
r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

convert UCSC SNP SQL dump to VCF

------------------------------------------------------------------------
r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

hapmap2vcf convertor

------------------------------------------------------------------------
r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/vcf.c

 * added comments
 * VCF->BCF is not possible without knowing the sequence dictionary before hand...

------------------------------------------------------------------------
r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/vcf.c

 * put n_smpl to "bcf1_t" to simplify API a little

------------------------------------------------------------------------
r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/index.c

fixed a bug in indexing

------------------------------------------------------------------------
r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_pileup.c

 * fixed a bug in capQ
 * valgrind identifies a use of uninitialised value, but I have not fixed it.

------------------------------------------------------------------------
r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bgzip.c
   M /trunk/samtools/razip.c

 * fixed a bug in razip: -c will delete the input file
 * copy tabix/bgzip to here

------------------------------------------------------------------------
r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-14 (r727)
 * allow to change the capQ parameter at the command line

------------------------------------------------------------------------
r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bcftools/vcfutils.pl
   M /trunk/samtools/misc/samtools.pl

 * added varFilter to vcfutils.pl
 * reimplement realn(). now it performs a local alignment
 * added cap_mapQ() to cap mapping quality when there are many substitutions

------------------------------------------------------------------------
r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   A /trunk/samtools/bcftools/bcf2qcall.c
   M /trunk/samtools/bcftools/call1.c

 * convert BCF to QCALL input

------------------------------------------------------------------------
r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_md.c

dynamic band width in realignment

------------------------------------------------------------------------
r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_plcmd.c

fixed a bug in realignment

------------------------------------------------------------------------
r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/prob1.c

fixed a minor issue

------------------------------------------------------------------------
r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_md.c

fixed a bug in realignment

------------------------------------------------------------------------
r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c

minor changes. It is BUGGY now!

------------------------------------------------------------------------
r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/kaln.c
   M /trunk/samtools/kaln.h

 * aggressive gapped aligner is implemented in calmd.
 * distinguish gap_open and gap_end_open in banded alignment
 * make tview accepts alignment with heading and tailing D

------------------------------------------------------------------------
r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools

Add svn:ignore properties for generated files that don't appear in "make all".

------------------------------------------------------------------------
r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
Changed paths:
   M /trunk/samtools
   M /trunk/samtools/bcftools
   M /trunk/samtools/misc

Add svn:ignore properties listing the generated files.
(Except for *.o, which we'll assume is in global-ignores.)

------------------------------------------------------------------------
r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/sample.c
   M /trunk/samtools/sample.h

 * samtools-0.1.8-13 (r715)
 * fixed a bug in identifying SM across files
 * bcftools: estimate heterozygosity
 * bcftools: allow to skip sites without reference bases

------------------------------------------------------------------------
r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h

quite a lot changes to the contrast caller, but I still feel something is missing...

------------------------------------------------------------------------
r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/vcfutils.pl

 * changed 3.434 to 4.343 (typo!)
 * fixed a bug in the contrast caller
 * calculate heterozygosity

------------------------------------------------------------------------
r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/call1.c

SNP calling from the GL field

------------------------------------------------------------------------
r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcf.c

fixed another problem

------------------------------------------------------------------------
r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/vcf.c

 * fixed bugs in parsing VCF
 * parser now works with GT/GQ/DP/PL/GL

------------------------------------------------------------------------
r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   M /trunk/samtools/bcftools/prob1.c

Do not compile _BCF_QUAD by default

------------------------------------------------------------------------
r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/call1.c

Write the correct ALT and PL in the SNP calling mode.

------------------------------------------------------------------------
r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfutils.pl

more commands for my own uses

------------------------------------------------------------------------
r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
Changed paths:
   A /trunk/samtools/bcftools/vcfutils.pl

Utilities for processing VCF

------------------------------------------------------------------------
r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h

preliminary contrast variant caller

------------------------------------------------------------------------
r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/call1.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h

z' and z'' can be calculated

------------------------------------------------------------------------
r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
   M /trunk/samtools/bcftools/prob1.c
   D /trunk/samtools/bcftools/vcfout.c

 * rename vcfout.c as call1.c
 * prepare to add two-sample comparison

------------------------------------------------------------------------
r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfout.c

fixed a bug in calculating the t statistics

------------------------------------------------------------------------
r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcftools/kfunc.c
   M /trunk/samtools/bcftools/vcfout.c

 * samtools-0.1.8-13 (r698)
 * perform one-tailed t-test for baseQ, mapQ and endDist

------------------------------------------------------------------------
r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/kfunc.c

added regularized incomplete beta function

------------------------------------------------------------------------
r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_plcmd.c

change the default correlation coefficient

------------------------------------------------------------------------
r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/vcfout.c

print QUAL as floating numbers

------------------------------------------------------------------------
r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/examples/Makefile
   A /trunk/samtools/sample.c
   A /trunk/samtools/sample.h

 * samtools-0.1.8-12 (r692)
 * group data by samples in "mpileup -g"

------------------------------------------------------------------------
r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   D /trunk/samtools/bam_mcns.c
   D /trunk/samtools/bam_mcns.h
   M /trunk/samtools/bam_plcmd.c

remove VCF output in mpileup

------------------------------------------------------------------------
r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h

 * use the revised MAQ error model for mpileup
 * prepare to remove the independent model from mpileup

------------------------------------------------------------------------
r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   A /trunk/samtools/errmod.c
   A /trunk/samtools/errmod.h
   M /trunk/samtools/ksort.h

added revised MAQ error model

------------------------------------------------------------------------
r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h
   M /trunk/samtools/bcftools/vcfout.c

allow to read the prior from the error output. EM iteration is working.

------------------------------------------------------------------------
r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/main.c
   M /trunk/samtools/bcftools/vcf.c

 * write a little more VCF header
 * concatenate BCFs

------------------------------------------------------------------------
r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/bcf.tex

use float for QUAL

------------------------------------------------------------------------
r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/prob1.c

faster for large sample size (in principle)

------------------------------------------------------------------------
r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bcftools/prob1.c

 * a numerically stable method to calculate z_{jk}
 * currently slower than the old method but will be important for large sample size
 * in principle, we can speed up for large n, but have not tried

------------------------------------------------------------------------
r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfout.c

fixed an issue in parsing integer

------------------------------------------------------------------------
r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c

do not print refname if file is converted from VCF

------------------------------------------------------------------------
r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/vcf.c

 * parse PL
 * fixed a bug in parsing VCF

------------------------------------------------------------------------
r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/main.c
   M /trunk/samtools/bcftools/vcf.c
   M /trunk/samtools/bcftools/vcfout.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/kstring.c

 * fixed a bug in kstrtok@kstring.c
 * preliminary VCF parser (not parse everything for now)
 * improved view interface

------------------------------------------------------------------------
r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/vcfout.c
   M /trunk/samtools/kstring.c
   M /trunk/samtools/kstring.h

 * improved kstring (added kstrtok)
 * removed the limit on the format string length in bcftools
 * use kstrtok to parse format which fixed a bug in the old code

------------------------------------------------------------------------
r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
Changed paths:
   A /trunk/samtools/bcftools/README
   M /trunk/samtools/bcftools/vcfout.c

help messages

------------------------------------------------------------------------
r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcfout.c

perform single-tail test for ED4

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r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   M /trunk/samtools/bcftools/kfunc.c
   M /trunk/samtools/bcftools/vcfout.c

 * test depth, end distance and HWE

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r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/kfunc.c

reimplement incomplete gamma functions. no copy-paste

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r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bcftools/fet.c
   M /trunk/samtools/bcftools/prob1.c
   M /trunk/samtools/bcftools/prob1.h
   M /trunk/samtools/bcftools/vcfout.c

 * bcftools: add HWE (no testing for now)
 * record end dist in a 2x2 table, not avg, std any more

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r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
Changed paths:
   A /trunk/samtools/bcftools/kfunc.c

 * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
 * Not using Numerical Recipe due to licensing issues

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r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
Changed paths:
   A /trunk/samtools/bcftools/fet.c

Fisher's exact test

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r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/examples/Makefile

 * samtools-0.1.8-11 (r672)
 * collect more stats for allele balance test in bcftools (not yet)

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r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/main.c

 * the code base is stablized again.
 * I will delay the vcf parser, which is quite complicated but with little value for now

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r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/examples/Makefile

minor

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r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcftools/vcf.c

unfinished vcf parser

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r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bcftools/Makefile
   M /trunk/samtools/bcftools/bcf.c
   M /trunk/samtools/bcftools/bcf.h
   M /trunk/samtools/bcftools/bcfutils.c
   M /trunk/samtools/bcftools/index.c
   M /trunk/samtools/bcftools/main.c
   A /trunk/samtools/bcftools/vcf.c
   M /trunk/samtools/bcftools/vcfout.c

 * added prelimiary VCF parser (not finished)
 * change struct a bit

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r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bcftools/bcf.c

 * allow to set min base q
 * fixed a bug in mpileup -u

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r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
Changed paths:
   A /trunk/samtools/bcftools/bcf.tex

spec

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r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/examples/Makefile

added more examples

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r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bcftools/Makefile

fixed compilation error

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r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   D /trunk/samtools/bcf.c
   D /trunk/samtools/bcf.h
   A /trunk/samtools/bcftools
   A /trunk/samtools/bcftools/Makefile
   A /trunk/samtools/bcftools/bcf.c
   A /trunk/samtools/bcftools/bcf.h
   A /trunk/samtools/bcftools/bcfutils.c
   A /trunk/samtools/bcftools/index.c
   A /trunk/samtools/bcftools/main.c
   A /trunk/samtools/bcftools/prob1.c
   A /trunk/samtools/bcftools/prob1.h
   A /trunk/samtools/bcftools/vcfout.c

move bcftools to samtools

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r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c

fixed another minor bug

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r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bcf.c

 * samtools-0.1.8-10 (r658)
 * fixed a bug in bam2bcf when the reference is N

------------------------------------------------------------------------
r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h

 * fixed a bug
 * treat ambiguous ref base as the fifth base

------------------------------------------------------------------------
r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
Changed paths:
   M /trunk/bcftools/bcf.c
   M /trunk/samtools/bcf.c

missing a column in VCF output...

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r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcf.c

fixed a memory leak

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r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bcf.c

fixed a bug in bcf reader

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r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam2bcf.c

fixed a bug

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r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam2bcf.c
   M /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-9 (r649)
 * lossless representation of PL in BCF output

------------------------------------------------------------------------
r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   A /trunk/samtools/bam2bcf.c
   A /trunk/samtools/bam2bcf.h
   M /trunk/samtools/bam_plcmd.c
   A /trunk/samtools/bcf.c
   A /trunk/samtools/bcf.h

Generate binary VCF

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r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-8 (r644)
 * mpileup becomes a little stable again
 * the method is slightly different, but is more theoretically correct
 * snp calling is O(n^2) instead of O(n^3)

------------------------------------------------------------------------
r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c

 * fixed a STUPID bug, which cost me a lot of time.
 * I am going to clean up mcns a little bit

------------------------------------------------------------------------
r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_mcns.h
   M /trunk/samtools/bam_plcmd.c

supposedly this is THE correct implementation, but more testing is needed

------------------------------------------------------------------------
r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c

NOT ready yet. Going to make further changes...

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r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-7 (r639)
 * fixed the reference allele assignment

------------------------------------------------------------------------
r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_mcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-6 (r638)
 * skip isnan/isinf in case of float underflow
 * added the flat prior
 * fixed an issue where there are no reads supporting the reference

------------------------------------------------------------------------
r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c

minor changes

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r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_mcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

minor tweaks

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r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_mcns.h
   M /trunk/samtools/bam_plcmd.c

posterior expectation FINALLY working. I am so tired...

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r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c

another minor fix to mpileup

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r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c

added the format column

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r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_mcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

added an alternative prior

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r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_mcns.h
   M /trunk/samtools/bam_plcmd.c

calculate posterior allele frequency

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r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-3 (r627)
 * multi-sample snp calling appears to work. More tests needed.

------------------------------------------------------------------------
r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_mcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_tview.c

 * preliminary multisample SNP caller.
 * something looks not so right, but it largely works

------------------------------------------------------------------------
r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_mcns.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.8-2 (r617)
 * allele frequency calculation apparently works...

------------------------------------------------------------------------
r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   A /trunk/samtools/bam_mcns.c
   A /trunk/samtools/bam_mcns.h
   M /trunk/samtools/bam_plcmd.c

 * added mutli-sample framework. It is not working, yet.
 * improved the mpileup interface

------------------------------------------------------------------------
r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/Makefile

 * samtools-0.1.8-1 (r615)
 * allow to get mpileup at required sites

------------------------------------------------------------------------
r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

Release samtools-0.1.8

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r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c

fixed a compiling issue for Windows

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r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_sort.c

fixed a bug in sorting when output to stdout (by Peter Chines)

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r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/NEWS
   M /trunk/samtools/bam_plcmd.c

change the command line option of pileup

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r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_pileup.c
   A /trunk/samtools/examples/toy.fa
   A /trunk/samtools/examples/toy.sam

make pileup work with CIGAR with I/D at the beginning or in the end

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r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_tview.c

 * make tview more friendly
 * a temporary remedy for an issue in indel calling

------------------------------------------------------------------------
r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-r607
 * improved the genotype accuracy for indels
 * use the SOAPsnp model for SNP calling by default.

------------------------------------------------------------------------
r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/misc/Makefile

removed a debugging example

------------------------------------------------------------------------
r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-.1.7-18 (r605)
 * fixed an issue when a deletion and mismatch occur at the same time
   and the base quality is higher than 40 (if -I40).

------------------------------------------------------------------------
r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/misc/Makefile

fixed a minor bug in idxstats

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r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_index.c

fixed a minor bug in indexing

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r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam.c

change printf() to puts in exporting

------------------------------------------------------------------------
r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c

minor fix. No actual effect.

------------------------------------------------------------------------
r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile

added Makefile targets to compile shared/dynamic library

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r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-17 (r596)
 * also keep the number of coor-less reads in the index file

------------------------------------------------------------------------
r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-16 (r595)
 * write additional information to bam index

------------------------------------------------------------------------
r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_index.c

fixed a bug for unmapped sequences in indexing

------------------------------------------------------------------------
r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/samtools.1

rename iterf as iter

------------------------------------------------------------------------
r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-15 (r592)
 * fixed a few minor memory leaks in the new pileup code
 * improved the functionality of mpileup

------------------------------------------------------------------------
r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-14 (r591)
 * elementary multi-way pileup. More testing and more functionality to be done.

------------------------------------------------------------------------
r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-13 (r590)
 * added mpileup APIs. No compiling errors, but not tested at all. It is late.

------------------------------------------------------------------------
r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-12 (r589)
 * added iterator-like APIs for pileup

------------------------------------------------------------------------
r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-11 (r588)
 * ported a few improvements from tabix back to samtools

------------------------------------------------------------------------
r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-10 (r587)
 * added iterator interface for bam_fetch (ported back from tabix)

------------------------------------------------------------------------
r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   A /trunk/samtools/bam_reheader.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c

 * samtools-0.1.7-9 (r586)
 * added "reheader" to replace the BAM header

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r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kstring.h

 * samtools-0.1.7-8 (r585)
 * speed up "view"

------------------------------------------------------------------------
r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/kstring.h
   M /trunk/samtools/misc/wgsim_eval.pl

 * samtools-0.1.7-7 (r584)
 * ported tabix BGZF to samtools
 * flush BGZF after writing the BAM header and between alignment boundaries

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r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
Changed paths:
   A /trunk/samtools/misc/varfilter.py

Initial release on behalf of Aylwyn Scally
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r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
Changed paths:
   M /trunk/samtools/samtools.1

Added a note about the indels coordinates
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r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
Changed paths:
   M /trunk/samtools/misc/sam2vcf.pl

Added the possibility to print or not to print the reference allele
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r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
Changed paths:
   M /trunk/samtools/sam_header.c

More descriptive message for space separated tags
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r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
Changed paths:
   M /trunk/samtools/misc/sam2vcf.pl

Speedup with -i, no need to query the reference all the time
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r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
Changed paths:
   M /trunk/samtools/sam_header.c

Fixed the order of sequences in the header
------------------------------------------------------------------------
r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
Changed paths:
   M /trunk/samtools/misc/sam2vcf.pl

Added possibility to select indels only and fixed a bug in reporting homozygous indels.
------------------------------------------------------------------------
r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
Changed paths:
   M /trunk/samtools/bam.c

Improve the invalid 'BAM\1' magic number error message, and also print it
when no bytes can be read from the alleged BAM file, e.g., in the common
user error case when a SAM file has accidentally been supplied.

------------------------------------------------------------------------
r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
Changed paths:
   M /trunk/samtools/AUTHORS
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/sam_header.c

Improved efficiency of header parsing
------------------------------------------------------------------------
r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
Changed paths:
   M /trunk/samtools/misc/export2sam.pl

Updated export2sam.pl by Chris Saunders from Illumina.


------------------------------------------------------------------------
r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
Changed paths:
   M /trunk/samtools/misc/samtools.pl

Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
------------------------------------------------------------------------
r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
Changed paths:
   M /trunk/samtools/misc/sam2vcf.pl

Print an error for pileups in simple format
------------------------------------------------------------------------
r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c

added a hidden option in pileup to output the base position (for Erin)

------------------------------------------------------------------------
r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
Changed paths:
   M /trunk/samtools/misc/sam2vcf.pl

Added possibility to specify a custom column title for the data column
------------------------------------------------------------------------
r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
Changed paths:
   M /trunk/samtools/bam_plcmd.c

Added the -d option to limit maximum depth for indels.
------------------------------------------------------------------------
r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
Changed paths:
   M /trunk/samtools/misc/sam2vcf.pl

Added VCF header
------------------------------------------------------------------------
r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl
   M /trunk/samtools/misc/wgsim.c

 * samtools-0.1.7-6
 * fixed a bug in faidx

------------------------------------------------------------------------
r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
Changed paths:
   M /trunk/samtools/faidx.c

Put the right filename in the error message.

------------------------------------------------------------------------
r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-5 (r528)
 * further add new consensus generation strategy

------------------------------------------------------------------------
r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
Changed paths:
   M /trunk/samtools/knetfile.c

Fixed a bug in knet_seek
------------------------------------------------------------------------
r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
Changed paths:
   M /trunk/samtools/misc/sam2vcf.pl

Small fix in VCF format: dot for the empty INFO field
------------------------------------------------------------------------
r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
Changed paths:
   M /trunk/samtools/sam_header.c

Allow tabs in the CO header field
------------------------------------------------------------------------
r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/Makefile.mingw

Depend on libbam.a rather than the phony target, so that samtools is not
unnecessarily rebuilt every time.  Also clean bgzip.

------------------------------------------------------------------------
r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/Makefile.mingw

Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
is defined.  Also introduce $(KNETFILE_O) which can be set to empty to
facilitate non-knet builds.

------------------------------------------------------------------------
r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.7-4 (r522)
 * fixed a bug in "view -r"
 * added a new option "view -R" to read required read groups from a file

------------------------------------------------------------------------
r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.7-3 (r521)
 * calmd: optionally mask matching bases as N

------------------------------------------------------------------------
r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl

 * samtools-0.1.7-2 (r520)
 * fixed a few issues with compilation in Windows (on behalf of John)
 * choose a random base as the consensus (for population genetics studies)

------------------------------------------------------------------------
r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
Changed paths:
   M /trunk/samtools/Makefile

Put libraries at the end, so they can resolve references from libbam.a
as well, even with old-fashioned linkers.

Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
the freshly built library, not some other libbam.a lying around the system.

------------------------------------------------------------------------
r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/misc/Makefile

Also clean *.exe (for Cygwin users using this makefile).

------------------------------------------------------------------------
r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_index.c

Index files should be opened in binary mode, not text mode.

------------------------------------------------------------------------
r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
Changed paths:
   A /trunk/samtools/examples/bam2bed.c

another example program

------------------------------------------------------------------------
r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/wgsim_eval.pl
   M /trunk/samtools/sam.c

 * samtools-0.1.7-1 (r515)
 * report an error when .fai contains duplicated names, instead of segfault

------------------------------------------------------------------------
r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam.c

Format 'c'-encoded auxiliary fields correctly, as *signed* integers.

------------------------------------------------------------------------
r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.mingw

Update Makefile.mingw for the same reason

------------------------------------------------------------------------
r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile

Fixed a bug in compiling razip

------------------------------------------------------------------------
r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

Release samtools-0.1.7 (r510)

------------------------------------------------------------------------
r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.6-22 (r509)
 * forget to fix a similar problem in glfgen

------------------------------------------------------------------------
r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.6-21 (r508)
 * fixed a potential bug in the indel caller towards the end of a chromosome

------------------------------------------------------------------------
r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.6-19 (r494)
 * allow to convert Illumina quality (64 based) to the BAM quality

------------------------------------------------------------------------
r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_header.c

 * samtools-0.1.6-18 (r493)
 * fixed the bugs due to improperly incorporating Petr's header parser
 * a little code clean up in sam_header.c

------------------------------------------------------------------------
r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
Changed paths:
   M /trunk/samtools/sam_header.c

Added sam_header_line_free call for sam_header_parse2
------------------------------------------------------------------------
r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
Changed paths:
   M /trunk/samtools/sam_view.c

 * BUGGY VERSION
 * fixed a minor bug

------------------------------------------------------------------------
r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/sam.c

 * BUGGY VERSION
 * improved the interface a bit
 * bug unfixed

------------------------------------------------------------------------
r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/sam_header.c
   M /trunk/samtools/sam_header.h

 * BUGGY VERSION. Please NOT use it.
 * Fixed a minor bug, but the major bug is still there.

------------------------------------------------------------------------
r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/kaln.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_header.c
   M /trunk/samtools/sam_header.h
   M /trunk/samtools/sam_view.c

 * This revision is SERIOUSLY BUGGY. Please NOT use it.
 * Start to incorporate header parsing from Petr Danecek

------------------------------------------------------------------------
r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
Changed paths:
   M /trunk/samtools/sam_header.c
   M /trunk/samtools/sam_header.h

Now possible to merge multiple HeaderDict dictionaries
------------------------------------------------------------------------
r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
Changed paths:
   M /trunk/samtools/sam_header.c


------------------------------------------------------------------------
r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
Changed paths:
   A /trunk/samtools/sam_header.c
   A /trunk/samtools/sam_header.h


------------------------------------------------------------------------
r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/examples/Makefile

 * samtools-0.1.6-17 (r484)
 * fixed a memory leak in rmdupse
 * fixed a bug in parsing @RG header lines
 * test rmdup in examples/

------------------------------------------------------------------------
r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.6-16 (r483)
 * unify the interface of rmdup and rmdupse
 * a new bug found in rg2lib(). Have not been fixed yet.

------------------------------------------------------------------------
r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/klist.h

 * samtools-0.1.6-15 (r482)
 * rewrite rmdupse
 * rmdupse is now library aware

------------------------------------------------------------------------
r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.6-14 (r480)
 * rmdup is now RG aware

------------------------------------------------------------------------
r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

added a small unitity to parse SRA XML files

------------------------------------------------------------------------
r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.6-13 (r479)
 * merge: optionally use file names as RG tags

------------------------------------------------------------------------
r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kaln.c

 * samtools-0.1.6-12 (r478)
 * fixed a bug in the indel caller

------------------------------------------------------------------------
r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.6-11 (r477)
 * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)

------------------------------------------------------------------------
r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
Changed paths:
   A /trunk/samtools/misc/sam2vcf.pl

Added the sam2vcf.pl script.
------------------------------------------------------------------------
r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/kaln.c
   A /trunk/samtools/kaln.h

Unfinished modification. Please do not use this revision...

------------------------------------------------------------------------
r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
Changed paths:
   M /trunk/samtools/knetfile.c

Removed the offending knet_seek message.
------------------------------------------------------------------------
r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
Changed paths:
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/razf.c

Bug fix - faidx on RAZF compressed files now working.
------------------------------------------------------------------------
r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
Changed paths:
   M /trunk/samtools/samtools.1

Clarify the meaning of a region like "chr2:1,000,000".

------------------------------------------------------------------------
r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/novo2sam.pl

Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)

------------------------------------------------------------------------
r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile.mingw
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.6-9 (r470)
 * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)

------------------------------------------------------------------------
r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.6-9 (r469)
 * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.

------------------------------------------------------------------------
r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl

 * samtools-0.1.6-7 (r468)
 * make merge stable

------------------------------------------------------------------------
r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
Changed paths:
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzip.c
   M /trunk/samtools/razf.c
   M /trunk/samtools/razip.c

Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
------------------------------------------------------------------------
r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.6-6 (r466)
 * do not crash calmd when some sequences are absent from the reference.

------------------------------------------------------------------------
r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/knetfile.c

Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
no way to seek on a pipe and the messages always appear.

------------------------------------------------------------------------
r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
Changed paths:
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/razf.c

A bug fix, "samtools view" is now working again.
------------------------------------------------------------------------
r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/faidx.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h
   M /trunk/samtools/razf.c
   M /trunk/samtools/razf.h

 * samtools-0.1.6-5 (r462)
 * Added knetfile support in razf and faidx (on behalf of Petr Danecek)

------------------------------------------------------------------------
r460 | lh3lh3 | 2009-09-09 07:06:22 -0400 (Wed, 09 Sep 2009) | 2 lines
Changed paths:
   M /trunk/samtools/samtools.1

fixed a formatting issue

------------------------------------------------------------------------
r459 | lh3lh3 | 2009-09-08 18:14:08 -0400 (Tue, 08 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.6-4 (r459)
 * make sort output the result to stdout when -o is in use

------------------------------------------------------------------------
r458 | lh3lh3 | 2009-09-07 05:10:28 -0400 (Mon, 07 Sep 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/faidx.c
   M /trunk/samtools/faidx.h
   M /trunk/samtools/samtools.1

 * samtools-0.1.6-2 (r458)
 * added more interface to faidx (by Nils)
 * updated documentation

------------------------------------------------------------------------
r457 | lh3lh3 | 2009-09-05 16:12:04 -0400 (Sat, 05 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.6-2 (r457)
 * get rid of three assert() in bam_sort.c

------------------------------------------------------------------------
r456 | jmarshall | 2009-09-04 12:46:25 -0400 (Fri, 04 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/razf.c

Return NULL from _razf_open() (and hence razf_open()/razf_open2())
when opening the file fails.

------------------------------------------------------------------------
r453 | lh3lh3 | 2009-09-02 08:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1
   D /trunk/samtools/source.dot

Release samtools-0.1.6

------------------------------------------------------------------------
r451 | lh3lh3 | 2009-09-02 05:44:48 -0400 (Wed, 02 Sep 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.5-34 (r451)
 * applied the patch by John
 * improved the help message a little bit

------------------------------------------------------------------------
r450 | lh3lh3 | 2009-09-02 04:55:55 -0400 (Wed, 02 Sep 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_color.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-33 (r450)
 * fixed a bug in bam_color.c (on behalf of Nils Homer)

------------------------------------------------------------------------
r449 | lh3lh3 | 2009-08-29 15:36:41 -0400 (Sat, 29 Aug 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl

 * samtools-0.1.5-32 (r449)
 * fillmd: fixed a bug in modifying MD/NM tags
 * in import, give a warning if the read is aligned but there is no CIGAR.

------------------------------------------------------------------------
r448 | lh3lh3 | 2009-08-19 04:44:28 -0400 (Wed, 19 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/wgsim_eval.pl

 * samtools-0.1.5-31 (r448)
 * fixed an issue when the last CIGAR is I or D

------------------------------------------------------------------------
r447 | lh3lh3 | 2009-08-17 04:34:57 -0400 (Mon, 17 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-30 (r447)
 * fixed a bug in bam_aux_get(): 'A' is not checked

------------------------------------------------------------------------
r446 | lh3lh3 | 2009-08-17 04:33:17 -0400 (Mon, 17 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * 

------------------------------------------------------------------------
r444 | lh3lh3 | 2009-08-11 05:02:36 -0400 (Tue, 11 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-28 (r444)
 * bug in "merge -n"

------------------------------------------------------------------------
r443 | lh3lh3 | 2009-08-11 04:29:11 -0400 (Tue, 11 Aug 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-27 (r443)
 * SEQ and QUAL can be "*"
 * parse CIGAR "=" and "X" as "M"

------------------------------------------------------------------------
r442 | lh3lh3 | 2009-08-07 16:56:38 -0400 (Fri, 07 Aug 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/md5.c
   M /trunk/samtools/misc/md5.h
   M /trunk/samtools/misc/md5fa.c

 * samtools-0.1.5-26 (r442)
 * replace RSA Inc md5.* with ones under permissive lincense
 * fixed a bug in detecting unsorted bam in pileup

------------------------------------------------------------------------
r441 | bhandsaker | 2009-08-05 09:41:28 -0400 (Wed, 05 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/bgzip.c

Change copyright notices now that MIT has approved open source distribution.

------------------------------------------------------------------------
r440 | lh3lh3 | 2009-08-05 05:44:24 -0400 (Wed, 05 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-25 (r436)
 * in flagstats, do not report singletons if both ends are unmapped

------------------------------------------------------------------------
r439 | lh3lh3 | 2009-08-04 17:16:51 -0400 (Tue, 04 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/maq2sam.c

fixed a SERIOUS bug in setting 0x20 flag

------------------------------------------------------------------------
r438 | lh3lh3 | 2009-08-04 16:50:43 -0400 (Tue, 04 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

fixed two minor bugs (suggested by Tim M Storm)

------------------------------------------------------------------------
r437 | lh3lh3 | 2009-08-04 04:13:24 -0400 (Tue, 04 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-24 (r435)
 * fixed a typo

------------------------------------------------------------------------
r434 | lh3lh3 | 2009-08-03 05:40:42 -0400 (Mon, 03 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-23 (r434)
 * in tview, press 'r' to show read names rather than sequences

------------------------------------------------------------------------
r433 | lh3lh3 | 2009-08-02 14:13:35 -0400 (Sun, 02 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/knetfile.c

 * tried to fixed the buggy FTP random access in Windows. FAILED.
 * anyway, MinGW seems to have problem with "%lld".

------------------------------------------------------------------------
r432 | lh3lh3 | 2009-08-01 19:32:07 -0400 (Sat, 01 Aug 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile.mingw
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/faidx.c
   M /trunk/samtools/razf.c
   A /trunk/samtools/win32/libcurses.a
   A /trunk/samtools/win32/xcurses.h

 * samtools-0.1.5-22 (r432)
 * faidx: fixed compitability issue with _WIN32
 * razf: fixed potential compitability issue with _WIN32
 * PDCurses support in Windows

------------------------------------------------------------------------
r431 | lh3lh3 | 2009-08-01 18:34:54 -0400 (Sat, 01 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/win32/libz.a

replace the GnuWin32 version of libz.a with my own build with MinGW.

------------------------------------------------------------------------
r430 | lh3lh3 | 2009-08-01 18:21:07 -0400 (Sat, 01 Aug 2009) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c

add comments

------------------------------------------------------------------------
r429 | lh3lh3 | 2009-08-01 17:41:19 -0400 (Sat, 01 Aug 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile.mingw
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.5-21 (r428)
 * knetfile.c is now compatible with mingw-winsock

------------------------------------------------------------------------
r428 | lh3lh3 | 2009-07-31 19:39:07 -0400 (Fri, 31 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.mingw

simplify MinGW Makefile

------------------------------------------------------------------------
r427 | lh3lh3 | 2009-07-31 19:30:54 -0400 (Fri, 31 Jul 2009) | 5 lines
Changed paths:
   A /trunk/samtools/Makefile.mingw
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/win32
   A /trunk/samtools/win32/libz.a
   A /trunk/samtools/win32/zconf.h
   A /trunk/samtools/win32/zlib.h

 * samtools-0.1.5-20 (r427)
 * MinGW support. At least SAM<->BAM conversion is working. Other
   functionality are not tested at the moment.
 * zlib headers and Windows version of libz.a are included in win32/

------------------------------------------------------------------------
r426 | lh3lh3 | 2009-07-31 18:32:09 -0400 (Fri, 31 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-19 (r426)
 * fixed a bug caused by recent modifications. Sorry.

------------------------------------------------------------------------
r425 | lh3lh3 | 2009-07-31 18:23:51 -0400 (Fri, 31 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bgzf.c

compatible with Windows binary files

------------------------------------------------------------------------
r424 | lh3lh3 | 2009-07-31 05:19:59 -0400 (Fri, 31 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl

 * samtools-0.1.5-18 (r423)
 * output additional information in pileup indel lines, for the purepose
   of debugging at the moment
 * in tview, optionally allow to treat reference skip as deletion

------------------------------------------------------------------------
r423 | lh3lh3 | 2009-07-30 17:00:36 -0400 (Thu, 30 Jul 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/psl2sam.pl

convert BLAT psl to SAM.

------------------------------------------------------------------------
r422 | lh3lh3 | 2009-07-30 06:24:39 -0400 (Thu, 30 Jul 2009) | 6 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-17 (r422)
 * fixed a but in knetfile.c when seek type is not SEEK_SET
 * write an empty BGZF block to every BGZF file
 * check BGZF EOF marker in bam_header_read()
 * update ChangeLog

------------------------------------------------------------------------
r421 | lh3lh3 | 2009-07-30 05:03:39 -0400 (Thu, 30 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-16 (r421)
 * in view and pileup, load header from FASTA index if the input is SAM.

------------------------------------------------------------------------
r420 | lh3lh3 | 2009-07-29 04:18:55 -0400 (Wed, 29 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/maq2sam.c

do not set "read 1" if reads are not mapped in the PE mode of maq

------------------------------------------------------------------------
r419 | lh3lh3 | 2009-07-28 04:52:33 -0400 (Tue, 28 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/samtools.pl
   M /trunk/samtools/misc/wgsim_eval.pl

 * samtools-0.1.5-15 (r419)
 * in sam_open(), return NULL when the file cannot be opened.
 * make wgsim_eval.pl more robust to imperfect SAM
 * add "unique" command to samtools.pl

------------------------------------------------------------------------
r418 | lh3lh3 | 2009-07-24 09:04:19 -0400 (Fri, 24 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/wgsim_eval.pl

skip @header lines in SAM

------------------------------------------------------------------------
r417 | lh3lh3 | 2009-07-24 07:42:38 -0400 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-14 (r417)
 * more help in "samtools view" due to the recent changes.

------------------------------------------------------------------------
r416 | lh3lh3 | 2009-07-24 07:34:30 -0400 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-17 (r416)
 * support import/export SAM with string tags

------------------------------------------------------------------------
r415 | lh3lh3 | 2009-07-24 06:39:26 -0400 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h
   M /trunk/samtools/sam_view.c

 * samtools-0.1.5-12 (r415)
 * FLAG now can be in HEX

------------------------------------------------------------------------
r414 | lh3lh3 | 2009-07-22 17:03:49 -0400 (Wed, 22 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/kstring.h

fixed a compiling error (thank Ken for fixing it)

------------------------------------------------------------------------
r412 | lh3lh3 | 2009-07-21 17:19:40 -0400 (Tue, 21 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/kstring.c
   M /trunk/samtools/kstring.h

Implemented Boyer-Moore search in the kstring library.

------------------------------------------------------------------------
r409 | lh3lh3 | 2009-07-17 12:10:20 -0400 (Fri, 17 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_index.c

do not include knetfile.h when _USE_KNETFILE is not defined

------------------------------------------------------------------------
r408 | lh3lh3 | 2009-07-17 10:29:21 -0400 (Fri, 17 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c

 * samtools-0.1.5-11 (r408)
 * force to overwirte existing MD if it is different from the one calculated
   from fillmd.
 * bgzf.c: improved the compatibility with Windows headers

------------------------------------------------------------------------
r407 | lh3lh3 | 2009-07-17 09:46:56 -0400 (Fri, 17 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.h

 * samtools-0.1.5-10 (r407)
 * implemented bam_aux_del() to remove a tag
 * fillmd: generate the NM tag
 * fillmd: cmd interface improvement

------------------------------------------------------------------------
r406 | lh3lh3 | 2009-07-16 18:30:40 -0400 (Thu, 16 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile

Sorry. The old Makefile is for PDCurses...

------------------------------------------------------------------------
r405 | lh3lh3 | 2009-07-16 18:30:11 -0400 (Thu, 16 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-9 (r405)
 * improved the compatibility with PDCurses a little bit

------------------------------------------------------------------------
r404 | lh3lh3 | 2009-07-16 18:23:52 -0400 (Thu, 16 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-8 (r404)
 * compatible with PDCurses

------------------------------------------------------------------------
r403 | lh3lh3 | 2009-07-16 17:39:39 -0400 (Thu, 16 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kseq.h

 * samtools-0.1.5-7 (r403)
 * fixed a bug in kseq.h for binary files (text files are fine)

------------------------------------------------------------------------
r402 | lh3lh3 | 2009-07-16 06:49:53 -0400 (Thu, 16 Jul 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c

 * samtools-0.1.5-6 (r402)
 * fixed compiling error when "-D_USE_NETFILE" is not applied
 * improve portability to MinGW

------------------------------------------------------------------------
r398 | lh3lh3 | 2009-07-13 05:21:36 -0400 (Mon, 13 Jul 2009) | 3 lines
Changed paths:
   A /trunk/bam-lite/bam.h (from /trunk/samtools/bam.h:395)
   A /trunk/bam-lite/bam_lite.c (from /trunk/samtools/bam_lite.c:395)
   D /trunk/samtools/bam_lite.c

 * move bam_lite.c to bam-lite
 * copy bam.h to bam-lite

------------------------------------------------------------------------
r395 | lh3lh3 | 2009-07-13 05:12:57 -0400 (Mon, 13 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_lite.c
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-5 (r395)
 * added bam_pileup_file() and removed bam_lpileup_file()

------------------------------------------------------------------------
r394 | lh3lh3 | 2009-07-12 19:35:10 -0400 (Sun, 12 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.5-4 (r394)
 * http_proxy support in knetfile library (check http_proxy ENV)

------------------------------------------------------------------------
r393 | lh3lh3 | 2009-07-12 18:57:07 -0400 (Sun, 12 Jul 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.5-3 (r393)
 * knetfile now supports HTTP (no proxy at the moment)
 * fixed a potential issue in knetfile on opening ordinary file, although I have
   not seen the sideeffect so far.

------------------------------------------------------------------------
r392 | lh3lh3 | 2009-07-12 13:50:55 -0400 (Sun, 12 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/samtools.1

Remove the warning in tview

------------------------------------------------------------------------
r391 | lh3lh3 | 2009-07-12 13:42:43 -0400 (Sun, 12 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-2 (r391)
 * do not show a blank screen when no reads mapped

------------------------------------------------------------------------
r390 | lh3lh3 | 2009-07-09 09:01:42 -0400 (Thu, 09 Jul 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.h
   A /trunk/samtools/bam_lite.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.5-1 (r390)
 * removed useless _IOLIB in bam.h. This should cause no change at all.
 * added bam_lite.c for light-weight BAM reading

------------------------------------------------------------------------
r385 | lh3lh3 | 2009-07-07 11:53:29 -0400 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c

Release samtools-0.1.5c (fixed a bug in piping)

------------------------------------------------------------------------
r383 | lh3lh3 | 2009-07-07 06:39:55 -0400 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c

Release samtools-0.1.5b (BUG! so embarrassing!)

------------------------------------------------------------------------
r381 | lh3lh3 | 2009-07-07 06:20:06 -0400 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)

------------------------------------------------------------------------
r373 | lh3lh3 | 2009-07-07 05:26:57 -0400 (Tue, 07 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

Release samtools-0.1.5

------------------------------------------------------------------------
r372 | lh3lh3 | 2009-07-07 04:49:27 -0400 (Tue, 07 Jul 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c

 * samtools-0.1.4-23 (r372)
 * keep header text if "view -t" is used (by Gerton)

------------------------------------------------------------------------
r371 | lh3lh3 | 2009-07-06 20:13:32 -0400 (Mon, 06 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/samtools.1

update documentation

------------------------------------------------------------------------
r370 | bhandsaker | 2009-07-02 17:24:34 -0400 (Thu, 02 Jul 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile

Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.

------------------------------------------------------------------------
r369 | lh3lh3 | 2009-07-02 08:36:53 -0400 (Thu, 02 Jul 2009) | 4 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-22 (r369)
 * in pileup, optionally print E2 and U2
 * remove the debugging code in bam_aux_get() (Drat!)

------------------------------------------------------------------------
r368 | lh3lh3 | 2009-07-02 06:32:26 -0400 (Thu, 02 Jul 2009) | 6 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/faidx.c
   M /trunk/samtools/faidx.h
   M /trunk/samtools/glf.c

 * samtools-0.1.4-21 (r368)
 * propagate errors rather than exit or complain assertion failure. Assertion
   should be only used for checking internal bugs, but not for external input
   inconsistency. I was just a bit lazy.
 * small memory leak may be present on failure, though

------------------------------------------------------------------------
r367 | lh3lh3 | 2009-06-30 11:18:42 -0400 (Tue, 30 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c

reduce the chance of blocking in FTP connection

------------------------------------------------------------------------
r366 | lh3lh3 | 2009-06-30 10:35:21 -0400 (Tue, 30 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c

minor changes to knetfile: invalid fd equals -1 rather than 0

------------------------------------------------------------------------
r365 | lh3lh3 | 2009-06-30 09:04:30 -0400 (Tue, 30 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.4-20 (r365)
 * download the BAM index file if it is not found in the current working directory.

------------------------------------------------------------------------
r364 | lh3lh3 | 2009-06-30 07:39:07 -0400 (Tue, 30 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/knetfile.c

 * samtools-0.1.4-19 (r364)
 * knetfile: report error when the file is not present on FTP

------------------------------------------------------------------------
r363 | lh3lh3 | 2009-06-29 18:23:32 -0400 (Mon, 29 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.4-18 (r363)
 * knetfile: do not trigger network communication in FTP seek (lazy seek)
 * bgzf: cache recent blocks (disabled by default)

------------------------------------------------------------------------
r362 | lh3lh3 | 2009-06-25 16:04:34 -0400 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bgzf.c

write changelog

------------------------------------------------------------------------
r361 | lh3lh3 | 2009-06-25 16:03:10 -0400 (Thu, 25 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-17 (r361)
 * if a file is given on FTP, search locally for the BAM index

------------------------------------------------------------------------
r360 | lh3lh3 | 2009-06-25 15:44:52 -0400 (Thu, 25 Jun 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

 * samtools-0.1.4-16 (r360)
 * report more information in index when the input is not sorted
 * change the behaviour of knet_seek() such that it returns 0 on success
 * support knetfile library in BGZF

------------------------------------------------------------------------
r359 | lh3lh3 | 2009-06-25 12:10:55 -0400 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/knetfile.c
   M /trunk/samtools/knetfile.h

fixed bugs in knetfile.*

------------------------------------------------------------------------
r358 | lh3lh3 | 2009-06-25 08:53:19 -0400 (Thu, 25 Jun 2009) | 2 lines
Changed paths:
   A /trunk/samtools/knetfile.h

this is the header file

------------------------------------------------------------------------
r357 | lh3lh3 | 2009-06-25 08:52:03 -0400 (Thu, 25 Jun 2009) | 3 lines
Changed paths:
   A /trunk/samtools/knetfile.c

 * open a file at FTP
 * preliminary version

------------------------------------------------------------------------
r354 | lh3lh3 | 2009-06-24 09:02:25 -0400 (Wed, 24 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-15 (r354)
 * fixed a memory leak in bam_view1(), although samtools is not using this routine.

------------------------------------------------------------------------
r351 | lh3lh3 | 2009-06-17 19:16:26 -0400 (Wed, 17 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/faidx.c

 * samtools-0.1.4-13 (r351)
 * make faidx more tolerant to empty lines right before or after > lines
 * hope this does not introduce new bugs...

------------------------------------------------------------------------
r350 | lh3lh3 | 2009-06-16 09:37:01 -0400 (Tue, 16 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-13 (r350)
 * fixed a small memory leak in pileup, caused by recent modifications

------------------------------------------------------------------------
r347 | lh3lh3 | 2009-06-13 16:20:49 -0400 (Sat, 13 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.4-12 (r347)
 * added `-S' to pileup, similar to `view -S' 

------------------------------------------------------------------------
r346 | lh3lh3 | 2009-06-13 12:52:31 -0400 (Sat, 13 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.4-11 (r346)
 * allow to select a read group at view command-line

------------------------------------------------------------------------
r344 | lh3lh3 | 2009-06-13 09:06:24 -0400 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/examples/calDepth.c

added more comments

------------------------------------------------------------------------
r343 | lh3lh3 | 2009-06-13 09:01:22 -0400 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/examples/calDepth.c

nothing really

------------------------------------------------------------------------
r342 | lh3lh3 | 2009-06-13 08:58:48 -0400 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/examples/Makefile
   A /trunk/samtools/examples/calDepth.c

added an example of calculating read depth

------------------------------------------------------------------------
r341 | lh3lh3 | 2009-06-13 08:00:08 -0400 (Sat, 13 Jun 2009) | 6 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   A /trunk/samtools/bam_color.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h

 * samtools-0.1.4-10 (r341)
 * only include key APIs in libbam.a
 * move color-specific routines to bam_color.c
 * update documentations
 * remove the support of -q in pileup

------------------------------------------------------------------------
r340 | lh3lh3 | 2009-06-13 06:17:14 -0400 (Sat, 13 Jun 2009) | 6 lines
Changed paths:
   M /trunk/samtools/INSTALL
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/razf.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.4-9 (r340)
 * added a warning to razf.c if zlib<1.2.2.1
 * fixed a compilation warning
 * fixed a segfault caused by @RG parsing
 * detect NCURSES in bam_tview.c

------------------------------------------------------------------------
r339 | lh3lh3 | 2009-06-13 05:35:19 -0400 (Sat, 13 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/INSTALL

update INSTALL

------------------------------------------------------------------------
r338 | lh3lh3 | 2009-06-12 19:15:24 -0400 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kstring.h
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.4-8 (r338)
 * parse the @RG header lines and allow to choose library at the "samtools view"
   command line

------------------------------------------------------------------------
r337 | lh3lh3 | 2009-06-12 16:25:50 -0400 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.4-7 (r337)
 * bgzf.c: support mode string "wu": uncompressed output
 * "samtools view" support "-u" command-line option

------------------------------------------------------------------------
r336 | lh3lh3 | 2009-06-12 12:20:12 -0400 (Fri, 12 Jun 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/misc/Makefile
   M /trunk/samtools/razf.c
   M /trunk/samtools/razf.h
   M /trunk/samtools/razip.c

 * no changes to samtools itself
 * remove zlib source codes
 * make RAZF reading compatible with old version of zlib
 * on old version of zlib, writing is not available

------------------------------------------------------------------------
r335 | lh3lh3 | 2009-06-12 11:47:33 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   D /trunk/samtools/zlib

remove zlib for simplification...

------------------------------------------------------------------------
r334 | lh3lh3 | 2009-06-12 10:43:36 -0400 (Fri, 12 Jun 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-6 (r334)
 * do not export bam_aux_get_core() for Bio::DB::Sam because it has already
   been implemented in that.
 * this version works with the latest Bio::DB::Sam (20090612)

------------------------------------------------------------------------
r333 | lh3lh3 | 2009-06-12 10:33:42 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog

update ChangeLog

------------------------------------------------------------------------
r332 | lh3lh3 | 2009-06-12 10:21:21 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/AUTHORS
   M /trunk/samtools/Makefile
   M /trunk/samtools/misc/Makefile

fixed minor things in Makefile

------------------------------------------------------------------------
r331 | lh3lh3 | 2009-06-12 10:07:05 -0400 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-5 (r3310
 * no change to samtools itself. Version number is increased to reflect the
   changes in the Makefile building system.

------------------------------------------------------------------------
r330 | lh3lh3 | 2009-06-12 10:03:38 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/AUTHORS
   D /trunk/samtools/README

update information...

------------------------------------------------------------------------
r329 | lh3lh3 | 2009-06-12 09:52:21 -0400 (Fri, 12 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/novo2sam.pl

 * updated novoalign converter by Colin Hercus et al.
 * this version works with indels

------------------------------------------------------------------------
r328 | lh3lh3 | 2009-06-12 09:50:53 -0400 (Fri, 12 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/INSTALL
   M /trunk/samtools/Makefile
   M /trunk/samtools/misc/Makefile
   M /trunk/samtools/zlib/Makefile

 * update Makefile
 * update INSTALL instruction

------------------------------------------------------------------------
r327 | lh3lh3 | 2009-06-12 09:18:29 -0400 (Fri, 12 Jun 2009) | 4 lines
Changed paths:
   A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.generic:325)
   D /trunk/samtools/Makefile.am
   D /trunk/samtools/Makefile.generic
   D /trunk/samtools/Makefile.lite
   D /trunk/samtools/autogen.sh
   D /trunk/samtools/cleanup.sh
   D /trunk/samtools/configure.ac
   A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.generic:305)
   D /trunk/samtools/misc/Makefile.am
   D /trunk/samtools/misc/Makefile.generic
   M /trunk/samtools/razf.c
   A /trunk/samtools/zlib
   A /trunk/samtools/zlib/Makefile
   A /trunk/samtools/zlib/adler32.c
   A /trunk/samtools/zlib/compress.c
   A /trunk/samtools/zlib/crc32.c
   A /trunk/samtools/zlib/crc32.h
   A /trunk/samtools/zlib/deflate.c
   A /trunk/samtools/zlib/deflate.h
   A /trunk/samtools/zlib/gzio.c
   A /trunk/samtools/zlib/infback.c
   A /trunk/samtools/zlib/inffast.c
   A /trunk/samtools/zlib/inffast.h
   A /trunk/samtools/zlib/inffixed.h
   A /trunk/samtools/zlib/inflate.c
   A /trunk/samtools/zlib/inflate.h
   A /trunk/samtools/zlib/inftrees.c
   A /trunk/samtools/zlib/inftrees.h
   A /trunk/samtools/zlib/trees.c
   A /trunk/samtools/zlib/trees.h
   A /trunk/samtools/zlib/uncompr.c
   A /trunk/samtools/zlib/zconf.h
   A /trunk/samtools/zlib/zlib.h
   A /trunk/samtools/zlib/zutil.c
   A /trunk/samtools/zlib/zutil.h
   D /trunk/samtools/zutil.h

 * added zlib-1.2.3 as razip requires that
 * prepare to changed back to the Makefile building system
 * unfinished! (will be soon)

------------------------------------------------------------------------
r326 | lh3lh3 | 2009-06-12 09:12:03 -0400 (Fri, 12 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

Unfinished

------------------------------------------------------------------------
r325 | lh3lh3 | 2009-06-10 11:27:59 -0400 (Wed, 10 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.4-4 (r325)
 * further avoid wrong consensus calls in repetitive regions.

------------------------------------------------------------------------
r324 | lh3lh3 | 2009-06-10 10:56:17 -0400 (Wed, 10 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h

 * samtools-0.1.4-3 (r324)
 * make maqcns generate the correct call in repetitive regions.
 * allow filtering on mapQ at the pileup command line

------------------------------------------------------------------------
r323 | lh3lh3 | 2009-06-10 05:04:21 -0400 (Wed, 10 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.3.2 (r322)
 * indels and SNPs use different mapping quality threshold

------------------------------------------------------------------------
r322 | lh3lh3 | 2009-06-10 05:03:22 -0400 (Wed, 10 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/export2sam.pl

fixed a typo

------------------------------------------------------------------------
r321 | lh3lh3 | 2009-06-09 04:21:48 -0400 (Tue, 09 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

just typo. no real change

------------------------------------------------------------------------
r320 | lh3lh3 | 2009-06-08 09:32:51 -0400 (Mon, 08 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

a little bit code cleanup

------------------------------------------------------------------------
r319 | lh3lh3 | 2009-06-08 09:22:33 -0400 (Mon, 08 Jun 2009) | 4 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.3.1
 * change default parameters
 * optionally print filtered variants

------------------------------------------------------------------------
r318 | lh3lh3 | 2009-06-08 09:14:26 -0400 (Mon, 08 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.3.0
 * combine snpFilter and indelFilter

------------------------------------------------------------------------
r317 | lh3lh3 | 2009-06-08 06:31:42 -0400 (Mon, 08 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.2.3
 * change a default parameter

------------------------------------------------------------------------
r316 | lh3lh3 | 2009-06-08 06:11:06 -0400 (Mon, 08 Jun 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c

 * samtools-0.1.4-2 (r316)
 * pileup: cap mapping quality at 60 (by default)
 * pileup: always calculate RMS mapq
 * pileup: allow to output variant sites only

------------------------------------------------------------------------
r312 | lh3lh3 | 2009-06-04 08:01:10 -0400 (Thu, 04 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.2.2
 * added pileup2fq

------------------------------------------------------------------------
r311 | lh3lh3 | 2009-06-03 04:40:40 -0400 (Wed, 03 Jun 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * in snpFilter, suppress non-SNP sites

------------------------------------------------------------------------
r310 | lh3lh3 | 2009-06-01 09:35:13 -0400 (Mon, 01 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.2.1
 * fixed a typo

------------------------------------------------------------------------
r309 | lh3lh3 | 2009-06-01 09:04:39 -0400 (Mon, 01 Jun 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.2.0
 * snpFilter

------------------------------------------------------------------------
r306 | lh3lh3 | 2009-05-28 06:49:35 -0400 (Thu, 28 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bgzf.c

 * minor changes to bgzf: return NULL if fd == -1
 * suggested by {kdj,jm18}@sanger.ac.uk

------------------------------------------------------------------------
r305 | lh3lh3 | 2009-05-28 06:16:08 -0400 (Thu, 28 May 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/interpolate_sam.pl

Script for paired-end pileup, contributed by Stephen Montgomery.

------------------------------------------------------------------------
r304 | lh3lh3 | 2009-05-28 06:08:49 -0400 (Thu, 28 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c

 * samtools-0.1.4-1 (r304)
 * fixed a minor bug in printing headers

------------------------------------------------------------------------
r297 | lh3lh3 | 2009-05-21 11:06:16 -0400 (Thu, 21 May 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/maq2sam.c
   M /trunk/samtools/samtools.1

Release samtools-0.1.4

------------------------------------------------------------------------
r296 | lh3lh3 | 2009-05-21 07:53:14 -0400 (Thu, 21 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-24 (r296)
 * another similar bug in the indel caller

------------------------------------------------------------------------
r295 | lh3lh3 | 2009-05-21 07:50:28 -0400 (Thu, 21 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-23 (r295)
 * fixed a critical bug in the indel caller

------------------------------------------------------------------------
r294 | lh3lh3 | 2009-05-20 08:00:20 -0400 (Wed, 20 May 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_stat.c

added a missing header file

------------------------------------------------------------------------
r293 | lh3lh3 | 2009-05-19 18:44:25 -0400 (Tue, 19 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-22 (r293)
 * open tview in the dot-view mode by default

------------------------------------------------------------------------
r292 | lh3lh3 | 2009-05-18 16:01:23 -0400 (Mon, 18 May 2009) | 6 lines
Changed paths:
   M /trunk/samtools/samtools.1

Added a note to the manual. Currently SAMtools used unaligned words in
several places. Although this does not cause bus errors to me, it may
affect portability. Please see the "Bus error" wiki page for more
information. Also thank James Bonfields for pointing this out.


------------------------------------------------------------------------
r286 | lh3lh3 | 2009-05-14 10:23:13 -0400 (Thu, 14 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-21 (286)
 * declare bam_aux_get_core() in bam.h

------------------------------------------------------------------------
r276 | lh3lh3 | 2009-05-13 05:07:55 -0400 (Wed, 13 May 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-20 (r276)
 * remove bam1_t::hash again. We need to modify the Perl API anyway to
   make it work with the latest SVN.
 * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index

------------------------------------------------------------------------
r275 | lh3lh3 | 2009-05-12 16:14:10 -0400 (Tue, 12 May 2009) | 4 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam.h
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-19 (r275)
 * a minor change to the bam1_t struct: added back "void *hash" for the
   backward compatibility with Bio::DB::Sam

------------------------------------------------------------------------
r273 | lh3lh3 | 2009-05-12 09:28:39 -0400 (Tue, 12 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-18 (r273)
 * rmdupse: do not remove unmapped reads

------------------------------------------------------------------------
r272 | lh3lh3 | 2009-05-12 09:20:00 -0400 (Tue, 12 May 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_rmdupse.c

change a parameter. It does nothing

------------------------------------------------------------------------
r271 | lh3lh3 | 2009-05-12 09:17:58 -0400 (Tue, 12 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile.am
   M /trunk/samtools/Makefile.generic
   M /trunk/samtools/Makefile.lite
   A /trunk/samtools/bam_rmdupse.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/configure.ac

 * samtools-0.1.3-17 (r271)
 * added 'rmdupse' command

------------------------------------------------------------------------
r267 | lh3lh3 | 2009-05-05 17:31:41 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.3-16 (r267)
 * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs

------------------------------------------------------------------------
r266 | lh3lh3 | 2009-05-05 17:23:27 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-15 (r266)
 * report an error if a non-* reference is present while @SQ is absent

------------------------------------------------------------------------
r265 | lh3lh3 | 2009-05-05 17:09:00 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.3-14 (r262)
 * make samopen() recognize @SQ header lines

------------------------------------------------------------------------
r261 | lh3lh3 | 2009-05-05 10:10:30 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam_view.c

 * samtools-0.1.3-13 (r260)
 * report error for file I/O error

------------------------------------------------------------------------
r260 | lh3lh3 | 2009-05-05 10:01:16 -0400 (Tue, 05 May 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.am

update Makefile.am

------------------------------------------------------------------------
r259 | lh3lh3 | 2009-05-05 09:52:25 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/sam.c
   M /trunk/samtools/sam.h

 * samtools-0.1.3-12 (r259)
 * use the new I/O interface in pileup

------------------------------------------------------------------------
r258 | lh3lh3 | 2009-05-05 09:33:22 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile.generic
   M /trunk/samtools/Makefile.lite
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/sam.c
   A /trunk/samtools/sam.h
   A /trunk/samtools/sam_view.c

 * samtools-0.1.3-11 (r258)
 * unify the interface to BAM and SAM I/O

------------------------------------------------------------------------
r257 | lh3lh3 | 2009-05-05 04:53:35 -0400 (Tue, 05 May 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile.lite
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-10 (r257)
 * allow hex with "pileup -m"

------------------------------------------------------------------------
r256 | lh3lh3 | 2009-05-04 14:16:50 -0400 (Mon, 04 May 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-9 (r256)
 * fixed a bug in bam_lpileup.c
 * I do not know if this also fixes the bug causing assertion failure in the tview

------------------------------------------------------------------------
r251 | lh3lh3 | 2009-04-28 08:53:23 -0400 (Tue, 28 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-8 (r251)
 * fixed a bug when there are reads without coordinates

------------------------------------------------------------------------
r250 | lh3lh3 | 2009-04-28 08:43:33 -0400 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
   A /trunk/samtools/AUTHORS
   A /trunk/samtools/README
   M /trunk/samtools/cleanup.sh

added missing files

------------------------------------------------------------------------
r249 | lh3lh3 | 2009-04-28 08:37:16 -0400 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.generic
   M /trunk/samtools/Makefile.lite
   M /trunk/samtools/configure.ac
   M /trunk/samtools/misc/Makefile.generic

improve large file support in compilation

------------------------------------------------------------------------
r248 | lh3lh3 | 2009-04-28 08:33:24 -0400 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/INSTALL

update INSTALL

------------------------------------------------------------------------
r247 | lh3lh3 | 2009-04-28 08:28:50 -0400 (Tue, 28 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.am
   M /trunk/samtools/autogen.sh
   M /trunk/samtools/cleanup.sh
   M /trunk/samtools/configure.ac
   A /trunk/samtools/misc/Makefile.am

fixed various issues about the GNU building scripts

------------------------------------------------------------------------
r246 | lh3lh3 | 2009-04-28 08:10:23 -0400 (Tue, 28 Apr 2009) | 4 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   D /trunk/samtools/Makefile
   A /trunk/samtools/Makefile.am
   A /trunk/samtools/Makefile.generic
   A /trunk/samtools/autogen.sh
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   A /trunk/samtools/cleanup.sh
   A /trunk/samtools/configure.ac
   D /trunk/samtools/misc/Makefile
   A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)

 * samtools-0.1.3-7 (r246)
 * incorporated revisions from Nils Homer
 * enhanced support of displaying color-space reads

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r244 | lh3lh3 | 2009-04-25 06:49:40 -0400 (Sat, 25 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-6 (r244)
 * fixed segfault for unmapped reads

------------------------------------------------------------------------
r243 | lh3lh3 | 2009-04-24 16:27:26 -0400 (Fri, 24 Apr 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-5 (r243)
 * fixed a long existing bug which may cause memory leak
 * check MD
 * consensus calling now works with "=", but indel calling not

------------------------------------------------------------------------
r242 | lh3lh3 | 2009-04-24 15:44:46 -0400 (Fri, 24 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_md.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-4 (r242)
 * fixed a memory leak

------------------------------------------------------------------------
r240 | lh3lh3 | 2009-04-24 11:40:18 -0400 (Fri, 24 Apr 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/Makefile.lite
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   A /trunk/samtools/bam_md.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-3 (r240)
 * generate MD tag
 * generate "=" bases
 * the plain pileup now support "=" bases, but consensus calling and glfgen may fail

------------------------------------------------------------------------
r239 | lh3lh3 | 2009-04-24 07:08:20 -0400 (Fri, 24 Apr 2009) | 5 lines
Changed paths:
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_aux.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-2 (r239)
 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
 * removed bam_aux_init()/bam_aux_destroy()
 * added tagview for testing bam_aux

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r235 | lh3lh3 | 2009-04-21 18:17:39 -0400 (Tue, 21 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.3-1
 * fixed a bug in pileup: the first read in a chromosome may not be printed

------------------------------------------------------------------------
r232 | lh3lh3 | 2009-04-16 10:25:43 -0400 (Thu, 16 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.lite

a missing file in Makefile.lite

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r227 | lh3lh3 | 2009-04-15 17:02:53 -0400 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c

Release samtools-0.1.3

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r223 | lh3lh3 | 2009-04-15 09:31:32 -0400 (Wed, 15 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-28
 * make samtools more robust to weird input such as empty file

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r222 | lh3lh3 | 2009-04-15 09:05:33 -0400 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/samtools.1

prepare for release 0.1.3

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r221 | lh3lh3 | 2009-04-15 08:32:14 -0400 (Wed, 15 Apr 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/blast2sam.pl

convert NCBI-BLASTN to SAM

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r220 | lh3lh3 | 2009-04-15 08:18:19 -0400 (Wed, 15 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-27
 * fixed a small memory leak in tview

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r219 | lh3lh3 | 2009-04-15 08:00:08 -0400 (Wed, 15 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_rmdup.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-26
 * fixed a bug in rmdup when there are unmapped reads

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r218 | lh3lh3 | 2009-04-14 17:28:58 -0400 (Tue, 14 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS

proposed NEWS for the new release (have not yet)

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r216 | lh3lh3 | 2009-04-14 17:10:46 -0400 (Tue, 14 Apr 2009) | 4 lines
Changed paths:
   M /trunk/samtools/misc/samtools.pl

 * samtools.pl-0.1.1
 * improve indelFilter to avoid filtering true indels. The new filter relies
   on the new pileup indel line implemented in samtools-0.1.2-25

------------------------------------------------------------------------
r215 | lh3lh3 | 2009-04-14 17:04:19 -0400 (Tue, 14 Apr 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

 * samtools-0.1.2-25
 * change the pileup indel line to shows the number of alignments actually
   containing indels

------------------------------------------------------------------------
r211 | lh3lh3 | 2009-04-13 07:07:13 -0400 (Mon, 13 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog

update ChangeLog from "svn log"

------------------------------------------------------------------------
r210 | lh3lh3 | 2009-04-12 15:57:05 -0400 (Sun, 12 Apr 2009) | 4 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kseq.h

 * samtools-0.1.2-24
 * in merge, gives a warning rather than error if the target sequence length is different
 * allow empty header

------------------------------------------------------------------------
r209 | lh3lh3 | 2009-04-12 15:32:44 -0400 (Sun, 12 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-23
 * recognize '*' at the QUAL field

------------------------------------------------------------------------
r208 | lh3lh3 | 2009-04-12 15:08:02 -0400 (Sun, 12 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kseq.h

 * samtools-0.1.2-22
 * the field separater is TAB only, now

------------------------------------------------------------------------
r207 | lh3lh3 | 2009-04-08 10:18:03 -0400 (Wed, 08 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/examples/ex1.sam.gz

 * fixed the problem in the example alignment due to the bug in fixmate

------------------------------------------------------------------------
r206 | lh3lh3 | 2009-04-08 10:15:05 -0400 (Wed, 08 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_mate.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/soap2sam.pl

 * samtools-0.1.2-21
 * fixed a nasty bug in `fixmate'

------------------------------------------------------------------------
r205 | lh3lh3 | 2009-04-08 05:57:08 -0400 (Wed, 08 Apr 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/bowtie2sam.pl
   M /trunk/samtools/misc/soap2sam.pl
   M /trunk/samtools/misc/wgsim_eval.pl

make the script robust to the bugs in SOAP-2.1.7

------------------------------------------------------------------------
r200 | lh3lh3 | 2009-04-02 10:14:56 -0400 (Thu, 02 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-20
 * check if file is truncated in flagstat

------------------------------------------------------------------------
r199 | lh3lh3 | 2009-04-02 10:09:10 -0400 (Thu, 02 Apr 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-19
 * print the header if requested

------------------------------------------------------------------------
r193 | lh3lh3 | 2009-03-27 11:09:50 -0400 (Fri, 27 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-18
 * fixed a minor bug reported by Nils Homer

------------------------------------------------------------------------
r185 | lh3lh3 | 2009-03-24 07:50:32 -0400 (Tue, 24 Mar 2009) | 2 lines
Changed paths:
   A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184)
   D /trunk/samtools/Makefile.std
   A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184)
   D /trunk/samtools/misc/Makefile.std

rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...

------------------------------------------------------------------------
r184 | lh3lh3 | 2009-03-24 06:36:38 -0400 (Tue, 24 Mar 2009) | 4 lines
Changed paths:
   D /trunk/samtools/Makefile
   A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183)
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bam_tview.c
   M /trunk/samtools/bamtk.c
   D /trunk/samtools/misc/Makefile
   A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182)
   M /trunk/samtools/samtools.1

 * samtools-0.1.2-17
 * incorporating Nils' changes
 * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils)

------------------------------------------------------------------------
r183 | lh3lh3 | 2009-03-24 06:30:23 -0400 (Tue, 24 Mar 2009) | 4 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/kseq.h
   A /trunk/samtools/kstring.c
   A /trunk/samtools/kstring.h

 * samtools-0.1.2-16
 * made pileup take a list of proposed indels. An insertion is N at the moment.
 * added my kstring library for a bit complex parsing of the position list.

------------------------------------------------------------------------
r169 | lh3lh3 | 2009-03-12 09:40:14 -0400 (Thu, 12 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/soap2sam.pl

 * soap2sam.pl-0.1.2
 * more robust to truncated soap output

------------------------------------------------------------------------
r168 | lh3lh3 | 2009-03-11 06:49:00 -0400 (Wed, 11 Mar 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile.lite

added bam_stat.o to Makefile.lite

------------------------------------------------------------------------
r167 | lh3lh3 | 2009-03-10 18:11:31 -0400 (Tue, 10 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-15
 * generate RMS of mapQ instead of max mapQ

------------------------------------------------------------------------
r166 | lh3lh3 | 2009-03-10 18:06:45 -0400 (Tue, 10 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/glf.c
   M /trunk/samtools/glf.h
   M /trunk/samtools/misc/Makefile

 * samtools-0.1.2-14
 * implemented GLFv3

------------------------------------------------------------------------
r159 | lh3lh3 | 2009-03-03 06:26:08 -0500 (Tue, 03 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-13
 * fixed a minor bug in displaying pileup

------------------------------------------------------------------------
r158 | lh3lh3 | 2009-03-03 06:24:16 -0500 (Tue, 03 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-12
 * optionally print SAM header

------------------------------------------------------------------------
r153 | lh3lh3 | 2009-03-02 05:45:28 -0500 (Mon, 02 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/glf.c

 * samtools-0.1.2-11
 * use "GLF\3" as the magic for GLFv3 files

------------------------------------------------------------------------
r152 | lh3lh3 | 2009-03-02 05:39:09 -0500 (Mon, 02 Mar 2009) | 5 lines
Changed paths:
   M /trunk/samtools/Makefile
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/glf.c
   M /trunk/samtools/glf.h

 * samtools-0.1.2-10
 * fixed a bug in import: core.bin is undefined for unmapped reads
 * this bug can be alleviated (not completely solved) in bam_index.c
 * update to GLFv3: pos is changed to offset for better compression

------------------------------------------------------------------------
r151 | lh3lh3 | 2009-03-01 10:18:43 -0500 (Sun, 01 Mar 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/wgsim.c

 * wgsim-0.2.3
 * fixed a bug in simulating indels

------------------------------------------------------------------------
r145 | lh3lh3 | 2009-02-26 14:43:57 -0500 (Thu, 26 Feb 2009) | 4 lines
Changed paths:
   M /trunk/samtools/misc/wgsim.c

 * wgsim-0.2.2
 * allow to print mismatch information as fastq comment. MAQ does
   not like long read names.

------------------------------------------------------------------------
r141 | lh3lh3 | 2009-02-26 09:53:03 -0500 (Thu, 26 Feb 2009) | 6 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/misc/wgsim.c
   M /trunk/samtools/misc/wgsim_eval.pl

 * wgsim-0.2.1
 * fixed a bug about color read coordinates
 * fixed a bug in read names
 * wgsim_eval.pl-0.1.3
 * make the script work with color reads

------------------------------------------------------------------------
r140 | lh3lh3 | 2009-02-26 09:02:57 -0500 (Thu, 26 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/Makefile
   M /trunk/samtools/misc/wgsim.c

 * wgsim: added a note

------------------------------------------------------------------------
r139 | lh3lh3 | 2009-02-26 06:39:08 -0500 (Thu, 26 Feb 2009) | 7 lines
Changed paths:
   M /trunk/samtools/misc/wgsim.c
   M /trunk/samtools/misc/wgsim_eval.pl

 * wgsim-0.2.0
 * considerable code clean up
 * print number of substitutions/indels/errors on each read
 * potentially support SOLiD simulation, though not tested at the moment
 * wgsim_eval.pl-0.1.2
 * change in accordant with wgsim

------------------------------------------------------------------------
r129 | lh3lh3 | 2009-02-18 17:23:27 -0500 (Wed, 18 Feb 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-9
 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks

------------------------------------------------------------------------
r128 | bhandsaker | 2009-02-18 14:06:57 -0500 (Wed, 18 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bamtk.c

Fix annoying segv when invalid region specified.

------------------------------------------------------------------------
r127 | lh3lh3 | 2009-02-17 05:49:55 -0500 (Tue, 17 Feb 2009) | 2 lines
Changed paths:
   D /trunk/samtools/misc/indel_filter.pl
   A /trunk/samtools/misc/samtools.pl

 * move indel_filter.pl to samtools.pl

------------------------------------------------------------------------
r126 | lh3lh3 | 2009-02-14 16:22:30 -0500 (Sat, 14 Feb 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_mate.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-7
 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP

------------------------------------------------------------------------
r125 | lh3lh3 | 2009-02-13 04:54:45 -0500 (Fri, 13 Feb 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-7
 * fixed a minor bug in flagstat

------------------------------------------------------------------------
r124 | lh3lh3 | 2009-02-12 06:15:32 -0500 (Thu, 12 Feb 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/misc/indel_filter.pl

 * samtools-0.1.2-6
 * improve indel caller by setting maximum window size

------------------------------------------------------------------------
r123 | lh3lh3 | 2009-02-12 05:30:29 -0500 (Thu, 12 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bamtk.c

 * output max mapping quality in indel line

------------------------------------------------------------------------
r122 | lh3lh3 | 2009-02-11 05:59:10 -0500 (Wed, 11 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/misc/maq2sam.c

fixed a bug in generating tag AM

------------------------------------------------------------------------
r121 | lh3lh3 | 2009-02-03 05:43:11 -0500 (Tue, 03 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bamtk.c

fixed a potential memory problem in indexing

------------------------------------------------------------------------
r120 | bhandsaker | 2009-02-02 10:52:52 -0500 (Mon, 02 Feb 2009) | 2 lines
Changed paths:
   M /trunk/samtools/Makefile

Pass LIBS to recursive targets to facilitate building at Broad.

------------------------------------------------------------------------
r119 | lh3lh3 | 2009-02-02 05:12:15 -0500 (Mon, 02 Feb 2009) | 4 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/bam_plcmd.c
   M /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-3
 * fixed a bug in generating GLFv2 for indels
 * improve flagstat report a little bit

------------------------------------------------------------------------
r118 | lh3lh3 | 2009-01-29 07:33:23 -0500 (Thu, 29 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   A /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-1
 * added flagstat command

------------------------------------------------------------------------
r116 | lh3lh3 | 2009-01-28 08:31:12 -0500 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

Release SAMtools-0.1.2

------------------------------------------------------------------------
r115 | lh3lh3 | 2009-01-28 07:54:08 -0500 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/indel_filter.pl

Script for filtering indel results

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r114 | lh3lh3 | 2009-01-25 06:45:37 -0500 (Sun, 25 Jan 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/zoom2sam.pl

convert ZOOM to SAM

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r113 | lh3lh3 | 2009-01-24 09:25:07 -0500 (Sat, 24 Jan 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/novo2sam.pl

add a script to convert novo alignment to SAM

------------------------------------------------------------------------
r112 | lh3lh3 | 2009-01-23 15:57:39 -0500 (Fri, 23 Jan 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/ChangeLog.old
   M /trunk/samtools/samtools.1

update documentation and ChangeLog

------------------------------------------------------------------------
r111 | lh3lh3 | 2009-01-23 14:22:59 -0500 (Fri, 23 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.1-19
 * fixed a bug in "merge" command line

------------------------------------------------------------------------
r110 | lh3lh3 | 2009-01-22 10:36:48 -0500 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/Makefile
   A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
   M /trunk/samtools/misc/export2sam.pl
   A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
   A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
   A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)

 * merge from branches/dev/
 * all future development will happen here

------------------------------------------------------------------------
r109 | lh3lh3 | 2009-01-22 10:14:27 -0500 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/COPYING
   M /trunk/samtools/ChangeLog
   A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
   M /trunk/samtools/Makefile
   A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/examples/00README.txt
   A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
   D /trunk/samtools/examples/ex1.fa.fai
   M /trunk/samtools/examples/ex1.sam.gz
   M /trunk/samtools/faidx.c
   A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
   M /trunk/samtools/glf.h
   M /trunk/samtools/misc/Makefile
   M /trunk/samtools/misc/maq2sam.c
   M /trunk/samtools/razf.c
   M /trunk/samtools/source.dot

 * Merge from branches/dev/
 * all future development will happen here at trunk/

------------------------------------------------------------------------
r79 | bhandsaker | 2009-01-07 16:42:15 -0500 (Wed, 07 Jan 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_tview.c

Fix problem with compiling without curses.

------------------------------------------------------------------------
r63 | lh3lh3 | 2008-12-22 10:58:02 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
   A /trunk/samtools (from /branches/dev/samtools:62)

Create trunk copy

------------------------------------------------------------------------
r62 | lh3lh3 | 2008-12-22 10:55:13 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/NEWS
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/samtools.1

Release samtools-0.1.1

------------------------------------------------------------------------
r61 | lh3lh3 | 2008-12-22 10:46:08 -0500 (Mon, 22 Dec 2008) | 10 lines
Changed paths:
   M /branches/dev/samtools/bam_aux.c
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bam_plcmd.c
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/razf.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-66
 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
 * fixed a memory leak in parsing a region
 * changed pileup a little bit when -s is in use: output ^ and $
 * when a bam is not indexed, output more meaningful error message
 * fixed a bug in indexing for small alignment
 * fixed a bug in the viewer when we come to the end of a reference file
 * updated documentation
 * prepare to release 0.1.1

------------------------------------------------------------------------
r60 | lh3lh3 | 2008-12-22 10:10:16 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/examples
   A /branches/dev/samtools/examples/00README.txt
   A /branches/dev/samtools/examples/ex1.fa
   A /branches/dev/samtools/examples/ex1.fa.fai
   A /branches/dev/samtools/examples/ex1.sam.gz

example

------------------------------------------------------------------------
r59 | lh3lh3 | 2008-12-22 04:38:15 -0500 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/ChangeLog

update ChangeLog

------------------------------------------------------------------------
r58 | lh3lh3 | 2008-12-20 18:06:00 -0500 (Sat, 20 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/misc/export2sam.pl

 * added comments
 * fixed several bugs 

------------------------------------------------------------------------
r57 | lh3lh3 | 2008-12-20 10:44:20 -0500 (Sat, 20 Dec 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/misc/export2sam.pl

convert Export format to SAM; not thoroughly tested

------------------------------------------------------------------------
r56 | lh3lh3 | 2008-12-19 17:13:28 -0500 (Fri, 19 Dec 2008) | 6 lines
Changed paths:
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bam_plcmd.c
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c
   A /branches/dev/samtools/source.dot

 * samtools-0.1.0-65
 * pileup: generate maq-like simple output
 * pileup: allow to output pileup at required sites
 * source.dot: source file relationship graph
 * tview: fixed a minor bug

------------------------------------------------------------------------
r55 | lh3lh3 | 2008-12-19 15:10:26 -0500 (Fri, 19 Dec 2008) | 2 lines
Changed paths:
   D /branches/dev/samtools/misc/all2sam.pl

remove all2sam.pl

------------------------------------------------------------------------
r54 | lh3lh3 | 2008-12-16 17:34:25 -0500 (Tue, 16 Dec 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/COPYING
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/faidx.h
   M /branches/dev/samtools/khash.h
   M /branches/dev/samtools/kseq.h
   M /branches/dev/samtools/ksort.h
   M /branches/dev/samtools/samtools.1

Added copyright information and a bit more documentation. No code change.

------------------------------------------------------------------------
r53 | lh3lh3 | 2008-12-16 08:40:18 -0500 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam.c
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-64
 * improved efficiency of the indel caller for spliced alignments

------------------------------------------------------------------------
r52 | lh3lh3 | 2008-12-16 05:28:20 -0500 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam.c
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_aux.c
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-63
 * a bit code cleanup: reduce the dependency between source files

------------------------------------------------------------------------
r51 | lh3lh3 | 2008-12-15 09:29:32 -0500 (Mon, 15 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bam_plcmd.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-62
 * fixed a memory leak

------------------------------------------------------------------------
r50 | lh3lh3 | 2008-12-15 09:00:13 -0500 (Mon, 15 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/ChangeLog
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/samtools.1

update documentation, ChangeLog and a comment

------------------------------------------------------------------------
r49 | lh3lh3 | 2008-12-15 08:36:43 -0500 (Mon, 15 Dec 2008) | 6 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bam_maqcns.h
   M /branches/dev/samtools/bam_pileup.c
   A /branches/dev/samtools/bam_plcmd.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-61
 * moved pileup command to a separate source file
 * added indel caller
 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
 * updated documentation

------------------------------------------------------------------------
r48 | lh3lh3 | 2008-12-12 08:55:36 -0500 (Fri, 12 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-60
 * fixed another bug in maqcns when there is a nearby deletion

------------------------------------------------------------------------
r47 | lh3lh3 | 2008-12-12 08:42:16 -0500 (Fri, 12 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-59
 * pileup: outputing consensus is now optional
 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
   I am not quite sure why the previous version may have problem.

------------------------------------------------------------------------
r46 | lh3lh3 | 2008-12-12 06:44:56 -0500 (Fri, 12 Dec 2008) | 6 lines
Changed paths:
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-58
 * add maq consensus to pileup. However, I will move this part to a new
   command as strictly speaking, consensus callin is not part of pileup,
   and imposing it would make it harder to generate for other language
   bindings.

------------------------------------------------------------------------
r45 | bhandsaker | 2008-12-11 15:43:56 -0500 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/bgzf.c

Fix bug in tell() after reads that consume to the exact end of a block.

------------------------------------------------------------------------
r44 | lh3lh3 | 2008-12-11 04:36:53 -0500 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/samtools.1

update manual

------------------------------------------------------------------------
r43 | lh3lh3 | 2008-12-11 04:25:36 -0500 (Thu, 11 Dec 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-57
 * fixed a bug in parser when there is auxiliary fields
 * made the parser a bit more robust

------------------------------------------------------------------------
r42 | lh3lh3 | 2008-12-10 09:57:29 -0500 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/bgzf.c

 * samtools-0.1.0-56
 * fixed a bug in bgzf (only reading is affected)
 * fixed a typo in bam_index.c
 * in bam_index.c, check potential bugs in the underlying I/O library

------------------------------------------------------------------------
r41 | lh3lh3 | 2008-12-10 07:53:08 -0500 (Wed, 10 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/samtools.1

update manual

------------------------------------------------------------------------
r40 | lh3lh3 | 2008-12-10 06:52:10 -0500 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-55
 * tried to make pileup work with clipping (previously not), though NOT tested
 * removed -v from pileup
 * made pileup take the reference sequence

------------------------------------------------------------------------
r39 | lh3lh3 | 2008-12-09 06:59:28 -0500 (Tue, 09 Dec 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-54
 * in parser, recognize "=", rather than ",", as a match
 * in parser, correctl parse "=" at the MRNM field.

------------------------------------------------------------------------
r38 | lh3lh3 | 2008-12-09 06:39:07 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/maq2sam.c

fixed a bug in handling maq flag 64 and 192

------------------------------------------------------------------------
r37 | lh3lh3 | 2008-12-09 04:53:46 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/md5fa.c

also calculate unordered md5sum check

------------------------------------------------------------------------
r36 | lh3lh3 | 2008-12-09 04:46:21 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/md5fa.c

fixed a minor bug when there are space in the sequence

------------------------------------------------------------------------
r35 | lh3lh3 | 2008-12-09 04:40:45 -0500 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/md5fa.c

fixed a potential memory leak

------------------------------------------------------------------------
r34 | lh3lh3 | 2008-12-08 09:52:17 -0500 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bamtk.c

 * fixed a bug in import: bin is wrongly calculated

------------------------------------------------------------------------
r33 | lh3lh3 | 2008-12-08 09:08:01 -0500 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/all2sam.pl

nothing, really

------------------------------------------------------------------------
r32 | lh3lh3 | 2008-12-08 07:56:02 -0500 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/kseq.h
   M /branches/dev/samtools/misc/Makefile
   A /branches/dev/samtools/misc/md5.c
   A /branches/dev/samtools/misc/md5.h
   A /branches/dev/samtools/misc/md5fa.c

 * fixed two warnings in kseq.h
 * added md5sum utilities

------------------------------------------------------------------------
r31 | lh3lh3 | 2008-12-08 06:35:29 -0500 (Mon, 08 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bamtk.c
   A /branches/dev/samtools/kseq.h
   D /branches/dev/samtools/kstream.h

 * samtools-0.1.0-52
 * replace kstream with kseq. kseq is a superset of kstream. I need the
   extra functions in kseq.h.
 * also compile stand-alone faidx

------------------------------------------------------------------------
r30 | lh3lh3 | 2008-12-08 06:17:04 -0500 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_sort.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-51
 * sorting by read names is available

------------------------------------------------------------------------
r29 | lh3lh3 | 2008-12-08 05:29:02 -0500 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam.c
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bam_sort.c
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/misc/maq2sam.c

 * samtools-0.1.0-50
 * format change to meet the latest specification

------------------------------------------------------------------------
r28 | lh3lh3 | 2008-12-04 11:09:21 -0500 (Thu, 04 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/misc/maq2sam.c

 * minor change in maqcns: special care when n==0
 * change maq2sam to meet the latest specification

------------------------------------------------------------------------
r27 | lh3lh3 | 2008-12-04 10:55:44 -0500 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/razf.c
   M /branches/dev/samtools/razf.h

considerable code clean up in razf

------------------------------------------------------------------------
r26 | lh3lh3 | 2008-12-04 10:08:18 -0500 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/ChangeLog
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/faidx.c

make RAZF optional in faidx.c

------------------------------------------------------------------------
r25 | lh3lh3 | 2008-12-01 10:27:22 -0500 (Mon, 01 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_aux.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-49
 * added routines for retrieving aux data, NOT TESTED YET!

------------------------------------------------------------------------
r24 | lh3lh3 | 2008-12-01 09:29:43 -0500 (Mon, 01 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/bam.c
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/bgzf.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-48
 * bgzf: fixed a potential integer overflow on 32-it machines
 * maqcns: set the minimum combined quality as 0
 * supporting hex strings

------------------------------------------------------------------------
r23 | lh3lh3 | 2008-11-27 12:14:37 -0500 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-47
 * fixed the bug in maqcns

------------------------------------------------------------------------
r22 | lh3lh3 | 2008-11-27 12:08:11 -0500 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam.h
   A /branches/dev/samtools/bam_maqcns.c
   A /branches/dev/samtools/bam_maqcns.h
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c
   A /branches/dev/samtools/glf.h

 * samtools-0.1.0-46
 * add MAQ consensus caller, currently BUGGY!

------------------------------------------------------------------------
r21 | lh3lh3 | 2008-11-27 08:51:28 -0500 (Thu, 27 Nov 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-45
 * tview: display padded alignment (but not P operation)
 * better coordinates and reference sequence

------------------------------------------------------------------------
r19 | lh3lh3 | 2008-11-27 04:26:05 -0500 (Thu, 27 Nov 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/ChangeLog

new ChangeLog

------------------------------------------------------------------------
r18 | lh3lh3 | 2008-11-27 04:24:45 -0500 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
   D /branches/dev/samtools/ChangeLog
   A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)

Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
the log of my personal SVN repository.

------------------------------------------------------------------------
r17 | lh3lh3 | 2008-11-27 04:22:55 -0500 (Thu, 27 Nov 2008) | 6 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/bgzf.c

 * samtools-0.1.0-44
 * declare fseeko and ftello as some Linux may not do this by default and
   missing these declarations will make bgzf buggy
 * get rid of some harmless warings
 * use BGZF by default, now

------------------------------------------------------------------------
r16 | lh3lh3 | 2008-11-26 16:19:11 -0500 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/razf.c

 * samtools-0.1.0-43
 * fixed a bug in razf_read()
 * give more warnings when the file is truncated (or due to bugs in I/O library)

------------------------------------------------------------------------
r15 | lh3lh3 | 2008-11-26 15:41:39 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/bgzf.c

fixed a bug in bgzf.c at the end of the file

------------------------------------------------------------------------
r14 | lh3lh3 | 2008-11-26 12:05:18 -0500 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-42
 * a lot happened to RAZF, although samtools itself is untouched. Better
   also update the version number anyway to avoid confusion

------------------------------------------------------------------------
r13 | lh3lh3 | 2008-11-26 12:03:48 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/razf.c

a change from Jue, but I think it should not matter

------------------------------------------------------------------------
r12 | lh3lh3 | 2008-11-26 11:48:14 -0500 (Wed, 26 Nov 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/razf.c

fixed a potential bug in razf. However, it seems still buggy, just
rarely happens, very rarely.

------------------------------------------------------------------------
r11 | lh3lh3 | 2008-11-26 09:02:56 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/razf.c

fixed a bug in razf, with the help of Jue

------------------------------------------------------------------------
r10 | lh3lh3 | 2008-11-26 06:55:32 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/bam_index.c

remove a comment

------------------------------------------------------------------------
r9 | lh3lh3 | 2008-11-26 06:37:05 -0500 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/razf.c
   M /branches/dev/samtools/razf.h

 * Jue has updated razf to realize Bob's scheme

------------------------------------------------------------------------
r7 | lh3lh3 | 2008-11-25 15:37:37 -0500 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/samtools.1

the manual page

------------------------------------------------------------------------
r6 | lh3lh3 | 2008-11-25 15:37:16 -0500 (Tue, 25 Nov 2008) | 3 lines
Changed paths:
   A /branches/dev/samtools/ChangeLog
   A /branches/dev/samtools/Makefile
   A /branches/dev/samtools/bam.c
   A /branches/dev/samtools/bam.h
   A /branches/dev/samtools/bam_aux.c
   A /branches/dev/samtools/bam_endian.h
   A /branches/dev/samtools/bam_import.c
   A /branches/dev/samtools/bam_index.c
   A /branches/dev/samtools/bam_lpileup.c
   A /branches/dev/samtools/bam_pileup.c
   A /branches/dev/samtools/bam_sort.c
   A /branches/dev/samtools/bam_tview.c
   A /branches/dev/samtools/bamtk.c
   A /branches/dev/samtools/bgzf.c
   A /branches/dev/samtools/bgzf.h
   A /branches/dev/samtools/bgzip.c
   A /branches/dev/samtools/faidx.c
   A /branches/dev/samtools/faidx.h
   A /branches/dev/samtools/khash.h
   A /branches/dev/samtools/ksort.h
   A /branches/dev/samtools/kstream.h
   A /branches/dev/samtools/misc
   A /branches/dev/samtools/misc/Makefile
   A /branches/dev/samtools/misc/all2sam.pl
   A /branches/dev/samtools/misc/maq2sam.c
   A /branches/dev/samtools/razf.c
   A /branches/dev/samtools/razf.h
   A /branches/dev/samtools/razip.c
   A /branches/dev/samtools/zutil.h

The initial version of samtools, replicated from my local SVN repository.
The current version is: 0.1.0-42. All future development will happen here.

------------------------------------------------------------------------
r5 | lh3lh3 | 2008-11-25 15:30:49 -0500 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools

samtools (C version)

------------------------------------------------------------------------
genometools-1.5.1/src/external/samtools-0.1.18/INSTALL000066400000000000000000000022601211610345200220720ustar00rootroot00000000000000System Requirements
===================

SAMtools depends on the zlib library . Version 1.2.3+ is
preferred and with 1.2.3+ you can compile razip and use it to compress a FASTA
file. SAMtools' faidx is able to index a razip-compressed FASTA file to save
diskspace. Older zlib also works with SAMtools, but razip cannot be compiled.

The text-based viewer (tview) requires the GNU ncurses library
, which comes with Mac OS X and most of
the modern Linux/Unix distributions. If you do not have this library installed,
you can still compile the rest of SAMtools by manually changing:
`-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and
comment out the line starting with `LIBCURSES='.


Compilation
===========

Type `make' to compile samtools. If you have zlib >= 1.2.2.1, you can compile
razip with `make razip'.


Installation
============

Copy `samtools', `bcftools/bcftools' and other executables/scripts in `misc' to
a location you want (e.g. a directory in your $PATH). You may also copy
`samtools.1' and `bcftools/bcftools.1' to a directory in your $MANPATH such
that the `man' command may find the manual.
genometools-1.5.1/src/external/samtools-0.1.18/Makefile000066400000000000000000000052701211610345200225050ustar00rootroot00000000000000CC=			gcc
CFLAGS=		-g -Wall -O2 -fPIC #-m64 #-arch ppc
DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
KNETFILE_O=	knetfile.o
LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
AOBJS=		bam_tview.o bam_plcmd.o sam_view.o	\
			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
			cut_target.o phase.o bam2depth.o
PROG=		samtools
INCLUDES=	-I.
SUBDIRS=	. bcftools misc
LIBPATH=
LIBCURSES=	-lncurses # -lXCurses

.SUFFIXES:.c .o

.c.o:
		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

all-recur lib-recur clean-recur cleanlocal-recur install-recur:
		@target=`echo $@ | sed s/-recur//`; \
		wdir=`pwd`; \
		list='$(SUBDIRS)'; for subdir in $$list; do \
			cd $$subdir; \
			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
			cd $$wdir; \
		done;

all:$(PROG)

.PHONY:all lib clean cleanlocal
.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur

lib:libbam.a

libbam.a:$(LOBJS)
		$(AR) -csru $@ $(LOBJS)

samtools:lib-recur $(AOBJS)
		$(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz

razip:razip.o razf.o $(KNETFILE_O)
		$(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz

bgzip:bgzip.o bgzf.o $(KNETFILE_O)
		$(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz

razip.o:razf.h
bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
sam.o:sam.h bam.h
bam_import.o:bam.h kseq.h khash.h razf.h
bam_pileup.o:bam.h razf.h ksort.h
bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
bam_lpileup.o:bam.h ksort.h
bam_tview.o:bam.h faidx.h
bam_sort.o:bam.h ksort.h razf.h
bam_md.o:bam.h faidx.h
sam_header.o:sam_header.h khash.h
bcf.o:bcftools/bcf.h
bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
bam2bcf_indel.o:bam2bcf.h
errmod.o:errmod.h
phase.o:bam.h khash.h ksort.h
bamtk.o:bam.h

faidx.o:faidx.h razf.h khash.h
faidx_main.o:faidx.h razf.h


libbam.1.dylib-local:$(LOBJS)
		libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz

libbam.so.1-local:$(LOBJS)
		$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz

dylib:
		@$(MAKE) cleanlocal; \
		case `uname` in \
			Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
			Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
			*) echo 'Unknown OS';; \
		esac


cleanlocal:
		rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib

clean:cleanlocal-recur
genometools-1.5.1/src/external/samtools-0.1.18/Makefile.mingw000066400000000000000000000040541211610345200236240ustar00rootroot00000000000000CC=			gcc.exe
AR=			ar.exe
CFLAGS=		-g -Wall -O2
DFLAGS=		-D_USE_KNETFILE -D_CURSES_LIB=2
KNETFILE_O=	knetfile.o
LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \
			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bedidx.o
AOBJS=		bam_tview.o bam_plcmd.o sam_view.o \
			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
			cut_target.o phase.o bam_cat.o bam2depth.o
BCFOBJS=	bcftools/bcf.o bcftools/fet.o bcftools/bcf2qcall.o bcftools/bcfutils.o \
			bcftools/call1.o bcftools/index.o bcftools/kfunc.o bcftools/em.o \
			bcftools/kmin.o bcftools/prob1.o bcftools/vcf.o bcftools/mut.o
PROG=		samtools.exe bcftools.exe
INCLUDES=	-I. -Iwin32
SUBDIRS=	.
LIBPATH=

.SUFFIXES:.c .o

.c.o:
		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

all:$(PROG)

.PHONY:all lib clean cleanlocal
.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur

lib:libbam.a

libbam.a:$(LOBJS)
		$(AR) -cru $@ $(LOBJS)

samtools.exe:$(AOBJS) libbam.a $(BCFOBJS)
		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(BCFOBJS) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz -lcurses -lws2_32

bcftools.exe:$(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o
		$(CC) $(CFLAGS) -o $@ $(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o -lm -Lwin32 -lz -lws2_32

razip.o:razf.h
bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
sam.o:sam.h bam.h
bam_import.o:bam.h kseq.h khash.h razf.h
bam_pileup.o:bam.h razf.h ksort.h
bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
bam_lpileup.o:bam.h ksort.h
bam_tview.o:bam.h faidx.h
bam_sort.o:bam.h ksort.h razf.h
bam_md.o:bam.h faidx.h
sam_header.o:sam_header.h khash.h
bcf.o:bcftools/bcf.h
bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
bam2bcf_indel.o:bam2bcf.h
errmod.o:errmod.h

faidx.o:faidx.h razf.h khash.h
faidx_main.o:faidx.h razf.h

clean:
		rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
genometools-1.5.1/src/external/samtools-0.1.18/NEWS000066400000000000000000000654251211610345200215540ustar00rootroot00000000000000Beta Release 0.1.18 (2 September, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in samtools:

 * Support the new =/X CIGAR operators (by Peter Cock).

 * Allow to subsample BAM while keeping the pairing intact (view -s).

 * Implemented variant distance bias as a new filter (by Petr Danecek).

 * Bugfix: huge memory usage during indexing

 * Bugfix: use of uninitialized variable in mpileup (rare)

 * Bugfix: wrong BAQ probability (rare)

Notable changes in bcftools:

 * Support indel in the contrast caller.

 * Bugfix: LRT2=nan in rare cases

(0.1.18: 2 September 2011, r982:295)



Beta Release 0.1.17 (6 July, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

With the maturity of `mpileup' and the lack of update in the `pileup' command,
the `pileup' command is now formally dropped. Most of the pileup functionality,
such as outputting mapping quality and read positions, have been added
`mpileup'.

Since this release, `bcftools view' is able to perform contrast SNP calling
(option -T) for discovering de novo and/or somatic mutations between a pair of
samples or in a family trio. Potential mutations are scored by a log likelihood
ratio, which is very simple in math, but should be comparable to more
sophisticated methods. Note that getting the score is only the very first step.
A lot more need to be done to reduce systematical errors due to mapping and
reference errors and structural variations.

Other notable changes in samtools:

 * Improved sorting order checking during indexing.

 * Improved region parsing. Colons in reference sequence names are parsed
   properly.

 * Fixed an issue where mpileup does not apply BAQ for the first few reads when
   a region is specified.

 * Fixed an issue where `faidx' does not work with FASTA files with long lines.

 * Bugfix: wrong SP genotype information in the BCF output.

Other notable changes in bcftools:

 * Output the ML esitmate of the allele count.

 * Added the HWE plus F<0 filter to varFilter. For multiple samples, it
   effectively filters false heterozygous calls around centromeres.

 * For association mapping, perform both 1-degree and 2-degree test. The
   2-degree test is conservative but more robust to HWE violation.

(0.1.17: 6 July 2011, r973:277)



Beta Release 0.1.16 (21 April, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in samtools:

 * Support the new SAM/BAM type `B' in the latest SAM spec v1.4.

 * When the output file of `samtools merge' exists, do not overwrite it unless
   a new command-line option `-f' is applied.

 * Bugfix: BED support is not working when the input BED is not sorted.

 * Bugfix: some reads without coordinates but given on the reverse strand are
   lost in merging.

Notable changes in bcftools:

 * Code cleanup: separated max-likelihood inference and Bayesian inference.

 * Test Hardy-Weinberg equilibrium with a likelihood-ratio test.

 * Provided another association test P-value by likelihood-ratio test.

 * Use Brent's method to estimate the site allele frequency when EM converges
   slowly. The resulting ML estimate of allele frequnecy is more accurate.

 * Added the `ldpair' command, which computes r^2 between SNP pairs given in
   an input file.

Also, the `pileup' command, which has been deprecated by `mpileup' since
version 0.1.10, will be dropped in the next release. The old `pileup' command
is substandard and causing a lot of confusion.

(0.1.16: 21 April 2011, r963:234)



Beta Release 0.1.15 (10 April, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Noteable changes:

 * Allow to perform variant calling or to extract information in multiple
   regions specified by a BED file (`samtools mpileup -l', `samtools view -L'
   and `bcftools view -l').

 * Added the `depth' command to samtools to compute the per-base depth with a
   simpler interface. File `bam2depth.c', which implements this command, is the
   recommended example on how to use the mpileup APIs.

 * Estimate genotype frequencies with ML; perform chi^2 based Hardy-Weinberg
   test using this estimate.

 * For `samtools view', when `-R' is specified, drop read groups in the header
   that are not contained in the specified file.

 * For `samtools flagstat', separate QC-pass and QC-fail reads.

 * Improved the command line help of `samtools mpileup' and `bcftools view'.

 * Use a global variable to control the verbose level of samtools stderr
   output. Nonetheless, it has not been full utilized.

 * Fixed an issue in association test which may report false associations,
   possibly due to floating point underflow.

(0.1.15: 10 April 2011, r949:203)



Beta release 0.1.14 (21 March, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release implements a method for testing associations for case-control
data. The method does not call genotypes but instead sums over all genotype
configurations to compute a chi^2 based test statistics. It can be potentially
applied to comparing a pair of samples (e.g. a tumor-normal pair), but this
has not been evaluated on real data.

Another new feature is to make X chromosome variant calls when female and male
samples are both present. The user needs to provide a file indicating the
ploidy of each sample (see also manual bcftools/bcftools.1).

Other notable changes:

 * Added `bcftools view -F' to parse BCF files generated by samtools r921 or
   older which encodes PL in a different way.

 * Changed the behavior of `bcftools view -s'. Now when a list of samples is
   provided, the samples in the output will be reordered to match the ordering
   in the sample list. This change is mainly designed for association test.

 * Sped up `bcftools view -v' for target sequencing given thousands of samples.
   Also added a new option `view -d' to skip loci where only a few samples are
   covered by reads.

 * Dropped HWE test. This feature has never been implemented properly. An EM
   should be much better. To be implemented in future.

 * Added the `cat' command to samtools. This command concatenate BAMs with
   identical sequence dictionaries in an efficient way. Modified from bam_cat.c
   written by Chris Saunders.

 * Added `samtools view -1' to write BAMs at a low compression level but twice
   faster to create. The `sort' command generates temporary files at a low
   compression level as well.

 * Added `samtools mpileup -6' to accept "BAM" with Illumina 1.3+ quality
   strings (strictly speaking, such a file is not BAM).

 * Added `samtools mpileup -L' to skip INDEL calling in regions with
   excessively high coverage. Such regions dramatically slow down mpileup.

 * Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc.

(0.1.14: 21 March 2011, r933:170)



Beta release 0.1.13 (1 March, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The most important though largely invisible modification is the change of the
order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
spec v4.1. The change means that 0.1.13 is not backward compatible with VCF/BCF
generated by samtools older than r921 inclusive.  VCF/BCF generated by the new
samtools will contain a line `##fileformat=VCFv4.1' as well as the samtools
version number.

Single Individual Haplotyping (SIH) is added as an experimental feature. It
originally aims to produce haploid consensus from fosmid pool sequencing, but
also works with short-read data. For short reads, phased blocks are usually too
short to be useful in many applications, but they can help to rule out part of
SNPs close to INDELs or between copies of CNVs.


Other notable changes in samtools:

 * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
   calling. This reduces the power but improves specificity.

 * Improved sorting order checking in indexing. Now indexing is the preferred way
   to check if a BAM is sorted.

 * Added a switch `-E' to mpileup and calmd. This option uses an alternative way
   to apply BAQ, which increases sensistivity, especially to MNPs, at the cost of
   a little loss in specificity.

 * Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.

 * Added `mpileup -m' to allow fine control of the collection of INDEL candidates.

 * Added `mpileup -S' to compute per-sample strand bias P-value.

 * Added `mpileup -G' to exclude read groups in variant calling.

 * Fixed segfault in indel calling related to unmapped and refskip reads.

 * Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
   genotypes for longer short INDELs, typically over 10bp.

 * Fixed a bug in tview on big-endian machines.

 * Fixed a very rare memory issue in bam_md.c

 * Fixed an out-of-boundary bug in mpileup when the read base is `N'.

 * Fixed a compiling error when the knetfile library is not used. Fixed a
   library compiling error due to the lack of bam_nt16_nt4_table[] table.
   Suppress a compiling warning related to the latest zlib.


Other notable changes in bcftools:

 * Updated the BCF spec.

 * Added the `FQ' VCF INFO field, which gives the phred-scaled probability
   of all samples being the same (identical to the reference or all homozygous
   variants). Option `view -f' has been dropped.

 * Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
   similar to "samtools.pl pileup2fq".

 * Make sure the GT FORMAT field is always the first FORMAT to conform the VCF
   spec. Drop bcf-fix.pl.

 * Output bcftools specific INFO and FORMAT in the VCF header.

 * Added `view -s' to call variants from a subset of samples.

 * Properly convert VCF to BCF with a user provided sequence dictionary. Nonetheless,
   custom fields are still unparsed and will be stored as a missing value.

 * Fixed a minor bug in Fisher's exact test; the results are rarely changed.


(0.1.13: 1 March 2011, r926:134)



Beta release 0.1.12a (2 December, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is another bug fix release:

 * Fixed a memory violation in mpileup, which causes segfault. Release
   0.1.9 and above are affected.

 * Fixed a memory violation in the indel caller, which does not causes
   segfault, but may potentially affect deletion calls in an unexpected
   way. Release 0.1.10 and above are affected.

 * Fixed a bug in computing r-square in bcftools. Few are using this
   functionality and it only has minor effect.

 * Fixed a memory leak in bam_fetch().

 * Fixed a bug in writing meta information to the BAM index for the last
   sequence. This bug is invisible to most users, but it is a bug anyway.

 * Fixed a bug in bcftools which causes false "DP4=0,0,0,0" annotations.

(0.1.12: 2 December 2010, r862)



Beta release 0.1.11 (21 November, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is mainly a bug fix release:

 * Fixed a bug in random retrieval (since 0.1.8). It occurs when reads
   are retrieved from a small region containing no reads.

 * Fixed a bug in pileup (since 0.1.9). The bug causes an assertion
   failure when the first CIGAR operation is a deletion.

 * Improved fault tolerence in remote access.

One minor feature has been implemented in bcftools:

 * Added a reference-free variant calling mode. In this mode, a site is
   regarded as a variat iff the sample(s) contains two or more alleles;
   the meaning of the QUAL field in the VCF output is changed
   accordingly. Effectively, the reference allele is irrelevant to the
   result in the new mode, although the reference sequence has to be
   used in realignment when SAMtools computes genotype likelihoods.

In addition, since 0.1.10, the `pileup' command has been deprecated by
`mpileup' which is more powerful and more accurate. The `pileup' command
will not be removed in the next few releases, but new features will not
be added.

(0.1.11: 21 November 2010, r851)



Beta Release 0.1.10 (16 November, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release is featured as the first major improvement to the indel
caller. The method is similar to the old one implemented in the pileup
command, but the details are handled more carefully both in theory and
in practice. As a result, the new indel caller usually gives more
accurate indel calls, though at the cost of sensitivity. The caller is
implemented in the mpileup command and is invoked by default. It works
with multiple samples.

Other notable changes:

 * With the -r option, the calmd command writes the difference between
   the original base quality and the BAQ capped base quality at the BQ
   tag but does not modify the base quality. Please use -Ar to overwrite
   the original base quality (the 0.1.9 behavior).

 * Allow to set a maximum per-sample read depth to reduce memory. In
   0.1.9, most of memory is wasted for the ultra high read depth in some
   regions (e.g. the chr1 centromere).

 * Optionally write per-sample read depth and per-sample strand bias
   P-value.

 * Compute equal-tail (Bayesian) credible interval of site allele
   frequency at the CI95 VCF annotation.

 * Merged the vcfutils.pl varFilter and filter4vcf for better SNP/indel
   filtering.

(0.1.10: 16 November 2010, r829)



Beta Release 0.1.9 (27 October, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release is featured as the first major improvement to the samtools'
SNP caller.  It comes with a revised MAQ error model, the support of
multi-sample SNP calling and the computation of base alignment quality
(BAQ).

The revised MAQ error model is based on the original model. It solves an
issue of miscalling SNPs in repetitive regions. Althought such SNPs can
usually be filtered at a later step, they mess up unfiltered calls. This
is a theoretical flaw in the original model. The revised MAQ model
deprecates the orginal MAQ model and the simplified SOAPsnp model.

Multi-sample SNP calling is separated in two steps. The first is done by
samtools mpileup and the second by a new program, bcftools, which is
included in the samtools source code tree. Multi-sample SNP calling also
works for single sample and has the advantage of enabling more powerful
filtration. It is likely to deprecate pileup in future once a proper
indel calling method is implemented.

BAQ is the Phred-scaled probability of a read base being wrongly
aligned. Capping base quality by BAQ has been shown to be very effective
in suppressing false SNPs caused by misalignments around indels or in
low-complexity regions with acceptable compromise on computation
time. This strategy is highly recommended and can be used with other SNP
callers as well.

In addition to the three major improvements, other notable changes are:

 * Changes to the pileup format. A reference skip (the N CIGAR operator)
   is shown as '<' or '>' depending on the strand. Tview is also changed
   accordingly.

 * Accelerated pileup. The plain pileup is about 50% faster.

 * Regional merge. The merge command now accepts a new option to merge
   files in a specified region.

 * Fixed a bug in bgzip and razip which causes source files to be
   deleted even if option -c is applied.

 * In APIs, propogate errors to downstream callers and make samtools
   return non-zero values once errors occur.

(0.1.9: 27 October 2010, r783)



Beta Release 0.1.8 (11 July, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable functional changes:

 * Added the `reheader' command which replaces a BAM header with a new
   header. This command is much faster than replacing header by
   BAM->SAM->BAM conversions.

 * Added the `mpileup' command which computes the pileup of multiple
   alignments.

 * The `index' command now stores the number of mapped and unmapped
   reads in the index file. This information can be retrieved quickly by
   the new `idxstats' command.

 * By default, pileup used the SOAPsnp model for SNP calling. This
   avoids the floating overflow in the MAQ model which leads to spurious
   calls in repetitive regions, although these calls will be immediately
   filtered by varFilter.

 * The `tview' command now correctly handles CIGARs like 7I10M and
   10M1P1I10M which cause assertion failure in earlier versions.

 * Tview accepts a region like `=10,000' where `=' stands for the
   current sequence name. This saves typing for long sequence names.

 * Added the `-d' option to `pileup' which avoids slow indel calling
   in ultradeep regions by subsampling reads locally.

 * Added the `-R' option to `view' which retrieves alignments in read
   groups listed in the specified file.

Performance improvements:

 * The BAM->SAM conversion is up to twice faster, depending on the
   characteristic of the input.

 * Parsing SAM headers with a lot of reference sequences is now much
   faster.

 * The number of lseek() calls per query is reduced when the query
   region contains no read alignments.

Bug fixes:

 * Fixed an issue in the indel caller that leads to miscall of indels.
   Note that this solution may not work well when the sequencing indel
   error rate is higher than the rate of SNPs.

 * Fixed another issue in the indel caller which may lead to incorrect
   genotype.

 * Fixed a bug in `sort' when option `-o' is applied.

 * Fixed a bug in `view -r'.

APIs and other changes:

 * Added iterator interfaces to random access and pileup. The callback
   interfaces directly call the iterator interfaces.

 * The BGZF blocks holding the BAM header are indepedent of alignment
   BGZF blocks. Alignment records shorter than 64kB is guaranteed to be
   fully contained in one BGZF block. This change is fully compatible
   with the old version of samtools/picard.

Changes in other utilities:

 * Updated export2sam.pl by Chris Saunders.

 * Improved the sam2vcf.pl script.

 * Added a Python version of varfilter.py by Aylwyn Scally.

(0.1.8: 11 July 2010, r613)



Beta Release 0.1.7 (10 November, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * Improved the indel caller in complex scenariors, in particular for
   long reads. The indel caller is now able to make reasonable indel
   calls from Craig Venter capillary reads.

 * Rewrote single-end duplicate removal with improved
   performance. Paired-end reads are not touched.

 * Duplicate removal is now library aware. Samtools remove potential
   PCR/optical dupliates inside a library rather than across libraries.

 * SAM header is now fully parsed, although this functionality is not
   used in merging and so on.

 * In samtools merge, optionally take the input file name as RG-ID and
   attach the RG tag to each alignment.

 * Added FTP support in the RAZF library. RAZF-compressed reference
   sequence can be retrieved remotely.

 * Improved network support for Win32.

 * Samtools sort and merge are now stable.

Changes in other utilities:

 * Implemented sam2vcf.pl that converts the pileup format to the VCF
   format.

 * This release of samtools is known to work with the latest
   Bio-Samtools Perl module.

(0.1.7: 10 November 2009, r510)



Beta Release 0.1.6 (2 September, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * In tview, do not show a blank screen when no reads mapped to the
   corresponding region.

 * Implemented native HTTP support in the BGZF library. Samtools is now
   able to directly open a BAM file on HTTP. HTTP proxy is also
   supported via the "http_proxy" environmental variable.

 * Samtools is now compitable with the MinGW (win32) compiler and the
   PDCurses library.

 * The calmd (or fillmd) command now calculates the NM tag and replaces
   MD tags if they are wrong.

 * The view command now recognizes and optionally prints FLAG in HEXs or
   strings to make a SAM file more friendly to human eyes. This is a
   samtools-C extension, not implemented in Picard for the time
   being. Please type `samtools view -?' for more information.

 * BAM files now have an end-of-file (EOF) marker to facilitate
   truncation detection. A warning will be given if an on-disk BAM file
   does not have this marker. The warning will be seen on BAM files
   generated by an older version of samtools. It does NO harm.

 * New key bindings in tview: `r' to show read names and `s' to show
   reference skip (N operation) as deletions.

 * Fixed a bug in `samtools merge -n'.

 * Samtools merge now optionally copies the header of a user specified
   SAM file to the resultant BAM output.

 * Samtools pileup/tview works with a CIGAR with the first or the last
   operation is an indel.

 * Fixed a bug in bam_aux_get().


Changes in other utilies:

 * Fixed wrong FLAG in maq2sam.


(0.1.6: 2 September 2009, r453)



Beta Release 0.1.5 (7 July, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * Support opening a BAM alignment on FTP. Users can now use "tview" to
   view alignments at the NCBI ftp site. Please read manual for more
   information.

 * In library, propagate errors rather than exit or complain assertion
   failure.

 * Simplified the building system and fixed compiling errors caused by
   zlib<1.2.2.1.

 * Fixed an issue about lost header information when a SAM is imported
   with "view -t".

 * Implemented "samtool.pl varFilter" which filters both SNPs and short
   indels. This command replaces "indelFilter".

 * Implemented "samtools.pl pileup2fq" to generate FASTQ consensus from
   pileup output.

 * In pileup, cap mapping quality at 60. This helps filtering when
   different aligners are in use.

 * In pileup, allow to output variant sites only.

 * Made pileup generate correct calls in repetitive region. At the same
   time, I am considering to implement a simplified model in SOAPsnp,
   although this has not happened yet.

 * In view, added '-u' option to output BAM without compression. This
   option is preferred when the output is piped to other commands.

 * In view, added '-l' and '-r' to get the alignments for one library or
   read group. The "@RG" header lines are now partially parsed.

 * Do not include command line utilities to libbam.a.

 * Fixed memory leaks in pileup and bam_view1().

 * Made faidx more tolerant to empty lines right before or after FASTA >
   lines.


Changes in other utilities:

 * Updated novo2sam.pl by Colin Hercus, the key developer of novoalign.


This release involves several modifications to the key code base which
may potentially introduce new bugs even though we have tried to minimize
this by testing on several examples. Please let us know if you catch
bugs.

(0.1.5: 7 July 2009, r373)



Beta Release 0.1.4 (21 May, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * Added the 'rmdupse' command: removing duplicates for SE reads.

 * Fixed a critical bug in the indel caller: clipped alignments are not
   processed correctly.

 * Fixed a bug in the tview: gapped alignment may be incorrectly
   displayed.

 * Unified the interface to BAM and SAM I/O. This is done by
   implementing a wrapper on top of the old APIs and therefore old APIs
   are still valid. The new I/O APIs also recognize the @SQ header
   lines.

 * Generate the MD tag.

 * Generate "=" bases. However, the indel caller will not work when "="
   bases are present.

 * Enhanced support of color-read display (by Nils Homer).

 * Implemented the GNU building system. However, currently the building
   system does not generate libbam.a. We will improve this later. For
   the time being, `make -f Makefile.generic' is preferred.

 * Fixed a minor bug in pileup: the first read in a chromosome may be
   skipped.

 * Fixed bugs in bam_aux.c. These bugs do not affect other components as
   they were not used previously.

 * Output the 'SM' tag from maq2sam.

(0.1.4: 21 May 2009, r297)



Beta Release 0.1.3 (15 April, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in SAMtools:

 * SAMtools is more consistent with the specification: a) '*' in the
   QUAL field is allowed; b) the field separator is TAB only and SPACE
   is treated as a character in a field; c) empty header is allowed.

 * Implemented GLFv3 support in pileup.

 * Fixed a severe bug in fixmate: strand information is wrongly
   overwritten.

 * Fixed a bug in alignment retrieval: alignments bridging n*16384bp are
   not correctly retrieved sometimes.

 * Fixed a bug in rmdup: segfault if unmapped reads are present.

 * Move indel_filter.pl to samtools.pl and improved the filtering by
   checking the actual number of alignments containing indels. The indel
   pileup line is also changed a little to make this filtration easier.

 * Fixed a minor bug in indexing: the bin number of an unmapped read is
   wrongly calculated.

 * Added `flagstat' command to show statistics on the FLAG field.

 * Improved indel caller by setting the maximum window size in local
   realignment.

Changes in other utilities:

 * Fixed a bug in maq2sam: a tag name is obsolete.

 * Improvement to wgsim: a) added support for SOLiD read simulation; b)
   show the number of substitutions/indels/errors in read name; c)
   considerable code clean up.

 * Various converters: improved functionality in general.

 * Updated the example SAM due to the previous bug in fixmate.

(0.1.3: 15 April 2009, r227)



Beta Release 0.1.2 (28 January, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in SAMtools:

 * Implemented a Bayesian indel caller. The new caller generate scores
   and genotype and is potentially more accurate than Maq's indel
   caller. The pileup format is also changed accordingly.

 * Implemented rmdup command: remove potential PCR duplicates. Note that
   this command ONLY works for FR orientation and requires ISIZE is
   correctly set.

 * Added fixmate command: fill in mate coordinates, ISIZE and mate
   related flags from a name-sorted alignment.

 * Fixed a bug in indexing: reads bridging 16x kbp were not retrieved.

 * Allow to select reads shown in the pileup output with a mask.

 * Generate GLFv2 from pileup.

 * Added two more flags for flagging PCR/optical duplicates and for QC
   failure.

 * Fixed a bug in sort command: name sorting for large alignment did not
   work.

 * Allow to completely disable RAZF (using Makefile.lite) as some people
   have problem to compile it.

 * Fixed a bug in import command when there are reads without
   coordinates.

 * Fixed a bug in tview: clipping broke the alignment viewer.

 * Fixed a compiling error when _NO_CURSES is applied.

 * Fixed a bug in merge command.

Changes in other utilities:

 * Added wgsim, a paired-end reads simulator. Wgsim was adapted from
   maq's reads simulator. Colin Hercus further improved it to allow
   longer indels.

 * Added wgsim_eval.pl, a script that evaluates the accuracy of
   alignment on reads generated by wgsim.

 * Added soap2sam.pl, a SOAP2->SAM converter. This converter does not
   work properly when multiple hits are output.

 * Added bowtie2sam.pl, a Bowtie->SAM converter. Only the top hit will
   be retained when multiple hits are present.

 * Fixed a bug in export2sam.pl for QC reads.

 * Support RG tag at MAQ->SAM converter.

 * Added novo2sam.pl, a NovoAlign->SAM converter. Multiple hits and
   indel are not properly handled, though.

 * Added zoom2sam.pl, a ZOOM->SAM converter. It only works with the
   default Illumina output.

(0.1.2: 28 January 2008; r116)



Beta Release 0.1.1 (22 December, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The is the first public release of samtools. For more information,
please check the manual page `samtools.1' and the samtools website
http://samtools.sourceforge.net
genometools-1.5.1/src/external/samtools-0.1.18/bam.c000066400000000000000000000271541211610345200217550ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include "bam.h"
#include "bam_endian.h"
#include "kstring.h"
#include "sam_header.h"

int bam_is_be = 0, bam_verbose = 2;
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";

/**************************
 * CIGAR related routines *
 **************************/

uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
{
	uint32_t k, end;
	end = c->pos;
	for (k = 0; k < c->n_cigar; ++k) {
		int op = cigar[k] & BAM_CIGAR_MASK;
		if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
			end += cigar[k] >> BAM_CIGAR_SHIFT;
	}
	return end;
}

int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
{
	uint32_t k;
	int32_t l = 0;
	for (k = 0; k < c->n_cigar; ++k) {
		int op = cigar[k] & BAM_CIGAR_MASK;
		if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP || op == BAM_CEQUAL || op == BAM_CDIFF)
			l += cigar[k] >> BAM_CIGAR_SHIFT;
	}
	return l;
}

/********************
 * BAM I/O routines *
 ********************/

bam_header_t *bam_header_init()
{
	bam_is_be = bam_is_big_endian();
	return (bam_header_t*)calloc(1, sizeof(bam_header_t));
}

void bam_header_destroy(bam_header_t *header)
{
	int32_t i;
	extern void bam_destroy_header_hash(bam_header_t *header);
	if (header == 0) return;
	if (header->target_name) {
		for (i = 0; i < header->n_targets; ++i)
			free(header->target_name[i]);
		free(header->target_name);
		free(header->target_len);
	}
	free(header->text);
	if (header->dict) sam_header_free(header->dict);
	if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
	bam_destroy_header_hash(header);
	free(header);
}

bam_header_t *bam_header_read(bamFile fp)
{
	bam_header_t *header;
	char buf[4];
	int magic_len;
	int32_t i = 1, name_len;
	// check EOF
	i = bgzf_check_EOF(fp);
	if (i < 0) {
		// If the file is a pipe, checking the EOF marker will *always* fail
		// with ESPIPE.  Suppress the error message in this case.
		if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
	}
	else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
	// read "BAM1"
	magic_len = bam_read(fp, buf, 4);
	if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
		fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
		return 0;
	}
	header = bam_header_init();
	// read plain text and the number of reference sequences
	bam_read(fp, &header->l_text, 4);
	if (bam_is_be) bam_swap_endian_4p(&header->l_text);
	header->text = (char*)calloc(header->l_text + 1, 1);
	bam_read(fp, header->text, header->l_text);
	bam_read(fp, &header->n_targets, 4);
	if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
	// read reference sequence names and lengths
	header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
	header->target_len = (uint32_t*)calloc(header->n_targets, 4);
	for (i = 0; i != header->n_targets; ++i) {
		bam_read(fp, &name_len, 4);
		if (bam_is_be) bam_swap_endian_4p(&name_len);
		header->target_name[i] = (char*)calloc(name_len, 1);
		bam_read(fp, header->target_name[i], name_len);
		bam_read(fp, &header->target_len[i], 4);
		if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
	}
	return header;
}

int bam_header_write(bamFile fp, const bam_header_t *header)
{
	char buf[4];
	int32_t i, name_len, x;
	// write "BAM1"
	strncpy(buf, "BAM\001", 4);
	bam_write(fp, buf, 4);
	// write plain text and the number of reference sequences
	if (bam_is_be) {
		x = bam_swap_endian_4(header->l_text);
		bam_write(fp, &x, 4);
		if (header->l_text) bam_write(fp, header->text, header->l_text);
		x = bam_swap_endian_4(header->n_targets);
		bam_write(fp, &x, 4);
	} else {
		bam_write(fp, &header->l_text, 4);
		if (header->l_text) bam_write(fp, header->text, header->l_text);
		bam_write(fp, &header->n_targets, 4);
	}
	// write sequence names and lengths
	for (i = 0; i != header->n_targets; ++i) {
		char *p = header->target_name[i];
		name_len = strlen(p) + 1;
		if (bam_is_be) {
			x = bam_swap_endian_4(name_len);
			bam_write(fp, &x, 4);
		} else bam_write(fp, &name_len, 4);
		bam_write(fp, p, name_len);
		if (bam_is_be) {
			x = bam_swap_endian_4(header->target_len[i]);
			bam_write(fp, &x, 4);
		} else bam_write(fp, &header->target_len[i], 4);
	}
	bgzf_flush(fp);
	return 0;
}

static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
{
	uint8_t *s;
	uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
	s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
	for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
	while (s < data + data_len) {
		uint8_t type;
		s += 2; // skip key
		type = toupper(*s); ++s; // skip type
		if (type == 'C' || type == 'A') ++s;
		else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
		else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
		else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
		else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
		else if (type == 'B') {
			int32_t n, Bsize = bam_aux_type2size(*s);
			memcpy(&n, s + 1, 4);
			if (1 == Bsize) {
			} else if (2 == Bsize) {
				for (i = 0; i < n; i += 2)
					bam_swap_endian_2p(s + 5 + i);
			} else if (4 == Bsize) {
				for (i = 0; i < n; i += 4)
					bam_swap_endian_4p(s + 5 + i);
			}
			bam_swap_endian_4p(s+1); 
		}
	}
}

int bam_read1(bamFile fp, bam1_t *b)
{
	bam1_core_t *c = &b->core;
	int32_t block_len, ret, i;
	uint32_t x[8];

	assert(BAM_CORE_SIZE == 32);
	if ((ret = bam_read(fp, &block_len, 4)) != 4) {
		if (ret == 0) return -1; // normal end-of-file
		else return -2; // truncated
	}
	if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3;
	if (bam_is_be) {
		bam_swap_endian_4p(&block_len);
		for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
	}
	c->tid = x[0]; c->pos = x[1];
	c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
	c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
	c->l_qseq = x[4];
	c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
	b->data_len = block_len - BAM_CORE_SIZE;
	if (b->m_data < b->data_len) {
		b->m_data = b->data_len;
		kroundup32(b->m_data);
		b->data = (uint8_t*)realloc(b->data, b->m_data);
	}
	if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
	b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
	if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
	return 4 + block_len;
}

inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
{
	uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
	int i;
	assert(BAM_CORE_SIZE == 32);
	x[0] = c->tid;
	x[1] = c->pos;
	x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
	x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
	x[4] = c->l_qseq;
	x[5] = c->mtid;
	x[6] = c->mpos;
	x[7] = c->isize;
	bgzf_flush_try(fp, 4 + block_len);
	if (bam_is_be) {
		for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
		y = block_len;
		bam_write(fp, bam_swap_endian_4p(&y), 4);
		swap_endian_data(c, data_len, data);
	} else bam_write(fp, &block_len, 4);
	bam_write(fp, x, BAM_CORE_SIZE);
	bam_write(fp, data, data_len);
	if (bam_is_be) swap_endian_data(c, data_len, data);
	return 4 + block_len;
}

int bam_write1(bamFile fp, const bam1_t *b)
{
	return bam_write1_core(fp, &b->core, b->data_len, b->data);
}

char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
{
	uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
	int i;
	const bam1_core_t *c = &b->core;
	kstring_t str;
	str.l = str.m = 0; str.s = 0;

	kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str);
	if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); }
	else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag);
	else { // BAM_OFSTR
		for (i = 0; i < 16; ++i)
			if ((c->flag & 1<tid < 0) kputsn("*\t", 2, &str);
	else {
		if (header) kputs(header->target_name[c->tid] , &str);
		else kputw(c->tid, &str);
		kputc('\t', &str);
	}
	kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
	if (c->n_cigar == 0) kputc('*', &str);
	else {
		for (i = 0; i < c->n_cigar; ++i) {
			kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
			kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
		}
	}
	kputc('\t', &str);
	if (c->mtid < 0) kputsn("*\t", 2, &str);
	else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
	else {
		if (header) kputs(header->target_name[c->mtid], &str);
		else kputw(c->mtid, &str);
		kputc('\t', &str);
	}
	kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str);
	if (c->l_qseq) {
		for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
		kputc('\t', &str);
		if (t[0] == 0xff) kputc('*', &str);
		else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
	} else kputsn("*\t*", 3, &str);
	s = bam1_aux(b);
	while (s < b->data + b->data_len) {
		uint8_t type, key[2];
		key[0] = s[0]; key[1] = s[1];
		s += 2; type = *s; ++s;
		kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str);
		if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; }
		else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; }
		else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; }
		else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; }
		else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; }
		else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; }
		else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; }
		else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
		else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
		else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
		else if (type == 'B') {
			uint8_t sub_type = *(s++);
			int32_t n;
			memcpy(&n, s, 4);
			s += 4; // no point to the start of the array
			kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
			for (i = 0; i < n; ++i) {
				kputc(',', &str);
				if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
				else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
				else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
				else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
				else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
				else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
				else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
			}
		}
	}
	return str.s;
}

char *bam_format1(const bam_header_t *header, const bam1_t *b)
{
	return bam_format1_core(header, b, BAM_OFDEC);
}

void bam_view1(const bam_header_t *header, const bam1_t *b)
{
	char *s = bam_format1(header, b);
	puts(s);
	free(s);
}

int bam_validate1(const bam_header_t *header, const bam1_t *b)
{
	char *s;

	if (b->core.tid < -1 || b->core.mtid < -1) return 0;
	if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;

	if (b->data_len < b->core.l_qname) return 0;
	s = memchr(bam1_qname(b), '\0', b->core.l_qname);
	if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;

	// FIXME: Other fields could also be checked, especially the auxiliary data

	return 1;
}

// FIXME: we should also check the LB tag associated with each alignment
const char *bam_get_library(bam_header_t *h, const bam1_t *b)
{
	const uint8_t *rg;
	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
	if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB");
	rg = bam_aux_get(b, "RG");
	return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
}
genometools-1.5.1/src/external/samtools-0.1.18/bam.h000066400000000000000000000603231211610345200217550ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008-2010 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li  */

#ifndef BAM_BAM_H
#define BAM_BAM_H

/*!
  @header

  BAM library provides I/O and various operations on manipulating files
  in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map)
  format. It now supports importing from or exporting to SAM, sorting,
  merging, generating pileup, and quickly retrieval of reads overlapped
  with a specified region.

  @copyright Genome Research Ltd.
 */

#define BAM_VERSION "0.1.18 (r982:295)"

#include 
#include 
#include 
#include 

#ifndef BAM_LITE
#define BAM_VIRTUAL_OFFSET16
#include "bgzf.h"
/*! @abstract BAM file handler */
typedef BGZF *bamFile;
#define bam_open(fn, mode) bgzf_open(fn, mode)
#define bam_dopen(fd, mode) bgzf_fdopen(fd, mode)
#define bam_close(fp) bgzf_close(fp)
#define bam_read(fp, buf, size) bgzf_read(fp, buf, size)
#define bam_write(fp, buf, size) bgzf_write(fp, buf, size)
#define bam_tell(fp) bgzf_tell(fp)
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
#else
#define BAM_TRUE_OFFSET
#ifndef S_SPLINT_S
#include 
#endif
typedef gzFile bamFile;
#define bam_open(fn, mode) gzopen(fn, mode)
#define bam_dopen(fd, mode) gzdopen(fd, mode)
#define bam_close(fp) gzclose(fp)
#define bam_read(fp, buf, size) gzread(fp, buf, size)
/* no bam_write/bam_tell/bam_seek() here */
#endif

/*@ignore@*/
/*! @typedef
  @abstract Structure for the alignment header.
  @field n_targets   number of reference sequences
  @field target_name names of the reference sequences
  @field target_len  lengths of the referene sequences
  @field dict        header dictionary
  @field hash        hash table for fast name lookup
  @field rg2lib      hash table for @RG-ID -> LB lookup
  @field l_text      length of the plain text in the header
  @field text        plain text

  @discussion Field hash points to null by default. It is a private
  member.
 */
typedef struct {
	int32_t n_targets;
	char **target_name;
	uint32_t *target_len;
	void *dict, *hash, *rg2lib;
	size_t l_text, n_text;
	char *text;
} bam_header_t;

/*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */
#define BAM_FPAIRED        1
/*! @abstract the read is mapped in a proper pair */
#define BAM_FPROPER_PAIR   2
/*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */
#define BAM_FUNMAP         4
/*! @abstract the mate is unmapped */
#define BAM_FMUNMAP        8
/*! @abstract the read is mapped to the reverse strand */
#define BAM_FREVERSE      16
/*! @abstract the mate is mapped to the reverse strand */
#define BAM_FMREVERSE     32
/*! @abstract this is read1 */
#define BAM_FREAD1        64
/*! @abstract this is read2 */
#define BAM_FREAD2       128
/*! @abstract not primary alignment */
#define BAM_FSECONDARY   256
/*! @abstract QC failure */
#define BAM_FQCFAIL      512
/*! @abstract optical or PCR duplicate */
#define BAM_FDUP        1024

#define BAM_OFDEC          0
#define BAM_OFHEX          1
#define BAM_OFSTR          2

/*! @abstract defautl mask for pileup */
#define BAM_DEF_MASK (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)

#define BAM_CORE_SIZE   sizeof(bam1_core_t)

/**
 * Describing how CIGAR operation/length is packed in a 32-bit integer.
 */
#define BAM_CIGAR_SHIFT 4
#define BAM_CIGAR_MASK  ((1 << BAM_CIGAR_SHIFT) - 1)

/*
  CIGAR operations.
 */
/*! @abstract CIGAR: M = match or mismatch*/
#define BAM_CMATCH      0
/*! @abstract CIGAR: I = insertion to the reference */
#define BAM_CINS        1
/*! @abstract CIGAR: D = deletion from the reference */
#define BAM_CDEL        2
/*! @abstract CIGAR: N = skip on the reference (e.g. spliced alignment) */
#define BAM_CREF_SKIP   3
/*! @abstract CIGAR: S = clip on the read with clipped sequence
  present in qseq */
#define BAM_CSOFT_CLIP  4
/*! @abstract CIGAR: H = clip on the read with clipped sequence trimmed off */
#define BAM_CHARD_CLIP  5
/*! @abstract CIGAR: P = padding */
#define BAM_CPAD        6
/*! @abstract CIGAR: equals = match */
#define BAM_CEQUAL        7
/*! @abstract CIGAR: X = mismatch */
#define BAM_CDIFF        8

/*! @typedef
  @abstract Structure for core alignment information.
  @field  tid     chromosome ID, defined by bam_header_t
  @field  pos     0-based leftmost coordinate
  @field  strand  strand; 0 for forward and 1 otherwise
  @field  bin     bin calculated by bam_reg2bin()
  @field  qual    mapping quality
  @field  l_qname length of the query name
  @field  flag    bitwise flag
  @field  n_cigar number of CIGAR operations
  @field  l_qseq  length of the query sequence (read)
 */
typedef struct {
	int32_t tid;
	int32_t pos;
	uint32_t bin:16, qual:8, l_qname:8;
	uint32_t flag:16, n_cigar:16;
	int32_t l_qseq;
	int32_t mtid;
	int32_t mpos;
	int32_t isize;
} bam1_core_t;

/*! @typedef
  @abstract Structure for one alignment.
  @field  core       core information about the alignment
  @field  l_aux      length of auxiliary data
  @field  data_len   current length of bam1_t::data
  @field  m_data     maximum length of bam1_t::data
  @field  data       all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux

  @discussion Notes:
 
   1. qname is zero tailing and core.l_qname includes the tailing '\0'.
   2. l_qseq is calculated from the total length of an alignment block
      on reading or from CIGAR.
 */
typedef struct {
	bam1_core_t core;
	int l_aux, data_len, m_data;
	uint8_t *data;
} bam1_t;

typedef struct __bam_iter_t *bam_iter_t;

#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
#define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)

/*! @function
  @abstract  Get the CIGAR array
  @param  b  pointer to an alignment
  @return    pointer to the CIGAR array

  @discussion In the CIGAR array, each element is a 32-bit integer. The
  lower 4 bits gives a CIGAR operation and the higher 28 bits keep the
  length of a CIGAR.
 */
#define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))

/*! @function
  @abstract  Get the name of the query
  @param  b  pointer to an alignment
  @return    pointer to the name string, null terminated
 */
#define bam1_qname(b) ((char*)((b)->data))

/*! @function
  @abstract  Get query sequence
  @param  b  pointer to an alignment
  @return    pointer to sequence

  @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
  8 for T and 15 for N. Two bases are packed in one byte with the base
  at the higher 4 bits having smaller coordinate on the read. It is
  recommended to use bam1_seqi() macro to get the base.
 */
#define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)

/*! @function
  @abstract  Get query quality
  @param  b  pointer to an alignment
  @return    pointer to quality string
 */
#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))

/*! @function
  @abstract  Get a base on read
  @param  s  Query sequence returned by bam1_seq()
  @param  i  The i-th position, 0-based
  @return    4-bit integer representing the base.
 */
#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)

/*! @function
  @abstract  Get query sequence and quality
  @param  b  pointer to an alignment
  @return    pointer to the concatenated auxiliary data
 */
#define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2)

#ifndef kroundup32
/*! @function
  @abstract  Round an integer to the next closest power-2 integer.
  @param  x  integer to be rounded (in place)
  @discussion x will be modified.
 */
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

/*!
  @abstract Whether the machine is big-endian; modified only in
  bam_header_init().
 */
extern int bam_is_be;

/*!
  @abstract Verbose level between 0 and 3; 0 is supposed to disable all
  debugging information, though this may not have been implemented.
 */
extern int bam_verbose;

/*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
extern unsigned char bam_nt16_table[256];

/*! @abstract Table for converting a 4-bit encoded nucleotide to a letter. */
extern char *bam_nt16_rev_table;

extern char bam_nt16_nt4_table[];

#ifdef __cplusplus
extern "C" {
#endif

	/*********************
	 * Low-level SAM I/O *
	 *********************/

	/*! @abstract TAM file handler */
	typedef struct __tamFile_t *tamFile;

	/*!
	  @abstract   Open a SAM file for reading, either uncompressed or compressed by gzip/zlib.
	  @param  fn  SAM file name
	  @return     SAM file handler
	 */
	tamFile sam_open(const char *fn);

	/*!
	  @abstract   Close a SAM file handler
	  @param  fp  SAM file handler
	 */
	void sam_close(tamFile fp);

	/*!
	  @abstract      Read one alignment from a SAM file handler
	  @param  fp     SAM file handler
	  @param  header header information (ordered names of chromosomes)
	  @param  b      read alignment; all members in b will be updated
	  @return        0 if successful; otherwise negative
	 */
	int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b);

	/*!
	  @abstract       Read header information from a TAB-delimited list file.
	  @param  fn_list file name for the list
	  @return         a pointer to the header structure

	  @discussion Each line in this file consists of chromosome name and
	  the length of chromosome.
	 */
	bam_header_t *sam_header_read2(const char *fn_list);

	/*!
	  @abstract       Read header from a SAM file (if present)
	  @param  fp      SAM file handler
	  @return         pointer to header struct; 0 if no @SQ lines available
	 */
	bam_header_t *sam_header_read(tamFile fp);

	/*!
	  @abstract       Parse @SQ lines a update a header struct
	  @param  h       pointer to the header struct to be updated
	  @return         number of target sequences

	  @discussion bam_header_t::{n_targets,target_len,target_name} will
	  be destroyed in the first place.
	 */
	int sam_header_parse(bam_header_t *h);
	int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);

	/*!
	  @abstract       Parse @RG lines a update a header struct
	  @param  h       pointer to the header struct to be updated
	  @return         number of @RG lines

	  @discussion bam_header_t::rg2lib will be destroyed in the first
	  place.
	 */
	int sam_header_parse_rg(bam_header_t *h);

#define sam_write1(header, b) bam_view1(header, b)


	/********************************
	 * APIs for string dictionaries *
	 ********************************/

	int bam_strmap_put(void *strmap, const char *rg, const char *lib);
	const char *bam_strmap_get(const void *strmap, const char *rg);
	void *bam_strmap_dup(const void*);
	void *bam_strmap_init();
	void bam_strmap_destroy(void *strmap);


	/*********************
	 * Low-level BAM I/O *
	 *********************/

	/*!
	  @abstract Initialize a header structure.
	  @return   the pointer to the header structure

	  @discussion This function also modifies the global variable
	  bam_is_be.
	 */
	bam_header_t *bam_header_init();

	/*!
	  @abstract        Destroy a header structure.
	  @param  header  pointer to the header
	 */
	void bam_header_destroy(bam_header_t *header);

	/*!
	  @abstract   Read a header structure from BAM.
	  @param  fp  BAM file handler, opened by bam_open()
	  @return     pointer to the header structure

	  @discussion The file position indicator must be placed at the
	  beginning of the file. Upon success, the position indicator will
	  be set at the start of the first alignment.
	 */
	bam_header_t *bam_header_read(bamFile fp);

	/*!
	  @abstract      Write a header structure to BAM.
	  @param  fp     BAM file handler
	  @param  header pointer to the header structure
	  @return        always 0 currently
	 */
	int bam_header_write(bamFile fp, const bam_header_t *header);

	/*!
	  @abstract   Read an alignment from BAM.
	  @param  fp  BAM file handler
	  @param  b   read alignment; all members are updated.
	  @return     number of bytes read from the file

	  @discussion The file position indicator must be
	  placed right before an alignment. Upon success, this function
	  will set the position indicator to the start of the next
	  alignment. This function is not affected by the machine
	  endianness.
	 */
	int bam_read1(bamFile fp, bam1_t *b);

	/*!
	  @abstract Write an alignment to BAM.
	  @param  fp       BAM file handler
	  @param  c        pointer to the bam1_core_t structure
	  @param  data_len total length of variable size data related to
	                   the alignment
	  @param  data     pointer to the concatenated data
	  @return          number of bytes written to the file

	  @discussion This function is not affected by the machine
	  endianness.
	 */
	int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data);

	/*!
	  @abstract   Write an alignment to BAM.
	  @param  fp  BAM file handler
	  @param  b   alignment to write
	  @return     number of bytes written to the file

	  @abstract It is equivalent to:
	    bam_write1_core(fp, &b->core, b->data_len, b->data)
	 */
	int bam_write1(bamFile fp, const bam1_t *b);

	/*! @function
	  @abstract  Initiate a pointer to bam1_t struct
	 */
#define bam_init1() ((bam1_t*)calloc((size_t) 1, sizeof(bam1_t)))

	/*! @function
	  @abstract  Free the memory allocated for an alignment.
	  @param  b  pointer to an alignment
	 */
#define bam_destroy1(b) do {					\
		if (b!=NULL) { free((b)->data); free(b); }	\
	} while (0==1)

	/*!
	  @abstract       Format a BAM record in the SAM format
	  @param  header  pointer to the header structure
	  @param  b       alignment to print
	  @return         a pointer to the SAM string
	 */
	char *bam_format1(const bam_header_t *header, const bam1_t *b);

	char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of);

	/*!
	  @abstract       Check whether a BAM record is plausibly valid
	  @param  header  associated header structure, or NULL if unavailable
	  @param  b       alignment to validate
	  @return         0 if the alignment is invalid; non-zero otherwise

	  @discussion  Simple consistency check of some of the fields of the
	  alignment record.  If the header is provided, several additional checks
	  are made.  Not all fields are checked, so a non-zero result is not a
	  guarantee that the record is valid.  However it is usually good enough
	  to detect when bam_seek() has been called with a virtual file offset
	  that is not the offset of an alignment record.
	 */
	int bam_validate1(const bam_header_t *header, const bam1_t *b);

	const char *bam_get_library(bam_header_t *header, const bam1_t *b);


	/***************
	 * pileup APIs *
	 ***************/

	/*! @typedef
	  @abstract Structure for one alignment covering the pileup position.
	  @field  b      pointer to the alignment
	  @field  qpos   position of the read base at the pileup site, 0-based
	  @field  indel  indel length; 0 for no indel, positive for ins and negative for del
	  @field  is_del 1 iff the base on the padded read is a deletion
	  @field  level  the level of the read in the "viewer" mode

	  @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
	  difference between the two functions is that the former does not
	  set bam_pileup1_t::level, while the later does. Level helps the
	  implementation of alignment viewers, but calculating this has some
	  overhead.
	 */
	typedef struct {
		bam1_t *b;
		int32_t qpos;
		int indel, level;
		uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28;
	} bam_pileup1_t;

	typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);

	struct __bam_plp_t;
	typedef struct __bam_plp_t *bam_plp_t;

	bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data);
	int bam_plp_push(bam_plp_t iter, const bam1_t *b);
	const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
	const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
	void bam_plp_set_mask(bam_plp_t iter, int mask);
	void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt);
	void bam_plp_reset(bam_plp_t iter);
	void bam_plp_destroy(bam_plp_t iter);

	struct __bam_mplp_t;
	typedef struct __bam_mplp_t *bam_mplp_t;

	bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data);
	void bam_mplp_destroy(bam_mplp_t iter);
	void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt);
	int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);

	/*! @typedef
	  @abstract    Type of function to be called by bam_plbuf_push().
	  @param  tid  chromosome ID as is defined in the header
	  @param  pos  start coordinate of the alignment, 0-based
	  @param  n    number of elements in pl array
	  @param  pl   array of alignments
	  @param  data user provided data
	  @discussion  See also bam_plbuf_push(), bam_plbuf_init() and bam_pileup1_t.
	 */
	typedef int (*bam_pileup_f)(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);

	typedef struct {
		bam_plp_t iter;
		bam_pileup_f func;
		void *data;
	} bam_plbuf_t;

	void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask);
	void bam_plbuf_reset(bam_plbuf_t *buf);
	bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data);
	void bam_plbuf_destroy(bam_plbuf_t *buf);
	int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf);

	int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data);

	struct __bam_lplbuf_t;
	typedef struct __bam_lplbuf_t bam_lplbuf_t;

	void bam_lplbuf_reset(bam_lplbuf_t *buf);

	/*! @abstract  bam_plbuf_init() equivalent with level calculated. */
	bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data);

	/*! @abstract  bam_plbuf_destroy() equivalent with level calculated. */
	void bam_lplbuf_destroy(bam_lplbuf_t *tv);

	/*! @abstract  bam_plbuf_push() equivalent with level calculated. */
	int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *buf);


	/*********************
	 * BAM indexing APIs *
	 *********************/

	struct __bam_index_t;
	typedef struct __bam_index_t bam_index_t;

	/*!
	  @abstract   Build index for a BAM file.
	  @discussion Index file "fn.bai" will be created.
	  @param  fn  name of the BAM file
	  @return     always 0 currently
	 */
	int bam_index_build(const char *fn);

	/*!
	  @abstract   Load index from file "fn.bai".
	  @param  fn  name of the BAM file (NOT the index file)
	  @return     pointer to the index structure
	 */
	bam_index_t *bam_index_load(const char *fn);

	/*!
	  @abstract    Destroy an index structure.
	  @param  idx  pointer to the index structure
	 */
	void bam_index_destroy(bam_index_t *idx);

	/*! @typedef
	  @abstract      Type of function to be called by bam_fetch().
	  @param  b     the alignment
	  @param  data  user provided data
	 */
	typedef int (*bam_fetch_f)(const bam1_t *b, void *data);

	/*!
	  @abstract Retrieve the alignments that are overlapped with the
	  specified region.

	  @discussion A user defined function will be called for each
	  retrieved alignment ordered by its start position.

	  @param  fp    BAM file handler
	  @param  idx   pointer to the alignment index
	  @param  tid   chromosome ID as is defined in the header
	  @param  beg   start coordinate, 0-based
	  @param  end   end coordinate, 0-based
	  @param  data  user provided data (will be transferred to func)
	  @param  func  user defined function
	 */
	int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func);

	bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end);
	int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b);
	void bam_iter_destroy(bam_iter_t iter);

	/*!
	  @abstract       Parse a region in the format: "chr2:100,000-200,000".
	  @discussion     bam_header_t::hash will be initialized if empty.
	  @param  header  pointer to the header structure
	  @param  str     string to be parsed
	  @param  ref_id  the returned chromosome ID
	  @param  begin   the returned start coordinate
	  @param  end     the returned end coordinate
	  @return         0 on success; -1 on failure
	 */
	int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);


	/**************************
	 * APIs for optional tags *
	 **************************/

	/*!
	  @abstract       Retrieve data of a tag
	  @param  b       pointer to an alignment struct
	  @param  tag     two-character tag to be retrieved

	  @return  pointer to the type and data. The first character is the
	  type that can be 'iIsScCdfAZH'.

	  @discussion  Use bam_aux2?() series to convert the returned data to
	  the corresponding type.
	*/
	uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);

	int32_t bam_aux2i(const uint8_t *s);
	float bam_aux2f(const uint8_t *s);
	double bam_aux2d(const uint8_t *s);
	char bam_aux2A(const uint8_t *s);
	char *bam_aux2Z(const uint8_t *s);

	int bam_aux_del(bam1_t *b, uint8_t *s);
	void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
	uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2]); // an alias of bam_aux_get()


	/*****************
	 * Miscellaneous *
	 *****************/

	/*!  
	  @abstract Calculate the rightmost coordinate of an alignment on the
	  reference genome.

	  @param  c      pointer to the bam1_core_t structure
	  @param  cigar  the corresponding CIGAR array (from bam1_t::cigar)
	  @return        the rightmost coordinate, 0-based
	*/
	uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar);

	/*!
	  @abstract      Calculate the length of the query sequence from CIGAR.
	  @param  c      pointer to the bam1_core_t structure
	  @param  cigar  the corresponding CIGAR array (from bam1_t::cigar)
	  @return        length of the query sequence
	*/
	int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar);

#ifdef __cplusplus
}
#endif

/*!
  @abstract    Calculate the minimum bin that contains a region [beg,end).
  @param  beg  start of the region, 0-based
  @param  end  end of the region, 0-based
  @return      bin
 */
static inline int bam_reg2bin(uint32_t beg, uint32_t end)
{
	--end;
	if (beg>>14 == end>>14) return 4681 + (beg>>14);
	if (beg>>17 == end>>17) return  585 + (beg>>17);
	if (beg>>20 == end>>20) return   73 + (beg>>20);
	if (beg>>23 == end>>23) return    9 + (beg>>23);
	if (beg>>26 == end>>26) return    1 + (beg>>26);
	return 0;
}

/*!
  @abstract     Copy an alignment
  @param  bdst  destination alignment struct
  @param  bsrc  source alignment struct
  @return       pointer to the destination alignment struct
 */
static inline bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
{
	uint8_t *data = bdst->data;
	int m_data = bdst->m_data;   // backup data and m_data
	if (m_data < bsrc->data_len) { // double the capacity
		m_data = bsrc->data_len; kroundup32(m_data);
		data = (uint8_t*)realloc(data, m_data);
	}
	memcpy(data, bsrc->data, bsrc->data_len); // copy var-len data
	*bdst = *bsrc; // copy the rest
	// restore the backup
	bdst->m_data = m_data;
	bdst->data = data;
	return bdst;
}

/*!
  @abstract     Duplicate an alignment
  @param  src   source alignment struct
  @return       pointer to the destination alignment struct
 */
static inline bam1_t *bam_dup1(const bam1_t *src)
{
	bam1_t *b;
	b = bam_init1();
	*b = *src;
	b->m_data = b->data_len;
	b->data = (uint8_t*)calloc(b->data_len, 1);
	memcpy(b->data, src->data, b->data_len);
	return b;
}

static inline int bam_aux_type2size(int x)
{
	if (x == 'C' || x == 'c' || x == 'A') return 1;
	else if (x == 'S' || x == 's') return 2;
	else if (x == 'I' || x == 'i' || x == 'f') return 4;
	else return 0;
}
/*@end@*/


#endif
genometools-1.5.1/src/external/samtools-0.1.18/bam2bcf.c000066400000000000000000000244111211610345200225030ustar00rootroot00000000000000#include 
#include 
#include "bam.h"
#include "kstring.h"
#include "bam2bcf.h"
#include "errmod.h"
#include "bcftools/bcf.h"

extern	void ks_introsort_uint32_t(size_t n, uint32_t a[]);

#define CALL_ETA 0.03f
#define CALL_MAX 256
#define CALL_DEFTHETA 0.83f
#define DEF_MAPQ 20

#define CAP_DIST 25

bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
{
	bcf_callaux_t *bca;
	if (theta <= 0.) theta = CALL_DEFTHETA;
	bca = calloc(1, sizeof(bcf_callaux_t));
	bca->capQ = 60;
	bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
	bca->min_baseQ = min_baseQ;
	bca->e = errmod_init(1. - theta);
	bca->min_frac = 0.002;
	bca->min_support = 1;
	return bca;
}

void bcf_call_destroy(bcf_callaux_t *bca)
{
	if (bca == 0) return;
	errmod_destroy(bca->e);
	free(bca->bases); free(bca->inscns); free(bca);
}
/* ref_base is the 4-bit representation of the reference base. It is
 * negative if we are looking at an indel. */
int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
{
    static int *var_pos = NULL, nvar_pos = 0;
	int i, n, ref4, is_indel, ori_depth = 0;
	memset(r, 0, sizeof(bcf_callret1_t));
	if (ref_base >= 0) {
		ref4 = bam_nt16_nt4_table[ref_base];
		is_indel = 0;
	} else ref4 = 4, is_indel = 1;
	if (_n == 0) return -1;
	// enlarge the bases array if necessary
	if (bca->max_bases < _n) {
		bca->max_bases = _n;
		kroundup32(bca->max_bases);
		bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
	}
	// fill the bases array
	memset(r, 0, sizeof(bcf_callret1_t));
	for (i = n = 0; i < _n; ++i) {
		const bam_pileup1_t *p = pl + i;
		int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
		// set base
		if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
		++ori_depth;
		baseQ = q = is_indel? p->aux&0xff : (int)bam1_qual(p->b)[p->qpos]; // base/indel quality
		seqQ = is_indel? (p->aux>>8&0xff) : 99;
		if (q < bca->min_baseQ) continue;
		if (q > seqQ) q = seqQ;
		mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
		mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
		if (q > mapQ) q = mapQ;
		if (q > 63) q = 63;
		if (q < 4) q = 4;
		if (!is_indel) {
			b = bam1_seqi(bam1_seq(p->b), p->qpos); // base
			b = bam_nt16_nt4_table[b? b : ref_base]; // b is the 2-bit base
			is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
		} else {
			b = p->aux>>16&0x3f;
			is_diff = (b != 0);
		}
		bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
		// collect annotations
		if (b < 4) r->qsum[b] += q;
		++r->anno[0<<2|is_diff<<1|bam1_strand(p->b)];
		min_dist = p->b->core.l_qseq - 1 - p->qpos;
		if (min_dist > p->qpos) min_dist = p->qpos;
		if (min_dist > CAP_DIST) min_dist = CAP_DIST;
		r->anno[1<<2|is_diff<<1|0] += baseQ;
		r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
		r->anno[2<<2|is_diff<<1|0] += mapQ;
		r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
		r->anno[3<<2|is_diff<<1|0] += min_dist;
		r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
	}
	r->depth = n; r->ori_depth = ori_depth;
	// glfgen
	errmod_cal(bca->e, n, 5, bca->bases, r->p);

    // Calculate the Variant Distance Bias (make it optional?)
    if ( nvar_pos < _n ) {
        nvar_pos = _n;
        var_pos = realloc(var_pos,sizeof(int)*nvar_pos);
    }
    int alt_dp=0, read_len=0;
    for (i=0; i<_n; i++) {
        const bam_pileup1_t *p = pl + i;
        if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base ) 
            continue;

        var_pos[alt_dp] = p->qpos;
        if ( (bam1_cigar(p->b)[0]&BAM_CIGAR_MASK)==4 )
            var_pos[alt_dp] -= bam1_cigar(p->b)[0]>>BAM_CIGAR_SHIFT;

        alt_dp++;
        read_len += p->b->core.l_qseq;
    }
    float mvd=0;
    int j;
    n=0;
    for (i=0; imvd[0] = n ? mvd/n : 0;
    r->mvd[1] = alt_dp;
    r->mvd[2] = alt_dp ? read_len/alt_dp : 0;

	return r->depth;
}


void calc_vdb(int n, const bcf_callret1_t *calls, bcf_call_t *call)
{
    // Variant distance bias. Samples merged by means of DP-weighted average.

    float weight=0, tot_prob=0;

    int i;
    for (i=0; i2*mu ? 0 : sin(mvd*3.14/2/mu) / (4*mu/3.14);
        }
        else
        {
            // Scaled gaussian curve, crude approximation, but behaves well. Using fixed depth for bigger depths.
            if ( dp>5 )
                dp = 5;
            float sigma2 = (read_len/1.9/(dp+1)) * (read_len/1.9/(dp+1));
            float norm   = 1.125*sqrt(2*3.14*sigma2);
            float mu     = read_len/2.9;
            if ( mvd < mu )
                prob = exp(-(mvd-mu)*(mvd-mu)/2/sigma2)/norm;
            else
                prob = exp(-(mvd-mu)*(mvd-mu)/3.125/sigma2)/norm;
        }

        //fprintf(stderr,"dp=%d mvd=%d read_len=%d -> prob=%f\n", dp,mvd,read_len,prob);
        tot_prob += prob*dp;
        weight += dp;
    }
    tot_prob = weight ? tot_prob/weight : 1; 
    //fprintf(stderr,"prob=%f\n", tot_prob);
    call->vdb = tot_prob;
}

int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
{
	int ref4, i, j, qsum[4];
	int64_t tmp;
	if (ref_base >= 0) {
		call->ori_ref = ref4 = bam_nt16_nt4_table[ref_base];
		if (ref4 > 4) ref4 = 4;
	} else call->ori_ref = -1, ref4 = 0;
	// calculate qsum
	memset(qsum, 0, 4 * sizeof(int));
	for (i = 0; i < n; ++i)
		for (j = 0; j < 4; ++j)
			qsum[j] += calls[i].qsum[j];
	for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
	// find the top 2 alleles
	for (i = 1; i < 4; ++i) // insertion sort
		for (j = i; j > 0 && qsum[j] < qsum[j-1]; --j)
			tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
	// set the reference allele and alternative allele(s)
	for (i = 0; i < 5; ++i) call->a[i] = -1;
	call->unseen = -1;
	call->a[0] = ref4;
	for (i = 3, j = 1; i >= 0; --i) {
		if ((qsum[i]&3) != ref4) {
			if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
			else break;
		}
	}
	if (ref_base >= 0) { // for SNPs, find the "unseen" base
		if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
			call->unseen = j, call->a[j++] = qsum[i]&3;
		call->n_alleles = j;
	} else {
		call->n_alleles = j;
		if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
	}
	// set the PL array
	if (call->n < n) {
		call->n = n;
		call->PL = realloc(call->PL, 15 * n);
	}
	{
		int x, g[15], z;
		double sum_min = 0.;
		x = call->n_alleles * (call->n_alleles + 1) / 2;
		// get the possible genotypes
		for (i = z = 0; i < call->n_alleles; ++i)
			for (j = 0; j <= i; ++j)
				g[z++] = call->a[j] * 5 + call->a[i];
		for (i = 0; i < n; ++i) {
			uint8_t *PL = call->PL + x * i;
			const bcf_callret1_t *r = calls + i;
			float min = 1e37;
			for (j = 0; j < x; ++j)
				if (min > r->p[g[j]]) min = r->p[g[j]];
			sum_min += min;
			for (j = 0; j < x; ++j) {
				int y;
				y = (int)(r->p[g[j]] - min + .499);
				if (y > 255) y = 255;
				PL[j] = y;
			}
		}
//		if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);
		call->shift = (int)(sum_min + .499);
	}
	// combine annotations
	memset(call->anno, 0, 16 * sizeof(int));
	for (i = call->depth = call->ori_depth = 0, tmp = 0; i < n; ++i) {
		call->depth += calls[i].depth;
		call->ori_depth += calls[i].ori_depth;
		for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
	}

    calc_vdb(n, calls, call);

	return 0;
}

int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
				 const bcf_callaux_t *bca, const char *ref)
{
	extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
	kstring_t s;
	int i, j;
	b->n_smpl = bc->n;
	b->tid = tid; b->pos = pos; b->qual = 0;
	s.s = b->str; s.m = b->m_str; s.l = 0;
	kputc('\0', &s);
	if (bc->ori_ref < 0) { // an indel
		// write REF
		kputc(ref[pos], &s);
		for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
		kputc('\0', &s);
		// write ALT
		kputc(ref[pos], &s);
		for (i = 1; i < 4; ++i) {
			if (bc->a[i] < 0) break;
			if (i > 1) {
				kputc(',', &s); kputc(ref[pos], &s);
			}
			if (bca->indel_types[bc->a[i]] < 0) { // deletion
				for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
					kputc(ref[pos+1+j], &s);
			} else { // insertion; cannot be a reference unless a bug
				char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
				for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
					kputc("ACGTN"[(int)inscns[j]], &s);
				for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
			}
		}
		kputc('\0', &s);
	} else { // a SNP
		kputc("ACGTN"[bc->ori_ref], &s); kputc('\0', &s);
		for (i = 1; i < 5; ++i) {
			if (bc->a[i] < 0) break;
			if (i > 1) kputc(',', &s);
			kputc(bc->unseen == i? 'X' : "ACGT"[bc->a[i]], &s);
		}
		kputc('\0', &s);
	}
	kputc('\0', &s);
	// INFO
	if (bc->ori_ref < 0) kputs("INDEL;", &s);
	kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
	for (i = 0; i < 16; ++i) {
		if (i) kputc(',', &s);
		kputw(bc->anno[i], &s);
	}
    if ( bc->vdb!=1 )
    {
        ksprintf(&s, ";VDB=%.4f", bc->vdb);
    }
	kputc('\0', &s);
	// FMT
	kputs("PL", &s);
	if (bcr) {
		kputs(":DP", &s);
		if (is_SP) kputs(":SP", &s);
	}
	kputc('\0', &s);
	b->m_str = s.m; b->str = s.s; b->l_str = s.l;
	bcf_sync(b);
	memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
	if (bcr) {
		uint16_t *dp = (uint16_t*)b->gi[1].data;
		int32_t *sp = is_SP? b->gi[2].data : 0;
		for (i = 0; i < bc->n; ++i) {
			bcf_callret1_t *p = bcr + i;
			dp[i] = p->depth < 0xffff? p->depth : 0xffff;
			if (is_SP) {
				if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
					|| p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
				{
					sp[i] = 0;
				} else {
					double left, right, two;
					int x;
					kt_fisher_exact(p->anno[0], p->anno[1], p->anno[2], p->anno[3], &left, &right, &two);
					x = (int)(-4.343 * log(two) + .499);
					if (x > 255) x = 255;
					sp[i] = x;
				}
			}
		}
	}
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam2bcf.h000066400000000000000000000030311211610345200225030ustar00rootroot00000000000000#ifndef BAM2BCF_H
#define BAM2BCF_H

#include 
#include "errmod.h"
#include "bcftools/bcf.h"

#define B2B_INDEL_NULL 10000

typedef struct __bcf_callaux_t {
	int capQ, min_baseQ;
	int openQ, extQ, tandemQ; // for indels
	int min_support; // for collecting indel candidates
	double min_frac; // for collecting indel candidates
	// for internal uses
	int max_bases;
	int indel_types[4];
	int maxins, indelreg;
	char *inscns;
	uint16_t *bases;
	errmod_t *e;
	void *rghash;
} bcf_callaux_t;

typedef struct {
	int depth, ori_depth, qsum[4];
	int anno[16];
	float p[25];
    int mvd[3]; // mean variant distance, number of variant reads, average read length
} bcf_callret1_t;

typedef struct {
	int a[5]; // alleles: ref, alt, alt2, alt3
	int n, n_alleles, shift, ori_ref, unseen;
	int anno[16], depth, ori_depth;
	uint8_t *PL;
    float vdb; // variant distance bias
} bcf_call_t;

#ifdef __cplusplus
extern "C" {
#endif

	bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
	void bcf_call_destroy(bcf_callaux_t *bca);
	int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
	int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
	int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
					 const bcf_callaux_t *bca, const char *ref);
	int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
						  const void *rghash);

#ifdef __cplusplus
}
#endif

#endif
genometools-1.5.1/src/external/samtools-0.1.18/bam2bcf_indel.c000066400000000000000000000414201211610345200236550ustar00rootroot00000000000000#include 
#include 
#include 
#include "bam.h"
#include "bam2bcf.h"
#include "kaln.h"
#include "kprobaln.h"
#include "khash.h"
KHASH_SET_INIT_STR(rg)

#include "ksort.h"
KSORT_INIT_GENERIC(uint32_t)

#define MINUS_CONST 0x10000000
#define INDEL_WINDOW_SIZE 50

void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
{
	const char *s, *p, *q, *r, *t;
	khash_t(rg) *hash;
	if (list == 0 || hdtext == 0) return _hash;
	if (_hash == 0) _hash = kh_init(rg);
	hash = (khash_t(rg)*)_hash;
	if ((s = strstr(hdtext, "@RG\t")) == 0) return hash;
	do {
		t = strstr(s + 4, "@RG\t"); // the next @RG
		if ((p = strstr(s, "\tID:")) != 0) p += 4;
		if ((q = strstr(s, "\tPL:")) != 0) q += 4;
		if (p && q && (t == 0 || (p < t && q < t))) { // ID and PL are both present
			int lp, lq;
			char *x;
			for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
			for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
			x = calloc((lp > lq? lp : lq) + 1, 1);
			for (r = q; *r && *r != '\t' && *r != '\n'; ++r) x[r-q] = *r;
			if (strstr(list, x)) { // insert ID to the hash table
				khint_t k;
				int ret;
				for (r = p; *r && *r != '\t' && *r != '\n'; ++r) x[r-p] = *r;
				x[r-p] = 0;
				k = kh_get(rg, hash, x);
				if (k == kh_end(hash)) k = kh_put(rg, hash, x, &ret);
				else free(x);
			} else free(x);
		}
		s = t;
	} while (s);
	return hash;
}

void bcf_call_del_rghash(void *_hash)
{
	khint_t k;
	khash_t(rg) *hash = (khash_t(rg)*)_hash;
	if (hash == 0) return;
	for (k = kh_begin(hash); k < kh_end(hash); ++k)
		if (kh_exist(hash, k))
			free((char*)kh_key(hash, k));
	kh_destroy(rg, hash);
}

static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
{
	int k, x = c->pos, y = 0, last_y = 0;
	*_tpos = c->pos;
	for (k = 0; k < c->n_cigar; ++k) {
		int op = cigar[k] & BAM_CIGAR_MASK;
		int l = cigar[k] >> BAM_CIGAR_SHIFT;
		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
			if (c->pos > tpos) return y;
			if (x + l > tpos) {
				*_tpos = tpos;
				return y + (tpos - x);
			}
			x += l; y += l;
			last_y = y;
		} else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
		else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
			if (x + l > tpos) {
				*_tpos = is_left? x : x + l;
				return y;
			}
			x += l;
		}
	}
	*_tpos = x;
	return last_y;
}
// FIXME: check if the inserted sequence is consistent with the homopolymer run
// l is the relative gap length and l_run is the length of the homopolymer on the reference
static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
{
	int q, qh;
	q = bca->openQ + bca->extQ * (abs(l) - 1);
	qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000;
	return q < qh? q : qh;
}

static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
{
	int i, j, max = 0, max_i = pos, score = 0;
	l = abs(l);
	for (i = pos + 1, j = 0; ref[i]; ++i, ++j) {
		if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1;
		else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1;
		if (score < 0) break;
		if (max < score) max = score, max_i = i;
	}
	return max_i - pos;
}

int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
					  const void *rghash)
{
	int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
	int N, K, l_run, ref_type, n_alt;
	char *inscns = 0, *ref2, *query, **ref_sample;
	khash_t(rg) *hash = (khash_t(rg)*)rghash;
	if (ref == 0 || bca == 0) return -1;
	// mark filtered reads
	if (rghash) {
		N = 0;
		for (s = N = 0; s < n; ++s) {
			for (i = 0; i < n_plp[s]; ++i) {
				bam_pileup1_t *p = plp[s] + i;
				const uint8_t *rg = bam_aux_get(p->b, "RG");
				p->aux = 1; // filtered by default
				if (rg) {
					khint_t k = kh_get(rg, hash, (const char*)(rg + 1));
					if (k != kh_end(hash)) p->aux = 0, ++N; // not filtered
				}
			}
		}
		if (N == 0) return -1; // no reads left
	}
	// determine if there is a gap
	for (s = N = 0; s < n; ++s) {
		for (i = 0; i < n_plp[s]; ++i)
			if (plp[s][i].indel != 0) break;
		if (i < n_plp[s]) break;
	}
	if (s == n) return -1; // there is no indel at this position.
	for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads
	{ // find out how many types of indels are present
		int m, n_alt = 0, n_tot = 0;
		uint32_t *aux;
		aux = calloc(N + 1, 4);
		m = max_rd_len = 0;
		aux[m++] = MINUS_CONST; // zero indel is always a type
		for (s = 0; s < n; ++s) {
			for (i = 0; i < n_plp[s]; ++i) {
				const bam_pileup1_t *p = plp[s] + i;
				if (rghash == 0 || p->aux == 0) {
					++n_tot;
					if (p->indel != 0) {
						++n_alt;
						aux[m++] = MINUS_CONST + p->indel;
					}
				}
				j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b));
				if (j > max_rd_len) max_rd_len = j;
			}
		}
		ks_introsort(uint32_t, m, aux);
		// squeeze out identical types
		for (i = 1, n_types = 1; i < m; ++i)
			if (aux[i] != aux[i-1]) ++n_types;
		if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
			free(aux); return -1;
		}
		if (n_types >= 64) {
			free(aux);
			if (bam_verbose >= 2) 
				fprintf(stderr, "[%s] excessive INDEL alleles at position %d. Skip the position.\n", __func__, pos + 1);
			return -1;
		}
		types = (int*)calloc(n_types, sizeof(int));
		t = 0;
		types[t++] = aux[0] - MINUS_CONST; 
		for (i = 1; i < m; ++i)
			if (aux[i] != aux[i-1])
				types[t++] = aux[i] - MINUS_CONST;
		free(aux);
		for (t = 0; t < n_types; ++t)
			if (types[t] == 0) break;
		ref_type = t; // the index of the reference type (0)
	}
	{ // calculate left and right boundary
		left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
		right = pos + INDEL_WINDOW_SIZE;
		if (types[0] < 0) right -= types[0];
		// in case the alignments stand out the reference
		for (i = pos; i < right; ++i)
			if (ref[i] == 0) break;
		right = i;
	}
	/* The following block fixes a long-existing flaw in the INDEL
	 * calling model: the interference of nearby SNPs. However, it also
	 * reduces the power because sometimes, substitutions caused by
	 * indels are not distinguishable from true mutations. Multiple
	 * sequence realignment helps to increase the power.
	 */
	{ // construct per-sample consensus
		int L = right - left + 1, max_i, max2_i;
		uint32_t *cns, max, max2;
		char *ref0, *r;
		ref_sample = calloc(n, sizeof(void*));
		cns = calloc(L, 4);
		ref0 = calloc(L, 1);
		for (i = 0; i < right - left; ++i)
			ref0[i] = bam_nt16_table[(int)ref[i+left]];
		for (s = 0; s < n; ++s) {
			r = ref_sample[s] = calloc(L, 1);
			memset(cns, 0, sizeof(int) * L);
			// collect ref and non-ref counts
			for (i = 0; i < n_plp[s]; ++i) {
				bam_pileup1_t *p = plp[s] + i;
				bam1_t *b = p->b;
				uint32_t *cigar = bam1_cigar(b);
				uint8_t *seq = bam1_seq(b);
				int x = b->core.pos, y = 0;
				for (k = 0; k < b->core.n_cigar; ++k) {
					int op = cigar[k]&0xf;
					int j, l = cigar[k]>>4;
					if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
						for (j = 0; j < l; ++j)
							if (x + j >= left && x + j < right)
								cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;
						x += l; y += l;
					} else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
					else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
				}
			}
			// determine the consensus
			for (i = 0; i < right - left; ++i) r[i] = ref0[i];
			max = max2 = 0; max_i = max2_i = -1;
			for (i = 0; i < right - left; ++i) {
				if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i;
				else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i;
			}
			if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1;
			if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
			if (max_i >= 0) r[max_i] = 15;
			if (max2_i >= 0) r[max2_i] = 15;
//			for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
		}
		free(ref0); free(cns);
	}
	{ // the length of the homopolymer run around the current position
		int c = bam_nt16_table[(int)ref[pos + 1]];
		if (c == 15) l_run = 1;
		else {
			for (i = pos + 2; ref[i]; ++i)
				if (bam_nt16_table[(int)ref[i]] != c) break;
			l_run = i;
			for (i = pos; i >= 0; --i)
				if (bam_nt16_table[(int)ref[i]] != c) break;
			l_run -= i + 1;
		}
	}
	// construct the consensus sequence
	max_ins = types[n_types - 1]; // max_ins is at least 0
	if (max_ins > 0) {
		int *inscns_aux = calloc(4 * n_types * max_ins, sizeof(int));
		// count the number of occurrences of each base at each position for each type of insertion
		for (t = 0; t < n_types; ++t) {
			if (types[t] > 0) {
				for (s = 0; s < n; ++s) {
					for (i = 0; i < n_plp[s]; ++i) {
						bam_pileup1_t *p = plp[s] + i;
						if (p->indel == types[t]) {
							uint8_t *seq = bam1_seq(p->b);
							for (k = 1; k <= p->indel; ++k) {
								int c = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos + k)];
								if (c < 4) ++inscns_aux[(t*max_ins+(k-1))*4 + c];
							}
						}
					}
				}
			}
		}
		// use the majority rule to construct the consensus
		inscns = calloc(n_types * max_ins, 1);
		for (t = 0; t < n_types; ++t) {
			for (j = 0; j < types[t]; ++j) {
				int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*4];
				for (k = 0; k < 4; ++k)
					if (ia[k] > max)
						max = ia[k], max_k = k;
				inscns[t*max_ins + j] = max? max_k : 4;
			}
		}
		free(inscns_aux);
	}
	// compute the likelihood given each type of indel for each read
	max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
	ref2  = calloc(max_ref2, 1);
	query = calloc(right - left + max_rd_len + max_ins + 2, 1);
	score1 = calloc(N * n_types, sizeof(int));
	score2 = calloc(N * n_types, sizeof(int));
	bca->indelreg = 0;
	for (t = 0; t < n_types; ++t) {
		int l, ir;
		kpa_par_t apf1 = { 1e-4, 1e-2, 10 }, apf2 = { 1e-6, 1e-3, 10 };
		apf1.bw = apf2.bw = abs(types[t]) + 3;
		// compute indelreg
		if (types[t] == 0) ir = 0;
		else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
		else ir = est_indelreg(pos, ref, -types[t], 0);
		if (ir > bca->indelreg) bca->indelreg = ir;
//		fprintf(stderr, "%d, %d, %d\n", pos, types[t], ir);
		// realignment
		for (s = K = 0; s < n; ++s) {
			// write ref2
			for (k = 0, j = left; j <= pos; ++j)
				ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
			if (types[t] <= 0) j += -types[t];
			else for (l = 0; l < types[t]; ++l)
					 ref2[k++] = inscns[t*max_ins + l];
			for (; j < right && ref[j]; ++j)
				ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
			for (; k < max_ref2; ++k) ref2[k] = 4;
			if (j < right) right = j;
			// align each read to ref2
			for (i = 0; i < n_plp[s]; ++i, ++K) {
				bam_pileup1_t *p = plp[s] + i;
				int qbeg, qend, tbeg, tend, sc, kk;
				uint8_t *seq = bam1_seq(p->b);
				uint32_t *cigar = bam1_cigar(p->b);
				if (p->b->core.flag&4) continue; // unmapped reads
				// FIXME: the following loop should be better moved outside; nonetheless, realignment should be much slower anyway.
				for (kk = 0; kk < p->b->core.n_cigar; ++kk)
					if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break;
				if (kk < p->b->core.n_cigar) continue;
				// FIXME: the following skips soft clips, but using them may be more sensitive.
				// determine the start and end of sequences for alignment
				qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left,  0, &tbeg);
				qend = tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend);
				if (types[t] < 0) {
					int l = -types[t];
					tbeg = tbeg - l > left?  tbeg - l : left;
				}
				// write the query sequence
				for (l = qbeg; l < qend; ++l)
					query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
				{ // do realignment; this is the bottleneck
					const uint8_t *qual = bam1_qual(p->b), *bq;
					uint8_t *qq;
					qq = calloc(qend - qbeg, 1);
					bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
					if (bq) ++bq; // skip type
					for (l = qbeg; l < qend; ++l) {
						qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l];
						if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
						if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
					}
					sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
									(uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0);
					l = (int)(100. * sc / (qend - qbeg) + .499); // used for adjusting indelQ below
					if (l > 255) l = 255;
					score1[K*n_types + t] = score2[K*n_types + t] = sc<<8 | l;
					if (sc > 5) {
						sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
										(uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0);
						l = (int)(100. * sc / (qend - qbeg) + .499);
						if (l > 255) l = 255;
						score2[K*n_types + t] = sc<<8 | l;
					}
					free(qq);
				}
/*
				for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
					fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);
				fputc('\n', stderr);
				for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], stderr);
				fputc('\n', stderr);
				fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam1_qname(p->b), qbeg, tbeg, sc);
*/
			}
		}
	}
	free(ref2); free(query);
	{ // compute indelQ
		int *sc, tmp, *sumq;
		sc   = alloca(n_types * sizeof(int));
		sumq = alloca(n_types * sizeof(int));
		memset(sumq, 0, sizeof(int) * n_types);
		for (s = K = 0; s < n; ++s) {
			for (i = 0; i < n_plp[s]; ++i, ++K) {
				bam_pileup1_t *p = plp[s] + i;
				int *sct = &score1[K*n_types], indelQ1, indelQ2, seqQ, indelQ;
				for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
				for (t = 1; t < n_types; ++t) // insertion sort
					for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
						tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
				/* errmod_cal() assumes that if the call is wrong, the
				 * likelihoods of other events are equal. This is about
				 * right for substitutions, but is not desired for
				 * indels. To reuse errmod_cal(), I have to make
				 * compromise for multi-allelic indels.
				 */
				if ((sc[0]&0x3f) == ref_type) {
					indelQ1 = (sc[1]>>14) - (sc[0]>>14);
					seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run);
				} else {
					for (t = 0; t < n_types; ++t) // look for the reference type
						if ((sc[t]&0x3f) == ref_type) break;
					indelQ1 = (sc[t]>>14) - (sc[0]>>14);
					seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run);
				}
				tmp = sc[0]>>6 & 0xff;
				indelQ1 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ1 + .499); // reduce indelQ
				sct = &score2[K*n_types];
				for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
				for (t = 1; t < n_types; ++t) // insertion sort
					for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
						tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
				if ((sc[0]&0x3f) == ref_type) {
					indelQ2 = (sc[1]>>14) - (sc[0]>>14);
				} else {
					for (t = 0; t < n_types; ++t) // look for the reference type
						if ((sc[t]&0x3f) == ref_type) break;
					indelQ2 = (sc[t]>>14) - (sc[0]>>14);
				}
				tmp = sc[0]>>6 & 0xff;
				indelQ2 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ2 + .499);
				// pick the smaller between indelQ1 and indelQ2
				indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2;
				if (indelQ > 255) indelQ = 255;
				if (seqQ > 255) seqQ = 255;
				p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total
				sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
//				fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ);
			}
		}
		// determine bca->indel_types[] and bca->inscns
		bca->maxins = max_ins;
		bca->inscns = realloc(bca->inscns, bca->maxins * 4);
		for (t = 0; t < n_types; ++t)
			sumq[t] = sumq[t]<<6 | t;
		for (t = 1; t < n_types; ++t) // insertion sort
			for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j)
				tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp;
		for (t = 0; t < n_types; ++t) // look for the reference type
			if ((sumq[t]&0x3f) == ref_type) break;
		if (t) { // then move the reference type to the first
			tmp = sumq[t];
			for (; t > 0; --t) sumq[t] = sumq[t-1];
			sumq[0] = tmp;
		}
		for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL;
		for (t = 0; t < 4 && t < n_types; ++t) {
			bca->indel_types[t] = types[sumq[t]&0x3f];
			memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins);
		}
		// update p->aux
		for (s = n_alt = 0; s < n; ++s) {
			for (i = 0; i < n_plp[s]; ++i) {
				bam_pileup1_t *p = plp[s] + i;
				int x = types[p->aux>>16&0x3f];
				for (j = 0; j < 4; ++j)
					if (x == bca->indel_types[j]) break;
				p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff));
				if ((p->aux>>16&0x3f) > 0) ++n_alt;
//				fprintf(stderr, "X pos=%d read=%d:%d name=%s call=%d type=%d q=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), p->aux>>16&63, bca->indel_types[p->aux>>16&63], p->aux&0xff, p->aux>>8&0xff);
			}
		}		
	}
	free(score1); free(score2);
	// free
	for (i = 0; i < n; ++i) free(ref_sample[i]);
	free(ref_sample);
	free(types); free(inscns);
	return n_alt > 0? 0 : -1;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam2depth.c000066400000000000000000000107061211610345200230570ustar00rootroot00000000000000/* This program demonstrates how to generate pileup from multiple BAMs
 * simutaneously, to achieve random access and to use the BED interface.
 * To compile this program separately, you may:
 *
 *   gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -L. -lbam -lz
 */
#include 
#include 
#include 
#include 
#include "bam.h"

typedef struct {     // auxiliary data structure
	bamFile fp;      // the file handler
	bam_iter_t iter; // NULL if a region not specified
	int min_mapQ;    // mapQ filter
} aux_t;

void *bed_read(const char *fn); // read a BED or position list file
void bed_destroy(void *_h);     // destroy the BED data structure
int bed_overlap(const void *_h, const char *chr, int beg, int end); // test if chr:beg-end overlaps

// This function reads a BAM alignment from one BAM file.
static int read_bam(void *data, bam1_t *b) // read level filters better go here to avoid pileup
{
	aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
	int ret = aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
	if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
	return ret;
}

#ifdef _MAIN_BAM2DEPTH
int main(int argc, char *argv[])
#else
int main_depth(int argc, char *argv[])
#endif
{
	int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0;
	const bam_pileup1_t **plp;
	char *reg = 0; // specified region
	void *bed = 0; // BED data structure
	bam_header_t *h = 0; // BAM header of the 1st input
	aux_t **data;
	bam_mplp_t mplp;

	// parse the command line
	while ((n = getopt(argc, argv, "r:b:q:Q:")) >= 0) {
		switch (n) {
			case 'r': reg = strdup(optarg); break;   // parsing a region requires a BAM header
			case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
			case 'q': baseQ = atoi(optarg); break;   // base quality threshold
			case 'Q': mapQ = atoi(optarg); break;    // mapping quality threshold
		}
	}
	if (optind == argc) {
		fprintf(stderr, "Usage: bam2depth [-r reg] [-q baseQthres] [-Q mapQthres] [-b in.bed]  [...]\n");
		return 1;
	}

	// initialize the auxiliary data structures
	n = argc - optind; // the number of BAMs on the command line
	data = calloc(n, sizeof(void*)); // data[i] for the i-th input
	beg = 0; end = 1<<30; tid = -1;  // set the default region
	for (i = 0; i < n; ++i) {
		bam_header_t *htmp;
		data[i] = calloc(1, sizeof(aux_t));
		data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM
		data[i]->min_mapQ = mapQ;                    // set the mapQ filter
		htmp = bam_header_read(data[i]->fp);         // read the BAM header
		if (i == 0) {
			h = htmp; // keep the header of the 1st BAM
			if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region
		} else bam_header_destroy(htmp); // if not the 1st BAM, trash the header
		if (tid >= 0) { // if a region is specified and parsed successfully
			bam_index_t *idx = bam_index_load(argv[optind+i]);  // load the index
			data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator
			bam_index_destroy(idx); // the index is not needed any more; phase out of the memory
		}
	}

	// the core multi-pileup loop
	mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
	n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
	plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp)
	while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
		if (pos < beg || pos >= end) continue; // out of range; skip
		if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip
		fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster
		for (i = 0; i < n; ++i) { // base level filters have to go here
			int j, m = 0;
			for (j = 0; j < n_plp[i]; ++j) {
				const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know
				if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos
				else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality
			}
			printf("\t%d", n_plp[i] - m); // this the depth to output
		}
		putchar('\n');
	}
	free(n_plp); free(plp);
	bam_mplp_destroy(mplp);

	bam_header_destroy(h);
	for (i = 0; i < n; ++i) {
		bam_close(data[i]->fp);
		if (data[i]->iter) bam_iter_destroy(data[i]->iter);
		free(data[i]);
	}
	free(data); free(reg);
	if (bed) bed_destroy(bed);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_aux.c000066400000000000000000000116111211610345200226210ustar00rootroot00000000000000#include 
#include "bam.h"
#include "khash.h"
typedef char *str_p;
KHASH_MAP_INIT_STR(s, int)
KHASH_MAP_INIT_STR(r2l, str_p)

void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
{
	int ori_len = b->data_len;
	b->data_len += 3 + len;
	b->l_aux += 3 + len;
	if (b->m_data < b->data_len) {
		b->m_data = b->data_len;
		kroundup32(b->m_data);
		b->data = (uint8_t*)realloc(b->data, b->m_data);
	}
	b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
	b->data[ori_len + 2] = type;
	memcpy(b->data + ori_len + 3, data, len);
}

uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
{
	return bam_aux_get(b, tag);
}

#define __skip_tag(s) do { \
		int type = toupper(*(s)); \
		++(s); \
		if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
		else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \
		else (s) += bam_aux_type2size(type); \
	} while(0)

uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
{
	uint8_t *s;
	int y = tag[0]<<8 | tag[1];
	s = bam1_aux(b);
	while (s < b->data + b->data_len) {
		int x = (int)s[0]<<8 | s[1];
		s += 2;
		if (x == y) return s;
		__skip_tag(s);
	}
	return 0;
}
// s MUST BE returned by bam_aux_get()
int bam_aux_del(bam1_t *b, uint8_t *s)
{
	uint8_t *p, *aux;
	aux = bam1_aux(b);
	p = s - 2;
	__skip_tag(s);
	memmove(p, s, b->l_aux - (s - aux));
	b->data_len -= s - p;
	b->l_aux -= s - p;
	return 0;
}

int bam_aux_drop_other(bam1_t *b, uint8_t *s)
{
	if (s) {
		uint8_t *p, *aux;
		aux = bam1_aux(b);
		p = s - 2;
		__skip_tag(s);
		memmove(aux, p, s - p);
		b->data_len -= b->l_aux - (s - p);
		b->l_aux = s - p;
	} else {
		b->data_len -= b->l_aux;
		b->l_aux = 0;
	}
	return 0;
}

void bam_init_header_hash(bam_header_t *header)
{
	if (header->hash == 0) {
		int ret, i;
		khiter_t iter;
		khash_t(s) *h;
		header->hash = h = kh_init(s);
		for (i = 0; i < header->n_targets; ++i) {
			iter = kh_put(s, h, header->target_name[i], &ret);
			kh_value(h, iter) = i;
		}
	}
}

void bam_destroy_header_hash(bam_header_t *header)
{
	if (header->hash)
		kh_destroy(s, (khash_t(s)*)header->hash);
}

int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
{
	khint_t k;
	khash_t(s) *h = (khash_t(s)*)header->hash;
	k = kh_get(s, h, seq_name);
	return k == kh_end(h)? -1 : kh_value(h, k);
}

int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end)
{
	char *s;
	int i, l, k, name_end;
	khiter_t iter;
	khash_t(s) *h;

	bam_init_header_hash(header);
	h = (khash_t(s)*)header->hash;

	*ref_id = *beg = *end = -1;
	name_end = l = strlen(str);
	s = (char*)malloc(l+1);
	// remove space
	for (i = k = 0; i < l; ++i)
		if (!isspace(str[i])) s[k++] = str[i];
	s[k] = 0; l = k;
	// determine the sequence name
	for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
	if (i >= 0) name_end = i;
	if (name_end < l) { // check if this is really the end
		int n_hyphen = 0;
		for (i = name_end + 1; i < l; ++i) {
			if (s[i] == '-') ++n_hyphen;
			else if (!isdigit(s[i]) && s[i] != ',') break;
		}
		if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
		s[name_end] = 0;
		iter = kh_get(s, h, s);
		if (iter == kh_end(h)) { // cannot find the sequence name
			iter = kh_get(s, h, str); // try str as the name
			if (iter == kh_end(h)) {
				if (bam_verbose >= 2) fprintf(stderr, "[%s] fail to determine the sequence name.\n", __func__);
				free(s); return -1;
			} else s[name_end] = ':', name_end = l;
		}
	} else iter = kh_get(s, h, str);
	*ref_id = kh_val(h, iter);
	// parse the interval
	if (name_end < l) {
		for (i = k = name_end + 1; i < l; ++i)
			if (s[i] != ',') s[k++] = s[i];
		s[k] = 0;
		*beg = atoi(s + name_end + 1);
		for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
		*end = i < k? atoi(s + i + 1) : 1<<29;
		if (*beg > 0) --*beg;
	} else *beg = 0, *end = 1<<29;
	free(s);
	return *beg <= *end? 0 : -1;
}

int32_t bam_aux2i(const uint8_t *s)
{
	int type;
	if (s == 0) return 0;
	type = *s++;
	if (type == 'c') return (int32_t)*(int8_t*)s;
	else if (type == 'C') return (int32_t)*(uint8_t*)s;
	else if (type == 's') return (int32_t)*(int16_t*)s;
	else if (type == 'S') return (int32_t)*(uint16_t*)s;
	else if (type == 'i' || type == 'I') return *(int32_t*)s;
	else return 0;
}

float bam_aux2f(const uint8_t *s)
{
	int type;
	type = *s++;
	if (s == 0) return 0.0;
	if (type == 'f') return *(float*)s;
	else return 0.0;
}

double bam_aux2d(const uint8_t *s)
{
	int type;
	type = *s++;
	if (s == 0) return 0.0;
	if (type == 'd') return *(double*)s;
	else return 0.0;
}

char bam_aux2A(const uint8_t *s)
{
	int type;
	type = *s++;
	if (s == 0) return 0;
	if (type == 'A') return *(char*)s;
	else return 0;
}

char *bam_aux2Z(const uint8_t *s)
{
	int type;
	type = *s++;
	if (s == 0) return 0;
	if (type == 'Z' || type == 'H') return (char*)s;
	else return 0;
}

#ifdef _WIN32
double drand48()
{
	return (double)rand() / RAND_MAX;
}
#endif
genometools-1.5.1/src/external/samtools-0.1.18/bam_cat.c000066400000000000000000000132401211610345200225730ustar00rootroot00000000000000/*

bam_cat -- efficiently concatenates bam files

bam_cat can be used to concatenate BAM files. Under special
circumstances, it can be used as an alternative to 'samtools merge' to
concatenate multiple sorted files into a single sorted file. For this
to work each file must be sorted, and the sorted files must be given
as command line arguments in order such that the final read in file i
is less than or equal to the first read in file i+1.

This code is derived from the bam_reheader function in samtools 0.1.8
and modified to perform concatenation by Chris Saunders on behalf of
Illumina.


########## License:

The MIT License

Original SAMtools work copyright (c) 2008-2009 Genome Research Ltd.
Modified SAMtools work copyright (c) 2010 Illumina, Inc.

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

*/


/*
makefile:
"""
CC=gcc
CFLAGS+=-g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I$(SAMTOOLS_DIR)
LDFLAGS+=-L$(SAMTOOLS_DIR)
LDLIBS+=-lbam -lz

all:bam_cat
"""
*/


#include 
#include 
#include 

#include "bgzf.h"
#include "bam.h"

#define BUF_SIZE 0x10000

#define GZIPID1 31
#define GZIPID2 139

#define BGZF_EMPTY_BLOCK_SIZE 28


int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam)
{
    BGZF *fp;
    FILE* fp_file;
    uint8_t *buf;
    uint8_t ebuf[BGZF_EMPTY_BLOCK_SIZE];
    const int es=BGZF_EMPTY_BLOCK_SIZE;
    int i;
    
    fp = strcmp(outbam, "-")? bgzf_open(outbam, "w") : bgzf_fdopen(fileno(stdout), "w");
    if (fp == 0) {
        fprintf(stderr, "[%s] ERROR: fail to open output file '%s'.\n", __func__, outbam);
        return 1;
    }
    if (h) bam_header_write(fp, h);
    
    buf = (uint8_t*) malloc(BUF_SIZE);
    for(i = 0; i < nfn; ++i){
        BGZF *in;
        bam_header_t *old;
        int len,j;
        
        in = strcmp(fn[i], "-")? bam_open(fn[i], "r") : bam_dopen(fileno(stdin), "r");
        if (in == 0) {
            fprintf(stderr, "[%s] ERROR: fail to open file '%s'.\n", __func__, fn[i]);
            return -1;
        }
        if (in->open_mode != 'r') return -1;
        
        old = bam_header_read(in);
		if (h == 0 && i == 0) bam_header_write(fp, old);
        
        if (in->block_offset < in->block_length) {
            bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
            bgzf_flush(fp);
        }
        
        j=0;
#ifdef _USE_KNETFILE
        fp_file=fp->x.fpw;
        while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0) {
#else  
        fp_file=fp->file;
        while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) {
#endif
            if(len= 0) {
		switch (c) {
			case 'h': {
        		tamFile fph = sam_open(optarg);
		        if (fph == 0) {
    		        fprintf(stderr, "[%s] ERROR: fail to read the header from '%s'.\n", __func__, argv[1]);
        		    return 1;
	        	}
	    	    h = sam_header_read(fph);
    	    	sam_close(fph);
				break;
			}
			case 'o': outfn = strdup(optarg); break;
		}
	}
	if (argc - optind < 2) {
        fprintf(stderr, "Usage: samtools cat [-h header.sam] [-o out.bam]   [...]\n");
        return 1;
    }
    ret = bam_cat(argc - optind, argv + optind, h, outfn? outfn : "-");
	free(outfn);
	return ret;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_color.c000066400000000000000000000053631211610345200231510ustar00rootroot00000000000000#include 
#include "bam.h"

/*!
 @abstract     Get the color encoding the previous and current base
 @param b      pointer to an alignment
 @param i      The i-th position, 0-based
 @return       color

 @discussion   Returns 0 no color information is found.
 */
char bam_aux_getCSi(bam1_t *b, int i)
{
	uint8_t *c = bam_aux_get(b, "CS");
	char *cs = NULL;

	// return the base if the tag was not found
	if(0 == c) return 0;

	cs = bam_aux2Z(c);
	// adjust for strandedness and leading adaptor
	if(bam1_strand(b)) i = strlen(cs) - 1 - i;
	else i++;
	return cs[i];
}

/*!
 @abstract     Get the color quality of the color encoding the previous and current base
 @param b      pointer to an alignment
 @param i      The i-th position, 0-based
 @return       color quality

 @discussion   Returns 0 no color information is found.
 */
char bam_aux_getCQi(bam1_t *b, int i)
{
	uint8_t *c = bam_aux_get(b, "CQ");
	char *cq = NULL;
	
	// return the base if the tag was not found
	if(0 == c) return 0;

	cq = bam_aux2Z(c);
	// adjust for strandedness
	if(bam1_strand(b)) i = strlen(cq) - 1 - i;
	return cq[i];
}

char bam_aux_nt2int(char a)
{
	switch(toupper(a)) {
		case 'A':
			return 0;
			break;
		case 'C':
			return 1;
			break;
		case 'G':
			return 2;
			break;
		case 'T':
			return 3;
			break;
		default:
			return 4;
			break;
	}
}

char bam_aux_ntnt2cs(char a, char b)
{
	a = bam_aux_nt2int(a);
	b = bam_aux_nt2int(b);
	if(4 == a || 4 == b) return '4';
	return "0123"[(int)(a ^ b)];
}

/*!
 @abstract     Get the color error profile at the give position    
 @param b      pointer to an alignment
 @return       the original color if the color was an error, '-' (dash) otherwise

 @discussion   Returns 0 no color information is found.
 */
char bam_aux_getCEi(bam1_t *b, int i)
{
	int cs_i;
	uint8_t *c = bam_aux_get(b, "CS");
	char *cs = NULL;
	char prev_b, cur_b;
	char cur_color, cor_color;

	// return the base if the tag was not found
	if(0 == c) return 0;
	
	cs = bam_aux2Z(c);

	// adjust for strandedness and leading adaptor
	if(bam1_strand(b)) { //reverse strand
		cs_i = strlen(cs) - 1 - i;
		// get current color
		cur_color = cs[cs_i];
		// get previous base.  Note: must rc adaptor
		prev_b = (cs_i == 1) ? "TGCAN"[(int)bam_aux_nt2int(cs[0])] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i+1)];
		// get current base
		cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)]; 
	}
	else {
		cs_i=i+1;
		// get current color
		cur_color = cs[cs_i];
		// get previous base
		prev_b = (0 == i) ? cs[0] : bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i-1)];
		// get current base
		cur_b = bam_nt16_rev_table[bam1_seqi(bam1_seq(b), i)];
	}

	// corrected color
	cor_color = bam_aux_ntnt2cs(prev_b, cur_b);

	if(cur_color == cor_color) { 
		return '-';
	}
	else {
		return cur_color;
	}
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_endian.h000066400000000000000000000020501211610345200232640ustar00rootroot00000000000000#ifndef BAM_ENDIAN_H
#define BAM_ENDIAN_H

#include 

static inline int bam_is_big_endian()
{
	long one= 1;
	return !(*((char *)(&one)));
}
static inline uint16_t bam_swap_endian_2(uint16_t v)
{
	return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
}
static inline void *bam_swap_endian_2p(void *x)
{
	*(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x);
	return x;
}
static inline uint32_t bam_swap_endian_4(uint32_t v)
{
	v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
	return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
}
static inline void *bam_swap_endian_4p(void *x)
{
	*(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x);
	return x;
}
static inline uint64_t bam_swap_endian_8(uint64_t v)
{
	v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
	v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
	return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
}
static inline void *bam_swap_endian_8p(void *x)
{
	*(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x);
	return x;
}

#endif
genometools-1.5.1/src/external/samtools-0.1.18/bam_import.c000066400000000000000000000377501211610345200233520ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include 
#include 
#ifdef _WIN32
#include 
#endif
#include "kstring.h"
#include "bam.h"
#include "sam_header.h"
#include "kseq.h"
#include "khash.h"

KSTREAM_INIT(gzFile, gzread, 16384)
KHASH_MAP_INIT_STR(ref, uint64_t)

void bam_init_header_hash(bam_header_t *header);
void bam_destroy_header_hash(bam_header_t *header);
int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);

unsigned char bam_nt16_table[256] = {
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	 1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
	15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
	15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
};

unsigned short bam_char2flag_table[256] = {
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
	BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
	0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
};

char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";

struct __tamFile_t {
	gzFile fp;
	kstream_t *ks;
	kstring_t *str;
	uint64_t n_lines;
	int is_first;
};

char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
{
	char **list = 0, *s;
	int n = 0, dret, m = 0;
	gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
	kstream_t *ks;
	kstring_t *str;
	str = (kstring_t*)calloc(1, sizeof(kstring_t));
	ks = ks_init(fp);
	while (ks_getuntil(ks, '\n', str, &dret) > 0) {
		if (n == m) {
			m = m? m << 1 : 16;
			list = (char**)realloc(list, m * sizeof(char*));
		}
		if (str->s[str->l-1] == '\r')
			str->s[--str->l] = '\0';
		s = list[n++] = (char*)calloc(str->l + 1, 1);
		strcpy(s, str->s);
	}
	ks_destroy(ks);
	gzclose(fp);
	free(str->s); free(str);
	*_n = n;
	return list;
}

static bam_header_t *hash2header(const kh_ref_t *hash)
{
	bam_header_t *header;
	khiter_t k;
	header = bam_header_init();
	header->n_targets = kh_size(hash);
	header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
	header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
	for (k = kh_begin(hash); k != kh_end(hash); ++k) {
		if (kh_exist(hash, k)) {
			int i = (int)kh_value(hash, k);
			header->target_name[i] = (char*)kh_key(hash, k);
			header->target_len[i] = kh_value(hash, k)>>32;
		}
	}
	bam_init_header_hash(header);
	return header;
}
bam_header_t *sam_header_read2(const char *fn)
{
	bam_header_t *header;
	int c, dret, ret, error = 0;
	gzFile fp;
	kstream_t *ks;
	kstring_t *str;
	kh_ref_t *hash;
	khiter_t k;
	if (fn == 0) return 0;
	fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
	if (fp == 0) return 0;
	hash = kh_init(ref);
	ks = ks_init(fp);
	str = (kstring_t*)calloc(1, sizeof(kstring_t));
	while (ks_getuntil(ks, 0, str, &dret) > 0) {
		char *s = strdup(str->s);
		int len, i;
		i = kh_size(hash);
		ks_getuntil(ks, 0, str, &dret);
		len = atoi(str->s);
		k = kh_put(ref, hash, s, &ret);
		if (ret == 0) {
			fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
			error = 1;
		}
		kh_value(hash, k) = (uint64_t)len<<32 | i;
		if (dret != '\n')
			while ((c = ks_getc(ks)) != '\n' && c != -1);
	}
	ks_destroy(ks);
	gzclose(fp);
	free(str->s); free(str);
	fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
	if (error) return 0;
	header = hash2header(hash);
	kh_destroy(ref, hash);
	return header;
}
static inline uint8_t *alloc_data(bam1_t *b, int size)
{
	if (b->m_data < size) {
		b->m_data = size;
		kroundup32(b->m_data);
		b->data = (uint8_t*)realloc(b->data, b->m_data);
	}
	return b->data;
}
static inline void parse_error(int64_t n_lines, const char * __restrict msg)
{
	fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
	abort();
}
static inline void append_text(bam_header_t *header, kstring_t *str)
{
	size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
	kroundup32(x); kroundup32(y);
	if (x < y) 
    {
        header->n_text = y;
        header->text = (char*)realloc(header->text, y);
        if ( !header->text ) 
        {
            fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
            abort();
        }
    }
    // Sanity check
    if ( header->l_text+str->l+1 >= header->n_text )
    {
        fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,header->n_text,x,y);
        abort();
    }
	strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
	header->l_text += str->l + 1;
	header->text[header->l_text] = 0;
}

int sam_header_parse(bam_header_t *h)
{
	char **tmp;
	int i;
	free(h->target_len); free(h->target_name);
	h->n_targets = 0; h->target_len = 0; h->target_name = 0;
	if (h->l_text < 3) return 0;
	if (h->dict == 0) h->dict = sam_header_parse2(h->text);
	tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
	if (h->n_targets == 0) return 0;
	h->target_name = calloc(h->n_targets, sizeof(void*));
	for (i = 0; i < h->n_targets; ++i)
		h->target_name[i] = strdup(tmp[i]);
	free(tmp);
	tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
	h->target_len = calloc(h->n_targets, 4);
	for (i = 0; i < h->n_targets; ++i)
		h->target_len[i] = atoi(tmp[i]);
	free(tmp);
	return h->n_targets;
}

bam_header_t *sam_header_read(tamFile fp)
{
	int ret, dret;
	bam_header_t *header = bam_header_init();
	kstring_t *str = fp->str;
	while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
		str->s[str->l] = dret; // note that str->s is NOT null terminated!!
		append_text(header, str);
		if (dret != '\n') {
			ret = ks_getuntil(fp->ks, '\n', str, &dret);
			str->s[str->l] = '\n'; // NOT null terminated!!
			append_text(header, str);
		}
		++fp->n_lines;
	}
	sam_header_parse(header);
	bam_init_header_hash(header);
	fp->is_first = 1;
	return header;
}

int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
{
	int ret, doff, doff0, dret, z = 0;
	bam1_core_t *c = &b->core;
	kstring_t *str = fp->str;
	kstream_t *ks = fp->ks;

	if (fp->is_first) {
		fp->is_first = 0;
		ret = str->l;
	} else {
		do { // special consideration for empty lines
			ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
			if (ret >= 0) z += str->l + 1;
		} while (ret == 0);
	}
	if (ret < 0) return -1;
	++fp->n_lines;
	doff = 0;

	{ // name
		c->l_qname = strlen(str->s) + 1;
		memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
		doff += c->l_qname;
	}
	{ // flag
		long flag;
		char *s;
		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
		flag = strtol((char*)str->s, &s, 0);
		if (*s) { // not the end of the string
			flag = 0;
			for (s = str->s; *s; ++s)
				flag |= bam_char2flag_table[(int)*s];
		}
		c->flag = flag;
	}
	{ // tid, pos, qual
		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
		if (c->tid < 0 && strcmp(str->s, "*")) {
			if (header->n_targets == 0) {
				fprintf(stderr, "[sam_read1] missing header? Abort!\n");
				exit(1);
			} else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
		}
		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
		if (ret < 0) return -2;
	}
	{ // cigar
		char *s, *t;
		int i, op;
		long x;
		c->n_cigar = 0;
		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
		z += str->l + 1;
		if (str->s[0] != '*') {
			for (s = str->s; *s; ++s) {
				if ((isalpha(*s)) || (*s=='=')) ++c->n_cigar;
				else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
			}
			b->data = alloc_data(b, doff + c->n_cigar * 4);
			for (i = 0, s = str->s; i != c->n_cigar; ++i) {
				x = strtol(s, &t, 10);
				op = toupper(*t);
				if (op == 'M') op = BAM_CMATCH;
				else if (op == 'I') op = BAM_CINS;
				else if (op == 'D') op = BAM_CDEL;
				else if (op == 'N') op = BAM_CREF_SKIP;
				else if (op == 'S') op = BAM_CSOFT_CLIP;
				else if (op == 'H') op = BAM_CHARD_CLIP;
				else if (op == 'P') op = BAM_CPAD;
				else if (op == '=') op = BAM_CEQUAL;
				else if (op == 'X') op = BAM_CDIFF;
				else parse_error(fp->n_lines, "invalid CIGAR operation");
				s = t + 1;
				bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
			}
			if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
			c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
			doff += c->n_cigar * 4;
		} else {
			if (!(c->flag&BAM_FUNMAP)) {
				fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
				c->flag |= BAM_FUNMAP;
			}
			c->bin = bam_reg2bin(c->pos, c->pos + 1);
		}
	}
	{ // mtid, mpos, isize
		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
		c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
		c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
		c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
		if (ret < 0) return -4;
	}
	{ // seq and qual
		int i;
		uint8_t *p = 0;
		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
		z += str->l + 1;
		if (strcmp(str->s, "*")) {
			c->l_qseq = strlen(str->s);
			if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b))) {
			  fprintf(stderr, "Line %ld, sequence length %i vs %i from CIGAR\n",
				  (long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));
			  parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
			}
			p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
			memset(p, 0, (c->l_qseq+1)/2);
			for (i = 0; i < c->l_qseq; ++i)
				p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
		} else c->l_qseq = 0;
		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
		z += str->l + 1;
		if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
			parse_error(fp->n_lines, "sequence and quality are inconsistent");
		p += (c->l_qseq+1)/2;
		if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
		else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
		doff += c->l_qseq + (c->l_qseq+1)/2;
	}
	doff0 = doff;
	if (dret != '\n' && dret != '\r') { // aux
		while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
			uint8_t *s, type, key[2];
			z += str->l + 1;
			if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
				parse_error(fp->n_lines, "missing colon in auxiliary data");
			key[0] = str->s[0]; key[1] = str->s[1];
			type = str->s[3];
			s = alloc_data(b, doff + 3) + doff;
			s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
			if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
				s = alloc_data(b, doff + 2) + doff;
				*s++ = 'A'; *s = str->s[5];
				doff += 2;
			} else if (type == 'I' || type == 'i') {
				long long x;
				s = alloc_data(b, doff + 5) + doff;
				x = (long long)atoll(str->s + 5);
				if (x < 0) {
					if (x >= -127) {
						*s++ = 'c'; *(int8_t*)s = (int8_t)x;
						s += 1; doff += 2;
					} else if (x >= -32767) {
						*s++ = 's'; *(int16_t*)s = (int16_t)x;
						s += 2; doff += 3;
					} else {
						*s++ = 'i'; *(int32_t*)s = (int32_t)x;
						s += 4; doff += 5;
						if (x < -2147483648ll)
							fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
									(long long)fp->n_lines, x);
					}
				} else {
					if (x <= 255) {
						*s++ = 'C'; *s++ = (uint8_t)x;
						doff += 2;
					} else if (x <= 65535) {
						*s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
						s += 2; doff += 3;
					} else {
						*s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
						s += 4; doff += 5;
						if (x > 4294967295ll)
							fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
									(long long)fp->n_lines, x);
					}
				}
			} else if (type == 'f') {
				s = alloc_data(b, doff + 5) + doff;
				*s++ = 'f';
				*(float*)s = (float)atof(str->s + 5);
				s += 4; doff += 5;
			} else if (type == 'd') {
				s = alloc_data(b, doff + 9) + doff;
				*s++ = 'd';
				*(float*)s = (float)atof(str->s + 9);
				s += 8; doff += 9;
			} else if (type == 'Z' || type == 'H') {
				int size = 1 + (str->l - 5) + 1;
				if (type == 'H') { // check whether the hex string is valid
					int i;
					if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
					for (i = 0; i < str->l - 5; ++i) {
						int c = toupper(str->s[5 + i]);
						if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
							parse_error(fp->n_lines, "invalid hex character");
					}
				}
				s = alloc_data(b, doff + size) + doff;
				*s++ = type;
				memcpy(s, str->s + 5, str->l - 5);
				s[str->l - 5] = 0;
				doff += size;
			} else if (type == 'B') {
				int32_t n = 0, Bsize, k = 0, size;
				char *p;
				if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
				Bsize = bam_aux_type2size(str->s[5]); // the size of each element
				for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
					if (*p == ',') ++n;
				p = str->s + 7; // now p points to the first number in the array
				size = 6 + Bsize * n; // total number of bytes allocated to this tag
				s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
				*s++ = 'B'; *s++ = str->s[5];
				memcpy(s, &n, 4); s += 4; // write the number of elements
				if (str->s[5] == 'c')      while (p < str->s + str->l) ((int8_t*)s)[k++]   = (int8_t)strtol(p, &p, 0),   ++p;
				else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++]  = (uint8_t)strtol(p, &p, 0),  ++p;
				else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++]  = (int16_t)strtol(p, &p, 0),  ++p; // FIXME: avoid unaligned memory
				else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
				else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++]  = (int32_t)strtol(p, &p, 0),  ++p;
				else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
				else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++]    = (float)strtod(p, &p),       ++p;
				else parse_error(fp->n_lines, "unrecognized array type");
				s += Bsize * n; doff += size;
			} else parse_error(fp->n_lines, "unrecognized type");
			if (dret == '\n' || dret == '\r') break;
		}
	}
	b->l_aux = doff - doff0;
	b->data_len = doff;
	return z;
}

tamFile sam_open(const char *fn)
{
	tamFile fp;
	gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
	if (gzfp == 0) return 0;
	fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
	fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
	fp->fp = gzfp;
	fp->ks = ks_init(fp->fp);
	return fp;
}

void sam_close(tamFile fp)
{
	if (fp) {
		ks_destroy(fp->ks);
		gzclose(fp->fp);
		free(fp->str->s); free(fp->str);
		free(fp);
	}
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_index.c000066400000000000000000000515341211610345200231430ustar00rootroot00000000000000#include 
#include 
#include "bam.h"
#include "khash.h"
#include "ksort.h"
#include "bam_endian.h"
#ifdef _USE_KNETFILE
#include "knetfile.h"
#endif

/*!
  @header

  Alignment indexing. Before indexing, BAM must be sorted based on the
  leftmost coordinate of alignments. In indexing, BAM uses two indices:
  a UCSC binning index and a simple linear index. The binning index is
  efficient for alignments spanning long distance, while the auxiliary
  linear index helps to reduce unnecessary seek calls especially for
  short alignments.

  The UCSC binning scheme was suggested by Richard Durbin and Lincoln
  Stein and is explained by Kent et al. (2002). In this scheme, each bin
  represents a contiguous genomic region which can be fully contained in
  another bin; each alignment is associated with a bin which represents
  the smallest region containing the entire alignment. The binning
  scheme is essentially another representation of R-tree. A distinct bin
  uniquely corresponds to a distinct internal node in a R-tree. Bin A is
  a child of Bin B if region A is contained in B.

  In BAM, each bin may span 2^29, 2^26, 2^23, 2^20, 2^17 or 2^14 bp. Bin
  0 spans a 512Mbp region, bins 1-8 span 64Mbp, 9-72 8Mbp, 73-584 1Mbp,
  585-4680 128Kbp and bins 4681-37449 span 16Kbp regions. If we want to
  find the alignments overlapped with a region [rbeg,rend), we need to
  calculate the list of bins that may be overlapped the region and test
  the alignments in the bins to confirm the overlaps. If the specified
  region is short, typically only a few alignments in six bins need to
  be retrieved. The overlapping alignments can be quickly fetched.

 */

#define BAM_MIN_CHUNK_GAP 32768
// 1<<14 is the size of minimum bin.
#define BAM_LIDX_SHIFT    14

#define BAM_MAX_BIN 37450 // =(8^6-1)/7+1

typedef struct {
	uint64_t u, v;
} pair64_t;

#define pair64_lt(a,b) ((a).u < (b).u)
KSORT_INIT(off, pair64_t, pair64_lt)

typedef struct {
	uint32_t m, n;
	pair64_t *list;
} bam_binlist_t;

typedef struct {
	int32_t n, m;
	uint64_t *offset;
} bam_lidx_t;

KHASH_MAP_INIT_INT(i, bam_binlist_t)

struct __bam_index_t {
	int32_t n;
	uint64_t n_no_coor; // unmapped reads without coordinate
	khash_t(i) **index;
	bam_lidx_t *index2;
};

// requirement: len <= LEN_MASK
static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
{
	khint_t k;
	bam_binlist_t *l;
	int ret;
	k = kh_put(i, h, bin, &ret);
	l = &kh_value(h, k);
	if (ret) { // not present
		l->m = 1; l->n = 0;
		l->list = (pair64_t*)calloc(l->m, 16);
	}
	if (l->n == l->m) {
		l->m <<= 1;
		l->list = (pair64_t*)realloc(l->list, l->m * 16);
	}
	l->list[l->n].u = beg; l->list[l->n++].v = end;
}

static inline void insert_offset2(bam_lidx_t *index2, bam1_t *b, uint64_t offset)
{
	int i, beg, end;
	beg = b->core.pos >> BAM_LIDX_SHIFT;
	end = (bam_calend(&b->core, bam1_cigar(b)) - 1) >> BAM_LIDX_SHIFT;
	if (index2->m < end + 1) {
		int old_m = index2->m;
		index2->m = end + 1;
		kroundup32(index2->m);
		index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
		memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
	}
	if (beg == end) {
		if (index2->offset[beg] == 0) index2->offset[beg] = offset;
	} else {
		for (i = beg; i <= end; ++i)
			if (index2->offset[i] == 0) index2->offset[i] = offset;
	}
	index2->n = end + 1;
}

static void merge_chunks(bam_index_t *idx)
{
#if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16)
	khash_t(i) *index;
	int i, l, m;
	khint_t k;
	for (i = 0; i < idx->n; ++i) {
		index = idx->index[i];
		for (k = kh_begin(index); k != kh_end(index); ++k) {
			bam_binlist_t *p;
			if (!kh_exist(index, k) || kh_key(index, k) == BAM_MAX_BIN) continue;
			p = &kh_value(index, k);
			m = 0;
			for (l = 1; l < p->n; ++l) {
#ifdef BAM_TRUE_OFFSET
				if (p->list[m].v + BAM_MIN_CHUNK_GAP > p->list[l].u) p->list[m].v = p->list[l].v;
#else
				if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
#endif
				else p->list[++m] = p->list[l];
			} // ~for(l)
			p->n = m + 1;
		} // ~for(k)
	} // ~for(i)
#endif // defined(BAM_TRUE_OFFSET) || defined(BAM_BGZF)
}

static void fill_missing(bam_index_t *idx)
{
	int i, j;
	for (i = 0; i < idx->n; ++i) {
		bam_lidx_t *idx2 = &idx->index2[i];
		for (j = 1; j < idx2->n; ++j)
			if (idx2->offset[j] == 0)
				idx2->offset[j] = idx2->offset[j-1];
	}
}

bam_index_t *bam_index_core(bamFile fp)
{
	bam1_t *b;
	bam_header_t *h;
	int i, ret;
	bam_index_t *idx;
	uint32_t last_bin, save_bin;
	int32_t last_coor, last_tid, save_tid;
	bam1_core_t *c;
	uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;

	idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
	b = (bam1_t*)calloc(1, sizeof(bam1_t));
	h = bam_header_read(fp);
	c = &b->core;

	idx->n = h->n_targets;
	bam_header_destroy(h);
	idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
	for (i = 0; i < idx->n; ++i) idx->index[i] = kh_init(i);
	idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));

	save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
	save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu;
	n_mapped = n_unmapped = n_no_coor = off_end = 0;
	off_beg = off_end = bam_tell(fp);
	while ((ret = bam_read1(fp, b)) >= 0) {
		if (c->tid < 0) ++n_no_coor;
		if (last_tid < c->tid || (last_tid >= 0 && c->tid < 0)) { // change of chromosomes
			last_tid = c->tid;
			last_bin = 0xffffffffu;
		} else if ((uint32_t)last_tid > (uint32_t)c->tid) {
			fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr\n",
					bam1_qname(b), last_tid+1, c->tid+1);
			return NULL;
		} else if ((int32_t)c->tid >= 0 && last_coor > c->pos) {
			fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n",
					bam1_qname(b), last_coor, c->pos, c->tid+1);
			return NULL;
		}
		if (c->tid >= 0 && !(c->flag & BAM_FUNMAP)) insert_offset2(&idx->index2[b->core.tid], b, last_off);
		if (c->bin != last_bin) { // then possibly write the binning index
			if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
				insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
			if (last_bin == 0xffffffffu && save_tid != 0xffffffffu) { // write the meta element
				off_end = last_off;
				insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, off_end);
				insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
				n_mapped = n_unmapped = 0;
				off_beg = off_end;
			}
			save_off = last_off;
			save_bin = last_bin = c->bin;
			save_tid = c->tid;
			if (save_tid < 0) break;
		}
		if (bam_tell(fp) <= last_off) {
			fprintf(stderr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n",
					(unsigned long long)bam_tell(fp), (unsigned long long)last_off);
			return NULL;
		}
		if (c->flag & BAM_FUNMAP) ++n_unmapped;
		else ++n_mapped;
		last_off = bam_tell(fp);
		last_coor = b->core.pos;
	}
	if (save_tid >= 0) {
		insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
		insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
		insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
	}
	merge_chunks(idx);
	fill_missing(idx);
	if (ret >= 0) {
		while ((ret = bam_read1(fp, b)) >= 0) {
			++n_no_coor;
			if (c->tid >= 0 && n_no_coor) {
				fprintf(stderr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
				return NULL;
			}
		}
	}
	if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
	free(b->data); free(b);
	idx->n_no_coor = n_no_coor;
	return idx;
}

void bam_index_destroy(bam_index_t *idx)
{
	khint_t k;
	int i;
	if (idx == 0) return;
	for (i = 0; i < idx->n; ++i) {
		khash_t(i) *index = idx->index[i];
		bam_lidx_t *index2 = idx->index2 + i;
		for (k = kh_begin(index); k != kh_end(index); ++k) {
			if (kh_exist(index, k))
				free(kh_value(index, k).list);
		}
		kh_destroy(i, index);
		free(index2->offset);
	}
	free(idx->index); free(idx->index2);
	free(idx);
}

void bam_index_save(const bam_index_t *idx, FILE *fp)
{
	int32_t i, size;
	khint_t k;
	fwrite("BAI\1", 1, 4, fp);
	if (bam_is_be) {
		uint32_t x = idx->n;
		fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
	} else fwrite(&idx->n, 4, 1, fp);
	for (i = 0; i < idx->n; ++i) {
		khash_t(i) *index = idx->index[i];
		bam_lidx_t *index2 = idx->index2 + i;
		// write binning index
		size = kh_size(index);
		if (bam_is_be) { // big endian
			uint32_t x = size;
			fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
		} else fwrite(&size, 4, 1, fp);
		for (k = kh_begin(index); k != kh_end(index); ++k) {
			if (kh_exist(index, k)) {
				bam_binlist_t *p = &kh_value(index, k);
				if (bam_is_be) { // big endian
					uint32_t x;
					x = kh_key(index, k); fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
					x = p->n; fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
					for (x = 0; (int)x < p->n; ++x) {
						bam_swap_endian_8p(&p->list[x].u);
						bam_swap_endian_8p(&p->list[x].v);
					}
					fwrite(p->list, 16, p->n, fp);
					for (x = 0; (int)x < p->n; ++x) {
						bam_swap_endian_8p(&p->list[x].u);
						bam_swap_endian_8p(&p->list[x].v);
					}
				} else {
					fwrite(&kh_key(index, k), 4, 1, fp);
					fwrite(&p->n, 4, 1, fp);
					fwrite(p->list, 16, p->n, fp);
				}
			}
		}
		// write linear index (index2)
		if (bam_is_be) {
			int x = index2->n;
			fwrite(bam_swap_endian_4p(&x), 4, 1, fp);
		} else fwrite(&index2->n, 4, 1, fp);
		if (bam_is_be) { // big endian
			int x;
			for (x = 0; (int)x < index2->n; ++x)
				bam_swap_endian_8p(&index2->offset[x]);
			fwrite(index2->offset, 8, index2->n, fp);
			for (x = 0; (int)x < index2->n; ++x)
				bam_swap_endian_8p(&index2->offset[x]);
		} else fwrite(index2->offset, 8, index2->n, fp);
	}
	{ // write the number of reads coor-less records.
		uint64_t x = idx->n_no_coor;
		if (bam_is_be) bam_swap_endian_8p(&x);
		fwrite(&x, 8, 1, fp);
	}
	fflush(fp);
}

static bam_index_t *bam_index_load_core(FILE *fp)
{
	int i;
	char magic[4];
	bam_index_t *idx;
	if (fp == 0) {
		fprintf(stderr, "[bam_index_load_core] fail to load index.\n");
		return 0;
	}
	fread(magic, 1, 4, fp);
	if (strncmp(magic, "BAI\1", 4)) {
		fprintf(stderr, "[bam_index_load] wrong magic number.\n");
		fclose(fp);
		return 0;
	}
	idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));	
	fread(&idx->n, 4, 1, fp);
	if (bam_is_be) bam_swap_endian_4p(&idx->n);
	idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
	idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t));
	for (i = 0; i < idx->n; ++i) {
		khash_t(i) *index;
		bam_lidx_t *index2 = idx->index2 + i;
		uint32_t key, size;
		khint_t k;
		int j, ret;
		bam_binlist_t *p;
		index = idx->index[i] = kh_init(i);
		// load binning index
		fread(&size, 4, 1, fp);
		if (bam_is_be) bam_swap_endian_4p(&size);
		for (j = 0; j < (int)size; ++j) {
			fread(&key, 4, 1, fp);
			if (bam_is_be) bam_swap_endian_4p(&key);
			k = kh_put(i, index, key, &ret);
			p = &kh_value(index, k);
			fread(&p->n, 4, 1, fp);
			if (bam_is_be) bam_swap_endian_4p(&p->n);
			p->m = p->n;
			p->list = (pair64_t*)malloc(p->m * 16);
			fread(p->list, 16, p->n, fp);
			if (bam_is_be) {
				int x;
				for (x = 0; x < p->n; ++x) {
					bam_swap_endian_8p(&p->list[x].u);
					bam_swap_endian_8p(&p->list[x].v);
				}
			}
		}
		// load linear index
		fread(&index2->n, 4, 1, fp);
		if (bam_is_be) bam_swap_endian_4p(&index2->n);
		index2->m = index2->n;
		index2->offset = (uint64_t*)calloc(index2->m, 8);
		fread(index2->offset, index2->n, 8, fp);
		if (bam_is_be)
			for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
	}
	if (fread(&idx->n_no_coor, 8, 1, fp) == 0) idx->n_no_coor = 0;
	if (bam_is_be) bam_swap_endian_8p(&idx->n_no_coor);
	return idx;
}

bam_index_t *bam_index_load_local(const char *_fn)
{
	FILE *fp;
	char *fnidx, *fn;

	if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) {
		const char *p;
		int l = strlen(_fn);
		for (p = _fn + l - 1; p >= _fn; --p)
			if (*p == '/') break;
		fn = strdup(p + 1);
	} else fn = strdup(_fn);
	fnidx = (char*)calloc(strlen(fn) + 5, 1);
	strcpy(fnidx, fn); strcat(fnidx, ".bai");
	fp = fopen(fnidx, "rb");
	if (fp == 0) { // try "{base}.bai"
		char *s = strstr(fn, "bam");
		if (s == fn + strlen(fn) - 3) {
			strcpy(fnidx, fn);
			fnidx[strlen(fn)-1] = 'i';
			fp = fopen(fnidx, "rb");
		}
	}
	free(fnidx); free(fn);
	if (fp) {
		bam_index_t *idx = bam_index_load_core(fp);
		fclose(fp);
		return idx;
	} else return 0;
}

#ifdef _USE_KNETFILE
static void download_from_remote(const char *url)
{
	const int buf_size = 1 * 1024 * 1024;
	char *fn;
	FILE *fp;
	uint8_t *buf;
	knetFile *fp_remote;
	int l;
	if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
	l = strlen(url);
	for (fn = (char*)url + l - 1; fn >= url; --fn)
		if (*fn == '/') break;
	++fn; // fn now points to the file name
	fp_remote = knet_open(url, "r");
	if (fp_remote == 0) {
		fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
		return;
	}
	if ((fp = fopen(fn, "wb")) == 0) {
		fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
		knet_close(fp_remote);
		return;
	}
	buf = (uint8_t*)calloc(buf_size, 1);
	while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
		fwrite(buf, 1, l, fp);
	free(buf);
	fclose(fp);
	knet_close(fp_remote);
}
#else
static void download_from_remote(const char *url)
{
	return;
}
#endif

bam_index_t *bam_index_load(const char *fn)
{
	bam_index_t *idx;
	idx = bam_index_load_local(fn);
	if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) {
		char *fnidx = calloc(strlen(fn) + 5, 1);
		strcat(strcpy(fnidx, fn), ".bai");
		fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
		download_from_remote(fnidx);
		idx = bam_index_load_local(fn);
	}
	if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
	return idx;
}

int bam_index_build2(const char *fn, const char *_fnidx)
{
	char *fnidx;
	FILE *fpidx;
	bamFile fp;
	bam_index_t *idx;
	if ((fp = bam_open(fn, "r")) == 0) {
		fprintf(stderr, "[bam_index_build2] fail to open the BAM file.\n");
		return -1;
	}
	idx = bam_index_core(fp);
	bam_close(fp);
	if(idx == 0) {
		fprintf(stderr, "[bam_index_build2] fail to index the BAM file.\n");
		return -1;
	}
	if (_fnidx == 0) {
		fnidx = (char*)calloc(strlen(fn) + 5, 1);
		strcpy(fnidx, fn); strcat(fnidx, ".bai");
	} else fnidx = strdup(_fnidx);
	fpidx = fopen(fnidx, "wb");
	if (fpidx == 0) {
		fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
		free(fnidx);
		return -1;
	}
	bam_index_save(idx, fpidx);
	bam_index_destroy(idx);
	fclose(fpidx);
	free(fnidx);
	return 0;
}

int bam_index_build(const char *fn)
{
	return bam_index_build2(fn, 0);
}

int bam_index(int argc, char *argv[])
{
	if (argc < 2) {
		fprintf(stderr, "Usage: samtools index  [out.index]\n");
		return 1;
	}
	if (argc >= 3) bam_index_build2(argv[1], argv[2]);
	else bam_index_build(argv[1]);
	return 0;
}

int bam_idxstats(int argc, char *argv[])
{
	bam_index_t *idx;
	bam_header_t *header;
	bamFile fp;
	int i;
	if (argc < 2) {
		fprintf(stderr, "Usage: samtools idxstats \n");
		return 1;
	}
	fp = bam_open(argv[1], "r");
	if (fp == 0) { fprintf(stderr, "[%s] fail to open BAM.\n", __func__); return 1; }
	header = bam_header_read(fp);
	bam_close(fp);
	idx = bam_index_load(argv[1]);
	if (idx == 0) { fprintf(stderr, "[%s] fail to load the index.\n", __func__); return 1; }
	for (i = 0; i < idx->n; ++i) {
		khint_t k;
		khash_t(i) *h = idx->index[i];
		printf("%s\t%d", header->target_name[i], header->target_len[i]);
		k = kh_get(i, h, BAM_MAX_BIN);
		if (k != kh_end(h))
			printf("\t%llu\t%llu", (long long)kh_val(h, k).list[1].u, (long long)kh_val(h, k).list[1].v);
		else printf("\t0\t0");
		putchar('\n');
	}
	printf("*\t0\t0\t%llu\n", (long long)idx->n_no_coor);
	bam_header_destroy(header);
	bam_index_destroy(idx);
	return 0;
}

static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[BAM_MAX_BIN])
{
	int i = 0, k;
	if (beg >= end) return 0;
	if (end >= 1u<<29) end = 1u<<29;
	--end;
	list[i++] = 0;
	for (k =    1 + (beg>>26); k <=    1 + (end>>26); ++k) list[i++] = k;
	for (k =    9 + (beg>>23); k <=    9 + (end>>23); ++k) list[i++] = k;
	for (k =   73 + (beg>>20); k <=   73 + (end>>20); ++k) list[i++] = k;
	for (k =  585 + (beg>>17); k <=  585 + (end>>17); ++k) list[i++] = k;
	for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
	return i;
}

static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
{
	uint32_t rbeg = b->core.pos;
	uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
	return (rend > beg && rbeg < end);
}

struct __bam_iter_t {
	int from_first; // read from the first record; no random access
	int tid, beg, end, n_off, i, finished;
	uint64_t curr_off;
	pair64_t *off;
};

// bam_fetch helper function retrieves 
bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
{
	uint16_t *bins;
	int i, n_bins, n_off;
	pair64_t *off;
	khint_t k;
	khash_t(i) *index;
	uint64_t min_off;
	bam_iter_t iter = 0;

	if (beg < 0) beg = 0;
	if (end < beg) return 0;
	// initialize iter
	iter = calloc(1, sizeof(struct __bam_iter_t));
	iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
	//
	bins = (uint16_t*)calloc(BAM_MAX_BIN, 2);
	n_bins = reg2bins(beg, end, bins);
	index = idx->index[tid];
	if (idx->index2[tid].n > 0) {
		min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
			: idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT];
		if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
			int n = beg>>BAM_LIDX_SHIFT;
			if (n > idx->index2[tid].n) n = idx->index2[tid].n;
			for (i = n - 1; i >= 0; --i)
				if (idx->index2[tid].offset[i] != 0) break;
			if (i >= 0) min_off = idx->index2[tid].offset[i];
		}
	} else min_off = 0; // tabix 0.1.2 may produce such index files
	for (i = n_off = 0; i < n_bins; ++i) {
		if ((k = kh_get(i, index, bins[i])) != kh_end(index))
			n_off += kh_value(index, k).n;
	}
	if (n_off == 0) {
		free(bins); return iter;
	}
	off = (pair64_t*)calloc(n_off, 16);
	for (i = n_off = 0; i < n_bins; ++i) {
		if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
			int j;
			bam_binlist_t *p = &kh_value(index, k);
			for (j = 0; j < p->n; ++j)
				if (p->list[j].v > min_off) off[n_off++] = p->list[j];
		}
	}
	free(bins);
	if (n_off == 0) {
		free(off); return iter;
	}
	{
		bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
		int l;
		ks_introsort(off, n_off, off);
		// resolve completely contained adjacent blocks
		for (i = 1, l = 0; i < n_off; ++i)
			if (off[l].v < off[i].v)
				off[++l] = off[i];
		n_off = l + 1;
		// resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
		for (i = 1; i < n_off; ++i)
			if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
		{ // merge adjacent blocks
#if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16)
			for (i = 1, l = 0; i < n_off; ++i) {
#ifdef BAM_TRUE_OFFSET
				if (off[l].v + BAM_MIN_CHUNK_GAP > off[i].u) off[l].v = off[i].v;
#else
				if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
#endif
				else off[++l] = off[i];
			}
			n_off = l + 1;
#endif
		}
		bam_destroy1(b);
	}
	iter->n_off = n_off; iter->off = off;
	return iter;
}

pair64_t *get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int *cnt_off)
{ // for pysam compatibility
	bam_iter_t iter;
	pair64_t *off;
	iter = bam_iter_query(idx, tid, beg, end);
	off = iter->off; *cnt_off = iter->n_off;
	free(iter);
	return off;
}

void bam_iter_destroy(bam_iter_t iter)
{
	if (iter) { free(iter->off); free(iter); }
}

int bam_iter_read(bamFile fp, bam_iter_t iter, bam1_t *b)
{
	int ret;
	if (iter && iter->finished) return -1;
	if (iter == 0 || iter->from_first) {
		ret = bam_read1(fp, b);
		if (ret < 0 && iter) iter->finished = 1;
		return ret;
	}
	if (iter->off == 0) return -1;
	for (;;) {
		if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
			if (iter->i == iter->n_off - 1) { ret = -1; break; } // no more chunks
			if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
			if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
				bam_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
				iter->curr_off = bam_tell(fp);
			}
			++iter->i;
		}
		if ((ret = bam_read1(fp, b)) >= 0) {
			iter->curr_off = bam_tell(fp);
			if (b->core.tid != iter->tid || b->core.pos >= iter->end) { // no need to proceed
				ret = bam_validate1(NULL, b)? -1 : -5; // determine whether end of region or error
				break;
			}
			else if (is_overlap(iter->beg, iter->end, b)) return ret;
		} else break; // end of file or error
	}
	iter->finished = 1;
	return ret;
}

int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func)
{
	int ret;
	bam_iter_t iter;
	bam1_t *b;
	b = bam_init1();
	iter = bam_iter_query(idx, tid, beg, end);
	while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
	bam_iter_destroy(iter);
	bam_destroy1(b);
	return (ret == -1)? 0 : ret;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_lpileup.c000066400000000000000000000115601211610345200235010ustar00rootroot00000000000000#include 
#include 
#include 
#include "bam.h"
#include "ksort.h"

#define TV_GAP 2

typedef struct __freenode_t {
	uint32_t level:28, cnt:4;
	struct __freenode_t *next;
} freenode_t, *freenode_p;

#define freenode_lt(a,b) ((a)->cnt < (b)->cnt || ((a)->cnt == (b)->cnt && (a)->level < (b)->level))
KSORT_INIT(node, freenode_p, freenode_lt)

/* Memory pool, similar to the one in bam_pileup.c */
typedef struct {
	int cnt, n, max;
	freenode_t **buf;
} mempool_t;

static mempool_t *mp_init()
{
	return (mempool_t*)calloc(1, sizeof(mempool_t));
}
static void mp_destroy(mempool_t *mp)
{
	int k;
	for (k = 0; k < mp->n; ++k) free(mp->buf[k]);
	free(mp->buf); free(mp);
}
static inline freenode_t *mp_alloc(mempool_t *mp)
{
	++mp->cnt;
	if (mp->n == 0) return (freenode_t*)calloc(1, sizeof(freenode_t));
	else return mp->buf[--mp->n];
}
static inline void mp_free(mempool_t *mp, freenode_t *p)
{
	--mp->cnt; p->next = 0; p->cnt = TV_GAP;
	if (mp->n == mp->max) {
		mp->max = mp->max? mp->max<<1 : 256;
		mp->buf = (freenode_t**)realloc(mp->buf, sizeof(freenode_t*) * mp->max);
	}
	mp->buf[mp->n++] = p;
}

/* core part */
struct __bam_lplbuf_t {
	int max, n_cur, n_pre;
	int max_level, *cur_level, *pre_level;
	mempool_t *mp;
	freenode_t **aux, *head, *tail;
	int n_nodes, m_aux;
	bam_pileup_f func;
	void *user_data;
	bam_plbuf_t *plbuf;
};

void bam_lplbuf_reset(bam_lplbuf_t *buf)
{
	freenode_t *p, *q;
	bam_plbuf_reset(buf->plbuf);
	for (p = buf->head; p->next;) {
		q = p->next;
		mp_free(buf->mp, p);
		p = q;
	}
	buf->head = buf->tail;
	buf->max_level = 0;
	buf->n_cur = buf->n_pre = 0;
	buf->n_nodes = 0;
}

static int tview_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
	bam_lplbuf_t *tv = (bam_lplbuf_t*)data;
	freenode_t *p;
	int i, l, max_level;
	// allocate memory if necessary
	if (tv->max < n) { // enlarge
		tv->max = n;
		kroundup32(tv->max);
		tv->cur_level = (int*)realloc(tv->cur_level, sizeof(int) * tv->max);
		tv->pre_level = (int*)realloc(tv->pre_level, sizeof(int) * tv->max);
	}
	tv->n_cur = n;
	// update cnt
	for (p = tv->head; p->next; p = p->next)
		if (p->cnt > 0) --p->cnt;
	// calculate cur_level[]
	max_level = 0;
	for (i = l = 0; i < n; ++i) {
		const bam_pileup1_t *p = pl + i;
		if (p->is_head) {
			if (tv->head->next && tv->head->cnt == 0) { // then take a free slot
				freenode_t *p = tv->head->next;
				tv->cur_level[i] = tv->head->level;
				mp_free(tv->mp, tv->head);
				tv->head = p;
				--tv->n_nodes;
			} else tv->cur_level[i] = ++tv->max_level;
		} else {
			tv->cur_level[i] = tv->pre_level[l++];
			if (p->is_tail) { // then return a free slot
				tv->tail->level = tv->cur_level[i];
				tv->tail->next = mp_alloc(tv->mp);
				tv->tail = tv->tail->next;
				++tv->n_nodes;
			}
		}
		if (tv->cur_level[i] > max_level) max_level = tv->cur_level[i];
		((bam_pileup1_t*)p)->level = tv->cur_level[i];
	}
	assert(l == tv->n_pre);
	tv->func(tid, pos, n, pl, tv->user_data);
	// sort the linked list
	if (tv->n_nodes) {
		freenode_t *q;
		if (tv->n_nodes + 1 > tv->m_aux) { // enlarge
			tv->m_aux = tv->n_nodes + 1;
			kroundup32(tv->m_aux);
			tv->aux = (freenode_t**)realloc(tv->aux, sizeof(void*) * tv->m_aux);
		}
		for (p = tv->head, i = l = 0; p->next;) {
			if (p->level > max_level) { // then discard this entry
				q = p->next;
				mp_free(tv->mp, p);
				p = q;
			} else {
				tv->aux[i++] = p;
				p = p->next;
			}
		}
		tv->aux[i] = tv->tail; // add a proper tail for the loop below
		tv->n_nodes = i;
		if (tv->n_nodes) {
			ks_introsort(node, tv->n_nodes, tv->aux);
			for (i = 0; i < tv->n_nodes; ++i) tv->aux[i]->next = tv->aux[i+1];
			tv->head = tv->aux[0];
		} else tv->head = tv->tail;
	}
	// clean up
	tv->max_level = max_level;
	memcpy(tv->pre_level, tv->cur_level, tv->n_cur * 4);
	// squeeze out terminated levels
	for (i = l = 0; i < n; ++i) {
		const bam_pileup1_t *p = pl + i;
		if (!p->is_tail)
			tv->pre_level[l++] = tv->pre_level[i];
	}
	tv->n_pre = l;
/*
	fprintf(stderr, "%d\t", pos+1);
	for (i = 0; i < n; ++i) {
		const bam_pileup1_t *p = pl + i;
		if (p->is_head) fprintf(stderr, "^");
		if (p->is_tail) fprintf(stderr, "$");
		fprintf(stderr, "%d,", p->level);
	}
	fprintf(stderr, "\n");
*/
	return 0;
}

bam_lplbuf_t *bam_lplbuf_init(bam_pileup_f func, void *data)
{
	bam_lplbuf_t *tv;
	tv = (bam_lplbuf_t*)calloc(1, sizeof(bam_lplbuf_t));
	tv->mp = mp_init();
	tv->head = tv->tail = mp_alloc(tv->mp);
	tv->func = func;
	tv->user_data = data;
	tv->plbuf = bam_plbuf_init(tview_func, tv);
	return (bam_lplbuf_t*)tv;
}

void bam_lplbuf_destroy(bam_lplbuf_t *tv)
{
	freenode_t *p, *q;
	free(tv->cur_level); free(tv->pre_level);
	bam_plbuf_destroy(tv->plbuf);
	free(tv->aux);
	for (p = tv->head; p->next;) {
		q = p->next;
		mp_free(tv->mp, p); p = q;
	}
	mp_free(tv->mp, p);
	assert(tv->mp->cnt == 0);
	mp_destroy(tv->mp);
	free(tv);
}

int bam_lplbuf_push(const bam1_t *b, bam_lplbuf_t *tv)
{
	return bam_plbuf_push(b, tv->plbuf);
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_mate.c000066400000000000000000000047541211610345200227640ustar00rootroot00000000000000#include 
#include 
#include "bam.h"

// currently, this function ONLY works if each read has one hit
void bam_mating_core(bamFile in, bamFile out)
{
	bam_header_t *header;
	bam1_t *b[2];
	int curr, has_prev;

	header = bam_header_read(in);
	bam_header_write(out, header);

	b[0] = bam_init1();
	b[1] = bam_init1();
	curr = 0; has_prev = 0;
	while (bam_read1(in, b[curr]) >= 0) {
		bam1_t *cur = b[curr], *pre = b[1-curr];
		if (has_prev) {
			if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
				cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
				pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
				if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
					&& !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)))
				{
					uint32_t cur5, pre5;
					cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos;
					pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
					cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
				} else cur->core.isize = pre->core.isize = 0;
				if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
				else cur->core.flag &= ~BAM_FMREVERSE;
				if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
				else pre->core.flag &= ~BAM_FMREVERSE;
				if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
				if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
				bam_write1(out, pre);
				bam_write1(out, cur);
				has_prev = 0;
			} else { // unpaired or singleton
				pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
				if (pre->core.flag & BAM_FPAIRED) {
					pre->core.flag |= BAM_FMUNMAP;
					pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
				}
				bam_write1(out, pre);
			}
		} else has_prev = 1;
		curr = 1 - curr;
	}
	if (has_prev) bam_write1(out, b[1-curr]);
	bam_header_destroy(header);
	bam_destroy1(b[0]);
	bam_destroy1(b[1]);
}

int bam_mating(int argc, char *argv[])
{
	bamFile in, out;
	if (argc < 3) {
		fprintf(stderr, "samtools fixmate  \n");
		return 1;
	}
	in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
    out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
	bam_mating_core(in, out);
	bam_close(in); bam_close(out);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_md.c000066400000000000000000000310701211610345200224250ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include "faidx.h"
#include "sam.h"
#include "kstring.h"
#include "kaln.h"
#include "kprobaln.h"

#define USE_EQUAL 1
#define DROP_TAG  2
#define BIN_QUAL  4
#define UPDATE_NM 8
#define UPDATE_MD 16
#define HASH_QNM  32

char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };

int bam_aux_drop_other(bam1_t *b, uint8_t *s);

void bam_fillmd1_core(bam1_t *b, char *ref, int flag, int max_nm)
{
	uint8_t *seq = bam1_seq(b);
	uint32_t *cigar = bam1_cigar(b);
	bam1_core_t *c = &b->core;
	int i, x, y, u = 0;
	kstring_t *str;
	int32_t old_nm_i = -1, nm = 0;

	str = (kstring_t*)calloc(1, sizeof(kstring_t));
	for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
		int j, l = cigar[i]>>4, op = cigar[i]&0xf;
		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
			for (j = 0; j < l; ++j) {
				int z = y + j;
				int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
				if (ref[x+j] == 0) break; // out of boundary
				if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
					if (flag&USE_EQUAL) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
					++u;
				} else {
					kputw(u, str); kputc(ref[x+j], str);
					u = 0; ++nm;
				}
			}
			if (j < l) break;
			x += l; y += l;
		} else if (op == BAM_CDEL) {
			kputw(u, str); kputc('^', str);
			for (j = 0; j < l; ++j) {
				if (ref[x+j] == 0) break;
				kputc(ref[x+j], str);
			}
			u = 0;
			if (j < l) break;
			x += l; nm += l;
		} else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
			y += l;
			if (op == BAM_CINS) nm += l;
		} else if (op == BAM_CREF_SKIP) {
			x += l;
		}
	}
	kputw(u, str);
	// apply max_nm
	if (max_nm > 0 && nm >= max_nm) {
		for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
			int j, l = cigar[i]>>4, op = cigar[i]&0xf;
			if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
				for (j = 0; j < l; ++j) {
					int z = y + j;
					int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
					if (ref[x+j] == 0) break; // out of boundary
					if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
						seq[z/2] |= (z&1)? 0x0f : 0xf0;
						bam1_qual(b)[z] = 0;
					}
				}
				if (j < l) break;
				x += l; y += l;
			} else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
			else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
		}
	}
	// update NM
	if (flag & UPDATE_NM) {
		uint8_t *old_nm = bam_aux_get(b, "NM");
		if (c->flag & BAM_FUNMAP) return;
		if (old_nm) old_nm_i = bam_aux2i(old_nm);
		if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
		else if (nm != old_nm_i) {
			fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
			bam_aux_del(b, old_nm);
			bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
		}
	}
	// update MD
	if (flag & UPDATE_MD) {
		uint8_t *old_md = bam_aux_get(b, "MD");
		if (c->flag & BAM_FUNMAP) return;
		if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
		else {
			int is_diff = 0;
			if (strlen((char*)old_md+1) == str->l) {
				for (i = 0; i < str->l; ++i)
					if (toupper(old_md[i+1]) != toupper(str->s[i]))
						break;
				if (i < str->l) is_diff = 1;
			} else is_diff = 1;
			if (is_diff) {
				fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s);
				bam_aux_del(b, old_md);
				bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
			}
		}
	}
	// drop all tags but RG
	if (flag&DROP_TAG) {
		uint8_t *q = bam_aux_get(b, "RG");
		bam_aux_drop_other(b, q);
	}
	// reduce the resolution of base quality
	if (flag&BIN_QUAL) {
		uint8_t *qual = bam1_qual(b);
		for (i = 0; i < b->core.l_qseq; ++i)
			if (qual[i] >= 3) qual[i] = qual[i]/10*10 + 7;
	}
	free(str->s); free(str);
}

void bam_fillmd1(bam1_t *b, char *ref, int flag)
{
	bam_fillmd1_core(b, ref, flag, 0);
}

int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
{
	uint8_t *seq = bam1_seq(b), *qual = bam1_qual(b);
	uint32_t *cigar = bam1_cigar(b);
	bam1_core_t *c = &b->core;
	int i, x, y, mm, q, len, clip_l, clip_q;
	double t;
	if (thres < 0) thres = 40; // set the default
	mm = q = len = clip_l = clip_q = 0;
	for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
		int j, l = cigar[i]>>4, op = cigar[i]&0xf;
		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
			for (j = 0; j < l; ++j) {
				int z = y + j;
				int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
				if (ref[x+j] == 0) break; // out of boundary
				if (c2 != 15 && c1 != 15 && qual[z] >= 13) { // not ambiguous
					++len;
					if (c1 && c1 != c2 && qual[z] >= 13) { // mismatch
						++mm;
						q += qual[z] > 33? 33 : qual[z];
					}
				}
			}
			if (j < l) break;
			x += l; y += l; len += l;
		} else if (op == BAM_CDEL) {
			for (j = 0; j < l; ++j)
				if (ref[x+j] == 0) break;
			if (j < l) break;
			x += l;
		} else if (op == BAM_CSOFT_CLIP) {
			for (j = 0; j < l; ++j) clip_q += qual[y+j];
			clip_l += l;
			y += l;
		} else if (op == BAM_CHARD_CLIP) {
			clip_q += 13 * l;
			clip_l += l;
		} else if (op == BAM_CINS) y += l;
		else if (op == BAM_CREF_SKIP) x += l;
	}
	for (i = 0, t = 1; i < mm; ++i)
		t *= (double)len / (i+1);
	t = q - 4.343 * log(t) + clip_q / 5.;
	if (t > thres) return -1;
	if (t < 0) t = 0;
	t = sqrt((thres - t) / thres) * thres;
//	fprintf(stderr, "%s %lf %d\n", bam1_qname(b), t, q);
	return (int)(t + .499);
}

int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
{
	int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1;
	uint32_t *cigar = bam1_cigar(b);
	bam1_core_t *c = &b->core;
	kpa_par_t conf = kpa_par_def;
	uint8_t *bq = 0, *zq = 0, *qual = bam1_qual(b);
	if ((c->flag & BAM_FUNMAP) || b->core.l_qseq == 0) return -1; // do nothing
	// test if BQ or ZQ is present
	if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
	if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
	if (bq && zq) { // remove the ZQ tag
		bam_aux_del(b, zq-1);
		zq = 0;
	}
	if (bq || zq) {
		if ((apply_baq && zq) || (!apply_baq && bq)) return -3; // in both cases, do nothing
		if (bq && apply_baq) { // then convert BQ to ZQ
			for (i = 0; i < c->l_qseq; ++i)
				qual[i] = qual[i] + 64 < bq[i]? 0 : qual[i] - ((int)bq[i] - 64);
			*(bq - 3) = 'Z';
		} else if (zq && !apply_baq) { // then convert ZQ to BQ
			for (i = 0; i < c->l_qseq; ++i)
				qual[i] += (int)zq[i] - 64;
			*(zq - 3) = 'B';
		}
		return 0;
	}
	// find the start and end of the alignment	
	x = c->pos, y = 0, yb = ye = xb = xe = -1;
	for (k = 0; k < c->n_cigar; ++k) {
		int op, l;
		op = cigar[k]&0xf; l = cigar[k]>>4;
		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
			if (yb < 0) yb = y;
			if (xb < 0) xb = x;
			ye = y + l; xe = x + l;
			x += l; y += l;
		} else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
		else if (op == BAM_CDEL) x += l;
		else if (op == BAM_CREF_SKIP) return -1; // do nothing if there is a reference skip
	}
	// set bandwidth and the start and the end
	bw = 7;
	if (abs((xe - xb) - (ye - yb)) > bw)
		bw = abs((xe - xb) - (ye - yb)) + 3;
	conf.bw = bw;
	xb -= yb + bw/2; if (xb < 0) xb = 0;
	xe += c->l_qseq - ye + bw/2;
	if (xe - xb - c->l_qseq > bw)
		xb += (xe - xb - c->l_qseq - bw) / 2, xe -= (xe - xb - c->l_qseq - bw) / 2;
	{ // glocal
		uint8_t *s, *r, *q, *seq = bam1_seq(b), *bq;
		int *state;
		bq = calloc(c->l_qseq + 1, 1);
		memcpy(bq, qual, c->l_qseq);
		s = calloc(c->l_qseq, 1);
		for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)];
		r = calloc(xe - xb, 1);
		for (i = xb; i < xe; ++i) {
			if (ref[i] == 0) { xe = i; break; }
			r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]];
		}
		state = calloc(c->l_qseq, sizeof(int));
		q = calloc(c->l_qseq, 1);
		kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
		if (!extend_baq) { // in this block, bq[] is capped by base quality qual[]
			for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
				int op = cigar[k]&0xf, l = cigar[k]>>4;
				if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
					for (i = y; i < y + l; ++i) {
						if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
						else bq[i] = bq[i] < q[i]? bq[i] : q[i];
					}
					x += l; y += l;
				} else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
				else if (op == BAM_CDEL) x += l;
			}
			for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ
		} else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!)
			uint8_t *left, *rght;
			left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1);
			for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
				int op = cigar[k]&0xf, l = cigar[k]>>4;
				if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
					for (i = y; i < y + l; ++i)
						bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i];
					for (left[y] = bq[y], i = y + 1; i < y + l; ++i)
						left[i] = bq[i] > left[i-1]? bq[i] : left[i-1];
					for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i)
						rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1];
					for (i = y; i < y + l; ++i)
						bq[i] = left[i] < rght[i]? left[i] : rght[i];
					x += l; y += l;
				} else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
				else if (op == BAM_CDEL) x += l;
			}
			for (i = 0; i < c->l_qseq; ++i) bq[i] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ
			free(left); free(rght);
		}
		if (apply_baq) {
			for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual
			bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq);
		} else bam_aux_append(b, "BQ", 'Z', c->l_qseq + 1, bq);
		free(bq); free(s); free(r); free(q); free(state);
	}
	return 0;
}

int bam_prob_realn(bam1_t *b, const char *ref)
{
	return bam_prob_realn_core(b, ref, 1);
}

int bam_fillmd(int argc, char *argv[])
{
	int c, flt_flag, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag;
	samfile_t *fp, *fpout = 0;
	faidx_t *fai;
	char *ref = 0, mode_w[8], mode_r[8];
	bam1_t *b;

	flt_flag = UPDATE_NM | UPDATE_MD;
	is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0;
	mode_w[0] = mode_r[0] = 0;
	strcpy(mode_r, "r"); strcpy(mode_w, "w");
	while ((c = getopt(argc, argv, "EqreuNhbSC:n:Ad")) >= 0) {
		switch (c) {
		case 'r': is_realn = 1; break;
		case 'e': flt_flag |= USE_EQUAL; break;
		case 'd': flt_flag |= DROP_TAG; break;
		case 'q': flt_flag |= BIN_QUAL; break;
		case 'h': flt_flag |= HASH_QNM; break;
		case 'N': flt_flag &= ~(UPDATE_MD|UPDATE_NM); break;
		case 'b': is_bam_out = 1; break;
		case 'u': is_uncompressed = is_bam_out = 1; break;
		case 'S': is_sam_in = 1; break;
		case 'n': max_nm = atoi(optarg); break;
		case 'C': capQ = atoi(optarg); break;
		case 'A': baq_flag |= 1; break;
		case 'E': baq_flag |= 2; break;
		default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
		}
	}
	if (!is_sam_in) strcat(mode_r, "b");
	if (is_bam_out) strcat(mode_w, "b");
	else strcat(mode_w, "h");
	if (is_uncompressed) strcat(mode_w, "u");
	if (optind + 1 >= argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   samtools fillmd [-eubrS]  \n\n");
		fprintf(stderr, "Options: -e       change identical bases to '='\n");
		fprintf(stderr, "         -u       uncompressed BAM output (for piping)\n");
		fprintf(stderr, "         -b       compressed BAM output\n");
		fprintf(stderr, "         -S       the input is SAM with header\n");
		fprintf(stderr, "         -A       modify the quality string\n");
		fprintf(stderr, "         -r       compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n");
		fprintf(stderr, "         -E       extended BAQ for better sensitivity but lower specificity\n\n");
		return 1;
	}
	fp = samopen(argv[optind], mode_r, 0);
	if (fp == 0) return 1;
	if (is_sam_in && (fp->header == 0 || fp->header->n_targets == 0)) {
		fprintf(stderr, "[bam_fillmd] input SAM does not have header. Abort!\n");
		return 1;
	}
	fpout = samopen("-", mode_w, fp->header);
	fai = fai_load(argv[optind+1]);

	b = bam_init1();
	while ((ret = samread(fp, b)) >= 0) {
		if (b->core.tid >= 0) {
			if (tid != b->core.tid) {
				free(ref);
				ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
				tid = b->core.tid;
				if (ref == 0)
					fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
							fp->header->target_name[tid]);
			}
			if (is_realn) bam_prob_realn_core(b, ref, baq_flag);
			if (capQ > 10) {
				int q = bam_cap_mapQ(b, ref, capQ);
				if (b->core.qual > q) b->core.qual = q;
			}
			if (ref) bam_fillmd1_core(b, ref, flt_flag, max_nm);
		}
		samwrite(fpout, b);
	}
	bam_destroy1(b);

	free(ref);
	fai_destroy(fai);
	samclose(fp); samclose(fpout);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_pileup.c000066400000000000000000000312321211610345200233230ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include "sam.h"

typedef struct {
	int k, x, y, end;
} cstate_t;

static cstate_t g_cstate_null = { -1, 0, 0, 0 };

typedef struct __linkbuf_t {
	bam1_t b;
	uint32_t beg, end;
	cstate_t s;
	struct __linkbuf_t *next;
} lbnode_t;

/* --- BEGIN: Memory pool */

typedef struct {
	int cnt, n, max;
	lbnode_t **buf;
} mempool_t;

static mempool_t *mp_init()
{
	mempool_t *mp;
	mp = (mempool_t*)calloc(1, sizeof(mempool_t));
	return mp;
}
static void mp_destroy(mempool_t *mp)
{
	int k;
	for (k = 0; k < mp->n; ++k) {
		free(mp->buf[k]->b.data);
		free(mp->buf[k]);
	}
	free(mp->buf);
	free(mp);
}
static inline lbnode_t *mp_alloc(mempool_t *mp)
{
	++mp->cnt;
	if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t));
	else return mp->buf[--mp->n];
}
static inline void mp_free(mempool_t *mp, lbnode_t *p)
{
	--mp->cnt; p->next = 0; // clear lbnode_t::next here
	if (mp->n == mp->max) {
		mp->max = mp->max? mp->max<<1 : 256;
		mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max);
	}
	mp->buf[mp->n++] = p;
}

/* --- END: Memory pool */

/* --- BEGIN: Auxiliary functions */

/* s->k: the index of the CIGAR operator that has just been processed.
   s->x: the reference coordinate of the start of s->k
   s->y: the query coordiante of the start of s->k
 */
static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
{
#define _cop(c) ((c)&BAM_CIGAR_MASK)
#define _cln(c) ((c)>>BAM_CIGAR_SHIFT)

	bam1_t *b = p->b;
	bam1_core_t *c = &b->core;
	uint32_t *cigar = bam1_cigar(b);
	int k, is_head = 0;
	// determine the current CIGAR operation
//	fprintf(stderr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam1_qname(b), pos, s->end, s->k, s->x, s->y);
	if (s->k == -1) { // never processed
		is_head = 1;
		if (c->n_cigar == 1) { // just one operation, save a loop
		  if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0;
		} else { // find the first match or deletion
			for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
				int op = _cop(cigar[k]);
				int l = _cln(cigar[k]);
				if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CEQUAL || op == BAM_CDIFF) break;
				else if (op == BAM_CREF_SKIP) s->x += l;
				else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
			}
			assert(k < c->n_cigar);
			s->k = k;
		}
	} else { // the read has been processed before
		int op, l = _cln(cigar[s->k]);
		if (pos - s->x >= l) { // jump to the next operation
			assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
			op = _cop(cigar[s->k+1]);
			if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop
			  if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
				s->x += l;
				++s->k;
			} else { // find the next M/D/N/=/X
			  if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
				s->x += l;
				for (k = s->k + 1; k < c->n_cigar; ++k) {
					op = _cop(cigar[k]), l = _cln(cigar[k]);
					if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break;
					else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
				}
				s->k = k;
			}
			assert(s->k < c->n_cigar); // otherwise a bug
		} // else, do nothing
	}
	{ // collect pileup information
		int op, l;
		op = _cop(cigar[s->k]); l = _cln(cigar[s->k]);
		p->is_del = p->indel = p->is_refskip = 0;
		if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
			int op2 = _cop(cigar[s->k+1]);
			int l2 = _cln(cigar[s->k+1]);
			if (op2 == BAM_CDEL) p->indel = -(int)l2;
			else if (op2 == BAM_CINS) p->indel = l2;
			else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
				int l3 = 0;
				for (k = s->k + 2; k < c->n_cigar; ++k) {
					op2 = _cop(cigar[k]); l2 = _cln(cigar[k]);
					if (op2 == BAM_CINS) l3 += l2;
					else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break;
				}
				if (l3 > 0) p->indel = l3;
			}
		}
		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
			p->qpos = s->y + (pos - s->x);
		} else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
			p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!
			p->is_refskip = (op == BAM_CREF_SKIP);
		} // cannot be other operations; otherwise a bug
		p->is_head = (pos == c->pos); p->is_tail = (pos == s->end);
	}
	return 1;
}

/* --- END: Auxiliary functions */

/*******************
 * pileup iterator *
 *******************/

struct __bam_plp_t {
	mempool_t *mp;
	lbnode_t *head, *tail, *dummy;
	int32_t tid, pos, max_tid, max_pos;
	int is_eof, flag_mask, max_plp, error, maxcnt;
	bam_pileup1_t *plp;
	// for the "auto" interface only
	bam1_t *b;
	bam_plp_auto_f func;
	void *data;
};

bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
{
	bam_plp_t iter;
	iter = calloc(1, sizeof(struct __bam_plp_t));
	iter->mp = mp_init();
	iter->head = iter->tail = mp_alloc(iter->mp);
	iter->dummy = mp_alloc(iter->mp);
	iter->max_tid = iter->max_pos = -1;
	iter->flag_mask = BAM_DEF_MASK;
	iter->maxcnt = 8000;
	if (func) {
		iter->func = func;
		iter->data = data;
		iter->b = bam_init1();
	}
	return iter;
}

void bam_plp_destroy(bam_plp_t iter)
{
	mp_free(iter->mp, iter->dummy);
	mp_free(iter->mp, iter->head);
	if (iter->mp->cnt != 0)
		fprintf(stderr, "[bam_plp_destroy] memory leak: %d. Continue anyway.\n", iter->mp->cnt);
	mp_destroy(iter->mp);
	if (iter->b) bam_destroy1(iter->b);
	free(iter->plp);
	free(iter);
}

const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
{
	if (iter->error) { *_n_plp = -1; return 0; }
	*_n_plp = 0;
	if (iter->is_eof && iter->head->next == 0) return 0;
	while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) {
		int n_plp = 0;
		lbnode_t *p, *q;
		// write iter->plp at iter->pos
		iter->dummy->next = iter->head;
		for (p = iter->head, q = iter->dummy; p->next; q = p, p = p->next) {
			if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
				q->next = p->next; mp_free(iter->mp, p); p = q;
			} else if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup
				if (n_plp == iter->max_plp) { // then double the capacity
					iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256;
					iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
				}
				iter->plp[n_plp].b = &p->b;
				if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true...
			}
		}
		iter->head = iter->dummy->next; // dummy->next may be changed
		*_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos;
		// update iter->tid and iter->pos
		if (iter->head->next) {
			if (iter->tid > iter->head->b.core.tid) {
				fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__);
				iter->error = 1;
				*_n_plp = -1;
				return 0;
			}
		}
		if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence
			iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
		} else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid
			iter->pos = iter->head->beg; // jump to the next position
		} else ++iter->pos; // scan contiguously
		// return
		if (n_plp) return iter->plp;
		if (iter->is_eof && iter->head->next == 0) break;
	}
	return 0;
}

int bam_plp_push(bam_plp_t iter, const bam1_t *b)
{
	if (iter->error) return -1;
	if (b) {
		if (b->core.tid < 0) return 0;
		if (b->core.flag & iter->flag_mask) return 0;
		if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt) return 0;
		bam_copy1(&iter->tail->b, b);
		iter->tail->beg = b->core.pos; iter->tail->end = bam_calend(&b->core, bam1_cigar(b));
		iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
		if (b->core.tid < iter->max_tid) {
			fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
			iter->error = 1;
			return -1;
		}
		if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
			fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
			iter->error = 1;
			return -1;
		}
		iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
		if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
			iter->tail->next = mp_alloc(iter->mp);
			iter->tail = iter->tail->next;
		}
	} else iter->is_eof = 1;
	return 0;
}

const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
{
	const bam_pileup1_t *plp;
	if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; }
	if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
	else { // no pileup line can be obtained; read alignments
		*_n_plp = 0;
		if (iter->is_eof) return 0;
		while (iter->func(iter->data, iter->b) >= 0) {
			if (bam_plp_push(iter, iter->b) < 0) {
				*_n_plp = -1;
				return 0;
			}
			if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
			// otherwise no pileup line can be returned; read the next alignment.
		}
		bam_plp_push(iter, 0);
		if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
		return 0;
	}
}

void bam_plp_reset(bam_plp_t iter)
{
	lbnode_t *p, *q;
	iter->max_tid = iter->max_pos = -1;
	iter->tid = iter->pos = 0;
	iter->is_eof = 0;
	for (p = iter->head; p->next;) {
		q = p->next;
		mp_free(iter->mp, p);
		p = q;
	}
	iter->head = iter->tail;
}

void bam_plp_set_mask(bam_plp_t iter, int mask)
{
	iter->flag_mask = mask < 0? BAM_DEF_MASK : (BAM_FUNMAP | mask);
}

void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
{
	iter->maxcnt = maxcnt;
}

/*****************
 * callback APIs *
 *****************/

int bam_pileup_file(bamFile fp, int mask, bam_pileup_f func, void *func_data)
{
	bam_plbuf_t *buf;
	int ret;
	bam1_t *b;
	b = bam_init1();
	buf = bam_plbuf_init(func, func_data);
	bam_plbuf_set_mask(buf, mask);
	while ((ret = bam_read1(fp, b)) >= 0)
		bam_plbuf_push(b, buf);
	bam_plbuf_push(0, buf);
	bam_plbuf_destroy(buf);
	bam_destroy1(b);
	return 0;
}

void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
{
	bam_plp_set_mask(buf->iter, mask);
}

void bam_plbuf_reset(bam_plbuf_t *buf)
{
	bam_plp_reset(buf->iter);
}

bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
{
	bam_plbuf_t *buf;
	buf = calloc(1, sizeof(bam_plbuf_t));
	buf->iter = bam_plp_init(0, 0);
	buf->func = func;
	buf->data = data;
	return buf;
}

void bam_plbuf_destroy(bam_plbuf_t *buf)
{
	bam_plp_destroy(buf->iter);
	free(buf);
}

int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
{
	int ret, n_plp, tid, pos;
	const bam_pileup1_t *plp;
	ret = bam_plp_push(buf->iter, b);
	if (ret < 0) return ret;
	while ((plp = bam_plp_next(buf->iter, &tid, &pos, &n_plp)) != 0)
		buf->func(tid, pos, n_plp, plp, buf->data);
	return 0;
}

/***********
 * mpileup *
 ***********/

struct __bam_mplp_t {
	int n;
	uint64_t min, *pos;
	bam_plp_t *iter;
	int *n_plp;
	const bam_pileup1_t **plp;
};

bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
{
	int i;
	bam_mplp_t iter;
	iter = calloc(1, sizeof(struct __bam_mplp_t));
	iter->pos = calloc(n, 8);
	iter->n_plp = calloc(n, sizeof(int));
	iter->plp = calloc(n, sizeof(void*));
	iter->iter = calloc(n, sizeof(void*));
	iter->n = n;
	iter->min = (uint64_t)-1;
	for (i = 0; i < n; ++i) {
		iter->iter[i] = bam_plp_init(func, data[i]);
		iter->pos[i] = iter->min;
	}
	return iter;
}

void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt)
{
	int i;
	for (i = 0; i < iter->n; ++i)
		iter->iter[i]->maxcnt = maxcnt;
}

void bam_mplp_destroy(bam_mplp_t iter)
{
	int i;
	for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]);
	free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp);
	free(iter);
}

int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
{
	int i, ret = 0;
	uint64_t new_min = (uint64_t)-1;
	for (i = 0; i < iter->n; ++i) {
		if (iter->pos[i] == iter->min) {
			int tid, pos;
			iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]);
			iter->pos[i] = (uint64_t)tid<<32 | pos;
		}
		if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i];
	}
	iter->min = new_min;
	if (new_min == (uint64_t)-1) return 0;
	*_tid = new_min>>32; *_pos = (uint32_t)new_min;
	for (i = 0; i < iter->n; ++i) {
		if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line"
			n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
			++ret;
		} else n_plp[i] = 0, plp[i] = 0;
	}
	return ret;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_plcmd.c000066400000000000000000000461501211610345200231310ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include 
#include "sam.h"
#include "faidx.h"
#include "kstring.h"

static inline int printw(int c, FILE *fp)
{
	char buf[16];
	int l, x;
	if (c == 0) return fputc('0', fp);
	for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
	if (c < 0) buf[l++] = '-';
	buf[l] = 0;
	for (x = 0; x < l/2; ++x) {
		int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
	}
	fputs(buf, fp);
	return 0;
}

static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
{
	int j;
	if (p->is_head) {
		putchar('^');
		putchar(p->b->core.qual > 93? 126 : p->b->core.qual + 33);
	}
	if (!p->is_del) {
		int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
		if (ref) {
			int rb = pos < ref_len? ref[pos] : 'N';
			if (c == '=' || bam_nt16_table[c] == bam_nt16_table[rb]) c = bam1_strand(p->b)? ',' : '.';
			else c = bam1_strand(p->b)? tolower(c) : toupper(c);
		} else {
			if (c == '=') c = bam1_strand(p->b)? ',' : '.';
			else c = bam1_strand(p->b)? tolower(c) : toupper(c);
		}
		putchar(c);
	} else putchar(p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*');
	if (p->indel > 0) {
		putchar('+'); printw(p->indel, stdout);
		for (j = 1; j <= p->indel; ++j) {
			int c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
			putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
		}
	} else if (p->indel < 0) {
		printw(p->indel, stdout);
		for (j = 1; j <= -p->indel; ++j) {
			int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
			putchar(bam1_strand(p->b)? tolower(c) : toupper(c));
		}
	}
	if (p->is_tail) putchar('$');
}

#include 
#include "bam2bcf.h"
#include "sample.h"

#define MPLP_GLF   0x10
#define MPLP_NO_COMP 0x20
#define MPLP_NO_ORPHAN 0x40
#define MPLP_REALN   0x80
#define MPLP_FMT_DP 0x100
#define MPLP_FMT_SP 0x200
#define MPLP_NO_INDEL 0x400
#define MPLP_EXT_BAQ 0x800
#define MPLP_ILLUMINA13 0x1000
#define MPLP_IGNORE_RG 0x2000
#define MPLP_PRINT_POS 0x4000
#define MPLP_PRINT_MAPQ 0x8000

void *bed_read(const char *fn);
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);

typedef struct {
	int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth;
	int openQ, extQ, tandemQ, min_support; // for indels
	double min_frac; // for indels
	char *reg, *pl_list;
	faidx_t *fai;
	void *bed, *rghash;
} mplp_conf_t;

typedef struct {
	bamFile fp;
	bam_iter_t iter;
	bam_header_t *h;
	int ref_id;
	char *ref;
	const mplp_conf_t *conf;
} mplp_aux_t;

typedef struct {
	int n;
	int *n_plp, *m_plp;
	bam_pileup1_t **plp;
} mplp_pileup_t;

static int mplp_func(void *data, bam1_t *b)
{
	extern int bam_realn(bam1_t *b, const char *ref);
	extern int bam_prob_realn_core(bam1_t *b, const char *ref, int);
	extern int bam_cap_mapQ(bam1_t *b, char *ref, int thres);
	mplp_aux_t *ma = (mplp_aux_t*)data;
	int ret, skip = 0;
	do {
		int has_ref;
		ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
		if (ret < 0) break;
		if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
			skip = 1;
			continue;
		}
		if (ma->conf->bed) { // test overlap
			skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
			if (skip) continue;
		}
		if (ma->conf->rghash) { // exclude read groups
			uint8_t *rg = bam_aux_get(b, "RG");
			skip = (rg && bcf_str2id(ma->conf->rghash, (const char*)(rg+1)) >= 0);
			if (skip) continue;
		}
		if (ma->conf->flag & MPLP_ILLUMINA13) {
			int i;
			uint8_t *qual = bam1_qual(b);
			for (i = 0; i < b->core.l_qseq; ++i)
				qual[i] = qual[i] > 31? qual[i] - 31 : 0;
		}
		has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
		skip = 0;
		if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1);
		if (has_ref && ma->conf->capQ_thres > 10) {
			int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres);
			if (q < 0) skip = 1;
			else if (b->core.qual > q) b->core.qual = q;
		}
		else if (b->core.qual < ma->conf->min_mq) skip = 1; 
		else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&1) && !(b->core.flag&2)) skip = 1;
	} while (skip);
	return ret;
}

static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
					   int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
{
	int i, j;
	memset(m->n_plp, 0, m->n * sizeof(int));
	for (i = 0; i < n; ++i) {
		for (j = 0; j < n_plp[i]; ++j) {
			const bam_pileup1_t *p = plp[i] + j;
			uint8_t *q;
			int id = -1;
			q = ignore_rg? 0 : bam_aux_get(p->b, "RG");
			if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
			if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
			if (id < 0 || id >= m->n) {
				assert(q); // otherwise a bug
				fprintf(stderr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]);
				exit(1);
			}
			if (m->n_plp[id] == m->m_plp[id]) {
				m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
				m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
			}
			m->plp[id][m->n_plp[id]++] = *p;
		}
	}
}

static int mpileup(mplp_conf_t *conf, int n, char **fn)
{
	extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
	extern void bcf_call_del_rghash(void *rghash);
	mplp_aux_t **data;
	int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
	const bam_pileup1_t **plp;
	bam_mplp_t iter;
	bam_header_t *h = 0;
	char *ref;
	void *rghash = 0;

	bcf_callaux_t *bca = 0;
	bcf_callret1_t *bcr = 0;
	bcf_call_t bc;
	bcf_t *bp = 0;
	bcf_hdr_t *bh = 0;

	bam_sample_t *sm = 0;
	kstring_t buf;
	mplp_pileup_t gplp;

	memset(&gplp, 0, sizeof(mplp_pileup_t));
	memset(&buf, 0, sizeof(kstring_t));
	memset(&bc, 0, sizeof(bcf_call_t));
	data = calloc(n, sizeof(void*));
	plp = calloc(n, sizeof(void*));
	n_plp = calloc(n, sizeof(int*));
	sm = bam_smpl_init();

	// read the header and initialize data
	for (i = 0; i < n; ++i) {
		bam_header_t *h_tmp;
		data[i] = calloc(1, sizeof(mplp_aux_t));
		data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
		data[i]->conf = conf;
		h_tmp = bam_header_read(data[i]->fp);
		data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
		bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
		rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
		if (conf->reg) {
			int beg, end;
			bam_index_t *idx;
			idx = bam_index_load(fn[i]);
			if (idx == 0) {
				fprintf(stderr, "[%s] fail to load index for %d-th input.\n", __func__, i+1);
				exit(1);
			}
			if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
				fprintf(stderr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
				exit(1);
			}
			if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
			data[i]->iter = bam_iter_query(idx, tid, beg, end);
			bam_index_destroy(idx);
		}
		if (i == 0) h = h_tmp;
		else {
			// FIXME: to check consistency
			bam_header_destroy(h_tmp);
		}
	}
	gplp.n = sm->n;
	gplp.n_plp = calloc(sm->n, sizeof(int));
	gplp.m_plp = calloc(sm->n, sizeof(int));
	gplp.plp = calloc(sm->n, sizeof(void*));

	fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
	// write the VCF header
	if (conf->flag & MPLP_GLF) {
		kstring_t s;
		bh = calloc(1, sizeof(bcf_hdr_t));
		s.l = s.m = 0; s.s = 0;
		bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
		for (i = 0; i < h->n_targets; ++i) {
			kputs(h->target_name[i], &s);
			kputc('\0', &s);
		}
		bh->l_nm = s.l;
		bh->name = malloc(s.l);
		memcpy(bh->name, s.s, s.l);
		s.l = 0;
		for (i = 0; i < sm->n; ++i) {
			kputs(sm->smpl[i], &s); kputc('\0', &s);
		}
		bh->l_smpl = s.l;
		bh->sname = malloc(s.l);
		memcpy(bh->sname, s.s, s.l);
		bh->txt = malloc(strlen(BAM_VERSION) + 64);
		bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
		free(s.s);
		bcf_hdr_sync(bh);
		bcf_hdr_write(bp, bh);
		bca = bcf_call_init(-1., conf->min_baseQ);
		bcr = calloc(sm->n, sizeof(bcf_callret1_t));
		bca->rghash = rghash;
		bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
		bca->min_frac = conf->min_frac;
		bca->min_support = conf->min_support;
	}
	if (tid0 >= 0 && conf->fai) { // region is set
		ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
		ref_tid = tid0;
		for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
	} else ref_tid = -1, ref = 0;
	iter = bam_mplp_init(n, mplp_func, (void**)data);
	max_depth = conf->max_depth;
	if (max_depth * sm->n > 1<<20)
		fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
	if (max_depth * sm->n < 8000) {
		max_depth = 8000 / sm->n;
		fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth);
	}
	max_indel_depth = conf->max_indel_depth * sm->n;
	bam_mplp_set_maxcnt(iter, max_depth);
	while (bam_mplp_auto(iter, &tid, &pos, n_plp, plp) > 0) {
		if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
		if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
		if (tid != ref_tid) {
			free(ref); ref = 0;
			if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
			for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
			ref_tid = tid;
		}
		if (conf->flag & MPLP_GLF) {
			int total_depth, _ref0, ref16;
			bcf1_t *b = calloc(1, sizeof(bcf1_t));
			for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
			group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
			_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
			ref16 = bam_nt16_table[_ref0];
			for (i = 0; i < gplp.n; ++i)
				bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
			bcf_call_combine(gplp.n, bcr, ref16, &bc);
			bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
						 (conf->flag&MPLP_FMT_SP), 0, 0);
			bcf_write(bp, bh, b);
			bcf_destroy(b);
			// call indels
			if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
				for (i = 0; i < gplp.n; ++i)
					bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
				if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
					b = calloc(1, sizeof(bcf1_t));
					bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
								 (conf->flag&MPLP_FMT_SP), bca, ref);
					bcf_write(bp, bh, b);
					bcf_destroy(b);
				}
			}
		} else {
			printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
			for (i = 0; i < n; ++i) {
				int j;
				printf("\t%d\t", n_plp[i]);
				if (n_plp[i] == 0) {
					printf("*\t*"); // FIXME: printf() is very slow...
					if (conf->flag & MPLP_PRINT_POS) printf("\t*");
				} else {
					for (j = 0; j < n_plp[i]; ++j)
						pileup_seq(plp[i] + j, pos, ref_len, ref);
					putchar('\t');
					for (j = 0; j < n_plp[i]; ++j) {
						const bam_pileup1_t *p = plp[i] + j;
						int c = bam1_qual(p->b)[p->qpos] + 33;
						if (c > 126) c = 126;
						putchar(c);
					}
					if (conf->flag & MPLP_PRINT_MAPQ) {
						putchar('\t');
						for (j = 0; j < n_plp[i]; ++j) {
							int c = plp[i][j].b->core.qual + 33;
							if (c > 126) c = 126;
							putchar(c);
						}
					}
					if (conf->flag & MPLP_PRINT_POS) {
						putchar('\t');
						for (j = 0; j < n_plp[i]; ++j) {
							if (j > 0) putchar(',');
							printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
						}
					}
				}
			}
			putchar('\n');
		}
	}

	bcf_close(bp);
	bam_smpl_destroy(sm); free(buf.s);
	for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
	free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
	bcf_call_del_rghash(rghash);
	bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
	bam_mplp_destroy(iter);
	bam_header_destroy(h);
	for (i = 0; i < n; ++i) {
		bam_close(data[i]->fp);
		if (data[i]->iter) bam_iter_destroy(data[i]->iter);
		free(data[i]);
	}
	free(data); free(plp); free(ref); free(n_plp);
	return 0;
}

#define MAX_PATH_LEN 1024
static int read_file_list(const char *file_list,int *n,char **argv[])
{
    char buf[MAX_PATH_LEN];
    int len, nfiles;
    char **files;

    FILE *fh = fopen(file_list,"r");
    if ( !fh )
    {
        fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
        return 1;
    }

    // Speed is not an issue here, determine the number of files by reading the file twice
    nfiles = 0;
    while ( fgets(buf,MAX_PATH_LEN,fh) ) nfiles++;

    if ( fseek(fh, 0L, SEEK_SET) )
    {
        fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
        return 1;
    }

    files = calloc(nfiles,sizeof(char*));
    nfiles = 0;
    while ( fgets(buf,MAX_PATH_LEN,fh) ) 
    {
        len = strlen(buf);
        while ( len>0 && isspace(buf[len-1]) ) len--;
        if ( !len ) continue;

        files[nfiles] = malloc(sizeof(char)*(len+1)); 
        strncpy(files[nfiles],buf,len);
        files[nfiles][len] = 0;
        nfiles++;
    }
    fclose(fh);
    if ( !nfiles )
    {
        fprintf(stderr,"No files read from %s\n", file_list);
        return 1;
    }
    *argv = files;
    *n    = nfiles;
    return 0;
}
#undef MAX_PATH_LEN

int bam_mpileup(int argc, char *argv[])
{
	int c;
    const char *file_list = NULL;
    char **fn = NULL;
    int nfiles = 0, use_orphan = 0;
	mplp_conf_t mplp;
	memset(&mplp, 0, sizeof(mplp_conf_t));
	#define MPLP_PRINT_POS 0x4000
	mplp.max_mq = 60;
	mplp.min_baseQ = 13;
	mplp.capQ_thres = 0;
	mplp.max_depth = 250; mplp.max_indel_depth = 250;
	mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
	mplp.min_frac = 0.002; mplp.min_support = 1;
	mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
	while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6Os")) >= 0) {
		switch (c) {
		case 'f':
			mplp.fai = fai_load(optarg);
			if (mplp.fai == 0) return 1;
			break;
		case 'd': mplp.max_depth = atoi(optarg); break;
		case 'r': mplp.reg = strdup(optarg); break;
		case 'l': mplp.bed = bed_read(optarg); break;
		case 'P': mplp.pl_list = strdup(optarg); break;
		case 'g': mplp.flag |= MPLP_GLF; break;
		case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
		case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
		case 'B': mplp.flag &= ~MPLP_REALN; break;
		case 'D': mplp.flag |= MPLP_FMT_DP; break;
		case 'S': mplp.flag |= MPLP_FMT_SP; break;
		case 'I': mplp.flag |= MPLP_NO_INDEL; break;
		case 'E': mplp.flag |= MPLP_EXT_BAQ; break;
		case '6': mplp.flag |= MPLP_ILLUMINA13; break;
		case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
		case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
		case 'O': mplp.flag |= MPLP_PRINT_POS; break;
		case 'C': mplp.capQ_thres = atoi(optarg); break;
		case 'M': mplp.max_mq = atoi(optarg); break;
		case 'q': mplp.min_mq = atoi(optarg); break;
		case 'Q': mplp.min_baseQ = atoi(optarg); break;
        case 'b': file_list = optarg; break;
		case 'o': mplp.openQ = atoi(optarg); break;
		case 'e': mplp.extQ = atoi(optarg); break;
		case 'h': mplp.tandemQ = atoi(optarg); break;
		case 'A': use_orphan = 1; break;
		case 'F': mplp.min_frac = atof(optarg); break;
		case 'm': mplp.min_support = atoi(optarg); break;
		case 'L': mplp.max_indel_depth = atoi(optarg); break;
		case 'G': {
				FILE *fp_rg;
				char buf[1024];
				mplp.rghash = bcf_str2id_init();
				if ((fp_rg = fopen(optarg, "r")) == 0)
					fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
				while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
					bcf_str2id_add(mplp.rghash, strdup(buf));
				fclose(fp_rg);
			}
			break;
		}
	}
	if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
	if (argc == 1) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
		fprintf(stderr, "Input options:\n\n");
		fprintf(stderr, "       -6           assume the quality is in the Illumina-1.3+ encoding\n");
		fprintf(stderr, "       -A           count anomalous read pairs\n");
		fprintf(stderr, "       -B           disable BAQ computation\n");
		fprintf(stderr, "       -b FILE      list of input BAM files [null]\n");
		fprintf(stderr, "       -C INT       parameter for adjusting mapQ; 0 to disable [0]\n");
		fprintf(stderr, "       -d INT       max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
		fprintf(stderr, "       -E           extended BAQ for higher sensitivity but lower specificity\n");
		fprintf(stderr, "       -f FILE      faidx indexed reference sequence file [null]\n");
		fprintf(stderr, "       -G FILE      exclude read groups listed in FILE [null]\n");
		fprintf(stderr, "       -l FILE      list of positions (chr pos) or regions (BED) [null]\n");
		fprintf(stderr, "       -M INT       cap mapping quality at INT [%d]\n", mplp.max_mq);
		fprintf(stderr, "       -r STR       region in which pileup is generated [null]\n");
		fprintf(stderr, "       -R           ignore RG tags\n");
		fprintf(stderr, "       -q INT       skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
		fprintf(stderr, "       -Q INT       skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
		fprintf(stderr, "\nOutput options:\n\n");
		fprintf(stderr, "       -D           output per-sample DP in BCF (require -g/-u)\n");
		fprintf(stderr, "       -g           generate BCF output (genotype likelihoods)\n");
		fprintf(stderr, "       -O           output base positions on reads (disabled by -g/-u)\n");
		fprintf(stderr, "       -s           output mapping quality (disabled by -g/-u)\n");
		fprintf(stderr, "       -S           output per-sample strand bias P-value in BCF (require -g/-u)\n");
		fprintf(stderr, "       -u           generate uncompress BCF output\n");
		fprintf(stderr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
		fprintf(stderr, "       -e INT       Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
		fprintf(stderr, "       -F FLOAT     minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
		fprintf(stderr, "       -h INT       coefficient for homopolymer errors [%d]\n", mplp.tandemQ);
		fprintf(stderr, "       -I           do not perform indel calling\n");
		fprintf(stderr, "       -L INT       max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
		fprintf(stderr, "       -m INT       minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
		fprintf(stderr, "       -o INT       Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
		fprintf(stderr, "       -P STR       comma separated list of platforms for indels [all]\n");
		fprintf(stderr, "\n");
		fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
		return 1;
	}
    if (file_list) {
        if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
        mpileup(&mplp,nfiles,fn);
        for (c=0; c
#include 
#include "bgzf.h"
#include "bam.h"

#define BUF_SIZE 0x10000

int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
{
	BGZF *fp;
	bam_header_t *old;
	int len;
	uint8_t *buf;
	if (in->open_mode != 'r') return -1;
	buf = malloc(BUF_SIZE);
	old = bam_header_read(in);
	fp = bgzf_fdopen(fd, "w");
	bam_header_write(fp, h);
	if (in->block_offset < in->block_length) {
		bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
		bgzf_flush(fp);
	}
#ifdef _USE_KNETFILE
	while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
		fwrite(buf, 1, len, fp->x.fpw);
#else
	while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
		fwrite(buf, 1, len, fp->file);
#endif
	free(buf);
	fp->block_offset = in->block_offset = 0;
	bgzf_close(fp);
	return 0;
}

int main_reheader(int argc, char *argv[])
{
	bam_header_t *h;
	BGZF *in;
	if (argc != 3) {
		fprintf(stderr, "Usage: samtools reheader  \n");
		return 1;
	}
	{ // read the header
		tamFile fph = sam_open(argv[1]);
		if (fph == 0) {
			fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
			return 1;
		}
		h = sam_header_read(fph);
		sam_close(fph);
	}
	in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
	if (in == 0) {
		fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[2]);
		return 1;
	}
	bam_reheader(in, h, fileno(stdout));
	bgzf_close(in);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_rmdup.c000066400000000000000000000127771211610345200231710ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include "sam.h"

typedef bam1_t *bam1_p;

#include "khash.h"
KHASH_SET_INIT_STR(name)
KHASH_MAP_INIT_INT64(pos, bam1_p)

#define BUFFER_SIZE 0x40000

typedef struct {
	uint64_t n_checked, n_removed;
	khash_t(pos) *best_hash;
} lib_aux_t;
KHASH_MAP_INIT_STR(lib, lib_aux_t)

typedef struct {
	int n, max;
	bam1_t **a;
} tmp_stack_t;

static inline void stack_insert(tmp_stack_t *stack, bam1_t *b)
{
	if (stack->n == stack->max) {
		stack->max = stack->max? stack->max<<1 : 0x10000;
		stack->a = (bam1_t**)realloc(stack->a, sizeof(bam1_t*) * stack->max);
	}
	stack->a[stack->n++] = b;
}

static inline void dump_best(tmp_stack_t *stack, samfile_t *out)
{
	int i;
	for (i = 0; i != stack->n; ++i) {
		samwrite(out, stack->a[i]);
		bam_destroy1(stack->a[i]);
	}
	stack->n = 0;
}

static void clear_del_set(khash_t(name) *del_set)
{
	khint_t k;
	for (k = kh_begin(del_set); k < kh_end(del_set); ++k)
		if (kh_exist(del_set, k))
			free((char*)kh_key(del_set, k));
	kh_clear(name, del_set);
}

static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
{
	khint_t k = kh_get(lib, aux, lib);
	if (k == kh_end(aux)) {
		int ret;
		char *p = strdup(lib);
		lib_aux_t *q;
		k = kh_put(lib, aux, p, &ret);
		q = &kh_val(aux, k);
		q->n_checked = q->n_removed = 0;
		q->best_hash = kh_init(pos);
		return q;
	} else return &kh_val(aux, k);
}

static void clear_best(khash_t(lib) *aux, int max)
{
	khint_t k;
	for (k = kh_begin(aux); k != kh_end(aux); ++k) {
		if (kh_exist(aux, k)) {
			lib_aux_t *q = &kh_val(aux, k);
			if (kh_size(q->best_hash) >= max)
				kh_clear(pos, q->best_hash);
		}
	}
}

static inline int sum_qual(const bam1_t *b)
{
	int i, q;
	uint8_t *qual = bam1_qual(b);
	for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
	return q;
}

void bam_rmdup_core(samfile_t *in, samfile_t *out)
{
	bam1_t *b;
	int last_tid = -1, last_pos = -1;
	tmp_stack_t stack;
	khint_t k;
	khash_t(lib) *aux;
	khash_t(name) *del_set;
	
	aux = kh_init(lib);
	del_set = kh_init(name);
	b = bam_init1();
	memset(&stack, 0, sizeof(tmp_stack_t));

	kh_resize(name, del_set, 4 * BUFFER_SIZE);
	while (samread(in, b) >= 0) {
		bam1_core_t *c = &b->core;
		if (c->tid != last_tid || last_pos != c->pos) {
			dump_best(&stack, out); // write the result
			clear_best(aux, BUFFER_SIZE);
			if (c->tid != last_tid) {
				clear_best(aux, 0);
				if (kh_size(del_set)) { // check
					fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
					clear_del_set(del_set);
				}
				if ((int)c->tid == -1) { // append unmapped reads
					samwrite(out, b);
					while (samread(in, b) >= 0) samwrite(out, b);
					break;
				}
				last_tid = c->tid;
				fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", in->header->target_name[c->tid]);
			}
		}
		if (!(c->flag&BAM_FPAIRED) || (c->flag&(BAM_FUNMAP|BAM_FMUNMAP)) || (c->mtid >= 0 && c->tid != c->mtid)) {
			samwrite(out, b);
		} else if (c->isize > 0) { // paired, head
			uint64_t key = (uint64_t)c->pos<<32 | c->isize;
			const char *lib;
			lib_aux_t *q;
			int ret;
			lib = bam_get_library(in->header, b);
			q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
			++q->n_checked;
			k = kh_put(pos, q->best_hash, key, &ret);
			if (ret == 0) { // found in best_hash
				bam1_t *p = kh_val(q->best_hash, k);
				++q->n_removed;
				if (sum_qual(p) < sum_qual(b)) { // the current alignment is better; this can be accelerated in principle
					kh_put(name, del_set, strdup(bam1_qname(p)), &ret); // p will be removed
					bam_copy1(p, b); // replaced as b
				} else kh_put(name, del_set, strdup(bam1_qname(b)), &ret); // b will be removed
				if (ret == 0)
					fprintf(stderr, "[bam_rmdup_core] inconsistent BAM file for pair '%s'. Continue anyway.\n", bam1_qname(b));
			} else { // not found in best_hash
				kh_val(q->best_hash, k) = bam_dup1(b);
				stack_insert(&stack, kh_val(q->best_hash, k));
			}
		} else { // paired, tail
			k = kh_get(name, del_set, bam1_qname(b));
			if (k != kh_end(del_set)) {
				free((char*)kh_key(del_set, k));
				kh_del(name, del_set, k);
			} else samwrite(out, b);
		}
		last_pos = c->pos;
	}

	for (k = kh_begin(aux); k != kh_end(aux); ++k) {
		if (kh_exist(aux, k)) {
			lib_aux_t *q = &kh_val(aux, k);			
			dump_best(&stack, out);
			fprintf(stderr, "[bam_rmdup_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
					(long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
			kh_destroy(pos, q->best_hash);
			free((char*)kh_key(aux, k));
		}
	}
	kh_destroy(lib, aux);

	clear_del_set(del_set);
	kh_destroy(name, del_set);
	free(stack.a);
	bam_destroy1(b);
}

void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se);

int bam_rmdup(int argc, char *argv[])
{
	int c, is_se = 0, force_se = 0;
	samfile_t *in, *out;
	while ((c = getopt(argc, argv, "sS")) >= 0) {
		switch (c) {
		case 's': is_se = 1; break;
		case 'S': force_se = is_se = 1; break;
		}
	}
	if (optind + 2 > argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:  samtools rmdup [-sS]  \n\n");
		fprintf(stderr, "Option: -s    rmdup for SE reads\n");
		fprintf(stderr, "        -S    treat PE reads as SE in rmdup (force -s)\n\n");
		return 1;
	}
	in = samopen(argv[optind], "rb", 0);
	out = samopen(argv[optind+1], "wb", in->header);
	if (in == 0 || out == 0) {
		fprintf(stderr, "[bam_rmdup] fail to read/write input files\n");
		return 1;
	}
	if (is_se) bam_rmdupse_core(in, out, force_se);
	else bam_rmdup_core(in, out);
	samclose(in); samclose(out);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_rmdupse.c000066400000000000000000000100371211610345200235040ustar00rootroot00000000000000#include 
#include "sam.h"
#include "khash.h"
#include "klist.h"

#define QUEUE_CLEAR_SIZE 0x100000
#define MAX_POS 0x7fffffff

typedef struct {
	int endpos;
	uint32_t score:31, discarded:1;
	bam1_t *b;
} elem_t, *elem_p;
#define __free_elem(p) bam_destroy1((p)->data.b)
KLIST_INIT(q, elem_t, __free_elem)
typedef klist_t(q) queue_t;

KHASH_MAP_INIT_INT(best, elem_p)
typedef khash_t(best) besthash_t;

typedef struct {
	uint64_t n_checked, n_removed;
	besthash_t *left, *rght;
} lib_aux_t;
KHASH_MAP_INIT_STR(lib, lib_aux_t)

static lib_aux_t *get_aux(khash_t(lib) *aux, const char *lib)
{
	khint_t k = kh_get(lib, aux, lib);
	if (k == kh_end(aux)) {
		int ret;
		char *p = strdup(lib);
		lib_aux_t *q;
		k = kh_put(lib, aux, p, &ret);
		q = &kh_val(aux, k);
		q->left = kh_init(best);
		q->rght = kh_init(best);
		q->n_checked = q->n_removed = 0;
		return q;
	} else return &kh_val(aux, k);
}

static inline int sum_qual(const bam1_t *b)
{
	int i, q;
	uint8_t *qual = bam1_qual(b);
	for (i = q = 0; i < b->core.l_qseq; ++i) q += qual[i];
	return q;
}

static inline elem_t *push_queue(queue_t *queue, const bam1_t *b, int endpos, int score)
{
	elem_t *p = kl_pushp(q, queue);
	p->discarded = 0;
	p->endpos = endpos; p->score = score;
	if (p->b == 0) p->b = bam_init1();
	bam_copy1(p->b, b);
	return p;
}

static void clear_besthash(besthash_t *h, int32_t pos)
{
	khint_t k;
	for (k = kh_begin(h); k != kh_end(h); ++k)
		if (kh_exist(h, k) && kh_val(h, k)->endpos <= pos)
			kh_del(best, h, k);
}

static void dump_alignment(samfile_t *out, queue_t *queue, int32_t pos, khash_t(lib) *h)
{
	if (queue->size > QUEUE_CLEAR_SIZE || pos == MAX_POS) {
		khint_t k;
		while (1) {
			elem_t *q;
			if (queue->head == queue->tail) break;
			q = &kl_val(queue->head);
			if (q->discarded) {
				q->b->data_len = 0;
				kl_shift(q, queue, 0);
				continue;
			}
			if ((q->b->core.flag&BAM_FREVERSE) && q->endpos > pos) break;
			samwrite(out, q->b);
			q->b->data_len = 0;
			kl_shift(q, queue, 0);
		}
		for (k = kh_begin(h); k != kh_end(h); ++k) {
			if (kh_exist(h, k)) {
				clear_besthash(kh_val(h, k).left, pos);
				clear_besthash(kh_val(h, k).rght, pos);
			}
		}
	}
}

void bam_rmdupse_core(samfile_t *in, samfile_t *out, int force_se)
{
	bam1_t *b;
	queue_t *queue;
	khint_t k;
	int last_tid = -2;
	khash_t(lib) *aux;

	aux = kh_init(lib);
	b = bam_init1();
	queue = kl_init(q);
	while (samread(in, b) >= 0) {
		bam1_core_t *c = &b->core;
		int endpos = bam_calend(c, bam1_cigar(b));
		int score = sum_qual(b);
		
		if (last_tid != c->tid) {
			if (last_tid >= 0) dump_alignment(out, queue, MAX_POS, aux);
			last_tid = c->tid;
		} else dump_alignment(out, queue, c->pos, aux);
		if ((c->flag&BAM_FUNMAP) || ((c->flag&BAM_FPAIRED) && !force_se)) {
			push_queue(queue, b, endpos, score);
		} else {
			const char *lib;
			lib_aux_t *q;
			besthash_t *h;
			uint32_t key;
			int ret;
			lib = bam_get_library(in->header, b);
			q = lib? get_aux(aux, lib) : get_aux(aux, "\t");
			++q->n_checked;
			h = (c->flag&BAM_FREVERSE)? q->rght : q->left;
			key = (c->flag&BAM_FREVERSE)? endpos : c->pos;
			k = kh_put(best, h, key, &ret);
			if (ret == 0) { // in the hash table
				elem_t *p = kh_val(h, k);
				++q->n_removed;
				if (p->score < score) {
					if (c->flag&BAM_FREVERSE) { // mark "discarded" and push the queue
						p->discarded = 1;
						kh_val(h, k) = push_queue(queue, b, endpos, score);
					} else { // replace
						p->score = score; p->endpos = endpos;
						bam_copy1(p->b, b);
					}
				} // otherwise, discard the alignment
			} else kh_val(h, k) = push_queue(queue, b, endpos, score);
		}
	}
	dump_alignment(out, queue, MAX_POS, aux);

	for (k = kh_begin(aux); k != kh_end(aux); ++k) {
		if (kh_exist(aux, k)) {
			lib_aux_t *q = &kh_val(aux, k);
			fprintf(stderr, "[bam_rmdupse_core] %lld / %lld = %.4lf in library '%s'\n", (long long)q->n_removed,
					(long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
			kh_destroy(best, q->left); kh_destroy(best, q->rght);
			free((char*)kh_key(aux, k));
		}
	}
	kh_destroy(lib, aux);
	bam_destroy1(b);
	kl_destroy(q, queue);
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_sort.c000066400000000000000000000326041211610345200230200ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include "bam.h"
#include "ksort.h"

static int g_is_by_qname = 0;

static inline int strnum_cmp(const char *a, const char *b)
{
	char *pa, *pb;
	pa = (char*)a; pb = (char*)b;
	while (*pa && *pb) {
		if (isdigit(*pa) && isdigit(*pb)) {
			long ai, bi;
			ai = strtol(pa, &pa, 10);
			bi = strtol(pb, &pb, 10);
			if (ai != bi) return aibi? 1 : 0;
		} else {
			if (*pa != *pb) break;
			++pa; ++pb;
		}
	}
	if (*pa == *pb)
		return (pa-a) < (pb-b)? -1 : (pa-a) > (pb-b)? 1 : 0;
	return *pa<*pb? -1 : *pa>*pb? 1 : 0;
}

#define HEAP_EMPTY 0xffffffffffffffffull

typedef struct {
	int i;
	uint64_t pos, idx;
	bam1_t *b;
} heap1_t;

#define __pos_cmp(a, b) ((a).pos > (b).pos || ((a).pos == (b).pos && ((a).i > (b).i || ((a).i == (b).i && (a).idx > (b).idx))))

static inline int heap_lt(const heap1_t a, const heap1_t b)
{
	if (g_is_by_qname) {
		int t;
		if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
		t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
		return (t > 0 || (t == 0 && __pos_cmp(a, b)));
	} else return __pos_cmp(a, b);
}

KSORT_INIT(heap, heap1_t, heap_lt)

static void swap_header_targets(bam_header_t *h1, bam_header_t *h2)
{
	bam_header_t t;
	t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets;
	t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name;
	t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len;
}

static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
{
	int tempi;
	char *temps;
	tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
	temps = h1->text, h1->text = h2->text, h2->text = temps;
}

#define MERGE_RG     1
#define MERGE_UNCOMP 2
#define MERGE_LEVEL1 4
#define MERGE_FORCE  8

/*!
  @abstract    Merge multiple sorted BAM.
  @param  is_by_qname whether to sort by query name
  @param  out  output BAM file name
  @param  headers  name of SAM file from which to copy '@' header lines,
                   or NULL to copy them from the first file to be merged
  @param  n    number of files to be merged
  @param  fn   names of files to be merged

  @discussion Padding information may NOT correctly maintained. This
  function is NOT thread safe.
 */
int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn,
					int flag, const char *reg)
{
	bamFile fpout, *fp;
	heap1_t *heap;
	bam_header_t *hout = 0;
	bam_header_t *hheaders = NULL;
	int i, j, *RG_len = 0;
	uint64_t idx = 0;
	char **RG = 0;
	bam_iter_t *iter = 0;

	if (headers) {
		tamFile fpheaders = sam_open(headers);
		if (fpheaders == 0) {
			const char *message = strerror(errno);
			fprintf(stderr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);
			return -1;
		}
		hheaders = sam_header_read(fpheaders);
		sam_close(fpheaders);
	}

	g_is_by_qname = by_qname;
	fp = (bamFile*)calloc(n, sizeof(bamFile));
	heap = (heap1_t*)calloc(n, sizeof(heap1_t));
	iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t));
	// prepare RG tag
	if (flag & MERGE_RG) {
		RG = (char**)calloc(n, sizeof(void*));
		RG_len = (int*)calloc(n, sizeof(int));
		for (i = 0; i != n; ++i) {
			int l = strlen(fn[i]);
			const char *s = fn[i];
			if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;
			for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
			++j; l -= j;
			RG[i] = calloc(l + 1, 1);
			RG_len[i] = l;
			strncpy(RG[i], s + j, l);
		}
	}
	// read the first
	for (i = 0; i != n; ++i) {
		bam_header_t *hin;
		fp[i] = bam_open(fn[i], "r");
		if (fp[i] == 0) {
			int j;
			fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);
			for (j = 0; j < i; ++j) bam_close(fp[j]);
			free(fp); free(heap);
			// FIXME: possible memory leak
			return -1;
		}
		hin = bam_header_read(fp[i]);
		if (i == 0) { // the first BAM
			hout = hin;
		} else { // validate multiple baf
			int min_n_targets = hout->n_targets;
			if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets;

			for (j = 0; j < min_n_targets; ++j)
				if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) {
					fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n",
							hout->target_name[j], hin->target_name[j], fn[i]);
					return -1;
				}

			// If this input file has additional target reference sequences,
			// add them to the headers to be output
			if (hin->n_targets > hout->n_targets) {
				swap_header_targets(hout, hin);
				// FIXME Possibly we should also create @SQ text headers
				// for the newly added reference sequences
			}

			bam_header_destroy(hin);
		}
	}

	if (hheaders) {
		// If the text headers to be swapped in include any @SQ headers,
		// check that they are consistent with the existing binary list
		// of reference information.
		if (hheaders->n_targets > 0) {
			if (hout->n_targets != hheaders->n_targets) {
				fprintf(stderr, "[bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences\n", headers);
				if (!reg) return -1;
			}
			for (j = 0; j < hout->n_targets; ++j)
				if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {
					fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence\n", hheaders->target_name[j], headers);
					if (!reg) return -1;
				}
		}

		swap_header_text(hout, hheaders);
		bam_header_destroy(hheaders);
	}

	if (reg) {
		int tid, beg, end;
		if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) {
			fprintf(stderr, "[%s] Malformated region string or undefined reference name\n", __func__);
			return -1;
		}
		for (i = 0; i < n; ++i) {
			bam_index_t *idx;
			idx = bam_index_load(fn[i]);
			iter[i] = bam_iter_query(idx, tid, beg, end);
			bam_index_destroy(idx);
		}
	}

	for (i = 0; i < n; ++i) {
		heap1_t *h = heap + i;
		h->i = i;
		h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
		if (bam_iter_read(fp[i], iter[i], h->b) >= 0) {
			h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b);
			h->idx = idx++;
		}
		else h->pos = HEAP_EMPTY;
	}
	if (flag & MERGE_UNCOMP) fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu");
	else if (flag & MERGE_LEVEL1) fpout = strcmp(out, "-")? bam_open(out, "w1") : bam_dopen(fileno(stdout), "w1");
	else fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
	if (fpout == 0) {
		fprintf(stderr, "[%s] fail to create the output file.\n", __func__);
		return -1;
	}
	bam_header_write(fpout, hout);
	bam_header_destroy(hout);

	ks_heapmake(heap, n, heap);
	while (heap->pos != HEAP_EMPTY) {
		bam1_t *b = heap->b;
		if (flag & MERGE_RG) {
			uint8_t *rg = bam_aux_get(b, "RG");
			if (rg) bam_aux_del(b, rg);
			bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
		}
		bam_write1_core(fpout, &b->core, b->data_len, b->data);
		if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
			heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b);
			heap->idx = idx++;
		} else if (j == -1) {
			heap->pos = HEAP_EMPTY;
			free(heap->b->data); free(heap->b);
			heap->b = 0;
		} else fprintf(stderr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);
		ks_heapadjust(heap, 0, n, heap);
	}

	if (flag & MERGE_RG) {
		for (i = 0; i != n; ++i) free(RG[i]);
		free(RG); free(RG_len);
	}
	for (i = 0; i != n; ++i) {
		bam_iter_destroy(iter[i]);
		bam_close(fp[i]);
	}
	bam_close(fpout);
	free(fp); free(heap); free(iter);
	return 0;
}

int bam_merge(int argc, char *argv[])
{
	int c, is_by_qname = 0, flag = 0, ret = 0;
	char *fn_headers = NULL, *reg = 0;

	while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) {
		switch (c) {
		case 'r': flag |= MERGE_RG; break;
		case 'f': flag |= MERGE_FORCE; break;
		case 'h': fn_headers = strdup(optarg); break;
		case 'n': is_by_qname = 1; break;
		case '1': flag |= MERGE_LEVEL1; break;
		case 'u': flag |= MERGE_UNCOMP; break;
		case 'R': reg = strdup(optarg); break;
		}
	}
	if (optind + 2 >= argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   samtools merge [-nr] [-h inh.sam]    [...]\n\n");
		fprintf(stderr, "Options: -n       sort by read names\n");
		fprintf(stderr, "         -r       attach RG tag (inferred from file names)\n");
		fprintf(stderr, "         -u       uncompressed BAM output\n");
		fprintf(stderr, "         -f       overwrite the output BAM if exist\n");
		fprintf(stderr, "         -1       compress level 1\n");
		fprintf(stderr, "         -R STR   merge file in the specified region STR [all]\n");
		fprintf(stderr, "         -h FILE  copy the header in FILE to  [in1.bam]\n\n");
		fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
		fprintf(stderr, "      must provide the correct header with -h, or uses Picard which properly maintains\n");
		fprintf(stderr, "      the header dictionary in merging.\n\n");
		return 1;
	}
	if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {
		FILE *fp = fopen(argv[optind], "rb");
		if (fp != NULL) {
			fclose(fp);
			fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]);
			return 1;
		}
	}
	if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
	free(reg);
	free(fn_headers);
	return ret;
}

typedef bam1_t *bam1_p;

static inline int bam1_lt(const bam1_p a, const bam1_p b)
{
	if (g_is_by_qname) {
		int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
		return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)))));
	} else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
}
KSORT_INIT(sort, bam1_p, bam1_lt)

static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
{
	char *name, mode[3];
	int i;
	bamFile fp;
	ks_mergesort(sort, k, buf, 0);
	name = (char*)calloc(strlen(prefix) + 20, 1);
	if (n >= 0) {
		sprintf(name, "%s.%.4d.bam", prefix, n);
		strcpy(mode, "w1");
	} else {
		sprintf(name, "%s.bam", prefix);
		strcpy(mode, "w");
	}
	fp = is_stdout? bam_dopen(fileno(stdout), mode) : bam_open(name, mode);
	if (fp == 0) {
		fprintf(stderr, "[sort_blocks] fail to create file %s.\n", name);
		free(name);
		// FIXME: possible memory leak
		return;
	}
	free(name);
	bam_header_write(fp, h);
	for (i = 0; i < k; ++i)
		bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data);
	bam_close(fp);
}

/*!
  @abstract Sort an unsorted BAM file based on the chromosome order
  and the leftmost position of an alignment

  @param  is_by_qname whether to sort by query name
  @param  fn       name of the file to be sorted
  @param  prefix   prefix of the output and the temporary files; upon
	                   sucessess, prefix.bam will be written.
  @param  max_mem  approxiate maximum memory (very inaccurate)

  @discussion It may create multiple temporary subalignment files
  and then merge them by calling bam_merge_core(). This function is
  NOT thread safe.
 */
void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t max_mem, int is_stdout)
{
	int n, ret, k, i;
	size_t mem;
	bam_header_t *header;
	bamFile fp;
	bam1_t *b, **buf;

	g_is_by_qname = is_by_qname;
	n = k = 0; mem = 0;
	fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
	if (fp == 0) {
		fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn);
		return;
	}
	header = bam_header_read(fp);
	buf = (bam1_t**)calloc(max_mem / BAM_CORE_SIZE, sizeof(bam1_t*));
	// write sub files
	for (;;) {
		if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));
		b = buf[k];
		if ((ret = bam_read1(fp, b)) < 0) break;
		mem += ret;
		++k;
		if (mem >= max_mem) {
			sort_blocks(n++, k, buf, prefix, header, 0);
			mem = 0; k = 0;
		}
	}
	if (ret != -1)
		fprintf(stderr, "[bam_sort_core] truncated file. Continue anyway.\n");
	if (n == 0) sort_blocks(-1, k, buf, prefix, header, is_stdout);
	else { // then merge
		char **fns, *fnout;
		fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n+1);
		sort_blocks(n++, k, buf, prefix, header, 0);
		fnout = (char*)calloc(strlen(prefix) + 20, 1);
		if (is_stdout) sprintf(fnout, "-");
		else sprintf(fnout, "%s.bam", prefix);
		fns = (char**)calloc(n, sizeof(char*));
		for (i = 0; i < n; ++i) {
			fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
			sprintf(fns[i], "%s.%.4d.bam", prefix, i);
		}
		bam_merge_core(is_by_qname, fnout, 0, n, fns, 0, 0);
		free(fnout);
		for (i = 0; i < n; ++i) {
			unlink(fns[i]);
			free(fns[i]);
		}
		free(fns);
	}
	for (k = 0; k < max_mem / BAM_CORE_SIZE; ++k) {
		if (buf[k]) {
			free(buf[k]->data);
			free(buf[k]);
		}
	}
	free(buf);
	bam_header_destroy(header);
	bam_close(fp);
}

void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
{
	bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0);
}

int bam_sort(int argc, char *argv[])
{
	size_t max_mem = 500000000;
	int c, is_by_qname = 0, is_stdout = 0;
	while ((c = getopt(argc, argv, "nom:")) >= 0) {
		switch (c) {
		case 'o': is_stdout = 1; break;
		case 'n': is_by_qname = 1; break;
		case 'm': max_mem = atol(optarg); break;
		}
	}
	if (optind + 2 > argc) {
		fprintf(stderr, "Usage: samtools sort [-on] [-m ]  \n");
		return 1;
	}
	bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_stat.c000066400000000000000000000062021211610345200227770ustar00rootroot00000000000000#include 
#include 
#include "bam.h"

typedef struct {
	long long n_reads[2], n_mapped[2], n_pair_all[2], n_pair_map[2], n_pair_good[2];
	long long n_sgltn[2], n_read1[2], n_read2[2];
	long long n_dup[2];
	long long n_diffchr[2], n_diffhigh[2];
} bam_flagstat_t;

#define flagstat_loop(s, c) do {										\
		int w = ((c)->flag & BAM_FQCFAIL)? 1 : 0;	 					\
		++(s)->n_reads[w];												\
		if ((c)->flag & BAM_FPAIRED) {									\
			++(s)->n_pair_all[w];										\
			if ((c)->flag & BAM_FPROPER_PAIR) ++(s)->n_pair_good[w];	\
			if ((c)->flag & BAM_FREAD1) ++(s)->n_read1[w];				\
			if ((c)->flag & BAM_FREAD2) ++(s)->n_read2[w];				\
			if (((c)->flag & BAM_FMUNMAP) && !((c)->flag & BAM_FUNMAP)) ++(s)->n_sgltn[w];	\
			if (!((c)->flag & BAM_FUNMAP) && !((c)->flag & BAM_FMUNMAP)) { \
				++(s)->n_pair_map[w];									\
				if ((c)->mtid != (c)->tid) {							\
					++(s)->n_diffchr[w];								\
					if ((c)->qual >= 5) ++(s)->n_diffhigh[w];			\
				}														\
			}															\
		}																\
		if (!((c)->flag & BAM_FUNMAP)) ++(s)->n_mapped[w];				\
		if ((c)->flag & BAM_FDUP) ++(s)->n_dup[w];						\
	} while (0)

bam_flagstat_t *bam_flagstat_core(bamFile fp)
{
	bam_flagstat_t *s;
	bam1_t *b;
	bam1_core_t *c;
	int ret;
	s = (bam_flagstat_t*)calloc(1, sizeof(bam_flagstat_t));
	b = bam_init1();
	c = &b->core;
	while ((ret = bam_read1(fp, b)) >= 0)
		flagstat_loop(s, c);
	bam_destroy1(b);
	if (ret != -1)
		fprintf(stderr, "[bam_flagstat_core] Truncated file? Continue anyway.\n");
	return s;
}
int bam_flagstat(int argc, char *argv[])
{
	bamFile fp;
	bam_header_t *header;
	bam_flagstat_t *s;
	if (argc == optind) {
		fprintf(stderr, "Usage: samtools flagstat \n");
		return 1;
	}
	fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
	assert(fp);
	header = bam_header_read(fp);
	s = bam_flagstat_core(fp);
	printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
	printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
	printf("%lld + %lld mapped (%.2f%%:%.2f%%)\n", s->n_mapped[0], s->n_mapped[1], (float)s->n_mapped[0] / s->n_reads[0] * 100.0, (float)s->n_mapped[1] / s->n_reads[1] * 100.0);
	printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
	printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
	printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
	printf("%lld + %lld properly paired (%.2f%%:%.2f%%)\n", s->n_pair_good[0], s->n_pair_good[1], (float)s->n_pair_good[0] / s->n_pair_all[0] * 100.0, (float)s->n_pair_good[1] / s->n_pair_all[1] * 100.0);
	printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
	printf("%lld + %lld singletons (%.2f%%:%.2f%%)\n", s->n_sgltn[0], s->n_sgltn[1], (float)s->n_sgltn[0] / s->n_pair_all[0] * 100.0, (float)s->n_sgltn[1] / s->n_pair_all[1] * 100.0);
	printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
	printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
	free(s);
	bam_header_destroy(header);
	bam_close(fp);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bam_tview.c000066400000000000000000000324371211610345200231730ustar00rootroot00000000000000#undef _HAVE_CURSES

#if _CURSES_LIB == 0
#elif _CURSES_LIB == 1
#include 
#ifndef NCURSES_VERSION
#warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
#else
#define _HAVE_CURSES
#endif
#elif _CURSES_LIB == 2
#include 
#define _HAVE_CURSES
#else
#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
#endif

#ifdef _HAVE_CURSES
#include 
#include 
#include 
#include 
#include "bam.h"
#include "faidx.h"
#include "bam2bcf.h"

char bam_aux_getCEi(bam1_t *b, int i);
char bam_aux_getCSi(bam1_t *b, int i);
char bam_aux_getCQi(bam1_t *b, int i);

#define TV_MIN_ALNROW 2
#define TV_MAX_GOTO  40
#define TV_LOW_MAPQ  10

#define TV_COLOR_MAPQ   0
#define TV_COLOR_BASEQ  1
#define TV_COLOR_NUCL   2
#define TV_COLOR_COL    3
#define TV_COLOR_COLQ   4

#define TV_BASE_NUCL 0
#define TV_BASE_COLOR_SPACE 1

typedef struct {
	int mrow, mcol;
	WINDOW *wgoto, *whelp;

	bam_index_t *idx;
	bam_lplbuf_t *lplbuf;
	bam_header_t *header;
	bamFile fp;
	int curr_tid, left_pos;
	faidx_t *fai;
	bcf_callaux_t *bca;

	int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
	char *ref;
} tview_t;

int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
	extern unsigned char bam_nt16_table[256];
	tview_t *tv = (tview_t*)data;
	int i, j, c, rb, attr, max_ins = 0;
	uint32_t call = 0;
	if (pos < tv->left_pos || tv->ccol > tv->mcol) return 0; // out of screen
	// print referece
	rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
	for (i = tv->last_pos + 1; i < pos; ++i) {
		if (i%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", i+1);
		c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
		mvaddch(1, tv->ccol++, c);
	}
	if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
	{ // call consensus
		bcf_callret1_t bcr;
		int qsum[4], a1, a2, tmp;
		double p[3], prior = 30;
		bcf_call_glfgen(n, pl, bam_nt16_table[rb], tv->bca, &bcr);
		for (i = 0; i < 4; ++i) qsum[i] = bcr.qsum[i]<<2 | i;
		for (i = 1; i < 4; ++i) // insertion sort
			for (j = i; j > 0 && qsum[j] > qsum[j-1]; --j)
				tmp = qsum[j], qsum[j] = qsum[j-1], qsum[j-1] = tmp;
		a1 = qsum[0]&3; a2 = qsum[1]&3;
		p[0] = bcr.p[a1*5+a1]; p[1] = bcr.p[a1*5+a2] + prior; p[2] = bcr.p[a2*5+a2];
		if ("ACGT"[a1] != toupper(rb)) p[0] += prior + 3;
		if ("ACGT"[a2] != toupper(rb)) p[2] += prior + 3;
		if (p[0] < p[1] && p[0] < p[2]) call = (1<>16&0xf];
	i = (call&0xffff)/10+1;
	if (i > 4) i = 4;
	attr |= COLOR_PAIR(i);
	if (c == toupper(rb)) c = '.';
	attron(attr);
	mvaddch(2, tv->ccol, c);
	attroff(attr);
	if(tv->ins) {
		// calculate maximum insert
		for (i = 0; i < n; ++i) {
			const bam_pileup1_t *p = pl + i;
			if (p->indel > 0 && max_ins < p->indel) max_ins = p->indel;
		}
	}
	// core loop
	for (j = 0; j <= max_ins; ++j) {
		for (i = 0; i < n; ++i) {
			const bam_pileup1_t *p = pl + i;
			int row = TV_MIN_ALNROW + p->level - tv->row_shift;
			if (j == 0) {
				if (!p->is_del) {
					if (tv->base_for == TV_BASE_COLOR_SPACE && 
							(c = bam_aux_getCSi(p->b, p->qpos))) {
						c = bam_aux_getCSi(p->b, p->qpos);
						// assume that if we found one color, we will be able to get the color error
						if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.';
					} else {
						if (tv->show_name) {
							char *name = bam1_qname(p->b);
							c = (p->qpos + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos];
						} else {
							c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)];
							if (tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
						}
					}
				} else c = p->is_refskip? (bam1_strand(p->b)? '<' : '>') : '*';
			} else { // padding
				if (j > p->indel) c = '*';
				else { // insertion
					if (tv->base_for ==  TV_BASE_NUCL) {
						if (tv->show_name) {
							char *name = bam1_qname(p->b);
							c = (p->qpos + j + 1 >= p->b->core.l_qname)? ' ' : name[p->qpos + j];
						} else {
							c = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + j)];
							if (j == 0 && tv->is_dot && toupper(c) == toupper(rb)) c = bam1_strand(p->b)? ',' : '.';
						}
					} else {
						c = bam_aux_getCSi(p->b, p->qpos + j);
						if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos + j)) c = bam1_strand(p->b)? ',' : '.';
					}
				}
			}
			if (row > TV_MIN_ALNROW && row < tv->mrow) {
				int x;
				attr = 0;
				if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
						|| (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
				if (tv->color_for == TV_COLOR_BASEQ) {
					x = bam1_qual(p->b)[p->qpos]/10 + 1;
					if (x > 4) x = 4;
					attr |= COLOR_PAIR(x);
				} else if (tv->color_for == TV_COLOR_MAPQ) {
					x = p->b->core.qual/10 + 1;
					if (x > 4) x = 4;
					attr |= COLOR_PAIR(x);
				} else if (tv->color_for == TV_COLOR_NUCL) {
					x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
					attr |= COLOR_PAIR(x);
				} else if(tv->color_for == TV_COLOR_COL) {
					x = 0;
					switch(bam_aux_getCSi(p->b, p->qpos)) {
						case '0': x = 0; break;
						case '1': x = 1; break;
						case '2': x = 2; break;
						case '3': x = 3; break;
						case '4': x = 4; break;
						default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
					}
					x+=5;
					attr |= COLOR_PAIR(x);
				} else if(tv->color_for == TV_COLOR_COLQ) {
					x = bam_aux_getCQi(p->b, p->qpos);
					if(0 == x) x = bam1_qual(p->b)[p->qpos];
					x = x/10 + 1;
					if (x > 4) x = 4;
					attr |= COLOR_PAIR(x);
				}
				attron(attr);
				mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
				attroff(attr);
			}
		}
		c = j? '*' : rb;
		if (c == '*') {
			attr = COLOR_PAIR(8);
			attron(attr);
			mvaddch(1, tv->ccol++, c);
			attroff(attr);
		} else mvaddch(1, tv->ccol++, c);
	}
	tv->last_pos = pos;
	return 0;
}

tview_t *tv_init(const char *fn, const char *fn_fa)
{
	tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
	tv->is_dot = 1;
	tv->fp = bam_open(fn, "r");
	bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
	assert(tv->fp);
	tv->header = bam_header_read(tv->fp);
	tv->idx = bam_index_load(fn);
	if (tv->idx == 0) exit(1);
	tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
	if (fn_fa) tv->fai = fai_load(fn_fa);
	tv->bca = bcf_call_init(0.83, 13);
	tv->ins = 1;

	initscr();
	keypad(stdscr, TRUE);
	clear();
	noecho();
	cbreak();
	tv->mrow = 24; tv->mcol = 80;
	getmaxyx(stdscr, tv->mrow, tv->mcol);
	tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
	tv->whelp = newwin(29, 40, 5, 5);
	tv->color_for = TV_COLOR_MAPQ;
	start_color();
	init_pair(1, COLOR_BLUE, COLOR_BLACK);
	init_pair(2, COLOR_GREEN, COLOR_BLACK);
	init_pair(3, COLOR_YELLOW, COLOR_BLACK);
	init_pair(4, COLOR_WHITE, COLOR_BLACK);
	init_pair(5, COLOR_GREEN, COLOR_BLACK);
	init_pair(6, COLOR_CYAN, COLOR_BLACK);
	init_pair(7, COLOR_YELLOW, COLOR_BLACK);
	init_pair(8, COLOR_RED, COLOR_BLACK);
	init_pair(9, COLOR_BLUE, COLOR_BLACK);
	return tv;
}

void tv_destroy(tview_t *tv)
{
	delwin(tv->wgoto); delwin(tv->whelp);
	endwin();

	bam_lplbuf_destroy(tv->lplbuf);
	bcf_call_destroy(tv->bca);
	bam_index_destroy(tv->idx);
	if (tv->fai) fai_destroy(tv->fai);
	free(tv->ref);
	bam_header_destroy(tv->header);
	bam_close(tv->fp);
	free(tv);
}

int tv_fetch_func(const bam1_t *b, void *data)
{
	tview_t *tv = (tview_t*)data;
	if (tv->no_skip) {
		uint32_t *cigar = bam1_cigar(b); // this is cheating...
		int i;
		for (i = 0; i core.n_cigar; ++i) {
			if ((cigar[i]&0xf) == BAM_CREF_SKIP)
				cigar[i] = cigar[i]>>4<<4 | BAM_CDEL;
		}
	}
	bam_lplbuf_push(b, tv->lplbuf);
	return 0;
}

int tv_draw_aln(tview_t *tv, int tid, int pos)
{
	// reset
	clear();
	tv->curr_tid = tid; tv->left_pos = pos;
	tv->last_pos = tv->left_pos - 1;
	tv->ccol = 0;
	// print ref and consensus
	if (tv->fai) {
		char *str;
		if (tv->ref) free(tv->ref);
		str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
		sprintf(str, "%s:%d-%d", tv->header->target_name[tv->curr_tid], tv->left_pos + 1, tv->left_pos + tv->mcol);
		tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
		free(str);
	}
	// draw aln
	bam_lplbuf_reset(tv->lplbuf);
	bam_fetch(tv->fp, tv->idx, tv->curr_tid, tv->left_pos, tv->left_pos + tv->mcol, tv, tv_fetch_func);
	bam_lplbuf_push(0, tv->lplbuf);

	while (tv->ccol < tv->mcol) {
		int pos = tv->last_pos + 1;
		if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
		mvaddch(1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
		++tv->last_pos;
	}
	return 0;
}

static void tv_win_goto(tview_t *tv, int *tid, int *pos)
{
	char str[256], *p;
	int i, l = 0;
	wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
	mvwprintw(tv->wgoto, 1, 2, "Goto: ");
	for (;;) {
		int c = wgetch(tv->wgoto);
		wrefresh(tv->wgoto);
		if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
			--l;
		} else if (c == KEY_ENTER || c == '\012' || c == '\015') {
			int _tid = -1, _beg, _end;
			if (str[0] == '=') {
				_beg = strtol(str+1, &p, 10) - 1;
				if (_beg > 0) {
					*pos = _beg;
					return;
				}
			} else {
				bam_parse_region(tv->header, str, &_tid, &_beg, &_end);
				if (_tid >= 0) {
					*tid = _tid; *pos = _beg;
					return;
				}
			}
		} else if (isgraph(c)) {
			if (l < TV_MAX_GOTO) str[l++] = c;
		} else if (c == '\027') l = 0;
		else if (c == '\033') return;
		str[l] = '\0';
		for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
		mvwprintw(tv->wgoto, 1, 8, "%s", str);
	}
}

static void tv_win_help(tview_t *tv) {
	int r = 1;
	WINDOW *win = tv->whelp;
	wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
	mvwprintw(win, r++, 2, "        -=-    Help    -=- ");
	r++;
	mvwprintw(win, r++, 2, "?          This window");
	mvwprintw(win, r++, 2, "Arrows     Small scroll movement");
	mvwprintw(win, r++, 2, "h,j,k,l    Small scroll movement");
	mvwprintw(win, r++, 2, "H,J,K,L    Large scroll movement");
	mvwprintw(win, r++, 2, "ctrl-H     Scroll 1k left");
	mvwprintw(win, r++, 2, "ctrl-L     Scroll 1k right");
	mvwprintw(win, r++, 2, "space      Scroll one screen");
	mvwprintw(win, r++, 2, "backspace  Scroll back one screen");
	mvwprintw(win, r++, 2, "g          Go to specific location");
	mvwprintw(win, r++, 2, "m          Color for mapping qual");
	mvwprintw(win, r++, 2, "n          Color for nucleotide");
	mvwprintw(win, r++, 2, "b          Color for base quality");
	mvwprintw(win, r++, 2, "c          Color for cs color");
	mvwprintw(win, r++, 2, "z          Color for cs qual");
	mvwprintw(win, r++, 2, ".          Toggle on/off dot view");
	mvwprintw(win, r++, 2, "s          Toggle on/off ref skip");
	mvwprintw(win, r++, 2, "r          Toggle on/off rd name");
	mvwprintw(win, r++, 2, "N          Turn on nt view");
	mvwprintw(win, r++, 2, "C          Turn on cs view");
	mvwprintw(win, r++, 2, "i          Toggle on/off ins");
	mvwprintw(win, r++, 2, "q          Exit");
	r++;
	mvwprintw(win, r++, 2, "Underline:      Secondary or orphan");
	mvwprintw(win, r++, 2, "Blue:    0-9    Green: 10-19");
	mvwprintw(win, r++, 2, "Yellow: 20-29   White: >=30");
	wrefresh(win);
	wgetch(win);
}

void tv_loop(tview_t *tv)
{
	int tid, pos;
	tid = tv->curr_tid; pos = tv->left_pos;
	while (1) {
		int c = getch();
		switch (c) {
			case '?': tv_win_help(tv); break;
			case '\033':
			case 'q': goto end_loop;
			case '/': 
			case 'g': tv_win_goto(tv, &tid, &pos); break;
			case 'm': tv->color_for = TV_COLOR_MAPQ; break;
			case 'b': tv->color_for = TV_COLOR_BASEQ; break;
			case 'n': tv->color_for = TV_COLOR_NUCL; break;
			case 'c': tv->color_for = TV_COLOR_COL; break;
			case 'z': tv->color_for = TV_COLOR_COLQ; break;
			case 's': tv->no_skip = !tv->no_skip; break;
			case 'r': tv->show_name = !tv->show_name; break;
			case KEY_LEFT:
			case 'h': --pos; break;
			case KEY_RIGHT:
			case 'l': ++pos; break;
			case KEY_SLEFT:
			case 'H': pos -= 20; break;
			case KEY_SRIGHT:
			case 'L': pos += 20; break;
			case '.': tv->is_dot = !tv->is_dot; break;
			case 'N': tv->base_for = TV_BASE_NUCL; break;
			case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
			case 'i': tv->ins = !tv->ins; break;
			case '\010': pos -= 1000; break;
			case '\014': pos += 1000; break;
			case ' ': pos += tv->mcol; break;
			case KEY_UP:
			case 'j': --tv->row_shift; break;
			case KEY_DOWN:
			case 'k': ++tv->row_shift; break;
			case KEY_BACKSPACE:
			case '\177': pos -= tv->mcol; break;
			case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
			default: continue;
		}
		if (pos < 0) pos = 0;
		if (tv->row_shift < 0) tv->row_shift = 0;
		tv_draw_aln(tv, tid, pos);
	}
end_loop:
	return;
}

int bam_tview_main(int argc, char *argv[])
{
	tview_t *tv;
	if (argc == 1) {
		fprintf(stderr, "Usage: bamtk tview  [ref.fasta]\n");
		return 1;
	}
	tv = tv_init(argv[1], (argc == 2)? 0 : argv[2]);
	tv_draw_aln(tv, 0, 0);
	tv_loop(tv);
	tv_destroy(tv);
	return 0;
}
#else // #ifdef _HAVE_CURSES
#include 
#warning "No curses library is available; tview is disabled."
int bam_tview_main(int argc, char *argv[])
{
	fprintf(stderr, "[bam_tview_main] The ncurses library is unavailable; tview is not compiled.\n");
	return 1;
}
#endif // #ifdef _HAVE_CURSES
genometools-1.5.1/src/external/samtools-0.1.18/bamtk.c000066400000000000000000000111441211610345200223040ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include "bam.h"

#ifdef _USE_KNETFILE
#include "knetfile.h"
#endif

int bam_taf2baf(int argc, char *argv[]);
int bam_mpileup(int argc, char *argv[]);
int bam_merge(int argc, char *argv[]);
int bam_index(int argc, char *argv[]);
int bam_sort(int argc, char *argv[]);
int bam_tview_main(int argc, char *argv[]);
int bam_mating(int argc, char *argv[]);
int bam_rmdup(int argc, char *argv[]);
int bam_flagstat(int argc, char *argv[]);
int bam_fillmd(int argc, char *argv[]);
int bam_idxstats(int argc, char *argv[]);
int main_samview(int argc, char *argv[]);
int main_import(int argc, char *argv[]);
int main_reheader(int argc, char *argv[]);
int main_cut_target(int argc, char *argv[]);
int main_phase(int argc, char *argv[]);
int main_cat(int argc, char *argv[]);
int main_depth(int argc, char *argv[]);
int main_bam2fq(int argc, char *argv[]);

int faidx_main(int argc, char *argv[]);

static int usage()
{
	fprintf(stderr, "\n");
	fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
	fprintf(stderr, "Version: %s\n\n", BAM_VERSION);
	fprintf(stderr, "Usage:   samtools  [options]\n\n");
	fprintf(stderr, "Command: view        SAM<->BAM conversion\n");
	fprintf(stderr, "         sort        sort alignment file\n");
	fprintf(stderr, "         mpileup     multi-way pileup\n");
	fprintf(stderr, "         depth       compute the depth\n");
	fprintf(stderr, "         faidx       index/extract FASTA\n");
#if _CURSES_LIB != 0
	fprintf(stderr, "         tview       text alignment viewer\n");
#endif
	fprintf(stderr, "         index       index alignment\n");
	fprintf(stderr, "         idxstats    BAM index stats (r595 or later)\n");
	fprintf(stderr, "         fixmate     fix mate information\n");
	fprintf(stderr, "         flagstat    simple stats\n");
	fprintf(stderr, "         calmd       recalculate MD/NM tags and '=' bases\n");
	fprintf(stderr, "         merge       merge sorted alignments\n");
	fprintf(stderr, "         rmdup       remove PCR duplicates\n");
	fprintf(stderr, "         reheader    replace BAM header\n");
	fprintf(stderr, "         cat         concatenate BAMs\n");
	fprintf(stderr, "         targetcut   cut fosmid regions (for fosmid pool only)\n");
	fprintf(stderr, "         phase       phase heterozygotes\n");
	fprintf(stderr, "\n");
#ifdef _WIN32
	fprintf(stderr, "\
Note: The Windows version of SAMtools is mainly designed for read-only\n\
      operations, such as viewing the alignments and generating the pileup.\n\
      Binary files generated by the Windows version may be buggy.\n\n");
#endif
	return 1;
}

int main(int argc, char *argv[])
{
#ifdef _WIN32
	setmode(fileno(stdout), O_BINARY);
	setmode(fileno(stdin),  O_BINARY);
#ifdef _USE_KNETFILE
	knet_win32_init();
#endif
#endif
	if (argc < 2) return usage();
	if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
	else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
	else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
	else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
	else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
	else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
	else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(argc-1, argv+1);
	else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
	else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
	else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
	else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
	else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
	else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
	else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
	else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
	else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
	else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
	else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
	else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
	else if (strcmp(argv[1], "pileup") == 0) {
		fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
		return 1;
	}
#if _CURSES_LIB != 0
	else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif
	else {
		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
		return 1;
	}
	return 0;	
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/000077500000000000000000000000001211610345200226545ustar00rootroot00000000000000genometools-1.5.1/src/external/samtools-0.1.18/bcftools/Makefile000066400000000000000000000023061211610345200243150ustar00rootroot00000000000000CC=			gcc
CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
LOBJS=		bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
OMISC=		..
AOBJS=		call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o
PROG=		bcftools
INCLUDES=	
SUBDIRS=	.

.SUFFIXES:.c .o

.c.o:
		$(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@

all-recur lib-recur clean-recur cleanlocal-recur install-recur:
		@target=`echo $@ | sed s/-recur//`; \
		wdir=`pwd`; \
		list='$(SUBDIRS)'; for subdir in $$list; do \
			cd $$subdir; \
			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
			cd $$wdir; \
		done;

all:$(PROG)

lib:libbcf.a

libbcf.a:$(LOBJS)
		$(AR) -csru $@ $(LOBJS)

bcftools:lib $(AOBJS)
		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz

bcf.o:bcf.h
vcf.o:bcf.h
index.o:bcf.h
bcfutils.o:bcf.h
prob1.o:prob1.h bcf.h
call1.o:prob1.h bcf.h
bcf2qcall.o:bcf.h
main.o:bcf.h

bcf.pdf:bcf.tex
		pdflatex bcf

cleanlocal:
		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*

clean:cleanlocal-recur
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/README000066400000000000000000000036561211610345200235460ustar00rootroot00000000000000The view command of bcftools calls variants, tests Hardy-Weinberg
equilibrium (HWE), tests allele balances and estimates allele frequency.

This command calls a site as a potential variant if P(ref|D,F) is below
0.9 (controlled by the -p option), where D is data and F is the prior
allele frequency spectrum (AFS).

The view command performs two types of allele balance tests, both based
on Fisher's exact test for 2x2 contingency tables with the row variable
being reference allele or not. In the first table, the column variable
is strand. Two-tail P-value is taken. We test if variant bases tend to
come from one strand. In the second table, the column variable is
whether a base appears in the first or the last 11bp of the read.
One-tail P-value is taken. We test if variant bases tend to occur
towards the end of reads, which is usually an indication of
misalignment.

Site allele frequency is estimated in two ways. In the first way, the
frequency is esimated as \argmax_f P(D|f) under the assumption of
HWE. Prior AFS is not used. In the second way, the frequency is
estimated as the posterior expectation of allele counts \sum_k
kP(k|D,F), dividied by the total number of haplotypes. HWE is not
assumed, but the estimate depends on the prior AFS. The two estimates
largely agree when the signal is strong, but may differ greatly on weak
sites as in this case, the prior plays an important role.

To test HWE, we calculate the posterior distribution of genotypes
(ref-hom, het and alt-hom). Chi-square test is performed. It is worth
noting that the model used here is prior dependent and assumes HWE,
which is different from both models for allele frequency estimate. The
new model actually yields a third estimate of site allele frequency.

The estimate allele frequency spectrum is printed to stderr per 64k
sites. The estimate is in fact only the first round of a EM
procedure. The second model (not the model for HWE testing) is used to
estimate the AFS.genometools-1.5.1/src/external/samtools-0.1.18/bcftools/bcf.c000066400000000000000000000204171211610345200235560ustar00rootroot00000000000000#include 
#include 
#include 
#include "kstring.h"
#include "bcf.h"

bcf_t *bcf_open(const char *fn, const char *mode)
{
	bcf_t *b;
	b = calloc(1, sizeof(bcf_t));
	if (strchr(mode, 'w')) {
		b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdout), mode);
	} else {
		b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
	}
#ifndef BCF_LITE
	b->fp->owned_file = 1;
#endif
	return b;
}

int bcf_close(bcf_t *b)
{
	int ret;
	if (b == 0) return 0;
	ret = bgzf_close(b->fp);
	free(b);
	return ret;
}

int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h)
{
	if (b == 0 || h == 0) return -1;
	bgzf_write(b->fp, "BCF\4", 4);
	bgzf_write(b->fp, &h->l_nm, 4);
	bgzf_write(b->fp, h->name, h->l_nm);
	bgzf_write(b->fp, &h->l_smpl, 4);
	bgzf_write(b->fp, h->sname, h->l_smpl);
	bgzf_write(b->fp, &h->l_txt, 4);
	bgzf_write(b->fp, h->txt, h->l_txt);
	bgzf_flush(b->fp);
	return 16 + h->l_nm + h->l_smpl + h->l_txt;
}

bcf_hdr_t *bcf_hdr_read(bcf_t *b)
{
	uint8_t magic[4];
	bcf_hdr_t *h;
	if (b == 0) return 0;
	h = calloc(1, sizeof(bcf_hdr_t));
	bgzf_read(b->fp, magic, 4);
	bgzf_read(b->fp, &h->l_nm, 4);
	h->name = malloc(h->l_nm);
	bgzf_read(b->fp, h->name, h->l_nm);
	bgzf_read(b->fp, &h->l_smpl, 4);
	h->sname = malloc(h->l_smpl);
	bgzf_read(b->fp, h->sname, h->l_smpl);
	bgzf_read(b->fp, &h->l_txt, 4);
	h->txt = malloc(h->l_txt);
	bgzf_read(b->fp, h->txt, h->l_txt);
	bcf_hdr_sync(h);
	return h;
}

void bcf_hdr_destroy(bcf_hdr_t *h)
{
	if (h == 0) return;
	free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns);
	free(h);
}

static inline char **cnt_null(int l, char *str, int *_n)
{
	int n = 0;
	char *p, **list;
	*_n = 0;
	if (l == 0 || str == 0) return 0;
	for (p = str; p != str + l; ++p)
		if (*p == 0) ++n;
	*_n = n;
	list = calloc(n, sizeof(void*));
	list[0] = str;
	for (p = str, n = 1; p < str + l - 1; ++p)
		if (*p == 0) list[n++] = p + 1;
	return list;
}

int bcf_hdr_sync(bcf_hdr_t *b)
{
	if (b == 0) return -1;
	if (b->ns) free(b->ns);
	if (b->sns) free(b->sns);
	if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
	else b->ns = 0, b->n_ref = 0;
	b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
	return 0;
}

int bcf_sync(bcf1_t *b)
{
	char *p, *tmp[5];
	int i, n, n_smpl = b->n_smpl;
	ks_tokaux_t aux;
	// set ref, alt, flt, info, fmt
	b->ref = b->alt = b->flt = b->info = b->fmt = 0;
	for (p = b->str, n = 0; p < b->str + b->l_str; ++p) {
		if (*p == 0 && p+1 != b->str + b->l_str) {
			if (n == 5) {
				++n;
				break;
			} else tmp[n++] = p + 1;
		}
	}
	if (n != 5) {
		fprintf(stderr, "[%s] incorrect number of fields (%d != 5) at %d:%d\n", __func__, n, b->tid, b->pos);
		return -1;
	}
	b->ref = tmp[0]; b->alt = tmp[1]; b->flt = tmp[2]; b->info = tmp[3]; b->fmt = tmp[4];
	// set n_alleles
	if (*b->alt == 0) b->n_alleles = 1;
	else {
		for (p = b->alt, n = 1; *p; ++p)
			if (*p == ',') ++n;
		b->n_alleles = n + 1;
	}
	// set n_gi and gi[i].fmt
	for (p = b->fmt, n = 1; *p; ++p)
		if (*p == ':') ++n;
	if (n > b->m_gi) {
		int old_m = b->m_gi;
		b->m_gi = n;
		kroundup32(b->m_gi);
		b->gi = realloc(b->gi, b->m_gi * sizeof(bcf_ginfo_t));
		memset(b->gi + old_m, 0, (b->m_gi - old_m) * sizeof(bcf_ginfo_t));
	}
	b->n_gi = n;
	for (p = kstrtok(b->fmt, ":", &aux), n = 0; p; p = kstrtok(0, 0, &aux))
		b->gi[n++].fmt = bcf_str2int(p, aux.p - p);
	// set gi[i].len
	for (i = 0; i < b->n_gi; ++i) {
		if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
			b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
		} else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
			b->gi[i].len = 2;
		} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
			b->gi[i].len = 1;
		} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
			b->gi[i].len = 4;
		} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
			b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2 * 4;
		}
		b->gi[i].data = realloc(b->gi[i].data, n_smpl * b->gi[i].len);
	}
	return 0;
}

int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
{
	int i, l = 0;
	if (b == 0) return -1;
	bgzf_write(bp->fp, &b->tid, 4);
	bgzf_write(bp->fp, &b->pos, 4);
	bgzf_write(bp->fp, &b->qual, 4);
	bgzf_write(bp->fp, &b->l_str, 4);
	bgzf_write(bp->fp, b->str, b->l_str);
	l = 12 + b->l_str;
	for (i = 0; i < b->n_gi; ++i) {
		bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
		l += b->gi[i].len * h->n_smpl;
	}
	return l;
}

int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
{
	int i, l = 0;
	if (b == 0) return -1;
	if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
	b->n_smpl = h->n_smpl;
	bgzf_read(bp->fp, &b->pos, 4);
	bgzf_read(bp->fp, &b->qual, 4);
	bgzf_read(bp->fp, &b->l_str, 4);
	if (b->l_str > b->m_str) {
		b->m_str = b->l_str;
		kroundup32(b->m_str);
		b->str = realloc(b->str, b->m_str);
	}
	bgzf_read(bp->fp, b->str, b->l_str);
	l = 12 + b->l_str;
	if (bcf_sync(b) < 0) return -2;
	for (i = 0; i < b->n_gi; ++i) {
		bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
		l += b->gi[i].len * h->n_smpl;
	}
	return l;
}

int bcf_destroy(bcf1_t *b)
{
	int i;
	if (b == 0) return -1;
	free(b->str);
	for (i = 0; i < b->m_gi; ++i)
		free(b->gi[i].data);
	free(b->gi);
	free(b);
	return 0;
}

static inline void fmt_str(const char *p, kstring_t *s)
{
	if (*p == 0) kputc('.', s);
	else kputs(p, s);
}

void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
{
	int i, j, x;
	s->l = 0;
	if (h->n_ref) kputs(h->ns[b->tid], s);
	else kputw(b->tid, s);
	kputc('\t', s);
	kputw(b->pos + 1, s); kputc('\t', s);
	fmt_str(b->str, s); kputc('\t', s);
	fmt_str(b->ref, s); kputc('\t', s);
	fmt_str(b->alt, s); kputc('\t', s);
	ksprintf(s, "%.3g", b->qual); kputc('\t', s);
	fmt_str(b->flt, s); kputc('\t', s);
	fmt_str(b->info, s);
	if (b->fmt[0]) {
		kputc('\t', s);
		fmt_str(b->fmt, s);
	}
	x = b->n_alleles * (b->n_alleles + 1) / 2;
	if (b->n_gi == 0) return;
	for (j = 0; j < h->n_smpl; ++j) {
		kputc('\t', s);
		for (i = 0; i < b->n_gi; ++i) {
			if (i) kputc(':', s);
			if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
				uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
				int k;
				for (k = 0; k < x; ++k) {
					if (k > 0) kputc(',', s);
					kputw(d[k], s);
				}
			} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
				kputw(((uint16_t*)b->gi[i].data)[j], s);
			} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
				kputw(((uint8_t*)b->gi[i].data)[j], s);
			} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
				kputw(((int32_t*)b->gi[i].data)[j], s);
			} else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
				int y = ((uint8_t*)b->gi[i].data)[j];
				if (y>>7&1) {
					kputsn("./.", 3, s);
				} else {
					kputc('0' + (y>>3&7), s);
					kputc("/|"[y>>6&1], s);
					kputc('0' + (y&7), s);
				}
			} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
				float *d = (float*)b->gi[i].data + j * x;
				int k;
				//printf("- %lx\n", d);
				for (k = 0; k < x; ++k) {
					if (k > 0) kputc(',', s);
					ksprintf(s, "%.2f", d[k]);
				}
			} else kputc('.', s); // custom fields
		}
	}
}

char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
{
	kstring_t s;
	s.l = s.m = 0; s.s = 0;
	bcf_fmt_core(h, b, &s);
	return s.s;
}

int bcf_append_info(bcf1_t *b, const char *info, int l)
{
	int shift = b->fmt - b->str;
	int l_fmt = b->l_str - shift;
	char *ori = b->str;
	if (b->l_str + l > b->m_str) { // enlarge if necessary
		b->m_str = b->l_str + l;
		kroundup32(b->m_str);
		b->str = realloc(b->str, b->m_str);
	}
	memmove(b->str + shift + l, b->str + shift, l_fmt); // move the FORMAT field
	memcpy(b->str + shift - 1, info, l); // append to the INFO field
	b->str[shift + l - 1] = '\0';
	b->fmt = b->str + shift + l;
	b->l_str += l;
	if (ori != b->str) bcf_sync(b); // synchronize when realloc changes the pointer
	return 0;
}

int bcf_cpy(bcf1_t *r, const bcf1_t *b)
{
	char *t1 = r->str;
	bcf_ginfo_t *t2 = r->gi;
	int i, t3 = r->m_str, t4 = r->m_gi;
	*r = *b;
	r->str = t1; r->gi = t2; r->m_str = t3; r->m_gi = t4;
	if (r->m_str < b->m_str) {
		r->m_str = b->m_str;
		r->str = realloc(r->str, r->m_str);
	}
	memcpy(r->str, b->str, r->m_str);
	bcf_sync(r); // calling bcf_sync() is simple but inefficient
	for (i = 0; i < r->n_gi; ++i)
		memcpy(r->gi[i].data, b->gi[i].data, r->n_smpl * r->gi[i].len);
	return 0;
}

int bcf_is_indel(const bcf1_t *b)
{
	char *p;
	if (strlen(b->ref) > 1) return 1;
	for (p = b->alt; *p; ++p)
		if (*p != ',' && p[1] != ',' && p[1] != '\0')
			return 1;
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/bcf.h000066400000000000000000000153051211610345200235630ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2010 Broad Institute

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li  */

#ifndef BCF_H
#define BCF_H

#define BCF_VERSION "0.1.17-dev (r973:277)"

#include 
#include 

#ifndef BCF_LITE
#include "bgzf.h"
typedef BGZF *bcfFile;
#else
typedef gzFile bcfFile;
#define bgzf_open(fn, mode) gzopen(fn, mode)
#define bgzf_fdopen(fd, mode) gzdopen(fd, mode)
#define bgzf_close(fp) gzclose(fp)
#define bgzf_read(fp, buf, len) gzread(fp, buf, len)
#define bgzf_write(fp, buf, len)
#define bgzf_flush(fp)
#endif

/*
  A member in the structs below is said to "primary" if its content
  cannot be inferred from other members in any of structs below; a
  member is said to be "derived" if its content can be derived from
  other members. For example, bcf1_t::str is primary as this comes from
  the input data, while bcf1_t::info is derived as it can always be
  correctly set if we know bcf1_t::str. Derived members are for quick
  access to the content and must be synchronized with the primary data.
 */

typedef struct {
	uint32_t fmt; // format of the block, set by bcf_str2int(). 
	int len; // length of data for each individual
	void *data; // concatenated data
	// derived info: fmt, len (<-bcf1_t::fmt)
} bcf_ginfo_t;

typedef struct {
	int32_t tid, pos; // refID and 0-based position
	int32_t l_str, m_str; // length and the allocated size of ->str
	float qual; // SNP quality
	char *str; // concatenated string of variable length strings in VCF (from col.2 to col.7)
	char *ref, *alt, *flt, *info, *fmt; // they all point to ->str; no memory allocation
	int n_gi, m_gi; // number and the allocated size of geno fields
	bcf_ginfo_t *gi; // array of geno fields
	int n_alleles, n_smpl; // number of alleles and samples
	// derived info: ref, alt, flt, info, fmt (<-str), n_gi (<-fmt), n_alleles (<-alt), n_smpl (<-bcf_hdr_t::n_smpl)
} bcf1_t;

typedef struct {
	int32_t n_ref, n_smpl; // number of reference sequences and samples
	int32_t l_nm; // length of concatenated sequence names; 0 padded
	int32_t l_smpl; // length of concatenated sample names; 0 padded
	int32_t l_txt; // length of header text (lines started with ##)
	char *name, *sname, *txt; // concatenated sequence names, sample names and header text
	char **ns, **sns; // array of sequence and sample names; point to name and sname, respectively
	// derived info: n_ref (<-name), n_smpl (<-sname), ns (<-name), sns (<-sname)
} bcf_hdr_t;

typedef struct {
	int is_vcf; // if the file in operation is a VCF
	void *v; // auxillary data structure for VCF
	bcfFile fp; // file handler for BCF
} bcf_t;

struct __bcf_idx_t;
typedef struct __bcf_idx_t bcf_idx_t;

#ifdef __cplusplus
extern "C" {
#endif

	// open a BCF file; for BCF file only
	bcf_t *bcf_open(const char *fn, const char *mode);
	// close file
	int bcf_close(bcf_t *b);
	// read one record from BCF; return -1 on end-of-file, and <-1 for errors
	int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b);
	// call this function if b->str is changed
	int bcf_sync(bcf1_t *b);
	// write a BCF record
	int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b);
	// read the BCF header; BCF only
	bcf_hdr_t *bcf_hdr_read(bcf_t *b);
	// write the BCF header
	int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h);
	// set bcf_hdr_t::ns and bcf_hdr_t::sns
	int bcf_hdr_sync(bcf_hdr_t *b);
	// destroy the header
	void bcf_hdr_destroy(bcf_hdr_t *h);
	// destroy a record
	int bcf_destroy(bcf1_t *b);
	// BCF->VCF conversion
	char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b);
	// append more info
	int bcf_append_info(bcf1_t *b, const char *info, int l);
	// copy
	int bcf_cpy(bcf1_t *r, const bcf1_t *b);

	// open a VCF or BCF file if "b" is set in "mode"
	bcf_t *vcf_open(const char *fn, const char *mode);
	// close a VCF/BCF file
	int vcf_close(bcf_t *bp);
	// read the VCF/BCF header
	bcf_hdr_t *vcf_hdr_read(bcf_t *bp);
	// read the sequence dictionary from a separate file; required for VCF->BCF conversion
	int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn);
	// read a VCF/BCF record; return -1 on end-of-file and <-1 for errors
	int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);
	// write the VCF header
	int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h);
	// write a VCF record
	int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b);

	// keep the first n alleles and discard the rest
	int bcf_shrink_alt(bcf1_t *b, int n);
	// convert GL to PL
	int bcf_gl2pl(bcf1_t *b);
	// if the site is an indel
	int bcf_is_indel(const bcf1_t *b);
	bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list);
	int bcf_subsam(int n_smpl, int *list, bcf1_t *b);
	// move GT to the first FORMAT field
	int bcf_fix_gt(bcf1_t *b);
	// update PL generated by old samtools
	int bcf_fix_pl(bcf1_t *b);
	// convert PL to GLF-like 10-likelihood GL
	int bcf_gl10(const bcf1_t *b, uint8_t *gl);
	// convert up to 4 INDEL alleles to GLF-like 10-likelihood GL
	int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl);

	// string hash table
	void *bcf_build_refhash(bcf_hdr_t *h);
	void bcf_str2id_destroy(void *_hash);
	void bcf_str2id_thorough_destroy(void *_hash);
	int bcf_str2id_add(void *_hash, const char *str);
	int bcf_str2id(void *_hash, const char *str);
	void *bcf_str2id_init();

	// indexing related functions
	int bcf_idx_build(const char *fn);
	uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg);
	int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *end);
	bcf_idx_t *bcf_idx_load(const char *fn);
	void bcf_idx_destroy(bcf_idx_t *idx);

#ifdef __cplusplus
}
#endif

static inline uint32_t bcf_str2int(const char *str, int l)
{
	int i;
	uint32_t x = 0;
	for (i = 0; i < l && i < 4; ++i) {
		if (str[i] == 0) return x;
		x = x<<8 | str[i];
	}
	return x;
}

#endif
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/bcf.tex000066400000000000000000000101711211610345200241300ustar00rootroot00000000000000\documentclass[10pt,pdftex]{article}
\usepackage{color}
\definecolor{gray}{rgb}{0.7,0.7,0.7}

\setlength{\topmargin}{0.0cm}
\setlength{\textheight}{21.5cm}
\setlength{\oddsidemargin}{0cm} 
\setlength{\textwidth}{16.5cm}
\setlength{\columnsep}{0.6cm}

\begin{document}

\begin{center}
\begin{tabular}{|l|l|l|l|l|}
\hline
\multicolumn{2}{|c|}{\bf Field} & \multicolumn{1}{c|}{\bf Descrption} & \multicolumn{1}{c|}{\bf Type} & \multicolumn{1}{c|}{\bf Value} \\\hline\hline
\multicolumn{2}{|l|}{\sf magic} & Magic string & {\tt char[4]} & {\tt BCF\char92 4} \\\hline
\multicolumn{2}{|l|}{\sf l\_seqnm} & Length of concatenated sequence names & {\tt int32\_t} & \\\hline
\multicolumn{2}{|l|}{\sf seqnm} & Concatenated names, {\tt NULL} padded & {\tt char[{\sf l\_seqnm}]} & \\\hline
\multicolumn{2}{|l|}{\sf l\_smpl} & Length of concatenated sample names & {\tt int32\_t} & \\\hline
\multicolumn{2}{|l|}{\sf smpl} & Concatenated sample names & {\tt char[{\sf l\_smpl}]} & \\\hline
\multicolumn{2}{|l|}{\sf l\_meta} & Length of the meta text (double-hash lines)& {\tt int32\_t} & \\\hline
\multicolumn{2}{|l|}{\sf meta} & Meta text, {\tt NULL} terminated & {\tt char[{\sf l\_meta}]} & \\\hline
\multicolumn{5}{|c|}{\it \color{gray}{List of records until the end of the file}}\\\cline{2-5}
& {\sf seq\_id} & Reference sequence ID & {\tt int32\_t} & \\\cline{2-5}
& {\sf pos} & Position & {\tt int32\_t} & \\\cline{2-5}
& {\sf qual} & Variant quality & {\tt float} & \\\cline{2-5}
& {\sf l\_str} & Length of {\sf str} & {\tt int32\_t} & \\\cline{2-5}
& {\sf str} & {\tt ID+REF+ALT+FILTER+INFO+FORMAT}, {\tt NULL} padded & {\tt char[{\sf l\_str}]} &\\\cline{2-5}
& \multicolumn{4}{c|}{Blocks of data; \#blocks and formats defined by {\tt FORMAT} (table below)}\\
\hline
\end{tabular}
\end{center}

\begin{center}
\begin{tabular}{clp{9cm}}
\hline
\multicolumn{1}{l}{\bf Field} & \multicolumn{1}{l}{\bf Type} & \multicolumn{1}{l}{\bf Description} \\\hline
{\tt DP} & {\tt uint16\_t[n]} & Read depth \\
{\tt GL} & {\tt float[n*G]} & Log10 likelihood of data; $G=\frac{A(A+1)}{2}$, $A=\#\{alleles\}$\\
{\tt GT} & {\tt uint8\_t[n]} & {\tt missing\char60\char60 7 | phased\char60\char60 6 | allele1\char60\char60 3 | allele2} \\
{\tt \_GT} & {\tt uint8\_t+uint8\_t[n*P]} & {Generic GT; the first int equals the max ploidy $P$. If the highest bit is set,
	the allele is not present (e.g. due to different ploidy between samples).} \\
{\tt GQ} & {\tt uint8\_t[n]} & {Genotype quality}\\
{\tt HQ} & {\tt uint8\_t[n*2]} & {Haplotype quality}\\
{\tt \_HQ} & {\tt uint8\_t+uint8\_t[n*P]} & {Generic HQ}\\
{\tt IBD} & {\tt uint32\_t[n*2]} & {IBD}\\
{\tt \_IBD} & {\tt uint8\_t+uint32\_t[n*P]} & {Generic IBD}\\
{\tt PL} & {\tt uint8\_t[n*G]} & {Phred-scaled likelihood of data}\\
{\tt PS} & {\tt uint32\_t[n]} & {Phase set}\\
%{\tt SP} & {\tt uint8\_t[n]} & {Strand bias P-value (bcftools only)}\\
\emph{Integer} & {\tt int32\_t[n*X]} & {Fix-sized custom Integer; $X$ defined in the header}\\
\emph{Numeric} & {\tt double[n*X]} & {Fix-sized custom Numeric}\\
\emph{String} & {\tt uint32\_t+char*} & {\tt NULL} padded concat. strings (int equals to the length) \\
\hline
\end{tabular}
\end{center}

\begin{itemize}
\item A BCF file is in the {\tt BGZF} format.
\item All multi-byte numbers are little-endian.
\item In a string, a missing value `.' is an empty C string ``{\tt
    \char92 0}'' (not ``{\tt .\char92 0}'')
\item For {\tt GL} and {\tt PL}, likelihoods of genotypes appear in the
  order of alleles in {\tt REF} and then {\tt ALT}. For example, if {\tt
    REF=C}, {\tt ALT=T,A}, likelihoods appear in the order of {\tt
    CC,CT,TT,CA,TA,AA} (NB: the ordering is different from the one in the original
	BCF proposal).
\item Predefined {\tt FORMAT} fields can be missing from VCF headers, but custom {\tt FORMAT} fields
	are required to be explicitly defined in the headers.
\item A {\tt FORMAT} field with its name starting with `{\tt \_}' is specific to BCF only.
	It gives an alternative binary representation of the corresponding VCF field, in case
	the default representation is unable to keep the genotype information,
	for example, when the ploidy is not 2 or there are more than 8 alleles.
\end{itemize}

\end{document}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/bcf2qcall.c000066400000000000000000000057241211610345200246610ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include "bcf.h"

static int8_t nt4_table[256] = {
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4 /*'-'*/, 4, 4,
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
};

static int read_I16(bcf1_t *b, int anno[16])
{
	char *p;
	int i;
	if ((p = strstr(b->info, "I16=")) == 0) return -1;
	p += 4;
	for (i = 0; i < 16; ++i) {
		anno[i] = strtol(p, &p, 10);
		if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
		++p;
	}
	return 0;
}

int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b)
{
	int a[4], k, g[10], l, map[4], k1, j, i, i0, anno[16], dp, mq, d_rest;
	char *s;
	if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
	if (i == b->n_gi) return -1; // no PL
	if (read_I16(b, anno) != 0) return -1; // no I16; FIXME: can be improved
	d_rest = dp = anno[0] + anno[1] + anno[2] + anno[3];
	if (dp == 0) return -1; // depth is zero
	mq = (int)(sqrt((double)(anno[9] + anno[11]) / dp) + .499);
	i0 = i;
	a[0] = nt4_table[(int)b->ref[0]];
	if (a[0] > 3) return -1; // ref is not A/C/G/T
	a[1] = a[2] = a[3] = -2; // -1 has a special meaning
	if (b->alt[0] == 0) return -1; // no alternate allele
	map[0] = map[1] = map[2] = map[3] = -2;
	map[a[0]] = 0;
	for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) {
		if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base
		a[k+1] = nt4_table[(int)*s];
		if (a[k+1] >= 0) map[a[k+1]] = k+1;
		else k1 = k+1;
		if (s[1] == 0) break;
	}
	for (k = 0; k < 4; ++k)
		if (map[k] < 0) map[k] = k1;
	for (i = 0; i < h->n_smpl; ++i) {
		int d;
		uint8_t *p = b->gi[i0].data + i * b->gi[i0].len;
		for (j = 0; j < b->gi[i0].len; ++j)
			if (p[j]) break;
		d = (int)((double)d_rest / (h->n_smpl - i) + .499);
		if (d == 0) d = 1;
		if (j == b->gi[i0].len) d = 0;
		d_rest -= d;
		for (k = j = 0; k < 4; ++k) {
			for (l = k; l < 4; ++l) {
				int t, x = map[k], y = map[l];
				if (x > y) t = x, x = y, y = t; // swap
				g[j++] = p[y * (y+1) / 2 + x];
			}
		}
		printf("%s\t%d\t%c", h->ns[b->tid], b->pos+1, *b->ref);
		printf("\t%d\t%d\t0", d, mq);
		for (j = 0; j < 10; ++j)
			printf("\t%d", g[j]);
		printf("\t%s\n", h->sns[i]);
	}
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/bcfutils.c000066400000000000000000000237661211610345200246510ustar00rootroot00000000000000#include 
#include 
#include "bcf.h"
#include "kstring.h"
#include "khash.h"
KHASH_MAP_INIT_STR(str2id, int)

#ifdef _WIN32
#define srand48(x) srand(x)
#define drand48() ((double)rand() / RAND_MAX)
#endif

// FIXME: valgrind report a memory leak in this function. Probably it does not get deallocated...
void *bcf_build_refhash(bcf_hdr_t *h)
{
	khash_t(str2id) *hash;
	int i, ret;
	hash = kh_init(str2id);
	for (i = 0; i < h->n_ref; ++i) {
		khint_t k;
		k = kh_put(str2id, hash, h->ns[i], &ret); // FIXME: check ret
		kh_val(hash, k) = i;
	}
	return hash;
}

void *bcf_str2id_init()
{
	return kh_init(str2id);
}

void bcf_str2id_destroy(void *_hash)
{
	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
	if (hash) kh_destroy(str2id, hash); // Note that strings are not freed.
}

void bcf_str2id_thorough_destroy(void *_hash)
{
	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
	khint_t k;
	if (hash == 0) return;
	for (k = 0; k < kh_end(hash); ++k)
		if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
	kh_destroy(str2id, hash);
}

int bcf_str2id(void *_hash, const char *str)
{
	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
	khint_t k;
	if (!hash) return -1;
	k = kh_get(str2id, hash, str);
	return k == kh_end(hash)? -1 : kh_val(hash, k);
}

int bcf_str2id_add(void *_hash, const char *str)
{
	khint_t k;
	int ret;
	khash_t(str2id) *hash = (khash_t(str2id)*)_hash;
	if (!hash) return -1;
	k = kh_put(str2id, hash, str, &ret);
	if (ret == 0) return kh_val(hash, k);
	kh_val(hash, k) = kh_size(hash) - 1;
	return kh_val(hash, k);
}

int bcf_shrink_alt(bcf1_t *b, int n)
{
	char *p;
	int i, j, k, n_smpl = b->n_smpl;
	if (b->n_alleles <= n) return -1;
	// update ALT
	if (n > 1) {
		for (p = b->alt, k = 1; *p; ++p)
			if (*p == ',' && ++k == n) break;
		*p = '\0';
	} else p = b->alt, *p = '\0';
	++p;
	memmove(p, b->flt, b->str + b->l_str - b->flt);
	b->l_str -= b->flt - p;
	// update PL
	for (i = 0; i < b->n_gi; ++i) {
		bcf_ginfo_t *g = b->gi + i;
		if (g->fmt == bcf_str2int("PL", 2)) {
			int l, x = b->n_alleles * (b->n_alleles + 1) / 2;
			uint8_t *d = (uint8_t*)g->data;
			g->len = n * (n + 1) / 2;
			for (l = k = 0; l < n_smpl; ++l) {
				uint8_t *dl = d + l * x;
				for (j = 0; j < g->len; ++j) d[k++] = dl[j];
			}
		} // FIXME: to add GL
	}
	b->n_alleles = n;
	bcf_sync(b);
	return 0;
}

int bcf_gl2pl(bcf1_t *b)
{
	char *p;
	int i, n_smpl = b->n_smpl;
	bcf_ginfo_t *g;
	float *d0;
	uint8_t *d1;
	if (strstr(b->fmt, "PL")) return -1;
	if ((p = strstr(b->fmt, "GL")) == 0) return -1;
	*p = 'P';
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == bcf_str2int("GL", 2))
			break;
	g = b->gi + i;
	g->fmt = bcf_str2int("PL", 2);
	g->len /= 4; // 4 == sizeof(float)
	d0 = (float*)g->data; d1 = (uint8_t*)g->data;
	for (i = 0; i < n_smpl * g->len; ++i) {
		int x = (int)(-10. * d0[i] + .499);
		if (x > 255) x = 255;
		if (x < 0) x = 0;
		d1[i] = x;
	}
	return 0;
}
/* FIXME: this function will fail given AB:GTX:GT. BCFtools never
 * produces such FMT, but others may do. */
int bcf_fix_gt(bcf1_t *b)
{
	char *s;
	int i;
	uint32_t tmp;
	bcf_ginfo_t gt;
	// check the presence of the GT FMT
	if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first
	if (s[3] != '\0' && s[3] != ':') return 0; // :GTX in fact
	tmp = bcf_str2int("GT", 2);
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == tmp) break;
	if (i == b->n_gi) return 0; // no GT in b->gi; probably a bug...
	gt = b->gi[i];
	// move GT to the first
	for (; i > 0; --i) b->gi[i] = b->gi[i-1];
	b->gi[0] = gt;
	memmove(b->fmt + 3, b->fmt, s + 1 - b->fmt);
	b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
	return 0;
}

int bcf_fix_pl(bcf1_t *b)
{
	int i;
	uint32_t tmp;
	uint8_t *PL, *swap;
	bcf_ginfo_t *gi;
	// pinpoint PL
	tmp = bcf_str2int("PL", 2);
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == tmp) break;
	if (i == b->n_gi) return 0;
	// prepare
	gi = b->gi + i;
	PL = (uint8_t*)gi->data;
	swap = alloca(gi->len);
	// loop through individuals
	for (i = 0; i < b->n_smpl; ++i) {
		int k, l, x;
		uint8_t *PLi = PL + i * gi->len;
		memcpy(swap, PLi, gi->len);
		for (k = x = 0; k < b->n_alleles; ++k)
			for (l = k; l < b->n_alleles; ++l)
				PLi[l*(l+1)/2 + k] = swap[x++];
	}
	return 0;
}

int bcf_smpl_covered(const bcf1_t *b)
{
	int i, j, n = 0;
	uint32_t tmp;
	bcf_ginfo_t *gi;
	// pinpoint PL
	tmp = bcf_str2int("PL", 2);
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == tmp) break;
	if (i == b->n_gi) return 0;
	// count how many samples having PL!=[0..0]
	gi = b->gi + i;
	for (i = 0; i < b->n_smpl; ++i) {
		uint8_t *PLi = ((uint8_t*)gi->data) + i * gi->len;
		for (j = 0; j < gi->len; ++j)
			if (PLi[j]) break;
		if (j < gi->len) ++n;
	}
	return n;
}

static void *locate_field(const bcf1_t *b, const char *fmt, int l)
{
	int i;
	uint32_t tmp;
	tmp = bcf_str2int(fmt, l);
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == tmp) break;
	return i == b->n_gi? 0 : b->gi[i].data;
}

int bcf_anno_max(bcf1_t *b)
{
	int k, max_gq, max_sp, n_het;
	kstring_t str;
	uint8_t *gt, *gq;
	int32_t *sp;
	max_gq = max_sp = n_het = 0;
	gt = locate_field(b, "GT", 2);
	if (gt == 0) return -1;
	gq = locate_field(b, "GQ", 2);
	sp = locate_field(b, "SP", 2);
	if (sp)
		for (k = 0; k < b->n_smpl; ++k)
			if (gt[k]&0x3f)
				max_sp = max_sp > (int)sp[k]? max_sp : sp[k];
	if (gq)
		for (k = 0; k < b->n_smpl; ++k)
			if (gt[k]&0x3f)
				max_gq = max_gq > (int)gq[k]? max_gq : gq[k];
	for (k = 0; k < b->n_smpl; ++k) {
		int a1, a2;
		a1 = gt[k]&7; a2 = gt[k]>>3&7;
		if ((!a1 && a2) || (!a2 && a1)) { // a het
			if (gq == 0) ++n_het;
			else if (gq[k] >= 20) ++n_het;
		}
	}
	if (n_het) max_sp -= (int)(4.343 * log(n_het) + .499);
	if (max_sp < 0) max_sp = 0;
	memset(&str, 0, sizeof(kstring_t));
	if (*b->info) kputc(';', &str);
	ksprintf(&str, "MXSP=%d;MXGQ=%d", max_sp, max_gq);
	bcf_append_info(b, str.s, str.l);
	free(str.s);
	return 0;
}

// FIXME: only data are shuffled; the header is NOT
int bcf_shuffle(bcf1_t *b, int seed)
{
	int i, j, *a;
	if (seed > 0) srand48(seed);
	a = malloc(b->n_smpl * sizeof(int));
	for (i = 0; i < b->n_smpl; ++i) a[i] = i;
	for (i = b->n_smpl; i > 1; --i) {
		int tmp;
		j = (int)(drand48() * i);
		tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;
	}
	for (j = 0; j < b->n_gi; ++j) {
		bcf_ginfo_t *gi = b->gi + j;
		uint8_t *swap, *data = (uint8_t*)gi->data;
		swap = malloc(gi->len * b->n_smpl);
		for (i = 0; i < b->n_smpl; ++i)
			memcpy(swap + gi->len * a[i], data + gi->len * i, gi->len);
		free(gi->data);
		gi->data = swap;
	}
	free(a);
	return 0;
}

bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int *list)
{
	int i, ret, j;
	khint_t k;
	bcf_hdr_t *h;
	khash_t(str2id) *hash;
	kstring_t s;
	s.l = s.m = 0; s.s = 0;
	hash = kh_init(str2id);
	for (i = 0; i < h0->n_smpl; ++i) {
		k = kh_put(str2id, hash, h0->sns[i], &ret);
		kh_val(hash, k) = i;
	}
	for (i = j = 0; i < n; ++i) {
		k = kh_get(str2id, hash, samples[i]);
		if (k != kh_end(hash)) {
			list[j++] = kh_val(hash, k);
			kputs(samples[i], &s); kputc('\0', &s);
		}
	}
	if (j < n) fprintf(stderr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
	kh_destroy(str2id, hash);
	h = calloc(1, sizeof(bcf_hdr_t));
	*h = *h0;
	h->ns = 0; h->sns = 0;
	h->name = malloc(h->l_nm); memcpy(h->name, h0->name, h->l_nm);
	h->txt = calloc(1, h->l_txt + 1); memcpy(h->txt, h0->txt, h->l_txt);
	h->l_smpl = s.l; h->sname = s.s;
	bcf_hdr_sync(h);
	return h;
}

int bcf_subsam(int n_smpl, int *list, bcf1_t *b)
{
	int i, j;
	for (j = 0; j < b->n_gi; ++j) {
		bcf_ginfo_t *gi = b->gi + j;
		uint8_t *swap;
		swap = malloc(gi->len * b->n_smpl);
		for (i = 0; i < n_smpl; ++i)
			memcpy(swap + i * gi->len, (uint8_t*)gi->data + list[i] * gi->len, gi->len);
		free(gi->data);
		gi->data = swap;
	}
	b->n_smpl = n_smpl;
	return 0;
}

static int8_t nt4_table[128] = {
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4 /*'-'*/, 4, 4,
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4, -1, 4, 4, 4,  4, 4, 4, 4
};

int bcf_gl10(const bcf1_t *b, uint8_t *gl)
{
	int a[4], k, l, map[4], k1, j, i;
	const bcf_ginfo_t *PL;
	char *s;
	if (b->ref[1] != 0 || b->n_alleles > 4) return -1; // ref is not a single base or >4 alleles
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
	if (i == b->n_gi) return -1; // no PL
	PL = b->gi + i;
	a[0] = nt4_table[(int)b->ref[0]];
	if (a[0] > 3 || a[0] < 0) return -1; // ref is not A/C/G/T
	a[1] = a[2] = a[3] = -2; // -1 has a special meaning
	if (b->alt[0] == 0) return -1; // no alternate allele
	map[0] = map[1] = map[2] = map[3] = -2;
	map[a[0]] = 0;
	for (k = 0, s = b->alt, k1 = -1; k < 3 && *s; ++k, s += 2) {
		if (s[1] != ',' && s[1] != 0) return -1; // ALT is not single base
		a[k+1] = nt4_table[(int)*s];
		if (a[k+1] >= 0) map[a[k+1]] = k+1;
		else k1 = k + 1;
		if (s[1] == 0) break; // the end of the ALT string
	}
	for (k = 0; k < 4; ++k)
		if (map[k] < 0) map[k] = k1;
	for (i = 0; i < b->n_smpl; ++i) {
		const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
		uint8_t *g = gl + 10 * i;
		for (k = j = 0; k < 4; ++k) {
			for (l = k; l < 4; ++l) {
				int t, x = map[k], y = map[l];
				if (x > y) t = x, x = y, y = t; // make sure x is the smaller
				g[j++] = p[y * (y+1) / 2 + x];
			}
		}
	}
	return 0;
}

int bcf_gl10_indel(const bcf1_t *b, uint8_t *gl)
{
	int k, l, j, i;
	const bcf_ginfo_t *PL;
	if (b->alt[0] == 0) return -1; // no alternate allele
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
	if (i == b->n_gi) return -1; // no PL
	PL = b->gi + i;
	for (i = 0; i < b->n_smpl; ++i) {
		const uint8_t *p = PL->data + i * PL->len; // the PL for the i-th individual
		uint8_t *g = gl + 10 * i;
		for (k = j = 0; k < 4; ++k) {
			for (l = k; l < 4; ++l) {
				int t, x = k, y = l;
				if (x > y) t = x, x = y, y = t; // make sure x is the smaller
				x = y * (y+1) / 2 + x;
				g[j++] = x < PL->len? p[x] : 255;
			}
		}
	}
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/call1.c000066400000000000000000000556121211610345200240250ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include "bcf.h"
#include "prob1.h"
#include "kstring.h"
#include "time.h"

#ifdef _WIN32
#define srand48(x) srand(x)
#define lrand48() rand()
#endif

#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)

#define VC_NO_GENO 2
#define VC_BCFOUT  4
#define VC_CALL    8
#define VC_VARONLY 16
#define VC_VCFIN   32
#define VC_UNCOMP  64
#define VC_KEEPALT 256
#define VC_ACGT_ONLY 512
#define VC_QCALL   1024
#define VC_CALL_GT 2048
#define VC_ADJLD   4096
#define VC_NO_INDEL 8192
#define VC_ANNO_MAX 16384
#define VC_FIX_PL   32768
#define VC_EM       0x10000
#define VC_PAIRCALL 0x20000
#define VC_QCNT     0x40000

typedef struct {
	int flag, prior_type, n1, n_sub, *sublist, n_perm;
	uint32_t *trio_aux;
	char *prior_file, **subsam, *fn_dict;
	uint8_t *ploidy;
	double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
	void *bed;
} viewconf_t;

void *bed_read(const char *fn);
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);

typedef struct {
	double p[4];
	int mq, depth, is_tested, d[4];
} anno16_t;

static double ttest(int n1, int n2, int a[4])
{
	extern double kf_betai(double a, double b, double x);
	double t, v, u1, u2;
	if (n1 == 0 || n2 == 0 || n1 + n2 < 3) return 1.0;
	u1 = (double)a[0] / n1; u2 = (double)a[2] / n2;
	if (u1 <= u2) return 1.;
	t = (u1 - u2) / sqrt(((a[1] - n1 * u1 * u1) + (a[3] - n2 * u2 * u2)) / (n1 + n2 - 2) * (1./n1 + 1./n2));
	v = n1 + n2 - 2;
//	printf("%d,%d,%d,%d,%lf,%lf,%lf\n", a[0], a[1], a[2], a[3], t, u1, u2);
	return t < 0.? 1. : .5 * kf_betai(.5*v, .5, v/(v+t*t));
}

static int test16_core(int anno[16], anno16_t *a)
{
	extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
	double left, right;
	int i;
	a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
	memcpy(a->d, anno, 4 * sizeof(int));
	a->depth = anno[0] + anno[1] + anno[2] + anno[3];
	a->is_tested = (anno[0] + anno[1] > 0 && anno[2] + anno[3] > 0);
	if (a->depth == 0) return -1;
	a->mq = (int)(sqrt((anno[9] + anno[11]) / a->depth) + .499);
	kt_fisher_exact(anno[0], anno[1], anno[2], anno[3], &left, &right, &a->p[0]);
	for (i = 1; i < 4; ++i)
		a->p[i] = ttest(anno[0] + anno[1], anno[2] + anno[3], anno+4*i);
	return 0;
}

static int test16(bcf1_t *b, anno16_t *a)
{
	char *p;
	int i, anno[16];
	a->p[0] = a->p[1] = a->p[2] = a->p[3] = 1.;
	a->d[0] = a->d[1] = a->d[2] = a->d[3] = 0.;
	a->mq = a->depth = a->is_tested = 0;
	if ((p = strstr(b->info, "I16=")) == 0) return -1;
	p += 4;
	for (i = 0; i < 16; ++i) {
		errno = 0; anno[i] = strtol(p, &p, 10);
		if (anno[i] == 0 && (errno == EINVAL || errno == ERANGE)) return -2;
		++p;
	}
	return test16_core(anno, a);
}

static void rm_info(bcf1_t *b, const char *key)
{
	char *p, *q;
	if ((p = strstr(b->info, key)) == 0) return;
	for (q = p; *q && *q != ';'; ++q);
	if (p > b->info && *(p-1) == ';') --p;
	memmove(p, q, b->l_str - (q - b->str));
	b->l_str -= q - p;
	bcf_sync(b);
}

static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[10], int cons_llr, int64_t cons_gt)
{
	kstring_t s;
	int has_I16, is_var;
	double fq, r;
	anno16_t a;

	has_I16 = test16(b, &a) >= 0? 1 : 0;
	rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!

	memset(&s, 0, sizeof(kstring_t));
	kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
	kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
	kputs(b->info, &s);
	if (b->info[0]) kputc(';', &s);
	{ // print EM
		if (em[0] >= 0) ksprintf(&s, "AF1=%.4g", 1 - em[0]);
		if (em[4] >= 0 && em[4] <= 0.05) ksprintf(&s, ";G3=%.4g,%.4g,%.4g;HWE=%.3g", em[3], em[2], em[1], em[4]);
		if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
		if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
		if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
	}
	if (cons_llr > 0) {
		ksprintf(&s, ";CLR=%d", cons_llr);
		if (cons_gt > 0)
			ksprintf(&s, ";UGT=%c%c%c;CGT=%c%c%c", cons_gt&0xff, cons_gt>>8&0xff, cons_gt>>16&0xff,
				     cons_gt>>32&0xff, cons_gt>>40&0xff, cons_gt>>48&0xff);
	}
	if (pr == 0) { // if pr is unset, return
		kputc('\0', &s); kputs(b->fmt, &s); kputc('\0', &s);
		free(b->str);
		b->m_str = s.m; b->l_str = s.l; b->str = s.s;
		bcf_sync(b);
		return 1;
	}

	is_var = (pr->p_ref < pref);
	r = is_var? pr->p_ref : pr->p_var;

//	ksprintf(&s, ";CI95=%.4g,%.4g", pr->cil, pr->cih); // FIXME: when EM is not used, ";" should be omitted!
	ksprintf(&s, ";AC1=%d", pr->ac);
	if (has_I16) ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
	fq = pr->p_ref_folded < 0.5? -4.343 * log(pr->p_ref_folded) : 4.343 * log(pr->p_var_folded);
	if (fq < -999) fq = -999;
	if (fq > 999) fq = 999;
	ksprintf(&s, ";FQ=%.3g", fq);
	if (pr->cmp[0] >= 0.) { // two sample groups
		int i, q[3];
		for (i = 1; i < 3; ++i) {
			double x = pr->cmp[i] + pr->cmp[0]/2.;
			q[i] = x == 0? 255 : (int)(-4.343 * log(x) + .499);
			if (q[i] > 255) q[i] = 255;
		}
		if (pr->perm_rank >= 0) ksprintf(&s, ";PR=%d", pr->perm_rank);
		// ksprintf(&s, ";LRT3=%.3g", pr->lrt);
		ksprintf(&s, ";PCHI2=%.3g;PC2=%d,%d", q[1], q[2], pr->p_chi2);
	}
	if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
	kputc('\0', &s);
	kputs(b->fmt, &s); kputc('\0', &s);
	free(b->str);
	b->m_str = s.m; b->l_str = s.l; b->str = s.s;
	b->qual = r < 1e-100? 999 : -4.343 * log(r);
	if (b->qual > 999) b->qual = 999;
	bcf_sync(b);
	if (!is_var) bcf_shrink_alt(b, 1);
	else if (!(flag&VC_KEEPALT))
		bcf_shrink_alt(b, pr->rank0 < 2? 2 : pr->rank0+1);
	if (is_var && (flag&VC_CALL_GT)) { // call individual genotype
		int i, x, old_n_gi = b->n_gi;
		s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
		kputs(":GT:GQ", &s); kputc('\0', &s);
		b->m_str = s.m; b->l_str = s.l; b->str = s.s;
		bcf_sync(b);
		for (i = 0; i < b->n_smpl; ++i) {
			x = bcf_p1_call_gt(pa, pr->f_exp, i);
			((uint8_t*)b->gi[old_n_gi].data)[i] = (x&3) == 0? 1<<3|1 : (x&3) == 1? 1 : 0;
			((uint8_t*)b->gi[old_n_gi+1].data)[i] = x>>2;
		}
	}
	return is_var;
}

static char **read_samples(const char *fn, int *_n)
{
	gzFile fp;
	kstream_t *ks;
	kstring_t s;
	int dret, n = 0, max = 0;
	char **sam = 0;
	*_n = 0;
	s.l = s.m = 0; s.s = 0;
	fp = gzopen(fn, "r");
	if (fp == 0) return 0; // fail to open file
	ks = ks_init(fp);
	while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
		int l;
		if (max == n) {
			max = max? max<<1 : 4;
			sam = realloc(sam, sizeof(void*)*max);
		}
		l = s.l;
		sam[n] = malloc(s.l + 2);
		strcpy(sam[n], s.s);
		sam[n][l+1] = 2; // by default, diploid
		if (dret != '\n') {
			if (ks_getuntil(ks, 0, &s, &dret) >= 0) { // read ploidy, 1 or 2
				int x = (int)s.s[0] - '0';
				if (x == 1 || x == 2) sam[n][l+1] = x;
				else fprintf(stderr, "(%s) ploidy can only be 1 or 2; assume diploid\n", __func__);
			}
			if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
		}
		++n;
	}
	ks_destroy(ks);
	gzclose(fp);
	free(s.s);
	*_n = n;
	return sam;
}

static void write_header(bcf_hdr_t *h)
{
	kstring_t str;
	str.l = h->l_txt? h->l_txt - 1 : 0;
	str.m = str.l + 1; str.s = h->txt;
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
//	if (!strstr(str.s, "##INFO=\n", &str);
	if (!strstr(str.s, "##INFO=\n", &str);
    if (!strstr(str.s, "##INFO=\n", &str);
    if (!strstr(str.s, "##INFO=\n", &str);
    if (!strstr(str.s, "##INFO=\n", &str);
    if (!strstr(str.s, "##INFO=\n", &str);
    if (!strstr(str.s, "##INFO=\n", &str);
    if (!strstr(str.s, "##INFO=\n", &str);
    if (!strstr(str.s, "##FORMAT=\n", &str);
    if (!strstr(str.s, "##FORMAT=\n", &str);
    if (!strstr(str.s, "##FORMAT=\n", &str);
	if (!strstr(str.s, "##FORMAT=\n", &str);
	if (!strstr(str.s, "##FORMAT=\n", &str);
	if (!strstr(str.s, "##FORMAT=\n", &str);
	h->l_txt = str.l + 1; h->txt = str.s;
}

double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);

int bcfview(int argc, char *argv[])
{
	extern int bcf_2qcall(bcf_hdr_t *h, bcf1_t *b);
	extern void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x);
	extern int bcf_fix_gt(bcf1_t *b);
	extern int bcf_anno_max(bcf1_t *b);
	extern int bcf_shuffle(bcf1_t *b, int seed);
	extern uint32_t *bcf_trio_prep(int is_x, int is_son);
	extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
	extern int bcf_pair_call(const bcf1_t *b);
	extern int bcf_min_diff(const bcf1_t *b);

	bcf_t *bp, *bout = 0;
	bcf1_t *b, *blast;
	int c, *seeds = 0;
	uint64_t n_processed = 0, qcnt[256];
	viewconf_t vc;
	bcf_p1aux_t *p1 = 0;
	bcf_hdr_t *hin, *hout;
	int tid, begin, end;
	char moder[4], modew[4];

	tid = begin = end = -1;
	memset(&vc, 0, sizeof(viewconf_t));
	vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1;
	memset(qcnt, 0, 8 * 256);
	while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Y")) >= 0) {
		switch (c) {
		case '1': vc.n1 = atoi(optarg); break;
		case 'l': vc.bed = bed_read(optarg); break;
		case 'D': vc.fn_dict = strdup(optarg); break;
		case 'F': vc.flag |= VC_FIX_PL; break;
		case 'N': vc.flag |= VC_ACGT_ONLY; break;
		case 'G': vc.flag |= VC_NO_GENO; break;
		case 'A': vc.flag |= VC_KEEPALT; break;
		case 'b': vc.flag |= VC_BCFOUT; break;
		case 'S': vc.flag |= VC_VCFIN; break;
		case 'c': vc.flag |= VC_CALL; break;
		case 'e': vc.flag |= VC_EM; break;
		case 'v': vc.flag |= VC_VARONLY | VC_CALL; break;
		case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
		case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
		case 'I': vc.flag |= VC_NO_INDEL; break;
		case 'M': vc.flag |= VC_ANNO_MAX; break;
		case 'Y': vc.flag |= VC_QCNT; break;
		case 't': vc.theta = atof(optarg); break;
		case 'p': vc.pref = atof(optarg); break;
		case 'i': vc.indel_frac = atof(optarg); break;
		case 'Q': vc.flag |= VC_QCALL; break;
		case 'L': vc.flag |= VC_ADJLD; break;
		case 'U': vc.n_perm = atoi(optarg); break;
		case 'C': vc.min_lrt = atof(optarg); break;
		case 'X': vc.min_perm_p = atof(optarg); break;
		case 'd': vc.min_smpl_frac = atof(optarg); break;
		case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
			vc.ploidy = calloc(vc.n_sub + 1, 1);
			for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
			tid = -1;
			break;
		case 'T':
			if (strcmp(optarg, "trioauto") == 0) vc.trio_aux = bcf_trio_prep(0, 0);
			else if (strcmp(optarg, "trioxd") == 0) vc.trio_aux = bcf_trio_prep(1, 0);
			else if (strcmp(optarg, "trioxs") == 0) vc.trio_aux = bcf_trio_prep(1, 1);
			else if (strcmp(optarg, "pair") == 0) vc.flag |= VC_PAIRCALL;
			else {
				fprintf(stderr, "[%s] Option '-T' can only take value trioauto, trioxd or trioxs.\n", __func__);
				return 1;
			}
			break;
		case 'P':
			if (strcmp(optarg, "full") == 0) vc.prior_type = MC_PTYPE_FULL;
			else if (strcmp(optarg, "cond2") == 0) vc.prior_type = MC_PTYPE_COND2;
			else if (strcmp(optarg, "flat") == 0) vc.prior_type = MC_PTYPE_FLAT;
			else vc.prior_file = strdup(optarg);
			break;
		}
	}
	if (argc == optind) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage: bcftools view [options]  [reg]\n\n");
		fprintf(stderr, "Input/output options:\n\n");
		fprintf(stderr, "       -A        keep all possible alternate alleles at variant sites\n");
		fprintf(stderr, "       -b        output BCF instead of VCF\n");
		fprintf(stderr, "       -D FILE   sequence dictionary for VCF->BCF conversion [null]\n");
		fprintf(stderr, "       -F        PL generated by r921 or before (which generate old ordering)\n");
		fprintf(stderr, "       -G        suppress all individual genotype information\n");
		fprintf(stderr, "       -l FILE   list of sites (chr pos) or regions (BED) to output [all sites]\n");
		fprintf(stderr, "       -L        calculate LD for adjacent sites\n");
		fprintf(stderr, "       -N        skip sites where REF is not A/C/G/T\n");
		fprintf(stderr, "       -Q        output the QCALL likelihood format\n");
		fprintf(stderr, "       -s FILE   list of samples to use [all samples]\n");
		fprintf(stderr, "       -S        input is VCF\n");
		fprintf(stderr, "       -u        uncompressed BCF output (force -b)\n");
		fprintf(stderr, "\nConsensus/variant calling options:\n\n");
		fprintf(stderr, "       -c        SNP calling (force -e)\n");
		fprintf(stderr, "       -d FLOAT  skip loci where less than FLOAT fraction of samples covered [0]\n");
		fprintf(stderr, "       -e        likelihood based analyses\n");
		fprintf(stderr, "       -g        call genotypes at variant sites (force -c)\n");
		fprintf(stderr, "       -i FLOAT  indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
		fprintf(stderr, "       -I        skip indels\n");
		fprintf(stderr, "       -p FLOAT  variant if P(ref|D)BCF conversion please specify the sequence dictionary with -D\n", __func__);
		return 1;
	}
	if (vc.n1 <= 0) vc.n_perm = 0; // TODO: give a warning here!
	if (vc.n_perm > 0) {
		seeds = malloc(vc.n_perm * sizeof(int));
		srand48(time(0));
		for (c = 0; c < vc.n_perm; ++c) seeds[c] = lrand48();
	}
	b = calloc(1, sizeof(bcf1_t));
	blast = calloc(1, sizeof(bcf1_t));
	strcpy(moder, "r");
	if (!(vc.flag & VC_VCFIN)) strcat(moder, "b");
	strcpy(modew, "w");
	if (vc.flag & VC_BCFOUT) strcat(modew, "b");
	if (vc.flag & VC_UNCOMP) strcat(modew, "u");
	bp = vcf_open(argv[optind], moder);
	hin = hout = vcf_hdr_read(bp);
	if (vc.fn_dict && (vc.flag & VC_VCFIN))
		vcf_dictread(bp, hin, vc.fn_dict);
	bout = vcf_open("-", modew);
	if (!(vc.flag & VC_QCALL)) {
		if (vc.n_sub) {
			vc.sublist = calloc(vc.n_sub, sizeof(int));
			hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
		}
		if (vc.flag & VC_CALL) write_header(hout);
		vcf_hdr_write(bout, hout);
	}
	if (vc.flag & VC_CALL) {
		p1 = bcf_p1_init(hout->n_smpl, vc.ploidy);
		if (vc.prior_file) {
			if (bcf_p1_read_prior(p1, vc.prior_file) < 0) {
				fprintf(stderr, "[%s] fail to read the prior AFS.\n", __func__);
				return 1;
			}
		} else bcf_p1_init_prior(p1, vc.prior_type, vc.theta);
		if (vc.n1 > 0 && vc.min_lrt > 0.) { // set n1
			bcf_p1_set_n1(p1, vc.n1);
			bcf_p1_init_subprior(p1, vc.prior_type, vc.theta);
		}
		if (vc.indel_frac > 0.) bcf_p1_indel_prior(p1, vc.indel_frac); // otherwise use the default indel_frac
	}
	if (optind + 1 < argc && !(vc.flag&VC_VCFIN)) {
		void *str2id = bcf_build_refhash(hout);
		if (bcf_parse_region(str2id, argv[optind+1], &tid, &begin, &end) >= 0) {
			bcf_idx_t *idx;
			idx = bcf_idx_load(argv[optind]);
			if (idx) {
				uint64_t off;
				off = bcf_idx_query(idx, tid, begin);
				if (off == 0) {
					fprintf(stderr, "[%s] no records in the query region.\n", __func__);
					return 1; // FIXME: a lot of memory leaks...
				}
				bgzf_seek(bp->fp, off, SEEK_SET);
				bcf_idx_destroy(idx);
			}
		}
	}
	while (vcf_read(bp, hin, b) > 0) {
		int is_indel, cons_llr = -1;
		int64_t cons_gt = -1;
		double em[10];
		if ((vc.flag & VC_VARONLY) && strcmp(b->alt, "X") == 0) continue;
		if ((vc.flag & VC_VARONLY) && vc.min_smpl_frac > 0.) {
			extern int bcf_smpl_covered(const bcf1_t *b);
			int n = bcf_smpl_covered(b);
			if ((double)n / b->n_smpl < vc.min_smpl_frac) continue;
		}
		if (vc.n_sub) bcf_subsam(vc.n_sub, vc.sublist, b);
		if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
		is_indel = bcf_is_indel(b);
		if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
		if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
			int x;
			if (b->ref[0] == 0 || b->ref[1] != 0) continue;
			x = toupper(b->ref[0]);
			if (x != 'A' && x != 'C' && x != 'G' && x != 'T') continue;
		}
		if (vc.bed && !bed_overlap(vc.bed, hin->ns[b->tid], b->pos, b->pos + strlen(b->ref))) continue;
		if (tid >= 0) {
			int l = strlen(b->ref);
			l = b->pos + (l > 0? l : 1);
			if (b->tid != tid || b->pos >= end) break;
			if (!(l > begin && end > b->pos)) continue;
		}
		++n_processed;
		if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference
			int x = bcf_min_diff(b);
			if (x > 255) x = 255;
			if (x >= 0) ++qcnt[x];
		}
		if (vc.flag & VC_QCALL) { // output QCALL format; STOP here
			bcf_2qcall(hout, b);
			continue;
		}
		if (vc.trio_aux) // do trio calling
			bcf_trio_call(vc.trio_aux, b, &cons_llr, &cons_gt);
		else if (vc.flag & VC_PAIRCALL)
			cons_llr = bcf_pair_call(b);
		if (vc.flag & (VC_CALL|VC_ADJLD|VC_EM)) bcf_gl2pl(b);
		if (vc.flag & VC_EM) bcf_em1(b, vc.n1, 0x1ff, em);
		else {
			int i;
			for (i = 0; i < 9; ++i) em[i] = -1.;
		}
		if (vc.flag & VC_CALL) { // call variants
			bcf_p1rst_t pr;
			int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
			if (n_processed % 100000 == 0) {
				fprintf(stderr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
				bcf_p1_dump_afs(p1);
			}
			if (pr.p_ref >= vc.pref && (vc.flag & VC_VARONLY)) continue;
			if (vc.n_perm && vc.n1 > 0 && pr.p_chi2 < vc.min_perm_p) { // permutation test
				bcf_p1rst_t r;
				int i, n = 0;
				for (i = 0; i < vc.n_perm; ++i) {
#ifdef BCF_PERM_LRT // LRT based permutation is much faster but less robust to artifacts
					double x[10];
					bcf_shuffle(b, seeds[i]);
					bcf_em1(b, vc.n1, 1<<7, x);
					if (x[7] < em[7]) ++n;
#else
					bcf_shuffle(b, seeds[i]);
					bcf_p1_cal(b, 1, p1, &r);
					if (pr.p_chi2 >= r.p_chi2) ++n;
#endif
				}
				pr.perm_rank = n;
			}
			if (calret >= 0) update_bcf1(b, p1, &pr, vc.pref, vc.flag, em, cons_llr, cons_gt);
		} else if (vc.flag & VC_EM) update_bcf1(b, 0, 0, 0, vc.flag, em, cons_llr, cons_gt);
		if (vc.flag & VC_ADJLD) { // compute LD
			double f[4], r2;
			if ((r2 = bcf_pair_freq(blast, b, f)) >= 0) {
				kstring_t s;
				s.m = s.l = 0; s.s = 0;
				if (*b->info) kputc(';', &s);
				ksprintf(&s, "NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3f", r2, f[0], f[1], f[2], f[3]);
				bcf_append_info(b, s.s, s.l);
				free(s.s);
			}
			bcf_cpy(blast, b);
		}
		if (vc.flag & VC_ANNO_MAX) bcf_anno_max(b);
		if (vc.flag & VC_NO_GENO) { // do not output GENO fields
			b->n_gi = 0;
			b->fmt[0] = '\0';
			b->l_str = b->fmt - b->str + 1;
		} else bcf_fix_gt(b);
		vcf_write(bout, hout, b);
	}
	if (vc.prior_file) free(vc.prior_file);
	if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
	if (hin != hout) bcf_hdr_destroy(hout);
	bcf_hdr_destroy(hin);
	bcf_destroy(b); bcf_destroy(blast);
	vcf_close(bp); vcf_close(bout);
	if (vc.fn_dict) free(vc.fn_dict);
	if (vc.ploidy) free(vc.ploidy);
	if (vc.trio_aux) free(vc.trio_aux);
	if (vc.n_sub) {
		int i;
		for (i = 0; i < vc.n_sub; ++i) free(vc.subsam[i]);
		free(vc.subsam); free(vc.sublist);
	}
	if (vc.bed) bed_destroy(vc.bed);
	if (vc.flag & VC_QCNT)
		for (c = 0; c < 256; ++c)
			fprintf(stderr, "QT\t%d\t%lld\n", c, (long long)qcnt[c]);
	if (seeds) free(seeds);
	if (p1) bcf_p1_destroy(p1);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/em.c000066400000000000000000000214311211610345200234220ustar00rootroot00000000000000#include 
#include 
#include 
#include "bcf.h"
#include "kmin.h"

static double g_q2p[256];

#define ITER_MAX 50
#define ITER_TRY 10
#define EPS 1e-5

extern double kf_gammaq(double, double);

/*
	Generic routines
 */
// get the 3 genotype likelihoods
static double *get_pdg3(const bcf1_t *b)
{
	double *pdg;
	const uint8_t *PL = 0;
	int i, PL_len = 0;
	// initialize g_q2p if necessary
	if (g_q2p[0] == 0.)
		for (i = 0; i < 256; ++i)
			g_q2p[i] = pow(10., -i / 10.);
	// set PL and PL_len
	for (i = 0; i < b->n_gi; ++i) {
		if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
			PL = (const uint8_t*)b->gi[i].data;
			PL_len = b->gi[i].len;
			break;
		}
	}
	if (i == b->n_gi) return 0; // no PL
	// fill pdg
	pdg = malloc(3 * b->n_smpl * sizeof(double));
	for (i = 0; i < b->n_smpl; ++i) {
		const uint8_t *pi = PL + i * PL_len;
		double *p = pdg + i * 3;
		p[0] = g_q2p[pi[2]]; p[1] = g_q2p[pi[1]]; p[2] = g_q2p[pi[0]];
	}
	return pdg;
}

// estimate site allele frequency in a very naive and inaccurate way
static double est_freq(int n, const double *pdg)
{
	int i, gcnt[3], tmp1;
	// get a rough estimate of the genotype frequency
	gcnt[0] = gcnt[1] = gcnt[2] = 0;
	for (i = 0; i < n; ++i) {
		const double *p = pdg + i * 3;
		if (p[0] != 1. || p[1] != 1. || p[2] != 1.) {
			int which = p[0] > p[1]? 0 : 1;
			which = p[which] > p[2]? which : 2;
			++gcnt[which];
		}
	}
	tmp1 = gcnt[0] + gcnt[1] + gcnt[2];
	return (tmp1 == 0)? -1.0 : (.5 * gcnt[1] + gcnt[2]) / tmp1;
}

/*
	Single-locus EM
 */

typedef struct {
	int beg, end;
	const double *pdg;
} minaux1_t;

static double prob1(double f, void *data)
{
	minaux1_t *a = (minaux1_t*)data;
	double p = 1., l = 0., f3[3];
	int i;
//	printf("brent %lg\n", f);
	if (f < 0 || f > 1) return 1e300;
	f3[0] = (1.-f)*(1.-f); f3[1] = 2.*f*(1.-f); f3[2] = f*f;
	for (i = a->beg; i < a->end; ++i) {
		const double *pdg = a->pdg + i * 3;
		p *= pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2];
		if (p < 1e-200) l -= log(p), p = 1.;
	}
	return l - log(p);
}

// one EM iteration for allele frequency estimate
static double freq_iter(double *f, const double *_pdg, int beg, int end)
{
	double f0 = *f, f3[3], err;
	int i;
//	printf("em %lg\n", *f);
	f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
	for (i = beg, f0 = 0.; i < end; ++i) {
		const double *pdg = _pdg + i * 3;
		f0 += (pdg[1] * f3[1] + 2. * pdg[2] * f3[2])
			/ (pdg[0] * f3[0] + pdg[1] * f3[1] + pdg[2] * f3[2]);
	}
	f0 /= (end - beg) * 2;
	err = fabs(f0 - *f);
	*f = f0;
	return err;
}

/* The following function combines EM and Brent's method. When the signal from
 * the data is strong, EM is faster but sometimes, EM may converge very slowly.
 * When this happens, we switch to Brent's method. The idea is learned from
 * Rasmus Nielsen.
 */
static double freqml(double f0, int beg, int end, const double *pdg)
{
	int i;
	double f;
	for (i = 0, f = f0; i < ITER_TRY; ++i)
		if (freq_iter(&f, pdg, beg, end) < EPS) break;
	if (i == ITER_TRY) { // haven't converged yet; try Brent's method
		minaux1_t a;
		a.beg = beg; a.end = end; a.pdg = pdg;
		kmin_brent(prob1, f0 == f? .5*f0 : f0, f, (void*)&a, EPS, &f);
	}
	return f;
}

// one EM iteration for genotype frequency estimate
static double g3_iter(double g[3], const double *_pdg, int beg, int end)
{
	double err, gg[3];
	int i;
	gg[0] = gg[1] = gg[2] = 0.;
//	printf("%lg,%lg,%lg\n", g[0], g[1], g[2]);
	for (i = beg; i < end; ++i) {
		double sum, tmp[3];
		const double *pdg = _pdg + i * 3;
		tmp[0] = pdg[0] * g[0]; tmp[1] = pdg[1] * g[1]; tmp[2] = pdg[2] * g[2];
		sum = (tmp[0] + tmp[1] + tmp[2]) * (end - beg);
		gg[0] += tmp[0] / sum; gg[1] += tmp[1] / sum; gg[2] += tmp[2] / sum;
	}
	err = fabs(gg[0] - g[0]) > fabs(gg[1] - g[1])? fabs(gg[0] - g[0]) : fabs(gg[1] - g[1]);
	err = err > fabs(gg[2] - g[2])? err : fabs(gg[2] - g[2]);
	g[0] = gg[0]; g[1] = gg[1]; g[2] = gg[2];
	return err;
}

// perform likelihood ratio test
static double lk_ratio_test(int n, int n1, const double *pdg, double f3[3][3])
{
	double r;
	int i;
	for (i = 0, r = 1.; i < n1; ++i) {
		const double *p = pdg + i * 3;
		r *= (p[0] * f3[1][0] + p[1] * f3[1][1] + p[2] * f3[1][2])
			/ (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
	}
	for (; i < n; ++i) {
		const double *p = pdg + i * 3;
		r *= (p[0] * f3[2][0] + p[1] * f3[2][1] + p[2] * f3[2][2])
			/ (p[0] * f3[0][0] + p[1] * f3[0][1] + p[2] * f3[0][2]);
	}
	return r;
}

// x[0]: ref frequency
// x[1..3]: alt-alt, alt-ref, ref-ref frequenc
// x[4]: HWE P-value
// x[5..6]: group1 freq, group2 freq
// x[7]: 1-degree P-value
// x[8]: 2-degree P-value
int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10])
{
	double *pdg;
	int i, n, n2;
	if (b->n_alleles < 2) return -1; // one allele only
	// initialization
	if (n1 < 0 || n1 > b->n_smpl) n1 = 0;
	if (flag & 1<<7) flag |= 7<<5; // compute group freq if LRT is required
	if (flag & 0xf<<1) flag |= 0xf<<1;
	n = b->n_smpl; n2 = n - n1;
	pdg = get_pdg3(b);
	if (pdg == 0) return -1;
	for (i = 0; i < 10; ++i) x[i] = -1.; // set to negative
	{
		if ((x[0] = est_freq(n, pdg)) < 0.) {
			free(pdg);
			return -1; // no data
		}
		x[0] = freqml(x[0], 0, n, pdg);
	}
	if (flag & (0xf<<1|3<<8)) { // estimate the genotype frequency and test HWE
		double *g = x + 1, f3[3], r;
		f3[0] = g[0] = (1 - x[0]) * (1 - x[0]);
		f3[1] = g[1] = 2 * x[0] * (1 - x[0]);
		f3[2] = g[2] = x[0] * x[0];
		for (i = 0; i < ITER_MAX; ++i)
			if (g3_iter(g, pdg, 0, n) < EPS) break;
		// Hardy-Weinberg equilibrium (HWE)
		for (i = 0, r = 1.; i < n; ++i) {
			double *p = pdg + i * 3;
			r *= (p[0] * g[0] + p[1] * g[1] + p[2] * g[2]) / (p[0] * f3[0] + p[1] * f3[1] + p[2] * f3[2]);
		}
		x[4] = kf_gammaq(.5, log(r));
	}
	if ((flag & 7<<5) && n1 > 0 && n1 < n) { // group frequency
		x[5] = freqml(x[0], 0, n1, pdg);
		x[6] = freqml(x[0], n1, n, pdg);
	}
	if ((flag & 1<<7) && n1 > 0 && n1 < n) { // 1-degree P-value
		double f[3], f3[3][3], tmp;
		f[0] = x[0]; f[1] = x[5]; f[2] = x[6];
		for (i = 0; i < 3; ++i)
			f3[i][0] = (1-f[i])*(1-f[i]), f3[i][1] = 2*f[i]*(1-f[i]), f3[i][2] = f[i]*f[i];
		tmp = log(lk_ratio_test(n, n1, pdg, f3));
		if (tmp < 0) tmp = 0;
		x[7] = kf_gammaq(.5, tmp);
	}
	if ((flag & 3<<8) && n1 > 0 && n1 < n) { // 2-degree P-value
		double g[3][3], tmp;
		for (i = 0; i < 3; ++i) memcpy(g[i], x + 1, 3 * sizeof(double));
		for (i = 0; i < ITER_MAX; ++i)
			if (g3_iter(g[1], pdg, 0, n1) < EPS) break;
		for (i = 0; i < ITER_MAX; ++i)
			if (g3_iter(g[2], pdg, n1, n) < EPS) break;
		tmp = log(lk_ratio_test(n, n1, pdg, g));
		if (tmp < 0) tmp = 0;
		x[8] = kf_gammaq(1., tmp);
	}
	// free
	free(pdg);
	return 0;
}

/*
	Two-locus EM (LD)
 */

#define _G1(h, k) ((h>>1&1) + (k>>1&1))
#define _G2(h, k) ((h&1) + (k&1))

// 0: the previous site; 1: the current site
static int pair_freq_iter(int n, double *pdg[2], double f[4])
{
	double ff[4];
	int i, k, h;
//	printf("%lf,%lf,%lf,%lf\n", f[0], f[1], f[2], f[3]);
	memset(ff, 0, 4 * sizeof(double));
	for (i = 0; i < n; ++i) {
		double *p[2], sum, tmp;
		p[0] = pdg[0] + i * 3; p[1] = pdg[1] + i * 3;
		for (k = 0, sum = 0.; k < 4; ++k)
			for (h = 0; h < 4; ++h)
				sum += f[k] * f[h] * p[0][_G1(k,h)] * p[1][_G2(k,h)];
		for (k = 0; k < 4; ++k) {
			tmp = f[0] * (p[0][_G1(0,k)] * p[1][_G2(0,k)] + p[0][_G1(k,0)] * p[1][_G2(k,0)])
				+ f[1] * (p[0][_G1(1,k)] * p[1][_G2(1,k)] + p[0][_G1(k,1)] * p[1][_G2(k,1)])
				+ f[2] * (p[0][_G1(2,k)] * p[1][_G2(2,k)] + p[0][_G1(k,2)] * p[1][_G2(k,2)])
				+ f[3] * (p[0][_G1(3,k)] * p[1][_G2(3,k)] + p[0][_G1(k,3)] * p[1][_G2(k,3)]);
			ff[k] += f[k] * tmp / sum;
		}
	}
	for (k = 0; k < 4; ++k) f[k] = ff[k] / (2 * n);
	return 0;
}

double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4])
{
	const bcf1_t *b[2];
	int i, j, n_smpl;
	double *pdg[2], flast[4], r, f0[2];
	// initialize others
	if (b0->n_smpl != b1->n_smpl) return -1; // different number of samples
	n_smpl = b0->n_smpl;
	b[0] = b0; b[1] = b1;
	f[0] = f[1] = f[2] = f[3] = -1.;
	if (b[0]->n_alleles < 2 || b[1]->n_alleles < 2) return -1; // one allele only
	pdg[0] = get_pdg3(b0); pdg[1] = get_pdg3(b1);
	if (pdg[0] == 0 || pdg[1] == 0) {
		free(pdg[0]); free(pdg[1]);
		return -1;
	}
	// set the initial value
	f0[0] = est_freq(n_smpl, pdg[0]);
	f0[1] = est_freq(n_smpl, pdg[1]);
	f[0] = (1 - f0[0]) * (1 - f0[1]); f[3] = f0[0] * f0[1];
	f[1] = (1 - f0[0]) * f0[1]; f[2] = f0[0] * (1 - f0[1]);
	// iteration
	for (j = 0; j < ITER_MAX; ++j) {
		double eps = 0;
		memcpy(flast, f, 4 * sizeof(double));
		pair_freq_iter(n_smpl, pdg, f);
		for (i = 0; i < 4; ++i) {
			double x = fabs(f[i] - flast[i]);
			if (x > eps) eps = x;
		}
		if (eps < EPS) break;
	}
	// free
	free(pdg[0]); free(pdg[1]);
	{ // calculate r^2
		double p[2], q[2], D;
		p[0] = f[0] + f[1]; q[0] = 1 - p[0];
		p[1] = f[0] + f[2]; q[1] = 1 - p[1];
		D = f[0] * f[3] - f[1] * f[2];
		r = sqrt(D * D / (p[0] * p[1] * q[0] * q[1]));
//		printf("R(%lf,%lf,%lf,%lf)=%lf\n", f[0], f[1], f[2], f[3], r);
		if (isnan(r)) r = -1.;
	}
	return r;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/fet.c000066400000000000000000000060621211610345200236020ustar00rootroot00000000000000#include 
#include 

/* This program is implemented with ideas from this web page:
 *
 *   http://www.langsrud.com/fisher.htm
 */

// log\binom{n}{k}
static double lbinom(int n, int k)
{
	if (k == 0 || n == k) return 0;
	return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
}

// n11  n12  | n1_
// n21  n22  | n2_
//-----------+----
// n_1  n_2  | n

// hypergeometric distribution
static double hypergeo(int n11, int n1_, int n_1, int n)
{
	return exp(lbinom(n1_, n11) + lbinom(n-n1_, n_1-n11) - lbinom(n, n_1));
}

typedef struct {
	int n11, n1_, n_1, n;
	double p;
} hgacc_t;

// incremental version of hypergenometric distribution
static double hypergeo_acc(int n11, int n1_, int n_1, int n, hgacc_t *aux)
{
	if (n1_ || n_1 || n) {
		aux->n11 = n11; aux->n1_ = n1_; aux->n_1 = n_1; aux->n = n;
	} else { // then only n11 changed; the rest fixed
		if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
			if (n11 == aux->n11 + 1) { // incremental
				aux->p *= (double)(aux->n1_ - aux->n11) / n11
					* (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1);
				aux->n11 = n11;
				return aux->p;
			}
			if (n11 == aux->n11 - 1) { // incremental
				aux->p *= (double)aux->n11 / (aux->n1_ - n11)
					* (aux->n11 + aux->n - aux->n1_ - aux->n_1) / (aux->n_1 - n11);
				aux->n11 = n11;
				return aux->p;
			}
		}
		aux->n11 = n11;
	}
	aux->p = hypergeo(aux->n11, aux->n1_, aux->n_1, aux->n);
	return aux->p;
}

double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two)
{
	int i, j, max, min;
	double p, q, left, right;
	hgacc_t aux;
	int n1_, n_1, n;

	n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n
	max = (n_1 < n1_) ? n_1 : n1_; // max n11, for right tail
	min = n1_ + n_1 - n;
	if (min < 0) min = 0; // min n11, for left tail
	*two = *_left = *_right = 1.;
	if (min == max) return 1.; // no need to do test
	q = hypergeo_acc(n11, n1_, n_1, n, &aux); // the probability of the current table
	// left tail
	p = hypergeo_acc(min, 0, 0, 0, &aux);
	for (left = 0., i = min + 1; p < 0.99999999 * q; ++i) // loop until underflow
		left += p, p = hypergeo_acc(i, 0, 0, 0, &aux);
	--i;
	if (p < 1.00000001 * q) left += p;
	else --i;
	// right tail
	p = hypergeo_acc(max, 0, 0, 0, &aux);
	for (right = 0., j = max - 1; p < 0.99999999 * q; --j) // loop until underflow
		right += p, p = hypergeo_acc(j, 0, 0, 0, &aux);
	++j;
	if (p < 1.00000001 * q) right += p;
	else ++j;
	// two-tail
	*two = left + right;
	if (*two > 1.) *two = 1.;
	// adjust left and right
	if (abs(i - n11) < abs(j - n11)) right = 1. - left + q;
	else left = 1.0 - right + q;
	*_left = left; *_right = right;
	return q;
}

#ifdef FET_MAIN
#include 

int main(int argc, char *argv[])
{
	char id[1024];
	int n11, n12, n21, n22;
	double left, right, twotail, prob;

	while (scanf("%s%d%d%d%d", id, &n11, &n12, &n21, &n22) == 5) {
		prob = kt_fisher_exact(n11, n12, n21, n22, &left, &right, &twotail);
		printf("%s\t%d\t%d\t%d\t%d\t%.6g\t%.6g\t%.6g\t%.6g\n", id, n11, n12, n21, n22,
				prob, left, right, twotail);
	}
	return 0;
}
#endif
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/index.c000066400000000000000000000200421211610345200241250ustar00rootroot00000000000000#include 
#include 
#include 
#include "bam_endian.h"
#include "kstring.h"
#include "bcf.h"
#ifdef _USE_KNETFILE
#include "knetfile.h"
#endif

#define TAD_LIDX_SHIFT 13

typedef struct {
	int32_t n, m;
	uint64_t *offset;
} bcf_lidx_t;

struct __bcf_idx_t {
	int32_t n;
	bcf_lidx_t *index2;
};

/************
 * indexing *
 ************/

static inline void insert_offset2(bcf_lidx_t *index2, int _beg, int _end, uint64_t offset)
{
	int i, beg, end;
	beg = _beg >> TAD_LIDX_SHIFT;
	end = (_end - 1) >> TAD_LIDX_SHIFT;
	if (index2->m < end + 1) {
		int old_m = index2->m;
		index2->m = end + 1;
		kroundup32(index2->m);
		index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
		memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
	}
	if (beg == end) {
		if (index2->offset[beg] == 0) index2->offset[beg] = offset;
	} else {
		for (i = beg; i <= end; ++i)
			if (index2->offset[i] == 0) index2->offset[i] = offset;
	}
	if (index2->n < end + 1) index2->n = end + 1;
}

bcf_idx_t *bcf_idx_core(bcf_t *bp, bcf_hdr_t *h)
{
	bcf_idx_t *idx;
	int32_t last_coor, last_tid;
	uint64_t last_off;
	kstring_t *str;
	BGZF *fp = bp->fp;
	bcf1_t *b;
	int ret;

	b = calloc(1, sizeof(bcf1_t));
	str = calloc(1, sizeof(kstring_t));
	idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t));
	idx->n = h->n_ref;
	idx->index2 = calloc(h->n_ref, sizeof(bcf_lidx_t));

	last_tid = 0xffffffffu;
	last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
	while ((ret = bcf_read(bp, h, b)) > 0) {
		int end, tmp;
		if (last_tid != b->tid) { // change of chromosomes
			last_tid = b->tid;
		} else if (last_coor > b->pos) {
			fprintf(stderr, "[bcf_idx_core] the input is out of order\n");
			free(str->s); free(str); free(idx); bcf_destroy(b);
			return 0;
		}
		tmp = strlen(b->ref);
		end = b->pos + (tmp > 0? tmp : 1);
		insert_offset2(&idx->index2[b->tid], b->pos, end, last_off);
		last_off = bgzf_tell(fp);
		last_coor = b->pos;
	}
	free(str->s); free(str); bcf_destroy(b);
	return idx;
}

void bcf_idx_destroy(bcf_idx_t *idx)
{
	int i;
	if (idx == 0) return;
	for (i = 0; i < idx->n; ++i) free(idx->index2[i].offset);
	free(idx->index2);
	free(idx);
}

/******************
 * index file I/O *
 ******************/

void bcf_idx_save(const bcf_idx_t *idx, BGZF *fp)
{
	int32_t i, ti_is_be;
	ti_is_be = bam_is_big_endian();
	bgzf_write(fp, "BCI\4", 4);
	if (ti_is_be) {
		uint32_t x = idx->n;
		bgzf_write(fp, bam_swap_endian_4p(&x), 4);
	} else bgzf_write(fp, &idx->n, 4);
	for (i = 0; i < idx->n; ++i) {
		bcf_lidx_t *index2 = idx->index2 + i;
		// write linear index (index2)
		if (ti_is_be) {
			int x = index2->n;
			bgzf_write(fp, bam_swap_endian_4p(&x), 4);
		} else bgzf_write(fp, &index2->n, 4);
		if (ti_is_be) { // big endian
			int x;
			for (x = 0; (int)x < index2->n; ++x)
				bam_swap_endian_8p(&index2->offset[x]);
			bgzf_write(fp, index2->offset, 8 * index2->n);
			for (x = 0; (int)x < index2->n; ++x)
				bam_swap_endian_8p(&index2->offset[x]);
		} else bgzf_write(fp, index2->offset, 8 * index2->n);
	}
}

static bcf_idx_t *bcf_idx_load_core(BGZF *fp)
{
	int i, ti_is_be;
	char magic[4];
	bcf_idx_t *idx;
	ti_is_be = bam_is_big_endian();
	if (fp == 0) {
		fprintf(stderr, "[%s] fail to load index.\n", __func__);
		return 0;
	}
	bgzf_read(fp, magic, 4);
	if (strncmp(magic, "BCI\4", 4)) {
		fprintf(stderr, "[%s] wrong magic number.\n", __func__);
		return 0;
	}
	idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t));	
	bgzf_read(fp, &idx->n, 4);
	if (ti_is_be) bam_swap_endian_4p(&idx->n);
	idx->index2 = (bcf_lidx_t*)calloc(idx->n, sizeof(bcf_lidx_t));
	for (i = 0; i < idx->n; ++i) {
		bcf_lidx_t *index2 = idx->index2 + i;
		int j;
		bgzf_read(fp, &index2->n, 4);
		if (ti_is_be) bam_swap_endian_4p(&index2->n);
		index2->m = index2->n;
		index2->offset = (uint64_t*)calloc(index2->m, 8);
		bgzf_read(fp, index2->offset, index2->n * 8);
		if (ti_is_be)
			for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
	}
	return idx;
}

bcf_idx_t *bcf_idx_load_local(const char *fnidx)
{
	BGZF *fp;
	fp = bgzf_open(fnidx, "r");
	if (fp) {
		bcf_idx_t *idx = bcf_idx_load_core(fp);
		bgzf_close(fp);
		return idx;
	} else return 0;
}

#ifdef _USE_KNETFILE
static void download_from_remote(const char *url)
{
	const int buf_size = 1 * 1024 * 1024;
	char *fn;
	FILE *fp;
	uint8_t *buf;
	knetFile *fp_remote;
	int l;
	if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
	l = strlen(url);
	for (fn = (char*)url + l - 1; fn >= url; --fn)
		if (*fn == '/') break;
	++fn; // fn now points to the file name
	fp_remote = knet_open(url, "r");
	if (fp_remote == 0) {
		fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
		return;
	}
	if ((fp = fopen(fn, "w")) == 0) {
		fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
		knet_close(fp_remote);
		return;
	}
	buf = (uint8_t*)calloc(buf_size, 1);
	while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
		fwrite(buf, 1, l, fp);
	free(buf);
	fclose(fp);
	knet_close(fp_remote);
}
#else
static void download_from_remote(const char *url)
{
	return;
}
#endif

static char *get_local_version(const char *fn)
{
    struct stat sbuf;
	char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
	strcat(strcpy(fnidx, fn), ".bci");
	if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
		char *p, *url;
		int l = strlen(fnidx);
		for (p = fnidx + l - 1; p >= fnidx; --p)
			if (*p == '/') break;
		url = fnidx; fnidx = strdup(p + 1);
		if (stat(fnidx, &sbuf) == 0) {
			free(url);
			return fnidx;
		}
		fprintf(stderr, "[%s] downloading the index file...\n", __func__);
		download_from_remote(url);
		free(url);
	}
    if (stat(fnidx, &sbuf) == 0) return fnidx;
	free(fnidx); return 0;
}

bcf_idx_t *bcf_idx_load(const char *fn)
{
	bcf_idx_t *idx;
    char *fname = get_local_version(fn);
	if (fname == 0) return 0;
	idx = bcf_idx_load_local(fname);
    free(fname);
	return idx;
}

int bcf_idx_build2(const char *fn, const char *_fnidx)
{
	char *fnidx;
	BGZF *fpidx;
	bcf_t *bp;
	bcf_idx_t *idx;
	bcf_hdr_t *h;
	if ((bp = bcf_open(fn, "r")) == 0) {
		fprintf(stderr, "[bcf_idx_build2] fail to open the BAM file.\n");
		return -1;
	}
	h = bcf_hdr_read(bp);
	idx = bcf_idx_core(bp, h);
	bcf_close(bp);
	if (_fnidx == 0) {
		fnidx = (char*)calloc(strlen(fn) + 5, 1);
		strcpy(fnidx, fn); strcat(fnidx, ".bci");
	} else fnidx = strdup(_fnidx);
	fpidx = bgzf_open(fnidx, "w");
	if (fpidx == 0) {
		fprintf(stderr, "[bcf_idx_build2] fail to create the index file.\n");
		free(fnidx);
		return -1;
	}
	bcf_idx_save(idx, fpidx);
	bcf_idx_destroy(idx);
	bgzf_close(fpidx);
	free(fnidx);
	return 0;
}

int bcf_idx_build(const char *fn)
{
	return bcf_idx_build2(fn, 0);
}

/********************************************
 * parse a region in the format chr:beg-end *
 ********************************************/

int bcf_parse_region(void *str2id, const char *str, int *tid, int *begin, int *end)
{
	char *s, *p;
	int i, l, k;
	l = strlen(str);
	p = s = (char*)malloc(l+1);
	/* squeeze out "," */
	for (i = k = 0; i != l; ++i)
		if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
	s[k] = 0;
	for (i = 0; i != k; ++i) if (s[i] == ':') break;
	s[i] = 0;
	if ((*tid = bcf_str2id(str2id, s)) < 0) {
		free(s);
		return -1;
	}
	if (i == k) { /* dump the whole sequence */
		*begin = 0; *end = 1<<29; free(s);
		return 0;
	}
	for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
	*begin = atoi(p);
	if (i < k) {
		p = s + i + 1;
		*end = atoi(p);
	} else *end = 1<<29;
	if (*begin > 0) --*begin;
	free(s);
	if (*begin > *end) return -1;
	return 0;
}

/*******************************
 * retrieve a specified region *
 *******************************/

uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg)
{
	uint64_t min_off, *offset;
	int i;
	if (beg < 0) beg = 0;
	offset = idx->index2[tid].offset;
	for (i = beg>>TAD_LIDX_SHIFT; i < idx->index2[tid].n && offset[i] == 0; ++i);
	min_off = (i == idx->index2[tid].n)? offset[idx->index2[tid].n-1] : offset[i];
	return min_off;
}

int bcf_main_index(int argc, char *argv[])
{
	if (argc == 1) {
		fprintf(stderr, "Usage: bcftools index \n");
		return 1;
	}
	bcf_idx_build(argv[1]);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/kfunc.c000066400000000000000000000115401211610345200241270ustar00rootroot00000000000000#include 


/* Log gamma function
 * \log{\Gamma(z)}
 * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245
 */
double kf_lgamma(double z)
{
	double x = 0;
	x += 0.1659470187408462e-06 / (z+7);
	x += 0.9934937113930748e-05 / (z+6);
	x -= 0.1385710331296526     / (z+5);
	x += 12.50734324009056      / (z+4);
	x -= 176.6150291498386      / (z+3);
	x += 771.3234287757674      / (z+2);
	x -= 1259.139216722289      / (z+1);
	x += 676.5203681218835      / z;
	x += 0.9999999999995183;
	return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);
}

/* complementary error function
 * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt
 * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66
 */
double kf_erfc(double x)
{
	const double p0 = 220.2068679123761;
	const double p1 = 221.2135961699311;
	const double p2 = 112.0792914978709;
	const double p3 = 33.912866078383;
	const double p4 = 6.37396220353165;
	const double p5 = .7003830644436881;
	const double p6 = .03526249659989109;
	const double q0 = 440.4137358247522;
	const double q1 = 793.8265125199484;
	const double q2 = 637.3336333788311;
	const double q3 = 296.5642487796737;
	const double q4 = 86.78073220294608;
	const double q5 = 16.06417757920695;
	const double q6 = 1.755667163182642;
	const double q7 = .08838834764831844;
	double expntl, z, p;
	z = fabs(x) * M_SQRT2;
	if (z > 37.) return x > 0.? 0. : 2.;
	expntl = exp(z * z * - .5);
	if (z < 10. / M_SQRT2) // for small z
	    p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0)
			/ (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0);
	else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65)))));
	return x > 0.? 2. * p : 2. * (1. - p);
}

/* The following computes regularized incomplete gamma functions.
 * Formulas are taken from Wiki, with additional input from Numerical
 * Recipes in C (for modified Lentz's algorithm) and AS245
 * (http://lib.stat.cmu.edu/apstat/245).
 *
 * A good online calculator is available at:
 *
 *   http://www.danielsoper.com/statcalc/calc23.aspx
 *
 * It calculates upper incomplete gamma function, which equals
 * kf_gammaq(s,z)*tgamma(s).
 */

#define KF_GAMMA_EPS 1e-14
#define KF_TINY 1e-290

// regularized lower incomplete gamma function, by series expansion
static double _kf_gammap(double s, double z)
{
	double sum, x;
	int k;
	for (k = 1, sum = x = 1.; k < 100; ++k) {
		sum += (x *= z / (s + k));
		if (x / sum < KF_GAMMA_EPS) break;
	}
	return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum));
}
// regularized upper incomplete gamma function, by continued fraction
static double _kf_gammaq(double s, double z)
{
	int j;
	double C, D, f;
	f = 1. + z - s; C = f; D = 0.;
	// Modified Lentz's algorithm for computing continued fraction
	// See Numerical Recipes in C, 2nd edition, section 5.2
	for (j = 1; j < 100; ++j) {
		double a = j * (s - j), b = (j<<1) + 1 + z - s, d;
		D = b + a * D;
		if (D < KF_TINY) D = KF_TINY;
		C = b + a / C;
		if (C < KF_TINY) C = KF_TINY;
		D = 1. / D;
		d = C * D;
		f *= d;
		if (fabs(d - 1.) < KF_GAMMA_EPS) break;
	}
	return exp(s * log(z) - z - kf_lgamma(s) - log(f));
}

double kf_gammap(double s, double z)
{
	return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z);
}

double kf_gammaq(double s, double z)
{
	return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z);
}

/* Regularized incomplete beta function. The method is taken from
 * Numerical Recipe in C, 2nd edition, section 6.4. The following web
 * page calculates the incomplete beta function, which equals
 * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b):
 *
 *   http://www.danielsoper.com/statcalc/calc36.aspx
 */
static double kf_betai_aux(double a, double b, double x)
{
	double C, D, f;
	int j;
	if (x == 0.) return 0.;
	if (x == 1.) return 1.;
	f = 1.; C = f; D = 0.;
	// Modified Lentz's algorithm for computing continued fraction
	for (j = 1; j < 200; ++j) {
		double aa, d;
		int m = j>>1;
		aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1))
			: m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m));
		D = 1. + aa * D;
		if (D < KF_TINY) D = KF_TINY;
		C = 1. + aa / C;
		if (C < KF_TINY) C = KF_TINY;
		D = 1. / D;
		d = C * D;
		f *= d;
		if (fabs(d - 1.) < KF_GAMMA_EPS) break;
	}
	return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f;
}
double kf_betai(double a, double b, double x)
{
	return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x);
}

#ifdef KF_MAIN
#include 
int main(int argc, char *argv[])
{
	double x = 5.5, y = 3;
	double a, b;
	printf("erfc(%lg): %lg, %lg\n", x, erfc(x), kf_erfc(x));
	printf("upper-gamma(%lg,%lg): %lg\n", x, y, kf_gammaq(y, x)*tgamma(y));
	a = 2; b = 2; x = 0.5;
	printf("incomplete-beta(%lg,%lg,%lg): %lg\n", a, b, x, kf_betai(a, b, x) / exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b)));
	return 0;
}
#endif
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/kmin.c000066400000000000000000000161451211610345200237650ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008, 2010 by Attractive Chaos 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Hooke-Jeeves algorithm for nonlinear minimization
 
   Based on the pseudocodes by Bell and Pike (CACM 9(9):684-685), and
   the revision by Tomlin and Smith (CACM 12(11):637-638). Both of the
   papers are comments on Kaupe's Algorithm 178 "Direct Search" (ACM
   6(6):313-314). The original algorithm was designed by Hooke and
   Jeeves (ACM 8:212-229). This program is further revised according to
   Johnson's implementation at Netlib (opt/hooke.c).
 
   Hooke-Jeeves algorithm is very simple and it works quite well on a
   few examples. However, it might fail to converge due to its heuristic
   nature. A possible improvement, as is suggested by Johnson, may be to
   choose a small r at the beginning to quickly approach to the minimum
   and a large r at later step to hit the minimum.
 */

#include 
#include 
#include 
#include "kmin.h"

static double __kmin_hj_aux(kmin_f func, int n, double *x1, void *data, double fx1, double *dx, int *n_calls)
{
	int k, j = *n_calls;
	double ftmp;
	for (k = 0; k != n; ++k) {
		x1[k] += dx[k];
		ftmp = func(n, x1, data); ++j;
		if (ftmp < fx1) fx1 = ftmp;
		else { /* search the opposite direction */
			dx[k] = 0.0 - dx[k];
			x1[k] += dx[k] + dx[k];
			ftmp = func(n, x1, data); ++j;
			if (ftmp < fx1) fx1 = ftmp;
			else x1[k] -= dx[k]; /* back to the original x[k] */
		}
	}
	*n_calls = j;
	return fx1; /* here: fx1=f(n,x1) */
}

double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls)
{
	double fx, fx1, *x1, *dx, radius;
	int k, n_calls = 0;
	x1 = (double*)calloc(n, sizeof(double));
	dx = (double*)calloc(n, sizeof(double));
	for (k = 0; k != n; ++k) { /* initial directions, based on MGJ */
		dx[k] = fabs(x[k]) * r;
		if (dx[k] == 0) dx[k] = r;
	}
	radius = r;
	fx1 = fx = func(n, x, data); ++n_calls;
	for (;;) {
		memcpy(x1, x, n * sizeof(double)); /* x1 = x */
		fx1 = __kmin_hj_aux(func, n, x1, data, fx, dx, &n_calls);
		while (fx1 < fx) {
			for (k = 0; k != n; ++k) {
				double t = x[k];
				dx[k] = x1[k] > x[k]? fabs(dx[k]) : 0.0 - fabs(dx[k]);
				x[k] = x1[k];
				x1[k] = x1[k] + x1[k] - t;
			}
			fx = fx1;
			if (n_calls >= max_calls) break;
			fx1 = func(n, x1, data); ++n_calls;
			fx1 = __kmin_hj_aux(func, n, x1, data, fx1, dx, &n_calls);
			if (fx1 >= fx) break;
			for (k = 0; k != n; ++k)
				if (fabs(x1[k] - x[k]) > .5 * fabs(dx[k])) break;
			if (k == n) break;
		}
		if (radius >= eps) {
			if (n_calls >= max_calls) break;
			radius *= r;
			for (k = 0; k != n; ++k) dx[k] *= r;
		} else break; /* converge */
	}
	free(x1); free(dx);
	return fx1;
}

// I copied this function somewhere several years ago with some of my modifications, but I forgot the source.
double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin)
{
	double bound, u, r, q, fu, tmp, fa, fb, fc, c;
	const double gold1 = 1.6180339887;
	const double gold2 = 0.3819660113;
	const double tiny = 1e-20;
	const int max_iter = 100;

	double e, d, w, v, mid, tol1, tol2, p, eold, fv, fw;
	int iter;

	fa = func(a, data); fb = func(b, data);
	if (fb > fa) { // swap, such that f(a) > f(b)
		tmp = a; a = b; b = tmp;
		tmp = fa; fa = fb; fb = tmp;
	}
	c = b + gold1 * (b - a), fc = func(c, data); // golden section extrapolation
	while (fb > fc) {
		bound = b + 100.0 * (c - b); // the farthest point where we want to go
		r = (b - a) * (fb - fc);
		q = (b - c) * (fb - fa);
		if (fabs(q - r) < tiny) { // avoid 0 denominator
			tmp = q > r? tiny : 0.0 - tiny;
		} else tmp = q - r;
		u = b - ((b - c) * q - (b - a) * r) / (2.0 * tmp); // u is the parabolic extrapolation point
		if ((b > u && u > c) || (b < u && u < c)) { // u lies between b and c
			fu = func(u, data);
			if (fu < fc) { // (b,u,c) bracket the minimum
				a = b; b = u; fa = fb; fb = fu;
				break;
			} else if (fu > fb) { // (a,b,u) bracket the minimum
				c = u; fc = fu;
				break;
			}
			u = c + gold1 * (c - b); fu = func(u, data); // golden section extrapolation
		} else if ((c > u && u > bound) || (c < u && u < bound)) { // u lies between c and bound
			fu = func(u, data);
			if (fu < fc) { // fb > fc > fu
				b = c; c = u; u = c + gold1 * (c - b);
				fb = fc; fc = fu; fu = func(u, data);
			} else { // (b,c,u) bracket the minimum
				a = b; b = c; c = u;
				fa = fb; fb = fc; fc = fu;
				break;
			}
		} else if ((u > bound && bound > c) || (u < bound && bound < c)) { // u goes beyond the bound
			u = bound; fu = func(u, data);
		} else { // u goes the other way around, use golden section extrapolation
			u = c + gold1 * (c - b); fu = func(u, data);
		}
		a = b; b = c; c = u;
		fa = fb; fb = fc; fc = fu;
	}
	if (a > c) u = a, a = c, c = u; // swap

	// now, afb and fb tol1) {
			// related to parabolic interpolation
			r = (b - w) * (fb - fv);
			q = (b - v) * (fb - fw);
			p = (b - v) * q - (b - w) * r;
			q = 2.0 * (q - r);
			if (q > 0.0) p = 0.0 - p;
			else q = 0.0 - q;
			eold = e; e = d;
			if (fabs(p) >= fabs(0.5 * q * eold) || p <= q * (a - b) || p >= q * (c - b)) {
				d = gold2 * (e = (b >= mid ? a - b : c - b));
			} else {
				d = p / q; u = b + d; // actual parabolic interpolation happens here
				if (u - a < tol2 || c - u < tol2)
					d = (mid > b)? tol1 : 0.0 - tol1;
			}
		} else d = gold2 * (e = (b >= mid ? a - b : c - b)); // golden section interpolation
		u = fabs(d) >= tol1 ? b + d : b + (d > 0.0? tol1 : -tol1);
		fu = func(u, data);
		if (fu <= fb) { // u is the minimum point so far
			if (u >= b) a = b;
			else c = b;
			v = w; w = b; b = u; fv = fw; fw = fb; fb = fu;
		} else { // adjust (a,c) and (u,v,w)
			if (u < b) a = u;
			else c = u;
			if (fu <= fw || w == b) {
				v = w; w = u;
				fv = fw; fw = fu;
			} else if (fu <= fv || v == b || v == w) {
				v = u; fv = fu;
			}
		}
	}
	*xmin = b;
	return fb;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/kmin.h000066400000000000000000000031231211610345200237620ustar00rootroot00000000000000/*
   Copyright (c) 2008, 2010 by Attractive Chaos 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

#ifndef KMIN_H
#define KMIN_H

#define KMIN_RADIUS  0.5
#define KMIN_EPS     1e-7
#define KMIN_MAXCALL 50000

typedef double (*kmin_f)(int, double*, void*);
typedef double (*kmin1_f)(double, void*);

#ifdef __cplusplus
extern "C" {
#endif

	double kmin_hj(kmin_f func, int n, double *x, void *data, double r, double eps, int max_calls);
	double kmin_brent(kmin1_f func, double a, double b, void *data, double tol, double *xmin);

#ifdef __cplusplus
}
#endif

#endif
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/main.c000066400000000000000000000120201211610345200237370ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include "bcf.h"

#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 0x10000)

int bcfview(int argc, char *argv[]);
int bcf_main_index(int argc, char *argv[]);

#define BUF_SIZE 0x10000

int bcf_cat(int n, char * const *fn)
{
	int i;
	bcf_t *out;
	uint8_t *buf;
	buf = malloc(BUF_SIZE);
	out = bcf_open("-", "w");
	for (i = 0; i < n; ++i) {
		bcf_t *in;
		bcf_hdr_t *h;
		off_t end;
		struct stat s;
		in = bcf_open(fn[i], "r");
		h = bcf_hdr_read(in);
		if (i == 0) bcf_hdr_write(out, h);
		bcf_hdr_destroy(h);
#ifdef _USE_KNETFILE
		fstat(knet_fileno(in->fp->x.fpr), &s);
		end = s.st_size - 28;
		while (knet_tell(in->fp->x.fpr) < end) {
			int size = knet_tell(in->fp->x.fpr) + BUF_SIZE < end? BUF_SIZE : end - knet_tell(in->fp->x.fpr);
			knet_read(in->fp->x.fpr, buf, size);
			fwrite(buf, 1, size, out->fp->x.fpw);
		}
#else
		abort(); // FIXME: not implemented
#endif
		bcf_close(in);
	}
	bcf_close(out);
	free(buf);
	return 0;
}

extern double bcf_pair_freq(const bcf1_t *b0, const bcf1_t *b1, double f[4]);

int bcf_main_ldpair(int argc, char *argv[])
{
	bcf_t *fp;
	bcf_hdr_t *h;
	bcf1_t *b0, *b1;
	bcf_idx_t *idx;
	kstring_t str;
	void *str2id;
	gzFile fplist;
	kstream_t *ks;
	int dret, lineno = 0;
	if (argc < 3) {
		fprintf(stderr, "Usage: bcftools ldpair  \n");
		return 1;
	}
	fplist = gzopen(argv[2], "rb");
	ks = ks_init(fplist);
	memset(&str, 0, sizeof(kstring_t));
	fp = bcf_open(argv[1], "rb");
	h = bcf_hdr_read(fp);
	str2id = bcf_build_refhash(h);
	idx = bcf_idx_load(argv[1]);
	if (idx == 0) {
		fprintf(stderr, "[%s] No bcf index is found. Abort!\n", __func__);
		return 1;
	}
	b0 = calloc(1, sizeof(bcf1_t));
	b1 = calloc(1, sizeof(bcf1_t));
	while (ks_getuntil(ks, '\n', &str, &dret) >= 0) {
		char *p, *q;
		int k;
		int tid0 = -1, tid1 = -1, pos0 = -1, pos1 = -1;
		++lineno;
		for (p = q = str.s, k = 0; *p; ++p) {
			if (*p == ' ' || *p == '\t') {
				*p = '\0';
				if (k == 0) tid0 = bcf_str2id(str2id, q);
				else if (k == 1) pos0 = atoi(q) - 1;
				else if (k == 2) tid1 = strcmp(q, "=")? bcf_str2id(str2id, q) : tid0;
				else if (k == 3) pos1 = atoi(q) - 1;
				q = p + 1;
				++k;
			}
		}
		if (k == 3) pos1 = atoi(q) - 1;
		if (tid0 >= 0 && tid1 >= 0 && pos0 >= 0 && pos1 >= 0) {
			uint64_t off;
			double r, f[4];
			off = bcf_idx_query(idx, tid0, pos0);
			bgzf_seek(fp->fp, off, SEEK_SET);
			while (bcf_read(fp, h, b0) >= 0 && b0->pos != pos0);
			off = bcf_idx_query(idx, tid1, pos1);
			bgzf_seek(fp->fp, off, SEEK_SET);
			while (bcf_read(fp, h, b1) >= 0 && b1->pos != pos1);
			r = bcf_pair_freq(b0, b1, f);
			r *= r;
			printf("%s\t%d\t%s\t%d\t%.4g\t%.4g\t%.4g\t%.4g\t%.4g\n", h->ns[tid0], pos0+1, h->ns[tid1], pos1+1,
				r, f[0], f[1], f[2], f[3]);
		} //else fprintf(stderr, "[%s] Parse error at line %d.\n", __func__, lineno);
	}
	bcf_destroy(b0); bcf_destroy(b1);
	bcf_idx_destroy(idx);
	bcf_str2id_destroy(str2id);
	bcf_hdr_destroy(h);
	bcf_close(fp);
	free(str.s);
	ks_destroy(ks);
	gzclose(fplist);
	return 0;
}

int bcf_main_ld(int argc, char *argv[])
{
	bcf_t *fp;
	bcf_hdr_t *h;
	bcf1_t **b, *b0;
	int i, j, m, n;
	double f[4];
	if (argc == 1) {
		fprintf(stderr, "Usage: bcftools ld \n");
		return 1;
	}
	fp = bcf_open(argv[1], "rb");
	h = bcf_hdr_read(fp);
	// read the entire BCF
	m = n = 0; b = 0;
	b0 = calloc(1, sizeof(bcf1_t));
	while (bcf_read(fp, h, b0) >= 0) {
		if (m == n) {
			m = m? m<<1 : 16;
			b = realloc(b, sizeof(void*) * m);
		}
		b[n] = calloc(1, sizeof(bcf1_t));
		bcf_cpy(b[n++], b0);
	}
	bcf_destroy(b0);
	// compute pair-wise r^2
	printf("%d\n", n); // the number of loci
	for (i = 0; i < n; ++i) {
		printf("%s:%d", h->ns[b[i]->tid], b[i]->pos + 1);
		for (j = 0; j < i; ++j) {
			double r = bcf_pair_freq(b[i], b[j], f);
			printf("\t%.3f", r*r);
		}
		printf("\t1.000\n");
	}
	// free
	for (i = 0; i < n; ++i) bcf_destroy(b[i]);
	free(b);
	bcf_hdr_destroy(h);
	bcf_close(fp);
	return 0;
}

int main(int argc, char *argv[])
{
	if (argc == 1) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Program: bcftools (Tools for data in the VCF/BCF formats)\n");
		fprintf(stderr, "Version: %s\n\n", BCF_VERSION);
		fprintf(stderr, "Usage:   bcftools  \n\n");
		fprintf(stderr, "Command: view      print, extract, convert and call SNPs from BCF\n");
		fprintf(stderr, "         index     index BCF\n");
		fprintf(stderr, "         cat       concatenate BCFs\n");
		fprintf(stderr, "         ld        compute all-pair r^2\n");
		fprintf(stderr, "         ldpair    compute r^2 between requested pairs\n");
		fprintf(stderr, "\n");
		return 1;
	}
	if (strcmp(argv[1], "view") == 0) return bcfview(argc-1, argv+1);
	else if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
	else if (strcmp(argv[1], "ld") == 0) return bcf_main_ld(argc-1, argv+1);
	else if (strcmp(argv[1], "ldpair") == 0) return bcf_main_ldpair(argc-1, argv+1);
	else if (strcmp(argv[1], "cat") == 0) return bcf_cat(argc-2, argv+2); // cat is different ...
	else {
		fprintf(stderr, "[main] Unrecognized command.\n");
		return 1;
	}
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/mut.c000066400000000000000000000073501211610345200236320ustar00rootroot00000000000000#include 
#include 
#include "bcf.h"

#define MAX_GENO 359

int8_t seq_bitcnt[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
char *seq_nt16rev = "XACMGRSVTWYHKDBN";

uint32_t *bcf_trio_prep(int is_x, int is_son)
{
	int i, j, k, n, map[10];
	uint32_t *ret;
	ret = calloc(MAX_GENO, 4);
	for (i = 0, k = 0; i < 4; ++i)
		for (j = i; j < 4; ++j)
			map[k++] = 1<n_smpl != 3) return -1; // not a trio
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
	if (i == b->n_gi) return -1; // no PL
	gl10 = alloca(10 * b->n_smpl);
	if (bcf_gl10(b, gl10) < 0) {
		if (bcf_gl10_indel(b, gl10) < 0) return -1;
	}
	PL = b->gi + i;
	for (i = 0, k = 0; i < 4; ++i)
		for (j = i; j < 4; ++j)
			map[k++] = seq_nt16rev[1<data)[j * PL->len] != 0) break;
	if (j < 3) { // we need to go through the complex procedure
		uint8_t *g[3];
		int minc = 1<<30, minc_j = -1, minf = 0, gtf = 0, gtc = 0;
		g[0] = gl10;
		g[1] = gl10 + 10;
		g[2] = gl10 + 20;
		for (j = 1; j <= (int)prep[0]; ++j) { // compute LK with constraint
			int sum = g[0][prep[j]&0xff] + g[1][prep[j]>>8&0xff] + g[2][prep[j]>>16&0xff];
			if (sum < minc) minc = sum, minc_j = j;
		}
		gtc |= map[prep[minc_j]&0xff]; gtc |= map[prep[minc_j]>>8&0xff]<<8; gtc |= map[prep[minc_j]>>16]<<16;
		for (j = 0; j < 3; ++j) { // compute LK without constraint
			int min = 1<<30, min_k = -1;
			for (k = 0; k < 10; ++k)
				if (g[j][k] < min) min = g[j][k], min_k = k;
			gtf |= map[min_k]<<(j*8);
			minf += min;
		}
		*llr = minc - minf; *gt = (int64_t)gtc<<32 | gtf;
	} else *llr = 0, *gt = -1;
	return 0;
}

int bcf_pair_call(const bcf1_t *b)
{
	int i, j, k;
	const bcf_ginfo_t *PL;
	if (b->n_smpl != 2) return -1; // not a pair
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
	if (i == b->n_gi) return -1; // no PL
	PL = b->gi + i;
	for (j = 0; j < 2; ++j) // check if ref hom is the most probable in all members
		if (((uint8_t*)PL->data)[j * PL->len] != 0) break;
	if (j < 2) { // we need to go through the complex procedure
		uint8_t *g[2];
		int minc = 1<<30, minf = 0;
		g[0] = PL->data;
		g[1] = (uint8_t*)PL->data + PL->len;
		for (j = 0; j < PL->len; ++j) // compute LK with constraint
			minc = minc < g[0][j] + g[1][j]? minc : g[0][j] + g[1][j];
		for (j = 0; j < 2; ++j) { // compute LK without constraint
			int min = 1<<30;
			for (k = 0; k < PL->len; ++k)
				min = min < g[j][k]? min : g[j][k];
			minf += min;
		}
		return minc - minf;
	} else return 0;
}

int bcf_min_diff(const bcf1_t *b)
{
	int i, min = 1<<30;
	const bcf_ginfo_t *PL;
	for (i = 0; i < b->n_gi; ++i)
		if (b->gi[i].fmt == bcf_str2int("PL", 2)) break;
	if (i == b->n_gi) return -1; // no PL
	PL = b->gi + i;
	for (i = 0; i < b->n_smpl; ++i) {
		int m1, m2, j;
		const uint8_t *p = (uint8_t*)PL->data;
		m1 = m2 = 1<<30;
		for (j = 0; j < PL->len; ++j) {
			if ((int)p[j] < m1) m2 = m1, m1 = p[j];
			else if ((int)p[j] < m2) m2 = p[j];
		}
		min = min < m2 - m1? min : m2 - m1;
	}
	return min;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/prob1.c000066400000000000000000000436511211610345200240540ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include 
#include "prob1.h"

#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)

#define MC_MAX_EM_ITER 16
#define MC_EM_EPS 1e-5
#define MC_DEF_INDEL 0.15

unsigned char seq_nt4_table[256] = {
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4 /*'-'*/, 4, 4,
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
};

struct __bcf_p1aux_t {
	int n, M, n1, is_indel;
	uint8_t *ploidy; // haploid or diploid ONLY
	double *q2p, *pdg; // pdg -> P(D|g)
	double *phi, *phi_indel;
	double *z, *zswap; // aux for afs
	double *z1, *z2, *phi1, *phi2; // only calculated when n1 is set
	double **hg; // hypergeometric distribution
	double *lf; // log factorial
	double t, t1, t2;
	double *afs, *afs1; // afs: accumulative AFS; afs1: site posterior distribution
	const uint8_t *PL; // point to PL
	int PL_len;
};

void bcf_p1_indel_prior(bcf_p1aux_t *ma, double x)
{
	int i;
	for (i = 0; i < ma->M; ++i)
		ma->phi_indel[i] = ma->phi[i] * x;
	ma->phi_indel[ma->M] = 1. - ma->phi[ma->M] * x;
}

static void init_prior(int type, double theta, int M, double *phi)
{
	int i;
	if (type == MC_PTYPE_COND2) {
		for (i = 0; i <= M; ++i)
			phi[i] = 2. * (i + 1) / (M + 1) / (M + 2);
	} else if (type == MC_PTYPE_FLAT) {
		for (i = 0; i <= M; ++i)
			phi[i] = 1. / (M + 1);
	} else {
		double sum;
		for (i = 0, sum = 0.; i < M; ++i)
			sum += (phi[i] = theta / (M - i));
		phi[M] = 1. - sum;
	}
}

void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta)
{
	init_prior(type, theta, ma->M, ma->phi);
	bcf_p1_indel_prior(ma, MC_DEF_INDEL);
}

void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta)
{
	if (ma->n1 <= 0 || ma->n1 >= ma->M) return;
	init_prior(type, theta, 2*ma->n1, ma->phi1);
	init_prior(type, theta, 2*(ma->n - ma->n1), ma->phi2);
}

int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn)
{
	gzFile fp;
	kstring_t s;
	kstream_t *ks;
	long double sum;
	int dret, k;
	memset(&s, 0, sizeof(kstring_t));
	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
	ks = ks_init(fp);
	memset(ma->phi, 0, sizeof(double) * (ma->M + 1));
	while (ks_getuntil(ks, '\n', &s, &dret) >= 0) {
		if (strstr(s.s, "[afs] ") == s.s) {
			char *p = s.s + 6;
			for (k = 0; k <= ma->M; ++k) {
				int x;
				double y;
				x = strtol(p, &p, 10);
				if (x != k && (errno == EINVAL || errno == ERANGE)) return -1;
				++p;
				y = strtod(p, &p);
				if (y == 0. && (errno == EINVAL || errno == ERANGE)) return -1;
				ma->phi[ma->M - k] += y;
			}
		}
	}
	ks_destroy(ks);
	gzclose(fp);
	free(s.s);
	for (sum = 0., k = 0; k <= ma->M; ++k) sum += ma->phi[k];
	fprintf(stderr, "[prior]");
	for (k = 0; k <= ma->M; ++k) ma->phi[k] /= sum;
	for (k = 0; k <= ma->M; ++k) fprintf(stderr, " %d:%.3lg", k, ma->phi[ma->M - k]);
	fputc('\n', stderr);
	for (sum = 0., k = 1; k < ma->M; ++k) sum += ma->phi[ma->M - k] * (2.* k * (ma->M - k) / ma->M / (ma->M - 1));
	fprintf(stderr, "[%s] heterozygosity=%lf, ", __func__, (double)sum);
	for (sum = 0., k = 1; k <= ma->M; ++k) sum += k * ma->phi[ma->M - k] / ma->M;
	fprintf(stderr, "theta=%lf\n", (double)sum);
	bcf_p1_indel_prior(ma, MC_DEF_INDEL);
	return 0;
}

bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy)
{
	bcf_p1aux_t *ma;
	int i;
	ma = calloc(1, sizeof(bcf_p1aux_t));
	ma->n1 = -1;
	ma->n = n; ma->M = 2 * n;
	if (ploidy) {
		ma->ploidy = malloc(n);
		memcpy(ma->ploidy, ploidy, n);
		for (i = 0, ma->M = 0; i < n; ++i) ma->M += ploidy[i];
		if (ma->M == 2 * n) {
			free(ma->ploidy);
			ma->ploidy = 0;
		}
	}
	ma->q2p = calloc(256, sizeof(double));
	ma->pdg = calloc(3 * ma->n, sizeof(double));
	ma->phi = calloc(ma->M + 1, sizeof(double));
	ma->phi_indel = calloc(ma->M + 1, sizeof(double));
	ma->phi1 = calloc(ma->M + 1, sizeof(double));
	ma->phi2 = calloc(ma->M + 1, sizeof(double));
	ma->z = calloc(ma->M + 1, sizeof(double));
	ma->zswap = calloc(ma->M + 1, sizeof(double));
	ma->z1 = calloc(ma->M + 1, sizeof(double)); // actually we do not need this large
	ma->z2 = calloc(ma->M + 1, sizeof(double));
	ma->afs = calloc(ma->M + 1, sizeof(double));
	ma->afs1 = calloc(ma->M + 1, sizeof(double));
	ma->lf = calloc(ma->M + 1, sizeof(double));
	for (i = 0; i < 256; ++i)
		ma->q2p[i] = pow(10., -i / 10.);
	for (i = 0; i <= ma->M; ++i) ma->lf[i] = lgamma(i + 1);
	bcf_p1_init_prior(ma, MC_PTYPE_FULL, 1e-3); // the simplest prior
	return ma;
}

int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
{
	if (n1 == 0 || n1 >= b->n) return -1;
	if (b->M != b->n * 2) {
		fprintf(stderr, "[%s] unable to set `n1' when there are haploid samples.\n", __func__);
		return -1;
	}
	b->n1 = n1;
	return 0;
}

void bcf_p1_destroy(bcf_p1aux_t *ma)
{
	if (ma) {
		int k;
		free(ma->lf);
		if (ma->hg && ma->n1 > 0) {
			for (k = 0; k <= 2*ma->n1; ++k) free(ma->hg[k]);
			free(ma->hg);
		}
		free(ma->ploidy); free(ma->q2p); free(ma->pdg);
		free(ma->phi); free(ma->phi_indel); free(ma->phi1); free(ma->phi2);
		free(ma->z); free(ma->zswap); free(ma->z1); free(ma->z2);
		free(ma->afs); free(ma->afs1);
		free(ma);
	}
}

static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
{
	int i, j;
	long *p, tmp;
	p = alloca(b->n_alleles * sizeof(long));
	memset(p, 0, sizeof(long) * b->n_alleles);
	for (j = 0; j < ma->n; ++j) {
		const uint8_t *pi = ma->PL + j * ma->PL_len;
		double *pdg = ma->pdg + j * 3;
		pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
		for (i = 0; i < b->n_alleles; ++i)
			p[i] += (int)pi[(i+1)*(i+2)/2-1];
	}
	for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
	for (i = 1; i < b->n_alleles; ++i) // insertion sort
		for (j = i; j > 0 && p[j] < p[j-1]; --j)
			tmp = p[j], p[j] = p[j-1], p[j-1] = tmp;
	for (i = b->n_alleles - 1; i >= 0; --i)
		if ((p[i]&0xf) == 0) break;
	return i;
}

int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
{
	double sum, g[3];
	double max, f3[3], *pdg = ma->pdg + k * 3;
	int q, i, max_i, ploidy;
	ploidy = ma->ploidy? ma->ploidy[k] : 2;
	if (ploidy == 2) {
		f3[0] = (1.-f0)*(1.-f0); f3[1] = 2.*f0*(1.-f0); f3[2] = f0*f0;
	} else {
		f3[0] = 1. - f0; f3[1] = 0; f3[2] = f0;
	}
	for (i = 0, sum = 0.; i < 3; ++i)
		sum += (g[i] = pdg[i] * f3[i]);
	for (i = 0, max = -1., max_i = 0; i < 3; ++i) {
		g[i] /= sum;
		if (g[i] > max) max = g[i], max_i = i;
	}
	max = 1. - max;
	if (max < 1e-308) max = 1e-308;
	q = (int)(-4.343 * log(max) + .499);
	if (q > 99) q = 99;
	return q<<2|max_i;
}

#define TINY 1e-20

static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
{
	double *z[2], *tmp, *pdg;
	int _j, last_min, last_max;
	assert(beg == 0 || ma->M == ma->n*2);
	z[0] = ma->z;
	z[1] = ma->zswap;
	pdg = ma->pdg;
	memset(z[0], 0, sizeof(double) * (ma->M + 1));
	memset(z[1], 0, sizeof(double) * (ma->M + 1));
	z[0][0] = 1.;
	last_min = last_max = 0;
	ma->t = 0.;
	if (ma->M == ma->n * 2) {
		int M = 0;
		for (_j = beg; _j < ma->n; ++_j) {
			int k, j = _j - beg, _min = last_min, _max = last_max, M0;
			double p[3], sum;
			M0 = M; M += 2;
			pdg = ma->pdg + _j * 3;
			p[0] = pdg[0]; p[1] = 2. * pdg[1]; p[2] = pdg[2];
			for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
			for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
			_max += 2;
			if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
			if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
			for (k = _min < 2? 2 : _min; k <= _max; ++k)
				z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
			for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
			ma->t += log(sum / (M * (M - 1.)));
			for (k = _min; k <= _max; ++k) z[1][k] /= sum;
			if (_min >= 1) z[1][_min-1] = 0.;
			if (_min >= 2) z[1][_min-2] = 0.;
			if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
			if (_j == ma->n1 - 1) { // set pop1; ma->n1==-1 when unset
				ma->t1 = ma->t;
				memcpy(ma->z1, z[1], sizeof(double) * (ma->n1 * 2 + 1));
			}
			tmp = z[0]; z[0] = z[1]; z[1] = tmp;
			last_min = _min; last_max = _max;
		}
		//for (_j = 0; _j < last_min; ++_j) z[0][_j] = 0.; // TODO: are these necessary?
		//for (_j = last_max + 1; _j < ma->M; ++_j) z[0][_j] = 0.;
	} else { // this block is very similar to the block above; these two might be merged in future
		int j, M = 0;
		for (j = 0; j < ma->n; ++j) {
			int k, M0, _min = last_min, _max = last_max;
			double p[3], sum;
			pdg = ma->pdg + j * 3;
			for (; _min < _max && z[0][_min] < TINY; ++_min) z[0][_min] = z[1][_min] = 0.;
			for (; _max > _min && z[0][_max] < TINY; --_max) z[0][_max] = z[1][_max] = 0.;
			M0 = M;
			M += ma->ploidy[j];
			if (ma->ploidy[j] == 1) {
				p[0] = pdg[0]; p[1] = pdg[2];
				_max++;
				if (_min == 0) k = 0, z[1][k] = (M0+1-k) * p[0] * z[0][k];
				for (k = _min < 1? 1 : _min; k <= _max; ++k)
					z[1][k] = (M0+1-k) * p[0] * z[0][k] + k * p[1] * z[0][k-1];
				for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
				ma->t += log(sum / M);
				for (k = _min; k <= _max; ++k) z[1][k] /= sum;
				if (_min >= 1) z[1][_min-1] = 0.;
				if (j < ma->n - 1) z[1][_max+1] = 0.;
			} else if (ma->ploidy[j] == 2) {
				p[0] = pdg[0]; p[1] = 2 * pdg[1]; p[2] = pdg[2];
				_max += 2;
				if (_min == 0) k = 0, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k];
				if (_min <= 1) k = 1, z[1][k] = (M0-k+1) * (M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1];
				for (k = _min < 2? 2 : _min; k <= _max; ++k)
					z[1][k] = (M0-k+1)*(M0-k+2) * p[0] * z[0][k] + k*(M0-k+2) * p[1] * z[0][k-1] + k*(k-1)* p[2] * z[0][k-2];
				for (k = _min, sum = 0.; k <= _max; ++k) sum += z[1][k];
				ma->t += log(sum / (M * (M - 1.)));
				for (k = _min; k <= _max; ++k) z[1][k] /= sum;
				if (_min >= 1) z[1][_min-1] = 0.;
				if (_min >= 2) z[1][_min-2] = 0.;
				if (j < ma->n - 1) z[1][_max+1] = z[1][_max+2] = 0.;
			}
			tmp = z[0]; z[0] = z[1]; z[1] = tmp;
			last_min = _min; last_max = _max;
		}
	}
	if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
}

static void mc_cal_y(bcf_p1aux_t *ma)
{
	if (ma->n1 > 0 && ma->n1 < ma->n && ma->M == ma->n * 2) { // NB: ma->n1 is ineffective when there are haploid samples
		int k;
		long double x;
		memset(ma->z1, 0, sizeof(double) * (2 * ma->n1 + 1));
		memset(ma->z2, 0, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
		ma->t1 = ma->t2 = 0.;
		mc_cal_y_core(ma, ma->n1);
		ma->t2 = ma->t;
		memcpy(ma->z2, ma->z, sizeof(double) * (2 * (ma->n - ma->n1) + 1));
		mc_cal_y_core(ma, 0);
		// rescale z
		x = expl(ma->t - (ma->t1 + ma->t2));
		for (k = 0; k <= ma->M; ++k) ma->z[k] *= x;
	} else mc_cal_y_core(ma, 0);
}

#define CONTRAST_TINY 1e-30

extern double kf_gammaq(double s, double z); // incomplete gamma function for chi^2 test

static inline double chi2_test(int a, int b, int c, int d)
{
	double x, z;
	x = (double)(a+b) * (c+d) * (b+d) * (a+c);
	if (x == 0.) return 1;
	z = a * d - b * c;
	return kf_gammaq(.5, .5 * z * z * (a+b+c+d) / x);
}

// chi2=(a+b+c+d)(ad-bc)^2/[(a+b)(c+d)(a+c)(b+d)]
static inline double contrast2_aux(const bcf_p1aux_t *p1, double sum, int k1, int k2, double x[3])
{
	double p = p1->phi[k1+k2] * p1->z1[k1] * p1->z2[k2] / sum * p1->hg[k1][k2];
	int n1 = p1->n1, n2 = p1->n - p1->n1;
	if (p < CONTRAST_TINY) return -1;
	if (.5*k1/n1 < .5*k2/n2) x[1] += p;
	else if (.5*k1/n1 > .5*k2/n2) x[2] += p;
	else x[0] += p;
	return p * chi2_test(k1, k2, (n1<<1) - k1, (n2<<1) - k2);
}

static double contrast2(bcf_p1aux_t *p1, double ret[3])
{
	int k, k1, k2, k10, k20, n1, n2;
	double sum;
	// get n1 and n2
	n1 = p1->n1; n2 = p1->n - p1->n1;
	if (n1 <= 0 || n2 <= 0) return 0.;
	if (p1->hg == 0) { // initialize the hypergeometric distribution
		/* NB: the hg matrix may take a lot of memory when there are many samples. There is a way
		   to avoid precomputing this matrix, but it is slower and quite intricate. The following
		   computation in this block can be accelerated with a similar strategy, but perhaps this
		   is not a serious concern for now. */
		double tmp = lgamma(2*(n1+n2)+1) - (lgamma(2*n1+1) + lgamma(2*n2+1));
		p1->hg = calloc(2*n1+1, sizeof(void*));
		for (k1 = 0; k1 <= 2*n1; ++k1) {
			p1->hg[k1] = calloc(2*n2+1, sizeof(double));
			for (k2 = 0; k2 <= 2*n2; ++k2)
				p1->hg[k1][k2] = exp(lgamma(k1+k2+1) + lgamma(p1->M-k1-k2+1) - (lgamma(k1+1) + lgamma(k2+1) + lgamma(2*n1-k1+1) + lgamma(2*n2-k2+1) + tmp));
		}
	}
	{ // compute
		long double suml = 0;
		for (k = 0; k <= p1->M; ++k) suml += p1->phi[k] * p1->z[k];
		sum = suml;
	}
	{ // get the max k1 and k2
		double max;
		int max_k;
		for (k = 0, max = 0, max_k = -1; k <= 2*n1; ++k) {
			double x = p1->phi1[k] * p1->z1[k];
			if (x > max) max = x, max_k = k;
		}
		k10 = max_k;
		for (k = 0, max = 0, max_k = -1; k <= 2*n2; ++k) {
			double x = p1->phi2[k] * p1->z2[k];
			if (x > max) max = x, max_k = k;
		}
		k20 = max_k;
	}
	{ // We can do the following with one nested loop, but that is an O(N^2) thing. The following code block is much faster for large N.
		double x[3], y;
		long double z = 0., L[2];
		x[0] = x[1] = x[2] = 0; L[0] = L[1] = 0;
		for (k1 = k10; k1 >= 0; --k1) {
			for (k2 = k20; k2 >= 0; --k2) {
				if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
				else z += y;
			}
			for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
				if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
				else z += y;
			}
		}
		ret[0] = x[0]; ret[1] = x[1]; ret[2] = x[2];
		x[0] = x[1] = x[2] = 0;
		for (k1 = k10 + 1; k1 <= 2*n1; ++k1) {
			for (k2 = k20; k2 >= 0; --k2) {
				if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
				else z += y;
			}
			for (k2 = k20 + 1; k2 <= 2*n2; ++k2) {
				if ((y = contrast2_aux(p1, sum, k1, k2, x)) < 0) break;
				else z += y;
			}
		}
		ret[0] += x[0]; ret[1] += x[1]; ret[2] += x[2];
		if (ret[0] + ret[1] + ret[2] < 0.95) { // in case of bad things happened
			ret[0] = ret[1] = ret[2] = 0; L[0] = L[1] = 0;
			for (k1 = 0, z = 0.; k1 <= 2*n1; ++k1)
				for (k2 = 0; k2 <= 2*n2; ++k2)
					if ((y = contrast2_aux(p1, sum, k1, k2, ret)) >= 0) z += y;
			if (ret[0] + ret[1] + ret[2] < 0.95) // It seems that this may be caused by floating point errors. I do not really understand why...
				z = 1.0, ret[0] = ret[1] = ret[2] = 1./3;
		}
		return (double)z;
	}
}

static double mc_cal_afs(bcf_p1aux_t *ma, double *p_ref_folded, double *p_var_folded)
{
	int k;
	long double sum = 0., sum2;
	double *phi = ma->is_indel? ma->phi_indel : ma->phi;
	memset(ma->afs1, 0, sizeof(double) * (ma->M + 1));
	mc_cal_y(ma);
	// compute AFS
	for (k = 0, sum = 0.; k <= ma->M; ++k)
		sum += (long double)phi[k] * ma->z[k];
	for (k = 0; k <= ma->M; ++k) {
		ma->afs1[k] = phi[k] * ma->z[k] / sum;
		if (isnan(ma->afs1[k]) || isinf(ma->afs1[k])) return -1.;
	}
	// compute folded variant probability
	for (k = 0, sum = 0.; k <= ma->M; ++k)
		sum += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
	for (k = 1, sum2 = 0.; k < ma->M; ++k)
		sum2 += (long double)(phi[k] + phi[ma->M - k]) / 2. * ma->z[k];
	*p_var_folded = sum2 / sum;
	*p_ref_folded = (phi[k] + phi[ma->M - k]) / 2. * (ma->z[ma->M] + ma->z[0]) / sum;
	// the expected frequency
	for (k = 0, sum = 0.; k <= ma->M; ++k) {
		ma->afs[k] += ma->afs1[k];
		sum += k * ma->afs1[k];
	}
	return sum / ma->M;
}

int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst)
{
	int i, k;
	long double sum = 0.;
	ma->is_indel = bcf_is_indel(b);
	rst->perm_rank = -1;
	// set PL and PL_len
	for (i = 0; i < b->n_gi; ++i) {
		if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
			ma->PL = (uint8_t*)b->gi[i].data;
			ma->PL_len = b->gi[i].len;
			break;
		}
	}
	if (i == b->n_gi) return -1; // no PL
	if (b->n_alleles < 2) return -1; // FIXME: find a better solution
	// 
	rst->rank0 = cal_pdg(b, ma);
	rst->f_exp = mc_cal_afs(ma, &rst->p_ref_folded, &rst->p_var_folded);
	rst->p_ref = ma->afs1[ma->M];
	for (k = 0, sum = 0.; k < ma->M; ++k)
		sum += ma->afs1[k];
	rst->p_var = (double)sum;
	{ // compute the allele count
		double max = -1;
		rst->ac = -1;
		for (k = 0; k <= ma->M; ++k)
			if (max < ma->z[k]) max = ma->z[k], rst->ac = k;
		rst->ac = ma->M - rst->ac;
	}
	// calculate f_flat and f_em
	for (k = 0, sum = 0.; k <= ma->M; ++k)
		sum += (long double)ma->z[k];
	rst->f_flat = 0.;
	for (k = 0; k <= ma->M; ++k) {
		double p = ma->z[k] / sum;
		rst->f_flat += k * p;
	}
	rst->f_flat /= ma->M;
	{ // estimate equal-tail credible interval (95% level)
		int l, h;
		double p;
		for (i = 0, p = 0.; i <= ma->M; ++i)
			if (p + ma->afs1[i] > 0.025) break;
			else p += ma->afs1[i];
		l = i;
		for (i = ma->M, p = 0.; i >= 0; --i)
			if (p + ma->afs1[i] > 0.025) break;
			else p += ma->afs1[i];
		h = i;
		rst->cil = (double)(ma->M - h) / ma->M; rst->cih = (double)(ma->M - l) / ma->M;
	}
	if (ma->n1 > 0) { // compute LRT
		double max0, max1, max2;
		for (k = 0, max0 = -1; k <= ma->M; ++k)
			if (max0 < ma->z[k]) max0 = ma->z[k];
		for (k = 0, max1 = -1; k <= ma->n1 * 2; ++k)
			if (max1 < ma->z1[k]) max1 = ma->z1[k];
		for (k = 0, max2 = -1; k <= ma->M - ma->n1 * 2; ++k)
			if (max2 < ma->z2[k]) max2 = ma->z2[k];
		rst->lrt = log(max1 * max2 / max0);
		rst->lrt = rst->lrt < 0? 1 : kf_gammaq(.5, rst->lrt);
	} else rst->lrt = -1.0;
	rst->cmp[0] = rst->cmp[1] = rst->cmp[2] = rst->p_chi2 = -1.0;
	if (do_contrast && rst->p_var > 0.5) // skip contrast2() if the locus is a strong non-variant
		rst->p_chi2 = contrast2(ma, rst->cmp);
	return 0;
}

void bcf_p1_dump_afs(bcf_p1aux_t *ma)
{
	int k;
	fprintf(stderr, "[afs]");
	for (k = 0; k <= ma->M; ++k)
		fprintf(stderr, " %d:%.3lf", k, ma->afs[ma->M - k]);
	fprintf(stderr, "\n");
	memset(ma->afs, 0, sizeof(double) * (ma->M + 1));
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/prob1.h000066400000000000000000000023141211610345200240500ustar00rootroot00000000000000#ifndef BCF_PROB1_H
#define BCF_PROB1_H

#include "bcf.h"

struct __bcf_p1aux_t;
typedef struct __bcf_p1aux_t bcf_p1aux_t;

typedef struct {
	int rank0, perm_rank; // NB: perm_rank is always set to -1 by bcf_p1_cal()
	int ac; // ML alternative allele count
	double f_exp, f_flat, p_ref_folded, p_ref, p_var_folded, p_var;
	double cil, cih;
	double cmp[3], p_chi2, lrt; // used by contrast2()
} bcf_p1rst_t;

#define MC_PTYPE_FULL  1
#define MC_PTYPE_COND2 2
#define MC_PTYPE_FLAT  3

#ifdef __cplusplus
extern "C" {
#endif

	bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy);
	void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
	void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
	void bcf_p1_destroy(bcf_p1aux_t *ma);
	int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
	int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
	void bcf_p1_dump_afs(bcf_p1aux_t *ma);
	int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
	int bcf_p1_set_n1(bcf_p1aux_t *b, int n1);
	void bcf_p1_set_folded(bcf_p1aux_t *p1a); // only effective when set_n1() is not called

	int bcf_em1(const bcf1_t *b, int n1, int flag, double x[10]);

#ifdef __cplusplus
}
#endif

#endif
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/vcf.c000066400000000000000000000153171211610345200236050ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include "bcf.h"
#include "kstring.h"
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 4096)

typedef struct {
	gzFile fp;
	FILE *fpout;
	kstream_t *ks;
	void *refhash;
	kstring_t line;
	int max_ref;
} vcf_t;

bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
{
	kstring_t meta, smpl;
	int dret;
	vcf_t *v;
	bcf_hdr_t *h;
	if (!bp->is_vcf) return bcf_hdr_read(bp);
	h = calloc(1, sizeof(bcf_hdr_t));
	v = (vcf_t*)bp->v;
	v->line.l = 0;
	memset(&meta, 0, sizeof(kstring_t));
	memset(&smpl, 0, sizeof(kstring_t));
	while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
		if (v->line.l < 2) continue;
		if (v->line.s[0] != '#') return 0; // no sample line
		if (v->line.s[0] == '#' && v->line.s[1] == '#') {
			kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
		} else if (v->line.s[0] == '#') {
			int k;
			ks_tokaux_t aux;
			char *p;
			for (p = kstrtok(v->line.s, "\t\n", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
				if (k >= 9) {
					kputsn(p, aux.p - p, &smpl);
					kputc('\0', &smpl);
				}
			}
			break;
		}
	}
	kputc('\0', &meta);
	h->name = 0;
	h->sname = smpl.s; h->l_smpl = smpl.l;
	h->txt = meta.s; h->l_txt = meta.l;
	bcf_hdr_sync(h);
	return h;
}

bcf_t *vcf_open(const char *fn, const char *mode)
{
	bcf_t *bp;
	vcf_t *v;
	if (strchr(mode, 'b')) return bcf_open(fn, mode);
	bp = calloc(1, sizeof(bcf_t));
	v = calloc(1, sizeof(vcf_t));
	bp->is_vcf = 1;
	bp->v = v;
	v->refhash = bcf_str2id_init();
	if (strchr(mode, 'r')) {
		v->fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
		v->ks = ks_init(v->fp);
	} else if (strchr(mode, 'w'))
		v->fpout = strcmp(fn, "-")? fopen(fn, "w") : stdout;
	return bp;
}

int vcf_dictread(bcf_t *bp, bcf_hdr_t *h, const char *fn)
{
	vcf_t *v;
	gzFile fp;
	kstream_t *ks;
	kstring_t s, rn;
	int dret;
	if (bp == 0) return -1;
	if (!bp->is_vcf) return 0;
	s.l = s.m = 0; s.s = 0;
	rn.m = rn.l = h->l_nm; rn.s = h->name;
	v = (vcf_t*)bp->v;
	fp = gzopen(fn, "r");
	ks = ks_init(fp);
	while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
		bcf_str2id_add(v->refhash, strdup(s.s));
		kputs(s.s, &rn); kputc('\0', &rn);
		if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
	}
	ks_destroy(ks);
	gzclose(fp);
	h->l_nm = rn.l; h->name = rn.s;
	bcf_hdr_sync(h);
	free(s.s);
	return 0;
}

int vcf_close(bcf_t *bp)
{
	vcf_t *v;
	if (bp == 0) return -1;
	if (!bp->is_vcf) return bcf_close(bp);
	v = (vcf_t*)bp->v;
	if (v->fp) {
		ks_destroy(v->ks);
		gzclose(v->fp);
	}
	if (v->fpout) fclose(v->fpout);
	free(v->line.s);
	bcf_str2id_thorough_destroy(v->refhash);
	free(v);
	free(bp);
	return 0;
}

int vcf_hdr_write(bcf_t *bp, const bcf_hdr_t *h)
{
	vcf_t *v = (vcf_t*)bp->v;
	int i, has_ver = 0;
	if (!bp->is_vcf) return bcf_hdr_write(bp, h);
	if (h->l_txt > 0) {
		if (strstr(h->txt, "##fileformat=")) has_ver = 1;
		if (has_ver == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
		fwrite(h->txt, 1, h->l_txt - 1, v->fpout);
	}
	if (h->l_txt == 0) fprintf(v->fpout, "##fileformat=VCFv4.1\n");
	fprintf(v->fpout, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
	for (i = 0; i < h->n_smpl; ++i)
		fprintf(v->fpout, "\t%s", h->sns[i]);
	fputc('\n', v->fpout);
	return 0;
}

int vcf_write(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
{
	vcf_t *v = (vcf_t*)bp->v;
	extern void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s);
	if (!bp->is_vcf) return bcf_write(bp, h, b);
	bcf_fmt_core(h, b, &v->line);
	fwrite(v->line.s, 1, v->line.l, v->fpout);
	fputc('\n', v->fpout);
	return v->line.l + 1;
}

int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
{
	int dret, k, i, sync = 0;
	vcf_t *v = (vcf_t*)bp->v;
	char *p, *q;
	kstring_t str, rn;
	ks_tokaux_t aux, a2;
	if (!bp->is_vcf) return bcf_read(bp, h, b);
	v->line.l = 0;
	str.l = 0; str.m = b->m_str; str.s = b->str;
	rn.l = rn.m = h->l_nm; rn.s = h->name;
	if (ks_getuntil(v->ks, '\n', &v->line, &dret) < 0) return -1;
	b->n_smpl = h->n_smpl;
	for (p = kstrtok(v->line.s, "\t", &aux), k = 0; p; p = kstrtok(0, 0, &aux), ++k) {
		*(char*)aux.p = 0;
		if (k == 0) { // ref
			int tid = bcf_str2id(v->refhash, p);
			if (tid < 0) {
				tid = bcf_str2id_add(v->refhash, strdup(p));
				kputs(p, &rn); kputc('\0', &rn);
				sync = 1;
			}
			b->tid = tid;
		} else if (k == 1) { // pos
			b->pos = atoi(p) - 1;
		} else if (k == 5) { // qual
			b->qual = (p[0] >= '0' && p[0] <= '9')? atof(p) : 0;
		} else if (k <= 8) { // variable length strings
			kputs(p, &str); kputc('\0', &str);
			b->l_str = str.l; b->m_str = str.m; b->str = str.s;
			if (k == 8) bcf_sync(b);
		} else { // k > 9
			if (strncmp(p, "./.", 3) == 0) {
				for (i = 0; i < b->n_gi; ++i) {
					if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
						((uint8_t*)b->gi[i].data)[k-9] = 1<<7;
					} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
						((uint8_t*)b->gi[i].data)[k-9] = 0;
					} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
						((int32_t*)b->gi[i].data)[k-9] = 0;
					} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
						((uint16_t*)b->gi[i].data)[k-9] = 0;
					} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
						int y = b->n_alleles * (b->n_alleles + 1) / 2;
						memset((uint8_t*)b->gi[i].data + (k - 9) * y, 0, y);
					} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
						int y = b->n_alleles * (b->n_alleles + 1) / 2;
						memset((float*)b->gi[i].data + (k - 9) * y, 0, y * 4);
					}
				}
				goto endblock;
			}
			for (q = kstrtok(p, ":", &a2), i = 0; q && i < b->n_gi; q = kstrtok(0, 0, &a2), ++i) {
				if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
					((uint8_t*)b->gi[i].data)[k-9] = (q[0] - '0')<<3 | (q[2] - '0') | (q[1] == '/'? 0 : 1) << 6;
				} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
					double _x = strtod(q, &q);
					int x = (int)(_x + .499);
					if (x > 255) x = 255;
					((uint8_t*)b->gi[i].data)[k-9] = x;
				} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
					int x = strtol(q, &q, 10);
					if (x > 0xffff) x = 0xffff;
					((uint32_t*)b->gi[i].data)[k-9] = x;
				} else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
					int x = strtol(q, &q, 10);
					if (x > 0xffff) x = 0xffff;
					((uint16_t*)b->gi[i].data)[k-9] = x;
				} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
					int x, y, j;
					uint8_t *data = (uint8_t*)b->gi[i].data;
					y = b->n_alleles * (b->n_alleles + 1) / 2;
					for (j = 0; j < y; ++j) {
						x = strtol(q, &q, 10);
						if (x > 255) x = 255;
						data[(k-9) * y + j] = x;
						++q;
					}
				} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
					int j, y;
					float x, *data = (float*)b->gi[i].data;
					y = b->n_alleles * (b->n_alleles + 1) / 2;
					for (j = 0; j < y; ++j) {
						x = strtod(q, &q);
						data[(k-9) * y + j] = x > 0? -x/10. : x;
						++q;
					}
				}
			}
		endblock: i = i;
		}
	}
	h->l_nm = rn.l; h->name = rn.s;
	if (sync) bcf_hdr_sync(h);
	return v->line.l + 1;
}
genometools-1.5.1/src/external/samtools-0.1.18/bcftools/vcfutils.pl000077500000000000000000000365331211610345200250650ustar00rootroot00000000000000#!/usr/bin/perl -w

# Author: lh3

use strict;
use warnings;
use Getopt::Std;

&main;
exit;

sub main {
  &usage if (@ARGV < 1);
  my $command = shift(@ARGV);
  my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
			  hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats,
			  gapstats=>\&gapstats, splitchr=>\&splitchr, vcf2fq=>\&vcf2fq);
  die("Unknown command \"$command\".\n") if (!defined($func{$command}));
  &{$func{$command}};
}

sub splitchr {
  my %opts = (l=>5000000);
  getopts('l:', \%opts);
  my $l = $opts{l};
  die(qq/Usage: vcfutils.pl splitchr [-l $opts{l}] \n/) if (@ARGV == 0 && -t STDIN);
  while (<>) {
	my @t = split;
	my $last = 0;
	for (my $i = 0; $i < $t[1];) {
	  my $e = ($t[1] - $i) / $l < 1.1? $t[1] : $i + $l;
	  print "$t[0]:".($i+1)."-$e\n";
	  $i = $e;
	}
  }
}

sub subsam {
  die(qq/Usage: vcfutils.pl subsam  [samples]\n/) if (@ARGV == 0);
  my ($fh, %h);
  my $fn = shift(@ARGV);
  my @col;
  open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die;
  $h{$_} = 1 for (@ARGV);
  while (<$fh>) {
	if (/^##/) {
	  print;
	} elsif (/^#/) {
	  my @t = split;
	  my @s = @t[0..8]; # all fixed fields + FORMAT
	  for (9 .. $#t) {
		if ($h{$t[$_]}) {
		  push(@s, $t[$_]);
		  push(@col, $_);
		}
	  }
	  pop(@s) if (@s == 9); # no sample selected; remove the FORMAT field
	  print join("\t", @s), "\n";
	} else {
	  my @t = split;
	  if (@col == 0) {
		print join("\t", @t[0..7]), "\n";
	  } else {
		print join("\t", @t[0..8], map {$t[$_]} @col), "\n";
	  }
	}
  }
  close($fh);
}

sub listsam {
  die(qq/Usage: vcfutils.pl listsam \n/) if (@ARGV == 0 && -t STDIN);
  while (<>) {
	if (/^#/ && !/^##/) {
	  my @t = split;
	  print join("\n", @t[9..$#t]), "\n";
	  exit;
	}
  }
}

sub fillac {
  die(qq/Usage: vcfutils.pl fillac \n\nNote: The GT field MUST BE present and always appear as the first field.\n/) if (@ARGV == 0 && -t STDIN);
  while (<>) {
	if (/^#/) {
	  print;
	} else {
	  my @t = split;
	  my @c = (0, 0);
	  my $n = 0;
	  my $s = -1;
	  @_ = split(":", $t[8]);
	  for (0 .. $#_) {
		if ($_[$_] eq 'GT') { $s = $_; last; }
	  }
	  if ($s < 0) {
		print join("\t", @t), "\n";
		next;
	  }
	  for (9 .. $#t) {
		if ($t[$_] =~ /^0,0,0/) {
		} elsif ($t[$_] =~ /^([^\s:]+:){$s}(\d+).(\d+)/) {
		  ++$c[$2]; ++$c[$3];
		  $n += 2;
		}
	  }
	  my $AC = "AC=" . join("\t", @c[1..$#c]) . ";AN=$n";
	  my $info = $t[7];
	  $info =~ s/(;?)AC=(\d+)//;
	  $info =~ s/(;?)AN=(\d+)//;
	  if ($info eq '.') {
		$info = $AC;
	  } else {
		$info .= ";$AC";
	  }
	  $t[7] = $info;
	  print join("\t", @t), "\n";
	}
  }
}

sub ldstats {
  my %opts = (t=>0.9);
  getopts('t:', \%opts);
  die("Usage: vcfutils.pl ldstats [-t $opts{t}] \n") if (@ARGV == 0 && -t STDIN);
  my $cutoff = $opts{t};
  my ($last, $lastchr) = (0x7fffffff, '');
  my ($x, $y, $n) = (0, 0, 0);
  while (<>) {
	if (/^([^#\s]+)\s(\d+)/) {
	  my ($chr, $pos) = ($1, $2);
	  if (/NEIR=([\d\.]+)/) {
		++$n;
		++$y, $x += $pos - $last if ($lastchr eq $chr && $pos > $last && $1 > $cutoff);
	  }
	  $last = $pos; $lastchr = $chr;
	}
  }
  print "Number of SNP intervals in strong LD (r > $opts{t}): $y\n";
  print "Fraction: ", $y/$n, "\n";
  print "Length: $x\n";
}

sub qstats {
  my %opts = (r=>'', s=>0.02, v=>undef);
  getopts('r:s:v', \%opts);
  die("Usage: vcfutils.pl qstats [-r ref.vcf] \n
Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #joint ts/tv #joint/#ref #joint/#non-indel \n") if (@ARGV == 0 && -t STDIN);
  my %ts = (AG=>1, GA=>1, CT=>1, TC=>1);
  my %h = ();
  my $is_vcf = defined($opts{v})? 1 : 0;
  if ($opts{r}) { # read the reference positions
	my $fh;
	open($fh, $opts{r}) || die;
	while (<$fh>) {
	  next if (/^#/);
	  if ($is_vcf) {
		my @t = split;
		$h{$t[0],$t[1]} = $t[4];
	  } else {
		$h{$1,$2} = 1 if (/^(\S+)\s+(\d+)/);
	  }
	}
	close($fh);
  }
  my $hsize = scalar(keys %h);
  my @a;
  while (<>) {
	next if (/^#/);
	my @t = split;
	next if (length($t[3]) != 1 || uc($t[3]) eq 'N');
	$t[3] = uc($t[3]); $t[4] = uc($t[4]);
	my @s = split(',', $t[4]);
	$t[5] = 3 if ($t[5] eq '.' || $t[5] < 0);
	next if (length($s[0]) != 1);
	my $hit;
	if ($is_vcf) {
	  $hit = 0;
	  my $aa = $h{$t[0],$t[1]};
	  if (defined($aa)) {
		my @aaa = split(",", $aa);
		for (@aaa) {
		  $hit = 1 if ($_ eq $s[0]);
		}
	  }
	} else {
	  $hit = defined($h{$t[0],$t[1]})? 1 : 0;
	}
	push(@a, [$t[5], ($t[4] eq '.' || $t[4] eq $t[3])? 0 : 1, $ts{$t[3].$s[0]}? 1 : 0, $hit]);
  }
  push(@a, [-1, 0, 0, 0]); # end marker
  die("[qstats] No SNP data!\n") if (@a == 0);
  @a = sort {$b->[0]<=>$a->[0]} @a;
  my $next = $opts{s};
  my $last = $a[0];
  my @c = (0, 0, 0, 0);
  my @lc;
  $lc[1] = $lc[2] = 0;
  for my $p (@a) {
	if ($p->[0] == -1 || ($p->[0] != $last && $c[0]/@a > $next)) {
	  my @x;
	  $x[0] = sprintf("%.4f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
	  $x[1] = sprintf("%.4f", $hsize? $c[3] / $hsize : 0);
	  $x[2] = sprintf("%.4f", $c[3] / $c[1]);
	  my $a = $c[1] - $lc[1];
	  my $b = $c[2] - $lc[2];
	  $x[3] = sprintf("%.4f", $a-$b? $b / ($a-$b) : 100);
	  print join("\t", $last, @c, @x), "\n";
	  $next = $c[0]/@a + $opts{s};
	  $lc[1] = $c[1]; $lc[2] = $c[2];
	}
	++$c[0]; $c[1] += $p->[1]; $c[2] += $p->[2]; $c[3] += $p->[3];
	$last = $p->[0];
  }
}

sub varFilter {
  my %opts = (d=>2, D=>10000000, a=>2, W=>10, Q=>10, w=>3, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, G=>0, S=>1000, e=>1e-4);
  getopts('pd:D:W:Q:w:a:1:2:3:4:G:S:e:', \%opts);
  die(qq/
Usage:   vcfutils.pl varFilter [options] 

Options: -Q INT    minimum RMS mapping quality for SNPs [$opts{Q}]
         -d INT    minimum read depth [$opts{d}]
         -D INT    maximum read depth [$opts{D}]
         -a INT    minimum number of alternate bases [$opts{a}]
         -w INT    SNP within INT bp around a gap to be filtered [$opts{w}]
         -W INT    window size for filtering adjacent gaps [$opts{W}]
         -1 FLOAT  min P-value for strand bias (given PV4) [$opts{1}]
         -2 FLOAT  min P-value for baseQ bias [$opts{2}]
         -3 FLOAT  min P-value for mapQ bias [$opts{3}]
         -4 FLOAT  min P-value for end distance bias [$opts{4}]
		 -e FLOAT  min P-value for HWE (plus F<0) [$opts{e}]
         -p        print filtered variants

Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools.
\n/) if (@ARGV == 0 && -t STDIN);

  # calculate the window size
  my ($ol, $ow) = ($opts{W}, $opts{w});
  my $max_dist = $ol > $ow? $ol : $ow;
  # the core loop
  my @staging; # (indel_filtering_score, flt_tag, indel_span; chr, pos, ...)
  while (<>) {
	my @t = split;
    if (/^#/) {
	  print; next;
	}
	next if ($t[4] eq '.'); # skip non-var sites
    next if ($t[3] eq 'N'); # skip sites with unknown ref ('N')
	# check if the site is a SNP
	my $type = 1; # SNP
	if (length($t[3]) > 1) {
	  $type = 2; # MNP
	  my @s = split(',', $t[4]);
	  for (@s) {
		$type = 3 if (length != length($t[3]));
	  }
	} else {
	  my @s = split(',', $t[4]);
	  for (@s) {
		$type = 3 if (length > 1);
	  }
	}
	# clear the out-of-range elements
	while (@staging) {
      # Still on the same chromosome and the first element's window still affects this position?
	  last if ($staging[0][3] eq $t[0] && $staging[0][4] + $staging[0][2] + $max_dist >= $t[1]);
	  varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much
	}
	my $flt = 0;
	# parse annotations
	my ($dp, $mq, $dp_alt) = (-1, -1, -1);
	if ($t[7] =~ /DP4=(\d+),(\d+),(\d+),(\d+)/i) {
	  $dp = $1 + $2 + $3 + $4;
	  $dp_alt = $3 + $4;
	}
	if ($t[7] =~ /DP=(\d+)/i) {
	  $dp = $1;
	}
	$mq = $1 if ($t[7] =~ /MQ=(\d+)/i);
	# the depth and mapQ filter
	if ($dp >= 0) {
	  if ($dp < $opts{d}) {
		$flt = 2;
	  } elsif ($dp > $opts{D}) {
		$flt = 3;
	  }
	}
	$flt = 4 if ($dp_alt >= 0 && $dp_alt < $opts{a});
	$flt = 1 if ($flt == 0 && $mq >= 0 && $mq < $opts{Q});
	$flt = 7 if ($flt == 0 && /PV4=([^,]+),([^,]+),([^,]+),([^,;\t]+)/
				 && ($1<$opts{1} || $2<$opts{2} || $3<$opts{3} || $4<$opts{4}));
	$flt = 8 if ($flt == 0 && ((/MXGQ=(\d+)/ && $1 < $opts{G}) || (/MXSP=(\d+)/ && $1 >= $opts{S})));
	# HWE filter
	if ($t[7] =~ /G3=([^;,]+),([^;,]+),([^;,]+).*HWE=([^;,]+)/ && $4 < $opts{e}) {
		my $p = 2*$1 + $2;
		my $f = ($p > 0 && $p < 1)? 1 - $2 / ($p * (1-$p)) : 0;
		$flt = 9 if ($f < 0);
	}

	my $score = $t[5] * 100 + $dp_alt;
	my $rlen = length($t[3]) - 1; # $indel_score<0 for SNPs
	if ($flt == 0) {
	  if ($type == 3) { # an indel
		# filtering SNPs and MNPs
		for my $x (@staging) {
		  next if (($x->[0]&3) == 3 || $x->[1] || $x->[4] + $x->[2] + $ow < $t[1]);
		  $x->[1] = 5;
		}
		# check the staging list for indel filtering
		for my $x (@staging) {
		  next if (($x->[0]&3) != 3 || $x->[1] || $x->[4] + $x->[2] + $ol < $t[1]);
		  if ($x->[0]>>2 < $score) {
			$x->[1] = 6;
		  } else {
			$flt = 6; last;
		  }
		}
	  } else { # SNP or MNP
		for my $x (@staging) {
		  next if (($x->[0]&3) != 3 || $x->[4] + $x->[2] + $ow < $t[1]);
		  if ($x->[4] + length($x->[7]) - 1 == $t[1] && substr($x->[7], -1, 1) eq substr($t[4], 0, 1)
			  && length($x->[7]) - length($x->[6]) == 1) {
			$x->[1] = 5;
		  } else { $flt = 5; }
		  last;
		}
		# check MNP
		for my $x (@staging) {
		  next if (($x->[0]&3) == 3 || $x->[4] + $x->[2] < $t[1]);
		  if ($x->[0]>>2 < $score) {
			$x->[1] = 8;
		  } else {
			$flt = 8; last;
		  }
		}
	  }
	}
	push(@staging, [$score<<2|$type, $flt, $rlen, @t]);
  }
  # output the last few elements in the staging list
  while (@staging) {
	varFilter_aux(shift @staging, $opts{p});
  }
}

sub varFilter_aux {
  my ($first, $is_print) = @_;
  if ($first->[1] == 0) {
	print join("\t", @$first[3 .. @$first-1]), "\n";
  } elsif ($is_print) {
	print STDERR join("\t", substr("UQdDaGgPMS", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
  }
}

sub gapstats {
  my (@c0, @c1);
  $c0[$_] = $c1[$_] = 0 for (0 .. 10000);
  while (<>) {
	next if (/^#/);
	my @t = split;
	next if (length($t[3]) == 1 && $t[4] =~ /^[A-Za-z](,[A-Za-z])*$/); # not an indel
	my @s = split(',', $t[4]);
	for my $x (@s) {
	  my $l = length($x) - length($t[3]) + 5000;
	  if ($x =~ /^-/) {
		$l = -(length($x) - 1) + 5000;
	  } elsif ($x =~ /^\+/) {
		$l = length($x) - 1 + 5000;
	  }
	  $c0[$l] += 1 / @s;
	}
  }
  for (my $i = 0; $i < 10000; ++$i) {
	next if ($c0[$i] == 0);
	$c1[0] += $c0[$i];
	$c1[1] += $c0[$i] if (($i-5000)%3 == 0);
	printf("C\t%d\t%.2f\n", ($i-5000), $c0[$i]);
  }
  printf("3\t%d\t%d\t%.3f\n", $c1[0], $c1[1], $c1[1]/$c1[0]);
}

sub ucscsnp2vcf {
  die("Usage: vcfutils.pl \n") if (@ARGV == 0 && -t STDIN);
  print "##fileformat=VCFv4.0\n";
  print join("\t", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"), "\n";
  while (<>) {
	my @t = split("\t");
	my $indel = ($t[9] =~ /^[ACGT](\/[ACGT])+$/)? 0 : 1;
	my $pos = $t[2] + 1;
	my @alt;
	push(@alt, $t[7]);
	if ($t[6] eq '-') {
	  $t[9] = reverse($t[9]);
	  $t[9] =~ tr/ACGTRYMKWSNacgtrymkwsn/TGCAYRKMWSNtgcayrkmwsn/;
	}
	my @a = split("/", $t[9]);
	for (@a) {
	  push(@alt, $_) if ($_ ne $alt[0]);
	}
	if ($indel) {
	  --$pos;
	  for (0 .. $#alt) {
		$alt[$_] =~ tr/-//d;
		$alt[$_] = "N$alt[$_]";
	  }
	}
	my $ref = shift(@alt);
	my $af = $t[13] > 0? ";AF=$t[13]" : '';
	my $valid = ($t[12] eq 'unknown')? '' : ";valid=$t[12]";
	my $info = "molType=$t[10];class=$t[11]$valid$af";
	print join("\t", $t[1], $pos, $t[4], $ref, join(",", @alt), 0, '.', $info), "\n";
  }
}

sub hapmap2vcf {
  die("Usage: vcfutils.pl  \n") if (@ARGV == 0);
  my $fn = shift(@ARGV);
  # parse UCSC SNP
  warn("Parsing UCSC SNPs...\n");
  my ($fh, %map);
  open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die;
  while (<$fh>) {
	my @t = split;
	next if ($t[3] - $t[2] != 1); # not SNP
	@{$map{$t[4]}} = @t[1,3,7];
  }
  close($fh);
  # write VCF
  warn("Writing VCF...\n");
  print "##fileformat=VCFv4.0\n";
  while (<>) {
	my @t = split;
	if ($t[0] eq 'rs#') { # the first line
	  print join("\t", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", @t[11..$#t]), "\n";
	} else {
	  next unless ($map{$t[0]});
	  next if (length($t[1]) != 3); # skip non-SNPs
	  my $a = \@{$map{$t[0]}};
	  my $ref = $a->[2];
	  my @u = split('/', $t[1]);
	  if ($u[1] eq $ref) {
		$u[1] = $u[0]; $u[0] = $ref;
	  } elsif ($u[0] ne $ref) { next; }
	  my $alt = $u[1];
	  my %w;
	  $w{$u[0]} = 0; $w{$u[1]} = 1;
	  my @s = (@$a[0,1], $t[0], $ref, $alt, 0, '.', '.', 'GT');
	  my $is_tri = 0;
	  for (@t[11..$#t]) {
		if ($_ eq 'NN') {
		  push(@s, './.');
		} else {
		  my @a = ($w{substr($_,0,1)}, $w{substr($_,1,1)});
		  if (!defined($a[0]) || !defined($a[1])) {
			$is_tri = 1;
			last;
		  }
		  push(@s, "$a[0]/$a[1]");
		}
	  }
	  next if ($is_tri);
	  print join("\t", @s), "\n";
	}
  }
}

sub vcf2fq {
  my %opts = (d=>3, D=>100000, Q=>10, l=>5);
  getopts('d:D:Q:l:', \%opts);
  die(qq/
Usage:   vcfutils.pl vcf2fq [options] 

Options: -d INT    minimum depth          [$opts{d}]
         -D INT    maximum depth          [$opts{D}]
         -Q INT    min RMS mapQ           [$opts{Q}]
         -l INT    INDEL filtering window [$opts{l}]
\n/) if (@ARGV == 0 && -t STDIN);

  my ($last_chr, $seq, $qual, $last_pos, @gaps);
  my $_Q = $opts{Q};
  my $_d = $opts{d};
  my $_D = $opts{D};

  my %het = (AC=>'M', AG=>'R', AT=>'W', CA=>'M', CG=>'S', CT=>'Y',
			 GA=>'R', GC=>'S', GT=>'K', TA=>'W', TC=>'Y', TG=>'K');

  $last_chr = '';
  while (<>) {
	next if (/^#/);
	my @t = split;
	if ($last_chr ne $t[0]) {
	  &v2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l}) if ($last_chr);
	  ($last_chr, $last_pos) = ($t[0], 0);
	  $seq = $qual = '';
	  @gaps = ();
	}
	die("[vcf2fq] unsorted input\n") if ($t[1] - $last_pos < 0);
	if ($t[1] - $last_pos > 1) {
	  $seq .= 'n' x ($t[1] - $last_pos - 1);
	  $qual .= '!' x ($t[1] - $last_pos - 1);
	}
	if (length($t[3]) == 1 && $t[7] !~ /INDEL/ && $t[4] =~ /^([A-Za-z.])(,[A-Za-z])*$/) { # a SNP or reference
	  my ($ref, $alt) = ($t[3], $1);
	  my ($b, $q);
	  $q = $1 if ($t[7] =~ /FQ=(-?[\d\.]+)/);
	  if ($q < 0) {
		$_ = ($t[7] =~ /AF1=([\d\.]+)/)? $1 : 0;
		$b = ($_ < .5 || $alt eq '.')? $ref : $alt;
		$q = -$q;
	  } else {
		$b = $het{"$ref$alt"};
		$b ||= 'N';
	  }
	  $b = lc($b);
	  $b = uc($b) if (($t[7] =~ /MQ=(\d+)/ && $1 >= $_Q) && ($t[7] =~ /DP=(\d+)/ && $1 >= $_d && $1 <= $_D));
	  $q = int($q + 33 + .499);
	  $q = chr($q <= 126? $q : 126);
	  $seq .= $b;
	  $qual .= $q;
	} elsif ($t[4] ne '.') { # an INDEL
	  push(@gaps, [$t[1], length($t[3])]);
	}
	$last_pos = $t[1];
  }
  &v2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l});
}

sub v2q_post_process {
  my ($chr, $seq, $qual, $gaps, $l) = @_;
  for my $g (@$gaps) {
	my $beg = $g->[0] > $l? $g->[0] - $l : 0;
	my $end = $g->[0] + $g->[1] + $l;
	$end = length($$seq) if ($end > length($$seq));
	substr($$seq, $beg, $end - $beg) = lc(substr($$seq, $beg, $end - $beg));
  }
  print "\@$chr\n"; &v2q_print_str($seq);
  print "+\n"; &v2q_print_str($qual);
}

sub v2q_print_str {
  my ($s) = @_;
  my $l = length($$s);
  for (my $i = 0; $i < $l; $i += 60) {
	print substr($$s, $i, 60), "\n";
  }
}

sub usage {
  die(qq/
Usage:   vcfutils.pl  []\n
Command: subsam       get a subset of samples
         listsam      list the samples
         fillac       fill the allele count field
         qstats       SNP stats stratified by QUAL

         hapmap2vcf   convert the hapmap format to VCF
         ucscsnp2vcf  convert UCSC SNP SQL dump to VCF

         varFilter    filtering short variants (*)
         vcf2fq       VCF->fastq (**)

Notes: Commands with description endting with (*) may need bcftools
       specific annotations.
\n/);
}
genometools-1.5.1/src/external/samtools-0.1.18/bedidx.c000066400000000000000000000074521211610345200224540ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 

#ifdef _WIN32
#define drand48() ((double)rand() / RAND_MAX)
#endif

#include "ksort.h"
KSORT_INIT_GENERIC(uint64_t)

#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 8192)

typedef struct {
	int n, m;
	uint64_t *a;
	int *idx;
} bed_reglist_t;

#include "khash.h"
KHASH_MAP_INIT_STR(reg, bed_reglist_t)

#define LIDX_SHIFT 13

typedef kh_reg_t reghash_t;

int *bed_index_core(int n, uint64_t *a, int *n_idx)
{
	int i, j, m, *idx;
	m = *n_idx = 0; idx = 0;
	for (i = 0; i < n; ++i) {
		int beg, end;
		beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT;
		if (m < end + 1) {
			int oldm = m;
			m = end + 1;
			kroundup32(m);
			idx = realloc(idx, m * sizeof(int));
			for (j = oldm; j < m; ++j) idx[j] = -1;
		}
		if (beg == end) {
			if (idx[beg] < 0) idx[beg] = i;
		} else {
			for (j = beg; j <= end; ++j)
				if (idx[j] < 0) idx[j] = i;
		}
		*n_idx = end + 1;
	}
	return idx;
}

void bed_index(void *_h)
{
	reghash_t *h = (reghash_t*)_h;
	khint_t k;
	for (k = 0; k < kh_end(h); ++k) {
		if (kh_exist(h, k)) {
			bed_reglist_t *p = &kh_val(h, k);
			if (p->idx) free(p->idx);
			ks_introsort(uint64_t, p->n, p->a);
			p->idx = bed_index_core(p->n, p->a, &p->m);
		}
	}
}

int bed_overlap_core(const bed_reglist_t *p, int beg, int end)
{
	int i, min_off;
	if (p->n == 0) return 0;
	min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT];
	if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here
		int n = beg>>LIDX_SHIFT;
		if (n > p->n) n = p->n;
		for (i = n - 1; i >= 0; --i)
			if (p->idx[i] >= 0) break;
		min_off = i >= 0? p->idx[i] : 0;
	}
	for (i = min_off; i < p->n; ++i) {
		if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed
		if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end)
			return 1; // find the overlap; return
	}
	return 0;
}

int bed_overlap(const void *_h, const char *chr, int beg, int end)
{
	const reghash_t *h = (const reghash_t*)_h;
	khint_t k;
	if (!h) return 0;
	k = kh_get(reg, h, chr);
	if (k == kh_end(h)) return 0;
	return bed_overlap_core(&kh_val(h, k), beg, end);
}

void *bed_read(const char *fn)
{
	reghash_t *h = kh_init(reg);
	gzFile fp;
	kstream_t *ks;
	int dret;
	kstring_t *str;
	// read the list
	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
	if (fp == 0) return 0;
	str = calloc(1, sizeof(kstring_t));
	ks = ks_init(fp);
	while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name
		int beg = -1, end = -1;
		bed_reglist_t *p;
		khint_t k = kh_get(reg, h, str->s);
		if (k == kh_end(h)) { // absent from the hash table
			int ret;
			char *s = strdup(str->s);
			k = kh_put(reg, h, s, &ret);
			memset(&kh_val(h, k), 0, sizeof(bed_reglist_t));
		}
		p = &kh_val(h, k);
		if (dret != '\n') { // if the lines has other characters
			if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
				beg = atoi(str->s); // begin
				if (dret != '\n') {
					if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
						end = atoi(str->s); // end
						if (end < beg) end = -1;
					}
				}
			}
		}
		if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line
		if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column
		if (beg >= 0 && end > beg) {
			if (p->n == p->m) {
				p->m = p->m? p->m<<1 : 4;
				p->a = realloc(p->a, p->m * 8);
			}
			p->a[p->n++] = (uint64_t)beg<<32 | end;
		}
	}
	ks_destroy(ks);
	gzclose(fp);
	free(str->s); free(str);
	bed_index(h);
	return h;
}

void bed_destroy(void *_h)
{
	reghash_t *h = (reghash_t*)_h;
	khint_t k;
	for (k = 0; k < kh_end(h); ++k) {
		if (kh_exist(h, k)) {
			free(kh_val(h, k).a);
			free(kh_val(h, k).idx);
			free((char*)kh_key(h, k));
		}
	}
	kh_destroy(reg, h);
}
genometools-1.5.1/src/external/samtools-0.1.18/bgzf.c000066400000000000000000000467731211610345200221560ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology

   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
   in the Software without restriction, including without limitation the rights
   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   copies of the Software, and to permit persons to whom the Software is
   furnished to do so, subject to the following conditions:

   The above copyright notice and this permission notice shall be included in
   all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.
*/

/*
  2009-06-29 by lh3: cache recent uncompressed blocks.
  2009-06-25 by lh3: optionally use my knetfile library to access file on a FTP.
  2009-06-12 by lh3: support a mode string like "wu" where 'u' for uncompressed output */

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include "bgzf.h"

#include "khash.h"
typedef struct {
	int size;
	uint8_t *block;
	int64_t end_offset;
} cache_t;
KHASH_MAP_INIT_INT64(cache, cache_t)

#if defined(_WIN32) || defined(_MSC_VER)
#define ftello(fp) ftell(fp)
#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
#else
extern off_t ftello(FILE *stream);
extern int fseeko(FILE *stream, off_t offset, int whence);
#endif

typedef int8_t bgzf_byte_t;

static const int DEFAULT_BLOCK_SIZE = 64 * 1024;
static const int MAX_BLOCK_SIZE = 64 * 1024;

static const int BLOCK_HEADER_LENGTH = 18;
static const int BLOCK_FOOTER_LENGTH = 8;

static const int GZIP_ID1 = 31;
static const int GZIP_ID2 = 139;
static const int CM_DEFLATE = 8;
static const int FLG_FEXTRA = 4;
static const int OS_UNKNOWN = 255;
static const int BGZF_ID1 = 66; // 'B'
static const int BGZF_ID2 = 67; // 'C'
static const int BGZF_LEN = 2;
static const int BGZF_XLEN = 6; // BGZF_LEN+4

static const int GZIP_WINDOW_BITS = -15; // no zlib header
static const int Z_DEFAULT_MEM_LEVEL = 8;


inline
void
static
packInt16(uint8_t* buffer, uint16_t value)
{
    buffer[0] = value;
    buffer[1] = value >> 8;
}

inline
int
static
unpackInt16(const uint8_t* buffer)
{
    return (buffer[0] | (buffer[1] << 8));
}

inline
void
static
packInt32(uint8_t* buffer, uint32_t value)
{
    buffer[0] = value;
    buffer[1] = value >> 8;
    buffer[2] = value >> 16;
    buffer[3] = value >> 24;
}

static inline
int
bgzf_min(int x, int y)
{
    return (x < y) ? x : y;
}

static
void
report_error(BGZF* fp, const char* message) {
    fp->error = message;
}

int bgzf_check_bgzf(const char *fn)
{
    BGZF *fp;
    uint8_t buf[10],magic[10]="\037\213\010\4\0\0\0\0\0\377";
    int n;

    if ((fp = bgzf_open(fn, "r")) == 0) 
    {
        fprintf(stderr, "[bgzf_check_bgzf] failed to open the file: %s\n",fn);
        return -1;
    }

#ifdef _USE_KNETFILE
    n = knet_read(fp->x.fpr, buf, 10);
#else
    n = fread(buf, 1, 10, fp->file);
#endif
    bgzf_close(fp);

    if ( n!=10 ) 
        return -1;

    if ( !memcmp(magic, buf, 10) ) return 1;
    return 0;
}

static BGZF *bgzf_read_init()
{
	BGZF *fp;
	fp = calloc(1, sizeof(BGZF));
    fp->uncompressed_block_size = MAX_BLOCK_SIZE;
    fp->uncompressed_block = malloc(MAX_BLOCK_SIZE);
    fp->compressed_block_size = MAX_BLOCK_SIZE;
    fp->compressed_block = malloc(MAX_BLOCK_SIZE);
	fp->cache_size = 0;
	fp->cache = kh_init(cache);
	return fp;
}

static
BGZF*
open_read(int fd)
{
#ifdef _USE_KNETFILE
    knetFile *file = knet_dopen(fd, "r");
#else
    FILE* file = fdopen(fd, "r");
#endif
    BGZF* fp;
	if (file == 0) return 0;
	fp = bgzf_read_init();
    fp->file_descriptor = fd;
    fp->open_mode = 'r';
#ifdef _USE_KNETFILE
    fp->x.fpr = file;
#else
    fp->file = file;
#endif
    return fp;
}

static
BGZF*
open_write(int fd, int compress_level) // compress_level==-1 for the default level
{
    FILE* file = fdopen(fd, "w");
    BGZF* fp;
	if (file == 0) return 0;
	fp = malloc(sizeof(BGZF));
    fp->file_descriptor = fd;
    fp->open_mode = 'w';
    fp->owned_file = 0;
	fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
	if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
#ifdef _USE_KNETFILE
    fp->x.fpw = file;
#else
    fp->file = file;
#endif
    fp->uncompressed_block_size = DEFAULT_BLOCK_SIZE;
    fp->uncompressed_block = NULL;
    fp->compressed_block_size = MAX_BLOCK_SIZE;
    fp->compressed_block = malloc(MAX_BLOCK_SIZE);
    fp->block_address = 0;
    fp->block_offset = 0;
    fp->block_length = 0;
    fp->error = NULL;
    return fp;
}

BGZF*
bgzf_open(const char* __restrict path, const char* __restrict mode)
{
    BGZF* fp = NULL;
    if (strchr(mode, 'r') || strchr(mode, 'R')) { /* The reading mode is preferred. */
#ifdef _USE_KNETFILE
		knetFile *file = knet_open(path, mode);
		if (file == 0) return 0;
		fp = bgzf_read_init();
		fp->file_descriptor = -1;
		fp->open_mode = 'r';
		fp->x.fpr = file;
#else
		int fd, oflag = O_RDONLY;
#ifdef _WIN32
		oflag |= O_BINARY;
#endif
		fd = open(path, oflag);
		if (fd == -1) return 0;
        fp = open_read(fd);
#endif
    } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
		int fd, compress_level = -1, oflag = O_WRONLY | O_CREAT | O_TRUNC;
#ifdef _WIN32
		oflag |= O_BINARY;
#endif
		fd = open(path, oflag, 0666);
		if (fd == -1) return 0;
		{ // set compress_level
			int i;
			for (i = 0; mode[i]; ++i)
				if (mode[i] >= '0' && mode[i] <= '9') break;
			if (mode[i]) compress_level = (int)mode[i] - '0';
			if (strchr(mode, 'u')) compress_level = 0;
		}
        fp = open_write(fd, compress_level);
    }
    if (fp != NULL) fp->owned_file = 1;
    return fp;
}

BGZF*
bgzf_fdopen(int fd, const char * __restrict mode)
{
	if (fd == -1) return 0;
    if (mode[0] == 'r' || mode[0] == 'R') {
        return open_read(fd);
    } else if (mode[0] == 'w' || mode[0] == 'W') {
		int i, compress_level = -1;
		for (i = 0; mode[i]; ++i)
			if (mode[i] >= '0' && mode[i] <= '9') break;
		if (mode[i]) compress_level = (int)mode[i] - '0';
		if (strchr(mode, 'u')) compress_level = 0;
        return open_write(fd, compress_level);
    } else {
        return NULL;
    }
}

static
int
deflate_block(BGZF* fp, int block_length)
{
    // Deflate the block in fp->uncompressed_block into fp->compressed_block.
    // Also adds an extra field that stores the compressed block length.

    bgzf_byte_t* buffer = fp->compressed_block;
    int buffer_size = fp->compressed_block_size;

    // Init gzip header
    buffer[0] = GZIP_ID1;
    buffer[1] = GZIP_ID2;
    buffer[2] = CM_DEFLATE;
    buffer[3] = FLG_FEXTRA;
    buffer[4] = 0; // mtime
    buffer[5] = 0;
    buffer[6] = 0;
    buffer[7] = 0;
    buffer[8] = 0;
    buffer[9] = OS_UNKNOWN;
    buffer[10] = BGZF_XLEN;
    buffer[11] = 0;
    buffer[12] = BGZF_ID1;
    buffer[13] = BGZF_ID2;
    buffer[14] = BGZF_LEN;
    buffer[15] = 0;
    buffer[16] = 0; // placeholder for block length
    buffer[17] = 0;

    // loop to retry for blocks that do not compress enough
    int input_length = block_length;
    int compressed_length = 0;
    while (1) {
        z_stream zs;
        zs.zalloc = NULL;
        zs.zfree = NULL;
        zs.next_in = fp->uncompressed_block;
        zs.avail_in = input_length;
        zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
        zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;

        int status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED,
                                  GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
        if (status != Z_OK) {
            report_error(fp, "deflate init failed");
            return -1;
        }
        status = deflate(&zs, Z_FINISH);
        if (status != Z_STREAM_END) {
            deflateEnd(&zs);
            if (status == Z_OK) {
                // Not enough space in buffer.
                // Can happen in the rare case the input doesn't compress enough.
                // Reduce the amount of input until it fits.
                input_length -= 1024;
                if (input_length <= 0) {
                    // should never happen
                    report_error(fp, "input reduction failed");
                    return -1;
                }
                continue;
            }
            report_error(fp, "deflate failed");
            return -1;
        }
        status = deflateEnd(&zs);
        if (status != Z_OK) {
            report_error(fp, "deflate end failed");
            return -1;
        }
        compressed_length = zs.total_out;
        compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
        if (compressed_length > MAX_BLOCK_SIZE) {
            // should never happen
            report_error(fp, "deflate overflow");
            return -1;
        }
        break;
    }

    packInt16((uint8_t*)&buffer[16], compressed_length-1);
    uint32_t crc = crc32(0L, NULL, 0L);
    crc = crc32(crc, fp->uncompressed_block, input_length);
    packInt32((uint8_t*)&buffer[compressed_length-8], crc);
    packInt32((uint8_t*)&buffer[compressed_length-4], input_length);

    int remaining = block_length - input_length;
    if (remaining > 0) {
        if (remaining > input_length) {
            // should never happen (check so we can use memcpy)
            report_error(fp, "remainder too large");
            return -1;
        }
        memcpy(fp->uncompressed_block,
               fp->uncompressed_block + input_length,
               remaining);
    }
    fp->block_offset = remaining;
    return compressed_length;
}

static
int
inflate_block(BGZF* fp, int block_length)
{
    // Inflate the block in fp->compressed_block into fp->uncompressed_block

    z_stream zs;
	int status;
    zs.zalloc = NULL;
    zs.zfree = NULL;
    zs.next_in = fp->compressed_block + 18;
    zs.avail_in = block_length - 16;
    zs.next_out = fp->uncompressed_block;
    zs.avail_out = fp->uncompressed_block_size;

    status = inflateInit2(&zs, GZIP_WINDOW_BITS);
    if (status != Z_OK) {
        report_error(fp, "inflate init failed");
        return -1;
    }
    status = inflate(&zs, Z_FINISH);
    if (status != Z_STREAM_END) {
        inflateEnd(&zs);
        report_error(fp, "inflate failed");
        return -1;
    }
    status = inflateEnd(&zs);
    if (status != Z_OK) {
        report_error(fp, "inflate failed");
        return -1;
    }
    return zs.total_out;
}

static
int
check_header(const bgzf_byte_t* header)
{
    return (header[0] == GZIP_ID1 &&
            header[1] == (bgzf_byte_t) GZIP_ID2 &&
            header[2] == Z_DEFLATED &&
            (header[3] & FLG_FEXTRA) != 0 &&
            unpackInt16((uint8_t*)&header[10]) == BGZF_XLEN &&
            header[12] == BGZF_ID1 &&
            header[13] == BGZF_ID2 &&
            unpackInt16((uint8_t*)&header[14]) == BGZF_LEN);
}

static void free_cache(BGZF *fp)
{
	khint_t k;
	khash_t(cache) *h = (khash_t(cache)*)fp->cache;
	if (fp->open_mode != 'r') return;
	for (k = kh_begin(h); k < kh_end(h); ++k)
		if (kh_exist(h, k)) free(kh_val(h, k).block);
	kh_destroy(cache, h);
}

static int load_block_from_cache(BGZF *fp, int64_t block_address)
{
	khint_t k;
	cache_t *p;
	khash_t(cache) *h = (khash_t(cache)*)fp->cache;
	k = kh_get(cache, h, block_address);
	if (k == kh_end(h)) return 0;
	p = &kh_val(h, k);
	if (fp->block_length != 0) fp->block_offset = 0;
	fp->block_address = block_address;
	fp->block_length = p->size;
	memcpy(fp->uncompressed_block, p->block, MAX_BLOCK_SIZE);
#ifdef _USE_KNETFILE
	knet_seek(fp->x.fpr, p->end_offset, SEEK_SET);
#else
	fseeko(fp->file, p->end_offset, SEEK_SET);
#endif
	return p->size;
}

static void cache_block(BGZF *fp, int size)
{
	int ret;
	khint_t k;
	cache_t *p;
	khash_t(cache) *h = (khash_t(cache)*)fp->cache;
	if (MAX_BLOCK_SIZE >= fp->cache_size) return;
	if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) {
		/* A better way would be to remove the oldest block in the
		 * cache, but here we remove a random one for simplicity. This
		 * should not have a big impact on performance. */
		for (k = kh_begin(h); k < kh_end(h); ++k)
			if (kh_exist(h, k)) break;
		if (k < kh_end(h)) {
			free(kh_val(h, k).block);
			kh_del(cache, h, k);
		}
	}
	k = kh_put(cache, h, fp->block_address, &ret);
	if (ret == 0) return; // if this happens, a bug!
	p = &kh_val(h, k);
	p->size = fp->block_length;
	p->end_offset = fp->block_address + size;
	p->block = malloc(MAX_BLOCK_SIZE);
	memcpy(kh_val(h, k).block, fp->uncompressed_block, MAX_BLOCK_SIZE);
}

int
bgzf_read_block(BGZF* fp)
{
    bgzf_byte_t header[BLOCK_HEADER_LENGTH];
	int count, size = 0, block_length, remaining;
#ifdef _USE_KNETFILE
    int64_t block_address = knet_tell(fp->x.fpr);
	if (load_block_from_cache(fp, block_address)) return 0;
    count = knet_read(fp->x.fpr, header, sizeof(header));
#else
    int64_t block_address = ftello(fp->file);
	if (load_block_from_cache(fp, block_address)) return 0;
    count = fread(header, 1, sizeof(header), fp->file);
#endif
    if (count == 0) {
        fp->block_length = 0;
        return 0;
    }
	size = count;
    if (count != sizeof(header)) {
        report_error(fp, "read failed");
        return -1;
    }
    if (!check_header(header)) {
        report_error(fp, "invalid block header");
        return -1;
    }
    block_length = unpackInt16((uint8_t*)&header[16]) + 1;
    bgzf_byte_t* compressed_block = (bgzf_byte_t*) fp->compressed_block;
    memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
    remaining = block_length - BLOCK_HEADER_LENGTH;
#ifdef _USE_KNETFILE
    count = knet_read(fp->x.fpr, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
#else
    count = fread(&compressed_block[BLOCK_HEADER_LENGTH], 1, remaining, fp->file);
#endif
    if (count != remaining) {
        report_error(fp, "read failed");
        return -1;
    }
	size += count;
    count = inflate_block(fp, block_length);
    if (count < 0) return -1;
    if (fp->block_length != 0) {
        // Do not reset offset if this read follows a seek.
        fp->block_offset = 0;
    }
    fp->block_address = block_address;
    fp->block_length = count;
	cache_block(fp, size);
    return 0;
}

int
bgzf_read(BGZF* fp, void* data, int length)
{
    if (length <= 0) {
        return 0;
    }
    if (fp->open_mode != 'r') {
        report_error(fp, "file not open for reading");
        return -1;
    }

    int bytes_read = 0;
    bgzf_byte_t* output = data;
    while (bytes_read < length) {
        int copy_length, available = fp->block_length - fp->block_offset;
		bgzf_byte_t *buffer;
        if (available <= 0) {
            if (bgzf_read_block(fp) != 0) {
                return -1;
            }
            available = fp->block_length - fp->block_offset;
            if (available <= 0) {
                break;
            }
        }
        copy_length = bgzf_min(length-bytes_read, available);
        buffer = fp->uncompressed_block;
        memcpy(output, buffer + fp->block_offset, copy_length);
        fp->block_offset += copy_length;
        output += copy_length;
        bytes_read += copy_length;
    }
    if (fp->block_offset == fp->block_length) {
#ifdef _USE_KNETFILE
        fp->block_address = knet_tell(fp->x.fpr);
#else
        fp->block_address = ftello(fp->file);
#endif
        fp->block_offset = 0;
        fp->block_length = 0;
    }
    return bytes_read;
}

int bgzf_flush(BGZF* fp)
{
    while (fp->block_offset > 0) {
        int count, block_length;
		block_length = deflate_block(fp, fp->block_offset);
        if (block_length < 0) return -1;
#ifdef _USE_KNETFILE
        count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
#else
        count = fwrite(fp->compressed_block, 1, block_length, fp->file);
#endif
        if (count != block_length) {
            report_error(fp, "write failed");
            return -1;
        }
        fp->block_address += block_length;
    }
    return 0;
}

int bgzf_flush_try(BGZF *fp, int size)
{
	if (fp->block_offset + size > fp->uncompressed_block_size)
		return bgzf_flush(fp);
	return -1;
}

int bgzf_write(BGZF* fp, const void* data, int length)
{
	const bgzf_byte_t *input = data;
	int block_length, bytes_written;
    if (fp->open_mode != 'w') {
        report_error(fp, "file not open for writing");
        return -1;
    }

    if (fp->uncompressed_block == NULL)
        fp->uncompressed_block = malloc(fp->uncompressed_block_size);

    input = data;
    block_length = fp->uncompressed_block_size;
    bytes_written = 0;
    while (bytes_written < length) {
        int copy_length = bgzf_min(block_length - fp->block_offset, length - bytes_written);
        bgzf_byte_t* buffer = fp->uncompressed_block;
        memcpy(buffer + fp->block_offset, input, copy_length);
        fp->block_offset += copy_length;
        input += copy_length;
        bytes_written += copy_length;
        if (fp->block_offset == block_length) {
            if (bgzf_flush(fp) != 0) {
                break;
            }
        }
    }
    return bytes_written;
}

int bgzf_close(BGZF* fp)
{
    if (fp->open_mode == 'w') {
        if (bgzf_flush(fp) != 0) return -1;
		{ // add an empty block
			int count, block_length = deflate_block(fp, 0);
#ifdef _USE_KNETFILE
			count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
#else
			count = fwrite(fp->compressed_block, 1, block_length, fp->file);
#endif
		}
#ifdef _USE_KNETFILE
        if (fflush(fp->x.fpw) != 0) {
#else
        if (fflush(fp->file) != 0) {
#endif
            report_error(fp, "flush failed");
            return -1;
        }
    }
    if (fp->owned_file) {
#ifdef _USE_KNETFILE
		int ret;
		if (fp->open_mode == 'w') ret = fclose(fp->x.fpw);
		else ret = knet_close(fp->x.fpr);
        if (ret != 0) return -1;
#else
        if (fclose(fp->file) != 0) return -1;
#endif
    }
    free(fp->uncompressed_block);
    free(fp->compressed_block);
	free_cache(fp);
    free(fp);
    return 0;
}

void bgzf_set_cache_size(BGZF *fp, int cache_size)
{
	if (fp) fp->cache_size = cache_size;
}

int bgzf_check_EOF(BGZF *fp)
{
	static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
	uint8_t buf[28];
	off_t offset;
#ifdef _USE_KNETFILE
	offset = knet_tell(fp->x.fpr);
	if (knet_seek(fp->x.fpr, -28, SEEK_END) != 0) return -1;
	knet_read(fp->x.fpr, buf, 28);
	knet_seek(fp->x.fpr, offset, SEEK_SET);
#else
	offset = ftello(fp->file);
	if (fseeko(fp->file, -28, SEEK_END) != 0) return -1;
	fread(buf, 1, 28, fp->file);
	fseeko(fp->file, offset, SEEK_SET);
#endif
	return (memcmp(magic, buf, 28) == 0)? 1 : 0;
}

int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
{
	int block_offset;
	int64_t block_address;

    if (fp->open_mode != 'r') {
        report_error(fp, "file not open for read");
        return -1;
    }
    if (where != SEEK_SET) {
        report_error(fp, "unimplemented seek option");
        return -1;
    }
    block_offset = pos & 0xFFFF;
    block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
#ifdef _USE_KNETFILE
    if (knet_seek(fp->x.fpr, block_address, SEEK_SET) != 0) {
#else
    if (fseeko(fp->file, block_address, SEEK_SET) != 0) {
#endif
        report_error(fp, "seek failed");
        return -1;
    }
    fp->block_length = 0;  // indicates current block is not loaded
    fp->block_address = block_address;
    fp->block_offset = block_offset;
    return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/bgzf.h000066400000000000000000000113331211610345200221430ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology

   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
   in the Software without restriction, including without limitation the rights
   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   copies of the Software, and to permit persons to whom the Software is
   furnished to do so, subject to the following conditions:

   The above copyright notice and this permission notice shall be included in
   all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.
*/

#ifndef __BGZF_H
#define __BGZF_H

#include 
#include 
#ifndef S_SPLINT_S
#include 
#endif
#ifdef _USE_KNETFILE
#include "knetfile.h"
#endif

//typedef int8_t bool;

/*@ignore@*/
typedef struct {
    int file_descriptor;
    char open_mode;  // 'r' or 'w'
    int16_t owned_file, compress_level;
#ifdef _USE_KNETFILE
	union {
		knetFile *fpr;
		FILE *fpw;
	} x;
#else
    FILE* file;
#endif
    int uncompressed_block_size;
    int compressed_block_size;
    void* uncompressed_block;
    void* compressed_block;
    int64_t block_address;
    int block_length;
    int block_offset;
	int cache_size;
    const char* error;
	void *cache; // a pointer to a hash table
} BGZF;

#ifdef __cplusplus
extern "C" {
#endif

/*
 * Open an existing file descriptor for reading or writing.
 * Mode must be either "r" or "w".
 * A subsequent bgzf_close will not close the file descriptor.
 * Returns null on error.
 */
#ifdef S_SPLINT_S
BGZF* bgzf_fdopen(int fd, const char* mode);
#else
BGZF* bgzf_fdopen(int fd, const char* __restrict mode);
#endif

/*
 * Open the specified file for reading or writing.
 * Mode must be either "r" or "w".
 * Returns null on error.
 */
#ifdef S_SPLINT_S
BGZF* bgzf_open(const char* path, const char*  mode);
#else
BGZF* bgzf_open(const char* path, const char* __restrict mode);
#endif

/*
 * Close the BGZ file and free all associated resources.
 * Does not close the underlying file descriptor if created with bgzf_fdopen.
 * Returns zero on success, -1 on error.
 */
int bgzf_close(BGZF* fp);

/*
 * Read up to length bytes from the file storing into data.
 * Returns the number of bytes actually read.
 * Returns zero on end of file.
 * Returns -1 on error.
 */
int bgzf_read(BGZF* fp, void* data, int length);

/*
 * Write length bytes from data to the file.
 * Returns the number of bytes written.
 * Returns -1 on error.
 */
int bgzf_write(BGZF* fp, const void* data, int length);

/*
 * Return a virtual file pointer to the current location in the file.
 * No interpetation of the value should be made, other than a subsequent
 * call to bgzf_seek can be used to position the file at the same point.
 * Return value is non-negative on success.
 * Returns -1 on error.
 */
#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))

/*
 * Set the file to read from the location specified by pos, which must
 * be a value previously returned by bgzf_tell for this file (but not
 * necessarily one returned by this file handle).
 * The where argument must be SEEK_SET.
 * Seeking on a file opened for write is not supported.
 * Returns zero on success, -1 on error.
 */
int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);

/*
 * Set the cache size. Zero to disable. By default, caching is
 * disabled. The recommended cache size for frequent random access is
 * about 8M bytes.
 */
void bgzf_set_cache_size(BGZF *fp, int cache_size);

int bgzf_check_EOF(BGZF *fp);
int bgzf_read_block(BGZF* fp);
int bgzf_flush(BGZF* fp);
int bgzf_flush_try(BGZF *fp, int size);
int bgzf_check_bgzf(const char *fn);

#ifdef __cplusplus
}
#endif

static inline int bgzf_getc(BGZF *fp)
{
	int c;
	if (fp->block_offset >= fp->block_length) {
		if (bgzf_read_block(fp) != 0) return -2; /* error */
		if (fp->block_length == 0) return -1; /* end-of-file */
	}
	c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
    if (fp->block_offset == fp->block_length) {
#ifdef _USE_KNETFILE
        fp->block_address = knet_tell(fp->x.fpr);
#else
        fp->block_address = ftello(fp->file);
#endif
        fp->block_offset = 0;
        fp->block_length = 0;
    }
	return c;
}
/*@end@*/

#endif
genometools-1.5.1/src/external/samtools-0.1.18/bgzip.c000066400000000000000000000134171211610345200223260ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology

   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
   in the Software without restriction, including without limitation the rights
   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   copies of the Software, and to permit persons to whom the Software is
   furnished to do so, subject to the following conditions:

   The above copyright notice and this permission notice shall be included in
   all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include "bgzf.h"

static const int WINDOW_SIZE = 64 * 1024;

static int bgzip_main_usage()
{
	fprintf(stderr, "\n");
	fprintf(stderr, "Usage:   bgzip [options] [file] ...\n\n");
	fprintf(stderr, "Options: -c      write on standard output, keep original files unchanged\n");
	fprintf(stderr, "         -d      decompress\n");
	fprintf(stderr, "         -f      overwrite files without asking\n");
	fprintf(stderr, "         -b INT  decompress at virtual file pointer INT\n");
	fprintf(stderr, "         -s INT  decompress INT bytes in the uncompressed file\n");
	fprintf(stderr, "         -h      give this help\n");
	fprintf(stderr, "\n");
	return 1;
}

static int write_open(const char *fn, int is_forced)
{
	int fd = -1;
	char c;
	if (!is_forced) {
		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
			fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
			scanf("%c", &c);
			if (c != 'Y' && c != 'y') {
				fprintf(stderr, "[bgzip] not overwritten\n");
				exit(1);
			}
		}
	}
	if (fd < 0) {
		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
			fprintf(stderr, "[bgzip] %s: Fail to write\n", fn);
			exit(1);
		}
	}
	return fd;
}

static void fail(BGZF* fp)
{
    fprintf(stderr, "Error: %s\n", fp->error);
    exit(1);
}

int main(int argc, char **argv)
{
	int c, compress, pstdout, is_forced;
	BGZF *fp;
	void *buffer;
	long start, end, size;

	compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
	while((c  = getopt(argc, argv, "cdhfb:s:")) >= 0){
		switch(c){
		case 'h': return bgzip_main_usage();
		case 'd': compress = 0; break;
		case 'c': pstdout = 1; break;
		case 'b': start = atol(optarg); break;
		case 's': size = atol(optarg); break;
		case 'f': is_forced = 1; break;
		}
	}
	if (size >= 0) end = start + size;
	if (end >= 0 && end < start) {
		fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);
		return 1;
	}
	if (compress == 1) {
		struct stat sbuf;
		int f_src = fileno(stdin);
		int f_dst = fileno(stdout);

		if ( argc>optind )
		{
			if ( stat(argv[optind],&sbuf)<0 ) 
			{ 
				fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
				return 1; 
			}

			if ((f_src = open(argv[optind], O_RDONLY)) < 0) {
				fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
				return 1;
			}

			if (pstdout)
				f_dst = fileno(stdout);
			else
			{
				char *name = malloc(strlen(argv[optind]) + 5);
				strcpy(name, argv[optind]);
				strcat(name, ".gz");
				f_dst = write_open(name, is_forced);
				if (f_dst < 0) return 1;
				free(name);
			}
		}
		else if (!pstdout && isatty(fileno((FILE *)stdout)) )
			return bgzip_main_usage();

		fp = bgzf_fdopen(f_dst, "w");
		buffer = malloc(WINDOW_SIZE);
		while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
			if (bgzf_write(fp, buffer, c) < 0) fail(fp);
		// f_dst will be closed here
		if (bgzf_close(fp) < 0) fail(fp);
		if (argc > optind && !pstdout) unlink(argv[optind]);
		free(buffer);
		close(f_src);
		return 0;
	} else {
		struct stat sbuf;
		int f_dst;

		if ( argc>optind )
		{
			if ( stat(argv[optind],&sbuf)<0 )
			{
				fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
				return 1;
			}
			char *name;
			int len = strlen(argv[optind]);
			if ( strcmp(argv[optind]+len-3,".gz") )
			{
				fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]);
				return 1;
			}
			fp = bgzf_open(argv[optind], "r");
			if (fp == NULL) {
				fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]);
				return 1;
			}

			if (pstdout) {
				f_dst = fileno(stdout);
			}
			else {
				name = strdup(argv[optind]);
				name[strlen(name) - 3] = '\0';
				f_dst = write_open(name, is_forced);
				free(name);
			}
		}
		else if (!pstdout && isatty(fileno((FILE *)stdin)) )
			return bgzip_main_usage();
		else
		{
			f_dst = fileno(stdout);
			fp = bgzf_fdopen(fileno(stdin), "r");
			if (fp == NULL) {
				fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
				return 1;
			}
		}
		buffer = malloc(WINDOW_SIZE);
		if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp);
		while (1) {
			if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);
			else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
			if (c == 0) break;
			if (c < 0) fail(fp);
			start += c;
			write(f_dst, buffer, c);
			if (end >= 0 && start >= end) break;
		}
		free(buffer);
		if (bgzf_close(fp) < 0) fail(fp);
		if (!pstdout) unlink(argv[optind]);
		return 0;
	}
}
genometools-1.5.1/src/external/samtools-0.1.18/cut_target.c000066400000000000000000000130431211610345200233470ustar00rootroot00000000000000#include 
#include 
#include 
#include "bam.h"
#include "errmod.h"
#include "faidx.h"

#define ERR_DEP 0.83f

typedef struct {
	int e[2][3], p[2][2];
} score_param_t;

/* Note that although the two matrics have 10 parameters in total, only 4
 * (probably 3) are free.  Changing the scoring matrices in a sort of symmetric
 * way will not change the result. */
static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} };

typedef struct {
	int min_baseQ, tid, max_bases;
	uint16_t *bases;
	bamFile fp;
	bam_header_t *h;
	char *ref;
	faidx_t *fai;
	errmod_t *em;
} ct_t;

static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp)
{
	int i, j, ret, tmp, k, sum[4], qual;
	float q[16];
	if (n > g->max_bases) { // enlarge g->bases
		g->max_bases = n;
		kroundup32(g->max_bases);
		g->bases = realloc(g->bases, g->max_bases * 2);
	}
	for (i = k = 0; i < n; ++i) {
		const bam_pileup1_t *p = plp + i;
		uint8_t *seq;
		int q, baseQ, b;
		if (p->is_refskip || p->is_del) continue;
		baseQ = bam1_qual(p->b)[p->qpos];
		if (baseQ < g->min_baseQ) continue;
		seq = bam1_seq(p->b);
		b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)];
		if (b > 3) continue;
		q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
		if (q < 4) q = 4;
		if (q > 63) q = 63;
		g->bases[k++] = q<<5 | bam1_strand(p->b)<<4 | b;
	}
	if (k == 0) return 0;
	errmod_cal(g->em, k, 4, g->bases, q);
	for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i;
	for (i = 1; i < 4; ++i) // insertion sort
		for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
			tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
	qual = (sum[1]>>2) - (sum[0]>>2);
	k = k < 256? k : 255;
	ret = (qual < 63? qual : 63) << 2 | (sum[0]&3);
	return ret<<8|k;
}

static void process_cns(bam_header_t *h, int tid, int l, uint16_t *cns)
{
	int i, f[2][2], *prev, *curr, *swap_tmp, s;
	uint8_t *b; // backtrack array
	b = calloc(l, 1);
	f[0][0] = f[0][1] = 0;
	prev = f[0]; curr = f[1];
	// fill the backtrack matrix
	for (i = 0; i < l; ++i) {
		int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2;
		int tmp0, tmp1;
		// compute f[0]
		tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0)
		tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1)
		if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0;
		else curr[0] = tmp1, b[i] = 1;
		// compute f[1]
		tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0)
		tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1)
		if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1;
		else curr[1] = tmp1, b[i] |= 1<<1;
		// swap
		swap_tmp = prev; prev = curr; curr = swap_tmp;
	}
	// backtrack
	s = prev[0] > prev[1]? 0 : 1;
	for (i = l - 1; i > 0; --i) {
		b[i] |= s<<2;
		s = b[i]>>s&1;
	}
	// print
	for (i = 0, s = -1; i <= l; ++i) {
		if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) {
			if (s >= 0) {
				int j;
				printf("%s:%d-%d\t0\t%s\t%d\t60\t%dM\t*\t0\t0\t", h->target_name[tid], s+1, i, h->target_name[tid], s+1, i-s);
				for (j = s; j < i; ++j) {
					int c = cns[j]>>8;
					if (c == 0) putchar('N');
					else putchar("ACGT"[c&3]);
				}
				putchar('\t');
				for (j = s; j < i; ++j)
					putchar(33 + (cns[j]>>8>>2));
				putchar('\n');
			}
			//if (s >= 0) printf("%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s);
			s = -1;
		} else if ((b[i]>>2&3) && s < 0) s = i;
	}
	free(b);
}

static int read_aln(void *data, bam1_t *b)
{
	extern int bam_prob_realn_core(bam1_t *b, const char *ref, int flag);
	ct_t *g = (ct_t*)data;
	int ret, len;
	ret = bam_read1(g->fp, b);
	if (ret >= 0 && g->fai && b->core.tid >= 0 && (b->core.flag&4) == 0) {
		if (b->core.tid != g->tid) { // then load the sequence
			free(g->ref);
			g->ref = fai_fetch(g->fai, g->h->target_name[b->core.tid], &len);
			g->tid = b->core.tid;
		}
		bam_prob_realn_core(b, g->ref, 1<<1|1);
	}
	return ret;
}

int main_cut_target(int argc, char *argv[])
{
	int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
	const bam_pileup1_t *p;
	bam_plp_t plp;
	uint16_t *cns;
	ct_t g;

	memset(&g, 0, sizeof(ct_t));
	g.min_baseQ = 13; g.tid = -1;
	while ((c = getopt(argc, argv, "f:Q:i:o:0:1:2:")) >= 0) {
		switch (c) {
			case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff
			case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY
			case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE
			case '1': g_param.e[1][1] = atoi(optarg); break;
			case '2': g_param.e[1][2] = atoi(optarg); break;
			case 'f': g.fai = fai_load(optarg);
				if (g.fai == 0) fprintf(stderr, "[%s] fail to load the fasta index.\n", __func__);
				break;
		}
	}
	if (argc == optind) {
		fprintf(stderr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] [-f ref] \n");
		return 1;
	}
	l = max_l = 0; cns = 0;
	g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
	g.h = bam_header_read(g.fp);
	g.em = errmod_init(1 - ERR_DEP);
	plp = bam_plp_init(read_aln, &g);
	while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) {
		if (tid < 0) break;
		if (tid != lasttid) { // change of chromosome
			if (cns) process_cns(g.h, lasttid, l, cns);
			if (max_l < g.h->target_len[tid]) {
				max_l = g.h->target_len[tid];
				kroundup32(max_l);
				cns = realloc(cns, max_l * 2);
			}
			l = g.h->target_len[tid];
			memset(cns, 0, max_l * 2);
			lasttid = tid;
		}
		cns[pos] = gencns(&g, n, p);
		lastpos = pos;
	}
	process_cns(g.h, lasttid, l, cns);
	free(cns);
	bam_header_destroy(g.h);
	bam_plp_destroy(plp);
	bam_close(g.fp);
	if (g.fai) {
		fai_destroy(g.fai); free(g.ref);
	}
	errmod_destroy(g.em);
	free(g.bases);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/errmod.c000066400000000000000000000066351211610345200225070ustar00rootroot00000000000000#include 
#include "errmod.h"
#include "ksort.h"
KSORT_INIT_GENERIC(uint16_t)

typedef struct __errmod_coef_t {
	double *fk, *beta, *lhet;
} errmod_coef_t;

typedef struct {
	double fsum[16], bsum[16];
	uint32_t c[16];
} call_aux_t;

static errmod_coef_t *cal_coef(double depcorr, double eta)
{
	int k, n, q;
	long double sum, sum1;
	double *lC;
	errmod_coef_t *ec;

	ec = calloc(1, sizeof(errmod_coef_t));
	// initialize ->fk
	ec->fk = (double*)calloc(256, sizeof(double));
	ec->fk[0] = 1.0;
	for (n = 1; n != 256; ++n)
		ec->fk[n] = pow(1. - depcorr, n) * (1.0 - eta) + eta;
	// initialize ->coef
	ec->beta = (double*)calloc(256 * 256 * 64, sizeof(double));
	lC = (double*)calloc(256 * 256, sizeof(double));
	for (n = 1; n != 256; ++n) {
		double lgn = lgamma(n+1);
		for (k = 1; k <= n; ++k)
			lC[n<<8|k] = lgn - lgamma(k+1) - lgamma(n-k+1);
	}
	for (q = 1; q != 64; ++q) {
		double e = pow(10.0, -q/10.0);
		double le = log(e);
		double le1 = log(1.0 - e);
		for (n = 1; n <= 255; ++n) {
			double *beta = ec->beta + (q<<16|n<<8);
			sum1 = sum = 0.0;
			for (k = n; k >= 0; --k, sum1 = sum) {
				sum = sum1 + expl(lC[n<<8|k] + k*le + (n-k)*le1);
				beta[k] = -10. / M_LN10 * logl(sum1 / sum);
			}
		}
	}
	// initialize ->lhet
	ec->lhet = (double*)calloc(256 * 256, sizeof(double));
	for (n = 0; n < 256; ++n)
		for (k = 0; k < 256; ++k)
			ec->lhet[n<<8|k] = lC[n<<8|k] - M_LN2 * n;
	free(lC);
	return ec;
}

errmod_t *errmod_init(float depcorr)
{
	errmod_t *em;
	em = (errmod_t*)calloc(1, sizeof(errmod_t));
	em->depcorr = depcorr;
	em->coef = cal_coef(depcorr, 0.03);
	return em;
}

void errmod_destroy(errmod_t *em)
{
	if (em == 0) return;
	free(em->coef->lhet); free(em->coef->fk); free(em->coef->beta);
	free(em->coef); free(em);
}
// qual:6, strand:1, base:4
int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q)
{
	call_aux_t aux;
	int i, j, k, w[32];

	if (m > m) return -1;
	memset(q, 0, m * m * sizeof(float));
	if (n == 0) return 0;
	// calculate aux.esum and aux.fsum
	if (n > 255) { // then sample 255 bases
		ks_shuffle(uint16_t, n, bases);
		n = 255;
	}
	ks_introsort(uint16_t, n, bases);
	memset(w, 0, 32 * sizeof(int));
	memset(&aux, 0, sizeof(call_aux_t));
	for (j = n - 1; j >= 0; --j) { // calculate esum and fsum
		uint16_t b = bases[j];
		int q = b>>5 < 4? 4 : b>>5;
		if (q > 63) q = 63;
		k = b&0x1f;
		aux.fsum[k&0xf] += em->coef->fk[w[k]];
		aux.bsum[k&0xf] += em->coef->fk[w[k]] * em->coef->beta[q<<16|n<<8|aux.c[k&0xf]];
		++aux.c[k&0xf];
		++w[k];
	}
	// generate likelihood
	for (j = 0; j != m; ++j) {
		float tmp1, tmp3;
		int tmp2, bar_e;
		// homozygous
		for (k = 0, tmp1 = tmp3 = 0.0, tmp2 = 0; k != m; ++k) {
			if (k == j) continue;
			tmp1 += aux.bsum[k]; tmp2 += aux.c[k]; tmp3 += aux.fsum[k];
		}
		if (tmp2) {
			bar_e = (int)(tmp1 / tmp3 + 0.499);
			if (bar_e > 63) bar_e = 63;
			q[j*m+j] = tmp1;
		}
		// heterozygous
		for (k = j + 1; k < m; ++k) {
			int cjk = aux.c[j] + aux.c[k];
			for (i = 0, tmp2 = 0, tmp1 = tmp3 = 0.0; i < m; ++i) {
				if (i == j || i == k) continue;
				tmp1 += aux.bsum[i]; tmp2 += aux.c[i]; tmp3 += aux.fsum[i];
			}
			if (tmp2) {
				bar_e = (int)(tmp1 / tmp3 + 0.499);
				if (bar_e > 63) bar_e = 63;
				q[j*m+k] = q[k*m+j] = -4.343 * em->coef->lhet[cjk<<8|aux.c[k]] + tmp1;
			} else q[j*m+k] = q[k*m+j] = -4.343 * em->coef->lhet[cjk<<8|aux.c[k]]; // all the bases are either j or k
		}
		for (k = 0; k != m; ++k) if (q[j*m+k] < 0.0) q[j*m+k] = 0.0;
	}
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/errmod.h000066400000000000000000000006721211610345200225070ustar00rootroot00000000000000#ifndef ERRMOD_H
#define ERRMOD_H

#include 

struct __errmod_coef_t;

typedef struct {
	double depcorr;
	struct __errmod_coef_t *coef;
} errmod_t;

errmod_t *errmod_init(float depcorr);
void errmod_destroy(errmod_t *em);

/*
	n: number of bases
	m: maximum base
	bases[i]: qual:6, strand:1, base:4
	q[i*m+j]: phred-scaled likelihood of (i,j)
 */
int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q);

#endif
genometools-1.5.1/src/external/samtools-0.1.18/examples/000077500000000000000000000000001211610345200226575ustar00rootroot00000000000000genometools-1.5.1/src/external/samtools-0.1.18/examples/00README.txt000066400000000000000000000015661211610345200245250ustar00rootroot00000000000000File ex1.fa contains two sequences cut from the human genome
build36. They were exatracted with command:

  samtools faidx human_b36.fa 2:2043966-2045540 20:67967-69550

Sequence names were changed manually for simplicity. File ex1.sam.gz
contains MAQ alignments exatracted with:

  (samtools view NA18507_maq.bam 2:2044001-2045500;
   samtools view NA18507_maq.bam 20:68001-69500)

and processed with `samtools fixmate' to make it self-consistent as a
standalone alignment.

To try samtools, you may run the following commands:

  samtools faidx ex1.fa                 # index the reference FASTA
  samtools import ex1.fa.fai ex1.sam.gz ex1.bam   # SAM->BAM
  samtools index ex1.bam                # index BAM
  samtools tview ex1.bam ex1.fa         # view alignment
  samtools pileup -cf ex1.fa ex1.bam    # pileup and consensus
  samtools pileup -cf ex1.fa -t ex1.fa.fai ex1.sam.gz

genometools-1.5.1/src/external/samtools-0.1.18/examples/Makefile000066400000000000000000000036571211610345200243320ustar00rootroot00000000000000all:../libbam.a ../samtools ../bcftools/bcftools \
	ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz ex1.bcf calDepth
		@echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;

ex1.fa.fai:ex1.fa
		../samtools faidx ex1.fa
ex1.bam:ex1.sam.gz ex1.fa.fai
		../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
ex1.bam.bai:ex1.bam
		../samtools index ex1.bam
ex1.pileup.gz:ex1.bam ex1.fa
		../samtools mpileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
ex1.glf:ex1.bam ex1.fa
		../samtools mpileup -gf ex1.fa ex1.bam > ex1.glf
ex1.glfview.gz:ex1.glf
		../samtools glfview ex1.glf | gzip > ex1.glfview.gz
ex1a.bam:ex1.bam
		../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view -bS - > $@
ex1b.bam:ex1.bam
		../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"b";print}}' | ../samtools view -bS - > $@
ex1f.rg:
		(echo "@RG	ID:ex1	LB:ex1	SM:ex1"; echo "@RG	ID:ex1a	LB:ex1	SM:ex1"; echo "@RG	ID:ex1b	LB:ex1b	SM:ex1b") > $@
ex1f.bam:ex1.bam ex1a.bam ex1b.bam ex1f.rg
		../samtools merge -rh ex1f.rg $@ ex1.bam ex1a.bam ex1b.bam
ex1f-rmduppe.bam:ex1f.bam
		../samtools rmdup ex1f.bam $@
ex1f-rmdupse.bam:ex1f.bam
		../samtools rmdup -S ex1f.bam $@

ex1.bcf:ex1.bam ex1.fa.fai
		../samtools mpileup -gf ex1.fa ex1.bam > $@

../bcftools/bcftools:
		(cd ../bcftools; make bcftools)

../samtools:
		(cd ..; make samtools)

../libbam.a:
		(cd ..; make libbam.a)

calDepth:../libbam.a calDepth.c
		gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz

clean:
		rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf

# ../samtools pileup ex1.bam|perl -ape '$_=$F[4];s/(\d+)(??{".{$1}"})|\^.//g;@_=(tr/A-Z//,tr/a-z//);$_=join("\t",@F[0,1],@_)."\n"'

# ../samtools pileup -cf ex1.fa ex1.bam|perl -ape '$_=$F[8];s/\^.//g;s/(\d+)(??{".{$1}"})|\^.//g;@_=(tr/A-Za-z//,tr/,.//);$_=join("\t",@F[0,1],@_)."\n"'
genometools-1.5.1/src/external/samtools-0.1.18/examples/bam2bed.c000066400000000000000000000026241211610345200243230ustar00rootroot00000000000000#include 
#include "sam.h"
static int fetch_func(const bam1_t *b, void *data)
{
	samfile_t *fp = (samfile_t*)data;
	uint32_t *cigar = bam1_cigar(b);
	const bam1_core_t *c = &b->core;
	int i, l;
	if (b->core.tid < 0) return 0;
	for (i = l = 0; i < c->n_cigar; ++i) {
		int op = cigar[i]&0xf;
		if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
			l += cigar[i]>>4;
	}
	printf("%s\t%d\t%d\t%s\t%d\t%c\n", fp->header->target_name[c->tid],
		   c->pos, c->pos + l, bam1_qname(b), c->qual, (c->flag&BAM_FREVERSE)? '-' : '+');
	return 0;
}
int main(int argc, char *argv[])
{
	samfile_t *fp;
	if (argc == 1) {
		fprintf(stderr, "Usage: bam2bed  [region]\n");
		return 1;
	}
	if ((fp = samopen(argv[1], "rb", 0)) == 0) {
		fprintf(stderr, "bam2bed: Fail to open BAM file %s\n", argv[1]);
		return 1;
	}
	if (argc == 2) { /* if a region is not specified */
		bam1_t *b = bam_init1();
		while (samread(fp, b) >= 0) fetch_func(b, fp);
		bam_destroy1(b);
	} else {
		int ref, beg, end;
		bam_index_t *idx;
		if ((idx = bam_index_load(argv[1])) == 0) {
			fprintf(stderr, "bam2bed: BAM indexing file is not available.\n");
			return 1;
		}
		bam_parse_region(fp->header, argv[2], &ref, &beg, &end);
		if (ref < 0) {
			fprintf(stderr, "bam2bed: Invalid region %s\n", argv[2]);
			return 1;
		}
		bam_fetch(fp->x.bam, idx, ref, beg, end, fp, fetch_func);
		bam_index_destroy(idx);
	}
	samclose(fp);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/examples/calDepth.c000066400000000000000000000032411211610345200245470ustar00rootroot00000000000000#include 
#include "sam.h"

typedef struct {
  int beg, end;
  samfile_t *in;
} tmpstruct_t;

// callback for bam_fetch()
static int fetch_func(const bam1_t *b, void *data)
{
  bam_plbuf_t *buf = (bam_plbuf_t*)data;
  bam_plbuf_push(b, buf);
  return 0;
}
// callback for bam_plbuf_init()
static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
  tmpstruct_t *tmp = (tmpstruct_t*)data;
  if ((int)pos >= tmp->beg && (int)pos < tmp->end)
    printf("%s\t%d\t%d\n", tmp->in->header->target_name[tid], pos + 1, n);
  return 0;
}

int main(int argc, char *argv[])
{
  tmpstruct_t tmp;
  if (argc == 1) {
    fprintf(stderr, "Usage: calDepth  [region]\n");
    return 1;
  }
  tmp.beg = 0; tmp.end = 0x7fffffff;
  tmp.in = samopen(argv[1], "rb", 0);
  if (tmp.in == 0) {
    fprintf(stderr, "Fail to open BAM file %s\n", argv[1]);
    return 1;
  }
  if (argc == 2) { // if a region is not specified
    sampileup(tmp.in, -1, pileup_func, &tmp);
  } else {
    int ref;
    bam_index_t *idx;
    bam_plbuf_t *buf;
    idx = bam_index_load(argv[1]); // load BAM index
    if (idx == 0) {
      fprintf(stderr, "BAM indexing file is not available.\n");
      return 1;
    }
    bam_parse_region(tmp.in->header, argv[2], &ref, &tmp.beg, &tmp.end); // parse the region
    if (ref < 0) {
      fprintf(stderr, "Invalid region %s\n", argv[2]);
      return 1;
    }
    buf = bam_plbuf_init(pileup_func, &tmp); // initialize pileup
    bam_fetch(tmp.in->x.bam, idx, ref, tmp.beg, tmp.end, buf, fetch_func);
    bam_plbuf_push(0, buf); // finalize pileup
    bam_index_destroy(idx);
    bam_plbuf_destroy(buf);
  }
  samclose(tmp.in);
  return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/examples/ex1.fa000066400000000000000000000062311211610345200236660ustar00rootroot00000000000000>seq1
CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCT
GTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCAC
GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAG
TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTC
AGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAA
CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACC
AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT
CTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
ATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGC
AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAAC
AACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACAC
ATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATAC
CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCT
TTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT
TCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT
GCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT
ACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGA
ACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTG
TGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTA
CGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAG
TCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC
TTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC
TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTG
TTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGG
AGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATA
TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTC
TCCCTCGTCTTCTTA
>seq2
TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAG
CTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT
TATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTT
CAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA
AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC
ATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAG
GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCAT
CAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATT
TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTA
AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA
ATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT
TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATA
AAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACC
TCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATA
GATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATT
AATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA
AATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGT
AAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATAT
AACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAAT
ACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGAT
GATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG
CGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATA
GCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAA
AAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAA
TTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGC
CAGAAAAAAATATTTACAGTAACT
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genometools-1.5.1/src/external/samtools-0.1.18/faidx.c000066400000000000000000000250201211610345200222770ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include "faidx.h"
#include "khash.h"

typedef struct {
	int32_t line_len, line_blen;
	int64_t len;
	uint64_t offset;
} faidx1_t;
KHASH_MAP_INIT_STR(s, faidx1_t)

#ifndef _NO_RAZF
#include "razf.h"
#else
#ifdef _WIN32
#define ftello(fp) ftell(fp)
#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
#else
extern off_t ftello(FILE *stream);
extern int fseeko(FILE *stream, off_t offset, int whence);
#endif
#define RAZF FILE
#define razf_read(fp, buf, size) fread(buf, 1, size, fp)
#define razf_open(fn, mode) fopen(fn, mode)
#define razf_close(fp) fclose(fp)
#define razf_seek(fp, offset, whence) fseeko(fp, offset, whence)
#define razf_tell(fp) ftello(fp)
#endif
#ifdef _USE_KNETFILE
#include "knetfile.h"
#endif

struct __faidx_t {
	RAZF *rz;
	int n, m;
	char **name;
	khash_t(s) *hash;
};

#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

static inline void fai_insert_index(faidx_t *idx, const char *name, int len, int line_len, int line_blen, uint64_t offset)
{
	khint_t k;
	int ret;
	faidx1_t t;
	if (idx->n == idx->m) {
		idx->m = idx->m? idx->m<<1 : 16;
		idx->name = (char**)realloc(idx->name, sizeof(void*) * idx->m);
	}
	idx->name[idx->n] = strdup(name);
	k = kh_put(s, idx->hash, idx->name[idx->n], &ret);
	t.len = len; t.line_len = line_len; t.line_blen = line_blen; t.offset = offset;
	kh_value(idx->hash, k) = t;
	++idx->n;
}

faidx_t *fai_build_core(RAZF *rz)
{
	char c, *name;
	int l_name, m_name, ret;
	int line_len, line_blen, state;
	int l1, l2;
	faidx_t *idx;
	uint64_t offset;
	int64_t len;

	idx = (faidx_t*)calloc(1, sizeof(faidx_t));
	idx->hash = kh_init(s);
	name = 0; l_name = m_name = 0;
	len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0;
	while (razf_read(rz, &c, 1)) {
		if (c == '\n') { // an empty line
			if (state == 1) {
				offset = razf_tell(rz);
				continue;
			} else if ((state == 0 && len < 0) || state == 2) continue;
		}
		if (c == '>') { // fasta header
			if (len >= 0)
				fai_insert_index(idx, name, len, line_len, line_blen, offset);
			l_name = 0;
			while ((ret = razf_read(rz, &c, 1)) != 0 && !isspace(c)) {
				if (m_name < l_name + 2) {
					m_name = l_name + 2;
					kroundup32(m_name);
					name = (char*)realloc(name, m_name);
				}
				name[l_name++] = c;
			}
			name[l_name] = '\0';
			if (ret == 0) {
				fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
				free(name); fai_destroy(idx);
				return 0;
			}
			if (c != '\n') while (razf_read(rz, &c, 1) && c != '\n');
			state = 1; len = 0;
			offset = razf_tell(rz);
		} else {
			if (state == 3) {
				fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name);
				free(name); fai_destroy(idx);
				return 0;
			}
			if (state == 2) state = 3;
			l1 = l2 = 0;
			do {
				++l1;
				if (isgraph(c)) ++l2;
			} while ((ret = razf_read(rz, &c, 1)) && c != '\n');
			if (state == 3 && l2) {
				fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name);
				free(name); fai_destroy(idx);
				return 0;
			}
			++l1; len += l2;
			if (state == 1) line_len = l1, line_blen = l2, state = 0;
			else if (state == 0) {
				if (l1 != line_len || l2 != line_blen) state = 2;
			}
		}
	}
	fai_insert_index(idx, name, len, line_len, line_blen, offset);
	free(name);
	return idx;
}

void fai_save(const faidx_t *fai, FILE *fp)
{
	khint_t k;
	int i;
	for (i = 0; i < fai->n; ++i) {
		faidx1_t x;
		k = kh_get(s, fai->hash, fai->name[i]);
		x = kh_value(fai->hash, k);
#ifdef _WIN32
		fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len);
#else
		fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len);
#endif
	}
}

faidx_t *fai_read(FILE *fp)
{
	faidx_t *fai;
	char *buf, *p;
	int len, line_len, line_blen;
#ifdef _WIN32
	long offset;
#else
	long long offset;
#endif
	fai = (faidx_t*)calloc(1, sizeof(faidx_t));
	fai->hash = kh_init(s);
	buf = (char*)calloc(0x10000, 1);
	while (!feof(fp) && fgets(buf, 0x10000, fp)) {
		for (p = buf; *p && isgraph(*p); ++p);
		*p = 0; ++p;
#ifdef _WIN32
		sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len);
#else
		sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
#endif
		fai_insert_index(fai, buf, len, line_len, line_blen, offset);
	}
	free(buf);
	return fai;
}

void fai_destroy(faidx_t *fai)
{
	int i;
	for (i = 0; i < fai->n; ++i) free(fai->name[i]);
	free(fai->name);
	kh_destroy(s, fai->hash);
	if (fai->rz) razf_close(fai->rz);
	free(fai);
}

int fai_build(const char *fn)
{
	char *str;
	RAZF *rz;
	FILE *fp;
	faidx_t *fai;
	str = (char*)calloc(strlen(fn) + 5, 1);
	sprintf(str, "%s.fai", fn);
	rz = razf_open(fn, "r");
	if (rz == 0) {
		fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
		free(str);
		return -1;
	}
	fai = fai_build_core(rz);
	razf_close(rz);
	fp = fopen(str, "wb");
	if (fp == 0) {
		fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
		fai_destroy(fai); free(str);
		return -1;
	}
	fai_save(fai, fp);
	fclose(fp);
	free(str);
	fai_destroy(fai);
	return 0;
}

#ifdef _USE_KNETFILE
FILE *download_and_open(const char *fn)
{
    const int buf_size = 1 * 1024 * 1024;
    uint8_t *buf;
    FILE *fp;
    knetFile *fp_remote;
    const char *url = fn;
    const char *p;
    int l = strlen(fn);
    for (p = fn + l - 1; p >= fn; --p)
        if (*p == '/') break;
    fn = p + 1;

    // First try to open a local copy
    fp = fopen(fn, "r");
    if (fp)
        return fp;

    // If failed, download from remote and open
    fp_remote = knet_open(url, "rb");
    if (fp_remote == 0) {
        fprintf(stderr, "[download_from_remote] fail to open remote file %s\n",url);
        return NULL;
    }
    if ((fp = fopen(fn, "wb")) == 0) {
        fprintf(stderr, "[download_from_remote] fail to create file in the working directory %s\n",fn);
        knet_close(fp_remote);
        return NULL;
    }
    buf = (uint8_t*)calloc(buf_size, 1);
    while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
        fwrite(buf, 1, l, fp);
    free(buf);
    fclose(fp);
    knet_close(fp_remote);

    return fopen(fn, "r");
}
#endif

faidx_t *fai_load(const char *fn)
{
	char *str;
	FILE *fp;
	faidx_t *fai;
	str = (char*)calloc(strlen(fn) + 5, 1);
	sprintf(str, "%s.fai", fn);

#ifdef _USE_KNETFILE
    if (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)
    {
        fp = download_and_open(str);
        if ( !fp )
        {
            fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
            free(str);
            return 0;
        }
    }
    else
#endif
        fp = fopen(str, "rb");
	if (fp == 0) {
		fprintf(stderr, "[fai_load] build FASTA index.\n");
		fai_build(fn);
		fp = fopen(str, "rb");
		if (fp == 0) {
			fprintf(stderr, "[fai_load] fail to open FASTA index.\n");
			free(str);
			return 0;
		}
	}

	fai = fai_read(fp);
	fclose(fp);

	fai->rz = razf_open(fn, "rb");
	free(str);
	if (fai->rz == 0) {
		fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
		return 0;
	}
	return fai;
}

char *fai_fetch(const faidx_t *fai, const char *str, int *len)
{
	char *s, c;
	int i, l, k, name_end;
	khiter_t iter;
	faidx1_t val;
	khash_t(s) *h;
	int beg, end;

	beg = end = -1;
	h = fai->hash;
	name_end = l = strlen(str);
	s = (char*)malloc(l+1);
	// remove space
	for (i = k = 0; i < l; ++i)
		if (!isspace(str[i])) s[k++] = str[i];
	s[k] = 0; l = k;
	// determine the sequence name
	for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
	if (i >= 0) name_end = i;
	if (name_end < l) { // check if this is really the end
		int n_hyphen = 0;
		for (i = name_end + 1; i < l; ++i) {
			if (s[i] == '-') ++n_hyphen;
			else if (!isdigit(s[i]) && s[i] != ',') break;
		}
		if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
		s[name_end] = 0;
		iter = kh_get(s, h, s);
		if (iter == kh_end(h)) { // cannot find the sequence name
			iter = kh_get(s, h, str); // try str as the name
			if (iter == kh_end(h)) {
				*len = 0;
			free(s); return 0;
			} else s[name_end] = ':', name_end = l;
		}
	} else iter = kh_get(s, h, str);
	val = kh_value(h, iter);
	// parse the interval
	if (name_end < l) {
		for (i = k = name_end + 1; i < l; ++i)
			if (s[i] != ',') s[k++] = s[i];
		s[k] = 0;
		beg = atoi(s + name_end + 1);
		for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
		end = i < k? atoi(s + i + 1) : val.len;
		if (beg > 0) --beg;
	} else beg = 0, end = val.len;
	if (beg >= val.len) beg = val.len;
	if (end >= val.len) end = val.len;
	if (beg > end) beg = end;
	free(s);

	// now retrieve the sequence
	l = 0;
	s = (char*)malloc(end - beg + 2);
	razf_seek(fai->rz, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
	while (razf_read(fai->rz, &c, 1) == 1 && l < end - beg && !fai->rz->z_err)
		if (isgraph(c)) s[l++] = c;
	s[l] = '\0';
	*len = l;
	return s;
}

int faidx_main(int argc, char *argv[])
{
	if (argc == 1) {
		fprintf(stderr, "Usage: faidx  [ [...]]\n");
		return 1;
	} else {
		if (argc == 2) fai_build(argv[1]);
		else {
			int i, j, k, l;
			char *s;
			faidx_t *fai;
			fai = fai_load(argv[1]);
			if (fai == 0) return 1;
			for (i = 2; i != argc; ++i) {
				printf(">%s\n", argv[i]);
				s = fai_fetch(fai, argv[i], &l);
				for (j = 0; j < l; j += 60) {
					for (k = 0; k < 60 && k < l - j; ++k)
						putchar(s[j + k]);
					putchar('\n');
				}
				free(s);
			}
			fai_destroy(fai);
		}
	}
	return 0;
}

int faidx_fetch_nseq(const faidx_t *fai) 
{
	return fai->n;
}

char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len)
{
	int l;
	char c;
    khiter_t iter;
    faidx1_t val;
	char *seq=NULL;

    // Adjust position
    iter = kh_get(s, fai->hash, c_name);
    if(iter == kh_end(fai->hash)) return 0;
    val = kh_value(fai->hash, iter);
	if(p_end_i < p_beg_i) p_beg_i = p_end_i;
    if(p_beg_i < 0) p_beg_i = 0;
    else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
    if(p_end_i < 0) p_end_i = 0;
    else if(val.len <= p_end_i) p_end_i = val.len - 1;

    // Now retrieve the sequence 
	l = 0;
	seq = (char*)malloc(p_end_i - p_beg_i + 2);
	razf_seek(fai->rz, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
	while (razf_read(fai->rz, &c, 1) == 1 && l < p_end_i - p_beg_i + 1)
		if (isgraph(c)) seq[l++] = c;
	seq[l] = '\0';
	*len = l;
	return seq;
}

#ifdef FAIDX_MAIN
int main(int argc, char *argv[]) { return faidx_main(argc, argv); }
#endif
genometools-1.5.1/src/external/samtools-0.1.18/faidx.h000066400000000000000000000061641211610345200223140ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li  */

#ifndef FAIDX_H
#define FAIDX_H

/*!
  @header

  Index FASTA files and extract subsequence.

  @copyright The Wellcome Trust Sanger Institute.
 */

struct __faidx_t;
typedef struct __faidx_t faidx_t;

#ifdef __cplusplus
extern "C" {
#endif

	/*!
	  @abstract   Build index for a FASTA or razip compressed FASTA file.
	  @param  fn  FASTA file name
	  @return     0 on success; or -1 on failure
	  @discussion File "fn.fai" will be generated.
	 */
	int fai_build(const char *fn);

	/*!
	  @abstract    Distroy a faidx_t struct.
	  @param  fai  Pointer to the struct to be destroyed
	 */
	void fai_destroy(faidx_t *fai);

	/*!
	  @abstract   Load index from "fn.fai".
	  @param  fn  File name of the FASTA file
	 */
	faidx_t *fai_load(const char *fn);

	/*!
	  @abstract    Fetch the sequence in a region.
	  @param  fai  Pointer to the faidx_t struct
	  @param  reg  Region in the format "chr2:20,000-30,000"
	  @param  len  Length of the region
	  @return      Pointer to the sequence; null on failure

	  @discussion The returned sequence is allocated by malloc family
	  and should be destroyed by end users by calling free() on it.
	 */
	char *fai_fetch(const faidx_t *fai, const char *reg, int *len);

	/*!
	  @abstract	   Fetch the number of sequences. 
	  @param  fai  Pointer to the faidx_t struct
	  @return	   The number of sequences
	 */
	int faidx_fetch_nseq(const faidx_t *fai);

	/*!
	  @abstract    Fetch the sequence in a region.
	  @param  fai  Pointer to the faidx_t struct
	  @param  c_name Region name
	  @param  p_beg_i  Beginning position number (zero-based)
	  @param  p_end_i  End position number (zero-based)
	  @param  len  Length of the region
	  @return      Pointer to the sequence; null on failure

	  @discussion The returned sequence is allocated by malloc family
	  and should be destroyed by end users by calling free() on it.
	 */
	char *faidx_fetch_seq(const faidx_t *fai, char *c_name, int p_beg_i, int p_end_i, int *len);

#ifdef __cplusplus
}
#endif

#endif
genometools-1.5.1/src/external/samtools-0.1.18/kaln.c000066400000000000000000000355761211610345200221520ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2003-2006, 2008, 2009, by Heng Li 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include 
#include "kaln.h"

#define FROM_M 0
#define FROM_I 1
#define FROM_D 2

typedef struct {
	int i, j;
	unsigned char ctype;
} path_t;

int aln_sm_blosum62[] = {
/*	 A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  *  X */
	 4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0,-4, 0,
	-1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3,-4,-1,
	-2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3,-4,-1,
	-2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3,-4,-1,
	 0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-4,-2,
	-1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2,-4,-1,
	-1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2,-4,-1,
	 0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3,-4,-1,
	-2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3,-4,-1,
	-1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3,-4,-1,
	-1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1,-4,-1,
	-1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2,-4,-1,
	-1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1,-4,-1,
	-2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1,-4,-1,
	-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2,-4,-2,
	 1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2,-4, 0,
	 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0,-4, 0,
	-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3,-4,-2,
	-2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1,-4,-1,
	 0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4,-4,-1,
	-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4, 1,-4,
	 0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-4,-1
};

int aln_sm_blast[] = {
	1, -3, -3, -3, -2,
	-3, 1, -3, -3, -2,
	-3, -3, 1, -3, -2,
	-3, -3, -3, 1, -2,
	-2, -2, -2, -2, -2
};

int aln_sm_qual[] = {
	  0, -23, -23, -23, 0,
	-23,   0, -23, -23, 0,
	-23, -23,   0, -23, 0,
	-23, -23, -23,   0, 0,
	  0,   0,   0,   0, 0
};

ka_param_t ka_param_blast = {  5,  2,   5, 2, aln_sm_blast, 5, 50 };
ka_param_t ka_param_aa2aa = { 10,  2,  10, 2, aln_sm_blosum62, 22, 50 };

ka_param2_t ka_param2_qual  = { 37, 11, 37, 11, 37, 11, 0, 0, aln_sm_qual, 5, 50 };

static uint32_t *ka_path2cigar32(const path_t *path, int path_len, int *n_cigar)
{
	int i, n;
	uint32_t *cigar;
	unsigned char last_type;

	if (path_len == 0 || path == 0) {
		*n_cigar = 0;
		return 0;
	}

	last_type = path->ctype;
	for (i = n = 1; i < path_len; ++i) {
		if (last_type != path[i].ctype) ++n;
		last_type = path[i].ctype;
	}
	*n_cigar = n;
	cigar = (uint32_t*)calloc(*n_cigar, 4);

	cigar[0] = 1u << 4 | path[path_len-1].ctype;
	last_type = path[path_len-1].ctype;
	for (i = path_len - 2, n = 0; i >= 0; --i) {
		if (path[i].ctype == last_type) cigar[n] += 1u << 4;
		else {
			cigar[++n] = 1u << 4 | path[i].ctype;
			last_type = path[i].ctype;
		}
	}

	return cigar;
}

/***************************/
/* START OF common_align.c */
/***************************/

#define SET_INF(s) (s).M = (s).I = (s).D = MINOR_INF;

#define set_M(MM, cur, p, sc)							\
{														\
	if ((p)->M >= (p)->I) {								\
		if ((p)->M >= (p)->D) {							\
			(MM) = (p)->M + (sc); (cur)->Mt = FROM_M;	\
		} else {										\
			(MM) = (p)->D + (sc); (cur)->Mt = FROM_D;	\
		}												\
	} else {											\
		if ((p)->I > (p)->D) {							\
			(MM) = (p)->I + (sc); (cur)->Mt = FROM_I;	\
		} else {										\
			(MM) = (p)->D + (sc); (cur)->Mt = FROM_D;	\
		}												\
	}													\
}
#define set_I(II, cur, p)								\
{														\
	if ((p)->M - gap_open > (p)->I) {					\
		(cur)->It = FROM_M;								\
		(II) = (p)->M - gap_open - gap_ext;				\
	} else {											\
		(cur)->It = FROM_I;								\
		(II) = (p)->I - gap_ext;						\
	}													\
}
#define set_end_I(II, cur, p)							\
{														\
	if (gap_end_ext >= 0) {								\
		if ((p)->M - gap_end_open > (p)->I) {			\
			(cur)->It = FROM_M;							\
			(II) = (p)->M - gap_end_open - gap_end_ext;	\
		} else {										\
			(cur)->It = FROM_I;							\
			(II) = (p)->I - gap_end_ext;				\
		}												\
	} else set_I(II, cur, p);							\
}
#define set_D(DD, cur, p)								\
{														\
	if ((p)->M - gap_open > (p)->D) {					\
		(cur)->Dt = FROM_M;								\
		(DD) = (p)->M - gap_open - gap_ext;				\
	} else {											\
		(cur)->Dt = FROM_D;								\
		(DD) = (p)->D - gap_ext;						\
	}													\
}
#define set_end_D(DD, cur, p)							\
{														\
	if (gap_end_ext >= 0) {								\
		if ((p)->M - gap_end_open > (p)->D) {			\
			(cur)->Dt = FROM_M;							\
			(DD) = (p)->M - gap_end_open - gap_end_ext;	\
		} else {										\
			(cur)->Dt = FROM_D;							\
			(DD) = (p)->D - gap_end_ext;				\
		}												\
	} else set_D(DD, cur, p);							\
}

typedef struct {
	uint8_t Mt:3, It:2, Dt:3;
} dpcell_t;

typedef struct {
	int M, I, D;
} dpscore_t;

/***************************
 * banded global alignment *
 ***************************/
uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar)
{
	int i, j;
	dpcell_t **dpcell, *q;
	dpscore_t *curr, *last, *s;
	int b1, b2, tmp_end;
	int *mat, end, max = 0;
	uint8_t type, ctype;
	uint32_t *cigar = 0;

	int gap_open, gap_ext, gap_end_open, gap_end_ext, b;
	int *score_matrix, N_MATRIX_ROW;

	/* initialize some align-related parameters. just for compatibility */
	gap_open = ap->gap_open;
	gap_ext = ap->gap_ext;
	gap_end_open = ap->gap_end_open;
	gap_end_ext = ap->gap_end_ext;
	b = ap->band_width;
	score_matrix = ap->matrix;
	N_MATRIX_ROW = ap->row;

	if (n_cigar) *n_cigar = 0;
	if (len1 == 0 || len2 == 0) return 0;

	/* calculate b1 and b2 */
	if (len1 > len2) {
		b1 = len1 - len2 + b;
		b2 = b;
	} else {
		b1 = b;
		b2 = len2 - len1 + b;
	}
	if (b1 > len1) b1 = len1;
	if (b2 > len2) b2 = len2;
	--seq1; --seq2;

	/* allocate memory */
	end = (b1 + b2 <= len1)? (b1 + b2 + 1) : (len1 + 1);
	dpcell = (dpcell_t**)malloc(sizeof(dpcell_t*) * (len2 + 1));
	for (j = 0; j <= len2; ++j)
		dpcell[j] = (dpcell_t*)malloc(sizeof(dpcell_t) * end);
	for (j = b2 + 1; j <= len2; ++j)
		dpcell[j] -= j - b2;
	curr = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
	last = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
	
	/* set first row */
	SET_INF(*curr); curr->M = 0;
	for (i = 1, s = curr + 1; i < b1; ++i, ++s) {
		SET_INF(*s);
		set_end_D(s->D, dpcell[0] + i, s - 1);
	}
	s = curr; curr = last; last = s;

	/* core dynamic programming, part 1 */
	tmp_end = (b2 < len2)? b2 : len2 - 1;
	for (j = 1; j <= tmp_end; ++j) {
		q = dpcell[j]; s = curr; SET_INF(*s);
		set_end_I(s->I, q, last);
		end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
		++s; ++q;
		for (i = 1; i != end; ++i, ++s, ++q) {
			set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
			set_I(s->I, q, last + i);
			set_D(s->D, q, s - 1);
		}
		set_M(s->M, q, last + i - 1, mat[seq1[i]]);
		set_D(s->D, q, s - 1);
		if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
			set_end_I(s->I, q, last + i);
		} else s->I = MINOR_INF;
		s = curr; curr = last; last = s;
	}
	/* last row for part 1, use set_end_D() instead of set_D() */
	if (j == len2 && b2 != len2 - 1) {
		q = dpcell[j]; s = curr; SET_INF(*s);
		set_end_I(s->I, q, last);
		end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
		++s; ++q;
		for (i = 1; i != end; ++i, ++s, ++q) {
			set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
			set_I(s->I, q, last + i);
			set_end_D(s->D, q, s - 1);
		}
		set_M(s->M, q, last + i - 1, mat[seq1[i]]);
		set_end_D(s->D, q, s - 1);
		if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
			set_end_I(s->I, q, last + i);
		} else s->I = MINOR_INF;
		s = curr; curr = last; last = s;
		++j;
	}

	/* core dynamic programming, part 2 */
	for (; j <= len2 - b2 + 1; ++j) {
		SET_INF(curr[j - b2]);
		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
		end = j + b1 - 1;
		for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i != end; ++i, ++s, ++q) {
			set_M(s->M, q, last + i - 1, mat[seq1[i]]);
			set_I(s->I, q, last + i);
			set_D(s->D, q, s - 1);
		}
		set_M(s->M, q, last + i - 1, mat[seq1[i]]);
		set_D(s->D, q, s - 1);
		s->I = MINOR_INF;
		s = curr; curr = last; last = s;
	}

	/* core dynamic programming, part 3 */
	for (; j < len2; ++j) {
		SET_INF(curr[j - b2]);
		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
		for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
			set_M(s->M, q, last + i - 1, mat[seq1[i]]);
			set_I(s->I, q, last + i);
			set_D(s->D, q, s - 1);
		}
		set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
		set_end_I(s->I, q, last + i);
		set_D(s->D, q, s - 1);
		s = curr; curr = last; last = s;
	}
	/* last row */
	if (j == len2) {
		SET_INF(curr[j - b2]);
		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
		for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
			set_M(s->M, q, last + i - 1, mat[seq1[i]]);
			set_I(s->I, q, last + i);
			set_end_D(s->D, q, s - 1);
		}
		set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
		set_end_I(s->I, q, last + i);
		set_end_D(s->D, q, s - 1);
		s = curr; curr = last; last = s;
	}

	*_score = last[len1].M;
	if (n_cigar) { /* backtrace */
		path_t *p, *path = (path_t*)malloc(sizeof(path_t) * (len1 + len2 + 2));
		i = len1; j = len2;
		q = dpcell[j] + i;
		s = last + len1;
		max = s->M; type = q->Mt; ctype = FROM_M;
		if (s->I > max) { max = s->I; type = q->It; ctype = FROM_I; }
		if (s->D > max) { max = s->D; type = q->Dt; ctype = FROM_D; }

		p = path;
		p->ctype = ctype; p->i = i; p->j = j; /* bug fixed 040408 */
		++p;
		do {
			switch (ctype) {
			case FROM_M: --i; --j; break;
			case FROM_I: --j; break;
			case FROM_D: --i; break;
			}
			q = dpcell[j] + i;
			ctype = type;
			switch (type) {
			case FROM_M: type = q->Mt; break;
			case FROM_I: type = q->It; break;
			case FROM_D: type = q->Dt; break;
			}
			p->ctype = ctype; p->i = i; p->j = j;
			++p;
		} while (i || j);
		cigar = ka_path2cigar32(path, p - path - 1, n_cigar);
		free(path);
	}

	/* free memory */
	for (j = b2 + 1; j <= len2; ++j)
		dpcell[j] += j - b2;
	for (j = 0; j <= len2; ++j)
		free(dpcell[j]);
	free(dpcell);
	free(curr); free(last);

	return cigar;
}

typedef struct {
	int M, I, D;
} score_aux_t;

#define MINUS_INF -0x40000000

// matrix: len2 rows and len1 columns
int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap)
{
	
#define __score_aux(_p, _q0, _sc, _io, _ie, _do, _de) {					\
		int t1, t2;														\
		score_aux_t *_q;												\
		_q = _q0;														\
		_p->M = _q->M >= _q->I? _q->M : _q->I;							\
		_p->M = _p->M >= _q->D? _p->M : _q->D;							\
		_p->M += (_sc);													\
		++_q;      t1 = _q->M - _io - _ie; t2 = _q->I - _ie; _p->I = t1 >= t2? t1 : t2; \
		_q = _p-1; t1 = _q->M - _do - _de; t2 = _q->D - _de; _p->D = t1 >= t2? t1 : t2; \
	}

	int i, j, bw, scmat_size = ap->row, *scmat = ap->matrix, ret;
	const uint8_t *seq1, *seq2;
	score_aux_t *curr, *last, *swap;
	bw = abs(len1 - len2) + ap->band_width;
	i = len1 > len2? len1 : len2;
	if (bw > i + 1) bw = i + 1;
	seq1 = _seq1 - 1; seq2 = _seq2 - 1;
	curr = calloc(len1 + 2, sizeof(score_aux_t));
	last = calloc(len1 + 2, sizeof(score_aux_t));
	{ // the zero-th row
		int x, end = len1;
		score_aux_t *p;
		j = 0;
		x = j + bw; end = len1 < x? len1 : x; // band end
		p = curr;
		p->M = 0; p->I = p->D = MINUS_INF;
		for (i = 1, p = &curr[1]; i <= end; ++i, ++p)
			p->M = p->I = MINUS_INF, p->D = -(ap->edo + ap->ede * i);
		p->M = p->I = p->D = MINUS_INF;
		swap = curr; curr = last; last = swap;
	}
	for (j = 1; j < len2; ++j) {
		int x, beg = 0, end = len1, *scrow, col_end;
		score_aux_t *p;
		x = j - bw; beg =    0 > x?    0 : x; // band start
		x = j + bw; end = len1 < x? len1 : x; // band end
		if (beg == 0) { // from zero-th column
			p = curr;
			p->M = p->D = MINUS_INF; p->I = -(ap->eio + ap->eie * j);
			++beg; // then beg = 1
		}
		scrow = scmat + seq2[j] * scmat_size;
		if (end == len1) col_end = 1, --end;
		else col_end = 0;
		for (i = beg, p = &curr[beg]; i <= end; ++i, ++p)
			__score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->iio, ap->iie, ap->ido, ap->ide);
		if (col_end) {
			__score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->eio, ap->eie, ap->ido, ap->ide);
			++p;
		}
		p->M = p->I = p->D = MINUS_INF;
//		for (i = 0; i <= len1; ++i) printf("(%d,%d,%d) ", curr[i].M, curr[i].I, curr[i].D); putchar('\n');
		swap = curr; curr = last; last = swap;
	}
	{ // the last row
		int x, beg = 0, *scrow;
		score_aux_t *p;
		j = len2;
		x = j - bw; beg = 0 > x?    0 : x; // band start
		if (beg == 0) { // from zero-th column
			p = curr;
			p->M = p->D = MINUS_INF; p->I = -(ap->eio + ap->eie * j);
			++beg; // then beg = 1
		}
		scrow = scmat + seq2[j] * scmat_size;
		for (i = beg, p = &curr[beg]; i < len1; ++i, ++p)
			__score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->iio, ap->iie, ap->edo, ap->ede);
		__score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->eio, ap->eie, ap->edo, ap->ede);
//		for (i = 0; i <= len1; ++i) printf("(%d,%d,%d) ", curr[i].M, curr[i].I, curr[i].D); putchar('\n');
	}
	ret = curr[len1].M >= curr[len1].I? curr[len1].M : curr[len1].I;
	ret = ret >= curr[len1].D? ret : curr[len1].D;
	free(curr); free(last);
	return ret;
}

#ifdef _MAIN
int main(int argc, char *argv[])
{
//	int len1 = 35, len2 = 35;
//	uint8_t *seq1 = (uint8_t*)"\0\0\3\3\2\0\0\0\1\0\2\1\2\1\3\2\3\3\3\0\2\3\2\1\1\3\3\3\2\3\3\1\0\0\1";
//	uint8_t *seq2 = (uint8_t*)"\0\0\3\3\2\0\0\0\1\0\2\1\2\1\3\2\3\3\3\0\2\3\2\1\1\3\3\3\2\3\3\1\0\1\0";
	int len1 = 4, len2 = 4;
	uint8_t *seq1 = (uint8_t*)"\1\0\0\1";
	uint8_t *seq2 = (uint8_t*)"\1\0\1\0";
	int sc;
//	ka_global_core(seq1, 2, seq2, 1, &ka_param_qual, &sc, 0);
	sc = ka_global_score(seq1, len1, seq2, len2, &ka_param2_qual);
	printf("%d\n", sc);
	return 0;
}
#endif
genometools-1.5.1/src/external/samtools-0.1.18/kaln.h000066400000000000000000000040301211610345200221340ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2003-2006, 2008, 2009 by Heng Li 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

#ifndef LH3_KALN_H_
#define LH3_KALN_H_

#include 

#define MINOR_INF -1073741823

typedef struct {
	int gap_open;
	int gap_ext;
	int gap_end_open;
	int gap_end_ext;

	int *matrix;
	int row;
	int band_width;
} ka_param_t;

typedef struct {
	int iio, iie, ido, ide;
	int eio, eie, edo, ede;
	int *matrix;
	int row;
	int band_width;
} ka_param2_t;

#ifdef __cplusplus
extern "C" {
#endif

	uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap,
							 int *_score, int *n_cigar);
	int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap);
#ifdef __cplusplus
}
#endif

extern ka_param_t ka_param_blast; /* = { 5, 2, 5, 2, aln_sm_blast, 5, 50 }; */
extern ka_param_t ka_param_qual; // only use this for global alignment!!!
extern ka_param2_t ka_param2_qual; // only use this for global alignment!!!

#endif
genometools-1.5.1/src/external/samtools-0.1.18/khash.h000066400000000000000000000426271211610345200223230ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008, 2009, 2011 by Attractive Chaos 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/*
  An example:

#include "khash.h"
KHASH_MAP_INIT_INT(32, char)
int main() {
	int ret, is_missing;
	khiter_t k;
	khash_t(32) *h = kh_init(32);
	k = kh_put(32, h, 5, &ret);
	if (!ret) kh_del(32, h, k);
	kh_value(h, k) = 10;
	k = kh_get(32, h, 10);
	is_missing = (k == kh_end(h));
	k = kh_get(32, h, 5);
	kh_del(32, h, k);
	for (k = kh_begin(h); k != kh_end(h); ++k)
		if (kh_exist(h, k)) kh_value(h, k) = 1;
	kh_destroy(32, h);
	return 0;
}
*/

/*
  2011-02-14 (0.2.5):

    * Allow to declare global functions.

  2009-09-26 (0.2.4):

    * Improve portability

  2008-09-19 (0.2.3):

	* Corrected the example
	* Improved interfaces

  2008-09-11 (0.2.2):

	* Improved speed a little in kh_put()

  2008-09-10 (0.2.1):

	* Added kh_clear()
	* Fixed a compiling error

  2008-09-02 (0.2.0):

	* Changed to token concatenation which increases flexibility.

  2008-08-31 (0.1.2):

	* Fixed a bug in kh_get(), which has not been tested previously.

  2008-08-31 (0.1.1):

	* Added destructor
*/


#ifndef __AC_KHASH_H
#define __AC_KHASH_H

/*!
  @header

  Generic hash table library.

  @copyright Heng Li
 */

#define AC_VERSION_KHASH_H "0.2.5"

#include 
#include 
#include 

/* compipler specific configuration */

#if UINT_MAX == 0xffffffffu
typedef unsigned int khint32_t;
#elif ULONG_MAX == 0xffffffffu
typedef unsigned long khint32_t;
#endif

#if ULONG_MAX == ULLONG_MAX
typedef unsigned long khint64_t;
#else
typedef unsigned long long khint64_t;
#endif

#ifdef _MSC_VER
#define inline __inline
#endif

typedef khint32_t khint_t;
typedef khint_t khiter_t;

#define __ac_HASH_PRIME_SIZE 32
static const khint32_t __ac_prime_list[__ac_HASH_PRIME_SIZE] =
{
  0ul,          3ul,          11ul,         23ul,         53ul,
  97ul,         193ul,        389ul,        769ul,        1543ul,
  3079ul,       6151ul,       12289ul,      24593ul,      49157ul,
  98317ul,      196613ul,     393241ul,     786433ul,     1572869ul,
  3145739ul,    6291469ul,    12582917ul,   25165843ul,   50331653ul,
  100663319ul,  201326611ul,  402653189ul,  805306457ul,  1610612741ul,
  3221225473ul, 4294967291ul
};

#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))

static const double __ac_HASH_UPPER = 0.77;

#define KHASH_DECLARE(name, khkey_t, khval_t)		 					\
	typedef struct {													\
		khint_t n_buckets, size, n_occupied, upper_bound;				\
		khint32_t *flags;												\
		khkey_t *keys;													\
		khval_t *vals;													\
	} kh_##name##_t;													\
	extern kh_##name##_t *kh_init_##name();								\
	extern void kh_destroy_##name(kh_##name##_t *h);					\
	extern void kh_clear_##name(kh_##name##_t *h);						\
	extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); 	\
	extern void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \
	extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \
	extern void kh_del_##name(kh_##name##_t *h, khint_t x);

#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
	typedef struct {													\
		khint_t n_buckets, size, n_occupied, upper_bound;				\
		khint32_t *flags;												\
		khkey_t *keys;													\
		khval_t *vals;													\
	} kh_##name##_t;													\
	SCOPE kh_##name##_t *kh_init_##name() {								\
		return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t));		\
	}																	\
	SCOPE void kh_destroy_##name(kh_##name##_t *h)						\
	{																	\
		if (h) {														\
			free(h->keys); free(h->flags);								\
			free(h->vals);												\
			free(h);													\
		}																\
	}																	\
	SCOPE void kh_clear_##name(kh_##name##_t *h)						\
	{																	\
		if (h && h->flags) {											\
			memset(h->flags, 0xaa, ((h->n_buckets>>4) + 1) * sizeof(khint32_t)); \
			h->size = h->n_occupied = 0;								\
		}																\
	}																	\
	SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) 	\
	{																	\
		if (h->n_buckets) {												\
			khint_t inc, k, i, last;									\
			k = __hash_func(key); i = k % h->n_buckets;					\
			inc = 1 + k % (h->n_buckets - 1); last = i;					\
			while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
				if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
				else i += inc;											\
				if (i == last) return h->n_buckets;						\
			}															\
			return __ac_iseither(h->flags, i)? h->n_buckets : i;		\
		} else return 0;												\
	}																	\
	SCOPE void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
	{																	\
		khint32_t *new_flags = 0;										\
		khint_t j = 1;													\
		{																\
			khint_t t = __ac_HASH_PRIME_SIZE - 1;						\
			while (__ac_prime_list[t] > new_n_buckets) --t;				\
			new_n_buckets = __ac_prime_list[t+1];						\
			if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0;	\
			else {														\
				new_flags = (khint32_t*)malloc(((new_n_buckets>>4) + 1) * sizeof(khint32_t));	\
				memset(new_flags, 0xaa, ((new_n_buckets>>4) + 1) * sizeof(khint32_t)); \
				if (h->n_buckets < new_n_buckets) {						\
					h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
					if (kh_is_map)										\
						h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
				}														\
			}															\
		}																\
		if (j) {														\
			for (j = 0; j != h->n_buckets; ++j) {						\
				if (__ac_iseither(h->flags, j) == 0) {					\
					khkey_t key = h->keys[j];							\
					khval_t val;										\
					if (kh_is_map) val = h->vals[j];					\
					__ac_set_isdel_true(h->flags, j);					\
					while (1) {											\
						khint_t inc, k, i;								\
						k = __hash_func(key);							\
						i = k % new_n_buckets;							\
						inc = 1 + k % (new_n_buckets - 1);				\
						while (!__ac_isempty(new_flags, i)) {			\
							if (i + inc >= new_n_buckets) i = i + inc - new_n_buckets; \
							else i += inc;								\
						}												\
						__ac_set_isempty_false(new_flags, i);			\
						if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { \
							{ khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
							if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
							__ac_set_isdel_true(h->flags, i);			\
						} else {										\
							h->keys[i] = key;							\
							if (kh_is_map) h->vals[i] = val;			\
							break;										\
						}												\
					}													\
				}														\
			}															\
			if (h->n_buckets > new_n_buckets) {							\
				h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \
				if (kh_is_map)											\
					h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \
			}															\
			free(h->flags);												\
			h->flags = new_flags;										\
			h->n_buckets = new_n_buckets;								\
			h->n_occupied = h->size;									\
			h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
		}																\
	}																	\
	SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
	{																	\
		khint_t x;														\
		if (h->n_occupied >= h->upper_bound) {							\
			if (h->n_buckets > (h->size<<1)) kh_resize_##name(h, h->n_buckets - 1); \
			else kh_resize_##name(h, h->n_buckets + 1);					\
		}																\
		{																\
			khint_t inc, k, i, site, last;								\
			x = site = h->n_buckets; k = __hash_func(key); i = k % h->n_buckets; \
			if (__ac_isempty(h->flags, i)) x = i;						\
			else {														\
				inc = 1 + k % (h->n_buckets - 1); last = i;				\
				while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
					if (__ac_isdel(h->flags, i)) site = i;				\
					if (i + inc >= h->n_buckets) i = i + inc - h->n_buckets; \
					else i += inc;										\
					if (i == last) { x = site; break; }					\
				}														\
				if (x == h->n_buckets) {								\
					if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
					else x = i;											\
				}														\
			}															\
		}																\
		if (__ac_isempty(h->flags, x)) {								\
			h->keys[x] = key;											\
			__ac_set_isboth_false(h->flags, x);							\
			++h->size; ++h->n_occupied;									\
			*ret = 1;													\
		} else if (__ac_isdel(h->flags, x)) {							\
			h->keys[x] = key;											\
			__ac_set_isboth_false(h->flags, x);							\
			++h->size;													\
			*ret = 2;													\
		} else *ret = 0;												\
		return x;														\
	}																	\
	SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)				\
	{																	\
		if (x != h->n_buckets && !__ac_iseither(h->flags, x)) {			\
			__ac_set_isdel_true(h->flags, x);							\
			--h->size;													\
		}																\
	}

#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
	KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)

/* --- BEGIN OF HASH FUNCTIONS --- */

/*! @function
  @abstract     Integer hash function
  @param  key   The integer [khint32_t]
  @return       The hash value [khint_t]
 */
#define kh_int_hash_func(key) (khint32_t)(key)
/*! @function
  @abstract     Integer comparison function
 */
#define kh_int_hash_equal(a, b) ((a) == (b))
/*! @function
  @abstract     64-bit integer hash function
  @param  key   The integer [khint64_t]
  @return       The hash value [khint_t]
 */
#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
/*! @function
  @abstract     64-bit integer comparison function
 */
#define kh_int64_hash_equal(a, b) ((a) == (b))
/*! @function
  @abstract     const char* hash function
  @param  s     Pointer to a null terminated string
  @return       The hash value
 */
static inline khint_t __ac_X31_hash_string(const char *s)
{
	khint_t h = *s;
	if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
	return h;
}
/*! @function
  @abstract     Another interface to const char* hash function
  @param  key   Pointer to a null terminated string [const char*]
  @return       The hash value [khint_t]
 */
#define kh_str_hash_func(key) __ac_X31_hash_string(key)
/*! @function
  @abstract     Const char* comparison function
 */
#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)

/* --- END OF HASH FUNCTIONS --- */

/* Other necessary macros... */

/*!
  @abstract Type of the hash table.
  @param  name  Name of the hash table [symbol]
 */
#define khash_t(name) kh_##name##_t

/*! @function
  @abstract     Initiate a hash table.
  @param  name  Name of the hash table [symbol]
  @return       Pointer to the hash table [khash_t(name)*]
 */
#define kh_init(name) kh_init_##name()

/*! @function
  @abstract     Destroy a hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
 */
#define kh_destroy(name, h) kh_destroy_##name(h)

/*! @function
  @abstract     Reset a hash table without deallocating memory.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
 */
#define kh_clear(name, h) kh_clear_##name(h)

/*! @function
  @abstract     Resize a hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  s     New size [khint_t]
 */
#define kh_resize(name, h, s) kh_resize_##name(h, s)

/*! @function
  @abstract     Insert a key to the hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  k     Key [type of keys]
  @param  r     Extra return code: 0 if the key is present in the hash table;
                1 if the bucket is empty (never used); 2 if the element in
				the bucket has been deleted [int*]
  @return       Iterator to the inserted element [khint_t]
 */
#define kh_put(name, h, k, r) kh_put_##name(h, k, r)

/*! @function
  @abstract     Retrieve a key from the hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  k     Key [type of keys]
  @return       Iterator to the found element, or kh_end(h) is the element is absent [khint_t]
 */
#define kh_get(name, h, k) kh_get_##name(h, k)

/*! @function
  @abstract     Remove a key from the hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  k     Iterator to the element to be deleted [khint_t]
 */
#define kh_del(name, h, k) kh_del_##name(h, k)


/*! @function
  @abstract     Test whether a bucket contains data.
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  x     Iterator to the bucket [khint_t]
  @return       1 if containing data; 0 otherwise [int]
 */
#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))

/*! @function
  @abstract     Get key given an iterator
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  x     Iterator to the bucket [khint_t]
  @return       Key [type of keys]
 */
#define kh_key(h, x) ((h)->keys[x])

/*! @function
  @abstract     Get value given an iterator
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  x     Iterator to the bucket [khint_t]
  @return       Value [type of values]
  @discussion   For hash sets, calling this results in segfault.
 */
#define kh_val(h, x) ((h)->vals[x])

/*! @function
  @abstract     Alias of kh_val()
 */
#define kh_value(h, x) ((h)->vals[x])

/*! @function
  @abstract     Get the start iterator
  @param  h     Pointer to the hash table [khash_t(name)*]
  @return       The start iterator [khint_t]
 */
#define kh_begin(h) (khint_t)(0)

/*! @function
  @abstract     Get the end iterator
  @param  h     Pointer to the hash table [khash_t(name)*]
  @return       The end iterator [khint_t]
 */
#define kh_end(h) ((h)->n_buckets)

/*! @function
  @abstract     Get the number of elements in the hash table
  @param  h     Pointer to the hash table [khash_t(name)*]
  @return       Number of elements in the hash table [khint_t]
 */
#define kh_size(h) ((h)->size)

/*! @function
  @abstract     Get the number of buckets in the hash table
  @param  h     Pointer to the hash table [khash_t(name)*]
  @return       Number of buckets in the hash table [khint_t]
 */
#define kh_n_buckets(h) ((h)->n_buckets)

/* More conenient interfaces */

/*! @function
  @abstract     Instantiate a hash set containing integer keys
  @param  name  Name of the hash table [symbol]
 */
#define KHASH_SET_INIT_INT(name)										\
	KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)

/*! @function
  @abstract     Instantiate a hash map containing integer keys
  @param  name  Name of the hash table [symbol]
  @param  khval_t  Type of values [type]
 */
#define KHASH_MAP_INIT_INT(name, khval_t)								\
	KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)

/*! @function
  @abstract     Instantiate a hash map containing 64-bit integer keys
  @param  name  Name of the hash table [symbol]
 */
#define KHASH_SET_INIT_INT64(name)										\
	KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)

/*! @function
  @abstract     Instantiate a hash map containing 64-bit integer keys
  @param  name  Name of the hash table [symbol]
  @param  khval_t  Type of values [type]
 */
#define KHASH_MAP_INIT_INT64(name, khval_t)								\
	KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)

typedef const char *kh_cstr_t;
/*! @function
  @abstract     Instantiate a hash map containing const char* keys
  @param  name  Name of the hash table [symbol]
 */
#define KHASH_SET_INIT_STR(name)										\
	KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)

/*! @function
  @abstract     Instantiate a hash map containing const char* keys
  @param  name  Name of the hash table [symbol]
  @param  khval_t  Type of values [type]
 */
#define KHASH_MAP_INIT_STR(name, khval_t)								\
	KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)

#endif /* __AC_KHASH_H */
genometools-1.5.1/src/external/samtools-0.1.18/klist.h000066400000000000000000000066201211610345200223440ustar00rootroot00000000000000#ifndef _LH3_KLIST_H
#define _LH3_KLIST_H

#include 

#define KMEMPOOL_INIT(name, kmptype_t, kmpfree_f)						\
	typedef struct {													\
		size_t cnt, n, max;												\
		kmptype_t **buf;												\
	} kmp_##name##_t;													\
	static inline kmp_##name##_t *kmp_init_##name() {					\
		return calloc(1, sizeof(kmp_##name##_t));						\
	}																	\
	static inline void kmp_destroy_##name(kmp_##name##_t *mp) {			\
		size_t k;														\
		for (k = 0; k < mp->n; ++k) {									\
			kmpfree_f(mp->buf[k]); free(mp->buf[k]);					\
		}																\
		free(mp->buf); free(mp);										\
	}																	\
	static inline kmptype_t *kmp_alloc_##name(kmp_##name##_t *mp) {		\
		++mp->cnt;														\
		if (mp->n == 0) return calloc(1, sizeof(kmptype_t));			\
		return mp->buf[--mp->n];										\
	}																	\
	static inline void kmp_free_##name(kmp_##name##_t *mp, kmptype_t *p) { \
		--mp->cnt;														\
		if (mp->n == mp->max) {											\
			mp->max = mp->max? mp->max<<1 : 16;							\
			mp->buf = realloc(mp->buf, sizeof(void*) * mp->max);		\
		}																\
		mp->buf[mp->n++] = p;											\
	}

#define kmempool_t(name) kmp_##name##_t
#define kmp_init(name) kmp_init_##name()
#define kmp_destroy(name, mp) kmp_destroy_##name(mp)
#define kmp_alloc(name, mp) kmp_alloc_##name(mp)
#define kmp_free(name, mp, p) kmp_free_##name(mp, p)

#define KLIST_INIT(name, kltype_t, kmpfree_t)							\
	struct __kl1_##name {												\
		kltype_t data;													\
		struct __kl1_##name *next;										\
	};																	\
	typedef struct __kl1_##name kl1_##name;								\
	KMEMPOOL_INIT(name, kl1_##name, kmpfree_t)							\
	typedef struct {													\
		kl1_##name *head, *tail;										\
		kmp_##name##_t *mp;												\
		size_t size;													\
	} kl_##name##_t;													\
	static inline kl_##name##_t *kl_init_##name() {						\
		kl_##name##_t *kl = calloc(1, sizeof(kl_##name##_t));			\
		kl->mp = kmp_init(name);										\
		kl->head = kl->tail = kmp_alloc(name, kl->mp);					\
		kl->head->next = 0;												\
		return kl;														\
	}																	\
	static inline void kl_destroy_##name(kl_##name##_t *kl) {			\
		kl1_##name *p;													\
		for (p = kl->head; p != kl->tail; p = p->next)					\
			kmp_free(name, kl->mp, p);									\
		kmp_free(name, kl->mp, p);										\
		kmp_destroy(name, kl->mp);										\
		free(kl);														\
	}																	\
	static inline kltype_t *kl_pushp_##name(kl_##name##_t *kl) {		\
		kl1_##name *q, *p = kmp_alloc(name, kl->mp);					\
		q = kl->tail; p->next = 0; kl->tail->next = p; kl->tail = p;	\
		++kl->size;														\
		return &q->data;												\
	}																	\
	static inline int kl_shift_##name(kl_##name##_t *kl, kltype_t *d) { \
		kl1_##name *p;													\
		if (kl->head->next == 0) return -1;								\
		--kl->size;														\
		p = kl->head; kl->head = kl->head->next;						\
		if (d) *d = p->data;											\
		kmp_free(name, kl->mp, p);										\
		return 0;														\
	}

#define kliter_t(name) kl1_##name
#define klist_t(name) kl_##name##_t
#define kl_val(iter) ((iter)->data)
#define kl_next(iter) ((iter)->next)
#define kl_begin(kl) ((kl)->head)
#define kl_end(kl) ((kl)->tail)

#define kl_init(name) kl_init_##name()
#define kl_destroy(name, kl) kl_destroy_##name(kl)
#define kl_pushp(name, kl) kl_pushp_##name(kl)
#define kl_shift(name, kl, d) kl_shift_##name(kl, d)

#endif
genometools-1.5.1/src/external/samtools-0.1.18/knetfile.c000066400000000000000000000436341211610345200230200ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008 by Genome Research Ltd (GRL).
                 2010 by Attractive Chaos 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Probably I will not do socket programming in the next few years and
   therefore I decide to heavily annotate this file, for Linux and
   Windows as well.  -ac */

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

#ifndef _WIN32
#include 
#include 
#include 
#endif

#include "knetfile.h"

/* In winsock.h, the type of a socket is SOCKET, which is: "typedef
 * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed
 * integer -1. In knetfile.c, I use "int" for socket type
 * throughout. This should be improved to avoid confusion.
 *
 * In Linux/Mac, recv() and read() do almost the same thing. You can see
 * in the header file that netread() is simply an alias of read(). In
 * Windows, however, they are different and using recv() is mandatory.
 */

/* This function tests if the file handler is ready for reading (or
 * writing if is_read==0). */
static int socket_wait(int fd, int is_read)
{
	fd_set fds, *fdr = 0, *fdw = 0;
	struct timeval tv;
	int ret;
	tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
	FD_ZERO(&fds);
	FD_SET(fd, &fds);
	if (is_read) fdr = &fds;
	else fdw = &fds;
	ret = select(fd+1, fdr, fdw, 0, &tv);
#ifndef _WIN32
	if (ret == -1) perror("select");
#else
	if (ret == 0)
		fprintf(stderr, "select time-out\n");
	else if (ret == SOCKET_ERROR)
		fprintf(stderr, "select: %d\n", WSAGetLastError());
#endif
	return ret;
}

#ifndef _WIN32
/* This function does not work with Windows due to the lack of
 * getaddrinfo() in winsock. It is addapted from an example in "Beej's
 * Guide to Network Programming" (http://beej.us/guide/bgnet/). */
static int socket_connect(const char *host, const char *port)
{
#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)

	int on = 1, fd;
	struct linger lng = { 0, 0 };
	struct addrinfo hints, *res = 0;
	memset(&hints, 0, sizeof(struct addrinfo));
	hints.ai_family = AF_UNSPEC;
	hints.ai_socktype = SOCK_STREAM;
	/* In Unix/Mac, getaddrinfo() is the most convenient way to get
	 * server information. */
	if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
	if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
	/* The following two setsockopt() are used by ftplib
	 * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they
	 * necessary. */
	if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
	if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
	if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
	freeaddrinfo(res);
	return fd;
}
#else
/* MinGW's printf has problem with "%lld" */
char *int64tostr(char *buf, int64_t x)
{
	int cnt;
	int i = 0;
	do {
		buf[i++] = '0' + x % 10;
		x /= 10;
	} while (x);
	buf[i] = 0;
	for (cnt = i, i = 0; i < cnt/2; ++i) {
		int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c;
	}
	return buf;
}

int64_t strtoint64(const char *buf)
{
	int64_t x;
	for (x = 0; *buf != '\0'; ++buf)
		x = x * 10 + ((int64_t) *buf - 48);
	return x;
}
/* In windows, the first thing is to establish the TCP connection. */
int knet_win32_init()
{
	WSADATA wsaData;
	return WSAStartup(MAKEWORD(2, 2), &wsaData);
}
void knet_win32_destroy()
{
	WSACleanup();
}
/* A slightly modfied version of the following function also works on
 * Mac (and presummably Linux). However, this function is not stable on
 * my Mac. It sometimes works fine but sometimes does not. Therefore for
 * non-Windows OS, I do not use this one. */
static SOCKET socket_connect(const char *host, const char *port)
{
#define __err_connect(func)										\
	do {														\
		fprintf(stderr, "%s: %d\n", func, WSAGetLastError());	\
		return -1;												\
	} while (0)

	int on = 1;
	SOCKET fd;
	struct linger lng = { 0, 0 };
	struct sockaddr_in server;
	struct hostent *hp = 0;
	// open socket
	if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket");
	if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt");
	if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt");
	// get host info
	if (isalpha(host[0])) hp = gethostbyname(host);
	else {
		struct in_addr addr;
		addr.s_addr = inet_addr(host);
		hp = gethostbyaddr((char*)&addr, 4, AF_INET);
	}
	if (hp == 0) __err_connect("gethost");
	// connect
	server.sin_addr.s_addr = *((unsigned long*)hp->h_addr);
	server.sin_family= AF_INET;
	server.sin_port = htons(atoi(port));
	if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect");
	// freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!)
	return fd;
}
#endif

static off_t my_netread(int fd, void *buf, off_t len)
{
	off_t rest = len, curr, l = 0;
	/* recv() and read() may not read the required length of data with
	 * one call. They have to be called repeatedly. */
	while (rest) {
		if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading
		curr = netread(fd, buf + l, rest);
		/* According to the glibc manual, section 13.2, a zero returned
		 * value indicates end-of-file (EOF), which should mean that
		 * read() will not return zero if EOF has not been met but data
		 * are not immediately available. */
		if (curr == 0) break;
		l += curr; rest -= curr;
	}
	return l;
}

/*************************
 * FTP specific routines *
 *************************/

static int kftp_get_response(knetFile *ftp)
{
#ifndef _WIN32
	unsigned char c;
#else
	char c;
#endif
	int n = 0;
	char *p;
	if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0;
	while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
		//fputc(c, stderr);
		if (n >= ftp->max_response) {
			ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256;
			ftp->response = realloc(ftp->response, ftp->max_response);
		}
		ftp->response[n++] = c;
		if (c == '\n') {
			if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2])
				&& ftp->response[3] != '-') break;
			n = 0;
			continue;
		}
	}
	if (n < 2) return -1;
	ftp->response[n-2] = 0;
	return strtol(ftp->response, &p, 0);
}

static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get)
{
	if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
	netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
	return is_get? kftp_get_response(ftp) : 0;
}

static int kftp_pasv_prep(knetFile *ftp)
{
	char *p;
	int v[6];
	kftp_send_cmd(ftp, "PASV\r\n", 1);
	for (p = ftp->response; *p && *p != '('; ++p);
	if (*p != '(') return -1;
	++p;
	sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
	memcpy(ftp->pasv_ip, v, 4 * sizeof(int));
	ftp->pasv_port = (v[4]<<8&0xff00) + v[5];
	return 0;
}


static int kftp_pasv_connect(knetFile *ftp)
{
	char host[80], port[10];
	if (ftp->pasv_port == 0) {
		fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n");
		return -1;
	}
	sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]);
	sprintf(port, "%d", ftp->pasv_port);
	ftp->fd = socket_connect(host, port);
	if (ftp->fd == -1) return -1;
	return 0;
}

int kftp_connect(knetFile *ftp)
{
	ftp->ctrl_fd = socket_connect(ftp->host, ftp->port);
	if (ftp->ctrl_fd == -1) return -1;
	kftp_get_response(ftp);
	kftp_send_cmd(ftp, "USER anonymous\r\n", 1);
	kftp_send_cmd(ftp, "PASS kftp@\r\n", 1);
	kftp_send_cmd(ftp, "TYPE I\r\n", 1);
	return 0;
}

int kftp_reconnect(knetFile *ftp)
{
	if (ftp->ctrl_fd != -1) {
		netclose(ftp->ctrl_fd);
		ftp->ctrl_fd = -1;
	}
	netclose(ftp->fd);
	ftp->fd = -1;
	return kftp_connect(ftp);
}

// initialize ->type, ->host, ->retr and ->size
knetFile *kftp_parse_url(const char *fn, const char *mode)
{
	knetFile *fp;
	char *p;
	int l;
	if (strstr(fn, "ftp://") != fn) return 0;
	for (p = (char*)fn + 6; *p && *p != '/'; ++p);
	if (*p != '/') return 0;
	l = p - fn - 6;
	fp = calloc(1, sizeof(knetFile));
	fp->type = KNF_TYPE_FTP;
	fp->fd = -1;
	/* the Linux/Mac version of socket_connect() also recognizes a port
	 * like "ftp", but the Windows version does not. */
	fp->port = strdup("21");
	fp->host = calloc(l + 1, 1);
	if (strchr(mode, 'c')) fp->no_reconnect = 1;
	strncpy(fp->host, fn + 6, l);
	fp->retr = calloc(strlen(p) + 8, 1);
	sprintf(fp->retr, "RETR %s\r\n", p);
    fp->size_cmd = calloc(strlen(p) + 8, 1);
    sprintf(fp->size_cmd, "SIZE %s\r\n", p);
	fp->seek_offset = 0;
	return fp;
}
// place ->fd at offset off
int kftp_connect_file(knetFile *fp)
{
	int ret;
	long long file_size;
	if (fp->fd != -1) {
		netclose(fp->fd);
		if (fp->no_reconnect) kftp_get_response(fp);
	}
	kftp_pasv_prep(fp);
    kftp_send_cmd(fp, fp->size_cmd, 1);
#ifndef _WIN32
    if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 )
    {
        fprintf(stderr,"[kftp_connect_file] %s\n", fp->response);
        return -1;
    }
#else
	const char *p = fp->response;
	while (*p != ' ') ++p;
	while (*p < '0' || *p > '9') ++p;
	file_size = strtoint64(p);
#endif
	fp->file_size = file_size;
	if (fp->offset>=0) {
		char tmp[32];
#ifndef _WIN32
		sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
#else
		strcpy(tmp, "REST ");
		int64tostr(tmp + 5, fp->offset);
		strcat(tmp, "\r\n");
#endif
		kftp_send_cmd(fp, tmp, 1);
	}
	kftp_send_cmd(fp, fp->retr, 0);
	kftp_pasv_connect(fp);
	ret = kftp_get_response(fp);
	if (ret != 150) {
		fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
		netclose(fp->fd);
		fp->fd = -1;
		return -1;
	}
	fp->is_ready = 1;
	return 0;
}


/**************************
 * HTTP specific routines *
 **************************/

knetFile *khttp_parse_url(const char *fn, const char *mode)
{
	knetFile *fp;
	char *p, *proxy, *q;
	int l;
	if (strstr(fn, "http://") != fn) return 0;
	// set ->http_host
	for (p = (char*)fn + 7; *p && *p != '/'; ++p);
	l = p - fn - 7;
	fp = calloc(1, sizeof(knetFile));
	fp->http_host = calloc(l + 1, 1);
	strncpy(fp->http_host, fn + 7, l);
	fp->http_host[l] = 0;
	for (q = fp->http_host; *q && *q != ':'; ++q);
	if (*q == ':') *q++ = 0;
	// get http_proxy
	proxy = getenv("http_proxy");
	// set ->host, ->port and ->path
	if (proxy == 0) {
		fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name.
		fp->port = strdup(*q? q : "80");
		fp->path = strdup(*p? p : "/");
	} else {
		fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
		for (q = fp->host; *q && *q != ':'; ++q);
		if (*q == ':') *q++ = 0; 
		fp->port = strdup(*q? q : "80");
		fp->path = strdup(fn);
	}
	fp->type = KNF_TYPE_HTTP;
	fp->ctrl_fd = fp->fd = -1;
	fp->seek_offset = 0;
	return fp;
}

int khttp_connect_file(knetFile *fp)
{
	int ret, l = 0;
	char *buf, *p;
	if (fp->fd != -1) netclose(fp->fd);
	fp->fd = socket_connect(fp->host, fp->port);
	buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
	l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host);
    l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
	l += sprintf(buf + l, "\r\n");
	netwrite(fp->fd, buf, l);
	l = 0;
	while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
		if (buf[l] == '\n' && l >= 3)
			if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
		++l;
	}
	buf[l] = 0;
	if (l < 14) { // prematured header
		netclose(fp->fd);
		fp->fd = -1;
		return -1;
	}
	ret = strtol(buf + 8, &p, 0); // HTTP return code
	if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file
		off_t rest = fp->offset;
		while (rest) {
			off_t l = rest < 0x10000? rest : 0x10000;
			rest -= my_netread(fp->fd, buf, l);
		}
	} else if (ret != 206 && ret != 200) {
		free(buf);
		fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret);
		netclose(fp->fd);
		fp->fd = -1;
		return -1;
	}
	free(buf);
	fp->is_ready = 1;
	return 0;
}

/********************
 * Generic routines *
 ********************/

knetFile *knet_open(const char *fn, const char *mode)
{
	knetFile *fp = 0;
	if (mode[0] != 'r') {
		fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n");
		return 0;
	}
	if (strstr(fn, "ftp://") == fn) {
		fp = kftp_parse_url(fn, mode);
		if (fp == 0) return 0;
		if (kftp_connect(fp) == -1) {
			knet_close(fp);
			return 0;
		}
		kftp_connect_file(fp);
	} else if (strstr(fn, "http://") == fn) {
		fp = khttp_parse_url(fn, mode);
		if (fp == 0) return 0;
		khttp_connect_file(fp);
	} else { // local file
#ifdef _WIN32
		/* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may
		 * be undefined on some systems, although it is defined on my
		 * Mac and the Linux I have tested on. */
		int fd = open(fn, O_RDONLY | O_BINARY);
#else		
		int fd = open(fn, O_RDONLY);
#endif
		if (fd == -1) {
			perror("open");
			return 0;
		}
		fp = (knetFile*)calloc(1, sizeof(knetFile));
		fp->type = KNF_TYPE_LOCAL;
		fp->fd = fd;
		fp->ctrl_fd = -1;
	}
	if (fp && fp->fd == -1) {
		knet_close(fp);
		return 0;
	}
	return fp;
}

knetFile *knet_dopen(int fd, const char *mode)
{
	knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile));
	fp->type = KNF_TYPE_LOCAL;
	fp->fd = fd;
	return fp;
}

off_t knet_read(knetFile *fp, void *buf, off_t len)
{
	off_t l = 0;
	if (fp->fd == -1) return 0;
	if (fp->type == KNF_TYPE_FTP) {
		if (fp->is_ready == 0) {
			if (!fp->no_reconnect) kftp_reconnect(fp);
			kftp_connect_file(fp);
		}
	} else if (fp->type == KNF_TYPE_HTTP) {
		if (fp->is_ready == 0)
			khttp_connect_file(fp);
	}
	if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX
		off_t rest = len, curr;
		while (rest) {
			do {
				curr = read(fp->fd, buf + l, rest);
			} while (curr < 0 && EINTR == errno);
			if (curr < 0) return -1;
			if (curr == 0) break;
			l += curr; rest -= curr;
		}
	} else l = my_netread(fp->fd, buf, len);
	fp->offset += l;
	return l;
}

off_t knet_seek(knetFile *fp, int64_t off, int whence)
{
	if (whence == SEEK_SET && off == fp->offset) return 0;
	if (fp->type == KNF_TYPE_LOCAL) {
		/* Be aware that lseek() returns the offset after seeking,
		 * while fseek() returns zero on success. */
		off_t offset = lseek(fp->fd, off, whence);
		if (offset == -1) {
            // Be silent, it is OK for knet_seek to fail when the file is streamed
            // fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
			return -1;
		}
		fp->offset = offset;
		return 0;
	}
    else if (fp->type == KNF_TYPE_FTP) 
    {
        if (whence==SEEK_CUR)
            fp->offset += off;
        else if (whence==SEEK_SET)
            fp->offset = off;
        else if ( whence==SEEK_END)
            fp->offset = fp->file_size+off;
		fp->is_ready = 0;
		return 0;
	} 
    else if (fp->type == KNF_TYPE_HTTP) 
    {
		if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future?
			fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n");
			errno = ESPIPE;
			return -1;
		}
        if (whence==SEEK_CUR)
            fp->offset += off;
        else if (whence==SEEK_SET)
            fp->offset = off;
		fp->is_ready = 0;
		return 0;
	}
	errno = EINVAL;
    fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
	return -1;
}

int knet_close(knetFile *fp)
{
	if (fp == 0) return 0;
	if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific
	if (fp->fd != -1) {
		/* On Linux/Mac, netclose() is an alias of close(), but on
		 * Windows, it is an alias of closesocket(). */
		if (fp->type == KNF_TYPE_LOCAL) close(fp->fd);
		else netclose(fp->fd);
	}
	free(fp->host); free(fp->port);
	free(fp->response); free(fp->retr); // FTP specific
	free(fp->path); free(fp->http_host); // HTTP specific
	free(fp);
	return 0;
}

#ifdef KNETFILE_MAIN
int main(void)
{
	char *buf;
	knetFile *fp;
	int type = 4, l;
#ifdef _WIN32
	knet_win32_init();
#endif
	buf = calloc(0x100000, 1);
	if (type == 0) {
		fp = knet_open("knetfile.c", "r");
		knet_seek(fp, 1000, SEEK_SET);
	} else if (type == 1) { // NCBI FTP, large file
		fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r");
		knet_seek(fp, 2500000000ll, SEEK_SET);
		l = knet_read(fp, buf, 255);
	} else if (type == 2) {
		fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r");
		knet_seek(fp, 1000, SEEK_SET);
	} else if (type == 3) {
		fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r");
		knet_seek(fp, 1000, SEEK_SET);
	} else if (type == 4) {
		fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
		knet_read(fp, buf, 10000);
		knet_seek(fp, 20000, SEEK_SET);
		knet_seek(fp, 10000, SEEK_SET);
		l = knet_read(fp, buf+10000, 10000000) + 10000;
	}
	if (type != 4 && type != 1) {
		knet_read(fp, buf, 255);
		buf[255] = 0;
		printf("%s\n", buf);
	} else write(fileno(stdout), buf, l);
	knet_close(fp);
	free(buf);
	return 0;
}
#endif
genometools-1.5.1/src/external/samtools-0.1.18/knetfile.h000066400000000000000000000031131211610345200230110ustar00rootroot00000000000000#ifndef KNETFILE_H
#define KNETFILE_H

#include 
#include 

#ifndef _WIN32
#define netread(fd, ptr, len) read(fd, ptr, len)
#define netwrite(fd, ptr, len) write(fd, ptr, len)
#define netclose(fd) close(fd)
#else
#include 
#define netread(fd, ptr, len) recv(fd, ptr, len, 0)
#define netwrite(fd, ptr, len) send(fd, ptr, len, 0)
#define netclose(fd) closesocket(fd)
#endif

// FIXME: currently I/O is unbuffered

#define KNF_TYPE_LOCAL 1
#define KNF_TYPE_FTP   2
#define KNF_TYPE_HTTP  3

typedef struct knetFile_s {
	int type, fd;
	int64_t offset;
	char *host, *port;

	// the following are for FTP only
	int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready;
	char *response, *retr, *size_cmd;
	int64_t seek_offset; // for lazy seek
    int64_t file_size;

	// the following are for HTTP only
	char *path, *http_host;
} knetFile;

#define knet_tell(fp) ((fp)->offset)
#define knet_fileno(fp) ((fp)->fd)

#ifdef __cplusplus
extern "C" {
#endif

#ifdef _WIN32
	int knet_win32_init();
	void knet_win32_destroy();
#endif

	knetFile *knet_open(const char *fn, const char *mode);

	/* 
	   This only works with local files.
	 */
	knetFile *knet_dopen(int fd, const char *mode);

	/*
	  If ->is_ready==0, this routine updates ->fd; otherwise, it simply
	  reads from ->fd.
	 */
	off_t knet_read(knetFile *fp, void *buf, off_t len);

	/*
	  This routine only sets ->offset and ->is_ready=0. It does not
	  communicate with the FTP server.
	 */
	off_t knet_seek(knetFile *fp, int64_t off, int whence);
	int knet_close(knetFile *fp);

#ifdef __cplusplus
}
#endif

#endif
genometools-1.5.1/src/external/samtools-0.1.18/kprobaln.c000066400000000000000000000244201211610345200230170ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2003-2006, 2008-2010, by Heng Li 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include 
#include "kprobaln.h"

/*****************************************
 * Probabilistic banded glocal alignment *
 *****************************************/

#define EI .25
#define EM .33333333333

static float g_qual2prob[256];

#define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; }

kpa_par_t kpa_par_def = { 0.001, 0.1, 10 };
kpa_par_t kpa_par_alt = { 0.0001, 0.01, 10 };

/*
  The topology of the profile HMM:

           /\             /\        /\             /\
           I[1]           I[k-1]    I[k]           I[L]
            ^   \      \    ^    \   ^   \      \   ^
            |    \      \   |     \  |    \      \  |
    M[0]   M[1] -> ... -> M[k-1] -> M[k] -> ... -> M[L]   M[L+1]
                \      \/        \/      \/      /
                 \     /\        /\      /\     /
                       -> D[k-1] -> D[k] ->

   M[0] points to every {M,I}[k] and every {M,I}[k] points M[L+1].

   On input, _ref is the reference sequence and _query is the query
   sequence. Both are sequences of 0/1/2/3/4 where 4 stands for an
   ambiguous residue. iqual is the base quality. c sets the gap open
   probability, gap extension probability and band width.

   On output, state and q are arrays of length l_query. The higher 30
   bits give the reference position the query base is matched to and the
   lower two bits can be 0 (an alignment match) or 1 (an
   insertion). q[i] gives the phred scaled posterior probability of
   state[i] being wrong.
 */
int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual,
			   const kpa_par_t *c, int *state, uint8_t *q)
{
	double **f, **b = 0, *s, m[9], sI, sM, bI, bM, pb;
	float *qual, *_qual;
	const uint8_t *ref, *query;
	int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;

	/*** initialization ***/
	is_backward = state && q? 1 : 0;
	ref = _ref - 1; query = _query - 1; // change to 1-based coordinate
	bw = l_ref > l_query? l_ref : l_query;
	if (bw > c->bw) bw = c->bw;
	if (bw < abs(l_ref - l_query)) bw = abs(l_ref - l_query);
	bw2 = bw * 2 + 1;
	// allocate the forward and backward matrices f[][] and b[][] and the scaling array s[]
	f = calloc(l_query+1, sizeof(void*));
	if (is_backward) b = calloc(l_query+1, sizeof(void*));
	for (i = 0; i <= l_query; ++i) {
		f[i] = calloc(bw2 * 3 + 6, sizeof(double)); // FIXME: this is over-allocated for very short seqs
		if (is_backward) b[i] = calloc(bw2 * 3 + 6, sizeof(double));
	}
	s = calloc(l_query+2, sizeof(double)); // s[] is the scaling factor to avoid underflow
	// initialize qual
	_qual = calloc(l_query, sizeof(float));
	if (g_qual2prob[0] == 0)
		for (i = 0; i < 256; ++i)
			g_qual2prob[i] = pow(10, -i/10.);
	for (i = 0; i < l_query; ++i) _qual[i] = g_qual2prob[iqual? iqual[i] : 30];
	qual = _qual - 1;
	// initialize transition probability
	sM = sI = 1. / (2 * l_query + 2); // the value here seems not to affect results; FIXME: need proof
	m[0*3+0] = (1 - c->d - c->d) * (1 - sM); m[0*3+1] = m[0*3+2] = c->d * (1 - sM);
	m[1*3+0] = (1 - c->e) * (1 - sI); m[1*3+1] = c->e * (1 - sI); m[1*3+2] = 0.;
	m[2*3+0] = 1 - c->e; m[2*3+1] = 0.; m[2*3+2] = c->e;
	bM = (1 - c->d) / l_ref; bI = c->d / l_ref; // (bM+bI)*l_ref==1
	/*** forward ***/
	// f[0]
	set_u(k, bw, 0, 0);
	f[0][k] = s[0] = 1.;
	{ // f[1]
		double *fi = f[1], sum;
		int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1, _beg, _end;
		for (k = beg, sum = 0.; k <= end; ++k) {
			int u;
			double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] * EM;
			set_u(u, bw, 1, k);
			fi[u+0] = e * bM; fi[u+1] = EI * bI;
			sum += fi[u] + fi[u+1];
		}
		// rescale
		s[1] = sum;
		set_u(_beg, bw, 1, beg); set_u(_end, bw, 1, end); _end += 2;
		for (k = _beg; k <= _end; ++k) fi[k] /= sum;
	}
	// f[2..l_query]
	for (i = 2; i <= l_query; ++i) {
		double *fi = f[i], *fi1 = f[i-1], sum, qli = qual[i];
		int beg = 1, end = l_ref, x, _beg, _end;
		uint8_t qyi = query[i];
		x = i - bw; beg = beg > x? beg : x; // band start
		x = i + bw; end = end < x? end : x; // band end
		for (k = beg, sum = 0.; k <= end; ++k) {
			int u, v11, v01, v10;
			double e;
			e = (ref[k] > 3 || qyi > 3)? 1. : ref[k] == qyi? 1. - qli : qli * EM;
			set_u(u, bw, i, k); set_u(v11, bw, i-1, k-1); set_u(v10, bw, i-1, k); set_u(v01, bw, i, k-1);
			fi[u+0] = e * (m[0] * fi1[v11+0] + m[3] * fi1[v11+1] + m[6] * fi1[v11+2]);
			fi[u+1] = EI * (m[1] * fi1[v10+0] + m[4] * fi1[v10+1]);
			fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2];
			sum += fi[u] + fi[u+1] + fi[u+2];
//			fprintf(stderr, "F (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]); // DEBUG
		}
		// rescale
		s[i] = sum;
		set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2;
		for (k = _beg, sum = 1./sum; k <= _end; ++k) fi[k] *= sum;
	}
	{ // f[l_query+1]
		double sum;
		for (k = 1, sum = 0.; k <= l_ref; ++k) {
			int u;
			set_u(u, bw, l_query, k);
			if (u < 3 || u >= bw2*3+3) continue;
		    sum += f[l_query][u+0] * sM + f[l_query][u+1] * sI;
		}
		s[l_query+1] = sum; // the last scaling factor
	}
	{ // compute likelihood
		double p = 1., Pr1 = 0.;
		for (i = 0; i <= l_query + 1; ++i) {
			p *= s[i];
			if (p < 1e-100) Pr1 += -4.343 * log(p), p = 1.;
		}
		Pr1 += -4.343 * log(p * l_ref * l_query);
		Pr = (int)(Pr1 + .499);
		if (!is_backward) { // skip backward and MAP
			for (i = 0; i <= l_query; ++i) free(f[i]);
			free(f); free(s); free(_qual);
			return Pr;
		}
	}
	/*** backward ***/
	// b[l_query] (b[l_query+1][0]=1 and thus \tilde{b}[][]=1/s[l_query+1]; this is where s[l_query+1] comes from)
	for (k = 1; k <= l_ref; ++k) {
		int u;
		double *bi = b[l_query];
		set_u(u, bw, l_query, k);
		if (u < 3 || u >= bw2*3+3) continue;
		bi[u+0] = sM / s[l_query] / s[l_query+1]; bi[u+1] = sI / s[l_query] / s[l_query+1];
	}
	// b[l_query-1..1]
	for (i = l_query - 1; i >= 1; --i) {
		int beg = 1, end = l_ref, x, _beg, _end;
		double *bi = b[i], *bi1 = b[i+1], y = (i > 1), qli1 = qual[i+1];
		uint8_t qyi1 = query[i+1];
		x = i - bw; beg = beg > x? beg : x;
		x = i + bw; end = end < x? end : x;
		for (k = end; k >= beg; --k) {
			int u, v11, v01, v10;
			double e;
			set_u(u, bw, i, k); set_u(v11, bw, i+1, k+1); set_u(v10, bw, i+1, k); set_u(v01, bw, i, k+1);
			e = (k >= l_ref? 0 : (ref[k+1] > 3 || qyi1 > 3)? 1. : ref[k+1] == qyi1? 1. - qli1 : qli1 * EM) * bi1[v11];
			bi[u+0] = e * m[0] + EI * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e.
			bi[u+1] = e * m[3] + EI * m[4] * bi1[v10+1];
			bi[u+2] = (e * m[6] + m[8] * bi[v01+2]) * y;
//			fprintf(stderr, "B (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]); // DEBUG
		}
		// rescale
		set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2;
		for (k = _beg, y = 1./s[i]; k <= _end; ++k) bi[k] *= y;
	}
	{ // b[0]
		int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1;
		double sum = 0.;
		for (k = end; k >= beg; --k) {
			int u;
			double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] * EM;
			set_u(u, bw, 1, k);
			if (u < 3 || u >= bw2*3+3) continue;
		    sum += e * b[1][u+0] * bM + EI * b[1][u+1] * bI;
		}
		set_u(k, bw, 0, 0);
		pb = b[0][k] = sum / s[0]; // if everything works as is expected, pb == 1.0
	}
	is_diff = fabs(pb - 1.) > 1e-7? 1 : 0;
	/*** MAP ***/
	for (i = 1; i <= l_query; ++i) {
		double sum = 0., *fi = f[i], *bi = b[i], max = 0.;
		int beg = 1, end = l_ref, x, max_k = -1;
		x = i - bw; beg = beg > x? beg : x;
		x = i + bw; end = end < x? end : x;
		for (k = beg; k <= end; ++k) {
			int u;
			double z;
			set_u(u, bw, i, k);
			z = fi[u+0] * bi[u+0]; if (z > max) max = z, max_k = (k-1)<<2 | 0; sum += z;
			z = fi[u+1] * bi[u+1]; if (z > max) max = z, max_k = (k-1)<<2 | 1; sum += z;
		}
		max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0
		if (state) state[i-1] = max_k;
		if (q) k = (int)(-4.343 * log(1. - max) + .499), q[i-1] = k > 100? 99 : k;
#ifdef _MAIN
		fprintf(stderr, "(%.10lg,%.10lg) (%d,%d:%c,%c:%d) %lg\n", pb, sum, i-1, max_k>>2,
				"ACGT"[query[i]], "ACGT"[ref[(max_k>>2)+1]], max_k&3, max); // DEBUG
#endif
	}
	/*** free ***/
	for (i = 0; i <= l_query; ++i) {
		free(f[i]); free(b[i]);
	}
	free(f); free(b); free(s); free(_qual);
	return Pr;
}

#ifdef _MAIN
#include 
int main(int argc, char *argv[])
{
	uint8_t conv[256], *iqual, *ref, *query;
	int c, l_ref, l_query, i, q = 30, b = 10, P;
	while ((c = getopt(argc, argv, "b:q:")) >= 0) {
		switch (c) {
		case 'b': b = atoi(optarg); break;
		case 'q': q = atoi(optarg); break;
		}
	}
	if (optind + 2 > argc) {
		fprintf(stderr, "Usage: %s [-q %d] [-b %d]  \n", argv[0], q, b); // example: acttc attc
		return 1;
	}
	memset(conv, 4, 256);
	conv['a'] = conv['A'] = 0; conv['c'] = conv['C'] = 1;
	conv['g'] = conv['G'] = 2; conv['t'] = conv['T'] = 3;
	ref = (uint8_t*)argv[optind]; query = (uint8_t*)argv[optind+1];
	l_ref = strlen((char*)ref); l_query = strlen((char*)query);
	for (i = 0; i < l_ref; ++i) ref[i] = conv[ref[i]];
	for (i = 0; i < l_query; ++i) query[i] = conv[query[i]];
	iqual = malloc(l_query);
	memset(iqual, q, l_query);
	kpa_par_def.bw = b;
	P = kpa_glocal(ref, l_ref, query, l_query, iqual, &kpa_par_alt, 0, 0);
	fprintf(stderr, "%d\n", P);
	free(iqual);
	return 0;
}
#endif
genometools-1.5.1/src/external/samtools-0.1.18/kprobaln.h000066400000000000000000000030401211610345200230170ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2003-2006, 2008, 2009 by Heng Li 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

#ifndef LH3_KPROBALN_H_
#define LH3_KPROBALN_H_

#include 

typedef struct {
	float d, e;
	int bw;
} kpa_par_t;

#ifdef __cplusplus
extern "C" {
#endif

	int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual,
				   const kpa_par_t *c, int *state, uint8_t *q);

#ifdef __cplusplus
}
#endif

extern kpa_par_t kpa_par_def, kpa_par_alt;

#endif
genometools-1.5.1/src/external/samtools-0.1.18/kseq.h000066400000000000000000000201121211610345200221510ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008, 2009, 2011 Attractive Chaos 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Last Modified: 18AUG2011 */

#ifndef AC_KSEQ_H
#define AC_KSEQ_H

#include 
#include 
#include 

#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
#define KS_SEP_TAB   1 // isspace() && !' '
#define KS_SEP_MAX   1

#define __KS_TYPE(type_t)						\
	typedef struct __kstream_t {				\
		unsigned char *buf;						\
		int begin, end, is_eof;					\
		type_t f;								\
	} kstream_t;

#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)

#define __KS_BASIC(type_t, __bufsize)								\
	static inline kstream_t *ks_init(type_t f)						\
	{																\
		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));	\
		ks->f = f;													\
		ks->buf = malloc(__bufsize);								\
		return ks;													\
	}																\
	static inline void ks_destroy(kstream_t *ks)					\
	{																\
		if (ks) {													\
			free(ks->buf);											\
			free(ks);												\
		}															\
	}

#define __KS_GETC(__read, __bufsize)						\
	static inline int ks_getc(kstream_t *ks)				\
	{														\
		if (ks->is_eof && ks->begin >= ks->end) return -1;	\
		if (ks->begin >= ks->end) {							\
			ks->begin = 0;									\
			ks->end = __read(ks->f, ks->buf, __bufsize);	\
			if (ks->end < __bufsize) ks->is_eof = 1;		\
			if (ks->end == 0) return -1;					\
		}													\
		return (int)ks->buf[ks->begin++];					\
	}

#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
	size_t l, m;
	char *s;
} kstring_t;
#endif

#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

#define __KS_GETUNTIL(__read, __bufsize)								\
	static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
	{																	\
		if (dret) *dret = 0;											\
		str->l = append? str->l : 0;									\
		if (ks->begin >= ks->end && ks->is_eof) return -1;				\
		for (;;) {														\
			int i;														\
			if (ks->begin >= ks->end) {									\
				if (!ks->is_eof) {										\
					ks->begin = 0;										\
					ks->end = __read(ks->f, ks->buf, __bufsize);		\
					if (ks->end < __bufsize) ks->is_eof = 1;			\
					if (ks->end == 0) break;							\
				} else break;											\
			}															\
			if (delimiter > KS_SEP_MAX) {								\
				for (i = ks->begin; i < ks->end; ++i)					\
					if (ks->buf[i] == delimiter) break;					\
			} else if (delimiter == KS_SEP_SPACE) {						\
				for (i = ks->begin; i < ks->end; ++i)					\
					if (isspace(ks->buf[i])) break;						\
			} else if (delimiter == KS_SEP_TAB) {						\
				for (i = ks->begin; i < ks->end; ++i)					\
					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
			} else i = 0; /* never come to here! */						\
			if (str->m - str->l < i - ks->begin + 1) {					\
				str->m = str->l + (i - ks->begin) + 1;					\
				kroundup32(str->m);										\
				str->s = (char*)realloc(str->s, str->m);				\
			}															\
			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
			str->l = str->l + (i - ks->begin);							\
			ks->begin = i + 1;											\
			if (i < ks->end) {											\
				if (dret) *dret = ks->buf[i];							\
				break;													\
			}															\
		}																\
		if (str->s == 0) {												\
			str->m = 1;													\
			str->s = (char*)calloc(1, 1);								\
		}																\
		str->s[str->l] = '\0';											\
		return str->l;													\
	} \
	static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
	{ return ks_getuntil2(ks, delimiter, str, dret, 0); }

#define KSTREAM_INIT(type_t, __read, __bufsize) \
	__KS_TYPE(type_t)							\
	__KS_BASIC(type_t, __bufsize)				\
	__KS_GETC(__read, __bufsize)				\
	__KS_GETUNTIL(__read, __bufsize)

#define __KSEQ_BASIC(type_t)											\
	static inline kseq_t *kseq_init(type_t fd)							\
	{																	\
		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));					\
		s->f = ks_init(fd);												\
		return s;														\
	}																	\
	static inline void kseq_rewind(kseq_t *ks)							\
	{																	\
		ks->last_char = 0;												\
		ks->f->is_eof = ks->f->begin = ks->f->end = 0;					\
	}																	\
	static inline void kseq_destroy(kseq_t *ks)							\
	{																	\
		if (!ks) return;												\
		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
		ks_destroy(ks->f);												\
		free(ks);														\
	}

/* Return value:
   >=0  length of the sequence (normal)
   -1   end-of-file
   -2   truncated quality string
 */
#define __KSEQ_READ \
	static int kseq_read(kseq_t *seq) \
	{ \
		int c; \
		kstream_t *ks = seq->f; \
		if (seq->last_char == 0) { /* then jump to the next header line */ \
			while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
			if (c == -1) return -1; /* end of file */ \
			seq->last_char = c; \
		} /* else: the first header char has been read in the previous call */ \
		seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
		if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
		if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); /* read FASTA/Q comment */ \
		if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
			seq->seq.m = 256; \
			seq->seq.s = (char*)malloc(seq->seq.m); \
		} \
		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
			seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
			ks_getuntil2(ks, '\n', &seq->seq, 0, 1); /* read the rest of the line */ \
		} \
		if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */	\
		if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
			seq->seq.m = seq->seq.l + 2; \
			kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
			seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
		} \
		seq->seq.s[seq->seq.l] = 0;	/* null terminated string */ \
		if (c != '+') return seq->seq.l; /* FASTA */ \
		if (seq->qual.m < seq->seq.m) {	/* allocate memory for qual in case insufficient */ \
			seq->qual.m = seq->seq.m; \
			seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
		} \
		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
		if (c == -1) return -2; /* error: no quality string */ \
		while (ks_getuntil2(ks, '\n', &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
		seq->last_char = 0;	/* we have not come to the next header line */ \
		if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
		return seq->seq.l; \
	}

#define __KSEQ_TYPE(type_t)						\
	typedef struct {							\
		kstring_t name, comment, seq, qual;		\
		int last_char;							\
		kstream_t *f;							\
	} kseq_t;

#define KSEQ_INIT(type_t, __read)				\
	KSTREAM_INIT(type_t, __read, 16384)			\
	__KSEQ_TYPE(type_t)							\
	__KSEQ_BASIC(type_t)						\
	__KSEQ_READ

#endif
genometools-1.5.1/src/external/samtools-0.1.18/ksort.h000066400000000000000000000234531211610345200223630ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li  */

/*
  2008-11-16 (0.1.4):

    * Fixed a bug in introsort() that happens in rare cases.

  2008-11-05 (0.1.3):

    * Fixed a bug in introsort() for complex comparisons.

	* Fixed a bug in mergesort(). The previous version is not stable.

  2008-09-15 (0.1.2):

	* Accelerated introsort. On my Mac (not on another Linux machine),
	  my implementation is as fast as std::sort on random input.

	* Added combsort and in introsort, switch to combsort if the
	  recursion is too deep.

  2008-09-13 (0.1.1):

	* Added k-small algorithm

  2008-09-05 (0.1.0):

	* Initial version

*/

#ifndef AC_KSORT_H
#define AC_KSORT_H

#include 
#include 

typedef struct {
	void *left, *right;
	int depth;
} ks_isort_stack_t;

#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }

#define KSORT_INIT(name, type_t, __sort_lt)								\
	void ks_mergesort_##name(size_t n, type_t array[], type_t temp[])	\
	{																	\
		type_t *a2[2], *a, *b;											\
		int curr, shift;												\
																		\
		a2[0] = array;													\
		a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n);		\
		for (curr = 0, shift = 0; (1ul<> 1) - 1; i != (size_t)(-1); --i)				\
			ks_heapadjust_##name(i, lsize, l);							\
	}																	\
	void ks_heapsort_##name(size_t lsize, type_t l[])					\
	{																	\
		size_t i;														\
		for (i = lsize - 1; i > 0; --i) {								\
			type_t tmp;													\
			tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
		}																\
	}																	\
	inline void __ks_insertsort_##name(type_t *s, type_t *t)			\
	{																	\
		type_t *i, *j, swap_tmp;										\
		for (i = s + 1; i < t; ++i)										\
			for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) {			\
				swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp;			\
			}															\
	}																	\
	void ks_combsort_##name(size_t n, type_t a[])						\
	{																	\
		const double shrink_factor = 1.2473309501039786540366528676643; \
		int do_swap;													\
		size_t gap = n;													\
		type_t tmp, *i, *j;												\
		do {															\
			if (gap > 2) {												\
				gap = (size_t)(gap / shrink_factor);					\
				if (gap == 9 || gap == 10) gap = 11;					\
			}															\
			do_swap = 0;												\
			for (i = a; i < a + n - gap; ++i) {							\
				j = i + gap;											\
				if (__sort_lt(*j, *i)) {								\
					tmp = *i; *i = *j; *j = tmp;						\
					do_swap = 1;										\
				}														\
			}															\
		} while (do_swap || gap > 2);									\
		if (gap != 1) __ks_insertsort_##name(a, a + n);					\
	}																	\
	void ks_introsort_##name(size_t n, type_t a[])						\
	{																	\
		int d;															\
		ks_isort_stack_t *top, *stack;									\
		type_t rp, swap_tmp;											\
		type_t *s, *t, *i, *j, *k;										\
																		\
		if (n < 1) return;												\
		else if (n == 2) {												\
			if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
			return;														\
		}																\
		for (d = 2; 1ul<>1) + 1;					\
				if (__sort_lt(*k, *i)) {								\
					if (__sort_lt(*k, *j)) k = j;						\
				} else k = __sort_lt(*j, *i)? i : j;					\
				rp = *k;												\
				if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; }	\
				for (;;) {												\
					do ++i; while (__sort_lt(*i, rp));					\
					do --j; while (i <= j && __sort_lt(rp, *j));		\
					if (j <= i) break;									\
					swap_tmp = *i; *i = *j; *j = swap_tmp;				\
				}														\
				swap_tmp = *i; *i = *t; *t = swap_tmp;					\
				if (i-s > t-i) {										\
					if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
					s = t-i > 16? i+1 : t;								\
				} else {												\
					if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
					t = i-s > 16? i-1 : s;								\
				}														\
			} else {													\
				if (top == stack) {										\
					free(stack);										\
					__ks_insertsort_##name(a, a+n);						\
					return;												\
				} else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
			}															\
		}																\
	}																	\
	/* This function is adapted from: http://ndevilla.free.fr/median/ */ \
	/* 0 <= kk < n */													\
	type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk)			\
	{																	\
		type_t *low, *high, *k, *ll, *hh, *mid;							\
		low = arr; high = arr + n - 1; k = arr + kk;					\
		for (;;) {														\
			if (high <= low) return *k;									\
			if (high == low + 1) {										\
				if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
				return *k;												\
			}															\
			mid = low + (high - low) / 2;								\
			if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
			if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
			if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);	\
			KSORT_SWAP(type_t, *mid, *(low+1));							\
			ll = low + 1; hh = high;									\
			for (;;) {													\
				do ++ll; while (__sort_lt(*ll, *low));					\
				do --hh; while (__sort_lt(*low, *hh));					\
				if (hh < ll) break;										\
				KSORT_SWAP(type_t, *ll, *hh);							\
			}															\
			KSORT_SWAP(type_t, *low, *hh);								\
			if (hh <= k) low = ll;										\
			if (hh >= k) high = hh - 1;									\
		}																\
	}																	\
	void ks_shuffle_##name(size_t n, type_t a[])						\
	{																	\
		int i, j;														\
		for (i = n; i > 1; --i) {										\
			type_t tmp;													\
			j = (int)(drand48() * i);									\
			tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;					\
		}																\
	}

#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a)

#define ks_lt_generic(a, b) ((a) < (b))
#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)

typedef const char *ksstr_t;

#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)

#endif
genometools-1.5.1/src/external/samtools-0.1.18/kstring.c000066400000000000000000000124001211610345200226630ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include "kstring.h"

int ksprintf(kstring_t *s, const char *fmt, ...)
{
	va_list ap;
	int l;
	va_start(ap, fmt);
	l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'.
	va_end(ap);
	if (l + 1 > s->m - s->l) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
		va_start(ap, fmt);
		l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
	}
	va_end(ap);
	s->l += l;
	return l;
}

char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux)
{
	const char *p, *start;
	if (sep) { // set up the table
		if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished
		aux->finished = 0;
		if (sep[1]) {
			aux->sep = -1;
			aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
			for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f);
		} else aux->sep = sep[0];
	}
	if (aux->finished) return 0;
	else if (str) aux->p = str - 1, aux->finished = 0;
	if (aux->sep < 0) {
		for (p = start = aux->p + 1; *p; ++p)
			if (aux->tab[*p>>6]>>(*p&0x3f)&1) break;
	} else {
		for (p = start = aux->p + 1; *p; ++p)
			if (*p == aux->sep) break;
	}
	aux->p = p; // end of token
	if (*p == 0) aux->finished = 1; // no more tokens
	return (char*)start;
}

// s MUST BE a null terminated string; l = strlen(s)
int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
{
	int i, n, max, last_char, last_start, *offsets, l;
	n = 0; max = *_max; offsets = *_offsets;
	l = strlen(s);
	
#define __ksplit_aux do {												\
		if (_offsets) {													\
			s[i] = 0;													\
			if (n == max) {												\
				max = max? max<<1 : 2;									\
				offsets = (int*)realloc(offsets, sizeof(int) * max);	\
			}															\
			offsets[n++] = last_start;									\
		} else ++n;														\
	} while (0)

	for (i = 0, last_char = last_start = 0; i <= l; ++i) {
		if (delimiter == 0) {
			if (isspace(s[i]) || s[i] == 0) {
				if (isgraph(last_char)) __ksplit_aux; // the end of a field
			} else {
				if (isspace(last_char) || last_char == 0) last_start = i;
			}
		} else {
			if (s[i] == delimiter || s[i] == 0) {
				if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field
			} else {
				if (last_char == delimiter || last_char == 0) last_start = i;
			}
		}
		last_char = s[i];
	}
	*_max = max; *_offsets = offsets;
	return n;
}

/**********************
 * Boyer-Moore search *
 **********************/

typedef unsigned char ubyte_t;

// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
static int *ksBM_prep(const ubyte_t *pat, int m)
{
	int i, *suff, *prep, *bmGs, *bmBc;
	prep = calloc(m + 256, sizeof(int));
	bmGs = prep; bmBc = prep + m;
	{ // preBmBc()
		for (i = 0; i < 256; ++i) bmBc[i] = m;
		for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
	}
	suff = calloc(m, sizeof(int));
	{ // suffixes()
		int f = 0, g;
		suff[m - 1] = m;
		g = m - 1;
		for (i = m - 2; i >= 0; --i) {
			if (i > g && suff[i + m - 1 - f] < i - g)
				suff[i] = suff[i + m - 1 - f];
			else {
				if (i < g) g = i;
				f = i;
				while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g;
				suff[i] = f - g;
			}
		}
	}
	{ // preBmGs()
		int j = 0;
		for (i = 0; i < m; ++i) bmGs[i] = m;
		for (i = m - 1; i >= 0; --i)
			if (suff[i] == i + 1)
				for (; j < m - 1 - i; ++j)
					if (bmGs[j] == m)
						bmGs[j] = m - 1 - i;
		for (i = 0; i <= m - 2; ++i)
			bmGs[m - 1 - suff[i]] = m - 1 - i;
	}
	free(suff);
	return prep;
}

void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep)
{
	int i, j, *prep = 0, *bmGs, *bmBc;
	const ubyte_t *str, *pat;
	str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat;
	prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep;
	if (_prep && *_prep == 0) *_prep = prep;
	bmGs = prep; bmBc = prep + m;
	j = 0;
	while (j <= n - m) {
		for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i);
		if (i >= 0) {
			int max = bmBc[str[i+j]] - m + 1 + i;
			if (max < bmGs[i]) max = bmGs[i];
			j += max;
		} else return (void*)(str + j);
	}
	if (_prep == 0) free(prep);
	return 0;
}

char *kstrstr(const char *str, const char *pat, int **_prep)
{
	return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
}

char *kstrnstr(const char *str, const char *pat, int n, int **_prep)
{
	return (char*)kmemmem(str, n, pat, strlen(pat), _prep);
}

/***********************
 * The main() function *
 ***********************/

#ifdef KSTRING_MAIN
#include 
int main()
{
	kstring_t *s;
	int *fields, n, i;
	ks_tokaux_t aux;
	char *p;
	s = (kstring_t*)calloc(1, sizeof(kstring_t));
	// test ksprintf()
	ksprintf(s, " abcdefg:    %d ", 100);
	printf("'%s'\n", s->s);
	// test ksplit()
	fields = ksplit(s, 0, &n);
	for (i = 0; i < n; ++i)
		printf("field[%d] = '%s'\n", i, s->s + fields[i]);
	// test kstrtok()
	s->l = 0;
	for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) {
		kputsn(p, aux.p - p, s);
		kputc('\n', s);
	}
	printf("%s", s->s);
	// free
	free(s->s); free(s); free(fields);

	{
		static char *str = "abcdefgcdgcagtcakcdcd";
		static char *pat = "cd";
		char *ret, *s = str;
		int *prep = 0;
		while ((ret = kstrstr(s, pat, &prep)) != 0) {
			printf("match: %s\n", ret);
			s = ret + prep[0];
		}
		free(prep);
	}
	return 0;
}
#endif
genometools-1.5.1/src/external/samtools-0.1.18/kstring.h000066400000000000000000000051451211610345200227000ustar00rootroot00000000000000#ifndef KSTRING_H
#define KSTRING_H

#include 
#include 
#include 

#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
	size_t l, m;
	char *s;
} kstring_t;
#endif

typedef struct {
	uint64_t tab[4];
	int sep, finished;
	const char *p; // end of the current token
} ks_tokaux_t;

#ifdef __cplusplus
extern "C" {
#endif

	int ksprintf(kstring_t *s, const char *fmt, ...);
	int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
	char *kstrstr(const char *str, const char *pat, int **_prep);
	char *kstrnstr(const char *str, const char *pat, int n, int **_prep);
	void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep);

	/* kstrtok() is similar to strtok_r() except that str is not
	 * modified and both str and sep can be NULL. For efficiency, it is
	 * actually recommended to set both to NULL in the subsequent calls
	 * if sep is not changed. */
	char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux);

#ifdef __cplusplus
}
#endif
	
static inline int kputsn(const char *p, int l, kstring_t *s)
{
	if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
	memcpy(s->s + s->l, p, l);
	s->l += l;
	s->s[s->l] = 0;
	return l;
}

static inline int kputs(const char *p, kstring_t *s)
{
	return kputsn(p, strlen(p), s);
}

static inline int kputc(int c, kstring_t *s)
{
	if (s->l + 1 >= s->m) {
		s->m = s->l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
	s->s[s->l++] = c;
	s->s[s->l] = 0;
	return c;
}

static inline int kputw(int c, kstring_t *s)
{
	char buf[16];
	int l, x;
	if (c == 0) return kputc('0', s);
	for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
	if (c < 0) buf[l++] = '-';
	if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
	for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
	s->s[s->l] = 0;
	return 0;
}

static inline int kputuw(unsigned c, kstring_t *s)
{
	char buf[16];
	int l, i;
	unsigned x;
	if (c == 0) return kputc('0', s);
	for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
	if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
	for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
	s->s[s->l] = 0;
	return 0;
}

static inline int *ksplit(kstring_t *s, int delimiter, int *n)
{
	int max = 0, *offsets = 0;
	*n = ksplit_core(s->s, delimiter, &max, &offsets);
	return offsets;
}

#endif
genometools-1.5.1/src/external/samtools-0.1.18/misc/000077500000000000000000000000001211610345200217745ustar00rootroot00000000000000genometools-1.5.1/src/external/samtools-0.1.18/misc/HmmGlocal.java000066400000000000000000000150741211610345200245110ustar00rootroot00000000000000import java.io.*;
import java.lang.*;

public class HmmGlocal
{
	private double[] qual2prob;
	private double cd, ce; // gap open probility [1e-3], gap extension probability [0.1]
	private int cb; // band width [7]

	public HmmGlocal(final double d, final double e, final int b) {
		cd = d; ce = e; cb = b;
		qual2prob = new double[256];
		for (int i = 0; i < 256; ++i)
			qual2prob[i] = Math.pow(10, -i/10.);
	}
	private static int set_u(final int b, final int i, final int k) {
		int x = i - b;
		x = x > 0? x : 0;
		return (k + 1 - x) * 3;
	}
	public int hmm_glocal(final byte[] _ref, final byte[] _query, final byte[] _iqual, int[] state, byte[] q) {
		int i, k;
		/*** initialization ***/
		// change coordinates
		int l_ref = _ref.length;
		byte[] ref = new byte[l_ref+1];
		for (i = 0; i < l_ref; ++i) ref[i+1] = _ref[i]; // FIXME: this is silly...
		int l_query = _query.length;
		byte[] query = new byte[l_query+1];
		double[] qual = new double[l_query+1];
		for (i = 0; i < l_query; ++i) {
			query[i+1] = _query[i];
			qual[i+1] = qual2prob[_iqual[i]];
		}
		// set band width
		int bw2, bw = l_ref > l_query? l_ref : l_query;
		if (bw > cb) bw = cb;
		if (bw < Math.abs(l_ref - l_query)) bw = Math.abs(l_ref - l_query);
		bw2 = bw * 2 + 1;
		// allocate the forward and backward matrices f[][] and b[][] and the scaling array s[]
		double[][] f = new double[l_query+1][bw2*3 + 6];
		double[][] b = new double[l_query+1][bw2*3 + 6];
		double[] s = new double[l_query+2];
		// initialize transition probabilities
		double sM, sI, bM, bI;
		sM = sI = 1. / (2 * l_query + 2);
		bM = (1 - cd) / l_query; bI = cd / l_query; // (bM+bI)*l_query==1
		double[] m = new double[9];
		m[0*3+0] = (1 - cd - cd) * (1 - sM); m[0*3+1] = m[0*3+2] = cd * (1 - sM);
		m[1*3+0] = (1 - ce) * (1 - sI); m[1*3+1] = ce * (1 - sI); m[1*3+2] = 0.;
		m[2*3+0] = 1 - ce; m[2*3+1] = 0.; m[2*3+2] = ce;
		/*** forward ***/
		// f[0]
		f[0][set_u(bw, 0, 0)] = s[0] = 1.;
		{ // f[1]
			double[] fi = f[1];
			double sum;
			int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1, _beg, _end;
			for (k = beg, sum = 0.; k <= end; ++k) {
				int u;
				double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] / 3.;
				u = set_u(bw, 1, k);
				fi[u+0] = e * bM; fi[u+1] = .25 * bI;
				sum += fi[u] + fi[u+1];
			}
			// rescale
			s[1] = sum;
			_beg = set_u(bw, 1, beg); _end = set_u(bw, 1, end); _end += 2;
			for (k = _beg; k <= _end; ++k) fi[k] /= sum;
		}
		// f[2..l_query]
		for (i = 2; i <= l_query; ++i) {
			double[] fi = f[i], fi1 = f[i-1];
			double sum, qli = qual[i];
			int beg = 1, end = l_ref, x, _beg, _end;
			byte qyi = query[i];
			x = i - bw; beg = beg > x? beg : x; // band start
			x = i + bw; end = end < x? end : x; // band end
			for (k = beg, sum = 0.; k <= end; ++k) {
				int u, v11, v01, v10;
				double e;
				e = (ref[k] > 3 || qyi > 3)? 1. : ref[k] == qyi? 1. - qli : qli / 3.;
				u = set_u(bw, i, k); v11 = set_u(bw, i-1, k-1); v10 = set_u(bw, i-1, k); v01 = set_u(bw, i, k-1);
				fi[u+0] = e * (m[0] * fi1[v11+0] + m[3] * fi1[v11+1] + m[6] * fi1[v11+2]);
				fi[u+1] = .25 * (m[1] * fi1[v10+0] + m[4] * fi1[v10+1]);
				fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2];
				sum += fi[u] + fi[u+1] + fi[u+2];
				//System.out.println("("+i+","+k+";"+u+"): "+fi[u]+","+fi[u+1]+","+fi[u+2]);
			}
			// rescale
			s[i] = sum;
			_beg = set_u(bw, i, beg); _end = set_u(bw, i, end); _end += 2;
			for (k = _beg, sum = 1./sum; k <= _end; ++k) fi[k] *= sum;
		}
		{ // f[l_query+1]
			double sum;
			for (k = 1, sum = 0.; k <= l_ref; ++k) {
				int u = set_u(bw, l_query, k);
				if (u < 3 || u >= bw2*3+3) continue;
				sum += f[l_query][u+0] * sM + f[l_query][u+1] * sI;
			}
			s[l_query+1] = sum; // the last scaling factor
		}
		/*** backward ***/
		// b[l_query] (b[l_query+1][0]=1 and thus \tilde{b}[][]=1/s[l_query+1]; this is where s[l_query+1] comes from)
		for (k = 1; k <= l_ref; ++k) {
			int u = set_u(bw, l_query, k);
			double[] bi = b[l_query];
			if (u < 3 || u >= bw2*3+3) continue;
			bi[u+0] = sM / s[l_query] / s[l_query+1]; bi[u+1] = sI / s[l_query] / s[l_query+1];
		}
		// b[l_query-1..1]
		for (i = l_query - 1; i >= 1; --i) {
			int beg = 1, end = l_ref, x, _beg, _end;
			double[] bi = b[i], bi1 = b[i+1];
			double y = (i > 1)? 1. : 0., qli1 = qual[i+1];
			byte qyi1 = query[i+1];
			x = i - bw; beg = beg > x? beg : x;
			x = i + bw; end = end < x? end : x;
			for (k = end; k >= beg; --k) {
				int u, v11, v01, v10;
				double e;
				u = set_u(bw, i, k); v11 = set_u(bw, i+1, k+1); v10 = set_u(bw, i+1, k); v01 = set_u(bw, i, k+1);
				e = (k >= l_ref? 0 : (ref[k+1] > 3 || qyi1 > 3)? 1. : ref[k+1] == qyi1? 1. - qli1 : qli1 / 3.) * bi1[v11];
				bi[u+0] = e * m[0] + .25 * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e.
				bi[u+1] = e * m[3] + .25 * m[4] * bi1[v10+1];
				bi[u+2] = (e * m[6] + m[8] * bi[v01+2]) * y;
			}
			// rescale
			_beg = set_u(bw, i, beg); _end = set_u(bw, i, end); _end += 2;
			for (k = _beg, y = 1./s[i]; k <= _end; ++k) bi[k] *= y;
		}
		double pb;
		{ // b[0]
			int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1;
			double sum = 0.;
			for (k = end; k >= beg; --k) {
				int u = set_u(bw, 1, k);
				double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] / 3.;
				if (u < 3 || u >= bw2*3+3) continue;
				sum += e * b[1][u+0] * bM + .25 * b[1][u+1] * bI;
			}
			pb = b[0][set_u(bw, 0, 0)] = sum / s[0]; // if everything works as is expected, pb == 1.0
		}
		int is_diff = Math.abs(pb - 1.) > 1e-7? 1 : 0;
		/*** MAP ***/
		for (i = 1; i <= l_query; ++i) {
			double sum = 0., max = 0.;
			double[] fi = f[i], bi = b[i];
			int beg = 1, end = l_ref, x, max_k = -1;
			x = i - bw; beg = beg > x? beg : x;
			x = i + bw; end = end < x? end : x;
			for (k = beg; k <= end; ++k) {
				int u = set_u(bw, i, k);
				double z;
				sum += (z = fi[u+0] * bi[u+0]); if (z > max) { max = z; max_k = (k-1)<<2 | 0; }
				sum += (z = fi[u+1] * bi[u+1]); if (z > max) { max = z; max_k = (k-1)<<2 | 1; }
			}
			max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0
			if (state != null) state[i-1] = max_k;
			if (q != null) {
				k = (int)(-4.343 * Math.log(1. - max) + .499);
				q[i-1] = (byte)(k > 100? 99 : k);
			}
			//System.out.println("("+pb+","+sum+")"+" ("+(i-1)+","+(max_k>>2)+","+(max_k&3)+","+max+")");
		}
		return 0;
	}

	public static void main(String[] args) {
		byte[] ref = {'\0', '\1', '\3', '\3', '\1'};
		byte[] query = {'\0', '\3', '\3', '\1'};
		byte[] qual = new byte[4];
		qual[0] = qual[1] = qual[2] = qual[3] = (byte)20;
		HmmGlocal hg = new HmmGlocal(1e-3, 0.1, 7);
		hg.hmm_glocal(ref, query, qual, null, null);
	}
}genometools-1.5.1/src/external/samtools-0.1.18/misc/Makefile000066400000000000000000000025641211610345200234430ustar00rootroot00000000000000CC=			gcc
CXX=		g++
CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
CXXFLAGS=	$(CFLAGS)
DFLAGS=		-D_FILE_OFFSET_BITS=64
OBJS=		
PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk
INCLUDES=	-I..
SUBDIRS=	.

.SUFFIXES:.c .o

.c.o:
		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

all:$(PROG)

lib-recur all-recur clean-recur cleanlocal-recur install-recur:
		@target=`echo $@ | sed s/-recur//`; \
		wdir=`pwd`; \
		list='$(SUBDIRS)'; for subdir in $$list; do \
			cd $$subdir; \
			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
				INCLUDES="$(INCLUDES)" $$target || exit 1; \
			cd $$wdir; \
		done;

lib:

seqtk:seqtk.o
		$(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz

wgsim:wgsim.o
		$(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz

md5fa:md5.o md5fa.o md5.h ../kseq.h
		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz

md5sum-lite:md5sum-lite.o
		$(CC) $(CFLAGS) -o $@ md5sum-lite.o

md5sum-lite.o:md5.c md5.h
		$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c

maq2sam-short:maq2sam.c
		$(CC) $(CFLAGS) -o $@ maq2sam.c -lz

maq2sam-long:maq2sam.c
		$(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz

md5fa.o:md5.h md5fa.c
		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c

seqtk.o:seqtk.c ../khash.h ../kseq.h
		$(CC) $(CFLAGS) -c -I.. -o $@ seqtk.c

wgsim.o:wgsim.c ../kseq.h
		$(CC) $(CFLAGS) -c -I.. -o $@ wgsim.c

cleanlocal:
		rm -fr gmon.out *.o a.out *.exe *.dSYM $(PROG) *~ *.a

clean:cleanlocal-recur
genometools-1.5.1/src/external/samtools-0.1.18/misc/blast2sam.pl000077500000000000000000000045571211610345200242370ustar00rootroot00000000000000#!/usr/bin/perl -w

use strict;
use warnings;
use Getopt::Std;

&blast2sam;

sub blast2sam {
  my %opts = ();
  getopts('s', \%opts);
  die("Usage: blast2sam.pl \n") if (-t STDIN && @ARGV == 0);
  my ($qlen, $slen, $q, $s, $qbeg, $qend, @sam, @cigar, @cmaux, $show_seq);
  $show_seq = defined($opts{s});
  @sam = (); @sam[0,4,6..8,10] = ('', 255, '*', 0, 0, '*');
  while (<>) {
	if (@cigar && (/^Query=/ || /Score =.*bits.*Expect/)) { # print
	  &blast_print_sam(\@sam, \@cigar, \@cmaux, $qlen - $qend);
	  @cigar = ();
	}
	if (/^Query= (\S+)/) {
	  $sam[0] = $1;
	} elsif (/\((\S+)\s+letters\)/) {
	  $qlen = $1; $qlen =~ s/,//g;
	} elsif (/^>(\S+)/) {
	  $sam[2] = $1;
	} elsif (/Length = (\d+)/) {
	  $slen = $1;
	} elsif (/Score =\s+(\S+) bits.+Expect(\(\d+\))? = (\S+)/) { # the start of an alignment block
	  my ($as, $ev) = (int($1 + .499), $3);
	  $ev = "1$ev" if ($ev =~ /^e/);
	  @sam[1,3,9,11,12] = (0, 0, '', "AS:i:$as", "EV:Z:$ev");
	  @cigar = (); $qbeg = 0;
	  @cmaux = (0, 0, 0, '');
	} elsif (/Strand = (\S+) \/ (\S+)/) {
	  $sam[1] |= 0x10 if ($2 eq 'Minus');
	} elsif (/Query\:\s(\d+)\s*(\S+)\s(\d+)/) {
	  $q = $2;
	  unless ($qbeg) {
		$qbeg = $1;
		push(@cigar, ($1-1) . "H") if ($1 > 1);
	  }
	  $qend = $3;
	  if ($show_seq) {
		my $x = $q;
		$x =~ s/-//g; $sam[9] .= $x;
	  }
	} elsif (/Sbjct\:\s(\d+)\s*(\S+)\s(\d+)/) {
	  $s = $2;
	  if ($sam[1] & 0x10) {
		$sam[3] = $3;
	  } else {
		$sam[3] = $1 unless ($sam[3]);
	  }
	  &aln2cm(\@cigar, \$q, \$s, \@cmaux);
	}
  }
  &blast_print_sam(\@sam, \@cigar, \@cmaux, $qlen - $qend);
}

sub blast_print_sam {
  my ($sam, $cigar, $cmaux, $qrest) = @_;
  push(@$cigar, $cmaux->[1] . substr("MDI", $cmaux->[0], 1));
  push(@$cigar, $qrest . 'H') if ($qrest);
  if ($sam->[1] & 0x10) {
	@$cigar = reverse(@$cigar);
	$sam->[9] = reverse($sam->[9]);
	$sam->[9] =~ tr/atgcrymkswATGCRYMKSW/tacgyrkmswTACGYRKMSW/;
  }
  $sam->[9] = '*' if (!$sam->[9]);
  $sam->[5] = join('', @$cigar);
  print join("\t", @$sam), "\n";
}

sub aln2cm {
  my ($cigar, $q, $s, $cmaux) = @_;
  my $l = length($$q);
  for (my $i = 0; $i < $l; ++$i) {
	my $op;
	# set $op
	if (substr($$q, $i, 1) eq '-') { $op = 2; }
	elsif (substr($$s, $i, 1) eq '-') { $op = 1; }
	else { $op = 0; }
	# for CIGAR
	if ($cmaux->[0] == $op) {
	  ++$cmaux->[1];
	} else {
	  push(@$cigar, $cmaux->[1] . substr("MDI", $cmaux->[0], 1));
	  $cmaux->[0] = $op; $cmaux->[1] = 1;
	}
  }
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/bowtie2sam.pl000077500000000000000000000041001211610345200244030ustar00rootroot00000000000000#!/usr/bin/perl -w

# Contact: lh3
# Version: 0.1.1

use strict;
use warnings;
use Getopt::Std;

&bowtie2sam;
exit;

sub bowtie2sam {
  my %opts = ();
  die("Usage: bowtie2sam.pl \n") if (@ARGV == 0 && -t STDIN);
  # core loop
  my (@s, $last, @staging, $k, $best_s, $subbest_s, $best_k);
  $last = '';
  while (<>) {
	my ($name, $nm) = &bowtie2sam_aux($_, \@s); # read_name, number of mismatches
	if ($name eq $last) {
	  # I do not know whether the multiple hits are ordered on the
	  # number of mismatches. I assume they are not and so I have to
	  # keep all these multiple hits in memory.
	  @{$staging[$k]} = @s;
	  if ($best_s > $nm) {
		$subbest_s = $best_s;
		$best_s = $nm;
		$best_k = $k;
	  } elsif ($subbest_s > $nm) {
		$subbest_s = $nm;
	  }
	  ++$k;
	} else {
	  if ($last) {
		if ($best_s == $subbest_s) {
		  $staging[$best_k][4] = 0;
		} elsif ($subbest_s - $best_s == 1) {
		  $staging[$best_k][4] = 15 if ($staging[$best_k][4] > 15);
		}
		print join("\t", @{$staging[$best_k]}), "\n";
	  }
	  $k = 1; $best_s = $nm; $subbest_s = 1000; $best_k = 0;
	  @{$staging[0]} = @s;
	  $last = $name;
	}
  }
  print join("\t", @{$staging[$best_k]}), "\n" if ($best_k >= 0);
}

sub bowtie2sam_aux {
  my ($line, $s) = @_;
  chomp($line);
  my @t = split("\t", $line);
  my $ret;
  @$s = ();
  # read name
  $s->[0] = $ret = $t[0];
  $s->[0] =~ s/\/[12]$//g;
  # initial flag (will be updated later)
  $s->[1] = 0;
  # read & quality
  $s->[9] = $t[4]; $s->[10] = $t[5];
  # cigar
  $s->[5] = length($s->[9]) . "M";
  # coor
  $s->[2] = $t[2]; $s->[3] = $t[3] + 1;
  $s->[1] |= 0x10 if ($t[1] eq '-');
  # mapQ
  $s->[4] = $t[6] == 0? 25 : 0;
  # mate coordinate
  $s->[6] = '*'; $s->[7] = $s->[8] = 0;
  # aux
  my $nm = @t - 7;
  push(@$s, "NM:i:" . (@t-7));
  push(@$s, "X$nm:i:" . ($t[6]+1));
  my $md = '';
  if ($t[7]) {
	$_ = $t[7];
	my $a = 0;
	while (/(\d+):[ACGTN]>([ACGTN])/gi) {
	  my ($y, $z) = ($1, $2);
	  $md .= (int($y)-$a) . $z;
	  $a += $y - $a + 1;
	}
	$md .= length($s->[9]) - $a;
  } else {
	$md = length($s->[9]);
  }
  push(@$s, "MD:Z:$md");
  return ($ret, $nm);
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/export2sam.pl000077500000000000000000000442141211610345200244450ustar00rootroot00000000000000#!/usr/bin/env perl
#
#
# export2sam.pl converts GERALD export files to SAM format.
#
#
#
########## License:
#
# The MIT License
#
# Original SAMtools work copyright (c) 2008-2009 Genome Research Ltd.
# Modified SAMtools work copyright (c) 2010 Illumina, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
# 
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#
#
#
########## ChangeLog:
#
# Version: 2.3.1 (18MAR2011)
#
#   - Restore file '-' as stdin input.
#
# Version: 2.3.0 (24JAN2011)
#
#   - Add support for export reserved chromosome name "CONTROL",
#       which is translated to optional field "XC:Z:CONTROL".
#   - Check for ".gz" file extension on export files and open
#       these as gzip pipes when the extension is found.
#
# Version: 2.2.0 (16NOV2010)
#
#   - Remove any leading zeros in export fields: RUNNO,LANE,TILE,X,Y
#   - For export records with reserved chromosome name identifiers
#       "QC" and "RM", add the optional field "XC:Z:QC" or "XC:Z:RM"
#       to the SAM record, so that these cases can be distinguished
#       from other unmatched reads.
#
# Version: 2.1.0 (21SEP2010)
#
#   - Additional export record error checking.
#   - Convert export records with chromomsome value of "RM" to unmapped 
#       SAM records.
#
# Version: 2.0.0 (15FEB2010)
#
#   Script updated by Illumina in conjunction with CASAVA 1.7.0
#   release.
#
#   Major changes are as follows:
#   - The CIGAR string has been updated to include all gaps from
#       ELANDv2 alignments.
#   - The ELAND single read alignment score is always stored in the
#       optional "SM" field and the ELAND paired read alignment score
#       is stored in the optional "AS" field when it exists.
#   - The MAPQ value is set to the higher of the two alignment scores,
#       but no greater than 254, i.e. min(254,max(SM,AS))
#   - The SAM "proper pair" bit (0x0002) is now set for read pairs
#       meeting ELAND's expected orientation and insert size criteria.
#   - The default quality score translation is set for export files
#       which contain Phread+64 quality values. An option,
#       "--qlogodds", has been added to translate quality values from
#       the Solexa+64 format used in export files prior to Pipeline
#       1.3
#   - The export match descriptor is now reverse-complemented when
#       necessary such that it always corresponds to the forward
#       strand of the reference, to be consistent with other
#       information in the SAM record. It is now written to the
#       optional 'XD' field (rather than 'MD') to acknowledge its
#       minor differences from the samtools match descriptor (see
#       additional detail below).
#   - An option, "--nofilter", has been added to include reads which
#       have failed primary analysis quality filtration. Such reads
#       will have the corresponding SAM flag bit (0x0200) set.
#   - Labels in the export 'contig' field are preserved by setting
#       RNAME to "$export_chromosome/$export_contig" when the contig
#       label exists.
#
#
# Contact: lh3
# Version: 0.1.2 (03JAN2009)
#
#
#
########## Known Conversion Limitations:
#
# - Export records for reads that map to a position < 1 (allowed
#     in export format), are converted to unmapped reads in the SAM
#     record.
# - Export records contain the reserved chromosome names: "NM",
#     "QC","RM" and "CONTROL". "NM" indicates that the aligner could
#     not map the read to the reference sequence set. "QC" means that
#     the aligner did not attempt to map the read due to some
#     technical limitation. "RM" means that the read mapped to a set
#     of 'contaminant' sequences specified in GERALD's RNA-seq
#     workflow. "CONTROL" means that the read is a control. All of
#     these alignment types are collapsed to the single unmapped
#     alignment state in the SAM record, but the optional SAM "XC"
#     field is used to record the original reserved chromosome name of
#     the read for all but the "NM" case.
# - The export match descriptor is slightly different than the
#     samtools match descriptor. For this reason it is stored in the
#     optional SAM field 'XD' (and not 'MD'). Note that the export
#     match descriptor differs from the samtools version in two
#     respects: (1) indels are explicitly closed with the '$'
#     character and (2) insertions must be enumerated in the match
#     descriptor. For example a 35-base read with a two-base insertion
#     is described as: 20^2$14
#
#
#

my $version = "2.3.1";

use strict;
use warnings;

use Getopt::Long;
use File::Spec;
use List::Util qw(min max);


use constant {
  EXPORT_MACHINE => 0,
  EXPORT_RUNNO => 1,
  EXPORT_LANE => 2,
  EXPORT_TILE => 3,
  EXPORT_X => 4,
  EXPORT_Y => 5,
  EXPORT_INDEX => 6,
  EXPORT_READNO => 7,
  EXPORT_READ => 8,
  EXPORT_QUAL => 9,
  EXPORT_CHROM => 10,
  EXPORT_CONTIG => 11,
  EXPORT_POS => 12,
  EXPORT_STRAND => 13, 
  EXPORT_MD => 14,
  EXPORT_SEMAP => 15,
  EXPORT_PEMAP => 16,
  EXPORT_PASSFILT => 21,
  EXPORT_SIZE => 22,
};


use constant {
  SAM_QNAME => 0,
  SAM_FLAG => 1,
  SAM_RNAME => 2,
  SAM_POS => 3,
  SAM_MAPQ => 4,
  SAM_CIGAR => 5,
  SAM_MRNM => 6,
  SAM_MPOS => 7,
  SAM_ISIZE => 8,
  SAM_SEQ => 9,
  SAM_QUAL => 10,
};


# function prototypes for Richard's code
sub match_desc_to_cigar($);
sub match_desc_frag_length($);
sub reverse_compl_match_descriptor($);
sub write_header($;$;$);


&export2sam;
exit;




sub export2sam {

  my $cmdline = $0 . " " . join(" ",@ARGV);
  my $arg_count = scalar @ARGV;
  my $progname = (File::Spec->splitpath($0))[2];

  my $is_logodds_qvals = 0; # if true, assume files contain logodds (i.e. "solexa") quality values
  my $is_nofilter = 0;
  my $read1file;
  my $read2file;
  my $print_version = 0;
  my $help = 0;

  my $result = GetOptions( "qlogodds" => \$is_logodds_qvals, 
                           "nofilter" => \$is_nofilter,
                           "read1=s"  => \$read1file,
                           "read2=s"  => \$read2file,
                           "version"  => \$print_version,
                           "help"     => \$help );

  my $usage = <) {
    $export_line_count++;
    my (@s1, @s2);
    &export2sam_aux($_, $export_line_count, \@s1, \@conv_table, $is_paired, 1, $is_nofilter);
    if ($is_paired) {
      my $read2line = <$fh2>;
      if(not $read2line){
        die("\nERROR: read1 and read2 export files do not contain the same number of reads.\n  Extra reads observed in read1 file at line no: $export_line_count.\n\n");
      }
      &export2sam_aux($read2line, $export_line_count, \@s2, \@conv_table, $is_paired, 2, $is_nofilter);

      if (@s1 && @s2) { # then set mate coordinate
        if($s1[SAM_QNAME] ne $s2[SAM_QNAME]){
          die("\nERROR: Non-paired reads in export files on line: $export_line_count.\n  Read1: $_  Read2: $read2line\n");
        }

        my $isize = 0;
        if ($s1[SAM_RNAME] ne '*' && $s1[SAM_RNAME] eq $s2[SAM_RNAME]) { # then calculate $isize
          my $x1 = ($s1[SAM_FLAG] & 0x10)? $s1[SAM_POS] + length($s1[SAM_SEQ]) : $s1[SAM_POS];
          my $x2 = ($s2[SAM_FLAG] & 0x10)? $s2[SAM_POS] + length($s2[SAM_SEQ]) : $s2[SAM_POS];
          $isize = $x2 - $x1;
        }

        foreach ([\@s1,\@s2,$isize],[\@s2,\@s1,-$isize]){ 
          my ($sa,$sb,$is) = @{$_};
          if ($sb->[SAM_RNAME] ne '*') {
            $sa->[SAM_MRNM] = ($sb->[SAM_RNAME] eq $sa->[SAM_RNAME]) ? "=" : $sb->[SAM_RNAME];
            $sa->[SAM_MPOS] = $sb->[SAM_POS];
            $sa->[SAM_ISIZE] = $is;
            $sa->[SAM_FLAG] |= 0x20 if ($sb->[SAM_FLAG] & 0x10);
          } else {
            $sa->[SAM_FLAG] |= 0x8;
          }
        } 
      }
    }
    print join("\t", @s1), "\n" if (@s1);
    print join("\t", @s2), "\n" if (@s2 && $is_paired);
  }
  close($fh1);
  if($is_paired) {
    while(my $read2line = <$fh2>){
      $export_line_count++;
      die("\nERROR: read1 and read2 export files do not contain the same number of reads.\n  Extra reads observed in read2 file at line no: $export_line_count.\n\n");
    }
    close($fh2);
  }
}

sub export2sam_aux {
  my ($line, $line_no, $s, $ct, $is_paired, $read_no, $is_nofilter) = @_;
  chomp($line);
  my @t = split("\t", $line);
  if(scalar(@t) < EXPORT_SIZE) {
    my $msg="\nERROR: Unexpected number of fields in export record on line $line_no of read$read_no export file. Found " . scalar(@t) . " fields but expected " . EXPORT_SIZE . ".\n";
    $msg.="\t...erroneous export record:\n" . $line . "\n\n";
    die($msg);
  }
  @$s = ();
  my $isPassFilt = ($t[EXPORT_PASSFILT] eq 'Y');
  return if(not ($isPassFilt or $is_nofilter));
  # read name
  my $samQnamePrefix = $t[EXPORT_MACHINE] . (($t[EXPORT_RUNNO] ne "") ? "_" .  int($t[EXPORT_RUNNO]) : "");
  $s->[SAM_QNAME] = join(':', $samQnamePrefix, int($t[EXPORT_LANE]), int($t[EXPORT_TILE]),
                         int($t[EXPORT_X]), int($t[EXPORT_Y]));
  # initial flag (will be updated later)
  $s->[SAM_FLAG] = 0;
  if($is_paired) {
    if($t[EXPORT_READNO] != $read_no){
      die("\nERROR: read$read_no export file contains record with read number: " .$t[EXPORT_READNO] . " on line: $line_no\n\n");
    }
    $s->[SAM_FLAG] |= 1 | 1<<(5 + $read_no);
  }
  $s->[SAM_FLAG] |= 0x200 if (not $isPassFilt);

  # read & quality
  my $is_export_rev = ($t[EXPORT_STRAND] eq 'R');
  if ($is_export_rev) { # then reverse the sequence and quality
    $s->[SAM_SEQ] = reverse($t[EXPORT_READ]);
    $s->[SAM_SEQ] =~ tr/ACGTacgt/TGCAtgca/;
    $s->[SAM_QUAL] = reverse($t[EXPORT_QUAL]);
  } else {
    $s->[SAM_SEQ] = $t[EXPORT_READ];
    $s->[SAM_QUAL] = $t[EXPORT_QUAL];
  }
  my @convqual = ();
  foreach (unpack('C*', $s->[SAM_QUAL])){
    my $val=$ct->[$_];
    if(not defined $val){
      my $msg="\nERROR: can't interpret export quality value: " . $_ . " in read$read_no export file, line: $line_no\n";
      if( $_ < 64 ) { $msg .= "  Use --qlogodds flag to translate logodds (solexa) quality values.\n"; }
      die($msg . "\n");
    }
    push @convqual,$val;
  }

  $s->[SAM_QUAL] = pack('C*',@convqual); # change coding


  # coor
  my $has_coor = 0;
  $s->[SAM_RNAME] = "*";
  if (($t[EXPORT_CHROM] eq 'NM') or
      ($t[EXPORT_CHROM] eq 'QC') or
      ($t[EXPORT_CHROM] eq 'RM') or
      ($t[EXPORT_CHROM] eq 'CONTROL')) {
    $s->[SAM_FLAG] |= 0x4; # unmapped
    push(@$s,"XC:Z:".$t[EXPORT_CHROM]) if($t[EXPORT_CHROM] ne 'NM');
  } elsif ($t[EXPORT_CHROM] =~ /(\d+):(\d+):(\d+)/) {
    $s->[SAM_FLAG] |= 0x4; # TODO: should I set BAM_FUNMAP in this case?
    push(@$s, "H0:i:$1", "H1:i:$2", "H2:i:$3")
  } elsif ($t[EXPORT_POS] < 1) {
    $s->[SAM_FLAG] |= 0x4; # unmapped
  } else {
    $s->[SAM_RNAME] = $t[EXPORT_CHROM];
    $s->[SAM_RNAME] .= "/" . $t[EXPORT_CONTIG] if($t[EXPORT_CONTIG] ne '');
    $has_coor = 1;
  }
  $s->[SAM_POS] = $has_coor? $t[EXPORT_POS] : 0;

#  print STDERR "t[14] = " . $t[14] . "\n";
  my $matchDesc = '';
  $s->[SAM_CIGAR] = "*";
  if($has_coor){
    $matchDesc = ($is_export_rev) ? reverse_compl_match_descriptor($t[EXPORT_MD]) : $t[EXPORT_MD];

    if($matchDesc =~ /\^/){
      # construct CIGAR string using Richard's function
      $s->[SAM_CIGAR] = match_desc_to_cigar($matchDesc); # indel processing
    } else {
      $s->[SAM_CIGAR] = length($s->[SAM_SEQ]) . "M";
    }
  }

#  print STDERR "cigar_string = $cigar_string\n";

  $s->[SAM_FLAG] |= 0x10 if ($has_coor && $is_export_rev);
  if($has_coor){
    my $semap = ($t[EXPORT_SEMAP] ne '') ? $t[EXPORT_SEMAP] : 0;
    my $pemap = 0;
    if($is_paired) {
      $pemap = ($t[EXPORT_PEMAP] ne '') ? $t[EXPORT_PEMAP] : 0;

      # set `proper pair' bit if non-blank, non-zero PE alignment score:
      $s->[SAM_FLAG] |= 0x02 if ($pemap > 0);
    }
    $s->[SAM_MAPQ] = min(254,max($semap,$pemap));
  } else {
    $s->[SAM_MAPQ] = 0;
  }
  # mate coordinate
  $s->[SAM_MRNM] = '*';
  $s->[SAM_MPOS] = 0;
  $s->[SAM_ISIZE] = 0;
  # aux
  push(@$s, "BC:Z:$t[EXPORT_INDEX]") if ($t[EXPORT_INDEX]);
  if($has_coor){
    # The export match descriptor differs slightly from the samtools match descriptor.
    # In order for the converted SAM files to be as compliant as possible,
    # we put the export match descriptor in optional field 'XD' rather than 'MD':
    push(@$s, "XD:Z:$matchDesc");
    push(@$s, "SM:i:$t[EXPORT_SEMAP]") if ($t[EXPORT_SEMAP] ne '');
    push(@$s, "AS:i:$t[EXPORT_PEMAP]") if ($is_paired and ($t[EXPORT_PEMAP] ne ''));
  }
}



#
# the following code is taken from Richard Shaw's sorted2sam.pl file
#
sub reverse_compl_match_descriptor($)
{
#    print "\nREVERSING THE MATCH DESCRIPTOR!\n";
    my ($match_desc) = @_;
    my $rev_compl_match_desc = reverse($match_desc);
    $rev_compl_match_desc =~ tr/ACGT\^\$/TGCA\$\^/;

    # Unreverse the digits of numbers.
    $rev_compl_match_desc = join('',
                                 map {($_ =~ /\d+/)
                                      ? join('', reverse(split('', $_)))
                                      : $_} split(/(\d+)/,
                                                  $rev_compl_match_desc));

    return $rev_compl_match_desc;
}



sub match_desc_to_cigar($)
{
    my ($match_desc) = @_;

    my @match_desc_parts = split(/(\^.*?\$)/, $match_desc);
    my $cigar_str = '';
    my $cigar_del_ch = 'D';
    my $cigar_ins_ch = 'I';
    my $cigar_match_ch = 'M';

    foreach my $match_desc_part (@match_desc_parts) {
        next if (!$match_desc_part);

        if ($match_desc_part =~ /^\^([ACGTN]+)\$$/) {
            # Deletion
            $cigar_str .= (length($1) . $cigar_del_ch);
        } elsif ($match_desc_part =~ /^\^(\d+)\$$/) {
            # Insertion
            $cigar_str .= ($1 . $cigar_ins_ch);
        } else {
            $cigar_str .= (match_desc_frag_length($match_desc_part)
                           . $cigar_match_ch);
        }
    }

    return $cigar_str;
}


#------------------------------------------------------------------------------

sub match_desc_frag_length($)
                           {
    my ($match_desc_str) = @_;
    my $len = 0;

    my @match_desc_fields = split(/([ACGTN]+)/, $match_desc_str);

    foreach my $match_desc_field (@match_desc_fields) {
        next if ($match_desc_field eq '');

        $len += (($match_desc_field =~ /(\d+)/)
                 ? $1 : length($match_desc_field));
    }

    return $len;
}


# argument holds the command line
sub write_header($;$;$) 
{
	my ($progname,$version,$cl) = @_;
	my $complete_header = "";
	$complete_header .= "\@PG\tID:$progname\tVN:$version\tCL:$cl\n";

	return $complete_header;
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/interpolate_sam.pl000077500000000000000000000116041211610345200255240ustar00rootroot00000000000000#!/usr/bin/perl
use strict;

###Builds interpolated pileup from SAM file
##@description counts bases between paired ends and piles up single end reads.
##@output, uses a #header for the RNAME and then the number of reads per base
##@author sm8@sanger.ac.uk, Stephen B. Montgomery

##@caveats
##Requires RNAME to have format as per example
##      chromosome:NCBI36:18:1:76117153:1
##      supercontig::NT_113883:1:137703:1
##      clone::AC138827.3:1:149397:1
##Expects simple CIGAR characters, M, I and D
##Expects SAM file to be sorted.
##Expects 0x0010 to mark second read in PE file (as has been the observed case from MAQ output) (important for line 77)

##Verify and read in SAM file
my $sam_file = $ARGV[0];
if(!defined($sam_file)) { die("No sam file defined on arg 1"); }
unless(-f $sam_file) { die("Sam file does not exist: $sam_file"); }
open(SAM, $sam_file) || die("Cannot open sam file"); 

##Globals
my $current_location = ""; ##Current RNAME being processed
my $current_size = 0; ##Size of sequence region being processed
my $current_position = 1; ##Current base being processed
my $open = 0; ##Number of open reads (PE reads that have not been closed)
my %close = (); ##Hash of closing positions, when the current_position gets to this position it subtracts the
    ##contained value from those open and deletes the indexed position from the hash

while (my $line = ) {
    my @tokens = split /\t/, $line;
    
    if ($current_location ne $tokens[2]) { ##Start a new sequence region 
        for (my $i = $current_position; $i <= $current_size; $i++) { ##Close the previous sequence region
            if (defined($close{$i})) {
                $open = $open - $close{$i};
                delete $close{$i};
            }
            print $open . "\n";
        }
        if ($current_location ne "") {
            print "\n";
        }
        
        ##Initiate a new sequence region
        my @location_tokens = split /:/, $tokens[2]; 
        $current_position = 1;
        $current_location = $tokens[2];
        $current_size = $location_tokens[4];
        $open = 0;
        %close = (); 
        print "#" . $tokens[2] . "\n";
        
        ##Print pileup to just before the first read (will be 0)
        for (my $current_position = 1; $current_position < $tokens[3]; $current_position++) {
            print $open . "\n";
        }
        $current_position = $tokens[3];
        
    } else { ##Sequence region already open
        if ($tokens[3] > $current_position) { ##If the new read's position is greater than the current position
                                                ##cycle through to catch up to the current position
            for (my $i = $current_position; $i < $tokens[3]; $i++) {
                if (defined($close{$i})) {
                    $open = $open - $close{$i};
                    delete $close{$i};
                }
                print $open . "\n";
            }
            $current_position = $tokens[3];
        }
    }
    $open++; ##Increment the number of open reads
    
    if (($tokens[1] & 0x0080 || $tokens[1] & 0x0040) && $tokens[1] & 0x0010 && $tokens[1] & 0x0002) { ##if second read of mate pair, add close condition
        $open--;
        my $parsed_cig = &parseCigar($tokens[5]);
        my $seq_region_end = $tokens[3] + $parsed_cig->{'M'} + $parsed_cig->{'D'} - 1;
        if (!defined($close{$seq_region_end + 1})) { $close{$seq_region_end + 1} = 0; }
        $close{$seq_region_end + 1} = $close{$seq_region_end + 1} + 1;
    } elsif (!($tokens[1] & 0x0001) || !($tokens[1] & 0x0002)) { ##if unpaired, add close condition
        my $parsed_cig = &parseCigar($tokens[5]);
        my $seq_region_end = $tokens[3] + $parsed_cig->{'M'} + $parsed_cig->{'D'} - 1;
        if (!defined($close{$seq_region_end + 1})) { $close{$seq_region_end + 1} = 0; }
        $close{$seq_region_end + 1} = $close{$seq_region_end + 1} + 1;
    } else {
        #do nothing
    }
}
for (my $i = $current_position; $i <= $current_size; $i++) {  ##Finish up the last sequence region
    if (defined($close{$i})) {
        $open = $open - $close{$i};
        delete $close{$i};
    }
    print $open . "\n";
}
print "\n";
close(SAM);
exit(0);

##reads and tokenizes simple cigarline
sub parseCigar() {
    my $cigar_line = shift;
    $cigar_line =~ s/([0-9]*[A-Z]{1})/$1\t/g;
    my @cigar_tokens = split /\t/, $cigar_line;
    my %parsed = ('M' => 0,
                  'I' => 0,
                  'D' => 0);
    my @events = ();
    for(my $i = 0; $i < scalar(@cigar_tokens); $i++) {
        if ($cigar_tokens[$i] =~ /([0-9]+)([A-Z]{1})/g) {
            if (!defined($parsed{$2})) { $parsed{$2} = 0; }
            my $nt = $2;
            if ($nt ne "M" && $nt ne "D"  && $nt ne "I") { $nt = "M"; }
            $parsed{$nt} += $1;
            my %event_el = ("t" => $nt,
                            "n" => $1);
            push @events, \%event_el;
        }
    }
    $parsed{'events'} = \@events;
    return \%parsed;
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/maq2sam.c000066400000000000000000000107651211610345200235120ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include 

#define PACKAGE_VERSION "r439"

//#define MAQ_LONGREADS

#ifdef MAQ_LONGREADS
#  define MAX_READLEN 128
#else
#  define MAX_READLEN 64
#endif

#define MAX_NAMELEN 36
#define MAQMAP_FORMAT_OLD 0
#define MAQMAP_FORMAT_NEW -1

#define PAIRFLAG_FF      0x01
#define PAIRFLAG_FR      0x02
#define PAIRFLAG_RF      0x04
#define PAIRFLAG_RR      0x08
#define PAIRFLAG_PAIRED  0x10
#define PAIRFLAG_DIFFCHR 0x20
#define PAIRFLAG_NOMATCH 0x40
#define PAIRFLAG_SW      0x80

typedef struct
{
	uint8_t seq[MAX_READLEN]; /* the last base is the single-end mapping quality. */
	uint8_t size, map_qual, info1, info2, c[2], flag, alt_qual;
	uint32_t seqid, pos;
	int dist;
	char name[MAX_NAMELEN];
} maqmap1_t;

typedef struct
{
	int format, n_ref;
	char **ref_name;
	uint64_t n_mapped_reads;
	maqmap1_t *mapped_reads;
} maqmap_t;

maqmap_t *maq_new_maqmap()
{
	maqmap_t *mm = (maqmap_t*)calloc(1, sizeof(maqmap_t));
	mm->format = MAQMAP_FORMAT_NEW;
	return mm;
}
void maq_delete_maqmap(maqmap_t *mm)
{
	int i;
	if (mm == 0) return;
	for (i = 0; i < mm->n_ref; ++i)
		free(mm->ref_name[i]);
	free(mm->ref_name);
	free(mm->mapped_reads);
	free(mm);
}
maqmap_t *maqmap_read_header(gzFile fp)
{
	maqmap_t *mm;
	int k, len;
	mm = maq_new_maqmap();
	gzread(fp, &mm->format, sizeof(int));
	if (mm->format != MAQMAP_FORMAT_NEW) {
		if (mm->format > 0) {
			fprintf(stderr, "** Obsolete map format is detected. Please use 'mapass2maq' command to convert the format.\n");
			exit(3);
		}
		assert(mm->format == MAQMAP_FORMAT_NEW);
	}
	gzread(fp, &mm->n_ref, sizeof(int));
	mm->ref_name = (char**)calloc(mm->n_ref, sizeof(char*));
	for (k = 0; k != mm->n_ref; ++k) {
		gzread(fp, &len, sizeof(int));
		mm->ref_name[k] = (char*)malloc(len * sizeof(char));
		gzread(fp, mm->ref_name[k], len);
	}
	/* read number of mapped reads */
	gzread(fp, &mm->n_mapped_reads, sizeof(uint64_t));
	return mm;
}

void maq2tam_core(gzFile fp, const char *rg)
{
	maqmap_t *mm;
	maqmap1_t mm1, *m1;
	int ret;
	m1 = &mm1;
	mm = maqmap_read_header(fp);
	while ((ret = gzread(fp, m1, sizeof(maqmap1_t))) == sizeof(maqmap1_t)) {
		int j, flag = 0, se_mapq = m1->seq[MAX_READLEN-1];
		if (m1->flag) flag |= 1;
		if ((m1->flag&PAIRFLAG_PAIRED) || ((m1->flag&PAIRFLAG_SW) && m1->flag != 192)) flag |= 2;
		if (m1->flag == 192) flag |= 4;
		if (m1->flag == 64) flag |= 8;
		if (m1->pos&1) flag |= 0x10;
		if ((flag&1) && m1->dist != 0) {
			int c;
			if (m1->dist > 0) {
				if (m1->flag&(PAIRFLAG_FF|PAIRFLAG_RF)) c = 0;
				else if (m1->flag&(PAIRFLAG_FR|PAIRFLAG_RR)) c = 1;
				else c = m1->pos&1;				
			} else {
				if (m1->flag&(PAIRFLAG_FF|PAIRFLAG_FR)) c = 0;
				else if (m1->flag&(PAIRFLAG_RF|PAIRFLAG_RR)) c = 1;
				else c = m1->pos&1;
			}
			if (c) flag |= 0x20;
		}
		if (m1->flag) {
			int l = strlen(m1->name);
			if (m1->name[l-2] == '/') {
				flag |= (m1->name[l-1] == '1')? 0x40 : 0x80;
				m1->name[l-2] = '\0';
			}
		}
		printf("%s\t%d\t", m1->name, flag);
		printf("%s\t%d\t", mm->ref_name[m1->seqid], (m1->pos>>1)+1);
		if (m1->flag == 130) {
			int c = (int8_t)m1->seq[MAX_READLEN-1];
			printf("%d\t", m1->alt_qual);
			if (c == 0) printf("%dM\t", m1->size);
			else {
				if (c > 0) printf("%dM%dI%dM\t", m1->map_qual, c, m1->size - m1->map_qual - c);
				else printf("%dM%dD%dM\t", m1->map_qual, -c, m1->size - m1->map_qual);
			}
			se_mapq = 0; // zero SE mapQ for reads aligned by SW
		} else {
			if (flag&4) printf("0\t*\t");
			else printf("%d\t%dM\t", m1->map_qual, m1->size);
		}
		printf("*\t0\t%d\t", m1->dist);
		for (j = 0; j != m1->size; ++j) {
			if (m1->seq[j] == 0) putchar('N');
			else putchar("ACGT"[m1->seq[j]>>6&3]);
		}
		putchar('\t');
		for (j = 0; j != m1->size; ++j)
			putchar((m1->seq[j]&0x3f) + 33);
		putchar('\t');
		if (rg) printf("RG:Z:%s\t", rg);
		if (flag&4) { // unmapped
			printf("MF:i:%d\n", m1->flag);
		} else {
			printf("MF:i:%d\t", m1->flag);
			if (m1->flag) printf("AM:i:%d\tSM:i:%d\t", m1->alt_qual, se_mapq);
			printf("NM:i:%d\tUQ:i:%d\tH0:i:%d\tH1:i:%d\n", m1->info1&0xf, m1->info2, m1->c[0], m1->c[1]);
		}
	}
	if (ret > 0)
		fprintf(stderr, "Truncated! Continue anyway.\n");
	maq_delete_maqmap(mm);
}

int main(int argc, char *argv[])
{
	gzFile fp;
	if (argc == 1) {
		fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
		fprintf(stderr, "Usage: maq2sam  []\n");
		return 1;
	}
	fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
	maq2tam_core(fp, argc > 2? argv[2] : 0);
	gzclose(fp);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/md5.c000066400000000000000000000215631211610345200226340ustar00rootroot00000000000000/*
 * This code implements the MD5 message-digest algorithm.
 * The algorithm is due to Ron Rivest.	This code was
 * written by Colin Plumb in 1993, no copyright is claimed.
 * This code is in the public domain; do with it what you wish.
 *
 * Equivalent code is available from RSA Data Security, Inc.
 * This code has been tested against that, and is equivalent,
 * except that you don't need to include two pages of legalese
 * with every copy.
 *
 * To compute the message digest of a chunk of bytes, declare an
 * MD5Context structure, pass it to MD5Init, call MD5Update as
 * needed on buffers full of bytes, and then call MD5Final, which
 * will fill a supplied 16-byte array with the digest.
 */

/* Brutally hacked by John Walker back from ANSI C to K&R (no
   prototypes) to maintain the tradition that Netfone will compile
   with Sun's original "cc". */

#include 
#include "md5.h"

#ifndef HIGHFIRST
#define byteReverse(buf, len)	/* Nothing */
#else
/*
 * Note: this code is harmless on little-endian machines.
 */
void byteReverse(buf, longs)
    unsigned char *buf; unsigned longs;
{
    uint32_t t;
    do {
	t = (uint32_t) ((unsigned) buf[3] << 8 | buf[2]) << 16 |
	    ((unsigned) buf[1] << 8 | buf[0]);
	*(uint32_t *) buf = t;
	buf += 4;
    } while (--longs);
}
#endif

void MD5Transform(uint32_t buf[4], uint32_t in[16]);


/*
 * Start MD5 accumulation.  Set bit count to 0 and buffer to mysterious
 * initialization constants.
 */
void MD5Init(ctx)
    struct MD5Context *ctx;
{
    ctx->buf[0] = 0x67452301;
    ctx->buf[1] = 0xefcdab89;
    ctx->buf[2] = 0x98badcfe;
    ctx->buf[3] = 0x10325476;

    ctx->bits[0] = 0;
    ctx->bits[1] = 0;
}

/*
 * Update context to reflect the concatenation of another buffer full
 * of bytes.
 */
void MD5Update(ctx, buf, len)
    struct MD5Context *ctx; unsigned char *buf; unsigned len;
{
    uint32_t t;

    /* Update bitcount */

    t = ctx->bits[0];
    if ((ctx->bits[0] = t + ((uint32_t) len << 3)) < t)
	ctx->bits[1]++; 	/* Carry from low to high */
    ctx->bits[1] += len >> 29;

    t = (t >> 3) & 0x3f;	/* Bytes already in shsInfo->data */

    /* Handle any leading odd-sized chunks */

    if (t) {
	unsigned char *p = (unsigned char *) ctx->in + t;

	t = 64 - t;
	if (len < t) {
	    memcpy(p, buf, len);
	    return;
	}
	memcpy(p, buf, t);
	byteReverse(ctx->in, 16);
	MD5Transform(ctx->buf, (uint32_t *) ctx->in);
	buf += t;
	len -= t;
    }
    /* Process data in 64-byte chunks */

    while (len >= 64) {
	memcpy(ctx->in, buf, 64);
	byteReverse(ctx->in, 16);
	MD5Transform(ctx->buf, (uint32_t *) ctx->in);
	buf += 64;
	len -= 64;
    }

    /* Handle any remaining bytes of data. */

    memcpy(ctx->in, buf, len);
}

/*
 * Final wrapup - pad to 64-byte boundary with the bit pattern 
 * 1 0* (64-bit count of bits processed, MSB-first)
 */
void MD5Final(digest, ctx)
    unsigned char digest[16]; struct MD5Context *ctx;
{
    unsigned count;
    unsigned char *p;

    /* Compute number of bytes mod 64 */
    count = (ctx->bits[0] >> 3) & 0x3F;

    /* Set the first char of padding to 0x80.  This is safe since there is
       always at least one byte free */
    p = ctx->in + count;
    *p++ = 0x80;

    /* Bytes of padding needed to make 64 bytes */
    count = 64 - 1 - count;

    /* Pad out to 56 mod 64 */
    if (count < 8) {
	/* Two lots of padding:  Pad the first block to 64 bytes */
	memset(p, 0, count);
	byteReverse(ctx->in, 16);
	MD5Transform(ctx->buf, (uint32_t *) ctx->in);

	/* Now fill the next block with 56 bytes */
	memset(ctx->in, 0, 56);
    } else {
	/* Pad block to 56 bytes */
	memset(p, 0, count - 8);
    }
    byteReverse(ctx->in, 14);

    /* Append length in bits and transform */
    ((uint32_t *) ctx->in)[14] = ctx->bits[0];
    ((uint32_t *) ctx->in)[15] = ctx->bits[1];

    MD5Transform(ctx->buf, (uint32_t *) ctx->in);
    byteReverse((unsigned char *) ctx->buf, 4);
    memcpy(digest, ctx->buf, 16);
    memset(ctx, 0, sizeof(ctx));        /* In case it's sensitive */
}


/* The four core functions - F1 is optimized somewhat */

/* #define F1(x, y, z) (x & y | ~x & z) */
#define F1(x, y, z) (z ^ (x & (y ^ z)))
#define F2(x, y, z) F1(z, x, y)
#define F3(x, y, z) (x ^ y ^ z)
#define F4(x, y, z) (y ^ (x | ~z))

/* This is the central step in the MD5 algorithm. */
#define MD5STEP(f, w, x, y, z, data, s) \
	( w += f(x, y, z) + data,  w = w<>(32-s),  w += x )

/*
 * The core of the MD5 algorithm, this alters an existing MD5 hash to
 * reflect the addition of 16 longwords of new data.  MD5Update blocks
 * the data and converts bytes into longwords for this routine.
 */
void MD5Transform(buf, in)
    uint32_t buf[4]; uint32_t in[16];
{
    register uint32_t a, b, c, d;

    a = buf[0];
    b = buf[1];
    c = buf[2];
    d = buf[3];

    MD5STEP(F1, a, b, c, d, in[0] + 0xd76aa478, 7);
    MD5STEP(F1, d, a, b, c, in[1] + 0xe8c7b756, 12);
    MD5STEP(F1, c, d, a, b, in[2] + 0x242070db, 17);
    MD5STEP(F1, b, c, d, a, in[3] + 0xc1bdceee, 22);
    MD5STEP(F1, a, b, c, d, in[4] + 0xf57c0faf, 7);
    MD5STEP(F1, d, a, b, c, in[5] + 0x4787c62a, 12);
    MD5STEP(F1, c, d, a, b, in[6] + 0xa8304613, 17);
    MD5STEP(F1, b, c, d, a, in[7] + 0xfd469501, 22);
    MD5STEP(F1, a, b, c, d, in[8] + 0x698098d8, 7);
    MD5STEP(F1, d, a, b, c, in[9] + 0x8b44f7af, 12);
    MD5STEP(F1, c, d, a, b, in[10] + 0xffff5bb1, 17);
    MD5STEP(F1, b, c, d, a, in[11] + 0x895cd7be, 22);
    MD5STEP(F1, a, b, c, d, in[12] + 0x6b901122, 7);
    MD5STEP(F1, d, a, b, c, in[13] + 0xfd987193, 12);
    MD5STEP(F1, c, d, a, b, in[14] + 0xa679438e, 17);
    MD5STEP(F1, b, c, d, a, in[15] + 0x49b40821, 22);

    MD5STEP(F2, a, b, c, d, in[1] + 0xf61e2562, 5);
    MD5STEP(F2, d, a, b, c, in[6] + 0xc040b340, 9);
    MD5STEP(F2, c, d, a, b, in[11] + 0x265e5a51, 14);
    MD5STEP(F2, b, c, d, a, in[0] + 0xe9b6c7aa, 20);
    MD5STEP(F2, a, b, c, d, in[5] + 0xd62f105d, 5);
    MD5STEP(F2, d, a, b, c, in[10] + 0x02441453, 9);
    MD5STEP(F2, c, d, a, b, in[15] + 0xd8a1e681, 14);
    MD5STEP(F2, b, c, d, a, in[4] + 0xe7d3fbc8, 20);
    MD5STEP(F2, a, b, c, d, in[9] + 0x21e1cde6, 5);
    MD5STEP(F2, d, a, b, c, in[14] + 0xc33707d6, 9);
    MD5STEP(F2, c, d, a, b, in[3] + 0xf4d50d87, 14);
    MD5STEP(F2, b, c, d, a, in[8] + 0x455a14ed, 20);
    MD5STEP(F2, a, b, c, d, in[13] + 0xa9e3e905, 5);
    MD5STEP(F2, d, a, b, c, in[2] + 0xfcefa3f8, 9);
    MD5STEP(F2, c, d, a, b, in[7] + 0x676f02d9, 14);
    MD5STEP(F2, b, c, d, a, in[12] + 0x8d2a4c8a, 20);

    MD5STEP(F3, a, b, c, d, in[5] + 0xfffa3942, 4);
    MD5STEP(F3, d, a, b, c, in[8] + 0x8771f681, 11);
    MD5STEP(F3, c, d, a, b, in[11] + 0x6d9d6122, 16);
    MD5STEP(F3, b, c, d, a, in[14] + 0xfde5380c, 23);
    MD5STEP(F3, a, b, c, d, in[1] + 0xa4beea44, 4);
    MD5STEP(F3, d, a, b, c, in[4] + 0x4bdecfa9, 11);
    MD5STEP(F3, c, d, a, b, in[7] + 0xf6bb4b60, 16);
    MD5STEP(F3, b, c, d, a, in[10] + 0xbebfbc70, 23);
    MD5STEP(F3, a, b, c, d, in[13] + 0x289b7ec6, 4);
    MD5STEP(F3, d, a, b, c, in[0] + 0xeaa127fa, 11);
    MD5STEP(F3, c, d, a, b, in[3] + 0xd4ef3085, 16);
    MD5STEP(F3, b, c, d, a, in[6] + 0x04881d05, 23);
    MD5STEP(F3, a, b, c, d, in[9] + 0xd9d4d039, 4);
    MD5STEP(F3, d, a, b, c, in[12] + 0xe6db99e5, 11);
    MD5STEP(F3, c, d, a, b, in[15] + 0x1fa27cf8, 16);
    MD5STEP(F3, b, c, d, a, in[2] + 0xc4ac5665, 23);

    MD5STEP(F4, a, b, c, d, in[0] + 0xf4292244, 6);
    MD5STEP(F4, d, a, b, c, in[7] + 0x432aff97, 10);
    MD5STEP(F4, c, d, a, b, in[14] + 0xab9423a7, 15);
    MD5STEP(F4, b, c, d, a, in[5] + 0xfc93a039, 21);
    MD5STEP(F4, a, b, c, d, in[12] + 0x655b59c3, 6);
    MD5STEP(F4, d, a, b, c, in[3] + 0x8f0ccc92, 10);
    MD5STEP(F4, c, d, a, b, in[10] + 0xffeff47d, 15);
    MD5STEP(F4, b, c, d, a, in[1] + 0x85845dd1, 21);
    MD5STEP(F4, a, b, c, d, in[8] + 0x6fa87e4f, 6);
    MD5STEP(F4, d, a, b, c, in[15] + 0xfe2ce6e0, 10);
    MD5STEP(F4, c, d, a, b, in[6] + 0xa3014314, 15);
    MD5STEP(F4, b, c, d, a, in[13] + 0x4e0811a1, 21);
    MD5STEP(F4, a, b, c, d, in[4] + 0xf7537e82, 6);
    MD5STEP(F4, d, a, b, c, in[11] + 0xbd3af235, 10);
    MD5STEP(F4, c, d, a, b, in[2] + 0x2ad7d2bb, 15);
    MD5STEP(F4, b, c, d, a, in[9] + 0xeb86d391, 21);

    buf[0] += a;
    buf[1] += b;
    buf[2] += c;
    buf[3] += d;
}

/* lh3: the following code is added by me */

#ifdef MD5SUM_MAIN
#include 
#include 
#include 
#define HEX_STR "0123456789abcdef"

static void md5_one(const char *fn)
{
	unsigned char buf[4096], digest[16];
	MD5_CTX md5;
	int l;
	FILE *fp;

	fp = strcmp(fn, "-")? fopen(fn, "r") : stdin;
	if (fp == 0) {
		fprintf(stderr, "md5sum: %s: No such file or directory\n", fn);
		exit(1);
	}
	MD5Init(&md5);
	while ((l = fread(buf, 1, 4096, fp)) > 0)
		MD5Update(&md5, buf, l);
	MD5Final(digest, &md5);
	if (fp != stdin) fclose(fp);
	for (l = 0; l < 16; ++l)
		printf("%c%c", HEX_STR[digest[l]>>4&0xf], HEX_STR[digest[l]&0xf]);
	printf("  %s\n", fn);
}
int main(int argc, char *argv[])
{
	int i;
	if (argc == 1) md5_one("-");
	else for (i = 1; i < argc; ++i) md5_one(argv[i]);
	return 0;
}
#endif
genometools-1.5.1/src/external/samtools-0.1.18/misc/md5.h000066400000000000000000000032451211610345200226360ustar00rootroot00000000000000/*
  This file is adapted from a program in this page:

  http://www.fourmilab.ch/md5/

  The original source code does not work on 64-bit machines due to the
  wrong typedef "uint32". I also added prototypes.

  -lh3
 */

#ifndef MD5_H
#define MD5_H

/*  The following tests optimise behaviour on little-endian
    machines, where there is no need to reverse the byte order
    of 32 bit words in the MD5 computation.  By default,
    HIGHFIRST is defined, which indicates we're running on a
    big-endian (most significant byte first) machine, on which
    the byteReverse function in md5.c must be invoked. However,
    byteReverse is coded in such a way that it is an identity
    function when run on a little-endian machine, so calling it
    on such a platform causes no harm apart from wasting time. 
    If the platform is known to be little-endian, we speed
    things up by undefining HIGHFIRST, which defines
    byteReverse as a null macro.  Doing things in this manner
    insures we work on new platforms regardless of their byte
    order.  */

#define HIGHFIRST

#if __LITTLE_ENDIAN__ != 0
#undef HIGHFIRST
#endif

#include 

struct MD5Context {
        uint32_t buf[4];
        uint32_t bits[2];
        unsigned char in[64];
};

void MD5Init(struct MD5Context *ctx);
void MD5Update(struct MD5Context *ctx, unsigned char *buf, unsigned len);
void MD5Final(unsigned char digest[16], struct MD5Context *ctx);

/*
 * This is needed to make RSAREF happy on some MS-DOS compilers.
 */
typedef struct MD5Context MD5_CTX;

/*  Define CHECK_HARDWARE_PROPERTIES to have main,c verify
    byte order and uint32_t settings.  */
#define CHECK_HARDWARE_PROPERTIES

#endif /* !MD5_H */
genometools-1.5.1/src/external/samtools-0.1.18/misc/md5fa.c000066400000000000000000000030161211610345200231340ustar00rootroot00000000000000#include 
#include 
#include "md5.h"
#include "kseq.h"

#define HEX_STR "0123456789abcdef"

KSEQ_INIT(gzFile, gzread)

static void md5_one(const char *fn)
{
	MD5_CTX md5_one, md5_all;
	int l, i, k;
	gzFile fp;
	kseq_t *seq;
	unsigned char unordered[16], digest[16];

	for (l = 0; l < 16; ++l) unordered[l] = 0;
	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
	if (fp == 0) {
		fprintf(stderr, "md5fa: %s: No such file or directory\n", fn);
		exit(1);
	}
	
	MD5Init(&md5_all);
	seq = kseq_init(fp);
	while ((l = kseq_read(seq)) >= 0) {
		for (i = k = 0; i < seq->seq.l; ++i) {
			if (islower(seq->seq.s[i])) seq->seq.s[k++] = toupper(seq->seq.s[i]);
			else if (isupper(seq->seq.s[i])) seq->seq.s[k++] = seq->seq.s[i];
		}
		MD5Init(&md5_one);
		MD5Update(&md5_one, (unsigned char*)seq->seq.s, k);
		MD5Final(digest, &md5_one);
		for (l = 0; l < 16; ++l) {
			printf("%c%c", HEX_STR[digest[l]>>4&0xf], HEX_STR[digest[l]&0xf]);
			unordered[l] ^= digest[l];
		}
		printf("  %s  %s\n", fn, seq->name.s);
		MD5Update(&md5_all, (unsigned char*)seq->seq.s, k);
	}
	MD5Final(digest, &md5_all);
	kseq_destroy(seq);
	for (l = 0; l < 16; ++l)
		printf("%c%c", HEX_STR[digest[l]>>4&0xf], HEX_STR[digest[l]&0xf]);
	printf("  %s  >ordered\n", fn);
	for (l = 0; l < 16; ++l)
		printf("%c%c", HEX_STR[unordered[l]>>4&0xf], HEX_STR[unordered[l]&0xf]);
	printf("  %s  >unordered\n", fn);
}

int main(int argc, char *argv[])
{
	int i;
	if (argc == 1) md5_one("-");
	else for (i = 1; i < argc; ++i) md5_one(argv[i]);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/novo2sam.pl000077500000000000000000000135451211610345200241100ustar00rootroot00000000000000#!/usr/bin/perl -w

# Contact: lh3
# Version: 0.1.3

#Modified by Zayed Albertyn(zayed.albertyn@gmail.com) & Colin Hercus(colin@novocraft.com)

#use strict;
#use warnings;
use Data::Dumper;
use Getopt::Std;

&novo2sam;
exit;

sub mating {
  my ($s1, $s2) = @_;
  my $isize = 0;
  if ($s1->[2] ne '*' && $s1->[2] eq $s2->[2]) { # then calculate $isize
	my $x1 = ($s1->[1] & 0x10)? $s1->[3] + length($s1->[9]) : $s1->[3];
	my $x2 = ($s2->[1] & 0x10)? $s2->[3] + length($s2->[9]) : $s2->[3];
	$isize = $x2 - $x1;
  }
  # update mate coordinate
  if ($s2->[2] ne '*') {
	@$s1[6..8] = (($s2->[2] eq $s1->[2])? "=" : $s2->[2], $s2->[3], $isize);
	$s1->[1] |= 0x20 if ($s2->[1] & 0x10);
  } else {
	$s1->[1] |= 0x8;
  }
  if ($s1->[2] ne '*') {
	@$s2[6..8] = (($s1->[2] eq $s2->[2])? "=" : $s1->[2], $s1->[3], -$isize);
	$s2->[1] |= 0x20 if ($s1->[1] & 0x10);
  } else {
	$s2->[1] |= 0x8;
  }
}

sub novo2sam {
  my %opts = ();
  getopts("p", \%opts);
  die("Usage: novo2sam.pl [-p] \n") if (@ARGV == 0);
  my $is_paired = defined($opts{p});
  # core loop
  my @s1 = ();
  my @s2 = ();
  my ($s_last, $s_curr) = (\@s1, \@s2);
  while (<>) {
	next if (/^#/);
	next if (/(QC|NM)\s*$/ || /(R\s+\d+)\s*$/);
	&novo2sam_aux($_, $s_curr, $is_paired);
	if (@$s_last != 0 && $s_last->[0] eq $s_curr->[0]) {
	  &mating($s_last, $s_curr);
	  print join("\t", @$s_last), "\n";
	  print join("\t", @$s_curr), "\n";
	  @$s_last = (); @$s_curr = ();
	} else {
	  print join("\t", @$s_last), "\n" if (@$s_last != 0);
	  my $s = $s_last; $s_last = $s_curr; $s_curr = $s;
	}
  }
  print join("\t", @$s_last), "\n" if (@$s_last != 0);
}

sub novo2sam_aux {
  my ($line, $s, $is_paired) = @_;

  chomp($line);
  my @t = split(/\s+/, $line);
  my @variations =  @t[13 .. $#t];
  @$s = ();
  return if ($t[4] ne 'U');
  my $len = length($t[2]);
  # read name
  $s->[0] = substr($t[0], 1);
  $s->[0] =~ s/\/[12]$//g;
  # initial flag (will be updated later)
  $s->[1] = 0;
  $s->[1] |= 1 | 1<<($t[1] eq 'L'? 6 : 7);
  $s->[1] |= 2 if ($t[10] eq '.');
  # read & quality
  if ($t[9] eq 'R') {
	$s->[9] = reverse($t[2]);
	$s->[10] = reverse($t[3]);
	$s->[9] =~ tr/ACGTRYMKWSNacgtrymkwsn/TGCAYRKMWSNtgcayrkmwsn/;
  } else {
	$s->[9] = $t[2]; $s->[10] = $t[3];
  }
  # cigar
   my $cigarstring ="";
  if (scalar @variations ==0 ) {
 	 $s->[5] = $len . "M"; # IMPORTANT: this cigar is not correct for gapped alignment
  } else {
	#convert to correct CIGAR
	my $tmpstr =  join" ",@variations ;
	if ( $tmpstr=~ /\+|\-/ ) {
		$cigarstring  = cigar_method($line,\@variations,$len);
		$s->[5]=$cigarstring;
	} else {
		$s->[5]=$len. "M";
	}
}  

# coor
  $s->[2] = substr($t[7], 1); $s->[3] = $t[8];
  $s->[1] |= 0x10 if ($t[9] eq 'R');
  # mapQ
  $s->[4] = $t[5] > $t[6]? $t[5] : $t[6];
  # mate coordinate
  $s->[6] = '*'; $s->[7] = $s->[8] = 0;
  # aux
  push(@$s, "NM:i:".(@t-13));
  my $md = '';
  $md = mdtag($md,$line,\@variations,$len);
  push(@$s, "MD:Z:$md");

}

sub mdtag {
	my $oldmd = shift;
	my $line = shift;
	my $ref =shift;
	my $rdlen  = shift;
	my @variations = @$ref;
	my $string="";
	my $mdtag="";
	my $t=1;
	my $q=1;
	my $deleteflag=0;
	my $len =0;
	foreach $string (@variations) {
		my ($indeltype,$insert) = indeltype($string);
		if ($indeltype eq "+") {
			$len = length ($insert);
			$q+=$len;
                  next;
		}
		my $pos = $1 if $string =~ /^(\d+)/;
		$len = $pos - $t;	
		if ($len !=0 || ($deleteflag eq 1 && $indeltype eq ">")) {
			$mdtag.=$len;
		}	
		$t+=$len;
		$q+=$len;
		if ($indeltype eq ">") {
			$mdtag.=$insert;
			$deleteflag=0;
		      $t+=1;
		      $q+=1;
		}
		if ($indeltype eq "-") {
			my $deletedbase = $2 if $string =~ /(\d+)\-([A-Za-z]+)/;
			if ($deleteflag == 0 ) {
				$mdtag.="^";
			}
			$mdtag.=$deletedbase;
			$deleteflag=1;
			$t+=1;
		}
	}
	$len = $rdlen - $q + 1;
	if ($len > 0) {
		$mdtag.="$len";
	}
#	print "In:$line\n";
#	print "MD: OLD => NEW\nMD: $oldmd => $mdtag\n\n";

	return $mdtag;
}

sub indeltype {
	my $string =  shift;
	my $insert="";
	my $indeltype;
               if ($string =~ /([A-Za-z]+)\>/) {
                        $indeltype=">";
                        $insert=$1;
                } elsif ($string =~ /\-/) {
                        $indeltype="-";
                } elsif ($string =~ /\+([A-Za-z]+)/) {
                        $indeltype="+";
                        $insert=$1;
                }
	 return ($indeltype,$insert);
	
}


sub cigar_method {
	my $line = shift;
	my $ref =shift;
	my $rdlen  = shift;
	my @variations = @$ref;
	my $string="";
	my $type="";
	my $t =1;
	my $q=1;
	my $indeltype="";
	my $cigar=  "";	
	my $insert = "";
	my $len=0;
	my @cig=();
	foreach $string (@variations) {
		next if $string =~  />/;
		my $pos = $1 if $string =~ /^(\d+)/;
		
		if ($string =~ /\+([A-Za-z]+)/) {	
			$indeltype="+";
			$insert = $1;
		}elsif ($string =~ /\-([A-Za-z]+)/) {
			$indeltype="-";
			$insert = $1;
		}
#print "$pos $indeltype $insert $t $q\n";	
		$len = $pos - $t;
		if ( $len > 0) {
			$cigar.=$len."M";
			push(@cig,$len."M");
		}
		$t+=$len;
		$q+=$len;

		if ($indeltype eq "-") {
			$cigar.="D";
			push(@cig,"D");
			$t++;
		}
		if ($indeltype eq "+") {
			$len = length ($insert);
			if ($len == 1) {
				$cigar.="I";
				push(@cig,"I");
			}
			if ($len > 1) {
				$cigar.=$len."I";
				push(@cig,$len."I")
			}
			$q+=$len;
		}
		$insert="";
	}
	$len= $rdlen - $q + 1;
	if ($len > 0) {
		$cigar.=$len."M"; 
		push(@cig,$len."M");
	}
	
      $cigar = newcigar($cigar,'D');
      $cigar = newcigar($cigar,'I');
	
	#print "$line\n";
	#print "c CIGAR:\t$cigar\n\n";
	return $cigar;

}



sub newcigar {
	my $cigar = shift;
	my $char = shift;
	my $new = "";
	my $copy = $cigar;
#print "$cigar\n";
	$copy =~ s/^($char+)/$1;/g;
#print "$copy\n";
	$copy =~ s/([^0-9$char])($char+)/$1;$2;/g;
#print "$copy\n";
	my @parts = split(/;/,$copy);
	my $el="";
	foreach $el (@parts) {
#print "$el\n";
		if ($el =~ /^$char+$/) {
			$new.=length($el).$char;
		}else {
			$new.=$el;
		}

	}
     return  $new;
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/psl2sam.pl000077500000000000000000000037461211610345200237270ustar00rootroot00000000000000#!/usr/bin/perl -w

# Author: lh3

# This script calculates a score using the BLAST scoring
# system. However, I am not sure how to count gap opens and gap
# extensions. It seems to me that column 5-8 are not what I am
# after. This script counts gaps from the last three columns. It does
# not generate reference skip (N) in the CIGAR as it is not easy to
# directly tell which gaps correspond to introns.

use strict;
use warnings;
use Getopt::Std;

my %opts = (a=>1, b=>3, q=>5, r=>2);
getopts('a:b:q:r:', \%opts);
die("Usage: psl2sam.pl [-a $opts{a}] [-b $opts{b}] [-q $opts{q}] [-r $opts{r}] \n") if (@ARGV == 0 && -t STDIN);

my @stack;
my $last = '';
my ($a, $b, $q, $r) = ($opts{a}, $opts{b}, $opts{q}, $opts{r});
while (<>) {
  next unless (/^\d/);
  my @t = split;
  my @s;
  my $cigar = '';
  if ($t[8] eq '-') {
	my $tmp = $t[11];
	$t[11] = $t[10] - $t[12];
	$t[12] = $t[10] - $tmp;
  }
  @s[0..4] = ($t[9], (($t[8] eq '+')? 0 : 16), $t[13], $t[15]+1, 0);
  @s[6..10] = ('*', 0, 0, '*', '*');
  $cigar .= $t[11].'H' if ($t[11]); # 5'-end clipping
  my @x = split(',', $t[18]);
  my @y = split(',', $t[19]);
  my @z = split(',', $t[20]);
  my ($y0, $z0) = ($y[0], $z[0]);
  my ($gap_open, $gap_ext) = (0, 0, 0);
  for (1 .. $t[17]-1) {
	my $ly = $y[$_] - $y[$_-1] - $x[$_-1];
	my $lz = $z[$_] - $z[$_-1] - $x[$_-1];
	if ($ly < $lz) { # del: the reference gap is longer
	  ++$gap_open;
	  $gap_ext += $lz - $ly;
	  $cigar .= ($y[$_] - $y0) . 'M';
	  $cigar .= ($lz - $ly) . 'D';
	  ($y0, $z0) = ($y[$_], $z[$_]);
	} elsif ($lz < $ly) { # ins: the query gap is longer
	  ++$gap_open;
	  $gap_ext += $ly - $lz;
	  $cigar .= ($z[$_] - $z0) . 'M';
	  $cigar .= ($ly - $lz) . 'I';
	  ($y0, $z0) = ($y[$_], $z[$_]);
	}
  }
  $cigar .= ($t[12] - $y0) . 'M';
  $cigar .= ($t[10] - $t[12]).'H' if ($t[10] != $t[12]); # 3'-end clipping
  $s[5] = $cigar;
  my $score = $a * $t[0] - $b * $t[1] - $q * $gap_open - $r * $gap_ext;
  $score = 0 if ($score < 0);
  $s[11] = "AS:i:$score";
  print join("\t", @s), "\n";
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/sam2vcf.pl000077500000000000000000000173111211610345200237000ustar00rootroot00000000000000#!/usr/bin/perl -w
# 
# VCF specs: http://www.1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf3.3
# 
# Contact: pd3@sanger
# Version: 2010-04-23

use strict;
use warnings;
use Carp;

my $opts = parse_params();
do_pileup_to_vcf($opts);

exit;

#---------------

sub error
{
    my (@msg) = @_;
    if ( scalar @msg ) { croak(@msg); }
    die
        "Usage: sam2vcf.pl [OPTIONS] < in.pileup > out.vcf\n",
        "Options:\n",
        "   -h, -?, --help                  This help message.\n",
        "   -i, --indels-only               Ignore SNPs.\n",
        "   -r, --refseq           The reference sequence, required when indels are present.\n",
        "   -R, --keep-ref                  Print reference alleles as well.\n",
        "   -s, --snps-only                 Ignore indels.\n",
        "   -t, --column-title      The column title.\n",
        "\n";
}


sub parse_params
{
    my %opts = ();

    $opts{fh_in}  = *STDIN;
    $opts{fh_out} = *STDOUT;

    while (my $arg=shift(@ARGV))
    {
        if ( $arg eq '-R' || $arg eq '--keep-ref' ) { $opts{keep_ref}=1; next; }
        if ( $arg eq '-r' || $arg eq '--refseq' ) { $opts{refseq}=shift(@ARGV); next; }
        if ( $arg eq '-t' || $arg eq '--column-title' ) { $opts{title}=shift(@ARGV); next; }
        if ( $arg eq '-s' || $arg eq '--snps-only' ) { $opts{snps_only}=1; next; }
        if ( $arg eq '-i' || $arg eq '--indels-only' ) { $opts{indels_only}=1; next; }
        if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }

        error("Unknown parameter \"$arg\". Run -h for help.\n");
    }
    return \%opts;
}

sub iupac_to_gtype
{
    my ($ref,$base) = @_;
    my %iupac = (
            'K' => ['G','T'],
            'M' => ['A','C'],
            'S' => ['C','G'],
            'R' => ['A','G'],
            'W' => ['A','T'],
            'Y' => ['C','T'],
            );
    if ( !exists($iupac{$base}) ) 
    { 
        if ( $base ne 'A' && $base ne 'C' && $base ne 'G' && $base ne 'T' ) { error("FIXME: what is this [$base]?\n"); }
        if ( $ref eq $base ) { return ('.','0/0'); }
        return ($base,'1/1');
    }
    my $gt = $iupac{$base};
    if ( $$gt[0] eq $ref  ) { return ($$gt[1],'0/1'); }
    elsif ( $$gt[1] eq $ref ) { return ($$gt[0],'0/1'); }
    return ("$$gt[0],$$gt[1]",'1/2');
}


sub parse_indel
{
    my ($cons) = @_;
    if ( $cons=~/^-/ ) 
    { 
        my $len = length($');
        return "D$len"; 
    }
    elsif ( $cons=~/^\+/ ) { return "I$'"; }
    elsif ( $cons eq '*' ) { return undef; }
    error("FIXME: could not parse [$cons]\n");
}


# An example of the pileup format:
#   1       3000011 C       C       32      0       98      1       ^~,     A
#   1       3002155 *       +T/+T   53      119     52      5       +T      *       4       1       0
#   1       3003094 *       -TT/-TT 31      164     60      11      -TT     *       5       6       0
#   1       3073986 *       */-AAAAAAAAAAAAAA       3       3       45      9       *       -AAAAAAAAAAAAAA 7       2       0
#
sub do_pileup_to_vcf
{
    my ($opts) = @_;

    my $fh_in  = $$opts{fh_in};
    my $fh_out = $$opts{fh_out};
    my ($prev_chr,$prev_pos,$prev_ref);
    my $refseq;
    my $ignore_indels = $$opts{snps_only} ? 1 : 0;
    my $ignore_snps   = $$opts{indels_only} ? 1 : 0;
    my $keep_ref      = $$opts{keep_ref} ? 1 : 0;
    my $title = exists($$opts{title}) ? $$opts{title} : 'data';

    print $fh_out 
        qq[##fileformat=VCFv3.3\n],
        qq[##INFO=DP,1,Integer,"Total Depth"\n],
        qq[##FORMAT=GT,1,String,"Genotype"\n],
        qq[##FORMAT=GQ,1,Integer,"Genotype Quality"\n],
        qq[##FORMAT=DP,1,Integer,"Read Depth"\n],
        qq[#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t$title\n]
        ;

    while (my $line=<$fh_in>)
    {
        chomp($line);
        my (@items) = split(/\t/,$line);
        if ( scalar @items<8 ) 
        { 
            error("\nToo few columns, does not look like output of 'samtools pileup -c': $line\n"); 
        }
        my ($chr,$pos,$ref,$cons,$cons_qual,$snp_qual,$rms_qual,$depth,$a1,$a2) = @items;
        $ref  = uc($ref);
        $cons = uc($cons);

        my ($alt,$gt);
        if ( $ref eq '*' )
        {
            # An indel is involved.
            if ( $ignore_indels )
            { 
                $prev_ref = $ref;
                $prev_pos = $pos;
                $prev_chr = $chr;
                next; 
            }

            if (!defined $prev_chr || $chr ne $prev_chr || $pos ne $prev_pos) 
            {
                if ( !$$opts{refseq} ) { error("Cannot do indels without the reference.\n"); }
                if ( !$refseq ) { $refseq = Fasta->new(file=>$$opts{refseq}); }
                $ref = $refseq->get_base($chr,$pos);
                $ref = uc($ref);
            }
            else { $ref = $prev_ref; }

            # One of the alleles can be a reference and it can come in arbitrary order. In some
            #   cases */* can be encountered. In such a case, look in the additional columns.
            my ($al1,$al2) = split(m{/},$cons);
            if ( $al1 eq $al2 && $al1 eq '*' ) { $al1=$a1; $al2=$a2; }
            my $alt1 = parse_indel($al1);
            my $alt2 = parse_indel($al2);
            if ( !$alt1 && !$alt2 ) { error("FIXME: could not parse indel:\n", $line); }
            if ( !$alt1 ) 
            { 
                $alt=$alt2; 
                $gt='0/1'; 
            }
            elsif ( !$alt2 ) 
            { 
                $alt=$alt1; 
                $gt='0/1'; 
            }
            elsif ( $alt1 eq $alt2 )
            { 
                $alt="$alt1"; 
                $gt='1/1'; 
            }
            else
            { 
                $alt="$alt1,$alt2"; 
                $gt='1/2'; 
            }
        }
        else
        {
            if ( $ignore_snps || (!$keep_ref && $ref eq $cons) ) 
            { 
                $prev_ref = $ref;
                $prev_pos = $pos;
                $prev_chr = $chr;
                next; 
            }

            # SNP
            ($alt,$gt) = iupac_to_gtype($ref,$cons);
        }

        print $fh_out "$chr\t$pos\t.\t$ref\t$alt\t$snp_qual\t0\tDP=$depth\tGT:GQ:DP\t$gt:$cons_qual:$depth\n";

        $prev_ref = $ref;
        $prev_pos = $pos;
        $prev_chr = $chr;
    }
}


#------------- Fasta --------------------
#
# Uses samtools to get a requested base from a fasta file. For efficiency, preloads
#   a chunk to memory. The size of the cached sequence can be controlled by the 'size'
#   parameter.
#
package Fasta;

use strict;
use warnings;
use Carp;

sub Fasta::new
{
    my ($class,@args) = @_;
    my $self = {@args};
    bless $self, ref($class) || $class;
    if ( !$$self{file} ) { $self->throw(qq[Missing the parameter "file"\n]); }
    $$self{chr}  = undef;
    $$self{from} = undef;
    $$self{to}   = undef;
    if ( !$$self{size} ) { $$self{size}=10_000_000; }
    bless $self, ref($class) || $class;
    return $self;
}

sub read_chunk
{
    my ($self,$chr,$pos) = @_;
    my $to = $pos + $$self{size};
    my $cmd = "samtools faidx $$self{file} $chr:$pos-$to";
    my @out = `$cmd`;
    if ( $? ) { $self->throw("$cmd: $!"); }
    my $line = shift(@out);
    if ( !($line=~/^>$chr:(\d+)-(\d+)/) ) { $self->throw("Could not parse: $line"); }
    $$self{chr}  = $chr;
    $$self{from} = $1;
    $$self{to}   = $2;
    my $chunk = '';
    while ($line=shift(@out))
    {
        chomp($line);
        $chunk .= $line;
    }
    $$self{chunk} = $chunk;
    return;
}

sub get_base
{
    my ($self,$chr,$pos) = @_;
    if ( !$$self{chr} || $chr ne $$self{chr} || $pos<$$self{from} || $pos>$$self{to} )
    {
        $self->read_chunk($chr,$pos);
    }
    my $idx = $pos - $$self{from};
    return substr($$self{chunk},$idx,1);
}

sub throw
{
    my ($self,@msg) = @_;
    croak(@msg);
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/samtools.pl000077500000000000000000000337331211610345200242060ustar00rootroot00000000000000#!/usr/bin/perl -w

# Author: lh3

use strict;
use warnings;
use Getopt::Std;

my $version = '0.3.3';
&usage if (@ARGV < 1);

my $command = shift(@ARGV);
my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, plp2vcf=>\&plp2vcf,
			unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr, sam2fq=>\&sam2fq);

die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
exit(0);

#
# showALEN
#

sub showALEN {
  die(qq/Usage: samtools.pl showALEN \n/) if (@ARGV == 0 && -t STDIN);
  while (<>) {
	my @t = split;
	next if (/^\@/ || @t < 11);
	my $l = 0;
	$_ = $t[5];
	s/(\d+)[MI]/$l+=$1/eg;
	print join("\t", @t[0..5]), "\t$l\t", join("\t", @t[6..$#t]), "\n";
  }
}

#
# varFilter
#

#
# Filtration code:
#
# d low depth
# D high depth
# W too many SNPs in a window (SNP only)
# G close to a high-quality indel (SNP only)
# Q low RMS mapping quality (SNP only)
# g close to another indel with higher quality (indel only)
# s low SNP quality (SNP only)
# i low indel quality (indel only)

sub varFilter {
  my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, S=>'', i=>'');
  getopts('pq:d:D:l:Q:w:W:N:G:S:i:', \%opts);
  die(qq/
Usage:   samtools.pl varFilter [options] 

Options: -Q INT    minimum RMS mapping quality for SNPs [$opts{Q}]
         -q INT    minimum RMS mapping quality for gaps [$opts{q}]
         -d INT    minimum read depth [$opts{d}]
         -D INT    maximum read depth [$opts{D}]
         -S INT    minimum SNP quality [$opts{S}]
         -i INT    minimum indel quality [$opts{i}]

         -G INT    min indel score for nearby SNP filtering [$opts{G}]
         -w INT    SNP within INT bp around a gap to be filtered [$opts{w}]

         -W INT    window size for filtering dense SNPs [$opts{W}]
         -N INT    max number of SNPs in a window [$opts{N}]

         -l INT    window size for filtering adjacent gaps [$opts{l}]

         -p        print filtered variants
\n/) if (@ARGV == 0 && -t STDIN);

  # calculate the window size
  my ($ol, $ow, $oW) = ($opts{l}, $opts{w}, $opts{W});
  my $max_dist = $ol > $ow? $ol : $ow;
  $max_dist = $oW if ($max_dist < $oW);
  # the core loop
  my @staging; # (indel_filtering_score, flt_tag)
  while (<>) {
	my @t = split;
	next if (uc($t[2]) eq uc($t[3]) || $t[3] eq '*/*'); # skip non-var sites
	# clear the out-of-range elements
	while (@staging) {
      # Still on the same chromosome and the first element's window still affects this position?  
	  last if ($staging[0][3] eq $t[0] && $staging[0][4] + $staging[0][2] + $max_dist >= $t[1]);
	  varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much
	}
	my ($flt, $score) = (0, -1);
	# first a simple filter
	if ($t[7] < $opts{d}) {
	  $flt = 2;
	} elsif ($t[7] > $opts{D}) {
	  $flt = 3;
	}
    if ($t[2] eq '*') { # an indel
        if ($opts{i} && $opts{i}>$t[5]) { $flt = 8; }
    }
    elsif ($opts{S} && $opts{S}>$t[5]) { $flt = 7; }    # SNP

	# site dependent filters
    my $len=0;
	if ($flt == 0) {
	  if ($t[2] eq '*') { # an indel
        # If deletion, remember the length of the deletion
        my ($a,$b) = split(m{/},$t[3]);
        my $alen = length($a) - 1;
        my $blen = length($b) - 1;
        if ( $alen>$blen )
        {
            if ( substr($a,0,1) eq '-' ) { $len=$alen; }
        }
        elsif ( substr($b,0,1) eq '-' ) { $len=$blen; }

		$flt = 1 if ($t[6] < $opts{q});
		# filtering SNPs
		if ($t[5] >= $opts{G}) {
		  for my $x (@staging) {
            # Is it a SNP and is it outside the SNP filter window?
			next if ($x->[0] >= 0 || $x->[4] + $x->[2] + $ow < $t[1]);
			$x->[1] = 5 if ($x->[1] == 0);
		  }
		}
		# calculate the filtering score (different from indel quality)
		$score = $t[5];
		$score += $opts{s} * $t[10] if ($t[8] ne '*');
		$score += $opts{s} * $t[11] if ($t[9] ne '*');
		# check the staging list for indel filtering
		for my $x (@staging) {
          # Is it a SNP and is it outside the gap filter window
		  next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ol < $t[1]);
		  if ($x->[0] < $score) {
			$x->[1] = 6;
		  } else {
			$flt = 6; last;
		  }
		}
	  } else { # a SNP
		$flt = 1 if ($t[6] < $opts{Q});
		# check adjacent SNPs
		my $k = 1;
		for my $x (@staging) {
		  ++$k if ($x->[0] < 0 && $x->[4] + $x->[2] + $oW >= $t[1] && ($x->[1] == 0 || $x->[1] == 4 || $x->[1] == 5));
		}
		# filtering is necessary
		if ($k > $opts{N}) {
		  $flt = 4;
		  for my $x (@staging) {
			 $x->[1] = 4 if ($x->[0] < 0 && $x->[4] + $x->[2] + $oW >= $t[1] && $x->[1] == 0);
		  }
		} else { # then check gap filter
		  for my $x (@staging) {
			next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ow < $t[1]);
			if ($x->[0] >= $opts{G}) {
			  $flt = 5; last;
			}
		  }
		}
	  }
	}
	push(@staging, [$score, $flt, $len, @t]);
  }
  # output the last few elements in the staging list
  while (@staging) {
	varFilter_aux(shift @staging, $opts{p});
  }
}

sub varFilter_aux {
  my ($first, $is_print) = @_;
  if ($first->[1] == 0) {
	print join("\t", @$first[3 .. @$first-1]), "\n";
  } elsif ($is_print) {
	print STDERR join("\t", substr("UQdDWGgsiX", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
  }
}

#
# pileup2fq
#

sub pileup2fq {
  my %opts = (d=>3, D=>255, Q=>25, G=>25, l=>10);
  getopts('d:D:Q:G:l:', \%opts);
  die(qq/
Usage:   samtools.pl pileup2fq [options] 

Options: -d INT    minimum depth        [$opts{d}]
         -D INT    maximum depth        [$opts{D}]
         -Q INT    min RMS mapQ         [$opts{Q}]
         -G INT    minimum indel score  [$opts{G}]
         -l INT    indel filter winsize [$opts{l}]\n
/) if (@ARGV == 0 && -t STDIN);

  my ($last_chr, $seq, $qual, @gaps, $last_pos);
  my $_Q = $opts{Q};
  my $_d = $opts{d};
  my $_D = $opts{D};

  $last_chr = '';
  while (<>) {
	my @t = split;
	if ($last_chr ne $t[0]) {
	  &p2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l}) if ($last_chr);
	  $last_chr = $t[0];
	  $last_pos = 0;
	  $seq = ''; $qual = '';
	  @gaps = ();
	}
	if ($t[1] - $last_pos != 1) {
	  $seq .= 'n' x ($t[1] - $last_pos - 1);
	  $qual .= '!' x ($t[1] - $last_pos - 1);
	}
	if ($t[2] eq '*') {
	  push(@gaps, $t[1]) if ($t[5] >= $opts{G});
	} else {
	  $seq .= ($t[6] >= $_Q && $t[7] >= $_d && $t[7] <= $_D)? uc($t[3]) : lc($t[3]);
	  my $q = $t[4] + 33;
	  $q = 126 if ($q > 126);
	  $qual .= chr($q);
	}
	$last_pos = $t[1];
  }
  &p2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l});
}

sub p2q_post_process {
  my ($chr, $seq, $qual, $gaps, $l) = @_;
  &p2q_filter_gaps($seq, $gaps, $l);
  print "\@$chr\n"; &p2q_print_str($seq);
  print "+\n"; &p2q_print_str($qual);
}

sub p2q_filter_gaps {
  my ($seq, $gaps, $l) = @_;
  for my $g (@$gaps) {
	my $x = $g > $l? $g - $l : 0;
	substr($$seq, $x, $l + $l) = lc(substr($$seq, $x, $l + $l));
  }
}

sub p2q_print_str {
  my ($s) = @_;
  my $l = length($$s);
  for (my $i = 0; $i < $l; $i += 60) {
	print substr($$s, $i, 60), "\n";
  }
}

#
# sam2fq
#

sub sam2fq {
  my %opts = (n=>20, p=>'');
  getopts('n:p:', \%opts);
  die("Usage: samtools.pl sam2fq [-n 20] [-p ] \n") if (@ARGV == 0 && -t STDIN);
  if ($opts{p} && $opts{n} > 1) {
	my $pre = $opts{p};
	my @fh;
	for (0 .. $opts{n}-1) {
	  open($fh[$_], sprintf("| gzip > $pre.%.3d.fq.gz", $_)) || die;
	}
	my $i = 0;
	while (<>) {
	  next if (/^@/);
	  chomp;
	  my @t = split("\t");
	  next if ($t[9] eq '*');
	  my ($name, $seq, $qual);
	  if ($t[1] & 16) { # reverse strand
		$seq = reverse($t[9]);
		$qual = reverse($t[10]);
		$seq =~ tr/ACGTacgt/TGCAtgca/;
	  } else {
		($seq, $qual) = @t[9,10];
	  }
	  $name = $t[0];
	  $name .= "/1" if ($t[1] & 0x40);
	  $name .= "/2" if ($t[1] & 0x80);
	  print {$fh[$i]} "\@$name\n$seq\n";
	  if ($qual ne '*') {
		print {$fh[$i]} "+\n$qual\n";
	  }
	  $i = 0 if (++$i == $opts{n});
	}
	close($fh[$_]) for (0 .. $opts{n}-1);
  } else {
	die("To be implemented.\n");
  }
}

#
# sra2hdr
#

# This subroutine does not use an XML parser. It requires that the SRA
# XML files are properly formated.
sub sra2hdr {
  my %opts = ();
  getopts('', \%opts);
  die("Usage: samtools.pl sra2hdr \n") if (@ARGV == 0);
  my $pre = $ARGV[0];
  my $fh;
  # read sample
  my $sample = 'UNKNOWN';
  open($fh, "$pre.sample.xml") || die;
  while (<$fh>) {
	$sample = $1 if (/) {
	if (/\s*(\S+)\s*<\/LIBRARY_NAME>/i) {
	  $exp2lib{$exp} = $1;
	}
  }
  close($fh);
  # read run
  my ($run, @fn);
  open($fh, "$pre.run.xml") || die;
  while (<$fh>) {
	if (//i) {
	  if (@fn == 1) {
		print STDERR "$fn[0]\t$run\n";
	  } else {
		for (0 .. $#fn) {
		  print STDERR "$fn[$_]\t$run", "_", $_+1, "\n";
		}
	  }
	}
  }
  close($fh);
}

#
# unique
#

sub unique {
  my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3);
  getopts('Qf:q:r:a:b:m', \%opts);
  die("Usage: samtools.pl unique [-f $opts{f}] \n") if (@ARGV == 0 && -t STDIN);
  my $last = '';
  my $recal_Q = !defined($opts{Q});
  my $multi_only = defined($opts{m});
  my @a;
  while (<>) {
	my $score = -1;
	print $_ if (/^\@/);
	$score = $1 if (/AS:i:(\d+)/);
	my @t = split("\t");
	next if (@t < 11);
	if ($score < 0) { # AS tag is unavailable
	  my $cigar = $t[5];
	  my ($mm, $go, $ge) = (0, 0, 0);
	  $cigar =~ s/(\d+)[ID]/++$go,$ge+=$1/eg;
	  $cigar = $t[5];
	  $cigar =~ s/(\d+)M/$mm+=$1/eg;
	  $score = $mm * $opts{a} - $go * $opts{q} - $ge * $opts{r}; # no mismatches...
	}
	$score = 1 if ($score < 1);
	if ($t[0] ne $last) {
	  &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
	  $last = $t[0];
	}
	push(@a, [$score, \@t]);
  }
  &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
}

sub unique_aux {
  my ($a, $fac, $is_recal, $multi_only) = @_;
  my ($max, $max2, $max_i) = (0, 0, -1);
  for (my $i = 0; $i < @$a; ++$i) {
	if ($a->[$i][0] > $max) {
	  $max2 = $max; $max = $a->[$i][0]; $max_i = $i;
	} elsif ($a->[$i][0] > $max2) {
	  $max2 = $a->[$i][0];
	}
  }
  if ($is_recal) {
	if (!$multi_only || @$a > 1) {
	  my $q = int($fac * ($max - $max2) / $max + .499);
	  $q = 250 if ($q > 250);
	  $a->[$max_i][1][4] = $q < 250? $q : 250;
	}
  }
  print join("\t", @{$a->[$max_i][1]});
  @$a = ();
}

#
# uniqcmp: compare two SAM files
#

sub uniqcmp {
  my %opts = (q=>10, s=>100);
  getopts('pq:s:', \%opts);
  die("Usage: samtools.pl uniqcmp  \n") if (@ARGV < 2);
  my ($fh, %a);
  warn("[uniqcmp] read the first file...\n");
  &uniqcmp_aux($ARGV[0], \%a, 0);
  warn("[uniqcmp] read the second file...\n");
  &uniqcmp_aux($ARGV[1], \%a, 1);
  warn("[uniqcmp] stats...\n");
  my @cnt;
  $cnt[$_] = 0 for (0..9);
  for my $x (keys %a) {
	my $p = $a{$x};
	my $z;
	if (defined($p->[0]) && defined($p->[1])) {
	  $z = ($p->[0][0] == $p->[1][0] && $p->[0][1] eq $p->[1][1] && abs($p->[0][2] - $p->[1][2]) < $opts{s})? 0 : 1;
	  if ($p->[0][3] >= $opts{q} && $p->[1][3] >= $opts{q}) {
		++$cnt[$z*3+0];
	  } elsif ($p->[0][3] >= $opts{q}) {
		++$cnt[$z*3+1];
	  } elsif ($p->[1][3] >= $opts{q}) {
		++$cnt[$z*3+2];
	  }
	  print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
		$p->[0][5]-$p->[1][5], "\n" if ($z && defined($opts{p}) && ($p->[0][3] >= $opts{q} || $p->[1][3] >= $opts{q}));
	} elsif (defined($p->[0])) {
	  ++$cnt[$p->[0][3]>=$opts{q}? 6 : 7];
	  print STDERR "$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t*\t0\t*\t",
		$p->[0][5], "\n" if (defined($opts{p}) && $p->[0][3] >= $opts{q});
	} else {
	  print STDERR "$x\t*\t0\t*\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
		-$p->[1][5], "\n" if (defined($opts{p}) && $p->[1][3] >= $opts{q});
	  ++$cnt[$p->[1][3]>=$opts{q}? 8 : 9];
	}
  }
  print "Consistent (high, high):   $cnt[0]\n";
  print "Consistent (high, low ):   $cnt[1]\n";
  print "Consistent (low , high):   $cnt[2]\n";
  print "Inconsistent (high, high): $cnt[3]\n";
  print "Inconsistent (high, low ): $cnt[4]\n";
  print "Inconsistent (low , high): $cnt[5]\n";
  print "Second missing (high):     $cnt[6]\n";
  print "Second missing (low ):     $cnt[7]\n";
  print "First  missing (high):     $cnt[8]\n";
  print "First  missing (low ):     $cnt[9]\n";
}

sub uniqcmp_aux {
  my ($fn, $a, $which) = @_;
  my $fh;
  $fn = "samtools view $fn |" if ($fn =~ /\.bam/);
  open($fh, $fn) || die;
  while (<$fh>) {
	my @t = split;
	next if (@t < 11);
#	my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0;
	my $l = 0;
	my ($x, $nm) = (0, 0);
	$nm = $1 if (/NM:i:(\d+)/);
	$_ = $t[5];
	s/(\d+)[MI]/$x+=$1/eg;
	@{$a->{$t[0]}[$which]} = (($t[1]&0x10)? 1 : 0, $t[2], $t[3]-$l, $t[4], "$x:$nm", $x - 4 * $nm);
  }
  close($fh);
}

sub plp2vcf {
  while (<>) {
	my @t = split;
	next if ($t[3] eq '*/*');
	if ($t[2] eq '*') { # indel
	  my @s = split("/", $t[3]);
	  my (@a, @b);
	  my ($ref, $alt);
	  for (@s) {
		next if ($_ eq '*');
		if (/^-/) {
		  push(@a, 'N'.substr($_, 1));
		  push(@b, 'N');
		} elsif (/^\+/) {
		  push(@a, 'N');
		  push(@b, 'N'.substr($_, 1));
		}
	  }
	  if ($a[0] && $a[1]) {
		if (length($a[0]) < length($a[1])) {
		  $ref = $a[1];
		  $alt = ($b[0] . ('N' x (length($a[1]) - length($a[0])))) . ",$b[1]";
		} elsif (length($a[0]) > length($a[1])) {
		  $ref = $a[0];
		  $alt = ($b[1] . ('N' x (length($a[0]) - length($a[1])))) . ",$b[0]";
		} else {
		  $ref = $a[0];
		  $alt = ($b[0] eq $b[1])? $b[0] : "$b[0],$b[1]";
		}
	  } else {
		$ref = $a[0]; $alt = $b[0];
	  }
	  print join("\t", @t[0,1], '.', $ref, $alt, $t[5], '.', '.'), "\n";
	} else { # SNP
	}
  }
}

#
# Usage
#

sub usage {
  die(qq/
Program: samtools.pl (helper script for SAMtools)
Version: $version
Contact: Heng Li \n
Usage:   samtools.pl  []\n
Command: varFilter     filtering SNPs and short indels
         pileup2fq     generate fastq from `pileup -c'
         showALEN      print alignment length (ALEN) following CIGAR
\n/);
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/seqtk.c000066400000000000000000000550461211610345200233010ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 

#include "kseq.h"
KSEQ_INIT(gzFile, gzread)

typedef struct {
	int n, m;
	uint64_t *a;
} reglist_t;

#include "khash.h"
KHASH_MAP_INIT_STR(reg, reglist_t)

typedef kh_reg_t reghash_t;

reghash_t *stk_reg_read(const char *fn)
{
	reghash_t *h = kh_init(reg);
	gzFile fp;
	kstream_t *ks;
	int dret;
	kstring_t *str;
	// read the list
	str = calloc(1, sizeof(kstring_t));
	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
	ks = ks_init(fp);
	while (ks_getuntil(ks, 0, str, &dret) >= 0) {
		int beg = -1, end = -1;
		reglist_t *p;
		khint_t k = kh_get(reg, h, str->s);
		if (k == kh_end(h)) {
			int ret;
			char *s = strdup(str->s);
			k = kh_put(reg, h, s, &ret);
			memset(&kh_val(h, k), 0, sizeof(reglist_t));
		}
		p = &kh_val(h, k);
		if (dret != '\n') {
			if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
				beg = atoi(str->s);
				if (dret != '\n') {
					if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
						end = atoi(str->s);
						if (end < 0) end = -1;
					}
				}
			}
		}
		// skip the rest of the line
		if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
		if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column
		if (beg < 0) beg = 0, end = INT_MAX;
		if (p->n == p->m) {
			p->m = p->m? p->m<<1 : 4;
			p->a = realloc(p->a, p->m * 8);
		}
		p->a[p->n++] = (uint64_t)beg<<32 | end;
	}
	ks_destroy(ks);
	gzclose(fp);
	free(str->s); free(str);
	return h;
}

void stk_reg_destroy(reghash_t *h)
{
	khint_t k;
	for (k = 0; k < kh_end(h); ++k) {
		if (kh_exist(h, k)) {
			free(kh_val(h, k).a);
			free((char*)kh_key(h, k));
		}
	}
	kh_destroy(reg, h);
}

/* constant table */

unsigned char seq_nt16_table[256] = {
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15 /*'-'*/,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
	15,15, 5, 6,  8,15, 7, 9,  0,10,15,15, 15,15,15,15,
	15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
	15,15, 5, 6,  8,15, 7, 9,  0,10,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
	15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
};

char *seq_nt16_rev_table = "XACMGRSVTWYHKDBN";
unsigned char seq_nt16to4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
int bitcnt_table[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };

/* composition */
int stk_comp(int argc, char *argv[])
{
	gzFile fp;
	kseq_t *seq;
	int l, c, upper_only = 0;
	reghash_t *h = 0;
	reglist_t dummy;
	while ((c = getopt(argc, argv, "ur:")) >= 0) {
		switch (c) {
			case 'u': upper_only = 1; break;
			case 'r': h = stk_reg_read(optarg); break;
		}
	}
	if (argc == optind) {
		fprintf(stderr, "Usage:  seqtk comp [-u] [-r in.bed] \n\n");
		fprintf(stderr, "Output format: chr, length, #A, #C, #G, #T, #2, #3, #4, #CpG, #tv, #ts, #CpG-ts\n");
		return 1;
	}
	fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
	seq = kseq_init(fp);
	dummy.n= dummy.m = 1; dummy.a = calloc(1, 8);
	while ((l = kseq_read(seq)) >= 0) {
		int i, k;
		reglist_t *p = 0;
		if (h) {
			khint_t k = kh_get(reg, h, seq->name.s);
			if (k != kh_end(h)) p = &kh_val(h, k);
		} else {
			p = &dummy;
			dummy.a[0] = l;
		}
		for (k = 0; p && k < p->n; ++k) {
			int beg = p->a[k]>>32, end = p->a[k]&0xffffffff;
			int la, lb, lc, na, nb, nc, cnt[11];
			if (beg > 0) la = seq->seq.s[beg-1], lb = seq_nt16_table[la], lc = bitcnt_table[lb];
			else la = 'a', lb = -1, lc = 0;
			na = seq->seq.s[beg]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb];
			memset(cnt, 0, 11 * sizeof(int));
			for (i = beg; i < end; ++i) {
				int is_CpG = 0, a, b, c;
				a = na; b = nb; c = nc;
				na = seq->seq.s[i+1]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb];
				if (b == 2 || b == 10) { // C or Y
					if (nb == 4 || nb == 5) is_CpG = 1;
				} else if (b == 4 || b == 5) { // G or R
					if (lb == 2 || lb == 10) is_CpG = 1;
				}
				if (upper_only == 0 || isupper(a)) {
					if (c > 1) ++cnt[c+2];
					if (c == 1) ++cnt[seq_nt16to4_table[b]];
					if (b == 10 || b == 5) ++cnt[9];
					else if (c == 2) {
						++cnt[8];
					}
					if (is_CpG) {
						++cnt[7];
						if (b == 10 || b == 5) ++cnt[10];
					}
				}
				la = a; lb = b; lc = c;
			}
			if (h) printf("%s\t%d\t%d", seq->name.s, beg, end);
			else printf("%s\t%d", seq->name.s, l);
			for (i = 0; i < 11; ++i) printf("\t%d", cnt[i]);
			putchar('\n');
		}
		fflush(stdout);
	}
	free(dummy.a);
	kseq_destroy(seq);
	gzclose(fp);
	return 0;
}

int stk_randbase(int argc, char *argv[])
{
	gzFile fp;
	kseq_t *seq;
	int l;
	if (argc == 1) {
		fprintf(stderr, "Usage: seqtk randbase \n");
		return 1;
	}
	fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
	seq = kseq_init(fp);
	while ((l = kseq_read(seq)) >= 0) {
		int i;
		printf(">%s", seq->name.s);
		for (i = 0; i < l; ++i) {
			int c, b, a, j, k, m;
			b = seq->seq.s[i];
			c = seq_nt16_table[b];
			a = bitcnt_table[c];
			if (a == 2) {
				m = (drand48() < 0.5);
				for (j = k = 0; j < 4; ++j) {
					if ((1<seq.s[i] = islower(b)? "acgt"[j] : "ACGT"[j];
			}
			if (i%60 == 0) putchar('\n');
			putchar(seq->seq.s[i]);
		}
		putchar('\n');
	}
	kseq_destroy(seq);
	gzclose(fp);
	return 0;
}

int stk_hety(int argc, char *argv[])
{
	gzFile fp;
	kseq_t *seq;
	int l, c, win_size = 50000, n_start = 5, win_step, is_lower_mask = 0;
	char *buf;
	uint32_t cnt[3];
	if (argc == 1) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   seqtk hety [options] \n\n");
		fprintf(stderr, "Options: -w INT   window size [%d]\n", win_size);
		fprintf(stderr, "         -t INT   # start positions in a window [%d]\n", n_start);
		fprintf(stderr, "         -m       treat lowercases as masked\n");
		fprintf(stderr, "\n");
		return 1;
	}
	while ((c = getopt(argc, argv, "w:t:m")) >= 0) {
		switch (c) {
		case 'w': win_size = atoi(optarg); break;
		case 't': n_start = atoi(optarg); break;
		case 'm': is_lower_mask = 1; break;
		}
	}
	fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
	seq = kseq_init(fp);
	win_step = win_size / n_start;
	buf = calloc(win_size, 1);
	while ((l = kseq_read(seq)) >= 0) {
		int x, i, y, z, next = 0;
		cnt[0] = cnt[1] = cnt[2] = 0;
		for (i = 0; i <= l; ++i) {
			if ((i >= win_size && i % win_step == 0) || i == l) {
				if (i == l && l >= win_size) {
					for (y = l - win_size; y < next; ++y) --cnt[(int)buf[y % win_size]];
				}
				if (cnt[1] + cnt[2] > 0)
					printf("%s\t%d\t%d\t%.2lf\t%d\t%d\n", seq->name.s, next, i,
						   (double)cnt[2] / (cnt[1] + cnt[2]) * win_size, cnt[1] + cnt[2], cnt[2]);
				next = i;
			}
			if (i < l) {
				y = i % win_size;
				c = seq->seq.s[i];
				if (is_lower_mask && islower(c)) c = 'N';
				c = seq_nt16_table[c];
				x = bitcnt_table[c];
				if (i >= win_size) --cnt[(int)buf[y]];
				buf[y] = z = x > 2? 0 : x == 2? 2 : 1;
				++cnt[z];
			}
		}
	}
	free(buf);
	kseq_destroy(seq);
	gzclose(fp);
	return 0;
}

/* fq2fa */
int stk_fq2fa(int argc, char *argv[])
{
	gzFile fp;
	kseq_t *seq;
	char *buf;
	int l, i, c, qual_thres = 0, linelen = 60;
	while ((c = getopt(argc, argv, "q:l:")) >= 0) {
		switch (c) {
			case 'q': qual_thres = atoi(optarg); break;
			case 'l': linelen = atoi(optarg); break;
		}
	}
	if (argc == optind) {
		fprintf(stderr, "Usage: seqtk fq2fa [-q qualThres=0] [-l lineLen=60] \n");
		return 1;
	}
	buf = linelen > 0? malloc(linelen + 1) : 0;
	fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
	seq = kseq_init(fp);
	while ((l = kseq_read(seq)) >= 0) {
		if (seq->qual.l && qual_thres > 0) {
			for (i = 0; i < l; ++i)
				if (seq->qual.s[i] - 33 < qual_thres)
					seq->seq.s[i] = tolower(seq->seq.s[i]);
		}
		putchar('>');
		if (seq->comment.l) {
			fputs(seq->name.s, stdout);
			putchar(' ');
			puts(seq->comment.s);
		} else puts(seq->name.s);
		if (buf) { // multi-line
			for (i = 0; i < l; i += linelen) {
				int x = i + linelen < l? linelen : l - i;
				memcpy(buf, seq->seq.s + i, x);
				buf[x] = 0;
				puts(buf);
			}
		} else puts(seq->seq.s);
	}
	free(buf);
	kseq_destroy(seq);
	gzclose(fp);
	return 0;
}

int stk_maskseq(int argc, char *argv[])
{
	khash_t(reg) *h = kh_init(reg);
	gzFile fp;
	kseq_t *seq;
	int l, i, j, c, is_complement = 0, is_lower = 0;
	khint_t k;
	while ((c = getopt(argc, argv, "cl")) >= 0) {
		switch (c) {
		case 'c': is_complement = 1; break;
		case 'l': is_lower = 1; break;
		}
	}
	if (argc - optind < 2) {
		fprintf(stderr, "Usage:   seqtk maskseq [-cl]  \n\n");
		fprintf(stderr, "Options: -c     mask the complement regions\n");
		fprintf(stderr, "         -l     soft mask (to lower cases)\n");
		return 1;
	}
	h = stk_reg_read(argv[optind+1]);
	// maskseq
	fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
	seq = kseq_init(fp);
	while ((l = kseq_read(seq)) >= 0) {
		k = kh_get(reg, h, seq->name.s);
		if (k == kh_end(h)) { // not found in the hash table
			if (is_complement) {
				for (j = 0; j < l; ++j)
					seq->seq.s[j] = is_lower? tolower(seq->seq.s[j]) : 'N';
			}
		} else {
			reglist_t *p = &kh_val(h, k);
			if (!is_complement) {
				for (i = 0; i < p->n; ++i) {
					int beg = p->a[i]>>32, end = p->a[i];
					if (beg >= seq->seq.l) {
						fprintf(stderr, "[maskseq] start position >= the sequence length.\n");
						continue;
					}
					if (end >= seq->seq.l) end = seq->seq.l;
					if (is_lower) for (j = beg; j < end; ++j) seq->seq.s[j] = tolower(seq->seq.s[j]);
					else for (j = beg; j < end; ++j) seq->seq.s[j] = 'N';
				}
			} else {
				int8_t *mask = calloc(seq->seq.l, 1);
				for (i = 0; i < p->n; ++i) {
					int beg = p->a[i]>>32, end = p->a[i];
					if (end >= seq->seq.l) end = seq->seq.l;
					for (j = beg; j < end; ++j) mask[j] = 1;
				}
				for (j = 0; j < l; ++j)
					if (mask[j] == 0) seq->seq.s[j] = is_lower? tolower(seq->seq.s[j]) : 'N';
				free(mask);
			}
		}
		printf(">%s", seq->name.s);
		for (j = 0; j < seq->seq.l; ++j) {
			if (j%60 == 0) putchar('\n');
			putchar(seq->seq.s[j]);
		}
		putchar('\n');
	}
	// free
	kseq_destroy(seq);
	gzclose(fp);
	stk_reg_destroy(h);
	return 0;
}

/* subseq */

int stk_subseq(int argc, char *argv[])
{
	khash_t(reg) *h = kh_init(reg);
	gzFile fp;
	kseq_t *seq;
	int l, i, j, c, is_tab = 0;
	khint_t k;
	while ((c = getopt(argc, argv, "t")) >= 0) {
		switch (c) {
		case 't': is_tab = 1; break;
		}
	}
	if (optind + 2 > argc) {
		fprintf(stderr, "Usage: seqtk subseq [-t]  \n\n");
		fprintf(stderr, "Note: Use 'samtools faidx' if only a few regions are intended.\n");
		return 1;
	}
	h = stk_reg_read(argv[optind+1]);
	// subseq
	fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
	seq = kseq_init(fp);
	while ((l = kseq_read(seq)) >= 0) {
		reglist_t *p;
		k = kh_get(reg, h, seq->name.s);
		if (k == kh_end(h)) continue;
		p = &kh_val(h, k);
		for (i = 0; i < p->n; ++i) {
			int beg = p->a[i]>>32, end = p->a[i];
			if (beg >= seq->seq.l) {
				fprintf(stderr, "[subseq] %s: %d >= %ld\n", seq->name.s, beg, seq->seq.l);
				continue;
			}
			if (end > seq->seq.l) end = seq->seq.l;
			if (is_tab == 0) {
				printf("%c%s", seq->qual.l == seq->seq.l? '@' : '>', seq->name.s);
				if (end == INT_MAX) {
					if (beg) printf(":%d", beg+1);
				} else printf(":%d-%d", beg+1, end);
			} else printf("%s\t%d\t", seq->name.s, beg + 1);
			if (end > seq->seq.l) end = seq->seq.l;
			for (j = 0; j < end - beg; ++j) {
				if (is_tab == 0 && j % 60 == 0) putchar('\n');
				putchar(seq->seq.s[j + beg]);
			}
			putchar('\n');
			if (seq->qual.l != seq->seq.l || is_tab) continue;
			printf("+");
			for (j = 0; j < end - beg; ++j) {
				if (j % 60 == 0) putchar('\n');
				putchar(seq->qual.s[j + beg]);
			}
			putchar('\n');
		}
	}
	// free
	kseq_destroy(seq);
	gzclose(fp);
	stk_reg_destroy(h);
	return 0;
}

/* mergefa */
int stk_mergefa(int argc, char *argv[])
{
	gzFile fp[2];
	kseq_t *seq[2];
	int i, l, c, is_intersect = 0, is_haploid = 0, qual = 0, is_mask = 0;
	while ((c = getopt(argc, argv, "himq:")) >= 0) {
		switch (c) {
			case 'i': is_intersect = 1; break;
			case 'h': is_haploid = 1; break;
			case 'm': is_mask = 1; break;
			case 'q': qual = atoi(optarg); break;
		}
	}
	if (is_mask && is_intersect) {
		fprintf(stderr, "[%s] `-i' and `-h' cannot be applied at the same time.\n", __func__);
		return 1;
	}
	if (optind + 2 > argc) {
		fprintf(stderr, "\nUsage: seqtk mergefa [options]  \n\n");
		fprintf(stderr, "Options: -q INT   quality threshold [0]\n");
		fprintf(stderr, "         -i       take intersection\n");
		fprintf(stderr, "         -m       convert to lowercase when one of the input base is N.\n");
		fprintf(stderr, "         -h       suppress hets in the input\n\n");
		return 1;
	}
	for (i = 0; i < 2; ++i) {
		fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
		seq[i] = kseq_init(fp[i]);
	}
	while (kseq_read(seq[0]) >= 0) {
		int min_l, c[2], is_upper;
		kseq_read(seq[1]);
		if (strcmp(seq[0]->name.s, seq[1]->name.s))
			fprintf(stderr, "[%s] Different sequence names: %s != %s\n", __func__, seq[0]->name.s, seq[1]->name.s);
		if (seq[0]->seq.l != seq[1]->seq.l)
			fprintf(stderr, "[%s] Unequal sequence length: %ld != %ld\n", __func__, seq[0]->seq.l, seq[1]->seq.l);
		min_l = seq[0]->seq.l < seq[1]->seq.l? seq[0]->seq.l : seq[1]->seq.l;
		printf(">%s", seq[0]->name.s);
		for (l = 0; l < min_l; ++l) {
			c[0] = seq[0]->seq.s[l]; c[1] = seq[1]->seq.s[l];
			if (seq[0]->qual.l && seq[0]->qual.s[l] - 33 < qual) c[0] = tolower(c[0]);
			if (seq[1]->qual.l && seq[1]->qual.s[l] - 33 < qual) c[1] = tolower(c[1]);
			if (is_intersect) is_upper = (isupper(c[0]) || isupper(c[1]))? 1 : 0;
			else if (is_mask) is_upper = (isupper(c[0]) || isupper(c[1]))? 1 : 0;
			else is_upper = (isupper(c[0]) && isupper(c[1]))? 1 : 0;
			c[0] = seq_nt16_table[c[0]]; c[1] = seq_nt16_table[c[1]];
			if (c[0] == 0) c[0] = 15;
			if (c[1] == 0) c[1] = 15;
			if (is_haploid && (bitcnt_table[c[0]] > 1 || bitcnt_table[c[1]] > 1)) is_upper = 0;
			if (is_intersect) {
				c[0] = c[0] & c[1];
				if (c[0] == 0) is_upper = 0;
			} else if (is_mask) {
				if (c[0] == 15 || c[1] == 15) is_upper = 0;
				c[0] = c[0] & c[1];
				if (c[0] == 0) is_upper = 0;
			} else c[0] = c[0] | c[1];
			c[0] = seq_nt16_rev_table[c[0]];
			if (!is_upper) c[0] = tolower(c[0]);
			if (l%60 == 0) putchar('\n');
			putchar(c[0]);
		}
		putchar('\n');
	}
	return 0;
}

int stk_famask(int argc, char *argv[])
{
	gzFile fp[2];
	kseq_t *seq[2];
	int i, l;
	if (argc < 3) {
		fprintf(stderr, "Usage: seqtk famask  \n");
		return 1;
	}
	for (i = 0; i < 2; ++i) {
		fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
		seq[i] = kseq_init(fp[i]);
	}
	while (kseq_read(seq[0]) >= 0) {
		int min_l, c[2];
		kseq_read(seq[1]);
		if (strcmp(seq[0]->name.s, seq[1]->name.s))
			fprintf(stderr, "[%s] Different sequence names: %s != %s\n", __func__, seq[0]->name.s, seq[1]->name.s);
		if (seq[0]->seq.l != seq[1]->seq.l)
			fprintf(stderr, "[%s] Unequal sequence length: %ld != %ld\n", __func__, seq[0]->seq.l, seq[1]->seq.l);
		min_l = seq[0]->seq.l < seq[1]->seq.l? seq[0]->seq.l : seq[1]->seq.l;
		printf(">%s", seq[0]->name.s);
		for (l = 0; l < min_l; ++l) {
			c[0] = seq[0]->seq.s[l]; c[1] = seq[1]->seq.s[l];
			if (c[1] == 'x') c[0] = tolower(c[0]);
			else if (c[1] != 'X') c[0] = c[1];
			if (l%60 == 0) putchar('\n');
			putchar(c[0]);
		}
		putchar('\n');
	}
	return 0;
}

int stk_mutfa(int argc, char *argv[])
{
	khash_t(reg) *h = kh_init(reg);
	gzFile fp;
	kseq_t *seq;
	kstream_t *ks;
	int l, i, dret;
	kstring_t *str;
	khint_t k;
	if (argc < 3) {
		fprintf(stderr, "Usage: seqtk mutfa  \n\n");
		fprintf(stderr, "Note:  contains at least four columns per line which are:\n");
		fprintf(stderr, "      'chr  1-based-pos  any  base-changed-to'.\n");
		return 1;
	}
	// read the list
	str = calloc(1, sizeof(kstring_t));
	fp = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
	ks = ks_init(fp);
	while (ks_getuntil(ks, 0, str, &dret) >= 0) {
		char *s = strdup(str->s);
		int beg = 0, ret;
		reglist_t *p;
		k = kh_get(reg, h, s);
		if (k == kh_end(h)) {
			k = kh_put(reg, h, s, &ret);
			memset(&kh_val(h, k), 0, sizeof(reglist_t));
		}
		p = &kh_val(h, k);
		if (ks_getuntil(ks, 0, str, &dret) > 0) beg = atol(str->s) - 1; // 2nd col
		ks_getuntil(ks, 0, str, &dret); // 3rd col
		ks_getuntil(ks, 0, str, &dret); // 4th col
		// skip the rest of the line
		if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
		if (isalpha(str->s[0]) && str->l == 1) {
			if (p->n == p->m) {
				p->m = p->m? p->m<<1 : 4;
				p->a = realloc(p->a, p->m * 8);
			}
			p->a[p->n++] = (uint64_t)beg<<32 | str->s[0];
		}
	}
	ks_destroy(ks);
	gzclose(fp);
	free(str->s); free(str);
	// mutfa
	fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
	seq = kseq_init(fp);
	while ((l = kseq_read(seq)) >= 0) {
		reglist_t *p;
		k = kh_get(reg, h, seq->name.s);
		if (k != kh_end(h)) {
			p = &kh_val(h, k);
			for (i = 0; i < p->n; ++i) {
				int beg = p->a[i]>>32;
				if (beg < seq->seq.l)
					seq->seq.s[beg] = (int)p->a[i];
			}
		}
		printf(">%s", seq->name.s);
		for (i = 0; i < l; ++i) {
			if (i%60 == 0) putchar('\n');
			putchar(seq->seq.s[i]);
		}
		putchar('\n');
	}
	// free
	kseq_destroy(seq);
	gzclose(fp);
	for (k = 0; k < kh_end(h); ++k) {
		if (kh_exist(h, k)) {
			free(kh_val(h, k).a);
			free((char*)kh_key(h, k));
		}
	}
	kh_destroy(reg, h);
	return 0;
}

int stk_listhet(int argc, char *argv[])
{
	gzFile fp;
	kseq_t *seq;
	int i, l;
	if (argc == 1) {
		fprintf(stderr, "Usage: seqtk listhet \n");
		return 1;
	}
	fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
	seq = kseq_init(fp);
	while ((l = kseq_read(seq)) >= 0) {
		for (i = 0; i < l; ++i) {
			int b = seq->seq.s[i];
			if (bitcnt_table[seq_nt16_table[b]] == 2)
				printf("%s\t%d\t%c\n", seq->name.s, i+1, b);
		}
	}
	kseq_destroy(seq);
	gzclose(fp);
	return 0;
}

/* cutN */
static int cutN_min_N_tract = 1000;
static int cutN_nonN_penalty = 10;

static int find_next_cut(const kseq_t *ks, int k, int *begin, int *end)
{
	int i, b, e;
	while (k < ks->seq.l) {
		if (seq_nt16_table[(int)ks->seq.s[k]] == 15) {
			int score, max;
			score = 0; e = max = -1;
			for (i = k; i < ks->seq.l && score >= 0; ++i) { /* forward */
				if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score;
				else score -= cutN_nonN_penalty;
				if (score > max) max = score, e = i;
			}
			score = 0; b = max = -1;
			for (i = e; i >= 0 && score >= 0; --i) { /* backward */
				if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score;
				else score -= cutN_nonN_penalty;
				if (score > max) max = score, b = i;
			}
			if (e + 1 - b >= cutN_min_N_tract) {
				*begin = b;
				*end = e + 1;
				return *end;
			}
			k = e + 1;
		} else ++k;
	}
	return -1;
}
static void print_seq(FILE *fpout, const kseq_t *ks, int begin, int end)
{
	int i;
	if (begin >= end) return; // FIXME: why may this happen? Understand it!
	fprintf(fpout, ">%s:%d-%d", ks->name.s, begin+1, end);
	for (i = begin; i < end && i < ks->seq.l; ++i) {
		if ((i - begin)%60 == 0) fputc('\n', fpout);
		fputc(ks->seq.s[i], fpout);
	}
	fputc('\n', fpout);
}
int stk_cutN(int argc, char *argv[])
{
	int c, l, gap_only = 0;
	gzFile fp;
	kseq_t *ks;
	while ((c = getopt(argc, argv, "n:p:g")) >= 0) {
		switch (c) {
		case 'n': cutN_min_N_tract = atoi(optarg); break;
		case 'p': cutN_nonN_penalty = atoi(optarg); break;
		case 'g': gap_only = 1; break;
		default: return 1;
		}
	}
	if (argc == optind) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   seqtk cutN [options] \n\n");
		fprintf(stderr, "Options: -n INT    min size of N tract [%d]\n", cutN_min_N_tract);
		fprintf(stderr, "         -p INT    penalty for a non-N [%d]\n", cutN_nonN_penalty);
		fprintf(stderr, "         -g        print gaps only, no sequence\n\n");
		return 1;
	}
	fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
	ks = kseq_init(fp);
	while ((l = kseq_read(ks)) >= 0) {
		int k = 0, begin = 0, end = 0;
		while (find_next_cut(ks, k, &begin, &end) >= 0) {
			if (begin != 0) {
				if (gap_only) printf("%s\t%d\t%d\n", ks->name.s, begin, end);
				else print_seq(stdout, ks, k, begin);
			}
			k = end;
		}
		if (!gap_only) print_seq(stdout, ks, k, l);
	}
	kseq_destroy(ks);
	gzclose(fp);
	return 0;
}

/* main function */
static int usage()
{
	fprintf(stderr, "\n");
	fprintf(stderr, "Usage:   seqtk  \n\n");
	fprintf(stderr, "Command: comp      get the nucleotide composite of FASTA/Q\n");
	fprintf(stderr, "         hety      regional heterozygosity\n");
	fprintf(stderr, "         fq2fa     convert FASTQ to FASTA\n");
	fprintf(stderr, "         subseq    extract subsequences from FASTA/Q\n");
	fprintf(stderr, "         maskseq   mask sequences\n");
	fprintf(stderr, "         mutfa     point mutate FASTA at specified positions\n");
	fprintf(stderr, "         mergefa   merge two FASTA/Q files\n");
	fprintf(stderr, "         randbase  choose a random base from hets\n");
	fprintf(stderr, "         cutN      cut sequence at long N\n");
	fprintf(stderr, "         listhet   extract the position of each het\n");
	fprintf(stderr, "\n");
	return 1;
}

int main(int argc, char *argv[])
{
	if (argc == 1) return usage();
	if (strcmp(argv[1], "comp") == 0) stk_comp(argc-1, argv+1);
	else if (strcmp(argv[1], "hety") == 0) stk_hety(argc-1, argv+1);
	else if (strcmp(argv[1], "fq2fa") == 0) stk_fq2fa(argc-1, argv+1);
	else if (strcmp(argv[1], "subseq") == 0) stk_subseq(argc-1, argv+1);
	else if (strcmp(argv[1], "maskseq") == 0) stk_maskseq(argc-1, argv+1);
	else if (strcmp(argv[1], "mutfa") == 0) stk_mutfa(argc-1, argv+1);
	else if (strcmp(argv[1], "mergefa") == 0) stk_mergefa(argc-1, argv+1);
	else if (strcmp(argv[1], "randbase") == 0) stk_randbase(argc-1, argv+1);
	else if (strcmp(argv[1], "cutN") == 0) stk_cutN(argc-1, argv+1);
	else if (strcmp(argv[1], "listhet") == 0) stk_listhet(argc-1, argv+1);
	else if (strcmp(argv[1], "famask") == 0) stk_famask(argc-1, argv+1);
	else {
		fprintf(stderr, "[main] unrecognized commad '%s'. Abort!\n", argv[1]);
		return 1;
	}
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/soap2sam.pl000077500000000000000000000052101211610345200240570ustar00rootroot00000000000000#!/usr/bin/perl -w

# Contact: lh3
# Version: 0.1.1

use strict;
use warnings;
use Getopt::Std;

&soap2sam;
exit;

sub mating {
  my ($s1, $s2) = @_;
  my $isize = 0;
  if ($s1->[2] ne '*' && $s1->[2] eq $s2->[2]) { # then calculate $isize
	my $x1 = ($s1->[1] & 0x10)? $s1->[3] + length($s1->[9]) : $s1->[3];
	my $x2 = ($s2->[1] & 0x10)? $s2->[3] + length($s2->[9]) : $s2->[3];
	$isize = $x2 - $x1;
  }
  # update mate coordinate
  if ($s2->[2] ne '*') {
	@$s1[6..8] = (($s2->[2] eq $s1->[2])? "=" : $s2->[2], $s2->[3], $isize);
	$s1->[1] |= 0x20 if ($s2->[1] & 0x10);
  } else {
	$s1->[1] |= 0x8;
  }
  if ($s1->[2] ne '*') {
	@$s2[6..8] = (($s1->[2] eq $s2->[2])? "=" : $s1->[2], $s1->[3], -$isize);
	$s2->[1] |= 0x20 if ($s1->[1] & 0x10);
  } else {
	$s2->[1] |= 0x8;
  }
}

sub soap2sam {
  my %opts = ();
  getopts("p", \%opts);
  die("Usage: soap2sam.pl [-p] \n") if (@ARGV == 0 && -t STDIN);
  my $is_paired = defined($opts{p});
  # core loop
  my @s1 = ();
  my @s2 = ();
  my ($s_last, $s_curr) = (\@s1, \@s2);
  while (<>) {
	s/[\177-\377]|[\000-\010]|[\012-\040]//g;
	next if (&soap2sam_aux($_, $s_curr, $is_paired) < 0);
	if (@$s_last != 0 && $s_last->[0] eq $s_curr->[0]) {
	  &mating($s_last, $s_curr);
	  print join("\t", @$s_last), "\n";
	  print join("\t", @$s_curr), "\n";
	  @$s_last = (); @$s_curr = ();
	} else {
	  print join("\t", @$s_last), "\n" if (@$s_last != 0);
	  my $s = $s_last; $s_last = $s_curr; $s_curr = $s;
	}
  }
  print join("\t", @$s_last), "\n" if (@$s_last != 0);
}

sub soap2sam_aux {
  my ($line, $s, $is_paired) = @_;
  chomp($line);
  my @t = split(/\s+/, $line);
  return -1 if (@t < 9 || $line =~ /^\s/ || !$t[0]);
  @$s = ();
  # fix SOAP-2.1.x bugs
  @t = @t[0..2,4..$#t] unless ($t[3] =~ /^\d+$/);
  # read name
  $s->[0] = $t[0];
  $s->[0] =~ s/\/[12]$//g;
  # initial flag (will be updated later)
  $s->[1] = 0;
  $s->[1] |= 1 | 1<<($t[4] eq 'a'? 6 : 7);
  $s->[1] |= 2 if ($is_paired);
  # read & quality
  $s->[9] = $t[1];
  $s->[10] = (length($t[2]) > length($t[1]))? substr($t[2], 0, length($t[1])) : $t[2];
  # cigar
  $s->[5] = length($s->[9]) . "M";
  # coor
  $s->[2] = $t[7]; $s->[3] = $t[8];
  $s->[1] |= 0x10 if ($t[6] eq '-');
  # mapQ
  $s->[4] = $t[3] == 1? 30 : 0;
  # mate coordinate
  $s->[6] = '*'; $s->[7] = $s->[8] = 0;
  # aux
  push(@$s, "NM:i:$t[9]");
  my $md = '';
  if ($t[9]) {
	my @x;
	for (10 .. $#t) {
	  push(@x, sprintf("%.3d,$1", $2)) if ($t[$_] =~ /^([ACGT])->(\d+)/i);
	}
	@x = sort(@x);
	my $a = 0;
	for (@x) {
	  my ($y, $z) = split(",");
	  $md .= (int($y)-$a) . $z;
	  $a += $y - $a + 1;
	}
	$md .= length($t[1]) - $a;
  } else {
	$md = length($t[1]);
  }
  push(@$s, "MD:Z:$md");
  return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/varfilter.py000077500000000000000000000132271211610345200243540ustar00rootroot00000000000000#!/software/bin/python

# Author: lh3, converted to python and modified to add -C option by Aylwyn Scally
#
# About:
#   varfilter.py is a port of Heng's samtools.pl varFilter script into 
#   python, with an additional -C INT option. This option sets a minimum 
#   consensus score, above which the script will output a pileup line 
#   wherever it _could have_ called a variant, even if none is actually 
#   called (i.e. hom-ref positions). This is important if you want to
#   subsequently merge the calls with those for another individual to get a
#   synoptic view of calls at each site. Without this option, and in all 
#   other respects, it behaves like samtools.pl varFilter.
#   
#   Aylwyn Scally as6@sanger.ac.uk


# Filtration code:
#
# C low CNS quality (hom-ref only)
# d low depth
# D high depth
# W too many SNPs in a window (SNP only)
# G close to a high-quality indel (SNP only)
# Q low RMS mapping quality (SNP only)
# g close to another indel with higher quality (indel only)
# s low SNP quality (SNP only)
# i low indel quality (indel only)


import sys
import getopt

def usage():
	print '''usage: varfilter.py [options] [cns-pileup]

Options: -Q INT	minimum RMS mapping quality for SNPs
		 -q INT	minimum RMS mapping quality for gaps
		 -d INT	minimum read depth 
		 -D INT	maximum read depth
		 -S INT	minimum SNP quality
		 -i INT	minimum indel quality
		 -C INT	minimum consensus quality for hom-ref sites

		 -G INT	min indel score for nearby SNP filtering
		 -w INT	SNP within INT bp around a gap to be filtered

		 -W INT	window size for filtering dense SNPs
		 -N INT	max number of SNPs in a window

		 -l INT	window size for filtering adjacent gaps

		 -p print filtered variants'''

def varFilter_aux(first, is_print):
	try:
		if first[1] == 0:
			sys.stdout.write("\t".join(first[4:]) + "\n")
		elif is_print:
			sys.stderr.write("\t".join(["UQdDWGgsiCX"[first[1]]] + first[4:]) + "\n")
	except IOError:
		sys.exit()
 
mindepth = 3
maxdepth = 100
gapgapwin = 30
minsnpmapq = 25
mingapmapq = 10
minindelscore = 25
scorefactor = 100
snpgapwin = 10
densesnpwin = 10
densesnps = 2
printfilt = False
minsnpq = 0
minindelq = 0
mincnsq = 0

try:
	options, args = getopt.gnu_getopt(sys.argv[1:], 'pq:d:D:l:Q:w:W:N:G:S:i:C:', [])
except getopt.GetoptError:
	usage()
	sys.exit(2)
for (oflag, oarg) in options:
	if oflag == '-d': mindepth = int(oarg)
	if oflag == '-D': maxdepth = int(oarg)
	if oflag == '-l': gapgapwin = int(oarg)
	if oflag == '-Q': minsnpmapq = int(oarg)
	if oflag == '-q': mingapmapq = int(oarg)
	if oflag == '-G': minindelscore = int(oarg)
	if oflag == '-s': scorefactor = int(oarg)
	if oflag == '-w': snpgapwin = int(oarg)
	if oflag == '-W': densesnpwin = int(oarg)
	if oflag == '-C': mincnsq = int(oarg)
	if oflag == '-N': densesnps = int(oarg)
	if oflag == '-p': printfilt = True
	if oflag == '-S': minsnpq = int(oarg)
	if oflag == '-i': minindelq = int(oarg)

if len(args) < 1:
	inp = sys.stdin
else:
	inp = open(args[0])

# calculate the window size
max_dist = max(gapgapwin, snpgapwin, densesnpwin)

staging = []
for t in (line.strip().split() for line in inp):
	(flt, score) = (0, -1)
	# non-var sites
	if t[3] == '*/*':
		continue
	is_snp = t[2].upper() != t[3].upper()
	if not (is_snp or mincnsq):
		continue
	# clear the out-of-range elements
	while staging:
		# Still on the same chromosome and the first element's window still affects this position?  
		if staging[0][4] == t[0] and int(staging[0][5]) + staging[0][2] + max_dist >= int(t[1]):
			break
		varFilter_aux(staging.pop(0), printfilt)
	
	# first a simple filter
	if int(t[7]) < mindepth:
		flt = 2
	elif int(t[7]) > maxdepth:
		flt = 3
	if t[2] == '*': # an indel
		if minindelq and minindelq > int(t[5]):
			flt = 8
	elif is_snp:
		if minsnpq and minsnpq> int(t[5]):
			flt = 7
	else:
		if mincnsq and mincnsq > int(t[4]):
			flt = 9

	# site dependent filters
	dlen = 0
	if flt == 0:
		if t[2] == '*': # an indel
			# If deletion, remember the length of the deletion
			(a,b) = t[3].split('/')
			alen = len(a) - 1
			blen = len(b) - 1
			if alen>blen:
				if a[0] == '-': dlen=alen 
			elif b[0] == '-': dlen=blen 

			if int(t[6]) < mingapmapq:
				flt = 1
			# filtering SNPs
			if int(t[5]) >= minindelscore:
				for x in (y for y in staging if y[3]):
					# Is it a SNP and is it outside the SNP filter window?
					if x[0] >= 0 or int(x[5]) + x[2] + snpgapwin < int(t[1]):
						continue
					if x[1] == 0:
						x[1] = 5
			
			# calculate the filtering score (different from indel quality)
			score = int(t[5])
			if t[8] != '*':
				score += scorefactor * int(t[10])
			if t[9] != '*':
				score += scorefactor * int(t[11])
			# check the staging list for indel filtering
			for x in (y for y in staging if y[3]):
			  # Is it a SNP and is it outside the gap filter window
				if x[0] < 0 or int(x[5]) + x[2] + gapgapwin < int(t[1]):
					continue
				if x[0] < score:
					x[1] = 6
				else:
					flt = 6
					break
		else: # a SNP or hom-ref
			if int(t[6]) < minsnpmapq:
				flt = 1
			# check adjacent SNPs
			k = 1
			for x in (y for y in staging if y[3]):
				if x[0] < 0 and int(x[5]) + x[2] + densesnpwin >= int(t[1]) and (x[1] == 0 or x[1] == 4 or x[1] == 5):
					k += 1
			
			# filtering is necessary
			if k > densesnps:
				flt = 4
				for x in (y for y in staging if y[3]):
					if x[0] < 0 and int(x[5]) + x[2] + densesnpwin >= int(t[1]) and x[1] == 0:
						x[1] = 4
			else: # then check gap filter
				for x in (y for y in staging if y[3]):
					if x[0] < 0 or int(x[5]) + x[2] + snpgapwin < int(t[1]):
						continue
					if x[0] >= minindelscore:
						flt = 5
						break
	
	staging.append([score, flt, dlen, is_snp] + t)
  
# output the last few elements in the staging list
while staging:
	varFilter_aux(staging.pop(0), printfilt)
genometools-1.5.1/src/external/samtools-0.1.18/misc/wgsim.c000066400000000000000000000340731211610345200232750ustar00rootroot00000000000000/* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).
                 2011 Heng Li 

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* This program is separated from maq's read simulator with Colin
 * Hercus' modification to allow longer indels. */

#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include 
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)

#define PACKAGE_VERSION "0.3.0"

const uint8_t nst_nt4_table[256] = {
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 5 /*'-'*/, 4, 4,
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
};

/* Simple normal random number generator, copied from genran.c */

double ran_normal()
{ 
	static int iset = 0; 
	static double gset; 
	double fac, rsq, v1, v2; 
	if (iset == 0) {
		do { 
			v1 = 2.0 * drand48() - 1.0;
			v2 = 2.0 * drand48() - 1.0; 
			rsq = v1 * v1 + v2 * v2;
		} while (rsq >= 1.0 || rsq == 0.0);
		fac = sqrt(-2.0 * log(rsq) / rsq); 
		gset = v1 * fac; 
		iset = 1;
		return v2 * fac;
	} else {
		iset = 0;
		return gset;
	}
}

/* wgsim */

enum muttype_t {NOCHANGE = 0, INSERT = 0x1000, SUBSTITUTE = 0xe000, DELETE = 0xf000};
typedef unsigned short mut_t;
static mut_t mutmsk = (mut_t)0xf000;

typedef struct {
	int l, m; /* length and maximum buffer size */
	mut_t *s; /* sequence */
} mutseq_t;

static double ERR_RATE = 0.02;
static double MUT_RATE = 0.001;
static double INDEL_FRAC = 0.15;
static double INDEL_EXTEND = 0.3;
static double MAX_N_RATIO = 0.1;

void wgsim_mut_diref(const kseq_t *ks, int is_hap, mutseq_t *hap1, mutseq_t *hap2)
{
	int i, deleting = 0;
	mutseq_t *ret[2];

	ret[0] = hap1; ret[1] = hap2;
	ret[0]->l = ks->seq.l; ret[1]->l = ks->seq.l;
	ret[0]->m = ks->seq.m; ret[1]->m = ks->seq.m;
	ret[0]->s = (mut_t *)calloc(ks->seq.m, sizeof(mut_t));
	ret[1]->s = (mut_t *)calloc(ks->seq.m, sizeof(mut_t));
	for (i = 0; i != ks->seq.l; ++i) {
		int c;
		c = ret[0]->s[i] = ret[1]->s[i] = (mut_t)nst_nt4_table[(int)ks->seq.s[i]];
        if (deleting) {
            if (drand48() < INDEL_EXTEND) {
                if (deleting & 1) ret[0]->s[i] |= DELETE;
                if (deleting & 2) ret[1]->s[i] |= DELETE;
                continue;
            } else deleting = 0;
        }
		if (c < 4 && drand48() < MUT_RATE) { // mutation
			if (drand48() >= INDEL_FRAC) { // substitution
				double r = drand48();
				c = (c + (int)(r * 3.0 + 1)) & 3;
				if (is_hap || drand48() < 0.333333) { // hom
					ret[0]->s[i] = ret[1]->s[i] = SUBSTITUTE|c;
				} else { // het
					ret[drand48()<0.5?0:1]->s[i] = SUBSTITUTE|c;
				}
			} else { // indel
				if (drand48() < 0.5) { // deletion
					if (is_hap || drand48() < 0.333333) { // hom-del
						ret[0]->s[i] = ret[1]->s[i] = DELETE;
                        deleting = 3;
					} else { // het-del
                        deleting = drand48()<0.5?1:2;
						ret[deleting-1]->s[i] = DELETE;
					}
				} else { // insertion
                    int num_ins = 0, ins = 0;
                    do {
                        num_ins++;
                        ins = (ins << 2) | (int)(drand48() * 4.0);
                    } while (num_ins < 4 && drand48() < INDEL_EXTEND);

					if (is_hap || drand48() < 0.333333) { // hom-ins
						ret[0]->s[i] = ret[1]->s[i] = (num_ins << 12) | (ins << 4) | c;
					} else { // het-ins
						ret[drand48()<0.5?0:1]->s[i] = (num_ins << 12) | (ins << 4) | c;
					}
				}
			}
		}
	}
}
void wgsim_print_mutref(const char *name, const kseq_t *ks, mutseq_t *hap1, mutseq_t *hap2)
{
	int i;
	for (i = 0; i != ks->seq.l; ++i) {
		int c[3];
		c[0] = nst_nt4_table[(int)ks->seq.s[i]];
		c[1] = hap1->s[i]; c[2] = hap2->s[i];
		if (c[0] >= 4) continue;
		if ((c[1] & mutmsk) != NOCHANGE || (c[2] & mutmsk) != NOCHANGE) {
			printf("%s\t%d\t", name, i+1);
			if (c[1] == c[2]) { // hom
				if ((c[1]&mutmsk) == SUBSTITUTE) { // substitution
					printf("%c\t%c\t-\n", "ACGTN"[c[0]], "ACGTN"[c[1]&0xf]);
				} else if ((c[1]&mutmsk) == DELETE) { // del
					printf("%c\t-\t-\n", "ACGTN"[c[0]]);
				} else if (((c[1] & mutmsk) >> 12) <= 5) { // ins
					printf("-\t");
                    int n = (c[1]&mutmsk) >> 12, ins = c[1] >> 4;
                    while (n > 0) {
                        putchar("ACGTN"[ins & 0x3]);
						ins >>= 2;
                        n--;
                    }
                    printf("\t-\n");
				}  else assert(0);
			} else { // het
				if ((c[1]&mutmsk) == SUBSTITUTE || (c[2]&mutmsk) == SUBSTITUTE) { // substitution
					printf("%c\t%c\t+\n", "ACGTN"[c[0]], "XACMGRSVTWYHKDBN"[1<<(c[1]&0x3)|1<<(c[2]&0x3)]);
				} else if ((c[1]&mutmsk) == DELETE) {
					printf("%c\t-\t+\n", "ACGTN"[c[0]]);
				} else if ((c[2]&mutmsk) == DELETE) {
					printf("%c\t-\t+\n", "ACGTN"[c[0]]);
				} else if (((c[1] & mutmsk) >> 12) <= 4) { // ins1
					printf("-\t");
                    int n = (c[1]&mutmsk) >> 12, ins = c[1] >> 4;
                    while (n > 0) {
                        putchar("ACGTN"[ins & 0x3]);
						ins >>= 2;
                        n--;
                    }
                    printf("\t+\n");
				} else if (((c[2] & mutmsk) >> 12) <= 5) { // ins2
					printf("-\t");
                    int n = (c[2]&mutmsk) >> 12, ins = c[2] >> 4;
                    while (n > 0) {
                        putchar("ACGTN"[ins & 0x3]);
                        ins >>= 2;
                        n--;
                    }
                    printf("\t+\n");
				} else assert(0);
			}
		}
	}
}

void wgsim_core(FILE *fpout1, FILE *fpout2, const char *fn, int is_hap, uint64_t N, int dist, int std_dev, int size_l, int size_r)
{
	kseq_t *ks;
    mutseq_t rseq[2];
	gzFile fp_fa;
	uint64_t tot_len, ii;
	int i, l, n_ref;
	char *qstr;
	int size[2], Q, max_size;
	uint8_t *tmp_seq[2];
    mut_t *target;

	l = size_l > size_r? size_l : size_r;
	qstr = (char*)calloc(l+1, 1);
	tmp_seq[0] = (uint8_t*)calloc(l+2, 1);
	tmp_seq[1] = (uint8_t*)calloc(l+2, 1);
	size[0] = size_l; size[1] = size_r;
	max_size = size_l > size_r? size_l : size_r;

	Q = (ERR_RATE == 0.0)? 'I' : (int)(-10.0 * log(ERR_RATE) / log(10.0) + 0.499) + 33;

	fp_fa = gzopen(fn, "r");
	ks = kseq_init(fp_fa);
	tot_len = n_ref = 0;
	fprintf(stderr, "[%s] calculating the total length of the reference sequence...\n", __func__);
	while ((l = kseq_read(ks)) >= 0) {
		tot_len += l;
		++n_ref;
	}
	fprintf(stderr, "[%s] %d sequences, total length: %llu\n", __func__, n_ref, (long long)tot_len);
	kseq_destroy(ks);
	gzclose(fp_fa);

	fp_fa = gzopen(fn, "r");
	ks = kseq_init(fp_fa);
	while ((l = kseq_read(ks)) >= 0) {
		uint64_t n_pairs = (uint64_t)((long double)l / tot_len * N + 0.5);
		if (l < dist + 3 * std_dev) {
			fprintf(stderr, "[%s] skip sequence '%s' as it is shorter than %d!\n", __func__, ks->name.s, dist + 3 * std_dev);
			continue;
		}

		// generate mutations and print them out
		wgsim_mut_diref(ks, is_hap, rseq, rseq+1);
		wgsim_print_mutref(ks->name.s, ks, rseq, rseq+1);

		for (ii = 0; ii != n_pairs; ++ii) { // the core loop
			double ran;
			int d, pos, s[2], is_flip = 0;
			int n_sub[2], n_indel[2], n_err[2], ext_coor[2], j, k;
			FILE *fpo[2];

			do { // avoid boundary failure
				ran = ran_normal();
				ran = ran * std_dev + dist;
				d = (int)(ran + 0.5);
				d = d > max_size? d : max_size;
				pos = (int)((l - d + 1) * drand48());
			} while (pos < 0 || pos >= ks->seq.l || pos + d - 1 >= ks->seq.l);

			// flip or not
			if (drand48() < 0.5) {
				fpo[0] = fpout1; fpo[1] = fpout2;
				s[0] = size[0]; s[1] = size[1];
			} else {
				fpo[1] = fpout1; fpo[0] = fpout2;
				s[1] = size[0]; s[0] = size[1];
				is_flip = 1;
			}

			// generate the read sequences
			target = rseq[drand48()<0.5?0:1].s; // haplotype from which the reads are generated
			n_sub[0] = n_sub[1] = n_indel[0] = n_indel[1] = n_err[0] = n_err[1] = 0;

#define __gen_read(x, start, iter) do {									\
				for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < ks->seq.l && k < s[x]; iter) {	\
					int c = target[i], mut_type = c & mutmsk;			\
					if (ext_coor[x] < 0) {								\
						if (mut_type != NOCHANGE && mut_type != SUBSTITUTE) continue; \
						ext_coor[x] = i;								\
					}													\
					if (mut_type == DELETE) ++n_indel[x];				\
					else if (mut_type == NOCHANGE || mut_type == SUBSTITUTE) { \
						tmp_seq[x][k++] = c & 0xf;						\
						if (mut_type == SUBSTITUTE) ++n_sub[x];			\
					} else {											\
						int n, ins;										\
						++n_indel[x];									\
						tmp_seq[x][k++] = c & 0xf;						\
						for (n = mut_type>>12, ins = c>>4; n > 0 && k < s[x]; --n, ins >>= 2) \
							tmp_seq[x][k++] = ins & 0x3;				\
					}													\
				}														\
				if (k != s[x]) ext_coor[x] = -10;						\
			} while (0)

			__gen_read(0, pos, ++i);
			__gen_read(1, pos + d - 1, --i);
			for (k = 0; k < s[1]; ++k) tmp_seq[1][k] = tmp_seq[1][k] < 4? 3 - tmp_seq[1][k] : 4; // complement
			if (ext_coor[0] < 0 || ext_coor[1] < 0) { // fail to generate the read(s)
				--ii;
				continue;
			}

			// generate sequencing errors
			for (j = 0; j < 2; ++j) {
				int n_n = 0;
				for (i = 0; i < s[j]; ++i) {
					int c = tmp_seq[j][i];
					if (c >= 4) { // actually c should be never larger than 4 if everything is correct
						c = 4;
						++n_n;
					} else if (drand48() < ERR_RATE) {
						// c = (c + (int)(drand48() * 3.0 + 1)) & 3; // random sequencing errors
						c = (c + 1) & 3; // recurrent sequencing errors
						++n_err[j];
					}
					tmp_seq[j][i] = c;
				}
				if ((double)n_n / s[j] > MAX_N_RATIO) break;
			}
			if (j < 2) { // too many ambiguous bases on one of the reads
				--ii;
				continue;
			}

			// print
			for (j = 0; j < 2; ++j) {
				for (i = 0; i < s[j]; ++i) qstr[i] = Q;
				qstr[i] = 0;
				fprintf(fpo[j], "@%s_%u_%u_%d:%d:%d_%d:%d:%d_%llx/%d\n", ks->name.s, ext_coor[0]+1, ext_coor[1]+1,
						n_err[0], n_sub[0], n_indel[0], n_err[1], n_sub[1], n_indel[1],
						(long long)ii, j==0? is_flip+1 : 2-is_flip);
				for (i = 0; i < s[j]; ++i)
					fputc("ACGTN"[(int)tmp_seq[j][i]], fpo[j]);
				fprintf(fpo[j], "\n+\n%s\n", qstr);
			}
		}
		free(rseq[0].s); free(rseq[1].s);
	}
	kseq_destroy(ks);
	gzclose(fp_fa);
	free(qstr);
	free(tmp_seq[0]); free(tmp_seq[1]);
}

static int simu_usage()
{
	fprintf(stderr, "\n");
	fprintf(stderr, "Program: wgsim (short read simulator)\n");
	fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
	fprintf(stderr, "Contact: Heng Li \n\n");
	fprintf(stderr, "Usage:   wgsim [options]   \n\n");
	fprintf(stderr, "Options: -e FLOAT      base error rate [%.3f]\n", ERR_RATE);
	fprintf(stderr, "         -d INT        outer distance between the two ends [500]\n");
	fprintf(stderr, "         -s INT        standard deviation [50]\n");
	fprintf(stderr, "         -N INT        number of read pairs [1000000]\n");
	fprintf(stderr, "         -1 INT        length of the first read [70]\n");
	fprintf(stderr, "         -2 INT        length of the second read [70]\n");
	fprintf(stderr, "         -r FLOAT      rate of mutations [%.4f]\n", MUT_RATE);
	fprintf(stderr, "         -R FLOAT      fraction of indels [%.2f]\n", INDEL_FRAC);
	fprintf(stderr, "         -X FLOAT      probability an indel is extended [%.2f]\n", INDEL_EXTEND);
	fprintf(stderr, "         -S INT        seed for random generator [-1]\n");
	fprintf(stderr, "         -h            haplotype mode\n");
	fprintf(stderr, "\n");
	return 1;
}

int main(int argc, char *argv[])
{
	int64_t N;
	int dist, std_dev, c, size_l, size_r, is_hap = 0;
	FILE *fpout1, *fpout2;
	int seed = -1;

	N = 1000000; dist = 500; std_dev = 50;
	size_l = size_r = 70;
	while ((c = getopt(argc, argv, "e:d:s:N:1:2:r:R:hX:S:")) >= 0) {
		switch (c) {
		case 'd': dist = atoi(optarg); break;
		case 's': std_dev = atoi(optarg); break;
		case 'N': N = atoi(optarg); break;
		case '1': size_l = atoi(optarg); break;
		case '2': size_r = atoi(optarg); break;
		case 'e': ERR_RATE = atof(optarg); break;
		case 'r': MUT_RATE = atof(optarg); break;
		case 'R': INDEL_FRAC = atof(optarg); break;
		case 'X': INDEL_EXTEND = atof(optarg); break;
		case 'S': seed = atoi(optarg); break;
		case 'h': is_hap = 1; break;
		}
	}
	if (argc - optind < 3) return simu_usage();
	fpout1 = fopen(argv[optind+1], "w");
	fpout2 = fopen(argv[optind+2], "w");
	if (!fpout1 || !fpout2) {
		fprintf(stderr, "[wgsim] file open error\n");
		return 1;
	}
	srand48(seed > 0? seed : time(0));
	wgsim_core(fpout1, fpout2, argv[optind], is_hap, N, dist, std_dev, size_l, size_r);

	fclose(fpout1); fclose(fpout2);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/wgsim_eval.pl000077500000000000000000000052511211610345200244740ustar00rootroot00000000000000#!/usr/bin/perl -w

# Contact: lh3
# Version: 0.1.5

use strict;
use warnings;
use Getopt::Std;

&wgsim_eval;
exit;

sub wgsim_eval {
  my %opts = (g=>5);
  getopts('pcag:', \%opts);
  die("Usage: wgsim_eval.pl [-pca] [-g $opts{g}] \n") if (@ARGV == 0 && -t STDIN);
  my (@c0, @c1, %fnfp);
  my ($max_q, $flag) = (0, 0);
  my $gap = $opts{g};
  $flag |= 1 if (defined $opts{p});
  $flag |= 2 if (defined $opts{c});
  while (<>) {
	next if (/^\@/);
	my @t = split("\t");
	next if (@t < 11);
	my $line = $_;
	my ($q, $is_correct, $chr, $left, $rght) = (int($t[4]/10), 1, $t[2], $t[3], $t[3]);
	$max_q = $q if ($q > $max_q);
	# right coordinate
	$_ = $t[5]; s/(\d+)[MDN]/$rght+=$1,'x'/eg;
	--$rght;
	# correct for soft clipping
	my ($left0, $rght0) = ($left, $rght);
	$left -= $1 if (/^(\d+)[SH]/);
	$rght += $1 if (/(\d+)[SH]$/);
	$left0 -= $1 if (/(\d+)[SH]$/);
	$rght0 += $1 if (/^(\d+)[SH]/);
	# skip unmapped reads
	next if (($t[1]&0x4) || $chr eq '*');
	# parse read name and check
	if ($t[0] =~ /^(\S+)_(\d+)_(\d+)_/) {
	  if ($1 ne $chr) { # different chr
		$is_correct = 0;
	  } else {
		if ($flag & 2) {
		  if (($t[1]&0x40) && !($t[1]&0x10)) { # F3, forward
			$is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
		  } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse
			$is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap);
		  } elsif (($t[1]&0x80) && !($t[1]&0x10)) { # R3, forward
			$is_correct = 0 if (abs($3 - $left) > $gap && abs($3 - $left0) > $gap);
		  } else { # R3, reverse
			$is_correct = 0 if (abs($2 - $rght) > $gap && abs($3 - $rght0) > $gap);
		  }
		} else {
		  if ($t[1] & 0x10) { # reverse
			$is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap); # in case of indels that are close to the end of a reads
		  } else {
			$is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
		  }
		}
	  }
	} else {
	  warn("[wgsim_eval] read '$t[0]' was not generated by wgsim?\n");
	  next;
	}
	++$c0[$q];
	++$c1[$q] unless ($is_correct);
	@{$fnfp{$t[4]}} = (0, 0) unless (defined $fnfp{$t[4]});
	++$fnfp{$t[4]}[0];
	++$fnfp{$t[4]}[1] unless ($is_correct);
	print STDERR $line if (($flag&1) && !$is_correct && $q > 0);
  }
  # print
  my ($cc0, $cc1) = (0, 0);
  if (!defined($opts{a})) {
	for (my $i = $max_q; $i >= 0; --$i) {
	  $c0[$i] = 0 unless (defined $c0[$i]);
	  $c1[$i] = 0 unless (defined $c1[$i]);
	  $cc0 += $c0[$i]; $cc1 += $c1[$i];
	  printf("%.2dx %12d / %-12d  %12d  %.3e\n", $i, $c1[$i], $c0[$i], $cc0, $cc1/$cc0) if ($cc0);
	}
  } else {
	for (reverse(sort {$a<=>$b} (keys %fnfp))) {
	  next if ($_ == 0);
	  $cc0 += $fnfp{$_}[0];
	  $cc1 += $fnfp{$_}[1];
	  print join("\t", $_, $cc0, $cc1), "\n";
	}
  }
}
genometools-1.5.1/src/external/samtools-0.1.18/misc/zoom2sam.pl000077500000000000000000000045351211610345200241120ustar00rootroot00000000000000#!/usr/bin/perl -w

# Contact: lh3
# Version: 0.1.0

use strict;
use warnings;
use Getopt::Std;

&zoom2sam;
exit;

sub mating {
  my ($s1, $s2) = @_;
  my $isize = 0;
  if ($s1->[2] ne '*' && $s1->[2] eq $s2->[2]) { # then calculate $isize
	my $x1 = ($s1->[1] & 0x10)? $s1->[3] + length($s1->[9]) : $s1->[3];
	my $x2 = ($s2->[1] & 0x10)? $s2->[3] + length($s2->[9]) : $s2->[3];
	$isize = $x2 - $x1;
  }
  # update mate coordinate
  if ($s2->[2] ne '*') {
	@$s1[6..8] = (($s2->[2] eq $s1->[2])? "=" : $s2->[2], $s2->[3], $isize);
	$s1->[1] |= 0x20 if ($s2->[1] & 0x10);
  } else {
	$s1->[1] |= 0x8;
  }
  if ($s1->[2] ne '*') {
	@$s2[6..8] = (($s1->[2] eq $s2->[2])? "=" : $s1->[2], $s1->[3], -$isize);
	$s2->[1] |= 0x20 if ($s1->[1] & 0x10);
  } else {
	$s2->[1] |= 0x8;
  }
}

sub zoom2sam {
  my %opts = ();
  getopts("p", \%opts);
  die("Usage: zoom2sam.pl [-p]  
Warnings: This script only supports the default Illumina outputs.\n") if (@ARGV < 2);
  my $is_paired = defined($opts{p});
  my $len = shift(@ARGV);
  # core loop
  my @s1 = ();
  my @s2 = ();
  my ($s_last, $s_curr) = (\@s1, \@s2);
  while (<>) {
	&zoom2sam_aux($_, $s_curr, $is_paired, $len);
	if (@$s_last != 0 && $s_last->[0] eq $s_curr->[0]) {
	  &mating($s_last, $s_curr);
	  print join("\t", @$s_last), "\n";
	  print join("\t", @$s_curr), "\n";
	  @$s_last = (); @$s_curr = ();
	} else {
	  print join("\t", @$s_last), "\n" if (@$s_last != 0);
	  my $s = $s_last; $s_last = $s_curr; $s_curr = $s;
	}
  }
  print join("\t", @$s_last), "\n" if (@$s_last != 0);
}

sub zoom2sam_aux {
  my ($line, $s, $is_paired, $len) = @_;
  chomp($line);
  my @t = split("\t", $line);
  @$s = ();
  # read name
  $s->[0] = $t[0];
  # initial flag (will be updated later)
  $s->[1] = 0;
  $s->[1] |= 1 | 1<<6 if ($s->[0] =~ /_F$/);
  $s->[1] |= 1 | 1<<7 if ($s->[0] =~ /_R$/);
  $s->[1] |= 2 if ($is_paired);
  # read & quality
  $s->[9] = "*"; $s->[10] = "*";
  # cigar
  $s->[5] = $len . "M";
  # coor
  my @s = split(/\s+/, $t[1]);
  $s->[2] = $s[0];
  $t[1] =~ /:(\d+)$/;
  $s->[3] = $1 + 1;
  if ($s->[0] =~ /_[FR]$/) {
	my $u = ($s->[0] =~ /_F$/)? 1 : 0;
	my $w = ($t[2] eq '+')? 1 : 0;
	$s->[1] |= 0x10 if ($u ^ $w);
	$s->[0] =~ s/_[FR]$//;
  } else {
	$s->[1] |= 0x10 if ($t[2] eq '-');
  }
  # mapQ
  $s->[4] = 30;
  # mate coordinate
  $s->[6] = '*'; $s->[7] = $s->[8] = 0;
  # aux
  push(@$s, "NM:i:$t[3]");
}
genometools-1.5.1/src/external/samtools-0.1.18/phase.c000066400000000000000000000505231211610345200223120ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include 
#include "bam.h"
#include "errmod.h"

#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)

#define MAX_VARS 256
#define FLIP_PENALTY 2
#define FLIP_THRES 4
#define MASK_THRES 3

#define FLAG_FIX_CHIMERA 0x1
#define FLAG_LIST_EXCL   0x4
#define FLAG_DROP_AMBI   0x8

typedef struct {
	// configurations, initialized in the main function
	int flag, k, min_baseQ, min_varLOD, max_depth;
	// other global variables
	int vpos_shift;
	bamFile fp;
	char *pre;
	bamFile out[3];
	// alignment queue
	int n, m;
	bam1_t **b;
} phaseg_t;

typedef struct {
	int8_t seq[MAX_VARS]; // TODO: change to dynamic memory allocation!
	int vpos, beg, end;
	uint32_t vlen:16, single:1, flip:1, phase:1, phased:1, ambig:1;
	uint32_t in:16, out:16; // in-phase and out-phase
} frag_t, *frag_p;

#define rseq_lt(a,b) ((a)->vpos < (b)->vpos)

#include "khash.h"
KHASH_SET_INIT_INT64(set64)
KHASH_MAP_INIT_INT64(64, frag_t)

typedef khash_t(64) nseq_t;

#include "ksort.h"
KSORT_INIT(rseq, frag_p, rseq_lt)

static char nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };

static inline uint64_t X31_hash_string(const char *s)
{
	uint64_t h = *s;
	if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
	return h;
}

static void count1(int l, const uint8_t *seq, int *cnt)
{
	int i, j, n_ambi;
	uint32_t z, x;
	if (seq[l-1] == 0) return; // do nothing is the last base is ambiguous
	for (i = n_ambi = 0; i < l; ++i) // collect ambiguous bases
		if (seq[i] == 0) ++n_ambi;
	if (l - n_ambi <= 1) return; // only one SNP
	for (x = 0; x < 1u<>j&1;
				++j;
			}
			z = z<<1 | c;
		}
		++cnt[z];
	}
}

static int **count_all(int l, int vpos, nseq_t *hash)
{
	khint_t k;
	int i, j, **cnt;
	uint8_t *seq;
	seq = calloc(l, 1);
	cnt = calloc(vpos, sizeof(void*));
	for (i = 0; i < vpos; ++i) cnt[i] = calloc(1<vpos >= vpos || f->single) continue; // out of region; or singleton
			if (f->vlen == 1) { // such reads should be flagged as deleted previously if everything is right
				f->single = 1;
				continue;
			}
			for (j = 1; j < f->vlen; ++j) {
				for (i = 0; i < l; ++i)
					seq[i] = j < l - 1 - i? 0 : f->seq[j - (l - 1 - i)];
				count1(l, seq, cnt[f->vpos + j]);
			}
		}
	}
	free(seq);
	return cnt;
}

// phasing
static int8_t *dynaprog(int l, int vpos, int **w)
{
	int *f[2], *curr, *prev, max, i;
	int8_t **b, *h = 0;
	uint32_t x, z = 1u<<(l-1), mask = (1u<>1; y1 = xc>>1;
			c0 = prev[y0] + wi[x] + wi[xc];
			c1 = prev[y1] + wi[x] + wi[xc];
			if (c0 > c1) bi[x] = 0, curr[x] = c0;
			else bi[x] = 1, curr[x] = c1;
		}
		tmp = prev; prev = curr; curr = tmp; // swap
	}
	{ // backtrack
		uint32_t max_x = 0;
		int which = 0;
		h = calloc(vpos, 1);
		for (x = 0, max = 0, max_x = 0; x < z; ++x)
			if (prev[x] > max) max = prev[x], max_x = x;
		for (i = vpos - 1, x = max_x; i >= 0; --i) {
			h[i] = which? (~x&1) : (x&1);
			which = b[i][x]? !which : which;
			x = b[i][x]? (~x&mask)>>1 : x>>1;
		}
	}
	// free
	for (i = 0; i < vpos; ++i) free(b[i]);
	free(f[0]); free(f[1]); free(b);
	return h;
}

// phase each fragment
static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip)
{
	khint_t k;
	uint64_t *pcnt;
	uint32_t *left, *rght, max;
	left = rght = 0; max = 0;
	pcnt = calloc(vpos, 8);
	for (k = 0; k < kh_end(hash); ++k) {
		if (kh_exist(hash, k)) {
			int i, c[2];
			frag_t *f = &kh_val(hash, k);
			if (f->vpos >= vpos) continue;
			// get the phase
			c[0] = c[1] = 0;
			for (i = 0; i < f->vlen; ++i) {
				if (f->seq[i] == 0) continue;
				++c[f->seq[i] == path[f->vpos + i] + 1? 0 : 1];
			}
			f->phase = c[0] > c[1]? 0 : 1;
			f->in = c[f->phase]; f->out = c[1 - f->phase];
			f->phased = f->in == f->out? 0 : 1;
			f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0;
			// fix chimera
			f->flip = 0;
			if (flip && c[0] >= 3 && c[1] >= 3) {
				int sum[2], m, mi, md;
				if (f->vlen > max) { // enlarge the array
					max = f->vlen;
					kroundup32(max);
					left = realloc(left, max * 4);
					rght = realloc(rght, max * 4);
				}
				for (i = 0, sum[0] = sum[1] = 0; i < f->vlen; ++i) { // get left counts
					if (f->seq[i]) {
						int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
						++sum[c == path[f->vpos + i]? 0 : 1];
					}
					left[i] = sum[1]<<16 | sum[0];
				}
				for (i = f->vlen - 1, sum[0] = sum[1] = 0; i >= 0; --i) { // get right counts
					if (f->seq[i]) {
						int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
						++sum[c == path[f->vpos + i]? 0 : 1];
					}
					rght[i] = sum[1]<<16 | sum[0];
				}
				// find the best flip point
				for (i = m = 0, mi = -1, md = -1; i < f->vlen - 1; ++i) {
					int a[2];
					a[0] = (left[i]&0xffff) + (rght[i+1]>>16&0xffff) - (rght[i+1]&0xffff) * FLIP_PENALTY;
					a[1] = (left[i]>>16&0xffff) + (rght[i+1]&0xffff) - (rght[i+1]>>16&0xffff) * FLIP_PENALTY;
					if (a[0] > a[1]) {
						if (a[0] > m) m = a[0], md = 0, mi = i;
					} else {
						if (a[1] > m) m = a[1], md = 1, mi = i;
					}
				}
				if (m - c[0] >= FLIP_THRES && m - c[1] >= FLIP_THRES) { // then flip
					f->flip = 1;
					if (md == 0) { // flip the tail
						for (i = mi + 1; i < f->vlen; ++i)
							if (f->seq[i] == 1) f->seq[i] = 2;
							else if (f->seq[i] == 2) f->seq[i] = 1;
					} else { // flip the head
						for (i = 0; i <= mi; ++i)
							if (f->seq[i] == 1) f->seq[i] = 2;
							else if (f->seq[i] == 2) f->seq[i] = 1;
					}
				}
			}
			// update pcnt[]
			if (!f->single) {
				for (i = 0; i < f->vlen; ++i) {
					int c;
					if (f->seq[i] == 0) continue;
					c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
					if (c == path[f->vpos + i]) {
						if (f->phase == 0) ++pcnt[f->vpos + i];
						else pcnt[f->vpos + i] += 1ull<<32;
					} else {
						if (f->phase == 0) pcnt[f->vpos + i] += 1<<16;
						else pcnt[f->vpos + i] += 1ull<<48;
					}
				}
			}
		}
	}
	free(left); free(rght);
	return pcnt;
}

static uint64_t *genmask(int vpos, const uint64_t *pcnt, int *_n)
{
	int i, max = 0, max_i = -1, m = 0, n = 0, beg = 0, score = 0;
	uint64_t *list = 0;
	for (i = 0; i < vpos; ++i) {
		uint64_t x = pcnt[i];
		int c[4], pre = score, s;
		c[0] = x&0xffff; c[1] = x>>16&0xffff; c[2] = x>>32&0xffff; c[3] = x>>48&0xffff;
		s = (c[1] + c[3] == 0)? -(c[0] + c[2]) : (c[1] + c[3] - 1);
		if (c[3] > c[2]) s += c[3] - c[2];
		if (c[1] > c[0]) s += c[1] - c[0];
		score += s;
		if (score < 0) score = 0;
		if (pre == 0 && score > 0) beg = i; // change from zero to non-zero
		if ((i == vpos - 1 || score == 0) && max >= MASK_THRES) {
			if (n == m) {
				m = m? m<<1 : 4;
				list = realloc(list, m * 8);
			}
			list[n++] = (uint64_t)beg<<32 | max_i;
			i = max_i; // reset i to max_i
			score = 0;
		} else if (score > max) max = score, max_i = i;
		if (score == 0) max = 0;
	}
	*_n = n;
	return list;
}

// trim heading and tailing ambiguous bases; mark deleted and remove sequence
static int clean_seqs(int vpos, nseq_t *hash)
{
	khint_t k;
	int ret = 0;
	for (k = 0; k < kh_end(hash); ++k) {
		if (kh_exist(hash, k)) {
			frag_t *f = &kh_val(hash, k);
			int beg, end, i;
			if (f->vpos >= vpos) {
				ret = 1;
				continue;
			}
			for (i = 0; i < f->vlen; ++i)
				if (f->seq[i] != 0) break;
			beg = i;
			for (i = f->vlen - 1; i >= 0; --i)
				if (f->seq[i] != 0) break;
			end = i + 1;
			if (end - beg <= 0) kh_del(64, hash, k);
			else {
				if (beg != 0) memmove(f->seq, f->seq + beg, end - beg);
				f->vpos += beg; f->vlen = end - beg;
				f->single = f->vlen == 1? 1 : 0;
			}
		}
	}
	return ret;
}

static void dump_aln(phaseg_t *g, int min_pos, const nseq_t *hash)
{
	int i, is_flip, drop_ambi;
	drop_ambi = g->flag & FLAG_DROP_AMBI;
	is_flip = (drand48() < 0.5);
	for (i = 0; i < g->n; ++i) {
		int end, which;
		uint64_t key;
		khint_t k;
		bam1_t *b = g->b[i];
		key = X31_hash_string(bam1_qname(b));
		end = bam_calend(&b->core, bam1_cigar(b));
		if (end > min_pos) break;
		k = kh_get(64, hash, key);
		if (k == kh_end(hash)) which = 3;
		else {
			frag_t *f = &kh_val(hash, k);
			if (f->ambig) which = drop_ambi? 2 : 3;
			else if (f->phased && f->flip) which = 2;
			else if (f->phased == 0) which = 3;
			else { // phased and not flipped
				char c = 'Y';
				which = f->phase;
				bam_aux_append(b, "ZP", 'A', 1, (uint8_t*)&c);
			}
			if (which < 2 && is_flip) which = 1 - which; // increase the randomness
		}
		if (which == 3) which = (drand48() < 0.5);
		bam_write1(g->out[which], b);
		bam_destroy1(b);
		g->b[i] = 0;
	}
	memmove(g->b, g->b + i, (g->n - i) * sizeof(void*));
	g->n -= i;
}

static int phase(phaseg_t *g, const char *chr, int vpos, uint64_t *cns, nseq_t *hash)
{
	int i, j, n_seqs = kh_size(hash), n_masked = 0, min_pos;
	khint_t k;
	frag_t **seqs;
	int8_t *path, *sitemask;
	uint64_t *pcnt, *regmask;

	if (vpos == 0) return 0;
	i = clean_seqs(vpos, hash); // i is true if hash has an element with its vpos >= vpos
	min_pos = i? cns[vpos]>>32 : 0x7fffffff;
	if (vpos == 1) {
		printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1);
		printf("M0\t%s\t%d\t%d\t%c\t%c\t%d\t0\t0\t0\t0\n//\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1,
			"ACGTX"[cns[0]&3], "ACGTX"[cns[0]>>16&3], g->vpos_shift + 1);
		for (k = 0; k < kh_end(hash); ++k) {
			if (kh_exist(hash, k)) {
				frag_t *f = &kh_val(hash, k);
				if (f->vpos) continue;
				f->flip = 0;
				if (f->seq[0] == 0) f->phased = 0;
				else f->phased = 1, f->phase = f->seq[0] - 1;
			}
		}
		dump_aln(g, min_pos, hash);
		++g->vpos_shift;
		return 1;
	}
	{ // phase
		int **cnt;
		uint64_t *mask;
		printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[vpos-1]>>32) + 1);
		sitemask = calloc(vpos, 1);
		cnt = count_all(g->k, vpos, hash);
		path = dynaprog(g->k, vpos, cnt);
		for (i = 0; i < vpos; ++i) free(cnt[i]);
		free(cnt);
		pcnt = fragphase(vpos, path, hash, 0); // do not fix chimeras when masking
		mask = genmask(vpos, pcnt, &n_masked);
		regmask = calloc(n_masked, 8);
		for (i = 0; i < n_masked; ++i) {
			regmask[i] = cns[mask[i]>>32]>>32<<32 | cns[(uint32_t)mask[i]]>>32;
			for (j = mask[i]>>32; j <= (int32_t)mask[i]; ++j)
				sitemask[j] = 1;
		}
		free(mask);
		if (g->flag & FLAG_FIX_CHIMERA) {
			free(pcnt);
			pcnt = fragphase(vpos, path, hash, 1);
		}
	}
	for (i = 0; i < n_masked; ++i)
		printf("FL\t%s\t%d\t%d\n", chr, (int)(regmask[i]>>32) + 1, (int)regmask[i] + 1);
	for (i = 0; i < vpos; ++i) {
		uint64_t x = pcnt[i];
		int8_t c[2];
		c[0] = (cns[i]&0xffff)>>2 == 0? 4 : (cns[i]&3);
		c[1] = (cns[i]>>16&0xffff)>>2 == 0? 4 : (cns[i]>>16&3);
		printf("M%d\t%s\t%d\t%d\t%c\t%c\t%d\t%d\t%d\t%d\t%d\n", sitemask[i]+1, chr, (int)(cns[0]>>32) + 1, (int)(cns[i]>>32) + 1, "ACGTX"[c[path[i]]], "ACGTX"[c[1-path[i]]],
			i + g->vpos_shift + 1, (int)(x&0xffff), (int)(x>>16&0xffff), (int)(x>>32&0xffff), (int)(x>>48&0xffff));
	}
	free(path); free(pcnt); free(regmask); free(sitemask);
	seqs = calloc(n_seqs, sizeof(void*));
	for (k = 0, i = 0; k < kh_end(hash); ++k) 
		if (kh_exist(hash, k) && kh_val(hash, k).vpos < vpos && !kh_val(hash, k).single)
			seqs[i++] = &kh_val(hash, k);
	n_seqs = i;
	ks_introsort_rseq(n_seqs, seqs);
	for (i = 0; i < n_seqs; ++i) {
		frag_t *f = seqs[i];
		printf("EV\t0\t%s\t%d\t40\t%dM\t*\t0\t0\t", chr, f->vpos + 1 + g->vpos_shift, f->vlen);
		for (j = 0; j < f->vlen; ++j) {
			uint32_t c = cns[f->vpos + j];
			if (f->seq[j] == 0) putchar('N');
			else putchar("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)]);
		}
		printf("\t*\tYP:i:%d\tYF:i:%d\tYI:i:%d\tYO:i:%d\tYS:i:%d\n", f->phase, f->flip, f->in, f->out, f->beg+1);
	}
	free(seqs);
	printf("//\n");
	fflush(stdout);
	g->vpos_shift += vpos;
	dump_aln(g, min_pos, hash);
	return vpos;
}

static void update_vpos(int vpos, nseq_t *hash)
{
	khint_t k;
	for (k = 0; k < kh_end(hash); ++k) {
		if (kh_exist(hash, k)) {
			frag_t *f = &kh_val(hash, k);
			if (f->vpos < vpos) kh_del(64, hash, k); // TODO: if frag_t::seq is allocated dynamically, free it
			else f->vpos -= vpos;
		}
	}
}

static nseq_t *shrink_hash(nseq_t *hash) // TODO: to implement
{
	return hash;
}

static int readaln(void *data, bam1_t *b)
{
	phaseg_t *g = (phaseg_t*)data;
	int ret;
	ret = bam_read1(g->fp, b);
	if (ret < 0) return ret;
	if (!(b->core.flag & (BAM_FUNMAP|BAM_FSECONDARY|BAM_FQCFAIL|BAM_FDUP)) && g->pre) {
		if (g->n == g->m) {
			g->m = g->m? g->m<<1 : 16;
			g->b = realloc(g->b, g->m * sizeof(void*));
		}
		g->b[g->n++] = bam_dup1(b);
	}
	return ret;
}

static khash_t(set64) *loadpos(const char *fn, bam_header_t *h)
{
	gzFile fp;
	kstream_t *ks;
	int ret, dret;
	kstring_t *str;
	khash_t(set64) *hash;

	hash = kh_init(set64);
	str = calloc(1, sizeof(kstring_t));
	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
	ks = ks_init(fp);
	while (ks_getuntil(ks, 0, str, &dret) >= 0) {
		int tid = bam_get_tid(h, str->s);
		if (tid >= 0 && dret != '\n') {
			if (ks_getuntil(ks, 0, str, &dret) >= 0) {
				uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
				kh_put(set64, hash, x, &ret);
			} else break;
		}
		if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
		if (dret < 0) break;
	}
	ks_destroy(ks);
	gzclose(fp);
	free(str->s); free(str);
	return hash;
}

static int gl2cns(float q[16])
{
	int i, j, min_ij;
	float min, min2;
	min = min2 = 1e30; min_ij = -1;
	for (i = 0; i < 4; ++i) {
		for (j = i; j < 4; ++j) {
			if (q[i<<2|j] < min) min_ij = i<<2|j, min2 = min, min = q[i<<2|j];
			else if (q[i<<2|j] < min2) min2 = q[i<<2|j];
		}
	}
	return (min_ij>>2&3) == (min_ij&3)? 0 : 1<<18 | (min_ij>>2&3)<<16 | (min_ij&3) | (int)(min2 - min + .499) << 2;
}

int main_phase(int argc, char *argv[])
{
	extern void bam_init_header_hash(bam_header_t *header);
	int c, tid, pos, vpos = 0, n, lasttid = -1, max_vpos = 0;
	const bam_pileup1_t *plp;
	bam_plp_t iter;
	bam_header_t *h;
	nseq_t *seqs;
	uint64_t *cns = 0;
	phaseg_t g;
	char *fn_list = 0;
	khash_t(set64) *set = 0;
	errmod_t *em;
	uint16_t *bases;

	memset(&g, 0, sizeof(phaseg_t));
	g.flag = FLAG_FIX_CHIMERA;
	g.min_varLOD = 37; g.k = 13; g.min_baseQ = 13; g.max_depth = 256;
	while ((c = getopt(argc, argv, "Q:eFq:k:b:l:D:A:")) >= 0) {
		switch (c) {
			case 'D': g.max_depth = atoi(optarg); break;
			case 'q': g.min_varLOD = atoi(optarg); break;
			case 'Q': g.min_baseQ = atoi(optarg); break;
			case 'k': g.k = atoi(optarg); break;
			case 'F': g.flag &= ~FLAG_FIX_CHIMERA; break;
			case 'e': g.flag |= FLAG_LIST_EXCL; break;
			case 'A': g.flag |= FLAG_DROP_AMBI; break;
			case 'b': g.pre = strdup(optarg); break;
			case 'l': fn_list = strdup(optarg); break;
		}
	}
	if (argc == optind) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   samtools phase [options] \n\n");
		fprintf(stderr, "Options: -k INT    block length [%d]\n", g.k);
		fprintf(stderr, "         -b STR    prefix of BAMs to output [null]\n");
		fprintf(stderr, "         -q INT    min het phred-LOD [%d]\n", g.min_varLOD);
		fprintf(stderr, "         -Q INT    min base quality in het calling [%d]\n", g.min_baseQ);
		fprintf(stderr, "         -D INT    max read depth [%d]\n", g.max_depth);
//		fprintf(stderr, "         -l FILE   list of sites to phase [null]\n");
		fprintf(stderr, "         -F        do not attempt to fix chimeras\n");
		fprintf(stderr, "         -A        drop reads with ambiguous phase\n");
//		fprintf(stderr, "         -e        do not discover SNPs (effective with -l)\n");
		fprintf(stderr, "\n");
		return 1;
	}
	g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
	h = bam_header_read(g.fp);
	if (fn_list) { // read the list of sites to phase
		bam_init_header_hash(h);
		set = loadpos(fn_list, h);
		free(fn_list);
	} else g.flag &= ~FLAG_LIST_EXCL;
	if (g.pre) { // open BAMs to write
		char *s = malloc(strlen(g.pre) + 20);
		strcpy(s, g.pre); strcat(s, ".0.bam"); g.out[0] = bam_open(s, "w");
		strcpy(s, g.pre); strcat(s, ".1.bam"); g.out[1] = bam_open(s, "w");
		strcpy(s, g.pre); strcat(s, ".chimera.bam"); g.out[2] = bam_open(s, "w");
		for (c = 0; c <= 2; ++c) bam_header_write(g.out[c], h);
		free(s);
	}

	iter = bam_plp_init(readaln, &g);
	g.vpos_shift = 0;
	seqs = kh_init(64);
	em = errmod_init(1. - 0.83);
	bases = calloc(g.max_depth, 2);
	printf("CC\n");
	printf("CC\tDescriptions:\nCC\n");
	printf("CC\t  CC      comments\n");
	printf("CC\t  PS      start of a phase set\n");
	printf("CC\t  FL      filtered region\n");
	printf("CC\t  M[012]  markers; 0 for singletons, 1 for phased and 2 for filtered\n");
	printf("CC\t  EV      supporting reads; SAM format\n");
	printf("CC\t  //      end of a phase set\nCC\n");
	printf("CC\tFormats of PS, FL and M[012] lines (1-based coordinates):\nCC\n");
	printf("CC\t  PS  chr  phaseSetStart  phaseSetEnd\n");
	printf("CC\t  FL  chr  filterStart    filterEnd\n");
	printf("CC\t  M?  chr  PS  pos  allele0  allele1  hetIndex  #supports0  #errors0  #supp1  #err1\n");
	printf("CC\nCC\n");
	fflush(stdout);
	while ((plp = bam_plp_auto(iter, &tid, &pos, &n)) != 0) {
		int i, k, c, tmp, dophase = 1, in_set = 0;
		float q[16];
		if (tid < 0) break;
		if (tid != lasttid) { // change of chromosome
			g.vpos_shift = 0;
			if (lasttid >= 0) {
				seqs = shrink_hash(seqs);
				phase(&g, h->target_name[lasttid], vpos, cns, seqs);
				update_vpos(0x7fffffff, seqs);
			}
			lasttid = tid;
			vpos = 0;
		}
		if (set && kh_get(set64, set, (uint64_t)tid<<32 | pos) != kh_end(set)) in_set = 1;
		if (n > g.max_depth) continue; // do not proceed if the depth is too high
		// fill the bases array and check if there is a variant
		for (i = k = 0; i < n; ++i) {
			const bam_pileup1_t *p = plp + i;
			uint8_t *seq;
			int q, baseQ, b;
			if (p->is_del || p->is_refskip) continue;
			baseQ = bam1_qual(p->b)[p->qpos];
			if (baseQ < g.min_baseQ) continue;
			seq = bam1_seq(p->b);
			b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)];
			if (b > 3) continue;
			q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
			if (q < 4) q = 4;
			if (q > 63) q = 63;
			bases[k++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
		}
		if (k == 0) continue;
		errmod_cal(em, k, 4, bases, q); // compute genotype likelihood
		c = gl2cns(q); // get the consensus
		// tell if to proceed
		if (set && (g.flag&FLAG_LIST_EXCL) && !in_set) continue; // not in the list
		if (!in_set && (c&0xffff)>>2 < g.min_varLOD) continue; // not a variant
		// add the variant
		if (vpos == max_vpos) {
			max_vpos = max_vpos? max_vpos<<1 : 128;
			cns = realloc(cns, max_vpos * 8);
		}
		cns[vpos] = (uint64_t)pos<<32 | c;
		for (i = 0; i < n; ++i) {
			const bam_pileup1_t *p = plp + i;
			uint64_t key;
			khint_t k;
			uint8_t *seq = bam1_seq(p->b);
			frag_t *f;
			if (p->is_del || p->is_refskip) continue;
			if (p->b->core.qual == 0) continue;
			// get the base code
			c = nt16_nt4_table[(int)bam1_seqi(seq, p->qpos)];
			if (c == (cns[vpos]&3)) c = 1;
			else if (c == (cns[vpos]>>16&3)) c = 2;
			else c = 0;
			// write to seqs
			key = X31_hash_string(bam1_qname(p->b));
			k = kh_put(64, seqs, key, &tmp);
			f = &kh_val(seqs, k);
			if (tmp == 0) { // present in the hash table
				if (vpos - f->vpos + 1 < MAX_VARS) {
					f->vlen = vpos - f->vpos + 1;
					f->seq[f->vlen-1] = c;
					f->end = bam_calend(&p->b->core, bam1_cigar(p->b));
				}
				dophase = 0;
			} else { // absent
				memset(f->seq, 0, MAX_VARS);
				f->beg = p->b->core.pos;
				f->end = bam_calend(&p->b->core, bam1_cigar(p->b));
				f->vpos = vpos, f->vlen = 1, f->seq[0] = c, f->single = f->phased = f->flip = f->ambig = 0;
			}
		}
		if (dophase) {
			seqs = shrink_hash(seqs);
			phase(&g, h->target_name[tid], vpos, cns, seqs);
			update_vpos(vpos, seqs);
			cns[0] = cns[vpos];
			vpos = 0;
		}
		++vpos;
	}
	if (tid >= 0) phase(&g, h->target_name[tid], vpos, cns, seqs);
	bam_header_destroy(h);
	bam_plp_destroy(iter);
	bam_close(g.fp);
	kh_destroy(64, seqs);
	kh_destroy(set64, set);
	free(cns);
	errmod_destroy(em);
	free(bases);
	if (g.pre) {
		for (c = 0; c <= 2; ++c) bam_close(g.out[c]);
		free(g.pre); free(g.b);
	}
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/razf.c000066400000000000000000000574271211610345200221660ustar00rootroot00000000000000/*
 * RAZF : Random Access compressed(Z) File
 * Version: 1.0
 * Release Date: 2008-10-27
 *
 * Copyright 2008, Jue Ruan , Heng Li 
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
 * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
 * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
 * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
 * SUCH DAMAGE.
 */

#ifndef _NO_RAZF

#include 
#include 
#include 
#include 
#include 
#include "razf.h"


#if ZLIB_VERNUM < 0x1221
struct _gz_header_s {
    int     text;
    uLong   time;
    int     xflags;
    int     os;
    Bytef   *extra;
    uInt    extra_len;
    uInt    extra_max;
    Bytef   *name;
    uInt    name_max;
    Bytef   *comment;
    uInt    comm_max;
    int     hcrc;
    int     done;
};
#warning "zlib < 1.2.2.1; RAZF writing is disabled."
#endif

#define DEF_MEM_LEVEL 8

static inline uint32_t byte_swap_4(uint32_t v){
	v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
	return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
}

static inline uint64_t byte_swap_8(uint64_t v){
	v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
	v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
	return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
}

static inline int is_big_endian(){
	int x = 0x01;
	char *c = (char*)&x;
	return (c[0] != 0x01);
}

#ifndef _RZ_READONLY
static void add_zindex(RAZF *rz, int64_t in, int64_t out){
	if(rz->index->size == rz->index->cap){
		rz->index->cap = rz->index->cap * 1.5 + 2;
		rz->index->cell_offsets = realloc(rz->index->cell_offsets, sizeof(int) * rz->index->cap);
		rz->index->bin_offsets  = realloc(rz->index->bin_offsets, sizeof(int64_t) * (rz->index->cap/RZ_BIN_SIZE + 1));
	}
	if(rz->index->size % RZ_BIN_SIZE == 0) rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE] = out;
	rz->index->cell_offsets[rz->index->size] = out - rz->index->bin_offsets[rz->index->size / RZ_BIN_SIZE];
	rz->index->size ++;
}

static void save_zindex(RAZF *rz, int fd){
	int32_t i, v32;
	int is_be;
	is_be = is_big_endian();
	if(is_be) write(fd, &rz->index->size, sizeof(int));
	else {
		v32 = byte_swap_4((uint32_t)rz->index->size);
		write(fd, &v32, sizeof(uint32_t));
	}
	v32 = rz->index->size / RZ_BIN_SIZE + 1;
	if(!is_be){
		for(i=0;iindex->bin_offsets[i]  = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
		for(i=0;iindex->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
	}
	write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
	write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
}
#endif

#ifdef _USE_KNETFILE
static void load_zindex(RAZF *rz, knetFile *fp){
#else
static void load_zindex(RAZF *rz, int fd){
#endif
	int32_t i, v32;
	int is_be;
	if(!rz->load_index) return;
	if(rz->index == NULL) rz->index = malloc(sizeof(ZBlockIndex));
	is_be = is_big_endian();
#ifdef _USE_KNETFILE
	knet_read(fp, &rz->index->size, sizeof(int));
#else
	read(fd, &rz->index->size, sizeof(int));
#endif
	if(!is_be) rz->index->size = byte_swap_4((uint32_t)rz->index->size);
	rz->index->cap = rz->index->size;
	v32 = rz->index->size / RZ_BIN_SIZE + 1;
	rz->index->bin_offsets  = malloc(sizeof(int64_t) * v32);
#ifdef _USE_KNETFILE
	knet_read(fp, rz->index->bin_offsets, sizeof(int64_t) * v32);
#else
	read(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
#endif
	rz->index->cell_offsets = malloc(sizeof(int) * rz->index->size);
#ifdef _USE_KNETFILE
	knet_read(fp, rz->index->cell_offsets, sizeof(int) * rz->index->size);
#else
	read(fd, rz->index->cell_offsets, sizeof(int) * rz->index->size);
#endif
	if(!is_be){
		for(i=0;iindex->bin_offsets[i] = byte_swap_8((uint64_t)rz->index->bin_offsets[i]);
		for(i=0;iindex->size;i++) rz->index->cell_offsets[i] = byte_swap_4((uint32_t)rz->index->cell_offsets[i]);
	}
}

#ifdef _RZ_READONLY
static RAZF* razf_open_w(int fd)
{
	fprintf(stderr, "[razf_open_w] Writing is not available with zlib ver < 1.2.2.1\n");
	return 0;
}
#else
static RAZF* razf_open_w(int fd){
	RAZF *rz;
#ifdef _WIN32
	setmode(fd, O_BINARY);
#endif
	rz = calloc(1, sizeof(RAZF));
	rz->mode = 'w';
#ifdef _USE_KNETFILE
    rz->x.fpw = fd;
#else
	rz->filedes = fd;
#endif
	rz->stream = calloc(sizeof(z_stream), 1);
	rz->inbuf  = malloc(RZ_BUFFER_SIZE);
	rz->outbuf = malloc(RZ_BUFFER_SIZE);
	rz->index = calloc(sizeof(ZBlockIndex), 1);
	deflateInit2(rz->stream, RZ_COMPRESS_LEVEL, Z_DEFLATED, WINDOW_BITS + 16, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY);
	rz->stream->avail_out = RZ_BUFFER_SIZE;
	rz->stream->next_out  = rz->outbuf;
	rz->header = calloc(sizeof(gz_header), 1);
	rz->header->os    = 0x03; //Unix
	rz->header->text  = 0;
	rz->header->time  = 0;
	rz->header->extra = malloc(7);
	strncpy((char*)rz->header->extra, "RAZF", 4);
	rz->header->extra[4] = 1; // obsolete field
	// block size = RZ_BLOCK_SIZE, Big-Endian
	rz->header->extra[5] = RZ_BLOCK_SIZE >> 8;
	rz->header->extra[6] = RZ_BLOCK_SIZE & 0xFF;
	rz->header->extra_len = 7;
	rz->header->name = rz->header->comment  = 0;
	rz->header->hcrc = 0;
	deflateSetHeader(rz->stream, rz->header);
	rz->block_pos = rz->block_off = 0;
	return rz;
}

static void _razf_write(RAZF* rz, const void *data, int size){
	int tout;
	rz->stream->avail_in = size;
	rz->stream->next_in  = (void*)data;
	while(1){
		tout = rz->stream->avail_out;
		deflate(rz->stream, Z_NO_FLUSH);
		rz->out += tout - rz->stream->avail_out;
		if(rz->stream->avail_out) break;
#ifdef _USE_KNETFILE
		write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
#else
		write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
#endif
		rz->stream->avail_out = RZ_BUFFER_SIZE;
		rz->stream->next_out  = rz->outbuf;
		if(rz->stream->avail_in == 0) break;
	};
	rz->in += size - rz->stream->avail_in;
	rz->block_off += size - rz->stream->avail_in;
}

static void razf_flush(RAZF *rz){
	uint32_t tout;
	if(rz->buf_len){
		_razf_write(rz, rz->inbuf, rz->buf_len);
		rz->buf_off = rz->buf_len = 0;
	}
	if(rz->stream->avail_out){
#ifdef _USE_KNETFILE    
		write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
#else        
		write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
#endif
		rz->stream->avail_out = RZ_BUFFER_SIZE;
		rz->stream->next_out  = rz->outbuf;
	}
	while(1){
		tout = rz->stream->avail_out;
		deflate(rz->stream, Z_FULL_FLUSH);
		rz->out += tout - rz->stream->avail_out;
		if(rz->stream->avail_out == 0){
#ifdef _USE_KNETFILE    
			write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
#else            
			write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
#endif
			rz->stream->avail_out = RZ_BUFFER_SIZE;
			rz->stream->next_out  = rz->outbuf;
		} else break;
	}
	rz->block_pos = rz->out;
	rz->block_off = 0;
}

static void razf_end_flush(RAZF *rz){
	uint32_t tout;
	if(rz->buf_len){
		_razf_write(rz, rz->inbuf, rz->buf_len);
		rz->buf_off = rz->buf_len = 0;
	}
	while(1){
		tout = rz->stream->avail_out;
		deflate(rz->stream, Z_FINISH);
		rz->out += tout - rz->stream->avail_out;
		if(rz->stream->avail_out < RZ_BUFFER_SIZE){
#ifdef _USE_KNETFILE        
			write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
#else            
			write(rz->filedes, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
#endif
			rz->stream->avail_out = RZ_BUFFER_SIZE;
			rz->stream->next_out  = rz->outbuf;
		} else break;
	}
}

static void _razf_buffered_write(RAZF *rz, const void *data, int size){
	int i, n;
	while(1){
		if(rz->buf_len == RZ_BUFFER_SIZE){
			_razf_write(rz, rz->inbuf, rz->buf_len);
			rz->buf_len = 0;
		}
		if(size + rz->buf_len < RZ_BUFFER_SIZE){
			for(i=0;iinbuf + rz->buf_len)[i] = ((char*)data)[i];
			rz->buf_len += size;
			return;
		} else {
			n = RZ_BUFFER_SIZE - rz->buf_len;
			for(i=0;iinbuf + rz->buf_len)[i] = ((char*)data)[i];
			size -= n;
			data += n;
			rz->buf_len += n;
		}
	}
}

int razf_write(RAZF* rz, const void *data, int size){
	int ori_size, n;
	int64_t next_block;
	ori_size = size;
	next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE;
	while(rz->in + rz->buf_len + size >= next_block){
		n = next_block - rz->in - rz->buf_len;
		_razf_buffered_write(rz, data, n);
		data += n;
		size -= n;
		razf_flush(rz);
		add_zindex(rz, rz->in, rz->out);
		next_block = ((rz->in / RZ_BLOCK_SIZE) + 1) * RZ_BLOCK_SIZE;
	}
	_razf_buffered_write(rz, data, size);
	return ori_size;
}
#endif

/* gzip flag byte */
#define ASCII_FLAG   0x01 /* bit 0 set: file probably ascii text */
#define HEAD_CRC     0x02 /* bit 1 set: header CRC present */
#define EXTRA_FIELD  0x04 /* bit 2 set: extra field present */
#define ORIG_NAME    0x08 /* bit 3 set: original file name present */
#define COMMENT      0x10 /* bit 4 set: file comment present */
#define RESERVED     0xE0 /* bits 5..7: reserved */

static int _read_gz_header(unsigned char *data, int size, int *extra_off, int *extra_len){
	int method, flags, n, len;
	if(size < 2) return 0;
	if(data[0] != 0x1f || data[1] != 0x8b) return 0;
	if(size < 4) return 0;
	method = data[2];
	flags  = data[3];
	if(method != Z_DEFLATED || (flags & RESERVED)) return 0;
	n = 4 + 6; // Skip 6 bytes
	*extra_off = n + 2;
	*extra_len = 0;
	if(flags & EXTRA_FIELD){
		if(size < n + 2) return 0;
		len = ((int)data[n + 1] << 8) | data[n];
		n += 2;
		*extra_off = n;
		while(len){
			if(n >= size) return 0;
			n ++;
			len --;
		}
		*extra_len = n - (*extra_off);
	}
	if(flags & ORIG_NAME) while(n < size && data[n++]);
	if(flags & COMMENT) while(n < size && data[n++]);
	if(flags & HEAD_CRC){
		if(n + 2 > size) return 0;
		n += 2;
	}
	return n;
}

#ifdef _USE_KNETFILE
static RAZF* razf_open_r(knetFile *fp, int _load_index){
#else
static RAZF* razf_open_r(int fd, int _load_index){
#endif
	RAZF *rz;
	int ext_off, ext_len;
	int n, is_be, ret;
	int64_t end;
	unsigned char c[] = "RAZF";
	rz = calloc(1, sizeof(RAZF));
	rz->mode = 'r';
#ifdef _USE_KNETFILE
    rz->x.fpr = fp;
#else
#ifdef _WIN32
	setmode(fd, O_BINARY);
#endif
	rz->filedes = fd;
#endif
	rz->stream = calloc(sizeof(z_stream), 1);
	rz->inbuf  = malloc(RZ_BUFFER_SIZE);
	rz->outbuf = malloc(RZ_BUFFER_SIZE);
	rz->end = rz->src_end = 0x7FFFFFFFFFFFFFFFLL;
#ifdef _USE_KNETFILE
    n = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
#else
	n = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
#endif
	ret = _read_gz_header(rz->inbuf, n, &ext_off, &ext_len);
	if(ret == 0){
		PLAIN_FILE:
		rz->in = n;
		rz->file_type = FILE_TYPE_PLAIN;
		memcpy(rz->outbuf, rz->inbuf, n);
		rz->buf_len = n;
		free(rz->stream);
		rz->stream = NULL;
		return rz;
	}
	rz->header_size = ret;
	ret = inflateInit2(rz->stream, -WINDOW_BITS);
	if(ret != Z_OK){ inflateEnd(rz->stream); goto PLAIN_FILE;}
	rz->stream->avail_in = n - rz->header_size;
	rz->stream->next_in  = rz->inbuf + rz->header_size;
	rz->stream->avail_out = RZ_BUFFER_SIZE;
	rz->stream->next_out  = rz->outbuf;
	rz->file_type = FILE_TYPE_GZ;
	rz->in = rz->header_size;
	rz->block_pos = rz->header_size;
	rz->next_block_pos = rz->header_size;
	rz->block_off = 0;
	if(ext_len < 7 || memcmp(rz->inbuf + ext_off, c, 4) != 0) return rz;
	if(((((unsigned char*)rz->inbuf)[ext_off + 5] << 8) | ((unsigned char*)rz->inbuf)[ext_off + 6]) != RZ_BLOCK_SIZE){
		fprintf(stderr, " -- WARNING: RZ_BLOCK_SIZE is not %d, treat source as gz file.  in %s -- %s:%d --\n", RZ_BLOCK_SIZE, __FUNCTION__, __FILE__, __LINE__);
		return rz;
	}
	rz->load_index = _load_index;
	rz->file_type = FILE_TYPE_RZ;
#ifdef _USE_KNETFILE
	if(knet_seek(fp, -16, SEEK_END) == -1){
#else
	if(lseek(fd, -16, SEEK_END) == -1){
#endif
		UNSEEKABLE:
		rz->seekable = 0;
		rz->index = NULL;
		rz->src_end = rz->end = 0x7FFFFFFFFFFFFFFFLL;
	} else {
		is_be = is_big_endian();
		rz->seekable = 1;
#ifdef _USE_KNETFILE
        knet_read(fp, &end, sizeof(int64_t));
#else
		read(fd, &end, sizeof(int64_t));
#endif        
		if(!is_be) rz->src_end = (int64_t)byte_swap_8((uint64_t)end);
		else rz->src_end = end;

#ifdef _USE_KNETFILE
		knet_read(fp, &end, sizeof(int64_t));
#else
		read(fd, &end, sizeof(int64_t));
#endif        
		if(!is_be) rz->end = (int64_t)byte_swap_8((uint64_t)end);
		else rz->end = end;
		if(n > rz->end){
			rz->stream->avail_in -= n - rz->end;
			n = rz->end;
		}
		if(rz->end > rz->src_end){
#ifdef _USE_KNETFILE
            knet_seek(fp, rz->in, SEEK_SET);
#else
			lseek(fd, rz->in, SEEK_SET);
#endif
			goto UNSEEKABLE;
		}
#ifdef _USE_KNETFILE
        knet_seek(fp, rz->end, SEEK_SET);
		if(knet_tell(fp) != rz->end){
			knet_seek(fp, rz->in, SEEK_SET);
#else
		if(lseek(fd, rz->end, SEEK_SET) != rz->end){
			lseek(fd, rz->in, SEEK_SET);
#endif
			goto UNSEEKABLE;
		}
#ifdef _USE_KNETFILE
		load_zindex(rz, fp);
		knet_seek(fp, n, SEEK_SET);
#else
		load_zindex(rz, fd);
		lseek(fd, n, SEEK_SET);
#endif
	}
	return rz;
}

#ifdef _USE_KNETFILE
RAZF* razf_dopen(int fd, const char *mode){
    if (strstr(mode, "r")) fprintf(stderr,"[razf_dopen] implement me\n");
    else if(strstr(mode, "w")) return razf_open_w(fd);
	return NULL;
}

RAZF* razf_dopen2(int fd, const char *mode)
{
    fprintf(stderr,"[razf_dopen2] implement me\n");
    return NULL;
}
#else
RAZF* razf_dopen(int fd, const char *mode){
	if(strstr(mode, "r")) return razf_open_r(fd, 1);
	else if(strstr(mode, "w")) return razf_open_w(fd);
	else return NULL;
}

RAZF* razf_dopen2(int fd, const char *mode)
{
	if(strstr(mode, "r")) return razf_open_r(fd, 0);
	else if(strstr(mode, "w")) return razf_open_w(fd);
	else return NULL;
}
#endif

static inline RAZF* _razf_open(const char *filename, const char *mode, int _load_index){
	int fd;
	RAZF *rz;
	if(strstr(mode, "r")){
#ifdef _USE_KNETFILE
        knetFile *fd = knet_open(filename, "r");
        if (fd == 0) {
            fprintf(stderr, "[_razf_open] fail to open %s\n", filename);
            return NULL;
        }
#else
#ifdef _WIN32
		fd = open(filename, O_RDONLY | O_BINARY);
#else
		fd = open(filename, O_RDONLY);
#endif
#endif
		if(fd < 0) return NULL;
		rz = razf_open_r(fd, _load_index);
	} else if(strstr(mode, "w")){
#ifdef _WIN32
		fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC | O_BINARY, 0666);
#else
		fd = open(filename, O_WRONLY | O_CREAT | O_TRUNC, 0666);
#endif
		if(fd < 0) return NULL;
		rz = razf_open_w(fd);
	} else return NULL;
	return rz;
}

RAZF* razf_open(const char *filename, const char *mode){
	return _razf_open(filename, mode, 1);
}

RAZF* razf_open2(const char *filename, const char *mode){
	return _razf_open(filename, mode, 0);
}

int razf_get_data_size(RAZF *rz, int64_t *u_size, int64_t *c_size){
	int64_t n;
	if(rz->mode != 'r' && rz->mode != 'R') return 0;
	switch(rz->file_type){
		case FILE_TYPE_PLAIN:
			if(rz->end == 0x7fffffffffffffffLL){
#ifdef _USE_KNETFILE
				if(knet_seek(rz->x.fpr, 0, SEEK_CUR) == -1) return 0;
                n = knet_tell(rz->x.fpr);
				knet_seek(rz->x.fpr, 0, SEEK_END);
                rz->end = knet_tell(rz->x.fpr);
				knet_seek(rz->x.fpr, n, SEEK_SET);
#else
				if((n = lseek(rz->filedes, 0, SEEK_CUR)) == -1) return 0;
				rz->end = lseek(rz->filedes, 0, SEEK_END);
				lseek(rz->filedes, n, SEEK_SET);
#endif                
			}
			*u_size = *c_size = rz->end;
			return 1;
		case FILE_TYPE_GZ:
			return 0;
		case FILE_TYPE_RZ:
			if(rz->src_end == rz->end) return 0;
			*u_size = rz->src_end;
			*c_size = rz->end;
			return 1;
		default:
			return 0;
	}
}

static int _razf_read(RAZF* rz, void *data, int size){
	int ret, tin;
	if(rz->z_eof || rz->z_err) return 0;
	if (rz->file_type == FILE_TYPE_PLAIN) {
#ifdef _USE_KNETFILE
		ret = knet_read(rz->x.fpr, data, size);
#else
		ret = read(rz->filedes, data, size);
#endif        
		if (ret == 0) rz->z_eof = 1;
		return ret;
	}
	rz->stream->avail_out = size;
	rz->stream->next_out  = data;
	while(rz->stream->avail_out){
		if(rz->stream->avail_in == 0){
			if(rz->in >= rz->end){ rz->z_eof = 1; break; }
			if(rz->end - rz->in < RZ_BUFFER_SIZE){
#ifdef _USE_KNETFILE
				rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, rz->end -rz->in);
#else
				rz->stream->avail_in = read(rz->filedes, rz->inbuf, rz->end -rz->in);
#endif        
			} else {
#ifdef _USE_KNETFILE
				rz->stream->avail_in = knet_read(rz->x.fpr, rz->inbuf, RZ_BUFFER_SIZE);
#else
				rz->stream->avail_in = read(rz->filedes, rz->inbuf, RZ_BUFFER_SIZE);
#endif        
			}
			if(rz->stream->avail_in == 0){
				rz->z_eof = 1;
				break;
			}
			rz->stream->next_in = rz->inbuf;
		}
		tin = rz->stream->avail_in;
		ret = inflate(rz->stream, Z_BLOCK);
		rz->in += tin - rz->stream->avail_in;
		if(ret == Z_NEED_DICT || ret == Z_MEM_ERROR || ret == Z_DATA_ERROR){
			fprintf(stderr, "[_razf_read] inflate error: %d %s (at %s:%d)\n", ret, rz->stream->msg ? rz->stream->msg : "", __FILE__, __LINE__);
			rz->z_err = 1;
			break;
		}
		if(ret == Z_STREAM_END){
			rz->z_eof = 1;
			break;
		}
		if ((rz->stream->data_type&128) && !(rz->stream->data_type&64)){
			rz->buf_flush = 1;
			rz->next_block_pos = rz->in;
			break;
		}
	}
	return size - rz->stream->avail_out;
}

int razf_read(RAZF *rz, void *data, int size){
	int ori_size, i;
	ori_size = size;
	while(size > 0){
		if(rz->buf_len){
			if(size < rz->buf_len){
				for(i=0;ioutbuf + rz->buf_off)[i];
				rz->buf_off += size;
				rz->buf_len -= size;
				data += size;
				rz->block_off += size;
				size = 0;
				break;
			} else {
				for(i=0;ibuf_len;i++) ((char*)data)[i] = ((char*)rz->outbuf + rz->buf_off)[i];
				data += rz->buf_len;
				size -= rz->buf_len;
				rz->block_off += rz->buf_len;
				rz->buf_off = 0;
				rz->buf_len = 0;
				if(rz->buf_flush){
					rz->block_pos = rz->next_block_pos;
					rz->block_off = 0;
					rz->buf_flush = 0;
				}
			}
		} else if(rz->buf_flush){
			rz->block_pos = rz->next_block_pos;
			rz->block_off = 0;
			rz->buf_flush = 0;
		}
		if(rz->buf_flush) continue;
		rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
		if(rz->z_eof && rz->buf_len == 0) break;
	}
	rz->out += ori_size - size;
	return ori_size - size;
}

int razf_skip(RAZF* rz, int size){
	int ori_size;
	ori_size = size;
	while(size > 0){
		if(rz->buf_len){
			if(size < rz->buf_len){
				rz->buf_off += size;
				rz->buf_len -= size;
				rz->block_off += size;
				size = 0;
				break;
			} else {
				size -= rz->buf_len;
				rz->buf_off = 0;
				rz->buf_len = 0;
				rz->block_off += rz->buf_len;
				if(rz->buf_flush){
					rz->block_pos = rz->next_block_pos;
					rz->block_off = 0;
					rz->buf_flush = 0;
				}
			}
		} else if(rz->buf_flush){
			rz->block_pos = rz->next_block_pos;
			rz->block_off = 0;
			rz->buf_flush = 0;
		}
		if(rz->buf_flush) continue;
		rz->buf_len = _razf_read(rz, rz->outbuf, RZ_BUFFER_SIZE);
		if(rz->z_eof || rz->z_err) break;
	}
	rz->out += ori_size - size;
	return ori_size - size;
}

static void _razf_reset_read(RAZF *rz, int64_t in, int64_t out){
#ifdef _USE_KNETFILE
	knet_seek(rz->x.fpr, in, SEEK_SET);
#else
	lseek(rz->filedes, in, SEEK_SET);
#endif
	rz->in  = in;
	rz->out = out;
	rz->block_pos = in;
	rz->next_block_pos = in;
	rz->block_off = 0;
	rz->buf_flush = 0;
	rz->z_eof = rz->z_err = 0;
	inflateReset(rz->stream);
	rz->stream->avail_in = 0;
	rz->buf_off = rz->buf_len = 0;
}

int64_t razf_jump(RAZF *rz, int64_t block_start, int block_offset){
	int64_t pos;
	rz->z_eof = 0;
	if(rz->file_type == FILE_TYPE_PLAIN){
		rz->buf_off = rz->buf_len = 0;
		pos = block_start + block_offset;
#ifdef _USE_KNETFILE
		knet_seek(rz->x.fpr, pos, SEEK_SET);
        pos = knet_tell(rz->x.fpr);
#else
		pos = lseek(rz->filedes, pos, SEEK_SET);
#endif
		rz->out = rz->in = pos;
		return pos;
	}
	if(block_start == rz->block_pos && block_offset >= rz->block_off) {
		block_offset -= rz->block_off;
		goto SKIP; // Needn't reset inflate
	}
	if(block_start  == 0) block_start = rz->header_size; // Automaticly revist wrong block_start
	_razf_reset_read(rz, block_start, 0);
	SKIP:
	if(block_offset) razf_skip(rz, block_offset);
	return rz->block_off;
}

int64_t razf_seek(RAZF* rz, int64_t pos, int where){
	int64_t idx;
	int64_t seek_pos, new_out;
	rz->z_eof = 0;
	if (where == SEEK_CUR) pos += rz->out;
	else if (where == SEEK_END) pos += rz->src_end;
	if(rz->file_type == FILE_TYPE_PLAIN){
#ifdef _USE_KNETFILE
		knet_seek(rz->x.fpr, pos, SEEK_SET);
        seek_pos = knet_tell(rz->x.fpr);
#else
		seek_pos = lseek(rz->filedes, pos, SEEK_SET);
#endif
		rz->buf_off = rz->buf_len = 0;
		rz->out = rz->in = seek_pos;
		return seek_pos;
	} else if(rz->file_type == FILE_TYPE_GZ){
		if(pos >= rz->out) goto SKIP;
		return rz->out;
	}
	if(pos == rz->out) return pos;
	if(pos > rz->src_end) return rz->out;
	if(!rz->seekable || !rz->load_index){
		if(pos >= rz->out) goto SKIP;
	}
	idx = pos / RZ_BLOCK_SIZE - 1;
	seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
	new_out  = (idx + 1) * RZ_BLOCK_SIZE;
	if(pos > rz->out && new_out <= rz->out) goto SKIP;
	_razf_reset_read(rz, seek_pos, new_out);
	SKIP:
	razf_skip(rz, (int)(pos - rz->out));
	return rz->out;
}

uint64_t razf_tell2(RAZF *rz)
{
	/*
	if (rz->load_index) {
		int64_t idx, seek_pos;
		idx = rz->out / RZ_BLOCK_SIZE - 1;
		seek_pos = (idx < 0)? rz->header_size:(rz->index->cell_offsets[idx] + rz->index->bin_offsets[idx / RZ_BIN_SIZE]);
		if (seek_pos != rz->block_pos || rz->out%RZ_BLOCK_SIZE != rz->block_off)
			fprintf(stderr, "[razf_tell2] inconsistent block offset: (%lld, %lld) != (%lld, %lld)\n",
					(long long)seek_pos, (long long)rz->out%RZ_BLOCK_SIZE, (long long)rz->block_pos, (long long) rz->block_off);
	}
	*/
	return (uint64_t)rz->block_pos<<16 | (rz->block_off&0xffff);
}

int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where)
{
	if (where != SEEK_SET) return -1;
	return razf_jump(rz, voffset>>16, voffset&0xffff);
}

void razf_close(RAZF *rz){
	if(rz->mode == 'w'){
#ifndef _RZ_READONLY
		razf_end_flush(rz);
		deflateEnd(rz->stream);
#ifdef _USE_KNETFILE
		save_zindex(rz, rz->x.fpw);
		if(is_big_endian()){
			write(rz->x.fpw, &rz->in, sizeof(int64_t));
			write(rz->x.fpw, &rz->out, sizeof(int64_t));
		} else {
			uint64_t v64 = byte_swap_8((uint64_t)rz->in);
			write(rz->x.fpw, &v64, sizeof(int64_t));
			v64 = byte_swap_8((uint64_t)rz->out);
			write(rz->x.fpw, &v64, sizeof(int64_t));
		}
#else
		save_zindex(rz, rz->filedes);
		if(is_big_endian()){
			write(rz->filedes, &rz->in, sizeof(int64_t));
			write(rz->filedes, &rz->out, sizeof(int64_t));
		} else {
			uint64_t v64 = byte_swap_8((uint64_t)rz->in);
			write(rz->filedes, &v64, sizeof(int64_t));
			v64 = byte_swap_8((uint64_t)rz->out);
			write(rz->filedes, &v64, sizeof(int64_t));
		}
#endif
#endif
	} else if(rz->mode == 'r'){
		if(rz->stream) inflateEnd(rz->stream);
	}
	if(rz->inbuf) free(rz->inbuf);
	if(rz->outbuf) free(rz->outbuf);
	if(rz->header){
		free(rz->header->extra);
		free(rz->header->name);
		free(rz->header->comment);
		free(rz->header);
	}
	if(rz->index){
		free(rz->index->bin_offsets);
		free(rz->index->cell_offsets);
		free(rz->index);
	}
	free(rz->stream);
#ifdef _USE_KNETFILE
    if (rz->mode == 'r')
        knet_close(rz->x.fpr);
    if (rz->mode == 'w')
        close(rz->x.fpw);
#else
	close(rz->filedes);
#endif
	free(rz);
}

#endif
genometools-1.5.1/src/external/samtools-0.1.18/razf.h000066400000000000000000000100511211610345200221510ustar00rootroot00000000000000 /*-
 * RAZF : Random Access compressed(Z) File
 * Version: 1.0
 * Release Date: 2008-10-27
 *
 * Copyright 2008, Jue Ruan , Heng Li 
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
 * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
 * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
 * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
 * SUCH DAMAGE.
 */


#ifndef __RAZF_RJ_H
#define __RAZF_RJ_H

#include 
#include 
#include "zlib.h"

#ifdef _USE_KNETFILE
#include "knetfile.h"
#endif

#if ZLIB_VERNUM < 0x1221
#define _RZ_READONLY
struct _gz_header_s;
typedef struct _gz_header_s _gz_header;
#define gz_header _gz_header
#endif

#define WINDOW_BITS   15

#ifndef RZ_BLOCK_SIZE
#define RZ_BLOCK_SIZE (1<mode from HEAD to TYPE after call inflateReset */
	int buf_off, buf_len;
	int z_err, z_eof;
	int seekable;
	/* Indice where the source is seekable */
	int load_index;
	/* set has_index to 0 in mode 'w', then index will be discarded */
} RAZF;

#ifdef __cplusplus
extern "C" {
#endif

	RAZF* razf_dopen(int data_fd, const char *mode);
	RAZF *razf_open(const char *fn, const char *mode);
	int razf_write(RAZF* rz, const void *data, int size);
	int razf_read(RAZF* rz, void *data, int size);
	int64_t razf_seek(RAZF* rz, int64_t pos, int where);
	void razf_close(RAZF* rz);

#define razf_tell(rz) ((rz)->out)

	RAZF* razf_open2(const char *filename, const char *mode);
	RAZF* razf_dopen2(int fd, const char *mode);
	uint64_t razf_tell2(RAZF *rz);
	int64_t razf_seek2(RAZF *rz, uint64_t voffset, int where);

#ifdef __cplusplus
}
#endif

#endif
genometools-1.5.1/src/external/samtools-0.1.18/razip.c000066400000000000000000000100161211610345200223300ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include 
#include "razf.h"

#define WINDOW_SIZE 4096

static int razf_main_usage()
{
	printf("\n");
	printf("Usage:   razip [options] [file] ...\n\n");
	printf("Options: -c      write on standard output, keep original files unchanged\n");
	printf("         -d      decompress\n");
	printf("         -l      list compressed file contents\n");
	printf("         -b INT  decompress at INT position in the uncompressed file\n");
	printf("         -s INT  decompress INT bytes in the uncompressed file\n");
	printf("         -h      give this help\n");
	printf("\n");
	return 0;
}

static int write_open(const char *fn, int is_forced)
{
	int fd = -1;
	char c;
	if (!is_forced) {
		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
			printf("razip: %s already exists; do you wish to overwrite (y or n)? ", fn);
			scanf("%c", &c);
			if (c != 'Y' && c != 'y') {
				printf("razip: not overwritten\n");
				exit(1);
			}
		}
	}
	if (fd < 0) {
		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
			fprintf(stderr, "razip: %s: Fail to write\n", fn);
			exit(1);
		}
	}
	return fd;
}

int main(int argc, char **argv)
{
	int c, compress, pstdout, is_forced;
	RAZF *rz;
	void *buffer;
	long start, end, size;

	compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
	while((c  = getopt(argc, argv, "cdlhfb:s:")) >= 0){
		switch(c){
		case 'h': return razf_main_usage();
		case 'd': compress = 0; break;
		case 'c': pstdout = 1; break;
		case 'l': compress = 2; break;
		case 'b': start = atol(optarg); break;
		case 's': size = atol(optarg); break;
		case 'f': is_forced = 1; break;
		}
	}
	if (size >= 0) end = start + size;
	if(end >= 0 && end < start){
		fprintf(stderr, " -- Illegal region: [%ld, %ld] --\n", start, end);
		return 1;
	}
	if(compress == 1){
		int f_src, f_dst = -1;
		if(argc > optind){
			if((f_src = open(argv[optind], O_RDONLY)) < 0){
				fprintf(stderr, " -- Cannot open file: %s --\n", argv[optind]);
				return 1;
			}
			if(pstdout){
				f_dst = fileno(stdout);
			} else {
				char *name = malloc(sizeof(strlen(argv[optind]) + 5));
				strcpy(name, argv[optind]);
				strcat(name, ".rz");
				f_dst = write_open(name, is_forced);
				if (f_dst < 0) return 1;
				free(name);
			}
		} else if(pstdout){ 
			f_src = fileno(stdin);
			f_dst = fileno(stdout);
		} else return razf_main_usage();
		rz = razf_dopen(f_dst, "w");
		buffer = malloc(WINDOW_SIZE);
		while((c = read(f_src, buffer, WINDOW_SIZE)) > 0) razf_write(rz, buffer, c);
		razf_close(rz); // f_dst will be closed here
		if (argc > optind && !pstdout) unlink(argv[optind]);
		free(buffer);
		close(f_src);
		return 0;
	} else {
		if(argc <= optind) return razf_main_usage();
		if(compress == 2){
			rz = razf_open(argv[optind], "r");
			if(rz->file_type == FILE_TYPE_RZ) {
							printf("%20s%20s%7s %s\n", "compressed", "uncompressed", "ratio", "name");
				printf("%20lld%20lld%6.1f%% %s\n", (long long)rz->end, (long long)rz->src_end, rz->end * 100.0f / rz->src_end,
					   argv[optind]);
			} else fprintf(stdout, "%s is not a regular rz file\n", argv[optind]);
		} else {
			int f_dst;
			if (argc > optind && !pstdout) {
				char *name;
				if (strstr(argv[optind], ".rz") - argv[optind] != strlen(argv[optind]) - 3) {
					printf("razip: %s: unknown suffix -- ignored\n", argv[optind]);
					return 1;
				}
				name = strdup(argv[optind]);
				name[strlen(name) - 3] = '\0';
				f_dst = write_open(name, is_forced);
				free(name);
			} else f_dst = fileno(stdout);
			rz = razf_open(argv[optind], "r");
			buffer = malloc(WINDOW_SIZE);
			razf_seek(rz, start, SEEK_SET);
			while(1){
				if(end < 0) c = razf_read(rz, buffer, WINDOW_SIZE);
				else c = razf_read(rz, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
				if(c <= 0) break;
				start += c;
				write(f_dst, buffer, c);
				if(end >= 0 && start >= end) break;
			}
			free(buffer);
			if (!pstdout) unlink(argv[optind]);
		}
		razf_close(rz);
		return 0;
	}
}

genometools-1.5.1/src/external/samtools-0.1.18/sam.c000066400000000000000000000133731211610345200217740ustar00rootroot00000000000000#include 
#include 
#include "faidx.h"
#include "sam.h"

#define TYPE_BAM  1
#define TYPE_READ 2

bam_header_t *bam_header_dup(const bam_header_t *h0)
{
	bam_header_t *h;
	int i;
	h = bam_header_init();
	*h = *h0;
	h->hash = h->dict = h->rg2lib = 0;
	h->text = (char*)calloc(h->l_text + 1, 1);
	memcpy(h->text, h0->text, h->l_text);
	h->target_len = (uint32_t*)calloc(h->n_targets, 4);
	h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
	for (i = 0; i < h->n_targets; ++i) {
		h->target_len[i] = h0->target_len[i];
		h->target_name[i] = strdup(h0->target_name[i]);
	}
	return h;
}
static void append_header_text(bam_header_t *header, char* text, int len)
{
	int x = header->l_text + 1;
	int y = header->l_text + len + 1; // 1 byte null
	if (text == 0) return;
	kroundup32(x); 
	kroundup32(y);
	if (x < y) header->text = (char*)realloc(header->text, y);
	strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
	header->l_text += len;
	header->text[header->l_text] = 0;
}

samfile_t *samopen(const char *fn, const char *mode, const void *aux)
{
	samfile_t *fp;
	fp = (samfile_t*)calloc(1, sizeof(samfile_t));
	if (strchr(mode, 'r')) { // read
		fp->type |= TYPE_READ;
		if (strchr(mode, 'b')) { // binary
			fp->type |= TYPE_BAM;
			fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
			if (fp->x.bam == 0) goto open_err_ret;
			fp->header = bam_header_read(fp->x.bam);
		} else { // text
			fp->x.tamr = sam_open(fn);
			if (fp->x.tamr == 0) goto open_err_ret;
			fp->header = sam_header_read(fp->x.tamr);
			if (fp->header->n_targets == 0) { // no @SQ fields
				if (aux) { // check if aux is present
					bam_header_t *textheader = fp->header;
					fp->header = sam_header_read2((const char*)aux);
					if (fp->header == 0) goto open_err_ret;
					append_header_text(fp->header, textheader->text, textheader->l_text);
					bam_header_destroy(textheader);
				}
				if (fp->header->n_targets == 0 && bam_verbose >= 1)
					fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
			} else if (bam_verbose >= 2) fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
		}
	} else if (strchr(mode, 'w')) { // write
		fp->header = bam_header_dup((const bam_header_t*)aux);
		if (strchr(mode, 'b')) { // binary
			char bmode[3];
			int i, compress_level = -1;
			for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break;
			if (mode[i]) compress_level = mode[i] - '0';
			if (strchr(mode, 'u')) compress_level = 0;
			bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0;
			fp->type |= TYPE_BAM;
			fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
			if (fp->x.bam == 0) goto open_err_ret;
			bam_header_write(fp->x.bam, fp->header);
		} else { // text
			// open file
			fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
			if (fp->x.tamr == 0) goto open_err_ret;
			if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2;
			else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2;
			else fp->type |= BAM_OFDEC<<2;
			// write header
			if (strchr(mode, 'h')) {
				int i;
				bam_header_t *alt;
				// parse the header text 
				alt = bam_header_init();
				alt->l_text = fp->header->l_text; alt->text = fp->header->text;
				sam_header_parse(alt);
				alt->l_text = 0; alt->text = 0;
				// check if there are @SQ lines in the header
				fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); // FIXME: better to skip the trailing NULL
				if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
					if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1)
						fprintf(stderr, "[samopen] inconsistent number of target sequences. Output the text header.\n");
				} else { // then dump ->target_{name,len}
					for (i = 0; i < fp->header->n_targets; ++i)
						fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
				}
				bam_header_destroy(alt);
			}
		}
	}
	return fp;

open_err_ret:
	free(fp);
	return 0;
}

void samclose(samfile_t *fp)
{
	if (fp == 0) return;
	if (fp->header) bam_header_destroy(fp->header);
	if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
	else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
	else fclose(fp->x.tamw);
	free(fp);
}

int samread(samfile_t *fp, bam1_t *b)
{
	if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
	if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
	else return sam_read1(fp->x.tamr, fp->header, b);
}

int samwrite(samfile_t *fp, const bam1_t *b)
{
	if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
	if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
	else {
		char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
		int l = strlen(s);
		fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
		free(s);
		return l + 1;
	}
}

int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
{
	bam_plbuf_t *buf;
	int ret;
	bam1_t *b;
	b = bam_init1();
	buf = bam_plbuf_init(func, func_data);
	bam_plbuf_set_mask(buf, mask);
	while ((ret = samread(fp, b)) >= 0)
		bam_plbuf_push(b, buf);
	bam_plbuf_push(0, buf);
	bam_plbuf_destroy(buf);
	bam_destroy1(b);
	return 0;
}

char *samfaipath(const char *fn_ref)
{
	char *fn_list = 0;
	if (fn_ref == 0) return 0;
	fn_list = calloc(strlen(fn_ref) + 5, 1);
	strcat(strcpy(fn_list, fn_ref), ".fai");
	if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
		if (access(fn_ref, R_OK) == -1) {
			fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
		} else {
			if (bam_verbose >= 3) fprintf(stderr, "[samfaipath] build FASTA index...\n");
			if (fai_build(fn_ref) == -1) {
				fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
				free(fn_list); fn_list = 0;
			}
		}
	}
	return fn_list;
}
genometools-1.5.1/src/external/samtools-0.1.18/sam.h000066400000000000000000000051301211610345200217710ustar00rootroot00000000000000#ifndef BAM_SAM_H
#define BAM_SAM_H

#include "bam.h"

/*!
  @header

  This file provides higher level of I/O routines and unifies the APIs
  for SAM and BAM formats. These APIs are more convenient and
  recommended.

  @copyright Genome Research Ltd.
 */

/*@ignore@*/
/*! @typedef
  @abstract SAM/BAM file handler
  @field  type    type of the handler; bit 1 for BAM, 2 for reading and bit 3-4 for flag format
  @field  bam   BAM file handler; valid if (type&1) == 1
  @field  tamr  SAM file handler for reading; valid if type == 2
  @field  tamw  SAM file handler for writing; valid if type == 0
  @field  header  header struct
 */
typedef struct {
	int type;
	union {
		tamFile tamr;
		bamFile bam;
		FILE *tamw;
	} x;
	bam_header_t *header;
} samfile_t;

#ifdef __cplusplus
extern "C" {
#endif

	/*!
	  @abstract     Open a SAM/BAM file

	  @param fn SAM/BAM file name; "-" is recognized as stdin (for
	  reading) or stdout (for writing).

	  @param mode open mode /[rw](b?)(u?)(h?)([xX]?)/: 'r' for reading,
	  'w' for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output,
	  'h' for outputing header in SAM, 'x' for HEX flag and 'X' for
	  string flag. If 'b' present, it must immediately follow 'r' or
	  'w'. Valid modes are "r", "w", "wh", "wx", "whx", "wX", "whX",
	  "rb", "wb" and "wbu" exclusively.

	  @param aux auxiliary data; if mode[0]=='w', aux points to
	  bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM
	  are absent, aux points the file name of the list of the reference;
	  aux is not used otherwise. If @SQ header lines are present in SAM,
	  aux is not used, either.

	  @return       SAM/BAM file handler
	 */
	samfile_t *samopen(const char *fn, const char *mode, const void *aux);

	/*!
	  @abstract     Close a SAM/BAM handler
	  @param  fp    file handler to be closed
	 */
	void samclose(samfile_t *fp);

	/*!
	  @abstract     Read one alignment
	  @param  fp    file handler
	  @param  b     alignment
	  @return       bytes read
	 */
	int samread(samfile_t *fp, bam1_t *b);

	/*!
	  @abstract     Write one alignment
	  @param  fp    file handler
	  @param  b     alignment
	  @return       bytes written
	 */
	int samwrite(samfile_t *fp, const bam1_t *b);

	/*!
	  @abstract     Get the pileup for a whole alignment file
	  @param  fp    file handler
	  @param  mask  mask transferred to bam_plbuf_set_mask()
	  @param  func  user defined function called in the pileup process
	  #param  data  user provided data for func()
	 */
	int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data);

	char *samfaipath(const char *fn_ref);

#ifdef __cplusplus
}
#endif
/*@end@*/

#endif
genometools-1.5.1/src/external/samtools-0.1.18/sam_header.c000066400000000000000000000454721211610345200233110ustar00rootroot00000000000000#include "sam_header.h"
#include 
#include 
#include 
#include 
#include 

#include "khash.h"
KHASH_MAP_INIT_STR(str, const char *)

struct _HeaderList
{
    struct _HeaderList *last;   // Hack: Used and maintained only by list_append_to_end. Maintained in the root node only.
    struct _HeaderList *next;
    void *data;
};
typedef struct _HeaderList list_t;
typedef list_t HeaderDict;

typedef struct
{
    char key[2];
    char *value;
}
HeaderTag;

typedef struct
{
    char type[2];
    list_t *tags;
}
HeaderLine;

const char *o_hd_tags[] = {"SO","GO",NULL};
const char *r_hd_tags[] = {"VN",NULL};

const char *o_sq_tags[] = {"AS","M5","UR","SP",NULL};
const char *r_sq_tags[] = {"SN","LN",NULL};
const char *u_sq_tags[] = {"SN",NULL};

const char *o_rg_tags[] = {"CN","DS","DT","FO","KS","LB","PG","PI","PL","PU","SM",NULL};
const char *r_rg_tags[] = {"ID",NULL};
const char *u_rg_tags[] = {"ID",NULL};

const char *o_pg_tags[] = {"VN","CL",NULL};
const char *r_pg_tags[] = {"ID",NULL};

const char *types[]          = {"HD","SQ","RG","PG","CO",NULL};
const char **optional_tags[] = {o_hd_tags,o_sq_tags,o_rg_tags,o_pg_tags,NULL,NULL};
const char **required_tags[] = {r_hd_tags,r_sq_tags,r_rg_tags,r_pg_tags,NULL,NULL};
const char **unique_tags[]   = {NULL,     u_sq_tags,u_rg_tags,NULL,NULL,NULL};


static void debug(const char *format, ...)
{
    va_list ap;
    va_start(ap, format);
    vfprintf(stderr, format, ap);
    va_end(ap);
}

#if 0
// Replaced by list_append_to_end
static list_t *list_prepend(list_t *root, void *data)
{
    list_t *l = malloc(sizeof(list_t));
    l->next = root;
    l->data = data;
    return l;
}
#endif

// Relies on the root->last being correct. Do not use with the other list_*
//  routines unless they are fixed to modify root->last as well.
static list_t *list_append_to_end(list_t *root, void *data)
{
    list_t *l = malloc(sizeof(list_t));
    l->last = l;
    l->next = NULL;
    l->data = data;

    if ( !root )
        return l;

    root->last->next = l;
    root->last = l;
    return root;
}

static list_t *list_append(list_t *root, void *data)
{
    list_t *l = root;
    while (l && l->next)
        l = l->next;
    if ( l ) 
    {
        l->next = malloc(sizeof(list_t));
        l = l->next;
    }
    else
    {
        l = malloc(sizeof(list_t));
        root = l;
    }
    l->data = data;
    l->next = NULL;
    return root;
}

static void list_free(list_t *root)
{
    list_t *l = root;
    while (root)
    {
        l = root;
        root = root->next;
        free(l);
    }
}



// Look for a tag "XY" in a predefined const char *[] array.
static int tag_exists(const char *tag, const char **tags)
{
    int itag=0;
    if ( !tags ) return -1;
    while ( tags[itag] )
    {
        if ( tags[itag][0]==tag[0] && tags[itag][1]==tag[1] ) return itag; 
        itag++;
    }
    return -1;
}



// Mimics the behaviour of getline, except it returns pointer to the next chunk of the text
//  or NULL if everything has been read. The lineptr should be freed by the caller. The
//  newline character is stripped.
static const char *nextline(char **lineptr, size_t *n, const char *text)
{
    int len;
    const char *to = text;

    if ( !*to ) return NULL;

    while ( *to && *to!='\n' && *to!='\r' ) to++;
    len = to - text + 1;

    if ( *to )
    {
        // Advance the pointer for the next call
        if ( *to=='\n' ) to++;
        else if ( *to=='\r' && *(to+1)=='\n' ) to+=2;
    }
    if ( !len )
        return to;

    if ( !*lineptr ) 
    {
        *lineptr = malloc(len);
        *n = len;
    }
    else if ( *nkey[0] = name[0];
    tag->key[1] = name[1];
    tag->value = malloc(len+1);
    memcpy(tag->value,value_from,len+1);
    tag->value[len] = 0;
    return tag;
}

static HeaderTag *header_line_has_tag(HeaderLine *hline, const char *key)
{
    list_t *tags = hline->tags;
    while (tags)
    {
        HeaderTag *tag = tags->data;
        if ( tag->key[0]==key[0] && tag->key[1]==key[1] ) return tag;
        tags = tags->next;
    }
    return NULL;
}


// Return codes:
//   0 .. different types or unique tags differ or conflicting tags, cannot be merged
//   1 .. all tags identical -> no need to merge, drop one
//   2 .. the unique tags match and there are some conflicting tags (same tag, different value) -> error, cannot be merged nor duplicated
//   3 .. there are some missing complementary tags and no unique conflict -> can be merged into a single line
static int sam_header_compare_lines(HeaderLine *hline1, HeaderLine *hline2)
{
    HeaderTag *t1, *t2;

    if ( hline1->type[0]!=hline2->type[0] || hline1->type[1]!=hline2->type[1] )
        return 0;

    int itype = tag_exists(hline1->type,types);
    if ( itype==-1 ) {
		debug("[sam_header_compare_lines] Unknown type [%c%c]\n", hline1->type[0],hline1->type[1]);
		return -1; // FIXME (lh3): error; I do not know how this will be handled in Petr's code
	}

    if ( unique_tags[itype] )
    {
        t1 = header_line_has_tag(hline1,unique_tags[itype][0]);
        t2 = header_line_has_tag(hline2,unique_tags[itype][0]);
        if ( !t1 || !t2 ) // this should never happen, the unique tags are required
            return 2;

        if ( strcmp(t1->value,t2->value) )
            return 0;   // the unique tags differ, cannot be merged
    }
    if ( !required_tags[itype] && !optional_tags[itype] )
    {
        t1 = hline1->tags->data;
        t2 = hline2->tags->data;
        if ( !strcmp(t1->value,t2->value) ) return 1; // identical comments
        return 0;
    }

    int missing=0, itag=0;
    while ( required_tags[itype] && required_tags[itype][itag] )
    {
        t1 = header_line_has_tag(hline1,required_tags[itype][itag]);
        t2 = header_line_has_tag(hline2,required_tags[itype][itag]);
        if ( !t1 && !t2 )
            return 2;       // this should never happen
        else if ( !t1 || !t2 )
            missing = 1;    // there is some tag missing in one of the hlines
        else if ( strcmp(t1->value,t2->value) )
        {
            if ( unique_tags[itype] )
                return 2;   // the lines have a matching unique tag but have a conflicting tag
                    
            return 0;    // the lines contain conflicting tags, cannot be merged
        }
        itag++;
    }
    itag = 0;
    while ( optional_tags[itype] && optional_tags[itype][itag] )
    {
        t1 = header_line_has_tag(hline1,optional_tags[itype][itag]);
        t2 = header_line_has_tag(hline2,optional_tags[itype][itag]);
        if ( !t1 && !t2 )
        {
            itag++;
            continue;
        }
        if ( !t1 || !t2 )
            missing = 1;    // there is some tag missing in one of the hlines
        else if ( strcmp(t1->value,t2->value) )
        {
            if ( unique_tags[itype] )
                return 2;   // the lines have a matching unique tag but have a conflicting tag

            return 0;   // the lines contain conflicting tags, cannot be merged
        }
        itag++;
    }
    if ( missing ) return 3;    // there are some missing complementary tags with no conflicts, can be merged
    return 1;
}


static HeaderLine *sam_header_line_clone(const HeaderLine *hline)
{
    list_t *tags;
    HeaderLine *out = malloc(sizeof(HeaderLine));
    out->type[0] = hline->type[0];
    out->type[1] = hline->type[1];
    out->tags = NULL;

    tags = hline->tags;
    while (tags)
    {
        HeaderTag *old = tags->data;

        HeaderTag *new = malloc(sizeof(HeaderTag));
        new->key[0] = old->key[0];
        new->key[1] = old->key[1];
        new->value  = strdup(old->value);
        out->tags = list_append(out->tags, new);

        tags = tags->next;
    }
    return out;
}

static int sam_header_line_merge_with(HeaderLine *out_hline, const HeaderLine *tmpl_hline)
{
    list_t *tmpl_tags;

    if ( out_hline->type[0]!=tmpl_hline->type[0] || out_hline->type[1]!=tmpl_hline->type[1] )
        return 0;
    
    tmpl_tags = tmpl_hline->tags;
    while (tmpl_tags)
    {
        HeaderTag *tmpl_tag = tmpl_tags->data;
        HeaderTag *out_tag  = header_line_has_tag(out_hline, tmpl_tag->key);
        if ( !out_tag )
        {
            HeaderTag *tag = malloc(sizeof(HeaderTag));
            tag->key[0] = tmpl_tag->key[0];
            tag->key[1] = tmpl_tag->key[1];
            tag->value  = strdup(tmpl_tag->value);
            out_hline->tags = list_append(out_hline->tags,tag);
        }
        tmpl_tags = tmpl_tags->next;
    }
    return 1;
}


static HeaderLine *sam_header_line_parse(const char *headerLine)
{
    HeaderLine *hline;
    HeaderTag *tag;
    const char *from, *to;
    from = headerLine;

    if ( *from != '@' ) {
		debug("[sam_header_line_parse] expected '@', got [%s]\n", headerLine);
		return 0;
	}
    to = ++from;

    while (*to && *to!='\t') to++;
    if ( to-from != 2 ) {
		debug("[sam_header_line_parse] expected '@XY', got [%s]\nHint: The header tags must be tab-separated.\n", headerLine);
		return 0;
	}
    
    hline = malloc(sizeof(HeaderLine));
    hline->type[0] = from[0];
    hline->type[1] = from[1];
    hline->tags = NULL;

    int itype = tag_exists(hline->type, types);
    
    from = to;
    while (*to && *to=='\t') to++;
    if ( to-from != 1 ) {
        debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
		return 0;
	}
    from = to;
    while (*from)
    {
        while (*to && *to!='\t') to++;

        if ( !required_tags[itype] && !optional_tags[itype] )
        {
            // CO is a special case, it can contain anything, including tabs
            if ( *to ) { to++; continue; }
            tag = new_tag("  ",from,to-1);
        }
        else
            tag = new_tag(from,from+3,to-1);

        if ( header_line_has_tag(hline,tag->key) ) 
                debug("The tag '%c%c' present (at least) twice on line [%s]\n", tag->key[0],tag->key[1], headerLine);
        hline->tags = list_append(hline->tags, tag);

        from = to;
        while (*to && *to=='\t') to++;
        if ( *to && to-from != 1 ) {
			debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
			return 0;
		}

        from = to;
    }
    return hline;
}


// Must be of an existing type, all tags must be recognised and all required tags must be present
static int sam_header_line_validate(HeaderLine *hline)
{
    list_t *tags;
    HeaderTag *tag;
    int itype, itag;
    
    // Is the type correct?
    itype = tag_exists(hline->type, types);
    if ( itype==-1 ) 
    {
        debug("The type [%c%c] not recognised.\n", hline->type[0],hline->type[1]);
        return 0;
    }

    // Has all required tags?
    itag = 0;
    while ( required_tags[itype] && required_tags[itype][itag] )
    {
        if ( !header_line_has_tag(hline,required_tags[itype][itag]) )
        {
            debug("The tag [%c%c] required for [%c%c] not present.\n", required_tags[itype][itag][0],required_tags[itype][itag][1],
                hline->type[0],hline->type[1]);
            return 0;
        }
        itag++;
    }

    // Are all tags recognised?
    tags = hline->tags;
    while ( tags )
    {
        tag = tags->data;
        if ( !tag_exists(tag->key,required_tags[itype]) && !tag_exists(tag->key,optional_tags[itype]) )
        {
            debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]);
            return 0;
        }
        tags = tags->next;
    }

    return 1;
}


static void print_header_line(FILE *fp, HeaderLine *hline)
{
    list_t *tags = hline->tags;
    HeaderTag *tag;

    fprintf(fp, "@%c%c", hline->type[0],hline->type[1]);
    while (tags)
    {
        tag = tags->data;

        fprintf(fp, "\t");
        if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
            fprintf(fp, "%c%c:", tag->key[0],tag->key[1]);
        fprintf(fp, "%s", tag->value);

        tags = tags->next;
    }
    fprintf(fp,"\n");
}


static void sam_header_line_free(HeaderLine *hline)
{
    list_t *tags = hline->tags;
    while (tags)
    {
        HeaderTag *tag = tags->data;
        free(tag->value);
        free(tag);
        tags = tags->next;
    }
    list_free(hline->tags);
    free(hline);
}

void sam_header_free(void *_header)
{
	HeaderDict *header = (HeaderDict*)_header;
    list_t *hlines = header;
    while (hlines)
    {
        sam_header_line_free(hlines->data);
        hlines = hlines->next;
    }
    list_free(header);
}

HeaderDict *sam_header_clone(const HeaderDict *dict)
{
    HeaderDict *out = NULL;
    while (dict)
    {
        HeaderLine *hline = dict->data;
        out = list_append(out, sam_header_line_clone(hline));
        dict = dict->next;
    }
    return out;
}

// Returns a newly allocated string
char *sam_header_write(const void *_header)
{
	const HeaderDict *header = (const HeaderDict*)_header;
    char *out = NULL;
    int len=0, nout=0;
    const list_t *hlines;

    // Calculate the length of the string to allocate
    hlines = header;
    while (hlines)
    {
        len += 4;   // @XY and \n

        HeaderLine *hline = hlines->data;
        list_t *tags = hline->tags;
        while (tags)
        {
            HeaderTag *tag = tags->data;
            len += strlen(tag->value) + 1;                  // \t
            if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
                len += strlen(tag->value) + 3;              // XY:
            tags = tags->next;
        }
        hlines = hlines->next;
    }

    nout = 0;
    out  = malloc(len+1);
    hlines = header;
    while (hlines)
    {
        HeaderLine *hline = hlines->data;

        nout += sprintf(out+nout,"@%c%c",hline->type[0],hline->type[1]);

        list_t *tags = hline->tags;
        while (tags)
        {
            HeaderTag *tag = tags->data;
            nout += sprintf(out+nout,"\t");
            if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
                nout += sprintf(out+nout,"%c%c:", tag->key[0],tag->key[1]);
            nout += sprintf(out+nout,"%s", tag->value);
            tags = tags->next;
        }
        hlines = hlines->next;
        nout += sprintf(out+nout,"\n");
    }
    out[len] = 0;
    return out;
}

void *sam_header_parse2(const char *headerText)
{
    list_t *hlines = NULL;
    HeaderLine *hline;
    const char *text;
    char *buf=NULL;
    size_t nbuf = 0;
	int tovalidate = 0;

    if ( !headerText )
		return 0;

    text = headerText;
    while ( (text=nextline(&buf, &nbuf, text)) )
    {
        hline = sam_header_line_parse(buf);
        if ( hline && (!tovalidate || sam_header_line_validate(hline)) )
            // With too many (~250,000) reference sequences the header parsing was too slow with list_append.
            hlines = list_append_to_end(hlines, hline);
        else
        {
			if (hline) sam_header_line_free(hline);
			sam_header_free(hlines);
            if ( buf ) free(buf);
            return NULL;
        }
    }
    if ( buf ) free(buf);

    return hlines;
}

void *sam_header2tbl(const void *_dict, char type[2], char key_tag[2], char value_tag[2])
{
	const HeaderDict *dict = (const HeaderDict*)_dict;
    const list_t *l   = dict;
    khash_t(str) *tbl = kh_init(str);
    khiter_t k;
    int ret;

	if (_dict == 0) return tbl; // return an empty (not null) hash table
    while (l)
    {
        HeaderLine *hline = l->data;
        if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] ) 
        {
            l = l->next;
            continue;
        }
        
        HeaderTag *key, *value;
        key   = header_line_has_tag(hline,key_tag);
        value = header_line_has_tag(hline,value_tag); 
        if ( !key || !value )
        {
            l = l->next;
            continue;
        }
        
        k = kh_get(str, tbl, key->value);
        if ( k != kh_end(tbl) )
            debug("[sam_header_lookup_table] They key %s not unique.\n", key->value);
        k = kh_put(str, tbl, key->value, &ret);
        kh_value(tbl, k) = value->value;

        l = l->next;
    }
    return tbl;
}

char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n)
{
	const HeaderDict *dict = (const HeaderDict*)_dict;
    const list_t *l   = dict;
    int max, n;
	char **ret;

	ret = 0; *_n = max = n = 0;
    while (l)
    {
        HeaderLine *hline = l->data;
        if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] ) 
        {
            l = l->next;
            continue;
        }
        
        HeaderTag *key;
        key   = header_line_has_tag(hline,key_tag);
        if ( !key )
        {
            l = l->next;
            continue;
        }

		if (n == max) {
			max = max? max<<1 : 4;
			ret = realloc(ret, max * sizeof(void*));
		}
		ret[n++] = key->value;

        l = l->next;
    }
	*_n = n;
    return ret;
}

const char *sam_tbl_get(void *h, const char *key)
{
	khash_t(str) *tbl = (khash_t(str)*)h;
	khint_t k;
	k = kh_get(str, tbl, key);
	return k == kh_end(tbl)? 0 : kh_val(tbl, k);
}

int sam_tbl_size(void *h)
{
	khash_t(str) *tbl = (khash_t(str)*)h;
	return h? kh_size(tbl) : 0;
}

void sam_tbl_destroy(void *h)
{
	khash_t(str) *tbl = (khash_t(str)*)h;
	kh_destroy(str, tbl);
}

void *sam_header_merge(int n, const void **_dicts)
{
	const HeaderDict **dicts = (const HeaderDict**)_dicts;
    HeaderDict *out_dict;
    int idict, status;

    if ( n<2 ) return NULL;

    out_dict = sam_header_clone(dicts[0]);

    for (idict=1; idictdata, out_hlines->data);
                if ( status==0 )
                {
                    out_hlines = out_hlines->next;
                    continue;
                }
                
                if ( status==2 ) 
                {
                    print_header_line(stderr,tmpl_hlines->data);
                    print_header_line(stderr,out_hlines->data);
                    debug("Conflicting lines, cannot merge the headers.\n");
					return 0;
                }
                if ( status==3 )
                    sam_header_line_merge_with(out_hlines->data, tmpl_hlines->data);

                inserted = 1;
                break;
            }
            if ( !inserted )
                out_dict = list_append(out_dict, sam_header_line_clone(tmpl_hlines->data));

            tmpl_hlines = tmpl_hlines->next;
        }
    }

    return out_dict;
}


genometools-1.5.1/src/external/samtools-0.1.18/sam_header.h000066400000000000000000000012031211610345200232760ustar00rootroot00000000000000#ifndef __SAM_HEADER_H__
#define __SAM_HEADER_H__

#ifdef __cplusplus
extern "C" {
#endif

	void *sam_header_parse2(const char *headerText);
	void *sam_header_merge(int n, const void **dicts);
	void sam_header_free(void *header);
	char *sam_header_write(const void *headerDict);   // returns a newly allocated string

	char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n);

	void *sam_header2tbl(const void *dict, char type[2], char key_tag[2], char value_tag[2]);
	const char *sam_tbl_get(void *h, const char *key);
	int sam_tbl_size(void *h);
	void sam_tbl_destroy(void *h);

#ifdef __cplusplus
}
#endif

#endif
genometools-1.5.1/src/external/samtools-0.1.18/sam_view.c000066400000000000000000000324221211610345200230220ustar00rootroot00000000000000#include 
#include 
#include 
#include 
#include 
#include "sam_header.h"
#include "sam.h"
#include "faidx.h"
#include "kstring.h"
#include "khash.h"
KHASH_SET_INIT_STR(rg)

// When counting records instead of printing them,
// data passed to the bam_fetch callback is encapsulated in this struct.
typedef struct {
	bam_header_t *header;
	int *count;
} count_func_data_t;

typedef khash_t(rg) *rghash_t;

// FIXME: we'd better use no global variables...
static rghash_t g_rghash = 0;
static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
static float g_subsam = -1;
static char *g_library, *g_rg;
static void *g_bed;

void *bed_read(const char *fn);
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);

static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
{
	if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
		return 1;
	if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
		return 1;
	if (g_subsam > 0.) {
		int x = (int)(g_subsam + .499);
		uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + x;
		if (k%1024 / 1024.0 >= g_subsam - x) return 1;
	}
	if (g_rg || g_rghash) {
		uint8_t *s = bam_aux_get(b, "RG");
		if (s) {
			if (g_rg) return (strcmp(g_rg, (char*)(s + 1)) == 0)? 0 : 1;
			if (g_rghash) {
				khint_t k = kh_get(rg, g_rghash, (char*)(s + 1));
				return (k != kh_end(g_rghash))? 0 : 1;
			}
		}
	}
	if (g_library) {
		const char *p = bam_get_library((bam_header_t*)h, b);
		return (p && strcmp(p, g_library) == 0)? 0 : 1;
	}
	return 0;
}

static char *drop_rg(char *hdtxt, rghash_t h, int *len)
{
	char *p = hdtxt, *q, *r, *s;
	kstring_t str;
	memset(&str, 0, sizeof(kstring_t));
	while (1) {
		int toprint = 0;
		q = strchr(p, '\n');
		if (q == 0) q = p + strlen(p);
		if (q - p < 3) break; // the line is too short; then stop
		if (strncmp(p, "@RG\t", 4) == 0) {
			int c;
			khint_t k;
			if ((r = strstr(p, "\tID:")) != 0) {
				r += 4;
				for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s);
				c = *s; *s = '\0';
				k = kh_get(rg, h, r);
				*s = c;
				if (k != kh_end(h)) toprint = 1;
			}
		} else toprint = 1;
		if (toprint) {
			kputsn(p, q - p, &str); kputc('\n', &str);
		}
		p = q + 1;
	}
	*len = str.l;
	return str.s;
}

// callback function for bam_fetch() that prints nonskipped records
static int view_func(const bam1_t *b, void *data)
{
	if (!__g_skip_aln(((samfile_t*)data)->header, b))
		samwrite((samfile_t*)data, b);
	return 0;
}

// callback function for bam_fetch() that counts nonskipped records
static int count_func(const bam1_t *b, void *data)
{
	if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) {
		(*((count_func_data_t*)data)->count)++;
	}
	return 0;
}

static int usage(int is_long_help);

int main_samview(int argc, char *argv[])
{
	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
	int of_type = BAM_OFDEC, is_long_help = 0;
	int count = 0;
	samfile_t *in = 0, *out = 0;
	char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0;

	/* parse command-line options */
	strcpy(in_mode, "r"); strcpy(out_mode, "w");
	while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:")) >= 0) {
		switch (c) {
		case 's': g_subsam = atof(optarg); break;
		case 'c': is_count = 1; break;
		case 'S': is_bamin = 0; break;
		case 'b': is_bamout = 1; break;
		case 't': fn_list = strdup(optarg); is_bamin = 0; break;
		case 'h': is_header = 1; break;
		case 'H': is_header_only = 1; break;
		case 'o': fn_out = strdup(optarg); break;
		case 'f': g_flag_on = strtol(optarg, 0, 0); break;
		case 'F': g_flag_off = strtol(optarg, 0, 0); break;
		case 'q': g_min_mapQ = atoi(optarg); break;
		case 'u': compress_level = 0; break;
		case '1': compress_level = 1; break;
		case 'l': g_library = strdup(optarg); break;
		case 'L': g_bed = bed_read(optarg); break;
		case 'r': g_rg = strdup(optarg); break;
		case 'R': fn_rg = strdup(optarg); break;
		case 'x': of_type = BAM_OFHEX; break;
		case 'X': of_type = BAM_OFSTR; break;
		case '?': is_long_help = 1; break;
		case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
		default: return usage(is_long_help);
		}
	}
	if (compress_level >= 0) is_bamout = 1;
	if (is_header_only) is_header = 1;
	if (is_bamout) strcat(out_mode, "b");
	else {
		if (of_type == BAM_OFHEX) strcat(out_mode, "x");
		else if (of_type == BAM_OFSTR) strcat(out_mode, "X");
	}
	if (is_bamin) strcat(in_mode, "b");
	if (is_header) strcat(out_mode, "h");
	if (compress_level >= 0) {
		char tmp[2];
		tmp[0] = compress_level + '0'; tmp[1] = '\0';
		strcat(out_mode, tmp);
	}
	if (argc == optind) return usage(is_long_help); // potential memory leak...

	// read the list of read groups
	if (fn_rg) {
		FILE *fp_rg;
		char buf[1024];
		int ret;
		g_rghash = kh_init(rg);
		fp_rg = fopen(fn_rg, "r");
		while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but bear me...
			kh_put(rg, g_rghash, strdup(buf), &ret); // we'd better check duplicates...
		fclose(fp_rg);
	}

	// generate the fn_list if necessary
	if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
	// open file handlers
	if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
		fprintf(stderr, "[main_samview] fail to open \"%s\" for reading.\n", argv[optind]);
		ret = 1;
		goto view_end;
	}
	if (in->header == 0) {
		fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", argv[optind]);
		ret = 1;
		goto view_end;
	}
	if (g_rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
		char *tmp;
		int l;
		tmp = drop_rg(in->header->text, g_rghash, &l);
		free(in->header->text);
		in->header->text = tmp;
		in->header->l_text = l;
	}
	if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
		fprintf(stderr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
		ret = 1;
		goto view_end;
	}
	if (is_header_only) goto view_end; // no need to print alignments

	if (argc == optind + 1) { // convert/print the entire file
		bam1_t *b = bam_init1();
		int r;
		while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
			if (!__g_skip_aln(in->header, b)) {
				if (!is_count) samwrite(out, b); // write the alignment to `out'
				count++;
			}
		}
		if (r < -1) {
			fprintf(stderr, "[main_samview] truncated file.\n");
			ret = 1;
		}
		bam_destroy1(b);
	} else { // retrieve alignments in specified regions
		int i;
		bam_index_t *idx = 0;
		if (is_bamin) idx = bam_index_load(argv[optind]); // load BAM index
		if (idx == 0) { // index is unavailable
			fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM files.\n");
			ret = 1;
			goto view_end;
		}
		for (i = optind + 1; i < argc; ++i) {
			int tid, beg, end, result;
			bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200'
			if (tid < 0) { // reference name is not found
				fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
				continue;
			}
			// fetch alignments
			if (is_count) {
				count_func_data_t count_data = { in->header, &count };
				result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func);
			} else
				result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func);
			if (result < 0) {
				fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
				ret = 1;
				break;
			}
		}
		bam_index_destroy(idx); // destroy the BAM index
	}

view_end:
	if (is_count && ret == 0) {
		printf("%d\n", count);
	}
	// close files, free and return
	free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
	if (g_bed) bed_destroy(g_bed);
	if (g_rghash) {
		khint_t k;
		for (k = 0; k < kh_end(g_rghash); ++k)
			if (kh_exist(g_rghash, k)) free((char*)kh_key(g_rghash, k));
		kh_destroy(rg, g_rghash);
	}
	samclose(in);
	if (!is_count)
		samclose(out);
	return ret;
}

static int usage(int is_long_help)
{
	fprintf(stderr, "\n");
	fprintf(stderr, "Usage:   samtools view [options] | [region1 [...]]\n\n");
	fprintf(stderr, "Options: -b       output BAM\n");
	fprintf(stderr, "         -h       print header for the SAM output\n");
	fprintf(stderr, "         -H       print header only (no alignments)\n");
	fprintf(stderr, "         -S       input is SAM\n");
	fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
	fprintf(stderr, "         -1       fast compression (force -b)\n");
	fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
	fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
	fprintf(stderr, "         -c       print only the count of matching records\n");
	fprintf(stderr, "         -L FILE  output alignments overlapping the input BED FILE [null]\n");
	fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
	fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
	fprintf(stderr, "         -o FILE  output file name [stdout]\n");
	fprintf(stderr, "         -R FILE  list of read groups to be outputted [null]\n");
	fprintf(stderr, "         -f INT   required flag, 0 for unset [0]\n");
	fprintf(stderr, "         -F INT   filtering flag, 0 for unset [0]\n");
	fprintf(stderr, "         -q INT   minimum mapping quality [0]\n");
	fprintf(stderr, "         -l STR   only output reads in library STR [null]\n");
	fprintf(stderr, "         -r STR   only output reads in read group STR [null]\n");
	fprintf(stderr, "         -s FLOAT fraction of templates to subsample; integer part as seed [-1]\n");
	fprintf(stderr, "         -?       longer help\n");
	fprintf(stderr, "\n");
	if (is_long_help)
		fprintf(stderr, "Notes:\n\
\n\
  1. By default, this command assumes the file on the command line is in\n\
     the BAM format and it prints the alignments in SAM. If `-t' is\n\
     applied, the input file is assumed to be in the SAM format. The\n\
     file supplied with `-t' is SPACE/TAB delimited with the first two\n\
     fields of each line consisting of the reference name and the\n\
     corresponding sequence length. The `.fai' file generated by `faidx'\n\
     can be used here. This file may be empty if reads are unaligned.\n\
\n\
  2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.\n\
\n\
  3. BAM->SAM conversion: `samtools view in.bam'.\n\
\n\
  4. A region should be presented in one of the following formats:\n\
     `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\
     specified, the input alignment file must be an indexed BAM file.\n\
\n\
  5. Option `-u' is preferred over `-b' when the output is piped to\n\
     another samtools command.\n\
\n\
  6. In a string FLAG, each character represents one bit with\n\
     p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped),\n\
     U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse)\n\
     1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), \n\
     f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and\n\
     `-X' are samtools-C specific. Picard and older samtools do not\n\
     support HEX or string flags.\n\
\n");
	return 1;
}

int main_import(int argc, char *argv[])
{
	int argc2, ret;
	char **argv2;
	if (argc != 4) {
		fprintf(stderr, "Usage: bamtk import   \n");
		return 1;
	}
	argc2 = 6;
	argv2 = calloc(6, sizeof(char*));
	argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2];
	ret = main_samview(argc2, argv2);
	free(argv2);
	return ret;
}

int8_t seq_comp_table[16] = { 0, 8, 4, 12, 2, 10, 9, 14, 1, 6, 5, 13, 3, 11, 7, 15 };

int main_bam2fq(int argc, char *argv[])
{
	bamFile fp;
	bam_header_t *h;
	bam1_t *b;
	int8_t *buf;
	int max_buf;
	if (argc == 1) {
		fprintf(stderr, "Usage: samtools bam2fq \n");
		return 1;
	}
	fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
	if (fp == 0) return 1;
	h = bam_header_read(fp);
	b = bam_init1();
	buf = 0;
	max_buf = 0;
	while (bam_read1(fp, b) >= 0) {
		int i, qlen = b->core.l_qseq;
		uint8_t *seq;
		putchar('@'); fputs(bam1_qname(b), stdout);
		if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
		else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
		else putchar('\n');
		if (max_buf < qlen + 1) {
			max_buf = qlen + 1;
			kroundup32(max_buf);
			buf = realloc(buf, max_buf);
		}
		buf[qlen] = 0;
		seq = bam1_seq(b);
		for (i = 0; i < qlen; ++i)
			buf[i] = bam1_seqi(seq, i);
		if (b->core.flag & 16) { // reverse complement
			for (i = 0; i < qlen>>1; ++i) {
				int8_t t = seq_comp_table[buf[qlen - 1 - i]];
				buf[qlen - 1 - i] = seq_comp_table[buf[i]];
				buf[i] = t;
			}
			if (qlen&1) buf[i] = seq_comp_table[buf[i]];
		}
		for (i = 0; i < qlen; ++i)
			buf[i] = bam_nt16_rev_table[buf[i]];
		puts((char*)buf);
		puts("+");
		seq = bam1_qual(b);
		for (i = 0; i < qlen; ++i)
			buf[i] = 33 + seq[i];
		if (b->core.flag & 16) { // reverse
			for (i = 0; i < qlen>>1; ++i) {
				int8_t t = buf[qlen - 1 - i];
				buf[qlen - 1 - i] = buf[i];
				buf[i] = t;
			}
		}
		puts((char*)buf);
	}
	free(buf);
	bam_destroy1(b);
	bam_header_destroy(h);
	bam_close(fp);
	return 0;
}
genometools-1.5.1/src/external/samtools-0.1.18/sample.c000066400000000000000000000056501211610345200224740ustar00rootroot00000000000000#include 
#include 
#include "sample.h"
#include "khash.h"
KHASH_MAP_INIT_STR(sm, int)

bam_sample_t *bam_smpl_init(void)
{
	bam_sample_t *s;
	s = calloc(1, sizeof(bam_sample_t));
	s->rg2smid = kh_init(sm);
	s->sm2id = kh_init(sm);
	return s;
}

void bam_smpl_destroy(bam_sample_t *sm)
{
	int i;
	khint_t k;
	khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
	if (sm == 0) return;
	for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
	free(sm->smpl);
	for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
		if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
	kh_destroy(sm, sm->rg2smid);
	kh_destroy(sm, sm->sm2id);
	free(sm);
}

static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
{
	khint_t k_rg, k_sm;
	int ret;
	khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
	k_rg = kh_get(sm, rg2smid, key);
	if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
	k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
	k_sm = kh_get(sm, sm2id, val);
	if (k_sm == kh_end(sm2id)) { // absent
		if (sm->n == sm->m) {
			sm->m = sm->m? sm->m<<1 : 1;
			sm->smpl = realloc(sm->smpl, sizeof(void*) * sm->m);
		}
		sm->smpl[sm->n] = strdup(val);
		k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
		kh_val(sm2id, k_sm) = sm->n++;
	}
	kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
}

int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
{
	const char *p = txt, *q, *r;
	kstring_t buf, first_sm;
	int n = 0;
	khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
	if (txt == 0) {
		add_pair(sm, sm2id, fn, fn);
		return 0;
	}
	memset(&buf, 0, sizeof(kstring_t));
    memset(&first_sm, 0, sizeof(kstring_t));
	while ((q = strstr(p, "@RG")) != 0) {
		p = q + 3;
		r = q = 0;
		if ((q = strstr(p, "\tID:")) != 0) q += 4;
		if ((r = strstr(p, "\tSM:")) != 0) r += 4;
		if (r && q) {
			char *u, *v;
			int oq, or;
			for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
			for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
			oq = *u; or = *v; *u = *v = '\0';
			buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
			add_pair(sm, sm2id, buf.s, r);
            if ( !first_sm.s )
                kputs(r,&first_sm); 
			*u = oq; *v = or;
		} else break;
		p = q > r? q : r;
		++n;
	}
	if (n == 0) add_pair(sm, sm2id, fn, fn);
    // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
    //  use the tag instead.
    else if ( n==1 && first_sm.s )
        add_pair(sm,sm2id,fn,first_sm.s);
    if ( first_sm.s )
        free(first_sm.s);

//	add_pair(sm, sm2id, fn, fn);
	free(buf.s);
	return 0;
}

int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
{
	khint_t k;
	khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
	if (rg) {
		str->l = 0;
		kputs(fn, str); kputc('/', str); kputs(rg, str);
		k = kh_get(sm, rg2smid, str->s);
	} else k = kh_get(sm, rg2smid, fn);
	return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
}
genometools-1.5.1/src/external/samtools-0.1.18/sample.h000066400000000000000000000006141211610345200224740ustar00rootroot00000000000000#ifndef BAM_SAMPLE_H
#define BAM_SAMPLE_H

#include "kstring.h"

typedef struct {
	int n, m;
	char **smpl;
	void *rg2smid, *sm2id;
} bam_sample_t;

bam_sample_t *bam_smpl_init(void);
int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt);
int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str);
void bam_smpl_destroy(bam_sample_t *sm);

#endif
genometools-1.5.1/src/external/samtools-0.1.18/win32/000077500000000000000000000000001211610345200220035ustar00rootroot00000000000000genometools-1.5.1/src/external/samtools-0.1.18/win32/xcurses.h000066400000000000000000001413731211610345200236610ustar00rootroot00000000000000/* Public Domain Curses */

/* $Id: curses.h,v 1.295 2008/07/15 17:13:25 wmcbrine Exp $ */

/*----------------------------------------------------------------------*
 *                              PDCurses                                *
 *----------------------------------------------------------------------*/

#ifndef __PDCURSES__
#define __PDCURSES__ 1

/*man-start**************************************************************

PDCurses definitions list:  (Only define those needed)

    XCURSES         True if compiling for X11.
    PDC_RGB         True if you want to use RGB color definitions
                    (Red = 1, Green = 2, Blue = 4) instead of BGR.
    PDC_WIDE        True if building wide-character support.
    PDC_DLL_BUILD   True if building a Win32 DLL.
    NCURSES_MOUSE_VERSION   Use the ncurses mouse API instead
                            of PDCurses' traditional mouse API.

PDCurses portable platform definitions list:

    PDC_BUILD       Defines API build version.
    PDCURSES        Enables access to PDCurses-only routines.
    XOPEN           Always true.
    SYSVcurses      True if you are compiling for SYSV portability.
    BSDcurses       True if you are compiling for BSD portability.

**man-end****************************************************************/

#define PDC_BUILD 3401
#define PDCURSES        1      /* PDCurses-only routines */
#define XOPEN           1      /* X/Open Curses routines */
#define SYSVcurses      1      /* System V Curses routines */
#define BSDcurses       1      /* BSD Curses routines */
#define CHTYPE_LONG     1      /* size of chtype; long */

/*----------------------------------------------------------------------*/

#include 
#include 
#include              /* Required by X/Open usage below */

#ifdef PDC_WIDE
# include 
#endif

#if defined(__cplusplus) || defined(__cplusplus__) || defined(__CPLUSPLUS)
extern "C"
{
# define bool _bool
#endif

/*----------------------------------------------------------------------
 *
 *  PDCurses Manifest Constants
 *
 */

#ifndef FALSE
# define FALSE 0
#endif
#ifndef TRUE
# define TRUE 1
#endif
#ifndef NULL
# define NULL (void *)0
#endif
#ifndef ERR
# define ERR (-1)
#endif
#ifndef OK
# define OK 0
#endif

/*----------------------------------------------------------------------
 *
 *  PDCurses Type Declarations
 *
 */

typedef unsigned char bool;    /* PDCurses Boolean type */

#ifdef CHTYPE_LONG
# if _LP64
typedef unsigned int chtype;
# else
typedef unsigned long chtype;  /* 16-bit attr + 16-bit char */
# endif
#else
typedef unsigned short chtype; /* 8-bit attr + 8-bit char */
#endif

#ifdef PDC_WIDE
typedef chtype cchar_t;
#endif

typedef chtype attr_t;

/*----------------------------------------------------------------------
 *
 *  PDCurses Mouse Interface -- SYSVR4, with extensions
 *
 */

typedef struct
{
    int x;           /* absolute column, 0 based, measured in characters */
    int y;           /* absolute row, 0 based, measured in characters */
    short button[3]; /* state of each button */
    int changes;     /* flags indicating what has changed with the mouse */
} MOUSE_STATUS;

#define BUTTON_RELEASED         0x0000
#define BUTTON_PRESSED          0x0001
#define BUTTON_CLICKED          0x0002
#define BUTTON_DOUBLE_CLICKED   0x0003
#define BUTTON_TRIPLE_CLICKED   0x0004
#define BUTTON_MOVED            0x0005  /* PDCurses */
#define WHEEL_SCROLLED          0x0006  /* PDCurses */
#define BUTTON_ACTION_MASK      0x0007  /* PDCurses */

#define PDC_BUTTON_SHIFT        0x0008  /* PDCurses */
#define PDC_BUTTON_CONTROL      0x0010  /* PDCurses */
#define PDC_BUTTON_ALT          0x0020  /* PDCurses */
#define BUTTON_MODIFIER_MASK    0x0038  /* PDCurses */

#define MOUSE_X_POS             (Mouse_status.x)
#define MOUSE_Y_POS             (Mouse_status.y)

/*
 * Bits associated with the .changes field:
 *   3         2         1         0
 * 210987654321098765432109876543210
 *                                 1 <- button 1 has changed
 *                                10 <- button 2 has changed
 *                               100 <- button 3 has changed
 *                              1000 <- mouse has moved
 *                             10000 <- mouse position report
 *                            100000 <- mouse wheel up
 *                           1000000 <- mouse wheel down
 */

#define PDC_MOUSE_MOVED         0x0008
#define PDC_MOUSE_POSITION      0x0010
#define PDC_MOUSE_WHEEL_UP      0x0020
#define PDC_MOUSE_WHEEL_DOWN    0x0040

#define A_BUTTON_CHANGED        (Mouse_status.changes & 7)
#define MOUSE_MOVED             (Mouse_status.changes & PDC_MOUSE_MOVED)
#define MOUSE_POS_REPORT        (Mouse_status.changes & PDC_MOUSE_POSITION)
#define BUTTON_CHANGED(x)       (Mouse_status.changes & (1 << ((x) - 1)))
#define BUTTON_STATUS(x)        (Mouse_status.button[(x) - 1])
#define MOUSE_WHEEL_UP          (Mouse_status.changes & PDC_MOUSE_WHEEL_UP)
#define MOUSE_WHEEL_DOWN        (Mouse_status.changes & PDC_MOUSE_WHEEL_DOWN)

/* mouse bit-masks */

#define BUTTON1_RELEASED        0x00000001L
#define BUTTON1_PRESSED         0x00000002L
#define BUTTON1_CLICKED         0x00000004L
#define BUTTON1_DOUBLE_CLICKED  0x00000008L
#define BUTTON1_TRIPLE_CLICKED  0x00000010L
#define BUTTON1_MOVED           0x00000010L /* PDCurses */

#define BUTTON2_RELEASED        0x00000020L
#define BUTTON2_PRESSED         0x00000040L
#define BUTTON2_CLICKED         0x00000080L
#define BUTTON2_DOUBLE_CLICKED  0x00000100L
#define BUTTON2_TRIPLE_CLICKED  0x00000200L
#define BUTTON2_MOVED           0x00000200L /* PDCurses */

#define BUTTON3_RELEASED        0x00000400L
#define BUTTON3_PRESSED         0x00000800L
#define BUTTON3_CLICKED         0x00001000L
#define BUTTON3_DOUBLE_CLICKED  0x00002000L
#define BUTTON3_TRIPLE_CLICKED  0x00004000L
#define BUTTON3_MOVED           0x00004000L /* PDCurses */

/* For the ncurses-compatible functions only, BUTTON4_PRESSED and 
   BUTTON5_PRESSED are returned for mouse scroll wheel up and down; 
   otherwise PDCurses doesn't support buttons 4 and 5 */

#define BUTTON4_RELEASED        0x00008000L
#define BUTTON4_PRESSED         0x00010000L
#define BUTTON4_CLICKED         0x00020000L
#define BUTTON4_DOUBLE_CLICKED  0x00040000L
#define BUTTON4_TRIPLE_CLICKED  0x00080000L

#define BUTTON5_RELEASED        0x00100000L
#define BUTTON5_PRESSED         0x00200000L
#define BUTTON5_CLICKED         0x00400000L
#define BUTTON5_DOUBLE_CLICKED  0x00800000L
#define BUTTON5_TRIPLE_CLICKED  0x01000000L

#define MOUSE_WHEEL_SCROLL      0x02000000L /* PDCurses */
#define BUTTON_MODIFIER_SHIFT   0x04000000L /* PDCurses */
#define BUTTON_MODIFIER_CONTROL 0x08000000L /* PDCurses */
#define BUTTON_MODIFIER_ALT     0x10000000L /* PDCurses */

#define ALL_MOUSE_EVENTS        0x1fffffffL
#define REPORT_MOUSE_POSITION   0x20000000L

/* ncurses mouse interface */

typedef unsigned long mmask_t;

typedef struct
{
        short id;       /* unused, always 0 */
        int x, y, z;    /* x, y same as MOUSE_STATUS; z unused */
        mmask_t bstate; /* equivalent to changes + button[], but
                           in the same format as used for mousemask() */
} MEVENT;

#ifdef NCURSES_MOUSE_VERSION
# define BUTTON_SHIFT   BUTTON_MODIFIER_SHIFT
# define BUTTON_CONTROL BUTTON_MODIFIER_CONTROL
# define BUTTON_CTRL    BUTTON_MODIFIER_CONTROL
# define BUTTON_ALT     BUTTON_MODIFIER_ALT
#else
# define BUTTON_SHIFT   PDC_BUTTON_SHIFT
# define BUTTON_CONTROL PDC_BUTTON_CONTROL
# define BUTTON_ALT     PDC_BUTTON_ALT
#endif

/*----------------------------------------------------------------------
 *
 *  PDCurses Structure Definitions
 *
 */

typedef struct _win       /* definition of a window */
{
    int   _cury;          /* current pseudo-cursor */
    int   _curx;
    int   _maxy;          /* max window coordinates */
    int   _maxx;
    int   _begy;          /* origin on screen */
    int   _begx;
    int   _flags;         /* window properties */
    chtype _attrs;        /* standard attributes and colors */
    chtype _bkgd;         /* background, normally blank */
    bool  _clear;         /* causes clear at next refresh */
    bool  _leaveit;       /* leaves cursor where it is */
    bool  _scroll;        /* allows window scrolling */
    bool  _nodelay;       /* input character wait flag */
    bool  _immed;         /* immediate update flag */
    bool  _sync;          /* synchronise window ancestors */
    bool  _use_keypad;    /* flags keypad key mode active */
    chtype **_y;          /* pointer to line pointer array */
    int   *_firstch;      /* first changed character in line */
    int   *_lastch;       /* last changed character in line */
    int   _tmarg;         /* top of scrolling region */
    int   _bmarg;         /* bottom of scrolling region */
    int   _delayms;       /* milliseconds of delay for getch() */
    int   _parx, _pary;   /* coords relative to parent (0,0) */
    struct _win *_parent; /* subwin's pointer to parent win */
} WINDOW;

/* Avoid using the SCREEN struct directly -- use the corresponding 
   functions if possible. This struct may eventually be made private. */

typedef struct
{
    bool  alive;          /* if initscr() called, and not endwin() */
    bool  autocr;         /* if cr -> lf */
    bool  cbreak;         /* if terminal unbuffered */
    bool  echo;           /* if terminal echo */
    bool  raw_inp;        /* raw input mode (v. cooked input) */
    bool  raw_out;        /* raw output mode (7 v. 8 bits) */
    bool  audible;        /* FALSE if the bell is visual */
    bool  mono;           /* TRUE if current screen is mono */
    bool  resized;        /* TRUE if TERM has been resized */
    bool  orig_attr;      /* TRUE if we have the original colors */
    short orig_fore;      /* original screen foreground color */
    short orig_back;      /* original screen foreground color */
    int   cursrow;        /* position of physical cursor */
    int   curscol;        /* position of physical cursor */
    int   visibility;     /* visibility of cursor */
    int   orig_cursor;    /* original cursor size */
    int   lines;          /* new value for LINES */
    int   cols;           /* new value for COLS */
    unsigned long _trap_mbe;       /* trap these mouse button events */
    unsigned long _map_mbe_to_key; /* map mouse buttons to slk */
    int   mouse_wait;              /* time to wait (in ms) for a
                                      button release after a press, in 
                                      order to count it as a click */
    int   slklines;                /* lines in use by slk_init() */
    WINDOW *slk_winptr;            /* window for slk */
    int   linesrippedoff;          /* lines ripped off via ripoffline() */
    int   linesrippedoffontop;     /* lines ripped off on 
                                      top via ripoffline() */
    int   delaytenths;             /* 1/10ths second to wait block
                                      getch() for */
    bool  _preserve;               /* TRUE if screen background
                                      to be preserved */
    int   _restore;                /* specifies if screen background
                                      to be restored, and how */
    bool  save_key_modifiers;      /* TRUE if each key modifiers saved
                                      with each key press */
    bool  return_key_modifiers;    /* TRUE if modifier keys are
                                      returned as "real" keys */
    bool  key_code;                /* TRUE if last key is a special key;
                                      used internally by get_wch() */
#ifdef XCURSES
    int   XcurscrSize;    /* size of Xcurscr shared memory block */
    bool  sb_on;
    int   sb_viewport_y;
    int   sb_viewport_x;
    int   sb_total_y;
    int   sb_total_x;
    int   sb_cur_y;
    int   sb_cur_x;
#endif
    short line_color;     /* color of line attributes - default -1 */
} SCREEN;

/*----------------------------------------------------------------------
 *
 *  PDCurses External Variables
 *
 */

#ifdef PDC_DLL_BUILD
# ifdef CURSES_LIBRARY
#  define PDCEX __declspec(dllexport) extern
# else
#  define PDCEX __declspec(dllimport)
# endif
#else
# define PDCEX extern
#endif

PDCEX  int          LINES;        /* terminal height */
PDCEX  int          COLS;         /* terminal width */
PDCEX  WINDOW       *stdscr;      /* the default screen window */
PDCEX  WINDOW       *curscr;      /* the current screen image */
PDCEX  SCREEN       *SP;          /* curses variables */
PDCEX  MOUSE_STATUS Mouse_status;
PDCEX  int          COLORS;
PDCEX  int          COLOR_PAIRS;
PDCEX  int          TABSIZE;
PDCEX  chtype       acs_map[];    /* alternate character set map */
PDCEX  char         ttytype[];    /* terminal name/description */

/*man-start**************************************************************

PDCurses Text Attributes
========================

Originally, PDCurses used a short (16 bits) for its chtype. To include 
color, a number of things had to be sacrificed from the strict Unix and 
System V support. The main problem was fitting all character attributes 
and color into an unsigned char (all 8 bits!).

Today, PDCurses by default uses a long (32 bits) for its chtype, as in 
System V. The short chtype is still available, by undefining CHTYPE_LONG 
and rebuilding the library.

The following is the structure of a win->_attrs chtype:

short form:

-------------------------------------------------
|15|14|13|12|11|10| 9| 8| 7| 6| 5| 4| 3| 2| 1| 0|
-------------------------------------------------
  color number |  attrs |   character eg 'a'

The available non-color attributes are bold, reverse and blink. Others 
have no effect. The high order char is an index into an array of 
physical colors (defined in color.c) -- 32 foreground/background color 
pairs (5 bits) plus 3 bits for other attributes.

long form:

----------------------------------------------------------------------------
|31|30|29|28|27|26|25|24|23|22|21|20|19|18|17|16|15|14|13|12|..| 3| 2| 1| 0|
----------------------------------------------------------------------------
      color number      |     modifiers         |      character eg 'a'

The available non-color attributes are bold, underline, invisible, 
right-line, left-line, protect, reverse and blink. 256 color pairs (8 
bits), 8 bits for other attributes, and 16 bits for character data.

**man-end****************************************************************/

/*** Video attribute macros ***/

#define A_NORMAL      (chtype)0

#ifdef CHTYPE_LONG
# define A_ALTCHARSET (chtype)0x00010000
# define A_RIGHTLINE  (chtype)0x00020000
# define A_LEFTLINE   (chtype)0x00040000
# define A_INVIS      (chtype)0x00080000
# define A_UNDERLINE  (chtype)0x00100000
# define A_REVERSE    (chtype)0x00200000
# define A_BLINK      (chtype)0x00400000
# define A_BOLD       (chtype)0x00800000

# define A_ATTRIBUTES (chtype)0xffff0000
# define A_CHARTEXT   (chtype)0x0000ffff
# define A_COLOR      (chtype)0xff000000

# define A_ITALIC     A_INVIS
# define A_PROTECT    (A_UNDERLINE | A_LEFTLINE | A_RIGHTLINE)

# define PDC_ATTR_SHIFT  19
# define PDC_COLOR_SHIFT 24
#else
# define A_BOLD       (chtype)0x0100  /* X/Open */
# define A_REVERSE    (chtype)0x0200  /* X/Open */
# define A_BLINK      (chtype)0x0400  /* X/Open */

# define A_ATTRIBUTES (chtype)0xff00  /* X/Open */
# define A_CHARTEXT   (chtype)0x00ff  /* X/Open */
# define A_COLOR      (chtype)0xf800  /* System V */

# define A_ALTCHARSET A_NORMAL        /* X/Open */
# define A_PROTECT    A_NORMAL        /* X/Open */
# define A_UNDERLINE  A_NORMAL        /* X/Open */

# define A_LEFTLINE   A_NORMAL
# define A_RIGHTLINE  A_NORMAL
# define A_ITALIC     A_NORMAL
# define A_INVIS      A_NORMAL

# define PDC_ATTR_SHIFT   8
# define PDC_COLOR_SHIFT 11
#endif

#define A_STANDOUT    (A_REVERSE | A_BOLD) /* X/Open */
#define A_DIM         A_NORMAL

#define CHR_MSK       A_CHARTEXT           /* Obsolete */
#define ATR_MSK       A_ATTRIBUTES         /* Obsolete */
#define ATR_NRM       A_NORMAL             /* Obsolete */

/* For use with attr_t -- X/Open says, "these shall be distinct", so 
   this is a non-conforming implementation. */

#define WA_ALTCHARSET A_ALTCHARSET
#define WA_BLINK      A_BLINK
#define WA_BOLD       A_BOLD
#define WA_DIM        A_DIM
#define WA_INVIS      A_INVIS
#define WA_LEFT       A_LEFTLINE
#define WA_PROTECT    A_PROTECT
#define WA_REVERSE    A_REVERSE
#define WA_RIGHT      A_RIGHTLINE
#define WA_STANDOUT   A_STANDOUT
#define WA_UNDERLINE  A_UNDERLINE

#define WA_HORIZONTAL A_NORMAL
#define WA_LOW        A_NORMAL
#define WA_TOP        A_NORMAL
#define WA_VERTICAL   A_NORMAL

/*** Alternate character set macros ***/

/* 'w' = 32-bit chtype; acs_map[] index | A_ALTCHARSET
   'n' = 16-bit chtype; it gets the fallback set because no bit is 
         available for A_ALTCHARSET */

#ifdef CHTYPE_LONG
# define ACS_PICK(w, n) ((chtype)w | A_ALTCHARSET)
#else
# define ACS_PICK(w, n) ((chtype)n)
#endif

/* VT100-compatible symbols -- box chars */

#define ACS_ULCORNER  ACS_PICK('l', '+')
#define ACS_LLCORNER  ACS_PICK('m', '+')
#define ACS_URCORNER  ACS_PICK('k', '+')
#define ACS_LRCORNER  ACS_PICK('j', '+')
#define ACS_RTEE      ACS_PICK('u', '+')
#define ACS_LTEE      ACS_PICK('t', '+')
#define ACS_BTEE      ACS_PICK('v', '+')
#define ACS_TTEE      ACS_PICK('w', '+')
#define ACS_HLINE     ACS_PICK('q', '-')
#define ACS_VLINE     ACS_PICK('x', '|')
#define ACS_PLUS      ACS_PICK('n', '+')

/* VT100-compatible symbols -- other */

#define ACS_S1        ACS_PICK('o', '-')
#define ACS_S9        ACS_PICK('s', '_')
#define ACS_DIAMOND   ACS_PICK('`', '+')
#define ACS_CKBOARD   ACS_PICK('a', ':')
#define ACS_DEGREE    ACS_PICK('f', '\'')
#define ACS_PLMINUS   ACS_PICK('g', '#')
#define ACS_BULLET    ACS_PICK('~', 'o')

/* Teletype 5410v1 symbols -- these are defined in SysV curses, but
   are not well-supported by most terminals. Stick to VT100 characters
   for optimum portability. */

#define ACS_LARROW    ACS_PICK(',', '<')
#define ACS_RARROW    ACS_PICK('+', '>')
#define ACS_DARROW    ACS_PICK('.', 'v')
#define ACS_UARROW    ACS_PICK('-', '^')
#define ACS_BOARD     ACS_PICK('h', '#')
#define ACS_LANTERN   ACS_PICK('i', '*')
#define ACS_BLOCK     ACS_PICK('0', '#')

/* That goes double for these -- undocumented SysV symbols. Don't use
   them. */

#define ACS_S3        ACS_PICK('p', '-')
#define ACS_S7        ACS_PICK('r', '-')
#define ACS_LEQUAL    ACS_PICK('y', '<')
#define ACS_GEQUAL    ACS_PICK('z', '>')
#define ACS_PI        ACS_PICK('{', 'n')
#define ACS_NEQUAL    ACS_PICK('|', '+')
#define ACS_STERLING  ACS_PICK('}', 'L')

/* Box char aliases */

#define ACS_BSSB      ACS_ULCORNER
#define ACS_SSBB      ACS_LLCORNER
#define ACS_BBSS      ACS_URCORNER
#define ACS_SBBS      ACS_LRCORNER
#define ACS_SBSS      ACS_RTEE
#define ACS_SSSB      ACS_LTEE
#define ACS_SSBS      ACS_BTEE
#define ACS_BSSS      ACS_TTEE
#define ACS_BSBS      ACS_HLINE
#define ACS_SBSB      ACS_VLINE
#define ACS_SSSS      ACS_PLUS

/* cchar_t aliases */

#ifdef PDC_WIDE
# define WACS_ULCORNER (&(acs_map['l']))
# define WACS_LLCORNER (&(acs_map['m']))
# define WACS_URCORNER (&(acs_map['k']))
# define WACS_LRCORNER (&(acs_map['j']))
# define WACS_RTEE     (&(acs_map['u']))
# define WACS_LTEE     (&(acs_map['t']))
# define WACS_BTEE     (&(acs_map['v']))
# define WACS_TTEE     (&(acs_map['w']))
# define WACS_HLINE    (&(acs_map['q']))
# define WACS_VLINE    (&(acs_map['x']))
# define WACS_PLUS     (&(acs_map['n']))

# define WACS_S1       (&(acs_map['o']))
# define WACS_S9       (&(acs_map['s']))
# define WACS_DIAMOND  (&(acs_map['`']))
# define WACS_CKBOARD  (&(acs_map['a']))
# define WACS_DEGREE   (&(acs_map['f']))
# define WACS_PLMINUS  (&(acs_map['g']))
# define WACS_BULLET   (&(acs_map['~']))

# define WACS_LARROW   (&(acs_map[',']))
# define WACS_RARROW   (&(acs_map['+']))
# define WACS_DARROW   (&(acs_map['.']))
# define WACS_UARROW   (&(acs_map['-']))
# define WACS_BOARD    (&(acs_map['h']))
# define WACS_LANTERN  (&(acs_map['i']))
# define WACS_BLOCK    (&(acs_map['0']))

# define WACS_S3       (&(acs_map['p']))
# define WACS_S7       (&(acs_map['r']))
# define WACS_LEQUAL   (&(acs_map['y']))
# define WACS_GEQUAL   (&(acs_map['z']))
# define WACS_PI       (&(acs_map['{']))
# define WACS_NEQUAL   (&(acs_map['|']))
# define WACS_STERLING (&(acs_map['}']))

# define WACS_BSSB     WACS_ULCORNER
# define WACS_SSBB     WACS_LLCORNER
# define WACS_BBSS     WACS_URCORNER
# define WACS_SBBS     WACS_LRCORNER
# define WACS_SBSS     WACS_RTEE
# define WACS_SSSB     WACS_LTEE
# define WACS_SSBS     WACS_BTEE
# define WACS_BSSS     WACS_TTEE
# define WACS_BSBS     WACS_HLINE
# define WACS_SBSB     WACS_VLINE
# define WACS_SSSS     WACS_PLUS
#endif

/*** Color macros ***/

#define COLOR_BLACK   0

#ifdef PDC_RGB        /* RGB */
# define COLOR_RED    1
# define COLOR_GREEN  2
# define COLOR_BLUE   4
#else                 /* BGR */
# define COLOR_BLUE   1
# define COLOR_GREEN  2
# define COLOR_RED    4
#endif

#define COLOR_CYAN    (COLOR_BLUE | COLOR_GREEN)
#define COLOR_MAGENTA (COLOR_RED | COLOR_BLUE)
#define COLOR_YELLOW  (COLOR_RED | COLOR_GREEN)

#define COLOR_WHITE   7

/*----------------------------------------------------------------------
 *
 *  Function and Keypad Key Definitions.
 *  Many are just for compatibility.
 *
 */

#define KEY_CODE_YES  0x100  /* If get_wch() gives a key code */

#define KEY_BREAK     0x101  /* Not on PC KBD */
#define KEY_DOWN      0x102  /* Down arrow key */
#define KEY_UP        0x103  /* Up arrow key */
#define KEY_LEFT      0x104  /* Left arrow key */
#define KEY_RIGHT     0x105  /* Right arrow key */
#define KEY_HOME      0x106  /* home key */
#define KEY_BACKSPACE 0x107  /* not on pc */
#define KEY_F0        0x108  /* function keys; 64 reserved */

#define KEY_DL        0x148  /* delete line */
#define KEY_IL        0x149  /* insert line */
#define KEY_DC        0x14a  /* delete character */
#define KEY_IC        0x14b  /* insert char or enter ins mode */
#define KEY_EIC       0x14c  /* exit insert char mode */
#define KEY_CLEAR     0x14d  /* clear screen */
#define KEY_EOS       0x14e  /* clear to end of screen */
#define KEY_EOL       0x14f  /* clear to end of line */
#define KEY_SF        0x150  /* scroll 1 line forward */
#define KEY_SR        0x151  /* scroll 1 line back (reverse) */
#define KEY_NPAGE     0x152  /* next page */
#define KEY_PPAGE     0x153  /* previous page */
#define KEY_STAB      0x154  /* set tab */
#define KEY_CTAB      0x155  /* clear tab */
#define KEY_CATAB     0x156  /* clear all tabs */
#define KEY_ENTER     0x157  /* enter or send (unreliable) */
#define KEY_SRESET    0x158  /* soft/reset (partial/unreliable) */
#define KEY_RESET     0x159  /* reset/hard reset (unreliable) */
#define KEY_PRINT     0x15a  /* print/copy */
#define KEY_LL        0x15b  /* home down/bottom (lower left) */
#define KEY_ABORT     0x15c  /* abort/terminate key (any) */
#define KEY_SHELP     0x15d  /* short help */
#define KEY_LHELP     0x15e  /* long help */
#define KEY_BTAB      0x15f  /* Back tab key */
#define KEY_BEG       0x160  /* beg(inning) key */
#define KEY_CANCEL    0x161  /* cancel key */
#define KEY_CLOSE     0x162  /* close key */
#define KEY_COMMAND   0x163  /* cmd (command) key */
#define KEY_COPY      0x164  /* copy key */
#define KEY_CREATE    0x165  /* create key */
#define KEY_END       0x166  /* end key */
#define KEY_EXIT      0x167  /* exit key */
#define KEY_FIND      0x168  /* find key */
#define KEY_HELP      0x169  /* help key */
#define KEY_MARK      0x16a  /* mark key */
#define KEY_MESSAGE   0x16b  /* message key */
#define KEY_MOVE      0x16c  /* move key */
#define KEY_NEXT      0x16d  /* next object key */
#define KEY_OPEN      0x16e  /* open key */
#define KEY_OPTIONS   0x16f  /* options key */
#define KEY_PREVIOUS  0x170  /* previous object key */
#define KEY_REDO      0x171  /* redo key */
#define KEY_REFERENCE 0x172  /* ref(erence) key */
#define KEY_REFRESH   0x173  /* refresh key */
#define KEY_REPLACE   0x174  /* replace key */
#define KEY_RESTART   0x175  /* restart key */
#define KEY_RESUME    0x176  /* resume key */
#define KEY_SAVE      0x177  /* save key */
#define KEY_SBEG      0x178  /* shifted beginning key */
#define KEY_SCANCEL   0x179  /* shifted cancel key */
#define KEY_SCOMMAND  0x17a  /* shifted command key */
#define KEY_SCOPY     0x17b  /* shifted copy key */
#define KEY_SCREATE   0x17c  /* shifted create key */
#define KEY_SDC       0x17d  /* shifted delete char key */
#define KEY_SDL       0x17e  /* shifted delete line key */
#define KEY_SELECT    0x17f  /* select key */
#define KEY_SEND      0x180  /* shifted end key */
#define KEY_SEOL      0x181  /* shifted clear line key */
#define KEY_SEXIT     0x182  /* shifted exit key */
#define KEY_SFIND     0x183  /* shifted find key */
#define KEY_SHOME     0x184  /* shifted home key */
#define KEY_SIC       0x185  /* shifted input key */

#define KEY_SLEFT     0x187  /* shifted left arrow key */
#define KEY_SMESSAGE  0x188  /* shifted message key */
#define KEY_SMOVE     0x189  /* shifted move key */
#define KEY_SNEXT     0x18a  /* shifted next key */
#define KEY_SOPTIONS  0x18b  /* shifted options key */
#define KEY_SPREVIOUS 0x18c  /* shifted prev key */
#define KEY_SPRINT    0x18d  /* shifted print key */
#define KEY_SREDO     0x18e  /* shifted redo key */
#define KEY_SREPLACE  0x18f  /* shifted replace key */
#define KEY_SRIGHT    0x190  /* shifted right arrow */
#define KEY_SRSUME    0x191  /* shifted resume key */
#define KEY_SSAVE     0x192  /* shifted save key */
#define KEY_SSUSPEND  0x193  /* shifted suspend key */
#define KEY_SUNDO     0x194  /* shifted undo key */
#define KEY_SUSPEND   0x195  /* suspend key */
#define KEY_UNDO      0x196  /* undo key */

/* PDCurses-specific key definitions -- PC only */

#define ALT_0         0x197
#define ALT_1         0x198
#define ALT_2         0x199
#define ALT_3         0x19a
#define ALT_4         0x19b
#define ALT_5         0x19c
#define ALT_6         0x19d
#define ALT_7         0x19e
#define ALT_8         0x19f
#define ALT_9         0x1a0
#define ALT_A         0x1a1
#define ALT_B         0x1a2
#define ALT_C         0x1a3
#define ALT_D         0x1a4
#define ALT_E         0x1a5
#define ALT_F         0x1a6
#define ALT_G         0x1a7
#define ALT_H         0x1a8
#define ALT_I         0x1a9
#define ALT_J         0x1aa
#define ALT_K         0x1ab
#define ALT_L         0x1ac
#define ALT_M         0x1ad
#define ALT_N         0x1ae
#define ALT_O         0x1af
#define ALT_P         0x1b0
#define ALT_Q         0x1b1
#define ALT_R         0x1b2
#define ALT_S         0x1b3
#define ALT_T         0x1b4
#define ALT_U         0x1b5
#define ALT_V         0x1b6
#define ALT_W         0x1b7
#define ALT_X         0x1b8
#define ALT_Y         0x1b9
#define ALT_Z         0x1ba

#define CTL_LEFT      0x1bb  /* Control-Left-Arrow */
#define CTL_RIGHT     0x1bc
#define CTL_PGUP      0x1bd
#define CTL_PGDN      0x1be
#define CTL_HOME      0x1bf
#define CTL_END       0x1c0

#define KEY_A1        0x1c1  /* upper left on Virtual keypad */
#define KEY_A2        0x1c2  /* upper middle on Virt. keypad */
#define KEY_A3        0x1c3  /* upper right on Vir. keypad */
#define KEY_B1        0x1c4  /* middle left on Virt. keypad */
#define KEY_B2        0x1c5  /* center on Virt. keypad */
#define KEY_B3        0x1c6  /* middle right on Vir. keypad */
#define KEY_C1        0x1c7  /* lower left on Virt. keypad */
#define KEY_C2        0x1c8  /* lower middle on Virt. keypad */
#define KEY_C3        0x1c9  /* lower right on Vir. keypad */

#define PADSLASH      0x1ca  /* slash on keypad */
#define PADENTER      0x1cb  /* enter on keypad */
#define CTL_PADENTER  0x1cc  /* ctl-enter on keypad */
#define ALT_PADENTER  0x1cd  /* alt-enter on keypad */
#define PADSTOP       0x1ce  /* stop on keypad */
#define PADSTAR       0x1cf  /* star on keypad */
#define PADMINUS      0x1d0  /* minus on keypad */
#define PADPLUS       0x1d1  /* plus on keypad */
#define CTL_PADSTOP   0x1d2  /* ctl-stop on keypad */
#define CTL_PADCENTER 0x1d3  /* ctl-enter on keypad */
#define CTL_PADPLUS   0x1d4  /* ctl-plus on keypad */
#define CTL_PADMINUS  0x1d5  /* ctl-minus on keypad */
#define CTL_PADSLASH  0x1d6  /* ctl-slash on keypad */
#define CTL_PADSTAR   0x1d7  /* ctl-star on keypad */
#define ALT_PADPLUS   0x1d8  /* alt-plus on keypad */
#define ALT_PADMINUS  0x1d9  /* alt-minus on keypad */
#define ALT_PADSLASH  0x1da  /* alt-slash on keypad */
#define ALT_PADSTAR   0x1db  /* alt-star on keypad */
#define ALT_PADSTOP   0x1dc  /* alt-stop on keypad */
#define CTL_INS       0x1dd  /* ctl-insert */
#define ALT_DEL       0x1de  /* alt-delete */
#define ALT_INS       0x1df  /* alt-insert */
#define CTL_UP        0x1e0  /* ctl-up arrow */
#define CTL_DOWN      0x1e1  /* ctl-down arrow */
#define CTL_TAB       0x1e2  /* ctl-tab */
#define ALT_TAB       0x1e3
#define ALT_MINUS     0x1e4
#define ALT_EQUAL     0x1e5
#define ALT_HOME      0x1e6
#define ALT_PGUP      0x1e7
#define ALT_PGDN      0x1e8
#define ALT_END       0x1e9
#define ALT_UP        0x1ea  /* alt-up arrow */
#define ALT_DOWN      0x1eb  /* alt-down arrow */
#define ALT_RIGHT     0x1ec  /* alt-right arrow */
#define ALT_LEFT      0x1ed  /* alt-left arrow */
#define ALT_ENTER     0x1ee  /* alt-enter */
#define ALT_ESC       0x1ef  /* alt-escape */
#define ALT_BQUOTE    0x1f0  /* alt-back quote */
#define ALT_LBRACKET  0x1f1  /* alt-left bracket */
#define ALT_RBRACKET  0x1f2  /* alt-right bracket */
#define ALT_SEMICOLON 0x1f3  /* alt-semi-colon */
#define ALT_FQUOTE    0x1f4  /* alt-forward quote */
#define ALT_COMMA     0x1f5  /* alt-comma */
#define ALT_STOP      0x1f6  /* alt-stop */
#define ALT_FSLASH    0x1f7  /* alt-forward slash */
#define ALT_BKSP      0x1f8  /* alt-backspace */
#define CTL_BKSP      0x1f9  /* ctl-backspace */
#define PAD0          0x1fa  /* keypad 0 */

#define CTL_PAD0      0x1fb  /* ctl-keypad 0 */
#define CTL_PAD1      0x1fc
#define CTL_PAD2      0x1fd
#define CTL_PAD3      0x1fe
#define CTL_PAD4      0x1ff
#define CTL_PAD5      0x200
#define CTL_PAD6      0x201
#define CTL_PAD7      0x202
#define CTL_PAD8      0x203
#define CTL_PAD9      0x204

#define ALT_PAD0      0x205  /* alt-keypad 0 */
#define ALT_PAD1      0x206
#define ALT_PAD2      0x207
#define ALT_PAD3      0x208
#define ALT_PAD4      0x209
#define ALT_PAD5      0x20a
#define ALT_PAD6      0x20b
#define ALT_PAD7      0x20c
#define ALT_PAD8      0x20d
#define ALT_PAD9      0x20e

#define CTL_DEL       0x20f  /* clt-delete */
#define ALT_BSLASH    0x210  /* alt-back slash */
#define CTL_ENTER     0x211  /* ctl-enter */

#define SHF_PADENTER  0x212  /* shift-enter on keypad */
#define SHF_PADSLASH  0x213  /* shift-slash on keypad */
#define SHF_PADSTAR   0x214  /* shift-star  on keypad */
#define SHF_PADPLUS   0x215  /* shift-plus  on keypad */
#define SHF_PADMINUS  0x216  /* shift-minus on keypad */
#define SHF_UP        0x217  /* shift-up on keypad */
#define SHF_DOWN      0x218  /* shift-down on keypad */
#define SHF_IC        0x219  /* shift-insert on keypad */
#define SHF_DC        0x21a  /* shift-delete on keypad */

#define KEY_MOUSE     0x21b  /* "mouse" key */
#define KEY_SHIFT_L   0x21c  /* Left-shift */
#define KEY_SHIFT_R   0x21d  /* Right-shift */
#define KEY_CONTROL_L 0x21e  /* Left-control */
#define KEY_CONTROL_R 0x21f  /* Right-control */
#define KEY_ALT_L     0x220  /* Left-alt */
#define KEY_ALT_R     0x221  /* Right-alt */
#define KEY_RESIZE    0x222  /* Window resize */
#define KEY_SUP       0x223  /* Shifted up arrow */
#define KEY_SDOWN     0x224  /* Shifted down arrow */

#define KEY_MIN       KEY_BREAK      /* Minimum curses key value */
#define KEY_MAX       KEY_SDOWN      /* Maximum curses key */

#define KEY_F(n)      (KEY_F0 + (n))

/*----------------------------------------------------------------------
 *
 *  PDCurses Function Declarations
 *
 */

/* Standard */

int     addch(const chtype);
int     addchnstr(const chtype *, int);
int     addchstr(const chtype *);
int     addnstr(const char *, int);
int     addstr(const char *);
int     attroff(chtype);
int     attron(chtype);
int     attrset(chtype);
int     attr_get(attr_t *, short *, void *);
int     attr_off(attr_t, void *);
int     attr_on(attr_t, void *);
int     attr_set(attr_t, short, void *);
int     baudrate(void);
int     beep(void);
int     bkgd(chtype);
void    bkgdset(chtype);
int     border(chtype, chtype, chtype, chtype, chtype, chtype, chtype, chtype);
int     box(WINDOW *, chtype, chtype);
bool    can_change_color(void);
int     cbreak(void); 
int     chgat(int, attr_t, short, const void *);
int     clearok(WINDOW *, bool);
int     clear(void);
int     clrtobot(void);
int     clrtoeol(void);
int     color_content(short, short *, short *, short *);
int     color_set(short, void *);
int     copywin(const WINDOW *, WINDOW *, int, int, int, int, int, int, int);
int     curs_set(int);
int     def_prog_mode(void);
int     def_shell_mode(void);
int     delay_output(int);
int     delch(void);
int     deleteln(void);
void    delscreen(SCREEN *); 
int     delwin(WINDOW *);
WINDOW *derwin(WINDOW *, int, int, int, int);
int     doupdate(void);
WINDOW *dupwin(WINDOW *);
int     echochar(const chtype);
int     echo(void);
int     endwin(void);
char    erasechar(void);
int     erase(void);
void    filter(void);
int     flash(void);
int     flushinp(void);
chtype  getbkgd(WINDOW *);
int     getnstr(char *, int);
int     getstr(char *);
WINDOW *getwin(FILE *);
int     halfdelay(int);
bool    has_colors(void);
bool    has_ic(void);
bool    has_il(void);
int     hline(chtype, int);
void    idcok(WINDOW *, bool);
int     idlok(WINDOW *, bool);
void    immedok(WINDOW *, bool);
int     inchnstr(chtype *, int);
int     inchstr(chtype *);
chtype  inch(void);
int     init_color(short, short, short, short);
int     init_pair(short, short, short);
WINDOW *initscr(void);
int     innstr(char *, int);
int     insch(chtype);
int     insdelln(int);
int     insertln(void);
int     insnstr(const char *, int);
int     insstr(const char *);
int     instr(char *);
int     intrflush(WINDOW *, bool);
bool    isendwin(void);
bool    is_linetouched(WINDOW *, int);
bool    is_wintouched(WINDOW *);
char   *keyname(int);
int     keypad(WINDOW *, bool);
char    killchar(void);
int     leaveok(WINDOW *, bool);
char   *longname(void);
int     meta(WINDOW *, bool);
int     move(int, int);
int     mvaddch(int, int, const chtype);
int     mvaddchnstr(int, int, const chtype *, int);
int     mvaddchstr(int, int, const chtype *);
int     mvaddnstr(int, int, const char *, int);
int     mvaddstr(int, int, const char *);
int     mvchgat(int, int, int, attr_t, short, const void *);
int     mvcur(int, int, int, int);
int     mvdelch(int, int);
int     mvderwin(WINDOW *, int, int);
int     mvgetch(int, int);
int     mvgetnstr(int, int, char *, int);
int     mvgetstr(int, int, char *);
int     mvhline(int, int, chtype, int);
chtype  mvinch(int, int);
int     mvinchnstr(int, int, chtype *, int);
int     mvinchstr(int, int, chtype *);
int     mvinnstr(int, int, char *, int);
int     mvinsch(int, int, chtype);
int     mvinsnstr(int, int, const char *, int);
int     mvinsstr(int, int, const char *);
int     mvinstr(int, int, char *);
int     mvprintw(int, int, const char *, ...);
int     mvscanw(int, int, const char *, ...);
int     mvvline(int, int, chtype, int);
int     mvwaddchnstr(WINDOW *, int, int, const chtype *, int);
int     mvwaddchstr(WINDOW *, int, int, const chtype *);
int     mvwaddch(WINDOW *, int, int, const chtype);
int     mvwaddnstr(WINDOW *, int, int, const char *, int);
int     mvwaddstr(WINDOW *, int, int, const char *);
int     mvwchgat(WINDOW *, int, int, int, attr_t, short, const void *);
int     mvwdelch(WINDOW *, int, int);
int     mvwgetch(WINDOW *, int, int);
int     mvwgetnstr(WINDOW *, int, int, char *, int);
int     mvwgetstr(WINDOW *, int, int, char *);
int     mvwhline(WINDOW *, int, int, chtype, int);
int     mvwinchnstr(WINDOW *, int, int, chtype *, int);
int     mvwinchstr(WINDOW *, int, int, chtype *);
chtype  mvwinch(WINDOW *, int, int);
int     mvwinnstr(WINDOW *, int, int, char *, int);
int     mvwinsch(WINDOW *, int, int, chtype);
int     mvwinsnstr(WINDOW *, int, int, const char *, int);
int     mvwinsstr(WINDOW *, int, int, const char *);
int     mvwinstr(WINDOW *, int, int, char *);
int     mvwin(WINDOW *, int, int);
int     mvwprintw(WINDOW *, int, int, const char *, ...);
int     mvwscanw(WINDOW *, int, int, const char *, ...);
int     mvwvline(WINDOW *, int, int, chtype, int);
int     napms(int);
WINDOW *newpad(int, int);
SCREEN *newterm(const char *, FILE *, FILE *);
WINDOW *newwin(int, int, int, int);
int     nl(void);
int     nocbreak(void);
int     nodelay(WINDOW *, bool);
int     noecho(void);
int     nonl(void);
void    noqiflush(void);
int     noraw(void);
int     notimeout(WINDOW *, bool);
int     overlay(const WINDOW *, WINDOW *);
int     overwrite(const WINDOW *, WINDOW *);
int     pair_content(short, short *, short *);
int     pechochar(WINDOW *, chtype);
int     pnoutrefresh(WINDOW *, int, int, int, int, int, int);
int     prefresh(WINDOW *, int, int, int, int, int, int);
int     printw(const char *, ...);
int     putwin(WINDOW *, FILE *);
void    qiflush(void);
int     raw(void);
int     redrawwin(WINDOW *);
int     refresh(void);
int     reset_prog_mode(void);
int     reset_shell_mode(void);
int     resetty(void);
int     ripoffline(int, int (*)(WINDOW *, int));
int     savetty(void);
int     scanw(const char *, ...);
int     scr_dump(const char *);
int     scr_init(const char *);
int     scr_restore(const char *);
int     scr_set(const char *);
int     scrl(int);
int     scroll(WINDOW *);
int     scrollok(WINDOW *, bool);
SCREEN *set_term(SCREEN *);
int     setscrreg(int, int);
int     slk_attroff(const chtype);
int     slk_attr_off(const attr_t, void *);
int     slk_attron(const chtype);
int     slk_attr_on(const attr_t, void *);
int     slk_attrset(const chtype);
int     slk_attr_set(const attr_t, short, void *);
int     slk_clear(void);
int     slk_color(short);
int     slk_init(int);
char   *slk_label(int);
int     slk_noutrefresh(void);
int     slk_refresh(void);
int     slk_restore(void);
int     slk_set(int, const char *, int);
int     slk_touch(void);
int     standend(void);
int     standout(void);
int     start_color(void);
WINDOW *subpad(WINDOW *, int, int, int, int);
WINDOW *subwin(WINDOW *, int, int, int, int);
int     syncok(WINDOW *, bool);
chtype  termattrs(void);
attr_t  term_attrs(void);
char   *termname(void);
void    timeout(int);
int     touchline(WINDOW *, int, int);
int     touchwin(WINDOW *);
int     typeahead(int);
int     untouchwin(WINDOW *);
void    use_env(bool);
int     vidattr(chtype);
int     vid_attr(attr_t, short, void *);
int     vidputs(chtype, int (*)(int));
int     vid_puts(attr_t, short, void *, int (*)(int));
int     vline(chtype, int);
int     vw_printw(WINDOW *, const char *, va_list);
int     vwprintw(WINDOW *, const char *, va_list);
int     vw_scanw(WINDOW *, const char *, va_list);
int     vwscanw(WINDOW *, const char *, va_list);
int     waddchnstr(WINDOW *, const chtype *, int);
int     waddchstr(WINDOW *, const chtype *);
int     waddch(WINDOW *, const chtype);
int     waddnstr(WINDOW *, const char *, int);
int     waddstr(WINDOW *, const char *);
int     wattroff(WINDOW *, chtype);
int     wattron(WINDOW *, chtype);
int     wattrset(WINDOW *, chtype);
int     wattr_get(WINDOW *, attr_t *, short *, void *);
int     wattr_off(WINDOW *, attr_t, void *);
int     wattr_on(WINDOW *, attr_t, void *);
int     wattr_set(WINDOW *, attr_t, short, void *);
void    wbkgdset(WINDOW *, chtype);
int     wbkgd(WINDOW *, chtype);
int     wborder(WINDOW *, chtype, chtype, chtype, chtype,
                chtype, chtype, chtype, chtype);
int     wchgat(WINDOW *, int, attr_t, short, const void *);
int     wclear(WINDOW *);
int     wclrtobot(WINDOW *);
int     wclrtoeol(WINDOW *);
int     wcolor_set(WINDOW *, short, void *);
void    wcursyncup(WINDOW *);
int     wdelch(WINDOW *);
int     wdeleteln(WINDOW *);
int     wechochar(WINDOW *, const chtype);
int     werase(WINDOW *);
int     wgetch(WINDOW *);
int     wgetnstr(WINDOW *, char *, int);
int     wgetstr(WINDOW *, char *);
int     whline(WINDOW *, chtype, int);
int     winchnstr(WINDOW *, chtype *, int);
int     winchstr(WINDOW *, chtype *);
chtype  winch(WINDOW *);
int     winnstr(WINDOW *, char *, int);
int     winsch(WINDOW *, chtype);
int     winsdelln(WINDOW *, int);
int     winsertln(WINDOW *);
int     winsnstr(WINDOW *, const char *, int);
int     winsstr(WINDOW *, const char *);
int     winstr(WINDOW *, char *);
int     wmove(WINDOW *, int, int);
int     wnoutrefresh(WINDOW *);
int     wprintw(WINDOW *, const char *, ...);
int     wredrawln(WINDOW *, int, int);
int     wrefresh(WINDOW *);
int     wscanw(WINDOW *, const char *, ...);
int     wscrl(WINDOW *, int);
int     wsetscrreg(WINDOW *, int, int);
int     wstandend(WINDOW *);
int     wstandout(WINDOW *);
void    wsyncdown(WINDOW *);
void    wsyncup(WINDOW *);
void    wtimeout(WINDOW *, int);
int     wtouchln(WINDOW *, int, int, int);
int     wvline(WINDOW *, chtype, int);

/* Wide-character functions */

#ifdef PDC_WIDE
int     addnwstr(const wchar_t *, int);
int     addwstr(const wchar_t *);
int     add_wch(const cchar_t *);
int     add_wchnstr(const cchar_t *, int);
int     add_wchstr(const cchar_t *);
int     border_set(const cchar_t *, const cchar_t *, const cchar_t *, 
                   const cchar_t *, const cchar_t *, const cchar_t *, 
                   const cchar_t *, const cchar_t *);
int     box_set(WINDOW *, const cchar_t *, const cchar_t *);
int     echo_wchar(const cchar_t *);
int     erasewchar(wchar_t *);
int     getbkgrnd(cchar_t *);
int     getcchar(const cchar_t *, wchar_t *, attr_t *, short *, void *);
int     getn_wstr(wint_t *, int);
int     get_wch(wint_t *);
int     get_wstr(wint_t *);
int     hline_set(const cchar_t *, int);
int     innwstr(wchar_t *, int);
int     ins_nwstr(const wchar_t *, int);
int     ins_wch(const cchar_t *);
int     ins_wstr(const wchar_t *);
int     inwstr(wchar_t *);
int     in_wch(cchar_t *);
int     in_wchnstr(cchar_t *, int);
int     in_wchstr(cchar_t *);
char   *key_name(wchar_t);
int     killwchar(wchar_t *);
int     mvaddnwstr(int, int, const wchar_t *, int);
int     mvaddwstr(int, int, const wchar_t *);
int     mvadd_wch(int, int, const cchar_t *);
int     mvadd_wchnstr(int, int, const cchar_t *, int);
int     mvadd_wchstr(int, int, const cchar_t *);
int     mvgetn_wstr(int, int, wint_t *, int);
int     mvget_wch(int, int, wint_t *);
int     mvget_wstr(int, int, wint_t *);
int     mvhline_set(int, int, const cchar_t *, int);
int     mvinnwstr(int, int, wchar_t *, int);
int     mvins_nwstr(int, int, const wchar_t *, int);
int     mvins_wch(int, int, const cchar_t *);
int     mvins_wstr(int, int, const wchar_t *);
int     mvinwstr(int, int, wchar_t *);
int     mvin_wch(int, int, cchar_t *);
int     mvin_wchnstr(int, int, cchar_t *, int);
int     mvin_wchstr(int, int, cchar_t *);
int     mvvline_set(int, int, const cchar_t *, int);
int     mvwaddnwstr(WINDOW *, int, int, const wchar_t *, int);
int     mvwaddwstr(WINDOW *, int, int, const wchar_t *);
int     mvwadd_wch(WINDOW *, int, int, const cchar_t *);
int     mvwadd_wchnstr(WINDOW *, int, int, const cchar_t *, int);
int     mvwadd_wchstr(WINDOW *, int, int, const cchar_t *);
int     mvwgetn_wstr(WINDOW *, int, int, wint_t *, int);
int     mvwget_wch(WINDOW *, int, int, wint_t *);
int     mvwget_wstr(WINDOW *, int, int, wint_t *);
int     mvwhline_set(WINDOW *, int, int, const cchar_t *, int);
int     mvwinnwstr(WINDOW *, int, int, wchar_t *, int);
int     mvwins_nwstr(WINDOW *, int, int, const wchar_t *, int);
int     mvwins_wch(WINDOW *, int, int, const cchar_t *);
int     mvwins_wstr(WINDOW *, int, int, const wchar_t *);
int     mvwin_wch(WINDOW *, int, int, cchar_t *);
int     mvwin_wchnstr(WINDOW *, int, int, cchar_t *, int);
int     mvwin_wchstr(WINDOW *, int, int, cchar_t *);
int     mvwinwstr(WINDOW *, int, int, wchar_t *);
int     mvwvline_set(WINDOW *, int, int, const cchar_t *, int);
int     pecho_wchar(WINDOW *, const cchar_t*);
int     setcchar(cchar_t*, const wchar_t*, const attr_t, short, const void*);
int     slk_wset(int, const wchar_t *, int);
int     unget_wch(const wchar_t);
int     vline_set(const cchar_t *, int);
int     waddnwstr(WINDOW *, const wchar_t *, int);
int     waddwstr(WINDOW *, const wchar_t *);
int     wadd_wch(WINDOW *, const cchar_t *);
int     wadd_wchnstr(WINDOW *, const cchar_t *, int);
int     wadd_wchstr(WINDOW *, const cchar_t *);
int     wbkgrnd(WINDOW *, const cchar_t *);
void    wbkgrndset(WINDOW *, const cchar_t *);
int     wborder_set(WINDOW *, const cchar_t *, const cchar_t *,
                    const cchar_t *, const cchar_t *, const cchar_t *, 
                    const cchar_t *, const cchar_t *, const cchar_t *);
int     wecho_wchar(WINDOW *, const cchar_t *);
int     wgetbkgrnd(WINDOW *, cchar_t *);
int     wgetn_wstr(WINDOW *, wint_t *, int);
int     wget_wch(WINDOW *, wint_t *);
int     wget_wstr(WINDOW *, wint_t *);
int     whline_set(WINDOW *, const cchar_t *, int);
int     winnwstr(WINDOW *, wchar_t *, int);
int     wins_nwstr(WINDOW *, const wchar_t *, int);
int     wins_wch(WINDOW *, const cchar_t *);
int     wins_wstr(WINDOW *, const wchar_t *);
int     winwstr(WINDOW *, wchar_t *);
int     win_wch(WINDOW *, cchar_t *);
int     win_wchnstr(WINDOW *, cchar_t *, int);
int     win_wchstr(WINDOW *, cchar_t *);
wchar_t *wunctrl(cchar_t *);
int     wvline_set(WINDOW *, const cchar_t *, int);
#endif

/* Quasi-standard */

chtype  getattrs(WINDOW *);
int     getbegx(WINDOW *);
int     getbegy(WINDOW *);
int     getmaxx(WINDOW *);
int     getmaxy(WINDOW *);
int     getparx(WINDOW *);
int     getpary(WINDOW *);
int     getcurx(WINDOW *);
int     getcury(WINDOW *);
void    traceoff(void);
void    traceon(void);
char   *unctrl(chtype);

int     crmode(void);
int     nocrmode(void);
int     draino(int);
int     resetterm(void);
int     fixterm(void);
int     saveterm(void);
int     setsyx(int, int);

int     mouse_set(unsigned long);
int     mouse_on(unsigned long);
int     mouse_off(unsigned long);
int     request_mouse_pos(void);
int     map_button(unsigned long);
void    wmouse_position(WINDOW *, int *, int *);
unsigned long getmouse(void);
unsigned long getbmap(void);

/* ncurses */

int     assume_default_colors(int, int);
const char *curses_version(void);
bool    has_key(int);
int     use_default_colors(void);
int     wresize(WINDOW *, int, int);

int     mouseinterval(int);
mmask_t mousemask(mmask_t, mmask_t *);
bool    mouse_trafo(int *, int *, bool);
int     nc_getmouse(MEVENT *);
int     ungetmouse(MEVENT *);
bool    wenclose(const WINDOW *, int, int);
bool    wmouse_trafo(const WINDOW *, int *, int *, bool);

/* PDCurses */

int     addrawch(chtype);
int     insrawch(chtype);
bool    is_termresized(void);
int     mvaddrawch(int, int, chtype);
int     mvdeleteln(int, int);
int     mvinsertln(int, int);
int     mvinsrawch(int, int, chtype);
int     mvwaddrawch(WINDOW *, int, int, chtype);
int     mvwdeleteln(WINDOW *, int, int);
int     mvwinsertln(WINDOW *, int, int);
int     mvwinsrawch(WINDOW *, int, int, chtype);
int     raw_output(bool);
int     resize_term(int, int);
WINDOW *resize_window(WINDOW *, int, int);
int     waddrawch(WINDOW *, chtype);
int     winsrawch(WINDOW *, chtype);
char    wordchar(void);

#ifdef PDC_WIDE
wchar_t *slk_wlabel(int);
#endif

void    PDC_debug(const char *, ...);
int     PDC_ungetch(int);
int     PDC_set_blink(bool);
int     PDC_set_line_color(short);
void    PDC_set_title(const char *);

int     PDC_clearclipboard(void);
int     PDC_freeclipboard(char *);
int     PDC_getclipboard(char **, long *);
int     PDC_setclipboard(const char *, long);

unsigned long PDC_get_input_fd(void);
unsigned long PDC_get_key_modifiers(void);
int     PDC_return_key_modifiers(bool);
int     PDC_save_key_modifiers(bool);

#ifdef XCURSES
WINDOW *Xinitscr(int, char **);
void    XCursesExit(void);
int     sb_init(void);
int     sb_set_horz(int, int, int);
int     sb_set_vert(int, int, int);
int     sb_get_horz(int *, int *, int *);
int     sb_get_vert(int *, int *, int *);
int     sb_refresh(void);
#endif

/*** Functions defined as macros ***/

/* getch() and ungetch() conflict with some DOS libraries */

#define getch()            wgetch(stdscr)
#define ungetch(ch)        PDC_ungetch(ch)

#define COLOR_PAIR(n)      (((chtype)(n) << PDC_COLOR_SHIFT) & A_COLOR)
#define PAIR_NUMBER(n)     (((n) & A_COLOR) >> PDC_COLOR_SHIFT)

/* These will _only_ work as macros */

#define getbegyx(w, y, x)  (y = getbegy(w), x = getbegx(w))
#define getmaxyx(w, y, x)  (y = getmaxy(w), x = getmaxx(w))
#define getparyx(w, y, x)  (y = getpary(w), x = getparx(w))
#define getyx(w, y, x)     (y = getcury(w), x = getcurx(w))

#define getsyx(y, x)       { if (curscr->_leaveit) (y)=(x)=-1; \
                             else getyx(curscr,(y),(x)); }

#ifdef NCURSES_MOUSE_VERSION
# define getmouse(x) nc_getmouse(x)
#endif

/* return codes from PDC_getclipboard() and PDC_setclipboard() calls */

#define PDC_CLIP_SUCCESS         0
#define PDC_CLIP_ACCESS_ERROR    1
#define PDC_CLIP_EMPTY           2
#define PDC_CLIP_MEMORY_ERROR    3

/* PDCurses key modifier masks */

#define PDC_KEY_MODIFIER_SHIFT   1
#define PDC_KEY_MODIFIER_CONTROL 2
#define PDC_KEY_MODIFIER_ALT     4
#define PDC_KEY_MODIFIER_NUMLOCK 8

#if defined(__cplusplus) || defined(__cplusplus__) || defined(__CPLUSPLUS)
# undef bool
}
#endif

#endif  /* __PDCURSES__ */
genometools-1.5.1/src/external/samtools-0.1.18/win32/zconf.h000066400000000000000000000225101211610345200232730ustar00rootroot00000000000000/* zconf.h -- configuration of the zlib compression library
 * Copyright (C) 1995-2005 Jean-loup Gailly.
 * For conditions of distribution and use, see copyright notice in zlib.h
 */

/* @(#) $Id$ */

#ifndef ZCONF_H
#define ZCONF_H

/*
 * If you *really* need a unique prefix for all types and library functions,
 * compile with -DZ_PREFIX. The "standard" zlib should be compiled without it.
 */
#ifdef Z_PREFIX
#  define deflateInit_          z_deflateInit_
#  define deflate               z_deflate
#  define deflateEnd            z_deflateEnd
#  define inflateInit_          z_inflateInit_
#  define inflate               z_inflate
#  define inflateEnd            z_inflateEnd
#  define deflateInit2_         z_deflateInit2_
#  define deflateSetDictionary  z_deflateSetDictionary
#  define deflateCopy           z_deflateCopy
#  define deflateReset          z_deflateReset
#  define deflateParams         z_deflateParams
#  define deflateBound          z_deflateBound
#  define deflatePrime          z_deflatePrime
#  define inflateInit2_         z_inflateInit2_
#  define inflateSetDictionary  z_inflateSetDictionary
#  define inflateSync           z_inflateSync
#  define inflateSyncPoint      z_inflateSyncPoint
#  define inflateCopy           z_inflateCopy
#  define inflateReset          z_inflateReset
#  define inflateBack           z_inflateBack
#  define inflateBackEnd        z_inflateBackEnd
#  define compress              z_compress
#  define compress2             z_compress2
#  define compressBound         z_compressBound
#  define uncompress            z_uncompress
#  define adler32               z_adler32
#  define crc32                 z_crc32
#  define get_crc_table         z_get_crc_table
#  define zError                z_zError

#  define alloc_func            z_alloc_func
#  define free_func             z_free_func
#  define in_func               z_in_func
#  define out_func              z_out_func
#  define Byte                  z_Byte
#  define uInt                  z_uInt
#  define uLong                 z_uLong
#  define Bytef                 z_Bytef
#  define charf                 z_charf
#  define intf                  z_intf
#  define uIntf                 z_uIntf
#  define uLongf                z_uLongf
#  define voidpf                z_voidpf
#  define voidp                 z_voidp
#endif

#if defined(__MSDOS__) && !defined(MSDOS)
#  define MSDOS
#endif
#if (defined(OS_2) || defined(__OS2__)) && !defined(OS2)
#  define OS2
#endif
#if defined(_WINDOWS) && !defined(WINDOWS)
#  define WINDOWS
#endif
#if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__)
#  ifndef WIN32
#    define WIN32
#  endif
#endif
#if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32)
#  if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__)
#    ifndef SYS16BIT
#      define SYS16BIT
#    endif
#  endif
#endif

/*
 * Compile with -DMAXSEG_64K if the alloc function cannot allocate more
 * than 64k bytes at a time (needed on systems with 16-bit int).
 */
#ifdef SYS16BIT
#  define MAXSEG_64K
#endif
#ifdef MSDOS
#  define UNALIGNED_OK
#endif

#ifdef __STDC_VERSION__
#  ifndef STDC
#    define STDC
#  endif
#  if __STDC_VERSION__ >= 199901L
#    ifndef STDC99
#      define STDC99
#    endif
#  endif
#endif
#if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus))
#  define STDC
#endif
#if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__))
#  define STDC
#endif
#if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32))
#  define STDC
#endif
#if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__))
#  define STDC
#endif

#if defined(__OS400__) && !defined(STDC)    /* iSeries (formerly AS/400). */
#  define STDC
#endif

#ifndef STDC
#  ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */
#    define const       /* note: need a more gentle solution here */
#  endif
#endif

/* Some Mac compilers merge all .h files incorrectly: */
#if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__)
#  define NO_DUMMY_DECL
#endif

/* Maximum value for memLevel in deflateInit2 */
#ifndef MAX_MEM_LEVEL
#  ifdef MAXSEG_64K
#    define MAX_MEM_LEVEL 8
#  else
#    define MAX_MEM_LEVEL 9
#  endif
#endif

/* Maximum value for windowBits in deflateInit2 and inflateInit2.
 * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files
 * created by gzip. (Files created by minigzip can still be extracted by
 * gzip.)
 */
#ifndef MAX_WBITS
#  define MAX_WBITS   15 /* 32K LZ77 window */
#endif

/* The memory requirements for deflate are (in bytes):
            (1 << (windowBits+2)) +  (1 << (memLevel+9))
 that is: 128K for windowBits=15  +  128K for memLevel = 8  (default values)
 plus a few kilobytes for small objects. For example, if you want to reduce
 the default memory requirements from 256K to 128K, compile with
     make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7"
 Of course this will generally degrade compression (there's no free lunch).

   The memory requirements for inflate are (in bytes) 1 << windowBits
 that is, 32K for windowBits=15 (default value) plus a few kilobytes
 for small objects.
*/

                        /* Type declarations */

#ifndef OF /* function prototypes */
#  ifdef STDC
#    define OF(args)  args
#  else
#    define OF(args)  ()
#  endif
#endif

/* The following definitions for FAR are needed only for MSDOS mixed
 * model programming (small or medium model with some far allocations).
 * This was tested only with MSC; for other MSDOS compilers you may have
 * to define NO_MEMCPY in zutil.h.  If you don't need the mixed model,
 * just define FAR to be empty.
 */
#ifdef SYS16BIT
#  if defined(M_I86SM) || defined(M_I86MM)
     /* MSC small or medium model */
#    define SMALL_MEDIUM
#    ifdef _MSC_VER
#      define FAR _far
#    else
#      define FAR far
#    endif
#  endif
#  if (defined(__SMALL__) || defined(__MEDIUM__))
     /* Turbo C small or medium model */
#    define SMALL_MEDIUM
#    ifdef __BORLANDC__
#      define FAR _far
#    else
#      define FAR far
#    endif
#  endif
#endif

#if defined(WINDOWS) || defined(WIN32)
   /* If building or using zlib as a DLL, define ZLIB_DLL.
    * This is not mandatory, but it offers a little performance increase.
    */
#  ifdef ZLIB_DLL
#    if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500))
#      ifdef ZLIB_INTERNAL
#        define ZEXTERN extern __declspec(dllexport)
#      else
#        define ZEXTERN extern __declspec(dllimport)
#      endif
#    endif
#  endif  /* ZLIB_DLL */
   /* If building or using zlib with the WINAPI/WINAPIV calling convention,
    * define ZLIB_WINAPI.
    * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI.
    */
#  ifdef ZLIB_WINAPI
#    ifdef FAR
#      undef FAR
#    endif
#    include 
     /* No need for _export, use ZLIB.DEF instead. */
     /* For complete Windows compatibility, use WINAPI, not __stdcall. */
#    define ZEXPORT WINAPI
#    ifdef WIN32
#      define ZEXPORTVA WINAPIV
#    else
#      define ZEXPORTVA FAR CDECL
#    endif
#  endif
#endif

#if defined (__BEOS__)
#  ifdef ZLIB_DLL
#    ifdef ZLIB_INTERNAL
#      define ZEXPORT   __declspec(dllexport)
#      define ZEXPORTVA __declspec(dllexport)
#    else
#      define ZEXPORT   __declspec(dllimport)
#      define ZEXPORTVA __declspec(dllimport)
#    endif
#  endif
#endif

#ifndef ZEXTERN
#  define ZEXTERN extern
#endif
#ifndef ZEXPORT
#  define ZEXPORT
#endif
#ifndef ZEXPORTVA
#  define ZEXPORTVA
#endif

#ifndef FAR
#  define FAR
#endif

#if !defined(__MACTYPES__)
typedef unsigned char  Byte;  /* 8 bits */
#endif
typedef unsigned int   uInt;  /* 16 bits or more */
typedef unsigned long  uLong; /* 32 bits or more */

#ifdef SMALL_MEDIUM
   /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */
#  define Bytef Byte FAR
#else
   typedef Byte  FAR Bytef;
#endif
typedef char  FAR charf;
typedef int   FAR intf;
typedef uInt  FAR uIntf;
typedef uLong FAR uLongf;

#ifdef STDC
   typedef void const *voidpc;
   typedef void FAR   *voidpf;
   typedef void       *voidp;
#else
   typedef Byte const *voidpc;
   typedef Byte FAR   *voidpf;
   typedef Byte       *voidp;
#endif

#if 0           /* HAVE_UNISTD_H -- this line is updated by ./configure */
#  include  /* for off_t */
#  include     /* for SEEK_* and off_t */
#  ifdef VMS
#    include    /* for off_t */
#  endif
#  define z_off_t off_t
#endif
#ifndef SEEK_SET
#  define SEEK_SET        0       /* Seek from beginning of file.  */
#  define SEEK_CUR        1       /* Seek from current position.  */
#  define SEEK_END        2       /* Set file pointer to EOF plus "offset" */
#endif
#ifndef z_off_t
#  define z_off_t long
#endif

#if defined(__OS400__)
#  define NO_vsnprintf
#endif

#if defined(__MVS__)
#  define NO_vsnprintf
#  ifdef FAR
#    undef FAR
#  endif
#endif

/* MVS linker does not support external names larger than 8 bytes */
#if defined(__MVS__)
#   pragma map(deflateInit_,"DEIN")
#   pragma map(deflateInit2_,"DEIN2")
#   pragma map(deflateEnd,"DEEND")
#   pragma map(deflateBound,"DEBND")
#   pragma map(inflateInit_,"ININ")
#   pragma map(inflateInit2_,"ININ2")
#   pragma map(inflateEnd,"INEND")
#   pragma map(inflateSync,"INSY")
#   pragma map(inflateSetDictionary,"INSEDI")
#   pragma map(compressBound,"CMBND")
#   pragma map(inflate_table,"INTABL")
#   pragma map(inflate_fast,"INFA")
#   pragma map(inflate_copyright,"INCOPY")
#endif

#endif /* ZCONF_H */
genometools-1.5.1/src/external/samtools-0.1.18/win32/zlib.h000066400000000000000000002012141211610345200231140ustar00rootroot00000000000000/* zlib.h -- interface of the 'zlib' general purpose compression library
  version 1.2.3, July 18th, 2005

  Copyright (C) 1995-2005 Jean-loup Gailly and Mark Adler

  This software is provided 'as-is', without any express or implied
  warranty.  In no event will the authors be held liable for any damages
  arising from the use of this software.

  Permission is granted to anyone to use this software for any purpose,
  including commercial applications, and to alter it and redistribute it
  freely, subject to the following restrictions:

  1. The origin of this software must not be misrepresented; you must not
     claim that you wrote the original software. If you use this software
     in a product, an acknowledgment in the product documentation would be
     appreciated but is not required.
  2. Altered source versions must be plainly marked as such, and must not be
     misrepresented as being the original software.
  3. This notice may not be removed or altered from any source distribution.

  Jean-loup Gailly        Mark Adler
  jloup@gzip.org          madler@alumni.caltech.edu


  The data format used by the zlib library is described by RFCs (Request for
  Comments) 1950 to 1952 in the files http://www.ietf.org/rfc/rfc1950.txt
  (zlib format), rfc1951.txt (deflate format) and rfc1952.txt (gzip format).
*/

#ifndef ZLIB_H
#define ZLIB_H

#include "zconf.h"

#ifdef __cplusplus
extern "C" {
#endif

#define ZLIB_VERSION "1.2.3"
#define ZLIB_VERNUM 0x1230

/*
     The 'zlib' compression library provides in-memory compression and
  decompression functions, including integrity checks of the uncompressed
  data.  This version of the library supports only one compression method
  (deflation) but other algorithms will be added later and will have the same
  stream interface.

     Compression can be done in a single step if the buffers are large
  enough (for example if an input file is mmap'ed), or can be done by
  repeated calls of the compression function.  In the latter case, the
  application must provide more input and/or consume the output
  (providing more output space) before each call.

     The compressed data format used by default by the in-memory functions is
  the zlib format, which is a zlib wrapper documented in RFC 1950, wrapped
  around a deflate stream, which is itself documented in RFC 1951.

     The library also supports reading and writing files in gzip (.gz) format
  with an interface similar to that of stdio using the functions that start
  with "gz".  The gzip format is different from the zlib format.  gzip is a
  gzip wrapper, documented in RFC 1952, wrapped around a deflate stream.

     This library can optionally read and write gzip streams in memory as well.

     The zlib format was designed to be compact and fast for use in memory
  and on communications channels.  The gzip format was designed for single-
  file compression on file systems, has a larger header than zlib to maintain
  directory information, and uses a different, slower check method than zlib.

     The library does not install any signal handler. The decoder checks
  the consistency of the compressed data, so the library should never
  crash even in case of corrupted input.
*/

typedef voidpf (*alloc_func) OF((voidpf opaque, uInt items, uInt size));
typedef void   (*free_func)  OF((voidpf opaque, voidpf address));

struct internal_state;

typedef struct z_stream_s {
    Bytef    *next_in;  /* next input byte */
    uInt     avail_in;  /* number of bytes available at next_in */
    uLong    total_in;  /* total nb of input bytes read so far */

    Bytef    *next_out; /* next output byte should be put there */
    uInt     avail_out; /* remaining free space at next_out */
    uLong    total_out; /* total nb of bytes output so far */

    char     *msg;      /* last error message, NULL if no error */
    struct internal_state FAR *state; /* not visible by applications */

    alloc_func zalloc;  /* used to allocate the internal state */
    free_func  zfree;   /* used to free the internal state */
    voidpf     opaque;  /* private data object passed to zalloc and zfree */

    int     data_type;  /* best guess about the data type: binary or text */
    uLong   adler;      /* adler32 value of the uncompressed data */
    uLong   reserved;   /* reserved for future use */
} z_stream;

typedef z_stream FAR *z_streamp;

/*
     gzip header information passed to and from zlib routines.  See RFC 1952
  for more details on the meanings of these fields.
*/
typedef struct gz_header_s {
    int     text;       /* true if compressed data believed to be text */
    uLong   time;       /* modification time */
    int     xflags;     /* extra flags (not used when writing a gzip file) */
    int     os;         /* operating system */
    Bytef   *extra;     /* pointer to extra field or Z_NULL if none */
    uInt    extra_len;  /* extra field length (valid if extra != Z_NULL) */
    uInt    extra_max;  /* space at extra (only when reading header) */
    Bytef   *name;      /* pointer to zero-terminated file name or Z_NULL */
    uInt    name_max;   /* space at name (only when reading header) */
    Bytef   *comment;   /* pointer to zero-terminated comment or Z_NULL */
    uInt    comm_max;   /* space at comment (only when reading header) */
    int     hcrc;       /* true if there was or will be a header crc */
    int     done;       /* true when done reading gzip header (not used
                           when writing a gzip file) */
} gz_header;

typedef gz_header FAR *gz_headerp;

/*
   The application must update next_in and avail_in when avail_in has
   dropped to zero. It must update next_out and avail_out when avail_out
   has dropped to zero. The application must initialize zalloc, zfree and
   opaque before calling the init function. All other fields are set by the
   compression library and must not be updated by the application.

   The opaque value provided by the application will be passed as the first
   parameter for calls of zalloc and zfree. This can be useful for custom
   memory management. The compression library attaches no meaning to the
   opaque value.

   zalloc must return Z_NULL if there is not enough memory for the object.
   If zlib is used in a multi-threaded application, zalloc and zfree must be
   thread safe.

   On 16-bit systems, the functions zalloc and zfree must be able to allocate
   exactly 65536 bytes, but will not be required to allocate more than this
   if the symbol MAXSEG_64K is defined (see zconf.h). WARNING: On MSDOS,
   pointers returned by zalloc for objects of exactly 65536 bytes *must*
   have their offset normalized to zero. The default allocation function
   provided by this library ensures this (see zutil.c). To reduce memory
   requirements and avoid any allocation of 64K objects, at the expense of
   compression ratio, compile the library with -DMAX_WBITS=14 (see zconf.h).

   The fields total_in and total_out can be used for statistics or
   progress reports. After compression, total_in holds the total size of
   the uncompressed data and may be saved for use in the decompressor
   (particularly if the decompressor wants to decompress everything in
   a single step).
*/

                        /* constants */

#define Z_NO_FLUSH      0
#define Z_PARTIAL_FLUSH 1 /* will be removed, use Z_SYNC_FLUSH instead */
#define Z_SYNC_FLUSH    2
#define Z_FULL_FLUSH    3
#define Z_FINISH        4
#define Z_BLOCK         5
/* Allowed flush values; see deflate() and inflate() below for details */

#define Z_OK            0
#define Z_STREAM_END    1
#define Z_NEED_DICT     2
#define Z_ERRNO        (-1)
#define Z_STREAM_ERROR (-2)
#define Z_DATA_ERROR   (-3)
#define Z_MEM_ERROR    (-4)
#define Z_BUF_ERROR    (-5)
#define Z_VERSION_ERROR (-6)
/* Return codes for the compression/decompression functions. Negative
 * values are errors, positive values are used for special but normal events.
 */

#define Z_NO_COMPRESSION         0
#define Z_BEST_SPEED             1
#define Z_BEST_COMPRESSION       9
#define Z_DEFAULT_COMPRESSION  (-1)
/* compression levels */

#define Z_FILTERED            1
#define Z_HUFFMAN_ONLY        2
#define Z_RLE                 3
#define Z_FIXED               4
#define Z_DEFAULT_STRATEGY    0
/* compression strategy; see deflateInit2() below for details */

#define Z_BINARY   0
#define Z_TEXT     1
#define Z_ASCII    Z_TEXT   /* for compatibility with 1.2.2 and earlier */
#define Z_UNKNOWN  2
/* Possible values of the data_type field (though see inflate()) */

#define Z_DEFLATED   8
/* The deflate compression method (the only one supported in this version) */

#define Z_NULL  0  /* for initializing zalloc, zfree, opaque */

#define zlib_version zlibVersion()
/* for compatibility with versions < 1.0.2 */

                        /* basic functions */

ZEXTERN const char * ZEXPORT zlibVersion OF((void));
/* The application can compare zlibVersion and ZLIB_VERSION for consistency.
   If the first character differs, the library code actually used is
   not compatible with the zlib.h header file used by the application.
   This check is automatically made by deflateInit and inflateInit.
 */

/*
ZEXTERN int ZEXPORT deflateInit OF((z_streamp strm, int level));

     Initializes the internal stream state for compression. The fields
   zalloc, zfree and opaque must be initialized before by the caller.
   If zalloc and zfree are set to Z_NULL, deflateInit updates them to
   use default allocation functions.

     The compression level must be Z_DEFAULT_COMPRESSION, or between 0 and 9:
   1 gives best speed, 9 gives best compression, 0 gives no compression at
   all (the input data is simply copied a block at a time).
   Z_DEFAULT_COMPRESSION requests a default compromise between speed and
   compression (currently equivalent to level 6).

     deflateInit returns Z_OK if success, Z_MEM_ERROR if there was not
   enough memory, Z_STREAM_ERROR if level is not a valid compression level,
   Z_VERSION_ERROR if the zlib library version (zlib_version) is incompatible
   with the version assumed by the caller (ZLIB_VERSION).
   msg is set to null if there is no error message.  deflateInit does not
   perform any compression: this will be done by deflate().
*/


ZEXTERN int ZEXPORT deflate OF((z_streamp strm, int flush));
/*
    deflate compresses as much data as possible, and stops when the input
  buffer becomes empty or the output buffer becomes full. It may introduce some
  output latency (reading input without producing any output) except when
  forced to flush.

    The detailed semantics are as follows. deflate performs one or both of the
  following actions:

  - Compress more input starting at next_in and update next_in and avail_in
    accordingly. If not all input can be processed (because there is not
    enough room in the output buffer), next_in and avail_in are updated and
    processing will resume at this point for the next call of deflate().

  - Provide more output starting at next_out and update next_out and avail_out
    accordingly. This action is forced if the parameter flush is non zero.
    Forcing flush frequently degrades the compression ratio, so this parameter
    should be set only when necessary (in interactive applications).
    Some output may be provided even if flush is not set.

  Before the call of deflate(), the application should ensure that at least
  one of the actions is possible, by providing more input and/or consuming
  more output, and updating avail_in or avail_out accordingly; avail_out
  should never be zero before the call. The application can consume the
  compressed output when it wants, for example when the output buffer is full
  (avail_out == 0), or after each call of deflate(). If deflate returns Z_OK
  and with zero avail_out, it must be called again after making room in the
  output buffer because there might be more output pending.

    Normally the parameter flush is set to Z_NO_FLUSH, which allows deflate to
  decide how much data to accumualte before producing output, in order to
  maximize compression.

    If the parameter flush is set to Z_SYNC_FLUSH, all pending output is
  flushed to the output buffer and the output is aligned on a byte boundary, so
  that the decompressor can get all input data available so far. (In particular
  avail_in is zero after the call if enough output space has been provided
  before the call.)  Flushing may degrade compression for some compression
  algorithms and so it should be used only when necessary.

    If flush is set to Z_FULL_FLUSH, all output is flushed as with
  Z_SYNC_FLUSH, and the compression state is reset so that decompression can
  restart from this point if previous compressed data has been damaged or if
  random access is desired. Using Z_FULL_FLUSH too often can seriously degrade
  compression.

    If deflate returns with avail_out == 0, this function must be called again
  with the same value of the flush parameter and more output space (updated
  avail_out), until the flush is complete (deflate returns with non-zero
  avail_out). In the case of a Z_FULL_FLUSH or Z_SYNC_FLUSH, make sure that
  avail_out is greater than six to avoid repeated flush markers due to
  avail_out == 0 on return.

    If the parameter flush is set to Z_FINISH, pending input is processed,
  pending output is flushed and deflate returns with Z_STREAM_END if there
  was enough output space; if deflate returns with Z_OK, this function must be
  called again with Z_FINISH and more output space (updated avail_out) but no
  more input data, until it returns with Z_STREAM_END or an error. After
  deflate has returned Z_STREAM_END, the only possible operations on the
  stream are deflateReset or deflateEnd.

    Z_FINISH can be used immediately after deflateInit if all the compression
  is to be done in a single step. In this case, avail_out must be at least
  the value returned by deflateBound (see below). If deflate does not return
  Z_STREAM_END, then it must be called again as described above.

    deflate() sets strm->adler to the adler32 checksum of all input read
  so far (that is, total_in bytes).

    deflate() may update strm->data_type if it can make a good guess about
  the input data type (Z_BINARY or Z_TEXT). In doubt, the data is considered
  binary. This field is only for information purposes and does not affect
  the compression algorithm in any manner.

    deflate() returns Z_OK if some progress has been made (more input
  processed or more output produced), Z_STREAM_END if all input has been
  consumed and all output has been produced (only when flush is set to
  Z_FINISH), Z_STREAM_ERROR if the stream state was inconsistent (for example
  if next_in or next_out was NULL), Z_BUF_ERROR if no progress is possible
  (for example avail_in or avail_out was zero). Note that Z_BUF_ERROR is not
  fatal, and deflate() can be called again with more input and more output
  space to continue compressing.
*/


ZEXTERN int ZEXPORT deflateEnd OF((z_streamp strm));
/*
     All dynamically allocated data structures for this stream are freed.
   This function discards any unprocessed input and does not flush any
   pending output.

     deflateEnd returns Z_OK if success, Z_STREAM_ERROR if the
   stream state was inconsistent, Z_DATA_ERROR if the stream was freed
   prematurely (some input or output was discarded). In the error case,
   msg may be set but then points to a static string (which must not be
   deallocated).
*/


/*
ZEXTERN int ZEXPORT inflateInit OF((z_streamp strm));

     Initializes the internal stream state for decompression. The fields
   next_in, avail_in, zalloc, zfree and opaque must be initialized before by
   the caller. If next_in is not Z_NULL and avail_in is large enough (the exact
   value depends on the compression method), inflateInit determines the
   compression method from the zlib header and allocates all data structures
   accordingly; otherwise the allocation will be deferred to the first call of
   inflate.  If zalloc and zfree are set to Z_NULL, inflateInit updates them to
   use default allocation functions.

     inflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough
   memory, Z_VERSION_ERROR if the zlib library version is incompatible with the
   version assumed by the caller.  msg is set to null if there is no error
   message. inflateInit does not perform any decompression apart from reading
   the zlib header if present: this will be done by inflate().  (So next_in and
   avail_in may be modified, but next_out and avail_out are unchanged.)
*/


ZEXTERN int ZEXPORT inflate OF((z_streamp strm, int flush));
/*
    inflate decompresses as much data as possible, and stops when the input
  buffer becomes empty or the output buffer becomes full. It may introduce
  some output latency (reading input without producing any output) except when
  forced to flush.

  The detailed semantics are as follows. inflate performs one or both of the
  following actions:

  - Decompress more input starting at next_in and update next_in and avail_in
    accordingly. If not all input can be processed (because there is not
    enough room in the output buffer), next_in is updated and processing
    will resume at this point for the next call of inflate().

  - Provide more output starting at next_out and update next_out and avail_out
    accordingly.  inflate() provides as much output as possible, until there
    is no more input data or no more space in the output buffer (see below
    about the flush parameter).

  Before the call of inflate(), the application should ensure that at least
  one of the actions is possible, by providing more input and/or consuming
  more output, and updating the next_* and avail_* values accordingly.
  The application can consume the uncompressed output when it wants, for
  example when the output buffer is full (avail_out == 0), or after each
  call of inflate(). If inflate returns Z_OK and with zero avail_out, it
  must be called again after making room in the output buffer because there
  might be more output pending.

    The flush parameter of inflate() can be Z_NO_FLUSH, Z_SYNC_FLUSH,
  Z_FINISH, or Z_BLOCK. Z_SYNC_FLUSH requests that inflate() flush as much
  output as possible to the output buffer. Z_BLOCK requests that inflate() stop
  if and when it gets to the next deflate block boundary. When decoding the
  zlib or gzip format, this will cause inflate() to return immediately after
  the header and before the first block. When doing a raw inflate, inflate()
  will go ahead and process the first block, and will return when it gets to
  the end of that block, or when it runs out of data.

    The Z_BLOCK option assists in appending to or combining deflate streams.
  Also to assist in this, on return inflate() will set strm->data_type to the
  number of unused bits in the last byte taken from strm->next_in, plus 64
  if inflate() is currently decoding the last block in the deflate stream,
  plus 128 if inflate() returned immediately after decoding an end-of-block
  code or decoding the complete header up to just before the first byte of the
  deflate stream. The end-of-block will not be indicated until all of the
  uncompressed data from that block has been written to strm->next_out.  The
  number of unused bits may in general be greater than seven, except when
  bit 7 of data_type is set, in which case the number of unused bits will be
  less than eight.

    inflate() should normally be called until it returns Z_STREAM_END or an
  error. However if all decompression is to be performed in a single step
  (a single call of inflate), the parameter flush should be set to
  Z_FINISH. In this case all pending input is processed and all pending
  output is flushed; avail_out must be large enough to hold all the
  uncompressed data. (The size of the uncompressed data may have been saved
  by the compressor for this purpose.) The next operation on this stream must
  be inflateEnd to deallocate the decompression state. The use of Z_FINISH
  is never required, but can be used to inform inflate that a faster approach
  may be used for the single inflate() call.

     In this implementation, inflate() always flushes as much output as
  possible to the output buffer, and always uses the faster approach on the
  first call. So the only effect of the flush parameter in this implementation
  is on the return value of inflate(), as noted below, or when it returns early
  because Z_BLOCK is used.

     If a preset dictionary is needed after this call (see inflateSetDictionary
  below), inflate sets strm->adler to the adler32 checksum of the dictionary
  chosen by the compressor and returns Z_NEED_DICT; otherwise it sets
  strm->adler to the adler32 checksum of all output produced so far (that is,
  total_out bytes) and returns Z_OK, Z_STREAM_END or an error code as described
  below. At the end of the stream, inflate() checks that its computed adler32
  checksum is equal to that saved by the compressor and returns Z_STREAM_END
  only if the checksum is correct.

    inflate() will decompress and check either zlib-wrapped or gzip-wrapped
  deflate data.  The header type is detected automatically.  Any information
  contained in the gzip header is not retained, so applications that need that
  information should instead use raw inflate, see inflateInit2() below, or
  inflateBack() and perform their own processing of the gzip header and
  trailer.

    inflate() returns Z_OK if some progress has been made (more input processed
  or more output produced), Z_STREAM_END if the end of the compressed data has
  been reached and all uncompressed output has been produced, Z_NEED_DICT if a
  preset dictionary is needed at this point, Z_DATA_ERROR if the input data was
  corrupted (input stream not conforming to the zlib format or incorrect check
  value), Z_STREAM_ERROR if the stream structure was inconsistent (for example
  if next_in or next_out was NULL), Z_MEM_ERROR if there was not enough memory,
  Z_BUF_ERROR if no progress is possible or if there was not enough room in the
  output buffer when Z_FINISH is used. Note that Z_BUF_ERROR is not fatal, and
  inflate() can be called again with more input and more output space to
  continue decompressing. If Z_DATA_ERROR is returned, the application may then
  call inflateSync() to look for a good compression block if a partial recovery
  of the data is desired.
*/


ZEXTERN int ZEXPORT inflateEnd OF((z_streamp strm));
/*
     All dynamically allocated data structures for this stream are freed.
   This function discards any unprocessed input and does not flush any
   pending output.

     inflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state
   was inconsistent. In the error case, msg may be set but then points to a
   static string (which must not be deallocated).
*/

                        /* Advanced functions */

/*
    The following functions are needed only in some special applications.
*/

/*
ZEXTERN int ZEXPORT deflateInit2 OF((z_streamp strm,
                                     int  level,
                                     int  method,
                                     int  windowBits,
                                     int  memLevel,
                                     int  strategy));

     This is another version of deflateInit with more compression options. The
   fields next_in, zalloc, zfree and opaque must be initialized before by
   the caller.

     The method parameter is the compression method. It must be Z_DEFLATED in
   this version of the library.

     The windowBits parameter is the base two logarithm of the window size
   (the size of the history buffer). It should be in the range 8..15 for this
   version of the library. Larger values of this parameter result in better
   compression at the expense of memory usage. The default value is 15 if
   deflateInit is used instead.

     windowBits can also be -8..-15 for raw deflate. In this case, -windowBits
   determines the window size. deflate() will then generate raw deflate data
   with no zlib header or trailer, and will not compute an adler32 check value.

     windowBits can also be greater than 15 for optional gzip encoding. Add
   16 to windowBits to write a simple gzip header and trailer around the
   compressed data instead of a zlib wrapper. The gzip header will have no
   file name, no extra data, no comment, no modification time (set to zero),
   no header crc, and the operating system will be set to 255 (unknown).  If a
   gzip stream is being written, strm->adler is a crc32 instead of an adler32.

     The memLevel parameter specifies how much memory should be allocated
   for the internal compression state. memLevel=1 uses minimum memory but
   is slow and reduces compression ratio; memLevel=9 uses maximum memory
   for optimal speed. The default value is 8. See zconf.h for total memory
   usage as a function of windowBits and memLevel.

     The strategy parameter is used to tune the compression algorithm. Use the
   value Z_DEFAULT_STRATEGY for normal data, Z_FILTERED for data produced by a
   filter (or predictor), Z_HUFFMAN_ONLY to force Huffman encoding only (no
   string match), or Z_RLE to limit match distances to one (run-length
   encoding). Filtered data consists mostly of small values with a somewhat
   random distribution. In this case, the compression algorithm is tuned to
   compress them better. The effect of Z_FILTERED is to force more Huffman
   coding and less string matching; it is somewhat intermediate between
   Z_DEFAULT and Z_HUFFMAN_ONLY. Z_RLE is designed to be almost as fast as
   Z_HUFFMAN_ONLY, but give better compression for PNG image data. The strategy
   parameter only affects the compression ratio but not the correctness of the
   compressed output even if it is not set appropriately.  Z_FIXED prevents the
   use of dynamic Huffman codes, allowing for a simpler decoder for special
   applications.

      deflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
   memory, Z_STREAM_ERROR if a parameter is invalid (such as an invalid
   method). msg is set to null if there is no error message.  deflateInit2 does
   not perform any compression: this will be done by deflate().
*/

ZEXTERN int ZEXPORT deflateSetDictionary OF((z_streamp strm,
                                             const Bytef *dictionary,
                                             uInt  dictLength));
/*
     Initializes the compression dictionary from the given byte sequence
   without producing any compressed output. This function must be called
   immediately after deflateInit, deflateInit2 or deflateReset, before any
   call of deflate. The compressor and decompressor must use exactly the same
   dictionary (see inflateSetDictionary).

     The dictionary should consist of strings (byte sequences) that are likely
   to be encountered later in the data to be compressed, with the most commonly
   used strings preferably put towards the end of the dictionary. Using a
   dictionary is most useful when the data to be compressed is short and can be
   predicted with good accuracy; the data can then be compressed better than
   with the default empty dictionary.

     Depending on the size of the compression data structures selected by
   deflateInit or deflateInit2, a part of the dictionary may in effect be
   discarded, for example if the dictionary is larger than the window size in
   deflate or deflate2. Thus the strings most likely to be useful should be
   put at the end of the dictionary, not at the front. In addition, the
   current implementation of deflate will use at most the window size minus
   262 bytes of the provided dictionary.

     Upon return of this function, strm->adler is set to the adler32 value
   of the dictionary; the decompressor may later use this value to determine
   which dictionary has been used by the compressor. (The adler32 value
   applies to the whole dictionary even if only a subset of the dictionary is
   actually used by the compressor.) If a raw deflate was requested, then the
   adler32 value is not computed and strm->adler is not set.

     deflateSetDictionary returns Z_OK if success, or Z_STREAM_ERROR if a
   parameter is invalid (such as NULL dictionary) or the stream state is
   inconsistent (for example if deflate has already been called for this stream
   or if the compression method is bsort). deflateSetDictionary does not
   perform any compression: this will be done by deflate().
*/

ZEXTERN int ZEXPORT deflateCopy OF((z_streamp dest,
                                    z_streamp source));
/*
     Sets the destination stream as a complete copy of the source stream.

     This function can be useful when several compression strategies will be
   tried, for example when there are several ways of pre-processing the input
   data with a filter. The streams that will be discarded should then be freed
   by calling deflateEnd.  Note that deflateCopy duplicates the internal
   compression state which can be quite large, so this strategy is slow and
   can consume lots of memory.

     deflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not
   enough memory, Z_STREAM_ERROR if the source stream state was inconsistent
   (such as zalloc being NULL). msg is left unchanged in both source and
   destination.
*/

ZEXTERN int ZEXPORT deflateReset OF((z_streamp strm));
/*
     This function is equivalent to deflateEnd followed by deflateInit,
   but does not free and reallocate all the internal compression state.
   The stream will keep the same compression level and any other attributes
   that may have been set by deflateInit2.

      deflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
   stream state was inconsistent (such as zalloc or state being NULL).
*/

ZEXTERN int ZEXPORT deflateParams OF((z_streamp strm,
                                      int level,
                                      int strategy));
/*
     Dynamically update the compression level and compression strategy.  The
   interpretation of level and strategy is as in deflateInit2.  This can be
   used to switch between compression and straight copy of the input data, or
   to switch to a different kind of input data requiring a different
   strategy. If the compression level is changed, the input available so far
   is compressed with the old level (and may be flushed); the new level will
   take effect only at the next call of deflate().

     Before the call of deflateParams, the stream state must be set as for
   a call of deflate(), since the currently available input may have to
   be compressed and flushed. In particular, strm->avail_out must be non-zero.

     deflateParams returns Z_OK if success, Z_STREAM_ERROR if the source
   stream state was inconsistent or if a parameter was invalid, Z_BUF_ERROR
   if strm->avail_out was zero.
*/

ZEXTERN int ZEXPORT deflateTune OF((z_streamp strm,
                                    int good_length,
                                    int max_lazy,
                                    int nice_length,
                                    int max_chain));
/*
     Fine tune deflate's internal compression parameters.  This should only be
   used by someone who understands the algorithm used by zlib's deflate for
   searching for the best matching string, and even then only by the most
   fanatic optimizer trying to squeeze out the last compressed bit for their
   specific input data.  Read the deflate.c source code for the meaning of the
   max_lazy, good_length, nice_length, and max_chain parameters.

     deflateTune() can be called after deflateInit() or deflateInit2(), and
   returns Z_OK on success, or Z_STREAM_ERROR for an invalid deflate stream.
 */

ZEXTERN uLong ZEXPORT deflateBound OF((z_streamp strm,
                                       uLong sourceLen));
/*
     deflateBound() returns an upper bound on the compressed size after
   deflation of sourceLen bytes.  It must be called after deflateInit()
   or deflateInit2().  This would be used to allocate an output buffer
   for deflation in a single pass, and so would be called before deflate().
*/

ZEXTERN int ZEXPORT deflatePrime OF((z_streamp strm,
                                     int bits,
                                     int value));
/*
     deflatePrime() inserts bits in the deflate output stream.  The intent
  is that this function is used to start off the deflate output with the
  bits leftover from a previous deflate stream when appending to it.  As such,
  this function can only be used for raw deflate, and must be used before the
  first deflate() call after a deflateInit2() or deflateReset().  bits must be
  less than or equal to 16, and that many of the least significant bits of
  value will be inserted in the output.

      deflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source
   stream state was inconsistent.
*/

ZEXTERN int ZEXPORT deflateSetHeader OF((z_streamp strm,
                                         gz_headerp head));
/*
      deflateSetHeader() provides gzip header information for when a gzip
   stream is requested by deflateInit2().  deflateSetHeader() may be called
   after deflateInit2() or deflateReset() and before the first call of
   deflate().  The text, time, os, extra field, name, and comment information
   in the provided gz_header structure are written to the gzip header (xflag is
   ignored -- the extra flags are set according to the compression level).  The
   caller must assure that, if not Z_NULL, name and comment are terminated with
   a zero byte, and that if extra is not Z_NULL, that extra_len bytes are
   available there.  If hcrc is true, a gzip header crc is included.  Note that
   the current versions of the command-line version of gzip (up through version
   1.3.x) do not support header crc's, and will report that it is a "multi-part
   gzip file" and give up.

      If deflateSetHeader is not used, the default gzip header has text false,
   the time set to zero, and os set to 255, with no extra, name, or comment
   fields.  The gzip header is returned to the default state by deflateReset().

      deflateSetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source
   stream state was inconsistent.
*/

/*
ZEXTERN int ZEXPORT inflateInit2 OF((z_streamp strm,
                                     int  windowBits));

     This is another version of inflateInit with an extra parameter. The
   fields next_in, avail_in, zalloc, zfree and opaque must be initialized
   before by the caller.

     The windowBits parameter is the base two logarithm of the maximum window
   size (the size of the history buffer).  It should be in the range 8..15 for
   this version of the library. The default value is 15 if inflateInit is used
   instead. windowBits must be greater than or equal to the windowBits value
   provided to deflateInit2() while compressing, or it must be equal to 15 if
   deflateInit2() was not used. If a compressed stream with a larger window
   size is given as input, inflate() will return with the error code
   Z_DATA_ERROR instead of trying to allocate a larger window.

     windowBits can also be -8..-15 for raw inflate. In this case, -windowBits
   determines the window size. inflate() will then process raw deflate data,
   not looking for a zlib or gzip header, not generating a check value, and not
   looking for any check values for comparison at the end of the stream. This
   is for use with other formats that use the deflate compressed data format
   such as zip.  Those formats provide their own check values. If a custom
   format is developed using the raw deflate format for compressed data, it is
   recommended that a check value such as an adler32 or a crc32 be applied to
   the uncompressed data as is done in the zlib, gzip, and zip formats.  For
   most applications, the zlib format should be used as is. Note that comments
   above on the use in deflateInit2() applies to the magnitude of windowBits.

     windowBits can also be greater than 15 for optional gzip decoding. Add
   32 to windowBits to enable zlib and gzip decoding with automatic header
   detection, or add 16 to decode only the gzip format (the zlib format will
   return a Z_DATA_ERROR).  If a gzip stream is being decoded, strm->adler is
   a crc32 instead of an adler32.

     inflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
   memory, Z_STREAM_ERROR if a parameter is invalid (such as a null strm). msg
   is set to null if there is no error message.  inflateInit2 does not perform
   any decompression apart from reading the zlib header if present: this will
   be done by inflate(). (So next_in and avail_in may be modified, but next_out
   and avail_out are unchanged.)
*/

ZEXTERN int ZEXPORT inflateSetDictionary OF((z_streamp strm,
                                             const Bytef *dictionary,
                                             uInt  dictLength));
/*
     Initializes the decompression dictionary from the given uncompressed byte
   sequence. This function must be called immediately after a call of inflate,
   if that call returned Z_NEED_DICT. The dictionary chosen by the compressor
   can be determined from the adler32 value returned by that call of inflate.
   The compressor and decompressor must use exactly the same dictionary (see
   deflateSetDictionary).  For raw inflate, this function can be called
   immediately after inflateInit2() or inflateReset() and before any call of
   inflate() to set the dictionary.  The application must insure that the
   dictionary that was used for compression is provided.

     inflateSetDictionary returns Z_OK if success, Z_STREAM_ERROR if a
   parameter is invalid (such as NULL dictionary) or the stream state is
   inconsistent, Z_DATA_ERROR if the given dictionary doesn't match the
   expected one (incorrect adler32 value). inflateSetDictionary does not
   perform any decompression: this will be done by subsequent calls of
   inflate().
*/

ZEXTERN int ZEXPORT inflateSync OF((z_streamp strm));
/*
    Skips invalid compressed data until a full flush point (see above the
  description of deflate with Z_FULL_FLUSH) can be found, or until all
  available input is skipped. No output is provided.

    inflateSync returns Z_OK if a full flush point has been found, Z_BUF_ERROR
  if no more input was provided, Z_DATA_ERROR if no flush point has been found,
  or Z_STREAM_ERROR if the stream structure was inconsistent. In the success
  case, the application may save the current current value of total_in which
  indicates where valid compressed data was found. In the error case, the
  application may repeatedly call inflateSync, providing more input each time,
  until success or end of the input data.
*/

ZEXTERN int ZEXPORT inflateCopy OF((z_streamp dest,
                                    z_streamp source));
/*
     Sets the destination stream as a complete copy of the source stream.

     This function can be useful when randomly accessing a large stream.  The
   first pass through the stream can periodically record the inflate state,
   allowing restarting inflate at those points when randomly accessing the
   stream.

     inflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not
   enough memory, Z_STREAM_ERROR if the source stream state was inconsistent
   (such as zalloc being NULL). msg is left unchanged in both source and
   destination.
*/

ZEXTERN int ZEXPORT inflateReset OF((z_streamp strm));
/*
     This function is equivalent to inflateEnd followed by inflateInit,
   but does not free and reallocate all the internal decompression state.
   The stream will keep attributes that may have been set by inflateInit2.

      inflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
   stream state was inconsistent (such as zalloc or state being NULL).
*/

ZEXTERN int ZEXPORT inflatePrime OF((z_streamp strm,
                                     int bits,
                                     int value));
/*
     This function inserts bits in the inflate input stream.  The intent is
  that this function is used to start inflating at a bit position in the
  middle of a byte.  The provided bits will be used before any bytes are used
  from next_in.  This function should only be used with raw inflate, and
  should be used before the first inflate() call after inflateInit2() or
  inflateReset().  bits must be less than or equal to 16, and that many of the
  least significant bits of value will be inserted in the input.

      inflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source
   stream state was inconsistent.
*/

ZEXTERN int ZEXPORT inflateGetHeader OF((z_streamp strm,
                                         gz_headerp head));
/*
      inflateGetHeader() requests that gzip header information be stored in the
   provided gz_header structure.  inflateGetHeader() may be called after
   inflateInit2() or inflateReset(), and before the first call of inflate().
   As inflate() processes the gzip stream, head->done is zero until the header
   is completed, at which time head->done is set to one.  If a zlib stream is
   being decoded, then head->done is set to -1 to indicate that there will be
   no gzip header information forthcoming.  Note that Z_BLOCK can be used to
   force inflate() to return immediately after header processing is complete
   and before any actual data is decompressed.

      The text, time, xflags, and os fields are filled in with the gzip header
   contents.  hcrc is set to true if there is a header CRC.  (The header CRC
   was valid if done is set to one.)  If extra is not Z_NULL, then extra_max
   contains the maximum number of bytes to write to extra.  Once done is true,
   extra_len contains the actual extra field length, and extra contains the
   extra field, or that field truncated if extra_max is less than extra_len.
   If name is not Z_NULL, then up to name_max characters are written there,
   terminated with a zero unless the length is greater than name_max.  If
   comment is not Z_NULL, then up to comm_max characters are written there,
   terminated with a zero unless the length is greater than comm_max.  When
   any of extra, name, or comment are not Z_NULL and the respective field is
   not present in the header, then that field is set to Z_NULL to signal its
   absence.  This allows the use of deflateSetHeader() with the returned
   structure to duplicate the header.  However if those fields are set to
   allocated memory, then the application will need to save those pointers
   elsewhere so that they can be eventually freed.

      If inflateGetHeader is not used, then the header information is simply
   discarded.  The header is always checked for validity, including the header
   CRC if present.  inflateReset() will reset the process to discard the header
   information.  The application would need to call inflateGetHeader() again to
   retrieve the header from the next gzip stream.

      inflateGetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source
   stream state was inconsistent.
*/

/*
ZEXTERN int ZEXPORT inflateBackInit OF((z_streamp strm, int windowBits,
                                        unsigned char FAR *window));

     Initialize the internal stream state for decompression using inflateBack()
   calls.  The fields zalloc, zfree and opaque in strm must be initialized
   before the call.  If zalloc and zfree are Z_NULL, then the default library-
   derived memory allocation routines are used.  windowBits is the base two
   logarithm of the window size, in the range 8..15.  window is a caller
   supplied buffer of that size.  Except for special applications where it is
   assured that deflate was used with small window sizes, windowBits must be 15
   and a 32K byte window must be supplied to be able to decompress general
   deflate streams.

     See inflateBack() for the usage of these routines.

     inflateBackInit will return Z_OK on success, Z_STREAM_ERROR if any of
   the paramaters are invalid, Z_MEM_ERROR if the internal state could not
   be allocated, or Z_VERSION_ERROR if the version of the library does not
   match the version of the header file.
*/

typedef unsigned (*in_func) OF((void FAR *, unsigned char FAR * FAR *));
typedef int (*out_func) OF((void FAR *, unsigned char FAR *, unsigned));

ZEXTERN int ZEXPORT inflateBack OF((z_streamp strm,
                                    in_func in, void FAR *in_desc,
                                    out_func out, void FAR *out_desc));
/*
     inflateBack() does a raw inflate with a single call using a call-back
   interface for input and output.  This is more efficient than inflate() for
   file i/o applications in that it avoids copying between the output and the
   sliding window by simply making the window itself the output buffer.  This
   function trusts the application to not change the output buffer passed by
   the output function, at least until inflateBack() returns.

     inflateBackInit() must be called first to allocate the internal state
   and to initialize the state with the user-provided window buffer.
   inflateBack() may then be used multiple times to inflate a complete, raw
   deflate stream with each call.  inflateBackEnd() is then called to free
   the allocated state.

     A raw deflate stream is one with no zlib or gzip header or trailer.
   This routine would normally be used in a utility that reads zip or gzip
   files and writes out uncompressed files.  The utility would decode the
   header and process the trailer on its own, hence this routine expects
   only the raw deflate stream to decompress.  This is different from the
   normal behavior of inflate(), which expects either a zlib or gzip header and
   trailer around the deflate stream.

     inflateBack() uses two subroutines supplied by the caller that are then
   called by inflateBack() for input and output.  inflateBack() calls those
   routines until it reads a complete deflate stream and writes out all of the
   uncompressed data, or until it encounters an error.  The function's
   parameters and return types are defined above in the in_func and out_func
   typedefs.  inflateBack() will call in(in_desc, &buf) which should return the
   number of bytes of provided input, and a pointer to that input in buf.  If
   there is no input available, in() must return zero--buf is ignored in that
   case--and inflateBack() will return a buffer error.  inflateBack() will call
   out(out_desc, buf, len) to write the uncompressed data buf[0..len-1].  out()
   should return zero on success, or non-zero on failure.  If out() returns
   non-zero, inflateBack() will return with an error.  Neither in() nor out()
   are permitted to change the contents of the window provided to
   inflateBackInit(), which is also the buffer that out() uses to write from.
   The length written by out() will be at most the window size.  Any non-zero
   amount of input may be provided by in().

     For convenience, inflateBack() can be provided input on the first call by
   setting strm->next_in and strm->avail_in.  If that input is exhausted, then
   in() will be called.  Therefore strm->next_in must be initialized before
   calling inflateBack().  If strm->next_in is Z_NULL, then in() will be called
   immediately for input.  If strm->next_in is not Z_NULL, then strm->avail_in
   must also be initialized, and then if strm->avail_in is not zero, input will
   initially be taken from strm->next_in[0 .. strm->avail_in - 1].

     The in_desc and out_desc parameters of inflateBack() is passed as the
   first parameter of in() and out() respectively when they are called.  These
   descriptors can be optionally used to pass any information that the caller-
   supplied in() and out() functions need to do their job.

     On return, inflateBack() will set strm->next_in and strm->avail_in to
   pass back any unused input that was provided by the last in() call.  The
   return values of inflateBack() can be Z_STREAM_END on success, Z_BUF_ERROR
   if in() or out() returned an error, Z_DATA_ERROR if there was a format
   error in the deflate stream (in which case strm->msg is set to indicate the
   nature of the error), or Z_STREAM_ERROR if the stream was not properly
   initialized.  In the case of Z_BUF_ERROR, an input or output error can be
   distinguished using strm->next_in which will be Z_NULL only if in() returned
   an error.  If strm->next is not Z_NULL, then the Z_BUF_ERROR was due to
   out() returning non-zero.  (in() will always be called before out(), so
   strm->next_in is assured to be defined if out() returns non-zero.)  Note
   that inflateBack() cannot return Z_OK.
*/

ZEXTERN int ZEXPORT inflateBackEnd OF((z_streamp strm));
/*
     All memory allocated by inflateBackInit() is freed.

     inflateBackEnd() returns Z_OK on success, or Z_STREAM_ERROR if the stream
   state was inconsistent.
*/

ZEXTERN uLong ZEXPORT zlibCompileFlags OF((void));
/* Return flags indicating compile-time options.

    Type sizes, two bits each, 00 = 16 bits, 01 = 32, 10 = 64, 11 = other:
     1.0: size of uInt
     3.2: size of uLong
     5.4: size of voidpf (pointer)
     7.6: size of z_off_t

    Compiler, assembler, and debug options:
     8: DEBUG
     9: ASMV or ASMINF -- use ASM code
     10: ZLIB_WINAPI -- exported functions use the WINAPI calling convention
     11: 0 (reserved)

    One-time table building (smaller code, but not thread-safe if true):
     12: BUILDFIXED -- build static block decoding tables when needed
     13: DYNAMIC_CRC_TABLE -- build CRC calculation tables when needed
     14,15: 0 (reserved)

    Library content (indicates missing functionality):
     16: NO_GZCOMPRESS -- gz* functions cannot compress (to avoid linking
                          deflate code when not needed)
     17: NO_GZIP -- deflate can't write gzip streams, and inflate can't detect
                    and decode gzip streams (to avoid linking crc code)
     18-19: 0 (reserved)

    Operation variations (changes in library functionality):
     20: PKZIP_BUG_WORKAROUND -- slightly more permissive inflate
     21: FASTEST -- deflate algorithm with only one, lowest compression level
     22,23: 0 (reserved)

    The sprintf variant used by gzprintf (zero is best):
     24: 0 = vs*, 1 = s* -- 1 means limited to 20 arguments after the format
     25: 0 = *nprintf, 1 = *printf -- 1 means gzprintf() not secure!
     26: 0 = returns value, 1 = void -- 1 means inferred string length returned

    Remainder:
     27-31: 0 (reserved)
 */


                        /* utility functions */

/*
     The following utility functions are implemented on top of the
   basic stream-oriented functions. To simplify the interface, some
   default options are assumed (compression level and memory usage,
   standard memory allocation functions). The source code of these
   utility functions can easily be modified if you need special options.
*/

ZEXTERN int ZEXPORT compress OF((Bytef *dest,   uLongf *destLen,
                                 const Bytef *source, uLong sourceLen));
/*
     Compresses the source buffer into the destination buffer.  sourceLen is
   the byte length of the source buffer. Upon entry, destLen is the total
   size of the destination buffer, which must be at least the value returned
   by compressBound(sourceLen). Upon exit, destLen is the actual size of the
   compressed buffer.
     This function can be used to compress a whole file at once if the
   input file is mmap'ed.
     compress returns Z_OK if success, Z_MEM_ERROR if there was not
   enough memory, Z_BUF_ERROR if there was not enough room in the output
   buffer.
*/

ZEXTERN int ZEXPORT compress2 OF((Bytef *dest,   uLongf *destLen,
                                  const Bytef *source, uLong sourceLen,
                                  int level));
/*
     Compresses the source buffer into the destination buffer. The level
   parameter has the same meaning as in deflateInit.  sourceLen is the byte
   length of the source buffer. Upon entry, destLen is the total size of the
   destination buffer, which must be at least the value returned by
   compressBound(sourceLen). Upon exit, destLen is the actual size of the
   compressed buffer.

     compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
   memory, Z_BUF_ERROR if there was not enough room in the output buffer,
   Z_STREAM_ERROR if the level parameter is invalid.
*/

ZEXTERN uLong ZEXPORT compressBound OF((uLong sourceLen));
/*
     compressBound() returns an upper bound on the compressed size after
   compress() or compress2() on sourceLen bytes.  It would be used before
   a compress() or compress2() call to allocate the destination buffer.
*/

ZEXTERN int ZEXPORT uncompress OF((Bytef *dest,   uLongf *destLen,
                                   const Bytef *source, uLong sourceLen));
/*
     Decompresses the source buffer into the destination buffer.  sourceLen is
   the byte length of the source buffer. Upon entry, destLen is the total
   size of the destination buffer, which must be large enough to hold the
   entire uncompressed data. (The size of the uncompressed data must have
   been saved previously by the compressor and transmitted to the decompressor
   by some mechanism outside the scope of this compression library.)
   Upon exit, destLen is the actual size of the compressed buffer.
     This function can be used to decompress a whole file at once if the
   input file is mmap'ed.

     uncompress returns Z_OK if success, Z_MEM_ERROR if there was not
   enough memory, Z_BUF_ERROR if there was not enough room in the output
   buffer, or Z_DATA_ERROR if the input data was corrupted or incomplete.
*/


typedef voidp gzFile;

ZEXTERN gzFile ZEXPORT gzopen  OF((const char *path, const char *mode));
/*
     Opens a gzip (.gz) file for reading or writing. The mode parameter
   is as in fopen ("rb" or "wb") but can also include a compression level
   ("wb9") or a strategy: 'f' for filtered data as in "wb6f", 'h' for
   Huffman only compression as in "wb1h", or 'R' for run-length encoding
   as in "wb1R". (See the description of deflateInit2 for more information
   about the strategy parameter.)

     gzopen can be used to read a file which is not in gzip format; in this
   case gzread will directly read from the file without decompression.

     gzopen returns NULL if the file could not be opened or if there was
   insufficient memory to allocate the (de)compression state; errno
   can be checked to distinguish the two cases (if errno is zero, the
   zlib error is Z_MEM_ERROR).  */

ZEXTERN gzFile ZEXPORT gzdopen  OF((int fd, const char *mode));
/*
     gzdopen() associates a gzFile with the file descriptor fd.  File
   descriptors are obtained from calls like open, dup, creat, pipe or
   fileno (in the file has been previously opened with fopen).
   The mode parameter is as in gzopen.
     The next call of gzclose on the returned gzFile will also close the
   file descriptor fd, just like fclose(fdopen(fd), mode) closes the file
   descriptor fd. If you want to keep fd open, use gzdopen(dup(fd), mode).
     gzdopen returns NULL if there was insufficient memory to allocate
   the (de)compression state.
*/

ZEXTERN int ZEXPORT gzsetparams OF((gzFile file, int level, int strategy));
/*
     Dynamically update the compression level or strategy. See the description
   of deflateInit2 for the meaning of these parameters.
     gzsetparams returns Z_OK if success, or Z_STREAM_ERROR if the file was not
   opened for writing.
*/

ZEXTERN int ZEXPORT    gzread  OF((gzFile file, voidp buf, unsigned len));
/*
     Reads the given number of uncompressed bytes from the compressed file.
   If the input file was not in gzip format, gzread copies the given number
   of bytes into the buffer.
     gzread returns the number of uncompressed bytes actually read (0 for
   end of file, -1 for error). */

ZEXTERN int ZEXPORT    gzwrite OF((gzFile file,
                                   voidpc buf, unsigned len));
/*
     Writes the given number of uncompressed bytes into the compressed file.
   gzwrite returns the number of uncompressed bytes actually written
   (0 in case of error).
*/

ZEXTERN int ZEXPORTVA   gzprintf OF((gzFile file, const char *format, ...));
/*
     Converts, formats, and writes the args to the compressed file under
   control of the format string, as in fprintf. gzprintf returns the number of
   uncompressed bytes actually written (0 in case of error).  The number of
   uncompressed bytes written is limited to 4095. The caller should assure that
   this limit is not exceeded. If it is exceeded, then gzprintf() will return
   return an error (0) with nothing written. In this case, there may also be a
   buffer overflow with unpredictable consequences, which is possible only if
   zlib was compiled with the insecure functions sprintf() or vsprintf()
   because the secure snprintf() or vsnprintf() functions were not available.
*/

ZEXTERN int ZEXPORT gzputs OF((gzFile file, const char *s));
/*
      Writes the given null-terminated string to the compressed file, excluding
   the terminating null character.
      gzputs returns the number of characters written, or -1 in case of error.
*/

ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
/*
      Reads bytes from the compressed file until len-1 characters are read, or
   a newline character is read and transferred to buf, or an end-of-file
   condition is encountered.  The string is then terminated with a null
   character.
      gzgets returns buf, or Z_NULL in case of error.
*/

ZEXTERN int ZEXPORT    gzputc OF((gzFile file, int c));
/*
      Writes c, converted to an unsigned char, into the compressed file.
   gzputc returns the value that was written, or -1 in case of error.
*/

ZEXTERN int ZEXPORT    gzgetc OF((gzFile file));
/*
      Reads one byte from the compressed file. gzgetc returns this byte
   or -1 in case of end of file or error.
*/

ZEXTERN int ZEXPORT    gzungetc OF((int c, gzFile file));
/*
      Push one character back onto the stream to be read again later.
   Only one character of push-back is allowed.  gzungetc() returns the
   character pushed, or -1 on failure.  gzungetc() will fail if a
   character has been pushed but not read yet, or if c is -1. The pushed
   character will be discarded if the stream is repositioned with gzseek()
   or gzrewind().
*/

ZEXTERN int ZEXPORT    gzflush OF((gzFile file, int flush));
/*
     Flushes all pending output into the compressed file. The parameter
   flush is as in the deflate() function. The return value is the zlib
   error number (see function gzerror below). gzflush returns Z_OK if
   the flush parameter is Z_FINISH and all output could be flushed.
     gzflush should be called only when strictly necessary because it can
   degrade compression.
*/

ZEXTERN z_off_t ZEXPORT    gzseek OF((gzFile file,
                                      z_off_t offset, int whence));
/*
      Sets the starting position for the next gzread or gzwrite on the
   given compressed file. The offset represents a number of bytes in the
   uncompressed data stream. The whence parameter is defined as in lseek(2);
   the value SEEK_END is not supported.
     If the file is opened for reading, this function is emulated but can be
   extremely slow. If the file is opened for writing, only forward seeks are
   supported; gzseek then compresses a sequence of zeroes up to the new
   starting position.

      gzseek returns the resulting offset location as measured in bytes from
   the beginning of the uncompressed stream, or -1 in case of error, in
   particular if the file is opened for writing and the new starting position
   would be before the current position.
*/

ZEXTERN int ZEXPORT    gzrewind OF((gzFile file));
/*
     Rewinds the given file. This function is supported only for reading.

   gzrewind(file) is equivalent to (int)gzseek(file, 0L, SEEK_SET)
*/

ZEXTERN z_off_t ZEXPORT    gztell OF((gzFile file));
/*
     Returns the starting position for the next gzread or gzwrite on the
   given compressed file. This position represents a number of bytes in the
   uncompressed data stream.

   gztell(file) is equivalent to gzseek(file, 0L, SEEK_CUR)
*/

ZEXTERN int ZEXPORT gzeof OF((gzFile file));
/*
     Returns 1 when EOF has previously been detected reading the given
   input stream, otherwise zero.
*/

ZEXTERN int ZEXPORT gzdirect OF((gzFile file));
/*
     Returns 1 if file is being read directly without decompression, otherwise
   zero.
*/

ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
/*
     Flushes all pending output if necessary, closes the compressed file
   and deallocates all the (de)compression state. The return value is the zlib
   error number (see function gzerror below).
*/

ZEXTERN const char * ZEXPORT gzerror OF((gzFile file, int *errnum));
/*
     Returns the error message for the last error which occurred on the
   given compressed file. errnum is set to zlib error number. If an
   error occurred in the file system and not in the compression library,
   errnum is set to Z_ERRNO and the application may consult errno
   to get the exact error code.
*/

ZEXTERN void ZEXPORT gzclearerr OF((gzFile file));
/*
     Clears the error and end-of-file flags for file. This is analogous to the
   clearerr() function in stdio. This is useful for continuing to read a gzip
   file that is being written concurrently.
*/

                        /* checksum functions */

/*
     These functions are not related to compression but are exported
   anyway because they might be useful in applications using the
   compression library.
*/

ZEXTERN uLong ZEXPORT adler32 OF((uLong adler, const Bytef *buf, uInt len));
/*
     Update a running Adler-32 checksum with the bytes buf[0..len-1] and
   return the updated checksum. If buf is NULL, this function returns
   the required initial value for the checksum.
   An Adler-32 checksum is almost as reliable as a CRC32 but can be computed
   much faster. Usage example:

     uLong adler = adler32(0L, Z_NULL, 0);

     while (read_buffer(buffer, length) != EOF) {
       adler = adler32(adler, buffer, length);
     }
     if (adler != original_adler) error();
*/

ZEXTERN uLong ZEXPORT adler32_combine OF((uLong adler1, uLong adler2,
                                          z_off_t len2));
/*
     Combine two Adler-32 checksums into one.  For two sequences of bytes, seq1
   and seq2 with lengths len1 and len2, Adler-32 checksums were calculated for
   each, adler1 and adler2.  adler32_combine() returns the Adler-32 checksum of
   seq1 and seq2 concatenated, requiring only adler1, adler2, and len2.
*/

ZEXTERN uLong ZEXPORT crc32   OF((uLong crc, const Bytef *buf, uInt len));
/*
     Update a running CRC-32 with the bytes buf[0..len-1] and return the
   updated CRC-32. If buf is NULL, this function returns the required initial
   value for the for the crc. Pre- and post-conditioning (one's complement) is
   performed within this function so it shouldn't be done by the application.
   Usage example:

     uLong crc = crc32(0L, Z_NULL, 0);

     while (read_buffer(buffer, length) != EOF) {
       crc = crc32(crc, buffer, length);
     }
     if (crc != original_crc) error();
*/

ZEXTERN uLong ZEXPORT crc32_combine OF((uLong crc1, uLong crc2, z_off_t len2));

/*
     Combine two CRC-32 check values into one.  For two sequences of bytes,
   seq1 and seq2 with lengths len1 and len2, CRC-32 check values were
   calculated for each, crc1 and crc2.  crc32_combine() returns the CRC-32
   check value of seq1 and seq2 concatenated, requiring only crc1, crc2, and
   len2.
*/


                        /* various hacks, don't look :) */

/* deflateInit and inflateInit are macros to allow checking the zlib version
 * and the compiler's view of z_stream:
 */
ZEXTERN int ZEXPORT deflateInit_ OF((z_streamp strm, int level,
                                     const char *version, int stream_size));
ZEXTERN int ZEXPORT inflateInit_ OF((z_streamp strm,
                                     const char *version, int stream_size));
ZEXTERN int ZEXPORT deflateInit2_ OF((z_streamp strm, int  level, int  method,
                                      int windowBits, int memLevel,
                                      int strategy, const char *version,
                                      int stream_size));
ZEXTERN int ZEXPORT inflateInit2_ OF((z_streamp strm, int  windowBits,
                                      const char *version, int stream_size));
ZEXTERN int ZEXPORT inflateBackInit_ OF((z_streamp strm, int windowBits,
                                         unsigned char FAR *window,
                                         const char *version,
                                         int stream_size));
#define deflateInit(strm, level) \
        deflateInit_((strm), (level),       ZLIB_VERSION, sizeof(z_stream))
#define inflateInit(strm) \
        inflateInit_((strm),                ZLIB_VERSION, sizeof(z_stream))
#define deflateInit2(strm, level, method, windowBits, memLevel, strategy) \
        deflateInit2_((strm),(level),(method),(windowBits),(memLevel),\
                      (strategy),           ZLIB_VERSION, sizeof(z_stream))
#define inflateInit2(strm, windowBits) \
        inflateInit2_((strm), (windowBits), ZLIB_VERSION, sizeof(z_stream))
#define inflateBackInit(strm, windowBits, window) \
        inflateBackInit_((strm), (windowBits), (window), \
        ZLIB_VERSION, sizeof(z_stream))


#if !defined(ZUTIL_H) && !defined(NO_DUMMY_DECL)
    struct internal_state {int dummy;}; /* hack for buggy compilers */
#endif

ZEXTERN const char   * ZEXPORT zError           OF((int));
ZEXTERN int            ZEXPORT inflateSyncPoint OF((z_streamp z));
ZEXTERN const uLongf * ZEXPORT get_crc_table    OF((void));

#ifdef __cplusplus
}
#endif

#endif /* ZLIB_H */
genometools-1.5.1/src/external/sqlite-3.7.10/000077500000000000000000000000001211610345200205025ustar00rootroot00000000000000genometools-1.5.1/src/external/sqlite-3.7.10/sqlite3.c000066400000000000000000217457161211610345200222610ustar00rootroot00000000000000/******************************************************************************
** This file is an amalgamation of many separate C source files from SQLite
** version 3.7.10.  By combining all the individual C code files into this
** single large file, the entire code can be compiled as a single translation
** unit.  This allows many compilers to do optimizations that would not be
** possible if the files were compiled separately.  Performance improvements
** of 5% or more are commonly seen when SQLite is compiled as a single
** translation unit.
**
** This file is all you need to compile SQLite.  To use SQLite in other
** programs, you need this file and the "sqlite3.h" header file that defines
** the programming interface to the SQLite library.  (If you do not have
** the "sqlite3.h" header file at hand, you will find a copy embedded within
** the text of this file.  Search for "Begin file sqlite3.h" to find the start
** of the embedded sqlite3.h header file.) Additional code files may be needed
** if you want a wrapper to interface SQLite with your choice of programming
** language. The code for the "sqlite3" command-line shell is also in a
** separate file. This file contains only code for the core SQLite library.
*/
#define SQLITE_CORE 1
#define SQLITE_AMALGAMATION 1
#ifndef SQLITE_PRIVATE
# define SQLITE_PRIVATE static
#endif
#ifndef SQLITE_API
# define SQLITE_API
#endif
/************** Begin file sqliteInt.h ***************************************/
/*
** 2001 September 15
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
** Internal interface definitions for SQLite.
**
*/
#ifndef _SQLITEINT_H_
#define _SQLITEINT_H_

/*
** These #defines should enable >2GB file support on POSIX if the
** underlying operating system supports it.  If the OS lacks
** large file support, or if the OS is windows, these should be no-ops.
**
** Ticket #2739:  The _LARGEFILE_SOURCE macro must appear before any
** system #includes.  Hence, this block of code must be the very first
** code in all source files.
**
** Large file support can be disabled using the -DSQLITE_DISABLE_LFS switch
** on the compiler command line.  This is necessary if you are compiling
** on a recent machine (ex: Red Hat 7.2) but you want your code to work
** on an older machine (ex: Red Hat 6.0).  If you compile on Red Hat 7.2
** without this option, LFS is enable.  But LFS does not exist in the kernel
** in Red Hat 6.0, so the code won't work.  Hence, for maximum binary
** portability you should omit LFS.
**
** Similar is true for Mac OS X.  LFS is only supported on Mac OS X 9 and later.
*/
#ifndef SQLITE_DISABLE_LFS
# define _LARGE_FILE       1
# ifndef _FILE_OFFSET_BITS
#   define _FILE_OFFSET_BITS 64
# endif
# define _LARGEFILE_SOURCE 1
#endif

/*
** Include the configuration header output by 'configure' if we're using the
** autoconf-based build
*/
#ifdef _HAVE_SQLITE_CONFIG_H
#include "config.h"
#endif

/************** Include sqliteLimit.h in the middle of sqliteInt.h ***********/
/************** Begin file sqliteLimit.h *************************************/
/*
** 2007 May 7
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
**
** This file defines various limits of what SQLite can process.
*/

/*
** The maximum length of a TEXT or BLOB in bytes.   This also
** limits the size of a row in a table or index.
**
** The hard limit is the ability of a 32-bit signed integer
** to count the size: 2^31-1 or 2147483647.
*/
#ifndef SQLITE_MAX_LENGTH
# define SQLITE_MAX_LENGTH 1000000000
#endif

/*
** This is the maximum number of
**
**    * Columns in a table
**    * Columns in an index
**    * Columns in a view
**    * Terms in the SET clause of an UPDATE statement
**    * Terms in the result set of a SELECT statement
**    * Terms in the GROUP BY or ORDER BY clauses of a SELECT statement.
**    * Terms in the VALUES clause of an INSERT statement
**
** The hard upper limit here is 32676.  Most database people will
** tell you that in a well-normalized database, you usually should
** not have more than a dozen or so columns in any table.  And if
** that is the case, there is no point in having more than a few
** dozen values in any of the other situations described above.
*/
#ifndef SQLITE_MAX_COLUMN
# define SQLITE_MAX_COLUMN 2000
#endif

/*
** The maximum length of a single SQL statement in bytes.
**
** It used to be the case that setting this value to zero would
** turn the limit off.  That is no longer true.  It is not possible
** to turn this limit off.
*/
#ifndef SQLITE_MAX_SQL_LENGTH
# define SQLITE_MAX_SQL_LENGTH 1000000000
#endif

/*
** The maximum depth of an expression tree. This is limited to
** some extent by SQLITE_MAX_SQL_LENGTH. But sometime you might
** want to place more severe limits on the complexity of an
** expression.
**
** A value of 0 used to mean that the limit was not enforced.
** But that is no longer true.  The limit is now strictly enforced
** at all times.
*/
#ifndef SQLITE_MAX_EXPR_DEPTH
# define SQLITE_MAX_EXPR_DEPTH 1000
#endif

/*
** The maximum number of terms in a compound SELECT statement.
** The code generator for compound SELECT statements does one
** level of recursion for each term.  A stack overflow can result
** if the number of terms is too large.  In practice, most SQL
** never has more than 3 or 4 terms.  Use a value of 0 to disable
** any limit on the number of terms in a compount SELECT.
*/
#ifndef SQLITE_MAX_COMPOUND_SELECT
# define SQLITE_MAX_COMPOUND_SELECT 500
#endif

/*
** The maximum number of opcodes in a VDBE program.
** Not currently enforced.
*/
#ifndef SQLITE_MAX_VDBE_OP
# define SQLITE_MAX_VDBE_OP 25000
#endif

/*
** The maximum number of arguments to an SQL function.
*/
#ifndef SQLITE_MAX_FUNCTION_ARG
# define SQLITE_MAX_FUNCTION_ARG 127
#endif

/*
** The maximum number of in-memory pages to use for the main database
** table and for temporary tables.  The SQLITE_DEFAULT_CACHE_SIZE
*/
#ifndef SQLITE_DEFAULT_CACHE_SIZE
# define SQLITE_DEFAULT_CACHE_SIZE  2000
#endif
#ifndef SQLITE_DEFAULT_TEMP_CACHE_SIZE
# define SQLITE_DEFAULT_TEMP_CACHE_SIZE  500
#endif

/*
** The default number of frames to accumulate in the log file before
** checkpointing the database in WAL mode.
*/
#ifndef SQLITE_DEFAULT_WAL_AUTOCHECKPOINT
# define SQLITE_DEFAULT_WAL_AUTOCHECKPOINT  1000
#endif

/*
** The maximum number of attached databases.  This must be between 0
** and 62.  The upper bound on 62 is because a 64-bit integer bitmap
** is used internally to track attached databases.
*/
#ifndef SQLITE_MAX_ATTACHED
# define SQLITE_MAX_ATTACHED 10
#endif


/*
** The maximum value of a ?nnn wildcard that the parser will accept.
*/
#ifndef SQLITE_MAX_VARIABLE_NUMBER
# define SQLITE_MAX_VARIABLE_NUMBER 999
#endif

/* Maximum page size.  The upper bound on this value is 65536.  This a limit
** imposed by the use of 16-bit offsets within each page.
**
** Earlier versions of SQLite allowed the user to change this value at
** compile time. This is no longer permitted, on the grounds that it creates
** a library that is technically incompatible with an SQLite library
** compiled with a different limit. If a process operating on a database
** with a page-size of 65536 bytes crashes, then an instance of SQLite
** compiled with the default page-size limit will not be able to rollback
** the aborted transaction. This could lead to database corruption.
*/
#ifdef SQLITE_MAX_PAGE_SIZE
# undef SQLITE_MAX_PAGE_SIZE
#endif
#define SQLITE_MAX_PAGE_SIZE 65536


/*
** The default size of a database page.
*/
#ifndef SQLITE_DEFAULT_PAGE_SIZE
# define SQLITE_DEFAULT_PAGE_SIZE 1024
#endif
#if SQLITE_DEFAULT_PAGE_SIZE>SQLITE_MAX_PAGE_SIZE
# undef SQLITE_DEFAULT_PAGE_SIZE
# define SQLITE_DEFAULT_PAGE_SIZE SQLITE_MAX_PAGE_SIZE
#endif

/*
** Ordinarily, if no value is explicitly provided, SQLite creates databases
** with page size SQLITE_DEFAULT_PAGE_SIZE. However, based on certain
** device characteristics (sector-size and atomic write() support),
** SQLite may choose a larger value. This constant is the maximum value
** SQLite will choose on its own.
*/
#ifndef SQLITE_MAX_DEFAULT_PAGE_SIZE
# define SQLITE_MAX_DEFAULT_PAGE_SIZE 8192
#endif
#if SQLITE_MAX_DEFAULT_PAGE_SIZE>SQLITE_MAX_PAGE_SIZE
# undef SQLITE_MAX_DEFAULT_PAGE_SIZE
# define SQLITE_MAX_DEFAULT_PAGE_SIZE SQLITE_MAX_PAGE_SIZE
#endif


/*
** Maximum number of pages in one database file.
**
** This is really just the default value for the max_page_count pragma.
** This value can be lowered (or raised) at run-time using that the
** max_page_count macro.
*/
#ifndef SQLITE_MAX_PAGE_COUNT
# define SQLITE_MAX_PAGE_COUNT 1073741823
#endif

/*
** Maximum length (in bytes) of the pattern in a LIKE or GLOB
** operator.
*/
#ifndef SQLITE_MAX_LIKE_PATTERN_LENGTH
# define SQLITE_MAX_LIKE_PATTERN_LENGTH 50000
#endif

/*
** Maximum depth of recursion for triggers.
**
** A value of 1 means that a trigger program will not be able to itself
** fire any triggers. A value of 0 means that no trigger programs at all
** may be executed.
*/
#ifndef SQLITE_MAX_TRIGGER_DEPTH
# define SQLITE_MAX_TRIGGER_DEPTH 1000
#endif

/************** End of sqliteLimit.h *****************************************/
/************** Continuing where we left off in sqliteInt.h ******************/

/* Disable nuisance warnings on Borland compilers */
#if defined(__BORLANDC__)
#pragma warn -rch /* unreachable code */
#pragma warn -ccc /* Condition is always true or false */
#pragma warn -aus /* Assigned value is never used */
#pragma warn -csu /* Comparing signed and unsigned */
#pragma warn -spa /* Suspicious pointer arithmetic */
#endif

/* Needed for various definitions... */
#ifndef _GNU_SOURCE
# define _GNU_SOURCE
#endif

/*
** Include standard header files as necessary
*/
#ifdef HAVE_STDINT_H
#include 
#endif
#ifdef HAVE_INTTYPES_H
#include 
#endif

/*
** The following macros are used to cast pointers to integers and
** integers to pointers.  The way you do this varies from one compiler
** to the next, so we have developed the following set of #if statements
** to generate appropriate macros for a wide range of compilers.
**
** The correct "ANSI" way to do this is to use the intptr_t type.
** Unfortunately, that typedef is not available on all compilers, or
** if it is available, it requires an #include of specific headers
** that vary from one machine to the next.
**
** Ticket #3860:  The llvm-gcc-4.2 compiler from Apple chokes on
** the ((void*)&((char*)0)[X]) construct.  But MSVC chokes on ((void*)(X)).
** So we have to define the macros in different ways depending on the
** compiler.
*/
#if defined(__PTRDIFF_TYPE__)  /* This case should work for GCC */
# define SQLITE_INT_TO_PTR(X)  ((void*)(__PTRDIFF_TYPE__)(X))
# define SQLITE_PTR_TO_INT(X)  ((int)(__PTRDIFF_TYPE__)(X))
#elif !defined(__GNUC__)       /* Works for compilers other than LLVM */
# define SQLITE_INT_TO_PTR(X)  ((void*)&((char*)0)[X])
# define SQLITE_PTR_TO_INT(X)  ((int)(((char*)X)-(char*)0))
#elif defined(HAVE_STDINT_H)   /* Use this case if we have ANSI headers */
# define SQLITE_INT_TO_PTR(X)  ((void*)(intptr_t)(X))
# define SQLITE_PTR_TO_INT(X)  ((int)(intptr_t)(X))
#else                          /* Generates a warning - but it always works */
# define SQLITE_INT_TO_PTR(X)  ((void*)(X))
# define SQLITE_PTR_TO_INT(X)  ((int)(X))
#endif

/*
** The SQLITE_THREADSAFE macro must be defined as 0, 1, or 2.
** 0 means mutexes are permanently disable and the library is never
** threadsafe.  1 means the library is serialized which is the highest
** level of threadsafety.  2 means the libary is multithreaded - multiple
** threads can use SQLite as long as no two threads try to use the same
** database connection at the same time.
**
** Older versions of SQLite used an optional THREADSAFE macro.
** We support that for legacy.
*/
#if !defined(SQLITE_THREADSAFE)
#if defined(THREADSAFE)
# define SQLITE_THREADSAFE THREADSAFE
#else
# define SQLITE_THREADSAFE 1 /* IMP: R-07272-22309 */
#endif
#endif

/*
** Powersafe overwrite is on by default.  But can be turned off using
** the -DSQLITE_POWERSAFE_OVERWRITE=0 command-line option.
*/
#ifndef SQLITE_POWERSAFE_OVERWRITE
# define SQLITE_POWERSAFE_OVERWRITE 1
#endif

/*
** The SQLITE_DEFAULT_MEMSTATUS macro must be defined as either 0 or 1.
** It determines whether or not the features related to
** SQLITE_CONFIG_MEMSTATUS are available by default or not. This value can
** be overridden at runtime using the sqlite3_config() API.
*/
#if !defined(SQLITE_DEFAULT_MEMSTATUS)
# define SQLITE_DEFAULT_MEMSTATUS 1
#endif

/*
** Exactly one of the following macros must be defined in order to
** specify which memory allocation subsystem to use.
**
**     SQLITE_SYSTEM_MALLOC          // Use normal system malloc()
**     SQLITE_WIN32_MALLOC           // Use Win32 native heap API
**     SQLITE_MEMDEBUG               // Debugging version of system malloc()
**
** On Windows, if the SQLITE_WIN32_MALLOC_VALIDATE macro is defined and the
** assert() macro is enabled, each call into the Win32 native heap subsystem
** will cause HeapValidate to be called.  If heap validation should fail, an
** assertion will be triggered.
**
** (Historical note:  There used to be several other options, but we've
** pared it down to just these three.)
**
** If none of the above are defined, then set SQLITE_SYSTEM_MALLOC as
** the default.
*/
#if defined(SQLITE_SYSTEM_MALLOC)+defined(SQLITE_WIN32_MALLOC)+defined(SQLITE_MEMDEBUG)>1
# error "At most one of the following compile-time configuration options\
 is allows: SQLITE_SYSTEM_MALLOC, SQLITE_WIN32_MALLOC, SQLITE_MEMDEBUG"
#endif
#if defined(SQLITE_SYSTEM_MALLOC)+defined(SQLITE_WIN32_MALLOC)+defined(SQLITE_MEMDEBUG)==0
# define SQLITE_SYSTEM_MALLOC 1
#endif

/*
** If SQLITE_MALLOC_SOFT_LIMIT is not zero, then try to keep the
** sizes of memory allocations below this value where possible.
*/
#if !defined(SQLITE_MALLOC_SOFT_LIMIT)
# define SQLITE_MALLOC_SOFT_LIMIT 1024
#endif

/*
** We need to define _XOPEN_SOURCE as follows in order to enable
** recursive mutexes on most Unix systems.  But Mac OS X is different.
** The _XOPEN_SOURCE define causes problems for Mac OS X we are told,
** so it is omitted there.  See ticket #2673.
**
** Later we learn that _XOPEN_SOURCE is poorly or incorrectly
** implemented on some systems.  So we avoid defining it at all
** if it is already defined or if it is unneeded because we are
** not doing a threadsafe build.  Ticket #2681.
**
** See also ticket #2741.
*/
#if !defined(_XOPEN_SOURCE) && !defined(__DARWIN__) && !defined(__APPLE__) && SQLITE_THREADSAFE
#  define _XOPEN_SOURCE 500  /* Needed to enable pthread recursive mutexes */
#endif

/*
** The TCL headers are only needed when compiling the TCL bindings.
*/
#if defined(SQLITE_TCL) || defined(TCLSH)
# include 
#endif

/*
** Many people are failing to set -DNDEBUG=1 when compiling SQLite.
** Setting NDEBUG makes the code smaller and run faster.  So the following
** lines are added to automatically set NDEBUG unless the -DSQLITE_DEBUG=1
** option is set.  Thus NDEBUG becomes an opt-in rather than an opt-out
** feature.
*/
#if !defined(NDEBUG) && !defined(SQLITE_DEBUG)
# define NDEBUG 1
#endif

/*
** The testcase() macro is used to aid in coverage testing.  When
** doing coverage testing, the condition inside the argument to
** testcase() must be evaluated both true and false in order to
** get full branch coverage.  The testcase() macro is inserted
** to help ensure adequate test coverage in places where simple
** condition/decision coverage is inadequate.  For example, testcase()
** can be used to make sure boundary values are tested.  For
** bitmask tests, testcase() can be used to make sure each bit
** is significant and used at least once.  On switch statements
** where multiple cases go to the same block of code, testcase()
** can insure that all cases are evaluated.
**
*/
#ifdef SQLITE_COVERAGE_TEST
SQLITE_PRIVATE   void sqlite3Coverage(int);
# define testcase(X)  if( X ){ sqlite3Coverage(__LINE__); }
#else
# define testcase(X)
#endif

/*
** The TESTONLY macro is used to enclose variable declarations or
** other bits of code that are needed to support the arguments
** within testcase() and assert() macros.
*/
#if !defined(NDEBUG) || defined(SQLITE_COVERAGE_TEST)
# define TESTONLY(X)  X
#else
# define TESTONLY(X)
#endif

/*
** Sometimes we need a small amount of code such as a variable initialization
** to setup for a later assert() statement.  We do not want this code to
** appear when assert() is disabled.  The following macro is therefore
** used to contain that setup code.  The "VVA" acronym stands for
** "Verification, Validation, and Accreditation".  In other words, the
** code within VVA_ONLY() will only run during verification processes.
*/
#ifndef NDEBUG
# define VVA_ONLY(X)  X
#else
# define VVA_ONLY(X)
#endif

/*
** The ALWAYS and NEVER macros surround boolean expressions which
** are intended to always be true or false, respectively.  Such
** expressions could be omitted from the code completely.  But they
** are included in a few cases in order to enhance the resilience
** of SQLite to unexpected behavior - to make the code "self-healing"
** or "ductile" rather than being "brittle" and crashing at the first
** hint of unplanned behavior.
**
** In other words, ALWAYS and NEVER are added for defensive code.
**
** When doing coverage testing ALWAYS and NEVER are hard-coded to
** be true and false so that the unreachable code then specify will
** not be counted as untested code.
*/
#if defined(SQLITE_COVERAGE_TEST)
# define ALWAYS(X)      (1)
# define NEVER(X)       (0)
#elif !defined(NDEBUG)
# define ALWAYS(X)      ((X)?1:(assert(0),0))
# define NEVER(X)       ((X)?(assert(0),1):0)
#else
# define ALWAYS(X)      (X)
# define NEVER(X)       (X)
#endif

/*
** Return true (non-zero) if the input is a integer that is too large
** to fit in 32-bits.  This macro is used inside of various testcase()
** macros to verify that we have tested SQLite for large-file support.
*/
#define IS_BIG_INT(X)  (((X)&~(i64)0xffffffff)!=0)

/*
** The macro unlikely() is a hint that surrounds a boolean
** expression that is usually false.  Macro likely() surrounds
** a boolean expression that is usually true.  GCC is able to
** use these hints to generate better code, sometimes.
*/
#if defined(__GNUC__) && 0
# define likely(X)    __builtin_expect((X),1)
# define unlikely(X)  __builtin_expect((X),0)
#else
# define likely(X)    !!(X)
# define unlikely(X)  !!(X)
#endif

/************** Include sqlite3.h in the middle of sqliteInt.h ***************/
/************** Begin file sqlite3.h *****************************************/
/*
** 2001 September 15
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
** This header file defines the interface that the SQLite library
** presents to client programs.  If a C-function, structure, datatype,
** or constant definition does not appear in this file, then it is
** not a published API of SQLite, is subject to change without
** notice, and should not be referenced by programs that use SQLite.
**
** Some of the definitions that are in this file are marked as
** "experimental".  Experimental interfaces are normally new
** features recently added to SQLite.  We do not anticipate changes
** to experimental interfaces but reserve the right to make minor changes
** if experience from use "in the wild" suggest such changes are prudent.
**
** The official C-language API documentation for SQLite is derived
** from comments in this file.  This file is the authoritative source
** on how SQLite interfaces are suppose to operate.
**
** The name of this file under configuration management is "sqlite.h.in".
** The makefile makes some minor changes to this file (such as inserting
** the version number) and changes its name to "sqlite3.h" as
** part of the build process.
*/
#ifndef _SQLITE3_H_
#define _SQLITE3_H_
#include      /* Needed for the definition of va_list */

/*
** Make sure we can call this stuff from C++.
*/
#if 0
extern "C" {
#endif


/*
** Add the ability to override 'extern'
*/
#ifndef SQLITE_EXTERN
# define SQLITE_EXTERN extern
#endif

#ifndef SQLITE_API
# define SQLITE_API
#endif


/*
** These no-op macros are used in front of interfaces to mark those
** interfaces as either deprecated or experimental.  New applications
** should not use deprecated interfaces - they are support for backwards
** compatibility only.  Application writers should be aware that
** experimental interfaces are subject to change in point releases.
**
** These macros used to resolve to various kinds of compiler magic that
** would generate warning messages when they were used.  But that
** compiler magic ended up generating such a flurry of bug reports
** that we have taken it all out and gone back to using simple
** noop macros.
*/
#define SQLITE_DEPRECATED
#define SQLITE_EXPERIMENTAL

/*
** Ensure these symbols were not defined by some previous header file.
*/
#ifdef SQLITE_VERSION
# undef SQLITE_VERSION
#endif
#ifdef SQLITE_VERSION_NUMBER
# undef SQLITE_VERSION_NUMBER
#endif

/*
** CAPI3REF: Compile-Time Library Version Numbers
**
** ^(The [SQLITE_VERSION] C preprocessor macro in the sqlite3.h header
** evaluates to a string literal that is the SQLite version in the
** format "X.Y.Z" where X is the major version number (always 3 for
** SQLite3) and Y is the minor version number and Z is the release number.)^
** ^(The [SQLITE_VERSION_NUMBER] C preprocessor macro resolves to an integer
** with the value (X*1000000 + Y*1000 + Z) where X, Y, and Z are the same
** numbers used in [SQLITE_VERSION].)^
** The SQLITE_VERSION_NUMBER for any given release of SQLite will also
** be larger than the release from which it is derived.  Either Y will
** be held constant and Z will be incremented or else Y will be incremented
** and Z will be reset to zero.
**
** Since version 3.6.18, SQLite source code has been stored in the
** Fossil configuration management
** system.  ^The SQLITE_SOURCE_ID macro evaluates to
** a string which identifies a particular check-in of SQLite
** within its configuration management system.  ^The SQLITE_SOURCE_ID
** string contains the date and time of the check-in (UTC) and an SHA1
** hash of the entire source tree.
**
** See also: [sqlite3_libversion()],
** [sqlite3_libversion_number()], [sqlite3_sourceid()],
** [sqlite_version()] and [sqlite_source_id()].
*/
#define SQLITE_VERSION        "3.7.10"
#define SQLITE_VERSION_NUMBER 3007010
#define SQLITE_SOURCE_ID      "2012-01-16 13:28:40 ebd01a8deffb5024a5d7494eef800d2366d97204"

/*
** CAPI3REF: Run-Time Library Version Numbers
** KEYWORDS: sqlite3_version, sqlite3_sourceid
**
** These interfaces provide the same information as the [SQLITE_VERSION],
** [SQLITE_VERSION_NUMBER], and [SQLITE_SOURCE_ID] C preprocessor macros
** but are associated with the library instead of the header file.  ^(Cautious
** programmers might include assert() statements in their application to
** verify that values returned by these interfaces match the macros in
** the header, and thus insure that the application is
** compiled with matching library and header files.
**
** 
    ** assert( sqlite3_libversion_number()==SQLITE_VERSION_NUMBER );
** assert( strcmp(sqlite3_sourceid(),SQLITE_SOURCE_ID)==0 );
** assert( strcmp(sqlite3_libversion(),SQLITE_VERSION)==0 );
** 
    )^
**
** ^The sqlite3_version[] string constant contains the text of [SQLITE_VERSION]
** macro.  ^The sqlite3_libversion() function returns a pointer to the
** to the sqlite3_version[] string constant.  The sqlite3_libversion()
** function is provided for use in DLLs since DLL users usually do not have
** direct access to string constants within the DLL.  ^The
** sqlite3_libversion_number() function returns an integer equal to
** [SQLITE_VERSION_NUMBER].  ^The sqlite3_sourceid() function returns
** a pointer to a string constant whose value is the same as the
** [SQLITE_SOURCE_ID] C preprocessor macro.
**
** See also: [sqlite_version()] and [sqlite_source_id()].
*/
SQLITE_API const char sqlite3_version[] = SQLITE_VERSION;
SQLITE_API const char *sqlite3_libversion(void);
SQLITE_API const char *sqlite3_sourceid(void);
SQLITE_API int sqlite3_libversion_number(void);

/*
** CAPI3REF: Run-Time Library Compilation Options Diagnostics
**
** ^The sqlite3_compileoption_used() function returns 0 or 1
** indicating whether the specified option was defined at
** compile time.  ^The SQLITE_ prefix may be omitted from the
** option name passed to sqlite3_compileoption_used().
**
** ^The sqlite3_compileoption_get() function allows iterating
** over the list of options that were defined at compile time by
** returning the N-th compile time option string.  ^If N is out of range,
** sqlite3_compileoption_get() returns a NULL pointer.  ^The SQLITE_
** prefix is omitted from any strings returned by
** sqlite3_compileoption_get().
**
** ^Support for the diagnostic functions sqlite3_compileoption_used()
** and sqlite3_compileoption_get() may be omitted by specifying the
** [SQLITE_OMIT_COMPILEOPTION_DIAGS] option at compile time.
**
** See also: SQL functions [sqlite_compileoption_used()] and
** [sqlite_compileoption_get()] and the [compile_options pragma].
*/
#ifndef SQLITE_OMIT_COMPILEOPTION_DIAGS
SQLITE_API int sqlite3_compileoption_used(const char *zOptName);
SQLITE_API const char *sqlite3_compileoption_get(int N);
#endif

/*
** CAPI3REF: Test To See If The Library Is Threadsafe
**
** ^The sqlite3_threadsafe() function returns zero if and only if
** SQLite was compiled with mutexing code omitted due to the
** [SQLITE_THREADSAFE] compile-time option being set to 0.
**
** SQLite can be compiled with or without mutexes.  When
** the [SQLITE_THREADSAFE] C preprocessor macro is 1 or 2, mutexes
** are enabled and SQLite is threadsafe.  When the
** [SQLITE_THREADSAFE] macro is 0,
** the mutexes are omitted.  Without the mutexes, it is not safe
** to use SQLite concurrently from more than one thread.
**
** Enabling mutexes incurs a measurable performance penalty.
** So if speed is of utmost importance, it makes sense to disable
** the mutexes.  But for maximum safety, mutexes should be enabled.
** ^The default behavior is for mutexes to be enabled.
**
** This interface can be used by an application to make sure that the
** version of SQLite that it is linking against was compiled with
** the desired setting of the [SQLITE_THREADSAFE] macro.
**
** This interface only reports on the compile-time mutex setting
** of the [SQLITE_THREADSAFE] flag.  If SQLite is compiled with
** SQLITE_THREADSAFE=1 or =2 then mutexes are enabled by default but
** can be fully or partially disabled using a call to [sqlite3_config()]
** with the verbs [SQLITE_CONFIG_SINGLETHREAD], [SQLITE_CONFIG_MULTITHREAD],
** or [SQLITE_CONFIG_MUTEX].  ^(The return value of the
** sqlite3_threadsafe() function shows only the compile-time setting of
** thread safety, not any run-time changes to that setting made by
** sqlite3_config(). In other words, the return value from sqlite3_threadsafe()
** is unchanged by calls to sqlite3_config().)^
**
** See the [threading mode] documentation for additional information.
*/
SQLITE_API int sqlite3_threadsafe(void);

/*
** CAPI3REF: Database Connection Handle
** KEYWORDS: {database connection} {database connections}
**
** Each open SQLite database is represented by a pointer to an instance of
** the opaque structure named "sqlite3".  It is useful to think of an sqlite3
** pointer as an object.  The [sqlite3_open()], [sqlite3_open16()], and
** [sqlite3_open_v2()] interfaces are its constructors, and [sqlite3_close()]
** is its destructor.  There are many other interfaces (such as
** [sqlite3_prepare_v2()], [sqlite3_create_function()], and
** [sqlite3_busy_timeout()] to name but three) that are methods on an
** sqlite3 object.
*/
typedef struct sqlite3 sqlite3;

/*
** CAPI3REF: 64-Bit Integer Types
** KEYWORDS: sqlite_int64 sqlite_uint64
**
** Because there is no cross-platform way to specify 64-bit integer types
** SQLite includes typedefs for 64-bit signed and unsigned integers.
**
** The sqlite3_int64 and sqlite3_uint64 are the preferred type definitions.
** The sqlite_int64 and sqlite_uint64 types are supported for backwards
** compatibility only.
**
** ^The sqlite3_int64 and sqlite_int64 types can store integer values
** between -9223372036854775808 and +9223372036854775807 inclusive.  ^The
** sqlite3_uint64 and sqlite_uint64 types can store integer values
** between 0 and +18446744073709551615 inclusive.
*/
#ifdef SQLITE_INT64_TYPE
  typedef SQLITE_INT64_TYPE sqlite_int64;
  typedef unsigned SQLITE_INT64_TYPE sqlite_uint64;
#elif defined(_MSC_VER) || defined(__BORLANDC__)
  typedef __int64 sqlite_int64;
  typedef unsigned __int64 sqlite_uint64;
#else
  typedef long long int sqlite_int64;
  typedef unsigned long long int sqlite_uint64;
#endif
typedef sqlite_int64 sqlite3_int64;
typedef sqlite_uint64 sqlite3_uint64;

/*
** If compiling for a processor that lacks floating point support,
** substitute integer for floating-point.
*/
#ifdef SQLITE_OMIT_FLOATING_POINT
# define double sqlite3_int64
#endif

/*
** CAPI3REF: Closing A Database Connection
**
** ^The sqlite3_close() routine is the destructor for the [sqlite3] object.
** ^Calls to sqlite3_close() return SQLITE_OK if the [sqlite3] object is
** successfully destroyed and all associated resources are deallocated.
**
** Applications must [sqlite3_finalize | finalize] all [prepared statements]
** and [sqlite3_blob_close | close] all [BLOB handles] associated with
** the [sqlite3] object prior to attempting to close the object.  ^If
** sqlite3_close() is called on a [database connection] that still has
** outstanding [prepared statements] or [BLOB handles], then it returns
** SQLITE_BUSY.
**
** ^If [sqlite3_close()] is invoked while a transaction is open,
** the transaction is automatically rolled back.
**
** The C parameter to [sqlite3_close(C)] must be either a NULL
** pointer or an [sqlite3] object pointer obtained
** from [sqlite3_open()], [sqlite3_open16()], or
** [sqlite3_open_v2()], and not previously closed.
** ^Calling sqlite3_close() with a NULL pointer argument is a
** harmless no-op.
*/
SQLITE_API int sqlite3_close(sqlite3 *);

/*
** The type for a callback function.
** This is legacy and deprecated.  It is included for historical
** compatibility and is not documented.
*/
typedef int (*sqlite3_callback)(void*,int,char**, char**);

/*
** CAPI3REF: One-Step Query Execution Interface
**
** The sqlite3_exec() interface is a convenience wrapper around
** [sqlite3_prepare_v2()], [sqlite3_step()], and [sqlite3_finalize()],
** that allows an application to run multiple statements of SQL
** without having to use a lot of C code.
**
** ^The sqlite3_exec() interface runs zero or more UTF-8 encoded,
** semicolon-separate SQL statements passed into its 2nd argument,
** in the context of the [database connection] passed in as its 1st
** argument.  ^If the callback function of the 3rd argument to
** sqlite3_exec() is not NULL, then it is invoked for each result row
** coming out of the evaluated SQL statements.  ^The 4th argument to
** sqlite3_exec() is relayed through to the 1st argument of each
** callback invocation.  ^If the callback pointer to sqlite3_exec()
** is NULL, then no callback is ever invoked and result rows are
** ignored.
**
** ^If an error occurs while evaluating the SQL statements passed into
** sqlite3_exec(), then execution of the current statement stops and
** subsequent statements are skipped.  ^If the 5th parameter to sqlite3_exec()
** is not NULL then any error message is written into memory obtained
** from [sqlite3_malloc()] and passed back through the 5th parameter.
** To avoid memory leaks, the application should invoke [sqlite3_free()]
** on error message strings returned through the 5th parameter of
** of sqlite3_exec() after the error message string is no longer needed.
** ^If the 5th parameter to sqlite3_exec() is not NULL and no errors
** occur, then sqlite3_exec() sets the pointer in its 5th parameter to
** NULL before returning.
**
** ^If an sqlite3_exec() callback returns non-zero, the sqlite3_exec()
** routine returns SQLITE_ABORT without invoking the callback again and
** without running any subsequent SQL statements.
**
** ^The 2nd argument to the sqlite3_exec() callback function is the
** number of columns in the result.  ^The 3rd argument to the sqlite3_exec()
** callback is an array of pointers to strings obtained as if from
** [sqlite3_column_text()], one for each column.  ^If an element of a
** result row is NULL then the corresponding string pointer for the
** sqlite3_exec() callback is a NULL pointer.  ^The 4th argument to the
** sqlite3_exec() callback is an array of pointers to strings where each
** entry represents the name of corresponding result column as obtained
** from [sqlite3_column_name()].
**
** ^If the 2nd parameter to sqlite3_exec() is a NULL pointer, a pointer
** to an empty string, or a pointer that contains only whitespace and/or
** SQL comments, then no SQL statements are evaluated and the database
** is not changed.
**
** Restrictions:
**
** 
      
** 
    •  The application must insure that the 1st parameter to sqlite3_exec()
**      is a valid and open [database connection].
** 
    •  The application must not close [database connection] specified by
**      the 1st parameter to sqlite3_exec() while sqlite3_exec() is running.
** 
    •  The application must not modify the SQL statement text passed into
**      the 2nd parameter of sqlite3_exec() while sqlite3_exec() is running.
** 
    
*/
SQLITE_API int sqlite3_exec(
  sqlite3*,                                  /* An open database */
  const char *sql,                           /* SQL to be evaluated */
  int (*callback)(void*,int,char**,char**),  /* Callback function */
  void *,                                    /* 1st argument to callback */
  char **errmsg                              /* Error msg written here */
);

/*
** CAPI3REF: Result Codes
** KEYWORDS: SQLITE_OK {error code} {error codes}
** KEYWORDS: {result code} {result codes}
**
** Many SQLite functions return an integer result code from the set shown
** here in order to indicate success or failure.
**
** New error codes may be added in future versions of SQLite.
**
** See also: [SQLITE_IOERR_READ | extended result codes],
** [sqlite3_vtab_on_conflict()] [SQLITE_ROLLBACK | result codes].
*/
#define SQLITE_OK           0   /* Successful result */
/* beginning-of-error-codes */
#define SQLITE_ERROR        1   /* SQL error or missing database */
#define SQLITE_INTERNAL     2   /* Internal logic error in SQLite */
#define SQLITE_PERM         3   /* Access permission denied */
#define SQLITE_ABORT        4   /* Callback routine requested an abort */
#define SQLITE_BUSY         5   /* The database file is locked */
#define SQLITE_LOCKED       6   /* A table in the database is locked */
#define SQLITE_NOMEM        7   /* A malloc() failed */
#define SQLITE_READONLY     8   /* Attempt to write a readonly database */
#define SQLITE_INTERRUPT    9   /* Operation terminated by sqlite3_interrupt()*/
#define SQLITE_IOERR       10   /* Some kind of disk I/O error occurred */
#define SQLITE_CORRUPT     11   /* The database disk image is malformed */
#define SQLITE_NOTFOUND    12   /* Unknown opcode in sqlite3_file_control() */
#define SQLITE_FULL        13   /* Insertion failed because database is full */
#define SQLITE_CANTOPEN    14   /* Unable to open the database file */
#define SQLITE_PROTOCOL    15   /* Database lock protocol error */
#define SQLITE_EMPTY       16   /* Database is empty */
#define SQLITE_SCHEMA      17   /* The database schema changed */
#define SQLITE_TOOBIG      18   /* String or BLOB exceeds size limit */
#define SQLITE_CONSTRAINT  19   /* Abort due to constraint violation */
#define SQLITE_MISMATCH    20   /* Data type mismatch */
#define SQLITE_MISUSE      21   /* Library used incorrectly */
#define SQLITE_NOLFS       22   /* Uses OS features not supported on host */
#define SQLITE_AUTH        23   /* Authorization denied */
#define SQLITE_FORMAT      24   /* Auxiliary database format error */
#define SQLITE_RANGE       25   /* 2nd parameter to sqlite3_bind out of range */
#define SQLITE_NOTADB      26   /* File opened that is not a database file */
#define SQLITE_ROW         100  /* sqlite3_step() has another row ready */
#define SQLITE_DONE        101  /* sqlite3_step() has finished executing */
/* end-of-error-codes */

/*
** CAPI3REF: Extended Result Codes
** KEYWORDS: {extended error code} {extended error codes}
** KEYWORDS: {extended result code} {extended result codes}
**
** In its default configuration, SQLite API routines return one of 26 integer
** [SQLITE_OK | result codes].  However, experience has shown that many of
** these result codes are too coarse-grained.  They do not provide as
** much information about problems as programmers might like.  In an effort to
** address this, newer versions of SQLite (version 3.3.8 and later) include
** support for additional result codes that provide more detailed information
** about errors. The extended result codes are enabled or disabled
** on a per database connection basis using the
** [sqlite3_extended_result_codes()] API.
**
** Some of the available extended result codes are listed here.
** One may expect the number of extended result codes will be expand
** over time.  Software that uses extended result codes should expect
** to see new result codes in future releases of SQLite.
**
** The SQLITE_OK result code will never be extended.  It will always
** be exactly zero.
*/
#define SQLITE_IOERR_READ              (SQLITE_IOERR | (1<<8))
#define SQLITE_IOERR_SHORT_READ        (SQLITE_IOERR | (2<<8))
#define SQLITE_IOERR_WRITE             (SQLITE_IOERR | (3<<8))
#define SQLITE_IOERR_FSYNC             (SQLITE_IOERR | (4<<8))
#define SQLITE_IOERR_DIR_FSYNC         (SQLITE_IOERR | (5<<8))
#define SQLITE_IOERR_TRUNCATE          (SQLITE_IOERR | (6<<8))
#define SQLITE_IOERR_FSTAT             (SQLITE_IOERR | (7<<8))
#define SQLITE_IOERR_UNLOCK            (SQLITE_IOERR | (8<<8))
#define SQLITE_IOERR_RDLOCK            (SQLITE_IOERR | (9<<8))
#define SQLITE_IOERR_DELETE            (SQLITE_IOERR | (10<<8))
#define SQLITE_IOERR_BLOCKED           (SQLITE_IOERR | (11<<8))
#define SQLITE_IOERR_NOMEM             (SQLITE_IOERR | (12<<8))
#define SQLITE_IOERR_ACCESS            (SQLITE_IOERR | (13<<8))
#define SQLITE_IOERR_CHECKRESERVEDLOCK (SQLITE_IOERR | (14<<8))
#define SQLITE_IOERR_LOCK              (SQLITE_IOERR | (15<<8))
#define SQLITE_IOERR_CLOSE             (SQLITE_IOERR | (16<<8))
#define SQLITE_IOERR_DIR_CLOSE         (SQLITE_IOERR | (17<<8))
#define SQLITE_IOERR_SHMOPEN           (SQLITE_IOERR | (18<<8))
#define SQLITE_IOERR_SHMSIZE           (SQLITE_IOERR | (19<<8))
#define SQLITE_IOERR_SHMLOCK           (SQLITE_IOERR | (20<<8))
#define SQLITE_IOERR_SHMMAP            (SQLITE_IOERR | (21<<8))
#define SQLITE_IOERR_SEEK              (SQLITE_IOERR | (22<<8))
#define SQLITE_LOCKED_SHAREDCACHE      (SQLITE_LOCKED |  (1<<8))
#define SQLITE_BUSY_RECOVERY           (SQLITE_BUSY   |  (1<<8))
#define SQLITE_CANTOPEN_NOTEMPDIR      (SQLITE_CANTOPEN | (1<<8))
#define SQLITE_CORRUPT_VTAB            (SQLITE_CORRUPT | (1<<8))
#define SQLITE_READONLY_RECOVERY       (SQLITE_READONLY | (1<<8))
#define SQLITE_READONLY_CANTLOCK       (SQLITE_READONLY | (2<<8))

/*
** CAPI3REF: Flags For File Open Operations
**
** These bit values are intended for use in the
** 3rd parameter to the [sqlite3_open_v2()] interface and
** in the 4th parameter to the [sqlite3_vfs.xOpen] method.
*/
#define SQLITE_OPEN_READONLY         0x00000001  /* Ok for sqlite3_open_v2() */
#define SQLITE_OPEN_READWRITE        0x00000002  /* Ok for sqlite3_open_v2() */
#define SQLITE_OPEN_CREATE           0x00000004  /* Ok for sqlite3_open_v2() */
#define SQLITE_OPEN_DELETEONCLOSE    0x00000008  /* VFS only */
#define SQLITE_OPEN_EXCLUSIVE        0x00000010  /* VFS only */
#define SQLITE_OPEN_AUTOPROXY        0x00000020  /* VFS only */
#define SQLITE_OPEN_URI              0x00000040  /* Ok for sqlite3_open_v2() */
#define SQLITE_OPEN_MAIN_DB          0x00000100  /* VFS only */
#define SQLITE_OPEN_TEMP_DB          0x00000200  /* VFS only */
#define SQLITE_OPEN_TRANSIENT_DB     0x00000400  /* VFS only */
#define SQLITE_OPEN_MAIN_JOURNAL     0x00000800  /* VFS only */
#define SQLITE_OPEN_TEMP_JOURNAL     0x00001000  /* VFS only */
#define SQLITE_OPEN_SUBJOURNAL       0x00002000  /* VFS only */
#define SQLITE_OPEN_MASTER_JOURNAL   0x00004000  /* VFS only */
#define SQLITE_OPEN_NOMUTEX          0x00008000  /* Ok for sqlite3_open_v2() */
#define SQLITE_OPEN_FULLMUTEX        0x00010000  /* Ok for sqlite3_open_v2() */
#define SQLITE_OPEN_SHAREDCACHE      0x00020000  /* Ok for sqlite3_open_v2() */
#define SQLITE_OPEN_PRIVATECACHE     0x00040000  /* Ok for sqlite3_open_v2() */
#define SQLITE_OPEN_WAL              0x00080000  /* VFS only */

/* Reserved:                         0x00F00000 */

/*
** CAPI3REF: Device Characteristics
**
** The xDeviceCharacteristics method of the [sqlite3_io_methods]
** object returns an integer which is a vector of the these
** bit values expressing I/O characteristics of the mass storage
** device that holds the file that the [sqlite3_io_methods]
** refers to.
**
** The SQLITE_IOCAP_ATOMIC property means that all writes of
** any size are atomic.  The SQLITE_IOCAP_ATOMICnnn values
** mean that writes of blocks that are nnn bytes in size and
** are aligned to an address which is an integer multiple of
** nnn are atomic.  The SQLITE_IOCAP_SAFE_APPEND value means
** that when data is appended to a file, the data is appended
** first then the size of the file is extended, never the other
** way around.  The SQLITE_IOCAP_SEQUENTIAL property means that
** information is written to disk in the same order as calls
** to xWrite().  The SQLITE_IOCAP_POWERSAFE_OVERWRITE property means that
** after reboot following a crash or power loss, the only bytes in a
** file that were written at the application level might have changed
** and that adjacent bytes, even bytes within the same sector are
** guaranteed to be unchanged.
*/
#define SQLITE_IOCAP_ATOMIC                 0x00000001
#define SQLITE_IOCAP_ATOMIC512              0x00000002
#define SQLITE_IOCAP_ATOMIC1K               0x00000004
#define SQLITE_IOCAP_ATOMIC2K               0x00000008
#define SQLITE_IOCAP_ATOMIC4K               0x00000010
#define SQLITE_IOCAP_ATOMIC8K               0x00000020
#define SQLITE_IOCAP_ATOMIC16K              0x00000040
#define SQLITE_IOCAP_ATOMIC32K              0x00000080
#define SQLITE_IOCAP_ATOMIC64K              0x00000100
#define SQLITE_IOCAP_SAFE_APPEND            0x00000200
#define SQLITE_IOCAP_SEQUENTIAL             0x00000400
#define SQLITE_IOCAP_UNDELETABLE_WHEN_OPEN  0x00000800
#define SQLITE_IOCAP_POWERSAFE_OVERWRITE    0x00001000

/*
** CAPI3REF: File Locking Levels
**
** SQLite uses one of these integer values as the second
** argument to calls it makes to the xLock() and xUnlock() methods
** of an [sqlite3_io_methods] object.
*/
#define SQLITE_LOCK_NONE          0
#define SQLITE_LOCK_SHARED        1
#define SQLITE_LOCK_RESERVED      2
#define SQLITE_LOCK_PENDING       3
#define SQLITE_LOCK_EXCLUSIVE     4

/*
** CAPI3REF: Synchronization Type Flags
**
** When SQLite invokes the xSync() method of an
** [sqlite3_io_methods] object it uses a combination of
** these integer values as the second argument.
**
** When the SQLITE_SYNC_DATAONLY flag is used, it means that the
** sync operation only needs to flush data to mass storage.  Inode
** information need not be flushed. If the lower four bits of the flag
** equal SQLITE_SYNC_NORMAL, that means to use normal fsync() semantics.
** If the lower four bits equal SQLITE_SYNC_FULL, that means
** to use Mac OS X style fullsync instead of fsync().
**
** Do not confuse the SQLITE_SYNC_NORMAL and SQLITE_SYNC_FULL flags
** with the [PRAGMA synchronous]=NORMAL and [PRAGMA synchronous]=FULL
** settings.  The [synchronous pragma] determines when calls to the
** xSync VFS method occur and applies uniformly across all platforms.
** The SQLITE_SYNC_NORMAL and SQLITE_SYNC_FULL flags determine how
** energetic or rigorous or forceful the sync operations are and
** only make a difference on Mac OSX for the default SQLite code.
** (Third-party VFS implementations might also make the distinction
** between SQLITE_SYNC_NORMAL and SQLITE_SYNC_FULL, but among the
** operating systems natively supported by SQLite, only Mac OSX
** cares about the difference.)
*/
#define SQLITE_SYNC_NORMAL        0x00002
#define SQLITE_SYNC_FULL          0x00003
#define SQLITE_SYNC_DATAONLY      0x00010

/*
** CAPI3REF: OS Interface Open File Handle
**
** An [sqlite3_file] object represents an open file in the
** [sqlite3_vfs | OS interface layer].  Individual OS interface
** implementations will
** want to subclass this object by appending additional fields
** for their own use.  The pMethods entry is a pointer to an
** [sqlite3_io_methods] object that defines methods for performing
** I/O operations on the open file.
*/
typedef struct sqlite3_file sqlite3_file;
struct sqlite3_file {
  const struct sqlite3_io_methods *pMethods;  /* Methods for an open file */
};

/*
** CAPI3REF: OS Interface File Virtual Methods Object
**
** Every file opened by the [sqlite3_vfs.xOpen] method populates an
** [sqlite3_file] object (or, more commonly, a subclass of the
** [sqlite3_file] object) with a pointer to an instance of this object.
** This object defines the methods used to perform various operations
** against the open file represented by the [sqlite3_file] object.
**
** If the [sqlite3_vfs.xOpen] method sets the sqlite3_file.pMethods element
** to a non-NULL pointer, then the sqlite3_io_methods.xClose method
** may be invoked even if the [sqlite3_vfs.xOpen] reported that it failed.  The
** only way to prevent a call to xClose following a failed [sqlite3_vfs.xOpen]
** is for the [sqlite3_vfs.xOpen] to set the sqlite3_file.pMethods element
** to NULL.
**
** The flags argument to xSync may be one of [SQLITE_SYNC_NORMAL] or
** [SQLITE_SYNC_FULL].  The first choice is the normal fsync().
** The second choice is a Mac OS X style fullsync.  The [SQLITE_SYNC_DATAONLY]
** flag may be ORed in to indicate that only the data of the file
** and not its inode needs to be synced.
**
** The integer values to xLock() and xUnlock() are one of
** 
      
** 
    •  [SQLITE_LOCK_NONE],
** 
    •  [SQLITE_LOCK_SHARED],
** 
    •  [SQLITE_LOCK_RESERVED],
** 
    •  [SQLITE_LOCK_PENDING], or
** 
    •  [SQLITE_LOCK_EXCLUSIVE].
** 
    
** xLock() increases the lock. xUnlock() decreases the lock.
** The xCheckReservedLock() method checks whether any database connection,
** either in this process or in some other process, is holding a RESERVED,
** PENDING, or EXCLUSIVE lock on the file.  It returns true
** if such a lock exists and false otherwise.
**
** The xFileControl() method is a generic interface that allows custom
** VFS implementations to directly control an open file using the
** [sqlite3_file_control()] interface.  The second "op" argument is an
** integer opcode.  The third argument is a generic pointer intended to
** point to a structure that may contain arguments or space in which to
** write return values.  Potential uses for xFileControl() might be
** functions to enable blocking locks with timeouts, to change the
** locking strategy (for example to use dot-file locks), to inquire
** about the status of a lock, or to break stale locks.  The SQLite
** core reserves all opcodes less than 100 for its own use.
** A [SQLITE_FCNTL_LOCKSTATE | list of opcodes] less than 100 is available.
** Applications that define a custom xFileControl method should use opcodes
** greater than 100 to avoid conflicts.  VFS implementations should
** return [SQLITE_NOTFOUND] for file control opcodes that they do not
** recognize.
**
** The xSectorSize() method returns the sector size of the
** device that underlies the file.  The sector size is the
** minimum write that can be performed without disturbing
** other bytes in the file.  The xDeviceCharacteristics()
** method returns a bit vector describing behaviors of the
** underlying device:
**
** 
      
** 
    •  [SQLITE_IOCAP_ATOMIC]
** 
    •  [SQLITE_IOCAP_ATOMIC512]
** 
    •  [SQLITE_IOCAP_ATOMIC1K]
** 
    •  [SQLITE_IOCAP_ATOMIC2K]
** 
    •  [SQLITE_IOCAP_ATOMIC4K]
** 
    •  [SQLITE_IOCAP_ATOMIC8K]
** 
    •  [SQLITE_IOCAP_ATOMIC16K]
** 
    •  [SQLITE_IOCAP_ATOMIC32K]
** 
    •  [SQLITE_IOCAP_ATOMIC64K]
** 
    •  [SQLITE_IOCAP_SAFE_APPEND]
** 
    •  [SQLITE_IOCAP_SEQUENTIAL]
** 
    
**
** The SQLITE_IOCAP_ATOMIC property means that all writes of
** any size are atomic.  The SQLITE_IOCAP_ATOMICnnn values
** mean that writes of blocks that are nnn bytes in size and
** are aligned to an address which is an integer multiple of
** nnn are atomic.  The SQLITE_IOCAP_SAFE_APPEND value means
** that when data is appended to a file, the data is appended
** first then the size of the file is extended, never the other
** way around.  The SQLITE_IOCAP_SEQUENTIAL property means that
** information is written to disk in the same order as calls
** to xWrite().
**
** If xRead() returns SQLITE_IOERR_SHORT_READ it must also fill
** in the unread portions of the buffer with zeros.  A VFS that
** fails to zero-fill short reads might seem to work.  However,
** failure to zero-fill short reads will eventually lead to
** database corruption.
*/
typedef struct sqlite3_io_methods sqlite3_io_methods;
struct sqlite3_io_methods {
  int iVersion;
  int (*xClose)(sqlite3_file*);
  int (*xRead)(sqlite3_file*, void*, int iAmt, sqlite3_int64 iOfst);
  int (*xWrite)(sqlite3_file*, const void*, int iAmt, sqlite3_int64 iOfst);
  int (*xTruncate)(sqlite3_file*, sqlite3_int64 size);
  int (*xSync)(sqlite3_file*, int flags);
  int (*xFileSize)(sqlite3_file*, sqlite3_int64 *pSize);
  int (*xLock)(sqlite3_file*, int);
  int (*xUnlock)(sqlite3_file*, int);
  int (*xCheckReservedLock)(sqlite3_file*, int *pResOut);
  int (*xFileControl)(sqlite3_file*, int op, void *pArg);
  int (*xSectorSize)(sqlite3_file*);
  int (*xDeviceCharacteristics)(sqlite3_file*);
  /* Methods above are valid for version 1 */
  int (*xShmMap)(sqlite3_file*, int iPg, int pgsz, int, void volatile**);
  int (*xShmLock)(sqlite3_file*, int offset, int n, int flags);
  void (*xShmBarrier)(sqlite3_file*);
  int (*xShmUnmap)(sqlite3_file*, int deleteFlag);
  /* Methods above are valid for version 2 */
  /* Additional methods may be added in future releases */
};

/*
** CAPI3REF: Standard File Control Opcodes
**
** These integer constants are opcodes for the xFileControl method
** of the [sqlite3_io_methods] object and for the [sqlite3_file_control()]
** interface.
**
** The [SQLITE_FCNTL_LOCKSTATE] opcode is used for debugging.  This
** opcode causes the xFileControl method to write the current state of
** the lock (one of [SQLITE_LOCK_NONE], [SQLITE_LOCK_SHARED],
** [SQLITE_LOCK_RESERVED], [SQLITE_LOCK_PENDING], or [SQLITE_LOCK_EXCLUSIVE])
** into an integer that the pArg argument points to. This capability
** is used during testing and only needs to be supported when SQLITE_TEST
** is defined.
**
** The [SQLITE_FCNTL_SIZE_HINT] opcode is used by SQLite to give the VFS
** layer a hint of how large the database file will grow to be during the
** current transaction.  This hint is not guaranteed to be accurate but it
** is often close.  The underlying VFS might choose to preallocate database
** file space based on this hint in order to help writes to the database
** file run faster.
**
** The [SQLITE_FCNTL_CHUNK_SIZE] opcode is used to request that the VFS
** extends and truncates the database file in chunks of a size specified
** by the user. The fourth argument to [sqlite3_file_control()] should
** point to an integer (type int) containing the new chunk-size to use
** for the nominated database. Allocating database file space in large
** chunks (say 1MB at a time), may reduce file-system fragmentation and
** improve performance on some systems.
**
** The [SQLITE_FCNTL_FILE_POINTER] opcode is used to obtain a pointer
** to the [sqlite3_file] object associated with a particular database
** connection.  See the [sqlite3_file_control()] documentation for
** additional information.
**
** ^(The [SQLITE_FCNTL_SYNC_OMITTED] opcode is generated internally by
** SQLite and sent to all VFSes in place of a call to the xSync method
** when the database connection has [PRAGMA synchronous] set to OFF.)^
** Some specialized VFSes need this signal in order to operate correctly
** when [PRAGMA synchronous | PRAGMA synchronous=OFF] is set, but most
** VFSes do not need this signal and should silently ignore this opcode.
** Applications should not call [sqlite3_file_control()] with this
** opcode as doing so may disrupt the operation of the specialized VFSes
** that do require it.
**
** ^The [SQLITE_FCNTL_WIN32_AV_RETRY] opcode is used to configure automatic
** retry counts and intervals for certain disk I/O operations for the
** windows [VFS] in order to provide robustness in the presence of
** anti-virus programs.  By default, the windows VFS will retry file read,
** file write, and file delete operations up to 10 times, with a delay
** of 25 milliseconds before the first retry and with the delay increasing
** by an additional 25 milliseconds with each subsequent retry.  This
** opcode allows these two values (10 retries and 25 milliseconds of delay)
** to be adjusted.  The values are changed for all database connections
** within the same process.  The argument is a pointer to an array of two
** integers where the first integer i the new retry count and the second
** integer is the delay.  If either integer is negative, then the setting
** is not changed but instead the prior value of that setting is written
** into the array entry, allowing the current retry settings to be
** interrogated.  The zDbName parameter is ignored.
**
** ^The [SQLITE_FCNTL_PERSIST_WAL] opcode is used to set or query the
** persistent [WAL | Write AHead Log] setting.  By default, the auxiliary
** write ahead log and shared memory files used for transaction control
** are automatically deleted when the latest connection to the database
** closes.  Setting persistent WAL mode causes those files to persist after
** close.  Persisting the files is useful when other processes that do not
** have write permission on the directory containing the database file want
** to read the database file, as the WAL and shared memory files must exist
** in order for the database to be readable.  The fourth parameter to
** [sqlite3_file_control()] for this opcode should be a pointer to an integer.
** That integer is 0 to disable persistent WAL mode or 1 to enable persistent
** WAL mode.  If the integer is -1, then it is overwritten with the current
** WAL persistence setting.
**
** ^The [SQLITE_FCNTL_POWERSAFE_OVERWRITE] opcode is used to set or query the
** persistent "powersafe-overwrite" or "PSOW" setting.  The PSOW setting
** determines the [SQLITE_IOCAP_POWERSAFE_OVERWRITE] bit of the
** xDeviceCharacteristics methods. The fourth parameter to
** [sqlite3_file_control()] for this opcode should be a pointer to an integer.
** That integer is 0 to disable zero-damage mode or 1 to enable zero-damage
** mode.  If the integer is -1, then it is overwritten with the current
** zero-damage mode setting.
**
** ^The [SQLITE_FCNTL_OVERWRITE] opcode is invoked by SQLite after opening
** a write transaction to indicate that, unless it is rolled back for some
** reason, the entire database file will be overwritten by the current
** transaction. This is used by VACUUM operations.
**
** ^The [SQLITE_FCNTL_VFSNAME] opcode can be used to obtain the names of
** all [VFSes] in the VFS stack.  The names are of all VFS shims and the
** final bottom-level VFS are written into memory obtained from
** [sqlite3_malloc()] and the result is stored in the char* variable
** that the fourth parameter of [sqlite3_file_control()] points to.
** The caller is responsible for freeing the memory when done.  As with
** all file-control actions, there is no guarantee that this will actually
** do anything.  Callers should initialize the char* variable to a NULL
** pointer in case this file-control is not implemented.  This file-control
** is intended for diagnostic use only.
*/
#define SQLITE_FCNTL_LOCKSTATE               1
#define SQLITE_GET_LOCKPROXYFILE             2
#define SQLITE_SET_LOCKPROXYFILE             3
#define SQLITE_LAST_ERRNO                    4
#define SQLITE_FCNTL_SIZE_HINT               5
#define SQLITE_FCNTL_CHUNK_SIZE              6
#define SQLITE_FCNTL_FILE_POINTER            7
#define SQLITE_FCNTL_SYNC_OMITTED            8
#define SQLITE_FCNTL_WIN32_AV_RETRY          9
#define SQLITE_FCNTL_PERSIST_WAL            10
#define SQLITE_FCNTL_OVERWRITE              11
#define SQLITE_FCNTL_VFSNAME                12
#define SQLITE_FCNTL_POWERSAFE_OVERWRITE    13

/*
** CAPI3REF: Mutex Handle
**
** The mutex module within SQLite defines [sqlite3_mutex] to be an
** abstract type for a mutex object.  The SQLite core never looks
** at the internal representation of an [sqlite3_mutex].  It only
** deals with pointers to the [sqlite3_mutex] object.
**
** Mutexes are created using [sqlite3_mutex_alloc()].
*/
typedef struct sqlite3_mutex sqlite3_mutex;

/*
** CAPI3REF: OS Interface Object
**
** An instance of the sqlite3_vfs object defines the interface between
** the SQLite core and the underlying operating system.  The "vfs"
** in the name of the object stands for "virtual file system".  See
** the [VFS | VFS documentation] for further information.
**
** The value of the iVersion field is initially 1 but may be larger in
** future versions of SQLite.  Additional fields may be appended to this
** object when the iVersion value is increased.  Note that the structure
** of the sqlite3_vfs object changes in the transaction between
** SQLite version 3.5.9 and 3.6.0 and yet the iVersion field was not
** modified.
**
** The szOsFile field is the size of the subclassed [sqlite3_file]
** structure used by this VFS.  mxPathname is the maximum length of
** a pathname in this VFS.
**
** Registered sqlite3_vfs objects are kept on a linked list formed by
** the pNext pointer.  The [sqlite3_vfs_register()]
** and [sqlite3_vfs_unregister()] interfaces manage this list
** in a thread-safe way.  The [sqlite3_vfs_find()] interface
** searches the list.  Neither the application code nor the VFS
** implementation should use the pNext pointer.
**
** The pNext field is the only field in the sqlite3_vfs
** structure that SQLite will ever modify.  SQLite will only access
** or modify this field while holding a particular static mutex.
** The application should never modify anything within the sqlite3_vfs
** object once the object has been registered.
**
** The zName field holds the name of the VFS module.  The name must
** be unique across all VFS modules.
**
** [[sqlite3_vfs.xOpen]]
** ^SQLite guarantees that the zFilename parameter to xOpen
** is either a NULL pointer or string obtained
** from xFullPathname() with an optional suffix added.
** ^If a suffix is added to the zFilename parameter, it will
** consist of a single "-" character followed by no more than
** 11 alphanumeric and/or "-" characters.
** ^SQLite further guarantees that
** the string will be valid and unchanged until xClose() is
** called. Because of the previous sentence,
** the [sqlite3_file] can safely store a pointer to the
** filename if it needs to remember the filename for some reason.
** If the zFilename parameter to xOpen is a NULL pointer then xOpen
** must invent its own temporary name for the file.  ^Whenever the
** xFilename parameter is NULL it will also be the case that the
** flags parameter will include [SQLITE_OPEN_DELETEONCLOSE].
**
** The flags argument to xOpen() includes all bits set in
** the flags argument to [sqlite3_open_v2()].  Or if [sqlite3_open()]
** or [sqlite3_open16()] is used, then flags includes at least
** [SQLITE_OPEN_READWRITE] | [SQLITE_OPEN_CREATE].
** If xOpen() opens a file read-only then it sets *pOutFlags to
** include [SQLITE_OPEN_READONLY].  Other bits in *pOutFlags may be set.
**
** ^(SQLite will also add one of the following flags to the xOpen()
** call, depending on the object being opened:
**
** 
      
** 
    •   [SQLITE_OPEN_MAIN_DB]
** 
    •   [SQLITE_OPEN_MAIN_JOURNAL]
** 
    •   [SQLITE_OPEN_TEMP_DB]
** 
    •   [SQLITE_OPEN_TEMP_JOURNAL]
** 
    •   [SQLITE_OPEN_TRANSIENT_DB]
** 
    •   [SQLITE_OPEN_SUBJOURNAL]
** 
    •   [SQLITE_OPEN_MASTER_JOURNAL]
** 
    •   [SQLITE_OPEN_WAL]
** 
    )^
**
** The file I/O implementation can use the object type flags to
** change the way it deals with files.  For example, an application
** that does not care about crash recovery or rollback might make
** the open of a journal file a no-op.  Writes to this journal would
** also be no-ops, and any attempt to read the journal would return
** SQLITE_IOERR.  Or the implementation might recognize that a database
** file will be doing page-aligned sector reads and writes in a random
** order and set up its I/O subsystem accordingly.
**
** SQLite might also add one of the following flags to the xOpen method:
**
** 
      
** 
    •  [SQLITE_OPEN_DELETEONCLOSE]
** 
    •  [SQLITE_OPEN_EXCLUSIVE]
** 
    
**
** The [SQLITE_OPEN_DELETEONCLOSE] flag means the file should be
** deleted when it is closed.  ^The [SQLITE_OPEN_DELETEONCLOSE]
** will be set for TEMP databases and their journals, transient
** databases, and subjournals.
**
** ^The [SQLITE_OPEN_EXCLUSIVE] flag is always used in conjunction
** with the [SQLITE_OPEN_CREATE] flag, which are both directly
** analogous to the O_EXCL and O_CREAT flags of the POSIX open()
** API.  The SQLITE_OPEN_EXCLUSIVE flag, when paired with the
** SQLITE_OPEN_CREATE, is used to indicate that file should always
** be created, and that it is an error if it already exists.
** It is not used to indicate the file should be opened
** for exclusive access.
**
** ^At least szOsFile bytes of memory are allocated by SQLite
** to hold the  [sqlite3_file] structure passed as the third
** argument to xOpen.  The xOpen method does not have to
** allocate the structure; it should just fill it in.  Note that
** the xOpen method must set the sqlite3_file.pMethods to either
** a valid [sqlite3_io_methods] object or to NULL.  xOpen must do
** this even if the open fails.  SQLite expects that the sqlite3_file.pMethods
** element will be valid after xOpen returns regardless of the success
** or failure of the xOpen call.
**
** [[sqlite3_vfs.xAccess]]
** ^The flags argument to xAccess() may be [SQLITE_ACCESS_EXISTS]
** to test for the existence of a file, or [SQLITE_ACCESS_READWRITE] to
** test whether a file is readable and writable, or [SQLITE_ACCESS_READ]
** to test whether a file is at least readable.   The file can be a
** directory.
**
** ^SQLite will always allocate at least mxPathname+1 bytes for the
** output buffer xFullPathname.  The exact size of the output buffer
** is also passed as a parameter to both  methods. If the output buffer
** is not large enough, [SQLITE_CANTOPEN] should be returned. Since this is
** handled as a fatal error by SQLite, vfs implementations should endeavor
** to prevent this by setting mxPathname to a sufficiently large value.
**
** The xRandomness(), xSleep(), xCurrentTime(), and xCurrentTimeInt64()
** interfaces are not strictly a part of the filesystem, but they are
** included in the VFS structure for completeness.
** The xRandomness() function attempts to return nBytes bytes
** of good-quality randomness into zOut.  The return value is
** the actual number of bytes of randomness obtained.
** The xSleep() method causes the calling thread to sleep for at
** least the number of microseconds given.  ^The xCurrentTime()
** method returns a Julian Day Number for the current date and time as
** a floating point value.
** ^The xCurrentTimeInt64() method returns, as an integer, the Julian
** Day Number multiplied by 86400000 (the number of milliseconds in
** a 24-hour day).
** ^SQLite will use the xCurrentTimeInt64() method to get the current
** date and time if that method is available (if iVersion is 2 or
** greater and the function pointer is not NULL) and will fall back
** to xCurrentTime() if xCurrentTimeInt64() is unavailable.
**
** ^The xSetSystemCall(), xGetSystemCall(), and xNestSystemCall() interfaces
** are not used by the SQLite core.  These optional interfaces are provided
** by some VFSes to facilitate testing of the VFS code. By overriding
** system calls with functions under its control, a test program can
** simulate faults and error conditions that would otherwise be difficult
** or impossible to induce.  The set of system calls that can be overridden
** varies from one VFS to another, and from one version of the same VFS to the
** next.  Applications that use these interfaces must be prepared for any
** or all of these interfaces to be NULL or for their behavior to change
** from one release to the next.  Applications must not attempt to access
** any of these methods if the iVersion of the VFS is less than 3.
*/
typedef struct sqlite3_vfs sqlite3_vfs;
typedef void (*sqlite3_syscall_ptr)(void);
struct sqlite3_vfs {
  int iVersion;            /* Structure version number (currently 3) */
  int szOsFile;            /* Size of subclassed sqlite3_file */
  int mxPathname;          /* Maximum file pathname length */
  sqlite3_vfs *pNext;      /* Next registered VFS */
  const char *zName;       /* Name of this virtual file system */
  void *pAppData;          /* Pointer to application-specific data */
  int (*xOpen)(sqlite3_vfs*, const char *zName, sqlite3_file*,
               int flags, int *pOutFlags);
  int (*xDelete)(sqlite3_vfs*, const char *zName, int syncDir);
  int (*xAccess)(sqlite3_vfs*, const char *zName, int flags, int *pResOut);
  int (*xFullPathname)(sqlite3_vfs*, const char *zName, int nOut, char *zOut);
  void *(*xDlOpen)(sqlite3_vfs*, const char *zFilename);
  void (*xDlError)(sqlite3_vfs*, int nByte, char *zErrMsg);
  void (*(*xDlSym)(sqlite3_vfs*,void*, const char *zSymbol))(void);
  void (*xDlClose)(sqlite3_vfs*, void*);
  int (*xRandomness)(sqlite3_vfs*, int nByte, char *zOut);
  int (*xSleep)(sqlite3_vfs*, int microseconds);
  int (*xCurrentTime)(sqlite3_vfs*, double*);
  int (*xGetLastError)(sqlite3_vfs*, int, char *);
  /*
  ** The methods above are in version 1 of the sqlite_vfs object
  ** definition.  Those that follow are added in version 2 or later
  */
  int (*xCurrentTimeInt64)(sqlite3_vfs*, sqlite3_int64*);
  /*
  ** The methods above are in versions 1 and 2 of the sqlite_vfs object.
  ** Those below are for version 3 and greater.
  */
  int (*xSetSystemCall)(sqlite3_vfs*, const char *zName, sqlite3_syscall_ptr);
  sqlite3_syscall_ptr (*xGetSystemCall)(sqlite3_vfs*, const char *zName);
  const char *(*xNextSystemCall)(sqlite3_vfs*, const char *zName);
  /*
  ** The methods above are in versions 1 through 3 of the sqlite_vfs object.
  ** New fields may be appended in figure versions.  The iVersion
  ** value will increment whenever this happens.
  */
};

/*
** CAPI3REF: Flags for the xAccess VFS method
**
** These integer constants can be used as the third parameter to
** the xAccess method of an [sqlite3_vfs] object.  They determine
** what kind of permissions the xAccess method is looking for.
** With SQLITE_ACCESS_EXISTS, the xAccess method
** simply checks whether the file exists.
** With SQLITE_ACCESS_READWRITE, the xAccess method
** checks whether the named directory is both readable and writable
** (in other words, if files can be added, removed, and renamed within
** the directory).
** The SQLITE_ACCESS_READWRITE constant is currently used only by the
** [temp_store_directory pragma], though this could change in a future
** release of SQLite.
** With SQLITE_ACCESS_READ, the xAccess method
** checks whether the file is readable.  The SQLITE_ACCESS_READ constant is
** currently unused, though it might be used in a future release of
** SQLite.
*/
#define SQLITE_ACCESS_EXISTS    0
#define SQLITE_ACCESS_READWRITE 1   /* Used by PRAGMA temp_store_directory */
#define SQLITE_ACCESS_READ      2   /* Unused */

/*
** CAPI3REF: Flags for the xShmLock VFS method
**
** These integer constants define the various locking operations
** allowed by the xShmLock method of [sqlite3_io_methods].  The
** following are the only legal combinations of flags to the
** xShmLock method:
**
** 
      
** 
    •   SQLITE_SHM_LOCK | SQLITE_SHM_SHARED
** 
    •   SQLITE_SHM_LOCK | SQLITE_SHM_EXCLUSIVE
** 
    •   SQLITE_SHM_UNLOCK | SQLITE_SHM_SHARED
** 
    •   SQLITE_SHM_UNLOCK | SQLITE_SHM_EXCLUSIVE
** 
    
**
** When unlocking, the same SHARED or EXCLUSIVE flag must be supplied as
** was given no the corresponding lock.
**
** The xShmLock method can transition between unlocked and SHARED or
** between unlocked and EXCLUSIVE.  It cannot transition between SHARED
** and EXCLUSIVE.
*/
#define SQLITE_SHM_UNLOCK       1
#define SQLITE_SHM_LOCK         2
#define SQLITE_SHM_SHARED       4
#define SQLITE_SHM_EXCLUSIVE    8

/*
** CAPI3REF: Maximum xShmLock index
**
** The xShmLock method on [sqlite3_io_methods] may use values
** between 0 and this upper bound as its "offset" argument.
** The SQLite core will never attempt to acquire or release a
** lock outside of this range
*/
#define SQLITE_SHM_NLOCK        8


/*
** CAPI3REF: Initialize The SQLite Library
**
** ^The sqlite3_initialize() routine initializes the
** SQLite library.  ^The sqlite3_shutdown() routine
** deallocates any resources that were allocated by sqlite3_initialize().
** These routines are designed to aid in process initialization and
** shutdown on embedded systems.  Workstation applications using
** SQLite normally do not need to invoke either of these routines.
**
** A call to sqlite3_initialize() is an "effective" call if it is
** the first time sqlite3_initialize() is invoked during the lifetime of
** the process, or if it is the first time sqlite3_initialize() is invoked
** following a call to sqlite3_shutdown().  ^(Only an effective call
** of sqlite3_initialize() does any initialization.  All other calls
** are harmless no-ops.)^
**
** A call to sqlite3_shutdown() is an "effective" call if it is the first
** call to sqlite3_shutdown() since the last sqlite3_initialize().  ^(Only
** an effective call to sqlite3_shutdown() does any deinitialization.
** All other valid calls to sqlite3_shutdown() are harmless no-ops.)^
**
** The sqlite3_initialize() interface is threadsafe, but sqlite3_shutdown()
** is not.  The sqlite3_shutdown() interface must only be called from a
** single thread.  All open [database connections] must be closed and all
** other SQLite resources must be deallocated prior to invoking
** sqlite3_shutdown().
**
** Among other things, ^sqlite3_initialize() will invoke
** sqlite3_os_init().  Similarly, ^sqlite3_shutdown()
** will invoke sqlite3_os_end().
**
** ^The sqlite3_initialize() routine returns [SQLITE_OK] on success.
** ^If for some reason, sqlite3_initialize() is unable to initialize
** the library (perhaps it is unable to allocate a needed resource such
** as a mutex) it returns an [error code] other than [SQLITE_OK].
**
** ^The sqlite3_initialize() routine is called internally by many other
** SQLite interfaces so that an application usually does not need to
** invoke sqlite3_initialize() directly.  For example, [sqlite3_open()]
** calls sqlite3_initialize() so the SQLite library will be automatically
** initialized when [sqlite3_open()] is called if it has not be initialized
** already.  ^However, if SQLite is compiled with the [SQLITE_OMIT_AUTOINIT]
** compile-time option, then the automatic calls to sqlite3_initialize()
** are omitted and the application must call sqlite3_initialize() directly
** prior to using any other SQLite interface.  For maximum portability,
** it is recommended that applications always invoke sqlite3_initialize()
** directly prior to using any other SQLite interface.  Future releases
** of SQLite may require this.  In other words, the behavior exhibited
** when SQLite is compiled with [SQLITE_OMIT_AUTOINIT] might become the
** default behavior in some future release of SQLite.
**
** The sqlite3_os_init() routine does operating-system specific
** initialization of the SQLite library.  The sqlite3_os_end()
** routine undoes the effect of sqlite3_os_init().  Typical tasks
** performed by these routines include allocation or deallocation
** of static resources, initialization of global variables,
** setting up a default [sqlite3_vfs] module, or setting up
** a default configuration using [sqlite3_config()].
**
** The application should never invoke either sqlite3_os_init()
** or sqlite3_os_end() directly.  The application should only invoke
** sqlite3_initialize() and sqlite3_shutdown().  The sqlite3_os_init()
** interface is called automatically by sqlite3_initialize() and
** sqlite3_os_end() is called by sqlite3_shutdown().  Appropriate
** implementations for sqlite3_os_init() and sqlite3_os_end()
** are built into SQLite when it is compiled for Unix, Windows, or OS/2.
** When [custom builds | built for other platforms]
** (using the [SQLITE_OS_OTHER=1] compile-time
** option) the application must supply a suitable implementation for
** sqlite3_os_init() and sqlite3_os_end().  An application-supplied
** implementation of sqlite3_os_init() or sqlite3_os_end()
** must return [SQLITE_OK] on success and some other [error code] upon
** failure.
*/
SQLITE_API int sqlite3_initialize(void);
SQLITE_API int sqlite3_shutdown(void);
SQLITE_API int sqlite3_os_init(void);
SQLITE_API int sqlite3_os_end(void);

/*
** CAPI3REF: Configuring The SQLite Library
**
** The sqlite3_config() interface is used to make global configuration
** changes to SQLite in order to tune SQLite to the specific needs of
** the application.  The default configuration is recommended for most
** applications and so this routine is usually not necessary.  It is
** provided to support rare applications with unusual needs.
**
** The sqlite3_config() interface is not threadsafe.  The application
** must insure that no other SQLite interfaces are invoked by other
** threads while sqlite3_config() is running.  Furthermore, sqlite3_config()
** may only be invoked prior to library initialization using
** [sqlite3_initialize()] or after shutdown by [sqlite3_shutdown()].
** ^If sqlite3_config() is called after [sqlite3_initialize()] and before
** [sqlite3_shutdown()] then it will return SQLITE_MISUSE.
** Note, however, that ^sqlite3_config() can be called as part of the
** implementation of an application-defined [sqlite3_os_init()].
**
** The first argument to sqlite3_config() is an integer
** [configuration option] that determines
** what property of SQLite is to be configured.  Subsequent arguments
** vary depending on the [configuration option]
** in the first argument.
**
** ^When a configuration option is set, sqlite3_config() returns [SQLITE_OK].
** ^If the option is unknown or SQLite is unable to set the option
** then this routine returns a non-zero [error code].
*/
SQLITE_API int sqlite3_config(int, ...);

/*
** CAPI3REF: Configure database connections
**
** The sqlite3_db_config() interface is used to make configuration
** changes to a [database connection].  The interface is similar to
** [sqlite3_config()] except that the changes apply to a single
** [database connection] (specified in the first argument).
**
** The second argument to sqlite3_db_config(D,V,...)  is the
** [SQLITE_DBCONFIG_LOOKASIDE | configuration verb] - an integer code
** that indicates what aspect of the [database connection] is being configured.
** Subsequent arguments vary depending on the configuration verb.
**
** ^Calls to sqlite3_db_config() return SQLITE_OK if and only if
** the call is considered successful.
*/
SQLITE_API int sqlite3_db_config(sqlite3*, int op, ...);

/*
** CAPI3REF: Memory Allocation Routines
**
** An instance of this object defines the interface between SQLite
** and low-level memory allocation routines.
**
** This object is used in only one place in the SQLite interface.
** A pointer to an instance of this object is the argument to
** [sqlite3_config()] when the configuration option is
** [SQLITE_CONFIG_MALLOC] or [SQLITE_CONFIG_GETMALLOC].
** By creating an instance of this object
** and passing it to [sqlite3_config]([SQLITE_CONFIG_MALLOC])
** during configuration, an application can specify an alternative
** memory allocation subsystem for SQLite to use for all of its
** dynamic memory needs.
**
** Note that SQLite comes with several [built-in memory allocators]
** that are perfectly adequate for the overwhelming majority of applications
** and that this object is only useful to a tiny minority of applications
** with specialized memory allocation requirements.  This object is
** also used during testing of SQLite in order to specify an alternative
** memory allocator that simulates memory out-of-memory conditions in
** order to verify that SQLite recovers gracefully from such
** conditions.
**
** The xMalloc, xRealloc, and xFree methods must work like the
** malloc(), realloc() and free() functions from the standard C library.
** ^SQLite guarantees that the second argument to
** xRealloc is always a value returned by a prior call to xRoundup.
**
** xSize should return the allocated size of a memory allocation
** previously obtained from xMalloc or xRealloc.  The allocated size
** is always at least as big as the requested size but may be larger.
**
** The xRoundup method returns what would be the allocated size of
** a memory allocation given a particular requested size.  Most memory
** allocators round up memory allocations at least to the next multiple
** of 8.  Some allocators round up to a larger multiple or to a power of 2.
** Every memory allocation request coming in through [sqlite3_malloc()]
** or [sqlite3_realloc()] first calls xRoundup.  If xRoundup returns 0,
** that causes the corresponding memory allocation to fail.
**
** The xInit method initializes the memory allocator.  (For example,
** it might allocate any require mutexes or initialize internal data
** structures.  The xShutdown method is invoked (indirectly) by
** [sqlite3_shutdown()] and should deallocate any resources acquired
** by xInit.  The pAppData pointer is used as the only parameter to
** xInit and xShutdown.
**
** SQLite holds the [SQLITE_MUTEX_STATIC_MASTER] mutex when it invokes
** the xInit method, so the xInit method need not be threadsafe.  The
** xShutdown method is only called from [sqlite3_shutdown()] so it does
** not need to be threadsafe either.  For all other methods, SQLite
** holds the [SQLITE_MUTEX_STATIC_MEM] mutex as long as the
** [SQLITE_CONFIG_MEMSTATUS] configuration option is turned on (which
** it is by default) and so the methods are automatically serialized.
** However, if [SQLITE_CONFIG_MEMSTATUS] is disabled, then the other
** methods must be threadsafe or else make their own arrangements for
** serialization.
**
** SQLite will never invoke xInit() more than once without an intervening
** call to xShutdown().
*/
typedef struct sqlite3_mem_methods sqlite3_mem_methods;
struct sqlite3_mem_methods {
  void *(*xMalloc)(int);         /* Memory allocation function */
  void (*xFree)(void*);          /* Free a prior allocation */
  void *(*xRealloc)(void*,int);  /* Resize an allocation */
  int (*xSize)(void*);           /* Return the size of an allocation */
  int (*xRoundup)(int);          /* Round up request size to allocation size */
  int (*xInit)(void*);           /* Initialize the memory allocator */
  void (*xShutdown)(void*);      /* Deinitialize the memory allocator */
  void *pAppData;                /* Argument to xInit() and xShutdown() */
};

/*
** CAPI3REF: Configuration Options
** KEYWORDS: {configuration option}
**
** These constants are the available integer configuration options that
** can be passed as the first argument to the [sqlite3_config()] interface.
**
** New configuration options may be added in future releases of SQLite.
** Existing configuration options might be discontinued.  Applications
** should check the return code from [sqlite3_config()] to make sure that
** the call worked.  The [sqlite3_config()] interface will return a
** non-zero [error code] if a discontinued or unsupported configuration option
** is invoked.
**
** 
    
** [[SQLITE_CONFIG_SINGLETHREAD]] 
    SQLITE_CONFIG_SINGLETHREAD
    
** 
    There are no arguments to this option.  ^This option sets the
** [threading mode] to Single-thread.  In other words, it disables
** all mutexing and puts SQLite into a mode where it can only be used
** by a single thread.   ^If SQLite is compiled with
** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then
** it is not possible to change the [threading mode] from its default
** value of Single-thread and so [sqlite3_config()] will return
** [SQLITE_ERROR] if called with the SQLITE_CONFIG_SINGLETHREAD
** configuration option.
    
**
** [[SQLITE_CONFIG_MULTITHREAD]] 
    SQLITE_CONFIG_MULTITHREAD
    
** 
    There are no arguments to this option.  ^This option sets the
** [threading mode] to Multi-thread.  In other words, it disables
** mutexing on [database connection] and [prepared statement] objects.
** The application is responsible for serializing access to
** [database connections] and [prepared statements].  But other mutexes
** are enabled so that SQLite will be safe to use in a multi-threaded
** environment as long as no two threads attempt to use the same
** [database connection] at the same time.  ^If SQLite is compiled with
** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then
** it is not possible to set the Multi-thread [threading mode] and
** [sqlite3_config()] will return [SQLITE_ERROR] if called with the
** SQLITE_CONFIG_MULTITHREAD configuration option.
    
**
** [[SQLITE_CONFIG_SERIALIZED]] 
    SQLITE_CONFIG_SERIALIZED
    
** 
    There are no arguments to this option.  ^This option sets the
** [threading mode] to Serialized. In other words, this option enables
** all mutexes including the recursive
** mutexes on [database connection] and [prepared statement] objects.
** In this mode (which is the default when SQLite is compiled with
** [SQLITE_THREADSAFE=1]) the SQLite library will itself serialize access
** to [database connections] and [prepared statements] so that the
** application is free to use the same [database connection] or the
** same [prepared statement] in different threads at the same time.
** ^If SQLite is compiled with
** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then
** it is not possible to set the Serialized [threading mode] and
** [sqlite3_config()] will return [SQLITE_ERROR] if called with the
** SQLITE_CONFIG_SERIALIZED configuration option.
    
**
** [[SQLITE_CONFIG_MALLOC]] 
    SQLITE_CONFIG_MALLOC
    
** 
     ^(This option takes a single argument which is a pointer to an
** instance of the [sqlite3_mem_methods] structure.  The argument specifies
** alternative low-level memory allocation routines to be used in place of
** the memory allocation routines built into SQLite.)^ ^SQLite makes
** its own private copy of the content of the [sqlite3_mem_methods] structure
** before the [sqlite3_config()] call returns.
    
**
** [[SQLITE_CONFIG_GETMALLOC]] 
    SQLITE_CONFIG_GETMALLOC
    
** 
     ^(This option takes a single argument which is a pointer to an
** instance of the [sqlite3_mem_methods] structure.  The [sqlite3_mem_methods]
** structure is filled with the currently defined memory allocation routines.)^
** This option can be used to overload the default memory allocation
** routines with a wrapper that simulations memory allocation failure or
** tracks memory usage, for example. 
    
**
** [[SQLITE_CONFIG_MEMSTATUS]] 
    SQLITE_CONFIG_MEMSTATUS
    
** 
     ^This option takes single argument of type int, interpreted as a
** boolean, which enables or disables the collection of memory allocation
** statistics. ^(When memory allocation statistics are disabled, the
** following SQLite interfaces become non-operational:
**   
      
**   
    •  [sqlite3_memory_used()]
**   
    •  [sqlite3_memory_highwater()]
**   
    •  [sqlite3_soft_heap_limit64()]
**   
    •  [sqlite3_status()]
**   
    )^
** ^Memory allocation statistics are enabled by default unless SQLite is
** compiled with [SQLITE_DEFAULT_MEMSTATUS]=0 in which case memory
** allocation statistics are disabled by default.
** 
    
**
** [[SQLITE_CONFIG_SCRATCH]] 
    SQLITE_CONFIG_SCRATCH
    
** 
     ^This option specifies a static memory buffer that SQLite can use for
** scratch memory.  There are three arguments:  A pointer an 8-byte
** aligned memory buffer from which the scratch allocations will be
** drawn, the size of each scratch allocation (sz),
** and the maximum number of scratch allocations (N).  The sz
** argument must be a multiple of 16.
** The first argument must be a pointer to an 8-byte aligned buffer
** of at least sz*N bytes of memory.
** ^SQLite will use no more than two scratch buffers per thread.  So
** N should be set to twice the expected maximum number of threads.
** ^SQLite will never require a scratch buffer that is more than 6
** times the database page size. ^If SQLite needs needs additional
** scratch memory beyond what is provided by this configuration option, then
** [sqlite3_malloc()] will be used to obtain the memory needed.
    
**
** [[SQLITE_CONFIG_PAGECACHE]] 
    SQLITE_CONFIG_PAGECACHE
    
** 
     ^This option specifies a static memory buffer that SQLite can use for
** the database page cache with the default page cache implementation.
** This configuration should not be used if an application-define page
** cache implementation is loaded using the SQLITE_CONFIG_PCACHE2 option.
** There are three arguments to this option: A pointer to 8-byte aligned
** memory, the size of each page buffer (sz), and the number of pages (N).
** The sz argument should be the size of the largest database page
** (a power of two between 512 and 32768) plus a little extra for each
** page header.  ^The page header size is 20 to 40 bytes depending on
** the host architecture.  ^It is harmless, apart from the wasted memory,
** to make sz a little too large.  The first
** argument should point to an allocation of at least sz*N bytes of memory.
** ^SQLite will use the memory provided by the first argument to satisfy its
** memory needs for the first N pages that it adds to cache.  ^If additional
** page cache memory is needed beyond what is provided by this option, then
** SQLite goes to [sqlite3_malloc()] for the additional storage space.
** The pointer in the first argument must
** be aligned to an 8-byte boundary or subsequent behavior of SQLite
** will be undefined.
    
**
** [[SQLITE_CONFIG_HEAP]] 
    SQLITE_CONFIG_HEAP
    
** 
     ^This option specifies a static memory buffer that SQLite will use
** for all of its dynamic memory allocation needs beyond those provided
** for by [SQLITE_CONFIG_SCRATCH] and [SQLITE_CONFIG_PAGECACHE].
** There are three arguments: An 8-byte aligned pointer to the memory,
** the number of bytes in the memory buffer, and the minimum allocation size.
** ^If the first pointer (the memory pointer) is NULL, then SQLite reverts
** to using its default memory allocator (the system malloc() implementation),
** undoing any prior invocation of [SQLITE_CONFIG_MALLOC].  ^If the
** memory pointer is not NULL and either [SQLITE_ENABLE_MEMSYS3] or
** [SQLITE_ENABLE_MEMSYS5] are defined, then the alternative memory
** allocator is engaged to handle all of SQLites memory allocation needs.
** The first pointer (the memory pointer) must be aligned to an 8-byte
** boundary or subsequent behavior of SQLite will be undefined.
** The minimum allocation size is capped at 2**12. Reasonable values
** for the minimum allocation size are 2**5 through 2**8.
    
**
** [[SQLITE_CONFIG_MUTEX]] 
    SQLITE_CONFIG_MUTEX
    
** 
     ^(This option takes a single argument which is a pointer to an
** instance of the [sqlite3_mutex_methods] structure.  The argument specifies
** alternative low-level mutex routines to be used in place
** the mutex routines built into SQLite.)^  ^SQLite makes a copy of the
** content of the [sqlite3_mutex_methods] structure before the call to
** [sqlite3_config()] returns. ^If SQLite is compiled with
** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then
** the entire mutexing subsystem is omitted from the build and hence calls to
** [sqlite3_config()] with the SQLITE_CONFIG_MUTEX configuration option will
** return [SQLITE_ERROR].
    
**
** [[SQLITE_CONFIG_GETMUTEX]] 
    SQLITE_CONFIG_GETMUTEX
    
** 
     ^(This option takes a single argument which is a pointer to an
** instance of the [sqlite3_mutex_methods] structure.  The
** [sqlite3_mutex_methods]
** structure is filled with the currently defined mutex routines.)^
** This option can be used to overload the default mutex allocation
** routines with a wrapper used to track mutex usage for performance
** profiling or testing, for example.   ^If SQLite is compiled with
** the [SQLITE_THREADSAFE | SQLITE_THREADSAFE=0] compile-time option then
** the entire mutexing subsystem is omitted from the build and hence calls to
** [sqlite3_config()] with the SQLITE_CONFIG_GETMUTEX configuration option will
** return [SQLITE_ERROR].
    
**
** [[SQLITE_CONFIG_LOOKASIDE]] 
    SQLITE_CONFIG_LOOKASIDE
    
** 
     ^(This option takes two arguments that determine the default
** memory allocation for the lookaside memory allocator on each
** [database connection].  The first argument is the
** size of each lookaside buffer slot and the second is the number of
** slots allocated to each database connection.)^  ^(This option sets the
** default lookaside size. The [SQLITE_DBCONFIG_LOOKASIDE]
** verb to [sqlite3_db_config()] can be used to change the lookaside
** configuration on individual connections.)^ 
    
**
** [[SQLITE_CONFIG_PCACHE2]] 
    SQLITE_CONFIG_PCACHE2
    
** 
     ^(This option takes a single argument which is a pointer to
** an [sqlite3_pcache_methods2] object.  This object specifies the interface
** to a custom page cache implementation.)^  ^SQLite makes a copy of the
** object and uses it for page cache memory allocations.
    
**
** [[SQLITE_CONFIG_GETPCACHE2]] 
    SQLITE_CONFIG_GETPCACHE2
    
** 
     ^(This option takes a single argument which is a pointer to an
** [sqlite3_pcache_methods2] object.  SQLite copies of the current
** page cache implementation into that object.)^ 
    
**
** [[SQLITE_CONFIG_LOG]] 
    SQLITE_CONFIG_LOG
    
** 
     ^The SQLITE_CONFIG_LOG option takes two arguments: a pointer to a
** function with a call signature of void(*)(void*,int,const char*),
** and a pointer to void. ^If the function pointer is not NULL, it is
** invoked by [sqlite3_log()] to process each logging event.  ^If the
** function pointer is NULL, the [sqlite3_log()] interface becomes a no-op.
** ^The void pointer that is the second argument to SQLITE_CONFIG_LOG is
** passed through as the first parameter to the application-defined logger
** function whenever that function is invoked.  ^The second parameter to
** the logger function is a copy of the first parameter to the corresponding
** [sqlite3_log()] call and is intended to be a [result code] or an
** [extended result code].  ^The third parameter passed to the logger is
** log message after formatting via [sqlite3_snprintf()].
** The SQLite logging interface is not reentrant; the logger function
** supplied by the application must not invoke any SQLite interface.
** In a multi-threaded application, the application-defined logger
** function must be threadsafe. 
    
**
** [[SQLITE_CONFIG_URI]] 
    SQLITE_CONFIG_URI
** 
     This option takes a single argument of type int. If non-zero, then
** URI handling is globally enabled. If the parameter is zero, then URI handling
** is globally disabled. If URI handling is globally enabled, all filenames
** passed to [sqlite3_open()], [sqlite3_open_v2()], [sqlite3_open16()] or
** specified as part of [ATTACH] commands are interpreted as URIs, regardless
** of whether or not the [SQLITE_OPEN_URI] flag is set when the database
** connection is opened. If it is globally disabled, filenames are
** only interpreted as URIs if the SQLITE_OPEN_URI flag is set when the
** database connection is opened. By default, URI handling is globally
** disabled. The default value may be changed by compiling with the
** [SQLITE_USE_URI] symbol defined.
**
** [[SQLITE_CONFIG_PCACHE]] [[SQLITE_CONFIG_GETPCACHE]]
** 
    SQLITE_CONFIG_PCACHE and SQLITE_CONFNIG_GETPCACHE
** 
     These options are obsolete and should not be used by new code.
** They are retained for backwards compatibility but are now no-ops.
** 
    
*/
#define SQLITE_CONFIG_SINGLETHREAD  1  /* nil */
#define SQLITE_CONFIG_MULTITHREAD   2  /* nil */
#define SQLITE_CONFIG_SERIALIZED    3  /* nil */
#define SQLITE_CONFIG_MALLOC        4  /* sqlite3_mem_methods* */
#define SQLITE_CONFIG_GETMALLOC     5  /* sqlite3_mem_methods* */
#define SQLITE_CONFIG_SCRATCH       6  /* void*, int sz, int N */
#define SQLITE_CONFIG_PAGECACHE     7  /* void*, int sz, int N */
#define SQLITE_CONFIG_HEAP          8  /* void*, int nByte, int min */
#define SQLITE_CONFIG_MEMSTATUS     9  /* boolean */
#define SQLITE_CONFIG_MUTEX        10  /* sqlite3_mutex_methods* */
#define SQLITE_CONFIG_GETMUTEX     11  /* sqlite3_mutex_methods* */
/* previously SQLITE_CONFIG_CHUNKALLOC 12 which is now unused. */
#define SQLITE_CONFIG_LOOKASIDE    13  /* int int */
#define SQLITE_CONFIG_PCACHE       14  /* no-op */
#define SQLITE_CONFIG_GETPCACHE    15  /* no-op */
#define SQLITE_CONFIG_LOG          16  /* xFunc, void* */
#define SQLITE_CONFIG_URI          17  /* int */
#define SQLITE_CONFIG_PCACHE2      18  /* sqlite3_pcache_methods2* */
#define SQLITE_CONFIG_GETPCACHE2   19  /* sqlite3_pcache_methods2* */

/*
** CAPI3REF: Database Connection Configuration Options
**
** These constants are the available integer configuration options that
** can be passed as the second argument to the [sqlite3_db_config()] interface.
**
** New configuration options may be added in future releases of SQLite.
** Existing configuration options might be discontinued.  Applications
** should check the return code from [sqlite3_db_config()] to make sure that
** the call worked.  ^The [sqlite3_db_config()] interface will return a
** non-zero [error code] if a discontinued or unsupported configuration option
** is invoked.
**
** 
    
** 
    SQLITE_DBCONFIG_LOOKASIDE
    
** 
     ^This option takes three additional arguments that determine the
** [lookaside memory allocator] configuration for the [database connection].
** ^The first argument (the third parameter to [sqlite3_db_config()] is a
** pointer to a memory buffer to use for lookaside memory.
** ^The first argument after the SQLITE_DBCONFIG_LOOKASIDE verb
** may be NULL in which case SQLite will allocate the
** lookaside buffer itself using [sqlite3_malloc()]. ^The second argument is the
** size of each lookaside buffer slot.  ^The third argument is the number of
** slots.  The size of the buffer in the first argument must be greater than
** or equal to the product of the second and third arguments.  The buffer
** must be aligned to an 8-byte boundary.  ^If the second argument to
** SQLITE_DBCONFIG_LOOKASIDE is not a multiple of 8, it is internally
** rounded down to the next smaller multiple of 8.  ^(The lookaside memory
** configuration for a database connection can only be changed when that
** connection is not currently using lookaside memory, or in other words
** when the "current value" returned by
** [sqlite3_db_status](D,[SQLITE_CONFIG_LOOKASIDE],...) is zero.
** Any attempt to change the lookaside memory configuration when lookaside
** memory is in use leaves the configuration unchanged and returns
** [SQLITE_BUSY].)^
    
**
** 
    SQLITE_DBCONFIG_ENABLE_FKEY
    
** 
     ^This option is used to enable or disable the enforcement of
** [foreign key constraints].  There should be two additional arguments.
** The first argument is an integer which is 0 to disable FK enforcement,
** positive to enable FK enforcement or negative to leave FK enforcement
** unchanged.  The second parameter is a pointer to an integer into which
** is written 0 or 1 to indicate whether FK enforcement is off or on
** following this call.  The second parameter may be a NULL pointer, in
** which case the FK enforcement setting is not reported back. 
    
**
** 
    SQLITE_DBCONFIG_ENABLE_TRIGGER
    
** 
     ^This option is used to enable or disable [CREATE TRIGGER | triggers].
** There should be two additional arguments.
** The first argument is an integer which is 0 to disable triggers,
** positive to enable triggers or negative to leave the setting unchanged.
** The second parameter is a pointer to an integer into which
** is written 0 or 1 to indicate whether triggers are disabled or enabled
** following this call.  The second parameter may be a NULL pointer, in
** which case the trigger setting is not reported back. 
    
**
** 
    
*/
#define SQLITE_DBCONFIG_LOOKASIDE       1001  /* void* int int */
#define SQLITE_DBCONFIG_ENABLE_FKEY     1002  /* int int* */
#define SQLITE_DBCONFIG_ENABLE_TRIGGER  1003  /* int int* */


/*
** CAPI3REF: Enable Or Disable Extended Result Codes
**
** ^The sqlite3_extended_result_codes() routine enables or disables the
** [extended result codes] feature of SQLite. ^The extended result
** codes are disabled by default for historical compatibility.
*/
SQLITE_API int sqlite3_extended_result_codes(sqlite3*, int onoff);

/*
** CAPI3REF: Last Insert Rowid
**
** ^Each entry in an SQLite table has a unique 64-bit signed
** integer key called the [ROWID | "rowid"]. ^The rowid is always available
** as an undeclared column named ROWID, OID, or _ROWID_ as long as those
** names are not also used by explicitly declared columns. ^If
** the table has a column of type [INTEGER PRIMARY KEY] then that column
** is another alias for the rowid.
**
** ^This routine returns the [rowid] of the most recent
** successful [INSERT] into the database from the [database connection]
** in the first argument.  ^As of SQLite version 3.7.7, this routines
** records the last insert rowid of both ordinary tables and [virtual tables].
** ^If no successful [INSERT]s
** have ever occurred on that database connection, zero is returned.
**
** ^(If an [INSERT] occurs within a trigger or within a [virtual table]
** method, then this routine will return the [rowid] of the inserted
** row as long as the trigger or virtual table method is running.
** But once the trigger or virtual table method ends, the value returned
** by this routine reverts to what it was before the trigger or virtual
** table method began.)^
**
** ^An [INSERT] that fails due to a constraint violation is not a
** successful [INSERT] and does not change the value returned by this
** routine.  ^Thus INSERT OR FAIL, INSERT OR IGNORE, INSERT OR ROLLBACK,
** and INSERT OR ABORT make no changes to the return value of this
** routine when their insertion fails.  ^(When INSERT OR REPLACE
** encounters a constraint violation, it does not fail.  The
** INSERT continues to completion after deleting rows that caused
** the constraint problem so INSERT OR REPLACE will always change
** the return value of this interface.)^
**
** ^For the purposes of this routine, an [INSERT] is considered to
** be successful even if it is subsequently rolled back.
**
** This function is accessible to SQL statements via the
** [last_insert_rowid() SQL function].
**
** If a separate thread performs a new [INSERT] on the same
** database connection while the [sqlite3_last_insert_rowid()]
** function is running and thus changes the last insert [rowid],
** then the value returned by [sqlite3_last_insert_rowid()] is
** unpredictable and might not equal either the old or the new
** last insert [rowid].
*/
SQLITE_API sqlite3_int64 sqlite3_last_insert_rowid(sqlite3*);

/*
** CAPI3REF: Count The Number Of Rows Modified
**
** ^This function returns the number of database rows that were changed
** or inserted or deleted by the most recently completed SQL statement
** on the [database connection] specified by the first parameter.
** ^(Only changes that are directly specified by the [INSERT], [UPDATE],
** or [DELETE] statement are counted.  Auxiliary changes caused by
** triggers or [foreign key actions] are not counted.)^ Use the
** [sqlite3_total_changes()] function to find the total number of changes
** including changes caused by triggers and foreign key actions.
**
** ^Changes to a view that are simulated by an [INSTEAD OF trigger]
** are not counted.  Only real table changes are counted.
**
** ^(A "row change" is a change to a single row of a single table
** caused by an INSERT, DELETE, or UPDATE statement.  Rows that
** are changed as side effects of [REPLACE] constraint resolution,
** rollback, ABORT processing, [DROP TABLE], or by any other
** mechanisms do not count as direct row changes.)^
**
** A "trigger context" is a scope of execution that begins and
** ends with the script of a [CREATE TRIGGER | trigger].
** Most SQL statements are
** evaluated outside of any trigger.  This is the "top level"
** trigger context.  If a trigger fires from the top level, a
** new trigger context is entered for the duration of that one
** trigger.  Subtriggers create subcontexts for their duration.
**
** ^Calling [sqlite3_exec()] or [sqlite3_step()] recursively does
** not create a new trigger context.
**
** ^This function returns the number of direct row changes in the
** most recent INSERT, UPDATE, or DELETE statement within the same
** trigger context.
**
** ^Thus, when called from the top level, this function returns the
** number of changes in the most recent INSERT, UPDATE, or DELETE
** that also occurred at the top level.  ^(Within the body of a trigger,
** the sqlite3_changes() interface can be called to find the number of
** changes in the most recently completed INSERT, UPDATE, or DELETE
** statement within the body of the same trigger.
** However, the number returned does not include changes
** caused by subtriggers since those have their own context.)^
**
** See also the [sqlite3_total_changes()] interface, the
** [count_changes pragma], and the [changes() SQL function].
**
** If a separate thread makes changes on the same database connection
** while [sqlite3_changes()] is running then the value returned
** is unpredictable and not meaningful.
*/
SQLITE_API int sqlite3_changes(sqlite3*);

/*
** CAPI3REF: Total Number Of Rows Modified
**
** ^This function returns the number of row changes caused by [INSERT],
** [UPDATE] or [DELETE] statements since the [database connection] was opened.
** ^(The count returned by sqlite3_total_changes() includes all changes
** from all [CREATE TRIGGER | trigger] contexts and changes made by
** [foreign key actions]. However,
** the count does not include changes used to implement [REPLACE] constraints,
** do rollbacks or ABORT processing, or [DROP TABLE] processing.  The
** count does not include rows of views that fire an [INSTEAD OF trigger],
** though if the INSTEAD OF trigger makes changes of its own, those changes
** are counted.)^
** ^The sqlite3_total_changes() function counts the changes as soon as
** the statement that makes them is completed (when the statement handle
** is passed to [sqlite3_reset()] or [sqlite3_finalize()]).
**
** See also the [sqlite3_changes()] interface, the
** [count_changes pragma], and the [total_changes() SQL function].
**
** If a separate thread makes changes on the same database connection
** while [sqlite3_total_changes()] is running then the value
** returned is unpredictable and not meaningful.
*/
SQLITE_API int sqlite3_total_changes(sqlite3*);

/*
** CAPI3REF: Interrupt A Long-Running Query
**
** ^This function causes any pending database operation to abort and
** return at its earliest opportunity. This routine is typically
** called in response to a user action such as pressing "Cancel"
** or Ctrl-C where the user wants a long query operation to halt
** immediately.
**
** ^It is safe to call this routine from a thread different from the
** thread that is currently running the database operation.  But it
** is not safe to call this routine with a [database connection] that
** is closed or might close before sqlite3_interrupt() returns.
**
** ^If an SQL operation is very nearly finished at the time when
** sqlite3_interrupt() is called, then it might not have an opportunity
** to be interrupted and might continue to completion.
**
** ^An SQL operation that is interrupted will return [SQLITE_INTERRUPT].
** ^If the interrupted SQL operation is an INSERT, UPDATE, or DELETE
** that is inside an explicit transaction, then the entire transaction
** will be rolled back automatically.
**
** ^The sqlite3_interrupt(D) call is in effect until all currently running
** SQL statements on [database connection] D complete.  ^Any new SQL statements
** that are started after the sqlite3_interrupt() call and before the
** running statements reaches zero are interrupted as if they had been
** running prior to the sqlite3_interrupt() call.  ^New SQL statements
** that are started after the running statement count reaches zero are
** not effected by the sqlite3_interrupt().
** ^A call to sqlite3_interrupt(D) that occurs when there are no running
** SQL statements is a no-op and has no effect on SQL statements
** that are started after the sqlite3_interrupt() call returns.
**
** If the database connection closes while [sqlite3_interrupt()]
** is running then bad things will likely happen.
*/
SQLITE_API void sqlite3_interrupt(sqlite3*);

/*
** CAPI3REF: Determine If An SQL Statement Is Complete
**
** These routines are useful during command-line input to determine if the
** currently entered text seems to form a complete SQL statement or
** if additional input is needed before sending the text into
** SQLite for parsing.  ^These routines return 1 if the input string
** appears to be a complete SQL statement.  ^A statement is judged to be
** complete if it ends with a semicolon token and is not a prefix of a
** well-formed CREATE TRIGGER statement.  ^Semicolons that are embedded within
** string literals or quoted identifier names or comments are not
** independent tokens (they are part of the token in which they are
** embedded) and thus do not count as a statement terminator.  ^Whitespace
** and comments that follow the final semicolon are ignored.
**
** ^These routines return 0 if the statement is incomplete.  ^If a
** memory allocation fails, then SQLITE_NOMEM is returned.
**
** ^These routines do not parse the SQL statements thus
** will not detect syntactically incorrect SQL.
**
** ^(If SQLite has not been initialized using [sqlite3_initialize()] prior
** to invoking sqlite3_complete16() then sqlite3_initialize() is invoked
** automatically by sqlite3_complete16().  If that initialization fails,
** then the return value from sqlite3_complete16() will be non-zero
** regardless of whether or not the input SQL is complete.)^
**
** The input to [sqlite3_complete()] must be a zero-terminated
** UTF-8 string.
**
** The input to [sqlite3_complete16()] must be a zero-terminated
** UTF-16 string in native byte order.
*/
SQLITE_API int sqlite3_complete(const char *sql);
SQLITE_API int sqlite3_complete16(const void *sql);

/*
** CAPI3REF: Register A Callback To Handle SQLITE_BUSY Errors
**
** ^This routine sets a callback function that might be invoked whenever
** an attempt is made to open a database table that another thread
** or process has locked.
**
** ^If the busy callback is NULL, then [SQLITE_BUSY] or [SQLITE_IOERR_BLOCKED]
** is returned immediately upon encountering the lock.  ^If the busy callback
** is not NULL, then the callback might be invoked with two arguments.
**
** ^The first argument to the busy handler is a copy of the void* pointer which
** is the third argument to sqlite3_busy_handler().  ^The second argument to
** the busy handler callback is the number of times that the busy handler has
** been invoked for this locking event.  ^If the
** busy callback returns 0, then no additional attempts are made to
** access the database and [SQLITE_BUSY] or [SQLITE_IOERR_BLOCKED] is returned.
** ^If the callback returns non-zero, then another attempt
** is made to open the database for reading and the cycle repeats.
**
** The presence of a busy handler does not guarantee that it will be invoked
** when there is lock contention. ^If SQLite determines that invoking the busy
** handler could result in a deadlock, it will go ahead and return [SQLITE_BUSY]
** or [SQLITE_IOERR_BLOCKED] instead of invoking the busy handler.
** Consider a scenario where one process is holding a read lock that
** it is trying to promote to a reserved lock and
** a second process is holding a reserved lock that it is trying
** to promote to an exclusive lock.  The first process cannot proceed
** because it is blocked by the second and the second process cannot
** proceed because it is blocked by the first.  If both processes
** invoke the busy handlers, neither will make any progress.  Therefore,
** SQLite returns [SQLITE_BUSY] for the first process, hoping that this
** will induce the first process to release its read lock and allow
** the second process to proceed.
**
** ^The default busy callback is NULL.
**
** ^The [SQLITE_BUSY] error is converted to [SQLITE_IOERR_BLOCKED]
** when SQLite is in the middle of a large transaction where all the
** changes will not fit into the in-memory cache.  SQLite will
** already hold a RESERVED lock on the database file, but it needs
** to promote this lock to EXCLUSIVE so that it can spill cache
** pages into the database file without harm to concurrent
** readers.  ^If it is unable to promote the lock, then the in-memory
** cache will be left in an inconsistent state and so the error
** code is promoted from the relatively benign [SQLITE_BUSY] to
** the more severe [SQLITE_IOERR_BLOCKED].  ^This error code promotion
** forces an automatic rollback of the changes.  See the
** 
** CorruptionFollowingBusyError wiki page for a discussion of why
** this is important.
**
** ^(There can only be a single busy handler defined for each
** [database connection].  Setting a new busy handler clears any
** previously set handler.)^  ^Note that calling [sqlite3_busy_timeout()]
** will also set or clear the busy handler.
**
** The busy callback should not take any actions which modify the
** database connection that invoked the busy handler.  Any such actions
** result in undefined behavior.
**
** A busy handler must not close the database connection
** or [prepared statement] that invoked the busy handler.
*/
SQLITE_API int sqlite3_busy_handler(sqlite3*, int(*)(void*,int), void*);

/*
** CAPI3REF: Set A Busy Timeout
**
** ^This routine sets a [sqlite3_busy_handler | busy handler] that sleeps
** for a specified amount of time when a table is locked.  ^The handler
** will sleep multiple times until at least "ms" milliseconds of sleeping
** have accumulated.  ^After at least "ms" milliseconds of sleeping,
** the handler returns 0 which causes [sqlite3_step()] to return
** [SQLITE_BUSY] or [SQLITE_IOERR_BLOCKED].
**
** ^Calling this routine with an argument less than or equal to zero
** turns off all busy handlers.
**
** ^(There can only be a single busy handler for a particular
** [database connection] any any given moment.  If another busy handler
** was defined  (using [sqlite3_busy_handler()]) prior to calling
** this routine, that other busy handler is cleared.)^
*/
SQLITE_API int sqlite3_busy_timeout(sqlite3*, int ms);

/*
** CAPI3REF: Convenience Routines For Running Queries
**
** This is a legacy interface that is preserved for backwards compatibility.
** Use of this interface is not recommended.
**
** Definition: A result table is memory data structure created by the
** [sqlite3_get_table()] interface.  A result table records the
** complete query results from one or more queries.
**
** The table conceptually has a number of rows and columns.  But
** these numbers are not part of the result table itself.  These
** numbers are obtained separately.  Let N be the number of rows
** and M be the number of columns.
**
** A result table is an array of pointers to zero-terminated UTF-8 strings.
** There are (N+1)*M elements in the array.  The first M pointers point
** to zero-terminated strings that  contain the names of the columns.
** The remaining entries all point to query results.  NULL values result
** in NULL pointers.  All other values are in their UTF-8 zero-terminated
** string representation as returned by [sqlite3_column_text()].
**
** A result table might consist of one or more memory allocations.
** It is not safe to pass a result table directly to [sqlite3_free()].
** A result table should be deallocated using [sqlite3_free_table()].
**
** ^(As an example of the result table format, suppose a query result
** is as follows:
**
** 
    **        Name        | Age
**        -----------------------
**        Alice       | 43
**        Bob         | 28
**        Cindy       | 21
** 
    
**
** There are two column (M==2) and three rows (N==3).  Thus the
** result table has 8 entries.  Suppose the result table is stored
** in an array names azResult.  Then azResult holds this content:
**
** 
    **        azResult[0] = "Name";
**        azResult[1] = "Age";
**        azResult[2] = "Alice";
**        azResult[3] = "43";
**        azResult[4] = "Bob";
**        azResult[5] = "28";
**        azResult[6] = "Cindy";
**        azResult[7] = "21";
** 
    )^
**
** ^The sqlite3_get_table() function evaluates one or more
** semicolon-separated SQL statements in the zero-terminated UTF-8
** string of its 2nd parameter and returns a result table to the
** pointer given in its 3rd parameter.
**
** After the application has finished with the result from sqlite3_get_table(),
** it must pass the result table pointer to sqlite3_free_table() in order to
** release the memory that was malloced.  Because of the way the
** [sqlite3_malloc()] happens within sqlite3_get_table(), the calling
** function must not try to call [sqlite3_free()] directly.  Only
** [sqlite3_free_table()] is able to release the memory properly and safely.
**
** The sqlite3_get_table() interface is implemented as a wrapper around
** [sqlite3_exec()].  The sqlite3_get_table() routine does not have access
** to any internal data structures of SQLite.  It uses only the public
** interface defined here.  As a consequence, errors that occur in the
** wrapper layer outside of the internal [sqlite3_exec()] call are not
** reflected in subsequent calls to [sqlite3_errcode()] or
** [sqlite3_errmsg()].
*/
SQLITE_API int sqlite3_get_table(
  sqlite3 *db,          /* An open database */
  const char *zSql,     /* SQL to be evaluated */
  char ***pazResult,    /* Results of the query */
  int *pnRow,           /* Number of result rows written here */
  int *pnColumn,        /* Number of result columns written here */
  char **pzErrmsg       /* Error msg written here */
);
SQLITE_API void sqlite3_free_table(char **result);

/*
** CAPI3REF: Formatted String Printing Functions
**
** These routines are work-alikes of the "printf()" family of functions
** from the standard C library.
**
** ^The sqlite3_mprintf() and sqlite3_vmprintf() routines write their
** results into memory obtained from [sqlite3_malloc()].
** The strings returned by these two routines should be
** released by [sqlite3_free()].  ^Both routines return a
** NULL pointer if [sqlite3_malloc()] is unable to allocate enough
** memory to hold the resulting string.
**
** ^(The sqlite3_snprintf() routine is similar to "snprintf()" from
** the standard C library.  The result is written into the
** buffer supplied as the second parameter whose size is given by
** the first parameter. Note that the order of the
** first two parameters is reversed from snprintf().)^  This is an
** historical accident that cannot be fixed without breaking
** backwards compatibility.  ^(Note also that sqlite3_snprintf()
** returns a pointer to its buffer instead of the number of
** characters actually written into the buffer.)^  We admit that
** the number of characters written would be a more useful return
** value but we cannot change the implementation of sqlite3_snprintf()
** now without breaking compatibility.
**
** ^As long as the buffer size is greater than zero, sqlite3_snprintf()
** guarantees that the buffer is always zero-terminated.  ^The first
** parameter "n" is the total size of the buffer, including space for
** the zero terminator.  So the longest string that can be completely
** written will be n-1 characters.
**
** ^The sqlite3_vsnprintf() routine is a varargs version of sqlite3_snprintf().
**
** These routines all implement some additional formatting
** options that are useful for constructing SQL statements.
** All of the usual printf() formatting options apply.  In addition, there
** is are "%q", "%Q", and "%z" options.
**
** ^(The %q option works like %s in that it substitutes a nul-terminated
** string from the argument list.  But %q also doubles every '\'' character.
** %q is designed for use inside a string literal.)^  By doubling each '\''
** character it escapes that character and allows it to be inserted into
** the string.
**
** For example, assume the string variable zText contains text as follows:
**
** 
    **  char *zText = "It's a happy day!";
** 
    
**
** One can use this text in an SQL statement as follows:
**
** 
    **  char *zSQL = sqlite3_mprintf("INSERT INTO table VALUES('%q')", zText);
**  sqlite3_exec(db, zSQL, 0, 0, 0);
**  sqlite3_free(zSQL);
** 
    
**
** Because the %q format string is used, the '\'' character in zText
** is escaped and the SQL generated is as follows:
**
** 
    **  INSERT INTO table1 VALUES('It''s a happy day!')
** 
    
**
** This is correct.  Had we used %s instead of %q, the generated SQL
** would have looked like this:
**
** 
    **  INSERT INTO table1 VALUES('It's a happy day!');
** 
    
**
** This second example is an SQL syntax error.  As a general rule you should
** always use %q instead of %s when inserting text into a string literal.
**
** ^(The %Q option works like %q except it also adds single quotes around
** the outside of the total string.  Additionally, if the parameter in the
** argument list is a NULL pointer, %Q substitutes the text "NULL" (without
** single quotes).)^  So, for example, one could say:
**
** 
    **  char *zSQL = sqlite3_mprintf("INSERT INTO table VALUES(%Q)", zText);
**  sqlite3_exec(db, zSQL, 0, 0, 0);
**  sqlite3_free(zSQL);
** 
    
**
** The code above will render a correct SQL statement in the zSQL
** variable even if the zText variable is a NULL pointer.
**
** ^(The "%z" formatting option works like "%s" but with the
** addition that after the string has been read and copied into
** the result, [sqlite3_free()] is called on the input string.)^
*/
SQLITE_API char *sqlite3_mprintf(const char*,...);
SQLITE_API char *sqlite3_vmprintf(const char*, va_list);
SQLITE_API char *sqlite3_snprintf(int,char*,const char*, ...);
SQLITE_API char *sqlite3_vsnprintf(int,char*,const char*, va_list);

/*
** CAPI3REF: Memory Allocation Subsystem
**
** The SQLite core uses these three routines for all of its own
** internal memory allocation needs. "Core" in the previous sentence
** does not include operating-system specific VFS implementation.  The
** Windows VFS uses native malloc() and free() for some operations.
**
** ^The sqlite3_malloc() routine returns a pointer to a block
** of memory at least N bytes in length, where N is the parameter.
** ^If sqlite3_malloc() is unable to obtain sufficient free
** memory, it returns a NULL pointer.  ^If the parameter N to
** sqlite3_malloc() is zero or negative then sqlite3_malloc() returns
** a NULL pointer.
**
** ^Calling sqlite3_free() with a pointer previously returned
** by sqlite3_malloc() or sqlite3_realloc() releases that memory so
** that it might be reused.  ^The sqlite3_free() routine is
** a no-op if is called with a NULL pointer.  Passing a NULL pointer
** to sqlite3_free() is harmless.  After being freed, memory
** should neither be read nor written.  Even reading previously freed
** memory might result in a segmentation fault or other severe error.
** Memory corruption, a segmentation fault, or other severe error
** might result if sqlite3_free() is called with a non-NULL pointer that
** was not obtained from sqlite3_malloc() or sqlite3_realloc().
**
** ^(The sqlite3_realloc() interface attempts to resize a
** prior memory allocation to be at least N bytes, where N is the
** second parameter.  The memory allocation to be resized is the first
** parameter.)^ ^ If the first parameter to sqlite3_realloc()
** is a NULL pointer then its behavior is identical to calling
** sqlite3_malloc(N) where N is the second parameter to sqlite3_realloc().
** ^If the second parameter to sqlite3_realloc() is zero or
** negative then the behavior is exactly the same as calling
** sqlite3_free(P) where P is the first parameter to sqlite3_realloc().
** ^sqlite3_realloc() returns a pointer to a memory allocation
** of at least N bytes in size or NULL if sufficient memory is unavailable.
** ^If M is the size of the prior allocation, then min(N,M) bytes
** of the prior allocation are copied into the beginning of buffer returned
** by sqlite3_realloc() and the prior allocation is freed.
** ^If sqlite3_realloc() returns NULL, then the prior allocation
** is not freed.
**
** ^The memory returned by sqlite3_malloc() and sqlite3_realloc()
** is always aligned to at least an 8 byte boundary, or to a
** 4 byte boundary if the [SQLITE_4_BYTE_ALIGNED_MALLOC] compile-time
** option is used.
**
** In SQLite version 3.5.0 and 3.5.1, it was possible to define
** the SQLITE_OMIT_MEMORY_ALLOCATION which would cause the built-in
** implementation of these routines to be omitted.  That capability
** is no longer provided.  Only built-in memory allocators can be used.
**
** The Windows OS interface layer calls
** the system malloc() and free() directly when converting
** filenames between the UTF-8 encoding used by SQLite
** and whatever filename encoding is used by the particular Windows
** installation.  Memory allocation errors are detected, but
** they are reported back as [SQLITE_CANTOPEN] or
** [SQLITE_IOERR] rather than [SQLITE_NOMEM].
**
** The pointer arguments to [sqlite3_free()] and [sqlite3_realloc()]
** must be either NULL or else pointers obtained from a prior
** invocation of [sqlite3_malloc()] or [sqlite3_realloc()] that have
** not yet been released.
**
** The application must not read or write any part of
** a block of memory after it has been released using
** [sqlite3_free()] or [sqlite3_realloc()].
*/
SQLITE_API void *sqlite3_malloc(int);
SQLITE_API void *sqlite3_realloc(void*, int);
SQLITE_API void sqlite3_free(void*);

/*
** CAPI3REF: Memory Allocator Statistics
**
** SQLite provides these two interfaces for reporting on the status
** of the [sqlite3_malloc()], [sqlite3_free()], and [sqlite3_realloc()]
** routines, which form the built-in memory allocation subsystem.
**
** ^The [sqlite3_memory_used()] routine returns the number of bytes
** of memory currently outstanding (malloced but not freed).
** ^The [sqlite3_memory_highwater()] routine returns the maximum
** value of [sqlite3_memory_used()] since the high-water mark
** was last reset.  ^The values returned by [sqlite3_memory_used()] and
** [sqlite3_memory_highwater()] include any overhead
** added by SQLite in its implementation of [sqlite3_malloc()],
** but not overhead added by the any underlying system library
** routines that [sqlite3_malloc()] may call.
**
** ^The memory high-water mark is reset to the current value of
** [sqlite3_memory_used()] if and only if the parameter to
** [sqlite3_memory_highwater()] is true.  ^The value returned
** by [sqlite3_memory_highwater(1)] is the high-water mark
** prior to the reset.
*/
SQLITE_API sqlite3_int64 sqlite3_memory_used(void);
SQLITE_API sqlite3_int64 sqlite3_memory_highwater(int resetFlag);

/*
** CAPI3REF: Pseudo-Random Number Generator
**
** SQLite contains a high-quality pseudo-random number generator (PRNG) used to
** select random [ROWID | ROWIDs] when inserting new records into a table that
** already uses the largest possible [ROWID].  The PRNG is also used for
** the build-in random() and randomblob() SQL functions.  This interface allows
** applications to access the same PRNG for other purposes.
**
** ^A call to this routine stores N bytes of randomness into buffer P.
**
** ^The first time this routine is invoked (either internally or by
** the application) the PRNG is seeded using randomness obtained
** from the xRandomness method of the default [sqlite3_vfs] object.
** ^On all subsequent invocations, the pseudo-randomness is generated
** internally and without recourse to the [sqlite3_vfs] xRandomness
** method.
*/
SQLITE_API void sqlite3_randomness(int N, void *P);

/*
** CAPI3REF: Compile-Time Authorization Callbacks
**
** ^This routine registers an authorizer callback with a particular
** [database connection], supplied in the first argument.
** ^The authorizer callback is invoked as SQL statements are being compiled
** by [sqlite3_prepare()] or its variants [sqlite3_prepare_v2()],
** [sqlite3_prepare16()] and [sqlite3_prepare16_v2()].  ^At various
** points during the compilation process, as logic is being created
** to perform various actions, the authorizer callback is invoked to
** see if those actions are allowed.  ^The authorizer callback should
** return [SQLITE_OK] to allow the action, [SQLITE_IGNORE] to disallow the
** specific action but allow the SQL statement to continue to be
** compiled, or [SQLITE_DENY] to cause the entire SQL statement to be
** rejected with an error.  ^If the authorizer callback returns
** any value other than [SQLITE_IGNORE], [SQLITE_OK], or [SQLITE_DENY]
** then the [sqlite3_prepare_v2()] or equivalent call that triggered
** the authorizer will fail with an error message.
**
** When the callback returns [SQLITE_OK], that means the operation
** requested is ok.  ^When the callback returns [SQLITE_DENY], the
** [sqlite3_prepare_v2()] or equivalent call that triggered the
** authorizer will fail with an error message explaining that
** access is denied.
**
** ^The first parameter to the authorizer callback is a copy of the third
** parameter to the sqlite3_set_authorizer() interface. ^The second parameter
** to the callback is an integer [SQLITE_COPY | action code] that specifies
** the particular action to be authorized. ^The third through sixth parameters
** to the callback are zero-terminated strings that contain additional
** details about the action to be authorized.
**
** ^If the action code is [SQLITE_READ]
** and the callback returns [SQLITE_IGNORE] then the
** [prepared statement] statement is constructed to substitute
** a NULL value in place of the table column that would have
** been read if [SQLITE_OK] had been returned.  The [SQLITE_IGNORE]
** return can be used to deny an untrusted user access to individual
** columns of a table.
** ^If the action code is [SQLITE_DELETE] and the callback returns
** [SQLITE_IGNORE] then the [DELETE] operation proceeds but the
** [truncate optimization] is disabled and all rows are deleted individually.
**
** An authorizer is used when [sqlite3_prepare | preparing]
** SQL statements from an untrusted source, to ensure that the SQL statements
** do not try to access data they are not allowed to see, or that they do not
** try to execute malicious statements that damage the database.  For
** example, an application may allow a user to enter arbitrary
** SQL queries for evaluation by a database.  But the application does
** not want the user to be able to make arbitrary changes to the
** database.  An authorizer could then be put in place while the
** user-entered SQL is being [sqlite3_prepare | prepared] that
** disallows everything except [SELECT] statements.
**
** Applications that need to process SQL from untrusted sources
** might also consider lowering resource limits using [sqlite3_limit()]
** and limiting database size using the [max_page_count] [PRAGMA]
** in addition to using an authorizer.
**
** ^(Only a single authorizer can be in place on a database connection
** at a time.  Each call to sqlite3_set_authorizer overrides the
** previous call.)^  ^Disable the authorizer by installing a NULL callback.
** The authorizer is disabled by default.
**
** The authorizer callback must not do anything that will modify
** the database connection that invoked the authorizer callback.
** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their
** database connections for the meaning of "modify" in this paragraph.
**
** ^When [sqlite3_prepare_v2()] is used to prepare a statement, the
** statement might be re-prepared during [sqlite3_step()] due to a
** schema change.  Hence, the application should ensure that the
** correct authorizer callback remains in place during the [sqlite3_step()].
**
** ^Note that the authorizer callback is invoked only during
** [sqlite3_prepare()] or its variants.  Authorization is not
** performed during statement evaluation in [sqlite3_step()], unless
** as stated in the previous paragraph, sqlite3_step() invokes
** sqlite3_prepare_v2() to reprepare a statement after a schema change.
*/
SQLITE_API int sqlite3_set_authorizer(
  sqlite3*,
  int (*xAuth)(void*,int,const char*,const char*,const char*,const char*),
  void *pUserData
);

/*
** CAPI3REF: Authorizer Return Codes
**
** The [sqlite3_set_authorizer | authorizer callback function] must
** return either [SQLITE_OK] or one of these two constants in order
** to signal SQLite whether or not the action is permitted.  See the
** [sqlite3_set_authorizer | authorizer documentation] for additional
** information.
**
** Note that SQLITE_IGNORE is also used as a [SQLITE_ROLLBACK | return code]
** from the [sqlite3_vtab_on_conflict()] interface.
*/
#define SQLITE_DENY   1   /* Abort the SQL statement with an error */
#define SQLITE_IGNORE 2   /* Don't allow access, but don't generate an error */

/*
** CAPI3REF: Authorizer Action Codes
**
** The [sqlite3_set_authorizer()] interface registers a callback function
** that is invoked to authorize certain SQL statement actions.  The
** second parameter to the callback is an integer code that specifies
** what action is being authorized.  These are the integer action codes that
** the authorizer callback may be passed.
**
** These action code values signify what kind of operation is to be
** authorized.  The 3rd and 4th parameters to the authorization
** callback function will be parameters or NULL depending on which of these
** codes is used as the second parameter.  ^(The 5th parameter to the
** authorizer callback is the name of the database ("main", "temp",
** etc.) if applicable.)^  ^The 6th parameter to the authorizer callback
** is the name of the inner-most trigger or view that is responsible for
** the access attempt or NULL if this access attempt is directly from
** top-level SQL code.
*/
/******************************************* 3rd ************ 4th ***********/
#define SQLITE_CREATE_INDEX          1   /* Index Name      Table Name      */
#define SQLITE_CREATE_TABLE          2   /* Table Name      NULL            */
#define SQLITE_CREATE_TEMP_INDEX     3   /* Index Name      Table Name      */
#define SQLITE_CREATE_TEMP_TABLE     4   /* Table Name      NULL            */
#define SQLITE_CREATE_TEMP_TRIGGER   5   /* Trigger Name    Table Name      */
#define SQLITE_CREATE_TEMP_VIEW      6   /* View Name       NULL            */
#define SQLITE_CREATE_TRIGGER        7   /* Trigger Name    Table Name      */
#define SQLITE_CREATE_VIEW           8   /* View Name       NULL            */
#define SQLITE_DELETE                9   /* Table Name      NULL            */
#define SQLITE_DROP_INDEX           10   /* Index Name      Table Name      */
#define SQLITE_DROP_TABLE           11   /* Table Name      NULL            */
#define SQLITE_DROP_TEMP_INDEX      12   /* Index Name      Table Name      */
#define SQLITE_DROP_TEMP_TABLE      13   /* Table Name      NULL            */
#define SQLITE_DROP_TEMP_TRIGGER    14   /* Trigger Name    Table Name      */
#define SQLITE_DROP_TEMP_VIEW       15   /* View Name       NULL            */
#define SQLITE_DROP_TRIGGER         16   /* Trigger Name    Table Name      */
#define SQLITE_DROP_VIEW            17   /* View Name       NULL            */
#define SQLITE_INSERT               18   /* Table Name      NULL            */
#define SQLITE_PRAGMA               19   /* Pragma Name     1st arg or NULL */
#define SQLITE_READ                 20   /* Table Name      Column Name     */
#define SQLITE_SELECT               21   /* NULL            NULL            */
#define SQLITE_TRANSACTION          22   /* Operation       NULL            */
#define SQLITE_UPDATE               23   /* Table Name      Column Name     */
#define SQLITE_ATTACH               24   /* Filename        NULL            */
#define SQLITE_DETACH               25   /* Database Name   NULL            */
#define SQLITE_ALTER_TABLE          26   /* Database Name   Table Name      */
#define SQLITE_REINDEX              27   /* Index Name      NULL            */
#define SQLITE_ANALYZE              28   /* Table Name      NULL            */
#define SQLITE_CREATE_VTABLE        29   /* Table Name      Module Name     */
#define SQLITE_DROP_VTABLE          30   /* Table Name      Module Name     */
#define SQLITE_FUNCTION             31   /* NULL            Function Name   */
#define SQLITE_SAVEPOINT            32   /* Operation       Savepoint Name  */
#define SQLITE_COPY                  0   /* No longer used */

/*
** CAPI3REF: Tracing And Profiling Functions
**
** These routines register callback functions that can be used for
** tracing and profiling the execution of SQL statements.
**
** ^The callback function registered by sqlite3_trace() is invoked at
** various times when an SQL statement is being run by [sqlite3_step()].
** ^The sqlite3_trace() callback is invoked with a UTF-8 rendering of the
** SQL statement text as the statement first begins executing.
** ^(Additional sqlite3_trace() callbacks might occur
** as each triggered subprogram is entered.  The callbacks for triggers
** contain a UTF-8 SQL comment that identifies the trigger.)^
**
** ^The callback function registered by sqlite3_profile() is invoked
** as each SQL statement finishes.  ^The profile callback contains
** the original statement text and an estimate of wall-clock time
** of how long that statement took to run.  ^The profile callback
** time is in units of nanoseconds, however the current implementation
** is only capable of millisecond resolution so the six least significant
** digits in the time are meaningless.  Future versions of SQLite
** might provide greater resolution on the profiler callback.  The
** sqlite3_profile() function is considered experimental and is
** subject to change in future versions of SQLite.
*/
SQLITE_API void *sqlite3_trace(sqlite3*, void(*xTrace)(void*,const char*), void*);
SQLITE_API SQLITE_EXPERIMENTAL void *sqlite3_profile(sqlite3*,
   void(*xProfile)(void*,const char*,sqlite3_uint64), void*);

/*
** CAPI3REF: Query Progress Callbacks
**
** ^The sqlite3_progress_handler(D,N,X,P) interface causes the callback
** function X to be invoked periodically during long running calls to
** [sqlite3_exec()], [sqlite3_step()] and [sqlite3_get_table()] for
** database connection D.  An example use for this
** interface is to keep a GUI updated during a large query.
**
** ^The parameter P is passed through as the only parameter to the
** callback function X.  ^The parameter N is the number of
** [virtual machine instructions] that are evaluated between successive
** invocations of the callback X.
**
** ^Only a single progress handler may be defined at one time per
** [database connection]; setting a new progress handler cancels the
** old one.  ^Setting parameter X to NULL disables the progress handler.
** ^The progress handler is also disabled by setting N to a value less
** than 1.
**
** ^If the progress callback returns non-zero, the operation is
** interrupted.  This feature can be used to implement a
** "Cancel" button on a GUI progress dialog box.
**
** The progress handler callback must not do anything that will modify
** the database connection that invoked the progress handler.
** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their
** database connections for the meaning of "modify" in this paragraph.
**
*/
SQLITE_API void sqlite3_progress_handler(sqlite3*, int, int(*)(void*), void*);

/*
** CAPI3REF: Opening A New Database Connection
**
** ^These routines open an SQLite database file as specified by the
** filename argument. ^The filename argument is interpreted as UTF-8 for
** sqlite3_open() and sqlite3_open_v2() and as UTF-16 in the native byte
** order for sqlite3_open16(). ^(A [database connection] handle is usually
** returned in *ppDb, even if an error occurs.  The only exception is that
** if SQLite is unable to allocate memory to hold the [sqlite3] object,
** a NULL will be written into *ppDb instead of a pointer to the [sqlite3]
** object.)^ ^(If the database is opened (and/or created) successfully, then
** [SQLITE_OK] is returned.  Otherwise an [error code] is returned.)^ ^The
** [sqlite3_errmsg()] or [sqlite3_errmsg16()] routines can be used to obtain
** an English language description of the error following a failure of any
** of the sqlite3_open() routines.
**
** ^The default encoding for the database will be UTF-8 if
** sqlite3_open() or sqlite3_open_v2() is called and
** UTF-16 in the native byte order if sqlite3_open16() is used.
**
** Whether or not an error occurs when it is opened, resources
** associated with the [database connection] handle should be released by
** passing it to [sqlite3_close()] when it is no longer required.
**
** The sqlite3_open_v2() interface works like sqlite3_open()
** except that it accepts two additional parameters for additional control
** over the new database connection.  ^(The flags parameter to
** sqlite3_open_v2() can take one of
** the following three values, optionally combined with the
** [SQLITE_OPEN_NOMUTEX], [SQLITE_OPEN_FULLMUTEX], [SQLITE_OPEN_SHAREDCACHE],
** [SQLITE_OPEN_PRIVATECACHE], and/or [SQLITE_OPEN_URI] flags:)^
**
** 
    
** ^(
    [SQLITE_OPEN_READONLY]
    
** 
    The database is opened in read-only mode.  If the database does not
** already exist, an error is returned.
    )^
**
** ^(
    [SQLITE_OPEN_READWRITE]
    
** 
    The database is opened for reading and writing if possible, or reading
** only if the file is write protected by the operating system.  In either
** case the database must already exist, otherwise an error is returned.
    )^
**
** ^(
    [SQLITE_OPEN_READWRITE] | [SQLITE_OPEN_CREATE]
    
** 
    The database is opened for reading and writing, and is created if
** it does not already exist. This is the behavior that is always used for
** sqlite3_open() and sqlite3_open16().
    )^
** 
    
**
** If the 3rd parameter to sqlite3_open_v2() is not one of the
** combinations shown above optionally combined with other
** [SQLITE_OPEN_READONLY | SQLITE_OPEN_* bits]
** then the behavior is undefined.
**
** ^If the [SQLITE_OPEN_NOMUTEX] flag is set, then the database connection
** opens in the multi-thread [threading mode] as long as the single-thread
** mode has not been set at compile-time or start-time.  ^If the
** [SQLITE_OPEN_FULLMUTEX] flag is set then the database connection opens
** in the serialized [threading mode] unless single-thread was
** previously selected at compile-time or start-time.
** ^The [SQLITE_OPEN_SHAREDCACHE] flag causes the database connection to be
** eligible to use [shared cache mode], regardless of whether or not shared
** cache is enabled using [sqlite3_enable_shared_cache()].  ^The
** [SQLITE_OPEN_PRIVATECACHE] flag causes the database connection to not
** participate in [shared cache mode] even if it is enabled.
**
** ^The fourth parameter to sqlite3_open_v2() is the name of the
** [sqlite3_vfs] object that defines the operating system interface that
** the new database connection should use.  ^If the fourth parameter is
** a NULL pointer then the default [sqlite3_vfs] object is used.
**
** ^If the filename is ":memory:", then a private, temporary in-memory database
** is created for the connection.  ^This in-memory database will vanish when
** the database connection is closed.  Future versions of SQLite might
** make use of additional special filenames that begin with the ":" character.
** It is recommended that when a database filename actually does begin with
** a ":" character you should prefix the filename with a pathname such as
** "./" to avoid ambiguity.
**
** ^If the filename is an empty string, then a private, temporary
** on-disk database will be created.  ^This private database will be
** automatically deleted as soon as the database connection is closed.
**
** [[URI filenames in sqlite3_open()]] 
    URI Filenames
    
**
** ^If [URI filename] interpretation is enabled, and the filename argument
** begins with "file:", then the filename is interpreted as a URI. ^URI
** filename interpretation is enabled if the [SQLITE_OPEN_URI] flag is
** set in the fourth argument to sqlite3_open_v2(), or if it has
** been enabled globally using the [SQLITE_CONFIG_URI] option with the
** [sqlite3_config()] method or by the [SQLITE_USE_URI] compile-time option.
** As of SQLite version 3.7.7, URI filename interpretation is turned off
** by default, but future releases of SQLite might enable URI filename
** interpretation by default.  See "[URI filenames]" for additional
** information.
**
** URI filenames are parsed according to RFC 3986. ^If the URI contains an
** authority, then it must be either an empty string or the string
** "localhost". ^If the authority is not an empty string or "localhost", an
** error is returned to the caller. ^The fragment component of a URI, if
** present, is ignored.
**
** ^SQLite uses the path component of the URI as the name of the disk file
** which contains the database. ^If the path begins with a '/' character,
** then it is interpreted as an absolute path. ^If the path does not begin
** with a '/' (meaning that the authority section is omitted from the URI)
** then the path is interpreted as a relative path.
** ^On windows, the first component of an absolute path
** is a drive specification (e.g. "C:").
**
** [[core URI query parameters]]
** The query component of a URI may contain parameters that are interpreted
** either by SQLite itself, or by a [VFS | custom VFS implementation].
** SQLite interprets the following three query parameters:
**
** 
      
**   
    •  vfs: ^The "vfs" parameter may be used to specify the name of
**     a VFS object that provides the operating system interface that should
**     be used to access the database file on disk. ^If this option is set to
**     an empty string the default VFS object is used. ^Specifying an unknown
**     VFS is an error. ^If sqlite3_open_v2() is used and the vfs option is
**     present, then the VFS specified by the option takes precedence over
**     the value passed as the fourth parameter to sqlite3_open_v2().
**
**   
    •  mode: ^(The mode parameter may be set to either "ro", "rw" or
**     "rwc". Attempting to set it to any other value is an error)^.
**     ^If "ro" is specified, then the database is opened for read-only
**     access, just as if the [SQLITE_OPEN_READONLY] flag had been set in the
**     third argument to sqlite3_prepare_v2(). ^If the mode option is set to
**     "rw", then the database is opened for read-write (but not create)
**     access, as if SQLITE_OPEN_READWRITE (but not SQLITE_OPEN_CREATE) had
**     been set. ^Value "rwc" is equivalent to setting both
**     SQLITE_OPEN_READWRITE and SQLITE_OPEN_CREATE. ^If sqlite3_open_v2() is
**     used, it is an error to specify a value for the mode parameter that is
**     less restrictive than that specified by the flags passed as the third
**     parameter.
**
**   
    •  cache: ^The cache parameter may be set to either "shared" or
**     "private". ^Setting it to "shared" is equivalent to setting the
**     SQLITE_OPEN_SHAREDCACHE bit in the flags argument passed to
**     sqlite3_open_v2(). ^Setting the cache parameter to "private" is
**     equivalent to setting the SQLITE_OPEN_PRIVATECACHE bit.
**     ^If sqlite3_open_v2() is used and the "cache" parameter is present in
**     a URI filename, its value overrides any behaviour requested by setting
**     SQLITE_OPEN_PRIVATECACHE or SQLITE_OPEN_SHAREDCACHE flag.
** 
    
**
** ^Specifying an unknown parameter in the query component of a URI is not an
** error.  Future versions of SQLite might understand additional query
** parameters.  See "[query parameters with special meaning to SQLite]" for
** additional information.
**
** [[URI filename examples]] 
    URI filename examples
    
**
** 
** 
     URI filenames  Results
** 
     file:data.db 
**          Open the file "data.db" in the current directory.
** 
     file:/home/fred/data.db
    
**          file:///home/fred/data.db 
    
**          file://localhost/home/fred/data.db 
         		
**          Open the database file "/home/fred/data.db".
** 
     file://darkstar/home/fred/data.db 
**          An error. "darkstar" is not a recognized authority.
** 
    
**          file:///C:/Documents%20and%20Settings/fred/Desktop/data.db
**      Windows only: Open the file "data.db" on fred's desktop on drive
**          C:. Note that the %20 escaping in this example is not strictly
**          necessary - space characters can be used literally
**          in URI filenames.
** 
     file:data.db?mode=ro&cache=private 
**          Open file "data.db" in the current directory for read-only access.
**          Regardless of whether or not shared-cache mode is enabled by
**          default, use a private cache.
** 
     file:/home/fred/data.db?vfs=unix-nolock 
**          Open file "/home/fred/data.db". Use the special VFS "unix-nolock".
** 
     file:data.db?mode=readonly 
**          An error. "readonly" is not a valid option for the "mode" parameter.
** 
    
**
** ^URI hexadecimal escape sequences (%HH) are supported within the path and
** query components of a URI. A hexadecimal escape sequence consists of a
** percent sign - "%" - followed by exactly two hexadecimal digits
** specifying an octet value. ^Before the path or query components of a
** URI filename are interpreted, they are encoded using UTF-8 and all
** hexadecimal escape sequences replaced by a single byte containing the
** corresponding octet. If this process generates an invalid UTF-8 encoding,
** the results are undefined.
**
** Note to Windows users:  The encoding used for the filename argument
** of sqlite3_open() and sqlite3_open_v2() must be UTF-8, not whatever
** codepage is currently defined.  Filenames containing international
** characters must be converted to UTF-8 prior to passing them into
** sqlite3_open() or sqlite3_open_v2().
*/
SQLITE_API int sqlite3_open(
  const char *filename,   /* Database filename (UTF-8) */
  sqlite3 **ppDb          /* OUT: SQLite db handle */
);
SQLITE_API int sqlite3_open16(
  const void *filename,   /* Database filename (UTF-16) */
  sqlite3 **ppDb          /* OUT: SQLite db handle */
);
SQLITE_API int sqlite3_open_v2(
  const char *filename,   /* Database filename (UTF-8) */
  sqlite3 **ppDb,         /* OUT: SQLite db handle */
  int flags,              /* Flags */
  const char *zVfs        /* Name of VFS module to use */
);

/*
** CAPI3REF: Obtain Values For URI Parameters
**
** These are utility routines, useful to VFS implementations, that check
** to see if a database file was a URI that contained a specific query
** parameter, and if so obtains the value of that query parameter.
**
** If F is the database filename pointer passed into the xOpen() method of
** a VFS implementation when the flags parameter to xOpen() has one or
** more of the [SQLITE_OPEN_URI] or [SQLITE_OPEN_MAIN_DB] bits set and
** P is the name of the query parameter, then
** sqlite3_uri_parameter(F,P) returns the value of the P
** parameter if it exists or a NULL pointer if P does not appear as a
** query parameter on F.  If P is a query parameter of F
** has no explicit value, then sqlite3_uri_parameter(F,P) returns
** a pointer to an empty string.
**
** The sqlite3_uri_boolean(F,P,B) routine assumes that P is a boolean
** parameter and returns true (1) or false (0) according to the value
** of P.  The value of P is true if it is "yes" or "true" or "on" or
** a non-zero number and is false otherwise.  If P is not a query parameter
** on F then sqlite3_uri_boolean(F,P,B) returns (B!=0).
**
** The sqlite3_uri_int64(F,P,D) routine converts the value of P into a
** 64-bit signed integer and returns that integer, or D if P does not
** exist.  If the value of P is something other than an integer, then
** zero is returned.
**
** If F is a NULL pointer, then sqlite3_uri_parameter(F,P) returns NULL and
** sqlite3_uri_boolean(F,P,B) returns B.  If F is not a NULL pointer and
** is not a database file pathname pointer that SQLite passed into the xOpen
** VFS method, then the behavior of this routine is undefined and probably
** undesirable.
*/
SQLITE_API const char *sqlite3_uri_parameter(const char *zFilename, const char *zParam);
SQLITE_API int sqlite3_uri_boolean(const char *zFile, const char *zParam, int bDefault);
SQLITE_API sqlite3_int64 sqlite3_uri_int64(const char*, const char*, sqlite3_int64);


/*
** CAPI3REF: Error Codes And Messages
**
** ^The sqlite3_errcode() interface returns the numeric [result code] or
** [extended result code] for the most recent failed sqlite3_* API call
** associated with a [database connection]. If a prior API call failed
** but the most recent API call succeeded, the return value from
** sqlite3_errcode() is undefined.  ^The sqlite3_extended_errcode()
** interface is the same except that it always returns the
** [extended result code] even when extended result codes are
** disabled.
**
** ^The sqlite3_errmsg() and sqlite3_errmsg16() return English-language
** text that describes the error, as either UTF-8 or UTF-16 respectively.
** ^(Memory to hold the error message string is managed internally.
** The application does not need to worry about freeing the result.
** However, the error string might be overwritten or deallocated by
** subsequent calls to other SQLite interface functions.)^
**
** When the serialized [threading mode] is in use, it might be the
** case that a second error occurs on a separate thread in between
** the time of the first error and the call to these interfaces.
** When that happens, the second error will be reported since these
** interfaces always report the most recent result.  To avoid
** this, each thread can obtain exclusive use of the [database connection] D
** by invoking [sqlite3_mutex_enter]([sqlite3_db_mutex](D)) before beginning
** to use D and invoking [sqlite3_mutex_leave]([sqlite3_db_mutex](D)) after
** all calls to the interfaces listed here are completed.
**
** If an interface fails with SQLITE_MISUSE, that means the interface
** was invoked incorrectly by the application.  In that case, the
** error code and message may or may not be set.
*/
SQLITE_API int sqlite3_errcode(sqlite3 *db);
SQLITE_API int sqlite3_extended_errcode(sqlite3 *db);
SQLITE_API const char *sqlite3_errmsg(sqlite3*);
SQLITE_API const void *sqlite3_errmsg16(sqlite3*);

/*
** CAPI3REF: SQL Statement Object
** KEYWORDS: {prepared statement} {prepared statements}
**
** An instance of this object represents a single SQL statement.
** This object is variously known as a "prepared statement" or a
** "compiled SQL statement" or simply as a "statement".
**
** The life of a statement object goes something like this:
**
** 
      
** 
    1.  Create the object using [sqlite3_prepare_v2()] or a related
**      function.
** 
    2.  Bind values to [host parameters] using the sqlite3_bind_*()
**      interfaces.
** 
    3.  Run the SQL by calling [sqlite3_step()] one or more times.
** 
    4.  Reset the statement using [sqlite3_reset()] then go back
**      to step 2.  Do this zero or more times.
** 
    5.  Destroy the object using [sqlite3_finalize()].
** 
    
**
** Refer to documentation on individual methods above for additional
** information.
*/
typedef struct sqlite3_stmt sqlite3_stmt;

/*
** CAPI3REF: Run-time Limits
**
** ^(This interface allows the size of various constructs to be limited
** on a connection by connection basis.  The first parameter is the
** [database connection] whose limit is to be set or queried.  The
** second parameter is one of the [limit categories] that define a
** class of constructs to be size limited.  The third parameter is the
** new limit for that construct.)^
**
** ^If the new limit is a negative number, the limit is unchanged.
** ^(For each limit category SQLITE_LIMIT_NAME there is a
** [limits | hard upper bound]
** set at compile-time by a C preprocessor macro called
** [limits | SQLITE_MAX_NAME].
** (The "_LIMIT_" in the name is changed to "_MAX_".))^
** ^Attempts to increase a limit above its hard upper bound are
** silently truncated to the hard upper bound.
**
** ^Regardless of whether or not the limit was changed, the
** [sqlite3_limit()] interface returns the prior value of the limit.
** ^Hence, to find the current value of a limit without changing it,
** simply invoke this interface with the third parameter set to -1.
**
** Run-time limits are intended for use in applications that manage
** both their own internal database and also databases that are controlled
** by untrusted external sources.  An example application might be a
** web browser that has its own databases for storing history and
** separate databases controlled by JavaScript applications downloaded
** off the Internet.  The internal databases can be given the
** large, default limits.  Databases managed by external sources can
** be given much smaller limits designed to prevent a denial of service
** attack.  Developers might also want to use the [sqlite3_set_authorizer()]
** interface to further control untrusted SQL.  The size of the database
** created by an untrusted script can be contained using the
** [max_page_count] [PRAGMA].
**
** New run-time limit categories may be added in future releases.
*/
SQLITE_API int sqlite3_limit(sqlite3*, int id, int newVal);

/*
** CAPI3REF: Run-Time Limit Categories
** KEYWORDS: {limit category} {*limit categories}
**
** These constants define various performance limits
** that can be lowered at run-time using [sqlite3_limit()].
** The synopsis of the meanings of the various limits is shown below.
** Additional information is available at [limits | Limits in SQLite].
**
** 
    
** [[SQLITE_LIMIT_LENGTH]] ^(
    SQLITE_LIMIT_LENGTH
    
** 
    The maximum size of any string or BLOB or table row, in bytes.
    )^
**
** [[SQLITE_LIMIT_SQL_LENGTH]] ^(
    SQLITE_LIMIT_SQL_LENGTH
    
** 
    The maximum length of an SQL statement, in bytes.
    )^
**
** [[SQLITE_LIMIT_COLUMN]] ^(
    SQLITE_LIMIT_COLUMN
    
** 
    The maximum number of columns in a table definition or in the
** result set of a [SELECT] or the maximum number of columns in an index
** or in an ORDER BY or GROUP BY clause.
    )^
**
** [[SQLITE_LIMIT_EXPR_DEPTH]] ^(
    SQLITE_LIMIT_EXPR_DEPTH
    
** 
    The maximum depth of the parse tree on any expression.
    )^
**
** [[SQLITE_LIMIT_COMPOUND_SELECT]] ^(
    SQLITE_LIMIT_COMPOUND_SELECT
    
** 
    The maximum number of terms in a compound SELECT statement.
    )^
**
** [[SQLITE_LIMIT_VDBE_OP]] ^(
    SQLITE_LIMIT_VDBE_OP
    
** 
    The maximum number of instructions in a virtual machine program
** used to implement an SQL statement.  This limit is not currently
** enforced, though that might be added in some future release of
** SQLite.
    )^
**
** [[SQLITE_LIMIT_FUNCTION_ARG]] ^(
    SQLITE_LIMIT_FUNCTION_ARG
    
** 
    The maximum number of arguments on a function.
    )^
**
** [[SQLITE_LIMIT_ATTACHED]] ^(
    SQLITE_LIMIT_ATTACHED
    
** 
    The maximum number of [ATTACH | attached databases].)^
    
**
** [[SQLITE_LIMIT_LIKE_PATTERN_LENGTH]]
** ^(
    SQLITE_LIMIT_LIKE_PATTERN_LENGTH
    
** 
    The maximum length of the pattern argument to the [LIKE] or
** [GLOB] operators.
    )^
**
** [[SQLITE_LIMIT_VARIABLE_NUMBER]]
** ^(
    SQLITE_LIMIT_VARIABLE_NUMBER
    
** 
    The maximum index number of any [parameter] in an SQL statement.)^
**
** [[SQLITE_LIMIT_TRIGGER_DEPTH]] ^(
    SQLITE_LIMIT_TRIGGER_DEPTH
    
** 
    The maximum depth of recursion for triggers.
    )^
** 
    
*/
#define SQLITE_LIMIT_LENGTH                    0
#define SQLITE_LIMIT_SQL_LENGTH                1
#define SQLITE_LIMIT_COLUMN                    2
#define SQLITE_LIMIT_EXPR_DEPTH                3
#define SQLITE_LIMIT_COMPOUND_SELECT           4
#define SQLITE_LIMIT_VDBE_OP                   5
#define SQLITE_LIMIT_FUNCTION_ARG              6
#define SQLITE_LIMIT_ATTACHED                  7
#define SQLITE_LIMIT_LIKE_PATTERN_LENGTH       8
#define SQLITE_LIMIT_VARIABLE_NUMBER           9
#define SQLITE_LIMIT_TRIGGER_DEPTH            10

/*
** CAPI3REF: Compiling An SQL Statement
** KEYWORDS: {SQL statement compiler}
**
** To execute an SQL query, it must first be compiled into a byte-code
** program using one of these routines.
**
** The first argument, "db", is a [database connection] obtained from a
** prior successful call to [sqlite3_open()], [sqlite3_open_v2()] or
** [sqlite3_open16()].  The database connection must not have been closed.
**
** The second argument, "zSql", is the statement to be compiled, encoded
** as either UTF-8 or UTF-16.  The sqlite3_prepare() and sqlite3_prepare_v2()
** interfaces use UTF-8, and sqlite3_prepare16() and sqlite3_prepare16_v2()
** use UTF-16.
**
** ^If the nByte argument is less than zero, then zSql is read up to the
** first zero terminator. ^If nByte is non-negative, then it is the maximum
** number of  bytes read from zSql.  ^When nByte is non-negative, the
** zSql string ends at either the first '\000' or '\u0000' character or
** the nByte-th byte, whichever comes first. If the caller knows
** that the supplied string is nul-terminated, then there is a small
** performance advantage to be gained by passing an nByte parameter that
** is equal to the number of bytes in the input string including
** the nul-terminator bytes as this saves SQLite from having to
** make a copy of the input string.
**
** ^If pzTail is not NULL then *pzTail is made to point to the first byte
** past the end of the first SQL statement in zSql.  These routines only
** compile the first statement in zSql, so *pzTail is left pointing to
** what remains uncompiled.
**
** ^*ppStmt is left pointing to a compiled [prepared statement] that can be
** executed using [sqlite3_step()].  ^If there is an error, *ppStmt is set
** to NULL.  ^If the input text contains no SQL (if the input is an empty
** string or a comment) then *ppStmt is set to NULL.
** The calling procedure is responsible for deleting the compiled
** SQL statement using [sqlite3_finalize()] after it has finished with it.
** ppStmt may not be NULL.
**
** ^On success, the sqlite3_prepare() family of routines return [SQLITE_OK];
** otherwise an [error code] is returned.
**
** The sqlite3_prepare_v2() and sqlite3_prepare16_v2() interfaces are
** recommended for all new programs. The two older interfaces are retained
** for backwards compatibility, but their use is discouraged.
** ^In the "v2" interfaces, the prepared statement
** that is returned (the [sqlite3_stmt] object) contains a copy of the
** original SQL text. This causes the [sqlite3_step()] interface to
** behave differently in three ways:
**
** 
      
** 
    1. 
** ^If the database schema changes, instead of returning [SQLITE_SCHEMA] as it
** always used to do, [sqlite3_step()] will automatically recompile the SQL
** statement and try to run it again.
** 
      2. 
**
** 
    2. 
** ^When an error occurs, [sqlite3_step()] will return one of the detailed
** [error codes] or [extended error codes].  ^The legacy behavior was that
** [sqlite3_step()] would only return a generic [SQLITE_ERROR] result code
** and the application would have to make a second call to [sqlite3_reset()]
** in order to find the underlying cause of the problem. With the "v2" prepare
** interfaces, the underlying reason for the error is returned immediately.
** 
      3. 
**
** 
    3. 
** ^If the specific value bound to [parameter | host parameter] in the
** WHERE clause might influence the choice of query plan for a statement,
** then the statement will be automatically recompiled, as if there had been
** a schema change, on the first  [sqlite3_step()] call following any change
** to the [sqlite3_bind_text | bindings] of that [parameter].
** ^The specific value of WHERE-clause [parameter] might influence the
** choice of query plan if the parameter is the left-hand side of a [LIKE]
** or [GLOB] operator or if the parameter is compared to an indexed column
** and the [SQLITE_ENABLE_STAT3] compile-time option is enabled.
** the
** 
      4. 
** 
    
*/
SQLITE_API int sqlite3_prepare(
  sqlite3 *db,            /* Database handle */
  const char *zSql,       /* SQL statement, UTF-8 encoded */
  int nByte,              /* Maximum length of zSql in bytes. */
  sqlite3_stmt **ppStmt,  /* OUT: Statement handle */
  const char **pzTail     /* OUT: Pointer to unused portion of zSql */
);
SQLITE_API int sqlite3_prepare_v2(
  sqlite3 *db,            /* Database handle */
  const char *zSql,       /* SQL statement, UTF-8 encoded */
  int nByte,              /* Maximum length of zSql in bytes. */
  sqlite3_stmt **ppStmt,  /* OUT: Statement handle */
  const char **pzTail     /* OUT: Pointer to unused portion of zSql */
);
SQLITE_API int sqlite3_prepare16(
  sqlite3 *db,            /* Database handle */
  const void *zSql,       /* SQL statement, UTF-16 encoded */
  int nByte,              /* Maximum length of zSql in bytes. */
  sqlite3_stmt **ppStmt,  /* OUT: Statement handle */
  const void **pzTail     /* OUT: Pointer to unused portion of zSql */
);
SQLITE_API int sqlite3_prepare16_v2(
  sqlite3 *db,            /* Database handle */
  const void *zSql,       /* SQL statement, UTF-16 encoded */
  int nByte,              /* Maximum length of zSql in bytes. */
  sqlite3_stmt **ppStmt,  /* OUT: Statement handle */
  const void **pzTail     /* OUT: Pointer to unused portion of zSql */
);

/*
** CAPI3REF: Retrieving Statement SQL
**
** ^This interface can be used to retrieve a saved copy of the original
** SQL text used to create a [prepared statement] if that statement was
** compiled using either [sqlite3_prepare_v2()] or [sqlite3_prepare16_v2()].
*/
SQLITE_API const char *sqlite3_sql(sqlite3_stmt *pStmt);

/*
** CAPI3REF: Determine If An SQL Statement Writes The Database
**
** ^The sqlite3_stmt_readonly(X) interface returns true (non-zero) if
** and only if the [prepared statement] X makes no direct changes to
** the content of the database file.
**
** Note that [application-defined SQL functions] or
** [virtual tables] might change the database indirectly as a side effect.
** ^(For example, if an application defines a function "eval()" that
** calls [sqlite3_exec()], then the following SQL statement would
** change the database file through side-effects:
**
** 
    **    SELECT eval('DELETE FROM t1') FROM t2;
** 
    
**
** But because the [SELECT] statement does not change the database file
** directly, sqlite3_stmt_readonly() would still return true.)^
**
** ^Transaction control statements such as [BEGIN], [COMMIT], [ROLLBACK],
** [SAVEPOINT], and [RELEASE] cause sqlite3_stmt_readonly() to return true,
** since the statements themselves do not actually modify the database but
** rather they control the timing of when other statements modify the
** database.  ^The [ATTACH] and [DETACH] statements also cause
** sqlite3_stmt_readonly() to return true since, while those statements
** change the configuration of a database connection, they do not make
** changes to the content of the database files on disk.
*/
SQLITE_API int sqlite3_stmt_readonly(sqlite3_stmt *pStmt);

/*
** CAPI3REF: Determine If A Prepared Statement Has Been Reset
**
** ^The sqlite3_stmt_busy(S) interface returns true (non-zero) if the
** [prepared statement] S has been stepped at least once using
** [sqlite3_step(S)] but has not run to completion and/or has not
** been reset using [sqlite3_reset(S)].  ^The sqlite3_stmt_busy(S)
** interface returns false if S is a NULL pointer.  If S is not a
** NULL pointer and is not a pointer to a valid [prepared statement]
** object, then the behavior is undefined and probably undesirable.
**
** This interface can be used in combination [sqlite3_next_stmt()]
** to locate all prepared statements associated with a database
** connection that are in need of being reset.  This can be used,
** for example, in diagnostic routines to search for prepared
** statements that are holding a transaction open.
*/
SQLITE_API int sqlite3_stmt_busy(sqlite3_stmt*);

/*
** CAPI3REF: Dynamically Typed Value Object
** KEYWORDS: {protected sqlite3_value} {unprotected sqlite3_value}
**
** SQLite uses the sqlite3_value object to represent all values
** that can be stored in a database table. SQLite uses dynamic typing
** for the values it stores.  ^Values stored in sqlite3_value objects
** can be integers, floating point values, strings, BLOBs, or NULL.
**
** An sqlite3_value object may be either "protected" or "unprotected".
** Some interfaces require a protected sqlite3_value.  Other interfaces
** will accept either a protected or an unprotected sqlite3_value.
** Every interface that accepts sqlite3_value arguments specifies
** whether or not it requires a protected sqlite3_value.
**
** The terms "protected" and "unprotected" refer to whether or not
** a mutex is held.  An internal mutex is held for a protected
** sqlite3_value object but no mutex is held for an unprotected
** sqlite3_value object.  If SQLite is compiled to be single-threaded
** (with [SQLITE_THREADSAFE=0] and with [sqlite3_threadsafe()] returning 0)
** or if SQLite is run in one of reduced mutex modes
** [SQLITE_CONFIG_SINGLETHREAD] or [SQLITE_CONFIG_MULTITHREAD]
** then there is no distinction between protected and unprotected
** sqlite3_value objects and they can be used interchangeably.  However,
** for maximum code portability it is recommended that applications
** still make the distinction between protected and unprotected
** sqlite3_value objects even when not strictly required.
**
** ^The sqlite3_value objects that are passed as parameters into the
** implementation of [application-defined SQL functions] are protected.
** ^The sqlite3_value object returned by
** [sqlite3_column_value()] is unprotected.
** Unprotected sqlite3_value objects may only be used with
** [sqlite3_result_value()] and [sqlite3_bind_value()].
** The [sqlite3_value_blob | sqlite3_value_type()] family of
** interfaces require protected sqlite3_value objects.
*/
typedef struct Mem sqlite3_value;

/*
** CAPI3REF: SQL Function Context Object
**
** The context in which an SQL function executes is stored in an
** sqlite3_context object.  ^A pointer to an sqlite3_context object
** is always first parameter to [application-defined SQL functions].
** The application-defined SQL function implementation will pass this
** pointer through into calls to [sqlite3_result_int | sqlite3_result()],
** [sqlite3_aggregate_context()], [sqlite3_user_data()],
** [sqlite3_context_db_handle()], [sqlite3_get_auxdata()],
** and/or [sqlite3_set_auxdata()].
*/
typedef struct sqlite3_context sqlite3_context;

/*
** CAPI3REF: Binding Values To Prepared Statements
** KEYWORDS: {host parameter} {host parameters} {host parameter name}
** KEYWORDS: {SQL parameter} {SQL parameters} {parameter binding}
**
** ^(In the SQL statement text input to [sqlite3_prepare_v2()] and its variants,
** literals may be replaced by a [parameter] that matches one of following
** templates:
**
** 
      
** 
    •   ?
** 
    •   ?NNN
** 
    •   :VVV
** 
    •   @VVV
** 
    •   $VVV
** 
    
**
** In the templates above, NNN represents an integer literal,
** and VVV represents an alphanumeric identifier.)^  ^The values of these
** parameters (also called "host parameter names" or "SQL parameters")
** can be set using the sqlite3_bind_*() routines defined here.
**
** ^The first argument to the sqlite3_bind_*() routines is always
** a pointer to the [sqlite3_stmt] object returned from
** [sqlite3_prepare_v2()] or its variants.
**
** ^The second argument is the index of the SQL parameter to be set.
** ^The leftmost SQL parameter has an index of 1.  ^When the same named
** SQL parameter is used more than once, second and subsequent
** occurrences have the same index as the first occurrence.
** ^The index for named parameters can be looked up using the
** [sqlite3_bind_parameter_index()] API if desired.  ^The index
** for "?NNN" parameters is the value of NNN.
** ^The NNN value must be between 1 and the [sqlite3_limit()]
** parameter [SQLITE_LIMIT_VARIABLE_NUMBER] (default value: 999).
**
** ^The third argument is the value to bind to the parameter.
**
** ^(In those routines that have a fourth argument, its value is the
** number of bytes in the parameter.  To be clear: the value is the
** number of bytes in the value, not the number of characters.)^
** ^If the fourth parameter is negative, the length of the string is
** the number of bytes up to the first zero terminator.
** If a non-negative fourth parameter is provided to sqlite3_bind_text()
** or sqlite3_bind_text16() then that parameter must be the byte offset
** where the NUL terminator would occur assuming the string were NUL
** terminated.  If any NUL characters occur at byte offsets less than
** the value of the fourth parameter then the resulting string value will
** contain embedded NULs.  The result of expressions involving strings
** with embedded NULs is undefined.
**
** ^The fifth argument to sqlite3_bind_blob(), sqlite3_bind_text(), and
** sqlite3_bind_text16() is a destructor used to dispose of the BLOB or
** string after SQLite has finished with it.  ^The destructor is called
** to dispose of the BLOB or string even if the call to sqlite3_bind_blob(),
** sqlite3_bind_text(), or sqlite3_bind_text16() fails.
** ^If the fifth argument is
** the special value [SQLITE_STATIC], then SQLite assumes that the
** information is in static, unmanaged space and does not need to be freed.
** ^If the fifth argument has the value [SQLITE_TRANSIENT], then
** SQLite makes its own private copy of the data immediately, before
** the sqlite3_bind_*() routine returns.
**
** ^The sqlite3_bind_zeroblob() routine binds a BLOB of length N that
** is filled with zeroes.  ^A zeroblob uses a fixed amount of memory
** (just an integer to hold its size) while it is being processed.
** Zeroblobs are intended to serve as placeholders for BLOBs whose
** content is later written using
** [sqlite3_blob_open | incremental BLOB I/O] routines.
** ^A negative value for the zeroblob results in a zero-length BLOB.
**
** ^If any of the sqlite3_bind_*() routines are called with a NULL pointer
** for the [prepared statement] or with a prepared statement for which
** [sqlite3_step()] has been called more recently than [sqlite3_reset()],
** then the call will return [SQLITE_MISUSE].  If any sqlite3_bind_()
** routine is passed a [prepared statement] that has been finalized, the
** result is undefined and probably harmful.
**
** ^Bindings are not cleared by the [sqlite3_reset()] routine.
** ^Unbound parameters are interpreted as NULL.
**
** ^The sqlite3_bind_* routines return [SQLITE_OK] on success or an
** [error code] if anything goes wrong.
** ^[SQLITE_RANGE] is returned if the parameter
** index is out of range.  ^[SQLITE_NOMEM] is returned if malloc() fails.
**
** See also: [sqlite3_bind_parameter_count()],
** [sqlite3_bind_parameter_name()], and [sqlite3_bind_parameter_index()].
*/
SQLITE_API int sqlite3_bind_blob(sqlite3_stmt*, int, const void*, int n, void(*)(void*));
SQLITE_API int sqlite3_bind_double(sqlite3_stmt*, int, double);
SQLITE_API int sqlite3_bind_int(sqlite3_stmt*, int, int);
SQLITE_API int sqlite3_bind_int64(sqlite3_stmt*, int, sqlite3_int64);
SQLITE_API int sqlite3_bind_null(sqlite3_stmt*, int);
SQLITE_API int sqlite3_bind_text(sqlite3_stmt*, int, const char*, int n, void(*)(void*));
SQLITE_API int sqlite3_bind_text16(sqlite3_stmt*, int, const void*, int, void(*)(void*));
SQLITE_API int sqlite3_bind_value(sqlite3_stmt*, int, const sqlite3_value*);
SQLITE_API int sqlite3_bind_zeroblob(sqlite3_stmt*, int, int n);

/*
** CAPI3REF: Number Of SQL Parameters
**
** ^This routine can be used to find the number of [SQL parameters]
** in a [prepared statement].  SQL parameters are tokens of the
** form "?", "?NNN", ":AAA", "$AAA", or "@AAA" that serve as
** placeholders for values that are [sqlite3_bind_blob | bound]
** to the parameters at a later time.
**
** ^(This routine actually returns the index of the largest (rightmost)
** parameter. For all forms except ?NNN, this will correspond to the
** number of unique parameters.  If parameters of the ?NNN form are used,
** there may be gaps in the list.)^
**
** See also: [sqlite3_bind_blob|sqlite3_bind()],
** [sqlite3_bind_parameter_name()], and
** [sqlite3_bind_parameter_index()].
*/
SQLITE_API int sqlite3_bind_parameter_count(sqlite3_stmt*);

/*
** CAPI3REF: Name Of A Host Parameter
**
** ^The sqlite3_bind_parameter_name(P,N) interface returns
** the name of the N-th [SQL parameter] in the [prepared statement] P.
** ^(SQL parameters of the form "?NNN" or ":AAA" or "@AAA" or "$AAA"
** have a name which is the string "?NNN" or ":AAA" or "@AAA" or "$AAA"
** respectively.
** In other words, the initial ":" or "$" or "@" or "?"
** is included as part of the name.)^
** ^Parameters of the form "?" without a following integer have no name
** and are referred to as "nameless" or "anonymous parameters".
**
** ^The first host parameter has an index of 1, not 0.
**
** ^If the value N is out of range or if the N-th parameter is
** nameless, then NULL is returned.  ^The returned string is
** always in UTF-8 encoding even if the named parameter was
** originally specified as UTF-16 in [sqlite3_prepare16()] or
** [sqlite3_prepare16_v2()].
**
** See also: [sqlite3_bind_blob|sqlite3_bind()],
** [sqlite3_bind_parameter_count()], and
** [sqlite3_bind_parameter_index()].
*/
SQLITE_API const char *sqlite3_bind_parameter_name(sqlite3_stmt*, int);

/*
** CAPI3REF: Index Of A Parameter With A Given Name
**
** ^Return the index of an SQL parameter given its name.  ^The
** index value returned is suitable for use as the second
** parameter to [sqlite3_bind_blob|sqlite3_bind()].  ^A zero
** is returned if no matching parameter is found.  ^The parameter
** name must be given in UTF-8 even if the original statement
** was prepared from UTF-16 text using [sqlite3_prepare16_v2()].
**
** See also: [sqlite3_bind_blob|sqlite3_bind()],
** [sqlite3_bind_parameter_count()], and
** [sqlite3_bind_parameter_index()].
*/
SQLITE_API int sqlite3_bind_parameter_index(sqlite3_stmt*, const char *zName);

/*
** CAPI3REF: Reset All Bindings On A Prepared Statement
**
** ^Contrary to the intuition of many, [sqlite3_reset()] does not reset
** the [sqlite3_bind_blob | bindings] on a [prepared statement].
** ^Use this routine to reset all host parameters to NULL.
*/
SQLITE_API int sqlite3_clear_bindings(sqlite3_stmt*);

/*
** CAPI3REF: Number Of Columns In A Result Set
**
** ^Return the number of columns in the result set returned by the
** [prepared statement]. ^This routine returns 0 if pStmt is an SQL
** statement that does not return data (for example an [UPDATE]).
**
** See also: [sqlite3_data_count()]
*/
SQLITE_API int sqlite3_column_count(sqlite3_stmt *pStmt);

/*
** CAPI3REF: Column Names In A Result Set
**
** ^These routines return the name assigned to a particular column
** in the result set of a [SELECT] statement.  ^The sqlite3_column_name()
** interface returns a pointer to a zero-terminated UTF-8 string
** and sqlite3_column_name16() returns a pointer to a zero-terminated
** UTF-16 string.  ^The first parameter is the [prepared statement]
** that implements the [SELECT] statement. ^The second parameter is the
** column number.  ^The leftmost column is number 0.
**
** ^The returned string pointer is valid until either the [prepared statement]
** is destroyed by [sqlite3_finalize()] or until the statement is automatically
** reprepared by the first call to [sqlite3_step()] for a particular run
** or until the next call to
** sqlite3_column_name() or sqlite3_column_name16() on the same column.
**
** ^If sqlite3_malloc() fails during the processing of either routine
** (for example during a conversion from UTF-8 to UTF-16) then a
** NULL pointer is returned.
**
** ^The name of a result column is the value of the "AS" clause for
** that column, if there is an AS clause.  If there is no AS clause
** then the name of the column is unspecified and may change from
** one release of SQLite to the next.
*/
SQLITE_API const char *sqlite3_column_name(sqlite3_stmt*, int N);
SQLITE_API const void *sqlite3_column_name16(sqlite3_stmt*, int N);

/*
** CAPI3REF: Source Of Data In A Query Result
**
** ^These routines provide a means to determine the database, table, and
** table column that is the origin of a particular result column in
** [SELECT] statement.
** ^The name of the database or table or column can be returned as
** either a UTF-8 or UTF-16 string.  ^The _database_ routines return
** the database name, the _table_ routines return the table name, and
** the origin_ routines return the column name.
** ^The returned string is valid until the [prepared statement] is destroyed
** using [sqlite3_finalize()] or until the statement is automatically
** reprepared by the first call to [sqlite3_step()] for a particular run
** or until the same information is requested
** again in a different encoding.
**
** ^The names returned are the original un-aliased names of the
** database, table, and column.
**
** ^The first argument to these interfaces is a [prepared statement].
** ^These functions return information about the Nth result column returned by
** the statement, where N is the second function argument.
** ^The left-most column is column 0 for these routines.
**
** ^If the Nth column returned by the statement is an expression or
** subquery and is not a column value, then all of these functions return
** NULL.  ^These routine might also return NULL if a memory allocation error
** occurs.  ^Otherwise, they return the name of the attached database, table,
** or column that query result column was extracted from.
**
** ^As with all other SQLite APIs, those whose names end with "16" return
** UTF-16 encoded strings and the other functions return UTF-8.
**
** ^These APIs are only available if the library was compiled with the
** [SQLITE_ENABLE_COLUMN_METADATA] C-preprocessor symbol.
**
** If two or more threads call one or more of these routines against the same
** prepared statement and column at the same time then the results are
** undefined.
**
** If two or more threads call one or more
** [sqlite3_column_database_name | column metadata interfaces]
** for the same [prepared statement] and result column
** at the same time then the results are undefined.
*/
SQLITE_API const char *sqlite3_column_database_name(sqlite3_stmt*,int);
SQLITE_API const void *sqlite3_column_database_name16(sqlite3_stmt*,int);
SQLITE_API const char *sqlite3_column_table_name(sqlite3_stmt*,int);
SQLITE_API const void *sqlite3_column_table_name16(sqlite3_stmt*,int);
SQLITE_API const char *sqlite3_column_origin_name(sqlite3_stmt*,int);
SQLITE_API const void *sqlite3_column_origin_name16(sqlite3_stmt*,int);

/*
** CAPI3REF: Declared Datatype Of A Query Result
**
** ^(The first parameter is a [prepared statement].
** If this statement is a [SELECT] statement and the Nth column of the
** returned result set of that [SELECT] is a table column (not an
** expression or subquery) then the declared type of the table
** column is returned.)^  ^If the Nth column of the result set is an
** expression or subquery, then a NULL pointer is returned.
** ^The returned string is always UTF-8 encoded.
**
** ^(For example, given the database schema:
**
** CREATE TABLE t1(c1 VARIANT);
**
** and the following statement to be compiled:
**
** SELECT c1 + 1, c1 FROM t1;
**
** this routine would return the string "VARIANT" for the second result
** column (i==1), and a NULL pointer for the first result column (i==0).)^
**
** ^SQLite uses dynamic run-time typing.  ^So just because a column
** is declared to contain a particular type does not mean that the
** data stored in that column is of the declared type.  SQLite is
** strongly typed, but the typing is dynamic not static.  ^Type
** is associated with individual values, not with the containers
** used to hold those values.
*/
SQLITE_API const char *sqlite3_column_decltype(sqlite3_stmt*,int);
SQLITE_API const void *sqlite3_column_decltype16(sqlite3_stmt*,int);

/*
** CAPI3REF: Evaluate An SQL Statement
**
** After a [prepared statement] has been prepared using either
** [sqlite3_prepare_v2()] or [sqlite3_prepare16_v2()] or one of the legacy
** interfaces [sqlite3_prepare()] or [sqlite3_prepare16()], this function
** must be called one or more times to evaluate the statement.
**
** The details of the behavior of the sqlite3_step() interface depend
** on whether the statement was prepared using the newer "v2" interface
** [sqlite3_prepare_v2()] and [sqlite3_prepare16_v2()] or the older legacy
** interface [sqlite3_prepare()] and [sqlite3_prepare16()].  The use of the
** new "v2" interface is recommended for new applications but the legacy
** interface will continue to be supported.
**
** ^In the legacy interface, the return value will be either [SQLITE_BUSY],
** [SQLITE_DONE], [SQLITE_ROW], [SQLITE_ERROR], or [SQLITE_MISUSE].
** ^With the "v2" interface, any of the other [result codes] or
** [extended result codes] might be returned as well.
**
** ^[SQLITE_BUSY] means that the database engine was unable to acquire the
** database locks it needs to do its job.  ^If the statement is a [COMMIT]
** or occurs outside of an explicit transaction, then you can retry the
** statement.  If the statement is not a [COMMIT] and occurs within an
** explicit transaction then you should rollback the transaction before
** continuing.
**
** ^[SQLITE_DONE] means that the statement has finished executing
** successfully.  sqlite3_step() should not be called again on this virtual
** machine without first calling [sqlite3_reset()] to reset the virtual
** machine back to its initial state.
**
** ^If the SQL statement being executed returns any data, then [SQLITE_ROW]
** is returned each time a new row of data is ready for processing by the
** caller. The values may be accessed using the [column access functions].
** sqlite3_step() is called again to retrieve the next row of data.
**
** ^[SQLITE_ERROR] means that a run-time error (such as a constraint
** violation) has occurred.  sqlite3_step() should not be called again on
** the VM. More information may be found by calling [sqlite3_errmsg()].
** ^With the legacy interface, a more specific error code (for example,
** [SQLITE_INTERRUPT], [SQLITE_SCHEMA], [SQLITE_CORRUPT], and so forth)
** can be obtained by calling [sqlite3_reset()] on the
** [prepared statement].  ^In the "v2" interface,
** the more specific error code is returned directly by sqlite3_step().
**
** [SQLITE_MISUSE] means that the this routine was called inappropriately.
** Perhaps it was called on a [prepared statement] that has
** already been [sqlite3_finalize | finalized] or on one that had
** previously returned [SQLITE_ERROR] or [SQLITE_DONE].  Or it could
** be the case that the same database connection is being used by two or
** more threads at the same moment in time.
**
** For all versions of SQLite up to and including 3.6.23.1, a call to
** [sqlite3_reset()] was required after sqlite3_step() returned anything
** other than [SQLITE_ROW] before any subsequent invocation of
** sqlite3_step().  Failure to reset the prepared statement using
** [sqlite3_reset()] would result in an [SQLITE_MISUSE] return from
** sqlite3_step().  But after version 3.6.23.1, sqlite3_step() began
** calling [sqlite3_reset()] automatically in this circumstance rather
** than returning [SQLITE_MISUSE].  This is not considered a compatibility
** break because any application that ever receives an SQLITE_MISUSE error
** is broken by definition.  The [SQLITE_OMIT_AUTORESET] compile-time option
** can be used to restore the legacy behavior.
**
** Goofy Interface Alert: In the legacy interface, the sqlite3_step()
** API always returns a generic error code, [SQLITE_ERROR], following any
** error other than [SQLITE_BUSY] and [SQLITE_MISUSE].  You must call
** [sqlite3_reset()] or [sqlite3_finalize()] in order to find one of the
** specific [error codes] that better describes the error.
** We admit that this is a goofy design.  The problem has been fixed
** with the "v2" interface.  If you prepare all of your SQL statements
** using either [sqlite3_prepare_v2()] or [sqlite3_prepare16_v2()] instead
** of the legacy [sqlite3_prepare()] and [sqlite3_prepare16()] interfaces,
** then the more specific [error codes] are returned directly
** by sqlite3_step().  The use of the "v2" interface is recommended.
*/
SQLITE_API int sqlite3_step(sqlite3_stmt*);

/*
** CAPI3REF: Number of columns in a result set
**
** ^The sqlite3_data_count(P) interface returns the number of columns in the
** current row of the result set of [prepared statement] P.
** ^If prepared statement P does not have results ready to return
** (via calls to the [sqlite3_column_int | sqlite3_column_*()] of
** interfaces) then sqlite3_data_count(P) returns 0.
** ^The sqlite3_data_count(P) routine also returns 0 if P is a NULL pointer.
** ^The sqlite3_data_count(P) routine returns 0 if the previous call to
** [sqlite3_step](P) returned [SQLITE_DONE].  ^The sqlite3_data_count(P)
** will return non-zero if previous call to [sqlite3_step](P) returned
** [SQLITE_ROW], except in the case of the [PRAGMA incremental_vacuum]
** where it always returns zero since each step of that multi-step
** pragma returns 0 columns of data.
**
** See also: [sqlite3_column_count()]
*/
SQLITE_API int sqlite3_data_count(sqlite3_stmt *pStmt);

/*
** CAPI3REF: Fundamental Datatypes
** KEYWORDS: SQLITE_TEXT
**
** ^(Every value in SQLite has one of five fundamental datatypes:
**
** 
      
** 
    •  64-bit signed integer
** 
    •  64-bit IEEE floating point number
** 
    •  string
** 
    •  BLOB
** 
    •  NULL
** 
    )^
**
** These constants are codes for each of those types.
**
** Note that the SQLITE_TEXT constant was also used in SQLite version 2
** for a completely different meaning.  Software that links against both
** SQLite version 2 and SQLite version 3 should use SQLITE3_TEXT, not
** SQLITE_TEXT.
*/
#define SQLITE_INTEGER  1
#define SQLITE_FLOAT    2
#define SQLITE_BLOB     4
#define SQLITE_NULL     5
#ifdef SQLITE_TEXT
# undef SQLITE_TEXT
#else
# define SQLITE_TEXT     3
#endif
#define SQLITE3_TEXT     3

/*
** CAPI3REF: Result Values From A Query
** KEYWORDS: {column access functions}
**
** These routines form the "result set" interface.
**
** ^These routines return information about a single column of the current
** result row of a query.  ^In every case the first argument is a pointer
** to the [prepared statement] that is being evaluated (the [sqlite3_stmt*]
** that was returned from [sqlite3_prepare_v2()] or one of its variants)
** and the second argument is the index of the column for which information
** should be returned. ^The leftmost column of the result set has the index 0.
** ^The number of columns in the result can be determined using
** [sqlite3_column_count()].
**
** If the SQL statement does not currently point to a valid row, or if the
** column index is out of range, the result is undefined.
** These routines may only be called when the most recent call to
** [sqlite3_step()] has returned [SQLITE_ROW] and neither
** [sqlite3_reset()] nor [sqlite3_finalize()] have been called subsequently.
** If any of these routines are called after [sqlite3_reset()] or
** [sqlite3_finalize()] or after [sqlite3_step()] has returned
** something other than [SQLITE_ROW], the results are undefined.
** If [sqlite3_step()] or [sqlite3_reset()] or [sqlite3_finalize()]
** are called from a different thread while any of these routines
** are pending, then the results are undefined.
**
** ^The sqlite3_column_type() routine returns the
** [SQLITE_INTEGER | datatype code] for the initial data type
** of the result column.  ^The returned value is one of [SQLITE_INTEGER],
** [SQLITE_FLOAT], [SQLITE_TEXT], [SQLITE_BLOB], or [SQLITE_NULL].  The value
** returned by sqlite3_column_type() is only meaningful if no type
** conversions have occurred as described below.  After a type conversion,
** the value returned by sqlite3_column_type() is undefined.  Future
** versions of SQLite may change the behavior of sqlite3_column_type()
** following a type conversion.
**
** ^If the result is a BLOB or UTF-8 string then the sqlite3_column_bytes()
** routine returns the number of bytes in that BLOB or string.
** ^If the result is a UTF-16 string, then sqlite3_column_bytes() converts
** the string to UTF-8 and then returns the number of bytes.
** ^If the result is a numeric value then sqlite3_column_bytes() uses
** [sqlite3_snprintf()] to convert that value to a UTF-8 string and returns
** the number of bytes in that string.
** ^If the result is NULL, then sqlite3_column_bytes() returns zero.
**
** ^If the result is a BLOB or UTF-16 string then the sqlite3_column_bytes16()
** routine returns the number of bytes in that BLOB or string.
** ^If the result is a UTF-8 string, then sqlite3_column_bytes16() converts
** the string to UTF-16 and then returns the number of bytes.
** ^If the result is a numeric value then sqlite3_column_bytes16() uses
** [sqlite3_snprintf()] to convert that value to a UTF-16 string and returns
** the number of bytes in that string.
** ^If the result is NULL, then sqlite3_column_bytes16() returns zero.
**
** ^The values returned by [sqlite3_column_bytes()] and
** [sqlite3_column_bytes16()] do not include the zero terminators at the end
** of the string.  ^For clarity: the values returned by
** [sqlite3_column_bytes()] and [sqlite3_column_bytes16()] are the number of
** bytes in the string, not the number of characters.
**
** ^Strings returned by sqlite3_column_text() and sqlite3_column_text16(),
** even empty strings, are always zero-terminated.  ^The return
** value from sqlite3_column_blob() for a zero-length BLOB is a NULL pointer.
**
** ^The object returned by [sqlite3_column_value()] is an
** [unprotected sqlite3_value] object.  An unprotected sqlite3_value object
** may only be used with [sqlite3_bind_value()] and [sqlite3_result_value()].
** If the [unprotected sqlite3_value] object returned by
** [sqlite3_column_value()] is used in any other way, including calls
** to routines like [sqlite3_value_int()], [sqlite3_value_text()],
** or [sqlite3_value_bytes()], then the behavior is undefined.
**
** These routines attempt to convert the value where appropriate.  ^For
** example, if the internal representation is FLOAT and a text result
** is requested, [sqlite3_snprintf()] is used internally to perform the
** conversion automatically.  ^(The following table details the conversions
** that are applied:
**
** 
    
** 
** 
     Internal
    Type     		 Requested
    Type     		  Conversion
**
** 
      NULL     INTEGER    Result is 0
** 
      NULL      FLOAT     Result is 0.0
** 
      NULL       TEXT     Result is NULL pointer
** 
      NULL       BLOB     Result is NULL pointer
** 
     INTEGER    FLOAT     Convert from integer to float
** 
     INTEGER     TEXT     ASCII rendering of the integer
** 
     INTEGER     BLOB     Same as INTEGER->TEXT
** 
      FLOAT    INTEGER    Convert from float to integer
** 
      FLOAT      TEXT     ASCII rendering of the float
** 
      FLOAT      BLOB     Same as FLOAT->TEXT
** 
      TEXT     INTEGER    Use atoi()
** 
      TEXT      FLOAT     Use atof()
** 
      TEXT       BLOB     No change
** 
      BLOB     INTEGER    Convert to TEXT then use atoi()
** 
      BLOB      FLOAT     Convert to TEXT then use atof()
** 
      BLOB       TEXT     Add a zero terminator if needed
** 
    
** 
    )^
**
** The table above makes reference to standard C library functions atoi()
** and atof().  SQLite does not really use these functions.  It has its
** own equivalent internal routines.  The atoi() and atof() names are
** used in the table for brevity and because they are familiar to most
** C programmers.
**
** Note that when type conversions occur, pointers returned by prior
** calls to sqlite3_column_blob(), sqlite3_column_text(), and/or
** sqlite3_column_text16() may be invalidated.
** Type conversions and pointer invalidations might occur
** in the following cases:
**
** 
      
** 
    •  The initial content is a BLOB and sqlite3_column_text() or
**      sqlite3_column_text16() is called.  A zero-terminator might
**      need to be added to the string.
      • 
** 
    •  The initial content is UTF-8 text and sqlite3_column_bytes16() or
**      sqlite3_column_text16() is called.  The content must be converted
**      to UTF-16.
      • 
** 
    •  The initial content is UTF-16 text and sqlite3_column_bytes() or
**      sqlite3_column_text() is called.  The content must be converted
**      to UTF-8.
      • 
** 
    
**
** ^Conversions between UTF-16be and UTF-16le are always done in place and do
** not invalidate a prior pointer, though of course the content of the buffer
** that the prior pointer references will have been modified.  Other kinds
** of conversion are done in place when it is possible, but sometimes they
** are not possible and in those cases prior pointers are invalidated.
**
** The safest and easiest to remember policy is to invoke these routines
** in one of the following ways:
**
** 
      
**  
    • sqlite3_column_text() followed by sqlite3_column_bytes()
      • 
**  
    • sqlite3_column_blob() followed by sqlite3_column_bytes()
      • 
**  
    • sqlite3_column_text16() followed by sqlite3_column_bytes16()
      • 
** 
    
**
** In other words, you should call sqlite3_column_text(),
** sqlite3_column_blob(), or sqlite3_column_text16() first to force the result
** into the desired format, then invoke sqlite3_column_bytes() or
** sqlite3_column_bytes16() to find the size of the result.  Do not mix calls
** to sqlite3_column_text() or sqlite3_column_blob() with calls to
** sqlite3_column_bytes16(), and do not mix calls to sqlite3_column_text16()
** with calls to sqlite3_column_bytes().
**
** ^The pointers returned are valid until a type conversion occurs as
** described above, or until [sqlite3_step()] or [sqlite3_reset()] or
** [sqlite3_finalize()] is called.  ^The memory space used to hold strings
** and BLOBs is freed automatically.  Do not pass the pointers returned
** [sqlite3_column_blob()], [sqlite3_column_text()], etc. into
** [sqlite3_free()].
**
** ^(If a memory allocation error occurs during the evaluation of any
** of these routines, a default value is returned.  The default value
** is either the integer 0, the floating point number 0.0, or a NULL
** pointer.  Subsequent calls to [sqlite3_errcode()] will return
** [SQLITE_NOMEM].)^
*/
SQLITE_API const void *sqlite3_column_blob(sqlite3_stmt*, int iCol);
SQLITE_API int sqlite3_column_bytes(sqlite3_stmt*, int iCol);
SQLITE_API int sqlite3_column_bytes16(sqlite3_stmt*, int iCol);
SQLITE_API double sqlite3_column_double(sqlite3_stmt*, int iCol);
SQLITE_API int sqlite3_column_int(sqlite3_stmt*, int iCol);
SQLITE_API sqlite3_int64 sqlite3_column_int64(sqlite3_stmt*, int iCol);
SQLITE_API const unsigned char *sqlite3_column_text(sqlite3_stmt*, int iCol);
SQLITE_API const void *sqlite3_column_text16(sqlite3_stmt*, int iCol);
SQLITE_API int sqlite3_column_type(sqlite3_stmt*, int iCol);
SQLITE_API sqlite3_value *sqlite3_column_value(sqlite3_stmt*, int iCol);

/*
** CAPI3REF: Destroy A Prepared Statement Object
**
** ^The sqlite3_finalize() function is called to delete a [prepared statement].
** ^If the most recent evaluation of the statement encountered no errors
** or if the statement is never been evaluated, then sqlite3_finalize() returns
** SQLITE_OK.  ^If the most recent evaluation of statement S failed, then
** sqlite3_finalize(S) returns the appropriate [error code] or
** [extended error code].
**
** ^The sqlite3_finalize(S) routine can be called at any point during
** the life cycle of [prepared statement] S:
** before statement S is ever evaluated, after
** one or more calls to [sqlite3_reset()], or after any call
** to [sqlite3_step()] regardless of whether or not the statement has
** completed execution.
**
** ^Invoking sqlite3_finalize() on a NULL pointer is a harmless no-op.
**
** The application must finalize every [prepared statement] in order to avoid
** resource leaks.  It is a grievous error for the application to try to use
** a prepared statement after it has been finalized.  Any use of a prepared
** statement after it has been finalized can result in undefined and
** undesirable behavior such as segfaults and heap corruption.
*/
SQLITE_API int sqlite3_finalize(sqlite3_stmt *pStmt);

/*
** CAPI3REF: Reset A Prepared Statement Object
**
** The sqlite3_reset() function is called to reset a [prepared statement]
** object back to its initial state, ready to be re-executed.
** ^Any SQL statement variables that had values bound to them using
** the [sqlite3_bind_blob | sqlite3_bind_*() API] retain their values.
** Use [sqlite3_clear_bindings()] to reset the bindings.
**
** ^The [sqlite3_reset(S)] interface resets the [prepared statement] S
** back to the beginning of its program.
**
** ^If the most recent call to [sqlite3_step(S)] for the
** [prepared statement] S returned [SQLITE_ROW] or [SQLITE_DONE],
** or if [sqlite3_step(S)] has never before been called on S,
** then [sqlite3_reset(S)] returns [SQLITE_OK].
**
** ^If the most recent call to [sqlite3_step(S)] for the
** [prepared statement] S indicated an error, then
** [sqlite3_reset(S)] returns an appropriate [error code].
**
** ^The [sqlite3_reset(S)] interface does not change the values
** of any [sqlite3_bind_blob|bindings] on the [prepared statement] S.
*/
SQLITE_API int sqlite3_reset(sqlite3_stmt *pStmt);

/*
** CAPI3REF: Create Or Redefine SQL Functions
** KEYWORDS: {function creation routines}
** KEYWORDS: {application-defined SQL function}
** KEYWORDS: {application-defined SQL functions}
**
** ^These functions (collectively known as "function creation routines")
** are used to add SQL functions or aggregates or to redefine the behavior
** of existing SQL functions or aggregates.  The only differences between
** these routines are the text encoding expected for
** the second parameter (the name of the function being created)
** and the presence or absence of a destructor callback for
** the application data pointer.
**
** ^The first parameter is the [database connection] to which the SQL
** function is to be added.  ^If an application uses more than one database
** connection then application-defined SQL functions must be added
** to each database connection separately.
**
** ^The second parameter is the name of the SQL function to be created or
** redefined.  ^The length of the name is limited to 255 bytes in a UTF-8
** representation, exclusive of the zero-terminator.  ^Note that the name
** length limit is in UTF-8 bytes, not characters nor UTF-16 bytes.
** ^Any attempt to create a function with a longer name
** will result in [SQLITE_MISUSE] being returned.
**
** ^The third parameter (nArg)
** is the number of arguments that the SQL function or
** aggregate takes. ^If this parameter is -1, then the SQL function or
** aggregate may take any number of arguments between 0 and the limit
** set by [sqlite3_limit]([SQLITE_LIMIT_FUNCTION_ARG]).  If the third
** parameter is less than -1 or greater than 127 then the behavior is
** undefined.
**
** ^The fourth parameter, eTextRep, specifies what
** [SQLITE_UTF8 | text encoding] this SQL function prefers for
** its parameters.  Every SQL function implementation must be able to work
** with UTF-8, UTF-16le, or UTF-16be.  But some implementations may be
** more efficient with one encoding than another.  ^An application may
** invoke sqlite3_create_function() or sqlite3_create_function16() multiple
** times with the same function but with different values of eTextRep.
** ^When multiple implementations of the same function are available, SQLite
** will pick the one that involves the least amount of data conversion.
** If there is only a single implementation which does not care what text
** encoding is used, then the fourth argument should be [SQLITE_ANY].
**
** ^(The fifth parameter is an arbitrary pointer.  The implementation of the
** function can gain access to this pointer using [sqlite3_user_data()].)^
**
** ^The sixth, seventh and eighth parameters, xFunc, xStep and xFinal, are
** pointers to C-language functions that implement the SQL function or
** aggregate. ^A scalar SQL function requires an implementation of the xFunc
** callback only; NULL pointers must be passed as the xStep and xFinal
** parameters. ^An aggregate SQL function requires an implementation of xStep
** and xFinal and NULL pointer must be passed for xFunc. ^To delete an existing
** SQL function or aggregate, pass NULL pointers for all three function
** callbacks.
**
** ^(If the ninth parameter to sqlite3_create_function_v2() is not NULL,
** then it is destructor for the application data pointer.
** The destructor is invoked when the function is deleted, either by being
** overloaded or when the database connection closes.)^
** ^The destructor is also invoked if the call to
** sqlite3_create_function_v2() fails.
** ^When the destructor callback of the tenth parameter is invoked, it
** is passed a single argument which is a copy of the application data
** pointer which was the fifth parameter to sqlite3_create_function_v2().
**
** ^It is permitted to register multiple implementations of the same
** functions with the same name but with either differing numbers of
** arguments or differing preferred text encodings.  ^SQLite will use
** the implementation that most closely matches the way in which the
** SQL function is used.  ^A function implementation with a non-negative
** nArg parameter is a better match than a function implementation with
** a negative nArg.  ^A function where the preferred text encoding
** matches the database encoding is a better
** match than a function where the encoding is different.
** ^A function where the encoding difference is between UTF16le and UTF16be
** is a closer match than a function where the encoding difference is
** between UTF8 and UTF16.
**
** ^Built-in functions may be overloaded by new application-defined functions.
**
** ^An application-defined function is permitted to call other
** SQLite interfaces.  However, such calls must not
** close the database connection nor finalize or reset the prepared
** statement in which the function is running.
*/
SQLITE_API int sqlite3_create_function(
  sqlite3 *db,
  const char *zFunctionName,
  int nArg,
  int eTextRep,
  void *pApp,
  void (*xFunc)(sqlite3_context*,int,sqlite3_value**),
  void (*xStep)(sqlite3_context*,int,sqlite3_value**),
  void (*xFinal)(sqlite3_context*)
);
SQLITE_API int sqlite3_create_function16(
  sqlite3 *db,
  const void *zFunctionName,
  int nArg,
  int eTextRep,
  void *pApp,
  void (*xFunc)(sqlite3_context*,int,sqlite3_value**),
  void (*xStep)(sqlite3_context*,int,sqlite3_value**),
  void (*xFinal)(sqlite3_context*)
);
SQLITE_API int sqlite3_create_function_v2(
  sqlite3 *db,
  const char *zFunctionName,
  int nArg,
  int eTextRep,
  void *pApp,
  void (*xFunc)(sqlite3_context*,int,sqlite3_value**),
  void (*xStep)(sqlite3_context*,int,sqlite3_value**),
  void (*xFinal)(sqlite3_context*),
  void(*xDestroy)(void*)
);

/*
** CAPI3REF: Text Encodings
**
** These constant define integer codes that represent the various
** text encodings supported by SQLite.
*/
#define SQLITE_UTF8           1
#define SQLITE_UTF16LE        2
#define SQLITE_UTF16BE        3
#define SQLITE_UTF16          4    /* Use native byte order */
#define SQLITE_ANY            5    /* sqlite3_create_function only */
#define SQLITE_UTF16_ALIGNED  8    /* sqlite3_create_collation only */

/*
** CAPI3REF: Deprecated Functions
** DEPRECATED
**
** These functions are [deprecated].  In order to maintain
** backwards compatibility with older code, these functions continue
** to be supported.  However, new applications should avoid
** the use of these functions.  To help encourage people to avoid
** using these functions, we are not going to tell you what they do.
*/
#ifndef SQLITE_OMIT_DEPRECATED
SQLITE_API SQLITE_DEPRECATED int sqlite3_aggregate_count(sqlite3_context*);
SQLITE_API SQLITE_DEPRECATED int sqlite3_expired(sqlite3_stmt*);
SQLITE_API SQLITE_DEPRECATED int sqlite3_transfer_bindings(sqlite3_stmt*, sqlite3_stmt*);
SQLITE_API SQLITE_DEPRECATED int sqlite3_global_recover(void);
SQLITE_API SQLITE_DEPRECATED void sqlite3_thread_cleanup(void);
SQLITE_API SQLITE_DEPRECATED int sqlite3_memory_alarm(void(*)(void*,sqlite3_int64,int),void*,sqlite3_int64);
#endif

/*
** CAPI3REF: Obtaining SQL Function Parameter Values
**
** The C-language implementation of SQL functions and aggregates uses
** this set of interface routines to access the parameter values on
** the function or aggregate.
**
** The xFunc (for scalar functions) or xStep (for aggregates) parameters
** to [sqlite3_create_function()] and [sqlite3_create_function16()]
** define callbacks that implement the SQL functions and aggregates.
** The 3rd parameter to these callbacks is an array of pointers to
** [protected sqlite3_value] objects.  There is one [sqlite3_value] object for
** each parameter to the SQL function.  These routines are used to
** extract values from the [sqlite3_value] objects.
**
** These routines work only with [protected sqlite3_value] objects.
** Any attempt to use these routines on an [unprotected sqlite3_value]
** object results in undefined behavior.
**
** ^These routines work just like the corresponding [column access functions]
** except that  these routines take a single [protected sqlite3_value] object
** pointer instead of a [sqlite3_stmt*] pointer and an integer column number.
**
** ^The sqlite3_value_text16() interface extracts a UTF-16 string
** in the native byte-order of the host machine.  ^The
** sqlite3_value_text16be() and sqlite3_value_text16le() interfaces
** extract UTF-16 strings as big-endian and little-endian respectively.
**
** ^(The sqlite3_value_numeric_type() interface attempts to apply
** numeric affinity to the value.  This means that an attempt is
** made to convert the value to an integer or floating point.  If
** such a conversion is possible without loss of information (in other
** words, if the value is a string that looks like a number)
** then the conversion is performed.  Otherwise no conversion occurs.
** The [SQLITE_INTEGER | datatype] after conversion is returned.)^
**
** Please pay particular attention to the fact that the pointer returned
** from [sqlite3_value_blob()], [sqlite3_value_text()], or
** [sqlite3_value_text16()] can be invalidated by a subsequent call to
** [sqlite3_value_bytes()], [sqlite3_value_bytes16()], [sqlite3_value_text()],
** or [sqlite3_value_text16()].
**
** These routines must be called from the same thread as
** the SQL function that supplied the [sqlite3_value*] parameters.
*/
SQLITE_API const void *sqlite3_value_blob(sqlite3_value*);
SQLITE_API int sqlite3_value_bytes(sqlite3_value*);
SQLITE_API int sqlite3_value_bytes16(sqlite3_value*);
SQLITE_API double sqlite3_value_double(sqlite3_value*);
SQLITE_API int sqlite3_value_int(sqlite3_value*);
SQLITE_API sqlite3_int64 sqlite3_value_int64(sqlite3_value*);
SQLITE_API const unsigned char *sqlite3_value_text(sqlite3_value*);
SQLITE_API const void *sqlite3_value_text16(sqlite3_value*);
SQLITE_API const void *sqlite3_value_text16le(sqlite3_value*);
SQLITE_API const void *sqlite3_value_text16be(sqlite3_value*);
SQLITE_API int sqlite3_value_type(sqlite3_value*);
SQLITE_API int sqlite3_value_numeric_type(sqlite3_value*);

/*
** CAPI3REF: Obtain Aggregate Function Context
**
** Implementations of aggregate SQL functions use this
** routine to allocate memory for storing their state.
**
** ^The first time the sqlite3_aggregate_context(C,N) routine is called
** for a particular aggregate function, SQLite
** allocates N of memory, zeroes out that memory, and returns a pointer
** to the new memory. ^On second and subsequent calls to
** sqlite3_aggregate_context() for the same aggregate function instance,
** the same buffer is returned.  Sqlite3_aggregate_context() is normally
** called once for each invocation of the xStep callback and then one
** last time when the xFinal callback is invoked.  ^(When no rows match
** an aggregate query, the xStep() callback of the aggregate function
** implementation is never called and xFinal() is called exactly once.
** In those cases, sqlite3_aggregate_context() might be called for the
** first time from within xFinal().)^
**
** ^The sqlite3_aggregate_context(C,N) routine returns a NULL pointer if N is
** less than or equal to zero or if a memory allocate error occurs.
**
** ^(The amount of space allocated by sqlite3_aggregate_context(C,N) is
** determined by the N parameter on first successful call.  Changing the
** value of N in subsequent call to sqlite3_aggregate_context() within
** the same aggregate function instance will not resize the memory
** allocation.)^
**
** ^SQLite automatically frees the memory allocated by
** sqlite3_aggregate_context() when the aggregate query concludes.
**
** The first parameter must be a copy of the
** [sqlite3_context | SQL function context] that is the first parameter
** to the xStep or xFinal callback routine that implements the aggregate
** function.
**
** This routine must be called from the same thread in which
** the aggregate SQL function is running.
*/
SQLITE_API void *sqlite3_aggregate_context(sqlite3_context*, int nBytes);

/*
** CAPI3REF: User Data For Functions
**
** ^The sqlite3_user_data() interface returns a copy of
** the pointer that was the pUserData parameter (the 5th parameter)
** of the [sqlite3_create_function()]
** and [sqlite3_create_function16()] routines that originally
** registered the application defined function.
**
** This routine must be called from the same thread in which
** the application-defined function is running.
*/
SQLITE_API void *sqlite3_user_data(sqlite3_context*);

/*
** CAPI3REF: Database Connection For Functions
**
** ^The sqlite3_context_db_handle() interface returns a copy of
** the pointer to the [database connection] (the 1st parameter)
** of the [sqlite3_create_function()]
** and [sqlite3_create_function16()] routines that originally
** registered the application defined function.
*/
SQLITE_API sqlite3 *sqlite3_context_db_handle(sqlite3_context*);

/*
** CAPI3REF: Function Auxiliary Data
**
** The following two functions may be used by scalar SQL functions to
** associate metadata with argument values. If the same value is passed to
** multiple invocations of the same SQL function during query execution, under
** some circumstances the associated metadata may be preserved. This may
** be used, for example, to add a regular-expression matching scalar
** function. The compiled version of the regular expression is stored as
** metadata associated with the SQL value passed as the regular expression
** pattern.  The compiled regular expression can be reused on multiple
** invocations of the same function so that the original pattern string
** does not need to be recompiled on each invocation.
**
** ^The sqlite3_get_auxdata() interface returns a pointer to the metadata
** associated by the sqlite3_set_auxdata() function with the Nth argument
** value to the application-defined function. ^If no metadata has been ever
** been set for the Nth argument of the function, or if the corresponding
** function parameter has changed since the meta-data was set,
** then sqlite3_get_auxdata() returns a NULL pointer.
**
** ^The sqlite3_set_auxdata() interface saves the metadata
** pointed to by its 3rd parameter as the metadata for the N-th
** argument of the application-defined function.  Subsequent
** calls to sqlite3_get_auxdata() might return this data, if it has
** not been destroyed.
** ^If it is not NULL, SQLite will invoke the destructor
** function given by the 4th parameter to sqlite3_set_auxdata() on
** the metadata when the corresponding function parameter changes
** or when the SQL statement completes, whichever comes first.
**
** SQLite is free to call the destructor and drop metadata on any
** parameter of any function at any time.  ^The only guarantee is that
** the destructor will be called before the metadata is dropped.
**
** ^(In practice, metadata is preserved between function calls for
** expressions that are constant at compile time. This includes literal
** values and [parameters].)^
**
** These routines must be called from the same thread in which
** the SQL function is running.
*/
SQLITE_API void *sqlite3_get_auxdata(sqlite3_context*, int N);
SQLITE_API void sqlite3_set_auxdata(sqlite3_context*, int N, void*, void (*)(void*));


/*
** CAPI3REF: Constants Defining Special Destructor Behavior
**
** These are special values for the destructor that is passed in as the
** final argument to routines like [sqlite3_result_blob()].  ^If the destructor
** argument is SQLITE_STATIC, it means that the content pointer is constant
** and will never change.  It does not need to be destroyed.  ^The
** SQLITE_TRANSIENT value means that the content will likely change in
** the near future and that SQLite should make its own private copy of
** the content before returning.
**
** The typedef is necessary to work around problems in certain
** C++ compilers.  See ticket #2191.
*/
typedef void (*sqlite3_destructor_type)(void*);
#define SQLITE_STATIC      ((sqlite3_destructor_type)0)
#define SQLITE_TRANSIENT   ((sqlite3_destructor_type)-1)

/*
** CAPI3REF: Setting The Result Of An SQL Function
**
** These routines are used by the xFunc or xFinal callbacks that
** implement SQL functions and aggregates.  See
** [sqlite3_create_function()] and [sqlite3_create_function16()]
** for additional information.
**
** These functions work very much like the [parameter binding] family of
** functions used to bind values to host parameters in prepared statements.
** Refer to the [SQL parameter] documentation for additional information.
**
** ^The sqlite3_result_blob() interface sets the result from
** an application-defined function to be the BLOB whose content is pointed
** to by the second parameter and which is N bytes long where N is the
** third parameter.
**
** ^The sqlite3_result_zeroblob() interfaces set the result of
** the application-defined function to be a BLOB containing all zero
** bytes and N bytes in size, where N is the value of the 2nd parameter.
**
** ^The sqlite3_result_double() interface sets the result from
** an application-defined function to be a floating point value specified
** by its 2nd argument.
**
** ^The sqlite3_result_error() and sqlite3_result_error16() functions
** cause the implemented SQL function to throw an exception.
** ^SQLite uses the string pointed to by the
** 2nd parameter of sqlite3_result_error() or sqlite3_result_error16()
** as the text of an error message.  ^SQLite interprets the error
** message string from sqlite3_result_error() as UTF-8. ^SQLite
** interprets the string from sqlite3_result_error16() as UTF-16 in native
** byte order.  ^If the third parameter to sqlite3_result_error()
** or sqlite3_result_error16() is negative then SQLite takes as the error
** message all text up through the first zero character.
** ^If the third parameter to sqlite3_result_error() or
** sqlite3_result_error16() is non-negative then SQLite takes that many
** bytes (not characters) from the 2nd parameter as the error message.
** ^The sqlite3_result_error() and sqlite3_result_error16()
** routines make a private copy of the error message text before
** they return.  Hence, the calling function can deallocate or
** modify the text after they return without harm.
** ^The sqlite3_result_error_code() function changes the error code
** returned by SQLite as a result of an error in a function.  ^By default,
** the error code is SQLITE_ERROR.  ^A subsequent call to sqlite3_result_error()
** or sqlite3_result_error16() resets the error code to SQLITE_ERROR.
**
** ^The sqlite3_result_toobig() interface causes SQLite to throw an error
** indicating that a string or BLOB is too long to represent.
**
** ^The sqlite3_result_nomem() interface causes SQLite to throw an error
** indicating that a memory allocation failed.
**
** ^The sqlite3_result_int() interface sets the return value
** of the application-defined function to be the 32-bit signed integer
** value given in the 2nd argument.
** ^The sqlite3_result_int64() interface sets the return value
** of the application-defined function to be the 64-bit signed integer
** value given in the 2nd argument.
**
** ^The sqlite3_result_null() interface sets the return value
** of the application-defined function to be NULL.
**
** ^The sqlite3_result_text(), sqlite3_result_text16(),
** sqlite3_result_text16le(), and sqlite3_result_text16be() interfaces
** set the return value of the application-defined function to be
** a text string which is represented as UTF-8, UTF-16 native byte order,
** UTF-16 little endian, or UTF-16 big endian, respectively.
** ^SQLite takes the text result from the application from
** the 2nd parameter of the sqlite3_result_text* interfaces.
** ^If the 3rd parameter to the sqlite3_result_text* interfaces
** is negative, then SQLite takes result text from the 2nd parameter
** through the first zero character.
** ^If the 3rd parameter to the sqlite3_result_text* interfaces
** is non-negative, then as many bytes (not characters) of the text
** pointed to by the 2nd parameter are taken as the application-defined
** function result.  If the 3rd parameter is non-negative, then it
** must be the byte offset into the string where the NUL terminator would
** appear if the string where NUL terminated.  If any NUL characters occur
** in the string at a byte offset that is less than the value of the 3rd
** parameter, then the resulting string will contain embedded NULs and the
** result of expressions operating on strings with embedded NULs is undefined.
** ^If the 4th parameter to the sqlite3_result_text* interfaces
** or sqlite3_result_blob is a non-NULL pointer, then SQLite calls that
** function as the destructor on the text or BLOB result when it has
** finished using that result.
** ^If the 4th parameter to the sqlite3_result_text* interfaces or to
** sqlite3_result_blob is the special constant SQLITE_STATIC, then SQLite
** assumes that the text or BLOB result is in constant space and does not
** copy the content of the parameter nor call a destructor on the content
** when it has finished using that result.
** ^If the 4th parameter to the sqlite3_result_text* interfaces
** or sqlite3_result_blob is the special constant SQLITE_TRANSIENT
** then SQLite makes a copy of the result into space obtained from
** from [sqlite3_malloc()] before it returns.
**
** ^The sqlite3_result_value() interface sets the result of
** the application-defined function to be a copy the
** [unprotected sqlite3_value] object specified by the 2nd parameter.  ^The
** sqlite3_result_value() interface makes a copy of the [sqlite3_value]
** so that the [sqlite3_value] specified in the parameter may change or
** be deallocated after sqlite3_result_value() returns without harm.
** ^A [protected sqlite3_value] object may always be used where an
** [unprotected sqlite3_value] object is required, so either
** kind of [sqlite3_value] object can be used with this interface.
**
** If these routines are called from within the different thread
** than the one containing the application-defined function that received
** the [sqlite3_context] pointer, the results are undefined.
*/
SQLITE_API void sqlite3_result_blob(sqlite3_context*, const void*, int, void(*)(void*));
SQLITE_API void sqlite3_result_double(sqlite3_context*, double);
SQLITE_API void sqlite3_result_error(sqlite3_context*, const char*, int);
SQLITE_API void sqlite3_result_error16(sqlite3_context*, const void*, int);
SQLITE_API void sqlite3_result_error_toobig(sqlite3_context*);
SQLITE_API void sqlite3_result_error_nomem(sqlite3_context*);
SQLITE_API void sqlite3_result_error_code(sqlite3_context*, int);
SQLITE_API void sqlite3_result_int(sqlite3_context*, int);
SQLITE_API void sqlite3_result_int64(sqlite3_context*, sqlite3_int64);
SQLITE_API void sqlite3_result_null(sqlite3_context*);
SQLITE_API void sqlite3_result_text(sqlite3_context*, const char*, int, void(*)(void*));
SQLITE_API void sqlite3_result_text16(sqlite3_context*, const void*, int, void(*)(void*));
SQLITE_API void sqlite3_result_text16le(sqlite3_context*, const void*, int,void(*)(void*));
SQLITE_API void sqlite3_result_text16be(sqlite3_context*, const void*, int,void(*)(void*));
SQLITE_API void sqlite3_result_value(sqlite3_context*, sqlite3_value*);
SQLITE_API void sqlite3_result_zeroblob(sqlite3_context*, int n);

/*
** CAPI3REF: Define New Collating Sequences
**
** ^These functions add, remove, or modify a [collation] associated
** with the [database connection] specified as the first argument.
**
** ^The name of the collation is a UTF-8 string
** for sqlite3_create_collation() and sqlite3_create_collation_v2()
** and a UTF-16 string in native byte order for sqlite3_create_collation16().
** ^Collation names that compare equal according to [sqlite3_strnicmp()] are
** considered to be the same name.
**
** ^(The third argument (eTextRep) must be one of the constants:
** 
      
** 
    •  [SQLITE_UTF8],
** 
    •  [SQLITE_UTF16LE],
** 
    •  [SQLITE_UTF16BE],
** 
    •  [SQLITE_UTF16], or
** 
    •  [SQLITE_UTF16_ALIGNED].
** 
    )^
** ^The eTextRep argument determines the encoding of strings passed
** to the collating function callback, xCallback.
** ^The [SQLITE_UTF16] and [SQLITE_UTF16_ALIGNED] values for eTextRep
** force strings to be UTF16 with native byte order.
** ^The [SQLITE_UTF16_ALIGNED] value for eTextRep forces strings to begin
** on an even byte address.
**
** ^The fourth argument, pArg, is an application data pointer that is passed
** through as the first argument to the collating function callback.
**
** ^The fifth argument, xCallback, is a pointer to the collating function.
** ^Multiple collating functions can be registered using the same name but
** with different eTextRep parameters and SQLite will use whichever
** function requires the least amount of data transformation.
** ^If the xCallback argument is NULL then the collating function is
** deleted.  ^When all collating functions having the same name are deleted,
** that collation is no longer usable.
**
** ^The collating function callback is invoked with a copy of the pArg
** application data pointer and with two strings in the encoding specified
** by the eTextRep argument.  The collating function must return an
** integer that is negative, zero, or positive
** if the first string is less than, equal to, or greater than the second,
** respectively.  A collating function must always return the same answer
** given the same inputs.  If two or more collating functions are registered
** to the same collation name (using different eTextRep values) then all
** must give an equivalent answer when invoked with equivalent strings.
** The collating function must obey the following properties for all
** strings A, B, and C:
**
** 
      
** 
    1.  If A==B then B==A.
** 
    2.  If A==B and B==C then A==C.
** 
    3.  If A<B THEN B>A.
** 
    4.  If A<B and B<C then A<C.
** 
    
**
** If a collating function fails any of the above constraints and that
** collating function is  registered and used, then the behavior of SQLite
** is undefined.
**
** ^The sqlite3_create_collation_v2() works like sqlite3_create_collation()
** with the addition that the xDestroy callback is invoked on pArg when
** the collating function is deleted.
** ^Collating functions are deleted when they are overridden by later
** calls to the collation creation functions or when the
** [database connection] is closed using [sqlite3_close()].
**
** ^The xDestroy callback is not called if the
** sqlite3_create_collation_v2() function fails.  Applications that invoke
** sqlite3_create_collation_v2() with a non-NULL xDestroy argument should
** check the return code and dispose of the application data pointer
** themselves rather than expecting SQLite to deal with it for them.
** This is different from every other SQLite interface.  The inconsistency
** is unfortunate but cannot be changed without breaking backwards
** compatibility.
**
** See also:  [sqlite3_collation_needed()] and [sqlite3_collation_needed16()].
*/
SQLITE_API int sqlite3_create_collation(
  sqlite3*,
  const char *zName,
  int eTextRep,
  void *pArg,
  int(*xCompare)(void*,int,const void*,int,const void*)
);
SQLITE_API int sqlite3_create_collation_v2(
  sqlite3*,
  const char *zName,
  int eTextRep,
  void *pArg,
  int(*xCompare)(void*,int,const void*,int,const void*),
  void(*xDestroy)(void*)
);
SQLITE_API int sqlite3_create_collation16(
  sqlite3*,
  const void *zName,
  int eTextRep,
  void *pArg,
  int(*xCompare)(void*,int,const void*,int,const void*)
);

/*
** CAPI3REF: Collation Needed Callbacks
**
** ^To avoid having to register all collation sequences before a database
** can be used, a single callback function may be registered with the
** [database connection] to be invoked whenever an undefined collation
** sequence is required.
**
** ^If the function is registered using the sqlite3_collation_needed() API,
** then it is passed the names of undefined collation sequences as strings
** encoded in UTF-8. ^If sqlite3_collation_needed16() is used,
** the names are passed as UTF-16 in machine native byte order.
** ^A call to either function replaces the existing collation-needed callback.
**
** ^(When the callback is invoked, the first argument passed is a copy
** of the second argument to sqlite3_collation_needed() or
** sqlite3_collation_needed16().  The second argument is the database
** connection.  The third argument is one of [SQLITE_UTF8], [SQLITE_UTF16BE],
** or [SQLITE_UTF16LE], indicating the most desirable form of the collation
** sequence function required.  The fourth parameter is the name of the
** required collation sequence.)^
**
** The callback function should register the desired collation using
** [sqlite3_create_collation()], [sqlite3_create_collation16()], or
** [sqlite3_create_collation_v2()].
*/
SQLITE_API int sqlite3_collation_needed(
  sqlite3*,
  void*,
  void(*)(void*,sqlite3*,int eTextRep,const char*)
);
SQLITE_API int sqlite3_collation_needed16(
  sqlite3*,
  void*,
  void(*)(void*,sqlite3*,int eTextRep,const void*)
);

#ifdef SQLITE_HAS_CODEC
/*
** Specify the key for an encrypted database.  This routine should be
** called right after sqlite3_open().
**
** The code to implement this API is not available in the public release
** of SQLite.
*/
SQLITE_API int sqlite3_key(
  sqlite3 *db,                   /* Database to be rekeyed */
  const void *pKey, int nKey     /* The key */
);

/*
** Change the key on an open database.  If the current database is not
** encrypted, this routine will encrypt it.  If pNew==0 or nNew==0, the
** database is decrypted.
**
** The code to implement this API is not available in the public release
** of SQLite.
*/
SQLITE_API int sqlite3_rekey(
  sqlite3 *db,                   /* Database to be rekeyed */
  const void *pKey, int nKey     /* The new key */
);

/*
** Specify the activation key for a SEE database.  Unless
** activated, none of the SEE routines will work.
*/
SQLITE_API void sqlite3_activate_see(
  const char *zPassPhrase        /* Activation phrase */
);
#endif

#ifdef SQLITE_ENABLE_CEROD
/*
** Specify the activation key for a CEROD database.  Unless
** activated, none of the CEROD routines will work.
*/
SQLITE_API void sqlite3_activate_cerod(
  const char *zPassPhrase        /* Activation phrase */
);
#endif

/*
** CAPI3REF: Suspend Execution For A Short Time
**
** The sqlite3_sleep() function causes the current thread to suspend execution
** for at least a number of milliseconds specified in its parameter.
**
** If the operating system does not support sleep requests with
** millisecond time resolution, then the time will be rounded up to
** the nearest second. The number of milliseconds of sleep actually
** requested from the operating system is returned.
**
** ^SQLite implements this interface by calling the xSleep()
** method of the default [sqlite3_vfs] object.  If the xSleep() method
** of the default VFS is not implemented correctly, or not implemented at
** all, then the behavior of sqlite3_sleep() may deviate from the description
** in the previous paragraphs.
*/
SQLITE_API int sqlite3_sleep(int);

/*
** CAPI3REF: Name Of The Folder Holding Temporary Files
**
** ^(If this global variable is made to point to a string which is
** the name of a folder (a.k.a. directory), then all temporary files
** created by SQLite when using a built-in [sqlite3_vfs | VFS]
** will be placed in that directory.)^  ^If this variable
** is a NULL pointer, then SQLite performs a search for an appropriate
** temporary file directory.
**
** It is not safe to read or modify this variable in more than one
** thread at a time.  It is not safe to read or modify this variable
** if a [database connection] is being used at the same time in a separate
** thread.
** It is intended that this variable be set once
** as part of process initialization and before any SQLite interface
** routines have been called and that this variable remain unchanged
** thereafter.
**
** ^The [temp_store_directory pragma] may modify this variable and cause
** it to point to memory obtained from [sqlite3_malloc].  ^Furthermore,
** the [temp_store_directory pragma] always assumes that any string
** that this variable points to is held in memory obtained from
** [sqlite3_malloc] and the pragma may attempt to free that memory
** using [sqlite3_free].
** Hence, if this variable is modified directly, either it should be
** made NULL or made to point to memory obtained from [sqlite3_malloc]
** or else the use of the [temp_store_directory pragma] should be avoided.
*/
SQLITE_API char *sqlite3_temp_directory;

/*
** CAPI3REF: Test For Auto-Commit Mode
** KEYWORDS: {autocommit mode}
**
** ^The sqlite3_get_autocommit() interface returns non-zero or
** zero if the given database connection is or is not in autocommit mode,
** respectively.  ^Autocommit mode is on by default.
** ^Autocommit mode is disabled by a [BEGIN] statement.
** ^Autocommit mode is re-enabled by a [COMMIT] or [ROLLBACK].
**
** If certain kinds of errors occur on a statement within a multi-statement
** transaction (errors including [SQLITE_FULL], [SQLITE_IOERR],
** [SQLITE_NOMEM], [SQLITE_BUSY], and [SQLITE_INTERRUPT]) then the
** transaction might be rolled back automatically.  The only way to
** find out whether SQLite automatically rolled back the transaction after
** an error is to use this function.
**
** If another thread changes the autocommit status of the database
** connection while this routine is running, then the return value
** is undefined.
*/
SQLITE_API int sqlite3_get_autocommit(sqlite3*);

/*
** CAPI3REF: Find The Database Handle Of A Prepared Statement
**
** ^The sqlite3_db_handle interface returns the [database connection] handle
** to which a [prepared statement] belongs.  ^The [database connection]
** returned by sqlite3_db_handle is the same [database connection]
** that was the first argument
** to the [sqlite3_prepare_v2()] call (or its variants) that was used to
** create the statement in the first place.
*/
SQLITE_API sqlite3 *sqlite3_db_handle(sqlite3_stmt*);

/*
** CAPI3REF: Return The Filename For A Database Connection
**
** ^The sqlite3_db_filename(D,N) interface returns a pointer to a filename
** associated with database N of connection D.  ^The main database file
** has the name "main".  If there is no attached database N on the database
** connection D, or if database N is a temporary or in-memory database, then
** a NULL pointer is returned.
**
** ^The filename returned by this function is the output of the
** xFullPathname method of the [VFS].  ^In other words, the filename
** will be an absolute pathname, even if the filename used
** to open the database originally was a URI or relative pathname.
*/
SQLITE_API const char *sqlite3_db_filename(sqlite3 *db, const char *zDbName);

/*
** CAPI3REF: Find the next prepared statement
**
** ^This interface returns a pointer to the next [prepared statement] after
** pStmt associated with the [database connection] pDb.  ^If pStmt is NULL
** then this interface returns a pointer to the first prepared statement
** associated with the database connection pDb.  ^If no prepared statement
** satisfies the conditions of this routine, it returns NULL.
**
** The [database connection] pointer D in a call to
** [sqlite3_next_stmt(D,S)] must refer to an open database
** connection and in particular must not be a NULL pointer.
*/
SQLITE_API sqlite3_stmt *sqlite3_next_stmt(sqlite3 *pDb, sqlite3_stmt *pStmt);

/*
** CAPI3REF: Commit And Rollback Notification Callbacks
**
** ^The sqlite3_commit_hook() interface registers a callback
** function to be invoked whenever a transaction is [COMMIT | committed].
** ^Any callback set by a previous call to sqlite3_commit_hook()
** for the same database connection is overridden.
** ^The sqlite3_rollback_hook() interface registers a callback
** function to be invoked whenever a transaction is [ROLLBACK | rolled back].
** ^Any callback set by a previous call to sqlite3_rollback_hook()
** for the same database connection is overridden.
** ^The pArg argument is passed through to the callback.
** ^If the callback on a commit hook function returns non-zero,
** then the commit is converted into a rollback.
**
** ^The sqlite3_commit_hook(D,C,P) and sqlite3_rollback_hook(D,C,P) functions
** return the P argument from the previous call of the same function
** on the same [database connection] D, or NULL for
** the first call for each function on D.
**
** The commit and rollback hook callbacks are not reentrant.
** The callback implementation must not do anything that will modify
** the database connection that invoked the callback.  Any actions
** to modify the database connection must be deferred until after the
** completion of the [sqlite3_step()] call that triggered the commit
** or rollback hook in the first place.
** Note that running any other SQL statements, including SELECT statements,
** or merely calling [sqlite3_prepare_v2()] and [sqlite3_step()] will modify
** the database connections for the meaning of "modify" in this paragraph.
**
** ^Registering a NULL function disables the callback.
**
** ^When the commit hook callback routine returns zero, the [COMMIT]
** operation is allowed to continue normally.  ^If the commit hook
** returns non-zero, then the [COMMIT] is converted into a [ROLLBACK].
** ^The rollback hook is invoked on a rollback that results from a commit
** hook returning non-zero, just as it would be with any other rollback.
**
** ^For the purposes of this API, a transaction is said to have been
** rolled back if an explicit "ROLLBACK" statement is executed, or
** an error or constraint causes an implicit rollback to occur.
** ^The rollback callback is not invoked if a transaction is
** automatically rolled back because the database connection is closed.
**
** See also the [sqlite3_update_hook()] interface.
*/
SQLITE_API void *sqlite3_commit_hook(sqlite3*, int(*)(void*), void*);
SQLITE_API void *sqlite3_rollback_hook(sqlite3*, void(*)(void *), void*);

/*
** CAPI3REF: Data Change Notification Callbacks
**
** ^The sqlite3_update_hook() interface registers a callback function
** with the [database connection] identified by the first argument
** to be invoked whenever a row is updated, inserted or deleted.
** ^Any callback set by a previous call to this function
** for the same database connection is overridden.
**
** ^The second argument is a pointer to the function to invoke when a
** row is updated, inserted or deleted.
** ^The first argument to the callback is a copy of the third argument
** to sqlite3_update_hook().
** ^The second callback argument is one of [SQLITE_INSERT], [SQLITE_DELETE],
** or [SQLITE_UPDATE], depending on the operation that caused the callback
** to be invoked.
** ^The third and fourth arguments to the callback contain pointers to the
** database and table name containing the affected row.
** ^The final callback parameter is the [rowid] of the row.
** ^In the case of an update, this is the [rowid] after the update takes place.
**
** ^(The update hook is not invoked when internal system tables are
** modified (i.e. sqlite_master and sqlite_sequence).)^
**
** ^In the current implementation, the update hook
** is not invoked when duplication rows are deleted because of an
** [ON CONFLICT | ON CONFLICT REPLACE] clause.  ^Nor is the update hook
** invoked when rows are deleted using the [truncate optimization].
** The exceptions defined in this paragraph might change in a future
** release of SQLite.
**
** The update hook implementation must not do anything that will modify
** the database connection that invoked the update hook.  Any actions
** to modify the database connection must be deferred until after the
** completion of the [sqlite3_step()] call that triggered the update hook.
** Note that [sqlite3_prepare_v2()] and [sqlite3_step()] both modify their
** database connections for the meaning of "modify" in this paragraph.
**
** ^The sqlite3_update_hook(D,C,P) function
** returns the P argument from the previous call
** on the same [database connection] D, or NULL for
** the first call on D.
**
** See also the [sqlite3_commit_hook()] and [sqlite3_rollback_hook()]
** interfaces.
*/
SQLITE_API void *sqlite3_update_hook(
  sqlite3*,
  void(*)(void *,int ,char const *,char const *,sqlite3_int64),
  void*
);

/*
** CAPI3REF: Enable Or Disable Shared Pager Cache
** KEYWORDS: {shared cache}
**
** ^(This routine enables or disables the sharing of the database cache
** and schema data structures between [database connection | connections]
** to the same database. Sharing is enabled if the argument is true
** and disabled if the argument is false.)^
**
** ^Cache sharing is enabled and disabled for an entire process.
** This is a change as of SQLite version 3.5.0. In prior versions of SQLite,
** sharing was enabled or disabled for each thread separately.
**
** ^(The cache sharing mode set by this interface effects all subsequent
** calls to [sqlite3_open()], [sqlite3_open_v2()], and [sqlite3_open16()].
** Existing database connections continue use the sharing mode
** that was in effect at the time they were opened.)^
**
** ^(This routine returns [SQLITE_OK] if shared cache was enabled or disabled
** successfully.  An [error code] is returned otherwise.)^
**
** ^Shared cache is disabled by default. But this might change in
** future releases of SQLite.  Applications that care about shared
** cache setting should set it explicitly.
**
** See Also:  [SQLite Shared-Cache Mode]
*/
SQLITE_API int sqlite3_enable_shared_cache(int);

/*
** CAPI3REF: Attempt To Free Heap Memory
**
** ^The sqlite3_release_memory() interface attempts to free N bytes
** of heap memory by deallocating non-essential memory allocations
** held by the database library.   Memory used to cache database
** pages to improve performance is an example of non-essential memory.
** ^sqlite3_release_memory() returns the number of bytes actually freed,
** which might be more or less than the amount requested.
** ^The sqlite3_release_memory() routine is a no-op returning zero
** if SQLite is not compiled with [SQLITE_ENABLE_MEMORY_MANAGEMENT].
**
** See also: [sqlite3_db_release_memory()]
*/
SQLITE_API int sqlite3_release_memory(int);

/*
** CAPI3REF: Free Memory Used By A Database Connection
**
** ^The sqlite3_db_release_memory(D) interface attempts to free as much heap
** memory as possible from database connection D. Unlike the
** [sqlite3_release_memory()] interface, this interface is effect even
** when then [SQLITE_ENABLE_MEMORY_MANAGEMENT] compile-time option is
** omitted.
**
** See also: [sqlite3_release_memory()]
*/
SQLITE_API int sqlite3_db_release_memory(sqlite3*);

/*
** CAPI3REF: Impose A Limit On Heap Size
**
** ^The sqlite3_soft_heap_limit64() interface sets and/or queries the
** soft limit on the amount of heap memory that may be allocated by SQLite.
** ^SQLite strives to keep heap memory utilization below the soft heap
** limit by reducing the number of pages held in the page cache
** as heap memory usages approaches the limit.
** ^The soft heap limit is "soft" because even though SQLite strives to stay
** below the limit, it will exceed the limit rather than generate
** an [SQLITE_NOMEM] error.  In other words, the soft heap limit
** is advisory only.
**
** ^The return value from sqlite3_soft_heap_limit64() is the size of
** the soft heap limit prior to the call, or negative in the case of an
** error.  ^If the argument N is negative
** then no change is made to the soft heap limit.  Hence, the current
** size of the soft heap limit can be determined by invoking
** sqlite3_soft_heap_limit64() with a negative argument.
**
** ^If the argument N is zero then the soft heap limit is disabled.
**
** ^(The soft heap limit is not enforced in the current implementation
** if one or more of following conditions are true:
**
** 
      
** 
    •  The soft heap limit is set to zero.
** 
    •  Memory accounting is disabled using a combination of the
**      [sqlite3_config]([SQLITE_CONFIG_MEMSTATUS],...) start-time option and
**      the [SQLITE_DEFAULT_MEMSTATUS] compile-time option.
** 
    •  An alternative page cache implementation is specified using
**      [sqlite3_config]([SQLITE_CONFIG_PCACHE2],...).
** 
    •  The page cache allocates from its own memory pool supplied
**      by [sqlite3_config]([SQLITE_CONFIG_PAGECACHE],...) rather than
**      from the heap.
** 
    )^
**
** Beginning with SQLite version 3.7.3, the soft heap limit is enforced
** regardless of whether or not the [SQLITE_ENABLE_MEMORY_MANAGEMENT]
** compile-time option is invoked.  With [SQLITE_ENABLE_MEMORY_MANAGEMENT],
** the soft heap limit is enforced on every memory allocation.  Without
** [SQLITE_ENABLE_MEMORY_MANAGEMENT], the soft heap limit is only enforced
** when memory is allocated by the page cache.  Testing suggests that because
** the page cache is the predominate memory user in SQLite, most
** applications will achieve adequate soft heap limit enforcement without
** the use of [SQLITE_ENABLE_MEMORY_MANAGEMENT].
**
** The circumstances under which SQLite will enforce the soft heap limit may
** changes in future releases of SQLite.
*/
SQLITE_API sqlite3_int64 sqlite3_soft_heap_limit64(sqlite3_int64 N);

/*
** CAPI3REF: Deprecated Soft Heap Limit Interface
** DEPRECATED
**
** This is a deprecated version of the [sqlite3_soft_heap_limit64()]
** interface.  This routine is provided for historical compatibility
** only.  All new applications should use the
** [sqlite3_soft_heap_limit64()] interface rather than this one.
*/
SQLITE_API SQLITE_DEPRECATED void sqlite3_soft_heap_limit(int N);


/*
** CAPI3REF: Extract Metadata About A Column Of A Table
**
** ^This routine returns metadata about a specific column of a specific
** database table accessible using the [database connection] handle
** passed as the first function argument.
**
** ^The column is identified by the second, third and fourth parameters to
** this function. ^The second parameter is either the name of the database
** (i.e. "main", "temp", or an attached database) containing the specified
** table or NULL. ^If it is NULL, then all attached databases are searched
** for the table using the same algorithm used by the database engine to
** resolve unqualified table references.
**
** ^The third and fourth parameters to this function are the table and column
** name of the desired column, respectively. Neither of these parameters
** may be NULL.
**
** ^Metadata is returned by writing to the memory locations passed as the 5th
** and subsequent parameters to this function. ^Any of these arguments may be
** NULL, in which case the corresponding element of metadata is omitted.
**
** ^(
    
** 
** 
     Parameter  Output
    Type     		  Description
**
** 
     5th  const char*  Data type
** 
     6th  const char*  Name of default collation sequence
** 
     7th  int          True if column has a NOT NULL constraint
** 
     8th  int          True if column is part of the PRIMARY KEY
** 
     9th  int          True if column is [AUTOINCREMENT]
** 
    
** 
    )^
**
** ^The memory pointed to by the character pointers returned for the
** declaration type and collation sequence is valid only until the next
** call to any SQLite API function.
**
** ^If the specified table is actually a view, an [error code] is returned.
**
** ^If the specified column is "rowid", "oid" or "_rowid_" and an
** [INTEGER PRIMARY KEY] column has been explicitly declared, then the output
** parameters are set for the explicitly declared column. ^(If there is no
** explicitly declared [INTEGER PRIMARY KEY] column, then the output
** parameters are set as follows:
**
** 
    **     data type: "INTEGER"
**     collation sequence: "BINARY"
**     not null: 0
**     primary key: 1
**     auto increment: 0
** 
    )^
**
** ^(This function may load one or more schemas from database files. If an
** error occurs during this process, or if the requested table or column
** cannot be found, an [error code] is returned and an error message left
** in the [database connection] (to be retrieved using sqlite3_errmsg()).)^
**
** ^This API is only available if the library was compiled with the
** [SQLITE_ENABLE_COLUMN_METADATA] C-preprocessor symbol defined.
*/
SQLITE_API int sqlite3_table_column_metadata(
  sqlite3 *db,                /* Connection handle */
  const char *zDbName,        /* Database name or NULL */
  const char *zTableName,     /* Table name */
  const char *zColumnName,    /* Column name */
  char const **pzDataType,    /* OUTPUT: Declared data type */
  char const **pzCollSeq,     /* OUTPUT: Collation sequence name */
  int *pNotNull,              /* OUTPUT: True if NOT NULL constraint exists */
  int *pPrimaryKey,           /* OUTPUT: True if column part of PK */
  int *pAutoinc               /* OUTPUT: True if column is auto-increment */
);

/*
** CAPI3REF: Load An Extension
**
** ^This interface loads an SQLite extension library from the named file.
**
** ^The sqlite3_load_extension() interface attempts to load an
** SQLite extension library contained in the file zFile.
**
** ^The entry point is zProc.
** ^zProc may be 0, in which case the name of the entry point
** defaults to "sqlite3_extension_init".
** ^The sqlite3_load_extension() interface returns
** [SQLITE_OK] on success and [SQLITE_ERROR] if something goes wrong.
** ^If an error occurs and pzErrMsg is not 0, then the
** [sqlite3_load_extension()] interface shall attempt to
** fill *pzErrMsg with error message text stored in memory
** obtained from [sqlite3_malloc()]. The calling function
** should free this memory by calling [sqlite3_free()].
**
** ^Extension loading must be enabled using
** [sqlite3_enable_load_extension()] prior to calling this API,
** otherwise an error will be returned.
**
** See also the [load_extension() SQL function].
*/
SQLITE_API int sqlite3_load_extension(
  sqlite3 *db,          /* Load the extension into this database connection */
  const char *zFile,    /* Name of the shared library containing extension */
  const char *zProc,    /* Entry point.  Derived from zFile if 0 */
  char **pzErrMsg       /* Put error message here if not 0 */
);

/*
** CAPI3REF: Enable Or Disable Extension Loading
**
** ^So as not to open security holes in older applications that are
** unprepared to deal with extension loading, and as a means of disabling
** extension loading while evaluating user-entered SQL, the following API
** is provided to turn the [sqlite3_load_extension()] mechanism on and off.
**
** ^Extension loading is off by default. See ticket #1863.
** ^Call the sqlite3_enable_load_extension() routine with onoff==1
** to turn extension loading on and call it with onoff==0 to turn
** it back off again.
*/
SQLITE_API int sqlite3_enable_load_extension(sqlite3 *db, int onoff);

/*
** CAPI3REF: Automatically Load Statically Linked Extensions
**
** ^This interface causes the xEntryPoint() function to be invoked for
** each new [database connection] that is created.  The idea here is that
** xEntryPoint() is the entry point for a statically linked SQLite extension
** that is to be automatically loaded into all new database connections.
**
** ^(Even though the function prototype shows that xEntryPoint() takes
** no arguments and returns void, SQLite invokes xEntryPoint() with three
** arguments and expects and integer result as if the signature of the
** entry point where as follows:
**
** 
    **    int xEntryPoint(
**      sqlite3 *db,
**      const char **pzErrMsg,
**      const struct sqlite3_api_routines *pThunk
**    );
** 
    )^
**
** If the xEntryPoint routine encounters an error, it should make *pzErrMsg
** point to an appropriate error message (obtained from [sqlite3_mprintf()])
** and return an appropriate [error code].  ^SQLite ensures that *pzErrMsg
** is NULL before calling the xEntryPoint().  ^SQLite will invoke
** [sqlite3_free()] on *pzErrMsg after xEntryPoint() returns.  ^If any
** xEntryPoint() returns an error, the [sqlite3_open()], [sqlite3_open16()],
** or [sqlite3_open_v2()] call that provoked the xEntryPoint() will fail.
**
** ^Calling sqlite3_auto_extension(X) with an entry point X that is already
** on the list of automatic extensions is a harmless no-op. ^No entry point
** will be called more than once for each database connection that is opened.
**
** See also: [sqlite3_reset_auto_extension()].
*/
SQLITE_API int sqlite3_auto_extension(void (*xEntryPoint)(void));

/*
** CAPI3REF: Reset Automatic Extension Loading
**
** ^This interface disables all automatic extensions previously
** registered using [sqlite3_auto_extension()].
*/
SQLITE_API void sqlite3_reset_auto_extension(void);

/*
** The interface to the virtual-table mechanism is currently considered
** to be experimental.  The interface might change in incompatible ways.
** If this is a problem for you, do not use the interface at this time.
**
** When the virtual-table mechanism stabilizes, we will declare the
** interface fixed, support it indefinitely, and remove this comment.
*/

/*
** Structures used by the virtual table interface
*/
typedef struct sqlite3_vtab sqlite3_vtab;
typedef struct sqlite3_index_info sqlite3_index_info;
typedef struct sqlite3_vtab_cursor sqlite3_vtab_cursor;
typedef struct sqlite3_module sqlite3_module;

/*
** CAPI3REF: Virtual Table Object
** KEYWORDS: sqlite3_module {virtual table module}
**
** This structure, sometimes called a "virtual table module",
** defines the implementation of a [virtual tables].
** This structure consists mostly of methods for the module.
**
** ^A virtual table module is created by filling in a persistent
** instance of this structure and passing a pointer to that instance
** to [sqlite3_create_module()] or [sqlite3_create_module_v2()].
** ^The registration remains valid until it is replaced by a different
** module or until the [database connection] closes.  The content
** of this structure must not change while it is registered with
** any database connection.
*/
struct sqlite3_module {
  int iVersion;
  int (*xCreate)(sqlite3*, void *pAux,
               int argc, const char *const*argv,
               sqlite3_vtab **ppVTab, char**);
  int (*xConnect)(sqlite3*, void *pAux,
               int argc, const char *const*argv,
               sqlite3_vtab **ppVTab, char**);
  int (*xBestIndex)(sqlite3_vtab *pVTab, sqlite3_index_info*);
  int (*xDisconnect)(sqlite3_vtab *pVTab);
  int (*xDestroy)(sqlite3_vtab *pVTab);
  int (*xOpen)(sqlite3_vtab *pVTab, sqlite3_vtab_cursor **ppCursor);
  int (*xClose)(sqlite3_vtab_cursor*);
  int (*xFilter)(sqlite3_vtab_cursor*, int idxNum, const char *idxStr,
                int argc, sqlite3_value **argv);
  int (*xNext)(sqlite3_vtab_cursor*);
  int (*xEof)(sqlite3_vtab_cursor*);
  int (*xColumn)(sqlite3_vtab_cursor*, sqlite3_context*, int);
  int (*xRowid)(sqlite3_vtab_cursor*, sqlite3_int64 *pRowid);
  int (*xUpdate)(sqlite3_vtab *, int, sqlite3_value **, sqlite3_int64 *);
  int (*xBegin)(sqlite3_vtab *pVTab);
  int (*xSync)(sqlite3_vtab *pVTab);
  int (*xCommit)(sqlite3_vtab *pVTab);
  int (*xRollback)(sqlite3_vtab *pVTab);
  int (*xFindFunction)(sqlite3_vtab *pVtab, int nArg, const char *zName,
                       void (**pxFunc)(sqlite3_context*,int,sqlite3_value**),
                       void **ppArg);
  int (*xRename)(sqlite3_vtab *pVtab, const char *zNew);
  /* The methods above are in version 1 of the sqlite_module object. Those
  ** below are for version 2 and greater. */
  int (*xSavepoint)(sqlite3_vtab *pVTab, int);
  int (*xRelease)(sqlite3_vtab *pVTab, int);
  int (*xRollbackTo)(sqlite3_vtab *pVTab, int);
};

/*
** CAPI3REF: Virtual Table Indexing Information
** KEYWORDS: sqlite3_index_info
**
** The sqlite3_index_info structure and its substructures is used as part
** of the [virtual table] interface to
** pass information into and receive the reply from the [xBestIndex]
** method of a [virtual table module].  The fields under **Inputs** are the
** inputs to xBestIndex and are read-only.  xBestIndex inserts its
** results into the **Outputs** fields.
**
** ^(The aConstraint[] array records WHERE clause constraints of the form:
**
** 
    column OP expr
    
**
** where OP is =, <, <=, >, or >=.)^  ^(The particular operator is
** stored in aConstraint[].op using one of the
** [SQLITE_INDEX_CONSTRAINT_EQ | SQLITE_INDEX_CONSTRAINT_ values].)^
** ^(The index of the column is stored in
** aConstraint[].iColumn.)^  ^(aConstraint[].usable is TRUE if the
** expr on the right-hand side can be evaluated (and thus the constraint
** is usable) and false if it cannot.)^
**
** ^The optimizer automatically inverts terms of the form "expr OP column"
** and makes other simplifications to the WHERE clause in an attempt to
** get as many WHERE clause terms into the form shown above as possible.
** ^The aConstraint[] array only reports WHERE clause terms that are
** relevant to the particular virtual table being queried.
**
** ^Information about the ORDER BY clause is stored in aOrderBy[].
** ^Each term of aOrderBy records a column of the ORDER BY clause.
**
** The [xBestIndex] method must fill aConstraintUsage[] with information
** about what parameters to pass to xFilter.  ^If argvIndex>0 then
** the right-hand side of the corresponding aConstraint[] is evaluated
** and becomes the argvIndex-th entry in argv.  ^(If aConstraintUsage[].omit
** is true, then the constraint is assumed to be fully handled by the
** virtual table and is not checked again by SQLite.)^
**
** ^The idxNum and idxPtr values are recorded and passed into the
** [xFilter] method.
** ^[sqlite3_free()] is used to free idxPtr if and only if
** needToFreeIdxPtr is true.
**
** ^The orderByConsumed means that output from [xFilter]/[xNext] will occur in
** the correct order to satisfy the ORDER BY clause so that no separate
** sorting step is required.
**
** ^The estimatedCost value is an estimate of the cost of doing the
** particular lookup.  A full scan of a table with N entries should have
** a cost of N.  A binary search of a table of N entries should have a
** cost of approximately log(N).
*/
struct sqlite3_index_info {
  /* Inputs */
  int nConstraint;           /* Number of entries in aConstraint */
  struct sqlite3_index_constraint {
     int iColumn;              /* Column on left-hand side of constraint */
     unsigned char op;         /* Constraint operator */
     unsigned char usable;     /* True if this constraint is usable */
     int iTermOffset;          /* Used internally - xBestIndex should ignore */
  } *aConstraint;            /* Table of WHERE clause constraints */
  int nOrderBy;              /* Number of terms in the ORDER BY clause */
  struct sqlite3_index_orderby {
     int iColumn;              /* Column number */
     unsigned char desc;       /* True for DESC.  False for ASC. */
  } *aOrderBy;               /* The ORDER BY clause */
  /* Outputs */
  struct sqlite3_index_constraint_usage {
    int argvIndex;           /* if >0, constraint is part of argv to xFilter */
    unsigned char omit;      /* Do not code a test for this constraint */
  } *aConstraintUsage;
  int idxNum;                /* Number used to identify the index */
  char *idxStr;              /* String, possibly obtained from sqlite3_malloc */
  int needToFreeIdxStr;      /* Free idxStr using sqlite3_free() if true */
  int orderByConsumed;       /* True if output is already ordered */
  double estimatedCost;      /* Estimated cost of using this index */
};

/*
** CAPI3REF: Virtual Table Constraint Operator Codes
**
** These macros defined the allowed values for the
** [sqlite3_index_info].aConstraint[].op field.  Each value represents
** an operator that is part of a constraint term in the wHERE clause of
** a query that uses a [virtual table].
*/
#define SQLITE_INDEX_CONSTRAINT_EQ    2
#define SQLITE_INDEX_CONSTRAINT_GT    4
#define SQLITE_INDEX_CONSTRAINT_LE    8
#define SQLITE_INDEX_CONSTRAINT_LT    16
#define SQLITE_INDEX_CONSTRAINT_GE    32
#define SQLITE_INDEX_CONSTRAINT_MATCH 64

/*
** CAPI3REF: Register A Virtual Table Implementation
**
** ^These routines are used to register a new [virtual table module] name.
** ^Module names must be registered before
** creating a new [virtual table] using the module and before using a
** preexisting [virtual table] for the module.
**
** ^The module name is registered on the [database connection] specified
** by the first parameter.  ^The name of the module is given by the
** second parameter.  ^The third parameter is a pointer to
** the implementation of the [virtual table module].   ^The fourth
** parameter is an arbitrary client data pointer that is passed through
** into the [xCreate] and [xConnect] methods of the virtual table module
** when a new virtual table is be being created or reinitialized.
**
** ^The sqlite3_create_module_v2() interface has a fifth parameter which
** is a pointer to a destructor for the pClientData.  ^SQLite will
** invoke the destructor function (if it is not NULL) when SQLite
** no longer needs the pClientData pointer.  ^The destructor will also
** be invoked if the call to sqlite3_create_module_v2() fails.
** ^The sqlite3_create_module()
** interface is equivalent to sqlite3_create_module_v2() with a NULL
** destructor.
*/
SQLITE_API int sqlite3_create_module(
  sqlite3 *db,               /* SQLite connection to register module with */
  const char *zName,         /* Name of the module */
  const sqlite3_module *p,   /* Methods for the module */
  void *pClientData          /* Client data for xCreate/xConnect */
);
SQLITE_API int sqlite3_create_module_v2(
  sqlite3 *db,               /* SQLite connection to register module with */
  const char *zName,         /* Name of the module */
  const sqlite3_module *p,   /* Methods for the module */
  void *pClientData,         /* Client data for xCreate/xConnect */
  void(*xDestroy)(void*)     /* Module destructor function */
);

/*
** CAPI3REF: Virtual Table Instance Object
** KEYWORDS: sqlite3_vtab
**
** Every [virtual table module] implementation uses a subclass
** of this object to describe a particular instance
** of the [virtual table].  Each subclass will
** be tailored to the specific needs of the module implementation.
** The purpose of this superclass is to define certain fields that are
** common to all module implementations.
**
** ^Virtual tables methods can set an error message by assigning a
** string obtained from [sqlite3_mprintf()] to zErrMsg.  The method should
** take care that any prior string is freed by a call to [sqlite3_free()]
** prior to assigning a new string to zErrMsg.  ^After the error message
** is delivered up to the client application, the string will be automatically
** freed by sqlite3_free() and the zErrMsg field will be zeroed.
*/
struct sqlite3_vtab {
  const sqlite3_module *pModule;  /* The module for this virtual table */
  int nRef;                       /* NO LONGER USED */
  char *zErrMsg;                  /* Error message from sqlite3_mprintf() */
  /* Virtual table implementations will typically add additional fields */
};

/*
** CAPI3REF: Virtual Table Cursor Object
** KEYWORDS: sqlite3_vtab_cursor {virtual table cursor}
**
** Every [virtual table module] implementation uses a subclass of the
** following structure to describe cursors that point into the
** [virtual table] and are used
** to loop through the virtual table.  Cursors are created using the
** [sqlite3_module.xOpen | xOpen] method of the module and are destroyed
** by the [sqlite3_module.xClose | xClose] method.  Cursors are used
** by the [xFilter], [xNext], [xEof], [xColumn], and [xRowid] methods
** of the module.  Each module implementation will define
** the content of a cursor structure to suit its own needs.
**
** This superclass exists in order to define fields of the cursor that
** are common to all implementations.
*/
struct sqlite3_vtab_cursor {
  sqlite3_vtab *pVtab;      /* Virtual table of this cursor */
  /* Virtual table implementations will typically add additional fields */
};

/*
** CAPI3REF: Declare The Schema Of A Virtual Table
**
** ^The [xCreate] and [xConnect] methods of a
** [virtual table module] call this interface
** to declare the format (the names and datatypes of the columns) of
** the virtual tables they implement.
*/
SQLITE_API int sqlite3_declare_vtab(sqlite3*, const char *zSQL);

/*
** CAPI3REF: Overload A Function For A Virtual Table
**
** ^(Virtual tables can provide alternative implementations of functions
** using the [xFindFunction] method of the [virtual table module].
** But global versions of those functions
** must exist in order to be overloaded.)^
**
** ^(This API makes sure a global version of a function with a particular
** name and number of parameters exists.  If no such function exists
** before this API is called, a new function is created.)^  ^The implementation
** of the new function always causes an exception to be thrown.  So
** the new function is not good for anything by itself.  Its only
** purpose is to be a placeholder function that can be overloaded
** by a [virtual table].
*/
SQLITE_API int sqlite3_overload_function(sqlite3*, const char *zFuncName, int nArg);

/*
** The interface to the virtual-table mechanism defined above (back up
** to a comment remarkably similar to this one) is currently considered
** to be experimental.  The interface might change in incompatible ways.
** If this is a problem for you, do not use the interface at this time.
**
** When the virtual-table mechanism stabilizes, we will declare the
** interface fixed, support it indefinitely, and remove this comment.
*/

/*
** CAPI3REF: A Handle To An Open BLOB
** KEYWORDS: {BLOB handle} {BLOB handles}
**
** An instance of this object represents an open BLOB on which
** [sqlite3_blob_open | incremental BLOB I/O] can be performed.
** ^Objects of this type are created by [sqlite3_blob_open()]
** and destroyed by [sqlite3_blob_close()].
** ^The [sqlite3_blob_read()] and [sqlite3_blob_write()] interfaces
** can be used to read or write small subsections of the BLOB.
** ^The [sqlite3_blob_bytes()] interface returns the size of the BLOB in bytes.
*/
typedef struct sqlite3_blob sqlite3_blob;

/*
** CAPI3REF: Open A BLOB For Incremental I/O
**
** ^(This interfaces opens a [BLOB handle | handle] to the BLOB located
** in row iRow, column zColumn, table zTable in database zDb;
** in other words, the same BLOB that would be selected by:
**
** 
    **     SELECT zColumn FROM zDb.zTable WHERE [rowid] = iRow;
** 
    )^
**
** ^If the flags parameter is non-zero, then the BLOB is opened for read
** and write access. ^If it is zero, the BLOB is opened for read access.
** ^It is not possible to open a column that is part of an index or primary
** key for writing. ^If [foreign key constraints] are enabled, it is
** not possible to open a column that is part of a [child key] for writing.
**
** ^Note that the database name is not the filename that contains
** the database but rather the symbolic name of the database that
** appears after the AS keyword when the database is connected using [ATTACH].
** ^For the main database file, the database name is "main".
** ^For TEMP tables, the database name is "temp".
**
** ^(On success, [SQLITE_OK] is returned and the new [BLOB handle] is written
** to *ppBlob. Otherwise an [error code] is returned and *ppBlob is set
** to be a null pointer.)^
** ^This function sets the [database connection] error code and message
** accessible via [sqlite3_errcode()] and [sqlite3_errmsg()] and related
** functions. ^Note that the *ppBlob variable is always initialized in a
** way that makes it safe to invoke [sqlite3_blob_close()] on *ppBlob
** regardless of the success or failure of this routine.
**
** ^(If the row that a BLOB handle points to is modified by an
** [UPDATE], [DELETE], or by [ON CONFLICT] side-effects
** then the BLOB handle is marked as "expired".
** This is true if any column of the row is changed, even a column
** other than the one the BLOB handle is open on.)^
** ^Calls to [sqlite3_blob_read()] and [sqlite3_blob_write()] for
** an expired BLOB handle fail with a return code of [SQLITE_ABORT].
** ^(Changes written into a BLOB prior to the BLOB expiring are not
** rolled back by the expiration of the BLOB.  Such changes will eventually
** commit if the transaction continues to completion.)^
**
** ^Use the [sqlite3_blob_bytes()] interface to determine the size of
** the opened blob.  ^The size of a blob may not be changed by this
** interface.  Use the [UPDATE] SQL command to change the size of a
** blob.
**
** ^The [sqlite3_bind_zeroblob()] and [sqlite3_result_zeroblob()] interfaces
** and the built-in [zeroblob] SQL function can be used, if desired,
** to create an empty, zero-filled blob in which to read or write using
** this interface.
**
** To avoid a resource leak, every open [BLOB handle] should eventually
** be released by a call to [sqlite3_blob_close()].
*/
SQLITE_API int sqlite3_blob_open(
  sqlite3*,
  const char *zDb,
  const char *zTable,
  const char *zColumn,
  sqlite3_int64 iRow,
  int flags,
  sqlite3_blob **ppBlob
);

/*
** CAPI3REF: Move a BLOB Handle to a New Row
**
** ^This function is used to move an existing blob handle so that it points
** to a different row of the same database table. ^The new row is identified
** by the rowid value passed as the second argument. Only the row can be
** changed. ^The database, table and column on which the blob handle is open
** remain the same. Moving an existing blob handle to a new row can be
** faster than closing the existing handle and opening a new one.
**
** ^(The new row must meet the same criteria as for [sqlite3_blob_open()] -
** it must exist and there must be either a blob or text value stored in
** the nominated column.)^ ^If the new row is not present in the table, or if
** it does not contain a blob or text value, or if another error occurs, an
** SQLite error code is returned and the blob handle is considered aborted.
** ^All subsequent calls to [sqlite3_blob_read()], [sqlite3_blob_write()] or
** [sqlite3_blob_reopen()] on an aborted blob handle immediately return
** SQLITE_ABORT. ^Calling [sqlite3_blob_bytes()] on an aborted blob handle
** always returns zero.
**
** ^This function sets the database handle error code and message.
*/
SQLITE_API SQLITE_EXPERIMENTAL int sqlite3_blob_reopen(sqlite3_blob *, sqlite3_int64);

/*
** CAPI3REF: Close A BLOB Handle
**
** ^Closes an open [BLOB handle].
**
** ^Closing a BLOB shall cause the current transaction to commit
** if there are no other BLOBs, no pending prepared statements, and the
** database connection is in [autocommit mode].
** ^If any writes were made to the BLOB, they might be held in cache
** until the close operation if they will fit.
**
** ^(Closing the BLOB often forces the changes
** out to disk and so if any I/O errors occur, they will likely occur
** at the time when the BLOB is closed.  Any errors that occur during
** closing are reported as a non-zero return value.)^
**
** ^(The BLOB is closed unconditionally.  Even if this routine returns
** an error code, the BLOB is still closed.)^
**
** ^Calling this routine with a null pointer (such as would be returned
** by a failed call to [sqlite3_blob_open()]) is a harmless no-op.
*/
SQLITE_API int sqlite3_blob_close(sqlite3_blob *);

/*
** CAPI3REF: Return The Size Of An Open BLOB
**
** ^Returns the size in bytes of the BLOB accessible via the
** successfully opened [BLOB handle] in its only argument.  ^The
** incremental blob I/O routines can only read or overwriting existing
** blob content; they cannot change the size of a blob.
**
** This routine only works on a [BLOB handle] which has been created
** by a prior successful call to [sqlite3_blob_open()] and which has not
** been closed by [sqlite3_blob_close()].  Passing any other pointer in
** to this routine results in undefined and probably undesirable behavior.
*/
SQLITE_API int sqlite3_blob_bytes(sqlite3_blob *);

/*
** CAPI3REF: Read Data From A BLOB Incrementally
**
** ^(This function is used to read data from an open [BLOB handle] into a
** caller-supplied buffer. N bytes of data are copied into buffer Z
** from the open BLOB, starting at offset iOffset.)^
**
** ^If offset iOffset is less than N bytes from the end of the BLOB,
** [SQLITE_ERROR] is returned and no data is read.  ^If N or iOffset is
** less than zero, [SQLITE_ERROR] is returned and no data is read.
** ^The size of the blob (and hence the maximum value of N+iOffset)
** can be determined using the [sqlite3_blob_bytes()] interface.
**
** ^An attempt to read from an expired [BLOB handle] fails with an
** error code of [SQLITE_ABORT].
**
** ^(On success, sqlite3_blob_read() returns SQLITE_OK.
** Otherwise, an [error code] or an [extended error code] is returned.)^
**
** This routine only works on a [BLOB handle] which has been created
** by a prior successful call to [sqlite3_blob_open()] and which has not
** been closed by [sqlite3_blob_close()].  Passing any other pointer in
** to this routine results in undefined and probably undesirable behavior.
**
** See also: [sqlite3_blob_write()].
*/
SQLITE_API int sqlite3_blob_read(sqlite3_blob *, void *Z, int N, int iOffset);

/*
** CAPI3REF: Write Data Into A BLOB Incrementally
**
** ^This function is used to write data into an open [BLOB handle] from a
** caller-supplied buffer. ^N bytes of data are copied from the buffer Z
** into the open BLOB, starting at offset iOffset.
**
** ^If the [BLOB handle] passed as the first argument was not opened for
** writing (the flags parameter to [sqlite3_blob_open()] was zero),
** this function returns [SQLITE_READONLY].
**
** ^This function may only modify the contents of the BLOB; it is
** not possible to increase the size of a BLOB using this API.
** ^If offset iOffset is less than N bytes from the end of the BLOB,
** [SQLITE_ERROR] is returned and no data is written.  ^If N is
** less than zero [SQLITE_ERROR] is returned and no data is written.
** The size of the BLOB (and hence the maximum value of N+iOffset)
** can be determined using the [sqlite3_blob_bytes()] interface.
**
** ^An attempt to write to an expired [BLOB handle] fails with an
** error code of [SQLITE_ABORT].  ^Writes to the BLOB that occurred
** before the [BLOB handle] expired are not rolled back by the
** expiration of the handle, though of course those changes might
** have been overwritten by the statement that expired the BLOB handle
** or by other independent statements.
**
** ^(On success, sqlite3_blob_write() returns SQLITE_OK.
** Otherwise, an  [error code] or an [extended error code] is returned.)^
**
** This routine only works on a [BLOB handle] which has been created
** by a prior successful call to [sqlite3_blob_open()] and which has not
** been closed by [sqlite3_blob_close()].  Passing any other pointer in
** to this routine results in undefined and probably undesirable behavior.
**
** See also: [sqlite3_blob_read()].
*/
SQLITE_API int sqlite3_blob_write(sqlite3_blob *, const void *z, int n, int iOffset);

/*
** CAPI3REF: Virtual File System Objects
**
** A virtual filesystem (VFS) is an [sqlite3_vfs] object
** that SQLite uses to interact
** with the underlying operating system.  Most SQLite builds come with a
** single default VFS that is appropriate for the host computer.
** New VFSes can be registered and existing VFSes can be unregistered.
** The following interfaces are provided.
**
** ^The sqlite3_vfs_find() interface returns a pointer to a VFS given its name.
** ^Names are case sensitive.
** ^Names are zero-terminated UTF-8 strings.
** ^If there is no match, a NULL pointer is returned.
** ^If zVfsName is NULL then the default VFS is returned.
**
** ^New VFSes are registered with sqlite3_vfs_register().
** ^Each new VFS becomes the default VFS if the makeDflt flag is set.
** ^The same VFS can be registered multiple times without injury.
** ^To make an existing VFS into the default VFS, register it again
** with the makeDflt flag set.  If two different VFSes with the
** same name are registered, the behavior is undefined.  If a
** VFS is registered with a name that is NULL or an empty string,
** then the behavior is undefined.
**
** ^Unregister a VFS with the sqlite3_vfs_unregister() interface.
** ^(If the default VFS is unregistered, another VFS is chosen as
** the default.  The choice for the new VFS is arbitrary.)^
*/
SQLITE_API sqlite3_vfs *sqlite3_vfs_find(const char *zVfsName);
SQLITE_API int sqlite3_vfs_register(sqlite3_vfs*, int makeDflt);
SQLITE_API int sqlite3_vfs_unregister(sqlite3_vfs*);

/*
** CAPI3REF: Mutexes
**
** The SQLite core uses these routines for thread
** synchronization. Though they are intended for internal
** use by SQLite, code that links against SQLite is
** permitted to use any of these routines.
**
** The SQLite source code contains multiple implementations
** of these mutex routines.  An appropriate implementation
** is selected automatically at compile-time.  ^(The following
** implementations are available in the SQLite core:
**
** 
      
** 
    •    SQLITE_MUTEX_OS2
** 
    •    SQLITE_MUTEX_PTHREADS
** 
    •    SQLITE_MUTEX_W32
** 
    •    SQLITE_MUTEX_NOOP
** 
    )^
**
** ^The SQLITE_MUTEX_NOOP implementation is a set of routines
** that does no real locking and is appropriate for use in
** a single-threaded application.  ^The SQLITE_MUTEX_OS2,
** SQLITE_MUTEX_PTHREADS, and SQLITE_MUTEX_W32 implementations
** are appropriate for use on OS/2, Unix, and Windows.
**
** ^(If SQLite is compiled with the SQLITE_MUTEX_APPDEF preprocessor
** macro defined (with "-DSQLITE_MUTEX_APPDEF=1"), then no mutex
** implementation is included with the library. In this case the
** application must supply a custom mutex implementation using the
** [SQLITE_CONFIG_MUTEX] option of the sqlite3_config() function
** before calling sqlite3_initialize() or any other public sqlite3_
** function that calls sqlite3_initialize().)^
**
** ^The sqlite3_mutex_alloc() routine allocates a new
** mutex and returns a pointer to it. ^If it returns NULL
** that means that a mutex could not be allocated.  ^SQLite
** will unwind its stack and return an error.  ^(The argument
** to sqlite3_mutex_alloc() is one of these integer constants:
**
** 
      
** 
    •   SQLITE_MUTEX_FAST
** 
    •   SQLITE_MUTEX_RECURSIVE
** 
    •   SQLITE_MUTEX_STATIC_MASTER
** 
    •   SQLITE_MUTEX_STATIC_MEM
** 
    •   SQLITE_MUTEX_STATIC_MEM2
** 
    •   SQLITE_MUTEX_STATIC_PRNG
** 
    •   SQLITE_MUTEX_STATIC_LRU
** 
    •   SQLITE_MUTEX_STATIC_LRU2
** 
    )^
**
** ^The first two constants (SQLITE_MUTEX_FAST and SQLITE_MUTEX_RECURSIVE)
** cause sqlite3_mutex_alloc() to create
** a new mutex.  ^The new mutex is recursive when SQLITE_MUTEX_RECURSIVE
** is used but not necessarily so when SQLITE_MUTEX_FAST is used.
** The mutex implementation does not need to make a distinction
** between SQLITE_MUTEX_RECURSIVE and SQLITE_MUTEX_FAST if it does
** not want to.  ^SQLite will only request a recursive mutex in
** cases where it really needs one.  ^If a faster non-recursive mutex
** implementation is available on the host platform, the mutex subsystem
** might return such a mutex in response to SQLITE_MUTEX_FAST.
**
** ^The other allowed parameters to sqlite3_mutex_alloc() (anything other
** than SQLITE_MUTEX_FAST and SQLITE_MUTEX_RECURSIVE) each return
** a pointer to a static preexisting mutex.  ^Six static mutexes are
** used by the current version of SQLite.  Future versions of SQLite
** may add additional static mutexes.  Static mutexes are for internal
** use by SQLite only.  Applications that use SQLite mutexes should
** use only the dynamic mutexes returned by SQLITE_MUTEX_FAST or
** SQLITE_MUTEX_RECURSIVE.
**
** ^Note that if one of the dynamic mutex parameters (SQLITE_MUTEX_FAST
** or SQLITE_MUTEX_RECURSIVE) is used then sqlite3_mutex_alloc()
** returns a different mutex on every call.  ^But for the static
** mutex types, the same mutex is returned on every call that has
** the same type number.
**
** ^The sqlite3_mutex_free() routine deallocates a previously
** allocated dynamic mutex.  ^SQLite is careful to deallocate every
** dynamic mutex that it allocates.  The dynamic mutexes must not be in
** use when they are deallocated.  Attempting to deallocate a static
** mutex results in undefined behavior.  ^SQLite never deallocates
** a static mutex.
**
** ^The sqlite3_mutex_enter() and sqlite3_mutex_try() routines attempt
** to enter a mutex.  ^If another thread is already within the mutex,
** sqlite3_mutex_enter() will block and sqlite3_mutex_try() will return
** SQLITE_BUSY.  ^The sqlite3_mutex_try() interface returns [SQLITE_OK]
** upon successful entry.  ^(Mutexes created using
** SQLITE_MUTEX_RECURSIVE can be entered multiple times by the same thread.
** In such cases the,
** mutex must be exited an equal number of times before another thread
** can enter.)^  ^(If the same thread tries to enter any other
** kind of mutex more than once, the behavior is undefined.
** SQLite will never exhibit
** such behavior in its own use of mutexes.)^
**
** ^(Some systems (for example, Windows 95) do not support the operation
** implemented by sqlite3_mutex_try().  On those systems, sqlite3_mutex_try()
** will always return SQLITE_BUSY.  The SQLite core only ever uses
** sqlite3_mutex_try() as an optimization so this is acceptable behavior.)^
**
** ^The sqlite3_mutex_leave() routine exits a mutex that was
** previously entered by the same thread.   ^(The behavior
** is undefined if the mutex is not currently entered by the
** calling thread or is not currently allocated.  SQLite will
** never do either.)^
**
** ^If the argument to sqlite3_mutex_enter(), sqlite3_mutex_try(), or
** sqlite3_mutex_leave() is a NULL pointer, then all three routines
** behave as no-ops.
**
** See also: [sqlite3_mutex_held()] and [sqlite3_mutex_notheld()].
*/
SQLITE_API sqlite3_mutex *sqlite3_mutex_alloc(int);
SQLITE_API void sqlite3_mutex_free(sqlite3_mutex*);
SQLITE_API void sqlite3_mutex_enter(sqlite3_mutex*);
SQLITE_API int sqlite3_mutex_try(sqlite3_mutex*);
SQLITE_API void sqlite3_mutex_leave(sqlite3_mutex*);

/*
** CAPI3REF: Mutex Methods Object
**
** An instance of this structure defines the low-level routines
** used to allocate and use mutexes.
**
** Usually, the default mutex implementations provided by SQLite are
** sufficient, however the user has the option of substituting a custom
** implementation for specialized deployments or systems for which SQLite
** does not provide a suitable implementation. In this case, the user
** creates and populates an instance of this structure to pass
** to sqlite3_config() along with the [SQLITE_CONFIG_MUTEX] option.
** Additionally, an instance of this structure can be used as an
** output variable when querying the system for the current mutex
** implementation, using the [SQLITE_CONFIG_GETMUTEX] option.
**
** ^The xMutexInit method defined by this structure is invoked as
** part of system initialization by the sqlite3_initialize() function.
** ^The xMutexInit routine is called by SQLite exactly once for each
** effective call to [sqlite3_initialize()].
**
** ^The xMutexEnd method defined by this structure is invoked as
** part of system shutdown by the sqlite3_shutdown() function. The
** implementation of this method is expected to release all outstanding
** resources obtained by the mutex methods implementation, especially
** those obtained by the xMutexInit method.  ^The xMutexEnd()
** interface is invoked exactly once for each call to [sqlite3_shutdown()].
**
** ^(The remaining seven methods defined by this structure (xMutexAlloc,
** xMutexFree, xMutexEnter, xMutexTry, xMutexLeave, xMutexHeld and
** xMutexNotheld) implement the following interfaces (respectively):
**
** 
      
**   
    •   [sqlite3_mutex_alloc()] 
      • 
**   
    •   [sqlite3_mutex_free()] 
      • 
**   
    •   [sqlite3_mutex_enter()] 
      • 
**   
    •   [sqlite3_mutex_try()] 
      • 
**   
    •   [sqlite3_mutex_leave()] 
      • 
**   
    •   [sqlite3_mutex_held()] 
      • 
**   
    •   [sqlite3_mutex_notheld()] 
      • 
** 
    )^
**
** The only difference is that the public sqlite3_XXX functions enumerated
** above silently ignore any invocations that pass a NULL pointer instead
** of a valid mutex handle. The implementations of the methods defined
** by this structure are not required to handle this case, the results
** of passing a NULL pointer instead of a valid mutex handle are undefined
** (i.e. it is acceptable to provide an implementation that segfaults if
** it is passed a NULL pointer).
**
** The xMutexInit() method must be threadsafe.  ^It must be harmless to
** invoke xMutexInit() multiple times within the same process and without
** intervening calls to xMutexEnd().  Second and subsequent calls to
** xMutexInit() must be no-ops.
**
** ^xMutexInit() must not use SQLite memory allocation ([sqlite3_malloc()]
** and its associates).  ^Similarly, xMutexAlloc() must not use SQLite memory
** allocation for a static mutex.  ^However xMutexAlloc() may use SQLite
** memory allocation for a fast or recursive mutex.
**
** ^SQLite will invoke the xMutexEnd() method when [sqlite3_shutdown()] is
** called, but only if the prior call to xMutexInit returned SQLITE_OK.
** If xMutexInit fails in any way, it is expected to clean up after itself
** prior to returning.
*/
typedef struct sqlite3_mutex_methods sqlite3_mutex_methods;
struct sqlite3_mutex_methods {
  int (*xMutexInit)(void);
  int (*xMutexEnd)(void);
  sqlite3_mutex *(*xMutexAlloc)(int);
  void (*xMutexFree)(sqlite3_mutex *);
  void (*xMutexEnter)(sqlite3_mutex *);
  int (*xMutexTry)(sqlite3_mutex *);
  void (*xMutexLeave)(sqlite3_mutex *);
  int (*xMutexHeld)(sqlite3_mutex *);
  int (*xMutexNotheld)(sqlite3_mutex *);
};

/*
** CAPI3REF: Mutex Verification Routines
**
** The sqlite3_mutex_held() and sqlite3_mutex_notheld() routines
** are intended for use inside assert() statements.  ^The SQLite core
** never uses these routines except inside an assert() and applications
** are advised to follow the lead of the core.  ^The SQLite core only
** provides implementations for these routines when it is compiled
** with the SQLITE_DEBUG flag.  ^External mutex implementations
** are only required to provide these routines if SQLITE_DEBUG is
** defined and if NDEBUG is not defined.
**
** ^These routines should return true if the mutex in their argument
** is held or not held, respectively, by the calling thread.
**
** ^The implementation is not required to provide versions of these
** routines that actually work. If the implementation does not provide working
** versions of these routines, it should at least provide stubs that always
** return true so that one does not get spurious assertion failures.
**
** ^If the argument to sqlite3_mutex_held() is a NULL pointer then
** the routine should return 1.   This seems counter-intuitive since
** clearly the mutex cannot be held if it does not exist.  But
** the reason the mutex does not exist is because the build is not
** using mutexes.  And we do not want the assert() containing the
** call to sqlite3_mutex_held() to fail, so a non-zero return is
** the appropriate thing to do.  ^The sqlite3_mutex_notheld()
** interface should also return 1 when given a NULL pointer.
*/
#ifndef NDEBUG
SQLITE_API int sqlite3_mutex_held(sqlite3_mutex*);
SQLITE_API int sqlite3_mutex_notheld(sqlite3_mutex*);
#endif

/*
** CAPI3REF: Mutex Types
**
** The [sqlite3_mutex_alloc()] interface takes a single argument
** which is one of these integer constants.
**
** The set of static mutexes may change from one SQLite release to the
** next.  Applications that override the built-in mutex logic must be
** prepared to accommodate additional static mutexes.
*/
#define SQLITE_MUTEX_FAST             0
#define SQLITE_MUTEX_RECURSIVE        1
#define SQLITE_MUTEX_STATIC_MASTER    2
#define SQLITE_MUTEX_STATIC_MEM       3  /* sqlite3_malloc() */
#define SQLITE_MUTEX_STATIC_MEM2      4  /* NOT USED */
#define SQLITE_MUTEX_STATIC_OPEN      4  /* sqlite3BtreeOpen() */
#define SQLITE_MUTEX_STATIC_PRNG      5  /* sqlite3_random() */
#define SQLITE_MUTEX_STATIC_LRU       6  /* lru page list */
#define SQLITE_MUTEX_STATIC_LRU2      7  /* NOT USED */
#define SQLITE_MUTEX_STATIC_PMEM      7  /* sqlite3PageMalloc() */

/*
** CAPI3REF: Retrieve the mutex for a database connection
**
** ^This interface returns a pointer the [sqlite3_mutex] object that
** serializes access to the [database connection] given in the argument
** when the [threading mode] is Serialized.
** ^If the [threading mode] is Single-thread or Multi-thread then this
** routine returns a NULL pointer.
*/
SQLITE_API sqlite3_mutex *sqlite3_db_mutex(sqlite3*);

/*
** CAPI3REF: Low-Level Control Of Database Files
**
** ^The [sqlite3_file_control()] interface makes a direct call to the
** xFileControl method for the [sqlite3_io_methods] object associated
** with a particular database identified by the second argument. ^The
** name of the database is "main" for the main database or "temp" for the
** TEMP database, or the name that appears after the AS keyword for
** databases that are added using the [ATTACH] SQL command.
** ^A NULL pointer can be used in place of "main" to refer to the
** main database file.
** ^The third and fourth parameters to this routine
** are passed directly through to the second and third parameters of
** the xFileControl method.  ^The return value of the xFileControl
** method becomes the return value of this routine.
**
** ^The SQLITE_FCNTL_FILE_POINTER value for the op parameter causes
** a pointer to the underlying [sqlite3_file] object to be written into
** the space pointed to by the 4th parameter.  ^The SQLITE_FCNTL_FILE_POINTER
** case is a short-circuit path which does not actually invoke the
** underlying sqlite3_io_methods.xFileControl method.
**
** ^If the second parameter (zDbName) does not match the name of any
** open database file, then SQLITE_ERROR is returned.  ^This error
** code is not remembered and will not be recalled by [sqlite3_errcode()]
** or [sqlite3_errmsg()].  The underlying xFileControl method might
** also return SQLITE_ERROR.  There is no way to distinguish between
** an incorrect zDbName and an SQLITE_ERROR return from the underlying
** xFileControl method.
**
** See also: [SQLITE_FCNTL_LOCKSTATE]
*/
SQLITE_API int sqlite3_file_control(sqlite3*, const char *zDbName, int op, void*);

/*
** CAPI3REF: Testing Interface
**
** ^The sqlite3_test_control() interface is used to read out internal
** state of SQLite and to inject faults into SQLite for testing
** purposes.  ^The first parameter is an operation code that determines
** the number, meaning, and operation of all subsequent parameters.
**
** This interface is not for use by applications.  It exists solely
** for verifying the correct operation of the SQLite library.  Depending
** on how the SQLite library is compiled, this interface might not exist.
**
** The details of the operation codes, their meanings, the parameters
** they take, and what they do are all subject to change without notice.
** Unlike most of the SQLite API, this function is not guaranteed to
** operate consistently from one release to the next.
*/
SQLITE_API int sqlite3_test_control(int op, ...);

/*
** CAPI3REF: Testing Interface Operation Codes
**
** These constants are the valid operation code parameters used
** as the first argument to [sqlite3_test_control()].
**
** These parameters and their meanings are subject to change
** without notice.  These values are for testing purposes only.
** Applications should not use any of these parameters or the
** [sqlite3_test_control()] interface.
*/
#define SQLITE_TESTCTRL_FIRST                    5
#define SQLITE_TESTCTRL_PRNG_SAVE                5
#define SQLITE_TESTCTRL_PRNG_RESTORE             6
#define SQLITE_TESTCTRL_PRNG_RESET               7
#define SQLITE_TESTCTRL_BITVEC_TEST              8
#define SQLITE_TESTCTRL_FAULT_INSTALL            9
#define SQLITE_TESTCTRL_BENIGN_MALLOC_HOOKS     10
#define SQLITE_TESTCTRL_PENDING_BYTE            11
#define SQLITE_TESTCTRL_ASSERT                  12
#define SQLITE_TESTCTRL_ALWAYS                  13
#define SQLITE_TESTCTRL_RESERVE                 14
#define SQLITE_TESTCTRL_OPTIMIZATIONS           15
#define SQLITE_TESTCTRL_ISKEYWORD               16
#define SQLITE_TESTCTRL_SCRATCHMALLOC           17
#define SQLITE_TESTCTRL_LOCALTIME_FAULT         18
#define SQLITE_TESTCTRL_EXPLAIN_STMT            19
#define SQLITE_TESTCTRL_LAST                    19

/*
** CAPI3REF: SQLite Runtime Status
**
** ^This interface is used to retrieve runtime status information
** about the performance of SQLite, and optionally to reset various
** highwater marks.  ^The first argument is an integer code for
** the specific parameter to measure.  ^(Recognized integer codes
** are of the form [status parameters | SQLITE_STATUS_...].)^
** ^The current value of the parameter is returned into *pCurrent.
** ^The highest recorded value is returned in *pHighwater.  ^If the
** resetFlag is true, then the highest record value is reset after
** *pHighwater is written.  ^(Some parameters do not record the highest
** value.  For those parameters
** nothing is written into *pHighwater and the resetFlag is ignored.)^
** ^(Other parameters record only the highwater mark and not the current
** value.  For these latter parameters nothing is written into *pCurrent.)^
**
** ^The sqlite3_status() routine returns SQLITE_OK on success and a
** non-zero [error code] on failure.
**
** This routine is threadsafe but is not atomic.  This routine can be
** called while other threads are running the same or different SQLite
** interfaces.  However the values returned in *pCurrent and
** *pHighwater reflect the status of SQLite at different points in time
** and it is possible that another thread might change the parameter
** in between the times when *pCurrent and *pHighwater are written.
**
** See also: [sqlite3_db_status()]
*/
SQLITE_API int sqlite3_status(int op, int *pCurrent, int *pHighwater, int resetFlag);


/*
** CAPI3REF: Status Parameters
** KEYWORDS: {status parameters}
**
** These integer constants designate various run-time status parameters
** that can be returned by [sqlite3_status()].
**
** 
    
** [[SQLITE_STATUS_MEMORY_USED]] ^(
    SQLITE_STATUS_MEMORY_USED
    
** 
    This parameter is the current amount of memory checked out
** using [sqlite3_malloc()], either directly or indirectly.  The
** figure includes calls made to [sqlite3_malloc()] by the application
** and internal memory usage by the SQLite library.  Scratch memory
** controlled by [SQLITE_CONFIG_SCRATCH] and auxiliary page-cache
** memory controlled by [SQLITE_CONFIG_PAGECACHE] is not included in
** this parameter.  The amount returned is the sum of the allocation
** sizes as reported by the xSize method in [sqlite3_mem_methods].
    )^
**
** [[SQLITE_STATUS_MALLOC_SIZE]] ^(
    SQLITE_STATUS_MALLOC_SIZE
    
** 
    This parameter records the largest memory allocation request
** handed to [sqlite3_malloc()] or [sqlite3_realloc()] (or their
** internal equivalents).  Only the value returned in the
** *pHighwater parameter to [sqlite3_status()] is of interest.
** The value written into the *pCurrent parameter is undefined.
    )^
**
** [[SQLITE_STATUS_MALLOC_COUNT]] ^(
    SQLITE_STATUS_MALLOC_COUNT
    
** 
    This parameter records the number of separate memory allocations
** currently checked out.
    )^
**
** [[SQLITE_STATUS_PAGECACHE_USED]] ^(
    SQLITE_STATUS_PAGECACHE_USED
    
** 
    This parameter returns the number of pages used out of the
** [pagecache memory allocator] that was configured using
** [SQLITE_CONFIG_PAGECACHE].  The
** value returned is in pages, not in bytes.
    )^
**
** [[SQLITE_STATUS_PAGECACHE_OVERFLOW]]
** ^(
    SQLITE_STATUS_PAGECACHE_OVERFLOW
    
** 
    This parameter returns the number of bytes of page cache
** allocation which could not be satisfied by the [SQLITE_CONFIG_PAGECACHE]
** buffer and where forced to overflow to [sqlite3_malloc()].  The
** returned value includes allocations that overflowed because they
** where too large (they were larger than the "sz" parameter to
** [SQLITE_CONFIG_PAGECACHE]) and allocations that overflowed because
** no space was left in the page cache.
    )^
**
** [[SQLITE_STATUS_PAGECACHE_SIZE]] ^(
    SQLITE_STATUS_PAGECACHE_SIZE
    
** 
    This parameter records the largest memory allocation request
** handed to [pagecache memory allocator].  Only the value returned in the
** *pHighwater parameter to [sqlite3_status()] is of interest.
** The value written into the *pCurrent parameter is undefined.
    )^
**
** [[SQLITE_STATUS_SCRATCH_USED]] ^(
    SQLITE_STATUS_SCRATCH_USED
    
** 
    This parameter returns the number of allocations used out of the
** [scratch memory allocator] configured using
** [SQLITE_CONFIG_SCRATCH].  The value returned is in allocations, not
** in bytes.  Since a single thread may only have one scratch allocation
** outstanding at time, this parameter also reports the number of threads
** using scratch memory at the same time.
    )^
**
** [[SQLITE_STATUS_SCRATCH_OVERFLOW]] ^(
    SQLITE_STATUS_SCRATCH_OVERFLOW
    
** 
    This parameter returns the number of bytes of scratch memory
** allocation which could not be satisfied by the [SQLITE_CONFIG_SCRATCH]
** buffer and where forced to overflow to [sqlite3_malloc()].  The values
** returned include overflows because the requested allocation was too
** larger (that is, because the requested allocation was larger than the
** "sz" parameter to [SQLITE_CONFIG_SCRATCH]) and because no scratch buffer
** slots were available.
** 
    )^
**
** [[SQLITE_STATUS_SCRATCH_SIZE]] ^(
    SQLITE_STATUS_SCRATCH_SIZE
    
** 
    This parameter records the largest memory allocation request
** handed to [scratch memory allocator].  Only the value returned in the
** *pHighwater parameter to [sqlite3_status()] is of interest.
** The value written into the *pCurrent parameter is undefined.
    )^
**
** [[SQLITE_STATUS_PARSER_STACK]] ^(
    SQLITE_STATUS_PARSER_STACK
    
** 
    This parameter records the deepest parser stack.  It is only
** meaningful if SQLite is compiled with [YYTRACKMAXSTACKDEPTH].
    )^
** 
    
**
** New status parameters may be added from time to time.
*/
#define SQLITE_STATUS_MEMORY_USED          0
#define SQLITE_STATUS_PAGECACHE_USED       1
#define SQLITE_STATUS_PAGECACHE_OVERFLOW   2
#define SQLITE_STATUS_SCRATCH_USED         3
#define SQLITE_STATUS_SCRATCH_OVERFLOW     4
#define SQLITE_STATUS_MALLOC_SIZE          5
#define SQLITE_STATUS_PARSER_STACK         6
#define SQLITE_STATUS_PAGECACHE_SIZE       7
#define SQLITE_STATUS_SCRATCH_SIZE         8
#define SQLITE_STATUS_MALLOC_COUNT         9

/*
** CAPI3REF: Database Connection Status
**
** ^This interface is used to retrieve runtime status information
** about a single [database connection].  ^The first argument is the
** database connection object to be interrogated.  ^The second argument
** is an integer constant, taken from the set of
** [SQLITE_DBSTATUS options], that
** determines the parameter to interrogate.  The set of
** [SQLITE_DBSTATUS options] is likely
** to grow in future releases of SQLite.
**
** ^The current value of the requested parameter is written into *pCur
** and the highest instantaneous value is written into *pHiwtr.  ^If
** the resetFlg is true, then the highest instantaneous value is
** reset back down to the current value.
**
** ^The sqlite3_db_status() routine returns SQLITE_OK on success and a
** non-zero [error code] on failure.
**
** See also: [sqlite3_status()] and [sqlite3_stmt_status()].
*/
SQLITE_API int sqlite3_db_status(sqlite3*, int op, int *pCur, int *pHiwtr, int resetFlg);

/*
** CAPI3REF: Status Parameters for database connections
** KEYWORDS: {SQLITE_DBSTATUS options}
**
** These constants are the available integer "verbs" that can be passed as
** the second argument to the [sqlite3_db_status()] interface.
**
** New verbs may be added in future releases of SQLite. Existing verbs
** might be discontinued. Applications should check the return code from
** [sqlite3_db_status()] to make sure that the call worked.
** The [sqlite3_db_status()] interface will return a non-zero error code
** if a discontinued or unsupported verb is invoked.
**
** 
    
** [[SQLITE_DBSTATUS_LOOKASIDE_USED]] ^(
    SQLITE_DBSTATUS_LOOKASIDE_USED
    
** 
    This parameter returns the number of lookaside memory slots currently
** checked out.
    )^
**
** [[SQLITE_DBSTATUS_LOOKASIDE_HIT]] ^(
    SQLITE_DBSTATUS_LOOKASIDE_HIT
    
** 
    This parameter returns the number malloc attempts that were
** satisfied using lookaside memory. Only the high-water value is meaningful;
** the current value is always zero.)^
**
** [[SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE]]
** ^(
    SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE
    
** 
    This parameter returns the number malloc attempts that might have
** been satisfied using lookaside memory but failed due to the amount of
** memory requested being larger than the lookaside slot size.
** Only the high-water value is meaningful;
** the current value is always zero.)^
**
** [[SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL]]
** ^(
    SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL
    
** 
    This parameter returns the number malloc attempts that might have
** been satisfied using lookaside memory but failed due to all lookaside
** memory already being in use.
** Only the high-water value is meaningful;
** the current value is always zero.)^
**
** [[SQLITE_DBSTATUS_CACHE_USED]] ^(
    SQLITE_DBSTATUS_CACHE_USED
    
** 
    This parameter returns the approximate number of of bytes of heap
** memory used by all pager caches associated with the database connection.)^
** ^The highwater mark associated with SQLITE_DBSTATUS_CACHE_USED is always 0.
**
** [[SQLITE_DBSTATUS_SCHEMA_USED]] ^(
    SQLITE_DBSTATUS_SCHEMA_USED
    
** 
    This parameter returns the approximate number of of bytes of heap
** memory used to store the schema for all databases associated
** with the connection - main, temp, and any [ATTACH]-ed databases.)^
** ^The full amount of memory used by the schemas is reported, even if the
** schema memory is shared with other database connections due to
** [shared cache mode] being enabled.
** ^The highwater mark associated with SQLITE_DBSTATUS_SCHEMA_USED is always 0.
**
** [[SQLITE_DBSTATUS_STMT_USED]] ^(
    SQLITE_DBSTATUS_STMT_USED
    
** 
    This parameter returns the approximate number of of bytes of heap
** and lookaside memory used by all prepared statements associated with
** the database connection.)^
** ^The highwater mark associated with SQLITE_DBSTATUS_STMT_USED is always 0.
** 
    
**
** [[SQLITE_DBSTATUS_CACHE_HIT]] ^(
    SQLITE_DBSTATUS_CACHE_HIT
    
** 
    This parameter returns the number of pager cache hits that have
** occurred.)^ ^The highwater mark associated with SQLITE_DBSTATUS_CACHE_HIT
** is always 0.
** 
    
**
** [[SQLITE_DBSTATUS_CACHE_MISS]] ^(
    SQLITE_DBSTATUS_CACHE_MISS
    
** 
    This parameter returns the number of pager cache misses that have
** occurred.)^ ^The highwater mark associated with SQLITE_DBSTATUS_CACHE_MISS
** is always 0.
** 
    
** 
    
*/
#define SQLITE_DBSTATUS_LOOKASIDE_USED       0
#define SQLITE_DBSTATUS_CACHE_USED           1
#define SQLITE_DBSTATUS_SCHEMA_USED          2
#define SQLITE_DBSTATUS_STMT_USED            3
#define SQLITE_DBSTATUS_LOOKASIDE_HIT        4
#define SQLITE_DBSTATUS_LOOKASIDE_MISS_SIZE  5
#define SQLITE_DBSTATUS_LOOKASIDE_MISS_FULL  6
#define SQLITE_DBSTATUS_CACHE_HIT            7
#define SQLITE_DBSTATUS_CACHE_MISS           8
#define SQLITE_DBSTATUS_MAX                  8   /* Largest defined DBSTATUS */


/*
** CAPI3REF: Prepared Statement Status
**
** ^(Each prepared statement maintains various
** [SQLITE_STMTSTATUS counters] that measure the number
** of times it has performed specific operations.)^  These counters can
** be used to monitor the performance characteristics of the prepared
** statements.  For example, if the number of table steps greatly exceeds
** the number of table searches or result rows, that would tend to indicate
** that the prepared statement is using a full table scan rather than
** an index.
**
** ^(This interface is used to retrieve and reset counter values from
** a [prepared statement].  The first argument is the prepared statement
** object to be interrogated.  The second argument
** is an integer code for a specific [SQLITE_STMTSTATUS counter]
** to be interrogated.)^
** ^The current value of the requested counter is returned.
** ^If the resetFlg is true, then the counter is reset to zero after this
** interface call returns.
**
** See also: [sqlite3_status()] and [sqlite3_db_status()].
*/
SQLITE_API int sqlite3_stmt_status(sqlite3_stmt*, int op,int resetFlg);

/*
** CAPI3REF: Status Parameters for prepared statements
** KEYWORDS: {SQLITE_STMTSTATUS counter} {SQLITE_STMTSTATUS counters}
**
** These preprocessor macros define integer codes that name counter
** values associated with the [sqlite3_stmt_status()] interface.
** The meanings of the various counters are as follows:
**
** 
    
** [[SQLITE_STMTSTATUS_FULLSCAN_STEP]] 
    SQLITE_STMTSTATUS_FULLSCAN_STEP
    
** 
    ^This is the number of times that SQLite has stepped forward in
** a table as part of a full table scan.  Large numbers for this counter
** may indicate opportunities for performance improvement through
** careful use of indices.
    
**
** [[SQLITE_STMTSTATUS_SORT]] 
    SQLITE_STMTSTATUS_SORT
    
** 
    ^This is the number of sort operations that have occurred.
** A non-zero value in this counter may indicate an opportunity to
** improvement performance through careful use of indices.
    
**
** [[SQLITE_STMTSTATUS_AUTOINDEX]] 
    SQLITE_STMTSTATUS_AUTOINDEX
    
** 
    ^This is the number of rows inserted into transient indices that
** were created automatically in order to help joins run faster.
** A non-zero value in this counter may indicate an opportunity to
** improvement performance by adding permanent indices that do not
** need to be reinitialized each time the statement is run.
    
** 
    
*/
#define SQLITE_STMTSTATUS_FULLSCAN_STEP     1
#define SQLITE_STMTSTATUS_SORT              2
#define SQLITE_STMTSTATUS_AUTOINDEX         3

/*
** CAPI3REF: Custom Page Cache Object
**
** The sqlite3_pcache type is opaque.  It is implemented by
** the pluggable module.  The SQLite core has no knowledge of
** its size or internal structure and never deals with the
** sqlite3_pcache object except by holding and passing pointers
** to the object.
**
** See [sqlite3_pcache_methods2] for additional information.
*/
typedef struct sqlite3_pcache sqlite3_pcache;

/*
** CAPI3REF: Custom Page Cache Object
**
** The sqlite3_pcache_page object represents a single page in the
** page cache.  The page cache will allocate instances of this
** object.  Various methods of the page cache use pointers to instances
** of this object as parameters or as their return value.
**
** See [sqlite3_pcache_methods2] for additional information.
*/
typedef struct sqlite3_pcache_page sqlite3_pcache_page;
struct sqlite3_pcache_page {
  void *pBuf;        /* The content of the page */
  void *pExtra;      /* Extra information associated with the page */
};

/*
** CAPI3REF: Application Defined Page Cache.
** KEYWORDS: {page cache}
**
** ^(The [sqlite3_config]([SQLITE_CONFIG_PCACHE2], ...) interface can
** register an alternative page cache implementation by passing in an
** instance of the sqlite3_pcache_methods2 structure.)^
** In many applications, most of the heap memory allocated by
** SQLite is used for the page cache.
** By implementing a
** custom page cache using this API, an application can better control
** the amount of memory consumed by SQLite, the way in which
** that memory is allocated and released, and the policies used to
** determine exactly which parts of a database file are cached and for
** how long.
**
** The alternative page cache mechanism is an
** extreme measure that is only needed by the most demanding applications.
** The built-in page cache is recommended for most uses.
**
** ^(The contents of the sqlite3_pcache_methods2 structure are copied to an
** internal buffer by SQLite within the call to [sqlite3_config].  Hence
** the application may discard the parameter after the call to
** [sqlite3_config()] returns.)^
**
** [[the xInit() page cache method]]
** ^(The xInit() method is called once for each effective
** call to [sqlite3_initialize()])^
** (usually only once during the lifetime of the process). ^(The xInit()
** method is passed a copy of the sqlite3_pcache_methods2.pArg value.)^
** The intent of the xInit() method is to set up global data structures
** required by the custom page cache implementation.
** ^(If the xInit() method is NULL, then the
** built-in default page cache is used instead of the application defined
** page cache.)^
**
** [[the xShutdown() page cache method]]
** ^The xShutdown() method is called by [sqlite3_shutdown()].
** It can be used to clean up
** any outstanding resources before process shutdown, if required.
** ^The xShutdown() method may be NULL.
**
** ^SQLite automatically serializes calls to the xInit method,
** so the xInit method need not be threadsafe.  ^The
** xShutdown method is only called from [sqlite3_shutdown()] so it does
** not need to be threadsafe either.  All other methods must be threadsafe
** in multithreaded applications.
**
** ^SQLite will never invoke xInit() more than once without an intervening
** call to xShutdown().
**
** [[the xCreate() page cache methods]]
** ^SQLite invokes the xCreate() method to construct a new cache instance.
** SQLite will typically create one cache instance for each open database file,
** though this is not guaranteed. ^The
** first parameter, szPage, is the size in bytes of the pages that must
** be allocated by the cache.  ^szPage will always a power of two.  ^The
** second parameter szExtra is a number of bytes of extra storage
** associated with each page cache entry.  ^The szExtra parameter will
** a number less than 250.  SQLite will use the
** extra szExtra bytes on each page to store metadata about the underlying
** database page on disk.  The value passed into szExtra depends
** on the SQLite version, the target platform, and how SQLite was compiled.
** ^The third argument to xCreate(), bPurgeable, is true if the cache being
** created will be used to cache database pages of a file stored on disk, or
** false if it is used for an in-memory database. The cache implementation
** does not have to do anything special based with the value of bPurgeable;
** it is purely advisory.  ^On a cache where bPurgeable is false, SQLite will
** never invoke xUnpin() except to deliberately delete a page.
** ^In other words, calls to xUnpin() on a cache with bPurgeable set to
** false will always have the "discard" flag set to true.
** ^Hence, a cache created with bPurgeable false will
** never contain any unpinned pages.
**
** [[the xCachesize() page cache method]]
** ^(The xCachesize() method may be called at any time by SQLite to set the
** suggested maximum cache-size (number of pages stored by) the cache
** instance passed as the first argument. This is the value configured using
** the SQLite "[PRAGMA cache_size]" command.)^  As with the bPurgeable
** parameter, the implementation is not required to do anything with this
** value; it is advisory only.
**
** [[the xPagecount() page cache methods]]
** The xPagecount() method must return the number of pages currently
** stored in the cache, both pinned and unpinned.
**
** [[the xFetch() page cache methods]]
** The xFetch() method locates a page in the cache and returns a pointer to
** an sqlite3_pcache_page object associated with that page, or a NULL pointer.
** The pBuf element of the returned sqlite3_pcache_page object will be a
** pointer to a buffer of szPage bytes used to store the content of a
** single database page.  The pExtra element of sqlite3_pcache_page will be
** a pointer to the szExtra bytes of extra storage that SQLite has requested
** for each entry in the page cache.
**
** The page to be fetched is determined by the key. ^The minimum key value
** is 1.  After it has been retrieved using xFetch, the page is considered
** to be "pinned".
**
** If the requested page is already in the page cache, then the page cache
** implementation must return a pointer to the page buffer with its content
** intact.  If the requested page is not already in the cache, then the
** cache implementation should use the value of the createFlag
** parameter to help it determined what action to take:
**
** 
** 
     createFlag  Behaviour when page is not already in cache
** 
     0  Do not allocate a new page.  Return NULL.
** 
     1  Allocate a new page if it easy and convenient to do so.
**                 Otherwise return NULL.
** 
     2  Make every effort to allocate a new page.  Only return
**                 NULL if allocating a new page is effectively impossible.
** 
    
**
** ^(SQLite will normally invoke xFetch() with a createFlag of 0 or 1.  SQLite
** will only use a createFlag of 2 after a prior call with a createFlag of 1
** failed.)^  In between the to xFetch() calls, SQLite may
** attempt to unpin one or more cache pages by spilling the content of
** pinned pages to disk and synching the operating system disk cache.
**
** [[the xUnpin() page cache method]]
** ^xUnpin() is called by SQLite with a pointer to a currently pinned page
** as its second argument.  If the third parameter, discard, is non-zero,
** then the page must be evicted from the cache.
** ^If the discard parameter is
** zero, then the page may be discarded or retained at the discretion of
** page cache implementation. ^The page cache implementation
** may choose to evict unpinned pages at any time.
**
** The cache must not perform any reference counting. A single
** call to xUnpin() unpins the page regardless of the number of prior calls
** to xFetch().
**
** [[the xRekey() page cache methods]]
** The xRekey() method is used to change the key value associated with the
** page passed as the second argument. If the cache
** previously contains an entry associated with newKey, it must be
** discarded. ^Any prior cache entry associated with newKey is guaranteed not
** to be pinned.
**
** When SQLite calls the xTruncate() method, the cache must discard all
** existing cache entries with page numbers (keys) greater than or equal
** to the value of the iLimit parameter passed to xTruncate(). If any
** of these pages are pinned, they are implicitly unpinned, meaning that
** they can be safely discarded.
**
** [[the xDestroy() page cache method]]
** ^The xDestroy() method is used to delete a cache allocated by xCreate().
** All resources associated with the specified cache should be freed. ^After
** calling the xDestroy() method, SQLite considers the [sqlite3_pcache*]
** handle invalid, and will not use it with any other sqlite3_pcache_methods2
** functions.
**
** [[the xShrink() page cache method]]
** ^SQLite invokes the xShrink() method when it wants the page cache to
** free up as much of heap memory as possible.  The page cache implementation
** is not obligated to free any memory, but well-behaved implementations should
** do their best.
*/
typedef struct sqlite3_pcache_methods2 sqlite3_pcache_methods2;
struct sqlite3_pcache_methods2 {
  int iVersion;
  void *pArg;
  int (*xInit)(void*);
  void (*xShutdown)(void*);
  sqlite3_pcache *(*xCreate)(int szPage, int szExtra, int bPurgeable);
  void (*xCachesize)(sqlite3_pcache*, int nCachesize);
  int (*xPagecount)(sqlite3_pcache*);
  sqlite3_pcache_page *(*xFetch)(sqlite3_pcache*, unsigned key, int createFlag);
  void (*xUnpin)(sqlite3_pcache*, sqlite3_pcache_page*, int discard);
  void (*xRekey)(sqlite3_pcache*, sqlite3_pcache_page*,
      unsigned oldKey, unsigned newKey);
  void (*xTruncate)(sqlite3_pcache*, unsigned iLimit);
  void (*xDestroy)(sqlite3_pcache*);
  void (*xShrink)(sqlite3_pcache*);
};

/*
** This is the obsolete pcache_methods object that has now been replaced
** by sqlite3_pcache_methods2.  This object is not used by SQLite.  It is
** retained in the header file for backwards compatibility only.
*/
typedef struct sqlite3_pcache_methods sqlite3_pcache_methods;
struct sqlite3_pcache_methods {
  void *pArg;
  int (*xInit)(void*);
  void (*xShutdown)(void*);
  sqlite3_pcache *(*xCreate)(int szPage, int bPurgeable);
  void (*xCachesize)(sqlite3_pcache*, int nCachesize);
  int (*xPagecount)(sqlite3_pcache*);
  void *(*xFetch)(sqlite3_pcache*, unsigned key, int createFlag);
  void (*xUnpin)(sqlite3_pcache*, void*, int discard);
  void (*xRekey)(sqlite3_pcache*, void*, unsigned oldKey, unsigned newKey);
  void (*xTruncate)(sqlite3_pcache*, unsigned iLimit);
  void (*xDestroy)(sqlite3_pcache*);
};


/*
** CAPI3REF: Online Backup Object
**
** The sqlite3_backup object records state information about an ongoing
** online backup operation.  ^The sqlite3_backup object is created by
** a call to [sqlite3_backup_init()] and is destroyed by a call to
** [sqlite3_backup_finish()].
**
** See Also: [Using the SQLite Online Backup API]
*/
typedef struct sqlite3_backup sqlite3_backup;

/*
** CAPI3REF: Online Backup API.
**
** The backup API copies the content of one database into another.
** It is useful either for creating backups of databases or
** for copying in-memory databases to or from persistent files.
**
** See Also: [Using the SQLite Online Backup API]
**
** ^SQLite holds a write transaction open on the destination database file
** for the duration of the backup operation.
** ^The source database is read-locked only while it is being read;
** it is not locked continuously for the entire backup operation.
** ^Thus, the backup may be performed on a live source database without
** preventing other database connections from
** reading or writing to the source database while the backup is underway.
**
** ^(To perform a backup operation:
**   
      
**     
    1. sqlite3_backup_init() is called once to initialize the
**         backup,
**     
    2. sqlite3_backup_step() is called one or more times to transfer
**         the data between the two databases, and finally
**     
    3. sqlite3_backup_finish() is called to release all resources
**         associated with the backup operation.
**   
    )^
** There should be exactly one call to sqlite3_backup_finish() for each
** successful call to sqlite3_backup_init().
**
** [[sqlite3_backup_init()]] sqlite3_backup_init()
**
** ^The D and N arguments to sqlite3_backup_init(D,N,S,M) are the
** [database connection] associated with the destination database
** and the database name, respectively.
** ^The database name is "main" for the main database, "temp" for the
** temporary database, or the name specified after the AS keyword in
** an [ATTACH] statement for an attached database.
** ^The S and M arguments passed to
** sqlite3_backup_init(D,N,S,M) identify the [database connection]
** and database name of the source database, respectively.
** ^The source and destination [database connections] (parameters S and D)
** must be different or else sqlite3_backup_init(D,N,S,M) will fail with
** an error.
**
** ^If an error occurs within sqlite3_backup_init(D,N,S,M), then NULL is
** returned and an error code and error message are stored in the
** destination [database connection] D.
** ^The error code and message for the failed call to sqlite3_backup_init()
** can be retrieved using the [sqlite3_errcode()], [sqlite3_errmsg()], and/or
** [sqlite3_errmsg16()] functions.
** ^A successful call to sqlite3_backup_init() returns a pointer to an
** [sqlite3_backup] object.
** ^The [sqlite3_backup] object may be used with the sqlite3_backup_step() and
** sqlite3_backup_finish() functions to perform the specified backup
** operation.
**
** [[sqlite3_backup_step()]] sqlite3_backup_step()
**
** ^Function sqlite3_backup_step(B,N) will copy up to N pages between
** the source and destination databases specified by [sqlite3_backup] object B.
** ^If N is negative, all remaining source pages are copied.
** ^If sqlite3_backup_step(B,N) successfully copies N pages and there
** are still more pages to be copied, then the function returns [SQLITE_OK].
** ^If sqlite3_backup_step(B,N) successfully finishes copying all pages
** from source to destination, then it returns [SQLITE_DONE].
** ^If an error occurs while running sqlite3_backup_step(B,N),
** then an [error code] is returned. ^As well as [SQLITE_OK] and
** [SQLITE_DONE], a call to sqlite3_backup_step() may return [SQLITE_READONLY],
** [SQLITE_NOMEM], [SQLITE_BUSY], [SQLITE_LOCKED], or an
** [SQLITE_IOERR_ACCESS | SQLITE_IOERR_XXX] extended error code.
**
** ^(The sqlite3_backup_step() might return [SQLITE_READONLY] if
** 
      
** 
    1.  the destination database was opened read-only, or
** 
    2.  the destination database is using write-ahead-log journaling
** and the destination and source page sizes differ, or
** 
    3.  the destination database is an in-memory database and the
** destination and source page sizes differ.
** 
    )^
**
** ^If sqlite3_backup_step() cannot obtain a required file-system lock, then
** the [sqlite3_busy_handler | busy-handler function]
** is invoked (if one is specified). ^If the
** busy-handler returns non-zero before the lock is available, then
** [SQLITE_BUSY] is returned to the caller. ^In this case the call to
** sqlite3_backup_step() can be retried later. ^If the source
** [database connection]
** is being used to write to the source database when sqlite3_backup_step()
** is called, then [SQLITE_LOCKED] is returned immediately. ^Again, in this
** case the call to sqlite3_backup_step() can be retried later on. ^(If
** [SQLITE_IOERR_ACCESS | SQLITE_IOERR_XXX], [SQLITE_NOMEM], or
** [SQLITE_READONLY] is returned, then
** there is no point in retrying the call to sqlite3_backup_step(). These
** errors are considered fatal.)^  The application must accept
** that the backup operation has failed and pass the backup operation handle
** to the sqlite3_backup_finish() to release associated resources.
**
** ^The first call to sqlite3_backup_step() obtains an exclusive lock
** on the destination file. ^The exclusive lock is not released until either
** sqlite3_backup_finish() is called or the backup operation is complete
** and sqlite3_backup_step() returns [SQLITE_DONE].  ^Every call to
** sqlite3_backup_step() obtains a [shared lock] on the source database that
** lasts for the duration of the sqlite3_backup_step() call.
** ^Because the source database is not locked between calls to
** sqlite3_backup_step(), the source database may be modified mid-way
** through the backup process.  ^If the source database is modified by an
** external process or via a database connection other than the one being
** used by the backup operation, then the backup will be automatically
** restarted by the next call to sqlite3_backup_step(). ^If the source
** database is modified by the using the same database connection as is used
** by the backup operation, then the backup database is automatically
** updated at the same time.
**
** [[sqlite3_backup_finish()]] sqlite3_backup_finish()
**
** When sqlite3_backup_step() has returned [SQLITE_DONE], or when the
** application wishes to abandon the backup operation, the application
** should destroy the [sqlite3_backup] by passing it to sqlite3_backup_finish().
** ^The sqlite3_backup_finish() interfaces releases all
** resources associated with the [sqlite3_backup] object.
** ^If sqlite3_backup_step() has not yet returned [SQLITE_DONE], then any
** active write-transaction on the destination database is rolled back.
** The [sqlite3_backup] object is invalid
** and may not be used following a call to sqlite3_backup_finish().
**
** ^The value returned by sqlite3_backup_finish is [SQLITE_OK] if no
** sqlite3_backup_step() errors occurred, regardless or whether or not
** sqlite3_backup_step() completed.
** ^If an out-of-memory condition or IO error occurred during any prior
** sqlite3_backup_step() call on the same [sqlite3_backup] object, then
** sqlite3_backup_finish() returns the corresponding [error code].
**
** ^A return of [SQLITE_BUSY] or [SQLITE_LOCKED] from sqlite3_backup_step()
** is not a permanent error and does not affect the return value of
** sqlite3_backup_finish().
**
** [[sqlite3_backup__remaining()]] [[sqlite3_backup_pagecount()]]
** sqlite3_backup_remaining() and sqlite3_backup_pagecount()
**
** ^Each call to sqlite3_backup_step() sets two values inside
** the [sqlite3_backup] object: the number of pages still to be backed
** up and the total number of pages in the source database file.
** The sqlite3_backup_remaining() and sqlite3_backup_pagecount() interfaces
** retrieve these two values, respectively.
**
** ^The values returned by these functions are only updated by
** sqlite3_backup_step(). ^If the source database is modified during a backup
** operation, then the values are not updated to account for any extra
** pages that need to be updated or the size of the source database file
** changing.
**
** Concurrent Usage of Database Handles
**
** ^The source [database connection] may be used by the application for other
** purposes while a backup operation is underway or being initialized.
** ^If SQLite is compiled and configured to support threadsafe database
** connections, then the source database connection may be used concurrently
** from within other threads.
**
** However, the application must guarantee that the destination
** [database connection] is not passed to any other API (by any thread) after
** sqlite3_backup_init() is called and before the corresponding call to
** sqlite3_backup_finish().  SQLite does not currently check to see
** if the application incorrectly accesses the destination [database connection]
** and so no error code is reported, but the operations may malfunction
** nevertheless.  Use of the destination database connection while a
** backup is in progress might also also cause a mutex deadlock.
**
** If running in [shared cache mode], the application must
** guarantee that the shared cache used by the destination database
** is not accessed while the backup is running. In practice this means
** that the application must guarantee that the disk file being
** backed up to is not accessed by any connection within the process,
** not just the specific connection that was passed to sqlite3_backup_init().
**
** The [sqlite3_backup] object itself is partially threadsafe. Multiple
** threads may safely make multiple concurrent calls to sqlite3_backup_step().
** However, the sqlite3_backup_remaining() and sqlite3_backup_pagecount()
** APIs are not strictly speaking threadsafe. If they are invoked at the
** same time as another thread is invoking sqlite3_backup_step() it is
** possible that they return invalid values.
*/
SQLITE_API sqlite3_backup *sqlite3_backup_init(
  sqlite3 *pDest,                        /* Destination database handle */
  const char *zDestName,                 /* Destination database name */
  sqlite3 *pSource,                      /* Source database handle */
  const char *zSourceName                /* Source database name */
);
SQLITE_API int sqlite3_backup_step(sqlite3_backup *p, int nPage);
SQLITE_API int sqlite3_backup_finish(sqlite3_backup *p);
SQLITE_API int sqlite3_backup_remaining(sqlite3_backup *p);
SQLITE_API int sqlite3_backup_pagecount(sqlite3_backup *p);

/*
** CAPI3REF: Unlock Notification
**
** ^When running in shared-cache mode, a database operation may fail with
** an [SQLITE_LOCKED] error if the required locks on the shared-cache or
** individual tables within the shared-cache cannot be obtained. See
** [SQLite Shared-Cache Mode] for a description of shared-cache locking.
** ^This API may be used to register a callback that SQLite will invoke
** when the connection currently holding the required lock relinquishes it.
** ^This API is only available if the library was compiled with the
** [SQLITE_ENABLE_UNLOCK_NOTIFY] C-preprocessor symbol defined.
**
** See Also: [Using the SQLite Unlock Notification Feature].
**
** ^Shared-cache locks are released when a database connection concludes
** its current transaction, either by committing it or rolling it back.
**
** ^When a connection (known as the blocked connection) fails to obtain a
** shared-cache lock and SQLITE_LOCKED is returned to the caller, the
** identity of the database connection (the blocking connection) that
** has locked the required resource is stored internally. ^After an
** application receives an SQLITE_LOCKED error, it may call the
** sqlite3_unlock_notify() method with the blocked connection handle as
** the first argument to register for a callback that will be invoked
** when the blocking connections current transaction is concluded. ^The
** callback is invoked from within the [sqlite3_step] or [sqlite3_close]
** call that concludes the blocking connections transaction.
**
** ^(If sqlite3_unlock_notify() is called in a multi-threaded application,
** there is a chance that the blocking connection will have already
** concluded its transaction by the time sqlite3_unlock_notify() is invoked.
** If this happens, then the specified callback is invoked immediately,
** from within the call to sqlite3_unlock_notify().)^
**
** ^If the blocked connection is attempting to obtain a write-lock on a
** shared-cache table, and more than one other connection currently holds
** a read-lock on the same table, then SQLite arbitrarily selects one of
** the other connections to use as the blocking connection.
**
** ^(There may be at most one unlock-notify callback registered by a
** blocked connection. If sqlite3_unlock_notify() is called when the
** blocked connection already has a registered unlock-notify callback,
** then the new callback replaces the old.)^ ^If sqlite3_unlock_notify() is
** called with a NULL pointer as its second argument, then any existing
** unlock-notify callback is canceled. ^The blocked connections
** unlock-notify callback may also be canceled by closing the blocked
** connection using [sqlite3_close()].
**
** The unlock-notify callback is not reentrant. If an application invokes
** any sqlite3_xxx API functions from within an unlock-notify callback, a
** crash or deadlock may be the result.
**
** ^Unless deadlock is detected (see below), sqlite3_unlock_notify() always
** returns SQLITE_OK.
**
** Callback Invocation Details
**
** When an unlock-notify callback is registered, the application provides a
** single void* pointer that is passed to the callback when it is invoked.
** However, the signature of the callback function allows SQLite to pass
** it an array of void* context pointers. The first argument passed to
** an unlock-notify callback is a pointer to an array of void* pointers,
** and the second is the number of entries in the array.
**
** When a blocking connections transaction is concluded, there may be
** more than one blocked connection that has registered for an unlock-notify
** callback. ^If two or more such blocked connections have specified the
** same callback function, then instead of invoking the callback function
** multiple times, it is invoked once with the set of void* context pointers
** specified by the blocked connections bundled together into an array.
** This gives the application an opportunity to prioritize any actions
** related to the set of unblocked database connections.
**
** Deadlock Detection
**
** Assuming that after registering for an unlock-notify callback a
** database waits for the callback to be issued before taking any further
** action (a reasonable assumption), then using this API may cause the
** application to deadlock. For example, if connection X is waiting for
** connection Y's transaction to be concluded, and similarly connection
** Y is waiting on connection X's transaction, then neither connection
** will proceed and the system may remain deadlocked indefinitely.
**
** To avoid this scenario, the sqlite3_unlock_notify() performs deadlock
** detection. ^If a given call to sqlite3_unlock_notify() would put the
** system in a deadlocked state, then SQLITE_LOCKED is returned and no
** unlock-notify callback is registered. The system is said to be in
** a deadlocked state if connection A has registered for an unlock-notify
** callback on the conclusion of connection B's transaction, and connection
** B has itself registered for an unlock-notify callback when connection
** A's transaction is concluded. ^Indirect deadlock is also detected, so
** the system is also considered to be deadlocked if connection B has
** registered for an unlock-notify callback on the conclusion of connection
** C's transaction, where connection C is waiting on connection A. ^Any
** number of levels of indirection are allowed.
**
** The "DROP TABLE" Exception
**
** When a call to [sqlite3_step()] returns SQLITE_LOCKED, it is almost
** always appropriate to call sqlite3_unlock_notify(). There is however,
** one exception. When executing a "DROP TABLE" or "DROP INDEX" statement,
** SQLite checks if there are any currently executing SELECT statements
** that belong to the same connection. If there are, SQLITE_LOCKED is
** returned. In this case there is no "blocking connection", so invoking
** sqlite3_unlock_notify() results in the unlock-notify callback being
** invoked immediately. If the application then re-attempts the "DROP TABLE"
** or "DROP INDEX" query, an infinite loop might be the result.
**
** One way around this problem is to check the extended error code returned
** by an sqlite3_step() call. ^(If there is a blocking connection, then the
** extended error code is set to SQLITE_LOCKED_SHAREDCACHE. Otherwise, in
** the special "DROP TABLE/INDEX" case, the extended error code is just
** SQLITE_LOCKED.)^
*/
SQLITE_API int sqlite3_unlock_notify(
  sqlite3 *pBlocked,                          /* Waiting connection */
  void (*xNotify)(void **apArg, int nArg),    /* Callback function to invoke */
  void *pNotifyArg                            /* Argument to pass to xNotify */
);


/*
** CAPI3REF: String Comparison
**
** ^The [sqlite3_strnicmp()] API allows applications and extensions to
** compare the contents of two buffers containing UTF-8 strings in a
** case-independent fashion, using the same definition of case independence
** that SQLite uses internally when comparing identifiers.
*/
SQLITE_API int sqlite3_strnicmp(const char *, const char *, int);

/*
** CAPI3REF: Error Logging Interface
**
** ^The [sqlite3_log()] interface writes a message into the error log
** established by the [SQLITE_CONFIG_LOG] option to [sqlite3_config()].
** ^If logging is enabled, the zFormat string and subsequent arguments are
** used with [sqlite3_snprintf()] to generate the final output string.
**
** The sqlite3_log() interface is intended for use by extensions such as
** virtual tables, collating functions, and SQL functions.  While there is
** nothing to prevent an application from calling sqlite3_log(), doing so
** is considered bad form.
**
** The zFormat string must not be NULL.
**
** To avoid deadlocks and other threading problems, the sqlite3_log() routine
** will not use dynamically allocated memory.  The log message is stored in
** a fixed-length buffer on the stack.  If the log message is longer than
** a few hundred characters, it will be truncated to the length of the
** buffer.
*/
SQLITE_API void sqlite3_log(int iErrCode, const char *zFormat, ...);

/*
** CAPI3REF: Write-Ahead Log Commit Hook
**
** ^The [sqlite3_wal_hook()] function is used to register a callback that
** will be invoked each time a database connection commits data to a
** [write-ahead log] (i.e. whenever a transaction is committed in
** [journal_mode | journal_mode=WAL mode]).
**
** ^The callback is invoked by SQLite after the commit has taken place and
** the associated write-lock on the database released, so the implementation
** may read, write or [checkpoint] the database as required.
**
** ^The first parameter passed to the callback function when it is invoked
** is a copy of the third parameter passed to sqlite3_wal_hook() when
** registering the callback. ^The second is a copy of the database handle.
** ^The third parameter is the name of the database that was written to -
** either "main" or the name of an [ATTACH]-ed database. ^The fourth parameter
** is the number of pages currently in the write-ahead log file,
** including those that were just committed.
**
** The callback function should normally return [SQLITE_OK].  ^If an error
** code is returned, that error will propagate back up through the
** SQLite code base to cause the statement that provoked the callback
** to report an error, though the commit will have still occurred. If the
** callback returns [SQLITE_ROW] or [SQLITE_DONE], or if it returns a value
** that does not correspond to any valid SQLite error code, the results
** are undefined.
**
** A single database handle may have at most a single write-ahead log callback
** registered at one time. ^Calling [sqlite3_wal_hook()] replaces any
** previously registered write-ahead log callback. ^Note that the
** [sqlite3_wal_autocheckpoint()] interface and the
** [wal_autocheckpoint pragma] both invoke [sqlite3_wal_hook()] and will
** those overwrite any prior [sqlite3_wal_hook()] settings.
*/
SQLITE_API void *sqlite3_wal_hook(
  sqlite3*,
  int(*)(void *,sqlite3*,const char*,int),
  void*
);

/*
** CAPI3REF: Configure an auto-checkpoint
**
** ^The [sqlite3_wal_autocheckpoint(D,N)] is a wrapper around
** [sqlite3_wal_hook()] that causes any database on [database connection] D
** to automatically [checkpoint]
** after committing a transaction if there are N or
** more frames in the [write-ahead log] file.  ^Passing zero or
** a negative value as the nFrame parameter disables automatic
** checkpoints entirely.
**
** ^The callback registered by this function replaces any existing callback
** registered using [sqlite3_wal_hook()].  ^Likewise, registering a callback
** using [sqlite3_wal_hook()] disables the automatic checkpoint mechanism
** configured by this function.
**
** ^The [wal_autocheckpoint pragma] can be used to invoke this interface
** from SQL.
**
** ^Every new [database connection] defaults to having the auto-checkpoint
** enabled with a threshold of 1000 or [SQLITE_DEFAULT_WAL_AUTOCHECKPOINT]
** pages.  The use of this interface
** is only necessary if the default setting is found to be suboptimal
** for a particular application.
*/
SQLITE_API int sqlite3_wal_autocheckpoint(sqlite3 *db, int N);

/*
** CAPI3REF: Checkpoint a database
**
** ^The [sqlite3_wal_checkpoint(D,X)] interface causes database named X
** on [database connection] D to be [checkpointed].  ^If X is NULL or an
** empty string, then a checkpoint is run on all databases of
** connection D.  ^If the database connection D is not in
** [WAL | write-ahead log mode] then this interface is a harmless no-op.
**
** ^The [wal_checkpoint pragma] can be used to invoke this interface
** from SQL.  ^The [sqlite3_wal_autocheckpoint()] interface and the
** [wal_autocheckpoint pragma] can be used to cause this interface to be
** run whenever the WAL reaches a certain size threshold.
**
** See also: [sqlite3_wal_checkpoint_v2()]
*/
SQLITE_API int sqlite3_wal_checkpoint(sqlite3 *db, const char *zDb);

/*
** CAPI3REF: Checkpoint a database
**
** Run a checkpoint operation on WAL database zDb attached to database
** handle db. The specific operation is determined by the value of the
** eMode parameter:
**
** 
    
** 
    SQLITE_CHECKPOINT_PASSIVE
    
**   Checkpoint as many frames as possible without waiting for any database
**   readers or writers to finish. Sync the db file if all frames in the log
**   are checkpointed. This mode is the same as calling
**   sqlite3_wal_checkpoint(). The busy-handler callback is never invoked.
**
** 
    SQLITE_CHECKPOINT_FULL
    
**   This mode blocks (calls the busy-handler callback) until there is no
**   database writer and all readers are reading from the most recent database
**   snapshot. It then checkpoints all frames in the log file and syncs the
**   database file. This call blocks database writers while it is running,
**   but not database readers.
**
** 
    SQLITE_CHECKPOINT_RESTART
    
**   This mode works the same way as SQLITE_CHECKPOINT_FULL, except after
**   checkpointing the log file it blocks (calls the busy-handler callback)
**   until all readers are reading from the database file only. This ensures
**   that the next client to write to the database file restarts the log file
**   from the beginning. This call blocks database writers while it is running,
**   but not database readers.
** 
    
**
** If pnLog is not NULL, then *pnLog is set to the total number of frames in
** the log file before returning. If pnCkpt is not NULL, then *pnCkpt is set to
** the total number of checkpointed frames (including any that were already
** checkpointed when this function is called). *pnLog and *pnCkpt may be
** populated even if sqlite3_wal_checkpoint_v2() returns other than SQLITE_OK.
** If no values are available because of an error, they are both set to -1
** before returning to communicate this to the caller.
**
** All calls obtain an exclusive "checkpoint" lock on the database file. If
** any other process is running a checkpoint operation at the same time, the
** lock cannot be obtained and SQLITE_BUSY is returned. Even if there is a
** busy-handler configured, it will not be invoked in this case.
**
** The SQLITE_CHECKPOINT_FULL and RESTART modes also obtain the exclusive
** "writer" lock on the database file. If the writer lock cannot be obtained
** immediately, and a busy-handler is configured, it is invoked and the writer
** lock retried until either the busy-handler returns 0 or the lock is
** successfully obtained. The busy-handler is also invoked while waiting for
** database readers as described above. If the busy-handler returns 0 before
** the writer lock is obtained or while waiting for database readers, the
** checkpoint operation proceeds from that point in the same way as
** SQLITE_CHECKPOINT_PASSIVE - checkpointing as many frames as possible
** without blocking any further. SQLITE_BUSY is returned in this case.
**
** If parameter zDb is NULL or points to a zero length string, then the
** specified operation is attempted on all WAL databases. In this case the
** values written to output parameters *pnLog and *pnCkpt are undefined. If
** an SQLITE_BUSY error is encountered when processing one or more of the
** attached WAL databases, the operation is still attempted on any remaining
** attached databases and SQLITE_BUSY is returned to the caller. If any other
** error occurs while processing an attached database, processing is abandoned
** and the error code returned to the caller immediately. If no error
** (SQLITE_BUSY or otherwise) is encountered while processing the attached
** databases, SQLITE_OK is returned.
**
** If database zDb is the name of an attached database that is not in WAL
** mode, SQLITE_OK is returned and both *pnLog and *pnCkpt set to -1. If
** zDb is not NULL (or a zero length string) and is not the name of any
** attached database, SQLITE_ERROR is returned to the caller.
*/
SQLITE_API int sqlite3_wal_checkpoint_v2(
  sqlite3 *db,                    /* Database handle */
  const char *zDb,                /* Name of attached database (or NULL) */
  int eMode,                      /* SQLITE_CHECKPOINT_* value */
  int *pnLog,                     /* OUT: Size of WAL log in frames */
  int *pnCkpt                     /* OUT: Total number of frames checkpointed */
);

/*
** CAPI3REF: Checkpoint operation parameters
**
** These constants can be used as the 3rd parameter to
** [sqlite3_wal_checkpoint_v2()].  See the [sqlite3_wal_checkpoint_v2()]
** documentation for additional information about the meaning and use of
** each of these values.
*/
#define SQLITE_CHECKPOINT_PASSIVE 0
#define SQLITE_CHECKPOINT_FULL    1
#define SQLITE_CHECKPOINT_RESTART 2

/*
** CAPI3REF: Virtual Table Interface Configuration
**
** This function may be called by either the [xConnect] or [xCreate] method
** of a [virtual table] implementation to configure
** various facets of the virtual table interface.
**
** If this interface is invoked outside the context of an xConnect or
** xCreate virtual table method then the behavior is undefined.
**
** At present, there is only one option that may be configured using
** this function. (See [SQLITE_VTAB_CONSTRAINT_SUPPORT].)  Further options
** may be added in the future.
*/
SQLITE_API int sqlite3_vtab_config(sqlite3*, int op, ...);

/*
** CAPI3REF: Virtual Table Configuration Options
**
** These macros define the various options to the
** [sqlite3_vtab_config()] interface that [virtual table] implementations
** can use to customize and optimize their behavior.
**
** 
    
** 
    SQLITE_VTAB_CONSTRAINT_SUPPORT
** 
    Calls of the form
** [sqlite3_vtab_config](db,SQLITE_VTAB_CONSTRAINT_SUPPORT,X) are supported,
** where X is an integer.  If X is zero, then the [virtual table] whose
** [xCreate] or [xConnect] method invoked [sqlite3_vtab_config()] does not
** support constraints.  In this configuration (which is the default) if
** a call to the [xUpdate] method returns [SQLITE_CONSTRAINT], then the entire
** statement is rolled back as if [ON CONFLICT | OR ABORT] had been
** specified as part of the users SQL statement, regardless of the actual
** ON CONFLICT mode specified.
**
** If X is non-zero, then the virtual table implementation guarantees
** that if [xUpdate] returns [SQLITE_CONSTRAINT], it will do so before
** any modifications to internal or persistent data structures have been made.
** If the [ON CONFLICT] mode is ABORT, FAIL, IGNORE or ROLLBACK, SQLite
** is able to roll back a statement or database transaction, and abandon
** or continue processing the current SQL statement as appropriate.
** If the ON CONFLICT mode is REPLACE and the [xUpdate] method returns
** [SQLITE_CONSTRAINT], SQLite handles this as if the ON CONFLICT mode
** had been ABORT.
**
** Virtual table implementations that are required to handle OR REPLACE
** must do so within the [xUpdate] method. If a call to the
** [sqlite3_vtab_on_conflict()] function indicates that the current ON
** CONFLICT policy is REPLACE, the virtual table implementation should
** silently replace the appropriate rows within the xUpdate callback and
** return SQLITE_OK. Or, if this is not possible, it may return
** SQLITE_CONSTRAINT, in which case SQLite falls back to OR ABORT
** constraint handling.
** 
    
*/
#define SQLITE_VTAB_CONSTRAINT_SUPPORT 1

/*
** CAPI3REF: Determine The Virtual Table Conflict Policy
**
** This function may only be called from within a call to the [xUpdate] method
** of a [virtual table] implementation for an INSERT or UPDATE operation. ^The
** value returned is one of [SQLITE_ROLLBACK], [SQLITE_IGNORE], [SQLITE_FAIL],
** [SQLITE_ABORT], or [SQLITE_REPLACE], according to the [ON CONFLICT] mode
** of the SQL statement that triggered the call to the [xUpdate] method of the
** [virtual table].
*/
SQLITE_API int sqlite3_vtab_on_conflict(sqlite3 *);

/*
** CAPI3REF: Conflict resolution modes
**
** These constants are returned by [sqlite3_vtab_on_conflict()] to
** inform a [virtual table] implementation what the [ON CONFLICT] mode
** is for the SQL statement being evaluated.
**
** Note that the [SQLITE_IGNORE] constant is also used as a potential
** return value from the [sqlite3_set_authorizer()] callback and that
** [SQLITE_ABORT] is also a [result code].
*/
#define SQLITE_ROLLBACK 1
/* #define SQLITE_IGNORE 2 // Also used by sqlite3_authorizer() callback */
#define SQLITE_FAIL     3
/* #define SQLITE_ABORT 4  // Also an error code */
#define SQLITE_REPLACE  5



/*
** Undo the hack that converts floating point types to integer for
** builds on processors without floating point support.
*/
#ifdef SQLITE_OMIT_FLOATING_POINT
# undef double
#endif

#if 0
}  /* End of the 'extern "C"' block */
#endif
#endif

/*
** 2010 August 30
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
*/

#ifndef _SQLITE3RTREE_H_
#define _SQLITE3RTREE_H_


#if 0
extern "C" {
#endif

typedef struct sqlite3_rtree_geometry sqlite3_rtree_geometry;

/*
** Register a geometry callback named zGeom that can be used as part of an
** R-Tree geometry query as follows:
**
**   SELECT ... FROM  WHERE  MATCH $zGeom(... params ...)
*/
SQLITE_API int sqlite3_rtree_geometry_callback(
  sqlite3 *db,
  const char *zGeom,
  int (*xGeom)(sqlite3_rtree_geometry *, int nCoord, double *aCoord, int *pRes),
  void *pContext
);


/*
** A pointer to a structure of the following type is passed as the first
** argument to callbacks registered using rtree_geometry_callback().
*/
struct sqlite3_rtree_geometry {
  void *pContext;                 /* Copy of pContext passed to s_r_g_c() */
  int nParam;                     /* Size of array aParam[] */
  double *aParam;                 /* Parameters passed to SQL geom function */
  void *pUser;                    /* Callback implementation user data */
  void (*xDelUser)(void *);       /* Called by SQLite to clean up pUser */
};


#if 0
}  /* end of the 'extern "C"' block */
#endif

#endif  /* ifndef _SQLITE3RTREE_H_ */


/************** End of sqlite3.h *********************************************/
/************** Continuing where we left off in sqliteInt.h ******************/
/************** Include hash.h in the middle of sqliteInt.h ******************/
/************** Begin file hash.h ********************************************/
/*
** 2001 September 22
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
** This is the header file for the generic hash-table implemenation
** used in SQLite.
*/
#ifndef _SQLITE_HASH_H_
#define _SQLITE_HASH_H_

/* Forward declarations of structures. */
typedef struct Hash Hash;
typedef struct HashElem HashElem;

/* A complete hash table is an instance of the following structure.
** The internals of this structure are intended to be opaque -- client
** code should not attempt to access or modify the fields of this structure
** directly.  Change this structure only by using the routines below.
** However, some of the "procedures" and "functions" for modifying and
** accessing this structure are really macros, so we can't really make
** this structure opaque.
**
** All elements of the hash table are on a single doubly-linked list.
** Hash.first points to the head of this list.
**
** There are Hash.htsize buckets.  Each bucket points to a spot in
** the global doubly-linked list.  The contents of the bucket are the
** element pointed to plus the next _ht.count-1 elements in the list.
**
** Hash.htsize and Hash.ht may be zero.  In that case lookup is done
** by a linear search of the global list.  For small tables, the
** Hash.ht table is never allocated because if there are few elements
** in the table, it is faster to do a linear search than to manage
** the hash table.
*/
struct Hash {
  unsigned int htsize;      /* Number of buckets in the hash table */
  unsigned int count;       /* Number of entries in this table */
  HashElem *first;          /* The first element of the array */
  struct _ht {              /* the hash table */
    int count;                 /* Number of entries with this hash */
    HashElem *chain;           /* Pointer to first entry with this hash */
  } *ht;
};

/* Each element in the hash table is an instance of the following
** structure.  All elements are stored on a single doubly-linked list.
**
** Again, this structure is intended to be opaque, but it can't really
** be opaque because it is used by macros.
*/
struct HashElem {
  HashElem *next, *prev;       /* Next and previous elements in the table */
  void *data;                  /* Data associated with this element */
  const char *pKey; int nKey;  /* Key associated with this element */
};

/*
** Access routines.  To delete, insert a NULL pointer.
*/
SQLITE_PRIVATE void sqlite3HashInit(Hash*);
SQLITE_PRIVATE void *sqlite3HashInsert(Hash*, const char *pKey, int nKey, void *pData);
SQLITE_PRIVATE void *sqlite3HashFind(const Hash*, const char *pKey, int nKey);
SQLITE_PRIVATE void sqlite3HashClear(Hash*);

/*
** Macros for looping over all elements of a hash table.  The idiom is
** like this:
**
**   Hash h;
**   HashElem *p;
**   ...
**   for(p=sqliteHashFirst(&h); p; p=sqliteHashNext(p)){
**     SomeStructure *pData = sqliteHashData(p);
**     // do something with pData
**   }
*/
#define sqliteHashFirst(H)  ((H)->first)
#define sqliteHashNext(E)   ((E)->next)
#define sqliteHashData(E)   ((E)->data)
/* #define sqliteHashKey(E)    ((E)->pKey) // NOT USED */
/* #define sqliteHashKeysize(E) ((E)->nKey)  // NOT USED */

/*
** Number of entries in a hash table
*/
/* #define sqliteHashCount(H)  ((H)->count) // NOT USED */

#endif /* _SQLITE_HASH_H_ */

/************** End of hash.h ************************************************/
/************** Continuing where we left off in sqliteInt.h ******************/
/************** Include parse.h in the middle of sqliteInt.h *****************/
/************** Begin file parse.h *******************************************/
#define TK_SEMI                            1
#define TK_EXPLAIN                         2
#define TK_QUERY                           3
#define TK_PLAN                            4
#define TK_BEGIN                           5
#define TK_TRANSACTION                     6
#define TK_DEFERRED                        7
#define TK_IMMEDIATE                       8
#define TK_EXCLUSIVE                       9
#define TK_COMMIT                         10
#define TK_END                            11
#define TK_ROLLBACK                       12
#define TK_SAVEPOINT                      13
#define TK_RELEASE                        14
#define TK_TO                             15
#define TK_TABLE                          16
#define TK_CREATE                         17
#define TK_IF                             18
#define TK_NOT                            19
#define TK_EXISTS                         20
#define TK_TEMP                           21
#define TK_LP                             22
#define TK_RP                             23
#define TK_AS                             24
#define TK_COMMA                          25
#define TK_ID                             26
#define TK_INDEXED                        27
#define TK_ABORT                          28
#define TK_ACTION                         29
#define TK_AFTER                          30
#define TK_ANALYZE                        31
#define TK_ASC                            32
#define TK_ATTACH                         33
#define TK_BEFORE                         34
#define TK_BY                             35
#define TK_CASCADE                        36
#define TK_CAST                           37
#define TK_COLUMNKW                       38
#define TK_CONFLICT                       39
#define TK_DATABASE                       40
#define TK_DESC                           41
#define TK_DETACH                         42
#define TK_EACH                           43
#define TK_FAIL                           44
#define TK_FOR                            45
#define TK_IGNORE                         46
#define TK_INITIALLY                      47
#define TK_INSTEAD                        48
#define TK_LIKE_KW                        49
#define TK_MATCH                          50
#define TK_NO                             51
#define TK_KEY                            52
#define TK_OF                             53
#define TK_OFFSET                         54
#define TK_PRAGMA                         55
#define TK_RAISE                          56
#define TK_REPLACE                        57
#define TK_RESTRICT                       58
#define TK_ROW                            59
#define TK_TRIGGER                        60
#define TK_VACUUM                         61
#define TK_VIEW                           62
#define TK_VIRTUAL                        63
#define TK_REINDEX                        64
#define TK_RENAME                         65
#define TK_CTIME_KW                       66
#define TK_ANY                            67
#define TK_OR                             68
#define TK_AND                            69
#define TK_IS                             70
#define TK_BETWEEN                        71
#define TK_IN                             72
#define TK_ISNULL                         73
#define TK_NOTNULL                        74
#define TK_NE                             75
#define TK_EQ                             76
#define TK_GT                             77
#define TK_LE                             78
#define TK_LT                             79
#define TK_GE                             80
#define TK_ESCAPE                         81
#define TK_BITAND                         82
#define TK_BITOR                          83
#define TK_LSHIFT                         84
#define TK_RSHIFT                         85
#define TK_PLUS                           86
#define TK_MINUS                          87
#define TK_STAR                           88
#define TK_SLASH                          89
#define TK_REM                            90
#define TK_CONCAT                         91
#define TK_COLLATE                        92
#define TK_BITNOT                         93
#define TK_STRING                         94
#define TK_JOIN_KW                        95
#define TK_CONSTRAINT                     96
#define TK_DEFAULT                        97
#define TK_NULL                           98
#define TK_PRIMARY                        99
#define TK_UNIQUE                         100
#define TK_CHECK                          101
#define TK_REFERENCES                     102
#define TK_AUTOINCR                       103
#define TK_ON                             104
#define TK_INSERT                         105
#define TK_DELETE                         106
#define TK_UPDATE                         107
#define TK_SET                            108
#define TK_DEFERRABLE                     109
#define TK_FOREIGN                        110
#define TK_DROP                           111
#define TK_UNION                          112
#define TK_ALL                            113
#define TK_EXCEPT                         114
#define TK_INTERSECT                      115
#define TK_SELECT                         116
#define TK_DISTINCT                       117
#define TK_DOT                            118
#define TK_FROM                           119
#define TK_JOIN                           120
#define TK_USING                          121
#define TK_ORDER                          122
#define TK_GROUP                          123
#define TK_HAVING                         124
#define TK_LIMIT                          125
#define TK_WHERE                          126
#define TK_INTO                           127
#define TK_VALUES                         128
#define TK_INTEGER                        129
#define TK_FLOAT                          130
#define TK_BLOB                           131
#define TK_REGISTER                       132
#define TK_VARIABLE                       133
#define TK_CASE                           134
#define TK_WHEN                           135
#define TK_THEN                           136
#define TK_ELSE                           137
#define TK_INDEX                          138
#define TK_ALTER                          139
#define TK_ADD                            140
#define TK_TO_TEXT                        141
#define TK_TO_BLOB                        142
#define TK_TO_NUMERIC                     143
#define TK_TO_INT                         144
#define TK_TO_REAL                        145
#define TK_ISNOT                          146
#define TK_END_OF_FILE                    147
#define TK_ILLEGAL                        148
#define TK_SPACE                          149
#define TK_UNCLOSED_STRING                150
#define TK_FUNCTION                       151
#define TK_COLUMN                         152
#define TK_AGG_FUNCTION                   153
#define TK_AGG_COLUMN                     154
#define TK_CONST_FUNC                     155
#define TK_UMINUS                         156
#define TK_UPLUS                          157

/************** End of parse.h ***********************************************/
/************** Continuing where we left off in sqliteInt.h ******************/
#include 
#include 
#include 
#include 
#include 

/*
** If compiling for a processor that lacks floating point support,
** substitute integer for floating-point
*/
#ifdef SQLITE_OMIT_FLOATING_POINT
# define double sqlite_int64
# define float sqlite_int64
# define LONGDOUBLE_TYPE sqlite_int64
# ifndef SQLITE_BIG_DBL
#   define SQLITE_BIG_DBL (((sqlite3_int64)1)<<50)
# endif
# define SQLITE_OMIT_DATETIME_FUNCS 1
# define SQLITE_OMIT_TRACE 1
# undef SQLITE_MIXED_ENDIAN_64BIT_FLOAT
# undef SQLITE_HAVE_ISNAN
#endif
#ifndef SQLITE_BIG_DBL
# define SQLITE_BIG_DBL (1e99)
#endif

/*
** OMIT_TEMPDB is set to 1 if SQLITE_OMIT_TEMPDB is defined, or 0
** afterward. Having this macro allows us to cause the C compiler
** to omit code used by TEMP tables without messy #ifndef statements.
*/
#ifdef SQLITE_OMIT_TEMPDB
#define OMIT_TEMPDB 1
#else
#define OMIT_TEMPDB 0
#endif

/*
** The "file format" number is an integer that is incremented whenever
** the VDBE-level file format changes.  The following macros define the
** the default file format for new databases and the maximum file format
** that the library can read.
*/
#define SQLITE_MAX_FILE_FORMAT 4
#ifndef SQLITE_DEFAULT_FILE_FORMAT
# define SQLITE_DEFAULT_FILE_FORMAT 4
#endif

/*
** Determine whether triggers are recursive by default.  This can be
** changed at run-time using a pragma.
*/
#ifndef SQLITE_DEFAULT_RECURSIVE_TRIGGERS
# define SQLITE_DEFAULT_RECURSIVE_TRIGGERS 0
#endif

/*
** Provide a default value for SQLITE_TEMP_STORE in case it is not specified
** on the command-line
*/
#ifndef SQLITE_TEMP_STORE
# define SQLITE_TEMP_STORE 1
#endif

/*
** GCC does not define the offsetof() macro so we'll have to do it
** ourselves.
*/
#ifndef offsetof
#define offsetof(STRUCTURE,FIELD) ((int)((char*)&((STRUCTURE*)0)->FIELD))
#endif

/*
** Check to see if this machine uses EBCDIC.  (Yes, believe it or
** not, there are still machines out there that use EBCDIC.)
*/
#if 'A' == '\301'
# define SQLITE_EBCDIC 1
#else
# define SQLITE_ASCII 1
#endif

/*
** Integers of known sizes.  These typedefs might change for architectures
** where the sizes very.  Preprocessor macros are available so that the
** types can be conveniently redefined at compile-type.  Like this:
**
**         cc '-DUINTPTR_TYPE=long long int' ...
*/
#ifndef UINT32_TYPE
# ifdef HAVE_UINT32_T
#  define UINT32_TYPE uint32_t
# else
#  define UINT32_TYPE unsigned int
# endif
#endif
#ifndef UINT16_TYPE
# ifdef HAVE_UINT16_T
#  define UINT16_TYPE uint16_t
# else
#  define UINT16_TYPE unsigned short int
# endif
#endif
#ifndef INT16_TYPE
# ifdef HAVE_INT16_T
#  define INT16_TYPE int16_t
# else
#  define INT16_TYPE short int
# endif
#endif
#ifndef UINT8_TYPE
# ifdef HAVE_UINT8_T
#  define UINT8_TYPE uint8_t
# else
#  define UINT8_TYPE unsigned char
# endif
#endif
#ifndef INT8_TYPE
# ifdef HAVE_INT8_T
#  define INT8_TYPE int8_t
# else
#  define INT8_TYPE signed char
# endif
#endif
#ifndef LONGDOUBLE_TYPE
# define LONGDOUBLE_TYPE long double
#endif
typedef sqlite_int64 i64;          /* 8-byte signed integer */
typedef sqlite_uint64 u64;         /* 8-byte unsigned integer */
typedef UINT32_TYPE u32;           /* 4-byte unsigned integer */
typedef UINT16_TYPE u16;           /* 2-byte unsigned integer */
typedef INT16_TYPE i16;            /* 2-byte signed integer */
typedef UINT8_TYPE u8;             /* 1-byte unsigned integer */
typedef INT8_TYPE i8;              /* 1-byte signed integer */

/*
** SQLITE_MAX_U32 is a u64 constant that is the maximum u64 value
** that can be stored in a u32 without loss of data.  The value
** is 0x00000000ffffffff.  But because of quirks of some compilers, we
** have to specify the value in the less intuitive manner shown:
*/
#define SQLITE_MAX_U32  ((((u64)1)<<32)-1)

/*
** The datatype used to store estimates of the number of rows in a
** table or index.  This is an unsigned integer type.  For 99.9% of
** the world, a 32-bit integer is sufficient.  But a 64-bit integer
** can be used at compile-time if desired.
*/
#ifdef SQLITE_64BIT_STATS
 typedef u64 tRowcnt;    /* 64-bit only if requested at compile-time */
#else
 typedef u32 tRowcnt;    /* 32-bit is the default */
#endif

/*
** Macros to determine whether the machine is big or little endian,
** evaluated at runtime.
*/
#ifdef SQLITE_AMALGAMATION
SQLITE_PRIVATE const int sqlite3one = 1;
#else
SQLITE_PRIVATE const int sqlite3one;
#endif
#if defined(i386) || defined(__i386__) || defined(_M_IX86)\
                             || defined(__x86_64) || defined(__x86_64__)
# define SQLITE_BIGENDIAN    0
# define SQLITE_LITTLEENDIAN 1
# define SQLITE_UTF16NATIVE  SQLITE_UTF16LE
#else
# define SQLITE_BIGENDIAN    (*(char *)(&sqlite3one)==0)
# define SQLITE_LITTLEENDIAN (*(char *)(&sqlite3one)==1)
# define SQLITE_UTF16NATIVE (SQLITE_BIGENDIAN?SQLITE_UTF16BE:SQLITE_UTF16LE)
#endif

/*
** Constants for the largest and smallest possible 64-bit signed integers.
** These macros are designed to work correctly on both 32-bit and 64-bit
** compilers.
*/
#define LARGEST_INT64  (0xffffffff|(((i64)0x7fffffff)<<32))
#define SMALLEST_INT64 (((i64)-1) - LARGEST_INT64)

/*
** Round up a number to the next larger multiple of 8.  This is used
** to force 8-byte alignment on 64-bit architectures.
*/
#define ROUND8(x)     (((x)+7)&~7)

/*
** Round down to the nearest multiple of 8
*/
#define ROUNDDOWN8(x) ((x)&~7)

/*
** Assert that the pointer X is aligned to an 8-byte boundary.  This
** macro is used only within assert() to verify that the code gets
** all alignment restrictions correct.
**
** Except, if SQLITE_4_BYTE_ALIGNED_MALLOC is defined, then the
** underlying malloc() implemention might return us 4-byte aligned
** pointers.  In that case, only verify 4-byte alignment.
*/
#ifdef SQLITE_4_BYTE_ALIGNED_MALLOC
# define EIGHT_BYTE_ALIGNMENT(X)   ((((char*)(X) - (char*)0)&3)==0)
#else
# define EIGHT_BYTE_ALIGNMENT(X)   ((((char*)(X) - (char*)0)&7)==0)
#endif


/*
** An instance of the following structure is used to store the busy-handler
** callback for a given sqlite handle.
**
** The sqlite.busyHandler member of the sqlite struct contains the busy
** callback for the database handle. Each pager opened via the sqlite
** handle is passed a pointer to sqlite.busyHandler. The busy-handler
** callback is currently invoked only from within pager.c.
*/
typedef struct BusyHandler BusyHandler;
struct BusyHandler {
  int (*xFunc)(void *,int);  /* The busy callback */
  void *pArg;                /* First arg to busy callback */
  int nBusy;                 /* Incremented with each busy call */
};

/*
** Name of the master database table.  The master database table
** is a special table that holds the names and attributes of all
** user tables and indices.
*/
#define MASTER_NAME       "sqlite_master"
#define TEMP_MASTER_NAME  "sqlite_temp_master"

/*
** The root-page of the master database table.
*/
#define MASTER_ROOT       1

/*
** The name of the schema table.
*/
#define SCHEMA_TABLE(x)  ((!OMIT_TEMPDB)&&(x==1)?TEMP_MASTER_NAME:MASTER_NAME)

/*
** A convenience macro that returns the number of elements in
** an array.
*/
#define ArraySize(X)    ((int)(sizeof(X)/sizeof(X[0])))

/*
** The following value as a destructor means to use sqlite3DbFree().
** This is an internal extension to SQLITE_STATIC and SQLITE_TRANSIENT.
*/
#define SQLITE_DYNAMIC   ((sqlite3_destructor_type)sqlite3DbFree)

/*
** When SQLITE_OMIT_WSD is defined, it means that the target platform does
** not support Writable Static Data (WSD) such as global and static variables.
** All variables must either be on the stack or dynamically allocated from
** the heap.  When WSD is unsupported, the variable declarations scattered
** throughout the SQLite code must become constants instead.  The SQLITE_WSD
** macro is used for this purpose.  And instead of referencing the variable
** directly, we use its constant as a key to lookup the run-time allocated
** buffer that holds real variable.  The constant is also the initializer
** for the run-time allocated buffer.
**
** In the usual case where WSD is supported, the SQLITE_WSD and GLOBAL
** macros become no-ops and have zero performance impact.
*/
#ifdef SQLITE_OMIT_WSD
  #define SQLITE_WSD const
  #define GLOBAL(t,v) (*(t*)sqlite3_wsd_find((void*)&(v), sizeof(v)))
  #define sqlite3GlobalConfig GLOBAL(struct Sqlite3Config, sqlite3Config)
SQLITE_API   int sqlite3_wsd_init(int N, int J);
SQLITE_API   void *sqlite3_wsd_find(void *K, int L);
#else
  #define SQLITE_WSD
  #define GLOBAL(t,v) v
  #define sqlite3GlobalConfig sqlite3Config
#endif

/*
** The following macros are used to suppress compiler warnings and to
** make it clear to human readers when a function parameter is deliberately
** left unused within the body of a function. This usually happens when
** a function is called via a function pointer. For example the
** implementation of an SQL aggregate step callback may not use the
** parameter indicating the number of arguments passed to the aggregate,
** if it knows that this is enforced elsewhere.
**
** When a function parameter is not used at all within the body of a function,
** it is generally named "NotUsed" or "NotUsed2" to make things even clearer.
** However, these macros may also be used to suppress warnings related to
** parameters that may or may not be used depending on compilation options.
** For example those parameters only used in assert() statements. In these
** cases the parameters are named as per the usual conventions.
*/
#define UNUSED_PARAMETER(x) (void)(x)
#define UNUSED_PARAMETER2(x,y) UNUSED_PARAMETER(x),UNUSED_PARAMETER(y)

/*
** Forward references to structures
*/
typedef struct AggInfo AggInfo;
typedef struct AuthContext AuthContext;
typedef struct AutoincInfo AutoincInfo;
typedef struct Bitvec Bitvec;
typedef struct CollSeq CollSeq;
typedef struct Column Column;
typedef struct Db Db;
typedef struct Schema Schema;
typedef struct Expr Expr;
typedef struct ExprList ExprList;
typedef struct ExprSpan ExprSpan;
typedef struct FKey FKey;
typedef struct FuncDestructor FuncDestructor;
typedef struct FuncDef FuncDef;
typedef struct FuncDefHash FuncDefHash;
typedef struct IdList IdList;
typedef struct Index Index;
typedef struct IndexSample IndexSample;
typedef struct KeyClass KeyClass;
typedef struct KeyInfo KeyInfo;
typedef struct Lookaside Lookaside;
typedef struct LookasideSlot LookasideSlot;
typedef struct Module Module;
typedef struct NameContext NameContext;
typedef struct Parse Parse;
typedef struct RowSet RowSet;
typedef struct Savepoint Savepoint;
typedef struct Select Select;
typedef struct SrcList SrcList;
typedef struct StrAccum StrAccum;
typedef struct Table Table;
typedef struct TableLock TableLock;
typedef struct Token Token;
typedef struct Trigger Trigger;
typedef struct TriggerPrg TriggerPrg;
typedef struct TriggerStep TriggerStep;
typedef struct UnpackedRecord UnpackedRecord;
typedef struct VTable VTable;
typedef struct VtabCtx VtabCtx;
typedef struct Walker Walker;
typedef struct WherePlan WherePlan;
typedef struct WhereInfo WhereInfo;
typedef struct WhereLevel WhereLevel;

/*
** Defer sourcing vdbe.h and btree.h until after the "u8" and
** "BusyHandler" typedefs. vdbe.h also requires a few of the opaque
** pointer types (i.e. FuncDef) defined above.
*/
/************** Include btree.h in the middle of sqliteInt.h *****************/
/************** Begin file btree.h *******************************************/
/*
** 2001 September 15
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
** This header file defines the interface that the sqlite B-Tree file
** subsystem.  See comments in the source code for a detailed description
** of what each interface routine does.
*/
#ifndef _BTREE_H_
#define _BTREE_H_

/* TODO: This definition is just included so other modules compile. It
** needs to be revisited.
*/
#define SQLITE_N_BTREE_META 10

/*
** If defined as non-zero, auto-vacuum is enabled by default. Otherwise
** it must be turned on for each database using "PRAGMA auto_vacuum = 1".
*/
#ifndef SQLITE_DEFAULT_AUTOVACUUM
  #define SQLITE_DEFAULT_AUTOVACUUM 0
#endif

#define BTREE_AUTOVACUUM_NONE 0        /* Do not do auto-vacuum */
#define BTREE_AUTOVACUUM_FULL 1        /* Do full auto-vacuum */
#define BTREE_AUTOVACUUM_INCR 2        /* Incremental vacuum */

/*
** Forward declarations of structure
*/
typedef struct Btree Btree;
typedef struct BtCursor BtCursor;
typedef struct BtShared BtShared;


SQLITE_PRIVATE int sqlite3BtreeOpen(
  sqlite3_vfs *pVfs,       /* VFS to use with this b-tree */
  const char *zFilename,   /* Name of database file to open */
  sqlite3 *db,             /* Associated database connection */
  Btree **ppBtree,         /* Return open Btree* here */
  int flags,               /* Flags */
  int vfsFlags             /* Flags passed through to VFS open */
);

/* The flags parameter to sqlite3BtreeOpen can be the bitwise or of the
** following values.
**
** NOTE:  These values must match the corresponding PAGER_ values in
** pager.h.
*/
#define BTREE_OMIT_JOURNAL  1  /* Do not create or use a rollback journal */
#define BTREE_NO_READLOCK   2  /* Omit readlocks on readonly files */
#define BTREE_MEMORY        4  /* This is an in-memory DB */
#define BTREE_SINGLE        8  /* The file contains at most 1 b-tree */
#define BTREE_UNORDERED    16  /* Use of a hash implementation is OK */

SQLITE_PRIVATE int sqlite3BtreeClose(Btree*);
SQLITE_PRIVATE int sqlite3BtreeSetCacheSize(Btree*,int);
SQLITE_PRIVATE int sqlite3BtreeSetSafetyLevel(Btree*,int,int,int);
SQLITE_PRIVATE int sqlite3BtreeSyncDisabled(Btree*);
SQLITE_PRIVATE int sqlite3BtreeSetPageSize(Btree *p, int nPagesize, int nReserve, int eFix);
SQLITE_PRIVATE int sqlite3BtreeGetPageSize(Btree*);
SQLITE_PRIVATE int sqlite3BtreeMaxPageCount(Btree*,int);
SQLITE_PRIVATE u32 sqlite3BtreeLastPage(Btree*);
SQLITE_PRIVATE int sqlite3BtreeSecureDelete(Btree*,int);
SQLITE_PRIVATE int sqlite3BtreeGetReserve(Btree*);
SQLITE_PRIVATE int sqlite3BtreeSetAutoVacuum(Btree *, int);
SQLITE_PRIVATE int sqlite3BtreeGetAutoVacuum(Btree *);
SQLITE_PRIVATE int sqlite3BtreeBeginTrans(Btree*,int);
SQLITE_PRIVATE int sqlite3BtreeCommitPhaseOne(Btree*, const char *zMaster);
SQLITE_PRIVATE int sqlite3BtreeCommitPhaseTwo(Btree*, int);
SQLITE_PRIVATE int sqlite3BtreeCommit(Btree*);
SQLITE_PRIVATE int sqlite3BtreeRollback(Btree*);
SQLITE_PRIVATE int sqlite3BtreeBeginStmt(Btree*,int);
SQLITE_PRIVATE int sqlite3BtreeCreateTable(Btree*, int*, int flags);
SQLITE_PRIVATE int sqlite3BtreeIsInTrans(Btree*);
SQLITE_PRIVATE int sqlite3BtreeIsInReadTrans(Btree*);
SQLITE_PRIVATE int sqlite3BtreeIsInBackup(Btree*);
SQLITE_PRIVATE void *sqlite3BtreeSchema(Btree *, int, void(*)(void *));
SQLITE_PRIVATE int sqlite3BtreeSchemaLocked(Btree *pBtree);
SQLITE_PRIVATE int sqlite3BtreeLockTable(Btree *pBtree, int iTab, u8 isWriteLock);
SQLITE_PRIVATE int sqlite3BtreeSavepoint(Btree *, int, int);

SQLITE_PRIVATE const char *sqlite3BtreeGetFilename(Btree *);
SQLITE_PRIVATE const char *sqlite3BtreeGetJournalname(Btree *);
SQLITE_PRIVATE int sqlite3BtreeCopyFile(Btree *, Btree *);

SQLITE_PRIVATE int sqlite3BtreeIncrVacuum(Btree *);

/* The flags parameter to sqlite3BtreeCreateTable can be the bitwise OR
** of the flags shown below.
**
** Every SQLite table must have either BTREE_INTKEY or BTREE_BLOBKEY set.
** With BTREE_INTKEY, the table key is a 64-bit integer and arbitrary data
** is stored in the leaves.  (BTREE_INTKEY is used for SQL tables.)  With
** BTREE_BLOBKEY, the key is an arbitrary BLOB and no content is stored
** anywhere - the key is the content.  (BTREE_BLOBKEY is used for SQL
** indices.)
*/
#define BTREE_INTKEY     1    /* Table has only 64-bit signed integer keys */
#define BTREE_BLOBKEY    2    /* Table has keys only - no data */

SQLITE_PRIVATE int sqlite3BtreeDropTable(Btree*, int, int*);
SQLITE_PRIVATE int sqlite3BtreeClearTable(Btree*, int, int*);
SQLITE_PRIVATE void sqlite3BtreeTripAllCursors(Btree*, int);

SQLITE_PRIVATE void sqlite3BtreeGetMeta(Btree *pBtree, int idx, u32 *pValue);
SQLITE_PRIVATE int sqlite3BtreeUpdateMeta(Btree*, int idx, u32 value);

/*
** The second parameter to sqlite3BtreeGetMeta or sqlite3BtreeUpdateMeta
** should be one of the following values. The integer values are assigned
** to constants so that the offset of the corresponding field in an
** SQLite database header may be found using the following formula:
**
**   offset = 36 + (idx * 4)
**
** For example, the free-page-count field is located at byte offset 36 of
** the database file header. The incr-vacuum-flag field is located at
** byte offset 64 (== 36+4*7).
*/
#define BTREE_FREE_PAGE_COUNT     0
#define BTREE_SCHEMA_VERSION      1
#define BTREE_FILE_FORMAT         2
#define BTREE_DEFAULT_CACHE_SIZE  3
#define BTREE_LARGEST_ROOT_PAGE   4
#define BTREE_TEXT_ENCODING       5
#define BTREE_USER_VERSION        6
#define BTREE_INCR_VACUUM         7

SQLITE_PRIVATE int sqlite3BtreeCursor(
  Btree*,                              /* BTree containing table to open */
  int iTable,                          /* Index of root page */
  int wrFlag,                          /* 1 for writing.  0 for read-only */
  struct KeyInfo*,                     /* First argument to compare function */
  BtCursor *pCursor                    /* Space to write cursor structure */
);
SQLITE_PRIVATE int sqlite3BtreeCursorSize(void);
SQLITE_PRIVATE void sqlite3BtreeCursorZero(BtCursor*);

SQLITE_PRIVATE int sqlite3BtreeCloseCursor(BtCursor*);
SQLITE_PRIVATE int sqlite3BtreeMovetoUnpacked(
  BtCursor*,
  UnpackedRecord *pUnKey,
  i64 intKey,
  int bias,
  int *pRes
);
SQLITE_PRIVATE int sqlite3BtreeCursorHasMoved(BtCursor*, int*);
SQLITE_PRIVATE int sqlite3BtreeDelete(BtCursor*);
SQLITE_PRIVATE int sqlite3BtreeInsert(BtCursor*, const void *pKey, i64 nKey,
                                  const void *pData, int nData,
                                  int nZero, int bias, int seekResult);
SQLITE_PRIVATE int sqlite3BtreeFirst(BtCursor*, int *pRes);
SQLITE_PRIVATE int sqlite3BtreeLast(BtCursor*, int *pRes);
SQLITE_PRIVATE int sqlite3BtreeNext(BtCursor*, int *pRes);
SQLITE_PRIVATE int sqlite3BtreeEof(BtCursor*);
SQLITE_PRIVATE int sqlite3BtreePrevious(BtCursor*, int *pRes);
SQLITE_PRIVATE int sqlite3BtreeKeySize(BtCursor*, i64 *pSize);
SQLITE_PRIVATE int sqlite3BtreeKey(BtCursor*, u32 offset, u32 amt, void*);
SQLITE_PRIVATE const void *sqlite3BtreeKeyFetch(BtCursor*, int *pAmt);
SQLITE_PRIVATE const void *sqlite3BtreeDataFetch(BtCursor*, int *pAmt);
SQLITE_PRIVATE int sqlite3BtreeDataSize(BtCursor*, u32 *pSize);
SQLITE_PRIVATE int sqlite3BtreeData(BtCursor*, u32 offset, u32 amt, void*);
SQLITE_PRIVATE void sqlite3BtreeSetCachedRowid(BtCursor*, sqlite3_int64);
SQLITE_PRIVATE sqlite3_int64 sqlite3BtreeGetCachedRowid(BtCursor*);

SQLITE_PRIVATE char *sqlite3BtreeIntegrityCheck(Btree*, int *aRoot, int nRoot, int, int*);
SQLITE_PRIVATE struct Pager *sqlite3BtreePager(Btree*);

SQLITE_PRIVATE int sqlite3BtreePutData(BtCursor*, u32 offset, u32 amt, void*);
SQLITE_PRIVATE void sqlite3BtreeCacheOverflow(BtCursor *);
SQLITE_PRIVATE void sqlite3BtreeClearCursor(BtCursor *);

SQLITE_PRIVATE int sqlite3BtreeSetVersion(Btree *pBt, int iVersion);

#ifndef NDEBUG
SQLITE_PRIVATE int sqlite3BtreeCursorIsValid(BtCursor*);
#endif

#ifndef SQLITE_OMIT_BTREECOUNT
SQLITE_PRIVATE int sqlite3BtreeCount(BtCursor *, i64 *);
#endif

#ifdef SQLITE_TEST
SQLITE_PRIVATE int sqlite3BtreeCursorInfo(BtCursor*, int*, int);
SQLITE_PRIVATE void sqlite3BtreeCursorList(Btree*);
#endif

#ifndef SQLITE_OMIT_WAL
SQLITE_PRIVATE   int sqlite3BtreeCheckpoint(Btree*, int, int *, int *);
#endif

/*
** If we are not using shared cache, then there is no need to
** use mutexes to access the BtShared structures.  So make the
** Enter and Leave procedures no-ops.
*/
#ifndef SQLITE_OMIT_SHARED_CACHE
SQLITE_PRIVATE   void sqlite3BtreeEnter(Btree*);
SQLITE_PRIVATE   void sqlite3BtreeEnterAll(sqlite3*);
#else
# define sqlite3BtreeEnter(X)
# define sqlite3BtreeEnterAll(X)
#endif

#if !defined(SQLITE_OMIT_SHARED_CACHE) && SQLITE_THREADSAFE
SQLITE_PRIVATE   int sqlite3BtreeSharable(Btree*);
SQLITE_PRIVATE   void sqlite3BtreeLeave(Btree*);
SQLITE_PRIVATE   void sqlite3BtreeEnterCursor(BtCursor*);
SQLITE_PRIVATE   void sqlite3BtreeLeaveCursor(BtCursor*);
SQLITE_PRIVATE   void sqlite3BtreeLeaveAll(sqlite3*);
#ifndef NDEBUG
  /* These routines are used inside assert() statements only. */
SQLITE_PRIVATE   int sqlite3BtreeHoldsMutex(Btree*);
SQLITE_PRIVATE   int sqlite3BtreeHoldsAllMutexes(sqlite3*);
SQLITE_PRIVATE   int sqlite3SchemaMutexHeld(sqlite3*,int,Schema*);
#endif
#else

# define sqlite3BtreeSharable(X) 0
# define sqlite3BtreeLeave(X)
# define sqlite3BtreeEnterCursor(X)
# define sqlite3BtreeLeaveCursor(X)
# define sqlite3BtreeLeaveAll(X)

# define sqlite3BtreeHoldsMutex(X) 1
# define sqlite3BtreeHoldsAllMutexes(X) 1
# define sqlite3SchemaMutexHeld(X,Y,Z) 1
#endif


#endif /* _BTREE_H_ */

/************** End of btree.h ***********************************************/
/************** Continuing where we left off in sqliteInt.h ******************/
/************** Include vdbe.h in the middle of sqliteInt.h ******************/
/************** Begin file vdbe.h ********************************************/
/*
** 2001 September 15
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
** Header file for the Virtual DataBase Engine (VDBE)
**
** This header defines the interface to the virtual database engine
** or VDBE.  The VDBE implements an abstract machine that runs a
** simple program to access and modify the underlying database.
*/
#ifndef _SQLITE_VDBE_H_
#define _SQLITE_VDBE_H_
/* #include  */

/*
** A single VDBE is an opaque structure named "Vdbe".  Only routines
** in the source file sqliteVdbe.c are allowed to see the insides
** of this structure.
*/
typedef struct Vdbe Vdbe;

/*
** The names of the following types declared in vdbeInt.h are required
** for the VdbeOp definition.
*/
typedef struct VdbeFunc VdbeFunc;
typedef struct Mem Mem;
typedef struct SubProgram SubProgram;

/*
** A single instruction of the virtual machine has an opcode
** and as many as three operands.  The instruction is recorded
** as an instance of the following structure:
*/
struct VdbeOp {
  u8 opcode;          /* What operation to perform */
  signed char p4type; /* One of the P4_xxx constants for p4 */
  u8 opflags;         /* Mask of the OPFLG_* flags in opcodes.h */
  u8 p5;              /* Fifth parameter is an unsigned character */
  int p1;             /* First operand */
  int p2;             /* Second parameter (often the jump destination) */
  int p3;             /* The third parameter */
  union {             /* fourth parameter */
    int i;                 /* Integer value if p4type==P4_INT32 */
    void *p;               /* Generic pointer */
    char *z;               /* Pointer to data for string (char array) types */
    i64 *pI64;             /* Used when p4type is P4_INT64 */
    double *pReal;         /* Used when p4type is P4_REAL */
    FuncDef *pFunc;        /* Used when p4type is P4_FUNCDEF */
    VdbeFunc *pVdbeFunc;   /* Used when p4type is P4_VDBEFUNC */
    CollSeq *pColl;        /* Used when p4type is P4_COLLSEQ */
    Mem *pMem;             /* Used when p4type is P4_MEM */
    VTable *pVtab;         /* Used when p4type is P4_VTAB */
    KeyInfo *pKeyInfo;     /* Used when p4type is P4_KEYINFO */
    int *ai;               /* Used when p4type is P4_INTARRAY */
    SubProgram *pProgram;  /* Used when p4type is P4_SUBPROGRAM */
    int (*xAdvance)(BtCursor *, int *);
  } p4;
#ifdef SQLITE_DEBUG
  char *zComment;          /* Comment to improve readability */
#endif
#ifdef VDBE_PROFILE
  int cnt;                 /* Number of times this instruction was executed */
  u64 cycles;              /* Total time spent executing this instruction */
#endif
};
typedef struct VdbeOp VdbeOp;


/*
** A sub-routine used to implement a trigger program.
*/
struct SubProgram {
  VdbeOp *aOp;                  /* Array of opcodes for sub-program */
  int nOp;                      /* Elements in aOp[] */
  int nMem;                     /* Number of memory cells required */
  int nCsr;                     /* Number of cursors required */
  int nOnce;                    /* Number of OP_Once instructions */
  void *token;                  /* id that may be used to recursive triggers */
  SubProgram *pNext;            /* Next sub-program already visited */
};

/*
** A smaller version of VdbeOp used for the VdbeAddOpList() function because
** it takes up less space.
*/
struct VdbeOpList {
  u8 opcode;          /* What operation to perform */
  signed char p1;     /* First operand */
  signed char p2;     /* Second parameter (often the jump destination) */
  signed char p3;     /* Third parameter */
};
typedef struct VdbeOpList VdbeOpList;

/*
** Allowed values of VdbeOp.p4type
*/
#define P4_NOTUSED    0   /* The P4 parameter is not used */
#define P4_DYNAMIC  (-1)  /* Pointer to a string obtained from sqliteMalloc() */
#define P4_STATIC   (-2)  /* Pointer to a static string */
#define P4_COLLSEQ  (-4)  /* P4 is a pointer to a CollSeq structure */
#define P4_FUNCDEF  (-5)  /* P4 is a pointer to a FuncDef structure */
#define P4_KEYINFO  (-6)  /* P4 is a pointer to a KeyInfo structure */
#define P4_VDBEFUNC (-7)  /* P4 is a pointer to a VdbeFunc structure */
#define P4_MEM      (-8)  /* P4 is a pointer to a Mem*    structure */
#define P4_TRANSIENT  0   /* P4 is a pointer to a transient string */
#define P4_VTAB     (-10) /* P4 is a pointer to an sqlite3_vtab structure */
#define P4_MPRINTF  (-11) /* P4 is a string obtained from sqlite3_mprintf() */
#define P4_REAL     (-12) /* P4 is a 64-bit floating point value */
#define P4_INT64    (-13) /* P4 is a 64-bit signed integer */
#define P4_INT32    (-14) /* P4 is a 32-bit signed integer */
#define P4_INTARRAY (-15) /* P4 is a vector of 32-bit integers */
#define P4_SUBPROGRAM  (-18) /* P4 is a pointer to a SubProgram structure */
#define P4_ADVANCE  (-19) /* P4 is a pointer to BtreeNext() or BtreePrev() */

/* When adding a P4 argument using P4_KEYINFO, a copy of the KeyInfo structure
** is made.  That copy is freed when the Vdbe is finalized.  But if the
** argument is P4_KEYINFO_HANDOFF, the passed in pointer is used.  It still
** gets freed when the Vdbe is finalized so it still should be obtained
** from a single sqliteMalloc().  But no copy is made and the calling
** function should *not* try to free the KeyInfo.
*/
#define P4_KEYINFO_HANDOFF (-16)
#define P4_KEYINFO_STATIC  (-17)

/*
** The Vdbe.aColName array contains 5n Mem structures, where n is the
** number of columns of data returned by the statement.
*/
#define COLNAME_NAME     0
#define COLNAME_DECLTYPE 1
#define COLNAME_DATABASE 2
#define COLNAME_TABLE    3
#define COLNAME_COLUMN   4
#ifdef SQLITE_ENABLE_COLUMN_METADATA
# define COLNAME_N        5      /* Number of COLNAME_xxx symbols */
#else
# ifdef SQLITE_OMIT_DECLTYPE
#   define COLNAME_N      1      /* Store only the name */
# else
#   define COLNAME_N      2      /* Store the name and decltype */
# endif
#endif

/*
** The following macro converts a relative address in the p2 field
** of a VdbeOp structure into a negative number so that
** sqlite3VdbeAddOpList() knows that the address is relative.  Calling
** the macro again restores the address.
*/
#define ADDR(X)  (-1-(X))

/*
** The makefile scans the vdbe.c source file and creates the "opcodes.h"
** header file that defines a number for each opcode used by the VDBE.
*/
/************** Include opcodes.h in the middle of vdbe.h ********************/
/************** Begin file opcodes.h *****************************************/
/* Automatically generated.  Do not edit */
/* See the mkopcodeh.awk script for details */
#define OP_Goto                                 1
#define OP_Gosub                                2
#define OP_Return                               3
#define OP_Yield                                4
#define OP_HaltIfNull                           5
#define OP_Halt                                 6
#define OP_Integer                              7
#define OP_Int64                                8
#define OP_Real                               130   /* same as TK_FLOAT    */
#define OP_String8                             94   /* same as TK_STRING   */
#define OP_String                               9
#define OP_Null                                10
#define OP_Blob                                11
#define OP_Variable                            12
#define OP_Move                                13
#define OP_Copy                                14
#define OP_SCopy                               15
#define OP_ResultRow                           16
#define OP_Concat                              91   /* same as TK_CONCAT   */
#define OP_Add                                 86   /* same as TK_PLUS     */
#define OP_Subtract                            87   /* same as TK_MINUS    */
#define OP_Multiply                            88   /* same as TK_STAR     */
#define OP_Divide                              89   /* same as TK_SLASH    */
#define OP_Remainder                           90   /* same as TK_REM      */
#define OP_CollSeq                             17
#define OP_Function                            18
#define OP_BitAnd                              82   /* same as TK_BITAND   */
#define OP_BitOr                               83   /* same as TK_BITOR    */
#define OP_ShiftLeft                           84   /* same as TK_LSHIFT   */
#define OP_ShiftRight                          85   /* same as TK_RSHIFT   */
#define OP_AddImm                              20
#define OP_MustBeInt                           21
#define OP_RealAffinity                        22
#define OP_ToText                             141   /* same as TK_TO_TEXT  */
#define OP_ToBlob                             142   /* same as TK_TO_BLOB  */
#define OP_ToNumeric                          143   /* same as TK_TO_NUMERIC*/
#define OP_ToInt                              144   /* same as TK_TO_INT   */
#define OP_ToReal                             145   /* same as TK_TO_REAL  */
#define OP_Eq                                  76   /* same as TK_EQ       */
#define OP_Ne                                  75   /* same as TK_NE       */
#define OP_Lt                                  79   /* same as TK_LT       */
#define OP_Le                                  78   /* same as TK_LE       */
#define OP_Gt                                  77   /* same as TK_GT       */
#define OP_Ge                                  80   /* same as TK_GE       */
#define OP_Permutation                         23
#define OP_Compare                             24
#define OP_Jump                                25
#define OP_And                                 69   /* same as TK_AND      */
#define OP_Or                                  68   /* same as TK_OR       */
#define OP_Not                                 19   /* same as TK_NOT      */
#define OP_BitNot                              93   /* same as TK_BITNOT   */
#define OP_Once                                26
#define OP_If                                  27
#define OP_IfNot                               28
#define OP_IsNull                              73   /* same as TK_ISNULL   */
#define OP_NotNull                             74   /* same as TK_NOTNULL  */
#define OP_Column                              29
#define OP_Affinity                            30
#define OP_MakeRecord                          31
#define OP_Count                               32
#define OP_Savepoint                           33
#define OP_AutoCommit                          34
#define OP_Transaction                         35
#define OP_ReadCookie                          36
#define OP_SetCookie                           37
#define OP_VerifyCookie                        38
#define OP_OpenRead                            39
#define OP_OpenWrite                           40
#define OP_OpenAutoindex                       41
#define OP_OpenEphemeral                       42
#define OP_SorterOpen                          43
#define OP_OpenPseudo                          44
#define OP_Close                               45
#define OP_SeekLt                              46
#define OP_SeekLe                              47
#define OP_SeekGe                              48
#define OP_SeekGt                              49
#define OP_Seek                                50
#define OP_NotFound                            51
#define OP_Found                               52
#define OP_IsUnique                            53
#define OP_NotExists                           54
#define OP_Sequence                            55
#define OP_NewRowid                            56
#define OP_Insert                              57
#define OP_InsertInt                           58
#define OP_Delete                              59
#define OP_ResetCount                          60
#define OP_SorterCompare                       61
#define OP_SorterData                          62
#define OP_RowKey                              63
#define OP_RowData                             64
#define OP_Rowid                               65
#define OP_NullRow                             66
#define OP_Last                                67
#define OP_SorterSort                          70
#define OP_Sort                                71
#define OP_Rewind                              72
#define OP_SorterNext                          81
#define OP_Prev                                92
#define OP_Next                                95
#define OP_SorterInsert                        96
#define OP_IdxInsert                           97
#define OP_IdxDelete                           98
#define OP_IdxRowid                            99
#define OP_IdxLT                              100
#define OP_IdxGE                              101
#define OP_Destroy                            102
#define OP_Clear                              103
#define OP_CreateIndex                        104
#define OP_CreateTable                        105
#define OP_ParseSchema                        106
#define OP_LoadAnalysis                       107
#define OP_DropTable                          108
#define OP_DropIndex                          109
#define OP_DropTrigger                        110
#define OP_IntegrityCk                        111
#define OP_RowSetAdd                          112
#define OP_RowSetRead                         113
#define OP_RowSetTest                         114
#define OP_Program                            115
#define OP_Param                              116
#define OP_FkCounter                          117
#define OP_FkIfZero                           118
#define OP_MemMax                             119
#define OP_IfPos                              120
#define OP_IfNeg                              121
#define OP_IfZero                             122
#define OP_AggStep                            123
#define OP_AggFinal                           124
#define OP_Checkpoint                         125
#define OP_JournalMode                        126
#define OP_Vacuum                             127
#define OP_IncrVacuum                         128
#define OP_Expire                             129
#define OP_TableLock                          131
#define OP_VBegin                             132
#define OP_VCreate                            133
#define OP_VDestroy                           134
#define OP_VOpen                              135
#define OP_VFilter                            136
#define OP_VColumn                            137
#define OP_VNext                              138
#define OP_VRename                            139
#define OP_VUpdate                            140
#define OP_Pagecount                          146
#define OP_MaxPgcnt                           147
#define OP_Trace                              148
#define OP_Noop                               149
#define OP_Explain                            150


/* Properties such as "out2" or "jump" that are specified in
** comments following the "case" for each opcode in the vdbe.c
** are encoded into bitvectors as follows:
*/
#define OPFLG_JUMP            0x0001  /* jump:  P2 holds jmp target */
#define OPFLG_OUT2_PRERELEASE 0x0002  /* out2-prerelease: */
#define OPFLG_IN1             0x0004  /* in1:   P1 is an input */
#define OPFLG_IN2             0x0008  /* in2:   P2 is an input */
#define OPFLG_IN3             0x0010  /* in3:   P3 is an input */
#define OPFLG_OUT2            0x0020  /* out2:  P2 is an output */
#define OPFLG_OUT3            0x0040  /* out3:  P3 is an output */
#define OPFLG_INITIALIZER {\
/*   0 */ 0x00, 0x01, 0x01, 0x04, 0x04, 0x10, 0x00, 0x02,\
/*   8 */ 0x02, 0x02, 0x02, 0x02, 0x02, 0x00, 0x24, 0x24,\
/*  16 */ 0x00, 0x00, 0x00, 0x24, 0x04, 0x05, 0x04, 0x00,\
/*  24 */ 0x00, 0x01, 0x01, 0x05, 0x05, 0x00, 0x00, 0x00,\
/*  32 */ 0x02, 0x00, 0x00, 0x00, 0x02, 0x10, 0x00, 0x00,\
/*  40 */ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x11, 0x11,\
/*  48 */ 0x11, 0x11, 0x08, 0x11, 0x11, 0x11, 0x11, 0x02,\
/*  56 */ 0x02, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,\
/*  64 */ 0x00, 0x02, 0x00, 0x01, 0x4c, 0x4c, 0x01, 0x01,\
/*  72 */ 0x01, 0x05, 0x05, 0x15, 0x15, 0x15, 0x15, 0x15,\
/*  80 */ 0x15, 0x01, 0x4c, 0x4c, 0x4c, 0x4c, 0x4c, 0x4c,\
/*  88 */ 0x4c, 0x4c, 0x4c, 0x4c, 0x01, 0x24, 0x02, 0x01,\
/*  96 */ 0x08, 0x08, 0x00, 0x02, 0x01, 0x01, 0x02, 0x00,\
/* 104 */ 0x02, 0x02, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,\
/* 112 */ 0x0c, 0x45, 0x15, 0x01, 0x02, 0x00, 0x01, 0x08,\
/* 120 */ 0x05, 0x05, 0x05, 0x00, 0x00, 0x00, 0x02, 0x00,\
/* 128 */ 0x01, 0x00, 0x02, 0x00, 0x00, 0x00, 0x00, 0x00,\
/* 136 */ 0x01, 0x00, 0x01, 0x00, 0x00, 0x04, 0x04, 0x04,\
/* 144 */ 0x04, 0x04, 0x02, 0x02, 0x00, 0x00, 0x00,}

/************** End of opcodes.h *********************************************/
/************** Continuing where we left off in vdbe.h ***********************/

/*
** Prototypes for the VDBE interface.  See comments on the implementation
** for a description of what each of these routines does.
*/
SQLITE_PRIVATE Vdbe *sqlite3VdbeCreate(sqlite3*);
SQLITE_PRIVATE int sqlite3VdbeAddOp0(Vdbe*,int);
SQLITE_PRIVATE int sqlite3VdbeAddOp1(Vdbe*,int,int);
SQLITE_PRIVATE int sqlite3VdbeAddOp2(Vdbe*,int,int,int);
SQLITE_PRIVATE int sqlite3VdbeAddOp3(Vdbe*,int,int,int,int);
SQLITE_PRIVATE int sqlite3VdbeAddOp4(Vdbe*,int,int,int,int,const char *zP4,int);
SQLITE_PRIVATE int sqlite3VdbeAddOp4Int(Vdbe*,int,int,int,int,int);
SQLITE_PRIVATE int sqlite3VdbeAddOpList(Vdbe*, int nOp, VdbeOpList const *aOp);
SQLITE_PRIVATE void sqlite3VdbeAddParseSchemaOp(Vdbe*,int,char*);
SQLITE_PRIVATE void sqlite3VdbeChangeP1(Vdbe*, u32 addr, int P1);
SQLITE_PRIVATE void sqlite3VdbeChangeP2(Vdbe*, u32 addr, int P2);
SQLITE_PRIVATE void sqlite3VdbeChangeP3(Vdbe*, u32 addr, int P3);
SQLITE_PRIVATE void sqlite3VdbeChangeP5(Vdbe*, u8 P5);
SQLITE_PRIVATE void sqlite3VdbeJumpHere(Vdbe*, int addr);
SQLITE_PRIVATE void sqlite3VdbeChangeToNoop(Vdbe*, int addr);
SQLITE_PRIVATE void sqlite3VdbeChangeP4(Vdbe*, int addr, const char *zP4, int N);
SQLITE_PRIVATE void sqlite3VdbeUsesBtree(Vdbe*, int);
SQLITE_PRIVATE VdbeOp *sqlite3VdbeGetOp(Vdbe*, int);
SQLITE_PRIVATE int sqlite3VdbeMakeLabel(Vdbe*);
SQLITE_PRIVATE void sqlite3VdbeRunOnlyOnce(Vdbe*);
SQLITE_PRIVATE void sqlite3VdbeDelete(Vdbe*);
SQLITE_PRIVATE void sqlite3VdbeDeleteObject(sqlite3*,Vdbe*);
SQLITE_PRIVATE void sqlite3VdbeMakeReady(Vdbe*,Parse*);
SQLITE_PRIVATE int sqlite3VdbeFinalize(Vdbe*);
SQLITE_PRIVATE void sqlite3VdbeResolveLabel(Vdbe*, int);
SQLITE_PRIVATE int sqlite3VdbeCurrentAddr(Vdbe*);
#ifdef SQLITE_DEBUG
SQLITE_PRIVATE   int sqlite3VdbeAssertMayAbort(Vdbe *, int);
SQLITE_PRIVATE   void sqlite3VdbeTrace(Vdbe*,FILE*);
#endif
SQLITE_PRIVATE void sqlite3VdbeResetStepResult(Vdbe*);
SQLITE_PRIVATE void sqlite3VdbeRewind(Vdbe*);
SQLITE_PRIVATE int sqlite3VdbeReset(Vdbe*);
SQLITE_PRIVATE void sqlite3VdbeSetNumCols(Vdbe*,int);
SQLITE_PRIVATE int sqlite3VdbeSetColName(Vdbe*, int, int, const char *, void(*)(void*));
SQLITE_PRIVATE void sqlite3VdbeCountChanges(Vdbe*);
SQLITE_PRIVATE sqlite3 *sqlite3VdbeDb(Vdbe*);
SQLITE_PRIVATE void sqlite3VdbeSetSql(Vdbe*, const char *z, int n, int);
SQLITE_PRIVATE void sqlite3VdbeSwap(Vdbe*,Vdbe*);
SQLITE_PRIVATE VdbeOp *sqlite3VdbeTakeOpArray(Vdbe*, int*, int*);
SQLITE_PRIVATE sqlite3_value *sqlite3VdbeGetValue(Vdbe*, int, u8);
SQLITE_PRIVATE void sqlite3VdbeSetVarmask(Vdbe*, int);
#ifndef SQLITE_OMIT_TRACE
SQLITE_PRIVATE   char *sqlite3VdbeExpandSql(Vdbe*, const char*);
#endif

SQLITE_PRIVATE void sqlite3VdbeRecordUnpack(KeyInfo*,int,const void*,UnpackedRecord*);
SQLITE_PRIVATE int sqlite3VdbeRecordCompare(int,const void*,UnpackedRecord*);
SQLITE_PRIVATE UnpackedRecord *sqlite3VdbeAllocUnpackedRecord(KeyInfo *, char *, int, char **);

#ifndef SQLITE_OMIT_TRIGGER
SQLITE_PRIVATE void sqlite3VdbeLinkSubProgram(Vdbe *, SubProgram *);
#endif


#ifndef NDEBUG
SQLITE_PRIVATE   void sqlite3VdbeComment(Vdbe*, const char*, ...);
# define VdbeComment(X)  sqlite3VdbeComment X
SQLITE_PRIVATE   void sqlite3VdbeNoopComment(Vdbe*, const char*, ...);
# define VdbeNoopComment(X)  sqlite3VdbeNoopComment X
#else
# define VdbeComment(X)
# define VdbeNoopComment(X)
#endif

#endif

/************** End of vdbe.h ************************************************/
/************** Continuing where we left off in sqliteInt.h ******************/
/************** Include pager.h in the middle of sqliteInt.h *****************/
/************** Begin file pager.h *******************************************/
/*
** 2001 September 15
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
** This header file defines the interface that the sqlite page cache
** subsystem.  The page cache subsystem reads and writes a file a page
** at a time and provides a journal for rollback.
*/

#ifndef _PAGER_H_
#define _PAGER_H_

/*
** Default maximum size for persistent journal files. A negative
** value means no limit. This value may be overridden using the
** sqlite3PagerJournalSizeLimit() API. See also "PRAGMA journal_size_limit".
*/
#ifndef SQLITE_DEFAULT_JOURNAL_SIZE_LIMIT
  #define SQLITE_DEFAULT_JOURNAL_SIZE_LIMIT -1
#endif

/*
** The type used to represent a page number.  The first page in a file
** is called page 1.  0 is used to represent "not a page".
*/
typedef u32 Pgno;

/*
** Each open file is managed by a separate instance of the "Pager" structure.
*/
typedef struct Pager Pager;

/*
** Handle type for pages.
*/
typedef struct PgHdr DbPage;

/*
** Page number PAGER_MJ_PGNO is never used in an SQLite database (it is
** reserved for working around a windows/posix incompatibility). It is
** used in the journal to signify that the remainder of the journal file
** is devoted to storing a master journal name - there are no more pages to
** roll back. See comments for function writeMasterJournal() in pager.c
** for details.
*/
#define PAGER_MJ_PGNO(x) ((Pgno)((PENDING_BYTE/((x)->pageSize))+1))

/*
** Allowed values for the flags parameter to sqlite3PagerOpen().
**
** NOTE: These values must match the corresponding BTREE_ values in btree.h.
*/
#define PAGER_OMIT_JOURNAL  0x0001    /* Do not use a rollback journal */
#define PAGER_NO_READLOCK   0x0002    /* Omit readlocks on readonly files */
#define PAGER_MEMORY        0x0004    /* In-memory database */

/*
** Valid values for the second argument to sqlite3PagerLockingMode().
*/
#define PAGER_LOCKINGMODE_QUERY      -1
#define PAGER_LOCKINGMODE_NORMAL      0
#define PAGER_LOCKINGMODE_EXCLUSIVE   1

/*
** Numeric constants that encode the journalmode.
*/
#define PAGER_JOURNALMODE_QUERY     (-1)  /* Query the value of journalmode */
#define PAGER_JOURNALMODE_DELETE      0   /* Commit by deleting journal file */
#define PAGER_JOURNALMODE_PERSIST     1   /* Commit by zeroing journal header */
#define PAGER_JOURNALMODE_OFF         2   /* Journal omitted.  */
#define PAGER_JOURNALMODE_TRUNCATE    3   /* Commit by truncating journal */
#define PAGER_JOURNALMODE_MEMORY      4   /* In-memory journal file */
#define PAGER_JOURNALMODE_WAL         5   /* Use write-ahead logging */

/*
** The remainder of this file contains the declarations of the functions
** that make up the Pager sub-system API. See source code comments for
** a detailed description of each routine.
*/

/* Open and close a Pager connection. */
SQLITE_PRIVATE int sqlite3PagerOpen(
  sqlite3_vfs*,
  Pager **ppPager,
  const char*,
  int,
  int,
  int,
  void(*)(DbPage*)
);
SQLITE_PRIVATE int sqlite3PagerClose(Pager *pPager);
SQLITE_PRIVATE int sqlite3PagerReadFileheader(Pager*, int, unsigned char*);

/* Functions used to configure a Pager object. */
SQLITE_PRIVATE void sqlite3PagerSetBusyhandler(Pager*, int(*)(void *), void *);
SQLITE_PRIVATE int sqlite3PagerSetPagesize(Pager*, u32*, int);
SQLITE_PRIVATE int sqlite3PagerMaxPageCount(Pager*, int);
SQLITE_PRIVATE void sqlite3PagerSetCachesize(Pager*, int);
SQLITE_PRIVATE void sqlite3PagerShrink(Pager*);
SQLITE_PRIVATE void sqlite3PagerSetSafetyLevel(Pager*,int,int,int);
SQLITE_PRIVATE int sqlite3PagerLockingMode(Pager *, int);
SQLITE_PRIVATE int sqlite3PagerSetJournalMode(Pager *, int);
SQLITE_PRIVATE int sqlite3PagerGetJournalMode(Pager*);
SQLITE_PRIVATE int sqlite3PagerOkToChangeJournalMode(Pager*);
SQLITE_PRIVATE i64 sqlite3PagerJournalSizeLimit(Pager *, i64);
SQLITE_PRIVATE sqlite3_backup **sqlite3PagerBackupPtr(Pager*);

/* Functions used to obtain and release page references. */
SQLITE_PRIVATE int sqlite3PagerAcquire(Pager *pPager, Pgno pgno, DbPage **ppPage, int clrFlag);
#define sqlite3PagerGet(A,B,C) sqlite3PagerAcquire(A,B,C,0)
SQLITE_PRIVATE DbPage *sqlite3PagerLookup(Pager *pPager, Pgno pgno);
SQLITE_PRIVATE void sqlite3PagerRef(DbPage*);
SQLITE_PRIVATE void sqlite3PagerUnref(DbPage*);

/* Operations on page references. */
SQLITE_PRIVATE int sqlite3PagerWrite(DbPage*);
SQLITE_PRIVATE void sqlite3PagerDontWrite(DbPage*);
SQLITE_PRIVATE int sqlite3PagerMovepage(Pager*,DbPage*,Pgno,int);
SQLITE_PRIVATE int sqlite3PagerPageRefcount(DbPage*);
SQLITE_PRIVATE void *sqlite3PagerGetData(DbPage *);
SQLITE_PRIVATE void *sqlite3PagerGetExtra(DbPage *);

/* Functions used to manage pager transactions and savepoints. */
SQLITE_PRIVATE void sqlite3PagerPagecount(Pager*, int*);
SQLITE_PRIVATE int sqlite3PagerBegin(Pager*, int exFlag, int);
SQLITE_PRIVATE int sqlite3PagerCommitPhaseOne(Pager*,const char *zMaster, int);
SQLITE_PRIVATE int sqlite3PagerExclusiveLock(Pager*);
SQLITE_PRIVATE int sqlite3PagerSync(Pager *pPager);
SQLITE_PRIVATE int sqlite3PagerCommitPhaseTwo(Pager*);
SQLITE_PRIVATE int sqlite3PagerRollback(Pager*);
SQLITE_PRIVATE int sqlite3PagerOpenSavepoint(Pager *pPager, int n);
SQLITE_PRIVATE int sqlite3PagerSavepoint(Pager *pPager, int op, int iSavepoint);
SQLITE_PRIVATE int sqlite3PagerSharedLock(Pager *pPager);

SQLITE_PRIVATE int sqlite3PagerCheckpoint(Pager *pPager, int, int*, int*);
SQLITE_PRIVATE int sqlite3PagerWalSupported(Pager *pPager);
SQLITE_PRIVATE int sqlite3PagerWalCallback(Pager *pPager);
SQLITE_PRIVATE int sqlite3PagerOpenWal(Pager *pPager, int *pisOpen);
SQLITE_PRIVATE int sqlite3PagerCloseWal(Pager *pPager);

/* Functions used to query pager state and configuration. */
SQLITE_PRIVATE u8 sqlite3PagerIsreadonly(Pager*);
SQLITE_PRIVATE int sqlite3PagerRefcount(Pager*);
SQLITE_PRIVATE int sqlite3PagerMemUsed(Pager*);
SQLITE_PRIVATE const char *sqlite3PagerFilename(Pager*);
SQLITE_PRIVATE const sqlite3_vfs *sqlite3PagerVfs(Pager*);
SQLITE_PRIVATE sqlite3_file *sqlite3PagerFile(Pager*);
SQLITE_PRIVATE const char *sqlite3PagerJournalname(Pager*);
SQLITE_PRIVATE int sqlite3PagerNosync(Pager*);
SQLITE_PRIVATE void *sqlite3PagerTempSpace(Pager*);
SQLITE_PRIVATE int sqlite3PagerIsMemdb(Pager*);
SQLITE_PRIVATE void sqlite3PagerCacheStat(Pager *, int, int, int *);
SQLITE_PRIVATE void sqlite3PagerClearCache(Pager *);

/* Functions used to truncate the database file. */
SQLITE_PRIVATE void sqlite3PagerTruncateImage(Pager*,Pgno);

#if defined(SQLITE_HAS_CODEC) && !defined(SQLITE_OMIT_WAL)
SQLITE_PRIVATE void *sqlite3PagerCodec(DbPage *);
#endif

/* Functions to support testing and debugging. */
#if !defined(NDEBUG) || defined(SQLITE_TEST)
SQLITE_PRIVATE   Pgno sqlite3PagerPagenumber(DbPage*);
SQLITE_PRIVATE   int sqlite3PagerIswriteable(DbPage*);
#endif
#ifdef SQLITE_TEST
SQLITE_PRIVATE   int *sqlite3PagerStats(Pager*);
SQLITE_PRIVATE   void sqlite3PagerRefdump(Pager*);
  void disable_simulated_io_errors(void);
  void enable_simulated_io_errors(void);
#else
# define disable_simulated_io_errors()
# define enable_simulated_io_errors()
#endif

#endif /* _PAGER_H_ */

/************** End of pager.h ***********************************************/
/************** Continuing where we left off in sqliteInt.h ******************/
/************** Include pcache.h in the middle of sqliteInt.h ****************/
/************** Begin file pcache.h ******************************************/
/*
** 2008 August 05
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
** This header file defines the interface that the sqlite page cache
** subsystem.
*/

#ifndef _PCACHE_H_

typedef struct PgHdr PgHdr;
typedef struct PCache PCache;

/*
** Every page in the cache is controlled by an instance of the following
** structure.
*/
struct PgHdr {
  sqlite3_pcache_page *pPage;    /* Pcache object page handle */
  void *pData;                   /* Page data */
  void *pExtra;                  /* Extra content */
  PgHdr *pDirty;                 /* Transient list of dirty pages */
  Pgno pgno;                     /* Page number for this page */
  Pager *pPager;                 /* The pager this page is part of */
#ifdef SQLITE_CHECK_PAGES
  u32 pageHash;                  /* Hash of page content */
#endif
  u16 flags;                     /* PGHDR flags defined below */

  /**********************************************************************
  ** Elements above are public.  All that follows is private to pcache.c
  ** and should not be accessed by other modules.
  */
  i16 nRef;                      /* Number of users of this page */
  PCache *pCache;                /* Cache that owns this page */

  PgHdr *pDirtyNext;             /* Next element in list of dirty pages */
  PgHdr *pDirtyPrev;             /* Previous element in list of dirty pages */
};

/* Bit values for PgHdr.flags */
#define PGHDR_DIRTY             0x002  /* Page has changed */
#define PGHDR_NEED_SYNC         0x004  /* Fsync the rollback journal before
                                       ** writing this page to the database */
#define PGHDR_NEED_READ         0x008  /* Content is unread */
#define PGHDR_REUSE_UNLIKELY    0x010  /* A hint that reuse is unlikely */
#define PGHDR_DONT_WRITE        0x020  /* Do not write content to disk */

/* Initialize and shutdown the page cache subsystem */
SQLITE_PRIVATE int sqlite3PcacheInitialize(void);
SQLITE_PRIVATE void sqlite3PcacheShutdown(void);

/* Page cache buffer management:
** These routines implement SQLITE_CONFIG_PAGECACHE.
*/
SQLITE_PRIVATE void sqlite3PCacheBufferSetup(void *, int sz, int n);

/* Create a new pager cache.
** Under memory stress, invoke xStress to try to make pages clean.
** Only clean and unpinned pages can be reclaimed.
*/
SQLITE_PRIVATE void sqlite3PcacheOpen(
  int szPage,                    /* Size of every page */
  int szExtra,                   /* Extra space associated with each page */
  int bPurgeable,                /* True if pages are on backing store */
  int (*xStress)(void*, PgHdr*), /* Call to try to make pages clean */
  void *pStress,                 /* Argument to xStress */
  PCache *pToInit                /* Preallocated space for the PCache */
);

/* Modify the page-size after the cache has been created. */
SQLITE_PRIVATE void sqlite3PcacheSetPageSize(PCache *, int);

/* Return the size in bytes of a PCache object.  Used to preallocate
** storage space.
*/
SQLITE_PRIVATE int sqlite3PcacheSize(void);

/* One release per successful fetch.  Page is pinned until released.
** Reference counted.
*/
SQLITE_PRIVATE int sqlite3PcacheFetch(PCache*, Pgno, int createFlag, PgHdr**);
SQLITE_PRIVATE void sqlite3PcacheRelease(PgHdr*);

SQLITE_PRIVATE void sqlite3PcacheDrop(PgHdr*);         /* Remove page from cache */
SQLITE_PRIVATE void sqlite3PcacheMakeDirty(PgHdr*);    /* Make sure page is marked dirty */
SQLITE_PRIVATE void sqlite3PcacheMakeClean(PgHdr*);    /* Mark a single page as clean */
SQLITE_PRIVATE void sqlite3PcacheCleanAll(PCache*);    /* Mark all dirty list pages as clean */

/* Change a page number.  Used by incr-vacuum. */
SQLITE_PRIVATE void sqlite3PcacheMove(PgHdr*, Pgno);

/* Remove all pages with pgno>x.  Reset the cache if x==0 */
SQLITE_PRIVATE void sqlite3PcacheTruncate(PCache*, Pgno x);

/* Get a list of all dirty pages in the cache, sorted by page number */
SQLITE_PRIVATE PgHdr *sqlite3PcacheDirtyList(PCache*);

/* Reset and close the cache object */
SQLITE_PRIVATE void sqlite3PcacheClose(PCache*);

/* Clear flags from pages of the page cache */
SQLITE_PRIVATE void sqlite3PcacheClearSyncFlags(PCache *);

/* Discard the contents of the cache */
SQLITE_PRIVATE void sqlite3PcacheClear(PCache*);

/* Return the total number of outstanding page references */
SQLITE_PRIVATE int sqlite3PcacheRefCount(PCache*);

/* Increment the reference count of an existing page */
SQLITE_PRIVATE void sqlite3PcacheRef(PgHdr*);

SQLITE_PRIVATE int sqlite3PcachePageRefcount(PgHdr*);

/* Return the total number of pages stored in the cache */
SQLITE_PRIVATE int sqlite3PcachePagecount(PCache*);

#if defined(SQLITE_CHECK_PAGES) || defined(SQLITE_DEBUG)
/* Iterate through all dirty pages currently stored in the cache. This
** interface is only available if SQLITE_CHECK_PAGES is defined when the
** library is built.
*/
SQLITE_PRIVATE void sqlite3PcacheIterateDirty(PCache *pCache, void (*xIter)(PgHdr *));
#endif

/* Set and get the suggested cache-size for the specified pager-cache.
**
** If no global maximum is configured, then the system attempts to limit
** the total number of pages cached by purgeable pager-caches to the sum
** of the suggested cache-sizes.
*/
SQLITE_PRIVATE void sqlite3PcacheSetCachesize(PCache *, int);
#ifdef SQLITE_TEST
SQLITE_PRIVATE int sqlite3PcacheGetCachesize(PCache *);
#endif

/* Free up as much memory as possible from the page cache */
SQLITE_PRIVATE void sqlite3PcacheShrink(PCache*);

#ifdef SQLITE_ENABLE_MEMORY_MANAGEMENT
/* Try to return memory used by the pcache module to the main memory heap */
SQLITE_PRIVATE int sqlite3PcacheReleaseMemory(int);
#endif

#ifdef SQLITE_TEST
SQLITE_PRIVATE void sqlite3PcacheStats(int*,int*,int*,int*);
#endif

SQLITE_PRIVATE void sqlite3PCacheSetDefault(void);

#endif /* _PCACHE_H_ */

/************** End of pcache.h **********************************************/
/************** Continuing where we left off in sqliteInt.h ******************/

/************** Include os.h in the middle of sqliteInt.h ********************/
/************** Begin file os.h **********************************************/
/*
** 2001 September 16
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
******************************************************************************
**
** This header file (together with is companion C source-code file
** "os.c") attempt to abstract the underlying operating system so that
** the SQLite library will work on both POSIX and windows systems.
**
** This header file is #include-ed by sqliteInt.h and thus ends up
** being included by every source file.
*/
#ifndef _SQLITE_OS_H_
#define _SQLITE_OS_H_

/*
** Figure out if we are dealing with Unix, Windows, or some other
** operating system.  After the following block of preprocess macros,
** all of SQLITE_OS_UNIX, SQLITE_OS_WIN, SQLITE_OS_OS2, and SQLITE_OS_OTHER
** will defined to either 1 or 0.  One of the four will be 1.  The other
** three will be 0.
*/
#if defined(SQLITE_OS_OTHER)
# if SQLITE_OS_OTHER==1
#   undef SQLITE_OS_UNIX
#   define SQLITE_OS_UNIX 0
#   undef SQLITE_OS_WIN
#   define SQLITE_OS_WIN 0
#   undef SQLITE_OS_OS2
#   define SQLITE_OS_OS2 0
# else
#   undef SQLITE_OS_OTHER
# endif
#endif
#if !defined(SQLITE_OS_UNIX) && !defined(SQLITE_OS_OTHER)
# define SQLITE_OS_OTHER 0
# ifndef SQLITE_OS_WIN
#   if defined(_WIN32) || defined(WIN32) || defined(__CYGWIN__) || defined(__MINGW32__) || defined(__BORLANDC__)
#     define SQLITE_OS_WIN 1
#     define SQLITE_OS_UNIX 0
#     define SQLITE_OS_OS2 0
#   elif defined(__EMX__) || defined(_OS2) || defined(OS2) || defined(_OS2_) || defined(__OS2__)
#     define SQLITE_OS_WIN 0
#     define SQLITE_OS_UNIX 0
#     define SQLITE_OS_OS2 1
#   else
#     define SQLITE_OS_WIN 0
#     define SQLITE_OS_UNIX 1
#     define SQLITE_OS_OS2 0
#  endif
# else
#  define SQLITE_OS_UNIX 0
#  define SQLITE_OS_OS2 0
# endif
#else
# ifndef SQLITE_OS_WIN
#  define SQLITE_OS_WIN 0
# endif
#endif

/*
** Define the maximum size of a temporary filename
*/
#if SQLITE_OS_WIN
# include 
# define SQLITE_TEMPNAME_SIZE (MAX_PATH+50)
#elif SQLITE_OS_OS2
# if (__GNUC__ > 3 || __GNUC__ == 3 && __GNUC_MINOR__ >= 3) && defined(OS2_HIGH_MEMORY)
#  include  /* has to be included before os2.h for linking to work */
# endif
# define INCL_DOSDATETIME
# define INCL_DOSFILEMGR
# define INCL_DOSERRORS
# define INCL_DOSMISC
# define INCL_DOSPROCESS
# define INCL_DOSMODULEMGR
# define INCL_DOSSEMAPHORES
# include 
# include 
# define SQLITE_TEMPNAME_SIZE (CCHMAXPATHCOMP)
#else
# define SQLITE_TEMPNAME_SIZE 200
#endif

/*
** Determine if we are dealing with Windows NT.
*/
#if defined(_WIN32_WINNT)
# define SQLITE_OS_WINNT 1
#else
# define SQLITE_OS_WINNT 0
#endif

/*
** Determine if we are dealing with WindowsCE - which has a much
** reduced API.
*/
#if defined(_WIN32_WCE)
# define SQLITE_OS_WINCE 1
#else
# define SQLITE_OS_WINCE 0
#endif

/* If the SET_FULLSYNC macro is not defined above, then make it
** a no-op
*/
#ifndef SET_FULLSYNC
# define SET_FULLSYNC(x,y)
#endif

/*
** The default size of a disk sector
*/
#ifndef SQLITE_DEFAULT_SECTOR_SIZE
# define SQLITE_DEFAULT_SECTOR_SIZE 4096
#endif

/*
** Temporary files are named starting with this prefix followed by 16 random
** alphanumeric characters, and no file extension. They are stored in the
** OS's standard temporary file directory, and are deleted prior to exit.
** If sqlite is being embedded in another program, you may wish to change the
** prefix to reflect your program's name, so that if your program exits
** prematurely, old temporary files can be easily identified. This can be done
** using -DSQLITE_TEMP_FILE_PREFIX=myprefix_ on the compiler command line.
**
** 2006-10-31:  The default prefix used to be "sqlite_".  But then
** Mcafee started using SQLite in their anti-virus product and it
** started putting files with the "sqlite" name in the c:/temp folder.
** This annoyed many windows users.  Those users would then do a
** Google search for "sqlite", find the telephone numbers of the
** developers and call to wake them up at night and complain.
** For this reason, the default name prefix is changed to be "sqlite"
** spelled backwards.  So the temp files are still identified, but
** anybody smart enough to figure out the code is also likely smart
** enough to know that calling the developer will not help get rid
** of the file.
*/
#ifndef SQLITE_TEMP_FILE_PREFIX
# define SQLITE_TEMP_FILE_PREFIX "etilqs_"
#endif

/*
** The following values may be passed as the second argument to
** sqlite3OsLock(). The various locks exhibit the following semantics:
**
** SHARED:    Any number of processes may hold a SHARED lock simultaneously.
** RESERVED:  A single process may hold a RESERVED lock on a file at
**            any time. Other processes may hold and obtain new SHARED locks.
** PENDING:   A single process may hold a PENDING lock on a file at
**            any one time. Existing SHARED locks may persist, but no new
**            SHARED locks may be obtained by other processes.
** EXCLUSIVE: An EXCLUSIVE lock precludes all other locks.
**
** PENDING_LOCK may not be passed directly to sqlite3OsLock(). Instead, a
** process that requests an EXCLUSIVE lock may actually obtain a PENDING
** lock. This can be upgraded to an EXCLUSIVE lock by a subsequent call to
** sqlite3OsLock().
*/
#define NO_LOCK         0
#define SHARED_LOCK     1
#define RESERVED_LOCK   2
#define PENDING_LOCK    3
#define EXCLUSIVE_LOCK  4

/*
** File Locking Notes:  (Mostly about windows but also some info for Unix)
**
** We cannot use LockFileEx() or UnlockFileEx() on Win95/98/ME because
** those functions are not available.  So we use only LockFile() and
** UnlockFile().
**
** LockFile() prevents not just writing but also reading by other processes.
** A SHARED_LOCK is obtained by locking a single randomly-chosen
** byte out of a specific range of bytes. The lock byte is obtained at
** random so two separate readers can probably access the file at the
** same time, unless they are unlucky and choose the same lock byte.
** An EXCLUSIVE_LOCK is obtained by locking all bytes in the range.
** There can only be one writer.  A RESERVED_LOCK is obtained by locking
** a single byte of the file that is designated as the reserved lock byte.
** A PENDING_LOCK is obtained by locking a designated byte different from
** the RESERVED_LOCK byte.
**
** On WinNT/2K/XP systems, LockFileEx() and UnlockFileEx() are available,
** which means we can use reader/writer locks.  When reader/writer locks
** are used, the lock is placed on the same range of bytes that is used
** for probabilistic locking in Win95/98/ME.  Hence, the locking scheme
** will support two or more Win95 readers or two or more WinNT readers.
** But a single Win95 reader will lock out all WinNT readers and a single
** WinNT reader will lock out all other Win95 readers.
**
** The following #defines specify the range of bytes used for locking.
** SHARED_SIZE is the number of bytes available in the pool from which
** a random byte is selected for a shared lock.  The pool of bytes for
** shared locks begins at SHARED_FIRST.
**
** The same locking strategy and
** byte ranges are used for Unix.  This leaves open the possiblity of having
** clients on win95, winNT, and unix all talking to the same shared file
** and all locking correctly.  To do so would require that samba (or whatever
** tool is being used for file sharing) implements locks correctly between
** windows and unix.  I'm guessing that isn't likely to happen, but by
** using the same locking range we are at least open to the possibility.
**
** Locking in windows is manditory.  For this reason, we cannot store
** actual data in the bytes used for locking.  The pager never allocates
** the pages involved in locking therefore.  SHARED_SIZE is selected so
** that all locks will fit on a single page even at the minimum page size.
** PENDING_BYTE defines the beginning of the locks.  By default PENDING_BYTE
** is set high so that we don't have to allocate an unused page except
** for very large databases.  But one should test the page skipping logic
** by setting PENDING_BYTE low and running the entire regression suite.
**
** Changing the value of PENDING_BYTE results in a subtly incompatible
** file format.  Depending on how it is changed, you might not notice
** the incompatibility right away, even running a full regression test.
** The default location of PENDING_BYTE is the first byte past the
** 1GB boundary.
**
*/
#ifdef SQLITE_OMIT_WSD
# define PENDING_BYTE     (0x40000000)
#else
# define PENDING_BYTE      sqlite3PendingByte
#endif
#define RESERVED_BYTE     (PENDING_BYTE+1)
#define SHARED_FIRST      (PENDING_BYTE+2)
#define SHARED_SIZE       510

/*
** Wrapper around OS specific sqlite3_os_init() function.
*/
SQLITE_PRIVATE int sqlite3OsInit(void);

/*
** Functions for accessing sqlite3_file methods
*/
SQLITE_PRIVATE int sqlite3OsClose(sqlite3_file*);
SQLITE_PRIVATE int sqlite3OsRead(sqlite3_file*, void*, int amt, i64 offset);
SQLITE_PRIVATE int sqlite3OsWrite(sqlite3_file*, const void*, int amt, i64 offset);
SQLITE_PRIVATE int sqlite3OsTruncate(sqlite3_file*, i64 size);
SQLITE_PRIVATE int sqlite3OsSync(sqlite3_file*, int);
SQLITE_PRIVATE int sqlite3OsFileSize(sqlite3_file*, i64 *pSize);
SQLITE_PRIVATE int sqlite3OsLock(sqlite3_file*, int);
SQLITE_PRIVATE int sqlite3OsUnlock(sqlite3_file*, int);
SQLITE_PRIVATE int sqlite3OsCheckReservedLock(sqlite3_file *id, int *pResOut);
SQLITE_PRIVATE int sqlite3OsFileControl(sqlite3_file*,int,void*);
SQLITE_PRIVATE void sqlite3OsFileControlHint(sqlite3_file*,int,void*);
#define SQLITE_FCNTL_DB_UNCHANGED 0xca093fa0
SQLITE_PRIVATE int sqlite3OsSectorSize(sqlite3_file *id);
SQLITE_PRIVATE int sqlite3OsDeviceCharacteristics(sqlite3_file *id);
SQLITE_PRIVATE int sqlite3OsShmMap(sqlite3_file *,int,int,int,void volatile **);
SQLITE_PRIVATE int sqlite3OsShmLock(sqlite3_file *id, int, int, int);
SQLITE_PRIVATE void sqlite3OsShmBarrier(sqlite3_file *id);
SQLITE_PRIVATE int sqlite3OsShmUnmap(sqlite3_file *id, int);


/*
** Functions for accessing sqlite3_vfs methods
*/
SQLITE_PRIVATE int sqlite3OsOpen(sqlite3_vfs *, const char *, sqlite3_file*, int, int *);
SQLITE_PRIVATE int sqlite3OsDelete(sqlite3_vfs *, const char *, int);
SQLITE_PRIVATE int sqlite3OsAccess(sqlite3_vfs *, const char *, int, int *pResOut);
SQLITE_PRIVATE int sqlite3OsFullPathname(sqlite3_vfs *, const char *, int, char *);
#ifndef SQLITE_OMIT_LOAD_EXTENSION
SQLITE_PRIVATE void *sqlite3OsDlOpen(sqlite3_vfs *, const char *);
SQLITE_PRIVATE void sqlite3OsDlError(sqlite3_vfs *, int, char *);
SQLITE_PRIVATE void (*sqlite3OsDlSym(sqlite3_vfs *, void *, const char *))(void);
SQLITE_PRIVATE void sqlite3OsDlClose(sqlite3_vfs *, void *);
#endif /* SQLITE_OMIT_LOAD_EXTENSION */
SQLITE_PRIVATE int sqlite3OsRandomness(sqlite3_vfs *, int, char *);
SQLITE_PRIVATE int sqlite3OsSleep(sqlite3_vfs *, int);
SQLITE_PRIVATE int sqlite3OsCurrentTimeInt64(sqlite3_vfs *, sqlite3_int64*);

/*
** Convenience functions for opening and closing files using
** sqlite3_malloc() to obtain space for the file-handle structure.
*/
SQLITE_PRIVATE int sqlite3OsOpenMalloc(sqlite3_vfs *, const char *, sqlite3_file **, int,int*);
SQLITE_PRIVATE int sqlite3OsCloseFree(sqlite3_file *);

#endif /* _SQLITE_OS_H_ */

/************** End of os.h **************************************************/
/************** Continuing where we left off in sqliteInt.h ******************/
/************** Include mutex.h in the middle of sqliteInt.h *****************/
/************** Begin file mutex.h *******************************************/
/*
** 2007 August 28
**
** The author disclaims copyright to this source code.  In place of
** a legal notice, here is a blessing:
**
**    May you do good and not evil.
**    May you find forgiveness for yourself and forgive others.
**    May you share freely, never taking more than you give.
**
*************************************************************************
**
** This file contains the common header for all mutex implementations.
** The sqliteInt.h header #includes this file so that it is available
** to all source files.  We break it out in an effort to keep the code
** better organized.
**
** NOTE:  source files should *not* #include this header file directly.
** Source files should #include the sqliteInt.h file and let that file
** include this one indirectly.
*/


/*
** Figure out what version of the code to use.  The choices are
**
**   SQLITE_MUTEX_OMIT         No mutex logic.  Not even stubs.  The
**                             mutexes implemention cannot be overridden
**                             at start-time.
**
**   SQLITE_MUTEX_NOOP         For single-threaded applications.  No
**                             mutual exclusion is provided.  But this
**                             implementation can be overridden at
**                             start-time.
**
**   SQLITE_MUTEX_PTHREADS     For multi-threaded applications on Unix.
**
**   SQLITE_MUTEX_W32          For multi-threaded applications on Win32.
**
**   SQLITE_MUTEX_OS2          For multi-threaded applications on OS/2.
*/
#if !SQLITE_THREADSAFE
# define SQLITE_MUTEX_OMIT
#endif
#if SQLITE_THREADSAFE && !defined(SQLITE_MUTEX_NOOP)
#  if SQLITE_OS_UNIX
#    define SQLITE_MUTEX_PTHREADS
#  elif SQLITE_OS_WIN
#    define SQLITE_MUTEX_W32
#  elif SQLITE_OS_OS2
#    define SQLITE_MUTEX_OS2
#  else
#    define SQLITE_MUTEX_NOOP
#  endif
#endif

#ifdef SQLITE_MUTEX_OMIT
/*
** If this is a no-op implementation, implement everything as macros.
*/
#define sqlite3_mutex_alloc(X)    ((sqlite3_mutex*)8)
#define sqlite3_mutex_free(X)
#define sqlite3_mutex_enter(X)
#define sqlite3_mutex_try(X)      SQLITE_OK
#define sqlite3_mutex_leave(X)
#define sqlite3_mutex_held(X)     ((void)(X),1)
#define sqlite3_mutex_notheld(X)  ((void)(X),1)
#define sqlite3MutexAlloc(X)      ((sqlite3_mutex*)8)
#define sqlite3MutexInit()        SQLITE_OK
#define sqlite3MutexEnd()
#define MUTEX_LOGIC(X)
#else
#define MUTEX_LOGIC(X)            X
#endif /* defined(SQLITE_MUTEX_OMIT) */

/************** End of mutex.h ***********************************************/
/************** Continuing where we left off in sqliteInt.h ******************/


/*
** Each database file to be accessed by the system is an instance
** of the following structure.  There are normally two of these structures
** in the sqlite.aDb[] array.  aDb[0] is the main database file and
** aDb[1] is the database file used to hold temporary tables.  Additional
** databases may be attached.
*/
struct Db {
  char *zName;         /* Name of this database */
  Btree *pBt;          /* The B*Tree structure for this database file */
  u8 inTrans;          /* 0: not writable.  1: Transaction.  2: Checkpoint */
  u8 safety_level;     /* How aggressive at syncing data to disk */
  Schema *pSchema;     /* Pointer to database schema (possibly shared) */
};

/*
** An instance of the following structure stores a database schema.
**
** Most Schema objects are associated with a Btree.  The exception is
** the Schema for the TEMP databaes (sqlite3.aDb[1]) which is free-standing.
** In shared cache mode, a single Schema object can be shared by multiple
** Btrees that refer to the same underlying BtShared object.
**
** Schema objects are automatically deallocated when the last Btree that
** references them is destroyed.   The TEMP Schema is manually freed by
** sqlite3_close().
*
** A thread must be holding a mutex on the corresponding Btree in order
** to access Schema content.  This implies that the thread must also be
** holding a mutex on the sqlite3 connection pointer that owns the Btree.
** For a TEMP Schema, only the connection mutex is required.
*/
struct Schema {
  int schema_cookie;   /* Database schema version number for this file */
  int iGeneration;     /* Generation counter.  Incremented with each change */
  Hash tblHash;        /* All tables indexed by name */
  Hash idxHash;        /* All (named) indices indexed by name */
  Hash trigHash;       /* All triggers indexed by name */
  Hash fkeyHash;       /* All foreign keys by referenced table name */
  Table *pSeqTab;      /* The sqlite_sequence table used by AUTOINCREMENT */
  u8 file_format;      /* Schema format version for this file */
  u8 enc;              /* Text encoding used by this database */
  u16 flags;           /* Flags associated with this schema */
  int cache_size;      /* Number of pages to use in the cache */
};

/*
** These macros can be used to test, set, or clear bits in the
** Db.pSchema->flags field.
*/
#define DbHasProperty(D,I,P)     (((D)->aDb[I].pSchema->flags&(P))==(P))
#define DbHasAnyProperty(D,I,P)  (((D)->aDb[I].pSchema->flags&(P))!=0)
#define DbSetProperty(D,I,P)     (D)->aDb[I].pSchema->flags|=(P)
#define DbClearProperty(D,I,P)   (D)->aDb[I].pSchema->flags&=~(P)

/*
** Allowed values for the DB.pSchema->flags field.
**
** The DB_SchemaLoaded flag is set after the database schema has been
** read into internal hash tables.
**
** DB_UnresetViews means that one or more views have column names that
** have been filled out.  If the schema changes, these column names might
** changes and so the view will need to be reset.
*/
#define DB_SchemaLoaded    0x0001  /* The schema has been loaded */
#define DB_UnresetViews    0x0002  /* Some views have defined column names */
#define DB_Empty           0x0004  /* The file is empty (length 0 bytes) */

/*
** The number of different kinds of things that can be limited
** using the sqlite3_limit() interface.
*/
#define SQLITE_N_LIMIT (SQLITE_LIMIT_TRIGGER_DEPTH+1)

/*
** Lookaside malloc is a set of fixed-size buffers that can be used
** to satisfy small transient memory allocation requests for objects
** associated with a particular database connection.  The use of
** lookaside malloc provides a significant performance enhancement
** (approx 10%) by avoiding numerous malloc/free requests while parsing
** SQL statements.
**
** The Lookaside structure holds configuration information about the
** lookaside malloc subsystem.  Each available memory allocation in
** the lookaside subsystem is stored on a linked list of LookasideSlot
** objects.
**
** Lookaside allocations are only allowed for objects that are associated
** with a particular database connection.  Hence, schema information cannot
** be stored in lookaside because in shared cache mode the schema information
** is shared by multiple database connections.  Therefore, while parsing
** schema information, the Lookaside.bEnabled flag is cleared so that
** lookaside allocations are not used to construct the schema objects.
*/
struct Lookaside {
  u16 sz;                 /* Size of each buffer in bytes */
  u8 bEnabled;            /* False to disable new lookaside allocations */
  u8 bMalloced;           /* True if pStart obtained from sqlite3_malloc() */
  int nOut;               /* Number of buffers currently checked out */
  int mxOut;              /* Highwater mark for nOut */
  int anStat[3];          /* 0: hits.  1: size misses.  2: full misses */
  LookasideSlot *pFree;   /* List of available buffers */
  void *pStart;           /* First byte of available memory space */
  void *pEnd;             /* First byte past end of available space */
};
struct LookasideSlot {
  LookasideSlot *pNext;    /* Next buffer in the list of free buffers */
};

/*
** A hash table for function definitions.
**
** Hash each FuncDef structure into one of the FuncDefHash.a[] slots.
** Collisions are on the FuncDef.pHash chain.
*/
struct FuncDefHash {
  FuncDef *a[23];       /* Hash table for functions */
};

/*
** Each database connection is an instance of the following structure.
**
** The sqlite.lastRowid records the last insert rowid generated by an
** insert statement.  Inserts on views do not affect its value.  Each
** trigger has its own context, so that lastRowid can be updated inside
** triggers as usual.  The previous value will be restored once the trigger
** exits.  Upon entering a before or instead of trigger, lastRowid is no
** longer (since after version 2.8.12) reset to -1.
**
** The sqlite.nChange does not count changes within triggers and keeps no
** context.  It is reset at start of sqlite3_exec.
** The sqlite.lsChange represents the number of changes made by the last
** insert, update, or delete statement.  It remains constant throughout the
** length of a statement and is then updated by OP_SetCounts.  It keeps a
** context stack just like lastRowid so that the count of changes
** within a trigger is not seen outside the trigger.  Changes to views do not
** affect the value of lsChange.
** The sqlite.csChange keeps track of the number of current changes (since
** the last statement) and is used to update sqlite_lsChange.
**
** The member variables sqlite.errCode, sqlite.zErrMsg and sqlite.zErrMsg16
** store the most recent error code and, if applicable, string. The
** internal function sqlite3Error() is used to set these variables
** consistently.
*/
struct sqlite3 {
  sqlite3_vfs *pVfs;            /* OS Interface */
  int nDb;                      /* Number of backends currently in use */
  Db *aDb;                      /* All backends */
  int flags;                    /* Miscellaneous flags. See below */
  unsigned int openFlags;       /* Flags passed to sqlite3_vfs.xOpen() */
  int errCode;                  /* Most recent error code (SQLITE_*) */
  int errMask;                  /* & result codes with this before returning */
  u8 autoCommit;                /* The auto-commit flag. */
  u8 temp_store;                /* 1: file 2: memory 0: default */
  u8 mallocFailed;              /* True if we have seen a malloc failure */
  u8 dfltLockMode;              /* Default locking-mode for attached dbs */
  signed char nextAutovac;      /* Autovac setting after VACUUM if >=0 */
  u8 suppressErr;               /* Do not issue error messages if true */
  u8 vtabOnConflict;            /* Value to return for s3_vtab_on_conflict() */
  int nextPagesize;             /* Pagesize after VACUUM if >0 */
  int nTable;                   /* Number of tables in the database */
  CollSeq *pDfltColl;           /* The default collating sequence (BINARY) */
  i64 lastRowid;                /* ROWID of most recent insert (see above) */
  u32 magic;                    /* Magic number for detect library misuse */
  int nChange;                  /* Value returned by sqlite3_changes() */
  int nTotalChange;             /* Value returned by sqlite3_total_changes() */
  sqlite3_mutex *mutex;         /* Connection mutex */
  int aLimit[SQLITE_N_LIMIT];   /* Limits */
  struct sqlite3InitInfo {      /* Information used during initialization */
    int iDb;                    /* When back is being initialized */
    int newTnum;                /* Rootpage of table being initialized */
    u8 busy;                    /* TRUE if currently initializing */
    u8 orphanTrigger;           /* Last statement is orphaned TEMP trigger */
  } init;
  int nExtension;               /* Number of loaded extensions */
  void **aExtension;            /* Array of shared library handles */
  struct Vdbe *pVdbe;           /* List of active virtual machines */
  int activeVdbeCnt;            /* Number of VDBEs currently executing */
  int writeVdbeCnt;             /* Number of active VDBEs that are writing */
  int vdbeExecCnt;              /* Number of nested calls to VdbeExec() */
  void (*xTrace)(void*,const char*);        /* Trace function */
  void *pTraceArg;                          /* Argument to the trace function */
  void (*xProfile)(void*,const char*,u64);  /* Profiling function */
  void *pProfileArg;                        /* Argument to profile function */
  void *pCommitArg;                 /* Argument to xCommitCallback() */
  int (*xCommitCallback)(void*);    /* Invoked at every commit. */
  void *pRollbackArg;               /* Argument to xRollbackCallback() */
  void (*xRollbackCallback)(void*); /* Invoked at every commit. */
  void *pUpdateArg;
  void (*xUpdateCallback)(void*,int, const char*,const char*,sqlite_int64);
#ifndef SQLITE_OMIT_WAL
  int (*xWalCallback)(void *, sqlite3 *, const char *, int);
  void *pWalArg;
#endif
  void(*xCollNeeded)(void*,sqlite3*,int eTextRep,const char*);
  void(*xCollNeeded16)(void*,sqlite3*,int eTextRep,const void*);
  void *pCollNeededArg;
  sqlite3_value *pErr;          /* Most recent error message */
  char *zErrMsg;                /* Most recent error message (UTF-8 encoded) */
  char *zErrMsg16;              /* Most recent error message (UTF-16 encoded) */
  union {
    volatile int isInterrupted; /* True if sqlite3_interrupt has been called */
    double notUsed1;            /* Spacer */
  } u1;
  Lookaside lookaside;          /* Lookaside malloc configuration */
#ifndef SQLITE_OMIT_AUTHORIZATION
  int (*xAuth)(void*,int,const char*,const char*,const char*,const char*);
                                /* Access authorization function */
  void *pAuthArg;               /* 1st argument to the access auth function */
#endif
#ifndef SQLITE_OMIT_PROGRESS_CALLBACK
  int (*xProgress)(void *);     /* The progress callback */
  void *pProgressArg;           /* Argument to the progress callback */
  int nProgressOps;             /* Number of opcodes for progress callback */
#endif
#ifndef SQLITE_OMIT_VIRTUALTABLE
  Hash aModule;                 /* populated by sqlite3_create_module() */
  VtabCtx *pVtabCtx;            /* Context for active vtab connect/create */
  VTable **aVTrans;             /* Virtual tables with open transactions */
  int nVTrans;                  /* Allocated size of aVTrans */
  VTable *pDisconnect;    /* Disconnect these in next sqlite3_prepare() */
#endif
  FuncDefHash aFunc;            /* Hash table of connection functions */
  Hash aCollSeq;                /* All collating sequences */
  BusyHandler busyHandler;      /* Busy callback */
  int busyTimeout;              /* Busy handler timeout, in msec */
  Db aDbStatic[2];              /* Static space for the 2 default backends */
  Savepoint *pSavepoint;        /* List of active savepoints */
  int nSavepoint;               /* Number of non-transaction savepoints */
  int nStatement;               /* Number of nested statement-transactions  */
  u8 isTransactionSavepoint;    /* True if the outermost savepoint is a TS */
  i64 nDeferredCons;            /* Net deferred constraints this transaction. */
  int *pnBytesFreed;            /* If not NULL, increment this in DbFree() */

#ifdef SQLITE_ENABLE_UNLOCK_NOTIFY
  /* The following variables are all protected by the STATIC_MASTER
  ** mutex, not by sqlite3.mutex. They are used by code in notify.c.
  **
  ** When X.pUnlockConnection==Y, that means that X is waiting for Y to
  ** unlock so that it can proceed.
  **
  ** When X.pBlockingConnection==Y, that means that something that X tried
  ** tried to do recently failed with an SQLITE_LOCKED error due to locks
  ** held by Y.
  */
  sqlite3 *pBlockingConnection; /* Connection that caused SQLITE_LOCKED */
  sqlite3 *pUnlockConnection;           /* Connection to watch for unlock */
  void *pUnlockArg;                     /* Argument to xUnlockNotify */
  void (*xUnlockNotify)(void **, int);  /* Unlock notify callback */
  sqlite3 *pNextBlocked;        /* Next in list of all blocked connections */
#endif
};

/*
** A macro to discover the encoding of a database.
*/
#define ENC(db) ((db)->aDb[0].pSchema->enc)

/*
** Possible values for the sqlite3.flags.
*/
#define SQLITE_VdbeTrace      0x00000100  /* True to trace VDBE execution */
#define SQLITE_InternChanges  0x00000200  /* Uncommitted Hash table changes */
#define SQLITE_FullColNames   0x00000400  /* Show full column names on SELECT */
#define SQLITE_ShortColNames  0x00000800  /* Show short columns names */
#define SQLITE_CountRows      0x00001000  /* Count rows changed by INSERT, */
                                          /*   DELETE, or UPDATE and return */
                                          /*   the count using a callback. */
#define SQLITE_NullCallback   0x00002000  /* Invoke the callback once if the */
                                          /*   result set is empty */
#define SQLITE_SqlTrace       0x00004000  /* Debug print SQL as it executes */
#define SQLITE_VdbeListing    0x00008000  /* Debug listings of VDBE programs */
#define SQLITE_WriteSchema    0x00010000  /* OK to update SQLITE_MASTER */
#define SQLITE_NoReadlock     0x00020000  /* Readlocks are omitted when
                                          ** accessing read-only databases */
#define SQLITE_IgnoreChecks   0x00040000  /* Do not enforce check constraints */
#define SQLITE_ReadUncommitted 0x0080000  /* For shared-cache mode */
#define SQLITE_LegacyFileFmt  0x00100000  /* Create new databases in format 1 */
#define SQLITE_FullFSync      0x00200000  /* Use full fsync on the backend */
#define SQLITE_CkptFullFSync  0x00400000  /* Use full fsync for checkpoint */
#define SQLITE_RecoveryMode   0x00800000  /* Ignore schema errors */
#define SQLITE_ReverseOrder   0x01000000  /* Reverse unordered SELECTs */
#define SQLITE_RecTriggers    0x02000000  /* Enable recursive triggers */
#define SQLITE_ForeignKeys    0x04000000  /* Enforce foreign key constraints  */
#define SQLITE_AutoIndex      0x08000000  /* Enable automatic indexes */
#define SQLITE_PreferBuiltin  0x10000000  /* Preference to built-in funcs */
#define SQLITE_LoadExtension  0x20000000  /* Enable load_extension */
#define SQLITE_EnableTrigger  0x40000000  /* True to enable triggers */

/*
** Bits of the sqlite3.flags field that are used by the
** sqlite3_test_control(SQLITE_TESTCTRL_OPTIMIZATIONS,...) interface.
** These must be the low-order bits of the flags field.
*/
#define SQLITE_QueryFlattener 0x01        /* Disable query flattening */
#define SQLITE_ColumnCache    0x02        /* Disable the column cache */
#define SQLITE_IndexSort      0x04        /* Disable indexes for sorting */
#define SQLITE_IndexSearch    0x08        /* Disable indexes for searching */
#define SQLITE_IndexCover     0x10        /* Disable index covering table */
#define SQLITE_GroupByOrder   0x20        /* Disable GROUPBY cover of ORDERBY */
#define SQLITE_FactorOutConst 0x40        /* Disable factoring out constants */
#define SQLITE_IdxRealAsInt   0x80        /* Store REAL as INT in indices */
#define SQLITE_DistinctOpt    0x80        /* DISTINCT using indexes */
#define SQLITE_OptMask        0xff        /* Mask of all disablable opts */

/*
** Possible values for the sqlite.magic field.
** The numbers are obtained at random and have no special meaning, other
** than being distinct from one another.
*/
#define SQLITE_MAGIC_OPEN     0xa029a697  /* Database is open */
#define SQLITE_MAGIC_CLOSED   0x9f3c2d33  /* Database is closed */
#define SQLITE_MAGIC_SICK     0x4b771290  /* Error and awaiting close */
#define SQLITE_MAGIC_BUSY     0xf03b7906  /* Database currently in use */
#define SQLITE_MAGIC_ERROR    0xb5357930  /* An SQLITE_MISUSE error occurred */

/*
** Each SQL function is defined by an instance of the following
** structure.  A pointer to this structure is stored in the sqlite.aFunc
** hash table.  When multiple functions have the same name, the hash table
** points to a linked list of these structures.
*/
struct FuncDef {
  i16 nArg;            /* Number of arguments.  -1 means unlimited */
  u8 iPrefEnc;         /* Preferred text encoding (SQLITE_UTF8, 16LE, 16BE) */
  u8 flags;            /* Some combination of SQLITE_FUNC_* */
  void *pUserData;     /* User data parameter */
  FuncDef *pNext;      /* Next function with same name */
  void (*xFunc)(sqlite3_context*,int,sqlite3_value**); /* Regular function */
  void (*xStep)(sqlite3_context*,int,sqlite3_value**); /* Aggregate step */
  void (*xFinalize)(sqlite3_context*);                /* Aggregate finalizer */
  char *zName;         /* SQL name of the function. */
  FuncDef *pHash;      /* Next with a different name but the same hash */
  FuncDestructor *pDestructor;   /* Reference counted destructor function */
};

/*
** This structure encapsulates a user-function destructor callback (as
** configured using create_function_v2()) and a reference counter. When
** create_function_v2() is called to create a function with a destructor,
** a single object of this type is allocated. FuncDestructor.nRef is set to
** the number of FuncDef objects created (either 1 or 3, depending on whether
** or not the specified encoding is SQLITE_ANY). The FuncDef.pDestructor
** member of each of the new FuncDef objects is set to point to the allocated
** FuncDestructor.
**
** Thereafter, when one of the FuncDef objects is deleted, the reference
** count on this object is decremented. When it reaches 0, the destructor
** is invoked and the FuncDestructor structure freed.
*/
struct FuncDestructor {
  int nRef;
  void (*xDestroy)(void *);
  void *pUserData;
};

/*
** Possible values for FuncDef.flags
*/
#define SQLITE_FUNC_LIKE     0x01 /* Candidate for the LIKE optimization */
#define SQLITE_FUNC_CASE     0x02 /* Case-sensitive LIKE-type function */
#define SQLITE_FUNC_EPHEM    0x04 /* Ephemeral.  Delete with VDBE */
#define SQLITE_FUNC_NEEDCOLL 0x08 /* sqlite3GetFuncCollSeq() might be called */
#define SQLITE_FUNC_PRIVATE  0x10 /* Allowed for internal use only */
#define SQLITE_FUNC_COUNT    0x20 /* Built-in count(*) aggregate */
#define SQLITE_FUNC_COALESCE 0x40 /* Built-in coalesce() or ifnull() function */

/*
** The following three macros, FUNCTION(), LIKEFUNC() and AGGREGATE() are
** used to create the initializers for the FuncDef structures.
**
**   FUNCTION(zName, nArg, iArg, bNC, xFunc)
**     Used to create a scalar function definition of a function zName
**     implemented by C function xFunc that accepts nArg arguments. The
**     value passed as iArg is cast to a (void*) and made available
**     as the user-data (sqlite3_user_data()) for the function. If
**     argument bNC is true, then the SQLITE_FUNC_NEEDCOLL flag is set.
**
**   AGGREGATE(zName, nArg, iArg, bNC, xStep, xFinal)
**     Used to create an aggregate function definition implemented by
**     the C functions xStep and xFinal. The first four parameters
**     are interpreted in the same way as the first 4 parameters to
**     FUNCTION().
**
**   LIKEFUNC(zName, nArg, pArg, flags)
**     Used to create a scalar function definition of a function zName
**     that accepts nArg arguments and is implemented by a call to C
**     function likeFunc. Argument pArg is cast to a (void *) and made
**     available as the function user-data (sqlite3_user_data()). The
**     FuncDef.flags variable is set to the value passed as the flags
**     parameter.
*/
#define FUNCTION(zName, nArg, iArg, bNC, xFunc) \
  {nArg, SQLITE_UTF8, bNC*SQLITE_FUNC_NEEDCOLL, \
   SQLITE_INT_TO_PTR(iArg), 0, xFunc, 0, 0, #zName, 0, 0}
#define STR_FUNCTION(zName, nArg, pArg, bNC, xFunc) \
  {nArg, SQLITE_UTF8, bNC*SQLITE_FUNC_NEEDCOLL, \
   pArg, 0, xFunc, 0, 0, #zName, 0, 0}
#define LIKEFUNC(zName, nArg, arg, flags) \
  {nArg, SQLITE_UTF8, flags, (void *)arg, 0, likeFunc, 0, 0, #zName, 0, 0}
#define AGGREGATE(zName, nArg, arg, nc, xStep, xFinal) \
  {nArg, SQLITE_UTF8, nc*SQLITE_FUNC_NEEDCOLL, \
   SQLITE_INT_TO_PTR(arg), 0, 0, xStep,xFinal,#zName,0,0}

/*
** All current savepoints are stored in a linked list starting at
** sqlite3.pSavepoint. The first element in the list is the most recently
** opened savepoint. Savepoints are added to the list by the vdbe
** OP_Savepoint instruction.
*/
struct Savepoint {
  char *zName;                        /* Savepoint name (nul-terminated) */
  i64 nDeferredCons;                  /* Number of deferred fk violations */
  Savepoint *pNext;                   /* Parent savepoint (if any) */
};

/*
** The following are used as the second parameter to sqlite3Savepoint(),
** and as the P1 argument to the OP_Savepoint instruction.
*/
#define SAVEPOINT_BEGIN      0
#define SAVEPOINT_RELEASE    1
#define SAVEPOINT_ROLLBACK   2


/*
** Each SQLite module (virtual table definition) is defined by an
** instance of the following structure, stored in the sqlite3.aModule
** hash table.
*/
struct Module {
  const sqlite3_module *pModule;       /* Callback pointers */
  const char *zName;                   /* Name passed to create_module() */
  void *pAux;                          /* pAux passed to create_module() */
  void (*xDestroy)(void *);            /* Module destructor function */
};

/*
** information about each column of an SQL table is held in an instance
** of this structure.
*/
struct Column {
  char *zName;     /* Name of this column */
  Expr *pDflt;     /* Default value of this column */
  char *zDflt;     /* Original text of the default value */
  char *zType;     /* Data type for this column */
  char *zColl;     /* Collating sequence.  If NULL, use the default */
  u8 notNull;      /* True if there is a NOT NULL constraint */
  u8 isPrimKey;    /* True if this column is part of the PRIMARY KEY */
  char affinity;   /* One of the SQLITE_AFF_... values */
#ifndef SQLITE_OMIT_VIRTUALTABLE
  u8 isHidden;     /* True if this column is 'hidden' */
#endif
};

/*
** A "Collating Sequence" is defined by an instance of the following
** structure. Conceptually, a collating sequence consists of a name and
** a comparison routine that defines the order of that sequence.
**
** There may two separate implementations of the collation function, one
** that processes text in UTF-8 encoding (CollSeq.xCmp) and another that
** processes text encoded in UTF-16 (CollSeq.xCmp16), using the machine
** native byte order. When a collation sequence is invoked, SQLite selects
** the version that will require the least expensive encoding
** translations, if any.
**
** The CollSeq.pUser member variable is an extra parameter that passed in
** as the first argument to the UTF-8 comparison function, xCmp.
** CollSeq.pUser16 is the equivalent for the UTF-16 comparison function,
** xCmp16.
**
** If both CollSeq.xCmp and CollSeq.xCmp16 are NULL, it means that the
** collating sequence is undefined.  Indices built on an undefined
** collating sequence may not be read or written.
*/
struct CollSeq {
  char *zName;          /* Name of the collating sequence, UTF-8 encoded */
  u8 enc;               /* Text encoding handled by xCmp() */
  void *pUser;          /* First argument to xCmp() */
  int (*xCmp)(void*,int, const void*, int, const void*);
  void (*xDel)(void*);  /* Destructor for pUser */
};

/*
** A sort order can be either ASC or DESC.
*/
#define SQLITE_SO_ASC       0  /* Sort in ascending order */
#define SQLITE_SO_DESC      1  /* Sort in ascending order */

/*
** Column affinity types.
**
** These used to have mnemonic name like 'i' for SQLITE_AFF_INTEGER and
** 't' for SQLITE_AFF_TEXT.  But we can save a little space and improve
** the speed a little by numbering the values consecutively.
**
** But rather than start with 0 or 1, we begin with 'a'.  That way,
** when multiple affinity types are concatenated into a string and
** used as the P4 operand, they will be more readable.
**
** Note also that the numeric types are grouped together so that testing
** for a numeric type is a single comparison.
*/
#define SQLITE_AFF_TEXT     'a'
#define SQLITE_AFF_NONE     'b'
#define SQLITE_AFF_NUMERIC  'c'
#define SQLITE_AFF_INTEGER  'd'
#define SQLITE_AFF_REAL     'e'

#define sqlite3IsNumericAffinity(X)  ((X)>=SQLITE_AFF_NUMERIC)

/*
** The SQLITE_AFF_MASK values masks off the significant bits of an
** affinity value.
*/
#define SQLITE_AFF_MASK     0x67

/*
** Additional bit values that can be ORed with an affinity without
** changing the affinity.
*/
#define SQLITE_JUMPIFNULL   0x08  /* jumps if either operand is NULL */
#define SQLITE_STOREP2      0x10  /* Store result in reg[P2] rather than jump */
#define SQLITE_NULLEQ       0x80  /* NULL=NULL */

/*
** An object of this type is created for each virtual table present in
** the database schema.
**
** If the database schema is shared, then there is one instance of this
** structure for each database connection (sqlite3*) that uses the shared
** schema. This is because each database connection requires its own unique
** instance of the sqlite3_vtab* handle used to access the virtual table
** implementation. sqlite3_vtab* handles can not be shared between
** database connections, even when the rest of the in-memory database
** schema is shared, as the implementation often stores the database
** connection handle passed to it via the xConnect() or xCreate() method
** during initialization internally. This database connection handle may
** then be used by the virtual table implementation to access real tables
** within the database. So that they appear as part of the callers
** transaction, these accesses need to be made via the same database
** connection as that used to execute SQL operations on the virtual table.
**
** All VTable objects that correspond to a single table in a shared
** database schema are initially stored in a linked-list pointed to by
** the Table.pVTable member variable of the corresponding Table object.
** When an sqlite3_prepare() operation is required to access the virtual
** table, it searches the list for the VTable that corresponds to the
** database connection doing the preparing so as to use the correct
** sqlite3_vtab* handle in the compiled query.
**
** When an in-memory Table object is deleted (for example when the
** schema is being reloaded for some reason), the VTable objects are not
** deleted and the sqlite3_vtab* handles are not xDisconnect()ed
** immediately. Instead, they are moved from the Table.pVTable list to
** another linked list headed by the sqlite3.pDisconnect member of the
** corresponding sqlite3 structure. They are then deleted/xDisconnected
** next time a statement is prepared using said sqlite3*. This is done
** to avoid deadlock issues involving multiple sqlite3.mutex mutexes.
** Refer to comments above function sqlite3VtabUnlockList() for an
** explanation as to why it is safe to add an entry to an sqlite3.pDisconnect
** list without holding the corresponding sqlite3.mutex mutex.
**
** The memory for objects of this type is always allocated by
** sqlite3DbMalloc(), using the connection handle stored in VTable.db as
** the first argument.
*/
struct VTable {
  sqlite3 *db;              /* Database connection associated with this table */
  Module *pMod;             /* Pointer to module implementation */
  sqlite3_vtab *pVtab;      /* Pointer to vtab instance */
  int nRef;                 /* Number of pointers to this structure */
  u8 bConstraint;           /* True if constraints are supported */
  int iSavepoint;           /* Depth of the SAVEPOINT stack */
  VTable *pNext;            /* Next in linked list (see above) */
};

/*
** Each SQL table is represented in memory by an instance of the
** following structure.
**
** Table.zName is the name of the table.  The case of the original
** CREATE TABLE statement is stored, but case is not significant for
** comparisons.
**
** Table.nCol is the number of columns in this table.  Table.aCol is a
** pointer to an array of Column structures, one for each column.
**
** If the table has an INTEGER PRIMARY KEY, then Table.iPKey is the index of
** the column that is that key.   Otherwise Table.iPKey is negative.  Note
** that the datatype of the PRIMARY KEY must be INTEGER for this field to
** be set.  An INTEGER PRIMARY KEY is used as the rowid for each row of
** the table.  If a table has no INTEGER PRIMARY KEY, then a random rowid
** is generated for each row of the table.  TF_HasPrimaryKey is set if
** the table has any PRIMARY KEY, INTEGER or otherwise.
**
** Table.tnum is the page number for the root BTree page of the table in the
** database file.  If Table.iDb is the index of the database table backend
** in sqlite.aDb[].  0 is for the main database and 1 is for the file that
** holds temporary tables and indices.  If TF_Ephemeral is set
** then the table is stored in a file that is automatically deleted
** when the VDBE cursor to the table is closed.  In this case Table.tnum
** refers VDBE cursor number that holds the table open, not to the root
** page number.  Transient tables are used to hold the results of a
** sub-query that appears instead of a real table name in the FROM clause
** of a SELECT statement.
*/
struct Table {
  char *zName;         /* Name of the table or view */
  int iPKey;           /* If not negative, use aCol[iPKey] as the primary key */
  int nCol;            /* Number of columns in this table */
  Column *aCol;        /* Information about each column */
  Index *pIndex;       /* List of SQL indexes on this table. */
  int tnum;            /* Root BTree node for this table (see note above) */
  tRowcnt nRowEst;     /* Estimated rows in table - from sqlite_stat1 table */
  Select *pSelect;     /* NULL for tables.  Points to definition if a view. */
  u16 nRef;            /* Number of pointers to this Table */
  u8 tabFlags;         /* Mask of TF_* values */
  u8 keyConf;          /* What to do in case of uniqueness conflict on iPKey */
  FKey *pFKey;         /* Linked list of all foreign keys in this table */
  char *zColAff;       /* String defining the affinity of each column */
#ifndef SQLITE_OMIT_CHECK
  Expr *pCheck;        /* The AND of all CHECK constraints */
#endif
#ifndef SQLITE_OMIT_ALTERTABLE
  int addColOffset;    /* Offset in CREATE TABLE stmt to add a new column */
#endif
#ifndef SQLITE_OMIT_VIRTUALTABLE
  VTable *pVTable;     /* List of VTable objects. */
  int nModuleArg;      /* Number of arguments to the module */
  char **azModuleArg;  /* Text of all module args. [0] is module name */
#endif
  Trigger *pTrigger;   /* List of triggers stored in pSchema */
  Schema *pSchema;     /* Schema that contains this table */
  Table *pNextZombie;  /* Next on the Parse.pZombieTab list */
};

/*
** Allowed values for Tabe.tabFlags.
*/
#define TF_Readonly        0x01    /* Read-only system table */
#define TF_Ephemeral       0x02    /* An ephemeral table */
#define TF_HasPrimaryKey   0x04    /* Table has a primary key */
#define TF_Autoincrement   0x08    /* Integer primary key is autoincrement */
#define TF_Virtual         0x10    /* Is a virtual table */
#define TF_NeedMetadata    0x20    /* aCol[].zType and aCol[].pColl missing */



/*
** Test to see whether or not a table is a virtual table.  This is
** done as a macro so that it will be optimized out when virtual
** table support is omitted from the build.
*/
#ifndef SQLITE_OMIT_VIRTUALTABLE
#  define IsVirtual(X)      (((X)->tabFlags & TF_Virtual)!=0)
#  define IsHiddenColumn(X) ((X)->isHidden)
#else
#  define IsVirtual(X)      0
#  define IsHiddenColumn(X) 0
#endif

/*
** Each foreign key constraint is an instance of the following structure.
**
** A foreign key is associated with two tables.  The "from" table is
** the table that contains the REFERENCES clause that creates the foreign
** key.  The "to" table is the table that is named in the REFERENCES clause.
** Consider this example:
**
**     CREATE TABLE ex1(
**       a INTEGER PRIMARY KEY,
**       b INTEGER CONSTRAINT fk1 REFERENCES ex2(x)
**     );
**
** For foreign key "fk1", the from-table is "ex1" and the to-table is "ex2".
**
** Each REFERENCES clause generates an instance of the following structure
** which is attached to the from-table.  The to-table need not exist when
** the from-table is created.  The existence of the to-table is not checked.
*/
struct FKey {
  Table *pFrom;     /* Table containing the REFERENCES clause (aka: Child) */
  FKey *pNextFrom;  /* Next foreign key in pFrom */
  char *zTo;        /* Name of table that the key points to (aka: Parent) */
  FKey *pNextTo;    /* Next foreign key on table named zTo */
  FKey *pPrevTo;    /* Previous foreign key on table named zTo */
  int nCol;         /* Number of columns in this key */
  /* EV: R-30323-21917 */
  u8 isDeferred;    /* True if constraint checking is deferred till COMMIT */
  u8 aAction[2];          /* ON DELETE and ON UPDATE actions, respectively */
  Trigger *apTrigger[2];  /* Triggers for aAction[] actions */
  struct sColMap {  /* Mapping of columns in pFrom to columns in zTo */
    int iFrom;         /* Index of column in pFrom */
    char *zCol;        /* Name of column in zTo.  If 0 use PRIMARY KEY */
  } aCol[1];        /* One entry for each of nCol column s */
};

/*
** SQLite supports many different ways to resolve a constraint
** error.  ROLLBACK processing means that a constraint violation
** causes the operation in process to fail and for the current transaction
** to be rolled back.  ABORT processing means the operation in process
** fails and any prior changes from that one operation are backed out,
** but the transaction is not rolled back.  FAIL processing means that
** the operation in progress stops and returns an error code.  But prior
** changes due to the same operation are not backed out and no rollback
** occurs.  IGNORE means that the particular row that caused the constraint
** error is not inserted or updated.  Processing continues and no error
** is returned.  REPLACE means that preexisting database rows that caused
** a UNIQUE constraint violation are removed so that the new insert or
** update can proceed.  Processing continues and no error is reported.
**
** RESTRICT, SETNULL, and CASCADE actions apply only to foreign keys.
** RESTRICT is the same as ABORT for IMMEDIATE foreign keys and the
** same as ROLLBACK for DEFERRED keys.  SETNULL means that the foreign
** key is set to NULL.  CASCADE means that a DELETE or UPDATE of the
** referenced table row is propagated into the row that holds the
** foreign key.
**
** The following symbolic values are used to record which type
** of action to take.
*/
#define OE_None     0   /* There is no constraint to check */
#define OE_Rollback 1   /* Fail the operation and rollback the transaction */
#define OE_Abort    2   /* Back out changes but do no rollback transaction */
#define OE_Fail     3   /* Stop the operation but leave all prior changes */
#define OE_Ignore   4   /* Ignore the error. Do not do the INSERT or UPDATE */
#define OE_Replace  5   /* Delete existing record, then do INSERT or UPDATE */

#define OE_Restrict 6   /* OE_Abort for IMMEDIATE, OE_Rollback for DEFERRED */
#define OE_SetNull  7   /* Set the foreign key value to NULL */
#define OE_SetDflt  8   /* Set the foreign key value to its default */
#define OE_Cascade  9   /* Cascade the changes */

#define OE_Default  99  /* Do whatever the default action is */


/*
** An instance of the following structure is passed as the first
** argument to sqlite3VdbeKeyCompare and is used to control the
** comparison of the two index keys.
*/
struct KeyInfo {
  sqlite3 *db;        /* The database connection */
  u8 enc;             /* Text encoding - one of the SQLITE_UTF* values */
  u16 nField;         /* Number of entries in aColl[] */
  u8 *aSortOrder;     /* Sort order for each column.  May be NULL */
  CollSeq *aColl[1];  /* Collating sequence for each term of the key */
};

/*
** An instance of the following structure holds information about a
** single index record that has already been parsed out into individual
** values.
**
** A record is an object that contains one or more fields of data.
** Records are used to store the content of a table row and to store
** the key of an index.  A blob encoding of a record is created by
** the OP_MakeRecord opcode of the VDBE and is disassembled by the
** OP_Column opcode.
**
** This structure holds a record that has already been disassembled
** into its constituent fields.
*/
struct UnpackedRecord {
  KeyInfo *pKeyInfo;  /* Collation and sort-order information */
  u16 nField;         /* Number of entries in apMem[] */
  u8 flags;           /* Boolean settings.  UNPACKED_... below */
  i64 rowid;          /* Used by UNPACKED_PREFIX_SEARCH */
  Mem *aMem;          /* Values */
};

/*
** Allowed values of UnpackedRecord.flags
*/
#define UNPACKED_INCRKEY       0x01  /* Make this key an epsilon larger */
#define UNPACKED_PREFIX_MATCH  0x02  /* A prefix match is considered OK */
#define UNPACKED_PREFIX_SEARCH 0x04  /* Ignore final (rowid) field */

/*
** Each SQL index is represented in memory by an
** instance of the following structure.
**
** The columns of the table that are to be indexed are described
** by the aiColumn[] field of this structure.  For example, suppose
** we have the following table and index:
**
**     CREATE TABLE Ex1(c1 int, c2 int, c3 text);
**     CREATE INDEX Ex2 ON Ex1(c3,c1);
**
** In the Table structure describing Ex1, nCol==3 because there are
** three columns in the table.  In the Index structure describing
** Ex2, nColumn==2 since 2 of the 3 columns of Ex1 are indexed.
** The value of aiColumn is {2, 0}.  aiColumn[0]==2 because the
** first column to be indexed (c3) has an index of 2 in Ex1.aCol[].
** The second column to be indexed (c1) has an index of 0 in
** Ex1.aCol[], hence Ex2.aiColumn[1]==0.
**
** The Index.onError field determines whether or not the indexed columns
** must be unique and what to do if they are not.  When Index.onError=OE_None,
** it means this is not a unique index.  Otherwise it is a unique index
** and the value of Index.onError indicate the which conflict resolution
** algorithm to employ whenever an attempt is made to insert a non-unique
** element.
*/
struct Index {
  char *zName;     /* Name of this index */
  int nColumn;     /* Number of columns in the table used by this index */
  int *aiColumn;   /* Which columns are used by this index.  1st is 0 */
  tRowcnt *aiRowEst; /* Result of ANALYZE: Est. rows selected by each column */
  Table *pTable;   /* The SQL table being indexed */
  int tnum;        /* Page containing root of this index in database file */
  u8 onError;      /* OE_Abort, OE_Ignore, OE_Replace, or OE_None */
  u8 autoIndex;    /* True if is automatically created (ex: by UNIQUE) */
  u8 bUnordered;   /* Use this index for == or IN queries only */
  char *zColAff;   /* String defining the affinity of each column */
  Index *pNext;    /* The next index associated with the same table */
  Schema *pSchema; /* Schema containing this index */
  u8 *aSortOrder;  /* Array of size Index.nColumn. True==DESC, False==ASC */
  char **azColl;   /* Array of collation sequence names for index */
#ifdef SQLITE_ENABLE_STAT3
  int nSample;             /* Number of elements in aSample[] */
  tRowcnt avgEq;           /* Average nEq value for key values not in aSample */
  IndexSample *aSample;    /* Samples of the left-most key */
#endif
};

/*
** Each sample stored in the sqlite_stat3 table is represented in memory
** using a structure of this type.  See documentation at the top of the
** analyze.c source file for additional information.
*/
struct IndexSample {
  union {
    char *z;        /* Value if eType is SQLITE_TEXT or SQLITE_BLOB */
    double r;       /* Value if eType is SQLITE_FLOAT */
    i64 i;          /* Value if eType is SQLITE_INTEGER */
  } u;
  u8 eType;         /* SQLITE_NULL, SQLITE_INTEGER ... etc. */
  int nByte;        /* Size in byte of text or blob. */
  tRowcnt nEq;      /* Est. number of rows where the key equals this sample */
  tRowcnt nLt;      /* Est. number of rows where key is less than this sample */
  tRowcnt nDLt;     /* Est. number of distinct keys less than this sample */
};

/*
** Each token coming out of the lexer is an instance of
** this structure.  Tokens are also used as part of an expression.
**
** Note if Token.z==0 then Token.dyn and Token.n are undefined and
** may contain random values.  Do not make any assumptions about Token.dyn
** and Token.n when Token.z==0.
*/
struct Token {
  const char *z;     /* Text of the token.  Not NULL-terminated! */
  unsigned int n;    /* Number of characters in this token */
};

/*
** An instance of this structure contains information needed to generate
** code for a SELECT that contains aggregate functions.
**
** If Expr.op==TK_AGG_COLUMN or TK_AGG_FUNCTION then Expr.pAggInfo is a
** pointer to this structure.  The Expr.iColumn field is the index in
** AggInfo.aCol[] or AggInfo.aFunc[] of information needed to generate
** code for that node.
**
** AggInfo.pGroupBy and AggInfo.aFunc.pExpr point to fields within the
** original Select structure that describes the SELECT statement.  These
** fields do not need to be freed when deallocating the AggInfo structure.
*/
struct AggInfo {
  u8 directMode;          /* Direct rendering mode means take data directly
                          ** from source tables rather than from accumulators */
  u8 useSortingIdx;       /* In direct mode, reference the sorting index rather
                          ** than the source table */
  int sortingIdx;         /* Cursor number of the sorting index */
  int sortingIdxPTab;     /* Cursor number of pseudo-table */
  ExprList *pGroupBy;     /* The group by clause */
  int nSortingColumn;     /* Number of columns in the sorting index */
  struct AggInfo_col {    /* For each column used in source tables */
    Table *pTab;             /* Source table */
    int iTable;              /* Cursor number of the source table */
    int iColumn;             /* Column number within the source table */
    int iSorterColumn;       /* Column number in the sorting index */
    int iMem;                /* Memory location that acts as accumulator */
    Expr *pExpr;             /* The original expression */
  } *aCol;
  int nColumn;            /* Number of used entries in aCol[] */
  int nColumnAlloc;       /* Number of slots allocated for aCol[] */
  int nAccumulator;       /* Number of columns that show through to the output.
                          ** Additional columns are used only as parameters to
                          ** aggregate functions */
  struct AggInfo_func {   /* For each aggregate function */
    Expr *pExpr;             /* Expression encoding the function */
    FuncDef *pFunc;          /* The aggregate function implementation */
    int iMem;                /* Memory location that acts as accumulator */
    int iDistinct;           /* Ephemeral table used to enforce DISTINCT */
  } *aFunc;
  int nFunc;              /* Number of entries in aFunc[] */
  int nFuncAlloc;         /* Number of slots allocated for aFunc[] */
};

/*
** The datatype ynVar is a signed integer, either 16-bit or 32-bit.
** Usually it is 16-bits.  But if SQLITE_MAX_VARIABLE_NUMBER is greater
** than 32767 we have to make it 32-bit.  16-bit is preferred because
** it uses less memory in the Expr object, which is a big memory user
** in systems with lots of prepared statements.  And few applications
** need more than about 10 or 20 variables.  But some extreme users want
** to have prepared statements with over 32767 variables, and for them
** the option is available (at compile-time).
*/
#if SQLITE_MAX_VARIABLE_NUMBER<=32767
typedef i16 ynVar;
#else
typedef int ynVar;
#endif

/*
** Each node of an expression in the parse tree is an instance
** of this structure.
**
** Expr.op is the opcode. The integer parser token codes are reused
** as opcodes here. For example, the parser defines TK_GE to be an integer
** code representing the ">=" operator. This same integer code is reused
** to represent the greater-than-or-equal-to operator in the expression
** tree.
**
** If the expression is an SQL literal (TK_INTEGER, TK_FLOAT, TK_BLOB,
** or TK_STRING), then Expr.token contains the text of the SQL literal. If
** the expression is a variable (TK_VARIABLE), then Expr.token contains the
** variable name. Finally, if the expression is an SQL function (TK_FUNCTION),
** then Expr.token contains the name of the function.
**
** Expr.pRight and Expr.pLeft are the left and right subexpressions of a
** binary operator. Either or both may be NULL.
**
** Expr.x.pList is a list of arguments if the expression is an SQL function,
** a CASE expression or an IN expression of the form " IN (, ...)".
** Expr.x.pSelect is used if the expression is a sub-select or an expression of
** the form " IN (SELECT ...)". If the EP_xIsSelect bit is set in the
** Expr.flags mask, then Expr.x.pSelect is valid. Otherwise, Expr.x.pList is
** valid.
**
** An expression of the form ID or ID.ID refers to a column in a table.
** For such expressions, Expr.op is set to TK_COLUMN and Expr.iTable is
** the integer cursor number of a VDBE cursor pointing to that table and
** Expr.iColumn is the column number for the specific column.  If the
** expression is used as a result in an aggregate SELECT, then the
** value is also stored in the Expr.iAgg column in the aggregate so that
** it can be accessed after all aggregates are computed.
**
** If the expression is an unbound variable marker (a question mark
** character '?' in the original SQL) then the Expr.iTable holds the index
** number for that variable.
**
** If the expression is a subquery then Expr.iColumn holds an integer
** register number containing the result of the subquery.  If the
** subquery gives a constant result, then iTable is -1.  If the subquery
** gives a different answer at different times during statement processing
** then iTable is the address of a subroutine that computes the subquery.
**
** If the Expr is of type OP_Column, and the table it is selecting from
** is a disk table or the "old.*" pseudo-table, then pTab points to the
** corresponding table definition.
**
** ALLOCATION NOTES:
**
** Expr objects can use a lot of memory space in database schema.  To
** help reduce memory requirements, sometimes an Expr object will be
** truncated.  And to reduce the number of memory allocations, sometimes
** two or more Expr objects will be stored in a single memory allocation,
** together with Expr.zToken strings.
**
** If the EP_Reduced and EP_TokenOnly flags are set when
** an Expr object is truncated.  When EP_Reduced is set, then all
** the child Expr objects in the Expr.pLeft and Expr.pRight subtrees
** are contained within the same memory allocation.  Note, however, that
** the subtrees in Expr.x.pList or Expr.x.pSelect are always separately
** allocated, regardless of whether or not EP_Reduced is set.
*/
struct Expr {
  u8 op;                 /* Operation performed by this node */
  char affinity;         /* The affinity of the column or 0 if not a column */
  u16 flags;             /* Various flags.  EP_* See below */
  union {
    char *zToken;          /* Token value. Zero terminated and dequoted */
    int iValue;            /* Non-negative integer value if EP_IntValue */
  } u;

  /* If the EP_TokenOnly flag is set in the Expr.flags mask, then no
  ** space is allocated for the fields below this point. An attempt to
  ** access them will result in a segfault or malfunction.
  *********************************************************************/

  Expr *pLeft;           /* Left subnode */
  Expr *pRight;          /* Right subnode */
  union {
    ExprList *pList;     /* Function arguments or in " IN ( IN ( and save them in the array . */
void              gth_region_factory_save(GthRegionFactory *region_factory,
                                          GtArray *nodes, GthInput *input);
GtStr*            gth_region_factory_get_seqid(GthRegionFactory*,
                                               unsigned long filenum,
                                               unsigned long seqnum);
long              gth_region_factory_offset(GthRegionFactory*,
                                            unsigned long filenum,
                                            unsigned long seqnum);

#endif
genometools-1.5.1/src/gth/run_header.c000066400000000000000000000146541211610345200177070ustar00rootroot00000000000000/*
  Copyright (c) 2003-2010 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/cstr_array.h"
#include "gth/indent.h"
#include "gth/showbool.h"
#include "gth/time.h"
#include "gth/call_info.h"
#include "gth/gthspeciestab.h"
#include "gth/run_header.h"
#include "gt_config.h"

/* The name of the splice site models. */
#define SPLICE_SITE_MODEL_NAME  "Bayesian"

/* The name of the generic species */
#define GENERIC_SPECIES_NAME    "generic"

static void show_overall_reference_type(GthAlphatype overallalphatype,
                                        unsigned int indentlevel,
                                        GtFile *outfp)
{
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "");
  switch (overallalphatype)
  {
    case DNA_ALPHA:
      gt_file_xprintf(outfp, "ESTcDNA");
      break;
    case PROTEIN_ALPHA:
      gt_file_xprintf(outfp, "Protein");
      break;
    case MIXED_ALPHA:
      gt_file_xprintf(outfp, "Mixed");
      break;
    default: gt_assert(0);
  }
  gt_file_xprintf(outfp, "\n");
}

static void show_xml_run_header(GthCallInfo *call_info, GthInput *input,
                                const char *timestring, const char *gth_version,
                                unsigned int indentlevel, const char **args)
{
  GtFile *outfp = call_info->out->outfp;
  unsigned long i;

  gth_indent(outfp, indentlevel);
  if (call_info->intermediate) {
    gt_file_xprintf(outfp, "
    \n");
  }
  else {
    gt_file_xprintf(outfp,
              "
    \n");
  }

  /* at least one genomic file defined */
  gt_assert(gth_input_num_of_gen_files(input));
  /* at least one reference file defined */
  gt_assert(gth_input_num_of_ref_files(input));

  /* show a readable version of GthCallInfo. That is, it is shown with wich
     parameters the program was called */

  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n", gth_version,
                  GT_BUILT, timestring);

  /* show genomic file names */
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  for (i = 0; i < gth_input_num_of_gen_files(input); i++) {
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "%s\n",
                    gth_input_get_genomic_filename(input, i));
  }

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");

  /* show reference file names */
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  for (i = 0; i < gth_input_num_of_ref_files(input); i++) {
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n",
                    gth_input_get_reference_filename(input, i),
                    gth_input_get_alphatype(input, i) == DNA_ALPHA
                    ? "ESTcDNA" : "Protein");
  }

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n", SPLICE_SITE_MODEL_NAME,
                  call_info->speciesnum ==  NUMOFSPECIES
                  ? GENERIC_SPECIES_NAME
                  : speciestab[call_info->speciesnum]);

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  /* output name of BSSM file */
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n",
                  gth_input_bssmfilename(input));

  /* output name of scorematrix */
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n",
                  gt_str_get(call_info->scorematrixfile));

  /* output searchmode */
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n",
                  GTH_SHOWBOOL(gth_input_forward(input)),
                  GTH_SHOWBOOL(gth_input_reverse(input)));

  /* output arguments as comment */
  gt_file_xprintf(outfp, "\n");

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");

  show_overall_reference_type(gth_input_overall_alphatype(input),
                              indentlevel, outfp);

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "
    \n");
}

void gth_run_header_show(GthCallInfo *call_info, GthInput *input,
                         const char *gth_version, unsigned int indentlevel,
                         const char **args)
{
  char *timestring;
  GtFile *outfp = call_info->out->outfp;

  /* determine time */
  timestring = gth_get_time();

  /* output XML header */
  if (call_info->out->xmlout) {
    show_xml_run_header(call_info, input, timestring, gth_version, indentlevel,
                        args);
  }
  else if (!call_info->out->gff3out) {
    gt_file_xprintf(outfp, "%c GenomeThreader %s (%s)\n", COMMENTCHAR,
                    gth_version, GT_BUILT);
    gt_file_xprintf(outfp, "%c Date run: %s\n", COMMENTCHAR, timestring);
    gt_file_xprintf(outfp, "%c Arguments: ", COMMENTCHAR);
    gt_cstr_array_show_genfile(args, outfp);
  }

  /* free */
  gt_free(timestring);
}
genometools-1.5.1/src/gth/run_header.h000066400000000000000000000021601211610345200177010ustar00rootroot00000000000000/*
  Copyright (c) 2003-2010 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RUN_HEADER_H
#define RUN_HEADER_H

#include "gth/stat.h"

/* output the run header in plain or XML format */
void gth_run_header_show(GthCallInfo*, GthInput*, const char *gth_version,
                         unsigned int indentlevel, const char **args);

#endif
genometools-1.5.1/src/gth/sa.c000066400000000000000000001275351211610345200162010ustar00rootroot00000000000000/*
  Copyright (c) 2003-2012 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/mathsupport.h"
#include "core/md5_seqid.h"
#include "core/safearith.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "extended/gff3_escaping.h"
#include "gth/default.h"
#include "gth/sa.h"
#include "gth/txt_sa_visitor.h"

#define SA_DELIMITERLINECHAR    '*'
#define CALCPOLYATAILWINDOW     50
#define MINIMUMPOLYATAILLENGTH  10

/* Keep in sync with gth_sas_are_equal()! */
struct GthSA {
  GthBacktracePath *backtrace_path;  /* the edit operations */
  unsigned long gen_total_length,    /* total length of the genomic sequence */
                gen_offset,          /* offset of the genomic sequence where
                                        this SA refers to */
                ref_total_length,    /* total length of reference sequence */
                gen_file_num,        /* genomic file number */
                gen_seq_num,         /* genomic sequence number */
                ref_file_num,        /* reference file number */
                ref_seq_num;         /* reference sequence number */
  GtStr *gen_id,                     /* contains id of genomic sequence */
        *ref_id,                     /* contains id of reference sequence */
        *gen_md5,                    /* contains MD5 of genomic sequence, if
                                        necessary */
        *ref_md5,                    /* contains MD5 of reference sequence, if
                                        necessary */
        *gen_desc,                   /* contains description of genomic
                                        sequence, if necessary */
        *ref_desc;                   /* contains description of reference
                                        sequence, if necessary */
  bool gen_strand_forward,           /* equals true, iff the alignment relates
                                        to the forward strand of the genomic
                                        sequence */
       ref_strand_forward;           /* equals true, iff the alignment relates
                                        to the forward strand of the reference
                                        sequence */
  GtArray *exons,                    /* contains the information about all
                                        exons */
          *introns;                  /* contains the information about all
                                        introns */
  GtRange polyAtailpos;              /* (GS2 = ppa), contains the positions of
                                        the  poly-A tail in the reference
                                        sequence. Iff both positions are equal
                                        to zero, no poly-A tail could be
                                        determined. */
  GthFlt alignmentscore,             /* the score of the alignment
                                        (GS2 = simscore) */
         coverage;                   /* coverage of the genomic DNA or cDNA
                                        segment, whichever is highest
                                        (GS2 = cvrge) */
  bool genomic_cov_is_highest;       /* (GS2 = no equivalent) */
  unsigned long cumlen_scored_exons, /* cumulative length of scored exons
                                        (GS2 = mlgth) */
                call_number;         /* the consecutive number of successful DP
                                        calls. not really usefull, only for
                                        compatibility with GS2 */
  GtStr *gff3_target_attribute;
};

GthSA* gth_sa_new(void)
{
  GthSA *sa;

  /* allocating space */
  sa = gt_calloc(1, sizeof *sa);

  /* initialize strings */
  sa->gen_id = gt_str_new();
  sa->ref_id = gt_str_new();

  /* initialize all arrays */
  sa->backtrace_path = gth_backtrace_path_new(GT_UNDEF_ULONG,
                                              GT_UNDEF_ULONG,
                                              0, /* ref_dp_start */
                                              GT_UNDEF_ULONG);
  sa->exons = gt_array_new(sizeof (Exoninfo));
  sa->introns = gt_array_new(sizeof (Introninfo));

  return sa;
}

GthSA* gth_sa_new_and_set(bool gen_strand_forward,
                          bool ref_strand_forward,
                          GthInput *input,
                          unsigned long gen_file_num,
                          unsigned long gen_seq_num,
                          unsigned long ref_file_num,
                          unsigned long ref_seq_num,
                          unsigned long call_number,
                          unsigned long gen_total_length,
                          unsigned long gen_offset,
                          unsigned long ref_total_length)
{
  GthSA *sa;

  /* alloc and init of arrays */
  sa = gth_sa_new();

  /* setting the strand directions */
  sa->gen_strand_forward = gen_strand_forward;
  sa->ref_strand_forward = ref_strand_forward;

  /* saving sequence ids */
  gth_input_save_gen_id(input, sa->gen_id, gen_file_num, gen_seq_num);
  gth_input_save_ref_id(input, sa->ref_id, ref_file_num, ref_seq_num);

  /* saving MD5s, if necessary */
  gth_input_save_gen_md5(input, &sa->gen_md5, gen_file_num, gen_seq_num);
  gth_input_save_ref_md5(input, &sa->ref_md5, ref_file_num, ref_seq_num);

  /* saving descriptions, if necessary */
  gth_input_save_gen_desc(input, &sa->gen_desc, gen_file_num, gen_seq_num);
  gth_input_save_ref_desc(input, &sa->ref_desc, ref_file_num, ref_seq_num);

  /* save the consecutive call number */
  sa->call_number = call_number;

  /* save total length of genomic sequence */
  sa->gen_total_length = gen_total_length;

  /* save genomic offset */
  sa->gen_offset = gen_offset;

  /* save total length of reference sequence */
  sa->ref_total_length = ref_total_length;
  gth_backtrace_path_set_ref_dp_length(sa->backtrace_path, ref_total_length);

  /* save file and sequence numbers */
  sa->gen_file_num = gen_file_num;
  sa->gen_seq_num = gen_seq_num;
  sa->ref_file_num = ref_file_num;
  sa->ref_seq_num = ref_seq_num;

  return sa;
}

void gth_sa_set(GthSA *sa, GthAlphatype ref_alphatype,
                unsigned long gen_dp_start, unsigned long gen_dp_length)
{
  gth_backtrace_path_set_gen_dp_start(sa->backtrace_path, gen_dp_start);
  gth_backtrace_path_set_gen_dp_length(sa->backtrace_path, gen_dp_length);
  gth_sa_set_score(sa, 0.0);
  gth_sa_set_coverage(sa, 0.0);
  gth_sa_set_highest_cov(sa, true);
  gth_sa_set_cumlen_scored_exons(sa, 0);
  /* reset edit operations */
  gth_backtrace_path_reset(sa->backtrace_path);
  gth_backtrace_path_set_alphatype(sa->backtrace_path, ref_alphatype);
  /* reset arrays */
  gt_array_reset(sa->exons);
  gt_array_reset(sa->introns);
}

void gth_sa_set_gen_dp_length(GthSA *sa, unsigned long gen_dp_length)
{
  gt_assert(sa);
  gth_backtrace_path_set_gen_dp_length(sa->backtrace_path, gen_dp_length);
}

void gth_sa_delete(GthSA *sa)
{
  if (!sa) return;
  gth_backtrace_path_delete(sa->backtrace_path);
  gt_array_delete(sa->exons);
  gt_array_delete(sa->introns);
  gt_str_delete(sa->gen_id);
  gt_str_delete(sa->ref_id);
  gt_str_delete(sa->gen_md5);
  gt_str_delete(sa->ref_md5);
  gt_str_delete(sa->gen_desc);
  gt_str_delete(sa->ref_desc);
  gt_str_delete(sa->gff3_target_attribute);
  gt_free(sa);
}

void gth_sa_show_exons(const GthSA *sa, GtFile *outfp)
{
  Exoninfo *exoninfo;
  unsigned long i;
  gt_assert(sa);
  for (i = 0; i < gt_array_size(sa->exons); i++) {
    exoninfo = (Exoninfo*) gt_array_get(sa->exons, i);
    gt_file_xprintf(outfp, "(%lu,%lu)", exoninfo->leftgenomicexonborder,
                    exoninfo->rightgenomicexonborder);
  }
  gt_file_xfputc('\n', outfp);
}

void gth_sa_get_exons(const GthSA *sa, GtArray *ranges)
{
  Exoninfo *exoninfo;
  unsigned long i;
  GtRange range;
  gt_assert(sa && ranges);
  for (i = 0; i < gt_array_size(sa->exons); i++) {
    exoninfo = gt_array_get(sa->exons, i);
    range.start = exoninfo->leftgenomicexonborder;
    range.end = exoninfo->rightgenomicexonborder;
    gt_array_add(ranges, range);
  }
}

#ifndef NDEBUG
bool gth_sa_exons_are_forward_and_consecutive(const GthSA *sa)
{
  GtArray *ranges;
  gt_assert(sa);
  ranges = gt_array_new(sizeof (GtRange));
  gth_sa_get_exons(sa, ranges);
  if (!gt_ranges_are_consecutive(ranges)) {
    gt_array_delete(ranges);
    return false;
  }
  gt_array_delete(ranges);
  return true;
}
#endif

GtRange gth_sa_range_forward(const GthSA *sa)
{
  GtRange range;
  unsigned long leftgenomicborder, rightgenomicborder;

  gt_assert(sa);

  leftgenomicborder  = ((Exoninfo*) gt_array_get_first(sa->exons))
                       ->leftgenomicexonborder;
  rightgenomicborder = ((Exoninfo*) gt_array_get_last(sa->exons))
                       ->rightgenomicexonborder;

  if (sa->gen_strand_forward) {
    range.start = leftgenomicborder;
    range.end = rightgenomicborder;
  }
  else {
    /* genomic offset is defined */
    gt_assert(sa->gen_offset != GT_UNDEF_ULONG);
    range.start  = sa->gen_total_length - 1
                   - (rightgenomicborder - sa->gen_offset)
                   + sa->gen_offset;
    range.end = sa->gen_total_length - 1
                - (leftgenomicborder - sa->gen_offset)
                + sa->gen_offset;
  }

  return range;
}

GtRange gth_sa_range_actual(const GthSA *sa)
{
  GtRange range;

  gt_assert(sa);

  range.start = ((Exoninfo*) gt_array_get_first(sa->exons))
                ->leftgenomicexonborder;
  range.end = ((Exoninfo*) gt_array_get_last(sa->exons))
              ->rightgenomicexonborder;

  return range;
}

GthFlt gth_sa_average_splice_site_prob(const GthSA *sa)
{
  unsigned long i, numofintrons;
  GthFlt averagepdpa = 0.0;
  Introninfo *introninfo;
  gt_assert(sa);
  numofintrons = gt_array_size(sa->introns);
  if (numofintrons > 0) {
    for (i = 0; i < numofintrons; i++) {
      introninfo = gt_array_get(sa->introns, i);
      averagepdpa += introninfo->donorsiteprobability;
      averagepdpa += introninfo->acceptorsiteprobability;
    }
    averagepdpa /= (2 * numofintrons);
  }
  return averagepdpa;
}

bool gth_sa_is_poor(const GthSA *sa, GthFlt minaveragessp)
{
  unsigned long num_of_introns;
  GthFlt averagepdpa;

  gt_assert(sa);

  num_of_introns = gt_array_size(sa->introns);
  averagepdpa = gth_sa_average_splice_site_prob(sa);

  if (num_of_introns == 0 &&
      sa->polyAtailpos.start > sa->polyAtailpos.end)
    return true;
  if (num_of_introns == 1 &&
      averagepdpa < (GthFlt) (1.5 * minaveragessp)) {
    return true;
  }
  if (num_of_introns > 1 && averagepdpa < minaveragessp)
    return true;

  return false;
}

bool gth_sa_B_is_better_than_A(const GthSA *saA, const GthSA *saB)
{
  GthFlt firstaveragepdpa, secondaveragepdpa;

  gt_assert(saA && saB);

  firstaveragepdpa  = gth_sa_average_splice_site_prob(saA);
  secondaveragepdpa = gth_sa_average_splice_site_prob(saB);

  if (gt_array_size(saA->introns) == 0 ||
      (gt_array_size(saB->introns) > 0 &&
       secondaveragepdpa > firstaveragepdpa)) {
    return true;
  }
  else
    return false;
}

unsigned long gth_sa_left_genomic_exon_border(const GthSA *sa,
                                              unsigned long exon)
{
  Exoninfo *exoninfo;
  gt_assert(sa);
  exoninfo = gth_sa_get_exon(sa, exon);
  return SHOWGENPOS(sa->gen_strand_forward,
                    sa->gen_total_length,
                    sa->gen_offset, exoninfo->leftgenomicexonborder);
}

unsigned long gth_sa_right_genomic_exon_border(const GthSA *sa,
                                               unsigned long exon)
{
  Exoninfo *exoninfo;
  gt_assert(sa);
  exoninfo = gth_sa_get_exon(sa, exon);
  return SHOWGENPOS(sa->gen_strand_forward,
                    sa->gen_total_length,
                    sa->gen_offset, exoninfo->rightgenomicexonborder);
}

double gth_sa_exon_score(const GthSA *sa, unsigned long exon)
{
  Exoninfo *exoninfo;
  gt_assert(sa);
  exoninfo = gth_sa_get_exon(sa, exon);
  return exoninfo->exonscore;
}

GtRange gth_sa_donor_site_range(const GthSA *sa, unsigned long intron)
{
  GtRange range;
  gt_assert(sa);
  range.start = gth_sa_left_intron_border(sa, intron);
  range.end = range.start + 1;
  return range;
}

GtRange gth_sa_acceptor_site_range(const GthSA *sa, unsigned long intron)
{
  GtRange range;
  gt_assert(sa);
  range.end = gth_sa_right_intron_border(sa, intron);
  range.start = range.end - 1;
  return range;
}

float gth_sa_donor_site_prob(const GthSA *sa, unsigned long intron)
{
  float prob;
  gt_assert(sa);
  prob = ((Introninfo*) gt_array_get(sa->introns, intron))
         ->donorsiteprobability;
  if (0.0005 > prob) /* return only three positions after decimal point */
    return 0.0;
  return prob;
}

float gth_sa_acceptor_site_prob(const GthSA *sa, unsigned long intron)
{
  float prob;
  gt_assert(sa);
  prob = ((Introninfo*) gt_array_get(sa->introns, intron))
         ->acceptorsiteprobability;
  if (0.0005 > prob) /* return only three positions after decimal point */
    return 0.0;
  return prob;
}

unsigned long gth_sa_genomic_exon_length(const GthSA *sa, unsigned long exon)
{
  Exoninfo *exoninfo;
  gt_assert(sa);
  exoninfo = gth_sa_get_exon(sa, exon);
  return exoninfo->rightgenomicexonborder - exoninfo->leftgenomicexonborder + 1;
}

unsigned long gth_sa_left_intron_border(const GthSA *sa, unsigned long intron)
{
  Exoninfo *exoninfo;
  gt_assert(sa);
  exoninfo = gth_sa_get_exon(sa, intron);
  return SHOWGENPOS(sa->gen_strand_forward,
                    sa->gen_total_length,
                    sa->gen_offset,
                    exoninfo->rightgenomicexonborder + 1);
}

unsigned long gth_sa_right_intron_border(const GthSA *sa, unsigned long intron)
{
  Exoninfo *exoninfo;
  gt_assert(sa);
  exoninfo = gth_sa_get_exon(sa, intron + 1);
  return SHOWGENPOS(sa->gen_strand_forward,
                    sa->gen_total_length,
                    sa->gen_offset,
                    exoninfo->leftgenomicexonborder - 1);
}

unsigned long gth_sa_intron_length(const GthSA *sa, unsigned long intron)
{
  Exoninfo *left_exon, *right_exon;
  gt_assert(sa);
  left_exon  = gth_sa_get_exon(sa, intron);
  right_exon = gth_sa_get_exon(sa, intron + 1);
  return right_exon->leftgenomicexonborder - left_exon->rightgenomicexonborder
         - 1;
}

GthBacktracePath* gth_sa_backtrace_path(const GthSA *sa)
{
  gt_assert(sa);
  return sa->backtrace_path;
}

Editoperation* gth_sa_get_editoperations(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_get(sa->backtrace_path);
}

unsigned long gth_sa_get_editoperations_length(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_length(sa->backtrace_path);
}

unsigned long gth_sa_indelcount(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_indelcount(sa->backtrace_path);
}

unsigned long gth_sa_gen_dp_length(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_gen_dp_length(sa->backtrace_path);
}

unsigned long gth_sa_gen_total_length(const GthSA *sa)
{
  gt_assert(sa);
  return sa->gen_total_length;
}

void gth_sa_set_gen_total_length(GthSA *sa, unsigned long gen_total_length)
{
  gt_assert(sa);
  sa->gen_total_length = gen_total_length;
}

unsigned long gth_sa_gen_offset(const GthSA *sa)
{
  gt_assert(sa);
  return sa->gen_offset;
}

void gth_sa_set_gen_offset(GthSA *sa, unsigned long gen_offset)
{
  gt_assert(sa);
  sa->gen_offset = gen_offset;
}

unsigned long gth_sa_ref_total_length(const GthSA *sa)
{
  gt_assert(sa);
  return sa->ref_total_length;
}

void gth_sa_set_ref_total_length(GthSA *sa, unsigned long reflen)
{
  gt_assert(sa);
  sa->ref_total_length = reflen;
  /* XXX: ??? */
  gth_backtrace_path_set_ref_dp_length(sa->backtrace_path, reflen);
}

unsigned long gth_sa_gen_dp_start(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_gen_dp_start(sa->backtrace_path);
}

unsigned long gth_sa_gen_dp_start_show(const GthSA *sa)
{
  gt_assert(sa);
  return SHOWGENPOS(sa->gen_strand_forward,
                    sa->gen_total_length,
                    sa->gen_offset,
                    gth_backtrace_path_gen_dp_start(sa->backtrace_path));
}

void gth_sa_set_gen_dp_start(GthSA *sa, unsigned long gen_dp_start)
{
  gt_assert(sa);
  gth_backtrace_path_set_gen_dp_start(sa->backtrace_path, gen_dp_start);
}

unsigned long gth_sa_gen_dp_end(const GthSA *sa)
{
  gt_assert(sa);
  return gth_sa_gen_dp_start(sa) + gth_sa_gen_dp_length(sa) - 1;
}

unsigned long gth_sa_gen_dp_end_show(const GthSA *sa)
{
  gt_assert(sa);
  return SHOWGENPOS(sa->gen_strand_forward,
                    sa->gen_total_length,
                    sa->gen_offset,
                    gth_sa_gen_dp_start(sa) + gth_sa_gen_dp_length(sa) - 1);
}

unsigned long gth_sa_gen_file_num(const GthSA *sa)
{
  gt_assert(sa);
  return sa->gen_file_num;
}

void gth_sa_set_gen_file_num(GthSA *sa, unsigned long filenum)
{
  gt_assert(sa);
  sa->gen_file_num = filenum;
}

unsigned long gth_sa_gen_seq_num(const GthSA *sa)
{
  gt_assert(sa);
  return sa->gen_seq_num;
}

void gth_sa_set_gen_seq_num(GthSA *sa, unsigned long seqnum)
{
  gt_assert(sa);
  sa->gen_seq_num = seqnum;
}

unsigned long gth_sa_ref_file_num(const GthSA *sa)
{
  gt_assert(sa);
  return sa->ref_file_num;
}

void gth_sa_set_ref_file_num(GthSA *sa, unsigned long filenum)
{
  gt_assert(sa);
  sa->ref_file_num = filenum;
}

unsigned long gth_sa_ref_seq_num(const GthSA *sa)
{
  gt_assert(sa);
  return sa->ref_seq_num;
}

void gth_sa_set_ref_seq_num(GthSA *sa, unsigned long seqnum)
{
  gt_assert(sa);
  sa->ref_seq_num = seqnum;
}

const char* gth_sa_gen_id(const GthSA *sa)
{
  gt_assert(sa);
  return gt_str_get(sa->gen_id);
}

GtStr* gth_sa_gen_id_str(const GthSA *sa)
{
  gt_assert(sa);
  return sa->gen_id;
}

void gth_sa_set_gen_id(GthSA *sa, const char *id)
{
  gt_assert(sa);
  gt_str_set(sa->gen_id, id);
}

const char* gth_sa_ref_id(const GthSA *sa)
{
  gt_assert(sa);
  return gt_str_get(sa->ref_id);
}

GtStr* gth_sa_ref_id_str(const GthSA *sa)
{
  gt_assert(sa);
  return sa->ref_id;
}

void gth_sa_set_ref_id(GthSA *sa, const char *id)
{
  gt_assert(sa);
  gt_str_set(sa->ref_id, id);
}

GtStr* gth_sa_gen_md5(const GthSA *sa)
{
  gt_assert(sa && sa->gen_md5);
  return sa->gen_md5;
}

GtStr* gth_sa_ref_md5(const GthSA *sa)
{
  gt_assert(sa && sa->ref_md5);
  return sa->ref_md5;
}

GtStr* gth_sa_gen_desc(const GthSA *sa)
{
  gt_assert(sa && sa->gen_desc);
  return sa->gen_desc;
}

GtStr* gth_sa_ref_desc(const GthSA *sa)
{
  gt_assert(sa && sa->ref_desc);
  return sa->ref_desc;
}

GtStrand gth_sa_gen_strand(const GthSA *sa)
{
  gt_assert(sa);
  return sa->gen_strand_forward ? GT_STRAND_FORWARD : GT_STRAND_REVERSE;
}

bool gth_sa_gen_strand_forward(const GthSA *sa)
{
  gt_assert(sa);
  return sa->gen_strand_forward;
}

char gth_sa_gen_strand_char(const GthSA *sa)
{
  gt_assert(sa);
  return SHOWSTRAND(sa->gen_strand_forward);
}

void gth_sa_set_gen_strand(GthSA *sa, bool forward)
{
  gt_assert(sa);
  sa->gen_strand_forward = forward;
}

bool gth_sa_ref_strand_forward(const GthSA *sa)
{
  gt_assert(sa);
  return sa->ref_strand_forward;
}

char gth_sa_ref_strand_char(const GthSA *sa)
{
  gt_assert(sa);
  return SHOWSTRAND(sa->ref_strand_forward);
}

void gth_sa_set_ref_strand(GthSA *sa, bool forward)
{
  gt_assert(sa);
  sa->ref_strand_forward = forward;
}

unsigned long gth_sa_genomiccutoff_start(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_genomiccutoff_start(sa->backtrace_path);
}

unsigned long gth_sa_referencecutoff_start(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_referencecutoff_start(sa->backtrace_path);
}

unsigned long gth_sa_eopcutoff_start(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_eopcutoff_start(sa->backtrace_path);
}

unsigned long gth_sa_genomiccutoff_end(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_genomiccutoff_end(sa->backtrace_path);
}

unsigned long gth_sa_referencecutoff_end(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_referencecutoff_end(sa->backtrace_path);
}

unsigned long gth_sa_eopcutoff_end(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_eopcutoff_end(sa->backtrace_path);
}

void gth_sa_set_cutoffs_start(GthSA *sa, Cutoffs *cutoffs)
{
 gt_assert(sa && cutoffs);
 gth_backtrace_path_set_cutoffs_start(sa->backtrace_path, cutoffs);
}

void gth_sa_set_cutoffs_end(GthSA *sa, Cutoffs *cutoffs)
{
 gt_assert(sa && cutoffs);
 gth_backtrace_path_set_cutoffs_end(sa->backtrace_path, cutoffs);
}

GthAlphatype gth_sa_alphatype(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_alphatype(sa->backtrace_path);
}

const char* gth_sa_alphastring(const GthSA *sa)
{
  gt_assert(sa);
  return gth_sa_alphatype(sa) == DNA_ALPHA ? "cDNA" : "Protein";
}

void gth_sa_set_alphatype(GthSA *sa, GthAlphatype alphatype)
{
  gt_assert(sa);
  gth_backtrace_path_set_alphatype(sa->backtrace_path, alphatype);
}

Exoninfo* gth_sa_get_exon(const GthSA *sa, unsigned long exon)
{
  gt_assert(sa && sa->exons);
  gt_assert(exon < gt_array_size(sa->exons));
  return gt_array_get(sa->exons, exon);
}

void gth_sa_add_exon(GthSA *sa, Exoninfo *exoninfo)
{
  gt_assert(sa && exoninfo);
  gt_array_add(sa->exons, *exoninfo);
}

unsigned long gth_sa_num_of_exons(const GthSA *sa)
{
  gt_assert(sa && sa->exons);
  return gt_array_size(sa->exons);
}

Introninfo* gth_sa_get_intron(const GthSA *sa, unsigned long intron)
{
  gt_assert(sa && sa->introns);
  gt_assert(intron < gt_array_size(sa->exons));
  return gt_array_get(sa->introns, intron);
}

void gth_sa_add_intron(GthSA *sa, Introninfo *introninfo)
{
  gt_assert(sa && introninfo);
  gt_array_add(sa->introns, *introninfo);
}

unsigned long gth_sa_num_of_introns(const GthSA *sa)
{
  gt_assert(sa && sa->introns);
  return gt_array_size(sa->introns);
}

void gth_sa_calc_polyAtailpos(GthSA *sa, const unsigned char *ref_seq_tran,
                              GtAlphabet *ref_alphabet)
{
  unsigned long ppa, mma, rightreferenceborder, referencelength;
  long i, leftreferenceborder;

  sa->polyAtailpos.start = 0;
  sa->polyAtailpos.end = 0;
  ppa = mma = 0;

  rightreferenceborder = ((Exoninfo*) gt_array_get_last(sa->exons))
                         ->rightreferenceexonborder;
  leftreferenceborder  = ((Exoninfo*) gt_array_get_first(sa->exons))
                         ->leftreferenceexonborder;

  /* setting i */
  referencelength = gth_sa_ref_total_length(sa);
  if ((rightreferenceborder + 1) >=
      (referencelength - 1 - CALCPOLYATAILWINDOW)) {
    i = gt_safe_cast2long(rightreferenceborder + 1);
  }
  else {
    if (referencelength < 1 + CALCPOLYATAILWINDOW)
      i = 0;
    else
      i =  referencelength - 1 - CALCPOLYATAILWINDOW;
  }

  for (/* i already set */; i < gt_safe_cast2long(referencelength); i++) {
    if (ref_seq_tran[i] == gt_alphabet_encode(ref_alphabet, 'A'))
      ppa++;
    else {
      if (ppa > 0 && mma < 1) {
        mma++;
        continue;
      }
      else {
        if (ppa >= MINIMUMPOLYATAILLENGTH)
          break;
        else {
          ppa = mma = 0;
          continue;
        }
      }
    }
  }

  if (ppa >= MINIMUMPOLYATAILLENGTH) {
    sa->polyAtailpos.start = gt_safe_cast2ulong(i - ppa - mma);
    sa->polyAtailpos.end = i - 1;
  }
  else {
    ppa = mma = 0;

    /* setting i */
    if ((leftreferenceborder - 1) <= CALCPOLYATAILWINDOW)
      i = leftreferenceborder - 1;
    else
      i =  CALCPOLYATAILWINDOW - 1;

    for (/* i already set */; i >= 0; i--) {
      if (ref_seq_tran[i] == gt_alphabet_encode(ref_alphabet, 'T'))
        ppa++;
      else {
        if (ppa > 0 && mma < 1) {
          mma++;
          continue;
        }
        else {
          if (ppa >= MINIMUMPOLYATAILLENGTH)
            break;
          else {
            ppa = mma = 0;
            continue;
          }
        }
      }
    }

    if (ppa >= MINIMUMPOLYATAILLENGTH) {
      sa->polyAtailpos.start  = gt_safe_cast2ulong(i + ppa + mma);
      sa->polyAtailpos.end = i + 1;
    }
  }
}

unsigned long gth_sa_polyAtail_start(const GthSA *sa)
{
  gt_assert(sa);
  return sa->polyAtailpos.start;
}

unsigned long gth_sa_polyAtail_stop(const GthSA *sa)
{
  gt_assert(sa);
  return sa->polyAtailpos.end;
}

void gth_sa_set_polyAtail_start(GthSA *sa, unsigned long start)
{
  gt_assert(sa);
  sa->polyAtailpos.start = start;
}

void gth_sa_set_polyAtail_stop(GthSA *sa, unsigned long stop)
{
  gt_assert(sa);
  sa->polyAtailpos.end = stop;
}

GthFlt gth_sa_score(const GthSA *sa)
{
  gt_assert(sa);
  return sa->alignmentscore;
}

void gth_sa_set_score(GthSA *sa, GthFlt score)
{
  gt_assert(sa);
  sa->alignmentscore = score;
}

GthFlt gth_sa_coverage(const GthSA *sa)
{
  gt_assert(sa);
  return sa->coverage;
}

void gth_sa_set_coverage(GthSA *sa, GthFlt coverage)
{
  gt_assert(sa);
  sa->coverage = coverage;
}

bool gth_sa_genomic_cov_is_highest(const GthSA *sa)
{
  gt_assert(sa);
  return sa->genomic_cov_is_highest;
}

char gth_sa_coverage_char(const GthSA *sa)
{
  gt_assert(sa);
  if (gth_sa_genomic_cov_is_highest(sa))
    return 'G';
  else {
    if (gth_sa_alphatype(sa) == DNA_ALPHA)
      return 'C';
    else
      return 'P';
  }
}

void gth_sa_set_highest_cov(GthSA *sa, bool genomic)
{
  gt_assert(sa);
  sa->genomic_cov_is_highest = genomic;
}

unsigned long gth_sa_cumlen_scored_exons(const GthSA *sa)
{
  gt_assert(sa);
  return sa->cumlen_scored_exons;
}

void gth_sa_set_cumlen_scored_exons(GthSA *sa, unsigned long cumlen)
{
  gt_assert(sa);
  sa->cumlen_scored_exons = cumlen;
}

unsigned long gth_sa_call_number(const GthSA *sa)
{
  gt_assert(sa);
  return sa->call_number;
}

static void set_gff3_target_attribute(GthSA *sa, bool md5ids)
{
  gt_assert(sa && !sa->gff3_target_attribute);
  sa->gff3_target_attribute = gt_str_new();
  if (md5ids) {
    gt_assert(sa->ref_md5);
    gt_str_append_cstr(sa->gff3_target_attribute, GT_MD5_SEQID_PREFIX);
    gt_str_append_str(sa->gff3_target_attribute, sa->ref_md5);
    gt_str_append_char(sa->gff3_target_attribute, ':');
  }
  gt_gff3_escape(sa->gff3_target_attribute, gt_str_get(sa->ref_id),
                 gt_str_length(sa->ref_id));
  gt_str_append_char(sa->gff3_target_attribute, ' ');
  gt_str_append_ulong(sa->gff3_target_attribute,
                      gth_sa_referencecutoff_start(sa) + 1); /* XXX: use
                                                                reference
                                                                dpstartpos */
  gt_str_append_char(sa->gff3_target_attribute, ' ');
  gt_str_append_ulong(sa->gff3_target_attribute,
                      gth_sa_ref_total_length(sa) - /* XXX */
                      gth_sa_referencecutoff_end(sa));
  gt_str_append_char(sa->gff3_target_attribute, ' ');
  if (sa->ref_strand_forward) {
    gt_str_append_char(sa->gff3_target_attribute,
                       GT_STRAND_CHARS[GT_STRAND_FORWARD]);
  }
  else {
    gt_str_append_char(sa->gff3_target_attribute,
                       GT_STRAND_CHARS[GT_STRAND_REVERSE]);
  }
}

const char* gth_sa_gff3_target_attribute(GthSA *sa, bool md5ids)
{
  gt_assert(sa);
  if (!sa->gff3_target_attribute && (md5ids || gt_str_length(sa->ref_id)))
    set_gff3_target_attribute(sa, md5ids);
  return gt_str_get(sa->gff3_target_attribute);
}

void gth_sa_determine_cutoffs(GthSA *sa, GthCutoffmode leadcutoffsmode,
                              GthCutoffmode termcutoffsmode,
                              unsigned long cutoffsminexonlen)
{
  gt_assert(sa);
  gth_backtrace_path_determine_cutoffs(sa->backtrace_path, leadcutoffsmode,
                                       termcutoffsmode, cutoffsminexonlen);
}

void gth_sa_cutoff_start(GthSA *sa)
{
  gt_assert(sa);
  gth_backtrace_path_cutoff_start(sa->backtrace_path);
}

void gth_sa_cutoff_end(GthSA *sa)
{
  gt_assert(sa);
  gth_backtrace_path_cutoff_end(sa->backtrace_path);
}

void gth_sa_cutoff_walked_path(GthSA *sa, const GthPathWalker *pw,
                               bool showeops, GtFile *outfp)
{
  gt_assert(sa && pw);
  gth_backtrace_path_cutoff_walked_path(sa->backtrace_path, pw, showeops,
                                        outfp);
}

void gth_sa_prepend(GthSA *sa, const GthBacktracePath *eops)
{
  gt_assert(sa && eops);
  gth_backtrace_path_prepend(sa->backtrace_path, eops);
}

void gth_sa_append(GthSA *sa, const GthBacktracePath *eops)
{
  gt_assert(sa && eops);
  gth_backtrace_path_append(sa->backtrace_path, eops);
}

void gth_sa_remove_zero_base_exons(GthSA *sa, GthStat *stat)
{
  gt_assert(sa);
  gth_backtrace_path_remove_zero_base_exons(sa->backtrace_path, stat);
}

bool gth_sa_contains_no_zero_base_exons(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_contains_no_zero_base_exons(sa->backtrace_path);
}

void gth_sa_echo_genomic_description(const GthSA *sa, GthInput *input,
                                     GtFile *outfp)
{
  gt_assert(sa && input);
  gth_input_echo_genomic_description(input, sa->gen_file_num,
                                     sa->gen_seq_num, outfp);
}

void gth_sa_echo_reference_description(const GthSA *sa, GthInput *input,
                                       GtFile *outfp)
{
  gt_assert(sa && input);
  gth_input_echo_reference_description(input, sa->ref_file_num,
                                       sa->ref_seq_num, outfp);
}

void gth_sa_echo_reference_sequence(const GthSA *sa, GthInput *input,
                                    bool format, GtFile *outfp)
{
  gt_assert(sa && input);
  gth_input_echo_reference_sequence(input, format, sa->ref_file_num,
                                    sa->ref_seq_num, sa->ref_strand_forward,
                                    outfp);
}

void gth_sa_echo_alignment(const GthSA *sa, unsigned long showintronmaxlen,
                           unsigned long translationtable,
                           bool wildcardimplosion, GthInput *input,
                           GtFile *outfp)
{
  unsigned long genomicstartcutoff, genomicendcutoff, genomictotalcutoff,
                referencestartcutoff, referenceendcutoff, referencetotalcutoff;
  bool reverse_subject_pos = false;
  const unsigned char *gen_seq_orig, *ref_seq_orig;
  GthSeqCon *ref_seq_con;
  GtAlphabet *ref_alphabet;

  gt_assert(sa && input);

  /* only for cosmetic reasons */
  genomicstartcutoff   = gth_sa_genomiccutoff_start(sa);
  genomicendcutoff     = gth_sa_genomiccutoff_end(sa);
  genomictotalcutoff   = genomicstartcutoff + genomicendcutoff;
  referencestartcutoff = gth_sa_referencecutoff_start(sa);
  referenceendcutoff   = gth_sa_referencecutoff_end(sa);
  referencetotalcutoff = referencestartcutoff + referenceendcutoff;

  /* make sure that the correct files are loaded */
  gth_input_load_reference_file(input, gth_sa_ref_file_num(sa), false);
  ref_seq_con = gth_input_current_ref_seq_con(input);
  ref_alphabet = gth_input_current_ref_alphabet(input);

  /* If the reverse complement of the genomic DNA is considered, this
     opition is needed for correct output of the genomic sequence positions
     by the function showalignmentgeneric() */
  if (!gth_sa_gen_strand_forward(sa))
    reverse_subject_pos = true;

  /* get genomic sequence */
  gen_seq_orig =
    gth_input_original_genomic_sequence(input, sa->gen_file_num,
                                        sa->gen_strand_forward)
    + gth_sa_gen_dp_start(sa);

  /* get reference sequence */
  if (gth_sa_ref_strand_forward(sa)) {
    ref_seq_orig =
      gth_seq_con_get_orig_seq(ref_seq_con, gth_sa_ref_seq_num(sa));
  }
  else {
    ref_seq_orig =
      gth_seq_con_get_orig_seq_rc(ref_seq_con, gth_sa_ref_seq_num(sa));
  }

  switch (gth_sa_alphatype(sa)) {
    case DNA_ALPHA:
      gthshowalignmentdna(outfp,ALIGNMENTLINEWIDTH,
                          gth_sa_get_editoperations(sa),
                          gth_sa_get_editoperations_length(sa),
                          gth_sa_indelcount(sa),
                          gen_seq_orig + genomicstartcutoff,
                          gth_sa_gen_dp_length(sa) - genomictotalcutoff,
                          ref_seq_orig + referencestartcutoff,
                          gth_sa_ref_total_length(sa) -
                          referencetotalcutoff,
                          gth_sa_gen_dp_start(sa) + genomicstartcutoff -
                          gth_sa_gen_offset(sa), referencestartcutoff,
                          gth_sa_gen_total_length(sa), showintronmaxlen,
                          ref_alphabet, reverse_subject_pos,
                          wildcardimplosion);
      break;
    case PROTEIN_ALPHA:
      gthshowalignmentprotein(outfp, ALIGNMENTLINEWIDTH,
                              gth_sa_get_editoperations(sa),
                              gth_sa_get_editoperations_length(sa),
                              gth_sa_indelcount(sa),
                              gen_seq_orig + genomicstartcutoff,
                              gth_sa_gen_dp_length(sa) - genomictotalcutoff,
                              ref_seq_orig + referencestartcutoff,
                              gth_sa_ref_total_length(sa) -
                              referencetotalcutoff,
                              gth_sa_gen_dp_start(sa) + genomicstartcutoff -
                              gth_sa_gen_offset(sa), referencestartcutoff,
                              gth_sa_gen_total_length(sa), showintronmaxlen,
                              ref_alphabet, translationtable,
                              gth_input_score_matrix(input),
                              gth_input_score_matrix_alpha(input),
                              reverse_subject_pos, wildcardimplosion);
      break;
    default: gt_assert(0);
  }
}

unsigned long gth_sa_get_alignment_lines(const GthSA *sa,
                                         unsigned char **first_line,
                                         unsigned char **second_line,
                                         unsigned char **third_line,
                                         unsigned long translationtable,
                                         GthInput *input)
{
  unsigned long genomicstartcutoff, genomicendcutoff, genomictotalcutoff,
                referencestartcutoff, referenceendcutoff, referencetotalcutoff;
  GT_UNUSED bool reverse_subject_pos = false;

  gt_assert(sa && first_line && second_line && third_line && input);

  /* only for cosmetic reasons */
  genomicstartcutoff   = gth_sa_genomiccutoff_start(sa);
  genomicendcutoff     = gth_sa_genomiccutoff_end(sa);
  genomictotalcutoff   = genomicstartcutoff + genomicendcutoff;
  referencestartcutoff = gth_sa_referencecutoff_start(sa);
  referenceendcutoff   = gth_sa_referencecutoff_end(sa);
  referencetotalcutoff = referencestartcutoff + referenceendcutoff;

  /* sequences */
  unsigned char *gen_seq_orig, *ref_seq_orig;
  unsigned long cols = 0;
  GthSeqCon *ref_seq_con;

  /* make sure that the correct files are loaded */
  gth_input_load_reference_file(input, gth_sa_ref_file_num(sa), false);
  ref_seq_con = gth_input_current_ref_seq_con(input);

  /* If the reverse complement of the genomic DNA is considered, this
     opition is needed for correct output of the genomic sequence positions
     by the function showalignmentgeneric() */
  if (!gth_sa_gen_strand_forward(sa))
    reverse_subject_pos = true;

  /* get genomic sequence */
  gen_seq_orig = (unsigned char*)
    gth_input_original_genomic_sequence(input, gth_sa_gen_file_num(sa),
                                        gth_sa_gen_strand_forward(sa))
    + gth_sa_gen_dp_start(sa);

  /* get reference sequence */
  if (gth_sa_ref_strand_forward(sa)) {
    ref_seq_orig =
      gth_seq_con_get_orig_seq(ref_seq_con, gth_sa_ref_seq_num(sa));
  }
  else {
    ref_seq_orig =
      gth_seq_con_get_orig_seq_rc(ref_seq_con, gth_sa_ref_seq_num(sa));
  }

  switch (gth_sa_alphatype(sa)) {
    case DNA_ALPHA:
      /* compute the two alignment lines */
      cols = gthfillthetwoalignmentlines(first_line,
                                         second_line,
                                         gen_seq_orig +
                                         genomicstartcutoff,
                                         gth_sa_gen_dp_length(sa) -
                                         genomictotalcutoff,
                                         ref_seq_orig +
                                         referencestartcutoff,
                                         gth_sa_ref_total_length(sa) -
                                         referencetotalcutoff,
                                         gth_sa_get_editoperations(sa),
                                         gth_sa_get_editoperations_length(sa),
                                         0,   /* linewidth not important here */
                                         0,   /* no short introns here */
                                         NULL,/* therefore no shortintroninfo */
                                         gth_sa_indelcount(sa));
      *third_line = NULL;
      break;
    case PROTEIN_ALPHA:
      /* compute the three alignment lines */
      cols = gthfillthethreealignmentlines(first_line,
                                           second_line,
                                           third_line,
                                           gth_sa_get_editoperations(sa),
                                           gth_sa_get_editoperations_length(sa),
                                           gth_sa_indelcount(sa),
                                           gen_seq_orig +
                                           genomicstartcutoff,
                                           gth_sa_gen_dp_length(sa) -
                                           genomictotalcutoff,
                                           ref_seq_orig +
                                           referencestartcutoff,
                                           gth_sa_ref_total_length(sa) -
                                           referencetotalcutoff,
                                           translationtable);
      break;
    default: gt_assert(0);
  }

  return cols;
}

bool gth_sa_is_valid(const GthSA *sa)
{
  gt_assert(sa);
  return gth_backtrace_path_is_valid(sa->backtrace_path);
}

void gth_sa_show(GthSA *sa, GthInput *input, GtFile *outfp)
{
  GthSAVisitor *sa_visitor;
  gt_assert(sa && input);
  gth_input_load_genomic_file(input, sa->gen_file_num, false);
  gth_input_load_reference_file(input, sa->ref_file_num, false);
  sa_visitor = gth_txt_sa_visitor_new(input,
                                      GTH_DEFAULT_GS2OUT,
                                      GTH_DEFAULT_DPMININTRONLENGTH,
                                      6, /* XXX */
                                      GTH_DEFAULT_SHOWINTRONMAXLEN,
                                      GTH_DEFAULT_TRANSLATIONTABLE,
                                      GTH_DEFAULT_SHOWSEQNUMS,
                                      outfp);
  gth_sa_visitor_visit_sa(sa_visitor, sa);
  gth_sa_visitor_delete(sa_visitor);
}

void gth_sa_save_ref_md5(GthSA *sa, GthInput *input)
{
  gt_assert(sa && input);
  gth_input_save_ref_md5(input, &sa->ref_md5, sa->ref_file_num,
                         sa->ref_seq_num);
}

bool gth_sas_are_equal(const GthSA *saA, const GthSA *saB)
{
  Exoninfo *exoninfoA, *exoninfoB;
  Introninfo *introninfoA, *introninfoB;
  unsigned long i;

  /* compare element 0 */
  if (gth_sa_alphatype(saA) != gth_sa_alphatype(saB))
    return false;

  /* compare element 1 */
  if (gth_backtrace_path_length(saA->backtrace_path) !=
      gth_backtrace_path_length(saB->backtrace_path)) {
    return false;
  }
  for (i = 0; i < gth_backtrace_path_length(saA->backtrace_path); i++) {
    if (((Editoperation*) gth_backtrace_path_get(saA->backtrace_path))[i] !=
        ((Editoperation*) gth_backtrace_path_get(saB->backtrace_path))[i]) {
      return false;
    }
  }

  /* element 2 has been removed (indelcount) */

  /* compare element 3 */
  if (gth_sa_gen_dp_length(saA) != gth_sa_gen_dp_length(saB))
    return false;

  /* compare element 4 */
  if (saA->gen_total_length != saB->gen_total_length)
    return false;

  /* compare element 5 */
  if (saA->gen_offset != saB->gen_offset)
    return false;

  /* compare element 6 */
  if (gth_sa_ref_total_length(saA) != gth_sa_ref_total_length(saB))
    return false;

  /* compare element 7 */
  if (gth_sa_gen_dp_start(saA) != gth_sa_gen_dp_start(saB))
    return false;

  /* element 8 has been removed (gen_dp_end) */

  /* compare element 9 */
  if (saA->gen_file_num != saB->gen_file_num)
    return false;

  /* compare element 10 */
  if (saA->gen_seq_num != saB->gen_seq_num)
    return false;

  /* compare element 11 */
  if (saA->ref_file_num != saB->ref_file_num)
    return false;

  /* compare element 12 */
  if (saA->ref_seq_num != saB->ref_seq_num)
    return false;

  /* compare element 13 */
  if (gt_str_cmp(saA->gen_id, saB->gen_id))
    return false;

  /* compare element 14 */
  if (gt_str_cmp(saA->ref_id, saB->ref_id))
    return false;

  /* compare element 15 */
  if (saA->gen_strand_forward != saB->gen_strand_forward)
    return false;

  /* compare element 16 */
  if (saA->ref_strand_forward != saB->ref_strand_forward)
    return false;

  /* compare element 17 */
  if (gth_sa_genomiccutoff_start(saA) != gth_sa_genomiccutoff_start(saB))
    return false;
  if (gth_sa_referencecutoff_start(saA) != gth_sa_referencecutoff_start(saB))
    return false;
  if (gth_sa_eopcutoff_start(saA) != gth_sa_eopcutoff_start(saB))
    return false;
  if (gth_sa_genomiccutoff_end(saA) != gth_sa_genomiccutoff_end(saB))
    return false;
  if (gth_sa_referencecutoff_end(saA) != gth_sa_referencecutoff_end(saB))
    return false;
  if (gth_sa_eopcutoff_end(saA) != gth_sa_eopcutoff_end(saB))
    return false;

  /* compare element 18 */
  if (gt_array_size(saA->exons) != gt_array_size(saB->exons))
    return false;
  for (i = 0; i < gt_array_size(saA->exons); i++) {
    exoninfoA = (Exoninfo*) gt_array_get(saA->exons, i);
    exoninfoB = (Exoninfo*) gt_array_get(saB->exons, i);
    if (exoninfoA->leftgenomicexonborder != exoninfoB->leftgenomicexonborder)
      return false;
    if (exoninfoA->rightgenomicexonborder != exoninfoB->rightgenomicexonborder)
      return false;
    if (exoninfoA->leftreferenceexonborder !=
        exoninfoB->leftreferenceexonborder) {
      return false;
    }
    if (exoninfoA->rightreferenceexonborder !=
        exoninfoB->rightreferenceexonborder) {
      return false;
    }
    if (!gt_double_equals_double(exoninfoA->exonscore, exoninfoB->exonscore)) {
      return false;
    }
  }

  /* compare element 19 */
  if (gt_array_size(saA->introns) != gt_array_size(saB->introns))
    return false;
  for (i = 0; i < gt_array_size(saA->introns); i++) {
    introninfoA = (Introninfo*) gt_array_get(saA->introns, i);
    introninfoB = (Introninfo*) gt_array_get(saB->introns, i);
    if (!gt_double_equals_double(introninfoA->donorsiteprobability,
                                 introninfoB->donorsiteprobability)) {
      return false;
    }
    if (!gt_double_equals_double(introninfoA->acceptorsiteprobability,
                                 introninfoB->acceptorsiteprobability)) {
      return false;
    }
    if (!gt_double_equals_double(introninfoA->donorsitescore,
                                 introninfoB->donorsitescore)) {
      return false;
    }
    if (!gt_double_equals_double(introninfoA->acceptorsitescore,
                                 introninfoB->acceptorsitescore)) {
      return false;
    }
  }

  /* compare element 20 */
  if (saA->polyAtailpos.start != saB->polyAtailpos.start)
    return false;
  if (saA->polyAtailpos.end != saB->polyAtailpos.end)
    return false;

  /* compare element 21 */
  if (saA->alignmentscore != saB->alignmentscore)
    return false;

  /* compare element 22 */
  if (saA->coverage != saB->coverage)
    return false;

  /* compare element 23 */
  if (saA->genomic_cov_is_highest != saB->genomic_cov_is_highest)
    return false;

  /* compare element 24 */
  if (saA->cumlen_scored_exons != saB->cumlen_scored_exons)
    return false;

  return true;
}
genometools-1.5.1/src/gth/sa.h000066400000000000000000000324421211610345200161760ustar00rootroot00000000000000/*
  Copyright (c) 2003-2009 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SA_H
#define SA_H

#include "core/array.h"
#include "core/error.h"
#include "core/file.h"
#include "core/str.h"
#include "core/strand.h"
#include "gth/backtrace_path.h"
#include "gth/bssm_param.h"
#include "gth/gthalphatype.h"
#include "gth/input.h"
#include "gth/stat.h"

/*
  This splice site score is used for protein spliced alignments, because
  for them no splice site scores are computed.
*/

#define UNDEFINED_SPLICE_SITE_SCORE     -1.0

/*
  This struct represents an exon. Thereby, the DNA positions always refer
  to the actual strand.
  Terminology: A DNA position can refer to the forward strand and to the
  actual strand. In the case that the considered position lies on the forward
  strand these are the same. In the case that the considered position lies on
  the reverse complement strand the following relation holds:
  pos_referring_to_actual_strand == total_genomic_length - 1 -
                                    pos_referring_to_forward_strand
*/

typedef struct {
  unsigned long leftgenomicexonborder,    /* the borders of the exons in the */
                rightgenomicexonborder,   /*  genomic sequence               */
                leftreferenceexonborder,  /* the borders of the exons in the */
                rightreferenceexonborder; /* reference sequence              */
  GthDbl exonscore;                       /* = exnscr                        */
} Exoninfo;

typedef struct {
  GthFlt donorsiteprobability,     /* (GS = itrscr) */
         acceptorsiteprobability;  /* (GS = itrscr) */
  GthDbl donorsitescore,           /* (GS = no equivalent) */
         acceptorsitescore;        /* (GS = no equivalent) */
} Introninfo;

/* The following structure bundles all information necessary to represent a
   spliced alignment. Keep in sync with gth_sas_are_equal()! */
typedef struct GthSA GthSA;

/* create a new spliced alignment (sa) */
GthSA*         gth_sa_new(void);
/* create a new sa and set the sequence ids and strand directions */
GthSA*         gth_sa_new_and_set(bool gen_strand_forward,
                                  bool ref_strand_forward,
                                  GthInput *input,
                                  unsigned long gen_file_num,
                                  unsigned long gen_seq_num,
                                  unsigned long ref_file_num,
                                  unsigned long ref_seq_num,
                                  unsigned long call_number,
                                  unsigned long gen_total_length,
                                  unsigned long gen_offset,
                                  unsigned long ref_total_length);
void            gth_sa_set(GthSA*, GthAlphatype ref_alphatype,
                           unsigned long gen_dp_start,
                           unsigned long gen_dp_length);
void            gth_sa_set_gen_dp_length(GthSA*, unsigned long gen_dp_length);
void            gth_sa_delete(GthSA*);
void            gth_sa_show_exons(const GthSA*, GtFile*);
void            gth_sa_get_exons(const GthSA*, GtArray *ranges);
bool            gth_sa_exons_are_forward_and_consecutive(const GthSA*);

/* returns the genomic range of  referring to the forward strand. */
GtRange         gth_sa_range_forward(const GthSA *sa);

/* returns the genomic range of  referring to the actual strand */
GtRange         gth_sa_range_actual(const GthSA *sa);

/* Returns the average splice site probability of spliced alignment .
   That is, the average probability of all donor and acceptor sites. If the
   spliced alignment contains no introns the average splice site probability is
   zero. */
GthFlt gth_sa_average_splice_site_prob(const GthSA *sa);

/* A spliced alignment  is ``poor'' if one of the following statements
   holds:
   - The number of introns equals zero and the polyA tail of the cDNA/EST is
     at the start of the spliced alignment
   - The number of introns equals one and the average splice site probability
     is less than 1.5 times the minimum average splice site probability
     .
   - The number of introns is greater than one and the average splice site
     probability is less than the minimum average splice site probability
     , which can be changed by a command line option (see
     manual). */
bool            gth_sa_is_poor(const GthSA *sa, GthFlt minaveragessp);

/* Consider two spliced alignments  and .
   Spliced alignment  is ``better'' than spliced alignment  if at
   least one of the following statements holds:
   -  has no introns.
   -  has at least one intron and the average splice site probability of
      is greater than the average splice site probability of . */
bool            gth_sa_B_is_better_than_A(const GthSA *saA, const GthSA *saB);

/* Returns the left genomic exon border for  of 
   (referring to the foward strand). */
unsigned long   gth_sa_left_genomic_exon_border(const GthSA*,
                                                unsigned long exon);

/* Returns the right genomic exon border for  of 
   (referring to the foward strand). */
unsigned long   gth_sa_right_genomic_exon_border(const GthSA*,
                                                 unsigned long exon);

double          gth_sa_exon_score(const GthSA*, unsigned long exon);
GtRange         gth_sa_donor_site_range(const GthSA*, unsigned long intron);
GtRange         gth_sa_acceptor_site_range(const GthSA*, unsigned long intron);
/* Return donor site probablity with three positions after decimal point. */
float           gth_sa_donor_site_prob(const GthSA*, unsigned long intron);
/* Return acceptor site probablity with three positions after decimal point. */
float           gth_sa_acceptor_site_prob(const GthSA*,
                                                      unsigned long intron);
unsigned long   gth_sa_genomic_exon_length(const GthSA*, unsigned long exon);
unsigned long   gth_sa_left_intron_border(const GthSA*, unsigned long intron);
unsigned long   gth_sa_right_intron_border(const GthSA*, unsigned long intron);
unsigned long   gth_sa_intron_length(const GthSA *, unsigned long intron);

/* XXX */
GthBacktracePath* gth_sa_backtrace_path(const GthSA*);
Editoperation*  gth_sa_get_editoperations(const GthSA*);
unsigned long   gth_sa_get_editoperations_length(const GthSA*);

unsigned long   gth_sa_indelcount(const GthSA*);
unsigned long   gth_sa_gen_dp_length(const GthSA*);
unsigned long   gth_sa_gen_total_length(const GthSA*);
void            gth_sa_set_gen_total_length(GthSA*, unsigned long);
unsigned long   gth_sa_gen_offset(const GthSA*);
void            gth_sa_set_gen_offset(GthSA*, unsigned long);
unsigned long   gth_sa_ref_total_length(const GthSA*);
void            gth_sa_set_ref_total_length(GthSA*, unsigned long);
unsigned long   gth_sa_gen_dp_start(const GthSA*);
unsigned long   gth_sa_gen_dp_start_show(const GthSA*);
void            gth_sa_set_gen_dp_start(GthSA*, unsigned long);
unsigned long   gth_sa_gen_dp_end(const GthSA*);
unsigned long   gth_sa_gen_dp_end_show(const GthSA*);
unsigned long   gth_sa_gen_file_num(const GthSA*);
void            gth_sa_set_gen_file_num(GthSA*, unsigned long);
unsigned long   gth_sa_gen_seq_num(const GthSA*);
void            gth_sa_set_gen_seq_num(GthSA*, unsigned long);
unsigned long   gth_sa_ref_file_num(const GthSA*);
void            gth_sa_set_ref_file_num(GthSA*, unsigned long);
unsigned long   gth_sa_ref_seq_num(const GthSA*);
void            gth_sa_set_ref_seq_num(GthSA*, unsigned long);
const char*     gth_sa_gen_id(const GthSA*);
GtStr*          gth_sa_gen_id_str(const GthSA*);
void            gth_sa_set_gen_id(GthSA*, const char*);
const char*     gth_sa_ref_id(const GthSA*);
GtStr*          gth_sa_ref_id_str(const GthSA*);
void            gth_sa_set_ref_id(GthSA*, const char*);
GtStr*          gth_sa_gen_md5(const GthSA*);
GtStr*          gth_sa_ref_md5(const GthSA*);
GtStr*          gth_sa_gen_desc(const GthSA*);
GtStr*          gth_sa_ref_desc(const GthSA*);
GtStrand        gth_sa_gen_strand(const GthSA*);
bool            gth_sa_gen_strand_forward(const GthSA*);
char            gth_sa_gen_strand_char(const GthSA*);
void            gth_sa_set_gen_strand(GthSA*, bool forward);
bool            gth_sa_ref_strand_forward(const GthSA*);
char            gth_sa_ref_strand_char(const GthSA*);
void            gth_sa_set_ref_strand(GthSA*, bool forward);
unsigned long   gth_sa_genomiccutoff_start(const GthSA*);
unsigned long   gth_sa_referencecutoff_start(const GthSA*);
unsigned long   gth_sa_eopcutoff_start(const GthSA*);
unsigned long   gth_sa_genomiccutoff_end(const GthSA*);
unsigned long   gth_sa_referencecutoff_end(const GthSA*);
unsigned long   gth_sa_eopcutoff_end(const GthSA*);
void            gth_sa_set_cutoffs_start(GthSA*, Cutoffs*);
void            gth_sa_set_cutoffs_end(GthSA*, Cutoffs*);
GthAlphatype    gth_sa_alphatype(const GthSA*);
const char*     gth_sa_alphastring(const GthSA*);
void            gth_sa_set_alphatype(GthSA*, GthAlphatype);
Exoninfo*       gth_sa_get_exon(const GthSA*, unsigned long);
void            gth_sa_add_exon(GthSA*, Exoninfo*);
unsigned long   gth_sa_num_of_exons(const GthSA*);
Introninfo*     gth_sa_get_intron(const GthSA*, unsigned long);
void            gth_sa_add_intron(GthSA*, Introninfo*);
unsigned long   gth_sa_num_of_introns(const GthSA*);
void            gth_sa_calc_polyAtailpos(GthSA*,
                                         const unsigned char *ref_seq_tran,
                                         GtAlphabet *ref_alpha);
unsigned long   gth_sa_polyAtail_start(const GthSA*);
unsigned long   gth_sa_polyAtail_stop(const GthSA*);
void            gth_sa_set_polyAtail_start(GthSA*, unsigned long);
void            gth_sa_set_polyAtail_stop(GthSA*, unsigned long);
GthFlt          gth_sa_score(const GthSA*);
void            gth_sa_set_score(GthSA*, GthFlt);
GthFlt          gth_sa_coverage(const GthSA*);
void            gth_sa_set_coverage(GthSA*, GthFlt);
bool            gth_sa_genomic_cov_is_highest(const GthSA*);
char            gth_sa_coverage_char(const GthSA*);
void            gth_sa_set_highest_cov(GthSA*, bool genomic);
unsigned long   gth_sa_cumlen_scored_exons(const GthSA*);
void            gth_sa_set_cumlen_scored_exons(GthSA*, unsigned long);
unsigned long   gth_sa_call_number(const GthSA*);
const char*     gth_sa_gff3_target_attribute(GthSA*, bool md5ids);
void            gth_sa_determine_cutoffs(GthSA*, GthCutoffmode leadcutoffsmode,
                                         GthCutoffmode termcutoffsmode,
                                         unsigned long cutoffsminexonlen);
void            gth_sa_cutoff_start(GthSA*);
void            gth_sa_cutoff_end(GthSA*);
void            gth_sa_cutoff_walked_path(GthSA*, const GthPathWalker*,
                                          bool showeops, GtFile*);
void            gth_sa_prepend(GthSA*, const GthBacktracePath*);
void            gth_sa_append(GthSA*, const GthBacktracePath*);
void            gth_sa_remove_zero_base_exons(GthSA*, GthStat *stat);
bool            gth_sa_contains_no_zero_base_exons(const GthSA*);
void            gth_sa_echo_genomic_description(const GthSA*, GthInput*,
                                                GtFile*);
void            gth_sa_echo_reference_description(const GthSA*, GthInput*,
                                                  GtFile*);
void            gth_sa_echo_reference_sequence(const GthSA*, GthInput*,
                                               bool format, GtFile*);
void            gth_sa_echo_alignment(const GthSA *sa,
                                      unsigned long showintronmaxlen,
                                      unsigned long translationtable,
                                      bool wildcardimplosion, GthInput *input,
                                      GtFile *outfp);
/* Fills the alignment lines ( and  for DNA alignments
   and , , and  for protein alignments). */
unsigned long   gth_sa_get_alignment_lines(const GthSA *sa,
                                           unsigned char **first_line,
                                           unsigned char **second_line,
                                           unsigned char **third_line,
                                           unsigned long translationtable,
                                           GthInput *input);
bool            gth_sa_is_valid(const GthSA*);
void            gth_sa_show(GthSA*, GthInput*, GtFile*);
void            gth_sa_save_ref_md5(GthSA*, GthInput*);

bool            gth_sas_are_equal(const GthSA*, const GthSA*);

#endif
genometools-1.5.1/src/gth/sa_cmp.c000066400000000000000000000051731211610345200170310ustar00rootroot00000000000000/*
  Copyright (c) 2003-2011 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "gth/sa.h"
#include "gth/sa_cmp.h"

/* is different from gt_range_compare()! */
static int compare_ranges(GtRange *rangeA, GtRange *rangeB)
{
  if ((rangeA->start  == rangeB->start) && (rangeA->end == rangeB->end))
    return 0;

  if ((rangeA->start < rangeB->start) ||
      ((rangeA->start == rangeB->start) && (rangeA->end > rangeB->end))) {
    return -1; /* rangeA '<' rangeB */
  }

  return 1; /* rangeA '>' rangeB */
}

/*
  The following function compares two spliced alignments according to their
  genomic positions. Thereby, the positions refering to the forward strand
  are considered.
*/
int gth_sa_cmp_genomic_forward(const void *dataA, const void *dataB)
{
  GthSA *saA = (GthSA*) dataA;
  GthSA *saB = (GthSA*) dataB;
  GtRange rangeA, rangeB;

  /* genomic file number comparison */
  if (gth_sa_gen_file_num(saA) < gth_sa_gen_file_num(saB))
    return -1; /* saA '<' saB */
  else if (gth_sa_gen_file_num(saA) > gth_sa_gen_file_num(saB))
    return 1;  /* saA '>' saB */

  rangeA = gth_sa_range_forward(saA);
  rangeB = gth_sa_range_forward(saB);

  return compare_ranges(&rangeA, &rangeB);
}

/*
  The following function compares two spliced alignments pointers according to
  their genomic positions. Thereby, the positions refering to the actual strand
  are considered.
*/
int gth_sa_cmp_genomic_actual(const void *dataA, const void *dataB)
{
  GthSA *saA= *(GthSA**) dataA;
  GthSA *saB= *(GthSA**) dataB;
  GtRange rangeA, rangeB;

  /* genomic file number comparison */
  if (gth_sa_gen_file_num(saA) < gth_sa_gen_file_num(saB))
    return -1; /* saA '<' saB */
  else if (gth_sa_gen_file_num(saA) > gth_sa_gen_file_num(saB))
    return 1;  /* saA '>' saB */

  rangeA = gth_sa_range_actual(saA);
  rangeB = gth_sa_range_actual(saB);

  return compare_ranges(&rangeA, &rangeB);
}
genometools-1.5.1/src/gth/sa_cmp.h000066400000000000000000000020271211610345200170310ustar00rootroot00000000000000/*
  Copyright (c) 2003-2011 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SA_CMP_H
#define SA_CMP_H

int gth_sa_cmp_genomic_forward(const void *dataA, const void *dataB);
int gth_sa_cmp_genomic_actual(const void *dataA, const void *dataB);

#endif
genometools-1.5.1/src/gth/sa_collection.c000066400000000000000000000460001211610345200203770ustar00rootroot00000000000000/*
  Copyright (c) 2003-2011 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "extended/rbtree.h"
#include "gth/sa_cmp.h"
#include "gth/sa_collection.h"

/*
  The following structure contains binary search trees of spliced alignments.
  They contain the same elements, but ordered according to different criteria.
  The tree rooted at  contains the spliced alignments primarily
  ordered according to their left genomic position (as the linked list in GS2).
  Thereby, the genomic positions always refer to the forward strand (in
  contrary to the rest of the program, where genomic positions always refer to
  the actual strand). The elements of the tree rooted at  are
  primarily ordered according to their reference ids. This tree is used to
  ensure that no alignment which ``spans'' another alignment (according to the
  function span_check()) is inserted into the trees.
*/
struct GthSACollection {
  GthDuplicateCheck duplicate_check;
  GtRBTree *rootlist,
           *rootEST;
  bool contains_sa;
};

typedef enum
{
  NOSPAN = 0,
  DISCARD,
  REPLACE,
  NUMOFSPANACTIONS
} Spancheck;

/*
  The following function checks if one of the two GthSA
  structures spans the other. This is checked on the basis of the left and
  right genomic border. If  is included in , DISCARD is returned.
  The other way around REPLACE is returned. If none of the both spans the other
  NOSPAN is returned;
*/
static Spancheck span_check(GthSA *saA, GthSA *saB)
{
  GtRange rangeA, rangeB;

  rangeA = gth_sa_range_forward(saA);
  rangeB = gth_sa_range_forward(saB);

  if ((rangeA.start <= rangeB.start) && (rangeA.end >= rangeB.end)) {
    /* discard saB */
    return DISCARD;
  }
  if ((rangeA.start >= rangeB.start) && (rangeA.end <= rangeB.end)) {
    /* replace saA by saB */
    return REPLACE;
  }
  return NOSPAN;
}

static int compare_strands(bool strandsignA, bool strandsignB)
{
  if (strandsignA && !strandsignB)
    return -1;
  if (!strandsignA && strandsignB)
    return 1;
  return 0;
}

/*
  This function is used to check if the tree rooted at 
  contains an alignment with the same ids and strand orientations.
  But the tree is ordered according to the function
  compare_duplicate_and_genomic_pos() given below.
*/

static int compare_duplicate(const void* dataA, const void* dataB,
                             void *cmpinfo)
{
  int rval;
  GthSA *saA = (GthSA*) dataA;
  GthSA *saB = (GthSA*) dataB;
  GthDuplicateCheck duplicate_check = *(GthDuplicateCheck*) cmpinfo;

  gt_assert(duplicate_check && duplicate_check != GTH_DC_NONE);

  if (duplicate_check == GTH_DC_ID &&
      (rval = gt_str_cmp(gth_sa_gen_id_str(saA), gth_sa_gen_id_str(saB)))) {
    return rval;
  }

  if ((duplicate_check == GTH_DC_DESC || duplicate_check == GTH_DC_BOTH) &&
      (rval = gt_str_cmp(gth_sa_gen_desc(saA), gth_sa_gen_desc(saB)))) {
    return rval;
  }

  if ((duplicate_check == GTH_DC_SEQ || duplicate_check == GTH_DC_BOTH) &&
      (rval = gt_str_cmp(gth_sa_gen_md5(saA), gth_sa_gen_md5(saB)))) {
    return rval;
  }

  if ((rval = compare_strands(gth_sa_gen_strand_forward(saA),
                              gth_sa_gen_strand_forward(saB)))) {
    return rval;
  }

  if (duplicate_check == GTH_DC_ID &&
      (rval = gt_str_cmp(gth_sa_ref_id_str(saA), gth_sa_ref_id_str(saB)))) {
    return rval;
  }

  if ((duplicate_check == GTH_DC_DESC || duplicate_check == GTH_DC_BOTH) &&
      (rval = gt_str_cmp(gth_sa_ref_desc(saA), gth_sa_ref_desc(saB)))) {
    return rval;
  }

  if ((duplicate_check == GTH_DC_SEQ || duplicate_check == GTH_DC_BOTH) &&
      (rval = gt_str_cmp(gth_sa_ref_md5(saA), gth_sa_ref_md5(saB)))) {
    return rval;
  }

  if ((rval = compare_strands(gth_sa_ref_strand_forward(saA),
                              gth_sa_ref_strand_forward(saB)))) {
    return rval;
  }

  return 0;
}

/*
  This function is used as ordering for the tree rooted at .
*/

static int compare_duplicate_and_genomic_pos(const void* dataA,
                                             const void* dataB,
                                             void *cmpinfo)
{
  int rval;

  if ((rval = compare_duplicate(dataA, dataB, cmpinfo)))
    return rval;

  return gth_sa_cmp_genomic_forward(dataA, dataB);
}

/*
  The following function is used as ordering for the tree rooted at .
*/

static int compare_sa(const void *dataA, const void *dataB, void *cmpinfo)
{
  GthSA *saA = (GthSA*) dataA;
  GthSA *saB = (GthSA*) dataB;
  GtRange rangeA, rangeB;
  GthDuplicateCheck duplicate_check = *(GthDuplicateCheck*) cmpinfo;

  if (saA == saB)
    return 0;

  rangeA = gth_sa_range_forward(saA);
  rangeB = gth_sa_range_forward(saB);

  if (duplicate_check != GTH_DC_NONE && !compare_duplicate(saA, saB, cmpinfo)) {
    Spancheck action = span_check(saA, saB);
    if (action == DISCARD)
      return 0;
    gt_assert(action != REPLACE);
  }

  /* genomic file number comparison */
  if (gth_sa_gen_file_num(saA) < gth_sa_gen_file_num(saB))
    return -1;
  if (gth_sa_gen_file_num(saA) > gth_sa_gen_file_num(saB))
    return 1;

  /* genomic file numbers are equal, compare ranges */
  if ((rangeA.start < rangeB.start) ||
      ((rangeA.start == rangeB.start) && (rangeA.end > rangeB.end))) {
    /* saA '<' saB */
    return -1;
  }
  else if (rangeA.start == rangeB.start && rangeA.end == rangeB.end) {
    int rval;
    /* some additional sorting criteria for the case when the two ranges are the
       same, this helps preventing ``random'' order of spliced alignments in a
       parallelized run */
    if (gth_sa_score(saA) < gth_sa_score(saB))
      return -1;
    if (gth_sa_score(saA) > gth_sa_score(saB))
      return 1;

    if (gth_sa_cumlen_scored_exons(saA) < gth_sa_cumlen_scored_exons(saB))
      return -1;
    if (gth_sa_cumlen_scored_exons(saA) > gth_sa_cumlen_scored_exons(saB))
      return 1;

    if (gth_sa_gen_strand_forward(saA) < gth_sa_gen_strand_forward(saB))
      return -1;
    if (gth_sa_gen_strand_forward(saA) > gth_sa_gen_strand_forward(saB))
      return 1;

    if (gth_sa_ref_strand_forward(saA) < gth_sa_ref_strand_forward(saB))
      return -1;
    if (gth_sa_ref_strand_forward(saA) > gth_sa_ref_strand_forward(saB))
      return 1;

    if ((rval = gt_str_cmp(gth_sa_ref_id_str(saA), gth_sa_ref_id_str(saB))))
      return rval;

    if (gth_sa_call_number(saA) < gth_sa_call_number(saB))
      return -1;
    if (gth_sa_call_number(saA) > gth_sa_call_number(saB))
      return 1;

    if (gth_sa_ref_file_num(saA) < gth_sa_ref_file_num(saB))
      return -1;
    if (gth_sa_ref_file_num(saA) > gth_sa_ref_file_num(saB))
      return 1;

    if (gth_sa_ref_seq_num(saA) < gth_sa_ref_seq_num(saB))
      return -1;
    if (gth_sa_ref_seq_num(saA) > gth_sa_ref_seq_num(saB))
      return 1;

    gt_assert(0);
  }

  /* saA '>' saB */
  return 1;
}

static void insert_alignment(GthSACollection *sa_collection, GthSA *saB,
                             bool use_rootEST)
{
  GT_UNUSED GthSA *saA = NULL;
  bool nodecreated;

  gt_assert(sa_collection && saB);

  /* insert spliced alignment into tree rooted at  */
  saA = (GthSA*) gt_rbtree_search_with_cmp(sa_collection->rootlist, saB,
                                           compare_sa,
                                           &sa_collection->duplicate_check,
                                           &nodecreated);
  /* insertion into binary tree succeeded */
  gt_assert(saA && nodecreated);

  if (use_rootEST) {
    /* insert spliced alignment into tree rooted at  */
    saA = (GthSA*) gt_rbtree_search_with_cmp(sa_collection->rootEST, saB,
                                             compare_duplicate_and_genomic_pos,
                                             &sa_collection->duplicate_check,
                                             &nodecreated);
    /* insertion into binary tree succeeded */
    gt_assert(saA && nodecreated);
  }
}

GthSACollection* gth_sa_collection_new(GthDuplicateCheck duplicate_check)
{
  GthSACollection *sa_collection= gt_calloc(1, sizeof *sa_collection);
  sa_collection->duplicate_check = duplicate_check;
  sa_collection->rootlist = gt_rbtree_new(compare_sa, (GtFree) gth_sa_delete,
                                          &sa_collection->duplicate_check);
  sa_collection->rootEST = gt_rbtree_new(compare_duplicate_and_genomic_pos,
                                         NULL,
                                         &sa_collection->duplicate_check);
  return sa_collection;
}

bool gth_sa_collection_insert_sa(GthSACollection *sa_collection, GthSA *saB,
                                 GthSAFilter *sa_filter, GthStat *stat)
{
  GthSA *saA = NULL, *spliced_alignmentptr = NULL, *satodel;
  Spancheck action;
  GtArray *alignmentstodelete;
  bool discard = false,
       replace = false;
  unsigned long i;

  /* filter */
  if (sa_filter) {
    if (gth_sa_filter_filter_sa(sa_filter, saB)) {
      /* discard saB.
         returning false to indicate that no element has been inserted */
      return false;
    }
  }

  if (sa_collection->duplicate_check != GTH_DC_NONE) {
    saA = (GthSA*) gt_rbtree_find_with_cmp(sa_collection->rootEST, saB,
                                           compare_duplicate,
                                           &sa_collection->duplicate_check);
  }

  if (saA == NULL) {
    /* no alignment with the same ids and strand orientations is in the tree or
       the duplicate check has been disabled, insert saB into both trees. */
    insert_alignment(sa_collection, saB,
                     sa_collection->duplicate_check != GTH_DC_NONE);
  }
  else {
    /* one or more alignments with the same ids and strand orientations exist
       in the tree. check if one of them spans the new alignment. */
    alignmentstodelete = gt_array_new(sizeof (GthSA*));

    /* check the actual one */
    action = span_check(saA, saB);
    switch (action) {
      case NOSPAN:
        /* nothing to do */
        break;
      case DISCARD:
        discard = true;
        break;
      case REPLACE:
        replace = true;
        gt_array_add(alignmentstodelete, saA);
        break;
      default: gt_assert(0);
    }

    /* going to the left */
    spliced_alignmentptr = gt_rbtree_previous_key(sa_collection->rootEST, saA,
                                              compare_duplicate_and_genomic_pos,
                                              &sa_collection->duplicate_check);

    while ((spliced_alignmentptr) &&
           (!compare_duplicate(saB, spliced_alignmentptr,
                               &sa_collection->duplicate_check))) {
      /* spliced_alignmentptr has the same ids and strand orientations:
         check if it spans saB */
      action = span_check(spliced_alignmentptr, saB);
      switch (action) {
        case NOSPAN:
          /* nothing to do */
          break;
        case DISCARD:
          discard = true;
          break;
        case REPLACE:
          replace = true;
          gt_array_add(alignmentstodelete, spliced_alignmentptr);
          break;
        default: gt_assert(0);
      }

      /* retrieving next alignment */
      spliced_alignmentptr = gt_rbtree_previous_key(sa_collection->rootEST,
                                              spliced_alignmentptr,
                                              compare_duplicate_and_genomic_pos,
                                              &sa_collection->duplicate_check);
    }

    /* going to right */
    spliced_alignmentptr = gt_rbtree_next_key(sa_collection->rootEST, saA,
                                              compare_duplicate_and_genomic_pos,
                                              &sa_collection->duplicate_check);
    while ((spliced_alignmentptr) &&
           (!compare_duplicate(saB, spliced_alignmentptr,
                               &sa_collection->duplicate_check))) {
      /* spliced_alignmentptr has the same ids and strand orientations:
         check if it spans saB */
      action = span_check(spliced_alignmentptr, saB);
      switch (action) {
        case NOSPAN:
          /* nothing to do */
          break;
        case DISCARD:
          discard = true;
          break;
        case REPLACE:
          replace = true;
          gt_array_add(alignmentstodelete, spliced_alignmentptr);
          break;
        default: gt_assert(0);
      }

      /* retrieving next alignment */
      spliced_alignmentptr = gt_rbtree_next_key(sa_collection->rootEST,
                                              spliced_alignmentptr,
                                              compare_duplicate_and_genomic_pos,
                                              &sa_collection->duplicate_check);

    }

    /* DISCARD and REPLACE are not true at the same time */
    gt_assert(!(discard && replace));
    if (discard) {
      gt_assert(saA);
      /* saB will be discarded
         returning false to indicate that no element has been inserted */
      gt_array_delete(alignmentstodelete);
      return false;
    }
    if (replace) {
      /* deleting all alignments which need to be replaced by saA */
      for (i = 0; i < gt_array_size(alignmentstodelete); i++) {
        satodel = *(GthSA**) gt_array_get(alignmentstodelete, i);
        (void) gt_rbtree_erase(sa_collection->rootEST, satodel);
        (void) gt_rbtree_erase(sa_collection->rootlist, satodel);
      }
    }

    /* free */
    gt_array_delete(alignmentstodelete);

    /* insert saB */
    gt_assert(sa_collection->duplicate_check != GTH_DC_NONE);
    insert_alignment(sa_collection, saB, true);
  }

  /* returning true to indicate that an element has been inserted */
  if (stat)
    gth_stat_increment_numofSAs(stat);
  sa_collection->contains_sa = true;
  return true;
}

static int storealignmentptr(void* data, GtRBTreeContext which,
                             GT_UNUSED unsigned long depth, void *actinfo)
{
  GthSA *sa = (GthSA*) data;
  GtArray *alignments = (GtArray*) actinfo;
  switch (which) {
    case GT_RBTREE_PREORDER:
    case GT_RBTREE_ENDORDER:
      break;
    case GT_RBTREE_POSTORDER:
    case GT_RBTREE_LEAF:
      gt_array_add(alignments, sa);
      break;
    default: gt_assert(0);
  }
  return 0;
}

/* The following function traverses the tree of alignments in 
   and returns all alignment pointers in the array. */
static GtArray* sa_collection_get_alignments(const GthSACollection
                                             *sa_collection)
{
  GtArray *alignments = gt_array_new(sizeof (GthSA*));
  GT_UNUSED int had_err;
  /* traverse the tree */
  had_err = gt_rbtree_walk(sa_collection->rootlist, storealignmentptr,
                           alignments);
  gt_assert(!had_err); /* storealignmentptr() is sane */
  return alignments;
}

bool gth_sa_collections_are_equal(const GthSACollection *sa_collectionA,
                                  const GthSACollection *sa_collectionB)
{
  GtArray *alignments_from_A, *alignments_from_B;
  unsigned long i;

  /* compute arrays of SAs from the trees */
  alignments_from_A = sa_collection_get_alignments(sa_collectionA);
  alignments_from_B = sa_collection_get_alignments(sa_collectionB);

  /* check if both arrays have the same size */
  if (gt_array_size(alignments_from_A) != gt_array_size(alignments_from_B)) {
    gt_array_delete(alignments_from_A);
    gt_array_delete(alignments_from_B);
    return false;
  }

  /* both arrays have the same size -> compare the individual SAs */
  for (i = 0; i < gt_array_size(alignments_from_A); i++) {
    if (!gth_sas_are_equal(*(GthSA**) gt_array_get(alignments_from_A, i),
                           *(GthSA**) gt_array_get(alignments_from_B, i))) {
      gt_array_delete(alignments_from_A);
      gt_array_delete(alignments_from_B);
      return false;
    }
  }

  /* free space */
  gt_array_delete(alignments_from_A);
  gt_array_delete(alignments_from_B);

  return true;
}

bool gth_sa_collection_contains_sa(const GthSACollection *sa_collection)
{
  gt_assert(sa_collection);
  return sa_collection->contains_sa;
}

void gth_sa_collection_traverse(const GthSACollection *sa_collection,
                                GthSAVisitor *sa_visitor, GthInput *input)
{
  GthSACollectionIterator *iterator;
  unsigned long num_of_sas = 0;
  GthSA *sa;
  gt_assert(sa_collection && sa_visitor && input);
  gth_sa_visitor_preface(sa_visitor);
  iterator = gth_sa_collection_iterator_new(sa_collection);
  while ((sa = gth_sa_collection_iterator_next(iterator))) {
    gth_input_load_genomic_file(input, gth_sa_gen_file_num(sa), false);
    gth_input_load_reference_file(input, gth_sa_ref_file_num(sa), false);
    gth_sa_visitor_visit_sa(sa_visitor, sa);
    num_of_sas++;
  }
  gth_sa_collection_iterator_delete(iterator);
  gth_sa_visitor_trailer(sa_visitor, num_of_sas);
}

void gth_sa_collection_set_md5s(GthSACollection *sa_collection, GthInput *input)
{
  gt_assert(sa_collection && input);
  if (gth_input_md5ids(input)) {
    GthSACollectionIterator *iterator;
    GthSA *sa;
    iterator = gth_sa_collection_iterator_new(sa_collection);
    while ((sa = gth_sa_collection_iterator_next(iterator))) {
      gth_input_load_genomic_file(input, gth_sa_gen_file_num(sa), false);
      gth_input_load_reference_file(input, gth_sa_ref_file_num(sa), false);
      gth_sa_save_ref_md5(sa, input);
    }
    gth_sa_collection_iterator_delete(iterator);
  }
}

void gth_sa_collection_delete(GthSACollection *sa_collection)
{
  if (!sa_collection) return;
  gt_rbtree_delete(sa_collection->rootlist);
  /* for the second tree no free function is needed, because all elements have
     been freed already by the previous redblacktreedestroy() */
  gt_rbtree_delete(sa_collection->rootEST);

  gt_free(sa_collection);
}

struct GthSACollectionIterator {
  GtArray *alignments;
  unsigned long counter;
};

GthSACollectionIterator* gth_sa_collection_iterator_new(const GthSACollection
                                                        *sa_collection)
{
  GthSACollectionIterator *iterator;
  gt_assert(sa_collection);
  iterator = gt_malloc(sizeof *iterator);
  iterator->alignments = sa_collection_get_alignments(sa_collection);
  iterator->counter = 0;
  return iterator;
}

GthSA* gth_sa_collection_iterator_next(GthSACollectionIterator *iterator)
{
  gt_assert(iterator);
  if (iterator->counter < gt_array_size(iterator->alignments))
    return *(GthSA**) gt_array_get(iterator->alignments, iterator->counter++);
  return NULL;
}

void gth_sa_collection_iterator_delete(GthSACollectionIterator *iterator)
{
  if (!iterator) return;
  gt_array_delete(iterator->alignments);
  gt_free(iterator);
}
genometools-1.5.1/src/gth/sa_collection.h000066400000000000000000000051021211610345200204020ustar00rootroot00000000000000/*
  Copyright (c) 2003-2011 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SA_COLLECTION_H
#define SA_COLLECTION_H

#include "gth/call_info.h"
#include "gth/input.h"
#include "gth/sa_visitor.h"
#include "gth/stat.h"

typedef struct GthSACollection GthSACollection;

GthSACollection* gth_sa_collection_new(GthDuplicateCheck duplicate_check);
/* Returns true, if  has passed the  and has been inserted into
   , otherwise false is returned.  is optional. */
bool          gth_sa_collection_insert_sa(GthSACollection*, GthSA *sa,
                                          GthSAFilter *sa_filter,
                                          GthStat *stat);
/* Checks if the given two spliced alignment collections are equal.
   They are equal if they contain exactly the same spliced alignments. */
bool          gth_sa_collections_are_equal(const GthSACollection*,
                                           const GthSACollection*);
/* Returns true if  contains at least on spliced alignment,
   false otherwise. */
bool          gth_sa_collection_contains_sa(const GthSACollection*);
void          gth_sa_collection_traverse(const GthSACollection*, GthSAVisitor*,
                                         GthInput*);
void          gth_sa_collection_set_md5s(GthSACollection*, GthInput*);
void          gth_sa_collection_delete(GthSACollection*);

typedef struct GthSACollectionIterator GthSACollectionIterator;

GthSACollectionIterator* gth_sa_collection_iterator_new(const GthSACollection*);
GthSA*                   gth_sa_collection_iterator_next(
                                                      GthSACollectionIterator*);
void                     gth_sa_collection_iterator_delete(
                                                      GthSACollectionIterator*);

#endif
genometools-1.5.1/src/gth/sa_filter.c000066400000000000000000000146771211610345200175500ustar00rootroot00000000000000/*
  Copyright (c) 2005-2010 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "gth/default.h"
#include "gth/sa_filter.h"

#define MINALIGNMENTSCORE_OPT_CSTR  "minalignmentscore"
#define MAXALIGNMENTSCORE_OPT_CSTR  "maxalignmentscore"
#define MINCOVERAGE_OPT_CSTR        "mincoverage"
#define MAXCOVERAGE_OPT_CSTR        "maxcoverage"

struct GthSAFilter {
  double min_alignmentscore,
         max_alignmentscore,
         min_coverage,
         max_coverage;
};

GthSAFilter* gth_sa_filter_new(void)
{
  GthSAFilter *sa_filter;
  sa_filter = gt_malloc(sizeof (GthSAFilter));
  sa_filter->min_alignmentscore = GTH_DEFAULT_MIN_ALIGNMENTSCORE;
  sa_filter->max_alignmentscore = GTH_DEFAULT_MAX_ALIGNMENTSCORE;
  sa_filter->min_coverage       = GTH_DEFAULT_MIN_COVERAGE;
  sa_filter->max_coverage       = GTH_DEFAULT_MAX_COVERAGE;
  return sa_filter;
}

static int sa_filter_check_arguments(void *data, GtError *err)
{
  GthSAFilter *sa_filter= (GthSAFilter*) data;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(sa_filter);

  if (sa_filter->min_alignmentscore > sa_filter->max_alignmentscore) {
    gt_error_set(err, "argument \"%.2f\" to option -%s must be smaller or "
                      "equal than argument \"%.2f\" to option -%s",
                 sa_filter->min_alignmentscore, MINALIGNMENTSCORE_OPT_CSTR,
                 sa_filter->max_alignmentscore, MAXALIGNMENTSCORE_OPT_CSTR);
    had_err = -1;
  }

  if (!had_err && sa_filter->min_coverage > sa_filter->max_coverage) {
    gt_error_set(err, "argument \"%.2f\" to option -%s must be smaller or "
                      "equal than argument \"%.2f\" to option -%s",
                 sa_filter->min_coverage, MINCOVERAGE_OPT_CSTR,
                 sa_filter->max_coverage, MAXCOVERAGE_OPT_CSTR);
    had_err = -1;
  }

  return had_err;
}

void gth_sa_filter_register_options(GtOptionParser *op, GthSAFilter *sa_filter,
                                    bool extended_options)
{
  GtOption *o;

  gt_assert(sa_filter && op);

  /* -minalignmentscore */
  o = gt_option_new_double_min_max(MINALIGNMENTSCORE_OPT_CSTR, "set the "
                                   "minimum alignment score for spliced "
                                   "alignments to be included into the set of "
                                   "spliced alignments",
                                   &sa_filter->min_alignmentscore,
                                   GTH_DEFAULT_MIN_ALIGNMENTSCORE,
                                   GTH_DEFAULT_MIN_ALIGNMENTSCORE,
                                   GTH_DEFAULT_MAX_ALIGNMENTSCORE);
  if (extended_options)
    gt_option_is_extended_option(o);
  gt_option_parser_add_option(op, o);

  /* -maxalignmentscore */
  o = gt_option_new_double_min_max(MAXALIGNMENTSCORE_OPT_CSTR, "set the "
                                   "maximum alignment score for spliced "
                                   "alignments to be included into the set of "
                                   "spliced alignments",
                                   &sa_filter->max_alignmentscore,
                                   GTH_DEFAULT_MAX_ALIGNMENTSCORE,
                                   GTH_DEFAULT_MIN_ALIGNMENTSCORE,
                                   GTH_DEFAULT_MAX_ALIGNMENTSCORE);
  if (extended_options)
    gt_option_is_extended_option(o);
  gt_option_parser_add_option(op, o);

  /* -mincoverage */
  o = gt_option_new_double_min_max(MINCOVERAGE_OPT_CSTR, "set the minimum "
                                   "coverage for spliced alignments to be "
                                   "included into the set of spliced "
                                   "alignments",
                                   &sa_filter->min_coverage,
                                   GTH_DEFAULT_MIN_COVERAGE,
                                   GTH_DEFAULT_MIN_COVERAGE,
                                   GTH_DEFAULT_MAX_COVERAGE);
  if (extended_options)
    gt_option_is_extended_option(o);
  gt_option_parser_add_option(op, o);

  /* -maxcoverage */
  o = gt_option_new_double_min_max(MAXCOVERAGE_OPT_CSTR, "set the maximum "
                                   "coverage for spliced alignments to be "
                                   "included into the set of spliced "
                                   "alignments",
                                   &sa_filter->max_coverage,
                                   GTH_DEFAULT_MAX_COVERAGE,
                                   GTH_DEFAULT_MIN_COVERAGE,
                                   GTH_DEFAULT_MAX_COVERAGE);
  if (extended_options)
    gt_option_is_extended_option(o);
  gt_option_parser_add_option(op, o);

  /* register hooks to check the arguments after the option parsing */
  gt_option_parser_register_hook(op, sa_filter_check_arguments, sa_filter);
}

bool gth_sa_filter_filter_sa(const GthSAFilter *sa_filter, GthSA *sa)
{
  gt_assert(sa_filter && sa);
  /* alignment score is larger or equal then default min value */
  gt_assert(gth_sa_score(sa) >= GTH_DEFAULT_MIN_ALIGNMENTSCORE);
  /* alignment score is smaller or equal then default max value */
  gt_assert(gth_sa_score(sa) <= GTH_DEFAULT_MAX_ALIGNMENTSCORE);
  /* coverage is larger or equal then default min value */
  gt_assert(gth_sa_coverage(sa) >= GTH_DEFAULT_MIN_COVERAGE);
  /* coverage score is smaller or equal then default max value */
  gt_assert(gth_sa_coverage(sa) <= GTH_DEFAULT_MAX_COVERAGE);

  /* filter */
  if (gth_sa_score(sa)    < sa_filter->min_alignmentscore ||
      gth_sa_score(sa)    > sa_filter->max_alignmentscore ||
      gth_sa_coverage(sa) < sa_filter->min_coverage       ||
      gth_sa_coverage(sa) > sa_filter->max_coverage) {
    return true;
  }
  return false;
}

void gth_sa_filter_delete(GthSAFilter *sa_filter)
{
  if (!sa_filter) return;
  gt_free(sa_filter);
}
genometools-1.5.1/src/gth/sa_filter.h000066400000000000000000000024731211610345200175440ustar00rootroot00000000000000/*
  Copyright (c) 2005-2009 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SA_FILTER_H
#define SA_FILTER_H

#include "core/option_api.h"
#include "gth/sa.h"

/* a filter for spliced alignments */
typedef struct GthSAFilter GthSAFilter;

GthSAFilter* gth_sa_filter_new(void);
void         gth_sa_filter_register_options(GtOptionParser*, GthSAFilter*,
                                            bool extended_options);
bool         gth_sa_filter_filter_sa(const GthSAFilter*, GthSA*);
void         gth_sa_filter_delete(GthSAFilter*);

#endif
genometools-1.5.1/src/gth/sa_visitor.c000066400000000000000000000036621211610345200177520ustar00rootroot00000000000000/*
  Copyright (c) 2008-2011 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "gth/sa_visitor_rep.h"

GthSAVisitor* gth_sa_visitor_create(const GthSAVisitorClass *savc)
{
  GthSAVisitor *sav;
  gt_assert(savc && savc->size);
  sav = gt_calloc(1, savc->size);
  sav->c_class = savc;
  return sav;
}

void* gth_sa_visitor_cast(GT_UNUSED const GthSAVisitorClass *savc,
                          GthSAVisitor *sav)
{
  gt_assert(savc && sav && sav->c_class == savc);
  return sav;
}

void gth_sa_visitor_preface(GthSAVisitor *sav)
{
  gt_assert(sav && sav->c_class);
  if (sav->c_class->preface)
    sav->c_class->preface(sav);
}

void gth_sa_visitor_visit_sa(GthSAVisitor *sav, GthSA *sa)
{
  gt_assert(sav && sa && sav->c_class && sav->c_class->visit_sa);
  sav->c_class->visit_sa(sav, sa);
}

void gth_sa_visitor_trailer(GthSAVisitor *sav, unsigned long num_of_sas)
{
  gt_assert(sav && sav->c_class);
  if (sav->c_class->trailer)
    sav->c_class->trailer(sav, num_of_sas);
}

void gth_sa_visitor_delete(GthSAVisitor *sav)
{
  if (!sav) return;
  gt_assert(sav->c_class);
  if (sav->c_class->free)
    sav->c_class->free(sav);
  gt_free(sav);
}
genometools-1.5.1/src/gth/sa_visitor.h000066400000000000000000000024141211610345200177510ustar00rootroot00000000000000/*
  Copyright (c) 2008-2011 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SA_VISITOR_H
#define SA_VISITOR_H

#include "gth/sa.h"

/* the ``spliced alignment visitor'' interface */
typedef struct GthSAVisitorClass GthSAVisitorClass;
typedef struct GthSAVisitor GthSAVisitor;

void gth_sa_visitor_preface(GthSAVisitor*);
void gth_sa_visitor_visit_sa(GthSAVisitor*, GthSA*);
void gth_sa_visitor_trailer(GthSAVisitor*, unsigned long num_of_sas);
void gth_sa_visitor_delete(GthSAVisitor*);

#endif
genometools-1.5.1/src/gth/sa_visitor_rep.h000066400000000000000000000026121211610345200206170ustar00rootroot00000000000000/*
  Copyright (c) 2008-2011 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SA_VISITOR_REP_H
#define SA_VISITOR_REP_H

#include "gth/sa_visitor.h"

/* the ``spliced alignment visitor'' interface */
struct GthSAVisitorClass {
  size_t size;
  void (*free)(GthSAVisitor*);
  void (*preface)(GthSAVisitor*);
  void (*visit_sa)(GthSAVisitor*, GthSA*);
  void (*trailer)(GthSAVisitor*, unsigned long num_of_sas);
};

struct GthSAVisitor {
  const GthSAVisitorClass *c_class;
};

GthSAVisitor* gth_sa_visitor_create(const GthSAVisitorClass*);
void*         gth_sa_visitor_cast(const GthSAVisitorClass*, GthSAVisitor*);

#endif
genometools-1.5.1/src/gth/seq_con.c000066400000000000000000000154561211610345200172230ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/class_alloc.h"
#include "core/ma_api.h"
#include "core/unused_api.h"
#include "gth/seq_con_rep.h"

struct GthSeqConClass {
  size_t size;
  GthSeqConDemandOrigSeqFunc demand_orig_seq;
  GthSeqConGetOrigSeqFunc get_orig_seq;
  GthSeqConGetTranSeqFunc get_tran_seq;
  GthSeqConGetOrigSeqRCFunc get_orig_seq_rc;
  GthSeqConGetTranSeqRCFunc get_tran_seq_rc;
  GthSeqConGetDescriptionFunc get_description;
  GthSeqConEchoDescriptionFunc echo_description;
  GthSeqConNumOfSeqsFunc num_of_seqs;
  GthSeqConTotalLengthFunc total_length;
  GthSeqConGetRangeFunc get_range;
  GthSeqConGetAlphabetFunc get_alphabet;
  GthSeqConFreeFunc free;
};

const GthSeqConClass* gth_seq_con_class_new(size_t size,
                                            GthSeqConDemandOrigSeqFunc
                                            demand_orig_seq,
                                            GthSeqConGetOrigSeqFunc
                                            get_orig_seq,
                                            GthSeqConGetTranSeqFunc
                                            get_tran_seq,
                                            GthSeqConGetOrigSeqRCFunc
                                            get_orig_seq_rc,
                                            GthSeqConGetTranSeqRCFunc
                                            get_tran_seq_rc,
                                            GthSeqConGetDescriptionFunc
                                            get_description,
                                            GthSeqConEchoDescriptionFunc
                                            echo_description,
                                            GthSeqConNumOfSeqsFunc num_of_seqs,
                                            GthSeqConTotalLengthFunc
                                            total_length,
                                            GthSeqConGetRangeFunc get_range,
                                            GthSeqConGetAlphabetFunc
                                            get_alphabet,
                                            GthSeqConFreeFunc free)
{
  GthSeqConClass *c_class = gt_class_alloc(sizeof *c_class);
  c_class->size = size;
  c_class->demand_orig_seq = demand_orig_seq;
  c_class->get_orig_seq = get_orig_seq;
  c_class->get_tran_seq = get_tran_seq;
  c_class->get_orig_seq_rc = get_orig_seq_rc;
  c_class->get_tran_seq_rc = get_tran_seq_rc;
  c_class->get_description = get_description;
  c_class->echo_description = echo_description;
  c_class->num_of_seqs = num_of_seqs;
  c_class->total_length = total_length;
  c_class->get_range = get_range;
  c_class->get_alphabet = get_alphabet;
  c_class->free = free;
  return c_class;
}

GthSeqCon* gth_seq_con_create(const GthSeqConClass *scc)
{
  GthSeqCon *sc;
  gt_assert(scc && scc->size);
  sc = gt_calloc(1, scc->size);
  sc->c_class = scc;
  sc->pvt = NULL; /* XXX */
  return sc;
}

void* gth_seq_con_cast(GT_UNUSED const GthSeqConClass *scc, GthSeqCon *sc)
{
  gt_assert(scc && sc && sc->c_class == scc);
  return sc;
}

void gth_seq_con_delete(GthSeqCon *sc)
{
  if (!sc) return;
  if (sc->c_class->free)
    sc->c_class->free(sc);
  gt_free(sc->pvt);
  gt_free(sc);
}

void gth_seq_con_demand_orig_seq(GthSeqCon *seq_con)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->demand_orig_seq);
  seq_con->c_class->demand_orig_seq(seq_con);
}
GtUchar* gth_seq_con_get_orig_seq(GthSeqCon *seq_con, unsigned long seq_num)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->get_orig_seq);
  return seq_con->c_class->get_orig_seq(seq_con, seq_num);
}

GtUchar* gth_seq_con_get_tran_seq(GthSeqCon *seq_con, unsigned long seq_num)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->get_tran_seq);
  return seq_con->c_class->get_tran_seq(seq_con, seq_num);
}

GtUchar* gth_seq_con_get_orig_seq_rc(GthSeqCon *seq_con, unsigned long seq_num)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->get_orig_seq_rc);
  return seq_con->c_class->get_orig_seq_rc(seq_con, seq_num);
}

GtUchar* gth_seq_con_get_tran_seq_rc(GthSeqCon *seq_con, unsigned long seq_num)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->get_tran_seq_rc);
  return seq_con->c_class->get_tran_seq_rc(seq_con, seq_num);
}

void gth_seq_con_get_description(GthSeqCon *seq_con, unsigned long seq_num,
                                 GtStr *desc)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->get_description);
  seq_con->c_class->get_description(seq_con, seq_num, desc);
}

void gth_seq_con_echo_description(GthSeqCon *seq_con, unsigned long seq_num,
                                  GtFile *outfp)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->echo_description);
  seq_con->c_class->echo_description(seq_con, seq_num, outfp);
}

unsigned long gth_seq_con_num_of_seqs(GthSeqCon *seq_con)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->num_of_seqs);
  return seq_con->c_class->num_of_seqs(seq_con);
}

unsigned long gth_seq_con_total_length(GthSeqCon *seq_con)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->total_length);
  return seq_con->c_class->total_length(seq_con);
}

GtRange gth_seq_con_get_range(GthSeqCon *seq_con, unsigned long seq_num)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->get_range);
  return seq_con->c_class->get_range(seq_con, seq_num);
}

GtRange gth_seq_con_get_relative_range(GthSeqCon *seq_con,
                                       unsigned long seq_num)
{
  GtRange relative_range, range;
  gt_assert(seq_con);
  gt_assert(seq_num < gth_seq_con_num_of_seqs(seq_con));
  range = gth_seq_con_get_range(seq_con, seq_num);
  relative_range.start = 0;
  relative_range.end = range.end - range.start;
  return relative_range;
}

unsigned long gth_seq_con_get_length(GthSeqCon *seq_con, unsigned long seq_num)
{
  GtRange range;
  gt_assert(seq_con);
  range = gth_seq_con_get_range(seq_con, seq_num);
  return gt_range_length(&range);
}

GtAlphabet* gth_seq_con_get_alphabet(GthSeqCon *seq_con)
{
  gt_assert(seq_con && seq_con->c_class && seq_con->c_class->get_alphabet);
  return seq_con->c_class->get_alphabet(seq_con);
}
genometools-1.5.1/src/gth/seq_con.h000066400000000000000000000052071211610345200172210ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SEQ_CON_H
#define SEQ_CON_H

#include "core/alphabet.h"
#include "core/file.h"
#include "core/range.h"
#include "core/str_api.h"
#include "core/types_api.h"

/* The sequence container class */
typedef struct GthSeqConClass GthSeqConClass;
typedef struct GthSeqCon GthSeqCon;

typedef GthSeqCon* (*GthSeqConConstructor)(const char *indexname,
                                           bool assign_rc, bool orig_seq,
                                           bool tran_seq);

void          gth_seq_con_delete(GthSeqCon*);
void          gth_seq_con_demand_orig_seq(GthSeqCon *seq_con);
GtUchar*      gth_seq_con_get_orig_seq(GthSeqCon *seq_con,
                                       unsigned long seq_num);
GtUchar*      gth_seq_con_get_tran_seq(GthSeqCon *seq_con,
                                       unsigned long seq_num);
GtUchar*      gth_seq_con_get_orig_seq_rc(GthSeqCon *seq_con,
                                          unsigned long seq_num);
GtUchar*      gth_seq_con_get_tran_seq_rc(GthSeqCon *seq_con,
                                          unsigned long seq_num);
void          gth_seq_con_get_description(GthSeqCon *seq_con,
                                          unsigned long seq_num, GtStr *desc);
void          gth_seq_con_echo_description(GthSeqCon *seq_con,
                                           unsigned long seq_num,
                                           GtFile *outfp);
unsigned long gth_seq_con_num_of_seqs(GthSeqCon *seq_con);
unsigned long gth_seq_con_total_length(GthSeqCon *seq_con);
GtRange       gth_seq_con_get_range(GthSeqCon *seq_con, unsigned long seq_num);

GtRange       gth_seq_con_get_relative_range(GthSeqCon *seq_con,
                                             unsigned long seq_num);
unsigned long gth_seq_con_get_length(GthSeqCon *seq_con, unsigned long seq_num);
GtAlphabet*   gth_seq_con_get_alphabet(GthSeqCon *seq_con);

#endif
genometools-1.5.1/src/gth/seq_con_rep.h000066400000000000000000000073671211610345200201000ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SEQ_CON_REP_H
#define SEQ_CON_REP_H

#include "gth/seq_con.h"

typedef void     (*GthSeqConDemandOrigSeqFunc)(GthSeqCon*);
typedef GtUchar* (*GthSeqConGetOrigSeqFunc)(GthSeqCon*, unsigned long seq_num);
typedef GtUchar* (*GthSeqConGetTranSeqFunc)(GthSeqCon*, unsigned long seq_num);
typedef GtUchar* (*GthSeqConGetOrigSeqRCFunc)(GthSeqCon*,
                                              unsigned long seq_num);
typedef GtUchar* (*GthSeqConGetTranSeqRCFunc)(GthSeqCon*,
                                              unsigned long seq_num);
typedef void     (*GthSeqConGetDescriptionFunc)(GthSeqCon*,
                                                unsigned long seq_num,
                                                GtStr *desc);
typedef void     (*GthSeqConEchoDescriptionFunc)(GthSeqCon*,
                                                 unsigned long seq_num,
                                                 GtFile *outfp);
typedef unsigned long (*GthSeqConNumOfSeqsFunc)(GthSeqCon*);
typedef unsigned long (*GthSeqConTotalLengthFunc)(GthSeqCon*);
typedef GtRange       (*GthSeqConGetRangeFunc)(GthSeqCon*,
                                               unsigned long seq_num);
typedef GtAlphabet*   (*GthSeqConGetAlphabetFunc)(GthSeqCon*);
typedef void          (*GthSeqConFreeFunc)(GthSeqCon*);

typedef struct GthSeqConMembers GthSeqConMembers;

struct GthSeqCon {
  const GthSeqConClass *c_class;
  GthSeqConMembers *pvt;
};

const GthSeqConClass* gth_seq_con_class_new(size_t size,
                                            GthSeqConDemandOrigSeqFunc
                                            demand_orig_seq,
                                            GthSeqConGetOrigSeqFunc
                                            get_orig_seq,
                                            GthSeqConGetTranSeqFunc
                                            get_tran_seq,
                                            GthSeqConGetOrigSeqRCFunc
                                            get_orig_seq_rc,
                                            GthSeqConGetTranSeqRCFunc
                                            get_tran_seq_rc,
                                            GthSeqConGetDescriptionFunc
                                            get_description,
                                            GthSeqConEchoDescriptionFunc
                                            echo_description,
                                            GthSeqConNumOfSeqsFunc num_of_seqs,
                                            GthSeqConTotalLengthFunc
                                            total_length,
                                            GthSeqConGetRangeFunc get_range,
                                            GthSeqConGetAlphabetFunc
                                            get_alphabet,
                                            GthSeqConFreeFunc free);
GthSeqCon*           gth_seq_con_create(const GthSeqConClass*);
void*                gth_seq_con_cast(const GthSeqConClass*, GthSeqCon*);

#endif
genometools-1.5.1/src/gth/showbool.h000066400000000000000000000015611211610345200174250ustar00rootroot00000000000000/*
  Copyright (c) 2009 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SHOWBOOL_H
#define SHOWBOOL_H

#define GTH_SHOWBOOL(B) ((B) ? "True" : "False")

#endif
genometools-1.5.1/src/gth/similarity_filter.c000066400000000000000000001176341211610345200213300ustar00rootroot00000000000000/*
  Copyright (c) 2003-2011 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/trans_table.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/warning_api.h"
#include "gth/chaining.h"
#include "gth/gtherror.h"
#include "gth/gthxml.h"
#include "gth/intermediate.h"
#include "gth/proc_sa_collection.h"
#include "gth/similarity_filter.h"

#define UNSUCCESSFULALIGNMENTSCORE      0.0

#define SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE 160
#define ICDELTASTRINGLENGTH                     40

#define SHOW_COMPUTE_MATCHES_STATUS_BUF_SIZE    160

typedef struct {
  unsigned long call_number;
  bool significant_match_found,
       max_call_number_reached,
       stop_amino_acid_warning;
} GthMatchInfo;

static void show_matrix_calculation_status(GthShowVerbose showverbose,
                                           bool gen_strand_forward,
                                           bool ref_strand_forward,
                                           bool introncutout,
                                           unsigned long chainctr,
                                           unsigned long num_of_chains,
                                           unsigned long icdelta,
                                           unsigned long gen_file_num,
                                           unsigned long num_of_gen_files,
                                           unsigned long ref_file_num,
                                           unsigned long num_of_ref_files,
                                           bool directmatches,
                                           bool verboseseqs,
                                           const char *gen_id,
                                           const char *ref_id)
{
  char buf[SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE],
       icdeltastring[ICDELTASTRINGLENGTH];
  GT_UNUSED int rval;

  if (introncutout) {
    rval =  snprintf(icdeltastring, ICDELTASTRINGLENGTH, ", icdelta=%lu",
                     icdelta);
    /* buffer icdeltastring[ICDELTASTRINGLENGTH] is large enough */
    gt_assert(rval <  ICDELTASTRINGLENGTH);
  }

  if (num_of_gen_files == 1 && num_of_ref_files == 1) {
    rval = snprintf(buf, SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE,
                    "d=%c, compute spliced alignment, genseq=%c, "
                    "chain=%lu/%lu, refseq=%c%s", SHOWSTRAND(directmatches),
                    SHOWSTRAND(gen_strand_forward),  chainctr + 1,
                    num_of_chains, SHOWSTRAND(ref_strand_forward),
                    introncutout ? icdeltastring : "");
  }
  else {
    rval = snprintf(buf, SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE,
                    "gf=%lu/%lu, d=%c, rf=%lu/%lu, compute spliced alignment, "
                    "gs=%c, chain=%lu/%lu, rs=%c%s", gen_file_num + 1,
                    num_of_gen_files, SHOWSTRAND(directmatches),
                    ref_file_num + 1, num_of_ref_files,
                    SHOWSTRAND(gen_strand_forward), chainctr + 1,
                    num_of_chains, SHOWSTRAND(ref_strand_forward),
                    introncutout ? icdeltastring : "");
  }
  /* buf[SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE] is large enough */
  gt_assert(rval <  SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE);
  showverbose(buf);

  if (verboseseqs) {
    rval = snprintf(buf, SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE,
                    "genomicid=%s, referenceid=%s", gen_id, ref_id);
    /* buf[SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE] is large enough */
    gt_assert(rval < SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE);
    showverbose(buf);
  }
}

static int callsahmt(bool call_dna_dp,
                     GthSA *sa,
                     bool forward,
                     unsigned long gen_file_num,
                     unsigned long ref_file_num,
                     GthChain *raw_chain,
                     unsigned long gen_total_length,
                     unsigned long gen_offset,
                     const GtRange *gen_seq_bounds,
                     const GtRange *gen_seq_bounds_rc,
                     const unsigned char *ref_seq_tran,
                     const unsigned char *ref_seq_orig,
                     unsigned long ref_total_length,
                     unsigned long ref_offset,
                     GthInput *input,
                     Introncutoutinfo *introncutoutinfo,
                     GthStat *stat,
                     unsigned long chainctr,
                     unsigned long num_of_chains,
                     unsigned long translationtable,
                     bool directmatches,
                     bool proteinexonpenal,
                     GthSpliceSiteModel *splice_site_model,
                     GthDPOptionsCore *dp_options_core,
                     GthDPOptionsEST *dp_options_est,
                     GthDPOptionsPostpro *dp_options_postpro,
                     GthDNACompletePathMatrixJT dna_complete_path_matrix_jt,
                     GthProteinCompletePathMatrixJT
                     protein_complete_path_matrix_jt,
                     GthOutput *out)
{
  int rval;
  GthChain *actual_chain, *contracted_chain, *used_chain;
  unsigned long icdelta = introncutoutinfo->icinitialdelta,
                iciterations = introncutoutinfo->iciterations;
  bool useintroncutout = introncutoutinfo->introncutout;
  /* initially useintron is set to the value of introncutoutinfo->introncutout,
     if the automatic intron cutotu technique is acitvated it can be set to
     true if an matrix allocation error (ERROR_MATRIX_ALLOCATION_FAILED) occurs
   */

  gt_assert(sa);

  actual_chain = gth_chain_new();
  contracted_chain = gth_chain_new();

  for (;;) {
    /* reset actualDPrange; */
    gt_array_set_size(actual_chain->forwardranges, 0);
    gt_array_set_size(actual_chain->reverseranges, 0);

    /* copy raw chain to actual chain */
    gth_chain_copy(actual_chain, raw_chain);

    /* shorten potential introns and compute spliced sequence, if the intron
       cutout technique is used */
    if (useintroncutout) {
      /* shorten potential introns */
      gth_chain_shorten_introns(actual_chain, icdelta,
                                introncutoutinfo->icminremintronlength,
                                gen_total_length, gen_offset, out->comments,
                                out->outfp);
    }
    else
      gth_chain_contract(contracted_chain, actual_chain);

    if (out->showverbose) {
      show_matrix_calculation_status(out->showverbose, forward,
                                     gth_sa_ref_strand_forward(sa),
                                     useintroncutout, chainctr, num_of_chains,
                                     icdelta, gen_file_num,
                                     gth_input_num_of_gen_files(input),
                                     ref_file_num,
                                     gth_input_num_of_ref_files(input),
                                     directmatches, out->verboseseqs,
                                     gth_sa_gen_id(sa), gth_sa_ref_id(sa));
    }

    /* allocate space for DP parameter */
    if (out->comments) {
      gt_file_xprintf(out->outfp, "%c alloc space for DP param "
                         "(genomicid=%s, referenceid=%s)\n", COMMENTCHAR,
                         gth_sa_gen_id(sa), gth_sa_ref_id(sa));
    }
    used_chain = useintroncutout ? actual_chain : contracted_chain;

    /* The variable 'forward' denotes the genomic strand on which the DP is
       applied. */
    if (forward) {
      if (call_dna_dp) {
        rval = gth_align_dna(sa, used_chain->forwardranges,
                             gth_input_current_gen_seq_tran(input),
                             gth_input_current_gen_seq_orig(input),
                             ref_seq_tran, ref_seq_orig, ref_total_length,
                             gth_input_current_gen_alphabet(input),
                             gth_input_current_ref_alphabet(input),
                             useintroncutout,
                             introncutoutinfo->autoicmaxmatrixsize,
                             out->showeops, out->comments, out->gs2out,
                             gen_seq_bounds, splice_site_model, dp_options_core,
                             dp_options_est, dp_options_postpro,
                             dna_complete_path_matrix_jt,
                             raw_chain->forward_jump_table, ref_offset, stat,
                             out->outfp);
      }
      else { /* call_protein_dp */
        rval = gth_align_protein(sa, used_chain->forwardranges,
                                 gth_input_current_gen_seq_tran(input),
                                 ref_seq_tran, ref_seq_orig, ref_total_length,
                                 gth_input_current_gen_alphabet(input),
                                 gth_input_current_ref_alphabet(input),
                                 input, useintroncutout,
                                 introncutoutinfo->autoicmaxmatrixsize,
                                 proteinexonpenal, out->showeops, out->comments,
                                 out->gs2out, translationtable, gen_seq_bounds,
                                 splice_site_model, dp_options_core,
                                 dp_options_postpro,
                                 protein_complete_path_matrix_jt,
                                 raw_chain->forward_jump_table, ref_offset,
                                 stat, out->outfp);
      }
    }
    else {
      /* the DP is called with the revers positions specifiers */
      if (call_dna_dp) {
        rval = gth_align_dna(sa, used_chain->reverseranges,
                             gth_input_current_gen_seq_tran_rc(input),
                             gth_input_current_gen_seq_orig_rc(input),
                             ref_seq_tran, ref_seq_orig, ref_total_length,
                             gth_input_current_gen_alphabet(input),
                             gth_input_current_ref_alphabet(input),
                             useintroncutout,
                             introncutoutinfo->autoicmaxmatrixsize,
                             out->showeops, out->comments, out->gs2out,
                             gen_seq_bounds_rc, splice_site_model,
                             dp_options_core, dp_options_est,
                             dp_options_postpro, dna_complete_path_matrix_jt,
                             raw_chain->reverse_jump_table, ref_offset, stat,
                             out->outfp);
      }
      else { /* call_protein_dp */
        rval = gth_align_protein(sa, used_chain->reverseranges,
                                 gth_input_current_gen_seq_tran_rc(input),
                                 ref_seq_tran, ref_seq_orig, ref_total_length,
                                 gth_input_current_gen_alphabet(input),
                                 gth_input_current_ref_alphabet(input),
                                 input, useintroncutout,
                                 introncutoutinfo->autoicmaxmatrixsize,
                                 proteinexonpenal, out->showeops, out->comments,
                                 out->gs2out, translationtable, gen_seq_bounds,
                                 splice_site_model, dp_options_core,
                                 dp_options_postpro,
                                 protein_complete_path_matrix_jt,
                                 raw_chain->reverse_jump_table, ref_offset,
                                 stat, out->outfp);
      }
    }

    if (rval == GTH_ERROR_DP_PARAMETER_ALLOCATION_FAILED)
      return GTH_ERROR_DP_PARAMETER_ALLOCATION_FAILED;

    /* handling of special error codes ERROR_CUTOUT_NOT_IN_INTRON and
       ERROR_MATRIX_ALLOCATION_FAILED from DP
       the only possible special error code given back by this function is
       ERROR_SA_COULD_NOT_BE_DETERMINED */
#ifndef NDEBUG
    if (!useintroncutout) gt_assert(rval != GTH_ERROR_CUTOUT_NOT_IN_INTRON);
#endif
    if (useintroncutout && rval == GTH_ERROR_CUTOUT_NOT_IN_INTRON) {
      /* the intron cutout technique failed -> increase counter */
      gth_stat_increment_numofunsuccessfulintroncutoutDPs(stat);
      if (--iciterations > 0) {
        /* if an iterations is left, increase icdelta, decrease the remaining
           iterations, and continue the while-loop */
        icdelta += introncutoutinfo->icdeltaincrease;
        continue;
      }
      else {
        /* no iteration left, discard SA */
        gth_stat_increment_numofundeterminedSAs(stat);
        gth_chain_delete(actual_chain);
        gth_chain_delete(contracted_chain);
        return GTH_ERROR_SA_COULD_NOT_BE_DETERMINED;
      }
    }
    else if (rval == GTH_ERROR_MATRIX_ALLOCATION_FAILED) {
      if (introncutoutinfo->autoicmaxmatrixsize > 0 && !useintroncutout) {
        /* if the automatic intron cutout technique is enabled and a ``normal''
           DP returned with the matrix allocation error, set useintroncutout,
           increase counter, and continue */
        if (out->showverbose) {
          out->showverbose("matrix allocation failed, use intron cutout "
                           "technique");
        }
        gth_stat_increment_numofautointroncutoutcalls(stat);
        useintroncutout = true;
        continue;
      }
      else {
        /* otherwise increase relevant statistics, free space and return with
           error */
        gth_stat_increment_numoffailedmatrixallocations(stat);
        gth_stat_increment_numofundeterminedSAs(stat);
        gth_chain_delete(actual_chain);
        gth_chain_delete(contracted_chain);
        return GTH_ERROR_SA_COULD_NOT_BE_DETERMINED;
      }
    }
    else if (rval) /* ``normal'' DP */
      return -1;
    break;
  }

#if 0
  if (out->comments) {
    gt_file_xprintf(out->outfp, "%c this SA has been computed:\n", COMMENTCHAR);
    gth_sa_show(sa, input, out->outfp);
  }
#endif

  /* free */
  gth_chain_delete(actual_chain);
  gth_chain_delete(contracted_chain);

  return 0;
}

/* the following function saves  by inserting it into  and
   sets  to true, if the insertion was successful */
static void save_sa(GthSACollection *sa_collection, GthSA *sa,
                    GthSAFilter *sa_filter, GthMatchInfo *match_info,
                    GthStat *stat)
{
  if (!gth_sa_collection_insert_sa(sa_collection, sa, sa_filter, stat)) {
    /* unsuccessful insertion; discard sa */
    gth_sa_delete(sa);
    match_info->call_number--;
  }
  else {
    /* else successful insertion */
    match_info->significant_match_found = true;
  }
}

static bool isunsuccessfulalignment(GthSA *sa,
                                    bool comments,
                                    GtFile *outfp)
{
  if (gth_sa_score(sa) <= UNSUCCESSFULALIGNMENTSCORE) {
    if (comments)
      gt_file_xprintf(outfp, "%c discard alignment\n", COMMENTCHAR);
    return true;
  }
  return false;
}

static int call_dna_DP(bool directmatches, GthCallInfo *call_info,
                       GthInput *input, GthStat *stat,
                       GthSACollection *sa_collection, GthSA *saA,
                       unsigned long gen_file_num,
                       unsigned long ref_file_num,
                       unsigned long gen_total_length,
                       unsigned long gen_offset,
                       const GtRange *gen_seq_bounds,
                       const GtRange *gen_seq_bounds_rc,
                       unsigned long ref_total_length, unsigned long ref_offset,
                       unsigned long chainctr,
                       unsigned long num_of_chains, GthMatchInfo *match_info,
                       const unsigned char *ref_seq_tran,
                       const unsigned char *ref_seq_orig,
                       const unsigned char *ref_seq_tran_rc,
                       const unsigned char *ref_seq_orig_rc,
                       GthChain *chain,
                       GthDNACompletePathMatrixJT dna_complete_path_matrix_jt,
                       GthProteinCompletePathMatrixJT
                       protein_complete_path_matrix_jt)
{
  int rval;
  bool bothstrandsanalyzed, firstdp = true,
       GT_UNUSED gs2outdirectmatches = directmatches;
  GthSA *saB = NULL;
  GtFile *outfp = call_info->out->outfp;

  if (directmatches ? gth_input_forward(input)
                    : gth_input_reverse(input)) {
    /* calculate alignment */
    rval = callsahmt(true, saA, directmatches, gen_file_num, ref_file_num,
                     chain, gen_total_length, gen_offset, gen_seq_bounds,
                     gen_seq_bounds_rc,
                     ref_seq_tran, ref_seq_orig, ref_total_length, ref_offset,
                     input, &call_info->simfilterparam.introncutoutinfo, stat,
                     chainctr, num_of_chains, call_info->translationtable,
                     directmatches, call_info->proteinexonpenal,
                     call_info->splice_site_model, call_info->dp_options_core,
                     call_info->dp_options_est, call_info->dp_options_postpro,
                     dna_complete_path_matrix_jt,
                     protein_complete_path_matrix_jt, call_info->out);
    if (rval && rval != GTH_ERROR_SA_COULD_NOT_BE_DETERMINED) {
                     /* ^ this error is treated below */
      return rval;
    }

    firstdp = false;
    bothstrandsanalyzed = gth_input_both(input);

    if (rval == GTH_ERROR_SA_COULD_NOT_BE_DETERMINED ||
        isunsuccessfulalignment(saA, call_info->out->comments, outfp)) {
      match_info->call_number--;
      /* if the spliced alignment was unsuccessful, it is deleted and the
         next hit is considered. */
      gth_sa_delete(saA);
      return 0; /* continue */
    }

    /* if not both strands are analyzed, we can save this alignment now.
       Otherwise we have to calculate the alignment to the other strand
       first and then save the better one. */
    if (!bothstrandsanalyzed)
      save_sa(sa_collection, saA, call_info->sa_filter, match_info, stat);
  }

  if (directmatches ? gth_input_reverse(input)
                    : gth_input_forward(input)) {
    if ((firstdp || gth_sa_is_poor(saA, call_info->minaveragessp)) &&
        !call_info->cdnaforwardonly) {
      if (firstdp) {
        /* space for first alignment is already allocated, bu we have to
           change the direction of the genomic and the reference strand */
        gth_sa_set_gen_strand(saA, !directmatches);
        gth_sa_set_ref_strand(saA, false);
      }
      else {
        /* allocating space for second alignment */
        saB = gth_sa_new_and_set(!directmatches, false, input,
                                 chain->gen_file_num, chain->gen_seq_num,
                                 chain->ref_file_num, chain->ref_seq_num,
                                 match_info->call_number, gen_total_length,
                                 gen_offset, ref_total_length);
      }

      /* setting gs2outdirectmatches (for compatibility) */
      gs2outdirectmatches = (bool) !directmatches;

      /* calculate alignment */
      rval = callsahmt(true, firstdp ? saA : saB, !directmatches,
                       gen_file_num, ref_file_num, chain, gen_total_length,
                       gen_offset, gen_seq_bounds, gen_seq_bounds_rc,
                       ref_seq_tran_rc, ref_seq_orig_rc, ref_total_length,
                       ref_offset, input,
                       &call_info->simfilterparam.introncutoutinfo, stat,
                       chainctr, num_of_chains, call_info->translationtable,
                       directmatches, call_info->proteinexonpenal,
                       call_info->splice_site_model, call_info->dp_options_core,
                       call_info->dp_options_est, call_info->dp_options_postpro,
                       dna_complete_path_matrix_jt,
                       protein_complete_path_matrix_jt, call_info->out);
      if (rval && rval != GTH_ERROR_SA_COULD_NOT_BE_DETERMINED) {
                       /* ^ this error is treated below */
        return rval;
      }

      if (firstdp) {
        if (rval == GTH_ERROR_SA_COULD_NOT_BE_DETERMINED ||
            isunsuccessfulalignment(saA, call_info->out->comments, outfp)) {
          /* for compatibility with GS2 */
          /* XXX: makes no sense. Possibly only if -gs2out is used. */
          match_info->significant_match_found= true;

          /* if the spliced alignment was unsuccessful, it is deleted and
             the next hit is considered. */
          gth_sa_delete(saA);
          return 0; /* continue */
        }

        save_sa(sa_collection, saA, call_info->sa_filter, match_info, stat);
      }
      else /* !firstdp */
      {
        if (rval == GTH_ERROR_SA_COULD_NOT_BE_DETERMINED ||
            isunsuccessfulalignment(saB, call_info->out->comments, outfp) ||
            !gth_sa_B_is_better_than_A(saA, saB)) {
          /* insert first SA */
          save_sa(sa_collection, saA, call_info->sa_filter, match_info, stat);
          /* discard second SA */
          gth_sa_delete(saB);
        }
        else {
          /* insert second SA */
          save_sa(sa_collection, saB, call_info->sa_filter, match_info, stat);
          /* free first SA */
          gth_sa_delete(saA);
        }
      }
    }
    else
      save_sa(sa_collection, saA, call_info->sa_filter, match_info, stat);
  }

  return 0;
}

static int call_protein_DP(bool directmatches,
                           GthCallInfo *call_info,
                           GthInput *input,
                           GthStat *stat,
                           GthSACollection *sa_collection,
                           GthSA *saA,
                           unsigned long gen_file_num,
                           unsigned long ref_file_num,
                           unsigned long gen_total_length,
                           unsigned long gen_offset,
                           const GtRange *gen_seq_bounds,
                           const GtRange *gen_seq_bounds_rc,
                           unsigned long ref_total_length,
                           unsigned long ref_offset,
                           unsigned long chainctr,
                           unsigned long num_of_chains,
                           GthMatchInfo *match_info,
                           const unsigned char *ref_seq_tran,
                           const unsigned char *ref_seq_orig,
                           GthChain *chain,
                           GthDNACompletePathMatrixJT
                           dna_complete_path_matrix_jt,
                           GthProteinCompletePathMatrixJT
                           protein_complete_path_matrix_jt)
{
  GtFile *outfp = call_info->out->outfp;
  int rval;

#ifndef NDEBUG
  /* strand is in searchmode */
  if (directmatches)
    gt_assert(gth_input_forward(input));
  else
    gt_assert(gth_input_reverse(input));
#endif

  /* calculate alignment */
  rval = callsahmt(false, saA, directmatches, gen_file_num, ref_file_num,
                   chain, gen_total_length, gen_offset, gen_seq_bounds,
                   gen_seq_bounds_rc, ref_seq_tran, ref_seq_orig,
                   ref_total_length, ref_offset, input,
                   &call_info->simfilterparam.introncutoutinfo, stat, chainctr,
                   num_of_chains, call_info->translationtable, directmatches,
                   call_info->proteinexonpenal, call_info->splice_site_model,
                   call_info->dp_options_core, call_info->dp_options_est,
                   call_info->dp_options_postpro, dna_complete_path_matrix_jt,
                   protein_complete_path_matrix_jt, call_info->out);
  if (rval && rval != GTH_ERROR_SA_COULD_NOT_BE_DETERMINED) {
                   /* ^ this error is treated below */
    return rval;
  }

  if (rval == GTH_ERROR_SA_COULD_NOT_BE_DETERMINED ||
      isunsuccessfulalignment(saA, call_info->out->comments, outfp)) {
    match_info->call_number--;
    /* if the spliced alignment was unsuccessful, it is deleted and the
       next hit is considered. */
    gth_sa_delete(saA);
    /* continue */
    return 0;
  }

  /* we can save the alignment now */
  save_sa(sa_collection, saA, call_info->sa_filter, match_info, stat);

  return 0;
}

static void show_no_match_line(GthAlphatype overallalphatype, GtFile *outfp)
{
  gt_file_xprintf(outfp, "\nNo significant ");
  switch (overallalphatype)
  {
    case DNA_ALPHA:
      gt_file_xprintf(outfp, "EST");
      break;
    case PROTEIN_ALPHA:
      gt_file_xprintf(outfp, "protein");
      break;
    default: gt_assert(0);
  }
  gt_file_xprintf(outfp, " matches were found.\n");
}

static GthChainCollection* match_and_chain(GthCallInfo *call_info,
                                           GthInput *input,
                                           GthStat *stat,
                                           unsigned long gen_file_num,
                                           unsigned long ref_file_num,
                                           bool directmatches,
                                           GthMatchInfo *match_info,
                                           const GthPlugins *plugins)
{
  GtFile *outfp = call_info->out->outfp;
  GthChainCollection *chain_collection = gth_chain_collection_new();

  /* compute the chains */
  gth_chaining(chain_collection, gen_file_num, ref_file_num, call_info, input,
               stat, directmatches, plugins);

  /* update statistics */
  gth_stat_increase_numofchains(stat,
                                gth_chain_collection_size(chain_collection));

  /* stop after chaining phase */
  if (call_info->simfilterparam.stopafterchaining) {
    gth_chain_collection_delete(chain_collection);
    return NULL;
  }

  if (call_info->out->showverbose)
    call_info->out->showverbose("calculate spliced alignment for every chain");

  if (!gth_chain_collection_size(chain_collection)) {
    /* no matches found -> return */
    if (!call_info->out->xmlout && !call_info->out->gff3out && !directmatches &&
        !match_info->significant_match_found) {
      show_no_match_line(gth_input_get_alphatype(input, ref_file_num), outfp);
    }
    gth_chain_collection_delete(chain_collection);
    return NULL;
  }

  return chain_collection;
}

static int calc_spliced_alignments(GthSACollection *sa_collection,
                                   GthChainCollection *chain_collection,
                                   GthCallInfo *call_info,
                                   GthInput *input,
                                   GthStat *stat,
                                   unsigned long gen_file_num,
                                   unsigned long ref_file_num,
                                   bool directmatches,
                                   GthMatchInfo *match_info,
                                   GthDNACompletePathMatrixJT
                                   dna_complete_path_matrix_jt,
                                   GthProteinCompletePathMatrixJT
                                   protein_complete_path_matrix_jt)
{
  const unsigned char *ref_seq_tran, *ref_seq_orig, *ref_seq_tran_rc = NULL,
                      *ref_seq_orig_rc = NULL;
  unsigned long chainctr, gen_offset = GT_UNDEF_ULONG, gen_total_length,
                ref_total_length;
  GtFile *outfp = call_info->out->outfp;
  GtRange gen_seq_bounds, gen_seq_bounds_rc;
  bool refseqisdna;
  GthChain *chain;
  GtRange range;
  GthSA *saA;
  int rval;

  gt_assert(sa_collection && chain_collection);

  refseqisdna = gth_input_ref_file_is_dna(input, ref_file_num);

  for (chainctr = 0;
       chainctr < gth_chain_collection_size(chain_collection);
       chainctr++) {
       chain = gth_chain_collection_get(chain_collection, chainctr);
    if (++match_info->call_number > call_info->firstalshown &&
        call_info->firstalshown > 0) {
      if (!(call_info->out->xmlout || call_info->out->gff3out))
        gt_file_xfputc('\n', outfp);
      else if (call_info->out->xmlout)
        gt_file_xprintf(outfp, "\n");

      match_info->max_call_number_reached = true;
      break; /* break out of loop */
    }

    /* compute considered genomic regions if not set by -frompos */
    if (!gth_input_use_substring_spec(input)) {
      gen_seq_bounds = gth_input_get_genomic_range(input, chain->gen_file_num,
                                                   chain->gen_seq_num);
      gen_total_length      = gt_range_length(&gen_seq_bounds);
      gen_offset            = gen_seq_bounds.start;
      gen_seq_bounds_rc     = gen_seq_bounds;
    }
    else {
      /* genomic multiseq contains exactly one sequence */
      gt_assert(gth_input_num_of_gen_seqs(input, chain->gen_file_num) == 1);
      gen_total_length = gth_input_genomic_file_total_length(input,
                                                             chain
                                                             ->gen_file_num);
      gen_seq_bounds.start    = gth_input_genomic_substring_from(input);
      gen_seq_bounds.end      = gth_input_genomic_substring_to(input);
      gen_offset              = 0;
      gen_seq_bounds_rc.start = gen_total_length - 1 - gen_seq_bounds.end;
      gen_seq_bounds_rc.end   = gen_total_length - 1 - gen_seq_bounds.start;
    }

    /* "retrieving" the reference sequence */
    range = gth_input_get_reference_range(input, chain->ref_file_num,
                                          chain->ref_seq_num);
    ref_seq_tran = gth_input_current_ref_seq_tran(input) + range.start;
    ref_seq_orig = gth_input_current_ref_seq_orig(input) + range.start;
    if (refseqisdna) {
      ref_seq_tran_rc = gth_input_current_ref_seq_tran_rc(input) + range.start;
      ref_seq_orig_rc = gth_input_current_ref_seq_orig_rc(input) + range.start;
    }
    ref_total_length = range.end - range.start + 1;

    /* check if protein sequences have a stop amino acid */
    if (!refseqisdna && !match_info->stop_amino_acid_warning &&
       ref_seq_orig[ref_total_length - 1] != GT_STOP_AMINO) {
      GtStr *ref_id = gt_str_new();
      gth_input_save_ref_id(input, ref_id, chain->ref_file_num,
                            chain->ref_seq_num);
      gt_warning("protein sequence '%s' (#%lu in file %s) does not end with a "
                 "stop amino acid ('%c'). If it is not a protein fragment you "
                 "should add a stop amino acid to improve the prediction. "
                 "For example with `gt seqtransform -addstopaminos` (see "
                 "http://genometools.org for details).", gt_str_get(ref_id),
                 chain->ref_seq_num,
                 gth_input_get_reference_filename(input, chain->ref_file_num),
                 GT_STOP_AMINO);
      match_info->stop_amino_acid_warning = true;
      gt_str_delete(ref_id);
    }

    /* allocating space for alignment */
    saA = gth_sa_new_and_set(directmatches, true, input, chain->gen_file_num,
                             chain->gen_seq_num, chain->ref_file_num,
                             chain->ref_seq_num, match_info->call_number,
                             gen_total_length, gen_offset, ref_total_length);

    /* extend the DP borders to the left and to the right */
    gth_chain_extend_borders(chain, &gen_seq_bounds, &gen_seq_bounds_rc,
                             gen_total_length, gen_offset);

    /* From here on the dp positions always refer to the forward strand of the
       genomic DNA. */

    /* call the Dynamic Programming */
    if (refseqisdna) {
      rval = call_dna_DP(directmatches, call_info, input, stat,
                         sa_collection, saA, gen_file_num, ref_file_num,
                         gen_total_length, gen_offset, &gen_seq_bounds,
                         &gen_seq_bounds_rc, ref_total_length, range.start,
                         chainctr, gth_chain_collection_size(chain_collection),
                         match_info, ref_seq_tran, ref_seq_orig,
                         ref_seq_tran_rc, ref_seq_orig_rc, chain,
                         dna_complete_path_matrix_jt,
                         protein_complete_path_matrix_jt);
    }
    else {
      rval = call_protein_DP(directmatches, call_info, input,
                             stat, sa_collection, saA, gen_file_num,
                             ref_file_num, gen_total_length, gen_offset,
                             &gen_seq_bounds, &gen_seq_bounds_rc,
                             ref_total_length, range.start, chainctr,
                             gth_chain_collection_size(chain_collection),
                             match_info, ref_seq_tran, ref_seq_orig, chain,
                             dna_complete_path_matrix_jt,
                             protein_complete_path_matrix_jt);
    }
    /* check return value */
    if (rval == GTH_ERROR_DP_PARAMETER_ALLOCATION_FAILED) {
      /* statistics bookkeeping */
      gth_stat_increment_numoffailedDPparameterallocations(stat);
      gth_stat_increment_numofundeterminedSAs(stat);
      /* free space */
      gth_sa_delete(saA);
      match_info->call_number--;
      continue; /* continue with the next DP range */
    }
    else if (rval)
      return -1;
  }

  if (!call_info->out->xmlout && !call_info->out->gff3out && !directmatches &&
      !match_info->significant_match_found &&
      match_info->call_number <= call_info->firstalshown) {
    show_no_match_line(gth_input_get_alphatype(input, ref_file_num), outfp);
  }

  return 0;
}

static void show_compute_matches_status(bool direct, GthShowVerbose showverbose,
                                        unsigned long gen_file_num,
                                        unsigned long num_of_gen_files,
                                        unsigned long ref_file_num,
                                        unsigned long num_of_ref_files)
{
  char buf[SHOW_COMPUTE_MATCHES_STATUS_BUF_SIZE];
  GT_UNUSED int rval;
  gt_assert(num_of_gen_files && num_of_ref_files );
  if (num_of_gen_files == 1 && num_of_ref_files == 1) {
    if (direct)
      showverbose("compute direct matches");
    else
      showverbose("compute palindromic matches");
  }
  else {
    if (direct) {
      rval = snprintf(buf, SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE,
                      "compute direct matches for genomic file (gf) %lu/%lu "
                      "and reference file (rf) %lu/%lu",
                      gen_file_num + 1, num_of_gen_files,
                      ref_file_num + 1, num_of_ref_files);
    }
    else {
      rval = snprintf(buf, SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE,
                      "compute palindromic matches for genomic file (gf) "
                      "%lu/%lu and reference file (rf) %lu/%lu",
                      gen_file_num + 1,  num_of_gen_files,
                      ref_file_num + 1,  num_of_ref_files);
    }
    /* buf[SHOW_COMPUTE_MATCHES_STATUS_BUF_SIZE] is large enough */
    gt_assert(rval < SHOW_MATRIX_CALCULATION_STATUS_BUF_SIZE);
    showverbose(buf);
  }
}

static int compute_sa_collection(GthSACollection *sa_collection,
                                 GthCallInfo *call_info,
                                 GthInput *input,
                                 GthStat *stat,
                                 const GthPlugins *plugins)
{
  GthChainCollection *chain_collection;
  GthMatchInfo match_info;
  unsigned long g, r;
  int rval = 0;

  match_info.call_number = 0;
  match_info.significant_match_found = false;
  match_info.max_call_number_reached = false;
  match_info.stop_amino_acid_warning = false;

  for (g = 0; g < gth_input_num_of_gen_files(input); g++) {
    for (r = 0; r < gth_input_num_of_ref_files(input); r++) {
      if (gth_input_get_alphatype(input, r) == DNA_ALPHA ||
          gth_input_forward(input)) {
        if (call_info->out->showverbose) {
          show_compute_matches_status(true, call_info->out->showverbose, g,
                                      gth_input_num_of_gen_files(input), r,
                                      gth_input_num_of_ref_files(input));
        }
        /* compute direct matches */
        chain_collection = match_and_chain(call_info, input, stat, g, r, true,
                                           &match_info, plugins);
        if (chain_collection) {
          rval = calc_spliced_alignments(sa_collection, chain_collection,
                                         call_info, input, stat, g, r, true,
                                         &match_info,
                                         plugins->dna_complete_path_matrix_jt,
                                         plugins
                                         ->protein_complete_path_matrix_jt);
          gth_chain_collection_delete(chain_collection);
          if (rval)
            break;
        }
      }
      if (match_info.max_call_number_reached)
        break;

      if (gth_input_get_alphatype(input, r) == DNA_ALPHA ||
          gth_input_reverse(input)) {
        if (call_info->out->showverbose) {
          show_compute_matches_status(false, call_info->out->showverbose, g,
                                      gth_input_num_of_gen_files(input), r,
                                      gth_input_num_of_ref_files(input));
        }
        /* compute reverse complemented (palindromic) matches */
        chain_collection = match_and_chain(call_info, input, stat, g, r, false,
                                           &match_info, plugins);
        if (chain_collection) {
          rval = calc_spliced_alignments(sa_collection, chain_collection,
                                         call_info, input, stat, g, r, false,
                                         &match_info,
                                         plugins->dna_complete_path_matrix_jt,
                                         plugins
                                         ->protein_complete_path_matrix_jt);
          gth_chain_collection_delete(chain_collection);
          if (rval)
            break;
        }
        if (match_info.max_call_number_reached)
          break;
      }
    }
  }

  return rval;
}

int gth_similarity_filter(GthCallInfo *call_info, GthInput *input,
                          GthStat *stat, unsigned int indentlevel,
                          const GthPlugins *plugins, GT_UNUSED GtError *err)
{
  GthSACollection *sa_collection; /* stores the calculated spliced alignments */

  gt_error_check(err);

  /* initialization */
  sa_collection = gth_sa_collection_new(call_info->duplicate_check);

  /* compute the spliced alignments */
  if (compute_sa_collection(sa_collection, call_info, input, stat, plugins)) {
    gth_sa_collection_delete(sa_collection);
    return -1;
  }

  /* process the alignments */
  gth_proc_sa_collection(sa_collection, call_info, input, stat, indentlevel);

  /* show XML trailer */
  if (call_info->out->xmlout) {
    gth_xml_show_trailer(call_info->intermediate, call_info->out->outfp);
  }

  /* output statistics */
  if (!call_info->out->gff3out)
    gth_stat_show(stat, true, call_info->out->xmlout, call_info->out->outfp);

#ifndef NDEBUG
  if (call_info->intermediate && call_info->out->outputfile) {
    /* intermediate output equals tree of alignments */
    gt_assert(gth_intermediate_output_is_correct(call_info->out->outputfile,
                                                 sa_collection, input,
                                                 &call_info->out->outfp, err));
  }
#endif

  /* free spliced alignment collection */
  gth_sa_collection_delete(sa_collection);

  return 0;
}
genometools-1.5.1/src/gth/similarity_filter.h000066400000000000000000000022031211610345200213160ustar00rootroot00000000000000/*
  Copyright (c) 2003-2009 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SIMILARITY_FILTER_H
#define SIMILARITY_FILTER_H

#include "gth/plugins.h"
#include "gth/stat.h"

int gth_similarity_filter(GthCallInfo*, GthInput*, GthStat*,
                          unsigned int indentlevel, const GthPlugins *plugins,
                          GtError*);

#endif
genometools-1.5.1/src/gth/splice_site_model.c000066400000000000000000000101571211610345200212500ustar00rootroot00000000000000/*
  Copyright (c) 2005-2010 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma_api.h"
#include "gth/default.h"
#include "gth/bssm_param.h"
#include "gth/splice_site_model_rep.h"

#define SET_PROB_VALUE(V, PROB)                           \
        ssm->V             = PROB;                        \
        ssm->log_##V       = (GthFlt) log(PROB); \
        ssm->log1minus_##V = (GthFlt) log(1.0 - (PROB))

GthSpliceSiteModel* gth_splice_site_model_new(void)
{
  GthSpliceSiteModel *ssm = gt_malloc(sizeof *ssm);

  ssm->useU12intronmodel = !GTH_DEFAULT_DISABLEU12INTRONMODEL;

  SET_PROB_VALUE(genericGTdonorprob, GTH_DEFAULT_GENERIC_GT_DONORPROB);
  SET_PROB_VALUE(nongenericGTdonorprob, GTH_DEFAULT_NONGENERIC_GT_DONORPROB);
  SET_PROB_VALUE(genericGCdonorprob, GTH_DEFAULT_GENERIC_GC_DONORPROB);
  SET_PROB_VALUE(nongenericGCdonorprob, GTH_DEFAULT_NONGENERIC_GC_DONORPROB);
  SET_PROB_VALUE(genericATdonorprob, GTH_DEFAULT_GENERIC_AT_DONORPROB);
  SET_PROB_VALUE(nongenericATdonorprob, GTH_DEFAULT_NONGENERIC_AT_DONORPROB);
  SET_PROB_VALUE(genericAGacceptorprob, GTH_DEFAULT_GENERIC_AG_ACCEPTORPROB);
  SET_PROB_VALUE(nongenericAGacceptorprob,
                 GTH_DEFAULT_NONGENERIC_AG_ACCEPTORPROB);
  SET_PROB_VALUE(genericACacceptorprob, GTH_DEFAULT_GENERIC_AC_ACCEPTORPROB);
  SET_PROB_VALUE(nongenericACacceptorprob,
                 GTH_DEFAULT_NONGENERIC_AC_ACCEPTORPROB);
  SET_PROB_VALUE(genericothersplicesitep,
                 GTH_DEFAULT_GENERIC_OTHERSPLICESITEPROB);
  SET_PROB_VALUE(nongenericothersplicesitep,
                 GTH_DEFAULT_NONGENERIC_OTHERSPLICESITEPROB);
  gth_splice_site_model_set_U12typedonorprob(ssm,
                                             GTH_DEFAULT_U12_TYPEDONORPROB);
  gth_splice_site_model_set_U12typedonorprob_one_mismatch(ssm,
                                      GTH_DEFAULT_U12_TYPEDONORPROBONEMISMATCH);

  ssm->bssm_param = NULL;

  return ssm;
}

void gth_splice_site_model_delete(GthSpliceSiteModel *ssm)
{
  if (!ssm) return;
  gth_bssm_param_delete(ssm->bssm_param);
  gt_free(ssm);
}

int gth_splice_site_model_load_bssm(GthSpliceSiteModel *ssm,
                                    const char *bssmfile, GtError *err)
{
  GtStr *bssmfilename;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(ssm && bssmfile && strlen(bssmfile));
  if (ssm->bssm_param) {
    gth_bssm_param_delete(ssm->bssm_param);
    ssm->bssm_param = NULL;
  }
  bssmfilename = gt_str_new();
  gt_str_append_cstr(bssmfilename, bssmfile);
  gt_str_append_char(bssmfilename, '.');
  gt_str_append_cstr(bssmfilename, BSSMFILEENDING);
  if (!(ssm->bssm_param = gth_bssm_param_load(gt_str_get(bssmfilename), err)))
    had_err = -1;
  gt_str_delete(bssmfilename);
  return had_err;
}

void gth_splice_site_model_U12intronmodel_set_usage(GthSpliceSiteModel *ssm,
                                                    bool useU12intronmodel)
{
  ssm->useU12intronmodel = useU12intronmodel;
}

void gth_splice_site_model_set_U12typedonorprob(GthSpliceSiteModel *ssm,
                                                GthFlt prob)
{
  SET_PROB_VALUE(U12typedonorprob, prob);
}

void gth_splice_site_model_set_U12typedonorprob_one_mismatch(GthSpliceSiteModel
                                                             *ssm,
                                                             GthFlt prob)
{
  SET_PROB_VALUE(U12typedonorprobonemismatch, prob);
}
genometools-1.5.1/src/gth/splice_site_model.h000066400000000000000000000037651211610345200212640ustar00rootroot00000000000000/*
  Copyright (c) 2005-2009 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SPLICE_SITE_MODEL_H
#define SPLICE_SITE_MODEL_H

#include "core/error.h"

/* generic splice site model */
typedef struct GthSpliceSiteModel GthSpliceSiteModel;

GthSpliceSiteModel* gth_splice_site_model_new(void);
void                gth_splice_site_model_delete(GthSpliceSiteModel*);
int                 gth_splice_site_model_load_bssm(GthSpliceSiteModel*,
                                                    const char *bssmfile,
                                                    GtError*);
void                gth_splice_site_model_U12intronmodel_set_usage(
                                                        GthSpliceSiteModel*,
                                                        bool useU12intronmodel);
void                gth_splice_site_model_set_U12typedonorprob(
                                                        GthSpliceSiteModel*,
                                                        GthFlt prob);
void                gth_splice_site_model_set_U12typedonorprob_one_mismatch(
                                                        GthSpliceSiteModel*,
                                                        GthFlt prob);

#endif
genometools-1.5.1/src/gth/splice_site_model_rep.h000066400000000000000000000066261211610345200221310ustar00rootroot00000000000000/*
  Copyright (c) 2005-2009 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SPLICE_SITE_MODEL_REP_H
#define SPLICE_SITE_MODEL_REP_H

#include "gth/splice_site_model.h"

struct GthSpliceSiteModel {
  /* the probabilities */
  GthFlt genericGTdonorprob,          /*     generic prob. of GT donor */
         nongenericGTdonorprob,       /* non-generic prob. of GT donor */
         genericGCdonorprob,          /*     generic prob. of GC donor */
         nongenericGCdonorprob,       /* non-generic prob. of GC donor */
         genericATdonorprob,          /*     generic prob. of AT donor */
         nongenericATdonorprob,       /* non-generic prob. of AT donor */
         genericAGacceptorprob,       /*     generic prob. of AG acceptor */
         nongenericAGacceptorprob,    /* non-generic prob. of AG acceptor */
         genericACacceptorprob,       /*     generic prob. of AC acceptor */
         nongenericACacceptorprob,    /* non-generic prob. of AC acceptor */
         genericothersplicesitep,     /*     generic prob. of other sp. sites */
         nongenericothersplicesitep;  /* non-generic prob. of other sp. sites */
  bool useU12intronmodel;             /* enable U12 intron model */
  GthFlt U12typedonorprob,            /* prob. of U12-type donor */
         U12typedonorprobonemismatch; /* prob. of U12-type donor with 1
                                         mismatch */

  /* the precomputed log values */
  GthFlt log_genericGTdonorprob,
         log1minus_genericGTdonorprob,
         log_nongenericGTdonorprob,
         log1minus_nongenericGTdonorprob,
         log_genericGCdonorprob,
         log1minus_genericGCdonorprob,
         log_nongenericGCdonorprob,
         log1minus_nongenericGCdonorprob,
         log_genericATdonorprob,
         log1minus_genericATdonorprob,
         log_nongenericATdonorprob,
         log1minus_nongenericATdonorprob,
         log_genericAGacceptorprob,
         log1minus_genericAGacceptorprob,
         log_nongenericAGacceptorprob,
         log1minus_nongenericAGacceptorprob,
         log_genericACacceptorprob,
         log1minus_genericACacceptorprob,
         log_nongenericACacceptorprob,
         log1minus_nongenericACacceptorprob,
         log_genericothersplicesitep,
         log1minus_genericothersplicesitep,
         log_nongenericothersplicesitep,
         log1minus_nongenericothersplicesitep,
         log_U12typedonorprob,
         log1minus_U12typedonorprob,
         log_U12typedonorprobonemismatch,
         log1minus_U12typedonorprobonemismatch;

  GthBSSMParam *bssm_param; /* contains bssm parameters or is NULL,
                              if generic parameters are used. */
};

#endif
genometools-1.5.1/src/gth/spliced_seq.c000066400000000000000000000132771211610345200200660ustar00rootroot00000000000000/*
  Copyright (c) 2004-2009 Gordon Gremme 
  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/range.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "gth/gthoutput.h"
#include "gth/spliced_seq.h"

static void fillsplicedseq(unsigned char *splicedseq,
                           const unsigned char *origseq, GtArray *ranges)
{
  const unsigned char *genomicptr;
  unsigned long i;
  gt_assert(ranges);
  for (i = 0; i < gt_array_size(ranges); i++) {
    for (genomicptr = origseq + ((GtRange*) gt_array_get(ranges, i))->start;
         genomicptr <= origseq +
                       ((GtRange*) gt_array_get(ranges, i))->end;
         *splicedseq++ = *genomicptr++);
  }
}

static void computepositionmapping(unsigned long *positionmapping,
                                   GtArray *ranges,
                                   GT_UNUSED unsigned long splicedseqlen)
{
  unsigned long i, rangecounter, templatepos = 0;
  for (rangecounter = 0; rangecounter < gt_array_size(ranges); rangecounter++) {
    for (i = ((GtRange*) gt_array_get(ranges, rangecounter))->start;
         i <= ((GtRange*) gt_array_get(ranges, rangecounter))->end;
         i++) {
      positionmapping[templatepos++] = i;
    }
  }
  gt_assert(templatepos == splicedseqlen);
}

GthSplicedSeq* gth_spliced_seq_new(const unsigned char *sequence,
                                   GtArray *ranges)
{
  GthSplicedSeq *spliced_seq = gt_malloc(sizeof *spliced_seq);

  gt_assert(sequence && ranges);

  spliced_seq->origseq = sequence;
  spliced_seq->ranges  = ranges;

  gt_assert(gt_ranges_are_consecutive(ranges));

  /* save total length of ranges */
  spliced_seq->splicedseqlen = gt_ranges_total_length(ranges);

  /* allocate space */
  spliced_seq->splicedseq = gt_malloc(sizeof (unsigned char) *
                                      spliced_seq->splicedseqlen);
  spliced_seq->positionmapping = gt_malloc(sizeof (unsigned long) *
                                           spliced_seq->splicedseqlen);

  /* processing */
  fillsplicedseq(spliced_seq->splicedseq, spliced_seq->origseq,
                 spliced_seq->ranges);

  /* compute position mapping */
  computepositionmapping(spliced_seq->positionmapping, spliced_seq->ranges,
                         spliced_seq->splicedseqlen);

  return spliced_seq;
}

GthSplicedSeq* gth_spliced_seq_new_with_comments(const unsigned char *sequence,
                                                 GtArray *ranges, bool comments,
                                                 GtFile *outfp)
{
  GthSplicedSeq *spliced_seq;
  gt_assert(sequence && ranges);
  spliced_seq = gth_spliced_seq_new(sequence, ranges);
  gt_assert(spliced_seq);
  if (comments) {
    double fraction = ((double) spliced_seq->splicedseqlen /
                       (double) gt_ranges_spanned_length(ranges)) * 100.0;
    /* fraction is valid percent value */
    gt_assert(fraction >= 0.0 && fraction <= 100.0);
    gt_file_xprintf(outfp,
                       "%c spliced sequence is %.2f%% of original sequence\n",
                       COMMENTCHAR, fraction);
  }
  return spliced_seq;
}

void gth_spliced_seq_delete(GthSplicedSeq *spliced_seq)
{
  if (!spliced_seq) return;
  gt_free(spliced_seq->splicedseq);
  gt_free(spliced_seq->positionmapping);
  gt_free(spliced_seq);
}

bool gth_spliced_seq_pos_is_border(const GthSplicedSeq *spliced_seq,
                                   unsigned long position)
{
  gt_assert(spliced_seq);
  /* position is legal */
  gt_assert(position < spliced_seq->splicedseqlen);
  if ((position + 1 < spliced_seq->splicedseqlen) &&
      (spliced_seq->positionmapping[position] + 1 !=
       spliced_seq->positionmapping[position+1])) {
    return true;
  }
  return false;
}

unsigned long gth_spliced_seq_border_length(const GthSplicedSeq *spliced_seq,
                                            unsigned long position)
{
  gt_assert(gth_spliced_seq_pos_is_border(spliced_seq, position));
  return spliced_seq->positionmapping[position+1] -
         spliced_seq->positionmapping[position] - 1;
}

unsigned long gth_spliced_seq_num_of_borders(const GthSplicedSeq *spliced_seq)
{
  unsigned long i, borders = 0;
  gt_assert(spliced_seq);
  for (i = 0; i < spliced_seq->splicedseqlen; i++) {
    if (gth_spliced_seq_pos_is_border(spliced_seq, i))
      borders++;
  }
  return borders;
}

static int cmpulong(const void *u1, const void *u2)
{
  return *(unsigned long*) u1 - *(unsigned long*) u2;
}

unsigned long gth_spliced_seq_orig_to_spliced_pos(const GthSplicedSeq
                                                  *spliced_seq,
                                                  unsigned long orig_pos)
{
  unsigned long *splicedposptr ;
  gt_assert(spliced_seq);
  splicedposptr = bsearch(&orig_pos, spliced_seq->positionmapping,
                          spliced_seq->splicedseqlen,
                          sizeof (unsigned long), cmpulong);
  if (splicedposptr)
    return splicedposptr - spliced_seq->positionmapping;
  return GT_UNDEF_ULONG;
}
genometools-1.5.1/src/gth/spliced_seq.h000066400000000000000000000050431211610345200200630ustar00rootroot00000000000000/*
  Copyright (c) 2004-2009 Gordon Gremme 
  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SPLICED_SEQ_H
#define SPLICED_SEQ_H

#include "core/array_api.h"
#include "core/file.h"

typedef struct {
  GtArray *ranges;                /* the ranges of the genomic sequence which
                                     have been used for processing */
  const unsigned char *origseq;   /* the original sequence */
        unsigned char *splicedseq;/* the processed sequence */
  unsigned long splicedseqlen,    /* the length of the processed sequence */
                *positionmapping; /* maps the positions on the spliced sequence
                                     back to the original sequence */
} GthSplicedSeq;

GthSplicedSeq* gth_spliced_seq_new(const unsigned char *sequence,
                                   GtArray *ranges);
GthSplicedSeq* gth_spliced_seq_new_with_comments(const unsigned char *sequence,
                                                 GtArray *ranges, bool comments,
                                                 GtFile *outfp);
void           gth_spliced_seq_delete(GthSplicedSeq*);
bool           gth_spliced_seq_pos_is_border(const GthSplicedSeq*,
                                             unsigned long position);
unsigned long  gth_spliced_seq_border_length(const GthSplicedSeq*,
                                             unsigned long position);
unsigned long  gth_spliced_seq_num_of_borders(const GthSplicedSeq*);
/* The following function computes the spliced sequence position of a given
   original position  of a position mapping  of length
    via binary search. */
unsigned long  gth_spliced_seq_orig_to_spliced_pos(const GthSplicedSeq*,
                                                   unsigned long orig_pos);

#endif
genometools-1.5.1/src/gth/stat.c000066400000000000000000000367271211610345200165530ustar00rootroot00000000000000/*
  Copyright (c) 2004-2010 Gordon Gremme 
  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/safearith.h"
#include "gth/default.h"
#include "gth/gthoutput.h"
#include "gth/time.h"
#include "gth/stat.h"

#define INFOCHAR\
        if (!stat->gthfilestat_mode) {          \
          gt_file_xprintf(outfp, "%c ", COMMENTCHAR); \
        }

struct GthStat {
  bool exondistri,       /* compute/output exon length distribution */
       introndistri,     /* compute/output intron length distribution */
       matchnumdistri,   /* compute/output match number distribution */
       refseqcovdistri,  /* compute/output reference sequence coverage
                            distribution */
       sa_stats,         /* compute/output spliced alignment statistics (e.g.,
                            alignment score and coverage distributions) */
       gthfilestat_mode; /* modify output for gthfilestat */

  unsigned long numofchains,             /* total number of computed chains */
       numofremovedzerobaseexons,        /* see function replacezerobaseexons()
                                            for explanation */
       numofautointroncutoutcalls,       /* number of times when the intron
                                            cutout technique was used
                                            automatically */
       numofunsuccessfulintroncutoutDPs, /* corresponds to
                                            ERROR_CUTOUT_NOT_IN_INTRON */
       numoffailedDPparameterallocations,/* correspoinds to
                                            ERROR_DP_PARAMETER_ALLOCATION_FAILED
                                          */
       numoffailedmatrixallocations,     /* corresponds to
                                            ERROR_MATRIX_ALLOCATION_FAILED */
       numofundeterminedSAs,             /* corresponds to
                                            ERROR_SA_COULD_NOT_BE_DETERMINED */
       numoffilteredpolyAtailmatches,    /* the number of filtered out matches
                                            which represent a matching poly(A)
                                            tail */

  /* memory statistics */
       numofSAs,                         /* number of computed SAs */
       numofPGLs_stored,                 /* number of stored PGLs */
       totalsizeofbacktracematricesinMB,
       numofbacktracematrixallocations;

  /* distributions */
  GtDiscDistri *exondistribution,
               *introndistribution,
               *matchnumdistribution,
               *refseqcoveragedistribution,
               *sa_alignment_score_distribution,
               *sa_coverage_distribution;
};

GthStat *gth_stat_new(void)
{
  GthStat *stat;

  stat = gt_malloc(sizeof (GthStat));

  stat->exondistri       = GTH_DEFAULT_EXONDISTRI;
  stat->introndistri     = GTH_DEFAULT_INTRONDISTRI;
  stat->matchnumdistri   = GTH_DEFAULT_MATCHNUMDISTRI;
  stat->refseqcovdistri  = GTH_DEFAULT_REFSEQCOVDISTRI;
  stat->sa_stats         = false;
  stat->gthfilestat_mode = false;

  stat->numofchains                       = 0;
  stat->numofremovedzerobaseexons         = 0;
  stat->numofautointroncutoutcalls        = 0;
  stat->numofunsuccessfulintroncutoutDPs  = 0;
  stat->numoffailedDPparameterallocations = 0;
  stat->numoffailedmatrixallocations      = 0;
  stat->numofundeterminedSAs              = 0;
  stat->numoffilteredpolyAtailmatches     = 0;

  /* init variables for memory statistics */
  stat->numofSAs                          = 0;
  stat->numofPGLs_stored                  = 0;
  stat->totalsizeofbacktracematricesinMB  = 0;
  stat->numofbacktracematrixallocations   = 0;

  /* init distributions */
  stat->exondistribution = gt_disc_distri_new();
  stat->introndistribution = gt_disc_distri_new();
  stat->matchnumdistribution = gt_disc_distri_new();
  stat->refseqcoveragedistribution = gt_disc_distri_new();
  stat->sa_alignment_score_distribution = gt_disc_distri_new();
  stat->sa_coverage_distribution = gt_disc_distri_new();

  return stat;
}

void gth_stat_enable_exondistri(GthStat *stat)
{
  gt_assert(stat);
  stat->exondistri = true;
}

void gth_stat_enable_introndistri(GthStat *stat)
{
  gt_assert(stat);
  stat->introndistri= true;
}

void gth_stat_enable_matchnumdistri(GthStat *stat)
{
  gt_assert(stat);
  stat->matchnumdistri = true;
}

void gth_stat_enable_refseqcovdistri(GthStat *stat)
{
  gt_assert(stat);
  stat->refseqcovdistri = true;
}

void gth_stat_enable_sa_stats(GthStat *stat)
{
  gt_assert(stat);
  stat->sa_stats = true;
}

void gth_stat_enable_gthfilestat_mode(GthStat *stat)
{
  gt_assert(stat);
  stat->gthfilestat_mode= true;
}

void gth_stat_increment_numofunsuccessfulintroncutoutDPs(GthStat *stat)
{
  gt_assert(stat);
  stat->numofunsuccessfulintroncutoutDPs++;
}

void gth_stat_increment_numofundeterminedSAs(GthStat *stat)
{
  gt_assert(stat);
  stat->numofundeterminedSAs++;
}

void gth_stat_increment_numofautointroncutoutcalls(GthStat *stat)
{
  gt_assert(stat);
  stat->numofautointroncutoutcalls++;
}

void gth_stat_increment_numoffailedmatrixallocations(GthStat *stat)
{
  gt_assert(stat);
  stat->numoffailedmatrixallocations++;
}

void gth_stat_increment_numoffailedDPparameterallocations(GthStat *stat)
{
  gt_assert(stat);
  stat->numoffailedDPparameterallocations++;
}

void gth_stat_increment_numofbacktracematrixallocations(GthStat *stat)
{
  gt_assert(stat);
  stat->numofbacktracematrixallocations++;
}

void gth_stat_increment_numofremovedzerobaseexons(GthStat *stat)
{
  gt_assert(stat);
  stat->numofremovedzerobaseexons++;
}

void gth_stat_increment_numofSAs(GthStat *stat)
{
  gt_assert(stat);
  stat->numofSAs++;
}

void gth_stat_increase_numofchains(GthStat *stat, unsigned long addend)
{
  gt_assert(stat);
  stat->numofchains += addend;
}

void gth_stat_increase_totalsizeofbacktracematricesinMB(GthStat *stat,
                                                        unsigned long addend)
{
  gt_assert(stat);
  gt_safe_add(stat->totalsizeofbacktracematricesinMB,
              stat->totalsizeofbacktracematricesinMB, addend);
}

void gth_stat_increase_numofPGLs_stored(GthStat *stat, unsigned long addend)
{
  gt_assert(stat);
  stat->numofPGLs_stored += addend;
}

unsigned long gth_stat_get_numofSAs(GthStat *stat)
{
  gt_assert(stat);
  return stat->numofSAs;
}

bool gth_stat_get_exondistri(GthStat *stat)
{
  gt_assert(stat);
  return stat->exondistri;
}

bool gth_stat_get_introndistri(GthStat *stat)
{
  gt_assert(stat);
  return stat->introndistri;
}

GtDiscDistri* gth_stat_get_exondistribution(GthStat *stat)
{
  gt_assert(stat);
  return stat->exondistribution;
}

GtDiscDistri* gth_stat_get_introndistribution(GthStat *stat)
{
  gt_assert(stat);
  return stat->introndistribution;
}

bool gth_stat_get_matchnumdistri(GthStat *stat)
{
  gt_assert(stat);
  return stat->matchnumdistri;
}

bool gth_stat_get_refseqcovdistri(GthStat *stat)
{
  gt_assert(stat);
  return stat->refseqcovdistri;
}

void gth_stat_add_to_matchnumdistri(GthStat *stat, unsigned long data)
{
  gt_assert(stat);
  if (stat->matchnumdistri)
    gt_disc_distri_add(stat->matchnumdistribution, data);
}

void gth_stat_add_to_refseqcovdistri(GthStat *stat, unsigned long data)
{
  gt_assert(stat);
  if (stat->refseqcovdistri)
    gt_disc_distri_add(stat->refseqcoveragedistribution, data);
}

void gth_stat_add_to_sa_alignment_score_distri(GthStat *stat,
                                               unsigned long data)
{
  gt_assert(stat);
  if (stat->sa_stats)
    gt_disc_distri_add(stat->sa_alignment_score_distribution, data);
}

void gth_stat_add_to_sa_coverage_distri(GthStat *stat, unsigned long data)
{
  gt_assert(stat);
  if (stat->sa_stats)
    gt_disc_distri_add(stat->sa_coverage_distribution, data);
}

static void outputgeneralstatistics(GthStat *stat, bool show_full_stats,
                                    GtFile *outfp)
{
  gt_assert(stat);
  if (show_full_stats) {
    gt_file_xprintf(outfp, "%c general statistics:\n", COMMENTCHAR);
    switch (stat->numofchains) {
      case 0:
        gt_file_xprintf(outfp, "%c no chain has been computed\n",
                           COMMENTCHAR);
        break;
      case 1:
        gt_file_xprintf(outfp, "%c 1 chain has been computed\n",
                           COMMENTCHAR);
        break;
      default:
        gt_file_xprintf(outfp, "%c %lu chains have been computed\n",
                        COMMENTCHAR, stat->numofchains);
    }
  }
}

static void outputmemorystatistics(GthStat *stat, bool show_full_stats,
                                   GtFile *outfp)
{
  gt_assert(stat);

  /* SA memory statistics */
  INFOCHAR;
  gt_file_xprintf(outfp, "memory statistics:\n");
  INFOCHAR;
  gt_file_xprintf(outfp, "%lu spliced alignments have been stored\n",
            stat->numofSAs);

  /* PGL memory statistics */
  INFOCHAR;
  gt_file_xprintf(outfp, "%lu predicted gene locations have been stored\n",
            stat->numofPGLs_stored);

  /* DP memory statistics */
  if (show_full_stats) {
    gt_file_xprintf(outfp,
              "%c %lu megabytes was the average size of the backtrace matrix\n",
              COMMENTCHAR, (stat->numofbacktracematrixallocations > 0
                           ? stat->totalsizeofbacktracematricesinMB /
                             stat->numofbacktracematrixallocations
                           : 0));
    switch (stat->numofbacktracematrixallocations) {
      case 0:
        gt_file_xprintf(outfp, "%c no backtrace matrix has been allocated\n",
                  COMMENTCHAR);
        break;
      case 1:
        gt_file_xprintf(outfp, "%c 1 backtrace matrix has been allocated\n",
                  COMMENTCHAR);
        break;
      default:
        gt_file_xprintf(outfp,"%c %lu backtrace matrices have been "
                        "allocated\n", COMMENTCHAR,
                        stat->numofbacktracematrixallocations);
    }
  }
}

void gth_stat_show(GthStat *stat, bool show_full_stats, bool xmlout,
                   GtFile *outfp)
{
  char *timestring;

  gt_assert(stat);

  /* begin XML comment */
  if (xmlout)
    gt_file_xprintf(outfp, "\n");
}

void gth_stat_delete(GthStat *stat)
{
  if (!stat) return;
  gt_disc_distri_delete(stat->exondistribution);
  gt_disc_distri_delete(stat->introndistribution);
  gt_disc_distri_delete(stat->matchnumdistribution);
  gt_disc_distri_delete(stat->refseqcoveragedistribution);
  gt_disc_distri_delete(stat->sa_alignment_score_distribution);
  gt_disc_distri_delete(stat->sa_coverage_distribution);
  gt_free(stat);
}
genometools-1.5.1/src/gth/stat.h000066400000000000000000000061521211610345200165450ustar00rootroot00000000000000/*
  Copyright (c) 2004-2009 Gordon Gremme 
  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef STAT_H
#define STAT_H

#include 
#include "core/disc_distri_api.h"
#include "core/error.h"

/* stores all kinds of gth related statistical information */
typedef struct GthStat GthStat;

GthStat*      gth_stat_new(void);
void          gth_stat_enable_exondistri(GthStat*);
void          gth_stat_enable_introndistri(GthStat*);
void          gth_stat_enable_matchnumdistri(GthStat*);
void          gth_stat_enable_refseqcovdistri(GthStat*);
void          gth_stat_enable_sa_stats(GthStat*);
void          gth_stat_enable_gthfilestat_mode(GthStat*);
void          gth_stat_increment_numofunsuccessfulintroncutoutDPs(GthStat*);
void          gth_stat_increment_numofundeterminedSAs(GthStat*);
void          gth_stat_increment_numofautointroncutoutcalls(GthStat*);
void          gth_stat_increment_numoffailedmatrixallocations(GthStat*);
void          gth_stat_increment_numoffailedDPparameterallocations(GthStat*);
void          gth_stat_increment_numofbacktracematrixallocations(GthStat*);
void          gth_stat_increment_numofremovedzerobaseexons(GthStat*);
void          gth_stat_increment_numofSAs(GthStat*);
void          gth_stat_increase_numofchains(GthStat*, unsigned long);
void          gth_stat_increase_totalsizeofbacktracematricesinMB(GthStat*,
                                                                 unsigned long);
void          gth_stat_increase_numofPGLs_stored(GthStat*, unsigned long);
unsigned long gth_stat_get_numofSAs(GthStat*);
bool          gth_stat_get_exondistri(GthStat*);
bool          gth_stat_get_introndistri(GthStat*);
GtDiscDistri* gth_stat_get_exondistribution(GthStat*);
GtDiscDistri* gth_stat_get_introndistribution(GthStat*);
bool          gth_stat_get_matchnumdistri(GthStat*);
bool          gth_stat_get_refseqcovdistri(GthStat*);
void          gth_stat_add_to_matchnumdistri(GthStat*, unsigned long);
void          gth_stat_add_to_refseqcovdistri(GthStat*, unsigned long);
void          gth_stat_add_to_sa_alignment_score_distri(GthStat*,
                                                        unsigned long);
void          gth_stat_add_to_sa_coverage_distri(GthStat*, unsigned long);
void          gth_stat_show(GthStat*, bool show_full_stats, bool xmlout,
                            GtFile*);
void          gth_stat_delete(GthStat*);

#endif
genometools-1.5.1/src/gth/time.c000066400000000000000000000033301211610345200165160ustar00rootroot00000000000000/*
  Copyright (c) 2005-2009 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/unused_api.h"
#include "gth/time.h"

#define TIMESTRINGLENGTH  80

char* gth_get_time(void)
{
  time_t utime;
  char *timestring;
  GT_UNUSED int rval;

  /* determine timestring */
  if (time(&utime) < 0) {
    timestring = gt_malloc(sizeof (char) * TIMESTRINGLENGTH);
    rval = snprintf(timestring, (size_t) TIMESTRINGLENGTH, "%s",
                    "time not available");
    gt_assert(rval < TIMESTRINGLENGTH);
    return timestring;
  }

  timestring = gt_malloc(sizeof (char) * TIMESTRINGLENGTH);
  if (strftime(timestring, (size_t) TIMESTRINGLENGTH, "%Y-%m-%d %H:%M:%S",
               localtime(&utime)) == 0) {
    rval = snprintf(timestring, (size_t) TIMESTRINGLENGTH, "%s",
                     "problem with time conversion");
    gt_assert(rval < TIMESTRINGLENGTH);
    return timestring;
  }

  return timestring;
}
genometools-1.5.1/src/gth/time.h000066400000000000000000000016421211610345200165270ustar00rootroot00000000000000/*
  Copyright (c) 2005-2009 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TIME_H
#define TIME_H

char* gth_get_time(void);

#endif
genometools-1.5.1/src/gth/txt_pgl_visitor.c000066400000000000000000000232721211610345200210270ustar00rootroot00000000000000/*
  Copyright (c) 2004-2011 Gordon Gremme 
  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/undef_api.h"
#include "gth/indent.h"
#include "gth/gthtrans.h"
#include "gth/pgl_visitor_rep.h"
#include "gth/txt_pgl_visitor.h"

#define PGLS_DELIMITERCHAR     '-'
#define PGL_DELIMITERLINECHAR  '*'

struct GthTxtPGLVisitor {
  const GthPGLVisitor parent_instance;
  GthInput *input;
  unsigned long translationtable;
  unsigned int indentlevel;
  GthOutput *out;
};

#define txt_pgl_visitor_cast(GV)\
        gth_pgl_visitor_cast(gth_txt_pgl_visitor_class(), GV)

static void outputAGSline(const GthAGS *ags, unsigned long agsnum,
                          GtFile *outfp)
{
  GthExonAGS *exon;
  unsigned long i;

  gt_file_xprintf(outfp, "AGS-%lu (",  agsnum + OUTPUTOFFSET);
  for (i = 0; i < gth_ags_num_of_exons(ags); i++) {
    exon = gth_ags_get_exon(ags, i);
    if (i > 0)
      gt_file_xfputc(',', outfp);
    gt_file_xprintf(outfp, "%lu  %lu", SHOWGENPOSAGS(exon->range.start),
                    SHOWGENPOSAGS(exon->range.end));
  }
  gt_file_xprintf(outfp, ")\n");
}

static void outputSCRline(const GthAGS *ags, GtFile *outfp)
{
  GthSpliceSiteProb *splicesiteprob;
  unsigned long i;

  gt_file_xprintf(outfp, "SCR   (");
  for (i = 0; i < gt_array_size(ags->exons) - 1; i++) {
    splicesiteprob = (GthSpliceSiteProb*) gt_array_get(ags->splicesiteprobs, i);
    gt_file_xprintf(outfp, "e %5.3f  d %5.3f a %5.3f,",
                    ((GthExonAGS*) gt_array_get(ags->exons, i))->score,
                    splicesiteprob->donorsiteprob,
                    splicesiteprob->acceptorsiteprob);
  }
  gt_file_xprintf(outfp, "e %5.3f)\n",
                  ((GthExonAGS*) gt_array_get(ags->exons, i))->score);
  gt_file_xfputc('\n', outfp);
}

static void output_exon_intron_lines(const GthAGS *ags, int widthforgenpos,
                                     GtFile *outfp)
{
  GthSpliceSiteProb *splicesiteprob;
  GthExonAGS *exon;
  unsigned long i, leftexonborder, rightexonborder, exonlength,
                leftintronborder = GT_UNDEF_ULONG, rightintronborder,
                intronlength;
  GthDbl exonscore;
  GthFlt donorsiteprob, acceptorsiteprob;

  for (i = 0; i < gt_array_size(ags->exons); i++) {
    exon            = (GthExonAGS*) gt_array_get(ags->exons, i);
    leftexonborder  = exon->range.start;
    rightexonborder = exon->range.end;
    exonlength      = rightexonborder - leftexonborder + 1;
    exonscore       = exon->score;

    if (i > 0) {
      rightintronborder = leftexonborder - 1;
      intronlength      = rightintronborder - leftintronborder + 1;
      splicesiteprob    = (GthSpliceSiteProb*)
                          gt_array_get(ags->splicesiteprobs, i-1);
      donorsiteprob     = splicesiteprob->donorsiteprob;
      acceptorsiteprob  = splicesiteprob->acceptorsiteprob;

      /* output intron */
      gt_file_xprintf(outfp,"    Intron %2lu %*lu %*lu (%4lu n);           "
                      "Pd: %5.3f  Pa: %5.3f\n",  i - 1 + OUTPUTOFFSET,
                      widthforgenpos, SHOWGENPOSAGS(leftintronborder),
                      widthforgenpos, SHOWGENPOSAGS(rightintronborder),
                      intronlength, donorsiteprob, acceptorsiteprob);
    }
    leftintronborder = rightexonborder + 1;

    /* output exon */
    gt_file_xprintf(outfp, "  Exon %2lu %*lu %*lu (%4lu n); score: %5.3f\n",
                    i + OUTPUTOFFSET, widthforgenpos,
                    SHOWGENPOSAGS(leftexonborder),
                    widthforgenpos,
                    SHOWGENPOSAGS(rightexonborder), exonlength, exonscore);
  }
  gt_file_xfputc('\n', outfp);
}

static void outputPGSlines(GtArray *alignments, GtFile *outfp)
{
  unsigned long i, j;
  GthSA *sa;

  for (i = 0; i < gt_array_size(alignments); i++) {
    sa = *(GthSA**) gt_array_get(alignments, i);

    gt_file_xprintf(outfp, "  PGS (");
    for (j = 0; j < gth_sa_num_of_exons(sa); j++) {
      if (j > 0)
        gt_file_xfputc(',', outfp);
      gt_file_xprintf(outfp, "%lu  %lu",
                      gth_sa_left_genomic_exon_border(sa, j),
                      gth_sa_right_genomic_exon_border(sa, j));
    }
    gt_file_xprintf(outfp, ")\t%s%c\n", gth_sa_ref_id(sa),
                       gth_sa_ref_strand_char(sa));
  }

  gt_file_xfputc('\n', outfp);
}

static void show_ags(const GthAGS *ags, unsigned long pglnum,
                     unsigned long agsnum, unsigned long translationtable,
                     GthInput *input, unsigned int indentlevel, GthOutput *out)
{
  GtFile *outfp = out->outfp;

  /* output AGS line */
  outputAGSline(ags, agsnum, out->outfp);

  /* output SCR line */
  outputSCRline(ags, out->outfp);

  /* output exon/intron lines */
  output_exon_intron_lines(ags, out->widthforgenpos, out->outfp);

  /* output PGS lines */
  outputPGSlines(ags->alignments, out->outfp);

  /* output 3-phase translation */
  gt_outputtranslationandorf(pglnum, ags, agsnum, translationtable, input,
                             indentlevel, out);

  /* output three final newlines */
  gt_file_xprintf(outfp, "\n\n\n");
}

static void show_pgl(GthPGL *pgl, unsigned long pglnum,
                     unsigned long translationtable, GthInput *input,
                     unsigned int indentlevel, GthOutput *out)
{
  unsigned long i;
  GtFile *outfp = out->outfp;

  gt_assert(!out->gff3out);

  if (out->xmlout) {
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
    indentlevel++;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n",
                     pglnum + OUTPUTOFFSET,
                     SHOWSTRAND(gth_pgl_is_forward(pgl)),
                     SHOWGENPOS(gth_pgl_is_forward(pgl),
                                gth_pgl_total_length(pgl),
                                gth_pgl_genomic_offset(pgl),
                                pgl->maxrange.start),
                     SHOWGENPOS(gth_pgl_is_forward(pgl),
                                gth_pgl_total_length(pgl),
                                gth_pgl_genomic_offset(pgl),
                                pgl->maxrange.end));
  }
  else {
    gt_file_xprintf(outfp, "PGL %3lu (%c strand):      %lu     %lu",
                    pglnum + OUTPUTOFFSET,
                    SHOWSTRAND(gth_pgl_is_forward(pgl)),
                    SHOWGENPOS(gth_pgl_is_forward(pgl),
                               gth_pgl_total_length(pgl),
                               gth_pgl_genomic_offset(pgl),
                               pgl->maxrange.start),
                    SHOWGENPOS(gth_pgl_is_forward(pgl),
                               gth_pgl_total_length(pgl),
                               gth_pgl_genomic_offset(pgl),
                               pgl->maxrange.end));
    if (out->pglgentemplate)
      gt_file_xprintf(outfp, " (genomic template '%s')", gth_pgl_gen_id(pgl));
    gt_file_xfputc('\n', outfp);
  }

  for (i = 0; i < gt_array_size(pgl->assemblies); i++) {
    show_ags(gth_pgl_get_ags(pgl, i), pglnum, i, translationtable, input,
             indentlevel, out);
  }

  if (out->xmlout) {
    indentlevel--;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
  }
}

static void txt_pgl_visitor_preface(GthPGLVisitor *pgl_visitor,
                                    unsigned long num_of_pgls)
{
  unsigned long i;
  GthTxtPGLVisitor *visitor = txt_pgl_visitor_cast(pgl_visitor);
  for (i = 0; i < DELIMITERLINELENGTH; i++)
    gt_file_xfputc(PGLS_DELIMITERCHAR, visitor->out->outfp);
  gt_file_xprintf(visitor->out->outfp, "\n\n");
  gt_file_xprintf(visitor->out->outfp,
                     "Predicted gene locations (%lu):\n\n\n", num_of_pgls);
}

static void txt_pgl_visitor_visit_pgl(GthPGLVisitor *pgl_visitor,
                                      GthPGL *pgl, unsigned long pglnum)
{
  GthTxtPGLVisitor *visitor = txt_pgl_visitor_cast(pgl_visitor);
  gt_assert(pgl);
  show_pgl(pgl, pglnum, visitor->translationtable, visitor->input,
           visitor->indentlevel, visitor->out);
}

const GthPGLVisitorClass* gth_txt_pgl_visitor_class()
{
  static const GthPGLVisitorClass pglvc = { sizeof (GthTxtPGLVisitor),
                                            NULL,
                                            txt_pgl_visitor_preface,
                                            NULL,
                                            txt_pgl_visitor_visit_pgl,
                                            NULL };
  return &pglvc;
}

GthPGLVisitor* gth_txt_pgl_visitor_new(GthInput *input,
                                       unsigned long translationtable,
                                       unsigned int indentlevel,
                                       GthOutput *out)
{
  GthPGLVisitor *pgl_visitor =
    gth_pgl_visitor_create(gth_txt_pgl_visitor_class());
  GthTxtPGLVisitor *visitor = txt_pgl_visitor_cast(pgl_visitor);
  visitor->input = input;
  visitor->translationtable = translationtable;
  visitor->indentlevel = indentlevel;
  visitor->out = out;
  return pgl_visitor;
}
genometools-1.5.1/src/gth/txt_pgl_visitor.h000066400000000000000000000027121211610345200210300ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TXT_PGL_VISITOR_H
#define TXT_PGL_VISITOR_H

#include "gth/input.h"
#include "gth/pgl_visitor.h"

/* implements the ``spliced alignment visitor'' interface */
typedef struct GthTxtPGLVisitor GthTxtPGLVisitor;

const GthPGLVisitorClass* gth_txt_pgl_visitor_class(void);
GthPGLVisitor*            gth_txt_pgl_visitor_new(GthInput*,
                                                  unsigned long
                                                  translationtable,
                                                  unsigned int indentlevel,
                                                  GthOutput*);

#endif
genometools-1.5.1/src/gth/txt_sa_visitor.c000066400000000000000000000277521211610345200206570ustar00rootroot00000000000000/*
  Copyright (c) 2004-2009 Gordon Gremme 
  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/undef_api.h"
#include "gth/sa_visitor_rep.h"
#include "gth/txt_sa_visitor.h"

#define SA_DELIMITERLINECHAR  '*'

struct GthTxtSAVisitor {
  const GthSAVisitor parent_instance;
  GthInput *input;
  bool gs2out,
       showseqnums;
  unsigned long minintronlength,
                widthforgenpos,
                showintronmaxlen,
                translationtable;
  GtFile *outfp;
};

#define txt_sa_visitor_cast(GV)\
        gth_sa_visitor_cast(gth_txt_sa_visitor_class(), GV)

static void showgthreferenceinformation(GthSA *sa, GthInput *input,
                                        bool showseqnums,
                                        GtFile *outfp)
{
  gt_assert(gth_sa_ref_file_num(sa) != GT_UNDEF_ULONG);

  switch (gth_sa_alphatype(sa)) {
    case DNA_ALPHA:
      gt_file_xprintf(outfp,
                         "EST Sequence: file=%s, strand=%c, description=",
                         gth_input_get_reference_filename(input,
                                                  gth_sa_ref_file_num(sa)),
                         gth_sa_ref_strand_char(sa));
      break;
    case PROTEIN_ALPHA:
      gt_file_xprintf(outfp, "Protein Sequence: file=%s, description=",
                         gth_input_get_reference_filename(input,
                                                 gth_sa_ref_file_num(sa)));
      break;
    default: gt_assert(0);
  }

  gth_sa_echo_reference_description(sa, input, outfp);

  if (showseqnums)
    gt_file_xprintf(outfp, ", seqnum=%lu",  gth_sa_ref_seq_num(sa));

  gt_file_xfputc('\n', outfp);
  gt_file_xfputc('\n', outfp);
}

static void showgs2referenceinformation(GthSA *sa, GtFile *outfp)
{
  gt_file_xprintf(outfp, "EST sequence %4lu %cstrand (File: %s%c)\n\n",
                     gth_sa_call_number(sa),
                     gth_sa_ref_strand_char(sa),
                     gth_sa_ref_id(sa),
                     gth_sa_ref_strand_char(sa));
}

static void showgthgenomicinformation(GthSA *sa, GthInput *input,
                                      bool showseqnums, GtFile *outfp)
{
  gt_assert(gth_sa_gen_file_num(sa) != GT_UNDEF_ULONG);

  gt_file_xprintf(outfp, "Genomic Template: file=%s, strand=%c, from=%lu, "
                            "to=%lu, description=",
                     gth_input_get_genomic_filename(input,
                                                    gth_sa_gen_file_num(sa)),
                     gth_sa_gen_strand_char(sa),
                     gth_sa_gen_dp_start_show(sa),
                     gth_sa_gen_dp_end_show(sa));

  gth_sa_echo_genomic_description(sa, input, outfp);

  if (showseqnums)
    gt_file_xprintf(outfp, ", seqnum=%lu",  gth_sa_gen_seq_num(sa));

  gt_file_xfputc('\n', outfp);
  gt_file_xfputc('\n', outfp);
}

/*
  The following function prints a PPA line, which shows the start and end
  position of the poly-A tail in the cDNA (iff a poly-A tail could be
  determined).
*/
static void showppaline(GthSA *sa, GtFile *outfp)
{
  if (gth_sa_polyAtail_start(sa) ||
      gth_sa_polyAtail_stop(sa)) {
    gt_file_xprintf(outfp,
                       " PPA                                  cDNA %6lu %6lu\n",
                       gth_sa_polyAtail_start(sa) + OUTPUTOFFSET,
                       gth_sa_polyAtail_stop(sa) + OUTPUTOFFSET);
  }
}

/* The following function prints the "classic" GeneSeqer2 MATCH line */
static void showmatchline(GthSA *sa, GtFile *outfp)
{
  gt_file_xprintf(outfp, "MATCH\t%s%c\t%s%c\t%5.3f\t%lu\t%5.3f\t%c\n",
                     gth_sa_gen_id(sa),
                     gth_sa_gen_strand_char(sa),
                     gth_sa_ref_id(sa),
                     gth_sa_ref_strand_char(sa),
                     gth_sa_score(sa),
                     gth_sa_cumlen_scored_exons(sa),
                     gth_sa_coverage(sa),
                     gth_sa_coverage_char(sa));
}

/*
  The following function prints the "classic" GeneSeqer2 PGS line
*/
static void showpgsline(GthSA *sa, GtFile *outfp)
{
  unsigned long i, numofexons;
  gt_assert(sa);
  numofexons = gth_sa_num_of_exons(sa);
  gt_file_xprintf(outfp, "PGS_%s%c_%s%c\t(",
                     gth_sa_gen_id(sa),
                     gth_sa_gen_strand_char(sa),
                     gth_sa_ref_id(sa),
                     gth_sa_ref_strand_char(sa));

  for (i = 0; i < numofexons; i++) {
    gt_file_xprintf(outfp, "%lu  %lu",
                    gth_sa_left_genomic_exon_border(sa, i),
                    gth_sa_right_genomic_exon_border(sa, i));
    if (i == numofexons - 1)
      gt_file_xprintf(outfp, ")\n\n");
    else
      gt_file_xfputc(',', outfp);
  }
}

static void showalignmentheader(GthSA *sa, bool gs2out, int widthforgenpos,
                                unsigned long minintronlength, GtFile *outfp)
{
  unsigned long i, leftreferenceexonborder, rightreferenceexonborder,
                referenceexonlength;
  GthDbl exonscore, donorsitescore, acceptorsitescore;
  GthFlt donorsiteprobability, acceptorsiteprobability;
  Exoninfo *exoninfo;
  Introninfo *introninfo;

  gt_file_xprintf(outfp, "Predicted gene structure");
  if (gs2out) {
    gt_file_xprintf(outfp, " (within gDNA segment %lu to %lu):\n",
                       gth_sa_gen_dp_start_show(sa),
                       gth_sa_gen_dp_end_show(sa));
  }
  else
    gt_file_xprintf(outfp, ":\n");
  gt_file_xfputc('\n', outfp);

  for (i = 0; i < gth_sa_num_of_exons(sa); i++) {
    exoninfo = gth_sa_get_exon(sa, i);
    leftreferenceexonborder  = exoninfo->leftreferenceexonborder;
    rightreferenceexonborder = exoninfo->rightreferenceexonborder;
    referenceexonlength      = rightreferenceexonborder
                               - leftreferenceexonborder + 1;
    exonscore                = exoninfo->exonscore;

    if (i > 0) {
      introninfo = gth_sa_get_intron(sa, i-1);
      donorsiteprobability    = introninfo->donorsiteprobability;
      donorsitescore          = introninfo->donorsitescore;
      acceptorsiteprobability = introninfo->acceptorsiteprobability;
      acceptorsitescore       = introninfo->acceptorsitescore;

      gt_file_xprintf(outfp, "  Intron %2lu %*lu %*lu (%4lu n); ",
                      i - 1 + OUTPUTOFFSET, widthforgenpos,
                      gth_sa_left_intron_border(sa, i-1),
                      widthforgenpos,
                      gth_sa_right_intron_border(sa, i-1),
                      gth_sa_intron_length(sa, i-1));

      gt_file_xprintf(outfp, "Pd: %5.3f ", donorsiteprobability);
      if (gth_sa_alphatype(sa) == DNA_ALPHA) {
        if (donorsitescore == 0.0)
          gt_file_xprintf(outfp, "(s:    0), ");
        else
          gt_file_xprintf(outfp, "(s: %4.2f), ", donorsitescore);
      }
      else
        gt_file_xprintf(outfp, "  ");
      gt_file_xprintf(outfp, "Pa: %5.3f ", acceptorsiteprobability);
      if (gth_sa_alphatype(sa) == DNA_ALPHA) {
        if (acceptorsitescore == 0.0)
          gt_file_xprintf(outfp, "(s:    0)");
        else
          gt_file_xprintf(outfp, "(s: %4.2f)", acceptorsitescore);
      }
      /* if the intron is shorter or equal than the minimum intron length two
         question marks are shown at the end of the line */
      if (gth_sa_intron_length(sa, i-1) <= minintronlength)
        gt_file_xprintf(outfp, " ??");
      gt_file_xfputc('\n', outfp);
    }

    gt_file_xprintf(outfp,
                    " Exon %2lu %*lu %*lu (%4lu n);  %s %6lu %6lu (%4lu %s); "
                    "score: %5.3f\n", i + OUTPUTOFFSET, widthforgenpos,
                    gth_sa_left_genomic_exon_border(sa, i),
                    widthforgenpos,
                    gth_sa_right_genomic_exon_border(sa, i),
                    gth_sa_genomic_exon_length(sa, i),
                    gth_sa_alphastring(sa),
                    leftreferenceexonborder  + OUTPUTOFFSET,
                    rightreferenceexonborder + OUTPUTOFFSET,
                    referenceexonlength,
                    gth_sa_alphatype(sa) == DNA_ALPHA
                    ? "n" : "aa",
                    exonscore);
  }

  /* showing PPA line (if an poly-A tail was determined) */
  if (gth_sa_alphatype(sa) == DNA_ALPHA)
    showppaline(sa, outfp);
  gt_file_xfputc('\n', outfp);

  /* showing MATCH line */
  showmatchline(sa, outfp);

  /* showing PGS line */
  showpgsline(sa, outfp);
}

static void showdelimiterline(GtFile *outfp)
{
  unsigned long i;
  for (i = 0; i < DELIMITERLINELENGTH; i++)
    gt_file_xfputc(SA_DELIMITERLINECHAR, outfp);
  gt_file_xfputc('\n', outfp);
}

static void show_spliced_alignment(GthSA *sa, GthInput *input, bool gs2out,
                                   unsigned long minintronlength,
                                   unsigned long widthforgenpos,
                                   unsigned long showintronmaxlen,
                                   unsigned long translationtable,
                                   bool showseqnums, GtFile *outfp)
{
  bool wildcardimplosion = false;

  showdelimiterline(outfp);

  if (gs2out) {
    /* all wildcards (N,S,Y,W,R,K,V,B,D,H,M) will be replaced by the wildcard N
       makes only sense for a DNA alphabet */
    wildcardimplosion = true;
    showgs2referenceinformation(sa, outfp);
    gth_sa_echo_reference_sequence(sa, input, true, outfp);
  }
  else {
    showgthreferenceinformation(sa, input, showseqnums, outfp);
    gth_sa_echo_reference_sequence(sa, input, true, outfp);
    showgthgenomicinformation(sa, input, showseqnums, outfp);
  }

  showalignmentheader(sa, gs2out, widthforgenpos, minintronlength, outfp);

  gt_file_xprintf(outfp,
                     "Alignment (genomic DNA sequence = upper lines):\n\n");

  gth_sa_echo_alignment(sa, showintronmaxlen, translationtable,
                        wildcardimplosion, input, outfp);
}

static void txt_sa_visitor_visit_sa(GthSAVisitor *sa_visitor, GthSA *sa)
{
  GthTxtSAVisitor *visitor = txt_sa_visitor_cast(sa_visitor);
  gt_assert(sa);
  show_spliced_alignment(sa, visitor->input, visitor->gs2out,
                         visitor->minintronlength, visitor->widthforgenpos,
                         visitor->showintronmaxlen, visitor->translationtable,
                         visitor->showseqnums, visitor->outfp);
}

const GthSAVisitorClass* gth_txt_sa_visitor_class()
{
  static const GthSAVisitorClass savc = { sizeof (GthTxtSAVisitor),
                                          NULL,
                                          NULL,
                                          txt_sa_visitor_visit_sa,
                                          NULL };
  return &savc;
}

GthSAVisitor* gth_txt_sa_visitor_new(GthInput *input, bool gs2out,
                                     unsigned long minintronlength,
                                     unsigned long widthforgenpos,
                                     unsigned long showintronmaxlen,
                                     unsigned long translationtable,
                                     bool showseqnums, GtFile *outfp)
{
  GthSAVisitor *sa_visitor = gth_sa_visitor_create(gth_txt_sa_visitor_class());
  GthTxtSAVisitor *visitor = txt_sa_visitor_cast(sa_visitor);
  visitor->input = input;
  visitor->gs2out = gs2out;
  visitor->minintronlength = minintronlength;
  visitor->widthforgenpos = widthforgenpos;
  visitor->showintronmaxlen = showintronmaxlen;
  visitor->translationtable = translationtable;
  visitor->showseqnums = showseqnums;
  visitor->outfp = outfp;
  return sa_visitor;
}
genometools-1.5.1/src/gth/txt_sa_visitor.h000066400000000000000000000032561211610345200206550ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TXT_SA_VISITOR_H
#define TXT_SA_VISITOR_H

#include "gth/sa_visitor.h"
#include "gth/input.h"

/* implements the ``spliced alignment visitor'' interface */
typedef struct GthTxtSAVisitor GthTxtSAVisitor;

const GthSAVisitorClass* gth_txt_sa_visitor_class(void);
GthSAVisitor*            gth_txt_sa_visitor_new(GthInput*,
                                                bool gs2out,
                                                unsigned long minintronlength,
                                                unsigned long widthforgenpos,
                                                unsigned long showintronmaxlen,
                                                unsigned long translationtable,
                                                bool showseqnums,
                                                GtFile *outfp);

#endif
genometools-1.5.1/src/gth/xml_final_sa_visitor.c000066400000000000000000000427531211610345200220070ustar00rootroot00000000000000/*
  Copyright (c) 2004-2011 Gordon Gremme 
  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/chardef.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "gth/indent.h"
#include "gth/sa_visitor_rep.h"
#include "gth/xml_final_sa_visitor.h"

struct GthXMLFinalSAVisitor {
  const GthSAVisitor parent_instance;
  unsigned long minintronlength,
                translationtable;
  GthInput *input;
  unsigned int indentlevel;
  GtFile *outfp;
};

#define xml_final_sa_visitor_cast(GV)\
        gth_sa_visitor_cast(gth_xml_final_sa_visitor_class(), GV)

static void xml_showgthreferenceinformation(GthSA *sa,
                                            GthInput *input,
                                            unsigned int indentlevel,
                                            GtFile *outfp)
{
  gt_assert(gth_sa_ref_file_num(sa) != GT_UNDEF_ULONG);

  gth_indent(outfp, indentlevel);

  switch (gth_sa_alphatype(sa)) {
    case DNA_ALPHA:
      gt_file_xprintf(outfp, "\n");
}

static void xml_showgthgenomicinformation(GthSA *sa,
                                          GthInput *input,
                                          unsigned int indentlevel,
                                          GtFile *outfp)
{
  gt_assert(gth_sa_gen_file_num(sa) != GT_UNDEF_ULONG);

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

/*
  The following function prints a PPA line, which shows the start and end
  position of the poly-A tail in the cDNA (iff a poly-A tail could be
  determined).
*/
static void xml_showppaline(GthSA *sa, unsigned int indentlevel,
                           GtFile *outfp)
{
  if (gth_sa_polyAtail_start(sa) ||
      gth_sa_polyAtail_stop(sa)) {
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp,
                       "\n",
                       gth_sa_polyAtail_start(sa) + OUTPUTOFFSET,
                       gth_sa_polyAtail_stop(sa) + OUTPUTOFFSET);
  }
}

/* The following function prints the "classic" GeneSeqer2 MATCH line */
static void xml_showmatchline(GthSA *sa, unsigned int indentlevel,
                              GtFile *outfp)
{
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n",
                       gth_sa_ref_id(sa),
                       gth_sa_ref_strand_char(sa));
  }
  else
    gt_file_xprintf(outfp, "ref_id=\"%s\">\n", gth_sa_ref_id(sa));

  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp,
                     "%.3f\n",
                     gth_sa_score(sa));
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu"
                     "\n",
                     gth_sa_cumlen_scored_exons(sa));
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

/*
  The following function prints the "classic" GeneSeqer2 PGS line
*/
static void xml_showpgsline(GthSA *sa, unsigned int indentlevel,
                            GtFile *outfp)
{
  unsigned long i, numofexons;
  gt_assert(sa);
  numofexons = gth_sa_num_of_exons(sa);
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n",
                     gth_sa_gen_id(sa), gth_sa_gen_strand_char(sa));
  gth_indent(outfp, indentlevel);
  if (gth_sa_alphatype(sa) == DNA_ALPHA) {
    gt_file_xprintf(outfp, "\n",
                       gth_sa_ref_id(sa), gth_sa_ref_strand_char(sa));
  }
  else {
    gt_file_xprintf(outfp, "\n",
                       gth_sa_ref_id(sa));
  }
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  for (i = 0; i < numofexons; i++) {
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n",
                    gth_sa_left_genomic_exon_border(sa, i),
                    gth_sa_right_genomic_exon_border(sa, i));
  }

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void xml_showalignmentheader(GthSA *sa,
                                    unsigned long minintronlength,
                                    unsigned int indentlevel, GtFile *outfp)
{
  unsigned long i, leftreferenceexonborder, rightreferenceexonborder,
                referenceexonlength;
  GthDbl exonscore, donorsitescore, acceptorsitescore;
  GthFlt donorsiteprobability, acceptorsiteprobability;
  Exoninfo *exoninfo;
  Introninfo *introninfo;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  for (i = 0; i < gth_sa_num_of_exons(sa); i++) {
    exoninfo = gth_sa_get_exon(sa, i);
    leftreferenceexonborder  = exoninfo->leftreferenceexonborder;
    rightreferenceexonborder = exoninfo->rightreferenceexonborder;
    referenceexonlength      = rightreferenceexonborder
                               - leftreferenceexonborder + 1;
    exonscore                = exoninfo->exonscore;

    if (i > 0) {
      introninfo = gth_sa_get_intron(sa, i-1);
      donorsiteprobability    = introninfo->donorsiteprobability;
      donorsitescore          = introninfo->donorsitescore;
      acceptorsiteprobability = introninfo->acceptorsiteprobability;
      acceptorsitescore       = introninfo->acceptorsitescore;

      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp, "\n",
                      i - 1 + OUTPUTOFFSET);
      indentlevel++;
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp,
                      "\n",
                      gth_sa_left_intron_border(sa, i-1),
                      gth_sa_right_intron_border(sa, i-1),
                      gth_sa_intron_length(sa, i-1));
      indentlevel++;
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp, "\n");
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp, "\n");
      indentlevel--;
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp, "\n");

      /* if the intron is shorter or equal than the minimal intron length an
         additional tag is shown */
      if (gth_sa_intron_length(sa, i-1) <= minintronlength) {
        gth_indent(outfp, indentlevel);
        gt_file_xprintf(outfp, "\n");
      }

      indentlevel--;
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp, "\n");
    }

    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n", i + OUTPUTOFFSET);
    indentlevel++;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n",
                    gth_sa_left_genomic_exon_border(sa, i),
                    gth_sa_right_genomic_exon_border(sa, i),
                    gth_sa_genomic_exon_length(sa, i));
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp,
                    "\n",
                    gth_sa_alphastring(sa),
                    leftreferenceexonborder  + OUTPUTOFFSET ,
                    rightreferenceexonborder + OUTPUTOFFSET ,
                    referenceexonlength, exonscore);
    indentlevel--;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
  }

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");

  /* showing PPA line (if an poly-A tail was determined) */
  if (gth_sa_alphatype(sa) == DNA_ALPHA)
    xml_showppaline(sa, indentlevel, outfp);

  /* showing MATCH line */
  xml_showmatchline(sa, indentlevel, outfp);

  /* showing PGS line */
  xml_showpgsline(sa, indentlevel, outfp);
}

static void showconcreteline(const unsigned char *alignmentline,
                             unsigned long cols, GtFile *outfp)
{
  unsigned long i;

  for (i = 0; i < cols; i++) {
    switch (alignmentline[i]) {
      case ABSTRACTGAPSYMBOL:
        gt_file_xfputc(CONCRETEGAPSYMBOL, outfp);
        break;
      case ABSTRACTINTRONSYMBOL:
        gt_file_xfputc(CONCRETEINTRONSYMBOL, outfp);
        break;
      default:
        gt_file_xfputc(alignmentline[i], outfp);
    }
  }
}

static void xml_final_show_spliced_alignment(GthSA *sa, GthInput *input,
                                             unsigned long minintronlength,
                                             unsigned long translationtable,
                                             unsigned int indentlevel,
                                             GtFile *outfp)
{
  unsigned char *first_line, *second_line, *third_line;
  GT_UNUSED bool reverse_subject_pos = false;
  unsigned long cols;

  gt_assert(sa && input);

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp,
                  "\n");
  indentlevel++;

  /* If the reverse complement of the genomic DNA is considered, this
     opition is needed for correct output of the genomic sequence positions
     by the function showalignmentgeneric() */
  if (!gth_sa_gen_strand_forward(sa))
    reverse_subject_pos = true;

  xml_showgthreferenceinformation(sa, input, indentlevel, outfp);

  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "");
  gth_sa_echo_reference_sequence(sa, input, false, outfp);
  gt_file_xprintf(outfp, "\n");
  indentlevel--;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  xml_showgthgenomicinformation(sa, input, indentlevel, outfp);

  xml_showalignmentheader(sa, minintronlength, indentlevel, outfp);

  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");

  /* compute the alignment lines */
  cols = gth_sa_get_alignment_lines(sa, &first_line, &second_line, &third_line,
                                    translationtable, input);

  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "");
  showconcreteline(first_line, cols, outfp);
  gt_file_xprintf(outfp, "\n");
  gth_indent(outfp, indentlevel);
  switch (gth_sa_alphatype(sa)) {
    case DNA_ALPHA:
      gt_file_xprintf(outfp, "");
      showconcreteline(second_line, cols, outfp);
      gt_file_xprintf(outfp, "\n");
      break;
    case PROTEIN_ALPHA:
      gt_file_xprintf(outfp, "");
      showconcreteline(second_line, cols, outfp);
      gt_file_xprintf(outfp, "\n");
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp, "");
      showconcreteline(third_line, cols, outfp);
      gt_file_xprintf(outfp, "\n");

      break;
    default: gt_assert(0);
  }

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");

  /* free */
  gt_free(first_line);
  gt_free(second_line);
  gt_free(third_line);
}

static void xml_final_sa_visitor_preface(GthSAVisitor *sa_visitor)
{
  GthXMLFinalSAVisitor *visitor = xml_final_sa_visitor_cast(sa_visitor);
  gth_indent(visitor->outfp, visitor->indentlevel);
  gt_file_xprintf(visitor->outfp, "\n");
}

static void xml_final_sa_visitor_visit_sa(GthSAVisitor *sa_visitor,
                                          GthSA *sa)
{
  GthXMLFinalSAVisitor *visitor = xml_final_sa_visitor_cast(sa_visitor);
  gt_assert(sa);
  xml_final_show_spliced_alignment(sa, visitor->input, visitor->minintronlength,
                                   visitor->translationtable,
                                   visitor->indentlevel, visitor->outfp);
}

static void  xml_final_sa_visitor_trailer(GthSAVisitor *sa_visitor,
                                          unsigned long num_of_sas)
{
  GthXMLFinalSAVisitor *visitor = xml_final_sa_visitor_cast(sa_visitor);
  visitor->indentlevel++;
  gth_indent(visitor->outfp, visitor->indentlevel);
  gt_file_xprintf(visitor->outfp, "%lu"
                  "\n", num_of_sas);
  gth_indent(visitor->outfp, visitor->indentlevel);
  gt_file_xprintf(visitor->outfp, "\n");
  visitor->indentlevel--;
}

const GthSAVisitorClass* gth_xml_final_sa_visitor_class()
{
  static const GthSAVisitorClass savc = { sizeof (GthXMLFinalSAVisitor),
                                          NULL,
                                          xml_final_sa_visitor_preface,
                                          xml_final_sa_visitor_visit_sa,
                                          xml_final_sa_visitor_trailer
                                        };
  return &savc;
}

GthSAVisitor* gth_xml_final_sa_visitor_new(GthInput *input,
                                           unsigned long minintronlength,
                                           unsigned long translationtable,
                                           unsigned int indentlevel,
                                           GtFile *outfp)
{
  GthSAVisitor *sa_visitor =
    gth_sa_visitor_create(gth_xml_final_sa_visitor_class());
  GthXMLFinalSAVisitor *visitor = xml_final_sa_visitor_cast(sa_visitor);
  visitor->input = input;
  visitor->minintronlength = minintronlength;
  visitor->translationtable = translationtable;
  visitor->indentlevel = indentlevel;
  visitor->outfp = outfp;
  return sa_visitor;
}
genometools-1.5.1/src/gth/xml_final_sa_visitor.h000066400000000000000000000032011211610345200217750ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef XML_FINAL_SA_VISITOR_H
#define XML_FINAL_SA_VISITOR_H

#include "gth/input.h"
#include "gth/sa_visitor.h"

/* implements the ``spliced alignment visitor'' interface */
typedef struct GthXMLFinalSAVisitor GthXMLFinalSAVisitor;

const GthSAVisitorClass* gth_xml_final_sa_visitor_class(void);
GthSAVisitor*            gth_xml_final_sa_visitor_new(GthInput*,
                                                      unsigned long
                                                      minintronlength,
                                                      unsigned long
                                                      translationtable,
                                                      unsigned int indentlevel,
                                                      GtFile *outfp);

#endif
genometools-1.5.1/src/gth/xml_inter_sa_visitor.c000066400000000000000000000321741211610345200220330ustar00rootroot00000000000000/*
  Copyright (c) 2004-2009 Gordon Gremme 
  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "gth/indent.h"
#include "gth/showbool.h"
#include "gth/intermediate.h"
#include "gth/sa_visitor_rep.h"
#include "gth/xml_inter_sa_visitor.h"

#define PRECISION  16

struct GthXMLInterSAVisitor {
  const GthSAVisitor parent_instance;
  GthInput *input;
  unsigned int indentlevel;
  GtFile *outfp;
};

#define xml_inter_sa_visitor_cast(GV)\
        gth_sa_visitor_cast(gth_xml_inter_sa_visitor_class(), GV)

static void showgenomicfilename(GthSA *sa, GthInput *input,
                                unsigned int indentlevel, GtFile *outfp)
{
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%s\n",
                     gth_input_get_genomic_filename(input,
                                                   gth_sa_gen_file_num(sa)));
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%s\n",
                     GTH_UNDEFINED_HASH);

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void showreferencefilename(GthSA *sa,
                                  GthInput *input,
                                  unsigned int indentlevel, GtFile *outfp)
{
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%s\n",
                     gth_input_get_reference_filename(input,
                                                 gth_sa_ref_file_num(sa)));
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%s\n",
                     GTH_UNDEFINED_HASH);

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void showalignmentcutoffs(GthSA *sa, unsigned int indentlevel,
                                 GtFile *outfp)
{
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_genomiccutoff_start(sa));
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_referencecutoff_start(sa));
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_eopcutoff_start(sa));
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_genomiccutoff_end(sa));
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_referencecutoff_end(sa));
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_eopcutoff_end(sa));
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void showexons(GthSA *sa, unsigned int indentlevel,
                      GtFile *outfp)
{
  Exoninfo *exoninfo;
  unsigned long i;

  for (i = 0; i < gth_sa_num_of_exons(sa); i++) {
    exoninfo = gth_sa_get_exon(sa, i);

    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
    indentlevel++;

    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp,
                    "%lu\n",
                    exoninfo->leftgenomicexonborder);
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp,
                    "%lu\n",
                    exoninfo->rightgenomicexonborder);
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp,
                    "%lu\n",
                    exoninfo->leftreferenceexonborder);
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "%lu\n",
                    exoninfo->rightreferenceexonborder);
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "%.*f\n", PRECISION,
                    exoninfo->exonscore);

    indentlevel--;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
  }
}

static void showintrons(GthSA *sa, bool dnaalpha,
                        unsigned int indentlevel, GtFile *outfp)
{
  Introninfo *introninfo;
  unsigned long i;

  for (i = 0; i < gth_sa_num_of_introns(sa); i++) {
    introninfo = gth_sa_get_intron(sa, i);

    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
    indentlevel++;

    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp,
                    "%.*f\n",
                    PRECISION, introninfo->donorsiteprobability);

    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp,
                    "%.*f\n",
                    PRECISION, introninfo->acceptorsiteprobability);

    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "%.*f\n",
                       PRECISION,
                       dnaalpha ? introninfo->donorsitescore
                                : UNDEFINED_SPLICE_SITE_SCORE);

    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "%.*f\n",
                       PRECISION,
                       dnaalpha ? introninfo->acceptorsitescore
                                : UNDEFINED_SPLICE_SITE_SCORE);

    indentlevel--;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
  }
}

static void showpolyAtailpos(GthSA *sa, unsigned int indentlevel,
                             GtFile *outfp)
{
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_polyAtail_start(sa));
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_polyAtail_stop(sa));

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void xml_inter_show_spliced_alignment(GthSA *sa, GthInput *input,
                                             unsigned int indentlevel,
                                             GtFile *outfp)
{
  bool dnaalpha = true;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp,
                  "\n");
  indentlevel++;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "");
  switch (gth_sa_alphatype(sa)) {
    case DNA_ALPHA:
      gt_file_xprintf(outfp, "DNA_ALPHA");
      break;
    case PROTEIN_ALPHA:
      gt_file_xprintf(outfp, "PROTEIN_ALPHA");
      dnaalpha = false;
      break;
    default: gt_assert(0);
  }
  gt_file_xprintf(outfp, "\n");

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;
  gth_backtrace_path_show_complete(gth_sa_backtrace_path(sa), true, indentlevel,
                                   outfp);
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_indelcount(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_gen_dp_length(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_gen_total_length(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_gen_offset(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_ref_total_length(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_gen_dp_start(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_gen_dp_end(sa));

  showgenomicfilename(sa, input, indentlevel, outfp);

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_gen_seq_num(sa));

  showreferencefilename(sa, input, indentlevel, outfp);

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu\n",
                     gth_sa_ref_seq_num(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%s\n", gth_sa_gen_id(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%s\n",
                  gth_sa_ref_id(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp,
                  "%s\n",
                  GTH_SHOWBOOL(gth_sa_gen_strand_forward(sa)));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp,
                    "%s\n",
                    GTH_SHOWBOOL(gth_sa_ref_strand_forward(sa)));

  showalignmentcutoffs(sa, indentlevel, outfp);

  showexons(sa, indentlevel, outfp);

  showintrons(sa, dnaalpha, indentlevel, outfp);

  showpolyAtailpos(sa, indentlevel, outfp);

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%.*f\n",
                  PRECISION, gth_sa_score(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%.*f\n", PRECISION,
                     gth_sa_coverage(sa));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%s"
                  "\n",
                  GTH_SHOWBOOL(gth_sa_genomic_cov_is_highest(sa)));

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "%lu"
                     "\n",
                     gth_sa_cumlen_scored_exons(sa));

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void xml_inter_sa_visitor_visit_sa(GthSAVisitor *sa_visitor,
                                          GthSA *sa)
{
  GthXMLInterSAVisitor *visitor = xml_inter_sa_visitor_cast(sa_visitor);
  gt_assert(sa);
  xml_inter_show_spliced_alignment(sa, visitor->input, visitor->indentlevel,
                                   visitor->outfp);
}

const GthSAVisitorClass* gth_xml_inter_sa_visitor_class()
{
  static const GthSAVisitorClass savc = { sizeof (GthXMLInterSAVisitor),
                                          NULL,
                                          NULL,
                                          xml_inter_sa_visitor_visit_sa,
                                          NULL };
  return &savc;
}

GthSAVisitor* gth_xml_inter_sa_visitor_new(GthInput *input,
                                           unsigned int indentlevel,
                                           GtFile *outfp)
{
  GthSAVisitor *sa_visitor =
    gth_sa_visitor_create(gth_xml_inter_sa_visitor_class());
  GthXMLInterSAVisitor *visitor = xml_inter_sa_visitor_cast(sa_visitor);
  visitor->input = input;
  visitor->indentlevel = indentlevel;
  visitor->outfp = outfp;
  return sa_visitor;
}

void gth_xml_inter_sa_visitor_set_outfp(GthSAVisitor *sa_visitor,
                                        GtFile *outfp)
{
  GthXMLInterSAVisitor *visitor = xml_inter_sa_visitor_cast(sa_visitor);
  visitor->outfp = outfp;
}
genometools-1.5.1/src/gth/xml_inter_sa_visitor.h000066400000000000000000000027441211610345200220400ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef XML_INTER_SA_VISITOR_H
#define XML_INTER_SA_VISITOR_H

#include "gth/sa_visitor.h"

/* implements the ``spliced alignment visitor'' interface */
typedef struct GthXMLInterSAVisitor GthXMLInterSAVisitor;

const GthSAVisitorClass* gth_xml_inter_sa_visitor_class(void);
GthSAVisitor*            gth_xml_inter_sa_visitor_new(GthInput*,
                                                      unsigned int indentlevel,
                                                      GtFile *outfp);
void                     gth_xml_inter_sa_visitor_set_outfp(GthSAVisitor*,
                                                            GtFile*);

#endif
genometools-1.5.1/src/gth/xml_pgl_visitor.c000066400000000000000000000277701211610345200210170ustar00rootroot00000000000000/*
  Copyright (c) 2004-2009 Gordon Gremme 
  Copyright (c) 2004-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/undef_api.h"
#include "core/unused_api.h"
#include "gth/indent.h"
#include "gth/gthtrans.h"
#include "gth/pgl_visitor_rep.h"
#include "gth/xml_pgl_visitor.h"

struct GthXMLPGLVisitor {
  const GthPGLVisitor parent_instance;
  GthInput *input;
  unsigned long translationtable;
  unsigned int indentlevel;
  GthOutput *out;
};

#define xml_pgl_visitor_cast(GV)\
        gth_pgl_visitor_cast(gth_xml_pgl_visitor_class(), GV)

static void xml_outputAGSline(const GthAGS *ags, unsigned long agsnum,
                              unsigned int indentlevel, GtFile *outfp)
{
  GthExonAGS *exon;
  unsigned long i;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n",
                  agsnum + OUTPUTOFFSET);
  indentlevel++;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  for (i = 0; i < gth_ags_num_of_exons(ags); i++) {
    exon = gth_ags_get_exon(ags, i);
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n",
                    SHOWGENPOSAGS(exon->range.start),
                    SHOWGENPOSAGS(exon->range.end));
  }

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void xml_outputSCRline(const GthAGS *ags, unsigned int indentlevel,
                              GtFile *outfp)
{
  GthSpliceSiteProb *splicesiteprob;
  unsigned long i;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  for (i = 0; i < gt_array_size(ags->exons) - 1; i++) {
    splicesiteprob = (GthSpliceSiteProb*) gt_array_get(ags->splicesiteprobs, i);
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n",
                       splicesiteprob->donorsiteprob,
                       splicesiteprob->acceptorsiteprob,
                       ((GthExonAGS*) gt_array_get(ags->exons, i))->score);
  }

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n",
                  ((GthExonAGS*) gt_array_get(ags->exons, i))->score);
  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void xml_output_exon_intron_lines(const GthAGS *ags,
                                         unsigned int indentlevel,
                                         GtFile *outfp)
{
  GthSpliceSiteProb *splicesiteprob;
  GthExonAGS *exon;
  unsigned long i, leftexonborder, rightexonborder, exonlength,
                leftintronborder = GT_UNDEF_ULONG, rightintronborder,
                intronlength;
  GthDbl exonscore;
  GthFlt donorsiteprob, acceptorsiteprob;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp,
                  "\n");
  indentlevel++;

  for (i = 0; i < gt_array_size(ags->exons); i++) {
    exon            = (GthExonAGS*) gt_array_get(ags->exons, i);
    leftexonborder  = exon->range.start;
    rightexonborder = exon->range.end;
    exonlength      = rightexonborder - leftexonborder + 1;
    exonscore       = exon->score;

    if (i > 0) {
      rightintronborder = leftexonborder - 1;
      intronlength      = rightintronborder - leftintronborder + 1;
      splicesiteprob    = (GthSpliceSiteProb*)
                          gt_array_get(ags->splicesiteprobs, i-1);
      donorsiteprob     = splicesiteprob->donorsiteprob;
      acceptorsiteprob  = splicesiteprob->acceptorsiteprob;

      /* output intron */
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp, "\n",  i - 1 + OUTPUTOFFSET,
                      donorsiteprob, acceptorsiteprob);
      indentlevel++;
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp,
                      "\n",
                      SHOWGENPOSAGS(leftintronborder),
                      SHOWGENPOSAGS(rightintronborder),  intronlength);
      indentlevel--;
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp, "\n");
    }
    leftintronborder = rightexonborder + 1;

    /* output exon */
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n",
                    i + OUTPUTOFFSET, exonscore);
    indentlevel++;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp,
                    "\n", SHOWGENPOSAGS(leftexonborder),
                    SHOWGENPOSAGS(rightexonborder), exonlength);
    indentlevel--;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
  }

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void xml_outputPGSlines(GtArray *alignments, unsigned int indentlevel,
                               GtFile *outfp)
{
  unsigned long i, j;
  GthSA *sa;

  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
  indentlevel++;

  for (i = 0; i < gt_array_size(alignments); i++) {
    sa = *(GthSA**) gt_array_get(alignments, i);

    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
    indentlevel++;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
    indentlevel++;

    for (j = 0; j < gth_sa_num_of_exons(sa); j++) {
      gth_indent(outfp, indentlevel);
      gt_file_xprintf(outfp, "\n",
                      gth_sa_left_genomic_exon_border(sa, j),
                      gth_sa_right_genomic_exon_border(sa, j));
    }
    indentlevel--;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
    gth_indent(outfp, indentlevel);
    if (gth_sa_alphatype(sa) == DNA_ALPHA) {
      gt_file_xprintf(outfp, "\n",
                         gth_sa_ref_id(sa),
                         gth_sa_ref_strand_char(sa));
    }
    else {
      gt_file_xprintf(outfp, "\n",
                         gth_sa_ref_id(sa));
    }
    indentlevel--;
    gth_indent(outfp, indentlevel);
    gt_file_xprintf(outfp, "\n");
  }

  indentlevel--;
  gth_indent(outfp, indentlevel);
  gt_file_xprintf(outfp, "\n");
}

static void xml_show_ags(const GthAGS *ags, unsigned long pglnum,
                         unsigned long agsnum, unsigned long translationtable,
                         GthInput *input, unsigned int indentlevel,
                         GthOutput *out)
{
  gth_indent(out->outfp, indentlevel);
  gt_file_xprintf(out->outfp, "\n");
  indentlevel++;

  /* output AGS line */
  xml_outputAGSline(ags, agsnum, indentlevel, out->outfp);

  /* output SCR line */
  xml_outputSCRline(ags, indentlevel, out->outfp);

  /* output exon/intron lines */
  xml_output_exon_intron_lines(ags, indentlevel, out->outfp);

  /* output PGS lines */
  xml_outputPGSlines(ags->alignments, indentlevel, out->outfp);

  /* output 3-phase translation */
  gt_outputtranslationandorf(pglnum, ags, agsnum, translationtable, input,
                          indentlevel, out);

  indentlevel--;
  gth_indent(out->outfp, indentlevel);
  gt_file_xprintf(out->outfp, "\n");
}

static void xml_show_pgl(GthPGL *pgl, unsigned long pglnum,
                         unsigned long translationtable, GthInput *input,
                         unsigned int indentlevel, GthOutput *out)
{
  unsigned long i;

  gth_indent(out->outfp, indentlevel);
  gt_file_xprintf(out->outfp, "\n");
  indentlevel++;
  gth_indent(out->outfp, indentlevel);
  gt_file_xprintf(out->outfp,
                     "\n",
                     pglnum + OUTPUTOFFSET,
                     SHOWSTRAND(gth_pgl_is_forward(pgl)),
                     SHOWGENPOS(gth_pgl_is_forward(pgl),
                                gth_pgl_total_length(pgl),
                                gth_pgl_genomic_offset(pgl),
                                pgl->maxrange.start),
                     SHOWGENPOS(gth_pgl_is_forward(pgl),
                                gth_pgl_total_length(pgl),
                                gth_pgl_genomic_offset(pgl),
                                pgl->maxrange.end));

  for (i = 0; i < gth_pgl_num_of_ags(pgl); i++) {
    xml_show_ags(gth_pgl_get_ags(pgl, i), pglnum, i, translationtable, input,
                 indentlevel, out);
  }

  indentlevel--;
  gth_indent(out->outfp, indentlevel);
  gt_file_xprintf(out->outfp, "\n");
}

static void xml_pgl_visitor_preface(GthPGLVisitor *pgl_visitor,
                                    GT_UNUSED unsigned long num_of_pgls)
{
  GthXMLPGLVisitor *visitor = xml_pgl_visitor_cast(pgl_visitor);
  gth_indent(visitor->out->outfp, visitor->indentlevel);
  gt_file_xprintf(visitor->out->outfp,
                     "\n");
}

static void xml_pgl_visitor_visit_pgl(GthPGLVisitor *pgl_visitor,
                                      GthPGL *pgl, unsigned long pglnum)
{
  GthXMLPGLVisitor *visitor = xml_pgl_visitor_cast(pgl_visitor);
  gt_assert(pgl);
  xml_show_pgl(pgl, pglnum, visitor->translationtable, visitor->input,
           visitor->indentlevel, visitor->out);
}

static void xml_pgl_visitor_trailer(GthPGLVisitor *pgl_visitor)
{
  GthXMLPGLVisitor *visitor = xml_pgl_visitor_cast(pgl_visitor);
  gth_indent(visitor->out->outfp, visitor->indentlevel);
  gt_file_xprintf(visitor->out->outfp, "\n");
}

const GthPGLVisitorClass* gth_xml_pgl_visitor_class()
{
  static const GthPGLVisitorClass pglvc = { sizeof (GthXMLPGLVisitor),
                                            NULL,
                                            xml_pgl_visitor_preface,
                                            NULL,
                                            xml_pgl_visitor_visit_pgl,
                                            xml_pgl_visitor_trailer };
  return &pglvc;
}

GthPGLVisitor* gth_xml_pgl_visitor_new(GthInput *input,
                                       unsigned long translationtable,
                                       unsigned int indentlevel, GthOutput *out)
{
  GthPGLVisitor *pgl_visitor =
    gth_pgl_visitor_create(gth_xml_pgl_visitor_class());
  GthXMLPGLVisitor *visitor = xml_pgl_visitor_cast(pgl_visitor);
  visitor->input = input;
  visitor->translationtable = translationtable;
  visitor->indentlevel = indentlevel;
  visitor->out = out;
  return pgl_visitor;
}
genometools-1.5.1/src/gth/xml_pgl_visitor.h000066400000000000000000000027121211610345200210110ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef XML_PGL_VISITOR_H
#define XML_PGL_VISITOR_H

#include "gth/input.h"
#include "gth/pgl_visitor.h"

/* implements the ``spliced alignment visitor'' interface */
typedef struct GthXMLPGLVisitor GthXMLPGLVisitor;

const GthPGLVisitorClass* gth_xml_pgl_visitor_class(void);
GthPGLVisitor*            gth_xml_pgl_visitor_new(GthInput*,
                                                  unsigned long
                                                  translationtable,
                                                  unsigned int indentlevel,
                                                  GthOutput*);

#endif
genometools-1.5.1/src/gtlua/000077500000000000000000000000001211610345200157475ustar00rootroot00000000000000genometools-1.5.1/src/gtlua/alphabet_lua.c000066400000000000000000000111021211610345200205270ustar00rootroot00000000000000 /*
  Copyright (c) 2007-2009 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "lauxlib.h"
#include "core/alphabet.h"
#include "extended/luahelper.h"
#include "gtlua/alphabet_lua.h"

static int alphabet_lua_new_protein(lua_State *L)
{
  GtAlphabet **alpha;
  gt_assert(L);
  alpha = lua_newuserdata(L, sizeof *alpha);
  gt_assert(alpha);
  *alpha = gt_alphabet_new_protein();
  gt_assert(*alpha);
  luaL_getmetatable(L, ALPHABET_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int alphabet_lua_new_empty(lua_State *L)
{
  GtAlphabet **alpha;
  gt_assert(L);
  alpha = lua_newuserdata(L, sizeof *alpha);
  gt_assert(alpha);
  *alpha = gt_alphabet_new_empty();
  gt_assert(*alpha);
  luaL_getmetatable(L, ALPHABET_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int alphabet_lua_new_dna(lua_State *L)
{
  GtAlphabet **alpha;
  gt_assert(L);
  alpha = lua_newuserdata(L, sizeof *alpha);
  gt_assert(alpha);
  *alpha = gt_alphabet_new_dna();
  gt_assert(*alpha);
  luaL_getmetatable(L, ALPHABET_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int alphabet_lua_add_mapping(lua_State *L)
{
  GtAlphabet **alpha;
  const char *characters;
  alpha = check_alphabet(L, 1);
  characters = luaL_checkstring(L, 2);
  luaL_argcheck(L, strlen(characters), 2,
                "mapping must contain at least one character");
  gt_alphabet_add_mapping(*alpha, characters);
  return 0;
}

static int alphabet_lua_add_wildcard(lua_State *L)
{
  GtAlphabet **alpha;
  const char *wildcard;
  alpha = check_alphabet(L, 1);
  wildcard = luaL_checkstring(L, 2);
  luaL_argcheck(L, strlen(wildcard) == 1, 2,
                "wildcard string must have length 0");
  gt_alphabet_add_wildcard(*alpha, wildcard[0]);
  return 0;
}

static int alphabet_lua_decode(lua_State *L)
{
  GtAlphabet **alpha;
  unsigned int code;
  char character;
  alpha = check_alphabet(L, 1);
  code = luaL_checkinteger(L, 2);
  /* XXX: too restrictive, does not consider wildcards */
  luaL_argcheck(L, code < gt_alphabet_size(*alpha), 2, "invalid code");
  character = gt_alphabet_decode(*alpha, code);
  lua_pushlstring(L, &character, 1);
  return 1;
}

static int alphabet_lua_size(lua_State *L)
{
  GtAlphabet **alpha;
  unsigned int size;
  alpha = check_alphabet(L, 1);
  size = gt_alphabet_size(*alpha);
  lua_pushinteger(L, size);
  return 1;
}

static int alphabet_lua_delete(lua_State *L)
{
  GtAlphabet **alpha;
  alpha = check_alphabet(L, 1);
  gt_alphabet_delete(*alpha);
  return 0;
}

static const struct luaL_Reg alphabet_lib_f [] = {
  { "alphabet_new_dna", alphabet_lua_new_dna },
  { "alphabet_new_protein", alphabet_lua_new_protein },
  { "alphabet_new_empty", alphabet_lua_new_empty },
  { NULL, NULL }
};

static const struct luaL_Reg alphabet_lib_m [] = {
  { "add_mapping", alphabet_lua_add_mapping },
  { "add_wildcard", alphabet_lua_add_wildcard },
  { "decode", alphabet_lua_decode },
  { "size", alphabet_lua_size },
  { NULL, NULL }
};

int gt_lua_open_alphabet(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, ALPHABET_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, alphabet_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, alphabet_lib_m);
  lua_pop(L, 1);
  luaL_register(L, "gt", alphabet_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}

void gt_lua_alphabet_push(lua_State *L, GtAlphabet *alpha)
{
  GtAlphabet **alphaptr;
  gt_assert(L && alpha);
  alphaptr = lua_newuserdata(L, sizeof (*alphaptr));
  *alphaptr = alpha;
  luaL_getmetatable(L, ALPHABET_METATABLE);
  lua_setmetatable(L, -2);
}
genometools-1.5.1/src/gtlua/alphabet_lua.h000066400000000000000000000036741211610345200205530ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ALPHABET_LUA_H
#define ALPHABET_LUA_H

#include "lua.h"
#include "core/alphabet.h"

/* exports the Alphabet class to Lua:

   -- Return a new protein alphabet.
   function alphabet_new_protein()

   -- Return a new DNA alphabet.
   function alphabet_new_dna()

   -- Return an empty alphabet.
   function alphabet_new_empty()

   -- Add the mapping of all given  to the given .
   -- The first character is the result of subsequent  calls.
   function alphabet:add_mapping(characters)

   -- Add  to .
   function alphabet:add_wildcard(characters)

   -- Return a string containing the decoded character of the  number.
   function alphabet:decode(code)

   -- Return the size of  as a number.
   function alphabet:size()
*/
int gt_lua_open_alphabet(lua_State*);

/* Push a  to Lua, takes ownership! */
void gt_lua_alphabet_push(lua_State*, GtAlphabet*);

#define ALPHABET_METATABLE  "GenomeTools.alphabet"
#define check_alphabet(L, POS) \
          (GtAlphabet**) luaL_checkudata(L, POS, ALPHABET_METATABLE)

#endif
genometools-1.5.1/src/gtlua/annotationsketch_lua.c000066400000000000000000000025411211610345200223320ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/assert_api.h"
#include "gtlua/canvas_lua.h"
#include "gtlua/diagram_lua.h"
#include "gtlua/image_info_lua.h"
#include "gtlua/layout_lua.h"
#include "gtlua/annotationsketch_lua.h"

int gt_lua_open_annotationsketch(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  gt_lua_open_canvas(L);
  gt_lua_open_diagram(L);
  gt_lua_open_imageinfo(L);
  gt_lua_open_layout(L);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/annotationsketch_lua.h000066400000000000000000000017501211610345200223400ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ANNOTATIONSKETCH_LUA_H
#define ANNOTATIONSKETCH_LUA_H

#include "lua.h"

int gt_lua_open_annotationsketch(lua_State*);

#endif
genometools-1.5.1/src/gtlua/bittab_lua.c000066400000000000000000000102701211610345200202210ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "core/bittab.h"
#include "core/error.h"
#include "extended/luahelper.h"
#include "gtlua/bittab_lua.h"
#include "gtlua/gtcore_lua.h"

#define BITTAB_METATABLE  "GenomeTools.bittab"
#define check_bittab(L, POS) \
        (GtBittab**) luaL_checkudata(L, POS, BITTAB_METATABLE)

static int bittab_lua_new(lua_State *L)
{
  long num_of_bits;
  GtBittab **bittab;
  gt_assert(L);
  num_of_bits = luaL_checklong(L, 1);
  luaL_argcheck(L, num_of_bits > 0, 1, "must be > 0");
  bittab = lua_newuserdata(L, sizeof (GtBittab*));
  gt_assert(bittab);
  *bittab = gt_bittab_new(num_of_bits);
  luaL_getmetatable(L, BITTAB_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static void get_bittab_and_bit(lua_State *L, GtBittab ***bittab, long *bit)
{
  *bittab = check_bittab(L, 1);
  *bit = luaL_checklong(L, 2);
  luaL_argcheck(L, *bit >= 0, 2, "bit number too small");
  luaL_argcheck(L, *bit < gt_bittab_size(**bittab), 2, "bit number too large");
}

static void get_two_bittabs(lua_State *L, GtBittab ***bt1, GtBittab ***bt2)
{
 *bt1 = check_bittab(L, 1);
 *bt2 = check_bittab(L, 2);
 luaL_argcheck(L, gt_bittab_size(**bt1) == gt_bittab_size(**bt2), 1,
               "bittabs have different sizes");
}

static int bittab_lua_set_bit(lua_State *L)
{
  GtBittab **bittab;
  long bit;
  get_bittab_and_bit(L, &bittab, &bit);
  gt_bittab_set_bit(*bittab, bit);
  return 0;
}

static int bittab_lua_unset_bit(lua_State *L)
{
  GtBittab **bittab;
  long bit;
  get_bittab_and_bit(L, &bittab, &bit);
  gt_bittab_unset_bit(*bittab, bit);
  return 0;
}

static int bittab_lua_complement(lua_State *L)
{
  GtBittab **dest, **src;
  get_two_bittabs(L, &dest, &src);
  gt_bittab_complement(*dest, *src);
  return 0;
}

static int bittab_lua_equal(lua_State *L)
{
  GtBittab **dest, **src;
  get_two_bittabs(L, &dest, &src);
  gt_bittab_equal(*dest, *src);
  return 0;
}

static int bittab_lua_and_equal(lua_State *L)
{
  GtBittab **dest, **src;
  get_two_bittabs(L, &dest, &src);
  gt_bittab_and_equal(*dest, *src);
  return 0;
}

static int bittab_lua_bit_is_set(lua_State *L)
{
  GtBittab **bittab;
  long bit;
  get_bittab_and_bit(L, &bittab, &bit);
  lua_pushboolean(L, gt_bittab_bit_is_set(*bittab, bit));
  return 1;
}

static int bittab_lua_delete(lua_State *L)
{
  GtBittab **bittab;
  bittab = check_bittab(L, 1);
  gt_bittab_delete(*bittab);
  return 0;
}

static const struct luaL_Reg bittab_lib_f [] = {
  { "bittab_new", bittab_lua_new },
  { NULL, NULL }
};

static const struct luaL_Reg bittab_lib_m [] = {
  { "set_bit", bittab_lua_set_bit },
  { "unset_bit", bittab_lua_unset_bit },
  { "complement", bittab_lua_complement },
  { "equal", bittab_lua_equal},
  { "and_equal", bittab_lua_and_equal},
  { "bit_is_set", bittab_lua_bit_is_set},
  { NULL, NULL }
};

int gt_lua_open_bittab(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, BITTAB_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, bittab_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, bittab_lib_m);
  lua_pop(L, 1);
  luaL_register(L, "gt", bittab_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/bittab_lua.h000066400000000000000000000033211211610345200202250ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef BITTAB_LUA_H
#define BITTAB_LUA_H

#include "lua.h"

/* exports the Bittab class to Lua:

   -- Returns a bittab with  many bits.
   function bittab_new(num_of_bits)

   -- Set  in .
   function bittab:set_bit(bit)

   -- Unset  in .
   function bittab:unset_bit(bit)

   -- Store the complement of bittab  in .
   --  and  must have the same size.
   function bittab:complement(src)

   -- Set  equal to bittab .
   --  and  must have the same size.
   function bittab:equal(src)

   -- Set  equal to the bitwise AND of  and .
   --  and  must have the same size.
   function bittab:and_equal(src)

   -- Returns true if  is set in , false otherwise.
   function bittab:bit_is_set(bit)
*/
int gt_lua_open_bittab(lua_State*);

#endif
genometools-1.5.1/src/gtlua/canvas_lua.c000066400000000000000000000102161211610345200202270ustar00rootroot00000000000000/*
  Copyright (c) 2008 Sascha Steinbiss 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef WITHOUT_CAIRO

#include "lauxlib.h"
#include "annotationsketch/canvas_cairo_file.h"
#include "annotationsketch/luastyle.h"
#include "core/error.h"
#include "extended/luahelper.h"
#include "gtlua/canvas_lua.h"
#include "gtlua/image_info_lua.h"

static int canvas_cairo_file_lua_new_generic(lua_State *L, GtGraphicsOutType t)
{
  GtCanvas **canvas;
  GtImageInfo **ii;
  unsigned int width,
               height;
  GtError *err;
  GtStyle *style;
  width = luaL_checkint(L, 1);
  height = luaL_checkint(L, 2);
  /* create canvas */
  style = gt_lua_get_style_from_registry(L);
  canvas = lua_newuserdata(L, sizeof (GtCanvas*));
  gt_assert(canvas);
  /* if a imageinfo object is passed, it must be correct type */
  if (lua_isnil(L, 3)) {
    err = gt_error_new();
    *canvas = gt_canvas_cairo_file_new(style, t, width, height, NULL, err);
  } else {
    ii = check_imageinfo(L, 3);
    err = gt_error_new();
    *canvas = gt_canvas_cairo_file_new(style, t, width, height, *ii, err);
  }
  if (gt_error_is_set(err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  luaL_getmetatable(L, CANVAS_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int canvas_cairo_file_lua_new_pdf(lua_State *L)
{
  return canvas_cairo_file_lua_new_generic(L, GT_GRAPHICS_PDF);
}

static int canvas_cairo_file_lua_new_png(lua_State *L)
{
  return canvas_cairo_file_lua_new_generic(L, GT_GRAPHICS_PNG);
}

static int canvas_cairo_file_lua_new_svg(lua_State *L)
{
  return canvas_cairo_file_lua_new_generic(L, GT_GRAPHICS_SVG);
}

static int canvas_cairo_file_lua_new_ps(lua_State *L)
{
  return canvas_cairo_file_lua_new_generic(L, GT_GRAPHICS_PS);
}

static int canvas_cairo_file_lua_to_file(lua_State *L)
{
  GtCanvas **canvas;
  GtCanvasCairoFile *ccf = NULL;
  GtError *err;
  const char *fn;
  int had_err = 0;
  canvas = check_canvas(L, 1);
  ccf = canvas_cairo_file_try_cast(*canvas);
  luaL_argcheck(L, ccf, 1, "must be a CanvasCairoFile object");
  fn = luaL_checkstring(L, 2);
  gt_assert(canvas);
  err = gt_error_new();
  had_err = gt_canvas_cairo_file_to_file(ccf, fn, err);
  if (had_err)
    return gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

static int canvas_lua_delete(lua_State *L)
{
  GtCanvas **canvas;
  canvas = check_canvas(L, 1);
  gt_canvas_delete(*canvas);
  return 0;
}

static const struct luaL_Reg canvas_lib_f [] = {
  { "canvas_cairo_file_new_png", canvas_cairo_file_lua_new_png },
  { "canvas_cairo_file_new_pdf", canvas_cairo_file_lua_new_pdf },
  { "canvas_cairo_file_new_ps", canvas_cairo_file_lua_new_ps },
  { "canvas_cairo_file_new_svg", canvas_cairo_file_lua_new_svg },
  { NULL, NULL }
};

static const struct luaL_Reg canvas_lib_m [] = {
  { "to_file", canvas_cairo_file_lua_to_file },
  { NULL, NULL }
};

int gt_lua_open_canvas(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, CANVAS_METATABLE);
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, canvas_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, canvas_lib_m);
  lua_pop(L, 1);
  luaL_register(L, "gt", canvas_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}

#endif
genometools-1.5.1/src/gtlua/canvas_lua.h000066400000000000000000000046711211610345200202440ustar00rootroot00000000000000/*
  Copyright (c) 2008 Sascha Steinbiss 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef CANVAS_LUA_H
#define CANVAS_LUA_H

#include "lua.h"

/* exports the Canvas class to Lua:

   -- Return a Canvas object which acts as a PNG drawing surface of
   -- width  to be passed to rendering functions as a visitor.
   -- An  object is filled with coordinate information if given.
   -- If not needed, pass nil as .
   function canvas_cairo_file_new_png(width, imageinfo)

   -- Return a Canvas object which acts as a PDF drawing surface of
   -- width  to be passed to rendering functions as a visitor.
   -- An  object is filled with coordinate information if given.
   function canvas_cairo_file_new_pdf(width, imageinfo)

   -- Return a Canvas object which acts as a PS drawing surface of
   -- width  to be passed to rendering functions as a visitor.
   -- An  object is filled with coordinate information if given.
   function canvas_cairo_file_new_ps(width, imageinfo)

   -- Return a Canvas object which acts as a SVG drawing surface of
   -- width  to be passed to rendering functions as a visitor.
   -- An  object is filled with coordinate information if given.
   function canvas_cairo_file_new_svg(width, imageinfo)

   -- Creates an image file with the given  which contains the
   -- contents of the canvas (only for objects created with
   -- ).
   function canvas:to_file(filename)
*/
int gt_lua_open_canvas(lua_State*);

#define CANVAS_METATABLE  "GenomeTools.canvas"
#define check_canvas(L, POS) \
              (GtCanvas**) luaL_checkudata(L, POS, CANVAS_METATABLE)

#endif
genometools-1.5.1/src/gtlua/cds_stream_lua.c000066400000000000000000000042211211610345200210770ustar00rootroot00000000000000/*
  Copyright (c) 2010 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "extended/cds_stream_api.h"
#include "extended/luahelper.h"
#include "gtlua/cds_stream_lua.h"
#include "gtlua/genome_stream_lua.h"
#include "gtlua/region_mapping_lua.h"

static int cds_stream_lua_new(lua_State *L)
{
  GtNodeStream **cds_stream, **in_stream;
  GtRegionMapping **region_mapping;
  in_stream = check_genome_stream(L, 1);
  region_mapping = check_region_mapping(L, 2);
  cds_stream = lua_newuserdata(L, sizeof (GtNodeStream*));
  gt_assert(cds_stream);
  *cds_stream = gt_cds_stream_new(*in_stream,
                                  gt_region_mapping_ref(*region_mapping),
                                  1, /* XXX */
                                  "gtscript",
                                  true, /* XXX */
                                  true, /* XXX */
                                  false /* XXX */);
  luaL_getmetatable(L, GENOME_STREAM_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static const struct luaL_Reg cds_stream_lib_f [] = {
  { "cds_stream_new", cds_stream_lua_new },
  { NULL, NULL }
};

int gt_lua_open_cds_stream(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_register(L, "gt", cds_stream_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/cds_stream_lua.h000066400000000000000000000027261211610345200211140ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef CDS_STREAM_LUA_H
#define CDS_STREAM_LUA_H

#include "lua.h"

/* exports the CDSStream class (which implements the GtNodeStream) interface
   to Lua:

   -- Returns a new CDS (coding sequence) stream object (a genome stream) which
   -- uses genome stream  as input.
   -- The CDS stream adds CDS features to exon features in .
   -- The given  is used to map the sequence regions given in
   --  to the actual sequence files necessary for computing the
   -- coding sequences.
   function cds_stream_new(in_stream, region_mapping)
*/
int gt_lua_open_cds_stream(lua_State*);

#endif
genometools-1.5.1/src/gtlua/csa_stream_lua.c000066400000000000000000000036571211610345200211100ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "extended/csa_stream_api.h"
#include "extended/luahelper.h"
#include "gtlua/genome_stream_lua.h"
#include "gtlua/csa_stream_lua.h"

static int csa_stream_lua_new(lua_State *L)
{
  GtNodeStream **csa_stream, **in_stream;
  long join_length;
  in_stream = check_genome_stream(L, 1);
  if (lua_gettop(L) >= 2) {
    join_length = luaL_checklong(L, 2);
    luaL_argcheck(L, join_length >= 0, 2, "must be >= 0");
  }
  else
    join_length = GT_DEFAULT_JOIN_LENGTH;
  csa_stream = lua_newuserdata(L, sizeof (GtNodeStream*));
  gt_assert(csa_stream);
  *csa_stream = gt_csa_stream_new(*in_stream, join_length);
  luaL_getmetatable(L, GENOME_STREAM_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static const struct luaL_Reg csa_stream_lib_f [] = {
  { "csa_stream_new", csa_stream_lua_new },
  { NULL, NULL }
};

int gt_lua_open_csa_stream(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_register(L, "gt", csa_stream_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/csa_stream_lua.h000066400000000000000000000026621211610345200211100ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef CSA_STREAM_LUA_H
#define CSA_STREAM_LUA_H

#include "lua.h"

/* exports the CSAStream class (which implements the GtNodeStream) interface
   to Lua:

   -- Returns a new CSA (consensus spliced alignment) stream object (a genome
   -- stream) which uses genome stream  as input.
   -- The CSA stream replaces spliced alignments with computed consensus spliced
   -- alignments.
   -- The optional  parameters sets the length for the spliced alignment
   -- clustering (default: 300).
   function csa_stream_new(in_stream, join)
*/
int gt_lua_open_csa_stream(lua_State*);

#endif
genometools-1.5.1/src/gtlua/diagram_lua.c000066400000000000000000000122451211610345200203640ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef WITHOUT_CAIRO

#include "lauxlib.h"
#include "annotationsketch/canvas.h"
#include "annotationsketch/diagram.h"
#include "extended/feature_index.h"
#include "annotationsketch/luastyle.h"
#include "core/error.h"
#include "extended/luahelper.h"
#include "gtlua/canvas_lua.h"
#include "gtlua/diagram_lua.h"
#include "gtlua/feature_index_lua.h"
#include "gtlua/genome_node_lua.h"
#include "gtlua/range_lua.h"
#include "core/unused_api.h"

static int diagram_lua_new(lua_State *L)
{
  GtDiagram **diagram;
  GtFeatureIndex **feature_index;
  GtRange *range;
  GtError *err;
  const char *seqid;
  GtStyle *style;
  bool has_seqid;
  /* get feature index */
  feature_index = check_feature_index(L, 1);
  /* get seqid */
  seqid = luaL_checkstring(L, 2);
  err = gt_error_new();
  if (gt_feature_index_has_seqid(*feature_index, &has_seqid, seqid, err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  luaL_argcheck(L, has_seqid,
                2, "feature index does not contain the given sequence id");
  /* get range */
  range = check_range(L, 3);
  /* create diagram */
  style = gt_lua_get_style_from_registry(L);
  diagram = lua_newuserdata(L, sizeof (GtDiagram*));
  gt_assert(diagram);
  err = gt_error_new();
  *diagram = gt_diagram_new(*feature_index, seqid, range, style, err);
  if (gt_error_is_set(err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  luaL_getmetatable(L, DIAGRAM_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static GtArray* genome_node_table_to_array(lua_State *L)
{
  lua_Integer i = 1;
  GtArray *nodes;
  GtGenomeNode **gn;
  GT_UNUSED const char *msg;
  bool error;
  /* make sure we got a table as first argument */
  luaL_checktype(L, 1, LUA_TTABLE);
  /* traverse table and save the ranges */
  nodes = gt_array_new(sizeof (GtGenomeNode*));
  lua_pushinteger(L, i);
  lua_gettable(L, 1);
  while (!lua_isnil(L, -1)) {
    error = false;
    gn = lua_touserdata(L, -1);
    if (gn && lua_getmetatable(L, -1)) {
      lua_getfield(L, LUA_REGISTRYINDEX, GENOME_NODE_METATABLE);
      if (lua_rawequal(L, -1, -2)) {
        lua_pop(L, 2); /* remove both metatables */
        gt_array_add(nodes, *gn);
      }
      else
        error = true;
    }
    else
      error = true;
    if (error) {
      /* we have a non-GenomeNode in the table */
      msg = lua_pushfstring(L, "expected %s as type of table entry %d",
                            GENOME_NODE_METATABLE, i);
      gt_array_delete(nodes);
      lua_error(L);
    }
    i++;
    lua_pop(L, 1); /* pop last result */
    lua_pushinteger(L, i);
    lua_gettable(L, 1);
  }
  return nodes;
}

static int diagram_lua_new_from_array(lua_State *L)
{
  GtDiagram **diagram;
  GtArray *nodes;
  GtRange range;
  GtStyle *style;
  /* get array */
  nodes = genome_node_table_to_array(L);
  /* get range */
  range.start = luaL_checklong(L, 2);
  range.end   = luaL_checklong(L, 3);
  luaL_argcheck(L, range.start > 0, 2, "must be > 0");
  luaL_argcheck(L, range.end > 0, 3, "must be > 0");
  luaL_argcheck(L, range.start <= range.end, 2, "must be <= endpos");
  /* create diagram */
  style = gt_lua_get_style_from_registry(L);
  diagram = lua_newuserdata(L, sizeof (GtDiagram*));
  gt_assert(diagram);
  *diagram = gt_diagram_new_from_array(nodes, &range, style);
  gt_array_delete(nodes);
  luaL_getmetatable(L, DIAGRAM_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int diagram_lua_delete(lua_State *L)
{
  GtDiagram **diagram;
  diagram = check_diagram(L, 1);
  gt_diagram_delete(*diagram);
  return 0;
}

static const struct luaL_Reg diagram_lib_f [] = {
  { "diagram_new", diagram_lua_new },
  { "diagram_new_from_array", diagram_lua_new_from_array },
  { NULL, NULL }
};

static const struct luaL_Reg diagram_lib_m [] = {
  { NULL, NULL }
};

int gt_lua_open_diagram(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, DIAGRAM_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, diagram_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, diagram_lib_m);
  lua_pop(L, 1);
  luaL_register(L, "gt", diagram_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}

#endif
genometools-1.5.1/src/gtlua/diagram_lua.h000066400000000000000000000031631211610345200203700ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef DIAGRAM_LUA_H
#define DIAGRAM_LUA_H

#include "lua.h"

/* exports the Diagram class to Lua:

   -- Return a diagram object which contains the genome nodes given in
   --  in the given  of the sequence region with sequence
   -- ID .
   function diagram_new(feature_index, range, seqid)

   -- Return a diagram object which contains the genome nodes given in
   -- . The range from  to  determines the visible
   -- region and should include the nodes in .
   function diagram_new_from_array(array, startpos, endpos)
*/
int gt_lua_open_diagram(lua_State*);

#define DIAGRAM_METATABLE  "GenomeTools.diagram"
#define check_diagram(L, POS) \
              (GtDiagram**) luaL_checkudata(L, POS, DIAGRAM_METATABLE)

#endif
genometools-1.5.1/src/gtlua/encseq_lua.c000066400000000000000000000734711211610345200202460ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "lauxlib.h"
#include "core/error.h"
#include "core/ma.h"
#include "core/str_array.h"
#include "core/unused_api.h"
#include "extended/luahelper.h"
#include "gtlua/alphabet_lua.h"
#include "gtlua/encseq_lua.h"
#include "gtlua/gtcore_lua.h"

#define ENCSEQ_BUFFER_METATABLE  "GenomeTools.encseq_buffer"

/* GtEncseqReader */

typedef struct {
  unsigned char *buf;
  unsigned long length;
} GtEncseqExtractedBuffer;

static void gt_lua_encseq_reader_push(lua_State *L, GtEncseqReader *reader)
{
  GtEncseqReader **readerptr;
  readerptr = lua_newuserdata(L, sizeof (GtEncseqReader*));
  *readerptr = reader;
  luaL_getmetatable(L, ENCSEQ_READER_METATABLE);
  lua_setmetatable(L, -2);
}

static int encseq_reader_lua_next_encoded_char(lua_State *L)
{
  GtEncseqReader **reader;
  unsigned char cc;
  reader = check_encseq_reader(L, 1);
  cc = gt_encseq_reader_next_encoded_char(*reader);
  lua_pushnumber(L, cc);
  return 1;
}

static int encseq_reader_lua_next_decoded_char(lua_State *L)
{
  GtEncseqReader **reader;
  char cc;
  reader = check_encseq_reader(L, 1);
  cc = gt_encseq_reader_next_decoded_char(*reader);
  lua_pushlstring(L, &cc, sizeof (char));
  return 1;
}

static int encseq_reader_lua_delete(lua_State *L)
{
  GtEncseqReader **reader;
  reader = check_encseq_reader(L, 1);
  gt_encseq_reader_delete(*reader);
  return 0;
}

static int encseq_reader_lua_reinit_with_readmode(lua_State *L)
{
  GtEncseq **encseq;
  GtEncseqReader **reader;
  unsigned long startpos;
  GtReadmode readmode;
  reader = check_encseq_reader(L, 1);
  encseq = check_encseq(L, 2);
  readmode = luaL_checknumber(L, 3);
  startpos = luaL_checknumber(L, 4);
  luaL_argcheck(L, startpos < gt_encseq_total_length(*encseq), 4,
                "cannot exceed total length of encoded sequence");
  gt_encseq_reader_reinit_with_readmode(*reader, *encseq, readmode, startpos);
  return 0;
}

/* GtEncseq */

static int encseq_lua_total_length(lua_State *L)
{
  GtEncseq **encseq;
  encseq = check_encseq(L, 1);
  lua_pushnumber(L, gt_encseq_total_length(*encseq));
  return 1;
}

static int encseq_lua_num_of_sequences(lua_State *L)
{
  GtEncseq **encseq;
  encseq = check_encseq(L, 1);
  lua_pushnumber(L, gt_encseq_num_of_sequences(*encseq));
  return 1;
}

static int encseq_lua_get_encoded_char(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long pos;
  int readmode;
  unsigned char cc;
  encseq = check_encseq(L, 1);
  pos = luaL_checknumber(L, 2);
  readmode = luaL_checknumber(L, 3);
  luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
                "cannot exceed total length of encoded sequence");
  cc = gt_encseq_get_encoded_char(*encseq, pos, readmode);
  lua_pushnumber(L, cc);
  return 1;
}

static int encseq_lua_get_decoded_char(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long pos;
  int readmode;
  char cc;
  encseq = check_encseq(L, 1);
  pos = luaL_checknumber(L, 2);
  readmode = luaL_checknumber(L, 3);
  luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
                "cannot exceed total length of encoded sequence");
  cc = gt_encseq_get_decoded_char(*encseq, pos, readmode);
  lua_pushlstring(L, &cc, sizeof (char));
  return 1;
}

static inline void push_values_as_table(lua_State *L, unsigned char *buf,
                                        unsigned long length)
{
  unsigned long i;
  gt_assert(buf && length > 0);
  lua_newtable(L);
  for (i = 0; i < length; i++) {
    /* lua_pushinteger(L, i+1); */ /* in Lua we index from 1 on */
    lua_pushinteger(L, buf[i]);
    lua_rawseti(L, -2, i+1);
  }
}

static int encseq_lua_push_buffer(lua_State *L, unsigned char *arr,
                                  unsigned long len)
{
  GtEncseqExtractedBuffer** buf;
  buf = lua_newuserdata(L, sizeof (GtEncseqExtractedBuffer*));
  gt_assert(buf);
  *buf = gt_malloc(sizeof (GtEncseqExtractedBuffer));
  gt_assert(*buf);
  (*buf)->buf = arr;
  (*buf)->length = len;
  luaL_getmetatable(L, ENCSEQ_BUFFER_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int encseq_lua_index_buffer(lua_State *L)
{
  GtEncseqExtractedBuffer **buf = luaL_checkudata(L, 1,
                                                  ENCSEQ_BUFFER_METATABLE);
  unsigned long num = luaL_checknumber(L, 2);
  luaL_argcheck(L, num <= (*buf)->length, 2,
                "must be inside extracted substring");
  lua_pushinteger(L, ((*buf)->buf)[num-1]);
  return 1;
}

static int encseq_lua_delete_buffer(lua_State *L)
{
  GtEncseqExtractedBuffer **buf = luaL_checkudata(L, 1,
                                                  ENCSEQ_BUFFER_METATABLE);
  gt_free((*buf)->buf);
  gt_free(*buf);
  return 0;
}

static int encseq_lua_extract_encoded(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long from, to;
  unsigned char *string;
  encseq = check_encseq(L, 1);
  from = luaL_checknumber(L, 2);
  to = luaL_checknumber(L, 3);
  luaL_argcheck(L, from <= to, 2, "must be <= range endposition");
  luaL_argcheck(L, to < gt_encseq_total_length(*encseq), 3,
                "cannot exceed total length of encoded sequence");
  string = gt_malloc((to - from + 1) * sizeof (unsigned char));
  gt_encseq_extract_encoded(*encseq, string, from, to);
  encseq_lua_push_buffer(L, string, (to - from + 1));
  return 1;
}

static int encseq_lua_extract_decoded(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long from, to;
  char *string;
  encseq = check_encseq(L, 1);
  from = luaL_checknumber(L, 2);
  to = luaL_checknumber(L, 3);
  luaL_argcheck(L, from <= to, 2, "must be <= range endposition");
  luaL_argcheck(L, to < gt_encseq_total_length(*encseq), 3,
                "cannot exceed total length of encoded sequence");
  string = gt_malloc((to - from + 1) * sizeof (char));
  gt_encseq_extract_decoded(*encseq, string, from, to);
  lua_pushlstring(L, string, (to - from + 1));
  gt_free(string);
  return 1;
}

static int encseq_lua_seqlength(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long pos;
  encseq = check_encseq(L, 1);
  pos = luaL_checknumber(L, 2);
  luaL_argcheck(L, pos < gt_encseq_num_of_sequences(*encseq), 2,
                "cannot exceed number of sequences");
  lua_pushnumber(L, gt_encseq_seqlength(*encseq, pos));
  return 1;
}

static int encseq_lua_seqstartpos(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long pos;
  encseq = check_encseq(L, 1);
  pos = luaL_checknumber(L, 2);
  luaL_argcheck(L, pos < gt_encseq_num_of_sequences(*encseq), 2,
                "cannot exceed number of sequences");
  lua_pushnumber(L, gt_encseq_seqstartpos(*encseq, pos));
  return 1;
}

static int encseq_lua_seqnum(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long pos;
  encseq = check_encseq(L, 1);
  pos = luaL_checknumber(L, 2);
  luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
                "cannot exceed total length of encoded sequence");
  lua_pushnumber(L, gt_encseq_seqnum(*encseq, pos));
  return 1;
}

static int encseq_lua_has_multiseq_support(lua_State *L)
{
  GtEncseq **encseq;
  encseq = check_encseq(L, 1);
  lua_pushboolean(L, gt_encseq_has_multiseq_support(*encseq));
  return 1;
}

static int encseq_lua_has_description_support(lua_State *L)
{
  GtEncseq **encseq;
  encseq = check_encseq(L, 1);
  lua_pushboolean(L, gt_encseq_has_description_support(*encseq));
  return 1;
}

static int encseq_lua_description(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long seqno, desclen;
  const char *string;
  encseq = check_encseq(L, 1);
  seqno = luaL_checknumber(L, 2);
  luaL_argcheck(L, seqno < gt_encseq_num_of_sequences(*encseq), 2,
                "cannot exceed number of sequences");
  string = gt_encseq_description(*encseq, &desclen, seqno);
  lua_pushlstring(L, string, desclen);
  return 1;
}

static int encseq_lua_num_of_files(lua_State *L)
{
  GtEncseq **encseq;
  encseq = check_encseq(L, 1);
  lua_pushnumber(L, gt_encseq_num_of_files(*encseq));
  return 1;
}

static int encseq_lua_effective_filelength(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long fileno;
  encseq = check_encseq(L, 1);
  fileno = luaL_checknumber(L, 2);
  luaL_argcheck(L, fileno < gt_encseq_num_of_files(*encseq), 2,
                "cannot exceed number of files");
  lua_pushnumber(L, gt_encseq_effective_filelength(*encseq, fileno));
  return 1;
}

static int encseq_lua_filestartpos(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long fileno;
  encseq = check_encseq(L, 1);
  fileno = luaL_checknumber(L, 2);
  luaL_argcheck(L, fileno < gt_encseq_num_of_files(*encseq), 2,
                "cannot exceed number of files");
  lua_pushnumber(L, gt_encseq_filestartpos(*encseq, fileno));
  return 1;
}

static int encseq_lua_filenum(lua_State *L)
{
  GtEncseq **encseq;
  unsigned long pos;
  encseq = check_encseq(L, 1);
  pos = luaL_checknumber(L, 2);
  luaL_argcheck(L, pos < gt_encseq_total_length(*encseq), 2,
                "cannot exceed total length of encoded sequence");
  lua_pushnumber(L, gt_encseq_filenum(*encseq, pos));
  return 1;
}

static int encseq_lua_filenames(lua_State *L)
{
  GtEncseq **encseq;
  const GtStrArray *filenames;
  unsigned long i;
  encseq = check_encseq(L, 1);
  filenames = gt_encseq_filenames(*encseq);
  lua_newtable(L);
  for (i = 0; i < gt_str_array_size(filenames); i++) {
    lua_pushinteger(L, i+1); /* in Lua we index from 1 on */
    lua_pushstring(L, gt_str_array_get(filenames, i));
    lua_rawset(L, -3);
  }
  return 1;
}

static int encseq_lua_alphabet(lua_State *L)
{
  GtEncseq **encseq;
  GtAlphabet *alpha;
  encseq = check_encseq(L, 1);
  gt_assert(*encseq);
  alpha = gt_alphabet_ref(gt_encseq_alphabet(*encseq));
  gt_lua_alphabet_push(L, alpha);
  return 1;
}

static int encseq_lua_mirror(lua_State *L)
{
  GtEncseq **encseq;
  GtError *err = gt_error_new();
  encseq = check_encseq(L, 1);
  gt_assert(*encseq);
  luaL_argcheck(L, !gt_encseq_is_mirrored(*encseq), 1, "is already mirrored");
  if (gt_encseq_mirror(*encseq, err) != 0)
    gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

static int encseq_lua_unmirror(lua_State *L)
{
  GtEncseq **encseq;
  encseq = check_encseq(L, 1);
  gt_assert(*encseq);
  luaL_argcheck(L, gt_encseq_is_mirrored(*encseq), 1, "is not mirrored");
  gt_encseq_unmirror(*encseq);
  return 0;
}

static int encseq_lua_is_mirrored(lua_State *L)
{
  GtEncseq **encseq;
  encseq = check_encseq(L, 1);
  gt_assert(*encseq);
  lua_pushboolean(L, gt_encseq_is_mirrored(*encseq));
  return 1;
}

static int encseq_lua_create_reader_with_readmode(lua_State *L)
{
  GtEncseq **encseq;
  GtEncseqReader *reader;
  unsigned long startpos;
  GtReadmode readmode;
  encseq = check_encseq(L, 1);
  readmode = luaL_checknumber(L, 2);
  startpos = luaL_checknumber(L, 3);
  luaL_argcheck(L, startpos < gt_encseq_total_length(*encseq), 3,
                "cannot exceed total length of encoded sequence");
  reader = gt_encseq_create_reader_with_readmode(*encseq, readmode, startpos);
  gt_assert(reader);
  gt_lua_encseq_reader_push(L, reader);
  return 1;
}

static int encseq_lua_delete(lua_State *L)
{
  GtEncseq **encseq;
  encseq = check_encseq(L, 1);
  gt_encseq_delete(*encseq);
  return 0;
}

/* GtEncseqEncoder */

static int encseq_encoder_lua_new(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = lua_newuserdata(L, sizeof (GtEncseqEncoder*));
  gt_assert(encoder);
  *encoder = gt_encseq_encoder_new();
  gt_assert(*encoder);
  luaL_getmetatable(L, ENCSEQ_ENCODER_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int encseq_encoder_lua_use_representation(lua_State *L)
{
  GtEncseqEncoder **encoder;
  const char *repr;
  GtError *err;
  encoder = check_encseq_encoder(L, 1);
  repr = luaL_checkstring(L, 2);
  gt_assert(*encoder);
  err = gt_error_new();
  if (gt_encseq_encoder_use_representation(*encoder, repr, err) != 0)
    gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

static int encseq_encoder_lua_representation(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  lua_pushstring(L, gt_str_get(gt_encseq_encoder_representation(*encoder)));
  return 1;
}

static int encseq_encoder_lua_use_symbolmap_file(lua_State *L)
{
  GtEncseqEncoder **encoder;
  const char *smapfile;
  GtError *err;
  encoder = check_encseq_encoder(L, 1);
  smapfile = luaL_checkstring(L, 2);
  gt_assert(*encoder);
  err = gt_error_new();
  if (gt_encseq_encoder_use_symbolmap_file(*encoder, smapfile, err) != 0)
    gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

static int encseq_encoder_lua_symbolmap_file(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  lua_pushstring(L, gt_encseq_encoder_symbolmap_file(*encoder));
  return 1;
}

static int encseq_encoder_lua_enable_description_support(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  gt_encseq_encoder_enable_description_support(*encoder);
  return 0;
}

static int encseq_encoder_lua_disable_description_support(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  gt_encseq_encoder_disable_description_support(*encoder);
  return 0;
}

static int encseq_encoder_lua_enable_multiseq_support(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  gt_encseq_encoder_enable_multiseq_support(*encoder);
  return 0;
}

static int encseq_encoder_lua_disable_multiseq_support(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  gt_encseq_encoder_disable_multiseq_support(*encoder);
  return 0;
}

static int encseq_encoder_lua_enable_lossless_support(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  gt_encseq_encoder_enable_lossless_support(*encoder);
  return 0;
}

static int encseq_encoder_lua_disable_lossless_support(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  gt_encseq_encoder_disable_lossless_support(*encoder);
  return 0;
}

static int encseq_encoder_lua_set_input_dna(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  gt_encseq_encoder_set_input_dna(*encoder);
  return 0;
}

static int encseq_encoder_lua_is_input_dna(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  lua_pushboolean(L, gt_encseq_encoder_is_input_dna(*encoder));
  return 1;
}

static int encseq_encoder_lua_set_input_protein(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  gt_encseq_encoder_set_input_protein(*encoder);
  return 0;
}

static int encseq_encoder_lua_is_input_protein(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_assert(*encoder);
  lua_pushboolean(L, gt_encseq_encoder_is_input_protein(*encoder));
  return 1;
}

static int encseq_encoder_lua_encode(lua_State *L)
{
  GtEncseqEncoder **encoder;
  GtStrArray *seqfiles = gt_str_array_new();
  GtError *err;
  const char *indexname;
  encoder = check_encseq_encoder(L, 1);
  err = gt_error_new();
  if (gt_lua_get_table_as_strarray(L, 2, seqfiles, err) != 0) {
    gt_str_array_delete(seqfiles);
    gt_lua_error(L, err);
  }
  indexname = luaL_checkstring(L, 3);
  gt_assert(*encoder);
  if (gt_encseq_encoder_encode(*encoder, seqfiles, indexname, err) != 0) {
    gt_str_array_delete(seqfiles);
    gt_lua_error(L, err);
  }
  gt_str_array_delete(seqfiles);
  gt_error_delete(err);
  return 0;
}

static int encseq_encoder_lua_delete(lua_State *L)
{
  GtEncseqEncoder **encoder;
  encoder = check_encseq_encoder(L, 1);
  gt_encseq_encoder_delete(*encoder);
  return 0;
}

/* GtEncseqLoader */

static int encseq_loader_lua_new(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = lua_newuserdata(L, sizeof (GtEncseqLoader*));
  gt_assert(loader);
  *loader = gt_encseq_loader_new();
  gt_assert(*loader);
  luaL_getmetatable(L, ENCSEQ_LOADER_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int encseq_loader_lua_enable_autosupport(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_enable_autosupport(*loader);
  return 0;
}

static int encseq_loader_lua_disable_autosupport(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_disable_autosupport(*loader);
  return 0;
}

static int encseq_loader_lua_require_description_support(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_require_description_support(*loader);
  return 0;
}

static int encseq_loader_lua_drop_description_support(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_drop_description_support(*loader);
  return 0;
}

static int encseq_loader_lua_require_multiseq_support(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_require_multiseq_support(*loader);
  return 0;
}

static int encseq_loader_lua_drop_multiseq_support(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_drop_multiseq_support(*loader);
  return 0;
}

static int encseq_loader_lua_require_lossless_support(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_require_lossless_support(*loader);
  return 0;
}

static int encseq_loader_lua_drop_lossless_support(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_drop_lossless_support(*loader);
  return 0;
}

static int encseq_loader_lua_mirror(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_mirror(*loader);
  return 0;
}

static int encseq_loader_lua_do_not_mirror(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_assert(*loader);
  gt_encseq_loader_do_not_mirror(*loader);
  return 0;
}

static int encseq_loader_lua_load(lua_State *L)
{
  GtEncseqLoader **loader;
  const char *indexname;
  GtError *err = gt_error_new();
  GtEncseq *encseq;
  loader = check_encseq_loader(L, 1);
  indexname = luaL_checkstring(L, 2);
  gt_assert(*loader);
  encseq = gt_encseq_loader_load(*loader, indexname, err);
  if (encseq == NULL)
    gt_lua_error(L, err);
  else {
    gt_lua_encseq_push(L, encseq);
  }
  gt_error_delete(err);
  return 1;
}

static int encseq_loader_lua_delete(lua_State *L)
{
  GtEncseqLoader **loader;
  loader = check_encseq_loader(L, 1);
  gt_encseq_loader_delete(*loader);
  return 0;
}

/* GtEncseqBuilder */

static int encseq_builder_lua_new(lua_State *L)
{
  GtEncseqBuilder **builder;
  GtAlphabet **alpha;
  builder = lua_newuserdata(L, sizeof (GtEncseqBuilder*));
  alpha = check_alphabet(L, 1);
  gt_assert(builder && *alpha);
  *builder = gt_encseq_builder_new(*alpha);
  gt_assert(*builder);
  luaL_getmetatable(L, ENCSEQ_BUILDER_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int encseq_builder_lua_enable_description_support(lua_State *L)
{
  GtEncseqBuilder **builder;
  builder = check_encseq_builder(L, 1);
  gt_assert(*builder);
  gt_encseq_builder_enable_description_support(*builder);
  return 0;
}

static int encseq_builder_lua_disable_description_support(lua_State *L)
{
  GtEncseqBuilder **builder;
  builder = check_encseq_builder(L, 1);
  gt_assert(*builder);
  gt_encseq_builder_disable_description_support(*builder);
  return 0;
}

static int encseq_builder_lua_enable_multiseq_support(lua_State *L)
{
  GtEncseqBuilder **builder;
  builder = check_encseq_builder(L, 1);
  gt_assert(*builder);
  gt_encseq_builder_enable_multiseq_support(*builder);
  return 0;
}

static int encseq_builder_lua_disable_multiseq_support(lua_State *L)
{
  GtEncseqBuilder **builder;
  builder = check_encseq_builder(L, 1);
  gt_assert(*builder);
  gt_encseq_builder_disable_multiseq_support(*builder);
  return 0;
}

static int encseq_builder_lua_add_str(lua_State *L)
{
  GtEncseqBuilder **builder;
  const char *str, *desc;
  builder = check_encseq_builder(L, 1);
  str = luaL_checkstring(L, 2);
  if (lua_isnil(L, 3))
    desc = "";
  else
    desc = luaL_checkstring(L, 3);
  gt_assert(*builder);
  gt_encseq_builder_add_cstr(*builder, str, strlen(str), desc);
  return 0;
}

static inline int gt_lua_get_table_as_uchararray(lua_State *L, int index,
                                                 unsigned char **outarray,
                                                 unsigned long *arrlen,
                                                 GtError *err)
{
  int had_err = 0, val;
  unsigned long i;
  unsigned char *arr;
  if (!lua_istable(L, index)) {
    gt_error_set(err, "argument is not a table");
    return -1;
  }
  *arrlen = lua_objlen(L, index);
  arr = gt_malloc(*arrlen * sizeof (unsigned char));
  for (i = 1; i <= *arrlen; i++)
  {
    lua_rawgeti(L, index, i);
    if (!lua_isnumber(L, -1)) {
      had_err = -1;
      gt_error_set(err, "input contains non-numeric value");
      break;
    }
    if (!had_err && (val = lua_tointeger(L, -1)) > UCHAR_MAX) {
      had_err = -1;
      gt_error_set(err, "input contains oversized encoded value");
    }
    if (!had_err)
      arr[i-1] = (unsigned char) val;
    lua_pop(L, 1);
  }
  *outarray = arr;
  return 0;
}

static int encseq_builder_lua_add_encoded(lua_State *L)
{
  GtEncseqBuilder **builder;
  const char *desc;
  unsigned char *arr = NULL;
  unsigned long arrlen = 0;
  GtError *err;
  builder = check_encseq_builder(L, 1);
  err = gt_error_new();
  if (gt_lua_get_table_as_uchararray(L, 2, &arr, &arrlen, err) != 0) {
    gt_lua_error(L, err);
  }
  if (lua_isnil(L, 3))
    desc = "";
  else
    desc = luaL_checkstring(L, 3);
  gt_assert(*builder);
  gt_encseq_builder_add_encoded_own(*builder, arr, arrlen, desc);
  gt_free(arr);
  gt_error_delete(err);
  return 0;
}

static int encseq_builder_lua_reset(lua_State *L)
{
  GtEncseqBuilder **builder;
  builder = check_encseq_builder(L, 1);
  gt_encseq_builder_reset(*builder);
  return 0;
}

static int encseq_builder_lua_build(lua_State *L)
{
  GtEncseqBuilder **builder;
  GtEncseq *encseq;
  GtError *err;
  builder = check_encseq_builder(L, 1);
  err = gt_error_new();
  encseq = gt_encseq_builder_build(*builder, err);
  if (encseq == NULL) {
    gt_lua_error(L, err);
  } else
    gt_lua_encseq_push(L, encseq);
  gt_error_delete(err);
  return 1;
}

static int encseq_builder_lua_delete(lua_State *L)
{
  GtEncseqBuilder **builder;
  builder = check_encseq_builder(L, 1);
  gt_encseq_builder_delete(*builder);
  return 0;
}

static const struct luaL_Reg encseq_lib_f [] = {
  { "encseq_encoder_new", encseq_encoder_lua_new },
  { "encseq_loader_new", encseq_loader_lua_new },
  { "encseq_builder_new", encseq_builder_lua_new },
  { NULL, NULL }
};

static const struct luaL_Reg encseq_reader_lib_m [] = {
  { "next_encoded_char", encseq_reader_lua_next_encoded_char },
  { "next_decoded_char", encseq_reader_lua_next_decoded_char },
  { "reinit_with_readmode", encseq_reader_lua_reinit_with_readmode },
  { NULL, NULL }
};

static const struct luaL_Reg encseq_encoder_lib_m [] = {
  { "use_representation", encseq_encoder_lua_use_representation },
  { "representation", encseq_encoder_lua_representation },
  { "use_symbolmap_file", encseq_encoder_lua_use_symbolmap_file },
  { "symbolmap_file", encseq_encoder_lua_symbolmap_file },
  { "enable_description_support",
                                encseq_encoder_lua_enable_description_support },
  { "disable_description_support",
                               encseq_encoder_lua_disable_description_support },
  { "enable_multiseq_support", encseq_encoder_lua_enable_multiseq_support },
  { "disable_multiseq_support", encseq_encoder_lua_disable_multiseq_support },
  { "enable_lossless_support", encseq_encoder_lua_enable_lossless_support },
  { "disable_lossless_support", encseq_encoder_lua_disable_lossless_support },
  { "set_input_dna", encseq_encoder_lua_set_input_dna },
  { "is_input_dna", encseq_encoder_lua_is_input_dna },
  { "set_input_protein", encseq_encoder_lua_set_input_protein },
  { "is_input_protein", encseq_encoder_lua_is_input_protein },
  { "encode", encseq_encoder_lua_encode },
  { NULL, NULL }
};

static const struct luaL_Reg encseq_loader_lib_m [] = {
  { "enable_autosupport", encseq_loader_lua_enable_autosupport },
  { "disable_autosupport", encseq_loader_lua_disable_autosupport },
  { "require_description_support",
                                encseq_loader_lua_require_description_support },
  { "drop_description_support", encseq_loader_lua_drop_description_support },
  { "require_multiseq_support", encseq_loader_lua_require_multiseq_support },
  { "drop_multiseq_support", encseq_loader_lua_drop_multiseq_support },
  { "require_lossless_support", encseq_loader_lua_require_lossless_support },
  { "drop_lossless_support", encseq_loader_lua_drop_lossless_support },
  { "mirror", encseq_loader_lua_mirror },
  { "do_not_mirror", encseq_loader_lua_do_not_mirror },
  { "load", encseq_loader_lua_load },
  { NULL, NULL }
};

static const struct luaL_Reg encseq_builder_lib_m [] = {
  { "enable_description_support",
                                encseq_builder_lua_enable_description_support },
  { "disable_description_support",
                               encseq_builder_lua_disable_description_support },
  { "enable_multiseq_support", encseq_builder_lua_enable_multiseq_support },
  { "disable_multiseq_support", encseq_builder_lua_disable_multiseq_support },
  { "add_string", encseq_builder_lua_add_str },
  { "add_encoded", encseq_builder_lua_add_encoded },
  { "build", encseq_builder_lua_build },
  { "reset", encseq_builder_lua_reset },
  { NULL, NULL }
};

static const struct luaL_Reg encseq_lib_m [] = {
  { "total_length", encseq_lua_total_length },
  { "num_of_sequences", encseq_lua_num_of_sequences },
  { "get_encoded_char", encseq_lua_get_encoded_char },
  { "get_decoded_char", encseq_lua_get_decoded_char },
  { "create_reader_with_readmode", encseq_lua_create_reader_with_readmode },
  { "extract_encoded", encseq_lua_extract_encoded },
  { "extract_decoded", encseq_lua_extract_decoded },
  { "seqlength", encseq_lua_seqlength },
  { "seqstartpos", encseq_lua_seqstartpos },
  { "seqnum", encseq_lua_seqnum },
  { "has_multiseq_support", encseq_lua_has_multiseq_support },
  { "has_description_support", encseq_lua_has_description_support },
  { "description", encseq_lua_description },
  { "filenames", encseq_lua_filenames },
  { "num_of_files", encseq_lua_num_of_files },
  { "effective_filelength", encseq_lua_effective_filelength },
  { "filestartpos", encseq_lua_filestartpos },
  { "filenum", encseq_lua_filenum },
  { "alphabet", encseq_lua_alphabet },
  { "mirror", encseq_lua_mirror },
  { "unmirror", encseq_lua_unmirror },
  { "is_mirrored", encseq_lua_is_mirrored },
  { NULL, NULL }
};

int gt_lua_open_encseq(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, ENCSEQ_METATABLE);
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, encseq_lua_delete);
  lua_settable(L, -3);
  luaL_register(L, NULL, encseq_lib_m);
  gt_lua_export_metatable(L, ENCSEQ_METATABLE);

  luaL_newmetatable(L, ENCSEQ_BUFFER_METATABLE);
  lua_pushcfunction(L, encseq_lua_index_buffer);
  lua_setfield(L, -2, "__index");
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, encseq_lua_delete_buffer);
  lua_settable(L, -3);
  lua_pop(L, 1);

  luaL_newmetatable(L, ENCSEQ_READER_METATABLE);
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, encseq_reader_lua_delete);
  lua_settable(L, -3);
  luaL_register(L, NULL, encseq_reader_lib_m);
  gt_lua_export_metatable(L, ENCSEQ_READER_METATABLE);

  luaL_newmetatable(L, ENCSEQ_ENCODER_METATABLE);
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, encseq_encoder_lua_delete);
  lua_settable(L, -3);
  luaL_register(L, NULL, encseq_encoder_lib_m);
  gt_lua_export_metatable(L, ENCSEQ_ENCODER_METATABLE);

  luaL_newmetatable(L, ENCSEQ_LOADER_METATABLE);
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, encseq_loader_lua_delete);
  lua_settable(L, -3);
  luaL_register(L, NULL, encseq_loader_lib_m);
  gt_lua_export_metatable(L, ENCSEQ_LOADER_METATABLE);

  luaL_newmetatable(L, ENCSEQ_BUILDER_METATABLE);
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, encseq_builder_lua_delete);
  lua_settable(L, -3);
  luaL_register(L, NULL, encseq_builder_lib_m);
  gt_lua_export_metatable(L, ENCSEQ_BUILDER_METATABLE);

  luaL_register(L, "gt", encseq_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}

void gt_lua_encseq_push(lua_State *L, GtEncseq *encseq)
{
  GtEncseq **encseqptr;
  gt_assert(L);
  encseqptr = lua_newuserdata(L, sizeof (GtEncseq*));
  *encseqptr = encseq;
  luaL_getmetatable(L, ENCSEQ_METATABLE);
  lua_setmetatable(L, -2);
}
genometools-1.5.1/src/gtlua/encseq_lua.h000066400000000000000000000040221211610345200202350ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ENCSEQ_LUA_H
#define ENCSEQ_LUA_H

#include "lua.h"
#include "core/encseq_api.h"

/* exports the Encseq class to Lua:      (XXX: document me)

   -- Returns a XXX with XXX.
   function ...(...)

*/
int gt_lua_open_encseq(lua_State*);

/* Push a  to Lua, takes ownership! */
void gt_lua_encseq_push(lua_State*, GtEncseq*);

#define ENCSEQ_METATABLE  "GenomeTools.encseq"
#define check_encseq(L, POS) \
        (GtEncseq**) luaL_checkudata(L, POS, ENCSEQ_METATABLE)

#define ENCSEQ_ENCODER_METATABLE  "GenomeTools.encseq_encoder"
#define check_encseq_encoder(L, POS) \
        (GtEncseqEncoder**) luaL_checkudata(L, POS, ENCSEQ_ENCODER_METATABLE)

#define ENCSEQ_LOADER_METATABLE  "GenomeTools.encseq_loader"
#define check_encseq_loader(L, POS) \
        (GtEncseqLoader**) luaL_checkudata(L, POS, ENCSEQ_LOADER_METATABLE)

#define ENCSEQ_BUILDER_METATABLE  "GenomeTools.encseq_builder"
#define check_encseq_builder(L, POS) \
        (GtEncseqBuilder**) luaL_checkudata(L, POS, ENCSEQ_BUILDER_METATABLE)

#define ENCSEQ_READER_METATABLE  "GenomeTools.encseq_reader"
#define check_encseq_reader(L, POS) \
        (GtEncseqReader**) luaL_checkudata(L, POS, ENCSEQ_READER_METATABLE)

#endif
genometools-1.5.1/src/gtlua/feature_index_lua.c000066400000000000000000000203741211610345200216040ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "core/unused_api.h"
#include "core/ma.h"
#include "extended/feature_index_memory_api.h"
#include "extended/feature_node.h"
#include "extended/luahelper.h"
#include "gtlua/feature_index_lua.h"
#include "gtlua/genome_node_lua.h"
#include "gtlua/range_lua.h"

static int feature_index_memory_lua_new(lua_State *L)
{
  GtFeatureIndex **feature_index;
  feature_index = lua_newuserdata(L, sizeof (GtFeatureIndex*));
  gt_assert(feature_index);
  *feature_index = gt_feature_index_memory_new();
  luaL_getmetatable(L, FEATURE_INDEX_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int feature_index_lua_add_region_node(lua_State *L)
{
  GtFeatureIndex **fi;
  GtGenomeNode **gn;
  GtRegionNode *rn;
  GtError *err;
  gt_assert(L);
  fi = check_feature_index(L, 1);
  gn = check_genome_node(L, 2);
  rn = gt_region_node_try_cast(*gn);
  luaL_argcheck(L, rn, 2, "not a region node");
  err = gt_error_new();
  if (gt_feature_index_add_region_node(*fi, rn, err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

static int feature_index_lua_add_gff3file(lua_State *L)
{
  GtFeatureIndex **fi;
  const char *filename;
  GtError *err;
  gt_assert(L);
  fi = check_feature_index(L, 1);
  filename = luaL_checkstring(L, 2);
  err = gt_error_new();
  if (gt_feature_index_add_gff3file(*fi, filename, err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

static int feature_index_lua_add_feature_node(lua_State *L)
{
  GtFeatureIndex **fi;
  GtGenomeNode **gn;
  GtFeatureNode *fn;
  GtStr *seqid;
  GtError *err;
  bool has_seqid;
  gt_assert(L);
  fi = check_feature_index(L, 1);
  gn = check_genome_node(L, 2);
  fn = gt_feature_node_cast(*gn);
  luaL_argcheck(L, fn, 2, "not a feature node");
  seqid = gt_genome_node_get_seqid(*gn);
  luaL_argcheck(L, seqid, 2, "feature does not have a sequence id");
  err = gt_error_new();
  if (gt_feature_index_has_seqid(*fi, &has_seqid, gt_str_get(seqid), err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  luaL_argcheck(L, has_seqid, 2,
                "feature index does not contain corresponding sequence region");
  err = gt_error_new();
  if (gt_feature_index_add_feature_node(*fi, fn, err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

static void push_features_as_table(lua_State *L, GtArray *features)
{
  unsigned long i;
  if (features && gt_array_size(features)) {
    /* push table containing feature references onto the stack */
    lua_newtable(L);
    for (i = 0; i < gt_array_size(features); i++) {
      lua_pushinteger(L, i+1); /* in Lua we index from 1 on */
      gt_lua_genome_node_push(L, gt_genome_node_ref(*(GtGenomeNode**)
                                                  gt_array_get(features, i)));
      lua_rawset(L, -3);
    }
  }
  else
    lua_pushnil(L);
}

static int feature_index_lua_get_features_for_seqid(lua_State *L)
{
  GtFeatureIndex **feature_index;
  const char *seqid;
  GtArray *features;
  GtError *err;
  feature_index = check_feature_index(L, 1);
  seqid = luaL_checkstring(L, 2);
  err = gt_error_new();
  features = gt_feature_index_get_features_for_seqid(*feature_index, seqid,
                                                     err);
  if (!features)
    return gt_lua_error(L, err);
  gt_error_delete(err);
  push_features_as_table(L, features);
  gt_array_delete(features);
  return 1;
}

static int feature_index_lua_get_features_for_range(lua_State *L)
{
  GtFeatureIndex **feature_index;
  const char *seqid;
  GtRange *range;
  GtError *err;
  bool has_seqid;
  GtArray *features;
  GT_UNUSED int had_err;

  feature_index = check_feature_index(L, 1);
  seqid = luaL_checkstring(L, 2);
  err = gt_error_new();
  if (gt_feature_index_has_seqid(*feature_index, &has_seqid, seqid, err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  luaL_argcheck(L, has_seqid, 2,
                "feature_index does not contain seqid");
  range = check_range(L, 3);
  features = gt_array_new(sizeof (GtGenomeNode*));
  err = gt_error_new();
  had_err = gt_feature_index_get_features_for_range(*feature_index, features,
                                                    seqid, range, err);
  if (had_err)
    return gt_lua_error(L, err);
  gt_error_delete(err);
  push_features_as_table(L, features);
  gt_array_delete(features);
  return 1;
}

static int feature_index_lua_get_first_seqid(lua_State *L)
{
  GtFeatureIndex **feature_index;
  char *seqid;
  GtError *err;
  feature_index = check_feature_index(L, 1);
  err = gt_error_new();
  seqid = gt_feature_index_get_first_seqid(*feature_index, err);
  if (gt_error_is_set(err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  if (seqid) {
    lua_pushstring(L, seqid);
    gt_free(seqid);
  } else
    lua_pushnil(L);
  return 1;
}

static int feature_index_lua_get_seqids(lua_State *L)
{
  GtFeatureIndex **feature_index;
  GtStrArray *seqids;
  GtError *err;
  feature_index = check_feature_index(L, 1);
  err = gt_error_new();
  seqids = gt_feature_index_get_seqids(*feature_index, err);
  if (!seqids)
    return gt_lua_error(L, err);
  gt_error_delete(err);
  /* push table containing sequence ids onto the stack */
  gt_lua_push_strarray_as_table(L, seqids);
  gt_str_array_delete(seqids);
  return 1;
}

static int feature_index_lua_get_range_for_seqid(lua_State *L)
{
  GtFeatureIndex **feature_index;
  const char *seqid;
  GtError *err;
  GtRange range;
  bool has_seqid;
  feature_index = check_feature_index(L, 1);
  seqid = luaL_checkstring(L, 2);
  err = gt_error_new();
  if (gt_feature_index_has_seqid(*feature_index, &has_seqid, seqid, err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  luaL_argcheck(L, has_seqid, 2,
                "feature_index does not contain seqid");
  err = gt_error_new();
  if (gt_feature_index_get_range_for_seqid(*feature_index, &range, seqid, err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  return gt_lua_range_push(L, range);
}

static int feature_index_lua_delete(lua_State *L)
{
  GtFeatureIndex **feature_index = check_feature_index(L, 1);
  gt_feature_index_delete(*feature_index);
  return 0;
}

static const struct luaL_Reg feature_index_lib_f [] = {
  { "feature_index_memory_new", feature_index_memory_lua_new },
  { NULL, NULL }
};

static const struct luaL_Reg feature_index_lib_m [] = {
  { "add_region_node", feature_index_lua_add_region_node },
  { "add_feature_node", feature_index_lua_add_feature_node },
  { "add_gff3file", feature_index_lua_add_gff3file },
  { "get_features_for_seqid", feature_index_lua_get_features_for_seqid },
  { "get_features_for_range", feature_index_lua_get_features_for_range },
  { "get_first_seqid", feature_index_lua_get_first_seqid },
  { "get_seqids", feature_index_lua_get_seqids },
  { "get_range_for_seqid", feature_index_lua_get_range_for_seqid },
  { NULL, NULL }
};

int gt_lua_open_feature_index(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, FEATURE_INDEX_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, feature_index_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, feature_index_lib_m);
  gt_lua_export_metatable(L, FEATURE_INDEX_METATABLE);
  luaL_register(L, "gt", feature_index_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/feature_index_lua.h000066400000000000000000000045331211610345200216100ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FEATURE_INDEX_LUA_H
#define FEATURE_INDEX_LUA_H

#include "lua.h"

/* exports the FeatureIndex class to Lua:

   -- Returns a new FeatureIndex object storing the index in memory.
   function feature_index_memory_new()

   -- Add all features from all sequence regions contained in  to
   -- .
   function feature_index:add_gff3file(gff3file)

   -- Add  to .
   function feature_index:add_region_node(region_node)

   -- Add  to , implicitly creating sequence
   -- region if not present before.
   function feature_index:add_feature_node(feature_node)

   -- Returns the feature nodes for sequence ID  in an array.
   function feature_index:get_features_for_seqid(seqid)

   -- Returns the genome features for sequence ID  within  in an
   -- array.
   function feature_index:get_features_for_range(seqid, range)

   -- Returns the first sequence ID stored in .
   function feature_index:get_first_seqid()

   -- Returns an array containins all sequence IDs stored in .
   function feature_index:get_seqids()

   -- Returns the range covered by features of sequence ID  in
   -- .
   function feature_index:get_range_for_seqid(seqid)
*/
int gt_lua_open_feature_index(lua_State*);

#define FEATURE_INDEX_METATABLE  "GenomeTools.feature_index"
#define check_feature_index(L, POS) \
          (GtFeatureIndex**) luaL_checkudata(L, POS, FEATURE_INDEX_METATABLE)

#endif
genometools-1.5.1/src/gtlua/feature_node_iterator_lua.c000066400000000000000000000071611211610345200233320ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "extended/feature_node_iterator_api.h"
#include "gtlua/genome_node_lua.h"
#include "gtlua/feature_node_iterator_lua.h"

#define GENOME_NODE_ITERATOR_METATABLE  "GenomeTools_genome.node_iterator"
#define check_gt_feature_node_iterator(L, POS) \
        (GtFeatureNodeIterator**) \
        luaL_checkudata(L, POS, GENOME_NODE_ITERATOR_METATABLE)

static int feature_node_iterator_lua_new(lua_State *L)
{
  GtFeatureNodeIterator **fni;
  GtFeatureNode **fn;
  gt_assert(L);
  fn = (GtFeatureNode**) check_genome_node(L, 1);
  fni = lua_newuserdata(L, sizeof (GtFeatureNodeIterator*));
  gt_assert(fni);
  *fni = gt_feature_node_iterator_new(*fn);
  luaL_getmetatable(L, GENOME_NODE_ITERATOR_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int feature_node_iterator_lua_new_direct(lua_State *L)
{
  GtFeatureNodeIterator **fni;
  GtFeatureNode **fn;
  gt_assert(L);
  fn = (GtFeatureNode**) check_genome_node(L, 1);
  fni = lua_newuserdata(L, sizeof (GtFeatureNodeIterator*));
  gt_assert(fni);
  *fni = gt_feature_node_iterator_new_direct(*fn);
  luaL_getmetatable(L, GENOME_NODE_ITERATOR_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int feature_node_iterator_lua_next(lua_State *L)
{
  GtFeatureNodeIterator **fni;
  GtFeatureNode *fn;
  fni = check_gt_feature_node_iterator(L, 1);
  fn = gt_feature_node_iterator_next(*fni);
  if (fn)
    gt_lua_genome_node_push(L, gt_genome_node_ref((GtGenomeNode*) fn));
  else
    lua_pushnil(L);
  return 1;
}

static int feature_node_iterator_lua_delete(lua_State *L)
{
  GtFeatureNodeIterator **gt_feature_node_iterator;
  gt_feature_node_iterator = check_gt_feature_node_iterator(L, 1);
  gt_feature_node_iterator_delete(*gt_feature_node_iterator);
  return 0;
}

static const struct luaL_Reg feature_node_iterator_lib_f [] = {
  { "feature_node_iterator_new", feature_node_iterator_lua_new },
  { "feature_node_iterator_new_direct", feature_node_iterator_lua_new_direct },
  { NULL, NULL }
};

static const struct luaL_Reg feature_node_iterator_lib_m [] = {
  { "next", feature_node_iterator_lua_next },
  { NULL, NULL }
};

int gt_lua_open_feature_node_iterator(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, GENOME_NODE_ITERATOR_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, feature_node_iterator_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, feature_node_iterator_lib_m);
  lua_pop(L, 1);
  luaL_register(L, "gt", feature_node_iterator_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/feature_node_iterator_lua.h000066400000000000000000000030331211610345200233310ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FEATURE_NODE_ITERATOR_LUA_H
#define FEATURE_NODE_ITERATOR_LUA_H

#include "lua.h"

/* exports the GenomeNodeIterator class to Lua:

   -- Returns a new genome node iterator which performs a depth-first traversel
   -- of  (including  itself).
   function feature_node_iterator_new(genome_node)

   -- Returns a noew genome node iterator wich iterates over all direct children
   -- of  (without  itself).
   function feature_node_iterator_new_direct(genome_node)

   -- Returns the next genome node for  or nil.
   function feature_node_iterator:next()
*/
int gt_lua_open_feature_node_iterator(lua_State*);

#endif
genometools-1.5.1/src/gtlua/feature_stream_lua.c000066400000000000000000000036221211610345200217650ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "extended/feature_stream_api.h"
#include "extended/luahelper.h"
#include "gtlua/genome_stream_lua.h"
#include "gtlua/feature_index_lua.h"
#include "gtlua/feature_stream_lua.h"

static int feature_stream_lua_new(lua_State *L)
{
  GtNodeStream **feature_stream, **in_stream;
  GtFeatureIndex **feature_index;
  feature_stream = lua_newuserdata(L, sizeof (GtNodeStream*));
  gt_assert(feature_stream);
  in_stream = check_genome_stream(L, 1);
  feature_index = check_feature_index(L, 2);
  *feature_stream = gt_feature_stream_new(*in_stream, *feature_index);
  luaL_getmetatable(L, GENOME_STREAM_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static const struct luaL_Reg feature_stream_lib_f [] = {
  { "feature_stream_new", feature_stream_lua_new },
  { NULL, NULL }
};

int gt_lua_open_feature_stream(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_register(L, "gt", feature_stream_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/feature_stream_lua.h000066400000000000000000000025711211610345200217740ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FEATURE_STREAM_LUA_H
#define FEATURE_STREAM_LUA_H

#include "lua.h"

/* exports the FeatureStream class (which implements the GtNodeStream) interface
   to Lua:

   -- Returns a new feature stream object (a genome stream) over 
   -- which uses the genome stream  as input.
   -- That is, all genome nodes which are pulled through the feature stream are
   -- added to the .
   function feature_stream_new(in_stream, feature_index)
*/
int gt_lua_open_feature_stream(lua_State*);

#endif
genometools-1.5.1/src/gtlua/feature_visitor_lua.c000066400000000000000000000035351211610345200221740ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "extended/feature_visitor.h"
#include "extended/luahelper.h"
#include "gtlua/feature_index_lua.h"
#include "gtlua/feature_visitor_lua.h"
#include "gtlua/genome_visitor_lua.h"

static int feature_visitor_lua_new(lua_State *L)
{
  GtNodeVisitor **feature_visitor;
  GtFeatureIndex **feature_index;
  feature_visitor = lua_newuserdata(L, sizeof (GtNodeVisitor*));
  gt_assert(feature_visitor);
  feature_index = check_feature_index(L, 1);
  *feature_visitor = gt_feature_visitor_new(*feature_index);
  luaL_getmetatable(L, GENOME_VISITOR_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static const struct luaL_Reg feature_visitor_lib_f [] = {
  { "feature_visitor_new", feature_visitor_lua_new },
  { NULL, NULL }
};

int gt_lua_open_feature_visitor(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_register(L, "gt", feature_visitor_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/feature_visitor_lua.h000066400000000000000000000024501211610345200221740ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FEATURE_VISITOR_LUA_H
#define FEATURE_VISITOR_LUA_H

#include "lua.h"

/* exports the FeatureVisitor class (which implements the GtNodeVisitor)
   interface to Lua:

   -- Returns a new feature visitor object over . That is, all
   -- genome nodes which are visited by the feature visitor are added to the
   -- .
   function feature_visitor_new(feature_index)
*/
int gt_lua_open_feature_visitor(lua_State*);

#endif
genometools-1.5.1/src/gtlua/genome_node_lua.c000066400000000000000000000274651211610345200212510ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "core/assert_api.h"
#include "extended/extract_feature_sequence.h"
#include "extended/genome_node.h"
#include "extended/gff3_output.h"
#include "extended/luahelper.h"
#include "gtlua/genome_node_lua.h"
#include "gtlua/genome_visitor_lua.h"
#include "gtlua/gt_lua.h"
#include "gtlua/range_lua.h"
#include "gtlua/region_mapping_lua.h"

static int feature_node_lua_new(lua_State *L)
{
  GtGenomeNode **gf;
  unsigned long startpos, endpos;
  GtStrand strand;
  const char *seqid, *type, *strand_str;
  size_t length;
  GtStr *seqid_str;
  gt_assert(L);
  /* get/check parameters */
  seqid = luaL_checkstring(L, 1);
  type = luaL_checkstring(L, 2);
  startpos = luaL_checklong(L, 3);
  endpos   = luaL_checklong(L, 4);
  luaL_argcheck(L, startpos > 0, 3, "must be > 0");
  luaL_argcheck(L, endpos > 0, 4, "must be > 0");
  luaL_argcheck(L, startpos <= endpos, 3, "must be <= endpos");
  strand_str = luaL_checklstring(L, 5, &length);
  luaL_argcheck(L, length == 1, 5, "strand string must have length 1");
  luaL_argcheck(L, (strand = gt_strand_get(strand_str[0])) !=
                    GT_NUM_OF_STRAND_TYPES, 5, "invalid strand");
  /* construct object */
  gf = lua_newuserdata(L, sizeof (GtGenomeNode*));
  seqid_str = gt_str_new_cstr(seqid);
  *gf = gt_feature_node_new(seqid_str, type, startpos, endpos, strand);
  gt_str_delete(seqid_str);
  gt_assert(*gf);
  luaL_getmetatable(L, GENOME_NODE_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int sequence_region_lua_new(lua_State *L)
{
  GtGenomeNode **rn;
  unsigned long startpos, endpos;
  const char *seqid;
  GtStr *seqid_str;
  gt_assert(L);
  /* get_check parameters */
  seqid = luaL_checkstring(L, 1);
  startpos = luaL_checklong(L, 2);
  endpos   = luaL_checklong(L, 3);
  luaL_argcheck(L, startpos > 0, 2, "must be > 0");
  luaL_argcheck(L, endpos > 0, 3, "must be > 0");
  luaL_argcheck(L, startpos <= endpos, 2, "must be <= endpos");
  /* construct object */
  rn = lua_newuserdata(L, sizeof (GtGenomeNode*));
  seqid_str = gt_str_new_cstr(seqid);
  *rn = gt_region_node_new(seqid_str, startpos, endpos);
  gt_str_delete(seqid_str);
  gt_assert(*rn);
  luaL_getmetatable(L, GENOME_NODE_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int genome_node_lua_get_filename(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  lua_pushstring(L, gt_genome_node_get_filename(*gn));
  return 1;
}

static int genome_node_lua_get_range(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  return gt_lua_range_push(L, gt_genome_node_get_range(*gn));
}

static int genome_node_lua_get_seqid(lua_State *L)
{
  GtStr *seqid;
  GtGenomeNode **gn = check_genome_node(L, 1);
  if ((seqid = gt_genome_node_get_seqid(*gn)))
    lua_pushstring(L, gt_str_get(seqid));
  else
    lua_pushnil(L);
  return 1;
}

static int feature_node_lua_get_strand(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  GtFeatureNode *fn;
  char strand_char[2];
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  strand_char[0] = GT_STRAND_CHARS[gt_feature_node_get_strand(fn)];
  strand_char[1] = '\0';
  lua_pushstring(L, strand_char);
  return 1;
}

static int feature_node_lua_get_source(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  GtFeatureNode *fn;
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  lua_pushstring(L, gt_feature_node_get_source(fn));
  return 1;
}

static int feature_node_lua_get_score(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  GtFeatureNode *fn;
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  if (gt_feature_node_score_is_defined(fn))
    lua_pushnumber(L, gt_feature_node_get_score(fn));
  else
    lua_pushnil(L);
  return 1;
}

static int feature_node_lua_get_attribute(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  const char *attr = NULL, *attrval = NULL;
  attr = luaL_checkstring(L, 2);
  GtFeatureNode *fn;
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  attrval = gt_feature_node_get_attribute(fn, attr);
  if (attrval)
    lua_pushstring(L, attrval);
  else
    lua_pushnil(L);
  return 1;
}

static int feature_node_lua_get_exons(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  GtArray *exons = gt_array_new(sizeof (GtGenomeNode*));
  unsigned long i = 0;
  GtFeatureNode *fn;
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  gt_feature_node_get_exons(fn, exons);
  lua_newtable(L);
  for (i = 0; i < gt_array_size(exons); i++) {
    lua_pushnumber(L, i+1);
    gt_lua_genome_node_push(L, (GtGenomeNode*)
                            gt_genome_node_ref(*(GtGenomeNode**)
                                               gt_array_get(exons, i)));
    lua_rawset(L, -3);
  }
  gt_array_delete(exons);
  return 1;
}

static int feature_node_lua_set_source(lua_State *L)
{
  const char *source;
  GtStr *source_str;
  GtGenomeNode **gn = check_genome_node(L, 1);
  GtFeatureNode *fn;
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  source = luaL_checkstring(L, 2);
  source_str = gt_str_new_cstr(source);
  gt_feature_node_set_source(fn, source_str);
  gt_str_delete(source_str);
  return 0;
}

static int genome_node_lua_accept(lua_State *L)
{
  GtGenomeNode **gn;
  GtNodeVisitor **gv;
  GtError *err;
  gn = check_genome_node(L, 1);
  gv = check_genome_visitor(L, 2);
  err = gt_error_new();
  if (gt_genome_node_accept(*gn, *gv, err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

static int genome_node_lua_add_child(lua_State *L)
{
  GtGenomeNode **parent, **child;
  GtFeatureNode *pf, *cf;
  parent = check_genome_node(L, 1);
  child  = check_genome_node(L, 2);
  pf = gt_feature_node_try_cast(*parent);
  luaL_argcheck(L, pf, 1, "not a feature node");
  cf = gt_feature_node_try_cast(*child);
  luaL_argcheck(L, cf, 2, "not a feature node");
  gt_feature_node_add_child(pf, (GtFeatureNode*)
                                gt_genome_node_ref((GtGenomeNode*) cf));
  return 0;
}

static int genome_node_lua_mark(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  gt_feature_node_mark(gt_feature_node_cast(*gn));
  return 0;
}

static int genome_node_lua_is_marked(lua_State *L)
{
  GtGenomeNode **gn = check_genome_node(L, 1);
  lua_pushboolean(L, gt_feature_node_is_marked(gt_feature_node_cast(*gn)));
  return 1;
}

static int genome_node_lua_contains_marked(lua_State *L)
{
  GtGenomeNode **gn;
  gn = check_genome_node(L, 1);
  lua_pushboolean(L,
                  gt_feature_node_contains_marked(gt_feature_node_cast(*gn)));
  return 1;
}

static int feature_node_lua_output_leading(lua_State *L)
{
  GtGenomeNode **gn;
  GtFeatureNode *fn;
  gn = check_genome_node(L, 1);
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  gt_gff3_output_leading(fn, NULL);
  return 0;
}

static int feature_node_lua_get_type(lua_State *L)
{
  GtGenomeNode **gn;
  GtFeatureNode *fn;
  gn = check_genome_node(L, 1);
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  lua_pushstring(L, gt_feature_node_get_type(fn));
  return 1;
}

static int feature_node_lua_extract_sequence(lua_State *L)
{
  GtGenomeNode **gn;
  GtFeatureNode *fn;
  const char *type;
  bool join;
  GtRegionMapping **region_mapping;
  GtStr *sequence;
  GtError *err;
  gn = check_genome_node(L, 1);
  /* make sure we get a feature node */
  fn = gt_feature_node_try_cast(*gn);
  luaL_argcheck(L, fn, 1, "not a feature node");
  type = luaL_checkstring(L, 2);
  join = lua_toboolean(L, 3);
  region_mapping = check_region_mapping(L, 4);
  err = gt_error_new();
  sequence = gt_str_new();
  if (gt_extract_feature_sequence(sequence, *gn, type, join, NULL, NULL,
                                  *region_mapping, err)) {
    gt_str_delete(sequence);
    return gt_lua_error(L, err);
  }
  if (gt_str_length(sequence))
    lua_pushstring(L, gt_str_get(sequence));
  else
    lua_pushnil(L);
  gt_str_delete(sequence);
  gt_error_delete(err);
  return 1;
}

static int feature_node_lua_remove_leaf(lua_State *L)
{
  GtGenomeNode **parent, **leaf;
  GtFeatureNode *pf, *lf;
  parent = check_genome_node(L, 1);
  leaf  = check_genome_node(L, 2);
  pf = gt_feature_node_try_cast(*parent);
  luaL_argcheck(L, pf, 1, "not a feature node");
  lf = gt_feature_node_try_cast(*leaf);
  luaL_argcheck(L, lf, 2, "not a feature node");
  gt_feature_node_remove_leaf(pf, lf);
  gt_genome_node_delete((GtGenomeNode*) lf);
  return 0;
}

static int genome_node_lua_delete(lua_State *L)
{
  GtGenomeNode **gn;
  gn = check_genome_node(L, 1);
  gt_genome_node_delete(*gn);
  return 0;
}

static const struct luaL_Reg genome_node_lib_f [] = {
  { "feature_node_new", feature_node_lua_new },
  { "region_node_new", sequence_region_lua_new },
  { NULL, NULL }
};

static const struct luaL_Reg genome_node_lib_m [] = {
  { "get_filename", genome_node_lua_get_filename },
  { "get_range", genome_node_lua_get_range },
  { "get_seqid", genome_node_lua_get_seqid },
  { "get_strand", feature_node_lua_get_strand },
  { "get_source", feature_node_lua_get_source },
  { "set_source", feature_node_lua_set_source },
  { "get_score", feature_node_lua_get_score },
  { "get_attribute", feature_node_lua_get_attribute },
  { "get_exons", feature_node_lua_get_exons },
  { "accept", genome_node_lua_accept },
  { "add_child", genome_node_lua_add_child },
  { "mark", genome_node_lua_mark },
  { "is_marked", genome_node_lua_is_marked },
  { "contains_marked", genome_node_lua_contains_marked },
  { "output_leading", feature_node_lua_output_leading },
  { "get_type", feature_node_lua_get_type },
  { "extract_sequence", feature_node_lua_extract_sequence },
  { "remove_leaf", feature_node_lua_remove_leaf },
  { NULL, NULL }
};

int gt_lua_open_genome_node(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, GENOME_NODE_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, genome_node_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, genome_node_lib_m);
  gt_lua_export_metatable(L, GENOME_NODE_METATABLE);
  luaL_register(L, "gt", genome_node_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}

void gt_lua_genome_node_push(lua_State *L, GtGenomeNode *gn)
{
  GtGenomeNode **gn_lua;
  gt_assert(L && gn);
  gn_lua = lua_newuserdata(L, sizeof (GtGenomeNode**));
  *gn_lua = gn;
  luaL_getmetatable(L, GENOME_NODE_METATABLE);
  lua_setmetatable(L, -2);
}
genometools-1.5.1/src/gtlua/genome_node_lua.h000066400000000000000000000073141211610345200212450ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GENOME_NODE_LUA_H
#define GENOME_NODE_LUA_H

#include "lua.h"
#include "extended/genome_node.h"

/* exports the GenomeNode interface and its implementors to Lua:

   -- Returns the filename of .
   function genome_node:get_filename()

   -- Returns the range of .
   function genome_node:get_range()

   -- Returns the sequence id of .
   function genome_node:get_seqid()

   -- Accept .
   function genome_node:accept(genome_visitor)

   -- Make  the parent of .
   function genome_node:is_part_of_genome_node(child_node)

   -- Mark .
   function genome_node:mark()

   -- Returns true if  is marked, false otherwise.
   function genome_node:is_marked()

   -- Returns true if  contains a marked node, false otherwise.
   function genome_node:contains_marked()

*/

/* exports the FeatureNode class to Lua:

   -- Create a new feature node on sequence with ID  and type 
   -- which lies from  to  on strand .
   --  and  always refer to the forward strand, therefore
   --  has to bo smaller or equal than .
   function feature_node_new(seqid, type, startpos, endpos, strand)

   -- Returns the strand of .
   function feature_node:get_strand()

   -- Returns the source of .
   function feature_node:get_source()

   -- Returns the score of .
   function feature_node:get_score()

   -- Returns the  attribute of .
   function feature_node:get_attribute(attrib)

   -- Returns an array containing the exons of .
   function feature_node:get_exons()

   -- Set the source of  to .
   function feature_node:set_source(source)

   -- Show leading part of GFF3 output for 
   function feature_node:output_leading()

   -- Return type of  as string.
   function feature_node:get_type()

   -- Extract the sequence of .
   -- If  is false and  has type  the sequence is
   -- returned (using  to get it).
   -- If  is true and  has children of type  their
   -- joined sequences are returned.
   -- If none of the above applies nil is returned.
   function feature_node:extract_sequence(type, join, region_mapping)

*/

/* exports the RegionNode class to Lua:

   -- Returns a new region node for sequence id  spanning .
   function region_node_new(seqid, range)
*/

int gt_lua_open_genome_node(lua_State*);

/* Push a  to Lua, takes ownership! */
void gt_lua_genome_node_push(lua_State*, GtGenomeNode*);

#define GENOME_NODE_METATABLE  "GenomeTools.genome_node"
#define check_genome_node(L, POS) \
                (GtGenomeNode**) luaL_checkudata(L, POS, GENOME_NODE_METATABLE)

#endif
genometools-1.5.1/src/gtlua/genome_stream_lua.c000066400000000000000000000067071211610345200216130ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "core/fileutils_api.h"
#include "extended/node_stream_api.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/luahelper.h"
#include "gtlua/genome_node_lua.h"
#include "gtlua/genome_stream_lua.h"

static int gff3_in_stream_lua_new_sorted(lua_State *L)
{
  GtNodeStream **gs;
  const char *filename;
  gt_assert(L);
  /* get/check parameters */
  filename = luaL_checkstring(L, 1);
  luaL_argcheck(L, gt_file_exists(filename), 1, "file does not exist");
  /* construct object */
  gs = lua_newuserdata(L, sizeof (GtNodeStream*));
  *gs = gt_gff3_in_stream_new_sorted(filename);
  gt_assert(*gs);
  luaL_getmetatable(L, GENOME_STREAM_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int gff3_out_stream_lua_new(lua_State *L)
{
  GtNodeStream **out_stream, **in_stream = check_genome_stream(L, 1);
  gt_assert(L);
  /* construct object */
  out_stream = lua_newuserdata(L, sizeof (GtNodeStream*));
  *out_stream = gt_gff3_out_stream_new(*in_stream, NULL);
  gt_assert(*out_stream);
  luaL_getmetatable(L, GENOME_STREAM_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int gt_node_stream_lua_next_tree(lua_State *L)
{
  GtNodeStream **gs = check_genome_stream(L, 1);
  GtGenomeNode *gn;
  GtError *err = gt_error_new();
  if (gt_node_stream_next(*gs, &gn, err))
    return gt_lua_error(L, err); /* handle error */
  else if (gn)
    gt_lua_genome_node_push(L, gn);
  else
    lua_pushnil(L);
  gt_error_delete(err);
  return 1;
}

static int gt_node_stream_lua_delete(lua_State *L)
{
  GtNodeStream **gs = check_genome_stream(L, 1);
  gt_node_stream_delete(*gs);
  return 0;
}

static const struct luaL_Reg gt_node_stream_lib_f [] = {
  { "gff3_in_stream_new_sorted", gff3_in_stream_lua_new_sorted },
  { "gff3_out_stream_new", gff3_out_stream_lua_new },
  { NULL, NULL }
};

static const struct luaL_Reg gt_node_stream_lib_m [] = {
  { "next_tree", gt_node_stream_lua_next_tree },
  { NULL, NULL }
};

int gt_lua_open_genome_stream(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, GENOME_STREAM_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, gt_node_stream_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, gt_node_stream_lib_m);
  lua_pop(L, 1);
  luaL_register(L, "gt", gt_node_stream_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/genome_stream_lua.h000066400000000000000000000033071211610345200216110ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GENOME_STREAM_LUA_H
#define GENOME_STREAM_LUA_H

#include "lua.h"

/* exports the GenomeStream interface and its implementors to Lua:
   -- Returns the next genome node for  or nil.
   function genome_stream:next_tree()
*/

/* exports the GFF3InStream class to Lua:
   -- Returns a new GFF3 input stream object for . The file 
   -- has to be a sorted GFF3 file.
   function gff3_in_stream_new_sorted(filename)
*/

/* exports the GFF3OutStream class to Lua:
   -- Returns a new GFF3 output stream which pulls its features from
   -- .
   function gff3_out_stream_new(genome_stream)
*/
int gt_lua_open_genome_stream(lua_State*);

#define GENOME_STREAM_METATABLE  "GenomeTools.genome_stream"
#define check_genome_stream(L, POS) \
          (GtNodeStream**) luaL_checkudata(L, POS, GENOME_STREAM_METATABLE)

#endif
genometools-1.5.1/src/gtlua/genome_visitor_lua.c000066400000000000000000000042271211610345200220120ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "extended/gff3_visitor_api.h"
#include "extended/luahelper.h"
#include "gtlua/genome_visitor_lua.h"

static int gff3_visitor_lua_new(lua_State *L)
{
  GtNodeVisitor **gv;
  gt_assert(L);
  /* construct object */
  gv = lua_newuserdata(L, sizeof (GtNodeVisitor*));
  *gv = gt_gff3_visitor_new(NULL);
  gt_assert(*gv);
  luaL_getmetatable(L, GENOME_VISITOR_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int gt_node_visitor_lua_delete(lua_State *L)
{
  GtNodeVisitor **gv = check_genome_visitor(L, 1);
  gt_node_visitor_delete(*gv);
  return 0;
}

static const struct luaL_Reg gt_node_visitor_lib_f [] = {
  { "gff3_visitor_new", gff3_visitor_lua_new },
  { NULL, NULL }
};

int gt_lua_open_genome_visitor(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, GENOME_VISITOR_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, gt_node_visitor_lua_delete);
  lua_settable(L, -3);
  lua_pop(L, 1);
  /* register functions */
  luaL_register(L, "gt", gt_node_visitor_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/genome_visitor_lua.h000066400000000000000000000025161211610345200220160ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GENOME_VISITOR_LUA_H
#define GENOME_VISITOR_LUA_H

#include "lua.h"

/* exports the GtNodeVisitor interface and its implementors to Lua:

*/

/* exports the GFF3Visitor class to Lua:
   -- Returns a new GFF3 visitor.
   function gff3_visitor_new()
*/

int gt_lua_open_genome_visitor(lua_State*);

#define GENOME_VISITOR_METATABLE  "GenomeTools.genome_visitor"
#define check_genome_visitor(L, POS) \
          (GtNodeVisitor**) luaL_checkudata(L, POS, GENOME_VISITOR_METATABLE)

#endif
genometools-1.5.1/src/gtlua/gt_lua.c000066400000000000000000000026241211610345200173720ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/assert_api.h"
#include "gtlua/gtcore_lua.h"
#include "gtlua/gtext_lua.h"
#include "gtlua/gt_lua.h"

#ifndef WITHOUT_CAIRO
#include "gtlua/annotationsketch_lua.h"
#endif

int gt_lua_open_lib(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  gt_lua_open_core(L); /* open core */
  gt_lua_open_extended(L); /* open extended */
#ifndef WITHOUT_CAIRO
  gt_lua_open_annotationsketch(L); /* open annotationsketch */
#endif
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/gt_lua.h000066400000000000000000000020021211610345200173650ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_LUA_H
#define GT_LUA_H

#include "lua.h"

/* Open GenomeTools library in Lua state . */
int                 gt_lua_open_lib(lua_State *L);

#endif
genometools-1.5.1/src/gtlua/gtcore_lua.c000066400000000000000000000030051211610345200202350ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/assert_api.h"
#include "gtlua/alphabet_lua.h"
#include "gtlua/bittab_lua.h"
#include "gtlua/encseq_lua.h"
#include "gtlua/gtcore_lua.h"
#include "gtlua/mathsupport_lua.h"
#include "gtlua/range_lua.h"
#include "gtlua/score_matrix_lua.h"
#include "gtlua/translate_lua.h"

int gt_lua_open_core(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  gt_lua_open_alphabet(L);
  gt_lua_open_bittab(L);
  gt_lua_open_encseq(L);
  gt_lua_open_mathsupport(L);
  gt_lua_open_range(L);
  gt_lua_open_score_matrix(L);
  gt_lua_open_translate(L);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/gtcore_lua.h000066400000000000000000000017101211610345200202430ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GTCORE_LUA_H
#define GTCORE_LUA_H

#include "lua.h"

int gt_lua_open_core(lua_State*);

#endif
genometools-1.5.1/src/gtlua/gtext_lua.c000066400000000000000000000035601211610345200201130ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/assert_api.h"
#include "gtlua/cds_stream_lua.h"
#include "gtlua/csa_stream_lua.h"
#include "gtlua/feature_index_lua.h"
#include "gtlua/feature_node_iterator_lua.h"
#include "gtlua/feature_stream_lua.h"
#include "gtlua/feature_visitor_lua.h"
#include "gtlua/genome_node_lua.h"
#include "gtlua/genome_stream_lua.h"
#include "gtlua/genome_visitor_lua.h"
#include "gtlua/gtext_lua.h"
#include "gtlua/region_mapping_lua.h"
#include "gtlua/stream_evaluator_lua.h"

int gt_lua_open_extended(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  gt_lua_open_cds_stream(L);
  gt_lua_open_csa_stream(L);
  gt_lua_open_feature_index(L);
  gt_lua_open_feature_node_iterator(L);
  gt_lua_open_feature_stream(L);
  gt_lua_open_feature_visitor(L);
  gt_lua_open_genome_node(L);
  gt_lua_open_genome_stream(L);
  gt_lua_open_genome_visitor(L);
  gt_lua_open_region_mapping(L);
  gt_lua_open_stream_evaluator(L);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/gtext_lua.h000066400000000000000000000017121211610345200201150ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GTEXT_LUA_H
#define GTEXT_LUA_H

#include "lua.h"

int gt_lua_open_extended(lua_State*);

#endif
genometools-1.5.1/src/gtlua/image_info_lua.c000066400000000000000000000107111211610345200210510ustar00rootroot00000000000000/*
  Copyright (c) 2008 Sascha Steinbiss 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef WITHOUT_CAIRO

#include 
#include 
#include "lauxlib.h"
#include "annotationsketch/image_info.h"
#include "annotationsketch/rec_map.h"
#include "core/error.h"
#include "extended/luahelper.h"
#include "gtlua/genome_node_lua.h"
#include "gtlua/image_info_lua.h"

static int imageinfo_lua_new(lua_State *L)
{
  GtImageInfo **ii;
  ii = lua_newuserdata(L, sizeof (GtImageInfo*));
  gt_assert(ii);
  *ii = gt_image_info_new();
  luaL_getmetatable(L, IMAGEINFO_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int imageinfo_lua_get_height(lua_State *L)
{
  GtImageInfo **ii;
  unsigned long height;
  GtError *err = NULL;
  ii = check_imageinfo(L, 1);
  gt_assert(ii);
  height = gt_image_info_get_height(*ii);
  if (height > DBL_MAX)
  {
    err = gt_error_new();
    gt_error_set(err, "image height exceeds %f!", DBL_MAX);
    return gt_lua_error(L, err);
  }
  else
    lua_pushnumber(L, (double) height);
  gt_error_delete(err);
  return 0;
}

static int imageinfo_lua_num_of_recmaps(lua_State *L)
{
  GtImageInfo **ii;
  unsigned long nof_rm;
  GtError *err = NULL;
  ii = check_imageinfo(L, 1);
  gt_assert(ii);
  nof_rm = gt_image_info_num_of_rec_maps(*ii);
  if (nof_rm > DBL_MAX)
  {
    err = gt_error_new();
    gt_error_set(err, "number of recmaps exceeds %f!", DBL_MAX);
    return gt_lua_error(L, err);
  }
  else
    lua_pushnumber(L, (double) nof_rm);
  gt_error_delete(err);
  return 0;
}

static void push_recmap_as_table(lua_State *L, const GtRecMap *rm)
{
  gt_assert(rm);
  lua_newtable(L);
  lua_pushstring(L, "nw_x");
  lua_pushnumber(L, gt_rec_map_get_northwest_x(rm));
  lua_rawset(L, -3);
  lua_pushstring(L, "nw_y");
  lua_pushnumber(L, gt_rec_map_get_northwest_y(rm));
  lua_rawset(L, -3);
  lua_pushstring(L, "se_x");
  lua_pushnumber(L, gt_rec_map_get_southeast_x(rm));
  lua_rawset(L, -3);
  lua_pushstring(L, "se_y");
  lua_pushnumber(L, gt_rec_map_get_southeast_y(rm));
  lua_rawset(L, -3);
  lua_pushstring(L, "feature_ref");
  gt_lua_genome_node_push(L, gt_genome_node_ref((GtGenomeNode*)
                                            gt_rec_map_get_genome_feature(rm)));
  lua_rawset(L, -3);
}

static int imageinfo_lua_recmaps_as_table(lua_State *L)
{
  GtImageInfo **ii;
  unsigned long num, i;
  ii = check_imageinfo(L, 1);
  gt_assert(ii);
  num = gt_image_info_num_of_rec_maps(*ii);
  if (num>0)
  {
    lua_newtable(L);
    for (i=0;i
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef IMAGE_INFO_LUA_H
#define IMAGE_INFO_LUA_H

#include "lua.h"

/* exports the Imageinfo class to Lua:

   -- returns a new ImageInfo object.
   function imageinfo_new()

   -- returns an array of tables with the fields "nw_x","nw_y","se_x","se_y" and
   -- "feature_ref" with the top left and bottom right coordinates in pixels or
   -- points and a GenomeNode reference per element drawn.
   function imageinfo:get_recmaps()
*/
int gt_lua_open_imageinfo(lua_State*);

#define IMAGEINFO_METATABLE  "GenomeTools.imageinfo"
#define check_imageinfo(L, POS) \
              (GtImageInfo**) luaL_checkudata(L, POS, IMAGEINFO_METATABLE)

#endif
genometools-1.5.1/src/gtlua/layout_lua.c000066400000000000000000000066331211610345200203010ustar00rootroot00000000000000/*
  Copyright (c) 2008-2010 Sascha Steinbiss 
  Copyright (c) 2008-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef WITHOUT_CAIRO

#include "lauxlib.h"
#include "annotationsketch/diagram.h"
#include "annotationsketch/layout.h"
#include "annotationsketch/luastyle.h"
#include "core/error.h"
#include "extended/luahelper.h"
#include "gtlua/canvas_lua.h"
#include "gtlua/diagram_lua.h"
#include "gtlua/layout_lua.h"

static int layout_lua_new(lua_State *L)
{
  GtLayout **layout;
  GtDiagram **diagram;
  unsigned int width;
  GtStyle *style;
  GtError *err;
  diagram = check_diagram(L, 1);
  width = luaL_checkint(L, 2);
  /* create layout */
  style = gt_lua_get_style_from_registry(L);
  layout = lua_newuserdata(L, sizeof (GtLayout*));
  gt_assert(layout);
  err = gt_error_new();
  *layout = gt_layout_new(*diagram, width, style, err);
  if (gt_error_is_set(err))
    return gt_lua_error(L, err);
  gt_error_delete(err);
  luaL_getmetatable(L, LAYOUT_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int layout_lua_sketch(lua_State *L)
{
  GtLayout **layout;
  GtCanvas **canvas;
  GtError *err;
  int had_err = 0;
  layout = check_layout(L, 1);
  canvas = check_canvas(L, 2);
  err = gt_error_new();
  had_err = gt_layout_sketch(*layout, *canvas, err);
  if (had_err < 0)
    return gt_lua_error(L, err);
  gt_error_delete(err);
  return 0;
}

static int layout_lua_get_height(lua_State *L)
{
  GtLayout **layout;
  GtError *err;
  int had_err = 0;
  unsigned long height;
  layout = check_layout(L, 1);
  err = gt_error_new();
  had_err = gt_layout_get_height(*layout, &height, err);
  lua_pushnumber(L, height);
  if (had_err < 0)
    return gt_lua_error(L, err);
  gt_error_delete(err);
  return 1;
}

static int layout_lua_delete(lua_State *L)
{
  GtLayout **layout;
  layout = check_layout(L, 1);
  gt_layout_delete(*layout);
  return 0;
}

static const struct luaL_Reg layout_lib_f [] = {
  { "layout_new", layout_lua_new },
  { NULL, NULL }
};

static const struct luaL_Reg layout_lib_m [] = {
  { "sketch", layout_lua_sketch },
  { "get_height", layout_lua_get_height },
  { NULL, NULL }
};

int gt_lua_open_layout(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, LAYOUT_METATABLE);
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, layout_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, layout_lib_m);
  lua_pop(L, 1);
  luaL_register(L, "gt", layout_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}

#endif
genometools-1.5.1/src/gtlua/layout_lua.h000066400000000000000000000027301211610345200203000ustar00rootroot00000000000000/*
  Copyright (c) 2008 Sascha Steinbiss 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LAYOUT_LUA_H
#define LAYOUT_LUA_H

#include "lua.h"

/* exports the Layout class to Lua:

   -- Return a Layout object which represents a layout of the content of
   --  with width .
   function layout_new(diagram, width)

   -- Return the height of the resulting .
   function layout:get_height(layout)

   -- Draw the content of the  on a given .
   function layout:sketch(layout, canvas)
*/
int gt_lua_open_layout(lua_State*);

#define LAYOUT_METATABLE  "GenomeTools.layout"
#define check_layout(L, POS) \
              (GtLayout**) luaL_checkudata(L, POS, LAYOUT_METATABLE)

#endif
genometools-1.5.1/src/gtlua/mathsupport_lua.c000066400000000000000000000027301211610345200213440ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "core/mathsupport.h"
#include "gtlua/mathsupport_lua.h"

static int gt_lua_mathsupport_rand_max(lua_State *L)
{
  unsigned long max = luaL_checknumber(L, 1);

  lua_pushnumber(L, gt_rand_max(max));
  return 1;
}

static const struct luaL_Reg mathsupport_lib_f [] = {
  { "rand_max", gt_lua_mathsupport_rand_max },
  { NULL, NULL }
};

int gt_lua_open_mathsupport(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_register(L, "gt", mathsupport_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/mathsupport_lua.h000066400000000000000000000021201211610345200213420ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef MATHSUPPORT_LUA_H
#define MATHSUPPORT_LUA_H

#include "lua.h"

/* exports the mathsupport module to Lua:

   -- Returns a random number between 0 and .
   function rand_max(val)
*/
int gt_lua_open_mathsupport(lua_State*);

#endif
genometools-1.5.1/src/gtlua/range_lua.c000066400000000000000000000117471211610345200200620ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "extended/luahelper.h"
#include "gtlua/range_lua.h"
#include "core/unused_api.h"

static int range_lua_new(lua_State *L)
{
  unsigned long startpos, endpos;
  GtRange *range;
  startpos = luaL_checklong(L, 1);
  endpos   = luaL_checklong(L, 2);
  luaL_argcheck(L, startpos > 0, 1, "must be > 0");
  luaL_argcheck(L, endpos > 0, 2, "must be > 0");
  luaL_argcheck(L, startpos <= endpos, 1, "must be <= endpos");
  range = lua_newuserdata(L, sizeof (GtRange));
  range->start = startpos;
  range->end   = endpos;
  luaL_getmetatable(L, RANGE_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int range_lua_get_start(lua_State *L)
{
  GtRange *range = check_range(L, 1);
  lua_pushinteger(L, range->start);
  return 1;
}

static int range_lua_get_end(lua_State *L)
{
  GtRange *range = check_range(L, 1);
  lua_pushinteger(L, range->end);
  return 1;
}

static int range_lua_overlap(lua_State *L)
{
  GtRange *range_a, *range_b;
  range_a = check_range(L, 1);
  range_b = check_range(L, 2);
  lua_pushboolean(L, gt_range_overlap(range_a, range_b));
  return 1;
}

static GtArray* range_table_to_array(lua_State *L)
{
  lua_Integer i = 1;
  GtArray *ranges;
  GtRange *range;
  GT_UNUSED const char *msg;
  bool error;
  /* make sure we got a table as first argument */
  luaL_checktype(L, 1, LUA_TTABLE);
  /* traverse table and save the ranges */
  ranges = gt_array_new(sizeof (GtRange));
  lua_pushinteger(L, i);
  lua_gettable(L, 1);
  while (!lua_isnil(L, -1)) {
    error = false;
    range = lua_touserdata(L, -1);
    if (range && lua_getmetatable(L, -1)) {
      lua_getfield(L, LUA_REGISTRYINDEX, RANGE_METATABLE);
      if (lua_rawequal(L, -1, -2)) {
        lua_pop(L, 2); /* remove both metatables */
        gt_array_add(ranges, *range);
      }
      else
        error = true;
    }
    else
      error = true;
    if (error) {
      /* we have a non range in the table */
      msg = lua_pushfstring(L, "expected %s as type of table entry %d",
                            RANGE_METATABLE, i);
      gt_array_delete(ranges);
      lua_error(L);
    }
    i++;
    lua_pop(L, 1); /* pop last result */
    lua_pushinteger(L, i);
    lua_gettable(L, 1);
  }
  return ranges;
}

static void push_range_array_as_table(lua_State *L, GtArray *ranges)
{
  unsigned long i;
  if (ranges && gt_array_size(ranges)) {
    lua_newtable(L);
    for (i = 0; i < gt_array_size(ranges); i++) {
      lua_pushinteger(L, i+1); /* in Lua we index from 1 on */
      gt_lua_range_push(L, *(GtRange*) gt_array_get(ranges, i));
      lua_rawset(L, -3);
    }
  }
  else
    lua_pushnil(L);
}

static int ranges_lua_sort(lua_State *L)
{
  GtArray *ranges;
  ranges = range_table_to_array(L);
  gt_ranges_sort(ranges);
  push_range_array_as_table(L, ranges);
  gt_array_delete(ranges);
  return 1;
}

static int ranges_lua_are_sorted(lua_State *L)
{
  GtArray *ranges;
  bool are_sorted;
  ranges = range_table_to_array(L);
  are_sorted = gt_ranges_are_sorted(ranges);
  gt_array_delete(ranges);
  lua_pushboolean(L, are_sorted);
  return 1;
}

static const struct luaL_Reg range_lib_f [] = {
  { "range_new", range_lua_new },
  { "ranges_sort", ranges_lua_sort},
  { "ranges_are_sorted", ranges_lua_are_sorted},
  { NULL, NULL }
};

static const struct luaL_Reg range_lib_m [] = {
  { "get_start", range_lua_get_start},
  { "get_end", range_lua_get_end},
  { "overlap", range_lua_overlap},
  { NULL, NULL }
};

int gt_lua_open_range(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, RANGE_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* register functions */
  luaL_register(L, NULL, range_lib_m);
  gt_lua_export_metatable(L, RANGE_METATABLE);
  luaL_register(L, "gt", range_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}

int gt_lua_range_push(lua_State *L, GtRange inrange)
{
  GtRange *outrange;
  gt_assert(L);
  outrange = lua_newuserdata(L, sizeof (GtRange));
  *outrange = inrange;
  luaL_getmetatable(L, RANGE_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}
genometools-1.5.1/src/gtlua/range_lua.h000066400000000000000000000036401211610345200200600ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RANGE_LUA_H
#define RANGE_LUA_H

#include "lua.h"
#include "core/range.h"

/* exports the Range class to Lua:

   -- Returns a new range object with start  and end .
   --  must be smaller or equal than .
   function range_new(startpos, endpos)

   -- Returns start of .
   function range:get_start()

   -- Returns end of .
   function range:get_end()

   -- Returns true if  and  overlap, false otherwise.
   function range:overlap(other_range)

   -- Returns an array containing the ranges from array  in sorted
   -- order.
   function ranges_sort(range_array)

   -- Returns true if the ranges in array  are sorted, false
   -- otherwise.
   function ranges_are_sorted(range_array)
*/
int gt_lua_open_range(lua_State*);

/* push a GtRange to Lua, returns 1 (number of elements pushed) */
int gt_lua_range_push(lua_State*, GtRange);

#define RANGE_METATABLE  "GenomeTools.range"
#define check_range(L, POS) \
          (GtRange*) luaL_checkudata(L, POS, RANGE_METATABLE)

#endif
genometools-1.5.1/src/gtlua/region_mapping_lua.c000066400000000000000000000050651211610345200217600ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "extended/luahelper.h"
#include "extended/region_mapping_api.h"
#include "gtlua/region_mapping_lua.h"
#include "gtlua/gtcore_lua.h"

static int region_mapping_lua_new_seqfile(lua_State *L)
{
  const char *seqfilename;
  GtStrArray *seqfile;
  GtRegionMapping **region_mapping;
  gt_assert(L);
  seqfilename = luaL_checkstring(L, 1);
  region_mapping = lua_newuserdata(L, sizeof (GtRegionMapping*));
  gt_assert(region_mapping);
  seqfile = gt_str_array_new();
  gt_str_array_add_cstr(seqfile, seqfilename);
  /* XXX: make second and third parameter available */
  *region_mapping = gt_region_mapping_new_seqfiles(seqfile, false, false);
  gt_str_array_delete(seqfile);
  luaL_getmetatable(L, REGION_MAPPING_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int region_mapping_lua_delete(lua_State *L)
{
  GtRegionMapping **region_mapping;
  region_mapping = check_region_mapping(L, 1);
  gt_region_mapping_delete(*region_mapping);
  return 0;
}

static const struct luaL_Reg region_mapping_lib_f [] = {
  { "region_mapping_new_seqfile", region_mapping_lua_new_seqfile },
  { NULL, NULL }
};

int gt_lua_open_region_mapping(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, REGION_MAPPING_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, region_mapping_lua_delete);
  lua_settable(L, -3);
  lua_pop(L, 1);
  /* register functions */
  luaL_register(L, "gt", region_mapping_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/region_mapping_lua.h000066400000000000000000000025111211610345200217560ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef REGION_MAPPING_LUA_H
#define REGION_MAPPING_LUA_H

#include "lua.h"

/* exports the RegionMapping class to Lua:

   -- Returns a new region mapping which maps everything onto sequence file
   -- .
   function region_mapping_new_seqfile(seqfile)
*/
int gt_lua_open_region_mapping(lua_State*);

#define REGION_MAPPING_METATABLE  "GenomeTools.region_mapping"
#define check_region_mapping(L, POS) \
        (GtRegionMapping**) luaL_checkudata(L, POS, REGION_MAPPING_METATABLE)

#endif
genometools-1.5.1/src/gtlua/score_matrix_lua.c000066400000000000000000000105561211610345200214620ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "core/score_matrix.h"
#include "extended/luahelper.h"
#include "gtlua/alphabet_lua.h"
#include "gtlua/score_matrix_lua.h"

#define SCOREMATRIX_METATABLE  "GenomeTools.score_matrix"
#define check_score_matrix(L, POS) \
        (GtScoreMatrix**) luaL_checkudata(L, POS, SCOREMATRIX_METATABLE)

static int score_matrix_lua_new_read_protein(lua_State *L)
{
  GtScoreMatrix **sm;
  const char *path;
  GtError *err;
  gt_assert(L);
  path = luaL_checkstring(L, 1);
  sm = lua_newuserdata(L, sizeof (GtScoreMatrix*));
  gt_assert(sm);
  err = gt_error_new();
  if (!(*sm = gt_score_matrix_new_read_protein(path, err)))
    return gt_lua_error(L, err); /* handle error */
  gt_error_delete(err);
  gt_assert(*sm);
  luaL_getmetatable(L, SCOREMATRIX_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int score_matrix_lua_new_read(lua_State *L)
{
  GtScoreMatrix **sm;
  GtAlphabet **alpha;
  const char *path;
  GtError *err;
  gt_assert(L);
  path = luaL_checkstring(L, 1);
  alpha = check_alphabet(L, 2);
  sm = lua_newuserdata(L, sizeof (GtScoreMatrix*));
  gt_assert(sm);
  err = gt_error_new();
  if (!(*sm = gt_score_matrix_new_read(path, *alpha, err)))
    return gt_lua_error(L, err); /* handle error */
  gt_error_delete(err);
  gt_assert(*sm);
  luaL_getmetatable(L, SCOREMATRIX_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int score_matrix_lua_get_dimension(lua_State *L)
{
  GtScoreMatrix **sm;
  unsigned int dimension;
  sm = check_score_matrix(L, 1);
  dimension = gt_score_matrix_get_dimension(*sm);
  lua_pushinteger(L, dimension);
  return 1;
}

static int score_matrix_lua_get_score(lua_State *L)
{
  GtScoreMatrix **sm;
  int idx1, idx2;
  int score;
  sm = check_score_matrix(L, 1);
  idx1 = luaL_checkint(L, 2);
  idx2 = luaL_checkint(L, 3);
  luaL_argcheck(L, idx1 >= 0, 2, "idx1 too small");
  luaL_argcheck(L, idx2 >= 0, 3, "idx2 too small");
  luaL_argcheck(L, idx1 < gt_score_matrix_get_dimension(*sm), 2,
                "idx1 too large");
  luaL_argcheck(L, idx2 < gt_score_matrix_get_dimension(*sm), 3,
                "idx2 too large");
  score = gt_score_matrix_get_score(*sm, idx1, idx2);
  lua_pushinteger(L, score);
  return 1;
}

static int score_matrix_lua_show(lua_State *L)
{
  GtScoreMatrix **sm;
  sm = check_score_matrix(L, 1);
  gt_score_matrix_show(*sm, stdout);
  return 0;
}

static int score_matrix_lua_delete(lua_State *L)
{
  GtScoreMatrix **sm;
  sm = check_score_matrix(L, 1);
  gt_score_matrix_delete(*sm);
  return 0;
}

static const struct luaL_Reg score_matrix_lib_f [] = {
  { "score_matrix_new_read_protein", score_matrix_lua_new_read_protein },
  { "score_matrix_new_read", score_matrix_lua_new_read},
  { NULL, NULL }
};

static const struct luaL_Reg score_matrix_lib_m [] = {
  { "get_dimension", score_matrix_lua_get_dimension },
  { "get_score", score_matrix_lua_get_score },
  { "show", score_matrix_lua_show },
  { NULL, NULL }
};

int gt_lua_open_score_matrix(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, SCOREMATRIX_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, score_matrix_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, score_matrix_lib_m);
  lua_pop(L, 1);
  luaL_register(L, "gt", score_matrix_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/score_matrix_lua.h000066400000000000000000000030461211610345200214630ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SCORE_MATRIX_LUA_H
#define SCORE_MATRIX_LUA_H

#include "lua.h"

/* exports the ScoreMatrix class to Lua:

   -- Returns a new protein score matrix object which has been read from file
   -- .
   function score_matrix_new_read_protein(path)

   -- Read in score matrix from  over given  and return it.
   function score_matrix_new_read(path, alphabet)

   -- Returns the dimension of the  as number.
   function score_matrix:get_dimension()

   -- Returns the score for , as number.
   function score_matrix:get_score(idx1, idx2)

   -- Show  on stdout.
   function score_matrix:show()
*/
int gt_lua_open_score_matrix(lua_State*);

#endif
genometools-1.5.1/src/gtlua/stream_evaluator_lua.c000066400000000000000000000074561211610345200223450ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "core/error.h"
#include "extended/luahelper.h"
#include "extended/stream_evaluator.h"
#include "gtlua/genome_stream_lua.h"
#include "gtlua/genome_visitor_lua.h"
#include "gtlua/gtext_lua.h"
#include "gtlua/stream_evaluator_lua.h"

#define STREAM_EVALUATOR_METATABLE  "GenomeTools.stream_evaluator"
#define check_stream_evaluator(L) \
        (GtStreamEvaluator**) luaL_checkudata(L, 1, STREAM_EVALUATOR_METATABLE)

static int stream_evaluator_lua_new(lua_State *L)
{
  GtStreamEvaluator **stream_evaluator;
  GtNodeStream **reality_stream, **prediction_stream;
  reality_stream = check_genome_stream(L, 1);
  prediction_stream = check_genome_stream(L, 2);
  stream_evaluator = lua_newuserdata(L, sizeof (GtStreamEvaluator*));
  *stream_evaluator = gt_stream_evaluator_new(*reality_stream,
                                              *prediction_stream,
                                              true, false, 0);
  luaL_getmetatable(L, STREAM_EVALUATOR_METATABLE);
  lua_setmetatable(L, -2);
  return 1;
}

static int stream_evaluator_lua_evaluate(lua_State *L)
{
  GtStreamEvaluator **stream_evaluator;
  GtNodeVisitor **genome_visitor;
  GtError *err;
  stream_evaluator = check_stream_evaluator(L);
  if (lua_gettop(L) >= 2) {
    genome_visitor = check_genome_visitor(L, 2);
  }
  else
    genome_visitor = NULL;
  err = gt_error_new();
  if (gt_stream_evaluator_evaluate(*stream_evaluator, false, false, false,
                                   genome_visitor ? *genome_visitor : NULL,
                                   err)) {
    return gt_lua_error(L, err);
  }
  gt_error_delete(err);
  return 0;
}

static int stream_evaluator_lua_show(lua_State *L)
{
  GtStreamEvaluator **stream_evaluator = check_stream_evaluator(L);
  gt_stream_evaluator_show(*stream_evaluator, NULL);
  return 0;
}

static int stream_evaluator_lua_delete(lua_State *L)
{
  GtStreamEvaluator **stream_evaluator;
  stream_evaluator = check_stream_evaluator(L);
  gt_stream_evaluator_delete(*stream_evaluator);
  return 0;
}

static const struct luaL_Reg stream_evaluator_lib_f [] = {
  { "stream_evaluator_new", stream_evaluator_lua_new },
  { NULL, NULL }
};

static const struct luaL_Reg stream_evaluator_lib_m [] = {
  { "evaluate", stream_evaluator_lua_evaluate },
  { "show", stream_evaluator_lua_show },
  { NULL, NULL }
};

int gt_lua_open_stream_evaluator(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_newmetatable(L, STREAM_EVALUATOR_METATABLE);
  /* metatable.__index = metatable */
  lua_pushvalue(L, -1); /* duplicate the metatable */
  lua_setfield(L, -2, "__index");
  /* set its _gc field */
  lua_pushstring(L, "__gc");
  lua_pushcfunction(L, stream_evaluator_lua_delete);
  lua_settable(L, -3);
  /* register functions */
  luaL_register(L, NULL, stream_evaluator_lib_m);
  lua_pop(L, 1);
  luaL_register(L, "gt", stream_evaluator_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/stream_evaluator_lua.h000066400000000000000000000027321211610345200223420ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef STREAM_EVALUATOR_LUA_H
#define STREAM_EVALUATOR_LUA_H

#include "lua.h"

/* exports the StreamEvaluator class to Lua:

   -- Returns a new stream evaluator object for the two genome streams
   --  and .
   function stream_evaluator_new(reality_stream, prediction_stream)

   -- Run evaluation of . All evaluated features are visited
   -- by the optional .
   function stream_evaluator:evaluate(genome_visitor)

   -- Show result of  on stdout.
   function stream_evaluator:show()
*/
int gt_lua_open_stream_evaluator(lua_State*);

#endif
genometools-1.5.1/src/gtlua/translate_lua.c000066400000000000000000000041471211610345200207570ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "lauxlib.h"
#include "core/codon_iterator_simple_api.h"
#include "core/translator.h"
#include "gtlua/translate_lua.h"

static int translate_dna_lua(lua_State *L)
{
  GtStr *protein;
  GtTranslator *tr;
  int rval;
  char translated;
  unsigned int frame;
  const char *dna = luaL_checkstring(L, 1);
  protein = gt_str_new();

  GtCodonIterator *ci = gt_codon_iterator_simple_new(dna,
                                                     strlen(dna),
                                                     NULL);
  tr = gt_translator_new(ci);
  rval = gt_translator_next(tr, &translated, &frame, NULL);
  while (!rval && translated) {
    gt_str_append_char(protein, translated);
    rval = gt_translator_next(tr, &translated, &frame, NULL);
  }
  lua_pushstring(L, gt_str_get(protein));
  gt_str_delete(protein);
  gt_translator_delete(tr);
  gt_codon_iterator_delete(ci);
  return 1;
}

static const struct luaL_Reg translate_lib_f [] = {
  { "translate_dna", translate_dna_lua },
  { NULL, NULL }
};

int gt_lua_open_translate(lua_State *L)
{
#ifndef NDEBUG
  int stack_size;
#endif
  gt_assert(L);
#ifndef NDEBUG
  stack_size = lua_gettop(L);
#endif
  luaL_register(L, "gt", translate_lib_f);
  lua_pop(L, 1);
  gt_assert(lua_gettop(L) == stack_size);
  return 1;
}
genometools-1.5.1/src/gtlua/translate_lua.h000066400000000000000000000020641211610345200207600ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TRANSLATE_LUA_H
#define TRANSLATE_LUA_H

#include "lua.h"

/* exports the translate module to Lua:

   -- Returns translated .
   function translate_dna(dna)
*/
int gt_lua_open_translate(lua_State*);

#endif
genometools-1.5.1/src/gtr.c000066400000000000000000000302421211610345200155740ustar00rootroot00000000000000/*
  Copyright (c) 2003-2011 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "gtr.h"
#include "gtt.h"
#include "interactive.h"
#include "lua.h"
#include "lauxlib.h"
#include "lualib.h"
#include "lfs.h"
#include "lpeg.h"
#include "md5.h"
#include "ldes56.h"
#include "core/cstr_array.h"
#include "core/ensure.h"
#include "core/fa.h"
#include "core/fileutils_api.h"
#include "core/gtdatapath.h"
#include "core/log.h"
#include "core/ma.h"
#include "core/thread_api.h"
#include "core/unit_testing.h"
#include "core/versionfunc.h"
#include "core/xansi_api.h"
#include "core/yarandom.h"
#include "extended/gtdatahelp.h"
#include "extended/luahelper.h"
#include "extended/toolbox.h"
#include "gtlua/gt_lua.h"

#ifndef WITHOUT_CAIRO
#include "annotationsketch/luastyle.h"
#include "annotationsketch/style.h"
#endif

struct GtR {
  bool test,
       interactive,
       debug,
       check64bit;
  unsigned int seed;
  GtStr *debugfp,
      *testspacepeak;
  GtToolbox *tools;
  GtHashmap *unit_tests;
  GtStr *test_only;
  lua_State *L;
#ifndef WITHOUT_CAIRO
  GtStyle *style;
#endif
  FILE *logfp;
};

GtR* gtr_new(GtError *err)
{
  GtR *gtr;
  int had_err = 0;
#ifndef WITHOUT_CAIRO
  GtStr *style_file = NULL;
#endif
  gtr = gt_calloc(1, sizeof (GtR));
  gtr->debugfp = gt_str_new();
  gtr->testspacepeak = gt_str_new();
  gtr->test_only = gt_str_new();
  gtr->L = luaL_newstate();
  if (!gtr->L) {
    gt_error_set(err, "out of memory (cannot create new lua state)");
    had_err = -1;
  }
  if (!had_err) {
    luaL_openlibs(gtr->L);    /* open the standard libraries */
    gt_lua_open_lib(gtr->L);  /* open the GenomeTools library */
    lua_pushcfunction(gtr->L, luaopen_lpeg);
    lua_pushstring(gtr->L, "lpeg");
    lua_call(gtr->L, 1, 0);   /* open LPeg library */
    lua_pushcfunction(gtr->L, luaopen_md5_core);
    lua_pushstring(gtr->L, "md5");
    lua_call(gtr->L, 1, 0);   /* open MD5 library */
    lua_pushcfunction(gtr->L, luaopen_lfs);
    lua_pushstring(gtr->L, "lfs");
    lua_call(gtr->L, 1, 0);   /* open Lua filesystem */
    lua_pushcfunction(gtr->L, luaopen_des56);
    lua_pushstring(gtr->L, "des56");
    lua_call(gtr->L, 1, 0);   /* open DES56 library */
    had_err = gt_lua_set_modules_path(gtr->L, err);
  }
#ifndef WITHOUT_CAIRO
  if (!had_err) {
    lua_settop(gtr->L, 0);
    if (!(gtr->style = gt_style_new_with_state(gtr->L)))
      had_err = -1;
  }
  if (!had_err) {
    if (!(style_file = gt_get_gtdata_path(gt_error_get_progname(err), err)))
      had_err = -1;
  }
  if (!had_err) {
    gt_str_append_cstr(style_file, "/sketch/default.style");
    if (gt_file_exists(gt_str_get(style_file))) {
      if (gt_style_load_file(gtr->style, gt_str_get(style_file), err))
        had_err = -1;
      else
        gt_lua_put_style_in_registry(gtr->L, gtr->style);
    }
  }
  gt_str_delete(style_file);
#endif
  if (had_err) {
    gt_free(gtr);
    return NULL;
  }
  return gtr;
}

static int show_gtr_help(const char *progname, void *data, GtError *err)
{
  int had_err;
  had_err = gt_toolbox_show(progname, data, err);
  if (!had_err)
    had_err = gt_gtdata_show_help(progname, NULL, err);
  return had_err;
}

GtOPrval gtr_parse(GtR *gtr, int *parsed_args, int argc, const char **argv,
                   GtError *err)
{
  GtOptionParser *op;
  GtOption *o, *only_option, *debug_option, *debugfp_option;
  GtOPrval oprval;

  gt_error_check(err);
  gt_assert(gtr);
  op = gt_option_parser_new("[option ...] [tool | script] [argument ...]",
                            "The GenomeTools (gt) genome analysis system "
                            "(http://genometools.org).");
  gt_option_parser_set_comment_func(op, show_gtr_help, gtr->tools);
  o = gt_option_new_bool("i",
                         "enter interactive mode after executing 'tool' or "
                         "'script'", >r->interactive, false);
  gt_option_hide_default(o);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_uint_min("j", "set number of parallel threads used at once",
                             >_jobs, 1, 1);
  gt_option_is_development_option(o);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_bool("test", "perform unit tests and exit", >r->test,
                         false);
  gt_option_hide_default(o);
  gt_option_parser_add_option(op, o);
  only_option = gt_option_new_string("only", "perform single unit test "
                                     "(requires -test)", gtr->test_only, "");
  gt_option_imply(only_option, o);
  gt_option_is_development_option(only_option);
  gt_option_hide_default(only_option);
  gt_option_parser_add_option(op, only_option);
  debug_option = gt_option_new_debug(>r->debug);
  gt_option_parser_add_option(op, debug_option);
  debugfp_option = gt_option_new_string("debugfp",
                                     "set file pointer for debugging output\n"
                                     "use ``stdout'' for standard output\n"
                                     "use ``stderr'' for standard error\n"
                                     "or any other string to use the "
                                     "corresponding file (will be overwritten "
                                     "without warning!)", gtr->debugfp,
                                     "stderr");
  gt_option_is_development_option(debugfp_option);
  gt_option_parser_add_option(op, debugfp_option);
  gt_option_imply(debugfp_option, debug_option);
  o = gt_option_new_uint("seed",
                         "set seed for random number generator manually\n"
                         "0 generates a seed from current time and process id",
                         >r->seed, 0);
  gt_option_is_development_option(o);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_bool("64bit", "exit with code 0 if this is a 64bit binary, "
                         "with 1 otherwise", >r->check64bit, false);
  gt_option_is_development_option(o);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_filename("testspacepeak", "alloc 64 MB and mmap the given "
                             "file", gtr->testspacepeak);
  gt_option_is_development_option(o);
  gt_option_parser_add_option(op, o);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

void gtr_register_components(GtR *gtr)
{
  gt_assert(gtr);
  /* add tools */
  gt_toolbox_delete(gtr->tools);
  gtr->tools = gtt_tools();
  /* add unit tests */
  gt_hashmap_delete(gtr->unit_tests);
  gtr->unit_tests = gtt_unit_tests();
}

static int check64bit(void)
{
  if (sizeof (unsigned long) == 8)
    return EXIT_SUCCESS;
  return EXIT_FAILURE;
}

static int run_tests(GtR *gtr, GtError *err)
{
  int test_err = 0, had_err = 0;
  char* key;
  void* value;
  gt_error_check(err);
  gt_assert(gtr);

  /* The following type assumptions are made in the GenomeTools library. */
  gt_ensure(had_err, sizeof (char) == 1);
  gt_ensure(had_err, sizeof (unsigned char) == 1);
  gt_ensure(had_err, sizeof (short) == 2);
  gt_ensure(had_err, sizeof (unsigned short) == 2);
  gt_ensure(had_err, sizeof (int) == 4);
  gt_ensure(had_err, sizeof (unsigned int) == 4);
  gt_ensure(had_err, sizeof (long) == 4 || sizeof (long) == 8);
  gt_ensure(had_err, sizeof (unsigned long) == 4 ||
                     sizeof (unsigned long) == 8);
  gt_ensure(had_err, sizeof (unsigned long) >= sizeof (size_t));
  gt_ensure(had_err, sizeof (long long) == 8);
  gt_ensure(had_err, sizeof (unsigned long long) == 8);

  /* show seed */
  printf("seed=%u\n", gtr->seed);
  gt_hashmap_unit_test(err);
  if (gtr->unit_tests) {
    if (gt_str_length(gtr->test_only) > 0) {
      key = gt_str_get(gtr->test_only);
      value = gt_hashmap_get(gtr->unit_tests, key);
      if (value) {
        had_err = gt_unit_test_run(key, value, &test_err, err);
        gt_assert(!had_err); /* cannot happen, gt_unit_test_run() is sane */
      }
      else {
        gt_error_set(err, "Test \"%s\" not found", key);
        return EXIT_FAILURE;
      }
    }
    else {
      had_err = gt_hashmap_foreach_in_key_order(gtr->unit_tests,
                                                gt_unit_test_run, &test_err,
                                                err);
      gt_assert(!had_err); /* cannot happen, gt_unit_test_run() is sane */
    }
  }
  if (test_err)
    return EXIT_FAILURE;
  return EXIT_SUCCESS;
}

static void enable_logging(const char *debugfp, FILE **logfp)
{
  gt_log_enable();
  if (!strcmp(debugfp, "stdout"))
    gt_log_set_fp(stdout);
  else if (!strcmp(debugfp, "stderr"))
    gt_log_set_fp(stderr);
  else {
    *logfp = gt_fa_xfopen(debugfp, "w");
    gt_log_set_fp(*logfp);
  }
}

int gtr_run(GtR *gtr, int argc, const char **argv, GtError *err)
{
  GtToolfunc toolfunc;
  GtTool *tool = NULL;
  char **nargv = NULL;
  void *mem, *map;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(gtr);
  if (gtr->debug)
    enable_logging(gt_str_get(gtr->debugfp), >r->logfp);
  gtr->seed = gt_ya_rand_init(gtr->seed);
  gt_log_log("seed=%u", gtr->seed);
  if (gtr->check64bit)
    return check64bit();
  if (gtr->test)
    return run_tests(gtr, err);
  if (gt_str_length(gtr->testspacepeak)) {
    mem = gt_malloc(1 << 26); /* alloc 64 MB */;
    map = gt_fa_xmmap_read(gt_str_get(gtr->testspacepeak), NULL);
    gt_fa_xmunmap(map);
    gt_free(mem);
  }
  if (argc == 0 && !gtr->interactive) {
    gt_error_set(err, "neither tool nor script specified; option -help lists "
                      "possible tools");
    had_err = -1;
  }
  if (!had_err && argc) {
    if (!gtr->tools || !gt_toolbox_has_tool(gtr->tools, argv[0])) {
      /* no tool found -> try to open script */
      if (gt_file_exists(argv[0])) {
        /* run script */
        nargv = gt_cstr_array_prefix_first(argv, gt_error_get_progname(err));
        gt_lua_set_arg(gtr->L, nargv[0], (const char**) nargv+1);
        if (luaL_dofile(gtr->L, argv[0])) {
          /* error */
          gt_assert(lua_isstring(gtr->L, -1)); /* error message on top */
          gt_error_set(err, "could not execute script %s",
                       lua_tostring(gtr->L, -1));
          had_err = -1;
          lua_pop(gtr->L, 1); /* pop error message */
        }
      }
      else {
        /* neither tool nor script found */
        gt_error_set(err, "neither tool nor script '%s' found; option -help "
                          "lists possible tools", argv[0]);
        had_err = -1;
      }
    }
    else {
      /* run tool */
      if (!(toolfunc = gt_toolbox_get(gtr->tools, argv[0]))) {
        tool = gt_toolbox_get_tool(gtr->tools, argv[0]);
        gt_assert(tool);
      }
      nargv = gt_cstr_array_prefix_first(argv, gt_error_get_progname(err));
      gt_error_set_progname(err, nargv[0]);
      if (toolfunc)
        had_err = toolfunc(argc, (const char**) nargv, err);
      else
        had_err = gt_tool_run(tool, argc, (const char**) nargv, err);
    }
  }
  gt_cstr_array_delete(nargv);
  if (!had_err && gtr->interactive) {
    gt_showshortversion(gt_error_get_progname(err));
    gt_lua_set_arg(gtr->L, gt_error_get_progname(err), argv);
    run_interactive_lua_interpreter(gtr->L);
  }
  if (had_err)
    return EXIT_FAILURE;
  return EXIT_SUCCESS;
}

void gtr_delete(GtR *gtr)
{
  if (!gtr) return;
  gt_fa_fclose(gtr->logfp);
  gt_str_delete(gtr->testspacepeak);
  gt_str_delete(gtr->debugfp);
  gt_str_delete(gtr->test_only);
  gt_toolbox_delete(gtr->tools);
  gt_hashmap_delete(gtr->unit_tests);
  if (gtr->L) lua_close(gtr->L);
#ifndef WITHOUT_CAIRO
  gt_style_delete_without_state(gtr->style);
#endif
  gt_free(gtr);
}
genometools-1.5.1/src/gtr.h000066400000000000000000000024531211610345200156040ustar00rootroot00000000000000/*
  Copyright (c) 2003-2011 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GTR_H
#define GTR_H

#include 
#include "core/init_api.h"
#include "core/error.h"
#include "core/option_api.h"

/* The GenomeTools runtime (gtr) */
typedef struct GtR GtR;

GtR*     gtr_new(GtError*);
GtOPrval gtr_parse(GtR*, int *parsed_args, int argc, const char **argv,
                   GtError*);
void     gtr_register_components(GtR*);
int      gtr_run(GtR*, int argc, const char **argv, GtError*);
void     gtr_delete(GtR*);

#endif
genometools-1.5.1/src/gtt.c000066400000000000000000000405401211610345200156000ustar00rootroot00000000000000/*
  Copyright (c) 2003-2013 Gordon Gremme 
  Copyright (c) 2003-2013 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "gtt.h"
#include "core/alphabet.h"
#include "core/array.h"
#include "core/array2dim_api.h"
#include "core/array2dim_sparse.h"
#include "core/array3dim.h"
#include "core/basename_api.h"
#include "core/bitpackarray.h"
#include "core/bitpackstring.h"
#include "core/bittab.h"
#include "core/bsearch.h"
#include "core/codon_iterator_encseq_api.h"
#include "core/codon_iterator_simple_api.h"
#include "core/colorspace.h"
#include "core/combinatorics.h"
#include "core/compact_ulong_store.h"
#include "core/countingsort.h"
#include "core/cstr.h"
#include "core/cstr_table.h"
#include "core/desc_buffer.h"
#include "core/disc_distri_api.h"
#include "core/dlist.h"
#include "core/dyn_bittab.h"
#include "core/encseq.h"
#include "core/grep_api.h"
#include "core/hashmap.h"
#include "core/hashtable.h"
#include "core/interval_tree.h"
#include "core/mathsupport.h"
#include "core/md5_seqid.h"
#include "core/quality.h"
#include "core/queue.h"
#include "core/sequence_buffer.h"
#include "core/splitter.h"
#include "core/symbol.h"
#include "core/tokenizer.h"
#include "core/translator.h"
#include "extended/alignment.h"
#include "extended/anno_db_gfflike_api.h"
#include "extended/elias_gamma.h"
#include "extended/encdesc.h"
#include "extended/evaluator.h"
#include "extended/feature_index.h"
#include "extended/feature_index_memory.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_escaping.h"
#include "extended/golomb.h"
#include "extended/hmm.h"
#include "extended/huffcode.h"
#include "extended/luaserialize.h"
#include "extended/popcount_tab.h"
#include "extended/ranked_list.h"
#include "extended/rbtree.h"
#include "extended/rmq.h"
#include "extended/splicedseq.h"
#include "extended/string_matching.h"
#include "extended/tag_value_map.h"
#include "extended/uint64hashtable.h"
#include "ltr/gt_ltrclustering.h"
#include "ltr/gt_ltrdigest.h"
#include "ltr/gt_ltrharvest.h"
#include "ltr/ltrelement.h"
#include "ltr/pbs.h"
#include "ltr/ppt.h"
#include "match/rdj-spmlist.h"
#include "match/rdj-strgraph.h"
#include "match/shu-encseq-gc.h"
#include "tools/gt_bed_to_gff3.h"
#include "tools/gt_cds.h"
#include "tools/gt_chain2dim.h"
#include "tools/gt_chseqids.h"
#include "tools/gt_clean.h"
#include "tools/gt_compreads.h"
#include "tools/gt_congruence.h"
#include "tools/gt_convertseq.h"
#include "tools/gt_csa.h"
#include "tools/gt_dev.h"
#include "tools/gt_dot.h"
#include "tools/gt_dupfeat.h"
#include "tools/gt_encseq.h"
#include "tools/gt_encseq2spm.h"
#include "tools/gt_eval.h"
#include "tools/gt_extractfeat.h"
#include "tools/gt_extractseq.h"
#include "tools/gt_featureindex.h"
#include "tools/gt_fingerprint.h"
#include "tools/gt_genomediff.h"
#include "tools/gt_gff3.h"
#include "tools/gt_gff3_to_gtf.h"
#include "tools/gt_gff3validator.h"
#include "tools/gt_gtf_to_gff3.h"
#include "tools/gt_hop.h"
#include "tools/gt_id_to_md5.h"
#include "tools/gt_interfeat.h"
#include "tools/gt_matchtool.h"
#include "tools/gt_matstat.h"
#include "tools/gt_maxpairs.h"
#include "tools/gt_md5_to_id.h"
#include "tools/gt_merge.h"
#include "tools/gt_mergefeat.h"
#include "tools/gt_mgth.h"
#include "tools/gt_mkfeatureindex.h"
#include "tools/gt_mkfmindex.h"
#include "tools/gt_mmapandread.h"
#include "tools/gt_orffinder.h"
#include "tools/gt_packedindex.h"
#include "tools/gt_prebwt.h"
#include "tools/gt_readjoiner.h"
#include "tools/gt_script_filter.h"
#include "tools/gt_select.h"
#include "tools/gt_seq.h"
#include "tools/gt_seqfilter.h"
#include "tools/gt_seqids.h"
#include "tools/gt_seqmutate.h"
#include "tools/gt_seqorder.h"
#include "tools/gt_seqstat.h"
#include "tools/gt_seqtransform.h"
#include "tools/gt_seqtranslate.h"
#include "tools/gt_sequniq.h"
#include "tools/gt_shredder.h"
#include "tools/gt_shulen.h"
#include "tools/gt_simreads.h"
#include "tools/gt_snpper.h"
#include "tools/gt_splicesiteinfo.h"
#include "tools/gt_splitfasta.h"
#include "tools/gt_stat.h"
#include "tools/gt_suffixerator.h"
#include "tools/gt_tagerator.h"
#include "tools/gt_tallymer.h"
#include "tools/gt_template.h"
#include "tools/gt_uniq.h"
#include "tools/gt_uniquesub.h"
#ifndef WITHOUT_CAIRO
#include "annotationsketch/block.h"
#include "annotationsketch/diagram.h"
#include "annotationsketch/gt_sketch.h"
#include "annotationsketch/gt_sketch_page.h"
#include "annotationsketch/image_info.h"
#include "annotationsketch/rec_map.h"
#include "annotationsketch/style.h"
#include "annotationsketch/track.h"
#endif

GtToolbox* gtt_tools(void)
{
  GtToolbox *tools = gt_toolbox_new();

  /* add tools */
  gt_toolbox_add_tool(tools, "orffinder", gt_orffinder());
  gt_toolbox_add(tools, "chseqids", gt_chseqids);
  gt_toolbox_add(tools, "clean", gt_clean);
  gt_toolbox_add(tools, "convertseq", gt_convertseq);
  gt_toolbox_add(tools, "matstat", gt_matstat);
  gt_toolbox_add(tools, "merge", gt_merge);
  gt_toolbox_add(tools, "mgth", gt_mgth);
  gt_toolbox_add(tools, "mkfmindex", gt_mkfmindex);
  gt_toolbox_add(tools, "mmapandread", gt_mmapandread);
  gt_toolbox_add(tools, "seqstat", gt_seqstat);
  gt_toolbox_add(tools, "suffixerator", gt_suffixerator);
  gt_toolbox_add(tools, "uniquesub", gt_uniquesub);
  gt_toolbox_add_hidden_tool(tools, "dev", gt_dev());
  gt_toolbox_add_hidden_tool(tools, "filter", gt_select());
  /* hidden "link from the mutate to the seqmutate tool for backward
     compatibility */
  gt_toolbox_add_hidden_tool(tools, "mutate", gt_seqmutate());
  gt_toolbox_add_hidden_tool(tools, "template", gt_template());
  gt_toolbox_add_tool(tools, "bed_to_gff3", gt_bed_to_gff3());
  gt_toolbox_add_tool(tools, "cds", gt_cds());
  gt_toolbox_add_tool(tools, "chain2dim", gt_chain2dim());
  gt_toolbox_add_tool(tools, "compreads", gt_compreads());
  gt_toolbox_add_tool(tools, "congruence", gt_congruence());
  gt_toolbox_add_tool(tools, "csa", gt_csa());
  gt_toolbox_add_tool(tools, "dot", gt_dot());
  gt_toolbox_add_tool(tools, "dupfeat", gt_dupfeat());
  gt_toolbox_add_tool(tools, "encseq", gt_encseq());
  gt_toolbox_add_tool(tools, "encseq2spm", gt_encseq2spm());
  gt_toolbox_add_tool(tools, "eval", gt_eval());
  gt_toolbox_add_tool(tools, "extractfeat", gt_extractfeat());
  gt_toolbox_add_tool(tools, "extractseq", gt_extractseq());
  gt_toolbox_add_tool(tools, "featureindex", gt_featureindex());
  gt_toolbox_add_tool(tools, "fingerprint", gt_fingerprint());
  gt_toolbox_add_tool(tools, "genomediff", gt_genomediff());
  gt_toolbox_add_tool(tools, "gff3", gt_gff3());
  gt_toolbox_add_tool(tools, "gff3_to_gtf", gt_gff3_to_gtf());
  gt_toolbox_add_tool(tools, "gff3validator", gt_gff3validator());
  gt_toolbox_add_tool(tools, "gtf_to_gff3", gt_gtf_to_gff3());
  gt_toolbox_add_tool(tools, "hop", gt_hop());
  gt_toolbox_add_tool(tools, "id_to_md5", gt_id_to_md5());
  gt_toolbox_add_tool(tools, "interfeat", gt_interfeat());
  gt_toolbox_add_tool(tools, "ltrclustering", gt_ltrclustering());
  gt_toolbox_add_tool(tools, "ltrdigest", gt_ltrdigest());
  gt_toolbox_add_tool(tools, "ltrharvest", gt_ltrharvest());
  gt_toolbox_add_tool(tools, "matchtool", gt_matchtool());
  gt_toolbox_add_tool(tools, "md5_to_id", gt_md5_to_id());
  gt_toolbox_add_tool(tools, "mergefeat", gt_mergefeat());
  gt_toolbox_add_tool(tools, "mkfeatureindex", gt_mkfeatureindex());
  gt_toolbox_add_tool(tools, "packedindex", gt_packedindex());
  gt_toolbox_add_tool(tools, "prebwt", gt_prebwt());
  gt_toolbox_add_tool(tools, "readjoiner", gt_readjoiner());
  gt_toolbox_add_tool(tools, "repfind", gt_repfind());
  gt_toolbox_add_tool(tools, "scriptfilter", gt_script_filter());
  gt_toolbox_add_tool(tools, "select", gt_select());
  gt_toolbox_add_tool(tools, "seq", gt_seq());
  gt_toolbox_add_tool(tools, "seqfilter", gt_seqfilter());
  gt_toolbox_add_tool(tools, "seqids", gt_seqids());
  gt_toolbox_add_tool(tools, "seqmutate", gt_seqmutate());
  gt_toolbox_add_tool(tools, "seqorder", gt_seqorder());
  gt_toolbox_add_tool(tools, "seqtransform", gt_seqtransform());
  gt_toolbox_add_tool(tools, "seqtranslate", gt_seqtranslate());
  gt_toolbox_add_tool(tools, "sequniq", gt_sequniq());
  gt_toolbox_add_tool(tools, "shredder", gt_shredder());
  gt_toolbox_add_tool(tools, "shulengthdist", gt_shulengthdist());
  gt_toolbox_add_tool(tools, "simreads", gt_simreads());
  gt_toolbox_add_tool(tools, "snpper", gt_snpper());
  gt_toolbox_add_tool(tools, "splicesiteinfo", gt_splicesiteinfo());
  gt_toolbox_add_tool(tools, "splitfasta", gt_splitfasta());
  gt_toolbox_add_tool(tools, "stat", gt_stat());
  gt_toolbox_add_tool(tools, "tagerator", gt_tagerator());
  gt_toolbox_add_tool(tools, "tallymer", gt_tallymer());
  gt_toolbox_add_tool(tools, "uniq", gt_uniq());
#ifndef WITHOUT_CAIRO
  gt_toolbox_add(tools, "sketch", gt_sketch);
  gt_toolbox_add_tool(tools, "sketch_page", gt_sketch_page());
#endif
  return tools;
}

GtHashmap* gtt_unit_tests(void)
{
  GtHashmap *unit_tests = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);

  /* add unit tests */

  gt_hashmap_add(unit_tests, "compactulongstore class",
                                              gt_compact_ulong_store_unit_test);
  gt_hashmap_add(unit_tests, "alphabet class", gt_alphabet_unit_test);
  gt_hashmap_add(unit_tests, "alignment class", gt_alignment_unit_test);
  gt_hashmap_add(unit_tests, "array class", gt_array_unit_test);
  gt_hashmap_add(unit_tests, "array example", gt_array_example);
  gt_hashmap_add(unit_tests, "array2dim example", gt_array2dim_example);
  gt_hashmap_add(unit_tests, "array2dim sparse example",
                                                   gt_array2dim_sparse_example);
  gt_hashmap_add(unit_tests, "array3dim example", gt_array3dim_example);
  gt_hashmap_add(unit_tests, "basename module", gt_basename_unit_test);
  gt_hashmap_add(unit_tests, "bit pack array class", gt_bitpackarray_unit_test);
  gt_hashmap_add(unit_tests, "bit pack string module",
                                                    gt_bitPackString_unit_test);
  gt_hashmap_add(unit_tests, "bittab class", gt_bittab_unit_test);
  gt_hashmap_add(unit_tests, "bittab example", gt_bittab_example);
  gt_hashmap_add(unit_tests, "bsearch module", gt_bsearch_unit_test);
  gt_hashmap_add(unit_tests, "codon iterator class, simple",
                                            gt_codon_iterator_simple_unit_test);
  gt_hashmap_add(unit_tests, "codon iterator class, encoded",
                                            gt_codon_iterator_encseq_unit_test);
  gt_hashmap_add(unit_tests, "color space module", gt_colorspace_unit_test);
  gt_hashmap_add(unit_tests, "combinatorics", gt_combinatorics_unit_test);
  gt_hashmap_add(unit_tests, "countingsort module", gt_countingsort_unit_test);
  gt_hashmap_add(unit_tests, "cstr module", gt_cstr_unit_test);
  gt_hashmap_add(unit_tests, "cstr table class", gt_cstr_table_unit_test);
  gt_hashmap_add(unit_tests, "description buffer class",
                                                      gt_desc_buffer_unit_test);
  gt_hashmap_add(unit_tests, "disc distri class", gt_disc_distri_unit_test);
  gt_hashmap_add(unit_tests, "dlist class", gt_dlist_unit_test);
  gt_hashmap_add(unit_tests, "dlist example", gt_dlist_example);
  gt_hashmap_add(unit_tests, "dynamic bittab class", gt_dyn_bittab_unit_test);
  gt_hashmap_add(unit_tests, "elias gamma class", gt_elias_gamma_unit_test);
  gt_hashmap_add(unit_tests, "encdesc class", gt_encdesc_unit_test);
  gt_hashmap_add(unit_tests, "encseq builder class",
                                                   gt_encseq_builder_unit_test);
  gt_hashmap_add(unit_tests, "encseq gc module", gt_encseq_gc_unit_test);
  gt_hashmap_add(unit_tests, "evaluator class", gt_evaluator_unit_test);
  gt_hashmap_add(unit_tests, "feature node iterator example",
                                             gt_feature_node_iterator_example);
  gt_hashmap_add(unit_tests, "feature node class", gt_feature_node_unit_test);
  gt_hashmap_add(unit_tests, "genome node class", gt_genome_node_unit_test);
  gt_hashmap_add(unit_tests, "gff3 escaping module",
                                                    gt_gff3_escaping_unit_test);
  gt_hashmap_add(unit_tests, "grep module", gt_grep_unit_test);
  gt_hashmap_add(unit_tests, "golomb class", gt_golomb_unit_test);
  gt_hashmap_add(unit_tests, "hashmap class", gt_hashmap_unit_test);
  gt_hashmap_add(unit_tests, "hashtable class", gt_hashtable_unit_test);
  gt_hashmap_add(unit_tests, "hmm class", gt_hmm_unit_test);
  gt_hashmap_add(unit_tests, "huffman coding class", gt_huffman_unit_test);
  gt_hashmap_add(unit_tests, "interval tree class", gt_interval_tree_unit_test);
  gt_hashmap_add(unit_tests, "Lua serializer module",
                                                   gt_lua_serializer_unit_test);
  gt_hashmap_add(unit_tests, "ltrelement module", gt_ltrelement_unit_test);
  gt_hashmap_add(unit_tests, "mathsupport module", gt_mathsupport_unit_test);
  gt_hashmap_add(unit_tests, "memory allocator module", gt_ma_unit_test);
  gt_hashmap_add(unit_tests, "MD5 seqid module", gt_md5_seqid_unit_test);
  gt_hashmap_add(unit_tests, "rdj: suffix-prefix matches list module",
                                                          gt_spmlist_unit_test);
  gt_hashmap_add(unit_tests, "PBS finder module", gt_pbs_unit_test);
  gt_hashmap_add(unit_tests, "PPT finder module", gt_ppt_unit_test);
  gt_hashmap_add(unit_tests, "popcount sorted tab", gt_popcount_tab_unit_test);
  gt_hashmap_add(unit_tests, "quality module", gt_quality_unit_test);
  gt_hashmap_add(unit_tests, "queue class", gt_queue_unit_test);
  gt_hashmap_add(unit_tests, "range class", gt_range_unit_test);
  gt_hashmap_add(unit_tests, "ranked list class", gt_ranked_list_unit_test);
  gt_hashmap_add(unit_tests, "red-black tree class", gt_rbtree_unit_test);
  gt_hashmap_add(unit_tests, "range minimum query class", gt_rmq_unit_test);
  gt_hashmap_add(unit_tests, "rdj: string graph class", gt_strgraph_unit_test);
  gt_hashmap_add(unit_tests, "red-black tree class", gt_rbtree_unit_test);
  gt_hashmap_add(unit_tests, "safearith example", gt_safearith_example);
  gt_hashmap_add(unit_tests, "safearith module", gt_safearith_unit_test);
  gt_hashmap_add(unit_tests, "sequence buffer class",
                                                  gt_sequence_buffer_unit_test);
  gt_hashmap_add(unit_tests, "splicedseq class", gt_splicedseq_unit_test);
  gt_hashmap_add(unit_tests, "splitter class", gt_splitter_unit_test);
  gt_hashmap_add(unit_tests, "string class", gt_str_unit_test);
  gt_hashmap_add(unit_tests, "string matching module",
                                                  gt_string_matching_unit_test);
  gt_hashmap_add(unit_tests, "symbol module", gt_symbol_unit_test);
  gt_hashmap_add(unit_tests, "tag value map class", gt_tag_value_map_unit_test);
  gt_hashmap_add(unit_tests, "tag value map example", gt_tag_value_map_example);
  gt_hashmap_add(unit_tests, "tokenizer class", gt_tokenizer_unit_test);
  gt_hashmap_add(unit_tests, "translator class", gt_translator_unit_test);
  gt_hashmap_add(unit_tests, "uint64hashtable", gt_uint64hashtable_unit_test);
#ifndef WITHOUT_CAIRO
  gt_hashmap_add(unit_tests, "block class", gt_block_unit_test);
  gt_hashmap_add(unit_tests, "diagram class", gt_diagram_unit_test);
  gt_hashmap_add(unit_tests, "style class", gt_style_unit_test);
  gt_hashmap_add(unit_tests, "element class", gt_element_unit_test);
  gt_hashmap_add(unit_tests, "memory feature index class",
                                             gt_feature_index_memory_unit_test);
  gt_hashmap_add(unit_tests, "database feature index class (GFF-like)",
                                                  gt_anno_db_gfflike_unit_test);
  gt_hashmap_add(unit_tests, "imageinfo class", gt_image_info_unit_test);
  gt_hashmap_add(unit_tests, "line class", gt_line_unit_test);
  gt_hashmap_add(unit_tests, "track class", gt_track_unit_test);
#endif

  return unit_tests;
}
genometools-1.5.1/src/gtt.h000066400000000000000000000022231211610345200156010ustar00rootroot00000000000000/*
  Copyright (c) 2003-2007 Gordon Gremme 
  Copyright (c) 2003-2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GTT_H
#define GTT_H

#include "core/fptr_api.h"
#include "core/hashmap.h"
#include "extended/toolbox.h"

/* The GenomeTools toolbox (gtt) module */

GtToolbox* gtt_tools(void);      /* return all GenomeTools tools */
GtHashmap* gtt_unit_tests(void); /* return all GenomeTools unit tests */

#endif
genometools-1.5.1/src/interactive.c000066400000000000000000000147251211610345200173250ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  This interactive Lua interpreter was heavily inspired by the original Lua
  interpreter (lua.c), therefore the copyright notice in lua.h also applies.
*/

#include 
#include 
#include 
#include 
#include "interactive.h"
#include "lauxlib.h"
#include "libtecla.h"
#include "core/assert_api.h"
#include "core/cstr_api.h"
#include "core/ma.h"
#include "core/unused_api.h"

static lua_State *globalL = NULL;

static void lstop(lua_State *L, GT_UNUSED lua_Debug *ar) {
  lua_sethook(L, NULL, 0, 0);
  luaL_error(L, "interrupted!");
}

static void laction (int i) {
  signal(i, SIG_DFL); /* if another SIGINT happens before lstop,
                         terminate process (default action) */
  lua_sethook(globalL, lstop, LUA_MASKCALL | LUA_MASKRET | LUA_MASKCOUNT, 1);
}

static int report(lua_State *L, int status) {
  if (status && !lua_isnil(L, -1)) {
    const char *msg = lua_tostring(L, -1);
    if (msg == NULL) msg = "(error object is not a string)";
    fprintf(stderr, "%s\n", msg);
    fflush(stderr);
    lua_pop(L, 1);
  }
  return status;
}

static int traceback(lua_State *L) {
  lua_getfield(L, LUA_GLOBALSINDEX, "debug");
  if (!lua_istable(L, -1)) {
    lua_pop(L, 1);
    return 1;
  }
  lua_getfield(L, -1, "traceback");
  if (!lua_isfunction(L, -1)) {
    lua_pop(L, 2);
    return 1;
  }
  lua_pushvalue(L, 1);  /* pass error message */
  lua_pushinteger(L, 2);  /* skip this function and traceback */
  lua_call(L, 2, 1);  /* call debug.traceback */
  return 1;
}

static int docall(lua_State *L, int narg, int clear) {
  int status;
  int base = lua_gettop(L) - narg;  /* function index */
  lua_pushcfunction(L, traceback);  /* push traceback function */
  lua_insert(L, base);  /* put it under chunk and args */
  signal(SIGINT, laction);
  status = lua_pcall(L, narg, (clear ? 0 : LUA_MULTRET), base);
  signal(SIGINT, SIG_DFL);
  lua_remove(L, base);  /* remove traceback function */
  /* force a complete garbage collection in case of errors */
  if (status != 0) lua_gc(L, LUA_GCCOLLECT, 0);
  return status;
}

static const char* get_prompt(lua_State *L, bool firstline) {
  const char *p;
  lua_getfield(L, LUA_GLOBALSINDEX, firstline ? "_PROMPT" : "_PROMPT2");
  p = lua_tostring(L, -1);
  if (p == NULL) p = (firstline ? "> " : ">> ");
  lua_pop(L, 1);  /* remove global */
  return p;
}

static int incomplete(lua_State *L, int status) {
  if (status == LUA_ERRSYNTAX) {
    size_t lmsg;
    const char *msg = lua_tolstring(L, -1, &lmsg);
    const char *tp = msg + lmsg - (sizeof (LUA_QL("")) - 1);
    if (strstr(msg, LUA_QL("")) == tp) {
      lua_pop(L, 1);
      return 1;
    }
  }
  return 0;  /* else... */
}

static int pushline(lua_State *L, bool firstline, GT_UNUSED GetLine *gl) {
  char buffer[BUFSIZ];
  char *b = buffer;
  size_t l;
  const char *prmt = get_prompt(L, firstline);
#ifdef CURSES
  if (!(b = gl_get_line(gl, prmt, NULL, 0)))
    return 0; /* no input */
#else
  b = buffer; /* use static buffer */
  fputs(prmt, stdout); fflush(stdout);/* show prompt */
  if (!fgets(b, BUFSIZ, stdin))  /* get line */
    return 0; /* no input */
#endif
  l = strlen(b);
  if (l > 0 && b[l-1] == '\n')  /* line ends with newline? */
    b[l-1] = '\0';  /* remove it */
  if (firstline && b[0] == '=')  /* first line starts with `=' ? */
    lua_pushfstring(L, "return %s", b+1);  /* change it to `return' */
  else
    lua_pushstring(L, b);
  return 1;
}

static int loadline(lua_State *L, GetLine *gl) {
  int status;
  lua_settop(L, 0);
  if (!pushline(L, true, gl))
    return -1;  /* no input */
  for (;;) {  /* repeat until gets a complete line */
    status = luaL_loadbuffer(L, lua_tostring(L, 1), lua_strlen(L, 1), "=stdin");
    if (!incomplete(L, status)) break;  /* cannot try to add lines? */
    if (!pushline(L, false, gl))  /* no more input? */
      return -1;
    lua_pushliteral(L, "\n");  /* add a new line... */
    lua_insert(L, -2);  /* ...between the two lines */
    lua_concat(L, 3);  /* join them */
  }
#ifdef CURSES
  if (lua_strlen(L, 1) > 0) { /* non-empty line? */
    char *line;
    GT_UNUSED int rval;
    /* save complete line in history */
    line = gt_cstr_dup(lua_tostring(L, 1));
    gt_cstr_rep(line, '\n', ' '); /* replace all newlines in  with blanks,
                                     because otherwise gl_append_history() would
                                     truncate  at the first newline */
    rval = gl_append_history(gl, line);
    gt_assert(!rval);
    gt_free(line);
  }
  lua_remove(L, 1);  /* remove line */
#endif
  return status;
}

static void dotty(lua_State *L, GetLine *gl) {
  int status;
  while ((status = loadline(L, gl)) != -1) {
    if (status == 0) status = docall(L, 0, 0);
    report(L, status);
    if (status == 0 && lua_gettop(L) > 0) {  /* any result to print? */
      lua_getglobal(L, "print");
      lua_insert(L, 1);
      if (lua_pcall(L, lua_gettop(L)-1, 0, 0) != 0)
        fprintf(stderr, "%s\n", lua_pushfstring(L,
                               "error calling " LUA_QL("print") " (%s)",
                               lua_tostring(L, -1)));
        fflush(stderr);
    }
  }
  lua_settop(L, 0);  /* clear stack */
  fputs("\n", stdout);
  fflush(stdout);
}

void run_interactive_lua_interpreter(lua_State *L)
{
#ifdef CURSES
  GetLine *gl;
  gl = new_GetLine(2048, 8096);
  gl_automatic_history(gl, 0); /* disable automatic history saving, we save
                                  complete input lines explicitly */
  if (!gl) {
    fprintf(stderr, "cannot create GetLine object\n");
    exit(EXIT_FAILURE);
  }
#endif
  globalL = L; /* for signal handling */
#ifdef CURSES
  dotty(L, gl);
  del_GetLine(gl);
#else
  dotty(L, NULL);
#endif
}
genometools-1.5.1/src/interactive.h000066400000000000000000000017201211610345200173210ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef INTERACTIVE_H
#define INTERACTIVE_H

#include "lua.h"

void run_interactive_lua_interpreter(lua_State*);

#endif
genometools-1.5.1/src/ltr/000077500000000000000000000000001211610345200154345ustar00rootroot00000000000000genometools-1.5.1/src/ltr/gt_ltrclustering.c000066400000000000000000000151521211610345200211770ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Kastens 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/ma.h"
#include "core/output_file_api.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "ltr/ltr_cluster_stream.h"
#include "ltr/ltr_classify_stream.h"
#include "ltr/gt_ltrclustering.h"

typedef struct {
  GtFile *outfp;
  GtOutputFileInfo *ofi;
  GtStr  *file_prefix;
  unsigned long psmall,
                plarge;
  double xdrop,
         identity;
  int wordsize;
} GtLTRClusteringArguments;

static void* gt_ltrclustering_arguments_new(void)
{
  GtLTRClusteringArguments *arguments = gt_calloc((size_t) 1,
                                                  sizeof (*arguments));
  arguments->ofi = gt_output_file_info_new();
  arguments->file_prefix = gt_str_new();
  return arguments;
}

static void gt_ltrclustering_arguments_delete(void *tool_arguments)
{
  GtLTRClusteringArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->file_prefix);
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_ltrclustering_option_parser_new(void *tool_arguments)
{
  GtLTRClusteringArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] indexname [GFF3_file ...]",
                            "Cluster features of LTRs.");

  /* -psmall */
  option = gt_option_new_ulong_min_max("psmall", "specify how many percent of"
                                       " the smaller sequence a match needs to"
                                       " cover in order to cluster the two"
                                       " sequences of the match.",
                                       &arguments->psmall, 0, 0, 100UL);

  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  /* -plarge */
  option = gt_option_new_ulong_min_max("plarge", "specify how many percent of"
                                       " the larger sequence a match needs to"
                                       " cover in order to cluster the two"
                                       " sequences of the match.",
                                       &arguments->plarge, 0, 0, 100UL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  gt_option_is_mandatory(option);

  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_min_args(op, 1U);

  return op;
}

static int gt_ltrclustering_runner(int argc, const char **argv,
                                       int parsed_args, void *tool_arguments,
                                       GtError *err)
{
  GtLTRClusteringArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream      = NULL,
               *last_stream         = NULL,
               *ltr_cluster_stream  = NULL,
               *ltr_classify_stream = NULL,
               *gff3_out_stream     = NULL;
  GtEncseqLoader *el;
  GtEncseq *encseq;
  int had_err = 0, arg = parsed_args;
  const char *indexname = argv[arg];

  gt_error_check(err);
  gt_assert(arguments);
  arg++;

  el = gt_encseq_loader_new();
  encseq = gt_encseq_loader_load(el, indexname, err);

  if (!encseq)
    had_err = -1;
  if (!had_err) {
    last_stream = gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - arg,
                                                                  argv + arg);
    last_stream = ltr_cluster_stream = gt_ltr_cluster_stream_new(last_stream,
                                                         encseq,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         10,
                                                         GT_UNDEF_INT,
                                                         GT_UNDEF_INT,
                                                         arguments->plarge,
                                                         arguments->psmall,
                                                         NULL,
                                                         err);
    last_stream = ltr_classify_stream = gt_ltr_classify_stream_new(last_stream,
                                                                   NULL,
                                                                   NULL,
                                                                   NULL,
                                                                   NULL,
                                                                   err);

    if (!ltr_classify_stream)
      had_err = -1;
    else
      last_stream = gff3_out_stream = gt_gff3_out_stream_new(last_stream,
                                                          arguments->outfp);
  }
  if (!had_err)
    had_err = gt_node_stream_pull(last_stream, err);

  gt_node_stream_delete(ltr_classify_stream);
  gt_node_stream_delete(ltr_cluster_stream);
  gt_node_stream_delete(gff3_in_stream);
  gt_node_stream_delete(gff3_out_stream);
  gt_encseq_loader_delete(el);
  gt_encseq_delete(encseq);

  return had_err;
}

GtTool* gt_ltrclustering(void)
{
  return gt_tool_new(gt_ltrclustering_arguments_new,
                  gt_ltrclustering_arguments_delete,
                  gt_ltrclustering_option_parser_new,
                  NULL,
                  gt_ltrclustering_runner);
}
genometools-1.5.1/src/ltr/gt_ltrclustering.h000066400000000000000000000017741211610345200212110ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Kastens 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_LTRCLUSTERING_H
#define GT_LTRCLUSTERING_H

#include "core/tool_api.h"

/* the ltrclustering tool */
GtTool* gt_ltrclustering(void);

#endif
genometools-1.5.1/src/ltr/gt_ltrdigest.c000066400000000000000000000465701211610345200203070ustar00rootroot00000000000000/*
  Copyright (c) 2008-2010 Sascha Steinbiss 
  Copyright (c) 2008-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#endif
#include 
#include "core/fileutils_api.h"
#include "core/log.h"
#include "core/logger.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/safearith.h"
#include "core/unused_api.h"
#include "core/warning_api.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "ltr/gt_ltrdigest.h"
#include "ltr/ltrdigest_def.h"
#include "ltr/ltrdigest_stream.h"
#include "ltr/ltrfileout_stream.h"
#include "core/encseq.h"

typedef struct GtLTRdigestOptions {
  GtPBSOptions  pbs_opts;
  GtPPTOptions  ppt_opts;
#ifdef HAVE_HMMER
  GtPdomOptions pdom_opts;
#endif
  GtStr *trna_lib, *prefix, *cutoffs;
  bool verbose;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
  unsigned long nthreads;
  unsigned int seqnamelen;
} GtLTRdigestOptions;

static void* gt_ltrdigest_arguments_new(void)
{
  GtLTRdigestOptions *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  memset(arguments, 0, sizeof *arguments);
#ifdef HAVE_HMMER
  arguments->pdom_opts.hmm_files = gt_str_array_new();
#endif
  arguments->trna_lib = gt_str_new();
  arguments->prefix = gt_str_new();
  arguments->cutoffs = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_ltrdigest_arguments_delete(void *tool_arguments)
{
  GtLTRdigestOptions *arguments = tool_arguments;
  if (!arguments) return;
#ifdef HAVE_HMMER
  gt_str_array_delete(arguments->pdom_opts.hmm_files);
#endif
  gt_str_delete(arguments->trna_lib);
  gt_str_delete(arguments->prefix);
  gt_str_delete(arguments->cutoffs);
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_ltrdigest_option_parser_new(void *tool_arguments)
{
  GtLTRdigestOptions *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *o, *ot, *oto;
#ifdef HAVE_HMMER
  GtOption *oh, *oc, *oeval;
  static const char *cutoffs[] = {"NONE", "GA", "TC", NULL};
#endif
  static GtRange pptlen_defaults           = { 8UL, 30UL},
                 uboxlen_defaults          = { 3UL, 30UL},
                 pbsalilen_defaults        = {11UL, 30UL},
                 pbsoffsetlen_defaults     = { 0UL,  5UL},
                 pbstrnaoffsetlen_defaults = { 0UL,  5UL};
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] gff3_file indexname",
                            "Identifies and annotates sequence features in LTR "
                            "retrotransposon candidates.");

  /* Output files */

  oto = gt_option_new_string("outfileprefix",
                             "prefix for output files (e.g. 'foo' will create "
                             "files called 'foo_*.csv' and 'foo_*.fas')\n"
                             "Omit this option for GFF3 output only.",
                             arguments->prefix,
                             NULL);
  gt_option_parser_add_option(op, oto);
  gt_option_hide_default(oto);

  o = gt_option_new_uint("seqnamelen",
                         "set maximal length of sequence names in FASTA headers"
                         " (e.g. for clustalw or similar tools)",
                         &arguments->seqnamelen,
                         20U);
  gt_option_parser_add_option(op, o);

  /* PPT search options */

  o = gt_option_new_range("pptlen",
                          "required PPT length range",
                          &arguments->ppt_opts.ppt_len,
                          &pptlen_defaults);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_range("uboxlen",
                          "required U-box length range",
                          &arguments->ppt_opts.ubox_len,
                          &uboxlen_defaults);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_uint("uboxdist",
                         "allowed U-box distance range from PPT",
                         &arguments->ppt_opts.max_ubox_dist, 0);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_uint("pptradius",
                         "radius around beginning of 3' LTR "
                         "to search for PPT",
                         &arguments->ppt_opts.radius,
                         30U);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_probability("pptrprob",
                                "purine emission probability inside PPT",
                                &arguments->ppt_opts.ppt_purine_prob,
                                PPT_PURINE_PROB);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);

  o = gt_option_new_probability("pptyprob",
                                "pyrimidine emission probability inside PPT",
                                &arguments->ppt_opts.ppt_pyrimidine_prob,
                                PPT_PYRIMIDINE_PROB);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);

  o = gt_option_new_probability("pptgprob",
                                "background G emission probability outside PPT",
                                &arguments->ppt_opts.bkg_g_prob,
                                BKG_G_PROB);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);

  o = gt_option_new_probability("pptcprob",
                                "background C emission probability outside PPT",
                                &arguments->ppt_opts.bkg_c_prob,
                                BKG_C_PROB);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);

  o = gt_option_new_probability("pptaprob",
                                "background A emission probability outside PPT",
                                &arguments->ppt_opts.bkg_a_prob,
                                BKG_A_PROB);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);

  o = gt_option_new_probability("ppttprob",
                                "background T emission probability outside PPT",
                                &arguments->ppt_opts.bkg_t_prob,
                                BKG_T_PROB);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);

  o = gt_option_new_probability("pptuprob",
                                "U/T emission probability inside U-box",
                                &arguments->ppt_opts.ubox_u_prob,
                                UBOX_U_PROB);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);

  /* PBS search options */

  ot = gt_option_new_filename("trnas",
                              "tRNA library in multiple FASTA format for PBS "
                              "detection\n"
                              "Omit this option to disable PBS search.",
                              arguments->trna_lib);
  gt_option_parser_add_option(op, ot);
  gt_option_hide_default(ot);

  o = gt_option_new_range("pbsalilen",
                          "required PBS/tRNA alignment length range",
                          &arguments->pbs_opts.alilen,
                          &pbsalilen_defaults);
  gt_option_parser_add_option(op, o);
  gt_option_imply(o, ot);

  o = gt_option_new_range("pbsoffset",
                          "allowed PBS offset from LTR boundary range",
                          &arguments->pbs_opts.offsetlen,
                          &pbsoffsetlen_defaults);
  gt_option_parser_add_option(op, o);
  gt_option_imply(o, ot);

  o = gt_option_new_range("pbstrnaoffset",
                          "allowed PBS/tRNA 3' end alignment offset range",
                          &arguments->pbs_opts.trnaoffsetlen,
                          &pbstrnaoffsetlen_defaults);
  gt_option_parser_add_option(op, o);
  gt_option_imply(o, ot);

  o = gt_option_new_uint("pbsmaxedist",
                         "maximal allowed PBS/tRNA alignment unit "
                         "edit distance",
                         &arguments->pbs_opts.max_edist,
                         1U);
  gt_option_parser_add_option(op, o);
  gt_option_imply(o, ot);

  o = gt_option_new_uint("pbsradius",
                         "radius around end of 5' LTR "
                         "to search for PBS",
                         &arguments->pbs_opts.radius,
                         30U);
  gt_option_parser_add_option(op, o);
  gt_option_imply(o, ot);

 /* Protein domain search options */

#ifdef HAVE_HMMER
  oh = gt_option_new_filename_array("hmms",
                                    "profile HMM models for domain detection "
                                    "(separate by spaces, finish with --) in "
                                    "HMMER3 format\n"
                                    "Omit this option to disable pHMM search.",
                                    arguments->pdom_opts.hmm_files);
  gt_option_parser_add_option(op, oh);

  oeval = gt_option_new_probability("pdomevalcutoff",
                                    "global E-value cutoff for pHMM search\n"
                                    "default 1E-6",
                                    &arguments->pdom_opts.evalue_cutoff,
                                    0.000001);
  gt_option_parser_add_option(op, oeval);
  gt_option_is_extended_option(oeval);
  gt_option_hide_default(oeval);
  gt_option_imply(oeval, oh);

  oc = gt_option_new_choice("pdomcutoff", "model-specific score cutoff\n"
                                       "choose from TC (trusted cutoff) | "
                                       "GA (gathering cutoff) | "
                                       "NONE (no cutoffs)",
                             arguments->cutoffs, cutoffs[0], cutoffs);
  gt_option_parser_add_option(op, oc);
  gt_option_is_extended_option(oeval);
  gt_option_imply(oeval, oh);

  o = gt_option_new_bool("aliout",
                         "output pHMM to amino acid sequence alignments",
                         &arguments->pdom_opts.write_alignments,
                         false);
  gt_option_parser_add_option(op, o);
  gt_option_imply(o, oh);
  gt_option_imply(o, oto);

  o = gt_option_new_bool("aaout",
                         "output amino acid sequences for protein domain "
                         "hits",
                         &arguments->pdom_opts.write_aaseqs,
                         false);
  gt_option_parser_add_option(op, o);
  gt_option_imply(o, oh);
  gt_option_imply(o, oto);

  o = gt_option_new_bool("allchains",
                           "output features from all chains and unchained "
                           "features, labeled with chain numbers",
                           &arguments->pdom_opts.output_all_chains,
                           false);
  gt_option_parser_add_option(op, o);
  gt_option_imply(o, oh);

  o = gt_option_new_uint("maxgaplen",
                         "maximal allowed gap size between fragments (in amino "
                         "acids) when chaining pHMM hits for a protein domain",
                         &arguments->pdom_opts.chain_max_gap_length,
                         50);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);
  gt_option_imply(o, oh);

  o = gt_option_new_ulong("threads",
                          "DEPRECATED, only included for compatibility reasons!"
                          " Use the -j parameter of the 'gt' call instead.",
                          &arguments->nthreads,
                          0);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);
#endif

  /* Extended PBS options */

  o = gt_option_new_int("pbsmatchscore",
                        "match score for PBS/tRNA alignments",
                        &arguments->pbs_opts.ali_score_match,
                        5);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);
  gt_option_imply(o, ot);

  o = gt_option_new_int("pbsmismatchscore",
                        "mismatch score for PBS/tRNA alignments",
                        &arguments->pbs_opts.ali_score_mismatch,
                        -10);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);
  gt_option_imply(o, ot);

  o = gt_option_new_int("pbsinsertionscore",
                        "insertion score for PBS/tRNA alignments",
                        &arguments->pbs_opts.ali_score_insertion,
                        -20);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);
  gt_option_imply(o, ot);

  o = gt_option_new_int("pbsdeletionscore",
                        "deletion score for PBS/tRNA alignments",
                        &arguments->pbs_opts.ali_score_deletion,
                        -20);
  gt_option_parser_add_option(op, o);
  gt_option_is_extended_option(o);
  gt_option_imply(o, ot);

  /* verbosity */

  o = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, o);

  /* output file options */

  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_min_max_args(op, 2U, 2U);

  return op;
}

int gt_ltrdigest_arguments_check(GT_UNUSED int rest_argc, void *tool_arguments,
                                 GtError* err)
{
  GtLTRdigestOptions *arguments = tool_arguments;
  int had_err  = 0;

  if (arguments->nthreads > 0) {
    gt_warning("The '-threads' option is deprecated. Please use the '-j'"
               "option of the 'gt' call instead, e.g.:\n"
               "  gt -j %lu ltrdigest ...", arguments->nthreads);
  }

  /* -trnas */
  if (!had_err && arguments->trna_lib && gt_str_length(arguments->trna_lib) > 0)
  {
    if (!gt_file_exists(gt_str_get(arguments->trna_lib)))
    {
      gt_error_set(err, "File '%s' does not exist!",
                        gt_str_get(arguments->trna_lib));
      had_err = -1;
    }
  }

  if (!had_err)
  {
    GtHMM *hmm;
    GtAlphabet *alpha;
    alpha = gt_alphabet_new_dna();
    hmm = gt_ppt_hmm_new(alpha, &arguments->ppt_opts);
    if (!hmm)
    {
      gt_error_set(err, "PPT HMM parameters are not valid!");
      had_err = -1;
    }
    else
      gt_hmm_delete(hmm);
    gt_alphabet_delete(alpha);
  }

  return had_err;
}

static int gt_ltrdigest_runner(GT_UNUSED int argc, const char **argv,
                               int parsed_args, void *tool_arguments,
                               GtError *err)
{
  GtLTRdigestOptions *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream   = NULL,
               *gff3_out_stream  = NULL,
               *ltrdigest_stream = NULL,
               *tab_out_stream   = NULL,
               *last_stream      = NULL;
  int had_err      = 0,
      tests_to_run = 0,
      arg = parsed_args;
  const char *indexname = argv[arg+1];
  GtLogger *logger = gt_logger_new(arguments->verbose,
                                   GT_LOGGER_DEFLT_PREFIX, stdout);
  GtEncseqLoader *el;
  GtEncseq *encseq;
  gt_error_check(err);
  gt_assert(arguments);

  /* Set sequence encoder options. Defaults are ok. */
  el = gt_encseq_loader_new();
  gt_encseq_loader_set_logger(el, logger);

  /* Open sequence file */
  encseq = gt_encseq_loader_load(el, indexname, err);
  if (!encseq)
    had_err = -1;

  /* Always search for PPT. */
  tests_to_run |= GT_LTRDIGEST_RUN_PPT;

  /* Open tRNA library if given. */
  if (!had_err && arguments->trna_lib
        && gt_str_length(arguments->trna_lib) > 0)
  {
    tests_to_run |= GT_LTRDIGEST_RUN_PBS;
   arguments->pbs_opts.trna_lib = gt_bioseq_new(gt_str_get(arguments->trna_lib),
                                                 err);
    if (gt_error_is_set(err))
      had_err = -1;
  }

#ifdef HAVE_HMMER
  /* Open HMMER files if given. */
  if (!had_err && gt_str_array_size(arguments->pdom_opts.hmm_files) > 0)
  {
    tests_to_run |= GT_LTRDIGEST_RUN_PDOM;
    if (!strcmp(gt_str_get(arguments->cutoffs), "GA")) {
      arguments->pdom_opts.cutoff = GT_PHMM_CUTOFF_GA;
    } else if (!strcmp(gt_str_get(arguments->cutoffs), "TC")) {
      arguments->pdom_opts.cutoff = GT_PHMM_CUTOFF_TC;
    } else if (!strcmp(gt_str_get(arguments->cutoffs), "NONE")) {
      arguments->pdom_opts.cutoff = GT_PHMM_CUTOFF_NONE;
    } else {
      gt_error_set(err, "invalid cutoff setting!");
      had_err = -1;
    }
  }
#endif

  if (!had_err)
  {
    /* set up stream flow
     * ------------------*/
    last_stream = gff3_in_stream  = gt_gff3_in_stream_new_sorted(argv[arg]);

    last_stream = ltrdigest_stream = gt_ltrdigest_stream_new(last_stream,
                                                  tests_to_run,
                                                  encseq,
                                                  &arguments->pbs_opts,
                                                  &arguments->ppt_opts,
#ifdef HAVE_HMMER
                                                  &arguments->pdom_opts,
#endif
                                                  err);
    if (!ltrdigest_stream)
      had_err = -1;
  }

  if (!had_err)
  {
    /* attach tabular output stream, if requested */
    if (gt_str_length(arguments->prefix) > 0)
    {
      last_stream = tab_out_stream = gt_ltr_fileout_stream_new(last_stream,
                                              tests_to_run,
                                              encseq,
                                              gt_str_get(arguments->prefix),
                                              &arguments->ppt_opts,
                                              &arguments->pbs_opts,
#ifdef HAVE_HMMER
                                              &arguments->pdom_opts,
#endif
                                              gt_str_get(arguments->trna_lib),
                                              argv[arg+1],
                                              argv[arg],
                                              arguments->seqnamelen,
                                              err);
#ifdef HAVE_HMMER
    if (arguments->pdom_opts.write_alignments)
      gt_ltr_fileout_stream_enable_pdom_alignment_output(tab_out_stream);
    if (arguments->pdom_opts.write_aaseqs)
      gt_ltr_fileout_stream_enable_aa_sequence_output(tab_out_stream);
#endif
    }

    last_stream = gff3_out_stream = gt_gff3_out_stream_new(last_stream,
                                                           arguments->outfp);

    /* pull the features through the stream and free them afterwards */
    had_err = gt_node_stream_pull(last_stream, err);
  }

  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(ltrdigest_stream);
  if (tab_out_stream != NULL)
    gt_node_stream_delete(tab_out_stream);
  gt_node_stream_delete(gff3_in_stream);

  gt_encseq_loader_delete(el);
  gt_encseq_delete(encseq);
  encseq = NULL;
  gt_bioseq_delete(arguments->pbs_opts.trna_lib);
  gt_logger_delete(logger);

  return had_err;
}

GtTool* gt_ltrdigest(void)
{
  return gt_tool_new(gt_ltrdigest_arguments_new,
                     gt_ltrdigest_arguments_delete,
                     gt_ltrdigest_option_parser_new,
                     gt_ltrdigest_arguments_check,
                     gt_ltrdigest_runner);
}
genometools-1.5.1/src/ltr/gt_ltrdigest.h000066400000000000000000000017451211610345200203070ustar00rootroot00000000000000/*
  Copyright (c) 2008 Sascha Steinbiss 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_LTRDIGEST_H
#define GT_LTRDIGEST_H

#include "core/tool_api.h"

/* the LTRdigest tool */
GtTool* gt_ltrdigest(void);

#endif
genometools-1.5.1/src/ltr/gt_ltrharvest.c000066400000000000000000000617071211610345200205030ustar00rootroot00000000000000/*
  Copyright (c) 2010-2012 Sascha Steinbiss 
  Copyright (c) 2007      David Ellinghaus 
  Copyright (c) 2007-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/option_api.h"
#include "core/unused_api.h"
#include "core/output_file_api.h"
#include "core/undef_api.h"
#include "core/versionfunc.h"
#include "extended/genome_node.h"
#include "extended/gff3_out_stream_api.h"
#include "ltr/ltr_four_char_motif.h"
#include "ltr/ltrharvest_stream.h"
#include "ltr/ltrharvest_fasta_out_stream.h"
#include "ltr/ltrharvest_tabout_stream.h"
#include "ltr/ltrharvest_tabout_visitor.h"
#include "ltr/gt_ltrharvest.h"

typedef struct {
  GtOutputFileInfo *ofi;
  GtFile *outfp;
  GtStr *str_indexname,
        *str_motif,
        *str_overlaps,
        *str_fastaoutputfilename,
        *str_fastaoutputfilenameinnerregion,
        *str_gff3filename;
  GtRange searchrange;
  unsigned long minseedlength,
                minltrlength,
                maxltrlength,
                mindistance,
                maxdistance,
                numofboundaries,
                offset;
  double similaritythreshold;
  int xdropbelowscore;
  GtXdropArbitraryscores arbitscores;
  unsigned int minlengthTSD,
               maxlengthTSD,
               allowedmismatches;
  unsigned int vicinity;
  bool bestoverlaps,
       nooverlaps,
       fastaoutput,
       fastaoutputinnerregion,
       gff3output,
       longoutput,
       scan,
       verbosemode;
  GtOption *optionmotif,
           *optionmotifmis,
           *optionoverlaps,
           *optionout,
           *optionoutinner,
           *optiongff3;
  GtLTRFourCharMotif *motif;
} LTRharvestArguments;

static void gt_ltrharvest_showopts(const LTRharvestArguments *lo)
{
  printf("# user defined options and values:\n");
  if (lo->verbosemode)
  {
    printf("#   verbosemode: On\n");
  }
  else
  {
    printf("#   verbosemode: Off\n");
  }
  printf("#   indexname: %s\n", gt_str_get(lo->str_indexname));
  if (lo->fastaoutput)
  {
    printf("#   outputfile: %s\n", gt_str_get(lo->str_fastaoutputfilename));
  }
  if (lo->fastaoutputinnerregion)
  {
    printf("#   outputfile inner region: %s\n",
        gt_str_get(lo->str_fastaoutputfilenameinnerregion));
  }
  if (lo->gff3output)
  {
    printf("#   outputfile gff3 format: %s\n",
           gt_str_get(lo->str_gff3filename));
  }
  printf("#   xdropbelowscore: %d\n", lo->xdropbelowscore);
  printf("#   similaritythreshold: %.2f\n", lo->similaritythreshold);
  printf("#   minseedlength: %lu\n", lo->minseedlength);
  printf("#   matchscore: %d\n", lo->arbitscores.mat);
  printf("#   mismatchscore: %d\n", lo->arbitscores.mis);
  printf("#   insertionscore: %d\n", lo->arbitscores.ins);
  printf("#   deletionscore: %d\n", lo->arbitscores.del);
  printf("#   minLTRlength: %lu\n",  lo->minltrlength);
  printf("#   maxLTRlength: %lu\n",  lo->maxltrlength);
  printf("#   minLTRdistance: %lu\n",  lo->mindistance);
  printf("#   maxLTRdistance: %lu\n",  lo->maxdistance);
  if (lo->nooverlaps)
  {
    printf("#   overlaps: no\n");
  }
  else
  {
    if (lo->bestoverlaps)
    {
      printf("#   overlaps: best\n");
    }
    else
    {
      printf("#   overlaps: all\n");
    }
  }
  printf("#   minTSDlength: %u\n",  lo->minlengthTSD);
  printf("#   maxTSDlength: %u\n",  lo->maxlengthTSD);
  printf("#   palindromic motif: %s\n", gt_str_get(lo->str_motif));
  printf("#   motifmismatchesallowed: %u\n", lo->allowedmismatches);
  printf("#   vicinity: %u nt\n", lo->vicinity);
  if (lo->searchrange.start != 0 ||
      lo->searchrange.end != 0)
  {
    printf("# ltrsearchseqrange=(%lu,%lu)\n",
          lo->searchrange.start,
          lo->searchrange.end);
  }
}

static void* gt_ltrharvest_arguments_new(void)
{
  LTRharvestArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  arguments->str_motif = gt_str_new();
  arguments->str_overlaps = gt_str_new();
  arguments->str_indexname = gt_str_new();
  arguments->str_fastaoutputfilename = gt_str_new();
  arguments->str_fastaoutputfilenameinnerregion = gt_str_new();
  arguments->str_gff3filename = gt_str_new();
  arguments->motif = gt_calloc((size_t) 1, sizeof (GtLTRFourCharMotif));
  return arguments;
}

static void gt_ltrharvest_arguments_delete(void *tool_arguments)
{
  LTRharvestArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->str_motif);
  gt_str_delete(arguments->str_overlaps);
  gt_str_delete(arguments->str_indexname);
  gt_str_delete(arguments->str_fastaoutputfilename);
  gt_str_delete(arguments->str_fastaoutputfilenameinnerregion);
  gt_str_delete(arguments->str_gff3filename);
  gt_option_delete(arguments->optiongff3);
  gt_option_delete(arguments->optionoutinner);
  gt_option_delete(arguments->optionout);
  gt_option_delete(arguments->optionmotif);
  gt_option_delete(arguments->optionmotifmis);
  gt_option_delete(arguments->optionoverlaps);
  gt_free(arguments->motif);
  gt_free(arguments);
}

static GtOptionParser* gt_ltrharvest_option_parser_new(void *tool_arguments)
{
  LTRharvestArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *optionindex,
           *optionltrsearchseqrange,
           *optionseed,
           *optionminlenltr,
           *optionmaxlenltr,
           *optionmindistltr,
           *optionmaxdistltr,
           *optionmintsd,
           *optionmaxtsd,
           *optionsimilar,
           *optionmotif,
           *optionmotifmis,
           *optionvic,
           *optionoverlaps,
           *optionxdrop,
           *optionmat,
           *optionmis,
           *optionins,
           *optiondel,
           *optionv,
           *optionoffset,
           *optionlongoutput,
           *optionout,
           *optionoutinner,
           *optiongff3,
           *optionscan;
  GtRange default_ltrsearchseqrange = {0,0};
  static const char *overlaps[] = {
    "best", /* the default */
    "no",
    "all",
    NULL
  };

  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] -index ",
                            "Predict LTR retrotransposons.");

  /* -index */
  optionindex = gt_option_new_string("index",
                             "specify the name of the enhanced suffix "
                             "array index (mandatory)",
                             arguments->str_indexname, NULL);
  gt_option_is_mandatory(optionindex);
  gt_option_parser_add_option(op, optionindex);

  /* -range */
  optionltrsearchseqrange
    = gt_option_new_range("range",
                          "specify range in the input sequence(s) in which LTR "
                          "pairs are searched",
                          &arguments->searchrange,
                          &default_ltrsearchseqrange);
  gt_option_parser_add_option(op, optionltrsearchseqrange);

  /* -seed */
  optionseed = gt_option_new_ulong_min("seed",
                               "specify minimum seed length for"
                               " exact repeats",
                               &arguments->minseedlength,
                               30UL,
                               1UL);
  gt_option_parser_add_option(op, optionseed);

  /* -minlenltr */
  optionminlenltr = gt_option_new_ulong_min_max("minlenltr",
                               "specify minimum length for each LTR",
                               &arguments->minltrlength,
                               100UL,
                               1UL,
                               GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, optionminlenltr);

  /* -maxlenltr */
  optionmaxlenltr = gt_option_new_ulong_min_max("maxlenltr",
                               "specify maximum length for each LTR",
                               &arguments->maxltrlength,
                               1000UL,
                               1UL,
                               GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, optionmaxlenltr);

  /* -mindistltr */
  optionmindistltr = gt_option_new_ulong_min_max("mindistltr",
                               "specify minimum distance of "
                               "LTR startpositions",
                               &arguments->mindistance,
                               1000UL,
                               1UL,
                               GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, optionmindistltr);

  /* -maxdistltr */
  optionmaxdistltr = gt_option_new_ulong_min_max("maxdistltr",
                               "specify maximum distance of "
                               "LTR startpositions",
                               &arguments->maxdistance,
                               15000UL,
                               1UL,
                               GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, optionmaxdistltr);

  /* -similar */
  optionsimilar = gt_option_new_double_min_max("similar",
                               "specify similaritythreshold in "
                               "range [1..100%]",
                               &arguments->similaritythreshold,
                               (double) 85.0,
                               (double) 0.0,
                               100.0);
  gt_option_parser_add_option(op, optionsimilar);

  /* -mintsd */
  optionmintsd = gt_option_new_uint_min_max("mintsd",
                              "specify minimum length for each TSD",
                               &arguments->minlengthTSD,
                               4U,
                               0,
                               GT_UNDEF_UINT);
  gt_option_parser_add_option(op, optionmintsd);

  /* -maxtsd */
  optionmaxtsd = gt_option_new_uint_min_max("maxtsd",
                              "specify maximum length for each TSD",
                               &arguments->maxlengthTSD,
                               20U,
                               0,
                               GT_UNDEF_UINT);
  gt_option_parser_add_option(op, optionmaxtsd);

  optionmotif = gt_option_new_string("motif",
                             "specify 2 nucleotides startmotif + "
                             "2 nucleotides endmotif: ****",
                             arguments->str_motif, NULL);
  gt_option_parser_add_option(op, optionmotif);
  arguments->optionmotif = gt_option_ref(optionmotif);

  /* -motifmis */
  optionmotifmis = gt_option_new_uint_min_max("motifmis",
                             "specify maximum number of "
                             "mismatches in motif [0,3]",
                             &arguments->allowedmismatches,
                             4U,
                             0,
                             3U);
  gt_option_parser_add_option(op, optionmotifmis);
  arguments->optionmotifmis = gt_option_ref(optionmotifmis);

  /* -vic */
  optionvic = gt_option_new_uint_min_max("vic",
                        "specify the number of nucleotides (to the left and "
                        "to the right) that will be searched "
                        "for TSDs and/or motifs around 5' and 3' boundary "
                        "of predicted LTR retrotransposons",
                        &arguments->vicinity,
                        60U,
                        1U,
                        500U);
  gt_option_parser_add_option(op, optionvic);

  /* -overlaps */
  optionoverlaps = gt_option_new_choice("overlaps",
               "specify no|best|all",
               arguments->str_overlaps,
               overlaps[0],
               overlaps);
  gt_option_parser_add_option(op, optionoverlaps);
  arguments->optionoverlaps = gt_option_ref(optionoverlaps);

  /* -xdrop */
  optionxdrop = gt_option_new_int_min("xdrop",
                        "specify xdropbelowscore for extension-alignment",
                        &arguments->xdropbelowscore,
                        5,
                        0);
  gt_option_parser_add_option(op, optionxdrop);

  /* -mat */
  optionmat = gt_option_new_int_min("mat",
                        "specify matchscore for extension-alignment",
                        &arguments->arbitscores.mat,
                        2,
                        1);
  gt_option_parser_add_option(op, optionmat);

  /* -mis */
  optionmis = gt_option_new_int_max("mis",
                        "specify mismatchscore for extension-alignment",
                        &arguments->arbitscores.mis,
                        -2,
                        -1);
  gt_option_parser_add_option(op, optionmis);

  /* -ins */
  optionins = gt_option_new_int_max("ins",
                        "specify insertionscore for extension-alignment",
                        &arguments->arbitscores.ins,
                        -3,
                        -1);
  gt_option_parser_add_option(op, optionins);

  /* -del */
  optiondel = gt_option_new_int_max("del",
                        "specify deletionscore for extension-alignment",
                        &arguments->arbitscores.del,
                        -3,
                        -1);
  gt_option_parser_add_option(op, optiondel);

  /* -v */
  optionv = gt_option_new_bool("v",
                           "verbose mode",
                           &arguments->verbosemode,
                           false);
  gt_option_parser_add_option(op, optionv);

  /* -longoutput */
  optionlongoutput = gt_option_new_bool("longoutput",
                           "additional motif/TSD output",
                           &arguments->longoutput,
                           false);
  gt_option_parser_add_option(op, optionlongoutput);

  /* -out */
  arguments->fastaoutput = false;
  optionout = gt_option_new_string("out",
                             "specify FASTA outputfilename",
                             arguments->str_fastaoutputfilename, NULL);
  gt_option_parser_add_option(op, optionout);
  arguments->optionout = gt_option_ref(optionout);

  /* -outinner */
  arguments->fastaoutputinnerregion = false;
  optionoutinner = gt_option_new_string("outinner",
                             "specify FASTA outputfilename for inner regions",
                             arguments->str_fastaoutputfilenameinnerregion,
                              NULL);
  gt_option_parser_add_option(op, optionoutinner);
  arguments->optionoutinner = gt_option_ref(optionoutinner);

  /* -gff3 */
  arguments->gff3output = false;
  optiongff3 = gt_option_new_string("gff3",
                                    "specify GFF3 outputfilename",
                                    arguments->str_gff3filename, NULL);
  gt_option_parser_add_option(op, optiongff3);
  arguments->optiongff3 = gt_option_ref(optiongff3);

  /* -offset */
  optionoffset = gt_option_new_ulong("offset",
                                     "offset added to GFF3 coordinates",
                                     &arguments->offset,
                                     0UL);
  gt_option_parser_add_option(op, optionoffset);
  gt_option_is_extended_option(optionoffset);

  /* -scan */
  optionscan = gt_option_new_bool("scan",
                                  "scan the index sequentially instead of "
                                  "mapping it into memory entirely",
                                  &arguments->scan,
                                  true);
  gt_option_parser_add_option(op, optionscan);
  gt_option_is_extended_option(optionscan);

  /* implications */
  gt_option_imply(optionmaxtsd, optionmintsd);
  gt_option_imply(optionmotifmis, optionmotif);

  gt_option_imply_either_2(optionlongoutput, optionmintsd, optionmotif);

  gt_option_parser_refer_to_manual(op);

  /* gt_output_file_register_options(op, &arguments->outfp, arguments->ofi); */

  return op;
}

static int gt_ltrharvest_arguments_check(GT_UNUSED int rest_argc,
                                           void *tool_arguments,
                                           GtError *err)
{
  LTRharvestArguments *arguments = tool_arguments;
  int had_err = 0;

  /* init */
  arguments->motif->firstleft   = (GtUchar) 't';
  arguments->motif->secondleft  = (GtUchar) 'g';
  arguments->motif->firstright  = (GtUchar) 'c';
  arguments->motif->secondright = (GtUchar) 'a';
  arguments->motif->allowedmismatches = arguments->allowedmismatches;

  if (gt_option_is_set(arguments->optionmotif))
  {
    if (gt_str_length(arguments->str_motif) != 4UL)
    {
      gt_error_set(err,
          "argument of -motif has not exactly 4 characters");
      had_err = -1;
    }
    if (!had_err) {
      arguments->motif->firstleft =
        (GtUchar) gt_str_get(arguments->str_motif)[0];
      arguments->motif->secondleft =
        (GtUchar) gt_str_get(arguments->str_motif)[1];
      arguments->motif->firstright =
        (GtUchar)  gt_str_get(arguments->str_motif)[2];
      arguments->motif->secondright =
        (GtUchar)  gt_str_get(arguments->str_motif)[3];
      /* default if motif specified */
      if (!gt_option_is_set(arguments->optionmotifmis))
      {
        arguments->motif->allowedmismatches = 0;
        arguments->allowedmismatches = 0;
      }
    }
  }
  if (!had_err) {
    if (gt_option_is_set(arguments->optionoverlaps))
    {
      if (strcmp(gt_str_get(arguments->str_overlaps), "no") == 0)
      {
        arguments->bestoverlaps = false;
        arguments->nooverlaps = true;
      }
      else if (strcmp(gt_str_get(arguments->str_overlaps), "best") == 0 )
      {
        arguments->bestoverlaps = true;
        arguments->nooverlaps = false;
      }
      else if (strcmp(gt_str_get(arguments->str_overlaps), "all") == 0 )
      {
        arguments->bestoverlaps = false;
        arguments->nooverlaps = false;
      }
      else
      {
        gt_assert(0); /* cannot happen */
      }
    }
    else
    {
      /* default is "best" */
      arguments->bestoverlaps = true;  /* take best prediction
                                          if overlap occurs, default */
      arguments->nooverlaps = false; /* overlapping predictions (not) allowed*/
    }
    /* if FASTA output is set */
    if (gt_option_is_set(arguments->optionout))
    {
      arguments->fastaoutput = true;
    }
    /* if FASTA output inner region is set */
    if (gt_option_is_set(arguments->optionoutinner))
    {
      arguments->fastaoutputinnerregion = true;
    }
    /* if GFF3 output is set */
    if (gt_option_is_set(arguments->optiongff3))
    {
      arguments->gff3output = true;
    }
  }
  return had_err;
}

static void gt_ltrharvest_showargsline(int argc, const char **argv)
{
  int i;
  gt_assert(argv && argc >= 1);
  printf("# args=");
  for (i=1; istr_indexname,
                                         arguments->searchrange,
                                         arguments->minseedlength,
                                         arguments->minltrlength,
                                         arguments->maxltrlength,
                                         arguments->mindistance,
                                         arguments->maxdistance,
                                         arguments->similaritythreshold,
                                         arguments->xdropbelowscore,
                                         arguments->arbitscores,
                                         arguments->motif,
                                         arguments->verbosemode,
                                         arguments->nooverlaps,
                                         arguments->bestoverlaps,
                                         arguments->scan,
                                         arguments->offset,
                                         arguments->minlengthTSD,
                                         arguments->maxlengthTSD,
                                         (unsigned long) arguments->vicinity,
                                         err);
  if (ltrh_stream == NULL)
    return -1;
  last_stream = ltrh_stream;

  encseq = gt_ltrharvest_stream_get_encseq(ltrh_stream);

  /* set visitors according to output parameter */
  if (!had_err && arguments->longoutput) {
    tabout_visitor = gt_ltrharvest_tabout_visitor_new_longoutput(encseq);
  } else {
    tabout_visitor = gt_ltrharvest_tabout_visitor_new();
  }

  /* create tabular output stream (traditional LTRharvest format) */
  tabout_stream = gt_ltrharvest_tabout_stream_new(last_stream, tabout_visitor);
  last_stream = tabout_stream;

  /* attach GFF3 output stream if requested */
  if (!had_err && arguments->gff3output) {
    gff3file = gt_file_open(GT_FILE_MODE_UNCOMPRESSED,
                            gt_str_get(arguments->str_gff3filename),
                            "w+",
                            err);
    if (gff3file == NULL) {
      had_err = -1;
    } else {
      gff3_out_stream = gt_gff3_out_stream_new(last_stream, gff3file);
      last_stream = gff3_out_stream;
    }
  }

  /* attach FASTA output stream if requested */
  if (!had_err && arguments->fastaoutput) {
    fastaoutfile = gt_file_open(GT_FILE_MODE_UNCOMPRESSED,
                                gt_str_get(arguments->str_fastaoutputfilename),
                                "w+",
                                err);
    if (fastaoutfile == NULL) {
      had_err = -1;
    } else {
      fasta_out_stream = gt_ltrharvest_fasta_out_stream_new(last_stream,
                                                            false,
                                                            encseq,
                                                            60UL,
                                                            fastaoutfile);
      last_stream = fasta_out_stream;
    }
  }

  /* attach FASTA inner region output stream if requested */
  if (!had_err && arguments->fastaoutputinnerregion) {
    fastainneroutfile = gt_file_open(GT_FILE_MODE_UNCOMPRESSED,
                      gt_str_get(arguments->str_fastaoutputfilenameinnerregion),
                      "w+", err);
    if (fastainneroutfile == NULL) {
      had_err = -1;
    } else {
      fasta_inner_out_stream = gt_ltrharvest_fasta_out_stream_new(last_stream,
                                                             true,
                                                             encseq,
                                                             60UL,
                                                             fastainneroutfile);
      last_stream = fasta_inner_out_stream;
    }
  }

  /* output arguments line */
  gt_ltrharvest_showargsline(argc, argv);

  /* show long parameters */
  if (arguments->verbosemode)
    gt_ltrharvest_showopts(arguments);

  /* print tabular output header */
  if (!had_err) {
    if (arguments->longoutput) {
      gt_ltrharvest_tabout_stream_printlongheader(arguments->minlengthTSD > 1U,
                                             arguments->allowedmismatches < 4U);
    } else {
      gt_ltrharvest_tabout_stream_printshortheader();
    }
  }

  /* pull the features through the stream and free them afterwards */
  if (!had_err)
    had_err = gt_node_stream_pull(last_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(tabout_stream);
  gt_node_stream_delete(fasta_out_stream);
  gt_node_stream_delete(fasta_inner_out_stream);
  gt_node_stream_delete(ltrh_stream);

  if (gff3file != NULL) gt_file_delete(gff3file);
  if (fastaoutfile != NULL) gt_file_delete(fastaoutfile);
  if (fastainneroutfile != NULL) gt_file_delete(fastainneroutfile);

  return had_err;
}

GtTool* gt_ltrharvest(void)
{
  return gt_tool_new(gt_ltrharvest_arguments_new,
                     gt_ltrharvest_arguments_delete,
                     gt_ltrharvest_option_parser_new,
                     gt_ltrharvest_arguments_check,
                     gt_ltrharvest_runner);
}
genometools-1.5.1/src/ltr/gt_ltrharvest.h000066400000000000000000000017511211610345200205010ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_LTRHARVEST_H
#define GT_LTRHARVEST_H

#include "core/tool_api.h"

/* the LTRharvest tool */
GtTool* gt_ltrharvest(void);

#endif
genometools-1.5.1/src/ltr/ltr_classify_stream.c000066400000000000000000000344741211610345200216650ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Kastens 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/array.h"
#include "core/bittab.h"
#include "core/class_alloc_lock.h"
#include "core/ma.h"
#include "core/cstr_api.h"
#include "core/hashmap.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "extended/feature_type.h"
#include "extended/genome_node.h"
#include "ltr/ltr_classify_stream.h"

struct GtLTRClassifyStream {
  const GtNodeStream parent_instance;
  GtNodeStream *in_stream;
  GtArray *nodes;
  GtHashmap *features;
  const char *famprefix;
  char **current_state;
  bool first_next;
  unsigned long next_index,
                *progress;
};

#define gt_ltr_classify_stream_cast(CS)\
        gt_node_stream_cast(gt_ltr_classify_stream_class(), CS);

static bool ltr_candidates_compatible(GtGenomeNode *candidate1,
                                      GtGenomeNode *candidate2,
                                      GtHashmap *features,
                                      GT_UNUSED GtError *err)
{
  GtGenomeNode *candidate;
  GtFeatureNode *curnode1,
                *curnode2;
  GtFeatureNodeIterator *fni1,
                        *fni2;
  GtHashmap *fnmap;
  const char *clid1,
             *clid2,
             *fnt;
  bool compatible = false,
       seen_a = false,
       first_ltr = true;
  unsigned long clnum1,
                clnum2;

  gt_error_check(err);
  gt_assert(candidate1 && candidate2);

  fni1 = gt_feature_node_iterator_new((GtFeatureNode*) candidate1);
  curnode1 = gt_feature_node_iterator_next(fni1);
  fni2 = gt_feature_node_iterator_new((GtFeatureNode*) candidate2);
  curnode2 = gt_feature_node_iterator_next(fni2);

  if (gt_feature_node_number_of_children(curnode1) <=
      gt_feature_node_number_of_children(curnode2)) {
    gt_feature_node_iterator_delete(fni2);
    candidate = candidate2;
  } else {
    gt_feature_node_iterator_delete(fni1);
    fni1 = fni2;
    candidate = candidate1;
  }
  fnmap = (GtHashmap*) gt_genome_node_get_user_data(candidate, "fnmap");

  while ((curnode1 = gt_feature_node_iterator_next(fni1)) != NULL) {
    fnt = gt_feature_node_get_type(curnode1);
    if ((strcmp(fnt, gt_ft_LTR_retrotransposon) == 0))
      continue;
    else if (strcmp(fnt, gt_ft_long_terminal_repeat) == 0) {
      if (first_ltr) {
        fnt = "lLTR";
        first_ltr = false;
      } else
        fnt = "rLTR";
    } else if (strcmp(fnt, gt_ft_protein_match) == 0) {
      fnt = gt_feature_node_get_attribute(curnode1, "name");
    }
    if (!fnt)
      continue;
    if (features != NULL)
      if (gt_hashmap_get(features, fnt) == NULL)
        continue;
    curnode2 = (GtFeatureNode*) gt_hashmap_get(fnmap, fnt);
    if (curnode2 != NULL) {
      clid1 = gt_feature_node_get_attribute(curnode1, "clid");
      if (clid1 != NULL)
        (void) sscanf(clid1, "%lu", &clnum1);
      else
        clnum1 = GT_UNDEF_ULONG;
      clid2 = gt_feature_node_get_attribute(curnode2, "clid");
      if (clid2 != NULL)
        (void) sscanf(clid2, "%lu", &clnum2);
      else
        clnum2 = GT_UNDEF_ULONG;
      if (clnum1 == clnum2) {
        if ((clnum1 != GT_UNDEF_ULONG) && (clnum2 != GT_UNDEF_ULONG))
          seen_a = true;
        compatible = true;
      }
      else if ((clnum1 == GT_UNDEF_ULONG && clnum2 != GT_UNDEF_ULONG) ||
               (clnum1 != GT_UNDEF_ULONG && clnum2 == GT_UNDEF_ULONG))
        compatible = true;
      else if (clnum1 != clnum2) {
        compatible = false;
        break;
      }
    }
  }
  gt_feature_node_iterator_delete(fni1);

  return (compatible && seen_a);
}

static bool ltr_group_compatible(GtArray *candidates, GtGenomeNode *candidate1,
                                 GtBittab *group, GtHashmap *features,
                                 GtError *err)
{
  GtArray *group_member;
  GtGenomeNode *candidate2;
  bool compatible = true;
  unsigned long i, index;

  gt_assert(candidates && candidate1 && group);
  gt_error_check(err);

  group_member = gt_array_new(sizeof(unsigned long));
  gt_bittab_get_all_bitnums(group, group_member);

  for (i = 0; i < gt_array_size(group_member); i++) {
    index = *(unsigned long*) gt_array_get(group_member, i);
    candidate2 = *(GtGenomeNode**) gt_array_get(candidates, index);
    if (!(compatible = ltr_candidates_compatible(candidate1, candidate2,
                                                 features, err)))
      break;
  }
  gt_array_delete(group_member);

  return compatible;
}

static int check_ambiguous_candidates(GtArray *candidates, GtArray *groups,
                                      GtHashmap *features,
                                      unsigned long *progress,
                                      GtError *err)
{
  GtGenomeNode *candidate;
  GtBittab *group;
  GtArray *compat_groups;
  int had_err = 0;
  unsigned long i,
                j;

  gt_error_check(err);
  gt_assert(candidates && groups);

  for (i = 0; i < gt_array_size(candidates); i++) {
    candidate = *(GtGenomeNode**) gt_array_get(candidates, i);
    if (gt_feature_node_try_cast(candidate) == NULL)
      continue;
    compat_groups = gt_array_new(sizeof(GtBittab*));
    for (j = 0; j < gt_array_size(groups); j++) {
      group = *(GtBittab**) gt_array_get(groups, j);
      if (ltr_group_compatible(candidates, candidate, group, features, err))
        gt_array_add(compat_groups, group);
    }
    if (gt_array_size(compat_groups) > 1UL) {
      for (j = 0; j < gt_array_size(groups); j++) {
        group = *(GtBittab**) gt_array_get(groups, j);
        gt_bittab_unset_bit(group, i);
        if (gt_bittab_count_set_bits(group) == 0)
          gt_array_rem(groups, j);
      }
    }
    gt_array_delete(compat_groups);
    if (progress != NULL)
      *progress = *progress + 1;
  }
  return had_err;
}

static int annotate_nodes(GtArray *candidates, GtArray *groups,
                          const char *famprefix, GtError *err)
{
  GtArray *group_member;
  GtBittab *group;
  GtFeatureNode *curnode;
  GtFeatureNodeIterator *fni = NULL;
  GtGenomeNode *gn;
  int had_err = 0;
  unsigned long i, j, index, famno = 0;

  gt_assert(candidates && groups);
  gt_error_check(err);

  for (i = 0; i < gt_array_size(groups); i++) {
    group = *(GtBittab**) gt_array_get(groups, i);
    group_member = gt_array_new(sizeof(unsigned long));
    gt_bittab_get_all_bitnums(group, group_member);
    if (gt_array_size(group_member) < 2UL) {
      gt_array_delete(group_member);
      continue;
    }
    for (j = 0; j < gt_array_size(group_member); j++) {
      index = *(unsigned long*) gt_array_get(group_member, j);
      gn = *(GtGenomeNode**) gt_array_get(candidates, index);
      fni = gt_feature_node_iterator_new((GtFeatureNode*) gn);
      curnode = gt_feature_node_iterator_next(fni);
      if (strcmp(gt_feature_node_get_type(curnode), gt_ft_repeat_region) == 0) {
        char fam[BUFSIZ];
        if (famprefix != NULL)
          (void) snprintf(fam, BUFSIZ, "%s%lu", famprefix, famno);
        else
          (void) snprintf(fam, BUFSIZ, "ltrfam_%lu", famno);
        gt_feature_node_set_attribute(curnode, "ltrfam", fam);
      } else {
        gt_feature_node_iterator_delete(fni);
        gt_error_set(err, "repeat_region is not root node");
        had_err = -1;
        break;
      }
      gt_feature_node_iterator_delete(fni);
    }
    gt_array_delete(group_member);
    if (had_err)
      break;
    famno++;
  }
  return had_err;
}

static void delete_hash(void *hash)
{
  gt_hashmap_delete((GtHashmap*) hash);
}

static void add_fnmap_to_candidates(GtArray *candidates)
{
  GtGenomeNode *gn;
  GtFeatureNode *curnode;
  GtFeatureNodeIterator *fni;
  GtHashmap *fnmap;
  bool first_ltr;
  const char *fnt;
  unsigned long i;

  for (i = 0; i < gt_array_size(candidates); i++) {
    gn = *(GtGenomeNode**) gt_array_get(candidates, i);
    if (gt_feature_node_try_cast(gn) == NULL)
      continue;
    first_ltr = true;
    fnmap = gt_hashmap_new(GT_HASH_STRING, gt_free_func, NULL);
    fni = gt_feature_node_iterator_new((GtFeatureNode*) gn);
    while ((curnode = gt_feature_node_iterator_next(fni)) != NULL) {
      fnt = gt_feature_node_get_type(curnode);
      if ((strcmp(fnt, gt_ft_repeat_region) == 0) ||
          (strcmp(fnt, gt_ft_LTR_retrotransposon) == 0))
        continue;
      else if (strcmp(fnt, gt_ft_long_terminal_repeat) == 0) {
        if (first_ltr) {
          fnt = "lLTR";
          first_ltr = false;
        } else
          fnt = "rLTR";
      } else if (strcmp(fnt, gt_ft_protein_match) == 0)
        fnt = gt_feature_node_get_attribute(curnode, "name");
      if (!fnt)
        continue;
      gt_hashmap_add(fnmap, (void*) gt_cstr_dup(fnt), (void*) curnode);
    }
    gt_genome_node_add_user_data(gn, "fnmap", (void*) fnmap, delete_hash);
    gt_feature_node_iterator_delete(fni);
    fni = NULL;
  }
}

static void remove_fnmap_from_candidates(GtArray *candidates)
{
  GtGenomeNode *gn;
  unsigned long i;

  for (i = 0; i < gt_array_size(candidates); i++) {
    gn = *(GtGenomeNode**) gt_array_get(candidates, i);
    if (gt_feature_node_try_cast(gn) == NULL)
      continue;
    gt_genome_node_release_user_data(gn, "fnmap");
  }
}

static int classify_ltrs(GtArray *candidates, GtHashmap *features,
                         const char *famprefix, char **current_state,
                         unsigned long *progress, GtError *err)
{
  GtBittab *group,
           *new_group;
  GtArray *groups;
  GtGenomeNode *candidate;
  bool sorted;
  int had_err = 0;
  unsigned long i, j, num_of_cands;

  gt_error_check(err);
  gt_assert(candidates);

  add_fnmap_to_candidates(candidates);
  num_of_cands = gt_array_size(candidates);
  groups = gt_array_new(sizeof(GtBittab*));

  if (current_state != NULL) {
    gt_free(*current_state);
    *current_state = gt_cstr_dup("Assigning candidates to families");
  }

  for (i = 0; i < num_of_cands; i++) {
    sorted = false;
    candidate = *(GtGenomeNode**) gt_array_get(candidates, i);
    if (gt_feature_node_try_cast(candidate) == NULL)
      continue;
    for (j = 0; j < gt_array_size(groups); j++) {
      group = *(GtBittab**) gt_array_get(groups, j);
      if (!sorted && ltr_group_compatible(candidates, candidate, group,
                                          features, err)) {
        gt_bittab_set_bit(group, i);
        sorted = true;
        break;
      }
    }
    if (!sorted) {
      new_group = gt_bittab_new(num_of_cands);
      gt_bittab_set_bit(new_group, i);
      gt_array_add(groups, new_group);
    }
    if (progress != NULL)
      *progress = *progress + 1;
  }
  if (current_state != NULL) {
    gt_free(*current_state);
    *current_state = gt_cstr_dup("Checking for ambiguity");
  }
  had_err = check_ambiguous_candidates(candidates, groups, features,
                                       progress, err);

  if (!had_err)
    had_err = annotate_nodes(candidates, groups, famprefix, err);

  for (i = 0; i < gt_array_size(groups); i++) {
    gt_bittab_delete(*(GtBittab**) gt_array_get(groups, i));
  }
  gt_array_delete(groups);
  remove_fnmap_from_candidates(candidates);

  return had_err;
}

static int gt_ltr_classify_stream_next(GtNodeStream *ns,
                                       GtGenomeNode **gn,
                                       GtError *err)
{
  GtLTRClassifyStream *lcs;
  GtGenomeNode *ref_gn;
  int had_err = 0;

  gt_error_check(err);
  lcs = gt_ltr_classify_stream_cast(ns);
  if (lcs->first_next) {
    while (!(had_err = gt_node_stream_next(lcs->in_stream, gn, err)) && *gn) {
      gt_assert(*gn && !had_err);
      ref_gn = gt_genome_node_ref(*gn);
      gt_array_add(lcs->nodes, ref_gn);
    }
    if (!had_err)
      had_err = classify_ltrs(lcs->nodes, lcs->features, lcs->famprefix,
                              lcs->current_state, lcs->progress, err);
    if (!had_err) {
      *gn = *(GtGenomeNode**) gt_array_get(lcs->nodes, lcs->next_index);
      lcs->next_index++;
      lcs->first_next = false;
      return 0;
    }
  } else {
    if (lcs->next_index >= gt_array_size(lcs->nodes))
      *gn = NULL;
    else {
      *gn = *(GtGenomeNode**) gt_array_get(lcs->nodes, lcs->next_index);
      lcs->next_index++;
    }
    return 0;
  }
  return had_err;
}

static void gt_ltr_classify_stream_free(GtNodeStream *ns)
{
  unsigned long i;
  GtLTRClassifyStream *lcs = gt_ltr_classify_stream_cast(ns);
  for (i = 0; i < gt_array_size(lcs->nodes); i++)
    gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(lcs->nodes, i));
  gt_array_delete(lcs->nodes);
  gt_node_stream_delete(lcs->in_stream);
}

const GtNodeStreamClass* gt_ltr_classify_stream_class(void)
{
  static const GtNodeStreamClass *nsc;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof(GtLTRClassifyStream),
                                   gt_ltr_classify_stream_free,
                                   gt_ltr_classify_stream_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

GtNodeStream* gt_ltr_classify_stream_new(GtNodeStream *in_stream,
                                         GtHashmap *features,
                                         const char *famprefix,
                                         char **current_state,
                                         unsigned long *progress,
                                         GT_UNUSED GtError *err)
{
  GtNodeStream *ns;
  GtLTRClassifyStream *lcs;
  ns = gt_node_stream_create(gt_ltr_classify_stream_class(), false);
  lcs = gt_ltr_classify_stream_cast(ns);
  lcs->in_stream = gt_node_stream_ref(in_stream);
  lcs->nodes = gt_array_new(sizeof(GtGenomeNode*));
  lcs->features = features;
  lcs->first_next = true;
  lcs->next_index = 0;
  lcs->famprefix = famprefix;
  lcs->progress = progress;
  lcs->current_state = current_state;
  return ns;
}
genometools-1.5.1/src/ltr/ltr_classify_stream.h000066400000000000000000000020201211610345200216500ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Kastens 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_CLASSIFY_STREAM_H
#define LTR_CLASSIFY_STREAM_H

#include "ltr/ltr_classify_stream_api.h"

const GtNodeStreamClass* gt_ltr_classify_stream_class(void);

#endif
genometools-1.5.1/src/ltr/ltr_classify_stream_api.h000066400000000000000000000027041211610345200225120ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Kastens 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_CLASSIFY_STREAM_API_H
#define LTR_CLASSIFY_STREAM_API_H

#include "core/error_api.h"
#include "core/hashmap_api.h"
#include "extended/node_stream_api.h"

typedef struct GtLTRClassifyStream GtLTRClassifyStream;

GtNodeStream* gt_ltr_classify_stream_new(GtNodeStream *in_stream,
                                         GtHashmap *features,
                                         const char *famprefix,
                                         char **current_state,
                                         unsigned long *progress,
                                         GtError *err);

#endif
genometools-1.5.1/src/ltr/ltr_cluster_prepare_seq_visitor.c000066400000000000000000000224351211610345200243150ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Steinbiss 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/array.h"
#include "core/class_alloc_lock.h"
#include "core/cstr_api.h"
#include "core/encseq_api.h"
#include "core/hashmap.h"
#include "core/log.h"
#include "core/str_api.h"
#include "core/str_array.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "extended/feature_type.h"
#include "extended/node_visitor_api.h"
#include "ltr/ltr_cluster_prepare_seq_visitor.h"

struct GtLTRClusterPrepareSeqVisitor {
  const GtNodeVisitor parent_instance;
  GtEncseq *src_encseq;
  GtHashmap *feat_to_encseq,
            *encseq_builders;
  GtStrArray *feat_to_encseq_keys;
};

static int extract_feature_seq(GtEncseqBuilder *b, const char *header,
                               GtStr *seqid, GtEncseq *encseq, GtRange range,
                               GT_UNUSED const char *fnt, GtError *err)
{
  char *buffer;
  int had_err = 0;
  unsigned long seqnum,
                startpos;

  (void) sscanf(gt_str_get(seqid), "seq%lu", &seqnum);
  if (seqnum >= gt_encseq_num_of_sequences(encseq)) {
    gt_error_set(err, "annotation encountered for sequence %lu, but the "
                      "supplied encoded sequence only contains sequences "
                      "0-%lu", seqnum, gt_encseq_num_of_sequences(encseq)-1);
    had_err = -1;
  }

  if (!had_err) {
    buffer = gt_calloc((size_t) gt_range_length(&range) + 1, sizeof (char));
    startpos = gt_encseq_seqstartpos(encseq, seqnum);
    gt_encseq_extract_decoded(encseq, buffer, startpos + range.start,
                              startpos + range.end);
    gt_encseq_builder_add_cstr(b, buffer, gt_range_length(&range), header);
    gt_free(buffer);
  }

  return had_err;
}

static int gt_ltr_cluster_prepare_seq_visitor_feature_node(GtNodeVisitor *nv,
                                               GtFeatureNode *fn,
                                               GtError *err)
{
  GtLTRClusterPrepareSeqVisitor *lcv;
  GtFeatureNode *curnode;
  GtFeatureNodeIterator *fni;
  GtStr *seqid = NULL;
  const char *fnt;
  char buffer[BUFSIZ];
  int had_err = 0;
  bool first_ltr = true;
  gt_error_check(err);

  lcv = gt_ltr_cluster_prepare_seq_visitor_cast(nv);
  gt_assert(lcv);
  gt_error_check(err);
  fni = gt_feature_node_iterator_new(fn);

  while (!had_err && (curnode = gt_feature_node_iterator_next(fni))) {
    GtFile *file = NULL;
    fnt = gt_feature_node_get_type(curnode);
    if (strcmp(fnt, gt_ft_repeat_region) == 0) {
      const char *rid;
      unsigned long id;
      seqid = gt_genome_node_get_seqid((GtGenomeNode*) curnode);
      rid = gt_feature_node_get_attribute(curnode, "ID");
      (void) sscanf(rid, "repeat_region%lu", &id);
      (void) snprintf(buffer, BUFSIZ, "%s_%lu", gt_str_get(seqid), id);
    } else if (strcmp(fnt, gt_ft_protein_match) == 0) {
      GtRange range;
      const char *attr;
      GtEncseqBuilder *eb;
      char header[BUFSIZ];
      attr = gt_feature_node_get_attribute(curnode, "name");
      if (!attr)
        continue;
      range = gt_genome_node_get_range((GtGenomeNode*) curnode);
      (void) snprintf(header, BUFSIZ, "%s_%lu_%lu", buffer, range.start,
                      range.end);
      if (!gt_hashmap_get(lcv->encseq_builders, attr)) {
        eb = gt_encseq_builder_new(gt_encseq_alphabet(lcv->src_encseq));
        gt_encseq_builder_create_ssp_tab(eb);
        gt_encseq_builder_create_sds_tab(eb);
        gt_encseq_builder_create_des_tab(eb);
        gt_hashmap_add(lcv->encseq_builders, gt_cstr_dup(attr),
                       eb);
        gt_log_log("builder %p added for feature %s", eb, attr);
        gt_str_array_add_cstr(lcv->feat_to_encseq_keys, attr);
      } else {
        eb = (GtEncseqBuilder*) gt_hashmap_get(lcv->encseq_builders, attr);
      }
      had_err = extract_feature_seq(eb, header, seqid, lcv->src_encseq, range,
                                    fnt, err);
      gt_file_delete(file);
    } else if (strcmp(fnt, gt_ft_LTR_retrotransposon) == 0)
      continue;
    else {
      char *tmp;
      GtRange range;
      GtEncseqBuilder *eb;
      char header[BUFSIZ];  /* XXX: use GtStr for safety */
      if (strcmp(fnt, gt_ft_long_terminal_repeat) == 0) {
        if (first_ltr) {
          tmp = gt_cstr_dup("lLTR");
          first_ltr = false;
        } else
          tmp = gt_cstr_dup("rLTR");
      } else
        tmp = gt_cstr_dup(fnt);
      range = gt_genome_node_get_range((GtGenomeNode*) curnode);
      if ((range.end - range.start + 1) < 10UL) {
        gt_free(tmp);
        continue;
      }
      (void) snprintf(header, BUFSIZ, "%s_%lu_%lu", buffer, range.start,
                      range.end);
      if (!gt_hashmap_get(lcv->encseq_builders, tmp)) {
        eb = gt_encseq_builder_new(gt_encseq_alphabet(lcv->src_encseq));
        gt_encseq_builder_create_ssp_tab(eb);
        gt_encseq_builder_create_sds_tab(eb);
        gt_encseq_builder_create_des_tab(eb);
        gt_hashmap_add(lcv->encseq_builders, gt_cstr_dup(tmp),
                       eb);
        gt_str_array_add_cstr(lcv->feat_to_encseq_keys, tmp);
      } else {
        eb = (GtEncseqBuilder*) gt_hashmap_get(lcv->encseq_builders, tmp);
      }
      had_err = extract_feature_seq(eb, header, seqid, lcv->src_encseq, range,
                                    fnt, err);
      gt_free(tmp);
      gt_file_delete(file);
    }
  }
  gt_feature_node_iterator_delete(fni);

  return had_err;
}

void gt_ltr_cluster_prepare_seq_visitor_free(GtNodeVisitor *v)
{
  GtLTRClusterPrepareSeqVisitor *lcv;
  lcv = gt_ltr_cluster_prepare_seq_visitor_cast(v);
  gt_encseq_delete(lcv->src_encseq);
  gt_str_array_delete(lcv->feat_to_encseq_keys);
  gt_hashmap_delete(lcv->feat_to_encseq);
  gt_hashmap_delete(lcv->encseq_builders);
}

const GtNodeVisitorClass* gt_ltr_cluster_prepare_seq_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc;
  gt_class_alloc_lock_enter();
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof(GtLTRClusterPrepareSeqVisitor),
                                gt_ltr_cluster_prepare_seq_visitor_free,
                                NULL,
                                gt_ltr_cluster_prepare_seq_visitor_feature_node,
                                NULL,
                                NULL,
                                NULL);
  }
  gt_class_alloc_lock_leave();
  return nvc;
}

GtNodeVisitor* gt_ltr_cluster_prepare_seq_visitor_new(GtEncseq *encseq,
                                                      GT_UNUSED GtError *err)
{
  GtNodeVisitor *nv;
  GtLTRClusterPrepareSeqVisitor *lcv;
  nv = gt_node_visitor_create(gt_ltr_cluster_prepare_seq_visitor_class());
  lcv = gt_ltr_cluster_prepare_seq_visitor_cast(nv);
  gt_assert(lcv);
  lcv->src_encseq = gt_encseq_ref(encseq);
  lcv->feat_to_encseq = NULL;
  lcv->encseq_builders = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
                                        (GtFree) gt_encseq_builder_delete);
  lcv->feat_to_encseq_keys = gt_str_array_new();
  return nv;
}

int gt_ltr_cluster_prepare_seq_finish_encseqs(void *key, void *value,
                                              void *data, GtError *err)
{
  GtLTRClusterPrepareSeqVisitor *v = (GtLTRClusterPrepareSeqVisitor*) data;
  GtEncseqBuilder *eb = (GtEncseqBuilder*) value;
  GtEncseq *encseq;
  int had_err = 0;
  const char *feature = (const char*) key;
  gt_assert(key && value);
  gt_error_check(err);

  encseq = gt_encseq_builder_build(eb, err);
  if (!encseq)
    had_err = -1;
  if (!had_err) {
    if (!v->feat_to_encseq) {
      v->feat_to_encseq = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
                                         (GtFree) gt_encseq_delete);
    }
    gt_assert(!gt_hashmap_get(v->feat_to_encseq, feature));
    gt_hashmap_add(v->feat_to_encseq, gt_cstr_dup(feature), encseq);
    gt_log_log("added encseq %p to hash for feature %s", encseq, feature);
  }
  return had_err;
}

GtHashmap* gt_ltr_cluster_prepare_seq_visitor_get_encseqs(
                                              GtLTRClusterPrepareSeqVisitor *v)
{
  gt_assert(v && v->encseq_builders);
  gt_log_log("finishing encseqs");
  if (!v->feat_to_encseq) {
    gt_log_log("starting...");
    (void) gt_hashmap_foreach(v->encseq_builders,
                              gt_ltr_cluster_prepare_seq_finish_encseqs,
                              v,
                              NULL);
  }
  return gt_hashmap_ref(v->feat_to_encseq);
}

GtStrArray* gt_ltr_cluster_prepare_seq_visitor_get_features(
                                              GtLTRClusterPrepareSeqVisitor *v)
{
  gt_assert(v && v->feat_to_encseq_keys);
  return gt_str_array_ref(v->feat_to_encseq_keys);
}
genometools-1.5.1/src/ltr/ltr_cluster_prepare_seq_visitor.h000066400000000000000000000036611211610345200243220ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Steinbiss 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_CLUSTER_PREPARE_SEQ_VISITOR_H
#define LTR_CLUSTER_PREPARE_SEQ_VISITOR_H

/* implements the ''node visitor'' interface */
typedef struct GtLTRClusterPrepareSeqVisitor GtLTRClusterPrepareSeqVisitor;

#include "core/array.h"
#include "core/encseq.h"
#include "core/str_array.h"
#include "extended/node_visitor.h"

const GtNodeVisitorClass* gt_ltr_cluster_prepare_seq_visitor_class(void);

GtNodeVisitor* gt_ltr_cluster_prepare_seq_visitor_new(GtEncseq *encseq,
                                                      GtError *err);
GtHashmap*      gt_ltr_cluster_prepare_seq_visitor_get_encseqs(
                                              GtLTRClusterPrepareSeqVisitor *v);
GtStrArray*     gt_ltr_cluster_prepare_seq_visitor_get_features(
                                              GtLTRClusterPrepareSeqVisitor *v);

#define gt_ltr_cluster_prepare_seq_visitor_cast(NV)\
        gt_node_visitor_cast(gt_ltr_cluster_prepare_seq_visitor_class(), NV)

#define gt_ltr_cluster_prepare_seq_visitor_try_cast(NV)\
        gt_node_visitor_try_cast(gt_ltr_cluster_prepare_seq_visitor_class(), NV)

#endif
genometools-1.5.1/src/ltr/ltr_cluster_stream.c000066400000000000000000000501411211610345200215160ustar00rootroot00000000000000/*
  Copyright (c) 2011      Sascha Kastens 
  Copyright (c)      2012 Sascha Steinbiss 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/array.h"
#include "core/class_alloc_lock.h"
#include "core/cstr_api.h"
#include "core/encseq.h"
#include "core/hashmap.h"
#include "core/log.h"
#include "core/ma.h"
#include "core/str_array.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "extended/clustered_set.h"
#include "extended/clustered_set_uf.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "extended/feature_type.h"
#include "extended/node_stream_api.h"
#include "extended/match.h"
#include "extended/match_iterator_api.h"
#include "extended/match_iterator_last.h"
#include "extended/match_iterator_open.h"
#include "ltr/ltr_cluster_stream.h"
#include "ltr/ltr_cluster_prepare_seq_visitor.h"
#include "match/sfx-run.h"

struct GtLTRClusterStream {
  const GtNodeStream parent_instance;
  GtNodeStream *in_stream;
  GtLTRClusterPrepareSeqVisitor *lcv;
  GtArray *nodes;
  GtHashmap *feat_to_encseq;
  GtStrArray *feat_to_encseq_keys;
  bool first_next;
  unsigned long psmall,
                plarge,
                next_index;
  int match_score, mismatch_cost, gap_open_cost,
      gap_ext_cost, xdrop, ydrop, zdrop, mscoregapped,
      mscoregapless, k;
  char **current_state;
};

#define gt_ltr_cluster_stream_cast(CS)\
        gt_node_stream_cast(gt_ltr_cluster_stream_class(), CS);

typedef struct GtMatchReference {
  unsigned long startpos, matchnum;
} GtMatchReference;

typedef struct GtMatchEdge {
unsigned long matchnum0, matchnum1;
unsigned long gap_size;
unsigned long edist;
unsigned long minlength;
} GtMatchEdge;

typedef struct GtMatchEdgeTable {
  GtArray *edges;
  unsigned long num_of_edges;
} GtMatchEdgeTable;

#define STORECLUSTEREDGEG(I, J, VALUE)\
matchedge.matchnum0 = I;\
matchedge.matchnum1 = J;\
matchedge.gap_size = VALUE;\
gt_array_add(matchedgetab.edges, matchedge);\
matchedgetab.num_of_edges++

#define STORECLUSTEREDGEED(I, J, ML, ED)\
matchedge.matchnum0 = I;\
matchedge.matchnum1 = J;\
matchedge.minlength = ML;\
matchedge.edist = ED;\
gt_array_add(matchedgetab.edges, matchedge);\
matchedgetab.num_of_edges++

static int cmpmatchreferences(const void *dataA, const void *dataB)
{
  GtMatchReference *mrefA = (GtMatchReference*) dataA;
  GtMatchReference *mrefB = (GtMatchReference*) dataB;
  if (mrefA->startpos < mrefB->startpos)
    return -1;
  if (mrefA->startpos > mrefB->startpos)
    return 1;
  return 0;
}

static GtMatchReference* gt_mirror_and_sort_matches(GtArray *matches)
{
  GtMatchReference *mref;
  GtMatch *match;
  GtRange rng_seq1, rng_seq2;
  unsigned long i, j;
  mref = gt_calloc((size_t) (gt_array_size(matches) * 2),
                   sizeof (GtMatchReference));
  for (i = 0, j = 0; i < gt_array_size(matches); i++, j+=2) {
    match = *(GtMatch**) gt_array_get(matches, i);
    gt_match_get_range_seq1(match, &rng_seq1);
    gt_match_get_range_seq2(match, &rng_seq2);
    mref[j].startpos = rng_seq1.start;
    mref[j].matchnum = i;
    mref[j+1].startpos = rng_seq2.start;
    mref[j+1].matchnum = i;
  }
  qsort (mref,
         (size_t) (2 * gt_array_size(matches)),
         sizeof (GtMatchReference),
         cmpmatchreferences);
  return mref;
}

static int gt_cluster_matches(GtClusteredSet *cs,
                              GtMatchEdgeTable *matchedgetab,
                              GtError *err)
{
  unsigned long i;
  for (i = 0; i < matchedgetab->num_of_edges; i++) {
     if (gt_clustered_set_merge_clusters(cs,
              ((GtMatchEdge*)(gt_array_get(matchedgetab->edges, i)))->matchnum0,
              ((GtMatchEdge*)(gt_array_get(matchedgetab->edges, i)))->matchnum1,
              err) != 0) {
       return -1;
    }
  }
  return 0;
}

static int cluster_sequences(GtArray *matches,
                             GtClusteredSet *cs,
                             GtHashmap *seqdesc2seqnum,
                             unsigned int psmall,
                             unsigned int plarge,
                             GtEncseq *encseq,
                             GtError *err)
{
  GtMatch *match;
  GtMatchEdgeTable matchedgetab;
  GtMatchEdge matchedge;
  GtRange rng_seq1,
          rng_seq2;
  int had_err = 0;
  unsigned long i,
                lsmall,
                llarge,
                matchlen1,
                matchlen2,
                num_of_seq,
                seqnum1 = 0,
                seqnum2 = 0;
  const char *seqid;

  num_of_seq = gt_encseq_num_of_sequences(encseq);
  gt_assert(matches && cs && seqdesc2seqnum && encseq);

  if (gt_clustered_set_num_of_elements(cs, err) != num_of_seq) {
    had_err = -1;
    gt_error_set(err,
                 "number of sequences (%lu) unequals number of elements in"
                 " clustered set (%lu)",
                 num_of_seq, gt_clustered_set_num_of_elements(cs, err));
  }
  if (!had_err) {
    matchedgetab.edges = gt_array_new(sizeof (GtMatchEdge));
    matchedgetab.num_of_edges = 0;

    for (i = 0; i < gt_array_size(matches); i++) {
      match = *(GtMatch**) gt_array_get(matches, i);
      gt_match_get_range_seq1(match, &rng_seq1);
      gt_match_get_range_seq2(match, &rng_seq2);

      matchlen1 =  gt_range_length(&rng_seq1);
      matchlen2 =  gt_range_length(&rng_seq2);

      seqid = gt_match_get_seqid1(match);
      if (gt_hashmap_get(seqdesc2seqnum, (void*) seqid) != NULL)
        seqnum1 = ((unsigned long) gt_hashmap_get(seqdesc2seqnum, seqid)) - 1;
      else {
        had_err = -1;
        gt_error_set(err, "key %s not found", seqid);
      }

      seqid = gt_match_get_seqid2(match);
      if (!had_err && gt_hashmap_get(seqdesc2seqnum, (void*) seqid) != NULL)
        seqnum2 = ((unsigned long) gt_hashmap_get(seqdesc2seqnum, seqid)) - 1;
      else {
        had_err = -1;
        gt_error_set(err, "key %s not found", seqid);
      }

      if (!had_err) {
        if (gt_encseq_seqlength(encseq, seqnum1) >
            gt_encseq_seqlength(encseq, seqnum2)) {
          llarge = gt_encseq_seqlength(encseq, seqnum1);
          lsmall = gt_encseq_seqlength(encseq, seqnum2);
        } else {
          lsmall = gt_encseq_seqlength(encseq, seqnum1);
          llarge = gt_encseq_seqlength(encseq, seqnum2);
        }
        if (((llarge * plarge)/100 <= matchlen1) &&
            ((lsmall * psmall)/100 <= matchlen1) &&
            ((llarge * plarge)/100 <= matchlen2) &&
            ((lsmall * psmall)/100 <= matchlen2)) {
          if (seqnum1 != seqnum2) {
            matchedge.matchnum0 = seqnum1;
            matchedge.matchnum1 = seqnum2;
            gt_array_add(matchedgetab.edges, matchedge);
            matchedgetab.num_of_edges++;
          }
        }
      }
    }
  }
  if (!had_err)
    if (gt_cluster_matches(cs, &matchedgetab, err) != 0)
      had_err = -1;
  if (!had_err)
    gt_array_delete(matchedgetab.edges);
  return had_err;
}

GT_UNUSED static int gt_cluster_matches_gap(GtArray *matches,
                                            GtClusteredSet *cs,
                                            unsigned long max_gap_size,
                                            GtError *err)
{
  GtMatchReference *mref;
  GtMatchEdgeTable matchedgetab;
  GtMatchEdge matchedge;
  GtMatch *match;
  GtRange range;
  unsigned long i,
                j,
                gap_size = 0,
                length = 0;
  unsigned long num_of_matches;
  int had_err;

  num_of_matches = gt_array_size(matches);
  if (gt_clustered_set_num_of_elements(cs, err) != num_of_matches) {
    had_err = -1;
    gt_error_set(err,
                 "number of matches (%lu) unequals number of elements in"
                 "clustered set (%lu)",
                 num_of_matches, gt_clustered_set_num_of_elements(cs, err));
  }
  if (!had_err) {
    matchedgetab.edges = gt_array_new(sizeof (GtMatchEdge));
    matchedgetab.num_of_edges = 0;

    mref = gt_mirror_and_sort_matches(matches);

    for (i = 0; i < (2 * (num_of_matches) - 1); i++) {
      for (j = i + 1; j < (2 * num_of_matches); j++) {
        match = *(GtMatch**) gt_array_get(matches, mref[i].matchnum);
        gt_match_get_range_seq1(match, &range);
        length = gt_range_length(&range);
        gap_size = mref[j].startpos - mref[i].startpos + length;

        if (gap_size > max_gap_size)
          break;
        if (mref[i].matchnum != mref[j].matchnum) {
          STORECLUSTEREDGEG(mref[i].matchnum, mref[j].matchnum, gap_size);
        }
      }
    }
    if (gt_cluster_matches(cs, &matchedgetab, err) != 0)
      had_err = -1;
    gt_array_delete(matchedgetab.edges);
    gt_free(mref);
  }
  return had_err;
}

static void free_hash(void *elem)
{
  gt_free(elem);
}

static int cluster_annotate_nodes(GtClusteredSet *cs, GtEncseq *encseq,
                                  const char *feature, GtArray *nodes,
                                  GtError *err)
{
  GtFeatureNodeIterator *fni;
  GtFeatureNode *curnode = NULL, *tmp;
  GtClusteredSetIterator *csi = NULL;
  GtGenomeNode *gn;
  GtHashmap *desc2node;
  GtStr *seqid = NULL;
  int had_err = 0;
  unsigned long num_of_clusters, i, elm;
  const char *fnt = NULL;
  char buffer[BUFSIZ], *real_feature;
  gt_error_check(err);

  if ((strcmp(feature, "lLTR") == 0) || (strcmp(feature, "rLTR") == 0))
    real_feature = gt_cstr_dup(gt_ft_long_terminal_repeat);
  else
    real_feature = gt_cstr_dup(feature);

  desc2node = gt_hashmap_new(GT_HASH_STRING, free_hash, NULL);
  for (i = 0; i < gt_array_size(nodes); i++) {
    gn = *(GtGenomeNode**) gt_array_get(nodes, i);
    if (gt_feature_node_try_cast(gn) == NULL)
      continue;
    fni = gt_feature_node_iterator_new((GtFeatureNode*) gn);
    while ((curnode = gt_feature_node_iterator_next(fni)) != NULL) {
      char header[BUFSIZ];
      fnt = gt_feature_node_get_type(curnode);
      if (strcmp(fnt, gt_ft_repeat_region) == 0) {
        const char *rid;
        unsigned long id;
        seqid = gt_genome_node_get_seqid((GtGenomeNode*) curnode);
        rid = gt_feature_node_get_attribute(curnode, "ID");
        (void) sscanf(rid, "repeat_region%lu", &id);
        (void) snprintf(buffer, BUFSIZ, "%s_%lu", gt_str_get(seqid), id);
      } else if (strcmp(fnt, gt_ft_protein_match) == 0) {
        GtRange range;
        const char *attr;
        attr = gt_feature_node_get_attribute(curnode, "name");
        if (!attr)
          continue;
        if (strcmp(feature, attr) != 0)
          continue;
        range = gt_genome_node_get_range((GtGenomeNode*) curnode);
        if ((range.end - range.start + 1) < 10UL)
          continue;
        (void) snprintf(header, BUFSIZ, "%s_%lu_%lu", buffer, range.start,
                        range.end);
        gt_hashmap_add(desc2node, (void*) gt_cstr_dup(header), (void*) curnode);
      } else if (strcmp(fnt, real_feature) == 0) {
        GtRange range;
        range = gt_genome_node_get_range((GtGenomeNode*) curnode);
        if ((range.end - range.start + 1) < 10UL)
          continue;
        (void) snprintf(header, BUFSIZ, "%s_%lu_%lu", buffer, range.start,
                        range.end);
        gt_hashmap_add(desc2node, (void*) gt_cstr_dup(header), (void*) curnode);
      }
    }
    gt_feature_node_iterator_delete(fni);
  }
  gt_free(real_feature);

  num_of_clusters = gt_clustered_set_num_of_clusters(cs, err);
  for (i = 0; i < num_of_clusters; i++) {
    csi = gt_clustered_set_get_iterator(cs, i ,err);
    if (csi != NULL) {
      while (!had_err && (gt_clustered_set_iterator_next(csi, &elm, err)
             != GT_CLUSTERED_SET_ITERATOR_STATUS_END)) {
        char clid[BUFSIZ];
        const char *encseqdesc;
        char *encseqid;
        unsigned long desclen;
        encseqdesc = gt_encseq_description(encseq, &desclen, elm);
        encseqid = gt_calloc((size_t) (desclen + 1), sizeof (char));
        (void) strncpy(encseqid, encseqdesc, (size_t) desclen);
        encseqid[desclen] = '\0';
        tmp = (GtFeatureNode*) gt_hashmap_get(desc2node, (void*) encseqid);
        (void) snprintf(clid, BUFSIZ, "%lu", i);
        gt_feature_node_set_attribute(tmp, "clid", clid);
        gt_free(encseqid);
      }
    }
    gt_clustered_set_iterator_delete(csi, err);
    csi = NULL;
  }
  gt_hashmap_delete(desc2node);
  return had_err;
}

static int process_feature(GtLTRClusterStream *lcs,
                           const char *feature,
                           GtError *err)
{
  GtArray *matches;
  GtMatchIterator *mi = NULL;
  GtMatch *match = NULL;
  GtMatchIteratorStatus status;
  GtEncseq *encseq;
  unsigned long i;
  int had_err = 0;

  if (lcs->current_state != NULL) {
    char tmp[BUFSIZ];
    gt_free(*lcs->current_state);
    (void) snprintf(tmp, BUFSIZ, "Clustering feature: %s", feature);
    *lcs->current_state = gt_cstr_dup(tmp);
  }
  matches = gt_array_new(sizeof(GtMatch*));
  encseq = (GtEncseq*) gt_hashmap_get(lcs->feat_to_encseq, feature);
  gt_log_log("found encseq %p for feature %s", encseq, feature);
  if (!had_err) {
    mi = gt_match_iterator_last_new(encseq, encseq, lcs->match_score,
                                        lcs->mismatch_cost,
                                        lcs->gap_open_cost,
                                        lcs->gap_ext_cost,
                                        lcs->xdrop,
                                        lcs->ydrop,
                                        lcs->zdrop,
                                        lcs->k,
                                        lcs->mscoregapped,
                                        lcs->mscoregapless, err);
    if (mi != NULL) {
      while ((status = gt_match_iterator_next(mi, &match, err))
             != GT_MATCHER_STATUS_END) {
        if (status == GT_MATCHER_STATUS_OK) {
          gt_array_add(matches, match);
        } else {
          gt_assert(status == GT_MATCHER_STATUS_ERROR);
          had_err = -1;
          break;
        }
      }
    } else
      had_err = -1;
  }
  if (!had_err) {
    GtClusteredSet *cs;
    GtHashmap *seqdesc2seqnum;
    GtMatch *tmp_match;
    const char *description;
    char *output;
    unsigned long desclen,
                  num_of_seq;

    seqdesc2seqnum = gt_hashmap_new(GT_HASH_STRING, free_hash, NULL);
    num_of_seq = gt_encseq_num_of_sequences(encseq);
    for (i = 0; i < num_of_seq; i++) {
      description = gt_encseq_description(encseq, &desclen, i);
      output = gt_calloc((size_t) (desclen + 1), sizeof (char));
      strncpy(output, description, (size_t) desclen);
      output[desclen] = '\0';
      gt_hashmap_add(seqdesc2seqnum, (void*) gt_cstr_dup(output),
                     (void*) (i + 1));
      gt_free(output);
    }
    cs = gt_clustered_set_union_find_new(num_of_seq, err);
    if (cs != NULL) {
      if (cluster_sequences(matches, cs, seqdesc2seqnum, (unsigned) lcs->psmall,
                            (unsigned) lcs->plarge, encseq, err) != 0) {
        had_err = -1;
      }
      if (!had_err) {
        (void) cluster_annotate_nodes(cs, encseq, feature, lcs->nodes, err);
      }
    } else
      had_err = -1;

    for (i = 0; i < gt_array_size(matches); i++) {
      tmp_match = *(GtMatch**) gt_array_get(matches, i);
      gt_match_delete(tmp_match);
    }
    gt_array_delete(matches);
    matches = NULL;
    gt_hashmap_delete(seqdesc2seqnum);
    gt_clustered_set_delete(cs, err);
  }
  gt_match_iterator_delete(mi);

  return had_err;
}

static int gt_ltr_cluster_stream_next(GtNodeStream *ns,
                                      GtGenomeNode **gn,
                                      GtError *err)
{
  GtLTRClusterStream *lcs;
  GtGenomeNode *ref_gn;
  int had_err = 0;
  unsigned long i = 0;

  gt_error_check(err);
  lcs = gt_ltr_cluster_stream_cast(ns);
  if (lcs->first_next) {
    while (!(had_err = gt_node_stream_next(lcs->in_stream, gn, err)) && *gn) {
      gt_assert(*gn && !had_err);
      ref_gn = gt_genome_node_ref(*gn);
      gt_array_add(lcs->nodes, ref_gn);
      had_err = gt_genome_node_accept(*gn, (GtNodeVisitor*) lcs->lcv, err);
      if (had_err) {
        gt_genome_node_delete(*gn);
        *gn = NULL;
        break;
      }
    }
    lcs->feat_to_encseq =
                       gt_ltr_cluster_prepare_seq_visitor_get_encseqs(lcs->lcv);
    lcs->feat_to_encseq_keys =
                      gt_ltr_cluster_prepare_seq_visitor_get_features(lcs->lcv);
    if (!had_err) {
      for (i = 0; i < gt_str_array_size(lcs->feat_to_encseq_keys); i++) {
        had_err = process_feature(lcs,
                                  gt_str_array_get(lcs->feat_to_encseq_keys, i),
                                  err);
        if (had_err)
          break;
      }
    }
    if (!had_err) {
      *gn = *(GtGenomeNode**) gt_array_get(lcs->nodes, lcs->next_index);
      lcs->next_index++;
      lcs->first_next = false;
      return 0;
    }
  } else {
    if (lcs->next_index >= gt_array_size(lcs->nodes))
      *gn = NULL;
    else {
      *gn = *(GtGenomeNode**) gt_array_get(lcs->nodes, lcs->next_index);
      lcs->next_index++;
    }
    return 0;
  }

  return had_err;
}

static void gt_ltr_cluster_stream_free(GtNodeStream *ns)
{
  unsigned long i;
  GtLTRClusterStream *lcs = gt_ltr_cluster_stream_cast(ns);
  gt_node_visitor_delete((GtNodeVisitor*) lcs->lcv);
  gt_hashmap_delete(lcs->feat_to_encseq);
  gt_str_array_delete(lcs->feat_to_encseq_keys);
  for (i = 0; i < gt_array_size(lcs->nodes); i++)
    gt_genome_node_delete(*(GtGenomeNode**) gt_array_get(lcs->nodes, i));
  gt_array_delete(lcs->nodes);
  gt_node_stream_delete(lcs->in_stream);
}

const GtNodeStreamClass* gt_ltr_cluster_stream_class(void)
{
  static const GtNodeStreamClass *nsc;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof(GtLTRClusterStream),
                                   gt_ltr_cluster_stream_free,
                                   gt_ltr_cluster_stream_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

GtNodeStream* gt_ltr_cluster_stream_new(GtNodeStream *in_stream,
                                        GtEncseq *encseq,
                                        int match_score,
                                        int mismatch_cost,
                                        int gap_open_cost,
                                        int gap_ext_cost,
                                        int xdrop,
                                        int ydrop,
                                        int zdrop,
                                        int k,
                                        int mscoregapped,
                                        int mscoregapless,
                                        unsigned long plarge,
                                        unsigned long psmall,
                                        char **current_state,
                                        GtError *err)
{
  GtNodeStream *ns;
  GtLTRClusterStream *lcs;
  ns = gt_node_stream_create(gt_ltr_cluster_stream_class(), false);
  lcs = gt_ltr_cluster_stream_cast(ns);
  lcs->in_stream = gt_node_stream_ref(in_stream);
  lcs->feat_to_encseq = NULL;
  lcs->feat_to_encseq_keys = NULL;
  lcs->nodes = gt_array_new(sizeof(GtGenomeNode*));
  lcs->lcv = gt_ltr_cluster_prepare_seq_visitor_cast(
                           gt_ltr_cluster_prepare_seq_visitor_new(encseq, err));
  lcs->first_next = true;
  lcs->next_index = 0;
  lcs->match_score = match_score;
  lcs->mismatch_cost = mismatch_cost;
  lcs->gap_open_cost = gap_open_cost;
  lcs->gap_ext_cost = gap_ext_cost;
  lcs->xdrop = xdrop;
  lcs->ydrop = ydrop;
  lcs->zdrop = zdrop;
  lcs->mscoregapped = mscoregapped;
  lcs->mscoregapless = mscoregapless;
  lcs->k = k;
  lcs->plarge = plarge;
  lcs->psmall = psmall;
  lcs->current_state = current_state;
  return ns;
}
genometools-1.5.1/src/ltr/ltr_cluster_stream.h000066400000000000000000000020141211610345200215170ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Kastens 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_CLUSTER_STREAM_H
#define LTR_CLUSTER_STREAM_H

#include "ltr/ltr_cluster_stream_api.h"

const GtNodeStreamClass* gt_ltr_cluster_stream_class(void);

#endif
genometools-1.5.1/src/ltr/ltr_cluster_stream_api.h000066400000000000000000000041361211610345200223570ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Kastens 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_CLUSTER_STREAM_API_H
#define LTR_CLUSTER_STREAM_API_H

#include "core/encseq_api.h"
#include "core/error_api.h"
#include "extended/node_stream_api.h"

typedef struct GtLTRClusterStream GtLTRClusterStream;

/* Implements the  interface.  annotates
   all LTR features with cluster IDs, based on matches. */
GtNodeStream* gt_ltr_cluster_stream_new(GtNodeStream *in_stream,
                                        GtEncseq *encseq,
                                        int match_score,
                                        int mismatch_cost,
                                        int gap_open_cost,
                                        int gap_ext_cost,
                                        int xdrop,
                                        int ydrop,
                                        int zdrop,
                                        int k,
                                        int mscoregapped,
                                        int mscoregapless,
                                        unsigned long plarge,
                                        unsigned long psmall,
                                        char **current_state,
                                        GtError *err);

#endif
genometools-1.5.1/src/ltr/ltr_four_char_motif.c000066400000000000000000000062611211610345200216340ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2007 David Ellinghaus 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "ltr/ltr_four_char_motif.h"

/* test the motif and encode the characters by using alpha */
int gt_ltr_four_char_motif_encode (GtLTRFourCharMotif *motif,
                                   const GtEncseq *encseq,
                                   GtError *err)
{
  const GtUchar *symbolmap;
  GtUchar c_tab[UCHAR_MAX+1];
  unsigned int i;

  symbolmap = gt_alphabet_symbolmap(gt_encseq_alphabet(encseq));
  if ( symbolmap[(unsigned int)motif->firstleft] == (GtUchar) UNDEFCHAR)
  {
    gt_error_set(err,"Illegal nucleotide character %c "
                      "as argument to option -motif", motif->firstleft);
    return -1;
  }
  if ( symbolmap[(unsigned int)motif->secondleft] == (GtUchar) UNDEFCHAR )
  {
    gt_error_set(err,"Illegal nucleotide character %c "
                      "as argument to option -motif", motif->secondleft);
    return -1;
  }
  if ( symbolmap[(unsigned int)motif->firstright] == (GtUchar) UNDEFCHAR )
  {
    gt_error_set(err,"Illegal nucleotide character %c "
                      "as argument to option -motif", motif->firstright);
    return -1;
  }
  if ( symbolmap[(unsigned int)motif->secondright] == (GtUchar) UNDEFCHAR )
  {
    gt_error_set(err,"Illegal nucleotide character %c "
                      "as argument to option -motif", motif->secondright);
    return -1;
  }

  for (i=0; i<=(unsigned int) UCHAR_MAX; i++)
  {
    c_tab[i] = (GtUchar) UNDEFCHAR;
  }
  /* define complementary symbols */
  c_tab[symbolmap['a']] = symbolmap['t'];
  c_tab[symbolmap['c']] = symbolmap['g'];
  c_tab[symbolmap['g']] = symbolmap['c'];
  c_tab[symbolmap['t']] = symbolmap['a'];

  /* if motif is not palindromic */
  if ( (c_tab[symbolmap[(unsigned int)motif->firstleft]] !=
       c_tab[c_tab[symbolmap[(unsigned int)motif->secondright]]])
           ||
      (c_tab[symbolmap[(unsigned int)motif->secondleft]] !=
       c_tab[c_tab[symbolmap[(unsigned int)motif->firstright]]]) )
  {
    gt_error_set(err, "Illegal motif, motif not palindromic");
    return -1;
  }

  /* encode the symbols */
  motif->firstleft = symbolmap[(unsigned int)motif->firstleft];
  motif->secondleft = symbolmap[(unsigned int)motif->secondleft];
  motif->firstright = symbolmap[(unsigned int)motif->firstright];
  motif->secondright = symbolmap[(unsigned int)motif->secondright];

  return 0;
}
genometools-1.5.1/src/ltr/ltr_four_char_motif.h000066400000000000000000000031531211610345200216360ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2007 David Ellinghaus 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_FOUR_CHAR_MOTIF_H
#define LTR_FOUR_CHAR_MOTIF_H

#include "core/chardef.h"
#include "core/encseq_api.h"

typedef struct
{
  GtStr *str_motif;
  GtUchar firstleft,     /* first character of left motif instance */
          secondleft,    /* second character of left motif instance */
          firstright,    /* first character of right motif instance */
          secondright;   /* second character of right motif instance */
  unsigned int allowedmismatches;   /* number of allowed mismatches  */
} GtLTRFourCharMotif;

int gt_ltr_four_char_motif_encode (GtLTRFourCharMotif *motif,
                                   const GtEncseq *encseq,
                                   GtError *err);

#endif
genometools-1.5.1/src/ltr/ltr_orf_annotator_stream.c000066400000000000000000000066311211610345200227150ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Steinbiss 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/class_alloc_lock.h"
#include "core/hashmap_api.h"
#include "extended/feature_type.h"
#include "extended/orf_finder_stream.h"
#include "ltr/ltr_orf_annotator_stream_api.h"

struct GtLTRORFAnnotatorStream {
  const GtNodeStream parent_instance;
  GtNodeStream *orf_stream;
  unsigned long *progress_loc;
  GtHashmap *types;
};

const GtNodeStreamClass* gt_ltr_orf_annotator_stream_class(void);

#define ltr_orf_annotator_stream_cast(NS)\
        gt_node_stream_cast(gt_ltr_orf_annotator_stream_class(), NS)

static int ltr_orf_annotator_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
                                         GtError *err)
{
  GtLTRORFAnnotatorStream *bs;
  gt_error_check(err);
  bs = ltr_orf_annotator_stream_cast(ns);
  if (bs->progress_loc != NULL)
    (*bs->progress_loc)++;
  return gt_node_stream_next(bs->orf_stream, gn, err);
}

static void ltr_orf_annotator_stream_free(GtNodeStream *ns)
{
  GtLTRORFAnnotatorStream *bs = ltr_orf_annotator_stream_cast(ns);
  gt_hashmap_delete(bs->types);
  gt_node_stream_delete(bs->orf_stream);
}

const GtNodeStreamClass* gt_ltr_orf_annotator_stream_class(void)
{
  static const GtNodeStreamClass *nsc = NULL;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof (GtLTRORFAnnotatorStream),
                                   ltr_orf_annotator_stream_free,
                                   ltr_orf_annotator_stream_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

GtNodeStream* gt_ltr_orf_annotator_stream_new(GtNodeStream *in_stream,
                                              GtEncseq *encseq,
                                              unsigned int min,
                                              unsigned int max,
                                              bool all,
                                              GtError *err)
{
  GtLTRORFAnnotatorStream *bs;
  GtNodeStream *ns;
  gt_assert(in_stream);
  ns = gt_node_stream_create(gt_ltr_orf_annotator_stream_class(), false);
  bs = ltr_orf_annotator_stream_cast(ns);
  bs->types = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
  bs->progress_loc = NULL;
  gt_hashmap_add(bs->types, gt_ft_LTR_retrotransposon, (void*) 1);
  bs->orf_stream = gt_orf_finder_stream_new(in_stream, encseq, bs->types, min,
                                            max, all, err);
  return ns;
}

void gt_ltr_orf_annotator_stream_set_progress_location(
                                                     GtLTRORFAnnotatorStream *s,
                                                     unsigned long *loc)
{
  gt_assert(s);
  s->progress_loc = loc;
}
genometools-1.5.1/src/ltr/ltr_orf_annotator_stream_api.h000066400000000000000000000033321211610345200235460ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Steinbiss 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_ORF_ANNOTATOR_STREAM_API_H
#define LTR_ORF_ANNOTATOR_STREAM_API_H

#include "core/encseq_api.h"
#include "core/error_api.h"
#include "extended/node_stream_api.h"

/* implements the ``node stream'' interface */
typedef struct GtLTRORFAnnotatorStream GtLTRORFAnnotatorStream;

GtNodeStream* gt_ltr_orf_annotator_stream_new(GtNodeStream *in_stream,
                                              GtEncseq *encseq,
                                              unsigned int min,
                                              unsigned int max,
                                              bool all,
                                              GtError *err);

void          gt_ltr_orf_annotator_stream_set_progress_location(
                                                       GtLTRORFAnnotatorStream*,
                                                       unsigned long*);
#endif
genometools-1.5.1/src/ltr/ltr_refseq_match_stream.c000066400000000000000000000352221211610345200225010ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Kastens 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/array.h"
#include "core/class_alloc_lock.h"
#include "core/cstr_api.h"
#include "core/encseq.h"
#include "core/fasta.h"
#include "core/hashmap.h"
#include "core/ma.h"
#include "core/str.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "extended/node_stream_api.h"
#include "extended/match.h"
#include "extended/match_blast.h"
#include "extended/match_iterator_api.h"
#include "extended/match_iterator_blast.h"
#include "ltr/ltr_refseq_match_stream.h"

#define ATTR_FLCAND "flcand"
#define ATTR_LTRFAM "ltrfam"
#define ATTR_TARGET "target"
#define ATTR_PARAMS "params"
#define NEW_FN_TYPE "nucleotide_match"
#define GT_BLAST_PATH_ENV "GT_BLAST_PATH"

struct GtLTRRefseqMatchStream {
  const GtNodeStream parent_instance;
  GtNodeStream *in_stream;
  GtArray *nodes;
  GtHashmap *header_to_fn;
  const char *indexname,
             *refseq_file,
             *seq_file,
             *source;
  unsigned long params_id,
                next_index;
  bool first_next,
       dust,
       flcands;
  int word_size,
      gapopen,
      gapextend,
      penalty,
      reward,
      num_threads;
  double evalue,
         xdrop,
         identity,
         min_ali_len_perc;
  const char *moreblast;
};

#define gt_ltr_refseq_match_stream_cast(GS)\
        gt_node_stream_cast(gt_ltr_refseq_match_stream_class(), GS);

static void gt_ltr_refseq_match_stream_free_hash_elem(void *elem)
{
  gt_free(elem);
}

static int gt_ltr_refseq_match_stream_extract_sequences(
                                                    GtLTRRefseqMatchStream *rms,
                                                    unsigned long *n_to_check,
                                                    GtError *err)
{
  GtStr *seqid;
  GtGenomeNode *gn;
  GtFeatureNode *curnode;
  GtFeatureNodeIterator *fni;
  GtRange range;
  GtFile *outfp;
  GtEncseqLoader *el = NULL;
  GtEncseq *encseq = NULL;
  char *buffer, header[BUFSIZ];
  const char *attr;
  int had_err = 0;
  unsigned long i,
                seqnum,
                startpos;

  gt_assert(rms);
  gt_error_check(err);
  outfp = gt_file_new(rms->seq_file, "w", err);
  if (!outfp)
    had_err = -1;

  if (!had_err) {
    el = gt_encseq_loader_new();
    encseq = gt_encseq_loader_load(el, rms->indexname, err);
    if (!encseq)
      had_err = -1;
  }

  if (!had_err) {
    for (i = 0; i < gt_array_size(rms->nodes); i++) {
      gn = *(GtGenomeNode**) gt_array_get(rms->nodes, i);
      fni = gt_feature_node_iterator_new((GtFeatureNode*) gn);
      curnode = gt_feature_node_iterator_next(fni);
      seqid = gt_genome_node_get_seqid((GtGenomeNode*) curnode);
      range = gt_genome_node_get_range((GtGenomeNode*) curnode);
      if (rms->flcands) {
        attr = gt_feature_node_get_attribute(curnode, ATTR_FLCAND);
        if (!attr) {
          gt_feature_node_iterator_delete(fni);
          continue;
        }
      }
      attr = gt_feature_node_get_attribute(curnode, ATTR_LTRFAM);
      if (attr != NULL)
        (void) snprintf(header, BUFSIZ, "%s_%s_%lu_%lu", attr,
                        gt_str_get(seqid), range.start, range.end);
      else
        (void) snprintf(header, BUFSIZ, "%s_%lu_%lu", gt_str_get(seqid),
                        range.start, range.end);
      gt_cstr_rep(header, ' ', '+');
      gt_hashmap_add(rms->header_to_fn, (void*) gt_cstr_dup(header),
                     (void*) curnode);
      (void) sscanf(gt_str_get(seqid), "seq%lu", &seqnum);
      buffer = gt_calloc((size_t) gt_range_length(&range) + 1, sizeof (char));
      startpos = gt_encseq_seqstartpos(encseq, seqnum);
      gt_encseq_extract_decoded(encseq, buffer, startpos + range.start - 1,
                                startpos + range.end - 1);
      (*n_to_check)++;
      gt_fasta_show_entry(header, buffer, gt_range_length(&range), 50UL, outfp);
      gt_free(buffer);
      gt_feature_node_iterator_delete(fni);
    }
    gt_file_delete(outfp);
  }

  return had_err;
}

static GtStrand gt_ltr_refseq_match_stream_determine_strand(GtMatchDirection d,
                                                            GtFeatureNode *fn)
{
  gt_assert(fn);
  if (gt_feature_node_get_strand(fn) == GT_STRAND_REVERSE) {
    if (d == GT_MATCH_DIRECT)
      return GT_STRAND_REVERSE;
    else
      return GT_STRAND_FORWARD;
  } else {
    if (d == GT_MATCH_REVERSE)
      return GT_STRAND_REVERSE;
    else
      return GT_STRAND_FORWARD;
  }
}

static void gt_ltr_refseq_match_stream_add_match_to_fn(
                                                    GtLTRRefseqMatchStream *rms,
                                                    GtMatch *match,
                                                    GT_UNUSED GtError *err)
{
  GtStr *seq;
  GtFeatureNode *fn;
  GtGenomeNode *new_node;
  GtMatchDirection dir;
  GtStrand str;
  GtRange fn_range, match_range1, match_range2;
  char target[BUFSIZ], *tmp, *tmp2, buf[BUFSIZ];
  const char *seqid1, *seqid2;
  unsigned long ali_length,
                fn_length,
                min_ali_length;
  double similarity;

  gt_assert(rms && match);
  gt_error_check(err);

  seqid1 = gt_match_get_seqid1(match);
  seqid2 = gt_match_get_seqid2(match);
  fn = (GtFeatureNode*) gt_hashmap_get(rms->header_to_fn, (void*) seqid1);
  fn_length = gt_genome_node_get_length((GtGenomeNode*) fn);
  fn_range = gt_genome_node_get_range((GtGenomeNode*) fn);
  min_ali_length = (unsigned long)
                                  ((rms->min_ali_len_perc / 100.0) * fn_length);
  ali_length = gt_match_blast_get_align_length((GtMatchBlast*) match);
  if (ali_length < min_ali_length) {
    gt_match_delete(match);
    return;
  }
  gt_match_get_range_seq1(match, &match_range1);
  gt_match_get_range_seq2(match, &match_range2);
  seq = gt_genome_node_get_seqid((GtGenomeNode*) fn);
  dir = gt_match_get_direction(match);
  str = gt_ltr_refseq_match_stream_determine_strand(dir, fn);
  similarity = gt_match_blast_get_similarity((GtMatchBlast*) match);
  new_node = gt_feature_node_new(seq, NEW_FN_TYPE,
                                 fn_range.start + match_range1.start,
                                 fn_range.start + match_range1.end, str);
  (void) snprintf(buf, BUFSIZ, "%.2f", similarity);
  gt_feature_node_set_attribute((GtFeatureNode*) new_node, "identity", buf);
  gt_feature_node_set_source((GtFeatureNode*) new_node,
                             gt_str_new_cstr(rms->source));
  if (rms->params_id != GT_UNDEF_ULONG) {
    char params_id[BUFSIZ];

    (void) snprintf(params_id, BUFSIZ, "%lu", rms->params_id);
    gt_feature_node_set_attribute((GtFeatureNode*) new_node, ATTR_PARAMS,
                                  params_id);
  }

  tmp = gt_cstr_dup(seqid2);
  tmp2 = strtok(tmp, " ");
  if (tmp2 != NULL) {
    GtStr *tmpstr = NULL;
    tmpstr = gt_str_new_cstr(gt_cstr_dup(tmp2));
    gt_free(tmp2);
    while ((tmp2 = strtok(NULL, " ")) != NULL) {
      gt_str_append_cstr(tmpstr, "%20");
      gt_str_append_cstr(tmpstr, gt_cstr_dup(tmp2));
      gt_free(tmp2);
    }
    (void) snprintf(target, BUFSIZ, "%s %lu %lu", gt_str_get(tmpstr),
                    match_range2.start, match_range2.end);
    gt_str_delete(tmpstr);
  } else
    (void) snprintf(target, BUFSIZ, "%s %lu %lu", seqid2, match_range2.start,
                    match_range2.end);
  gt_feature_node_set_attribute((GtFeatureNode*) new_node, ATTR_TARGET,
                                target);
  gt_feature_node_add_child(fn, (GtFeatureNode*) new_node);

  gt_match_delete(match);
}

static int gt_ltr_refseq_match_stream_refseq_match(GtLTRRefseqMatchStream *rms,
                                                   GtError *err)
{
  GtMatchIterator *mi = NULL;
  GtMatch *match = NULL;
  GtMatchIteratorStatus status;
  char makeblastdb_call[BUFSIZ],
       *env = NULL;
  int had_err = 0;

  gt_assert(rms);
  gt_error_check(err);
  env = getenv(GT_BLAST_PATH_ENV);
  if (env != NULL)
    (void) snprintf(makeblastdb_call, BUFSIZ,
                    "%s/makeblastdb -in %s -dbtype nucl -logfile "
                    "makeblastdb.txt",
                    env, rms->refseq_file);
  else
    (void) snprintf(makeblastdb_call, BUFSIZ,
                    "makeblastdb -in %s -dbtype nucl -logfile "
                    "makeblastdb.txt",
                    rms->refseq_file);
  had_err = system(makeblastdb_call);
  if (!had_err) {
    mi = gt_match_iterator_blastn_process_new(rms->seq_file,
                                              rms->refseq_file,
                                              rms->evalue,
                                              rms->dust,
                                              rms->word_size,
                                              rms->gapopen,
                                              rms->gapextend,
                                              rms->penalty,
                                              rms->reward,
                                              rms->identity,
                                              rms->num_threads,
                                              rms->xdrop,
                                              rms->moreblast,
                                              err);
    if (mi != NULL) {
      if ((status = gt_match_iterator_next(mi, &match, err))
           != GT_MATCHER_STATUS_OK) {
          gt_error_set(err, "Could not run BLASTN.");
          had_err = -1;
      } else {
          gt_ltr_refseq_match_stream_add_match_to_fn(rms, match, err);
          while ((status = gt_match_iterator_next(mi, &match, err))
                 != GT_MATCHER_STATUS_END) {
            if (status == GT_MATCHER_STATUS_OK) {
              gt_ltr_refseq_match_stream_add_match_to_fn(rms, match, err);
            } else
              had_err = -1;
          }
      }
    } else
      had_err = -1;
  } else
    gt_error_set(err, "Could not run makeblastdb.");

  return had_err;
}

static int gt_ltr_refseq_match_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
                                           GtError *err)
{
  GtLTRRefseqMatchStream *rms;
  GtGenomeNode *ref_gn;
  int had_err = 0;
  unsigned long n_to_check = 0;

  gt_error_check(err);
  rms = gt_ltr_refseq_match_stream_cast(ns);
  if (rms->first_next) {
    while (!(had_err = gt_node_stream_next(rms->in_stream, gn, err)) && *gn) {
      gt_assert(*gn && !had_err);
      ref_gn = gt_genome_node_ref(*gn);
      gt_array_add(rms->nodes, ref_gn);
    }
    if (!had_err)
      had_err = gt_ltr_refseq_match_stream_extract_sequences(rms, &n_to_check,
                                                             err);
    if (n_to_check > 0) {
      if (!had_err)
        had_err = gt_ltr_refseq_match_stream_refseq_match(rms, err);
      if (!had_err) {
        *gn = *(GtGenomeNode**) gt_array_get(rms->nodes, rms->next_index);
        rms->next_index++;
        rms->first_next = false;
        return 0;
      }
    }
  } else {
    if (rms->next_index >= gt_array_size(rms->nodes))
      *gn = NULL;
    else {
      *gn = *(GtGenomeNode**) gt_array_get(rms->nodes, rms->next_index);
      rms->next_index++;
    }
    return 0;
  }

  return had_err;
}

static void gt_ltr_refseq_match_stream_free(GtNodeStream *gs)
{
  GtLTRRefseqMatchStream *rms = gt_ltr_refseq_match_stream_cast(gs);

  gt_hashmap_delete(rms->header_to_fn);
  gt_node_stream_delete(rms->in_stream);
}

const GtNodeStreamClass* gt_ltr_refseq_match_stream_class(void)
{
  static const GtNodeStreamClass *gsc = NULL;
  gt_class_alloc_lock_enter();
  if (!gsc) {
    gsc = gt_node_stream_class_new(sizeof (GtLTRRefseqMatchStream),
                                   gt_ltr_refseq_match_stream_free,
                                   gt_ltr_refseq_match_stream_next);
  }
  gt_class_alloc_lock_leave();
  return gsc;
}

GtNodeStream* gt_ltr_refseq_match_stream_new(GtNodeStream *in_stream,
                                             const char *indexname,
                                             const char *refseq_file,
                                             const char *seq_file,
                                             double evalue,
                                             bool dust,
                                             int word_size,
                                             int gapopen,
                                             int gapextend,
                                             int penalty,
                                             int reward,
                                             int num_threads,
                                             double xdrop,
                                             double identity,
                                             const char *moreblast,
                                             bool flcands,
                                             double min_ali_len_perc,
                                             unsigned long params_id,
                                             const char *source,
                                             GT_UNUSED GtError *err)
{
  GtNodeStream *gs;
  GtLTRRefseqMatchStream *rms;
  gs = gt_node_stream_create(gt_ltr_refseq_match_stream_class(), false);
  rms = gt_ltr_refseq_match_stream_cast(gs);
  rms->in_stream = gt_node_stream_ref(in_stream);
  rms->nodes = gt_array_new(sizeof(GtGenomeNode*));
  rms->first_next = true;
  rms->params_id = params_id;
  rms->next_index = 0;
  rms->header_to_fn = gt_hashmap_new(GT_HASH_STRING,
                                     gt_ltr_refseq_match_stream_free_hash_elem,
                                     NULL);
  rms->indexname = indexname;
  rms->refseq_file = refseq_file;
  rms->seq_file = seq_file;
  rms->evalue = evalue;
  rms->dust = dust;
  rms->word_size = word_size;
  rms->gapopen = gapopen;
  rms->gapextend = gapextend;
  rms->penalty = penalty;
  rms->reward = reward;
  rms->num_threads = num_threads;
  rms->xdrop = xdrop;
  rms->identity = identity;
  rms->moreblast = moreblast;
  rms->flcands = flcands;
  rms->source = source;
  rms->min_ali_len_perc = min_ali_len_perc;

  return gs;
}
genometools-1.5.1/src/ltr/ltr_refseq_match_stream.h000066400000000000000000000020401211610345200224760ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Kastens 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_REFSEQ_MATCH_STREAM_H
#define LTR_REFSEQ_MATCH_STREAM_H

#include "ltr/ltr_refseq_match_stream_api.h"

const GtNodeStreamClass* gt_ltr_refseq_match_stream_class(void);

#endif
genometools-1.5.1/src/ltr/ltr_refseq_match_stream_api.h000066400000000000000000000051551211610345200233410ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Kastens 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_REFSEQ_MATCH_STREAM_API_H
#define LTR_REFSEQ_MATCH_STREAM_API_H

#include "core/error_api.h"
#include "extended/node_stream_api.h"

typedef struct GtLTRRefseqMatchStream GtLTRRefseqMatchStream;

/* Implements the  interface. 
   extracts the sequences for each  and matches them against
   a given set of reference sequences (). If a match is found
   the associated  will be extended by a new  of
   type 'nucleotide_match' */
GtNodeStream* gt_ltr_refseq_match_stream_new(GtNodeStream *in_stream,
                                             const char *indexname,
                                             const char *refseq_file,
                                             const char *seq_file,
                                             double evalue,
                                             bool dust,
                                             int word_size,
                                             int gapopen,
                                             int gapextend,
                                             int penalty,
                                             int reward,
                                             int num_threads,
                                             double xdrop,
                                             double identity,
                                             const char *moreblast,
                                             bool flcands,
                                             double min_ali_len_perc,
                                             unsigned long params_id,
                                             const char *source,
                                             GtError *err);

#endif
genometools-1.5.1/src/ltr/ltr_visitor.c000066400000000000000000000104721211610345200201640ustar00rootroot00000000000000/*
  Copyright (c) 2008 Sascha Steinbiss 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/class_alloc_lock.h"
#include "core/cstr_api.h"
#include "core/hashmap.h"
#include "core/ma.h"
#include "core/range.h"
#include "core/unused_api.h"
#include "extended/feature_type.h"
#include "extended/node_visitor_api.h"
#include "extended/region_node.h"
#include "ltr/ltr_visitor.h"

struct GtLTRVisitor {
  const GtNodeVisitor parent_instance;
  GtLTRElement *element;
};

#define gt_ltr_visitor_cast(GV)\
        gt_node_visitor_cast(gt_ltr_visitor_class(), GV)

static int gt_ltr_visitor_feature_node(GtNodeVisitor *nv, GtFeatureNode *fn,
                                       GT_UNUSED GtError *err)
{
  GtLTRVisitor *lv;
  GtRange node_range;
  GtArray *pdomarr = NULL;
  const char *pfamname;
  const char *fnt;
  lv = gt_ltr_visitor_cast(nv);
  gt_assert(lv);
  gt_error_check(err);

  fnt = gt_feature_node_get_type(fn);

  if (strcmp(fnt, gt_ft_LTR_retrotransposon) == 0)
  {
    lv->element->mainnode = fn;
  } else if (strcmp(fnt, gt_ft_long_terminal_repeat) == 0)
  {
    if (lv->element->leftLTR == NULL)
    {
      node_range = gt_genome_node_get_range((GtGenomeNode*) fn);
      lv->element->leftLTR = fn;
      /* compensate for 1-based node coords */
      lv->element->leftLTR_5 = node_range.start - 1;
      lv->element->leftLTR_3 = node_range.end - 1;
    }
    else
    {
      node_range = gt_genome_node_get_range((GtGenomeNode*) fn);
      lv->element->rightLTR = fn;
      /* compensate for 1-based node coords */
      lv->element->rightLTR_5 = node_range.start - 1;
      lv->element->rightLTR_3 = node_range.end - 1;
    }
  } else if (strcmp(fnt, gt_ft_target_site_duplication) == 0)
  {
    if (lv->element->leftTSD == NULL)
    {
      lv->element->leftTSD = fn;
    }
    else
    {
      lv->element->rightTSD = fn;
    }
  } else if (strcmp(fnt, gt_ft_RR_tract) == 0)
  {
    if (lv->element->ppt == NULL)
    {
      lv->element->ppt = fn;
    }
  } else if (strcmp(fnt, gt_ft_primer_binding_site) == 0)
  {
    if (lv->element->pbs == NULL)
    {
      lv->element->pbs = fn;
    }
  } else if (strcmp(fnt, gt_ft_protein_match) == 0)
  {
    if (!lv->element->pdoms)
    {
      lv->element->pdoms = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
                                          (GtFree) gt_array_delete);
    }
    pfamname = gt_feature_node_get_attribute(fn, "name");
    if (!(pdomarr = (GtArray*) gt_hashmap_get(lv->element->pdoms, pfamname)))
    {
      char *pfamcpy = gt_cstr_dup(pfamname);
      pdomarr = gt_array_new(sizeof (GtFeatureNode*));
      gt_hashmap_add(lv->element->pdoms, pfamcpy, pdomarr);
      if (lv->element->pdomorder != NULL)
        gt_array_add(lv->element->pdomorder, pfamcpy);
    }
    gt_array_add(pdomarr, fn);
  }
  return 0;
}

const GtNodeVisitorClass* gt_ltr_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  gt_class_alloc_lock_enter();
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRVisitor),
                                    NULL,
                                    NULL,
                                    gt_ltr_visitor_feature_node,
                                    NULL,
                                    NULL,
                                    NULL);
  }
  gt_class_alloc_lock_leave();
  return nvc;
}

GtNodeVisitor* gt_ltr_visitor_new(GtLTRElement *element)
{
  GtNodeVisitor *nv;
  GtLTRVisitor *lv;
  gt_assert(element);
  nv = gt_node_visitor_create(gt_ltr_visitor_class());
  lv = gt_ltr_visitor_cast(nv);
  lv->element = element;
  gt_assert(lv);
  return nv;
}
genometools-1.5.1/src/ltr/ltr_visitor.h000066400000000000000000000025461211610345200201740ustar00rootroot00000000000000/*
  Copyright (c) 2008 Sascha Steinbiss 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTR_VISITOR_H
#define LTR_VISITOR_H

/* Implements the  interface. */
typedef struct GtLTRVisitor GtLTRVisitor;

#include "extended/node_visitor.h"
#include "ltr/ltrelement.h"

const GtNodeVisitorClass* gt_ltr_visitor_class(void);
GtNodeVisitor*            gt_ltr_visitor_new(GtLTRElement *element);

#define gt_ltr_visitor_cast(GV)\
        gt_node_visitor_cast(gt_ltr_visitor_class(), GV)

#define gt_ltr_visitor_try_cast(GV)\
        gt_node_visitor_try_cast(gt_ltr_visitor_class(), GV)

#endif
genometools-1.5.1/src/ltr/ltrdigest_def.h000066400000000000000000000021671211610345200204320ustar00rootroot00000000000000/*
  Copyright (c) 2008 Sascha Steinbiss 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTRDIGEST_DEF_H
#define LTRDIGEST_DEF_H

#include "ltr/pbs.h"
#include "ltr/ppt.h"
#include "ltr/pdom.h"

enum GtLTRdigestRunScans {
  GT_LTRDIGEST_RUN_PPT  = 0x1,
  GT_LTRDIGEST_RUN_PBS  = 0x2,
  GT_LTRDIGEST_RUN_PDOM = 0x4
};

#define GT_LTRDIGEST_TAG "LTRdigest"

#endif
genometools-1.5.1/src/ltr/ltrdigest_stream.c000066400000000000000000000455061211610345200211660ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Sascha Steinbiss 
  Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/class_alloc_lock.h"
#include "core/log.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/range.h"
#include "core/str.h"
#include "core/unused_api.h"
#include "extended/node_stream_api.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "extended/reverse_api.h"
#include "ltr/ltrdigest_def.h"
#include "ltr/ltrdigest_stream.h"
#include "ltr/ltr_visitor.h"

struct GtLTRdigestStream {
  const GtNodeStream parent_instance;
  GtNodeStream *in_stream;
  GtEncseq *encseq;
  GtPBSOptions *pbs_opts;
  GtPPTOptions *ppt_opts;
#ifdef HAVE_HMMER
  GtPdomFinder *pdf;
  GtPdomOptions *pdom_opts;
#endif
  GtLTRVisitor *lv;
  GtStr *ltrdigest_tag;
  int tests_to_run;
  GtLTRElement element;
};

#define GT_ALIWIDTH 60

#define gt_ltrdigest_stream_cast(GS)\
        gt_node_stream_cast(gt_ltrdigest_stream_class(), GS)

#ifdef HAVE_HMMER
static int pdom_hit_attach_gff3(GtPdomModel *model, GtPdomModelHit *hit,
                                void *data, GT_UNUSED GtError *err)
{
  unsigned long i;
  GtRange rng;
  GtLTRdigestStream *ls = (GtLTRdigestStream *) data;
  GtStrand strand;
  gt_assert(model && hit);

  strand = gt_pdom_model_hit_get_best_strand(hit);
  /* do not use the hits on the non-predicted strand
      -- maybe identify nested elements ? */
  if (strand != gt_feature_node_get_strand(ls->element.mainnode))
    return 0;

  for (i=0;ipdom_opts->output_all_chains) {
      gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
                                                        ls->element.mainnode),
                               gt_ft_protein_match,
                               rng.start,
                               rng.end,
                               strand);
      gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_alignment",
                                   alignmentstring, (GtFree) gt_str_delete);
      gt_genome_node_add_user_data((GtGenomeNode*) gf, "pdom_aaseq",
                                   aastring, (GtFree) gt_str_delete);
      gt_feature_node_set_source((GtFeatureNode*) gf, ls->ltrdigest_tag);
      gt_feature_node_set_score((GtFeatureNode*) gf,
                                gt_pdom_single_hit_get_evalue(singlehit));
      gt_feature_node_set_phase((GtFeatureNode*) gf, frame);
      if (gt_pdom_model_get_name(model)) {
        gt_feature_node_add_attribute((GtFeatureNode*) gf, "name",
                                      gt_pdom_model_get_name(model));
      }
      if (gt_pdom_model_get_acc(model)) {
        gt_feature_node_add_attribute((GtFeatureNode*) gf, "id",
                                      gt_pdom_model_get_acc(model));
      }
      if (gt_pdom_single_hit_is_chained(singlehit)
            && ls->pdom_opts->output_all_chains) {
        GtStr *buffer;
        unsigned long i;
        GtArray *chains = gt_pdom_single_hit_get_chains(singlehit);
        gt_assert(chains != NULL);
        buffer = gt_str_new();
        for (i = 0; i < gt_array_size(chains); i++) {
          gt_str_append_cstr(buffer, gt_pdom_model_get_name(model));
          gt_str_append_char(buffer, ':');
          gt_str_append_ulong(buffer,
                              *(unsigned long*) gt_array_get(chains, i));
          if (i != gt_array_size(chains) - 1) {
            gt_str_append_char(buffer, ',');
          }
        }
        gt_feature_node_add_attribute((GtFeatureNode*) gf, "chains",
                                      gt_str_get(buffer));
        gt_str_delete(buffer);
      }
      gt_feature_node_add_child(ls->element.mainnode, (GtFeatureNode*) gf);
    }
  }
  return 0;
}
#endif

static void pbs_attach_results_to_gff3(GtPBSResults *results,
                                       GtLTRElement *element,
                                       GtStrand *canonical_strand,
                                       GtStr *tag)
{
  GtRange pbs_range;
  GtGenomeNode *gf;
  unsigned long i = 0;
  char buffer[BUFSIZ];
  GtPBSHit* hit = gt_pbs_results_get_ranked_hit(results, i++);
  if (*canonical_strand == GT_STRAND_UNKNOWN)
    *canonical_strand = gt_pbs_hit_get_strand(hit);
  else
  {
    /* do we have to satisfy a strand constraint?
     * then find best-scoring PBS on the given canonical strand */
    while (gt_pbs_hit_get_strand(hit) != *canonical_strand
             && i < gt_pbs_results_get_number_of_hits(results))
    {
      gt_log_log("dropping PBS because of nonconsistent strand: %s\n",
                 gt_feature_node_get_attribute(element->mainnode, "ID"));
      hit = gt_pbs_results_get_ranked_hit(results, i++);
    }
    /* if there is none, do not report a PBS */
    if (gt_pbs_hit_get_strand(hit) != *canonical_strand)
      return;
  }
  pbs_range = gt_pbs_hit_get_coords(hit);
  pbs_range.start++; pbs_range.end++;  /* GFF3 is 1-based */
  gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
                                                    element->mainnode),
                           gt_ft_primer_binding_site,
                           pbs_range.start,
                           pbs_range.end,
                           gt_pbs_hit_get_strand(hit));
  gt_feature_node_set_source((GtFeatureNode*) gf, tag);
  gt_feature_node_set_score((GtFeatureNode*) gf,
                            (float) gt_pbs_hit_get_score(hit));
  if (gt_pbs_hit_get_trna(hit) != NULL) {
    gt_feature_node_add_attribute((GtFeatureNode*) gf, "trna",
                                   gt_pbs_hit_get_trna(hit));
  }
  gt_feature_node_set_strand(element->mainnode, gt_pbs_hit_get_strand(hit));
  (void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_tstart(hit));
  gt_feature_node_add_attribute((GtFeatureNode*) gf, "trnaoffset", buffer);
  (void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_offset(hit));
  gt_feature_node_add_attribute((GtFeatureNode*) gf, "pbsoffset", buffer);
  (void) snprintf(buffer, BUFSIZ-1, "%lu", gt_pbs_hit_get_edist(hit));
  gt_feature_node_add_attribute((GtFeatureNode*) gf, "edist", buffer);
  gt_feature_node_add_child(element->mainnode, (GtFeatureNode*) gf);
}

static void ppt_attach_results_to_gff3(GtPPTResults *results,
                                       GtLTRElement *element,
                                       GtStrand *canonical_strand,
                                       GtStr *tag)
{
  GtRange ppt_range;
  unsigned long i = 0;
  GtGenomeNode *gf;
  GtPPTHit *hit = gt_ppt_results_get_ranked_hit(results, i++),
           *ubox;
  if (*canonical_strand == GT_STRAND_UNKNOWN)
    *canonical_strand = gt_ppt_hit_get_strand(hit);
  else
  {
    /* find best-scoring PPT on the given canonical strand */
    while (gt_ppt_hit_get_strand(hit) != *canonical_strand
             && i < gt_ppt_results_get_number_of_hits(results))
    {
      gt_log_log("dropping PPT because of nonconsistent strand: %s\n",
                 gt_feature_node_get_attribute(element->mainnode, "ID"));
      hit = gt_ppt_results_get_ranked_hit(results, i++);
    }
    /* if there is none, do not report a PPT */
    if (gt_ppt_hit_get_strand(hit) != *canonical_strand)
      return;
  }
  ppt_range = gt_ppt_hit_get_coords(hit);
  ppt_range.start++; ppt_range.end++;  /* GFF3 is 1-based */
  gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
                                                    element->mainnode),
                           gt_ft_RR_tract,
                           ppt_range.start,
                           ppt_range.end,
                           gt_ppt_hit_get_strand(hit));
  gt_feature_node_set_source((GtFeatureNode*) gf, tag);
  gt_feature_node_set_strand(element->mainnode, gt_ppt_hit_get_strand(hit));
  gt_feature_node_add_child(element->mainnode, (GtFeatureNode*) gf);
  if ((ubox = gt_ppt_hit_get_ubox(hit)) != NULL) {
    GtRange ubox_range = gt_ppt_hit_get_coords(ubox);
    ubox_range.start++; ubox_range.end++;
    gf = gt_feature_node_new(gt_genome_node_get_seqid((GtGenomeNode*)
                                                      element->mainnode),
                             gt_ft_U_box,
                             ubox_range.start,
                             ubox_range.end,
                             gt_ppt_hit_get_strand(ubox));
    gt_feature_node_set_source((GtFeatureNode*) gf, tag);
    gt_feature_node_set_strand(element->mainnode, gt_ppt_hit_get_strand(ubox));
    gt_feature_node_add_child(element->mainnode, (GtFeatureNode*) gf);
  }
}

static int run_ltrdigest(GtLTRElement *element, char *seq,
                         GtLTRdigestStream *ls,
#ifdef HAVE_HMMER
                         GtError *err)
#else
                         GT_UNUSED GtError *err)
#endif
{
  int had_err = 0;
  char *rev_seq;
  unsigned long seqlen = gt_ltrelement_length(element);
  GtStrand canonical_strand = GT_STRAND_UNKNOWN;

  /* create reverse strand sequence */
  rev_seq = gt_calloc((size_t) seqlen+1, sizeof (char));
  memcpy(rev_seq, seq, sizeof (char) * seqlen);
  had_err = gt_reverse_complement(rev_seq, seqlen, err);

  if (!had_err)
  {
#ifdef HAVE_HMMER
    /* Protein domain finding
     * ----------------------*/
    if (ls->tests_to_run & GT_LTRDIGEST_RUN_PDOM)
    {
      GtPdomResults *pdom_results = NULL;
      if (!ls->pdf)
      {
        gt_error_set(err, "No PdomFinder object found -- "
                          "how could that happen?");
        had_err = -1;
      } else
      {
        pdom_results = gt_pdom_finder_find(ls->pdf, (const char*) seq,
                                           (const char*) rev_seq, element, err);
        if (!pdom_results)
        {
          had_err = -1;
        } else {
          if (pdom_results && !gt_pdom_results_empty(pdom_results))
          {
            /* determine most likely strand from protein domain results */
            if (gt_double_compare(
                     gt_pdom_results_get_combined_evalue_fwd(pdom_results),
                     gt_pdom_results_get_combined_evalue_rev(pdom_results)) < 0)
              canonical_strand = GT_STRAND_FORWARD;
            else
              canonical_strand = GT_STRAND_REVERSE;
            gt_feature_node_set_strand(ls->element.mainnode, canonical_strand);
            /* create nodes for protein match annotations */
            (void) gt_pdom_results_foreach_domain_hit(pdom_results,
                                                      pdom_hit_attach_gff3,
                                                      ls,
                                                      err);
          }
          gt_pdom_results_delete(pdom_results);
        }
      }
    }
#endif

    /* PPT finding
     * -----------*/
    if (ls->tests_to_run & GT_LTRDIGEST_RUN_PPT)
    {
      GtPPTResults *ppt_results = NULL;
      ppt_results = gt_ppt_find((const char*) seq, (const char*) rev_seq,
                              element, ls->ppt_opts);
      if (gt_ppt_results_get_number_of_hits(ppt_results) > 0)
      {
        ppt_attach_results_to_gff3(ppt_results, element, &canonical_strand,
                                   ls->ltrdigest_tag);
      }
      gt_ppt_results_delete(ppt_results);
    }

    /* PBS finding
     * ----------- */
    if (ls->tests_to_run & GT_LTRDIGEST_RUN_PBS)
    {
      GtPBSResults *pbs_results = NULL;
      pbs_results = gt_pbs_find((const char*) seq, (const char*) rev_seq,
                                element, ls->pbs_opts, err);
       if (gt_pbs_results_get_number_of_hits(pbs_results) > 0)
       {
        pbs_attach_results_to_gff3(pbs_results, element, &canonical_strand,
                                   ls->ltrdigest_tag);
       }
       gt_pbs_results_delete(pbs_results);
    }
  }
  gt_free(rev_seq);
  return had_err;
}

static int gt_ltrdigest_stream_next(GtNodeStream *ns, GtGenomeNode **gn,
                                    GtError *err)
{
  GtLTRdigestStream *ls;
  GtFeatureNode *fn;
  int had_err;

  gt_error_check(err);
  ls = gt_ltrdigest_stream_cast(ns);

  /* initialize this element */
  memset(&ls->element, 0, sizeof (GtLTRElement));

  /* get annotations from parser */
  had_err = gt_node_stream_next(ls->in_stream, gn, err);
  if (!had_err && *gn)
  {
    GtFeatureNodeIterator *gni;
    GtFeatureNode *mygn;

   /* only process feature nodes */
   if (!(fn = gt_feature_node_try_cast(*gn)))
     return 0;

    /* fill LTRElement structure from GFF3 subgraph */
    gni = gt_feature_node_iterator_new(fn);
    for (mygn = fn; mygn != NULL; mygn = gt_feature_node_iterator_next(gni))
      (void) gt_genome_node_accept((GtGenomeNode*) mygn,
                                   (GtNodeVisitor*) ls->lv,
                                   err);
    gt_feature_node_iterator_delete(gni);
  }

  if (ls->element.mainnode != NULL)
  {
    unsigned long seqid;
    const char *sreg;
    char *seq;

    sreg = gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*)
                                               ls->element.mainnode));

    /* we assume that this is the correct numbering! */
    if (!sscanf(sreg,"seq%lu", &seqid))
    {
      gt_error_set(err, "Feature '%s' on line %u has invalid region identifier,"
                   "must be 'seqX' with X being a sequence number, but was "
                   "'%s'!",
                   gt_feature_node_get_attribute(ls->element.mainnode, "ID"),
                   gt_genome_node_get_line_number((GtGenomeNode*)
                                                  ls->element.mainnode),
                   gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*)
                                                       ls->element.mainnode)));
      had_err = -1;
    }
    if (!had_err)
    {
      if (seqid > gt_encseq_num_of_sequences(ls->encseq)-1) {
        gt_error_set(err, "Sequence region number exceeds number of sequences "
                          "in encoded sequence file: 'seq%lu'!", seqid);
        had_err = -1;
      }
    }
    if (!had_err)
    {
      GtUchar *symbolstring;
      unsigned long length, seqstartpos, seqlength;
      const GtAlphabet *alpha;

      seqstartpos = gt_encseq_seqstartpos(ls->encseq, seqid);
      seqlength = gt_encseq_seqlength(ls->encseq, seqid);

      if (ls->element.rightLTR_3 <= seqlength)
      {
        alpha        = gt_encseq_alphabet(ls->encseq);
        length       = gt_ltrelement_length(&ls->element);
        seq          = gt_malloc((size_t) (length+1) * sizeof (char));
        symbolstring = gt_malloc((size_t) (length+1) * sizeof (GtUchar));
        gt_encseq_extract_encoded(ls->encseq,
                                  symbolstring,
                                  seqstartpos + (ls->element.leftLTR_5),
                                  seqstartpos + (ls->element.leftLTR_5)
                                    + length - 1);
        gt_alphabet_decode_seq_to_cstr(alpha, seq, symbolstring, length);
        gt_free(symbolstring);

        /* run LTRdigest core routine */
        had_err = run_ltrdigest(&ls->element, seq, ls, err);

        gt_free(seq);
      }
      else
      {
        /* do not process elements whose positions exceed sequence boundaries
         (obviously annotation and sequence do not match!) */
        gt_error_set(err,
                     "Element '%s' exceeds sequence boundaries! (%lu > %lu)",
                     gt_feature_node_get_attribute(ls->element.mainnode, "ID"),
                     ls->element.rightLTR_3, seqlength);
        had_err = -1;
      }
    }
  }
  if (had_err) {
    gt_genome_node_delete(*gn);
    *gn = NULL;
  }
  return had_err;
}

static void gt_ltrdigest_stream_free(GtNodeStream *ns)
{
  GtLTRdigestStream *ls = gt_ltrdigest_stream_cast(ns);
  gt_node_visitor_delete((GtNodeVisitor*) ls->lv);
  gt_str_delete(ls->ltrdigest_tag);
  gt_node_stream_delete(ls->in_stream);
#ifdef HAVE_HMMER
  gt_pdom_finder_delete(ls->pdf);
#endif
}

const GtNodeStreamClass* gt_ltrdigest_stream_class(void)
{
  static const GtNodeStreamClass *nsc;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof (GtLTRdigestStream),
                                   gt_ltrdigest_stream_free,
                                   gt_ltrdigest_stream_next );
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

GtNodeStream* gt_ltrdigest_stream_new(GtNodeStream *in_stream,
                                      int tests_to_run,
                                      GtEncseq *encseq,
                                      GtPBSOptions *pbs_opts,
                                      GtPPTOptions *ppt_opts,
#ifdef HAVE_HMMER
                                      GtPdomOptions *pdom_opts,
                                      GtError *err)
#else
                                      GT_UNUSED GtError *err)
#endif
{
  GtNodeStream *ns;
  GtLTRdigestStream *ls;
  ns = gt_node_stream_create(gt_ltrdigest_stream_class(), true);
  ls = gt_ltrdigest_stream_cast(ns);
  ls->in_stream = gt_node_stream_ref(in_stream);
  ls->ppt_opts = ppt_opts;
  ls->pbs_opts = pbs_opts;
#ifdef HAVE_HMMER
  ls->pdom_opts = pdom_opts;
  ls->pdf = gt_pdom_finder_new(ls->pdom_opts->hmm_files,
                               ls->pdom_opts->evalue_cutoff,
                               ls->pdom_opts->chain_max_gap_length,
                               ls->pdom_opts->cutoff,
                               err);
#endif
  ls->tests_to_run = tests_to_run;
  ls->encseq = encseq;
  ls->ltrdigest_tag = gt_str_new_cstr(GT_LTRDIGEST_TAG);
  ls->lv = (GtLTRVisitor*) gt_ltr_visitor_new(&ls->element);
#ifdef HAVE_HMMER
  if (!ls->pdf)
  {
    /* An error occurred, do not return a stream.
       We assume that the error message has been set. */
    gt_node_stream_delete(ns);
    return NULL;
  } else
#endif
  return ns;
}
genometools-1.5.1/src/ltr/ltrdigest_stream.h000066400000000000000000000032631211610345200211650ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Sascha Steinbiss 
  Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTRDIGEST_STREAM_H
#define LTRDIGEST_STREAM_H

#include "core/error_api.h"
#include "extended/node_stream_api.h"
#include "ltr/pbs.h"
#include "ltr/ppt.h"
#ifdef HAVE_HMMER
#include "ltr/pdom.h"
#endif
#include "core/encseq.h"

/* implements the ``node stream'' interface */
typedef struct GtLTRdigestStream GtLTRdigestStream;

const GtNodeStreamClass* gt_ltrdigest_stream_class(void);

GtNodeStream* gt_ltrdigest_stream_new(GtNodeStream *in_stream,
                                      int tests_to_run,
                                      GtEncseq *encseq,
                                      GtPBSOptions *pbs_opts,
                                      GtPPTOptions *ppt_opts,
#ifdef HAVE_HMMER
                                      GtPdomOptions *pdom_opts,
#endif
                                      GtError *err);

#endif
genometools-1.5.1/src/ltr/ltrelement.c000066400000000000000000000123311211610345200177530ustar00rootroot00000000000000/*
  Copyright (c) 2008-2010 Sascha Steinbiss 
  Copyright (c) 2008-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/alphabet.h"
#include "core/cstr_api.h"
#include "core/ensure.h"
#include "core/ma.h"
#include "core/minmax.h"
#include "extended/reverse_api.h"
#include "ltr/ltrelement.h"

unsigned long gt_ltrelement_length(GtLTRElement *e)
{
  gt_assert(e && (e->leftLTR_3 >= e->leftLTR_5));
  return e->rightLTR_3 - e->leftLTR_5 + 1;
}

unsigned long gt_ltrelement_leftltrlen(GtLTRElement *e)
{
  gt_assert(e && (e->leftLTR_3 >= e->leftLTR_5));
  return e->leftLTR_3-e->leftLTR_5 + 1;
}

char* gt_ltrelement_get_sequence(unsigned long start, unsigned long end,
                                 GtStrand strand, GtEncseq *seq,
                                 unsigned long seqstartpos, GtError *err)
{
  char *out;
  int had_err = 0;
  GtUchar *symbolstring;
  const GtAlphabet *alpha;
  GtEncseqReader *esr;
  unsigned long len, i;

  gt_assert(seq && end >= start);
  gt_error_check(err);

  alpha = gt_encseq_alphabet(seq);
  len = end - start + 1;

  out          = gt_malloc((size_t) (len + 1) * sizeof (char));
  symbolstring = gt_malloc((size_t) (len + 1) * sizeof (GtUchar));

  esr = gt_encseq_create_reader_with_readmode(seq, GT_READMODE_FORWARD,
                                              seqstartpos + start);
  for (i=0;irightLTR_3 >= e->rightLTR_5));
  return e->rightLTR_3 - e->rightLTR_5 + 1;
}

int gt_ltrelement_format_description(GtLTRElement *e, unsigned int seqnamelen,
                                     char *buf, size_t buflen)
{
  int ret;
  char tmpstr[BUFSIZ];
  gt_assert(buf && e);

  (void) snprintf(tmpstr, MIN(BUFSIZ, (size_t) seqnamelen+1), "%s", e->seqid);
  tmpstr[seqnamelen+1] = '\0';
  gt_cstr_rep(tmpstr, ' ', '_');
  ret = snprintf(buf, buflen, "%s_%lu_%lu", tmpstr, e->leftLTR_5+1,
                 e->rightLTR_3+1);
  return ret;
}

int gt_ltrelement_unit_test(GtError *err)
{
  int had_err = 0;
  GtLTRElement element;
  char tmp[BUFSIZ];
  const char *fullseq =                           "aaaaaaaaaaaaaaaaaaaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "acatactaggatgctagaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatataggatcctaaggctac"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "aaaaaaaaaaaaaaaaaaaa";

  gt_error_check(err);

  /* check left LTR */
  element.leftLTR_5 = 20UL;
  element.leftLTR_3 = 119UL;
  gt_ensure(had_err, gt_ltrelement_leftltrlen(&element) == 100UL);
  memset(tmp, 0, BUFSIZ);
  memcpy(tmp, fullseq + (element.leftLTR_5 * sizeof (char)),
         (size_t) (element.leftLTR_3 - element.leftLTR_5+ 1) * sizeof (char));
  gt_ensure(had_err,
            strcmp(tmp, "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcg"
                        "aatatagcactgcatttcgaatatagtttcgaatatagcactgcattt"
                        "cgaa" ) == 0);

  /* check right LTR */
  element.rightLTR_5 = 520UL;
  element.rightLTR_3 = 619UL;
  gt_ensure(had_err, gt_ltrelement_rightltrlen(&element) == 100UL);
  memset(tmp, 0, BUFSIZ);
  memcpy(tmp, fullseq + (element.rightLTR_5 * sizeof (char)),
         (size_t) (element.rightLTR_3 - element.rightLTR_5+ 1) * sizeof (char));
  gt_ensure(had_err,
            strcmp(tmp, "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcg"
                        "aatatagcactgcatttcgaatatagtttcgaatatagcactgcattt"
                        "cgaa" ) == 0);

  return had_err;
}
genometools-1.5.1/src/ltr/ltrelement.h000066400000000000000000000045561211610345200177720ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Sascha Steinbiss 
  Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTRELEMENT_H
#define LTRELEMENT_H

#include "core/error.h"
#include "core/hashmap.h"
#include "core/range.h"
#include "core/seq.h"
#include "core/strand.h"
#include "extended/feature_node.h"
#include "core/encseq.h"

enum GtOffset {
  GT_OFFSET_END_LEFT_LTR,
  GT_OFFSET_END_RIGHT_LTR,
  GT_OFFSET_BEGIN_RIGHT_LTR,
  GT_OFFSET_BEGIN_LEFT_LTR
};

typedef struct GtLTRElement {
  unsigned long leftLTR_3,
                leftLTR_5,
                rightLTR_3,
                rightLTR_5;
  GtFeatureNode *mainnode,
                *leftLTR,
                *rightLTR,
                *leftTSD,
                *rightTSD,
                *ppt,
                *pbs;
  char *seqid;
  GtArray *pdomorder;
  GtHashmap *pdoms;
} GtLTRElement;

unsigned long gt_ltrelement_length(GtLTRElement *e);
char*         gt_ltrelement_get_sequence(unsigned long start,
                                         unsigned long end,
                                         GtStrand strand,
                                         GtEncseq *seq,
                                         unsigned long seqstartpos,
                                         GtError *err);
unsigned long gt_ltrelement_leftltrlen(GtLTRElement *e);
unsigned long gt_ltrelement_rightltrlen(GtLTRElement *e);
int           gt_ltrelement_format_description(GtLTRElement *e,
                                               unsigned int seqnamelen,
                                               char *buf, size_t buflen);
int           gt_ltrelement_unit_test(GtError *err);
#endif
genometools-1.5.1/src/ltr/ltrfileout_stream.c000066400000000000000000000653031211610345200213530ustar00rootroot00000000000000/*
  Copyright (c) 2008-2010 Sascha Steinbiss 
  Copyright (c) 2008-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#include 
#endif
#include 
#include 
#include "core/class_alloc_lock.h"
#include "core/cstr_api.h"
#include "core/fasta.h"
#include "core/hashmap.h"
#include "core/ma.h"
#include "core/minmax.h"
#include "core/range.h"
#include "core/str.h"
#include "core/unused_api.h"
#include "extended/node_stream_api.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "ltr/ltrfileout_stream.h"
#include "ltr/ltr_visitor.h"

#define GT_FSWIDTH         60UL
#define GT_MAXFILENAMELEN 256
#define GT_MAXFASTAHEADER 256

struct GtLTRFileOutStream {
  const GtNodeStream parent_instance;
  GtNodeStream *in_stream;
  GtEncseq *encseq;
  const char *fileprefix;
  GtFile *metadata_file,
            *tabout_file,
            *pbsout_file,
            *pptout_file,
            *ltr5out_file,
            *ltr3out_file,
            *elemout_file;
  GtHashmap *pdomout_files,
            *pdomali_files,
            *pdomaa_files;
  GtLTRVisitor *lv;
  int tests_to_run;
  unsigned int seqnamelen;
  GtLTRElement element;
  bool write_pdom_alignments,
       write_pdom_aaseqs;
};

#define gt_ltr_fileout_stream_cast(GS)\
        gt_node_stream_cast(gt_ltr_fileout_stream_class(), GS)

static int write_pdom(GtLTRFileOutStream *ls, GtArray *pdoms,
                      const char *pdomname, GtEncseq *seq,
                      unsigned long startpos, char *desc, GtError *err)
{
  int had_err = 0;
  GtFile *seqfile = NULL,
            *alifile = NULL,
            *aafile = NULL;
  unsigned long i = 0,
                seq_length = 0;
  GtStr *pdom_seq,
        *pdom_aaseq;
  gt_error_check(err);

  pdom_seq = gt_str_new();
  pdom_aaseq = gt_str_new();

  /* get protein domain output file */
  seqfile = (GtFile*) gt_hashmap_get(ls->pdomout_files, pdomname);
  if (seqfile == NULL)
  {
    /* no file opened for this domain yet, do it */
    char buffer[GT_MAXFILENAMELEN];
    (void) snprintf(buffer, (size_t) (GT_MAXFILENAMELEN-1), "%s_pdom_%s.fas",
                    ls->fileprefix, pdomname);
    seqfile = gt_file_xopen(buffer, "w+");
    gt_hashmap_add(ls->pdomout_files, gt_cstr_dup(pdomname), seqfile);
  }

  /* get protein alignment output file */
  if (ls->write_pdom_alignments)
  {
    alifile = (GtFile*) gt_hashmap_get(ls->pdomali_files, pdomname);
    if (alifile == NULL)
    {
      /* no file opened for this domain yet, do it */
      char buffer[GT_MAXFILENAMELEN];
      (void) snprintf(buffer, (size_t) (GT_MAXFILENAMELEN-1), "%s_pdom_%s.ali",
                      ls->fileprefix, pdomname);
      alifile = gt_file_xopen(buffer, "w+");
      gt_hashmap_add(ls->pdomali_files, gt_cstr_dup(pdomname), alifile);
    }
  }

  /* get amino acid sequence output file */
  if (ls->write_pdom_aaseqs)
  {
    aafile = (GtFile*) gt_hashmap_get(ls->pdomaa_files, pdomname);
    if (aafile == NULL)
    {
      /* no file opened for this domain yet, do it */
      char buffer[GT_MAXFILENAMELEN];
      (void) snprintf(buffer, (size_t) (GT_MAXFILENAMELEN-1),
                      "%s_pdom_%s_aa.fas",
                      ls->fileprefix, pdomname);
      aafile = gt_file_xopen(buffer, "w+");
      gt_hashmap_add(ls->pdomaa_files, gt_cstr_dup(pdomname), aafile);
    }
  }

  if (gt_array_size(pdoms) > 1UL)
  {
    for (i=1UL; i= 0);
    }
    if (gt_feature_node_get_strand(*(GtFeatureNode**) gt_array_get(pdoms, 0UL))
        == GT_STRAND_REVERSE)
    {
      gt_array_reverse(pdoms);
    }
  }

  /* output protein domain data */
  for (i=0;iwrite_pdom_alignments && ali)
    {
      char buf[BUFSIZ];
      /* write away alignment */
      (void) snprintf(buf, BUFSIZ-1, "Protein domain alignment in translated "
                                     "sequence for candidate\n'%s':\n\n",
                                     desc);
      gt_file_xwrite(alifile, buf, (size_t) strlen(buf) * sizeof (char));
      gt_file_xwrite(alifile, gt_str_get(ali),
                        (size_t) gt_str_length(ali) * sizeof (char));
      gt_file_xwrite(alifile, "---\n\n", 5 * sizeof (char));
    }
    if (ls->write_pdom_aaseqs && aaseq)
    {
      /* append amino acid sequence */
      gt_str_append_str(pdom_aaseq, aaseq);
    }
    gt_genome_node_release_user_data((GtGenomeNode*) fn, "pdom_alignment");
    gt_genome_node_release_user_data((GtGenomeNode*) fn, "pdom_aaseq");
    seq_length += gt_range_length(&pdom_rng);
    gt_free(tmpstr);
  }
  if (!had_err)
  {
    gt_fasta_show_entry(desc,
                        gt_str_get(pdom_seq),
                        seq_length,
                        GT_FSWIDTH,
                        seqfile);
    if (ls->write_pdom_aaseqs)
    {
      gt_fasta_show_entry(desc,
                          gt_str_get(pdom_aaseq),
                          gt_str_length(pdom_aaseq),
                          GT_FSWIDTH,
                          aafile);
    }
  }
  gt_str_delete(pdom_seq);
  gt_str_delete(pdom_aaseq);
  return had_err;
}

int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
{
  GtLTRFileOutStream *ls;
  GtFeatureNode *fn;
  GtRange lltr_rng, rltr_rng, rng, ppt_rng, pbs_rng;
  char *ppt_seq, *pbs_seq;
  int had_err;
  unsigned long i=0;

  gt_error_check(err);
  ls = gt_ltr_fileout_stream_cast(ns);

  /* initialize this element */
  memset(&ls->element, 0, sizeof (GtLTRElement));

  /* get annotations from parser */
  had_err = gt_node_stream_next(ls->in_stream, gn, err);
  if (!had_err && *gn)
  {
    GtFeatureNodeIterator* gni;
    GtFeatureNode *mygn;

    /* only process feature nodes */
    if (!(fn = gt_feature_node_try_cast(*gn)))
      return 0;

    ls->element.pdomorder = gt_array_new(sizeof (const char*));

    /* fill LTRElement structure from GFF3 subgraph */
    gni = gt_feature_node_iterator_new(fn);
    for (mygn = fn; mygn != NULL; mygn = gt_feature_node_iterator_next(gni))
      (void) gt_genome_node_accept((GtGenomeNode*) mygn,
                                   (GtNodeVisitor*) ls->lv,
                                   err);
    gt_feature_node_iterator_delete(gni);
  }

  if (ls->element.mainnode != NULL)
  {
    unsigned long seqnr, seqid_len, seqstartpos;
    GT_UNUSED unsigned long seqlength;
    char *outseq,
         desc[GT_MAXFASTAHEADER];
    GtRange ltr3_rng, ltr5_rng;
    GT_UNUSED GtRange elemrng;

    /* find sequence in GtEncseq */
    const char *sreg = gt_str_get(gt_genome_node_get_seqid((GtGenomeNode*)
                                                        ls->element.mainnode));
    (void) sscanf(sreg,"seq%lu", &seqnr);

    elemrng = gt_genome_node_get_range((GtGenomeNode*) ls->element.mainnode);
    seqstartpos = gt_encseq_seqstartpos(ls->encseq, seqnr);
    seqlength = gt_encseq_seqlength(ls->encseq, seqnr);

    ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char));
    (void) snprintf(ls->element.seqid,
                    MIN((size_t) seqid_len, (size_t) ls->seqnamelen)+1,
                    "%s",
                    gt_encseq_description(ls->encseq, &seqid_len, seqnr));
    gt_cstr_rep(ls->element.seqid, ' ', '_');
    if (seqid_len > (unsigned long) ls->seqnamelen)
      ls->element.seqid[ls->seqnamelen] = '\0';

    (void) gt_ltrelement_format_description(&ls->element,
                                            ls->seqnamelen,
                                            desc,
                                            (size_t) (GT_MAXFASTAHEADER-1));

    /* output basic retrotransposon data */
    lltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftLTR);
    rltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightLTR);
    rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.mainnode);
    gt_file_xprintf(ls->tabout_file,
                       "%lu\t%lu\t%lu\t%s\t%lu\t%lu\t%lu\t%lu\t%lu\t%lu\t",
                       rng.start,
                       rng.end,
                       gt_ltrelement_length(&ls->element),
                       ls->element.seqid,
                       lltr_rng.start,
                       lltr_rng.end,
                       gt_ltrelement_leftltrlen(&ls->element),
                       rltr_rng.start,
                       rltr_rng.end,
                       gt_ltrelement_rightltrlen(&ls->element));

    /* output TSDs */
    if (ls->element.leftTSD != NULL)
    {
      GtRange tsd_rng;
      GtStrand tsd_strand;
      char *tsd_seq;

      tsd_strand = gt_feature_node_get_strand(ls->element.leftTSD);
      tsd_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftTSD);
      tsd_seq = gt_ltrelement_get_sequence(tsd_rng.start-1, tsd_rng.end-1,
                                           tsd_strand, ls->encseq, seqstartpos,
                                           err);
      gt_file_xprintf(ls->tabout_file,
                         "%lu\t%lu\t%s\t",
                         tsd_rng.start,
                         tsd_rng.end,
                         tsd_seq);
      gt_free((char*) tsd_seq);
    } else gt_file_xprintf(ls->tabout_file, "\t\t\t");
    if (ls->element.rightTSD != NULL)
    {
      GtRange tsd_rng;
      GtStrand tsd_strand;
      char *tsd_seq;

      tsd_strand = gt_feature_node_get_strand(ls->element.rightTSD);
      tsd_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightTSD);
      tsd_seq = gt_ltrelement_get_sequence(tsd_rng.start-1, tsd_rng.end-1,
                                           tsd_strand, ls->encseq, seqstartpos,
                                           err);
      gt_file_xprintf(ls->tabout_file,
                         "%lu\t%lu\t%s\t",
                         tsd_rng.start,
                         tsd_rng.end,
                         tsd_seq);
      gt_free((char*) tsd_seq);
    } else gt_file_xprintf(ls->tabout_file, "\t\t\t");

    /* output PPT */
    if (ls->element.ppt != NULL)
    {
      GtStrand ppt_strand;
      ppt_strand = gt_feature_node_get_strand(ls->element.ppt);
      ppt_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.ppt);
      ppt_seq = gt_ltrelement_get_sequence(ppt_rng.start-1, ppt_rng.end-1,
                                           ppt_strand, ls->encseq, seqstartpos,
                                           err);
      gt_fasta_show_entry(desc, ppt_seq, gt_range_length(&ppt_rng),
                          GT_FSWIDTH, ls->pptout_file);
      gt_file_xprintf(ls->tabout_file,
                         "%lu\t%lu\t%s\t%c\t%d\t",
                         ppt_rng.start,
                         ppt_rng.end,
                         ppt_seq,
                         GT_STRAND_CHARS[ppt_strand],
                         (ppt_strand == GT_STRAND_FORWARD ?
                             abs((int) (rltr_rng.start - ppt_rng.end)) :
                             abs((int) (lltr_rng.end - ppt_rng.start))));
      gt_free((char*) ppt_seq);
    } else gt_file_xprintf(ls->tabout_file, "\t\t\t\t\t");

    /* output PBS */
    if (ls->element.pbs != NULL)
    {
      GtStrand pbs_strand;

      pbs_strand = gt_feature_node_get_strand(ls->element.pbs);
      pbs_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.pbs);
      pbs_seq = gt_ltrelement_get_sequence(pbs_rng.start-1, pbs_rng.end-1,
                                           pbs_strand, ls->encseq, seqstartpos,
                                           err);
      gt_fasta_show_entry(desc, pbs_seq, gt_range_length(&pbs_rng),
                          GT_FSWIDTH, ls->pbsout_file);
      gt_file_xprintf(ls->tabout_file,
                         "%lu\t%lu\t%c\t%s\t%s\t%s\t%s\t%s\t",
                         pbs_rng.start,
                         pbs_rng.end,
                         GT_STRAND_CHARS[pbs_strand],
                      gt_feature_node_get_attribute(ls->element.pbs, "trna"),
                      pbs_seq,
                      gt_feature_node_get_attribute(ls->element.pbs,
                                                    "pbsoffset"),
                      gt_feature_node_get_attribute(ls->element.pbs,
                                                    "trnaoffset"),
                      gt_feature_node_get_attribute(ls->element.pbs, "edist"));
      gt_free((char*) pbs_seq);
    } else gt_file_xprintf(ls->tabout_file, "\t\t\t\t\t\t\t\t");

    /* output protein domains */
    if (ls->element.pdoms != NULL)
    {
      GtStr *pdomorderstr = gt_str_new();
      for (i=0;ielement.pdomorder);i++)
      {
        const char* key = *(const char**) gt_array_get(ls->element.pdomorder,
                                                       i);
        GtArray *entry = (GtArray*) gt_hashmap_get(ls->element.pdoms, key);
        (void) write_pdom(ls, entry, key, ls->encseq, seqstartpos, desc, err);
      }

      if (GT_STRAND_REVERSE == gt_feature_node_get_strand(ls->element.mainnode))
        gt_array_reverse(ls->element.pdomorder);

      for (i=0;ielement.pdomorder);i++)
      {
        const char* name = *(const char**) gt_array_get(ls->element.pdomorder,
                                                        i);
        gt_str_append_cstr(pdomorderstr, name);
        if (i != gt_array_size(ls->element.pdomorder)-1)
          gt_str_append_cstr(pdomorderstr, "/");
      }
      gt_file_xprintf(ls->tabout_file, "%s", gt_str_get(pdomorderstr));
      gt_str_delete(pdomorderstr);
    }

    /* output LTRs (we just expect them to exist) */
    switch (gt_feature_node_get_strand(ls->element.mainnode))
    {
      case GT_STRAND_REVERSE:
        ltr5_rng = rltr_rng;
        ltr3_rng = lltr_rng;
        break;
      case GT_STRAND_FORWARD:
      default:
        ltr5_rng = lltr_rng;
        ltr3_rng = rltr_rng;
        break;
    }
    outseq = gt_ltrelement_get_sequence(ltr5_rng.start-1,
                              ltr5_rng.end-1,
                              gt_feature_node_get_strand(ls->element.mainnode),
                              ls->encseq, seqstartpos, err);
    gt_fasta_show_entry(desc,
                        outseq,
                        gt_range_length(<r5_rng),
                        GT_FSWIDTH,
                        ls->ltr5out_file);
    gt_free(outseq);
    outseq = gt_ltrelement_get_sequence(rng.start-1,
                              rng.end-1,
                              gt_feature_node_get_strand(ls->element.mainnode),
                              ls->encseq, seqstartpos, err);
    gt_fasta_show_entry(desc,
                        outseq,
                        gt_range_length(&rng),
                        GT_FSWIDTH,
                        ls->elemout_file);
    gt_free(outseq);

    /* output complete oriented element */
    outseq = gt_ltrelement_get_sequence(ltr3_rng.start-1,
                              ltr3_rng.end-1,
                              gt_feature_node_get_strand(ls->element.mainnode),
                              ls->encseq, seqstartpos, err);
    gt_fasta_show_entry(desc,
                        outseq,
                        gt_range_length(<r3_rng),
                        GT_FSWIDTH,
                        ls->ltr3out_file);
    gt_free(outseq);
    gt_file_xprintf(ls->tabout_file, "\n");
  }
  gt_hashmap_delete(ls->element.pdoms);
  gt_array_delete(ls->element.pdomorder);
  gt_free(ls->element.seqid);
  return had_err;
}

static void write_metadata(GtFile *metadata_file,
                           int tests_to_run,
                           GtPPTOptions *ppt_opts,
                           GtPBSOptions *pbs_opts,
#ifdef HAVE_HMMER
                           GtPdomOptions *pdom_opts,
#endif
                           const char *trnafilename,
                           const char *seqfilename,
                           const char *gfffilename)
{
  int buflen = 1024;
  char *buffer;

  buffer = gt_calloc((size_t) (buflen+1), sizeof (char));
  /* get working directory */
  while (getcwd(buffer, (size_t) buflen) == NULL) {
    buflen += 1024;
    buffer = gt_realloc(buffer, (buflen+1) * sizeof (char));
  }
  gt_assert(buffer && strlen(buffer) > 0);

  /* append working dir to relative paths if necessary */
  if (seqfilename[0] != '/')
    gt_file_xprintf(metadata_file,
                       "Sequence file used\t%s/%s\n", buffer, seqfilename);
  else
    gt_file_xprintf(metadata_file,
                       "Sequence file used\t%s\n", seqfilename);
  if (gfffilename[0] != '/')
    gt_file_xprintf(metadata_file,
                       "GFF3 input used\t%s/%s\n", buffer, gfffilename);
  else
    gt_file_xprintf(metadata_file,
                       "GFF3 input used\t%s\n", gfffilename);

  if (tests_to_run & GT_LTRDIGEST_RUN_PPT)
  {
    gt_file_xprintf(metadata_file,
                       "PPT length\t%lu-%lunt\t8-30nt\n",
                       ppt_opts->ppt_len.start,
                       ppt_opts->ppt_len.end);
    gt_file_xprintf(metadata_file,
                       "U-box length\t%lu-%lunt\t3-30nt\n",
                       ppt_opts->ubox_len.start,
                       ppt_opts->ubox_len.end);
    gt_file_xprintf(metadata_file,
                       "PPT search radius\t%u\t30\n", ppt_opts->radius);
  }

  if (tests_to_run & GT_LTRDIGEST_RUN_PBS)
  {
    if (trnafilename[0] != '/')
      gt_file_xprintf(metadata_file,
                         "tRNA library for PBS detection\t%s/%s\n",
                         buffer, trnafilename);
    else
      gt_file_xprintf(metadata_file,
                         "tRNA library for PBS detection\t%s\n",
                         trnafilename);
    gt_file_xprintf(metadata_file,
                       "allowed PBS/tRNA alignment length"
                       " range\t%lu-%lunt\t11-30nt\n",
                       pbs_opts->alilen.start,
                       pbs_opts->alilen.end);
    gt_file_xprintf(metadata_file,
                       "PBS/tRNA maximum unit edit distance\t%u\t1\n",
                       pbs_opts->max_edist);
    gt_file_xprintf(metadata_file,
                       "allowed PBS offset from 5' LTR range"
                       "\t%lu-%lunt\t0-5nt\n",
                       pbs_opts->offsetlen.start,
                       pbs_opts->offsetlen.end);
    gt_file_xprintf(metadata_file,
                       "allowed PBS offset from 3' tRNA end"
                       " range\t%lu-%lunt\t0-5nt\n",
                       pbs_opts->trnaoffsetlen.start,
                       pbs_opts->trnaoffsetlen.end);
    gt_file_xprintf(metadata_file,
                       "PBS search radius\t%d\t30\n", pbs_opts->radius);
  }

#ifdef HAVE_HMMER
  if (tests_to_run & GT_LTRDIGEST_RUN_PDOM)
  {
    unsigned long i;
    gt_file_xprintf(metadata_file,
                       "Protein domain models\t%lu (",
                       gt_str_array_size(pdom_opts->hmm_files));
    for (i=0;ihmm_files);i++)
    {
      gt_file_xprintf(metadata_file, "%s",
                         gt_str_array_get(pdom_opts->hmm_files, i));
      if (i != gt_str_array_size(pdom_opts->hmm_files)-1)
        gt_file_xprintf(metadata_file, ", ");
    }
    gt_file_xprintf(metadata_file, ")\n");
    gt_file_xprintf(metadata_file,
                       "pHMM e-value cutoff \t%g\t%g\n",
                       pdom_opts->evalue_cutoff,
                       0.000001);
    gt_file_xprintf(metadata_file,
                       "maximal allowed gap length between fragments to chain"
                       " \t%u\t%u\n",
                       pdom_opts->chain_max_gap_length,
                       50);
  }
#endif
  gt_file_xprintf(metadata_file, "\n");
  gt_free(buffer);
}

void gt_ltrfileout_stream_free(GtNodeStream *ns)
{
  GtLTRFileOutStream *ls = gt_ltr_fileout_stream_cast(ns);
  if (ls->tabout_file != NULL)
    gt_file_delete(ls->tabout_file);
  if (ls->metadata_file != NULL)
    gt_file_delete(ls->metadata_file);
  if (ls->pbsout_file != NULL)
    gt_file_delete(ls->pbsout_file);
  if (ls->pptout_file != NULL)
    gt_file_delete(ls->pptout_file);
  if (ls->ltr5out_file != NULL)
    gt_file_delete(ls->ltr5out_file);
  if (ls->ltr3out_file != NULL)
    gt_file_delete(ls->ltr3out_file);
  if (ls->elemout_file != NULL)
    gt_file_delete(ls->elemout_file);
  gt_hashmap_delete(ls->pdomout_files);
  gt_hashmap_delete(ls->pdomali_files);
  gt_hashmap_delete(ls->pdomaa_files);
  gt_node_visitor_delete((GtNodeVisitor*) ls->lv);
  gt_node_stream_delete(ls->in_stream);
}

const GtNodeStreamClass* gt_ltr_fileout_stream_class(void)
{
  static const GtNodeStreamClass *nsc;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof (GtLTRFileOutStream),
                                   gt_ltrfileout_stream_free,
                                   gt_ltrfileout_stream_next );
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

void gt_ltr_fileout_stream_enable_pdom_alignment_output(GtNodeStream *ns)
{
  GtLTRFileOutStream *ls;
  gt_assert(ns);

  ls = gt_ltr_fileout_stream_cast(ns);
  ls->write_pdom_alignments = true;
}

void gt_ltr_fileout_stream_enable_aa_sequence_output(GtNodeStream *ns)
{
  GtLTRFileOutStream *ls;
  gt_assert(ns);

  ls = gt_ltr_fileout_stream_cast(ns);
  ls->write_pdom_aaseqs = true;
}

GtNodeStream* gt_ltr_fileout_stream_new(GtNodeStream *in_stream,
                                     int tests_to_run,
                                     GtEncseq *encseq,
                                     char *file_prefix,
                                     GtPPTOptions *ppt_opts,
                                     GtPBSOptions *pbs_opts,
#ifdef HAVE_HMMER
                                     GtPdomOptions *pdom_opts,
#endif
                                     const char *trnafilename,
                                     const char *seqfilename,
                                     const char *gfffilename,
                                     unsigned int seqnamelen,
                                     GtError* err)
{
  GtNodeStream *ns;
  GtLTRFileOutStream *ls;
  char fn[GT_MAXFILENAMELEN];
  gt_error_check(err);

  gt_assert(file_prefix && in_stream && encseq && ppt_opts && pbs_opts
#ifdef HAVE_HMMER
    && pdom_opts
#endif
    );

  ns = gt_node_stream_create(gt_ltr_fileout_stream_class(), true);
  ls = gt_ltr_fileout_stream_cast(ns);

  /* ref GFF input stream and sequences*/
  ls->in_stream = gt_node_stream_ref(in_stream);
  ls->encseq = encseq;
  ls->tests_to_run = tests_to_run;
  ls->seqnamelen = seqnamelen;
  ls->write_pdom_alignments = false;
  ls->write_pdom_aaseqs = false;

  /* open outfiles */
  ls->fileprefix = file_prefix;
  (void) snprintf(fn, (size_t) (GT_MAXFILENAMELEN-1),
                  "%s_tabout.csv", file_prefix);
  ls->tabout_file = gt_file_open(GT_FILE_MODE_UNCOMPRESSED, fn, "w+", err);
  if (tests_to_run & GT_LTRDIGEST_RUN_PPT)
  {
    (void) snprintf(fn, (size_t) (GT_MAXFILENAMELEN-1),
                    "%s_ppt.fas", file_prefix);
    ls->pptout_file = gt_file_open(GT_FILE_MODE_UNCOMPRESSED, fn, "w+", err);
  }
  if (tests_to_run & GT_LTRDIGEST_RUN_PBS)
  {
    (void) snprintf(fn, (size_t) (GT_MAXFILENAMELEN-1),
                    "%s_pbs.fas", file_prefix);
    ls->pbsout_file = gt_file_open(GT_FILE_MODE_UNCOMPRESSED, fn, "w+", err);
  }
  (void) snprintf(fn, (size_t) (GT_MAXFILENAMELEN-1),
                   "%s_5ltr.fas", file_prefix);
  ls->ltr5out_file = gt_file_open(GT_FILE_MODE_UNCOMPRESSED, fn, "w+", err);
  (void) snprintf(fn, (size_t) (GT_MAXFILENAMELEN-1),
                  "%s_3ltr.fas", file_prefix);
  ls->ltr3out_file = gt_file_open(GT_FILE_MODE_UNCOMPRESSED, fn, "w+", err);
  (void) snprintf(fn, (size_t) (GT_MAXFILENAMELEN-1),
                  "%s_complete.fas", file_prefix);
  ls->elemout_file = gt_file_open(GT_FILE_MODE_UNCOMPRESSED, fn, "w+", err);
  (void) snprintf(fn, (size_t) (GT_MAXFILENAMELEN-1),
                  "%s_conditions.csv", file_prefix);
  ls->metadata_file = gt_file_open(GT_FILE_MODE_UNCOMPRESSED, fn, "w+", err);

  /* create hashmaps to hold protein domain output files */
  ls->pdomout_files = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
                                     (GtFree) gt_file_delete);
  ls->pdomali_files = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
                                     (GtFree) gt_file_delete);
  ls->pdomaa_files  = gt_hashmap_new(GT_HASH_STRING, gt_free_func,
                                     (GtFree) gt_file_delete);

  /* log run conditions in file */
  write_metadata(ls->metadata_file,
                 tests_to_run,
                 ppt_opts,
                 pbs_opts,
#ifdef HAVE_HMMER
                 pdom_opts,
#endif
                 trnafilename,
                 seqfilename,
                 gfffilename);

  /* print tabular outfile headline */
  gt_file_xprintf(ls->tabout_file,
              "element start\telement end\telement length\tsequence\t"
              "lLTR start\tlLTR end\tlLTR length\t"
              "rLTR start\trLTR end\trLTR length\t"
              "lTSD start\tlTSD end\tlTSD motif\t"
              "rTSD start\trTSD end\trTSD motif\t"
              "PPT start\tPPT end\tPPT motif\tPPT strand\tPPT offset");
  gt_file_xprintf(ls->tabout_file,
              "\tPBS start\tPBS end\tPBS strand\ttRNA\ttRNA motif\tPBS offset\t"
              "tRNA offset\tPBS/tRNA edist");
#ifdef HAVE_HMMER
  gt_file_xprintf(ls->tabout_file, "\tProtein domain hits");
#endif
  gt_file_xprintf(ls->tabout_file, "\n");

  /* create visitor */
  ls->lv = (GtLTRVisitor*) gt_ltr_visitor_new(&ls->element);
  return ns;
}
genometools-1.5.1/src/ltr/ltrfileout_stream.h000066400000000000000000000041521211610345200213530ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Sascha Steinbiss 
  Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTRFILEOUT_STREAM_H
#define LTRFILEOUT_STREAM_H

#include "core/bioseq.h"
#include "extended/node_stream_api.h"
#include "ltr/ltrdigest_def.h"
#include "core/encseq.h"

/* implements the ``node_stream'' interface */
typedef struct GtLTRFileOutStream GtLTRFileOutStream;

const GtNodeStreamClass* gt_ltr_fileout_stream_class(void);

GtNodeStream* gt_ltr_fileout_stream_new(GtNodeStream *in_stream,
                                        int tests_to_run,
                                        GtEncseq *encseq,
                                        char *file_prefix,
                                        GtPPTOptions *ppt_opts,
                                        GtPBSOptions *pbs_opts,
#ifdef HAVE_HMMER
                                        GtPdomOptions *pdom_opts,
#endif
                                        const char *trnafilename,
                                        const char *seqfilename,
                                        const char *gfffilename,
                                        unsigned int seqnamelen,
                                        GtError *err);

void          gt_ltr_fileout_stream_enable_pdom_alignment_output(GtNodeStream*);
void          gt_ltr_fileout_stream_enable_aa_sequence_output(GtNodeStream*);

#endif
genometools-1.5.1/src/ltr/ltrharvest_fasta_out_stream.c000066400000000000000000000030521211610345200234160ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/assert_api.h"
#include "core/unused_api.h"
#include "extended/node_visitor_api.h"
#include "extended/visitor_stream_api.h"
#include "ltr/ltrharvest_fasta_out_stream.h"
#include "ltr/ltrharvest_fasta_out_visitor.h"

GtNodeStream* gt_ltrharvest_fasta_out_stream_new(GtNodeStream *in_stream,
                                                 bool inner,
                                                 const GtEncseq *encseq,
                                                 unsigned long width,
                                                 GtFile *outfp)
{
  GtNodeVisitor *nv;
  nv = gt_ltrharvest_fasta_out_visitor_new(encseq, inner, width, outfp);
  return gt_visitor_stream_new(in_stream, nv);
}
genometools-1.5.1/src/ltr/ltrharvest_fasta_out_stream.h000066400000000000000000000025001211610345200234200ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTRHARVEST_FASTA_OUT_STREAM_H
#define LTRHARVEST_FASTA_OUT_STREAM_H

#include 
#include "core/encseq_api.h"
#include "core/file_api.h"
#include "extended/node_stream_api.h"

GtNodeStream* gt_ltrharvest_fasta_out_stream_new(GtNodeStream*, bool inner,
                                                 const GtEncseq *encseq,
                                                 unsigned long width,
                                                 GtFile *outfp);

#endif
genometools-1.5.1/src/ltr/ltrharvest_fasta_out_visitor.c000066400000000000000000000152301211610345200236230ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/array_api.h"
#include "core/class_alloc_lock.h"
#include "core/cstr_api.h"
#include "core/encseq_api.h"
#include "core/fasta.h"
#include "core/ma.h"
#include "core/parseutils.h"
#include "core/range.h"
#include "core/str_api.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/warning_api.h"
#include "extended/node_visitor_api.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "extended/feature_type.h"
#include "ltr/ltrharvest_fasta_out_visitor.h"

struct GtLTRharvestFastaOutVisitor {
  const GtNodeVisitor parent_instance;
  GtFile* outfp;
  unsigned long width;
  bool inner;
  const GtEncseq *encseq;
};

#define gt_ltrharvest_fasta_out_visitor_cast(GV)\
        gt_node_visitor_cast(gt_ltrharvest_fasta_out_visitor_class(), GV)

static int gt_ltrharvest_fasta_out_visitor_feature_node(GtNodeVisitor *nv,
                                                        GtFeatureNode *fn,
                                                        GT_UNUSED GtError *err)
{
  GtLTRharvestFastaOutVisitor *lv;
  GtFeatureNodeIterator *fni;
  GtFeatureNode *curnode = NULL,
                *leftltr = NULL,
                *rightltr = NULL,
                *ltr_retrotrans = NULL;
  int had_err = 0,
      added_ltr = 0;
  GtRange rng,
          outrng;
  unsigned long seqnum = GT_UNDEF_ULONG;
  const char *fnt;
  lv = gt_ltrharvest_fasta_out_visitor_cast(nv);
  gt_assert(lv);
  gt_error_check(err);

  /* traverse annotation subgraph and collect info */
  fni = gt_feature_node_iterator_new(fn);
  while (!had_err && (curnode = gt_feature_node_iterator_next(fni))) {
    fnt = gt_feature_node_get_type(curnode);

    if (strcmp(fnt, gt_ft_LTR_retrotransposon) == 0)
    {
      const char *val;
      ltr_retrotrans = curnode;
      val = gt_feature_node_get_attribute(curnode, "seq_number");
      if (val == NULL) {
        gt_error_set(err, "missing attribute \"seq_number\"");
        had_err = -1;
      }
      if (!had_err) {
        (void) gt_parse_ulong(&seqnum, val);
      }
    }
    if (strcmp(fnt, gt_ft_long_terminal_repeat) == 0)
    {
      switch (added_ltr) {
        case 0:
          leftltr = curnode;
          break;
        case 1:
          rightltr = curnode;
          break;
        default:
          gt_error_set(err,
                       "invalid number of LTR annotations: more than 2");
          had_err = -1;
      }
      added_ltr++;
    }
  }
  gt_feature_node_iterator_delete(fni);

  /* check for invalid annotations */
  if (!had_err && (!leftltr || !rightltr)) {
    gt_error_set(err, "missing LTR annotations");
    had_err = -1;
  }

  /* determine sequence interval to output */
  if (lv->inner) {
    gt_assert(leftltr && rightltr);
    rng = gt_genome_node_get_range((GtGenomeNode*) leftltr);
    outrng.start = rng.end + 1;
    rng = gt_genome_node_get_range((GtGenomeNode*) rightltr);
    outrng.end = rng.start - 1;
  } else {
    gt_assert(ltr_retrotrans);
    rng = gt_genome_node_get_range((GtGenomeNode*) ltr_retrotrans);
    outrng = rng;
  }

  /* output FASTA sequences */
  if (!had_err && ltr_retrotrans != NULL) {
    if (outrng.start < outrng.end) {
      char *buf;
      const char *seqdesc;
      GtStr *desc;
      unsigned long startpos,
                    seqdesclen;
      gt_assert(seqnum != GT_UNDEF_ULONG
                  && seqnum < gt_encseq_num_of_sequences(lv->encseq));
      seqdesc = gt_encseq_description(lv->encseq, &seqdesclen, seqnum);
      desc = gt_str_new();
      gt_str_append_cstr_nt(desc, seqdesc, seqdesclen);
      gt_str_append_cstr(desc, " (dbseq-nr ");
      gt_str_append_ulong(desc, seqnum);
      gt_str_append_cstr(desc, ") [");
      gt_str_append_ulong(desc, outrng.start);
      gt_str_append_cstr(desc, ",");
      gt_str_append_ulong(desc, outrng.end);
      gt_str_append_cstr(desc, "]");
      buf = gt_calloc((size_t) gt_range_length(&outrng) + 1, sizeof (char));
      startpos = gt_encseq_seqstartpos(lv->encseq, seqnum);
      gt_encseq_extract_decoded(lv->encseq, buf,
                                startpos + outrng.start - 1,
                                startpos + outrng.end - 1);
      gt_fasta_show_entry(gt_str_get(desc), buf, gt_range_length(&outrng),
                          lv->width, lv->outfp);
      gt_free(buf);
      gt_str_delete(desc);
    } else {
      GtRange rootrng;
      rootrng = gt_genome_node_get_range((GtGenomeNode*) ltr_retrotrans);
      gt_warning("trying to output empty%s sequence for candidate at "
                 "%lu-%lu on sequence %lu",
                 (lv->inner ? " inner" : ""),
                 rootrng.start,
                 rootrng.end,
                 seqnum);
    }
  }

  return had_err;
}

const GtNodeVisitorClass* gt_ltrharvest_fasta_out_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  gt_class_alloc_lock_enter();
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRharvestFastaOutVisitor),
                                   NULL,
                                   NULL,
                                   gt_ltrharvest_fasta_out_visitor_feature_node,
                                   NULL,
                                   NULL,
                                   NULL);
  }
  gt_class_alloc_lock_leave();
  return nvc;
}

GtNodeVisitor* gt_ltrharvest_fasta_out_visitor_new(const GtEncseq *encseq,
                                                   bool inner,
                                                   unsigned long width,
                                                   GtFile *outfp)
{
  GtNodeVisitor *nv;
  GtLTRharvestFastaOutVisitor *lv;
  gt_assert(encseq && outfp);
  nv = gt_node_visitor_create(gt_ltrharvest_fasta_out_visitor_class());
  lv = gt_ltrharvest_fasta_out_visitor_cast(nv);
  gt_assert(lv);
  lv->inner = inner;
  lv->outfp = outfp;
  lv->width = width;
  lv->encseq = encseq;
  return nv;
}
genometools-1.5.1/src/ltr/ltrharvest_fasta_out_visitor.h000066400000000000000000000031171211610345200236310ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTRHARVEST_FASTA_OUT_VISITOR_H
#define LTRHARVEST_FASTA_OUT_VISITOR_H

#include "core/encseq_api.h"
#include "core/file.h"
#include "extended/node_visitor.h"

/* Implements the  interface. */
typedef struct GtLTRharvestFastaOutVisitor GtLTRharvestFastaOutVisitor;

const GtNodeVisitorClass* gt_ltrharvest_fasta_out_visitor_class(void);
GtNodeVisitor*            gt_ltrharvest_fasta_out_visitor_new(const GtEncseq
                                                                        *encseq,
                                                            bool inner,
                                                            unsigned long width,
                                                            GtFile *outfp);

#endif
genometools-1.5.1/src/ltr/ltrharvest_stream.c000066400000000000000000001655361211610345200213710ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Sascha Steinbiss 
  Copyright (c) 2007      David Ellinghaus 
  Copyright (c) 2007-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include "core/array_api.h"
#include "core/arraydef.h"
#include "core/assert_api.h"
#include "core/class_alloc_lock.h"
#include "core/encseq_api.h"
#include "core/error_api.h"
#include "core/log.h"
#include "core/mathsupport.h"
#include "core/minmax.h"
#include "core/str_api.h"
#include "core/types_api.h"
#include "core/undef_api.h"
#include "extended/feature_type.h"
#include "extended/genome_node.h"
#include "extended/node_stream_api.h"
#include "match/esa-seqread.h"
#include "match/esa-maxpairs.h"
#include "match/esa-mmsearch.h"
#include "match/greedyedist.h"
#include "match/xdrop.h"
#include "ltr/ltrharvest_stream.h"

#define GT_LTRHARVEST_NAME "LTRharvest"

typedef struct
{
  unsigned long pos1,         /* first position of maximal repeat (seed) */
                offset,       /* second position = pos1 + offset */
                len,          /* length of maximal repeat  */
                contignumber; /* number of contig for this repeat */
} Repeat;

GT_DECLAREARRAYSTRUCT(Repeat);

/* The datatype RepeatInfo stores all maximal repeats (seeds) and */
/* information about the length and distance constraints. */
typedef struct
{
  GtArrayRepeat repeats; /* array of maximal repeats (seeds) */
  unsigned long lmin,        /* minimum allowed length of a LTR */
                lmax,        /* maximum allowed length of a LTR */
                dmin,        /* minimum distance between LTRs */
                dmax;        /* maximum distance between LTRs,
                                this values is determined as the minimum
                                of the corresponding option value and the
                                maximum length of any sequence in the encseq */
  GtRange ltrsearchseqrange; /* if start and end are 0, then no range */
} RepeatInfo;

/* The datatype SubRepeatInfo stores information about the maximal repeats */
/* for the TSD detection. */
typedef struct
{
  GtArrayRepeat repeats; /* array of maximal repeats for TSDs */
  unsigned long tsd_lmin,    /* minimal length of TSD */
                tsd_lmax,    /* maximal length of TSD */
                offset1, /* offset1 for absolute position 1 in sequence */
                offset2; /* offset2 for absolute position 2 in sequence */
                         /* pos1 < pos2 */
} SubRepeatInfo;

typedef struct
{
  unsigned long contignumber,   /* ordinal number of sequence in encseq */
                leftLTR_5,      /* 5' boundary of left LTR */
                leftLTR_3,      /* 3' boundary of left LTR */
                rightLTR_5,     /* 5' boundary of right LTR */
                rightLTR_3,     /* 3' boundary of right LTR */
                lenleftTSD,
                lenrightTSD;
  bool          tsd,            /* If true, then TSDs exist. */
                motif_near_tsd, /* If true, then motif near the TSD exists. */
                motif_far_tsd,  /* If true, then motif at the inner borders
                                   of LTRs exist. */
                lengthdistconstraint, /* If true, length and distance
                                         constraints are satisfied */
                skipped; /* if skipped then because of an overlap
                            with a higher similarity prediction or
                            because of "overlap=no" option */
  double similarity;     /* similarity value of LTRs */
} LTRboundaries;

GT_DECLAREARRAYSTRUCT(LTRboundaries);

typedef enum {
  GT_LTRHARVEST_STREAM_STATE_START,
  GT_LTRHARVEST_STREAM_STATE_REGIONS,
  GT_LTRHARVEST_STREAM_STATE_COMMENTS,
  GT_LTRHARVEST_STREAM_STATE_FEATURES
} GtLTRharvestStreamState;

struct GtLTRharvestStream
{
  const GtNodeStream parent_instance;
  RepeatInfo repeatinfo;
  GtStr *str_indexname;
  unsigned long minseedlength;
  double similaritythreshold;
  int xdropbelowscore;
  GtXdropArbitraryscores arbitscores;
  unsigned int allowedmismatches;
  GtLTRFourCharMotif *motif;
  unsigned long offset;
  unsigned int minlengthTSD,
               maxlengthTSD;
  unsigned long numofboundaries;
  unsigned long vicinityforcorrectboundaries;
  unsigned long prevseqnum;
  const LTRboundaries **bdptrtab;
  GtArrayLTRboundaries arrayLTRboundaries;
  const GtEncseq *encseq;
  Sequentialsuffixarrayreader *ssar;
  bool verbosemode;
  bool nooverlaps;
  bool bestoverlaps;
  unsigned long cur_elem_index;
  GtLTRharvestStreamState state;
};

#define gt_ltrharvest_stream_cast(GS)\
        gt_node_stream_cast(gt_ltrharvest_stream_class(), GS);

static int bdptrcompare(const void *a, const void *b)
{
  const LTRboundaries **bda, **bdb;

  bda = (const LTRboundaries **) a;
  bdb = (const LTRboundaries **) b;
  if ((*bda)->contignumber < (*bdb)->contignumber)
  {
    return -1;
  }
  if ((*bda)->contignumber > (*bdb)->contignumber)
  {
    return 1;
  }
  if ((*bda)->leftLTR_5 < (*bdb)->leftLTR_5)
  {
    return -1;
  }
  if ((*bda)->leftLTR_5 > (*bdb)->leftLTR_5)
  {
    return 1;
  }
  return 0;
}

static int gt_simpleexactselfmatchstore(void *info,
                                        const GtEncseq *encseq,
                                        unsigned long len,
                                        unsigned long pos1,
                                        unsigned long pos2,
                                        GT_UNUSED GtError *err)
{
  unsigned long distance;
  RepeatInfo *repeatinfo = (RepeatInfo *) info;

  gt_error_check(err);
  if (pos1 > pos2)
  {
    unsigned long tmp = pos1;
    pos1 = pos2;
    pos2 = tmp;
  }
  if (repeatinfo->ltrsearchseqrange.start > 0 ||
      repeatinfo->ltrsearchseqrange.end > 0)
  {
    if (pos1 < repeatinfo->ltrsearchseqrange.start  ||
        pos2 + len - 1 > repeatinfo->ltrsearchseqrange.end)
    {
      return 0;
    }
  }
  distance = pos2 - pos1;
  /*test maximal length of candidate pair and distance constraints*/
  if (len <= repeatinfo->lmax && repeatinfo->dmin <= distance
                              && distance <= repeatinfo->dmax)
  {
    const unsigned long seqnum1 = gt_encseq_seqnum(encseq,pos1);
    const unsigned long seqnum2 = gt_encseq_seqnum(encseq,pos2);

    if (seqnum1 == seqnum2)
    {
      Repeat *nextfreerepeatptr;

      GT_GETNEXTFREEINARRAY(nextfreerepeatptr,&repeatinfo->repeats,Repeat,32);
      nextfreerepeatptr->pos1 = pos1;
      nextfreerepeatptr->offset = distance;
      nextfreerepeatptr->len = len;
      nextfreerepeatptr->contignumber = seqnum1;
    }
  }
  return 0;
}

static int gt_subsimpleexactselfmatchstore(void *info,
                                            GT_UNUSED const GtEncseq *encseq,
                                            const GtQuerymatch *querymatch,
                                            GT_UNUSED const GtUchar *query,
                                            GT_UNUSED unsigned long
                                              query_totallength,
                                            GT_UNUSED GtError *err)
{
  Repeat *nextfreerepeatptr;
  SubRepeatInfo *sri = (SubRepeatInfo *) info;

  GT_GETNEXTFREEINARRAY (nextfreerepeatptr, &sri->repeats, Repeat, 10);
  nextfreerepeatptr->pos1 = sri->offset1 + gt_querymatch_dbstart(querymatch);
  nextfreerepeatptr->offset = sri->offset2 +
                              gt_querymatch_querystart(querymatch) -
                              (sri->offset1 +
                               gt_querymatch_dbstart(querymatch));
  nextfreerepeatptr->len = gt_querymatch_querylen(querymatch);
  return 0;
}

/* XXX: better directly sort the ArrayLTRboundaries */
static const LTRboundaries **sortedltrboundaries(unsigned long *numofboundaries,
                                                 const GtArrayLTRboundaries
                                                 *ltr)
{
  unsigned long countboundaries = 0, nextfill = 0;
  const LTRboundaries *bd, **bdptrtab;

  for (bd = ltr->spaceLTRboundaries; bd < ltr->spaceLTRboundaries +
                                          ltr->nextfreeLTRboundaries; bd++)
  {
    if (!bd->skipped)
    {
      countboundaries++;
    }
  }
  bdptrtab = gt_malloc(sizeof (LTRboundaries *) * countboundaries);
  nextfill = 0;
  for (bd = ltr->spaceLTRboundaries; bd < ltr->spaceLTRboundaries +
                                          ltr->nextfreeLTRboundaries; bd++)
  {
    if (!bd->skipped)
    {
      bdptrtab[nextfill++] = bd;
    }
  }
  qsort(bdptrtab,(size_t) countboundaries, sizeof (LTRboundaries *),
        bdptrcompare);
  *numofboundaries = countboundaries;
  return bdptrtab;
}

typedef struct
{
  unsigned int left, right;
} LTRMotifmismatches;

/*
 The following function searches for TSDs and/or a specified palindromic
 motif at the 5'-border of left LTR and 3'-border of right LTR. Thereby,
 all maximal repeats from the vicinity are processed one after another
 to find the TSD with the minimum deviation with regard to the boundary
 position from the x-drop alignment. If also a motif is searched,
 a simple motif check at the boundaries of the TSDs is performed.
 */

static void searchforbestTSDandormotifatborders(const SubRepeatInfo
                                                   *subrepeatinfo,
                                                const GtLTRharvestStream *lo,
                                                LTRboundaries *boundaries,
                                                LTRMotifmismatches *mismatches)
{
  unsigned long motifpos1,
                motifpos2,
                back, forward,
                oldleftLTR_5  = boundaries->leftLTR_5,
                oldrightLTR_3 = boundaries->rightLTR_3,
                difffromoldboundary1 = 0,
                difffromoldboundary2 = 0;
  LTRMotifmismatches tmp_mm;
  unsigned int hitcounter = 0;
  Repeat *rep;

  if (subrepeatinfo->repeats.nextfreeRepeat > 0)
  {
    boundaries->tsd = true;
  }
  boundaries->motif_near_tsd = false;

  for (rep = subrepeatinfo->repeats.spaceRepeat;
       rep < subrepeatinfo->repeats.spaceRepeat +
             subrepeatinfo->repeats.nextfreeRepeat; rep++)
  {
    /* motifpos1 is the first position after the left repeat */
    motifpos1 = rep->pos1 + rep->len;
    /* motifpos2 is two positions before the right repeat */
    motifpos2 = rep->pos1 + rep->offset - 2;

    for (back = 0; back < rep->len - subrepeatinfo->tsd_lmin + 1; back++)
    {
      for (forward = 0;
           forward < rep->len - subrepeatinfo->tsd_lmin + 1 - back;
           forward++)
      {
        tmp_mm.left = tmp_mm.right = 0;
        if (gt_encseq_get_encoded_char(/* Random access */ lo->encseq,
                                       motifpos1 - back, GT_READMODE_FORWARD)
            != lo->motif->firstleft)
        {
          tmp_mm.left++;
        }
        if (gt_encseq_get_encoded_char(/* Random access */ lo->encseq,
                                              motifpos1 + 1 - back,
                                              GT_READMODE_FORWARD)
            != lo->motif->secondleft)
        {
          tmp_mm.left++;
        }
        if (gt_encseq_get_encoded_char(/* Random access */ lo->encseq,
                                              motifpos2 + forward,
                                              GT_READMODE_FORWARD)
            != lo->motif->firstright)
        {
          tmp_mm.right++;
        }
        if (gt_encseq_get_encoded_char(/* Random access */ lo->encseq,
                                              motifpos2 + 1 + forward,
                                              GT_READMODE_FORWARD)
            != lo->motif->secondright)
        {
          tmp_mm.right++;
        }

        if (tmp_mm.left <= lo->motif->allowedmismatches
            && tmp_mm.right <= lo->motif->allowedmismatches)
        {
          const unsigned long tsd_len = rep->len - back - forward;

          /* TSD length not too big */
          if (tsd_len <= subrepeatinfo->tsd_lmax)
          {
            if (!boundaries->motif_near_tsd)
            {
              unsigned long max, min;

              /* save number of mismatches */
              *mismatches = tmp_mm;

              /* adjust boundaries */
              boundaries->motif_near_tsd = true;
              boundaries->leftLTR_5  = motifpos1 - back;
              boundaries->rightLTR_3 = motifpos2 + 1 + forward;

              /* store TSD length */
              boundaries->lenleftTSD = boundaries->lenrightTSD = tsd_len;

              max = MAX(oldleftLTR_5, boundaries->leftLTR_5);
              min = MIN(oldleftLTR_5, boundaries->leftLTR_5);
              difffromoldboundary1 = max - min;

              max = MAX(oldrightLTR_3, boundaries->rightLTR_3);
              min = MIN(oldrightLTR_3, boundaries->rightLTR_3);
              difffromoldboundary2 = max - min;

              hitcounter++;
            } else
            {
              unsigned long max, min, difffromnewboundary1,
                   difffromnewboundary2;

              /* test if hit is nearer to old boundaries than previous hit */
              max = MAX(oldleftLTR_5, motifpos1 - back);
              min = MIN(oldleftLTR_5, motifpos1 - back);
              difffromnewboundary1 = max - min;
              max = MAX(oldrightLTR_3, motifpos2 + 1 + forward);
              min = MIN(oldrightLTR_3, motifpos2 + 1 + forward);
              difffromnewboundary2 = max - min;

              if (difffromnewboundary1 + difffromnewboundary2 <
                  difffromoldboundary1 + difffromoldboundary2)
              {
                /* save number of mismatches */
                *mismatches = tmp_mm;

                /* adjust boundaries */
                boundaries->leftLTR_5  = motifpos1 - back;
                boundaries->rightLTR_3 = motifpos2 + 1 + forward;

                /* store TSD length */
                boundaries->lenleftTSD = boundaries->lenrightTSD = tsd_len;

                difffromoldboundary1 = difffromnewboundary1;
                difffromoldboundary2 = difffromnewboundary2;
                hitcounter++;
              }
            }
          }
        }
      }
    }
  }
}

/*
 The following function searches only for a specified palindromic motif
 at the 5'-border of left LTR and 3'-border of right LTR.
 */

static void searchformotifonlyborders(const GtLTRharvestStream *lo,
    LTRboundaries *boundaries,
    unsigned long startleftLTR,
    unsigned long endleftLTR,
    unsigned long startrightLTR,
    unsigned long endrightLTR,
    LTRMotifmismatches *motifmismatches)
{
  bool motif1 = false,
       motif2 = false;
  LTRMotifmismatches tmp_mm;
  unsigned int motifmismatches_frombestmatch = 0;
  unsigned long idx,
         oldleftLTR_5  = boundaries->leftLTR_5,
         oldrightLTR_3 = boundaries->rightLTR_3,
         difffromoldboundary = 0;

  /**** search for left motif around leftLTR_5 ****/

  for (idx = startleftLTR; idx < endleftLTR; idx++)
  {
    tmp_mm.left = 0;
    if (gt_encseq_get_encoded_char(/* XXX */ lo->encseq, idx,
                                          GT_READMODE_FORWARD)
        != lo->motif->firstleft)
    {
      tmp_mm.left++;
    }
    if (gt_encseq_get_encoded_char(/* XXX */ lo->encseq,
                                          idx+1,
                                          GT_READMODE_FORWARD) !=
        lo->motif->secondleft)
    {
      tmp_mm.left++;
    }
    if (tmp_mm.left + motifmismatches->left <= lo->motif->allowedmismatches)
    {
       /* first hit */
       if (!motif1)
       {
         unsigned long max, min;

         motifmismatches_frombestmatch = tmp_mm.left;
         boundaries->leftLTR_5 = idx;
         motif1 = true;
         max = MAX(oldleftLTR_5, boundaries->leftLTR_5);
         min = MIN(oldleftLTR_5, boundaries->leftLTR_5);
         difffromoldboundary = max - min;
       } else /* next hit */
       {
         unsigned long maxval, minval, difffromnewboundary;

         /* test if hit is nearer to old boundaries than previous hit */
         maxval = MAX(oldleftLTR_5, idx);
         minval = MIN(oldleftLTR_5, idx);
         difffromnewboundary = maxval - minval;

         if (difffromnewboundary < difffromoldboundary)
         {
           motifmismatches_frombestmatch = tmp_mm.left;
           boundaries->leftLTR_5 = idx;
           difffromoldboundary = difffromnewboundary;
         }
       }
    }
  }
  motifmismatches->left += motifmismatches_frombestmatch;
  motifmismatches_frombestmatch = 0;

  for (idx = startrightLTR + 1; idx <= endrightLTR; idx++)
  {
    tmp_mm.right = 0;
    if (gt_encseq_get_encoded_char(/* XXX */ lo->encseq, idx,
                                          GT_READMODE_FORWARD) !=
                       lo->motif->secondright)
    {
      tmp_mm.right++;
    }
    if (gt_encseq_get_encoded_char(/* XXX */ lo->encseq,idx-1,
                                          GT_READMODE_FORWARD) !=
                       lo->motif->firstright)
    {
      tmp_mm.right++;
    }
    if (tmp_mm.right + motifmismatches->right <= lo->motif->allowedmismatches)
    {
       /* first hit */
       if (!motif2)
       {
         unsigned long max, min;

         motifmismatches_frombestmatch = tmp_mm.right;
         boundaries->rightLTR_3 = idx;
         motif2 = true;
         max = MAX(oldrightLTR_3, boundaries->rightLTR_3);
         min = MIN(oldrightLTR_3, boundaries->rightLTR_3);
         difffromoldboundary = max - min;
       } else /* next hit */
       {
         unsigned long maxval, minval, difffromnewboundary;

         /* test if hit is nearer to old boundaries than previous hit */
         maxval = MAX(oldrightLTR_3, idx);
         minval = MIN(oldrightLTR_3, idx);
         difffromnewboundary = maxval - minval;
         if (difffromnewboundary < difffromoldboundary)
         {
           motifmismatches_frombestmatch = tmp_mm.right;
           boundaries->rightLTR_3 = idx;
           difffromoldboundary = difffromnewboundary;
         }
       }
    }
  }
  motifmismatches->right += motifmismatches_frombestmatch;
  if (motif1 && motif2)
  {
    boundaries->motif_near_tsd = true;
  } else
  {
    boundaries->motif_near_tsd = false;
  }
}

/*
 The following function searches for a specified palindromic motif at the
 3'-border of left LTR and the 5'-border of right LTR.
 */

static void searchformotifonlyinside(const GtLTRharvestStream *lo,
                                     LTRboundaries *boundaries,
                                     LTRMotifmismatches *motifmismatches)
{
  bool motif1 = false,
       motif2 = false;
  unsigned long startleftLTR,
         endleftLTR,
         startrightLTR,
         endrightLTR,
         oldleftLTR_3  = boundaries->leftLTR_3,
         oldrightLTR_5 = boundaries->rightLTR_5,
         difffromoldboundary = 0,
         idx;
  LTRMotifmismatches tmp_mm;
  unsigned int motifmismatches_frombestmatch = 0;

  /** vicinity of 3'-border of left LTR **/
  /* do not align over 5'border of left LTR,
     in case of need decrease alignment length */
  if ((boundaries->leftLTR_3 < lo->vicinityforcorrectboundaries)
      || (startleftLTR = boundaries->leftLTR_3 -
         lo->vicinityforcorrectboundaries + 1) <
      boundaries->leftLTR_5 + 2)
  {
    startleftLTR = boundaries->leftLTR_5 + 2;
  }
  /* do not align over 5'-border of right LTR */
  if ((endleftLTR = boundaries->leftLTR_3 +
       lo->vicinityforcorrectboundaries - 1) >
      boundaries->rightLTR_5 - 1)
  {
    endleftLTR = boundaries->rightLTR_5 - 1;
  }
  /** vicinity of 5'-border of right LTR **/
  /* do not align over 3'-border of left LTR */
  if ((startrightLTR = boundaries->rightLTR_5 -
         lo->vicinityforcorrectboundaries + 1)
       < boundaries->leftLTR_3 + 1)
  {
    startrightLTR = boundaries->leftLTR_3 + 1;
  }
  /* do not align over 3'border of right LTR */
  if ((endrightLTR = boundaries->rightLTR_5 +
       lo->vicinityforcorrectboundaries - 1) >
      boundaries->rightLTR_3 - 2)
  {
    endrightLTR = boundaries->rightLTR_3 - 2;
  }

  /**** search for right motif around leftLTR_3 ****/

  for (idx = startleftLTR + 1; idx <= endleftLTR; idx++)
  {
    tmp_mm.left = 0;
    if (gt_encseq_get_encoded_char(/* XXX */ lo->encseq, idx,
                                          GT_READMODE_FORWARD)
                       != lo->motif->secondright)
    {
      tmp_mm.left++;
    }
    if (gt_encseq_get_encoded_char(/* XXX */ lo->encseq,
                                          idx-1,
                                          GT_READMODE_FORWARD) !=
                       lo->motif->firstright)
    {
      tmp_mm.left++;
    }
    if (tmp_mm.left + motifmismatches->left <= lo->motif->allowedmismatches)
    {
       /* first hit */
       if (!motif1)
       {
         unsigned long maxval, minval;

         motifmismatches_frombestmatch = tmp_mm.left;
         boundaries->leftLTR_3 = idx;
         motif1 = true;
         maxval = MAX(oldleftLTR_3, boundaries->leftLTR_3);
         minval = MIN(oldleftLTR_3, boundaries->leftLTR_3);
         difffromoldboundary = maxval - minval;
       } else /* next hit */
       {
         unsigned long maxval, minval, difffromnewboundary;

         /* test if hit is nearer to old boundaries than previous hit */
         maxval = MAX(oldleftLTR_3, idx);
         minval = MIN(oldleftLTR_3, idx);
         difffromnewboundary = maxval - minval;

         if (difffromnewboundary < difffromoldboundary)
         {
           motifmismatches_frombestmatch = tmp_mm.left;
           boundaries->leftLTR_3 = idx;
           difffromoldboundary = difffromnewboundary;
         }
       }
    }
  }
  motifmismatches->left += motifmismatches_frombestmatch;
  motifmismatches_frombestmatch = 0;

  /**** search for left motif around rightLTR_5 ****/

  for (idx = startrightLTR ; idx < endrightLTR; idx++)
  {
    tmp_mm.right = 0;
    if (gt_encseq_get_encoded_char(/* XXX */ lo->encseq, idx,
                                          GT_READMODE_FORWARD)
                       != lo->motif->firstleft)
    {
      tmp_mm.right++;
    }
    if (gt_encseq_get_encoded_char(/* XXX */ lo->encseq, idx+1,
                                          GT_READMODE_FORWARD)
                       != lo->motif->secondleft)
    {
      tmp_mm.right++;
    }
    if (tmp_mm.right + motifmismatches->right <= lo->motif->allowedmismatches)
    {
       /* first hit */
       if (!motif2)
       {
         unsigned long maxval, minval;

         motifmismatches_frombestmatch = tmp_mm.right;
         boundaries->rightLTR_5 = idx;
         motif2 = true;
         maxval = MAX(oldrightLTR_5, boundaries->rightLTR_5);
         minval = MIN(oldrightLTR_5, boundaries->rightLTR_5);
         difffromoldboundary = maxval - minval;
       } else /* next hit */
       {
         unsigned long maxval, minval, difffromnewboundary;

         /* test if hit is nearer to old boundaries than previous hit */
         maxval = MAX(oldrightLTR_5, idx);
         minval = MIN(oldrightLTR_5, idx);
         difffromnewboundary = maxval - minval;

         if (difffromnewboundary < difffromoldboundary)
         {
           motifmismatches_frombestmatch = tmp_mm.right;
           boundaries->rightLTR_5 = idx;
           difffromoldboundary = difffromnewboundary;
         }
       }
    }
  }
  motifmismatches->right += motifmismatches_frombestmatch;
  if (motif1 && motif2)
  {
    boundaries->motif_far_tsd = true;
  } else
  {
    boundaries->motif_far_tsd = false;
  }
}

/*
 The following function searches for TSDs and/or a specified palindromic motif
 at the 5'-border of left LTR and 3'-border of right LTR.
 */

static int searchforTSDandorMotifoutside(
  const GtLTRharvestStream *lo,
  LTRboundaries *boundaries,
  LTRMotifmismatches *motifmismatches,
  GtError *err)
{
  unsigned long startleftLTR,
         endleftLTR,
         startrightLTR,
         endrightLTR,
         leftlen,
         rightlen,
         sequenceendpos,
         seqstartpos,
         seqlength;
  SubRepeatInfo subrepeatinfo;
  bool haserr = false;

  gt_error_check(err);

  /* check border cases */

  /* vicinity of 5'-border of left LTR */
  seqstartpos = gt_encseq_seqstartpos(lo->encseq, boundaries->contignumber);
  seqlength = gt_encseq_seqlength(lo->encseq, boundaries->contignumber);
  if (boundaries->contignumber == 0)
  {
    /* do not align over left sequence boundary,
       in case of need decrease alignment length */
    if (boundaries->leftLTR_5 < lo->vicinityforcorrectboundaries)
    {
      startleftLTR = seqstartpos;
    } else
    {
      startleftLTR = boundaries->leftLTR_5 - lo->vicinityforcorrectboundaries;
    }
  } else
  {
    /* do not align over left separator symbol
       in case of need decrease alignment length */
    if (boundaries->leftLTR_5 < lo->vicinityforcorrectboundaries)
    {
      startleftLTR = seqstartpos;
    } else
    {
      startleftLTR = boundaries->leftLTR_5 - lo->vicinityforcorrectboundaries;
      if (startleftLTR < seqstartpos && boundaries->leftLTR_5 >= seqstartpos)
      {
        startleftLTR = seqstartpos;
      }
    }
  }
  /* do not align over 3'-border of left LTR */
  endleftLTR = boundaries->leftLTR_5 + lo->vicinityforcorrectboundaries;
  if (endleftLTR > boundaries->leftLTR_3 - 2) /* -2 because of possible motif */
  {
    endleftLTR = boundaries->leftLTR_3 - 2;
  }
  leftlen = endleftLTR - startleftLTR + 1;

  /* vicinity of 3'-border of right LTR
     do not align over 5'border of right LTR */
  startrightLTR = boundaries->rightLTR_3 - lo->vicinityforcorrectboundaries;
  if (startrightLTR < boundaries->rightLTR_5 + 2) /* +2 for possible motif */
  {
    startrightLTR = boundaries->rightLTR_5 + 2;
  }
  sequenceendpos = seqstartpos + seqlength - 1;
  /* do not align into next sequence in case of need decrease alignment
     length */
  endrightLTR = boundaries->rightLTR_3 + lo->vicinityforcorrectboundaries;
  if (endrightLTR > sequenceendpos && boundaries->rightLTR_3 <= sequenceendpos)
  {
    endrightLTR = sequenceendpos;
  }
  rightlen = endrightLTR - startrightLTR + 1;

  /* now, search for correct boundaries */

  /* search for TSDs and/or motif */
  if (lo->minlengthTSD > 1U)
  {
    GtUchar *dbseq = gt_malloc(sizeof (*dbseq) * leftlen),
            *query = gt_malloc(sizeof (*query) * rightlen);

    gt_encseq_extract_encoded(lo->encseq,dbseq,startleftLTR,endleftLTR);
    gt_encseq_extract_encoded(lo->encseq,query,startrightLTR,endrightLTR);
    GT_INITARRAY(&subrepeatinfo.repeats, Repeat);
    subrepeatinfo.tsd_lmin = (unsigned long) lo->minlengthTSD;
    subrepeatinfo.tsd_lmax = (unsigned long) lo->maxlengthTSD;
    gt_assert(startleftLTR < startrightLTR);
    subrepeatinfo.offset1 = startleftLTR;
    subrepeatinfo.offset2 = startrightLTR;

    if (gt_sarrquerysubstringmatch(dbseq,
                                   leftlen,
                                   query,
                                   rightlen,
                                   lo->minlengthTSD,
                                   gt_encseq_alphabet(lo->encseq),
                                   gt_subsimpleexactselfmatchstore,
                                   &subrepeatinfo,
                                   NULL,
                                   err) != 0)
    {
       haserr = true;
    }
    gt_free(dbseq);
    gt_free(query);

    if (!haserr)
    {
      searchforbestTSDandormotifatborders(&subrepeatinfo,
                                          lo,
                                          boundaries,
                                          motifmismatches);
    }
    GT_FREEARRAY (&subrepeatinfo.repeats, Repeat);
  } else /* no search for TSDs, search for motif only */
  {
    searchformotifonlyborders(lo,
                              boundaries,
                              startleftLTR,
                              endleftLTR,
                              startrightLTR,
                              endrightLTR,
                              motifmismatches);
  }
  return haserr ? -1 : 0;
}

/*
 The following function searches for TSD and/or a specified palindromic motif
 at the borders of left LTR and the right LTR, respectively.
 */
static int gt_findcorrectboundaries(const GtLTRharvestStream *lo,
                                    LTRboundaries *boundaries,
                                    GtError *err)
{
  LTRMotifmismatches motifmismatches;

  gt_error_check(err);
  gt_log_log("searching for correct boundaries in vicinity...\n");
  /* first: 5'-border of left LTR and 3'-border of right LTR */

  motifmismatches.left = motifmismatches.right = 0;
  if (searchforTSDandorMotifoutside(lo,
                                    boundaries,
                                    &motifmismatches,
                                    err) != 0)
  {
    return -1;
  }

  /* second: 3'-border of left LTR and 5'-border of right LTR */
  if (lo->motif->allowedmismatches < 4U)
  {
    gt_log_log("second: searching for motif only around 3'border of left LTR "
               "and 5'-border of right LTR...\n");
    searchformotifonlyinside(lo,boundaries,&motifmismatches);
  }
  return 0;
}

static bool checklengthanddistanceconstraints(LTRboundaries *boundaries,
                                              const RepeatInfo *repeatinfo)
{
  unsigned long ulen, vlen, dist_between_LTRs;

  ulen = boundaries->leftLTR_3  - boundaries->leftLTR_5  + 1;
  vlen = boundaries->rightLTR_3 - boundaries->rightLTR_5 + 1;
  dist_between_LTRs = boundaries->rightLTR_5 - boundaries->leftLTR_5;
  if (ulen > repeatinfo->lmax
        || vlen > repeatinfo->lmax
        || ulen < repeatinfo->lmin
        || vlen < repeatinfo->lmin
        || dist_between_LTRs > repeatinfo->dmax
        || dist_between_LTRs < repeatinfo->dmin
        || boundaries->leftLTR_3 >= boundaries->rightLTR_5)
  {
    boundaries->lengthdistconstraint = false;
    boundaries->similarity = 0.0;
    return false;
  } else
  {
    boundaries->lengthdistconstraint = true;
    return true;
  }
}

static void adjustboundariesfromXdropextension(GtXdropbest xdropbest_left,
                                               GtXdropbest xdropbest_right,
                                               unsigned long seed1_startpos,
                                               unsigned long seed2_startpos,
                                               unsigned long seed1_endpos,
                                               unsigned long seed2_endpos,
                                               LTRboundaries *boundaries)
{
  /* left alignment */
  boundaries->leftLTR_5  = seed1_startpos - xdropbest_left.ivalue;
  boundaries->rightLTR_5 = seed2_startpos - xdropbest_left.jvalue;

  /* right alignment */
  boundaries->leftLTR_3  = seed1_endpos + xdropbest_right.ivalue;
  boundaries->rightLTR_3 = seed2_endpos + xdropbest_right.jvalue;
}

/*
 The following function applies the filter algorithms one after another
 to all candidate pairs.
*/
static int gt_searchforLTRs(GtLTRharvestStream *lo,
                            GtArrayLTRboundaries *arrayLTRboundaries,
                            GtError *err)
{
  GtXdropresources *xdropresources;
  GtXdropbest xdropbest_left, xdropbest_right;
#undef GT_GREEDY_BUFFER
#ifdef GT_GREEDY_BUFFER
  unsigned long maxulen = 0, maxvlen = 0;
  GtUchar *useq = NULL,
          *vseq = NULL;
#endif
  GtSeqabstract *sa_useq = gt_seqabstract_new_empty(),
                *sa_vseq = gt_seqabstract_new_empty();
  unsigned long edist;
  Repeat *repeatptr;
  LTRboundaries *boundaries;
  GtFrontResource *frontresource = gt_frontresource_new(100UL);
  bool haserr = false;

  gt_error_check(err);
  xdropresources = gt_xdrop_resources_new(&lo->arbitscores);
  for (repeatptr = lo->repeatinfo.repeats.spaceRepeat;
       repeatptr < lo->repeatinfo.repeats.spaceRepeat +
                   lo->repeatinfo.repeats.nextfreeRepeat; repeatptr++)
  {
    unsigned long alilen,
                  ulen,
                  vlen,
                  seqend,
                  seqstart = gt_encseq_seqstartpos(lo->encseq,
                                                   repeatptr->contignumber);

    seqend = seqstart + gt_encseq_seqlength(lo->encseq,
                                            repeatptr->contignumber);
    gt_assert(lo->repeatinfo.lmax >= repeatptr->len);
    alilen = lo->repeatinfo.lmax - repeatptr->len;
    /**** left (reverse) xdrop alignment ****/
    if (repeatptr->pos1 > 0)
    {
      gt_assert(seqstart <= repeatptr->pos1);
      if (alilen <= repeatptr->pos1 - seqstart)
      {
        gt_seqabstract_reinit_encseq(sa_useq,lo->encseq,alilen,0);
        gt_seqabstract_reinit_encseq(sa_vseq,lo->encseq,alilen,0);
      } else
      {
        gt_seqabstract_reinit_encseq(sa_useq,lo->encseq,
                                     repeatptr->pos1 - seqstart,0);
        gt_seqabstract_reinit_encseq(sa_vseq,lo->encseq,
                                     repeatptr->pos1 + repeatptr->offset
                                                     - seqstart,0);
      }
      gt_evalxdroparbitscoresextend(false,
                                    &xdropbest_left,
                                    xdropresources,
                                    sa_useq,
                                    sa_vseq,
                                    repeatptr->pos1,
                                    repeatptr->pos1 + repeatptr->offset,
                                    (GtXdropscore) lo->xdropbelowscore);
    } else
    {
      xdropbest_left.ivalue = 0;
      xdropbest_left.jvalue = 0;
      xdropbest_left.score = 0;
    }
    if (repeatptr->pos1 + repeatptr->len > 0)
    {
      gt_assert(seqend >= repeatptr->pos1 + repeatptr->offset + repeatptr->len);
      if (alilen <= seqend - (repeatptr->pos1 + repeatptr->offset +
                              repeatptr->len))
      {
        gt_seqabstract_reinit_encseq(sa_useq,lo->encseq,alilen,0);
        gt_seqabstract_reinit_encseq(sa_vseq,lo->encseq,alilen,0);
      } else
      {
        gt_seqabstract_reinit_encseq(sa_useq,lo->encseq,
                                     seqend - (repeatptr->pos1+repeatptr->len),
                                     0);
        gt_seqabstract_reinit_encseq(sa_vseq,lo->encseq,
                                     seqend - (repeatptr->pos1 +
                                               repeatptr->offset +
                                               repeatptr->len),0);
      }
      gt_evalxdroparbitscoresextend(true,
                                    &xdropbest_right,
                                    xdropresources,
                                    sa_useq,
                                    sa_vseq,
                                    repeatptr->pos1 + repeatptr->len,
                                    repeatptr->pos1 + repeatptr->offset +
                                    repeatptr->len,
                                    (GtXdropscore) lo->xdropbelowscore);
    } else
    {
      xdropbest_right.ivalue = 0;
      xdropbest_right.jvalue = 0;
      xdropbest_right.score = 0;
    }
    GT_GETNEXTFREEINARRAY(boundaries,arrayLTRboundaries,LTRboundaries,5);
    boundaries->contignumber = repeatptr->contignumber;
    boundaries->leftLTR_5 = 0;
    boundaries->leftLTR_3 = 0;
    boundaries->rightLTR_5 = 0;
    boundaries->rightLTR_3 = 0;
    boundaries->lenleftTSD = 0;
    boundaries->lenrightTSD = 0;
    boundaries->tsd = false;
    boundaries->motif_near_tsd = false;
    boundaries->motif_far_tsd = false;
    boundaries->skipped = false;
    boundaries->similarity = 0.0;

    /* store new boundaries-positions in boundaries */
    adjustboundariesfromXdropextension(
                   xdropbest_left,
                   xdropbest_right,
                   repeatptr->pos1,  /*seed1 startpos*/
                   repeatptr->pos1 + repeatptr->offset, /*seed2 startpos*/
                   repeatptr->pos1 + repeatptr->len - 1, /*seed1 endpos*/
                   repeatptr->pos1 + repeatptr->offset + repeatptr->len - 1,
                                                         /*seed2 endpos*/
                   boundaries);

    /* if search for motif and/or TSD */
    if (lo->motif->allowedmismatches < 4U || lo->minlengthTSD > 1U)
    {
      if (gt_findcorrectboundaries(lo, boundaries, err) != 0)
      {
        haserr = true;
        break;
      }

      /* if search for TSDs and (not) motif */
      if (boundaries->tsd &&
          (lo->motif->allowedmismatches >= 4U ||
          (boundaries->motif_near_tsd && boundaries->motif_far_tsd)))
      {
        /* predicted as full LTR-pair, keep it */
      } else
      {
        /* if search for motif only (and not TSD) */
        if (lo->minlengthTSD <= 1U &&
            boundaries->motif_near_tsd &&
            boundaries->motif_far_tsd)
        {
          /* predicted as full LTR-pair, keep it */
        } else
        {
          /* delete this LTR-pair candidate */
          arrayLTRboundaries->nextfreeLTRboundaries--;
          continue;
        }
      }
    }

    /* check length and distance constraints again */
    if (!checklengthanddistanceconstraints(boundaries, &lo->repeatinfo))
    {
      /* delete this LTR-pair candidate */
      arrayLTRboundaries->nextfreeLTRboundaries--;
      continue;
    }

    /* check similarity from candidate pair
       copy LTR sequences for greedyunitedist function */
    ulen = boundaries->leftLTR_3 - boundaries->leftLTR_5 + 1;
    vlen = boundaries->rightLTR_3 - boundaries->rightLTR_5 + 1;
#ifdef GT_GREEDY_BUFFER
    if (ulen > maxulen)
    {
      maxulen = ulen;
      useq = gt_realloc(useq, sizeof (*useq) * maxulen);
    }
    if (vlen > maxvlen)
    {
      maxvlen = vlen;
      vseq = gt_realloc(vseq, sizeof (*vseq) * maxvlen);
    }
    gt_encseq_extract_encoded(lo->encseq, useq, boundaries->leftLTR_5,
                                            boundaries->leftLTR_3);
    gt_encseq_extract_encoded(lo->encseq, vseq, boundaries->rightLTR_5,
                                            boundaries->rightLTR_3);
    gt_seqabstract_reinit_ptr(sa_useq,useq,ulen,0);
    gt_seqabstract_reinit_ptr(sa_vseq,vseq,vlen,0);
#else
    gt_seqabstract_reinit_encseq(sa_useq,lo->encseq,ulen,boundaries->leftLTR_5);
    gt_seqabstract_reinit_encseq(sa_vseq,lo->encseq,vlen,
                                 boundaries->rightLTR_5);
#endif
    edist = greedyunitedist(frontresource,sa_useq,sa_vseq);

    /* determine similarity */
    boundaries->similarity = 100.0 * (1.0 - (double) edist/MAX(ulen,vlen));

    if (gt_double_smaller_double(boundaries->similarity,
                                 lo->similaritythreshold))
    {
      /* delete this LTR-pair candidate */
      arrayLTRboundaries->nextfreeLTRboundaries--;
    }
  }
#ifdef GT_GREEDY_BUFFER
  FREESPACE(useq);
  FREESPACE(vseq);
#endif
  gt_xdrop_resources_delete(xdropresources);
  gt_seqabstract_delete(sa_useq);
  gt_seqabstract_delete(sa_vseq);
  gt_frontresource_delete(frontresource);
  return haserr ? -1 : 0;
}

/*
 The following function removes exact duplicates from the array of
 predicted LTR elements. Exact duplicates occur when
 different seeds are extended to same boundary coordinates.
 */
static void gt_removeduplicates(GtArrayLTRboundaries *arrayLTRboundaries)
{
  unsigned long i, j;
  unsigned long startpos_i, endpos_i, startpos_j, endpos_j;
  LTRboundaries *boundaries_i,
                *boundaries_j;

  for (i = 0; i < arrayLTRboundaries->nextfreeLTRboundaries; i++)
  {
    boundaries_i = &(arrayLTRboundaries->spaceLTRboundaries[i]);
    if (boundaries_i->skipped)
    {
      continue;
    }
    startpos_i = boundaries_i->leftLTR_5;
    endpos_i   = boundaries_i->rightLTR_3;

    for (j = i + 1; j < arrayLTRboundaries->nextfreeLTRboundaries; j++)
    {
      boundaries_j = &(arrayLTRboundaries->spaceLTRboundaries[j]);
      if (boundaries_j->skipped)
      {
        continue;
      }
      startpos_j = boundaries_j->leftLTR_5;
      endpos_j   = boundaries_j->rightLTR_3;

      if (startpos_i == startpos_j && endpos_i == endpos_j)
      {
        boundaries_j->skipped = true;
      }
    }
  }
}

/* The following function removes overlaps and deletes the prediction with
   a lower similarity value. If "nooverlapallowed" is set, then all
   overlapping predictions are deleted completely.
 */
static void gt_removeoverlapswithlowersimilarity(
  GtArrayLTRboundaries *arrayLTRboundaries,
  bool nooverlapallowed)
{
  unsigned long i, j;
  unsigned long startpos_i, endpos_i, startpos_j, endpos_j;
  LTRboundaries *boundaries_i,
                *boundaries_j;

  for (i = 0; i < arrayLTRboundaries->nextfreeLTRboundaries; i++)
  {
    boundaries_i = &(arrayLTRboundaries->spaceLTRboundaries[i]);
    if (boundaries_i->skipped)
    {
      continue;
    }
    startpos_i = boundaries_i->leftLTR_5;
    endpos_i   = boundaries_i->rightLTR_3;

    for (j = i + 1; j < arrayLTRboundaries->nextfreeLTRboundaries; j++)
    {
      boundaries_j = &(arrayLTRboundaries->spaceLTRboundaries[j]);
      if (boundaries_j->skipped)
      {
        continue;
      }
      startpos_j = boundaries_j->leftLTR_5;
      endpos_j   = boundaries_j->rightLTR_3;

      /* if overlap */
      if (!((endpos_i < startpos_j) || (endpos_j < startpos_i)))
      {
        if (nooverlapallowed)
        {
          /* All predictions in a cluster will be deleted. */

          /* take min(startpos_i, startpos_j) */
          if (startpos_j < startpos_i)
          {
            startpos_i = startpos_j;
          }
          /* take max(endpos_i, endpos_j) */
          if (endpos_i < endpos_j)
          {
            endpos_i = endpos_j;
          }
          /* delete both predictions */
          boundaries_i->skipped = true;
          boundaries_j->skipped = true;
        } else
        {
          /* take prediction with higher similarity */
          if (boundaries_i->similarity >= boundaries_j->similarity)
          {
            boundaries_j->skipped = true;
          } else
          {
            boundaries_i->skipped = true;
            break;
          }
        }
      }
    }
  }
}

static int gt_ltrharvest_stream_next(GtNodeStream *ns,
                                     GtGenomeNode **gn,
                                     GtError *err)
{
  int had_err = 0;
  GtLTRharvestStream *ltrh_stream = gt_ltrharvest_stream_cast(ns);

  gt_error_check(err);
  /* LTRharvest run */
  if (ltrh_stream->state == GT_LTRHARVEST_STREAM_STATE_START) {

    GT_INITARRAY(<rh_stream->repeatinfo.repeats, Repeat);
    ltrh_stream->prevseqnum = GT_UNDEF_ULONG;
    if (!had_err && gt_enumeratemaxpairs(ltrh_stream->ssar,
                      ltrh_stream->encseq,
                      gt_readmodeSequentialsuffixarrayreader(ltrh_stream->ssar),
                      (unsigned int) ltrh_stream->minseedlength,
                      gt_simpleexactselfmatchstore,
                      <rh_stream->repeatinfo,
                      err) != 0)
    {
      had_err = -1;
    }

    /* apply the filter algorithms */
    if (!had_err && gt_searchforLTRs(ltrh_stream,
                                     <rh_stream->arrayLTRboundaries,
                                     err) != 0)
    {
      had_err = -1;
    }

    /* not needed any longer */
    GT_FREEARRAY(<rh_stream->repeatinfo.repeats, Repeat);

    /* remove exact duplicates */
    if (!had_err)
    {
      gt_removeduplicates(<rh_stream->arrayLTRboundaries);
    }

    /* remove overlapping predictions if desired */
    if (!had_err && (ltrh_stream->nooverlaps || ltrh_stream->bestoverlaps))
    {
      gt_removeoverlapswithlowersimilarity(<rh_stream->arrayLTRboundaries,
                                            ltrh_stream->nooverlaps);
    }

    /* sort elements */
    if (!had_err)
    {
      ltrh_stream->bdptrtab =
        sortedltrboundaries(<rh_stream->numofboundaries,
                            <rh_stream->arrayLTRboundaries);
    }
    ltrh_stream->state = GT_LTRHARVEST_STREAM_STATE_REGIONS;
  }

  /* first stream out the region nodes */
  if (!had_err && ltrh_stream->state == GT_LTRHARVEST_STREAM_STATE_REGIONS) {
    bool skip = false;
    if (ltrh_stream->cur_elem_index < ltrh_stream->numofboundaries) {
      unsigned long seqnum, seqlength;
      GtGenomeNode *rn;
      GtStr *seqid;
      seqnum = ltrh_stream->bdptrtab[ltrh_stream->cur_elem_index]->contignumber;
      if (ltrh_stream->prevseqnum == GT_UNDEF_ULONG)
      {
        ltrh_stream->prevseqnum = seqnum;
      } else
      {
        while (ltrh_stream->prevseqnum == seqnum)
        {
          ltrh_stream->cur_elem_index++;
          if (ltrh_stream->cur_elem_index >= ltrh_stream->numofboundaries)
          {
            skip = true;
            break;
          }
          seqnum
            = ltrh_stream->bdptrtab[ltrh_stream->cur_elem_index]->contignumber;
        }
      }
      if (!skip)
      {
        ltrh_stream->prevseqnum = seqnum;
        seqlength = gt_encseq_seqlength(ltrh_stream->encseq, seqnum);
        seqid = gt_str_new_cstr("seq");
        gt_str_append_ulong(seqid, seqnum);
        rn = gt_region_node_new(seqid,
                                1 + ltrh_stream->offset,
                                seqlength + ltrh_stream->offset);
        gt_str_delete(seqid);
        *gn = rn;
        ltrh_stream->cur_elem_index++;
      } else
      {
        ltrh_stream->cur_elem_index = 0;
        ltrh_stream->state = GT_LTRHARVEST_STREAM_STATE_COMMENTS;
        *gn = NULL;
      }
    } else
    {
      ltrh_stream->cur_elem_index = 0;
      ltrh_stream->state = GT_LTRHARVEST_STREAM_STATE_COMMENTS;
      *gn = NULL;
    }
  }

  /* then stream out the comment nodes */
  if (!had_err && ltrh_stream->state == GT_LTRHARVEST_STREAM_STATE_COMMENTS)
  {
    bool skip = false;
    if (ltrh_stream->cur_elem_index < ltrh_stream->numofboundaries)
    {
      const char *desc;
      char buf[BUFSIZ];
      unsigned long desclen, seqnum;
      GtGenomeNode *cn;
      seqnum = ltrh_stream->bdptrtab[ltrh_stream->cur_elem_index]->contignumber;
      if (ltrh_stream->prevseqnum == GT_UNDEF_ULONG)
      {
        ltrh_stream->prevseqnum = seqnum;
      } else
      {
        while (ltrh_stream->prevseqnum == seqnum)
        {
          ltrh_stream->cur_elem_index++;
          if (ltrh_stream->cur_elem_index >= ltrh_stream->numofboundaries)
          {
            skip = true;
            break;
          }
          seqnum
            = ltrh_stream->bdptrtab[ltrh_stream->cur_elem_index]->contignumber;
        }
      }
      if (!skip)
      {
        ltrh_stream->prevseqnum = seqnum;
        desc = gt_encseq_description(ltrh_stream->encseq, &desclen, seqnum);
        (void) strncpy(buf, desc, (size_t) (desclen * sizeof (char)));
        buf[desclen] = '\0';
        cn = gt_comment_node_new(buf);
        *gn = cn;
        ltrh_stream->cur_elem_index++;
      } else
      {
        ltrh_stream->cur_elem_index = 0;
        ltrh_stream->state = GT_LTRHARVEST_STREAM_STATE_FEATURES;
        *gn = NULL;
      }
    } else
    {
      ltrh_stream->cur_elem_index = 0;
      ltrh_stream->state = GT_LTRHARVEST_STREAM_STATE_FEATURES;
      *gn = NULL;
    }
  }

  /* finally, stream out the features */
  if (!had_err && ltrh_stream->state == GT_LTRHARVEST_STREAM_STATE_FEATURES)
  {
    if (ltrh_stream->cur_elem_index <  ltrh_stream->numofboundaries)
    {
      GtStr *seqid, *source;
      char buf[BUFSIZ];
      GtGenomeNode *node, *parent;
      const LTRboundaries *elem =
        (ltrh_stream->bdptrtab[ltrh_stream->cur_elem_index]);
      unsigned long seqstartpos;

      seqstartpos = gt_encseq_seqstartpos(ltrh_stream->encseq,
                                          elem->contignumber);
      seqid = gt_str_new_cstr("seq");
      source = gt_str_new_cstr(GT_LTRHARVEST_NAME);

      gt_str_append_ulong(seqid, elem->contignumber);

      /* repeat_region */
      node = gt_feature_node_new(seqid,
                                 gt_ft_repeat_region,
                                 elem->leftLTR_5 - seqstartpos + 1
                                   - elem->lenleftTSD
                                   + ltrh_stream->offset,
                                 elem->rightLTR_3 - seqstartpos + 1
                                   + elem->lenrightTSD
                                   + ltrh_stream->offset,
                                 GT_STRAND_UNKNOWN);
      gt_feature_node_set_source((GtFeatureNode*) node, source);
      *gn = node;
      parent = node;
      if (ltrh_stream->motif->allowedmismatches < 4U)
      {
        node = gt_feature_node_new(seqid,
                                   gt_ft_inverted_repeat,
                                   elem->leftLTR_5 - seqstartpos + 1
                                     + ltrh_stream->offset,
                                   elem->leftLTR_5 - seqstartpos + 2
                                     + ltrh_stream->offset,
                                   GT_STRAND_UNKNOWN);
        gt_feature_node_set_source((GtFeatureNode*) node, source);
        gt_feature_node_add_child((GtFeatureNode*) parent,
                                  (GtFeatureNode*) node);
        node = gt_feature_node_new(seqid,
                                   gt_ft_inverted_repeat,
                                   elem->leftLTR_3 - seqstartpos
                                     + ltrh_stream->offset,
                                   elem->leftLTR_3 - seqstartpos + 1
                                     + ltrh_stream->offset,
                                   GT_STRAND_UNKNOWN);
        gt_feature_node_set_source((GtFeatureNode*) node, source);
        gt_feature_node_add_child((GtFeatureNode*) parent,
                                  (GtFeatureNode*) node);
        node = gt_feature_node_new(seqid,
                                   gt_ft_inverted_repeat,
                                   elem->rightLTR_5 - seqstartpos + 1
                                     + ltrh_stream->offset,
                                   elem->rightLTR_5 - seqstartpos + 2
                                     + ltrh_stream->offset,
                                   GT_STRAND_UNKNOWN);
        gt_feature_node_set_source((GtFeatureNode*) node, source);
        gt_feature_node_add_child((GtFeatureNode*) parent,
                                  (GtFeatureNode*) node);
        node = gt_feature_node_new(seqid,
                                   gt_ft_inverted_repeat,
                                   elem->rightLTR_3 - seqstartpos
                                     + ltrh_stream->offset,
                                   elem->rightLTR_3 - seqstartpos + 1
                                     + ltrh_stream->offset,
                                   GT_STRAND_UNKNOWN);
        gt_feature_node_set_source((GtFeatureNode*) node, source);
        gt_feature_node_add_child((GtFeatureNode*) parent,
                                  (GtFeatureNode*) node);
      }
      /* target_site_duplication */
      if (ltrh_stream->minlengthTSD > 1U)
      {
        node = gt_feature_node_new(seqid,
                                   gt_ft_target_site_duplication,
                                   elem->leftLTR_5 - seqstartpos + 1
                                     - elem->lenleftTSD
                                     + ltrh_stream->offset,
                                   elem->leftLTR_5 - seqstartpos
                                     + ltrh_stream->offset,
                                   GT_STRAND_UNKNOWN);
        gt_feature_node_set_source((GtFeatureNode*) node, source);
        gt_feature_node_add_child((GtFeatureNode*) parent,
                                  (GtFeatureNode*) node);
        node = gt_feature_node_new(seqid,
                                   gt_ft_target_site_duplication,
                                   elem->rightLTR_3 - seqstartpos + 2
                                     + ltrh_stream->offset,
                                   elem->rightLTR_3 - seqstartpos + 1
                                     + elem->lenrightTSD
                                     + ltrh_stream->offset,
                                   GT_STRAND_UNKNOWN);
        gt_feature_node_set_source((GtFeatureNode*) node, source);
        gt_feature_node_add_child((GtFeatureNode*) parent,
                                  (GtFeatureNode*) node);
      }
      /* LTR_retrotransposon */
      node = gt_feature_node_new(seqid,
                                 gt_ft_LTR_retrotransposon,
                                 elem->leftLTR_5 - seqstartpos + 1
                                   + ltrh_stream->offset,
                                 elem->rightLTR_3 - seqstartpos + 1
                                   + ltrh_stream->offset,
                                 GT_STRAND_UNKNOWN);
      gt_feature_node_set_source((GtFeatureNode*) node, source);
      (void) snprintf(buf, BUFSIZ-1, "%.2f", elem->similarity);
      gt_feature_node_set_attribute((GtFeatureNode*) node,
                                    "ltr_similarity",
                                    buf);
      (void) snprintf(buf, BUFSIZ-1, "%lu", elem->contignumber);
      gt_feature_node_set_attribute((GtFeatureNode*) node,
                                    "seq_number",
                                    buf);
      gt_feature_node_add_child((GtFeatureNode*) parent,
                                (GtFeatureNode*) node);
      parent = node;
      /* long_terminal_repeat */
      node = gt_feature_node_new(seqid,
                                 gt_ft_long_terminal_repeat,
                                 elem->leftLTR_5 - seqstartpos + 1
                                   + ltrh_stream->offset,
                                 elem->leftLTR_3 - seqstartpos + 1
                                   + ltrh_stream->offset,
                                 GT_STRAND_UNKNOWN);
      gt_feature_node_set_source((GtFeatureNode*) node, source);
      gt_feature_node_add_child((GtFeatureNode*) parent,
                                (GtFeatureNode*) node);
      node = gt_feature_node_new(seqid,
                                 gt_ft_long_terminal_repeat,
                                 elem->rightLTR_5 - seqstartpos + 1
                                   + ltrh_stream->offset,
                                 elem->rightLTR_3 - seqstartpos + 1
                                   + ltrh_stream->offset,
                                 GT_STRAND_UNKNOWN);
      gt_feature_node_set_source((GtFeatureNode*) node, source);
      gt_feature_node_add_child((GtFeatureNode*) parent,
                                (GtFeatureNode*) node);
      gt_str_delete(seqid);
      gt_str_delete(source);
      ltrh_stream->cur_elem_index++;
    } else
    {
      *gn = NULL;
    }
  }
  return had_err;
}

static void gt_ltrharvest_stream_free(GtNodeStream *ns)
{
  GtLTRharvestStream *ltrh_stream = gt_ltrharvest_stream_cast(ns);
  GT_FREEARRAY(<rh_stream->arrayLTRboundaries, LTRboundaries);
  if (ltrh_stream->ssar != NULL)
    gt_freeSequentialsuffixarrayreader(<rh_stream->ssar);
  if (ltrh_stream->bdptrtab != NULL)
    gt_free(ltrh_stream->bdptrtab);
}

const GtNodeStreamClass* gt_ltrharvest_stream_class(void)
{
  static const GtNodeStreamClass *nsc = NULL;
  gt_class_alloc_lock_enter();
  if (!nsc) {
    nsc = gt_node_stream_class_new(sizeof (GtLTRharvestStream),
                                   gt_ltrharvest_stream_free,
                                   gt_ltrharvest_stream_next);
  }
  gt_class_alloc_lock_leave();
  return nsc;
}

const GtEncseq* gt_ltrharvest_stream_get_encseq(GtNodeStream *ltrh_stream)
{
  GtLTRharvestStream *stream;
  gt_assert(ltrh_stream != NULL);
  stream = gt_ltrharvest_stream_cast(ltrh_stream);
  return stream->encseq;
}

GtNodeStream* gt_ltrharvest_stream_new(GtStr *str_indexname,
                                       GtRange searchrange,
                                       unsigned long minseedlength,
                                       unsigned long minltrlength,
                                       unsigned long maxltrlength,
                                       unsigned long mindistance,
                                       unsigned long maxdistance,
                                       double similaritythreshold,
                                       int xdropbelowscore,
                                       GtXdropArbitraryscores arbitscores,
                                       GtLTRFourCharMotif *motif,
                                       bool verbosemode,
                                       bool nooverlaps,
                                       bool bestoverlaps,
                                       bool scan,
                                       unsigned long offset,
                                       unsigned int minlengthTSD,
                                       unsigned int maxlengthTSD,
                                       unsigned long vicinity,
                                       GtError *err)
{
  int had_err = 0;
  unsigned long max_contiglength;
  GtNodeStream *ns = gt_node_stream_create(gt_ltrharvest_stream_class(), false);
  GtLTRharvestStream *ltrh_stream = gt_ltrharvest_stream_cast(ns);

  ltrh_stream->str_indexname = str_indexname;
  ltrh_stream->minseedlength = minseedlength;
  ltrh_stream->similaritythreshold = similaritythreshold;
  ltrh_stream->xdropbelowscore = xdropbelowscore;
  ltrh_stream->arbitscores = arbitscores;
  ltrh_stream->motif = motif;
  ltrh_stream->verbosemode = verbosemode;
  ltrh_stream->offset = offset;
  ltrh_stream->repeatinfo.ltrsearchseqrange = searchrange;
  ltrh_stream->minlengthTSD = minlengthTSD;
  ltrh_stream->maxlengthTSD = maxlengthTSD;
  ltrh_stream->nooverlaps = nooverlaps;
  ltrh_stream->bestoverlaps = bestoverlaps;
  ltrh_stream->vicinityforcorrectboundaries = vicinity;
  ltrh_stream->cur_elem_index = 0;
  ltrh_stream->state = GT_LTRHARVEST_STREAM_STATE_START;
  /* init array for maximal repeats */
  GT_INITARRAY(<rh_stream->arrayLTRboundaries, LTRboundaries);

  ltrh_stream->ssar =
    gt_newSequentialsuffixarrayreaderfromfile(gt_str_get(str_indexname),
                                                SARR_LCPTAB | SARR_SUFTAB |
                                                SARR_ESQTAB | SARR_DESTAB |
                                                SARR_SSPTAB | SARR_SDSTAB,
                                                scan
                                                  ? SEQ_scan
                                                  : SEQ_mappedboth,
                                                NULL,
                                                err);
  if (ltrh_stream->ssar == NULL)
  {
    gt_node_stream_delete(ns);
    return NULL;
  }
  /* get encseq associated with suffix array */
  ltrh_stream->encseq = gt_encseqSequentialsuffixarrayreader(ltrh_stream->ssar);
  max_contiglength = gt_encseq_max_seq_length(ltrh_stream->encseq);
  ltrh_stream->repeatinfo.dmax = MIN(maxdistance,max_contiglength);
  ltrh_stream->repeatinfo.dmin = mindistance;
  ltrh_stream->repeatinfo.lmin = minltrlength;
  ltrh_stream->repeatinfo.lmax = maxltrlength;

  /* encode motif according to encseq alphabet */
  had_err = gt_ltr_four_char_motif_encode(motif, ltrh_stream->encseq, err);
  if (had_err)
  {
    gt_node_stream_delete(ns);
    return NULL;
  }

  return had_err ? NULL : ns;
}
genometools-1.5.1/src/ltr/ltrharvest_stream.h000066400000000000000000000047301211610345200213620ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTRHARVEST_STREAM_H
#define LTRHARVEST_STREAM_H

#include "match/xdrop.h"
#include "extended/node_stream_api.h"
#include "ltr/ltr_four_char_motif.h"

/* implements the ``genome stream'' interface */
typedef struct GtLTRharvestStream GtLTRharvestStream;

const GtNodeStreamClass* gt_ltrharvest_stream_class(void);
GtNodeStream* gt_ltrharvest_stream_new(GtStr *str_indexname,
                                       GtRange searchrange,
                                       unsigned long minseedlength,
                                       unsigned long minltrlength,
                                       unsigned long maxltrlength,
                                       unsigned long mindistance,
                                       unsigned long maxdistance,
                                       double similaritythreshold,
                                       int xdropbelowscore,
                                       GtXdropArbitraryscores arbitscores,
                                       GtLTRFourCharMotif *motif,
                                       bool verbosemode,
                                       bool nooverlaps,
                                       bool bestoverlaps,
                                       bool scan,
                                       unsigned long offset,
                                       unsigned int minlengthTSD,
                                       unsigned int maxlengthTSD,
                                       unsigned long vicinity,
                                       GtError *err);

const GtEncseq* gt_ltrharvest_stream_get_encseq(GtNodeStream *ltrh_stream);
#endif
genometools-1.5.1/src/ltr/ltrharvest_tabout_stream.c000066400000000000000000000051541211610345200227340ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "extended/visitor_stream_api.h"
#include "ltr/ltrharvest_tabout_stream.h"
#include "ltr/ltrharvest_tabout_visitor.h"

GtNodeStream* gt_ltrharvest_tabout_stream_new(GtNodeStream *in_stream,
                                              GtNodeVisitor *v)
{
  return gt_visitor_stream_new(in_stream, v);
}

void gt_ltrharvest_tabout_stream_printshortheader(void)
{
  printf("# predictions are reported in the following way\n");
  printf("# s(ret) e(ret) l(ret) s(lLTR) e(lLTR) l(lLTR)"
      " s(rLTR) e(rLTR) l(rLTR) sim(LTRs) seq-nr \n");
  printf("# where:\n");
  printf("# s = starting position\n");
  printf("# e = ending position\n");
  printf("# l = length\n");
  printf("# ret = LTR-retrotransposon\n");
  printf("# lLTR = left LTR\n");
  printf("# rLTR = right LTR\n");
  printf("# sim = similarity\n");
  printf("# seq-nr = sequence number\n");
}

void gt_ltrharvest_tabout_stream_printlongheader(bool withtsd, bool withmotif)
{
  printf("# predictions are reported in the following way\n");
  printf("# s(ret) e(ret) l(ret) ");
  printf("s(lLTR) e(lLTR) l(lLTR)");
  if (withtsd)
  {
    printf(" TSD l(TSD)");
  }
  if (withmotif)
  {
    printf(" m(lLTR)");
  }
  printf(" s(rLTR) e(rLTR) l(rLTR)");
  if (withtsd)
  {
    printf(" TSD l(TSD)");
  }
  if (withmotif)
  {
    printf(" m(rLTR)");
  }
  printf(" sim(LTRs)");
  printf(" seq-nr");
  printf("\n# where:\n");
  printf("# s = starting position\n");
  printf("# e = ending position\n");
  printf("# l = length\n");
  if (withmotif)
  {
    printf("# m = motif\n");
  }
  printf("# ret = LTR-retrotransposon\n");
  printf("# lLTR = left LTR\n");
  printf("# rLTR = right LTR\n");
  if (withtsd)
  {
    printf("# TSD = target site duplication\n");
  }
  printf("# sim = similarity\n");
  printf("# seq-nr = sequence number\n");
}
genometools-1.5.1/src/ltr/ltrharvest_tabout_stream.h000066400000000000000000000025641211610345200227430ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTRHARVEST_TABOUT_STREAM_H
#define LTRHARVEST_TABOUT_STREAM_H

#include "extended/node_stream_api.h"
#include "extended/node_visitor_api.h"

/* Takes ownership of . */
GtNodeStream* gt_ltrharvest_tabout_stream_new(GtNodeStream *in_stream,
                                              GtNodeVisitor *v);
void          gt_ltrharvest_tabout_stream_printshortheader(void);
void          gt_ltrharvest_tabout_stream_printlongheader(bool withtsd,
                                                          bool withmotif);
#endif
genometools-1.5.1/src/ltr/ltrharvest_tabout_visitor.c000066400000000000000000000226201211610345200231350ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/array_api.h"
#include "core/class_alloc_lock.h"
#include "core/cstr_api.h"
#include "core/encseq_api.h"
#include "core/ma.h"
#include "core/parseutils.h"
#include "core/range.h"
#include "core/str_api.h"
#include "core/unused_api.h"
#include "extended/node_visitor_api.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "extended/feature_type.h"
#include "ltr/ltrharvest_tabout_visitor.h"

struct GtLTRharvestTaboutVisitor {
  const GtNodeVisitor parent_instance;
  bool longoutput;
  const GtEncseq *encseq;
};

#define gt_ltrharvest_tabout_visitor_cast(GV)\
        gt_node_visitor_cast(gt_ltrharvest_tabout_visitor_class(), GV)

static inline void
gt_ltrharvest_tabout_visitor_seq4feat(GtLTRharvestTaboutVisitor *nv,
                                      GtFeatureNode *fn, GtStr *out,
                                      unsigned long seqnum)
{
  char *buf;
  GtRange rng;
  unsigned long startpos;
  gt_assert(nv && fn && out);
  rng = gt_genome_node_get_range((GtGenomeNode*) fn);
  buf = gt_calloc((size_t) (gt_range_length(&rng)+1), sizeof (char));
  startpos = gt_encseq_seqstartpos(nv->encseq, seqnum);
  gt_encseq_extract_decoded(nv->encseq, buf,
                            startpos + rng.start - 1,
                            startpos + rng.end - 1);
  gt_str_append_cstr(out, buf);
  gt_free(buf);
}

static int gt_ltrharvest_tabout_visitor_feature_node(GtNodeVisitor *nv,
                                                     GtFeatureNode *fn,
                                                     GT_UNUSED GtError *err)
{
  GtLTRharvestTaboutVisitor *lv;
  GtFeatureNodeIterator *fni;
  GtFeatureNode *curnode = NULL,
                *leftltr = NULL,
                *rightltr = NULL,
                *ltr_retrotrans = NULL,
                *lefttsd = NULL,
                *righttsd = NULL,
                *leftmotif_5 = NULL,
                *leftmotif_3 = NULL,
                *rightmotif_5 = NULL,
                *rightmotif_3 = NULL;
  int had_err = 0,
      added_motifs = 0,
      added_tsd = 0,
      added_ltr = 0;
  GtStr *line;
  GtRange rng;
  bool no_element = false;
  unsigned long seqnum = 0;
  const char *fnt;
  char buf[BUFSIZ];
  lv = gt_ltrharvest_tabout_visitor_cast(nv);
  gt_assert(lv);
  gt_error_check(err);

  line = gt_str_new();
  /* traverse annotation subgraph and collect info */
  fni = gt_feature_node_iterator_new(fn);
  while (!had_err && (curnode = gt_feature_node_iterator_next(fni))) {
    fnt = gt_feature_node_get_type(curnode);

    if (strcmp(fnt, gt_ft_LTR_retrotransposon) == 0)
    {
      const char *val;
      ltr_retrotrans = curnode;
      val = gt_feature_node_get_attribute(curnode, "seq_number");
      if (val == NULL) {
        gt_error_set(err, "missing attribute \"seq_number\"");
        had_err = -1;
      }
      if (!had_err) {
        (void) gt_parse_ulong(&seqnum, val);
      }
    }
    if (strcmp(fnt, gt_ft_long_terminal_repeat) == 0)
    {
      switch (added_ltr) {
        case 0:
          leftltr = curnode;
          break;
        case 1:
          rightltr = curnode;
          break;
        default:
          gt_error_set(err,
                       "invalid number of LTR annotations: more than 2");
          had_err = -1;
      }
      added_ltr++;
    }
    if (strcmp(fnt, gt_ft_inverted_repeat) == 0)
    {
      switch (added_motifs) {
        case 0:
          leftmotif_5 = curnode;
          break;
        case 1:
          leftmotif_3 = curnode;
          break;
        case 2:
          rightmotif_5 = curnode;
          break;
        case 3:
          rightmotif_3 = curnode;
          break;
        default:
          gt_error_set(err,
                       "invalid number of motif annotations: more than 4");
          had_err = -1;
          break;
      }
      added_motifs++;
    }
    if (strcmp(fnt, gt_ft_target_site_duplication) == 0)
    {
      switch (added_tsd) {
        case 0:
          lefttsd = curnode;
          break;
        case 1:
          righttsd = curnode;
          break;
        default:
          gt_error_set(err,
                       "invalid number of TSD annotations: more than 2");
          had_err = -1;
      }
      added_tsd++;
    }
  }
  gt_feature_node_iterator_delete(fni);

  /* check for invalid annotations */
  if (!had_err && (!leftltr || !rightltr)) {
    gt_error_set(err, "missing LTR annotations");
    had_err = -1;
  }
  if (lv->longoutput) {
    if (!had_err && added_motifs > 0 && added_motifs != 4) {
      gt_error_set(err, "invalid number of motif annotations, != 4");
      had_err = -1;
    }
    if (!had_err && added_tsd > 0 && added_tsd != 2) {
      gt_error_set(err, "invalid number of TSD annotations, != 2");
      had_err = -1;
    }
  }

  /* output in tabular format */
  if (!had_err) {
    if (ltr_retrotrans != NULL) {
      /* whole element */
      rng = gt_genome_node_get_range((GtGenomeNode*) ltr_retrotrans);
      (void) snprintf(buf, BUFSIZ-1, "%lu  %lu  %lu  ", rng.start,
                      rng.end, gt_range_length(&rng));
      gt_str_append_cstr(line, buf);
    } else {
      no_element = true;
    }
  }

  if (!had_err && !no_element) {
    /* left LTR */
    rng = gt_genome_node_get_range((GtGenomeNode*) leftltr);
    (void) snprintf(buf, BUFSIZ-1, "%lu  %lu  %lu  ", rng.start,
                    rng.end, gt_range_length(&rng));
    gt_str_append_cstr(line, buf);
    /* left TSD */
    if (lv->longoutput && added_tsd > 0 ) {
      gt_assert(lefttsd);
      gt_ltrharvest_tabout_visitor_seq4feat(lv, lefttsd, line, seqnum);
      gt_str_append_cstr(line, "  ");
      rng = gt_genome_node_get_range((GtGenomeNode*) lefttsd);
      gt_str_append_ulong(line, gt_range_length(&rng));
      gt_str_append_cstr(line, "  ");
    }
    /* left motif */
    if (lv->longoutput && added_motifs > 0 ) {
      gt_assert(leftmotif_5 && leftmotif_3);
      gt_ltrharvest_tabout_visitor_seq4feat(lv, leftmotif_5, line, seqnum);
      gt_str_append_cstr(line, "..");
      gt_ltrharvest_tabout_visitor_seq4feat(lv, leftmotif_3, line, seqnum);
      gt_str_append_cstr(line, "  ");
    }

    /* right LTR */
    rng = gt_genome_node_get_range((GtGenomeNode*) rightltr);
    (void) snprintf(buf, BUFSIZ-1, "%lu  %lu  %lu  ", rng.start,
                    rng.end, gt_range_length(&rng));
    gt_str_append_cstr(line, buf);
    /* right TSD */
    if (lv->longoutput && added_tsd > 0 ) {
      gt_assert(righttsd);
      gt_ltrharvest_tabout_visitor_seq4feat(lv, righttsd, line, seqnum);
      gt_str_append_cstr(line, "  ");
      rng = gt_genome_node_get_range((GtGenomeNode*) righttsd);
      gt_str_append_ulong(line, gt_range_length(&rng));
      gt_str_append_cstr(line, "  ");
    }
    /* right motif */
    if (lv->longoutput && added_motifs > 0 ) {
      gt_assert(rightmotif_5 && rightmotif_3);
      gt_ltrharvest_tabout_visitor_seq4feat(lv, rightmotif_5, line, seqnum);
      gt_str_append_cstr(line, "..");
      gt_ltrharvest_tabout_visitor_seq4feat(lv, rightmotif_3, line, seqnum);
      gt_str_append_cstr(line, "  ");
    }

    gt_str_append_cstr(line, gt_feature_node_get_attribute(ltr_retrotrans,
                                                           "ltr_similarity"));
    gt_str_append_cstr(line, "  ");
    gt_str_append_ulong(line, seqnum);
    printf("%s\n", gt_str_get(line));
  }
  gt_str_delete(line);
  return had_err;
}

const GtNodeVisitorClass* gt_ltrharvest_tabout_visitor_class(void)
{
  static const GtNodeVisitorClass *nvc = NULL;
  gt_class_alloc_lock_enter();
  if (!nvc) {
    nvc = gt_node_visitor_class_new(sizeof (GtLTRharvestTaboutVisitor),
                                    NULL,
                                    NULL,
                                    gt_ltrharvest_tabout_visitor_feature_node,
                                    NULL,
                                    NULL,
                                    NULL);
  }
  gt_class_alloc_lock_leave();
  return nvc;
}

GtNodeVisitor* gt_ltrharvest_tabout_visitor_new(void)
{
  GtNodeVisitor *nv;
  GtLTRharvestTaboutVisitor *lv;
  nv = gt_node_visitor_create(gt_ltrharvest_tabout_visitor_class());
  lv = gt_ltrharvest_tabout_visitor_cast(nv);
  gt_assert(lv);
  lv->longoutput = false;
  lv->encseq = NULL;
  return nv;
}

GtNodeVisitor* gt_ltrharvest_tabout_visitor_new_longoutput(const GtEncseq
                                                                        *encseq)
{
  GtNodeVisitor *nv;
  GtLTRharvestTaboutVisitor *lv;
  gt_assert(encseq);
  nv = gt_node_visitor_create(gt_ltrharvest_tabout_visitor_class());
  lv = gt_ltrharvest_tabout_visitor_cast(nv);
  gt_assert(lv);
  lv->longoutput = true;
  lv->encseq = encseq;
  return nv;
}
genometools-1.5.1/src/ltr/ltrharvest_tabout_visitor.h000066400000000000000000000026021211610345200231400ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LTRHARVEST_TABOUT_VISITOR_H
#define LTRHARVEST_TABOUT_VISITOR_H

/* Implements the  interface. */
typedef struct GtLTRharvestTaboutVisitor GtLTRharvestTaboutVisitor;

#include "core/encseq_api.h"
#include "extended/node_visitor.h"

const GtNodeVisitorClass* gt_ltrharvest_tabout_visitor_class(void);
GtNodeVisitor*            gt_ltrharvest_tabout_visitor_new(void);
GtNodeVisitor*            gt_ltrharvest_tabout_visitor_new_longoutput(
                                                        const GtEncseq *encseq);

#endif
genometools-1.5.1/src/ltr/pbs.c000066400000000000000000000351451211610345200163740ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009 Sascha Steinbiss 
  Copyright (c) 2008-2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/minmax.h"
#include "core/xansi_api.h"
#include "core/array.h"
#include "core/bioseq.h"
#include "core/ensure.h"
#include "core/fa.h"
#include "core/fileutils_api.h"
#include "extended/reverse_api.h"
#include "extended/swalign.h"
#include "ltr/pbs.h"

struct GtPBSHit {
  unsigned long start,
                end,
                edist,
                offset,
                tstart,
                alilen;
  GtStrand strand;
  double score;
  const char *trna;
  GtPBSResults *res;
};

struct GtPBSResults {
  GtArray *hits;
  GtLTRElement *elem;
  GtPBSOptions *opts;
};

static GtPBSHit* gt_pbs_hit_new(unsigned long alilen, GtStrand strand,
                                const char *tRNA, unsigned long tstart,
                                unsigned long start, unsigned long end,
                                unsigned long offset, unsigned long edist,
                                double score, GtPBSResults *r)
{
  GtPBSHit *hit = gt_malloc(sizeof (GtPBSHit));
  hit->alilen  = alilen;
  hit->strand  = strand;
  hit->trna    = tRNA;
  hit->tstart  = tstart;
  hit->start   = start;
  hit->end     = end;
  hit->offset  = offset;
  hit->edist   = edist;
  hit->score   = score;
  hit->res     = r;
  return hit;
}

static GtPBSResults* gt_pbs_results_new(GtLTRElement *elem,
                                        GtPBSOptions *opts)
{
  GtPBSResults *res = gt_calloc((size_t) 1, sizeof (GtPBSResults));
  res->elem = elem;
  res->opts = opts;
  res->hits = gt_array_new(sizeof (GtPBSHit*));
  return res;
}

GtRange gt_pbs_hit_get_coords(const GtPBSHit *h)
{
  GtRange rng;
  gt_assert(h && h->end >= h->start);
  rng.start = h->start;
  rng.end = h->end;
  switch (h->strand)
  {
    case GT_STRAND_FORWARD:
    default:
      rng.start = h->res->elem->leftLTR_3 + 1 - h->res->opts->radius
                    + rng.start;
      rng.end = rng.start + (h->end - h->start);
      break;
    case GT_STRAND_REVERSE:
      rng.end = h->res->elem->rightLTR_5 - 1 + h->res->opts->radius - rng.start;
      rng.start = rng.end - (h->end - h->start);
      break;
  }
  gt_assert(gt_range_length(&rng) == (h->end - h->start + 1));
  return rng;
}

unsigned long gt_pbs_hit_get_offset(const GtPBSHit *h)
{
  gt_assert(h);
  return h->offset;
}

double gt_pbs_hit_get_score(const GtPBSHit *h)
{
  gt_assert(h);
  return h->score;
}

unsigned long gt_pbs_hit_get_edist(const GtPBSHit *h)
{
  gt_assert(h);
  return h->edist;
}

const char* gt_pbs_hit_get_trna(const GtPBSHit *h)
{
  gt_assert(h);
  return h->trna;
}

unsigned long gt_pbs_hit_get_tstart(const GtPBSHit *h)
{
  gt_assert(h);
  return h->tstart;
}

GtStrand gt_pbs_hit_get_strand(const GtPBSHit *h)
{
  gt_assert(h);
  return h->strand;
}

unsigned long gt_pbs_hit_get_alignment_length(const GtPBSHit *h)
{
  gt_assert(h);
  return h->alilen;
}

unsigned long gt_pbs_results_get_number_of_hits(const GtPBSResults *r)
{
  gt_assert(r);
  return gt_array_size(r->hits);
}

GtPBSHit* gt_pbs_results_get_ranked_hit(const GtPBSResults *r, unsigned long i)
{
  gt_assert(r);
  return *(GtPBSHit**) gt_array_get(r->hits, i);
}

static GtScoreFunction* gt_dna_scorefunc_new(GtAlphabet *a, int match,
                                             int mismatch, int insertion,
                                             int deletion)
{
  GtScoreMatrix *sm = gt_score_matrix_new(a);
  GtScoreFunction *sf = gt_score_function_new(sm, insertion, deletion);
  unsigned int m,n;

  for (m=0;m nr2) {
    return nr1 - nr2;
  } else {
    return nr2 - nr1;
  }
}

static void gt_pbs_add_hit(GtArray *hitlist, GtAlignment *ali, GtPBSOptions *o,
                           unsigned long trna_seqlen, const char *desc,
                           GtStrand strand, GtPBSResults *r)
{
  unsigned long dist;
  GtPBSHit *hit;
  unsigned long offset, alilen;
  GtRange urange, vrange;
  gt_assert(hitlist && desc);

  if (!ali) return;
  gt_assert(ali);

  dist = gt_alignment_eval(ali);
  urange = gt_alignment_get_urange(ali);
  vrange = gt_alignment_get_vrange(ali);
  offset = gt_ulongabs((unsigned long) o->radius, urange.start);
  alilen = gt_ulongabs(urange.end, urange.start)+1;

  if (dist <= (unsigned long) o->max_edist
        && offset <= o->offsetlen.end
        && offset >= o->offsetlen.start
        && alilen <= o->alilen.end
        && alilen >= o->alilen.start
        && vrange.start <= o->trnaoffsetlen.end
        && vrange.start >= o->trnaoffsetlen.start)
  {
    hit = gt_pbs_hit_new(alilen,
                         strand,
                         desc,
                         vrange.start,
                         urange.start,
                         urange.end,
                         offset,
                         dist,
                         gt_pbs_score_func(dist,
                                           offset,
                                           urange.end-urange.start+1,
                                           trna_seqlen,
                                           vrange.start),
                         r);
    gt_array_add(hitlist, hit);
  }
}

static int gt_pbs_hit_compare(const void *h1, const void *h2)
{
  GtPBSHit *hp1 = *(GtPBSHit**) h1;
  GtPBSHit *hp2 = *(GtPBSHit**) h2;

  return (gt_double_compare(hp2->score, hp1->score));
}

GtPBSResults* gt_pbs_find(const char *seq,
                          const char *rev_seq,
                          GtLTRElement *element,
                          GtPBSOptions *o,
                          GtError *err)
{
  GtSeq *seq_forward, *seq_rev;
  GtPBSResults *results;
  unsigned long j;
  GtAlignment *ali;
  GtAlphabet *a = gt_alphabet_new_dna();
  GtScoreFunction *sf = gt_dna_scorefunc_new(a,
                                             o->ali_score_match,
                                             o->ali_score_mismatch,
                                             o->ali_score_insertion,
                                             o->ali_score_deletion);

  gt_assert(seq && rev_seq && sf && a && element);

  results = gt_pbs_results_new(element, o);

  seq_forward = gt_seq_new(seq + (gt_ltrelement_leftltrlen(element))
                               - (o->radius),
                           (unsigned long) (2*o->radius + 1),
                           a);

  seq_rev     = gt_seq_new(rev_seq + (gt_ltrelement_rightltrlen(element))
                                   - (o->radius),
                           (unsigned long) (2*o->radius + 1),
                           a);

  for (j=0;jtrna_lib);j++)
  {
    GtSeq *trna_seq, *trna_from3;
    char *trna_from3_full;
    unsigned long trna_seqlen;

    trna_seq = gt_bioseq_get_seq(o->trna_lib, j);
    trna_seqlen = gt_seq_length(trna_seq);

    trna_from3_full = gt_calloc((size_t) trna_seqlen, sizeof (char));
    memcpy(trna_from3_full, gt_seq_get_orig(trna_seq),
           sizeof (char)*trna_seqlen);
    (void) gt_reverse_complement(trna_from3_full, trna_seqlen, err);
    trna_from3 = gt_seq_new_own(trna_from3_full, trna_seqlen, a);

    ali = gt_swalign(seq_forward, trna_from3, sf);
    gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
                   gt_seq_get_description(trna_seq), GT_STRAND_FORWARD,
                   results);
    gt_alignment_delete(ali);

    ali = gt_swalign(seq_rev, trna_from3, sf);
    gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
                   gt_seq_get_description(trna_seq), GT_STRAND_REVERSE,
                   results);
    gt_alignment_delete(ali);

    gt_seq_delete(trna_seq);
    gt_seq_delete(trna_from3);
  }
  gt_seq_delete(seq_forward);
  gt_seq_delete(seq_rev);
  gt_score_function_delete(sf);
  gt_alphabet_delete(a);
  gt_array_sort(results->hits, gt_pbs_hit_compare);
  return results;
}

void gt_pbs_results_delete(GtPBSResults *results)
{
    unsigned long i;
    if (!results) return;
    if (results->hits != NULL)
    {
      for (i=0;ihits);i++)
      {
        GtPBSHit *hit = *(GtPBSHit**) gt_array_get(results->hits, i);
        gt_free(hit);
      }
      gt_array_delete(results->hits);
    }
    gt_free(results);
}

int gt_pbs_unit_test(GtError *err)
{
  int had_err = 0;
  GtLTRElement element;
  GtPBSOptions o;
  GtStr *tmpfilename;
  FILE *tmpfp;
  GtPBSResults *res;
  GtPBSHit *hit;
  double score1, score2;
  GtRange rng;
  char *rev_seq,
       *seq,
       tmp[BUFSIZ];
  const char *fullseq =                           "aaaaaaaaaaaaaaaaaaaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "acatactaggatgctag" /* <- PBS forward */
                                     "aatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatag"
                                   /* PBS reverse -> */ "gatcctaaggctac"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "aaaaaaaaaaaaaaaaaaaa";

  /* notice previous errors */
  gt_error_check(err);

  /* create temporary tRNA library file */
  tmpfilename = gt_str_new();
  tmpfp = gt_xtmpfp(tmpfilename);
  fprintf(tmpfp, ">test1\nccccccccccccccctagcatcctagtatgtccc\n"
                 ">test2\ncccccccccgatcctagggctaccctttc\n");
  gt_fa_xfclose(tmpfp);
  gt_ensure(had_err, gt_file_exists(gt_str_get(tmpfilename)));

  /* setup testing parameters */
  o.radius = 30U;
  o.max_edist = 1U;
  o.alilen.start = 11UL;
  o.alilen.end = 30UL;
  o.offsetlen.start = 0UL;
  o.offsetlen.end = 5UL;
  o.trnaoffsetlen.start = 0UL;
  o.trnaoffsetlen.end =  40UL;
  o.ali_score_match = 5;
  o.ali_score_mismatch = -10;
  o.ali_score_insertion = o.ali_score_deletion = -20;
  o.trna_lib = gt_bioseq_new(gt_str_get(tmpfilename), err);
  gt_ensure(had_err, gt_bioseq_number_of_sequences(o.trna_lib) == 2UL);

  element.leftLTR_5 = 20UL;
  element.leftLTR_3 = 119UL;
  element.rightLTR_5 = 520UL;
  element.rightLTR_3 = 619UL;

  /* setup sequences */
  seq     = gt_malloc((size_t) 600 * sizeof (char));
  rev_seq = gt_malloc((size_t) 600 * sizeof (char));
  memcpy(seq,     fullseq + 20, (size_t) 600);
  memcpy(rev_seq, fullseq + 20, (size_t) 600);
  gt_ensure(had_err,
            !gt_reverse_complement(rev_seq, (unsigned long) 600, NULL));

  /* try to find PBS in sequences */
  res = gt_pbs_find(seq, rev_seq, &element, &o, err);
  gt_ensure(had_err, res != NULL);
  gt_ensure(had_err, gt_pbs_results_get_number_of_hits(res) == 2UL);

  /* check first hit on forward strand */
  hit = gt_pbs_results_get_ranked_hit(res, 0UL);
  gt_ensure(had_err, hit != NULL);
  gt_ensure(had_err, gt_pbs_hit_get_alignment_length(hit) == 17UL);
  gt_ensure(had_err, gt_pbs_hit_get_edist(hit) == 0UL);
  gt_ensure(had_err, gt_pbs_hit_get_offset(hit) == 0UL);
  gt_ensure(had_err, gt_pbs_hit_get_tstart(hit) == 3UL);
  gt_ensure(had_err, strcmp(gt_pbs_hit_get_trna(hit), "test1") == 0);
  rng = gt_pbs_hit_get_coords(hit);
  gt_ensure(had_err, rng.start == 120UL);
  gt_ensure(had_err, rng.end == 136UL);
  score1 = gt_pbs_hit_get_score(hit);
  gt_ensure(had_err, gt_pbs_hit_get_strand(hit) == GT_STRAND_FORWARD);
  memset(tmp, 0, BUFSIZ-1);
  memcpy(tmp, fullseq + (rng.start * sizeof (char)),
         (size_t) ((rng.end - rng.start + 1) * sizeof (char)));
  gt_ensure(had_err, strcmp(tmp, "acatactaggatgctag" ) == 0);

  /* check second hit on reverse strand */
  hit = gt_pbs_results_get_ranked_hit(res, 1UL);
  gt_ensure(had_err, hit != NULL);
  gt_ensure(had_err, gt_pbs_hit_get_alignment_length(hit) == 14UL);
  gt_ensure(had_err, gt_pbs_hit_get_edist(hit) == 1UL);
  gt_ensure(had_err, gt_pbs_hit_get_offset(hit) == 0UL);
  gt_ensure(had_err, gt_pbs_hit_get_tstart(hit) == 6UL);
  gt_ensure(had_err, strcmp(gt_pbs_hit_get_trna(hit), "test2") == 0);
  rng = gt_pbs_hit_get_coords(hit);
  gt_ensure(had_err, rng.start == 506UL);
  gt_ensure(had_err, rng.end == 519UL);
  score2 = gt_pbs_hit_get_score(hit);
  gt_ensure(had_err, gt_double_compare(score1, score2) > 0);
  gt_ensure(had_err, gt_pbs_hit_get_strand(hit) == GT_STRAND_REVERSE);
  memset(tmp, 0, BUFSIZ-1);
  memcpy(tmp, fullseq + (rng.start * sizeof (char)),
         (size_t) ((rng.end - rng.start + 1) * sizeof (char)));
  gt_ensure(had_err, strcmp(tmp, "gatcctaaggctac" ) == 0);

  /* clean up */
  gt_xremove(gt_str_get(tmpfilename));
  gt_ensure(had_err, !gt_file_exists(gt_str_get(tmpfilename)));
  gt_str_delete(tmpfilename);
  gt_bioseq_delete(o.trna_lib);
  gt_free(rev_seq);
  gt_free(seq);
  gt_pbs_results_delete(res);

  return had_err;
}
genometools-1.5.1/src/ltr/pbs.h000066400000000000000000000046201211610345200163730ustar00rootroot00000000000000/*
  Copyright (c) 2008 Sascha Steinbiss 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef PBS_H
#define PBS_H

#include "core/undef_api.h"
#include "core/bioseq.h"
#include "core/dlist.h"
#include "core/seq.h"
#include "core/strand.h"
#include "core/score_function.h"
#include "extended/alignment.h"
#include "ltr/ltrelement.h"

typedef struct GtPBSOptions {
  unsigned int radius,
               max_edist;
  GtRange alilen,
          offsetlen,
          trnaoffsetlen;
  int ali_score_match,
      ali_score_mismatch,
      ali_score_insertion,
      ali_score_deletion;
  GtBioseq *trna_lib;
} GtPBSOptions;

typedef struct GtPBSHit GtPBSHit;
typedef struct GtPBSResults GtPBSResults;

GtPBSResults*  gt_pbs_find(const char *seq,
                           const char *rev_seq,
                           GtLTRElement *element,
                           GtPBSOptions *o,
                           GtError *err);

GtRange        gt_pbs_hit_get_coords(const GtPBSHit*);
GtStrand       gt_pbs_hit_get_strand(const GtPBSHit*);
double         gt_pbs_hit_get_score(const GtPBSHit*);
unsigned long  gt_pbs_hit_get_edist(const GtPBSHit*);
unsigned long  gt_pbs_hit_get_offset(const GtPBSHit*);
unsigned long  gt_pbs_hit_get_tstart(const GtPBSHit*);
const char*    gt_pbs_hit_get_trna(const GtPBSHit*);
unsigned long  gt_pbs_hit_get_alignment_length(const GtPBSHit*);

unsigned long  gt_pbs_results_get_number_of_hits(const GtPBSResults*);
GtPBSHit*      gt_pbs_results_get_ranked_hit(const GtPBSResults*,
                                             unsigned long);
void           gt_pbs_results_delete(GtPBSResults*);

int            gt_pbs_unit_test(GtError*);

#endif
genometools-1.5.1/src/ltr/pdom.c000066400000000000000000001015501211610345200165410ustar00rootroot00000000000000/*
  Copyright (c) 2008-2010 Sascha Steinbiss 
  Copyright (c) 2008-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifdef HAVE_HMMER

#include 
#include 
#include 
#include 
#include 
#include 

#include "core/codon_api.h"
#include "core/codon_iterator_simple_api.h"
#include "core/log.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/minmax.h"
#include "core/thread_api.h"
#include "core/translator.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "extended/globalchaining.h"
#include "extended/reverse_api.h"
#include "ltr/pdom.h"

/* HMMER3 related includes */
#include "p7_config.h"
#include "easel.h"
#include "esl_alphabet.h"
#include "esl_getopts.h"
#include "esl_sq.h"
#include "esl_ssi.h"
#include "esl_sqio.h"
#include "esl_stopwatch.h"
#include "p7_config.h"
#ifdef HMMER_THREADS
#include "esl_threads.h"
#include "esl_workqueue.h"
#endif
#include "hmmer.h"

struct GtPdomFinder {
  GtStrArray *hmm_files;
  GtArray *models;
  GtLTRElement *elem;
  ESL_GETOPTS *getopts;
  double glob_eval_cutoff;
  bool reportall;
  unsigned int chain_max_gap_length;
};

struct GtPdomModel {
  P7_HMM *model;
  ESL_ALPHABET *abc;
  unsigned long reference_count;
};

struct GtPdomSingleHit {
  GtPhase phase;
  GtRange range;
  GtStr *aa_seq_model,
        *mline,
        *aa_seq_matched;
  double eval;
  bool chained;
  GtPdomModelHit *mhit;
  unsigned long reference_count;
  GtArray *chains;
};

struct GtPdomModelHit {
  P7_TOPHITS *hits_fwd, *hits_rev;
  GtStrand strand;
  GtArray *members;
  unsigned long reference_count;
  GtLTRElement *elem;
};

struct GtPdomResults {
  GtHashmap *domains;
  double combined_e_value_fwd,
         combined_e_value_rev;
  bool empty;
};

typedef struct GtPdomDomainTraverseInfo {
  GtPdomIteratorFunc func;
  void *data;
} GtPdomDomainTraverseInfo;

typedef struct GtPdomSharedMem {
  GtPdomFinder *gpf;
  unsigned long next_hmm;
  GtArray *hmms;
  GtStr **fwd, **rev;
  GtPdomResults *results;
  GtMutex *in_lock, *out_lock;
} GtPdomSharedMem;

/* --------------- GtPdomSingleHit ---------------------------------- */

#define gt_pdom_isgap(c) ((c) == ' ' || (c) == '.' || (c) == '_' \
                            || (c) == '-' || (c) == '~')

void gt_pdom_single_hit_format_alignment(const GtPdomSingleHit *sh,
                                         unsigned long width,
                                         GtStr *dest)
{
  unsigned long pos,
                match_start,
                match_end,
                i,
                len, modellen, matchlen;
  char *buffer, cpbuf[BUFSIZ];
  const char *model,
             *mline,
             *matched;
  gt_assert(sh && width > 0 && dest && width < BUFSIZ);
  buffer = gt_calloc(width+1, sizeof (char));
  model = gt_str_get(sh->aa_seq_model);
  mline = gt_str_get(sh->mline);
  matched = gt_str_get(sh->aa_seq_matched);
  gt_str_reset(dest);

  modellen = gt_str_length(sh->aa_seq_model);
  matchlen = gt_str_length(sh->aa_seq_matched);
  len = MAX(modellen, matchlen);

  match_end = sh->range.start - 1;
  if (width > len)
    width = len;
  for (pos = 0; pos + width < len; pos += width)
  {
    match_start = match_end + 1;
    for (i = pos; i < pos + width && matched[i] != '\0'; i++)
      if (!gt_pdom_isgap(matched[i])) match_end++;
    strncpy(buffer, model+pos, width);
    snprintf(cpbuf, BUFSIZ, "%6s %s\n", " ", buffer);
    gt_str_append_cstr(dest, cpbuf);
    strncpy(buffer, mline+pos, width);
    snprintf(cpbuf, BUFSIZ, "%6s %s\n", " ", buffer);
    gt_str_append_cstr(dest, cpbuf);
    strncpy(buffer, matched+pos, width);
    snprintf(cpbuf, BUFSIZ, "%6lu %s %6lu\n\n",
                            match_start,
                            buffer,
                            match_end);
    gt_str_append_cstr(dest, cpbuf);
  }
  if (pos < len)
  {
    unsigned long rest_len;
    rest_len = len - pos;
    match_start = match_end + 1;
    for (i = pos; i < len && matched[i] != '\0'; i++)
      if (!gt_pdom_isgap(matched[i])) match_end++;
    strncpy(buffer, model+pos, rest_len);
    buffer[rest_len]='\0';
    snprintf(cpbuf, BUFSIZ, "%6s %s\n", " ", buffer);
    gt_str_append_cstr(dest, cpbuf);
    strncpy(buffer, mline+pos, rest_len);
    snprintf(cpbuf, BUFSIZ, "%6s %s\n", " ", buffer);
    gt_str_append_cstr(dest, cpbuf);
    strncpy(buffer, matched+pos, rest_len);
    snprintf(cpbuf, BUFSIZ, "%6lu %s %6lu\n\n",
                            match_start,
                            buffer,
                            match_end);
    gt_str_append_cstr(dest, cpbuf);
  }
  gt_free(buffer);
}

void gt_pdom_single_hit_get_aaseq(const GtPdomSingleHit *sh,
                                  GtStr *dest)
{
  const char *matched;
  unsigned long i;
  gt_assert(sh && dest);
  gt_str_reset(dest);

  matched = gt_str_get(sh->aa_seq_matched);
  for (i = 0; i < gt_str_length(sh->aa_seq_matched); i++)
  {
    if (!gt_pdom_isgap(matched[i])) {
      /* replace stop codons by 'X'es */
      if (matched[i] == '*') {
        gt_str_append_char(dest, 'X');
      } else {
        gt_str_append_char(dest, toupper(matched[i]));
      }
    }
  }
}

static GtPdomSingleHit* gt_pdom_single_hit_new(P7_DOMAIN *singlehit,
                                               GtPdomModelHit *mhit)
{
  GtPdomSingleHit *hit;
  gt_assert(singlehit && singlehit->ad);
  hit = gt_calloc(1, sizeof (GtPdomSingleHit));
  hit->phase = gt_phase_get(singlehit->ad->sqname[0]);
  hit->range.start = singlehit->ad->sqfrom-1;
  hit->range.end = singlehit->ad->sqto-1;
  gt_log_log("create single hit %lu-%lu", hit->range.start, hit->range.end);
  gt_assert(gt_range_length(&(hit->range)) > 0);
  hit->mhit = mhit;
  hit->eval = singlehit->pvalue;
  if (singlehit->ad && singlehit->ad->aseq)
    hit->aa_seq_matched = gt_str_new_cstr(singlehit->ad->aseq);
  if (singlehit->ad && singlehit->ad->model)
    hit->aa_seq_model = gt_str_new_cstr(singlehit->ad->model);
  if (singlehit->ad && singlehit->ad->mline)
    hit->mline = gt_str_new_cstr(singlehit->ad->mline);
  gt_assert(hit->range.start <= hit->range.end);
  hit->chains = gt_array_new(sizeof (unsigned long));
  hit->chained = false;
  return hit;
}

GtPdomSingleHit* gt_pdom_single_hit_ref(GtPdomSingleHit *sh)
{
  gt_assert(sh);
  sh->reference_count++;
  return sh;
}

GtPhase gt_pdom_single_hit_get_phase(const GtPdomSingleHit *singlehit)
{
  gt_assert(singlehit);
  return singlehit->phase;
}

GtRange gt_pdom_single_hit_get_range(const GtPdomSingleHit *singlehit)
{
  GtRange retrng;
  gt_assert(singlehit);
  switch (singlehit->mhit->strand)
  {
    case GT_STRAND_FORWARD:
    default:
      retrng.start = singlehit->mhit->elem->leftLTR_5
                        + (singlehit->range.start) * GT_CODON_LENGTH
                        + (unsigned long) singlehit->phase;
      retrng.end   =  retrng.start
                        + (gt_range_length(&singlehit->range) - 1)
                           * GT_CODON_LENGTH;
      break;
    case GT_STRAND_REVERSE:
      retrng.start = singlehit->mhit->elem->rightLTR_3
                        - (singlehit->range.end+1) * GT_CODON_LENGTH
                        - (unsigned long) singlehit->phase;
      retrng.end   =  retrng.start
                        + (gt_range_length(&singlehit->range) - 1)
                           * GT_CODON_LENGTH;
      break;
  }
  gt_log_log("range: (%lu-%lu, phase %d) -> %lu-%lu (len %lu) strand: %c\n",
             singlehit->range.start, singlehit->range.end,
             singlehit->phase, retrng.start, retrng.end,
             gt_range_length(&retrng),
             GT_STRAND_CHARS[singlehit->mhit->strand]);
  return retrng;
}

double gt_pdom_single_hit_get_evalue(const GtPdomSingleHit *singlehit)
{
  gt_assert(singlehit);
  return singlehit->eval;
}

void gt_pdom_single_hit_set_chained(GtPdomSingleHit *singlehit,
                                    unsigned long cno)
{
  gt_assert(singlehit);
  gt_array_add(singlehit->chains, cno);
  gt_log_log("adding single hit %lu-%lu to chain %lu", singlehit->range.start,
                                                       singlehit->range.end,
                                                       cno);
  singlehit->chained = true;
}

bool gt_pdom_single_hit_is_chained(GtPdomSingleHit *singlehit)
{
  gt_assert(singlehit);
  return singlehit->chained;
}

GtArray* gt_pdom_single_hit_get_chains(GtPdomSingleHit *singlehit)
{
  gt_assert(singlehit);
  return singlehit->chains;
}

void gt_pdom_single_hit_delete(void *value)
{
  GtPdomSingleHit *sh;
  if (!value) return;
  sh = (GtPdomSingleHit*) value;
  if (sh->reference_count) {
    sh->reference_count--;
    return;
  }
  gt_str_delete(sh->aa_seq_matched);
  gt_str_delete(sh->aa_seq_model);
  gt_str_delete(sh->mline);
  gt_array_delete(sh->chains);
  gt_free(sh);
}

/* --------------- GtPdomModelHit ---------------------------------- */

static GtPdomModelHit* gt_pdom_model_hit_new(GtLTRElement *elem)
{
  GtPdomModelHit *hit;
  hit = gt_calloc(1, sizeof (GtPdomModelHit));
  hit->hits_fwd   = p7_tophits_Create();
  hit->hits_rev   = p7_tophits_Create();
  hit->strand     = GT_STRAND_UNKNOWN;
  hit->elem       = elem;
  hit->members = gt_array_new(sizeof (GtPdomSingleHit*));
  return hit;
}

GtPdomModelHit *gt_pdom_model_hit_ref(GtPdomModelHit *mh)
{
  gt_assert(mh);
  mh->reference_count++;
  return mh;
}

void gt_pdom_model_hit_add_single_hit(GtPdomModelHit *mh,
                                      GtPdomSingleHit *sh)
{
  gt_assert(mh && mh->members && sh);
  gt_array_add(mh->members, sh);
}

GtStrand gt_pdom_model_hit_get_best_strand(const GtPdomModelHit *h)
{
  gt_assert(h);
  return h->strand;
}

unsigned long gt_pdom_model_hit_num_of_single_hits(const GtPdomModelHit *h)
{
  gt_assert(h);
  return gt_array_size(h->members);
}

GtPdomSingleHit* gt_pdom_model_hit_single_hit(const GtPdomModelHit *h,
                                          unsigned long nth)
{
  gt_assert(h);
  return *(GtPdomSingleHit**) gt_array_get(h->members, nth);
}

void gt_pdom_model_hit_delete(void *value)
{
  GtPdomModelHit *hit;
  if (!value) return;
  hit = (GtPdomModelHit*) value;
  if (hit->reference_count) {
    hit->reference_count--;
    return;
  }
  if (hit->hits_fwd)
    p7_tophits_Destroy(hit->hits_fwd);
  if (hit->hits_rev)
    p7_tophits_Destroy(hit->hits_rev);
  if (hit->members)
  {
    unsigned long i;
    for (i=0;imembers);i++)
    {
      gt_pdom_single_hit_delete(*(GtPdomSingleHit**)
                                 gt_array_get(hit->members, i));
    }
    gt_array_delete(hit->members);
  }
  gt_free(hit);
}

/* --------------- GtPdomModel ------------------------------------ */

static GtPdomModel* gt_pdom_model_new(P7_HMM *model)
{
  GtPdomModel *newmodel;
  gt_assert(model);
  newmodel = gt_calloc(1, sizeof (GtPdomModel));
  newmodel->model = model;
  return newmodel;
}

GtPdomModel *gt_pdom_model_ref(GtPdomModel *m)
{
  gt_assert(m);
  m->reference_count++;
  return m;
}

const char* gt_pdom_model_get_name(const GtPdomModel *model)
{
  gt_assert(model);
  return model->model->name;
}

const char* gt_pdom_model_get_acc(const GtPdomModel *model)
{
  gt_assert(model);
  return model->model->acc;
}

void gt_pdom_model_delete(void *value)
{
  GtPdomModel *model;
  if (!value) return;
  model = (GtPdomModel*) value;
  if (model->reference_count) {
    model->reference_count--;
    return;
  }
  if (model->abc) esl_alphabet_Destroy(model->abc);
  p7_hmm_Destroy(model->model);
  gt_free(model);
}

/* --------------- GtPdomResults ---------------------------------- */

static GtPdomResults* gt_pdom_results_new(void)
{
  GtPdomResults *res;
  res = gt_calloc(1, sizeof (GtPdomResults));
  res->domains = gt_hashmap_new(GT_HASH_DIRECT, gt_pdom_model_delete,
                                gt_pdom_model_hit_delete);
  res->empty = TRUE;
  res->combined_e_value_fwd = res->combined_e_value_rev = 0.0;
  return res;
}

bool gt_pdom_results_empty(GtPdomResults *res)
{
  gt_assert(res);
  return res->empty;
}

double gt_pdom_results_get_combined_evalue_fwd(GtPdomResults *result)
{
  gt_assert(result);
  return result->combined_e_value_fwd;
}

double gt_pdom_results_get_combined_evalue_rev(GtPdomResults *result)
{
  gt_assert(result);
  return result->combined_e_value_rev;
}

void gt_pdom_results_delete(GtPdomResults *res)
{
  if (!res) return;
  gt_hashmap_delete(res->domains);
  gt_free(res);
}

/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */

static int visit_domain(void *key, void *value, void *data,
                        GT_UNUSED GtError *err)
{
  GtPdomModel *model = (GtPdomModel *) key;
  GtPdomModelHit *hit = (GtPdomModelHit*) value;
  GtPdomDomainTraverseInfo *info = (GtPdomDomainTraverseInfo*) data;
  return info->func(model, hit, info->data, err);
}

int gt_pdom_results_foreach_domain_hit(GtPdomResults *results,
                                       GtPdomIteratorFunc func,
                                       void *data,
                                       GtError *err)
{
  GtPdomDomainTraverseInfo info;
  info.func = func;
  info.data = data;
  return gt_hashmap_foreach(results->domains,
                            visit_domain,
                            &info,
                            err);
}

static inline void gt_hmmer_search(P7_PIPELINE *pli,
                                   char *in_seq,
                                   ESL_ALPHABET *abc,
                                   P7_OPROFILE *om,
                                   P7_BG *bg,
                                   char *seqdesc,
                                   P7_TOPHITS *hits,
                                   GT_UNUSED GtMutex *lock)
{
  ESL_SQ *sq = NULL;
  /* create and encode sequence */
  sq = esl_sq_CreateFrom(seqdesc, in_seq, "\0", "\0", NULL);
  esl_sq_Digitize(abc, sq);
  /* configure for new sequence */
  p7_pli_NewSeq(pli, sq);
  p7_bg_SetLength(bg, sq->n);
  p7_oprofile_ReconfigLength(om, sq->n);
  /* process this sequence */
  p7_Pipeline(pli, om, bg, sq, hits);
  /* cleanup */
  esl_sq_Destroy(sq);  /* XXX: reuse me? */
  p7_pipeline_Reuse(pli);
}

static void chainproc(GtChain *c, GtFragment *f,
                      GT_UNUSED unsigned long nof_frags,
                      GT_UNUSED unsigned long gap_length, void *data)
{
  unsigned long i,
                *chainno = (unsigned long*) data;

  gt_log_log("resulting chain has %ld GtFragments, score %ld",
             gt_chain_size(c),
             gt_chain_get_score(c));
  for (i = 0; i < gt_chain_size(c); i++)
  {
    GtFragment frag;
    frag = f[gt_chain_get_fragnum(c, i)];
    gt_log_log("(%lu %lu) (%lu %lu)", frag.startpos1, frag.endpos1,
                                          frag.startpos2, frag.endpos2);
    gt_pdom_single_hit_set_chained((GtPdomSingleHit*) frag.data, *chainno);
  }
  (*chainno)++;
  gt_log_log("\n");
}

static int gt_fragcmp(const void *frag1, const void *frag2)
{
  GtFragment *f1 = (GtFragment*) frag1;
  GtFragment *f2 = (GtFragment*) frag2;
  if (f1->startpos2 == f2->startpos2)
    return 0;
  else return (f1->startpos2 < f2->startpos2 ? -1 : 1);
}

static void* gt_pdom_per_domain_worker_thread(void *data)
{
  GtPdomSharedMem *shared;
  GtPdomModel *hmm;
  P7_PIPELINE *pli;
  P7_TOPHITS *hits = NULL;
  bool best_fwd = TRUE;
  GtFragment *frags;
  GtPdomModelHit *hit;

  shared = (GtPdomSharedMem*) data;

  P7_BG *bg = NULL;
  P7_PROFILE *gm = NULL;
  P7_OPROFILE *om = NULL;

  for (;;)
  {
    unsigned long h = 0,
                  d = 0,
                  nof_domains = 0;
    P7_DOMAIN *lastdom = NULL;

    gt_mutex_lock(shared->in_lock);
    /* Have all HMMs been distributed? If so, we are done here. */
    if (shared->next_hmm == gt_array_size(shared->gpf->models))
    {
      gt_mutex_unlock(shared->in_lock);
      return NULL;
    }

    /* Get work from HMM list */
    hmm = *(GtPdomModel**) gt_array_get(shared->gpf->models,
                                        shared->next_hmm);
    shared->next_hmm++;

    /* work claimed, release input */
    gt_mutex_unlock(shared->in_lock);

    /* prepare HMM for searching */
    pli = p7_pipeline_Create(shared->gpf->getopts, hmm->model->M, 400,
                             p7_SEARCH_SEQS);

    bg = p7_bg_Create(hmm->abc);
    gm = p7_profile_Create(hmm->model->M, hmm->abc);
    om = p7_oprofile_Create(hmm->model->M, hmm->abc);
    p7_ProfileConfig(hmm->model, bg, gm, 400, p7_LOCAL);
    p7_oprofile_Convert(gm, om);
    p7_pli_NewModel(pli, om, bg);

    hit = gt_pdom_model_hit_new(shared->gpf->elem);

    gt_hmmer_search(pli,
                    gt_str_get(shared->fwd[0]),
                    hmm->abc,
                    om,
                    bg,
                    "0+",
                    hit->hits_fwd,
                    shared->out_lock);
    gt_hmmer_search(pli,
                    gt_str_get(shared->fwd[1]),
                    hmm->abc,
                    om,
                    bg,
                    "1+",
                    hit->hits_fwd,
                    shared->out_lock);
    gt_hmmer_search(pli,
                    gt_str_get(shared->fwd[2]),
                    hmm->abc,
                    om,
                    bg,
                    "2+",
                    hit->hits_fwd,
                    shared->out_lock);
    gt_hmmer_search(pli,
                    gt_str_get(shared->rev[0]),
                    hmm->abc,
                    om,
                    bg,
                    "0-",
                    hit->hits_rev,
                    shared->out_lock);
    gt_hmmer_search(pli,
                    gt_str_get(shared->rev[1]),
                    hmm->abc,
                    om,
                    bg,
                    "1-",
                    hit->hits_rev,
                    shared->out_lock);
    gt_hmmer_search(pli,
                    gt_str_get(shared->rev[2]),
                    hmm->abc,
                    om,
                    bg,
                    "2-",
                    hit->hits_rev,
                    shared->out_lock);

    p7_tophits_Sort(hit->hits_fwd);
    p7_tophits_Sort(hit->hits_rev);
    p7_tophits_Threshold(hit->hits_fwd, pli);
    p7_tophits_Threshold(hit->hits_rev, pli);

    p7_pipeline_Destroy(pli);
    p7_oprofile_Destroy(om);
    p7_profile_Destroy(gm);
    p7_bg_Destroy(bg);

    /* check if there were any hits */
    if (hit->hits_fwd->nreported > 0 || hit->hits_rev->nreported > 0)
    {
      gt_log_log("N: %llu/%llu, nreported: %llu/%llu, nincluded: %llu/%llu",
                  (unsigned long long) hit->hits_fwd->N,
                  (unsigned long long) hit->hits_rev->N,
                  (unsigned long long) hit->hits_fwd->nreported,
                  (unsigned long long) hit->hits_rev->nreported,
                  (unsigned long long) hit->hits_fwd->nincluded,
                  (unsigned long long) hit->hits_rev->nincluded);
      shared->results->empty = FALSE;
      if (hit->hits_fwd->nreported > 0)
      {
        if (hit->hits_rev->nreported > 0)
        {
          if (gt_double_compare(hit->hits_fwd->hit[0]->score,
                                hit->hits_rev->hit[0]->score) < 0)
            best_fwd = FALSE;
        }
        else best_fwd = TRUE;
      }
      else best_fwd = FALSE;

      /* determine best-scoring strand */
      hits = (best_fwd ? hit->hits_fwd : hit->hits_rev);
      gt_assert(hits);

      /* determine number of domain hits, track single domain hits */
      for (h = 0; h < hits->N; h++) {
        if (hits->hit[h]->flags & p7_IS_REPORTED) {
          for (d = 0; d < hits->hit[h]->ndom; d++) {
            if (hits->hit[h]->dcl[d].is_reported) {
              nof_domains++;
              lastdom = &(hits->hit[h]->dcl[d]);
              gt_log_log("domain %s, from: %lu, to %lu, on %s (%lu/%d)",
                         hits->hit[h]->dcl[d].ad->hmmname,
                         hits->hit[h]->dcl[d].ad->sqfrom,
                         hits->hit[h]->dcl[d].ad->sqto,
                         hits->hit[h]->dcl[d].ad->sqname,
                         d+1,
                         hits->hit[h]->ndom);
            }
          }
        }
      }

      /* no need to chain if there is only one domain hit */
      if (nof_domains > 1)
      {
        unsigned long i = 0;
        gt_log_log("nof_domains: %lu", nof_domains);
        /* create GtFragment set for chaining */
        frags = (GtFragment*) gt_calloc(nof_domains, sizeof (GtFragment));
        for (h = 0; h < hits->N; h++) {
          if (hits->hit[h]->flags & p7_IS_REPORTED) {
            for (d = 0; d < hits->hit[h]->ndom; d++) {
              if (hits->hit[h]->dcl[d].is_reported) {
                P7_DOMAIN *dom = &(hits->hit[h]->dcl[d]);
                GtPdomSingleHit *sh = gt_pdom_single_hit_new(dom, hit);
                gt_pdom_model_hit_add_single_hit(hit, sh);
                frags[i].startpos1 = dom->ad->hmmfrom;
                frags[i].endpos1   = dom->ad->hmmto;
                frags[i].startpos2 = dom->ad->sqfrom;
                frags[i].endpos2   = dom->ad->sqto;
                /* let weight(f) be targetlength(f) multiplied by bitscore(f) */
                frags[i].weight    = (dom->ad->sqto - dom->ad->sqfrom + 1)
                                         * dom->bitscore;
                frags[i].data      = sh;
                i++;
              }
            }
          }
        }

        /* sort GtFragments by position */
        qsort(frags, nof_domains, sizeof (GtFragment), gt_fragcmp);
        for (i=0;igpf->chain_max_gap_length,
                              chainproc, &chainno);
        gt_free(frags);
      }
      else
      {
        /* single domain hit, no chaining necessary */
        if (lastdom != NULL) {
          GtPdomSingleHit *sh;
          sh = gt_pdom_single_hit_new(lastdom, hit);
          gt_pdom_model_hit_add_single_hit(hit, sh);
          gt_pdom_single_hit_set_chained(sh, 0UL);
        }
      }

      /* Lock results, we want to write to the result hashtable */
      gt_mutex_lock(shared->out_lock);

      /* register results */
      gt_hashmap_add(shared->results->domains,
                     gt_pdom_model_ref(hmm),
                     hit);
      if (best_fwd)
      {
        shared->results->combined_e_value_fwd
          += log(hit->hits_fwd->hit[0]->pvalue);
        hit->strand = GT_STRAND_FORWARD;
      }
      else
      {
        shared->results->combined_e_value_rev
          += log(hit->hits_rev->hit[0]->pvalue);
        hit->strand = GT_STRAND_REVERSE;
       }

      /* unlock results */
      gt_mutex_unlock(shared->out_lock);
    }
    else
      gt_pdom_model_hit_delete(hit);

  }
}

static void gt_pdom_run_threads(GtArray *hmms,
                                GtStr **fwd, GtStr **rev,
                                GtPdomResults *results,
                                GtPdomFinder *gpf)
{
  GtPdomSharedMem *shared;
  gt_assert(hmms && fwd && rev && results && gpf);

  shared = gt_calloc(1, sizeof (GtPdomSharedMem));

  shared->hmms = hmms;
  shared->fwd = fwd;
  shared->rev = rev;
  shared->next_hmm = 0;
  shared->results = results;
  shared->gpf = gpf;
  shared->in_lock = gt_mutex_new();
  shared->out_lock = gt_mutex_new();

  gt_multithread(gt_pdom_per_domain_worker_thread, shared, NULL);

  gt_mutex_delete(shared->in_lock);
  gt_mutex_delete(shared->out_lock);
  gt_free(shared);
}

GtPdomResults* gt_pdom_finder_find(GtPdomFinder *gpf, const char *seq,
                                   const char *rev_seq, GtLTRElement *element,
                                   GtError *err)
{
  GtStr *fwd[3], *rev[3];
  char translated;
  unsigned long seqlen;
  GtCodonIterator *ci;
  GtPdomResults *results = NULL;
  GtTranslatorStatus status;
  GtTranslator *tr;
  int i,
      had_err = 0;
  unsigned int frame;
  gt_assert(seq && rev_seq && strlen(seq) == strlen(rev_seq) && element);
  gt_error_check(err);

  seqlen = gt_ltrelement_length(element);
  gpf->elem = element;
  results = gt_pdom_results_new();

  for (i=0;i<3;i++)
  {
    fwd[i] = gt_str_new();
    rev[i] = gt_str_new();
  }

  ci = gt_codon_iterator_simple_new(seq, seqlen, NULL);
  gt_assert(ci);
  tr = gt_translator_new(ci);
  /* create translations */
  status = gt_translator_next(tr, &translated, &frame, err);
  while (status == GT_TRANSLATOR_OK && translated)
  {
    gt_str_append_char(fwd[frame], translated);
    status = gt_translator_next(tr, &translated, &frame, NULL);
  }
  if (status == GT_TRANSLATOR_ERROR) had_err = -1;

  if (!had_err)
  {
    gt_codon_iterator_delete(ci);
    ci = gt_codon_iterator_simple_new(rev_seq, seqlen, NULL);
    gt_translator_set_codon_iterator(tr, ci);
    status = gt_translator_next(tr, &translated, &frame, err);
    while (status == GT_TRANSLATOR_OK && translated)
    {
      gt_str_append_char(rev[frame], translated);
      status = gt_translator_next(tr, &translated, &frame, NULL);
    }
    if (status == GT_TRANSLATOR_ERROR) had_err = -1;
  }

  if (!had_err)
  {
    for (i=0;i<3;i++)
    {
      gt_assert(gt_str_length(fwd[i]) == (seqlen - i) / 3);
      gt_assert(gt_str_length(rev[i]) == (seqlen - i) / 3);
    }

    /* start worker threads */
    gt_pdom_run_threads(gpf->models, fwd, rev, results, gpf);
  }

  for (i=0;i<3;i++)
  {
    gt_str_delete(fwd[i]);
    gt_str_delete(rev[i]);
  }

  gt_codon_iterator_delete(ci);
  gt_translator_delete(tr);
  return results;
}

/* --------------- GtPdomFinder ------------------------------------- */

static int gt_pdom_finder_load_files(GtPdomFinder *gpf, GtStrArray *files,
                                     GtError *err)
{
  int had_err = 0;
  GtPdomModel *gpm = NULL;
  unsigned long i;
  gt_assert(gpf && files && err);
  for (i=0;iabc = abc;
      if (had_err) {
        if (hmmfp) p7_hmmfile_Close(hmmfp);
        break;
      }
    }
    if (!had_err) {
      gt_log_log("HMM file '%s' loaded.", hmmfile);
      gt_array_add(gpf->models, gpm);
    }
    if (hmmfp) p7_hmmfile_Close(hmmfp);
  }
  return had_err;
}

static void gt_pdom_clear_hmms(GtArray *hmms)
{
  unsigned long i;
  if (!hmms) return;
  for (i=0;i0", NULL,
    NULL,  "--cut_ga,--cut_nc,--cut_tc",
    "E-value cutoff for reporting significant sequence hits", 0 },
 { "-T", eslARG_REAL, FALSE, NULL, "x>0", NULL, NULL,
   "--cut_ga,--cut_nc,--cut_tc",
   "bit score cutoff for reporting significant sequence hits", 0 },
 { "-Z", eslARG_REAL, FALSE, NULL, "x>0", NULL, NULL,
   NULL, "set # of comparisons done, for E-value calculation", 0 },
 { "--domE", eslARG_REAL,"1000.0", NULL, "x>0", NULL, NULL,
   "--cut_ga,--cut_nc,--cut_tc",
   "E-value cutoff for reporting individual domains", 0 },
 { "--domT", eslARG_REAL, FALSE, NULL, "x>0", NULL, NULL,
   "--cut_ga,--cut_nc,--cut_tc",
   "bit score cutoff for reporting individual domains", 0 },
 { "--domZ", eslARG_REAL, FALSE, NULL, "x>0", NULL, NULL, NULL,
   "set # of significant seqs, for domain E-value calculation", 0 },
 { "--cut_ga", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,
   "--seqE,--seqT,--domE,--domT",
   "use GA gathering threshold bit score cutoffs in ", 0 },
 { "--cut_nc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,
   "--seqE,--seqT,--domE,--domT",
   "use NC noise threshold bit score cutoffs in ", 0 },
 { "--cut_tc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,
   "--seqE,--seqT,--domE,--domT",
   "use TC trusted threshold bit score cutoffs in ", 0 },
 { "--max", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL,
   "--F1,--F2,--F3", "Turn all heuristic filters off (less speed, more power)",
   0 },
 { "--F1", eslARG_REAL, "0.02", NULL, NULL, NULL, NULL,
   "--max", "Stage 1 (MSV) threshold: promote hits w/ P <= F1", 0 },
 { "--F2", eslARG_REAL, "1e-3", NULL, NULL, NULL, NULL,
   "--max", "Stage 2 (Vit) threshold: promote hits w/ P <= F2", 0 },
 { "--F3", eslARG_REAL, "1e-5", NULL, NULL, NULL, NULL,
   "--max", "Stage 3 (Fwd) threshold: promote hits w/ P <= F3", 0 },
 { "--nobias", eslARG_NONE, NULL, NULL, NULL, NULL, NULL,
   "--max", "turn off composition bias filter", 0 },
 { "--nonull2", eslARG_NONE, NULL, NULL, NULL, NULL, NULL, NULL,
   "turn off biased composition score corrections", 0 },
 { "--incE", eslARG_REAL,  "0.01", NULL, "x>0",     NULL,  NULL,  NULL,
   "consider sequences <= this E-value threshold as significant", 5 },
 { "--incdomE",    eslARG_REAL,  "0.01", NULL, "x>0",     NULL,  NULL,  NULL,
   "consider domains <= this E-value threshold as significant", 5 },
 { "--incT",       eslARG_REAL,   FALSE, NULL, NULL,      NULL,    NULL,  NULL,
   "consider sequences >= this score threshold as significant", 5 },
 { "--incdomT",    eslARG_REAL,   FALSE, NULL,  NULL,     NULL,  NULL,  NULL,
   "consider domains >= this score threshold as significant", 5 },
 { "--seed", eslARG_INT, "42", NULL, "n>=0", NULL, NULL, NULL,
 "set RNG seed to  (if 0: one-time arbitrary seed)", 0 },
 { "--acc", eslARG_NONE, FALSE, NULL, NULL, NULL, NULL, NULL,
   "output target accessions instead of names if possible", 0 },
 { "--noali", eslARG_NONE, FALSE, NULL, NULL, NULL,  NULL,  NULL,
   "don't output alignments, so output is smaller", 2 },
 {  0, 0, 0, 0, 0, 0, 0, 0, 0, 0 },
};

GtPdomFinder* gt_pdom_finder_new(GtStrArray *hmmfiles, double eval_cutoff,
                                 unsigned int chain_max_gap_length,
                                 GtPdomCutoff cutoff, GtError *err)
{
  int had_err = 0;
  GtPdomFinder *gpf;
  GtStr *cmd;   /* for HMMER3 parameterization, we need to construct a
                   virtual command line for Easel to parse, see below */
  gt_assert(hmmfiles && err);
  gpf = gt_calloc(1, sizeof (GtPdomFinder));
  gpf->getopts = esl_getopts_Create(gt_pdom_hmmer3_options);
  gpf->hmm_files = gt_str_array_ref(hmmfiles);
  gpf->chain_max_gap_length = chain_max_gap_length;
  gpf->models = gt_array_new(sizeof (struct GtPdomModel*));
  gpf->glob_eval_cutoff = eval_cutoff;
  had_err = gt_pdom_finder_load_files(gpf, hmmfiles, err);

  if (!had_err) {
    cmd = gt_str_new_cstr("--noali ");
    switch (cutoff) {
      case GT_PHMM_CUTOFF_GA:
        gt_str_append_cstr(cmd, "--cut_ga ");
        break;
      case GT_PHMM_CUTOFF_TC:
        gt_str_append_cstr(cmd, "--cut_tc ");
        break;
      case GT_PHMM_CUTOFF_NONE:
        gt_str_append_cstr(cmd, "-E ");
        gt_str_append_double(cmd, eval_cutoff, 100);
        gt_str_append_cstr(cmd, " ");
        break;
    }
    had_err = esl_opt_ProcessSpoof(gpf->getopts, gt_str_get(cmd));
    gt_str_delete(cmd);
  }

  p7_FLogsumInit();
  if (had_err)
  {
    gt_pdom_clear_hmms(gpf->models);
    gt_str_array_delete(gpf->hmm_files);
    gt_free(gpf);
    return NULL;
  } else return gpf;
}

void gt_pdom_finder_delete(GtPdomFinder *gpf)
{
  if (!gpf) return;
  gt_pdom_clear_hmms(gpf->models);
  if (gpf->getopts) esl_getopts_Destroy(gpf->getopts);
  gt_str_array_delete(gpf->hmm_files);
  gt_free(gpf);
}

#endif
genometools-1.5.1/src/ltr/pdom.h000066400000000000000000000110171211610345200165440ustar00rootroot00000000000000/*
  Copyright (c) 2008-2010 Sascha Steinbiss 
  Copyright (c) 2008-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef PDOM_H
#define PDOM_H

#ifdef HAVE_HMMER

#include "core/array.h"
#include "core/error.h"
#include "core/hashmap.h"
#include "core/strand.h"
#include "core/str_array.h"
#include "ltr/ltrelement.h"

typedef enum {
  GT_PHMM_CUTOFF_TC,
  GT_PHMM_CUTOFF_GA,
  GT_PHMM_CUTOFF_NONE
} GtPdomCutoff;

typedef struct GtPdomOptions {
  double evalue_cutoff;
  GtStrArray *hmm_files;
  unsigned int chain_max_gap_length;
  bool write_alignments,
       write_aaseqs,
       output_all_chains;
  GtPdomCutoff cutoff;
} GtPdomOptions;

typedef struct GtPdomFinder GtPdomFinder;
typedef struct GtPdomModel GtPdomModel;
typedef struct GtPdomSingleHit GtPdomSingleHit;
typedef struct GtPdomModelHit GtPdomModelHit;
typedef struct GtPdomResults GtPdomResults;

typedef int (*GtPdomIteratorFunc)(GtPdomModel *model, GtPdomModelHit *hit,
                                  void *data, GtError*);

/* acts as a factory for GtPdomResults */
GtPdomFinder*    gt_pdom_finder_new(GtStrArray *hmmfiles,
                                    double eval_cutoff,
                                    unsigned int chain_max_gap_length,
                                    GtPdomCutoff cutoff,
                                    GtError*);
unsigned int     gt_pdom_finder_get_nof_threads(const GtPdomFinder*);
unsigned int     gt_pdom_finder_get_max_gap_length(const GtPdomFinder*);
double           gt_pdom_finder_get_eval_cutoff(const GtPdomFinder*);
GtStrArray*      gt_pdom_finder_get_model_filenames(const GtPdomFinder*);
unsigned long    gt_pdom_finder_get_number_of_models(const GtPdomFinder*);
GtPdomModel*     gt_pdom_finder_get_model(const GtPdomModel*, unsigned long);
GtPdomResults*   gt_pdom_finder_find(GtPdomFinder*, const char *seq,
                                     const char *rev_seq, GtLTRElement*,
                                     GtError *err);
void             gt_pdom_finder_delete(GtPdomFinder*);

/* holds results for all models */
int              gt_pdom_results_foreach_domain_hit(GtPdomResults*,
                                                    GtPdomIteratorFunc,
                                                    void*,
                                                    GtError*);
bool             gt_pdom_results_empty(GtPdomResults*);
double           gt_pdom_results_get_combined_evalue_fwd(GtPdomResults*);
double           gt_pdom_results_get_combined_evalue_rev(GtPdomResults*);
void             gt_pdom_results_delete(GtPdomResults*);

/* holds information about a single domain model */
const char*      gt_pdom_model_get_name(const GtPdomModel*);
const char*      gt_pdom_model_get_acc(const GtPdomModel*);

/* holds hits for a single domain model */
unsigned long    gt_pdom_model_hit_num_of_single_hits(const GtPdomModelHit*);
GtPdomSingleHit* gt_pdom_model_hit_single_hit(const GtPdomModelHit*,
                                                   unsigned long i);
GtStrand         gt_pdom_model_hit_get_best_strand(const GtPdomModelHit*);

/* holds information about an individual hit */
GtPhase          gt_pdom_single_hit_get_phase(const GtPdomSingleHit*);
GtRange          gt_pdom_single_hit_get_range(const GtPdomSingleHit*);
double           gt_pdom_single_hit_get_evalue(const GtPdomSingleHit*);
void             gt_pdom_single_hit_format_alignment(const GtPdomSingleHit*,
                                                     unsigned long width,
                                                     GtStr *dest);
void             gt_pdom_single_hit_get_aaseq(const GtPdomSingleHit*,
                                              GtStr *dest);
bool             gt_pdom_single_hit_is_chained(GtPdomSingleHit *singlehit);
GtArray*         gt_pdom_single_hit_get_chains(GtPdomSingleHit *singlehit);

#endif
#endif
genometools-1.5.1/src/ltr/ppt.c000066400000000000000000000431001211610345200164010ustar00rootroot00000000000000/*
  Copyright (c) 2008-2011 Sascha Steinbiss 
  Copyright (c) 2008-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ensure.h"
#include "core/log.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/minmax.h"
#include "core/xansi_api.h"
#include "core/array.h"
#include "extended/reverse_api.h"
#include "ltr/ppt.h"

/* This enumeration defines the states in the PPT detection HMM. */
typedef enum {
  PPT_IN,
  PPT_OUT,
  PPT_UBOX,
  PPT_N,
  PPT_NOF_STATES
} GtPPTStates;

struct GtPPTHit {
  GtRange rng;
  double score;
  GtPPTStates state;
  GtPPTHit *ubox;
  GtStrand strand;
  GtPPTResults *res;
};

struct GtPPTResults {
  GtArray *hits;
  GtLTRElement *elem;
  GtPPTOptions *opts;
};

static GtPPTResults* gt_ppt_results_new(GtLTRElement *elem,
                                        GtPPTOptions *opts)
{
  GtPPTResults *res = gt_calloc((size_t) 1, sizeof (GtPPTResults));
  res->elem = elem;
  res->opts = opts;
  res->hits = gt_array_new(sizeof (GtPPTHit*));
  return res;
}

static GtPPTHit* gt_ppt_hit_new(GtStrand strand, GtPPTResults *r)
{
  GtPPTHit *h = gt_calloc((size_t) 1, sizeof (GtPPTHit));
  gt_assert(h);
  h->strand = strand;
  h->res = r;
  h->score = 0.0;
  return h;
}

GtRange gt_ppt_hit_get_coords(const GtPPTHit *h)
{
  GtRange rng;
  gt_assert(h);
  rng.start = h->rng.start;
  rng.end = h->rng.end;
  switch (h->strand)
  {
    case GT_STRAND_FORWARD:
    default:
      rng.start = h->res->elem->rightLTR_5 - 1 - h->res->opts->radius
                    + rng.start;
      rng.end = rng.start + (gt_range_length(&h->rng) - 1);
      break;
    case GT_STRAND_REVERSE:
      rng.end = h->res->elem->leftLTR_3 + 1 + h->res->opts->radius - rng.start;
      rng.start = rng.end - (gt_range_length(&h->rng) - 1);
      break;
  }
  gt_assert(gt_range_length(&rng) == gt_range_length(&h->rng));
  return rng;
}

GtPPTHit* gt_ppt_hit_get_ubox(const GtPPTHit *h)
{
  gt_assert(h);
  return h->ubox;
}

GtStrand gt_ppt_hit_get_strand(const GtPPTHit *h)
{
  gt_assert(h);
  return h->strand;
}

unsigned long gt_ppt_results_get_number_of_hits(GtPPTResults *r)
{
  gt_assert(r);
  return gt_array_size(r->hits);
}

GtPPTHit* gt_ppt_results_get_ranked_hit(GtPPTResults *r, unsigned long i)
{
  gt_assert(r);
  return *(GtPPTHit**) gt_array_get(r->hits, i);
}

GtHMM* gt_ppt_hmm_new(const GtAlphabet *alpha, GtPPTOptions *opts)
{
  GtHMM *hmm;
  double non_u_prob = 0.0;

  gt_assert(alpha);

  hmm = gt_hmm_new((unsigned int) PPT_NOF_STATES, gt_alphabet_size(alpha));

  /* set emission probabilities */
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_OUT,
                                  (unsigned int) gt_alphabet_encode(alpha, 'G'),
                                  opts->bkg_g_prob);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_OUT,
                                  (unsigned int) gt_alphabet_encode(alpha, 'A'),
                                  opts->bkg_a_prob);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_OUT,
                                  (unsigned int) gt_alphabet_encode(alpha, 'C'),
                                  opts->bkg_c_prob);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_OUT,
                                  (unsigned int) gt_alphabet_encode(alpha, 'T'),
                                  opts->bkg_t_prob);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_IN,
                                  (unsigned int) gt_alphabet_encode(alpha, 'G'),
                                  opts->ppt_purine_prob/2);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_IN,
                                  (unsigned int) gt_alphabet_encode(alpha, 'A'),
                                  opts->ppt_purine_prob/2);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_IN,
                                  (unsigned int) gt_alphabet_encode(alpha, 'C'),
                                  opts->ppt_pyrimidine_prob/2);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_IN,
                                  (unsigned int) gt_alphabet_encode(alpha, 'T'),
                                  opts->ppt_pyrimidine_prob/2);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_UBOX,
                                  (unsigned int) gt_alphabet_encode(alpha, 'T'),
                                  opts->ubox_u_prob);
  /* calculate non-U probabilities (still uniform, may be optimised) */
  non_u_prob = (1.0 - (opts->ubox_u_prob)) / ((double) 3);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_UBOX,
                                  (unsigned int) gt_alphabet_encode(alpha, 'G'),
                                  non_u_prob);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_UBOX,
                                  (unsigned int) gt_alphabet_encode(alpha, 'A'),
                                  non_u_prob);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_UBOX,
                                  (unsigned int) gt_alphabet_encode(alpha, 'C'),
                                  non_u_prob);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_N,
                                  (unsigned int) gt_alphabet_encode(alpha, 'G'),
                                  0.00);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_N,
                                  (unsigned int) gt_alphabet_encode(alpha, 'A'),
                                  0.00);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_N,
                                  (unsigned int) gt_alphabet_encode(alpha, 'C'),
                                  0.00);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_N,
                                  (unsigned int) gt_alphabet_encode(alpha, 'T'),
                                  0.00);
  gt_hmm_set_emission_probability(hmm, (unsigned int) PPT_N,
                                  (unsigned int) gt_alphabet_encode(alpha, 'N'),
                                  1.00);

  /* set transition probabilities */
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_OUT,
                                    (unsigned int) PPT_IN, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_OUT,
                                    (unsigned int) PPT_N, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_OUT,
                                    (unsigned int) PPT_UBOX, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_UBOX,
                                    (unsigned int) PPT_OUT, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_UBOX,
                                    (unsigned int) PPT_N, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_UBOX,
                                    (unsigned int) PPT_IN, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_IN,
                                    (unsigned int) PPT_UBOX, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_IN,
                                    (unsigned int) PPT_OUT, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_IN,
                                    (unsigned int) PPT_N, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_N,
                                    (unsigned int) PPT_UBOX, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_N,
                                    (unsigned int) PPT_OUT, 0.05);
  gt_hmm_set_transition_probability(hmm, (unsigned int) PPT_N,
                                    (unsigned int) PPT_IN, 0.05);
  gt_hmm_set_missing_transition_probabilities(hmm);

  if (!gt_hmm_is_valid(hmm))
  {
    gt_hmm_delete(hmm);
    return NULL;
  } else
    return hmm;
}

static inline double gt_ppt_score(unsigned long radius, unsigned long end)
{
  double ret;
  unsigned long r2;
  r2 = radius * radius;
  ret = ((double) r2
           - pow(fabs((double) radius - (double) end), 2.0))/(double) r2;
  return ret;
}

static int gt_ppt_hit_cmp(const void *h1, const void *h2)
{
  GtPPTHit* ph1 = *(GtPPTHit**) h1;
  GtPPTHit* ph2 = *(GtPPTHit**) h2;
  gt_assert(h1 && h2);
  return gt_double_compare(ph2->score, ph1->score);
}

static bool gt_ubox_ok(GtPPTHit *hit, GtRange uboxlen)
{
  gt_assert(hit);
  return (hit->state == PPT_UBOX
           && hit->rng.end-hit->rng.start+1 >= uboxlen.start
           && hit->rng.end-hit->rng.start+1 <= uboxlen.end);
}

static bool gt_ppt_ok(GtPPTHit *hit, GtRange pptlen)
{
  gt_assert(hit);
  return (hit->state == PPT_IN
           && hit->rng.end-hit->rng.start+1 >= pptlen.start
           && hit->rng.end-hit->rng.start+1 <= pptlen.end);
}

static void gt_group_hits(unsigned int *decoded, GtPPTResults *results,
                          unsigned long radius, GT_UNUSED const char *seq,
                          GtStrand strand)
{
  GtPPTHit *cur_hit = NULL,
           *potential_ubox = NULL;
  unsigned long i = 0;

  gt_assert(decoded && results && strand != GT_STRAND_UNKNOWN);

  /* group hits into stretches */
  cur_hit = gt_ppt_hit_new(strand, results);
  for (i = 0; i < 2 * radius - 1; i++)
  {
    cur_hit->state = (GtPPTStates) decoded[i];
    cur_hit->rng.end = i;
    if (decoded[i+1] != decoded[i] || i + 2 == 2 * radius)
    {
      switch (cur_hit->state)
      {
        case PPT_UBOX:
          if (gt_ubox_ok(cur_hit, results->opts->ubox_len)) {
            if (potential_ubox != NULL) {
              gt_free(potential_ubox);
              potential_ubox = NULL;
            }
            potential_ubox = cur_hit;
            cur_hit = NULL;
          }
          else
          {
            gt_free(cur_hit);
            cur_hit = NULL;
          }
          break;
        case PPT_IN:
          if (gt_ppt_ok(cur_hit, results->opts->ppt_len))
          {
            cur_hit->score = gt_ppt_score(radius, cur_hit->rng.end);
            gt_array_add(results->hits, cur_hit);
            if (potential_ubox != NULL)
            {
              if (cur_hit->rng.start - potential_ubox->rng.end
                    <= (unsigned long) results->opts->max_ubox_dist)
              {
                /* this PPT has a U-box, handle accordingly */
                cur_hit->ubox = potential_ubox;
              } else {
                gt_free(potential_ubox);
              }
              potential_ubox = NULL;
            }
            cur_hit = NULL;
          }
          else
          {
            if (potential_ubox != NULL) {
              gt_free(potential_ubox);
              potential_ubox = NULL;
            }
            gt_free(cur_hit);
            cur_hit = NULL;
          }
          break;
        default:
          if (potential_ubox != NULL) {
                gt_free(potential_ubox);
                potential_ubox = NULL;
          }
          gt_free(cur_hit);
          cur_hit = NULL;
          break;
      }
      if (i+2!=2*radius)
      {
        /* we assume that the current hit has been processed */
        gt_assert(cur_hit == NULL);
        cur_hit = gt_ppt_hit_new(strand, results);
        cur_hit->rng.start = i+1;
      }
    }
  }
  if (cur_hit != NULL)
    cur_hit->rng.end++;
  gt_free(potential_ubox);
}

GtPPTResults* gt_ppt_find(const char *seq,
                          const char *rev_seq,
                          GtLTRElement *element,
                          GtPPTOptions *o)
{
  unsigned int *encoded_seq=NULL,
               *decoded=NULL;
  GtAlphabet *alpha;
  GtHMM *hmm;
  GtPPTResults *results = NULL;
  unsigned long i = 0,
                radius = 0,
                seqlen = gt_ltrelement_length(element),
                ltrlen = 0;

  gt_assert(seq && rev_seq && element && o);

  results = gt_ppt_results_new(element, o);

  alpha = gt_alphabet_new_dna();
  hmm = gt_ppt_hmm_new(alpha, o);

  /* do PPT finding on forward strand
   * -------------------------------- */
  ltrlen = gt_ltrelement_rightltrlen(element);
  /* make sure that we do not cross the LTR boundary */
  radius = MIN((unsigned long) o->radius, ltrlen-1);
  /* encode sequence */
  encoded_seq = gt_malloc(sizeof (unsigned int) * seqlen);
  for (i=0;iradius, ltrlen-1);
  /* encode sequence */
  for (i=0;ihits, gt_ppt_hit_cmp);

  gt_free(encoded_seq);
  gt_free(decoded);
  gt_alphabet_delete(alpha);
  gt_hmm_delete(hmm);

  return results;
}

void gt_ppt_results_delete(GtPPTResults *results)
{
  unsigned long i;
  if (results == NULL) return;

  if (results->hits != NULL)
  {
    for (i=0;ihits);i++)
    {
      GtPPTHit * hit = *(GtPPTHit**) gt_array_get(results->hits,i);
      if (hit->ubox != NULL)
        gt_free(hit->ubox);
      gt_free(hit);
    }
    gt_array_delete(results->hits);
  }
  gt_free(results);
}

int gt_ppt_unit_test(GtError *err)
{
  int had_err = 0;
  GtPPTOptions o;
  GtPPTResults *rs;
  GtPPTHit *h;
  GtLTRElement element;
  GtRange rng;
  char *rev_seq,
       *seq,
       tmp[BUFSIZ];
  const char *fullseq =                           "aaaaaaaaaaaaaaaaaaaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "aaag"
                        "tcttctttct" /* <- PPT reverse */
                                  "aaaaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatttt"
                                   /* PPT forward -> */  "gggatagggggag"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "tatagcactgcatttcgaatatagtttcgaatatagcactgcatttcgaa"
                    "aaaaaaaaaaaaaaaaaaaa";

  seq     = gt_malloc(600 * sizeof (char));
  rev_seq = gt_malloc(600 * sizeof (char));
  memcpy(seq,     fullseq + 20, (size_t) 600);
  memcpy(rev_seq, fullseq + 20, (size_t) 600);
  gt_ensure(had_err, !gt_reverse_complement(rev_seq, 600UL, err));

  element.leftLTR_5 = 20UL;
  element.leftLTR_3 = 119UL;
  element.rightLTR_5 = 520UL;
  element.rightLTR_3 = 619UL;

  /* run PPT finding */
  memset(&o, 0, sizeof (GtPPTOptions));
  o.ppt_len.start = 5UL;
  o.ppt_len.end = 15UL;
  o.ubox_len.start = 2UL;
  o.ubox_len.end = 15UL;
  o.radius = 30U;
  o.ppt_pyrimidine_prob = PPT_PYRIMIDINE_PROB;
  o.ppt_purine_prob = PPT_PURINE_PROB;
  o.bkg_a_prob = BKG_A_PROB;
  o.bkg_g_prob = BKG_G_PROB;
  o.bkg_t_prob = BKG_T_PROB;
  o.bkg_c_prob = BKG_C_PROB;
  o.ubox_u_prob = UBOX_U_PROB;
  rs = gt_ppt_find(seq, rev_seq, &element, &o);

  gt_ensure(had_err, gt_ppt_results_get_number_of_hits(rs) == 2UL);
  h = gt_ppt_results_get_ranked_hit(rs, 0);
  gt_ensure(had_err, h);
  rng = gt_ppt_hit_get_coords(h);
  gt_ensure(had_err, rng.start == 507UL);
  gt_ensure(had_err, rng.end == 519UL);
  memset(tmp, 0, BUFSIZ);
  memcpy(tmp, fullseq + (rng.start * sizeof (char)),
         (size_t) ((rng.end - rng.start + 1) * sizeof (char)));
  gt_ensure(had_err, strcmp(tmp, "gggatagggggag" ) == 0);

  h = gt_ppt_results_get_ranked_hit(rs, 1UL);
  gt_ensure(had_err, h);
  rng = gt_ppt_hit_get_coords(h);
  gt_ensure(had_err, rng.start == 124UL);
  gt_ensure(had_err, rng.end == 133UL);
  memset(tmp, 0, BUFSIZ);
  memcpy(tmp, fullseq + (rng.start * sizeof (char)),
         (size_t) ((rng.end - rng.start + 1) * sizeof (char)));
  gt_ensure(had_err, strcmp(tmp, "tcttctttct" ) == 0);

  gt_free(rev_seq);
  gt_free(seq);

  gt_ppt_results_delete(rs);
  return had_err;
}
genometools-1.5.1/src/ltr/ppt.h000066400000000000000000000044331211610345200164140ustar00rootroot00000000000000/*
  Copyright (c) 2008-2011 Sascha Steinbiss 
  Copyright (c) 2008-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef PPT_H
#define PPT_H

#include "core/alphabet.h"
#include "core/range.h"
#include "core/strand.h"
#include "core/undef_api.h"
#include "extended/hmm.h"
#include "ltr/ltrelement.h"

#define PPT_PURINE_PROB     0.97
#define PPT_PYRIMIDINE_PROB 0.03
#define BKG_A_PROB          0.25
#define BKG_C_PROB          0.25
#define BKG_G_PROB          0.25
#define BKG_T_PROB          0.25
#define UBOX_U_PROB         0.91

typedef struct {
  GtRange ppt_len, ubox_len;
  double ppt_pyrimidine_prob,
         ppt_purine_prob,
         bkg_a_prob,
         bkg_g_prob,
         bkg_t_prob,
         bkg_c_prob,
         ubox_u_prob;
  unsigned int radius,
               max_ubox_dist;
} GtPPTOptions;

typedef struct GtPPTHit GtPPTHit;
typedef struct GtPPTResults GtPPTResults;

GtHMM*          gt_ppt_hmm_new(const GtAlphabet *alpha, GtPPTOptions *opts);

GtPPTResults*   gt_ppt_find(const char *seq,
                            const char *rev_seq,
                            GtLTRElement *element,
                            GtPPTOptions*);

GtRange         gt_ppt_hit_get_coords(const GtPPTHit*);
GtPPTHit*       gt_ppt_hit_get_ubox(const GtPPTHit*);
GtStrand        gt_ppt_hit_get_strand(const GtPPTHit*);

unsigned long   gt_ppt_results_get_number_of_hits(GtPPTResults*);
GtPPTHit*       gt_ppt_results_get_ranked_hit(GtPPTResults*, unsigned long);
void            gt_ppt_results_delete(GtPPTResults*);

int             gt_ppt_unit_test(GtError*);

#endif
genometools-1.5.1/src/lualib.c000066400000000000000000000012121211610345200162430ustar00rootroot00000000000000/*
* lualib.c -- Lua core and libraries in a single file
*/

#define luaall_c

#include "lapi.c"
#include "lcode.c"
#include "ldebug.c"
#include "ldo.c"
#include "ldump.c"
#include "lfunc.c"
#include "lgc.c"
#include "llex.c"
#include "lmem.c"
#include "lobject.c"
#include "lopcodes.c"
#include "lparser.c"
#include "lstate.c"
#include "lstring.c"
#include "ltable.c"
#include "ltm.c"
#include "lundump.c"
#include "lvm.c"
#include "lzio.c"

#include "lauxlib.c"
#include "lbaselib.c"
#include "ldblib.c"
#include "liolib.c"
#include "linit.c"
#include "lmathlib.c"
#include "loadlib.c"
#include "loslib.c"
#include "lstrlib.c"
#include "ltablib.c"
genometools-1.5.1/src/match/000077500000000000000000000000001211610345200157275ustar00rootroot00000000000000genometools-1.5.1/src/match/absdfstrans-def.h000066400000000000000000000020011211610345200211370ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ABSDFSTRANS_DEF_H
#define ABSDFSTRANS_DEF_H

typedef struct AbstractDfstransformer AbstractDfstransformer;

typedef struct Limdfsconstinfo Limdfsconstinfo;

#endif
genometools-1.5.1/src/match/absdfstrans-imp.h000066400000000000000000000071041211610345200211770ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ABSDFSTRANS_IMP_H
#define ABSDFSTRANS_IMP_H
#include "core/defined-types.h"
#include "absdfstrans-def.h"
#include "procmatch.h"

typedef unsigned long Aliasdfsstate;

#define DECLAREPTRDFSSTATE(V)\
        Aliasdfsstate * V

#undef SKDEBUG

typedef enum
{
  Limdfssuccess,  /* success of traversal */
  Limdfscontinue, /* no success, but still have the chance to find result */
  Limdfsstop      /* no success possible */
} Limdfsstatus;

typedef struct
{
  Limdfsstatus status;
  unsigned long pprefixlen, /* only defined if limdfsstatus = Limdfssuccess */
                distance;   /* only defined if limdfsstatus = Limdfssuccess */
} Limdfsresult;

struct AbstractDfstransformer
{
  size_t sizeofdfsstate;
  Limdfsconstinfo *(*allocatedfsconstinfo)(unsigned int alphasize);
  void (*initdfsconstinfo)(Limdfsconstinfo *dfsconstinfo,
                           unsigned int alphasize,
                           ...);
  void (*extractdfsconstinfo)(Processresult processresult,
                              void *processinfo,
                              const void *patterninfo,
                              Limdfsconstinfo *dfsconstinfo);
  void (*freedfsconstinfo)(Limdfsconstinfo **dfsconstinfo);
  void (*initrootLimdfsstate)(DECLAREPTRDFSSTATE(aliasstate),
                              Limdfsconstinfo *dfsconstinfo);
  void (*initLimdfsstackelem)(DECLAREPTRDFSSTATE(aliasstate));
  void (*freeLimdfsstackelem)(DECLAREPTRDFSSTATE(aliasstate));
  void (*copyLimdfsstate)(DECLAREPTRDFSSTATE(deststate),
                          const DECLAREPTRDFSSTATE(srcstate),
                          Limdfsconstinfo *dfsconstinfo);
  void (*fullmatchLimdfsstate)(Limdfsresult *limdfsresult,
                               DECLAREPTRDFSSTATE(aliascolumn),
                               unsigned long left,
                               unsigned long right,
                               unsigned long width,
                               unsigned long currentdepth,
                               Limdfsconstinfo *dfsconstinfo);
  void (*nextLimdfsstate)(const Limdfsconstinfo *dfsconstinfo,
                          DECLAREPTRDFSSTATE(aliasoutstate),
                          unsigned long currentdepth,
                          GtUchar currentchar,
                          const DECLAREPTRDFSSTATE(aliasinstate));
  void (*inplacenextLimdfsstate)(const Limdfsconstinfo *dfsconstinfo,
                                 DECLAREPTRDFSSTATE(aliasstate),
                                 unsigned long currentdepth,
                                 GtUchar currentchar);
#ifdef SKDEBUG
  void (*showLimdfsstate)(const DECLAREPTRDFSSTATE(aliasstate),
                          unsigned long currentdepth,
                          const Limdfsconstinfo *dfsconstinfo);
#endif
};

#endif
genometools-1.5.1/src/match/apmeoveridx.c000066400000000000000000000320541211610345200204220ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/ma_api.h"

#include "core/encseq.h"
#include "core/defined-types.h"
#include "apmeoveridx.h"
#include "absdfstrans-imp.h"
#include "initeqsvec.h"

#define UNDEFMAXLEQK      (mti->patternlength+1)
#define SUCCESSMAXLEQK    mti->patternlength

typedef struct
{
  unsigned long Pv,       /* the plus-vector for Myers Algorithm */
                Mv,       /* the minus-vector for Myers Algorithm */
                maxleqk;  /* \(\max\{i\in[0,m]\mid D(i)\leq k\}\) where
                          \(m\) is the length of the pattern, \(k\) is the
                          distance threshold, and \(D\) is
                          the current distance column */
  unsigned long lastdistvalue;   /* the score for the given depth */
} ApmeoveridxLimdfsstate;

typedef struct
{
  bool skpp;
  unsigned long maxintervalwidth,
                patternlength,
                maxdistance,
                *eqsvector;
} ApmeoveridxLimdfsconstinfo;

#ifdef SKDEBUG

static void showmaxleqvalue(FILE *fp,unsigned long maxleqk,
                            const Limdfsconstinfo *mti)
{
  if (maxleqk == UNDEFMAXLEQK)
  {
    fprintf(fp,"undefined");
  } else
  {
    fprintf(fp,"%lu",maxleqk);
  }
}

static void apme_showLimdfsstate(const DECLAREPTRDFSSTATE(aliascol),
                                 unsigned long currentdepth,
                                 const Limdfsconstinfo *mt)
{
  const ApmeoveridxLimdfsstate *col = (const ApmeoveridxLimdfsstate *) aliascol;
  const ApmeoveridxLimdfsconstinfo *mti =
                                        (const ApmeoveridxLimdfsconstinfo *) mt;

  if (col->maxleqk == UNDEFMAXLEQK)
  {
    printf("[]");
  } else
  {
    unsigned long idx, backmask, score = currentdepth;

    printf("[%lu",score);
    for (idx=1UL, backmask = 1UL; idx<=col->maxleqk; idx++, backmask <<= 1)
    {
      if (col->Pv & backmask)
      {
        score++;
      } else
      {
        if (col->Mv & backmask)
        {
          score--;
        }
      }
      printf(",%lu",score);
    }
    printf("] with maxleqk=%lu",col->maxleqk);
  }
}

static void verifycolumnvalues(const Limdfsconstinfo *mt,
                               const Limdfsstate *acol,
                               unsigned long startscore)
{
  unsigned long idx, score, minscore, mask, bfmaxleqk;
  const ApmeoveridxLimdfsstate *col = (const ApmeoveridxLimdfsstate *) acol;
  const ApmeoveridxLimdfsconstinfo *mti =
                                        (const ApmeoveridxLimdfsconstinfo *) mt;

  if (startscore <= mti->maxdistance)
  {
    bfmaxleqk = 0;
    minscore = startscore;
  } else
  {
    bfmaxleqk = UNDEFMAXLEQK;
    minscore = 0;
  }
  score = startscore;
  for (idx=1UL, mask = 1UL; idx <= mti->patternlength; idx++, mask <<= 1)
  {
    if (col->Pv & mask)
    {
      score++;
    } else
    {
      if (col->Mv & mask)
      {
        score--;
      }
    }
    if (score <= mti->maxdistance)
    {
      bfmaxleqk = idx;
      minscore = score;
    }
  }
  if (bfmaxleqk != col->maxleqk)
  {
    fprintf(stderr,"correct maxleqk = ");
    showmaxleqvalue(stderr,bfmaxleqk,mti);
    fprintf(stderr," != ");
    showmaxleqvalue(stderr,col->maxleqk,mti);
    fprintf(stderr," = col->maxleqk\n");
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  if (bfmaxleqk != UNDEFMAXLEQK && minscore != col->lastdistvalue)
  {
    fprintf(stderr,"correct score = %lu != %lu = col->score\n",
                 minscore,
                 col->lastdistvalue);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
}

#endif

static void apme_initdfsconstinfo(Limdfsconstinfo *mt,
                                  unsigned int alphasize,
                                  ...)
                                 /* Variable argument list is as follows:
                                    unsigned int alphasize
                                    const GtUchar *pattern,
                                    unsigned long patternlength,
                                    unsigned long maxdistance,
                                    unsigned long maxintervalwidth,
                                    bool skpp
                                 */
{
  va_list ap;
  const GtUchar *pattern;
  ApmeoveridxLimdfsconstinfo *mti = (ApmeoveridxLimdfsconstinfo *) mt;

  va_start(ap,alphasize);
  pattern = va_arg(ap, const GtUchar *);
  mti->patternlength = va_arg(ap, unsigned long);
  mti->maxdistance = va_arg(ap, unsigned long);
  mti->maxintervalwidth = va_arg(ap, unsigned long);
  mti->skpp = (bool) va_arg(ap, int);
  va_end(ap);
  gt_assert(mti->maxdistance < mti->patternlength);
  gt_initeqsvector(mti->eqsvector,(unsigned long) alphasize,
                pattern,mti->patternlength);
}

static Limdfsconstinfo *apme_allocatedfsconstinfo(unsigned int alphasize)
{
  ApmeoveridxLimdfsconstinfo *mti =
                                 gt_malloc(sizeof (ApmeoveridxLimdfsconstinfo));
  mti->eqsvector = gt_malloc(sizeof (*mti->eqsvector) * alphasize);
  return (Limdfsconstinfo*) mti;
}

static void apme_freedfsconstinfo(Limdfsconstinfo **mtptr)
{
  ApmeoveridxLimdfsconstinfo **mtiptr = (ApmeoveridxLimdfsconstinfo **) mtptr;
  gt_free((*mtiptr)->eqsvector);
  gt_free(*mtiptr);
  *mtiptr = NULL;
}

static void apme_initLimdfsstate(DECLAREPTRDFSSTATE(aliascolumn),
                                 Limdfsconstinfo *mt)
{
  ApmeoveridxLimdfsstate *column = (ApmeoveridxLimdfsstate *) aliascolumn;
  ApmeoveridxLimdfsconstinfo *mti = (ApmeoveridxLimdfsconstinfo *) mt;

  column->Mv = 0UL;
  if (mti->skpp)
  {
    column->Pv = 0UL; /* first column consists of 0 => skip pattern prefix */
    column->maxleqk = mti->patternlength;
    column->lastdistvalue = 0;
  } else
  {
    column->Pv = ~0UL; /* first column: 0 1 2 ... m */
    column->maxleqk = mti->maxdistance;
    column->lastdistvalue = mti->maxdistance;
  }
}

static void apme_fullmatchLimdfsstate(Limdfsresult *limdfsresult,
                                      DECLAREPTRDFSSTATE(aliascolumn),
                                      GT_UNUSED unsigned long leftbound,
                                      GT_UNUSED unsigned long rightbound,
                                      unsigned long width,
                                      GT_UNUSED unsigned long currentdepth,
                                      Limdfsconstinfo *mt)
{
  ApmeoveridxLimdfsstate *col = (ApmeoveridxLimdfsstate *) aliascolumn;
  ApmeoveridxLimdfsconstinfo *mti = (ApmeoveridxLimdfsconstinfo *) mt;

  if (col->maxleqk == UNDEFMAXLEQK)
  {
    limdfsresult->status = Limdfsstop; /* stop depth first traversal */
    return;
  }
  if (mti->maxintervalwidth == 0 || width == (unsigned long) 1)
  {
    if (col->maxleqk == SUCCESSMAXLEQK)
    {
      /* success with match of length plen */
      limdfsresult->status = Limdfssuccess;
      limdfsresult->pprefixlen = mti->patternlength;
      limdfsresult->distance = col->lastdistvalue;
      return;
    }
  } else
  {
    if (width <= (unsigned long) mti->maxintervalwidth)
    {
      /* success with match of length maxleqk */
      gt_assert(col->maxleqk > 0);
      limdfsresult->status = Limdfssuccess;
      limdfsresult->pprefixlen = col->maxleqk;
      limdfsresult->distance = col->lastdistvalue;
      return;
    }
  }
  /* continue with depth first traversal */
  limdfsresult->status = Limdfscontinue;
}

static void apme_nextLimdfsstate(const Limdfsconstinfo *mt,
                                 DECLAREPTRDFSSTATE(aliasoutcol),
                                 GT_UNUSED unsigned long currentdepth,
                                 GtUchar currentchar,
                                 const DECLAREPTRDFSSTATE(aliasincol))
{
  unsigned long Eq = 0, Xv, Xh, Ph, Mh, /* as in Myers Paper */
                backmask,               /* only one bit is on */
                idx,                    /* a counter */
                score;                  /* current score */
  ApmeoveridxLimdfsstate *outcol = (ApmeoveridxLimdfsstate *) aliasoutcol;
  const ApmeoveridxLimdfsstate *incol =
                                    (const ApmeoveridxLimdfsstate *) aliasincol;
  const ApmeoveridxLimdfsconstinfo *mti =
                                        (const ApmeoveridxLimdfsconstinfo *) mt;

  gt_assert(incol->maxleqk != UNDEFMAXLEQK);
  gt_assert(mti->maxintervalwidth > 0 || incol->maxleqk != SUCCESSMAXLEQK);
  gt_assert(currentchar != (GtUchar) SEPARATOR);
  if (currentchar != (GtUchar) WILDCARD)
  {
    Eq = mti->eqsvector[(unsigned long) currentchar];
  }
  Xv = Eq | incol->Mv;
  Xh = (((Eq & incol->Pv) + incol->Pv) ^ incol->Pv) | Eq;

  Ph = incol->Mv | ~ (Xh | incol->Pv);
  Mh = incol->Pv & Xh;

  Ph = (Ph << 1) | 1UL;
  outcol->Pv = (Mh << 1) | ~ (Xv | Ph);
  outcol->Mv = Ph & Xv;
  backmask = 1UL << incol->maxleqk;
  if (Eq & backmask || Mh & backmask)
  {
    outcol->maxleqk = incol->maxleqk + 1UL;
    outcol->lastdistvalue = incol->lastdistvalue;
  } else
  {
    if (Ph & backmask)
    {
      score = mti->maxdistance+1;
      outcol->maxleqk = UNDEFMAXLEQK;
      if (incol->maxleqk > 0)
      {
        for (idx = incol->maxleqk - 1, backmask >>= 1;
             /* Nothing */;
             backmask >>= 1)
        {
          if (outcol->Pv & backmask)
          {
            score--;
            if (score <= mti->maxdistance)
            {
              outcol->maxleqk = idx;
              outcol->lastdistvalue = score;
              break;
            }
          } else
          {
            if (outcol->Mv & backmask)
            {
              score++;
            }
          }
          if (idx > 0)
          {
            idx--;
          } else
          {
            break;
          }
        }
      }
    } else
    {
      outcol->maxleqk = incol->maxleqk;
      outcol->lastdistvalue = incol->lastdistvalue;
    }
  }
#ifdef SKDEBUG
  verifycolumnvalues(mti,outcol,currentdepth);
#endif
}

static void apme_inplacenextLimdfsstate(const Limdfsconstinfo *mt,
                                        DECLAREPTRDFSSTATE(aliascol),
                                        GT_UNUSED unsigned long currentdepth,
                                        GtUchar currentchar)
{
  unsigned long Eq = 0, Xv, Xh, Ph, Mh, /* as in Myers Paper */
                backmask,           /* only one bit is on */
                idx,                /* a counter */
                score;              /* current score */
  ApmeoveridxLimdfsstate *col = (ApmeoveridxLimdfsstate *) aliascol;
  const ApmeoveridxLimdfsconstinfo *mti =
                                        (const ApmeoveridxLimdfsconstinfo *) mt;

  gt_assert(col->maxleqk != UNDEFMAXLEQK);
  gt_assert(mti->maxintervalwidth > 0 || col->maxleqk != SUCCESSMAXLEQK);
  if (currentchar != (GtUchar) WILDCARD)
  {
    Eq = mti->eqsvector[(unsigned long) currentchar];
  }
  Xv = Eq | col->Mv;
  Xh = (((Eq & col->Pv) + col->Pv) ^ col->Pv) | Eq;

  Ph = col->Mv | ~ (Xh | col->Pv);
  Mh = col->Pv & Xh;

  Ph = (Ph << 1) | 1UL;
  col->Pv = (Mh << 1) | ~ (Xv | Ph);
  col->Mv = Ph & Xv;
  backmask = 1UL << col->maxleqk;
  if (Eq & backmask || Mh & backmask)
  {
    col->maxleqk++;
  } else
  {
    if (Ph & backmask)
    {
      unsigned long tmpmaxleqk = UNDEFMAXLEQK;
      score = mti->maxdistance+1;
      if (col->maxleqk > 0)
      {
        for (idx = col->maxleqk - 1, backmask >>= 1;
             /* Nothing */;
             backmask >>= 1)
        {
          if (col->Pv & backmask)
          {
            score--;
            if (score <= mti->maxdistance)
            {
              tmpmaxleqk = idx;
              col->lastdistvalue = score;
              break;
            }
          } else
          {
            if (col->Mv & backmask)
            {
              score++;
            }
          }
          if (idx > 0)
          {
            idx--;
          } else
          {
            break;
          }
        }
      }
      col->maxleqk = tmpmaxleqk;
    }
  }
}

const AbstractDfstransformer *gt_apme_AbstractDfstransformer(void)
{
  static const AbstractDfstransformer apme_adfst =
  {
    sizeof (ApmeoveridxLimdfsstate),
    apme_allocatedfsconstinfo,
    apme_initdfsconstinfo,
    NULL, /* no extractdfsconstinfo */
    apme_freedfsconstinfo,
    apme_initLimdfsstate,
    NULL,
    NULL,
    NULL,
    apme_fullmatchLimdfsstate,
    apme_nextLimdfsstate,
    apme_inplacenextLimdfsstate,
#ifdef SKDEBUG
    apme_showLimdfsstate,
#endif
  };
  return &apme_adfst;
}
genometools-1.5.1/src/match/apmeoveridx.h000066400000000000000000000017531211610345200204310ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef APMEOVERIDX_H
#define APMEOVERIDX_H
#include "absdfstrans-def.h"

const AbstractDfstransformer *gt_apme_AbstractDfstransformer(void);

#endif
genometools-1.5.1/src/match/asqg_writer.c000066400000000000000000000106611211610345200204260ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "core/log_api.h"
#include "match/asqg_writer.h"

struct GtAsqgWriter
{
  GtFile *file;
  const GtEncseq *encseq;
};

GtAsqgWriter* gt_asqg_writer_new(GtFile *file, const GtEncseq *encseq)
{
  GtAsqgWriter *aw;
  aw = gt_malloc(sizeof (*aw));
  aw->file = file;
  aw->encseq = encseq;
  return aw;
}

int gt_asqg_writer_show_header(GtAsqgWriter *aw, float erate,
    unsigned long minlen, const char *inputfilename, bool has_containments,
    bool has_transitives, GT_UNUSED GtError *err)
{
  gt_assert(aw != NULL);
  gt_file_xprintf(aw->file,
      "HT\tVN:i:%lu\tER:f:%g\tOL:i:%lu\tIN:Z:%s\tCN:i:%c\tTE:i:%c\n",
      GT_ASQG_VERSION, erate, minlen, inputfilename,
      has_containments ? '1' : '0', has_transitives ? '1' : '0');
  return 0;
}

static inline void gt_asqg_writer_show_vertex_line(GtFile *file,
    unsigned long seqnum, const char *sequence, bool subsequence)
{
  gt_file_xprintf(file, "VT\t%lu\t%s\tSS:i:%c\n", seqnum, sequence,
      subsequence ? '1' : '0');
}

int gt_asqg_writer_show_vertices(GtAsqgWriter *aw, GT_UNUSED GtError *err)
{
  const GtTwobitencoding *nextencoded;
  GtTwobitencoding code = 0;
  unsigned long seqnum = 0, nofseqs = gt_encseq_num_of_sequences(aw->encseq),
                pos = 0, next_stop, i,
                tlen = gt_encseq_total_length(aw->encseq), charsincode = 0;
  char *seqbuffer;
  bool last_seq = false;
  const char code2char[] = "acgt";
  gt_assert(aw != NULL);
  seqbuffer = gt_malloc(sizeof (*seqbuffer) *
      (gt_encseq_max_seq_length(aw->encseq) + 1UL));
  nextencoded = gt_encseq_twobitencoding_export(aw->encseq);
  i = 0;
  while (!last_seq)
  {
    if (seqnum + 1UL == nofseqs)
    {
      last_seq = true;
      next_stop = tlen - 1UL;
    }
    else
      next_stop = gt_encseq_seqstartpos(aw->encseq, seqnum + 1UL) - 1UL;
    for (/**/; i < next_stop; i++)
    {
      if (charsincode == 0)
      {
        code = *(nextencoded++);
        charsincode = (unsigned long)GT_UNITSIN2BITENC;
      }
      seqbuffer[pos++] = code2char[code >> ((--charsincode) << 1) & 3];
    }
    seqbuffer[pos] = '\0';
    gt_asqg_writer_show_vertex_line(aw->file, seqnum, seqbuffer, false);
    pos = 0;
    /* consume separator */
    i++;
    if (charsincode == 0)
    {
      code = *(nextencoded++);
      charsincode = (unsigned long)GT_UNITSIN2BITENC;
    }
    charsincode--;
    seqnum++;
  }
  gt_free(seqbuffer);
  return 0;
}

static inline void gt_asqg_writer_show_edge_line(GtFile *file,
    unsigned long seqnum1, unsigned long seqnum2, unsigned long start1,
    unsigned long end1, unsigned long seqlen1, unsigned long start2,
    unsigned long end2, unsigned long seqlen2, bool revcompl,
    unsigned long edist)
{
  gt_file_xprintf(file, "ED\t%lu %lu %lu %lu %lu %lu %lu %lu %c %lu\n",
      seqnum1, seqnum2, start1, end1, seqlen1, start2, end2, seqlen2,
      revcompl ? '1' : '0', edist);
}

void gt_spmproc_show_asgq(unsigned long suffix_readnum,
    unsigned long prefix_readnum, unsigned long length,
    bool suffixseq_direct, bool prefixseq_direct, void *asqg_writer)
{
  GtAsqgWriter *aw = asqg_writer;
  const unsigned long sl1 = gt_encseq_seqlength(aw->encseq, suffix_readnum),
                      sl2 = gt_encseq_seqlength(aw->encseq, prefix_readnum);
  gt_asqg_writer_show_edge_line(aw->file, suffix_readnum, prefix_readnum,
      suffixseq_direct ? sl1 - length : 0,
      suffixseq_direct ? sl1 - 1UL : length - 1UL, sl1,
      prefixseq_direct ? 0 : sl2 - length,
      prefixseq_direct ? length - 1UL : sl2 - 1UL, sl2,
      !suffixseq_direct || !prefixseq_direct, 0);
}

void gt_asqg_writer_delete(GtAsqgWriter *aw)
{
  gt_free(aw);
}
genometools-1.5.1/src/match/asqg_writer.h000066400000000000000000000055611211610345200204360ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ASQG_WRITER_H
#define ASQG_WRITER_H

#include "core/file.h"
#include "core/encseq.h"
#include "core/error.h"

/* The  class allows to write string graph information in
   the ASQG format of SGA (Simpsons and Durbin, 2012). */
typedef struct GtAsqgWriter GtAsqgWriter;

/*  is the supported version of the asqg format. */
#define GT_ASQG_VERSION 1UL

/* Creates a new  object, using  for output
   and  as source of information. */
GtAsqgWriter* gt_asqg_writer_new(GtFile *file, const GtEncseq *encseq);

/* Writes the header using the provided information:  is the
   minimal match length,  is a string to use as input filename,
    the error rate,  shall be true, if containments
   are present,  shall be true, if transitive edges are
   present. Returns 0 on success, -1 on error and sets . */
int           gt_asqg_writer_show_header(GtAsqgWriter *aw,
                                         float erate,
                                         unsigned long minlen,
                                         const char *inputfilename,
                                         bool has_containments,
                                         bool has_transitives,
                                         GtError *err);

/* Writes the vertices. Returns 0 on success, -1 on error and sets . */
int           gt_asqg_writer_show_vertices(GtAsqgWriter *aw,
                                           GtError *err);

/* Writes an edge using Readjoiner SPM information. */
void          gt_spmproc_show_asgq(unsigned long suffix_readnum,
                                   unsigned long prefix_readnum,
                                   unsigned long length,
                                   bool suffixseq_direct,
                                   bool prefixseq_direct,
                                   void *asqg_writer);

/* Deletes a  object. */
void          gt_asqg_writer_delete(GtAsqgWriter *aw);

#endif
genometools-1.5.1/src/match/bcktab.c000066400000000000000000001266011211610345200173270ustar00rootroot00000000000000/*
  Copyright (c) 2007-2011 Stefan Kurtz 
  Copyright (c) 2007-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#include 
#include 
#include 
#include 
#endif
#include "core/fa.h"
#include "core/chardef.h"
#include "core/error.h"
#include "core/format64.h"
#include "core/mapspec.h"
#include "core/mathsupport.h"
#include "core/minmax.h"
#include "core/safecast-gen.h"
#include "core/spacecalc.h"
#include "core/str.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "bcktab.h"
#include "esa-fileend.h"
#include "intcode-def.h"
#include "initbasepower.h"
#include "sfx-maprange.h"
#include "stamp.h"

#define GT_FROMCODE2SPECIALCODE(CODE,NUMOFCHARS)\
                               (((NUMOFCHARS) == 4U)\
                               ? ((CODE) >> 2)\
                               : (((CODE) - ((NUMOFCHARS)-1)) / (NUMOFCHARS)))

typedef struct
{
  unsigned long nonspecialsmaxbucketsize,
                specialsmaxbucketsize,
                maxbucketsize;
} GtMaxbucketinfo;

struct GtBcktab
{
  GtLeftborder leftborder;
  uint32_t *uintcountspecialcodes,
           **uintdistpfxidx;
  unsigned long *ulongcountspecialcodes,
                **ulongdistpfxidx,
                sizeofrep,
                pagesize,
                numofdistpfxidxcounters;
  unsigned int prefixlength,
               numofchars,
               optimalnumofbits;
  GtCodetype numofallcodes,
             numofspecialcodes,
             **multimappower,
             *basepower,
             *filltable;
  GtUchar *qgrambuffer;
  GtMaxbucketinfo maxbucketinfo;
  bool allocated,
       withspecialsuffixes,
       useulong;
  void *mappedptr;
  GtSfxmappedrange *mappedleftborder,
                   *mappedcountspecialcodes;
};

void gt_bcktab_leftborder_assign(GtLeftborder *lb,GtCodetype code,
                                 unsigned long value)
{
  gt_assert(lb != NULL);
  if (lb->ulongbounds != NULL)
  {
    lb->ulongbounds[code] = value;
  } else
  {
    gt_assert(value <= (unsigned long) UINT_MAX);
    gt_assert(lb->uintbounds != NULL);
    lb->uintbounds[code] = (uint32_t) value;
  }
}

unsigned long gt_bcktab_get_leftborder(const GtBcktab *bcktab,GtCodetype code)
{
  gt_assert(bcktab != NULL);
  if (bcktab->leftborder.ulongbounds != NULL)
  {
    return bcktab->leftborder.ulongbounds[code];
  }
  gt_assert(bcktab->leftborder.uintbounds != NULL);
  return (unsigned long) bcktab->leftborder.uintbounds[code];
}

static unsigned long gt_bcktab_distpfxidx_get(const GtBcktab *bcktab,
                                              unsigned int prefixindex,
                                              GtCodetype ordercode)
{
  if (bcktab->ulongdistpfxidx != NULL)
  {
    return bcktab->ulongdistpfxidx[prefixindex][ordercode];
  }
  gt_assert(bcktab->uintdistpfxidx != NULL);
  return (unsigned long) bcktab->uintdistpfxidx[prefixindex][ordercode];
}

static void gt_bcktab_distpfxidx_increment(const GtBcktab *bcktab,
                                           unsigned int prefixindex,
                                           GtCodetype ordercode)
{
  if (bcktab->ulongdistpfxidx != NULL)
  {
    bcktab->ulongdistpfxidx[prefixindex][ordercode]++;
  } else
  {
    gt_assert(bcktab->uintdistpfxidx != NULL);
    bcktab->uintdistpfxidx[prefixindex][ordercode]++;
  }
}

static unsigned long gt_bcktab_transformcode(unsigned long code,
                                             const void *data)
{
  unsigned int numofchars, *numofcharptr = (unsigned int *) data;

  numofchars = *numofcharptr;
  if (code >= (unsigned long) (numofchars - 1))
  {
    return GT_FROMCODE2SPECIALCODE(code,numofchars);
  } else
  {
    return 0;
  }
}

static void gt_bcktab_transform_minmax_code(unsigned long *mincode,
                                            unsigned long *maxcode,
                                            const void *data)
{
  *mincode = gt_bcktab_transformcode(*mincode,data);
  *maxcode = gt_bcktab_transformcode(*maxcode,data);
}

void gt_bcktab_storetmp(GtBcktab *bcktab)
{
  if (bcktab->useulong) {
    gt_Sfxmappedrange_storetmp_ulong(bcktab->mappedleftborder,
                                     &bcktab->leftborder.ulongbounds,
                                     true);
    if (bcktab->withspecialsuffixes)
    {
      gt_Sfxmappedrange_storetmp_ulong(bcktab->mappedcountspecialcodes,
                                       &bcktab->ulongcountspecialcodes,
                                       true);
    }
  } else {
    gt_Sfxmappedrange_storetmp_uint32(bcktab->mappedleftborder,
                                      &bcktab->leftborder.uintbounds,
                                      true);
    if (bcktab->withspecialsuffixes)
    {
      gt_Sfxmappedrange_storetmp_uint32(bcktab->mappedcountspecialcodes,
                                        &bcktab->uintcountspecialcodes,
                                        true);
    }
  }
}

void gt_bcktab_maprange_lb_cs(GtSfxmappedrangelist *sfxmrlist,GtBcktab *bcktab)
{
  bcktab->mappedleftborder
    = gt_Sfxmappedrange_new("leftborder",
                            bcktab->numofallcodes+1,
                            bcktab->useulong
                              ? GtSfxunsignedlong
                              : GtSfxuint32_t,
                            NULL,
                            NULL);
  gt_Sfxmappedrangelist_add(sfxmrlist,bcktab->mappedleftborder);
  if (bcktab->withspecialsuffixes)
  {
    bcktab->mappedcountspecialcodes
      = gt_Sfxmappedrange_new("countspecialcodes",
                              bcktab->numofspecialcodes,
                              bcktab->useulong
                                ? GtSfxunsignedlong
                                : GtSfxuint32_t,
                              gt_bcktab_transform_minmax_code,
                              &bcktab->numofchars);
    gt_Sfxmappedrangelist_add(sfxmrlist,bcktab->mappedcountspecialcodes);
  }
}

void gt_bcktab_assignboundsforpart(GtBcktab *bcktab,
                                   GtCodetype mincode,
                                   GtCodetype maxcode)
{
  void *tmpleftborder;

  tmpleftborder = gt_Sfxmappedrange_map(bcktab->mappedleftborder,
                                        mincode,
                                        maxcode);
  if (bcktab->useulong)
  {
    bcktab->leftborder.ulongbounds = (unsigned long *) tmpleftborder;
  } else
  {
    bcktab->leftborder.uintbounds = (uint32_t *) tmpleftborder;
  }
  if (bcktab->withspecialsuffixes)
  {
    void *tmpspecialcodes;

    tmpspecialcodes = gt_Sfxmappedrange_map(bcktab->mappedcountspecialcodes,
                                            mincode, maxcode);
    if (bcktab->useulong)
    {
      bcktab->ulongcountspecialcodes = (unsigned long *) tmpspecialcodes;
    } else
    {
      bcktab->uintcountspecialcodes = (uint32_t *) tmpspecialcodes;
    }
  }
}

static unsigned long gt_bcktab_numofdistpfxidxcounters(
                                             const GtCodetype *basepower,
                                             unsigned int prefixlength)
{
  if (prefixlength > 2U)
  {
    unsigned long numofcounters = 0;
    unsigned int idx;

    for (idx=1U; idx < prefixlength-1; idx++)
    {
      numofcounters += basepower[idx];
    }
    return numofcounters;
  }
  return 0;
}

static bool gt_bcktab_useulong(unsigned long maxvalue)
{
  return maxvalue <= (unsigned long) UINT_MAX ? false : true;
}

static uint64_t gt_bcktab_sizeoftable_generic(unsigned int prefixlength,
                                              unsigned long numofallcodes,
                                              unsigned long numofspecialcodes,
                                              bool useulong,
                                              const GtCodetype *basepower,
                                              bool countdistpfxidx,
                                              bool withspecialsuffixes)
{
  uint64_t sizeoftable;
  size_t sizeofbasetype;

  sizeofbasetype = useulong ? sizeof (unsigned long) : sizeof (uint32_t);
  sizeoftable = (uint64_t) sizeofbasetype * (uint64_t) (numofallcodes + 1);
  if (withspecialsuffixes)
  {
    sizeoftable += sizeofbasetype * (uint64_t) numofspecialcodes;
    if (countdistpfxidx)
    {
      sizeoftable += (uint64_t) sizeofbasetype *
                                gt_bcktab_numofdistpfxidxcounters(basepower,
                                                                  prefixlength);
    }
  }
  return sizeoftable;
}

uint64_t gt_bcktab_sizeoftable(unsigned int numofchars,
                               unsigned int prefixlength,
                               unsigned long maxvalue,
                               bool withspecialsuffixes)
{
  unsigned long numofallcodes, numofspecialcodes;
  uint64_t sizeofbuckettable;
  GtCodetype *basepower;

  if (withspecialsuffixes)
  {
    if (prefixlength >= 2U)
    {
      basepower = gt_initbasepower(numofchars,prefixlength-2);
    } else
    {
      basepower = NULL;
    }
    numofspecialcodes = gt_power_for_small_exponents(numofchars,prefixlength-1);
  } else
  {
    basepower = NULL;
    numofspecialcodes = 0;
  }
  numofallcodes = gt_power_for_small_exponents(numofchars,prefixlength);
  sizeofbuckettable
    = gt_bcktab_sizeoftable_generic(prefixlength,
                                    numofallcodes,
                                    numofspecialcodes,
                                    gt_bcktab_useulong(maxvalue),
                                    basepower,
                                    true,
                                    withspecialsuffixes);
  gt_free(basepower);
  return sizeofbuckettable;
}

unsigned long gt_bcktab_sizeofworkspace(unsigned int prefixlength)
{
  size_t size = sizeof (GtCodetype) * (prefixlength+1);
  size += sizeof (GtCodetype) * prefixlength;
  size += sizeof (GtBcktab);
  size += prefixlength;
  return (unsigned long) size;
}

static void ulong_setdistpfxidxptrs(unsigned long **ulongdistpfxidx,
                                    unsigned long *ptr,
                                    const GtCodetype *basepower,
                                    unsigned int prefixlength)
{
  unsigned int idx;

  ulongdistpfxidx[0] = ptr;
  for (idx=1U; idxwithspecialsuffixes);
  if (prefixlength > 2U)
  {
    if (bcktab->numofdistpfxidxcounters > 0)
    {
      unsigned long *ulongcounters;
      uint32_t *uintcounters;
      size_t allocsize;

      if (bcktab->useulong)
      {
        bcktab->ulongdistpfxidx = gt_malloc(sizeof (void *) * (prefixlength-1));
        allocsize = sizeof (*ulongcounters) * bcktab->numofdistpfxidxcounters;
        ulongcounters = gt_malloc(allocsize);
        memset(ulongcounters,0,allocsize);
        ulong_setdistpfxidxptrs(bcktab->ulongdistpfxidx,ulongcounters,
                                bcktab->basepower,prefixlength);
      } else
      {
        bcktab->uintdistpfxidx = gt_malloc(sizeof (void *) * (prefixlength-1));
        allocsize = sizeof (*uintcounters) * bcktab->numofdistpfxidxcounters;
        uintcounters = gt_malloc(allocsize);
        memset(uintcounters,0,allocsize);
        uint_setdistpfxidxptrs(bcktab->uintdistpfxidx,uintcounters,
                               bcktab->basepower,prefixlength);
      }
      gt_logger_log(logger,"sizeof (distpfxidx)=%lu bytes",
                            (unsigned long) allocsize);
    }
  }
}

static GtBcktab *gt_bcktab_new_withinit(unsigned int numofchars,
                                        unsigned int prefixlength,
                                        unsigned long maxvalue,
                                        bool withspecialsuffixes)
{
  GtBcktab *bcktab;
  uint64_t sizeofrep_uint64_t;

  bcktab = gt_malloc(sizeof *bcktab);
  bcktab->mappedptr = NULL;
  bcktab->mappedleftborder = NULL;
  bcktab->leftborder.ulongbounds = NULL;
  bcktab->leftborder.uintbounds = NULL;
  bcktab->mappedcountspecialcodes = NULL;
  bcktab->ulongcountspecialcodes = NULL;
  bcktab->uintcountspecialcodes = NULL;
  bcktab->ulongdistpfxidx = NULL;
  bcktab->uintdistpfxidx = NULL;
  bcktab->prefixlength = prefixlength;
  bcktab->withspecialsuffixes = withspecialsuffixes;
  bcktab->basepower = gt_initbasepower(numofchars,prefixlength);
  bcktab->numofchars = numofchars;
  bcktab->numofdistpfxidxcounters
    = gt_bcktab_numofdistpfxidxcounters(bcktab->basepower,prefixlength);
  bcktab->filltable = gt_initfilltable(numofchars,prefixlength);
  bcktab->numofallcodes = bcktab->basepower[prefixlength];
  bcktab->numofspecialcodes = bcktab->basepower[prefixlength-1];
  bcktab->multimappower = gt_initmultimappower(numofchars,prefixlength);
  bcktab->pagesize = (unsigned long) sysconf((int) _SC_PAGESIZE);
  bcktab->useulong = gt_bcktab_useulong(maxvalue);
  gt_assert(bcktab->pagesize % sizeof (unsigned long) == 0);
  bcktab->allocated = false;
  bcktab->qgrambuffer = gt_malloc(sizeof (*bcktab->qgrambuffer) * prefixlength);
  sizeofrep_uint64_t = gt_bcktab_sizeoftable_generic(
                                          prefixlength,
                                          bcktab->numofallcodes,
                                          bcktab->numofspecialcodes,
                                          bcktab->useulong,
                                          bcktab->basepower,
                                          true,
                                          withspecialsuffixes);
  bcktab->sizeofrep = CALLCASTFUNC(uint64_t,unsigned_long,sizeofrep_uint64_t);
  return bcktab;
}

GtBcktab *gt_bcktab_new(unsigned int numofchars,
                        unsigned int prefixlength,
                        unsigned long maxvalue,
                        bool storespecialcodes,
                        bool withspecialsuffixes,
                        GtLogger *logger,
                        GtError *err)
{
  GtBcktab *bcktab;
  bool haserr = false;

  bcktab = gt_bcktab_new_withinit(numofchars,prefixlength,maxvalue,
                                  withspecialsuffixes);
  bcktab->allocated = true;
  if (storespecialcodes && bcktab->numofallcodes > 0 &&
      bcktab->numofallcodes-1 > (unsigned long) MAXCODEVALUE)
  {
    gt_error_set(err,"alphasize^prefixlength-1 = " FormatGtCodetype
                     " does not fit into %u"
                     " bits: choose smaller value for prefixlength",
                     bcktab->numofallcodes-1,
                     CODEBITS);
    haserr = true;
  }
  if (!haserr)
  {
    size_t allocsize_bounds, allocsize_countspecialcodes = 0;
    if (bcktab->useulong)
    {
      allocsize_bounds = sizeof (*bcktab->leftborder.ulongbounds) *
                         (bcktab->numofallcodes+1);
      bcktab->leftborder.ulongbounds = gt_malloc(allocsize_bounds);
      memset(bcktab->leftborder.ulongbounds,0,allocsize_bounds);
      if (withspecialsuffixes)
      {
        allocsize_countspecialcodes = sizeof (*bcktab->ulongcountspecialcodes) *
                                      bcktab->numofspecialcodes;
        bcktab->ulongcountspecialcodes = gt_malloc(allocsize_countspecialcodes);
        memset(bcktab->ulongcountspecialcodes,0,allocsize_countspecialcodes);
      }
    } else
    {
      allocsize_bounds = sizeof (*bcktab->leftborder.uintbounds) *
                         (bcktab->numofallcodes+1);
      bcktab->leftborder.uintbounds = gt_malloc(allocsize_bounds);
      memset(bcktab->leftborder.uintbounds,0,allocsize_bounds);
      if (withspecialsuffixes)
      {
        allocsize_countspecialcodes = sizeof (*bcktab->uintcountspecialcodes) *
                                      bcktab->numofspecialcodes;
        bcktab->uintcountspecialcodes = gt_malloc(allocsize_countspecialcodes);
        memset(bcktab->uintcountspecialcodes,0,allocsize_countspecialcodes);
      }
    }
    gt_logger_log(logger,"sizeof (leftborder)=%lu bytes",
                (unsigned long) allocsize_bounds);
    if (withspecialsuffixes)
    {
      gt_logger_log(logger,"sizeof (countspecialcodes)=%lu bytes",
                (unsigned long) allocsize_countspecialcodes);
      allocdistpfxidxcounts(bcktab,prefixlength,logger);
    }
    gt_logger_log(logger,"sizeof (bcktab)=" Formatuint64_t " bytes",
              PRINTuint64_tcast(gt_bcktab_sizeoftable(numofchars,
                                                      prefixlength,
                                                      maxvalue,
                                                      withspecialsuffixes)));
  }
  if (haserr)
  {
    gt_bcktab_delete(bcktab);
    return NULL;
  }
  return bcktab;
}

static void assignbcktabmapspecification(GtMapspec *mapspec,
                                         void *data,
                                         bool writemode)
{
  GtBcktab *bcktab = (GtBcktab *) data;

  if (bcktab->useulong)
  {
    gt_mapspec_add_ulong(mapspec, bcktab->leftborder.ulongbounds,
                         (unsigned long) (bcktab->numofallcodes+1));
  } else
  {
    gt_mapspec_add_uint32(mapspec, bcktab->leftborder.uintbounds,
                          (unsigned long) (bcktab->numofallcodes+1));
  }
  if (bcktab->withspecialsuffixes)
  {
    if (bcktab->useulong)
    {
      gt_mapspec_add_ulong(mapspec, bcktab->ulongcountspecialcodes,
                           (unsigned long) bcktab->numofspecialcodes);
    } else
    {
      gt_mapspec_add_uint32(mapspec, bcktab->uintcountspecialcodes,
                            (unsigned long) bcktab->numofspecialcodes);
    }
    if (bcktab->numofdistpfxidxcounters > 0)
    {
      if (!writemode)
      {
        if (bcktab->useulong)
        {
          bcktab->ulongdistpfxidx = gt_malloc(sizeof (void *) *
                                              (bcktab->prefixlength-1));
        } else
        {
          bcktab->uintdistpfxidx = gt_malloc(sizeof (void *) *
                                             (bcktab->prefixlength-1));
        }
      }
      if (bcktab->useulong)
      {
        gt_mapspec_add_ulong(mapspec, bcktab->ulongdistpfxidx[0],
                             bcktab->numofdistpfxidxcounters);
      } else
      {
        gt_mapspec_add_uint32(mapspec, bcktab->uintdistpfxidx[0],
                              bcktab->numofdistpfxidxcounters);
      }
    }
  }
}

int gt_bcktab_flush_to_file(FILE *fp,const GtBcktab *bcktab,GtError *err)
{
  gt_error_check(err);
  return gt_mapspec_write(assignbcktabmapspecification, fp, (GtBcktab *) bcktab,
                          bcktab->sizeofrep, err);
}

static int fillbcktabmapspecstartptr(GtBcktab *bcktab,
                                     const char *indexname,
                                     GtError *err)
{
  bool haserr = false;
  GtStr *tmpfilename;

  gt_error_check(err);
  tmpfilename = gt_str_new_cstr(indexname);
  gt_str_append_cstr(tmpfilename,BCKTABSUFFIX);
  if (gt_mapspec_read(assignbcktabmapspecification,
                      bcktab,
                      tmpfilename,
                      bcktab->sizeofrep,
                      &bcktab->mappedptr,
                      err) != 0)
  {
    haserr = true;
  }
  gt_str_delete(tmpfilename);
  return haserr ? -1 : 0;
}

#define CHECKCOUNTSPECIALCODES
#ifdef CHECKCOUNTSPECIALCODES
static unsigned long fromcode2countspecialcodes(GtCodetype code,
                                                const GtBcktab *bcktab)
{
  if (code >= bcktab->filltable[bcktab->prefixlength-1])
  {
    GtCodetype ordercode = code - bcktab->filltable[bcktab->prefixlength-1];
    GtCodetype divisor = bcktab->filltable[bcktab->prefixlength-1] + 1;
    if (ordercode % divisor == 0)
    {
      ordercode /= divisor;
      if (bcktab->ulongcountspecialcodes != NULL)
      {
        return bcktab->ulongcountspecialcodes[ordercode];
      } else
      {
        gt_assert(bcktab->uintcountspecialcodes != NULL);
        return (unsigned long) bcktab->uintcountspecialcodes[ordercode];
      }
    }
  }
  return 0;
}

static void pfxidxpartialsums(unsigned long *count,
                              GtCodetype code,
                              const GtBcktab *bcktab)
{
  unsigned int prefixindex;
  unsigned long sum = 0, specialsinbucket;
  GtCodetype ordercode, divisor;

  memset(count,0,sizeof (*count) * (size_t) bcktab->prefixlength);
  for (prefixindex=bcktab->prefixlength-2; prefixindex>=1U; prefixindex--)
  {
    if (code >= bcktab->filltable[prefixindex])
    {
      ordercode = code - bcktab->filltable[prefixindex];
      divisor = bcktab->filltable[prefixindex] + 1;
      if (ordercode % divisor == 0)
      {
        ordercode /= divisor;
        count[prefixindex]
          = gt_bcktab_distpfxidx_get(bcktab,prefixindex-1,ordercode);
        sum += count[prefixindex];
      }
    } else
    {
      break;
    }
  }
  specialsinbucket = fromcode2countspecialcodes(code,bcktab);
  gt_assert(sum <= specialsinbucket);
  count[bcktab->prefixlength-1] = specialsinbucket - sum;
  if (bcktab->prefixlength > 2U)
  {
    for (prefixindex = bcktab->prefixlength-2; prefixindex>=1U; prefixindex--)
    {
      count[prefixindex] += count[prefixindex+1];
    }
#ifndef NDEBUG
    if (specialsinbucket != count[1])
    {
      fprintf(stderr,"code " FormatGtCodetype ": sum = %lu != %lu = count[1]\n",
              code,sum,count[1]);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
#endif
  }
}

void gt_bcktab_checkcountspecialcodes(const GtBcktab *bcktab)
{
  GtCodetype code;
  unsigned long *count;

  if (bcktab->prefixlength >= 2U)
  {
    count = gt_malloc(sizeof (*count) * bcktab->prefixlength);
    for (code=0; codenumofallcodes; code++)
    {
      pfxidxpartialsums(count, code, bcktab);
    }
    gt_free(count);
  }
}
#endif

GtBcktab *gt_bcktab_map(const char *indexname,
                        unsigned int numofchars,
                        unsigned int prefixlength,
                        unsigned long maxvalue,
                        bool withspecialsuffixes,
                        GtError *err)
{
  GtBcktab *bcktab;

  bcktab = gt_bcktab_new_withinit(numofchars,prefixlength,maxvalue,
                                  withspecialsuffixes);
  bcktab->allocated = false;
  if (fillbcktabmapspecstartptr(bcktab, indexname, err) != 0)
  {
    gt_bcktab_delete(bcktab);
    return NULL;
  }
  if (withspecialsuffixes)
  {
    if (bcktab->ulongdistpfxidx != NULL)
    {
      ulong_setdistpfxidxptrs(bcktab->ulongdistpfxidx,
                              bcktab->ulongdistpfxidx[0],
                              bcktab->basepower,bcktab->prefixlength);
    } else
    {
      if (bcktab->uintdistpfxidx != NULL)
      {
        uint_setdistpfxidxptrs(bcktab->uintdistpfxidx,
                               bcktab->uintdistpfxidx[0],
                               bcktab->basepower,bcktab->prefixlength);
      }
    }
#ifdef CHECKCOUNTSPECIALCODES
    gt_bcktab_checkcountspecialcodes(bcktab);
#endif
  }
  return bcktab;
}

void gt_bcktab_show(const GtBcktab *bcktab)
{
  unsigned int prefixindex;

  for (prefixindex=1U; prefixindex < bcktab->prefixlength-1; prefixindex++)
  {
    GtCodetype code;
    unsigned long sum = 0, value;
    for (code = 0; code < bcktab->basepower[prefixindex]; code++)
    {
      value = gt_bcktab_distpfxidx_get(bcktab,prefixindex-1,code);
      sum += value;
      printf("distpfxidx[%u][%lu]=%lu\n",prefixindex,code,value);
    }
    printf("sum %lu\n",sum);
  }
}

void gt_bcktab_leftborder_show(const GtBcktab *bcktab)
{
  GtCodetype idx;

  for (idx=0; idxnumofallcodes; idx++)
  {
    printf("leftborder[" FormatGtCodetype "]=%lu\n",idx,
                                    gt_bcktab_get_leftborder(bcktab,idx));
  }
}

int gt_bcktab_remap_all(GtBcktab *bcktab,GtError *err)
{
  bool haserr = false;
  void *tmp;

  if (bcktab->mappedleftborder != NULL)
  {
    tmp = gt_Sfxmappedrange_map_entire(bcktab->mappedleftborder,err);
    if (bcktab->useulong)
    {
      bcktab->leftborder.ulongbounds = (unsigned long *) tmp;
      if (bcktab->leftborder.ulongbounds == NULL)
      {
        haserr = true;
      }
    } else
    {
      bcktab->leftborder.uintbounds = (uint32_t *) tmp;
      if (bcktab->leftborder.uintbounds == NULL)
      {
        haserr = true;
      }
    }
  }
  if (!haserr &&
      bcktab->withspecialsuffixes && bcktab->mappedcountspecialcodes != NULL)
  {
    tmp = gt_Sfxmappedrange_map_entire(bcktab->mappedcountspecialcodes,err);
    if (bcktab->useulong)
    {
      bcktab->ulongcountspecialcodes = (unsigned long *) tmp;
      if (bcktab->ulongcountspecialcodes == NULL)
      {
        gt_fa_xmunmap(bcktab->leftborder.ulongbounds);
        haserr = true;
      }
    } else
    {
      bcktab->uintcountspecialcodes = (uint32_t *) tmp;
      if (bcktab->uintcountspecialcodes == NULL)
      {
        gt_fa_xmunmap(bcktab->leftborder.uintbounds);
        haserr = true;
      }
    }
  }
  return haserr ? -1 : 0;
}

void gt_bcktab_delete(GtBcktab *bcktab)
{
  if (bcktab == NULL)
  {
    return;
  }
  /*showbcktab(bcktabptr);*/
  if (bcktab->allocated)
  {
    gt_Sfxmappedrange_delete(bcktab->mappedleftborder);
    bcktab->mappedleftborder = NULL;
    gt_Sfxmappedrange_delete(bcktab->mappedcountspecialcodes);
    bcktab->mappedcountspecialcodes = NULL;
    gt_free(bcktab->ulongcountspecialcodes);
    gt_free(bcktab->uintcountspecialcodes);
    gt_free(bcktab->leftborder.ulongbounds);
    gt_free(bcktab->leftborder.uintbounds);
    if (bcktab->ulongdistpfxidx != NULL)
    {
      gt_free(bcktab->ulongdistpfxidx[0]);
    }
    if (bcktab->uintdistpfxidx != NULL)
    {
      gt_free(bcktab->uintdistpfxidx[0]);
    }
  } else
  {
    gt_assert(bcktab->mappedleftborder == NULL);
    gt_assert(bcktab->mappedcountspecialcodes == NULL);
    if (bcktab->mappedptr != NULL)
    {
      gt_fa_xmunmap(bcktab->mappedptr);
    }
    bcktab->mappedptr = NULL;
    if (bcktab->ulongdistpfxidx != NULL)
    {
      bcktab->ulongdistpfxidx[0] = NULL;
    }
    if (bcktab->uintdistpfxidx != NULL)
    {
      bcktab->uintdistpfxidx[0] = NULL;
    }
  }
  bcktab->leftborder.ulongbounds = NULL;
  bcktab->leftborder.uintbounds = NULL;
  bcktab->ulongcountspecialcodes = NULL;
  bcktab->uintcountspecialcodes = NULL;
  gt_free(bcktab->ulongdistpfxidx);
  bcktab->ulongdistpfxidx = NULL;
  gt_free(bcktab->uintdistpfxidx);
  bcktab->uintdistpfxidx = NULL;
  gt_multimappower_delete(bcktab->multimappower);
  gt_free(bcktab->filltable);
  bcktab->filltable = NULL;
  gt_free(bcktab->basepower);
  bcktab->basepower = NULL;
  gt_free(bcktab->qgrambuffer);
  bcktab->qgrambuffer = NULL;
  gt_free(bcktab);
}

void gt_bcktab_updatespecials(GtBcktab *bcktab,
                              GtCodetype code,
                              unsigned int prefixindex)
{
  GtCodetype specialcode;

  gt_assert(prefixindex > 0);
  gt_assert(prefixindex <= bcktab->prefixlength);
  gt_assert(code < bcktab->numofallcodes);
  if (prefixindex < bcktab->prefixlength-1)
  {
    GtCodetype ordercode = (code - bcktab->filltable[prefixindex])/
                           (bcktab->filltable[prefixindex]+1);
    gt_bcktab_distpfxidx_increment(bcktab,prefixindex-1,ordercode);
  }
  gt_assert(code >= (GtCodetype) (bcktab->numofchars-1));
  specialcode = GT_FROMCODE2SPECIALCODE(code,bcktab->numofchars);
  if (bcktab->ulongcountspecialcodes != NULL)
  {
    bcktab->ulongcountspecialcodes[specialcode]++;
  } else
  {
    gt_assert(bcktab->uintcountspecialcodes != NULL);
    bcktab->uintcountspecialcodes[specialcode]++;
  }
}

/* The following function is not used anymore */

void gt_bcktab_addfinalspecials(GtBcktab *bcktab,
                                unsigned long specialcharacters)
{
  if (bcktab->withspecialsuffixes)
  {
    GtCodetype specialcode;

    gt_assert(bcktab->filltable[0] >= (GtCodetype) (bcktab->numofchars-1));
    specialcode = GT_FROMCODE2SPECIALCODE(bcktab->filltable[0],
                                          bcktab->numofchars);
    if (bcktab->ulongcountspecialcodes != NULL)
    {
      bcktab->ulongcountspecialcodes[specialcode]
        += (unsigned long) (specialcharacters + 1);
    } else
    {
      gt_assert(bcktab->uintcountspecialcodes != NULL);
      bcktab->uintcountspecialcodes[specialcode]
        += (uint32_t) (specialcharacters + 1);
    }
  }
}

unsigned int gt_bcktab_calcboundsparts(GtBucketspecification *bucketspec,
                                       const GtBcktab *bcktab,
                                       GtCodetype code,
                                       GtCodetype maxcode,
                                       unsigned long totalwidth,
                                       unsigned int rightchar)
{
  bucketspec->left = gt_bcktab_get_leftborder(bcktab,code);
  if (code < maxcode)
  {
    unsigned long nextleftborder = gt_bcktab_get_leftborder(bcktab,code+1);

    if (nextleftborder > 0)
    {
      bucketspec->nonspecialsinbucket = nextleftborder - bucketspec->left;
    } else
    {
      bucketspec->nonspecialsinbucket = 0;
    }
  } else
  {
    gt_assert(totalwidth >= bucketspec->left);
    bucketspec->nonspecialsinbucket
      = (unsigned long) (totalwidth - bucketspec->left);
  }
  if (bcktab->withspecialsuffixes && rightchar == bcktab->numofchars - 1)
  {
    GtCodetype specialcode;

    gt_assert(code >= (GtCodetype) (bcktab->numofchars-1));
    specialcode = GT_FROMCODE2SPECIALCODE(code,bcktab->numofchars);
    if (bcktab->ulongcountspecialcodes != NULL)
    {
      bucketspec->specialsinbucket
        = bcktab->ulongcountspecialcodes[specialcode];
    } else
    {
      gt_assert(bcktab->uintcountspecialcodes != NULL);
      bucketspec->specialsinbucket
        = (unsigned long) bcktab->uintcountspecialcodes[specialcode];
    }
    if (bucketspec->nonspecialsinbucket >= bucketspec->specialsinbucket)
    {
      bucketspec->nonspecialsinbucket -= bucketspec->specialsinbucket;
    } else
    {
      bucketspec->nonspecialsinbucket = 0;
    }
  } else
  {
    bucketspec->specialsinbucket = 0;
  }
  return (rightchar < bcktab->numofchars - 1) ? (rightchar + 1) : 0;
}

void gt_bcktab_calcboundaries(GtBucketspecification *bucketspec,
                              const GtBcktab *bcktab,
                              GtCodetype code)
{
  gt_assert(code != bcktab->numofallcodes);
  (void) gt_bcktab_calcboundsparts(bucketspec,
                                   bcktab,
                                   code,
                                   bcktab->numofallcodes, /*codewithspecialsuffixes
                                    ? (unsigned int) (code % bcktab->numofchars)
                                    : 0);
}

unsigned long gt_bcktab_calcrightbounds(const GtBcktab *bcktab,
                                        GtCodetype code,
                                        GtCodetype maxcode,
                                        unsigned long totalwidth)
{
  return code < maxcode ? gt_bcktab_get_leftborder(bcktab,code+1) : totalwidth;
}

GtCodetype gt_bcktab_codedownscale(const GtBcktab *bcktab,
                                   GtCodetype code,
                                   unsigned int prefixindex,
                                   unsigned int maxprefixlen)
{
  unsigned int remain;

  code -= bcktab->filltable[maxprefixlen];
  remain = maxprefixlen-prefixindex;
  code %= (bcktab->filltable[remain]+1);
  code *= bcktab->basepower[remain];
  code += bcktab->filltable[prefixindex];
  return code;
}

void gt_bcktab_determinemaxsize(GtBcktab *bcktab,
                                GtCodetype mincode,
                                GtCodetype maxcode,
                                unsigned long partwidth)
{
  unsigned int rightchar = (unsigned int) (mincode % bcktab->numofchars);
  GtBucketspecification bucketspec;
  GtCodetype code;

#ifdef SKDEBUG
  printf("mincode=%lu,maxcode=%lu,partwidth=%lu,totallength=%lu\n",
          (unsigned long) mincode,(unsigned long) maxcode,
          partwidth,totallength);
#endif
  bcktab->maxbucketinfo.specialsmaxbucketsize = 1UL;
  bcktab->maxbucketinfo.nonspecialsmaxbucketsize = 1UL;
  bcktab->maxbucketinfo.maxbucketsize = 1UL;
  for (code = mincode; code <= maxcode; code++)
  {
    rightchar = gt_bcktab_calcboundsparts(&bucketspec,
                                          bcktab,
                                          code,
                                          maxcode,
                                          partwidth,
                                          rightchar);
    if (bucketspec.nonspecialsinbucket >
        bcktab->maxbucketinfo.nonspecialsmaxbucketsize)
    {
      bcktab->maxbucketinfo.nonspecialsmaxbucketsize
        = bucketspec.nonspecialsinbucket;
    }
    if (bucketspec.specialsinbucket >
        bcktab->maxbucketinfo.specialsmaxbucketsize)
    {
      bcktab->maxbucketinfo.specialsmaxbucketsize = bucketspec.specialsinbucket;
    }
    if (bucketspec.nonspecialsinbucket + bucketspec.specialsinbucket
        > bcktab->maxbucketinfo.maxbucketsize)
    {
      bcktab->maxbucketinfo.maxbucketsize = bucketspec.nonspecialsinbucket +
                                            bucketspec.specialsinbucket;
    }
  }
  /*
  gt_logger_log(logger,"maxbucket (specials)=%lu",
              bcktab->maxbucketinfo.specialsmaxbucketsize);
  gt_logger_log(logger,"maxbucket (nonspecials)=%lu",
              bcktab->maxbucketinfo.nonspecialsmaxbucketsize);
  gt_logger_log(logger,"maxbucket (all)=%lu",
              bcktab->maxbucketinfo.maxbucketsize);
  */
}

unsigned long gt_bcktab_nonspecialsmaxsize(const GtBcktab *bcktab)
{
  return bcktab->maxbucketinfo.nonspecialsmaxbucketsize;
}

unsigned int gt_bcktab_prefixlength(const GtBcktab *bcktab)
{
  return bcktab->prefixlength;
}

unsigned int gt_bcktab_singletonmaxprefixindex(const GtBcktab *bcktab,
                                               GtCodetype code)
{
  if (bcktab->prefixlength > 2U)
  {
    GtCodetype ordercode, divisor;
    unsigned int prefixindex;

    for (prefixindex=bcktab->prefixlength-2; prefixindex>=1U; prefixindex--)
    {
      if (code >= bcktab->filltable[prefixindex])
      {
        ordercode = code - bcktab->filltable[prefixindex];
        divisor = bcktab->filltable[prefixindex] + 1;
        if (ordercode % divisor == 0)
        {
          ordercode /= divisor;
          if (gt_bcktab_distpfxidx_get(bcktab,prefixindex-1,ordercode) > 0)
          {
            return prefixindex;
          }
        }
      } else
      {
        break;
      }
    }
  }
  return bcktab->prefixlength-1;
}

/* The following function is not used */

unsigned long gt_bcktab_distpfxidxpartialsums(const GtBcktab *bcktab,
                                              GtCodetype code,
                                              unsigned int lowerbound)
{
  GtCodetype ordercode, divisor;
  unsigned long sum = 0;
  unsigned int prefixindex;

  for (prefixindex=bcktab->prefixlength-2; prefixindex>lowerbound;
       prefixindex--)
  {
    if (code >= bcktab->filltable[prefixindex])
    {
      ordercode = code - bcktab->filltable[prefixindex];
      divisor = bcktab->filltable[prefixindex] + 1;
      if (ordercode % divisor == 0)
      {
        ordercode /= divisor;
        sum += gt_bcktab_distpfxidx_get(bcktab,prefixindex-1,ordercode);
      }
    } else
    {
      break;
    }
  }
  return sum;
}

unsigned int gt_bcktab_pfxidx2lcpvalues_uint8(unsigned int *minprefixindex,
                                              uint8_t *smalllcpvalues,
                                              unsigned long specialsinbucket,
                                              const GtBcktab *bcktab,
                                              GtCodetype code)
{
  unsigned int prefixindex, maxprefixindex = 0;
  unsigned long idx, value, insertpos;
  GtCodetype ordercode, divisor;

  gt_assert(smalllcpvalues != NULL);
  *minprefixindex = bcktab->prefixlength;
  insertpos = specialsinbucket;
  for (prefixindex=1U; prefixindexprefixlength-1; prefixindex++)
  {
    if (code >= bcktab->filltable[prefixindex])
    {
      ordercode = code - bcktab->filltable[prefixindex];
      divisor = bcktab->filltable[prefixindex] + 1;
      if (ordercode % divisor == 0)
      {
        ordercode /= divisor;
        value = gt_bcktab_distpfxidx_get(bcktab,prefixindex-1,ordercode);
        if (value > 0)
        {
          maxprefixindex = prefixindex;
          if (*minprefixindex > prefixindex)
          {
            *minprefixindex = prefixindex;
          }
          for (idx=0; idx < value; idx++)
          {
            gt_assert(insertpos > 0);
            smalllcpvalues[--insertpos] = (uint8_t) prefixindex;
          }
        }
      }
    }
  }
  if (insertpos > 0)
  {
    maxprefixindex = bcktab->prefixlength-1;
    if (*minprefixindex == bcktab->prefixlength)
    {
      *minprefixindex = bcktab->prefixlength-1;
    }
    while (insertpos > 0)
    {
      smalllcpvalues[--insertpos] = (uint8_t) (bcktab->prefixlength-1);
    }
  }
  return maxprefixindex;
}

unsigned int gt_bcktab_pfxidx2lcpvalues_Lcpvaluetype(
                                              unsigned int *minprefixindex,
                                              GtLcpvaluetype *bucketoflcpvalues,
                                              unsigned long specialsinbucket,
                                              const GtBcktab *bcktab,
                                              GtCodetype code)
{
  unsigned int prefixindex, maxprefixindex = 0;
  unsigned long idx, value, insertpos;
  GtCodetype ordercode, divisor;

  gt_assert(bucketoflcpvalues != NULL);
  *minprefixindex = bcktab->prefixlength;
  insertpos = specialsinbucket;
  for (prefixindex=1U; prefixindexprefixlength-1; prefixindex++)
  {
    if (code >= bcktab->filltable[prefixindex])
    {
      ordercode = code - bcktab->filltable[prefixindex];
      divisor = bcktab->filltable[prefixindex] + 1;
      if (ordercode % divisor == 0)
      {
        ordercode /= divisor;
        value = gt_bcktab_distpfxidx_get(bcktab,prefixindex-1,ordercode);
        if (value > 0)
        {
          maxprefixindex = prefixindex;
          if (*minprefixindex > prefixindex)
          {
            *minprefixindex = prefixindex;
          }
          for (idx=0; idx < value; idx++)
          {
            gt_assert(insertpos > 0);
            bucketoflcpvalues[--insertpos] = (GtLcpvaluetype) prefixindex;
          }
        }
      }
    }
  }
  if (insertpos > 0)
  {
    maxprefixindex = bcktab->prefixlength-1;
    if (*minprefixindex == bcktab->prefixlength)
    {
      *minprefixindex = bcktab->prefixlength-1;
    }
    while (insertpos > 0)
    {
      bucketoflcpvalues[--insertpos]
        = (GtLcpvaluetype) (bcktab->prefixlength-1);
    }
  }
  return maxprefixindex;
}

const GtCodetype **gt_bcktab_multimappower(const GtBcktab *bcktab)
{
  return (const GtCodetype **) bcktab->multimappower;
}

GtCodetype gt_bcktab_filltable(const GtBcktab *bcktab,unsigned int idx)
{
  return bcktab->filltable[idx];
}

GtLeftborder *gt_bcktab_leftborder(GtBcktab *bcktab)
{
  return &bcktab->leftborder;
}

GtCodetype gt_bcktab_numofallcodes(const GtBcktab *bcktab)
{
  return bcktab->numofallcodes;
}

unsigned long gt_bcktab_leftborderpartialsums(
                             unsigned long *saved_bucketswithoutwholeleaf,
                             unsigned long *numofsuffixestosort,
                             GtBcktab *bcktab)
{
  unsigned long code, largestbucketsize, sumbuckets, saved = 0, currentsize;

  gt_assert(bcktab->numofallcodes > 0);
  largestbucketsize = sumbuckets = gt_bcktab_get_leftborder(bcktab,0);
  for (code = 1UL; code < bcktab->numofallcodes; code++)
  {
    currentsize = gt_bcktab_get_leftborder(bcktab,code);
    sumbuckets += currentsize;
    if (largestbucketsize < currentsize)
    {
      largestbucketsize = currentsize;
    }
    gt_bcktab_leftborder_assign(&bcktab->leftborder,code,sumbuckets);
  }
  gt_bcktab_leftborder_assign(&bcktab->leftborder,bcktab->numofallcodes,
                              sumbuckets);
  if (saved_bucketswithoutwholeleaf != NULL)
  {
    *saved_bucketswithoutwholeleaf = saved;
  }
  if (numofsuffixestosort != NULL)
  {
    *numofsuffixestosort = sumbuckets;
  }
  return largestbucketsize;
}

size_t gt_bcktab_sizeforlcpvalues(const GtBcktab *bcktab)
{
  size_t sizespeciallcps, sizelcps;

  sizespeciallcps = sizeof (uint8_t) *
                    bcktab->maxbucketinfo.specialsmaxbucketsize;
  sizelcps
    = sizeof (unsigned long) * gt_bcktab_nonspecialsmaxsize(bcktab);
  return MAX(sizelcps,sizespeciallcps);
}

unsigned long gt_bcktab_maxbucketsize(const GtBcktab *bcktab)
{
  return bcktab->maxbucketinfo.maxbucketsize;
}

GtCodetype gt_bcktab_findfirstlarger(const GtBcktab *bcktab,
                                     unsigned long suftaboffset)
{
  GtCodetype left = 0, right = bcktab->numofallcodes, mid,
             found = bcktab->numofallcodes;
  unsigned long midval;

  while (left+1 < right)
  {
    mid = GT_DIV2(left+right);
    midval = gt_bcktab_get_leftborder(bcktab,mid);
    if (suftaboffset == midval)
    {
      return mid;
    }
    if (suftaboffset < midval)
    {
      found = mid;
      right = mid - 1;
    } else
    {
      left = mid + 1;
    }
  }
  return found;
}

#ifdef SKDEBUG
#include "qgram2code.h"
void gt_bcktab_consistencyofsuffix(int line,
                                   const GtEncseq *encseq,
                                   GtReadmode readmode,
                                   const GtBcktab *bcktab,
                                   const Suffixwithcode *suffix)
{
  unsigned int idx, firstspecial = bcktab->prefixlength, gramfirstspecial;
  GtCodetype qgramcode = 0;
  unsigned long totallength;
  GtUchar cc = 0;

  totallength = gt_encseq_total_length(encseq);
  for (idx=0; idxprefixlength; idx++)
  {
    if (suffix->startpos + idx >= totallength)
    {
      firstspecial = idx;
      break;
    }
    cc = gt_encseq_get_encoded_char(encseq,suffix->startpos + idx,
                                           readmode);
    if (ISSPECIAL(cc))
    {
      firstspecial = idx;
      break;
    }
    bcktab->qgrambuffer[idx] = cc;
  }
  for (idx=firstspecial; idxprefixlength; idx++)
  {
    bcktab->qgrambuffer[idx] = (GtUchar) (bcktab->numofchars-1);
  }
  gramfirstspecial = qgram2code(&qgramcode,
                                (const GtCodetype **) bcktab->multimappower,
                                bcktab->prefixlength,
                                bcktab->qgrambuffer);
  gt_assert(gramfirstspecial == bcktab->prefixlength);
  gt_assert(qgramcode == suffix->code);
  if (firstspecial != suffix->prefixindex)
  {
    fprintf(stderr,"line %d: code=%u: ",line,suffix->code);
    fprintf(stderr,"firstspecial = %u != %u = suffix->prefixindex\n",
                    firstspecial,suffix->prefixindex);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
}
#endif
genometools-1.5.1/src/match/bcktab.h000066400000000000000000000170001211610345200173240ustar00rootroot00000000000000/*
  Copyright (c) 2007-2011 Stefan Kurtz 
  Copyright (c) 2007-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef BCKTAB_H
#define BCKTAB_H

#include 
#include "core/error.h"
#include "core/intbits.h"
#include "core/codetype.h"
#include "core/logger_api.h"
#include "sfx-maprange.h"

#ifdef GT_LONGLCPVALUES
typedef unsigned long GtLcpvaluetype;
#define GT_LCPVALUE_MAX ULONG_MAX
#else
typedef uint32_t GtLcpvaluetype;
#define GT_LCPVALUE_MAX UINT32_MAX
#endif

typedef struct
{
  unsigned long left,
                nonspecialsinbucket,
                specialsinbucket;
} GtBucketspecification;

typedef struct
{
  uint32_t *uintbounds;
  unsigned long *ulongbounds;
} GtLeftborder;

typedef struct GtBcktab GtBcktab;

/*@unused@*/ static inline void gt_bcktab_leftborder_addcode(GtLeftborder *lb,
                                                             GtCodetype code)
{
  gt_assert(lb != NULL);
  if (lb->ulongbounds != NULL)
  {
    lb->ulongbounds[code]++;
  } else
  {
    gt_assert(lb->uintbounds[code] < (uint32_t) UINT_MAX);
    lb->uintbounds[code]++;
  }
}

/*@unused@*/ static inline unsigned long gt_bcktab_leftborder_insertionindex(
                                                  GtLeftborder *lb,
                                                  GtCodetype code)
{
  gt_assert(lb != NULL);
  if (lb->ulongbounds != NULL)
  {
    return --lb->ulongbounds[code];
  }
  gt_assert(lb->uintbounds != NULL);
  return (unsigned long) --lb->uintbounds[code];
}

void gt_bcktab_leftborder_assign(GtLeftborder *lb,GtCodetype code,
                                 unsigned long value);

unsigned long gt_bcktab_get_leftborder(const GtBcktab *bcktab,GtCodetype code);

GtBcktab *gt_bcktab_map(const char *indexname,
                        unsigned int numofchars,
                        unsigned int prefixlength,
                        unsigned long maxvalue,
                        bool withspecialsuffixes,
                        GtError *err);

void gt_bcktab_assignboundsforpart(GtBcktab *bcktab,
                                   GtCodetype mincode,
                                   GtCodetype maxcode);

int gt_bcktab_remap_all(GtBcktab *bcktab,GtError *err);

void gt_bcktab_delete(GtBcktab *bcktab);

GtBcktab *gt_bcktab_new(unsigned int numofchars,
                        unsigned int prefixlength,
                        unsigned long maxvalue,
                        bool storespecialcodes,
                        bool withspecialsuffixes,
                        GtLogger *logger,
                        GtError *err);

void gt_bcktab_updatespecials(GtBcktab *bcktab,
                              GtCodetype code,
                              unsigned int prefixindex);

GtCodetype gt_bcktab_codedownscale(const GtBcktab *bcktab,
                                   GtCodetype code,
                                   unsigned int prefixindex,
                                   unsigned int maxprefixlen);

int gt_bcktab_flush_to_file(FILE *fp,const GtBcktab *bcktab,GtError *err);

void gt_bcktab_storetmp(GtBcktab *bcktab);

void gt_bcktab_maprange_lb_cs(GtSfxmappedrangelist *sfxmrlist,GtBcktab *bcktab);

unsigned int gt_bcktab_calcboundsparts(GtBucketspecification *bucketspec,
                                       const GtBcktab *bcktab,
                                       GtCodetype code,
                                       GtCodetype maxcode,
                                       unsigned long totalwidth,
                                       unsigned int rightchar);

unsigned long gt_bcktab_calcrightbounds(const GtBcktab *bcktab,
                                        GtCodetype code,
                                        GtCodetype maxcode,
                                        unsigned long totalwidth);

unsigned long gt_bcktab_distpfxidxpartialsums(const GtBcktab *bcktab,
                                              GtCodetype code,
                                              unsigned int lowerbound);

void gt_bcktab_calcboundaries(GtBucketspecification *bucketspec,
                              const GtBcktab *bcktab,
                              GtCodetype code);

void gt_bcktab_determinemaxsize(GtBcktab *bcktab,
                                const GtCodetype mincode,
                                const GtCodetype maxcode,
                                unsigned long partwidth);

unsigned int gt_bcktab_singletonmaxprefixindex(const GtBcktab *bcktab,
                                               GtCodetype code);

unsigned int gt_bcktab_pfxidx2lcpvalues_uint8(unsigned int *minprefixindex,
                                              uint8_t *smalllcpvalues,
                                              unsigned long specialsinbucket,
                                              const GtBcktab *bcktab,
                                              GtCodetype code);

unsigned int gt_bcktab_pfxidx2lcpvalues_Lcpvaluetype(
                                              unsigned int *minprefixindex,
                                              GtLcpvaluetype *bucketoflcpvalues,
                                              unsigned long specialsinbucket,
                                              const GtBcktab *bcktab,
                                              GtCodetype code);

const GtCodetype **gt_bcktab_multimappower(const GtBcktab *bcktab);

GtCodetype gt_bcktab_filltable(const GtBcktab *bcktab,unsigned int idx);

GtLeftborder *gt_bcktab_leftborder(GtBcktab *bcktab);

GtCodetype gt_bcktab_numofallcodes(const GtBcktab *bcktab);

uint64_t gt_bcktab_sizeoftable(unsigned int numofchars,
                               unsigned int prefixlength,
                               unsigned long maxvalue,
                               bool withspecialsuffixes);

unsigned long gt_bcktab_sizeofworkspace(unsigned int prefixlength);

unsigned int gt_bcktab_prefixlength(const GtBcktab *bcktab);

unsigned long gt_bcktab_leftborderpartialsums(
                             unsigned long *saved_bucketswithoutwholeleaf,
                             unsigned long *numofsuffixestosort,
                             GtBcktab *bcktab);

size_t gt_bcktab_sizeforlcpvalues(const GtBcktab *bcktab);

unsigned long gt_bcktab_maxbucketsize(const GtBcktab *bcktab);

unsigned long gt_bcktab_nonspecialsmaxsize(const GtBcktab *bcktab);

void gt_bcktab_leftborder_show(const GtBcktab *bcktab);

GtCodetype gt_bcktab_findfirstlarger(const GtBcktab *bcktab,
                                     unsigned long suftaboffset);

#ifdef SKDEBUG
void gt_bcktab_checkcountspecialcodes(const GtBcktab *bcktab);

void gt_bcktab_consistencyofsuffix(int line,
                                   const GtEncseq *encseq,
                                   GtReadmode readmode,
                                   const GtBcktab *bcktab,
                                   const Suffixwithcode *suffix);
#endif
#endif
genometools-1.5.1/src/match/cgr_spacedseed.c000066400000000000000000000204221211610345200210260ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "core/ma_api.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "cgr_spacedseed.h"
#include "sarr-def.h"
#include "core/intbits.h"
#include "idx-limdfs.h"
#include "absdfstrans-def.h"
#include "spaced-seeds.h"
#include "iter-window.h"
#include "esa-map.h"

typedef struct
{
  unsigned long seedwidth, numofonepositions;
  unsigned char *onepositions;
  GtBitsequence seedbitvector;
} Spacedseed;

static Spacedseed *spacedseed_new(const char *seedstring, GtError *err)
{
  Spacedseed *spse;
  unsigned long idx, fillindex;
  bool haserr = false;

  spse = gt_malloc(sizeof (*spse));
  spse->seedwidth = spse->numofonepositions = 0;
  spse->seedbitvector = 0;
  spse->onepositions = NULL;
  for (idx = 0; seedstring[idx] != '\0'; idx++)
  {
    if (spse->seedwidth == (unsigned long) GT_INTWORDSIZE)
    {
      gt_error_set(err,"space seed cannot be longer than %u",
                       (unsigned int) GT_INTWORDSIZE);
      haserr = true;
      break;
    }
    spse->seedwidth++;
    if (seedstring[idx] == '1')
    {
      spse->numofonepositions++;
      spse->seedbitvector |= GT_ITHBIT(idx);
    }
  }
  if (!haserr)
  {
    spse->onepositions = gt_malloc(sizeof (*spse->onepositions) *
                                   spse->numofonepositions);
    for (fillindex = 0, idx = 0; seedstring[idx] != '\0'; idx++)
    {
      if (seedstring[idx] == '1')
      {
        spse->onepositions[fillindex++] = (unsigned char) idx;
      }
    }
  }
  if (haserr)
  {
    gt_free(spse);
    return NULL;
  }
  return spse;
}

static void spacedseed_delete(Spacedseed *spse)
{
  gt_free(spse->onepositions);
  gt_free(spse);
}

static void singlewindowmatchspacedseed(Limdfsresources *limdfsresources,
                                        const AbstractDfstransformer *dfst,
                                        const GtUchar *qptr,
                                        const Spacedseed *spse)
{
  gt_indexbasedspacedseeds(limdfsresources,
                        qptr,
                        spse->seedbitvector,
                        spse->seedwidth,
                        dfst);
}

static void singlequerymatchspacedseed(Limdfsresources *limdfsresources,
                                       const AbstractDfstransformer *dfst,
                                       const GtUchar *query,
                                       unsigned long querylen,
                                       const Spacedseed *spse)
{
  const GtUchar *qptr;
  unsigned long offset, skipvalue;

  if (spse->seedwidth > querylen)
  {
    return;
  }
  qptr = query;
  offset = 0;
  while (qptr <= query + querylen - spse->seedwidth)
  {
    skipvalue = containsspecialbytestring(qptr,offset,spse->seedwidth);
    if (skipvalue == spse->seedwidth)
    {
      offset = spse->seedwidth-1;
      singlewindowmatchspacedseed(limdfsresources,dfst,qptr,spse);
      qptr++;
    } else
    {
      offset = 0;
      qptr += (skipvalue+1);
    }
  }
}

static void cgr_showmatch(GT_UNUSED void *processinfo,
                      const GtIdxMatch *match)
{
  printf("%lu\t",match->dblen);
  printf("%lu\n",match->dbstartpos);
}

#ifdef WITHONLINE
static void onlinespacedseedsearch(const GtEncseq *encseq,
                                   const Spacedseed *spse,
                                   const GtUchar *qptr,qp)
{
  Windowiterator *wit;
  const GtUchar *buffer;
  unsigned long currentpos, totallength;
  unsigned long firstpos, windowschecked = 0;
  Bitsequence bitmask;
  bool matched;

  totallength = gt_encseq_total_length(encseq);
  wit = gt_windowiterator_new(encseq,spse->seedwidth,0,totallength);
  while (true)
  {
    buffer = gt_windowiterator_next(¤tpos,&firstpos,wit);
    if (buffer != NULL)
    {
      bitmask = FIRSTBIT;
      matched = true;
      for (idx=0; idx < spse->seedwidth; idx++)
      {
        if ((spse->seedbitvector & bitmask) && qptr[idx] != buffer[idx])
        {
          matched = false;
          break;
        }
        bitmask >>= 1;
      }
      if (matched)
      {
      }
    } else
    {
      break;
    }
  }
  gt_windowiterator_delete(wit);
}
#endif

int gt_matchspacedseed(bool withesa,
                    bool docompare,
                    const char *inputindex,
                    const GtStrArray *queryfilenames,
                    bool verbose,
                    GtError *err)
{
  Genericindex *genericindex = NULL;
  bool haserr = false;
  Spacedseed *spse;
  GtLogger *logger;

  logger = gt_logger_new(verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  /*
  spse = spacedseed_new("11011011000011011",err);
  */
  spse = spacedseed_new("111001001001010111",err);
  if (spse == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    genericindex = genericindex_new(inputindex,withesa,
                                    withesa && docompare,false,false,
                                    0,logger,err);
    if (genericindex == NULL)
    {
      haserr = true;
    }
  }
  if (!haserr && docompare)
  {
    gt_assert(genericindex != NULL);
    gt_assert(spse != NULL);
    /*
    iteroverallwords(genericindex->suffixarray->encseq,spse->seedwidth,
          0,gt_encseq_total_length(genericindex->suffixarray->encseq));
    iteroverallwords2(genericindex->suffixarray->encseq,spse->seedwidth,
            0,
            gt_encseq_total_length(genericindex->suffixarray->encseq));
    */
  }
  if (!haserr)
  {
    GtSeqIterator *seqit;
    const GtUchar *query;
    unsigned long querylen;
    char *desc = NULL;
    uint64_t unitnum;
    int retval;
    Limdfsresources *limdfsresources = NULL;
    const AbstractDfstransformer *dfst;
    const GtEncseq *encseq;

    dfst = gt_spse_AbstractDfstransformer();
    gt_assert(genericindex != NULL);
    limdfsresources = gt_newLimdfsresources(genericindex,
                                         true,
                                         0,
                                         (unsigned long) GT_INTWORDSIZE,
                                         false, /* keepexpandedonstack */
                                         cgr_showmatch,
                                         NULL, /* processmatch info */
                                         NULL, /* processresult */
                                         NULL, /* processresult info */
                                         dfst);
    encseq = genericindex_getencseq(genericindex);
    seqit = gt_seq_iterator_sequence_buffer_new(queryfilenames, err);
    if (!seqit)
      haserr = true;
    if (!haserr)
    {
      GtAlphabet *a = gt_encseq_alphabet(encseq);
      gt_seq_iterator_set_symbolmap(seqit, gt_alphabet_symbolmap(a));
      for (unitnum = 0; /* Nothing */; unitnum++)
      {
        retval = gt_seq_iterator_next(seqit,
                                     &query,
                                     &querylen,
                                     &desc,
                                     err);
        if (retval < 0)
        {
          haserr = true;
          break;
        }
        if (retval == 0)
        {
          break;
        }
        singlequerymatchspacedseed(limdfsresources,
                                   dfst,
                                   query,
                                   querylen,
                                   spse);
      }
      if (limdfsresources != NULL)
      {
        gt_freeLimdfsresources(&limdfsresources,dfst);
      }
      gt_seq_iterator_delete(seqit);
    }
  }
  genericindex_delete(genericindex);
  spacedseed_delete(spse);
  gt_logger_delete(logger);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/cgr_spacedseed.h000066400000000000000000000023501211610345200210330ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef CGR_SPACEDSEED_H
#define CGR_SPACEDSEED_H

#include 
#include "core/str.h"
#include "core/str_array_api.h"
#include "core/error_api.h"

int gt_matchspacedseed(bool withesa,
                    bool docompare,
                    const char *inputindex,
                    const GtStrArray *queryfilenames,
                    bool verbose,
                    GtError *err);

#endif
genometools-1.5.1/src/match/chain2dim.c000066400000000000000000001645261211610345200177470ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/error_api.h"
#include "core/minmax.h"
#include "core/mathsupport.h" /* for gt_double_equals_double */
#include "core/unused_api.h"
#include "core/ma.h"
#include "core/arraydef.h"
#include "core/logger.h"
#include "extended/rbtree.h"
#include "extended/ranked_list.h"
#include "chain2dim.h"
#include "prsqualint.h"

/*
  The basic information required for each match is stored
  in a structure of the following type. The user has to specify
  those components which are tagged `user defined'. The chaining
  algorithms computes the remaining components tagged 'compute'
  in chain.
*/

typedef struct
{
  GtChain2Dimpostype startpos[2], /* start of matches in the 2 dimensions,
                                 userdef */
                 endpos[2];  /* end of matches in the 2 dimensions, userdef */
  unsigned long firstinchain,   /* first element in chain, computed for all
                                   chainkinds but only used for local chaining
                                */
                previousinchain;  /* previous index in chain, compute */
  GtChain2Dimscoretype
         weight, /* weight of match, user defined */
         initialgap, /* gap to start of sequences, user defined */
         terminalgap, /* gap to last positions of match, user defined */
         score; /* score of highest scoreing chain ending here, compute */
} Matchchaininfo;

struct GtChain2Dimmatchtable
{
   Matchchaininfo *matches;
   GtChain2Dimscoretype largestdim0,
                        largestdim1;
   unsigned long nextfree,
                 allocated,
                 /* not NULL only for GLOBALCHAININGALLCHAINS */
                 allprevious,
                 *previouscount,
                 *previousbound,
                 *previoustab;
};

/*
  The following type defines the possible kinds of chaining.
  The mode can be one of the two following values.
*/

typedef enum
{
  GLOBALCHAINING,              /* global chaining without gap costs */
  GLOBALCHAININGWITHGAPCOST,   /* global chaining with L1 gap costs */
  GLOBALCHAININGWITHOVERLAPS,  /* chaining with overlaps */
  GLOBALCHAININGALLCHAINS,     /* global chaining with output of all chains */
  LOCALCHAININGMAX,            /* local chaining; one maximum is reported */
  LOCALCHAININGTHRESHOLD,      /* local chaining; all chains >= minscore */
  LOCALCHAININGBEST,           /* local chaining; k best local chains */
  LOCALCHAININGPERCENTAWAY     /* local chaining; percent away from best */
} GtChain2Dimkind;

static bool chain2dim_chainkind_global(GtChain2Dimkind chainkind)
{
  return (chainkind == GLOBALCHAINING ||
          chainkind == GLOBALCHAININGWITHGAPCOST ||
          chainkind == GLOBALCHAININGWITHOVERLAPS ||
          chainkind == GLOBALCHAININGALLCHAINS) ? true : false;
}

/*
  The following type defines the chain mode consisting of a chainkind.
  If chainkind = LOCALCHAININGTHRESHOLD, then an additional
  component minimumscore is used.
  If chainkind = LOCALCHAININGBEST, then  an additional
  component howmanybest is used.
  If chainkind = LOCALCHAININGPERCENTAWAY, then  an additional
  component percentawayfrombest is defined
*/

struct GtChain2Dimmode
{
  GtChain2Dimkind chainkind;
  GtChain2Dimpostype maxgapwidth;  /* 0 if undefined or
                                  otherwise maximal width of gap */
  GtChain2Dimscoretype minimumscore; /* only defined if
                                  chainkind = LOCALCHAININGTHRESHOLD */
  unsigned long howmanybest,   /* only defined if
                                  chainkind = LOCALCHAININGBEST */
                percentawayfrombest;  /* only defined if
                                         chainkind = LOCALCHAININGPERCENTAWAY */
};

typedef unsigned long GtChain2Dimref;

GT_DECLAREARRAYSTRUCT(GtChain2Dimref);

/*
  A chain consists of an array of references to chained matches.
  These refer to an array of matchchaininfos.
*/

struct GtChain2Dim
{
  GtArrayGtChain2Dimref chainedmatches;
  GtChain2Dimscoretype scoreofchain;
  bool storedinreverseorder;
};

GtChain2Dimmatchtable *gt_chain_matchtable_new(unsigned long numberofmatches)
{
  GtChain2Dimmatchtable *matchtable = gt_malloc(sizeof (*matchtable));
  matchtable->matches = gt_malloc(sizeof (*matchtable->matches) *
                                  numberofmatches);
  matchtable->nextfree = 0;
  matchtable->allocated = numberofmatches;
  matchtable->largestdim0 = matchtable->largestdim1 = 0;
  matchtable->previouscount = NULL;
  matchtable->previousbound = NULL;
  matchtable->previoustab = NULL;
  matchtable->allprevious = 0;
  return matchtable;
}

void gt_chain_matchtable_delete(GtChain2Dimmatchtable *matchtable)
{
  if (matchtable != NULL)
  {
    gt_free(matchtable->matches);
    gt_free(matchtable->previouscount);
    gt_free(matchtable->previousbound);
    gt_free(matchtable->previoustab);
    gt_free(matchtable);
  }
}

void gt_chain_matchtable_empty(GtChain2Dimmatchtable *matchtable)
{
  gt_assert(matchtable != NULL);
  matchtable->largestdim0 = matchtable->largestdim1 = 0;
  matchtable->nextfree = 0;
}

void gt_chain_matchtable_add(GtChain2Dimmatchtable *matchtable,
                             const GtChain2Dimmatchvalues *inmatch)
{
  Matchchaininfo *matchchaininfo;

  gt_assert(matchtable->nextfree < matchtable->allocated);
  gt_assert(inmatch->startpos[0] <= inmatch->endpos[0]);
  gt_assert(inmatch->startpos[1] <= inmatch->endpos[1]);
  matchchaininfo = matchtable->matches + matchtable->nextfree++;
  matchchaininfo->startpos[0] = inmatch->startpos[0];
  matchchaininfo->startpos[1] = inmatch->startpos[1];
  matchchaininfo->endpos[0] = inmatch->endpos[0];
  matchchaininfo->endpos[1] = inmatch->endpos[1];
  matchchaininfo->weight = inmatch->weight;
  if (matchtable->largestdim0 < (GtChain2Dimscoretype) inmatch->endpos[0])
  {
    matchtable->largestdim0 = (GtChain2Dimscoretype) inmatch->endpos[0];
  }
  if (matchtable->largestdim1 < (GtChain2Dimscoretype) inmatch->endpos[1])
  {
    matchtable->largestdim1 = (GtChain2Dimscoretype) inmatch->endpos[1];
  }
}

void gt_chain_fillthegapvalues(GtChain2Dimmatchtable *matchtable)
{
  Matchchaininfo *fiptr;

  for (fiptr = matchtable->matches;
       fiptr < matchtable->matches + matchtable->nextfree;
       fiptr++)
  {
    fiptr->initialgap
      = (GtChain2Dimscoretype) (fiptr->startpos[0] + fiptr->startpos[1]);
    fiptr->terminalgap
      = (GtChain2Dimscoretype) (matchtable->largestdim0 - fiptr->endpos[0] +
                                matchtable->largestdim1 - fiptr->endpos[1]);
  }
}

void gt_chain_applyweight(double weightfactor,
                          GtChain2Dimmatchtable *matchtable)
{
  if (!gt_double_equals_double(weightfactor, 1.0))
  {
    Matchchaininfo *fiptr;

    for (fiptr = matchtable->matches;
         fiptr < matchtable->matches + matchtable->nextfree;
         fiptr++)
    {
      fiptr->weight *= weightfactor;
    }
  }
}

#define MAKEENDPOINT(FID)       (FID)
#define FRAGIDENT(FRAG)         ((FRAG)->fpident)

#define GT_CHAIN2DIM_UNDEFPREVIOUS           matchtable->nextfree

#define GT_CHAIN2DIM_GETSTOREDSTARTPOINT(DIM,IDX)\
        matchtable->matches[IDX].startpos[DIM]
#define GT_CHAIN2DIM_GETSTOREDENDPOINT(DIM,IDX)\
        matchtable->matches[IDX].endpos[DIM]
#define GT_CHAIN2DIM_INITIALGAP(IDX)\
        matchtable->matches[IDX].initialgap
#define GT_CHAIN2DIM_TERMINALGAP(IDX)\
        matchtable->matches[IDX].terminalgap

typedef GtChain2Dimscoretype (*GtChain2Dimgapcostfunction)(
                                                  const GtChain2Dimmatchtable *,
                                                  unsigned long,
                                                  unsigned long);

typedef struct
{
  unsigned long fpident;
  GtChain2Dimpostype fpposition;
} GtChain2DimMatchpoint;

typedef struct
{
  GtRBTree *dictroot;
  unsigned long *endpointperm;
} GtChain2DimMatchstore;

typedef struct
{
  GtChain2Dimscoretype maxscore;
  unsigned long maxmatchnum;
  bool defined;
} GtChain2DimMaxmatchvalue;

/*
  The component isavailable is used to
  (1) indicate that some score is already stored (when generating the classes)
  (2) indicate that the class representative has not yet been processed
      further (after generation)
*/

typedef struct
{
  bool isavailable;
  GtChain2Dimscoretype score;
} GtChain2DimBestofclass;

static bool gt_chain2dim_overlapping(const GtChain2Dimmatchtable *matchtable,
                                     unsigned long i,
                                     unsigned long j)
{
  return (GT_CHAIN2DIM_GETSTOREDENDPOINT(0,i)
            >= GT_CHAIN2DIM_GETSTOREDSTARTPOINT(0,j) ||
          GT_CHAIN2DIM_GETSTOREDENDPOINT(1,i)
            >= GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1,j)) ? true : false;
}

static bool gt_chain2dim_colinear(const GtChain2Dimmatchtable *matchtable,
                                  int dim,
                                  unsigned long i,
                                  unsigned long j)
{
  return (GT_CHAIN2DIM_GETSTOREDENDPOINT(dim,i)
            < GT_CHAIN2DIM_GETSTOREDSTARTPOINT(dim,j)) ? true : false;
}

static bool gt_chain2dim_ovl_colinear(const GtChain2Dimmatchtable *matchtable,
                                      unsigned long i,
                                      unsigned long j)
{
  return (GT_CHAIN2DIM_GETSTOREDSTARTPOINT(0, i)
            < GT_CHAIN2DIM_GETSTOREDSTARTPOINT(0, j) &&
          GT_CHAIN2DIM_GETSTOREDENDPOINT(0, i)
            < GT_CHAIN2DIM_GETSTOREDENDPOINT(0, j)   &&
          GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1, i)
            < GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1, j) &&
          GT_CHAIN2DIM_GETSTOREDENDPOINT(1, i)
            < GT_CHAIN2DIM_GETSTOREDENDPOINT(1, j)) ? true : false;
}

static GtChain2Dimscoretype gapcostL1(const GtChain2Dimmatchtable *matchtable,
                                  unsigned long i,
                                  unsigned long j)
{
  return (GtChain2Dimscoretype)
         ((GT_CHAIN2DIM_GETSTOREDSTARTPOINT(0,j)
             - GT_CHAIN2DIM_GETSTOREDENDPOINT(0,i)) +
          (GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1,j)
             - GT_CHAIN2DIM_GETSTOREDENDPOINT(1,i)));
}

static GtChain2Dimscoretype gt_chain2dim_overlapcost(
                                    const GtChain2Dimmatchtable *matchtable,
                                    unsigned long i,
                                    unsigned long j)
{
  GtChain2Dimpostype overlaplength = 0;

  /* add overlap in first dimension */
  if (GT_CHAIN2DIM_GETSTOREDSTARTPOINT(0, j)
        <= GT_CHAIN2DIM_GETSTOREDENDPOINT(0, i))
  {
    overlaplength += GT_CHAIN2DIM_GETSTOREDENDPOINT(0, i)
                       - GT_CHAIN2DIM_GETSTOREDSTARTPOINT(0, j) + 1;
  }

  /* add overlap in second dimension */
  if (GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1, j)
        <= GT_CHAIN2DIM_GETSTOREDENDPOINT(1, i))
  {
    overlaplength += GT_CHAIN2DIM_GETSTOREDENDPOINT(1, i)
                       - GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1, j) + 1;
  }
  return (GtChain2Dimscoretype) overlaplength;
}

/*
  The Chebychev distance for two qhits h=(i,j) and h'=(i',j')
  is defined as:

                      max{|i'-i-q|,|j'-j-q|},

  whereas i+q-1 is the end point in i-dimension of match 1 and
  j+q-1 is the end point in j-dimension of match 1.
  In using the match specific end points, other than fixed values for q,
  following function generalizes to MEMs as well.
*/

static GtChain2Dimscoretype gapcostCc(const GtChain2Dimmatchtable *matchtable,
                                  unsigned long i,unsigned long j)
{
  GtChain2Dimpostype value1, value2;

  gt_assert(GT_CHAIN2DIM_GETSTOREDSTARTPOINT(0,j)
              > GT_CHAIN2DIM_GETSTOREDENDPOINT(0,i) &&
            GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1,j)
              > GT_CHAIN2DIM_GETSTOREDENDPOINT(1,i));
  value1 = GT_CHAIN2DIM_GETSTOREDSTARTPOINT(0,j)
             - GT_CHAIN2DIM_GETSTOREDENDPOINT(0,i) - 1,
  value2 = GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1,j)
             - GT_CHAIN2DIM_GETSTOREDENDPOINT(1,i) - 1;
  return (GtChain2Dimscoretype) MAX(value1,value2);
}

#define GT_MINARRAYSPACE(A,TYPE,MINLEN)\
        do {\
          if ((MINLEN) >= (A)->allocated##TYPE)\
          {\
            (A)->allocated##TYPE = MINLEN;\
            (A)->space##TYPE = gt_realloc_mem((A)->space##TYPE,\
                                              sizeof (TYPE) *\
                                              (A)->allocated##TYPE,\
                                              __FILE__, __LINE__);\
          }\
          gt_assert((A)->space##TYPE != NULL);\
        } while (false)

static void gt_chain2dim_chainingboundarycases(const GtChain2Dimmode *chainmode,
                                  GtChain2Dim *chain,
                                  const GtChain2Dimmatchtable *matchtable)
{
  chain->storedinreverseorder = false;
  if (matchtable->nextfree == 0)
  {
    chain->scoreofchain = 0;
    chain->chainedmatches.nextfreeGtChain2Dimref = 0;
  } else
  {
    if (matchtable->nextfree == 1UL)
    {
      chain->scoreofchain = matchtable->matches[0].weight;
      if (chainmode->chainkind == GLOBALCHAININGWITHGAPCOST)
      {
        chain->scoreofchain -= (GT_CHAIN2DIM_INITIALGAP(0)
                                  + GT_CHAIN2DIM_TERMINALGAP(0));
      }
      chain->chainedmatches.nextfreeGtChain2Dimref = 0;
      GT_STOREINARRAY(&chain->chainedmatches,GtChain2Dimref,32UL,0);
    }
  }
}

static void gt_chain2dim_retrace_previousinchain(GtChain2Dim *chain,
                                   const GtChain2Dimmatchtable *matchtable,
                                   unsigned long retracestart)
{
  unsigned long matchnum, lengthofchain;

  chain->storedinreverseorder = false;
  for (lengthofchain = 0, matchnum = retracestart;
       matchnum != GT_CHAIN2DIM_UNDEFPREVIOUS; lengthofchain++)
  {
    /* Use previousinchain */
    matchnum = matchtable->matches[matchnum].previousinchain;
  }
  GT_MINARRAYSPACE(&chain->chainedmatches,GtChain2Dimref,lengthofchain);
  chain->chainedmatches.nextfreeGtChain2Dimref = lengthofchain;
  for (matchnum = retracestart;
       matchnum != GT_CHAIN2DIM_UNDEFPREVIOUS;
       /* Use previousinchain */
       matchnum = matchtable->matches[matchnum].previousinchain)
  {
    gt_assert(lengthofchain > 0);
    lengthofchain--;
    chain->chainedmatches.spaceGtChain2Dimref[lengthofchain] = matchnum;
  }
  gt_assert(lengthofchain == 0);
}

typedef struct
{
  unsigned long level, son;
} GtChain2DimEdgelevel;

GT_DECLAREARRAYSTRUCT(GtChain2DimEdgelevel);

static void gt_chain2dim_nd_retrace_allprevious(
                                   GtArrayGtChain2DimEdgelevel *stack,
                                   GtChain2Dim *chain,
                                   const GtChain2Dimmatchtable *matchtable,
                                   unsigned long retracestart,
                                   GtChain2Dimprocessor chainprocessor,
                                   void *cpinfo)
{
  unsigned long idx;
  GtChain2DimEdgelevel *el;

  if (matchtable->previouscount[retracestart] == 0)
  {
    return;
  }
  gt_assert(stack->nextfreeGtChain2DimEdgelevel == 0);
  chain->storedinreverseorder = true;
  GT_MINARRAYSPACE(&chain->chainedmatches,GtChain2Dimref,32UL);
  chain->chainedmatches.spaceGtChain2Dimref[0] = retracestart;
  chain->chainedmatches.nextfreeGtChain2Dimref = 1UL;
  for (idx = matchtable->previousbound[retracestart];
       idx < matchtable->previousbound[retracestart] +
             matchtable->previouscount[retracestart]; idx++)
  {
    if (matchtable->previoustab[idx] != GT_CHAIN2DIM_UNDEFPREVIOUS)
    {
      GT_GETNEXTFREEINARRAY(el,stack,GtChain2DimEdgelevel,32UL);
      el->level = 1UL;
      el->son = matchtable->previoustab[idx];
    }
  }
  while (stack->nextfreeGtChain2DimEdgelevel > 0)
  {
    GtChain2DimEdgelevel father
      = stack->spaceGtChain2DimEdgelevel[--stack->nextfreeGtChain2DimEdgelevel];
    GT_MINARRAYSPACE(&chain->chainedmatches,GtChain2Dimref,father.level + 1);
    chain->chainedmatches.spaceGtChain2Dimref[father.level] = father.son;
    chain->chainedmatches.nextfreeGtChain2Dimref = father.level + 1;
    if (matchtable->previouscount[father.son] == 0)
    {
      chainprocessor(cpinfo,matchtable,chain);
    } else
    {
      for (idx = matchtable->previousbound[father.son];
           idx < matchtable->previousbound[father.son] +
                 matchtable->previouscount[father.son]; idx++)
      {
        if (matchtable->previoustab[idx] != GT_CHAIN2DIM_UNDEFPREVIOUS)
        {
          GT_GETNEXTFREEINARRAY(el,stack,GtChain2DimEdgelevel,32UL);
          el->level = father.level + 1;
          el->son = matchtable->previoustab[idx];
        }
      }
    }
  }
}

static bool gt_chain2dim_checkmaxgapwidth(const GtChain2Dimmatchtable
                                                                    *matchtable,
                                          GtChain2Dimpostype maxgapwidth,
                                          unsigned long leftmatch,
                                          unsigned long rightmatch)
{
  GtChain2Dimpostype gapwidth, startpoint, endpoint;

  startpoint = GT_CHAIN2DIM_GETSTOREDSTARTPOINT(0,rightmatch);
  endpoint = GT_CHAIN2DIM_GETSTOREDENDPOINT(0,leftmatch);
  if (startpoint <= endpoint)
  {
    gapwidth = 0;
  } else
  {
    gapwidth = startpoint - endpoint - 1;
  }
  if (gapwidth > maxgapwidth)
  {
    return false;
  }
  startpoint = GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1,rightmatch);
  endpoint = GT_CHAIN2DIM_GETSTOREDENDPOINT(1,leftmatch);
  if (startpoint <= endpoint)
  {
    gapwidth = 0;
  } else
  {
    gapwidth = startpoint - endpoint - 1;
  }
  if (gapwidth > maxgapwidth)
  {
    return false;
  }
  return true;
}

static void gt_chain2dim_bruteforcechainingscores(
                               const GtChain2Dimmode *chainmode,
                               GtChain2Dimmatchtable *matchtable,
                               GtChain2Dimgapcostfunction chaingapcostfunction)
{
  if (matchtable->nextfree > 1UL)
  {
    unsigned long rightmatch;

    matchtable->matches[0].firstinchain = 0;
    matchtable->matches[0].previousinchain = GT_CHAIN2DIM_UNDEFPREVIOUS;
    matchtable->matches[0].score = matchtable->matches[0].weight;
    if (chainmode->chainkind == GLOBALCHAININGWITHGAPCOST)
    {
      matchtable->matches[0].score -= (GT_CHAIN2DIM_INITIALGAP(0)
                                         + GT_CHAIN2DIM_TERMINALGAP(0));
    }
    for (rightmatch=1Ul; rightmatchnextfree; rightmatch++)
    {
      const GtChain2Dimscoretype weightright
        = matchtable->matches[rightmatch].weight;
      unsigned long leftmatch;
      GtChain2DimMaxmatchvalue localmaxmatch;

      localmaxmatch.defined = false;
      localmaxmatch.maxscore = 0;
      localmaxmatch.maxmatchnum = 0;
      for (leftmatch=0; leftmatchmaxgapwidth != 0 &&
            !gt_chain2dim_checkmaxgapwidth(matchtable,chainmode->maxgapwidth,
                                           leftmatch,rightmatch))
        {
          combinable = false;
        } else
        {
          if (chainmode->chainkind == GLOBALCHAININGWITHOVERLAPS)
          {
            combinable = gt_chain2dim_ovl_colinear(matchtable,leftmatch,
                                                   rightmatch);
          } else
          {
            if (gt_chain2dim_overlapping(matchtable,leftmatch,rightmatch))
            {
              combinable = false;
            } else
            {
              combinable = true;
            }
          }
        }
        if (combinable)
        {
          GtChain2Dimscoretype score = matchtable->matches[leftmatch].score;
          unsigned long previous;

          if (chainmode->chainkind == GLOBALCHAINING)
          {
            /* process chainkinds without gap costs */
            score += weightright;
            previous = leftmatch;
          } else
          {
            score -= chaingapcostfunction(matchtable,leftmatch,rightmatch);
            if (chainmode->chainkind == GLOBALCHAININGWITHGAPCOST)
            {
              score += (weightright + GT_CHAIN2DIM_TERMINALGAP(leftmatch)
                                    - GT_CHAIN2DIM_TERMINALGAP(rightmatch));
              previous = leftmatch;
            } else
            {
              if (score > 0)
              {
                score += weightright;
                previous = leftmatch;
              } else
              {
                score = weightright;
                previous = GT_CHAIN2DIM_UNDEFPREVIOUS;
              }
            }
          }
          if (!localmaxmatch.defined || localmaxmatch.maxscore < score)
          {
            localmaxmatch.maxscore = score;
            localmaxmatch.maxmatchnum = previous;
            localmaxmatch.defined = true;
          }
        }
      }
      if (localmaxmatch.defined)
      {
        matchtable->matches[rightmatch].previousinchain
          = localmaxmatch.maxmatchnum;
        if (localmaxmatch.maxmatchnum == GT_CHAIN2DIM_UNDEFPREVIOUS)
        {
          matchtable->matches[rightmatch].firstinchain = rightmatch;
        } else
        {
          matchtable->matches[rightmatch].firstinchain
            = matchtable->matches[localmaxmatch.maxmatchnum].firstinchain;
        }
        matchtable->matches[rightmatch].score = localmaxmatch.maxscore;
      } else
      {
        matchtable->matches[rightmatch].previousinchain
          = GT_CHAIN2DIM_UNDEFPREVIOUS;
        matchtable->matches[rightmatch].firstinchain = rightmatch;
        matchtable->matches[rightmatch].score = weightright;
        if (chainmode->chainkind == GLOBALCHAININGWITHGAPCOST)
        {
          matchtable->matches[rightmatch].score
            -= (GT_CHAIN2DIM_INITIALGAP(rightmatch)
                  + GT_CHAIN2DIM_TERMINALGAP(rightmatch));
        }
      }
    }
  }
}

static void gt_chain2dim_ndbfchainscores(GtChain2Dimmatchtable *matchtable)
{
  if (matchtable->nextfree > 1UL)
  {
    unsigned long rightmatch;

    matchtable->matches[0].firstinchain = 0;
    matchtable->matches[0].previousinchain = GT_CHAIN2DIM_UNDEFPREVIOUS;
    matchtable->matches[0].score = matchtable->matches[0].weight;
    matchtable->previouscount
      = gt_malloc(sizeof (*matchtable->previouscount) * matchtable->nextfree);
    matchtable->previousbound
      = gt_malloc(sizeof (*matchtable->previousbound) * matchtable->nextfree);
    matchtable->previouscount[0] = 0;
    for (rightmatch=1Ul; rightmatchnextfree; rightmatch++)
    {
      const GtChain2Dimscoretype weightright
        = matchtable->matches[rightmatch].weight;
      unsigned long leftmatch;
      GtChain2DimMaxmatchvalue localmaxmatch;
      unsigned long previouswithbestscore;

      localmaxmatch.defined = false;
      localmaxmatch.maxscore = 0;
      localmaxmatch.maxmatchnum = 0;
      previouswithbestscore = 0;
      for (leftmatch=0; leftmatchmatches[leftmatch].score;
          unsigned long previous;

          if (score > 0)
          {
            score += weightright;
            previous = leftmatch;
          } else
          {
            score = weightright;
            previous = GT_CHAIN2DIM_UNDEFPREVIOUS;
          }
          if (!localmaxmatch.defined)
          {
            localmaxmatch.maxscore = score;
            localmaxmatch.maxmatchnum = previous;
            localmaxmatch.defined = true;
            previouswithbestscore = 1UL;
          } else
          {
            if (localmaxmatch.maxscore < score)
            {
              localmaxmatch.maxscore = score;
              localmaxmatch.maxmatchnum = previous;
              previouswithbestscore = 1UL;
            } else
            {
              if (localmaxmatch.maxscore == score)
              {
                previouswithbestscore++;
              }
            }
          }
        }
      }
      if (localmaxmatch.defined)
      {
        gt_assert(previouswithbestscore > 0);
        matchtable->matches[rightmatch].previousinchain
          = localmaxmatch.maxmatchnum;
        matchtable->matches[rightmatch].score = localmaxmatch.maxscore;
        matchtable->previouscount[rightmatch] = previouswithbestscore;
      } else
      {
        matchtable->matches[rightmatch].previousinchain
          = GT_CHAIN2DIM_UNDEFPREVIOUS;
        matchtable->matches[rightmatch].score = weightright;
        matchtable->previouscount[rightmatch] = 0;
      }
    }
    matchtable->previousbound[0] = matchtable->previouscount[0];
    for (rightmatch=1UL; rightmatchnextfree; rightmatch++)
    {
      matchtable->previousbound[rightmatch]
        = matchtable->previousbound[rightmatch-1] +
          matchtable->previouscount[rightmatch];
    }
    matchtable->allprevious = matchtable->previousbound[matchtable->nextfree-1];
    matchtable->previoustab
      = gt_malloc(sizeof (*matchtable->previoustab) * matchtable->allprevious);
    for (rightmatch=1Ul; rightmatchnextfree; rightmatch++)
    {
      const GtChain2Dimscoretype weightright
        = matchtable->matches[rightmatch].weight;
      unsigned long leftmatch;

      if (matchtable->previouscount[rightmatch] == 0)
      {
        continue;
      }
      for (leftmatch=0; leftmatchmatches[leftmatch].score;
          unsigned long previous;

          if (score > 0)
          {
            score += weightright;
            previous = leftmatch;
          } else
          {
            score = weightright;
            previous = GT_CHAIN2DIM_UNDEFPREVIOUS;
          }
          if (score == matchtable->matches[rightmatch].score)
          {
            gt_assert(matchtable->previousbound[rightmatch] > 0);
            matchtable->previoustab[--matchtable->previousbound[rightmatch]]
              = previous;
          }
        }
      }
    }
  }
}

/*
  The following function compares match points. These are
  end points of matches in dimension 2.
  If the match points are identical, then the order is undefined.
*/

static int gt_chain2dim_cmpendMatchpoint2(const void* keya,
                                          const void* keyb,
                                          GT_UNUSED void *info)
{
  if (((GtChain2DimMatchpoint *) keya)->fpposition <
      ((GtChain2DimMatchpoint *) keyb)->fpposition)
  {
    return -1;
  }
  if (((GtChain2DimMatchpoint *) keya)->fpposition >
      ((GtChain2DimMatchpoint *) keyb)->fpposition)
  {
    return 1;
  }
  if (FRAGIDENT((GtChain2DimMatchpoint *) keya) <
      FRAGIDENT((GtChain2DimMatchpoint *) keyb))
  {
    return -1;
  }
  if (FRAGIDENT((GtChain2DimMatchpoint *) keya) >
      FRAGIDENT((GtChain2DimMatchpoint *) keyb))
  {
    return 1;
  }
  return 0;
}

static GtChain2Dimscoretype gt_chain2dim_evalpriority(bool addterminal,
                                     const GtChain2Dimmatchtable *matchtable,
                                     unsigned long matchnum)
{
  if (addterminal)
  {
    return matchtable->matches[matchnum].score
             - GT_CHAIN2DIM_TERMINALGAP(matchnum);
  }
  return matchtable->matches[matchnum].score;
}

static void gt_chain2dim_insertintodict(bool addterminal,
                                        const GtChain2Dimmatchtable *matchtable,
                                        GtChain2DimMatchstore *matchstore,
                                        GtChain2DimMatchpoint *qmatch2)
{
  GtChain2DimMatchpoint *retval2;
  bool nodecreated;

  retval2 = (GtChain2DimMatchpoint *) gt_rbtree_search(matchstore->dictroot,
                                                       qmatch2,
                                                       &nodecreated);
  gt_assert(retval2 != NULL);
  if (!nodecreated)
  {
    if (gt_chain2dim_evalpriority(addterminal,matchtable,FRAGIDENT(retval2)) <
        gt_chain2dim_evalpriority(addterminal,matchtable,FRAGIDENT(qmatch2)))
    {
      gt_assert(retval2->fpposition == qmatch2->fpposition);
      retval2->fpident = qmatch2->fpident;
    }
  }
}

static void gt_chain2dim_activatematchpoint(bool addterminal,
                               const GtChain2Dimmatchtable *matchtable,
                               GtChain2DimMatchstore *matchstore,
                               GtChain2DimMatchpoint *qmatch2)
{
  GtChain2DimMatchpoint *tmp2;
  GtChain2Dimscoretype qpriority;

  qpriority = gt_chain2dim_evalpriority(addterminal,matchtable,
                                        FRAGIDENT(qmatch2));
  tmp2 = (GtChain2DimMatchpoint *) gt_rbtree_previous_equal_key(
                                     matchstore->dictroot,
                                     qmatch2,
                                     gt_chain2dim_cmpendMatchpoint2,
                                     NULL);
  if (tmp2 == NULL ||
      qpriority > gt_chain2dim_evalpriority(addterminal,matchtable,
                                            FRAGIDENT(tmp2)))
  {
    gt_chain2dim_insertintodict(addterminal,matchtable,matchstore,qmatch2);
    while (true)
    {
      tmp2 = (GtChain2DimMatchpoint *) gt_rbtree_next_key(
                                               matchstore->dictroot,
                                               qmatch2,
                                               gt_chain2dim_cmpendMatchpoint2,
                                               NULL);
      if (tmp2 == NULL ||
          qpriority <= gt_chain2dim_evalpriority(addterminal,matchtable,
                                                 FRAGIDENT(tmp2)))
      {
        break;
      }
      if (gt_rbtree_erase(matchstore->dictroot, tmp2) != 0)
      {
        fprintf(stderr,"cannot delete successor node\n");
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
    }
  } else
  {
    gt_free(qmatch2);
  }
}

static void gt_chain2dim_evalmatchscore(const GtChain2Dimmode *chainmode,
                                        GtChain2Dimmatchtable *matchtable,
                                        GtChain2DimMatchstore *matchstore,
                                        bool gapsL1,
                                        unsigned long matchpointident,
                                        unsigned int presortdim)
{
  unsigned long previous;
  GtChain2Dimpostype startpos2;
  GtChain2DimMatchpoint *qmatch2;
  GtChain2Dimscoretype score;

  startpos2 = GT_CHAIN2DIM_GETSTOREDSTARTPOINT(1-presortdim,matchpointident);
  if (startpos2 == 0)
  {
    qmatch2 = NULL;
  } else
  {
    GtChain2DimMatchpoint keymatch2;

    keymatch2.fpposition = startpos2 - 1;  /* it is a start position */
    keymatch2.fpident = MAKEENDPOINT(matchpointident);
                       /* but considered as endpoint */
    qmatch2 = (GtChain2DimMatchpoint *) gt_rbtree_previous_equal_key(
                                                 matchstore->dictroot,
                                                 &keymatch2,
                                                 gt_chain2dim_cmpendMatchpoint2,
                                                 NULL);
    if (qmatch2 != NULL)
    {
      if (chainmode->maxgapwidth != 0 &&
          !gt_chain2dim_checkmaxgapwidth(matchtable,
                                         chainmode->maxgapwidth,
                                         FRAGIDENT(qmatch2),
                                         matchpointident))
      {
        qmatch2 = NULL;
      }
    }
  }
  if (qmatch2 == NULL)
  {
    score = matchtable->matches[matchpointident].weight;
    if (chainmode->chainkind == GLOBALCHAININGWITHGAPCOST)
    {
      score -= GT_CHAIN2DIM_INITIALGAP(matchpointident);
    }
    previous = GT_CHAIN2DIM_UNDEFPREVIOUS;
  } else
  {
    score = matchtable->matches[FRAGIDENT(qmatch2)].score;
    if (chainmode->chainkind == GLOBALCHAINING)
    {
      score += matchtable->matches[matchpointident].weight;
      previous = FRAGIDENT(qmatch2);
    } else
    {
      GtChain2Dimscoretype tmpgc;

      if (gapsL1)
      {
        tmpgc = gapcostL1(matchtable,FRAGIDENT(qmatch2),matchpointident);
      } else
      {
        tmpgc = gapcostCc(matchtable,FRAGIDENT(qmatch2),matchpointident);
      }
      if (chainmode->chainkind == GLOBALCHAININGWITHGAPCOST || score > tmpgc)
      {
        score += (matchtable->matches[matchpointident].weight - tmpgc);
        previous = FRAGIDENT(qmatch2);
      } else
      {
        score = matchtable->matches[matchpointident].weight;
        previous = GT_CHAIN2DIM_UNDEFPREVIOUS;
      }
    }
  }
  matchtable->matches[matchpointident].score = score;
  matchtable->matches[matchpointident].previousinchain = previous;
  if (previous == GT_CHAIN2DIM_UNDEFPREVIOUS)
  {
    matchtable->matches[matchpointident].firstinchain = matchpointident;
  } else
  {
    matchtable->matches[matchpointident].firstinchain
      = matchtable->matches[previous].firstinchain;
  }
}

static bool gt_chain2dim_isrightmaximal_chain(
                                        const GtChain2Dimmatchtable *matchtable,
                                        unsigned long currentmatch)
{
  if (currentmatch == matchtable->nextfree - 1)
  {
    return true;
  }
  /* Use previousinchain */
  if (matchtable->matches[currentmatch+1].previousinchain != currentmatch)
  {
    return true;
  }
  if (matchtable->matches[currentmatch+1].score <
      matchtable->matches[currentmatch].score)
  {
    return true;
  }
  return false;
}

/* The following function is called only for local chaining. As it is the
   only function which accesses firstinchain, this component is used
   only for local chaining */

static GtChain2DimBestofclass *gt_chain2dim_local_getclassrep(
                   GtChain2DimBestofclass *chainequivalenceclasses,
                   const GtChain2Dimmatchtable *matchtable,
                   unsigned long matchnum)
{
  return chainequivalenceclasses + matchtable->matches[matchnum].firstinchain;
}

/* The following function is called for local chaining only. */

static void gt_chain2dim_local_determineequivreps(
                                GtChain2DimBestofclass *chainequivalenceclasses,
                                const GtChain2Dimmatchtable *matchtable)
{
  unsigned long matchnum;
  GtChain2DimBestofclass *classptr, *classrep;

  for (classptr = chainequivalenceclasses;
       classptr < chainequivalenceclasses + matchtable->nextfree;
       classptr++)
  {
    classptr->isavailable = false;
  }
  for (matchnum=0; matchnumnextfree; matchnum++)
  {
    if (gt_chain2dim_isrightmaximal_chain(matchtable,matchnum))
    {
      classrep = gt_chain2dim_local_getclassrep(chainequivalenceclasses,
                                                matchtable,matchnum);
      if (!classrep->isavailable ||
          classrep->score < matchtable->matches[matchnum].score)
      {
        classrep->score = matchtable->matches[matchnum].score;
        classrep->isavailable = true;
      }
    }
  }
}

static bool gt_chain2dim_retrievemaximalscore(GtChain2Dimscoretype *maxscore,
                                              const GtChain2Dimmode *chainmode,
                                              const GtChain2Dimmatchtable
                                                *matchtable)
{
  unsigned long matchnum;
  GtChain2Dimscoretype tgap;
  bool maxscoredefined = false;

  *maxscore = 0;
  for (matchnum=0; matchnumnextfree; matchnum++)
  {
    if (gt_chain2dim_isrightmaximal_chain(matchtable,matchnum))
    {
      if (chainmode->chainkind == GLOBALCHAININGWITHGAPCOST)
      {
        tgap = GT_CHAIN2DIM_TERMINALGAP(matchnum);
      } else
      {
        tgap = 0;
      }
      if (!maxscoredefined ||
          *maxscore < matchtable->matches[matchnum].score - tgap)
      {
        *maxscore = matchtable->matches[matchnum].score - tgap;
        maxscoredefined = true;
      }
    }
  }
  return maxscoredefined;
}

static int comparescores(const void *key1,
                         const void *key2,
                         GT_UNUSED void *info)
{
  if (*((GtChain2Dimscoretype *) key1) < *(((GtChain2Dimscoretype *) key2)))
  {
    return -1;
  }
  if (*((GtChain2Dimscoretype *) key1) > *(((GtChain2Dimscoretype *) key2)))
  {
    return 1;
  }
  return 0;
}

/* The following function is called for local chaining only. */

static void retrieve_local_chainbestscores(bool *minscoredefined,
                                    GtChain2Dimscoretype *minscore,
                                    const GtChain2Dimmatchtable *matchtable,
                                    unsigned long howmanybest)
{
  unsigned long idx, matchnum = 0;
  GtChain2Dimscoretype *scores;
  GtRankedList *dictbestmatches;
  void *minkey;

  scores = gt_malloc(sizeof (*scores) * matchtable->nextfree);
  dictbestmatches = gt_ranked_list_new(howmanybest,comparescores,NULL,NULL);
  for (idx=0; idxnextfree; idx++)
  {
    if (gt_chain2dim_isrightmaximal_chain(matchtable,idx))
    {
      scores[matchnum] = matchtable->matches[idx].score;
      gt_ranked_list_insert(dictbestmatches,
                            (void *) (scores + matchnum));
      matchnum++;
    }
  }
  if (matchnum == 0)
  {
    *minscoredefined = false;
  } else
  {
    minkey = gt_ranked_list_last(dictbestmatches);
    gt_assert(minkey != NULL);
    *minscore = *((GtChain2Dimscoretype *) minkey);
    *minscoredefined = true;
  }
  gt_ranked_list_delete(dictbestmatches);
  gt_free(scores);
}

static void gt_chain2dim_retrievechainthreshold(
                             const GtChain2Dimmode *chainmode,
                             GtChain2Dimmatchtable *matchtable,
                             GtChain2Dim *chain,
                             GtChain2Dimscoretype minscore,
                             GtChain2DimBestofclass *chainequivalenceclasses,
                             GtChain2Dimprocessor chainprocessor,
                             void *cpinfo)
{
  unsigned long matchnum;
  GtArrayGtChain2DimEdgelevel stack;

  GT_INITARRAY(&stack,GtChain2DimEdgelevel);
  for (matchnum=0; matchnum < matchtable->nextfree; matchnum++)
  {
    if (gt_chain2dim_isrightmaximal_chain(matchtable,matchnum))
    {
      GtChain2Dimscoretype tgap;

      if (chainmode->chainkind == GLOBALCHAININGWITHGAPCOST)
      {
        tgap = GT_CHAIN2DIM_TERMINALGAP(matchnum);
      } else
      {
        tgap = 0;
      }
      if (matchtable->matches[matchnum].score - tgap >= minscore)
      {
        if (chainequivalenceclasses != NULL)
        {
          GtChain2DimBestofclass *classrep
            = gt_chain2dim_local_getclassrep(chainequivalenceclasses,
                                             matchtable,matchnum);

          gt_assert(classrep != NULL &&
                    !chain2dim_chainkind_global(chainmode->chainkind));
          if (classrep->isavailable &&
              classrep->score == matchtable->matches[matchnum].score - tgap)
          {
            chain->scoreofchain = classrep->score;
            classrep->isavailable = false;
            gt_chain2dim_retrace_previousinchain(chain, matchtable, matchnum);
            chainprocessor(cpinfo,matchtable,chain);
          }
        } else
        {
          chain->scoreofchain = matchtable->matches[matchnum].score - tgap;
          if (chainmode->chainkind != GLOBALCHAININGALLCHAINS)
          {
            gt_chain2dim_retrace_previousinchain(chain, matchtable,
                                                 matchnum);
            chainprocessor(cpinfo,matchtable,chain);
          } else
          {
            gt_chain2dim_nd_retrace_allprevious(&stack,chain, matchtable,
                                                matchnum,chainprocessor,
                                                cpinfo);
          }
        }
      }
    }
  }
  GT_FREEARRAY(&stack,GtChain2DimEdgelevel);
}

static int comparestartandend(const Matchchaininfo *sortedstartpoints,
                              const Matchchaininfo *sortedendpoints,
                              unsigned int presortdim)
{
  if (sortedstartpoints->startpos[presortdim] <
      sortedendpoints->endpos[presortdim])
  {
    return -1;
  }
  if (sortedstartpoints->startpos[presortdim] >
      sortedendpoints->endpos[presortdim])
  {
    return 1;
  }
  return -1;
}

static GtChain2DimMatchpoint *makeactivationpoint(
                                       const GtChain2Dimmatchtable *matchtable,
                                       unsigned long fpident,
                                       unsigned int postsortdim)
{
  GtChain2DimMatchpoint *fpptr;

  fpptr = gt_malloc(sizeof (*fpptr));
  gt_assert(fpptr != NULL);
  fpptr->fpident = MAKEENDPOINT(fpident);
  fpptr->fpposition = GT_CHAIN2DIM_GETSTOREDENDPOINT(postsortdim,fpident);
  return fpptr;
}

static void mergestartandendpoints(const GtChain2Dimmode *chainmode,
                                   GtChain2Dimmatchtable *matchtable,
                                   GtChain2DimMatchstore *matchstore,
                                   bool gapsL1,
                                   unsigned int presortdim)
{
  unsigned long xidx, startcount, endcount;
  const unsigned int postsortdim = 1U - presortdim;
  bool addterminal = (chainmode->chainkind == GLOBALCHAINING) ? false : true;

  matchstore->dictroot = gt_rbtree_new(gt_chain2dim_cmpendMatchpoint2,
                                       gt_free_func, NULL);
  for (xidx = 0, startcount = 0, endcount = 0;
       startcount < matchtable->nextfree &&
       endcount < matchtable->nextfree;
       xidx++)
  {
    if (comparestartandend(matchtable->matches + startcount,
                           matchtable->matches +
                           matchstore->endpointperm[endcount],
                           presortdim) < 0)
    {
      gt_chain2dim_evalmatchscore(chainmode,
                     matchtable,
                     matchstore,
                     gapsL1,
                     startcount,
                     presortdim);
      startcount++;
    } else
    {
      gt_chain2dim_activatematchpoint(addterminal,matchtable,matchstore,
                        makeactivationpoint(matchtable,
                                            matchstore->
                                            endpointperm[endcount],
                                            postsortdim));
      endcount++;
    }
  }
  while (startcount < matchtable->nextfree)
  {
    gt_chain2dim_evalmatchscore(chainmode,
                   matchtable,
                   matchstore,
                   gapsL1,
                   startcount,
                   presortdim);
    startcount++;
    xidx++;
  }
  while (endcount < matchtable->nextfree)
  {
    gt_chain2dim_activatematchpoint(addterminal,matchtable,matchstore,
                      makeactivationpoint(matchtable,
                                          matchstore->
                                          endpointperm[endcount],
                                          postsortdim));
    endcount++;
    xidx++;
  }
}

static unsigned int gt_chain2dim_findmaximalscores(
                                            const GtChain2Dimmode *chainmode,
                                            GtChain2Dim *chain,
                                            GtChain2Dimmatchtable *matchtable,
                                            GtChain2DimMatchstore *matchstore,
                                            GtChain2Dimprocessor chainprocessor,
                                            bool withequivclasses,
                                            void *cpinfo,
                                            GtLogger *logger)
{
  unsigned long matchnum;
  GtChain2Dimscoretype minscore = 0;
  GtChain2DimMatchpoint *maxpoint;
  GtChain2DimBestofclass *chainequivalenceclasses;
  unsigned int retval;
  bool minscoredefined = false;

  if (withequivclasses && !chain2dim_chainkind_global(chainmode->chainkind))
  {
    chainequivalenceclasses = gt_malloc(sizeof (*chainequivalenceclasses) *
                                        matchtable->nextfree);
    gt_chain2dim_local_determineequivreps(chainequivalenceclasses, matchtable);
  } else
  {
    chainequivalenceclasses = NULL;
  }
  switch (chainmode->chainkind)
  {
    case GLOBALCHAINING:
      maxpoint = gt_rbtree_maximum_key(matchstore->dictroot);
      gt_assert(maxpoint != NULL);
      matchnum = FRAGIDENT(maxpoint);
      minscore = matchtable->matches[matchnum].score;
      minscoredefined = true;
      break;
    case GLOBALCHAININGWITHGAPCOST:
    case GLOBALCHAININGWITHOVERLAPS:
    case GLOBALCHAININGALLCHAINS:
    case LOCALCHAININGMAX:
      minscoredefined
        = gt_chain2dim_retrievemaximalscore(&minscore,chainmode,matchtable);
      break;
    case LOCALCHAININGTHRESHOLD:
      minscore = chainmode->minimumscore;
      minscoredefined = true;
      break;
    case LOCALCHAININGBEST:
      retrieve_local_chainbestscores(&minscoredefined,
                                     &minscore,
                                     matchtable,
                                     chainmode->howmanybest);
      break;
    case LOCALCHAININGPERCENTAWAY:
      minscoredefined
        = gt_chain2dim_retrievemaximalscore(&minscore,chainmode,matchtable);
      if (minscoredefined)
      {
        minscore = (GtChain2Dimscoretype)
                   ((double) minscore *
                    (1.0 - (double) chainmode->percentawayfrombest/100.0));
      }
      break;
    default:
      fprintf(stderr,"chainkind = %d not valid\n",
               (int) chainmode->chainkind);
      exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  if (minscoredefined)
  {
    gt_logger_log(logger,
                  "compute %soptimal %s chains with score >= %ld",
                  chainmode->chainkind == GLOBALCHAININGALLCHAINS ? "all " : "",
                  chain2dim_chainkind_global(chainmode->chainkind) ? "global"
                                                                   : "local",
                  minscore);
    gt_chain2dim_retrievechainthreshold(chainmode,
                                        matchtable,
                                        chain,
                                        minscore,
                                        chainequivalenceclasses,
                                        chainprocessor,
                                        cpinfo);
    retval = 0;
  } else
  {
    retval = 1U;
  }
  if (chainequivalenceclasses != NULL)
  {
    gt_free(chainequivalenceclasses);
  }
  return retval;
}

static void makesortedendpointpermutation(unsigned long *perm,
                                          GtChain2Dimmatchtable *matchtable,
                                          unsigned int presortdim)
{
  unsigned long temp, *iptr, *jptr, i, moves = 0;

  for (i = 0; i < matchtable->nextfree; i++)
  {
    perm[i] = i;
  }
  for (iptr = perm + 1UL; iptr < perm + matchtable->nextfree; iptr++)
  {
    for (jptr = iptr; jptr > perm; jptr--)
    {
      if (GT_CHAIN2DIM_GETSTOREDENDPOINT(presortdim,*(jptr-1)) <=
          GT_CHAIN2DIM_GETSTOREDENDPOINT(presortdim,*jptr))
      {
        break;
      }
      temp = *(jptr-1);
      *(jptr-1) = *jptr;
      *jptr = temp;
      moves++;
    }
  }
}

static void fastchainingscores(const GtChain2Dimmode *chainmode,
                               GtChain2Dimmatchtable *matchtable,
                               GtChain2DimMatchstore *matchstore,
                               unsigned int presortdim,
                               bool gapsL1)
{
  matchstore->endpointperm
    = gt_malloc(sizeof (*matchstore->endpointperm) *
                matchtable->nextfree);
  makesortedendpointpermutation(matchstore->endpointperm,
                                matchtable,
                                presortdim);
  mergestartandendpoints(chainmode,
                         matchtable,
                         matchstore,
                         gapsL1,
                         presortdim);
  gt_free(matchstore->endpointperm);
}

static GtChain2Dimgapcostfunction assignchaingapcostfunction(
                                                      GtChain2Dimkind chainkind,
                                                      bool gapsL1)
{
  if (chainkind == GLOBALCHAININGWITHOVERLAPS)
  {
    return gt_chain2dim_overlapcost;
  }
  if (chainkind != GLOBALCHAININGALLCHAINS && chainkind != GLOBALCHAINING)
  {
    if (gapsL1)
    {
      return gapcostL1;
    }
    return gapcostCc;
  }
  return NULL;
}

/*EE
  The following function implements the different kinds of chaining
  algorithms for global and local chaining. The mode is specified
  by \texttt{chainmode}. There are \texttt{numofmatches} many matches,
  each specified in an array \texttt{matchtable} points to.
  \texttt{chain} is the array in which a chain is stored. However,
  do not further process a chain. Just use
  INITARRAY(&chain.chainedmatches,Uint) to initialize it before calling
  \textttt{fastchaining} and
  FREEARRAY(&chain.chainedmatches,Uint) to free the space after calling
  \textttt{fastchaining}. The function \texttt{chainprocessor} processes
  each chain found, and \texttt{cpinfo} is used as the first argument
  in each call to \texttt{chainprocessor}. The function returns
  0 upon success and otherwise, if an error occurs.
  Finally \texttt{gt_logger_log} is applied to each status message generated
  during the execution of \texttt{fastchaining}. If \texttt{gt_logger_log}
  is \texttt{NULL}, then nothing is generated and shown.
*/

void gt_chain_fastchaining(const GtChain2Dimmode *chainmode,
                           GtChain2Dim *chain,
                           GtChain2Dimmatchtable *matchtable,
                           bool gapsL1,
                           unsigned int presortdim,
                           bool withequivclasses,
                           GtChain2Dimprocessor chainprocessor,
                           void *cpinfo,
                           GtLogger *logger)
{
  GT_UNUSED unsigned int retval;
  GtChain2Dimgapcostfunction chaingapcostfunction;

  gt_assert(presortdim <= 1U);
  chaingapcostfunction
    = assignchaingapcostfunction(chainmode->chainkind,gapsL1);
  if (matchtable->nextfree > 1UL)
  {
    GtChain2DimMatchstore matchstore;

    gt_logger_log(logger,"compute chain scores");
    if (chainmode->chainkind == GLOBALCHAININGWITHOVERLAPS)
    {
      gt_chain2dim_bruteforcechainingscores(chainmode,matchtable,
                                            chaingapcostfunction);
    } else
    {
      if (chainmode->chainkind == GLOBALCHAININGALLCHAINS)
      {
        gt_chain2dim_ndbfchainscores(matchtable);
      } else
      {
        fastchainingscores(chainmode,
                           matchtable,
                           &matchstore,
                           presortdim,
                           gapsL1);
      }
    }
    gt_logger_log(logger,"retrieve optimal chains");
    retval = gt_chain2dim_findmaximalscores(chainmode,
                               chain,
                               matchtable,
                               &matchstore,
                               chainprocessor,
                               withequivclasses,
                               cpinfo,
                               logger);
    if (chainmode->chainkind != GLOBALCHAININGWITHOVERLAPS
        && chainmode->chainkind != GLOBALCHAININGALLCHAINS)
    {
      gt_rbtree_delete(matchstore.dictroot);
    }
  } else
  {
    gt_chain2dim_chainingboundarycases(chainmode, chain, matchtable);
    chainprocessor(cpinfo,matchtable,chain);
    retval = 0;
  }
  /* retval is not reported. */
}

static int cmpMatchchaininfo0(const void *keya,const void *keyb)
{
  if (((const Matchchaininfo *) keya)->startpos[0] <
      ((const Matchchaininfo *) keyb)->startpos[0])
  {
    return -1;
  }
  if (((const Matchchaininfo *) keya)->startpos[0] >
      ((const Matchchaininfo *) keyb)->startpos[0])
  {
    return 1;
  }
  return 0;
}

static int cmpMatchchaininfo1(const void *keya,const void *keyb)
{
  if (((const Matchchaininfo *) keya)->startpos[1] <
      ((const Matchchaininfo *) keyb)->startpos[1])
  {
    return -1;
  }
  if (((const Matchchaininfo *) keya)->startpos[1] >
      ((const Matchchaininfo *) keyb)->startpos[1])
  {
    return 1;
  }
  return 0;
}

typedef int (*Qsortcomparefunction)(const void *,const void *);

void gt_chain_possiblysortmatches(GtLogger *logger,
                                    GtChain2Dimmatchtable *matchtable,
                                    unsigned int presortdim)
{
  if (matchtable->nextfree > 1UL)
  {
    Qsortcomparefunction qsortcomparefunction;
    Matchchaininfo *fptr;
    bool matchesaresorted = true;

    gt_assert(presortdim <= 1U);
    qsortcomparefunction
      = (presortdim == 0) ? cmpMatchchaininfo0 : cmpMatchchaininfo1;
    for (fptr = matchtable->matches;
         fptr < matchtable->matches + matchtable->nextfree - 1;
         fptr++)
    {
      if (qsortcomparefunction((const void *) fptr,
                               (const void *) (fptr+1)) == 1)
      {
        matchesaresorted = false;
        break;
      }
    }
    if (!matchesaresorted)
    {
      gt_logger_log(logger,"input matches are not yet sorted => sort them");
      qsort(matchtable->matches,(size_t) matchtable->nextfree,
            sizeof (*matchtable->matches),qsortcomparefunction);
    } else
    {
      gt_logger_log(logger,"matches are already sorted w.r.t. dimension %u",
                    presortdim);
    }
  }
}

static int parselocalchainingparameter(GtChain2Dimmode *chainmode,
                                       const char *option,
                                       const char *lparam,
                                       GtError *err)
{
  Qualifiedinteger *qualint;

  qualint = gt_parsequalifiedinteger(option,lparam,err);
  if (qualint == NULL)
  {
    return -1;
  }
  switch (qualint->qualtag)
  {
    case Qualbestof:
      chainmode->chainkind = LOCALCHAININGBEST;
      chainmode->howmanybest = qualint->integervalue;
      break;
    case Qualpercentaway:
      chainmode->chainkind = LOCALCHAININGPERCENTAWAY;
      chainmode->percentawayfrombest = qualint->integervalue;
      break;
    case Qualabsolute:
      chainmode->chainkind = LOCALCHAININGTHRESHOLD;
      chainmode->minimumscore = (GtChain2Dimscoretype) qualint->integervalue;
      break;
  }
  gt_free(qualint);
  return 0;
}

static int parseglobalchainingparameter(GtChain2Dimmode *chainmode,
                                        const char *option,
                                        const char *gparam,
                                        GtError *err)
{
  if (strcmp(gparam,GT_CHAIN2DIM_GAPCOSTSWITCH) == 0)
  {
    chainmode->chainkind = GLOBALCHAININGWITHGAPCOST;
    return 0;
  }
  if (strcmp(gparam,GT_CHAIN2DIM_OVERLAPSWITCH) == 0)
  {
    chainmode->chainkind = GLOBALCHAININGWITHOVERLAPS;
    return 0;
  }
  if (strcmp(gparam,GT_CHAIN2DIM_ALLSWITCH) == 0)
  {
    chainmode->chainkind = GLOBALCHAININGALLCHAINS;
    return 0;
  }
  if (err != NULL)
  {
    gt_error_set(err,"argument of option -%s must be %s or %s: ",
                      option,
                      GT_CHAIN2DIM_GAPCOSTSWITCH,
                      GT_CHAIN2DIM_OVERLAPSWITCH);
  } else
  {
    fprintf(stderr,"argument of option -%s must be %s or %s: ",
                   option,
                   GT_CHAIN2DIM_GAPCOSTSWITCH,
                   GT_CHAIN2DIM_OVERLAPSWITCH);
  }
  return -1;
}

GtChain2Dimmode *gt_chain_chainmode_new(unsigned long maxgap,
                                        bool globalset,
                                        const char *globalargs,
                                        bool localset,
                                        const char *localargs,
                                        GtError *err)
{
  GtChain2Dimmode *chainmode;
  bool haserr = false;

  gt_assert(!(globalset && localset));
  chainmode = gt_malloc(sizeof (*chainmode));
  chainmode->chainkind = GLOBALCHAINING;
  chainmode->maxgapwidth = (GtChain2Dimpostype) maxgap;
  if (localset)
  {
    if (localargs == NULL)
    {
      chainmode->chainkind = LOCALCHAININGMAX;
    } else
    {
      if (parselocalchainingparameter(chainmode, "local", localargs, err) != 0)
      {
        haserr = true;
      }
    }
  }
  if (globalset)
  {
    if (globalargs == NULL)
    {
      chainmode->chainkind = GLOBALCHAINING;
    } else
    {
      if (parseglobalchainingparameter(chainmode, "global", globalargs,
                                       err) != 0)
      {
        haserr = true;
      }
    }
  }
  if (haserr)
  {
    gt_free(chainmode);
    return NULL;
  }
  return chainmode;
}

void gt_chain_chainmode_delete(GtChain2Dimmode *chainmode)
{
  if (chainmode != NULL)
  {
    gt_free(chainmode);
  }
}

GtChain2Dim *gt_chain_chain_new(void)
{
  GtChain2Dim *chain;

  chain = gt_malloc(sizeof (*chain));
  GT_INITARRAY(&chain->chainedmatches,GtChain2Dimref);
  return chain;
}

void gt_chain_chain_delete(GtChain2Dim *chain)
{
  if (chain != NULL)
  {
    GT_FREEARRAY(&chain->chainedmatches,GtChain2Dimref);
    gt_free(chain);
  }
}

GtChain2Dimscoretype gt_chain_chainscore(const GtChain2Dim *chain)
{
  return chain->scoreofchain;
}

unsigned long gt_chain_chainlength(const GtChain2Dim *chain)
{
  return chain->chainedmatches.nextfreeGtChain2Dimref;
}

bool gt_chain_storedinreverseorder(const GtChain2Dim *chain)
{
  return chain->storedinreverseorder;
}

void gt_chain_extractchainelem(GtChain2Dimmatchvalues *value,
                               const GtChain2Dimmatchtable *matchtable,
                               const GtChain2Dim *chain,unsigned long idx)
{
  const Matchchaininfo *fiptr;

  gt_assert(idx <  gt_chain_chainlength(chain) &&
            chain->chainedmatches.spaceGtChain2Dimref[idx] <
            matchtable->nextfree);
  fiptr = matchtable->matches +
          chain->chainedmatches.spaceGtChain2Dimref[idx];
  value->startpos[0] = fiptr->startpos[0];
  value->startpos[1] = fiptr->startpos[1];
  value->endpos[0] = fiptr->endpos[0];
  value->endpos[1] = fiptr->endpos[1];
  value->weight = fiptr->weight;
}

void gt_chain_printchainelem(FILE *outfp,const GtChain2Dimmatchvalues *value)
{
  fprintf(outfp,
          "%lu %lu %lu %lu"
          " %ld\n",value->startpos[0],
                   value->endpos[0],
                   value->startpos[1],
                   value->endpos[1],
                   value->weight);
}
genometools-1.5.1/src/match/chain2dim.h000066400000000000000000000135001211610345200177350ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef CHAIN2DIM_H
#define CHAIN2DIM_H

#include "core/error_api.h"
#include "core/logger.h"

/*
  The following string is used to trigger the usage of gap costs
  for global chaining.
*/

#define GT_CHAIN2DIM_GAPCOSTSWITCH        "gc"

/*
  The following string is used to trigger the use of a chaining algorithm
  allowing for overlaps between the hits.
*/

#define GT_CHAIN2DIM_OVERLAPSWITCH        "ov"

#define GT_CHAIN2DIM_ALLSWITCH            "all"

/* the followin type is used for the position values in the matches to be
   chained */

typedef unsigned long GtChain2Dimpostype;

/* the following type is used for scores of chains */

typedef long GtChain2Dimscoretype;

/* the anonymous type for a chain */

typedef struct GtChain2Dim GtChain2Dim;

/* the anonymous type for a table storing the matches */

typedef struct GtChain2Dimmatchtable GtChain2Dimmatchtable;

/* the following type is used for relevant values to output for a chained
   frgament */

typedef struct
{
  GtChain2Dimpostype startpos[2], /* start of matches in the 2 dimensions,
                                 userdef */
                 endpos[2];  /* end of matches in the 2 dimensions, userdef */
  GtChain2Dimscoretype weight; /* weight of match, user defined */
} GtChain2Dimmatchvalues;

/*
  the type of function to report chains.
*/

typedef void (*GtChain2Dimprocessor)(void *,
                                 const GtChain2Dimmatchtable *,
                                 const GtChain2Dim *);

/* the type of value describing how to chain */

typedef struct GtChain2Dimmode GtChain2Dimmode;

/* the constructor for tables of matches */

GtChain2Dimmatchtable *gt_chain_matchtable_new(unsigned long numberofmatches);

/* the destructor for tables of matches */

void gt_chain_matchtable_delete(GtChain2Dimmatchtable *matchtable);

/* the function for emptying a table of matches, without freeing the space */

void gt_chain_matchtable_empty(GtChain2Dimmatchtable *matchtable);

/* the following function adds the relevant values describing a match */

void gt_chain_matchtable_add(GtChain2Dimmatchtable *matchtable,
                                    const GtChain2Dimmatchvalues *inmatch);

/* the following functions reads a file describing matches in open format.
   It returns the corresponding table of matches. */

GtChain2Dimmatchtable *gt_chain_analyzeopenformatfile(double weightfactor,
                                                  const char *matchfile,
                                                  GtError *err);

/* the function to fill the gap values for all matches */

void gt_chain_fillthegapvalues(GtChain2Dimmatchtable *matchtable);

/* function to apply an additional weight to the elements to be chained */

void gt_chain_applyweight(double weightfactor,
                          GtChain2Dimmatchtable *matchtable);

/* the function to sort an array of matches */

void gt_chain_possiblysortmatches(GtLogger *logger,
                                  GtChain2Dimmatchtable *matchtable,
                                  unsigned int presortdim);

/* the constructor for chainmode objects. Use err = NULL to print
   error messages to stderr. */

GtChain2Dimmode *gt_chain_chainmode_new(unsigned long maxgap,
                                        bool globalset,
                                        const char *globalargs,
                                        bool localset,
                                        const char *localargs,
                                        GtError *err);

/* the destructor for chainmode objects */

void gt_chain_chainmode_delete(GtChain2Dimmode *chainmode);

/* the constructor for chains */

GtChain2Dim *gt_chain_chain_new(void);

/* the descructor for chains */

void gt_chain_chain_delete(GtChain2Dim *chain);

/* the function to perform the fast chaining algorithms */

void gt_chain_fastchaining(const GtChain2Dimmode *chainmode,
                           GtChain2Dim *chain,
                           GtChain2Dimmatchtable *matchtable,
                           bool gapsL1,
                           unsigned int presortdim,
                           bool withequivclasses,
                           GtChain2Dimprocessor chainprocessor,
                           void *cpinfo,
                           GtLogger *logger);

/* obtain the score of a chain */

GtChain2Dimscoretype gt_chain_chainscore(const GtChain2Dim *chain);

/* obtain the length of a chain */

unsigned long gt_chain_chainlength(const GtChain2Dim *chain);

/* return true iff chain is stored in reverse order */

bool gt_chain_storedinreverseorder(const GtChain2Dim *chain);

/* store the values of element idx in given chain in the first parameter */

void gt_chain_extractchainelem(GtChain2Dimmatchvalues *value,
                               const GtChain2Dimmatchtable *matchtable,
                               const GtChain2Dim *chain,
                               unsigned long idx);

/* print a chain element to the given file pointer */

void gt_chain_printchainelem(FILE *outfp,const GtChain2Dimmatchvalues *value);

#endif
genometools-1.5.1/src/match/chainofin.c000066400000000000000000000071301211610345200200320ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#endif
#include "core/fa.h"
#include "core/error_api.h"
#include "chain2dim.h"

#define READNUMS 5

#define CANNOTPARSELINE(S)\
        gt_error_set(err,"matchfile \"%s\", line %lu, column %lu: %s",\
                     matchfile,linenum+1,countcolumns+1,S)

static int numberoflinesinfile(unsigned long *linenum,
                               const char *filename,
                               GtError *err)
{
  FILE *fp;
  int cc;

  fp = gt_fa_fopen(filename,"r",err);
  *linenum = 0;
  if (fp == NULL)
  {
    return -1;
  }
  while ((cc = getc(fp)) != EOF)
  {
    if (cc == '\n')
    {
      (*linenum)++;
    }
  }
  gt_fa_fclose(fp);
  return 0;
}

GtChain2Dimmatchtable *gt_chain_analyzeopenformatfile(double weightfactor,
                                                  const char *matchfile,
                                                  GtError *err)
{
  GtChain2Dimmatchtable *matchtable;
  unsigned long linenum;
  long storeinteger[READNUMS];
  FILE *matchfp;
  bool haserr = false;
  GtChain2Dimmatchvalues fragment;

  if (numberoflinesinfile(&linenum,matchfile,err) != 0)
  {
    return NULL;
  }
  matchfp = gt_fa_fopen(matchfile,"r",err);
  if (matchfp == NULL)
  {
    return NULL;
  }
  matchtable = gt_chain_matchtable_new(linenum);
  for (linenum = 0; fscanf(matchfp,"%ld %ld %ld %ld %ld\n",
                           &storeinteger[0],
                           &storeinteger[1],
                           &storeinteger[2],
                           &storeinteger[3],
                           &storeinteger[4]) == READNUMS; linenum++)
  {
    unsigned long countcolumns;

    for (countcolumns = 0; countcolumns < (unsigned long) (READNUMS-1);
         countcolumns++)
    {
      if (storeinteger[countcolumns] < 0)
      {
        CANNOTPARSELINE("non-negative integer expected");
        haserr = true;
      }
    }
    if (storeinteger[0] > storeinteger[1])
    {
      CANNOTPARSELINE("startpos1 <= endpos1 expected");
      haserr = true;
      break;
    }
    if (storeinteger[2] > storeinteger[3])
    {
      CANNOTPARSELINE("startpos2 <= endpos2 expected");
      haserr = true;
      break;
    }
    fragment.startpos[0] = (GtChain2Dimpostype) storeinteger[0];
    fragment.endpos[0] = (GtChain2Dimpostype) storeinteger[1];
    fragment.startpos[1] = (GtChain2Dimpostype) storeinteger[2];
    fragment.endpos[1] = (GtChain2Dimpostype) storeinteger[3];
    fragment.weight
      = (GtChain2Dimscoretype) (weightfactor * (double) storeinteger[4]);
    gt_chain_matchtable_add(matchtable,&fragment);
    /*gt_chain_printchainelem(stdout,&fragment); */
  }
  gt_fa_fclose(matchfp);
  if (haserr)
  {
    gt_chain_matchtable_delete(matchtable);
    return NULL;
  }
  gt_chain_fillthegapvalues(matchtable);
  return matchtable;
}
genometools-1.5.1/src/match/cutendpfx.c000066400000000000000000000074671211610345200201110ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/chardef.h"
#include "core/codetype.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/ma_api.h"
#include "bcktab.h"
#include "cutendpfx.h"

struct Bucketenumerator
{
  const GtBcktab *bcktab; /* only need multimappower and filltable */
  unsigned int prefixlength,
               demandprefixlength;
  GtBucketspecification bucketspec;
  GtCodetype currentcode, lastcode;
};

static inline unsigned int prefixqgram2code(GtCodetype *code,
                                            const GtCodetype **multimappower,
                                            unsigned int qvalue,
                                            unsigned int qvalueprefix,
                                            const GtUchar *qgram)
{
  int i;
  GtCodetype tmpcode = 0;
  GtUchar a;

  gt_assert(qvalueprefix > 0);
  gt_assert(qvalue > qvalueprefix);
  for (i = (int) (qvalueprefix-1); i>=0; i--)
  {
    a = qgram[i];
    if (ISSPECIAL(a))
    {
      return (unsigned int) i;
    }
    tmpcode += multimappower[i][a];
  }
  *code = tmpcode;
  return qvalue;
}

Bucketenumerator *gt_newbucketenumerator(const GtBcktab *bcktab,
                                      unsigned int prefixlength,
                                      const GtUchar *demandprefix,
                                      unsigned int demandprefixlength)
{
  Bucketenumerator *bucketenumerator;
  GT_UNUSED unsigned int firstspecial;

  bucketenumerator = gt_malloc(sizeof *bucketenumerator);
  bucketenumerator->bcktab = bcktab;
  bucketenumerator->prefixlength = prefixlength;
  bucketenumerator->demandprefixlength = demandprefixlength;
  firstspecial = prefixqgram2code(&bucketenumerator->currentcode,
                                  gt_bcktab_multimappower(bcktab),
                                  prefixlength,
                                  demandprefixlength,
                                  demandprefix);
  gt_assert(firstspecial == prefixlength);
  bucketenumerator->lastcode
    = bucketenumerator->currentcode
      + gt_bcktab_filltable(bcktab,demandprefixlength);
  return bucketenumerator;
}

bool gt_nextbucketenumerator(Lcpinterval *itv,
                             Bucketenumerator *bucketenumerator)
{
  while (true)
  {
    if (bucketenumerator->currentcode > bucketenumerator->lastcode)
    {
      break;
    }
    gt_bcktab_calcboundaries(&bucketenumerator->bucketspec,
                             bucketenumerator->bcktab,
                             bucketenumerator->currentcode);
    bucketenumerator->currentcode++;
    if (bucketenumerator->bucketspec.nonspecialsinbucket > 0)
    {
      itv->left = bucketenumerator->bucketspec.left;
      itv->right = itv->left +
                   bucketenumerator->bucketspec.nonspecialsinbucket - 1;
      itv->offset = (unsigned long) bucketenumerator->demandprefixlength;
      return true;
    }
  }
  return false;
}

void gt_freebucketenumerator(Bucketenumerator *bucketenumerator)
{
  gt_free(bucketenumerator);
}
genometools-1.5.1/src/match/cutendpfx.h000066400000000000000000000030111211610345200200730ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef CUTENDPFX_H
#define CUTENDPFX_H

#include 
#include 
#include 
#include "core/types_api.h"
#include "lcpinterval.h"
#include "bcktab.h"

typedef struct Bucketenumerator Bucketenumerator;

Bucketenumerator *gt_newbucketenumerator(const GtBcktab *bcktab,
                                         unsigned int prefixlength,
                                         const GtUchar *demandprefix,
                                         unsigned int demandprefixlength);

bool gt_nextbucketenumerator(Lcpinterval *itv,
                             Bucketenumerator *bucketenumerator);

void gt_freebucketenumerator(Bucketenumerator *bucketenumerator);

#endif
genometools-1.5.1/src/match/dataalign.h000066400000000000000000000026151211610345200200300ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef DATAALIGN_H
#define DATAALIGN_H

#include 
#include "core/minmax.h"

/*
 * functionality to layout data at correct alignment (=> fewer
 * individual mallocs)
 */
enum {
  MAX_ALIGN_REQUIREMENT = 8,
  MIN_ALIGN_REQUREMENT = 4,
};

static inline unsigned long long
roundUp(unsigned long long v, unsigned long multipleOf)
{
  return v - v%multipleOf + multipleOf * (v%multipleOf?1:0);
}

static inline size_t
offsetAlign(size_t offset, size_t sizeOfVal2Align)
{
  size_t alignBase = MAX(MIN_ALIGN_REQUREMENT,
                         MIN(sizeOfVal2Align, MAX_ALIGN_REQUIREMENT));
  return roundUp(offset, alignBase);
}

#endif
genometools-1.5.1/src/match/dist-short.c000066400000000000000000000131621211610345200201760ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/assert_api.h"
#include "core/types_api.h"
#include "core/chardef.h"
#include "core/encseq.h"
#include "core/defined-types.h"
#include "initeqsvec.h"
#include "dist-short.h"

#define DECLARELOCALVARS\
        unsigned long Pv = ~0UL,\
                      Mv = 0,\
                      Eq,\
                      Xv,\
                      Xh,\
                      Ph,\
                      Mh,\
                      Ebit = (1UL << (ulen-1)),\
                      distval = ulen

#define COMPUTENEWDIST(CC)\
        gt_assert((CC) != (GtUchar) SEPARATOR);\
        if ((CC) != (GtUchar) WILDCARD)\
        {\
          Eq = eqsvector[(unsigned long) (CC)];\
        } else\
        {\
          Eq = 0;\
        }\
        Xv = Eq | Mv;\
        Xh = (((Eq & Pv) + Pv) ^ Pv) | Eq;\
        Ph = Mv | ~ (Xh | Pv);\
        Mh = Pv & Xh;\
        if (Ph & Ebit)\
        {\
          distval++;\
        } else\
        {\
          if (Mh & Ebit)\
          {\
            distval--;\
          }\
        }\
        /*\
           the original version of Myers included the statement\
           Ph <<= 1. As an effect, the first element of each column\
           was 0. We add a 1 to the shifted Ph vector. As a consequence,\
           we obtain an increment by 1 in the first column.\
        */\
        Ph = (Ph << 1) | 1UL;\
        Pv = (Mh << 1) | ~ (Xv | Ph);\
        Mv = Ph & Xv

unsigned long gt_distanceofshortstringsbytearray(unsigned long *eqsvector,
                                              unsigned int alphasize,
                                              const GtUchar *useq,
                                              unsigned long ulen,
                                              const GtUchar *vseq,
                                              unsigned long vlen)
{
  DECLARELOCALVARS;
  const GtUchar *vptr;

  gt_initeqsvector(eqsvector,(unsigned long) alphasize,useq,ulen);
  for (vptr = vseq; vptr < vseq + vlen; vptr++)
  {
    COMPUTENEWDIST(*vptr);
  }
  return distval;
}

unsigned long gt_distanceofshortstringsencseq(unsigned long *eqsvector,
                                           unsigned int alphasize,
                                           const GtUchar *useq,
                                           unsigned long ulen,
                                           const GtEncseq *encseq,
                                           unsigned long vstartpos,
                                           unsigned long vlen)
{
  DECLARELOCALVARS;
  GtUchar cc;
  unsigned long pos;

  gt_initeqsvector(eqsvector,(unsigned long) alphasize,useq,ulen);
  for (pos = vstartpos; pos < vstartpos + vlen; pos++)
  {
    cc = gt_encseq_get_encoded_char(encseq,pos,GT_READMODE_FORWARD);
    COMPUTENEWDIST(cc);
  }
  return distval;
}

unsigned long gt_reversesuffixmatch(unsigned long *eqsvector,
                                 unsigned int alphasize,
                                 const GtUchar *useq,
                                 unsigned long ulen,
                                 const GtUchar *vseq,
                                 unsigned long vlen,
                                 unsigned long maxdistance)
{
  DECLARELOCALVARS;
  const GtUchar *vptr;

  gt_initeqsvectorrev(eqsvector,(unsigned long) alphasize,useq,ulen);
  gt_assert(maxdistance > 0);
  for (vptr = vseq + vlen - 1; vptr >= vseq; vptr--)
  {
    COMPUTENEWDIST(*vptr);
    if (distval <= maxdistance)
    {
      break;
    }
  }
  /* gt_assert(distval <= maxdistance); */
  return (unsigned long) (vseq + vlen - vptr);
}

Definedunsignedlong gt_forwardprefixmatch(const GtEncseq *encseq,
                                       unsigned int alphasize,
                                       unsigned long startpos,
                                       bool nowildcards,
                                       unsigned long *eqsvector,
                                       const GtUchar *useq,
                                       unsigned long ulen,
                                       unsigned long maxdistance)
{
  DECLARELOCALVARS;
  unsigned long pos, totallength = gt_encseq_total_length(encseq);
  GtUchar cc;
  Definedunsignedlong result;

  gt_initeqsvector(eqsvector,(unsigned long) alphasize,useq,ulen);
  gt_assert(maxdistance > 0);
  for (pos = startpos; /* Nothing */; pos++)
  {
    gt_assert(pos - startpos <= (unsigned long) (ulen + maxdistance));
    cc = gt_encseq_get_encoded_char(encseq,pos,GT_READMODE_FORWARD);
    if (nowildcards && cc == (GtUchar) WILDCARD)
    {
      result.defined = false;
      result.valueunsignedlong = 0;
      return result;
    }
    COMPUTENEWDIST(cc);
    if (distval <= maxdistance || pos == totallength-1)
    {
      break;
    }
  }
  result.defined = true;
  result.valueunsignedlong = (unsigned long) (pos - startpos + 1);
  return result;
}
genometools-1.5.1/src/match/dist-short.h000066400000000000000000000052421211610345200202030ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef DIST_SHORT_H
#define DIST_SHORT_H
#include "core/defined-types.h"
#include "core/encseq_api.h"
#include "core/types_api.h"

unsigned long gt_distanceofshortstringsbytearray(unsigned long *eqsvector,
                                     unsigned int alphasize,
                                     const GtUchar *useq,
                                     unsigned long ulen,
                                     const GtUchar *vseq,
                                     unsigned long vlen);

unsigned long gt_distanceofshortstringsencseq(unsigned long *eqsvector,
                                           unsigned int alphasize,
                                           const GtUchar *useq,
                                           unsigned long ulen,
                                           const GtEncseq *encseq,
                                           unsigned long vstartpos,
                                           unsigned long vlen);

unsigned long gt_reversesuffixmatch(unsigned long *eqsvector,
                                 unsigned int alphasize,
                                 const GtUchar *useq,
                                 unsigned long ulen,
                                 const GtUchar *vseq,
                                 unsigned long vlen,
                                 unsigned long maxdistance);

Definedunsignedlong gt_forwardprefixmatch(const GtEncseq *encseq,
                                       unsigned int alphasize,
                                       unsigned long startpos,
                                       bool nowildcards,
                                       unsigned long *eqsvector,
                                       const GtUchar *useq,
                                       unsigned long ulen,
                                       unsigned long maxdistance);

#endif
genometools-1.5.1/src/match/echoseq.c000066400000000000000000000117601211610345200175270ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/alphabet.h"
#include "core/assert_api.h"
#include "core/chardef.h"
#include "core/error.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "core/encseq.h"

void gt_symbolstring2fasta(FILE *fpout,
                        const char *desc,
                        const GtAlphabet *alpha,
                        const GtUchar *w,
                        unsigned long wlen,
                        unsigned long width)
{
  unsigned long i, j;
  GtUchar currentchar;

  gt_assert(width > 0);
  if (desc == NULL)
  {
    fprintf(fpout,">\n");
  } else
  {
    fprintf(fpout,">%s\n",desc);
  }
  for (i = 0, j = 0; ; i++)
  {
    currentchar = w[i];
    if (currentchar == (GtUchar) SEPARATOR)
    {
      fprintf(fpout,"\n>\n");
      j = 0;
    } else
    {
      gt_alphabet_echo_pretty_symbol(alpha,fpout,currentchar);
    }
    if (i == wlen - 1)
    {
      fprintf(fpout,"\n");
      break;
    }
    if (currentchar != (GtUchar) SEPARATOR)
    {
      j++;
      if (j >= width)
      {
        fprintf(fpout,"\n");
        j = 0;
      }
    }
  }
}

void gt_encseq2symbolstring(FILE *fpout,
                            const GtEncseq *encseq,
                            GtReadmode readmode,
                            unsigned long start,
                            unsigned long wlen,
                            unsigned long width)
{
  unsigned long j, idx, lastpos;
  GtUchar currentchar;
  GtEncseqReader *esr;
  const GtAlphabet *alpha;

  esr = gt_encseq_create_reader_with_readmode(encseq, readmode, start);
  gt_assert(width > 0);
  lastpos = start + wlen - 1;
  alpha = gt_encseq_alphabet(encseq);
  for (idx = start, j = 0; /* Nothing */ ; idx++)
  {
    currentchar = gt_encseq_reader_next_encoded_char(esr);
    if (currentchar == (GtUchar) SEPARATOR)
    {
      fprintf(fpout,"\n>\n");
      j = 0;
    } else
    {
      gt_alphabet_echo_pretty_symbol(alpha,fpout,currentchar);
    }
    if (idx == lastpos)
    {
      fprintf(fpout,"\n");
      break;
    }
    if (currentchar != (GtUchar) SEPARATOR)
    {
      j++;
      if (j >= width)
      {
        fprintf(fpout,"\n");
        j = 0;
      }
    }
  }
  gt_encseq_reader_delete(esr);
}

void gt_fprintfencseq(FILE *fpout,
                      const GtEncseq *encseq,
                      unsigned long start,
                      unsigned long wlen)
{
  unsigned long idx;
  GtUchar currentchar;
  const GtAlphabet *alpha;

  alpha = gt_encseq_alphabet(encseq);
  for (idx = start; idx < start + wlen; idx++)
  {
    currentchar = gt_encseq_get_encoded_char(encseq,
                                                    idx,
                                                    GT_READMODE_FORWARD);
    gt_assert(ISNOTSPECIAL(currentchar));
    gt_alphabet_echo_pretty_symbol(alpha,fpout,currentchar);
  }
}

void gt_encseq2fastaoutput(FILE *fpout,
                           const char *desc,
                           const GtEncseq *encseq,
                           GtReadmode readmode,
                           unsigned long start,
                           unsigned long wlen,
                           unsigned long width)
{
  gt_assert(width > 0);
  if (desc == NULL)
  {
    fprintf(fpout,">\n");
  } else
  {
    fprintf(fpout,">%s\n",desc);
  }
  gt_encseq2symbolstring(fpout,
                         encseq,
                         readmode,
                         start,
                         wlen,
                         width);
}

int gt_echodescriptionandsequence(const GtStrArray *filenametab,GtError *err)
{
  GtSeqIterator *seqit;
  char *desc = NULL;
  const GtUchar *sequence;
  unsigned long seqlen;
  bool haserr = false;
  int retval;

  seqit = gt_seq_iterator_sequence_buffer_new(filenametab, err);
  if (!seqit)
    return -1;
  while (true)
  {
    retval = gt_seq_iterator_next(seqit,
                                 &sequence,
                                 &seqlen,
                                 &desc,
                                 err);
    if (retval < 0)
    {
      haserr = true;
      break;
    }
    if (retval == 0)
    {
      break;
    }
    gt_symbolstring2fasta(stdout,desc,NULL,sequence,seqlen,70UL);
  }
  gt_seq_iterator_delete(seqit);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/echoseq.h000066400000000000000000000041751211610345200175360ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ECHOSEQ_H
#define ECHOSEQ_H
#include 
#include "core/alphabet.h"
#include "core/error_api.h"
#include "core/types_api.h"
#include "core/str_array_api.h"
#include "core/readmode.h"

#include "core/encseq.h"

void gt_symbolstring2fasta(FILE *fpout,
                        const char *desc,
                        const GtAlphabet *alpha,
                        const GtUchar *w,
                        unsigned long wlen,
                        unsigned long width);

void gt_encseq2symbolstring(FILE *fpout,
                         const GtEncseq *encseq,
                         GtReadmode readmode,
                         unsigned long start,
                         unsigned long wlen,
                         unsigned long width);

void gt_fprintfencseq(FILE *fpout,
                   const GtEncseq *encseq,
                   unsigned long start,
                   unsigned long wlen);

void gt_encseq2fastaoutput(FILE *fpout,
                        const char *desc,
                        const GtEncseq *encseq,
                        GtReadmode readmode,
                        unsigned long start,
                        unsigned long wlen,
                        unsigned long width);

int gt_echodescriptionandsequence(const GtStrArray *filenametab,GtError *err);

#endif
genometools-1.5.1/src/match/eis-bitpackseqpos.h000066400000000000000000000054741211610345200215400ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BITPACKSEQPOS_H
#define EIS_BITPACKSEQPOS_H

/**
 * @file eis-bitpackseqpos.h
 * @brief Defines appropriate width routines for storing and retrieving
 * unsigned long values in/from BitString.
 */

#include "core/bitpackstring.h"

#ifndef _LP64
/** retrieve unsigned long from BitString */
#define gt_bsGetUlong gt_bsGetUInt32
/** store unsigned long in BitString */
#define gt_bsStoreUlong gt_bsStoreUInt32
/** read back array of unsigned long values in BitString */
#define gt_bsGetUniformUlongArray gt_bsGetUniformUInt32Array
/** read back array of unsigned long values in BitString */
#define gt_bsGetUniformUlongArrayAdd gt_bsGetUniformUInt32ArrayAdd
/** read back array of unsigned long values in BitString */
#define gt_bsGetNonUniformUlongArray gt_bsGetNonUniformUInt32Array
/** read back array of unsigned long values in BitString */
#define gt_bsGetNonUniformUlongArrayAdd gt_bsGetNonUniformUInt32ArrayAdd
/** store array of unsigned long values in BitString */
#define gt_bsStoreUniformUlongArray gt_bsStoreUniformUInt32Array
/** how many bits are required to store given unsigned long value */
#define requiredUlongBits gt_requiredUInt32Bits
#else
/** retrieve unsigned long from BitString */
#define gt_bsGetUlong gt_bsGetUInt64
/** store unsigned long in BitString */
#define gt_bsStoreUlong gt_bsStoreUInt64
/** read back array of unsigned long values in BitString */
#define gt_bsGetUniformUlongArray gt_bsGetUniformUInt64Array
/** read back array of unsigned long values in BitString */
#define gt_bsGetUniformUlongArrayAdd gt_bsGetUniformUInt64ArrayAdd
/** read back array of unsigned long values in BitString */
#define gt_bsGetNonUniformUlongArray gt_bsGetNonUniformUInt64Array
/** read back array of unsigned long values in BitString */
#define gt_bsGetNonUniformUlongArrayAdd gt_bsGetNonUniformUInt64ArrayAdd
/** store array of unsigned long values in BitString  */
#define gt_bsStoreUniformUlongArray gt_bsStoreUniformUInt64Array
/** how many bits are required to store given unsigned long value */
#define requiredUlongBits gt_requiredUInt64Bits
#endif

#endif
genometools-1.5.1/src/match/eis-blockcomp-construct.h000066400000000000000000000042601211610345200226530ustar00rootroot00000000000000/*
  Copyright (C) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BLOCKCOMP_CONSTRUCT_H
#define EIS_BLOCKCOMP_CONSTRUCT_H

#include "match/eis-encidxseq.h"

/**
 * @param alphabet ownership of alphabet is transferred to the sequence
 * index produced unless NULL is returned
 */
EISeq *
gt_newGenBlockEncIdxSeq(unsigned long totalLen, const char *projectName,
                     MRAEnc *alphabet, const struct seqStats *stats,
                     SeqDataReader BWTGenerator,
                     const struct seqBaseParam *params,
                     size_t numExtHeaders, const uint16_t *headerIDs,
                     const uint32_t *extHeaderSizes,
                     headerWriteFunc *extHeaderCallbacks,
                     void **headerCBData,
                     bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                     varExtBitsEstimator biVarBits, void *cbState,
                     GtError *err);

/**
 * @brief Load previously written block encoded sequence
 * representation.
 * @param alphabet
 * @param totalLen
 * Caution: ownership of alphabet changes to returned index.
 * @param projectName base name of corresponding suffixerator project
 * @param features select optional in-memory data structures for speed-up
 * @param err genometools error object reference
 * @return new encoded indexed sequence object reference
 */
EISeq *
gt_loadBlockEncIdxSeqGen(MRAEnc *alphabet,
                      const char *projectName, int features, GtError *err);

#endif
genometools-1.5.1/src/match/eis-blockcomp-param.c000066400000000000000000000026451211610345200217270ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "match/eis-blockcomp-param.h"
#include "match/eis-encidxseq.h"

void
gt_registerBlockEncOptions(GtOptionParser *op,
                           struct blockEncParams *paramOutput)
{
  GtOption *option;

  option = gt_option_new_uint_min("bsize", "specify size of blocks",
                                  ¶mOutput->blockSize, 8U, 1U);
  gt_option_parser_add_option(op, option);
  option = gt_option_new_uint_min("blbuck", "specify number of blocks per "
                                            "bucket",
                                  ¶mOutput->bucketBlocks, 8U, 1U);
  gt_option_parser_add_option(op, option);
}
genometools-1.5.1/src/match/eis-blockcomp-param.h000066400000000000000000000025541211610345200217330ustar00rootroot00000000000000/*
  Copyright (c) 2007,2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BLOCKCOMP_PARAM_H
#define EIS_BLOCKCOMP_PARAM_H

/**
 * @file eis-blockcomp-param.h
 * @brief Call gt_registerBlockEncOptions to add options for construction
 * of a block-compressed index to the option parser.
 */
#include "core/option_api.h"
#include "match/eis-encidxseq.h"

/**
 * @brief Add options for construction of a block-compressed index to
 * the option parser.
 * @param op
 * @param paramOutput user provided values will be stored here
 * @param err
 */
void
gt_registerBlockEncOptions(GtOptionParser *op,
                           struct blockEncParams *paramOutput);

#endif
genometools-1.5.1/src/match/eis-blockcomp.c000066400000000000000000003121351211610345200206270ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/**
 * \file eis-blockcomp.c
 * \brief Methods to build block-compressed representation of indexed
 * sequence and answer queries on said representation.
 * \author Thomas Jahns 
 */
/*
 * TODO:
 * - normalize use  of  seqIdx variable naming (seq, bseq etc.)
 */
#include 
#include 
#include 
#include 
#ifndef S_SPLINT_S
#include 
#endif
#include 
#include "core/assert_api.h"
#include "core/bitpackstring.h"
#include "match/dataalign.h"
#include "core/error.h"
#include "core/fa.h"
#include "core/log.h"
#include "core/minmax.h"
#include "core/str.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "eis-blockcomp-construct.h"
#include "match/eis-bitpackseqpos.h"
#include "match/eis-encidxseq.h"
#include "match/eis-encidxseq-priv.h"
#include "match/eis-seqranges.h"
#include "match/eis-seqblocktranslate.h"
#include "match/eis-seqdatasrc.h"

struct onDiskBlockCompIdx
{
  FILE *idxFP;                 /**< used for writing the index and
                                * if an mmap of the whole index
                                * isn't possible also for reading */
  GtStr *idxFN;                /**< stores the filename of idxFP */
  char *idxMMap;               /**< if mmapping of the constant- and
                                * variable-width strings succeeded,
                                * stores the base of the
                                * corresponding memory mapped file
                                * portion */
  off_t cwDataPos,             /**< constant width data of the index */
    varDataPos,                /**< variable width part */
    rangeEncPos;               /**< in-file position of special
                                *  symbol representation */
};

/**
 * mode in which to encode a range of the alphabet
 */
enum rangeStoreMode {
  DIRECT_SYM_ENCODE,          /**< direct sequence encoding (not implemented) */
  BLOCK_COMPOSITION_INCLUDE,  /**< encode as two bitstrings, one
                               * containing a sequence of constant
                               * width composition indices, one
                               * containing a sequence of variable
                               * width permutation indices */
  REGIONS_LIST,               /**< encode as linear list of sequence regions */
};

struct blockCompositionSeq
{
  struct encIdxSeq baseClass;
  struct onDiskBlockCompIdx externalData;
  struct compList compositionTable;
  struct seqRangeList *rangeEncs;
  struct extHeaderPos *extHeaderPos;
  size_t numExtHeaders;
  BitOffset maxVarExtBitsPerBucket, cwExtBitsPerBucket;
  /* maxVarBitsPerBucket, cwBits */
  MRAEnc *blockMapAlphabet, *rangeMapAlphabet;
  int *modes;
  unsigned bucketBlocks, blockSize, callBackDataOffsetBits, bitsPerUlong,
    bitsPerVarDiskOffset;
  AlphabetRangeSize blockMapAlphabetSize;
  Symbol blockEncFallback, rangeEncFallback;
  int numModes;
  unsigned *partialSymSumBits, *partialSymSumBitsSums, symSumBits;
};

static inline size_t
blockEncIdxSeqHeaderLength(const struct blockCompositionSeq *seqIdx,
                           size_t numExtHeaders,
                           const uint32_t *extHeaderSizes);

static int
openOnDiskData(const char *projectName, struct onDiskBlockCompIdx *idx,
               char *mode, GtError *err);

static void
initOnDiskBlockCompIdx(struct onDiskBlockCompIdx *idx,
                       size_t headerLen, off_t cwLen);

static void
destructOnDiskBlockCompIdx(struct onDiskBlockCompIdx *idx);

static size_t
writeIdxHeader(struct blockCompositionSeq *seqIdx,
               size_t numExtHeaders, const uint16_t *headerIDs,
               const uint32_t *extHeaderSizes,
               headerWriteFunc *extHeaderCallbacks,
               void **headerCBData,
               GtError *err);

static inline int
tryMMapOfIndex(struct onDiskBlockCompIdx *idxData);

static const struct encIdxSeqClass blockCompositionSeqClass;

static inline struct blockCompositionSeq *
encIdxSeq2blockCompositionSeq(struct encIdxSeq *seq)
{
  gt_assert(seq && seq->classInfo == &blockCompositionSeqClass);
  return (struct blockCompositionSeq *)((char *)seq
    - offsetof(struct blockCompositionSeq, baseClass));
}

static inline struct encIdxSeq *
blockCompositionSeq2encIdxSeq(struct blockCompositionSeq *seq)
{
  gt_assert(seq);
  return &(seq->baseClass);
}

static inline const struct blockCompositionSeq *
constEncIdxSeq2blockCompositionSeq(const struct encIdxSeq *seq)
{
  gt_assert(seq && seq->classInfo == &blockCompositionSeqClass);
  return (struct blockCompositionSeq *)((char *)seq
    - offsetof(struct blockCompositionSeq, baseClass));
}

static inline const struct encIdxSeq *
constBlockCompositionSeq2encIdxSeq(const struct blockCompositionSeq *seq)
{
  gt_assert(seq);
  return &(seq->baseClass);
}

struct appendState
{
  BitString compCache, permCache;
  BitOffset compCacheLen, permCacheLen, cwMemPos, varMemPos, varDiskOffset;
  off_t cwDiskOffset;
  unsigned varMemOldBits, cwMemOldBits;
};

static inline void
initAppendState(struct appendState *aState,
                const struct blockCompositionSeq *seqIdx);
static void
destructAppendState(struct appendState *aState);

static inline void
append2IdxOutput(struct appendState *state,
                 PermCompIndex permCompIdx[2],
                 unsigned bitsOfCompositionIdx, unsigned bitsOfPermutationIdx);

static BitOffset
appendCallBackOutput(struct appendState *state,
                     const struct blockCompositionSeq *seqIdx,
                     bitInsertFunc biFunc, unsigned long start,
                     unsigned long len, unsigned callBackDataOffsetBits,
                     void *cbState);

typedef unsigned long partialSymSum;

static inline partialSymSum *
newPartialSymSums(AlphabetRangeSize alphabetSize);

static inline void
deletePartialSymSums(partialSymSum *sums);

static inline void
addBlock2PartialSymSums(partialSymSum *sums, const Symbol *block,
                        unsigned blockSize);

static inline void
copyPartialSymSums(AlphabetRangeSize alphabetSize, partialSymSum *dest,
                   const partialSymSum *src);

static inline unsigned long
numBuckets(unsigned long seqLen, size_t bucketLen);

static inline off_t
cwSize(const struct blockCompositionSeq *seqIdx);

static inline BitOffset
vwBits(unsigned long seqLen, unsigned blockSize, unsigned bucketBlocks,
       unsigned maxPermIdxBits, varExtBitsEstimator biVarBits, void *cbState,
       struct varBitsEstimate *extVarBitsUpperBound);

static void
addRangeEncodedSyms(struct seqRangeList *rangeList, const Symbol *block,
                    unsigned blockSize, unsigned long blockNum,
                    const MRAEnc *alphabet, int selection, const int *rangeSel);

static int
updateIdxOutput(struct blockCompositionSeq *seqIdx,
                struct appendState *aState,
                const partialSymSum *buck);

static int
finalizeIdxOutput(struct blockCompositionSeq *seqIdx,
                  struct appendState *state);

static inline void
symSumBitsDefaultSetup(struct blockCompositionSeq *seqIdx);

#define newBlockEncIdxSeqErrRet()                                       \
  do {                                                                  \
    if (newSeqIdx->externalData.idxFP)                                  \
      destructOnDiskBlockCompIdx(&newSeqIdx->externalData);             \
    if (newSeqIdx->compositionTable.bitsPerCount)                       \
      gt_destructCompositionList(&newSeqIdx->compositionTable);         \
    if (newSeqIdx->rangeEncs)                                           \
      gt_deleteSeqRangeList(newSeqIdx->rangeEncs);                      \
    if (newSeqIdx->extHeaderPos)                                        \
      gt_free(newSeqIdx->extHeaderPos);                                 \
    if (newSeqIdx->partialSymSumBits)                                   \
      gt_free(newSeqIdx->partialSymSumBits);                            \
    if (newSeqIdx->extHeaderPos)                                        \
      gt_free(newSeqIdx->extHeaderPos);                                 \
    if (newSeqIdx) gt_free(newSeqIdx);                                  \
    if (modesCopy)                                                      \
      gt_free(modesCopy);                                               \
    if (blockMapAlphabet) gt_MRAEncDelete(blockMapAlphabet);            \
    if (rangeMapAlphabet) gt_MRAEncDelete(rangeMapAlphabet);            \
    return NULL;                                                        \
  } while (0)

static void
addBlock2OutputBuffer(
  struct blockCompositionSeq *newSeqIdx,
  partialSymSum *buck, unsigned long blockNum,
  Symbol *block, unsigned blockSize,
  const MRAEnc *alphabet, const int *modes,
  const MRAEnc *blockMapAlphabet, AlphabetRangeSize blockMapAlphabetSize,
  BitString permCompBSPreAlloc, unsigned *compositionPreAlloc,
  unsigned compositionIdxBits, struct appendState *aState)
{
  PermCompIndex permCompIdx[2];
  unsigned significantPermIdxBits;
  /* a. update superbucket table */
  addBlock2PartialSymSums(buck, block, blockSize);
  /* b. add ranges of differently encoded symbols to
   * corresponding representation */
  addRangeEncodedSyms(newSeqIdx->rangeEncs, block, blockSize,
                      blockNum, alphabet, REGIONS_LIST,
                      modes);
  /* c. add to table of composition/permutation indices */
  gt_MRAEncSymbolsTransform(blockMapAlphabet, block, blockSize);
  /* FIXME control remapping */
  /* currently invalid characters in input can seriously break this */
  gt_block2IndexPair(&newSeqIdx->compositionTable, blockSize,
                  blockMapAlphabetSize, block, permCompIdx,
                  &significantPermIdxBits,
                  permCompBSPreAlloc, compositionPreAlloc);
  append2IdxOutput(aState, permCompIdx, compositionIdxBits,
                   significantPermIdxBits);
}

static int
writeOutputBuffer(struct blockCompositionSeq *newSeqIdx,
                  struct appendState *aState, bitInsertFunc biFunc,
                  unsigned long lastUpdatePos, size_t bucketLen,
                  unsigned callBackDataOffsetBits, void *cbState,
                  const partialSymSum *buckLast)
{
  if (biFunc)
    if (appendCallBackOutput(aState, newSeqIdx, biFunc,
                             lastUpdatePos, bucketLen,
                             callBackDataOffsetBits, cbState)
        == (BitOffset)-1)
    {
      perror("error condition while writing block-compressed"
             " index data");
      return -1;
    }
  if (!updateIdxOutput(newSeqIdx, aState, buckLast))
  {
    perror("error condition while writing block-compressed"
           " index data");
    return -1;
  }
  return 1;
}

#define newBlockEncIdxSeqLoopErr()                      \
  destructAppendState(&aState);                         \
  deletePartialSymSums(buck);                           \
  deletePartialSymSums(buckLast);                       \
  gt_free(compositionPreAlloc);                         \
  gt_free(permCompBSPreAlloc);                          \
  gt_free(block);                                       \
  break

EISeq *
gt_newGenBlockEncIdxSeq(unsigned long totalLen, const char *projectName,
                        MRAEnc *alphabet, const struct seqStats *stats,
                        SeqDataReader BWTGenerator,
                        const struct seqBaseParam *params,
                        size_t numExtHeaders, const uint16_t *headerIDs,
                        const uint32_t *extHeaderSizes,
                        headerWriteFunc *extHeaderCallbacks,
                        void **headerCBData,
                        bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                        varExtBitsEstimator biVarBits, void *cbState,
                        GtError *err)
{
  struct blockCompositionSeq *newSeqIdx = NULL;
  AlphabetRangeSize blockMapAlphabetSize, totalAlphabetSize;
  size_t regionsEstimate=totalLen / 100;
  MRAEnc *blockMapAlphabet = NULL, *rangeMapAlphabet = NULL;
  BitOffset bitsPerComposition, bitsPerPermutation;
  unsigned compositionIdxBits, callBackDataOffsetBits,
    blockSize = params->encParams.blockEnc.blockSize,
    bucketBlocks = params->encParams.blockEnc.bucketBlocks;
  size_t bucketLen = (size_t)bucketBlocks * blockSize;
  int *modesCopy = NULL;
  struct varBitsEstimate biMaxExtSize;
  enum rangeStoreMode modes[] = { BLOCK_COMPOSITION_INCLUDE,
                                  REGIONS_LIST };
  gt_assert(projectName);
  gt_assert(params->encType == BWT_ON_BLOCK_ENC);
  gt_assert(blockSize > 0);
  gt_assert((biFunc && biVarBits) || (biFunc == NULL && biVarBits == NULL));
  gt_error_check(err);

  newSeqIdx = gt_calloc(sizeof (struct blockCompositionSeq), 1);
  newSeqIdx->bucketBlocks = bucketBlocks;
  newSeqIdx->bitsPerUlong = requiredUlongBits((newSeqIdx->baseClass.seqLen
                                                 = totalLen) - 1);
  newSeqIdx->baseClass.alphabet = alphabet;
  {
    size_t range, numAlphabetRanges = newSeqIdx->numModes =
      MRAEncGetNumRanges(alphabet);
    totalAlphabetSize = gt_MRAEncGetSize(alphabet);
    blockMapAlphabetSize = 0;
    newSeqIdx->modes = modesCopy = gt_malloc(sizeof (int) * numAlphabetRanges);
    for (range = 0; range < numAlphabetRanges; ++range)
    {
      modesCopy[range] = modes[range];
      switch (modes[range])
      {
      case BLOCK_COMPOSITION_INCLUDE:
        blockMapAlphabetSize += MRAEncGetRangeSize(alphabet, range);
        break;
      case DIRECT_SYM_ENCODE:
        /*< OUTLOOK: insert proper code to process ranges
         * to improve orthogonality */
        break;
      case REGIONS_LIST:
        /*< OUTLOOK: insert proper code to process ranges
         * to improve orthogonality */
        break;
      default:
        gt_log_log("Invalid encoding request.\n");
        newBlockEncIdxSeqErrRet();
        break;
      }
    }
    newSeqIdx->blockMapAlphabetSize = blockMapAlphabetSize;
    newSeqIdx->blockMapAlphabet = blockMapAlphabet =
      gt_MRAEncSecondaryMapping(alphabet, BLOCK_COMPOSITION_INCLUDE, modesCopy,
                             newSeqIdx->blockEncFallback = 0);
    newSeqIdx->rangeMapAlphabet = rangeMapAlphabet =
      gt_MRAEncSecondaryMapping(alphabet, REGIONS_LIST, modesCopy,
                             newSeqIdx->rangeEncFallback = 0);
    gt_assert(gt_MRAEncGetSize(blockMapAlphabet) == blockMapAlphabetSize);
    gt_assert(gt_MRAEncGetSize(rangeMapAlphabet)
           == totalAlphabetSize - blockMapAlphabetSize);
  }
  newSeqIdx->partialSymSumBits
    = gt_malloc(sizeof (newSeqIdx->partialSymSumBits[0])
                * blockMapAlphabetSize * 2);
  newSeqIdx->partialSymSumBitsSums
    = newSeqIdx->partialSymSumBits + blockMapAlphabetSize;
  if (stats)
  {
    unsigned long *symCounts;
    symCounts = gt_malloc(sizeof (symCounts[0]) * blockMapAlphabetSize);
    switch (stats->sourceAlphaType)
    {
    case sourceUInt8:
      memset(symCounts, 0,
             sizeof (symCounts[0]) * blockMapAlphabetSize);
      {
        Symbol eSym, bSym;
        unsigned i;
        for (i = 0; i <= UINT8_MAX; ++i)
          if (gt_MRAEncSymbolIsInSelectedRanges(
                alphabet, eSym = MRAEncMapSymbol(alphabet, i),
                BLOCK_COMPOSITION_INCLUDE, modesCopy)
              && ((bSym = MRAEncMapSymbol(blockMapAlphabet, eSym))
                  < blockMapAlphabetSize))
            symCounts[bSym]
              += stats->symbolDistributionTable[i];
#ifdef EIS_DEBUG
        for (i = 0; i < blockMapAlphabetSize; ++i)
        {
          gt_log_log("symCount[%"PRIuSymbol"]=%lu\n", (Symbol) i,
                  stats->symbolDistributionTable[i]);
        }
#endif /* EIS_DEBUG */
        if (blockMapAlphabetSize)
        {
          newSeqIdx->partialSymSumBitsSums[0] = 0;
          newSeqIdx->partialSymSumBits[0] = requiredUlongBits(symCounts[0]);
          for (i = 1; i < blockMapAlphabetSize; ++i)
          {
            newSeqIdx->partialSymSumBitsSums[i]
              = newSeqIdx->partialSymSumBitsSums[i - 1]
              + newSeqIdx->partialSymSumBits[i - 1];
            newSeqIdx->partialSymSumBits[i]
              = requiredUlongBits(symCounts[i]);
          }
#ifdef EIS_DEBUG
          for (i = 0; i < blockMapAlphabetSize; ++i)
          {
            gt_log_log("bitsPerSymSum[%"PRIuSymbol"]=%u\n", (Symbol)i,
                    newSeqIdx->partialSymSumBits[i]);
          }
#endif  /* EIS_DEBUG */
          newSeqIdx->symSumBits
            = newSeqIdx->partialSymSumBitsSums[blockMapAlphabetSize - 1]
            + newSeqIdx->partialSymSumBits[blockMapAlphabetSize - 1];
#ifdef EIS_DEBUG
          gt_log_log("symSumBits total: %u\n", newSeqIdx->symSumBits);
#endif  /* EIS_DEBUG */
        }
      }
      /* count special characters to estimate number of regions required */
      {
        Symbol eSym, rSym;
        unsigned long regionSymCount = 0;
        AlphabetRangeSize rangeMapAlphabetSize
          = gt_MRAEncGetSize(rangeMapAlphabet);
        unsigned i;
        for (i = 0; i <= UINT8_MAX; ++i)
          if (gt_MRAEncSymbolIsInSelectedRanges(
               alphabet, eSym = MRAEncMapSymbol(alphabet, i),
               REGIONS_LIST, modesCopy)
             && ((rSym = MRAEncMapSymbol(rangeMapAlphabet, eSym))
                 < rangeMapAlphabetSize))
            regionSymCount += stats->symbolDistributionTable[i];
        regionsEstimate = regionSymCount/20;
#ifdef EIS_DEBUG
        gt_log_log("Expected %lu symbols to encode in regions.\n",
                    regionSymCount);
#endif
      }
      break;
    default:
      symSumBitsDefaultSetup(newSeqIdx);
    }
    gt_free(symCounts);
  }
  else
  {
    symSumBitsDefaultSetup(newSeqIdx);
  }
  {
    int regionFeatures = SRL_NO_FEATURES;
    if (params->EISFeatureSet & EIS_FEATURE_REGION_SUMS)
      regionFeatures |= SRL_PARTIAL_SYMBOL_SUMS;
    newSeqIdx->rangeEncs = gt_newSeqRangeList(regionsEstimate, rangeMapAlphabet,
                                           regionFeatures);
  }
  newSeqIdx->baseClass.classInfo = &blockCompositionSeqClass;
  if (!gt_initCompositionList(&newSeqIdx->compositionTable, blockSize,
                           blockMapAlphabetSize))
  {
    gt_error_set(err, "Insufficient memory for selected block size %u and "
              "alphabet size %u, try smaller block size?\n", blockSize,
              blockMapAlphabetSize);
    newBlockEncIdxSeqErrRet();
  }
  bitsPerComposition = newSeqIdx->compositionTable.bitsPerCount
    * blockMapAlphabetSize;
  compositionIdxBits = newSeqIdx->compositionTable.compositionIdxBits;
  bitsPerPermutation = newSeqIdx->compositionTable.bitsPerSymbol * blockSize;
  newSeqIdx->blockSize = blockSize;
  newSeqIdx->cwExtBitsPerBucket = cwExtBitsPerPos * bucketLen;
  newSeqIdx->callBackDataOffsetBits = callBackDataOffsetBits
    = biFunc ? gt_requiredUInt64Bits(newSeqIdx->compositionTable.maxPermIdxBits
                                  * bucketBlocks) : 0;
  {
    BitOffset maxVarBitsTotal =
      vwBits(totalLen, blockSize, bucketBlocks,
             newSeqIdx->compositionTable.maxPermIdxBits,
             biVarBits, cbState, &biMaxExtSize);
    newSeqIdx->bitsPerVarDiskOffset = gt_requiredUInt64Bits(maxVarBitsTotal);
  }
  newSeqIdx->maxVarExtBitsPerBucket = biMaxExtSize.maxBitsPerBucket;
  {
    size_t headerLen = blockEncIdxSeqHeaderLength(newSeqIdx, numExtHeaders,
                                                  extHeaderSizes);
    if (!openOnDiskData(projectName, &newSeqIdx->externalData, "wb+",err))
      newBlockEncIdxSeqErrRet();
    initOnDiskBlockCompIdx(&newSeqIdx->externalData,
                           headerLen, cwSize(newSeqIdx));
  }
  /* At this point everything should be ready to receive the actual sequence
   * information, steps: */
  {
    int hadGtError = 0;
    do
    {
      {
        Symbol *block;
        unsigned *compositionPreAlloc;
        BitString permCompBSPreAlloc;
        partialSymSum *buck, *buckLast;
        block = gt_malloc(sizeof (Symbol) * blockSize);
        compositionPreAlloc = gt_malloc(sizeof (compositionPreAlloc[0])
                                        * blockMapAlphabetSize);
        permCompBSPreAlloc =
          gt_malloc(bitElemsAllocSize(bitsPerComposition + bitsPerPermutation)
                    * sizeof (BitElem));
        buck = newPartialSymSums(totalAlphabetSize);
        buckLast = newPartialSymSums(totalAlphabetSize);
        /* 2. read block sized chunks from bwttab and suffix array */
        {
          unsigned long numFullBlocks = totalLen / blockSize, blockNum,
            lastUpdatePos = 0;
          /* pos == totalLen - symbolsLeft */
          struct appendState aState;
          initAppendState(&aState, newSeqIdx);
          blockNum = 0;
          while (blockNum < numFullBlocks)
          {
            size_t readResult;
            /* 3. for each chunk: */
            readResult = SDRRead(BWTGenerator, block, blockSize);
            if (readResult != blockSize)
            {
              hadGtError = 1;
              perror("error condition while reading index data");
              break;
            }
            gt_MRAEncSymbolsTransform(alphabet, block, blockSize);
            addBlock2OutputBuffer(newSeqIdx, buck, blockNum,
                                  block, blockSize,
                                  alphabet, modesCopy,
                                  blockMapAlphabet, blockMapAlphabetSize,
                                  permCompBSPreAlloc, compositionPreAlloc,
                                  compositionIdxBits, &aState);
            /* update on-disk structure */
            if (!((++blockNum) % bucketBlocks))
            {
              unsigned long pos = blockNum * blockSize;
              if (writeOutputBuffer(newSeqIdx, &aState, biFunc, lastUpdatePos,
                                    bucketLen, callBackDataOffsetBits, cbState,
                                    buckLast) < 0)
              {
                hadGtError = 1;
                break;
              }
              /* update retained data */
              copyPartialSymSums(totalAlphabetSize, buckLast, buck);
              lastUpdatePos = pos;
            }
          }
          /* handle last chunk */
          if (!hadGtError)
          {
            unsigned long symbolsLeft = totalLen % blockSize;
            if (symbolsLeft)
            {
              size_t readResult;
              readResult = SDRRead(BWTGenerator, block, symbolsLeft);
              if (readResult < symbolsLeft)
              {
                hadGtError = 1;
                perror("error condition while reading index data");
                newBlockEncIdxSeqLoopErr();
              }
              else
              {
                gt_MRAEncSymbolsTransform(alphabet, block, symbolsLeft);
                memset(block + symbolsLeft, 0,
                       sizeof (Symbol) * (blockSize - symbolsLeft));
                addBlock2OutputBuffer(newSeqIdx, buck, blockNum,
                                      block, blockSize,
                                      alphabet, modesCopy,
                                      blockMapAlphabet, blockMapAlphabetSize,
                                      permCompBSPreAlloc, compositionPreAlloc,
                                      compositionIdxBits, &aState);
              }
            }
            if (lastUpdatePos <= totalLen)
            {
              /* one bucket still unfinished */
              if (writeOutputBuffer(newSeqIdx, &aState, biFunc, lastUpdatePos,
                                    totalLen - lastUpdatePos,
                                    callBackDataOffsetBits, cbState,
                                    buckLast) < 0)
              {
                hadGtError = 1;
                break;
              }
            }
            if (!finalizeIdxOutput(newSeqIdx, &aState))
            {
              hadGtError = 1;
              perror("error condition while writing block-compressed"
                     " index data");
              newBlockEncIdxSeqLoopErr();
            }
            if (!writeIdxHeader(newSeqIdx, numExtHeaders, headerIDs,
                                extHeaderSizes, extHeaderCallbacks,
                                headerCBData, err))
            {
              hadGtError = 1;
              perror("error condition while writing block-compressed"
                     " index header");
              newBlockEncIdxSeqLoopErr();
            }
            if (fflush(newSeqIdx->externalData.idxFP))
            {
              hadGtError = 1;
              perror("error condition while writing block-compressed"
                     " index header");
              newBlockEncIdxSeqLoopErr();
            }
            tryMMapOfIndex(&newSeqIdx->externalData);
          }
          if (hadGtError)
          {
            newBlockEncIdxSeqLoopErr();
          }
          /* 4. dealloc resources no longer required */
          destructAppendState(&aState);
          deletePartialSymSums(buck);
          deletePartialSymSums(buckLast);
        }
        /* 4. dealloc resources no longer required */
        gt_free(compositionPreAlloc);
        gt_free(permCompBSPreAlloc);
        gt_free(block);
      }
    } while (0);
    /* close bwttab and suffix array */
    if (hadGtError)
      newBlockEncIdxSeqErrRet();
  }
  return &(newSeqIdx->baseClass);
}

static void
deleteBlockEncIdxSeq(struct encIdxSeq *seq)
{
  struct blockCompositionSeq *bseq;
  gt_assert(seq && seq->classInfo == &blockCompositionSeqClass);
  bseq = encIdxSeq2blockCompositionSeq(seq);
  gt_free(bseq->extHeaderPos);
  gt_free(bseq->partialSymSumBits);
  destructOnDiskBlockCompIdx(&bseq->externalData);
  gt_destructCompositionList(&bseq->compositionTable);
  gt_MRAEncDelete(bseq->baseClass.alphabet);
  gt_MRAEncDelete(bseq->rangeMapAlphabet);
  gt_MRAEncDelete(bseq->blockMapAlphabet);
  gt_deleteSeqRangeList(bseq->rangeEncs);
  gt_free(bseq->modes);
  gt_free(bseq);
}

#define USE_SBLOCK_CACHE

static inline int
seqIdxUsesMMap(const struct blockCompositionSeq *seqIdx)
{
  return seqIdx->externalData.idxMMap != NULL;
}

/**
 * Since the sequence represented in the form of blocks is incomplete
 * without the information in corresponding regions, a superBlock
 * struct stores only information for the strings of composition and
 * permutation indices. The cwData string is prepended by partial
 * symbol sums and offsets in the global variable width string. Also
 * appended to the indices is extra information inserted by the
 * callback functions on index creation.
 */
struct superBlock
{
  unsigned varDataMemBase, cwIdxMemBase;
  BitString varData, cwData;
};

static inline size_t
superBlockCWMaxReadSize(const struct blockCompositionSeq *seqIdx);

static inline size_t
superBlockVarMaxReadSize(const struct blockCompositionSeq *seqIdx);

static inline BitOffset
superBlockCWBits(const struct blockCompositionSeq *seqIdx);

static inline size_t
superBlockMemSize(const struct blockCompositionSeq *seqIdx)
{
  if (seqIdxUsesMMap(seqIdx))
  {
    return sizeof (struct superBlock);
  }
  else
  {
    size_t offset;
    offset = offsetAlign(sizeof (struct superBlock), sizeof (BitElem));
    offset = offsetAlign(offset + superBlockCWMaxReadSize(seqIdx),
                         sizeof (BitElem));
    offset += superBlockVarMaxReadSize(seqIdx);
    return offsetAlign(offset, MAX_ALIGN_REQUIREMENT);
  }
}

static inline void
initEmptySuperBlock(struct superBlock *sBlock,
                    const struct blockCompositionSeq *seqIdx)
{
  if (!seqIdxUsesMMap(seqIdx))
  {
    size_t offset;
    sBlock->cwData = (BitString)
      ((char *)sBlock + (offset = offsetAlign(sizeof (*sBlock),
                                              sizeof (BitElem))));
    sBlock->varData = (BitString)
      ((char *)sBlock + (offset = offsetAlign(offset
                                              + superBlockCWMaxReadSize(seqIdx),
                                              sizeof (BitElem))));
  }
}

static struct superBlock *
newEmptySuperBlock(const struct blockCompositionSeq *seqIdx)
{
  struct superBlock *sBlock;
  sBlock = gt_malloc(superBlockMemSize(seqIdx));
  initEmptySuperBlock(sBlock, seqIdx);
  return sBlock;
}

static void
deleteSuperBlock(struct superBlock *sBlock)
{
  gt_free(sBlock);
}

static inline void
symSumBitsDefaultSetup(struct blockCompositionSeq *seqIdx)
{
  unsigned i;
  AlphabetRangeSize blockMapAlphabetSize = seqIdx->blockMapAlphabetSize;
  seqIdx->partialSymSumBitsSums[0] = 0;
  seqIdx->partialSymSumBits[0] = seqIdx->bitsPerUlong;
  for (i = 1; i < blockMapAlphabetSize; ++i)
    seqIdx->partialSymSumBitsSums[i] = seqIdx->partialSymSumBitsSums[i - 1]
      + (seqIdx->partialSymSumBits[i] = seqIdx->bitsPerUlong);
  seqIdx->symSumBits = blockMapAlphabetSize * seqIdx->bitsPerUlong;
#ifdef EIS_DEBUG
  gt_log_log("symSumBits=%u, blockMapAlphabetSize=%u\n",
          seqIdx->symSumBits, seqIdx->blockMapAlphabetSize);
#endif
  gt_assert(seqIdx->partialSymSumBitsSums[i - 1] + seqIdx->bitsPerUlong
         == seqIdx->symSumBits);
}

static inline unsigned long
sBlockGetPartialSymSum(struct superBlock *sBlock, Symbol sym,
                       const struct blockCompositionSeq *seqIdx)
{
  return gt_bsGetUlong(sBlock->cwData, seqIdx->partialSymSumBitsSums[sym]
                     + sBlock->cwIdxMemBase, seqIdx->partialSymSumBits[sym]);
}

static inline void
sBlockGetPartialSymSums(struct superBlock *sBlock,
                        const struct blockCompositionSeq *seqIdx,
                        unsigned long *sums)
{
  gt_bsGetNonUniformUlongArray(
    sBlock->cwData, sBlock->cwIdxMemBase, seqIdx->blockMapAlphabetSize,
    seqIdx->symSumBits, seqIdx->partialSymSumBits,
#ifdef _LP64
                             (uint64_t*) sums);
#else
                             (uint32_t*) sums);
#endif
}

static inline BitOffset
cwPreVarIdxBits(const struct blockCompositionSeq *seqIdx)
{
  return seqIdx->symSumBits;
}

static inline BitOffset
sBlockGetVarIdxOffset(const struct superBlock *sBlock,
                      const struct blockCompositionSeq *seqIdx)
{
  BitOffset offset = cwPreVarIdxBits(seqIdx) + sBlock->cwIdxMemBase;
  return gt_bsGetUInt64(sBlock->cwData, offset, seqIdx->bitsPerVarDiskOffset);
}

static inline BitOffset
cwPreCBOffsetBits(const struct blockCompositionSeq *seqIdx)
{
  BitOffset offset = cwPreVarIdxBits(seqIdx) + seqIdx->bitsPerVarDiskOffset;
  return offset;
}

static inline BitOffset
cwPreCompIdxBits(const struct blockCompositionSeq *seqIdx)
{
  BitOffset offset = cwPreCBOffsetBits(seqIdx) + seqIdx->callBackDataOffsetBits;
  return offset;
}

static inline BitOffset
sBlockGetCompIdxOffset(const struct superBlock *sBlock,
                       const struct blockCompositionSeq *seqIdx,
                       unsigned compIdxNum)
{
  BitOffset offset = sBlock->cwIdxMemBase + cwPreCompIdxBits(seqIdx)
    + compIdxNum * seqIdx->compositionTable.compositionIdxBits;
  return offset;
}

static inline BitOffset
cwPreCWExtBits(const struct blockCompositionSeq *seqIdx)
{
  BitOffset offset = cwPreCompIdxBits(seqIdx)
    + seqIdx->bucketBlocks * seqIdx->compositionTable.compositionIdxBits;
  return offset;
}

static inline BitOffset
sBlockCWExtBitsOffset(const struct superBlock *sBlock,
                      const struct blockCompositionSeq *seqIdx)
{
  BitOffset offset = cwPreCWExtBits(seqIdx) + sBlock->cwIdxMemBase;
  return offset;
}

static inline BitOffset
sBlockGetcbOffsetOffset(const struct superBlock *sBlock,
                        const struct blockCompositionSeq *seqIdx)
{
  BitOffset offset = cwPreCBOffsetBits(seqIdx) + sBlock->cwIdxMemBase;
  return offset;
}

static inline BitOffset
sBlockGetcbOffset(const struct superBlock *sBlock,
                  const struct blockCompositionSeq *seqIdx)
{
  BitOffset offset = sBlockGetcbOffsetOffset(sBlock, seqIdx);
  return gt_bsGetUInt64(sBlock->cwData, offset, seqIdx->callBackDataOffsetBits);
}

static inline PermCompIndex
sBlockGetCompIdx(const struct superBlock *sBlock, unsigned compIdxNum,
                 const struct blockCompositionSeq *seqIdx)
{
  BitOffset offset = sBlockGetCompIdxOffset(sBlock, seqIdx, compIdxNum);
  unsigned bitsPerCompositionIdx = seqIdx->compositionTable.compositionIdxBits;
  return gt_bsGetPermCompIndex(sBlock->cwData, offset, bitsPerCompositionIdx);
}

static inline unsigned long
blockNumFromPos(const struct blockCompositionSeq *seqIdx, unsigned long pos)
{
  return pos / seqIdx->blockSize;
}

static inline unsigned long
bucketNumFromPos(const struct blockCompositionSeq *seqIdx, unsigned long pos)
{
  return pos / (seqIdx->bucketBlocks * seqIdx->blockSize);
}

static inline unsigned long
bucketBasePos(const struct blockCompositionSeq *seqIdx, unsigned long bucketNum)
{
  return bucketNum * seqIdx->bucketBlocks * seqIdx->blockSize;
}

static inline unsigned long
bucketNumFromBlockNum(struct blockCompositionSeq *seqIdx,
                      unsigned long blockNum)
{
  return blockNum / seqIdx->bucketBlocks;
}

#define fetchSuperBlockErrRet()                    \
  do {                                             \
    if (!sBlockPreAlloc) deleteSuperBlock(retval); \
    return NULL;                                   \
  } while (0)

static struct superBlock *
fetchSuperBlock(const struct blockCompositionSeq *seqIdx,
                unsigned long bucketNum, struct superBlock *sBlockPreAlloc)
{
  struct superBlock *retval = NULL;
  gt_assert(seqIdx);
  gt_assert(bucketNum * seqIdx->bucketBlocks * seqIdx->blockSize
         <= seqIdx->baseClass.seqLen);
  if (sBlockPreAlloc)
    retval = sBlockPreAlloc;
  else
    retval = newEmptySuperBlock(seqIdx);
  if (seqIdxUsesMMap(seqIdx))
  {
    BitOffset bucketOffset = bucketNum * superBlockCWBits(seqIdx);
    BitOffset varDataOffset;
    retval->cwData = (BitString)(seqIdx->externalData.idxMMap
      + bucketOffset / bitElemBits * sizeof (BitElem));
    retval->cwIdxMemBase = bucketOffset%bitElemBits;

    varDataOffset = sBlockGetVarIdxOffset(retval, seqIdx);
    retval->varData = (BitString)(seqIdx->externalData.idxMMap
      + seqIdx->externalData.varDataPos - seqIdx->externalData.cwDataPos
      + varDataOffset/bitElemBits * sizeof (BitElem));
    retval->varDataMemBase = varDataOffset%bitElemBits;
  }
  else
  {
    FILE *idxFP;
    GT_UNUSED int ret;
    size_t superBlockCWDiskSize = superBlockCWMaxReadSize(seqIdx);
    BitOffset bucketOffset = bucketNum * superBlockCWBits(seqIdx);
    BitOffset varDataOffset;
    idxFP = seqIdx->externalData.idxFP;
    if (fseeko(idxFP, seqIdx->externalData.cwDataPos
              + bucketOffset / bitElemBits * sizeof (BitElem), SEEK_SET))
      fetchSuperBlockErrRet();
    if (fread(retval->cwData, 1, superBlockCWDiskSize, idxFP)
       != superBlockCWDiskSize)
      fetchSuperBlockErrRet();
    retval->cwIdxMemBase = bucketOffset%bitElemBits;
    varDataOffset = sBlockGetVarIdxOffset(retval, seqIdx);
    if (fseeko(idxFP, seqIdx->externalData.varDataPos
              + varDataOffset/bitElemBits * sizeof (BitElem), SEEK_SET))
      fetchSuperBlockErrRet();
    retval->varDataMemBase = varDataOffset%bitElemBits;
    ret = fread(retval->varData, sizeof (BitElem),
                superBlockVarMaxReadSize(seqIdx),
                idxFP);
    if (ferror(idxFP))
      fetchSuperBlockErrRet();
  }
  return retval;
}

static unsigned long
blockCompSeqSelect(GT_UNUSED struct encIdxSeq *seq, GT_UNUSED Symbol sym,
                   GT_UNUSED unsigned long count, GT_UNUSED union EISHint *hint)
{
  /* FIXME: implementation pending */
  abort();
  return 0;
}

/*
 * routines for management of super-Block-Cache, this does currently
 * use a simple direct-mapped caching
 */

static inline size_t
pos2CachePos(struct seqCache *sCache, unsigned long pos)
{
  return pos % sCache->numEntries;
}

static void
initSuperBlockSeqCache(struct seqCache *sBlockCache,
                       const struct blockCompositionSeq *seqIdx,
                       size_t numEntries)
{
  unsigned bucketBlocks, GT_UNUSED bucketLen, blockSize;
  size_t superBlockSize;

  gt_assert(seqIdx && sBlockCache);
  blockSize = seqIdx->blockSize;
  bucketLen = (bucketBlocks = seqIdx->bucketBlocks) * blockSize;
  superBlockSize = superBlockMemSize(seqIdx);
  sBlockCache->numEntries = numEntries;
  {
    void *temp = gt_malloc((sizeof (unsigned long) + superBlockSize
                           + sizeof (void *)) * numEntries);
    sBlockCache->cachedPos = temp;
    sBlockCache->entriesPtr = (void **)((char *)temp
                                        + sizeof (unsigned long) * numEntries);
    sBlockCache->entries =
                      (char *)temp + (sizeof (unsigned long) + sizeof (void *))
                         * numEntries;
  }
  {
    size_t i;
    for (i = 0; i < numEntries; ++i)
    {
      sBlockCache->entriesPtr[i] = (char *)sBlockCache->entries
        + superBlockSize * i;
      initEmptySuperBlock(sBlockCache->entriesPtr[i], seqIdx);
      sBlockCache->cachedPos[i] = -1;
    }
  }
}

static void
destructSuperBlockSeqCache(struct seqCache *sBlockCache)
{
  gt_free(sBlockCache->cachedPos);
}

static inline int
inSeqCache(struct seqCache *sCache, unsigned long pos)
{
  return sCache->cachedPos[pos2CachePos(sCache, pos)] == pos;
}

#ifdef USE_SBLOCK_CACHE
static struct superBlock *
cacheFetchSuperBlock(const struct blockCompositionSeq *seqIdx,
                     unsigned long superBlockNum, struct seqCache *sBlockCache)
{
  size_t cachePos = pos2CachePos(sBlockCache, superBlockNum);
  if (inSeqCache(sBlockCache, superBlockNum))
    return (struct superBlock *)sBlockCache->entriesPtr[cachePos];
  else
  {
    struct superBlock *sb =
      (struct superBlock *)sBlockCache->entriesPtr[cachePos];
    return fetchSuperBlock(seqIdx, superBlockNum, sb);
  }
}
#endif /* USE_SBLOCK_CACHE */

#define walkCompIndices(seqIdx, sBlock, numBlocks, cwOffset,              \
                        codeForCompIndex, varOffset)                      \
  do {                                                                    \
    unsigned blocksLeft = (numBlocks),                                    \
      bitsPerCompositionIdx =                                             \
      (seqIdx)->compositionTable.compositionIdxBits;                      \
    while (blocksLeft)                                                    \
    {                                                                     \
      PermCompIndex compIndex;                                            \
      compIndex = gt_bsGetPermCompIndex((sBlock)->cwData, cwIdxMemOffset, \
                                     bitsPerCompositionIdx);              \
      codeForCompIndex;                                                   \
      (varOffset) +=                                                      \
        (seqIdx)->compositionTable.permutations[compIndex].permIdxBits;   \
      (cwOffset) += bitsPerCompositionIdx;                                \
      --blocksLeft;                                                       \
    }                                                                     \
  } while (0)

#define walkCompIndicesPrefix(seqIdx, sBlock, blockNum, cwOffset,       \
                              codeForCompIndex, varOffset)              \
  do {                                                                  \
    cwOffset = sBlockGetCompIdxOffset(sBlock, seqIdx, 0);               \
    varOffset = sBlock->varDataMemBase;                                 \
    walkCompIndices(seqIdx, sBlock, blockNum, cwOffset,                 \
                    codeForCompIndex, varOffset);                       \
  } while (0)

static inline void
unpackBlock(const struct blockCompositionSeq *seqIdx,
            const struct superBlock *sBlock,
            BitOffset cwOffset, BitOffset varOffset, Symbol *block,
            unsigned sublen)
{
  unsigned varIdxBits, bitsPerCompositionIdx;
  PermCompIndex compIndex, permIndex;
  bitsPerCompositionIdx = seqIdx->compositionTable.compositionIdxBits;
  compIndex = gt_bsGetPermCompIndex(sBlock->cwData, cwOffset,
                                 bitsPerCompositionIdx);
  varIdxBits = seqIdx->compositionTable.permutations[compIndex].permIdxBits;
  permIndex = gt_bsGetPermCompIndex(sBlock->varData, varOffset, varIdxBits);
  indexPair2block(&seqIdx->compositionTable, seqIdx->blockSize,
                  compIndex, permIndex, block, sublen);
}

/*
 * regular, user-accessible query functions
 */
static Symbol *
blockCompSeqGetBlock(struct blockCompositionSeq *seqIdx, unsigned long blockNum,
                     struct blockEncIdxSeqHint *hint, int queryRangeEnc,
                     struct superBlock *sBlockPreFetch,
                     Symbol *blockPA)
{
  struct superBlock *sBlock;
  BitOffset varDataMemOffset, cwIdxMemOffset;
  GT_UNUSED unsigned long relBlockNum;
  unsigned blockSize;
  Symbol *block;
  gt_assert(seqIdx);
  blockSize = seqIdx->blockSize;
  if (blockNum * blockSize >= EISLength(&seqIdx->baseClass))
    return NULL;
  if (sBlockPreFetch)
    sBlock = sBlockPreFetch;
  else
  {
    unsigned long bucketNum = bucketNumFromBlockNum(seqIdx, blockNum);
#ifdef USE_SBLOCK_CACHE
    sBlock = cacheFetchSuperBlock(seqIdx, bucketNum,
                                  &hint->sBlockCache);
#else
    sBlock = fetchSuperBlock(seqIdx, bucketNum, NULL);
#endif
  }
  relBlockNum = blockNum % seqIdx->bucketBlocks;
  if (blockPA)
    block = blockPA;
  else
    block = gt_calloc(sizeof (Symbol), blockSize);
  walkCompIndicesPrefix(seqIdx, sBlock, blockNum % seqIdx->bucketBlocks,
                        cwIdxMemOffset, , varDataMemOffset);
  unpackBlock(seqIdx, sBlock, cwIdxMemOffset, varDataMemOffset, block,
              blockSize);
  if (queryRangeEnc)
    gt_SRLApplyRangesToSubString(seqIdx->rangeEncs,
                              block, blockNum * blockSize, blockSize,
                              blockNum * blockSize, &hint->rangeHint);
#ifndef USE_SBLOCK_CACHE
  if (!sBlockPreFetch)
    deleteSuperBlock(sBlock);
#endif
  return block;
}

static inline unsigned long
adjustPosRankForBlock(struct blockCompositionSeq *seqIdx,
                      struct superBlock *sBlock, unsigned long pos, Symbol bSym,
                      unsigned blockSize, unsigned long preBlockRankCount,
                      BitOffset cwIdxMemOffset, BitOffset varDataMemOffset,
                      unsigned bitsPerCompositionIdx)
{
  unsigned long rankCount = preBlockRankCount;
  unsigned inBlockPos;
  if ((inBlockPos = pos % blockSize)
      && symCountFromComposition(
        &seqIdx->compositionTable, seqIdx->blockMapAlphabetSize,
        gt_bsGetPermCompIndex(sBlock->cwData, cwIdxMemOffset,
                           bitsPerCompositionIdx), bSym))
  {
    Symbol block[blockSize];
    unsigned i;
    unpackBlock(seqIdx, sBlock, cwIdxMemOffset, varDataMemOffset, block,
                inBlockPos);
    for (i = 0; i < inBlockPos; ++i)
    {
      if (block[i] == bSym)
        ++rankCount;
    }
  }
  return rankCount;
}

/* Note: pos is meant exclusively, i.e. returns 0
   for any query where pos==0 because that corresponds to the empty prefix */
static unsigned long
blockCompSeqRank(struct encIdxSeq *eSeqIdx, Symbol eSym, unsigned long pos,
                 union EISHint *hint)
{
  struct blockCompositionSeq *seqIdx;
  unsigned long rankCount;
  gt_assert(eSeqIdx && eSeqIdx->classInfo == &blockCompositionSeqClass);
  seqIdx = encIdxSeq2blockCompositionSeq(eSeqIdx);
  gt_assert(gt_MRAEncSymbolIsInSelectedRanges(seqIdx->baseClass.alphabet,
                                        eSym, BLOCK_COMPOSITION_INCLUDE,
                                        seqIdx->modes) >= 0);
  if (gt_MRAEncSymbolIsInSelectedRanges(seqIdx->baseClass.alphabet, eSym,
                                     BLOCK_COMPOSITION_INCLUDE, seqIdx->modes))
  {
    BitOffset varDataMemOffset, cwIdxMemOffset;
    struct superBlock *sBlock;
    Symbol bSym = MRAEncMapSymbol(seqIdx->blockMapAlphabet, eSym);
    unsigned long blockNum, bucketNum;
    unsigned blockSize = seqIdx->blockSize, bitsPerCompositionIdx
      = seqIdx->compositionTable.compositionIdxBits;
    bucketNum = bucketNumFromPos(seqIdx, pos);
#ifdef USE_SBLOCK_CACHE
    sBlock = cacheFetchSuperBlock(seqIdx, bucketNum,
                                  &hint->bcHint.sBlockCache);
#else
    sBlock = fetchSuperBlock(seqIdx, bucketNum, NULL);
#endif
    rankCount = sBlockGetPartialSymSum(sBlock, bSym, seqIdx);
    blockNum = blockNumFromPos(seqIdx, pos);
    walkCompIndicesPrefix(
      seqIdx, sBlock, blockNum % seqIdx->bucketBlocks, cwIdxMemOffset,
      rankCount += symCountFromComposition(
        &seqIdx->compositionTable, seqIdx->blockMapAlphabetSize, compIndex,
        bSym);,
      varDataMemOffset);
    rankCount = adjustPosRankForBlock(
      seqIdx, sBlock, pos, bSym, blockSize, rankCount, cwIdxMemOffset,
      varDataMemOffset, bitsPerCompositionIdx);
    if (bSym == seqIdx->blockEncFallback)
    {
      unsigned long base = bucketBasePos(seqIdx, bucketNum);
      rankCount -= gt_SRLAllSymbolsCountInSeqRegion(
        seqIdx->rangeEncs, base, pos, &hint->bcHint.rangeHint);
    }
#ifndef USE_SBLOCK_CACHE
    deleteSuperBlock(sBlock);
#endif
  }
  else
  {
    rankCount = gt_SRLSymbolCountInSeqRegion(seqIdx->rangeEncs, 0, pos, eSym,
                                          &hint->bcHint.rangeHint);
  }
  return rankCount;
}

/* Note: pos is meant exclusively, i.e. returns 0
   for any query where pos==0 because that corresponds to the empty prefix */
static GtUlongPair
blockCompSeqPosPairRank(struct encIdxSeq *eSeqIdx, Symbol eSym,
                        unsigned long posA, unsigned long posB,
                        union EISHint *hint)
{
  struct blockCompositionSeq *seqIdx;
  GtUlongPair rankCounts;
  unsigned long bucketNum;
  gt_assert(eSeqIdx && eSeqIdx->classInfo == &blockCompositionSeqClass);
  gt_assert(posA <= posB);
  seqIdx = encIdxSeq2blockCompositionSeq(eSeqIdx);
  gt_assert(gt_MRAEncSymbolIsInSelectedRanges(seqIdx->baseClass.alphabet,
                                        eSym, BLOCK_COMPOSITION_INCLUDE,
                                        seqIdx->modes) >= 0);
  /* Only when both positions are in same bucket, special treatment
   * makes sense. */
  {
    unsigned long bucketNumA, bucketNumB;
    bucketNumA = bucketNumFromPos(seqIdx, posA);
    bucketNumB = bucketNumFromPos(seqIdx, posB);
    if (bucketNumA != bucketNumB)
    {
      rankCounts.a = blockCompSeqRank(eSeqIdx, eSym, posA, hint);
      rankCounts.b = blockCompSeqRank(eSeqIdx, eSym, posB, hint);
      return rankCounts;
    }
    bucketNum = bucketNumA;
  }
  if (gt_MRAEncSymbolIsInSelectedRanges(seqIdx->baseClass.alphabet, eSym,
                                     BLOCK_COMPOSITION_INCLUDE, seqIdx->modes))
  {
    BitOffset varDataMemOffset, cwIdxMemOffset;
    struct superBlock *sBlock;
    unsigned long blockNumA = blockNumFromPos(seqIdx, posA),
      blockNumB = blockNumFromPos(seqIdx, posB);
    Symbol bSym = MRAEncMapSymbol(seqIdx->blockMapAlphabet, eSym);
    unsigned blockSize = seqIdx->blockSize, bitsPerCompositionIdx
      = seqIdx->compositionTable.compositionIdxBits,
      inBucketBlockNumA = blockNumA % seqIdx->bucketBlocks,
      inBucketBlockNumB = blockNumB % seqIdx->bucketBlocks;
#ifdef USE_SBLOCK_CACHE
    sBlock = cacheFetchSuperBlock(seqIdx, bucketNum,
                                  &hint->bcHint.sBlockCache);
#else
    sBlock = fetchSuperBlock(seqIdx, bucketNum, NULL);
#endif
    rankCounts.a = sBlockGetPartialSymSum(sBlock, bSym, seqIdx);
    walkCompIndicesPrefix(
      seqIdx, sBlock, inBucketBlockNumA, cwIdxMemOffset,
      rankCounts.a += symCountFromComposition(
        &seqIdx->compositionTable, seqIdx->blockMapAlphabetSize, compIndex,
        bSym),
      varDataMemOffset);
    rankCounts.b = rankCounts.a;
    rankCounts.a =
      adjustPosRankForBlock(seqIdx, sBlock, posA, bSym, blockSize,
                            rankCounts.a, cwIdxMemOffset, varDataMemOffset,
                            bitsPerCompositionIdx);
    walkCompIndices(
      seqIdx, sBlock, inBucketBlockNumB - inBucketBlockNumA, cwIdxMemOffset,
      rankCounts.b += symCountFromComposition(
        &seqIdx->compositionTable, seqIdx->blockMapAlphabetSize, compIndex,
        bSym),
      varDataMemOffset);
    rankCounts.b =
      adjustPosRankForBlock(seqIdx, sBlock, posB, bSym, blockSize,
                            rankCounts.b, cwIdxMemOffset, varDataMemOffset,
                            bitsPerCompositionIdx);
    if (bSym == seqIdx->blockEncFallback)
    {
      unsigned long base = bucketBasePos(seqIdx, bucketNum);
      rankCounts.a -= gt_SRLAllSymbolsCountInSeqRegion(
        seqIdx->rangeEncs, base, posA, &hint->bcHint.rangeHint);
      rankCounts.b -= gt_SRLAllSymbolsCountInSeqRegion(
        seqIdx->rangeEncs, base, posB, &hint->bcHint.rangeHint);
    }
#ifndef USE_SBLOCK_CACHE
    deleteSuperBlock(sBlock);
#endif
  }
  else
  {
    rankCounts.a = gt_SRLSymbolCountInSeqRegion(seqIdx->rangeEncs, 0, posA,
                                                eSym, &hint->bcHint.rangeHint);
    rankCounts.b = gt_SRLSymbolCountInSeqRegion(seqIdx->rangeEncs, 0, posA,
                                                eSym, &hint->bcHint.rangeHint);
  }
  return rankCounts;
}

static void
blockCompSeqExpose(struct encIdxSeq *eSeqIdx, unsigned long pos, int flags,
                   struct extBitsRetrieval *retval, union EISHint *hint)
{
  struct blockCompositionSeq *seqIdx;
  gt_assert(eSeqIdx && eSeqIdx->classInfo == &blockCompositionSeqClass);
  gt_assert(retval);
  seqIdx = encIdxSeq2blockCompositionSeq(eSeqIdx);
  {
    struct superBlock *sBlock;
    unsigned long bucketNum, end;
    bucketNum = bucketNumFromPos(seqIdx, pos);
    retval->start = bucketBasePos(seqIdx, bucketNum);
    end = bucketBasePos(seqIdx, bucketNum + 1);
    if (end >= seqIdx->baseClass.seqLen)
      end = seqIdx->baseClass.seqLen;
    retval->len = end - retval->start;
#ifdef USE_SBLOCK_CACHE
    sBlock = cacheFetchSuperBlock(seqIdx, bucketNum,
                                  &hint->bcHint.sBlockCache);
#else
    sBlock = fetchSuperBlock(seqIdx, bucketNum, NULL);
#endif
    retval->cwOffset = sBlockCWExtBitsOffset(sBlock, seqIdx);
    if (flags & EBRF_PERSISTENT_CWBITS)
    {
      if (!(retval->flags & EBRF_PERSISTENT_CWBITS))
      {
          retval->varPart = gt_malloc(superBlockCWMaxReadSize(seqIdx));
      }
      memcpy(retval->cwPart, sBlock->cwData,
             superBlockCWMaxReadSize(seqIdx));
    }
    else
    {
      if (retval->flags & EBRF_PERSISTENT_CWBITS)
        gt_free(retval->cwPart);
      retval->cwPart = sBlock->cwData;
    }
    if (EBRF_RETRIEVE_VARBITS)
    {
      retval->varOffset = sBlockGetcbOffset(sBlock, seqIdx)
        + sBlock->varDataMemBase;
      if (flags & EBRF_PERSISTENT_VARBITS)
      {
        if (!(retval->flags & EBRF_PERSISTENT_VARBITS))
        {
          retval->varPart = gt_malloc(superBlockVarMaxReadSize(seqIdx));
        }
        memcpy(retval->varPart, sBlock->varData,
               superBlockVarMaxReadSize(seqIdx));
      }
      else
      {
        if (retval->flags & EBRF_PERSISTENT_VARBITS)
          gt_free(retval->varPart);
        retval->varPart = sBlock->varData;
      }
    }
    else
    {
      if (retval->flags & EBRF_PERSISTENT_VARBITS)
        gt_free(retval->varPart);
      retval->varPart = NULL;
      retval->varOffset = 0;
    }
#ifndef USE_SBLOCK_CACHE
    deleteSuperBlock(sBlock);
#endif
    retval->flags = flags;
  }
}

static inline void
adjustRanksForBlock(struct blockCompositionSeq *seqIdx,
                    struct superBlock *sBlock, unsigned long pos,
                    unsigned blockSize, unsigned long rankCounts[],
                    BitOffset cwIdxMemOffset, BitOffset varDataMemOffset)
{
  unsigned inBlockPos = pos % blockSize;
  if (inBlockPos)
  {
    Symbol block[blockSize];
    unsigned i;
    unpackBlock(seqIdx, sBlock, cwIdxMemOffset, varDataMemOffset, block,
                inBlockPos);
    for (i = 0; i < inBlockPos; ++i)
      ++(rankCounts[block[i]]);
  }
}

static void
blockCompSeqRangeRank(struct encIdxSeq *eSeqIdx, AlphabetRangeID range,
                      unsigned long pos, unsigned long *rankCounts,
                      union EISHint *hint)
{
  struct blockCompositionSeq *seqIdx;
  gt_assert(eSeqIdx && eSeqIdx->classInfo == &blockCompositionSeqClass);
  seqIdx = encIdxSeq2blockCompositionSeq(eSeqIdx);
  gt_assert(range < MRAEncGetNumRanges(EISGetAlphabet(eSeqIdx)));
  switch (seqIdx->modes[range])
  {
  case BLOCK_COMPOSITION_INCLUDE:
    {
      BitOffset varDataMemOffset, cwIdxMemOffset;
      struct superBlock *sBlock;
      unsigned long blockNum, bucketNum;
      unsigned blockSize = seqIdx->blockSize;
      bucketNum = bucketNumFromPos(seqIdx, pos);
#ifdef USE_SBLOCK_CACHE
      sBlock = cacheFetchSuperBlock(seqIdx, bucketNum,
                                    &hint->bcHint.sBlockCache);
#else
      sBlock = fetchSuperBlock(seqIdx, bucketNum, NULL);
#endif
      {
        sBlockGetPartialSymSums(sBlock, seqIdx, rankCounts);
        blockNum = blockNumFromPos(seqIdx, pos);
        walkCompIndicesPrefix(
          seqIdx, sBlock, blockNum % seqIdx->bucketBlocks, cwIdxMemOffset,
          addSymCountsFromComposition(&seqIdx->compositionTable,
                                      seqIdx->blockMapAlphabetSize, compIndex,
                                      rankCounts);,
          varDataMemOffset);
        adjustRanksForBlock(seqIdx, sBlock, pos, blockSize, rankCounts,
                            cwIdxMemOffset, varDataMemOffset);
        {
          unsigned long base = bucketBasePos(seqIdx, bucketNum);
          rankCounts[seqIdx->blockEncFallback]
            -= gt_SRLAllSymbolsCountInSeqRegion(
              seqIdx->rangeEncs, base, pos, &hint->bcHint.rangeHint);
        }
      }
#ifndef USE_SBLOCK_CACHE
      deleteSuperBlock(sBlock);
#endif
    }
    break;
  case REGIONS_LIST:
    {
      AlphabetRangeSize sym,
        rangeEncNumSyms = gt_MRAEncGetSize(seqIdx->rangeMapAlphabet);
      for (sym = 0; sym < rangeEncNumSyms; ++sym)
        rankCounts[sym] = gt_SRLSymbolCountInSeqRegion(
          seqIdx->rangeEncs, 0, pos,
          MRAEncRevMapSymbol(seqIdx->rangeMapAlphabet, sym),
          &hint->bcHint.rangeHint);
    }
    break;
  }
}

static void
blockCompSeqPosPairRangeRank(struct encIdxSeq *eSeqIdx, AlphabetRangeID range,
                             unsigned long posA, unsigned long posB,
                             unsigned long *rankCounts, union EISHint *hint)
{
  struct blockCompositionSeq *seqIdx;
  gt_assert(eSeqIdx && eSeqIdx->classInfo == &blockCompositionSeqClass);
  seqIdx = encIdxSeq2blockCompositionSeq(eSeqIdx);
  gt_assert(range < MRAEncGetNumRanges(EISGetAlphabet(eSeqIdx)));
  switch (seqIdx->modes[range])
  {
  case BLOCK_COMPOSITION_INCLUDE:
    {
      BitOffset varDataMemOffset, cwIdxMemOffset;
      struct superBlock *sBlock;
      AlphabetRangeSize rsize = MRAEncGetRangeSize(eSeqIdx->alphabet, range);
      /* Only when both positions are in same bucket, special treatment
       * makes sense. */
      unsigned long bucketNum = bucketNumFromPos(seqIdx, posA);
      if (bucketNum != bucketNumFromPos(seqIdx, posB))
      {
        blockCompSeqRangeRank(eSeqIdx, range, posA, rankCounts, hint);
        blockCompSeqRangeRank(eSeqIdx, range, posB, rankCounts + rsize, hint);
        return;
      }
#ifdef USE_SBLOCK_CACHE
      sBlock = cacheFetchSuperBlock(seqIdx, bucketNum,
                                    &hint->bcHint.sBlockCache);
#else
      sBlock = fetchSuperBlock(seqIdx, bucketNum, NULL);
#endif
      {
        unsigned long blockNumA = blockNumFromPos(seqIdx, posA),
          blockNumB = blockNumFromPos(seqIdx, posB);
        unsigned blockSize = seqIdx->blockSize,
          inBucketBlockNumA = blockNumA % seqIdx->bucketBlocks,
          inBucketBlockNumB = blockNumB % seqIdx->bucketBlocks;
        sBlockGetPartialSymSums(sBlock, seqIdx, rankCounts);
        walkCompIndicesPrefix(
          seqIdx, sBlock, inBucketBlockNumA, cwIdxMemOffset,
          addSymCountsFromComposition(&seqIdx->compositionTable,
                                      seqIdx->blockMapAlphabetSize, compIndex,
                                      rankCounts);,
          varDataMemOffset);
        memcpy(rankCounts + rsize, rankCounts, rsize * sizeof (rankCounts[0]));
        adjustRanksForBlock(seqIdx, sBlock, posA, blockSize, rankCounts,
                            cwIdxMemOffset, varDataMemOffset);
        walkCompIndices(
          seqIdx, sBlock, inBucketBlockNumB - inBucketBlockNumA, cwIdxMemOffset,
          addSymCountsFromComposition(&seqIdx->compositionTable,
                                      seqIdx->blockMapAlphabetSize, compIndex,
                                      rankCounts + rsize);,
          varDataMemOffset);
        adjustRanksForBlock(seqIdx, sBlock, posB, blockSize,
                            rankCounts + rsize,
                            cwIdxMemOffset, varDataMemOffset);
        {
          unsigned long base = bucketBasePos(seqIdx, bucketNum);
          rankCounts[seqIdx->blockEncFallback]
            -= gt_SRLAllSymbolsCountInSeqRegion(
              seqIdx->rangeEncs, base, posA, &hint->bcHint.rangeHint);
          rankCounts[rsize + seqIdx->blockEncFallback]
            -= gt_SRLAllSymbolsCountInSeqRegion(
              seqIdx->rangeEncs, base, posB, &hint->bcHint.rangeHint);
        }
      }
#ifndef USE_SBLOCK_CACHE
      deleteSuperBlock(sBlock);
#endif
    }
    break;
  case REGIONS_LIST:
    {
      AlphabetRangeSize sym,
        rangeEncNumSyms = gt_MRAEncGetSize(seqIdx->rangeMapAlphabet);
      for (sym = 0; sym < rangeEncNumSyms; ++sym)
        rankCounts[sym] = gt_SRLSymbolCountInSeqRegion(
          seqIdx->rangeEncs, 0, posA,
          MRAEncRevMapSymbol(seqIdx->rangeMapAlphabet, sym),
          &hint->bcHint.rangeHint);
      for (sym = 0; sym < rangeEncNumSyms; ++sym)
        rankCounts[sym + rangeEncNumSyms]
          = gt_SRLSymbolCountInSeqRegion(
            seqIdx->rangeEncs, 0, posB,
            MRAEncRevMapSymbol(seqIdx->rangeMapAlphabet, sym),
            &hint->bcHint.rangeHint);
    }
    break;
  }
}

static Symbol
blockCompSeqGet(struct encIdxSeq *seq, unsigned long pos, union EISHint *hint)
{
  Symbol sym;
  struct blockCompositionSeq *seqIdx;
  unsigned blockSize;
  gt_assert(seq && seq->classInfo == &blockCompositionSeqClass);
  if (pos >= seq->seqLen)
    return ~(Symbol)0;
  seqIdx = encIdxSeq2blockCompositionSeq(seq);
  blockSize = seqIdx->blockSize;
  {
    Symbol block[blockSize];
    blockCompSeqGetBlock(seqIdx, pos/blockSize, &(hint->bcHint), 1, NULL,
                         block);
    sym = block[pos%blockSize];
  }
  return sym;
}

static inline partialSymSum *
newPartialSymSums(AlphabetRangeSize alphabetSize)
{
  return gt_calloc(alphabetSize, sizeof (unsigned long));
}

static inline void
deletePartialSymSums(partialSymSum *sums)
{
  gt_free(sums);
}

static inline void
addBlock2PartialSymSums(partialSymSum *sums, const Symbol *block,
                        unsigned blockSize)
{
  unsigned i;
  for (i = 0; i < blockSize; ++i)
    ++(sums[block[i]]);
}

static inline void
copyPartialSymSums(AlphabetRangeSize alphabetSize, partialSymSum *dest,
                   const partialSymSum *src)
{
  memcpy(dest, src, sizeof (dest[0]) * alphabetSize);
}

static inline BitOffset
superBlockCWBits(const struct blockCompositionSeq *seqIdx)
{
  return seqIdx->symSumBits + seqIdx->bitsPerVarDiskOffset
    + seqIdx->callBackDataOffsetBits
    + seqIdx->compositionTable.compositionIdxBits * seqIdx->bucketBlocks
    + seqIdx->cwExtBitsPerBucket;
}

static inline size_t
superBlockCWMaxReadSize(const struct blockCompositionSeq *seqIdx)
{
  return bitElemsAllocSize(superBlockCWBits(seqIdx) + bitElemBits - 1)
    * sizeof (BitElem);
}

static inline size_t
superBlockVarMaxBits(const struct blockCompositionSeq *seqIdx)
{
  return seqIdx->compositionTable.maxPermIdxBits * seqIdx->bucketBlocks
    + seqIdx->maxVarExtBitsPerBucket;
}

static inline size_t
superBlockVarMaxReadSize(const struct blockCompositionSeq *seqIdx)
{
  return bitElemsAllocSize(superBlockVarMaxBits(seqIdx)
                           + bitElemBits - 1);
}

static inline unsigned long
numBuckets(unsigned long seqLen, size_t bucketLen)
{
  /* seqLen + 1 because the partial sums for seqLen are used  */
  return (seqLen + 1) / bucketLen + (((seqLen + 1) % bucketLen)?1:0);
}

static inline off_t
cwSize(const struct blockCompositionSeq *seqIdx)
{
  off_t cwLen;
  cwLen = bitElemsAllocSize(
    superBlockCWBits(seqIdx)
    * numBuckets(seqIdx->baseClass.seqLen,
                 seqIdx->bucketBlocks * seqIdx->blockSize)) * sizeof (BitElem);
  return cwLen;
}

static inline BitOffset
vwBitsSimple(unsigned long seqLen, unsigned blockSize, unsigned bucketBlocks,
             unsigned maxPermIdxBits, BitOffset maxVarExtBitsPerBucket)
{
  return numBuckets(seqLen, bucketBlocks * blockSize)
    * (maxPermIdxBits * bucketBlocks + maxVarExtBitsPerBucket);
}

static inline BitOffset
vwBits(unsigned long seqLen, unsigned blockSize, unsigned bucketBlocks,
       unsigned maxPermIdxBits, varExtBitsEstimator biVarBits, void *cbState,
       struct varBitsEstimate *extVarBitsUpperBound)
{
  size_t bucketLen = (size_t)bucketBlocks * blockSize;
  BitOffset maxVarBits = numBuckets(seqLen, bucketLen)
    * (maxPermIdxBits * bucketBlocks);
  if (biVarBits)
  {
    struct segmentDesc desc[2];
    struct varBitsEstimate *extVarBits, extVarBitsTemp;
    extVarBits = extVarBitsUpperBound?extVarBitsUpperBound:&extVarBitsTemp;
    desc[0].repeatCount = (seqLen + 1) / bucketLen;
    desc[0].len = bucketLen;
    desc[1].repeatCount = ((seqLen + 1) % bucketLen)?1:0;
    desc[1].len = seqLen % bucketLen;
    if (biVarBits(cbState, desc, sizeof (desc)/sizeof (desc[0]), extVarBits))
      maxVarBits += extVarBits->maxBitsTotal;
    else
      maxVarBits += numBuckets(seqLen, bucketLen)
        * extVarBits->maxBitsPerBucket;
  }
  else if (extVarBitsUpperBound)
  {
    extVarBitsUpperBound->maxBitsTotal
      = extVarBitsUpperBound->maxBitsPerBucket
      = extVarBitsUpperBound->maxBitsPerPos = 0;
  }
  return maxVarBits;
}

/**
 * @return 0 on error, 1 otherwise
 */
static int
openOnDiskData(const char *projectName, struct onDiskBlockCompIdx *idx,
               char *mode,GtError *err)
{
  GtStr *bdxName = gt_str_new_cstr(projectName);
  gt_str_append_cstr(bdxName, ".bdx");
  idx->idxFP = gt_fa_fopen(gt_str_get(bdxName), mode, err);
  idx->idxFN = gt_str_ref(bdxName);
  gt_str_delete(bdxName);
  if (!idx->idxFP)
    return 0;
  else
    return 1;
}

enum {
  EXT_HEADER_PREFIX_SIZE = 8,
  HEADER_PAGESIZE_ROUNDUP = 8192,
  HEADER_ID_BLOCK_LEN = 8,
};

static void
initOnDiskBlockCompIdx(struct onDiskBlockCompIdx *idx,
                       size_t headerLen, off_t cwLen)
{
  idx->cwDataPos = roundUp(headerLen, HEADER_PAGESIZE_ROUNDUP);
  idx->varDataPos = cwLen + idx->cwDataPos;
  idx->rangeEncPos = 0;
}

static void
destructOnDiskBlockCompIdx(struct onDiskBlockCompIdx *idx)
{
  if (idx->idxMMap)
    gt_fa_xmunmap(idx->idxMMap);
  if (idx->idxFP)
    gt_fa_xfclose(idx->idxFP);
  if (idx->idxFN)
    gt_str_delete(idx->idxFN);
}

static inline void
initAppendState(struct appendState *aState,
                const struct blockCompositionSeq *seqIdx)
{
  BitOffset compCacheLen = superBlockCWBits(seqIdx) + bitElemBits - 1,
    permCacheLen = superBlockVarMaxBits(seqIdx) + bitElemBits - 1;
  aState->compCacheLen = compCacheLen;
  aState->permCacheLen = permCacheLen;
  aState->compCache = gt_calloc(sizeof (BitElem),
                                bitElemsAllocSize(compCacheLen));
  aState->permCache = gt_calloc(sizeof (BitElem),
                                bitElemsAllocSize(permCacheLen));
  aState->cwMemPos = cwPreCompIdxBits(seqIdx);
  aState->cwDiskOffset = aState->varMemPos = aState->cwMemOldBits =
    aState->varDiskOffset = aState->varMemOldBits = 0;
}

static void
destructAppendState(struct appendState *aState)
{
  gt_free(aState->permCache);
  gt_free(aState->compCache);
}

/**
 * @return 0 on successfull update, <0 on error
 */
static inline void
append2IdxOutput(struct appendState *state,
                 PermCompIndex permCompIdx[2],
                 unsigned bitsOfCompositionIdx, unsigned bitsOfPermutationIdx)
{
  gt_assert(state->cwMemPos + bitsOfCompositionIdx <= state->compCacheLen);
  gt_bsStorePermCompIndex(state->compCache, state->cwMemPos,
                          bitsOfCompositionIdx, permCompIdx[0]);
  state->cwMemPos += bitsOfCompositionIdx;
  gt_assert(state->varMemPos + bitsOfPermutationIdx <= state->permCacheLen);
  gt_bsStorePermCompIndex(state->permCache, state->varMemPos,
                          bitsOfPermutationIdx, permCompIdx[1]);
  state->varMemPos += bitsOfPermutationIdx;
}

static BitOffset
appendCallBackOutput(struct appendState *state,
                     const struct blockCompositionSeq *seqIdx,
                     bitInsertFunc biFunc, unsigned long start,
                     unsigned long len, unsigned callBackDataOffsetBits,
                     void *cbState)
{
  BitOffset bitsWritten;
  gt_assert(state);
  if (callBackDataOffsetBits)
  {
    BitOffset offset = cwPreCBOffsetBits(seqIdx);
    gt_bsStoreUInt64(state->compCache, state->cwMemOldBits + offset,
                  callBackDataOffsetBits,
                  state->varMemPos - state->varMemOldBits);
  }
  bitsWritten = biFunc(state->compCache, state->cwMemOldBits
                       + cwPreCWExtBits(seqIdx),
                       state->permCache, state->varMemPos, start, len, cbState);
  if (bitsWritten == (BitOffset)-1)
    return bitsWritten;
  state->cwMemPos = cwPreCWExtBits(seqIdx) + state->cwMemOldBits
    + seqIdx->cwExtBitsPerBucket;
  state->varMemPos += bitsWritten;
  return bitsWritten;
}

/**
 * @return >0 on success, 0 on I/O-error
 */
static int
updateIdxOutput(struct blockCompositionSeq *seqIdx,
                struct appendState *aState,
                const partialSymSum *buck)
{
  size_t recordsExpected, cwBitElems;
  AlphabetRangeSize blockAlphabetSize;
  gt_assert(seqIdx && aState && buck);
  /* seek2/write constant width indices */
  if (!(seqIdx->externalData.cwDataPos + aState->cwDiskOffset
         < seqIdx->externalData.varDataPos
         + aState->varDiskOffset/bitElemBits * sizeof (BitElem)))
  {
    fprintf(stderr,"cwDatapos=%lu\n",
           (unsigned long) seqIdx->externalData.cwDataPos);
    fprintf(stderr,"cwDiskOffset=%lu\n",(unsigned long) aState->cwDiskOffset);
    fprintf(stderr,"varDataPos=%lu\n",
                   (unsigned long) seqIdx->externalData.varDataPos);
    fprintf(stderr,"bitElemBits=%lu\n",(unsigned long) bitElemBits);
    fprintf(stderr,"aState->varDiskOffset=%lu\n",
                    (unsigned long) aState->varDiskOffset);
    fprintf(stderr,"aState->varDiskOffset/bitElemBits=%lu\n",
                    (unsigned long) (aState->varDiskOffset/bitElemBits));
    fprintf(stderr,"sizeof (BitElem)=%lu\n",(unsigned long) sizeof (BitElem));
    fprintf(stderr,"aState->varDiskOffset/bitElemBits * sizeof (BitElem)=%lu\n",
            (unsigned long) (aState->varDiskOffset/bitElemBits *
                             sizeof (BitElem)));
    fprintf(stderr,"seqIdx->externalData.varDataPos + "
                   "aState->varDiskOffset/bitElemBits * sizeof (BitElem)=%lu\n",
            (unsigned long) (seqIdx->externalData.varDataPos +
                             aState->varDiskOffset/bitElemBits
                             * sizeof (BitElem)));
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  gt_assert(seqIdx->externalData.cwDataPos + aState->cwDiskOffset
         < seqIdx->externalData.varDataPos
         + aState->varDiskOffset/bitElemBits * sizeof (BitElem));
  blockAlphabetSize = seqIdx->blockMapAlphabetSize;
  /* put bucket data for count up to the beginning of the current
   * block into the cw BitString */
  gt_assert(sizeof (unsigned long) * CHAR_BIT >= seqIdx->bitsPerUlong);
  {
    Symbol i;
    for (i = 0; i < blockAlphabetSize; ++i)
    {
      gt_bsStoreUlong(aState->compCache,
                    aState->cwMemOldBits + seqIdx->partialSymSumBitsSums[i],
                    seqIdx->partialSymSumBits[i], buck[i]);
    }
  }
  /* append variable width offset position */
  gt_bsStoreUInt64(aState->compCache, aState->cwMemOldBits
                + cwPreVarIdxBits(seqIdx), seqIdx->bitsPerVarDiskOffset,
                aState->varDiskOffset);
  if (fseeko(seqIdx->externalData.idxFP,
            seqIdx->externalData.cwDataPos + aState->cwDiskOffset,
            SEEK_SET))
    return 0;
  cwBitElems = recordsExpected = aState->cwMemPos / bitElemBits;
  gt_xfwrite(aState->compCache, sizeof (BitElem), recordsExpected,
             seqIdx->externalData.idxFP);
  if ((aState->cwMemOldBits = aState->cwMemPos % bitElemBits))
    aState->compCache[0] = aState->compCache[recordsExpected];
  /* seek2/write variable width indices */
  if (fseeko(seqIdx->externalData.idxFP, seqIdx->externalData.varDataPos
            + aState->varDiskOffset/bitElemBits * sizeof (BitElem), SEEK_SET))
    return 0;
  recordsExpected = aState->varMemPos/bitElemBits;
  gt_xfwrite(aState->permCache, sizeof (BitElem), recordsExpected,
             seqIdx->externalData.idxFP);
  /* move last elem of permCache with unwritten bits to front */
  if (aState->varMemPos % bitElemBits)
    aState->permCache[0] = aState->permCache[recordsExpected];
  /* FIXME: this assumes that the string of variable width date does
   * indeed occupy at least one full bitElem */
  aState->cwDiskOffset += cwBitElems;
  aState->cwMemPos = cwPreCompIdxBits(seqIdx) + aState->cwMemOldBits;
  aState->varDiskOffset += aState->varMemPos - aState->varMemOldBits;
  aState->varMemOldBits = (aState->varMemPos %= bitElemBits);
  return 1;
}

/* Caution: EH??-headers are reserved for extension headers */
enum bdxHeader {
  BKSZ_HEADER_FIELD = 0x424b535a, /* block size */
  BBLK_HEADER_FIELD = 0x42424c4b, /* blocks per bucket */
  VOFF_HEADER_FIELD = 0x564f4646, /* variable string offset */
  ROFF_HEADER_FIELD = 0x524f4646, /* range encoding offset */
  NMRN_HEADER_FIELD = 0x4e4d524e, /* number of ranges */
  CBMB_HEADER_FIELD = 0x43424d42, /* block internal offset for ext
                                   * bits provided by callback */
  MEXB_HEADER_FIELD = 0x4d455842, /* maxVarExtBitsPerBucket */
  CEXB_HEADER_FIELD = 0x43455842, /* cwExtBitsPerBucket */
  SPBT_HEADER_FIELD = 0x53504254, /* bits stored for unsigned long values */
  SSBT_HEADER_FIELD = 0x53534254, /* block map alphabet size */
  BEFB_HEADER_FIELD = 0x42454642, /* block encoding fallback symbol */
  REFB_HEADER_FIELD = 0x52454642, /* range encoding fallback symbol */
  VDOB_HEADER_FIELD = 0x56444f42, /* bitsPerVarDiskOffset */
  SELE_HEADER_FIELD = 0x53454c45, /* sequence length */
  EH_HEADER_PREFIX = 0x45480000,  /* extension headers */
};

static const char bdxHeader[] = "BDX";

static inline off_t
extHeadersSizeAggregate(size_t numExtHeaders, const uint32_t *extHeaderSizes)
{
  off_t len = 0, i;
  for (i = 0; i < numExtHeaders; ++i)
    len += extHeaderSizes[i] + EXT_HEADER_PREFIX_SIZE;
  return len;
}

static inline size_t
blockEncIdxSeqHeaderLength(const struct blockCompositionSeq *seqIdx,
                           size_t numExtHeaders, const uint32_t *extHeaderSizes)
{
  size_t headerSize =
    4                           /* BDX identifier */
    + 4                         /* length field */
    + 8                         /* block size */
    + 8                         /* blocks per bucket */
    + 12                        /* offset of variable length data */
    + 12                        /* offset of range encodings */
    + 4 + 4                     /* bits used per seqpos */
    + 4 + 4                     /* bits used per variable bit offset */
    + 4 + 4 + 4 * seqIdx->blockMapAlphabetSize /* bit counts for partial sums */
    + 4 + 4                     /* block encoding fallback symbol */
    + 4 + 4                     /* range encoding fallback symbol */
    + 4 + 4                     /* num modes */
    + 4 + 8                     /* length of sequence */
    + 4 * seqIdx->numModes      /* one uint32_t for every mode */
    ;
  if (seqIdx->callBackDataOffsetBits)
    headerSize += 4 + 4         /* extra offset bits per constant block */
      + 4 + 8                   /* extension bits stored in constant block */
      + 4 + 8;                  /* variable area bits added per bucket max */

  headerSize += extHeadersSizeAggregate(numExtHeaders, extHeaderSizes);
  return headerSize;
}

struct extHeaderPos
{
  off_t pos;
  uint32_t headerID;
};

static inline void
appendExtHeaderPos(struct extHeaderPos **headerList, size_t numHeaders,
                   off_t pos, uint32_t headerID)
{
  *headerList = gt_realloc(*headerList,
                           sizeof (**headerList) * (numHeaders + 1));
  (*headerList)[numHeaders].pos = pos;
  (*headerList)[numHeaders].headerID = headerID;
};

static inline int
writeExtIdxHeader(FILE *fp, uint16_t headerID, size_t len,
                  headerWriteFunc cbFunc, void *cbData)
{
  uint32_t expHeader[2] =
    { EH_HEADER_PREFIX | headerID, len };
  gt_xfwrite(expHeader, sizeof (uint32_t), 2, fp);
  return cbFunc(fp, cbData);
}

#define writeIdxHeaderErrRet(retval)            \
  do {                                          \
    gt_free(buf);                               \
    return 0;                                   \
  } while (0)
/**
 * FIXME: this doesn't work on platforms with sizeof (uint32_t) != 4
 * or sizeof (int) < 4
 * @return 0 on error, header length in bytes on success
 */
static size_t
writeIdxHeader(struct blockCompositionSeq *seqIdx,
               size_t numExtHeaders, const uint16_t *headerIDs,
               const uint32_t *extHeaderSizes,
               headerWriteFunc *extHeaderCallbacks,
               void **headerCBData, GT_UNUSED GtError *err)
{
  FILE *fp;
  /* construct memory buffer with header data */
  size_t i, bufLen;
  off_t offset, len;
  char *buf;
  gt_assert(seqIdx && err);
  fp = seqIdx->externalData.idxFP;
  bufLen = blockEncIdxSeqHeaderLength(seqIdx, 0, NULL);
  buf = gt_malloc(bufLen);
  /* account for ext headers */
  len = roundUp(bufLen, HEADER_PAGESIZE_ROUNDUP);
  /* 1. 4 identifier bytes at offset 0 */
  strcpy(buf, bdxHeader);
  /* 2. header length */
  *(uint32_t *)(buf + 4) = len;
  /* 3. block size */
  offset = HEADER_ID_BLOCK_LEN;
  *(uint32_t *)(buf + offset) = BKSZ_HEADER_FIELD;
  *(uint32_t *)(buf + offset + 4) = seqIdx->blockSize;
  offset += 8;
  *(uint32_t *)(buf + offset) = BBLK_HEADER_FIELD;
  *(uint32_t *)(buf + offset + 4) = seqIdx->bucketBlocks;
  offset += 8;
  *(uint32_t *)(buf + offset) = VOFF_HEADER_FIELD;
  *(uint64_t *)(buf + offset + 4) = seqIdx->externalData.varDataPos;
  offset += 12;
  *(uint32_t *)(buf + offset) = ROFF_HEADER_FIELD;
  *(uint64_t *)(buf + offset + 4) = seqIdx->externalData.rangeEncPos;
  offset += 12;
  *(uint32_t *)(buf + offset) = SELE_HEADER_FIELD;
  *(uint64_t *)(buf + offset + 4) = seqIdx->baseClass.seqLen;
  offset += 12;
  *(uint32_t *)(buf + offset) = SPBT_HEADER_FIELD;
  *(uint32_t *)(buf + offset + 4) = seqIdx->bitsPerUlong;
  offset += 8;
  *(uint32_t *)(buf + offset) = VDOB_HEADER_FIELD;
  *(uint32_t *)(buf + offset + 4) = seqIdx->bitsPerVarDiskOffset;
  offset += 8;
  *(uint32_t *)(buf + offset) = SSBT_HEADER_FIELD;
  *(uint32_t *)(buf + offset + 4) = seqIdx->blockMapAlphabetSize;
  for (i = 0; i < seqIdx->blockMapAlphabetSize; ++i)
    *(uint32_t *)(buf + offset + 8 + 4*i) = seqIdx->partialSymSumBits[i];
  offset += 8 + 4 * seqIdx->blockMapAlphabetSize;
  *(uint32_t *)(buf + offset) = BEFB_HEADER_FIELD;
  *(uint32_t *)(buf + offset + 4) = seqIdx->blockEncFallback;
  offset += 8;
  *(uint32_t *)(buf + offset) = REFB_HEADER_FIELD;
  *(uint32_t *)(buf + offset + 4) = seqIdx->rangeEncFallback;
  offset += 8;
  *(uint32_t *)(buf + offset) = NMRN_HEADER_FIELD;
  *(uint32_t *)(buf + offset + 4) = seqIdx->numModes;
  offset += 8;
  for (i = 0; i < seqIdx->numModes; ++i)
  {
    *(uint32_t *)(buf + offset) = seqIdx->modes[i];
    offset += 4;
  }
  if (seqIdx->callBackDataOffsetBits)
  {
    *(uint32_t *)(buf + offset) = CBMB_HEADER_FIELD;
    *(uint32_t *)(buf + offset + 4) = seqIdx->callBackDataOffsetBits;
    offset += 8;
    *(uint32_t *)(buf + offset) = CEXB_HEADER_FIELD;
    *(uint64_t *)(buf + offset + 4) = seqIdx->cwExtBitsPerBucket;
    offset += 12;
    *(uint32_t *)(buf + offset) = MEXB_HEADER_FIELD;
    *(uint64_t *)(buf + offset + 4) = seqIdx->maxVarExtBitsPerBucket;
    offset += 12;
  }
  gt_assert(offset == bufLen);
  if (fseeko(fp, 0, SEEK_SET))
    writeIdxHeaderErrRet(0);
  gt_xfwrite(buf, bufLen, 1, fp);
  if (numExtHeaders)
  {
    off_t offsetTargetValue = bufLen;
    if (!writeExtIdxHeader(fp, headerIDs[0], extHeaderSizes[0],
                          extHeaderCallbacks[0], headerCBData[0]))
      writeIdxHeaderErrRet(0);
    else
      appendExtHeaderPos(&seqIdx->extHeaderPos, seqIdx->numExtHeaders++,
                         bufLen + EXT_HEADER_PREFIX_SIZE,
                         EH_HEADER_PREFIX | headerIDs[0]);
    for (i = 1; i < numExtHeaders; ++i)
    {
      offsetTargetValue += EXT_HEADER_PREFIX_SIZE + extHeaderSizes[i - 1];
      if (fseeko(fp, offsetTargetValue, SEEK_SET))
        writeIdxHeaderErrRet(0);
      if (!writeExtIdxHeader(fp, headerIDs[i], extHeaderSizes[i],
                            extHeaderCallbacks[i], headerCBData[i]))
        writeIdxHeaderErrRet(0);
      else
        appendExtHeaderPos(&seqIdx->extHeaderPos, seqIdx->numExtHeaders++,
                           offsetTargetValue + EXT_HEADER_PREFIX_SIZE,
                           EH_HEADER_PREFIX | headerIDs[0]);
    }
    offset = offsetTargetValue + EXT_HEADER_PREFIX_SIZE
      + extHeaderSizes[numExtHeaders - 1];
    gt_assert(offset >= ftello(fp));
  }
  gt_assert(seqIdx->externalData.cwDataPos == len);
  gt_free(buf);
  return len;
}

#define loadBlockEncIdxSeqErrRet()                                \
  do {                                                            \
    destructOnDiskBlockCompIdx(&newSeqIdx->externalData);         \
    if (newSeqIdx->compositionTable.bitsPerCount)                 \
      gt_destructCompositionList(&newSeqIdx->compositionTable);   \
    if (newSeqIdx->rangeEncs)                                     \
      gt_deleteSeqRangeList(newSeqIdx->rangeEncs);                \
    gt_free(newSeqIdx->extHeaderPos);                             \
    gt_free(newSeqIdx->partialSymSumBits);                        \
    gt_free(buf);                                                 \
    if (alphabet) gt_MRAEncDelete(alphabet);                      \
    gt_free(modesCopy);                                           \
    gt_free(blockMapAlphabet);                                    \
    gt_free(rangeMapAlphabet);                                    \
    gt_free(newSeqIdx);                                           \
    return NULL;                                                  \
  } while (0)

struct encIdxSeq *
gt_loadBlockEncIdxSeqGen(MRAEnc *alphabet,
                         const char *projectName, int features, GtError *err)
{
  struct blockCompositionSeq *newSeqIdx = NULL;
  Symbol blockMapAlphabetSize, GT_UNUSED totalAlphabetSize;
  MRAEnc *blockMapAlphabet = NULL, *rangeMapAlphabet = NULL;
  size_t headerLen;
  int *modesCopy = NULL;
  char *buf = NULL;
  gt_assert(projectName && err);
  newSeqIdx = gt_calloc(sizeof (struct blockCompositionSeq), 1);
  newSeqIdx->baseClass.alphabet = alphabet;
  newSeqIdx->baseClass.classInfo = &blockCompositionSeqClass;

  if (!openOnDiskData(projectName, &newSeqIdx->externalData, "rb",err)) {
    gt_error_set(err, "error reading data from disk");
    loadBlockEncIdxSeqErrRet();
  }
  {
    size_t offset = HEADER_ID_BLOCK_LEN;
    buf = gt_malloc(HEADER_ID_BLOCK_LEN);
    if (fread(buf, HEADER_ID_BLOCK_LEN, 1,
          newSeqIdx->externalData.idxFP) != 1) {
      gt_error_set(err, "error reading header id");
      loadBlockEncIdxSeqErrRet();
    }
    if (strcmp(buf, bdxHeader)!= 0) {
      gt_error_set(err, "header is not BDX found %s instead", buf);
      loadBlockEncIdxSeqErrRet();
    }
    newSeqIdx->externalData.cwDataPos = headerLen = *(uint32_t *)(buf + 4);
    buf = gt_realloc(buf, headerLen);
    if (fread(buf + HEADER_ID_BLOCK_LEN, headerLen - HEADER_ID_BLOCK_LEN,
             1, newSeqIdx->externalData.idxFP) != 1) {
      gt_error_set(err, "error reading header");
      loadBlockEncIdxSeqErrRet();
    }
    while (offset < headerLen)
    {
      uint32_t currentHeader;
      switch (currentHeader = *(uint32_t *)(buf + offset))
      {
      case SELE_HEADER_FIELD:
        newSeqIdx->baseClass.seqLen = *(uint64_t *)(buf + offset + 4);
        offset += 12;
        break;
      case BKSZ_HEADER_FIELD:
        newSeqIdx->blockSize = *(uint32_t *)(buf + offset + 4);
        offset += 8;
        break;
      case BBLK_HEADER_FIELD:
        newSeqIdx->bucketBlocks = *(uint32_t *)(buf + offset + 4);
        offset += 8;
        break;
      case VOFF_HEADER_FIELD:
        newSeqIdx->externalData.varDataPos
          = *(uint64_t *)(buf + offset + 4);
        offset += 12;
        break;
      case ROFF_HEADER_FIELD:
        newSeqIdx->externalData.rangeEncPos = *(uint64_t *)(buf + offset + 4);
        offset += 12;
        break;
      case NMRN_HEADER_FIELD:
        {
          size_t numModes = newSeqIdx->numModes
            = *(uint32_t *)(buf + (offset += 4));
          offset += 4;
          modesCopy = newSeqIdx->modes = gt_malloc(sizeof (int) * numModes);
          size_t j;
          for (j = 0; j < numModes; ++j)
          {
            modesCopy[j] = *(uint32_t *)(buf + offset);
            offset += 4;
          }
        }
        break;
      case CBMB_HEADER_FIELD:
        newSeqIdx->callBackDataOffsetBits = *(uint32_t *)(buf + offset + 4);
        offset += 8;
        break;
      case SPBT_HEADER_FIELD:
        newSeqIdx->bitsPerUlong = *(uint32_t *)(buf + offset + 4);
        offset += 8;
        break;
      case VDOB_HEADER_FIELD:
        newSeqIdx->bitsPerVarDiskOffset = *(uint32_t *)(buf + offset + 4);
        offset += 8;
        break;
      case SSBT_HEADER_FIELD:
        {
          size_t i;
          Symbol blockMapAlphabetSize = *(uint32_t *)(buf + offset + 4);
          newSeqIdx->partialSymSumBits
            = gt_malloc(sizeof (newSeqIdx->partialSymSumBits[0])
                        * blockMapAlphabetSize * 2);
          newSeqIdx->partialSymSumBitsSums
            = newSeqIdx->partialSymSumBits + blockMapAlphabetSize;
          if (blockMapAlphabetSize)
          {
            newSeqIdx->partialSymSumBits[0]= *(uint32_t *)(buf + offset + 8);
            newSeqIdx->partialSymSumBitsSums[0] = 0;
#ifdef EIS_DEBUG
            gt_log_log("partialSymSumBits[0]=%u\n",
                    newSeqIdx->partialSymSumBits[0]);
#endif
            for (i = 1; i < blockMapAlphabetSize; ++i)
            {
              newSeqIdx->partialSymSumBits[i]
                = *(uint32_t *)(buf + offset + 8 + 4*i);
#ifdef EIS_DEBUG
              gt_log_log("partialSymSumBits[%"PRIuSymbol"]=%u\n",
                      (Symbol)i, newSeqIdx->partialSymSumBits[i]);
#endif
              newSeqIdx->partialSymSumBitsSums[i] =
                newSeqIdx->partialSymSumBitsSums[i - 1]
                + newSeqIdx->partialSymSumBits[i - 1];
            }
            newSeqIdx->symSumBits
              = newSeqIdx->partialSymSumBitsSums[blockMapAlphabetSize - 1]
              + newSeqIdx->partialSymSumBits[blockMapAlphabetSize - 1];
          }
          offset += 8 + 4 * blockMapAlphabetSize;
        }
      case BEFB_HEADER_FIELD:
        newSeqIdx->blockEncFallback = *(uint32_t *)(buf + offset + 4);
        offset += 8;
        break;
      case REFB_HEADER_FIELD:
        newSeqIdx->rangeEncFallback = *(uint32_t *)(buf + offset + 4);
        offset += 8;
        break;
      case MEXB_HEADER_FIELD:
        newSeqIdx->maxVarExtBitsPerBucket = *(uint64_t *)(buf + offset + 4);
        offset += 12;
        break;
      case CEXB_HEADER_FIELD:
        newSeqIdx->cwExtBitsPerBucket = *(uint64_t *)(buf + offset + 4);
        offset += 12;
        break;
      case 0:
        /* empty header skip to next portion */
        offset = headerLen;
        break;
      default:
        if ((currentHeader & 0xffff0000L) == EH_HEADER_PREFIX)
        {
          uint32_t extHeaderLen = *(uint32_t *)(buf + offset + 4);
          offset += EXT_HEADER_PREFIX_SIZE;
          appendExtHeaderPos(&newSeqIdx->extHeaderPos,
                             newSeqIdx->numExtHeaders++,
                             offset, currentHeader);
          offset += extHeaderLen;
        }
        else
        {
          gt_error_set(err, "Unknown header field: %4s", buf + offset);
          loadBlockEncIdxSeqErrRet();
        }
      }
    }
    gt_assert(newSeqIdx->modes
           && newSeqIdx->bucketBlocks
           && newSeqIdx->numModes
           && offset == headerLen);
    /* compute values not read from header */
    if (!newSeqIdx->bitsPerUlong)
      newSeqIdx->bitsPerUlong =
        requiredUlongBits(newSeqIdx->baseClass.seqLen - 1);
    else if (newSeqIdx->bitsPerUlong !=
            requiredUlongBits(newSeqIdx->baseClass.seqLen - 1)) {
      gt_error_set(err, "bits per ulong wrong in header found %u, expected %u",
                   newSeqIdx->bitsPerUlong,
                   requiredUlongBits(newSeqIdx->baseClass.seqLen - 1));
      loadBlockEncIdxSeqErrRet();
    }
  }
  {
    AlphabetRangeID range, numAlphabetRanges = newSeqIdx->numModes =
      MRAEncGetNumRanges(alphabet);
    totalAlphabetSize = gt_MRAEncGetSize(alphabet);
    blockMapAlphabetSize = 0;
    for (range = 0; range < numAlphabetRanges; ++range)
    {
      switch (modesCopy[range])
      {
      case BLOCK_COMPOSITION_INCLUDE:
        blockMapAlphabetSize += MRAEncGetRangeSize(alphabet, range);
        break;
      case DIRECT_SYM_ENCODE:
        /*< FIXME: insert proper code to process direct encoding regions */
        break;
      case REGIONS_LIST:
        /*< FIXME: insert proper code to process ranges */
        break;
      default:
        gt_error_set(err, "Invalid encoding request.");
        loadBlockEncIdxSeqErrRet();
        break;
      }
    }
    newSeqIdx->blockMapAlphabet = blockMapAlphabet =
      gt_MRAEncSecondaryMapping(alphabet, BLOCK_COMPOSITION_INCLUDE, modesCopy,
                             newSeqIdx->blockEncFallback);
    newSeqIdx->rangeMapAlphabet = rangeMapAlphabet =
      gt_MRAEncSecondaryMapping(alphabet, REGIONS_LIST, modesCopy,
                             newSeqIdx->rangeEncFallback);
    newSeqIdx->blockMapAlphabetSize = blockMapAlphabetSize;
    gt_assert(gt_MRAEncGetSize(blockMapAlphabet) == blockMapAlphabetSize);
  }
  if (!newSeqIdx->partialSymSumBits && blockMapAlphabetSize)
  {
    newSeqIdx->partialSymSumBits
      = gt_malloc(sizeof (newSeqIdx->partialSymSumBits[0])
                  * blockMapAlphabetSize * 2);
    newSeqIdx->partialSymSumBitsSums
      = newSeqIdx->partialSymSumBits + blockMapAlphabetSize;
    symSumBitsDefaultSetup(newSeqIdx);
  }
  if (!gt_initCompositionList(&newSeqIdx->compositionTable,
                              newSeqIdx->blockSize,
                              blockMapAlphabetSize)) {
    gt_error_set(err, "error initialising composition list");
    loadBlockEncIdxSeqErrRet();
  }
  if (newSeqIdx->bitsPerVarDiskOffset == 0)
    newSeqIdx->bitsPerVarDiskOffset =
      gt_requiredUInt64Bits(
        vwBitsSimple(newSeqIdx->baseClass.seqLen, newSeqIdx->blockSize,
                     newSeqIdx->bucketBlocks,
                     newSeqIdx->compositionTable.maxPermIdxBits,
                     newSeqIdx->maxVarExtBitsPerBucket));

  if (fseeko(newSeqIdx->externalData.idxFP,
             newSeqIdx->externalData.rangeEncPos, SEEK_SET)) {
    gt_error_set(err, "error in fseeko");
    loadBlockEncIdxSeqErrRet();
  }
  {
    int regionFeatures = SRL_NO_FEATURES;
    if (features & EIS_FEATURE_REGION_SUMS)
      regionFeatures |= SRL_PARTIAL_SYMBOL_SUMS;
    if (!(newSeqIdx->rangeEncs =
          gt_SRLReadFromStream(newSeqIdx->externalData.idxFP, rangeMapAlphabet,
                            regionFeatures, err))) {
      gt_error_set(err, "error creating rangeEncs");
      loadBlockEncIdxSeqErrRet();
    }
  }
  tryMMapOfIndex(&newSeqIdx->externalData);
  gt_free(buf);
  return &newSeqIdx->baseClass;
}

static inline int
tryMMapOfIndex(struct onDiskBlockCompIdx *idxData)
{
  size_t len = idxData->rangeEncPos - idxData->cwDataPos;
  gt_assert(idxData && idxData->idxFP && idxData->idxMMap == NULL);
  idxData->idxMMap = gt_fa_mmap_generic_fd(fileno(idxData->idxFP),
                                           gt_str_get(idxData->idxFN),len,
                                           idxData->cwDataPos, false, false,
                                           NULL);
  return (idxData->idxMMap != NULL ? 0 : 1);
}

static FILE *
seekToHeader(const struct encIdxSeq *seqIdx, uint16_t headerID,
             uint32_t *lenRet)
{
  const struct blockCompositionSeq *bSeqIdx;
  size_t i;
  uint32_t query = headerID | EH_HEADER_PREFIX;
  gt_assert(seqIdx);
  bSeqIdx =
    constEncIdxSeq2blockCompositionSeq(seqIdx);
  for (i = 0; i < bSeqIdx->numExtHeaders; ++i)
  {
    if (bSeqIdx->extHeaderPos[i].headerID == query)
    {
      uint32_t headerPrefix[2];
      if (lenRet)
      {
        if (fseeko(bSeqIdx->externalData.idxFP,
                   bSeqIdx->extHeaderPos[i].pos - EXT_HEADER_PREFIX_SIZE,
                   SEEK_SET))
           return NULL;
        if (fread(headerPrefix, sizeof (headerPrefix[0]), 2,
                  bSeqIdx->externalData.idxFP) != 2)
          return NULL;
        *lenRet = headerPrefix[1];
      }
      else
        if (fseeko(bSeqIdx->externalData.idxFP, bSeqIdx->extHeaderPos[i].pos,
                   SEEK_SET))
          return NULL;
      return bSeqIdx->externalData.idxFP;
    }
  }
  return NULL;
}

/**
 * @return 0 on error, 1 on success
 */
static int
finalizeIdxOutput(struct blockCompositionSeq *seqIdx,
                  struct appendState *aState)
{
  off_t rangeEncPos;
  size_t recordsExpected;
  gt_assert(aState && seqIdx);
  gt_assert(aState->cwMemOldBits < bitElemBits
         && aState->cwMemOldBits + cwPreCompIdxBits(seqIdx)
         == aState->cwMemPos);
  gt_assert(aState->varMemOldBits < bitElemBits
         && aState->varMemOldBits == aState->varMemPos);
  if (aState->cwMemOldBits)
  {
    /* seek2/write variable width indices */
    if (fseeko(seqIdx->externalData.idxFP,
               seqIdx->externalData.cwDataPos
               + aState->cwDiskOffset * sizeof (BitElem), SEEK_SET))
      return 0;
    recordsExpected = 1;
    gt_xfwrite(aState->compCache, sizeof (BitElem), recordsExpected,
               seqIdx->externalData.idxFP);
    ++(aState->cwDiskOffset);
  }
  if (aState->varMemOldBits)
  {
    /* seek2/write variable width indices */
    if (fseeko(seqIdx->externalData.idxFP,
               seqIdx->externalData.varDataPos
               + aState->varDiskOffset/bitElemBits * sizeof (BitElem),
               SEEK_SET))
      return 0;
    recordsExpected = 1;
    gt_xfwrite(aState->permCache, sizeof (BitElem),
               recordsExpected,
               seqIdx->externalData.idxFP);
  }
  rangeEncPos = seqIdx->externalData.varDataPos
    + aState->varDiskOffset / bitElemBits * sizeof (BitElem)
    + ((aState->varDiskOffset%bitElemBits)?sizeof (BitElem):0);
  seqIdx->externalData.rangeEncPos = rangeEncPos;
  /* insert terminator so every search for a next range will find a
   * range just beyond the sequence end */
  gt_SRLAppendNewRange(seqIdx->rangeEncs,
                    seqIdx->baseClass.seqLen + seqIdx->blockSize, 1, 0);
  gt_SRLCompact(seqIdx->rangeEncs);
  if (fseeko(seqIdx->externalData.idxFP, rangeEncPos, SEEK_SET))
    return 0;
  if (!(gt_SRLSaveToStream(seqIdx->rangeEncs, seqIdx->externalData.idxFP)))
     return 0;
  return 1;
}

static void
addRangeEncodedSyms(struct seqRangeList *rangeList, const Symbol *block,
                    unsigned blockSize, unsigned long blockNum,
                    const MRAEnc *alphabet, int selection, const int *rangeSel)
{
  unsigned i;
  for (i = 0; i < blockSize; ++i)
  {
    gt_assert(gt_MRAEncSymbolIsInSelectedRanges(alphabet, block[i],
                                          selection, rangeSel) >= 0);
    if (gt_MRAEncSymbolIsInSelectedRanges(alphabet, block[i], selection,
                                          rangeSel)) {
      gt_SRLAddPosition(rangeList, blockNum * blockSize + i, block[i]);
    }
  }
}

static union EISHint *
newBlockCompSeqHint(const struct encIdxSeq *seq)
{
  union EISHint *hintret;
  const struct blockCompositionSeq *seqIdx;
  gt_assert(seq && seq->classInfo == &blockCompositionSeqClass);
  seqIdx = constEncIdxSeq2blockCompositionSeq(seq);
  hintret = gt_malloc(sizeof (union EISHint));
  gt_SRLInitListSearchHint(seqIdx->rangeEncs, &hintret->bcHint.rangeHint);
  /* FIXME: make cache size user-configurable */
  initSuperBlockSeqCache(&hintret->bcHint.sBlockCache, seqIdx, 32);
  return hintret;
}

static void
deleteBlockCompSeqHint(struct encIdxSeq *seq, union EISHint *hint)
{
  GT_UNUSED struct blockCompositionSeq *seqIdx;
  gt_assert(seq && seq->classInfo == &blockCompositionSeqClass);
  seqIdx = encIdxSeq2blockCompositionSeq(seq);
  destructSuperBlockSeqCache(&hint->bcHint.sBlockCache);
  gt_free(hint);
}

static int
printBlock(Symbol *block, unsigned blockSize, FILE *fp)
{
  unsigned i;
  int outCount = 0;
  for (i = 0; i < blockSize; ++i)
    outCount += fprintf(fp, " %d", (int)block[i]);
  return outCount;
}

enum {
  BUCKET_PLAIN                     = 0,
  BUCKET_PRINT_BITSTRING           = 1 <<  0,
  BUCKET_PRINT_BITSTRING_SEPARATOR = 1 <<  1,
  BUCKET_PRINT_BITSIZES            = 1 <<  2,
  BUCKET_PRINT_RANGES_OVERLAY      = 1 <<  3,
};

static int
printBucket(const struct blockCompositionSeq *seqIdx, unsigned long bucketNum,
            int flags, FILE *fp, union EISHint *hint)
{
  unsigned long lastBucket = bucketNumFromPos(seqIdx,
                                             EISLength(&seqIdx->baseClass)),
                start, end;
  AlphabetRangeSize i, blockMapAlphabetSize = seqIdx->blockMapAlphabetSize;
  int outCount = 0;
  gt_assert(seqIdx && fp && hint);
  if (bucketBasePos(seqIdx, bucketNum) >= EISLength(&seqIdx->baseClass))
  {
    gt_log_log("warning: querying bucket %lu"
            " beyond end of sequence!\n", bucketNum);
    bucketNum = lastBucket;
  }
  start = bucketBasePos(seqIdx, bucketNum);
  end = ((bucketNum < lastBucket)?
         bucketBasePos(seqIdx, bucketNum + 1):
         EISLength(&seqIdx->baseClass));
  outCount +=
    fprintf(fp, "# Inspecting bucket: %lu\n"
            "# bucket position start=%lu, end=%lu\n"
            "# partial symbol sums up to start:\n",
            bucketNum, start, end - 1);
  {
    struct superBlock *sBlock;
    BitOffset varDataMemOffset, cwIdxMemOffset, varIdxOffset;
    Symbol *block;
    unsigned blockSize = seqIdx->blockSize,
      idxBits = seqIdx->compositionTable.compositionIdxBits;
#ifdef USE_SBLOCK_CACHE
    sBlock = cacheFetchSuperBlock(seqIdx, bucketNum,
                                  &hint->bcHint.sBlockCache);
#else
    sBlock = fetchSuperBlock(seqIdx, bucketNum, NULL);
#endif
    block = gt_malloc(sizeof (block[0]) * seqIdx->blockSize);
    for (i = 0; i < blockMapAlphabetSize; ++i)
    {
      if (flags & BUCKET_PRINT_BITSIZES)
      {
        outCount += fprintf(fp, "# partial sum[%u] bits: %u\n", i,
                            seqIdx->partialSymSumBits[i]);
      }
      outCount +=
        fprintf(fp, "# partial sum[%u]=%lu\n", i,
                sBlockGetPartialSymSum(sBlock, i, seqIdx));
    }
    if (flags & BUCKET_PRINT_BITSIZES)
    {
      fprintf(fp, "# bit size of sBlockVarIdxOffset: %u\n",
              seqIdx->bitsPerVarDiskOffset);
    }
    fprintf(fp, "# sBlockVarIdxOffset=%llu\n",
            (varIdxOffset = sBlockGetVarIdxOffset(sBlock, seqIdx)));
    if (seqIdx->callBackDataOffsetBits)
      fprintf(fp, "# sBlockGetcbOffset=%llu\n",
              sBlockGetcbOffset(sBlock, seqIdx));
    i = 0;
    if (flags & BUCKET_PRINT_BITSIZES)
    {
      fprintf(fp, "# bits of constant width extension data: %llu\n",
              (unsigned long long)seqIdx->cwExtBitsPerBucket);
    }
    walkCompIndicesPrefix(
      seqIdx, sBlock, seqIdx->bucketBlocks, cwIdxMemOffset,
      outCount +=
      fprintf(
        fp, "# block %u: comp idx: %lu, permIdxBits=%u, perm idx: %lu =>",
        i, (unsigned long)compIndex,
        (unsigned)seqIdx->compositionTable.permutations[compIndex].permIdxBits,
        (unsigned long)gt_bsGetPermCompIndex(
          sBlock->varData, varDataMemOffset,
          seqIdx->compositionTable.permutations[compIndex].permIdxBits));
      unpackBlock(seqIdx, sBlock, cwIdxMemOffset, varDataMemOffset, block,
                  blockSize);
      outCount += printBlock(block, blockSize, fp);
      fputs("\n", fp);
      i++; , varDataMemOffset);
    gt_free(block);
    if (flags & BUCKET_PRINT_BITSTRING)
    {
      for (i = 0; i < blockMapAlphabetSize; ++i)
      {
        if (gt_bsPrint(fp, sBlock->cwData, seqIdx->partialSymSumBitsSums[i]
                    + sBlock->cwIdxMemBase, seqIdx->partialSymSumBits[i]))
          outCount += seqIdx->partialSymSumBits[i];
        if (flags & BUCKET_PRINT_BITSTRING_SEPARATOR)
          outCount += fputs("&", fp);
      }
      gt_bsPrint(fp, sBlock->cwData,
              cwPreVarIdxBits(seqIdx) + sBlock->cwIdxMemBase,
              seqIdx->bitsPerVarDiskOffset);
      if (flags & BUCKET_PRINT_BITSTRING_SEPARATOR)
        outCount += fputs("&", fp);
      if (seqIdx->callBackDataOffsetBits)
      {
        gt_bsPrint(fp, sBlock->cwData, sBlockGetcbOffsetOffset(sBlock, seqIdx),
                seqIdx->callBackDataOffsetBits);
        if (flags & BUCKET_PRINT_BITSTRING_SEPARATOR)
          outCount += fputs("&", fp);
      }
      walkCompIndicesPrefix(
        seqIdx, sBlock, seqIdx->bucketBlocks, cwIdxMemOffset,
        gt_bsPrint(fp, sBlock->cwData, cwIdxMemOffset, idxBits);
        if (flags & BUCKET_PRINT_BITSTRING_SEPARATOR)
          outCount += fputs("&", fp);, varDataMemOffset);
      gt_bsPrint(fp, sBlock->cwData, sBlockCWExtBitsOffset(sBlock, seqIdx),
              seqIdx->cwExtBitsPerBucket);
      fputs("\n# variable width string: \n", fp);
      walkCompIndicesPrefix(
        seqIdx, sBlock, seqIdx->bucketBlocks, cwIdxMemOffset,
        idxBits =
        seqIdx->compositionTable.permutations[compIndex].permIdxBits;
        gt_bsPrint(fp, sBlock->varData, varDataMemOffset, idxBits);
        if (flags & BUCKET_PRINT_BITSTRING_SEPARATOR)
          outCount += fputs("&", fp);, varDataMemOffset);
      if (bucketNum != lastBucket)
      {
        struct superBlock *nextSBlock;
        BitOffset nextVarIdxOffset;
#ifdef USE_SBLOCK_CACHE
        nextSBlock = cacheFetchSuperBlock(seqIdx, bucketNum + 1,
                                          &hint->bcHint.sBlockCache);
#else
        nextSBlock = fetchSuperBlock(seqIdx, bucketNum + 1, NULL);
#endif
        nextVarIdxOffset = sBlockGetVarIdxOffset(nextSBlock, seqIdx);
        gt_bsPrint(fp, sBlock->varData, varDataMemOffset,
                nextVarIdxOffset - varIdxOffset);
        fprintf(fp, "\n# varIdxOffset for next block: %llu",
                (unsigned long long)nextVarIdxOffset);
#ifndef USE_SBLOCK_CACHE
        deleteSuperBlock(sBlock);
#endif
      }
      fputs("\n", fp);
    }
    if (flags & BUCKET_PRINT_RANGES_OVERLAY)
    {
      fputs("# overlapping symbol ranges:\n", fp);
      gt_SRLPrintRangesInfo(seqIdx->rangeEncs, fp, start, end - start,
                         &hint->bcHint.rangeHint);
    }
  }
  return outCount;
}

unsigned
gt_blockEncIdxSeqSegmentLen(const struct blockEncParams *params)
{
  return params->blockSize * params->bucketBlocks;
}

static int
printBlockEncPosDiags(const EISeq *seq, unsigned long pos, FILE *fp,
                      EISHint hint)
{
  const struct blockCompositionSeq *seqIdx;
  int outCount = 0;
  unsigned long bucketNum;
  gt_assert(seq && seq->classInfo == &blockCompositionSeqClass);
  seqIdx = constEncIdxSeq2blockCompositionSeq(seq);
  bucketNum = bucketNumFromPos(seqIdx, pos);
  fputs("##################################################\n"
        "# This bucket:\n"
        "##################################################\n", fp);
  outCount += printBucket(seqIdx, bucketNum, BUCKET_PLAIN, fp, hint);
  if (bucketNum)
  {
    fputs("##################################################\n"
          "# Previous bucket:\n"
          "##################################################\n", fp);
    outCount += printBucket(seqIdx, bucketNum - 1, BUCKET_PLAIN, fp, hint);
  }
  if (bucketNum < bucketNumFromPos(seqIdx, EISLength(seq)))
  {
    fputs("##################################################\n"
          "# Next bucket:\n"
          "##################################################\n", fp);
    outCount += printBucket(seqIdx, bucketNum + 1, BUCKET_PLAIN, fp, hint);
  }
  return outCount;
}

static int
displayBlockEncBlock(const EISeq *seq, unsigned long pos, FILE *fp,
                     EISHint hint)
{
  const struct blockCompositionSeq *seqIdx;
  int outCount;
  unsigned long bucketNum;
  gt_assert(seq && seq->classInfo == &blockCompositionSeqClass);
  seqIdx = constEncIdxSeq2blockCompositionSeq(seq);
  bucketNum = bucketNumFromPos(seqIdx, pos);
  outCount = printBucket(seqIdx, bucketNum, BUCKET_PRINT_BITSTRING_SEPARATOR
                         | BUCKET_PRINT_BITSTRING | BUCKET_PRINT_BITSIZES
                         | BUCKET_PRINT_RANGES_OVERLAY, fp, hint);
  return outCount;
}

static const struct encIdxSeqClass blockCompositionSeqClass =
{
  .delete = deleteBlockEncIdxSeq,
  .rank = blockCompSeqRank,
  .posPairRank = blockCompSeqPosPairRank,
  .rangeRank = blockCompSeqRangeRank,
  .posPairRangeRank = blockCompSeqPosPairRangeRank,
  .select = blockCompSeqSelect,
  .get = blockCompSeqGet,
  .newHint = newBlockCompSeqHint,
  .deleteHint = deleteBlockCompSeqHint,
  .expose = blockCompSeqExpose,
  .seekToHeader = seekToHeader,
  .printPosDiags = printBlockEncPosDiags,
  .printExtPosDiags = displayBlockEncBlock,
};
genometools-1.5.1/src/match/eis-bwtseq-construct.c000066400000000000000000000222541211610345200222050ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq_metadata.h"
#include "core/log.h"
#include "match/sarr-def.h"
#include "match/esa-map.h"
#include "match/eis-bitpackseqpos.h"
#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-construct.h"
#include "match/eis-bwtseq-extinfo.h"
#include "match/eis-bwtseq-param.h"
#include "match/eis-bwtseq-priv.h"
#include "match/eis-encidxseq.h"
#include "match/eis-encidxseq-construct.h"

BWTSeq *
gt_availBWTSeq(const struct bwtParam *params, GtLogger *verbosity,
            GtError *err)
{
  struct BWTSeq *bwtSeq = NULL;
  Suffixarray suffixArray;
  unsigned long len;
  gt_assert(params && err);
  gt_error_check(err);
  if (streamsuffixarray(&suffixArray, SARR_SUFTAB | SARR_BWTTAB
                        | SARR_ESQTAB, gt_str_get(params->projectName),
                        verbosity, err))
  {
    gt_error_unset(err);
    if (streamsuffixarray(&suffixArray, SARR_SUFTAB | SARR_ESQTAB,
                          gt_str_get(params->projectName), verbosity, err))
    {
      GtEncseqMetadata *emd = NULL;
      gt_error_unset(err);
      emd = gt_encseq_metadata_new(gt_str_get(params->projectName), err);
      if (emd == NULL)
        return NULL;
      len = gt_encseq_metadata_total_length(emd);
      gt_encseq_metadata_delete(emd);
    } else {
      len = gt_encseq_total_length(suffixArray.encseq) + 1;
    }
  } else {
    len = gt_encseq_total_length(suffixArray.encseq) + 1;
  }
  bwtSeq = gt_availBWTSeqFromSA(params, &suffixArray, len, err);
  gt_freesuffixarray(&suffixArray);
  return bwtSeq;
}

BWTSeq *
gt_trSuftab2BWTSeq(const struct bwtParam *params, GtLogger *verbosity,
                GtError *err)
{
  struct BWTSeq *bwtSeq = NULL;
  Suffixarray suffixArray;
  unsigned long len;
  gt_assert(params && err);
  gt_error_check(err);
  do
  {
    if (streamsuffixarray(&suffixArray,
                          SARR_SUFTAB | SARR_BWTTAB | SARR_ESQTAB,
                          gt_str_get(params->projectName), verbosity, err))
    {
      gt_error_unset(err);
      if (streamsuffixarray(&suffixArray, SARR_SUFTAB | SARR_ESQTAB,
                            gt_str_get(params->projectName), verbosity, err))
      {
        gt_error_set(err, "suffix array project %s does not hold required "
                     "suffix array (.suf) and encoded sequence (.esq) "
                     "information!", gt_str_get(params->projectName));
        break;
      }
    }
    len = gt_encseq_total_length(suffixArray.encseq) + 1;
    bwtSeq = gt_createBWTSeqFromSA(params, &suffixArray, len, err);
    gt_freesuffixarray(&suffixArray);
  } while (0);
  return bwtSeq;
}

BWTSeq *
gt_availBWTSeqFromSA(const struct bwtParam *params, Suffixarray *sa,
                  unsigned long totalLen, GtError *err)
{
  BWTSeq *bwtSeq;
  gt_assert(sa && params && err);
  gt_error_check(err);
  /* try loading index */
  bwtSeq = gt_loadBWTSeqForSA(gt_str_get(params->projectName),
                              params->seqParams.encType,
                              params->seqParams.EISFeatureSet,
                              gt_encseq_alphabet(sa->encseq), err);
  /* if loading didn't work try on-demand creation */
  if (!bwtSeq)
  {
    gt_error_unset(err);
    bwtSeq = gt_createBWTSeqFromSA(params, sa, totalLen, err);
  }
  else
  {
    fputs("Using pre-computed sequence index.\n", stderr);
  }
  return bwtSeq;
}

enum {
  GT_ALPHABETHANDLING_DEFAULT = 0,
  GT_ALPHABETHANDLING_W_RANK  = 1,
};

static const enum rangeSortMode GTAlphabetRangeSort[][2] =
{
  { SORTMODE_VALUE, SORTMODE_UNDEFINED },
  { SORTMODE_VALUE, SORTMODE_RANK }
};

BWTSeq *
gt_loadBWTSeq(const char *projectName, int BWTOptFlags,
              GT_UNUSED GtLogger *verbosity, GtError *err)
{
  struct BWTSeq *bwtSeq = NULL;
  GtEncseq *encseq;
  GtEncseqLoader *el;
  gt_assert(projectName && err);
  gt_error_check(err);

  el = gt_encseq_loader_new();
  gt_encseq_loader_do_not_require_sds_tab(el);
  gt_encseq_loader_do_not_require_des_tab(el);
  gt_encseq_loader_do_not_require_ssp_tab(el);
  encseq = gt_encseq_loader_load(el, projectName, err);
  gt_encseq_loader_delete(el);

  if (encseq == NULL)
    return NULL;
  bwtSeq = gt_loadBWTSeqForSA(projectName, BWT_ON_BLOCK_ENC, BWTOptFlags,
                           gt_encseq_alphabet(encseq), err);
  gt_encseq_delete(encseq);
  return bwtSeq;
}

BWTSeq *
gt_loadBWTSeqForSA(const char *projectName, enum seqBaseEncoding encType,
                   int BWTOptFlags, const GtAlphabet *gtalphabet,
                   GtError *err)
{
  struct BWTSeq *bwtSeq = NULL;
  EISeq *seqIdx = NULL;
  MRAEnc *alphabet = NULL;
  gt_assert(projectName && gtalphabet && err);
  alphabet = gt_SANewMRAEnc(gtalphabet);
  seqIdx = gt_loadEncIdxSeqForSA(gtalphabet, projectName, encType,
                                 gt_convertBWTOptFlags2EISFeatures(BWTOptFlags),
                                 err);
  if (seqIdx != NULL)
  {
    bwtSeq = gt_newBWTSeq(seqIdx, alphabet,
                          GTAlphabetRangeSort[GT_ALPHABETHANDLING_DEFAULT]);
  }
  if (!bwtSeq)
  {
    gt_MRAEncDelete(alphabet);
    if (seqIdx)
    {
      gt_deleteEncIdxSeq(seqIdx);
    }
  }
  return bwtSeq;
}

BWTSeq *
gt_createBWTSeqFromSA(const struct bwtParam *params, Suffixarray *sa,
                   unsigned long totalLen, GtError *err)
{
  BWTSeq *bwtSeq = NULL;
  if (!sa->longest.defined)
  {
    gt_log_log("error: position of null-rotation/longest suffix not available"
               " for project %s\n", gt_str_get(params->projectName));
  }
  else
  {
    SuffixarrayFileInterface sai;
    gt_initSuffixarrayFileInterface(&sai, totalLen, sa);
    bwtSeq = gt_createBWTSeqFromSAI(params, &sai, err);
    gt_destructSuffixarrayFileInterface(&sai);
  }
  return bwtSeq;
}

static inline void
buildSpRTable(const struct bwtParam *params,
              unsigned long totalLen,
              const GtEncseq *encseq,
              GtReadmode readmode,
              SpecialsRankLookup **sprTable,
              const enum rangeSortMode **rangeSort)
{
  if (params->featureToggles & BWTReversiblySorted)
  {
    int sampleIntervalLog2 = params->sourceRankInterval;
    if (sampleIntervalLog2 == -1)
    {
      sampleIntervalLog2
        = gt_requiredUIntBits(requiredUlongBits(totalLen));
    }
    *sprTable = gt_newSpecialsRankLookup(encseq, readmode, sampleIntervalLog2);
  }
  *rangeSort = GTAlphabetRangeSort[sprTable?
                                   GT_ALPHABETHANDLING_W_RANK:
                                   GT_ALPHABETHANDLING_DEFAULT];
}

static BWTSeq *
gt_createBWTSeqFromSASS(const struct bwtParam *params, SASeqSrc *src,
                     SpecialsRankLookup *sprTable,
                     const enum rangeSortMode *rangeSort,
                     GtError *err);

BWTSeq *
gt_createBWTSeqFromSAI(const struct bwtParam *params,
                    SuffixarrayFileInterface *sai,
                    GtError *err)
{
  BWTSeq *bwtSeq;
  SpecialsRankLookup *sprTable = NULL;
  const enum rangeSortMode *rangeSort;
  gt_assert(sai && err && params);
  buildSpRTable(params, SAIGetLength(sai), SAIGetEncSeq(sai),
                SAIGetGtReadmode(sai), &sprTable, &rangeSort);
  bwtSeq = gt_createBWTSeqFromSASS(params, SAI2SASS(sai), sprTable, rangeSort,
                                err);
  if (sprTable)
    gt_deleteSpecialsRankLookup(sprTable);
  return bwtSeq;
}

BWTSeq *
gt_createBWTSeqFromSfxI(const struct bwtParam *params, sfxInterface *sfxi,
                     GtError *err)
{
  BWTSeq *bwtSeq;
  SpecialsRankLookup *sprTable = NULL;
  const enum rangeSortMode *rangeSort;
  gt_assert(sfxi && params && err);
  buildSpRTable(params, gt_SfxIGetLength(sfxi), gt_SfxIGetEncSeq(sfxi),
                gt_SfxIGetReadmode(sfxi), &sprTable, &rangeSort);
  bwtSeq = gt_createBWTSeqFromSASS(params, gt_SfxI2SASS(sfxi), sprTable,
                                   rangeSort,
                                   err);
  if (sprTable)
    gt_deleteSpecialsRankLookup(sprTable);
  return bwtSeq;
}

static BWTSeq *
gt_createBWTSeqFromSASS(const struct bwtParam *params, SASeqSrc *src,
                     SpecialsRankLookup *sprTable,
                     const enum rangeSortMode *rangeSort,
                     GtError *err)
{
  EISeq *seqIdx = NULL;
  BWTSeq *bwtSeq = NULL;
  seqIdx = gt_createBWTSeqGeneric(params, gt_createEncIdxSeqGen, src,
                               rangeSort, sprTable, err);
  if (seqIdx)
  {
    MRAEnc *alphabet = SASSNewMRAEnc(src);
    bwtSeq = gt_newBWTSeq(seqIdx, alphabet, rangeSort);
    if (!bwtSeq)
    {
      gt_deleteEncIdxSeq(seqIdx);
      gt_MRAEncDelete(alphabet);
    }
  }
  return bwtSeq;
}
genometools-1.5.1/src/match/eis-bwtseq-construct.h000066400000000000000000000077411211610345200222160ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_CONSTRUCT_H
#define EIS_BWTSEQ_CONSTRUCT_H

/**
 * \file eis-bwtseq-construct.h
 * Interface definitions for construction of an indexed representation of the
 * BWT of a sequence as presented by Manzini and Ferragina (Compressed
 * Representations of Sequences and Full-Text Indexes, 2006)
 * \author Thomas Jahns 
 */

#include "match/sarr-def.h"
#include "match/eis-bwtseq.h"
#include "match/eis-suffixerator-interface.h"
#include "match/eis-suffixarray-interface.h"

/**
 * \brief Loads (or creates if necessary) an encoded indexed sequence
 * object of the BWT transform.
 * @param params a struct holding parameter information for index construction
 * @param sa Suffixarray data structure to build BWT index from
 * @param totalLen length of sorted sequence (including terminator)
 * @param err genometools error object reference
 * @return reference to new BWT sequence object
 */
BWTSeq *
gt_availBWTSeqFromSA(const struct bwtParam *params, Suffixarray *sa,
                  unsigned long totalLen, GtError *err);

/**
 * \brief Loads an encoded indexed sequence object of the
 * BWT transform.
 * @param params a struct holding parameter information for index construction
 * @param sa Suffixarray data structure to build BWT index from
 * @param totalLen length of BWT sequence (including terminator symbol)
 * @param err genometools error object reference
 * @return reference to new BWT sequence object
 */
BWTSeq *
gt_loadBWTSeqForSA(const char *projectName, enum seqBaseEncoding encType,
                int BWTOptFlags, const GtAlphabet *gtalphabet,
                GtError *err);

/**
 * \brief Creates an encoded indexed sequence object of the BWT transform.
 * @param params a struct holding parameter information for index construction
 * @param si Suffixerator interface to read data for BWT index from
 * @param totalLen length of BWT sequence (including terminator symbol)
 * @param err genometools reference for core functions
 * @return reference to new BWT sequence object
 */
BWTSeq *
gt_createBWTSeqFromSfxI(const struct bwtParam *params, sfxInterface *si,
                     GtError *err);

/**
 * \brief Creates or loads an encoded indexed sequence object of the
 * BWT transform.
 * @param params a struct holding parameter information for index construction
 * @param sa suffix array to read data for BWT index from
 * @param totalLen length of BWT sequence (including terminator symbol)
 * @param err genometools reference for core functions
 * @return reference to new BWT sequence object
 */
BWTSeq *
gt_createBWTSeqFromSA(const struct bwtParam *params, Suffixarray *sa,
                   unsigned long totalLen, GtError *err);

/**
 * \brief Creates or loads an encoded indexed sequence object of the
 * BWT transform.
 * @param params a struct holding parameter information for index construction
 * @param sai interface to suffix array to read data for BWT index from
 * @param totalLen length of BWT sequence (including terminator symbol)
 * @param err genometools reference for core functions
 * @return reference to new BWT sequence object
 */
BWTSeq *
gt_createBWTSeqFromSAI(const struct bwtParam *params,
                    SuffixarrayFileInterface *sai,
                    GtError *err);

#endif
genometools-1.5.1/src/match/eis-bwtseq-context-param.c000066400000000000000000000026211211610345200227370ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "match/eis-bwtseq-context-param.h"

void
gt_registerCtxMapOptions(GtOptionParser *op, int *ilogOut)
{
 GtOption *option = gt_option_new_int_min_max(
    "ctxilog", "specify the interval of context sampling as log value\n"
    "parameter i means that each 2^i-th position of source is sampled for "
    "rank\n-1 => chooses default of log(log(sequence length))\n"
    "-2 => generates no map",
    ilogOut, CTX_MAP_ILOG_NOMAP, CTX_MAP_ILOG_AUTOSIZE,
    sizeof (unsigned long) * CHAR_BIT - 1);
  gt_option_parser_add_option(op, option);
}
genometools-1.5.1/src/match/eis-bwtseq-context-param.h000066400000000000000000000030021211610345200227360ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_CONTEXT_PARAM_H
#define EIS_BWTSEQ_CONTEXT_PARAM_H

#include 

#include "core/minmax.h"
#include "core/option_api.h"

/* #include "core/bitpackstring.h" Not necessary. Stefan */
#include "match/eis-bitpackseqpos.h"

enum ctxMapSize {
  CTX_MAP_ILOG_NOMAP = -2,
  CTX_MAP_ILOG_AUTOSIZE = -1,
};

void
gt_registerCtxMapOptions(GtOptionParser *op, int *ilogOut);

static inline bool
ctxMapILogIsValid(unsigned long seqLen, short mapIntervalLog2)
{
  return (mapIntervalLog2 == CTX_MAP_ILOG_NOMAP
          || mapIntervalLog2 == CTX_MAP_ILOG_AUTOSIZE
          || (mapIntervalLog2 >= 0
              && mapIntervalLog2
              < MIN(requiredUlongBits(seqLen),
                    sizeof (unsigned long) * CHAR_BIT)));
}

#endif
genometools-1.5.1/src/match/eis-bwtseq-context-priv.h000066400000000000000000000026141211610345200226260ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_CONTEXT_PRIV_H
#define EIS_BWTSEQ_CONTEXT_PRIV_H

#include "match/eis-bwtseq-context.h"

struct BWTSeqContextRetriever
{
  unsigned long mapInterval, mapMask;
  const BWTSeq *bwtSeq;
  BitString revMapMMap,         /**< holds the page aligned result
                                 * from mmap, later used in munmap  */
    revMap;                     /**< maps positions in the original
                                 * sequence to positions in the BWT */
  uint16_t mapIntervalLog2;
  uint16_t bitsPerUlong;
};

static inline unsigned long
numMapEntries(unsigned long seqLen, unsigned short mapIntervalLog2);

#endif
genometools-1.5.1/src/match/eis-bwtseq-context-siop.h000066400000000000000000000037571211610345200226310ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_CONTEXT_SIOP_H
#define EIS_BWTSEQ_CONTEXT_SIOP_H

#include 
#ifndef S_SPLINT_S
#include 
#endif

#include "match/eis-bitpackseqpos.h"
#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-context.h"
#include "match/eis-bwtseq-context-priv.h"
#include "match/eis-encidxseq.h"

static inline unsigned long
numMapEntries(unsigned long seqLen, unsigned short mapIntervalLog2)
{
  return (seqLen + (1<> mapIntervalLog2;
}

static inline struct SeqMark
BWTSeqCRNextMark(const BWTSeqContextRetriever *bwtSeqCR, unsigned long pos)
{
  unsigned long seqLen, mapMask;
  struct SeqMark nextMark;
  gt_assert(bwtSeqCR);
  seqLen = BWTSeqLength(bwtSeqCR->bwtSeq);
  gt_assert(pos < seqLen);
  mapMask = bwtSeqCR->mapMask;
  /* rounds up to next multiple of mapInterval */
  nextMark.textPos = (pos + mapMask) & ~mapMask;
  if (nextMark.textPos < seqLen)
  {
    nextMark.bwtPos
      = gt_bsGetUlong(bwtSeqCR->revMap,
                    (nextMark.textPos >> bwtSeqCR->mapIntervalLog2)
                    * bwtSeqCR->bitsPerUlong, bwtSeqCR->bitsPerUlong);
  }
  else
  {
    nextMark.textPos = seqLen - 1;
    nextMark.bwtPos = BWTSeqTerminatorPos(bwtSeqCR->bwtSeq);
  }
  return nextMark;
}

#endif
genometools-1.5.1/src/match/eis-bwtseq-context.c000066400000000000000000000321071211610345200216430ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include 

#include "core/bitpackstring.h"
#include "match/dataalign.h"
#include "core/fa.h"
#include "core/str.h"
#include "core/xansi_api.h"

#include "match/eis-bitpackseqpos.h"
#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-context.h"
#include "match/eis-bwtseq-context-priv.h"
#include "match/eis-seqdatasrc.h"

struct BWTSeqContextRetrieverFactory
{
  unsigned long seqLen, currentSfxPos, moduloMask;
  bool constructionComplete;
  unsigned short mapIntervalLog2;
  FILE *mapTableDiskBackingStore;
  GtStr *mapTableDBSPath;
};

#define die(msg) die_func(msg, __FILE__, __LINE__)

static inline void
die_func(const char *errMsg, const char *file, int line)
{
  fprintf(stderr, "error: %s: %s at %s, line %d", errMsg, strerror(errno),
          file, line);
  exit(GT_EXIT_PROGRAMMING_ERROR);
}

enum
{
  BLOCK_IO_SIZE = BUFSIZ / sizeof (unsigned long),
};

static void
initBWTSeqContextRetrieverFactory(BWTSeqContextRetrieverFactory *newFactory,
                                  unsigned long seqLen,
                                  short mapIntervalLog2)
{
  FILE *fp;
  gt_assert(ctxMapILogIsValid(seqLen, mapIntervalLog2));
  if (mapIntervalLog2 == CTX_MAP_ILOG_AUTOSIZE)
  {
    mapIntervalLog2 = gt_requiredUIntBits(requiredUlongBits(seqLen));
  }
  newFactory->seqLen = seqLen;
  newFactory->currentSfxPos = 0;
  newFactory->moduloMask = (1 << mapIntervalLog2) - 1;
  newFactory->mapIntervalLog2 = mapIntervalLog2;
  newFactory->constructionComplete = false;
  newFactory->mapTableDBSPath = gt_str_new();
  fp = newFactory->mapTableDiskBackingStore
    = gt_xtmpfp_generic(newFactory->mapTableDBSPath,
                        TMPFP_AUTOREMOVE | TMPFP_OPENBINARY);
  {
    off_t backingStoreSize = numMapEntries(seqLen, mapIntervalLog2), i;
    unsigned long buf[BLOCK_IO_SIZE];
    memset(buf, 0, sizeof (buf));
    for (i = BLOCK_IO_SIZE; i < backingStoreSize; i += BLOCK_IO_SIZE)
    {
      gt_xfwrite(buf, sizeof (buf[0]), BLOCK_IO_SIZE, fp);
    }
    {
      unsigned leftOver = backingStoreSize % BLOCK_IO_SIZE;
      if (leftOver > 0) {
        gt_xfwrite(buf, sizeof (buf[0]), leftOver, fp);
      }
    }
  }
}

BWTSeqContextRetrieverFactory *
gt_newBWTSeqContextRetrieverFactory(unsigned long seqLen, short mapIntervalLog2)
{
  BWTSeqContextRetrieverFactory *newFactory;
  newFactory = gt_malloc(sizeof (*newFactory));
  initBWTSeqContextRetrieverFactory(newFactory, seqLen, mapIntervalLog2);
  return newFactory;
}

static void
destructBWTSeqContextRetrieverFactory(BWTSeqContextRetrieverFactory *factory)
{
  gt_fa_xfclose(factory->mapTableDiskBackingStore);
  gt_str_delete(factory->mapTableDBSPath);
}

void
gt_deleteBWTSeqContextRetrieverFactory(BWTSeqContextRetrieverFactory *factory)
{
  destructBWTSeqContextRetrieverFactory(factory);
  gt_free(factory);
}

static inline void
addMapVal(BWTSeqContextRetrieverFactory *factory,
          unsigned long currentSfxPos, unsigned long origPos)
{
  off_t mapPos = ((off_t)origPos >> factory->mapIntervalLog2)
    * sizeof (unsigned long);
  unsigned long mapVal = currentSfxPos;
  FILE *fp = factory->mapTableDiskBackingStore;
  if (fseeko(fp, mapPos, SEEK_SET) == -1)
    die("failed to seek in backing store");
  gt_xfwrite(&mapVal, sizeof (mapVal), 1, fp);
}

/**
 * @return number of not processed suffix indices, i.e. 0 on success
 */
unsigned long
gt_BWTSCRFReadAdvance(BWTSeqContextRetrieverFactory *factory,
                   unsigned long chunkSize,
                   SeqDataReader readSfxIdx)
{
  unsigned long buf[BLOCK_IO_SIZE], sfxIdxLeft = chunkSize;
  gt_assert(factory);
  while (sfxIdxLeft)
  {
    unsigned long len = MIN(BLOCK_IO_SIZE, sfxIdxLeft);
    if (SDRRead(readSfxIdx, buf, len)
        != len)
    {
      fputs("error: short read when building context retriever!\n", stderr);
      abort();
    }
    gt_BWTSCRFMapAdvance(factory, buf, len);
    sfxIdxLeft -= len;
  }
  return chunkSize - sfxIdxLeft;
}

size_t
gt_BWTSCRFMapAdvance(BWTSeqContextRetrieverFactory *factory,
                  const unsigned long *src,
                  size_t len)
{
  unsigned long currentSfxPos;
  gt_assert(factory);
  currentSfxPos = factory->currentSfxPos;
  {
    size_t i;
    unsigned long mask = factory->moduloMask,
      seqLen = factory->seqLen;
    for (i = 0; i < len; ++i)
    {
      if (!(((src[i] + seqLen - 1)%seqLen) & mask))
        addMapVal(factory, currentSfxPos + i, ((src[i] + seqLen - 1)%seqLen));
    }
  }
  factory->currentSfxPos = currentSfxPos + len;
  return len;
}

bool
gt_BWTSCRFFinished(const BWTSeqContextRetrieverFactory *factory)
{
  return factory->currentSfxPos == factory->seqLen;
}

static inline void
readBS2Map(BWTSeqContextRetrieverFactory *factory,
           BWTSeqContextRetriever *gt_newBWTSeqCR);

static inline bool
BWTSeqCRMapOpen(unsigned short mapIntervalLog2,
                unsigned short bitsPerUlong,
                unsigned long seqLen,
                const char *projectName,
                bool createMapFile,
                BWTSeqContextRetriever *gt_newBWTSeqCR);

BWTSeqContextRetriever *
gt_BWTSCRFGet(BWTSeqContextRetrieverFactory *factory,
              const BWTSeq *bwtSeq,
              const char *projectName)
{
  unsigned short bitsPerUlong, mapIntervalLog2;
  BWTSeqContextRetriever *gt_newBWTSeqCR;
  gt_assert(factory && projectName);
  bitsPerUlong = requiredUlongBits(factory->seqLen - 1);
  gt_newBWTSeqCR = gt_malloc(sizeof (*gt_newBWTSeqCR));
  gt_newBWTSeqCR->mapIntervalLog2 = mapIntervalLog2 = factory->mapIntervalLog2;
  gt_newBWTSeqCR->bitsPerUlong = bitsPerUlong;
  gt_newBWTSeqCR->bwtSeq = bwtSeq;
  gt_newBWTSeqCR->mapInterval = 1 << factory->mapIntervalLog2;
  gt_newBWTSeqCR->mapMask = gt_newBWTSeqCR->mapInterval - 1;
  if (!BWTSeqCRMapOpen(mapIntervalLog2, bitsPerUlong, factory->seqLen,
                       projectName, true, gt_newBWTSeqCR))
  {
    gt_free(gt_newBWTSeqCR);
    return NULL;
  }
  readBS2Map(factory, gt_newBWTSeqCR);
  return gt_newBWTSeqCR;
}

static inline void
readBlock2Buf(FILE *fp,
              unsigned long *buf,
              size_t len,
              BitString bitstring,
              BitOffset offset,
              unsigned short bitsPerUlong)
{
  if (fread(buf, sizeof (buf[0]), len, fp) != len)
    die("short read when reading backing store");
  gt_bsStoreUniformUlongArray(bitstring, offset, bitsPerUlong, len,
#ifdef _LP64
                             (uint64_t*) buf);
#else
                             (uint32_t*) buf);
#endif
}

static inline void
readBS2Map(BWTSeqContextRetrieverFactory *factory,
           BWTSeqContextRetriever *gt_newBWTSeqCR)
{
  FILE *fp = factory->mapTableDiskBackingStore;
  unsigned long buf[BLOCK_IO_SIZE];
  off_t i, numFullBlocks, lastBlockLen;
  BitString revMap =  gt_newBWTSeqCR->revMap;
  BitOffset storePos = 0;
  unsigned bitsPerUlong = gt_newBWTSeqCR->bitsPerUlong;
  {
    off_t numEntries  = numMapEntries(factory->seqLen,
                                      factory->mapIntervalLog2);
    numFullBlocks = numEntries / BLOCK_IO_SIZE;
    lastBlockLen = numEntries % BLOCK_IO_SIZE;
  }
  if (fseeko(fp, 0, SEEK_SET) == -1)
    die("failed seek in backing store");
  for (i = 0; i < numFullBlocks; ++i )
  {
    readBlock2Buf(fp, buf, BLOCK_IO_SIZE, revMap, storePos, bitsPerUlong);
    storePos += bitsPerUlong * BLOCK_IO_SIZE;
  }
  readBlock2Buf(fp, buf, lastBlockLen, revMap, storePos, bitsPerUlong);
}

enum {
  HEADER_ENTRY_BITS = 16,
};

static inline bool
BWTSeqCRMapOpen(unsigned short mapIntervalLog2,
                unsigned short bitsPerUlong,
                unsigned long seqLen,
                const char *projectName,
                bool createMapFile,
                BWTSeqContextRetriever *gt_newBWTSeqCR)
{
  FILE *mapFile = NULL;
  BitString mapMap = NULL;
  GtStr *mapName = NULL;
  gt_assert(projectName);
  do {
    size_t headerBitElems = bitElemsAllocSize(2 * HEADER_ENTRY_BITS),
      headerSize = headerBitElems * sizeof (BitElem),
      mapSize = headerSize + sizeof (BitElem)
      * bitElemsAllocSize(bitsPerUlong * numMapEntries(
                            seqLen, mapIntervalLog2));
    mapName = gt_str_new_cstr(projectName);
    {
      char buf[1 + 4 + 3];
      snprintf(buf, sizeof (buf), ".%ucxm", (unsigned)mapIntervalLog2);
      gt_str_append_cstr(mapName, buf);
      if (createMapFile)
      {
        /* write header information, for reference to verify noone
         * toyed with the file name */
        BitElem headerBuf[headerBitElems];
        if (!(mapFile = gt_fa_fopen(gt_str_get(mapName), "w+b", NULL)))
          break;
        gt_bsStoreUInt16(headerBuf, 0, HEADER_ENTRY_BITS, mapIntervalLog2);
        gt_bsStoreUInt16(headerBuf, HEADER_ENTRY_BITS, HEADER_ENTRY_BITS,
                      bitsPerUlong);
        gt_xfwrite(headerBuf,  sizeof (headerBuf), 1, mapFile);
        if (fseeko(mapFile, mapSize - 1, SEEK_SET))
          break;
        /* write one byte so mmap works for full file */
        gt_xfwrite(&buf, 1, 1, mapFile);
        gt_xfflush(mapFile);
      }
      else
      {
        /* read header information, for reference to verify noone
         * toyed with the file name */
        BitElem headerBuf[headerBitElems];
        if (!(mapFile = gt_fa_fopen(gt_str_get(mapName), "rb", NULL)))
          break;
        if (fread(headerBuf,  sizeof (headerBuf), 1, mapFile) != 1)
          break;
        if (gt_bsGetUInt16(headerBuf, 0, HEADER_ENTRY_BITS) != mapIntervalLog2
            || (gt_bsGetUInt16(headerBuf, HEADER_ENTRY_BITS, HEADER_ENTRY_BITS)
                != bitsPerUlong))
        {
          fprintf(stderr, "error: context map file %s contains corrupted "
                  "data.\n", gt_str_get(mapName));
          break;
        }
      }
    }
    mapMap = gt_fa_mmap_generic_fd(fileno(mapFile), gt_str_get(mapName),
                                   mapSize, 0, createMapFile, false, NULL);
    gt_newBWTSeqCR->revMap = (gt_newBWTSeqCR->revMapMMap = mapMap) + headerSize;
  } while (0);
  if (mapName) gt_str_delete(mapName);
  if (mapFile) gt_fa_xfclose(mapFile);
  return mapMap != NULL;
}

BWTSeqContextRetriever *
gt_BWTSeqCRLoad(const BWTSeq *bwtSeq,
             const char *projectName,
             short mapIntervalLog2)
{
  unsigned long seqLen;
  unsigned short bitsPerUlong;
  BWTSeqContextRetriever *gt_newBWTSeqCR;
  gt_assert(bwtSeq && projectName);
  seqLen = BWTSeqLength(bwtSeq);
  bitsPerUlong = requiredUlongBits(seqLen - 1);
  gt_newBWTSeqCR = gt_malloc(sizeof (*gt_newBWTSeqCR));
  gt_newBWTSeqCR->bitsPerUlong = bitsPerUlong;
  gt_newBWTSeqCR->bwtSeq = bwtSeq;
  if (mapIntervalLog2 != CTX_MAP_ILOG_AUTOSIZE)
  {
    if (!BWTSeqCRMapOpen(mapIntervalLog2, bitsPerUlong, seqLen,
                         projectName, false, gt_newBWTSeqCR))
    {
      gt_free(gt_newBWTSeqCR);
      return NULL;
    }
  }
  else
  {
    short mapIntervalLog2Max = bitsPerUlong;
    mapIntervalLog2 = 0;
    while (!BWTSeqCRMapOpen(mapIntervalLog2, bitsPerUlong, seqLen,
                            projectName, false, gt_newBWTSeqCR)
           && mapIntervalLog2 < mapIntervalLog2Max)
      ++mapIntervalLog2;
    if (!gt_newBWTSeqCR->revMap)
    {
      gt_free(gt_newBWTSeqCR);
      return NULL;
    }
  }
  gt_newBWTSeqCR->mapIntervalLog2 = mapIntervalLog2;
  gt_newBWTSeqCR->mapInterval = 1 << mapIntervalLog2;
  gt_newBWTSeqCR->mapMask = gt_newBWTSeqCR->mapInterval - 1;
  return gt_newBWTSeqCR;
}

void
gt_deleteBWTSeqCR(BWTSeqContextRetriever *bwtSeqCR)
{
  gt_assert(bwtSeqCR);
  gt_fa_xmunmap(bwtSeqCR->revMapMMap);
  gt_free(bwtSeqCR);
}

void
gt_BWTSeqCRAccessSubseq(const BWTSeqContextRetriever *bwtSeqCR,
                     unsigned long start, size_t len, Symbol subseq[])
{
  struct SeqMark currentPos;
  struct extBitsRetrieval extBits;
  const BWTSeq *bwtSeq;
  initExtBitsRetrieval(&extBits);
  gt_assert(bwtSeqCR);
  gt_assert(start < BWTSeqLength(bwtSeqCR->bwtSeq));
  bwtSeq = bwtSeqCR->bwtSeq;
  {
    unsigned long end = start + len - 1;
    currentPos = BWTSeqCRNextMark(bwtSeqCR, end);
    gt_assert(currentPos.textPos >= end);
    while (currentPos.textPos > end)
    {
      currentPos.bwtPos = BWTSeqLFMap(bwtSeq, currentPos.bwtPos, &extBits);
      --currentPos.textPos;
    }
  }
  {
    unsigned long i = len;
    while (i)
    {
      --i;
      subseq[i] = BWTSeqGetSym(bwtSeq, currentPos.bwtPos);
      currentPos.bwtPos = BWTSeqLFMap(bwtSeq, currentPos.bwtPos, &extBits);
#ifndef NDEBUG
      --currentPos.textPos;
#endif
    }
  }
  gt_assert(currentPos.textPos + 1 == start);
}
genometools-1.5.1/src/match/eis-bwtseq-context.h000066400000000000000000000071731211610345200216550ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_CONTEXT_H
#define EIS_BWTSEQ_CONTEXT_H

/**
 * @file eis-bwtseq-context.h
 * @brief interface for generating arbitrary context from a
 * packedindex object
 */

#include "match/eis-seqdatasrc.h"

#include "match/eis-bwtseq-context-param.h"

typedef struct BWTSeqContextRetriever BWTSeqContextRetriever;

typedef struct BWTSeqContextRetrieverFactory BWTSeqContextRetrieverFactory;

/**
 * @param seqLen length of sequence to build context map for
 * @param mapIntervalLog2 unless equal to CTX_MAP_ILOG_NOMAP or
 * CTX_MAP_ILOG_AUTOSIZE compute map with interval 1<

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/chardef.h"
#include "core/log.h"
#include "core/minmax.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "match/eis-specialsrank.h"
#include "match/eis-bitpackseqpos.h"
#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-extinfo.h"
#include "match/eis-bwtseq-priv.h"
#include "match/eis-bwtseq-context.h"
#include "match/eis-headerid.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-sa-common.h"

/**
 * @file eis-bwtseq-extinfo.c generic methods for bwt index creation and
 * everything related to storing/retrieving locate information
 */

struct locateHeader
{
  unsigned long rot0Pos;
  unsigned locateInterval;
  int featureToggles;
};

enum {
  LOCATE_HEADER_SIZE = sizeof (struct locateHeader),
};

struct locateHeaderWriteInfo
{
  SASeqSrc *src;
  unsigned locateInterval;
  int featureToggles;
};

static int
writeLocateInfoHeader(FILE *fp, void *cbData)
{
  struct locateHeader headerData;
  Definedunsignedlong rot0Pos;
  const struct locateHeaderWriteInfo *headerSrc = cbData;
  gt_assert(cbData);
  headerData.locateInterval = headerSrc->locateInterval;
  rot0Pos = SASSGetRot0Pos(headerSrc->src);
  if (!rot0Pos.defined)
  {
    fputs("Invalid index construction: position of suffix 0 unknown!\n",
          stderr);
    abort();
  }
  headerData.rot0Pos = rot0Pos.valueunsignedlong;
  headerData.featureToggles = headerSrc->featureToggles;
  gt_xfwrite(&headerData, sizeof (headerData), 1, fp);
  return 1;
}

/**
 * @return 0 on error
 */
static inline int
readLocateInfoHeader(EISeq *seqIdx, struct locateHeader *headerData)
{
  FILE *fp;
  gt_assert(seqIdx && headerData);
  if (!(fp = EISSeekToHeader(seqIdx, LOCATE_INFO_IN_INDEX_HEADERID, NULL)))
    return 0;
  if (fread(headerData, sizeof (*headerData), 1, fp) != 1)
    return 0;
  return 1;
}

struct sortModeHeader
{
  uint32_t bitsPerOrigRank;
  const MRAEnc *alphabet;
  const enum rangeSortMode *rangeSort;
};

static inline uint32_t
computeSortModeHeaderSize(const MRAEnc *alphabet)
{
  return sizeof (uint32_t) + sizeof (int16_t) * MRAEncGetNumRanges(alphabet);
}

static int
writeRankSortHeader(FILE *fp, void *cbData)
{
  struct sortModeHeader *headerData = cbData;
  gt_assert(cbData);
  gt_xfwrite(&headerData->bitsPerOrigRank, sizeof (headerData->bitsPerOrigRank),
             1, fp);
  {
    size_t i, numRanges = MRAEncGetNumRanges(headerData->alphabet);
    for (i = 0; i < numRanges; ++i)
    {
      int16_t mode = headerData->rangeSort[i];
      gt_xfwrite(&mode, sizeof (mode), 1, fp);
    }
  }
  return 1;
}

static inline int
readRankSortHeader(EISeq *seqIdx, uint32_t *bitsPerOrigRank,
                   const MRAEnc *alphabet,
                   enum rangeSortMode *rangeSort)
{
  FILE *fp;
  gt_assert(seqIdx && alphabet && bitsPerOrigRank && rangeSort);
  if (!(fp = EISSeekToHeader(seqIdx, RANK_SORT_HEADERID, NULL)))
    return 0;
  if (fread(bitsPerOrigRank, sizeof (*bitsPerOrigRank), 1, fp) != 1)
    return 0;
  {
    uint16_t mode;
    size_t i, numRanges = MRAEncGetNumRanges(alphabet);
    for (i = 0; i < numRanges; ++i)
    {
      if (fread(&mode, sizeof (mode), 1, fp) != 1)
        return 0;
      rangeSort[i] = mode;
    }
  }
  return 1;
}

struct seqRevMapEntry
{
  unsigned long bwtPos, origPos;
};

struct addLocateInfoState
{
  unsigned long seqLen, extraLocMarksUpperBound;
  const MRAEnc *alphabet;
  const enum rangeSortMode *rangeSort;
  SeqDataReader readUlong;
  RandomSeqAccessor origSeqAccess;
  unsigned locateInterval, bitsPerOrigPos, bitsPerUlong,
    bitsPerOrigRank;
  const SpecialsRankLookup *sprTable;
  int featureToggles;
  size_t revMapQueueSize;
  struct seqRevMapEntry *revMapQueue;
  size_t origRanksQueueSize;
  unsigned long *origRanksQueue;
  BWTSeqContextRetrieverFactory *ctxFactory;
};

static inline unsigned
bitsPerPosUpperBoundWithoutSegmentAggregates(struct addLocateInfoState *state)
{
  unsigned bitsPerPos = 0;
  if (state->featureToggles & BWTLocateCount)
    /* bitsPerUlong is actually an upper bound of log(segmentLen) to
     * identify each locate mark */
    bitsPerPos += state->bitsPerUlong;
  bitsPerPos += state->bitsPerOrigPos; /* stored for every position */
  /* rank sorting data if needed */
  bitsPerPos += state->bitsPerOrigRank;
  return bitsPerPos;
}

static inline unsigned
bitsPerPosUpperBound(struct addLocateInfoState *state)
{
  unsigned bitsPerPos = bitsPerPosUpperBoundWithoutSegmentAggregates(state);
  if (state->featureToggles & BWTLocateCount)
    /* +1 to account for the contribution to count value (which will
     * actually use log(blockLen) instead of blockLen bits, i.e. less
     * than 1 bit per position) */
    bitsPerPos += 1;
  return bitsPerPos;
}

static bool
locBitsUpperBounds(void *cbState, struct segmentDesc *desc,
                   size_t numSegmentDesc, struct varBitsEstimate *result)
{
  struct addLocateInfoState *state = cbState;
  gt_assert(cbState);
  if (state->featureToggles & (BWTLocateCount | BWTLocateBitmap))
  {
    unsigned maxBitsPerPos = bitsPerPosUpperBound(state);
    result->maxBitsPerPos = maxBitsPerPos;
    if (desc)
    {
      size_t i, maxSegLen = 0;
      BitOffset maxBitsTotal = 0;
      unsigned long numSegmentsTotal = 0;
      unsigned bitsPerOrigRank = state->bitsPerOrigRank;
      for (i = 0; i < numSegmentDesc; ++i)
      {
        size_t len = desc[i].len;
        maxSegLen = MAX(len, maxSegLen);
        if (state->featureToggles & BWTLocateCount)
          maxBitsTotal += requiredUlongBits(len) * desc[i].repeatCount;
        numSegmentsTotal += desc[i].repeatCount;
      }
      maxBitsTotal +=
        (state->seqLen / state->locateInterval + state->extraLocMarksUpperBound)
        * (((state->featureToggles & BWTLocateCount) ?
            requiredUlongBits(maxSegLen) : 0)
           + state->bitsPerOrigPos);
      if (bitsPerOrigRank)
      {
        unsigned long maxRank = specialsRank(state->sprTable, state->seqLen);
        /* rank values stored */
        maxBitsTotal += maxRank * bitsPerOrigRank;
      }
      result->maxBitsPerBucket =
        /* locate marks and rank sorts */
        maxSegLen * bitsPerPosUpperBoundWithoutSegmentAggregates(state)
        /* count of locate marks */
        + ((state->featureToggles & BWTLocateCount) ?
           requiredUlongBits(maxSegLen) : 0);
      result->maxBitsTotal = maxBitsTotal;
      return true;
    }
    else
      return false;
  }
  else
  {
    result->maxBitsTotal = result->maxBitsPerBucket
      = result->maxBitsPerPos = 0;
    return false;
  }
}

static void
initAddLocateInfoState(struct addLocateInfoState *state,
                       RandomSeqAccessor origSeqAccess,
                       SeqDataReader readUlong,
                       const MRAEnc *alphabet, const struct seqStats *stats,
                       const enum rangeSortMode *rangeSort,
                       unsigned long srcLen, const struct bwtParam *params,
                       const SpecialsRankLookup *sprTable,
                       unsigned bitsPerOrigRank,
                       BWTSeqContextRetrieverFactory *ctxFactory)
{
  unsigned long lastPos;
  unsigned aggregationExpVal;
  unsigned locateInterval;
  gt_assert(state);
  state->alphabet = alphabet;
  state->seqLen = srcLen;
  state->rangeSort = rangeSort;
  state->readUlong = readUlong;
  state->origSeqAccess = origSeqAccess;
  state->featureToggles = params->featureToggles;
  aggregationExpVal = gt_estimateSegmentSize(¶ms->seqParams);
  locateInterval = params->locateInterval;
  lastPos = srcLen - 1;
  state->locateInterval = locateInterval;
  state->bitsPerUlong = requiredUlongBits(lastPos);
  state->bitsPerOrigRank = bitsPerOrigRank;
  state->sprTable = sprTable;
  if (locateInterval)
  {
    if (params->featureToggles & BWTReversiblySorted)
      state->bitsPerOrigPos = requiredUlongBits(lastPos/locateInterval);
    else
      state->bitsPerOrigPos = requiredUlongBits(lastPos);
    state->origRanksQueueSize = state->revMapQueueSize =aggregationExpVal;
    state->revMapQueue = gt_malloc(sizeof (state->revMapQueue[0])
                                   * state->revMapQueueSize);
    state->origRanksQueue = gt_malloc(sizeof (state->origRanksQueue[0])
                                      * state->origRanksQueueSize);
    state->bitsPerOrigRank = bitsPerOrigRank;
    /* if there are rank sorted symbols, but no rank sorting is
     * available, extra locate marks will be inserted, at most every
     * second position can be marked this way because for every
     * SORTMODE_VALUE -> SORTMODE_{RANk|UNDEF} transition there must be one
     * inverse transition */
    if (!(params->featureToggles & BWTReversiblySorted)
        && locateInterval > 1)
    {
      unsigned long stdLocMarks = srcLen / locateInterval,
        extraLocMarksUpperBound = MIN(srcLen/2, srcLen - stdLocMarks);
      if (stats)
      {
        unsigned long nonValSortSyms = 0;
        unsigned i;
        for (i = 0; i <= UINT8_MAX; ++i)
          if (MRAEncSymbolHasValidMapping(alphabet, i)
              && !gt_MRAEncSymbolIsInSelectedRanges(
                alphabet, MRAEncMapSymbol(alphabet, i),
                SORTMODE_VALUE, (int *)rangeSort))
            nonValSortSyms += stats->symbolDistributionTable[i];
        extraLocMarksUpperBound = MIN3(extraLocMarksUpperBound, nonValSortSyms,
                                       srcLen - nonValSortSyms);
      }
      state->extraLocMarksUpperBound = extraLocMarksUpperBound;
    }
    else
    {
      state->extraLocMarksUpperBound = 0;
    }
  }
  else
  {
    state->extraLocMarksUpperBound = 0;
    state->bitsPerOrigPos = state->bitsPerOrigRank = 0;
    state->origRanksQueueSize = state->revMapQueueSize = 0;
    state->origRanksQueue = NULL;
    state->revMapQueue = NULL;
  }
  state->ctxFactory = ctxFactory;
}

static void
destructAddLocateInfoState(struct addLocateInfoState *state)
{
  gt_free(state->revMapQueue);
  gt_free(state->origRanksQueue);
}

static inline int
isSortModeTransition(RandomSeqAccessor origSeqAccess, unsigned long seqLen,
                     const MRAEnc *alphabet,
                     const enum rangeSortMode *rangeSort,
                     unsigned long pos)
{
  Symbol syms[2];
  if (pos > 0 && pos < seqLen - 1)
  {
#ifndef NDEBUG
    int retcode =
#endif
      accessSequence(origSeqAccess, syms, pos - 1, 2);
    gt_assert(retcode == 2);
  }
  else if (pos == 0)
  {
#ifndef NDEBUG
    int retcode =
#endif
      accessSequence(origSeqAccess, syms + 1, 0, 1);
    gt_assert(retcode == 1);
    syms[0] = UNDEFBWTCHAR;
  }
  else /* pos == seqLen - 1 */
  {
#ifndef NDEBUG
    int retcode =
#endif
      accessSequence(origSeqAccess, syms, seqLen - 2, 1);
    gt_assert(retcode == 1);
    syms[1] = UNDEFBWTCHAR;
  }
  {
    AlphabetRangeID range[2];
    range[0] = MRAEncGetRangeOfSymbol(alphabet,
                                      MRAEncMapSymbol(alphabet, syms[0]));
    range[1] = MRAEncGetRangeOfSymbol(alphabet,
                                      MRAEncMapSymbol(alphabet, syms[1]));
    return rangeSort[range[0]] != rangeSort[range[1]];
  }
}

static BitOffset
addLocateInfo(BitString cwDest, BitOffset cwOffset,
              BitString varDest, BitOffset varOffset,
              GT_UNUSED unsigned long start, unsigned long len, void *cbState)
{
  BitOffset bitsWritten = 0;
  struct addLocateInfoState *state = cbState;
  unsigned bitsPerBWTPos, bitsPerOrigPos, bitsPerOrigRank;
  int retcode;
  unsigned locateInterval;
  gt_assert(varDest && cbState);
  locateInterval = state->locateInterval;
  /* 0. resize caches if necessary */
  if (locateInterval && len > state->revMapQueueSize)
  {
    state->revMapQueue = gt_realloc(state->revMapQueue,
                                    len * sizeof (state->revMapQueue[0]));
    state->revMapQueueSize = len;
  }
  if (state->sprTable && len > state->origRanksQueueSize)
  {
    state->origRanksQueue = gt_realloc(state->origRanksQueue,
                                          len *
                                          sizeof (state->origRanksQueue[0]));
    state->origRanksQueueSize = len;
  }
  bitsPerBWTPos = requiredUlongBits(len - 1);
  bitsPerOrigPos = state->bitsPerOrigPos;
  bitsPerOrigRank = state->bitsPerOrigRank;
  {
    unsigned long i, mapVal;
    size_t revMapQueueLen = 0, origRanksQueueLen = 0;
    int reversiblySorted = state->featureToggles & BWTReversiblySorted,
      locateBitmap = state->featureToggles & BWTLocateBitmap;
    /* read len suffix array indices from suftab */
    /* TODO: decide  on reasonable buffering of mapVal */
    for (i = 0; i < len; ++i)
    {
      /* add locate data if necessary */
      if (locateInterval)
      {
        int insertExtraLocateMark = 0;
        /* 1.a read array index*/
        if ((retcode = SDRRead(state->readUlong, &mapVal, 1)) != 1)
          return (BitOffset)-1;
        /* 1.b find current symbol and compare to special ranges */
        insertExtraLocateMark = !reversiblySorted &&
          isSortModeTransition(state->origSeqAccess, state->seqLen,
                               state->alphabet, state->rangeSort,
                               mapVal);
        /* 1.c check wether the index into the original sequence is an
         * even multiple of the sampling interval, or a not-reversible
         * sort mode transition occurred */
        if (!(mapVal % locateInterval) || insertExtraLocateMark)
        {
          /* 1.c.1 enter index into cache */
          state->revMapQueue[revMapQueueLen].bwtPos = i;
          state->revMapQueue[revMapQueueLen].origPos
            = reversiblySorted ? mapVal/state->locateInterval : mapVal;
          ++revMapQueueLen;
          /* 1.c.2 mark position in bwt sequence */
          if (locateBitmap)
            bsSetBit(cwDest, cwOffset + i);
        }
        else
          if (locateBitmap)
            gt_bsClearBit(cwDest, cwOffset + i);
      }
      /* and add data for extra sort information */
      if (bitsPerOrigRank)
      {
        Symbol BWTSym;
        const MRAEnc *alphabet = state->alphabet;
        if (mapVal != 0)
          accessSequence(state->origSeqAccess, &BWTSym, mapVal - 1, 1);
        else
          BWTSym = UNDEFBWTCHAR;
        if (state->rangeSort[MRAEncGetRangeOfSymbol(
                alphabet, MRAEncMapSymbol(alphabet, BWTSym))]
            == SORTMODE_RANK)
        {
          state->origRanksQueue[origRanksQueueLen++] =
            specialsRank(state->sprTable,
                         mapVal != 0 ? mapVal - 1 : state->seqLen - 1);
        }
      }
      if (state->ctxFactory)
      {
        gt_BWTSCRFMapAdvance(state->ctxFactory, &mapVal, 1);
      }
    }
    /* 2. copy revMapQueue into output */
    if (locateInterval)
    {
      int locateCount = state->featureToggles & BWTLocateCount;
      if (locateCount)
      {
        unsigned bitsPerCount = requiredUlongBits(len);
        gt_bsStoreUlong(varDest, varOffset + bitsWritten, bitsPerCount,
                      revMapQueueLen);
        bitsWritten += bitsPerCount;
      }
      for (i = 0; i < revMapQueueLen; ++i)
      {
        if (locateCount)
        {
          gt_bsStoreUlong(varDest, varOffset + bitsWritten, bitsPerBWTPos,
                        state->revMapQueue[i].bwtPos);
          bitsWritten += bitsPerBWTPos;
        }
        gt_bsStoreUlong(varDest, varOffset + bitsWritten, bitsPerOrigPos,
                      state->revMapQueue[i].origPos);
        bitsWritten += bitsPerOrigPos;
      }
    }
    if (bitsPerOrigRank)
    {
      unsigned bitsPerOrigRank = state->bitsPerOrigRank;
      if (origRanksQueueLen)
      {
        gt_bsStoreUniformUlongArray(varDest, varOffset + bitsWritten,
                                  bitsPerOrigRank, origRanksQueueLen,
#ifdef _LP64
                             (uint64_t*) state->origRanksQueue);
#else
                             (uint32_t*) state->origRanksQueue);
#endif
        bitsWritten += bitsPerOrigRank * origRanksQueueLen;
      }
    }
  }
  return bitsWritten;
}

static inline int
sortModeHeaderNeeded(const MRAEnc *alphabet,
                     const enum rangeSortMode *rangeSort,
                     const SpecialsRankLookup *sprTable)
{
  bool hasRankSortedRanges = false;
  AlphabetRangeID i, numRanges = MRAEncGetNumRanges(alphabet);
  for (i = 0; i < numRanges; ++i)
    hasRankSortedRanges |= (rangeSort[i] == SORTMODE_RANK?1:0);
  return (hasRankSortedRanges && sprTable);
}

EISeq *
gt_createBWTSeqGeneric(const struct bwtParam *params,
                       indexCreateFunc createIndex,
                       SASeqSrc *src,
                       const enum rangeSortMode rangeSort[],
                       const SpecialsRankLookup *sprTable,
                       GtError *err)
{
  struct encIdxSeq *baseSeqIdx = NULL;
  struct addLocateInfoState varState;
  bool varStateIsInitialized = false;
  unsigned locateInterval;
  BWTSeqContextRetrieverFactory *buildContextMap = NULL;
  gt_assert(src && params && err);
  gt_error_check(err);
  locateInterval = params->locateInterval;
  do
  {
    struct locateHeaderWriteInfo locHeaderData
      = { src, locateInterval, params->featureToggles };
    struct sortModeHeader sortModeHeader;
    void *p[] = { &locHeaderData , &sortModeHeader };
    uint16_t headerIDs[] = { LOCATE_INFO_IN_INDEX_HEADERID,
                             RANK_SORT_HEADERID };
    uint32_t headerSizes[] = { LOCATE_HEADER_SIZE,
                               0 };
    headerWriteFunc headerFuncs[] = { writeLocateInfoHeader,
                                      writeRankSortHeader };
    size_t numHeaders = 0;
    unsigned bitsPerOrigRank = 0;
    unsigned long totalLen = SASSGetLength(src);
    const MRAEnc *alphabet = SASSGetMRAEnc(src);
    MRAEnc *baseAlphabet = SASSNewMRAEnc(src);
    /* FIXME: this  has to work also when locateInterval == 0 and
     * sprTable != NULL */
    if (params->ctxMapILog != CTX_MAP_ILOG_NOMAP)
      buildContextMap = gt_newBWTSeqContextRetrieverFactory(totalLen,
                                                         params->ctxMapILog);
    if (locateInterval)
    {
      ++numHeaders;
      if (sortModeHeaderNeeded(alphabet, rangeSort, sprTable))
      {
        unsigned long
#ifndef NDEBUG
          origSeqLen = gt_encseq_total_length(
                                                gt_SPRTGetOrigEncseq(sprTable)),
#endif
          maxRank;
        gt_assert(origSeqLen == totalLen - 1);
        maxRank = specialsRank(sprTable, totalLen - 1);
        bitsPerOrigRank = sortModeHeader.bitsPerOrigRank
          = requiredUlongBits(maxRank);
        sortModeHeader.alphabet = alphabet;
        sortModeHeader.rangeSort = rangeSort;
        headerSizes[1] = computeSortModeHeaderSize(alphabet);
        ++numHeaders;
      }
      {
        SeqDataReader readSfxIdx = SASSCreateReader(src, SFX_REQUEST_SUFTAB);
        if (SDRIsValid(readSfxIdx))
        {
          initAddLocateInfoState(
            &varState, SASSGetOrigSeqAccessor(src), readSfxIdx,
            alphabet, SASSGetSeqStats(src), rangeSort, totalLen, params,
            bitsPerOrigRank?sprTable:NULL, bitsPerOrigRank,
            buildContextMap);
          varStateIsInitialized = true;
        }
        else
        {
          gt_error_set(err, "error: locate sampling requested but not available"
                       " for project %s\n", gt_str_get(params->projectName));
        }
      }
    }
    if (!(baseSeqIdx
          = createIndex(totalLen, gt_str_get(params->projectName), baseAlphabet,
                        SASSGetSeqStats(src),
                        SASSCreateReader(src, SFX_REQUEST_BWTTAB),
                        ¶ms->seqParams, numHeaders,
                        headerIDs, headerSizes, headerFuncs, p,
                        locateInterval?addLocateInfo:NULL,
                        /* one bit per position if using bitmap */
                        (params->featureToggles & BWTLocateBitmap)?1:0,
                        locateInterval?locBitsUpperBounds:NULL, &varState,
                        err)))
      break;
    if (buildContextMap)
    {
      if (!gt_BWTSCRFFinished(buildContextMap))
      {
        fputs("error: context table construction incomplete!\n", stderr);
      }
      else
      {
        BWTSeqContextRetriever *ctxRetrieve =
          gt_BWTSCRFGet(buildContextMap, NULL, gt_str_get(params->projectName));
        gt_deleteBWTSeqCR(ctxRetrieve);
      }
    }
  } while (0);
  if (buildContextMap)
    gt_deleteBWTSeqContextRetrieverFactory(buildContextMap);
  if (varStateIsInitialized)
    destructAddLocateInfoState(&varState);
  return baseSeqIdx;
}

static inline BitOffset
searchLocateCountMark(const BWTSeq *bwtSeq, unsigned long pos,
                      struct extBitsRetrieval *extBits)
{
  unsigned i, numMarks, bitsPerCount;
  BitOffset markOffset;
  EISRetrieveExtraBits(bwtSeq->seqIdx, pos, EBRF_RETRIEVE_CWBITS
                       | EBRF_RETRIEVE_VARBITS, extBits, bwtSeq->hint);
  markOffset = extBits->varOffset;
  bitsPerCount = requiredUlongBits(extBits->len);
  numMarks = gt_bsGetUlong(extBits->varPart, markOffset, bitsPerCount);
  if (numMarks)
  {
    unsigned bitsPerBWTPos = requiredUlongBits(extBits->len - 1),
      bitsPerOrigPos = requiredUlongBits(
        ((bwtSeq->featureToggles & BWTReversiblySorted) ?
         (BWTSeqLength(bwtSeq) - 1) / bwtSeq->locateSampleInterval :
         BWTSeqLength(bwtSeq) - 1));
    unsigned long cmpPos = pos - extBits->start;
    markOffset += bitsPerCount;
    for (i = 0; i < numMarks; ++i)
    {
      unsigned long markedPos = gt_bsGetUlong(extBits->varPart, markOffset,
                                     bitsPerBWTPos);
      if (markedPos < cmpPos)
        markOffset += bitsPerBWTPos + bitsPerOrigPos;
      else if (markedPos > cmpPos)
        break;
      else if (markedPos == cmpPos)
        return markOffset + bitsPerBWTPos;
    }
  }
  return 0;
}

int
gt_BWTSeqPosHasLocateInfo(const BWTSeq *bwtSeq, unsigned long pos,
                       struct extBitsRetrieval *extBits)
{
  if (bwtSeq->featureToggles & BWTLocateBitmap)
  {
    EISRetrieveExtraBits(bwtSeq->seqIdx, pos, EBRF_RETRIEVE_CWBITS, extBits,
                         bwtSeq->hint);
    return gt_bsGetBit(extBits->cwPart,
                       extBits->cwOffset + pos - extBits->start);
  }
  else if (bwtSeq->featureToggles & BWTLocateCount)
  {
    BitOffset markOffset = searchLocateCountMark(bwtSeq, pos, extBits);
    return markOffset != 0;
  }
#ifndef NDEBUG
  else
  {
    fputs("Trying to locate in BWT sequence index without locate information.",
          stderr);
    abort();
  }
#endif
  return 0;
}

unsigned long
gt_BWTSeqLocateMatch(const BWTSeq *bwtSeq, unsigned long pos,
                  struct extBitsRetrieval *extBits)
{
  if (bwtSeq->featureToggles & BWTLocateBitmap)
  {
    unsigned long nextLocate = pos;
    unsigned locateOffset = 0;
    while (!gt_BWTSeqPosHasLocateInfo(bwtSeq, nextLocate, extBits))
      nextLocate = BWTSeqLFMap(bwtSeq, nextLocate, extBits), ++locateOffset;
    EISRetrieveExtraBits(bwtSeq->seqIdx, nextLocate,
                         EBRF_RETRIEVE_CWBITS | EBRF_RETRIEVE_VARBITS,
                         extBits, bwtSeq->hint);
    {
      unsigned long maxPosVal = ((bwtSeq->featureToggles & BWTReversiblySorted)?
                          (BWTSeqLength(bwtSeq) - 1)
                          /bwtSeq->locateSampleInterval:
                          BWTSeqLength(bwtSeq) - 1);
      unsigned bitsPerCount = requiredUlongBits(extBits->len),
        bitsPerBWTPos = requiredUlongBits(extBits->len - 1),
        bitsPerOrigPos = requiredUlongBits(maxPosVal);
      BitOffset locateRecordIndex =
        gt_bs1BitsCount(extBits->cwPart, extBits->cwOffset,
                     nextLocate - extBits->start),
        locateRecordOffset = ((bwtSeq->featureToggles & BWTLocateCount?
                               bitsPerBWTPos:0) + bitsPerOrigPos)
        * locateRecordIndex
        + ((bwtSeq->featureToggles & BWTLocateCount)?bitsPerCount:0);
      unsigned long matchPos =
        gt_bsGetUlong(
          extBits->varPart, extBits->varOffset + locateRecordOffset
          + ((bwtSeq->featureToggles & BWTLocateCount)?bitsPerBWTPos:0),
          bitsPerOrigPos);
      if (bwtSeq->featureToggles & BWTReversiblySorted)
        matchPos = matchPos * bwtSeq->locateSampleInterval;
      matchPos += locateOffset;
      gt_assert(!(bwtSeq->featureToggles & BWTLocateCount)
             || gt_bsGetUlong(extBits->varPart,
                            extBits->varOffset + locateRecordOffset,
                            bitsPerBWTPos)
             == nextLocate - extBits->start);
      return matchPos;
    }
  }
  else if (bwtSeq->featureToggles & BWTLocateCount)
  {
    BitOffset markOffset;
    unsigned long nextLocate = pos, matchPos;
    unsigned locateOffset = 0;  /* mark is at most locateInterval
                                 * positions away */
    unsigned bitsPerOrigPos
      = requiredUlongBits(((bwtSeq->featureToggles & BWTReversiblySorted)?
                            (BWTSeqLength(bwtSeq) - 1)
                            /bwtSeq->locateSampleInterval:
                            BWTSeqLength(bwtSeq) - 1));
    while ((markOffset = searchLocateCountMark(bwtSeq, nextLocate,
                                               extBits)) == 0)
    {
      nextLocate = BWTSeqLFMap(bwtSeq, nextLocate, extBits);
      ++locateOffset;
      gt_assert(locateOffset <= BWTSeqLength(bwtSeq));
    }
    matchPos = gt_bsGetUlong(extBits->varPart, markOffset, bitsPerOrigPos);
    if (bwtSeq->featureToggles & BWTReversiblySorted)
        matchPos = matchPos * bwtSeq->locateSampleInterval;
    matchPos += locateOffset;
    return matchPos;
  }
  /* Internal error: Trying to locate in BWT sequence index without locate
     information. */
   abort();
   return 0; /* shut up compiler */
}

static inline BitOffset
locateVarBits(const BWTSeq *bwtSeq, struct extBitsRetrieval *extBits)
{
  BitOffset numLocBits = 0;
  unsigned bitsPerBWTPos = requiredUlongBits(extBits->len - 1),
    bitsPerOrigPos = requiredUlongBits(
      ((bwtSeq->featureToggles & BWTReversiblySorted) ?
       (BWTSeqLength(bwtSeq) - 1) / bwtSeq->locateSampleInterval :
       BWTSeqLength(bwtSeq) - 1));
  if (bwtSeq->featureToggles & BWTLocateBitmap)
  {
    unsigned numMarks = gt_bs1BitsCount(extBits->cwPart, extBits->cwOffset,
                                     extBits->len);
    numLocBits = numMarks * bitsPerOrigPos;
  }
  else if (bwtSeq->featureToggles & BWTLocateCount)
  {
    BitOffset markOffset = extBits->varOffset;
    unsigned bitsPerCount = requiredUlongBits(extBits->len);
    unsigned numMarks = gt_bsGetUlong(extBits->varPart, markOffset,
                                    bitsPerCount);
    numLocBits = bitsPerCount + numMarks * (bitsPerBWTPos + bitsPerOrigPos);
  }
  return numLocBits;
}

unsigned long
gt_BWTSeqGetRankSort(const BWTSeq *bwtSeq, unsigned long pos,
                  AlphabetRangeID range, struct extBitsRetrieval *extBits)
{
  BitOffset locVarBits;
  AlphabetRangeSize rSize;
  gt_assert(bwtSeq->rangeSort[range] == SORTMODE_RANK);
  EISRetrieveExtraBits(bwtSeq->seqIdx, pos, EBRF_RETRIEVE_CWBITS
                       | EBRF_RETRIEVE_VARBITS, extBits, bwtSeq->hint);
  locVarBits = locateVarBits(bwtSeq, extBits);
  rSize = MRAEncGetRangeSize(EISGetAlphabet(bwtSeq->seqIdx), range);
  {
    unsigned long ranks[rSize * 2];
    unsigned long BWTRankTotal = 0;
    AlphabetRangeSize i;
    EISPosPairRangeRank(bwtSeq->seqIdx, range, extBits->start, pos, ranks,
                        bwtSeq->hint);
    for (i = 0; i < rSize; ++i)
      BWTRankTotal += ranks[i + rSize] - ranks[i];
    return gt_bsGetUlong(extBits->varPart, extBits->varOffset + locVarBits
                       + bwtSeq->bitsPerOrigRank * BWTRankTotal,
                       bwtSeq->bitsPerOrigRank);
  }
}

void
gt_BWTSeqInitLocateHandling(BWTSeq *bwtSeq,
                         const enum rangeSortMode *defaultRangeSort)
{
  struct encIdxSeq *seqIdx;
  struct locateHeader locHeader;
  gt_assert(bwtSeq);
  seqIdx = bwtSeq->seqIdx;
  if (!readLocateInfoHeader(seqIdx, &locHeader)
      || !locHeader.locateInterval)
  {
    gt_log_log("Index does not contain locate information.\n"
            "Localization of matches will not be supported!");
    bwtSeq->locateSampleInterval = 0;
    bwtSeq->featureToggles = BWTBaseFeatures;
  }
  else
  {
    bwtSeq->locateSampleInterval = locHeader.locateInterval;
    bwtSeq->rot0Pos = locHeader.rot0Pos;
    /* FIXME: this really deserves its own header */
    bwtSeq->featureToggles = locHeader.featureToggles;

    if (readRankSortHeader(seqIdx, &bwtSeq->bitsPerOrigRank,
                           bwtSeq->alphabet, bwtSeq->rangeSort))
      ;
    else
    {
      AlphabetRangeID numRanges = MRAEncGetNumRanges(bwtSeq->alphabet);
      bwtSeq->bitsPerOrigRank = 0;
      memcpy(bwtSeq->rangeSort, defaultRangeSort,
             numRanges * sizeof (defaultRangeSort[0]));
    }
  }
}
genometools-1.5.1/src/match/eis-bwtseq-extinfo.h000066400000000000000000000067151211610345200216460ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_EXTINFO_H
#define EIS_BWTSEQ_EXTINFO_H

/**
 * @file eis-bwtseq-extinfo.h
 * @brief Routines to add and query extension information embedded in
 * the base sequence index.
 * - generic BWT index creation routine
 */

#include "match/eis-specialsrank.h"
#include "match/eis-bwtseq.h"
#include "match/eis-encidxseq.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-random-seqaccess.h"
#include "match/eis-sa-common.h"
#include "match/eis-seqdatasrc.h"

/** The constructor for the base index must conform to this
 * signature. */
typedef EISeq *(*indexCreateFunc)(
  unsigned long totalLen, const char *projectName, MRAEnc *alphabet,
  const struct seqStats *stats, SeqDataReader BWTGenerator,
  const struct seqBaseParam *params, size_t numExtHeaders,
  const uint16_t *headerIDs, const uint32_t *extHeaderSizes,
  headerWriteFunc *extHeaderCallbacks,
  void **headerCBData, bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
  varExtBitsEstimator biVarBits, void *cbState, GtError *err);

/**
 * To enrich a base index with the information required for a BWT
 * index, wrap the base index constructor in a call to gt_createBWTSeqGeneric.
 * @param params holds all parameters for both, the BWT sequence
 * object and the base index
 * @param createIndex wrapped constructor
 * @param src passed to createIndex and used as source of suffix array
 * @param totalLen length of the sorted sequence plus terminator symbol
 * @param alphabet encoding to use for symbols of the input sequence
 * @param specialRanges one value describing for each range of
 * alphabet how symbols in this range are sorted
 * @param readOrigSeq makes the original sequence available
 * @param origSeqState opaque sequence object to pass to readOrigSeq
 * @param readNextUlong stream reader for the values of the suffix
 * array
 * @param spReadState opaque suffix array source object to pass to
 * readNextUlong
 * @param lrepFunc reports the position of the null-rotation
 * @param lrepState passed to lrepFunc
 * @param err
 */
EISeq *
gt_createBWTSeqGeneric(const struct bwtParam *params,
                       indexCreateFunc createIndex,
                       SASeqSrc *src,
                       const enum rangeSortMode rangeSort[],
                       const SpecialsRankLookup *sprTable,
                       GtError *err);

int
gt_BWTSeqPosHasLocateInfo(const BWTSeq *bwtSeq, unsigned long pos,
                       struct extBitsRetrieval *extBits);

unsigned long
gt_BWTSeqGetRankSort(const BWTSeq *bwtSeq, unsigned long pos,
                  AlphabetRangeID range, struct extBitsRetrieval *extBits);

void
gt_BWTSeqInitLocateHandling(BWTSeq *bwtSeq,
                         const enum rangeSortMode *defaultRangeSort);

#endif
genometools-1.5.1/src/match/eis-bwtseq-param.c000066400000000000000000000106001211610345200212510ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/error.h"
#include "core/option_api.h"
#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-param.h"
#include "match/eis-bwtseq-context-param.h"
#include "match/eis-encidxseq-param.h"

void
gt_registerPackedIndexOptions(GtOptionParser *op,
                              struct bwtOptions *paramOutput,
                              int defaultOptimizationFlags,
                              const GtStr *projectName)
{
  GtOption *option;

  gt_registerEncIdxSeqOptions(op, ¶mOutput->final.seqParams);

  paramOutput->final.featureToggles = BWTBaseFeatures;

  option = gt_option_new_uint(
    "locfreq", "specify the locate frequency\n"
    "parameter i means that each i-th position of input string is stored\n"
    "0 => no locate information", ¶mOutput->final.locateInterval, 16U);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool(
    "locbitmap", "marked/unmarked positions for locate are stored as bitmaps\n"
    "this gives faster location of hits but increases the index by 1 bit per"
    " symbol", ¶mOutput->useLocateBitmap, true);
  gt_option_parser_add_option(op, option);
  paramOutput->useLocateBitmapOption = option;

  option = gt_option_new_bool(
    "sprank", "build rank table for special symbols\n"
    "this produces an index which can be used to regenerate the "
    "original sequence but increases the memory used during index creation",
    ¶mOutput->useSourceRank, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_int_min_max(
    "sprankilog", "specify the interval of rank sampling as log value\n"
    "parameter i means that each 2^i-th position of source is sampled for "
    "rank\nundefined => chooses default of log(log(sequence length))",
    ¶mOutput->final.sourceRankInterval, -1, -1,
    sizeof (unsigned long) * CHAR_BIT - 1);
  gt_option_parser_add_option(op, option);

  gt_registerCtxMapOptions(op, ¶mOutput->final.ctxMapILog);

  paramOutput->final.projectName = projectName;

  paramOutput->defaultOptimizationFlags = defaultOptimizationFlags;
}

static int
estimateBestLocateTypeFeature(const struct bwtOptions *paramOutput)
{
  if (!paramOutput->final.locateInterval)
    return BWTBaseFeatures;
  {
    /* two cases: we store 1 bit per position or log(segmentlen) for
     * each marked position plus one to note the number of marked positions */
    unsigned segmentLen = gt_estimateSegmentSize(¶mOutput->final.seqParams);
    if (segmentLen > (segmentLen + 1) * gt_requiredUIntBits(segmentLen)
                     / paramOutput->final.locateInterval)
      return BWTLocateCount;
    else
      return BWTLocateBitmap;
  }
}

void
gt_computePackedIndexDefaults(struct bwtOptions *paramOutput, int extraToggles)
{
  if (gt_option_is_set(paramOutput->useLocateBitmapOption))
    paramOutput->final.featureToggles
      |= (paramOutput->useLocateBitmap?BWTLocateBitmap:BWTLocateCount);
  else
    paramOutput->final.featureToggles
      |= estimateBestLocateTypeFeature(paramOutput);
  if (paramOutput->final.sourceRankInterval >= 0
      || paramOutput->useSourceRank)
    paramOutput->final.featureToggles |= BWTReversiblySorted;
  paramOutput->final.featureToggles |= extraToggles;
  paramOutput->final.seqParams.EISFeatureSet
    = gt_convertBWTOptFlags2EISFeatures(paramOutput->defaultOptimizationFlags);
}

int
gt_convertBWTOptFlags2EISFeatures(int BWTOptFlags)
{
  int EISFeatureSet = EIS_FEATURE_NONE;
  if (BWTOptFlags & BWTDEFOPT_LOW_RAM_OVERHEAD)
  {
    EISFeatureSet &= ~EIS_FEATURE_REGION_SUMS;
  }
  if (BWTOptFlags & BWTDEFOPT_FAST_RANK)
  {
    EISFeatureSet |= EIS_FEATURE_REGION_SUMS;
  }
  return EISFeatureSet;
}
genometools-1.5.1/src/match/eis-bwtseq-param.h000066400000000000000000000164311211610345200212660ustar00rootroot00000000000000/*
  Copyright (c) 2007,2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_PARAM_H
#define EIS_BWTSEQ_PARAM_H

/**
 * @file eis-bwtseq-param.h
 * @brief Routines to handle option processing for BWT index
 * construction and declaration of parameter types and corresponding
 * constant values.
 */

#include "core/option_api.h"

#include "match/eis-encidxseq-param.h"
/* #include "match/eis-bwtseq-context-param.h" not neccessary remove
 * Stefan */

/**
 * all parameters for building the BWT sequence index
 */
struct bwtParam
{
  struct seqBaseParam seqParams;  /**< holds extra parameter
                                   *   information specific to the
                                   *   base sequence storage */
  int featureToggles;             /**< set of bittoggles composed
                                   *   from enum BWTFeatures */
  unsigned locateInterval;        /**< store locate information
                                   * (mapping from BWT sequence to
                                   * original sequence for every nth
                                   * position in original sequence) at
                                   * this frequency, unless
                                   * locateInterval = 0, which implies
                                   * storing no locate information at
                                   * all */
  int sourceRankInterval;         /**< makes ranges which are sorted in
                                   * rank mode reversibly sorted:
                                   * -1:
                                   *     inactive
                                   * 0...sizeof (unsigned long)*CHAR_BIT:
                                   *     build accel table
                                   *     with 1<

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_PRIV_H
#define EIS_BWTSEQ_PRIV_H

#include "core/chardef.h"
#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-extinfo.h"
#include "match/eis-encidxseq.h"
#include "match/pckbucket.h"

enum {
  bwtTerminatorSym = SEPARATOR - 3,
};

struct BWTSeq
{
  struct encIdxSeq *seqIdx;
  MRAEnc *alphabet;
  size_t alphabetSize;
  EISHint hint;
  unsigned locateSampleInterval; /**< no sampling if 0 */
  Symbol bwtTerminatorFallback;  /**< the terminator symbol has been
                                  * flattened into this symbol for
                                  * storage reasons */
  AlphabetRangeID bwtTerminatorFallbackRange;
  unsigned long rot0Pos;
  unsigned long *count;
  int featureToggles;
  unsigned bitsPerOrigRank;
  enum rangeSortMode *rangeSort;
  Pckbuckettable *pckbuckettable;
};

struct BWTSeqExactMatchesIterator
{
  struct matchBound bounds;
  unsigned long nextMatchBWTPos;
  struct extBitsRetrieval extBits;
};

unsigned long
gt_BWTSeqLocateMatch(const BWTSeq *bwtSeq, unsigned long pos,
                  struct extBitsRetrieval *extBits);

BWTSeq *
gt_newBWTSeq(EISeq *seqIdx, MRAEnc *alphabet,
          const enum rangeSortMode *defaultRangeSort);

#endif
genometools-1.5.1/src/match/eis-bwtseq-sass.c000066400000000000000000000154001211610345200211250ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/unused_api.h"

#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-context.h"
#include "match/eis-bwtseq-sass.h"
#include "match/eis-encidxseq.h"
#include "match/eis-list-do.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-sa-common.h"
#include "match/eis-sa-common-priv.h"

typedef struct BWTSeqReaderState BWTSeqReaderState;

struct BWTSeqReaderState
{
  BWTSeqReaderState *next;
  struct BWTSASeqSrc *backLink;
  unsigned long nextReadPos;
};

struct BWTSASeqSrc
{
  struct SASeqSrc baseClass;
  const BWTSeq *bwtSeq;
  const BWTSeqContextRetriever *ctxMap;
  BWTSeqReaderState *readerStateList;
};

typedef struct BWTSASeqSrc BWTSASeqSrc;

static inline BWTSASeqSrc*
SASS2BWTSASS(SASeqSrc *baseClass)
{
  return (BWTSASeqSrc *)
    ((char *)baseClass - offsetof(BWTSASeqSrc, baseClass));
}

static inline const BWTSASeqSrc *
constSASS2BWTSASS(const SASeqSrc *baseClass)
{
  return (const BWTSASeqSrc *)
    ((const char *)baseClass - offsetof(BWTSASeqSrc, baseClass));
}

static inline SASeqSrc *
BWTSASS2SASS(BWTSASeqSrc *bwtSASS)
{
  return &bwtSASS->baseClass;
}

static inline const SASeqSrc *
constBWTSASS2SASS(const BWTSASeqSrc *bwtSASS)
{
  return &bwtSASS->baseClass;
}

static Definedunsignedlong
BWTSASSGetRot0Pos(const struct SASeqSrc *baseClass)
{
  Definedunsignedlong val
    = { BWTSeqTerminatorPos(constSASS2BWTSASS(baseClass)->bwtSeq), true };
  return val;
}

static void
gt_deleteBWTSeqSASS(struct SASeqSrc *baseClass)
{
  destructSASeqSrc(baseClass);
  ListDo(BWTSeqReaderState, SASS2BWTSASS(baseClass)->readerStateList,
         gt_free(p));
  gt_free(SASS2BWTSASS(baseClass));
}

static size_t
BWTSASSAccessOrigSeq(const void *state,
                     Symbol *dest,
                     unsigned long pos,
                     size_t len)
{
  const BWTSeqContextRetriever *ctxMap = state;
  gt_assert(state);
  gt_BWTSeqCRAccessSubseq(ctxMap, pos, len, dest);
  return len;
}

static MRAEnc *
BWTSASSNewMRAEnc(const SASeqSrc *src)
{
  const BWTSASeqSrc *bwtSASeqSrc;
  gt_assert(src);
  bwtSASeqSrc = constSASS2BWTSASS(src);
  return gt_MRAEncCopy(EISGetAlphabet(BWTSeqGetEncIdxSeq(bwtSASeqSrc->bwtSeq)));
}

static SeqDataReader
BWTSASSCreateReader(SASeqSrc *src, enum sfxDataRequest request);

SASeqSrc *
gt_BWTSeqNewSASeqSrc(const BWTSeq *bwtSeq, const BWTSeqContextRetriever *ctxMap)
{
  struct BWTSASeqSrc *newBWTSASeqSrc;
  gt_assert(bwtSeq);
  newBWTSASeqSrc = gt_malloc(sizeof (*newBWTSASeqSrc));
  {
    RandomSeqAccessor origSeqAccess;
    if (ctxMap)
    {
      origSeqAccess.accessFunc = BWTSASSAccessOrigSeq;
      origSeqAccess.state = (void *)ctxMap;
    }
    else
    {
      origSeqAccess.accessFunc = NULL;
      origSeqAccess.state = NULL;
    }
    initSASeqSrc(&newBWTSASeqSrc->baseClass,
                 BWTSeqLength(bwtSeq),
                 NULL,
                 BWTSASSCreateReader,
                 BWTSASSGetRot0Pos,
                 NULL,
                 origSeqAccess,
                 gt_deleteBWTSeqSASS,
                 BWTSASSNewMRAEnc,
                 NULL, NULL);   /* since BWTSeq can regenerate
                                 * arbitrary portions of all
                                 * associated data (when reversibly
                                 * sorted) no generator is necessary
                                 * and all readers just keep their state
                                 */
  }
  newBWTSASeqSrc->ctxMap = ctxMap;
  newBWTSASeqSrc->bwtSeq = bwtSeq;
  newBWTSASeqSrc->readerStateList = NULL;
  return &newBWTSASeqSrc->baseClass;
}

static size_t
BWTSASSReadSufTab(SeqDataSrc src, void *dest, size_t len)
{
  const BWTSeq *bwtSeq;
  struct extBitsRetrieval extBits;
  gt_assert(src);
  initExtBitsRetrieval(&extBits);
  bwtSeq = ((BWTSeqReaderState *)src)->backLink->bwtSeq;
  size_t i;
  unsigned long pos = ((BWTSeqReaderState *)src)->nextReadPos;
  for (i = 0; i < len; ++i)
    ((unsigned long *)dest)[i] = gt_BWTSeqLocateMatch(bwtSeq,
                                                      pos + i,
                                                      &extBits);
  ((BWTSeqReaderState *)src)->nextReadPos = pos + len;
  destructExtBitsRetrieval(&extBits);
  return len;
}

static SeqDataReader
BWTSASSMakeSufTabReader(GT_UNUSED BWTSASeqSrc *bwtSASeqSrc,
                        BWTSeqReaderState *state)
{
  SeqDataReader reader = { state, BWTSASSReadSufTab };
  return reader;
}

static size_t
BWTSASSReadBWT(SeqDataSrc src, void *dest, size_t len)
{
  const BWTSeq *bwtSeq;
  gt_assert(src);
  bwtSeq = ((BWTSeqReaderState *)src)->backLink->bwtSeq;
  size_t i;
  unsigned long pos = ((BWTSeqReaderState *)src)->nextReadPos;
  for (i = 0; i < len; ++i)
    ((Symbol *)dest)[i] = BWTSeqGetSym(bwtSeq, pos + i);
  ((BWTSeqReaderState *)src)->nextReadPos = pos + len;
  return len;
}

static SeqDataReader
BWTSASSMakeBWTReader(GT_UNUSED BWTSASeqSrc *bwtSASeqSrc,
                     BWTSeqReaderState *state)
{
  SeqDataReader reader = { state, BWTSASSReadBWT };
  return reader;
}

static BWTSeqReaderState *
BWTSeqSASSAddReaderState(BWTSASeqSrc *bwtSASeqSrc)
{
  BWTSeqReaderState *newReader = gt_malloc(sizeof (*newReader));
  gt_assert(bwtSASeqSrc);
  newReader->backLink = bwtSASeqSrc;
  newReader->nextReadPos = 0;
  newReader->next = bwtSASeqSrc->readerStateList;
  bwtSASeqSrc->readerStateList = newReader;
  return newReader;
}

static SeqDataReader
BWTSASSCreateReader(SASeqSrc *src, enum sfxDataRequest rtype)
{
  struct seqDataReader reader = { NULL, NULL};
  BWTSASeqSrc *bwtSASeqSrc;
  gt_assert(src);
  bwtSASeqSrc = SASS2BWTSASS(src);
  switch (rtype)
  {
  case SFX_REQUEST_SUFTAB:
    reader = BWTSASSMakeSufTabReader(bwtSASeqSrc,
                                     BWTSeqSASSAddReaderState(bwtSASeqSrc));
    break;
  case SFX_REQUEST_BWTTAB:
    reader = BWTSASSMakeBWTReader(bwtSASeqSrc,
                                  BWTSeqSASSAddReaderState(bwtSASeqSrc));
    break;
  default:
    fprintf(stderr, "error: unimplemented request: %d, %s: %d!\n", rtype,
            __FILE__, __LINE__);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  return reader;
}
genometools-1.5.1/src/match/eis-bwtseq-sass.h000066400000000000000000000020401211610345200211260ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_SASS_H
#define EIS_BWTSEQ_SASS_H

#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-context.h"
#include "match/eis-sa-common.h"

SASeqSrc *
gt_BWTSeqNewSASeqSrc(const BWTSeq *bwtSeq,
                     const BWTSeqContextRetriever *ctxMap);

#endif
genometools-1.5.1/src/match/eis-bwtseq-siop.h000066400000000000000000000217401211610345200211370ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_SIOP_H
#define EIS_BWTSEQ_SIOP_H

/* trivial operations on BWTSeq objects go here for speed */

#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-priv.h"
#include "stamp.h"

static inline const MRAEnc *
BWTSeqGetAlphabet(const BWTSeq *seq)
{
  return seq->alphabet;
}

static inline unsigned long
BWTSeqLength(const BWTSeq *seq)
{
  return EISLength(seq->seqIdx);
}

static inline unsigned long
BWTSeqTerminatorPos(const BWTSeq *bwtSeq)
{
  return bwtSeq->rot0Pos;
}

static inline bool
BWTSeqHasLocateInformation(const BWTSeq *bwtSeq)
{
  return bwtSeq->locateSampleInterval != 0;
}

static inline unsigned long
BWTSeqTransformedOcc(const BWTSeq *bwtSeq, Symbol tsym, unsigned long pos)
{
  gt_assert(bwtSeq);
  /* two counts must be treated specially:
   * 1. for the symbols mapped to the same value as the terminator
   * 2. for queries of the terminator itself */
  if (tsym < bwtSeq->bwtTerminatorFallback)
    return EISSymTransformedRank(bwtSeq->seqIdx, tsym, pos, bwtSeq->hint);
  else if (tsym > bwtSeq->bwtTerminatorFallback
           && tsym != bwtSeq->alphabetSize - 1)
    return EISSymTransformedRank(bwtSeq->seqIdx, tsym, pos, bwtSeq->hint);
  else if (tsym == bwtSeq->bwtTerminatorFallback)
    return EISSymTransformedRank(bwtSeq->seqIdx, tsym, pos, bwtSeq->hint)
      - ((pos > BWTSeqTerminatorPos(bwtSeq))?1:0);
  else /* tsym == not flattened terminator == alphabetSize - 1 */
  {
    gt_assert(tsym == bwtSeq->alphabetSize - 1);
    return (pos > BWTSeqTerminatorPos(bwtSeq))?1:0;
  }
}

static inline GtUlongPair
BWTSeqTransformedPosPairOcc(const BWTSeq *bwtSeq, Symbol tSym,
                            unsigned long posA, unsigned long posB)
{
  gt_assert(bwtSeq);
  /* two counts must be treated specially:
   * 1. for the symbols mapped to the same value as the terminator
   * 2. for queries of the terminator itself */
  if (tSym < bwtSeq->bwtTerminatorFallback)
    return EISSymTransformedPosPairRank(bwtSeq->seqIdx, tSym, posA, posB,
                                        bwtSeq->hint);
  else if (tSym > bwtSeq->bwtTerminatorFallback
           && tSym != bwtSeq->alphabetSize - 1)
    return EISSymTransformedPosPairRank(bwtSeq->seqIdx, tSym, posA, posB,
                                        bwtSeq->hint);
  else if (tSym == bwtSeq->bwtTerminatorFallback)
    return EISSymTransformedPosPairRank(bwtSeq->seqIdx, tSym, posA, posB,
                                        bwtSeq->hint);
/*       - ((pos > BWTSeqTerminatorPos(bwtSeq))?1:0); */
  else /* tSym == not flattened terminator == alphabetSize - 1 */
  {
    GtUlongPair occ;
    gt_assert(tSym == bwtSeq->alphabetSize - 1);
    occ.a = (posA > BWTSeqTerminatorPos(bwtSeq))?1:0;
    occ.b = (posB > BWTSeqTerminatorPos(bwtSeq))?1:0;
    return occ;
  }
}

static inline unsigned long
BWTSeqOcc(const BWTSeq *bwtSeq, Symbol sym, unsigned long pos)
{
  gt_assert(bwtSeq);
  Symbol tSym = MRAEncMapSymbol(BWTSeqGetAlphabet(bwtSeq), sym);
  return BWTSeqTransformedOcc(bwtSeq, tSym, pos);
}

static inline GtUlongPair
BWTSeqPosPairOcc(const BWTSeq *bwtSeq, Symbol sym, unsigned long posA,
                 unsigned long posB)
{
  gt_assert(bwtSeq);
  Symbol tSym = MRAEncMapSymbol(BWTSeqGetAlphabet(bwtSeq), sym);
  return BWTSeqTransformedPosPairOcc(bwtSeq, tSym, posA, posB);
}

static inline void
BWTSeqRangeOcc(const BWTSeq *bwtSeq, AlphabetRangeID range, unsigned long pos,
               unsigned long *rangeOccs)
{
  gt_assert(bwtSeq && rangeOccs);
  gt_assert(range < MRAEncGetNumRanges(BWTSeqGetAlphabet(bwtSeq)));
  EISRangeRank(bwtSeq->seqIdx, range, pos, rangeOccs, bwtSeq->hint);
  if (range == bwtSeq->bwtTerminatorFallbackRange)
  {
    const MRAEnc *alphabet = BWTSeqGetAlphabet(bwtSeq);
    AlphabetRangeSize
      termIdx = MRAEncMapSymbol(alphabet, bwtTerminatorSym)
      - MRAEncGetRangeBase(alphabet, range),
      fbIdx = bwtSeq->bwtTerminatorFallback
      - MRAEncGetRangeBase(alphabet, range);
    if (pos > BWTSeqTerminatorPos(bwtSeq))
    {
      rangeOccs[termIdx] = 1;
      --(rangeOccs[fbIdx]);
    }
    else
      rangeOccs[termIdx] = 0;
  }
}

static inline void
BWTSeqPosPairRangeOcc(const BWTSeq *bwtSeq, AlphabetRangeID range,
                      unsigned long posA, unsigned long posB,
                      unsigned long *rangeOccs)
{
  gt_assert(bwtSeq && rangeOccs);
  gt_assert(posA <= posB);
  gt_assert(range < MRAEncGetNumRanges(BWTSeqGetAlphabet(bwtSeq)));
  EISPosPairRangeRank(bwtSeq->seqIdx, range, posA, posB, rangeOccs,
                      bwtSeq->hint);
  if (range == bwtSeq->bwtTerminatorFallbackRange)
  {
    const MRAEnc *alphabet = BWTSeqGetAlphabet(bwtSeq);
    AlphabetRangeSize rSize = MRAEncGetRangeSize(alphabet, range),
      termIdx = MRAEncMapSymbol(alphabet, bwtTerminatorSym)
      - MRAEncGetRangeBase(alphabet, range),
      fbIdx = bwtSeq->bwtTerminatorFallback
      - MRAEncGetRangeBase(alphabet, range);
    memmove(rangeOccs + termIdx + 1, rangeOccs + termIdx,
            sizeof (rangeOccs[0]) * (rSize - 1));
    rangeOccs[termIdx] = rangeOccs[termIdx + rSize] = 0;
    if (posB > BWTSeqTerminatorPos(bwtSeq))
    {
      rangeOccs[termIdx + rSize] = 1;
      --(rangeOccs[fbIdx + rSize]);
      if (posA > BWTSeqTerminatorPos(bwtSeq))
      {
        rangeOccs[termIdx] = 1;
        --(rangeOccs[fbIdx]);
      }
      else
        rangeOccs[termIdx] = 0;
    }
    else
      rangeOccs[rSize + termIdx] = rangeOccs[termIdx] = 0;
  }
}

static inline unsigned long
BWTSeqLFMap(const BWTSeq *bwtSeq, unsigned long LPos,
            struct extBitsRetrieval *extBits)
{
  Symbol tSym = EISGetTransformedSym(bwtSeq->seqIdx, LPos, bwtSeq->hint);
  unsigned long FPos;
  const MRAEnc *alphabet = BWTSeqGetAlphabet(bwtSeq);
  if (LPos != BWTSeqTerminatorPos(bwtSeq))
  {
    AlphabetRangeID range = MRAEncGetRangeOfSymbol(alphabet, tSym);
    switch (bwtSeq->rangeSort[range])
    {
    case SORTMODE_VALUE:
      FPos = bwtSeq->count[tSym] + BWTSeqTransformedOcc(bwtSeq, tSym, LPos);
      break;
    case SORTMODE_RANK:
      FPos = bwtSeq->count[MRAEncGetRangeBase(alphabet, range)]
        + gt_BWTSeqGetRankSort(bwtSeq, LPos, range, extBits);
      break;
    case SORTMODE_UNDEFINED:
    default:
#ifndef _NDEBUG
      fputs("Requesting LF-map for symbol from range of undefined sorting.\n",
            stderr);
      abort();
#endif
      FPos = (unsigned long)-1;
      break;
    }
  }
  else
  {
    gt_assert(tSym == bwtSeq->bwtTerminatorFallback);
    FPos = bwtSeq->count[bwtSeq->alphabetSize - 1];
  }
  return FPos;
}

static inline unsigned long
BWTSeqAggCount(const BWTSeq *bwtSeq, Symbol sym)
{
  Symbol  tSym;
  gt_assert(bwtSeq);
  gt_assert(MRAEncSymbolHasValidMapping(BWTSeqGetAlphabet(bwtSeq), sym));
  tSym = MRAEncMapSymbol(BWTSeqGetAlphabet(bwtSeq), sym);
  return bwtSeq->count[tSym];
}

static inline unsigned long
BWTSeqAggTransformedCount(const BWTSeq *bwtSeq, Symbol tSym)
{
  gt_assert(bwtSeq);
  gt_assert(tSym <= bwtSeq->alphabetSize);
  return bwtSeq->count[tSym];
}

static inline struct matchBound *
BWTSeqIncrMatch(const BWTSeq *bwtSeq, struct matchBound *limits,
                Symbol nextSym)
{
  const MRAEnc *alphabet;
  Symbol curSym;
  gt_assert(bwtSeq && limits);
  gt_assert(limits->start < bwtSeq->count[bwtSeq->alphabetSize]
         && limits->end < bwtSeq->count[bwtSeq->alphabetSize]);
  alphabet = BWTSeqGetAlphabet(bwtSeq);
  curSym = MRAEncMapSymbol(alphabet, nextSym);
  gt_assert(MRAEncSymbolHasValidMapping(alphabet, curSym));
  limits->start = bwtSeq->count[curSym]
    + BWTSeqTransformedOcc(bwtSeq, curSym, limits->start);
  limits->end = bwtSeq->count[curSym]
    + BWTSeqTransformedOcc(bwtSeq, curSym, limits->end);
  return limits;
}

static inline const EISeq *
BWTSeqGetEncIdxSeq(const BWTSeq *bwtSeq)
{
  gt_assert(bwtSeq);
  return bwtSeq->seqIdx;
}

static inline Symbol
BWTSeqGetSym(const BWTSeq *bwtSeq, unsigned long pos)
{
  gt_assert(bwtSeq);
  return EISGetSym(bwtSeq->seqIdx, pos, bwtSeq->hint);
}

static inline bool
EMIGetNextMatch(struct BWTSeqExactMatchesIterator *iter, unsigned long *pos,
                const BWTSeq *bwtSeq)
{
  if (iter->nextMatchBWTPos < iter->bounds.end)
  {
    /*printf("nextMatchBWTPos=%lu\n",(unsigned long) iter->nextMatchBWTPos);*/
    *pos = gt_BWTSeqLocateMatch(bwtSeq, iter->nextMatchBWTPos, &iter->extBits);
    iter->nextMatchBWTPos++;
    return true;
  }
  else
    return false;
}

#endif
genometools-1.5.1/src/match/eis-bwtseq.c000066400000000000000000000524271211610345200201700ustar00rootroot00000000000000/*
  Copyright (c) 2007,2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/assert_api.h"
#include "match/dataalign.h"
#include "core/error.h"
#include "core/log.h"
#include "core/str.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/undef_api.h"
#include "core/yarandom.h"
#include "match/eis-bitpackseqpos.h"
#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-extinfo.h"
#include "match/eis-bwtseq-param.h"
#include "match/eis-bwtseq-priv.h"
#include "match/eis-bwtseq-context.h"
#include "match/eis-encidxseq.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-suffixerator-interface.h"
#include "match/eis-suffixarray-interface.h"
#include "match/esa-map.h"
#include "match/sarr-def.h"

/**
 * @param alphabet ownership of alphabet is with the newly produced
 * sequence object if return value is not 0
 */
static int
initBWTSeqFromEncSeqIdx(BWTSeq *bwtSeq, struct encIdxSeq *seqIdx,
                        MRAEnc *alphabet, unsigned long *counts,
                        enum rangeSortMode *rangeSort,
                        const enum rangeSortMode *defaultRangeSort)
{
  size_t alphabetSize;
  Symbol bwtTerminatorFlat;
  EISHint hint;
  gt_assert(bwtSeq && seqIdx);
  bwtSeq->alphabet = alphabet;
  alphabetSize = gt_MRAEncGetSize(alphabet);
  if (!alphabetSize)
    /* weird error, shouldn't happen, but I prefer error return to
     * segfault in case someone tampered with the input */
    return 0;
  /* FIXME: this should probably be handled in chardef.h to have a
   * unique mapping */
  /* FIXME: this assumes there is exactly two ranges */
  gt_MRAEncAddSymbolToRange(alphabet, bwtTerminatorSym, 1);
  gt_assert(gt_MRAEncGetSize(alphabet) ==  alphabetSize + 1);
  alphabetSize = gt_MRAEncGetSize(alphabet);
  bwtSeq->bwtTerminatorFallback = bwtTerminatorFlat
    = MRAEncMapSymbol(alphabet, UNDEFBWTCHAR);
  bwtSeq->bwtTerminatorFallbackRange = 1;
  bwtSeq->count = counts;
  bwtSeq->rangeSort = rangeSort;
  bwtSeq->seqIdx = seqIdx;
  bwtSeq->alphabetSize = alphabetSize;
  bwtSeq->hint = hint = newEISHint(seqIdx);
  {
    Symbol i;
    unsigned long len = EISLength(seqIdx), *count = bwtSeq->count;
    count[0] = 0;
    for (i = 0; i < bwtTerminatorFlat; ++i)
      count[i + 1] = count[i]
        + EISSymTransformedRank(seqIdx, i, len, hint);
    /* handle character which the terminator has been mapped to specially */
    count[i + 1] = count[i]
      + EISSymTransformedRank(seqIdx, i, len, hint) - 1;
    gt_assert(count[i + 1] >= count[i]);
    /* now we can finish the rest of the symbols */
    for (i += 2; i < alphabetSize; ++i)
      count[i] = count[i - 1]
        + EISSymTransformedRank(seqIdx, i - 1, len, hint);
    /* and finally place the 1-count for the terminator */
    count[i] = count[i - 1] + 1;
#ifdef EIS_DEBUG
    gt_log_log("count[alphabetSize]=%lu, len=%lu",count[alphabetSize], len);
    for (i = 0; i <= alphabetSize; ++i)
      gt_log_log("count[%u]=%lu", (unsigned)i, count[i]);
#endif
    gt_assert(count[alphabetSize] == len);
  }
  gt_BWTSeqInitLocateHandling(bwtSeq, defaultRangeSort);
  return 1;
}

/**
 * @param alphabet ownership of alphabet is with the newly produced
 * sequence object if return value is non-NULL
 */
BWTSeq *
gt_newBWTSeq(EISeq *seqIdx, MRAEnc *alphabet,
          const enum rangeSortMode *defaultRangeSort)
{
  BWTSeq *bwtSeq;
  unsigned long *counts;
  size_t countsOffset, rangeSortOffset, totalSize;
  enum rangeSortMode *rangeSort;
  unsigned alphabetSize;
  gt_assert(seqIdx);
  /* alphabetSize is increased by one to handle the flattened
   * terminator symbol correctly */
  alphabetSize = gt_MRAEncGetSize(alphabet) + 1;
  countsOffset = offsetAlign(sizeof (struct BWTSeq), sizeof (unsigned long));
  rangeSortOffset = offsetAlign(countsOffset
                                + sizeof (unsigned long) * (alphabetSize + 1),
                                sizeof (enum rangeSortMode));
  totalSize = rangeSortOffset + sizeof (enum rangeSortMode)
    * MRAEncGetNumRanges(alphabet);
  bwtSeq = gt_malloc(totalSize);
  bwtSeq->pckbuckettable = NULL;
  counts = (unsigned long *)((char  *)bwtSeq + countsOffset);
  rangeSort = (enum rangeSortMode *)((char *)bwtSeq + rangeSortOffset);
  if (!initBWTSeqFromEncSeqIdx(bwtSeq, seqIdx, alphabet, counts, rangeSort,
                               defaultRangeSort))
  {
    gt_free(bwtSeq);
    bwtSeq = NULL;
  }
  return bwtSeq;
}

void
gt_deleteBWTSeq(BWTSeq *bwtSeq)
{
  gt_MRAEncDelete(bwtSeq->alphabet);
  deleteEISHint(bwtSeq->seqIdx, bwtSeq->hint);
  gt_deleteEncIdxSeq(bwtSeq->seqIdx);
  gt_free(bwtSeq);
}

typedef struct
{
  const Mbtab **mbtab;
  unsigned int numofchars, maxdepth, depth;
  GtCodetype code;
} GtPrebwtstate;

static const Mbtab *gt_prebwt_next(GtPrebwtstate *prebwt,unsigned int cc)
{
  prebwt->code = prebwt->code * prebwt->numofchars + cc;
  prebwt->depth++;
  return prebwt->mbtab[prebwt->depth] + prebwt->code;
}

static inline void
getMatchBound(const BWTSeq *bwtSeq, const Symbol *query, size_t queryLen,
              struct matchBound *match, bool forward)
{
  const Symbol *qptr, *qend;
  unsigned int cc;
  const Mbtab *mbptr;
  GtPrebwtstate prebwt;

  gt_assert(bwtSeq && query);
  if (forward)
  {
    qptr = query;
    qend = query + queryLen;
  } else
  {
    qptr = query + queryLen - 1;
    qend = query - 1;
  }
  gt_assert(ISNOTSPECIAL(*qptr));
  cc = (unsigned int) *qptr;
  prebwt.mbtab = gt_bwtseq2mbtab((const FMindex *) bwtSeq);
  if (prebwt.mbtab != NULL)
  {
    prebwt.numofchars = gt_bwtseq2numofchars((const FMindex *) bwtSeq);
    prebwt.maxdepth = gt_bwtseq2maxdepth((const FMindex *) bwtSeq);
    prebwt.code = 0;
    prebwt.depth = 0;
    mbptr = gt_prebwt_next(&prebwt,cc);
    match->start = mbptr->lowerbound;
    match->end = mbptr->upperbound;
  } else
  {
    prebwt.numofchars = GT_UNDEF_UINT;
    prebwt.maxdepth = GT_UNDEF_UINT;
    prebwt.code = 0;
    prebwt.depth = GT_UNDEF_UINT;
    match->start = bwtSeq->count[cc];
    match->end   = bwtSeq->count[cc + 1];
  }
  qptr = forward ? (qptr+1) : (qptr-1);
  while (match->start < match->end && qptr != qend)
  {
    GtUlongPair occPair;

    gt_assert(ISNOTSPECIAL(*qptr));
    cc = (unsigned int) *qptr;
    if (prebwt.mbtab != NULL && prebwt.depth < prebwt.maxdepth)
    {
      mbptr = gt_prebwt_next(&prebwt,cc);
      match->start = mbptr->lowerbound;
      match->end = mbptr->upperbound;
    } else
    {
      occPair = BWTSeqTransformedPosPairOcc(bwtSeq, (Symbol) cc, match->start,
                                            match->end);
      match->start = bwtSeq->count[cc] + occPair.a;
      match->end   = bwtSeq->count[cc] + occPair.b;
    }
    qptr = forward ? (qptr+1) : (qptr-1);
  }
}

unsigned long gt_packedindexuniqueforward(const BWTSeq *bwtSeq,
                                          const GtUchar *qstart,
                                          const GtUchar *qend)
{
  GtUchar cc;
  const GtUchar *qptr;
  struct matchBound bwtbound;
  GtUlongPair seqpospair;
  Symbol curSym;
  const MRAEnc *alphabet;

  gt_assert(bwtSeq && qstart);
  alphabet = BWTSeqGetAlphabet(bwtSeq);
  qptr = qstart;
  cc = *qptr++;
#undef SKDEBUG
#ifdef SKDEBUG
  printf("# start cc=%u\n",cc);
#endif
  if (ISSPECIAL(cc))
  {
    return 0;
  }
  curSym = MRAEncMapSymbol(alphabet, cc);
  bwtbound.start = bwtSeq->count[curSym];
  bwtbound.end = bwtSeq->count[curSym+1];
#ifdef SKDEBUG
  printf("# bounds=%lu,%lu = %lu"
          "occurrences\n",
         bwtbound.start,
         bwtbound.end,
         bwtbound.end - bwtbound.start);
#endif
  while (qptr < qend && bwtbound.start + 1 < bwtbound.end)
  {
    cc = *qptr;
#ifdef SKDEBUG
    printf("# cc=%u\n",cc);
#endif
    if (ISSPECIAL (cc))
    {
      return 0;
    }
    curSym = MRAEncMapSymbol(alphabet, cc);
    seqpospair = BWTSeqTransformedPosPairOcc(bwtSeq, curSym,
                                             bwtbound.start,bwtbound.end);
    bwtbound.start = bwtSeq->count[curSym] + seqpospair.a;
    bwtbound.end = bwtSeq->count[curSym] + seqpospair.b;
#ifdef SKDEBUG
    printf("# bounds=%lu,%lu = %lu"
            "occurrences\n",
           bwtbound.start,
           bwtbound.end,
           bwtbound.end - bwtbound.start);
#endif
    qptr++;
  }
  if (bwtbound.start + 1 == bwtbound.end)
  {
    return (unsigned long) (qptr - qstart);
  }
  return 0;
}

unsigned long gt_packedindexmstatsforward(const BWTSeq *bwtSeq,
                                       unsigned long *witnessleftbound,
                                       const GtUchar *qstart,
                                       const GtUchar *qend)
{
  GtUchar cc;
  const GtUchar *qptr;
  unsigned long prevlbound;
  struct matchBound bwtbound;
  GtUlongPair seqpospair;
  Symbol curSym;
  unsigned long matchlength;
  const MRAEnc *alphabet;

  gt_assert(bwtSeq && qstart && qstart < qend);
  alphabet = BWTSeqGetAlphabet(bwtSeq);
  qptr = qstart;
  cc = *qptr;
#undef SKDEBUG
#ifdef SKDEBUG
  printf("# start cc=%u\n",cc);
#endif
  if (ISSPECIAL(cc))
  {
    return 0;
  }
  curSym = MRAEncMapSymbol(alphabet, cc);
  bwtbound.start = bwtSeq->count[curSym];
  bwtbound.end = bwtSeq->count[curSym+1];
  if (bwtbound.start >= bwtbound.end)
  {
    return 0;
  }
#ifdef SKDEBUG
  printf("# bounds=%lu,%lu = %lu"
          "occurrences\n",
         bwtbound.start,
         bwtbound.end,
         bwtbound.end - bwtbound.start);
#endif
  prevlbound = bwtbound.start;
  for (qptr++; qptr < qend; qptr++)
  {
    cc = *qptr;
#ifdef SKDEBUG
    printf("# cc=%u\n",cc);
#endif
    if (ISSPECIAL (cc))
    {
      break;
    }
    curSym = MRAEncMapSymbol(alphabet, cc);
    seqpospair = BWTSeqTransformedPosPairOcc(bwtSeq, curSym,
                                             bwtbound.start,bwtbound.end);
    bwtbound.start = bwtSeq->count[curSym] + seqpospair.a;
    bwtbound.end = bwtSeq->count[curSym] + seqpospair.b;
#ifdef SKDEBUG
    printf("# bounds=%lu,%lu = %lu"
            "occurrences\n",
           bwtbound.start,
           bwtbound.end,
           bwtbound.end - bwtbound.start);
#endif
    if (bwtbound.start >= bwtbound.end)
    {
      break;
    }
    prevlbound = bwtbound.start;
  }
  matchlength = (unsigned long) (qptr - qstart);
  if (witnessleftbound != NULL)
  {
    *witnessleftbound = prevlbound;
  }
  return matchlength;
}

unsigned long
gt_BWTSeqMatchCount(const BWTSeq *bwtSeq, const Symbol *query, size_t queryLen,
                 bool forward)
{
  struct matchBound match;
  gt_assert(bwtSeq && query);
  getMatchBound(bwtSeq, query, queryLen, &match, forward);
  if (match.end < match.start)
    return 0;
  else
    return match.end - match.start;
}

bool
gt_initEMIterator(BWTSeqExactMatchesIterator *iter, const BWTSeq *bwtSeq,
               const Symbol *query, size_t queryLen, bool forward)
{
  gt_assert(iter && bwtSeq && query);
  if (!bwtSeq->locateSampleInterval)
  {
    fputs("Index does not contain locate information.\n"
          "Localization of matches impossible!", stderr);
    return false;
  }
  getMatchBound(bwtSeq, query, queryLen, &iter->bounds, forward);
  iter->nextMatchBWTPos = iter->bounds.start;
  initExtBitsRetrieval(&iter->extBits);
  return true;
}

bool
gt_initEmptyEMIterator(BWTSeqExactMatchesIterator *iter, const BWTSeq *bwtSeq)
{
  gt_assert(iter && bwtSeq);
  if (!bwtSeq->locateSampleInterval)
  {
    fputs("Index does not contain locate information.\n"
          "Localization of matches impossible!", stderr);
    return false;
  }
  iter->bounds.start = iter->bounds.end = iter->nextMatchBWTPos = 0;
  initExtBitsRetrieval(&iter->extBits);
  return true;
}

struct BWTSeqExactMatchesIterator *
gt_newEMIterator(const BWTSeq *bwtSeq, const Symbol *query, size_t queryLen,
              bool forward)
{
  struct BWTSeqExactMatchesIterator *iter;
  gt_assert(bwtSeq && query);
  iter = gt_malloc(sizeof (*iter));
  if (gt_initEMIterator(iter, bwtSeq, query, queryLen,forward))
  {
    return iter;
  }
  gt_free(iter);
  return NULL;
}

bool
gt_reinitEMIterator(BWTSeqExactMatchesIterator *iter, const BWTSeq *bwtSeq,
                 const Symbol *query, size_t queryLen, bool forward)
{
  getMatchBound(bwtSeq, query, queryLen, &iter->bounds, forward);
  iter->nextMatchBWTPos = iter->bounds.start;
  return true;
}

void
gt_destructEMIterator(struct BWTSeqExactMatchesIterator *iter)
{
  destructExtBitsRetrieval(&iter->extBits);
}

void
gt_deleteEMIterator(struct BWTSeqExactMatchesIterator *iter)
{
  gt_free(iter);
}

unsigned long
gt_EMINumMatchesTotal(const struct BWTSeqExactMatchesIterator *iter)
{
  gt_assert(iter);
  if (iter->bounds.start > iter->bounds.end)
    return 0;
  else
    return iter->bounds.end - iter->bounds.start;
}

unsigned long
gt_EMINumMatchesLeft(const struct BWTSeqExactMatchesIterator *iter)
{
  gt_assert(iter);
  if (iter->nextMatchBWTPos > iter->bounds.end)
    return 0;
  else
    return iter->bounds.end - iter->bounds.start;
}

enum
{
  MAX_CONTEXT_LEN = 1000,
  MIN_CONTEXT_LEN = 1,
  CONTEXT_FRACTION = 128,
  MAX_NUM_CONTEXT_CHECKS = 1000,
  CONTEXT_INTERVAL = 128,
};

int
gt_BWTSeqVerifyIntegrity(BWTSeq *bwtSeq, const char *projectName,
                      int checkFlags,
                      unsigned long tickPrint, FILE *fp,
                      GtLogger *verbosity, GtError *err)
{
  Suffixarray suffixArray;
  struct extBitsRetrieval extBits;
  bool suffixArrayIsInitialized = false, extBitsAreInitialized = false;
  enum verifyBWTSeqErrCode retval = VERIFY_BWTSEQ_NO_ERROR;
  do
  {
    unsigned long seqLen;
    gt_assert(bwtSeq && projectName && err);
    gt_error_check(err);

    initExtBitsRetrieval(&extBits);
    extBitsAreInitialized = true;

    if (gt_mapsuffixarray(&suffixArray,
                       SARR_SUFTAB | SARR_ESQTAB, projectName, verbosity, err))
    {
      gt_error_set(err, "Cannot load reference suffix array project with"
                    " demand for suffix table file and encoded sequence"
                    " for project: %s", projectName);
      retval = VERIFY_BWTSEQ_REFLOAD_ERROR;
      break;
    }
    suffixArrayIsInitialized = true;
    seqLen = gt_encseq_total_length(suffixArray.encseq) + 1;
    if (BWTSeqLength(bwtSeq) != seqLen)
    {
      gt_error_set(err, "length mismatch for suffix array project %s and "
                "bwt sequence index", projectName);
      retval = VERIFY_BWTSEQ_LENCOMPARE_ERROR;
      break;
    }

    if (checkFlags & VERIFY_BWTSEQ_SUFVAL
        && BWTSeqHasLocateInformation(bwtSeq))
    {
      unsigned long i;
      for (i = 0; i < seqLen && retval == VERIFY_BWTSEQ_NO_ERROR; ++i)
      {
        if (gt_BWTSeqPosHasLocateInfo(bwtSeq, i, &extBits))
        {
          unsigned long sfxArrayValue = gt_BWTSeqLocateMatch(bwtSeq, i,
                                                             &extBits);
          if (sfxArrayValue != ESASUFFIXPTRGET(suffixArray.suftab,i))
          {
            gt_error_set(err, "Failed suffix array value comparison"
                          " at position %lu: %lu != %lu",
                          i, sfxArrayValue,
                          ESASUFFIXPTRGET(suffixArray.suftab,i));
            retval = VERIFY_BWTSEQ_SUFVAL_ERROR;
            break;
          }
        }
        if (tickPrint && !((i + 1) % tickPrint))
          putc('.', fp);
      }
      if (tickPrint)
        putc('\n', fp);
      if (retval != VERIFY_BWTSEQ_NO_ERROR)
        break;
    }
    else if (checkFlags & VERIFY_BWTSEQ_SUFVAL)
    {
      gt_error_set(err, "check of suffix array values was requested,"
                " but index contains no  locate information!");
      retval = VERIFY_BWTSEQ_SUFVAL_ERROR;
      break;
    }
    else if (!(checkFlags & VERIFY_BWTSEQ_SUFVAL)
             && BWTSeqHasLocateInformation(bwtSeq))
    {
      fputs("Not checking suftab values.\n", stderr);
    }
    if (BWTSeqHasLocateInformation(bwtSeq))
    {
      unsigned long nextLocate = BWTSeqTerminatorPos(bwtSeq);
      if (suffixArray.longest.defined &&
          suffixArray.longest.valueunsignedlong != nextLocate)
      {
        gt_error_set(err, "terminator/0-rotation position mismatch %lu"
                  " vs. %lu", suffixArray.longest.valueunsignedlong,
                  nextLocate);
        retval = VERIFY_BWTSEQ_TERMPOS_ERROR;
        break;
      }
      if ((checkFlags & VERIFY_BWTSEQ_LFMAPWALK)
          && (bwtSeq->featureToggles & BWTReversiblySorted))
      {
        unsigned long i = seqLen;
        /* handle first symbol specially because the encseq
         * will not return the terminator symbol */
        {
          Symbol sym = BWTSeqGetSym(bwtSeq, nextLocate);
          if (sym != UNDEFBWTCHAR)
          {
            gt_error_set(err, "symbol mismatch at position %lu: "
                      "%d vs. reference symbol %d", i - 1, (int)sym,
                      (int)UNDEFBWTCHAR);
            retval = VERIFY_BWTSEQ_LFMAPWALK_ERROR;
            break;
          }
          --i;
          nextLocate = BWTSeqLFMap(bwtSeq, nextLocate, &extBits);
        }
        while (i > 0)
        {
          Symbol symRef =
                         gt_encseq_get_encoded_char(suffixArray.encseq,
                                                          --i,
                                                          suffixArray.readmode);
          Symbol symCmp = BWTSeqGetSym(bwtSeq, nextLocate);
          if (symCmp != symRef)
          {
            gt_error_set(err, "symbol mismatch at position %lu: "
                      "%d vs. reference symbol %d", i, symCmp, symRef);
            retval = VERIFY_BWTSEQ_LFMAPWALK_ERROR;
            break;
          }
          nextLocate = BWTSeqLFMap(bwtSeq, nextLocate, &extBits);
        }
        if (retval != VERIFY_BWTSEQ_NO_ERROR)
          break;
      }
      else if ((checkFlags & VERIFY_BWTSEQ_LFMAPWALK)
               && !(bwtSeq->featureToggles & BWTReversiblySorted))
      {
        gt_error_set(err, "requested complete backwards regeneration in index"
                  " without regeneration capability");
        retval = VERIFY_BWTSEQ_LFMAPWALK_IMP_ERROR;
        break;
      }
    }
    if (checkFlags & VERIFY_BWTSEQ_CONTEXT)
    {
      BWTSeqContextRetriever *bwtSeqCR =
        gt_BWTSeqCRLoad(bwtSeq, projectName, CTX_MAP_ILOG_AUTOSIZE);
      if (!bwtSeqCR)
      {
        gt_error_set(err, "cannot load BWT sequence context access table"
                  " for project %s", projectName);
        retval = VERIFY_BWTSEQ_CONTEXT_LOADFAIL;
        break;
      }
      fputs("Checking context regeneration.\n", stderr);
      {
        unsigned long i, start, subSeqLen,
          maxSubSeqLen = MIN(MAX(MIN_CONTEXT_LEN, seqLen/CONTEXT_FRACTION),
                             MAX_CONTEXT_LEN),
          numTries = MIN(MAX_NUM_CONTEXT_CHECKS,
                         MAX(2, seqLen/CONTEXT_INTERVAL));
        Symbol *contextBuf = gt_malloc(sizeof (Symbol) * MAX_CONTEXT_LEN);
        GtEncseqReader *esr =
           gt_encseq_create_reader_with_readmode(suffixArray.encseq,
                                                 suffixArray.readmode,
                                                 0);
        for (i = 0; i < numTries && retval == VERIFY_BWTSEQ_NO_ERROR; ++i)
        {
          unsigned long j, end, inSubSeqLen;
          subSeqLen = random()%maxSubSeqLen + 1;
          start = random()%(seqLen - subSeqLen + 1);
          end = start + subSeqLen;
          inSubSeqLen = subSeqLen - ((end==seqLen)?1:0);
          gt_BWTSeqCRAccessSubseq(bwtSeqCR, start, subSeqLen, contextBuf);
          gt_encseq_reader_reinit_with_readmode(esr, suffixArray.encseq,
                                                suffixArray.readmode, start);
          for (j = 0; j < inSubSeqLen; ++j)
          {
            Symbol symRef = gt_encseq_reader_next_encoded_char(esr);
            Symbol symCmp = contextBuf[j];
            if (symCmp != symRef)
            {
              gt_error_set(err, "symbol mismatch at position %lu: "
                        "%d vs. reference symbol %d", start + j, (int)symCmp,
                        (int)symRef);
              retval = VERIFY_BWTSEQ_CONTEXT_SYMFAIL;
              break;
            }
          }
          while (j < subSeqLen)
          {
            Symbol symRef = UNDEFBWTCHAR;
            Symbol symCmp = contextBuf[j];
            if (symCmp != symRef)
            {
              gt_error_set(err, "symbol mismatch at position %lu: "
                        "%d vs. reference symbol %d", start + j, (int)symCmp,
                        (int)symRef);
              retval = VERIFY_BWTSEQ_CONTEXT_SYMFAIL;
              break;
            }
            ++j;
          }
        }
        if (retval == VERIFY_BWTSEQ_NO_ERROR)
          fputs("Context regeneration completed successfully.\n", stderr);
        gt_encseq_reader_delete(esr);
        gt_free(contextBuf);
      }
      gt_deleteBWTSeqCR(bwtSeqCR);
    }
  } while (0);
  if (suffixArrayIsInitialized) gt_freesuffixarray(&suffixArray);
  if (extBitsAreInitialized) destructExtBitsRetrieval(&extBits);
  return retval;
}
genometools-1.5.1/src/match/eis-bwtseq.h000066400000000000000000000464051211610345200201740ustar00rootroot00000000000000/*
  Copyright (c) 2007,2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_BWTSEQ_H
#define EIS_BWTSEQ_H

/**
 * \file eis-bwtseq.h
 * Interface definitions for querying an indexed representation of the
 * BWT of a sequence as presented by Manzini and Ferragina (Compressed
 * Representations of Sequences and Full-Text Indexes, 2006)
 */

#include "core/error.h"
#include "core/str.h"
#include "core/logger.h"
#include "match/eis-encidxseq.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-bwtseq-param.h"

/* TODO:
 * - implement other index types
 */

/**
 * Defines mode by which to derive sort of symbols in particular ranges
 */
enum rangeSortMode {
  SORTMODE_VALUE     = 0,
  SORTMODE_UNDEFINED = 1,
  SORTMODE_RANK      = 2,
};

/**
 * Stores column indices of the (virtual) matrix of rotations of the
 * input string used to construct the BWT, note that upper will
 * typically contain the lower value since rows are numbered from 0 at
 * the top to n-1 at the bottom.
 */
struct matchBound
{
  unsigned long start,                 /**< index of first boundary row */
    end;                        /**< index of second boundary row */
};

/** Object holding a BWT sequence index */

typedef struct BWTSeq BWTSeq;

/** Iterator of Matches produced by a search query from a BWT
 * sequence index */
typedef struct BWTSeqExactMatchesIterator BWTSeqExactMatchesIterator;

/**
 * \brief Creates or loads an encoded indexed sequence object of the
 * BWT transform.
 * @param params a struct holding parameter information for index construction
 * @param err genometools error object reference
 * @return reference to new BWT sequence object
 */
BWTSeq *
gt_availBWTSeq(const struct bwtParam *params, GtLogger *verbosity, GtError*);

/**
 * \brief Creates an encoded indexed sequence object of the BWT
 * transform by translating the information in a pre-existing suffix
 * array.
 * @param params a struct holding parameter information for index construction
 * @param err genometools error object reference
 * @return reference to new BWT sequence object
 */
BWTSeq *
gt_trSuftab2BWTSeq(const struct bwtParam *params, GtLogger *verbosity,
                GtError *err);

/**
 * \brief Loads an encoded indexed sequence object of the
 * BWT transform.
 * @param projectName
 * @param BWTOptFlags Selects in-memory features of sequence index to
 * use, see enum BWTOptionDefaultsOptimizationFlags for possible settings.
 * @param err genometools error object reference
 * @return reference to new BWT sequence object
 */
BWTSeq *
gt_loadBWTSeq(const char *projectName, int BWTOptFlags, GtLogger *verbosity,
              GtError *err);

/**
 * \brief Deallocate a previously loaded/created BWT sequence object.
 * @param bwtseq reference of object to delete
 */
void
gt_deleteBWTSeq(BWTSeq *bwtseq);

/**
 * \brief Query BWT sequence object for availability of added
 * information to locate matches.
 * @param bwtSeq reference of object to query
 * @return 0 if no locate information is present, non-zero otherwise
 */
static inline bool
BWTSeqHasLocateInformation(const BWTSeq *bwtSeq);

/**
 * \brief Retrieve alphabet transformation from BWT sequence object
 * @param bwtSeq reference of object to query for alphabet
 * @return read-only reference of alphabet associated with sequence
 */
static inline const MRAEnc *
BWTSeqGetAlphabet(const BWTSeq *bwtSeq);

/**
 * \brief Retrieve sequence index in which the BWT is stored
 * @param bwtSeq reference of object to query for index
 * @return read-only reference of index containing the sequence
 */
static inline const EISeq *
BWTSeqGetEncIdxSeq(const BWTSeq *bwtSeq);

/**
 * \brief Retrieve Symbol at given position in BWT
 * @param bwtSeq reference of object to query for index
 * @return read-only reference of index containing the sequence
 */
static inline Symbol
BWTSeqGetSym(const BWTSeq *bwtSeq, unsigned long pos);

/**
 * \brief Query length of stored sequence.
 * @param bwtSeq reference of object to query
 * @return length of sequence
 */
static inline unsigned long
BWTSeqLength(const BWTSeq *bwtSeq);

/**
 * @brief Query position of rotation 0 in suffix array (aka
 * longest) which also is the position of the terminator symbol in the
 * BWT.
 * @param bwtSeq reference of object to query
 * @return position of terminator
 */
static inline unsigned long
BWTSeqTerminatorPos(const BWTSeq *bwtSeq);

/**
 * \brief Query BWT sequence for the number of occurences of a symbol in a
 * given prefix.
 * @param bwtSeq reference of object to query
 * @param tSym transformed symbol (as obtained by
 * MRAEncMapSymbol(BWTSeqGetAlphabet(bwtSeq), origSym)
 * @param pos right bound of BWT prefix queried
 * @return number of occurrences of symbol up to but not including pos
 */
static inline unsigned long
BWTSeqTransformedOcc(const BWTSeq *bwtSeq, Symbol tSym, unsigned long pos);

/**
 * \brief Query BWT sequence for the number of occurences of a symbol in a
 * given prefix.
 * @param bwtSeq reference of object to query
 * @param sym symbol (from original alphabet)
 * @param pos right bound of BWT prefix queried
 * @return number of occurrences of symbol up to but not including pos
 */
static inline unsigned long
BWTSeqOcc(const BWTSeq *bwtSeq, Symbol sym, unsigned long pos);

/**
 * \brief Query BWT sequence for the number of occurences of a symbol
 * in two given prefixes.
 * @param bwtSeq reference of object to query
 * @param tSym transformed symbol (as obtained by
 * MRAEncMapSymbol(BWTSeqGetAlphabet(bwtSeq), origSym)
 * @param posA right bound of first BWT prefix queried
 * @param posA right bound of second BWT prefix queried
 * @return number of occurrences of symbol up to but not including
 * posA and posB respectively in fields a and b of returned struct
 */
static inline GtUlongPair
BWTSeqTransformedPosPairOcc(const BWTSeq *bwtSeq, Symbol tSym,
                            unsigned long posA, unsigned long posB);

/**
 * \brief Query BWT sequence for the number of occurences of a symbol
 * in two given prefixes.
 * @param bwtSeq reference of object to query
 * @param sym symbol (from original alphabet)
 * @param posA right bound of first BWT prefix queried
 * @param posB right bound of second BWT prefix queried
 * @return number of occurrences of symbol up to but not including
 * posA and posB respectively in fields a and b of returned struct
 */
static inline GtUlongPair
BWTSeqPosPairOcc(const BWTSeq *bwtSeq, Symbol sym,
                 unsigned long posA, unsigned long posB);

/**
 * \brief Query BWT sequence for the number of occurences of all symbols in a
 * given alphabet range and BWT sequence prefix.
 * @param bwtSeq reference of object to query
 * @param range range of symbols in alphabet to query
 * @param pos right bound of BWT prefix queried
 * @param rangeOccs occurrence counts for all symbols in range are written to
 * this array. The referenced memory must be sized appropriately to
 * accomodate as many symbols as are in range (MRAEncGetRangeSize if
 * in doubt) and rangeOccs[i] will hold the occurrence count of symbol
 * MRAEncRevMapSymbol(alphabet, i + MRAEncGetRangeBase(alphabet, range))
 */
static inline void
BWTSeqRangeOcc(const BWTSeq *bwtSeq, AlphabetRangeID range, unsigned long pos,
               unsigned long *rangeOccs);

/* XXX: range 0 for range = 0 for regular symbols;
   unsigned long rangeOcc[4]; */

/**
 * \brief Query BWT sequence for the number of occurences of all symbols in a
 * given alphabet range and two BWT sequence prefixes.
 * @param bwtSeq reference of object to query
 * @param range range of symbols in alphabet to query
 * @param posA right bound of first BWT prefix queried
 * @param posB right bound of second BWT prefix queried
 * @param rangeOccs occurrence counts for all symbols in range are written to
 * this array. The referenced memory must be sized appropriately to
 * accomodate two-times as many positions symbols as are in range
 * (use MRAEncGetRangeSize if in doubt) and rangeOccs[i] will hold the
 * occurrence count of symbol
 * MRAEncRevMapSymbol(alphabet, i + MRAEncGetRangeBase(alphabet, range))
 * up to position posA while the corresponding is true for
 * rangeOccs[rangeSize + i] concerning posB
 */
static inline void
BWTSeqPosPairRangeOcc(const BWTSeq *bwtSeq, AlphabetRangeID range,
                      unsigned long posA, unsigned long posB,
                      unsigned long *rangeOccs);

/**
 * \brief Given a position in the L-column of the matrix of rotations,
 * find the corresponding row in the F-column.
 * @param bwtSeq reference of object to query
 * @param pos row index for L-column
 * @param extBits modified in intermediate queries
 * @return index of corresponding row F-column
 */
static inline unsigned long
BWTSeqLFMap(const BWTSeq *bwtSeq, unsigned long pos,
            struct extBitsRetrieval *extBits);

/**
 * \brief Given a symbol, query the aggregate count of symbols with
 * lower index, this corresponds to the first row in the C-column of
 * standard literature on the BWT on which the given symbol is found.
 * @param bwtSeq reference of object to query
 * @param sym symbol to query counts sum for
 * @return aggregate count
 */
static inline unsigned long
BWTSeqAggCount(const BWTSeq *bwtSeq, Symbol sym);

/**
 * \brief Given a symbol, query the aggregate count of symbols with
 * lower index.
 *
 * This corresponds to the first row in the C-column of
 * standard literature on the BWT on which the given symbol is found,
 * this function takes a symbol already transformed into the stored
 * alphabet as argument.
 *
 * @param bwtSeq reference of object to query
 * @param tSym symbol to query counts sum for
 * reference for core functions @return aggregate count
 */
static inline unsigned long
BWTSeqAggTransformedCount(const BWTSeq *bwtSeq, Symbol tSym);

/**
 * \brief Given a query string find number of matches in original
 * sequence (of which the sequence object is a BWT).
 * @param bwtSeq reference of object to query
 * @param query symbol string to search matches for
 * @param queryLen length of query string
 * @param forward direction of processing the query
 * @return number of matches
 */
unsigned long
gt_BWTSeqMatchCount(const BWTSeq *bwtSeq, const Symbol *query, size_t queryLen,
                 bool forward);

/**
 * \brief Given a pair of limiting positions in the suffix array and a
 * symbol, compute the interval reached by matching one symbol further.
 * @param bwtSeq reference of sequence index to query
 * @param nextSym symbol by which to further restrict match
 * @param limits current restriction of match interval
 * @return limits, with bounds adjusted
 */
static inline struct matchBound *
BWTSeqIncrMatch(const BWTSeq *bwtSeq, struct matchBound *limits,
                Symbol nextSym);

/**
 * GtError conditions encountered upon integrity check.
 */
enum verifyBWTSeqErrCode
{
  VERIFY_BWTSEQ_NO_ERROR = 0,       /**< every check completed okay */
  VERIFY_BWTSEQ_REFLOAD_ERROR = -1, /**< failed to load suffix array for
                                     *   reference comparisons */
  VERIFY_BWTSEQ_LENCOMPARE_ERROR = -2, /* lengths of bwt sequence
                                        * index and loaded suffix arry
                                        * don't match */
  VERIFY_BWTSEQ_SUFVAL_ERROR = -3, /**< a marked suffix array value
                                    * stored in the bwt sequence index
                                    * does not match the value read directly
                                    * from the suffix array table */
  VERIFY_BWTSEQ_LFMAPWALK_ERROR = -4, /**< while traversing the bwt
                                       * sequence in reverse original sequence
                                       * order, the symbol retrieved
                                       * does not match the
                                       * corresponding symbol in the
                                       * encoded sequence */
  VERIFY_BWTSEQ_LFMAPWALK_IMP_ERROR = -5, /**< original sequence
                                           * regeneration was
                                           * requested,
                                           * but is impossible */
  VERIFY_BWTSEQ_TERMPOS_ERROR = -6, /**< the position of the
                                     * 0-rotation does not match */
  VERIFY_BWTSEQ_CONTEXT_SYMFAIL = -7, /**< context regeneration
                                       * delivered an incorrect symbol */
  VERIFY_BWTSEQ_CONTEXT_LOADFAIL = -8, /**< context regeneration
                                        * is impossible because the
                                        * context failed to load */
};

enum verifyBWTSeqFlags
{
  VERIFY_BWTSEQ_SUFVAL    = 1 << 0, /**< check stored suffix arrays */
  VERIFY_BWTSEQ_LFMAPWALK = 1 << 1, /**< performs full backwards
                                     * regeneration of original
                                     * sequence (if possible)
                                     */
  VERIFY_BWTSEQ_CONTEXT   = 1 << 2, /**< try some random context
                                     * regenerations
                                     */
};

/**
 * \brief Perform various checks on the burrows wheeler transform
 *
 * - inspect all sampled suffix array values for equality with
 *   corresponding value of mapped reference suffix array
 * - check wether the last-to-first traversal of the BWT sequence
 *   index delivers the reversed encoded sequence
 *
 * @param bwtSeq index to check
 * @param projectName suffix array to load as reference
 * @param tickPrint print a dot every time tickPrint many symbols have
 *                  been processed
 * @param fp dots printed to this file
 */
enum verifyBWTSeqErrCode
gt_BWTSeqVerifyIntegrity(BWTSeq *bwtSeq, const char *projectName,
                      int checkFlags,
                      unsigned long tickPrint, FILE *fp,
                      GtLogger *verbosity, GtError *err);

/**
 * \brief Given a query string produce iterator for all matches in
 * original sequence (of which the sequence object is a BWT).
 *
 * Warning: the iterator object will become invalid once the
 * corresponding bwt sequence object has been deleted.
 *
 * Warning: user must manage storage of iter manually
 *
 * @param iter points to storage for iterator
 * @param bwtSeq reference of bwt sequence object to use for matching
 * @param query symbol string to search matches for
 * @param queryLen length of query string
 * @param forward direction of processing the query
 * @return true if successfully initialized, false on error
 */
bool
gt_initEMIterator(BWTSeqExactMatchesIterator *iter, const BWTSeq *bwtSeq,
               const Symbol *query, size_t queryLen, bool forward);

/**
 * \brief Only initializes empty iterator for given
 * sequence object.
 *
 * Warning: the iterator object will become invalid once the
 * corresponding bwt sequence object has been deleted.
 *
 * Warning: user must manage storage of iter manually
 * @param iter points to storage for iterator
 * @param bwtSeq reference of bwt sequence object to use for matching
 * @return true if successfully initialized, false on error
 */
bool
gt_initEmptyEMIterator(BWTSeqExactMatchesIterator *iter, const BWTSeq *bwt);

/**
 * \brief Set up iterator for new query, iter must have been
 * initialized previously. Everything else is identical to
 * gt_initEMIterator.
 *
 * Warning: the iterator object will become invalid once the
 * corresponding bwt sequence object has been deleted.
 * @param iter points to storage for iterator
 * @param bwtSeq reference of bwt sequence object to use for matching
 * @param query symbol string to search matches for
 * @param queryLen length of query string
 * @param forward direction of processing the query
 * @return true if successfully initialized, false on error
 */
bool
gt_reinitEMIterator(BWTSeqExactMatchesIterator *iter, const BWTSeq *bwtSeq,
                 const Symbol *query, size_t queryLen, bool forward);
/**
 * \brief Destruct resources of matches iterator. Does not free the
 * storage of iterator itself.
 * Warning: user must manage storage of iter manually
 * @param iter reference to matches iterator
 */
void
gt_destructEMIterator(struct BWTSeqExactMatchesIterator *iter);

/**
 * \brief Given a query string produce iterator for all matches in
 * original sequence (of which the sequence object is a BWT).
 *
 * Warning: the iterator object will become invalid once the
 * corresponding bwt sequence object has been deleted.
 * @param bwtSeq reference of bwt sequence object to use for matching
 * @param query symbol string to search matches for
 * @param queryLen length of query string
 * @param forward direction of processing the query
 * @return reference of iterator object, NULL on error
 */
BWTSeqExactMatchesIterator *
gt_newEMIterator(const BWTSeq *bwtSeq, const Symbol *query, size_t queryLen,
              bool forward);

/**
 * \brief Deallocate an iterator object.
 * @param iter reference of iterator object
 */
void
gt_deleteEMIterator(BWTSeqExactMatchesIterator *iter);

/**
 * \brief Get position of next match from an iterator.
 * @param iter reference of iterator object
 * @param bwtSeq reference of bwt sequence object to use for matching
 * @param pos location of match will be stored here if a further match
 * is available, not modified otherwise
 * @return true if another match could be found, false otherwise
 */
static inline bool
EMIGetNextMatch(BWTSeqExactMatchesIterator *iter, unsigned long *pos,
                const BWTSeq *bwtSeq);

/**
 * \brief Query an iterator for the total number of matches.
 * @param iter reference of iterator object
 * @return total number of matches
 */
unsigned long
gt_EMINumMatchesTotal(const BWTSeqExactMatchesIterator *iter);

/**
 * \brief Query an iterator for the number of matches not yet
 * inspected via EMIGetNextMatch.
 * @param iter reference of iterator object
 * @return number of matches left
 */
unsigned long
gt_EMINumMatchesLeft(const BWTSeqExactMatchesIterator *iter);

/**
 * @brief for packed index (given as void pointer), compute the longest
 * prefix of string in range between qstart and qend that occurs exactly
 * once in the index.
 * @param packed index (given as void pointer)
 * @param qstart points to memory area where query is found
 * @param qend points to memory area immediately after the query
 * @param err
 * @return 0 if not unique, otherwise length of minmum unique prefix.
 */
unsigned long gt_packedindexuniqueforward(const BWTSeq *bwtseq,
                                       const GtUchar *qstart,
                                       const GtUchar *qend);

unsigned long gt_packedindexmstatsforward(const BWTSeq *bwtseq,
                                       unsigned long *witnessposition,
                                       const GtUchar *qstart,
                                       const GtUchar *qend);

#include "match/eis-bwtseq-siop.h"

#endif
genometools-1.5.1/src/match/eis-encidxseq-construct.c000066400000000000000000000226431211610345200226650ustar00rootroot00000000000000/*
  Copyright (C) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq_metadata.h"
#include "match/eis-blockcomp-construct.h"
#include "match/eis-encidxseq-construct.h"
#include "match/sarr-def.h"
#include "match/esa-map.h"
#include "core/log_api.h"

static EISeq *
gt_createEncIdxSeqFromSASeqSrc(SASeqSrc *src,
                            const char *projectName,
                            const struct seqBaseParam *params,
                            size_t numExtHeaders, const uint16_t *headerIDs,
                            const uint32_t *extHeaderSizes,
                            headerWriteFunc *extHeaderCallbacks,
                            void **headerCBData, bitInsertFunc biFunc,
                            BitOffset cwExtBitsPerPos,
                            varExtBitsEstimator biVarBits, void *cbState,
                            GtError *err);

EISeq *
gt_createEncIdxSeq(const char *projectName,
                const struct seqBaseParam *params,
                size_t numExtHeaders, const uint16_t *headerIDs,
                const uint32_t *extHeaderSizes,
                headerWriteFunc *extHeaderCallbacks, void **headerCBData,
                bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                varExtBitsEstimator biVarBits, void *cbState,
                GtLogger *verbosity, GtError *err)
{
  Suffixarray suffixArray;
  struct encIdxSeq *newSeqIdx;
  unsigned long length;
  gt_assert(projectName);
  /* map and interpret index project file */
  if (streamsuffixarray(&suffixArray,
                       SARR_SUFTAB | SARR_BWTTAB, projectName, verbosity, err))
    return NULL;
  length = gt_encseq_total_length(suffixArray.encseq) + 1;
  newSeqIdx = gt_createEncIdxSeqFromSA(&suffixArray, length,
                                      projectName, params,
                                      numExtHeaders, headerIDs,
                                      extHeaderSizes, extHeaderCallbacks,
                                      headerCBData, biFunc, cwExtBitsPerPos,
                                      biVarBits, cbState, err);
  gt_freesuffixarray(&suffixArray);
  return newSeqIdx;
}

EISeq *
gt_createEncIdxSeqFromSA(Suffixarray *sa, unsigned long totalLen,
                      const char *projectName,
                      const struct seqBaseParam *params,
                      size_t numExtHeaders, const uint16_t *headerIDs,
                      const uint32_t *extHeaderSizes,
                      headerWriteFunc *extHeaderCallbacks,
                      void **headerCBData,
                      bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                      varExtBitsEstimator biVarBits, void *cbState,
                      GtError *err)
{
  struct encIdxSeq *newSeqIdx;
  SuffixarrayFileInterface sai;
  gt_assert(sa && projectName && err);
  gt_initSuffixarrayFileInterface(&sai, totalLen, sa);
  newSeqIdx = gt_createEncIdxSeqFromSAI(
    &sai, projectName, params, numExtHeaders, headerIDs,
    extHeaderSizes, extHeaderCallbacks, headerCBData, biFunc, cwExtBitsPerPos,
    biVarBits, cbState, err);
  gt_destructSuffixarrayFileInterface(&sai);
  return newSeqIdx;
}

EISeq *
gt_createEncIdxSeqFromSAI(SuffixarrayFileInterface *sai,
                       const char *projectName,
                       const struct seqBaseParam *params,
                       size_t numExtHeaders, const uint16_t *headerIDs,
                       const uint32_t *extHeaderSizes,
                       headerWriteFunc *extHeaderCallbacks,
                       void **headerCBData,
                       bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                       varExtBitsEstimator biVarBits, void *cbState,
                       GtError *err)
{
  gt_assert(sai && projectName && err);
  return gt_createEncIdxSeqFromSASeqSrc(
    SAI2SASS(sai), projectName, params,
    numExtHeaders, headerIDs, extHeaderSizes,
    extHeaderCallbacks, headerCBData, biFunc,
    cwExtBitsPerPos, biVarBits, cbState, err);
}

EISeq *
gt_createEncIdxSeqFromSfxI(sfxInterface *sfxi,
                        const char *projectName,
                        const struct seqBaseParam *params,
                        size_t numExtHeaders, const uint16_t *headerIDs,
                        const uint32_t *extHeaderSizes,
                        headerWriteFunc *extHeaderCallbacks,
                        void **headerCBData,
                        bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                        varExtBitsEstimator biVarBits, void *cbState,
                        GtError *err)
{
  gt_assert(sfxi && projectName && err);
  return gt_createEncIdxSeqFromSASeqSrc(
    gt_SfxI2SASS(sfxi), projectName, params,
    numExtHeaders, headerIDs, extHeaderSizes,
    extHeaderCallbacks, headerCBData, biFunc,
    cwExtBitsPerPos, biVarBits, cbState, err);
}

static EISeq *
gt_createEncIdxSeqFromSASeqSrc(SASeqSrc *src,
                            const char *projectName,
                            const struct seqBaseParam *params,
                            size_t numExtHeaders, const uint16_t *headerIDs,
                            const uint32_t *extHeaderSizes,
                            headerWriteFunc *extHeaderCallbacks,
                            void **headerCBData, bitInsertFunc biFunc,
                            BitOffset cwExtBitsPerPos,
                            varExtBitsEstimator biVarBits, void *cbState,
                            GtError *err)
{
  SeqDataReader readSfxBWTSym;
  MRAEnc *alphabet;
  struct encIdxSeq *newSeqIdx;
  if (!SDRIsValid(readSfxBWTSym
                  = SASSCreateReader(src, SFX_REQUEST_BWTTAB)))
    return NULL;
  alphabet = SASSNewMRAEnc(src);
  newSeqIdx = gt_createEncIdxSeqGen(SASSGetLength(src), projectName,
                                 alphabet, SASSGetSeqStats(src),
                                 readSfxBWTSym, params,
                                 numExtHeaders, headerIDs, extHeaderSizes,
                                 extHeaderCallbacks, headerCBData, biFunc,
                                 cwExtBitsPerPos, biVarBits,
                                 cbState, err);
  if (!newSeqIdx)
    gt_MRAEncDelete(alphabet);
  return newSeqIdx;
}

EISeq *
gt_createEncIdxSeqGen(unsigned long totalLen, const char *projectName,
                   MRAEnc *alphabet, const struct seqStats *stats,
                   SeqDataReader seqGenerator,
                   const struct seqBaseParam *params,
                   size_t numExtHeaders, const uint16_t *headerIDs,
                   const uint32_t *extHeaderSizes,
                   headerWriteFunc *extHeaderCallbacks,
                   void **headerCBData,
                   bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                   varExtBitsEstimator biVarBits, void *cbState, GtError *err)
{
  EISeq *seqIdx = NULL;
  switch (params->encType)
  {
  case BWT_ON_BLOCK_ENC:
    seqIdx = gt_newGenBlockEncIdxSeq(totalLen, projectName, alphabet, stats,
                                  seqGenerator, params, numExtHeaders,
                                  headerIDs, extHeaderSizes, extHeaderCallbacks,
                                  headerCBData, biFunc, cwExtBitsPerPos,
                                  biVarBits, cbState, err);
    break;
  default:
    gt_error_set(err, "Illegal/unknown/unimplemented encoding requested!");
    break;
  }
  return seqIdx;
}

struct encIdxSeq *
gt_loadEncIdxSeqForSA(const GtAlphabet *gtalphabet,
                   const char *projectName,
                   enum seqBaseEncoding encType, int features, GtError *err)
{
  MRAEnc *alphabet;
  EISeq *seqIdx = NULL;
  gt_assert(gtalphabet!=NULL);
  alphabet = gt_SANewMRAEnc(gtalphabet);
  switch (encType)
  {
  case BWT_ON_BLOCK_ENC:
    seqIdx = gt_loadBlockEncIdxSeqGen(alphabet, projectName, features,
                                   err);
    break;
  default:
    gt_error_set(err, "Illegal/unknown/unimplemented encoding requested!");
    break;
  }
  gt_assert(seqIdx != NULL || gt_error_is_set(err));
  return seqIdx;
}

EISeq *
gt_loadEncIdxSeq(const char *projectName,
                 enum seqBaseEncoding encType, int features,
                 GT_UNUSED GtLogger *verbosity, GtError *err)
{
  struct encIdxSeq *newSeqIdx = NULL;
  GtEncseq *encseq = NULL;
  GtEncseqLoader *el = NULL;
  do
  {
    el = gt_encseq_loader_new();
    gt_encseq_loader_do_not_require_sds_tab(el);
    gt_encseq_loader_do_not_require_des_tab(el);
    gt_encseq_loader_do_not_require_ssp_tab(el);
    encseq = gt_encseq_loader_load(el, projectName, err);
    gt_encseq_loader_delete(el);
    if (encseq == NULL)
      break;
    newSeqIdx = gt_loadEncIdxSeqForSA(gt_encseq_alphabet(encseq),
                                      projectName,
                                      encType, features, err);
    gt_encseq_delete(encseq);
  } while (0);
  return newSeqIdx;
}
genometools-1.5.1/src/match/eis-encidxseq-construct.h000066400000000000000000000255761211610345200227020ustar00rootroot00000000000000/*
  Copyright (C) 2007,2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_ENCIDXSEQ_CONSTRUCT_H
#define EIS_ENCIDXSEQ_CONSTRUCT_H

/**
 * @file eis-encidxseq-construct.h
 * @brief Methods to construct encoded indexed sequence objects from a
 * variety of sources.
 * @author Thomas Jahns 
 */

#include "core/error.h"
#include "core/str.h"
#include "match/eis-encidxseq.h"
#include "match/eis-suffixerator-interface.h"
#include "match/eis-suffixarray-interface.h"
#include "match/sarr-def.h"

/**
 * \brief Construct block-encoded indexed sequence object and write
 * corresponding representation to disk.
 * @param si reference of suffixerator interface used to read
 * construction from
 * @param totalLen length of indexed sequence (including terminator
 * and separators)
 * @param projectName base name of corresponding suffixerator project
 * @param params parameters describing the composition of blocks,
 * buckets and construction of in memory structures
 * @param numExtHeaders number of extension headers to write via callbacks
 * @param headerIDs array of numExtHeaders ids to be used
 * for each extension header in turn
 * @param extHeaderSizes array of numExtHeaders sizes
 * representing the length of each extension header
 * @param extHeaderCallbacks array of numExtHeaders function pointers
 * each of which will be called once upon writing the header
 * @param headerCBData array of pointers passed as argument when the
 * corresponding header writing function is called
 * @param biFunc function to be called when a chunk of data has been
 * accumulated for a given region of sequence data
 * @param cwExtBitsPerPos exactly this many bits will be appended by
 * biFunc for each symbol of the input sequence
 * @param maxVarExtBitsPerPos at most this many bits will be appended to the
 * variable width part of the data
 * @param cbState will be passed on each call of biFunc
 * @param err genometools reference for core functions
 */
EISeq *
gt_createEncIdxSeqFromSfxI(sfxInterface *si,
                        const char *projectName,
                        const struct seqBaseParam *params,
                        size_t numExtHeaders, const uint16_t *headerIDs,
                        const uint32_t *extHeaderSizes,
                        headerWriteFunc *extHeaderCallbacks,
                        void **headerCBData, bitInsertFunc biFunc,
                        BitOffset cwExtBitsPerPos,
                        varExtBitsEstimator biVarBits, void *cbState,
                        GtError *err);

/**
 * \brief Construct block-encoded indexed sequence object and write
 * corresponding representation to disk.
 * @param sa reference of suffix-array data structure to read
 * construction from
 * @param totalLen length of indexed sequence (including terminator
 * and separators)
 * @param projectName base name of corresponding suffixerator project
 * @param params parameters describing the composition of blocks,
 * buckets and construction of in memory structures
 * @param numExtHeaders number of extension headers to write via callbacks
 * @param headerIDs array of numExtHeaders ids to be used
 * for each extension header in turn
 * @param extHeaderSizes array of numExtHeaders sizes
 * representing the length of each extension header
 * @param extHeaderCallbacks array of numExtHeaders function pointers
 * each of which will be called once upon writing the header
 * @param headerCBData array of pointers passed as argument when the
 * corresponding header writing function is called
 * @param biFunc function to be called when a chunk of data has been
 * accumulated for a given region of sequence data
 * @param cwExtBitsPerPos exactly this many bits will be appended by
 * biFunc for each symbol of the input sequence
 * @param maxVarExtBitsPerPos at most this many bits will be appended to the
 * variable width part of the data
 * @param cbState will be passed on each call of biFunc
 * @param err genometools reference for core functions
 */
EISeq *
gt_createEncIdxSeqFromSA(Suffixarray *sa,
                      unsigned long totalLen, const char *projectName,
                      const struct seqBaseParam *params,
                      size_t numExtHeaders, const uint16_t *headerIDs,
                      const uint32_t *extHeaderSizes,
                      headerWriteFunc *extHeaderCallbacks,
                      void **headerCBData,
                      bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                      varExtBitsEstimator biVarBits, void *cbState,
                      GtError *err);

/**
 * \brief Construct block-encoded indexed sequence object and write
 * corresponding representation to disk.
 * @param sai reference of state struct holding reference to
 * suffix-array data structure to read construction from and progress
 * information
 * @param alphabet encoding to use for the built sequence, "ownership"
 * of alphabet will pass to the returned object if no error occured.
 * @param totalLen length of indexed sequence (including terminator
 * and separators)
 * @param projectName base name of corresponding suffixerator project
 * @param params parameters describing the composition of blocks,
 * buckets and construction of in memory structures
 * @param numExtHeaders number of extension headers to write via callbacks
 * @param headerIDs array of numExtHeaders ids to be used
 * for each extension header in turn
 * @param extHeaderSizes array of numExtHeaders sizes
 * representing the length of each extension header
 * @param extHeaderCallbacks array of numExtHeaders function pointers
 * each of which will be called once upon writing the header
 * @param headerCBData array of pointers passed as argument when the
 * corresponding header writing function is called
 * @param biFunc function to be called when a chunk of data has been
 * accumulated for a given region of sequence data
 * @param cwExtBitsPerPos exactly this many bits will be appended by
 * biFunc for each symbol of the input sequence
 * @param maxVarExtBitsPerPos at most this many bits will be appended to the
 * variable width part of the data
 * @param cbState will be passed on each call of biFunc
 * @param err genometools reference for core functions
 */
EISeq *
gt_createEncIdxSeqFromSAI(SuffixarrayFileInterface *sai,
                       const char *projectName,
                       const struct seqBaseParam *params,
                       size_t numExtHeaders, const uint16_t *headerIDs,
                       const uint32_t *extHeaderSizes,
                       headerWriteFunc *extHeaderCallbacks,
                       void **headerCBData,
                       bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                       varExtBitsEstimator biVarBits, void *cbState,
                       GtError *err);

/**
 * \brief Construct indexed sequence object and write
 * corresponding representation to disk.
 * @param projectName base name of corresponding suffixerator project
 * @param params parameters for index construction
 * @param numExtHeaders number of extension headers to write via callbacks
 * @param headerIDs array of numExtHeaders ids to be used
 * for each extension header in turn
 * @param extHeaderSizes array of numExtHeaders sizes
 * representing the length of each extension header
 * @param extHeaderCallbacks array of numExtHeaders function pointers
 * each of which will be called once upon writing the header
 * @param headerCBData array of pointers passed as argument when the
 * corresponding header writing function is called
 * @param biFunc function to be called when a chunk of data has been
 * accumulated for a given region of sequence data
 * @param cwBitsPerPos exactly this many bits will be appended by
 * biFunc for each symbol of the input sequence
 * @param biVarBitsEstimate tell how many bits will be appended to the
 * variable width part of the data
 * @param cbState will be passed on each call of biFunc and biVarBits
 * @param err genometools error object reference
 * @return new encoded indexed sequence object reference
 */
EISeq *
gt_createEncIdxSeq(const char *projectName,
                const struct seqBaseParam *params,
                size_t numExtHeaders, const uint16_t *headerIDs,
                const uint32_t *extHeaderSizes,
                headerWriteFunc *extHeaderCallbacks, void **headerCBData,
                bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                varExtBitsEstimator biVarBits, void *cbState,
                GtLogger *verbosity, GtError *err);

/**
 * \brief Load previously written indexed sequence
 * representation for already opened suffix-array structure.
 * @param sa reference of suffix-array data structure to read
 * construction from
 * @param totalLen length of indexed sequence (including terminator
 * and separators)
 * @param projectName base name of corresponding suffixerator project
 * @param encType encoding type of loaded sequence index
 * @param features select optional in-memory structures
 * @param err genometools reference for core functions
 */
EISeq *
gt_loadEncIdxSeqForSA(const GtAlphabet *gtalphabet,
                      const char *projectName,
                      enum seqBaseEncoding encType, int features, GtError *err);

/**
 * \brief Load previously written block encoded sequence
 * representation.
 * @param projectName base name of corresponding suffixerator project
 * @param features select optional in-memory data structures for speed-up
 * @param err genometools error object reference
 * @return new encoded indexed sequence object reference
 */
EISeq *
gt_loadEncIdxSeq(const char *projectName,
              enum seqBaseEncoding encType, int features,
              GtLogger *verbosity, GtError *err);

EISeq *
gt_createEncIdxSeqGen(unsigned long totalLen, const char *projectName,
                   MRAEnc *alphabet, const struct seqStats *stats,
                   SeqDataReader seqGenerator,
                   const struct seqBaseParam *params,
                   size_t numExtHeaders, const uint16_t *headerIDs,
                   const uint32_t *extHeaderSizes,
                   headerWriteFunc *extHeaderCallbacks,
                   void **headerCBData,
                   bitInsertFunc biFunc, BitOffset cwExtBitsPerPos,
                   varExtBitsEstimator biVarBits, void *cbState, GtError *err);

#endif
genometools-1.5.1/src/match/eis-encidxseq-param.c000066400000000000000000000022511211610345200217320ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "match/eis-encidxseq-param.h"
#include "match/eis-blockcomp-param.h"

void
gt_registerEncIdxSeqOptions(GtOptionParser *op,
                            struct seqBaseParam *paramOutput)
{
  /* currently BWT_ON_BLOCK is fixed but might be extended in the future */
  paramOutput->encType = BWT_ON_BLOCK_ENC;
  gt_registerBlockEncOptions(op, ¶mOutput->encParams.blockEnc);
}
genometools-1.5.1/src/match/eis-encidxseq-param.h000066400000000000000000000107071211610345200217440ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_ENCIDXSEQ_PARAM_H
#define EIS_ENCIDXSEQ_PARAM_H

#include "core/option_api.h"

/**
 * @file eis-encidxseq-param.h
 * @brief Parameter definitions for index creation routines.
 */

/**
 * Select features to use for index in-memory representation.
 */
enum EISFeatureBits
{
  EIS_FEATURE_NONE = 0,           /**< fallback value */
  EIS_FEATURE_REGION_SUMS = 1<<0, /**< if set construct sum tables for
                                   *   the special symbol ranges
                                   *   use this on index loading if
                                   *   you want to use this index in
                                   *   many queries, omit if memory
                                   *   is very tight (e.g. on construction) */
};

/**
 * Parameters to construct a block composition compressed index.
 */
struct blockEncParams
{
  unsigned blockSize;         /**< number of symbols to combine in
                               * one block a lookup-table
                               * containing
                               * $alphabetsize^{blockSize}$ entries is
                               * required so adjust with caution */
  unsigned bucketBlocks;      /**< number of blocks for which to
                               * store partial symbol sums (lower
                               * values increase index size and
                               * decrease computations for lookup) */
};

/**
 * Names the type of encoding used:
 */
enum seqBaseEncoding {
  BWT_BASETYPE_AUTOSELECT,      /**< automatic, load any index present
                                 *     (currently not implemented) */
  BWT_ON_RLE,                   /**< use original fmindex run-length
                                 * encoding  */
  BWT_ON_BLOCK_ENC,             /**< do block compression by dividing
                                 * sequence into strings of
                                 * composition and permutation
                                 * indices */
  BWT_ON_WAVELET_TREE_ENC,      /**< encode sequence with wavelet-trees */
};

/**
 * Stores information to construct the underlying sequence object.
 */
union seqBaseEncParam
{
  struct blockEncParams blockEnc; /**< parameters for block encoding  */
/*   struct  */
/*   { */
/*   } RLEParams; */
/*   struct  */
/*   { */
/*   } waveletTreeParams; */
};

struct seqBaseParam
{
  enum seqBaseEncoding encType;  /**< encType selects the encoding
                                   *   method of the sequence index *
                                   *   storing the BWT sequence (see
                                   *   enum seqBaseEncoding). */
  int EISFeatureSet;              /**< bitwise or of EIS_FEATURE_NONE
                                   * and other features selectable via enum
                                   * EISFeatureBits (see eis-encidxseq.h) */
  union seqBaseEncParam encParams;/**< a union holding extra parameter
                                   *   information specific to the
                                   *   type selected via parameter
                                   *   encType */
};

void
gt_registerEncIdxSeqOptions(GtOptionParser *op,
                            struct seqBaseParam *paramOutput);

/**
 * @brief Given the construction parameters for a sequence index,
 * estimate how many symbols will be encoded together.
 *
 * Extension information can be expected to be stored at a intervals
 * corresponding to the return value of this function.
 * @param params paramters for sequence index construction
 * @param encType select which type of index will be constructed
 * @param err
 * @return number of symbols stored consecutively
 */
unsigned
gt_estimateSegmentSize(const struct seqBaseParam *params);

#endif
genometools-1.5.1/src/match/eis-encidxseq-priv.h000066400000000000000000000055231211610345200216240ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_ENCIDXSEQ_PRIV_H
#define EIS_ENCIDXSEQ_PRIV_H

#include 

#include "match/eis-mrangealphabet.h"
#include "match/eis-seqranges.h"
#include "match/eis-encidxseq.h"

struct encIdxSeqClass
{
  void (*delete)(EISeq *seq);
  unsigned long (*rank)(EISeq *seq, Symbol sym, unsigned long pos,
                 union EISHint *hint);
  GtUlongPair (*posPairRank)(EISeq *seq, Symbol tSym, unsigned long posA,
                                   unsigned long posB, union EISHint *hint);
  void (*rangeRank)(struct encIdxSeq *eSeqIdx, unsigned range,
                    unsigned long pos, unsigned long *rankCounts,
                    union EISHint *hint);
  void (*posPairRangeRank)(struct encIdxSeq *eSeqIdx, unsigned range,
                           unsigned long posA, unsigned long posB,
                           unsigned long *rankCounts, union EISHint *hint);
  unsigned long (*select)(EISeq *seq, Symbol sym, unsigned long count,
                   union EISHint *hint);
  Symbol (*get)(EISeq *seq, unsigned long pos, EISHint hint);
  union EISHint *(*newHint)(const EISeq *seq);
  void (*deleteHint)(EISeq *seq, EISHint hint);
  const MRAEnc *(*getAlphabet)(const EISeq *seq);
  void (*expose)(EISeq *seq, unsigned long pos, int persistent,
                 struct extBitsRetrieval *retval, union EISHint *hint);
  FILE *(*seekToHeader)(const EISeq *seq, uint16_t headerID,
                        uint32_t *lenRet);
  int (*printPosDiags)(const EISeq *seq, unsigned long pos, FILE *fp,
                       EISHint hint);
  int (*printExtPosDiags)(const EISeq *seq, unsigned long pos, FILE *fp,
                          EISHint hint);
};

struct encIdxSeq
{
  const struct encIdxSeqClass *classInfo;
  MRAEnc *alphabet;
  unsigned long seqLen;
};

struct seqCache
{
  size_t numEntries;
  unsigned long *cachedPos;
  void **entriesPtr;
  void *entries;
};

struct blockEncIdxSeqHint
{
  struct seqCache sBlockCache;
  seqRangeListSearchHint rangeHint;
};

union EISHint
{
  struct blockEncIdxSeqHint bcHint;
};

unsigned
gt_blockEncIdxSeqSegmentLen(const struct blockEncParams *params);

#endif
genometools-1.5.1/src/match/eis-encidxseq-siop.h000066400000000000000000000121221211610345200216070ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_ENCIDXSEQ_SIOP_H
#define EIS_ENCIDXSEQ_SIOP_H

#include 
#include "core/ma_api.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-encidxseq.h"
#include "match/eis-encidxseq-priv.h"

static inline unsigned long
EISLength(const EISeq *seq)
{
  return seq->seqLen;
}

static inline const MRAEnc *
EISGetAlphabet(const EISeq *seq)
{
  gt_assert(seq);
  return seq->alphabet;
}

static inline Symbol
EISGetSym(EISeq *seq, unsigned long pos, EISHint hint)
{
  gt_assert(seq && hint);
  return MRAEncRevMapSymbol(seq->alphabet,
                            seq->classInfo->get(seq, pos, hint));
}

static inline Symbol
EISGetTransformedSym(EISeq *seq, unsigned long pos, EISHint hint)
{
  gt_assert(seq && hint);
  return seq->classInfo->get(seq, pos, hint);
}

static inline unsigned long
EISRank(EISeq *seq, Symbol sym, unsigned long pos, union EISHint *hint)
{
  Symbol mSym;
  mSym = MRAEncMapSymbol(seq->alphabet, sym);
  return seq->classInfo->rank(seq, mSym, pos, hint);
}

static inline unsigned long
EISSymTransformedRank(EISeq *seq, Symbol tSym, unsigned long pos,
                      union EISHint *hint)
{
  gt_assert(tSym < gt_MRAEncGetSize(EISGetAlphabet(seq)));
  return seq->classInfo->rank(seq, tSym, pos, hint);
}

static inline GtUlongPair
EISPosPairRank(EISeq *seq, Symbol sym, unsigned long posA, unsigned long posB,
               union EISHint *hint)
{
  Symbol tSym;
  tSym = MRAEncMapSymbol(seq->alphabet, sym);
  return seq->classInfo->posPairRank(seq, tSym, posA, posB, hint);
}

static inline void
EISRangeRank(EISeq *seq, AlphabetRangeID range, unsigned long pos,
             unsigned long *rankCounts, union EISHint *hint)
{
  return seq->classInfo->rangeRank(seq, range, pos, rankCounts, hint);
}

static inline void
EISPosPairRangeRank(EISeq *seq, AlphabetRangeID range, unsigned long posA,
                    unsigned long posB, unsigned long *rankCounts,
                    union EISHint *hint)
{
  seq->classInfo->posPairRangeRank(seq, range, posA, posB, rankCounts, hint);
}

static inline GtUlongPair
EISSymTransformedPosPairRank(EISeq *seq, Symbol tSym, unsigned long posA,
                             unsigned long posB, union EISHint *hint)
{
  if (tSym >= gt_MRAEncGetSize(EISGetAlphabet(seq)))
  {
    fprintf(stderr,"tsym=%lu,gt_MRAEncGetSize(EISGetAlphabet(seq)=%lu\n",
           (unsigned long) tSym,
           (unsigned long) gt_MRAEncGetSize(EISGetAlphabet(seq)));
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  gt_assert(tSym < gt_MRAEncGetSize(EISGetAlphabet(seq)));
  return seq->classInfo->posPairRank(seq, tSym, posA, posB, hint);
}

static inline void
EISRetrieveExtraBits(EISeq *seq, unsigned long pos, int flags,
                     struct extBitsRetrieval *retval, union EISHint *hint)
{
  return seq->classInfo->expose(seq, pos, flags, retval, hint);
}

static inline void
initExtBitsRetrieval(struct extBitsRetrieval *r)
{
  memset(r, 0, sizeof (struct extBitsRetrieval));
}

static inline struct extBitsRetrieval *
newExtBitsRetrieval()
{
  struct extBitsRetrieval *retval
    = gt_malloc(sizeof (struct extBitsRetrieval));
  initExtBitsRetrieval(retval);
  return retval;
}

static inline void
destructExtBitsRetrieval(struct extBitsRetrieval *r)
{
  if ((r->flags & EBRF_PERSISTENT_CWBITS) && r->cwPart)
    gt_free(r->cwPart);
  if ((r->flags & EBRF_PERSISTENT_VARBITS) && r->varPart)
    gt_free(r->varPart);
}

static inline void
deleteExtBitsRetrieval(struct extBitsRetrieval *r)
{
  destructExtBitsRetrieval(r);
  gt_free(r);
}

static inline FILE *
EISSeekToHeader(const EISeq *seqIdx, uint16_t headerID,
                uint32_t *lenRet)
{
  gt_assert(seqIdx);
  return seqIdx->classInfo->seekToHeader(seqIdx, headerID, lenRet);
}

static inline EISHint
newEISHint(const EISeq *seq)
{
  return seq->classInfo->newHint(seq);
}

static inline void
deleteEISHint(EISeq *seq, EISHint hint)
{
  return seq->classInfo->deleteHint(seq, hint);
}

static inline int
EISPrintDiagsForPos(const EISeq *seq, unsigned long pos, FILE *fp, EISHint hint)
{
  if (seq->classInfo->printPosDiags)
    return seq->classInfo->printPosDiags(seq, pos, fp, hint);
  else
    return 0;
}

static inline int
EISPrintExtDiagsForPos(const EISeq *seq, unsigned long pos, FILE *fp,
                       EISHint hint)
{
  if (seq->classInfo->printExtPosDiags)
    return seq->classInfo->printExtPosDiags(seq, pos, fp, hint);
  else
    return 0;
}

#endif
genometools-1.5.1/src/match/eis-encidxseq.c000066400000000000000000000216051211610345200206400ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/log_api.h"
#include "core/yarandom.h"
#include "match/eis-encidxseq.h"
#include "match/eis-encidxseq-priv.h"
#include "match/esa-map.h"
#include "match/sarr-def.h"

enum {
  AVG_RANGE_RANK_INTERVAL = 128, /**< do range rank queries
                                  * approximately at this interval  */
};

void
gt_deleteEncIdxSeq(EISeq *seq)
{
  seq->classInfo->delete(seq);
}

const char *EISIntegrityCheckResultStrings[] =
{
  "no error in bwt comparison.",
  "reading from the index produced an incorrect symbol.",
  "reading from the BWT reference file failed or delivered a symbol"
  " not in the alphabet (bwt file corrupt?) ",
  "loading/mapping of the suffix array project failed. \n"
  "(did you generate the BWT?)",
  "the rank operation delivered a wrong count"
};

#define verifyIntegrityErrRet(retcode)                                  \
  {                                                                     \
    switch (retcode) {                                                  \
    case EIS_INTEGRITY_CHECK_INVALID_SYMBOL:                            \
      fprintf(stderr, "Comparision failed at position %lu"              \
              ", reference symbol: %u, symbol read: %u\n",              \
              pos, symOrig, symEnc);                                    \
      gt_error_set(err, "Invalid symbol encountered.");                 \
      break;                                                            \
    case EIS_INTEGRITY_CHECK_BWT_READ_ERROR:                            \
      fprintf(stderr, "Read of symbol failed at position %lu\n", pos);  \
      gt_error_set(err, "Failed reading reference BWT source.");        \
      break;                                                            \
    case EIS_INTEGRITY_CHECK_RANK_FAILED:                               \
      fprintf(stderr, "At position %lu"                                 \
              ", rank operation yielded  wrong count: %lu"              \
              ", expected %lu for symbol %d\n",                         \
              pos, rankQueryResult, rankExpect, rankCmpSym);            \
      gt_error_set(err, "Invalid rank result.");                        \
      break;                                                            \
    }                                                                   \
    EISPrintDiagsForPos(seqIdx, pos, stderr, hint);                     \
    retval = retcode;                                                   \
    break;                                                              \
  } do {} while (0)

/**
 * @param tickPrint if not zero, print a . every tickPrint symbols to
 * fp
 * @param fp descriptor to write progress marks to.
 * @return -1 on error, 0 on identity, >0 on inconsistency
 */
enum EISIntegrityCheckResults
gt_EISVerifyIntegrity(EISeq *seqIdx, const char *projectName,
                      unsigned long skip,
                      unsigned long tickPrint, FILE *fp, int chkFlags,
                      GtLogger *verbosity, GtError *err)
{
  FILE *bwtFP;
  unsigned long pos = 0,
                length = EISLength(seqIdx);
  Suffixarray suffixArray;
  Symbol symOrig;
  unsigned symEnc;
  EISHint hint;
  unsigned long rankQueryResult, rankExpect;
  const MRAEnc *alphabet;
  AlphabetRangeSize alphabetSize;
  AlphabetRangeID numRanges;
  enum EISIntegrityCheckResults retval = EIS_INTEGRITY_CHECK_NO_ERROR;
  /* two part process: enumerate all positions of original sequence
   * and verify that the query functions return correct values */
  if (streamsuffixarray(&suffixArray, SARR_BWTTAB, projectName, verbosity, err))
  {
    gt_error_set(err, "Cannot load suffix array project with"
                  " demand for BWT file\n");
    return EIS_INTEGRITY_CHECK_SA_LOAD_ERROR;
  }
  bwtFP = suffixArray.bwttabstream.fp;
  hint = newEISHint(seqIdx);
  alphabet = EISGetAlphabet(seqIdx);
  alphabetSize = gt_MRAEncGetSize(alphabet);
  numRanges = MRAEncGetNumRanges(alphabet);
  do
  {
    unsigned long rankTable[alphabetSize], rangeRanks[2][alphabetSize],
      pairRangeRanks[2* alphabetSize], lastRangeRankPos = 0;
    int symRead, rt = 0;
    AlphabetRangeID lastRangeID = 0;
    unsigned rankCmpSym;
    memset(rankTable, 0, sizeof (rankTable));
    memset(rangeRanks, 0, sizeof (rangeRanks));
    if (skip > 0)
    {
      unsigned sym;
      if (skip >= length)
      {
        gt_logger_log(verbosity, "Invalid skip request: %lld,"
                    " too large for sequence length: %lu",
                    (long long)skip, length);
        return -1;
      }
      fseeko(bwtFP, skip, SEEK_SET);
      for (sym = 0; sym <= (unsigned) GT_MAXALPHABETCHARACTER; ++sym)
        if (MRAEncSymbolHasValidMapping(alphabet, sym))
          rankTable[sym] = EISRank(seqIdx, sym, skip, hint);
      pos = skip;
    }
    while (retval == EIS_INTEGRITY_CHECK_NO_ERROR
           && (symRead = getc(bwtFP)) != EOF)
    {
      symOrig = MRAEncMapSymbol(alphabet, symRead);
      symEnc = EISGetTransformedSym(seqIdx, pos, hint);
      if (symEnc >= alphabetSize)
        verifyIntegrityErrRet(EIS_INTEGRITY_CHECK_INVALID_SYMBOL);
      if (symOrig >= alphabetSize)
        verifyIntegrityErrRet(EIS_INTEGRITY_CHECK_BWT_READ_ERROR);
      if (symEnc != symOrig)
        verifyIntegrityErrRet(EIS_INTEGRITY_CHECK_INVALID_SYMBOL);
      ++rankTable[symOrig];
      if (chkFlags & EIS_VERIFY_EXT_RANK)
      {
        for (rankCmpSym = 0; rankCmpSym < alphabetSize; ++rankCmpSym)
          if ((rankExpect = rankTable[rankCmpSym])
              != (rankQueryResult
                  = EISSymTransformedRank(seqIdx, rankCmpSym, pos + 1, hint)))
            verifyIntegrityErrRet(EIS_INTEGRITY_CHECK_RANK_FAILED);
      }
      else
      {
        rankCmpSym = symEnc;
        if ((rankExpect = rankTable[symEnc])
            != (rankQueryResult = EISSymTransformedRank(seqIdx, symEnc,
                                                        pos + 1, hint)))
          verifyIntegrityErrRet(EIS_INTEGRITY_CHECK_RANK_FAILED);
      }
      /* do rank for full range on some occasions */
      if (!(random() % AVG_RANGE_RANK_INTERVAL))
      {
        unsigned i;
        AlphabetRangeSize rangeSize;
        AlphabetRangeID range = random() % numRanges;
        Symbol rangeBase = MRAEncGetRangeBase(alphabet, range);
        rangeSize = MRAEncGetRangeSize(alphabet, range);
        EISRangeRank(seqIdx, range, pos + 1, rangeRanks[rt], hint);
        for (i = 0; i < rangeSize; ++i)
        {
          rankCmpSym = rangeBase + i;
          if ((rankQueryResult = rangeRanks[rt][i])
              != (rankExpect = rankTable[rankCmpSym]))
            verifyIntegrityErrRet(EIS_INTEGRITY_CHECK_RANK_FAILED);
        }
        if (retval)
          break;
        if (range == lastRangeID)
        {
          EISPosPairRangeRank(seqIdx, range, lastRangeRankPos, pos + 1,
                              pairRangeRanks, hint);
          for (i = 0; i < rangeSize; ++i)
          {
            rankCmpSym = rangeBase + i;
            if ((rankQueryResult = pairRangeRanks[rangeSize + i])
                != (rankExpect = rankTable[rankCmpSym]))
              verifyIntegrityErrRet(EIS_INTEGRITY_CHECK_RANK_FAILED);
            if ((rankQueryResult = pairRangeRanks[i])
                != (rankExpect = rangeRanks[rt ^ 1][i]))
              verifyIntegrityErrRet(EIS_INTEGRITY_CHECK_RANK_FAILED);
          }
          if (retval)
            break;
        }
        lastRangeID = range;
        lastRangeRankPos = pos + 1;
        rt ^= 1;
      }
      ++pos;
      if (tickPrint && !(pos % tickPrint))
        putc('.', fp);
    }
    if (retval)
      break;
    if (tickPrint)
      putc('\n', fp);
    if (ferror(bwtFP))
      verifyIntegrityErrRet(EIS_INTEGRITY_CHECK_BWT_READ_ERROR);
  } while (0);
  deleteEISHint(seqIdx, hint);
  gt_freesuffixarray(&suffixArray);
  return retval;
}

unsigned
gt_estimateSegmentSize(const struct seqBaseParam *params)
{
  unsigned segmentLen = 0;
  switch (params->encType)
  {
  case BWT_ON_BLOCK_ENC:
    segmentLen =
      gt_blockEncIdxSeqSegmentLen(¶ms->encParams.blockEnc);
    break;
  default:
    fputs("Illegal/unknown/unimplemented encoding requested!", stderr);
    abort();
    break;
  }
  return segmentLen;
}
genometools-1.5.1/src/match/eis-encidxseq.h000066400000000000000000000407211211610345200206450ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_ENCIDXSEQ_H
#define EIS_ENCIDXSEQ_H

/**
 * \file eis-encidxseq.h
 * Interface definitions for encoded indexed sequences.
 * \author Thomas Jahns 
 */
#include 
#include 

#include "core/bitpackstring.h"
#include "core/error.h"
#include "core/str.h"
#include "core/types_api.h"

#include "core/logger.h"
#include "match/eis-encidxseq-param.h"
#include "match/eis-headerid.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-seqdatasrc.h"

/**
 * callback function to insert variable width data into encidx
 * construction
 * @param dest bitstring to append data to (can hold at least as many
 * bits as specified in the constructor)
 * @param sOffset position in dest at which the callee may start
 * writing
 * @param start the data will be written together with the encoding of
 * symbols at position start up to position start + len
 * @param len see parameter start for description
 * @param cbState is passed on every call back of bitInsertFunc to
 * pass information that is kept across individual calls
 * @param err genometools error object reference
 * @return number of bits actually written, or (BitOffset)-1 if an
 * error occured
 */
typedef BitOffset (*bitInsertFunc)(BitString cwDest, BitOffset cwOffset,
                                   BitString varDest, BitOffset varOffset,
                                   unsigned long start, unsigned long len,
                                   void *cbState);

/**
 * Callback to insert one header field. The data written can later be
 * retrieved via EISSeekToHeader.
 */
typedef int (*headerWriteFunc)(FILE *fp, void *headerCBData);

/**
 * later inserted bits can be retrieved and will be presented in this
 * struct.
 * CAUTION: the bitstrings exposed in this manner become invalid if
 * delete is called for the corresponding sequence index.
 */
struct extBitsRetrieval
{
  BitOffset cwOffset,           /**< offset in constant-width string
                                 * at which data was earlier stored by
                                 * a bitInsertFunc */
            varOffset;          /**< offset in variable-width string
                                 * at which data was earlier stored by
                                 * a bitInsertFunc  */
  unsigned long start,          /**< start position of region for
                                 * which the retried information was
                                 * stored */
                len;            /**< length of region */
  BitString cwPart,             /**< string containing
                                 * constant-width part of data  */
    varPart;                    /**< string containg variable-width data */
  int flags;                    /**< flags for internal use (Don't touch) */
};

/**
 * Select which parts of the stored data to retrieve: only constant width
 * part or also from the variable part. Join with bitwise or to form a
 * request for extBitsRetrieval.
 */
enum extBitsRetrievalFlags
{
  EBRF_RETRIEVE_CWBITS = 0,        /**< retrieve the constant-width part */
  EBRF_PERSISTENT_CWBITS = 1<<0,   /**< make constant width string persistent,
                                    * i.e. survive further calls to
                                    * query functions */
  EBRF_RETRIEVE_VARBITS = 1<<1,    /**< retrieve variable-width string */
  EBRF_PERSISTENT_VARBITS = 1<<2,  /**< make variable-width string persistent,
                                    * i.e. survive further calls to
                                    * query functions */
};

/**
 * Stores the number of occurrences for every symbol of the input alphabet.
 */
struct seqStats
{
  unsigned long *symbolDistributionTable;   /**< indexed by symbol value */
  enum sourceEncType sourceAlphaType;       /**< defines alphabet width */
};

struct varBitsEstimate
{
  BitOffset maxBitsPerPos,
    maxBitsPerBucket,
    maxBitsTotal;
};

struct segmentDesc
{
  unsigned long repeatCount;
  size_t len;
};

/**
 * @brief Provides estimate of extension bits required by higher layer bit
 * insertion if segment size is known ahead of construction.
 * @param cbState higher layer state reference
 * @param segmentDescs describe segments used
 * @param numSegmentDesc number of descriptions
 * @return true if estimate is conclusive for maxVarExtBitsTotal and
 * maxBitsPerBucket of result
 */
typedef bool (*varExtBitsEstimator)(void *cbState, struct segmentDesc *desc,
                                    size_t numSegmentDesc,
                                    struct varBitsEstimate *result);

/** holds encoded indexed sequence object */
typedef struct encIdxSeq EISeq;
/** hints to speed up retrievals when accessing positions in sequence
 * (or at least close to one another) */
typedef union EISHint *EISHint;

/**
 * \brief Deallocate a previously loaded/created sequence object.
 * @param seq reference of object to delete
 */
void
gt_deleteEncIdxSeq(EISeq *seq);

/**
 * \brief Retrieve alphabet transformation from sequence object
 * @param seq reference of object to query for alphabet
 * @return read-only reference of alphabet associated with sequence
 */
static inline const MRAEnc *
EISGetAlphabet(const EISeq *seq);

/**
 * \brief Return number of occurrences of symbol sym in index up to
 * but not including given position.
 * @param seq sequence index object to query
 * @param sym original alphabet symbol to query occurrences of
 * @param pos occurences are counted up to this position
 * @param hint provides cache and direction information for queries
 * based on previous queries
 */
static inline unsigned long
EISRank(EISeq *seq, Symbol sym, unsigned long pos, union EISHint *hint);

/**
 * \brief Return number of occurrences of symbol tSym in index up to
 * but not including given position.
 * @param seq sequence index object to query
 * @param tSym symbol to query occurrences of, but already transformed
 * by input alphabet
 * @param pos occurences are counted up to this position
 * @param hint provides cache and direction information for queries
 * based on previous queries
 */
static inline unsigned long
EISSymTransformedRank(EISeq *seq, Symbol tSym, unsigned long pos,
                      union EISHint *hint);

/**
 * \brief Return number of occurrences of symbol sym in index up to
 * but not including given positions.
 *
 * precondition: posA <= posB
 * @param seq sequence index object to query
 * @param sym original alphabet symbol to query occurrences of
 * @param posA occurences are counted up to this position
 * @param posB as for posA occurences are counted up to this position
 * @param hint provides cache and direction information for queries
 * based on previous queries
 * @return members a and b of returned struct contain Occ results for
 * posA and posB respectively
 */
static inline GtUlongPair
EISPosPairRank(EISeq *seq, Symbol sym, unsigned long posA, unsigned long posB,
               union EISHint *hint);

/**
 * \brief Return number of occurrences of symbol sym in index up to
 * but not including given positions.
 *
 * precondition: posA <= posB
 * @param seq sequence index object to query
 * @param tSym symbol to query occurrences of, but already transformed
 * by input alphabet
 * @param posA occurences are counted up to this position
 * @param posB as for posA occurences are counted up to this position
 * @param hint provides cache and direction information for queries
 * based on previous queries
 * @return members a and b of returned struct contain Occ results for
 * posA and posB respectively
 */
static inline GtUlongPair
EISSymTransformedPosPairRank(EISeq *seq, Symbol tSym, unsigned long posA,
                             unsigned long posB, union EISHint *hint);

/**
 * \brief Return number of occurrences of all symbols in selected
 * range in index up to but not including given position.
 *
 * @param seq sequence index object to query
 * @param range compute rank counts for all symbols in this range
 * @param pos occurences are counted up to (but not including) this position
 * @param rankCounts ranks for all symbols in range are written to this
 * array. The referenced memory must be sized appropriately to
 * accomodate as many symbols as are in range (MRAEncGetRangeSize if
 * in doubt) and rankCounts[i] will hold the occurrence count of symbol
 * MRAEncRevMapSymbol(alphabet, i + MRAEncGetRangeBase(alphabet, range))
 * @param hint provides cache and direction information for queries
 * based on previous queries
 */
static inline void
EISRangeRank(EISeq *seq, AlphabetRangeID range, unsigned long pos,
             unsigned long *rankCounts, union EISHint *hint);

/**
 * \brief Return number of occurrences of all symbols in selected
 * range in index up to but not including given position.
 *
 * @param seq sequence index object to query
 * @param range compute rank counts for all symbols in this range
 * @param posA occurences are counted up to (but not including) this position
 * @param posB occurences are counted up to (but not including) this position
 * @param rankCounts ranks for all symbols in range are written to this
 * array. The referenced memory must be sized appropriately to
 * accomodate two-times as many positions symbols as are in range
 * (use MRAEncGetRangeSize if in doubt) and rankCounts[i] will hold the
 * occurrence count of symbol
 * MRAEncRevMapSymbol(alphabet, i + MRAEncGetRangeBase(alphabet, range))
 * up to position posA while the corresponding is true for
 * rankCounts[rangeSize + i] concerning posB
 * @param hint provides cache and direction information for queries
 * based on previous queries
 */
static inline void
EISPosPairRangeRank(EISeq *seq, AlphabetRangeID range, unsigned long posA,
                    unsigned long posB, unsigned long *rankCounts,
                    union EISHint *hint);

/**
 * Presents the bits previously stored by a bitInsertFunc callback.
 * @param seq
 * @param pos sequence position for which to retrieve corresponding
 * area
 * @param flags select which part of the extension bits to query
 * @param retval store information of retrieved bits here
 * @param hint provides cache and direction information for queries
 */
static inline void
EISRetrieveExtraBits(EISeq *seq, unsigned long pos, int flags,
                     struct extBitsRetrieval *retval, union EISHint *hint);

/**
 * \brief Initialize empty structure to hold retrieval results later.
 * @param r struct to initialize
 */
static inline void
initExtBitsRetrieval(struct extBitsRetrieval *r);

/**
 * \brief Allocate and initialize empty structure to hold retrieval
 * results later.
 * @return reference of new retrieval object
 */
static inline struct extBitsRetrieval *
newExtBitsRetrieval();

/**
 * \brief Destruct structure holding retrieval data, deallocates
 * referenced data as necessary.
 * @param r struct to destruct
 */
static inline void
destructExtBitsRetrieval(struct extBitsRetrieval *r);

/**
 * \brief Destruct structure holding retrieval data, deallocates
 * referenced data as necessary and the structure itself.
 * @param r struct to delete
 */
static inline void
deleteExtBitsRetrieval(struct extBitsRetrieval *r);

/**
 * \brief Find positions of nth symbol occurrence. TODO: NOT IMPLEMENTED
 */
unsigned long
EISSelect(EISeq *seq, Symbol sym, unsigned long count);

/**
 * \brief Query length of stored sequence.
 * @param seq indexed sequence object to query
 * @return length of sequence
 */
static inline unsigned long
EISLength(const EISeq *seq);

/**
 * \brief Return symbol at specified position. Comparable to c[pos] if the
 * sequence was stored straight in an array c.
 * @param seq indexed sequence object to be queried
 * @param pos position to retrieve symbol for
 * @param hint optional caching/hinting structure (improves average
 * retrieval time)
 * @return value of symbol as encoded in original alphabet
 */
static inline Symbol
EISGetSym(EISeq *seq, unsigned long pos, EISHint hint);

/**
 * \brief Return symbol at specified position. Comparable to c[pos] if the
 * sequence was stored straight in an array c. Returns value of
 * encoding, i.e. does not retranslate to original alphabet.
 * @param seq indexed sequence object to be queried
 * @param pos position to retrieve symbol for
 * @param hint optional caching/hinting structure (improves average
 * retrieval time)
 * @return value of symbol as processed by encoding alphabet
 */
static inline Symbol
EISGetTransformedSym(EISeq *seq, unsigned long pos, EISHint hint);

/**
 * \brief Construct new hinting structure to accelerate operations on
 * related positions.
 * @param seq reference of sequence object to use
 * @return new EISHint handle
 */
static inline EISHint
newEISHint(const EISeq *seq);

/**
 * Deallocate hinting data.
 * @param seq sequence associated
 * @param hint hint to free
 */
static inline void
deleteEISHint(EISeq *seq, EISHint hint);

/**
 * Possible outcome of index integrity check.
 */
enum EISIntegrityCheckResults
{
  EIS_INTEGRITY_CHECK_NO_ERROR = 0,   /**< all tests completed
                                       * without error */
  EIS_INTEGRITY_CHECK_INVALID_SYMBOL, /**< reading from the index
                                       *   produced an incorrect symbol  */
  EIS_INTEGRITY_CHECK_BWT_READ_ERROR, /**< reading from the BWT
                                       *   reference file failed or
                                       *   delivered a symbol not in
                                       *   the alphabet (bwt file
                                       *   corrupt?) */
  EIS_INTEGRITY_CHECK_SA_LOAD_ERROR,  /**< loading/mapping of the
                                       *   suffix array project failed
                                       *   (did you generate the BWT) */
  EIS_INTEGRITY_CHECK_RANK_FAILED     /**< the rank operation
                                       *   delivered a wrong count */
};

/** table of error descriptions indexed by return values of
 * gt_EISVerifyIntegrity  */
extern const char *EISIntegrityCheckResultStrings[];

/**
 * Select potentially expensive checks to perform on index.
 */
enum EISIntegrityCheckFlags
{
  EIS_VERIFY_BASIC = 0,         /**< just basic checks  */
  EIS_VERIFY_EXT_RANK = 1 << 0, /**< do rank queries for all
                                 * positions for all symbols in the
                                 * alphabet, not only for ranks changed */
};

/**
 * @brief Check wether index contains same symbols as reference
 * sequence and delivers correct rank counts.
 * @param seqIdx index to check
 * @param projectName name of corresponding suffix array project to
 * use as reference
 * @param skip omit this many symbols at the beginning
 * @param tickPrint print a dot every tickPrint symbols processed
 * @param fp print dots to this file pointer
 * @param chkFlags select additional tests (see enum EISIntegrityCheckFlags)
 */
enum EISIntegrityCheckResults
gt_EISVerifyIntegrity(EISeq *seqIdx, const char *projectName,
                      unsigned long skip,
                      unsigned long tickPrint, FILE *fp, int chkFlags,
                      GtLogger *verbosity, GtError *err);

/**
 * @brief Position file pointer at header written by upper layer.
 * @param seqIdx index to search header in
 * @param headerID number of header to search for
 * @param lenRet write length of header here
 * @return appropriate file pointer or NULL if header was not found
 */
static inline FILE *
EISSeekToHeader(const EISeq *seqIdx, uint16_t headerID,
                uint32_t *lenRet);

/**
 * Given a position write debugging output for surrounding sequence.
 * @param seqIdx sequence index to query
 * @param pos position for which to print context
 * @param fp print diagnostics to this file pointer
 * @param hint use this structure for hinting
 * @return 0 if an I/O error occured wrt fp
 */
static inline int
EISPrintDiagsForPos(const EISeq *seqIdx, unsigned long pos, FILE *fp,
                    EISHint hint);

#include "match/eis-encidxseq-siop.h"

#endif
genometools-1.5.1/src/match/eis-headerid.h000066400000000000000000000016771211610345200204360ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_HEADERID_H
#define EIS_HEADERID_H

enum {
  /* used by bwt sequence class */
  LOCATE_INFO_IN_INDEX_HEADERID = 1111,
  RANK_SORT_HEADERID            = 1112,
};

#endif
genometools-1.5.1/src/match/eis-list-do.h000066400000000000000000000024201211610345200202270ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_LIST_DO_H
#define EIS_LIST_DO_H

#define ListDo(type, initialPtr, NodeOp)        \
  do {                                          \
    type *p = initialPtr;                       \
    while (p)                                   \
    {                                           \
      type *next = p->next;                     \
      NodeOp;                                   \
      p = next;                                 \
    }                                           \
  } while (0)

#endif
genometools-1.5.1/src/match/eis-mrangealphabet-priv.h000066400000000000000000000037551211610345200226200ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_MRANGEALPHABET_PRIV_H
#define EIS_MRANGEALPHABET_PRIV_H

#include 
#include 
#include 

#include "match/eis-mrangealphabet.h"

struct multiRangeAlphabetEncoding
{
  enum sourceEncType encType;
  AlphabetRangeID numRanges;
  AlphabetRangeSize *rangeEndIndices, /*< maps to the last position + 1
                                       * for each range */
    *symbolsPerRange;   /*< gives number of symbols in each range */
};

struct multiRangeAlphabetEncodingUInt8
{
  struct multiRangeAlphabetEncoding baseClass;
  uint8_t mappings[UINT8_MAX+1], revMappings[UINT8_MAX+1];
};

typedef struct multiRangeAlphabetEncodingUInt8 MRAEncUInt8;

static inline MRAEncUInt8 *
MRAEnc2MRAEncUInt8(MRAEnc *mralpha)
{
  gt_assert(mralpha && mralpha->encType == sourceUInt8);
  return (MRAEncUInt8*)
    ((char *)mralpha - offsetof(MRAEncUInt8, baseClass));
}

static inline const MRAEncUInt8 *
constMRAEnc2MRAEncUInt8(const MRAEnc *mralpha)
{
  gt_assert(mralpha && mralpha->encType == sourceUInt8);
  return (const MRAEncUInt8*)
    ((char *)mralpha - offsetof(MRAEncUInt8, baseClass));
}

static inline MRAEnc*
MRAEncUInt82MRAEnc(MRAEncUInt8 *mralpha)
{
  gt_assert(mralpha);
  return &(mralpha->baseClass);
}

#endif
genometools-1.5.1/src/match/eis-mrangealphabet-siop.h000066400000000000000000000056701211610345200226100ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_MRANGEALPHABET_SIOP_H
#define EIS_MRANGEALPHABET_SIOP_H

#include "match/eis-mrangealphabet.h"
#include "match/eis-mrangealphabet-priv.h"

static inline MRAEnc *
MRAEncUInt8New(AlphabetRangeID numRanges, AlphabetRangeSize symbolsPerRange[],
               const uint8_t *mapping)
{
  return gt_newMultiRangeAlphabetEncodingUInt8(numRanges, symbolsPerRange,
                                            mapping);
}

static inline AlphabetRangeID
MRAEncGetNumRanges(const MRAEnc *mralpha)
{
  return mralpha->numRanges;
}

static inline AlphabetRangeSize
MRAEncGetRangeSize(const MRAEnc *mralpha, AlphabetRangeID range)
{
  gt_assert(mralpha);
  gt_assert(mralpha->numRanges > range);
  return mralpha->symbolsPerRange[range];
}

static inline Symbol
MRAEncGetRangeBase(const MRAEnc *mralpha, AlphabetRangeID range)
{
  gt_assert(mralpha && mralpha->numRanges > range);
  if (range == 0)
    return 0;
  else
    return mralpha->rangeEndIndices[range - 1];
}

static inline size_t
MRAEncGetDomainSize(const MRAEnc *mralpha)
{
  gt_assert(mralpha);
  switch (mralpha->encType)
  {
  case sourceUInt8:
    return UINT8_MAX + 1;
  default:
    abort();
  }
}

static inline Symbol
MRAEncMapSymbol(const MRAEnc *mralpha, Symbol sym)
{
  switch (mralpha->encType)
  {
  case sourceUInt8:
    return constMRAEnc2MRAEncUInt8(mralpha)->mappings[(uint8_t)sym];
  default:
    abort();
  }
}

static inline Symbol
MRAEncRevMapSymbol(const MRAEnc *mralpha, Symbol sym)
{
  switch (mralpha->encType)
  {
  case sourceUInt8:
    return constMRAEnc2MRAEncUInt8(mralpha)->revMappings[(uint8_t)sym];
  default:
    abort();
  }
}

static inline int
MRAEncSymbolHasValidMapping(const MRAEnc *mralpha, Symbol sym)
{
  switch (mralpha->encType)
  {
  case sourceUInt8:
    return mralpha->rangeEndIndices[mralpha->numRanges - 1] == UINT8_MAX
      || (constMRAEnc2MRAEncUInt8(mralpha)->mappings[(uint8_t)sym]
          != UNDEF_UCHAR);
  default:
    abort();
  }
}

static inline AlphabetRangeID
MRAEncGetRangeOfSymbol(const MRAEnc *mralpha, Symbol sym)
{
  AlphabetRangeID range = 0;
  gt_assert(mralpha && sym < gt_MRAEncGetSize(mralpha));
  while (sym >= mralpha->rangeEndIndices[range])
    ++range;
  return range;
}

#endif
genometools-1.5.1/src/match/eis-mrangealphabet.c000066400000000000000000000250111211610345200216220ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include "core/alphabet.h"
#include "core/assert_api.h"
#include "core/chardef.h"
#include "match/dataalign.h"
#include "core/ma_api.h"
#include "core/str.h"
#include "core/types_api.h"
#include "core/str_array.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-mrangealphabet-priv.h"
#include "core/unused_api.h"

MRAEnc *
gt_newMultiRangeAlphabetEncodingUInt8(AlphabetRangeID numRanges,
                                   const AlphabetRangeSize symbolsPerRange[],
                                   const uint8_t *mappings)
{
  MRAEncUInt8 *newAlpha = NULL;
  size_t rEIOffset = offsetAlign(
    sizeof (MRAEncUInt8),
    sizeof (newAlpha->baseClass.rangeEndIndices[0]));
  size_t sPROffset = offsetAlign(
    rEIOffset  +  sizeof (newAlpha->baseClass.rangeEndIndices[0]) * numRanges,
    sizeof (newAlpha->baseClass.symbolsPerRange[0]));
  AlphabetRangeID i;
  if ((newAlpha = gt_calloc(
         sPROffset
         + sizeof (newAlpha->baseClass.symbolsPerRange[0]) * numRanges,
         1)))
  {
    newAlpha->baseClass.rangeEndIndices
      = (AlphabetRangeSize *)((char *)newAlpha + rEIOffset);
    newAlpha->baseClass.symbolsPerRange
      = (AlphabetRangeSize *)((char *)newAlpha + sPROffset);
    newAlpha->baseClass.encType = sourceUInt8;
    newAlpha->baseClass.numRanges = numRanges;
    memset(newAlpha->mappings, UNDEF_UCHAR, UINT8_MAX+1);
    memset(newAlpha->revMappings, UNDEF_UCHAR, UINT8_MAX+1);
    newAlpha->baseClass.rangeEndIndices[0] =
      newAlpha->baseClass.symbolsPerRange[0] = symbolsPerRange[0];
    for (i = 1; i < numRanges; ++i)
    {
      newAlpha->baseClass.rangeEndIndices[i] =
        newAlpha->baseClass.rangeEndIndices[i-1]
        + (newAlpha->baseClass.symbolsPerRange[i] = symbolsPerRange[i]);
    }
    for (i = 0; i <= UINT8_MAX; ++i)
    {
      newAlpha->mappings[i] = mappings[i];
      newAlpha->revMappings[mappings[i]] = i;
    }
  }
  else
  {
    if (newAlpha)
    {
      if (newAlpha->baseClass.symbolsPerRange)
        gt_free(newAlpha->baseClass.symbolsPerRange);
      if (newAlpha->baseClass.rangeEndIndices)
        gt_free(newAlpha->baseClass.rangeEndIndices);
      gt_free(newAlpha);
    }
    return NULL;
  }
  return &(newAlpha->baseClass);
}

MRAEnc *
gt_MRAEncGTAlphaNew(const GtAlphabet *alpha)
{
  AlphabetRangeSize symsPerRange[2];
  uint8_t *mappings;
  MRAEnc *result;
  uint32_t numofchars = gt_alphabet_num_of_chars(alpha);
  mappings = gt_malloc(sizeof (uint8_t) * (UINT8_MAX + 1));
  memset(mappings, UNDEF_UCHAR, UINT8_MAX+1);
  {
    /* handle regular symbols */
    int i;
    for (i = 0; i < numofchars; ++i)
      mappings[i] = i;
    symsPerRange[0] = numofchars;
  }
  /* handle special symbols */
  mappings[WILDCARD] = numofchars;
  symsPerRange[1] = 1;
  result = gt_newMultiRangeAlphabetEncodingUInt8(2, symsPerRange, mappings);
  gt_free(mappings);
  return result;
}

MRAEnc *
gt_MRAEncCopy(const MRAEnc *alpha)
{
  gt_assert(alpha);
  switch (alpha->encType)
  {
  case sourceUInt8:
    {
      MRAEncUInt8 *newAlpha = NULL;
      const MRAEncUInt8 *srcAlpha = constMRAEnc2MRAEncUInt8(alpha);
      int numRanges = alpha->numRanges;
      gt_assert(numRanges > 0);
      if ((newAlpha = gt_calloc(sizeof (MRAEncUInt8), 1))
          && (newAlpha->baseClass.rangeEndIndices =
              gt_malloc(sizeof (newAlpha->baseClass.rangeEndIndices[0])
                        * numRanges))
          && (newAlpha->baseClass.symbolsPerRange =
              gt_malloc(sizeof (newAlpha->baseClass.rangeEndIndices[0])
                        * numRanges)))
      {
        newAlpha->baseClass.encType = sourceUInt8;
        newAlpha->baseClass.numRanges = srcAlpha->baseClass.numRanges;
        memcpy(newAlpha->mappings, srcAlpha->mappings, UINT8_MAX+1);
        memcpy(newAlpha->revMappings, srcAlpha->revMappings, UINT8_MAX+1);
        memcpy(newAlpha->baseClass.rangeEndIndices,
               srcAlpha->baseClass.rangeEndIndices,
               sizeof (newAlpha->baseClass.rangeEndIndices[0]) * numRanges);
        memcpy(newAlpha->baseClass.symbolsPerRange,
               srcAlpha->baseClass.symbolsPerRange,
               sizeof (newAlpha->baseClass.symbolsPerRange[0]) * numRanges);
        return &(newAlpha->baseClass);
      }
      else
      {
        if (newAlpha)
        {
          if (newAlpha->baseClass.symbolsPerRange)
            gt_free(newAlpha->baseClass.symbolsPerRange);
          if (newAlpha->baseClass.rangeEndIndices)
            gt_free(newAlpha->baseClass.rangeEndIndices);
          gt_free(newAlpha);
        }
        return NULL;
      }
    }
    break;
  default:
    return NULL;
    break;
  }
}

AlphabetRangeSize
gt_MRAEncGetSize(const MRAEnc *mralpha)
{
  AlphabetRangeID range, numRanges = mralpha->numRanges, sumRanges = 0;
  for (range = 0; range < numRanges; ++range)
  {
    sumRanges += mralpha->symbolsPerRange[range];
  }
  return sumRanges;
}

MRAEnc *
gt_MRAEncSecondaryMapping(const MRAEnc *srcAlpha, int selection,
                       const int *rangeSel, Symbol fallback)
{
  MRAEnc *newAlpha;
  switch (srcAlpha->encType)
  {
  case sourceUInt8:
    {
      GT_UNUSED const MRAEncUInt8 *ui8alpha;
      uint8_t *mappings, destSym;
      AlphabetRangeSize *newRanges, sym;
      AlphabetRangeID range, numRanges = MRAEncGetNumRanges(srcAlpha);
      ui8alpha = constMRAEnc2MRAEncUInt8(srcAlpha);
      mappings = gt_malloc(sizeof (uint8_t) * (UINT8_MAX + 1));
      memset(mappings, UNDEF_UCHAR, UINT8_MAX+1);
      newRanges = gt_malloc(sizeof (newRanges[0]) * numRanges);
      sym = 0;
      destSym = 0;
      for (range = 0; range < numRanges; ++range)
      {
        if (rangeSel[range] == selection)
        {
          for (; sym < srcAlpha->rangeEndIndices[range]; ++sym)
            mappings[sym] = destSym++;
          newRanges[range] = srcAlpha->symbolsPerRange[range];
        }
        else
        {
          for (; sym < srcAlpha->rangeEndIndices[range]; ++sym)
            mappings[sym] = fallback;
          newRanges[range] = 0;
        }
      }
      newAlpha = gt_newMultiRangeAlphabetEncodingUInt8(numRanges, newRanges,
                                                    mappings);
      gt_free(mappings);
      gt_free(newRanges);
    }
    break;
  default:
    abort();
    break;
  }
  return newAlpha;
}

MRAEnc *
gt_MRAEncAddSymbolToRange(MRAEnc *mralpha, Symbol sym, AlphabetRangeID range)
{
  Symbol insertPos, numSyms;
  gt_assert(mralpha && range < mralpha->numRanges);
  insertPos = mralpha->rangeEndIndices[range];
  numSyms = mralpha->rangeEndIndices[mralpha->numRanges - 1];
  switch (mralpha->encType)
  {
  case sourceUInt8:
    {
      MRAEncUInt8 *ui8alpha;
      ui8alpha = MRAEnc2MRAEncUInt8(mralpha);
      gt_assert(ui8alpha->mappings[sym] == UNDEF_UCHAR);
      /* first move all old mappings accordingly */
      {
        Symbol i;
        for (i = numSyms; i > insertPos; --i)
        {
          Symbol origSym = ui8alpha->revMappings[i - 1];
          ui8alpha->revMappings[i] = origSym;
          ui8alpha->mappings[origSym] += 1;
        }
      }
      /* do actual insertion */
      ui8alpha->mappings[sym] = insertPos;
      ui8alpha->revMappings[insertPos] = sym;
      /* adjust ranges */
      mralpha->symbolsPerRange[range] += 1;
      {
        AlphabetRangeID i;
        for (i = range; i < mralpha->numRanges; ++i)
        {
          mralpha->rangeEndIndices[i] += 1;
        }
      }
    }
    break;
  default:
    abort();
    break;
  }
  return mralpha;
}

/**
 * @return number of symbols actually read
 */
size_t
gt_MRAEncReadAndTransform(const MRAEnc *mralpha, FILE *fp,
                       size_t numSyms, Symbol *dest)
{
  int retval = 0;
  switch (mralpha->encType)
  {
  case sourceUInt8:
    {
      const MRAEncUInt8 *ui8alpha;
      size_t i;
      ui8alpha = constMRAEnc2MRAEncUInt8(mralpha);
      for (i = 0; i < numSyms; ++i)
      {
        int c = getc(fp);
        if (c != EOF)
          dest[i] = ui8alpha->mappings[c];
        else
          break;
      }
      retval = i;
    }
    break;
  default:
    abort();
    break;
  }
  return retval;
}

void
gt_MRAEncSymbolsTransform(const MRAEnc *mralpha, Symbol *symbols,
                          size_t numSyms)
{
  switch (mralpha->encType)
  {
  case sourceUInt8:
    {
      const MRAEncUInt8 *ui8alpha;
      size_t i;
      ui8alpha = constMRAEnc2MRAEncUInt8(mralpha);
      for (i = 0; i < numSyms; ++i)
      {
        symbols[i] = ui8alpha->mappings[symbols[i]];
      }
    }
    break;
  default:
    abort();
    break;
  }
}

void
gt_MRAEncSymbolsRevTransform(const MRAEnc *mralpha, Symbol *symbols,
                          size_t numSyms)
{
  switch (mralpha->encType)
  {
  case sourceUInt8:
    {
      const MRAEncUInt8 *ui8alpha;
      size_t i;
      ui8alpha = constMRAEnc2MRAEncUInt8(mralpha);
      for (i = 0; i < numSyms; ++i)
      {
        symbols[i] = ui8alpha->revMappings[symbols[i]];
      }
    }
    break;
  default:
    abort();
    break;
  }
}

int
gt_MRAEncSymbolIsInSelectedRanges(const MRAEnc *mralpha, Symbol sym,
                               int selection, const int *rangeSel)
{
  AlphabetRangeID range = 0;
  gt_assert(mralpha && rangeSel);
  while (range < mralpha->numRanges
         && sym >= mralpha->rangeEndIndices[range])
    ++range;
  if (range < mralpha->numRanges)
  {
    if (rangeSel[range] == selection
       && sym >= (mralpha->rangeEndIndices[range]
                  - mralpha->symbolsPerRange[range])
       /* implicitely: && sym < mralpha->rangeEndIndices[range] */)
      return 1;
    else
      return 0;
  }
  else
    return -1;
}

void
gt_MRAEncDelete(struct multiRangeAlphabetEncoding *mralpha)
{
  gt_assert(mralpha);
  switch (mralpha->encType)
  {
    MRAEncUInt8 *ui8alpha;
  case sourceUInt8:
    ui8alpha = MRAEnc2MRAEncUInt8(mralpha);
    gt_free(ui8alpha);
    break;
  default:
    abort();
    break;
  }
}
genometools-1.5.1/src/match/eis-mrangealphabet.h000066400000000000000000000214431211610345200216340ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_MRANGEALPHABET_H
#define EIS_MRANGEALPHABET_H

/**
 * \file eis-mrangealphabet.h
 * \brief Methods for an alphabet mapping where the alphabet is mapped
 * to multiple contiguous ranges.
 *
 * The mapping is constructed so that an alphabet with n symbols
 * is mapped to the range 0..n-1 and any symbol can be queried for
 * what range it belongs to.
 * \author Thomas Jahns 
 */

#include 
#include "core/alphabet.h"

/** symbols are stored in this scalar type */
typedef unsigned char Symbol;
#define PRIuSymbol "u"
/** let's assume 65536 ranges are enough */
typedef unsigned AlphabetRangeID;
/** Caution: sizeof (AlphabetRangeID) >= sizeof (AlphabetRangeSize)
 *           must be true, AlphabetRangeSize must be able to
 *           represent the total number of symbols */
typedef unsigned short AlphabetRangeSize;
/** retrieve symbol from BitString */
#define gt_bsGetSymbol gt_bsGetUInt8
/** store symbol in BitString */
#define gt_bsStoreSymbol gt_bsStoreUInt8
/** retrieve array of symbols from BitString  */
#define gt_bsGetUniformSymbolArray gt_bsGetUniformUInt8Array
/** store array of symbols in BitString  */
#define gt_bsStoreUniformSymbolArray gt_bsStoreUniformUInt8Array
/** how many bits are required to store given symbol value */
#define requiredSymbolBits gt_requiredUInt8Bits

/**
 * Describes an alphabet i.e. a mapping function from a given input
 * type to a contiguous range of integers which are divided into
 * multiple ranges, which are again continuous.
 */
typedef struct multiRangeAlphabetEncoding MRAEnc;

/** used to describe a symbol not occurring in the alphabet */
#define UNDEF_UCHAR ((unsigned char)~0)

/** select width of symbol input */
enum sourceEncType {
  sourceUnknown = 0,            /**< invalid/undefined  */
  sourceUInt8 = 1,              /**< input in the range 0..255 */
};

/**
 * \brief Create an alphabet to map a selection of unsigned characters
 * onto the resulting ranges.
 * @param numRanges number of distinct ranges the alphabet is to be
 * divided into.
 * @param symbolsPerRange gives the number of symbols for every range
 * @param mapping maps all uint8_t input symbols to values in the
 * range 0..sum(symbolsPerRange) or the input alphabet specific
 * value UNDEF_UCHAR
 */
static inline MRAEnc *
MRAEncUInt8New(AlphabetRangeID numRanges, AlphabetRangeSize symbolsPerRange[],
               const uint8_t *mapping);

/**
 * \brief Creates a mapping to two ranges (regular and special
 * symbols) from a given genometools alphabet.
 * @param alpha original alphabet
 */
MRAEnc *
gt_MRAEncGTAlphaNew(const GtAlphabet *alpha);

/**
 * \brief alias of MRAEncUInt8New
 */
MRAEnc *
gt_newMultiRangeAlphabetEncodingUInt8(AlphabetRangeID numRanges,
                                   const AlphabetRangeSize symbolsPerRange[],
                                   const uint8_t *mappings);

/**
 * @brief Copy constructor for multi-range alphabets
 * @param alpha alphabet to copy
 * @return new alphabet object
 */
MRAEnc *
gt_MRAEncCopy(const MRAEnc *alpha);

/**
 * \brief remap multirange alphabet by excluding some ranges
 *
 * Maps symbols from all included ranges to new values 0 to n where all
 * symbols from non-included ranges are mapped to fallback
 * @param srcAlpha alphabet to remap
 * @param selection ranges with this value in rangeSel are carried
 * over to new alphabet
 * @param rangeSel array of integer flags, if != selection for given
 * range => maps all symbols in range to fallback, otherwise append to
 * already mapped symbols
 * @param fallback symbol to map not-included ranges to
 */
MRAEnc *
gt_MRAEncSecondaryMapping(const MRAEnc *srcAlpha, int selection,
                       const int *rangeSel, Symbol fallback);

/**
 * \brief Inserts a previously unmapped symbol into a range.
 *
 * All successor ranges will therefore be shifted by one in the
 * resulting mapping.
 * @param mralpha alphabet object reference to add mapping to
 * @param sym input code to map
 * @param range number of range to insert new symbol into
 * @return same reference as mralpha but after destructive change
 */
MRAEnc *
gt_MRAEncAddSymbolToRange(MRAEnc *mralpha, Symbol sym, AlphabetRangeID range);

/**
 * \brief Query number of ranges in alphabet.
 * @param mralpha alphabet to query for number of ranges
 * @return number of ranges
 */
static inline AlphabetRangeID
MRAEncGetNumRanges(const MRAEnc *mralpha);

/**
 * \brief Query number of symbols in given range of alphabet.
 * @param mralpha alphabet to get range from
 * @param range
 */
static inline AlphabetRangeSize
MRAEncGetRangeSize(const MRAEnc *mralpha, AlphabetRangeID range);

/**
 * \brief Query symbol which starts range.
 * @param mralpha
 * @param range start symbol of range, symbols of range range from
 * MRAEncGetRangeBase(alph, range) to MRAEncGetRangeBase(alph, range + 1) - 1
 */
static inline Symbol
MRAEncGetRangeBase(const MRAEnc *mralpha, AlphabetRangeID range);

/**
 * @brief Get number of different symbols in alphabet.
 * @param mralpha
 * @return number of symbols in alphabet
 */
AlphabetRangeSize
gt_MRAEncGetSize(const MRAEnc *mralpha);

/**
 * @brief Get range of input symbols.
 * @param mralpha
 * @return size of original value range of symbols in alphabet
 * (i.e. 256 for 8 bit mapping)
 */
static size_t
MRAEncGetDomainSize(const MRAEnc *mralpha);

/**
 * \brief Look up code of symbol from input domain in output range.
 * @return output code or input specific code for illegal symbol (in
 * which case MRAEncSymbolHasValidMapping would have returned false).
 */
static inline Symbol
MRAEncMapSymbol(const MRAEnc *mralpha, Symbol sym);

/**
 * @brief Find wether a symbol from input is accurately represented in
 * the alphabet or illegal input.
 * @param mralpha
 * @param sym symbol to map
 * @return 0 if alphabet has no valid mapping, !0 otherwise
 */
static inline int
MRAEncSymbolHasValidMapping(const MRAEnc *mralpha, Symbol sym);

/**
 * @brief Apply reverse mapping of transformed symbol to input alphabet.
 * @param mralpha
 * @param sym symbol to un-map
 * @return inverse mapping of sym
 */
static inline Symbol
MRAEncRevMapSymbol(const MRAEnc *mralpha, Symbol sym);

/**
 * @brief Apply mapping of input string.
 * @param mralpha
 * @param symbols symbols to convert
 * @param numSyms length of symbols string
 */
void
gt_MRAEncSymbolsTransform(const MRAEnc *mralpha,
                          Symbol *symbols,
                          size_t numSyms);

/**
 * @brief Apply reverse mapping of string.
 * @param mralpha
 * @param symbols symbols to convert
 * @param numSyms length of symbols string
 */
void
gt_MRAEncSymbolsRevTransform(const MRAEnc *mralpha, Symbol *symbols,
                          size_t numSyms);
/**
 * @brief Query wether a symbol belongs to a selected range
 * @param mralpha alphabet to query
 * @param sym symbol to look-up range for
 * @param selection value to test rangeSel for
 * @param rangeSel array of codes for every range in alphabet, to be
 * compared with selection
 * @return > 0 if sym is included in a range r which has rangeSel[r]
 * == selection, 0 if sym is not in any selected range, and <0 if sym
 * is out of the alphabets range of symbols
 */
int
gt_MRAEncSymbolIsInSelectedRanges(const MRAEnc *mralpha, Symbol sym,
                               int selection, const int *rangeSel);

/**
 * @brief Query range for given symbol
 * @param mralpha alphabet to query
 * @param sym symbol to look-up range for (already transformed by
 * mapping corresponding to alphabet)
 * @return range id
 */
static inline AlphabetRangeID
MRAEncGetRangeOfSymbol(const MRAEnc *mralpha, Symbol sym);

/**
 * @brief Read symbols from file and transform according to
 * mapping.
 * @param mralpha
 * @param fp file pointer
 * @param numSyms read this many symbols
 * @param dest write converted symbols here
 * @return number of symbols actually read
 */
size_t
gt_MRAEncReadAndTransform(const MRAEnc *mralpha, FILE *fp,
                       size_t numSyms, Symbol *dest);

/**
 * @brief Delete alphabet object.
 * @param mralpha
 */
void
gt_MRAEncDelete(struct multiRangeAlphabetEncoding *mralpha);

#include "match/eis-mrangealphabet-siop.h"

#endif
genometools-1.5.1/src/match/eis-random-seqaccess.h000066400000000000000000000035601211610345200221120ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_RANDOM_SEQACCESS_H
#define EIS_RANDOM_SEQACCESS_H

/**
 * @file eis-construction-interface.h
 * @brief Abstract interface for suffix array sources.
 *
 * The function pointer types defined here are essentially the
 * interface used for index construction: a source for suffix array
 * and BWT sequence entries is characterized by an interface
 * conforming to these functions.
 */
#include 

#include "core/error.h"

#include "match/eis-mrangealphabet.h"

/**
 * \brief generic method to access the original encoded sequence
 * @return actual number of symbols acquired
 */
typedef size_t (*accessSeqSubStr)(const void *state,
                                  Symbol *dest,
                                  unsigned long pos,
                                  size_t len);

struct randomSeqAccessor
{
  accessSeqSubStr accessFunc;
  void *state;
};

typedef struct randomSeqAccessor RandomSeqAccessor;

static inline size_t
accessSequence(RandomSeqAccessor accessor, Symbol *dest, unsigned long pos,
               size_t len)
{
  return accessor.accessFunc(accessor.state, dest, pos, len);
}

#endif
genometools-1.5.1/src/match/eis-sa-common-priv.h000066400000000000000000000045401211610345200215300ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SA_COMMON_PRIV_H
#define EIS_SA_COMMON_PRIV_H

#include "eis-random-seqaccess.h"
#include "eis-sa-common.h"
#include "eis-sequencemultiread.h"

typedef SeqDataReader (*createReaderFunc)(SASeqSrc *src,
                                          enum sfxDataRequest request);

typedef SeqDataTranslator (*createTranslatorFunc)(SASeqSrc *src,
                                                  enum sfxDataRequest request);

typedef Definedunsignedlong (*getRot0PosFunc)(const SASeqSrc *src);

typedef const struct seqStats *(*getSeqStatsFunc)(const SASeqSrc *src);

typedef void (*deleteSASeqSrcFunc)(SASeqSrc *src);

typedef MRAEnc *(*newMRAEncFunc)(const SASeqSrc *src);

struct SASeqSrc
{
  unsigned long seqLen;
  createReaderFunc createReader;
  createTranslatorFunc createTranslator;
  getRot0PosFunc getRot0Pos;
  getSeqStatsFunc getSeqStats;
  RandomSeqAccessor origSequenceAccess;
  deleteSASeqSrcFunc deleteSASS;
  newMRAEncFunc newMRAEnc;
  MRAEnc *alphabet;
  struct seqReaderSet readerSet;
  struct saTaggedXltorStateList xltorStates;
};

static inline void
initSASeqSrc(SASeqSrc *src, unsigned long seqLen,
             createTranslatorFunc createTranslator,
             createReaderFunc createReader,
             getRot0PosFunc getRot0Pos, getSeqStatsFunc getSeqStats,
             RandomSeqAccessor origSeqAccess, deleteSASeqSrcFunc deleteSASS,
             newMRAEncFunc newSeqMRAEnc,
             generatorFunc generator, void *generatorState);

static inline void
destructSASeqSrc(SASeqSrc *src);

SeqDataReader
gt_SASSGenericCreateReader(SASeqSrc *src, enum sfxDataRequest request);

#endif
genometools-1.5.1/src/match/eis-sa-common-siop.h000066400000000000000000000100641211610345200215200ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SA_COMMON_SIOP_H
#define EIS_SA_COMMON_SIOP_H

#include "match/eis-sa-common.h"
#include "match/eis-sa-common-priv.h"

static inline GtUchar
sfxIdx2BWTSym(unsigned long sufIdx, const GtEncseq *encseq,
              GtReadmode readmode)
{
  return sufIdx != 0
    ? gt_encseq_get_encoded_char(encseq, sufIdx - 1, readmode)
    : (GtUchar) UNDEFBWTCHAR;
}

static inline size_t
EncSeqGetSubSeq(const GtEncseq *encseq, GtReadmode readmode,
                unsigned long pos, size_t len, GtUchar *subSeq)
{
  size_t i;
  gt_assert(encseq);
  for (i = 0; i < len; ++i)
    subSeq[i] = gt_encseq_get_encoded_char(encseq, pos + i, readmode);
  return len;
}

static inline SeqDataReader
SASSCreateReader(SASeqSrc *src, enum sfxDataRequest request)
{
  return src->createReader(src, request);
}

static inline Definedunsignedlong
SASSGetRot0Pos(const SASeqSrc *src)
{
  return src->getRot0Pos(src);
}

static inline unsigned long
SASSGetLength(const SASeqSrc *src)
{
  return src->seqLen;
}

static inline MRAEnc *
SASSNewMRAEnc(const SASeqSrc *src)
{
  return src->newMRAEnc(src);
}

static inline const MRAEnc *
SASSGetMRAEnc(SASeqSrc *src)
{
  return (src->alphabet ?
          src->alphabet : (src->alphabet = SASSNewMRAEnc(src)));
}

static inline const struct seqStats *
SASSGetSeqStats(const SASeqSrc *src)
{
  if (src->getSeqStats)
    return src->getSeqStats(src);
  else
    return NULL;
}

static inline size_t
SASSAccessSequence(const SASeqSrc *src, Symbol *dest,
                   unsigned long pos, size_t len)
{
  return accessSequence(src->origSequenceAccess, dest, pos, len);
}

static inline RandomSeqAccessor
SASSGetOrigSeqAccessor(const SASeqSrc *src)
{
  return src->origSequenceAccess;
}

static inline void
initSASeqSrc(SASeqSrc *src, unsigned long seqLen,
             createTranslatorFunc createTranslator,
             createReaderFunc createReader, getRot0PosFunc getRot0Pos,
             getSeqStatsFunc getSeqStats, RandomSeqAccessor origSeqAccess,
             deleteSASeqSrcFunc deleteSASS,
             newMRAEncFunc newMRAEnc,
             generatorFunc generator, void *generatorState)
{
  gt_assert(src);
  gt_assert(createReader || createTranslator);
  gt_assert(getRot0Pos);
  src->seqLen = seqLen;
  src->createTranslator = createTranslator;
  /* createTranslator is not NULL iff read from suffixerator */
  /* createReader is not NULL iff read from suffixarray */
  if (createTranslator && !createReader)
  {
    src->createReader = gt_SASSGenericCreateReader;
  } else
  {
    src->createReader = createReader;
  }
  src->getRot0Pos = getRot0Pos;
  src->getSeqStats = getSeqStats;
  src->origSequenceAccess = origSeqAccess;
  src->deleteSASS = deleteSASS;
  src->newMRAEnc = newMRAEnc;
  src->alphabet = NULL;
  gt_initEmptySeqReaderSet(&src->readerSet,
                           SFX_REQUEST_NONE,
                           (createTranslator != NULL) ? true : false,
                           sizeof (unsigned long),
                           generator, generatorState);
  gt_initSATaggedXltorStateList(&src->xltorStates);
}

static inline void
destructSASeqSrc(SASeqSrc *src)
{
  if (src->alphabet)
    gt_MRAEncDelete(src->alphabet);
  gt_destructSATaggedXltorStateList(&src->xltorStates);
  gt_destructSeqReaderSet(&src->readerSet);
}

static inline void
SASSDelete(SASeqSrc *src)
{
  src->deleteSASS(src);
}

#endif
genometools-1.5.1/src/match/eis-sa-common.c000066400000000000000000000067011211610345200205460ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/ma_api.h"
#include "core/encseq.h"
#include "match/eis-sa-common.h"

size_t gt_translateSuftab2BWT(void *translator,
                              void *voiddest,
                              const unsigned long *src,
                              size_t len)
{
  struct encSeqTrState *trState = (struct encSeqTrState *) translator;
  GtUchar *dest = (GtUchar *) voiddest;
  size_t idx;

  gt_assert(trState);
  for (idx = 0; idx < len; ++idx)
  {
    dest[idx] = sfxIdx2BWTSym(src[idx], trState->encseq,
                              trState->readmode);
  }
  return len * sizeof (GtUchar);
}

size_t gt_translateSuftab2BWTSuffixsortspace(
                                       void *translator,
                                       void *voiddest,
                                       const GtSuffixsortspace *suffixsortspace,
                                       unsigned long offset,
                                       size_t len)
{
  struct encSeqTrState *trState = (struct encSeqTrState *) translator;
  GtUchar *dest = (GtUchar *) voiddest;
  size_t idx;

  gt_assert(trState);
  for (idx = 0; idx < len; ++idx)
  {
    dest[idx]
      = sfxIdx2BWTSym(gt_suffixsortspace_getdirect(suffixsortspace,offset+idx),
                      trState->encseq, trState->readmode);
  }
  return len * sizeof (GtUchar);
}

struct saTaggedXltorStateLE
{
  struct saTaggedXltorStateLE *next;
  struct saTaggedXltorState state;
};

void
gt_initSATaggedXltorStateList(struct saTaggedXltorStateList *saXltorStateList)
{
  saXltorStateList->numXltors = 0;
  saXltorStateList->stateList = NULL;
}

void
gt_destructSATaggedXltorStateList(
  struct saTaggedXltorStateList *saXltorStateList)
{
  struct saTaggedXltorStateLE *next;
  gt_assert(saXltorStateList);
  next = saXltorStateList->stateList;
  while (next)
  {
    struct saTaggedXltorStateLE *prev = next;
    next = next->next;
    gt_free(prev);
  }
}

struct saTaggedXltorState *
gt_addSuffixarrayXltor(struct saTaggedXltorStateList *saXltorStateList,
                    enum sfxDataRequest request,
                    struct encSeqTrState state)
{
  struct saTaggedXltorStateLE *newSAXltorState;
  newSAXltorState = gt_malloc(sizeof (*newSAXltorState));
  newSAXltorState->state.typeTag = request;
  newSAXltorState->state.state = state;
  newSAXltorState->next = saXltorStateList->stateList;
  saXltorStateList->stateList = newSAXltorState;
  ++(saXltorStateList->numXltors);
  return &newSAXltorState->state;
}

SeqDataReader
gt_SASSGenericCreateReader(SASeqSrc *src, enum sfxDataRequest request)
{
  return gt_seqReaderSetRegisterConsumer(&src->readerSet, request,
                                      src->createTranslator(src, request));
}
genometools-1.5.1/src/match/eis-sa-common.h000066400000000000000000000106431211610345200205530ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/**
 * \file eis-suffixerator-interface.h
 * \brief Methods to call suffixerator functions through one object,
 * but have the same data available to multiple listeners.
 * \author Thomas Jahns 
 */
#ifndef EIS_SA_COMMON_H
#define EIS_SA_COMMON_H

#include 
#include "core/defined-types.h"
#include "core/encseq.h"
#include "core/types_api.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-random-seqaccess.h"
#include "match/eis-seqdatasrc.h"
#include "match/sfx-suffixgetset.h"

/**
 * Describes what kind of information will be read by a requestor:
 */
enum sfxDataRequest {
  SFX_REQUEST_NONE = 0,         /**< empty request, used for special purposes */
  SFX_REQUEST_SUFTAB = 1<<0,    /**< request for suffix array entries */
  SFX_REQUEST_BWTTAB = 1<<1,    /**< request for bwt table */
  SFX_REQUEST_ALL = SFX_REQUEST_SUFTAB |
                    SFX_REQUEST_BWTTAB, /**< used as bitmask  */
  SFX_REQUEST_ANY = SFX_REQUEST_ALL,             /**< used as bitmask  */
};

/**
 * @return Symbol at position sufIdx or UNDEFBWTCHAR i.e. the terminator
 */
static inline GtUchar
sfxIdx2BWTSym(unsigned long sufIdx, const GtEncseq *encseq,
              GtReadmode readmode);

static inline size_t
EncSeqGetSubSeq(const GtEncseq *encseq, GtReadmode readmode,
                unsigned long pos, size_t len, GtUchar *subStr);

struct encSeqTrState
{
  const GtEncseq *encseq;
  GtReadmode readmode;
};

/**
 * @brief Produce given length of symbols from the BWT by translating
 * an array of suffix indices, this version uses the values of
 * suffix array and encoded sequence instead of reading the BWT file.
 * @param state reference of a SuffixarrayFileInterface
 * @param dest write symbols here
 * @param src read suffix indices from here
 * @param len length of string to read
 */

size_t gt_translateSuftab2BWT(void *data,
                              void *voiddest,
                              const unsigned long *src,
                              size_t len);

size_t gt_translateSuftab2BWTSuffixsortspace(
                                       void *translator,
                                       void *voiddest,
                                       const GtSuffixsortspace *suffixsortspace,
                                       unsigned long offset,
                                       size_t len);

struct saTaggedXltorState
{
  enum sfxDataRequest typeTag;
  struct encSeqTrState state;
};

struct saTaggedXltorStateList
{
  size_t numXltors;
  struct saTaggedXltorStateLE *stateList;
};

void
gt_initSATaggedXltorStateList(struct saTaggedXltorStateList *saXltorStateList);

void
gt_destructSATaggedXltorStateList(
  struct saTaggedXltorStateList *saXltorStateList);

struct saTaggedXltorState *
gt_addSuffixarrayXltor(struct saTaggedXltorStateList *saXltorStateList,
                    enum sfxDataRequest request,
                    struct encSeqTrState state);

typedef struct SASeqSrc SASeqSrc;

static inline SeqDataReader
SASSCreateReader(SASeqSrc *src, enum sfxDataRequest request);

static inline Definedunsignedlong
SASSGetRot0Pos(const SASeqSrc *src);

static inline unsigned long
SASSGetLength(const SASeqSrc *src);

static inline MRAEnc *
SASSNewMRAEnc(const SASeqSrc *src);

static inline const MRAEnc *
SASSGetMRAEnc(SASeqSrc *src);

static inline const struct seqStats *
SASSGetSeqStats(const SASeqSrc *src);

static inline size_t
SASSAccessSequence(const SASeqSrc *src,
                   Symbol *dest,
                   unsigned long pos,
                   size_t len);

static inline RandomSeqAccessor
SASSGetOrigSeqAccessor(const SASeqSrc *src);

static inline void
SASSDelete(SASeqSrc *src);

#include "match/eis-sa-common-siop.h"

#endif
genometools-1.5.1/src/match/eis-seqblocktranslate.c000066400000000000000000000431751211610345200224040ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef NDEBUG
#include 
#endif

#include "core/bitpackstring.h"
#include "core/combinatorics.h"
#include "core/mathsupport.h"
#include "core/dynalloc.h"
#include "core/log.h"
#include "core/ma_api.h"
#include "core/unused_api.h"
#include "match/eis-seqblocktranslate.h"

#if 1
/**
 * Setup composition array for lexically maximal composition.
 * @param maxSym last symbol to represent (lexical maximum)
 * @param blockSize sum of symbol counts in composition
 * (i.e. composition contains this many symbols)
 * @param composition vector of symbol counts
 * @param symRMNZ points to index of rightmost non-zero symbol count
 * in composition vector (state of generating procedure)
 */
static inline void
initComposition(Symbol maxSym, unsigned blockSize,
                unsigned composition[maxSym + 1], unsigned *symRMNZ)
{
  memset(composition, 0, sizeof (composition[0]) * (maxSym));
  composition[*symRMNZ = maxSym] = blockSize;
}
#else
/**
 * Setup composition array for lexically minimal composition.
 * @param maxSym last symbol to represent (lexical maximum)
 * @param blockSize sum of symbol counts in composition
 * (i.e. composition contains this many symbols)
 * @param composition vector of symbol counts
 * @param symRMNZ points to index of rightmost non-zero symbol count
 * in composition vector (state of generating procedure)
 */
static inline void
initComposition(Symbol maxSym, unsigned blockSize,
                unsigned composition[maxSym + 1], unsigned *symLMNZ)
{
  memset(composition + 1, 0, sizeof (composition[0]) * (maxSym));
  composition[*symLMNZ = 0] = blockSize;
}
#endif

#if 1
/**
 * Compute lexically previous composition given any composition in
 * \link composition \endlink.
 * @param composition array[0..maxSym] of occurrence counts for each symbol
 * @param maxSym last symbol index of composition
 * @param symMNZ rightmost non-zero entry of composition[]
 */
static inline void
nextComposition(unsigned composition[],
                Symbol maxSym,
                unsigned *symRMNZ)
{
  ++composition[*symRMNZ - 1];
  if (!(--composition[*symRMNZ]))
  {
    --*symRMNZ;
  }
  else if (!(composition[maxSym]))
  {
    composition[maxSym] = composition[*symRMNZ];
    composition[*symRMNZ] = 0;
    *symRMNZ = maxSym;
  }
}
#else
/**
 * Compute lexically next composition given any composition in
 * \link composition \endlink.
 * @param composition array[0..maxSym] of occurrence counts for each symbol
 * @param maxSym last symbol index of composition
 * @param symMNZ rightmost non-zero entry of composition[]
 */
static inline void
nextComposition(unsigned composition[],
                Symbol maxSym,
                unsigned *symLMNZ)
{
  ++composition[*symLMNZ + 1];
  if (!(--composition[*symLMNZ]))
  {
    ++*symLMNZ;
  }
  else if (!(composition[0]))
  {
    composition[0] = composition[*symLMNZ];
    composition[*symLMNZ] = 0;
    *symLMNZ = 0;
  }
}
#endif

static int
initPermutationsList(const unsigned *composition, struct permList *permutation,
                     BitString permStore, BitOffset permOffset,
                     unsigned blockSize, unsigned alphabetSize,
                     unsigned bitsPerSymbol);

static void
destructPermutationsList(struct permList *permutation);

#ifdef EIS_DEBUG
static void
printComposition(FILE *fp, const unsigned *composition,
                 unsigned alphabetSize, unsigned blockSize);
#endif /* EIS_DEBUG */

static inline BitOffset
compListPermStartOffset(struct compList *list, unsigned numSyms)
{
  return list->numCompositions * list->bitsPerCount * numSyms;
}

#define gt_initCompositionListErrRet()                                  \
  do {                                                                  \
    if (newList->permutations)                                          \
    {                                                                   \
      unsigned i;                                                       \
      for (i = 0; i < cmpIdx; ++i)                                      \
        destructPermutationsList(newList->permutations + i );           \
      gt_free(newList->permutations);                                   \
    }                                                                   \
    if (newList->catCompsPerms)                                         \
      gt_free(newList->catCompsPerms);                                  \
    if (composition) gt_free(composition);                              \
    return 0;                                                           \
  } while (0)

int
gt_initCompositionList(struct compList *newList, unsigned blockSize,
                    unsigned alphabetSize)
{
  unsigned *composition = NULL;
  Symbol maxSym = alphabetSize - 1;
  BitOffset bitsPerComp, bitsPerCount, bitsPerPerm;
  size_t numCompositions, cmpIdx = 0;
  size_t maxNumPermutations = 0, numTotalPermutations;
  gt_assert(newList);
  newList->permutations = NULL;
  newList->catCompsPerms = NULL;
  if (!(composition = gt_malloc(sizeof (composition[0]) * alphabetSize)))
    gt_initCompositionListErrRet();
  bitsPerComp = alphabetSize * (bitsPerCount = gt_requiredUIntBits(blockSize));
  newList->bitsPerCount = bitsPerCount;
  numCompositions = newList->numCompositions =
    gt_combinatorics_binomial_simple(blockSize + maxSym, maxSym);
  numTotalPermutations = gt_combinatorics_i_pow(alphabetSize, blockSize);
  newList->compositionIdxBits = gt_requiredUInt64Bits(numCompositions - 1);
  newList->bitsPerSymbol = gt_requiredUIntBits(maxSym);
  bitsPerPerm = newList->bitsPerSymbol * blockSize;
  {
    size_t size = bitElemsAllocSize(numCompositions * bitsPerComp
                                    + numTotalPermutations * bitsPerPerm)
      * sizeof (BitElem);
    if (size == SIZE_MAX)
      gt_initCompositionListErrRet();
    newList->catCompsPerms = gt_malloc(size);
  }
  newList->permutations = gt_calloc(sizeof (struct permList), numCompositions);
  {
    unsigned symRMNZ;
    BitOffset offset = 0, permOffset =
      compListPermStartOffset(newList, alphabetSize);
#ifndef NDEBUG
    size_t permSum = 0;
#endif
    initComposition(maxSym, blockSize, composition, &symRMNZ);
    do
    {
#ifdef EIS_DEBUG
      printComposition(stderr, composition, alphabetSize, blockSize);
#endif /* EIS_DEBUG */
      gt_bsStoreUniformUIntArray(newList->catCompsPerms, offset,
                              bitsPerCount, alphabetSize, composition);
      gt_assert(cmpIdx > 1?(gt_bsCompare(newList->catCompsPerms, offset,
                                      bitsPerComp,
                              newList->catCompsPerms, offset - bitsPerComp,
                              bitsPerComp)>0):1);
      if (initPermutationsList(composition, newList->permutations + cmpIdx,
                               newList->catCompsPerms, permOffset, blockSize,
                               alphabetSize, newList->bitsPerSymbol))
        gt_initCompositionListErrRet();
#if defined(EIS_DEBUG) && !defined(NDEBUG)
      gt_log_log("%lu",
              (unsigned long)newList->permutations[cmpIdx].numPermutations);
#endif
#ifndef NDEBUG
      permSum += newList->permutations[cmpIdx].numPermutations;
#endif
      permOffset += newList->permutations[cmpIdx].numPermutations * bitsPerPerm;
      if (newList->permutations[cmpIdx].numPermutations > maxNumPermutations)
        maxNumPermutations = newList->permutations[cmpIdx].numPermutations;
      if (++cmpIdx < numCompositions)
        ;
      else
        break;
      offset += bitsPerComp;
      nextComposition(composition, maxSym, &symRMNZ);
    } while (1);
    /* verify that the last composition is indeed the lexically maximally */
    gt_assert(composition[0] == blockSize);
#if defined(EIS_DEBUG) && !defined(NDEBUG)
    gt_log_log("permSum=%lu, alphabetSize=%lu, blockSize=%d, "
            "pow(alphabetSize, blockSize)=%f",
            (unsigned long)permSum, (unsigned long)alphabetSize, blockSize,
            gt_power_for_small_exponents(alphabetSize, blockSize));
#endif
    gt_assert(permSum == gt_power_for_small_exponents(alphabetSize, blockSize));
  }
  newList->maxPermIdxBits = gt_requiredUInt64Bits(maxNumPermutations - 1);
  gt_free(composition);
  return 1;
}

void
gt_destructCompositionList(struct compList *clist)
{
  {
    unsigned i;
    for (i = 0; i < clist->numCompositions; ++i)
      destructPermutationsList(clist->permutations + i);
  }
  gt_free(clist->permutations);
  gt_free(clist->catCompsPerms);
}

struct compList *
gt_newCompositionList(unsigned blockSize, unsigned alphabetSize)
{
  struct compList *newList = NULL;
  if (!(newList = gt_calloc(1, sizeof (struct compList))))
    return NULL;
  if (!gt_initCompositionList(newList, blockSize, alphabetSize))
  {
    gt_free(newList);
    return NULL;
  }
  return newList;
}

void
gt_deleteCompositionList(struct compList *clist)
{
  gt_destructCompositionList(clist);
  gt_free(clist);
}

#ifdef EIS_DEBUG
/**
 * Compute number of digits a value would require when displayed in
 * selected number system (i.e. 2=binary, 10=decimal).
 * @param d value to be displayed
 * @param base number of symbols in output alphabet
 * @return number of digits required for output
 */
static inline int
digitPlaces(long d, int base)
{
  int l=1;
  while (d/=base)
    ++l;
  return l;
}

static void
printComposition(FILE *fp, const unsigned *composition,
                 unsigned alphabetSize, unsigned blockSize)
{
  Symbol sym;
  unsigned width = digitPlaces(blockSize, 10);
  for (sym = 0; sym < alphabetSize; ++sym)
  {
    fprintf(fp, "%*d ", width, composition[sym]);
  }
  fputs("\n", fp);
}
#endif /* EIS_DEBUG */

static void
initPermutation(Symbol *permutation, const unsigned *composition,
                unsigned alphabetSize);
static inline void
nextPermutation(Symbol *permutation, unsigned blockSize);

#ifdef EIS_DEBUG
static void
printPermutation(FILE *fp, Symbol *permutation, unsigned blockSize);
#endif /* EIS_DEBUG */

static int
initPermutationsList(const unsigned *composition, struct permList *permutation,
                     BitString permStore, BitOffset permOffset,
                     unsigned blockSize, unsigned alphabetSize,
                     unsigned bitsPerSymbol)
{
  size_t numPermutations = permutation->numPermutations =
    gt_combinatorics_multinomial(blockSize, alphabetSize, composition);
  if (numPermutations > 1)
    permutation->permIdxBits = gt_requiredUInt64Bits(numPermutations - 1);
  else
    permutation->permIdxBits = 0;
  Symbol *currentPermutation;
  BitOffset bitsPerPermutation = bitsPerSymbol * blockSize;
  if (!(currentPermutation = gt_malloc(sizeof (Symbol) * blockSize)))
    return -1;
  permutation->catPermsOffset = permOffset;
  initPermutation(currentPermutation, composition, alphabetSize);
  {
    size_t i = 0;
    BitOffset offset = permOffset;
    do
    {
      gt_bsStoreUniformSymbolArray(permStore, offset,
                                bitsPerSymbol, blockSize, currentPermutation);
#ifdef EIS_DEBUG
      printPermutation(stderr, currentPermutation, blockSize);
#endif /* EIS_DEBUG */
      gt_assert(i > 0?(gt_bsCompare(permStore, offset, bitsPerPermutation,
                              permStore,
                              offset - bitsPerPermutation,
                              bitsPerPermutation)>0):1);
      if (++i < numPermutations)
        ;
      else
        break;
      offset += bitsPerPermutation;
      nextPermutation(currentPermutation, blockSize);
    } while (1);
  }
  gt_free(currentPermutation);
  return 0;
}

static void
destructPermutationsList(GT_UNUSED struct permList *permutation)
{
/*   gt_free(permutation->catPerms); */
}

static void
initPermutation(Symbol *permutation, const unsigned *composition,
                unsigned alphabetSize)
{
  Symbol sym, *p = permutation;
  unsigned j;
  for (sym = 0; sym < alphabetSize; ++sym)
    for (j = 0; j < composition[sym]; ++j)
      *(p++) = sym;
}

static void
nextPermutation(Symbol *permutation, unsigned blockSize)
{
  /*
   * Every permutation represents a leaf in the decision tree
   * generating all permutations, thus given one permutation, we
   * ascend in the tree until we can make a decision resulting in a
   * lexically larger value.
   */
  unsigned upLvl = blockSize - 1;
  {
    Symbol maxSymInSuf = permutation[blockSize - 1];
    do
    {
      if (upLvl == 0 || maxSymInSuf > permutation[--upLvl])
        break;
      if (permutation[upLvl] > maxSymInSuf)
        maxSymInSuf = permutation[upLvl];
    } while (1);
  }
  /* now that we have found the branch point, descend again,
   * selecting first the next largest symbol */
  {
    Symbol saved = permutation[upLvl];
    Symbol swap = permutation[upLvl + 1];
    unsigned swapIdx = upLvl + 1;
    unsigned i;
    for (i = swapIdx + 1; i < blockSize; ++i)
    {
      if (permutation[i] > saved && permutation[i] < swap)
        swap = permutation[i], swapIdx = i;
    }
    permutation[upLvl] = swap;
    permutation[swapIdx] = saved;
  }
  for (++upLvl;upLvl < blockSize - 1; ++upLvl)
  {
    /* find minimal remaining symbol */
    unsigned i, minIdx = upLvl;
    Symbol minSym = permutation[upLvl];
    for (i = upLvl + 1; i < blockSize; ++i)
      if (permutation[i] < minSym)
        minSym = permutation[i], minIdx = i;
    permutation[minIdx] = permutation[upLvl];
    permutation[upLvl] = minSym;
  }
}

#ifdef EIS_DEBUG
static void
printPermutation(FILE *fp, Symbol *permutation, unsigned blockSize)
{
  unsigned i;
  if (blockSize)
    fprintf(fp, "%lu", (unsigned long)permutation[0]);
  for (i = 1; i < blockSize; ++i)
  {
    fprintf(fp, "%lu", (unsigned long)permutation[i]);
  }
  fputs("\n", fp);
}
#endif /* EIS_DEBUG */

int
gt_block2IndexPair(const struct compList *compositionTable,
                unsigned blockSize, unsigned alphabetSize,
                const Symbol *block, PermCompIndex idxOutput[2],
                unsigned *bitsOfPermIdx,
                BitString permCompPA, unsigned *compPA)
{
  unsigned bitsPerCount;
  BitOffset bitsPerComposition, bitsPerPermutation;
  BitString permCompBitString;
  gt_assert(compositionTable && idxOutput && block);
  gt_assert(blockSize > 0);
  bitsPerComposition = (bitsPerCount = compositionTable->bitsPerCount)
    * alphabetSize;
  bitsPerPermutation = compositionTable->bitsPerSymbol * blockSize;
  if (permCompPA)
    permCompBitString = permCompPA;
  else
    permCompBitString =
      gt_malloc(bitElemsAllocSize(bitsPerComposition + bitsPerPermutation)
                * sizeof (BitElem));
  {
    /* first compute composition from block */
    size_t i;
    unsigned *composition;
    if (compPA)
    {
      composition = compPA;
      memset(composition, 0, sizeof (composition[0])*alphabetSize);
    }
    else
      composition = gt_calloc(sizeof (composition[0]), alphabetSize);
    for (i = 0; i < blockSize; ++i)
    {
      ++composition[block[i]];
    }
    gt_bsStoreUniformUIntArray(permCompBitString, 0, bitsPerCount,
                            alphabetSize, composition);
    if (!compPA)
      gt_free(composition);
  }
  {
    /* do binary search for composition (simplified because the list
     * contains every composition possible and thus cmpresult will
     * become 0 at some point) */
    size_t compIndex = compositionTable->numCompositions / 2;
    size_t divStep = compIndex;
    int cmpresult;
    while ((cmpresult = gt_bsCompare(permCompBitString, 0, bitsPerComposition,
                                 compositionTable->catCompsPerms,
                                 compIndex * bitsPerComposition,
                                 bitsPerComposition)))
    {
      if (divStep > 1)
        divStep >>= 1; /* divStep /= 2 */
      if (cmpresult > 0)
        compIndex += divStep;
      else /* cmpresult < 0 */
        compIndex -= divStep;
    }
    idxOutput[0] = compIndex;
  }
  {
    const struct permList *permutation = compositionTable->permutations
      + idxOutput[0];
    if (bitsOfPermIdx)
      *bitsOfPermIdx = permutation->permIdxBits;
    if (permutation->numPermutations > 1)
    {
      /* build permutation bitstring */
      gt_bsStoreUniformSymbolArray(permCompBitString, bitsPerComposition,
                                compositionTable->bitsPerSymbol, blockSize,
                                block);
      /* do binary search for permutation */
      {
        size_t permIndex = permutation->numPermutations / 2;
        size_t divStep = permIndex;
        int cmpresult;
        while ((cmpresult = gt_bsCompare(permCompBitString, bitsPerComposition,
                                     bitsPerPermutation,
                                     compositionTable->catCompsPerms,
                                     permutation->catPermsOffset
                                     + permIndex * bitsPerPermutation,
                                     bitsPerPermutation)))
        {
          if (divStep > 1)
            divStep >>= 1; /* divStep /= 2 */
          if (cmpresult > 0)
            permIndex += divStep;
          else /* cmpresult < 0 */
            permIndex -= divStep;
        }
        idxOutput[1] = permIndex;
      }
    }
    else
        idxOutput[1] = 0;
  }
  if (!permCompPA)
    gt_free(permCompBitString);
  return 0;
}
genometools-1.5.1/src/match/eis-seqblocktranslate.h000066400000000000000000000176021211610345200224050ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SEQBLOCKTRANSLATE_H
#define EIS_SEQBLOCKTRANSLATE_H

/**
 * \file eis-seqblocktranslate.h
 * Translate fixed length substrings (q-words) to a pair of indices: one to
 * designate the composition counts and one to define the actual
 * sequence
 */
#include 
#include 
#include 

#include "match/eis-bitpackseqpos.h"
#include "match/eis-mrangealphabet.h"

/** store indices in this scalar */
typedef uint32_t PermCompIndex;
/** method to retrieve one index from a BitString */
#define gt_bsGetPermCompIndex gt_bsGetUInt32
/** method to store one index in a BitString */
#define gt_bsStorePermCompIndex gt_bsStoreUInt32

/**
 * For permutations common to one composition.
 */
struct permList
{
  size_t numPermutations;       /**< number of permutations this
                                 * composition produces  */
  unsigned permIdxBits;         /**< bits required to store values
                                 * from 0..numPermuations-1  */
  BitOffset catPermsOffset;     /**< offset into the table of all
                                 * permutations at which the
                                 * permutations corresponding to this
                                 * composition are stored */
};

/**
 * Holds the lists of compositions and permutations.
 */
struct compList
{
  size_t numCompositions;       /**< how many ways are there to choose
                                 *   q symbols from the given alphabet */
  struct permList *permutations;/**< reference of list of permutations */
  BitString catCompsPerms;      /**< bitstring with all compositions,
                                 *   followed by all permutations
                                 *   encoded in minimal space
                                 *   concatenated together */
  unsigned bitsPerCount,        /**< bits required to hold one value 0..q */
    bitsPerSymbol,              /**< bits for each symbol */
    compositionIdxBits,         /**< gt_log_2 of numcompositions */
    maxPermIdxBits;             /**< maximum bit length of permutation
                                 *   indices */
};

/**
 * @brief construct object to translate q-words to
 * composition/permutation index tuple
 * @param compList
 * @param blockSize length of q-words to encode
 * @param numSyms size of alphabet
 * @return 0 on error, !0 otherwise
 */
int
gt_initCompositionList(struct compList *compList, unsigned blockSize,
                    unsigned numSyms);
/**
 * Deallocate resources of composition list object, storage struct is not freed.
 * @param clist
 */
void
gt_destructCompositionList(struct compList *clist);

/**
 * @brief create new object to map q-words to composition/permutation
 * index tuples
 * @param blockSize length of q-words to map
 * @param alphabetSize
 * @return NULL on error
 */
struct compList *
gt_newCompositionList(unsigned blockSize, unsigned alphabetSize);

/**
 * Delete composition list object.
 * @param clist
 */
void
gt_deleteCompositionList(struct compList *clist);

/**
 * \brief Transforms a block-sized sequence of symbols to corresponding
 * index-pair representation of block-composition index.
 * @param compositionTable tables to use for lookup
 * @param blockSize length of encoded sequence blocks
 * @param alphabetSize encoded symbols are from range 0..(alphabetSize - 1)
 * @param block symbol sequence holding at least as many symbols as
 * required by seqIdx
 * @param idxOutput on return idxOutput[0] holds the composition
 * index, idxOutput[1] the permutation index.
 * @param bitsOfPermIdx if non-NULL, the number of significant bits
 * for the permutation index is stored here.
 * @param permCompPA if not NULL must point to a memory region of
 * sufficient size to hold the concatenated bistring representations
 * of composition and permutation, composition at offset 0,
 * permutation at offset compositionTable->bitsPerCount * alphabetSize.
 * @param compPA if not NULL must reference a memory region of
 * sufficient size to hold the composition representation as alphabet
 * range sized sequence.
 * @return -1 in case of memory exhaustion, cannot happen if both
 * permCompPA and compPA are valid preallocated memory regions, 0
 * otherwise.
 */
int
gt_block2IndexPair(const struct compList *compositionTable,
                unsigned blockSize, unsigned alphabetSize,
                const Symbol *block, PermCompIndex idxOutput[2],
                unsigned *bitsOfPermIdx,
                BitString permCompPA, unsigned *compPA);

/**
 * @brief Give q-word corresponding to pair of indices.
 * @param compositionTable
 * @param blockSize q-word length (must be same as used on construction)
 * @param compIdx composition index
 * @param permIdx permutation index
 * @param block write sequence of symbols here
 * @param subLen only unpack this many symbols
 */
static inline void
indexPair2block(const struct compList *compositionTable, unsigned blockSize,
                PermCompIndex compIdx, PermCompIndex permIdx,
                Symbol *block, unsigned subLen)
{
  unsigned bitsPerPermutation;
  struct permList *permutationList;
  gt_assert(compositionTable && block);
  gt_assert(subLen <= blockSize);
  bitsPerPermutation = compositionTable->bitsPerSymbol * blockSize;
  permutationList = compositionTable->permutations + compIdx;
  gt_bsGetUniformSymbolArray(
    compositionTable->catCompsPerms,
    permutationList->catPermsOffset + bitsPerPermutation * permIdx,
    compositionTable->bitsPerSymbol, subLen, block);
}

/**
 * @brief Find how often a symbol occurs in a composition given by index
 * @param compositionTable
 * @param alphabetSize
 * @param compIndex composition index
 * @param sym
 * @return number of symbol occurrences
 */
static inline unsigned
symCountFromComposition(struct compList *compositionTable,
                        unsigned alphabetSize,
                        PermCompIndex compIndex, Symbol sym)
{
  BitOffset bitsPerComp, bitsPerCount;
  gt_assert(compositionTable);
  bitsPerCount = compositionTable->bitsPerCount;
  bitsPerComp = bitsPerCount * alphabetSize;
  gt_assert(compIndex < compositionTable->numCompositions);
  return gt_bsGetUInt(compositionTable->catCompsPerms,
                   compIndex * bitsPerComp + sym * bitsPerCount,
                   bitsPerCount);
}

/**
 * @brief Add symbol occurrences for a composition given by index
 * @param compositionTable
 * @param alphabetSize
 * @param compIndex composition index
 * @param counts add occurrence counts to this array
 */
static inline void
addSymCountsFromComposition(struct compList *compositionTable,
                            unsigned alphabetSize,
                            PermCompIndex compIndex, unsigned long *counts)
{
  BitOffset bitsPerComp, bitsPerCount;
  gt_assert(compositionTable);
  bitsPerCount = compositionTable->bitsPerCount;
  bitsPerComp = bitsPerCount * alphabetSize;
  gt_assert(compIndex < compositionTable->numCompositions);
  gt_bsGetUniformUlongArrayAdd(compositionTable->catCompsPerms,
                             compIndex * bitsPerComp, bitsPerCount,
                             alphabetSize,
#ifdef _LP64
                             (uint64_t*) counts);
#else
                             (uint32_t*) counts);
#endif
}

#endif
genometools-1.5.1/src/match/eis-seqdatasrc.h000066400000000000000000000101111211610345200210020ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SEQDATASRC_H
#define EIS_SEQDATASRC_H
/**
 * \file eis-seqdatasrc.h
 * Abstract interface for sequential data sources.
 */
#include 
#include 

#include "core/error.h"
#include "stamp.h"
#include "sfx-suffixgetset.h"

/* sequential data source api */
typedef void *SeqDataSrc;
/**
 * @param len number of elements (objects) to read
 * @return number of elements read (less then len on end-of-file etc.)
 */
typedef size_t (*seqDataReadFunc)(SeqDataSrc src, void *dest, size_t len);

struct seqDataReader
{
  SeqDataSrc src;
  seqDataReadFunc readData;
};

typedef struct seqDataReader SeqDataReader;

static inline int
SDRIsValid(SeqDataReader sr)
{
  return sr.readData != NULL;
}

static inline size_t
SDRRead(SeqDataReader sr, void *dest, size_t len)
{
  return sr.readData(sr.src, dest, len);
}

/* while the above describes a data source, this is a corresponding sink */
typedef void *SeqDataDest;
typedef size_t (*seqDataWriteFunc)(SeqDataDest dest, const void *src,
                                   size_t len);

struct seqDataWriter
{
  seqDataWriteFunc writeData1;
  SeqDataDest dest;
};

typedef struct seqDataWriter SeqDataWriter;

static inline size_t
SDWWrite(SeqDataWriter sw, const void *src, size_t len)
{
  return sw.writeData1(sw.dest, src, len);
}

/* generic data translator api */
union translatorState
{
  void *ref;
  size_t elemSize;
};

typedef union translatorState TranslatorState;
/**
 * @return number of chars! written to dest
 */
typedef size_t (*seqDataTranslateFunc)(void *translator, void *dest,
                                       const unsigned long *src, size_t len);

typedef size_t (*seqDataTranslateSuffixsortspaceFunc)(
                               void *translator,
                               void *dest,
                               const GtSuffixsortspace *suffixsortspace,
                               unsigned long offset,
                               size_t len);

struct seqDataTranslator
{
  TranslatorState state;
  seqDataTranslateFunc translateData;
  seqDataTranslateSuffixsortspaceFunc translateDataSuffixsortspace;
};

typedef struct seqDataTranslator SeqDataTranslator;

static inline size_t
SDRTranslate(SeqDataTranslator xltor, void *dest, const unsigned long *src,
             size_t len)
{
  if (xltor.translateData != NULL)
  {
    return xltor.translateData(xltor.state.ref, dest, src, len);
  }
  /* fall back to zero-translation i.e. verbatim copy */
  memcpy(dest, src, len * xltor.state.elemSize);
  return len * xltor.state.elemSize;
}

static inline size_t
SDRTranslateSuffixsortspace(SeqDataTranslator xltor, void *dest,
                            const GtSuffixsortspace *suffixsortspace,
                            unsigned long offset, size_t len)
{
  if (xltor.translateDataSuffixsortspace != NULL)
  {
    return xltor.translateDataSuffixsortspace(xltor.state.ref, dest,
                                              suffixsortspace,
                                              offset, len);
  }
  /* fall back to zero-translation i.e. verbatim copy */
  {
    size_t idx;
    unsigned long *ulongdest = (unsigned long *) dest;
    for (idx = 0; idx < len; idx++)
    {
      ulongdest[idx] = gt_suffixsortspace_getdirect(suffixsortspace,offset+idx);
    }
  }
  /*memcpy(dest, src, len * xltor.state.elemSize); */
  return len * xltor.state.elemSize;
}

#endif
genometools-1.5.1/src/match/eis-seqranges-priv.h000066400000000000000000000042611211610345200216270ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SEQRANGES_PRIV_H
#define EIS_SEQRANGES_PRIV_H

#include "match/eis-bitpackseqpos.h"
#include "match/eis-seqranges.h"

typedef uint16_t regionLength;

struct seqRange
{
  unsigned long startPos;
  BitElem symLenStr[sizeof (unsigned long) / sizeof (BitElem)];
  /**< holds the bits required for the symbol stored and the length
   * of the range */
};

enum {
  symLenStrBits = sizeof (unsigned long) / sizeof (BitElem) * bitElemBits,
};

struct seqRangeList
{
  size_t numRangesStorable, numRanges;
  struct seqRange *ranges;
  unsigned long *partialSymSums;
  const MRAEnc *alphabet;
  unsigned symBits;
  unsigned long maxRangeLen;
};

static inline unsigned long
seqRangeLen(const struct seqRange *p, unsigned symBits)
{
  return gt_bsGetUlong(p->symLenStr, symBits, symLenStrBits - symBits);
}

static inline Symbol
seqRangeSym(const struct seqRange *p, unsigned symBits)
{
  return gt_bsGetSymbol(p->symLenStr, 0, symBits);
}

static inline void
seqRangeSetLen(struct seqRange *p, unsigned long len, unsigned symBits)
{
  return gt_bsStoreUlong(p->symLenStr, symBits, symLenStrBits - symBits, len);
}

static inline void
seqRangeSetSym(struct seqRange *p, Symbol sym, unsigned symBits)
{
  return gt_bsStoreSymbol(p->symLenStr, 0, symBits, sym);
}

static inline int
posIsInSeqRange(struct seqRange *p, unsigned long pos, unsigned symBits)
{
  return (pos >= p->startPos && pos < p->startPos + seqRangeLen(p, symBits));
}

#endif
genometools-1.5.1/src/match/eis-seqranges.c000066400000000000000000000564421211610345200206540ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/bsearch.h"
#include "core/error.h"
#include "core/ma_api.h"
#include "core/minmax.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"

#include "match/eis-seqranges.h"
#include "match/eis-seqranges-priv.h"

struct seqRangeList *
gt_newSeqRangeList(size_t rangesStartNum, const MRAEnc *alphabet,
                enum SRLFeatures features)
{
  struct seqRangeList *newList;
  newList = gt_malloc(sizeof (struct seqRangeList));
  newList->numRanges = 0;
  newList->numRangesStorable = rangesStartNum;
  newList->ranges = gt_malloc(sizeof (newList->ranges[0]) * rangesStartNum);
  if (features & SRL_PARTIAL_SYMBOL_SUMS)
    newList->partialSymSums = gt_malloc(sizeof (unsigned long)
                                        * gt_MRAEncGetSize(alphabet)
                                        * rangesStartNum);
  else
    newList->partialSymSums = NULL;
  newList->alphabet = alphabet;
  newList->symBits = requiredSymbolBits(gt_MRAEncGetSize(alphabet) - 1);
  if (newList->symBits)
    newList->maxRangeLen =
      (((unsigned long)1) << (symLenStrBits - newList->symBits)) - 1;
  else
    newList->maxRangeLen = ~(unsigned long)0;
  return newList;
}

void
gt_SRLCompact(struct seqRangeList *rangeList)
{
  gt_assert(rangeList);
  rangeList->ranges = gt_realloc(rangeList->ranges,
                                 sizeof (rangeList->ranges[0])
                                 * rangeList->numRanges);
  if (rangeList->partialSymSums)
    rangeList->partialSymSums =
      gt_realloc(rangeList->partialSymSums, sizeof (unsigned long)
                 * gt_MRAEncGetSize(rangeList->alphabet)
                 * rangeList->numRanges);
  rangeList->numRangesStorable = rangeList->numRanges;
}

void
gt_deleteSeqRangeList(struct seqRangeList *rangeList)
{
  gt_assert(rangeList);
  if (rangeList->ranges)
    gt_free(rangeList->ranges);
  if (rangeList->partialSymSums)
    gt_free(rangeList->partialSymSums);
  gt_free(rangeList);
}

void
gt_SRLAppendNewRange(struct seqRangeList *rangeList,
                  unsigned long pos,
                  unsigned long len,
                  Symbol esym)
{
  gt_assert(rangeList);
  if (len)
  {
    Symbol sym = MRAEncMapSymbol(rangeList->alphabet, esym);
    struct seqRange *p;
    unsigned long *pSums;
    size_t numRanges = rangeList->numRanges,
      numSyms = gt_MRAEncGetSize(rangeList->alphabet),
      numNewRanges = len/rangeList->maxRangeLen
      + ((len%rangeList->maxRangeLen)?1:0);
    unsigned symBits = rangeList->symBits;
    if (numRanges + numNewRanges > rangeList->numRangesStorable)
    {
      size_t newSize = numRanges + 2 * numNewRanges;
      rangeList->ranges = gt_realloc(rangeList->ranges,
                                     sizeof (struct seqRange) * newSize);
      if (rangeList->partialSymSums)
        rangeList->partialSymSums =
          gt_realloc(rangeList->partialSymSums, sizeof (unsigned long)
                     * numSyms * newSize);
      rangeList->numRangesStorable = newSize;
    }
    p = rangeList->ranges + numRanges;
    if (rangeList->partialSymSums)
      pSums = rangeList->partialSymSums + numSyms * numRanges;
    else
      pSums = NULL;
    while (len > rangeList->maxRangeLen)
    {
      p->startPos = pos;
      seqRangeSetSym(p, sym, symBits);
      seqRangeSetLen(p, rangeList->maxRangeLen, symBits);
      pos += rangeList->maxRangeLen;
      len -= rangeList->maxRangeLen;
      if (numRanges && pSums)
      {
        unsigned long *spDest = pSums, *spSrc = pSums - numSyms;
        size_t i;
        for (i = 0; i < numSyms; ++i)
        {
          *spDest++ = *spSrc++;
        }
        pSums[seqRangeSym(p - 1, symBits)] += seqRangeLen(p - 1, symBits);
        pSums += numSyms;
      }
      else if (pSums)
      {
        memset(pSums, 0, sizeof (unsigned long) * numSyms);
        pSums += numSyms;
      }
      ++p;
      ++numRanges;
    }
    if (len)
    {
      p->startPos = pos;
      seqRangeSetSym(p, sym, symBits);
      seqRangeSetLen(p, len, symBits);
      if (numRanges && pSums)
      {
        unsigned long *spDest = pSums, *spSrc = pSums - numSyms;
        size_t i;
        for (i = 0; i < numSyms; ++i)
        {
          *spDest++ = *spSrc++;
        }
        pSums[seqRangeSym(p - 1, symBits)] += seqRangeLen(p - 1, symBits);
        pSums += numSyms;
      }
      else if (pSums)
      {
        memset(pSums, 0, sizeof (unsigned long) * numSyms);
        pSums += numSyms;
      }
      ++numRanges;
    }
    gt_assert(numRanges == rangeList->numRanges + numNewRanges);
    rangeList->numRanges = numRanges;
  }
}

void
gt_SRLinsertNewRange(GT_UNUSED struct seqRangeList *rangeList,
                  GT_UNUSED unsigned long pos, GT_UNUSED unsigned long len,
                  GT_UNUSED Symbol esym)
{
  gt_assert(rangeList);
  abort();
/*   { */
/*     Symbol sym = MRAEncMapSymbol(rangeList->alphabet, esym); */
/*   } */
  /* currently not implemented because only append is currently
   * needed */
}

void
gt_SRLAddPosition(struct seqRangeList *rangeList, unsigned long pos,
                  Symbol esym)
{
  size_t numRanges;
  struct seqRange *lastRange;
  unsigned long lastRangeLen;
  unsigned symBits;
  Symbol sym;
  gt_assert(rangeList);
  sym = MRAEncMapSymbol(rangeList->alphabet, esym);
  numRanges = rangeList->numRanges;
  lastRange = rangeList->ranges + numRanges - 1;
  symBits = rangeList->symBits;
  if (numRanges)
    lastRangeLen = seqRangeLen(lastRange, symBits);

  if (numRanges && lastRange->startPos + lastRangeLen > pos)
  {
    /* TODO: search for range */
    gt_SRLinsertNewRange(rangeList, pos, 1, esym);
  }
  else if (numRanges
           && (seqRangeSym(lastRange, symBits) == sym)
           && (lastRange->startPos + lastRangeLen == pos)
           && (lastRangeLen < rangeList->maxRangeLen))
    seqRangeSetLen(lastRange, ++lastRangeLen, symBits);
  else
    gt_SRLAppendNewRange(rangeList, pos, 1, esym);
}

void
gt_SRLInitListSearchHint(struct seqRangeList *rangeList,
                      seqRangeListSearchHint *hint)
{
  gt_assert(rangeList && hint);
  *hint = rangeList->numRanges / 2;
}

static int
posSeqRangeOverlapCompare(const void *key, const void *elem, void *data)
{
  unsigned long pos;
  const struct seqRange *range;
  const struct seqRangeList *rangeList;
  pos = *(const unsigned long *)key;
  range = elem;
  rangeList = data;
  if (pos < range->startPos)
    return -1;
  else if (pos >= range->startPos + seqRangeLen(range, rangeList->symBits))
    return 1;
  else
    return 0;
}

int
gt_SRLOverlapsPosition(struct seqRangeList *rangeList, unsigned long pos,
                    seqRangeListSearchHint *hint, Symbol *symAtPos)
{
  size_t rangeIdx;
  struct seqRange *p;
  gt_assert(rangeList);
  if (hint)
    rangeIdx = *hint;
  else
    rangeIdx = rangeList->numRanges / 2;
  p = rangeList->ranges + rangeIdx;
  if (posIsInSeqRange(p, pos, rangeList->symBits))
  {
    if (symAtPos)
      *symAtPos = MRAEncRevMapSymbol(rangeList->alphabet,
                                     seqRangeSym(p, rangeList->symBits));
    return 1;
  }
  /* TODO: implement "else if" case to also look at next range */
  else
  {
    unsigned long searchPos = pos;
    struct seqRange *searchRes =
      gt_bsearch_data(&searchPos, rangeList->ranges, rangeList->numRanges,
                   sizeof (struct seqRange), posSeqRangeOverlapCompare,
                   rangeList);
    if (searchRes)
    {
      if (symAtPos)
        *symAtPos = seqRangeSym(searchRes, rangeList->symBits);
      if (hint)
        *hint = searchRes - rangeList->ranges;
      return 1;
    }
    else
      return 0;
  }
}

static int
posSeqRangeNextCompare(const void *key, const void *elem, void *data)
{
  unsigned long pos;
  const struct seqRange *range;
  const struct seqRangeList *rangeList;
  pos = *(const unsigned long *)key;
  range = elem;
  rangeList = data;
  if (pos < range->startPos)
    if (pos < range[-1].startPos + seqRangeLen(range - 1, rangeList->symBits))
      return -1;
    else
      return 0;
  else if (pos >= range->startPos + seqRangeLen(range, rangeList->symBits))
    return 1;
  else /* pos < range->startPos + range->len  && pos >= range->startPos */
    return 0;
}

#define rangeNextMatch(idx)                                  \
  ((ranges[idx].startPos >= pos                              \
    || ranges[idx].startPos + seqRangeLen(ranges + idx, symBits) > pos) \
   && ranges[idx - 1].startPos + seqRangeLen(ranges + idx - 1, symBits) <= pos)

/**
 * \brief Given a position and an optional search hint, find the next
 * range either overlapping or ahead of the position.
 * @param rangeList list of ranges to be searched
 * @param pos position to search range for
 * @param hint pointer to position of possibly near range
 * @return pointer to sequence range or NULL if no corresponding range
 * was found
 */
struct seqRange *
gt_SRLFindPositionNext(struct seqRangeList *rangeList, unsigned long pos,
                    seqRangeListSearchHint *hint)
{
  /* no ranges no matches in ranges */
  seqRangeListSearchHint hintCopy;
  size_t numRanges;
  struct seqRange *ranges;
  unsigned symBits;
  gt_assert(rangeList);
  ranges = rangeList->ranges;
  symBits = rangeList->symBits;
  if (hint)
    hintCopy = *hint;
  else
    gt_SRLInitListSearchHint(rangeList, &hintCopy);
  if ((numRanges = rangeList->numRanges) == 0)
  {
    return NULL;
  }
  if (ranges[0].startPos >= pos
      || pos < ranges[0].startPos + seqRangeLen(ranges + 0, symBits))
  {
    return ranges + 0;
  }
  else if (hintCopy && rangeNextMatch(hintCopy))
  {
    return ranges + hintCopy;
  }
  else if ((numRanges > hintCopy + 1) && rangeNextMatch(hintCopy + 1))
  {
    ++hintCopy;
    if (hint)
      *hint = hintCopy;
    return rangeList->ranges + hintCopy;
  }
  else if (hintCopy && rangeNextMatch(hintCopy - 1))
  {
    --hintCopy;
    if (hint)
      *hint = hintCopy;
    return rangeList->ranges + hintCopy;
  }
  else if (numRanges > 2)
  {
    unsigned long searchPos = pos;
    struct seqRange *searchRes =
      gt_bsearch_data(&searchPos, rangeList->ranges + 1,
                      rangeList->numRanges - 1, sizeof (struct seqRange),
                      posSeqRangeNextCompare, rangeList);
    if (searchRes && hint)
      *hint = searchRes - rangeList->ranges;
    return searchRes;
  }
  else /* numRanges <= 2 */
    return NULL;
}

static int
posSeqRangeLastCompare(const void *key, const void *elem)
{
  unsigned long pos;
  struct seqRange *range;
  pos = *(unsigned long *)key;
  range = (struct seqRange *)elem;
  if (pos >= range->startPos)
    if (pos < range[1].startPos)
      return 0;
    else
      return 1;
  else
    return -1;
}

#define rangeLastMatch(idx)                                             \
  (ranges[idx].startPos <= pos && ranges[idx + 1].startPos > pos)

/**
 * \brief Given a position and an optional search hint, find the next
 * range either overlapping or ahead of the position.
 * @param rangeList list of ranges to be searched
 * @param pos position to search range for
 * @param hint pointer to position of possibly near range
 * @return pointer to sequence range or NULL if no corresponding range
 * was found
 */
struct seqRange *
gt_SRLFindPositionLast(struct seqRangeList *rangeList, unsigned long pos,
                    seqRangeListSearchHint *hint)
{
  /* no ranges no matches in ranges */
  seqRangeListSearchHint hintCopy;
  size_t numRanges;
  struct seqRange *ranges;
  GT_UNUSED unsigned symBits;
  gt_assert(rangeList);
  ranges = rangeList->ranges;
  symBits = rangeList->symBits;
  if (hint)
    hintCopy = *hint;
  else
    gt_SRLInitListSearchHint(rangeList, &hintCopy);
  if ((numRanges = rangeList->numRanges) == 0)
  {
    return NULL;
  }
  if (ranges[0].startPos > pos)
    return NULL;
  else if (ranges[numRanges - 1].startPos <= pos)
  {
    return ranges + numRanges - 1;
  }
  else if ((hintCopy < numRanges - 1) && rangeLastMatch(hintCopy))
  {
    return ranges + hintCopy;
  }
  else if ((hintCopy < numRanges - 2) && rangeLastMatch(hintCopy + 1))
  {
    ++hintCopy;
    if (hint)
      *hint = hintCopy;
    return ranges + hintCopy;
  }
  else if (hintCopy && rangeLastMatch(hintCopy - 1))
  {
    --hintCopy;
    if (hint)
      *hint = hintCopy;
    return ranges + hintCopy;
  }
  else if (numRanges > 2)
  {
    unsigned long searchPos = pos;
    struct seqRange *searchRes =
      bsearch(&searchPos, ranges, rangeList->numRanges - 1,
              sizeof (struct seqRange), posSeqRangeLastCompare);
    if (searchRes && hint)
      *hint = searchRes - ranges;
    return searchRes;
  }
  else /* numRanges <= 2 */
    return NULL;
}

/**
 * @return 0 on error, >0 on success
 */
/* FIXME: convert to platform-independent variant */
int
gt_SRLSaveToStream(struct seqRangeList *rangeList, FILE *fp)
{
  size_t numRanges;
  gt_assert(rangeList && fp);
  numRanges = rangeList->numRanges;
  gt_xfwrite(&(rangeList->numRanges), sizeof (rangeList->numRanges), 1, fp);
  gt_xfwrite(rangeList->ranges, sizeof (struct seqRange), numRanges, fp);
  return 1;
}

/* FIXME: convert to platform-independent variant */
struct seqRangeList *
gt_SRLReadFromStream(FILE *fp, const MRAEnc *alphabet,
                  enum SRLFeatures features, GT_UNUSED GtError *err)
{
  struct seqRangeList *newRangeList;
  size_t numRanges;
  gt_assert(fp && err);
  newRangeList = gt_malloc(sizeof (struct seqRangeList));
  newRangeList->alphabet = alphabet;
  newRangeList->symBits = requiredSymbolBits(gt_MRAEncGetSize(alphabet) - 1);
  if (newRangeList->symBits)
    newRangeList->maxRangeLen =
      (((unsigned long)1) << (symLenStrBits - newRangeList->symBits)) - 1;
  else
    newRangeList->maxRangeLen = ~(unsigned long)0;
  gt_xfread(&(newRangeList->numRanges), sizeof (newRangeList->numRanges), 1,
            fp);
  numRanges = newRangeList->numRanges;
  newRangeList->partialSymSums = NULL;
  newRangeList->ranges = gt_malloc(sizeof (struct seqRange) *
                                   (newRangeList->numRangesStorable
                                   = numRanges));
  gt_xfread(newRangeList->ranges, sizeof (struct seqRange), numRanges, fp);
  if (features & SRL_PARTIAL_SYMBOL_SUMS)
  {
    unsigned long *partialSymSums;
    size_t numSyms = gt_MRAEncGetSize(alphabet), i;
    newRangeList->partialSymSums = partialSymSums =
     gt_malloc(sizeof (unsigned long) * gt_MRAEncGetSize(alphabet) * numRanges);
    memset(partialSymSums, 0, sizeof (unsigned long) * numSyms);
    for (i = 1; i < numRanges; ++i)
    {
      struct seqRange *lastRange = newRangeList->ranges + i - 1;
      Symbol lastSym = seqRangeSym(lastRange, newRangeList->symBits);
      memcpy(partialSymSums + i * numSyms, partialSymSums + (i - 1) * numSyms,
             sizeof (unsigned long) * numSyms);
      partialSymSums[i * numSyms + lastSym] +=
        seqRangeLen(lastRange, newRangeList->symBits);
    }
  }
  return newRangeList;
}

/**
 * @param occStore must be pre-initialized (either to some previous
 * count or zero) table of count for every symbol in alphabet,
 * i.e. indexing like occStore[sym] for every value of sym stored in
 * rangeList must be a valid memory reference.
 */
void
gt_SRLSymbolsInSeqRegion(struct seqRangeList *rangeList, unsigned long start,
                      unsigned long end, unsigned long *occStore,
                      seqRangeListSearchHint *hint)
{
  struct seqRange *p;
  /* find range next to start position */
  /* first solve special case where pos precedes very first list
   * entry, because we want to be able to look at the preceding range
   * in binary search */
  /* no ranges => no symbols in ranges */
  if (rangeList->numRanges == 0)
    return;
  p = gt_SRLFindPositionNext(rangeList, start, hint);
  /* no range overlapping or between start and end of sequence? */
  if (!p)
    return;
  /* iterate over ranges left */
  {
    unsigned long s = MAX(start, p->startPos);
    struct seqRange *maxRange = rangeList->ranges + rangeList->numRanges - 1;
    while (s <= end)
    {
      unsigned long overlap = MIN(p->startPos + seqRangeLen(p,
                                                            rangeList->symBits),
                                  end + 1) - s;
      occStore[MRAEncRevMapSymbol(rangeList->alphabet,
                                  seqRangeSym(p, rangeList->symBits))]
               += overlap;
      if (p == maxRange)
        break;
      s = (++p)->startPos;
    }
  }
}

unsigned long
gt_SRLSymbolCountInSeqRegion(struct seqRangeList *rangeList,
                          unsigned long start,
                          unsigned long end,
                          Symbol esym,
                          seqRangeListSearchHint *hint)
{
  const struct seqRange *p;
  if (rangeList->numRanges == 0)
    return 0;
  p = gt_SRLFindPositionNext(rangeList, start, NULL);
  if (p)
  {
    if (rangeList->partialSymSums)
    {
      const struct seqRange *q = gt_SRLFindPositionLast(rangeList, end, hint);
      if (!q)
      {
        /* in case
         * - end precedes first region
         * or
         * - start is after last region
         * no symbols can be encoded in range
         */
        return 0;
      }
      {
        size_t pOff = p - rangeList->ranges, qOff = q - rangeList->ranges;
        size_t numSyms = gt_MRAEncGetSize(rangeList->alphabet);
        unsigned long symCount;
        Symbol sym = MRAEncMapSymbol(rangeList->alphabet, esym);
        unsigned symBits = rangeList->symBits;
        symCount = rangeList->partialSymSums[qOff * numSyms + sym]
          - rangeList->partialSymSums[pOff * numSyms + sym];
        /* two special cases: start might be inside p and end inside q */
        if (sym == seqRangeSym(p, symBits) && start >= p->startPos)
          symCount -= start - p->startPos;
        if (sym == seqRangeSym(q, symBits))
        {
          regionLength lastOverlap = MIN(end - q->startPos,
                                         seqRangeLen(q, symBits));
          symCount += lastOverlap;
        }
        return symCount;
      }
    }
    else
    {
      unsigned long symCount = 0;
      unsigned long s = MAX(start, p->startPos);
      Symbol sym = MRAEncMapSymbol(rangeList->alphabet, esym);
      unsigned symBits = rangeList->symBits;
      struct seqRange *maxRange = rangeList->ranges + rangeList->numRanges - 1;
      while (s < end)
      {
        if (seqRangeSym(p, symBits) == sym)
          symCount += MIN(p->startPos + seqRangeLen(p, symBits), end) - s;
        if (p == maxRange)
          break;
        s = (++p)->startPos;
      }
      return symCount;
    }
  }
  else
    return 0;
}

unsigned long
gt_SRLAllSymbolsCountInSeqRegion(struct seqRangeList *rangeList,
                              unsigned long start,
                              unsigned long end,
                              seqRangeListSearchHint *hint)
{
  const struct seqRange *p;
  if (rangeList->numRanges == 0)
    return 0;
  p = gt_SRLFindPositionNext(rangeList, start, hint);
  if (p)
  {
    if (rangeList->partialSymSums)
    {
      const struct seqRange *q = gt_SRLFindPositionLast(rangeList, end, hint);
      if (!q)
      {
        /* in case
         * - end precedes first region
         * or
         * - start is after last region
         * no symbols can be encoded in range
         */
        return 0;
      }
      {
        size_t pOff = p - rangeList->ranges, qOff = q - rangeList->ranges;
        size_t numSyms = gt_MRAEncGetSize(rangeList->alphabet);
        unsigned long symCount = 0;
        Symbol sym;
        unsigned symBits = rangeList->symBits;
        for (sym = 0; sym < numSyms; ++sym)
        {
          symCount += rangeList->partialSymSums[qOff * numSyms + sym]
            - rangeList->partialSymSums[pOff * numSyms + sym];
          /* two special cases: start might be inside p and end inside q */
        }
        if (start >= p->startPos)
          symCount -= start - p->startPos;

        {
          regionLength lastOverlap = MIN(end - q->startPos,
                                         seqRangeLen(q, symBits));
          symCount += lastOverlap;
        }
        return symCount;
      }
    }
    else
    {
      unsigned long symCount = 0;
      unsigned long s = MAX(start, p->startPos);
      struct seqRange *maxRange = rangeList->ranges + rangeList->numRanges - 1;
      unsigned symBits = rangeList->symBits;
      while (s < end)
      {
        symCount += MIN(p->startPos + seqRangeLen(p, symBits), end) - s;
        if (p == maxRange)
          break;
        s = (++p)->startPos;
      }
      return symCount;
    }
  }
  else
    return 0;
}

void
gt_SRLApplyRangesToSubString(struct seqRangeList *rangeList,
                          Symbol *subString,
                          unsigned long start,
                          unsigned long len,
                          unsigned long subStringOffset,
                          seqRangeListSearchHint *hint)
{
  struct seqRange *nextRange;
  unsigned long inSeqPos = start;
  unsigned symBits = rangeList->symBits;
  gt_assert(rangeList);
  nextRange = gt_SRLFindPositionNext(rangeList, inSeqPos, hint);
  do {
    if (inSeqPos < nextRange->startPos)
    {
      inSeqPos = nextRange->startPos;
    }
    else
    {
      size_t i;
      unsigned maxSubstPos =
        MIN(nextRange->startPos + seqRangeLen(nextRange, symBits),
            start + len) - subStringOffset;
      Symbol sym = MRAEncRevMapSymbol(rangeList->alphabet,
                                      seqRangeSym(nextRange, symBits));
      for (i = inSeqPos - subStringOffset; i < maxSubstPos; ++i)
        subString[i] = sym;
      inSeqPos = subStringOffset + maxSubstPos;
      ++nextRange;
    }
  } while (inSeqPos < start + len);
}

int
gt_SRLPrintRangesInfo(struct seqRangeList *rangeList,
                   FILE *fp,
                   unsigned long start,
                   unsigned long len,
                   seqRangeListSearchHint *hint)
{
  struct seqRange *nextRange;
  unsigned long end = start + len;
  unsigned symBits = rangeList->symBits;
  int result = 0;
  gt_assert(rangeList);
  nextRange = gt_SRLFindPositionNext(rangeList, start, hint);
  while (nextRange->startPos < end)
  {
    if (rangeList->partialSymSums)
    {
      size_t numSyms = gt_MRAEncGetSize(rangeList->alphabet);
      size_t pOff = nextRange - rangeList->ranges;
      Symbol sym;
      fputs("# range partial sums:", fp);
      for (sym = 0; sym < numSyms; ++sym)
        fprintf(fp, " sum[%u]=%lu",
                MRAEncRevMapSymbol(rangeList->alphabet, sym),
                rangeList->partialSymSums[pOff * numSyms + sym]);
      fputs("\n", fp);
    }
    if (result +=
        fprintf(fp, "# range overlap: symbol %u, start=%lu, length=%lu\n",
                MRAEncRevMapSymbol(rangeList->alphabet,
                                   seqRangeSym(nextRange, symBits)),
                nextRange->startPos, seqRangeLen(nextRange, symBits)) < 0)
    {
      result = -1;
      break;
    }
    ++nextRange;
  }
  return result;
}
genometools-1.5.1/src/match/eis-seqranges.h000066400000000000000000000164121211610345200206520ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SEQRANGES_H
#define EIS_SEQRANGES_H

/**
 * @file eis-seqranges.h
 * @brief Store lists of ranges of symbols.
 *
 * This is intended to reduce the storage overhead introduced by the
 * presence of a special class of symbols in a sequence. These symbols
 * are generally expected to:
 * - be underrepresented in the sequence
 * - often form contiguous ranges
 * - require special treatment by algorithms
 */
#include 

#include "core/error.h"
#include "core/bitpackstring.h"

#include "match/eis-mrangealphabet.h"

/**
 * Select wether certain internal data structures are constructed with
 * these flags.
 */
enum SRLFeatures {
  SRL_NO_FEATURES = 0,              /**< build no special structures */
  SRL_PARTIAL_SYMBOL_SUMS = 1 << 0, /**< for every range also keep
                                     * sums of other special symbols
                                     * encountered up to the
                                     * beginning of the range */
};

/**
 * Used to remember previous queries.
 */
typedef size_t seqRangeListSearchHint;

/**
 * @brief Constructor for list of sequence ranges.
 * @param rangesStartNum allocate space for this many ranges
 * @param alphabet map stored symbols according to this alphabet
 * @param features see enum SRLFeatures for a description
 * @return newly constructed list
 */
struct seqRangeList *
gt_newSeqRangeList(size_t rangesStartNum, const MRAEnc *alphabet,
                enum SRLFeatures features);
/**
 * @brief Shrink the list according to the exact number of ranges stored.
 * @param rangeList
 */
void
gt_SRLCompact(struct seqRangeList *rangeList);

/**
 * @brief Destructor for sequence range lists.
 * @param rangeList
 */
void
gt_deleteSeqRangeList(struct seqRangeList *rangeList);

/**
 * @brief Add a new range at the end of the current list.
 * @param rangeList
 * @param pos start of new range
 * @param len length of new range
 * @param sym the range is a contiguous sequence of this symbol
 */
void
gt_SRLAppendNewRange(struct seqRangeList *rangeList,
                  unsigned long pos,
                  unsigned long len,
                  Symbol sym);

/**
 * @brief Add a new range of length one
 * @param rangeList
 * @param pos at this position
 * @param sym this symbol occurs
 */
void
gt_SRLAddPosition(struct seqRangeList *rangeList, unsigned long pos,
               Symbol sym);

/**
 * @brief Initialize a search hint by this function.
 * @param rangeList
 * @param hint points to storage
 */
void
gt_SRLInitListSearchHint(struct seqRangeList *rangeList,
                      seqRangeListSearchHint *hint);

/**
 * @brief Find the range overlapping or if no such range exists
 * follows pos.
 * @param rangeList
 * @param pos
 * @param hint
 * @return NULL if no range overlaps or succeeds pos
 */
struct seqRange *
gt_SRLFindPositionNext(struct seqRangeList *rangeList, unsigned long pos,
                    seqRangeListSearchHint *hint);

/**
 * @brief This predicate is true if position is within one of the
 * ranges of the range list.
 * @param rangeList
 * @param pos
 * @param hint
 * @param symAtPos if not NULL, the symbol of the range overlapping
 * pos is written to this address, if such a range exists
 * @return true if an overlap exits, false if not
 */
int
gt_SRLOverlapsPosition(struct seqRangeList *rangeList, unsigned long pos,
                    seqRangeListSearchHint *hint, Symbol *symAtPos);

/**
 * @brief For the sequence region [start..end-1] count the number of
 * occurrences for each symbol represented in the overlapping ranges.
 * @param rangeList
 * @param start
 * @param end
 * @param occStore for each symbol occStore[MRAEncMapSymbol(alphabet,
 * sym)] is set to the number of occurrences of sym, where alphabet is
 * the alphabet originally used in the constructor
 * @param hint
 */
void
gt_SRLSymbolsInSeqRegion(struct seqRangeList *rangeList, unsigned long start,
                      unsigned long end, unsigned long *occStore,
                      seqRangeListSearchHint *hint);

/**
 * @brief Compute the occurrence count for one symbol in a given region.
 * @param rangeList
 * @param start
 * @param end
 * @param sym only account for ranges matching this symbol
 * @param hint
 */
unsigned long
gt_SRLSymbolCountInSeqRegion(struct seqRangeList *rangeList,
                          unsigned long start,
                          unsigned long end,
                          Symbol sym,
                          seqRangeListSearchHint *hint);

/**
 * @brief Sum over the occurrence counts for all symbols in a given region.
 * @param rangeList
 * @param start
 * @param end
 * @param hint
 */
unsigned long
gt_SRLAllSymbolsCountInSeqRegion(struct seqRangeList *rangeList,
                              unsigned long start,
                              unsigned long end,
                              seqRangeListSearchHint *hint);

/**
 * @brief Overwrite all positions in a string that coincide with
 * ranges in the list with the symbol for that range.
 *
 * @param rangeList
 * @param subString write symbols in ranges at subStringOffset+i to subString[i]
 * @param start start only use ranges overlapping [start..end-1]
 * @param len
 * @param subStringOffset offset of subString relative to the
 * underlying sequence
 * @param hint
 */
void
gt_SRLApplyRangesToSubString(struct seqRangeList *rangeList,
                          Symbol *subString,
                          unsigned long start,
                          unsigned long len,
                          unsigned long subStringOffset,
                          seqRangeListSearchHint *hint);

/**
 * @brief Print text description of ranges overlapping the given
 * region.
 *
 * @param rangeList
 * @param fp print description to this file
 * @param start
 * @param len
 * @param hint
 * @return <0 in case of I/O error, >=0 otherwise.
 */
int
gt_SRLPrintRangesInfo(struct seqRangeList *rangeList,
                   FILE *fp,
                   unsigned long start,
                   unsigned long len,
                   seqRangeListSearchHint *hint);
/**
 * @brief Save a range list structure to file.
 * @param rangeList
 * @param fp file to save rangeList to
 * @return <0 if an error occurred
 */
int
gt_SRLSaveToStream(struct seqRangeList *rangeList, FILE *fp);

/**
 * @brief Restore a sequence range list from file.
 * @param fp read from this file
 * @param alphabet symbols are interpreted under this alphabet
 * @param features see enum SRLFeatures
 * @param err
 */
struct seqRangeList *
gt_SRLReadFromStream(FILE *fp, const MRAEnc *alphabet,
                  enum SRLFeatures features, GtError *err);

#endif
genometools-1.5.1/src/match/eis-sequencemultiread.c000066400000000000000000000271411211610345200223750ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 

#include "core/ma_api.h"
#include "core/unused_api.h"
#include "match/eis-sequencemultiread.h"
#include "match/sarr-def.h"
#include "match/eis-list-do.h"

struct seqReaderState
{
  struct seqReaderState *next;
  unsigned long nextReadPos;           /**< next position to be read/consumed */
  int tag;                      /**< set of bits defined by
                                 * application, can be used for value
                                 * or as bit set */
  SeqReaderSet *readerSet;
  consumerID id;
  void *dest;
  SeqDataTranslator xltor;
};

struct seqSinkState
{
  int tag;                      /**< set of bits defined by
                                 * application, can be used for value
                                 * or as bit set */
  consumerID id;
  SeqDataWriter writer;
};

static inline unsigned long
seqReaderSetGetConsumerNextPos(struct seqReaderState *consumer)
{
  gt_assert(consumer);
  return consumer->nextReadPos;
}

static inline void
seqReaderSetSetConsumerNextPos(struct seqReaderState *consumer,
                               unsigned long newPos)
{
  gt_assert(consumer && consumer->nextReadPos <= newPos);
  consumer->nextReadPos = newPos;
}

static void
seqReaderSetMove2Backlog(void *backlogState, const void *seqData,
                         unsigned long requestStart, size_t requestLen);

static size_t
seqReaderSetRead(void *state, void *dest, size_t len);

/*
int
gt_initSeqReaderSet(SeqReaderSet *readerSet, int initialSuperSet,
                 int numConsumers, int *tags, SeqDataTranslator xltors[],
                 SeqDataReader *generatedReaders, size_t seqElemSize,
                 generatorFunc generator, void *generatorState)
{
  int i;
  gt_initEmptySeqReaderSet(readerSet, initialSuperSet, seqElemSize,
                        generator, generatorState);
  for (i = 0; i < numConsumers; ++i)
  {
    generatedReaders[i]
      = gt_seqReaderSetRegisterConsumer(readerSet, tags[i], xltors[i]);
    if (!generatedReaders[i].readData)
      break;
  }
  return i;
}
*/

void
gt_initEmptySeqReaderSet(SeqReaderSet *readerSet, int initialSuperSet,
                         bool fromSuffixsortspace,
                         size_t seqElemSize, generatorFunc generator,
                         void *generatorState)
{
  readerSet->fromSuffixsortspace = fromSuffixsortspace;
  readerSet->tagSuperSet = initialSuperSet;
  readerSet->numAutoConsumers = readerSet->numConsumers = 0;
  readerSet->consumerList = NULL;
  readerSet->autoConsumerList = NULL;
  readerSet->backlogStartPos = 0;
  readerSet->backlogLen = readerSet->backlogSize = 0;
  readerSet->backlogElemSize = seqElemSize;
  readerSet->seqDataBacklog = NULL; /* only allocate backlog when it's
                                     * really needed! */
  readerSet->generatorState = generatorState;
  readerSet->generator = generator;
}

void
gt_destructSeqReaderSet(SeqReaderSet *readerSet)
{
  gt_assert(readerSet);
  ListDo(struct seqReaderState, readerSet->consumerList, gt_free(p));
  if (readerSet->autoConsumerList)
    gt_free(readerSet->autoConsumerList);
  if (readerSet->seqDataBacklog)
    gt_free(readerSet->seqDataBacklog);
}

SeqDataReader
gt_seqReaderSetRegisterConsumer(SeqReaderSet *readerSet, int tag,
                             SeqDataTranslator xltor)
{
  int availId = readerSet->numConsumers++;
  SeqDataReader reader;
  struct seqReaderState *state;
  gt_assert(readerSet);
  state = gt_malloc(sizeof (*state));
  state->readerSet = readerSet;
  state->id = availId;
  state->xltor = xltor;
  state->nextReadPos = 0;
  state->tag = tag;
  state->next = readerSet->consumerList;
  readerSet->consumerList = state;

  readerSet->tagSuperSet |= tag;

  reader.src = state;
  reader.readData = seqReaderSetRead;
  return reader;
}

bool
gt_seqReaderSetRegisterAutoConsumer(SeqReaderSet *readerSet, int tag,
                                 SeqDataWriter writer)
{
  int availId = readerSet->numConsumers++;
  gt_assert(false);
  gt_assert(readerSet);
  {
    struct seqSinkState *temp;
    if (!(temp = gt_realloc(readerSet->autoConsumerList,
                            sizeof (*temp) * (availId + 1))))
      return false;
    readerSet->autoConsumerList = temp;
  }
  {
    struct seqSinkState *state = readerSet->autoConsumerList + availId;
    state->id = availId;
    state->writer = writer;
    state->tag = tag;

    readerSet->tagSuperSet |= tag;
  }
  return true;
}

static size_t
seqReaderSetRead(void *src, void *dest, size_t len)
{
  struct seqReaderState *state = src;
  struct seqReaderSet *readerSet;
  unsigned long pos;
  size_t elemsLeft;
  gt_assert(src);
  readerSet = state->readerSet;
  elemsLeft = len;
  pos = seqReaderSetGetConsumerNextPos(state);
  while (elemsLeft)
  {
    if (pos >= readerSet->backlogStartPos + readerSet->backlogLen)
    {
      /* pos is in block that's governed by generator */
      size_t elemsGenerated =
        readerSet->generator(readerSet->generatorState, readerSet,
                             seqReaderSetMove2Backlog, dest, pos, elemsLeft,
                             state->xltor);
      seqReaderSetSetConsumerNextPos(state, pos += elemsGenerated);
      elemsLeft -= elemsGenerated;
      break;
    }
    else if (pos >= readerSet->backlogStartPos
             /* implicit because of above condition
                && pos < readerSet->backlogStartPos + readerSet->backlogLen */
      )
    {
      /* pos is in backlog */
      unsigned long subLen, charsWritten;

      subLen = MIN(elemsLeft, readerSet->backlogStartPos - pos
                              + readerSet->backlogLen);
      gt_assert(state->xltor.translateData == NULL);
      /*
      charsWritten = SDRTranslate(state->xltor, dest,
                                  (char *)readerSet->seqDataBacklog
                                  + (pos - readerSet->backlogStartPos)
                                  * readerSet->backlogElemSize,
                                  subLen);
      */
      memcpy(dest, (char *)readerSet->seqDataBacklog
                   + (pos - readerSet->backlogStartPos)
                   * readerSet->backlogElemSize,
             subLen * state->xltor.state.elemSize);
      charsWritten = subLen * state->xltor.state.elemSize;
      elemsLeft -= subLen;
      seqReaderSetSetConsumerNextPos(state, pos += subLen);
      dest = (char *)dest + charsWritten;
    }
    else
    {
      fprintf(stderr, "fatal error at file %s, line %d\n", __FILE__, __LINE__);
      abort();
    }
  }
  return len - elemsLeft;
}

#if 0
/* These might be needed later when translation results values are
 * kept in backlog too */
static inline unsigned long
seqReaderSetFindMinOpenRequestBySet(SeqReaderSet *readerSet, int setSpec)
{
  unsigned long min = -1;
  int i;
  gt_assert(readerSet);
  for (i = 0; i < readerSet->numConsumers; ++i)
    if (readerSet->consumers[i].tag & setSpec)
      min = MIN(min, readerSet->consumers[i].nextReadPos);
  return min;
}

static inline unsigned long
seqReaderSetFindMinOpenRequestByVal(SeqReaderSet *readerSet, int tagVal)
{
  unsigned long min = -1;
  int i;
  gt_assert(readerSet);
  for (i = 0; i < readerSet->numConsumers; ++i)
    if (readerSet->consumers[i].tag == tagVal)
      min = MIN(min, readerSet->consumers[i].nextReadPos);
  return min;
}
#endif

static inline unsigned long
seqReaderSetFindMinOpenRequest(SeqReaderSet *readerSet)
{
  struct seqReaderState *p;
  unsigned long min = -1;
  gt_assert(readerSet);
  p = readerSet->consumerList;
  while (p)
  {
    min = MIN(min, seqReaderSetGetConsumerNextPos(p));
    p = p->next;
  }
  return min;
}

static void
seqReaderSetMove2Backlog(void *backlogState, const void *seqData,
                         unsigned long requestStart, size_t requestLen)
{
  unsigned long requestMinPos;
  struct seqReaderSet *readerSet = backlogState;
  gt_assert(backlogState && (requestLen?(seqData!=NULL):1));
  requestMinPos = seqReaderSetFindMinOpenRequest(readerSet);
  /* 1. pass all data to be invalidated to automatic sinks */
  {
    int i, numAutoConsumers = readerSet->numAutoConsumers;
    struct seqSinkState *sinks = readerSet->autoConsumerList;
    /* The following must hold, as writer is not defined */
    gt_assert(numAutoConsumers == 0);
    for (i = 0; i < numAutoConsumers; ++i)
    {
      SDWWrite(sinks[i].writer, seqData, requestLen);
    }
  }
  /* 2. move still unread old values as far as possible to head of copy */
  gt_assert(requestMinPos >= readerSet->backlogStartPos);
  if (requestMinPos < readerSet->backlogStartPos + readerSet->backlogLen)
  {
    size_t backlogUnread
      = readerSet->backlogLen - requestMinPos + readerSet->backlogStartPos;
    memmove(readerSet->seqDataBacklog,
            (char *)readerSet->seqDataBacklog
            + (requestMinPos - readerSet->backlogStartPos)
            * readerSet->backlogElemSize,
            readerSet->backlogElemSize * backlogUnread);
    readerSet->backlogLen = backlogUnread;
    readerSet->backlogStartPos = requestMinPos;
  }
  else
  {
    readerSet->backlogLen = 0;
    readerSet->backlogStartPos = requestMinPos;
  }
  {
    unsigned long copyStartPos = MAX(requestMinPos, requestStart);
    size_t copyLen = requestLen - copyStartPos + requestStart;
    /* 3. extend backlog to also accept all invalidated values still needed */
    if (copyLen)
    {
      unsigned long *destSptr;

      size_t idx, backlogSizeLeft
        = readerSet->backlogSize - readerSet->backlogLen;
      if (copyLen > backlogSizeLeft)
      {
        size_t newSize = readerSet->backlogLen + copyLen;
        readerSet->seqDataBacklog
          = gt_realloc(readerSet->seqDataBacklog, readerSet->backlogElemSize
                       * newSize);
        readerSet->backlogSize = newSize;
      }
      destSptr = ((unsigned long *) readerSet->seqDataBacklog) +
                 readerSet->backlogLen;
      if (readerSet->fromSuffixsortspace)
      {
        GtSuffixsortspace *srcSptr = (GtSuffixsortspace *) seqData;
        for (idx = 0; idx< copyLen; idx++)
        {
          destSptr[idx]
            = gt_suffixsortspace_getdirect(srcSptr,
                                           copyStartPos - requestStart + idx);
        }
      } else
      {
        ESASuffixptr *srcSptr
          = ((ESASuffixptr *) seqData) + (copyStartPos - requestStart);
        for (idx = 0; idx< copyLen; idx++)
        {
          destSptr[idx] = ESASUFFIXPTRGET(srcSptr,idx);
        }
      }
      /*
      memcpy((char *)readerSet->seqDataBacklog
             + readerSet->backlogLen * readerSet->backlogElemSize,
             (char *)seqData
             + (copyStartPos - requestStart) * readerSet->backlogElemSize,
             readerSet->backlogElemSize * copyLen);
      */
      readerSet->backlogLen += copyLen;
    }
  }
}

static inline int
seqReaderSetGetConsumerTag(struct seqReaderState *state)
{
  gt_assert(state);
  return state->tag;
}

static inline void
seqReaderSetAdvanceConsumer(struct seqReaderState *state, size_t len)
{
  gt_assert(state);
  state->nextReadPos += len;
}
genometools-1.5.1/src/match/eis-sequencemultiread.h000066400000000000000000000067661211610345200224140ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SEQUENCEMULTIREAD_H
#define EIS_SEQUENCEMULTIREAD_H
/**
 * \file eis-sequencemultiread.h
 * Keeps information about multiple synchronous reads of sequence
 * data, where only one source and multiple consumers exist.
 */
#include "core/assert_api.h"
#include "core/minmax.h"
#include "match/eis-seqdatasrc.h"

/** every reader is identified by a unique scalar */
typedef unsigned consumerID;

/* moves data that can no longer be regenerated to the backlog */
typedef void (*move2BacklogFunc)(void *backlogState, const void *seqData,
                                 unsigned long requestStart, size_t requestLen);

/**
 * basic idea: let this function write the required data to output
 * and also call the move2Backlog callback if any data will be
 * invalidated after this call and is still required by other consumers
 * @return number of elements actually generated (might be short on eof etc.)
 */
typedef size_t (*generatorFunc)(void *generatorState, void *backlogState,
                                move2BacklogFunc move2Backlog, void *output,
                                unsigned long generateStart, size_t len,
                                SeqDataTranslator xltor);

typedef struct seqReaderSet SeqReaderSet;

struct seqReaderSet
{
  int numConsumers, numAutoConsumers;
  int tagSuperSet;
  struct seqReaderState *consumerList;
  struct seqSinkState *autoConsumerList;
  unsigned long backlogStartPos;
  bool fromSuffixsortspace;
  size_t backlogSize, backlogLen, backlogElemSize;
  void *seqDataBacklog, *generatorState;
  generatorFunc generator;
};

/**
 * @return numReaders if all consumers registered otherwise
 */
/*
int
gt_initSeqReaderSet(SeqReaderSet *readerSet, int initialSuperSet,
                 int numConsumers, int *tags, SeqDataTranslator xltors[],
                 SeqDataReader *generatedReaders, size_t seqElemSize,
                 generatorFunc generator, void *generatorState);
*/

void
gt_initEmptySeqReaderSet(SeqReaderSet *readerSet, int initialSuperSet,
                         bool fromSuffixsortspace,
                         size_t seqElemSize,
                         generatorFunc generator,
                         void *generatorState);

/**
 * @return readData field will be NULL on error -> test with
 * SDRIsValid */
SeqDataReader
gt_seqReaderSetRegisterConsumer(SeqReaderSet *readerSet, int tag,
                             SeqDataTranslator xltor);

/**
 * @brief The registered writer will be called automatically for any
 * data that is to be invalidated.
 *
 * @return false on error, true if successfully registered
 */
bool
gt_seqReaderSetRegisterAutoConsumer(SeqReaderSet *readerSet, int tag,
                                 SeqDataWriter writer);

void
gt_destructSeqReaderSet(SeqReaderSet *readerSet);

#endif
genometools-1.5.1/src/match/eis-specialsrank-priv.h000066400000000000000000000030661211610345200223200ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SPECIALSRANK_PRIV_H
#define EIS_SPECIALSRANK_PRIV_H

#include "match/eis-specialsrank.h"

typedef unsigned long (*RankReportFunc)(const SpecialsRankLookup *ranker,
                                 unsigned long pos);

struct specialsRankLookup
{
  RankReportFunc rankFunc;
  const GtEncseq *encseq;
  union
  {
    struct specialsRankTable
    {
      GtEncseqReader *scanState;
      unsigned long *rankSumSamples, numSamples, sampleInterval;
      GtReadmode readmode;
      unsigned sampleIntervalLog2;
    } sampleTable;
    unsigned long lastSeqPos;
  } implementationData;
};

static inline unsigned long
specialsRank(const SpecialsRankLookup *ranker, unsigned long pos)
{
  return ranker->rankFunc(ranker, pos);
}

#endif
genometools-1.5.1/src/match/eis-specialsrank.c000066400000000000000000000154251211610345200213370ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/assert_api.h"
#include "match/dataalign.h"
#include "core/ma_api.h"
#include "core/minmax.h"

#include "match/eis-specialsrank.h"
#include "match/eis-specialsrank-priv.h"

typedef struct specialsRankTable SpecialsRankTable;

static unsigned long
specialsRankFromSampleTable(const SpecialsRankLookup *rankTable,
                            unsigned long pos);

static unsigned long
specialsRankFromTermPos(const SpecialsRankLookup *rankTable,
                        unsigned long pos);

static inline struct specialsRankLookup *
allocSpecialsRankTable(const GtEncseq *encseq,
                       unsigned long lastSeqPos,
                       unsigned sampleIntervalLog2,
                       GtReadmode readmode)
{
  struct specialsRankTable *rankTable;
  struct specialsRankLookup *ranker;
  unsigned long numSamples = (lastSeqPos >> sampleIntervalLog2) + 1;

  ranker = gt_malloc(offsetAlign(sizeof (*ranker), sizeof (unsigned long))
                     + numSamples * sizeof (unsigned long));
  rankTable = &ranker->implementationData.sampleTable;
  rankTable->rankSumSamples
    = (unsigned long *)((char *)ranker + offsetAlign(sizeof (*ranker),
                                              sizeof (unsigned long)));
  rankTable->sampleIntervalLog2 = sampleIntervalLog2;
  rankTable->sampleInterval = ((unsigned long)1) << sampleIntervalLog2;
  rankTable->readmode = readmode;
  rankTable->numSamples = numSamples;
  rankTable->scanState = gt_encseq_create_reader_with_readmode(encseq,
                                                               readmode, 0);
  ranker->encseq = encseq;
  ranker->rankFunc = specialsRankFromSampleTable;
  return ranker;
}

static inline struct specialsRankLookup *
allocEmptySpecialsRankLookup(const GtEncseq *encseq,
                             unsigned long lastSeqPos)
{
  struct specialsRankLookup *ranker;
  ranker = gt_malloc(sizeof (*ranker));
  ranker->implementationData.lastSeqPos = lastSeqPos;
  ranker->rankFunc = specialsRankFromTermPos;
  ranker->encseq = encseq;
  return ranker;
}

static inline bool
nextRange(GtRange *range, GtSpecialrangeiterator *sri,
          GtReadmode readmode, unsigned long seqLastPos)
{
  bool hasNextRange = gt_specialrangeiterator_next(sri, range);
  if (hasNextRange)
  {
    if (GT_ISDIRREVERSE(readmode))
    {
      unsigned long temp = range->end;
      range->end = seqLastPos - range->start;
      range->start = seqLastPos - temp;
    }
  }
  else
    range->end = seqLastPos + 1, range->start = seqLastPos;
  return hasNextRange;
}

SpecialsRankLookup *
gt_newSpecialsRankLookup(const GtEncseq *encseq, GtReadmode readmode,
                         unsigned sampleIntervalLog2)
{
  struct specialsRankLookup *ranker;
  unsigned long seqLastPos, seqLen;
  unsigned long sampleInterval = ((unsigned long)1) << sampleIntervalLog2;
  gt_assert(encseq);
  gt_assert(sampleIntervalLog2 < sizeof (unsigned long) * CHAR_BIT);
  seqLastPos = gt_encseq_total_length(encseq);
  seqLen = seqLastPos + 1;
  if (gt_encseq_has_specialranges(encseq))
  {
    /* this sequence has some special characters */
    struct specialsRankTable *rankTable;
    GtSpecialrangeiterator *sri;
    unsigned long *sample, *maxSample, sum = 0, pos = 0, nextSamplePos;
    GtRange range = { 0, 0 };
    ranker = allocSpecialsRankTable(encseq, seqLen, sampleIntervalLog2,
                                    readmode);
    rankTable = &ranker->implementationData.sampleTable;
    sri = gt_specialrangeiterator_new(encseq, !GT_ISDIRREVERSE(readmode));
    sample = rankTable->rankSumSamples;
    maxSample = sample + rankTable->numSamples;
    *sample++ = sum;
    nextSamplePos = sampleInterval;
    nextRange(&range, sri, readmode, seqLastPos);
    while (sample < maxSample)
    {
      while (pos < nextSamplePos)
      {
        pos = MIN(MAX(pos, range.start), nextSamplePos);
        sum += MIN(range.end - pos, nextSamplePos - pos);
        pos = MIN(range.end, nextSamplePos);
        if (pos < nextSamplePos)
        {
          nextRange(&range, sri, readmode, seqLastPos);
        }
      }
      *sample++ = sum;
      nextSamplePos += sampleInterval;
    }
    gt_specialrangeiterator_delete(sri);
    sri = NULL;
  }
  else
  {
    /* While there is no special characters in this sequence, there
     * is of course the terminator */
    ranker = allocEmptySpecialsRankLookup(encseq, seqLastPos);
  }
  return ranker;
}

void
gt_deleteSpecialsRankLookup(SpecialsRankLookup *ranker)
{
  if (ranker->rankFunc == specialsRankFromSampleTable)
    gt_encseq_reader_delete(ranker->implementationData.sampleTable.scanState);
  gt_free(ranker);
}

static unsigned long
specialsRankFromSampleTable(const SpecialsRankLookup *ranker, unsigned long pos)
{
  const SpecialsRankTable *rankTable = &ranker->implementationData.sampleTable;
  unsigned long rankCount, samplePos, encSeqLen;
  gt_assert(ranker);
  encSeqLen = gt_encseq_total_length(ranker->encseq);
  gt_assert(pos <= encSeqLen + 1);
  samplePos = pos & ~(rankTable->sampleInterval - 1);
  {
    size_t sampleIdx = pos >> rankTable->sampleIntervalLog2;
    rankCount = rankTable->rankSumSamples[sampleIdx];
  }
  {
    const GtEncseq *encseq = ranker->encseq;
    GtEncseqReader *esr = rankTable->scanState;
    GtReadmode readmode = rankTable->readmode;
    unsigned long encseqQueryMax = MIN(pos, encSeqLen);
    if (samplePos < encseqQueryMax)
    {
      gt_encseq_reader_reinit_with_readmode(esr, encseq, readmode, samplePos);
      do {
        samplePos++;
        if (ISSPECIAL(gt_encseq_reader_next_encoded_char(esr)))
          ++rankCount;
      } while (samplePos < encseqQueryMax);
    }
    if (pos == encSeqLen + 1)
      ++rankCount;
  }
  return rankCount;
}

static unsigned long
specialsRankFromTermPos(const SpecialsRankLookup *ranker, unsigned long pos)
{
  gt_assert(pos <= ranker->implementationData.lastSeqPos + 1);
  return ((pos == ranker->implementationData.lastSeqPos + 1)?1:0);
}

const GtEncseq *
gt_SPRTGetOrigEncseq(const SpecialsRankLookup *ranker)
{
  return ranker->encseq;
}
genometools-1.5.1/src/match/eis-specialsrank.h000066400000000000000000000026071211610345200213420ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SPECIALSRANK_H
#define EIS_SPECIALSRANK_H

#include "core/encseq.h"

typedef struct specialsRankLookup SpecialsRankLookup;

SpecialsRankLookup *
gt_newSpecialsRankLookup(const GtEncseq *encseq, GtReadmode readmode,
                     unsigned sampleIntervalLog2);

void
gt_deleteSpecialsRankLookup(SpecialsRankLookup *table);

static inline unsigned long
specialsRank(const SpecialsRankLookup *rankTable, unsigned long pos);

const GtEncseq *
gt_SPRTGetOrigEncseq(const SpecialsRankLookup *rankTable);

#include "match/eis-specialsrank-priv.h"

#endif
genometools-1.5.1/src/match/eis-suffixarray-interface-priv.h000066400000000000000000000034451211610345200241430ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SUFFIXARRAY_INTERFACE_PRIV_H
#define EIS_SUFFIXARRAY_INTERFACE_PRIV_H

#include "eis-suffixarray-interface.h"

/**
 * Used to pass suffixarray to read from and alphabet to encode with
 * to readers.
 */
struct suffixarrayFileInterface
{
  struct SASeqSrc baseClass;
  struct saTaggedXltorStateList xltorStates;
  Suffixarray *sa;                      /**< the suffix array to read from */
  char numBWTFileReaders;
};

static inline SuffixarrayFileInterface *
SASS2SAI(SASeqSrc *baseClass)
{
  return (SuffixarrayFileInterface *)
    ((char *)baseClass - offsetof(SuffixarrayFileInterface, baseClass));
}

static inline const SuffixarrayFileInterface *
constSASS2SAI(const SASeqSrc *baseClass)
{
  return (const SuffixarrayFileInterface *)
    ((const char *)baseClass - offsetof(SuffixarrayFileInterface, baseClass));
}

static inline SASeqSrc *
SAI2SASS(SuffixarrayFileInterface *sai)
{
  return &sai->baseClass;
}

static inline const SASeqSrc *
constSAI2SASS(const SuffixarrayFileInterface *sai)
{
  return &sai->baseClass;
}

#endif
genometools-1.5.1/src/match/eis-suffixarray-interface-siop.h000066400000000000000000000026441211610345200241350ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SUFFIXARRAY_INTERFACE_SIOP_H
#define EIS_SUFFIXARRAY_INTERFACE_SIOP_H

#include "eis-suffixarray-interface.h"
#include "eis-suffixarray-interface-priv.h"

static inline MRAEnc *
SAINewMRAEnc(const SuffixarrayFileInterface *sai)
{
  return gt_SANewMRAEnc(gt_encseq_alphabet(sai->sa->encseq));
}

static inline const GtEncseq *
SAIGetEncSeq(const SuffixarrayFileInterface *sai)
{
  return sai->sa->encseq;
}

static inline GtReadmode
SAIGetGtReadmode(const SuffixarrayFileInterface *sai)
{
  return sai->sa->readmode;
}

static inline unsigned long
SAIGetLength(const SuffixarrayFileInterface *sai)
{
  return SASSGetLength(constSAI2SASS(sai));
}

#endif
genometools-1.5.1/src/match/eis-suffixarray-interface.c000066400000000000000000000157751211610345200231710ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/chardef.h"
#include "core/error.h"
#include "core/ma_api.h"
#include "core/unused_api.h"
#include "match/sarr-def.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-sa-common.h"
#include "match/eis-seqdatasrc.h"
#include "match/eis-suffixarray-interface.h"
#include "match/eis-suffixarray-interface-priv.h"

static void
gt_deleteSuffixarrayFileInterfaceBase(SASeqSrc *baseClass)
{
  gt_deleteSuffixarrayFileInterface(SASS2SAI(baseClass));
}

static struct seqDataReader
SAIBaseMakeReader(SASeqSrc *baseClass, enum sfxDataRequest rtype)
{
  return gt_SAIMakeReader(SASS2SAI(baseClass), rtype);
}

static Definedunsignedlong
SAIBaseGetRot0Pos(const SASeqSrc *baseClass)
{
  return gt_SAIGetRot0Pos(constSASS2SAI(baseClass));
}

static inline size_t
SAIBaseGetOrigSeq(const SASeqSrc *baseClass, Symbol *dest, unsigned long pos,
                  size_t len)
{
  return gt_SAIGetOrigSeq(constSASS2SAI(baseClass), dest, pos, len);
}

MRAEnc *
gt_SAIBaseNewMRAEnc(const SASeqSrc *baseClass)
{
  return SAINewMRAEnc(constSASS2SAI(baseClass));
}

static size_t
SAIGenerate(void *generatorState, void *backlogState,
            move2BacklogFunc move2Backlog, void *output,
            unsigned long generateStart, size_t len,
            SeqDataTranslator xltor);

void
gt_initSuffixarrayFileInterface(SuffixarrayFileInterface *sai,
                             unsigned long seqLen, Suffixarray *sa)
{
  {
    RandomSeqAccessor origSeqAccess = { gt_SAIGetOrigSeq, sai };
    initSASeqSrc(&sai->baseClass, seqLen, NULL, SAIBaseMakeReader,
                 SAIBaseGetRot0Pos, NULL,
                 origSeqAccess, gt_deleteSuffixarrayFileInterfaceBase,
                 gt_SAIBaseNewMRAEnc,
                 SAIGenerate, sai);
  }
  sai->sa = sa;
  sai->numBWTFileReaders = 0;
  gt_initSATaggedXltorStateList(&sai->xltorStates);
}

SuffixarrayFileInterface *
gt_newSuffixarrayFileInterface(Suffixarray *sa, unsigned long seqLen)
{
  SuffixarrayFileInterface *sai = gt_malloc(sizeof (*sai));
  gt_initSuffixarrayFileInterface(sai, seqLen, sa);
  return sai;
}

void
gt_destructSuffixarrayFileInterface(SuffixarrayFileInterface *sai)
{
  destructSASeqSrc(&sai->baseClass);
  gt_destructSATaggedXltorStateList(&sai->xltorStates);
}

void
gt_deleteSuffixarrayFileInterface(SuffixarrayFileInterface *sai)
{
  gt_destructSuffixarrayFileInterface(sai);
  gt_free(sai);
}

static size_t
SAIReadBWT(void *state, Symbol *dest, size_t len, GtError *err);

struct seqDataReader
gt_SAIMakeBWTReader(SuffixarrayFileInterface *sai)
{
  struct seqDataReader reader = { NULL, NULL};
  if (!sai->sa->bwttabstream.fp || sai->numBWTFileReaders > 0)
  {
    if (sai->sa->encseq)
    {
      struct encSeqTrState bwtReadState = {
        .readmode = sai->sa->readmode,
        .encseq = sai->sa->encseq
      };
      struct saTaggedXltorState *stateStore
        = gt_addSuffixarrayXltor(&sai->xltorStates,
                              SFX_REQUEST_BWTTAB, bwtReadState);
      struct seqDataTranslator xltor = {
        { .ref = &stateStore->state },
        gt_translateSuftab2BWT,
        gt_translateSuftab2BWTSuffixsortspace
      };

      reader = gt_seqReaderSetRegisterConsumer(&sai->baseClass.readerSet,
                                            SFX_REQUEST_BWTTAB, xltor);
    }
    else
    {
      fputs("error: bwt data not available for given project.\n", stderr);
    }
  }
  else
  {
    /* a .bwt file is available for reading */
    reader.readData = (seqDataReadFunc)SAIReadBWT;
    reader.src = sai;
    ++sai->numBWTFileReaders;
  }
  return reader;
}

struct seqDataReader
gt_SAIMakeSufTabReader(SuffixarrayFileInterface *sai)
{
  struct seqDataReader reader = { NULL, NULL};
  if (sai->sa->suftabstream_GtUlong.fp)
  {
    struct seqDataTranslator xltor = {
      { .elemSize = sizeof (unsigned long) }, NULL, NULL,
    };
    reader = gt_seqReaderSetRegisterConsumer(&sai->baseClass.readerSet,
                                             SFX_REQUEST_SUFTAB, xltor);
  }
  else
  {
    fputs("error: suffix array data not available for given project.\n",
          stderr);
  }
  return reader;
}

struct seqDataReader
gt_SAIMakeReader(SuffixarrayFileInterface *sai, enum sfxDataRequest rtype)
{
  struct seqDataReader reader = { NULL, NULL};
  switch (rtype)
  {
  case SFX_REQUEST_SUFTAB:
    reader = gt_SAIMakeSufTabReader(sai);
    break;
  case SFX_REQUEST_BWTTAB:
    reader = gt_SAIMakeBWTReader(sai);
    break;
  default:
    fprintf(stderr, "error: unimplemented request: %d, %s: %d!\n", rtype,
            __FILE__, __LINE__);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  return reader;
}

/**
 * @brief Read given length of symbols from the BWT, starting after last
 * position read.
 * @param state reference of a SuffixarrayFileInterface
 * @param dest write symbols here
 * @param len length of string to read
 * @return actual number of symbols read
 */
static size_t
SAIReadBWT(void *state, GtUchar *dest, size_t len, GT_UNUSED GtError *err)
{
  SuffixarrayFileInterface *sai = state;
  gt_assert(state);
  return fread(dest, sizeof (GtUchar), len, sai->sa->bwttabstream.fp);
}

size_t
gt_SAIGetOrigSeq(const void *state, Symbol *dest, unsigned long pos, size_t len)
{
  const SuffixarrayFileInterface *sai;
  gt_assert(state);
  sai = state;
  return EncSeqGetSubSeq(sai->sa->encseq, sai->sa->readmode, pos, len, dest);
}

Definedunsignedlong
gt_SAIGetRot0Pos(const void *state)
{
  const SuffixarrayFileInterface *sai = state;
  gt_assert(sai);
  return sai->sa->longest;
}

MRAEnc *
gt_SANewMRAEnc(const GtAlphabet *gtalphabet)
{
  MRAEnc *alphabet;
  gt_assert(gtalphabet != NULL);
  alphabet = gt_MRAEncGTAlphaNew(gtalphabet);
  gt_MRAEncAddSymbolToRange(alphabet, SEPARATOR, 1);
  return alphabet;
}

static size_t
SAIGenerate(void *generatorState, void *backlogState,
            move2BacklogFunc move2Backlog, void *output,
            unsigned long generateStart, size_t len,
            SeqDataTranslator xltor)
{
  size_t idx;
  SuffixarrayFileInterface *sai = generatorState;
  Suffixarray *sa;
  unsigned long buf[len];

  gt_assert(sai);
  sa = sai->sa;
  for (idx = 0; idx < len; ++idx)
  {
    if (gt_readnextfromstream_GtUlong(buf + idx,&sa->suftabstream_GtUlong) != 1)
    {
      break;
    }
  }
  move2Backlog(backlogState, buf, generateStart, idx);
  SDRTranslate(xltor, output, buf, idx);
  return idx;
}
genometools-1.5.1/src/match/eis-suffixarray-interface.h000066400000000000000000000065631211610345200231710ustar00rootroot00000000000000/*
  Copyright (C) 2007,2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_SUFFIXARRAY_INTERFACE_H
#define EIS_SUFFIXARRAY_INTERFACE_H

/**
 * \file eis-suffixarray-interface.h
 * Defines an interface deriving the abstract interface defined in
 * eis-sa-common.h for suffix array class objects (type SASeqSrc).
 */
#include 
#include "core/error.h"
#include "match/sarr-def.h"

#include "match/eis-mrangealphabet.h"
#include "match/eis-seqdatasrc.h"
#include "match/eis-sequencemultiread.h"

typedef struct suffixarrayFileInterface SuffixarrayFileInterface;

void
gt_initSuffixarrayFileInterface(SuffixarrayFileInterface *sai,
                             unsigned long seqLen,
                             Suffixarray *sa);

SuffixarrayFileInterface *
gt_newSuffixarrayFileInterface(Suffixarray *sa, unsigned long seqLen);

void
gt_destructSuffixarrayFileInterface(SuffixarrayFileInterface *sai);

void
gt_deleteSuffixarrayFileInterface(SuffixarrayFileInterface *sai);

SeqDataReader
gt_SAIMakeReader(SuffixarrayFileInterface *sai, enum sfxDataRequest rtype);

SeqDataReader
gt_SAIMakeBWTReader(SuffixarrayFileInterface *sai);

SeqDataReader
gt_SAIMakeSufTabReader(SuffixarrayFileInterface *sai);

/**
 * @brief Gets symbols of original sequence at given position.
 * @param state SuffixarrayFileInterface reference
 * @param dest write symbols here
 * @param pos get symbols starting at this position in original sequence
 * @param len length of string to read
 * @return actual number of symbols read
 */
size_t
gt_SAIGetOrigSeq(const void *state, Symbol *dest, unsigned long pos,
                 size_t len);

/**
 * @brief Query position of suffix starting at position 0, can be
 * undefined if not yet encountered.
 *
 * @param state reference of Suffixarray object
 * @return
 */
Definedunsignedlong
gt_SAIGetRot0Pos(const void *state);

/**
 * \brief Get reference for original sequence object.
 *
 * @param sai SuffixarrayFileInterface reference
 * @return reference of sequence object
 */
static inline const GtEncseq *
SAIGetEncSeq(const SuffixarrayFileInterface *sai);

static inline GtReadmode
SAIGetGtReadmode(const SuffixarrayFileInterface *sai);

static inline unsigned long
SAIGetLength(const SuffixarrayFileInterface *sai);

/**
 * @brief Query appropriate alphabet encoding for suffix array.
 * @param state reference of Suffixarray object
 * @return alphabet
 */
MRAEnc *
gt_SANewMRAEnc(const GtAlphabet *gtalphabet);

static inline MRAEnc *
SAINewMRAEnc(const SuffixarrayFileInterface *sai);

static inline struct SASeqSrc *
SAI2SASS(SuffixarrayFileInterface *sai);

/* visible for the compiler, but not meant for users to depend upon */
#include "eis-suffixarray-interface-siop.h"

#endif
genometools-1.5.1/src/match/eis-suffixerator-interface.c000066400000000000000000000322121211610345200233300ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include 

#include "match/dataalign.h"
#include "core/fa.h"
#include "core/filelengthvalues.h"
#include "core/logger.h"
#include "core/minmax.h"
#include "core/seq_iterator_api.h"
#include "core/str.h"
#include "core/str_array.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/codetype.h"
#include "core/encseq.h"

#include "match/eis-encidxseq.h"
#include "match/eis-sa-common.h"
#include "match/eis-sequencemultiread.h"
#include "match/eis-suffixerator-interface.h"

struct sfxInterface
{
  struct SASeqSrc baseClass;
  GtReadmode readmode;
  unsigned int prefixlength, numofparts, maximumspace;
  const Sfxstrategy *sfxstrategy;
  const GtAlphabet *alpha;
  const GtEncseq *encseq;
  struct seqStats *stats;
  Sfxiterator *sfi;
  Definedunsignedlong rot0Pos;
  /* data relevant to holding portions of the suffix array */
  unsigned long lastGeneratedLen, lastGeneratedStart;
  const GtSuffixsortspace *lastGeneratedSufTabSegment;
};

static SeqDataTranslator
SfxIRequest2XltorFunc(sfxInterface *sfxi,
                      enum sfxDataRequest rtype)
{
  SeqDataTranslator tr = { { NULL }, NULL };
  switch (rtype)
  {
    struct encSeqTrState readState;
    struct saTaggedXltorState *stateStore;
  case SFX_REQUEST_BWTTAB:
    readState.readmode = sfxi->readmode;
    readState.encseq = sfxi->encseq;
    stateStore = gt_addSuffixarrayXltor(&sfxi->baseClass.xltorStates,
                                        rtype, readState);
    tr.state.ref = &stateStore->state;
    tr.translateData = gt_translateSuftab2BWT;
    tr.translateDataSuffixsortspace = gt_translateSuftab2BWTSuffixsortspace;
    break;
  case SFX_REQUEST_SUFTAB:
    tr.state.elemSize = sizeof (unsigned long);
    gt_assert(tr.translateData == NULL);
    break;
  default:
    fprintf(stderr, "error: unimplemented request!\n");
    abort();
    break;
  }
  return tr;
}

static inline sfxInterface *
SASS2SfxI(SASeqSrc *baseClass)
{
  return (sfxInterface *)((char *)baseClass
                          - offsetof(sfxInterface, baseClass));
}

struct SASeqSrc *
gt_SfxI2SASS(sfxInterface *sfxi)
{
  return &sfxi->baseClass;
}

static inline const sfxInterface *
constSASS2SfxI(const SASeqSrc *baseClass)
{
  return (const sfxInterface *)((const char *)baseClass
                                - offsetof(sfxInterface, baseClass));
}

static SeqDataTranslator
SfxIBaseRequest2XltorFunc(SASeqSrc *baseClass,
                          enum sfxDataRequest rtype)
{
  return SfxIRequest2XltorFunc(SASS2SfxI(baseClass), rtype);
}

static Definedunsignedlong
SfxIBaseGetRot0Pos(const SASeqSrc *baseClass)
{
  return gt_SfxIGetRot0Pos(constSASS2SfxI(baseClass));
}

static const struct seqStats *
SfxIBaseGetSeqStats(const SASeqSrc *baseClass)
{
  return gt_SfxIGetSeqStats(constSASS2SfxI(baseClass));
}

static MRAEnc *
SfxIBaseNewMRAEnc(const SASeqSrc *baseClass)
{
  return gt_SfxINewMRAEnc(constSASS2SfxI(baseClass));
}

static void
gt_deleteSfxInterfaceBase(SASeqSrc *baseClass)
{
  gt_deleteSfxInterface(SASS2SfxI(baseClass));
}

static size_t
SfxIGenerate(void *iface,
             void *backlogState,
             move2BacklogFunc move2Backlog,
             void *output,
             unsigned long generateStart,
             size_t len,
             SeqDataTranslator xltor);

sfxInterface *
gt_newSfxInterface(GtReadmode readmode,
                unsigned int prefixlength,
                unsigned int numofparts,
                unsigned long maximumspace,
                const Sfxstrategy *sfxstrategy,
                const GtEncseq *encseq,
                GtTimer *sfxprogress,
                bool withprogressbar,
                unsigned long length,
                GtLogger *verbosity,
                GtError *err)
{
  return gt_newSfxInterfaceWithReaders(readmode,
                                       prefixlength,
                                       numofparts,
                                       maximumspace,
                                       sfxstrategy,
                                       0,
                                       NULL,
                                       NULL,
                                       encseq,
                                       sfxprogress,
                                       withprogressbar,
                                       length,
                                       verbosity,
                                       err);
}

static struct seqStats *
newSeqStatsFromCharDist(const GtEncseq *encseq,
                        const GtAlphabet *alpha, unsigned long len)
{
  struct seqStats *stats = NULL;
  unsigned i, numofchars;
  unsigned long regularSymsSum = 0;
  stats = gt_malloc(offsetAlign(sizeof (*stats), sizeof (unsigned long))
                    + (UINT8_MAX + 1) * sizeof (unsigned long));
  unsigned int numOfSeqs;

  numOfSeqs = gt_encseq_num_of_sequences(encseq);
  stats->sourceAlphaType = sourceUInt8;
  stats->symbolDistributionTable =
    (unsigned long *)((char *)stats + offsetAlign(sizeof (*stats),
                                                  sizeof (unsigned long)));
  memset(stats->symbolDistributionTable,
         0,
         sizeof (unsigned long) * (UINT8_MAX + 1));
  numofchars = gt_alphabet_num_of_chars(alpha);
  for (i = 0; i < numofchars; ++i)
  {
    stats->symbolDistributionTable[i]
      = (unsigned long) gt_encseq_charcount(encseq,(GtUchar) i);
    regularSymsSum += stats->symbolDistributionTable[i];
  }
  stats->symbolDistributionTable[WILDCARD] = len - regularSymsSum - numOfSeqs;
  stats->symbolDistributionTable[SEPARATOR] += numOfSeqs;
  stats->symbolDistributionTable[UNDEFBWTCHAR] += 1;
  return stats;
}

static void
deleteSeqStats(struct seqStats *stats)
{
  gt_free(stats);
}

#define gt_newSfxInterfaceWithReadersErrRet()        \
  do {                                            \
    if (sfxi->stats)                             \
      deleteSeqStats(sfxi->stats);               \
    if (sfxi) gt_free(sfxi);                    \
    sfxi = NULL;                                 \
  } while (0)

sfxInterface *
gt_newSfxInterfaceWithReaders(GtReadmode readmode,
                              unsigned int prefixlength,
                              unsigned int numofparts,
                              unsigned long maximumspace,
                              const Sfxstrategy *sfxstrategy,
                              size_t numReaders,
                              enum sfxDataRequest readerRequests[],
                              SeqDataReader readers[],
                              const GtEncseq *encseq,
                              GtTimer *sfxprogress,
                              bool withprogressbar,
                              unsigned long length,
                              GtLogger *verbosity, GtError *err)
{
  sfxInterface *sfxi = NULL;
  size_t idx;

  gt_error_check(err);
  sfxi = gt_calloc(1, sizeof (*sfxi));
  {
    RandomSeqAccessor origSeqAccess = { gt_SfxIGetOrigSeq, sfxi };
    initSASeqSrc(&sfxi->baseClass, length, SfxIBaseRequest2XltorFunc, NULL,
                 SfxIBaseGetRot0Pos, SfxIBaseGetSeqStats,
                 origSeqAccess, gt_deleteSfxInterfaceBase, SfxIBaseNewMRAEnc,
                 SfxIGenerate, sfxi);
  }
  sfxi->readmode = readmode;
  sfxi->encseq = encseq;
  sfxi->alpha = gt_encseq_alphabet(encseq);
  sfxi->stats = newSeqStatsFromCharDist(encseq,sfxi->alpha, length);
  if (!(sfxi->sfi = gt_Sfxiterator_new(encseq,
                                       readmode,
                                       prefixlength,
                                       numofparts,
                                       maximumspace,
                                       sfxstrategy,
                                       sfxprogress,
                                       withprogressbar,
                                       verbosity,
                                       err)))
  {
    gt_newSfxInterfaceWithReadersErrRet();
  }
  sfxi->rot0Pos.defined = false;

  sfxi->lastGeneratedStart = sfxi->lastGeneratedLen = 0;
  sfxi->lastGeneratedSufTabSegment = NULL;

  for (idx = 0; idx < numReaders; ++idx)
  {
    readers[idx] = gt_SfxIRegisterReader(sfxi, readerRequests[idx]);
    if (!readers[idx].readData)
    {
      gt_newSfxInterfaceWithReadersErrRet();
    }
  }
  return sfxi;
}

const Sfxiterator *gt_SfxInterface2Sfxiterator(const sfxInterface *sfxi)
{
  return sfxi->sfi;
}

void
gt_deleteSfxInterface(sfxInterface *sfxi)
{
  destructSASeqSrc(&sfxi->baseClass);
  (void) gt_Sfxiterator_delete(sfxi->sfi,NULL);
  sfxi->sfi = NULL;
  deleteSeqStats(sfxi->stats);
  gt_free(sfxi);
}

const GtAlphabet *
gt_SfxIGetAlphabet(const sfxInterface *si)
{
  return si->alpha;
}

MRAEnc *
gt_SfxINewMRAEnc(const sfxInterface *si)
{
  MRAEnc *alphabet;
  gt_assert(si);
  alphabet = gt_MRAEncGTAlphaNew(gt_SfxIGetAlphabet(si));
  gt_MRAEncAddSymbolToRange(alphabet, SEPARATOR, 1);
  return alphabet;
}

unsigned long
gt_SfxIGetLength(const sfxInterface *si)
{
  gt_assert(si);
  return si->baseClass.seqLen;
}

const struct seqStats *
gt_SfxIGetSeqStats(const sfxInterface *si)
{
  return si->stats;
}

Definedunsignedlong
gt_SfxIGetRot0Pos(const struct sfxInterface *si)
{
  return si->rot0Pos;
}

const GtEncseq *
gt_SfxIGetEncSeq(const sfxInterface *si)
{
  return si->encseq;
}

GtReadmode
gt_SfxIGetReadmode(const sfxInterface *si)
{
  return si->readmode;
}

SeqDataReader
gt_SfxIRegisterReader(sfxInterface *sfxi, enum sfxDataRequest rtype)
{
  return gt_seqReaderSetRegisterConsumer(
    &sfxi->baseClass.readerSet, rtype, SfxIRequest2XltorFunc(sfxi, rtype));
}

size_t
gt_SfxIGetOrigSeq(const void *state, Symbol *dest, unsigned long pos,
                  size_t len)
{
  const struct sfxInterface *sfxi;
  gt_assert(state);
  sfxi = state;
  return EncSeqGetSubSeq(sfxi->encseq, sfxi->readmode, pos, len, dest);
}

/** writes substring of suffix table to output, stores older data into
 * cache if necessary */
static size_t
SfxIGenerate(void *iface,
             void *backlogState,
             move2BacklogFunc move2Backlog,
             void *output,
             unsigned long generateStart,
             size_t len,
             SeqDataTranslator xltor)
{
  sfxInterface *sfxi = iface;
  size_t elemsLeft = len;
  gt_assert(sfxi && backlogState && move2Backlog && output);
  gt_assert(generateStart + len <= gt_SfxIGetLength(sfxi));
  do
  {
    if (generateStart < sfxi->lastGeneratedStart + sfxi->lastGeneratedLen)
    {
      size_t copyLen = MIN(elemsLeft, sfxi->lastGeneratedStart
                           + sfxi->lastGeneratedLen - generateStart),
        charsWritten =
        SDRTranslateSuffixsortspace(xltor, output,
                                    sfxi->lastGeneratedSufTabSegment,
                                    generateStart - sfxi->lastGeneratedStart,
                                    copyLen);
      generateStart += copyLen;
      elemsLeft -= copyLen;
      output = (char *)output + charsWritten;
    }
    /* 1. read next region of sequence by calling nextSfxIterator */
    if (elemsLeft)
    {

      move2Backlog(backlogState, sfxi->lastGeneratedSufTabSegment,
                   sfxi->lastGeneratedStart, sfxi->lastGeneratedLen);
      sfxi->lastGeneratedStart += sfxi->lastGeneratedLen;
      sfxi->lastGeneratedSufTabSegment
        = gt_Sfxiterator_next(&sfxi->lastGeneratedLen,
                              NULL,
                              sfxi->sfi);
      if (sfxi->lastGeneratedSufTabSegment != NULL)
      {
        /* size_t because the current approach cannot generate more
         * than memory will hold anyway */
        size_t pos, lastGeneratedLen = sfxi->lastGeneratedLen;

        if (!sfxi->rot0Pos.defined)
        {
          for (pos=0; pos < lastGeneratedLen; pos++)
          {
            if (gt_suffixsortspace_getdirect(sfxi->lastGeneratedSufTabSegment,
                                             pos) == 0)
            {
              sfxi->rot0Pos.defined = true;
              sfxi->rot0Pos.valueunsignedlong = sfxi->lastGeneratedStart + pos;
              break;
            }
          }
        }
        /* uncomment this to reenable synchronous writing of tables */
/*if (sfxi->lastGeneratedSufTabSegment == NULL */
/*    || suftab2file(&sfxi->outfileinfo, sfxi->lastGeneratedSufTabSegment, */
/*                   sfxi->so.readmode, sfxi->lastGeneratedLen, err) != 0) */
/*       break; */
      }
      else
        break;
    }
    /* 5. if positions in region don't suffice go back to step 3. */
  } while (elemsLeft);
  return len - elemsLeft;
}
genometools-1.5.1/src/match/eis-suffixerator-interface.h000066400000000000000000000171401211610345200233400ustar00rootroot00000000000000/*
  Copyright (C) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/**
 * \file eis-suffixerator-interface.h
 * \brief Methods to call suffixerator functions through one object,
 * but have the same data available to multiple listeners.
 * Conforms to the abstract interface defined in
 * eis-sa-common.h for suffix array class objects (type SASeqSrc).
 * \author Thomas Jahns 
 */
#ifndef EIS_SUFFIXERATOR_INTERFACE_H
#define EIS_SUFFIXERATOR_INTERFACE_H

#include "core/error.h"
#include "match/sfx-suffixer.h"
#include "match/eis-mrangealphabet.h"
#include "match/eis-seqdatasrc.h"
#include "match/eis-sa-common.h"

/**
 * opaque interface layer to retrieve arbitrary length portions of
 * the suffixarray
 */
typedef struct sfxInterface sfxInterface;

/**
 * @brief Create suffixerator interface object.
 *
 * @param so options for calling suffixerator
 * @param encseq object holding the sequences for suffixerator to
 * operate on
 * @param numofsequences number of sequences concatenated in encseq
 * @param sfxprogress timing device
 * @param length length of concatenated sequences plus terminator and
 * separators
 * @param alpha alphabet to use
 * generate statistics
 * @param verbosity used as argument of gt_logger_log
 * @param err
 * @return interface object reference
 */
sfxInterface *
gt_newSfxInterface(GtReadmode readmode,
                unsigned int prefixlength,
                unsigned int numofparts,
                unsigned long maximumspace,
                const Sfxstrategy *sfxstrategy,
                const GtEncseq *encseq,
                GtTimer *sfxprogress,
                bool withprogressbar,
                unsigned long length,
                GtLogger *verbosity,
                GtError *err);

/**
 * @brief Create suffixerator interface object with requestors already
 * in place.
 *
 * @param so options for calling suffixerator
 * @param numReaders number of readers to register at creation
 * @param requests reference of array with request type for each
 * reader
 * @param ids array to which, for each reader, one id is written (same
 * sequence as corresponding requests)
 * @param encseq object holding the sequences for suffixerator to
 * operate on
 * @param numofsequences number of sequences concatenated in encseq
 * @param sfxprogress timing device
 * @param length length of concatenated sequences plus terminator and
 * separators
 * @param alpha alphabet to use
 * generate statistics
 * @param verbosity used as argument of gt_logger_log
 * @param err
 * @return interface object reference
 */
sfxInterface *
gt_newSfxInterfaceWithReaders(GtReadmode readmode,
                           unsigned int prefixlength,
                           unsigned int numofparts,
                           unsigned long maximumspace,
                           const Sfxstrategy *sfxstrategy,
                           size_t numReaders,
                           enum sfxDataRequest readerRequests[],
                           SeqDataReader readers[],
                           const GtEncseq *encseq,
                           GtTimer *sfxprogress,
                           bool withprogressbar,
                           unsigned long length,
                           GtLogger *verbosity,
                           GtError *err);

/**
 * @brief get Sfxiterator from SfxInterface
 *
 * @param iface to take Sfxiterator from
 *
 */
const Sfxiterator *
gt_SfxInterface2Sfxiterator(const sfxInterface *iface);

/**
 * @brief Deallocate resources of suffixerator interface object.
 *
 * @param iface object to delete
 */
void
gt_deleteSfxInterface(sfxInterface *iface);

/**
 * @brief Dynamically cast to super class.
 *
 * @param sfxi reference to suffixerator interface object
 * @return reference of object of base class
 */
SASeqSrc *
gt_SfxI2SASS(sfxInterface *sfxi);

/**
 * \brief Constructs multiple range alphabet for sequence sorted by
 * suffixerator (i.e. alphabet includes separator symbol).
 *
 * @param si reference of interface to suffixerator
 * @return reference of newly created alphabet object
 */
MRAEnc *
gt_SfxINewMRAEnc(const sfxInterface *si);

/**
 * \brief Get reference for alphabet used to encode original sequence
 * object.
 *
 * @param si reference of interface to suffixerator
 * @return reference of alphabet object
 */
const GtAlphabet *
gt_SfxIGetAlphabet(const sfxInterface *si);

/**
 * \brief Get reference for original sequence object.
 *
 * @param si reference of interface to suffixerator
 * @return reference of sequence object
 */
const GtEncseq *
gt_SfxIGetEncSeq(const sfxInterface *si);

/**
 * @brief Get read mode used for suffix sorting.
 * @param si suffixerator interface object reference
 * @return read mode
 */
GtReadmode
gt_SfxIGetReadmode(const sfxInterface *si);

/**
 * \brief Get original sequence substring.
 *
 * @param si reference of interface to suffixerator
 * @param dest store read symbols here
 * @param pos position to start reading at
 * @param len number of symbols to read
 * @return number of symbols actually read
 */
size_t
gt_SfxIGetOrigSeq(const void *si, Symbol *dest, unsigned long pos, size_t len);

/**
 * \brief Query original sequence for statistics.
 *
 * @param si reference of interface to suffixerator
 * @return reference of struct holding statistics (symbol counts)
 */
const struct seqStats *
gt_SfxIGetSeqStats(const sfxInterface *si);

/**
 * @brief Query length @f$l@f$ of sequence sorted by suffixerator, including
 * the terminator and separator symbols (i.e.
 * @f[ l = \sum_{i=1}^n \left(|s_i| + 1\right)@f]
 * ).
 *
 * @param si reference of interface to suffixerator
 * @return length of sequence
 */
unsigned long
gt_SfxIGetLength(const sfxInterface *si);

/**
 * @brief Query position of suffix starting at position 0, can be
 * undefined if not yet encountered.
 *
 * @param si reference of interface to suffixerator
 * @return tuple of boolean (position is known) and position (if
 * known) or undefined value.
 */
Definedunsignedlong
gt_SfxIGetRot0Pos(const struct sfxInterface *si);

/**
 * @return >0 on success, 0 on error
 */
SeqDataReader
gt_SfxIRegisterReader(sfxInterface *iface, enum sfxDataRequest request);

#if 0
/**
 * \brief Reads portion of the BWT string produced by suffixerator.
 *
 * @param iface
 * @param id value returned by corresponding gt_SfxIRegisterReader call
 * @param len number of symbols to read
 * @param dest store read symbols here
 * @return number of symbols read (less than len implies end of file)
 */
size_t
readSfxIBWTRange(sfxInterface *iface, listenerID id, size_t len, GtUchar *dest);

/**
 * @return actual number of symbols read
 */
size_t
readSfxILCPRange(sfxInterface *iface, listenerID id, size_t len,
                 unsigned long *dest, GtError *err);

/**
 * @return actual number of symbols read
 */
size_t
readSfxISufTabRange(sfxInterface *iface, listenerID id, size_t len,
                    unsigned long *dest);
#endif

SeqDataReader
gt_SfxIRegisterReader(sfxInterface *iface, enum sfxDataRequest request);

#endif
genometools-1.5.1/src/match/eis-voiditf.c000066400000000000000000000455141211610345200203260ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/divmodmul.h"
#include "core/encseq_metadata.h"
#include "core/log_api.h"
#include "eis-bwtseq-construct.h"
#include "eis-bwtseq-priv.h"
#include "eis-bwtseq.h"
#include "eis-voiditf.h"
#include "procmatch.h"

/* XXX make use of the types declared by the EIS-tools, similar to
  the module core/bitpackarray.h */

unsigned long gt_bwtseqfirstmatch(const FMindex *fmindex,
                                  unsigned long bound)
{
  struct extBitsRetrieval extBits;
  unsigned long pos;

  initExtBitsRetrieval(&extBits);
  pos = gt_BWTSeqLocateMatch((const BWTSeq *) fmindex,bound,&extBits);
  destructExtBitsRetrieval(&extBits);
  return pos;
}

struct Bwtseqpositioniterator
{
  struct extBitsRetrieval extBits;
  const BWTSeq *bwtseq;
  unsigned long currentbound, upperbound;
};

Bwtseqpositioniterator *gt_Bwtseqpositioniterator_new(const FMindex *fmindex,
                                                      unsigned long lowerbound,
                                                      unsigned long upperbound)
{
  Bwtseqpositioniterator *bspi;

  bspi = gt_malloc(sizeof (*bspi));
  initExtBitsRetrieval(&bspi->extBits);
  bspi->bwtseq = (const BWTSeq *) fmindex;
  bspi->currentbound = lowerbound;
  bspi->upperbound = upperbound;
  return bspi;
}

bool gt_Bwtseqpositioniterator_next(unsigned long *pos,
                                    Bwtseqpositioniterator *bspi)
{
  if (bspi->currentbound < bspi->upperbound)
  {
    *pos = gt_BWTSeqLocateMatch(bspi->bwtseq,bspi->currentbound,&bspi->extBits);
    bspi->currentbound++;
    return true;
  }
  return false;
}

bool gt_BwtseqpositionwithoutSEPiterator_next(unsigned long *pos,
                                              Bwtseqpositioniterator *bspi)
{
  while (bspi->currentbound < bspi->upperbound)
  {
    GtUchar cc;

    if (bspi->currentbound != BWTSeqTerminatorPos(bspi->bwtseq))
    {
      cc = BWTSeqGetSym(bspi->bwtseq, bspi->currentbound);
    } else
    {
      cc = SEPARATOR;
    }
    if (cc != SEPARATOR)
    {
      *pos = gt_BWTSeqLocateMatch(bspi->bwtseq,
                                  bspi->currentbound,
                                  &bspi->extBits);
      bspi->currentbound++;
      return true;
    }
    bspi->currentbound++;
  }
  return false;
}

void gt_Bwtseqpositioniterator_delete(Bwtseqpositioniterator *bspi)
{
  destructExtBitsRetrieval(&bspi->extBits);
  gt_free(bspi);
}

struct BwtSeqpositionextractor
{
  struct extBitsRetrieval extBits;
  const BWTSeq *bwtseq;
  unsigned long upperbound;
};

BwtSeqpositionextractor *gt_newBwtSeqpositionextractor(
                                                     const FMindex *voidbwtseq,
                                                     unsigned long upperbound)
{
  BwtSeqpositionextractor *bspex;

  bspex = gt_malloc(sizeof (*bspex));
  initExtBitsRetrieval(&bspex->extBits);
  bspex->bwtseq = (const BWTSeq *) voidbwtseq;
  bspex->upperbound = upperbound;
  return bspex;
}

unsigned long gt_BwtSeqpositionextractor_extract(BwtSeqpositionextractor *bspex,
                                                 unsigned long lowerbound)
{
  unsigned long pos;

  gt_assert(lowerbound < bspex->upperbound);
  pos = gt_BWTSeqLocateMatch(bspex->bwtseq,lowerbound,&bspex->extBits);
  return pos;
}

void gt_freeBwtSeqpositionextractor(BwtSeqpositionextractor *bspex)
{
  destructExtBitsRetrieval(&(bspex->extBits));
  gt_free(bspex);
}

struct Bwtseqcontextiterator
{
  struct extBitsRetrieval extBits;
  const BWTSeq *bwtseq;
  unsigned long bound;
};

Bwtseqcontextiterator *gt_Bwtseqcontextiterator_new(const FMindex *fmindex,
                                                    unsigned long bound)
{
  Bwtseqcontextiterator *bsci;

  bsci = gt_malloc(sizeof (*bsci));
  initExtBitsRetrieval(&bsci->extBits);
  bsci->bwtseq = (const BWTSeq *) fmindex;
  bsci->bound = bound;
  return bsci;
}

GtUchar gt_bwtseqgetsymbol(unsigned long bound,const FMindex *fmindex)
{
  if (bound != BWTSeqTerminatorPos((const BWTSeq *) fmindex))
  {
    return BWTSeqGetSym((const BWTSeq *) fmindex, bound);
  }
  return SEPARATOR;
}

GtUchar gt_Bwtseqcontextiterator_next(unsigned long *bound,
                                      Bwtseqcontextiterator *bsci)
{
  GtUchar cc;

  if (bsci->bound != BWTSeqTerminatorPos(bsci->bwtseq))
  {
    cc = BWTSeqGetSym(bsci->bwtseq, bsci->bound);
  } else
  {
    cc = SEPARATOR;
  }
  *bound = bsci->bound = BWTSeqLFMap(bsci->bwtseq, bsci->bound, &bsci->extBits);
  return cc;
}

void gt_Bwtseqcontextiterator_delete(Bwtseqcontextiterator *bsci)
{
  if (bsci != NULL)
  {
    destructExtBitsRetrieval(&bsci->extBits);
    gt_free(bsci);
  }
}

FMindex *gt_loadvoidBWTSeqForSA(const char *indexname,
                                bool withpckbt,
                                GtError *err)
{
  BWTSeq *bwtseq = NULL;
  bool haserr = false;
  GtEncseqMetadata *emd;
  GtAlphabet *alphabet;

  emd = gt_encseq_metadata_new(indexname, err);
  if (emd == NULL) {
    gt_assert(gt_error_is_set(err));
    haserr = true;
  }
  if (!haserr) {
    alphabet = gt_encseq_metadata_alphabet(emd);
    if (alphabet == NULL)
    {
      gt_assert(gt_error_is_set(err));
      haserr = true;
    }
  }
  if (!haserr)
  {
    bwtseq = gt_loadBWTSeqForSA(indexname,
                                BWT_ON_BLOCK_ENC,
                                BWTDEFOPT_MULTI_QUERY,
                                alphabet,
                                err);
    if (bwtseq == NULL)
    {
      gt_assert(gt_error_is_set(err));
      haserr = true;
    }
  }
  if (!haserr)
  {
    if (withpckbt && gt_pckbuckettable_exists(indexname))
    {
      unsigned int numofchars = gt_alphabet_num_of_chars(alphabet);
      bwtseq->pckbuckettable = gt_pckbuckettable_map(indexname,numofchars,err);
      if (bwtseq->pckbuckettable == NULL)
      {
        gt_assert(gt_error_is_set(err));
        haserr = true;
      }
    } else
    {
      bwtseq->pckbuckettable = NULL;
    }
  }
  gt_encseq_metadata_delete(emd);
  if (haserr && bwtseq != NULL)
  {
    gt_deletevoidBWTSeq((FMindex *) bwtseq);
    bwtseq = NULL;
  }
  return haserr ? NULL : (FMindex *) bwtseq;
}

const Mbtab **gt_bwtseq2mbtab(const FMindex *fmindex)
{
  gt_assert(fmindex != NULL);
  if (((const BWTSeq *) fmindex)->pckbuckettable == NULL)
  {
    return NULL;
  }
  return (const Mbtab **)
         gt_pckbuckettable_mbtab_get(((const BWTSeq *) fmindex)
                                     ->pckbuckettable);
}

unsigned int gt_bwtseq2maxdepth(const FMindex *fmindex)
{
  gt_assert(fmindex != NULL);
  if (((const BWTSeq *) fmindex)->pckbuckettable == NULL)
  {
    return 0;
  }
  return gt_pckbuckettable_maxdepth_get(((const BWTSeq *) fmindex)
                                        ->pckbuckettable);
}

unsigned int gt_bwtseq2numofchars(const FMindex *fmindex)
{
  gt_assert(fmindex != NULL);
  if (((const BWTSeq *) fmindex)->pckbuckettable == NULL)
  {
    return 0;
  }
  return gt_pckbuckettable_numofchars_get(((const BWTSeq *) fmindex)
                                          ->pckbuckettable);
}

void gt_bwtrangesplitwithoutspecial(GtArrayBoundswithchar *bwci,
                                    unsigned long *rangeOccs,
                                    const FMindex *fmindex,
                                    unsigned long lbound,
                                    unsigned long ubound)
{
  const BWTSeq *bwtseq = (const BWTSeq *) fmindex;
  AlphabetRangeSize idx, rangesize;

  rangesize = MRAEncGetRangeSize(EISGetAlphabet(bwtseq->seqIdx),0);
  bwci->nextfreeBoundswithchar = 0;
  BWTSeqPosPairRangeOcc(bwtseq, 0, lbound, ubound,rangeOccs);
  for (idx = 0; idx < rangesize; idx++)
  {
    if (rangeOccs[idx] < rangeOccs[rangesize+idx])
    {
      bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar].inchar = idx;
      bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar].lbound
        = bwtseq->count[idx] + rangeOccs[idx];
      bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar++].rbound
        = bwtseq->count[idx] + rangeOccs[rangesize+idx];
    }
  }
}

unsigned long gt_bwtrangesplitallwithoutspecial(Mbtab *mbtab,
                                                unsigned long *rangeOccs,
                                                const FMindex *fmindex,
                                                unsigned long lbound,
                                                unsigned long ubound)
{
  const BWTSeq *bwtseq = (const BWTSeq *) fmindex;
  AlphabetRangeSize idx, rangesize
    = MRAEncGetRangeSize(EISGetAlphabet(bwtseq->seqIdx),0);

  gt_assert(sizeof (AlphabetRangeSize) <= sizeof (unsigned long));
  BWTSeqPosPairRangeOcc(bwtseq, 0, lbound, ubound,rangeOccs);
  for (idx = 0; idx < rangesize; idx++)
  {
    if (rangeOccs[idx] < rangeOccs[rangesize+idx])
    {
      mbtab[idx].lowerbound = bwtseq->count[idx] + rangeOccs[idx];
      mbtab[idx].upperbound = bwtseq->count[idx] + rangeOccs[rangesize+idx];
    } else
    {
      mbtab[idx].lowerbound = mbtab[idx].upperbound = 0;
    }
  }
  return (unsigned long) rangesize;
}

unsigned long gt_bwtrangesplitallwithspecial(Mbtab *mbtab,
                                             unsigned long *rangeOccs,
                                             const FMindex *voidBwtSeq,
                                             unsigned long lbound,
                                             unsigned long ubound)
{
  unsigned long char_idx, range_idx, rangebase;
  const BWTSeq *bwtseq = (const BWTSeq *) voidBwtSeq;
  const MRAEnc *alphabet = BWTSeqGetAlphabet(bwtseq);
  AlphabetRangeID numofranges = MRAEncGetNumRanges(alphabet);
  AlphabetRangeSize rangesize = 0, totalrange = 0;

  for (range_idx = 0; range_idx < (unsigned long) numofranges; range_idx++)
  {
    unsigned long rangeOcc_idx = 0;
    rangesize = MRAEncGetRangeSize(alphabet, range_idx);
    totalrange += rangesize;
    BWTSeqPosPairRangeOcc(bwtseq, range_idx, lbound, ubound,rangeOccs);
    rangebase = (unsigned long) MRAEncGetRangeBase(alphabet, range_idx);
    for (char_idx = rangebase;
         char_idx < rangebase + rangesize; char_idx++)
    {
      if (rangeOccs[rangeOcc_idx] < rangeOccs[rangesize+rangeOcc_idx])
      {
        mbtab[char_idx].lowerbound = bwtseq->count[char_idx] +
                                     rangeOccs[rangeOcc_idx];
        mbtab[char_idx].upperbound = bwtseq->count[char_idx] +
                                     rangeOccs[rangesize+rangeOcc_idx];
      } else
      {
        mbtab[char_idx].lowerbound = mbtab[char_idx].upperbound = 0;
      }
      rangeOcc_idx++;
    }
  }
  return totalrange;
}

/*
void bwtrangewithspecial(GT_UNUSED GtArrayBoundswithchar *bwci,
                         unsigned long *rangeOccs,
                         GT_UNUSED unsigned long numofchars,
                         const void *voidBwtSeq,
                         const Lcpinterval *parent)
{
  const BWTSeq *bwtseq = (const BWTSeq *) voidBwtSeq;

  AlphabetRangeSize rangesize
    = MRAEncGetRangeSize(EISGetAlphabet(bwtseq->seqIdx),1);
  gt_assert(rangesize < (AlphabetRangeSize) 4);
  BWTSeqPosPairRangeOcc(bwtseq, 1, parent->left, parent->right,rangeOccs);
    inchar = WILDCARD
    bwtcode = MRAEncMapSymbol(EISGetAlphabet(bwtseq->seqIdx),WILDCARD);
    idx = bwtcode -  MRAEncGetRangeBase(EISGetAlphabet(bwtseq->seqIdx),1);
    if (rangeOccs[idx] < rangeOccs[rangesize+idx])
    {
      pos = gt_BWTSeqLocateMatch((const BWTSeq *) fmindex,bound,&extBits);
    }
  }
}
*/

void gt_deletevoidBWTSeq(FMindex *fmindex)
{
  BWTSeq *bwtseq = (BWTSeq *) fmindex;

  if (bwtseq->pckbuckettable != NULL)
  {
    gt_pckbuckettable_delete(bwtseq->pckbuckettable);
    bwtseq->pckbuckettable = NULL;
  }
  gt_deleteBWTSeq(bwtseq);
}

unsigned long gt_voidpackedindexuniqueforward(const void *fmindex,
                                              GT_UNUSED unsigned long offset,
                                              GT_UNUSED unsigned long left,
                                              GT_UNUSED unsigned long right,
                                              GT_UNUSED unsigned long
                                                        *witnessposition,
                                              const GtUchar *qstart,
                                              const GtUchar *qend)
{
  return gt_packedindexuniqueforward((const BWTSeq *) fmindex,qstart,qend);
}

unsigned long gt_voidpackedfindfirstmatchconvert(const FMindex *fmindex,
                                                 unsigned long witnessbound,
                                                 unsigned long matchlength)
{
  const BWTSeq *bwtseq = (const BWTSeq *) fmindex;
  unsigned long startpos;

  startpos = gt_bwtseqfirstmatch(fmindex,witnessbound);
  gt_assert((bwtseq->seqIdx->seqLen-1) >= (startpos + matchlength));
  return (bwtseq->seqIdx->seqLen - 1) - (startpos + matchlength);
}

unsigned long gt_voidpackedindexmstatsforward(const void *fmindex,
                                              GT_UNUSED unsigned long offset,
                                              GT_UNUSED unsigned long left,
                                              GT_UNUSED unsigned long right,
                                              unsigned long *witnessposition,
                                              const GtUchar *qstart,
                                              const GtUchar *qend)
{
  const BWTSeq *bwtseq = (const BWTSeq *) fmindex;
  unsigned long matchlength;

  matchlength = gt_packedindexmstatsforward(bwtseq,witnessposition,qstart,qend);
  if (matchlength > 0 && witnessposition != NULL)
  {
    *witnessposition = gt_voidpackedfindfirstmatchconvert(fmindex,
                                                          *witnessposition,
                                                          matchlength);
  }
  return matchlength;
}

bool gt_pck_exactpatternmatching(const FMindex *fmindex,
                                 const GtUchar *pattern,
                                 unsigned long patternlength,
                                 unsigned long totallength,
                                 const GtUchar *dbsubstring,
                                 ProcessIdxMatch processmatch,
                                 void *processmatchinfo)
{
  BWTSeqExactMatchesIterator *bsemi;
  unsigned long dbstartpos, numofmatches;
  GtIdxMatch match;

  bsemi = gt_newEMIterator((const BWTSeq *) fmindex,
                           pattern,(size_t) patternlength, true);
  gt_assert(bsemi != NULL);
  numofmatches = gt_EMINumMatchesTotal(bsemi);
  match.dbabsolute = true;
  match.dblen = patternlength;
  match.dbsubstring = dbsubstring;
  match.querystartpos = 0;
  match.querylen = patternlength;
  match.distance = 0;
  match.alignment = NULL;
  while (EMIGetNextMatch(bsemi,&dbstartpos,(const BWTSeq *) fmindex))
  {
    gt_assert(totallength >= (dbstartpos + patternlength));
    match.dbstartpos = totallength - (dbstartpos + patternlength);
    processmatch(processmatchinfo,&match);
  }
  if (bsemi != NULL)
  {
    gt_deleteEMIterator(bsemi);
    bsemi = NULL;
  }
  return numofmatches > 0 ? true : false;
}

unsigned long gt_voidpackedindex_totallength_get(const FMindex *fmindex)
{
  unsigned long bwtlen = BWTSeqLength((const BWTSeq *) fmindex);

  gt_assert(bwtlen > 0);
  return bwtlen - 1;
}

unsigned long gt_pck_getShuStringLength(const FMindex *bwtSubject,
                                       const GtUchar *suffix,
                                       unsigned long suffixLength)
{
  GtUlongPair occPair;
  Symbol curChar;
  const GtUchar *qptr, *qend;
  const MRAEnc *alphabet;
  unsigned long start, end;

  gt_assert(bwtSubject && suffix);
  alphabet = BWTSeqGetAlphabet((const BWTSeq *) bwtSubject);

  qptr = suffix;
  qend = suffix + suffixLength;

  curChar = MRAEncMapSymbol(alphabet, *qptr);

  qptr++;
  start = ((const BWTSeq *) bwtSubject)->count[curChar];
  end = ((const BWTSeq *) bwtSubject)->count[curChar + 1];
  for (/* Nothing */; start < end && qptr < qend; qptr++)
  {
    curChar = MRAEncMapSymbol(alphabet, *qptr);
    occPair = BWTSeqTransformedPosPairOcc((const BWTSeq *) bwtSubject,
                                          curChar,
                                          start,
                                          end);
    start = ((const BWTSeq *) bwtSubject)->count[curChar] + occPair.a;
    end = ((const BWTSeq *) bwtSubject)->count[curChar] + occPair.b;
  }
  if (qptr == qend && start < end)
    return suffixLength + 1;
  else
    return qptr - suffix;
}

double gt_pck_getGCcontent(const FMindex *bwtSubject,
                           const GtAlphabet *alphabet)
{
  unsigned long  c, length;
  double gc;
  const MRAEnc *FM_alphabet;
  GtUchar c_sym;

  FM_alphabet = BWTSeqGetAlphabet((const BWTSeq *) bwtSubject);

  c_sym = MRAEncMapSymbol(FM_alphabet,
                          gt_alphabet_encode(alphabet, 'c'));
  length = ((const BWTSeq *) bwtSubject)->seqIdx->seqLen;

  c = ((const BWTSeq *) bwtSubject)->count[c_sym+1] -
    ((const BWTSeq *) bwtSubject)->count[c_sym];

  gc = c * 2 / (double) (length - 2);
  return gc;
}

unsigned long gt_pck_get_nonspecial_count(const FMindex *index)
{
  const BWTSeq *bwtseq = (const BWTSeq *) index;

  return BWTSeqAggTransformedCount(bwtseq,
                                   MRAEncGetRangeSize(BWTSeqGetAlphabet(bwtseq),
                                     0));
}

unsigned long gt_pck_special_occ_in_nonspecial_intervals(const FMindex *index)
{
  const BWTSeq *bwtseq = (const BWTSeq *) index;
  unsigned long count = 0,
                *rangeOccs, first_special_row;
  unsigned short idx, rangesize;

  rangesize = (unsigned short) MRAEncGetRangeSize(BWTSeqGetAlphabet(bwtseq), 1);
  rangeOccs = gt_calloc(rangesize, sizeof (unsigned long));
  first_special_row = gt_pck_get_nonspecial_count(index);
  BWTSeqRangeOcc(bwtseq, 1, first_special_row, rangeOccs);
  for (idx = 0; idx < rangesize; idx++)
    count += rangeOccs[idx];
  gt_free(rangeOccs);
  return count;
}

unsigned long gt_pck_exact_pattern_count(const FMindex *index,
                                         const GtUchar *pattern,
                                         unsigned long patternlength) {
  return gt_BWTSeqMatchCount((const BWTSeq *) index,
                              pattern,
                              (size_t) patternlength,
                              true); /* XXX check if this is right! */
}
genometools-1.5.1/src/match/eis-voiditf.h000066400000000000000000000175161211610345200203340ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EIS_VOIDITF_H
#define EIS_VOIDITF_H

#include "core/unused_api.h"
#include "core/encseq_api.h"

#include "splititv.h"
#include "procmatch.h"

/* The following type is just used to stronlgy type the functions
   using the FMindex (rather than using void pointers) */

typedef struct FMindex FMindex;

unsigned long gt_bwtseqfirstmatch(const FMindex *fmindex, unsigned long bound);

/** Iterator for positions defined by a lower and upper bound
 */

typedef struct Bwtseqpositioniterator Bwtseqpositioniterator;

Bwtseqpositioniterator *gt_Bwtseqpositioniterator_new(const FMindex *fmindex,
                                                      unsigned long lowerbound,
                                                      unsigned long upperbound);

bool gt_Bwtseqpositioniterator_next(unsigned long *pos,
                                    Bwtseqpositioniterator *bspi);

bool gt_BwtseqpositionwithoutSEPiterator_next(unsigned long *pos,
                                              Bwtseqpositioniterator *bspi);

GtUchar gt_bwtseqgetsymbol(unsigned long bound,const FMindex *fmindex);

void gt_Bwtseqpositioniterator_delete(Bwtseqpositioniterator *bspi);

typedef struct BwtSeqpositionextractor BwtSeqpositionextractor;

BwtSeqpositionextractor *gt_newBwtSeqpositionextractor(
                                                     const FMindex *voidbwtseq,
                                                     unsigned long upperbound);

unsigned long gt_BwtSeqpositionextractor_extract(BwtSeqpositionextractor *bspex,
                                                 unsigned long lowerbound);

void gt_freeBwtSeqpositionextractor(BwtSeqpositionextractor *bspex);

typedef struct Bwtseqcontextiterator Bwtseqcontextiterator;

Bwtseqcontextiterator *gt_Bwtseqcontextiterator_new(const FMindex *fmindex,
                                                    unsigned long bound);

GtUchar gt_Bwtseqcontextiterator_next(unsigned long *bound,
                                      Bwtseqcontextiterator *bsci);

void gt_Bwtseqcontextiterator_delete(Bwtseqcontextiterator *bsci);

void gt_bwtrangesplitwithoutspecial(GtArrayBoundswithchar *bwci,
                                    unsigned long *rangeOccs,
                                    const FMindex *fmindex,
                                    unsigned long lbound,
                                    unsigned long ubound);

FMindex *gt_loadvoidBWTSeqForSA(const char *indexname,
                                bool withpckbt,
                                GtError *err);

void gt_deletevoidBWTSeq(FMindex *packedindex);

/* the parameter is const void *, as this is required by the other
   indexed based methods */

unsigned long gt_voidpackedindexuniqueforward(const void *fmindex,
                                              GT_UNUSED unsigned long offset,
                                              GT_UNUSED unsigned long left,
                                              GT_UNUSED unsigned long right,
                                              GT_UNUSED unsigned long
                                                        *witnessposition,
                                              const GtUchar *qstart,
                                              const GtUchar *qend);

/* the parameter is const void *, as this is required by the other
   indexed based methods */

unsigned long gt_voidpackedindexmstatsforward(const void *fmindex,
                                              GT_UNUSED unsigned long offset,
                                              GT_UNUSED unsigned long left,
                                              GT_UNUSED unsigned long right,
                                              unsigned long *witnessposition,
                                              const GtUchar *qstart,
                                              const GtUchar *qend);

bool gt_pck_exactpatternmatching(const FMindex *fmindex,
                                 const GtUchar *pattern,
                                 unsigned long patternlength,
                                 unsigned long totallength,
                                 const GtUchar *dbsubstring,
                                 ProcessIdxMatch processmatch,
                                 void *processmatchinfo);

unsigned long gt_voidpackedfindfirstmatchconvert(const FMindex *fmindex,
                                                 unsigned long witnessbound,
                                                 unsigned long matchlength);

typedef struct
{
  unsigned long lowerbound, upperbound;
} Mbtab;

unsigned long gt_bwtrangesplitallwithoutspecial(Mbtab *mbtab,
                                                unsigned long *rangeOccs,
                                                const FMindex *fmindex,
                                                unsigned long lbound,
                                                unsigned long ubound);

unsigned int gt_bwtseq2maxdepth(const FMindex *fmindex);

unsigned int gt_bwtseq2numofchars(const FMindex *fmindex);

const Mbtab **gt_bwtseq2mbtab(const FMindex *fmindex);

/* this does currently not work, only for the root interval. This is due to the
 * sorting of the special chars, might be changed in future.
 * Only reliable information:
 * - Child intervals of standard alphabet
 * - type of special and the number, but not the interval (child intervals in
 *   special ranges do not necessarily form continuous intervals!) */
unsigned long gt_bwtrangesplitallwithspecial(Mbtab *mbtab,
                                             unsigned long *rangeOccs,
                                             const FMindex *voidBwtSeq,
                                             unsigned long lbound,
                                             unsigned long ubound);

unsigned long gt_voidpackedindex_totallength_get(const FMindex *fmindex);

/* returns the length of the matching prefix +1, that is it returns the
 * length of the shortest absent prefix */
unsigned long gt_pck_getShuStringLength(const FMindex* bwtSubject,
                                       const GtUchar* query,
                                       unsigned long queryLength);

/* returns the ½gc-content of the subject assuming fwd and rev sequence in the
 * index so that |g| == |c| */
double gt_pck_getGCcontent(const FMindex *bwtSubject,
                           const GtAlphabet *alphabet);

/* returns the count of all non special chars in the index, corresponding to the
 * first row in which a special char prefixes the rotation */
unsigned long gt_pck_get_nonspecial_count(const FMindex *index);

/* returns occurrences of special chars in the intervals of non special chars,
 * that is the number of rows that would be extended with a special. */
unsigned long gt_pck_special_occ_in_nonspecial_intervals(const FMindex *index);

/* counts the exact occurences of pattern in index returns 0 if pattern is not
 found */
unsigned long gt_pck_exact_pattern_count(const FMindex *index,
                                         const GtUchar *pattern,
                                         unsigned long patternlength);
#endif
genometools-1.5.1/src/match/emimergeesa.h000066400000000000000000000045071211610345200203710ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef EMIMERGEESA_H
#define EMIMERGEESA_H

#include "sarr-def.h"
#include "merger-trie.h"

#define SIZEOFMERGERESULTBUFFER BUFSIZ

/* make the type opaque */

typedef struct
{
  unsigned int idx;  /* index of genome in list of all genomes */
  unsigned long startpos;   /* in the range [0..totallength single index] */
} Indexedsuffix;

typedef struct
{
  unsigned int nextaccessidx,  /* in the range [0..SIZEOFMERGERESULTBUFFER] */
               nextstoreidx;   /* in the range [0..SIZEOFMERGERESULTBUFFER] */
  unsigned long lcptabstore[SIZEOFMERGERESULTBUFFER];
  Indexedsuffix suftabstore[SIZEOFMERGERESULTBUFFER];
  bool lastpage;
} Suflcpbuffer;

typedef struct
{
  uint64_t ident;              /* can be arbitrary large */
  unsigned int numofentries,   /* in the range [0..numofindexes-1] */
               numofindexes;   /* number of indexes */
  unsigned long *nextpostable; /* in the range [0..totallength single index] */
  Suflcpbuffer buf;
  Mergertrierep trierep;
  Suffixarray *suffixarraytable;
  unsigned int numofchars;
} Emissionmergedesa;

int gt_emissionmergedesa_stepdeleteandinsertothersuffixes(
                                    Emissionmergedesa *emmesa, GtError *err);

int gt_emissionmergedesa_init(Emissionmergedesa *emmesa,
                           const GtStrArray *indexnametab,
                           unsigned int demand,
                           GtLogger *logger,
                           GtError *err);

void gt_emissionmergedesa_wrap(Emissionmergedesa *emmesa);

#endif
genometools-1.5.1/src/match/encseq2offset.c000066400000000000000000000127301211610345200206450ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/chardef.h"
#include "core/ma_api.h"
#include "sarr-def.h"
#include "core/safecast-gen.h"

unsigned long *gt_encseqtable2sequenceoffsets(
                                    unsigned long *totallength,
                                    GtSpecialcharinfo *specialcharinfo,
                                    const Suffixarray *suffixarraytable,
                                    unsigned int numofindexes)
{
  unsigned int idx;
  GtUchar lastofprevious, firstofcurrent;
  unsigned long tmplength, numofsequences = 0, *sequenceoffsettable;
  uint64_t tmpspecialcharacters,
           tmpwildcards,
           tmpspecialranges,
           tmpwildcardranges,
           tmprealspecialranges,
           tmprealwildcardranges,
           tmpoffset;

  gt_assert(numofindexes > 0);
  sequenceoffsettable = gt_malloc(sizeof (*sequenceoffsettable) * numofindexes);
  tmpspecialcharacters = (uint64_t) (numofindexes-1);
  tmpwildcards = 0;
  tmpspecialranges = 0;
  tmpwildcardranges = 0;
  tmprealspecialranges = 0;
  tmprealwildcardranges = 0;
  for (idx=0; idx 0)
    {
      /* Random access */
      lastofprevious
        = gt_encseq_get_encoded_char(suffixarraytable[idx-1].encseq,
                                     tmplength-1,
                                     suffixarraytable[idx - 1].readmode);
      /* Random access */
      firstofcurrent
        = gt_encseq_get_encoded_char(suffixarraytable[idx].encseq,
                                     0,
                                     suffixarraytable[idx].readmode);
      if (ISSPECIAL(lastofprevious))
      {
        if (ISSPECIAL(firstofcurrent))
        {
          tmpspecialranges--;
          tmprealspecialranges--;
        }
      } else
      {
        if (ISNOTSPECIAL(firstofcurrent))
        {
          tmpspecialranges++;
          tmprealspecialranges++;
        }
      }
    }
    tmpoffset = (uint64_t) sequenceoffsettable[idx] +
       (uint64_t) gt_encseq_total_length(suffixarraytable[idx].encseq);
    (void) CALLCASTFUNC(uint64_t,unsigned_long,tmpoffset);
    (void) CALLCASTFUNC(uint64_t,unsigned_long,tmpspecialcharacters);
    (void) CALLCASTFUNC(uint64_t,unsigned_long,tmpwildcards);
    (void) CALLCASTFUNC(uint64_t,unsigned_long,tmpspecialranges);
    (void) CALLCASTFUNC(uint64_t,unsigned_long,tmpwildcardranges);
    (void) CALLCASTFUNC(uint64_t,unsigned_long,tmprealspecialranges);
    (void) CALLCASTFUNC(uint64_t,unsigned_long,tmprealwildcardranges);
    printf("# seqlen[%u] = %lu\n",
           idx,
           gt_encseq_total_length(suffixarraytable[idx].encseq));
  }
  tmplength = gt_encseq_total_length(suffixarraytable[numofindexes -1].encseq);
  *totallength = sequenceoffsettable[numofindexes-1] + tmplength;
  specialcharinfo->specialcharacters = (unsigned long) tmpspecialcharacters;
  specialcharinfo->wildcards = (unsigned long) tmpwildcards;
  specialcharinfo->specialranges = (unsigned long) tmpspecialranges;
  specialcharinfo->wildcardranges = (unsigned long) tmpwildcardranges;
  specialcharinfo->realspecialranges = (unsigned long) tmprealspecialranges;
  specialcharinfo->realwildcardranges = (unsigned long) tmprealwildcardranges;
  specialcharinfo->lengthofspecialprefix
    = gt_encseq_lengthofspecialprefix(suffixarraytable[0].encseq);
  specialcharinfo->lengthofwildcardprefix
    = gt_encseq_lengthofwildcardprefix(suffixarraytable[0].encseq);
  specialcharinfo->lengthofspecialsuffix
    = gt_encseq_lengthofspecialsuffix(suffixarraytable[idx-1].encseq);
  specialcharinfo->lengthofwildcardsuffix
    = gt_encseq_lengthofwildcardsuffix(suffixarraytable[idx-1].encseq);
  gt_assert(numofsequences > 0);
#ifndef NDEBUG
  gt_GtSpecialcharinfo_check(specialcharinfo,numofsequences - 1);
#endif
  return sequenceoffsettable;
}
genometools-1.5.1/src/match/encseq2offset.pr000066400000000000000000000006041211610345200210410ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
unsigned long *gt_encseqtable2sequenceoffsets(
                                    unsigned long *totallength,
                                    GtSpecialcharinfo *specialcharinfo,
                                    const Suffixarray *suffixarraytable,
                                    unsigned int numofindexes);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/enum-patt.c000066400000000000000000000117551211610345200200160ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/chardef.h"
#include "core/types_api.h"
#include "core/encseq.h"
#include "enum-patt.h"

 struct Enumpatterniterator
{
  unsigned long minpatternlen,
                maxpatternlen,
                samplecount,
                *patternstat;
  GtUchar *patternspace;
  const GtEncseq *sampleencseq;
  unsigned int alphasize;
  unsigned long totallength;
  GtEncseqReader *esr;
};

Enumpatterniterator *gt_newenumpatterniterator(unsigned long minpatternlen,
                                               unsigned long maxpatternlen,
                                               const GtEncseq *encseq,
                                               GtError *err)
{
  Enumpatterniterator *epi = NULL;
  unsigned long i;

  if (maxpatternlen < minpatternlen)
  {
    gt_error_set(err,"maxpatternlen=%lu < %lu",
                    maxpatternlen,
                    minpatternlen);
    return NULL;
  }
  epi = gt_malloc(sizeof *epi);
  epi->totallength = gt_encseq_total_length(encseq);
  if (epi->totallength <= (unsigned long) maxpatternlen)
  {
    gt_error_set(err,"totallength=%lu <= maxpatternlen = %lu",
                    epi->totallength,
                    maxpatternlen);
    gt_free(epi);
    return NULL;
  }
  epi->patternspace = gt_malloc(sizeof *epi->patternspace * maxpatternlen);
  epi->patternstat = gt_malloc(sizeof *epi->patternstat * (maxpatternlen+1));
  for (i=0; i<=maxpatternlen; i++)
  {
    epi->patternstat[i] = 0;
  }
  epi->minpatternlen = minpatternlen;
  epi->maxpatternlen = maxpatternlen;
  epi->sampleencseq = encseq;
  epi->samplecount = 0;
  epi->alphasize = gt_alphabet_num_of_chars(
                                           gt_encseq_alphabet(encseq));
  epi->esr = NULL;
  return epi;
}

static void reversesequenceinplace(GtUchar *s,unsigned long len)
{
  GtUchar *front, *back, tmp;

  for (front = s, back = s + len - 1; front < back; front++, back--)
  {
    tmp = *front;
    *front = *back;
    *back = tmp;
  }
}

const GtUchar *gt_nextEnumpatterniterator(unsigned long *patternlen,
                                       Enumpatterniterator *epi)
{
  unsigned long start;
  unsigned long j;
  GtUchar cc;

  if (epi->minpatternlen == epi->maxpatternlen)
  {
    *patternlen = epi->minpatternlen;
  } else
  {
    *patternlen = (unsigned long) (epi->minpatternlen +
                                   (random() %
                                      (epi->maxpatternlen -
                                       epi->minpatternlen+1)));
  }
  start =
        (unsigned long) (random() % (epi->totallength - *patternlen));
  gt_assert(start < (unsigned long) (epi->totallength - *patternlen));
  if (epi->esr == NULL) {
    epi->esr = gt_encseq_create_reader_with_readmode(epi->sampleencseq,
                                          GT_READMODE_FORWARD,
                                          start);
  } else {
    gt_encseq_reader_reinit_with_readmode(epi->esr, epi->sampleencseq,
                                          GT_READMODE_FORWARD,
                                          start);
  }

  for (j=0; j<*patternlen; j++)
  {
    cc = gt_encseq_reader_next_encoded_char(epi->esr);
    if (ISSPECIAL(cc))
    {
      cc = (GtUchar) (random() % epi->alphasize);
    }
    epi->patternspace[j] = cc;
  }
  if (epi->samplecount & 1)
  {
    reversesequenceinplace(epi->patternspace,*patternlen);
  }
  epi->samplecount++;
  epi->patternstat[*patternlen]++;
  return epi->patternspace;
}

void gt_showPatterndistribution(const Enumpatterniterator *epi)
{
  unsigned long i;
  double addprob, probsum = 0.0;

  printf("# %lu pattern with the following length distribution:\n",
         epi->samplecount);
  for (i=epi->minpatternlen; i<=epi->maxpatternlen; i++)
  {
    if (epi->patternstat[i] > 0)
    {
      addprob = (double) epi->patternstat[i] / epi->samplecount;
      probsum += addprob;
      printf("# %lu: %lu (prob=%.4f,cumulative=%.4f)\n",
             i,
             epi->patternstat[i],
             addprob,
             probsum);
    }
  }
}

void gt_freeEnumpatterniterator(Enumpatterniterator *epi)
{
  if (!epi) return;
  gt_free(epi->patternspace);
  gt_free(epi->patternstat);
  gt_encseq_reader_delete(epi->esr);
  gt_free(epi);
}
genometools-1.5.1/src/match/enum-patt.h000066400000000000000000000027271211610345200200220ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ENUM_PATT_H
#define ENUM_PATT_H

typedef struct Enumpatterniterator Enumpatterniterator;

Enumpatterniterator *gt_newenumpatterniterator(unsigned long minpatternlen,
                                            unsigned long maxpatternlen,
                                            const GtEncseq *encseq,
                                            GtError *err);

const GtUchar *gt_nextEnumpatterniterator(unsigned long *patternlen,
                                     Enumpatterniterator *epi);

void gt_showPatterndistribution(const Enumpatterniterator *epi);

void gt_freeEnumpatterniterator(Enumpatterniterator *epi);

#endif
genometools-1.5.1/src/match/esa-bottomup-errfind.inc000066400000000000000000000211501211610345200224670ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  THIS FILE IS GENERATED by
  scripts/gen-esa-bottomup.rb
  --key errfind
  --reader
  --absolute.
  DO NOT EDIT.
*/

#include 
#include "core/ma.h"
#include "esa-seqread.h"
/* no include for seqnumrelpos.h */

static void initBUinfo_errfind(GtBUinfo_errfind *,GtBUstate_errfind *);

static void freeBUinfo_errfind(GtBUinfo_errfind *,GtBUstate_errfind *);

static int processleafedge_errfind(bool,
    unsigned long,
    GtBUinfo_errfind *,
    unsigned long, /* position */
    GtBUstate_errfind *,
    GtError *err);

static int processbranchingedge_errfind(bool firstsucc,
    unsigned long,
    GtBUinfo_errfind *,
    unsigned long,
    unsigned long,
    GtBUinfo_errfind *,
    GtBUstate_errfind *,
    GtError *);

static int processlcpinterval_errfind(unsigned long,
    GtBUinfo_errfind *,
    GtBUstate_errfind *,
    GtError *err);

#define TOP_ESA_BOTTOMUP_errfind\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1]

#define POP_ESA_BOTTOMUP_errfind\
        (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo))

#define PUSH_ESA_BOTTOMUP_errfind(LCP,LB)\
        if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\
        {\
          gt_assert(stack->nextfreeGtBUItvinfo ==\
                    stack->allocatedGtBUItvinfo);\
          stack->spaceGtBUItvinfo\
            = allocateBUstack_errfind(stack->spaceGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo+incrementstacksize,\
                              bustate);\
          stack->allocatedGtBUItvinfo += incrementstacksize;\
        }\
        gt_assert(stack->spaceGtBUItvinfo != NULL);\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo++].rb = ULONG_MAX

typedef struct
{
  unsigned long lcp, lb, rb;
  GtBUinfo_errfind info;
} GtBUItvinfo_errfind;

typedef struct
{
  GtBUItvinfo_errfind *spaceGtBUItvinfo;
  unsigned long allocatedGtBUItvinfo,
                nextfreeGtBUItvinfo;
} GtArrayGtBUItvinfo_errfind;

GtArrayGtBUItvinfo_errfind *gt_GtArrayGtBUItvinfo_new_errfind(void)
{
  GtArrayGtBUItvinfo_errfind *stack = gt_malloc(sizeof (*stack));

  stack->spaceGtBUItvinfo = NULL;
  stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0;
  return stack;
}

void gt_GtArrayGtBUItvinfo_delete_errfind(GtArrayGtBUItvinfo_errfind *stack,
                                  GtBUstate_errfind *state)
{
  unsigned long idx;

  for (idx=0; idxallocatedGtBUItvinfo; idx++)
  {
    freeBUinfo_errfind(&stack->spaceGtBUItvinfo[idx].info,state);
  }
  gt_free(stack->spaceGtBUItvinfo);
  gt_free(stack);
}

static GtBUItvinfo_errfind *allocateBUstack_errfind(GtBUItvinfo_errfind *ptr,
                                   unsigned long currentallocated,
                                   unsigned long allocated,
                                   GtBUstate_errfind *state)
{
  unsigned long idx;
  GtBUItvinfo_errfind *itvinfo;

  itvinfo = gt_realloc(ptr,sizeof (*itvinfo) * allocated);
  gt_assert(allocated > currentallocated);
  for (idx=currentallocated; idxnextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_errfind.lcp)
    {
      if (TOP_ESA_BOTTOMUP_errfind.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_errfind(firstedge,
                          TOP_ESA_BOTTOMUP_errfind.lcp,
                          &TOP_ESA_BOTTOMUP_errfind.info,
                          previoussuffix,
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_errfind.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_errfind;
      lastinterval->rb = idx;
      if (processlcpinterval_errfind(lastinterval->lcp,
                             &lastinterval->info,
                             bustate,
                             err) != 0)
      {
        haserr = true;
      }
      if (lcpvalue <= TOP_ESA_BOTTOMUP_errfind.lcp)
      {
        if (TOP_ESA_BOTTOMUP_errfind.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (processbranchingedge_errfind(firstedge,
                   TOP_ESA_BOTTOMUP_errfind.lcp,
                   &TOP_ESA_BOTTOMUP_errfind.info,
                   lastinterval->lcp,
                   lastinterval->rb - lastinterval->lb + 1,
                   &lastinterval->info,
                   bustate,
                   err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_errfind.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        unsigned long lastintervallcp = lastinterval->lcp,
              lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP_errfind(lcpvalue,lastintervallb);
        if (processbranchingedge_errfind(true,
                       TOP_ESA_BOTTOMUP_errfind.lcp,
                       &TOP_ESA_BOTTOMUP_errfind.info,
                       lastintervallcp,
                       lastintervalrb - lastintervallb + 1,
                       NULL,
                       bustate,
                       err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_errfind(lcpvalue,idx);
        if (processleafedge_errfind(true,
                            TOP_ESA_BOTTOMUP_errfind.lcp,
                            &TOP_ESA_BOTTOMUP_errfind.info,
                            previoussuffix,
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP_errfind.lcp > 0)
  {
    /* no assignment to lastsuftabvalue */
    if (processleafedge_errfind(false,
                        TOP_ESA_BOTTOMUP_errfind.lcp,
                        &TOP_ESA_BOTTOMUP_errfind.info,
                        lastsuftabvalue,
                        bustate,
                        err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP_errfind.rb = idx;
      if (processlcpinterval_errfind(TOP_ESA_BOTTOMUP_errfind.lcp,
                             &TOP_ESA_BOTTOMUP_errfind.info,
                             bustate,
                             err) != 0)
      {
        haserr = true;
      }
    }
  }
  gt_GtArrayGtBUItvinfo_delete_errfind(stack,bustate);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup-maxpairs.inc000066400000000000000000000204241211610345200226650ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  THIS FILE IS GENERATED by
  scripts/gen-esa-bottomup.rb
  --key maxpairs
  --reader
  --absolute
  --no_process_lcpinterval.
  DO NOT EDIT.
*/

#include 
#include "core/ma.h"
#include "esa-seqread.h"
/* no include for seqnumrelpos.h */

static void initBUinfo_maxpairs(GtBUinfo_maxpairs *,GtBUstate_maxpairs *);

static void freeBUinfo_maxpairs(GtBUinfo_maxpairs *,GtBUstate_maxpairs *);

static int processleafedge_maxpairs(bool,
    unsigned long,
    GtBUinfo_maxpairs *,
    unsigned long, /* position */
    GtBUstate_maxpairs *,
    GtError *err);

static int processbranchingedge_maxpairs(bool firstsucc,
    unsigned long,
    GtBUinfo_maxpairs *,
    unsigned long,
    unsigned long,
    GtBUinfo_maxpairs *,
    GtBUstate_maxpairs *,
    GtError *);

/* no declaration of processlcpinterval_maxpairs */

#define TOP_ESA_BOTTOMUP_maxpairs\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1]

#define POP_ESA_BOTTOMUP_maxpairs\
        (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo))

#define PUSH_ESA_BOTTOMUP_maxpairs(LCP,LB)\
        if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\
        {\
          gt_assert(stack->nextfreeGtBUItvinfo ==\
                    stack->allocatedGtBUItvinfo);\
          stack->spaceGtBUItvinfo\
            = allocateBUstack_maxpairs(stack->spaceGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo+incrementstacksize,\
                              bustate);\
          stack->allocatedGtBUItvinfo += incrementstacksize;\
        }\
        gt_assert(stack->spaceGtBUItvinfo != NULL);\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo++].rb = ULONG_MAX

typedef struct
{
  unsigned long lcp, lb, rb;
  GtBUinfo_maxpairs info;
} GtBUItvinfo_maxpairs;

typedef struct
{
  GtBUItvinfo_maxpairs *spaceGtBUItvinfo;
  unsigned long allocatedGtBUItvinfo,
                nextfreeGtBUItvinfo;
} GtArrayGtBUItvinfo_maxpairs;

GtArrayGtBUItvinfo_maxpairs *gt_GtArrayGtBUItvinfo_new_maxpairs(void)
{
  GtArrayGtBUItvinfo_maxpairs *stack = gt_malloc(sizeof (*stack));

  stack->spaceGtBUItvinfo = NULL;
  stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0;
  return stack;
}

void gt_GtArrayGtBUItvinfo_delete_maxpairs(GtArrayGtBUItvinfo_maxpairs *stack,
                                  GtBUstate_maxpairs *state)
{
  unsigned long idx;

  for (idx=0; idxallocatedGtBUItvinfo; idx++)
  {
    freeBUinfo_maxpairs(&stack->spaceGtBUItvinfo[idx].info,state);
  }
  gt_free(stack->spaceGtBUItvinfo);
  gt_free(stack);
}

static GtBUItvinfo_maxpairs *allocateBUstack_maxpairs(GtBUItvinfo_maxpairs *ptr,
                                   unsigned long currentallocated,
                                   unsigned long allocated,
                                   GtBUstate_maxpairs *state)
{
  unsigned long idx;
  GtBUItvinfo_maxpairs *itvinfo;

  itvinfo = gt_realloc(ptr,sizeof (*itvinfo) * allocated);
  gt_assert(allocated > currentallocated);
  for (idx=currentallocated; idxnextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_maxpairs.lcp)
    {
      if (TOP_ESA_BOTTOMUP_maxpairs.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_maxpairs(firstedge,
                          TOP_ESA_BOTTOMUP_maxpairs.lcp,
                          &TOP_ESA_BOTTOMUP_maxpairs.info,
                          previoussuffix,
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_maxpairs.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_maxpairs;
      lastinterval->rb = idx;
      /* no call to processlcpinterval_maxpairs */
      if (lcpvalue <= TOP_ESA_BOTTOMUP_maxpairs.lcp)
      {
        if (TOP_ESA_BOTTOMUP_maxpairs.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (processbranchingedge_maxpairs(firstedge,
                   TOP_ESA_BOTTOMUP_maxpairs.lcp,
                   &TOP_ESA_BOTTOMUP_maxpairs.info,
                   lastinterval->lcp,
                   lastinterval->rb - lastinterval->lb + 1,
                   &lastinterval->info,
                   bustate,
                   err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_maxpairs.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        unsigned long lastintervallcp = lastinterval->lcp,
              lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP_maxpairs(lcpvalue,lastintervallb);
        if (processbranchingedge_maxpairs(true,
                       TOP_ESA_BOTTOMUP_maxpairs.lcp,
                       &TOP_ESA_BOTTOMUP_maxpairs.info,
                       lastintervallcp,
                       lastintervalrb - lastintervallb + 1,
                       NULL,
                       bustate,
                       err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_maxpairs(lcpvalue,idx);
        if (processleafedge_maxpairs(true,
                            TOP_ESA_BOTTOMUP_maxpairs.lcp,
                            &TOP_ESA_BOTTOMUP_maxpairs.info,
                            previoussuffix,
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP_maxpairs.lcp > 0)
  {
    /* no assignment to lastsuftabvalue */
    if (processleafedge_maxpairs(false,
                        TOP_ESA_BOTTOMUP_maxpairs.lcp,
                        &TOP_ESA_BOTTOMUP_maxpairs.info,
                        lastsuftabvalue,
                        bustate,
                        err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP_maxpairs.rb = idx;
      /* no call to processlcpinterval_maxpairs */
    }
  }
  gt_GtArrayGtBUItvinfo_delete_maxpairs(stack,bustate);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup-rdjce.inc000066400000000000000000000200771211610345200221340ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  THIS FILE IS GENERATED by
  scripts/gen-esa-bottomup.rb
  --key rdjce
  --reader
  --absolute
  --no_process_lcpinterval.
  DO NOT EDIT.
*/

#include 
#include "core/ma.h"
#include "esa-seqread.h"
/* no include for seqnumrelpos.h */

static void initBUinfo_rdjce(GtBUinfo_rdjce *,GtBUstate_rdjce *);

static void freeBUinfo_rdjce(GtBUinfo_rdjce *,GtBUstate_rdjce *);

static int processleafedge_rdjce(bool,
    unsigned long,
    GtBUinfo_rdjce *,
    unsigned long, /* position */
    GtBUstate_rdjce *,
    GtError *err);

static int processbranchingedge_rdjce(bool firstsucc,
    unsigned long,
    GtBUinfo_rdjce *,
    unsigned long,
    unsigned long,
    GtBUinfo_rdjce *,
    GtBUstate_rdjce *,
    GtError *);

/* no declaration of processlcpinterval_rdjce */

#define TOP_ESA_BOTTOMUP_rdjce\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1]

#define POP_ESA_BOTTOMUP_rdjce\
        (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo))

#define PUSH_ESA_BOTTOMUP_rdjce(LCP,LB)\
        if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\
        {\
          gt_assert(stack->nextfreeGtBUItvinfo ==\
                    stack->allocatedGtBUItvinfo);\
          stack->spaceGtBUItvinfo\
            = allocateBUstack_rdjce(stack->spaceGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo+incrementstacksize,\
                              bustate);\
          stack->allocatedGtBUItvinfo += incrementstacksize;\
        }\
        gt_assert(stack->spaceGtBUItvinfo != NULL);\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo++].rb = ULONG_MAX

typedef struct
{
  unsigned long lcp, lb, rb;
  GtBUinfo_rdjce info;
} GtBUItvinfo_rdjce;

typedef struct
{
  GtBUItvinfo_rdjce *spaceGtBUItvinfo;
  unsigned long allocatedGtBUItvinfo,
                nextfreeGtBUItvinfo;
} GtArrayGtBUItvinfo_rdjce;

GtArrayGtBUItvinfo_rdjce *gt_GtArrayGtBUItvinfo_new_rdjce(void)
{
  GtArrayGtBUItvinfo_rdjce *stack = gt_malloc(sizeof (*stack));

  stack->spaceGtBUItvinfo = NULL;
  stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0;
  return stack;
}

void gt_GtArrayGtBUItvinfo_delete_rdjce(GtArrayGtBUItvinfo_rdjce *stack,
                                  GtBUstate_rdjce *state)
{
  unsigned long idx;

  for (idx=0; idxallocatedGtBUItvinfo; idx++)
  {
    freeBUinfo_rdjce(&stack->spaceGtBUItvinfo[idx].info,state);
  }
  gt_free(stack->spaceGtBUItvinfo);
  gt_free(stack);
}

static GtBUItvinfo_rdjce *allocateBUstack_rdjce(GtBUItvinfo_rdjce *ptr,
                                   unsigned long currentallocated,
                                   unsigned long allocated,
                                   GtBUstate_rdjce *state)
{
  unsigned long idx;
  GtBUItvinfo_rdjce *itvinfo;

  itvinfo = gt_realloc(ptr,sizeof (*itvinfo) * allocated);
  gt_assert(allocated > currentallocated);
  for (idx=currentallocated; idxnextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_rdjce.lcp)
    {
      if (TOP_ESA_BOTTOMUP_rdjce.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_rdjce(firstedge,
                          TOP_ESA_BOTTOMUP_rdjce.lcp,
                          &TOP_ESA_BOTTOMUP_rdjce.info,
                          previoussuffix,
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_rdjce.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_rdjce;
      lastinterval->rb = idx;
      /* no call to processlcpinterval_rdjce */
      if (lcpvalue <= TOP_ESA_BOTTOMUP_rdjce.lcp)
      {
        if (TOP_ESA_BOTTOMUP_rdjce.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (processbranchingedge_rdjce(firstedge,
                   TOP_ESA_BOTTOMUP_rdjce.lcp,
                   &TOP_ESA_BOTTOMUP_rdjce.info,
                   lastinterval->lcp,
                   lastinterval->rb - lastinterval->lb + 1,
                   &lastinterval->info,
                   bustate,
                   err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_rdjce.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        unsigned long lastintervallcp = lastinterval->lcp,
              lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP_rdjce(lcpvalue,lastintervallb);
        if (processbranchingedge_rdjce(true,
                       TOP_ESA_BOTTOMUP_rdjce.lcp,
                       &TOP_ESA_BOTTOMUP_rdjce.info,
                       lastintervallcp,
                       lastintervalrb - lastintervallb + 1,
                       NULL,
                       bustate,
                       err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_rdjce(lcpvalue,idx);
        if (processleafedge_rdjce(true,
                            TOP_ESA_BOTTOMUP_rdjce.lcp,
                            &TOP_ESA_BOTTOMUP_rdjce.info,
                            previoussuffix,
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP_rdjce.lcp > 0)
  {
    /* no assignment to lastsuftabvalue */
    if (processleafedge_rdjce(false,
                        TOP_ESA_BOTTOMUP_rdjce.lcp,
                        &TOP_ESA_BOTTOMUP_rdjce.info,
                        lastsuftabvalue,
                        bustate,
                        err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP_rdjce.rb = idx;
      /* no call to processlcpinterval_rdjce */
    }
  }
  gt_GtArrayGtBUItvinfo_delete_rdjce(stack,bustate);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup-rdjcv.inc000066400000000000000000000200771211610345200221550ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  THIS FILE IS GENERATED by
  scripts/gen-esa-bottomup.rb
  --key rdjcv
  --reader
  --absolute
  --no_process_lcpinterval.
  DO NOT EDIT.
*/

#include 
#include "core/ma.h"
#include "esa-seqread.h"
/* no include for seqnumrelpos.h */

static void initBUinfo_rdjcv(GtBUinfo_rdjcv *,GtBUstate_rdjcv *);

static void freeBUinfo_rdjcv(GtBUinfo_rdjcv *,GtBUstate_rdjcv *);

static int processleafedge_rdjcv(bool,
    unsigned long,
    GtBUinfo_rdjcv *,
    unsigned long, /* position */
    GtBUstate_rdjcv *,
    GtError *err);

static int processbranchingedge_rdjcv(bool firstsucc,
    unsigned long,
    GtBUinfo_rdjcv *,
    unsigned long,
    unsigned long,
    GtBUinfo_rdjcv *,
    GtBUstate_rdjcv *,
    GtError *);

/* no declaration of processlcpinterval_rdjcv */

#define TOP_ESA_BOTTOMUP_rdjcv\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1]

#define POP_ESA_BOTTOMUP_rdjcv\
        (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo))

#define PUSH_ESA_BOTTOMUP_rdjcv(LCP,LB)\
        if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\
        {\
          gt_assert(stack->nextfreeGtBUItvinfo ==\
                    stack->allocatedGtBUItvinfo);\
          stack->spaceGtBUItvinfo\
            = allocateBUstack_rdjcv(stack->spaceGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo+incrementstacksize,\
                              bustate);\
          stack->allocatedGtBUItvinfo += incrementstacksize;\
        }\
        gt_assert(stack->spaceGtBUItvinfo != NULL);\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo++].rb = ULONG_MAX

typedef struct
{
  unsigned long lcp, lb, rb;
  GtBUinfo_rdjcv info;
} GtBUItvinfo_rdjcv;

typedef struct
{
  GtBUItvinfo_rdjcv *spaceGtBUItvinfo;
  unsigned long allocatedGtBUItvinfo,
                nextfreeGtBUItvinfo;
} GtArrayGtBUItvinfo_rdjcv;

GtArrayGtBUItvinfo_rdjcv *gt_GtArrayGtBUItvinfo_new_rdjcv(void)
{
  GtArrayGtBUItvinfo_rdjcv *stack = gt_malloc(sizeof (*stack));

  stack->spaceGtBUItvinfo = NULL;
  stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0;
  return stack;
}

void gt_GtArrayGtBUItvinfo_delete_rdjcv(GtArrayGtBUItvinfo_rdjcv *stack,
                                  GtBUstate_rdjcv *state)
{
  unsigned long idx;

  for (idx=0; idxallocatedGtBUItvinfo; idx++)
  {
    freeBUinfo_rdjcv(&stack->spaceGtBUItvinfo[idx].info,state);
  }
  gt_free(stack->spaceGtBUItvinfo);
  gt_free(stack);
}

static GtBUItvinfo_rdjcv *allocateBUstack_rdjcv(GtBUItvinfo_rdjcv *ptr,
                                   unsigned long currentallocated,
                                   unsigned long allocated,
                                   GtBUstate_rdjcv *state)
{
  unsigned long idx;
  GtBUItvinfo_rdjcv *itvinfo;

  itvinfo = gt_realloc(ptr,sizeof (*itvinfo) * allocated);
  gt_assert(allocated > currentallocated);
  for (idx=currentallocated; idxnextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_rdjcv.lcp)
    {
      if (TOP_ESA_BOTTOMUP_rdjcv.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_rdjcv(firstedge,
                          TOP_ESA_BOTTOMUP_rdjcv.lcp,
                          &TOP_ESA_BOTTOMUP_rdjcv.info,
                          previoussuffix,
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_rdjcv.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_rdjcv;
      lastinterval->rb = idx;
      /* no call to processlcpinterval_rdjcv */
      if (lcpvalue <= TOP_ESA_BOTTOMUP_rdjcv.lcp)
      {
        if (TOP_ESA_BOTTOMUP_rdjcv.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (processbranchingedge_rdjcv(firstedge,
                   TOP_ESA_BOTTOMUP_rdjcv.lcp,
                   &TOP_ESA_BOTTOMUP_rdjcv.info,
                   lastinterval->lcp,
                   lastinterval->rb - lastinterval->lb + 1,
                   &lastinterval->info,
                   bustate,
                   err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_rdjcv.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        unsigned long lastintervallcp = lastinterval->lcp,
              lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP_rdjcv(lcpvalue,lastintervallb);
        if (processbranchingedge_rdjcv(true,
                       TOP_ESA_BOTTOMUP_rdjcv.lcp,
                       &TOP_ESA_BOTTOMUP_rdjcv.info,
                       lastintervallcp,
                       lastintervalrb - lastintervallb + 1,
                       NULL,
                       bustate,
                       err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_rdjcv(lcpvalue,idx);
        if (processleafedge_rdjcv(true,
                            TOP_ESA_BOTTOMUP_rdjcv.lcp,
                            &TOP_ESA_BOTTOMUP_rdjcv.info,
                            previoussuffix,
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP_rdjcv.lcp > 0)
  {
    /* no assignment to lastsuftabvalue */
    if (processleafedge_rdjcv(false,
                        TOP_ESA_BOTTOMUP_rdjcv.lcp,
                        &TOP_ESA_BOTTOMUP_rdjcv.info,
                        lastsuftabvalue,
                        bustate,
                        err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP_rdjcv.rb = idx;
      /* no call to processlcpinterval_rdjcv */
    }
  }
  gt_GtArrayGtBUItvinfo_delete_rdjcv(stack,bustate);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup-shulen-RAM.inc000066400000000000000000000213251211610345200227550ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  THIS FILE IS GENERATED by
  scripts/gen-esa-bottomup.rb
  --key shulen
  --gtlcpvaluetypeset
  --absolute
  --no_process_lastvalue
  --no_process_lcpinterval
  --withlastfrompreviousbucket
  --additionaluint32bucket
  --no_declarations.
  DO NOT EDIT.
*/

#include 
#include "core/ma.h"
#include "esa-seqread.h"
/* no include for seqnumrelpos.h */

static int gt_esa_bottomup_RAM_previousfromlast_shulen(
                        unsigned long previoussuffix,
                        unsigned long lcpvalue,
                        GtArrayGtBUItvinfo_shulen *stack,
                        GtBUstate_shulen *bustate,
                        /* no parameter snrp */
                        GtError *err)
{
  const unsigned long incrementstacksize = 32UL;
  unsigned long idx = 0;
  GtBUItvinfo_shulen *lastinterval = NULL;
  bool haserr = false, firstedge,
       firstedgefromroot = bustate->firstedgefromroot;

    gt_assert(stack->nextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_shulen.lcp)
    {
      if (TOP_ESA_BOTTOMUP_shulen.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_shulen(firstedge,
                          TOP_ESA_BOTTOMUP_shulen.lcp,
                          &TOP_ESA_BOTTOMUP_shulen.info,
                          previoussuffix,
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_shulen.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_shulen;
      lastinterval->rb = idx + bustate->idxoffset;
      /* no call to processlcpinterval_shulen */
      if (lcpvalue <= TOP_ESA_BOTTOMUP_shulen.lcp)
      {
        if (TOP_ESA_BOTTOMUP_shulen.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (processbranchingedge_shulen(firstedge,
                   TOP_ESA_BOTTOMUP_shulen.lcp,
                   &TOP_ESA_BOTTOMUP_shulen.info,
                   lastinterval->lcp,
                   lastinterval->rb - lastinterval->lb + 1,
                   &lastinterval->info,
                   bustate,
                   err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_shulen.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        unsigned long lastintervallcp = lastinterval->lcp,
              lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP_shulen(lcpvalue,lastintervallb);
        if (processbranchingedge_shulen(true,
                       TOP_ESA_BOTTOMUP_shulen.lcp,
                       &TOP_ESA_BOTTOMUP_shulen.info,
                       lastintervallcp,
                       lastintervalrb - lastintervallb + 1,
                       NULL,
                       bustate,
                       err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_shulen(lcpvalue,idx + bustate->idxoffset);
        if (processleafedge_shulen(true,
                            TOP_ESA_BOTTOMUP_shulen.lcp,
                            &TOP_ESA_BOTTOMUP_shulen.info,
                            previoussuffix,
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  if (!haserr)
  {
    bustate->firstedgefromroot = firstedgefromroot;
  }
  return haserr ? -1 : 0;
}

static int gt_esa_bottomup_RAM_shulen(const unsigned long *bucketofsuffixes,
                        const uint32_t *bucketofsuffixes_uint32,
                        const GtLcpvaluetype *lcptab_bucket,
                        unsigned long numberofsuffixes,
                        GtArrayGtBUItvinfo_shulen *stack,
                        GtBUstate_shulen *bustate,
                        /* no parameter snrp */
                        GtError *err)
{
  const unsigned long incrementstacksize = 32UL;
  unsigned long lcpvalue,
                previoussuffix,
                idx;
  GtBUItvinfo_shulen *lastinterval = NULL;
  bool haserr = false, firstedge, firstedgefromroot;

  if (bustate->previousbucketlastsuffix == ULONG_MAX)
  {
    PUSH_ESA_BOTTOMUP_shulen(0,0);
    firstedgefromroot = true;
  } else
  {
    firstedgefromroot = bustate->firstedgefromroot;
  }
  gt_assert (numberofsuffixes > 0);
  for (idx = 0; !haserr && idx < numberofsuffixes-1; idx++)
  {
    lcpvalue = (unsigned long) lcptab_bucket[idx+1];
    previoussuffix = bucketofsuffixes != NULL ? bucketofsuffixes[idx]
                                 : (unsigned long)
                                   bucketofsuffixes_uint32[idx];
    gt_assert(stack->nextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_shulen.lcp)
    {
      if (TOP_ESA_BOTTOMUP_shulen.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_shulen(firstedge,
                          TOP_ESA_BOTTOMUP_shulen.lcp,
                          &TOP_ESA_BOTTOMUP_shulen.info,
                          previoussuffix,
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_shulen.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_shulen;
      lastinterval->rb = idx + bustate->idxoffset;
      /* no call to processlcpinterval_shulen */
      if (lcpvalue <= TOP_ESA_BOTTOMUP_shulen.lcp)
      {
        if (TOP_ESA_BOTTOMUP_shulen.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (processbranchingedge_shulen(firstedge,
                   TOP_ESA_BOTTOMUP_shulen.lcp,
                   &TOP_ESA_BOTTOMUP_shulen.info,
                   lastinterval->lcp,
                   lastinterval->rb - lastinterval->lb + 1,
                   &lastinterval->info,
                   bustate,
                   err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_shulen.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        unsigned long lastintervallcp = lastinterval->lcp,
              lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP_shulen(lcpvalue,lastintervallb);
        if (processbranchingedge_shulen(true,
                       TOP_ESA_BOTTOMUP_shulen.lcp,
                       &TOP_ESA_BOTTOMUP_shulen.info,
                       lastintervallcp,
                       lastintervalrb - lastintervallb + 1,
                       NULL,
                       bustate,
                       err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_shulen(lcpvalue,idx + bustate->idxoffset);
        if (processleafedge_shulen(true,
                            TOP_ESA_BOTTOMUP_shulen.lcp,
                            &TOP_ESA_BOTTOMUP_shulen.info,
                            previoussuffix,
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  }
  if (!haserr)
  {
    bustate->previousbucketlastsuffix
      = bucketofsuffixes != NULL ? bucketofsuffixes[numberofsuffixes-1]
                                 : (unsigned long)
                                   bucketofsuffixes_uint32[numberofsuffixes-1];
    bustate->firstedgefromroot = firstedgefromroot;
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup-shulen.inc000066400000000000000000000202061211610345200223350ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  THIS FILE IS GENERATED by
  scripts/gen-esa-bottomup.rb
  --key shulen
  --reader
  --absolute
  --no_process_lcpinterval.
  DO NOT EDIT.
*/

#include 
#include "core/ma.h"
#include "esa-seqread.h"
/* no include for seqnumrelpos.h */

static void initBUinfo_shulen(GtBUinfo_shulen *,GtBUstate_shulen *);

static void freeBUinfo_shulen(GtBUinfo_shulen *,GtBUstate_shulen *);

static int processleafedge_shulen(bool,
    unsigned long,
    GtBUinfo_shulen *,
    unsigned long, /* position */
    GtBUstate_shulen *,
    GtError *err);

static int processbranchingedge_shulen(bool firstsucc,
    unsigned long,
    GtBUinfo_shulen *,
    unsigned long,
    unsigned long,
    GtBUinfo_shulen *,
    GtBUstate_shulen *,
    GtError *);

/* no declaration of processlcpinterval_shulen */

#define TOP_ESA_BOTTOMUP_shulen\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1]

#define POP_ESA_BOTTOMUP_shulen\
        (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo))

#define PUSH_ESA_BOTTOMUP_shulen(LCP,LB)\
        if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\
        {\
          gt_assert(stack->nextfreeGtBUItvinfo ==\
                    stack->allocatedGtBUItvinfo);\
          stack->spaceGtBUItvinfo\
            = allocateBUstack_shulen(stack->spaceGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo+incrementstacksize,\
                              bustate);\
          stack->allocatedGtBUItvinfo += incrementstacksize;\
        }\
        gt_assert(stack->spaceGtBUItvinfo != NULL);\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo++].rb = ULONG_MAX

typedef struct
{
  unsigned long lcp, lb, rb;
  GtBUinfo_shulen info;
} GtBUItvinfo_shulen;

typedef struct
{
  GtBUItvinfo_shulen *spaceGtBUItvinfo;
  unsigned long allocatedGtBUItvinfo,
                nextfreeGtBUItvinfo;
} GtArrayGtBUItvinfo_shulen;

GtArrayGtBUItvinfo_shulen *gt_GtArrayGtBUItvinfo_new_shulen(void)
{
  GtArrayGtBUItvinfo_shulen *stack = gt_malloc(sizeof (*stack));

  stack->spaceGtBUItvinfo = NULL;
  stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0;
  return stack;
}

void gt_GtArrayGtBUItvinfo_delete_shulen(GtArrayGtBUItvinfo_shulen *stack,
                                  GtBUstate_shulen *state)
{
  unsigned long idx;

  for (idx=0; idxallocatedGtBUItvinfo; idx++)
  {
    freeBUinfo_shulen(&stack->spaceGtBUItvinfo[idx].info,state);
  }
  gt_free(stack->spaceGtBUItvinfo);
  gt_free(stack);
}

static GtBUItvinfo_shulen *allocateBUstack_shulen(GtBUItvinfo_shulen *ptr,
                                   unsigned long currentallocated,
                                   unsigned long allocated,
                                   GtBUstate_shulen *state)
{
  unsigned long idx;
  GtBUItvinfo_shulen *itvinfo;

  itvinfo = gt_realloc(ptr,sizeof (*itvinfo) * allocated);
  gt_assert(allocated > currentallocated);
  for (idx=currentallocated; idxnextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_shulen.lcp)
    {
      if (TOP_ESA_BOTTOMUP_shulen.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_shulen(firstedge,
                          TOP_ESA_BOTTOMUP_shulen.lcp,
                          &TOP_ESA_BOTTOMUP_shulen.info,
                          previoussuffix,
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_shulen.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_shulen;
      lastinterval->rb = idx;
      /* no call to processlcpinterval_shulen */
      if (lcpvalue <= TOP_ESA_BOTTOMUP_shulen.lcp)
      {
        if (TOP_ESA_BOTTOMUP_shulen.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (processbranchingedge_shulen(firstedge,
                   TOP_ESA_BOTTOMUP_shulen.lcp,
                   &TOP_ESA_BOTTOMUP_shulen.info,
                   lastinterval->lcp,
                   lastinterval->rb - lastinterval->lb + 1,
                   &lastinterval->info,
                   bustate,
                   err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_shulen.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        unsigned long lastintervallcp = lastinterval->lcp,
              lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP_shulen(lcpvalue,lastintervallb);
        if (processbranchingedge_shulen(true,
                       TOP_ESA_BOTTOMUP_shulen.lcp,
                       &TOP_ESA_BOTTOMUP_shulen.info,
                       lastintervallcp,
                       lastintervalrb - lastintervallb + 1,
                       NULL,
                       bustate,
                       err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_shulen(lcpvalue,idx);
        if (processleafedge_shulen(true,
                            TOP_ESA_BOTTOMUP_shulen.lcp,
                            &TOP_ESA_BOTTOMUP_shulen.info,
                            previoussuffix,
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP_shulen.lcp > 0)
  {
    /* no assignment to lastsuftabvalue */
    if (processleafedge_shulen(false,
                        TOP_ESA_BOTTOMUP_shulen.lcp,
                        &TOP_ESA_BOTTOMUP_shulen.info,
                        lastsuftabvalue,
                        bustate,
                        err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP_shulen.rb = idx;
      /* no call to processlcpinterval_shulen */
    }
  }
  gt_GtArrayGtBUItvinfo_delete_shulen(stack,bustate);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup-spmeq.inc000066400000000000000000000206641211610345200221740ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  THIS FILE IS GENERATED by
  scripts/gen-esa-bottomup.rb
  --key spmeq
  --no_process_lcpinterval.
  DO NOT EDIT.
*/

#include 
#include "core/ma.h"
#include "esa-seqread.h"
#include "seqnumrelpos.h"

static void initBUinfo_spmeq(GtBUinfo_spmeq *,GtBUstate_spmeq *);

static void freeBUinfo_spmeq(GtBUinfo_spmeq *,GtBUstate_spmeq *);

static int processleafedge_spmeq(bool,
    unsigned long,
    GtBUinfo_spmeq *,
    unsigned long, /* seqnum */
    unsigned long, /* relpos */
    GtBUstate_spmeq *,
    GtError *err);

static int processbranchingedge_spmeq(bool firstsucc,
    unsigned long,
    GtBUinfo_spmeq *,
    unsigned long,
    unsigned long,
    GtBUinfo_spmeq *,
    GtBUstate_spmeq *,
    GtError *);

/* no declaration of processlcpinterval_spmeq */

#define TOP_ESA_BOTTOMUP_spmeq\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1]

#define POP_ESA_BOTTOMUP_spmeq\
        (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo))

#define PUSH_ESA_BOTTOMUP_spmeq(LCP,LB)\
        if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\
        {\
          gt_assert(stack->nextfreeGtBUItvinfo ==\
                    stack->allocatedGtBUItvinfo);\
          stack->spaceGtBUItvinfo\
            = allocateBUstack_spmeq(stack->spaceGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo+incrementstacksize,\
                              bustate);\
          stack->allocatedGtBUItvinfo += incrementstacksize;\
        }\
        gt_assert(stack->spaceGtBUItvinfo != NULL);\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo++].rb = ULONG_MAX

typedef struct
{
  unsigned long lcp, lb, rb;
  GtBUinfo_spmeq info;
} GtBUItvinfo_spmeq;

typedef struct
{
  GtBUItvinfo_spmeq *spaceGtBUItvinfo;
  unsigned long allocatedGtBUItvinfo,
                nextfreeGtBUItvinfo;
} GtArrayGtBUItvinfo_spmeq;

GtArrayGtBUItvinfo_spmeq *gt_GtArrayGtBUItvinfo_new_spmeq(void)
{
  GtArrayGtBUItvinfo_spmeq *stack = gt_malloc(sizeof (*stack));

  stack->spaceGtBUItvinfo = NULL;
  stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0;
  return stack;
}

void gt_GtArrayGtBUItvinfo_delete_spmeq(GtArrayGtBUItvinfo_spmeq *stack,
                                  GtBUstate_spmeq *state)
{
  unsigned long idx;

  for (idx=0; idxallocatedGtBUItvinfo; idx++)
  {
    freeBUinfo_spmeq(&stack->spaceGtBUItvinfo[idx].info,state);
  }
  gt_free(stack->spaceGtBUItvinfo);
  gt_free(stack);
}

static GtBUItvinfo_spmeq *allocateBUstack_spmeq(GtBUItvinfo_spmeq *ptr,
                                   unsigned long currentallocated,
                                   unsigned long allocated,
                                   GtBUstate_spmeq *state)
{
  unsigned long idx;
  GtBUItvinfo_spmeq *itvinfo;

  itvinfo = gt_realloc(ptr,sizeof (*itvinfo) * allocated);
  gt_assert(allocated > currentallocated);
  for (idx=currentallocated; idx 0);
  for (idx = 0; !haserr && idx < numberofsuffixes-1; idx++)
  {
    lcpvalue = (unsigned long) lcptab_bucket[idx+1];
    previoussuffix = bucketofsuffixes[idx];
    gt_assert(stack->nextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_spmeq.lcp)
    {
      if (TOP_ESA_BOTTOMUP_spmeq.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_spmeq(firstedge,
                          TOP_ESA_BOTTOMUP_spmeq.lcp,
                          &TOP_ESA_BOTTOMUP_spmeq.info,
                          gt_seqnumrelpos_decode_seqnum(snrp,previoussuffix),
                          gt_seqnumrelpos_decode_relpos(snrp,previoussuffix),
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_spmeq.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_spmeq;
      lastinterval->rb = idx;
      /* no call to processlcpinterval_spmeq */
      if (lcpvalue <= TOP_ESA_BOTTOMUP_spmeq.lcp)
      {
        if (TOP_ESA_BOTTOMUP_spmeq.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (processbranchingedge_spmeq(firstedge,
                   TOP_ESA_BOTTOMUP_spmeq.lcp,
                   &TOP_ESA_BOTTOMUP_spmeq.info,
                   lastinterval->lcp,
                   lastinterval->rb - lastinterval->lb + 1,
                   &lastinterval->info,
                   bustate,
                   err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_spmeq.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        unsigned long lastintervallcp = lastinterval->lcp,
              lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP_spmeq(lcpvalue,lastintervallb);
        if (processbranchingedge_spmeq(true,
                       TOP_ESA_BOTTOMUP_spmeq.lcp,
                       &TOP_ESA_BOTTOMUP_spmeq.info,
                       lastintervallcp,
                       lastintervalrb - lastintervallb + 1,
                       NULL,
                       bustate,
                       err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_spmeq(lcpvalue,idx);
        if (processleafedge_spmeq(true,
                            TOP_ESA_BOTTOMUP_spmeq.lcp,
                            &TOP_ESA_BOTTOMUP_spmeq.info,
                            gt_seqnumrelpos_decode_seqnum(snrp,previoussuffix),
                            gt_seqnumrelpos_decode_relpos(snrp,previoussuffix),
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP_spmeq.lcp > 0)
  {
    unsigned long lastsuftabvalue = bucketofsuffixes[numberofsuffixes-1];
    if (processleafedge_spmeq(false,
                        TOP_ESA_BOTTOMUP_spmeq.lcp,
                        &TOP_ESA_BOTTOMUP_spmeq.info,
                        gt_seqnumrelpos_decode_seqnum(snrp,lastsuftabvalue),
                        gt_seqnumrelpos_decode_relpos(snrp,lastsuftabvalue),
                        bustate,
                        err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP_spmeq.rb = idx;
      /* no call to processlcpinterval_spmeq */
    }
  }
  stack->nextfreeGtBUItvinfo = 0; /* empty the stack */
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup-spmsk.inc000066400000000000000000000176251211610345200222070ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  THIS FILE IS GENERATED by
  scripts/gen-esa-bottomup.rb
  --key spmsk
  --no_process_branchingedge.
  DO NOT EDIT.
*/

#include 
#include "core/ma.h"
#include "esa-seqread.h"
#include "seqnumrelpos.h"

static void initBUinfo_spmsk(GtBUinfo_spmsk *,GtBUstate_spmsk *);

static void freeBUinfo_spmsk(GtBUinfo_spmsk *,GtBUstate_spmsk *);

static int processleafedge_spmsk(bool,
    unsigned long,
    GtBUinfo_spmsk *,
    unsigned long, /* seqnum */
    unsigned long, /* relpos */
    GtBUstate_spmsk *,
    GtError *err);

/* no declaration of processbranchingedge_spmsk */

static int processlcpinterval_spmsk(unsigned long,
    GtBUinfo_spmsk *,
    GtBUstate_spmsk *,
    GtError *err);

#define TOP_ESA_BOTTOMUP_spmsk\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1]

#define POP_ESA_BOTTOMUP_spmsk\
        (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo))

#define PUSH_ESA_BOTTOMUP_spmsk(LCP,LB)\
        if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\
        {\
          gt_assert(stack->nextfreeGtBUItvinfo ==\
                    stack->allocatedGtBUItvinfo);\
          stack->spaceGtBUItvinfo\
            = allocateBUstack_spmsk(stack->spaceGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo+incrementstacksize,\
                              bustate);\
          stack->allocatedGtBUItvinfo += incrementstacksize;\
        }\
        gt_assert(stack->spaceGtBUItvinfo != NULL);\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo++].rb = ULONG_MAX

typedef struct
{
  unsigned long lcp, lb, rb;
  GtBUinfo_spmsk info;
} GtBUItvinfo_spmsk;

typedef struct
{
  GtBUItvinfo_spmsk *spaceGtBUItvinfo;
  unsigned long allocatedGtBUItvinfo,
                nextfreeGtBUItvinfo;
} GtArrayGtBUItvinfo_spmsk;

GtArrayGtBUItvinfo_spmsk *gt_GtArrayGtBUItvinfo_new_spmsk(void)
{
  GtArrayGtBUItvinfo_spmsk *stack = gt_malloc(sizeof (*stack));

  stack->spaceGtBUItvinfo = NULL;
  stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0;
  return stack;
}

void gt_GtArrayGtBUItvinfo_delete_spmsk(GtArrayGtBUItvinfo_spmsk *stack,
                                  GtBUstate_spmsk *state)
{
  unsigned long idx;

  for (idx=0; idxallocatedGtBUItvinfo; idx++)
  {
    freeBUinfo_spmsk(&stack->spaceGtBUItvinfo[idx].info,state);
  }
  gt_free(stack->spaceGtBUItvinfo);
  gt_free(stack);
}

static GtBUItvinfo_spmsk *allocateBUstack_spmsk(GtBUItvinfo_spmsk *ptr,
                                   unsigned long currentallocated,
                                   unsigned long allocated,
                                   GtBUstate_spmsk *state)
{
  unsigned long idx;
  GtBUItvinfo_spmsk *itvinfo;

  itvinfo = gt_realloc(ptr,sizeof (*itvinfo) * allocated);
  gt_assert(allocated > currentallocated);
  for (idx=currentallocated; idx 0);
  for (idx = 0; !haserr && idx < numberofsuffixes-1; idx++)
  {
    lcpvalue = (unsigned long) lcptab_bucket[idx+1];
    previoussuffix = bucketofsuffixes[idx];
    gt_assert(stack->nextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_spmsk.lcp)
    {
      if (TOP_ESA_BOTTOMUP_spmsk.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_spmsk(firstedge,
                          TOP_ESA_BOTTOMUP_spmsk.lcp,
                          &TOP_ESA_BOTTOMUP_spmsk.info,
                          gt_seqnumrelpos_decode_seqnum(snrp,previoussuffix),
                          gt_seqnumrelpos_decode_relpos(snrp,previoussuffix),
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_spmsk.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_spmsk;
      lastinterval->rb = idx;
      if (processlcpinterval_spmsk(lastinterval->lcp,
                             &lastinterval->info,
                             bustate,
                             err) != 0)
      {
        haserr = true;
      }
      if (lcpvalue <= TOP_ESA_BOTTOMUP_spmsk.lcp)
      {
        if (TOP_ESA_BOTTOMUP_spmsk.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        /* no call to processbranchingedge_spmsk */
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_spmsk.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        PUSH_ESA_BOTTOMUP_spmsk(lcpvalue,lastintervallb);
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_spmsk(lcpvalue,idx);
        if (processleafedge_spmsk(true,
                            TOP_ESA_BOTTOMUP_spmsk.lcp,
                            &TOP_ESA_BOTTOMUP_spmsk.info,
                            gt_seqnumrelpos_decode_seqnum(snrp,previoussuffix),
                            gt_seqnumrelpos_decode_relpos(snrp,previoussuffix),
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP_spmsk.lcp > 0)
  {
    unsigned long lastsuftabvalue = bucketofsuffixes[numberofsuffixes-1];
    if (processleafedge_spmsk(false,
                        TOP_ESA_BOTTOMUP_spmsk.lcp,
                        &TOP_ESA_BOTTOMUP_spmsk.info,
                        gt_seqnumrelpos_decode_seqnum(snrp,lastsuftabvalue),
                        gt_seqnumrelpos_decode_relpos(snrp,lastsuftabvalue),
                        bustate,
                        err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP_spmsk.rb = idx;
      if (processlcpinterval_spmsk(TOP_ESA_BOTTOMUP_spmsk.lcp,
                             &TOP_ESA_BOTTOMUP_spmsk.info,
                             bustate,
                             err) != 0)
      {
        haserr = true;
      }
    }
  }
  stack->nextfreeGtBUItvinfo = 0; /* empty the stack */
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup-spmvar.inc000066400000000000000000000216201211610345200223500ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  THIS FILE IS GENERATED by
  scripts/gen-esa-bottomup.rb
  --key spmvar.
  DO NOT EDIT.
*/

#include 
#include "core/ma.h"
#include "esa-seqread.h"
#include "seqnumrelpos.h"

static void initBUinfo_spmvar(GtBUinfo_spmvar *,GtBUstate_spmvar *);

static void freeBUinfo_spmvar(GtBUinfo_spmvar *,GtBUstate_spmvar *);

static int processleafedge_spmvar(bool,
    unsigned long,
    GtBUinfo_spmvar *,
    unsigned long, /* seqnum */
    unsigned long, /* relpos */
    GtBUstate_spmvar *,
    GtError *err);

static int processbranchingedge_spmvar(bool firstsucc,
    unsigned long,
    GtBUinfo_spmvar *,
    unsigned long,
    unsigned long,
    GtBUinfo_spmvar *,
    GtBUstate_spmvar *,
    GtError *);

static int processlcpinterval_spmvar(unsigned long,
    GtBUinfo_spmvar *,
    GtBUstate_spmvar *,
    GtError *err);

#define TOP_ESA_BOTTOMUP_spmvar\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1]

#define POP_ESA_BOTTOMUP_spmvar\
        (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo))

#define PUSH_ESA_BOTTOMUP_spmvar(LCP,LB)\
        if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\
        {\
          gt_assert(stack->nextfreeGtBUItvinfo ==\
                    stack->allocatedGtBUItvinfo);\
          stack->spaceGtBUItvinfo\
            = allocateBUstack_spmvar(stack->spaceGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo+incrementstacksize,\
                              bustate);\
          stack->allocatedGtBUItvinfo += incrementstacksize;\
        }\
        gt_assert(stack->spaceGtBUItvinfo != NULL);\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo++].rb = ULONG_MAX

typedef struct
{
  unsigned long lcp, lb, rb;
  GtBUinfo_spmvar info;
} GtBUItvinfo_spmvar;

typedef struct
{
  GtBUItvinfo_spmvar *spaceGtBUItvinfo;
  unsigned long allocatedGtBUItvinfo,
                nextfreeGtBUItvinfo;
} GtArrayGtBUItvinfo_spmvar;

GtArrayGtBUItvinfo_spmvar *gt_GtArrayGtBUItvinfo_new_spmvar(void)
{
  GtArrayGtBUItvinfo_spmvar *stack = gt_malloc(sizeof (*stack));

  stack->spaceGtBUItvinfo = NULL;
  stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0;
  return stack;
}

void gt_GtArrayGtBUItvinfo_delete_spmvar(GtArrayGtBUItvinfo_spmvar *stack,
                                  GtBUstate_spmvar *state)
{
  unsigned long idx;

  for (idx=0; idxallocatedGtBUItvinfo; idx++)
  {
    freeBUinfo_spmvar(&stack->spaceGtBUItvinfo[idx].info,state);
  }
  gt_free(stack->spaceGtBUItvinfo);
  gt_free(stack);
}

static GtBUItvinfo_spmvar *allocateBUstack_spmvar(GtBUItvinfo_spmvar *ptr,
                                   unsigned long currentallocated,
                                   unsigned long allocated,
                                   GtBUstate_spmvar *state)
{
  unsigned long idx;
  GtBUItvinfo_spmvar *itvinfo;

  itvinfo = gt_realloc(ptr,sizeof (*itvinfo) * allocated);
  gt_assert(allocated > currentallocated);
  for (idx=currentallocated; idx 0);
  for (idx = 0; !haserr && idx < numberofsuffixes-1; idx++)
  {
    lcpvalue = (unsigned long) lcptab_bucket[idx+1];
    previoussuffix = bucketofsuffixes[idx];
    gt_assert(stack->nextfreeGtBUItvinfo > 0);
    if (lcpvalue <= TOP_ESA_BOTTOMUP_spmvar.lcp)
    {
      if (TOP_ESA_BOTTOMUP_spmvar.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (processleafedge_spmvar(firstedge,
                          TOP_ESA_BOTTOMUP_spmvar.lcp,
                          &TOP_ESA_BOTTOMUP_spmvar.info,
                          gt_seqnumrelpos_decode_seqnum(snrp,previoussuffix),
                          gt_seqnumrelpos_decode_relpos(snrp,previoussuffix),
                          bustate,
                          err) != 0)
      {
        haserr = true;
      }
    }
    gt_assert(lastinterval == NULL);
    while (!haserr && lcpvalue < TOP_ESA_BOTTOMUP_spmvar.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP_spmvar;
      lastinterval->rb = idx;
      if (processlcpinterval_spmvar(lastinterval->lcp,
                             &lastinterval->info,
                             bustate,
                             err) != 0)
      {
        haserr = true;
      }
      if (lcpvalue <= TOP_ESA_BOTTOMUP_spmvar.lcp)
      {
        if (TOP_ESA_BOTTOMUP_spmvar.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (processbranchingedge_spmvar(firstedge,
                   TOP_ESA_BOTTOMUP_spmvar.lcp,
                   &TOP_ESA_BOTTOMUP_spmvar.info,
                   lastinterval->lcp,
                   lastinterval->rb - lastinterval->lb + 1,
                   &lastinterval->info,
                   bustate,
                   err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      }
    }
    if (!haserr && lcpvalue > TOP_ESA_BOTTOMUP_spmvar.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallb = lastinterval->lb;
        unsigned long lastintervallcp = lastinterval->lcp,
              lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP_spmvar(lcpvalue,lastintervallb);
        if (processbranchingedge_spmvar(true,
                       TOP_ESA_BOTTOMUP_spmvar.lcp,
                       &TOP_ESA_BOTTOMUP_spmvar.info,
                       lastintervallcp,
                       lastintervalrb - lastintervallb + 1,
                       NULL,
                       bustate,
                       err) != 0)
        {
          haserr = true;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP_spmvar(lcpvalue,idx);
        if (processleafedge_spmvar(true,
                            TOP_ESA_BOTTOMUP_spmvar.lcp,
                            &TOP_ESA_BOTTOMUP_spmvar.info,
                            gt_seqnumrelpos_decode_seqnum(snrp,previoussuffix),
                            gt_seqnumrelpos_decode_relpos(snrp,previoussuffix),
                            bustate,
                            err) != 0)
        {
          haserr = true;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP_spmvar.lcp > 0)
  {
    unsigned long lastsuftabvalue = bucketofsuffixes[numberofsuffixes-1];
    if (processleafedge_spmvar(false,
                        TOP_ESA_BOTTOMUP_spmvar.lcp,
                        &TOP_ESA_BOTTOMUP_spmvar.info,
                        gt_seqnumrelpos_decode_seqnum(snrp,lastsuftabvalue),
                        gt_seqnumrelpos_decode_relpos(snrp,lastsuftabvalue),
                        bustate,
                        err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP_spmvar.rb = idx;
      if (processlcpinterval_spmvar(TOP_ESA_BOTTOMUP_spmvar.lcp,
                             &TOP_ESA_BOTTOMUP_spmvar.info,
                             bustate,
                             err) != 0)
      {
        haserr = true;
      }
    }
  }
  stack->nextfreeGtBUItvinfo = 0; /* empty the stack */
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup.c000066400000000000000000000353361211610345200205240ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "esa-bottomup.h"
#include "esa-seqread.h"
#include "esa_visitor.h"

#define TOP_ESA_BOTTOMUP\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo-1]
#define POP_ESA_BOTTOMUP\
        (stack->spaceGtBUItvinfo + (--stack->nextfreeGtBUItvinfo))

#define PUSH_ESA_BOTTOMUP(LCP,LB)\
        if (stack->nextfreeGtBUItvinfo >= stack->allocatedGtBUItvinfo)\
        {\
          gt_assert(stack->nextfreeGtBUItvinfo == stack->allocatedGtBUItvinfo);\
          stack->spaceGtBUItvinfo\
            = allocateBUstack(stack->spaceGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo,\
                              stack->allocatedGtBUItvinfo+incrementstacksize,\
                              ev);\
          stack->allocatedGtBUItvinfo += incrementstacksize;\
        }\
        gt_assert(stack->spaceGtBUItvinfo != NULL);\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lcp = LCP;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].lb = LB;\
        stack->spaceGtBUItvinfo[stack->nextfreeGtBUItvinfo].rb = ULONG_MAX;\
        stack->nextfreeGtBUItvinfo++

typedef struct
{
  unsigned long lcp, lb, rb;
  GtESAVisitorInfo *info;
} GtBUItvinfo;

struct GtArrayGtBUItvinfo
{
  GtBUItvinfo *spaceGtBUItvinfo;
  unsigned long allocatedGtBUItvinfo,
                nextfreeGtBUItvinfo;
};

GtArrayGtBUItvinfo *gt_GtArrayGtBUItvinfo_new(void)
{
  GtArrayGtBUItvinfo *stack = gt_malloc(sizeof (*stack));

  stack->spaceGtBUItvinfo = NULL;
  stack->allocatedGtBUItvinfo = stack->nextfreeGtBUItvinfo = 0;
  return stack;
}

void gt_GtArrayGtBUItvinfo_delete(GtArrayGtBUItvinfo *stack,
                                  GtESAVisitor *ev)
{
  unsigned long idx;

  for (idx=0; idxallocatedGtBUItvinfo; idx++)
  {
    gt_esa_visitor_info_delete(stack->spaceGtBUItvinfo[idx].info, ev);
  }
  gt_free(stack->spaceGtBUItvinfo);
  gt_free(stack);
}

#ifdef SKDEBUG
static void showstack(const GtBUItvinfo *stackspace,
                      unsigned long nextfreeItvinfo)
{
  unsigned long idx;

  for (idx=0; idx currentallocated);
  for (idx=currentallocated; idx 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (gt_esa_visitor_visit_leaf_edge(ev,
                                         firstedge,
                                         TOP_ESA_BOTTOMUP.lcp,
                                         TOP_ESA_BOTTOMUP.lb,
                                         TOP_ESA_BOTTOMUP.info,
                                         previoussuffix,
                                         err) != 0)
      {
        haserr = true;
        break;
      }
    }
    gt_assert(lastinterval == NULL);
    while (lcpvalue < TOP_ESA_BOTTOMUP.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP;
      lastinterval->rb = idx;
      if (gt_esa_visitor_visit_lcp_interval(ev,
                                            lastinterval->lcp,
                                            lastinterval->lb,
                                            lastinterval->rb,
                                            lastinterval->info,
                                            err) != 0)
      {
        haserr = true;
        break;
      }
      if (lcpvalue <= TOP_ESA_BOTTOMUP.lcp)
      {
        if (TOP_ESA_BOTTOMUP.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (gt_esa_visitor_visit_branching_edge(ev,
                                                firstedge,
                                                TOP_ESA_BOTTOMUP.lcp,
                                                TOP_ESA_BOTTOMUP.lb,
                                                TOP_ESA_BOTTOMUP.info,
                                                lastinterval->lcp,
                                                lastinterval->lb,
                                                lastinterval->rb,
                                                lastinterval->info,
                                                err) != 0)
        {
          haserr = true;
          break;
        }
        lastinterval = NULL;
      }
    }
    if (haserr)
    {
      break;
    }
    if (lcpvalue > TOP_ESA_BOTTOMUP.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallcp = lastinterval->lcp,
                      lastintervallb = lastinterval->lb,
                      lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP(lcpvalue,lastintervallb);
        if (gt_esa_visitor_visit_branching_edge(ev,
                                                true,
                                                TOP_ESA_BOTTOMUP.lcp,
                                                TOP_ESA_BOTTOMUP.lb,
                                                TOP_ESA_BOTTOMUP.info,
                                                lastintervallcp,
                                                lastintervallb,
                                                lastintervalrb,
                                                NULL,
                                                err) != 0)
        {
          haserr = true;
          break;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP(lcpvalue,idx);
        if (gt_esa_visitor_visit_leaf_edge(ev,
                                           true,
                                           TOP_ESA_BOTTOMUP.lcp,
                                           TOP_ESA_BOTTOMUP.lb,
                                           TOP_ESA_BOTTOMUP.info,
                                           previoussuffix,
                                           err) != 0)
        {
          haserr = true;
          break;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP.lcp > 0)
  {
    if (gt_esa_visitor_visit_leaf_edge(ev,
                                       false,
                                       TOP_ESA_BOTTOMUP.lcp,
                                       TOP_ESA_BOTTOMUP.lb,
                                       TOP_ESA_BOTTOMUP.info,
                                       lastsuftabvalue,
                                       err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP.rb = idx;
      if (gt_esa_visitor_visit_lcp_interval(ev,
                                            TOP_ESA_BOTTOMUP.lcp,
                                            TOP_ESA_BOTTOMUP.lb,
                                            TOP_ESA_BOTTOMUP.rb,
                                            TOP_ESA_BOTTOMUP.info,
                                            err) != 0)
      {
        haserr = true;
      }
    }
  }
  gt_GtArrayGtBUItvinfo_delete(stack, ev);
  return haserr ? -1 : 0;
}

int gt_esa_bottomup_RAM(const unsigned long *suftab,
                        const uint16_t *lcptab_bucket,
                        unsigned long nonspecials,
                        GtArrayGtBUItvinfo *stack,
                        GtESAVisitor *ev,
                        GtError *err)
{
  const unsigned long incrementstacksize = 32UL;
  unsigned long lcpvalue,
                previoussuffix = 0,
                idx;
  GtBUItvinfo *lastinterval = NULL;
  bool haserr = false, firstedge, firstedgefromroot = true;

  gt_assert(nonspecials > 0);
  PUSH_ESA_BOTTOMUP(0,0);
  for (idx = 0; idx < nonspecials-1; idx++)
  {
    lcpvalue = (unsigned long) lcptab_bucket[idx+1];
    previoussuffix = suftab[idx];
    if (lcpvalue <= TOP_ESA_BOTTOMUP.lcp)
    {
      if (TOP_ESA_BOTTOMUP.lcp > 0 || !firstedgefromroot)
      {
        firstedge = false;
      } else
      {
        firstedge = true;
        firstedgefromroot = false;
      }
      if (gt_esa_visitor_visit_leaf_edge(ev,
                                         firstedge,
                                         TOP_ESA_BOTTOMUP.lcp,
                                         TOP_ESA_BOTTOMUP.lb,
                                         TOP_ESA_BOTTOMUP.info,
                                         previoussuffix,
                                         err) != 0)
      {
        haserr = true;
        break;
      }
    }
    gt_assert(lastinterval == NULL);
    while (lcpvalue < TOP_ESA_BOTTOMUP.lcp)
    {
      lastinterval = POP_ESA_BOTTOMUP;
      lastinterval->rb = idx;
      if (gt_esa_visitor_visit_lcp_interval(ev,
                                            lastinterval->lcp,
                                            lastinterval->lb,
                                            lastinterval->rb,
                                            lastinterval->info,
                                            err) != 0)
      {
        haserr = true;
        break;
      }
      if (lcpvalue <= TOP_ESA_BOTTOMUP.lcp)
      {
        if (TOP_ESA_BOTTOMUP.lcp > 0 || !firstedgefromroot)
        {
          firstedge = false;
        } else
        {
          firstedge = true;
          firstedgefromroot = false;
        }
        if (gt_esa_visitor_visit_branching_edge(ev,
                                                firstedge,
                                                TOP_ESA_BOTTOMUP.lcp,
                                                TOP_ESA_BOTTOMUP.lb,
                                                TOP_ESA_BOTTOMUP.info,
                                                lastinterval->lcp,
                                                lastinterval->lb,
                                                lastinterval->rb,
                                                lastinterval->info,
                                                err) != 0)
        {
          haserr = true;
          break;
        }
        lastinterval = NULL;
      }
    }
    if (haserr)
    {
      break;
    }
    if (lcpvalue > TOP_ESA_BOTTOMUP.lcp)
    {
      if (lastinterval != NULL)
      {
        unsigned long lastintervallcp = lastinterval->lcp,
                      lastintervallb = lastinterval->lb,
                      lastintervalrb = lastinterval->rb;
        PUSH_ESA_BOTTOMUP(lcpvalue,lastintervallb);
        if (gt_esa_visitor_visit_branching_edge(ev,
                                                true,
                                                TOP_ESA_BOTTOMUP.lcp,
                                                TOP_ESA_BOTTOMUP.lb,
                                                TOP_ESA_BOTTOMUP.info,
                                                lastintervallcp,
                                                lastintervallb,
                                                lastintervalrb,
                                                NULL,
                                                err) != 0)
        {
          haserr = true;
          break;
        }
        lastinterval = NULL;
      } else
      {
        PUSH_ESA_BOTTOMUP(lcpvalue,idx);
        if (gt_esa_visitor_visit_leaf_edge(ev,
                                           true,
                                           TOP_ESA_BOTTOMUP.lcp,
                                           TOP_ESA_BOTTOMUP.lb,
                                           TOP_ESA_BOTTOMUP.info,
                                           previoussuffix,
                                           err) != 0)
        {
          haserr = true;
          break;
        }
      }
    }
  }
  gt_assert(stack->nextfreeGtBUItvinfo > 0);
  if (!haserr && TOP_ESA_BOTTOMUP.lcp > 0)
  {
    unsigned long lastsuftabvalue = suftab[nonspecials-1];
    if (gt_esa_visitor_visit_leaf_edge(ev,
                                       false,
                                       TOP_ESA_BOTTOMUP.lcp,
                                       TOP_ESA_BOTTOMUP.lb,
                                       TOP_ESA_BOTTOMUP.info,
                                       lastsuftabvalue,
                                       err) != 0)
    {
      haserr = true;
    } else
    {
      TOP_ESA_BOTTOMUP.rb = idx;
      if (gt_esa_visitor_visit_lcp_interval(ev,
                                            TOP_ESA_BOTTOMUP.lcp,
                                            TOP_ESA_BOTTOMUP.lb,
                                            TOP_ESA_BOTTOMUP.rb,
                                            TOP_ESA_BOTTOMUP.info,
                                            err) != 0)
      {
        haserr = true;
      }
    }
  }
  stack->nextfreeGtBUItvinfo = 0; /* empty the stack */
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-bottomup.h000066400000000000000000000033031211610345200205160ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_BOTTOMUP_H
#define ESA_BOTTOMUP_H

#include "core/logger_api.h"
#include "core/error_api.h"
#include "esa-seqread.h"
#include "esa_visitor.h"

typedef struct GtBUinfo GtBUinfo;
typedef struct GtBUstate GtBUstate;

typedef struct GtArrayGtBUItvinfo GtArrayGtBUItvinfo;

int gt_esa_bottomup(Sequentialsuffixarrayreader *ssar,
                    GtESAVisitor *ev,
                    GtError *err);

GtArrayGtBUItvinfo *gt_GtArrayGtBUItvinfo_new(void);

void gt_GtArrayGtBUItvinfo_delete(GtArrayGtBUItvinfo *stack,
                                  GtESAVisitor *ev);

int gt_esa_bottomup_RAM(const unsigned long *suftab,
                        const uint16_t *lcptab_bucket,
                        unsigned long nonspecials,
                        GtArrayGtBUItvinfo *stack,
                        GtESAVisitor *ev,
                        GtError *err);

#endif
genometools-1.5.1/src/match/esa-dfs.c000066400000000000000000000206061211610345200174210ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/ma_api.h"
#include "esa-seqread.h"
#include "esa-dfs.h"

#define ABOVETOP  stackspace[nextfreeItvinfo]
#define TOP       stackspace[nextfreeItvinfo-1]
#define BELOWTOP  stackspace[nextfreeItvinfo-2]

#define INCSTACKSIZE  32

#define PUSHDFS(D,B)\
        if (nextfreeItvinfo >= allocatedItvinfo)\
        {\
          gt_assert(nextfreeItvinfo == allocatedItvinfo);\
          stackspace = allocItvinfo(stackspace,\
                                    allocatedItvinfo,\
                                    allocatedItvinfo+INCSTACKSIZE,\
                                    allocateDfsinfo,\
                                    state);\
          allocatedItvinfo += INCSTACKSIZE;\
        }\
        gt_assert(stackspace != NULL);\
        stackspace[nextfreeItvinfo].depth = D;\
        stackspace[nextfreeItvinfo].lastisleafedge = B;\
        nextfreeItvinfo++

typedef struct
{
  bool lastisleafedge;
  unsigned long depth;
  Dfsinfo *dfsinfo;
} Itvinfo;

static Itvinfo *allocItvinfo(Itvinfo *ptr,
                             unsigned long currentallocated,
                             unsigned long allocated,
                             Dfsinfo *(*allocateDfsinfo)(Dfsstate *),
                             Dfsstate *state)
{
  unsigned long i;
  Itvinfo *itvinfo;

  itvinfo = gt_realloc(ptr,sizeof *ptr * allocated);
  if (allocateDfsinfo != NULL)
  {
    gt_assert(allocated > currentallocated);
    for (i=currentallocated; i= 2UL ? BELOWTOP.depth
                                                     : 0,
                              state,err) != 0)
      {
        haserr = true;
        break;
      }
      gt_assert(nextfreeItvinfo > 0);
      nextfreeItvinfo--;
    }
    if (haserr)
    {
      break;
    }
    if (currentlcp == TOP.depth)
    {
      if (firstrootedge && TOP.depth == 0)
      {
        firstedge = true;
        firstrootedge = false;
      } else
      {
        firstedge = false;
      }
      if (TOP.lastisleafedge)
      {
        if (processleafedge != NULL &&
            processleafedge(firstedge,TOP.depth,TOP.dfsinfo,
                            previoussuffix,state,err) != 0)
        {
          haserr = true;
          break;
        }
      } else
      {
        if (!firstedge)
        {
          gt_assert(nextfreeItvinfo < allocatedItvinfo);
        }
        if (processbranchedge != NULL &&
            processbranchedge(firstedge,
                              TOP.depth,
                              TOP.dfsinfo,
                              /*firstedge ? NULL : ABOVETOP.dfsinfo,*/
                              ABOVETOP.dfsinfo,
                              state,
                              err) != 0)
        {
          haserr = true;
          break;
        }
        TOP.lastisleafedge = true;
      }
    } else
    {
      PUSHDFS(currentlcp,true);
      if (BELOWTOP.lastisleafedge)
      {
        if (assignleftmostleaf != NULL)
        {
          assignleftmostleaf(TOP.dfsinfo,currentindex,state);
        }
        if (processleafedge != NULL &&
            processleafedge(true,
                            TOP.depth,
                            TOP.dfsinfo,
                            previoussuffix,
                            state,
                            err) != 0)
        {
          haserr = true;
          break;
        }
        BELOWTOP.lastisleafedge = false;
      } else
      {
        previouslcp = TOP.depth;
        if (processbranchedge != NULL &&
            processbranchedge(true,
                              previouslcp,
                              TOP.dfsinfo,
                              NULL, /* not used since firstsucc = true */
                              state,
                              err) != 0)
        {
          haserr = true;
          break;
        }
      }
    }
    gt_assert(!haserr);
  }
  freeItvinfo(stackspace,
              allocatedItvinfo,
              freeDfsinfo,
              state);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-dfs.h000066400000000000000000000050671211610345200174320ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_DFS_H
#define ESA_DFS_H
#include 
#include "core/error_api.h"
#include "core/unused_api.h"

#include "esa-seqread.h"

typedef struct Dfsinfo Dfsinfo;
typedef struct Dfsstate Dfsstate;

int gt_depthfirstesa(Sequentialsuffixarrayreader *ssar,
                  Dfsinfo *(*allocateDfsinfo)(Dfsstate *),
                  void(*freeDfsinfo)(Dfsinfo *,Dfsstate *),
                  int(*processleafedge)(bool,unsigned long,Dfsinfo *,
                                        unsigned long,Dfsstate *,
                                        GtError *),
                  int(*processbranchedge)(bool,
                                          unsigned long,
                                          Dfsinfo *,
                                          Dfsinfo *,
                                          Dfsstate *,
                                          GtError *),
                  int(*processcompletenode)(unsigned long,
                                            Dfsinfo *,
                                            unsigned long,
                                            Dfsstate *,
                                            GtError *),
                  void(*assignleftmostleaf)(Dfsinfo *,
                                            unsigned long,
                                            Dfsstate *),
                  void(*assignrightmostleaf)(Dfsinfo *,
                                             unsigned long,
                                             unsigned long,
                                             unsigned long,
                                             Dfsstate *),
                  Dfsstate *state,
                  GT_UNUSED GtLogger *logger,
                  GtError *err);

#endif
genometools-1.5.1/src/match/esa-fileend.h000066400000000000000000000036551211610345200202650ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_FILEEND_H
#define ESA_FILEEND_H

/*
  The following defines the suffix of an indexname to be used for an
  reverse complemented index. The length is also defined.
*/

#define RCMSUFFIX         ".rcm"

/*
  The following defines the suffix of an indexname to be used as
  a six frame index. The length is also defined.
*/

#define SIXFRAMESUFFIX    ".6fr"

/*
  The following defines the suffix of a file to store the
  table suftab.
*/

#define SUFTABSUFFIX  ".suf"

/*
  The following defines the suffix of a file to store the
  table lcptab.
*/

#define LCPTABSUFFIX  ".lcp"

/*
  The following defines the suffix of a file to store the
  large lcp table values.
*/

#define LARGELCPTABSUFFIX  ".llv"

/*
  The following defines the suffix of a file to store Burrows and
  Wheeler transform.
*/

#define BWTTABSUFFIX  ".bwt"

/*
  The following defines the suffix of a file to store bucket table.
*/

#define BCKTABSUFFIX  ".bck"

/*
  The following defines the suffix of the project file.
*/

/*
  The following defines the suffix of the project file.
*/

#define PROJECTFILESUFFIX ".prj"

#endif
genometools-1.5.1/src/match/esa-lcpintervals.c000066400000000000000000000241441211610345200213540ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/logger.h"
#include "core/unused_api.h"
#include "lcpinterval.h"
#include "esa-seqread.h"
#include "esa-lcpintervals.h"
#include "esa-dfs.h"
#include "esa-bottomup.h"
#include "esa_lcpintervals_visitor.h"

typedef struct  /* global information */
{
  Lcpinterval lastcompletenode;
  int (*processlcpinterval)(void *,const Lcpinterval *);
  void *processinfo;
} Elcpstate;

static Dfsinfo *allocateDfsinfo_elcp(GT_UNUSED Dfsstate *astate)
{
  return (Dfsinfo *) gt_malloc(sizeof (Lcpinterval));
}

static void freeDfsinfo_elcp(Dfsinfo *adfsinfo,GT_UNUSED Dfsstate *state)
{
  gt_free((Lcpinterval *) adfsinfo);
}

static void showbranchingedgeDFS(bool firstsucc,unsigned long fd,
                                 unsigned long flb,
                                 unsigned long sd,unsigned long slb)
{
  printf("B %c %lu %lu %lu %lu\n",firstsucc ? '1' : '0',fd,flb,sd,slb);
}

static int processleafedge_elcp(bool firstsucc,
                                unsigned long fatherdepth,
                                Dfsinfo *afather,
                                unsigned long leafnumber,
                                GT_UNUSED Dfsstate *astate,
                                GT_UNUSED GtError *err)
{
  Lcpinterval *father = (Lcpinterval *) afather;

  printf("L %c %lu %lu %lu\n",firstsucc ? '1' : '0',
                              fatherdepth,father->left,leafnumber);
  return 0;
}

static int processbranchedge_elcp(bool firstsucc,
                                  unsigned long fatherdepth,
                                  Dfsinfo *afather,
                                  Dfsinfo *ason,
                                  Dfsstate *astate,
                                  GT_UNUSED GtError *err)
{
  Lcpinterval *father = (Lcpinterval *) afather;
  Lcpinterval *son = (Lcpinterval *) ason;
  Elcpstate *state = (Elcpstate *) astate;

  if (son != NULL)
  {
    showbranchingedgeDFS(firstsucc,fatherdepth,father->left,son->offset,
                       son->left);
  } else
  {
    showbranchingedgeDFS(firstsucc,fatherdepth,father->left,
                       state->lastcompletenode.offset,
                       state->lastcompletenode.left);
  }
  return 0;
}

static int processcompletenode_elcp(
                          unsigned long nodeptrdepth,
                          Dfsinfo *anodeptr,
                          GT_UNUSED unsigned long nodeptrminusonedepth,
                          Dfsstate *astate,
                          GT_UNUSED GtError *err)
{
  Lcpinterval *nodeptr = (Lcpinterval *) anodeptr;
  Elcpstate *state = (Elcpstate *) astate;

  gt_assert(state != NULL);
  gt_assert(nodeptr != NULL);
  nodeptr->offset = state->lastcompletenode.offset = nodeptrdepth;
  state->lastcompletenode.left = nodeptr->left;
  state->lastcompletenode.right = nodeptr->right;
  if (state->processlcpinterval != NULL)
  {
    if (state->processlcpinterval(state->processinfo,
                                  &state->lastcompletenode) != 0)
    {
      return -1;
    }
  }
  return 0;
}

static void assignleftmostleaf_elcp(Dfsinfo *adfsinfo,
                                    unsigned long leftmostleaf,
                                    GT_UNUSED Dfsstate *dfsstate)
{
  ((Lcpinterval *) adfsinfo)->left = leftmostleaf;
}

static void assignrightmostleaf_elcp(Dfsinfo *adfsinfo,
                                     unsigned long currentindex,
                                     GT_UNUSED unsigned long previoussuffix,
                                     GT_UNUSED unsigned long currentlcp,
                                     GT_UNUSED Dfsstate *dfsstate)
{
  ((Lcpinterval *) adfsinfo)->right = currentindex;
}

static int gt_enumlcpvalues(bool outedges,
                            Sequentialsuffixarrayreader *ssar,
                            int (*processlcpinterval)(void *,
                                                      const Lcpinterval *),
                            void *processinfo,
                            GtLogger *logger,
                            GtError *err)
{
  Elcpstate *state;
  bool haserr = false;

  state = gt_malloc(sizeof (*state));
  if (outedges)
  {
    state->processlcpinterval = NULL;
    state->processinfo = NULL;
  } else
  {
    state->processlcpinterval = processlcpinterval;
    state->processinfo = processinfo;
  }
  if (gt_depthfirstesa(ssar,
                       allocateDfsinfo_elcp,
                       freeDfsinfo_elcp,
                       outedges ? processleafedge_elcp : NULL,
                       outedges ? processbranchedge_elcp : NULL,
                       processcompletenode_elcp,
                       assignleftmostleaf_elcp,
                       assignrightmostleaf_elcp,
                       (Dfsstate *) state,
                       logger,
                       err) != 0)
  {
    haserr = true;
  }
  if (!haserr && state->processlcpinterval != NULL)
  {
    state->lastcompletenode.offset = 0;
    state->lastcompletenode.left = 0;
    state->lastcompletenode.right
      = gt_Sequentialsuffixarrayreader_totallength(ssar);
    if (state->processlcpinterval(state->processinfo,
                                  &state->lastcompletenode) != 0)
    {
      haserr = true;
    }
  }
  gt_free(state);
  return haserr ? -1 : 0;
}

static int showlcpinterval(GT_UNUSED void *data,const Lcpinterval *lcpinterval)
{
  printf("N %lu %lu %lu\n",lcpinterval->offset,
                           lcpinterval->left,
                           lcpinterval->right);
  return 0;
}

int gt_runenumlcpvalues(const char *inputindex,
                        bool outedges,
                        bool bottomup,
                        GtLogger *logger,
                        GtError *err)
{
  bool haserr = false;
  Sequentialsuffixarrayreader *ssar;

  gt_error_check(err);
  ssar = gt_newSequentialsuffixarrayreaderfromfile(inputindex,
                                                   SARR_LCPTAB |
                                                   SARR_SUFTAB |
                                                   SARR_ESQTAB,
                                                   SEQ_scan,
                                                   logger,
                                                   err);
  if (ssar == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (bottomup)
    {
      GtESAVisitor *elv = gt_esa_lcpitvs_visitor_new();
      if (gt_esa_bottomup(ssar, elv, err) != 0)
      {
        haserr = true;
      }
      gt_esa_visitor_delete(elv);
    } else
    {
      if (gt_enumlcpvalues(outedges, ssar, showlcpinterval, NULL,
                           logger, err) != 0)
      {
        haserr = true;
      }
    }
  }
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  return haserr ? -1 : 0;
}

static int gt_esa_scantables(Sequentialsuffixarrayreader *ssar,
                             unsigned int mode,GtError *err)
{
  unsigned long lcpvalue,
                previoussuffix = 0,
                idx,
                nonspecials,
                sumsuftab = 0,
                sumlcptab = 0;
  bool haserr = false;

  nonspecials = gt_Sequentialsuffixarrayreader_nonspecials(ssar);
  if (mode == 1U)
  {
    for (idx = 0; idx < nonspecials; idx++)
    {
      int retval = gt_nextSequentiallcpvalue(&lcpvalue,ssar,err);

      if (retval < 0)
      {
        haserr = true;
        break;
      }
      if (retval == 0)
      {
        break;
      }
      sumlcptab += lcpvalue; /* silly but guarantees that loop is
                                not eliminated by compiler */
      retval = gt_nextSequentialsuftabvalue(&previoussuffix,ssar);
      gt_assert(retval >= 0);
      if (retval == 0)
      {
        break;
      }
      sumsuftab += previoussuffix; /* silly but guarantees that loop is
                                      not eliminated by compiler */
    }
  } else
  {
    if (mode == 2U)
    {
      for (idx = 0; !haserr && idx < nonspecials; idx++)
      {
        NEXTSEQUENTIALLCPTABVALUE(lcpvalue,ssar);
        sumlcptab += lcpvalue; /* silly but guarantees that loop is
                                  not eliminated by compiler */
        NEXTSEQUENTIALSUFTABVALUE(previoussuffix,ssar);
        sumsuftab += previoussuffix; /* silly but guarantees that loop is
                                        not eliminated by compiler */
      }
    } else
    {
      gt_error_set(err,"illegal mode %u: use 1 or 2",mode);
      haserr = true;
    }
  }
  if (!haserr)
  {
    printf("sumsuftab=%lu\n",sumsuftab);
    printf("sumlcptab=%lu\n",sumlcptab);
  }
  return haserr ? -1 : 0;
}

int gt_runscanesa(const char *inputindex, unsigned int mode,
                  GtLogger *logger,GtError *err)
{
  bool haserr = false;
  Sequentialsuffixarrayreader *ssar;

  gt_error_check(err);
  ssar = gt_newSequentialsuffixarrayreaderfromfile(inputindex,
                                                   SARR_LCPTAB |
                                                   SARR_SUFTAB |
                                                   SARR_ESQTAB,
                                                   SEQ_scan,
                                                   logger,
                                                   err);
  if (ssar == NULL)
  {
    haserr = true;
  }
  if (!haserr && gt_esa_scantables(ssar, mode, err) != 0)
  {
    haserr = true;
  }
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-lcpintervals.h000066400000000000000000000024151211610345200213560ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_LCPINTERVALS_H
#define ESA_LCPINTERVALS_H

#include "core/logger_api.h"
#include "core/error_api.h"

int gt_runenumlcpvalues(const char *inputindex,
                        bool outedges,
                        bool bottomup,
                        GtLogger *logger,
                        GtError *err);

int gt_runscanesa(const char *inputindex, unsigned int mode,
                  GtLogger *logger,GtError *err);

#endif
genometools-1.5.1/src/match/esa-lcpval.c000066400000000000000000000064221211610345200201260ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/unused_api.h"
#include "esa-lcpval.h"

 struct Lcpvalueiterator
{
  unsigned long relpos,
         lastsuftabentry;
  GtReadmode readmode;
  const GtEncseq *encseq;
  GtEncseqReader *esr1, *esr2;
};

Lcpvalueiterator *gt_newLcpvalueiterator(const GtEncseq *encseq,
                                         GtReadmode readmode)
{
  Lcpvalueiterator *lvi;

  lvi = gt_malloc(sizeof *lvi);
  lvi->esr1 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  lvi->esr2 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  lvi->encseq = encseq;
  lvi->relpos = 0;
  lvi->readmode = readmode;
  lvi->lastsuftabentry = 0;
  return lvi;
}

unsigned long gt_nextLcpvalueiterator(Lcpvalueiterator *lvi,
                                      bool firstpage,
                                      const ESASuffixptr *suftabptr,
                                      unsigned long numberofsuffixes)
{
  unsigned long lcpvalue;

  gt_assert(lvi->relpos < numberofsuffixes);
  if (firstpage && lvi->relpos == 0)
  {
    lcpvalue = 0;
  } else
  {
    GT_UNUSED int cmp;

    cmp = gt_encseq_check_comparetwosuffixes(lvi->encseq,
                                             lvi->readmode,
                                             &lcpvalue,
                                             false,
                                             false,
                                             0,
                                             lvi->lastsuftabentry,
                                             ESASUFFIXPTRGET(suftabptr,
                                                             lvi->relpos),
                                             lvi->esr1,
                                             lvi->esr2);
#ifndef NDEBUG
    if (cmp > 0)
    {
      fprintf(stderr,"pos=%lu"
              ": cmp %lu"
              " %lu = %d, lcpval=%lu\n",
              lvi->relpos,
              lvi->lastsuftabentry,
              ESASUFFIXPTRGET(suftabptr,lvi->relpos),
              cmp,
              lcpvalue);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
#endif
  }
  lvi->lastsuftabentry = ESASUFFIXPTRGET(suftabptr,lvi->relpos);
  if (lvi->relpos + 1 == numberofsuffixes)
  {
    lvi->relpos = 0;
  } else
  {
    lvi->relpos++;
  }
  return lcpvalue;
}

void gt_freeLcpvalueiterator(Lcpvalueiterator *lvi)
{
  if (lvi != NULL)
  {
    gt_encseq_reader_delete(lvi->esr1);
    gt_encseq_reader_delete(lvi->esr2);
    gt_free(lvi);
  }
}
genometools-1.5.1/src/match/esa-lcpval.h000066400000000000000000000026771211610345200201430ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_LCPVAL_H
#define ESA_LCPVAL_H

#include "core/readmode.h"
#include "core/encseq.h"
#include "match/sarr-def.h"

typedef struct Lcpvalueiterator Lcpvalueiterator;

Lcpvalueiterator *gt_newLcpvalueiterator(const GtEncseq *encseq,
                                      GtReadmode readmode);

unsigned long gt_nextLcpvalueiterator(Lcpvalueiterator *lvi,
                                      bool firstpage,
                                      const ESASuffixptr *suftabptr,
                                      unsigned long numberofsuffixes);

void gt_freeLcpvalueiterator(Lcpvalueiterator *lvi);

#endif
genometools-1.5.1/src/match/esa-map.c000066400000000000000000000426001211610345200174200ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#include 
#include 
#include 
#include 
#endif
#include "core/fa.h"
#include "core/fileutils.h"
#include "core/array.h"
#include "core/endianess_api.h"
#include "core/error.h"
#include "core/ma_api.h"
#include "core/format64.h"
#include "core/codetype.h"
#include "core/encseq.h"
#include "esa-fileend.h"
#include "esa-scanprj.h"
#include "sarr-def.h"

#define DBFILEKEY "dbfile="

#define INITBufferedfile(INDEXNAME,STREAM,TYPE,SUFFIX)\
        (STREAM)->fp = gt_fa_fopen_with_suffix(INDEXNAME,SUFFIX,"rb",err);\
        if ((STREAM)->fp == NULL)\
        {\
          haserr = true;\
          (STREAM)->bufferedfilespace = NULL;\
        } else\
        {\
          (STREAM)->nextread = 0;\
          (STREAM)->nextfree = 0;\
          (STREAM)->bufferedfilespace\
            = gt_malloc(sizeof *((STREAM)->bufferedfilespace)\
                        * (FILEBUFFERSIZE));\
        }

static int scanprjfileuintkeysviafileptr(Suffixarray *suffixarray,
                                         const char *indexname,
                                         GtLogger *logger,
                                         FILE *fpin,
                                         GtError *err)
{
  uint32_t integersize, littleendian, readmodeint, mirrored;
  unsigned int linenum;
  unsigned long currentlinelength;
  Definedunsignedlong maxbranchdepth;
  size_t dbfilelen = strlen(DBFILEKEY);
  bool haserr = false;
  GtScannedprjkeytable *scannedprjkeytable;
  GtStr *currentline;
  /* the following five variables are local as the parsed values are
     not required: they are determined by reading the encseq */
  GtSpecialcharinfo specialcharinfo;
  unsigned long totallength,
                numofsequences,
                numofdbsequences,
                numofquerysequences;

  gt_error_check(err);
  scannedprjkeytable = gt_scannedprjkeytable_new();
  GT_SCANNEDPRJKEY_ADD("totallength",&totallength,NULL);
  GT_SCANNEDPRJKEY_ADD("specialcharacters",
                       &specialcharinfo.specialcharacters,NULL);
  GT_SCANNEDPRJKEY_ADD("specialranges",
                       &specialcharinfo.specialranges,NULL);
  GT_SCANNEDPRJKEY_ADD("realspecialranges",
                       &specialcharinfo.realspecialranges,NULL);
  GT_SCANNEDPRJKEY_ADD("lengthofspecialprefix",
                       &specialcharinfo.lengthofspecialprefix,NULL);
  GT_SCANNEDPRJKEY_ADD("lengthofspecialsuffix",
                       &specialcharinfo.lengthofspecialsuffix,NULL);
  GT_SCANNEDPRJKEY_ADD("wildcards",
                       &specialcharinfo.wildcards,NULL);
  GT_SCANNEDPRJKEY_ADD("wildcardranges",
                       &specialcharinfo.wildcardranges,NULL);
  GT_SCANNEDPRJKEY_ADD("realwildcardranges",
                       &specialcharinfo.realwildcardranges,NULL);
  GT_SCANNEDPRJKEY_ADD("lengthofwildcardprefix",
                       &specialcharinfo.lengthofwildcardprefix,NULL);
  GT_SCANNEDPRJKEY_ADD("lengthofwildcardsuffix",
                       &specialcharinfo.lengthofwildcardsuffix,NULL);
  GT_SCANNEDPRJKEY_ADD("numofsequences",&numofsequences,NULL);
  GT_SCANNEDPRJKEY_ADD("numofdbsequences",&numofdbsequences,NULL);
  gt_scannedprjkey_add(scannedprjkeytable,"numofquerysequences",
                       &numofquerysequences,0,false,NULL);
  GT_SCANNEDPRJKEY_ADD("numberofallsortedsuffixes",
                       &suffixarray->numberofallsortedsuffixes,NULL);
  GT_SCANNEDPRJKEY_ADD("longest",&suffixarray->longest.valueunsignedlong,
                       &suffixarray->longest.defined);
  GT_SCANNEDPRJKEY_ADD("prefixlength",&suffixarray->prefixlength,NULL);
  GT_SCANNEDPRJKEY_ADD("largelcpvalues",
                       &suffixarray->numoflargelcpvalues.valueunsignedlong,
                       &suffixarray->numoflargelcpvalues.defined);
  gt_scannedprjkey_add(scannedprjkeytable,"averagelcp",
                       &suffixarray->averagelcp.valuedouble,
                       sizeof (suffixarray->averagelcp.valuedouble),
                       true,
                       &suffixarray->averagelcp.defined);
  GT_SCANNEDPRJKEY_ADD("maxbranchdepth",&maxbranchdepth.valueunsignedlong,
                       &maxbranchdepth.defined);
  GT_SCANNEDPRJKEY_ADD("integersize",&integersize,NULL);
  GT_SCANNEDPRJKEY_ADD("littleendian",&littleendian,NULL);
  GT_SCANNEDPRJKEY_ADD("readmode",&readmodeint,NULL);
  GT_SCANNEDPRJKEY_ADD("mirrored",&mirrored,NULL);
  currentline = gt_str_new();
  for (linenum = 0; gt_str_read_next_line(currentline, fpin) != EOF; linenum++)
  {
    currentlinelength = gt_str_length(currentline);
    if (dbfilelen <= (size_t) currentlinelength &&
        memcmp(DBFILEKEY,gt_str_get(currentline),dbfilelen) == 0)
    {
      /* Nothing */
    } else
    {
      if (gt_scannedprjkey_analyze(indexname,
                                   PROJECTFILESUFFIX,
                                   linenum,
                                   gt_str_get(currentline),
                                   currentlinelength,
                                   scannedprjkeytable,
                                   err) != 0)
      {
        haserr = true;
        break;
      }
    }
    gt_str_reset(currentline);
  }
  gt_str_delete(currentline);
  if (!haserr && gt_scannedprjkey_allkeysdefined(indexname,PROJECTFILESUFFIX,
                                                 scannedprjkeytable,
                                                 logger,err) != 0)
  {
    haserr = true;
  }
  if (!haserr && integersize != (uint32_t) 32 && integersize != (uint32_t) 64)
  {
    gt_error_set(err,"%s%s contains illegal line defining the integer size",
                 indexname,PROJECTFILESUFFIX);
    haserr = true;
  }
  if (!haserr && integersize != (uint32_t) (sizeof (unsigned long) * CHAR_BIT))
  {
    gt_error_set(err,"index was generated for %u-bit integers while "
                      "this program uses %u-bit integers",
                      (unsigned int) integersize,
                      (unsigned int) (sizeof (unsigned long) * CHAR_BIT));
    haserr = true;
  }
  if (!haserr)
  {
    if (gt_is_little_endian())
    {
      if (littleendian != (uint32_t) 1)
      {
        gt_error_set(err,"computer has little endian byte order, while index "
                         "was built on computer with big endian byte order");
        haserr = true;
      }
    } else
    {
      if (littleendian == (uint32_t) 1)
      {
        gt_error_set(err,"computer has big endian byte order, while index "
                         "was built on computer with little endian byte "
                         "order");
        haserr = true;
      }
    }
  }
  if (!haserr)
  {
    if (readmodeint > (uint32_t) 3)
    {
      gt_error_set(err,"illegal readmode %u",(unsigned int) readmodeint);
      haserr = true;
    }
    suffixarray->readmode = (GtReadmode) readmodeint;
  }
  if (!haserr)
  {
    if (mirrored > (uint32_t) 1)
    {
      gt_error_set(err,"illegal mirroring flag: only 0(=no mirroring) and "
                       "1 (=mirroring) is supported, but read %u",
                       (unsigned int) mirrored);
      haserr = true;
    }
    suffixarray->mirroredencseq = (mirrored == (uint32_t) 1);
  }
  gt_scannedprjkeytable_delete(scannedprjkeytable);
  return haserr ? -1 : 0;
}

static void initsuffixarray(Suffixarray *suffixarray)
{
  suffixarray->encseq = NULL;
  suffixarray->suftab = NULL;
  suffixarray->lcptab = NULL;
  suffixarray->llvtab = NULL;
  suffixarray->bwttab = NULL;
  suffixarray->bcktab = NULL;
  suffixarray->bwttabstream.fp = NULL;
  suffixarray->bwttabstream.bufferedfilespace = NULL;
  suffixarray->suftabstream_GtUlong.fp = NULL;
  suffixarray->suftabstream_GtUlong.bufferedfilespace = NULL;
#ifdef _LP64
  suffixarray->suftabstream_uint32_t.fp = NULL;
  suffixarray->suftabstream_uint32_t.bufferedfilespace = NULL;
#endif
  suffixarray->lcptabstream.fp = NULL;
  suffixarray->lcptabstream.bufferedfilespace = NULL;
  suffixarray->llvtabstream.fp = NULL;
  suffixarray->llvtabstream.bufferedfilespace = NULL;
  suffixarray->numberofallsortedsuffixes = 0;
}

static bool scanprjfileuintkeys(Suffixarray *suffixarray,
                                const char *indexname,
                                GtLogger *logger,
                                GtError *err)
{
  bool haserr = false;
  FILE *fp;

  gt_error_check(err);
  fp = gt_fa_fopen_with_suffix(indexname,PROJECTFILESUFFIX,"rb",err);
  if (fp == NULL)
  {
    haserr = true;
  }
  if (!haserr && scanprjfileuintkeysviafileptr(suffixarray,
                                               indexname,logger,
                                               fp,err) != 0)
  {
    haserr = true;
  }
  gt_fa_xfclose(fp);
  return haserr;
}

void gt_freesuffixarray(Suffixarray *suffixarray)
{
  gt_fa_xmunmap((void *) suffixarray->suftab);
  suffixarray->suftab = NULL;
  gt_fa_xmunmap((void *) suffixarray->lcptab);
  suffixarray->lcptab = NULL;
  gt_fa_xmunmap((void *) suffixarray->llvtab);
  suffixarray->llvtab = NULL;
  gt_fa_xmunmap((void *) suffixarray->bwttab);
  suffixarray->bwttab = NULL;
  gt_fa_xfclose(suffixarray->suftabstream_GtUlong.fp);
  suffixarray->suftabstream_GtUlong.fp = NULL;
  gt_free(suffixarray->suftabstream_GtUlong.bufferedfilespace);
#ifdef _LP64
  gt_fa_xfclose(suffixarray->suftabstream_uint32_t.fp);
  suffixarray->suftabstream_uint32_t.fp = NULL;
  gt_free(suffixarray->suftabstream_uint32_t.bufferedfilespace);
#endif
  gt_fa_xfclose(suffixarray->lcptabstream.fp);
  suffixarray->lcptabstream.fp = NULL;
  gt_free(suffixarray->lcptabstream.bufferedfilespace);
  gt_fa_xfclose(suffixarray->llvtabstream.fp);
  suffixarray->llvtabstream.fp = NULL;
  gt_free(suffixarray->llvtabstream.bufferedfilespace);
  gt_fa_xfclose(suffixarray->bwttabstream.fp);
  suffixarray->bwttabstream.fp = NULL;
  gt_free(suffixarray->bwttabstream.bufferedfilespace);
  gt_encseq_delete(suffixarray->encseq);
  suffixarray->encseq = NULL;
  if (suffixarray->bcktab != NULL)
  {
    gt_bcktab_delete(suffixarray->bcktab);
    suffixarray->bcktab = NULL;
  }
}

static int inputsuffixarray(bool map,
                            Suffixarray *suffixarray,
                            unsigned int demand,
                            const char *indexname,
                            GtLogger *logger,
                            GtError *err)
{
  bool haserr = false;
  GtEncseqLoader *el;
  unsigned long totallength = 0;

  gt_error_check(err);
  initsuffixarray(suffixarray);
  el = gt_encseq_loader_new();
  if (!(demand & SARR_DESTAB))
    gt_encseq_loader_do_not_require_des_tab(el);
  else
    gt_encseq_loader_require_des_tab(el);
  if (!(demand & SARR_SDSTAB))
    gt_encseq_loader_do_not_require_sds_tab(el);
  else
    gt_encseq_loader_require_sds_tab(el);
  if (!(demand & SARR_SSPTAB))
    gt_encseq_loader_do_not_require_ssp_tab(el);
  else
    gt_encseq_loader_require_ssp_tab(el);
  gt_encseq_loader_set_logger(el, logger);
  suffixarray->encseq = gt_encseq_loader_load(el, indexname, err);
  gt_encseq_loader_delete(el);
  if (suffixarray->encseq == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    haserr = scanprjfileuintkeys(suffixarray,indexname,logger,err);
  }
  if (!haserr
        && suffixarray->mirroredencseq
        && !gt_encseq_is_mirrored(suffixarray->encseq))
  {
    if (gt_encseq_mirror(suffixarray->encseq, err) != 0)
      haserr = true;
  }
  if (!haserr)
  {
    totallength = gt_encseq_total_length(suffixarray->encseq);
  }
  if (!haserr && (demand & SARR_SUFTAB))
  {
    if (map)
    {
      if (suffixarray->numberofallsortedsuffixes > 0)
      {
        suffixarray->suftab
          = gt_fa_mmap_check_size_with_suffix(indexname,
                                       SUFTABSUFFIX,
                                       suffixarray->numberofallsortedsuffixes,
                                       sizeof (*suffixarray->suftab),
                                       err);
        if (suffixarray->suftab == NULL)
        {
          haserr = true;
        }
      }
    } else
    {
#ifdef _LP64
      off_t filesize = gt_file_size_with_suffix(indexname,SUFTABSUFFIX);

      if (filesize == (off_t) sizeof (uint32_t) *
                              suffixarray->numberofallsortedsuffixes)
      {
        gt_logger_log(logger,"read suftab in units of 4 bytes");
        INITBufferedfile(indexname,&suffixarray->suftabstream_uint32_t,uint32_t,
                         SUFTABSUFFIX);
      } else
      {
        gt_logger_log(logger,"read suftab in units of 8 bytes");
        INITBufferedfile(indexname,&suffixarray->suftabstream_GtUlong,GtUlong,
                         SUFTABSUFFIX);
      }
#else
      gt_logger_log(logger,"read suftab in units of 4 bytes");
      INITBufferedfile(indexname,&suffixarray->suftabstream_GtUlong,GtUlong,
                       SUFTABSUFFIX);
#endif
    }
    if (!haserr && !suffixarray->longest.defined)
    {
      gt_error_set(err,"longest not defined");
      haserr = true;
    }
  }
  if (!haserr && (demand & SARR_LCPTAB))
  {
    if (map)
    {
      if (suffixarray->numberofallsortedsuffixes > 0)
      {
        suffixarray->lcptab
          = gt_fa_mmap_check_size_with_suffix(indexname,
                                         LCPTABSUFFIX,
                                         suffixarray->numberofallsortedsuffixes,
                                         sizeof (*suffixarray->lcptab),
                                         err);
        if (suffixarray->lcptab == NULL)
        {
          haserr = true;
        }
      }
    } else
    {
      INITBufferedfile(indexname,&suffixarray->lcptabstream,GtUchar,
                       LCPTABSUFFIX);
      if (!haserr &&
          fseek(suffixarray->lcptabstream.fp,(long) sizeof (GtUchar),SEEK_SET))
      {
        gt_error_set(err,"fseek(esastream) failed: %s",strerror(errno));
        haserr = true;
      }
    }
    if (!haserr && !suffixarray->numoflargelcpvalues.defined)
    {
      gt_error_set(err,"numoflargelcpvalues not defined");
      haserr = true;
    }
    if (!haserr && suffixarray->numoflargelcpvalues.valueunsignedlong > 0)
    {
      if (map)
      {
        suffixarray->llvtab
          = gt_fa_mmap_check_size_with_suffix(indexname,
                                           LARGELCPTABSUFFIX,
                                           (unsigned long)
                                           suffixarray->numoflargelcpvalues.
                                           valueunsignedlong,
                                           sizeof (*suffixarray->llvtab),
                                           err);
        if (suffixarray->llvtab == NULL)
        {
          haserr = true;
        }
      } else
      {
        INITBufferedfile(indexname,&suffixarray->llvtabstream,Largelcpvalue,
                         LARGELCPTABSUFFIX);
      }
    }
  }
  if (!haserr && (demand & SARR_BWTTAB))
  {
    if (map)
    {
      suffixarray->bwttab
        = gt_fa_mmap_check_size_with_suffix(indexname,
                                         BWTTABSUFFIX,
                                         totallength+1,
                                         sizeof (*suffixarray->bwttab),
                                         err);
      if (suffixarray->bwttab == NULL)
      {
        haserr = true;
      }
    } else
    {
      INITBufferedfile(indexname,&suffixarray->bwttabstream,GtUchar,
                       BWTTABSUFFIX);
    }
  }
  if (!haserr && (demand & SARR_BCKTAB))
  {
    suffixarray->bcktab
      = gt_bcktab_map(indexname,
                      gt_encseq_alphabetnumofchars(suffixarray->encseq),
                      suffixarray->prefixlength,
                      totallength+1,
                      true,
                      err);
    if (suffixarray->bcktab == NULL)
    {
      haserr = true;
    }
  }
  if (haserr)
  {
    gt_freesuffixarray(suffixarray);
  }
  return haserr ? -1 : 0;
}

int streamsuffixarray(Suffixarray *suffixarray,
                      unsigned int demand,
                      const char *indexname,
                      GtLogger *logger,
                      GtError *err)
{
  gt_error_check(err);
  return inputsuffixarray(false,
                          suffixarray,
                          demand,
                          indexname,
                          logger,
                          err);
}

int gt_mapsuffixarray(Suffixarray *suffixarray,
                      unsigned int demand,
                      const char *indexname,
                      GtLogger *logger,
                      GtError *err)
{
  gt_error_check(err);
  /* printf("sizeof (Suffixarray)=%lu\n",sizeof (Suffixarray)); */
  return inputsuffixarray(true,
                          suffixarray,
                          demand,
                          indexname,
                          logger,
                          err);
}
genometools-1.5.1/src/match/esa-map.h000066400000000000000000000026051211610345200174260ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_MAP_H
#define ESA_MAP_H
#include "sarr-def.h"

#include "core/logger.h"

void gt_freesuffixarray(Suffixarray *suffixarray);

int streamsuffixarray(Suffixarray *suffixarray,
                      unsigned int demand,
                      const char *indexname,
                      GtLogger *logger,
                      GtError *err);

int gt_mapsuffixarray(Suffixarray *suffixarray,
                   unsigned int demand,
                   const char *indexname,
                   GtLogger *logger,
                   GtError *err);

#endif
genometools-1.5.1/src/match/esa-maxpairs.c000066400000000000000000000272641211610345200205000ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/arraydef.h"
#include "core/unused_api.h"
#include "esa-seqread.h"
#include "esa-maxpairs.h"

#define ISLEFTDIVERSE   (GtUchar) (state->alphabetsize)
#define INITIALCHAR     (GtUchar) (state->alphabetsize+1)

#define CHECKCHAR(CC)\
        if (father->commonchar != (CC) || (CC) >= ISLEFTDIVERSE)\
        {\
          father->commonchar = ISLEFTDIVERSE;\
        }

#define NODEPOSLISTENTRY(NN,SYM)\
        (NN)->nodeposlist[SYM]

#define NODEPOSLISTLENGTH(NN,SYM)\
        NODEPOSLISTENTRY(NN,SYM).length

#define NODEPOSLISTSTART(NN,SYM)\
        NODEPOSLISTENTRY(NN,SYM).start

typedef struct
{
  unsigned long start,
                length;
} Listtype;

typedef struct /* information stored for each node of the lcp interval tree */
{
  GtUchar commonchar;
  unsigned long uniquecharposstart,
                uniquecharposlength; /* uniquecharpos[start..start+len-1] */
  Listtype *nodeposlist;
} GtBUinfo_maxpairs;

typedef struct  /* global information */
{
  bool initialized;
  unsigned int searchlength,
               alphabetsize;
  GtArrayGtUlong uniquechar,
              *poslist;
  const GtEncseq *encseq;
  GtReadmode readmode;
  Processmaxpairs processmaxpairs;
  void *processmaxpairsinfo;
} GtBUstate_maxpairs;

static void initBUinfo_maxpairs(GtBUinfo_maxpairs *buinfo,
                                GtBUstate_maxpairs *state)
{
  buinfo->nodeposlist = gt_malloc(sizeof (*buinfo->nodeposlist) *
                                  state->alphabetsize);
}

static void freeBUinfo_maxpairs(GtBUinfo_maxpairs *buinfo,
                                GT_UNUSED GtBUstate_maxpairs *state)
{
  gt_free(buinfo->nodeposlist);
}

static void add2poslist_maxpairs(GtBUstate_maxpairs *state,
                                 GtBUinfo_maxpairs *ninfo,
                                 unsigned int base,unsigned long leafnumber)
{
  GtArrayGtUlong *ptr;

  if (base >= state->alphabetsize)
  {
    ninfo->uniquecharposlength++;
    GT_STOREINARRAY(&state->uniquechar,GtUlong,4,leafnumber);
  } else
  {
    ptr = &state->poslist[base];
    GT_STOREINARRAY(ptr,GtUlong,4,leafnumber);
    NODEPOSLISTLENGTH(ninfo,base)++;
  }
}

static void concatlists_maxpairs(GtBUstate_maxpairs *state,
                                 GtBUinfo_maxpairs *father,
                                 GtBUinfo_maxpairs *son)
{
  unsigned int base;

  for (base = 0; base < state->alphabetsize; base++)
  {
    NODEPOSLISTLENGTH(father,base) += NODEPOSLISTLENGTH(son,base);
  }
  father->uniquecharposlength += son->uniquecharposlength;
}

static int cartproduct1_maxpairs(GtBUstate_maxpairs *state,
                                 unsigned long fatherdepth,
                                 const GtBUinfo_maxpairs *ninfo,
                                 unsigned int base,
                                 unsigned long leafnumber,GtError *err)
{
  Listtype *pl;
  unsigned long *spptr, *start;

  pl = &NODEPOSLISTENTRY(ninfo,base);
  start = state->poslist[base].spaceGtUlong + pl->start;
  for (spptr = start; spptr < start + pl->length; spptr++)
  {
    if (state->processmaxpairs(state->processmaxpairsinfo,state->encseq,
                               fatherdepth,leafnumber,*spptr,err) != 0)
    {
      return -1;
    }
  }
  return 0;
}

static int cartproduct2_maxpairs(GtBUstate_maxpairs *state,
                                 unsigned long fatherdepth,
                                 const GtBUinfo_maxpairs *ninfo1,
                                 unsigned int base1,
                                 const GtBUinfo_maxpairs *ninfo2,
                                 unsigned int base2,
                                 GtError *err)
{
  Listtype *pl1, *pl2;
  unsigned long *start1, *start2, *spptr1, *spptr2;

  pl1 = &NODEPOSLISTENTRY(ninfo1,base1);
  start1 = state->poslist[base1].spaceGtUlong + pl1->start;
  pl2 = &NODEPOSLISTENTRY(ninfo2,base2);
  start2 = state->poslist[base2].spaceGtUlong + pl2->start;
  for (spptr1 = start1; spptr1 < start1 + pl1->length; spptr1++)
  {
    for (spptr2 = start2; spptr2 < start2 + pl2->length; spptr2++)
    {
      if (state->processmaxpairs(state->processmaxpairsinfo,state->encseq,
                                 fatherdepth,*spptr1,*spptr2,err) != 0)
      {
        return -1;
      }
    }
  }
  return 0;
}

static void setpostabto0_maxpairs(GtBUstate_maxpairs *state)
{
  unsigned int base;

  if (!state->initialized)
  {
    for (base = 0; base < state->alphabetsize; base++)
    {
      state->poslist[base].nextfreeGtUlong = 0;
    }
    state->uniquechar.nextfreeGtUlong = 0;
    state->initialized = true;
  }
}

static int processleafedge_maxpairs(bool firstsucc,
                                    unsigned long fatherdepth,
                                    GtBUinfo_maxpairs *father,
                                    unsigned long leafnumber,
                                    GtBUstate_maxpairs *state,
                                    GtError *err)
{
  unsigned int base;
  unsigned long *start, *spptr;
  GtUchar leftchar;

#ifdef SKDEBUG
  printf("%s %lu firstsucc=%s, __func__," " depth(father)= %lu\n",
         leafnumber,
         firstsucc ? "true" : "false",
         fatherdepth);
#endif
  if (fatherdepth < (unsigned long) state->searchlength)
  {
    setpostabto0_maxpairs(state);
    return 0;
  }
  if (leafnumber == 0)
  {
    leftchar = INITIALCHAR;
  } else
  {
    /* Random access */
    leftchar = gt_encseq_get_encoded_char(state->encseq,
                                          leafnumber-1,
                                          state->readmode);
  }
  state->initialized = false;
#ifdef SKDEBUG
  printf("%s: leftchar %u\n",__func__,(unsigned int) leftchar);
#endif
  if (firstsucc)
  {
    father->commonchar = leftchar;
    father->uniquecharposlength = 0;
    father->uniquecharposstart = state->uniquechar.nextfreeGtUlong;
    for (base = 0; base < state->alphabetsize; base++)
    {
      NODEPOSLISTSTART(father,base) = state->poslist[base].nextfreeGtUlong;
      NODEPOSLISTLENGTH(father,base) = 0;
    }
    add2poslist_maxpairs(state,father,(unsigned int) leftchar,leafnumber);
    return 0;
  }
  if (father->commonchar != ISLEFTDIVERSE)
  {
    CHECKCHAR(leftchar);
  }
  if (father->commonchar == ISLEFTDIVERSE)
  {
    for (base = 0; base < state->alphabetsize; base++)
    {
      if (leftchar != (GtUchar) base)
      {
        if (cartproduct1_maxpairs(state,fatherdepth,father,base,leafnumber,
                                  err) != 0)
        {
          return -1;
        }
      }
    }
    start = state->uniquechar.spaceGtUlong +
            father->uniquecharposstart;
    for (spptr = start; spptr < start + father->uniquecharposlength; spptr++)
    {
      if (state->processmaxpairs(state->processmaxpairsinfo,state->encseq,
                                 fatherdepth,leafnumber,*spptr,err) != 0)
      {
        return -2;
      }
    }
  }
  add2poslist_maxpairs(state,father,(unsigned int) leftchar,leafnumber);
  return 0;
}

static int processbranchingedge_maxpairs(bool firstsucc,
                                         unsigned long fatherdepth,
                                         GtBUinfo_maxpairs *father,
                                         GT_UNUSED unsigned long sondepth,
                                         GT_UNUSED unsigned long sonwidth,
                                         GtBUinfo_maxpairs *son,
                                         GtBUstate_maxpairs *state,
                                         GtError *err)
{
  unsigned int chfather, chson;
  unsigned long *start, *spptr, *fptr, *fstart;

#ifdef SKDEBUG
  printf("%s firstsucc=%s, depth(father)= %lu\n",
          __func__,firstsucc ? "true" : "false",fatherdepth);
#endif
  if (fatherdepth < (unsigned long) state->searchlength)
  {
    setpostabto0_maxpairs(state);
    return 0;
  }
  state->initialized = false;
  if (firstsucc)
  {
    return 0;
  }
  if (father->commonchar != ISLEFTDIVERSE)
  {
    gt_assert(son != NULL);
#ifdef SKDEBUG
    printf("commonchar=%u\n",(unsigned int) son->commonchar);
#endif
    if (son->commonchar != ISLEFTDIVERSE)
    {
      CHECKCHAR(son->commonchar);
    } else
    {
      father->commonchar = ISLEFTDIVERSE;
    }
  }
  if (father->commonchar == ISLEFTDIVERSE)
  {
    start = state->uniquechar.spaceGtUlong + son->uniquecharposstart;
    for (chfather = 0; chfather < state->alphabetsize; chfather++)
    {
      for (chson = 0; chson < state->alphabetsize; chson++)
      {
        if (chson != chfather)
        {
          if (cartproduct2_maxpairs(state,fatherdepth,father,chfather,
                                    son,chson,err) != 0)
          {
            return -1;
          }
        }
      }
      for (spptr = start; spptr < start + son->uniquecharposlength; spptr++)
      {
        if (cartproduct1_maxpairs(state,fatherdepth,father,chfather,*spptr,
                                  err) != 0)
        {
          return -2;
        }
      }
    }
    fstart = state->uniquechar.spaceGtUlong +
             father->uniquecharposstart;
    for (fptr = fstart; fptr < fstart + father->uniquecharposlength; fptr++)
    {
      for (chson = 0; chson < state->alphabetsize; chson++)
      {
        if (cartproduct1_maxpairs(state,fatherdepth,son,chson,*fptr,err) != 0)
        {
          return -3;
        }
      }
      for (spptr = start; spptr < start + son->uniquecharposlength; spptr++)
      {
        if (state->processmaxpairs(state->processmaxpairsinfo,state->encseq,
                                   fatherdepth,*fptr,*spptr,err) != 0)
        {
          return -4;
        }
      }
    }
  }
  concatlists_maxpairs(state,father,son);
  return 0;
}

#include "esa-bottomup-maxpairs.inc"

int gt_enumeratemaxpairs(Sequentialsuffixarrayreader *ssar,
                         const GtEncseq *encseq,
                         GtReadmode readmode,
                         unsigned int searchlength,
                         Processmaxpairs processmaxpairs,
                         void *processmaxpairsinfo,
                         GtError *err)
{
  unsigned int base;
  GtArrayGtUlong *ptr;
  GtBUstate_maxpairs *state;
  bool haserr = false;

  state = gt_malloc(sizeof (*state));
  state->alphabetsize = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
  state->searchlength = searchlength;
  state->processmaxpairs = processmaxpairs;
  state->processmaxpairsinfo = processmaxpairsinfo;
  state->initialized = false;
  state->encseq = encseq;
  state->readmode = readmode;

  GT_INITARRAY(&state->uniquechar,GtUlong);
  state->poslist = gt_malloc(sizeof (*state->poslist) * state->alphabetsize);
  for (base = 0; base < state->alphabetsize; base++)
  {
    ptr = &state->poslist[base];
    GT_INITARRAY(ptr,GtUlong);
  }
  if (gt_esa_bottomup_maxpairs(ssar, state, err) != 0)
  {
    haserr = true;
  }
  GT_FREEARRAY(&state->uniquechar,GtUlong);
  for (base = 0; base < state->alphabetsize; base++)
  {
    ptr = &state->poslist[base];
    GT_FREEARRAY(ptr,GtUlong);
  }
  gt_free(state->poslist);
  gt_free(state);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-maxpairs.h000066400000000000000000000031301211610345200204670ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009 Stefan Kurtz 
  Copyright (c) 2007-2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_MAXPAIRS_H
#define ESA_MAXPAIRS_H

#include "core/error_api.h"
#include "core/encseq.h"
#include "esa-seqread.h"

typedef int (*Processmaxpairs)(void *,
                               const GtEncseq *,
                               unsigned long,
                               unsigned long,
                               unsigned long,
                               GtError *);

int gt_enumeratemaxpairs(Sequentialsuffixarrayreader *ssar,
                         const GtEncseq *encseq,
                         GtReadmode readmode,
                         unsigned int searchlength,
                         Processmaxpairs processmaxpairs,
                         void *processmaxpairsinfo,
                         GtError *err);

#endif
genometools-1.5.1/src/match/esa-merge.c000066400000000000000000000234321211610345200177440ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/unused_api.h"
#include "core/logger.h"
#include "core/encseq.h"
#include "core/ma_api.h"
#include "sarr-def.h"
#include "emimergeesa.h"
#include "merger-trie.h"
#include "lcpoverflow.h"

#include "esa-map.h"

static void fillandinsert(Mergertrierep *trierep,
                          unsigned int idx,
                          unsigned long suftabvalue,
                          Mergertrienode *node,
                          GT_UNUSED uint64_t ident)
{
  Suffixinfo sinfo;

  sinfo.idx = idx;
  sinfo.startpos = suftabvalue;
#ifdef WITHTRIEIDENT
  sinfo.ident = ident;
#endif
  gt_mergertrie_insertsuffix(trierep,node,&sinfo);
}

static int inputthesequences(unsigned int *numofchars,
                             unsigned long *nextpostable,
                             Suffixarray *suffixarraytable,
                             const GtStrArray *indexnametab,
                             unsigned int demand,
                             GtLogger *logger,
                             GtError *err)
{
  unsigned long idx;
  const char *indexname;

  gt_error_check(err);
  for (idx=0; idxroot,
                  (uint64_t) idx);
  }
  return 0;
}

/*@null@*/ static Mergertrienode *findlargestnodeleqlcpvalue(
                                          Mergertrienode *smallest,
                                          unsigned long lcpvalue,
                                          GtError *err)
{
  Mergertrienode *tmp;

  gt_error_check(err);
  for (tmp = smallest->parent; tmp != NULL; tmp = tmp->parent)
  {
    if (tmp->depth <= lcpvalue)
    {
      return tmp;
    }
  }
  gt_error_set(err,"path does not contain a node of depth <= %lu",
                lcpvalue);
  return NULL;
}

int gt_emissionmergedesa_stepdeleteandinsertothersuffixes(
                                 Emissionmergedesa *emmesa, GtError *err)
{
  Mergertrienode *tmpsmallestleaf, *tmplcpnode;
  Largelcpvalue tmpexception;
  GtUchar tmpsmalllcpvalue;
  int retval;
  unsigned long tmpsuftabvalue,
         tmplcpvalue,
         tmplastbranchdepth;
  unsigned int tmpidx;

  gt_error_check(err);
  for (emmesa->buf.nextstoreidx = 0;
      emmesa->numofentries > 0 &&
      emmesa->buf.nextstoreidx < (unsigned int) SIZEOFMERGERESULTBUFFER;
      emmesa->buf.nextstoreidx++)
  {
    tmpsmallestleaf = gt_mergertrie_findsmallestnode(&emmesa->trierep);
    tmplastbranchdepth = tmpsmallestleaf->parent->depth;
    tmpidx = tmpsmallestleaf->suffixinfo.idx;
    emmesa->buf.suftabstore[emmesa->buf.nextstoreidx].idx = tmpidx;
    emmesa->buf.suftabstore[emmesa->buf.nextstoreidx].startpos
      = tmpsmallestleaf->suffixinfo.startpos;
    if (emmesa->nextpostable[tmpidx] >
       gt_encseq_total_length(emmesa->suffixarraytable[tmpidx].encseq))
    {
      gt_mergertrie_deletesmallestpath(tmpsmallestleaf,&emmesa->trierep);
      emmesa->numofentries--;
    } else
    {
      retval = gt_readnextfromstream_GtUchar(&tmpsmalllcpvalue,
                                       &emmesa->suffixarraytable[tmpidx].
                                                lcptabstream);
      if (retval < 0)
      {
        return -1;
      }
      if (retval == 0)
      {
        gt_error_set(err,"file %s: line %d: unexpected end of file when "
                        "reading lcptab",__FILE__,__LINE__);
        return -2;
      }
      if (tmpsmalllcpvalue == LCPOVERFLOW)
      {
        retval = gt_readnextfromstream_Largelcpvalue(
                               &tmpexception,
                               &emmesa->suffixarraytable[tmpidx].llvtabstream);
        if (retval < 0)
        {
          return -3;
        }
        if (retval == 0)
        {
          gt_error_set(err,"file %s: line %d: unexpected end of file when "
                        "reading llvtab",__FILE__,__LINE__);
          return -4;
        }
        tmplcpvalue = tmpexception.value;
      } else
      {
        tmplcpvalue = (unsigned long) tmpsmalllcpvalue;
      }
      if (tmplcpvalue > tmplastbranchdepth)
      {
        tmplastbranchdepth = tmplcpvalue;
      }
      tmplcpnode = findlargestnodeleqlcpvalue(tmpsmallestleaf,tmplcpvalue,err);
      retval = gt_readnextfromstream_GtUlong(&tmpsuftabvalue,
                                         &emmesa->suffixarraytable[tmpidx].
                                         suftabstream_GtUlong);
      if (retval == 0)
      {
        gt_error_set(err,"file %s: line %d: unexpected end of file when "
                      "reading suftab",__FILE__,__LINE__);
        return -6;
      }
      emmesa->nextpostable[tmpidx]++;
      fillandinsert(&emmesa->trierep,
                    tmpidx,
                    tmpsuftabvalue,
                    tmplcpnode,
                    emmesa->ident++);
      tmpsmallestleaf = gt_mergertrie_findsmallestnode(&emmesa->trierep);
      gt_mergertrie_deletesmallestpath(tmpsmallestleaf,&emmesa->trierep);
    }
    if (emmesa->numofentries > 0)
    {
      emmesa->buf.lcptabstore[emmesa->buf.nextstoreidx]
        = tmplastbranchdepth;
      emmesa->buf.lastpage = false;
    } else
    {
      emmesa->buf.lastpage = true;
    }
  }
  return 0;
}

int gt_emissionmergedesa_init(Emissionmergedesa *emmesa,
                           const GtStrArray *indexnametab,
                           unsigned int demand,
                           GtLogger *logger,
                           GtError *err)
{
  unsigned int numofindexes;
  bool haserr = false;

  numofindexes = (unsigned int) gt_str_array_size(indexnametab);
  emmesa->buf.nextaccessidx = emmesa->buf.nextstoreidx = 0;
  emmesa->numofindexes = numofindexes;
  emmesa->numofentries = numofindexes;
  emmesa->ident = (uint64_t) numofindexes;
  emmesa->trierep.encseqreadinfo = NULL;
  emmesa->suffixarraytable = gt_malloc(sizeof *emmesa->suffixarraytable
                                       * numofindexes);
  emmesa->nextpostable = gt_malloc(sizeof *emmesa->nextpostable * numofindexes);
  if (inputthesequences(&emmesa->numofchars,
                        emmesa->nextpostable,
                        emmesa->suffixarraytable,
                        indexnametab,
                        demand,
                        logger,
                        err) != 0)
  {
    haserr = true;
    return -1;
  }
  if (!haserr && numofindexes > 1U)
  {
    unsigned int idx;

    emmesa->trierep.encseqreadinfo
      = gt_malloc(sizeof *emmesa->trierep.encseqreadinfo * numofindexes);
    for (idx = 0; idx < numofindexes; idx++)
    {
      emmesa->trierep.encseqreadinfo[idx].encseqptr
        = emmesa->suffixarraytable[idx].encseq;
      emmesa->trierep.encseqreadinfo[idx].readmode
        = emmesa->suffixarraytable[idx].readmode;
    }
    gt_mergertrie_initnodetable(&emmesa->trierep,(unsigned long) numofindexes,
                             numofindexes);
    if (insertfirstsuffixes(&emmesa->trierep,
                           emmesa->nextpostable,
                           emmesa->suffixarraytable,
                           numofindexes,
                           err) != 0)
    {
      gt_free(emmesa->trierep.encseqreadinfo);
      emmesa->trierep.encseqreadinfo = NULL;
      haserr = true;
    }
  }
  if (haserr)
  {
    gt_free(emmesa->suffixarraytable);
    gt_free(emmesa->nextpostable);
  }
  return haserr ? -1 : 0;
}

void gt_emissionmergedesa_wrap(Emissionmergedesa *emmesa)
{
  unsigned int idx;

  for (idx = 0; idx < emmesa->numofindexes; idx++)
  {
    gt_freesuffixarray(emmesa->suffixarraytable + idx);
  }
  gt_free(emmesa->suffixarraytable);
  gt_free(emmesa->trierep.encseqreadinfo);
  emmesa->trierep.encseqreadinfo = NULL;
  if (emmesa->numofindexes > 1U)
  {
    gt_mergertrie_delete(&emmesa->trierep);
  }
  gt_free(emmesa->nextpostable);
}
genometools-1.5.1/src/match/esa-minunique.c000066400000000000000000000154041211610345200206570ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/chardef.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "sarr-def.h"

#include "esa-splititv.h"
#include "esa-minunique.h"

unsigned long gt_suffixarrayuniqueforward (const void *genericindex,
                                       unsigned long offset,
                                       unsigned long left,
                                       unsigned long right,
                                       GT_UNUSED unsigned long
                                          *witnessposition,
                                       const GtUchar *qstart,
                                       const GtUchar *qend)
{
  Simplelcpinterval itv;
  const GtUchar *qptr;
  const Suffixarray *suffixarray = (const Suffixarray *) genericindex;
  unsigned long totallength;

  itv.left = left;
  itv.right = right;
  totallength = gt_encseq_total_length(suffixarray->encseq);
  for (qptr = qstart; /* Nothing */; qptr++, offset++)
  {
    if (itv.left < itv.right)
    {
      if (qptr >= qend || ISSPECIAL(*qptr) ||
          !gt_lcpintervalfindcharchildintv(suffixarray->encseq,
                                           suffixarray->readmode,
                                           totallength,
                                           suffixarray->suftab,
                                           &itv,
                                           *qptr,
                                           offset,
                                           itv.left,
                                           itv.right))
      {
        break;
      }
    } else
    {
      return offset;
    }
  }
  return 0;
}

unsigned long gt_suffixarraymstats (const void *genericindex,
                                    unsigned long offset,
                                    unsigned long left,
                                    unsigned long right,
                                    unsigned long *witnessposition,
                                    const GtUchar *qstart,
                                    const GtUchar *qend)
{
  Simplelcpinterval itv;
  const GtUchar *qptr;
  const Suffixarray *suffixarray = (const Suffixarray *) genericindex;
  unsigned long totallength;

  itv.left = left;
  itv.right = right;
  totallength = gt_encseq_total_length(suffixarray->encseq);
  for (qptr = qstart; /* Nothing */; qptr++, offset++)
  {
    gt_assert(itv.left <= itv.right);
    if (qptr >= qend || ISSPECIAL(*qptr) ||
        !gt_lcpintervalfindcharchildintv(suffixarray->encseq,
                                      suffixarray->readmode,
                                      totallength,
                                      suffixarray->suftab,
                                      &itv,
                                      *qptr,
                                      (unsigned long) offset,
                                      itv.left,itv.right))
    {
      if (witnessposition != NULL)
      {
        *witnessposition = ESASUFFIXPTRGET(suffixarray->suftab,itv.left);
      }
      break;
    }
  }
  return offset;
}

unsigned long gt_suffixarrayfindmums (const void *genericindex,
                                      unsigned long offset,
                                      unsigned long left,
                                      unsigned long right,
                                      unsigned long *witnessposition,
                                      const GtUchar *qstart,
                                      const GtUchar *qend)
{
  const Suffixarray *suffixarray = (const Suffixarray *) genericindex;
  Simplelcpinterval itv;
  const GtUchar *qptr;
  unsigned long totallength;

  itv.left = left;
  itv.right = right;
  totallength = gt_encseq_total_length(suffixarray->encseq);
  *witnessposition = ULONG_MAX;
  for (qptr = qstart; /* Nothing */; qptr++, offset++)
  {
    gt_assert(itv.left <= itv.right);
    if (qptr >= qend || ISSPECIAL(*qptr) ||
        !gt_lcpintervalfindcharchildintv(suffixarray->encseq,
                                         suffixarray->readmode,
                                         totallength,
                                         suffixarray->suftab,
                                         &itv,
                                         *qptr,
                                         offset,
                                         itv.left,
                                         itv.right))
    {
      if (itv.left == itv.right)
      {
        *witnessposition = ESASUFFIXPTRGET(suffixarray->suftab,itv.left);
      }
      break;
    }
  }
  return offset;
}

GtRange gt_suffixarrayfindinterval (const void *genericindex,
                                    unsigned long offset,
                                    unsigned long left,
                                    unsigned long right,
                                    unsigned long *matchlength,
                                    const GtUchar *qstart,
                                    const GtUchar *qend)
{
  const Suffixarray *suffixarray = (const Suffixarray *) genericindex;
  const GtUchar *qptr;
  unsigned long totallength = gt_encseq_total_length(suffixarray->encseq);
  GtRange result;

  gt_assert(qstart < qend);
  for (qptr = qstart; /* Nothing */; qptr++, offset++)
  {
    Simplelcpinterval itv;

    if (qptr >= qend || ISSPECIAL(*qptr) ||
        !gt_lcpintervalfindcharchildintv(suffixarray->encseq,
                                         suffixarray->readmode,
                                         totallength,
                                         suffixarray->suftab,
                                         &itv,
                                         *qptr,
                                         offset,
                                         left,
                                         right))
    {
      break;
    }
    gt_assert(itv.left <= itv.right);
    left = itv.left;
    right = itv.right;
  }
  *matchlength = (unsigned long) (qptr - qstart);
  result.start = left;
  result.end = right;
  return result;
}
genometools-1.5.1/src/match/esa-minunique.h000066400000000000000000000053411211610345200206630ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_MINUNIQUE_H
#define ESA_MINUNIQUE_H

#include "core/unused_api.h"
#include "core/types_api.h"
#include "core/range_api.h"

unsigned long gt_suffixarrayuniqueforward (const void *genericindex,
                                           unsigned long offset,
                                           unsigned long left,
                                           unsigned long right,
                                           GT_UNUSED unsigned long
                                              *witnessposition,
                                           const GtUchar *qstart,
                                           const GtUchar *qend);

unsigned long gt_suffixarraymstats (const void *genericindex,
                                    unsigned long offset,
                                    unsigned long left,
                                    unsigned long right,
                                    unsigned long *witnessposition,
                                    const GtUchar *qstart,
                                    const GtUchar *qend);

unsigned long gt_suffixarrayfindmums (const void *genericindex,
                                      unsigned long offset,
                                      unsigned long left,
                                      unsigned long right,
                                      unsigned long *witnessposition,
                                      const GtUchar *qstart,
                                      const GtUchar *qend);

GtRange gt_suffixarrayfindinterval (const void *genericindex,
                                    unsigned long offset,
                                    unsigned long left,
                                    unsigned long right,
                                    unsigned long *matchlength,
                                    const GtUchar *qstart,
                                    const GtUchar *qend);
#endif
genometools-1.5.1/src/match/esa-mmsearch.c000066400000000000000000000765231211610345200204550ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/minmax.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "core/types_api.h"
#include "core/timer_api.h"
#include "core/format64.h"
#include "sarr-def.h"
#include "revcompl.h"
#include "lcpinterval.h"
#include "esa-map.h"
#include "echoseq.h"
#include "sfx-apfxlen.h"
#include "sfx-suffixer.h"
#include "esa-minunique.h"
#include "esa-mmsearch.h"

typedef struct
{
  const GtUchar *sequence;
  bool reversecopy;
  const GtEncseq *encseq;
  GtReadmode readmode;
  unsigned long startpos, length;
} GtQueryrep;

typedef struct
{
  const GtQueryrep *queryrep;
  unsigned long offset; /* position relative to startpos */
} GtQuerysubstring;

static GtUchar gt_mmsearch_accessquery(const GtQueryrep *queryrep,
                                       unsigned long pos)
{
  unsigned long abspos;

  gt_assert(queryrep != NULL && pos < queryrep->length);
  abspos = queryrep->startpos + pos;
  if (queryrep->sequence != NULL)
  {
    gt_assert(queryrep->readmode == GT_READMODE_FORWARD);
    return queryrep->sequence[abspos];
  } else
  {
    gt_assert(queryrep->readmode != GT_READMODE_FORWARD &&
              queryrep->encseq != NULL);
    return gt_encseq_get_encoded_char(queryrep->encseq,abspos,
                                      queryrep->readmode);
  }
}

#define GT_MMSEARCH_COMPARE(OFFSET,LCPLEN)\
        sidx = (OFFSET) + (LCPLEN);\
        if (sidx < totallength)\
        {\
          gt_encseq_reader_reinit_with_readmode(esr,dbencseq,readmode,sidx);\
        }\
        for (/* Nothing */ ; /* Nothing */; sidx++, (LCPLEN)++)\
        {\
          if ((LCPLEN) >= (unsigned long) minmatchlength)\
          {\
            retcode = 0;\
            break;\
          }\
          if (sidx >= totallength)\
          {\
            retcode = -1;\
            break;\
          }\
          currentdbchar = gt_encseq_reader_next_encoded_char(esr);\
          currentquerychar = gt_mmsearch_accessquery(querysubstring->queryrep,\
                                         querysubstring->offset + (LCPLEN));\
          retcode = (int) (currentquerychar - currentdbchar);\
          if (retcode == 0)\
          {\
            if (ISSPECIAL(currentdbchar) && ISSPECIAL(currentquerychar))\
            {\
              retcode = -1;\
              break;\
            }\
          } else\
          {\
            break;\
          }\
        }

static bool gt_mmsearch(const GtEncseq *dbencseq,
                        GtEncseqReader *esr,
                        const ESASuffixptr *suftab,
                        GtReadmode readmode,
                        Lcpinterval *lcpitv,
                        const GtQuerysubstring *querysubstring,
                        unsigned long minmatchlength)
{
  unsigned long left, leftsave, mid, right, lpref, rpref,
                totallength, lcplen, sidx;
  int retcode = 0;
  GtUchar currentdbchar, currentquerychar;

  totallength = gt_encseq_total_length(dbencseq);
  leftsave = left = lcpitv->left;
  right = lcpitv->right;
  lcplen = lcpitv->offset;
  GT_MMSEARCH_COMPARE(ESASUFFIXPTRGET(suftab,left),lcplen);
  if (retcode > 0)
  {
    lpref = lcplen;
    lcplen = lcpitv->offset;
    GT_MMSEARCH_COMPARE(ESASUFFIXPTRGET(suftab,right),lcplen);
    if (retcode > 0)
    {
      return false;
    } else
    {
      rpref = lcplen;
      while (right > left + 1)
      {
        mid = GT_DIV2(left+right);
        lcplen = MIN(lpref,rpref);
        GT_MMSEARCH_COMPARE(ESASUFFIXPTRGET(suftab,mid),lcplen);
        if (retcode <= 0)
        {
          right = mid;
          rpref = lcplen;
        } else
        {
          left = mid;
          lpref = lcplen;
        }
      }
      lcpitv->left = right;
    }
  }

  left = leftsave;
  right = lcpitv->right;
  lcplen = lcpitv->offset;
  GT_MMSEARCH_COMPARE(ESASUFFIXPTRGET(suftab,left),lcplen);
  if (retcode < 0)
  {
    return false;
  } else
  {
    lpref = lcplen;
    lcplen = lcpitv->offset;
    GT_MMSEARCH_COMPARE(ESASUFFIXPTRGET(suftab,right),lcplen);
    if (retcode >= 0)
    {
      lcpitv->right = right;
    } else
    {
      rpref = lcplen;
      while (right > left + 1)
      {
        mid = GT_DIV2(left+right);
        lcplen = MIN(lpref,rpref);
        GT_MMSEARCH_COMPARE(ESASUFFIXPTRGET(suftab,mid),lcplen);
        if (retcode >= 0)
        {
          left = mid;
          lpref = lcplen;
        } else
        {
          right = mid;
          rpref = lcplen;
        }
      }
      lcpitv->right = left;
    }
  }
  return true;
}

struct GtMMsearchiterator
{
  Lcpinterval lcpitv;
  unsigned long sufindex;
  const ESASuffixptr *suftab;
  GtEncseqReader *esr;
};

static GtMMsearchiterator *gt_mmsearchiterator_new_generic(
                                       const GtEncseq *dbencseq,
                                       const ESASuffixptr *suftab,
                                       unsigned long leftbound,
                                       unsigned long rightbound,
                                       unsigned long itvoffset,
                                       GtReadmode readmode,
                                       const GtQuerysubstring *querysubstring,
                                       unsigned long minmatchlength)

{
  GtMMsearchiterator *mmsi = gt_malloc(sizeof *mmsi);

  mmsi->lcpitv.left = leftbound;
  mmsi->lcpitv.right = rightbound;
  mmsi->lcpitv.offset = itvoffset;
  mmsi->suftab = suftab;
  mmsi->esr = gt_encseq_create_reader_with_readmode(dbencseq, readmode, 0);
  if (!gt_mmsearch(dbencseq,mmsi->esr,suftab,readmode,&mmsi->lcpitv,
                   querysubstring,minmatchlength))
  {
    mmsi->lcpitv.left = 1UL;
    mmsi->lcpitv.right = 0;
  }
  mmsi->sufindex = mmsi->lcpitv.left;
  return mmsi;
}

GtMMsearchiterator *gt_mmsearchiterator_new_complete_olain(
                                   const GtEncseq *dbencseq,
                                   const void *voidsuftab, /* XXX */
                                   unsigned long leftbound,
                                   unsigned long rightbound,
                                   unsigned long itvoffset,
                                   GtReadmode readmode,
                                   const GtUchar *pattern,
                                   unsigned long patternlength)
{
  GtQueryrep queryrep;
  GtQuerysubstring querysubstring;
  const ESASuffixptr *suftab = (const ESASuffixptr *) voidsuftab; /* XXX */

  queryrep.sequence = pattern;
  queryrep.reversecopy = false;
  queryrep.encseq = NULL;
  queryrep.readmode = GT_READMODE_FORWARD;
  queryrep.startpos = 0;
  queryrep.length = (unsigned long) patternlength;
  querysubstring.queryrep = &queryrep;
  querysubstring.offset = 0;
  return gt_mmsearchiterator_new_generic(dbencseq,
                                         suftab,
                                         leftbound,
                                         rightbound,
                                         itvoffset,
                                         readmode,
                                         &querysubstring,
                                         patternlength);
}

unsigned long gt_mmsearchiterator_count(const GtMMsearchiterator *mmsi)
{
  if (mmsi->lcpitv.left > mmsi->lcpitv.right)
  {
    return 0;
  }
  return mmsi->lcpitv.right - mmsi->lcpitv.left + 1;
}

bool gt_mmsearchiterator_next(unsigned long *dbstart,GtMMsearchiterator *mmsi)
{
  if (mmsi->sufindex <= mmsi->lcpitv.right)
  {
    *dbstart = ESASUFFIXPTRGET(mmsi->suftab,mmsi->sufindex++);
    return true;
  }
  return false;
}

bool gt_mmsearchiterator_isempty(const GtMMsearchiterator *mmsi)
{
  return mmsi == NULL || mmsi->lcpitv.left > mmsi->lcpitv.right;
}

bool gt_mmsearchiterator_identical(const GtMMsearchiterator *mmsi1,
                                   const GtMMsearchiterator *mmsi2)
{
  gt_assert(mmsi1 != NULL);
  gt_assert(mmsi2 != NULL);
  return mmsi1->lcpitv.left == mmsi2->lcpitv.left &&
         mmsi1->lcpitv.right == mmsi2->lcpitv.right;
}

void gt_mmsearchiterator_delete(GtMMsearchiterator *mmsi)
{
  if (mmsi != NULL)
  {
    gt_encseq_reader_delete(mmsi->esr);
    gt_free(mmsi);
  }
}

static bool gt_mmsearch_isleftmaximal(const GtEncseq *dbencseq,
                                      GtReadmode readmode,
                                      unsigned long dbstart,
                                      const GtQuerysubstring *querysubstring)
{
  GtUchar dbleftchar;

  if (dbstart == 0 || querysubstring->offset == 0)
  {
    return true;
  }
  dbleftchar = gt_encseq_get_encoded_char(dbencseq, /* Random access */
                              dbstart-1,
                              readmode);
  if (ISSPECIAL(dbleftchar) ||
      dbleftchar != gt_mmsearch_accessquery(querysubstring->queryrep,
                                            querysubstring->offset-1))
  {
    return true;
  }
  return false;
}

static bool gt_mum_isleftmaximal(const GtEncseq *dbencseq,
                                 GtReadmode readmode,
                                 unsigned long dbstart,
                                 unsigned long queryoffset,
                                 const GtUchar *query)
{
  GtUchar dbleftchar;

  if (dbstart == 0 || queryoffset == 0)
  {
    return true;
  }
  dbleftchar = gt_encseq_get_encoded_char(dbencseq, /* Random access */
                                          dbstart-1,
                                          readmode);
  if (ISSPECIAL(dbleftchar) || dbleftchar != query[queryoffset-1])
  {
    return true;
  }
  return false;
}

static unsigned long gt_mmsearch_extendright(const GtEncseq *dbencseq,
                                             GtEncseqReader *esr,
                                             GtReadmode readmode,
                                             unsigned long totallength,
                                             unsigned long dbend,
                                             const GtQuerysubstring
                                               *querysubstring,
                                             unsigned long matchlength)
{
  GtUchar dbchar;
  unsigned long dbpos, querypos;

  if (dbend < totallength)
  {
    gt_encseq_reader_reinit_with_readmode(esr,dbencseq,readmode,dbend);
  }
  for (dbpos = dbend, querypos = querysubstring->offset + matchlength;
       dbpos < totallength &&
       querypos < querysubstring->queryrep->length;
       dbpos++, querypos++)
  {
    dbchar = gt_encseq_reader_next_encoded_char(esr);
    if (ISSPECIAL(dbchar) ||
        dbchar != gt_mmsearch_accessquery(querysubstring->queryrep,querypos))
    {
      break;
    }
  }
  return dbpos - dbend;
}

static int gt_queryuniquematch(bool selfmatch,
                               const Suffixarray *suffixarray,
                               uint64_t queryunitnum,
                               const GtQueryrep *queryrep,
                               unsigned long minmatchlength,
                               GtProcessquerymatch processquerymatch,
                               void *processquerymatchinfo,
                               GtQuerymatch *querymatchspaceptr,
                               GtError *err)
{
  unsigned long offset,
                totallength = gt_encseq_total_length(suffixarray->encseq),
                localqueryoffset = 0;
  uint64_t localqueryunitnum = queryunitnum;
  bool haserr = false;

  gt_assert(!selfmatch && queryrep->length >= minmatchlength);
  for (offset = 0; offset <= queryrep->length - minmatchlength; offset++)
  {
    unsigned long matchlen, dbstart;

    matchlen = gt_suffixarrayfindmums (suffixarray,
                                       0,
                                       0, /* leftbound */
                                       totallength, /* rightbound */
                                       &dbstart,
                                       queryrep->sequence + offset,
                                       queryrep->sequence + queryrep->length);
    if (dbstart != ULONG_MAX &&
        matchlen >= minmatchlength &&
        gt_mum_isleftmaximal(suffixarray->encseq,
                             suffixarray->readmode,
                             dbstart,
                             offset,
                             queryrep->sequence))
    {
      gt_querymatch_fill(querymatchspaceptr,
                         matchlen,
                         dbstart,
                         queryrep->readmode,
                         queryrep->reversecopy,
                         0, /* score */
                         0, /* edist */
                         selfmatch,
                         localqueryunitnum,
                         matchlen,
                         localqueryoffset);
      if (processquerymatch(processquerymatchinfo,
                            suffixarray->encseq,
                            querymatchspaceptr,
                            queryrep->sequence,
                            queryrep->length,
                            err) != 0)
      {
        haserr = true;
      }
    }
    if (!haserr)
    {
      if (queryrep->sequence[offset] == (GtUchar) SEPARATOR)
      {
        localqueryunitnum++;
        localqueryoffset = 0;
      } else
      {
        localqueryoffset++;
      }
    }
  }
  return haserr ? -1 : 0;
}

static int gt_querysubstringmatch_generic(
                                     bool selfmatch,
                                     const GtEncseq *dbencseq,
                                     const ESASuffixptr *suftabpart,
                                     GtReadmode readmode,
                                     unsigned long numberofsuffixes,
                                     uint64_t queryunitnum,
                                     const GtQueryrep *queryrep,
                                     unsigned long minmatchlength,
                                     GtProcessquerymatch processquerymatch,
                                     void *processquerymatchinfo,
                                     GtQuerymatch *querymatchspaceptr,
                                     GtError *err)
{
  GtMMsearchiterator *mmsi;
  unsigned long totallength, localqueryoffset = 0;
  uint64_t localqueryunitnum = queryunitnum;
  GtQuerysubstring querysubstring;
  bool haserr = false;

  gt_assert(numberofsuffixes > 0);
  totallength = gt_encseq_total_length(dbencseq);
  querysubstring.queryrep = queryrep;
  for (querysubstring.offset = 0;
       querysubstring.offset <= queryrep->length - minmatchlength;
       querysubstring.offset++)
  {
    unsigned long dbstart;

    mmsi = gt_mmsearchiterator_new_generic(dbencseq,
                                           suftabpart,
                                           0, /* leftbound */
                                           numberofsuffixes-1, /* rightbound */
                                           0, /* offset */
                                           readmode,
                                           &querysubstring,
                                           minmatchlength);
    while (!haserr && gt_mmsearchiterator_next(&dbstart,mmsi))
    {
      if (gt_mmsearch_isleftmaximal(dbencseq,
                                    readmode,
                                    dbstart,
                                    &querysubstring))
      {
        unsigned long extend = gt_mmsearch_extendright(dbencseq,
                                                       mmsi->esr,
                                                       readmode,
                                                       totallength,
                                                       dbstart + minmatchlength,
                                                       &querysubstring,
                                                       minmatchlength);
        gt_querymatch_fill(querymatchspaceptr,
                           minmatchlength + extend,
                           dbstart,
                           queryrep->readmode,
                           queryrep->reversecopy,
                           0, /* score */
                           0, /* edist */
                           selfmatch,
                           localqueryunitnum,
                           minmatchlength + extend,
                           localqueryoffset);
        if (processquerymatch(processquerymatchinfo,
                              dbencseq,
                              querymatchspaceptr,
                              queryrep->sequence,
                              queryrep->length,
                              err) != 0)
        {
          haserr = true;
        }
      }
    }
    gt_mmsearchiterator_delete(mmsi);
    mmsi = NULL;
    if (!haserr)
    {
      if (gt_mmsearch_accessquery(queryrep,querysubstring.offset)
          == (GtUchar) SEPARATOR)
      {
        localqueryunitnum++;
        localqueryoffset = 0;
      } else
      {
        localqueryoffset++;
      }
    }
  }
  return haserr ? -1 : 0;
}

static int gt_querysubstringmatch(bool selfmatch,
                                  const Suffixarray *suffixarray,
                                  uint64_t queryunitnum,
                                  const GtQueryrep *queryrep,
                                  unsigned long minmatchlength,
                                  GtProcessquerymatch processquerymatch,
                                  void *processquerymatchinfo,
                                  GtQuerymatch *querymatchspaceptr,
                                  GtError *err)
{
  return gt_querysubstringmatch_generic(selfmatch,
                              suffixarray->encseq,
                              suffixarray->suftab,
                              suffixarray->readmode,
                              gt_encseq_total_length(suffixarray->encseq) + 1,
                              queryunitnum,
                              queryrep,
                              minmatchlength,
                              processquerymatch,
                              processquerymatchinfo,
                              querymatchspaceptr,
                              err);
}

typedef int (*GtQuerysubstringmatchfunc)(bool,
                                         const Suffixarray *,
                                         uint64_t,
                                         const GtQueryrep *,
                                         unsigned long,
                                         GtProcessquerymatch,
                                         void *,
                                         GtQuerymatch *,
                                         GtError *);

static int gt_callenumquerymatches_withindex(
                            GtQuerysubstringmatchfunc findquerymatches,
                            const Suffixarray *suffixarray,
                            const GtStrArray *queryfiles,
                            bool forwardstrand,
                            bool reversestrand,
                            unsigned int userdefinedleastlength,
                            GtProcessquerybeforematching
                               processquerybeforematching,
                            GtProcessquerymatch processquerymatch,
                            void *processquerymatchinfo,
                            GtError *err)
{
  GtSeqIterator *seqit;
  bool haserr = false;

  seqit = gt_seq_iterator_sequence_buffer_new(queryfiles, err);
  if (seqit == NULL)
  {
    haserr = true;
  } else
  {
    GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
    const GtUchar *query;
    unsigned long querylen;
    int retval;
    uint64_t queryunitnum;
    GtUchar *queryreverse = NULL;
    unsigned long queryreverse_length = 0;
    char *desc = NULL;
    int mode;

    gt_seq_iterator_set_symbolmap(seqit,
                    gt_alphabet_symbolmap(gt_encseq_alphabet(
                                                        suffixarray->encseq)));
    for (queryunitnum = 0; /* Nothing */; queryunitnum++)
    {
      retval = gt_seq_iterator_next(seqit, &query, &querylen, &desc, err);
      if (retval < 0)
      {
        haserr = true;
        break;
      }
      if (retval == 0)
      {
        break;
      }
      if (querylen >= (unsigned long) userdefinedleastlength)
      {
        GtQueryrep queryrep;

        queryrep.encseq = NULL;
        queryrep.readmode = GT_READMODE_FORWARD;
        queryrep.startpos = 0;
        queryrep.length = querylen;
        for (mode = 0; mode <= 1; mode++)
        {
          if (mode == 0 && forwardstrand)
          {
            queryrep.sequence = query;
            queryrep.reversecopy = false;
            if (processquerybeforematching != NULL)
            {
              processquerybeforematching(processquerymatchinfo,desc,query,
                                         querylen,true);
            }
          } else
          {
            if (mode == 1 && reversestrand)
            {
              if (querylen > queryreverse_length)
              {
                queryreverse = gt_realloc(queryreverse,
                                          sizeof (*queryreverse) * querylen);
                queryreverse_length = querylen;
              }
              gt_copy_reversecomplement(queryreverse,query,querylen);
              queryrep.sequence = queryreverse;
              queryrep.reversecopy = true;
              if (processquerybeforematching != NULL)
              {
                processquerybeforematching(processquerymatchinfo,desc,
                                           queryreverse,querylen,false);
              }
            } else
            {
              queryrep.sequence = NULL;
              queryrep.reversecopy = false;
            }
          }
          if (queryrep.sequence != NULL)
          {
            int ret = findquerymatches(false,
                                       suffixarray,
                                       queryunitnum,
                                       &queryrep,
                                       (unsigned long) userdefinedleastlength,
                                       processquerymatch,
                                       processquerymatchinfo,
                                       querymatchspaceptr,
                                       err);
            if (ret != 0)
            {
              haserr = true;
              break;
            }
          }
        }
      }
    }
    gt_seq_iterator_delete(seqit);
    gt_free(queryreverse);
    gt_querymatch_delete(querymatchspaceptr);
  }
  return haserr ? -1 : 0;
}

int gt_callenumquerymatches(const char *indexname,
                            const GtStrArray *queryfiles,
                            bool findmums,
                            bool forwardstrand,
                            bool reversestrand,
                            unsigned int userdefinedleastlength,
                            GtProcessquerybeforematching
                              processquerybeforematching,
                            GtProcessquerymatch processquerymatch,
                            void *processquerymatchinfo,
                            GtLogger *logger,
                            GtError *err)
{
  Suffixarray suffixarray;
  bool haserr = false;

  if (gt_mapsuffixarray(&suffixarray,
                        SARR_ESQTAB | SARR_SUFTAB | SARR_SSPTAB,
                        indexname,
                        logger,
                        err) != 0)
  {
    haserr = true;
  } else
  {
    if (gt_callenumquerymatches_withindex(findmums
                                            ? gt_queryuniquematch
                                            : gt_querysubstringmatch,
                                          &suffixarray,
                                          queryfiles,
                                          forwardstrand,
                                          reversestrand,
                                          userdefinedleastlength,
                                          processquerybeforematching,
                                          processquerymatch,
                                          processquerymatchinfo,
                                          err) != 0)
    {
      haserr = true;
    }
  }
  gt_freesuffixarray(&suffixarray);
  return haserr ? -1 : 0;
}

int gt_callenumselfmatches(const char *indexname,
                           GtReadmode queryreadmode,
                           unsigned int userdefinedleastlength,
                           GtProcessquerymatch processquerymatch,
                           void *processquerymatchinfo,
                           GtLogger *logger,
                           GtError *err)
{
  Suffixarray suffixarray;
  bool haserr = false;

  gt_assert(queryreadmode != GT_READMODE_FORWARD);
  if (gt_mapsuffixarray(&suffixarray,
                        SARR_ESQTAB | SARR_SUFTAB | SARR_SSPTAB,
                        indexname,
                        logger,
                        err) != 0)
  {
    haserr = true;
  } else
  {
    unsigned long seqnum, numofsequences, seqlength, seqstartpos;
    GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
    GtQueryrep queryrep;

    numofsequences = gt_encseq_num_of_sequences(suffixarray.encseq);
    queryrep.sequence = NULL;
    queryrep.reversecopy = false;
    queryrep.encseq = suffixarray.encseq;
    queryrep.readmode = queryreadmode;
    for (seqnum = 0; seqnum < numofsequences; seqnum++)
    {
      seqstartpos = gt_encseq_seqstartpos(suffixarray.encseq, seqnum);
      seqlength = gt_encseq_seqlength(suffixarray.encseq, seqnum);
      if (seqlength >= (unsigned long) userdefinedleastlength)
      {
        queryrep.startpos = seqstartpos;
        queryrep.length = seqlength;
        if (gt_querysubstringmatch(true,
                                   &suffixarray,
                                   (uint64_t) seqnum,
                                   &queryrep,
                                   (unsigned long) userdefinedleastlength,
                                   processquerymatch,
                                   processquerymatchinfo,
                                   querymatchspaceptr,
                                   err) != 0)
        {
          haserr = true;
          break;
        }
      }
    }
    gt_querymatch_delete(querymatchspaceptr);
  }
  gt_freesuffixarray(&suffixarray);
  return haserr ? -1 : 0;
}

static int gt_constructsarrandrunmmsearch(
                 const GtEncseq *dbencseq,
                 GtReadmode readmode,
                 unsigned int prefixlength,
                 unsigned int numofparts,
                 unsigned long maximumspace,
                 const GtUchar *query,
                 unsigned long querylen,
                 unsigned int minlength,
                 GtProcessquerymatch processquerymatch,
                 void *processquerymatchinfo,
                 GtTimer *sfxprogress,
                 bool withprogressbar,
                 GtError *err)
{
  bool haserr = false;
  Sfxiterator *sfi;
  Sfxstrategy sfxstrategy;

  defaultsfxstrategy(&sfxstrategy,
                     gt_encseq_bitwise_cmp_ok(dbencseq) ? false : true);
  sfxstrategy.outsuftabonfile = false;
  sfi = gt_Sfxiterator_new(dbencseq,
                           readmode,
                           prefixlength,
                           numofparts,
                           maximumspace,
                           &sfxstrategy, /* sfxstrategy */
                           sfxprogress,
                           withprogressbar,
                           NULL, /* logger */
                           err);
  if (sfi == NULL)
  {
    haserr = true;
  } else
  {
    const GtSuffixsortspace *suffixsortspace;
    unsigned long numberofsuffixes;
    GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
    GtQueryrep queryrep;

    queryrep.sequence = query;
    queryrep.reversecopy = false;
    queryrep.encseq = NULL;
    queryrep.readmode = GT_READMODE_FORWARD;
    queryrep.startpos = 0;
    queryrep.length = (unsigned long) querylen;
    while (true)
    {
      suffixsortspace = gt_Sfxiterator_next(&numberofsuffixes,NULL,sfi);
      if (suffixsortspace == NULL)
      {
        break;
      }
      if (gt_querysubstringmatch_generic(
                                false,
                                dbencseq,
                                (const ESASuffixptr *)
                                gt_suffixsortspace_ulong_get(suffixsortspace),
                                readmode,
                                numberofsuffixes,
                                0,
                                &queryrep,
                                (unsigned long) minlength,
                                processquerymatch,
                                processquerymatchinfo,
                                querymatchspaceptr,
                                err) != 0)
      {
        haserr = true;
        break;
      }
    }
    gt_querymatch_delete(querymatchspaceptr);
  }
  if (gt_Sfxiterator_delete(sfi,err) != 0)
  {
    haserr = true;
  }
  return haserr ? -1 : 0;
}

int gt_sarrquerysubstringmatch(const GtUchar *dbseq,
                               unsigned long dblen,
                               const GtUchar *query,
                               unsigned long querylen,
                               unsigned int minlength,
                               GtAlphabet *alpha,
                               GtProcessquerymatch processquerymatch,
                               void *processquerymatchinfo,
                               GtLogger *logger,
                               GtError *err)
{
  unsigned int numofchars, recommendedprefixlength;
  bool haserr = false;
  GtEncseq *dbencseq;
  GtEncseqBuilder *eb;

  eb = gt_encseq_builder_new(alpha);
  gt_encseq_builder_disable_multiseq_support(eb);
  gt_encseq_builder_disable_description_support(eb);
  gt_encseq_builder_set_logger(eb, logger);
  gt_encseq_builder_add_encoded(eb, dbseq, dblen, NULL);
  dbencseq = gt_encseq_builder_build(eb, err);
  gt_encseq_builder_delete(eb);

  numofchars = gt_alphabet_num_of_chars(alpha);
  recommendedprefixlength
    = gt_recommendedprefixlength(numofchars,dblen,
                                 GT_RECOMMENDED_MULTIPLIER_DEFAULT,
                                 true);
  if (gt_constructsarrandrunmmsearch(dbencseq,
                                     GT_READMODE_FORWARD,
                                     recommendedprefixlength,
                                     1U, /* parts */
                                     0, /* maximumspace */
                                     query,
                                     querylen,
                                     minlength,
                                     processquerymatch,
                                     processquerymatchinfo,
                                     NULL,
                                     false,
                                     err) != 0)
  {
    haserr = true;
  }
  gt_encseq_delete(dbencseq);
  dbencseq = NULL;
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-mmsearch.h000066400000000000000000000100031211610345200204370ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_MMSEARCH_H
#define ESA_MMSEARCH_H
#include "core/error.h"
#include "core/encseq.h"
#include "querymatch.h"

typedef int (*GtProcessquerymatch)(void *,
                                   const GtEncseq *,
                                   const GtQuerymatch *,
                                   const GtUchar *query,
                                   unsigned long query_totallength,
                                   GtError *);

typedef void (*GtProcessquerybeforematching)(void *,const char *,
                                             const GtUchar *,unsigned long,
                                             bool);

typedef struct GtMMsearchiterator GtMMsearchiterator;

GtMMsearchiterator *gt_mmsearchiterator_new_complete_olain(
                                    const GtEncseq *dbencseq,
                                    const void *voidsuftab, /* XXX */
                                    unsigned long leftbound,
                                    unsigned long rightbound,
                                    unsigned long itvoffset,
                                    GtReadmode readmode,
                                    const GtUchar *pattern,
                                    unsigned long patternlength);

bool gt_mmsearchiterator_next(unsigned long *dbstart,GtMMsearchiterator *mmsi);

bool gt_mmsearchiterator_isempty(const GtMMsearchiterator *mmsi);

bool gt_mmsearchiterator_identical(const GtMMsearchiterator *mmsi1,
                                   const GtMMsearchiterator *mmsi2);

void gt_mmsearchiterator_delete(GtMMsearchiterator *mmsi);

unsigned long gt_mmsearchiterator_count(const GtMMsearchiterator *mmsi);

int gt_callenumquerymatches(const char *indexname,
                            const GtStrArray *queryfiles,
                            bool findmums,
                            bool forwardstrand,
                            bool reversestrand,
                            unsigned int userdefinedleastlength,
                            GtProcessquerybeforematching
                              processquerybeforematching,
                            GtProcessquerymatch processquerymatch,
                            void *processquerymatchinfo,
                            GtLogger *logger,
                            GtError *err);

int gt_callenumselfmatches(const char *indexname,
                           GtReadmode queryreadmode,
                           unsigned int userdefinedleastlength,
                           GtProcessquerymatch processquerymatch,
                           void *processquerymatchinfo,
                           GtLogger *logger,
                           GtError *err);

int gt_sarrquerysubstringmatch(const GtUchar *dbseq,
                               unsigned long dblen,
                               const GtUchar *query,
                               unsigned long querylen,
                               unsigned int minlength,
                               GtAlphabet *alpha,
                               GtProcessquerymatch processquerymatch,
                               void *processquerymatchinfo,
                               GtLogger *logger,
                               GtError *err);

#endif
genometools-1.5.1/src/match/esa-scanprj.c000066400000000000000000000237451211610345200203140ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include "core/error.h"
#include "core/str.h"
#include "core/ma.h"
#include "core/array.h"
#include "core/types_api.h"
#include "core/logger.h"
#include "core/format64.h"
#include "esa-scanprj.h"

typedef union
{
  uint32_t uint32value;
  uint64_t uint64value;
  double doublevalue;
} GtScannedprjvalue;

typedef struct
{
  const char *keystring;
  uint32_t *uint32valueptr;
  uint64_t *uint64valueptr;
  double *doublevalueptr;
  bool readdouble,
       ptrdefined,
       found,
       *readflag;
} GtScannedprjkey;

struct GtScannedprjkeytable
{
  GtArray *arr;
};

GtScannedprjkeytable *gt_scannedprjkeytable_new(void)
{
  GtScannedprjkeytable *scannedprjkeytable;

  scannedprjkeytable = gt_malloc(sizeof (*scannedprjkeytable));
  scannedprjkeytable->arr = gt_array_new(sizeof (GtScannedprjkey));
  return scannedprjkeytable;
}

void gt_scannedprjkeytable_delete(GtScannedprjkeytable *scannedprjkeytable)
{
  gt_array_delete(scannedprjkeytable->arr);
  gt_free(scannedprjkeytable);
}

void gt_scannedprjkey_add(GtScannedprjkeytable *scannedprjkeytable,
                          const char *keystring,
                          void *valueptr,
                          size_t sizeval,
                          bool readdouble,
                          bool *readflag)
{
  GtScannedprjkey rikvalue;

  rikvalue.keystring = keystring;
  rikvalue.readflag = readflag;
  rikvalue.readdouble = readdouble;
  if (readdouble)
  {
    gt_assert(sizeval == sizeof (double));
    rikvalue.uint32valueptr = NULL;
    rikvalue.uint64valueptr = NULL;
    rikvalue.doublevalueptr = valueptr;
    rikvalue.ptrdefined = true;
  } else
  {
    gt_assert(sizeval == 0 || sizeval == (size_t) 4 || sizeval == (size_t) 8);
    switch (sizeval)
    {
      case 0: rikvalue.uint32valueptr = NULL;
              rikvalue.uint64valueptr = NULL;
              rikvalue.ptrdefined = false;
              break;
      case 4: gt_assert(sizeof (uint32_t) == (size_t) 4);
              rikvalue.uint32valueptr = valueptr;
              rikvalue.uint64valueptr = NULL;
              rikvalue.ptrdefined = true;
              break;
      case 8: gt_assert(sizeof (uint64_t) == (size_t) 8);
              rikvalue.uint64valueptr = valueptr;
              rikvalue.uint32valueptr = NULL;
              rikvalue.ptrdefined = true;
              break;
    }
  }
  rikvalue.found = false;
  gt_array_add_elem(scannedprjkeytable->arr,&rikvalue,
                    sizeof (GtScannedprjkey));
}

static int gt_scannedprjkey_scanline(uint32_t *lengthofkey,
                                     GtScannedprjvalue *scannedprjvalue,
                                     const char *linebuffer,
                                     unsigned long linelength,
                                     GtError *err)
{
  unsigned long idx;
  bool haserr = false, found = false;
  int retval = 0;

  gt_error_check(err);
  for (idx=0; idxdoublevalue = readdouble;
        retval = 2;
      } else
      {
        int64_t readint;

        if (sscanf((const char *) (linebuffer + idx + 1),
                   FormatScanint64_t,
                   SCANint64_tcast(&readint)) != 1 || readint < (int64_t) 0)
        {
          gt_error_set(err,"cannot find non-negative integer in \"%*.*s\"",
                             (int) (linelength - (idx+1)),
                             (int) (linelength - (idx+1)),
                             linebuffer + idx + 1);
          return -1;
        }
        if (readint <= (int64_t) UINT32_MAX)
        {
          scannedprjvalue->uint32value = (uint32_t) readint;
          retval = 0;
        } else
        {
          scannedprjvalue->uint64value = (uint64_t) readint;
          retval = 1;
        }
      }
      break;
    }
  }
  if (!found)
  {
    gt_error_set(err,"missing equality symbol in \"%*.*s\"",
                       (int) linelength,
                       (int) linelength,
                       linebuffer);
    haserr = true;
  }
  return haserr ? -1 : retval;
}

int gt_scannedprjkey_allkeysdefined(
                               const char *indexname,
                               const char *suffix,
                               const GtScannedprjkeytable *scannedprjkeytable,
                               GtLogger *logger,
                               GtError *err)
{
  unsigned long idx;
  GtScannedprjkey *rikptr;

  gt_error_check(err);
  for (idx=0; idxarr); idx++)
  {
    rikptr = (GtScannedprjkey *) gt_array_get(scannedprjkeytable->arr,idx);
    if (rikptr->found)
    {
      if (rikptr->ptrdefined)
      {
        if (rikptr->uint32valueptr != NULL)
        {
          gt_logger_log(logger,"%s=%u",
                      rikptr->keystring,
                      (unsigned int) *(rikptr->uint32valueptr));
        } else
        {
          if (rikptr->uint64valueptr != NULL)
          {
            gt_logger_log(logger,"%s=" Formatuint64_t,
                        rikptr->keystring,
                        PRINTuint64_tcast(*(rikptr->uint64valueptr)));
          } else
          {
            if (rikptr->doublevalueptr != NULL)
            {
              gt_logger_log(logger,"%s=%.2f", rikptr->keystring,
                            *(rikptr->doublevalueptr));
            } else
            {
              gt_assert(false);
            }
          }
        }
      } else
      {
        gt_logger_log(logger,"%s=0",rikptr->keystring);
      }
      if (rikptr->readflag != NULL)
      {
        *(rikptr->readflag) = true;
      }
    } else
    {
      if (rikptr->readflag == NULL)
      {
        gt_error_set(err,"file %s%s: missing line beginning with \"%s=\"",
                     indexname, suffix, rikptr->keystring);
        return -1;
      }
      *(rikptr->readflag) = false;
    }
  }
  return 0;
}

int gt_scannedprjkey_analyze(const char *indexname,
                             const char *suffix,
                             unsigned int linenum,
                             const char *linebuffer,
                             unsigned long linelength,
                             GtScannedprjkeytable *scannedprjkeytable,
                             GtError *err)
{
  GtScannedprjkey *rikptr;
  bool found = false, haserr = false;
  unsigned long i;
  int retval;
  GtScannedprjvalue scannedprjvalue;
  uint32_t lengthofkey;

  gt_error_check(err);
  retval = gt_scannedprjkey_scanline(&lengthofkey,
                                     &scannedprjvalue,
                                     linebuffer,
                                     linelength,
                                     err);
  if (retval < 0)
  {
    haserr = true;
  } else
  {
    for (i=0; iarr); i++)
    {
      rikptr = gt_array_get(scannedprjkeytable->arr,i);
      if (memcmp(linebuffer, rikptr->keystring,(size_t) lengthofkey) == 0)
      {
        rikptr->found = true;
        if (rikptr->ptrdefined)
        {
          if (rikptr->uint32valueptr == NULL)
          {
            if (retval == 1)
            {
              *(rikptr->uint64valueptr) = scannedprjvalue.uint64value;
            } else
            {
              if (retval == 2)
              {
                gt_assert(rikptr->readdouble);
                *(rikptr->doublevalueptr) = scannedprjvalue.doublevalue;
              } else
              {
                gt_assert(retval == 0);
                *(rikptr->uint64valueptr)
                  = (uint64_t) scannedprjvalue.uint32value;
              }
            }
          } else
          {
            if (retval == 1)
            {
              gt_error_set(err,"uint64value " Formatuint64_t
                           " does not fit into %s",
                           PRINTuint64_tcast(scannedprjvalue.uint64value),
                           rikptr->keystring);
              haserr = true;
              break;
            }
            if (retval == 2)
            {
              gt_error_set(err,"double %.2f does not fit into %s",
                           scannedprjvalue.doublevalue,
                           rikptr->keystring);
              haserr = true;
              break;
            }
            *(rikptr->uint32valueptr) = scannedprjvalue.uint32value;
          }
        }
        found = true;
        break;
      }
    }
    if (!found)
    {
      gt_error_set(err,"file %s%s, line %u: cannot find key for \"%*.*s\"",
                    indexname,
                    suffix,
                    linenum,
                    (int) lengthofkey,
                    (int) lengthofkey,
                    linebuffer);
      haserr = true;
    }
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-scanprj.h000066400000000000000000000044721211610345200203150ustar00rootroot00000000000000/*
  Copyright (c) 2005-2007 Stefan Kurtz 
  Copyright (c) 2005-2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_SCANPRJ_H
#define ESA_SCANPRJ_H
#include "core/array.h"
#include "core/error.h"
#include "core/str.h"
#include "core/logger.h"

#define GT_SCANNEDPRJKEY_ADD(VALNAME,VAL,FORCEREAD)\
        gt_scannedprjkey_add(scannedprjkeytable,VALNAME,VAL,sizeof (*(VAL)),\
                             false,FORCEREAD)

typedef struct GtScannedprjkeytable GtScannedprjkeytable;

GtScannedprjkeytable *gt_scannedprjkeytable_new(void);

void gt_scannedprjkeytable_delete(GtScannedprjkeytable *scannedprjkeytable);

void gt_scannedprjkey_add(GtScannedprjkeytable *scannedprjkeytable,
                          const char *keystring,
                          void *valueptr,
                          size_t sizeval,
                          bool readdouble,
                          bool *readflag);

int gt_scannedprjkey_analyze(const char *indexname,
                             const char *suffix,
                             unsigned int linenum,
                             const char *linebuffer,
                             unsigned long linelength,
                             GtScannedprjkeytable *scannedprjkeytable,
                             GtError *err);

int gt_scannedprjkey_allkeysdefined(
                               const char *indexname,
                               const char *suffix,
                               const GtScannedprjkeytable *scannedprjkeytable,
                               GtLogger *logger,
                               GtError *err);

#endif
genometools-1.5.1/src/match/esa-seqread.c000066400000000000000000000210321211610345200202630ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/unused_api.h"
#include "core/ma_api.h"
#include "sarr-def.h"
#include "esa-seqread.h"
#include "esa-lcpval.h"
#include "lcpoverflow.h"
#include "esa-map.h"

Sequentialsuffixarrayreader *gt_newSequentialsuffixarrayreaderfromfile(
                                        const char *indexname,
                                        unsigned int demand,
                                        Sequentialaccesstype seqactype,
                                        GtLogger *logger,
                                        GtError *err)
{
  Sequentialsuffixarrayreader *ssar;

  ssar = gt_malloc(sizeof *ssar);
  ssar->suffixarray = gt_malloc(sizeof *ssar->suffixarray);
  gt_assert(seqactype == SEQ_mappedboth || seqactype == SEQ_scan);
  if ((seqactype == SEQ_mappedboth
         ? gt_mapsuffixarray : streamsuffixarray)(ssar->suffixarray,
                                                  demand,
                                                  indexname,
                                                  logger,
                                                  err) != 0)
  {
    gt_free(ssar->suffixarray);
    gt_free(ssar);
    return NULL;
  }
  ssar->nextsuftabindex = 0;
  ssar->nextlcptabindex = 1UL;
  ssar->largelcpindex = 0;
  ssar->seqactype = seqactype;
  ssar->suftab = NULL;
  gt_assert(ssar->suffixarray != NULL);
  ssar->encseq = ssar->suffixarray->encseq;
  ssar->readmode = ssar->suffixarray->readmode;
  ssar->numberofsuffixes = gt_encseq_total_length(ssar->encseq) + 1;
  ssar->nonspecials = gt_encseq_total_length(ssar->encseq) -
                      gt_encseq_specialcharacters(ssar->encseq);
  ssar->lvi = NULL;
  return ssar;
}

Sequentialsuffixarrayreader *gt_newSequentialsuffixarrayreaderfromRAM(
                                        const GtEncseq *encseq,
                                        GtReadmode readmode)
{
  Sequentialsuffixarrayreader *ssar;

  ssar = gt_malloc(sizeof *ssar);
  ssar->lvi = gt_newLcpvalueiterator(encseq,readmode);
  ssar->suffixarray = NULL;
  ssar->nextlcptabindex = 1UL; /* not required here */
  ssar->largelcpindex = 0; /* not required here */
  ssar->seqactype = SEQ_suftabfrommemory;
  ssar->readmode = readmode;
  ssar->encseq = encseq;
  ssar->numberofsuffixes = gt_encseq_total_length(encseq) + 1;
  ssar->nonspecials = gt_encseq_total_length(encseq) -
                      gt_encseq_specialcharacters(encseq);
  return ssar;
}

void gt_updateSequentialsuffixarrayreaderfromRAM(
                    Sequentialsuffixarrayreader *ssar,
                    const ESASuffixptr *suftab,
                    bool firstpage,
                    unsigned long numberofsuffixes)
{
  ssar->nextsuftabindex = 0;
  ssar->suftab = suftab;
  ssar->numberofsuffixes = numberofsuffixes;
  if (firstpage)
  {
    (void) gt_nextLcpvalueiterator(ssar->lvi,
                                   true,
                                   suftab,
                                   numberofsuffixes);
  }
}

void gt_freeSequentialsuffixarrayreader(Sequentialsuffixarrayreader **ssar)
{
  if ((*ssar)->suffixarray != NULL)
  {
    gt_freesuffixarray((*ssar)->suffixarray);
    gt_free((*ssar)->suffixarray);
  }
  gt_freeLcpvalueiterator((*ssar)->lvi);
  gt_free(*ssar);
}

int gt_nextSequentiallcpvalue(unsigned long *currentlcp,
                              Sequentialsuffixarrayreader *ssar,
                              GtError *err)
{
  GtUchar tmpsmalllcpvalue;
  int retval;

  switch (ssar->seqactype)
  {
    case SEQ_scan:
      retval = gt_readnextfromstream_GtUchar(&tmpsmalllcpvalue,
                                         &ssar->suffixarray->lcptabstream);
      if (retval > 0)
      {
        if (tmpsmalllcpvalue < LCPOVERFLOW)
        {
          *currentlcp = (unsigned long) tmpsmalllcpvalue;
        } else
        {
          Largelcpvalue tmpexception;

          retval = gt_readnextfromstream_Largelcpvalue(&tmpexception,
                                            &ssar->suffixarray->llvtabstream);
          if (retval == 0)
          {
            gt_error_set(err,"file %s: line %d: unexpected end of file when "
                             "reading llvtab",__FILE__,__LINE__);
            return -1;
          }
          *currentlcp = tmpexception.value;
        }
      } else
      {
        return 0;
      }
      break;
    case SEQ_mappedboth:
      if (ssar->nextlcptabindex < ssar->numberofsuffixes)
      {
        tmpsmalllcpvalue = ssar->suffixarray->lcptab[ssar->nextlcptabindex++];
        if (tmpsmalllcpvalue < LCPOVERFLOW)
        {
          *currentlcp = (unsigned long) tmpsmalllcpvalue;
        } else
        {
          gt_assert(ssar->suffixarray->llvtab[ssar->largelcpindex].position ==
                 ssar->nextlcptabindex-1);
          *currentlcp = ssar->suffixarray->llvtab[ssar->largelcpindex++].value;
        }
      } else
      {
        return 0;
      }
      break;
    case SEQ_suftabfrommemory:
      if (ssar->nextlcptabindex < ssar->numberofsuffixes)
      {
        *currentlcp = gt_nextLcpvalueiterator(ssar->lvi,
                                              true,
                                              ssar->suftab,
                                              ssar->numberofsuffixes);
        ssar->nextlcptabindex++;
      } else
      {
        return 0;
      }
      break;
  }
  return 1;
}

int gt_nextSequentialsuftabvalue(unsigned long *currentsuffix,
                                 Sequentialsuffixarrayreader *ssar)
{
  if (ssar->seqactype == SEQ_scan)
  {
#ifdef _LP64
    if (ssar->suffixarray->suftabstream_GtUlong.fp != NULL)
    {
      return gt_readnextfromstream_GtUlong(currentsuffix,
                                 &ssar->suffixarray->suftabstream_GtUlong);
    } else
    {
      uint32_t readvalue = 0;
      int ret = gt_readnextfromstream_uint32_t(
                                 &readvalue,
                                 &ssar->suffixarray->suftabstream_uint32_t);
      *currentsuffix = (unsigned long) readvalue;
      return ret;
    }
#else
     return gt_readnextfromstream_GtUlong(currentsuffix,
                                      &ssar->suffixarray->suftabstream_GtUlong);
#endif
  }
  if (ssar->seqactype == SEQ_mappedboth)
  {
    *currentsuffix = ESASUFFIXPTRGET(ssar->suffixarray->suftab,
                                     ssar->nextsuftabindex++);
    return 1;
  }
  *currentsuffix = ESASUFFIXPTRGET(ssar->suftab,ssar->nextsuftabindex++);
  return 1;
}

const GtEncseq *gt_encseqSequentialsuffixarrayreader(
                          const Sequentialsuffixarrayreader *ssar)
{
  return ssar->encseq;
}

GtReadmode gt_readmodeSequentialsuffixarrayreader(
                          const Sequentialsuffixarrayreader *ssar)
{
  return ssar->readmode;
}

const ESASuffixptr *gt_suftabSequentialsuffixarrayreader(
                        const Sequentialsuffixarrayreader *ssar)
{
  gt_assert(ssar->seqactype != SEQ_scan);
  if (ssar->seqactype == SEQ_mappedboth)
  {
    return ssar->suffixarray->suftab;
  }
  return ssar->suftab;
}

const Suffixarray *gt_suffixarraySequentialsuffixarrayreader(
              const Sequentialsuffixarrayreader *ssar)
{
  return ssar->suffixarray;
}

unsigned long gt_Sequentialsuffixarrayreader_nonspecials(
                          const Sequentialsuffixarrayreader *ssar)
{
  return ssar->nonspecials;
}

unsigned long gt_Sequentialsuffixarrayreader_totallength(
              const Sequentialsuffixarrayreader *ssar)
{
  gt_assert(ssar->numberofsuffixes > 0);
  return ssar->numberofsuffixes - 1;
}

unsigned int gt_Sequentialsuffixarrayreader_prefixlength(
              const Sequentialsuffixarrayreader *ssar)
{
  return ssar->suffixarray->prefixlength;
}

GtBcktab *gt_Sequentialsuffixarrayreader_bcktab(
              const Sequentialsuffixarrayreader *ssar)
{
  return ssar->suffixarray->bcktab;
}
genometools-1.5.1/src/match/esa-seqread.h000066400000000000000000000265671211610345200203120ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_SEQREAD_H
#define ESA_SEQREAD_H
#include 
#include "core/str.h"
#include "core/error.h"
#include "core/encseq.h"

#include "esa-lcpval.h"
#include "sarr-def.h"
#include "lcpoverflow.h"

typedef enum
{
  SEQ_scan,
  SEQ_mappedboth,
  SEQ_suftabfrommemory
} Sequentialaccesstype;

struct Sequentialsuffixarrayreader
{
  Suffixarray *suffixarray;
  unsigned long nonspecials,
         numberofsuffixes,
         nextsuftabindex, /* for SEQ_mappedboth | SEQ_suftabfrommemory */
         nextlcptabindex, /* for SEQ_mappedboth */
         largelcpindex;   /* SEQ_mappedboth */
  Sequentialaccesstype seqactype;
  Lcpvalueiterator *lvi;
  const ESASuffixptr *suftab;
  const GtEncseq *encseq;
  GtReadmode readmode;
};

typedef struct Sequentialsuffixarrayreader Sequentialsuffixarrayreader;

Sequentialsuffixarrayreader *gt_newSequentialsuffixarrayreaderfromRAM(
                                        const GtEncseq *encseq,
                                        GtReadmode readmode);

void gt_updateSequentialsuffixarrayreaderfromRAM(
                    Sequentialsuffixarrayreader *ssar,
                    const ESASuffixptr *suftab,
                    bool firstpage,
                    unsigned long numberofsuffixes);

int gt_nextSequentiallcpvalue(unsigned long *currentlcp,
                           Sequentialsuffixarrayreader *ssar,
                           GtError *err);

int gt_nextSequentialsuftabvalue(unsigned long *currentsuffix,
                                 Sequentialsuffixarrayreader *ssar);

#define NEXTSEQUENTIALSUFTABVALUE_SEQ_scan_generic(SUFTABVALUE,SSAR,TYPE)\
        {\
          GtBufferedfile_ ## TYPE *buf\
            = &(SSAR)->suffixarray->suftabstream_ ## TYPE;\
          if (buf->nextread >= buf->nextfree)\
          {\
            buf->nextfree\
              = (unsigned int) fread(buf->bufferedfilespace,\
                                     sizeof (*buf->bufferedfilespace),\
                                     (size_t) FILEBUFFERSIZE,\
                                     buf->fp);\
            if (ferror(buf->fp))\
            {\
              gt_error_set(err,"error when trying to read next %s",#TYPE);\
              haserr = true;\
            } else\
            {\
              buf->nextread = 0;\
              if (buf->nextfree == 0)\
              {\
                gt_error_set(err,"Missing value in suftab");\
                haserr = true;\
                break;\
              }\
            }\
          }\
          SUFTABVALUE = (unsigned long)buf->bufferedfilespace[buf->nextread++];\
        }

#ifdef _LP64
#define NEXTSEQUENTIALSUFTABVALUE_SEQ_scan(SUFTABVALUE,SSAR)\
        if ((SSAR)->suffixarray->suftabstream_GtUlong.fp != NULL)\
        {\
          NEXTSEQUENTIALSUFTABVALUE_SEQ_scan_generic(SUFTABVALUE,SSAR,GtUlong);\
        } else\
        {\
          NEXTSEQUENTIALSUFTABVALUE_SEQ_scan_generic(SUFTABVALUE,SSAR,\
                                                     uint32_t);\
        }
#else
#define NEXTSEQUENTIALSUFTABVALUE_SEQ_scan(SUFTABVALUE,SSAR)\
        NEXTSEQUENTIALSUFTABVALUE_SEQ_scan_generic(SUFTABVALUE,SSAR,GtUlong)
#endif

#define NEXTSEQUENTIALSUFTABVALUE(SUFTABVALUE,SSAR)\
        switch ((SSAR)->seqactype)\
        {\
          case SEQ_scan:\
            NEXTSEQUENTIALSUFTABVALUE_SEQ_scan(SUFTABVALUE,SSAR);\
            break;\
          case SEQ_mappedboth:\
            SUFTABVALUE = ESASUFFIXPTRGET((SSAR)->suffixarray->suftab,\
                                          (SSAR)->nextsuftabindex++);\
            break;\
          case SEQ_suftabfrommemory:\
            SUFTABVALUE = ESASUFFIXPTRGET((SSAR)->suftab,\
                                          (SSAR)->nextsuftabindex++);\
          break;\
        }

#define NEXTSEQUENTIALLCPTABVALUE(LCPVALUE,SSAR)\
        {\
          GtUchar tmpsmalllcpvalue;\
          if ((SSAR)->seqactype == SEQ_scan)\
          {\
            int retval = gt_readnextfromstream_GtUchar(&tmpsmalllcpvalue,\
                                        &(SSAR)->suffixarray->lcptabstream);\
            if (retval > 0)\
            {\
              if (tmpsmalllcpvalue < LCPOVERFLOW)\
              {\
                LCPVALUE = (unsigned long) tmpsmalllcpvalue;\
              } else\
              {\
                Largelcpvalue tmpexception;\
                retval = gt_readnextfromstream_Largelcpvalue(&tmpexception,\
                                        &(SSAR)->suffixarray->llvtabstream);\
                if (retval == 0)\
                {\
                  gt_error_set(err,"file %s: line %d: unexpected end "\
                                   "of file when reading llvtab",\
                                   __FILE__,__LINE__);\
                  haserr = true;\
                  break;\
                }\
                LCPVALUE = tmpexception.value;\
              }\
            } else\
            {\
              break;\
            }\
          } else\
          {\
            if ((SSAR)->seqactype == SEQ_mappedboth)\
            {\
              if ((SSAR)->nextlcptabindex < (SSAR)->numberofsuffixes)\
              {\
                tmpsmalllcpvalue\
                  = (SSAR)->suffixarray->lcptab[(SSAR)->nextlcptabindex++];\
                if (tmpsmalllcpvalue < LCPOVERFLOW)\
                {\
                  LCPVALUE = (unsigned long) tmpsmalllcpvalue;\
                } else\
                {\
                  gt_assert((SSAR)->suffixarray->llvtab[(SSAR)->largelcpindex]\
                             .position == (SSAR)->nextlcptabindex-1);\
                  LCPVALUE = (SSAR)->suffixarray->llvtab\
                                      [(SSAR)->largelcpindex++].value;\
                }\
              } else\
              {\
                break;\
              }\
            } else\
            {\
              if ((SSAR)->nextlcptabindex < (SSAR)->numberofsuffixes)\
              {\
                LCPVALUE = gt_nextLcpvalueiterator((SSAR)->lvi,\
                                                   true,\
                                                   (SSAR)->suftab,\
                                                   (SSAR)->numberofsuffixes);\
                (SSAR)->nextlcptabindex++;\
              } else\
              {\
                break;\
              }\
            }\
          }\
        }

#define NEXTSEQUENTIALLCPTABVALUEWITHLAST(LCPVALUE,LASTSUFTABVALUE,SSAR)\
        {\
          GtUchar tmpsmalllcpvalue;\
          if ((SSAR)->seqactype == SEQ_scan)\
          {\
            int retval = gt_readnextfromstream_GtUchar(&tmpsmalllcpvalue,\
                                        &(SSAR)->suffixarray->lcptabstream);\
            if (retval > 0)\
            {\
              if (tmpsmalllcpvalue < LCPOVERFLOW)\
              {\
                LCPVALUE = (unsigned long) tmpsmalllcpvalue;\
              } else\
              {\
                Largelcpvalue tmpexception;\
                retval = gt_readnextfromstream_Largelcpvalue(&tmpexception,\
                                        &(SSAR)->suffixarray->llvtabstream);\
                if (retval == 0)\
                {\
                  gt_error_set(err,"file %s: line %d: unexpected end "\
                                   "of file when reading llvtab",\
                                   __FILE__,__LINE__);\
                  haserr = true;\
                  break;\
                }\
                LCPVALUE = tmpexception.value;\
              }\
            } else\
            {\
              NEXTSEQUENTIALSUFTABVALUE_SEQ_scan(LASTSUFTABVALUE,SSAR);\
              break;\
            }\
          } else\
          {\
            if ((SSAR)->seqactype == SEQ_mappedboth)\
            {\
              if ((SSAR)->nextlcptabindex < (SSAR)->numberofsuffixes)\
              {\
                tmpsmalllcpvalue\
                  = (SSAR)->suffixarray->lcptab[(SSAR)->nextlcptabindex++];\
                if (tmpsmalllcpvalue < LCPOVERFLOW)\
                {\
                  LCPVALUE = (unsigned long) tmpsmalllcpvalue;\
                } else\
                {\
                  gt_assert((SSAR)->suffixarray->llvtab[(SSAR)->largelcpindex]\
                             .position == (SSAR)->nextlcptabindex-1);\
                  LCPVALUE = (SSAR)->suffixarray->llvtab\
                                      [(SSAR)->largelcpindex++].value;\
                }\
              } else\
              {\
                LASTSUFTABVALUE = ESASUFFIXPTRGET((SSAR)->suffixarray->suftab,\
                                                  (SSAR)->nextsuftabindex++);\
                break;\
              }\
            } else\
            {\
              if ((SSAR)->nextlcptabindex < (SSAR)->numberofsuffixes)\
              {\
                LCPVALUE = gt_nextLcpvalueiterator((SSAR)->lvi,\
                                                   true,\
                                                   (SSAR)->suftab,\
                                                   (SSAR)->numberofsuffixes);\
                (SSAR)->nextlcptabindex++;\
              } else\
              {\
                LASTSUFTABVALUE = ESASUFFIXPTRGET((SSAR)->suftab,\
                                                  (SSAR)->nextsuftabindex++);\
                break;\
              }\
            }\
          }\
        }

Sequentialsuffixarrayreader *gt_newSequentialsuffixarrayreaderfromfile(
                                        const char *indexname,
                                        unsigned int demand,
                                        Sequentialaccesstype seqactype,
                                        GtLogger *logger,
                                        GtError *err);

void gt_freeSequentialsuffixarrayreader(Sequentialsuffixarrayreader **ssar);

const GtEncseq *gt_encseqSequentialsuffixarrayreader(
                          const Sequentialsuffixarrayreader *ssar);

GtReadmode gt_readmodeSequentialsuffixarrayreader(
                          const Sequentialsuffixarrayreader *ssar);

unsigned long gt_Sequentialsuffixarrayreader_nonspecials(
                          const Sequentialsuffixarrayreader *ssar);

const ESASuffixptr *gt_suftabSequentialsuffixarrayreader(
                        const Sequentialsuffixarrayreader *ssar);

const Suffixarray *gt_suffixarraySequentialsuffixarrayreader(
              const Sequentialsuffixarrayreader *ssar);

unsigned long gt_Sequentialsuffixarrayreader_totallength(
              const Sequentialsuffixarrayreader *ssar);

unsigned int gt_Sequentialsuffixarrayreader_prefixlength(
              const Sequentialsuffixarrayreader *ssar);

GtBcktab *gt_Sequentialsuffixarrayreader_bcktab(
              const Sequentialsuffixarrayreader *ssar);

#endif
genometools-1.5.1/src/match/esa-shulen.c000066400000000000000000000474421211610345200201520ustar00rootroot00000000000000/*
  Copyright (c) 2010 Stefan Kurtz 
  Copyright (c) 2011 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "core/array2dim_api.h"
#include "core/logger.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "core/format64.h"
#undef SHUDEBUG
#ifdef SHUDEBUG
#include "core/encseq.h"
#endif
#include "esa-seqread.h"
#include "esa-splititv.h"
#include "shu_unitfile.h"
#include "esa-shulen.h"

typedef struct /* information stored for each node of the lcp interval tree */
{
  unsigned long *gnumdist;
#ifdef SHUDEBUG
  unsigned long id;
#endif
} GtBUinfo_shulen;

struct GtBUstate_shulen /* global information */
{
  unsigned long numofdbfiles;
  uint64_t **shulengthdist;
  const GtEncseq *encseq;
  unsigned long *file_to_genome_map;
#undef GENOMEDIFF_PAPER_IMPL
#ifdef GENOMEDIFF_PAPER_IMPL
  unsigned long *leafdist;
#endif
#ifdef SHUDEBUG
  unsigned long lastleafnumber,
                nextid;
#endif
  /* the remaining components are used for the genomediff function
     called from the suffixerator */
  unsigned long idxoffset,
                previousbucketlastsuffix;
  bool firstedgefromroot;
  GtShuUnitFileInfo *unit_info;
  void *stack;
};

static void resetgnumdist_shulen(GtBUinfo_shulen *father,
                                 unsigned long numofdbfiles)
{
  unsigned long idx;

#ifdef SHUDEBUG
  printf("reset node %lu\n",father->id);
#endif
  for (idx = 0; idx < numofdbfiles; idx++)
  {
    father->gnumdist[idx] = 0;
  }
}

static void initBUinfo_shulen(GtBUinfo_shulen *buinfo,
                              GT_UNUSED GtBUstate_shulen *state)
{
#ifdef SHUDEBUG
  buinfo->id = state->nextid++;
#endif
  buinfo->gnumdist = NULL;
}

static void freeBUinfo_shulen(GtBUinfo_shulen *buinfo,
                              GT_UNUSED GtBUstate_shulen *state)
{
  gt_free(buinfo->gnumdist);
}

static void contribute_shulen(GT_UNUSED int line,
                              uint64_t **shulengthdist,
                              unsigned long referidx,
                              unsigned long shulenidx,
                              unsigned long count,
                              unsigned long depth)
{
#ifdef SHUDEBUG
  printf("line %d: add[%lu][%lu]+=count=%lu*depth=%lu\n",line,referidx,
                                                        shulenidx,count,depth);
#endif
  shulengthdist[referidx][shulenidx] += count * depth;
}

#ifdef SHUDEBUG
static void shownode(int line,
                     const GtBUstate_shulen *state,
                     const char *kind,
                     const GtBUinfo_shulen *node)
{
  unsigned long idx;

  printf("line %d: %s(id=%lu,numofdbfiles=%lu):",line,kind,node->id,
                                                 state->numofdbfiles);
  for (idx=0; idx < state->numofdbfiles; idx++)
  {
    if (node->gnumdist[idx] > 0)
    {
      printf(" %lu->%lu",idx,node->gnumdist[idx]);
    }
  }
  printf("\n");
}
#endif

static void cartproduct_shulen(GtBUstate_shulen *state,
                               unsigned long depth,
                               const unsigned long *refnumdist,
                               const unsigned long *querynumdist)
{
  unsigned long referidx, shulenidx;

  for (referidx=0; referidx < state->numofdbfiles; referidx++)
  {
    if (refnumdist[referidx] > 0 && querynumdist[referidx] == 0)
    {
      for (shulenidx=0; shulenidx < state->numofdbfiles; shulenidx++)
      {
        if (querynumdist[shulenidx] > 0)
        {
          gt_assert(referidx != shulenidx);
          contribute_shulen(__LINE__,
                            state->shulengthdist,
                            referidx,
                            shulenidx,
                            querynumdist[shulenidx],
                            depth + 1);
        }
      }
    }
  }
}

static void shu_compute_leaf_edge_contrib(GtBUstate_shulen *state,
                                          const unsigned long *fathernumdist,
                                          unsigned long gnum,
                                          unsigned long fatherdepth)
{
  unsigned long idx;
#ifdef GENOMEDIFF_PAPER_IMPL
  gt_assert(state->leafdist != NULL);
  for (idx = 0; idx < state->numofdbfiles; idx++)
  {
    state->leafdist[idx] = 0;
  }
  state->leafdist[gnum] = 1UL;
  cartproduct_shulen(state,fatherdepth,fathernumdist,state->leafdist);
  cartproduct_shulen(state,fatherdepth,state->leafdist,fathernumdist);
#else
  for (idx = 0; idx < state->numofdbfiles; idx++)
  {
    if (idx != gnum && fathernumdist[idx] > 0)
    {
      contribute_shulen(__LINE__,
                        state->shulengthdist,
                        idx,
                        gnum,
                        1UL,
                        fatherdepth+1);
      if (fathernumdist[gnum] == 0)
      {
        contribute_shulen(__LINE__,
                          state->shulengthdist,
                          gnum,
                          idx,
                          fathernumdist[idx],
                          fatherdepth + 1);
      }
    }
  }
#endif
}

static int processleafedge_shulen(bool firstsucc,
                                  unsigned long fatherdepth,
                                  GtBUinfo_shulen *father,
                                  unsigned long leafnumber,
                                  GtBUstate_shulen *state,
                                  GT_UNUSED GtError *err)
{
  unsigned long gnum;

#ifdef SHUDEBUG
  printf("processleafedge %lu firstsucc=%s, "
         " depth(father)=%lu, path=",
         leafnumber,
         firstsucc ? "true" : "false",
         fatherdepth);
  if (fatherdepth > 0)
  {
    gt_encseq_showatstartposwithdepth(stdout,
                                      state->encseq,
                                      GT_READMODE_FORWARD,
                                      leafnumber,
                                      fatherdepth);
  }
  printf("\n");
#endif
  if (state->file_to_genome_map != NULL)
  {
    gnum = state->file_to_genome_map[gt_encseq_filenum(state->encseq,
                                                       leafnumber)];
  } else
  {
    gnum = gt_encseq_filenum(state->encseq,leafnumber);
  }
  if (firstsucc)
  {
    gt_assert(father != NULL);
    if (father->gnumdist == NULL)
    {
      father->gnumdist
        = gt_malloc(sizeof (*father->gnumdist) * state->numofdbfiles);
    }
    resetgnumdist_shulen(father,state->numofdbfiles);
#ifdef SHUDEBUG
    shownode(__LINE__,state,"father",father);
#endif
  } else
  {
#ifdef SHUDEBUG
    shownode(__LINE__,state,"father",father);
#endif
    shu_compute_leaf_edge_contrib(state,father->gnumdist,gnum,fatherdepth);
  }
  father->gnumdist[gnum]++;
#ifdef SHUDEBUG
  printf("gnumdist[id=%lu,filenum=%lu]=%lu\n",father->id,gnum,
                                              father->gnumdist[gnum]);
  state->lastleafnumber = leafnumber;
#endif
  return 0;
}

static int processbranchingedge_shulen(bool firstsucc,
                                       unsigned long fatherdepth,
                                       GtBUinfo_shulen *father,
                                       GT_UNUSED unsigned long sondepth,
                                       GT_UNUSED unsigned long sonwidth,
                                       GtBUinfo_shulen *son,
                                       GtBUstate_shulen *state,
                                       GT_UNUSED GtError *err)
{
  unsigned long idx;

#ifdef SHUDEBUG
  printf("%s firstsucc=%s, depth(father)=%lu,path=",__func__,
         firstsucc ? "true" : "false",fatherdepth);
  if (fatherdepth > 0)
  {
    gt_encseq_showatstartposwithdepth(stdout,
                                      state->encseq,
                                      GT_READMODE_FORWARD,
                                      state->lastleafnumber,
                                      fatherdepth);
  }
  printf("\n");
#endif
  if (firstsucc)
  {
    gt_assert(father != NULL);
    if (father->gnumdist == NULL)
    {
      father->gnumdist
        = gt_malloc(sizeof (*father->gnumdist) * state->numofdbfiles);
      resetgnumdist_shulen(father,state->numofdbfiles);
    }
#ifdef SHUDEBUG
    shownode(__LINE__,state,"father",father);
#endif
  } else
  {
#ifdef SHUDEBUG
    gt_assert(father != NULL);
    shownode(__LINE__,state,"father",father);
    gt_assert(son != NULL);
    shownode(__LINE__,state,"son",son);
#endif
    cartproduct_shulen(state, fatherdepth, father->gnumdist, son->gnumdist);
    cartproduct_shulen(state, fatherdepth, son->gnumdist, father->gnumdist);
  }
  if (son != NULL)
  {
    for (idx = 0; idx < state->numofdbfiles; idx++)
    {
      father->gnumdist[idx] += son->gnumdist[idx];
      son->gnumdist[idx] = 0;
#ifdef SHUDEBUG
      printf("gnumdist[id=%lu,filenum=%lu]=%lu\n",father->id,idx,
                                                  father->gnumdist[idx]);
      printf("gnumdist[id=%lu,filenum=%lu]=0\n",son->id,idx);
#endif
    }
  }
  return 0;
}

static uint64_t **shulengthdist_new(unsigned long numofdbfiles)
{
  unsigned long idx1, idx2;
  uint64_t **shulengthdist;

  gt_array2dim_malloc(shulengthdist,numofdbfiles,numofdbfiles);
  for (idx1=0; idx1 < numofdbfiles; idx1++)
  {
    for (idx2=0; idx2 < numofdbfiles; idx2++)
    {
      shulengthdist[idx1][idx2] = 0;
    }
  }
  return shulengthdist;
}

/*
  XXX: check what kind of const annotation is necesseay to
  make the contents of shulengthdist non-writable.
*/

static void shulengthdist_print(const GtStrArray *file_names,
                                const uint64_t * const*shulengthdist,
                                unsigned long numofdbfiles)
{
  unsigned long idx1, idx2;

  /*shulengthdist[0][0] = 0; for testing */
  printf("# sum of shulen\n%lu\n",numofdbfiles);
  for (idx2=0; idx2 < numofdbfiles; idx2++)
  {
    if (file_names != NULL)
    {
      printf("%s\t",gt_str_array_get(file_names,idx2));
    } else
    {
      printf("%lu\t",idx2);
    }
    for (idx1=0; idx1 < numofdbfiles; idx1++)
    {
      if (idx1 != idx2)
      {
        printf(Formatuint64_t"\t",
               PRINTuint64_tcast(shulengthdist[idx1][idx2]));
      } else
      {
        printf("0.000000\t");
      }
    }
    printf("\n");
  }
}

#include "esa-bottomup-shulen.inc"

int gt_multiesa2shulengthdist_print(Sequentialsuffixarrayreader *ssar,
                                    const GtEncseq *encseq,
                                    GtError *err)
{
  GtBUstate_shulen *state;
  bool haserr = false;

  state = gt_malloc(sizeof (*state));
  state->numofdbfiles = gt_encseq_num_of_files(encseq);
  state->encseq = encseq;
#ifdef GENOMEDIFF_PAPER_IMPL
  state->leafdist = gt_malloc(sizeof (*state->leafdist) * state->numofdbfiles);
#endif
#ifdef SHUDEBUG
  state->nextid = 0;
#endif
  state->shulengthdist = shulengthdist_new(state->numofdbfiles);
  if (gt_esa_bottomup_shulen(ssar, state, err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    shulengthdist_print(NULL,(const uint64_t * const*) state->shulengthdist,
                        state->numofdbfiles);
  }
  gt_array2dim_delete(state->shulengthdist);
#ifdef GENOMEDIFF_PAPER_IMPL
  gt_free(state->leafdist);
#endif
  gt_free(state);
  return haserr ? -1 : 0;
}

static unsigned long gt_esa2shulengthatposition(const Suffixarray *suffixarray,
                                                unsigned long totallength,
                                                unsigned long offset,
                                                unsigned long left,
                                                unsigned long right,
                                                const GtUchar *qstart,
                                                const GtUchar *qend)
{
  Simplelcpinterval itv;
  const GtUchar *qptr;

  gt_assert(left < right);
  itv.left = left;
  itv.right = right;
  /*printf("\n");*/
  for (qptr = qstart; /* Nothing */; qptr++, offset++)
  {
    if (itv.left <= itv.right)
    {
      /*
      if (qptr < qend)
      {
        printf("read %u\n",(unsigned int) *qptr);
      }
      */
      if (qptr >= qend || ISSPECIAL(*qptr) ||
          !gt_lcpintervalfindcharchildintv(suffixarray->encseq,
                                           suffixarray->readmode,
                                           totallength,
                                           suffixarray->suftab,
                                           &itv,
                                           *qptr,
                                           offset,
                                           itv.left,
                                           itv.right))
      {
        break;
      }
    } else
    {
      break;
    }
  }
  /*printf("add %lu\n",offset+1); */
  return offset+1;
}

static unsigned long gt_esa2shulengthquery(const Suffixarray *suffixarray,
                                           const GtUchar *query,
                                           unsigned long querylen)
{
  const GtUchar *qptr;
  unsigned long totalgmatchlength = 0, gmatchlength, remaining;
  unsigned long totallength = gt_encseq_total_length(suffixarray->encseq);

  for (qptr = query, remaining = querylen; remaining > 0; qptr++, remaining--)
  {
    if (ISSPECIAL(*qptr))
    {
      gmatchlength = 0;
    } else
    {
      gmatchlength = gt_esa2shulengthatposition(suffixarray,
                                              totallength,
                                              0,
                                              0,
                                              totallength,
                                              qptr,
                                              query+querylen);
    }
    totalgmatchlength += gmatchlength;
  }
  return totalgmatchlength;
}

int gt_esa2shulengthqueryfiles(unsigned long *totalgmatchlength,
                               const Suffixarray *suffixarray,
                               const GtStrArray *queryfilenames,
                               GtError *err)
{
  bool haserr = false;
  GtSeqIterator *seqit;
  const GtUchar *query;
  unsigned long querylen;
  char *desc = NULL;
  int retval;
  GtAlphabet *alphabet;

  gt_error_check(err);
  alphabet = gt_encseq_alphabet(suffixarray->encseq);
  gt_assert(gt_str_array_size(queryfilenames) == 1UL);
  seqit = gt_seq_iterator_sequence_buffer_new(queryfilenames, err);
  if (!seqit)
  {
    haserr = true;
  }
  if (!haserr)
  {
    gt_seq_iterator_set_symbolmap(seqit, gt_alphabet_symbolmap(alphabet));
    for (; /* Nothing */; )
    {
      retval = gt_seq_iterator_next(seqit,
                                   &query,
                                   &querylen,
                                   &desc,
                                   err);
      if (retval < 0)
      {
        haserr = true;
        break;
      }
      if (retval == 0)
      {
        break;
      }
      *totalgmatchlength += gt_esa2shulengthquery(suffixarray,query,querylen);
    }
    gt_seq_iterator_delete(seqit);
  }
  return haserr ? -1 : 0;
}

int gt_multiesa2shulengthdist(Sequentialsuffixarrayreader *ssar,
                              const GtEncseq *encseq,
                              uint64_t **shulen,
                              const GtShuUnitFileInfo *unit_info,
                              GtError *err)
{
  GtBUstate_shulen *bustate;
  bool haserr = false;

  bustate = gt_malloc(sizeof (*bustate));
  bustate->numofdbfiles = unit_info->num_of_genomes;
  bustate->file_to_genome_map = unit_info->map_files;
  bustate->encseq = encseq;
#ifdef GENOMEDIFF_PAPER_IMPL
  bustate->leafdist
    = gt_malloc(sizeof (*bustate->leafdist) * bustate->numofdbfiles);
#endif
#ifdef SHUDEBUG
  bustate->nextid = 0;
#endif
  bustate->shulengthdist = shulen;
  if (gt_esa_bottomup_shulen(ssar, bustate, err) != 0)
  {
    haserr = true;
  }
#ifdef GENOMEDIFF_PAPER_IMPL
  gt_free(bustate->leafdist);
#endif
  gt_free(bustate);
  return haserr ? -1 : 0;
}

GtBUstate_shulen *gt_sfx_multiesashulengthdist_new(const GtEncseq *encseq,
                                            GenomediffInfo *gd_info)
{
  GtBUstate_shulen *bustate;

  bustate = gt_malloc(sizeof (*bustate));
  bustate->encseq = encseq;
  bustate->previousbucketlastsuffix = ULONG_MAX;
  bustate->idxoffset = 0;
  bustate->firstedgefromroot = false;
#ifdef SHUDEBUG
  bustate->nextid = 0;
#endif
  if (gd_info == NULL)
    bustate->unit_info = gt_shu_unit_info_new(encseq);
  else
    bustate->unit_info = gd_info->unit_info;

  bustate->numofdbfiles = gt_encseq_num_of_files(encseq);
#ifdef GENOMEDIFF_PAPER_IMPL
  bustate->leafdist
    = gt_malloc(sizeof (*bustate->leafdist) * bustate->numofdbfiles);
#endif
  bustate->file_to_genome_map = bustate->unit_info->map_files;
  if (gd_info == NULL)
    bustate->shulengthdist = shulengthdist_new(bustate->numofdbfiles);
  else
    bustate->shulengthdist = gd_info->shulensums;

  bustate->stack = (void *) gt_GtArrayGtBUItvinfo_new_shulen();
  return bustate;
}

#include "esa-bottomup-shulen-RAM.inc"

int gt_sfx_multiesa2shulengthdist(GtBUstate_shulen *bustate,
                                  const unsigned long *bucketofsuffixes,
                                  const uint32_t *bucketofsuffixes_uint32,
                                  const GtLcpvaluetype *lcptab_bucket,
                                  unsigned long numberofsuffixes,
                                  GtError *err)
{
  bool haserr = false;

  if (bustate->previousbucketlastsuffix != ULONG_MAX &&
      gt_esa_bottomup_RAM_previousfromlast_shulen(
                                 bustate->previousbucketlastsuffix,
                                 (unsigned long) lcptab_bucket[0],
                                 bustate->stack,
                                 bustate,
                                 err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (gt_esa_bottomup_RAM_shulen(bucketofsuffixes,
                                   bucketofsuffixes_uint32,
                                   lcptab_bucket,
                                   numberofsuffixes,
                                   bustate->stack,
                                   bustate,
                                   err) != 0)
    {
      haserr = true;
    }
  }
  bustate->idxoffset += numberofsuffixes;
  return haserr ? -1 : 0;
}

int gt_sfx_multiesa2shulengthdist_last(GtBUstate_shulen *bustate,GtError *err)
{
  if (bustate->previousbucketlastsuffix != ULONG_MAX &&
      gt_esa_bottomup_RAM_previousfromlast_shulen(
                                 bustate->previousbucketlastsuffix,
                                 0,
                                 bustate->stack,
                                 bustate,
                                 err) != 0)
  {
    return -1;
  }
  return 0;
}

void gt_sfx_multiesashulengthdist_delete(GtBUstate_shulen *bustate,
                                         GenomediffInfo *gd_info)
{
  if (bustate == NULL)
  {
    return;
  }
  gt_assert(bustate->shulengthdist != NULL);
  if (gd_info == NULL) {
    shulengthdist_print(bustate->unit_info->file_names,
                        (const uint64_t * const*) bustate->shulengthdist,
                        bustate->numofdbfiles);
    gt_array2dim_delete(bustate->shulengthdist);
    gt_shu_unit_info_delete(bustate->unit_info);
  }
  gt_GtArrayGtBUItvinfo_delete_shulen(bustate->stack,bustate);
#ifdef GENOMEDIFF_PAPER_IMPL
  gt_free(bustate->leafdist);
#endif
  gt_free(bustate);
}
genometools-1.5.1/src/match/esa-shulen.h000066400000000000000000000052271211610345200201520ustar00rootroot00000000000000/*
  Copyright (c) 2010 Stefan Kurtz 
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_SHULEN_H
#define ESA_SHULEN_H

#include "core/encseq_api.h"
#include "core/error_api.h"
#include "core/str_array.h"
#include "match/esa-seqread.h"
#include "match/shu_unitfile.h"
#include "match/genomediff_opt.h"

typedef struct GtBUstate_shulen GtBUstate_shulen;

int gt_multiesa2shulengthdist_print(Sequentialsuffixarrayreader *ssar,
                                    const GtEncseq *encseq,
                                    GtError *err);

int gt_esa2shulengthqueryfiles(unsigned long *totalgmatchlength,
                               const Suffixarray *suffixarray,
                               const GtStrArray *queryfilenames,
                               GtError *err);

int gt_multiesa2shulengthdist(Sequentialsuffixarrayreader *ssar,
                              const GtEncseq *encseq,
                              uint64_t **shulen,
                              const GtShuUnitFileInfo *unit_info,
                              GtError *err);

GtBUstate_shulen *gt_sfx_multiesashulengthdist_new(const GtEncseq *encseq,
                                                   GenomediffInfo *gd_info);

int gt_sfx_multiesa2shulengthdist(GtBUstate_shulen *bustate,
                                  const unsigned long *bucketofsuffixes,
                                  const uint32_t *bucketofsuffixes_uint32,
                                  const GtLcpvaluetype *lcptab_bucket,
                                  unsigned long numberofsuffixes,
                                  GtError *err);

int gt_sfx_multiesa2shulengthdist_last(GtBUstate_shulen *bustate,
                                       GtError *err);

void gt_sfx_multiesashulengthdist_delete(GtBUstate_shulen *bustate,
                                         GenomediffInfo *gd_info);

#endif
genometools-1.5.1/src/match/esa-splititv.c000066400000000000000000000141631211610345200205240ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/types_api.h"

#include "esa-splititv.h"

#define SEQUENCE(ENCSEQ,POS) (((POS) == totallength) \
                             ? (GtUchar) SEPARATOR\
                             : gt_encseq_get_encoded_char(ENCSEQ, \
                                                                 POS, \
                                                                 readmode))

static unsigned long lcpintervalfindrightbound(const GtEncseq *encseq,
                                        GtReadmode readmode,
                                        unsigned long totallength,
                                        const ESASuffixptr *suftab,
                                        GtUchar cc,
                                        unsigned long offset,
                                        unsigned long left,
                                        unsigned long right)
{
  unsigned long pos, mid;
  GtUchar midcc;

  while (right > left+1)
  {
    mid = GT_DIV2(left+right);
    pos = ESASUFFIXPTRGET(suftab,mid) + offset;
    midcc = SEQUENCE(encseq,pos);
    if (cc < midcc)
    {
      right = mid;
    } else
    {
      left = mid;
    }
  }
  return left;
}

bool gt_lcpintervalfindcharchildintv(const GtEncseq *encseq,
                                     GtReadmode readmode,
                                     unsigned long totallength,
                                     const ESASuffixptr *suftab,
                                     Simplelcpinterval *itv,
                                     GtUchar cc,
                                     unsigned long offset,
                                     unsigned long left,
                                     unsigned long right)
{
  GtUchar leftcc, rightcc;
  unsigned long pos, rightbound, leftbound = left;

  pos = ESASUFFIXPTRGET(suftab,right) + offset;
  rightcc = SEQUENCE(encseq,pos);
  while (true)
  {
    pos = ESASUFFIXPTRGET(suftab,leftbound) + offset;
    leftcc = SEQUENCE(encseq,pos);
    if (leftcc == rightcc)
    {
      break;
    }
    rightbound = lcpintervalfindrightbound(encseq,readmode,
                                           totallength,suftab,leftcc,
                                           offset,leftbound,right);
    if (leftcc == cc)
    {
      itv->left = leftbound;
      itv->right = rightbound;
      return true;
    }
    if (leftcc > cc)
    {
      return false;
    }
    leftbound = rightbound+1;
  }
  if (leftcc == cc)
  {
    itv->left = leftbound;
    itv->right = right;
    return true;
  }
  return false;
}

#define ADDCURRENTLBOUND(V)\
        bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar].lbound = V

#define ADDPREVIOUSRBOUND(V)\
        if (bwci->nextfreeBoundswithchar > 0)\
        {\
          bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar-1].rbound = V;\
        }

#define ADDCURRENTINCHAR(V)\
        bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar++].inchar = V

void gt_lcpintervalsplitwithoutspecial(GtArrayBoundswithchar *bwci,
                                       const GtEncseq *encseq,
                                       GtReadmode readmode,
                                       unsigned long totallength,
                                       const ESASuffixptr *suftab,
                                       unsigned long parentoffset,
                                       unsigned long parentleft,
                                       unsigned long parentright)
{
  GtUchar leftcc, rightcc;
  unsigned long rightbound = 0, leftbound = parentleft;

  /* call gt_lcpintervalextendlcp and verify if interval can be extended by
     some character */
  bwci->nextfreeBoundswithchar = 0;
  rightcc = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,parentright) + parentoffset);
  while (true)
  {
    leftcc = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,leftbound) + parentoffset);
    gt_assert(bwci->nextfreeBoundswithchar < bwci->allocatedBoundswithchar);
    if (ISSPECIAL(leftcc))
    {
      ADDPREVIOUSRBOUND(rightbound);
      ADDCURRENTLBOUND(rightbound+1);
      return;
    }
    ADDPREVIOUSRBOUND(leftbound-1);
    ADDCURRENTLBOUND(leftbound);
    ADDCURRENTINCHAR(leftcc);
    if (leftcc == rightcc)
    {
      break;
    }
    rightbound = lcpintervalfindrightbound(encseq,readmode,totallength,suftab,
                                           leftcc,parentoffset,
                                           leftbound,parentright);
    leftbound = rightbound+1;
  }
  gt_assert(bwci->nextfreeBoundswithchar < bwci->allocatedBoundswithchar);
  ADDPREVIOUSRBOUND(parentright);
  ADDCURRENTLBOUND(parentright+1);
}

GtUchar gt_lcpintervalextendlcp(const GtEncseq *encseq,
                                GtReadmode readmode,
                                const ESASuffixptr *suftab,
                                unsigned long totallength,
                                GtUchar alphasize,
                                unsigned long parentoffset,
                                unsigned long parentleft,
                                unsigned long parentright)
{
  GtUchar ccl, ccr;

  ccl = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,parentleft) + parentoffset);
  ccr = SEQUENCE(encseq,ESASUFFIXPTRGET(suftab,parentright) + parentoffset);
  if (ccl != ccr || ISSPECIAL(ccl))
  {
    return alphasize;
  }
  gt_assert(ccl < alphasize);
  return ccl;
}
genometools-1.5.1/src/match/esa-splititv.h000066400000000000000000000047701211610345200205340ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_SPLITITV_H
#define ESA_SPLITITV_H

#include "core/arraydef.h"
#include "core/types_api.h"

#include "core/encseq.h"
#include "match/sarr-def.h"
#include "splititv.h"

typedef struct
{
  unsigned long left,
         right;
} Simplelcpinterval;

bool gt_lcpintervalfindcharchildintv(const GtEncseq *encseq,
                                  GtReadmode readmode,
                                  unsigned long totallength,
                                  const ESASuffixptr *suftab,
                                  Simplelcpinterval *itv,
                                  GtUchar cc,
                                  unsigned long offset,
                                  unsigned long left,
                                  unsigned long right);

void gt_lcpintervalsplitwithoutspecial(GtArrayBoundswithchar *bwci,
                                    const GtEncseq *encseq,
                                    GtReadmode readmode,
                                    unsigned long totallength,
                                    const ESASuffixptr *suftab,
                                    unsigned long parentoffset,
                                    unsigned long parentleft,
                                    unsigned long parentright);

GtUchar gt_lcpintervalextendlcp(const GtEncseq *encseq,
                           GtReadmode readmode,
                           const ESASuffixptr *suftab,
                           unsigned long totallength,
                           GtUchar alphasize,
                           unsigned long parentoffset,
                           unsigned long parentleft,
                           unsigned long parentright);

#endif
genometools-1.5.1/src/match/esa-spmitvs.c000066400000000000000000000047331211610345200203550ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "core/mathsupport.h"
#include "match/esa_spmitvs_visitor.h"
#include "esa-spmitvs.h"
#include "esa-bottomup.h"

int gt_process_spmitv(const char *inputindex, GtLogger *logger, GtError *err)
{
  bool haserr = false;
  Sequentialsuffixarrayreader *ssar;

  gt_error_check(err);
  ssar = gt_newSequentialsuffixarrayreaderfromfile(inputindex,
                                                   SARR_LCPTAB |
                                                   SARR_SUFTAB |
                                                   SARR_ESQTAB,
                                                   SEQ_scan,
                                                   logger,
                                                   err);
  if (ssar == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    GtESAVisitor *ev;
    unsigned long nonspecials;

    nonspecials = gt_Sequentialsuffixarrayreader_nonspecials(ssar);
    ev = gt_esa_spmitvs_visitor_new(
                              gt_encseqSequentialsuffixarrayreader(ssar),
                              gt_readmodeSequentialsuffixarrayreader(ssar),
                              gt_Sequentialsuffixarrayreader_prefixlength(ssar),
                              err);

    if (gt_esa_bottomup(ssar, ev, err) != 0)
    {
      haserr = true;
    } else
    {
      gt_esa_spmitvs_visitor_print_results((GtESASpmitvsVisitor*) ev,
                                           nonspecials);
    }
    gt_esa_visitor_delete(ev);
  }
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/esa-spmitvs.h000066400000000000000000000020231211610345200203500ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_SPMITVS_H
#define ESA_SPMITVS_H

#include "core/logger_api.h"
#include "core/error_api.h"

int gt_process_spmitv(const char *inputindex, GtLogger *logger, GtError *err);

#endif
genometools-1.5.1/src/match/esa-spmsk.c000066400000000000000000000133671211610345200200100ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/unused_api.h"
#include "core/readmode_api.h"
#include "core/error_api.h"
#include "core/arraydef.h"
#include "esa-bottomup.h"
#include "esa-spmsk.h"

typedef struct
{
  unsigned long firstinW;
} GtBUinfo_spmsk;

struct GtBUstate_spmsk /* global information */
{
  const GtEncseq *encseq;
  GtReadmode readmode;
  unsigned long totallength,
                minmatchlength,
                spmcounter,
                spaceforbucketprocessing;
  bool countspms,
       outputspms;
  GtArrayGtUlong Wset, Lset;
  /* Declare the stack as void as the real type
     GtArrayGtBUItvinfo_spmsk is declared later in esa-bottomup-spmsk.inc */
  void *stack;
};

static void initBUinfo_spmsk(GtBUinfo_spmsk *buinfo,
                             GT_UNUSED GtBUstate_spmsk *state)
{
  buinfo->firstinW = ULONG_MAX;
}

static void freeBUinfo_spmsk(GT_UNUSED GtBUinfo_spmsk *info,
                             GT_UNUSED GtBUstate_spmsk *state)
{
  return;
}

static int processleafedge_spmsk(bool firstedge,
                                 unsigned long fd,
                                 GtBUinfo_spmsk *finfo,
                                 unsigned long seqnum,
                                 unsigned long relpos,
                                 GtBUstate_spmsk *state,
                                 GT_UNUSED GtError *err)

{
  if (fd >= state->minmatchlength)
  {
    if (firstedge)
    {
      gt_assert(finfo != NULL);
      ((GtBUinfo_spmsk *) finfo)->firstinW = state->Wset.nextfreeGtUlong;
    }
    if (relpos == 0)
    {
      GT_STOREINARRAY(&state->Wset,GtUlong,128,seqnum);
    }
    if (relpos + fd == gt_encseq_seqlength(state->encseq,seqnum))
    {
      GT_STOREINARRAY(&state->Lset,GtUlong,128,seqnum);
    }
  }
  return 0;
}

static int processlcpinterval_spmsk(unsigned long lcp,
                                    GtBUinfo_spmsk *info,
                                    GtBUstate_spmsk *state,
                                    GT_UNUSED GtError *err)
{
  if (lcp >= state->minmatchlength)
  {
    unsigned long lidx, widx, firstpos;

    gt_assert(info != NULL);
    firstpos = ((GtBUinfo_spmsk *) info)->firstinW;
    for (lidx = 0; lidx < state->Lset.nextfreeGtUlong; lidx++)
    {
      if (state->outputspms)
      {
        unsigned long lpos = state->Lset.spaceGtUlong[lidx];

        for (widx = firstpos; widx < state->Wset.nextfreeGtUlong; widx++)
        {
          printf("%lu %lu %lu\n",lpos,state->Wset.spaceGtUlong[widx],lcp);
        }
      } else
      {
        gt_assert(state->countspms);
        if (firstpos < state->Wset.nextfreeGtUlong)
        {
          state->spmcounter += state->Wset.nextfreeGtUlong - firstpos;
        }
      }
    }
    state->Lset.nextfreeGtUlong = 0;
  } else
  {
    state->Wset.nextfreeGtUlong = 0;
  }
  return 0;
}

#include "esa-bottomup-spmsk.inc"

GtBUstate_spmsk *gt_spmsk_inl_new(const GtEncseq *encseq,
                            GtReadmode readmode,
                            unsigned long minmatchlength,
                            bool countspms,
                            bool outputspms,
                            GT_UNUSED const char *indexname)
{
  GtBUstate_spmsk *state = gt_malloc(sizeof (*state));

  state->encseq = encseq;
  state->readmode = readmode;
  state->totallength = gt_encseq_total_length(encseq);
  state->minmatchlength = minmatchlength;
  state->countspms = countspms;
  state->outputspms = outputspms;
  state->spmcounter = 0;
  state->stack = (void *) gt_GtArrayGtBUItvinfo_new();
  GT_INITARRAY(&state->Wset,GtUlong);
  GT_INITARRAY(&state->Lset,GtUlong);
  return state;
}

unsigned long gt_spmsk_inl_delete(GtBUstate_spmsk *state)
{
  if (state != NULL)
  {
    unsigned long tmpcount;

    GT_FREEARRAY(&state->Wset,GtUlong);
    GT_FREEARRAY(&state->Lset,GtUlong);
    gt_GtArrayGtBUItvinfo_delete_spmsk(
                 (GtArrayGtBUItvinfo_spmsk *) state->stack,state);
    tmpcount = state->spmcounter;
    gt_free(state);
    return tmpcount;
  }
  return 0;
}

int gt_spmsk_inl_process(void *data,
                         const unsigned long *seqnum_relpos_bucket,
                         const GtSeqnumrelpos *snrp,
                         const uint16_t *lcptab_bucket,
                         unsigned long nonspecials,
                         unsigned long spaceforbucketprocessing,
                         GtError *err)
{
  GtBUstate_spmsk *state = (GtBUstate_spmsk *) data;

  gt_assert(snrp != NULL);
  gt_assert(lcptab_bucket != NULL);
  state->spaceforbucketprocessing = spaceforbucketprocessing;
  if (gt_esa_bottomup_RAM_spmsk(seqnum_relpos_bucket,
                                lcptab_bucket,
                                nonspecials,
                                (GtArrayGtBUItvinfo_spmsk *) state->stack,
                                state,
                                snrp,
                                err) != 0)
  {
    return -1;
  }
  return 0;
}

void gt_spmsk_inl_process_end(GT_UNUSED void *data)
{
  return;
}
genometools-1.5.1/src/match/esa-spmsk.h000066400000000000000000000050411211610345200200030ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_SPMSK_H
#define ESA_SPMSK_H

#include 
#include "core/unused_api.h"
#include "core/error_api.h"
#include "core/encseq_api.h"
#include "seqnumrelpos.h"

typedef struct GtBUstate_spmsk GtBUstate_spmsk;

GtBUstate_spmsk *gt_spmsk_inl_new(const GtEncseq *encseq,
                                  GtReadmode readmode,
                                  unsigned long minmatchlength,
                                  bool countspms,
                                  bool outputspms,
                                  GT_UNUSED const char *indexname);

unsigned long gt_spmsk_inl_delete(GtBUstate_spmsk *state);

int gt_spmsk_inl_process(void *data,
                         const unsigned long *seqnum_relpos_bucket,
                         const GtSeqnumrelpos *snrp,
                         const uint16_t *lcptab_bucket,
                         unsigned long nonspecials,
                         unsigned long spaceforbucketprocessing,
                         /* this parameter can be 0 in case where
                            user defined memlimit or derived
                            memlimit is not available. If it is available
                            then, value is > 0 and gives the amount of space
                            in bytes which can be used in the bucket processing
                            without exceeding the given memlimit. Note
                            that after each part, the bucket processing
                            machinery must delete its space to a minimum,
                            as all space required adds up to the maximum.
                         */
                         GtError *err);

void gt_spmsk_inl_process_end(GT_UNUSED void *data);

#endif
genometools-1.5.1/src/match/esa_lcpintervals_visitor.c000066400000000000000000000070401211610345200232110ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/class_alloc_lock.h"
#include "core/unused_api.h"
#include "esa_visitor_rep.h"
#include "esa_lcpintervals_visitor.h"

struct GtESALcpintervalsVisitor {
  const GtESAVisitor parent_instance;
};

#define gt_esa_lcpitvs_visitor_cast(GV)\
        gt_esa_visitor_cast(gt_esa_lcpitvs_visitor_class(), GV)

static int gt_esa_lcpitvs_visitor_processleafedge(GT_UNUSED GtESAVisitor *ev,
                                                  bool firstsucc,
                                                  unsigned long fd,
                                                  GT_UNUSED unsigned long flb,
                                                  GT_UNUSED
                                                         GtESAVisitorInfo *info,
                                                  unsigned long leafnumber,
                                                  GT_UNUSED GtError *err)

{
  printf("L %c %lu %lu %lu\n", firstsucc ? '1' : '0', fd, flb, leafnumber);
  return 0;
}

static int gt_esa_lcpitvs_visitor_processbranchingedge(
                                                    GT_UNUSED GtESAVisitor *ev,
                                                    bool firstsucc,
                                                    unsigned long fd,
                                                    unsigned long flb,
                                                    GT_UNUSED
                                                        GtESAVisitorInfo *finfo,
                                                    unsigned long sd,
                                                    unsigned long slb,
                                                    GT_UNUSED unsigned long srb,
                                                    GT_UNUSED
                                                        GtESAVisitorInfo *sinfo,
                                                    GT_UNUSED GtError *err)
{
  printf("B %c %lu %lu %lu %lu\n", firstsucc ? '1' : '0', fd, flb, sd, slb);
  return 0;
}

static const GtESAVisitorClass* gt_esa_lcpitvs_visitor_class(void)
{
  static const GtESAVisitorClass *esc = NULL;
  gt_class_alloc_lock_enter();
  if (!esc) {
    esc = gt_esa_visitor_class_new(sizeof (GtESALcpintervalsVisitor),
                                   NULL,
                                   gt_esa_lcpitvs_visitor_processleafedge,
                                   gt_esa_lcpitvs_visitor_processbranchingedge,
                                   NULL,
                                   NULL,
                                   NULL);
  }
  gt_class_alloc_lock_leave();
  return esc;
}

GtESAVisitor* gt_esa_lcpitvs_visitor_new(void)
{
  GtESAVisitor *ev = gt_esa_visitor_create(gt_esa_lcpitvs_visitor_class());
  return ev;
}
genometools-1.5.1/src/match/esa_lcpintervals_visitor.h000066400000000000000000000021121211610345200232110ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_LCPINTERVALS_VISITOR_H
#define ESA_LCPINTERVALS_VISITOR_H

#include "match/esa_visitor.h"

typedef struct GtESALcpintervalsVisitor GtESALcpintervalsVisitor;

GtESAVisitor*            gt_esa_lcpitvs_visitor_new(void);

#endif
genometools-1.5.1/src/match/esa_spmitvs_visitor.c000066400000000000000000000203171211610345200222120ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/class_alloc_lock.h"
#include "core/mathsupport.h"
#include "core/unused_api.h"
#include "esa-seqread.h"
#include "esa-spmitvs.h"
#include "esa-bottomup.h"
#include "esa_visitor_rep.h"
#include "esa_spmitvs_visitor.h"

typedef struct
{
  unsigned long wholeleaf, wholeleafwidth, nowholeleaf, nowholeleafwidth;
} Lcpintervalcount;

struct GtESASpmitvsVisitor {
  const GtESAVisitor parent_instance;
  unsigned long unnecessaryleaves,
                totallength,
                currentleafindex,
                lastwholeleaf,
                maxlen;
  unsigned int prefixlength;
  Lcpintervalcount *wholeleafcount;
  const GtEncseq *encseq;
  GtReadmode readmode;
};

#define gt_esa_spmitvs_visitor_cast(GV)\
        gt_esa_visitor_cast(gt_esa_spmitvs_visitor_class(), GV)

static bool gt_esa_spmitvs_visitor_iswholeleaf(const GtEncseq *encseq,
                                               GtReadmode readmode,
                                               unsigned long leafnumber)
{
  return (leafnumber > 0)
    ? gt_encseq_position_is_separator(encseq,leafnumber - 1,readmode)
    : true;
}

static int gt_esa_spmitvs_visitor_processleafedge(GtESAVisitor *ev,
                                                  GT_UNUSED bool firstsucc,
                                                  unsigned long fd,
                                                  GT_UNUSED unsigned long flb,
                                                  GT_UNUSED
                                                         GtESAVisitorInfo *info,
                                                  unsigned long leafnumber,
                                                  GT_UNUSED GtError *err)

{
  GtESASpmitvsVisitor *esv;
  gt_assert(ev);
  esv = gt_esa_spmitvs_visitor_cast(ev);

  if (gt_esa_spmitvs_visitor_iswholeleaf(esv->encseq,esv->readmode,leafnumber))
  {
    gt_assert(esv->currentleafindex != esv->totallength);
    esv->lastwholeleaf = esv->currentleafindex;
  } else
  {
    if (leafnumber + fd < esv->totallength &&
        !gt_encseq_position_is_separator(esv->encseq,
                                         leafnumber + fd,
                                         esv->readmode))
    {
      esv->unnecessaryleaves++;
    }
  }
  esv->currentleafindex++;
  return 0;
}

static int gt_esa_spmitvs_visitor_processbranchingedge(GtESAVisitor *ev,
                                                    GT_UNUSED bool firstsucc,
                                                    unsigned long fd,
                                                    GT_UNUSED unsigned long flb,
                                                    GT_UNUSED
                                                        GtESAVisitorInfo *finfo,
                                                    unsigned long sd,
                                                    unsigned long slb,
                                                    unsigned long srb,
                                                    GT_UNUSED
                                                        GtESAVisitorInfo *sinfo,
                                                    GT_UNUSED GtError *err)
{
  GtESASpmitvsVisitor *esv;
  unsigned long idx;
  gt_assert(ev);
  esv = gt_esa_spmitvs_visitor_cast(ev);

  for (idx=fd+1; idxmaxlen);
    if (esv->lastwholeleaf != esv->totallength &&
        esv->lastwholeleaf >= slb)
    {
      gt_assert(esv->lastwholeleaf <= srb);
      esv->wholeleafcount[idx].wholeleaf++;
      esv->wholeleafcount[idx].wholeleafwidth += (srb - slb + 1);
    } else
    {
      esv->wholeleafcount[idx].nowholeleaf++;
      esv->wholeleafcount[idx].nowholeleafwidth += (srb - slb + 1);
    }
  }
  return 0;
}

static int gt_esa_spmitvs_visitor_processlcpinterval(GtESAVisitor *ev,
                                                     unsigned long lcp,
                                                     unsigned long lb,
                                                     unsigned long rb,
                                                     GT_UNUSED
                                                         GtESAVisitorInfo *info,
                                                     GT_UNUSED GtError *err)
{
  GtESASpmitvsVisitor *esv;
  gt_assert(ev);
  esv = gt_esa_spmitvs_visitor_cast(ev);

  if (esv->lastwholeleaf != esv->totallength &&
      esv->lastwholeleaf >= lb)
  {
    gt_assert(lcp <= (unsigned long) esv->maxlen);
    gt_assert(esv->lastwholeleaf <= rb);
    esv->wholeleafcount[lcp].wholeleaf++;
    esv->wholeleafcount[lcp].wholeleafwidth += (rb - lb + 1);
  } else
  {
    esv->wholeleafcount[lcp].nowholeleaf++;
    esv->wholeleafcount[lcp].nowholeleafwidth += (rb - lb + 1);
  }
  return 0;
}

void gt_esa_spmitvs_visitor_delete(GtESAVisitor *ev)
{
  GtESASpmitvsVisitor *esv;
  gt_assert(ev);
  esv = gt_esa_spmitvs_visitor_cast(ev);
  gt_free(esv->wholeleafcount);
}

const GtESAVisitorClass* gt_esa_spmitvs_visitor_class()
{
  static const GtESAVisitorClass *esc = NULL;
  gt_class_alloc_lock_enter();
  if (!esc) {
    esc = gt_esa_visitor_class_new(sizeof (GtESASpmitvsVisitor),
                                   gt_esa_spmitvs_visitor_delete,
                                   gt_esa_spmitvs_visitor_processleafedge,
                                   gt_esa_spmitvs_visitor_processbranchingedge,
                                   gt_esa_spmitvs_visitor_processlcpinterval,
                                   NULL,
                                   NULL);
  }
  gt_class_alloc_lock_leave();
  return esc;
}

GtESAVisitor* gt_esa_spmitvs_visitor_new(const GtEncseq *encseq,
                                         GtReadmode readmode,
                                         unsigned int prefixlength,
                                         GT_UNUSED GtError *err)
{
  GtESAVisitor *ev = gt_esa_visitor_create(gt_esa_spmitvs_visitor_class());
  GtESASpmitvsVisitor *esv = gt_esa_spmitvs_visitor_cast(ev);

  esv->encseq = encseq;
  esv->readmode = readmode;
  esv->maxlen = gt_encseq_max_seq_length(encseq);
  esv->unnecessaryleaves = 0;
  esv->totallength = gt_encseq_total_length(encseq);
  esv->currentleafindex = 0;
  esv->lastwholeleaf = esv->totallength; /* undefined */
  esv->prefixlength = prefixlength;
  esv->wholeleafcount = gt_malloc(sizeof (*esv->wholeleafcount) *
                                 (esv->maxlen+1));
  memset(esv->wholeleafcount, 0,
         sizeof (*esv->wholeleafcount) * (esv->maxlen+1));

  return ev;
}

void gt_esa_spmitvs_visitor_print_results(GtESASpmitvsVisitor *esv,
                                          unsigned long nonspecials)
{
  unsigned long idx;
  printf("unnecessaryleaves=%lu (%.2f)\n",
         esv->unnecessaryleaves,
         (double) esv->unnecessaryleaves/nonspecials);
  for (idx = 0; idx<= esv->maxlen; idx++)
  {
    if (esv->wholeleafcount[idx].wholeleaf != 0 ||
        esv->wholeleafcount[idx].nowholeleaf != 0)
    {
      printf("wholeleaf[%lu]:num=%lu (%.2f), ",idx,
             esv->wholeleafcount[idx].wholeleaf,
             (double) esv->wholeleafcount[idx].wholeleaf/
                      (esv->wholeleafcount[idx].wholeleaf+
                       esv->wholeleafcount[idx].nowholeleaf));
      printf("width=%lu (%.2f)\n",
              esv->wholeleafcount[idx].wholeleafwidth,
              (double) esv->wholeleafcount[idx].wholeleafwidth/
                       esv->totallength);
    }
  }
}
genometools-1.5.1/src/match/esa_spmitvs_visitor.h000066400000000000000000000033111211610345200222120ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_SPMITVS_VISITOR_H
#define ESA_SPMITVS_VISITOR_H

#include "core/encseq_api.h"
#include "core/error_api.h"
#include "core/logger.h"
#include "match/esa_visitor.h"

typedef struct GtESASpmitvsVisitor GtESASpmitvsVisitor;

const GtESAVisitorClass* gt_esa_spmitvs_visitor_class(void);
GtESAVisitor*            gt_esa_spmitvs_visitor_new(const GtEncseq *encseq,
                                                    GtReadmode readmode,
                                                    unsigned int prefixlength,
                                                    GtError *err);
void                     gt_esa_spmitvs_visitor_print_results(
                                                     GtESASpmitvsVisitor*,
                                                     unsigned long nonspecials);

#endif
genometools-1.5.1/src/match/esa_visitor.c000066400000000000000000000122071211610345200204240ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/assert_api.h"
#include "core/class_alloc.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "match/esa_visitor_rep.h"

/* the  interface */
struct GtESAVisitorClass {
  size_t size;
  GtESAVisitorFreeFunc free;
  GtESAVisitorLeafEdgeFunc leafedge_func;
  GtESAVisitorBranchingEdgeFunc branchingedge_func;
  GtESAVisitorLCPIntervalFunc lcpinterval_func;
  GtESAVisitorInfoCreatorFunc create_info_func;
  GtESAVisitorInfoDestructorFunc delete_info_func;
};

const GtESAVisitorClass*
gt_esa_visitor_class_new(size_t size,
                         GtESAVisitorFreeFunc free,
                         GtESAVisitorLeafEdgeFunc leafedge_func,
                         GtESAVisitorBranchingEdgeFunc branchingedge_func,
                         GtESAVisitorLCPIntervalFunc lcpinterval_func,
                         GtESAVisitorInfoCreatorFunc create_info_func,
                         GtESAVisitorInfoDestructorFunc delete_info_func)
{
  GtESAVisitorClass *c_class;
  gt_assert(size);
  c_class = gt_class_alloc(sizeof *c_class);
  c_class->size = size;
  c_class->free = free;
  c_class->leafedge_func = leafedge_func;
  c_class->branchingedge_func = branchingedge_func;
  c_class->lcpinterval_func = lcpinterval_func;
  c_class->create_info_func = create_info_func;
  c_class->delete_info_func = delete_info_func;
  return c_class;
}

GtESAVisitor* gt_esa_visitor_create(const GtESAVisitorClass *evc)
{
  GtESAVisitor *ev;
  gt_assert(evc && evc->size);
  ev = gt_calloc((size_t) 1, evc->size);
  ev->c_class = evc;
  return ev;
}

void* gt_esa_visitor_cast(GT_UNUSED const GtESAVisitorClass *evc,
                           GtESAVisitor *ev)
{
  gt_assert(evc && ev && ev->c_class == evc);
  return ev;
}

GtESAVisitorInfo* gt_esa_visitor_info_new(GtESAVisitor *ev)
{
  gt_assert(ev && ev->c_class);
  if (ev->c_class->create_info_func != NULL)
    return ev->c_class->create_info_func(ev);
  return NULL;
}

void gt_esa_visitor_info_delete(GtESAVisitorInfo *info, GtESAVisitor *ev)
{
  gt_assert(ev && ev->c_class);
  if (ev->c_class->delete_info_func != NULL)
    ev->c_class->delete_info_func(info, ev);
}

int gt_esa_visitor_visit_leaf_edge(GtESAVisitor *ev,
                                   bool firstsucc,
                                   unsigned long fd,
                                   unsigned long flb,
                                   GtESAVisitorInfo *info,
                                   unsigned long leafnumber,
                                   GtError *err)
{
  gt_error_check(err);
  gt_assert(ev && ev->c_class);
  if (ev->c_class->leafedge_func != NULL)
    return ev->c_class->leafedge_func(ev, firstsucc, fd, flb, info, leafnumber,
                                      err);
  return 0;
}

int gt_esa_visitor_visit_branching_edge(GtESAVisitor *ev,
                                        bool firstsucc,
                                        unsigned long fd,
                                        unsigned long flb,
                                        GtESAVisitorInfo *finfo,
                                        unsigned long sd,
                                        unsigned long slb,
                                        unsigned long srb,
                                        GtESAVisitorInfo *sinfo,
                                        GtError *err)
{
  gt_error_check(err);
  gt_assert(ev && ev->c_class);
  if (ev->c_class->branchingedge_func != NULL)
    return ev->c_class->branchingedge_func(ev, firstsucc, fd, flb, finfo, sd,
                                           slb, srb, sinfo, err);
  return 0;
}

int gt_esa_visitor_visit_lcp_interval(GtESAVisitor *ev,
                                      unsigned long lcp,
                                      unsigned long lb,
                                      unsigned long rb,
                                      GtESAVisitorInfo *info,
                                      GtError *err)
{
  gt_error_check(err);
  gt_assert(ev && ev->c_class);
  if (ev->c_class->lcpinterval_func != NULL)
    return ev->c_class->lcpinterval_func(ev, lcp, lb, rb, info, err);
  return 0;
}

void gt_esa_visitor_delete(GtESAVisitor *ev)
{
  if (!ev) return;
  gt_assert(ev->c_class);
  if (ev->c_class->free != NULL)
    ev->c_class->free(ev);
  gt_free(ev);
}
genometools-1.5.1/src/match/esa_visitor.h000066400000000000000000000057131211610345200204350ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_VISITOR_H
#define ESA_VISITOR_H

#include 
#include "core/error_api.h"

typedef struct GtESAVisitor GtESAVisitor;
typedef struct GtESAVisitorClass GtESAVisitorClass;
typedef struct GtESAVisitorInfo GtESAVisitorInfo;

void*             gt_esa_visitor_cast(const GtESAVisitorClass*, GtESAVisitor*);
int               gt_esa_visitor_visit_leaf_edge(GtESAVisitor*,
                                                 bool,
                                                 unsigned long,
                                                 unsigned long,
                                                 GtESAVisitorInfo*,
                                                 unsigned long,
                                                 GtError*);
int               gt_esa_visitor_visit_branching_edge(GtESAVisitor*,
                                                      bool,
                                                      unsigned long,
                                                      unsigned long,
                                                      GtESAVisitorInfo*,
                                                      unsigned long,
                                                      unsigned long,
                                                      unsigned long,
                                                      GtESAVisitorInfo*,
                                                      GtError*);
int               gt_esa_visitor_visit_lcp_interval(GtESAVisitor*,
                                                    unsigned long,
                                                    unsigned long,
                                                    unsigned long,
                                                    GtESAVisitorInfo*,
                                                    GtError*);
void              gt_esa_visitor_delete(GtESAVisitor *ev);

GtESAVisitorInfo* gt_esa_visitor_info_new(GtESAVisitor*);
void              gt_esa_visitor_info_delete(GtESAVisitorInfo*,
                                             GtESAVisitor*);

#endif
genometools-1.5.1/src/match/esa_visitor_rep.h000066400000000000000000000072041211610345200213000ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ESA_VISITOR_REP_H
#define ESA_VISITOR_REP_H

#include 
#include "match/esa_visitor.h"

typedef void              (*GtESAVisitorFreeFunc)(GtESAVisitor*);
typedef GtESAVisitorInfo* (*GtESAVisitorInfoCreatorFunc)(GtESAVisitor*);
typedef void              (*GtESAVisitorInfoDestructorFunc)(GtESAVisitorInfo*,
                                                            GtESAVisitor*);
typedef int               (*GtESAVisitorLeafEdgeFunc)(GtESAVisitor*,
                                                      bool,
                                                      unsigned long,
                                                      unsigned long,
                                                      GtESAVisitorInfo*,
                                                      unsigned long,
                                                      GtError*);
typedef int               (*GtESAVisitorBranchingEdgeFunc)(GtESAVisitor*,
                                                           bool,
                                                           unsigned long,
                                                           unsigned long,
                                                           GtESAVisitorInfo*,
                                                           unsigned long,
                                                           unsigned long,
                                                           unsigned long,
                                                           GtESAVisitorInfo*,
                                                           GtError*);
typedef int               (*GtESAVisitorLCPIntervalFunc)(GtESAVisitor*,
                                                         unsigned long,
                                                         unsigned long,
                                                         unsigned long,
                                                         GtESAVisitorInfo*,
                                                         GtError*);

typedef struct GtESAVisitorMembers GtESAVisitorMembers;

struct GtESAVisitor {
  const GtESAVisitorClass *c_class;
  GtESAVisitorMembers *members;
};

const GtESAVisitorClass* gt_esa_visitor_class_new(size_t size,
                                                GtESAVisitorFreeFunc,
                                                GtESAVisitorLeafEdgeFunc,
                                                GtESAVisitorBranchingEdgeFunc,
                                                GtESAVisitorLCPIntervalFunc,
                                                GtESAVisitorInfoCreatorFunc,
                                                GtESAVisitorInfoDestructorFunc);
GtESAVisitor*            gt_esa_visitor_create(const GtESAVisitorClass*);

#endif
genometools-1.5.1/src/match/firstcodes-accum.c000066400000000000000000000201371211610345200213310ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/intbits.h"
#include "core/types_api.h"
#include "core/codetype.h"
#include "core/divmodmul.h"
#include "core/encseq.h"
#include "core/log_api.h"
#include "kmercodes.h"
#include "firstcodes-buf.h"
#include "firstcodes-accum.h"

#define GT_FIRSTCODES_ACCUM(BUF,CODE,RELPOS)\
        {\
          if ((BUF)->accum_all || (((RELPOS) > 0) &&\
              GT_MARKSUBSTRING_CHECKMARK((BUF)->markprefix,CODE) &&\
              GT_MARKSUBSTRING_CHECKMARK((BUF)->marksuffix,CODE)))\
          {\
            if ((BUF)->nextfree == (BUF)->allocated)\
            {\
              (BUF)->flush_function((BUF)->fciptr);\
            }\
            gt_assert ((BUF)->nextfree < (BUF)->allocated);\
            (BUF)->spaceGtUlong[(BUF)->nextfree++] = CODE;\
          }\
        }

static void gt_firstcodes_accum_kmerscan_range(
                                         const GtBitsequence *twobitencoding,
                                         unsigned int kmersize,
                                         unsigned int minmatchlength,
                                         unsigned long startpos,
                                         unsigned long length,
                                         unsigned long maxunitindex,
                                         GtCodeposbuffer *buf)
{
  const unsigned long maskright = GT_MASKRIGHT(kmersize);
  const unsigned long lastpossiblepos = length - minmatchlength;
  const unsigned long lastfrelpos = length - kmersize;
  const unsigned int shiftleft = GT_MULT2(kmersize-1);
  unsigned int shiftright;
  unsigned long unitindex, frelpos;
  GtTwobitencoding currentencoding;
  GtCodetype cc, marksubstringtmpcode, fcode, rccode;

  gt_assert(kmersize <= (unsigned int) GT_UNITSIN2BITENC);
  fcode = gt_kmercode_at_position(twobitencoding, startpos, kmersize);
  rccode = gt_kmercode_complement(gt_kmercode_reverse(fcode,kmersize),
                                  maskright);
  GT_FIRSTCODES_ACCUM(buf,fcode,0UL);
  if (kmersize == minmatchlength)
  {
    GT_FIRSTCODES_ACCUM(buf,rccode,lastfrelpos);
  }
  unitindex = GT_DIVBYUNITSIN2BITENC(startpos + kmersize);
  currentencoding = twobitencoding[unitindex];
  shiftright = (unsigned int)
               GT_MULT2(GT_UNITSIN2BITENC - 1 -
                        GT_MODBYUNITSIN2BITENC(startpos + kmersize));
  for (frelpos = 1UL; frelpos <= lastfrelpos; frelpos++)
  {
    cc = (GtCodetype) (currentencoding >> shiftright) & 3;
    fcode = ((fcode << 2) | cc) & maskright;
    rccode = (rccode >> 2) | ((cc ^ 3UL) << shiftleft);
    if (frelpos <= lastpossiblepos)
    {
      GT_FIRSTCODES_ACCUM(buf,fcode,frelpos);
    }
    if (lastfrelpos - frelpos <= lastpossiblepos)
    {
      GT_FIRSTCODES_ACCUM(buf,rccode,lastfrelpos - frelpos);
    }
    if (shiftright > 0)
    {
      shiftright -= 2;
    } else
    {
      gt_assert(unitindex < maxunitindex-1 || frelpos == lastfrelpos);
      if (unitindex < maxunitindex-1)
      {
        currentencoding = twobitencoding[++unitindex];
        shiftright = (unsigned int) (GT_INTWORDSIZE-2);
      }
    }
  }
}

static void gt_firstcodes_accum_kmerscan_eqlen(
                                     const GtBitsequence *twobitencoding,
                                     unsigned long equallength,
                                     unsigned long totallength,
                                     unsigned long maxunitindex,
                                     unsigned int kmersize,
                                     unsigned int minmatchlength,
                                     GtCodeposbuffer *buf)
{
  unsigned long startpos;

  if (equallength >= (unsigned long) kmersize)
  {
    for (startpos = 0; startpos < totallength; startpos += equallength+1)
    {
      gt_firstcodes_accum_kmerscan_range(twobitencoding,
                                         kmersize,
                                         minmatchlength,
                                         startpos,
                                         equallength,
                                         maxunitindex,
                                         buf);
    }
  }
}

static void gt_firstcodes_accum_kmerscan(const GtEncseq *encseq,
                                         const GtBitsequence *twobitencoding,
                                         unsigned long totallength,
                                         unsigned long maxunitindex,
                                         unsigned int kmersize,
                                         unsigned int minmatchlength,
                                         GtCodeposbuffer *buf)
{
  unsigned long laststart = 0;

  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;

    sri = gt_specialrangeiterator_new(encseq,true);
    while (gt_specialrangeiterator_next(sri,&range)
           && range.start < totallength)
    {
      gt_assert(range.start >= laststart);
      if (range.start - laststart >= (unsigned long) minmatchlength)
      {
        gt_firstcodes_accum_kmerscan_range(twobitencoding,
                                           kmersize,
                                           minmatchlength,
                                           laststart,
                                           range.start - laststart,
                                           maxunitindex,
                                           buf);
      }
      laststart = range.end;
    }
    gt_specialrangeiterator_delete(sri);
  }
  if (totallength - laststart >= (unsigned long) minmatchlength)
  {
    gt_firstcodes_accum_kmerscan_range(twobitencoding,
                                       kmersize,
                                       minmatchlength,
                                       laststart,
                                       totallength - laststart,
                                       maxunitindex,
                                       buf);
  }
}

void gt_firstcodes_accum_runkmerscan(const GtEncseq *encseq,
                                     unsigned int kmersize,
                                     unsigned int minmatchlength,
                                     GtCodeposbuffer *buf)
{
  const GtTwobitencoding *twobitencoding
    = gt_encseq_twobitencoding_export(encseq);
  unsigned long totallength, maxunitindex;

  if (gt_encseq_is_mirrored(encseq))
  {
    totallength = (gt_encseq_total_length(encseq)-1)/2;
  } else
  {
    totallength = gt_encseq_total_length(encseq);
  }
  maxunitindex = gt_unitsoftwobitencoding(totallength) - 1;
  if (gt_encseq_accesstype_get(encseq) == GT_ACCESS_TYPE_EQUALLENGTH)
  {
    unsigned long equallength = gt_encseq_equallength(encseq);

    gt_assert(equallength >= (unsigned long) kmersize);
    gt_firstcodes_accum_kmerscan_eqlen(twobitencoding,
                                       equallength,
                                       totallength,
                                       maxunitindex,
                                       kmersize,
                                       minmatchlength,
                                       buf);
  } else
  {
    gt_firstcodes_accum_kmerscan(encseq,
                                 twobitencoding,
                                 totallength,
                                 maxunitindex,
                                 kmersize,
                                 minmatchlength,
                                 buf);
  }
}
genometools-1.5.1/src/match/firstcodes-accum.h000066400000000000000000000023131211610345200213320ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FIRSTCODES_ACCUM_H
#define FIRSTCODES_ACCUM_H

#include "core/encseq_api.h"
#include "match/firstcodes-buf.h"

void gt_firstcodes_accum_runkmerscan(const GtEncseq *encseq,
                                     unsigned int kmersize,
                                     unsigned int minmatchlength,
                                     GtCodeposbuffer *buf);

#endif
genometools-1.5.1/src/match/firstcodes-buf.h000066400000000000000000000026231211610345200210220ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FIRSTCODES_BUF_H
#define FIRSTCODES_BUF_H

#include "core/types_api.h"
#include "marksubstring.h"
#include "seqnumrelpos.h"

typedef void (*GtCodeposbufferflushfunction)(void *);

typedef struct
{
  unsigned long currentmincode,
                currentmaxcode,
                nextfree,
                allocated;
  Gtmarksubstring *markprefix,
                  *marksuffix;
  GtCodeposbufferflushfunction flush_function;
  GtUlongPair *spaceGtUlongPair;
  GtUlong *spaceGtUlong;
  GtSeqnumrelpos *snrp;
  void *fciptr;
  bool accum_all;
} GtCodeposbuffer;

#endif
genometools-1.5.1/src/match/firstcodes-cache.c000066400000000000000000000200211211610345200212740ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/arraydef.h"
#include "core/divmodmul.h"
#include "core/log_api.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "firstcodes-cache.h"
#include "firstcodes-spacelog.h"
#include 
#include 

typedef struct
{
  unsigned long afcindex, code;
} GtIndexwithcode;

struct GtArrayGtIndexwithcode
{
  GtIndexwithcode *spaceGtIndexwithcode;
  unsigned long width, nextfreeGtIndexwithcode, allocatedGtIndexwithcode;
  unsigned int depth;
};

GtArrayGtIndexwithcode *gt_firstcodes_binsearchcache_new(
                                      unsigned long differentcodes,
                                      unsigned int addbscache_depth,
                                      GtFirstcodesspacelog *fcsl)
{
  unsigned int depth = addbscache_depth +
                       (unsigned int) log10((double) differentcodes);
  while (true)
  {
    unsigned long allocated = 1UL << (depth+1);
    if (allocated < differentcodes && differentcodes/allocated >= 32UL)
    {
      GtArrayGtIndexwithcode *binsearchcache;
      size_t allocbytes;

      binsearchcache = gt_malloc(sizeof (*binsearchcache));
      binsearchcache->depth = depth;
      binsearchcache->nextfreeGtIndexwithcode = 0;
      binsearchcache->allocatedGtIndexwithcode = allocated;
      binsearchcache->width = differentcodes/allocated;
      allocbytes = sizeof (*binsearchcache->spaceGtIndexwithcode)
                   * binsearchcache->allocatedGtIndexwithcode;
      gt_assert(binsearchcache->width > 0);
      binsearchcache->spaceGtIndexwithcode = gt_malloc(allocbytes);
      gt_log_log("binsearchcache->depth=%u => %lu bytes",
                 binsearchcache->depth,
                 (unsigned long) allocbytes);
      GT_FCI_ADDWORKSPACE(fcsl,"binsearchcache",allocbytes);
      return binsearchcache;
    } else
    {
      if (depth > 0)
      {
        depth--;
      } else
      {
        break;
      }
    }
  }
  return NULL;
}

unsigned long gt_firstcodes_binsearchcache_width(const GtArrayGtIndexwithcode
                                                 *binsearchcache)
{
  return binsearchcache->width;
}

void gt_firstcodes_binsearchcache_set_index_code(GtArrayGtIndexwithcode
                                                 *binsearchcache,
                                                 unsigned long afcindex,
                                                 unsigned long code)
{
  if (binsearchcache->nextfreeGtIndexwithcode <
      binsearchcache->allocatedGtIndexwithcode)
  {
    binsearchcache->spaceGtIndexwithcode
      [binsearchcache->nextfreeGtIndexwithcode].afcindex = afcindex;
    binsearchcache->spaceGtIndexwithcode
      [binsearchcache->nextfreeGtIndexwithcode++].code = code;
  }
}

void gt_firstcodes_binsearchcache_check(GtArrayGtIndexwithcode *binsearchcache,
                                       GT_UNUSED const unsigned long
                                                                 *allfirstcodes,
                                       unsigned long differentcodes)
{
  if (binsearchcache != NULL)
  {
    unsigned long idx, current = binsearchcache->width;

    gt_assert(binsearchcache->spaceGtIndexwithcode != NULL);
    for (idx=0; idx < binsearchcache->nextfreeGtIndexwithcode &&
                current < differentcodes; idx++)
    {
      gt_assert(binsearchcache->spaceGtIndexwithcode[idx].afcindex == current);
      gt_assert(binsearchcache->spaceGtIndexwithcode[idx].code
                == allfirstcodes[current]);
      current += binsearchcache->width;
    }
  }
}

void gt_firstcodes_binsearchcache_delete(GtArrayGtIndexwithcode *binsearchcache,
                                         GtFirstcodesspacelog *fcsl)
{
  if (binsearchcache != NULL)
  {
    if (binsearchcache->spaceGtIndexwithcode != NULL)
    {
      GT_FCI_SUBTRACTWORKSPACE(fcsl,"binsearchcache");
      GT_FREEARRAY(binsearchcache,GtIndexwithcode);
    }
    gt_free (binsearchcache);
  }
}

unsigned long gt_firstcodes_find_accu(unsigned long *foundcode,
                                      const unsigned long *differences,
                                      unsigned long allfirstcodes0,
                                      unsigned long differentcodes,
                                      unsigned long differencemask,
                                      const GtArrayGtIndexwithcode
                                         *binsearchcache,
                                      unsigned long code)
{
  unsigned long leftptr = ULONG_MAX, rightptr = ULONG_MAX,
                foundindex = ULONG_MAX, previouscode = ULONG_MAX;

  if (code <= allfirstcodes0)
  {
    *foundcode = allfirstcodes0;
    return 0;
  }
  *foundcode = ULONG_MAX;
  if (binsearchcache != NULL)
  {
    const GtIndexwithcode *leftic, *midic, *rightic;
    unsigned int depth;

    gt_assert(binsearchcache->spaceGtIndexwithcode != NULL);
    leftic = binsearchcache->spaceGtIndexwithcode;
    rightic = binsearchcache->spaceGtIndexwithcode +
              binsearchcache->nextfreeGtIndexwithcode - 1;
    for (depth = 0; /* Nothing */; depth++)
    {
      midic = leftic + GT_DIV2((unsigned long) (rightic-leftic));
      if (code < midic->code)
      {
        foundindex = midic->afcindex;
        *foundcode = midic->code;
        if (depth < binsearchcache->depth)
        {
          rightic = midic - 1;
        } else
        {
          gt_assert(leftic->afcindex != ULONG_MAX &&
                    rightic->afcindex != ULONG_MAX);
          if (leftic > binsearchcache->spaceGtIndexwithcode)
          {
            leftptr = (leftic-1)->afcindex + 1;
            previouscode = (leftic-1)->code;
          } else
          {
            gt_assert(code > allfirstcodes0);
            leftptr = 1UL;
            previouscode = allfirstcodes0;
          }
          gt_assert(rightic->afcindex > 0);
          rightptr = rightic->afcindex - 1;
          break;
        }
      } else
      {
        if (code > midic->code)
        {
          if (depth < binsearchcache->depth)
          {
            leftic = midic + 1;
          } else
          {
            gt_assert(leftic->afcindex != ULONG_MAX &&
                      rightic->afcindex != ULONG_MAX);
            leftptr = leftic->afcindex + 1;
            previouscode = leftic->code;
            if (rightic < binsearchcache->spaceGtIndexwithcode +
                          binsearchcache->nextfreeGtIndexwithcode - 1)
            {
              gt_assert((rightic+1)->afcindex > 0);
              rightptr = (rightic+1)->afcindex - 1;
            } else
            {
              rightptr = differentcodes - 1;
            }
            break;
          }
        } else
        {
          gt_assert(midic->afcindex != ULONG_MAX);
          *foundcode = midic->code;
          return midic->afcindex;
        }
      }
    }
    gt_assert(leftptr != ULONG_MAX && rightptr != ULONG_MAX);
  } else
  {
    leftptr = 1UL;
    previouscode = allfirstcodes0;
    rightptr = differentcodes - 1;
  }
  if (leftptr <= rightptr)
  {
    unsigned long idx;

    for (idx = leftptr; idx <= rightptr; idx++)
    {
      previouscode += (differences[idx] & differencemask); /* extract diff */
      if (code <= previouscode)
      {
        *foundcode = previouscode;
        foundindex = idx;
        break;
      }
    }
  }
  return foundindex;
}
genometools-1.5.1/src/match/firstcodes-cache.h000066400000000000000000000050231211610345200213060ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FIRSTCODES_CACHE_H
#define FIRSTCODES_CACHE_H

#include "firstcodes-spacelog.h"

typedef struct GtArrayGtIndexwithcode GtArrayGtIndexwithcode;

GtArrayGtIndexwithcode *gt_firstcodes_binsearchcache_new(
                                      unsigned long differentcodes,
                                      unsigned int addbscache_depth,
                                      GtFirstcodesspacelog *fcsl);

void gt_firstcodes_binsearchcache_check(GtArrayGtIndexwithcode *binsearchcache,
                                       const unsigned long *allfirstcodes,
                                       unsigned long differentcodes);

void gt_firstcodes_binsearchcache_delete(GtArrayGtIndexwithcode *binsearchcache,
                                         GtFirstcodesspacelog *fcsl);

unsigned long gt_firstcodes_binsearchcache_width(const GtArrayGtIndexwithcode
                                                 *binsearchcache);

void gt_firstcodes_binsearchcache_set_index_code(GtArrayGtIndexwithcode
                                                 *binsearchcache,
                                                 unsigned long afcindex,
                                                 unsigned long code);

unsigned long gt_firstcodes_find_accu(
                                 unsigned long *foundcode,
                                 const unsigned long *differences,
                                 unsigned long allfirstcodes0,
                                 unsigned long differentcodes,
                                 unsigned long differencemask,
                                 const GtArrayGtIndexwithcode *binsearchcache,
                                 unsigned long code);

#endif
genometools-1.5.1/src/match/firstcodes-insert.c000066400000000000000000000224251211610345200215470ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/intbits.h"
#include "core/types_api.h"
#include "core/codetype.h"
#include "core/divmodmul.h"
#include "core/encseq.h"
#include "kmercodes.h"
#include "firstcodes-buf.h"
#include "firstcodes-insert.h"

#define GT_FIRSTCODES_INSERTSUFFIXES(BUF,CODE,SEQNUM,RELPOS)\
        {\
          if ((BUF)->currentmincode <= (CODE) &&\
              (CODE) <= (BUF)->currentmaxcode &&\
              GT_MARKSUBSTRING_CHECKMARK((BUF)->markprefix,CODE) &&\
              GT_MARKSUBSTRING_CHECKMARK((BUF)->marksuffix,CODE))\
          {\
            if ((BUF)->nextfree == (BUF)->allocated)\
            {\
              (BUF)->flush_function((BUF)->fciptr);\
            }\
            gt_assert ((BUF)->nextfree < (BUF)->allocated);\
            (BUF)->spaceGtUlongPair[(BUF)->nextfree].a = CODE;\
            (BUF)->spaceGtUlongPair[(BUF)->nextfree++].b\
              = gt_seqnumrelpos_encode((BUF)->snrp,SEQNUM,RELPOS);\
          }\
        }

static void gt_firstcodes_insert_kmerscan_range(
                                         const GtBitsequence *twobitencoding,
                                         unsigned int kmersize,
                                         unsigned int minmatchlength,
                                         unsigned long startpos,
                                         unsigned long length,
                                         unsigned long fseqnum,
                                         unsigned long rseqnum,
                                         unsigned long maxunitindex,
                                         GtCodeposbuffer *buf)
{
  const unsigned long maskright = GT_MASKRIGHT(kmersize);
  const unsigned long lastpossiblepos = length - minmatchlength;
  const unsigned long lastfrelpos = length - kmersize;
  const unsigned int shiftleft = GT_MULT2(kmersize-1);
  unsigned int shiftright;
  unsigned long unitindex, frelpos;
  GtTwobitencoding currentencoding;
  GtCodetype cc, marksubstringtmpcode, fcode, rccode;

  gt_assert(kmersize <= (unsigned int) GT_UNITSIN2BITENC);
  fcode = gt_kmercode_at_position(twobitencoding, startpos, kmersize);
  rccode = gt_kmercode_complement(gt_kmercode_reverse(fcode,kmersize),
                                  maskright);
  GT_FIRSTCODES_INSERTSUFFIXES(buf,fcode,fseqnum,0UL);
  if (kmersize == minmatchlength)
  {
    GT_FIRSTCODES_INSERTSUFFIXES(buf,rccode,rseqnum,lastfrelpos);
  }
  unitindex = GT_DIVBYUNITSIN2BITENC(startpos + kmersize);
  currentencoding = twobitencoding[unitindex];
  shiftright = (unsigned int)
               GT_MULT2(GT_UNITSIN2BITENC - 1 -
                        GT_MODBYUNITSIN2BITENC(startpos + kmersize));
  for (frelpos = 1UL; frelpos <= lastfrelpos; frelpos++)
  {
    cc = (GtCodetype) (currentencoding >> shiftright) & 3;
    fcode = ((fcode << 2) | cc) & maskright;
    rccode = (rccode >> 2) | ((cc ^ 3UL) << shiftleft);
    if (frelpos <= lastpossiblepos)
    {
      GT_FIRSTCODES_INSERTSUFFIXES(buf,fcode,fseqnum,frelpos);
    }
    if (lastfrelpos - frelpos <= lastpossiblepos)
    {
      GT_FIRSTCODES_INSERTSUFFIXES(buf,rccode,rseqnum,lastfrelpos - frelpos);
    }
    if (shiftright > 0)
    {
      shiftright -= 2;
    } else
    {
      gt_assert(unitindex < maxunitindex-1 || frelpos == lastfrelpos);
      if (unitindex < maxunitindex-1)
      {
        currentencoding = twobitencoding[++unitindex];
        shiftright = (unsigned int) (GT_INTWORDSIZE-2);
      }
    }
  }
}

static void gt_firstcodes_insert_kmerscan_eqlen(
                                     const GtBitsequence *twobitencoding,
                                     unsigned long equallength,
                                     unsigned long totallength,
                                     unsigned long numofsequences,
                                     unsigned long maxunitindex,
                                     unsigned int kmersize,
                                     unsigned int minmatchlength,
                                     GtCodeposbuffer *buf)
{
  unsigned long startpos, fseqnum;

  if (equallength >= (unsigned long) kmersize)
  {
    for (startpos = 0, fseqnum = 0; startpos < totallength;
         startpos += equallength+1, fseqnum++)
    {
      gt_firstcodes_insert_kmerscan_range(twobitencoding,
                                          kmersize,
                                          minmatchlength,
                                          startpos,
                                          equallength,
                                          fseqnum,
                                          numofsequences - 1 - fseqnum,
                                          maxunitindex,
                                          buf);
    }
  }
}

static void gt_firstcodes_insert_kmerscan(const GtEncseq *encseq,
                                          const GtBitsequence *twobitencoding,
                                          unsigned long totallength,
                                          unsigned long numofsequences,
                                          unsigned long maxunitindex,
                                          unsigned int kmersize,
                                          unsigned int minmatchlength,
                                          GtCodeposbuffer *buf)
{
  unsigned long laststart = 0, fseqnum = 0;

  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;

    sri = gt_specialrangeiterator_new(encseq,true);
    while (gt_specialrangeiterator_next(sri,&range)
           && range.start < totallength)
    {
      gt_assert(range.start >= laststart);
      if (range.start - laststart >= (unsigned long) minmatchlength)
      {
        gt_firstcodes_insert_kmerscan_range(twobitencoding,
                                            kmersize,
                                            minmatchlength,
                                            laststart,
                                            range.start - laststart,
                                            fseqnum,
                                            numofsequences - 1 - fseqnum,
                                            maxunitindex,
                                            buf);
      }
      laststart = range.end;
      fseqnum++;
    }
    gt_specialrangeiterator_delete(sri);
  }
  if (totallength - laststart >= (unsigned long) minmatchlength)
  {
    gt_firstcodes_insert_kmerscan_range(twobitencoding,
                                        kmersize,
                                        minmatchlength,
                                        laststart,
                                        totallength - laststart,
                                        fseqnum,
                                        numofsequences - 1 - fseqnum,
                                        maxunitindex,
                                        buf);
  }
}

void gt_firstcodes_insert_runkmerscan(const GtEncseq *encseq,
                                      unsigned int kmersize,
                                      unsigned int minmatchlength,
                                      GtCodeposbuffer *buf)
{
  const GtTwobitencoding *twobitencoding
    = gt_encseq_twobitencoding_export(encseq);
  unsigned long totallength, maxunitindex, numofsequences;

  gt_assert(minmatchlength>=kmersize);
  if (gt_encseq_is_mirrored(encseq))
  {
    totallength = (gt_encseq_total_length(encseq)-1)/2;
  } else
  {
    totallength = gt_encseq_total_length(encseq);
  }
  numofsequences = gt_encseq_num_of_sequences(encseq);
  maxunitindex = gt_unitsoftwobitencoding(totallength) - 1;
  if (gt_encseq_accesstype_get(encseq) == GT_ACCESS_TYPE_EQUALLENGTH)
  {
    unsigned long equallength = gt_encseq_equallength(encseq);

    gt_assert(equallength >= (unsigned long) kmersize);
    gt_firstcodes_insert_kmerscan_eqlen(twobitencoding,
                                        equallength,
                                        totallength,
                                        numofsequences,
                                        maxunitindex,
                                        kmersize,
                                        minmatchlength,
                                        buf);
  } else
  {
    gt_firstcodes_insert_kmerscan(encseq,
                                  twobitencoding,
                                  totallength,
                                  numofsequences,
                                  maxunitindex,
                                  kmersize,
                                  minmatchlength,
                                  buf);
  }
}
genometools-1.5.1/src/match/firstcodes-insert.h000066400000000000000000000023211211610345200215450ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FIRSTCODES_INSERT_H
#define FIRSTCODES_INSERT_H

#include "core/encseq_api.h"
#include "match/firstcodes-buf.h"

void gt_firstcodes_insert_runkmerscan(const GtEncseq *encseq,
                                      unsigned int kmersize,
                                      unsigned int minmatchlength,
                                      GtCodeposbuffer *buf);

#endif
genometools-1.5.1/src/match/firstcodes-psbuf.c000066400000000000000000000055761211610345200213720ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#endif
#include "core/fa.h"
#include "core/str_api.h"
#include "core/xansi_api.h"
#include "core/ma.h"
#include "core/log.h"
#include "firstcodes-psbuf.h"
#include "firstcodes-spacelog.h"

GtLeftborderOutbuffer *gt_leftborderbuffer_new(const char *name,
                                               GtFirstcodesspacelog *fcsl)
{
  GtLeftborderOutbuffer *lbbuf = gt_malloc(sizeof (*lbbuf));

  lbbuf->totalwrite = 0;
  lbbuf->outfilename = gt_str_new();
  lbbuf->fp = gt_xtmpfp(lbbuf->outfilename);
  lbbuf->nextfree = 0;
  lbbuf->allocated = 1024UL;
  lbbuf->name = gt_str_new_cstr(name);
  lbbuf->spaceuint32_t = gt_malloc(sizeof (*lbbuf->spaceuint32_t) *
                                   lbbuf->allocated);
  GT_FCI_ADDWORKSPACE(fcsl,name,
                      sizeof (*lbbuf->spaceuint32_t) * lbbuf->allocated);
  return lbbuf;
}

void gt_leftborderbuffer_flush(GtLeftborderOutbuffer *leftborderbuffer)
{
  gt_xfwrite(leftborderbuffer->spaceuint32_t,
             sizeof (*leftborderbuffer->spaceuint32_t),
             (size_t) leftborderbuffer->nextfree,
             leftborderbuffer->fp);
  leftborderbuffer->totalwrite += leftborderbuffer->nextfree;
  leftborderbuffer->nextfree = 0;
}

GtStr *gt_leftborderbuffer_delete(GtLeftborderOutbuffer *lbbuf,
                                  GtFirstcodesspacelog *fcsl,
                                  GT_UNUSED unsigned long expectedwritten)
{
  GtStr *outfilename;

  gt_assert(lbbuf != NULL);
  gt_leftborderbuffer_flush(lbbuf);
  gt_fa_fclose(lbbuf->fp);
  lbbuf->fp = NULL;
  gt_log_log("write %s to file %s (%lu units of size %u)",
             gt_str_get(lbbuf->name),
             gt_str_get(lbbuf->outfilename),
             lbbuf->totalwrite,(unsigned int) sizeof (*lbbuf->spaceuint32_t));
  gt_assert(lbbuf->spaceuint32_t != NULL);
  gt_free(lbbuf->spaceuint32_t);
  GT_FCI_SUBTRACTWORKSPACE(fcsl,gt_str_get(lbbuf->name));
  gt_assert(lbbuf->totalwrite == expectedwritten);
  outfilename = lbbuf->outfilename;
  gt_str_delete(lbbuf->name);
  gt_free(lbbuf);
  return outfilename;
}
genometools-1.5.1/src/match/firstcodes-psbuf.h000066400000000000000000000030531211610345200213630ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FIRSTCODES_PSBUF_H
#define FIRSTCODES_PSBUF_H

#include 
#include "core/unused_api.h"
#include "firstcodes-spacelog.h"

typedef struct
{
  uint32_t *spaceuint32_t;
  unsigned long nextfree, allocated, totalwrite;
  GtStr *outfilename, *name;
  FILE *fp;
} GtLeftborderOutbuffer;

GtLeftborderOutbuffer *gt_leftborderbuffer_new(const char *name,
                                               GtFirstcodesspacelog *fcsl);

void gt_leftborderbuffer_flush(GtLeftborderOutbuffer *leftborderbuffer);

GtStr *gt_leftborderbuffer_delete(GtLeftborderOutbuffer *lbbuf,
                                  GtFirstcodesspacelog *fcsl,
                                  GT_UNUSED unsigned long expectedwritten);

#endif
genometools-1.5.1/src/match/firstcodes-scan.c000066400000000000000000000274401211610345200211710ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/intbits.h"
#include "core/types_api.h"
#include "core/codetype.h"
#include "core/divmodmul.h"
#include "core/encseq.h"
#include "core/log_api.h"
#include "kmercodes.h"
#include "firstcodes-scan.h"

#undef WITHCHECK
#ifdef WITHCHECK
static void gt_firstcode_verifycodes(const GtBitsequence *twobitencoding,
                                     unsigned long position,
                                     unsigned int kmersize,
                                     GtCodetype fcode,
                                     GtCodetype rccode)
{
  GtCodetype bfcode = gt_kmercode_at_position(twobitencoding,position,kmersize),
             bfrccode = gt_kmercode_complement(
                                     gt_kmercode_reverse(bfcode,kmersize),
                                     GT_MASKRIGHT(kmersize));

  gt_assert(fcode == bfcode);
  if (rccode != bfrccode)
  {
    printf("position %lu: fcode=%lu,rccode=%lu != %lu\n",position,fcode,
            rccode,bfrccode);
    exit(EXIT_FAILURE);
  }
}
#endif

typedef void (*GtProcesskmercode)(GtCodetype,unsigned long,
                                  unsigned long,void *);

static GtTwobitencoding gt_firstcodes_kmerscan_range(
                                         const GtBitsequence *twobitencoding,
                                         GT_UNUSED bool withcheck,
                                         unsigned int kmersize,
                                         unsigned int minmatchlength,
                                         unsigned long startpos,
                                         unsigned long endpos,
                                         unsigned long fseqnum,
                                         unsigned long rseqnum,
                                         unsigned long maxunitindex,
                                         GtProcesskmercode processcode,
                                         void *data)
{
  GtTwobitencoding currentencoding, encodingsum = 0;
  unsigned int shiftright;
  const unsigned int shiftleft = GT_MULT2(kmersize-1);
  GtCodetype cc, fcode, rccode;
  unsigned long position, unitindex, frelpos;
  const unsigned long maskright = GT_MASKRIGHT(kmersize);
  const unsigned long lastpossiblepos = endpos - startpos - minmatchlength;
  const unsigned long lastfrelpos = endpos - startpos - kmersize;

  gt_assert(kmersize <= (unsigned int) GT_UNITSIN2BITENC);
  position = startpos;
  fcode = gt_kmercode_at_position(twobitencoding, position, kmersize);
  rccode = gt_kmercode_complement(gt_kmercode_reverse(fcode,kmersize),
                                  maskright);
  if (processcode != NULL)
  {
    processcode(fcode,fseqnum,0,data);
    if (lastfrelpos <= lastpossiblepos)
    {
      processcode(rccode,rseqnum,lastfrelpos,data);
    }
  }
  unitindex = GT_DIVBYUNITSIN2BITENC(startpos + kmersize);
  currentencoding = twobitencoding[unitindex];
  encodingsum += currentencoding;
  shiftright = (unsigned int)
               GT_MULT2(GT_UNITSIN2BITENC - 1 -
                        GT_MODBYUNITSIN2BITENC(startpos + kmersize));
  gt_assert(endpos >= (unsigned long) kmersize);
  endpos -= kmersize;
  frelpos = 1UL;
  while (position < endpos)
  {
    position++;
    cc = (GtCodetype) (currentencoding >> shiftright) & 3;
    fcode = ((fcode << 2) | cc) & maskright;
    rccode = (rccode >> 2) | ((cc ^ 3UL) << shiftleft);
    if (processcode != NULL)
    {
      gt_assert(lastfrelpos >= frelpos);
      if (frelpos <= lastpossiblepos)
      {
        processcode(fcode,fseqnum,frelpos,data);
      }
      if (lastfrelpos - frelpos <= lastpossiblepos)
      {
        processcode(rccode,rseqnum,lastfrelpos - frelpos,data);
      }
    }
#ifdef WITHCHECK
    if (withcheck)
    {
      gt_firstcode_verifycodes(twobitencoding,
                               position,
                               kmersize,
                               fcode,
                               rccode);
    }
#endif
    if (shiftright > 0)
    {
      shiftright -= 2;
    } else
    {
      gt_assert(unitindex < maxunitindex-1 || position == endpos);
      if (unitindex < maxunitindex-1)
      {
        currentencoding = twobitencoding[++unitindex];
        encodingsum += currentencoding;
        shiftright = (unsigned int) (GT_INTWORDSIZE-2);
      }
    }
    frelpos++;
  }
  return encodingsum;
}

unsigned long gt_firstcodes_kmerscan_eqlen(const GtBitsequence *twobitencoding,
                                           bool withcheck,
                                           unsigned long equallength,
                                           unsigned long totallength,
                                           unsigned long numofsequences,
                                           unsigned long maxunitindex,
                                           unsigned int kmersize,
                                           unsigned int minmatchlength,
                                           GtProcesskmercode processcode,
                                           void *data)
{
  unsigned long startpos, encodingsum = 0, fseqnum;

  if (equallength >= (unsigned long) minmatchlength)
  {
    for (startpos = 0, fseqnum = 0; startpos < totallength;
         startpos += equallength+1, fseqnum++)
    {
      encodingsum += (unsigned long) gt_firstcodes_kmerscan_range(
                                                  twobitencoding,
                                                  withcheck,
                                                  kmersize,
                                                  minmatchlength,
                                                  startpos,
                                                  startpos + equallength,
                                                  fseqnum,
                                                  numofsequences - 1 - fseqnum,
                                                  maxunitindex,
                                                  processcode,
                                                  data);
    }
  }
  return encodingsum;
}

unsigned long gt_firstcodes_kmerscan(const GtEncseq *encseq,
                                     const GtBitsequence *twobitencoding,
                                     bool withcheck,
                                     unsigned long totallength,
                                     unsigned long numofsequences,
                                     unsigned long maxunitindex,
                                     unsigned int kmersize,
                                     unsigned int minmatchlength,
                                     GtProcesskmercode processcode,
                                     void *data)
{
  unsigned long laststart = 0, encodingsum = 0, fseqnum = 0;

  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;

    sri = gt_specialrangeiterator_new(encseq,true);
    while (gt_specialrangeiterator_next(sri,&range)
           && range.start < totallength)
    {
      gt_assert(range.start >= laststart);
      if (range.start - laststart >= (unsigned long) minmatchlength)
      {
        encodingsum += (unsigned long) gt_firstcodes_kmerscan_range(
                                                twobitencoding,
                                                withcheck,
                                                kmersize,
                                                minmatchlength,
                                                laststart,
                                                range.start,
                                                fseqnum,
                                                numofsequences - 1 - fseqnum,
                                                maxunitindex,
                                                processcode,
                                                data);
      }
      laststart = range.end;
      fseqnum++;
    }
    gt_specialrangeiterator_delete(sri);
  }
  if (totallength - laststart >= (unsigned long) minmatchlength)
  {
    encodingsum += (unsigned long) gt_firstcodes_kmerscan_range(
                                              twobitencoding,
                                              withcheck,
                                              kmersize,
                                              minmatchlength,
                                              laststart,
                                              totallength,
                                              fseqnum,
                                              numofsequences - 1 - fseqnum,
                                              maxunitindex,
                                              processcode,
                                              data);
  }
  return encodingsum;
}

static void showcodes (GtCodetype code,
                       unsigned long seqnum,
                       unsigned long relpos,
                       GT_UNUSED void *data)
{
  printf("%c %lu %lu %lu\n",relpos == 0 ? 'T' : 'F',code,seqnum,relpos);
}

void gt_firstcode_runkmerscan(const GtEncseq *encseq,
                              unsigned int mode,
                              unsigned int kmersize,
                              unsigned int minmatchlength)
{
  const GtTwobitencoding *twobitencoding
    = gt_encseq_twobitencoding_export(encseq);
  unsigned long totallength, maxunitindex, encodingsum, numofsequences;
  bool withcheck = mode == 1U ? true : false;

  if (gt_encseq_is_mirrored(encseq))
  {
    totallength = (gt_encseq_total_length(encseq)-1)/2;
  } else
  {
    totallength = gt_encseq_total_length(encseq);
  }
  numofsequences = gt_encseq_num_of_sequences(encseq);
  maxunitindex = gt_unitsoftwobitencoding(totallength) - 1;
  gt_log_log("totallength=%lu,maxunitindex=%lu\n",totallength,maxunitindex);
  if (gt_encseq_accesstype_get(encseq) == GT_ACCESS_TYPE_EQUALLENGTH)
  {
    unsigned long equallength = gt_encseq_equallength(encseq);

    encodingsum = gt_firstcodes_kmerscan_eqlen(twobitencoding,
                                               withcheck,
                                               equallength,
                                               totallength,
                                               numofsequences,
                                               maxunitindex,
                                               kmersize,
                                               minmatchlength,
                                               mode == 2U ? showcodes : NULL,
                                               NULL);
  } else
  {
    encodingsum = gt_firstcodes_kmerscan(encseq,
                                         twobitencoding,
                                         withcheck,
                                         totallength,
                                         numofsequences,
                                         maxunitindex,
                                         kmersize,
                                         minmatchlength,
                                         mode == 2U ? showcodes : NULL,
                                         NULL);
  }
  gt_log_log("encodingsum = %lu\n",encodingsum);
}
genometools-1.5.1/src/match/firstcodes-scan.h000066400000000000000000000022101211610345200211620ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FIRSTCODES_SCAN_H
#define FIRSTCODES_SCAN_H

#include "core/encseq_api.h"

void gt_firstcode_runkmerscan(const GtEncseq *encseq,
                              unsigned int mode,
                              unsigned int kmersize,
                              unsigned int minmatchlength);

#endif
genometools-1.5.1/src/match/firstcodes-spacelog.c000066400000000000000000000243541211610345200220430ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#endif
#include "core/fa.h"
#include "core/ma.h"
#include "core/log_api.h"
#include "core/spacecalc.h"
#include "core/spacepeak.h"
#include "core/mathsupport.h"
#include "firstcodes-spacelog.h"

typedef struct
{
  const char *filename;
  int line;
  const char *title;
  size_t size;
  bool work;
} GtFirstcodespacelogentry;

struct GtFirstcodesspacelog
{
  size_t workspace,
         splitspace,
         spacepeak;
  double max_percent_difference;
  bool calc_difference;
  GtFirstcodespacelogentry *entries;
  unsigned long nextfree, allocated;
};

GtFirstcodesspacelog *gt_firstcodes_spacelog_new(void)
{
  GtFirstcodesspacelog *fcsl;

  fcsl = gt_malloc(sizeof (GtFirstcodesspacelog));
  fcsl->workspace = fcsl->splitspace = 0;
  fcsl->nextfree = fcsl->allocated = 0;
  fcsl->spacepeak = 0;
  fcsl->max_percent_difference = 0.0;
  fcsl->calc_difference = false;
  fcsl->entries = NULL;
  return fcsl;
}

void gt_firstcodes_spacelog_start_diff(GtFirstcodesspacelog *fcsl)
{
  fcsl->calc_difference = gt_ma_bookkeeping_enabled();
}

void gt_firstcodes_spacelog_stop_diff(GtFirstcodesspacelog *fcsl)
{
  fcsl->calc_difference = false;
}

size_t gt_firstcodes_spacelog_total(const GtFirstcodesspacelog *fcsl)
{
  return fcsl->workspace + fcsl->splitspace;
}

size_t gt_firstcodes_spacelog_workspace(const GtFirstcodesspacelog *fcsl)
{
  return fcsl->workspace;
}

size_t gt_firstcodes_spacelog_peak(const GtFirstcodesspacelog *fcsl)
{
  return fcsl->spacepeak;
}

static GtFirstcodespacelogentry *gt_spacelog_find(GtFirstcodesspacelog *fcsl,
                                                  const char *title)
{
  unsigned long idx;

  for (idx = 0; idx < fcsl->nextfree; idx++)
  {
    if (strcmp(fcsl->entries[idx].title,title) == 0)
    {
      return fcsl->entries + idx;
    }
  }
  return NULL;
}

static void gt_spacelog_updateaddentry(GtFirstcodespacelogentry *entry,
                                       const char *filename,int line,
                                       const char *title,size_t size,
                                       bool work)
{
  entry->filename = filename;
  entry->line = line;
  entry->title = title;
  entry->size = size;
  entry->work = work;
}

static void gt_spacelog_addentry(GtFirstcodesspacelog *fcsl,
                                 const char *filename,int line,
                                 const char *title,size_t size,
                                 bool work)
{
  gt_assert(fcsl->nextfree <= fcsl->allocated);
  if (fcsl->nextfree == fcsl->allocated)
  {
    fcsl->allocated += 16UL;
    fcsl->entries = gt_realloc(fcsl->entries,sizeof (*fcsl->entries) *
                                             fcsl->allocated);
  }
  gt_spacelog_updateaddentry(fcsl->entries + fcsl->nextfree,
                             filename,line,title,size,work);
  fcsl->nextfree++;
}

bool gt_firstcodes_spacelog_showentries(FILE *fp,
                                        const GtFirstcodesspacelog *fcsl)
{
  unsigned long idx;
  bool foundnonempty = false;

  for (idx = 0; idx < fcsl->nextfree; idx++)
  {
    if (fcsl->entries[idx].size > 0)
    {
      fprintf(fp,"%s %d %s %s %lu\n",
               fcsl->entries[idx].filename,
               fcsl->entries[idx].line,
               fcsl->entries[idx].title,
               fcsl->entries[idx].work ? "work" : "split",
               (unsigned long) fcsl->entries[idx].size);
      foundnonempty = true;
    }
  }
  return foundnonempty;
}

void gt_firstcodes_spacelog_delete(GtFirstcodesspacelog *fcsl)
{
  if (fcsl != NULL)
  {
#ifdef SKDEBUG
    if (gt_firstcodes_spacelog_showentries(stderr,fcsl))
    {
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
#endif
    gt_log_log("maximal difference between estimated and real space = %.2f%%",
               fcsl->max_percent_difference);
    gt_free(fcsl->entries);
    gt_free(fcsl);
  }
}

static void gt_firstcodes_subtract_error(const char *title,
                                         const char *filename,
                                         int line,
                                         size_t size,
                                         bool work,
                                         size_t sumspace)
{
  fprintf(stderr,"for title \"%s\" (from file %s, line %d) "
                 "in spacelog entries: "
                 "size=%lu > %lu=%sspace\n",title,filename,line,
                 (unsigned long) size,(unsigned long) sumspace,
                 work ? "work" : "split");
}

static void gt_firstcodes_updatemax(GtFirstcodesspacelog *fcsl)
{
  if (fcsl->workspace + fcsl->splitspace > fcsl->spacepeak)
  {
    fcsl->spacepeak = fcsl->workspace + fcsl->splitspace;
    gt_log_log("update spacepeak to %.2f MB",
               GT_MEGABYTES(fcsl->spacepeak));
  }
}

void gt_firstcodes_spacelog_add(GtFirstcodesspacelog *fcsl,
                                int line,
                                const char *filename,
                                bool add,
                                const char *title,
                                bool work,
                                size_t size)
{
  GtFirstcodespacelogentry *entry;
  size_t logspace;

  if (add)
  {
    entry = gt_spacelog_find(fcsl,title);
    if (entry != NULL)
    {
      if (entry->size != 0)
      {
        fprintf(stderr,"existing entry for title \"%s\""
                       "(from file %s, line %d) "
                       "in spacelog entries must have size 0\n",
                       title,filename,line);
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
      gt_spacelog_updateaddentry(entry,filename,line,title,size,work);
    } else
    {
      gt_spacelog_addentry(fcsl,filename,line,title,size,work);
    }
    if (work)
    {
      fcsl->workspace += size;
    } else
    {
      fcsl->splitspace += size;
    }
    gt_firstcodes_updatemax(fcsl);
  } else
  {
    entry = gt_spacelog_find(fcsl,title);
    if (entry == NULL)
    {
      fprintf(stderr,"cannot find title \"%s\" (from file %s, line %d) "
                     "in spacelog entries\n",title,filename,line);
      (void) gt_firstcodes_spacelog_showentries(stderr,fcsl);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    if ((entry->work && !work) || (!entry->work && work))
    {
      fprintf(stderr,"for title \"%s\" (from file %s, line %d) "
                     "in spacelog entries: inconsistent work/splitassignment\n",
               title,filename,line);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    if (work)
    {
      if (entry->size > fcsl->workspace)
      {
        gt_firstcodes_subtract_error(title, filename, line, entry->size, true,
                                     fcsl->workspace);
        (void) gt_firstcodes_spacelog_showentries(stderr,fcsl);
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
      fcsl->workspace -= entry->size;
    } else
    {
      if (entry->size > fcsl->splitspace)
      {
        gt_firstcodes_subtract_error(title, filename, line, entry->size, false,
                                     fcsl->splitspace);
        (void) gt_firstcodes_spacelog_showentries(stderr,fcsl);
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
      fcsl->splitspace -= entry->size;
    }
    if (size > 0)
    {
      size_t previous_size = entry->size;
      gt_spacelog_updateaddentry(entry,filename,line,title,size,work);
      if (work)
      {
        fcsl->workspace += size;
      } else
      {
        fcsl->splitspace += size;
      }
      if (size > previous_size)
      {
        add = true;
        size -= previous_size;
      } else
      {
        size = previous_size - size;
      }
      gt_firstcodes_updatemax(fcsl);
    } else
    {
      size = entry->size;
      entry->size = 0;
    }
  }
  logspace = fcsl->workspace+fcsl->splitspace;
  gt_log_log(
#ifdef SKDEBUG
             "file %s, line %d: "
#endif
             "%s %s= %.2f, %s, w=%.2f, s=%.2f, sum=%.2f MB",
#ifdef SKDEBUG
             filename,
             line,
#endif
             work ? "w" : "s",
             add ? "+" : "-",
             GT_MEGABYTES(size),
             title,
             GT_MEGABYTES(fcsl->workspace),
             GT_MEGABYTES(fcsl->splitspace),
             GT_MEGABYTES(logspace));
#ifdef SKDEBUG
  if (gt_ma_bookkeeping_enabled())
  {
    unsigned long realspace = gt_ma_get_space_current() +
                              gt_fa_get_space_current();
    gt_log_log("current space usage %.2f MB (%.2f+%.2f)",
                                GT_MEGABYTES(realspace),
                                GT_MEGABYTES(gt_ma_get_space_current()),
                                GT_MEGABYTES(gt_fa_get_space_current()));
    if (fcsl->calc_difference)
    {
      double percent_difference;

      if ((unsigned long) logspace > realspace)
      {
        fprintf(stderr,"overestimating logspace\n");
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
      if (realspace >= 1000000UL)
      {
        /*
        printf("realspace=%lu,logspace=%lu\n",realspace,
                                              (unsigned long) logspace);
        */
        percent_difference = 100.0 * (double) (realspace - logspace)/realspace;
        if (gt_double_larger_double(percent_difference,3.0))
        {
          fprintf(stderr,"space difference of %.2f%% is too large\n",
                       percent_difference);
          exit(GT_EXIT_PROGRAMMING_ERROR);
        }
        if (gt_double_smaller_double(fcsl->max_percent_difference,
                                     percent_difference))
        {
          fcsl->max_percent_difference = percent_difference;
        }
      }
    }
  }
#endif
}
genometools-1.5.1/src/match/firstcodes-spacelog.h000066400000000000000000000052421211610345200220430ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FIRSTCODES_SPACELOG_H
#define FIRSTCODES_SPACELOG_H

#include 
#include 

typedef struct GtFirstcodesspacelog GtFirstcodesspacelog;

GtFirstcodesspacelog *gt_firstcodes_spacelog_new(void);

void gt_firstcodes_spacelog_delete(GtFirstcodesspacelog *fcsl);

size_t gt_firstcodes_spacelog_total(const GtFirstcodesspacelog *fcsl);

size_t gt_firstcodes_spacelog_workspace(const GtFirstcodesspacelog *fcsl);

void gt_firstcodes_spacelog_start_diff(GtFirstcodesspacelog *fcsl);

void gt_firstcodes_spacelog_stop_diff(GtFirstcodesspacelog *fcsl);

size_t gt_firstcodes_spacelog_peak(const GtFirstcodesspacelog *fcsl);

bool gt_firstcodes_spacelog_showentries(FILE *fp,
                                        const GtFirstcodesspacelog *fcsl);

void gt_firstcodes_spacelog_add(GtFirstcodesspacelog *fcsl,
                                int line,
                                const char *filename,
                                bool add,
                                const char *title,
                                bool work,
                                size_t size);

#define GT_FCI_ADDWORKSPACE(FCSL,TAB,SIZE)\
        gt_firstcodes_spacelog_add(FCSL,__LINE__,__FILE__,true,TAB,true,SIZE)

#define GT_FCI_ADDSPLITSPACE(FCSL,TAB,SIZE)\
        gt_firstcodes_spacelog_add(FCSL,__LINE__,__FILE__,true,TAB,false,SIZE)

#define GT_FCI_SUBTRACTWORKSPACE(FCSL,TAB)\
        gt_firstcodes_spacelog_add(FCSL,__LINE__,__FILE__,false,TAB,true,0)

#define GT_FCI_SUBTRACTSPLITSPACE(FCSL,TAB)\
        gt_firstcodes_spacelog_add(FCSL,__LINE__,__FILE__,false,TAB,false,0)

#define GT_FCI_SUBTRACTADDWORKSPACE(FCSL,TAB,SIZE)\
        gt_firstcodes_spacelog_add(FCSL,__LINE__,__FILE__,false,TAB,true,SIZE)

#define GT_FCI_SUBTRACTADDSPLITSPACE(FCSL,TAB,SIZE)\
        gt_firstcodes_spacelog_add(FCSL,__LINE__,__FILE__,false,TAB,false,SIZE)

#endif
genometools-1.5.1/src/match/firstcodes-tab.c000066400000000000000000000556661211610345200210260ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/xansi_api.h"
#include "core/fa.h"
#include "core/assert_api.h"
#include "core/divmodmul.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#ifdef SKDEBUG
#include "core/disc_distri_api.h"
#endif
#include "core/log.h"
#include "core/spacecalc.h"
#include "core/hashmap-generic.h"
#include "core/arraydef.h"
#include "firstcodes-tab.h"
#include "firstcodes-psbuf.h"
#include "firstcodes-cache.h"

static void gt_firstcodes_countocc_new(GtFirstcodesspacelog *fcsl,
                                       GtFirstcodestab *fct,
                                       unsigned int bitsforcount,
                                       unsigned long numofsequences)
{
  if (bitsforcount < (unsigned int) (sizeof (GtCountAFCtype) * CHAR_BIT))
  {
    fct->countocc_small = gt_malloc((size_t) (numofsequences+1) *
                                    sizeof (*fct->countocc_small));
    GT_FCI_ADDWORKSPACE(fcsl,"countocc_small",
                        sizeof (*fct->countocc_small) *
                        (numofsequences+1));
  } else
  {
    fct->countocc_small = NULL;
  }
  fct->countocc_exceptions = ul_u32_gt_hashmap_new();
  gt_assert(fct->countocc_exceptions != NULL);
  fct->outfilenameleftborder = NULL;
  fct->leftborder_samples = NULL;
#ifdef _LP64
  GT_INITARRAY(&fct->bitchangepoints,GtUlong);
#endif
}

static void gt_firstcodes_countocc_set(GtFirstcodestab *fct,
                                       unsigned long *differences,
                                       unsigned long idx,
                                       unsigned long value)
{
  gt_assert(value > 0);
  if (fct->countocc_small == NULL)
  {
    if (value <= fct->countmax)
    {
      differences[idx] |= (value << fct->shiftforcounts);
    } else
    {
      differences[idx] &= fct->differencemask;
      ul_u32_gt_hashmap_add(fct->countocc_exceptions,idx,
                            (uint32_t) (value - fct->countmax));
      fct->hashmap_addcount++;
    }
  } else
  {
    if (value <= GT_FIRSTCODES_MAXSMALL)
    {
      fct->countocc_small[idx] = (GtCountAFCtype) value;
    } else
    {
      fct->countocc_small[idx] = 0;
      ul_u32_gt_hashmap_add(fct->countocc_exceptions,idx,
                            value - GT_FIRSTCODES_MAXSMALL);
      fct->hashmap_addcount++;
    }
  }
}

static void gt_firstcodes_countocc_increment(GtFirstcodestab *fct,
                                             unsigned long *differences,
                                             unsigned long idx,
                                             unsigned long inc)
{
  unsigned long count;

  if (fct->countocc_small == NULL)
  {
    if ((count = (differences[idx] >> fct->shiftforcounts)) > 0)
    {
      differences[idx] &= fct->differencemask;
      if (inc + count <= fct->countmax)
      {
        differences[idx] |= ((inc + count) << fct->shiftforcounts);
      } else
      {
        ul_u32_gt_hashmap_add(fct->countocc_exceptions,idx,
                              (uint32_t) (inc + count - fct->countmax));
        fct->hashmap_addcount++;
      }
    } else
    {
      uint32_t *valueptr = ul_u32_gt_hashmap_get(fct->countocc_exceptions,idx);

      gt_assert(valueptr != NULL && *valueptr + inc <= UINT32_MAX);
      (*valueptr) += inc;
      fct->hashmap_getcount++;
    }
  } else
  {
    if ((count = (unsigned long) fct->countocc_small[idx]) > 0)
    {
      if (inc + count <= GT_FIRSTCODES_MAXSMALL)
      {
        fct->countocc_small[idx] += inc;
      } else
      {
        ul_u32_gt_hashmap_add(fct->countocc_exceptions,idx,
                              inc + count - GT_FIRSTCODES_MAXSMALL);
        fct->countocc_small[idx] = 0;
        fct->hashmap_addcount++;
      }
    } else
    {
      uint32_t *valueptr = ul_u32_gt_hashmap_get(fct->countocc_exceptions,idx);

      gt_assert(valueptr != NULL && *valueptr + inc <= UINT32_MAX);
      (*valueptr) += inc;
      fct->hashmap_getcount++;
    }
  }
}

static void gt_firstcodes_countocc_resize(GtFirstcodesspacelog *fcsl,
                                          GtFirstcodestab *fct,
                                          unsigned long numofdifferentcodes)
{
  if (fct->countocc_small != NULL)
  {
    fct->countocc_small = gt_realloc(fct->countocc_small,
                                     sizeof (*fct->countocc_small) *
                                             (numofdifferentcodes+1));
    GT_FCI_SUBTRACTADDWORKSPACE(fcsl,"countocc_small",
                                sizeof (*fct->countocc_small) *
                                (numofdifferentcodes+1));
  }
}

#ifdef SKDEBUG

typedef struct
{
  unsigned long smallcount, smallsum,
                largecount, largesum,
                hugecount, hugesum;
} GtCountdistri_info;

static void gt_firstcodes_evaluate_distvalue(unsigned long key,
                                             unsigned long long value,
                                             void *data)
{
  GtCountdistri_info *cdi = (GtCountdistri_info *) data;

  gt_assert(value > 0);
  if (key <= UINT8_MAX)
  {
    cdi->smallcount++;
    cdi->smallsum += value;
  } else
  {
    if (key <= UINT16_MAX)
    {
      cdi->largecount++;
      cdi->largesum += value;
    } else
    {
      cdi->hugecount++;
      cdi->hugesum += value;
    }
  }
}

static void gt_firstcodes_evaluate_countdistri(const GtDiscDistri *countdistri)
{
  GtCountdistri_info cdi;
  unsigned long sum;
  size_t spacenow, spacedirectstore, spaceopt, spacewithhash;;

  cdi.smallcount = 0;
  cdi.smallsum = 0;
  cdi.largecount = 0;
  cdi.largesum = 0;
  cdi.hugecount = 0;
  cdi.hugesum = 0;
  gt_disc_distri_foreach(countdistri,gt_firstcodes_evaluate_distvalue,&cdi);
  sum = cdi.smallsum + cdi.largesum + cdi.hugesum;
  gt_log_log("small=%lu,%lu (%.2f)",cdi.smallcount,cdi.smallsum,
          (double) cdi.smallsum/sum);
  gt_log_log("large=%lu,%lu (%.2f)",cdi.largecount,cdi.largesum,
          (double) cdi.largesum/sum);
  gt_log_log("huge=%lu,%lu (%.2f)",cdi.hugecount,cdi.hugesum,
          (double) cdi.largesum/sum);
  spacenow = sizeof (uint32_t) * sum;
  spaceopt = sizeof (uint8_t) * sum;
  spacedirectstore = sizeof (uint32_t) * cdi.largesum;
  spacewithhash = (2 * sizeof (void *)) * cdi.largecount;
  gt_log_log("spacenow=%.2f, spaceopt (direct)=%2.f spaceopt (hash) =%.2f",
          GT_MEGABYTES(spacenow),
          GT_MEGABYTES(spaceopt+spacedirectstore),
          GT_MEGABYTES(spaceopt+spacewithhash));
}
#endif

unsigned long gt_firstcodes_remdups(unsigned long *allfirstcodes,
                                    GtFirstcodesspacelog *fcsl,
                                    GtFirstcodestab *fct,
                                    unsigned long numofsequences,
                                    Gtmarksubstring *markprefix,
                                    Gtmarksubstring *marksuffix,
                                    GtArrayGtIndexwithcode **binsearchcache,
                                    unsigned int addbscache_depth,
                                    bool withdistbits,
                                    GtLogger *logger)
{
  if (numofsequences == 0)
  {
    fct->differentcodes = 0;
  } else
  {
    unsigned long numofdifferentcodes = 1UL, storeidx, readidx, previouscode,
                  idx, maxdifference = 0, cachewidth, nextstorecache, lastocc,
                  storedvalue, diff, *distbits = NULL;
    unsigned int bitsformaxdifference, bitsforcount;

    previouscode = allfirstcodes[0];
    for (idx=1UL; idx < numofsequences; idx++)
    {
      unsigned long currentcode = allfirstcodes[idx];
      if (previouscode != currentcode)
      {
        numofdifferentcodes++;
        if (maxdifference < currentcode - previouscode)
        {
          maxdifference = currentcode - previouscode;
        }
        previouscode = currentcode;
      }
    }
    bitsformaxdifference = gt_determinebitspervalue(maxdifference);
    fct->differencemask = (1UL << bitsformaxdifference) - 1UL;
    gt_assert(sizeof (unsigned long) * CHAR_BIT >=
              (size_t) bitsformaxdifference);
    bitsforcount = (unsigned int)
                   sizeof (unsigned long) * CHAR_BIT - bitsformaxdifference;
    fct->countmax = (1UL << bitsforcount) - 1UL;
    fct->shiftforcounts = bitsformaxdifference;
    gt_logger_log(logger,"maximum difference of neighbored codes %lu (%u bits)",
                  maxdifference,bitsformaxdifference);
    /*
    printf("maxdifference=%lu,bitsformaxdifference=%u,bitsforcount=%u\n",
            maxdifference,bitsformaxdifference,bitsforcount);
    */
    gt_firstcodes_countocc_new(fcsl,fct,bitsforcount,numofsequences);
    gt_marksubstring_mark(markprefix,allfirstcodes[0]);
    gt_marksubstring_mark(marksuffix,allfirstcodes[0]);
    *binsearchcache
      = gt_firstcodes_binsearchcache_new(numofdifferentcodes,
                                         addbscache_depth,
                                         fcsl);
    cachewidth = (*binsearchcache) == NULL
                   ? 0
                   : gt_firstcodes_binsearchcache_width(*binsearchcache);
    nextstorecache = cachewidth;
    lastocc = 1UL; /* for first code */
    storedvalue = allfirstcodes[0];
    allfirstcodes[0] = 0;
    if (withdistbits)
    {
      distbits = gt_calloc((size_t) (64+1),sizeof (*distbits));
    }
    for (storeidx = 0, readidx = 1UL; readidx < numofsequences; readidx++)
    {
      unsigned long readvalue = allfirstcodes[readidx];

      if (storedvalue != readvalue)
      {
        if ((*binsearchcache) != NULL && storeidx == nextstorecache)
        {
          gt_firstcodes_binsearchcache_set_index_code(*binsearchcache,
                                                      nextstorecache,
                                                      storedvalue);
          nextstorecache += cachewidth;
        }
        gt_firstcodes_countocc_set(fct,allfirstcodes,storeidx,lastocc);
        lastocc = 1UL;
        storeidx++;
        gt_assert(storedvalue < readvalue);
        diff = readvalue - storedvalue;
        if (distbits != NULL)
        {
          distbits[gt_determinebitspervalue(diff)]++;
        }
        allfirstcodes[storeidx] = diff;
        storedvalue = readvalue;
        gt_marksubstring_mark(markprefix,readvalue);
        gt_marksubstring_mark(marksuffix,readvalue);
      } else
      {
        lastocc++;
      }
    }
    if (withdistbits)
    {
      int bits;

      gt_assert(distbits != NULL);
      for (bits = 0; bits <= 64; bits++)
      {
        if (distbits[bits] > 0)
        {
          printf("%d bits: %lu\n",bits,distbits[bits]);
        }
      }
      gt_free(distbits);
    }
    gt_firstcodes_countocc_set(fct,allfirstcodes,storeidx,lastocc);
    gt_assert(numofdifferentcodes == (unsigned long) (storeidx + 1));
    if (numofdifferentcodes < numofsequences)
    {
      /* reduce the memory requirement, as the duplicated elements are not
         needed */
      gt_firstcodes_countocc_resize(fcsl,fct,numofdifferentcodes);
    }
    fct->differentcodes = numofdifferentcodes;
  }
  gt_logger_log(logger,"number of different first codes=%lu (%.2f%%) "
                       "in %lu sequences",
                fct->differentcodes,
                100.00 * (double) fct->differentcodes/numofsequences,
                numofsequences);
  return fct->differentcodes;
}

unsigned long gt_firstcodes_accumulatecounts_merge(
                                        GtFirstcodestab *tab,
                                        unsigned long *differences,
                                        unsigned long differentcodes,
                                        const unsigned long *querystream_fst,
                                        const unsigned long *querystream_lst,
                                        unsigned long subjectindex,
                                        unsigned long subjectcode)
{
  unsigned long found = 0, lastocc = 0;
  const unsigned long *query = querystream_fst;

  gt_assert(subjectindex < differentcodes);
  while (query <= querystream_lst)
  {
    if (*query <= subjectcode)
    {
      if (*query == subjectcode)
      {
        lastocc++;
      }
      query++;
    } else
    {
      if (lastocc > 0)
      {
        gt_firstcodes_countocc_increment(tab,differences,subjectindex,lastocc);
        found += lastocc;
        lastocc = 0;
      }
      if (subjectindex < differentcodes - 1)
      {
        subjectindex++;
        /* extract diff */
        subjectcode += (differences[subjectindex] & tab->differencemask);
      } else
      {
        break;
      }
    }
  }
  if (lastocc > 0)
  {
    gt_firstcodes_countocc_increment(tab,differences,subjectindex,lastocc);
    found += lastocc;
    lastocc = 0;
  }
  return found;
}

static uint32_t gt_firstcodes_countocc_get(const GtFirstcodestab *fct,
                                           const unsigned long *differences,
                                           unsigned long idx)
{
  if (fct->countocc_small == NULL)
  {
    unsigned long count;

    if ((count = (differences[idx] >> fct->shiftforcounts)) > 0)
    {
      return (uint32_t) count;
    } else
    {
      uint32_t *valueptr = ul_u32_gt_hashmap_get(fct->countocc_exceptions,idx);

      gt_assert(valueptr != NULL);
      return *valueptr + (uint32_t) fct->countmax;
    }
  } else
  {
    if (fct->countocc_small[idx] > 0)
    {
      return (uint32_t) fct->countocc_small[idx];
    } else
    {
      uint32_t *valueptr = ul_u32_gt_hashmap_get(fct->countocc_exceptions,idx);

      gt_assert(valueptr != NULL);
      return *valueptr + (uint32_t) GT_FIRSTCODES_MAXSMALL;
    }
  }
}

#define GT_PARTIALSUM_LEFTBORDER_SET(BUF,VALUE)\
        if ((BUF)->nextfree == (BUF)->allocated)\
        {\
          gt_leftborderbuffer_flush(BUF);\
        }\
        (BUF)->spaceuint32_t[(BUF)->nextfree++] = (uint32_t) (VALUE);

#define GT_FIRSTCODES_ADD_SAMPLE(PARTSUM)\
        gt_assert(samplecount < fct->numofsamples);\
        fct->leftborder_samples[samplecount++] = PARTSUM

unsigned long gt_firstcodes_partialsums(GtFirstcodesspacelog *fcsl,
                                        GtFirstcodestab *fct,
                                        const unsigned long *differences,
                                        GT_UNUSED unsigned long
                                                            expectedlastpartsum)
{
  unsigned long idx, partsum, maxbucketsize, bitmask, samplecount = 0,
                spacewithhashmap = 0, spacewithouthashmap = 0;
  uint32_t currentcount;
  GtLeftborderOutbuffer *leftborderbuffer_all = NULL;
#ifdef _LP64
  const unsigned int btp = gt_determinebitspervalue(expectedlastpartsum);
  unsigned long exceedvalue = 1UL << GT_MODVALUEBITS;
#endif
#ifdef SKDEBUG
  GtDiscDistri *countdistri = gt_disc_distri_new();
#endif

  gt_assert(fct->differentcodes < UINT32_MAX);
  gt_log_log("hashmap_addcount=%lu (%.5f%%)",fct->hashmap_addcount,
                  100.0 * (double) fct->hashmap_addcount/
                                   fct->differentcodes);
  gt_log_log("hashmap_getcount=%lu (%.5f%%)",
                  fct->hashmap_getcount,
                  100.0 * (double) fct->hashmap_getcount/
                                   fct->differentcodes);

#ifdef _LP64
  if (btp <= GT_MODVALUEBITS)
  {
    fct->bitchangepoints.allocatedGtUlong = 0;
    fct->bitchangepoints.spaceGtUlong = NULL;
  } else
  {
    fct->bitchangepoints.allocatedGtUlong = 1UL << (btp - GT_MODVALUEBITS);
    gt_log_log("lastpartsum=%lu, bitchangepoints.allocated=%lu",
              expectedlastpartsum,fct->bitchangepoints.allocatedGtUlong);
    fct->bitchangepoints.spaceGtUlong
      = gt_malloc(sizeof (*fct->bitchangepoints.spaceGtUlong)
                  * fct->bitchangepoints.allocatedGtUlong);
  }
  fct->bitchangepoints.nextfreeGtUlong = 0;
#endif
  currentcount = gt_firstcodes_countocc_get(fct,differences,0);
  partsum = (unsigned long) currentcount;
  maxbucketsize = (unsigned long) currentcount;
#ifdef SKDEBUG
  gt_disc_distri_add(countdistri,(unsigned long) currentcount);
#endif
  fct->sampleshift = 9U;
  while (true)
  {
    fct->sampledistance = 1UL << fct->sampleshift;
    if (fct->sampledistance < fct->differentcodes)
    {
      break;
    }
    fct->sampleshift--;
  }
  bitmask = fct->sampledistance - 1;
  fct->numofsamples = 1UL + 1UL + fct->differentcodes/fct->sampledistance;
  fct->leftborder_samples = gt_malloc(sizeof (*fct->leftborder_samples) *
                                      fct->numofsamples);
  GT_FCI_ADDWORKSPACE(fcsl,"leftborder_samples",
                      sizeof (*fct->leftborder_samples) * fct->numofsamples);
  GT_FIRSTCODES_ADD_SAMPLE(partsum);
  leftborderbuffer_all = gt_leftborderbuffer_new("leftborder",fcsl);
  GT_PARTIALSUM_LEFTBORDER_SET(leftborderbuffer_all,partsum);
  for (idx = 1UL; idx < fct->differentcodes; idx++)
  {
    currentcount = gt_firstcodes_countocc_get(fct,differences,idx);
#ifdef _LP64
    gt_assert(currentcount <= GT_MODVALUEMASK);
#endif
#ifdef SKDEBUG
    gt_disc_distri_add(countdistri,(unsigned long) currentcount);
#endif
    if (maxbucketsize < (unsigned long) currentcount)
    {
      maxbucketsize = (unsigned long) currentcount;
    }
    partsum += currentcount;
#ifdef _LP64
    if (fct->bitchangepoints.allocatedGtUlong > 0 && partsum >= exceedvalue)
    {
      gt_assert(idx > 0 && fct->bitchangepoints.nextfreeGtUlong <
                           fct->bitchangepoints.allocatedGtUlong);
      gt_assert(fct->bitchangepoints.spaceGtUlong != NULL);
      fct->bitchangepoints.spaceGtUlong
        [fct->bitchangepoints.nextfreeGtUlong++] = idx-1;
      exceedvalue = ((exceedvalue >> GT_MODVALUEBITS) + 1) << GT_MODVALUEBITS;
    }
#endif
    if ((idx & bitmask) == 0)
    {
      GT_FIRSTCODES_ADD_SAMPLE(partsum);
    }
    GT_PARTIALSUM_LEFTBORDER_SET(leftborderbuffer_all,partsum);
  }
  GT_PARTIALSUM_LEFTBORDER_SET(leftborderbuffer_all,partsum);
  fct->outfilenameleftborder
      = gt_leftborderbuffer_delete(leftborderbuffer_all,fcsl,
                                   gt_firstcodes_leftborder_entries(fct));
  if (partsum > fct->leftborder_samples[samplecount-1])
  {
    GT_FIRSTCODES_ADD_SAMPLE(partsum);
  } else
  {
    gt_assert(partsum == fct->leftborder_samples[samplecount-1]);
  }
  gt_assert(expectedlastpartsum == partsum);
  fct->numofsamples = samplecount-1;
#ifdef SKDEBUG
  gt_firstcodes_evaluate_countdistri(countdistri);
  gt_disc_distri_delete(countdistri);
#endif
  if (fct->countocc_small != NULL)
  {
    gt_free(fct->countocc_small);
    GT_FCI_SUBTRACTWORKSPACE(fcsl,"countocc_small");
    fct->countocc_small = NULL;
  }
  if (fct->hashmap_addcount > 0 && gt_ma_bookkeeping_enabled())
  {
    spacewithhashmap = gt_ma_get_space_current() + gt_fa_get_space_current();
  }
  gt_hashtable_delete(fct->countocc_exceptions);
  if (fct->hashmap_addcount > 0 && gt_ma_bookkeeping_enabled())
  {
    unsigned long hashmapspace;

    spacewithouthashmap = gt_ma_get_space_current() + gt_fa_get_space_current();
    gt_assert(spacewithouthashmap < spacewithhashmap);
    hashmapspace = spacewithhashmap - spacewithouthashmap;
    gt_log_log("space for hashmap=%.2f (%lu bytes per entry)",
               GT_MEGABYTES(hashmapspace),hashmapspace/fct->hashmap_addcount);
  }
  fct->countocc_exceptions = NULL;
  return maxbucketsize;
}

unsigned long gt_firstcodes_get_sample(const GtFirstcodestab *fct,
                                       unsigned long idx)
{
  gt_assert(idx <= fct->numofsamples);
  return fct->leftborder_samples[idx];
}

unsigned long gt_firstcodes_get_leftborder(const GtFirstcodestab *fct,
                                           unsigned long idx)
{
#ifdef _LP64
  GT_CHANGEPOINT_GET(changepoint);

  return (unsigned long) fct->leftborder[idx]
                         + (changepoint << GT_MODVALUEBITS);
#else
  return (unsigned long) fct->leftborder[idx];
#endif
}

unsigned long gt_firstcodes_leftborder_entries(const GtFirstcodestab *fct)
{
  return fct->differentcodes + 1;
}

unsigned long gt_firstcodes_numofsamples(const GtFirstcodestab *fct)
{
  return fct->numofsamples;
}

unsigned long gt_firstcodes_findfirstsamplelarger(const GtFirstcodestab *fct,
                                                  unsigned long suftaboffset)
{
  unsigned long left = 0, right, mid, midval, found;

  right = found = fct->numofsamples;
  while (left+1 < right)
  {
    mid = GT_DIV2(left+right);
    midval = gt_firstcodes_get_sample(fct,mid);
    if (suftaboffset == midval)
    {
      return mid;
    }
    if (suftaboffset < midval)
    {
      found = mid;
      right = mid - 1;
    } else
    {
      left = mid + 1;
    }
  }
  gt_assert(suftaboffset <= gt_firstcodes_get_sample(fct,found));
  return found;
}

unsigned long gt_firstcodes_sample2full(const GtFirstcodestab *fct,
                                        unsigned long idx)
{
  gt_assert(idx <= fct->numofsamples);
  if (idx < fct->numofsamples)
  {
    return idx << fct->sampleshift;
  }
  return fct->differentcodes - 1;
}

void gt_firstcodes_samples_delete(GtFirstcodesspacelog *fcsl,
                                  GtFirstcodestab *fct)
{
  if (fct->leftborder_samples != NULL)
  {
    gt_free(fct->leftborder_samples);
    GT_FCI_SUBTRACTWORKSPACE(fcsl,"leftborder_samples");
    fct->leftborder_samples = NULL;
  }
}

void gt_firstcodes_countocc_delete(GtFirstcodesspacelog *fcsl,
                                   GtFirstcodestab *fct)
{
  if (fct->countocc_small != NULL)
  {
    GT_FCI_SUBTRACTWORKSPACE(fcsl,"countocc_small");
    gt_free(fct->countocc_small);
    fct->countocc_small = NULL;
  }
  gt_hashtable_delete(fct->countocc_exceptions);
  fct->countocc_exceptions = NULL;
}

void gt_firstcodes_tab_delete(GtFirstcodesspacelog *fcsl,GtFirstcodestab *fct)
{
  gt_firstcodes_samples_delete(fcsl,fct);
  gt_str_delete(fct->outfilenameleftborder);
  fct->outfilenameleftborder = NULL;
#ifdef _LP64
  GT_FREEARRAY(&fct->bitchangepoints,GtUlong);
#endif
}

void gt_firstcodes_countocc_setnull(GtFirstcodestab *fct)
{
  fct->leftborder = NULL;
  fct->countocc_small = NULL;
  fct->leftborder_samples = NULL;
  fct->countocc_exceptions = NULL;
  fct->differentcodes = 0;
  fct->hashmap_addcount = 0;
  fct->hashmap_getcount = 0;
  fct->outfilenameleftborder = NULL;
#ifdef _LP64
  GT_INITARRAY(&fct->bitchangepoints,GtUlong);
#endif
}

uint32_t **gt_firstcodes_leftborder_address(GtFirstcodestab *fct)
{
  return &fct->leftborder;
}

void gt_firstcodes_leftborder_remap(GtFirstcodestab *fct,uint32_t *ptr)
{
  fct->leftborder = ptr;
}

const GtStr *gt_firstcodes_outfilenameleftborder(const GtFirstcodestab *fct)
{
  return fct->outfilenameleftborder;
}
genometools-1.5.1/src/match/firstcodes-tab.h000066400000000000000000000136171211610345200210210ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FIRSTCODES_TAB_H
#define FIRSTCODES_TAB_H

#include 
#include "core/unused_api.h"
#include "core/str_api.h"
#include "core/hashmap-generic.h"
#include "core/logger_api.h"
#include "core/arraydef.h"
#include "marksubstring.h"
#include "firstcodes-spacelog.h"
#include "firstcodes-cache.h"

typedef uint8_t GtCountAFCtype;
#define GT_FIRSTCODES_MAXSMALL UINT8_MAX

typedef struct
{
  unsigned long differentcodes,
                numofsamples,
                sampledistance,
                hashmap_addcount,
                hashmap_getcount;
  unsigned int sampleshift;
  uint32_t *leftborder;
  GtCountAFCtype *countocc_small;
  GtHashtable *countocc_exceptions;
  unsigned long *leftborder_samples;
  GtStr *outfilenameleftborder;
  unsigned long differencemask, /* for extracting the difference */
                countmax;
  unsigned int shiftforcounts;
#ifdef _LP64
  GtArrayGtUlong bitchangepoints;
#endif
} GtFirstcodestab;

DECLARE_HASHMAP(unsigned long, ul, uint32_t, u32, static, inline)
DEFINE_HASHMAP(unsigned long, ul, uint32_t, u32, gt_ht_ul_elem_hash,
               gt_ht_ul_elem_cmp, NULL_DESTRUCTOR, NULL_DESTRUCTOR, static,
               inline)

#ifdef _LP64
#define GT_CHANGEPOINT_GET(CP)\
        unsigned long CP;\
        for (CP = 0; CP < fct->bitchangepoints.nextfreeGtUlong &&\
                     idx > fct->bitchangepoints.spaceGtUlong[CP]; CP++)\
            /* Nothing */ ;
#endif

#define GT_MODVALUEBITS 32U
#define GT_MODVALUEMASK UINT32_MAX

GT_UNUSED
static inline unsigned long gt_firstcodes_insertionindex(GtFirstcodestab *fct,
                                                         unsigned long idx)
{
#ifdef _LP64
  GT_CHANGEPOINT_GET(changepoint);
  gt_assert(idx < fct->differentcodes);
  if (fct->leftborder[idx] > 0)
  {
    return (unsigned long) --fct->leftborder[idx]
                           + (changepoint << GT_MODVALUEBITS);
  } else
  {
    gt_assert(changepoint > 0);
    changepoint--;
    fct->bitchangepoints.spaceGtUlong[changepoint]++;
    fct->leftborder[idx] = GT_MODVALUEMASK;
    return (unsigned long)
           fct->leftborder[idx] + (changepoint << GT_MODVALUEBITS);
  }
#else
  gt_assert(idx < fct->differentcodes && fct->leftborder[idx] > 0);
  return (unsigned long) --fct->leftborder[idx];
#endif
}

unsigned long gt_firstcodes_partialsums(GtFirstcodesspacelog *fcsl,
                                        GtFirstcodestab *fct,
                                        const unsigned long *differences,
                                        unsigned long expectedlastpartsum);

unsigned long gt_firstcodes_get_leftborder(const GtFirstcodestab *fct,
                                           unsigned long idx);

unsigned long gt_firstcodes_numofsamples(const GtFirstcodestab *fct);

unsigned long gt_firstcodes_findfirstsamplelarger(const GtFirstcodestab *fct,
                                                  unsigned long suftaboffset);

void gt_firstcodes_samples_delete(GtFirstcodesspacelog *fcsl,
                                  GtFirstcodestab *fct);

void gt_firstcodes_countocc_delete(GtFirstcodesspacelog *fcsl,
                                   GtFirstcodestab *fct);

void gt_firstcodes_tab_delete(GtFirstcodesspacelog *fcsl,
                              GtFirstcodestab *fct);

void gt_firstcodes_countocc_setnull(GtFirstcodestab *fct);

uint32_t **gt_firstcodes_leftborder_address(GtFirstcodestab *fct);

void gt_firstcodes_leftborder_remap(GtFirstcodestab *fct,uint32_t *ptr);

const GtStr *gt_firstcodes_outfilenameleftborder(const GtFirstcodestab *fct);

unsigned long gt_firstcodes_sample2full(const GtFirstcodestab *fct,
                                        unsigned long idx);

unsigned long gt_firstcodes_leftborder_entries(const GtFirstcodestab *fct);

unsigned long gt_firstcodes_leftborder_entries(const GtFirstcodestab *fct);

unsigned long gt_firstcodes_get_sample(const GtFirstcodestab *fct,
                                       unsigned long idx);

unsigned long gt_firstcodes_remdups(unsigned long *allfirstcodes,
                                    GtFirstcodesspacelog *fcsl,
                                    GtFirstcodestab *fct,
                                    unsigned long numofsequences,
                                    Gtmarksubstring *markprefix,
                                    Gtmarksubstring *marksuffix,
                                    GtArrayGtIndexwithcode **binsearchcache,
                                    unsigned int addbscache_depth,
                                    bool withdistbits,
                                    GtLogger *logger);

unsigned long gt_firstcodes_accumulatecounts_merge(
                                        GtFirstcodestab *tab,
                                        unsigned long *differences,
                                        unsigned long differentcodes,
                                        const unsigned long *querystream_fst,
                                        const unsigned long *querystream_lst,
                                        unsigned long subjectindex,
                                        unsigned long subjectcode);

#endif
genometools-1.5.1/src/match/firstcodes.c000066400000000000000000001632601211610345200202500ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/fa.h"
#include "core/arraydef.h"
#include "core/codetype.h"
#include "core/encseq.h"
#include "core/error_api.h"
#include "core/logger_api.h"
#include "core/mathsupport.h"
#include "core/radix_sort.h"
#include "core/showtime.h"
#include "core/spacecalc.h"
#include "core/spacepeak.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/minmax.h"
#ifdef GT_THREADS_ENABLED
#include "core/thread_api.h"
#endif
#include "firstcodes-buf.h"
#include "firstcodes-spacelog.h"
#include "firstcodes-tab.h"
#include "firstcodes-accum.h"
#include "firstcodes-insert.h"
#include "firstcodes-cache.h"
#include "firstcodes.h"
#include "marksubstring.h"
#include "seqnumrelpos.h"
#include "sfx-partssuf.h"
#include "sfx-shortreadsort.h"
#include "sfx-suffixer.h"
#include "spmsuftab.h"
#include "stamp.h"

typedef struct
{
  unsigned long firstcodehits,
                firstcodeposhits,
                countsequences,
                numofsequences,
                codebuffer_total,
                currentminindex,
                currentmaxindex,
                differentcodes, /* a copy of the same value as in tab */
                widthofpart;
  GtArrayGtIndexwithcode *binsearchcache;
  unsigned int flushcount,
               shiftright2index,
               marksuffixunits,
               markprefixunits,
               bitsforposref;
  GtRadixsortinfo *radixsort_code,
                  *radixsort_codepos;
  GtSpmsuftab *spmsuftab;
  GtSfxmappedrange *mappedleftborder,
                   *mappedallfirstcodes,
                   *mappedmarkprefix;
  unsigned long *allfirstcodes,
                allfirstcodes0_save;
  GtFirstcodesspacelog *fcsl;
  GtCodeposbuffer buf;
  GtFirstcodestab tab;
} GtFirstcodesinfo;

static double gt_firstcodes_round(double d)
{
  return floor(d + 0.5);
}

static unsigned long gt_kmercode2prefix_index(unsigned long idx,
                                              const void *data)
{
  const GtFirstcodesinfo *fci = (const GtFirstcodesinfo *) data;

  gt_assert(fci != NULL && idx < fci->differentcodes);
  return fci->allfirstcodes[idx] >> fci->shiftright2index;
}

static void gt_minmax_index_kmercode2prefix(unsigned long *minindex,
                                            unsigned long *maxindex,
                                            const void *data)
{
  *minindex = gt_kmercode2prefix_index(*minindex,data);
  *maxindex = gt_kmercode2prefix_index(*maxindex,data);
}

static void gt_storefirstcodes(void *processinfo,
                               GT_UNUSED bool firstinrange,
                               GT_UNUSED unsigned long pos,
                               GtCodetype code)
{
  GtFirstcodesinfo *fci = (GtFirstcodesinfo *) processinfo;

  gt_assert(fci != NULL && firstinrange &&
            fci->allfirstcodes != NULL &&
            fci->countsequences < fci->numofsequences);
  fci->allfirstcodes[fci->countsequences++] = code;
}

static void gt_firstcodes_restore_from_differences(GtFirstcodesinfo *fci)
{
  unsigned long idx;

  fci->allfirstcodes[0] = fci->allfirstcodes0_save;
  for (idx=1UL; idx < fci->differentcodes; idx++)
  {
    fci->allfirstcodes[idx]
      = (fci->allfirstcodes[idx] & fci->tab.differencemask)
        + fci->allfirstcodes[idx-1];
  }
}

static void gt_firstcodes_accumulatecounts_flush(void *data)
{
  GtFirstcodesinfo *fci = (GtFirstcodesinfo *) data;

  if (fci->buf.nextfree > 0)
  {
    unsigned long foundindex, foundcode;

    gt_assert(fci->allfirstcodes != NULL);
    fci->codebuffer_total += fci->buf.nextfree;
    gt_radixsort_inplace_sort(fci->radixsort_code,fci->buf.nextfree);
    foundindex = gt_firstcodes_find_accu(&foundcode,
                                         fci->allfirstcodes,
                                         fci->allfirstcodes0_save,
                                         fci->differentcodes,
                                         fci->tab.differencemask,
                                         fci->binsearchcache,
                                         fci->buf.spaceGtUlong[0]);
    if (foundindex != ULONG_MAX)
    {
      fci->firstcodehits
        += gt_firstcodes_accumulatecounts_merge(&fci->tab,
                                                fci->allfirstcodes,
                                                fci->differentcodes,
                                                fci->buf.spaceGtUlong,
                                                fci->buf.spaceGtUlong
                                                + fci->buf.nextfree - 1,
                                                foundindex,
                                                foundcode);
    }
    fci->flushcount++;
    fci->buf.nextfree = 0;
  }
}

const unsigned long *gt_firstcodes_find_insert(const GtFirstcodesinfo *fci,
                                               unsigned long code)
{
  const unsigned long *found = NULL, *leftptr = NULL, *midptr, *rightptr = NULL;

  leftptr = fci->allfirstcodes + fci->currentminindex;
  rightptr = fci->allfirstcodes + fci->currentmaxindex;
  while (leftptr <= rightptr)
  {
    midptr = leftptr + GT_DIV2((unsigned long) (rightptr-leftptr));
    if (code < *midptr)
    {
      rightptr = midptr - 1;
      found = midptr;
    } else
    {
      if (code > *midptr)
      {
        leftptr = midptr + 1;
      } else
      {
        return midptr;
      }
    }
  }
  return found;
}

static unsigned long gt_firstcodes_insertsuffixes_merge(
                                        GtFirstcodesinfo *fci,
                                        const GtUlongPair *querystream_fst,
                                        const unsigned long *subjectstream_fst)
{
  unsigned long found = 0, idx;
  const GtUlongPair *query = querystream_fst,
                    *querystream_lst = fci->buf.spaceGtUlongPair +
                                       fci->buf.nextfree - 1;
  const unsigned long *subject = subjectstream_fst,
                      *subjectstream_lst = fci->allfirstcodes +
                                           fci->currentmaxindex;

  while (query <= querystream_lst && subject <= subjectstream_lst)
  {
    if (query->a <= *subject)
    {
      if (query->a == *subject)
      {
        idx = gt_firstcodes_insertionindex(&fci->tab,
                                           (unsigned long)
                                           (subject - fci->allfirstcodes));
        gt_assert(idx < fci->firstcodehits + fci->numofsequences);
        gt_spmsuftab_set(fci->spmsuftab,idx,
                         gt_spmsuftab_usebitsforpositions(fci->spmsuftab)
                           ? gt_seqnumrelpos_decode_pos(fci->buf.snrp,query->b)
                           : query->b);
        found++;
      }
      query++;
    } else
    {
      subject++;
    }
  }
  return found;
}

static void gt_firstcodes_insertsuffixes_flush(void *data)
{
  GtFirstcodesinfo *fci = (GtFirstcodesinfo *) data;

  if (fci->buf.nextfree > 0)
  {
    const unsigned long *ptr;

    gt_assert(fci->allfirstcodes != NULL);
    fci->codebuffer_total += fci->buf.nextfree;
    gt_radixsort_inplace_sort(fci->radixsort_codepos,fci->buf.nextfree);
    ptr = gt_firstcodes_find_insert(fci,fci->buf.spaceGtUlongPair[0].a);
    if (ptr != NULL)
    {
      fci->firstcodeposhits
        += gt_firstcodes_insertsuffixes_merge(fci,fci->buf.spaceGtUlongPair,
                                              ptr);
    }
    fci->flushcount++;
    fci->buf.nextfree = 0;
  }
}

static void gt_firstcodes_checksuftab_bucket(const GtEncseq *encseq,
                                             GtReadmode readmode,
                                             GtEncseqReader *esr1,
                                             GtEncseqReader *esr2,
                                             unsigned long previoussuffix,
                                             bool previousdefined,
                                             const unsigned long
                                               *seqnum_relpos_bucket,
                                             const GtSeqnumrelpos *snrp,
                                             GT_UNUSED const uint16_t
                                               *lcptab_bucket,
                                             unsigned long numberofsuffixes)
{
  unsigned long idx, current, maxlcp,
                totallength = gt_encseq_total_length(encseq);
  const unsigned long depth = 0;
  GT_UNUSED int cmp;
  const bool specialsareequal = false, specialsareequalatdepth0 = false;

  gt_assert(!previousdefined || previoussuffix < totallength);
  for (idx = 0; idx < numberofsuffixes; idx++)
  {
    current = gt_seqnumrelpos_decode_pos(snrp,seqnum_relpos_bucket[idx]);
    if (previousdefined && idx < totallength)
    {
      gt_assert(current < totallength);
      cmp = gt_encseq_check_comparetwosuffixes(encseq,
                                               readmode,
                                               &maxlcp,
                                               specialsareequal,
                                               specialsareequalatdepth0,
                                               depth,
                                               previoussuffix,
                                               current,
                                               esr1,
                                               esr2);
      gt_assert(cmp <= 0);
      gt_assert(idx == 0 || maxlcp == (unsigned long) lcptab_bucket[idx]);
    }
    previoussuffix = current;
    previousdefined = true;
  }
}

static int gt_firstcodes_sortremaining(GtShortreadsortworkinfo *srsw,
                                       const GtEncseq *encseq,
                                       GtReadmode readmode,
                                       const GtSpmsuftab *spmsuftab,
                                       const GtSeqnumrelpos *snrp,
                                       const GtFirstcodestab *fct,
                                       unsigned long minindex,
                                       unsigned long maxindex,
                                       unsigned long sumofwidth,
                                       unsigned long spaceforbucketprocessing,
                                       unsigned long depth,
                                       GtFirstcodesintervalprocess itvprocess,
                                       GtFirstcodesintervalprocess_end
                                              itvprocess_end,
                                       void *itvprocessdata,
                                       bool withsuftabcheck,
                                       GtError *err)
{
  unsigned long current,
                next = GT_UNDEF_ULONG,
                idx,
                width,
                sumwidth = 0,
                previoussuffix = 0;
  GtShortreadsortresult srsresult;
  bool previousdefined = false, haserr = false;

  current = gt_firstcodes_get_leftborder(fct,minindex);
  for (idx = minindex; idx <= maxindex; idx++)
  {
    if (idx < maxindex)
    {
      next = gt_firstcodes_get_leftborder(fct,idx+1);
      gt_assert(current < next);
      width = next - current;
    } else
    {
      gt_assert(sumofwidth > current);
      width = sumofwidth - current;
    }
    sumwidth += width;
    gt_assert(sumwidth <= spmsuftab->numofentries);
    if (width >= 2UL)
    {
      gt_shortreadsort_firstcodes_sort(&srsresult,
                                       srsw,
                                       snrp,
                                       encseq,
                                       spmsuftab,
                                       current,
                                       width,
                                       depth,
                                       0);
      if (withsuftabcheck)
      {
        gt_firstcodes_checksuftab_bucket(encseq,
                                         readmode,
                                         NULL,
                                         NULL,
                                         previoussuffix,
                                         previousdefined,
                                         srsresult.suftab_bucket,
                                         snrp,
                                         srsresult.lcptab_bucket,
                                         width);
        previousdefined = true;
        previoussuffix
          = gt_seqnumrelpos_decode_pos(snrp,srsresult.suftab_bucket[width-1]);
      }
      if (itvprocess != NULL)
      {
        if (itvprocess(itvprocessdata,
                       srsresult.suftab_bucket,
                       snrp,srsresult.lcptab_bucket,width,
                       spaceforbucketprocessing,err) != 0)
        {
          haserr = true;
          break;
        }
      }
    } else
    {
      gt_assert(width == 1UL);
    }
    gt_assert(next != GT_UNDEF_ULONG);
    current = next;
  }
  if (itvprocess_end != NULL)
  {
    itvprocess_end(itvprocessdata);
  }
  return haserr ? -1 : 0;
}

#ifdef GT_THREADS_ENABLED

static unsigned long gt_firstcodes_findfirstlarger(const GtFirstcodestab *fct,
                                                   unsigned long start,
                                                   unsigned long end,
                                                   unsigned long offset)
{
  unsigned long left = start, right = end, found = end, mid, midval;

  while (left+1 < right)
  {
    mid = GT_DIV2(left+right);
    midval = gt_firstcodes_get_leftborder(fct,mid);
    if (offset == midval)
    {
      return mid;
    }
    if (offset < midval)
    {
      found = mid;
      right = mid - 1;
    } else
    {
      left = mid + 1;
    }
  }
  return found;
}

static unsigned long *gt_evenly_divide_part(const GtFirstcodestab *fct,
                                            unsigned long partminindex,
                                            unsigned long partmaxindex,
                                            unsigned long numofsuffixes,
                                            unsigned int numofparts)
{
  unsigned long *endindexes, widthofpart, offset;
  unsigned int part, remainder;

  gt_assert(partminindex < partmaxindex && numofparts >= 2U);
  widthofpart = numofsuffixes/numofparts;
  endindexes = gt_malloc(sizeof (*endindexes) * numofparts);
  offset = gt_firstcodes_get_leftborder(fct,partminindex);
  remainder = (unsigned int) (numofsuffixes % (unsigned long) numofparts);
  for (part=0; part < numofparts; part++)
  {
    if (remainder > 0)
    {
      offset += widthofpart + 1;
      remainder--;
    } else
    {
      offset += widthofpart;
    }
    if (part == numofparts - 1)
    {
      endindexes[part] = partmaxindex;
    } else
    {
      unsigned long start = (part == 0) ? partminindex : endindexes[part-1] + 1;

      endindexes[part] = gt_firstcodes_findfirstlarger(fct,start,partmaxindex,
                                                       offset);
      gt_assert(endindexes[part] <= partmaxindex);
    }
  }
  return endindexes;
}

typedef struct
{
  GtShortreadsortworkinfo *srsw;
  const GtEncseq *encseq;
  GtReadmode readmode;
  const GtSpmsuftab *spmsuftab;
  const GtSeqnumrelpos *snrp;
  const GtFirstcodestab *fct;
  unsigned long depth,
                minindex,
                maxindex,
                sumofwidth,
                spaceforbucketprocessing;
  bool withsuftabcheck;
  GtFirstcodesintervalprocess itvprocess;
  GtFirstcodesintervalprocess_end itvprocess_end;
  void *itvprocessdata;
  GtError *err;
  GtThread *thread;
} GtSortRemainingThreadinfo;

static void *gt_firstcodes_thread_caller_sortremaining(void *data)
{
  GtSortRemainingThreadinfo *threadinfo = (GtSortRemainingThreadinfo *) data;

  if (gt_firstcodes_sortremaining(threadinfo->srsw,
                                  threadinfo->encseq,
                                  threadinfo->readmode,
                                  threadinfo->spmsuftab,
                                  threadinfo->snrp,
                                  threadinfo->fct,
                                  threadinfo->minindex,
                                  threadinfo->maxindex,
                                  threadinfo->sumofwidth,
                                  threadinfo->spaceforbucketprocessing,
                                  threadinfo->depth,
                                  threadinfo->itvprocess,
                                  threadinfo->itvprocess_end,
                                  threadinfo->itvprocessdata,
                                  threadinfo->withsuftabcheck,
                                  threadinfo->err) != 0)
  {
    gt_assert(false);
  }
  return NULL;
}

static int gt_firstcodes_thread_sortremaining(
                                       GtShortreadsortworkinfo **srswtab,
                                       const GtEncseq *encseq,
                                       GtReadmode readmode,
                                       const GtSpmsuftab *spmsuftab,
                                       const GtSeqnumrelpos *snrp,
                                       const GtFirstcodestab *fct,
                                       unsigned long partminindex,
                                       unsigned long partmaxindex,
                                       unsigned long widthofpart,
                                       unsigned long sumofwidth,
                                       unsigned long spaceforbucketprocessing,
                                       unsigned long depth,
                                       GtFirstcodesintervalprocess itvprocess,
                                       GtFirstcodesintervalprocess_end
                                         itvprocess_end,
                                       void *itvprocessdatatab,
                                       bool withsuftabcheck,
                                       unsigned int threads,
                                       GtLogger *logger,
                                       GtError *err)
{
  unsigned int t;
  unsigned long sum = 0, *endindexes;
  GtSortRemainingThreadinfo *threadinfo;
  bool haserr = false;

  gt_assert(threads >= 2U);
  endindexes = gt_evenly_divide_part(fct,partminindex,partmaxindex,widthofpart,
                                     threads);
  threadinfo = gt_malloc(sizeof (*threadinfo) * threads);
  for (t=0; tbinsearchcache,fci->fcsl);
  if (fci->radixsort_codepos != NULL)
  {
    gt_radixsort_delete(fci->radixsort_codepos);
    GT_FCI_SUBTRACTWORKSPACE(fci->fcsl,"radixsort_codepos");
    fci->radixsort_codepos = NULL;
  }
  if (fci->mappedmarkprefix != NULL)
  {
    gt_Sfxmappedrange_delete(fci->mappedmarkprefix);
    gt_marksubstring_delete(fci->buf.markprefix,true);
  } else
  {
    gt_marksubstring_delete(fci->buf.markprefix,true);
    if (fci->buf.markprefix != NULL)
    {
      GT_FCI_SUBTRACTSPLITSPACE(fci->fcsl,"markprefix");
    }
  }
  fci->buf.markprefix = NULL;
  gt_marksubstring_delete(fci->buf.marksuffix,true);
  if (fci->buf.marksuffix != NULL)
  {
    GT_FCI_SUBTRACTWORKSPACE(fci->fcsl,"marksuffix");
  }
  fci->buf.marksuffix = NULL;
  if (fci->mappedallfirstcodes == NULL && fci->allfirstcodes != NULL)
  {
    gt_free(fci->allfirstcodes);
    fci->allfirstcodes = NULL;
    GT_FCI_SUBTRACTSPLITSPACE(fci->fcsl,"allfirstcodes");
  }
}

static unsigned long gt_firstcodes_idx2code(const GtFirstcodesinfo *fci,
                                            unsigned long idx)
{
  gt_assert(idx <= fci->differentcodes);
  if (idx == fci->differentcodes)
  {
    return fci->allfirstcodes[idx-1];
  }
  return fci->allfirstcodes[idx];
}

void gt_rungetencseqkmers(const GtEncseq *encseq,unsigned int kmersize)
{
  const GtReadmode readmode = GT_READMODE_FORWARD;

  getencseqkmers_twobitencoding(encseq,
                                readmode,
                                kmersize,
                                kmersize,
                                false,
                                NULL,
                                NULL,
                                NULL,
                                NULL);
}

static int gt_firstcodes_init(GtFirstcodesinfo *fci,
                              const GtEncseq *encseq,
                              unsigned int kmersize,
                              bool withsuftabcheck,
                              unsigned int minmatchlength,
                              GtError *err)
{
  unsigned long totallength, maxseqlength, maxrelpos;
  unsigned int logtotallength, bitsforrelpos, bitsforseqnum;
  bool haserr = false;

  maxseqlength = gt_encseq_max_seq_length(encseq);
  totallength = gt_encseq_total_length(encseq);
  logtotallength
    = (unsigned int) gt_firstcodes_round(log((double) totallength));
  if (logtotallength >= 8U)
  {
    fci->markprefixunits = MAX(8U,logtotallength - 8U);
  } else
  {
    fci->markprefixunits = MIN(kmersize/2U,8U);
  }
  if (fci->markprefixunits >= 2U)
  {
    fci->marksuffixunits = fci->markprefixunits - 1;
  } else
  {
    fci->marksuffixunits = fci->markprefixunits;
  }
  if (fci->marksuffixunits + fci->markprefixunits > kmersize)
  {
    if (fci->marksuffixunits % 2U == 0)
    {
      fci->marksuffixunits = fci->markprefixunits = kmersize/2U;
    } else
    {
      fci->marksuffixunits = kmersize/2;
      fci->markprefixunits = kmersize - fci->marksuffixunits;
    }
  }
  gt_log_log("markprefixunits=%u,marksuffixunits=%u",fci->markprefixunits,
                                                     fci->marksuffixunits);
  if (maxseqlength > (unsigned long) minmatchlength)
  {
    maxrelpos = maxseqlength - (unsigned long) minmatchlength;
  } else
  {
    maxrelpos = 0;
  }
  bitsforrelpos = gt_determinebitspervalue(maxrelpos);
  fci->buf.snrp = gt_seqnumrelpos_new(bitsforrelpos,encseq);
  fci->buf.accum_all = false;
  fci->buf.markprefix = NULL;
  fci->buf.marksuffix = NULL;
  fci->numofsequences = gt_encseq_num_of_sequences(encseq);
  gt_assert(fci->numofsequences > 0);
  bitsforseqnum = gt_determinebitspervalue(fci->numofsequences - 1);
  if (bitsforseqnum + bitsforrelpos > (unsigned int) GT_INTWORDSIZE)
  {
    gt_seqnumrelpos_delete(fci->buf.snrp);
    fci->buf.snrp = NULL;
    gt_error_set(err,"cannot process encoded sequences with %lu sequences "
                     "of length up to %lu (%u+%u bits)",
                     fci->numofsequences,maxseqlength,bitsforseqnum,
                     bitsforrelpos);
    haserr = true;
  }
  fci->fcsl = gt_firstcodes_spacelog_new();
  fci->spmsuftab = NULL;
  fci->radixsort_code = NULL;
  fci->radixsort_codepos = NULL;
  fci->buf.spaceGtUlongPair = NULL;
  fci->buf.spaceGtUlong = NULL;
  fci->mappedallfirstcodes = NULL;
  fci->mappedmarkprefix = NULL;
  fci->mappedleftborder = NULL;
  fci->binsearchcache = NULL;
  GT_FCI_ADDWORKSPACE(fci->fcsl,"encseq",(size_t) gt_encseq_sizeofrep(encseq));
  if (withsuftabcheck)
  {
    gt_firstcodes_spacelog_start_diff(fci->fcsl);
  }
  if (!haserr)
  {
    size_t sizeforcodestable
      = sizeof (*fci->allfirstcodes) * fci->numofsequences;
    fci->allfirstcodes = gt_malloc(sizeforcodestable);
    GT_FCI_ADDSPLITSPACE(fci->fcsl,"allfirstcodes",sizeforcodestable);
  } else
  {
    fci->allfirstcodes = NULL;
  }
  gt_firstcodes_countocc_setnull(&fci->tab);
  fci->countsequences = 0;
  fci->firstcodehits = 0;
  fci->firstcodeposhits = 0;
  fci->bitsforposref = bitsforseqnum + bitsforrelpos;
  return haserr ? -1 : 0;
}

static void gt_firstcodes_collectcodes(GtFirstcodesinfo *fci,
                                       const GtEncseq *encseq,
                                       GtReadmode readmode,
                                       unsigned int kmersize,
                                       unsigned int minmatchlength,
                                       unsigned int addbscache_depth,
                                       bool withdistbits,
                                       GtLogger *logger,
                                       GtTimer *timer)
{
  unsigned int numofchars;

  getencseqkmers_twobitencoding(encseq,
                                readmode,
                                kmersize,
                                minmatchlength,
                                true,
                                gt_storefirstcodes,
                                fci,
                                NULL,
                                NULL);
  fci->numofsequences = fci->countsequences;
  gt_logger_log(logger,"have stored %lu prefix codes",fci->numofsequences);
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "to sort initial prefixes",stdout);
  }
  gt_radixsort_inplace_ulong(fci->allfirstcodes,fci->numofsequences);
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "to remove duplicates",stdout);
  }
  numofchars = gt_encseq_alphabetnumofchars(encseq);
  gt_assert(numofchars == 4U);
  fci->buf.markprefix = gt_marksubstring_new(numofchars,kmersize,false,
                                            fci->markprefixunits);
  fci->shiftright2index = gt_marksubstring_shiftright(fci->buf.markprefix)
                          + GT_LOGWORDSIZE;
  GT_FCI_ADDSPLITSPACE(fci->fcsl,"markprefix",
                      (size_t) gt_marksubstring_size(fci->buf.markprefix));
  fci->buf.marksuffix = gt_marksubstring_new(numofchars,kmersize,true,
                                            fci->marksuffixunits);
  GT_FCI_ADDWORKSPACE(fci->fcsl,"marksuffix",
                      (size_t) gt_marksubstring_size(fci->buf.marksuffix));
  gt_assert(fci->allfirstcodes != NULL);
  fci->allfirstcodes0_save = fci->allfirstcodes[0];
  fci->differentcodes = gt_firstcodes_remdups(fci->allfirstcodes,
                                             fci->fcsl,
                                             &fci->tab,
                                             fci->numofsequences,
                                             fci->buf.markprefix,
                                             fci->buf.marksuffix,
                                             &fci->binsearchcache,
                                             addbscache_depth,
                                             withdistbits,
                                             logger);
  if (fci->differentcodes > 0 && fci->differentcodes < fci->numofsequences)
  {
    fci->allfirstcodes = gt_realloc(fci->allfirstcodes,
                                    sizeof (*fci->allfirstcodes) *
                                    fci->differentcodes);
    GT_FCI_SUBTRACTADDSPLITSPACE(fci->fcsl,"allfirstcodes",
                                 sizeof (*fci->allfirstcodes) *
                                 fci->differentcodes);
  }
}

static int gt_firstcodes_allocspace(GtFirstcodesinfo *fci,
                                    unsigned int numofparts,
                                    unsigned long maximumspace,
                                    unsigned long phase2extra,
                                    GtError *err)
{
  if (maximumspace > 0)
  {
    if ((unsigned long) gt_firstcodes_spacelog_total(fci->fcsl) +
                        phase2extra >= maximumspace)
    {
      gt_error_set(err,"already used %.2f MB of memory and need %.2f MB later "
                       "=> cannot compute index in at most %.2f MB",
                       GT_MEGABYTES(gt_firstcodes_spacelog_total(fci->fcsl)),
                       GT_MEGABYTES(phase2extra),
                       GT_MEGABYTES(maximumspace));
      return -1;
    } else
    {
      size_t remainspace = (size_t) maximumspace -
                           (gt_firstcodes_spacelog_total(fci->fcsl) +
                            phase2extra);

      fci->buf.allocated
        = gt_radixsort_max_num_of_entries_ulong(remainspace);
      if (fci->buf.allocated < fci->differentcodes/16UL)
      {
        fci->buf.allocated = fci->differentcodes/16UL;
      }
    }
  } else
  {
    if (numofparts == 0)
    {
      fci->buf.allocated = gt_radixsort_max_num_of_entries_ulong(
                                 gt_firstcodes_spacelog_total(fci->fcsl)/5UL);
    } else
    {
      fci->buf.allocated = fci->differentcodes/5;
    }
  }
  if (fci->buf.allocated < 16UL)
  {
    fci->buf.allocated = 16UL;
  }
  return 0;
}

static void gt_firstcodes_accumulatecounts_run(GtFirstcodesinfo *fci,
                                               const GtEncseq *encseq,
                                               unsigned int kmersize,
                                               unsigned int minmatchlength,
                                               GtLogger *logger,
                                               GtTimer *timer)
{
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "to accumulate counts",stdout);
  }
  gt_assert(fci->buf.allocated > 0);
  fci->radixsort_code = gt_radixsort_new_ulong(fci->buf.allocated);
  fci->buf.spaceGtUlong = gt_radixsort_space_ulong(fci->radixsort_code);
  GT_FCI_ADDWORKSPACE(fci->fcsl,"radixsort_code",
                      gt_radixsort_size(fci->radixsort_code));
  fci->buf.fciptr = fci; /* as we need to give fci to the flush function */
  fci->buf.flush_function = gt_firstcodes_accumulatecounts_flush;
  gt_logger_log(logger,"maximum space for accumulating counts %.2f MB",
                GT_MEGABYTES(gt_firstcodes_spacelog_total(fci->fcsl)));
  gt_firstcodes_accum_runkmerscan(encseq, kmersize, minmatchlength,&fci->buf);
  gt_firstcodes_accumulatecounts_flush(fci);
  gt_logger_log(logger,"codebuffer_total=%lu (%.3f%% of all suffixes)",
                fci->codebuffer_total,
                100.0 * (double) fci->codebuffer_total/
                                 gt_encseq_total_length(encseq));
  if (fci->firstcodehits > 0)
  {
    gt_assert(fci->flushcount > 0);
    gt_logger_log(logger,"firstcodehits=%lu (%.3f%% of all suffixes), "
                         "%u rounds (avg length %lu)",
                         fci->firstcodehits,
                         100.0 * (double) fci->firstcodehits/
                                          gt_encseq_total_length(encseq),
                         fci->flushcount,
                         fci->codebuffer_total/fci->flushcount);
  }
  gt_radixsort_delete(fci->radixsort_code);
  fci->radixsort_code = NULL;
  GT_FCI_SUBTRACTWORKSPACE(fci->fcsl,"radixsort_code");
}

static void gt_firstcodes_map_sections(GtFirstcodesinfo *fci,
                                       GtSfxmappedrangelist *sfxmrlist)
{
  fci->mappedmarkprefix
    = gt_Sfxmappedrange_new("markprefix",
                            gt_marksubstring_entries(fci->buf.markprefix),
                            GtSfxGtBitsequence,
                            gt_minmax_index_kmercode2prefix,
                            fci);
  gt_Sfxmappedrangelist_add(sfxmrlist,fci->mappedmarkprefix);
  if (fci->differentcodes > 0)
  {
    fci->mappedallfirstcodes = gt_Sfxmappedrange_new("allfirstcodes",
                                                    fci->differentcodes,
                                                    GtSfxunsignedlong,
                                                    NULL,
                                                    NULL);
    gt_Sfxmappedrangelist_add(sfxmrlist,fci->mappedallfirstcodes);
    fci->mappedleftborder = gt_Sfxmappedrange_new("leftborder",
                                                 fci->differentcodes+1,
                                                 GtSfxuint32_t,
                                                 NULL,
                                                 NULL);
    gt_Sfxmappedrangelist_add(sfxmrlist,fci->mappedleftborder);
  }
}

static int gt_firstcodes_auto_parts(GtFirstcodesinfo *fci,
                                    GtSfxmappedrangelist *sfxmrlist,
                                    unsigned int numofparts,
                                    unsigned long *maximumspace,
                                    unsigned long maxbucketsize,
                                    unsigned int kmersize,
                                    unsigned long totallength,
                                    unsigned long maxseqlength,
                                    unsigned long suftabentries,
                                    unsigned long phase2extra,
                                    GtError *err)
{
  int retval;
  unsigned long leftbordersize_all;

  if (numofparts == 0 && *maximumspace == 0)
  {
    *maximumspace = (unsigned long)
                    (gt_firstcodes_spacelog_peak(fci->fcsl) +
                     phase2extra +
                     gt_shortreadsort_size(true,maxbucketsize,
                                           maxseqlength - kmersize) +
                     4 * 4096);
  } else
  {
    gt_assert(*maximumspace > 0);
  }
  if (fci->mappedleftborder != NULL)
  {
    leftbordersize_all = gt_Sfxmappedrange_size_mapped(
                             fci->mappedleftborder,0,
                             gt_firstcodes_leftborder_entries(&fci->tab)-1);
  } else
  {
    leftbordersize_all = 0;
  }
  retval = gt_suftabparts_fit_memlimit(gt_firstcodes_spacelog_total(fci->fcsl)
                                           /*as this is subtracted*/
                                         + leftbordersize_all
                                         + phase2extra,
                                       *maximumspace,
                                       NULL,
                                       &fci->tab,
                                       sfxmrlist,
                                       totallength,
                                       fci->bitsforposref,
                                       0, /* special characters not used */
                                       suftabentries,
                                       false, /* suftabuint not used */
                                       err);
  if (retval < 0)
  {
    return -1;
  } else
  {
    gt_assert(retval > 0);
    return retval;
  }
}

static void gt_firstcodes_handle_tmp(GtFirstcodesinfo *fci,
                                     GtSuftabparts *suftabparts)
{
  gt_assert(fci->mappedleftborder != NULL);
  gt_Sfxmappedrange_usetmp(fci->mappedleftborder,
                           gt_firstcodes_outfilenameleftborder(&fci->tab),
                           (void **)
                             gt_firstcodes_leftborder_address(&fci->tab),
                           gt_firstcodes_leftborder_entries(&fci->tab),
                           true);
  if (gt_suftabparts_numofparts(suftabparts) > 1U)
  {
    gt_assert(fci->allfirstcodes != NULL);
    gt_assert(fci->mappedallfirstcodes != NULL);
    gt_Sfxmappedrange_storetmp_ulong(fci->mappedallfirstcodes,
                                     &fci->allfirstcodes,
                                     false);
    GT_FCI_SUBTRACTSPLITSPACE(fci->fcsl,"allfirstcodes");
    gt_assert(fci->allfirstcodes == NULL);
    gt_marksubstring_bits_null(fci->buf.markprefix,false);
    gt_assert(fci->mappedmarkprefix != NULL);
    gt_Sfxmappedrange_storetmp_bitsequence(fci->mappedmarkprefix,
                                           gt_marksubstring_bits_address(
                                                fci->buf.markprefix),
                                           false);
    GT_FCI_SUBTRACTSPLITSPACE(fci->fcsl,"markprefix");
    gt_marksubstring_bits_null(fci->buf.markprefix,true);
  } else
  {
    gt_Sfxmappedrange_delete(fci->mappedallfirstcodes);
    fci->mappedallfirstcodes = NULL;
    gt_Sfxmappedrange_delete(fci->mappedmarkprefix);
    fci->mappedmarkprefix = NULL;
  }
}

static void gt_firstcodes_allocsize_for_insertion(GtFirstcodesinfo *fci,
                                                  unsigned long maximumspace,
                                                  const GtSuftabparts
                                                    *suftabparts,
                                                  unsigned long phase2extra)
{
  if (maximumspace > 0)
  {
    const unsigned long maxrounds = 400UL;
    size_t used = gt_firstcodes_spacelog_workspace(fci->fcsl) +
                  phase2extra +
                  gt_suftabparts_largestsizemappedpartwise(suftabparts);

    if ((unsigned long) used < maximumspace)
    {
      fci->buf.allocated = gt_radixsort_max_num_of_entries_ulongpair(
                                                (size_t) maximumspace - used);
    } else
    {
      fci->buf.allocated /= 4UL;
    }
    if ((unsigned long) (fci->codebuffer_total+fci->numofsequences)/
                        fci->buf.allocated > maxrounds)
    {
      fci->buf.allocated
        = (fci->codebuffer_total+fci->numofsequences)/maxrounds;
    }
  } else
  {
    fci->buf.allocated /= 2UL;
  }
}

static int gt_firstcodes_process_part(GtFirstcodesinfo *fci,
                                      const GtEncseq *encseq,
                                      GtReadmode readmode,
                                      unsigned int kmersize,
                                      unsigned int minmatchlength,
                                      const GtSuftabparts *suftabparts,
                                      unsigned int part,
                                      unsigned long maximumspace,
#ifndef GT_THREADS_ENABLED
                                      GT_UNUSED
#endif
                                      unsigned int threads,
                                      unsigned long suftabentries,
                                      bool withsuftabcheck,
                                      GtShortreadsortworkinfo **srswtab,
                                      GtFirstcodesintervalprocess itvprocess,
                                      GtFirstcodesintervalprocess_end
                                        itvprocess_end,
                                      void *itvprocessdatatab,
                                      GtLogger *logger,
                                      GtTimer *timer,
                                      GtError *err)
{
  unsigned long spaceforbucketprocessing = 0;
  void *mapptr;
  bool haserr = false;

  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "to insert suffixes into buckets",stdout);
  }
  fci->widthofpart = gt_suftabparts_widthofpart(part,suftabparts);
  gt_logger_log(logger,"compute part %u (%.2f%% of all candidates)",part,
               (double) 100.0 * fci->widthofpart/suftabentries);
  fci->currentminindex = gt_suftabparts_minindex(part,suftabparts);
  fci->currentmaxindex = gt_suftabparts_maxindex(part,suftabparts);
  if (fci->mappedallfirstcodes != NULL)
  {
    fci->allfirstcodes
      = (unsigned long *)
        gt_Sfxmappedrange_map(fci->mappedallfirstcodes,
                              fci->currentminindex,
                              fci->currentmaxindex);
    GT_FCI_ADDSPLITSPACE(fci->fcsl,"allfirstcodes",
                         (size_t) gt_Sfxmappedrange_size_mapped(
                                        fci->mappedallfirstcodes,
                                        fci->currentminindex,
                                        fci->currentmaxindex));
  }
  gt_assert(fci->mappedleftborder != NULL);
  mapptr = gt_Sfxmappedrange_map(fci->mappedleftborder,
                                 fci->currentminindex,
                                 fci->currentmaxindex);
  gt_firstcodes_leftborder_remap(&fci->tab,(uint32_t *) mapptr);
  GT_FCI_ADDSPLITSPACE(fci->fcsl,"leftborder",
                       (size_t) gt_Sfxmappedrange_size_mapped(
                                               fci->mappedleftborder,
                                               fci->currentminindex,
                                               fci->currentmaxindex));
  if (fci->mappedmarkprefix != NULL)
  {
    mapptr = gt_Sfxmappedrange_map(fci->mappedmarkprefix,
                                   fci->currentminindex,
                                   fci->currentmaxindex);

    gt_marksubstring_bits_map(fci->buf.markprefix, (GtBitsequence *) mapptr);
    GT_FCI_ADDSPLITSPACE(fci->fcsl,"markprefix",
                         (size_t) gt_Sfxmappedrange_size_mapped(
                                               fci->mappedmarkprefix,
                                               fci->currentminindex,
                                               fci->currentmaxindex));
  }
  gt_logger_log(logger,"maximum space for part %u: %.2f MB",
                part,GT_MEGABYTES(gt_firstcodes_spacelog_total(fci->fcsl)));
  fci->buf.currentmincode = gt_firstcodes_idx2code(fci,fci->currentminindex);
  fci->buf.currentmaxcode = gt_firstcodes_idx2code(fci,fci->currentmaxindex);
  gt_spmsuftab_partoffset(fci->spmsuftab,
                          gt_suftabparts_offset(part,suftabparts));
  gt_firstcodes_insert_runkmerscan(encseq,
                                   kmersize,
                                   minmatchlength,
                                   &fci->buf);
  gt_firstcodes_insertsuffixes_flush(fci);
  if (fci->mappedmarkprefix != NULL)
  {
    gt_Sfxmappedrange_unmap(fci->mappedmarkprefix);
    GT_FCI_SUBTRACTSPLITSPACE(fci->fcsl,"markprefix");
  }
  if (fci->mappedallfirstcodes != NULL)
  {
    gt_Sfxmappedrange_unmap(fci->mappedallfirstcodes);
    GT_FCI_SUBTRACTSPLITSPACE(fci->fcsl,"allfirstcodes");
  }
  if (part == gt_suftabparts_numofparts(suftabparts) - 1)
  {
    gt_firstcode_delete_before_end(fci);
  }
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "to sort buckets of suffixes",stdout);
  }
  if (maximumspace > 0)
  {
    if ((unsigned long) gt_firstcodes_spacelog_total(fci->fcsl)
        < maximumspace)
    {
      spaceforbucketprocessing = maximumspace -
                                 (unsigned long)
                                 gt_firstcodes_spacelog_total(fci->fcsl);
      gt_log_log("space left for sortremaining: %.2f",
                 GT_MEGABYTES(spaceforbucketprocessing));
    } else
    {
      spaceforbucketprocessing = 0;
    }
  }
#ifdef GT_THREADS_ENABLED
  if (threads > 1U)
  {
    if (gt_firstcodes_thread_sortremaining(
                                   srswtab,
                                   encseq,
                                   readmode,
                                   fci->spmsuftab,
                                   fci->buf.snrp,
                                   &fci->tab,
                                   fci->currentminindex,
                                   fci->currentmaxindex,
                                   gt_suftabparts_widthofpart(part,suftabparts),
                                   gt_suftabparts_sumofwidth(part,suftabparts),
                                   spaceforbucketprocessing,
                                   (unsigned long) kmersize,
                                   itvprocess,
                                   itvprocess_end,
                                   itvprocessdatatab,
                                   withsuftabcheck,
                                   threads,
                                   logger,
                                   NULL) != 0)
    {
      haserr = true;
    }
  } else
#endif
  {
    if (gt_firstcodes_sortremaining(srswtab[0],
                                    encseq,
                                    readmode,
                                    fci->spmsuftab,
                                    fci->buf.snrp,
                                    &fci->tab,
                                    fci->currentminindex,
                                    fci->currentmaxindex,
                                    gt_suftabparts_sumofwidth(part,suftabparts),
                                    spaceforbucketprocessing,
                                    (unsigned long) kmersize,
                                    itvprocess,
                                    itvprocess_end,
                                    itvprocessdatatab == NULL
                                      ? NULL
                                      : ((void **) itvprocessdatatab)[0],
                                    withsuftabcheck,
                                    err) != 0)
    {
      haserr = true;
    }
  }
  if (fci->mappedleftborder != NULL)
  {
    gt_Sfxmappedrange_unmap(fci->mappedleftborder);
    GT_FCI_SUBTRACTSPLITSPACE(fci->fcsl,"leftborder");
  }
  return haserr ? -1 : 0;
}

int storefirstcodes_getencseqkmers_twobitencoding(const GtEncseq *encseq,
                                                  unsigned int kmersize,
                                                  unsigned int numofparts,
                                                  unsigned long maximumspace,
                                                  unsigned int minmatchlength,
                                                  bool withsuftabcheck,
                                                  bool onlyaccumulation,
                                                  bool onlyallfirstcodes,
                                                  GT_UNUSED
                                                  unsigned int addbscache_depth,
                                                  unsigned long phase2extra,
                    GT_UNUSED bool radixsmall,      /* set to true */
                    GT_UNUSED unsigned int radixparts, /* set to 2U */
                                                  GtFirstcodesintervalprocess
                                                    itvprocess,
                                                 GtFirstcodesintervalprocess_end
                                                     itvprocess_end,
                                                  void *itvprocessdatatab,
                                                  GtLogger *logger,
                                                  GtError *err)
{
  GtTimer *timer = NULL;
  GtFirstcodesinfo fci;
  size_t suftab_size = 0;
  unsigned int part, threadcount;
  unsigned long maxbucketsize, suftabentries = 0, largest_width,
                totallength = gt_encseq_total_length(encseq),
                maxseqlength = gt_encseq_max_seq_length(encseq);
  GtSfxmappedrangelist *sfxmrlist = NULL;
  GtSuftabparts *suftabparts = NULL;
  GtShortreadsortworkinfo **srswtab = NULL;
  const GtReadmode readmode = GT_READMODE_FORWARD;
  bool haserr = false;
#ifdef GT_THREADS_ENABLED
  const unsigned int threads = gt_jobs;
#else
  const unsigned int threads = 1U;
#endif

  if (maxseqlength < (unsigned long) minmatchlength)
  {
    return 0;
  }
  if (gt_firstcodes_init(&fci,
                         encseq,
                         kmersize,
                         withsuftabcheck,
                         minmatchlength,
                         err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    sfxmrlist = gt_Sfxmappedrangelist_new();
    if (gt_showtime_enabled())
    {
      timer = gt_timer_new_with_progress_description("to collect initial "
                                                     "prefixes");
      gt_timer_start(timer);
    }
    gt_firstcodes_collectcodes(&fci,
                               encseq,
                               readmode,
                               kmersize,
                               minmatchlength,
                               addbscache_depth,
                               onlyallfirstcodes,
                               logger,
                               timer);
    if (fci.differentcodes > 0 && onlyallfirstcodes)
    {
      gt_free(fci.allfirstcodes);
      fci.allfirstcodes = NULL;
      gt_marksubstring_delete(fci.buf.markprefix,true);
      gt_marksubstring_delete(fci.buf.marksuffix,true);
      gt_firstcodes_countocc_delete(fci.fcsl,&fci.tab);
      gt_firstcodes_binsearchcache_delete(fci.binsearchcache,fci.fcsl);
      gt_firstcodes_spacelog_delete(fci.fcsl);
      gt_seqnumrelpos_delete(fci.buf.snrp);
      gt_Sfxmappedrangelist_delete(sfxmrlist);
      fci.binsearchcache = NULL;
      if (timer != NULL)
      {
        gt_timer_delete(timer);
      }
      return 0;
    }
    fci.flushcount = 0;
    fci.codebuffer_total = 0;
    if (gt_firstcodes_allocspace(&fci,
                                 numofparts,
                                 maximumspace,
                                 phase2extra,
                                 err) != 0)
    {
      haserr = true;
    }
  }
  fci.buf.nextfree = 0;
  if (!haserr)
  {
    gt_firstcodes_accumulatecounts_run(&fci,
                                       encseq,
                                       kmersize,
                                       minmatchlength,
                                       logger,
                                       timer);
    suftabentries = fci.firstcodehits + fci.numofsequences;
    if (timer != NULL)
    {
      gt_timer_show_progress(timer,"to compute partial sums",stdout);
    }
    maxbucketsize = gt_firstcodes_partialsums(fci.fcsl,&fci.tab,
                                              fci.allfirstcodes,suftabentries);
    gt_firstcodes_restore_from_differences(&fci);
    gt_logger_log(logger,"maximum space after computing partial sums: %.2f MB",
                  GT_MEGABYTES(gt_firstcodes_spacelog_total(fci.fcsl)));
    gt_logger_log(logger,"maxbucketsize=%lu",maxbucketsize);
    gt_firstcodes_map_sections(&fci,sfxmrlist);
    if (numofparts == 0 || maximumspace > 0)
    {
      int retval = gt_firstcodes_auto_parts(&fci,
                                            sfxmrlist,
                                            numofparts,
                                            &maximumspace,
                                            maxbucketsize,
                                            kmersize,
                                            totallength,
                                            maxseqlength,
                                            suftabentries,
                                            phase2extra,
                                            err);
      if (retval < 0)
      {
        haserr = true;
      } else
      {
        numofparts = (unsigned int) retval;
      }
    }
  }
  if (!haserr)
  {
    gt_assert(numofparts > 0);
    suftabparts = gt_suftabparts_new(numofparts,
                                     NULL,
                                     &fci.tab,
                                     sfxmrlist,
                                     suftabentries,
                                     0,
                                     logger);
    gt_assert(suftabparts != NULL);
    gt_suftabparts_showallrecords(suftabparts,true);
    gt_assert(fci.allfirstcodes[fci.differentcodes - 1] ==
              gt_firstcodes_idx2code(&fci,
                                     gt_suftabparts_maxindex_last(suftabparts))
             );
    gt_Sfxmappedrangelist_delete(sfxmrlist);
    sfxmrlist = NULL;
    gt_firstcodes_samples_delete(fci.fcsl,&fci.tab);
    gt_assert(fci.buf.nextfree == 0);
    gt_firstcodes_handle_tmp(&fci,suftabparts);
    largest_width = gt_suftabparts_largest_width(suftabparts);
    fci.spmsuftab = gt_spmsuftab_new(largest_width,
                                     totallength,
                                     fci.bitsforposref,
                                     logger);
    suftab_size = gt_spmsuftab_requiredspace(largest_width,totallength,
                                             fci.bitsforposref);
    GT_FCI_ADDWORKSPACE(fci.fcsl,"suftab",suftab_size);
    fci.buf.flush_function = gt_firstcodes_insertsuffixes_flush;
    srswtab = gt_malloc(sizeof (*srswtab) * threads);
    for (threadcount = 0; threadcount < threads; threadcount++)
    {
      srswtab[threadcount]
        = gt_shortreadsort_new(maxbucketsize,maxseqlength - kmersize,
                               readmode,true,false);
    }
    GT_FCI_ADDWORKSPACE(fci.fcsl,"shortreadsort",
                        threads * gt_shortreadsort_size(true,maxbucketsize,
                                                        maxseqlength-kmersize));
    gt_firstcodes_allocsize_for_insertion(&fci,
                                          maximumspace,
                                          suftabparts,
                                          phase2extra);
    if (!onlyaccumulation)
    {
      fci.radixsort_codepos = gt_radixsort_new_ulongpair(fci.buf.allocated);
      GT_FCI_ADDWORKSPACE(fci.fcsl,"radixsort_codepos",
                          gt_radixsort_size(fci.radixsort_codepos));
      fci.buf.spaceGtUlongPair
        = gt_radixsort_space_ulongpair(fci.radixsort_codepos);
    }
    fci.codebuffer_total = 0;
    fci.flushcount = 0;
    for (part = 0; !haserr && !onlyaccumulation &&
                   part < gt_suftabparts_numofparts(suftabparts); part++)
    {
      if (gt_firstcodes_process_part(&fci,
                                     encseq,
                                     readmode,
                                     kmersize,
                                     minmatchlength,
                                     suftabparts,
                                     part,
                                     maximumspace,
                                     threads,
                                     suftabentries,
                                     withsuftabcheck,
                                     srswtab,
                                     itvprocess,
                                     itvprocess_end,
                                     itvprocessdatatab,
                                     logger,
                                     timer,
                                     err) != 0)
      {
        haserr = true;
      }
    }
  }
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "cleaning up",stdout);
  }
  if (!haserr)
  {
    GT_FCI_SUBTRACTWORKSPACE(fci.fcsl,"shortreadsort");
  }
  if (!haserr && !onlyaccumulation && srswtab != NULL)
  {
    unsigned long sumofstoredvalues = 0;

    for (threadcount=0; threadcount
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FIRSTCODES_H
#define FIRSTCODES_H

#include 
#include "core/log_api.h"
#include "core/error_api.h"
#include "core/encseq_api.h"
#include "seqnumrelpos.h"

typedef int (*GtFirstcodesintervalprocess)(void *,
                                           const unsigned long *,
                                           const GtSeqnumrelpos *,
                                           const uint16_t *,
                                           unsigned long,
                                           unsigned long,
                                           GtError *);

typedef void (*GtFirstcodesintervalprocess_end)(void *);

void gt_rungetencseqkmers(const GtEncseq *encseq,unsigned int kmersize);

int storefirstcodes_getencseqkmers_twobitencoding(
                    const GtEncseq *encseq,
                    unsigned int kmersize,
                    unsigned int numofparts,
                    unsigned long maximumspace,
                    unsigned int minmatchlength,
                    bool withsuftabcheck, /* set to false, only for tests */
                    bool onlyaccumulation, /* set to false, only for tests */
                    bool onlyallfirstcodes, /* set to false, only for tests */
                    GT_UNUSED unsigned int addbscache_depth, /* set to 5U */
                    unsigned long phase2extra, /* extra space needed in proc.
                                                  intervals */
                    bool radixsmall,      /* set to true */
                    unsigned int radixparts, /* set to 2U */
                    GtFirstcodesintervalprocess itvprocess,
                    GtFirstcodesintervalprocess_end itvprocess_end,
                    void *itvprocessdatatab,
                    GtLogger *logger,
                    GtError *err);

#endif
genometools-1.5.1/src/match/fmi-fwduni.c000066400000000000000000000074001211610345200201410ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/unused_api.h"
#include "fmindex.h"

#include "fmi-occ.gen"
#include "fmi-locate.pr"

unsigned long gt_skfmuniqueforward (const void *genericindex,
                                 GT_UNUSED unsigned long offset,
                                 GT_UNUSED unsigned long left,
                                 GT_UNUSED unsigned long right,
                                 GT_UNUSED unsigned long *witnessposition,
                                 const GtUchar *qstart,
                                 const GtUchar *qend)
{
  GtUchar cc;
  const GtUchar *qptr;
  GtUlongBound bwtbound;
  const Fmindex *fmindex = (Fmindex *) genericindex;

  gt_assert(qstart < qend);
  qptr = qstart;
  cc = *qptr++;
  if (ISSPECIAL(cc))
  {
    return 0;
  }
  bwtbound.lbound = fmindex->tfreq[cc];
  bwtbound.ubound = fmindex->tfreq[cc+1];
  while (qptr < qend && bwtbound.lbound + 1 < bwtbound.ubound)
  {
    cc = *qptr;
    if (ISSPECIAL (cc))
    {
      return 0;
    }
    bwtbound.lbound = fmindex->tfreq[cc] +
                      fmoccurrence (fmindex, cc, bwtbound.lbound);
    bwtbound.ubound = fmindex->tfreq[cc] +
                      fmoccurrence (fmindex, cc, bwtbound.ubound);
    qptr++;
  }
  if (bwtbound.lbound + 1 == bwtbound.ubound)
  {
    return (unsigned long) (qptr - qstart);
  }
  return 0;
}

unsigned long gt_skfmmstats (const void *genericindex,
                          GT_UNUSED unsigned long offset,
                          GT_UNUSED unsigned long left,
                          GT_UNUSED unsigned long right,
                          unsigned long *witnessposition,
                          const GtUchar *qstart,
                          const GtUchar *qend)
{
  GtUchar cc;
  const GtUchar *qptr;
  unsigned long prevlbound;
  unsigned long matchlength;
  GtUlongBound bwtbound;
  const Fmindex *fmindex = (Fmindex *) genericindex;

  gt_assert(qstart < qend);
  qptr = qstart;
  cc = *qptr;
  if (ISSPECIAL(cc))
  {
    return 0;
  }
  bwtbound.lbound = fmindex->tfreq[cc];
  bwtbound.ubound = fmindex->tfreq[cc+1];
  if (bwtbound.lbound >= bwtbound.ubound)
  {
    return 0;
  }
  prevlbound = bwtbound.lbound;
  for (qptr++; qptr < qend; qptr++)
  {
    cc = *qptr;
    if (ISSPECIAL (cc))
    {
      break;
    }
    bwtbound.lbound = fmindex->tfreq[cc] +
                      fmoccurrence (fmindex, cc, bwtbound.lbound);
    bwtbound.ubound = fmindex->tfreq[cc] +
                      fmoccurrence (fmindex, cc, bwtbound.ubound);
    if (bwtbound.lbound >= bwtbound.ubound)
    {
      break;
    }
    prevlbound = bwtbound.lbound;
  }
  matchlength = (unsigned long) (qptr - qstart);
  if (witnessposition != NULL)
  {
    unsigned long startpos = gt_fmfindtextpos (fmindex,prevlbound);
    gt_assert((fmindex->bwtlength-1) >= (startpos + matchlength));
    *witnessposition = (fmindex->bwtlength-1) - (startpos + matchlength);
  }
  return matchlength;
}
genometools-1.5.1/src/match/fmi-fwduni.pr000066400000000000000000000015721211610345200203440ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
unsigned long gt_skfmuniqueforward (const void *genericindex,
                                 GT_UNUSED unsigned long offset,
                                 GT_UNUSED unsigned long left,
                                 GT_UNUSED unsigned long right,
                                 GT_UNUSED unsigned long *witnessposition,
                                 const GtUchar *qstart,
                                 const GtUchar *qend);

unsigned long gt_skfmmstats (const void *genericindex,
                          GT_UNUSED unsigned long offset,
                          GT_UNUSED unsigned long left,
                          GT_UNUSED unsigned long right,
                          unsigned long *witnessposition,
                          const GtUchar *qstart,
                          const GtUchar *qend);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/fmi-keyval.c000066400000000000000000000102511211610345200201360ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/divmodmul.h"
#include "core/mathsupport.h"
#include "core/safecast-gen.h"
#include "fmindex.h"

unsigned long gt_determinenumberofspecialstostore(const GtSpecialcharinfo
                                                        *specialcharinfo)
{
  unsigned long addprefixsuffix = 0;

  if (specialcharinfo->lengthofspecialprefix > 0)
  {
    addprefixsuffix++;
  }
  if (specialcharinfo->lengthofspecialsuffix > 0)
  {
    addprefixsuffix++;
  }
  return specialcharinfo->realspecialranges + 1 - addprefixsuffix;
}

static unsigned long determinefmindexsize (const Fmindex *fm,
                                           const GtSpecialcharinfo
                                              *specialcharinfo,
                                           unsigned int suffixlength,
                                           bool storeindexpos)
{
  uint64_t sumsize = 0;

  sumsize +=
          (uint64_t) sizeof (unsigned long) * (uint64_t) TFREQSIZE(fm->mapsize);
  sumsize += (uint64_t) sizeof (unsigned long) *
             (uint64_t) SUPERBFREQSIZE(fm->mapsize,fm->nofsuperblocks);
  if (storeindexpos)
  {
    sumsize += (uint64_t) sizeof (unsigned long) *
               (uint64_t) MARKPOSTABLELENGTH(fm->bwtlength,fm->markdist);
  }
  if (suffixlength > 0)
  {
    sumsize += (uint64_t) sizeof (GtUlongBound) * (uint64_t) fm->numofcodes;
  }
  if (storeindexpos)
  {
    sumsize += (uint64_t) sizeof (GtPairBwtidx) *
               (uint64_t) gt_determinenumberofspecialstostore(specialcharinfo);
  }
  sumsize += (uint64_t) sizeof (GtUchar) *
             (uint64_t) BFREQSIZE(fm->mapsize,fm->nofblocks);
  return CALLCASTFUNC(uint64_t,unsigned_long,sumsize);
}

void gt_computefmkeyvalues (Fmindex *fm,
                            const GtSpecialcharinfo *specialcharinfo,
                            unsigned long bwtlength,
                            unsigned int log2bsize,
                            unsigned int log2markdist,
                            unsigned int numofchars,
                            unsigned int suffixlength,
                            bool storeindexpos)
{
  fm->mappedptr = NULL;
  fm->log2bsize = log2bsize;
  fm->log2markdist = log2markdist;
  fm->bwtlength = bwtlength;
  fm->log2superbsize = GT_MULT2 (fm->log2bsize);
  fm->bsize = (unsigned int) GT_POW2 (fm->log2bsize);
  fm->bsizehalve = GT_DIV2(fm->bsize);
  fm->superbsize = (unsigned int) GT_POW2 (fm->log2superbsize);
  fm->nofblocks = (unsigned long) (fm->bwtlength / fm->bsize) + 1;
  fm->nofsuperblocks = (unsigned long) (fm->bwtlength / fm->superbsize) + 2;
  fm->markdist = (unsigned long) GT_POW2 (fm->log2markdist);
  fm->markdistminus1 = (unsigned long) (fm->markdist - 1);
  fm->negatebsizeones = ~ (unsigned long) (fm->bsize - 1);
  fm->negatesuperbsizeones = ~ (unsigned long) (fm->superbsize - 1);
  fm->log2superbsizeminuslog2bsize = fm->log2superbsize - fm->log2bsize;
  fm->mapsize = numofchars+1;
  fm->suffixlength = suffixlength;
  if (fm->suffixlength > 0)
  {
    fm->numofcodes = gt_power_for_small_exponents(fm->mapsize-1,
                                                  fm->suffixlength);
  } else
  {
    fm->numofcodes = 0;
  }
  fm->sizeofindex = determinefmindexsize (fm,
                                          specialcharinfo,
                                          suffixlength,
                                          storeindexpos);
}
genometools-1.5.1/src/match/fmi-keyval.pr000066400000000000000000000012061211610345200203350ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
unsigned long gt_determinenumberofspecialstostore(const GtSpecialcharinfo
                                                        *specialcharinfo);

void gt_computefmkeyvalues (Fmindex *fm,
                            const GtSpecialcharinfo *specialcharinfo,
                            unsigned long bwtlength,
                            unsigned int log2bsize,
                            unsigned int log2markdist,
                            unsigned int numofchars,
                            unsigned int suffixlength,
                            bool storeindexpos);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/fmi-locate.c000066400000000000000000000046041211610345200201170ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/divmodmul.h"

#include "fmindex.h"
#include "fmi-occ.gen"

static unsigned long searchsmallestgeq(const GtPairBwtidx *left,
                                const GtPairBwtidx *right,
                                unsigned long key)
{
  const GtPairBwtidx *leftptr, *midptr, *rightptr, *found = NULL;
  unsigned long len;

  gt_assert(left != NULL);
  gt_assert(right != NULL);
  leftptr = left;
  rightptr = right;
  while (leftptr<=rightptr)
  {
    len = (unsigned long) (rightptr-leftptr);
    midptr = leftptr + GT_DIV2(len);
    if (key < midptr->bwtpos)
    {
      found = midptr;
      rightptr = midptr - 1;
    } else
    {
      if (key > midptr->bwtpos)
      {
        leftptr = midptr + 1;
      } else
      {
        return midptr->suftabvalue;
      }
    }
  }
  gt_assert(found != NULL);
  return found->suftabvalue;
}

unsigned long gt_fmfindtextpos (const Fmindex *fm,unsigned long idx)
{
  unsigned long offset = 0;
  GtUchar cc;

  while ((idx & fm->markdistminus1) != 0)
  {
    if (idx == fm->longestsuffixpos || ISSPECIAL(cc = ACCESSBWTTEXT(idx)))
    {
      unsigned long smallestgeq
               = searchsmallestgeq(fm->specpos.spaceGtPairBwtidx,
                                   fm->specpos.spaceGtPairBwtidx +
                                   fm->specpos.nextfreeGtPairBwtidx - 1,
                                   idx);
      return (smallestgeq + offset) % fm->bwtlength;
    }
    idx = fm->tfreq[cc] + fmoccurrence (fm, cc, idx);
    offset++;
  }
  return (fm->markpostable[idx / fm->markdist] + offset) % fm->bwtlength;
}
genometools-1.5.1/src/match/fmi-locate.pr000066400000000000000000000002121211610345200203050ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
unsigned long gt_fmfindtextpos (const Fmindex *fm,unsigned long idx);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/fmi-map.c000066400000000000000000000171051211610345200174250ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include "core/error.h"
#include "core/fileutils.h"
#include "core/fa.h"
#include "core/array.h"
#include "core/str.h"
#include "core/alphabet.h"
#include "core/logger.h"
#include "esa-scanprj.h"
#include "fmindex.h"

#include "fmi-keyval.pr"
#include "fmi-mapspec.pr"

bool gt_fmindexexists(const char *indexname)
{
  if (!gt_file_exists_with_suffix(indexname,FMASCIIFILESUFFIX))
  {
    return false;
  }
  if (!gt_file_exists_with_suffix(indexname,FMDATAFILESUFFIX))
  {
    return false;
  }
  return true;
}

static int scanfmafileviafileptr(Fmindex *fmindex,
                                 GtSpecialcharinfo *specialcharinfo,
                                 bool *storeindexpos,
                                 const char *indexname,
                                 FILE *fpin,
                                 GtLogger *logger,
                                 GtError *err)
{
  bool haserr = false;
  GtScannedprjkeytable *scannedprjkeytable;
  unsigned int intstoreindexpos;

  gt_error_check(err);
  scannedprjkeytable = gt_scannedprjkeytable_new();
  GT_SCANNEDPRJKEY_ADD("bwtlength",&fmindex->bwtlength,NULL);
  GT_SCANNEDPRJKEY_ADD("longest",&fmindex->longestsuffixpos,NULL);
  GT_SCANNEDPRJKEY_ADD("storeindexpos",&intstoreindexpos,NULL);
  GT_SCANNEDPRJKEY_ADD("log2blocksize",&fmindex->log2bsize,NULL);
  GT_SCANNEDPRJKEY_ADD("log2markdist",&fmindex->log2markdist,NULL);
  GT_SCANNEDPRJKEY_ADD("specialcharacters",
                       &specialcharinfo->specialcharacters,NULL);
  GT_SCANNEDPRJKEY_ADD("specialranges",&specialcharinfo->specialranges,NULL);
  GT_SCANNEDPRJKEY_ADD("realspecialranges",&specialcharinfo->realspecialranges,
                       NULL);
  GT_SCANNEDPRJKEY_ADD("lengthofspecialprefix",
                       &specialcharinfo->lengthofspecialprefix,NULL);
  GT_SCANNEDPRJKEY_ADD("lengthofspecialsuffix",
                       &specialcharinfo->lengthofspecialsuffix,NULL);
  GT_SCANNEDPRJKEY_ADD("wildcards",&specialcharinfo->wildcards,NULL);
  GT_SCANNEDPRJKEY_ADD("wildcardranges",&specialcharinfo->wildcardranges,NULL);
  GT_SCANNEDPRJKEY_ADD("realwildcardranges",
                       &specialcharinfo->realwildcardranges,NULL);
  GT_SCANNEDPRJKEY_ADD("lengthofwildcardprefix",
                       &specialcharinfo->lengthofwildcardprefix,NULL);
  GT_SCANNEDPRJKEY_ADD("lengthofwildcardsuffix",
                       &specialcharinfo->lengthofwildcardsuffix,NULL);
  GT_SCANNEDPRJKEY_ADD("suffixlength",&fmindex->suffixlength,NULL);
  if (!haserr)
  {
    GtStr *currentline;
    unsigned int linenum;

    currentline = gt_str_new();
    for (linenum = 0; gt_str_read_next_line(currentline, fpin) != EOF;
         linenum++)
    {
      if (gt_scannedprjkey_analyze(indexname,
                                   FMASCIIFILESUFFIX,
                                   linenum,
                                   gt_str_get(currentline),
                                   gt_str_length(currentline),
                                   scannedprjkeytable,
                                   err) != 0)
      {
        haserr = true;
        break;
      }
      gt_str_reset(currentline);
    }
    gt_str_delete(currentline);
  }
  if (!haserr && gt_scannedprjkey_allkeysdefined(indexname,FMASCIIFILESUFFIX,
                                                 scannedprjkeytable,
                                                 logger,err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (intstoreindexpos == 1U)
    {
      *storeindexpos = true;
    } else
    {
      if (intstoreindexpos == 0)
      {
        *storeindexpos = false;
      } else
      {
        gt_error_set(err,"illegal value in line matching \"storeindexpos=\"");
        haserr = true;
      }
    }
  }
  gt_scannedprjkeytable_delete(scannedprjkeytable);
  return haserr ? -1 : 0;
}

void gt_freefmindex(Fmindex *fmindex)
{
  if (fmindex->mappedptr != NULL)
  {
    gt_fa_xmunmap(fmindex->mappedptr);
  }
  if (fmindex->bwtformatching != NULL)
  {
    gt_encseq_delete(fmindex->bwtformatching);
    fmindex->bwtformatching = NULL;
  }
  gt_alphabet_delete((GtAlphabet *) fmindex->alphabet);
}

static GtEncseq *mapbwtencoding(const char *indexname,
                                GtLogger *logger,
                                GtError *err)
{
  GtEncseqLoader *el;
  GtEncseq *ret;
  gt_error_check(err);

  el = gt_encseq_loader_new();
  gt_encseq_loader_do_not_require_des_tab(el);
  gt_encseq_loader_do_not_require_ssp_tab(el);
  gt_encseq_loader_do_not_require_sds_tab(el);
  gt_encseq_loader_set_logger(el, logger);
  ret = gt_encseq_loader_load(el, indexname, err);
  gt_encseq_loader_delete(el);
  return ret;
}

int gt_mapfmindex (Fmindex *fmindex,const char *indexname,
                GtLogger *logger,GtError *err)
{
  FILE *fpin = NULL;
  bool haserr = false, storeindexpos = true;
  GtSpecialcharinfo specialcharinfo;

  gt_error_check(err);
  fmindex->mappedptr = NULL;
  fmindex->bwtformatching = NULL;
  fmindex->alphabet = NULL;
  fpin = gt_fa_fopen_with_suffix(indexname,FMASCIIFILESUFFIX,"rb",err);
  if (fpin == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (scanfmafileviafileptr(fmindex,
                              &specialcharinfo,
                              &storeindexpos,
                              indexname,
                              fpin,
                              logger,
                              err) != 0)
    {
      haserr = true;
    }
  }
  gt_fa_xfclose(fpin);
  if (!haserr)
  {
    fmindex->bwtformatching = mapbwtencoding(indexname,logger,err);
    if (fmindex->bwtformatching == NULL)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    fmindex->specpos.nextfreeGtPairBwtidx
      = (unsigned long) gt_determinenumberofspecialstostore(&specialcharinfo);
    fmindex->specpos.spaceGtPairBwtidx = NULL;
    fmindex->specpos.allocatedGtPairBwtidx = 0;
    fmindex->alphabet = gt_alphabet_ref(
                                  gt_encseq_alphabet(fmindex->bwtformatching));
    if (fmindex->alphabet == NULL)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    GtStr *tmpfilename;

    gt_computefmkeyvalues (fmindex,
                           &specialcharinfo,
                           fmindex->bwtlength,
                           fmindex->log2bsize,
                           fmindex->log2markdist,
                           gt_alphabet_num_of_chars(fmindex->alphabet),
                           fmindex->suffixlength,
                           storeindexpos);
    tmpfilename = gt_str_new_cstr(indexname);
    gt_str_append_cstr(tmpfilename,FMDATAFILESUFFIX);
    if (gt_fillfmmapspecstartptr(fmindex,storeindexpos,tmpfilename,err) != 0)
    {
      haserr = true;
    }
    gt_str_delete(tmpfilename);
  }
  if (haserr)
  {
    gt_freefmindex(fmindex);
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/fmi-map.pr000066400000000000000000000004061211610345200176200ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
bool gt_fmindexexists(const char *indexname);

void gt_freefmindex(Fmindex *fmindex);

int gt_mapfmindex (Fmindex *fmindex,const char *indexname,
                GtLogger *logger,GtError *err);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/fmi-mapspec.c000066400000000000000000000064611211610345200203030ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "core/mapspec.h"
#include "fmindex.h"

static void assignfmmapspecification(GtMapspec *mapspec,
                                     void *data,
                                     GT_UNUSED bool writemode)
{
  Fmindexwithoptions *fmwithoptions = (Fmindexwithoptions *) data;
  Fmindex *fmindex;

  fmindex = fmwithoptions->fmptr;
  gt_mapspec_add_ulong(mapspec, fmindex->tfreq,
                       (unsigned long) TFREQSIZE(fmindex->mapsize));
  gt_mapspec_add_ulong(mapspec, fmindex->superbfreq,
                       (unsigned long) SUPERBFREQSIZE(fmindex->mapsize,
                                                      fmindex->nofsuperblocks));
  gt_mapspec_add_ulong(mapspec, fmindex->markpostable,
                       fmwithoptions->storeindexpos
                       ? (unsigned long) MARKPOSTABLELENGTH(fmindex->bwtlength,
                                                            fmindex->markdist)
                       : 0);
  gt_mapspec_add_ulongbound(mapspec, fmindex->boundarray,
                            (unsigned long) fmindex->numofcodes);
  gt_mapspec_add_pairbwtindex(mapspec, fmindex->specpos.spaceGtPairBwtidx,
                              fmwithoptions->storeindexpos
                              ? fmindex->specpos.nextfreeGtPairBwtidx
                              : 0);
  gt_mapspec_add_uchar(mapspec, fmindex->bfreq,
                (unsigned long) BFREQSIZE(fmindex->mapsize,fmindex->nofblocks));
}

int gt_flushfmindex2file(FILE *fp,
                         Fmindex *fmindex,
                         bool storeindexpos,
                         GtError *err)
{
  Fmindexwithoptions fmwithoptions;

  gt_error_check(err);
  fmwithoptions.fmptr = fmindex;
  fmwithoptions.storeindexpos = storeindexpos;
  return gt_mapspec_write(assignfmmapspecification,fp,
                          (void *) &fmwithoptions,fmindex->sizeofindex,err);
}

int gt_fillfmmapspecstartptr(Fmindex *fmindex,
                             bool storeindexpos,
                             const GtStr *tmpfilename,
                             GtError *err)
{
  Fmindexwithoptions fmwithoptions;

  gt_error_check(err);
  fmwithoptions.fmptr = fmindex;
  fmwithoptions.storeindexpos = storeindexpos;
  return gt_mapspec_read(assignfmmapspecification,
                         (void *) &fmwithoptions,
                         tmpfilename,
                         fmindex->sizeofindex,
                         &fmindex->mappedptr,
                         err);
}
genometools-1.5.1/src/match/fmi-mapspec.pr000066400000000000000000000006531211610345200204770ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
int gt_flushfmindex2file(FILE *fp,
                         Fmindex *fmindex,
                         bool storeindexpos,
                         GtError *err);

int gt_fillfmmapspecstartptr(Fmindex *fmindex,
                             bool storeindexpos,
                             const GtStr *tmpfilename,
                             GtError *err);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/fmi-mkindex.c000066400000000000000000000167161211610345200203160ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/basename_api.h"
#include "core/divmodmul.h"
#include "core/option_api.h"
#include "core/versionfunc.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "fmindex.h"
#include "fmi-save.pr"
#include "fmi-keyval.pr"
#include "fmi-sufbwtstream.pr"

typedef struct
{
  bool noindexpos;
  GtStrArray *indexnametab;
  GtStr *leveldesc,
      *outfmindex;
} Mkfmcallinfo;

typedef struct
{
  const char *name;
  unsigned int log2bsize,
               log2markdist;
} Indexleveldesc;

static Indexleveldesc indexlevel[] =
{
  {"tiny",  7U, 6U},
  {"small", 7U, 4U},
  {"medium",5U, 3U},
  {"big",   4U, 2U}
};

static GtOPrval parsemkfmindex(Mkfmcallinfo *mkfmcallinfo,
                               int argc,
                               const char **argv,
                               GtError *err)
{
  GtOptionParser *op;
  GtOption *option, *optionfmout;
  GtOPrval oprval;
  int parsed_args;

  gt_error_check(err);
  mkfmcallinfo->indexnametab = gt_str_array_new();
  mkfmcallinfo->outfmindex = gt_str_new();
  mkfmcallinfo->leveldesc = gt_str_new();
  op = gt_option_parser_new("[option ...] -ii indexfile [...]",
                         "Compute FM-index.");
  gt_option_parser_set_mail_address(op, "");
  optionfmout = gt_option_new_string("fmout",
                             "specify name of FM-index to be generated\n"
                             "(mandatory if more than one input index "
                             "is specified)",
                             mkfmcallinfo->outfmindex, NULL);
  gt_option_parser_add_option(op, optionfmout);

  option = gt_option_new_filename_array("ii", "specify indices to be used",
                                        mkfmcallinfo->indexnametab);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("size",
                             "specify size (tiny, small, medium, big)",
                             mkfmcallinfo->leveldesc, "medium");
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("noindexpos",
                           "store no index positions (hence the positions of\n"
                           "matches in the index cannot be retrieved)",
                           &mkfmcallinfo->noindexpos,false);
  gt_option_parser_add_option(op, option);

  oprval = gt_option_parser_parse(op, &parsed_args, argc, argv, gt_versionfunc,
                                  err);
  if (oprval == GT_OPTION_PARSER_OK)
  {
    if (!gt_option_is_set(optionfmout))
    {
      if (gt_str_array_size(mkfmcallinfo->indexnametab) > 1UL)
      {
        gt_error_set(err,"if more than one index is given, then "
                          "option -fmout is mandatory");
        oprval = GT_OPTION_PARSER_ERROR;
      } else
      {
        char *basenameptr;

        basenameptr = gt_basename(gt_str_array_get(mkfmcallinfo->indexnametab,
                                  0));
        gt_str_set(mkfmcallinfo->outfmindex,basenameptr);
        gt_free(basenameptr);
      }
    }
  }
  gt_option_parser_delete(op);
  if (oprval == GT_OPTION_PARSER_OK && parsed_args != argc)
  {
    gt_error_set(err,"superfluous program parameters");
    oprval = GT_OPTION_PARSER_ERROR;
  }
  return oprval;
}

static void freemkfmcallinfo(Mkfmcallinfo *mkfmcallinfo)
{
  gt_str_array_delete(mkfmcallinfo->indexnametab);
  gt_str_delete(mkfmcallinfo->outfmindex);
  gt_str_delete(mkfmcallinfo->leveldesc);
}

static int levedescl2levelnum(const char *name,
                              unsigned int *log2bsize,
                              unsigned int *log2markdist)
{
  size_t i;

  gt_assert(name != NULL);
  for (i=0; ispecpos, GtPairBwtidx);
  gt_free (fm->bfreq);
  gt_free (fm->superbfreq);
  gt_free (fm->tfreq);
  gt_free (fm->markpostable);
  if (fm->suffixlength > 0)
  {
    gt_free(fm->boundarray);
  }
}

static int mkfmindexoptions(Mkfmcallinfo *mkfmcallinfo,
                            int argc,const char **argv,GtError *err)
{
  GtOPrval rval;
  int retval = 0;

  gt_error_check(err);
  rval = parsemkfmindex(mkfmcallinfo,argc,argv,err);
  if (rval == GT_OPTION_PARSER_ERROR)
  {
    retval = -1;
  } else
  {
    if (rval == GT_OPTION_PARSER_REQUESTS_EXIT)
    {
      retval = 2;
    }
  }
  return retval;
}

static int runmkfmindex(Mkfmcallinfo *mkfmcallinfo,GtLogger *logger,
                        GtError *err)
{
  Fmindex fm;
  unsigned int log2bsize,
               log2markdist;
  bool haserr = false;
  GtSpecialcharinfo specialcharinfo;

  gt_error_check(err);
  GT_INITARRAY(&fm.specpos, GtPairBwtidx);
  fm.bfreq = NULL;
  fm.superbfreq = NULL;
  fm.tfreq = NULL;
  fm.markpostable = NULL;
  fm.boundarray = NULL;
  fm.suffixlength = 0;

  if (levedescl2levelnum(gt_str_get(mkfmcallinfo->leveldesc),
                        &log2bsize,
                        &log2markdist) != 0)
  {
    gt_error_set(err,"undefined level \"%s\"",
                      gt_str_get(mkfmcallinfo->leveldesc));
    haserr = true;
  }
  if (!haserr && gt_sufbwt2fmindex(&fm,
                                   &specialcharinfo,
                                   log2bsize,
                                   log2markdist,
                                   gt_str_get(mkfmcallinfo->outfmindex),
                                   mkfmcallinfo->indexnametab,
                                   mkfmcallinfo->noindexpos ? false : true,
                                   logger,
                                   err) != 0)
  {
    haserr = true;
  }
  if (!haserr && gt_saveFmindex(gt_str_get(mkfmcallinfo->outfmindex),
                                &fm,
                                &specialcharinfo,
                                mkfmcallinfo->noindexpos ? false : true,
                                err) < 0)
  {
    haserr = true;
  }
  freeconstructedfmindex(&fm);
  return haserr ? -1 : 0;
}

int gt_parseargsandcallmkfmindex(int argc,const char **argv,GtError *err)
{
  Mkfmcallinfo mkfmcallinfo;
  int retval;
  bool haserr = false;

  retval = mkfmindexoptions(&mkfmcallinfo,argc,argv,err);
  if (retval == 0)
  {
    GtLogger *logger = gt_logger_new(false, GT_LOGGER_DEFLT_PREFIX, stdout);
    if (runmkfmindex(&mkfmcallinfo,logger,err) < 0)
    {
      haserr = true;
    }
    gt_logger_delete(logger);
    logger = NULL;
  } else
  {
    if (retval < 0)
    {
      haserr = true;
    }
  }
  freemkfmcallinfo(&mkfmcallinfo);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/fmi-mkindex.pr000066400000000000000000000002171211610345200205020ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
int gt_parseargsandcallmkfmindex(int argc,const char **argv,GtError *err);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/fmi-occ.gen000066400000000000000000000135541211610345200177470ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FMI_OCC_GEN
#define FMI_OCC_GEN

#define ACCESSBWTTEXT(POS)\
        gt_encseq_get_encoded_char(fm->bwtformatching,POS,\
                                          GT_READMODE_FORWARD)

static unsigned long fmoccurrence (const Fmindex *fm,GtUchar cc,
                                   unsigned long pos)
{
  unsigned long bwtidx,
         bwtlastidx,
         numofocc,
         idx,
         maxbfreqidx,
         ctimesnumofblocks = (unsigned long) (cc * fm->nofblocks),
         ctimesnumofsuperblocks = (unsigned long) (cc * fm->nofsuperblocks),
         posshiftbsizepow = pos >> (unsigned long) fm->log2bsize,
         posshiftsuperbsizepow = pos >> (unsigned long) fm->log2superbsize;

#ifdef SKDEBUG
  printf("bwtlength=%u,",(unsigned int) fm->bwtlength);
  printf("longestpos=%u,",(unsigned int) fm->longestsuffixpos);
  printf("bsize=%u,",(unsigned int) fm->bsize);
  printf("pos=%u,cc=%u\n",pos,cc);
#endif
  if ((pos <= fm->longestsuffixpos &&
       fm->longestsuffixpos - pos < (unsigned long) fm->bsize) ||
      (pos >  fm->longestsuffixpos &&
       pos - fm->longestsuffixpos < (unsigned long) fm->bsize))
  {                                    /* dollar in block */
    maxbfreqidx = ctimesnumofblocks + posshiftbsizepow;
    numofocc = fm->superbfreq[ctimesnumofsuperblocks + posshiftsuperbsizepow];
#ifdef SKDEBUG
    printf("case 0: numofocc = %u\n",numofocc);
#endif
    for (idx = ctimesnumofblocks +
               ((pos & fm->negatesuperbsizeones) >> fm->log2bsize);
         idx < maxbfreqidx; idx++)
    {
      numofocc += fm->bfreq[idx];
#ifdef SKDEBUG
      printf("case 1: numofocc = %u\n",numofocc);
#endif
    }
    for (bwtidx = (pos & fm->negatebsizeones); bwtidx < pos; bwtidx++)
    {
#ifdef SKDEBUG
      printf("access(%u)=%u,cc=%u\n",bwtidx,ACCESSBWTTEXT(bwtidx),cc);
#endif
      if (bwtidx != fm->longestsuffixpos && ACCESSBWTTEXT(bwtidx) == cc)
      {
        numofocc++;
#ifdef SKDEBUG
        printf("case 2: numofocc = %u\n",numofocc);
#endif
      }
    }
#ifdef SKDEBUG
    printf("(0) return %u\n",numofocc);
#endif
    return numofocc;
  }
  if ((pos & (fm->superbsize >> 1)) &&       /* first halve of superbuckets */
      fm->bwtlength - pos > (unsigned long) fm->superbsize)
  {
    maxbfreqidx = ctimesnumofblocks +
                  ((posshiftsuperbsizepow + 1) <<
                   fm->log2superbsizeminuslog2bsize);
    numofocc = fm->superbfreq[ctimesnumofsuperblocks +
                              posshiftsuperbsizepow + 1];
#ifdef SKDEBUG
    printf("case 3: numofocc %u\n",numofocc);
#endif
    for (idx = ctimesnumofblocks + posshiftbsizepow; idx < maxbfreqidx; idx++)
    {
      numofocc -= fm->bfreq[idx];
#ifdef SKDEBUG
      printf("case 4: numofocc %u\n",numofocc);
#endif
    }
    if (pos & fm->bsizehalve)            /* second halve of bucket */
    {
      numofocc += fm->bfreq[ctimesnumofblocks + posshiftbsizepow];
#ifdef SKDEBUG
      printf("case 5: numofocc %u\n",numofocc);
#endif
      bwtlastidx = (posshiftbsizepow + 1) << (unsigned long) fm->log2bsize;
      for (bwtidx = pos; bwtidx < bwtlastidx; bwtidx++)
      {
        if (ACCESSBWTTEXT(bwtidx) == cc)
        {
          numofocc--;
#ifdef SKDEBUG
          printf("case 6: numofocc = %u\n",numofocc);
#endif
        }
      }
    } else                               /* first halve of bucket */
    {
      for (bwtidx = (pos & fm->negatebsizeones); bwtidx < pos; bwtidx++)
      {
        if (ACCESSBWTTEXT(bwtidx) == cc)
        {
          numofocc++;
#ifdef SKDEBUG
          printf("case 7: numofocc = %u\n",numofocc);
#endif
        }
      }
    }
  } else                                 /* second halve of superbucket */
  {
    maxbfreqidx = ctimesnumofblocks + posshiftbsizepow;
    numofocc = fm->superbfreq[ctimesnumofsuperblocks + posshiftsuperbsizepow];
#ifdef SKDEBUG
    printf("case 8: numofocc = %u\n",numofocc);
#endif
    for (idx = ctimesnumofblocks +
               ((pos & fm->negatesuperbsizeones) >> fm->log2bsize);
         idx < maxbfreqidx; idx++)
    {
      numofocc += fm->bfreq[idx];
#ifdef SKDEBUG
      printf("case 9: numofocc = %u\n",numofocc);
#endif
    }
    if ((pos & fm->bsizehalve)           /* second halve of bucket */
        && (fm->bwtlength - pos > (unsigned long) fm->bsize))
    {
      numofocc += fm->bfreq[ctimesnumofblocks + posshiftbsizepow];
#ifdef SKDEBUG
      printf("case 10: numofocc = %u\n",numofocc);
#endif
      bwtlastidx = (pos & fm->negatebsizeones) + fm->bsize;
      for (bwtidx = pos; bwtidx < bwtlastidx; bwtidx++)
      {
        if (ACCESSBWTTEXT(bwtidx) == cc)
        {
          numofocc--;
#ifdef SKDEBUG
          printf("case 11: numofocc = %u\n",numofocc);
#endif
        }
      }
    } else                               /* first halve of bucket */
    {
      for (bwtidx = (pos & fm->negatebsizeones); bwtidx < pos; bwtidx++)
      {
        if (ACCESSBWTTEXT(bwtidx) == cc)
        {
          numofocc++;
#ifdef SKDEBUG
          printf("case 12: numofocc = %u\n",numofocc);
#endif
        }
      }
    }
  }
#ifdef SKDEBUG
  printf("(1) return %u\n",numofocc);
#endif
  return numofocc;
}

#endif
genometools-1.5.1/src/match/fmi-save.c000066400000000000000000000065741211610345200176160ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/fa.h"
#include "fmindex.h"

#include "fmi-mapspec.pr"

static int writefmascii(const char *indexname,
                        const Fmindex *fm,
                        const GtSpecialcharinfo *specialcharinfo,
                        bool storeindexpos,
                        GtError *err)
{
  FILE *fmafp;

  gt_error_check(err);
  fmafp = gt_fa_fopen_with_suffix(indexname,FMASCIIFILESUFFIX,"wb",err);
  if (fmafp == NULL)
  {
    return -1;
  }
  fprintf (fmafp, "bwtlength=%lu\n",
           fm->bwtlength);
  fprintf (fmafp, "longest=%lu\n",
                   fm->longestsuffixpos);
  fprintf (fmafp, "storeindexpos=%d\n", storeindexpos ? 1 : 0);
  fprintf (fmafp, "log2blocksize=%u\n", fm->log2bsize);
  fprintf (fmafp, "log2markdist=%u\n", fm->log2markdist);
  fprintf (fmafp, "specialcharacters=%lu\n",specialcharinfo->specialcharacters);
  fprintf (fmafp, "specialranges=%lu\n",specialcharinfo->specialranges);
  fprintf (fmafp, "realspecialranges=%lu\n",specialcharinfo->realspecialranges);
  fprintf (fmafp, "lengthofspecialprefix=%lu\n",
           specialcharinfo->lengthofspecialprefix);
  fprintf (fmafp, "lengthofspecialsuffix=%lu\n",
           specialcharinfo->lengthofspecialsuffix);
  fprintf (fmafp, "wildcards=%lu\n",specialcharinfo->wildcards);
  fprintf (fmafp, "wildcardranges=%lu\n",specialcharinfo->wildcardranges);
  fprintf (fmafp, "realwildcardranges=%lu\n",
                   specialcharinfo->realwildcardranges);
  fprintf (fmafp, "lengthofwildcardprefix=%lu\n",
           specialcharinfo->lengthofwildcardprefix);
  fprintf (fmafp, "lengthofwildcardsuffix=%lu\n",
           specialcharinfo->lengthofwildcardsuffix);
  fprintf (fmafp, "suffixlength=%u\n", fm->suffixlength);
  gt_fa_xfclose(fmafp);
  return 0;
}

static int writefmdata(const char *indexname,
                       Fmindex *fm,
                       bool storeindexpos,
                       GtError *err)
{
  FILE *fp;

  gt_error_check(err);
  fp = gt_fa_fopen_with_suffix(indexname,FMDATAFILESUFFIX,"wb",err);
  if (fp == NULL)
  {
    return -1;
  }
  if (gt_flushfmindex2file(fp,fm,storeindexpos,err) != 0)
  {
    return -2;
  }
  gt_fa_xfclose(fp);
  return 0;
}

int gt_saveFmindex(const char *indexname,Fmindex *fm,
                   const GtSpecialcharinfo *specialcharinfo,
                   bool storeindexpos,GtError *err)
{
  gt_error_check(err);
  if (writefmascii(indexname, fm, specialcharinfo,storeindexpos,err) != 0)
  {
    return -1;
  }
  if (writefmdata (indexname, fm, storeindexpos,err) != 0)
  {
    return -2;
  }
  return 0;
}
genometools-1.5.1/src/match/fmi-save.pr000066400000000000000000000003541211610345200200030ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
int gt_saveFmindex(const char *indexname,Fmindex *fm,
                   const GtSpecialcharinfo *specialcharinfo,
                   bool storeindexpos,GtError *err);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/fmi-sufbwtstream.c000066400000000000000000000365721211610345200214070ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/fa.h"
#include "core/alphabet.h"
#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/encseq_metadata.h"
#include "core/error.h"
#include "core/str.h"
#include "core/xansi_api.h"
#include "core/ma_api.h"

#include "emimergeesa.h"
#include "esa-fileend.h"
#include "fmindex.h"
#include "esa-map.h"

#include "encseq2offset.pr"
#include "fmi-keyval.pr"
#include "fmi-mapspec.pr"

static int copytheindexfile(const char *destindex,
                            const char *sourceindex,
                            const char *suffix,
                            uint64_t maxlength,
                            GtError *err)
{
  FILE *fpdest = NULL, *fpsource = NULL;
  int cc;
  bool haserr = false;

  gt_error_check(err);
  fpdest = gt_fa_fopen_with_suffix(destindex,suffix,"wb",err);
  if (fpdest == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    fpsource = gt_fa_fopen_with_suffix(sourceindex,suffix,"rb",err);
    if (fpsource == NULL)
    {
      haserr = true;
    }
  }
  printf("# cp %s%s %s%s\n",sourceindex,suffix,destindex,suffix);
  if (!haserr)
  {
    if (maxlength == 0)
    {
      while ((cc = fgetc(fpsource)) != EOF)
      {
        (void) putc(cc,fpdest);
      }
    } else
    {
      uint64_t pos;

      for (pos = 0; pos < maxlength; pos++)
      {
        if ((cc = fgetc(fpsource)) == EOF)
        {
          break;
        }
        (void) putc(cc,fpdest);
      }
    }
  }
  gt_fa_xfclose(fpdest);
  gt_fa_xfclose(fpsource);
  return haserr ? -1 : 0;
}

static void allocatefmtables(Fmindex *fm,
                             const GtSpecialcharinfo *specialcharinfo,
                             bool storeindexpos)
{
  fm->tfreq = gt_malloc(sizeof *fm->tfreq * TFREQSIZE(fm->mapsize));
  fm->superbfreq = gt_malloc(sizeof *fm->superbfreq
                             * SUPERBFREQSIZE(fm->mapsize,fm->nofsuperblocks));
  if (storeindexpos)
  {
    fm->markpostable = gt_malloc(sizeof *fm->markpostable
                                 * MARKPOSTABLELENGTH(fm->bwtlength,
                                                      fm->markdist));
    fm->specpos.nextfreeGtPairBwtidx = 0;
    fm->specpos.allocatedGtPairBwtidx
      = (unsigned long) gt_determinenumberofspecialstostore(specialcharinfo);
    printf("# %lu wildcards in the last %lu characters (%.2f)\n",
           (unsigned long) specialcharinfo->specialcharacters -
                           fm->specpos.allocatedGtPairBwtidx,
           specialcharinfo->specialcharacters,
            (double) (specialcharinfo->specialcharacters -
                      fm->specpos.allocatedGtPairBwtidx)/
                     specialcharinfo->specialcharacters);
    fm->specpos.spaceGtPairBwtidx
      = gt_malloc(sizeof *fm->specpos.spaceGtPairBwtidx
                  * fm->specpos.allocatedGtPairBwtidx);
  } else
  {
    GT_INITARRAY(&fm->specpos,GtPairBwtidx);
    fm->markpostable = NULL;
  }
  fm->bfreq = gt_malloc(sizeof *fm->bfreq
                        * BFREQSIZE(fm->mapsize,fm->nofblocks));
}

static void set0frequencies(Fmindex *fm)
{
  unsigned long i;

  for (i = 0; i < (unsigned long) TFREQSIZE(fm->mapsize); i++)
  {
    fm->tfreq[i] = 0;
  }
  for (i = 0; i < (unsigned long) BFREQSIZE(fm->mapsize,fm->nofblocks); i++)
  {
    fm->bfreq[i] = 0;
  }
  for (i = 0;
       i < (unsigned long) SUPERBFREQSIZE(fm->mapsize,fm->nofsuperblocks);
       i++)
  {
    fm->superbfreq[i] = 0;
  }
}

static void finalizefmfrequencies(Fmindex *fm)
{
  unsigned int j;
  unsigned long i, *freqptr;

  for (j = 2U; j <= fm->mapsize; j++)
  {
    fm->tfreq[j] += fm->tfreq[j - 1];
  }
  freqptr = fm->superbfreq;
  for (j = 0; j < fm->mapsize; j++)
  {
    for (i = (unsigned long) 2; i < fm->nofsuperblocks; i++)
    {
      freqptr[i] += freqptr[i-1];
    }
    freqptr += fm->nofsuperblocks;
  }
}

static void showconstructionmessage(const char *indexname,
                                    unsigned long totallength,
                                    unsigned long fmsize,
                                    unsigned int log2bsize,
                                    unsigned int log2markdist,
                                    unsigned int numofchars)
{
  printf("# construct fmindex \"%s\" for bsize=%lu, superbsize=%lu,",
          indexname,
          (unsigned long) GT_POW2(log2bsize),
          (unsigned long) GT_POW2(log2markdist));
  printf(" len=%lu, alphasize=%u: size ",
          totallength,
          numofchars);
  printf("%lu bytes, space overhead %.2f\n",
          fmsize,
          (double) fmsize/(double) (totallength+1));
}

static int nextesamergedsufbwttabvalues(Definedunsignedlong *longest,
                                       GtUchar *bwtvalue,
                                       unsigned long *suftabvalue,
                                       Emissionmergedesa *emmesa,
                                       const unsigned long *sequenceoffsettable,
                                       unsigned long bwtpos,
                                       GtError *err)
{
  Indexedsuffix indexedsuffix;

  gt_error_check(err);
  if (emmesa->buf.nextaccessidx >= emmesa->buf.nextstoreidx)
  {
    if (emmesa->numofentries == 0)
    {
      return 0;
    }
    if (gt_emissionmergedesa_stepdeleteandinsertothersuffixes(emmesa,err) != 0)
    {
      return -1;
    }
    if (emmesa->buf.nextstoreidx == 0)
    {
      return 0;
    }
    emmesa->buf.nextaccessidx = 0;
  }
  indexedsuffix = emmesa->buf.suftabstore[emmesa->buf.nextaccessidx];
  *suftabvalue = sequenceoffsettable[indexedsuffix.idx] +
                 indexedsuffix.startpos;
  if (indexedsuffix.startpos == 0)
  {
    if (indexedsuffix.idx == 0)
    {
      if (longest->defined)
      {
        gt_error_set(err,"longest is already defined as %lu",
                      longest->valueunsignedlong);
        return -2;
      }
      longest->defined = true;
      longest->valueunsignedlong = bwtpos;
      *bwtvalue = (GtUchar) UNDEFBWTCHAR;
    } else
    {
      *bwtvalue = (GtUchar) SEPARATOR;
    }
  } else
  {
    *bwtvalue
      = gt_encseq_get_encoded_char( /* Random access */
           emmesa->suffixarraytable[indexedsuffix.idx].encseq,
           indexedsuffix.startpos-1,
           emmesa->suffixarraytable[indexedsuffix.idx].readmode);
  }
  emmesa->buf.nextaccessidx++;
  return 1;
}

int gt_sufbwt2fmindex(Fmindex *fmindex,
                   GtSpecialcharinfo *specialcharinfo,
                   unsigned int log2bsize,
                   unsigned int log2markdist,
                   const char *outfmindex,
                   const GtStrArray *indexnametab,
                   bool storeindexpos,
                   GtLogger *logger,
                   GtError *err)
{
  Suffixarray suffixarray;
  Emissionmergedesa emmesa;
  GtUchar cc;
  unsigned long bwtpos,
         totallength = 0,
         suftabvalue = 0,
         *sequenceoffsettable = NULL,
         firstignorespecial = 0,
         nextmark,
         *markptr,
         nextprogress,
         tmpsuftabvalue,
         stepprogress;
  unsigned int numofchars = 0,
               suffixlength = 0,
               numofindexes;
  int retval;
  Definedunsignedlong longest = { false, 0 };
  GtPairBwtidx *pairptr;
  FILE *outbwt = NULL;
  GtStr *tmpfilename = NULL;
  bool haserr = false;

  gt_error_check(err);
  longest.defined = false;
  longest.valueunsignedlong = 0;
  numofindexes = (unsigned int) gt_str_array_size(indexnametab);
  if (numofindexes == 1U)
  {
    const char *indexname = gt_str_array_get(indexnametab,0);

    if (streamsuffixarray(&suffixarray,
                          SARR_BWTTAB | (storeindexpos ? SARR_SUFTAB : 0),
                          indexname,
                          logger,
                          err) != 0)
    {
      haserr = true;
    } else
    {
      totallength = gt_encseq_total_length(suffixarray.encseq);
    }
    if (!haserr && gt_specialcharinfo_read(specialcharinfo,indexname,err) != 0)
    {
      haserr = true;
    }
    if (!haserr)
    {
      numofchars = gt_alphabet_num_of_chars(
                               gt_encseq_alphabet(suffixarray.encseq));
      firstignorespecial = totallength - specialcharinfo->specialcharacters;
      if (gt_alphabet_to_file(gt_encseq_alphabet(suffixarray.encseq),
                              outfmindex, err) != 0)
      {
        haserr = true;
      }
    }
    if (!haserr)
    {
      if (copytheindexfile(outfmindex,
                            indexname,
                            BWTTABSUFFIX,
                            (uint64_t) firstignorespecial,
                            err) != 0)
      {
        haserr = true;
      }
    }
  } else
  {
    GtEncseqMetadata *emd = NULL;
    if (gt_emissionmergedesa_init(&emmesa,
                               indexnametab,
                               SARR_ESQTAB | SARR_SUFTAB | SARR_LCPTAB,
                               logger,
                               err) != 0)
    {
      haserr = true;
    }
    if (!haserr)
    {
      const char *indexname = NULL;
      indexname = gt_str_array_get(indexnametab,0);
      emd = gt_encseq_metadata_new(indexname, err);
      if (emd == NULL) {
        haserr = true;
      }
    }
    if (!haserr) {
      suffixlength = 0;
      if (gt_alphabet_to_file(gt_encseq_metadata_alphabet(emd),
                              outfmindex, err) != 0)
      {
        haserr = true;
      }
    }
    gt_encseq_metadata_delete(emd);
    if (!haserr)
    {
      sequenceoffsettable = gt_encseqtable2sequenceoffsets(&totallength,
                                                        specialcharinfo,
                                                        emmesa.suffixarraytable,
                                                        numofindexes);
      if (sequenceoffsettable == NULL)
      {
        haserr = true;
      }
    }
    if (!haserr)
    {
      longest.defined = false;
      longest.valueunsignedlong = 0;
      outbwt = gt_fa_fopen_with_suffix(outfmindex,BWTTABSUFFIX,"wb",err);
      if (outbwt == NULL)
      {
        haserr = true;
      }
    }
    if (!haserr)
    {
      numofchars = emmesa.numofchars;
      firstignorespecial = totallength - specialcharinfo->specialcharacters;
    }
  }
  if (!haserr)
  {
    printf("# firstignorespecial=%lu\n",
              firstignorespecial);
    gt_computefmkeyvalues (fmindex,
                        specialcharinfo,
                        totallength+1,
                        log2bsize,
                        log2markdist,
                        numofchars,
                        suffixlength,
                        storeindexpos);
    showconstructionmessage(outfmindex,
                            totallength,
                            fmindex->sizeofindex,
                            log2bsize,
                            log2markdist,
                            numofchars);
    allocatefmtables(fmindex,specialcharinfo,storeindexpos);
    set0frequencies(fmindex);
    if (storeindexpos)
    {
      markptr = fmindex->markpostable;
    } else
    {
      markptr = NULL;
    }
    nextprogress = stepprogress = totallength/78;
    for (bwtpos = 0, nextmark = 0; ; bwtpos++)
    {
      if (numofindexes == 1U)
      {
        if (storeindexpos)
        {
          retval = gt_readnextfromstream_GtUlong(&tmpsuftabvalue,
                                            &suffixarray.suftabstream_GtUlong);
          if (retval == 0)
          {
            break;
          }
          suftabvalue = (unsigned long) tmpsuftabvalue;
        }
        retval = gt_readnextfromstream_GtUchar(&cc,&suffixarray.bwttabstream);
        if (retval == 0)
        {
          break;
        }
      } else
      {
        retval = nextesamergedsufbwttabvalues(&longest,
                                              &cc,
                                              &suftabvalue,
                                              &emmesa,
                                              sequenceoffsettable,
                                              bwtpos,
                                              err);
        if (retval < 0)
        {
          haserr = true;
          break;
        }
        if (retval == 0)
        {
          break;
        }
        gt_xfwrite(&cc, sizeof (GtUchar), (size_t) 1, outbwt);
      }
      if (bwtpos == nextprogress)
      {
        if (bwtpos == stepprogress)
        {
          (void) putchar('#');
        }
        (void) putchar('.');
        (void) fflush(stdout);
        nextprogress += stepprogress;
      }
      if (storeindexpos && bwtpos == nextmark)
      {
        *markptr++ = suftabvalue;
        nextmark += fmindex->markdist;
      }
      if (ISBWTSPECIAL(cc))
      {
        if (storeindexpos && bwtpos < firstignorespecial)
        {
          pairptr = fmindex->specpos.spaceGtPairBwtidx +
                    fmindex->specpos.nextfreeGtPairBwtidx++;
          if (pairptr >= fmindex->specpos.spaceGtPairBwtidx +
                         fmindex->specpos.allocatedGtPairBwtidx)
          {
            gt_error_set(err,"program error: not enough space for specpos");
            haserr = true;
            break;
          }
          pairptr->bwtpos = bwtpos;
          pairptr->suftabvalue = suftabvalue;
        }
      } else
      {
        fmindex->tfreq[cc+1]++;
        fmindex->bfreq[(cc * fmindex->nofblocks) +
                       (bwtpos >> fmindex->log2bsize)]++;
        fmindex->superbfreq[(cc * fmindex->nofsuperblocks) +
                       (bwtpos >> fmindex->log2superbsize) + 1]++;
      }
    }
  }
  if (!haserr)
  {
    if (storeindexpos &&
        fmindex->specpos.allocatedGtPairBwtidx !=
        fmindex->specpos.nextfreeGtPairBwtidx)
    {
      gt_error_set(err,"program error: too much space for specpos: "
                    "allocated = %lu != %lu = used",
                    fmindex->specpos.allocatedGtPairBwtidx,
                    fmindex->specpos.nextfreeGtPairBwtidx);
      haserr = true;
    }
  }
  if (!haserr)
  {
    (void) putchar('\n');
    finalizefmfrequencies(fmindex);
    if (fmindex->suffixlength > 0)
    {
      fmindex->boundarray = gt_malloc(sizeof *fmindex->boundarray
                                      * fmindex->numofcodes);
    }
    if (numofindexes == 1U)
    {
      fmindex->longestsuffixpos = suffixarray.longest.valueunsignedlong;
      gt_freesuffixarray(&suffixarray);
    } else
    {
      if (!longest.defined)
      {
        gt_error_set(err,"longest is not defined after merging");
        haserr = true;
      }
      if (!haserr)
      {
        fmindex->longestsuffixpos = longest.valueunsignedlong;
      }
      gt_fa_xfclose(outbwt);
      gt_emissionmergedesa_wrap(&emmesa);
    }
  }
  gt_free(sequenceoffsettable);
  gt_free(tmpfilename);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/fmi-sufbwtstream.pr000066400000000000000000000007101211610345200215670ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
int gt_sufbwt2fmindex(Fmindex *fmindex,
                   GtSpecialcharinfo *specialcharinfo,
                   unsigned int log2bsize,
                   unsigned int log2markdist,
                   const char *outfmindex,
                   const GtStrArray *indexnametab,
                   bool storeindexpos,
                   GtLogger *logger,
                   GtError *err);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/fmindex.h000066400000000000000000000107171211610345200175400ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef FMINDEX_H
#define FMINDEX_H

#include 
#include "core/alphabet.h"
#include "core/arraydef.h"
#include "core/encseq.h"
#include "core/pairbwtidx.h"
#include "core/ulongbound.h"

/*
  TO DO:
  - free index if in the merging process all suffixes are inserted.

  - implement option -check to determine the exact size of the index
    for the different methods.

  - can we guarantee that in the BWT we only access positions smaller
    than
    firstignorespecial = fm->bwtlength - (specialcharacters + 1);
    Then we do not have to store so many special positions.

  - generate special versions of fmqhits for the following cases:
       -  GT_ACCESS_TYPE_DIRECTACCESS
       - specialcharacters == 0

    This means that the macros with the corresponding character
    accesses are replaced at compile time.

  - also for single input index generate bwt file if option
    -fmout is used.

  - can we, for a given alphabet, first determine all bounds like in
    binsplitinterval?

  - trenne uniquesub in uniquesub und uniquesub-esa auf.

  - integriere codierte BWTtab in den fmindex

  - Programmierrichtlinien: safe cast
                            single thread f"ahig
                            dynamische Allokation f"ur Dateinamen
                            flexible kombination von Optionen
*/

#define FMASCIIFILESUFFIX ".fma"
#define FMDATAFILESUFFIX  ".fmd"

#define MARKPOSTABLELENGTH(BWTLENGTH,MARKDIST)\
        (1 + ((BWTLENGTH) - 1) / (MARKDIST))

#define TFREQSIZE(MAPSIZE)\
        ((MAPSIZE) + 1)

#define BFREQSIZE(MAPSIZE,NOFBLOCKS)\
        ((MAPSIZE) * (NOFBLOCKS))

#define SUPERBFREQSIZE(MAPSIZE,NOFSUPERBLOCKS)\
        ((MAPSIZE) * (NOFSUPERBLOCKS))

GT_DECLAREARRAYSTRUCT(GtPairBwtidx);

typedef int(*FMprocessqhit)(void *,unsigned long,unsigned long);

typedef struct
{
  /* Note: do not use specialcharinfo of bwtformatching */
  GtEncseq *bwtformatching;
  GtUchar *bfreq;            /* bfreq[c][i] = #c in block i */
  unsigned long bwtlength,        /* also totallength + 1 */
         *tfreq,           /* tfreq[c] = #characters < c in text */
         *superbfreq,      /* superbfreq[c][i] = #c in all superblocks */
                           /* which are previous to superblock i */
         *markpostable,    /* sampling of entries from suffix array */
         longestsuffixpos,
         negatebsizeones,
         negatesuperbsizeones,
         markdistminus1;   /* markdist - 1 */
  GtArrayGtPairBwtidx specpos; /* positions of special characters */
  const GtAlphabet *alphabet;
  void *mappedptr; /* NULL or pointer to the mapped space block */
  unsigned int mapsize,      /* copy of alphabet.mapsize, used for searching */
           bsize,            /* size of block */
           bsizehalve,       /* DIV2(fm->bsize) */
           superbsize,       /* size of superblock */
           log2bsize,        /* gt_log_{2}(bsize) */
           log2superbsize,   /* gt_log_{2}(superbsize) */
           log2superbsizeminuslog2bsize, /* log{2}(superbsize)-log{2}(bsize) */
           log2markdist,     /* gt_log_{2}(markdist) */
           suffixlength;     /* len of suffix for which buckets are computed*/
  unsigned long sizeofindex; /* size of the fmindex in bytes */
  unsigned long nofblocks,          /* number of blocks (bwtlength/bsize + 1) */
         nofsuperblocks,     /* number of superblocks (bwtlength/superbsize+2)*/
         markdist,           /* multiple of entry num stored in suffix array */
         numofcodes;         /* number of entries in boundaries */
  GtUlongBound *boundarray;      /* corresponding boundaries */
} Fmindex;

typedef struct
{
  Fmindex *fmptr;
  bool storeindexpos;
} Fmindexwithoptions;

#endif
genometools-1.5.1/src/match/genomediff_opt.h000066400000000000000000000033311211610345200210650ustar00rootroot00000000000000/*
  Copyright (c) 2010 Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GENOMEDIFF_OPT_H
#define GENOMEDIFF_OPT_H

#include 

#include "core/encseq_options.h"
#include "core/error.h"
#include "core/option_api.h"
#include "core/str_array.h"
#include "match/index_options.h"
#include "match/shu_unitfile.h"

typedef struct GtGenomediffArguments {
  bool scan,
       verbose,
       with_esa,
       with_pck,
       with_units;
  int user_max_depth;
  unsigned long max_ln_n_fac;
  double divergence_abs_err, /* kr2 T */
         divergence_m, /* kr2 M */
         divergence_rel_err, /* kr2 E */
         divergence_threshold; /* kr2 THRESHOLD */
  GtEncseqOptions *loadopts;
  GtIndexOptions *idxopts;
  GtOption *ref_unitfile;
  GtStr *indexname,
        *indextype,
        *unitfile;
  GtStrArray *filenames;
} GtGenomediffArguments;

typedef struct GenomediffInfo {
  GtShuUnitFileInfo *unit_info;
  uint64_t **shulensums;
} GenomediffInfo;

#endif
genometools-1.5.1/src/match/giextract.c000066400000000000000000000670631211610345200201010ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009 Stefan Kurtz 
  Copyright (c) 2007-2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 
#ifndef S_SPLINT_S
#include 
#endif
#include "core/fileutils.h"
#include "core/fa.h"
#include "core/assert_api.h"
#include "core/divmodmul.h"
#include "core/error.h"
#include "core/fasta.h"
#include "core/fileutils.h"
#include "core/format64.h"
#include "core/ma_api.h"
#include "core/progressbar.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "core/xansi_api.h"
#include "giextract.h"
#include "echoseq.h"

#define COMPLETE(VALUE)\
        ((VALUE)->frompos == 1UL && (VALUE)->topos == 0)

#define EXTRABUF 128

#define CHECKPOSITIVE(VAL,FORMAT,WHICH)\
        if ((VAL) <= 0)\
        {\
          gt_error_set(err,"file \"%s\", line " Formatuint64_t \
                           ": illegal format: %s element = " FORMAT \
                           " is not a positive integer",\
                           gt_str_get(fileofkeystoextract),\
                           PRINTuint64_tcast(linenum+1),\
                           WHICH,\
                           VAL);\
          haserr = true;\
        }

typedef struct
{
  char *fastakey;
  unsigned long frompos, topos;
  bool markhit;
} Fastakeyquery;

static int comparefastakeys(const void *a,const void *b)
{
  int cmp = strcmp(((Fastakeyquery *) a)->fastakey,
                   ((Fastakeyquery *) b)->fastakey);

  if (cmp < 0)
  {
    return -1;
  }
  if (cmp > 0)
  {
    return 1;
  }
  if (((Fastakeyquery *) a)->frompos < ((Fastakeyquery *) b)->frompos)
  {
    return -1;
  }
  if (((Fastakeyquery *) a)->frompos > ((Fastakeyquery *) b)->frompos)
  {
    return 1;
  }
  if (((Fastakeyquery *) a)->topos < ((Fastakeyquery *) b)->topos)
  {
    return -1;
  }
  if (((Fastakeyquery *) a)->topos > ((Fastakeyquery *) b)->topos)
  {
    return 1;
  }
  return 0;
}

static unsigned long remdupsfastakeyqueries(Fastakeyquery *fastakeyqueries,
                                            unsigned long numofqueries,
                                            bool verbose)
{
  if (numofqueries == 0)
  {
    return 0;
  } else
  {
    Fastakeyquery *storeptr, *readptr;
    unsigned long newnumofqueries;

    for (storeptr = fastakeyqueries, readptr = fastakeyqueries+1;
         readptr < fastakeyqueries + numofqueries;
         readptr++)
    {
      if (strcmp(storeptr->fastakey,readptr->fastakey) != 0 ||
          storeptr->frompos != readptr->frompos ||
          storeptr->topos != readptr->topos)
      {
        storeptr++;
        if (storeptr != readptr)
        {
          size_t len;

          storeptr->frompos = readptr->frompos;
          storeptr->topos = readptr->topos;
          len = strlen(readptr->fastakey);
          storeptr->fastakey = gt_realloc(storeptr->fastakey,
                                          sizeof (char) * (len+1));
          strcpy(storeptr->fastakey,readptr->fastakey);
        }
      }
    }
    newnumofqueries = (unsigned long) (storeptr - fastakeyqueries + 1);
    if (newnumofqueries < numofqueries)
    {
      if (verbose)
      {
        printf("# removed %lu duplicate queries\n",
                numofqueries - newnumofqueries);
      }
      for (storeptr = fastakeyqueries + newnumofqueries;
           storeptr < fastakeyqueries + numofqueries;
           storeptr++)
      {
        gt_free(storeptr->fastakey);
        storeptr->fastakey = NULL;
      }
    }
    return newnumofqueries;
  }
}

static void fastakeyqueries_delete(Fastakeyquery *fastakeyqueries,
                                   unsigned long numofqueries)
{
  if (fastakeyqueries != NULL)
  {
    unsigned long idx;

    for (idx=0; idxfastakey = gt_malloc(sizeof (char) * (idx+1));
  } else
  {
    if (idx != (size_t) keysize)
    {
      gt_error_set(err,"key \"%*.*s\" is not of size %lu",(int) idx,
                   (int) idx,lineptr,keysize);
      haserr = true;
    }
  }
  if (!haserr)
  {
    strncpy(fastakeyptr->fastakey,lineptr,idx);
    fastakeyptr->fastakey[idx] = '\0';
    fastakeyptr->frompos = 1UL;
    fastakeyptr->topos = 0;
    if (sscanf(lineptr+idx,"%ld %ld\n",&readlongfrompos,&readlongtopos) == 2)
    {
      CHECKPOSITIVE(readlongfrompos,"%ld","second");
      if (!haserr)
      {
        fastakeyptr->frompos = (unsigned long) readlongfrompos;
        CHECKPOSITIVE(readlongtopos,"%ld","third");
      }
      if (!haserr)
      {
        fastakeyptr->topos = (unsigned long) readlongtopos;
      }
    }
  }
  if (!haserr)
  {
    fastakeyptr->markhit = false;
    if (!COMPLETE(fastakeyptr) && fastakeyptr->frompos > fastakeyptr->topos)
    {
      gt_error_set(err, "file \"%s\", line " Formatuint64_t
                        "illegal format: second value "
                        "%lu is larger than third value %lu",
                        gt_str_get(fileofkeystoextract),
                        PRINTuint64_tcast(linenum+1),
                        fastakeyptr->frompos,
                        fastakeyptr->topos);
      haserr = true;
    }
  }
  return haserr ? -1 : 0;
}

static Fastakeyquery *readfileofkeystoextract(bool verbose,
                                              unsigned long *numofqueries,
                                              const GtStr *fileofkeystoextract,
                                              GtError *err)
{
  FILE *fp;
  GtStr *currentline;
  bool haserr = false;
  uint64_t linenum;
  Fastakeyquery *fastakeyqueries;
#undef SKDEBUG
#ifdef SKDEBUG
  unsigned long i;
#endif

  gt_error_check(err);
  *numofqueries = gt_file_number_of_lines(gt_str_get(fileofkeystoextract));
  if (*numofqueries == 0)
  {
    gt_error_set(err,"empty file \"%s\" not allowed",
                 gt_str_get(fileofkeystoextract));
    return NULL;
  }
  fp = gt_fa_fopen(gt_str_get(fileofkeystoextract),"r",err);
  if (fp == NULL)
  {
    return NULL;
  }
  if (verbose)
  {
    printf("# opened keyfile \"%s\"\n",gt_str_get(fileofkeystoextract));
  }
  fastakeyqueries = gt_malloc(sizeof (*fastakeyqueries) * (*numofqueries));
  currentline = gt_str_new();
  for (linenum = 0; gt_str_read_next_line(currentline, fp) != EOF; linenum++)
  {
    if (extractkeyfromcurrentline(fastakeyqueries + linenum,
                                  0,
                                  currentline,
                                  linenum,
                                  fileofkeystoextract,
                                  err) != 0)
    {
      haserr = true;
      break;
    }
    gt_str_reset(currentline);
  }
  gt_str_delete(currentline);
  gt_fa_fclose(fp);
  if (haserr)
  {
    fastakeyqueries_delete(fastakeyqueries,*numofqueries);
    return NULL;
  }
  qsort(fastakeyqueries,(size_t) *numofqueries,sizeof (*fastakeyqueries),
        comparefastakeys);
  if (verbose)
  {
    printf("# %lu fastakey-queries successfully parsed and sorted\n",
            *numofqueries);
  }
  *numofqueries = remdupsfastakeyqueries(fastakeyqueries,*numofqueries,verbose);
#ifdef SKDEBUG
  for (i=0; i<*numofqueries; i++)
  {
    printf("%lu %s\n",i,fastakeyqueries[i].fastakey);
  }
#endif
  return fastakeyqueries;
}

static unsigned long searchdesinfastakeyqueries(const char *extractkey,
                                                const Fastakeyquery
                                                  *fastakeyqueries,
                                                unsigned long numofqueries)
{
  const Fastakeyquery *leftptr, *rightptr, *midptr;
  int cmp;

  leftptr = fastakeyqueries;
  rightptr = fastakeyqueries + numofqueries - 1;
  while (leftptr <= rightptr)
  {
    midptr = leftptr + GT_DIV2((unsigned long) (rightptr-leftptr));
    cmp = strcmp(extractkey,midptr->fastakey);
    if (cmp == 0)
    {
      if (midptr > fastakeyqueries &&
          strcmp(extractkey,(midptr-1)->fastakey) == 0)
      {
        rightptr = midptr - 1;
      } else
      {
        return (unsigned long) (midptr - fastakeyqueries);
      }
    } else
    {
      if (cmp < 0)
      {
        rightptr = midptr-1;
      } else
      {
        leftptr = midptr + 1;
      }
    }
  }
  return numofqueries;
}

static void outputnonmarked(const Fastakeyquery *fastakeyqueries,
                            unsigned long numofqueries)
{
  unsigned long idx, countmissing = 0;

  for (idx=0; idx 0)
      {
        gt_assert(i>0);
        secondpipe = i;
        break;
      }
      gt_assert(i>0);
      firstpipe = i;
    }
  }
  if (firstpipe == 0 || secondpipe == 0)
  {
    gt_error_set(err,"Cannot find key in description \"%s\"",desc);
    return NULL;
  }
  gt_assert(firstpipe < secondpipe);
  *keylen = secondpipe - firstpipe - 1;
  return desc + firstpipe + 1;
}

static int giextract_encodedseq2fasta(FILE *fpout,
                                      const GtEncseq *encseq,
                                      unsigned long seqnum,
                                      const Fastakeyquery *fastakeyquery,
                                      unsigned long linewidth,
                                      GT_UNUSED GtError *err)
{
  const char *desc;
  unsigned long desclen;
  bool haserr = false;

  desc = gt_encseq_description(encseq, &desclen, seqnum);
  gt_xfputc('>',fpout);
  if (fastakeyquery != NULL && !COMPLETE(fastakeyquery))
  {
    printf("%s %lu %lu ",fastakeyquery->fastakey,
                         fastakeyquery->frompos,
                         fastakeyquery->topos);
  }
  gt_xfwrite(desc,sizeof *desc,(size_t) desclen,fpout);
  if (!haserr)
  {
    unsigned long frompos, topos, seqstartpos, seqlength ;

    gt_xfputc('\n',fpout);
    seqstartpos = gt_encseq_seqstartpos(encseq, seqnum);
    seqlength = gt_encseq_seqlength(encseq, seqnum);
    if (fastakeyquery != NULL && !COMPLETE(fastakeyquery))
    {
      frompos = fastakeyquery->frompos-1;
      topos = fastakeyquery->topos - fastakeyquery->frompos + 1;
    } else
    {
      frompos = 0;
      topos = seqlength;
    }
    gt_encseq2symbolstring(fpout,
                           encseq,
                           GT_READMODE_FORWARD,
                           seqstartpos + frompos,
                           topos,
                           linewidth);
  }
  return haserr ? -1 : 0;
}

#define MAXFIXEDKEYSIZE 11

typedef struct
{
  char key[MAXFIXEDKEYSIZE+1];
  unsigned long seqnum;
} Fixedsizekey;

static int compareFixedkeys(const void *a,const void *b)
{
  const Fixedsizekey *fa = a;
  const Fixedsizekey *fb = b;
  return strcmp(((const Fixedsizekey *) fa)->key,
                ((const Fixedsizekey *) fb)->key);
}

#define GT_KEYSTABFILESUFFIX ".kys"

int gt_extractkeysfromdesfile(const char *indexname,
                              bool sortkeys,
                              GtLogger *logger,
                              GtError *err)
{
  FILE *fpin, *fpout = NULL;
  GtStr *line = NULL;
  const char *keyptr;
  unsigned long keylen, constantkeylen = 0, linenum;/* incorrectorder = 0;*/
  bool haserr = false, firstdesc = true;
  char *previouskey = NULL;
  Fixedsizekey *keytab = NULL, *keytabptr = NULL;
  GtEncseq *encseq = NULL;
  unsigned long numofentries = 0;
  const unsigned long linewidth = 60UL;

  fpin = gt_fa_fopen_with_suffix(indexname,GT_DESTABFILESUFFIX,"rb",err);
  if (fpin == NULL)
  {
    return -1;
  }
  if (!sortkeys)
  {
    fpout = gt_fa_fopen_with_suffix(indexname,GT_KEYSTABFILESUFFIX,"wb",err);
    if (fpout == NULL)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    line = gt_str_new();
  }
  for (linenum = 0; !haserr && gt_str_read_next_line(line, fpin) != EOF;
       linenum++)
  {
    keyptr = desc2key(&keylen,gt_str_get(line),err);
    if (keyptr == NULL)
    {
      haserr = true;
      break;
    }
    if (keylen == 0)
    {
      gt_error_set(err,"key of length 0 in \"%s\" not expected",
                   gt_str_get(line));
      haserr = true;
      break;
    }
    if (firstdesc)
    {
      if (keylen > (unsigned long) CHAR_MAX)
      {
        gt_error_set(err,"key \"%*.*s\" of length %lu not allowed; "
                         "no key must be larger than %d",
                          (int) keylen,(int) keylen,keyptr,keylen,CHAR_MAX);
        haserr = true;
        break;
      }
      constantkeylen = keylen;
      previouskey = gt_malloc(sizeof (char) * (constantkeylen+1));
      firstdesc = false;
      if (!sortkeys)
      {
        gt_xfputc((char) constantkeylen,fpout);
      } else
      {
        GtEncseqLoader *el;
        if (constantkeylen > (unsigned long) MAXFIXEDKEYSIZE)
        {
          gt_error_set(err,"key \"%*.*s\" of length %lu not allowed; "
                           "no key must be larger than %d",
                            (int) keylen,(int) keylen,keyptr,keylen,
                            MAXFIXEDKEYSIZE);
          haserr = true;
          break;
        }
        el = gt_encseq_loader_new();
        gt_encseq_loader_set_logger(el, logger);
        encseq = gt_encseq_loader_load(el, indexname, err);
        gt_encseq_loader_delete(el);
        if (encseq == NULL)
        {
          haserr = true;
          break;
        }
        numofentries = gt_encseq_num_of_sequences(encseq);
        gt_assert(numofentries > 0);
        keytab = gt_malloc(sizeof (*keytab) * numofentries);
        keytabptr = keytab;
      }
    } else
    {
      if (constantkeylen != keylen)
      {
        gt_error_set(err,"key \"%*.*s\" of length %lu: all keys must be of "
                         "the same length which for all previously seen "
                         "headers is %lu",
                         (int) keylen,(int) keylen,keyptr,keylen,
                         constantkeylen);
        haserr = true;
        break;
      }
      gt_assert(previouskey != NULL);
      if (!sortkeys && strncmp(previouskey,keyptr,(size_t) constantkeylen) >= 0)
      {
        gt_error_set(err,"previous key \"%s\" is not lexicographically smaller "
                         "than current key \"%*.*s\"",
                         previouskey,(int) keylen,(int) keylen,keyptr);
        haserr = true;
        break;
        /*
        printf("previous key \"%s\" (no %lu) is lexicographically larger "
               "than current key \"%*.*s\"\n",
               previouskey,linenum,(int) keylen,(int) keylen,keyptr);
        incorrectorder++;
        */
      }
    }
    if (!sortkeys)
    {
      gt_xfwrite(keyptr,sizeof *keyptr,(size_t) keylen,fpout);
      gt_xfputc('\0',fpout);
    } else
    {
      gt_assert(keytabptr != NULL);
      strncpy(keytabptr->key,keyptr,(size_t) constantkeylen);
      keytabptr->key[constantkeylen] = '\0';
      keytabptr->seqnum = linenum;
      keytabptr++;
    }
    strncpy(previouskey,keyptr,(size_t) constantkeylen);
    previouskey[constantkeylen] = '\0';
    gt_str_reset(line);
  }
  if (!haserr)
  {
    gt_logger_log(logger,"number of keys of length %lu = %lu",
                constantkeylen,linenum);
    /*
    gt_logger_log(logger,"number of incorrectly ordered keys = %lu",
                incorrectorder);
    */
  }
  gt_str_delete(line);
  gt_fa_fclose(fpin);
  gt_fa_fclose(fpout);
  gt_free(previouskey);
  if (!haserr && sortkeys)
  {
    gt_assert(keytabptr != NULL);
    gt_assert(numofentries > 0);
    gt_assert(keytabptr == keytab + numofentries);
    qsort(keytab,(size_t) numofentries,sizeof (*keytab),compareFixedkeys);
    gt_assert(keytabptr != NULL);
    for (keytabptr = keytab; !haserr && keytabptr < keytab + numofentries;
         keytabptr++)
    {
      if (giextract_encodedseq2fasta(stdout,
                                     encseq,
                                     keytabptr->seqnum,
                                     NULL,
                                     linewidth,
                                     err) != 0)
      {
        haserr = true;
        break;
      }
    }
  }
  if (encseq != NULL)
  {
    gt_encseq_delete(encseq);
    encseq = NULL;
  }
  gt_free(keytab);
  return haserr ? -1 : 0;
}

bool gt_deskeysfileexists(const char *indexname)
{
  return gt_file_exists_with_suffix(indexname,GT_KEYSTABFILESUFFIX);
}

static unsigned long searchfastaqueryindes(const char *extractkey,
                                           const char *keytab,
                                           unsigned long numofkeys,
                                           unsigned long keysize)
{
  unsigned long left = 0, right = numofkeys - 1, mid;
  int cmp;

  while (left <= right)
  {
    mid = left + GT_DIV2((unsigned long) (right-left));
    cmp = strcmp(extractkey,keytab + 1UL + mid * (keysize+1));
    if (cmp < 0)
    {
      gt_assert(mid > 0);
      right = mid-1;
    } else
    {
      if (cmp > 0)
      {
        left = mid+1;
      } else
      {
        gt_assert(mid < numofkeys);
        return mid;
      }
    }
  }
  return numofkeys;
}

static int itersearchoverallkeys(const GtEncseq *encseq,
                                 const char *keytab,
                                 unsigned long numofkeys,
                                 unsigned long keysize,
                                 const GtStr *fileofkeystoextract,
                                 unsigned long linewidth,
                                 GtError *err)
{
  FILE *fp;
  GtStr *currentline;
  uint64_t linenum;
  unsigned long seqnum, countmissing = 0;
  bool haserr = false;
  Fastakeyquery fastakeyquery;

  if (linewidth == 0)
  {
    gt_error_set(err,"use option width to specify line width for formatting");
    return -1;
  }
  fp = gt_fa_fopen(gt_str_get(fileofkeystoextract),"r",err);
  if (fp == NULL)
  {
    return -1;
  }
  currentline = gt_str_new();
  fastakeyquery.fastakey = gt_malloc(sizeof (char) * (keysize+1));
  for (linenum = 0; gt_str_read_next_line(currentline, fp) != EOF; linenum++)
  {
    if (extractkeyfromcurrentline(&fastakeyquery,
                                  keysize,
                                  currentline,
                                  linenum,
                                  fileofkeystoextract,
                                  err) != 0)
    {
      haserr = true;
      break;
    }
    seqnum = searchfastaqueryindes(fastakeyquery.fastakey,keytab,numofkeys,
                                   keysize);
    if (seqnum < numofkeys)
    {
      if (giextract_encodedseq2fasta(stdout,
                                     encseq,
                                     seqnum,
                                     &fastakeyquery,
                                     linewidth,
                                     err) != 0)
      {
        haserr = true;
        break;
      }
    } else
    {
      countmissing++;
    }
    gt_str_reset(currentline);
  }
  if (!haserr && countmissing > 0)
  {
    printf("# number of unsatified fastakey-queries: %lu\n",countmissing);
  }
  gt_str_delete(currentline);
  gt_fa_fclose(fp);
  gt_free(fastakeyquery.fastakey);
  return haserr ? - 1 : 0;
}

static int readkeysize(const char *indexname,GtError *err)
{
  FILE *fp;
  bool haserr = false;
  char cc;

  gt_error_check(err);
  fp = gt_fa_fopen_with_suffix(indexname,GT_KEYSTABFILESUFFIX,"rb",err);
  if (fp == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    GT_UNUSED size_t ret;

    ret = fread(&cc,sizeof cc, (size_t) 1, fp);
    if (ferror(fp))
    {
      gt_error_set(err,"error when trying to read first byte of file %s%s: %s",
                   indexname,GT_KEYSTABFILESUFFIX,strerror(errno));
      haserr = true;
    }
  }
  gt_assert(cc >= 0);
  gt_fa_xfclose(fp);
  return haserr ? -1 : (int) cc;
}

int gt_extractkeysfromfastaindex(const char *indexname,
                                 const GtStr *fileofkeystoextract,
                                 unsigned long linewidth,GtError *err)
{
  GtEncseq *encseq = NULL;
  GtEncseqLoader *el = NULL;
  bool haserr = false;
  unsigned long numofdbsequences = 0, keysize = 0;

  el = gt_encseq_loader_new();
  encseq = gt_encseq_loader_load(el, indexname, err);
  gt_encseq_loader_delete(el);
  if (encseq == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    int retval;

    numofdbsequences = gt_encseq_num_of_sequences(encseq);
    retval = readkeysize(indexname,err);
    if (retval < 0)
    {
      haserr = true;
    }
    keysize = (unsigned long) retval;
  }
  if (!haserr)
  {
    char *keytab;
    unsigned long keytablength;

    keytablength = 1UL + numofdbsequences * (keysize+1);
    keytab = gt_fa_mmap_check_size_with_suffix(indexname,
                                               GT_KEYSTABFILESUFFIX,
                                               keytablength,
                                               sizeof (GtUchar),
                                               err);
    if (keytab == NULL)
    {
      haserr = true;
    } else
    {
      if (itersearchoverallkeys(encseq,keytab,numofdbsequences,
                                keysize,fileofkeystoextract,
                                linewidth,err) != 0)
      {
        haserr = true;
      }
    }
    gt_fa_xmunmap(keytab);
  }
  if (encseq != NULL)
  {
    gt_encseq_delete(encseq);
    encseq = NULL;
  }
  return haserr ? -1 : 0;
}

int gt_extractkeysfromfastafile(bool verbose,
                                GtFile *outfp,
                                unsigned long width,
                                const GtStr *fileofkeystoextract,
                                GtStrArray *referencefiletab,
                                GtError *err)
{
  GtSeqIterator *seqit;
  const GtUchar *sequence;
  char *desc, *headerbufferspace = NULL, *keyspace = NULL;
  const char *keyptr;
  unsigned long allockeyspace = 0, len, keylen, numofqueries, keyposition,
                countmarkhit = 0;
  int had_err = 0;
  off_t totalsize;
  Fastakeyquery *fastakeyqueries;
  size_t headerbuffersize = 0, headerlength;

  gt_error_check(err);
  fastakeyqueries = readfileofkeystoextract(verbose,&numofqueries,
                                            fileofkeystoextract,err);
  if (fastakeyqueries == NULL)
  {
    return -1;
  }
  totalsize = gt_files_estimate_total_size(referencefiletab);
  if (verbose)
  {
    printf("# estimated total size is " Formatuint64_t "\n",
            PRINTuint64_tcast(totalsize));
  }
  seqit = gt_seq_iterator_sequence_buffer_new(referencefiletab, err);
  if (!seqit)
  {
    had_err = -1;
  }
  if (!had_err && verbose)
  {
    gt_progressbar_start(gt_seq_iterator_getcurrentcounter(seqit,
                                                          (unsigned long long)
                                                          totalsize),
                                                          (unsigned long long)
                                                          totalsize);
  }
  while (had_err != -1 && countmarkhit < numofqueries)
  {
    had_err = gt_seq_iterator_next(seqit, &sequence, &len, &desc, err);
    if (had_err != 1)
    {
      break;
    }
    keyptr = desc2key(&keylen,desc,err);
    if (keyptr == NULL)
    {
      had_err = -1;
    } else
    {
      if (allockeyspace < keylen)
      {
        keyspace = gt_realloc(keyspace,sizeof (*keyspace) * (keylen+1));
        allockeyspace = keylen;
      }
      gt_assert(keyspace != NULL);
      strncpy(keyspace,keyptr,(size_t) keylen);
      keyspace[keylen] = '\0';
      keyposition = searchdesinfastakeyqueries(keyspace,fastakeyqueries,
                                               numofqueries);
      if (keyposition < numofqueries)
      {
        while (keyposition < numofqueries &&
               strcmp(fastakeyqueries[keyposition].fastakey,keyspace) == 0)
        {
#ifndef NDEBUG
          if (fastakeyqueries[keyposition].markhit)
          {
            fprintf(stderr,"key %s was already found before\n",
                     fastakeyqueries[keyposition].fastakey);
            exit(GT_EXIT_PROGRAMMING_ERROR);
          }
#endif
          headerlength = strlen(desc);
          if (headerbuffersize < headerlength + EXTRABUF + 1)
          {
            headerbuffersize = headerlength + EXTRABUF + 1;
            headerbufferspace = gt_realloc(headerbufferspace,
                                           sizeof (*headerbufferspace)
                                           * headerbuffersize);
          }
          if (COMPLETE(fastakeyqueries + keyposition))
          {
            /*
            (void) snprintf(headerbufferspace,headerbuffersize,
                            "%*.*s complete %s",
                            (int) keylen,(int) keylen,keyspace,
                            desc);
            */
            gt_fasta_show_entry(desc, (const char *) sequence, len, width,
                                outfp);
          } else
          {
            (void) snprintf(headerbufferspace,headerbuffersize,
                            "%*.*s %lu %lu %s",
                            (int) keylen,(int) keylen,keyspace,
                            fastakeyqueries[keyposition].frompos,
                            fastakeyqueries[keyposition].topos,
                            desc);
            gt_fasta_show_entry(headerbufferspace,
                                (const char *)
                                (sequence+fastakeyqueries[keyposition].
                                                          frompos - 1),
                                fastakeyqueries[keyposition].topos -
                                fastakeyqueries[keyposition].frompos+1,
                                width, outfp);
          }
          fastakeyqueries[keyposition].markhit = true;
          countmarkhit++;
          keyposition++;
        }
      }
#ifdef SKDEBUG
      printf("%s 1 %lu\n",keyspace, len);
#endif
    }
  }
  gt_free(headerbufferspace);
  gt_free(keyspace);
  if (verbose)
  {
    gt_progressbar_stop();
  }
  if (verbose)
  {
    outputnonmarked(fastakeyqueries,numofqueries);
  }
  fastakeyqueries_delete(fastakeyqueries,numofqueries);
  gt_seq_iterator_delete(seqit);
  return had_err;
}
genometools-1.5.1/src/match/giextract.h000066400000000000000000000034101211610345200200700ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Stefan Kurtz 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GIEXTRACT_H
#define GIEXTRACT_H
#include 
#include "core/str_api.h"
#include "core/fileutils_api.h"
#include "core/error.h"
#include "core/logger.h"

int gt_extractkeysfromfastafile(bool verbose,
                                GtFile *outfp,
                                unsigned long width,
                                const GtStr *fileofkeystoextract,
                                GtStrArray *referencefiletab,
                                GtError *err);

int gt_extractkeysfromfastaindex(const char *indexname,
                                 const GtStr *fileofkeystoextract,
                                 unsigned long linewidth,GtError *err);

int gt_extractkeysfromdesfile(const char *indexname,
                              bool sortkeys,
                              GtLogger *logger,
                              GtError *err);

bool gt_deskeysfileexists(const char *indexname);

#endif
genometools-1.5.1/src/match/greedyedist.c000066400000000000000000000237261211610345200204150ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/chardef.h"
#include "core/ma_api.h"
#include "core/minmax.h"
#include "core/types_api.h"
#include "greedyedist.h"

#define GT_FRONT_STORE(GL,F,V)         F = V
#define GT_FRONT_ROWVALUE(FVAL)        *(FVAL)
#define GT_FRONT_MINUSINFINITY(GL)     ((GL)->integermin)

typedef long GtFrontvalue;

typedef struct
{
  long offset,   /* absolute base address of the front */
       width,    /* width of the front */
       left;     /* left boundary (negative), */
                 /* -left is relative address of entry */
} GtFrontspec;

/*
  A structure to store the global values.
*/

struct GtFrontResource
{
  unsigned long currentallocated;
  long ulen,
       vlen,
       integermin;
  GtFrontvalue *frontspace;
};

static unsigned long sumofoddnumbers(unsigned long max)
{
  return max * max;
}

GtFrontResource *gt_frontresource_new(unsigned long maxdist)
{
  GtFrontResource *ftres = gt_malloc(sizeof *ftres);

  ftres->currentallocated = sumofoddnumbers(maxdist);
  ftres->frontspace = gt_malloc(sizeof *ftres->frontspace
                                * ftres->currentallocated);
  return ftres;
}

void gt_frontresource_delete(GtFrontResource *ftres)
{
  if (ftres != NULL)
  {
    gt_free(ftres->frontspace);
    gt_free(ftres);
  }
}

#ifdef SKDEBUG
static void showfront(const GtFrontResource *ftres,
                      const GtFrontspec *fspec,
                      long r)
{
  GtFrontvalue *fval;
  long k;

  for (fval = ftres->frontspace + fspec->offset, k=fspec->left;
       k < fspec->left + fspec->width; k++, fval++)
  {
    if (r <= 0 || k <= -r || k >= r)
    {
      printf("(k=%ld)%ld ",k,GT_FRONT_ROWVALUE(fval));
    } else
    {
      printf("(k=%ld)undef ",k);
    }
  }
  (void) putchar('\n');
}
#endif

static void frontspecparms(const GtFrontResource *ftres,
                           GtFrontspec *fspec,
                           long p,
                           long r)
{
  if (r <= 0)
  {
    fspec->left = -p;
    fspec->width = p + p + 1;
  } else
  {
    fspec->left = MAX(-ftres->ulen,-p);
    fspec->width = MIN(ftres->vlen,p) - fspec->left + 1;
  }
#ifdef SKDEBUG
  printf("p=%ld,offset=%ld,left=%ld,width=%ld\n",p,
                                                 fspec->offset,
                                                 fspec->left,
                                                 fspec->width);
#endif
}

static long accessfront(const GtFrontResource *ftres,
                        GtFrontvalue *fval,
                        const GtFrontspec *fspec,
                        long k)
{
  if (fspec->left <= k && k < fspec->left + fspec->width)
  {
    return GT_FRONT_ROWVALUE(fval+k);
  }
  return GT_FRONT_MINUSINFINITY(ftres);
}

/*
  The following function evaluates an entry \(front(k,p)\) in a
  forward direction.
*/

static void evalentryforward(const GtSeqabstract *useq,
                             const GtSeqabstract *vseq,
                             GtFrontResource *ftres,
                             GtFrontvalue *fval,
                             const GtFrontspec *fspec,
                             long k)
{
  long value, t;
  GtFrontvalue *fptr;

#ifdef SKDEBUG
  printf("evalentryforward(k=%ld)\n",k);
#endif
  fptr = ftres->frontspace + fspec->offset - fspec->left;
  t = accessfront(ftres,fptr,fspec,k) + 1;         /* same diagonal */
#ifdef SKDEBUG
  printf("same: access(k=%ld)=%ld\n",k,t-1);
#endif

  value = accessfront(ftres,fptr,fspec,k-1);       /* diagonal below */
#ifdef SKDEBUG
  printf("below: access(k=%ld)=%ld\n",k-1,value);
#endif
  if (t < value)
  {
    t = value;
  }
  value = accessfront(ftres,fptr,fspec,k+1) + 1;     /* diagonal above */
#ifdef SKDEBUG
  printf("above: access(k=%ld)=%ld\n",k+1,value-1);
#endif
  if (t < value)
  {
    t = value;
  }
#ifdef SKDEBUG
  printf("maximum: t=%ld\n",t);   /* the maximum over three values */
#endif
  if (t < 0 || t+k < 0)             /* no negative value */
  {
    GT_FRONT_STORE(ftres,GT_FRONT_ROWVALUE(fval),GT_FRONT_MINUSINFINITY(ftres));
  } else
  {
    if (ftres->ulen != 0 && ftres->vlen != 0 &&
        t < ftres->ulen && t + k < ftres->vlen)
    {
      unsigned long lcp, minlen
        = (unsigned long) MIN(ftres->ulen - t,ftres->vlen - (t + k));
      lcp = gt_seqabstract_lcp(true,
                               useq,
                               vseq,
                               (unsigned long) t,
                               (unsigned long) (t + k),
                               minlen);
      t += lcp;
    }
    if (t > ftres->ulen || t + k > ftres->vlen)
    {
      GT_FRONT_STORE(ftres,GT_FRONT_ROWVALUE(fval),
                     GT_FRONT_MINUSINFINITY(ftres));
    } else
    {
      GT_FRONT_STORE(ftres,GT_FRONT_ROWVALUE(fval),t);
    }
  }
}

/*
  The following function evaluates a front in forward direction.
  It returns true if any of the returned values is at least 0.
*/

static bool evalfrontforward(const GtSeqabstract *useq,
                             const GtSeqabstract *vseq,
                             GtFrontResource *ftres,
                             const GtFrontspec *prevfspec,
                             const GtFrontspec *fspec,
                             long r)
{
  long k;
  bool defined = false;
  GtFrontvalue *fval;

  for (fval = ftres->frontspace + fspec->offset, k = fspec->left;
       k < fspec->left + fspec->width; k++, fval++)
  {
    if (r <= 0 || k <= -r || k >= r)
    {
      evalentryforward(useq,vseq,ftres,fval,prevfspec,k);
      if (GT_FRONT_ROWVALUE(fval) >= 0)
      {
        defined = true;
      }
#ifdef SKDEBUG
      printf("store front[k=%ld]=%ld ",k,GT_FRONT_ROWVALUE(fval));
      printf("at index %ld\n",(long) (fval-ftres->frontspace));
#endif
    } else
    {
#ifdef SKDEBUG
      printf("store front[k=%ld]=GT_FRONT_MINUSINFINITY ",k);
      printf("at index %ld\n",(long) (fval-ftres->frontspace));
#endif
      GT_FRONT_STORE(ftres,GT_FRONT_ROWVALUE(fval),
                     GT_FRONT_MINUSINFINITY(ftres));
    }
  }
#ifdef SKDEBUG
  printf("frontvalues[r=%ld]=",r);
  showfront(ftres,fspec,r);
#endif
  return defined;
}

/*
  The following function evaluates the entry \(front(0,0)\) in a
  forward direction.
*/

static void firstfrontforward(const GtSeqabstract *useq,
                              const GtSeqabstract *vseq,
                              GtFrontResource *ftres,
                              GtFrontspec *fspec)
{
  fspec->left = fspec->offset = 0;
  fspec->width = 1L;
  if (ftres->ulen == 0 || ftres->vlen == 0)
  {
    GT_FRONT_STORE(ftres,GT_FRONT_ROWVALUE(&ftres->frontspace[0]),0);
  } else
  {
    unsigned long lcp = gt_seqabstract_lcp(true,
                                           useq,
                                           vseq,
                                           0,
                                           0,
                                           (unsigned long)
                                           MIN(ftres->ulen,ftres->vlen));
    GT_FRONT_STORE(ftres,GT_FRONT_ROWVALUE(&ftres->frontspace[0]),(long) lcp);
  }
#ifdef SKDEBUG
  printf("forward front[0]=%ld\n",GT_FRONT_ROWVALUE(&ftres->frontspace[0]));
#endif
}

unsigned long greedyunitedist(GtFrontResource *ftres,
                              const GtSeqabstract *useq,
                              const GtSeqabstract *vseq)
{
  unsigned long realdistance, kval;
  long r;
  GtFrontspec frontspecspace[2], *fspec, *prevfspec;
  GtFrontvalue *fptr;

#ifdef SKDEBUG
  printf("unitedistcheckSEPgeneric(ulen=%lu,vlen=%lu)\n",ulenvalue,vlenvalue);
#endif
  gt_assert(gt_seqabstract_length_get(useq) < (unsigned long) LONG_MAX);
  gt_assert(gt_seqabstract_length_get(vseq) < (unsigned long) LONG_MAX);
  ftres->ulen = (long) gt_seqabstract_length_get(useq);
  ftres->vlen = (long) gt_seqabstract_length_get(vseq);
  ftres->integermin = -MAX(ftres->ulen,ftres->vlen);
  prevfspec = &frontspecspace[0];
  firstfrontforward(useq,vseq,ftres,prevfspec);
  if (ftres->ulen == ftres->vlen &&
      GT_FRONT_ROWVALUE(ftres->frontspace) == ftres->vlen)
  {
    realdistance = 0;
  } else
  {
    for (kval=1UL, r=1-MIN(ftres->ulen,ftres->vlen);
         /* Nothing */ ; kval++, r++)
    {
      if (prevfspec == &frontspecspace[0])
      {
        fspec = &frontspecspace[1];
      } else
      {
        fspec = &frontspecspace[0];
      }
      fspec->offset = prevfspec->offset + prevfspec->width;
      frontspecparms(ftres,fspec,(long) kval,r);
      while ((unsigned long) (fspec->offset + fspec->width)
             >= ftres->currentallocated)
      {
        ftres->currentallocated += kval+1;
        ftres->frontspace
          = gt_realloc(ftres->frontspace,
                       sizeof *ftres->frontspace * ftres->currentallocated);
      }
      (void) evalfrontforward(useq,vseq,ftres,prevfspec,fspec,r);
      fptr = ftres->frontspace + fspec->offset - fspec->left;
      if (accessfront(ftres,fptr,fspec,ftres->vlen - ftres->ulen)
          == ftres->ulen)
      {
        realdistance = kval;
        break;
      }
      if (prevfspec == &frontspecspace[0])
      {
        prevfspec = &frontspecspace[1];
      } else
      {
        prevfspec = &frontspecspace[0];
      }
    }
  }
#ifdef SKDEBUG
  printf("unitedistfrontSEP returns %ld\n",realdistance);
#endif
  return realdistance;
}
genometools-1.5.1/src/match/greedyedist.h000066400000000000000000000023721211610345200204140ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GREEDYEDIST_H
#define GREEDYEDIST_H

#include "match/seqabstract.h"

typedef struct GtFrontResource GtFrontResource;

GtFrontResource *gt_frontresource_new(unsigned long maxdist);

void gt_frontresource_delete(GtFrontResource *ftres);

unsigned long greedyunitedist(GtFrontResource *ftres,
                              const GtSeqabstract *useq,
                              const GtSeqabstract *vseq);

#endif
genometools-1.5.1/src/match/greedyfwdmat.c000066400000000000000000000344111211610345200205600ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include "core/alphabet.h"
#include "core/error.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "core/unused_api.h"
#include "core/defined-types.h"
#include "core/codetype.h"
#include "core/encseq.h"
#include "core/format64.h"
#include "core/ma_api.h"
#include "optionargmode.h"
#include "greedyfwdmat.h"
#include "initbasepower.h"

typedef struct
{
  bool showsequence,
       showquerypos,
       showsubjectpos;
  Definedunsignedlong minlength,
                      maxlength;
} Rangespecinfo;

typedef void (*Preprocessgmatchlength)(uint64_t,
                                       const char *,
                                       void *);
typedef void (*Processgmatchlength)(const GtAlphabet *,
                                    const GtUchar *,
                                    unsigned long,
                                    unsigned long,
                                    unsigned long,
                                    void *);
typedef void (*Postprocessgmatchlength)(const GtAlphabet *,
                                        uint64_t,
                                        const char *,
                                        const GtUchar *,
                                        unsigned long,
                                        void *);

typedef struct
{
  const void *genericindex;
  unsigned long totallength;
  const GtAlphabet *alphabet;
  Greedygmatchforwardfunction gmatchforward;
  Preprocessgmatchlength preprocessgmatchlength;
  Processgmatchlength processgmatchlength;
  Postprocessgmatchlength postprocessgmatchlength;
  void *processinfo;
  const GtEncseq *encseq;
} Substringinfo;

#ifndef NDEBUG
static void checkifsequenceisthere(const GtEncseq *encseq,
                                   unsigned long witnessposition,
                                   unsigned long gmatchlength,
                                   const GtUchar *qptr)
{
  unsigned long i;
  GtUchar cc;

  for (i=0; ipreprocessgmatchlength != NULL)
  {
    substringinfo->preprocessgmatchlength(unitnum,
                                          desc,
                                          substringinfo->processinfo);
  }
  if (((Rangespecinfo *) substringinfo->processinfo)->showsubjectpos ||
      substringinfo->encseq != NULL)
  {
    wptr = &witnessposition;
  } else
  {
    wptr = NULL;
  }
  for (qptr = query, remaining = querylen; remaining > 0; qptr++, remaining--)
  {
    gmatchlength = substringinfo->gmatchforward(substringinfo->genericindex,
                                                0,
                                                0,
                                                substringinfo->totallength,
                                                wptr,
                                                qptr,
                                                query+querylen);
    if (gmatchlength > 0)
    {
#ifndef NDEBUG
      if (substringinfo->encseq != NULL)
      {
        gt_assert(wptr != NULL);
        checkifsequenceisthere(substringinfo->encseq,
                               witnessposition,
                               gmatchlength,
                               qptr);
      }
#endif
      substringinfo->processgmatchlength(substringinfo->alphabet,
                                         query,
                                         gmatchlength,
                                         (unsigned long) (qptr-query),
                                         wptr == NULL
                                           ? (unsigned long) 0
                                           : witnessposition,
                                         substringinfo->processinfo);
    }
  }
  if (substringinfo->postprocessgmatchlength != NULL)
  {
    substringinfo->postprocessgmatchlength(substringinfo->alphabet,
                                           unitnum,
                                           desc,
                                           query,
                                           querylen,
                                           substringinfo->processinfo);
  }
}

static void showunitnum(uint64_t unitnum,
                        const char *desc,
                        GT_UNUSED void *info)
{
  printf("unit " Formatuint64_t, PRINTuint64_tcast(unitnum));
  if (desc != NULL && desc[0] != '\0')
  {
    printf(" (%s)",desc);
  }
  printf("\n");
}

static void showifinlengthrange(const GtAlphabet *alphabet,
                                const GtUchar *start,
                                unsigned long gmatchlength,
                                unsigned long querystart,
                                unsigned long subjectpos,
                                void *info)
{
  Rangespecinfo *rangespecinfo = (Rangespecinfo *) info;

  if ((!rangespecinfo->minlength.defined ||
      gmatchlength >= rangespecinfo->minlength.valueunsignedlong) &&
     (!rangespecinfo->maxlength.defined ||
      gmatchlength <= rangespecinfo->maxlength.valueunsignedlong))
  {
    if (rangespecinfo->showquerypos)
    {
      printf("%lu ",querystart);
    }
    printf("%lu",gmatchlength);
    if (rangespecinfo->showsubjectpos)
    {
      printf(" %lu",subjectpos);
    }
    if (rangespecinfo->showsequence)
    {
      (void) putchar(' ');
      gt_alphabet_decode_seq_to_fp(alphabet,stdout,start + querystart,
                                   gmatchlength);
    }
    (void) putchar('\n');
  }
}

int gt_findsubquerygmatchforward(const GtEncseq *encseq,
                              const void *genericindex,
                              unsigned long totallength,
                              Greedygmatchforwardfunction gmatchforward,
                              const GtAlphabet *alphabet,
                              const GtStrArray *queryfilenames,
                              Definedunsignedlong minlength,
                              Definedunsignedlong maxlength,
                              bool showsequence,
                              bool showquerypos,
                              bool showsubjectpos,
                              GtError *err)
{
  Substringinfo substringinfo;
  Rangespecinfo rangespecinfo;
  bool haserr = false;
  GtSeqIterator *seqit;
  const GtUchar *query;
  unsigned long querylen;
  char *desc = NULL;
  int retval;
  uint64_t unitnum;

  gt_error_check(err);
  substringinfo.genericindex = genericindex;
  substringinfo.totallength = totallength;
  rangespecinfo.minlength = minlength;
  rangespecinfo.maxlength = maxlength;
  rangespecinfo.showsequence = showsequence;
  rangespecinfo.showquerypos = showquerypos;
  rangespecinfo.showsubjectpos = showsubjectpos;
  substringinfo.preprocessgmatchlength = showunitnum;
  substringinfo.processgmatchlength = showifinlengthrange;
  substringinfo.postprocessgmatchlength = NULL;
  substringinfo.alphabet = alphabet;
  substringinfo.processinfo = &rangespecinfo;
  substringinfo.gmatchforward = gmatchforward;
  substringinfo.encseq = encseq;
  seqit = gt_seq_iterator_sequence_buffer_new(queryfilenames, err);
  if (!seqit)
    haserr = true;
  if (!haserr)
  {
    gt_seq_iterator_set_symbolmap(seqit, gt_alphabet_symbolmap(alphabet));
    for (unitnum = 0; /* Nothing */; unitnum++)
    {
      retval = gt_seq_iterator_next(seqit,
                                &query,
                                &querylen,
                                &desc,
                                err);
      if (retval < 0)
      {
        haserr = true;
        break;
      }
      if (retval == 0)
      {
        break;
      }
      gmatchposinsinglesequence(&substringinfo,
                                unitnum,
                                query,
                                querylen,
                                desc);
    }
    gt_seq_iterator_delete(seqit);
  }
  return haserr ? -1 : 0;
}

#ifdef WITHrunsubstringiteration
int runsubstringiteration(Greedygmatchforwardfunction gmatchforward,
                          const void *genericindex,
                          unsigned long totalwidth,
                          const unsigned long *leftborder,
                          const unsigned long *countspecialcodes,
                          const Alphabet *alphabet,
                          unsigned int prefixlength,
                          const GtStrArray *queryfilenames,
                          GtError *err)
{
  Substriter *substriter;
  Substring substring;
  bool haserr = false;
  int retval;
  unsigned int numofchars;
  unsigned long gmatchlength, gmatchlength2;
  GtCodetype maxcode;
  GtBucketspecification bucketspec;

  substriter->seqit = gt_seq_iterator_new(filenames,
                                      getsymbolmapAlphabet(alphabet),
                                      true);
  substriter = gt_substriter_new(queryfilenames,alphabet,prefixlength);
  numofchars = getnumofcharsAlphabet(alphabet);
  maxcode = ontheflybasepower(numofchars,prefixlength);
  while (true)
  {
    retval = gt_substriter_next(&substring,substriter,err);
    if (retval < 0)
    {
      haserr = true;
      break;
    }
    if (retval == 0)
    {
      break;
    }
    gt_assert(substring.remaining >= (unsigned long) prefixlength);
    gmatchlength = gmatchforward(genericindex,
                                 0,
                                 0,
                                 totalwidth,
                                 NULL,
                                 substring.currentptr,
                                 substring.currentptr + substring.remaining);
    if (leftborder != NULL)
    {
      gt_bcktab_calcboundaries(&bucketspec,
                               leftborder,
                               countspecialcodes,
                               substring.currentcode,
                               maxcode,
                               totalwidth,
                               substring.currentcode % numofchars,
                               numofchars);
      if (bucketspec.nonspecialsinbucket > 0)
      {
        gmatchlength2 = gmatchforward(genericindex,
                                      (unsigned long) prefixlength,
                                      bucketspec.left,
                                      bucketspec.left
                                        + bucketspec.nonspecialsinbucket - 1,
                                      NULL,
                                      substring.currentptr+prefixlength,
                                      substring.currentptr+substring.remaining);
#ifndef NDEBUG
        if (gmatchlength2 != gmatchlength)
        {
          fprintf(stderr,"at offset %lu:\n",(unsigned long)
                                              (substring.currentptr -
                                               substring.start));
          fprintf(stderr,"bucketspec=(%lu,%lu)\n",
                          bucketspec.left,
                          bucketspec.left+bucketspec.nonspecialsinbucket-1);
          fprintf(stderr,"gmatchlength2 = %lu != %lu = gmatchlength\n",
                          gmatchlength2,gmatchlength);
          exit(GT_EXIT_PROGRAMMING_ERROR);
        }
#endif
      }
    }
  }
  gt_substriter_delete(substriter);
  return haserr ? -1 : 0;
}

int runsubstringiteration(Greedygmatchforwardfunction gmatchforward,
                          const void *genericindex,
                          unsigned long totalwidth,
                          const unsigned long *leftborder,
                          const unsigned long *countspecialcodes,
                          const Alphabet *alphabet,
                          unsigned int prefixlength,
                          const GtStrArray *queryfilenames,
                          GtError *err)
{
  GtSeqIterator *seqit;
  const GtUchar *query;
  unsigned long querylen;
  char *desc = NULL;
  Substriter *substriter;
  Substring substring;
  bool haserr = false;
  int retval;
  unsigned int numofchars;
  unsigned long gmatchlength, gmatchlength2;
  GtCodetype maxcode;
  GtBucketspecification bucketspec;
  bool haserr = false;

  seqit = gt_seq_iterator_new(queryfilenames,getsymbolmapAlphabet(alphabet),
  *                          true);
  for (unitnum = 0; ; unitnum++)
  {
    retval = gt_seq_iterator_next(seqit,
                              &query,
                              &querylen,
                              &desc,
                              err);
    if (retval < 0)
    {
      haserr = true;
      break;
    }
    if (retval == 0)
    {
      break;
    }
  }
  gt_seq_iterator_delete(seqit);
  return haserr ? -1 : 0;
}
#endif
genometools-1.5.1/src/match/greedyfwdmat.h000066400000000000000000000053461211610345200205720ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GREEDYFWDMAT_H
#define GREEDYFWDMAT_H

#include 
#include "core/alphabet.h"
#include "core/error.h"
#include "core/types_api.h"
#include "core/str_array.h"
#include "core/defined-types.h"

#include "core/encseq.h"

typedef unsigned long (*Greedygmatchforwardfunction) (const void *,
                                                      unsigned long offset,
                                                      unsigned long left,
                                                      unsigned long right,
                                                      unsigned long *,
                                                      const GtUchar *,
                                                      const GtUchar *);

int gt_findsubquerygmatchforward(const GtEncseq *encseq,
                              const void *genericindex,
                              unsigned long totallength,
                              Greedygmatchforwardfunction gmatchforward,
                              const GtAlphabet *alphabet,
                              const GtStrArray *queryfilenames,
                              Definedunsignedlong minlength,
                              Definedunsignedlong maxlength,
                              bool showsequence,
                              bool showquerypos,
                              bool showsubjectpos,
                              GtError *err);

int runsubstringiteration(Greedygmatchforwardfunction gmatchforward,
                          const void *genericindex,
                          unsigned long totalwidth,
                          const unsigned long *leftborder,
                          const unsigned long *countspecialcodes,
                          const GtAlphabet *alphabet,
                          unsigned int prefixlength,
                          const GtStrArray *queryfilenames,
                          GtError *err);
#endif
genometools-1.5.1/src/match/hashfirstcodes.c000066400000000000000000000131261211610345200211070ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/codetype.h"
#include "core/encseq.h"
#include "core/showtime.h"
#include "core/unused_api.h"
#include "extended/uint64hashtable.h"
#include "hashfirstcodes.h"
#include "sfx-suffixer.h"

typedef struct
{
  GtUint64hashtable *table;
  unsigned long differentcodes;
  unsigned int kmersize;
  unsigned long *suftab;
  unsigned long finalpsum;
} GtHashfirstcodes;

static void gt_hashfirstcodes(void *processinfo,
                              GT_UNUSED bool firstinrange,
                              GT_UNUSED unsigned long pos,
                              GtCodetype code)
{
  GtHashfirstcodes *hashfirstcodes = (GtHashfirstcodes *) processinfo;

  if (!gt_uint64hashtable_search(hashfirstcodes->table,
                                 (uint64_t) code,
                                 true))
  {
    hashfirstcodes->differentcodes++;
  }
}

static void gt_hashremainingcodes(void *processinfo,
                                  bool firstinrange,
                                  GT_UNUSED unsigned long pos,
                                  GtCodetype code)
{
  GtUint64hashtable *table = (GtUint64hashtable *) processinfo;

  if (!firstinrange)
  {
    (void) gt_uint64hashtable_search(table,(uint64_t) code,false);
  }
}

static void gt_insertallcodeswithhashtable(void *processinfo,
                                           GT_UNUSED bool firstinrange,
                                           unsigned long pos,
                                           GtCodetype code)
{
  GtHashfirstcodes *hashfirstcodes = (GtHashfirstcodes *) processinfo;

  unsigned long idx = gt_uint64hashtable_insertionindex(hashfirstcodes->table,
                                                        (uint64_t) code);
  if (idx != ULONG_MAX)
  {
    gt_assert(idx < hashfirstcodes->finalpsum);
    hashfirstcodes->suftab[idx] = pos;
  }
}

void hashfirstcodes_getencseqkmers_twobitencoding(const GtEncseq *encseq,
                                                  unsigned int kmersize)
{
  GtTimer *timer = NULL;
  GtHashfirstcodes hashfirstcodes;
  unsigned long numofsequences, psum;
  GT_UNUSED unsigned long totallength;
  /*GT_UNUSED unsigned long countsum;*/
  const unsigned int spmopt = 45U;

  if (gt_showtime_enabled())
  {
    timer = gt_timer_new_with_progress_description("insert first codes into "
                                                   "hashtable");
    gt_timer_start(timer);
  }
  numofsequences = gt_encseq_num_of_sequences(encseq);
  totallength = gt_encseq_total_length(encseq);
  hashfirstcodes.table = gt_uint64hashtable_new((size_t) numofsequences);
  hashfirstcodes.differentcodes = 0;
  getencseqkmers_twobitencoding(encseq,
                                GT_READMODE_FORWARD,
                                kmersize,
                                kmersize,
                                true,
                                gt_hashfirstcodes,
                                &hashfirstcodes,
                                NULL,
                                NULL);
  printf("# number of different codes=%lu (%.4f) in %lu sequences\n",
          hashfirstcodes.differentcodes,
          (double) hashfirstcodes.differentcodes/numofsequences,
          numofsequences);
  /*countsum = gt_uint64hashtable_countsum_get(hashfirstcodes.table);*/
  gt_assert(gt_uint64hashtable_countsum_get(hashfirstcodes.table)
               == numofsequences);
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "accumulate counts",stdout);
  }
  getencseqkmers_twobitencoding(encseq,
                                GT_READMODE_FORWARD,
                                kmersize,
                                spmopt,
                                false,
                                gt_hashremainingcodes,
                                hashfirstcodes.table,
                                NULL,
                                NULL);
  psum = gt_uint64hashtable_partialsums(hashfirstcodes.table,timer);
  hashfirstcodes.suftab = gt_malloc((size_t) psum *
                                    sizeof (*hashfirstcodes.suftab));
  hashfirstcodes.finalpsum = psum;
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "insert suffixes into suffix table",
                                        stdout);
  }
  getencseqkmers_twobitencoding(encseq,
                                GT_READMODE_FORWARD,
                                kmersize,
                                spmopt,
                                false,
                                gt_insertallcodeswithhashtable,
                                &hashfirstcodes,
                                NULL,
                                NULL);
  gt_free(hashfirstcodes.suftab);
  gt_uint64hashtable_delete(hashfirstcodes.table);
  if (timer != NULL)
  {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
}
genometools-1.5.1/src/match/hashfirstcodes.h000066400000000000000000000020761211610345200211160ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef HASHFIRSTCODES_H
#define HASHFIRSTCODES_H

#include "core/encseq.h"

void hashfirstcodes_getencseqkmers_twobitencoding(const GtEncseq *encseq,
                                                  unsigned int kmersize);

#endif
genometools-1.5.1/src/match/idx-limdfs.c000066400000000000000000001451561211610345200201470ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/defined-types.h"
#include "core/ma_api.h"
#include "sarr-def.h"
#include "esa-splititv.h"
#include "eis-voiditf.h"
#include "esa-mmsearch.h"
#include "absdfstrans-imp.h"
#include "idx-limdfs.h"
#include "esa-map.h"
#include "idxlocalidp.h"
#include "esa-minunique.h"

#define DECLAREDFSSTATE(V)\
        Aliasdfsstate V[5]

struct Genericindex
{
  Suffixarray *suffixarray;
  unsigned long totallength;
  FMindex *packedindex;
  bool withesa;
  const Mbtab **mbtab;      /* only relevant for packedindex */
  unsigned int maxdepth;    /* maximaldepth of boundaries */
};

void genericindex_delete(Genericindex *genericindex)
{
  if (genericindex == NULL)
  {
    return;
  }
  gt_freesuffixarray(genericindex->suffixarray);
  gt_free(genericindex->suffixarray);
  if (genericindex->packedindex != NULL)
  {
    gt_deletevoidBWTSeq(genericindex->packedindex);
  }
  gt_free(genericindex);
}

const GtEncseq *genericindex_getencseq(const Genericindex *genericindex)
{
  gt_assert(genericindex->suffixarray->encseq != NULL);
  return genericindex->suffixarray->encseq;
}

const Suffixarray *genericindex_getsuffixarray(const Genericindex
                                                *genericindex)
{
  gt_assert(genericindex->suffixarray != NULL);
  return genericindex->suffixarray;
}

Genericindex *genericindex_new(const char *indexname,
                               bool withesa,
                               bool withencseq,
                               bool withdestab,
                               bool withssptab,
                               int userdefinedmaxdepth,
                               GtLogger *logger,
                               GtError *err)
{
  unsigned int demand = 0;
  bool haserr = false;
  Genericindex *genericindex;

  genericindex = gt_malloc(sizeof (*genericindex));
  if (withesa)
  {
    demand |= SARR_SUFTAB;
  }
  if (withencseq)
  {
    demand |= SARR_ESQTAB;
  }
  if (withdestab)
  {
    demand |= SARR_DESTAB;
  }
  if (withssptab)
  {
    demand |= SARR_SSPTAB;
  }
  genericindex->withesa = withesa;
  genericindex->suffixarray = gt_malloc(sizeof (*genericindex->suffixarray));
  if (gt_mapsuffixarray(genericindex->suffixarray,
                        demand,
                        indexname,
                        logger,
                        err) != 0)
  {
    haserr = true;
    genericindex->totallength = 0;
  } else
  {
    genericindex->totallength
      = gt_encseq_total_length(genericindex->suffixarray->encseq);
  }
  if (!haserr)
  {
    if (withesa && genericindex->suffixarray->readmode != GT_READMODE_FORWARD)
    {
      gt_error_set(err,"using option -esa you can only process index "
                       "in forward mode");
      haserr = true;
    } else
    {
      if (!withesa
            && genericindex->suffixarray->readmode != GT_READMODE_REVERSE)
      {
        gt_error_set(err,"with option -pck you can only process index "
                         "in reverse mode");
        haserr = true;
      }
    }
  }
  genericindex->packedindex = NULL;
  genericindex->mbtab = NULL;
  genericindex->maxdepth = 0;
  if (!haserr && !withesa)
  {
    genericindex->packedindex = gt_loadvoidBWTSeqForSA(indexname,true, err);
    if (genericindex->packedindex == NULL)
    {
      gt_assert(gt_error_is_set(err));
      haserr = true;
    }
  }
  if (!haserr && !withesa)
  {
    genericindex->mbtab = gt_bwtseq2mbtab(genericindex->packedindex);
    genericindex->maxdepth = gt_bwtseq2maxdepth(genericindex->packedindex);
    if (userdefinedmaxdepth >= 0 &&
        genericindex->maxdepth > (unsigned int) userdefinedmaxdepth)
    {
      genericindex->maxdepth = (unsigned int) userdefinedmaxdepth;
    }
  }
  if (haserr)
  {
    genericindex_delete(genericindex);
    return NULL;
  }
  return genericindex;
}

typedef struct
{
  unsigned long offset,
                leftbound,
                rightbound;
  GtCodetype code;
  GtUchar inchar;
} Indexbounds;

typedef struct
{
  Indexbounds lcpitv;
  DECLAREDFSSTATE(aliasstate);
  /* the following two components are only required if keepexpandedonstack
     is true */
  bool keeponstack;
  unsigned long previousstackelem;
} Lcpintervalwithinfo;

GT_DECLAREARRAYSTRUCT(Lcpintervalwithinfo);

struct Limdfsresources
{
  Limdfsconstinfo *dfsconstinfo;
  GtArrayBoundswithchar bwci;
  GtArrayLcpintervalwithinfo stack;
  Lcpintervalwithinfo copyofparent;
  DECLAREDFSSTATE(copyofcopyofparentstate);
  unsigned long parentindex;
  bool keepexpandedonstack;
  GtUchar alphasize;
  void *patterninfo;
  const Genericindex *genericindex;
  bool nowildcards;
  unsigned long maxintervalwidth;
  unsigned long *rangeOccs;
  const GtEncseq *encseq;
  GtArrayGtUlong mstatspos;
  GtUchar *currentpathspace;
  unsigned long allocatedpathspace;
  unsigned long numberofmatches;
  ProcessIdxMatch processmatch;
  void *processmatchinfo;
  Processresult processresult;
};

Limdfsresources *gt_newLimdfsresources(const Genericindex *genericindex,
                                    bool nowildcards,
                                    unsigned long maxintervalwidth,
                                    unsigned long maxpathlength,
                                    bool keepexpandedonstack,
                                    ProcessIdxMatch processmatch,
                                    void *processmatchinfo,
                                    Processresult processresult,
                                    void *patterninfo,
                                    const AbstractDfstransformer *adfst)
{
  Limdfsresources *limdfsresources;
  unsigned int numofchars;
  const GtEncseq *encseq;

  encseq = genericindex->suffixarray->encseq;
  numofchars = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
  limdfsresources = gt_malloc(sizeof *limdfsresources);
  limdfsresources->bwci.spaceBoundswithchar
    = gt_malloc(sizeof *limdfsresources->bwci.spaceBoundswithchar
                * (numofchars+1));
  limdfsresources->bwci.nextfreeBoundswithchar = 0;
  limdfsresources->bwci.allocatedBoundswithchar
    = (unsigned long) (numofchars+1);
  GT_INITARRAY(&limdfsresources->stack,Lcpintervalwithinfo);
  gt_assert(numofchars <= GT_MAXALPHABETCHARACTER);
  limdfsresources->alphasize = (GtUchar) numofchars;
  limdfsresources->processmatch = processmatch;
  limdfsresources->processmatchinfo = processmatchinfo;
  limdfsresources->processresult = processresult;
  limdfsresources->patterninfo = patterninfo;
  limdfsresources->genericindex = genericindex;
  limdfsresources->nowildcards = nowildcards;
  limdfsresources->encseq = encseq;
  limdfsresources->maxintervalwidth = maxintervalwidth;
  limdfsresources->keepexpandedonstack = keepexpandedonstack;
  if (maxpathlength > 0)
  {
    limdfsresources->currentpathspace
      = gt_malloc(sizeof *limdfsresources->currentpathspace
                  * maxpathlength);
    limdfsresources->allocatedpathspace = maxpathlength;
  } else
  {
    limdfsresources->currentpathspace = NULL;
  }
  /* Application specific */
  limdfsresources->dfsconstinfo
    = adfst->allocatedfsconstinfo((unsigned int) limdfsresources->alphasize);
  if (genericindex->withesa)
  {
    limdfsresources->rangeOccs = NULL;
  } else
  {
    limdfsresources->rangeOccs
      = gt_malloc(sizeof *limdfsresources->rangeOccs
                  * GT_MULT2(limdfsresources->alphasize));
  }
  GT_INITARRAY(&limdfsresources->mstatspos,GtUlong);
  if (maxintervalwidth > 0)
  {
    limdfsresources->mstatspos.spaceGtUlong
      = gt_malloc(sizeof *limdfsresources->mstatspos.spaceGtUlong
                  * maxintervalwidth);
    limdfsresources->mstatspos.allocatedGtUlong = maxintervalwidth;
  }
  if (adfst->initLimdfsstackelem != NULL &&
      !limdfsresources->keepexpandedonstack)
  {
    adfst->initLimdfsstackelem(limdfsresources->copyofcopyofparentstate);
    adfst->initLimdfsstackelem(limdfsresources->copyofparent.aliasstate);
  }
  return limdfsresources;
}

static void tracethestackelems(GtIdxMatch *match,
                               Limdfsresources *limdfsresources,
                               unsigned long pprefixlen,
                               const Lcpintervalwithinfo *runptr)
{
  unsigned long previous = 0;

  gt_reinitLocaliTracebackstate(limdfsresources->dfsconstinfo,
                             runptr->lcpitv.offset,
                             pprefixlen);
  do
  {
    if (previous > 0)
    {
      gt_assert(previous - 1 == runptr->lcpitv.offset);
    }
    previous = runptr->lcpitv.offset;
    gt_assert(previous > 0);
    gt_assert(runptr->previousstackelem <
              limdfsresources->stack.nextfreeLcpintervalwithinfo);
    gt_processelemLocaliTracebackstate(limdfsresources->dfsconstinfo,
                                    runptr->lcpitv.inchar,runptr->aliasstate);
    runptr = limdfsresources->stack.spaceLcpintervalwithinfo +
             runptr->previousstackelem;
  } while (runptr->lcpitv.offset > 0);
  match->alignment
    = gt_completealignmentfromLocaliTracebackstate(&match->querylen,
                                                limdfsresources->dfsconstinfo);
  gt_assert(pprefixlen >= match->querylen);
  match->querystartpos = pprefixlen - match->querylen;
}

static Lcpintervalwithinfo *allocateStackspace(Limdfsresources *limdfsresources,
                                               const AbstractDfstransformer
                                                      *adfst)
{
  GtArrayLcpintervalwithinfo *stack = &limdfsresources->stack;

  if (stack->nextfreeLcpintervalwithinfo >= stack->allocatedLcpintervalwithinfo)
  {
    unsigned long idx;
    const unsigned long addelems = 32UL;

    stack->spaceLcpintervalwithinfo
      = gt_realloc(stack->spaceLcpintervalwithinfo,
                   sizeof *stack->spaceLcpintervalwithinfo
                   * (stack->allocatedLcpintervalwithinfo + addelems));
    if (adfst->initLimdfsstackelem != NULL)
    {
      for (idx = stack->allocatedLcpintervalwithinfo;
           idx < stack->allocatedLcpintervalwithinfo + addelems; idx++)
      {
        adfst->initLimdfsstackelem(stack->spaceLcpintervalwithinfo[idx].
                                   aliasstate);
      }
    }
    stack->allocatedLcpintervalwithinfo += addelems;
  }
  return stack->spaceLcpintervalwithinfo + stack->nextfreeLcpintervalwithinfo++;
}

static void initlcpinfostack(Limdfsresources *limdfsresources,
                             const AbstractDfstransformer *adfst)
{
  Lcpintervalwithinfo *stackptr;

  limdfsresources->stack.nextfreeLcpintervalwithinfo = 0;
  stackptr = allocateStackspace(limdfsresources,adfst);
  stackptr->lcpitv.offset = 0;
  stackptr->lcpitv.leftbound = 0;
  stackptr->lcpitv.rightbound = limdfsresources->genericindex->withesa
                                ? limdfsresources->genericindex->totallength
                                : limdfsresources->genericindex->totallength+1;
  stackptr->lcpitv.code = 0;
  if (limdfsresources->keepexpandedonstack)
  {
    stackptr->previousstackelem = 0; /* Just to let it be defined */
    stackptr->keeponstack = true;
  }
  if (adfst->initrootLimdfsstate != NULL)
  {
    adfst->initrootLimdfsstate(stackptr->aliasstate,
                               limdfsresources->dfsconstinfo);
  }
}

void gt_freeLimdfsresources(Limdfsresources **ptrlimdfsresources,
                         const AbstractDfstransformer *adfst)
{
  Limdfsresources *limdfsresources = *ptrlimdfsresources;

  adfst->freedfsconstinfo(&limdfsresources->dfsconstinfo);
  GT_FREEARRAY(&limdfsresources->bwci,Boundswithchar);
  if (adfst->freeLimdfsstackelem != NULL)
  {
    unsigned long idx;

    for (idx = 0; idx < limdfsresources->stack.allocatedLcpintervalwithinfo;
         idx++)
    {
      adfst->freeLimdfsstackelem(limdfsresources->stack.
                                 spaceLcpintervalwithinfo[idx].aliasstate);
    }
    if (!limdfsresources->keepexpandedonstack)
    {
      adfst->freeLimdfsstackelem(limdfsresources->copyofcopyofparentstate);
      adfst->freeLimdfsstackelem(limdfsresources->copyofparent.aliasstate);
    }
  }
  GT_FREEARRAY(&limdfsresources->stack,Lcpintervalwithinfo);
  gt_free(limdfsresources->rangeOccs);
  gt_free(limdfsresources->currentpathspace);
  GT_FREEARRAY(&limdfsresources->mstatspos,GtUlong);
  gt_free(*ptrlimdfsresources);
}

/* enumerate the suffixes in an LCP-interval */

static void gen_esa_overinterval(const Genericindex *genericindex,
                                 ProcessIdxMatch processmatch,
                                 void *processmatchinfo,
                                 const Indexbounds *itv,
                                 GT_UNUSED unsigned long totallength,
                                 GtIdxMatch *match)
{
  unsigned long idx;

  for (idx = itv->leftbound; idx <= itv->rightbound; idx++)
  {
    match->dbstartpos = ESASUFFIXPTRGET(genericindex->suffixarray->suftab,idx);
    /* call processmatch */
    processmatch(processmatchinfo,match);
  }
}

static void esa_overinterval(Limdfsresources *limdfsresources,
                             const Indexbounds *itv,
                             GtIdxMatch *match)
{
  gen_esa_overinterval(limdfsresources->genericindex,
                       limdfsresources->processmatch,
                       limdfsresources->processmatchinfo,
                       itv,
                       limdfsresources->genericindex->totallength,
                       match);
  limdfsresources->numberofmatches += (itv->rightbound - itv->leftbound + 1);
}

static void gen_pck_overinterval(const Genericindex *genericindex,
                                 ProcessIdxMatch processmatch,
                                 void *processmatchinfo,
                                 const Indexbounds *itv,
                                 unsigned long totallength,
                                 GtIdxMatch *match)
{
  Bwtseqpositioniterator *bspi;
  unsigned long dbstartpos;

  gt_assert(itv->leftbound < itv->rightbound);
  bspi = gt_Bwtseqpositioniterator_new(genericindex->packedindex,
                                       itv->leftbound,itv->rightbound);
  while (gt_Bwtseqpositioniterator_next(&dbstartpos,bspi))
  {
    gt_assert(totallength >= (dbstartpos + itv->offset));
    /* call processmatch */
    match->dbstartpos = totallength - (dbstartpos + itv->offset);
    processmatch(processmatchinfo,match);
  }
  gt_Bwtseqpositioniterator_delete(bspi);
}

static void pck_overinterval(Limdfsresources *limdfsresources,
                             const Indexbounds *itv,
                             GtIdxMatch *match)
{
  gen_pck_overinterval(limdfsresources->genericindex,
                       limdfsresources->processmatch,
                       limdfsresources->processmatchinfo,
                       itv,
                       limdfsresources->genericindex->totallength,
                       match);
  limdfsresources->numberofmatches += (itv->rightbound - itv->leftbound);
}

static void storemstatsposition(void *processinfo,const GtIdxMatch *match)
{
  GtArrayGtUlong *mstatspos = (GtArrayGtUlong *) processinfo;

  GT_STOREINARRAY(mstatspos,GtUlong,32,match->dbstartpos);
}

static int comparepositions(const void *a, const void *b)
{
  if (*((unsigned long *) a) < *((unsigned long *) b))
  {
    return -1;
  }
  return 1;
}

GtArrayGtUlong *gt_fromitv2sortedmatchpositions(
                                             Limdfsresources *limdfsresources,
                                             unsigned long leftbound,
                                             unsigned long rightbound,
                                             unsigned long offset)
{
  Indexbounds itv;
  GtIdxMatch match;

  limdfsresources->mstatspos.nextfreeGtUlong = 0;
  itv.leftbound = leftbound;
  itv.rightbound = rightbound;
  itv.offset = (unsigned long) offset;
  match.dbabsolute = true;
  match.dblen = itv.offset;
  match.dbsubstring = limdfsresources->currentpathspace;
  match.querystartpos = 0;
  match.querylen = offset;
  match.distance = 0;
  match.alignment = NULL;
  (limdfsresources->genericindex->withesa
       ? gen_esa_overinterval
       : gen_pck_overinterval)
    (limdfsresources->genericindex,
     storemstatsposition,
     &limdfsresources->mstatspos,
     &itv,
     limdfsresources->genericindex->totallength,
     &match);
  qsort(limdfsresources->mstatspos.spaceGtUlong,
        (size_t) limdfsresources->mstatspos.nextfreeGtUlong,
        sizeof (unsigned long), comparepositions);
  if (limdfsresources->genericindex->withesa)
  {
    limdfsresources->numberofmatches += (rightbound - leftbound + 1);
  } else
  {
    limdfsresources->numberofmatches += (rightbound - leftbound);
  }
  return &limdfsresources->mstatspos;
}

static void initparentcopy(Limdfsresources *limdfsresources,
                           const AbstractDfstransformer *adfst)
{
  if (!limdfsresources->keepexpandedonstack)
  {
    if (adfst->copyLimdfsstate == NULL)
    {
      memcpy(limdfsresources->copyofcopyofparentstate,
             limdfsresources->copyofparent.aliasstate,
             adfst->sizeofdfsstate);
    } else
    {
      adfst->copyLimdfsstate(limdfsresources->copyofcopyofparentstate,
                             limdfsresources->copyofparent.aliasstate,
                             limdfsresources->dfsconstinfo);
    }
  }
}

static Lcpintervalwithinfo *expandsingleton(Limdfsresources *limdfsresources,
                                            unsigned long *resetvalue,
                                            bool notfirst,
                                            GtUchar cc,
                                            unsigned long currentdepth,
                                            const AbstractDfstransformer *adfst)
{
  if (limdfsresources->keepexpandedonstack)
  {
    Lcpintervalwithinfo *instate;
    Lcpintervalwithinfo *outstate;

    outstate = allocateStackspace(limdfsresources,adfst);
    outstate->keeponstack = true;
    outstate->lcpitv.offset = (unsigned long) currentdepth;
    outstate->lcpitv.inchar = cc;
    if (notfirst)
    {
      instate = outstate-1;
      gt_assert(limdfsresources->stack.nextfreeLcpintervalwithinfo >= 2UL);
      outstate->previousstackelem
        = limdfsresources->stack.nextfreeLcpintervalwithinfo - 2;
    } else
    {
      gt_assert(limdfsresources->parentindex <
                limdfsresources->stack.nextfreeLcpintervalwithinfo-1);
      *resetvalue = limdfsresources->stack.nextfreeLcpintervalwithinfo-1;
      instate = limdfsresources->stack.spaceLcpintervalwithinfo +
                limdfsresources->parentindex;
      outstate->previousstackelem = limdfsresources->parentindex;
    }
    gt_assert(instate < outstate);
    adfst->nextLimdfsstate(limdfsresources->dfsconstinfo,
                           outstate->aliasstate,
                           currentdepth,
                           cc,
                           instate->aliasstate);
    return outstate;
  }
  adfst->inplacenextLimdfsstate(limdfsresources->dfsconstinfo,
                                limdfsresources->copyofcopyofparentstate,
                                currentdepth,
                                cc);
  return NULL;
}

static void addpathchar(Limdfsresources *limdfsresources,unsigned long idx,
                        GtUchar cc)
{
  if (limdfsresources->currentpathspace != NULL)
  {
    gt_assert(idx < limdfsresources->allocatedpathspace);
    limdfsresources->currentpathspace[idx] = cc;
  }
}

/* iterate transformation algorithm over a sequence context */

static void esa_overcontext(Limdfsresources *limdfsresources,
                            const Indexbounds *child,
                            const AbstractDfstransformer *adfst)
{
  unsigned long pos, startpos;
  unsigned long resetvalue = 0;
  GtUchar cc;
  Limdfsresult limdfsresult;
  GtIdxMatch match;

  initparentcopy(limdfsresources,adfst);
  startpos = ESASUFFIXPTRGET(limdfsresources->genericindex->suffixarray->suftab,
                             child->leftbound);
#ifdef SKDEBUG
  printf("retrieve context of startpos=%lu\n",(unsigned long) startpos);
#endif
  for (pos = startpos + child->offset - 1;
       pos < limdfsresources->genericindex->totallength; pos++)
  {
    cc = gt_encseq_get_encoded_char(
                          limdfsresources->genericindex->suffixarray->encseq,
                          pos,
                          limdfsresources->genericindex->suffixarray->readmode);
    if (cc != (GtUchar) SEPARATOR &&
        (!limdfsresources->nowildcards || cc != (GtUchar) WILDCARD))
    {
#ifdef SKDEBUG
      printf("cc=%u\n",(unsigned int) cc);
#endif
      Lcpintervalwithinfo *outstate;

      addpathchar(limdfsresources,(unsigned long) (pos - startpos),cc);
      outstate = expandsingleton(limdfsresources,
                                 &resetvalue,
                                 (pos > startpos + child->offset - 1)
                                    ? true : false,
                                 cc,
                                 (unsigned long) (pos - startpos + 1),
                                 adfst);
      adfst->fullmatchLimdfsstate(&limdfsresult,
                                  limdfsresources->keepexpandedonstack
                                    ?  outstate->aliasstate
                                    :  limdfsresources->copyofcopyofparentstate,
                                  child->leftbound,
                                  child->leftbound,
                                  (unsigned long) 1,
                                  (unsigned long) (pos-startpos+1),
                                  limdfsresources->dfsconstinfo);
      if (limdfsresult.status == Limdfsstop)
      {
        break;
      }
      if (limdfsresult.status == Limdfssuccess)
      {
        match.dbabsolute = true;
        match.dbstartpos = startpos;
        match.dblen = pos - startpos + 1;
        match.dbsubstring = limdfsresources->currentpathspace;
        match.querylen = limdfsresult.pprefixlen;
        match.distance = limdfsresult.distance;
        if (limdfsresources->keepexpandedonstack)
        {
          tracethestackelems(&match,limdfsresources,limdfsresult.pprefixlen,
                             outstate);
        } else
        {
          match.querystartpos = 0;
          match.alignment = NULL;
        }
        /* call processmatch */
        limdfsresources->processmatch(limdfsresources->processmatchinfo,&match);
        limdfsresources->numberofmatches++;
        break;
      }
    } else
    {
      break; /* failure */
    }
  }
  if (limdfsresources->keepexpandedonstack)
  {
    gt_assert(resetvalue > 0);
    limdfsresources->stack.nextfreeLcpintervalwithinfo = resetvalue;
  }
}

/*
   the following function iterates to determine the smallest length
   at which the expanded pattern matches
*/

static void pck_overcontext(Limdfsresources *limdfsresources,
                            const Indexbounds *child,
                            const AbstractDfstransformer *adfst)
{
  GtUchar cc;
  unsigned long contextlength, resetvalue = 0;
  bool processinchar = true;
  unsigned long bound;
  Bwtseqcontextiterator *bsci;
  Limdfsresult limdfsresult;
  GtIdxMatch match;

  gt_assert(child != NULL);
  bound = child->leftbound;
  bsci
    = gt_Bwtseqcontextiterator_new(limdfsresources->genericindex->packedindex,
                                   bound);
  initparentcopy(limdfsresources,adfst);
#ifdef SKDEBUG
  printf("retrieve context for bound = %lu\n",(unsigned long) bound);
#endif
  for (contextlength = 0; /* nothing */; contextlength++)
  {
    if (processinchar)
    {
      cc = child->inchar;
      processinchar = false;
    } else
    {
      cc = gt_Bwtseqcontextiterator_next(&bound,bsci);
    }
    if (cc != (GtUchar) SEPARATOR &&
        (!limdfsresources->nowildcards || cc != (GtUchar) WILDCARD))
    {
      Lcpintervalwithinfo *outstate;
#ifdef SKDEBUG
      printf("cc=%u\n",(unsigned int) cc);
#endif
      addpathchar(limdfsresources,
                  (unsigned long) (child->offset - 1 + contextlength),cc);
      outstate = expandsingleton(limdfsresources,
                                 &resetvalue,
                                 (contextlength > 0) ? true : false,
                                 cc,
                                 (unsigned long) (child->offset+contextlength),
                                 adfst);
      adfst->fullmatchLimdfsstate(&limdfsresult,
                                  limdfsresources->keepexpandedonstack
                                    ? outstate->aliasstate
                                    : limdfsresources->copyofcopyofparentstate,
                                  bound,
                                  bound+1,
                                  (unsigned long) 1,
                                  (unsigned long) (child->offset+contextlength),
                                  limdfsresources->dfsconstinfo);
      if (limdfsresult.status == Limdfsstop)
      {
        break;
      }
      if (limdfsresult.status == Limdfssuccess)
      {
        unsigned long startpos;

        startpos = gt_bwtseqfirstmatch(
                                    limdfsresources->genericindex->packedindex,
                                    child->leftbound);
        match.dbabsolute = true;
        match.dbstartpos = limdfsresources->genericindex->totallength -
                           (startpos + child->offset);
        match.dblen = child->offset + contextlength;
        match.dbsubstring = limdfsresources->currentpathspace;
        match.querylen = limdfsresult.pprefixlen;
        match.distance = limdfsresult.distance;
        if (limdfsresources->keepexpandedonstack)
        {
          tracethestackelems(&match,limdfsresources,limdfsresult.pprefixlen,
                             outstate);
        } else
        {
          match.querystartpos = 0;
          match.alignment = NULL;
        }
        /* call processmatch */
        limdfsresources->processmatch(limdfsresources->processmatchinfo,&match);
        limdfsresources->numberofmatches++;
        break;
      }
    } else
    {
      break;
    }
  }
  if (limdfsresources->keepexpandedonstack)
  {
    gt_assert(resetvalue > 0);
    limdfsresources->stack.nextfreeLcpintervalwithinfo = resetvalue;
  }
  gt_Bwtseqcontextiterator_delete(bsci);
  bsci = NULL;
}

static const Lcpintervalwithinfo *currentparent(const Limdfsresources
                                                *limdfsresources)
{
  const Lcpintervalwithinfo *ptr;

  if (limdfsresources->keepexpandedonstack)
  {
    gt_assert(limdfsresources->parentindex <
              limdfsresources->stack.nextfreeLcpintervalwithinfo);
  }
  ptr = limdfsresources->keepexpandedonstack
           ? (limdfsresources->stack.spaceLcpintervalwithinfo +
              limdfsresources->parentindex)
           : &limdfsresources->copyofparent;
  return ptr;
}

/* the following function does not contain any iteration */

static void pushandpossiblypop(Limdfsresources *limdfsresources,
                               const Indexbounds *child,
                               const AbstractDfstransformer *adfst)
{
  Limdfsresult limdfsresult;
  unsigned long width;
  Lcpintervalwithinfo *stackptr;

#ifdef SKDEBUG
  printf("(2) nextLimdfsstate(");
  adfst->showLimdfsstate(currentparent(limdfsresources)->aliasstate,
                         (unsigned long) (child->offset-1),
                         limdfsresources->dfsconstinfo);
  printf(",%u)=",(unsigned int) child->inchar);
#endif
  stackptr = allocateStackspace(limdfsresources,adfst);
  adfst->nextLimdfsstate(limdfsresources->dfsconstinfo,
                         stackptr->aliasstate,
                         (unsigned long) child->offset,
                         child->inchar,
                         currentparent(limdfsresources)->aliasstate);
#ifdef SKDEBUG
  adfst->showLimdfsstate(stackptr->aliasstate,
                         (unsigned long) child->offset,
                         limdfsresources->dfsconstinfo);
  printf("\n");
#endif
  if (limdfsresources->genericindex->withesa)
  {
    width = child->rightbound - child->leftbound + 1;
  } else
  {
    width = child->rightbound - child->leftbound;
  }
  adfst->fullmatchLimdfsstate(&limdfsresult,
                              stackptr->aliasstate,
                              child->leftbound,
                              child->rightbound,
                              width,
                              (unsigned long) child->offset,
                              limdfsresources->dfsconstinfo);
  if (limdfsresult.status == Limdfscontinue)
  {
    stackptr->lcpitv = *child;
    if (limdfsresources->keepexpandedonstack)
    {
      stackptr->keeponstack = true;
      stackptr->previousstackelem = limdfsresources->parentindex;
    }
    return; /* no success, but still have the chance to find result */
  }
  if (limdfsresult.status == Limdfssuccess)
  {
    GtIdxMatch match;

    match.dbabsolute = true;
    match.querylen = limdfsresult.pprefixlen;
    match.distance = limdfsresult.distance;
    match.dblen = child->offset;
    match.dbsubstring = limdfsresources->currentpathspace;
    if (limdfsresources->keepexpandedonstack)
    {
      gt_assert(stackptr >= limdfsresources->stack.spaceLcpintervalwithinfo &&
                stackptr < limdfsresources->stack.spaceLcpintervalwithinfo +
                           limdfsresources->stack.nextfreeLcpintervalwithinfo);
      stackptr->lcpitv = *child;
      stackptr->keeponstack = true;
      stackptr->previousstackelem = limdfsresources->parentindex;
      tracethestackelems(&match,limdfsresources,limdfsresult.pprefixlen,
                         stackptr);
    } else
    {
      match.querystartpos = 0;
      match.alignment = NULL;
    }
    /* success with match of length pprefixlen */
    (limdfsresources->genericindex->withesa
         ? esa_overinterval
         : pck_overinterval) (limdfsresources,child,&match);
  }
  /* now status == Limdfssuccess || status == Limdfsstop */
  /* pop the element from the stack as there has been success or stop event */
  limdfsresources->stack.nextfreeLcpintervalwithinfo--;
}

static void processchildinterval(Limdfsresources *limdfsresources,
                                 const Indexbounds *child,
                                 const AbstractDfstransformer *adfst)
{
  if (child->leftbound + 1 < child->rightbound ||
      (limdfsresources->genericindex->withesa &&
       child->leftbound + 1 == child->rightbound))
  {
    pushandpossiblypop(limdfsresources, child, adfst);
  } else
  {
    if (limdfsresources->genericindex->withesa)
    {
      esa_overcontext(limdfsresources,child,adfst);
    } else
    {
      pck_overcontext(limdfsresources,child,adfst);
    }
  }
}

#ifdef SKDEBUG

static void showLCPinterval(bool withesa,const Indexbounds *itv)
{
  unsigned long width;

  width = withesa ? (itv->rightbound - itv->leftbound + 1)
                  : itv->rightbound - itv->leftbound;
  printf("(%lu,width=%lu)",(unsigned long) itv->offset,(unsigned long) width);
  printf("(%lu,%lu)",(unsigned long) itv->leftbound,
                     (unsigned long)
                     (withesa ? itv->rightbound : itv->rightbound-1));
}

#endif

static void esa_splitandprocess(Limdfsresources *limdfsresources,
                                const AbstractDfstransformer *adfst)
{
  unsigned long firstspecial;
  GtUchar extendchar;
  unsigned long idx;
  const Indexbounds *parent = &(currentparent(limdfsresources)->lcpitv);

  extendchar = gt_lcpintervalextendlcp(
                       limdfsresources->genericindex->suffixarray->encseq,
                       limdfsresources->genericindex->suffixarray->readmode,
                       limdfsresources->genericindex->suffixarray->suftab,
                       limdfsresources->genericindex->totallength,
                       limdfsresources->alphasize,
                       parent->offset,
                       parent->leftbound,
                       parent->rightbound);
  if (extendchar < limdfsresources->alphasize)
  {
    limdfsresources->bwci.spaceBoundswithchar[0].lbound = parent->leftbound;
    limdfsresources->bwci.spaceBoundswithchar[0].rbound = parent->rightbound;
    limdfsresources->bwci.spaceBoundswithchar[0].inchar = extendchar;
    limdfsresources->bwci.nextfreeBoundswithchar = 1UL;
  } else
  {
    limdfsresources->bwci.nextfreeBoundswithchar = 0;
    gt_lcpintervalsplitwithoutspecial(
                     &limdfsresources->bwci,
                     limdfsresources->genericindex->suffixarray->encseq,
                     limdfsresources->genericindex->suffixarray->readmode,
                     limdfsresources->genericindex->totallength,
                     limdfsresources->genericindex->suffixarray->suftab,
                     parent->offset,
                     parent->leftbound,
                     parent->rightbound);
  }
  firstspecial = parent->leftbound;
  for (idx = 0; idx < limdfsresources->bwci.nextfreeBoundswithchar; idx++)
  {
    Indexbounds child;

    /* reset as parentptr may have been moved */
    parent = &(currentparent(limdfsresources)->lcpitv);
    child.inchar = limdfsresources->bwci.spaceBoundswithchar[idx].inchar;
    child.offset = parent->offset+1;
    child.leftbound = limdfsresources->bwci.spaceBoundswithchar[idx].lbound;
    child.rightbound = limdfsresources->bwci.spaceBoundswithchar[idx].rbound;
    child.code = 0; /* not used, but we better define it */
    addpathchar(limdfsresources,(unsigned long) parent->offset,child.inchar);
#ifdef SKDEBUG
    printf("%u-child of ",(unsigned int) child.inchar);
    showLCPinterval(limdfsresources->genericindex->withesa,parent);
    printf(" is ");
    showLCPinterval(limdfsresources->genericindex->withesa,&child);
    printf("\n");
#endif
    processchildinterval(limdfsresources, &child, adfst);
    firstspecial = child.rightbound+1;
  }
  if (!limdfsresources->nowildcards)
  {
    Indexbounds child;
    unsigned long bound;

    child.inchar = (GtUchar) WILDCARD;
    child.offset = parent->offset+1;
    child.code = 0;  /* not used, but we better define it */
    for (bound = firstspecial; bound <= parent->rightbound; bound++)
    {
      child.leftbound = child.rightbound = bound;
      esa_overcontext(limdfsresources,&child,adfst);
    }
  }
}

static void smalldepthbwtrangesplitwithoutspecial(GtArrayBoundswithchar *bwci,
                                                  const Mbtab **mbtab,
                                                  GtUchar alphasize,
                                                  GtCodetype parentcode,
                                                  unsigned long childdepth)
{
  GtCodetype childcode;
  const Mbtab *mbptr;

  gt_assert(childdepth > 0);
  bwci->nextfreeBoundswithchar = 0;
  childcode = parentcode * alphasize;
  for (mbptr = mbtab[childdepth] + childcode;
       mbptr < mbtab[childdepth] + childcode + alphasize;
       mbptr++)
  {
    if (mbptr->lowerbound < mbptr->upperbound)
    {
      bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar].inchar
        = (GtUchar) (mbptr - (mbtab[childdepth] + childcode));
      bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar].lbound
        = mbptr->lowerbound;
      bwci->spaceBoundswithchar[bwci->nextfreeBoundswithchar++].rbound
        = mbptr->upperbound;
    }
  }
}

static void pck_splitandprocess(Limdfsresources *limdfsresources,
                                const AbstractDfstransformer *adfst)
{
  unsigned long idx;
  unsigned long sumwidth = 0;
  const Indexbounds *parent = &(currentparent(limdfsresources)->lcpitv);
  GtCodetype startcode;

  if (parent->offset < (unsigned long) limdfsresources->genericindex->maxdepth)
  {
    smalldepthbwtrangesplitwithoutspecial(&limdfsresources->bwci,
                                          limdfsresources->genericindex->mbtab,
                                          limdfsresources->alphasize,
                                          parent->code,
                                          (unsigned long) (parent->offset + 1));
    startcode = parent->code * limdfsresources->alphasize;
  } else
  {
    gt_bwtrangesplitwithoutspecial(&limdfsresources->bwci,
                                limdfsresources->rangeOccs,
                                limdfsresources->genericindex->packedindex,
                                parent->leftbound,
                                parent->rightbound);
    startcode = 0;
  }
  for (idx = 0; idx < limdfsresources->bwci.nextfreeBoundswithchar; idx++)
  {
    Indexbounds child;

    /* reset as parentptr may have been moved */
    parent = &(currentparent(limdfsresources)->lcpitv);
    child.inchar = limdfsresources->bwci.spaceBoundswithchar[idx].inchar;
    child.offset = parent->offset+1;
    child.leftbound = limdfsresources->bwci.spaceBoundswithchar[idx].lbound;
    child.rightbound = limdfsresources->bwci.spaceBoundswithchar[idx].rbound;
    gt_assert(child.inchar < limdfsresources->alphasize);
    child.code = startcode + child.inchar;
    addpathchar(limdfsresources,(unsigned long) parent->offset,child.inchar);
    sumwidth += child.rightbound - child.leftbound;
#ifdef SKDEBUG
    printf("%u-child of ",(unsigned int) child.inchar);
    showLCPinterval(limdfsresources->genericindex->withesa,parent);
    printf(" is ");
    showLCPinterval(limdfsresources->genericindex->withesa,&child);
    printf("\n");
#endif
    processchildinterval(limdfsresources, &child, adfst);
  }
  if (!limdfsresources->nowildcards)
  {
    unsigned long bound;
    Indexbounds child;

    for (bound = parent->leftbound + sumwidth;
         bound < parent->rightbound; bound++)
    {
      GtUchar cc = gt_bwtseqgetsymbol(bound,
                                   limdfsresources->genericindex->packedindex);

      child.offset = parent->offset+1;
      child.code = 0;  /* not used, but we better define it */
      if (cc != (GtUchar) SEPARATOR)
      {
        child.leftbound = bound;
        child.inchar = cc;
        pck_overcontext(limdfsresources,&child,adfst);
      }
    }
  }
}

#ifdef SKDEBUG
#define SHOWSTACKTOP(STACKPTR)\
        printf("top=");\
        showLCPinterval(limdfsresources->genericindex->withesa,\
                        &(STACKPTR)->lcpitv);\
        adfst->showLimdfsstate((STACKPTR)->aliasstate,\
                               (unsigned long) (STACKPTR)->lcpitv.offset,\
                               limdfsresources->dfsconstinfo);\
        printf("\n")
#else
#define SHOWSTACKTOP(STACKPTR) /* Nothing */
#endif

static void runlimdfs(Limdfsresources *limdfsresources,
                      const AbstractDfstransformer *adfst)
{
  Lcpintervalwithinfo *stackptr;

  gt_assert(adfst->sizeofdfsstate <=
            sizeof (limdfsresources->copyofparent.aliasstate));
  limdfsresources->numberofmatches = 0;
  initlcpinfostack(limdfsresources,adfst);
  while (limdfsresources->stack.nextfreeLcpintervalwithinfo > 0)
  {
    gt_assert(limdfsresources->stack.spaceLcpintervalwithinfo != NULL);
    /*
    printf("nextfreeLcpintervalwithinfo=%lu\n",
               limdfsresources->stack.nextfreeLcpintervalwithinfo);
    */
    stackptr = limdfsresources->stack.spaceLcpintervalwithinfo +
               limdfsresources->stack.nextfreeLcpintervalwithinfo - 1;
    SHOWSTACKTOP(stackptr);
    if (limdfsresources->keepexpandedonstack)
    {
      if (stackptr->keeponstack)
      {
        limdfsresources->parentindex
          = limdfsresources->stack.nextfreeLcpintervalwithinfo - 1;
      } else
      {
        limdfsresources->stack.nextfreeLcpintervalwithinfo--;
        continue;
      }
    } else
    {
      /* make a copy of the top most stack element to be used as source */
      if (adfst->copyLimdfsstate == NULL)
      {
        limdfsresources->copyofparent = *stackptr; /* make a copy */
      } else
      {
        limdfsresources->copyofparent.lcpitv = stackptr->lcpitv;
        adfst->copyLimdfsstate(limdfsresources->copyofparent.aliasstate,
                               stackptr->aliasstate,
                               limdfsresources->dfsconstinfo);
      }
      /* now parentptr always points to copyofparent */
    }
    if (currentparent(limdfsresources)->lcpitv.offset > 0)
    {
      addpathchar(limdfsresources,
                  (unsigned long)
                   (currentparent(limdfsresources)->lcpitv.offset-1),
                  currentparent(limdfsresources)->lcpitv.inchar);
    }
    gt_assert(limdfsresources->stack.nextfreeLcpintervalwithinfo > 0);
    /* now delete the top element from the stack as we have made a copy */
    if (limdfsresources->keepexpandedonstack)
    {
      stackptr->keeponstack = false;
    } else
    {
      limdfsresources->stack.nextfreeLcpintervalwithinfo--;
    }
    (limdfsresources->genericindex->withesa
        ? esa_splitandprocess
        : pck_splitandprocess) (limdfsresources,adfst);
  }
  if (adfst->extractdfsconstinfo != NULL)
  {
    adfst->extractdfsconstinfo(limdfsresources->processresult,
                               limdfsresources,
                               limdfsresources->patterninfo,
                               limdfsresources->dfsconstinfo);
  }
}

typedef enum
{
  Popitv,
  Splititv,
  Processitv,
  Pushitv,
  Processcontext
} Runlimdfsstate;

bool gt_indexbasedapproxpatternmatching(Limdfsresources *limdfsresources,
                                     const GtUchar *pattern,
                                     unsigned long patternlength,
                                     unsigned long maxdistance,
                                     unsigned long maxintervalwidth,
                                     bool skpp,
                                     const AbstractDfstransformer *adfst)
{
  adfst->initdfsconstinfo(limdfsresources->dfsconstinfo,
                          (unsigned int) limdfsresources->alphasize,
                          pattern,
                          patternlength,
                          maxdistance,
                          maxintervalwidth,
                          skpp);
  runlimdfs(limdfsresources,adfst);
  return (limdfsresources->numberofmatches > 0) ? true : false;
}

void gt_indexbasedmstats(Limdfsresources *limdfsresources,
                      const GtUchar *pattern,
                      unsigned long patternlength,
                      const AbstractDfstransformer *adfst)
{
  adfst->initdfsconstinfo(limdfsresources->dfsconstinfo,
                          (unsigned int) limdfsresources->alphasize,
                          pattern,
                          patternlength);
  runlimdfs(limdfsresources,adfst);
}

void gt_indexbasedspacedseeds(Limdfsresources *limdfsresources,
                           const GtUchar *pattern,
                           GtBitsequence seedbitvector,
                           unsigned long seedweight,
                           const AbstractDfstransformer *adfst)
{
  adfst->initdfsconstinfo(limdfsresources->dfsconstinfo,
                          (unsigned int) limdfsresources->alphasize,
                          pattern,
                          seedbitvector,
                          seedweight);
  runlimdfs(limdfsresources,adfst);
}

void gt_indexbasedlocali(Limdfsresources *limdfsresources,
                      long matchscore,
                      long mismatchscore,
                      long gapstart,
                      long gapextend,
                      unsigned long threshold,
                      const GtUchar *query,
                      unsigned long querylength,
                      const AbstractDfstransformer *adfst)
{
  adfst->initdfsconstinfo(limdfsresources->dfsconstinfo,
                          (unsigned int) limdfsresources->alphasize,
                          matchscore,
                          mismatchscore,
                          gapstart,
                          gapextend,
                          threshold,
                          query,
                          querylength);
  runlimdfs(limdfsresources,adfst);
}

unsigned long genericmstats(const Limdfsresources *limdfsresources,
                            const GtUchar *qstart,
                            const GtUchar *qend)
{
  if (limdfsresources->genericindex->withesa)
  {
    return gt_suffixarraymstats (limdfsresources->genericindex->suffixarray,
                              0,
                              0,
                              limdfsresources->genericindex->totallength,
                              NULL,
                              qstart,
                              qend);
  }
  return gt_voidpackedindexmstatsforward(limdfsresources->genericindex->
                                                       packedindex,
                                      0,
                                      0,
                                      limdfsresources->genericindex->
                                                       totallength,
                                      NULL,
                                      qstart,
                                      qend);
}

static bool esa_exactpatternmatching(const Suffixarray *suffixarray,
                                     const GtUchar *pattern,
                                     unsigned long patternlength,
                                     GT_UNUSED const GtUchar *dbsubstring,
                                     ProcessIdxMatch processmatch,
                                     void *processmatchinfo)
{
  GtMMsearchiterator *mmsi;
  unsigned long dbstartpos,
         totallength = gt_encseq_total_length(suffixarray->encseq);
  bool nomatches;
  GtIdxMatch match;

  mmsi = gt_mmsearchiterator_new_complete_olain(suffixarray->encseq,
                                           suffixarray->suftab,
                                           0,  /* leftbound */
                                           totallength, /* rightbound */
                                           0, /* offset */
                                           suffixarray->readmode,
                                           pattern,
                                           patternlength);
  nomatches = gt_mmsearchiterator_isempty(mmsi);
  match.dbabsolute = true;
  match.dblen = (unsigned long) patternlength;
  match.dbsubstring = pattern;
  match.querystartpos = 0;
  match.querylen = patternlength;
  match.distance = 0;
  match.alignment = NULL;
  while (gt_mmsearchiterator_next(&dbstartpos,mmsi))
  {
    /* call processmatch */
    match.dbstartpos = dbstartpos;
    processmatch(processmatchinfo,&match);
  }
  gt_mmsearchiterator_delete(mmsi);
  return nomatches ? false : true;
}

bool gt_indexbasedexactpatternmatching(const Limdfsresources *limdfsresources,
                                    const GtUchar *pattern,
                                    unsigned long patternlength)
{
  if (limdfsresources->genericindex->withesa)
  {
    return esa_exactpatternmatching(limdfsresources->genericindex->suffixarray,
                                    pattern,
                                    patternlength,
                                    limdfsresources->currentpathspace,
                                    limdfsresources->processmatch,
                                    limdfsresources->processmatchinfo);
  } else
  {
    return gt_pck_exactpatternmatching(
                                    limdfsresources->genericindex->packedindex,
                                    pattern,
                                    patternlength,
                                    limdfsresources->genericindex->totallength,
                                    limdfsresources->currentpathspace,
                                    limdfsresources->processmatch,
                                    limdfsresources->processmatchinfo);
  }
}

GtUchar gt_limdfs_getencodedchar(const Limdfsresources *limdfsresources,
                              unsigned long pos,
                              GtReadmode readmode)
{
  gt_assert(limdfsresources->encseq != NULL);

  return gt_encseq_get_encoded_char(limdfsresources->encseq,
                                           pos,
                                           readmode);
}

bool gt_intervalwidthleq(const Limdfsresources *limdfsresources,
                      unsigned long leftbound,unsigned long rightbound)
{
  unsigned long width;

  if (limdfsresources->genericindex->withesa)
  {
    if (leftbound > rightbound)
    {
      width = 0;
    } else
    {
      width = rightbound - leftbound + 1;
    }
  } else
  {
    if (leftbound >= rightbound)
    {
      width = 0;
    } else
    {
      width = rightbound - leftbound;
    }
  }
  if (width > 0 && width <= (unsigned long) limdfsresources->maxintervalwidth)
  {
    return true;
  }
  return false;
}

const FMindex *genericindex_get_packedindex(const Genericindex *genericindex)
{
  gt_assert(genericindex->packedindex != NULL);
  return genericindex->packedindex;
}

unsigned long genericindex_get_totallength(const Genericindex *genericindex)
{
  gt_assert(genericindex && genericindex->totallength != 0);
  return genericindex->totallength;
}

unsigned long esa_exact_pattern_count(const Suffixarray *suffixarray,
                                      const GtUchar *pattern,
                                      unsigned long patternlength) {
  GtMMsearchiterator *mmsi;
  unsigned long count,
                totallength = gt_encseq_total_length(suffixarray->encseq);

  mmsi = gt_mmsearchiterator_new_complete_olain(suffixarray->encseq,
                                           suffixarray->suftab,
                                           0,  /* leftbound */
                                           totallength, /* rightbound */
                                           0, /* offset */
                                           suffixarray->readmode,
                                           pattern,
                                           patternlength);

  count = gt_mmsearchiterator_count(mmsi);
  gt_mmsearchiterator_delete(mmsi);
  return count;
}

unsigned long gt_indexbased_exact_pattern_count(
                                              const Genericindex *genericindex,
                                              const GtUchar *pattern,
                                              unsigned long patternlength) {
  if (genericindex->withesa) {
    return esa_exact_pattern_count(genericindex->suffixarray,
                                    pattern,
                                    patternlength);
  }
  else {
    return gt_pck_exact_pattern_count(genericindex->packedindex,
                                       pattern,
                                       patternlength);
  }
}
genometools-1.5.1/src/match/idx-limdfs.h000066400000000000000000000126221211610345200201430ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef IDX_LIMDFS_H
#define IDX_LIMDFS_H

#include "core/arraydef.h"

#include "core/readmode.h"
#include "procmatch.h"
#include "core/logger.h"
#include "absdfstrans-def.h"
#include "core/intbits.h"
#include "match/eis-voiditf.h"
#include "match/sarr-def.h"

typedef struct Genericindex Genericindex;

void genericindex_delete(Genericindex *genericindex);

const GtEncseq *genericindex_getencseq(const Genericindex
                                                *genericindex);

const Suffixarray *genericindex_getsuffixarray(const Genericindex
                                                *genericindex);

Genericindex *genericindex_new(const char *indexname,
                               bool withesa,
                               bool withencseq,
                               bool withdestab,
                               bool withssptab,
                               int userdefinedmaxdepth,
                               GtLogger *logger,
                               GtError *err);

typedef struct Limdfsresources Limdfsresources;

Limdfsresources *gt_newLimdfsresources(const Genericindex *genericindex,
                                    bool nowildcards,
                                    unsigned long maxintervalwidth,
                                    unsigned long maxpathlength,
                                    bool keepexpandedonstack,
                                    ProcessIdxMatch processmatch,
                                    void *processmatchinfo,
                                    Processresult processresult,
                                    void *patterninfo,
                                    const AbstractDfstransformer *adfst);

void gt_freeLimdfsresources(Limdfsresources **ptrlimdfsresources,
                         const AbstractDfstransformer *adfst);

bool gt_indexbasedapproxpatternmatching(Limdfsresources *limdfsresources,
                                     const GtUchar *pattern,
                                     unsigned long patternlength,
                                     unsigned long maxdistance,
                                     unsigned long maxintervalwidth,
                                     bool skpp,
                                     const AbstractDfstransformer *adfst);

void gt_indexbasedmstats(Limdfsresources *limdfsresources,
                      const GtUchar *pattern,
                      unsigned long patternlength,
                      const AbstractDfstransformer *adfst);

void gt_indexbasedspacedseeds(Limdfsresources *limdfsresources,
                           const GtUchar *pattern,
                           GtBitsequence seedbitvector,
                           unsigned long seedweight,
                           const AbstractDfstransformer *adfst);

void gt_indexbasedlocali(Limdfsresources *limdfsresources,
                      long matchscore,
                      long mismatchscore,
                      long gapstart,
                      long gapextend,
                      unsigned long threshold,
                      const GtUchar *query,
                      unsigned long querylength,
                      const AbstractDfstransformer *adfst);

unsigned long genericmstats(const Limdfsresources *limdfsresources,
                            const GtUchar *qstart,
                            const GtUchar *qend);

bool gt_indexbasedexactpatternmatching(const Limdfsresources *limdfsresources,
                                    const GtUchar *pattern,
                                    unsigned long patternlength);

GtUchar gt_limdfs_getencodedchar(const Limdfsresources *limdfsresources,
                              unsigned long pos,
                              GtReadmode readmode);

bool gt_intervalwidthleq(const Limdfsresources *limdfsresources,
                      unsigned long leftbound,unsigned long rightbound);

GtArrayGtUlong *gt_fromitv2sortedmatchpositions(
                                          Limdfsresources *limdfsresources,
                                          unsigned long leftbound,
                                          unsigned long rightbound,
                                          unsigned long offset);

const FMindex *genericindex_get_packedindex(const Genericindex *genericindex);

unsigned long genericindex_get_totallength(const Genericindex *genericindex);

unsigned long gt_indexbased_exact_pattern_count(
                                              const Genericindex *genericindex,
                                              const GtUchar *pattern,
                                              unsigned long patternlength);

#endif
genometools-1.5.1/src/match/idxlocali.c000066400000000000000000000251741211610345200200540ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "core/ma_api.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "extended/alignment.h"
#include "sarr-def.h"
#include "core/intbits.h"
#include "core/format64.h"
#include "idx-limdfs.h"
#include "idxlocali.h"
#include "idxlocalidp.h"
#include "idxlocalisw.h"
#include "absdfstrans-def.h"
#include "esa-map.h"
#include "stamp.h"

typedef struct
{
  const GtUchar *characters;
  uint64_t queryunit;
  GtUchar wildcardshow;
  bool showalignment;
  const GtEncseq *encseq;
} Showmatchinfo;

static void showmatch(void *processinfo,const GtIdxMatch *match)
{
  Showmatchinfo *showmatchinfo = (Showmatchinfo *) processinfo;
  unsigned long seqnum;
  unsigned long relpos;

  if (match->dbabsolute)
  {
    unsigned long seqstartpos;
    seqnum = gt_encseq_seqnum(showmatchinfo->encseq, match->dbstartpos);
    seqstartpos = gt_encseq_seqstartpos(showmatchinfo->encseq, seqnum);
    gt_assert(seqstartpos <= match->dbstartpos);
    relpos = match->dbstartpos - seqstartpos;
  } else
  {
    relpos = match->dbstartpos;
    seqnum = match->dbseqnum;
  }
  printf("%lu\t%lu\t",seqnum,relpos);
  printf("%lu\t",match->dblen);
  printf("\t" Formatuint64_t "\t%lu\t%lu\t%lu\n",
              PRINTuint64_tcast(showmatchinfo->queryunit),
              match->querystartpos,
              match->querylen,
              match->distance);
  if (showmatchinfo->showalignment)
  {
    gt_alignment_show_with_mapped_chars(
                (const GtAlignment *) match->alignment,
                showmatchinfo->characters,
                showmatchinfo->wildcardshow,
                stdout);
  }
}

typedef struct
{
  const GtEncseq *encseq;
  GtBitsequence *hasmatch;
} Storematchinfo;

void gt_initstorematch(Storematchinfo *storematch,
                    const GtEncseq *encseq)
{
  unsigned long numofdbsequences = gt_encseq_num_of_sequences(encseq);

  storematch->encseq = encseq;
  GT_INITBITTAB(storematch->hasmatch,numofdbsequences);
}

static void storematch(void *info,const GtIdxMatch *match)
{
  Storematchinfo *storematch = (Storematchinfo *) info;
  unsigned long seqnum;

  if (match->dbabsolute)
  {
    seqnum = gt_encseq_seqnum(storematch->encseq,
                                           match->dbstartpos);
  } else
  {
    seqnum = match->dbseqnum;
  }
  if (!GT_ISIBITSET(storematch->hasmatch,seqnum))
  {
    GT_SETIBIT(storematch->hasmatch,seqnum);
  }
}

void gt_checkandresetstorematch(GT_UNUSED uint64_t queryunit,
                             Storematchinfo *storeonline,
                             Storematchinfo *storeoffline)
{
  unsigned long seqnum, countmatchseq = 0,
    numofdbsequences = gt_encseq_num_of_sequences(storeonline->encseq);

  for (seqnum = 0; seqnum < numofdbsequences; seqnum++)
  {
#ifndef NDEBUG
    if (GT_ISIBITSET(storeonline->hasmatch,seqnum) &&
        !GT_ISIBITSET(storeoffline->hasmatch,seqnum))
    {
      fprintf(stderr,"query " Formatuint64_t " refseq %lu: "
                     "online has match but offline not\n",
                     PRINTuint64_tcast(queryunit),seqnum);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    if (!GT_ISIBITSET(storeonline->hasmatch,seqnum) &&
        GT_ISIBITSET(storeoffline->hasmatch,seqnum))
    {
      fprintf(stderr,"query " Formatuint64_t " refseq %lu: "
                     "offline has match but online not\n",
                     PRINTuint64_tcast(queryunit),seqnum);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
#endif
    if (GT_ISIBITSET(storeonline->hasmatch,seqnum))
    {
      countmatchseq++;
    }
  }
  GT_CLEARBITTAB(storeonline->hasmatch,numofdbsequences);
  GT_CLEARBITTAB(storeoffline->hasmatch,numofdbsequences);
  printf("matching sequences: %lu\n",countmatchseq);
}

void gt_freestorematch(Storematchinfo *storematch)
{
  gt_free(storematch->hasmatch);
}

int gt_runidxlocali(const IdxlocaliOptions *idxlocalioptions,GtError *err)
{
  Genericindex *genericindex = NULL;
  bool haserr = false;
  GtLogger *logger;
  const GtEncseq *encseq = NULL;

  logger = gt_logger_new(idxlocalioptions->verbose,
                         GT_LOGGER_DEFLT_PREFIX, stdout);

  if (idxlocalioptions->doonline)
  {
    GtEncseqLoader *el;
    el = gt_encseq_loader_new();
    gt_encseq_loader_require_multiseq_support(el);
    gt_encseq_loader_drop_description_support(el);
    gt_encseq_loader_set_logger(el, logger);
    encseq = gt_encseq_loader_load(el, gt_str_get(idxlocalioptions->indexname),
                                   err);
    gt_encseq_loader_delete(el);
    if (encseq == NULL)
    {
      haserr = true;
    }
  } else
  {
    genericindex = genericindex_new(gt_str_get(idxlocalioptions->indexname),
                                    idxlocalioptions->withesa,
                                    idxlocalioptions->withesa ||
                                    idxlocalioptions->docompare,
                                    false,
                                    true,
                                    0,
                                    logger,
                                    err);
    if (genericindex == NULL)
    {
      haserr = true;
    } else
    {
      encseq = genericindex_getencseq(genericindex);
    }
  }
  if (!haserr)
  {
    GtSeqIterator *seqit;
    const GtUchar *query;
    unsigned long querylen;
    char *desc = NULL;
    int retval;
    Limdfsresources *limdfsresources = NULL;
    const AbstractDfstransformer *dfst;
    SWdpresource *swdpresource = NULL;
    Showmatchinfo showmatchinfo;
    ProcessIdxMatch processmatch;
    GtAlphabet *a;
    void *processmatchinfoonline, *processmatchinfooffline;
    Storematchinfo storeonline, storeoffline;

    a = gt_encseq_alphabet(encseq);
    if (idxlocalioptions->docompare)
    {
      processmatch = storematch;
      gt_initstorematch(&storeonline,encseq);
      gt_initstorematch(&storeoffline,encseq);
      processmatchinfoonline = &storeonline;
      processmatchinfooffline = &storeoffline;
    } else
    {
      processmatch = showmatch;
      showmatchinfo.encseq = encseq;
      showmatchinfo.characters = gt_alphabet_characters(a);
      showmatchinfo.wildcardshow = gt_alphabet_wildcard_show(a);
      showmatchinfo.showalignment = idxlocalioptions->showalignment;
      processmatchinfoonline = processmatchinfooffline = &showmatchinfo;
    }
    if (idxlocalioptions->doonline || idxlocalioptions->docompare)
    {
      swdpresource = gt_newSWdpresource(idxlocalioptions->matchscore,
                                     idxlocalioptions->mismatchscore,
                                     idxlocalioptions->gapextend,
                                     idxlocalioptions->threshold,
                                     idxlocalioptions->showalignment,
                                     processmatch,
                                     processmatchinfoonline);
    }
    dfst = gt_locali_AbstractDfstransformer();
    if (!idxlocalioptions->doonline || idxlocalioptions->docompare)
    {
      gt_assert(genericindex != NULL);
      limdfsresources = gt_newLimdfsresources(genericindex,
                                           true,
                                           0,
                                           0,    /* maxpathlength */
                                           true, /* keepexpandedonstack */
                                           processmatch,
                                           processmatchinfooffline,
                                           NULL, /* processresult */
                                           NULL, /* processresult info */
                                           dfst);
    }
    seqit = gt_seq_iterator_sequence_buffer_new(idxlocalioptions->queryfiles,
                                               err);
    if (!seqit)
      haserr = true;
    if (!haserr)
    {
      gt_seq_iterator_set_symbolmap(seqit, gt_alphabet_symbolmap(a));
      for (showmatchinfo.queryunit = 0; /* Nothing */;
           showmatchinfo.queryunit++)
      {
        retval = gt_seq_iterator_next(seqit,
                                     &query,
                                     &querylen,
                                     &desc,
                                     err);
        if (retval < 0)
        {
          haserr = true;
          break;
        }
        if (retval == 0)
        {
          break;
        }
        printf("process sequence " Formatuint64_t " of length %lu\n",
                PRINTuint64_tcast(showmatchinfo.queryunit),querylen);
        if (idxlocalioptions->doonline || idxlocalioptions->docompare)
        {
          gt_multiapplysmithwaterman(swdpresource,encseq,query,querylen);
        }
        if (!idxlocalioptions->doonline || idxlocalioptions->docompare)
        {
          gt_indexbasedlocali(limdfsresources,
                           idxlocalioptions->matchscore,
                           idxlocalioptions->mismatchscore,
                           idxlocalioptions->gapstart,
                           idxlocalioptions->gapextend,
                           idxlocalioptions->threshold,
                           query,
                           querylen,
                           dfst);
        }
        if (idxlocalioptions->docompare)
        {
          gt_checkandresetstorematch(showmatchinfo.queryunit,
                                  &storeonline,&storeoffline);
        }
      }
      if (limdfsresources != NULL)
      {
        gt_freeLimdfsresources(&limdfsresources,dfst);
      }
      if (swdpresource != NULL)
      {
        gt_freeSWdpresource(swdpresource);
        swdpresource = NULL;
      }
      gt_seq_iterator_delete(seqit);
    }
    if (idxlocalioptions->docompare)
    {
      gt_freestorematch(&storeonline);
      gt_freestorematch(&storeoffline);
    }
  }
  if (genericindex == NULL)
  {
    gt_encseq_delete((GtEncseq *) encseq);
    encseq = NULL;
  } else
  {
    genericindex_delete(genericindex);
  }
  gt_logger_delete(logger);
  logger = NULL;
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/idxlocali.h000066400000000000000000000027021211610345200200510ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#ifndef IDXLOCALI_H
#define IDXLOCALI_H

#include 
#include "core/str_array.h"
#include "core/str.h"
#include "core/option_api.h"
#include "core/error_api.h"

typedef struct
{
  GtStrArray *queryfiles;
  GtStr *indexname;
  GtOption *refoptionesaindex,
           *refoptionpckindex;
  bool withesa,
       verbose,
       showalignment,
       doonline,
       docompare;
  unsigned long threshold;
  long matchscore,
       mismatchscore,
       gapstart,
       gapextend;
} IdxlocaliOptions;

int gt_runidxlocali(const IdxlocaliOptions *idxlocalioptions,GtError *err);

#endif
genometools-1.5.1/src/match/idxlocalidp.c000066400000000000000000000621251211610345200203750ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma_api.h"
#include "core/types_api.h"
#include "core/chardef.h"
#include "core/unused_api.h"
#include "core/assert_api.h"
#include "core/ma_api.h"
#include "extended/alignment.h"
#include "absdfstrans-imp.h"
#include "idxlocalisw.h"
#include "idxlocalidp.h"

#define MINUSINFTY (-1L)

typedef struct
{
  unsigned long dbcurrent, dbprefixlen;
  unsigned long querypos, queryend;
  GtUchar *spaceGtUchardbsubstring;
  unsigned long allocatedGtUchardbsubstring;
  GtAlignment *alignment;
} LocaliTracebackstate;

struct Limdfsconstinfo
{
  Scorevalues scorevalues;
  const GtUchar *query;
  unsigned long maxcollen,
                querylength,
                threshold;
  LocaliTracebackstate tbs;
};

typedef enum
{
  Notraceback,
  Insertbit,
  Replacebit,
  Deletebit
} LocaliTracebit;

typedef struct
{
#undef AFFINE
#ifdef AFFINE
  Scoretype repcell,
            inscell,
            delcell;
#endif
  Scoretype bestcell;
  LocaliTracebit tracebit;
} LocaliMatrixvalue;

typedef struct
{
  LocaliMatrixvalue *colvalues;
  unsigned long lenval,
                pprefixlen,
                maxvalue;
} LocaliColumn;

typedef struct
{
  Limdfsstatus status;
  unsigned long qseqendpos;
  Scoretype alignmentscore;
} Idxlocaliresult;

#ifdef AFFINE
static inline Scoretype max2 (Scoretype a,Scoretype b)
{
  return (a < b) ? b : a;
}

static inline Scoretype max3 (Scoretype a,Scoretype b,Scoretype c)
{
  Scoretype temp;

  temp = (a < b) ? b : a;
  return (temp < c) ? c : temp;
}
#endif

#ifdef SKDEBUG
static void showscorecolumn(const LocaliColumn *column,
                            unsigned long querylength,
                            unsigned long currentdepth)
{
  gt_assert(column != NULL);
  printf("at depth %lu: ",currentdepth);
  if (column->colvalues == NULL)
  {
    gt_assert(column->lenval == 0);
    printf("empty column\n");
  } else
  {
    unsigned long idx;

    gt_assert(column->colvalues != NULL);
    for (idx = 0; idx <= querylength; idx++)
    {
      if (column->colvalues[idx].bestcell > 0)
      {
        printf("(%lu,%ld) ",idx,column->colvalues[idx].bestcell);
      }
    }
    printf("max=%lu\n",column->maxvalue);
  }
}

void locali_showLimdfsstate(const DECLAREPTRDFSSTATE(aliasstate),
                            unsigned long currentdepth,
                            const Limdfsconstinfo *lci)
{
  showscorecolumn((const LocaliColumn *) aliasstate,
                  lci->querylength,currentdepth);
}
#endif

#ifdef SKDEBUG
#define REALLOCMSG(COL)\
        printf("line %d: %salloc %lu entries",\
                __LINE__,(COL)->colvalues == NULL ? "m" : "re",\
                lci->maxcollen)

#define ATADDRESS(S,COL)\
        printf("%s at address %0X\n",S,(unsigned int) (COL)->colvalues)
#else
#define REALLOCMSG(COL) /* Nothing */
#define ATADDRESS(S,COL)  /* Nothing */
#endif

#define IDXLOCALIDP_UPDATEMAX(EXPR,BIT)\
        temp = EXPR;\
        if (temp > outcol->colvalues[i].bestcell)\
        {\
          outcol->colvalues[i].bestcell = temp;\
          outcol->colvalues[i].tracebit = BIT;\
        }

static void secondcolumn (const Limdfsconstinfo *lci,LocaliColumn *outcol,
                          GtUchar dbchar)
{
  unsigned long i;

  if (outcol->lenval < lci->maxcollen)
  {
    REALLOCMSG(outcol);
    outcol->colvalues = gt_realloc(outcol->colvalues,
                                   sizeof (LocaliMatrixvalue)
                                     * lci->maxcollen);
    outcol->lenval = lci->maxcollen;
    ATADDRESS("",outcol);
  }
#ifdef AFFINE
  outcol->colvalues[0].repcell = MINUSINFTY;
  outcol->colvalues[0].inscell = lci->scorevalues.gapstart +
                                 lci->scorevalues.gapextend;
  outcol->colvalues[0].delcell = MINUSINFTY;
#endif
  outcol->colvalues[0].bestcell = MINUSINFTY;
  outcol->colvalues[0].tracebit = Notraceback;
  outcol->maxvalue = 0;
  outcol->pprefixlen = 0;
  for (i = 1UL; i <= lci->querylength; i++)
  {
#ifdef AFFINE
    outcol->colvalues[i].delcell = MINUSINFTY;
    outcol->colvalues[i].inscell = MINUSINFTY;
    outcol->colvalues[i].repcell = REPLACEMENTSCORE(&lci->scorevalues,
                                                    dbchar,lci->query[i-1]);
    outcol->colvalues[i].bestcell = max2(outcol->colvalues[i].delcell,
                                         outcol->colvalues[i].repcell);
#else
    Scoretype temp;

    outcol->colvalues[i].bestcell = MINUSINFTY;
    outcol->colvalues[i].tracebit = Notraceback;
    if (outcol->colvalues[i-1].bestcell > 0)
    {
      IDXLOCALIDP_UPDATEMAX(outcol->colvalues[i-1].bestcell +
                lci->scorevalues.gapextend,Deletebit);
    }
    IDXLOCALIDP_UPDATEMAX(REPLACEMENTSCORE(&lci->scorevalues,
                               dbchar,lci->query[i-1]),Replacebit);
    IDXLOCALIDP_UPDATEMAX(lci->scorevalues.gapextend,Insertbit);
#endif
    if (outcol->colvalues[i].bestcell > 0 &&
        outcol->colvalues[i].bestcell > (Scoretype) outcol->maxvalue)
    {
      outcol->maxvalue = (unsigned long) outcol->colvalues[i].bestcell;
      outcol->pprefixlen = i;
    }
  }
}

static void nextcolumn (const Limdfsconstinfo *lci,
                        LocaliColumn *outcol,
                        const GtUchar dbchar,
                        const LocaliColumn *incol)
{
  unsigned long i;
#ifndef AFFINE
  Scoretype temp;
#endif

  gt_assert(outcol != incol);
  gt_assert(outcol->colvalues != incol->colvalues);
  gt_assert(incol->lenval >= lci->querylength+1);
  if (outcol->lenval < lci->querylength+1)
  {
    REALLOCMSG(outcol);
    outcol->colvalues = gt_realloc(outcol->colvalues,
                                   sizeof (LocaliMatrixvalue)
                                     * lci->maxcollen);
    outcol->lenval = lci->maxcollen;
    ATADDRESS("",outcol);
  }
  gt_assert(outcol->lenval >= lci->querylength+1);
#ifdef AFFINE
  outcol->colvalues[0].repcell = outcol->colvalues[0].delcell = MINUSINFTY;
  if (incol->colvalues[0].inscell > 0)
  {
    if (incol->colvalues[0].bestcell > 0)
    {
      outcol->colvalues[0].inscell
        = max2 (incol->colvalues[0].inscell + lci->scorevalues.gapextend,
                incol->colvalues[0].bestcell + lci->scorevalues.gapstart +
                                               lci->scorevalues.gapextend);
    } else
    {
      outcol->colvalues[0].inscell = incol->colvalues[0].inscell +
                                     lci->scorevalues.gapextend;
    }
  } else
  {
    if (incol->colvalues[0].bestcell > 0)
    {
      outcol->colvalues[0].inscell = incol->colvalues[0].bestcell +
                                     lci->scorevalues.gapstart +
                                     lci->scorevalues.gapextend;
    } else
    {
      outcol->colvalues[0].inscell = MINUSINFTY;
    }
  }
  outcol->colvalues[0].bestcell = max3 (outcol->colvalues[0].repcell,
                                        outcol->colvalues[0].inscell,
                                        outcol->colvalues[0].delcell);
#else
  outcol->colvalues[0].bestcell = MINUSINFTY;
  outcol->colvalues[0].tracebit = Notraceback;
#endif
  outcol->maxvalue = 0;
  outcol->pprefixlen = 0;
  for (i = 1UL; i <= lci->querylength; i++)
  {
#ifdef AFFINE
    if (incol->colvalues[i-1].bestcell > 0)
    {
      outcol->colvalues[i].repcell = incol->colvalues[i-1].bestcell +
                                     REPLACEMENTSCORE(&lci->scorevalues,
                                                      dbchar,lci->query[i-1]);
    } else
    {
      outcol->colvalues[i].repcell = MINUSINFTY;
    }
    if (incol->colvalues[i].inscell > 0)
    {
      if (incol->colvalues[i].bestcell > 0)
      {
        outcol->colvalues[i].inscell
          = max2 (incol->colvalues[i].inscell + lci->scorevalues.gapextend,
                  incol->colvalues[i].bestcell + lci->scorevalues.gapstart +
                                                 lci->scorevalues.gapextend);
      } else
      {
        outcol->colvalues[i].inscell = incol->colvalues[i].inscell +
                                       lci->scorevalues.gapextend;
      }
    } else
    {
      if (incol->colvalues[i].bestcell > 0)
      {
        outcol->colvalues[i].inscell = incol->colvalues[i].bestcell +
                                       lci->scorevalues.gapstart +
                                       lci->scorevalues.gapextend;
      } else
      {
        outcol->colvalues[i].inscell = MINUSINFTY;
      }
    }
    if (outcol->colvalues[i-1].delcell > 0)
    {
      if (outcol->colvalues[i-1].bestcell > 0)
      {
        outcol->colvalues[i].delcell
          = max2 (outcol->colvalues[i-1].delcell + lci->scorevalues.gapextend,
                  outcol->colvalues[i-1].bestcell + lci->scorevalues.gapstart +
                                                    lci->scorevalues.gapextend);
      } else
      {
        outcol->colvalues[i].delcell = outcol->colvalues[i-1].delcell +
                                       lci->scorevalues.gapextend;
      }
    } else
    {
      if (outcol->colvalues[i-1].bestcell > 0)
      {
        outcol->colvalues[i].delcell = outcol->colvalues[i-1].bestcell +
                                       lci->scorevalues.gapstart +
                                       lci->scorevalues.gapextend;
      } else
      {
        outcol->colvalues[i].delcell = MINUSINFTY;
      }
    }
    outcol->colvalues[i].bestcell = max3 (outcol->colvalues[i].repcell,
                                          outcol->colvalues[i].inscell,
                                          outcol->colvalues[i].delcell);
#else
    outcol->colvalues[i].bestcell = MINUSINFTY;
    outcol->colvalues[i].tracebit = Notraceback;
    if (outcol->colvalues[i-1].bestcell > 0)
    {
      IDXLOCALIDP_UPDATEMAX(outcol->colvalues[i-1].bestcell
                              + lci->scorevalues.gapextend,
                            Deletebit);
    }
    if (incol->colvalues[i-1].bestcell > 0)
    {
      IDXLOCALIDP_UPDATEMAX(incol->colvalues[i-1].bestcell +
                REPLACEMENTSCORE(&lci->scorevalues,
                                 dbchar,lci->query[i-1]),Replacebit);
    }
    if (incol->colvalues[i].bestcell > 0)
    {
      IDXLOCALIDP_UPDATEMAX(incol->colvalues[i].bestcell
                              + lci->scorevalues.gapextend,
                            Insertbit);
    }
#endif
    if (outcol->colvalues[i].bestcell > 0 &&
        outcol->colvalues[i].bestcell > (Scoretype) outcol->maxvalue)
    {
      outcol->maxvalue = (unsigned long) outcol->colvalues[i].bestcell;
      outcol->pprefixlen = i;
    }
  }
}

#ifdef AFFINE
static void inplacenextcolumn (const Limdfsconstinfo *lci,
                               const GtUchar dbchar,
                               LocaliColumn *column)
{
  unsigned long i;
  LocaliMatrixvalue nw, west;

  column->colvalues[0].repcell = column->colvalues[0].delcell = MINUSINFTY;
  if (column->colvalues[0].inscell > 0)
  {
    if (column->colvalues[0].bestcell > 0)
    {
      column->colvalues[0].inscell
        = max2 (column->colvalues[0].inscell + lci->scorevalues.gapextend,
                column->colvalues[0].bestcell + lci->scorevalues.gapstart +
                                                lci->scorevalues.gapextend);
    } else
    {
      column->colvalues[0].inscell
        = column->colvalues[0].inscell + lci->scorevalues.gapextend;
    }
  } else
  {
    if (column->colvalues[0].bestcell > 0)
    {
      column->colvalues[0].inscell = column->colvalues[0].bestcell +
                                     lci->scorevalues.gapstart +
                                     lci->scorevalues.gapextend;
    } else
    {
      column->colvalues[0].inscell = MINUSINFTY;
    }
  }
  column->colvalues[0].bestcell = max3 (column->colvalues[0].repcell,
                                        column->colvalues[0].inscell,
                                        column->colvalues[0].delcell);
  column->maxvalue = (unsigned long) max2(0,column->colvalues[0].bestcell);
  column->pprefixlen = 0;
  nw = column->colvalues[0];
  for (i = 1UL; i <= lci->querylength; i++)
  {
    west = column->colvalues[i];
    if (nw.bestcell > 0)
    {
      column->colvalues[i].repcell = nw.bestcell +
                                     REPLACEMENTSCORE(&lci->scorevalues,
                                                      dbchar,lci->query[i-1]);
    } else
    {
      column->colvalues[i].repcell = MINUSINFTY;
    }
    if (west.inscell > 0)
    {
      if (west.bestcell > 0)
      {
        column->colvalues[i].inscell
          = max2 (west.inscell + lci->scorevalues.gapextend,
                  west.bestcell + lci->scorevalues.gapstart
                                + lci->scorevalues.gapextend);
      } else
      {
        column->colvalues[i].inscell = west.inscell +
                                       lci->scorevalues.gapextend;
      }
    } else
    {
      if (west.bestcell > 0)
      {
        column->colvalues[i].inscell = west.bestcell +
                                       lci->scorevalues.gapstart +
                                       lci->scorevalues.gapextend;
      } else
      {
        column->colvalues[i].inscell = MINUSINFTY;
      }
    }
    if (column->colvalues[i-1].delcell > 0)
    {
      if (column->colvalues[i-1].bestcell > 0)
      {
        column->colvalues[i].delcell
          = max2 (column->colvalues[i-1].delcell + lci->scorevalues.gapextend,
                  column->colvalues[i-1].bestcell + lci->scorevalues.gapstart +
                                                    lci->scorevalues.gapextend);
      } else
      {
        column->colvalues[i].delcell = column->colvalues[i-1].delcell +
                                       lci->scorevalues.gapextend;
      }
    } else
    {
      if (column->colvalues[i-1].bestcell > 0)
      {
        column->colvalues[i].delcell = column->colvalues[i-1].bestcell +
                                       lci->scorevalues.gapstart +
                                       lci->scorevalues.gapextend;
      } else
      {
        column->colvalues[i].delcell = MINUSINFTY;
      }
    }
    nw = west;
    column->colvalues[i].bestcell = max3 (column->colvalues[i].repcell,
                                          column->colvalues[i].inscell,
                                          column->colvalues[i].delcell);
    if (column->colvalues[i].bestcell > 0 &&
        column->colvalues[i].bestcell > (Scoretype) column->maxvalue)
    {
      column->maxvalue = (unsigned long) column->colvalues[i].bestcell;
      column->pprefixlen = i;
    }
  }
}
#endif

static Limdfsconstinfo *locali_allocatedfsconstinfo (GT_UNUSED
                                                     unsigned int alphasize)
{
  Limdfsconstinfo *lci;

  lci = gt_malloc (sizeof (Limdfsconstinfo));
  lci->maxcollen = 0;
  lci->tbs.alignment = gt_alignment_new();
  lci->tbs.spaceGtUchardbsubstring = NULL;
  lci->tbs.allocatedGtUchardbsubstring = 0;
  return lci;
}

static void locali_initdfsconstinfo (Limdfsconstinfo *lci,
                                     unsigned int alphasize,...)
{
  va_list ap;

  va_start (ap, alphasize);
  lci->scorevalues.matchscore = va_arg (ap, Scoretype);
  lci->scorevalues.mismatchscore = va_arg (ap, Scoretype);
  lci->scorevalues.gapstart = va_arg (ap, Scoretype);
  lci->scorevalues.gapextend = va_arg (ap, Scoretype);
  lci->threshold = va_arg (ap, unsigned long);
  lci->query = va_arg (ap, const GtUchar *);
  lci->querylength = va_arg (ap, unsigned long);
  if (lci->maxcollen < lci->querylength + 1)
  {
    lci->maxcollen = lci->querylength+1;
  }
  va_end(ap);
}

static void locali_freedfsconstinfo (Limdfsconstinfo **lci)
{
  gt_alignment_delete((*lci)->tbs.alignment);
  (*lci)->tbs.alignment = NULL;
  gt_free((*lci)->tbs.spaceGtUchardbsubstring);
  (*lci)->tbs.spaceGtUchardbsubstring = NULL;
  gt_free (*lci);
  *lci = NULL;
}

static void locali_initrootLimdfsstate(DECLAREPTRDFSSTATE(aliasstate),
                                       Limdfsconstinfo *lci)
{
  LocaliColumn *column = (LocaliColumn *) aliasstate;

  if (column->lenval < lci->maxcollen)
  {
    REALLOCMSG(column);
    column->colvalues = gt_realloc(column->colvalues,
                                   sizeof (LocaliMatrixvalue)
                                      * lci->maxcollen);
    column->lenval = lci->maxcollen;
    ATADDRESS("",column);
  }
}

static void locali_initLimdfsstackelem (DECLAREPTRDFSSTATE (aliasstate))
{
  LocaliColumn *column = (LocaliColumn *) aliasstate;

  column->colvalues = NULL;
  column->lenval = 0;
}

static void locali_freeLimdfsstackelem (DECLAREPTRDFSSTATE (aliasstate))
{
  LocaliColumn *column = (LocaliColumn *) aliasstate;

  if (column ->colvalues != NULL)
  {
    ATADDRESS("free ",column);
    gt_free(column->colvalues);
    column->colvalues = NULL;
    column->lenval = 0;
  }
}

static void locali_copyLimdfsstate (DECLAREPTRDFSSTATE(deststate),
                                    const DECLAREPTRDFSSTATE(srcstate),
                                    Limdfsconstinfo *lci)
{
  LocaliColumn *destcol = (LocaliColumn *) deststate;
  const LocaliColumn *srccol = (const LocaliColumn *) srcstate;

  if (srccol->colvalues != NULL)
  {
    unsigned long idx;

    if (destcol->lenval < lci->maxcollen)
    {
      REALLOCMSG(destcol);
      destcol->colvalues = gt_realloc(destcol->colvalues,
                                      sizeof (LocaliMatrixvalue)
                                        * lci->maxcollen);
      destcol->lenval = lci->maxcollen;
      ATADDRESS("",destcol);
    }
#ifndef NDEBUG
    if (destcol->lenval < lci->querylength+1)
    {
      fprintf(stderr,"destcol->lenval = %lu < %lu lci->querylength+1\n",
                      destcol->lenval,lci->querylength+1);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    if (srccol->lenval < lci->querylength+1)
    {
      fprintf(stderr,"srccol->lenval = %lu < %lu lci->querylength+1\n",
                      srccol->lenval,lci->querylength+1);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
#endif
    for (idx = 0; idx<=lci->querylength; idx++)
    {
      destcol->colvalues[idx] = srccol->colvalues[idx];
    }
  }
  destcol->maxvalue = srccol->maxvalue;
  destcol->pprefixlen = srccol->pprefixlen;
}

static void locali_fullmatchLimdfsstate (Limdfsresult *limdfsresult,
                                         DECLAREPTRDFSSTATE(aliasstate),
                                         GT_UNUSED unsigned long leftbound,
                                         GT_UNUSED unsigned long rightbound,
                                         GT_UNUSED unsigned long width,
                                         GT_UNUSED unsigned long currentdepth,
                                         Limdfsconstinfo *lci)
{
  LocaliColumn *column = (LocaliColumn *) aliasstate;

  if (column->colvalues != NULL)
  {
    if (column->maxvalue >= lci->threshold)
    {
      limdfsresult->status = Limdfssuccess;
      limdfsresult->distance = column->maxvalue;
      limdfsresult->pprefixlen = column->pprefixlen;
    } else
    {
      if (column->maxvalue > 0)
      {
        limdfsresult->status = Limdfscontinue;
      } else
      {
        limdfsresult->status = Limdfsstop;
      }
    }
  } else
  {
    limdfsresult->status = Limdfscontinue;
  }
}

static void locali_nextLimdfsstate (const Limdfsconstinfo *lci,
                                    DECLAREPTRDFSSTATE (aliasoutcol),
                                    GT_UNUSED unsigned long currentdepth,
                                    GtUchar currentchar,
                                    const DECLAREPTRDFSSTATE (aliasincol))
{
  LocaliColumn *outcol = (LocaliColumn *) aliasoutcol;
  const LocaliColumn *incol = (const LocaliColumn *) aliasincol;

  if (currentdepth > 1UL)
  {
    nextcolumn (lci,outcol,currentchar,incol);
  } else
  {
    secondcolumn (lci, outcol, currentchar);
  }
}

#ifdef AFFINE
static void locali_inplacenextLimdfsstate (const Limdfsconstinfo *lci,
                                           DECLAREPTRDFSSTATE (aliasstate),
                                           GT_UNUSED unsigned long currentdepth,
                                           GtUchar currentchar)
{
  LocaliColumn *column = (LocaliColumn *) aliasstate;

  if (currentdepth > 1UL)
  {
    inplacenextcolumn (lci,currentchar,column);
  } else
  {
    secondcolumn (lci,column,currentchar);
  }
}
#endif

void gt_reinitLocaliTracebackstate(Limdfsconstinfo *lci,
                                unsigned long dbprefixlen,
                                unsigned long pprefixlen)
{
  LocaliTracebackstate *tbs = &lci->tbs;

  tbs->dbprefixlen = tbs->dbcurrent = dbprefixlen;
  tbs->queryend = tbs->querypos = pprefixlen;
  if (dbprefixlen > (unsigned long) tbs->allocatedGtUchardbsubstring)
  {
    tbs->spaceGtUchardbsubstring = gt_realloc(tbs->spaceGtUchardbsubstring,
                                            sizeof (GtUchar) * dbprefixlen);
  }
  gt_alignment_reset(tbs->alignment);
}

void gt_processelemLocaliTracebackstate(Limdfsconstinfo *lci,
                                     GtUchar currentchar,
                                     const void *aliasstate)
{
  LocaliTracebackstate *tbs = &lci->tbs;
  const LocaliColumn *column = (const LocaliColumn *) aliasstate;

  while (true)
  {
    /*
    printf(" coord(i=%lu,j=%lu) with ",tbs->querypos,
                                       (unsigned long) tbs->dbcurrent);
    printf("cellvalue=%ld, ",column->colvalues[tbs->querypos].bestcell);
    */
    switch (column->colvalues[tbs->querypos].tracebit)
    {
      case Insertbit:
        /* printf("insertbit\n"); */
        gt_alignment_add_insertion(tbs->alignment);
        gt_assert(tbs->dbcurrent > 0);
        tbs->dbcurrent--;
        tbs->spaceGtUchardbsubstring[tbs->dbcurrent] = currentchar;
        return;
      case Replacebit:
        /* printf("replacebit\n"); */
        gt_alignment_add_replacement(tbs->alignment);
        gt_assert(tbs->dbcurrent > 0);
        tbs->dbcurrent--;
        tbs->spaceGtUchardbsubstring[tbs->dbcurrent] = currentchar;
        gt_assert(tbs->querypos > 0);
        tbs->querypos--;
        return;
      case Deletebit:
        /* printf("deletebit\n"); */
        gt_alignment_add_deletion(tbs->alignment);
        gt_assert(tbs->querypos > 0);
        tbs->querypos--;
        break; /* stay in the same column => so next iteration */
      case Notraceback:
        fprintf(stderr,"tracebit = Notraceback not allowed\n");
        fprintf(stderr,"column->colvalues[tbs->querypos].bestcell=%ld\n",
                        column->colvalues[tbs->querypos].bestcell);
        exit(GT_EXIT_PROGRAMMING_ERROR);
      default:
        fprintf(stderr,"tracebit = %d not allowed\n",
                (int) column->colvalues[tbs->querypos].tracebit);
        exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  }
}

const void *gt_completealignmentfromLocaliTracebackstate(
                                        unsigned long *alignedquerylength,
                                        const Limdfsconstinfo *lci)
{
#ifndef NDEBUG
  Scoretype evalscore;
#endif
  const GtUchar *querysubstart;

#ifdef SKDEBUG
  gt_alignment_show_multieop_list(lci->tbs.alignment,stdout);
#endif
  gt_assert(lci->tbs.queryend >= lci->tbs.querypos);
  *alignedquerylength = lci->tbs.queryend - lci->tbs.querypos;
  querysubstart = lci->query + lci->tbs.querypos;
  gt_assert(querysubstart != NULL);
  gt_alignment_set_seqs(lci->tbs.alignment,
                        querysubstart,
                        *alignedquerylength,
                        lci->tbs.spaceGtUchardbsubstring,
                        (unsigned long) lci->tbs.dbprefixlen);
#ifndef NDEBUG
  evalscore = gt_alignment_eval_with_score(lci->tbs.alignment,
                                           lci->scorevalues.matchscore,
                                           lci->scorevalues.mismatchscore,
                                           lci->scorevalues.gapextend);
  if (evalscore < 0 || (unsigned long) evalscore < lci->threshold)
  {
    fprintf(stderr,"unexpected eval score %ld\n",evalscore);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
#endif
  return (const void *) lci->tbs.alignment;
}

const AbstractDfstransformer *gt_locali_AbstractDfstransformer (void)
{
  static const AbstractDfstransformer locali_adfst =
  {
    sizeof (LocaliColumn),
    locali_allocatedfsconstinfo,
    locali_initdfsconstinfo,
    NULL,
    locali_freedfsconstinfo,
    locali_initrootLimdfsstate,
    locali_initLimdfsstackelem,
    locali_freeLimdfsstackelem,
    locali_copyLimdfsstate,
    locali_fullmatchLimdfsstate,
    locali_nextLimdfsstate,
#ifdef AFFINE
    locali_inplacenextLimdfsstate,
#else
    NULL,
#endif
#ifdef SKDEBUG
    locali_showLimdfsstate
#endif /*  */
  };
  return &locali_adfst;
}
genometools-1.5.1/src/match/idxlocalidp.h000066400000000000000000000030701211610345200203740ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef IDXLOCALIDP_H
#define IDXLOCALIDP_H
#include "core/types_api.h"

#include "absdfstrans-def.h"

const AbstractDfstransformer *gt_locali_AbstractDfstransformer(void);

void gt_reinitLocaliTracebackstate(Limdfsconstinfo *lci,
                                unsigned long dbprefixlen,
                                unsigned long pprefixlen);

void gt_processelemLocaliTracebackstate(Limdfsconstinfo *lci,
                                     GtUchar currentchar,
                                     const void *aliasstate);

const void *gt_completealignmentfromLocaliTracebackstate(
                                      unsigned long *alignedquerylength,
                                      const Limdfsconstinfo *lci);

#endif
genometools-1.5.1/src/match/idxlocalisw.c000066400000000000000000000375041211610345200204260ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "core/encseq.h"
#include "core/ma_api.h"
#include "core/format64.h"
#include "extended/alignment.h"
#include "idxlocalisw.h"
#include "procmatch.h"

#define REPLACEMENTBIT   ((GtUchar) 1)
#define DELETIONBIT      (((GtUchar) 1) << 1)
#define INSERTIONBIT     (((GtUchar) 1) << 2)

typedef struct
{
  unsigned long umax,
                vmax;
} Maxscorecoord;

typedef GtUchar Retracebits;

static Scoretype swlocalsimilarityscore(Scoretype *scol,
                                        Maxscorecoord *maxpair,
                                        const Scorevalues *scorevalues,
                                        const GtUchar *useq,
                                        unsigned long ulen,
                                        const GtEncseq *vencseq,
                                        unsigned long startpos,
                                        unsigned long endpos)
{
  Scoretype val, we, nw, *scolptr, maximalscore = 0;
  const GtUchar *uptr;
  GtUchar vcurrent;
  unsigned long j;

  maxpair->umax = maxpair->vmax = 0;
  for (scolptr = scol; scolptr <= scol + ulen; scolptr++)
  {
    *scolptr = 0;
  }
  for (j = startpos; j < endpos; j++)
  {
    nw = 0;
    vcurrent = gt_encseq_get_encoded_char(vencseq,j,
                                                   GT_READMODE_FORWARD);
    gt_assert(vcurrent != (GtUchar) SEPARATOR);
    for (scolptr = scol+1, uptr = useq; uptr < useq + ulen; scolptr++, uptr++)
    {
      gt_assert(*uptr != (GtUchar) SEPARATOR);
      we = *scolptr;
      *scolptr = *(scolptr-1) + scorevalues->gapextend;
      if ((val = nw + REPLACEMENTSCORE(scorevalues,*uptr,vcurrent)) > *scolptr)
      {
        *scolptr = val;
      }
      if ((val = we + scorevalues->gapextend) > *scolptr)
      {
        *scolptr = val;
      }
      if (*scolptr < 0)
      {
        *scolptr = 0;
      } else
      {
        if (*scolptr > maximalscore)
        {
          maximalscore = *scolptr;
          maxpair->umax = (unsigned long) (uptr - useq + 1);
          maxpair->vmax = (unsigned long) (j - startpos + 1);
        }
      }
      nw = we;
    }
  }
  return maximalscore;
}

typedef struct
{
  Scoretype similarity;
  unsigned long lu;
  unsigned long lv;
} DPpoint;

typedef struct
{
  unsigned long len1,
                start1;
  unsigned long start2, len2;
  Scoretype similarity;
} DPregion;

static void swlocalsimilarityregion(DPpoint *scol,
                                    DPregion *maxentry,
                                    const Scorevalues *scorevalues,
                                    const GtUchar *useq,
                                    unsigned long ulen,
                                    const GtEncseq *vencseq,
                                    unsigned long startpos,
                                    unsigned long endpos)
{
  Scoretype val;
  DPpoint *scolptr, we, nw;
  const GtUchar *uptr;
  GtUchar vcurrent;
  unsigned long j;

  maxentry->similarity = 0;
  maxentry->len1 = 0;
  maxentry->len2 = 0;
  maxentry->start1 = 0;
  maxentry->start2 = 0;
  for (scolptr = scol; scolptr <= scol + ulen; scolptr++)
  {
    scolptr->similarity = 0;
    scolptr->lu = 0;
    scolptr->lv = 0;
  }
  for (j = startpos; j < endpos; j++)
  {
    vcurrent = gt_encseq_get_encoded_char(vencseq,j,
                                                   GT_READMODE_FORWARD);
    gt_assert(vcurrent != (GtUchar) SEPARATOR);
    nw = *scol;
    for (scolptr = scol+1, uptr = useq; uptr < useq + ulen; scolptr++, uptr++)
    {
      gt_assert(*uptr != (GtUchar) SEPARATOR);
      we = *scolptr;
      scolptr->similarity = (scolptr-1)->similarity + scorevalues->gapextend;
      scolptr->lu = (scolptr-1)->lu + 1;
      scolptr->lv = (scolptr-1)->lv;
      if ((val = nw.similarity + REPLACEMENTSCORE(scorevalues,*uptr,vcurrent))
               > scolptr->similarity)
      {
        scolptr->similarity = val;
        scolptr->lu = nw.lu + 1;
        scolptr->lv = nw.lv + 1;
      }
      if ((val = we.similarity + scorevalues->gapextend)
               > scolptr->similarity)
      {
        scolptr->similarity = val;
        scolptr->lu = we.lu;
        scolptr->lv = we.lv + 1;
      }
      if (scolptr->similarity < 0)
      {
        scolptr->similarity = 0;
        scolptr->lu = 0;
        scolptr->lv = 0;
      } else
      {
        if (scolptr->similarity > maxentry->similarity)
        {
          maxentry->similarity = scolptr->similarity;
          maxentry->len1 = scolptr->lu;
          maxentry->len2 = scolptr->lv;
          maxentry->start1 = (unsigned long) (uptr - useq) - scolptr->lu + 1;
          maxentry->start2 = (j - startpos) - scolptr->lv + 1;
        }
      }
      nw = we;
    }
  }
}

static void swmaximalDPedges(Retracebits *edges,
                             Scoretype *scol,
                             const Scorevalues *scorevalues,
                             const GtUchar *useq,
                             unsigned long ulen,
                             const GtEncseq *vencseq,
                             unsigned long startpos,
                             unsigned long endpos)
{
  Scoretype val, we, nw, *scolptr;
  const GtUchar *uptr;
  GtUchar vcurrent;
  unsigned long j;
  Retracebits *eptr;

  eptr = edges;
  *eptr = 0;
  for (*scol = 0, scolptr = scol+1, uptr = useq, eptr++; uptr < useq + ulen;
       scolptr++, uptr++, eptr++)
  {
    *scolptr = *(scolptr-1) + scorevalues->gapextend;
    *eptr = DELETIONBIT;
  }
  for (j = startpos; j < endpos; j++)
  {
    vcurrent = gt_encseq_get_encoded_char(vencseq,j,
                                                   GT_READMODE_FORWARD);
    gt_assert(vcurrent != (GtUchar) SEPARATOR);
    nw = *scol;
    *scol = nw + scorevalues->gapextend;
    *eptr = INSERTIONBIT;
    for (scolptr = scol+1, uptr = useq, eptr++; uptr < useq + ulen;
         scolptr++, uptr++, eptr++)
    {
      gt_assert(*uptr != (GtUchar) SEPARATOR);
      we = *scolptr;
      *scolptr = *(scolptr-1) + scorevalues->gapextend;
      *eptr = DELETIONBIT;
      if ((val = nw + REPLACEMENTSCORE(scorevalues,*uptr,vcurrent))
               >= *scolptr)
      {
        if (val == *scolptr)
        {
          *eptr = *eptr | REPLACEMENTBIT;
        } else
        {
          *eptr = REPLACEMENTBIT;
        }
        *scolptr = val;
      }
      if ((val = we + scorevalues->gapextend) >= *scolptr)
      {
        if (val == *scolptr)
        {
          *eptr = *eptr | INSERTIONBIT;
        } else
        {
          *eptr = INSERTIONBIT;
        }
        *scolptr = val;
      }
      nw = we;
    }
  }
}

static void swtracebackDPedges(GtAlignment *alignment,
                               unsigned long ulen,
                               const GtEncseq *encseq,
                               unsigned long vlen,
                               GtUchar *dbsubstring,
                               unsigned long startpos,
                               const Retracebits *edges)
{
  const Retracebits *eptr = edges + (ulen+1) * (vlen+1) - 1;

  while (true)
  {
    if (*eptr & DELETIONBIT)
    {
      gt_alignment_add_deletion(alignment);
      eptr--;
    } else
    {
      if (*eptr & REPLACEMENTBIT)
      {
        gt_alignment_add_replacement(alignment);
        eptr -= (ulen+2);
      } else
      {
        if (*eptr & INSERTIONBIT)
        {
          gt_alignment_add_insertion(alignment);
          eptr -= (ulen+1);
        } else
        {
          break;
        }
      }
      gt_assert(vlen > 0);
      vlen--;
      dbsubstring[vlen] = gt_encseq_get_encoded_char(encseq,
                                                           startpos + vlen,
                                                           GT_READMODE_FORWARD);
    }
  }
}

static void swproducealignment(GtAlignment *alignment,
                               GtUchar *dbsubstring,
                               Retracebits *edges,
                               Scoretype *scol,
                               const Scorevalues *scorevalues,
                               GT_UNUSED unsigned long scorethreshold,
                               const GtUchar *useq,
                               unsigned long ulen,
                               const GtEncseq *vencseq,
                               unsigned long startpos,
                               unsigned long endpos)
{
  unsigned long vlen = endpos - startpos;

  swmaximalDPedges(edges,scol,scorevalues,useq,ulen,vencseq,startpos,endpos);
  swtracebackDPedges(alignment,ulen,vencseq,vlen,dbsubstring,startpos,edges);
  gt_alignment_set_seqs(alignment,useq,ulen,dbsubstring,(unsigned long) vlen);
#ifndef NDEBUG
  {
    Scoretype evalscore;

    evalscore = gt_alignment_eval_with_score(alignment,
                                             scorevalues->matchscore,
                                             scorevalues->mismatchscore,
                                             scorevalues->gapextend);
    if (evalscore < 0 || (unsigned long) evalscore < scorethreshold)
    {
      fprintf(stderr,"unexpected eval score %ld\n",evalscore);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  }
#endif
}

struct SWdpresource
{
  bool showalignment;
  GtAlignment *alignment;
  Scorevalues scorevalues;
  Scoretype *swcol;
  unsigned long scorethreshold;
  DPpoint *swentrycol;
  GtUchar *dbsubstring;
  unsigned long allocatedswcol, allocatedmaxedges, allocateddbsubstring;
  Retracebits *maxedges;
  ProcessIdxMatch processmatch;
  void *processmatchinfo;
};

static void applysmithwaterman(SWdpresource *dpresource,
                               const GtEncseq *encseq,
                               unsigned long encsequnit,
                               unsigned long startpos,
                               unsigned long endpos,
                               const GtUchar *query,
                               unsigned long querylen)
{
  Scoretype score;
  Maxscorecoord maxpair;
  DPregion maxentry;

  if (dpresource->allocatedswcol < querylen + 1)
  {
    dpresource->allocatedswcol = querylen + 1;
    dpresource->swcol = gt_realloc(dpresource->swcol,
                                   sizeof *dpresource->swcol
                                   * dpresource->allocatedswcol);
    dpresource->swentrycol = gt_realloc(dpresource->swentrycol,
                                        sizeof *dpresource->swentrycol
                                        * dpresource->allocatedswcol);
  }
  score = swlocalsimilarityscore(dpresource->swcol,&maxpair,
                                 &dpresource->scorevalues,
                                 query,querylen,encseq,startpos,endpos);
  if (score >= (Scoretype) dpresource->scorethreshold)
  {
    GtIdxMatch match;

    swlocalsimilarityregion(dpresource->swentrycol,
                            &maxentry,
                            &dpresource->scorevalues,
                            query,maxpair.umax,
                            encseq,startpos,startpos + maxpair.vmax);
    gt_assert(maxentry.similarity == score);
    match.dbabsolute = false;
    match.dbstartpos = maxentry.start2;
    match.dblen = maxentry.len2;
    match.dbseqnum = encsequnit;
    match.querystartpos = maxentry.start1;
    match.querylen = maxentry.len1;
    gt_assert(maxentry.similarity >= 0);
    match.distance = (unsigned long) maxentry.similarity;
    if (dpresource->showalignment)
    {
      if (dpresource->allocatedmaxedges <
          (maxentry.len1 + 1) * (maxentry.len2 + 1))
      {
        dpresource->allocatedmaxedges
          = (maxentry.len1 + 1) * (maxentry.len2 + 1);
        dpresource->maxedges
          = gt_realloc(dpresource->maxedges,
                       sizeof *dpresource->maxedges
                       * dpresource->allocatedmaxedges);
      }
      gt_alignment_reset(dpresource->alignment);
      if (dpresource->allocateddbsubstring < (unsigned long) maxentry.len2)
      {
        dpresource->allocateddbsubstring = (unsigned long) maxentry.len2;
        dpresource->dbsubstring
          = gt_realloc(dpresource->dbsubstring,
                       sizeof *dpresource->dbsubstring
                       * dpresource->allocateddbsubstring);
      }
      swproducealignment(dpresource->alignment,
                         dpresource->dbsubstring,
                         dpresource->maxedges,
                         dpresource->swcol,
                         &dpresource->scorevalues,
                         dpresource->scorethreshold,
                         query + maxentry.start1,
                         maxentry.len1,
                         encseq,
                         startpos + maxentry.start2,
                         startpos + maxentry.start2 + maxentry.len2);
      match.alignment = dpresource->alignment;
      match.dbsubstring = dpresource->dbsubstring;
    } else
    {
      match.dbsubstring = NULL;
      match.alignment = NULL;
    }
    dpresource->processmatch(dpresource->processmatchinfo,&match);
  }
}

void gt_multiapplysmithwaterman(SWdpresource *dpresource,
                             const GtEncseq *encseq,
                             const GtUchar *query,
                             unsigned long querylen)
{
  unsigned long seqnum,
                seqstartpos,
                seqlength,
                numofdbsequences = gt_encseq_num_of_sequences(encseq);

  for (seqnum = 0; seqnum < numofdbsequences; seqnum++)
  {
    seqstartpos = gt_encseq_seqstartpos(encseq, seqnum);
    seqlength = gt_encseq_seqlength(encseq, seqnum);
    applysmithwaterman(dpresource,
                       encseq,
                       seqnum,
                       seqstartpos,
                       seqstartpos + seqlength,
                       query,
                       querylen);
  }
}

SWdpresource *gt_newSWdpresource(Scoretype matchscore,
                              Scoretype mismatchscore,
                              Scoretype gapextend,
                              unsigned long scorethreshold,
                              bool showalignment,
                              ProcessIdxMatch processmatch,
                              void *processmatchinfo)
{
  SWdpresource *swdpresource;

  swdpresource = gt_malloc(sizeof *swdpresource);
  swdpresource->showalignment = showalignment;
  swdpresource->scorevalues.matchscore = matchscore;
  swdpresource->scorevalues.mismatchscore = mismatchscore;
  swdpresource->scorevalues.gapextend = gapextend;
  swdpresource->scorethreshold = scorethreshold;
  swdpresource->alignment = gt_alignment_new();
  swdpresource->swcol = NULL;
  swdpresource->swentrycol = NULL;
  swdpresource->maxedges = NULL;
  swdpresource->allocatedswcol = 0;
  swdpresource->allocatedmaxedges = 0;
  swdpresource->processmatch = processmatch;
  swdpresource->processmatchinfo = processmatchinfo;
  swdpresource->dbsubstring = NULL;
  swdpresource->allocateddbsubstring = 0;
  return swdpresource;
}

void gt_freeSWdpresource(SWdpresource *swdpresource)
{
  gt_alignment_delete(swdpresource->alignment);
  swdpresource->alignment = NULL;
  gt_free(swdpresource->swcol);
  gt_free(swdpresource->swentrycol);
  gt_free(swdpresource->maxedges);
  gt_free(swdpresource->dbsubstring);
  swdpresource->allocatedswcol = 0;
  swdpresource->allocatedmaxedges = 0;
  gt_free(swdpresource);
}
genometools-1.5.1/src/match/idxlocalisw.h000066400000000000000000000040751211610345200204300ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef IDXLOCALISW_H
#define IDXLOCALISW_H
#include 
#include "core/encseq.h"
#include "procmatch.h"

typedef long Scoretype;

typedef struct
{
  Scoretype matchscore,   /* must be positive */
            mismatchscore,/* must be negative */
            gapstart,     /* must be negative */
            gapextend;    /* must be negative */
} Scorevalues;

#define REPLACEMENTSCORE(SV,A,B) (((A) != (B) || ISSPECIAL(A))\
                                   ? (SV)->mismatchscore\
                                   : (SV)->matchscore)

typedef struct SWdpresource SWdpresource;

SWdpresource *gt_newSWdpresource(Scoretype matchscore,
                              Scoretype mismatchscore,
                              Scoretype gapextend,
                              unsigned long scorethreshold,
                              bool showalignment,
                              ProcessIdxMatch processmatch,
                              void *processmatchinfo);

void gt_multiapplysmithwaterman(SWdpresource *dpresource,
                             const GtEncseq *encseq,
                             const GtUchar *query,
                             unsigned long querylen);

void gt_freeSWdpresource(SWdpresource *swdpresource);

#endif
genometools-1.5.1/src/match/index_options.c000066400000000000000000000547471211610345200207760ustar00rootroot00000000000000/*
  Copyright (c) 2007      Stefan Kurtz 
  Copyright (c)      2010 Sascha Steinbiss 
  Copyright (c)      2012 Dirk Willrodt 
  Copyright (c) 2007-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 

#include "core/basename_api.h"
#include "core/encseq_options.h"
#include "core/error.h"
#include "core/grep_api.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "core/option_api.h"
#include "core/spacecalc.h"
#include "core/str.h"
#include "core/str_array.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#ifndef S_SPLINT_S /* splint reports too many errors for the following */
#include "match/eis-bwtseq-param.h"
#endif
#include "match/index_options.h"

typedef enum {
  GT_INDEX_OPTIONS_UNDEFINED,
  GT_INDEX_OPTIONS_ESA,
  GT_INDEX_OPTIONS_PACKED
} GtIndexOptionsIndexType;

struct GtIndexOptions
{
  unsigned int numofparts,
               prefixlength;
  unsigned long maximumspace;
  GtStrArray *algbounds;
  GtReadmode readmode;
  bool outsuftab,
       outlcptab,
       outbwttab,
       outbcktab,
       outkystab,
       outkyssort,
       lcpdist,
       swallow_tail;
  GtStr *kysargumentstring,
        *indexname,
        *dir,
        *memlimit;
  Sfxstrategy sfxstrategy;
  GtEncseqOptions *encopts;
  GtIndexOptionsIndexType type;
  GtOption *option,
           *optionoutsuftab,
           *optionoutlcptab,
           *optionoutbwttab,
           *optionoutbcktab,
           *optionprefixlength,
           *optioncmpcharbychar,
           *optionnoshortreadsort,
           *optionspmopt,
           *optionstorespecialcodes,
           *optionmaxwidthrealmedian,
           *optionalgbounds,
           *optionparts,
           *optionmemlimit,
           *optiondifferencecover,
           *optionuserdefinedsortmaxdepth,
           *optionkys;
#ifndef S_SPLINT_S /* splint reports too many errors for the following and so
                      we exclude it */
  struct bwtOptions bwtIdxParams;
#endif
};

static GtIndexOptions* gt_index_options_new(void)
{
  GtIndexOptions *oi = gt_malloc(sizeof *oi);
  oi->algbounds = gt_str_array_new();
  oi->dir = gt_str_new_cstr("fwd");
  oi->indexname = NULL;
  oi->kysargumentstring = gt_str_new();
  oi->lcpdist = false;
  oi->maximumspace = 0UL; /* in bytes */
  oi->memlimit = gt_str_new();
  oi->numofparts = 1U;
  oi->option = NULL;
  oi->optionalgbounds = NULL;
  oi->optioncmpcharbychar = NULL;
  oi->optiondifferencecover = NULL;
  oi->optionmaxwidthrealmedian = NULL;
  oi->optionmemlimit = NULL;
  oi->optionoutbcktab = NULL;
  oi->optionoutbwttab = NULL;
  oi->optionoutlcptab = NULL;
  oi->optionoutsuftab = NULL;
  oi->optionparts = NULL;
  oi->optionprefixlength = NULL;
  oi->optionspmopt = NULL;
  oi->optionstorespecialcodes = NULL;
  oi->outbcktab = false;
  oi->outbwttab = false;
  oi->outkyssort = false;
  oi->outkystab = false;
  oi->outlcptab = false;
  oi->outsuftab = false; /* only defined for GT_INDEX_OPTIONS_ESA */
  oi->prefixlength = GT_PREFIXLENGTH_AUTOMATIC;
  oi->swallow_tail = false;
  oi->type = GT_INDEX_OPTIONS_UNDEFINED;
  return oi;
}

#define GT_IDXOPTS_READMAXBOUND(COMP,IDX)\
        if (!haserr)\
        {\
          arg = gt_str_array_get(algbounds, IDX);\
          if (sscanf(arg,"%ld", &readint) != 1 || readint <= 0)\
          {\
            gt_error_set(err,"option -algbds: all arguments must be positive " \
                             "numbers");\
            haserr = true;\
          }\
          sfxstrategy->COMP = (unsigned long) readint;\
        }

int gt_parse_algbounds(Sfxstrategy *sfxstrategy,
                       const GtStrArray *algbounds,
                       GtError *err)
{
  bool haserr = false;
  const char *arg;
  long readint;

  if (gt_str_array_size(algbounds) != 3UL)
  {
    gt_error_set(err,"option -algbds must have exactly 3 arguments");
    haserr = true;
  }
  GT_IDXOPTS_READMAXBOUND(maxinsertionsort, 0);
  GT_IDXOPTS_READMAXBOUND(maxbltriesort, 1UL);
  if (sfxstrategy->maxinsertionsort > sfxstrategy->maxbltriesort)
  {
    gt_error_set(err,"first argument of option -algbds must not be larger "
                     "than second argument");
    haserr = true;
  }
  GT_IDXOPTS_READMAXBOUND(maxcountingsort, 2UL);
  if (sfxstrategy->maxbltriesort > sfxstrategy->maxcountingsort)
  {
    gt_error_set(err,"second argument of option -algbds must not be larger "
                     "than third argument");
    haserr = true;
  }
  return haserr ? -1 : 0;
}

static int gt_index_options_check_set_create_opts(void *oip, GtError *err)
{
  int had_err = 0;
  GtIndexOptions *oi = (GtIndexOptions*) oip;
  gt_assert(oi != NULL && oi->type != GT_INDEX_OPTIONS_UNDEFINED);
  gt_error_check(err);
  /* readmode needs to be initialized to fwd */
  oi->readmode = (GtReadmode) 0;
  if (!had_err)
  {
    if (gt_option_is_set(oi->optionalgbounds))
    {
      if (gt_parse_algbounds(&oi->sfxstrategy,oi->algbounds,err) != 0)
      {
        had_err = -1;
      }
    } else
    {
      oi->sfxstrategy.maxinsertionsort = MAXINSERTIONSORTDEFAULT;
      oi->sfxstrategy.maxbltriesort = MAXBLTRIESORTDEFAULT;
      oi->sfxstrategy.maxcountingsort = MAXCOUNTINGSORTDEFAULT;
    }
  }
  if (!had_err && oi->sfxstrategy.kmerswithencseqreader &&
      oi->sfxstrategy.spmopt_minlength > 0)
  {
    gt_error_set(err,"options -spmopt  and -kmerswithencseqreader are "
                     "not compatible");
    had_err = -1;
  }
  if (!had_err
        && oi->optionmemlimit != NULL
        && gt_option_is_set(oi->optionmemlimit))
  {
    had_err = gt_option_parse_spacespec(&oi->maximumspace,"memlimit",
                                        oi->memlimit,err);
  }
  if (!had_err)
  {
    if (oi->sfxstrategy.maxinsertionsort > oi->sfxstrategy.maxbltriesort)
    {
      gt_error_set(err,"first argument of option -algbds must not be larger "
                       "than second argument");
      had_err = -1;
    } else
    {
      if (oi->sfxstrategy.maxbltriesort > oi->sfxstrategy.maxcountingsort)
      {
        gt_error_set(err,"second argument of option -algbds must not be larger "
                         "than third argument");
        had_err = -1;
      }
    }
  }
  return had_err;
}

static int gt_index_options_check_set_out_opts(void *oip, GtError *err)
{
  int had_err = 0;
  GtIndexOptions *oi = (GtIndexOptions*) oip;
  gt_assert(oi != NULL && oi->type != GT_INDEX_OPTIONS_UNDEFINED);
  gt_error_check(err);

  if (!had_err) {
    int retval;
    retval = gt_readmode_parse(gt_str_get(oi->dir), err);
    if (retval < 0) {
      had_err = -1;
    } else {
      oi->readmode = (GtReadmode) retval;
      if (oi->type == GT_INDEX_OPTIONS_PACKED
            && (oi->readmode == GT_READMODE_COMPL
                  || oi->readmode == GT_READMODE_REVCOMPL)) {
        gt_error_set(err,"construction of packed index not possible for "
                         "complemented and for reverse complemented sequences");
        had_err = -1;
      }
    }
  }
  if (!had_err && oi->type == GT_INDEX_OPTIONS_PACKED) {
#ifndef S_SPLINT_S
    gt_computePackedIndexDefaults(&oi->bwtIdxParams, BWTBaseFeatures);
#endif
  }
  if (!had_err && gt_option_is_set(oi->optionkys)) {
    oi->outkystab = true;
    if (strcmp(gt_str_get(oi->kysargumentstring), "sort") == 0) {
      oi->outkyssort = true;
    } else {
      if (strcmp(gt_str_get(oi->kysargumentstring),"nosort") != 0) {
        gt_error_set(err,"illegal argument to option -kys: either use no "
                         "argument or argument \"sort\"");
        had_err = -1;
      }
    }
  }

  return had_err;
}

static GtIndexOptions*
gt_index_options_register_generic_output(GtOptionParser *op,
                                         GtIndexOptions *idxo,
                                         GtStr *indexname,
                                         GtEncseqOptions *encopts)
{
  gt_assert(idxo != NULL);
  gt_assert(op != NULL && idxo->type != GT_INDEX_OPTIONS_UNDEFINED &&
            encopts != NULL);
  idxo->encopts = encopts;
  idxo->indexname = indexname != NULL ? gt_str_ref(indexname) : NULL;
  idxo->optionkys = gt_option_new_string("kys",
                                   "output/sort according to keys of the form "
                                   "|key| in fasta header",
                                   idxo->kysargumentstring,
                                   "nosort");
  gt_option_argument_is_optional(idxo->optionkys);
  gt_option_imply(idxo->optionkys, gt_encseq_options_sds_option(idxo->encopts));
  gt_option_parser_add_option(op, idxo->optionkys);

  gt_encseq_options_add_readmode_option(op, idxo->dir);

  if (idxo->type == GT_INDEX_OPTIONS_ESA)
  {
    idxo->optionoutsuftab = gt_option_new_bool("suf",
                                   "output suffix array (suftab) to file",
                                   &idxo->outsuftab,
                                   false);
    gt_option_parser_add_option(op, idxo->optionoutsuftab);

    idxo->optionoutlcptab = gt_option_new_bool("lcp",
                                   "output lcp table (lcptab) to file",
                                   &idxo->outlcptab,
                                   false);
    gt_option_parser_add_option(op, idxo->optionoutlcptab);

    idxo->option = gt_option_new_bool("lcpdist",
                              "output distributions of values in lcptab",
                              &idxo->lcpdist,
                              false);
    gt_option_is_extended_option(idxo->option);
    gt_option_imply(idxo->option, idxo->optionoutlcptab);
    gt_option_parser_add_option(op, idxo->option);

    idxo->option = gt_option_new_bool("swallow-tail",
                              "swallow the tail of the suffix array and lcptab",
                              &idxo->swallow_tail,
                              false);
    gt_option_is_development_option(idxo->option);
    gt_option_parser_add_option(op, idxo->option);

    idxo->optionoutbwttab = gt_option_new_bool("bwt",
                                   "output Burrows-Wheeler Transformation "
                                   "(bwttab) to file",
                                   &idxo->outbwttab,
                                   false);
    gt_option_exclude(idxo->optionspmopt, idxo->optionoutbwttab);
    gt_option_parser_add_option(op, idxo->optionoutbwttab);

    idxo->optionoutbcktab = gt_option_new_bool("bck",
                                "output bucket table to file",
                                &idxo->outbcktab,
                                false);
    gt_option_parser_add_option(op, idxo->optionoutbcktab);
  } else {
    idxo->optionoutsuftab
      = idxo->optionoutlcptab = idxo->optionoutbwttab = NULL;
    idxo->sfxstrategy.spmopt_minlength = 0;
#ifndef S_SPLINT_S
    gt_registerPackedIndexOptions(op,
                                  &idxo->bwtIdxParams,
                                  BWTDEFOPT_CONSTRUCTION,
                                  idxo->indexname);
#endif
  }

  gt_option_parser_register_hook(op, gt_index_options_check_set_out_opts, idxo);

  return idxo;
}

static GtIndexOptions* gt_index_options_register_generic_create(
                                                      GtOptionParser *op,
                                                      GtIndexOptionsIndexType t)
{
  GtIndexOptions *idxo;
  gt_assert(op != NULL && t != GT_INDEX_OPTIONS_UNDEFINED);
  idxo = gt_index_options_new();
  idxo->type = t;
  idxo->optionprefixlength = gt_option_new_uint_min("pl",
                                    "specify prefix length for bucket sort\n"
                                    "recommendation: use without argument;\n"
                                    "then a reasonable prefix length is "
                                    "automatically determined.",
                                    &idxo->prefixlength,
                                    GT_PREFIXLENGTH_AUTOMATIC,
                                    1U);
  gt_option_argument_is_optional(idxo->optionprefixlength);
  gt_option_parser_add_option(op, idxo->optionprefixlength);

  idxo->optionuserdefinedsortmaxdepth
    = gt_option_new_uint_min("sortmaxdepth","sort only up to the given depth.",
                             &idxo->sfxstrategy.userdefinedsortmaxdepth,
                             0,
                             1U);
  gt_option_parser_add_option(op, idxo->optionuserdefinedsortmaxdepth);
  gt_option_is_development_option(idxo->optionuserdefinedsortmaxdepth);

  idxo->optiondifferencecover = gt_option_new_uint_min("dc",
                                    "specify difference cover value",
                                    &idxo->sfxstrategy.differencecover,
                                    0,
                                    4U);
  gt_option_parser_add_option(op, idxo->optiondifferencecover);
  gt_option_exclude(idxo->optionuserdefinedsortmaxdepth,
                    idxo->optiondifferencecover);

  idxo->optioncmpcharbychar = gt_option_new_bool("cmpcharbychar",
                                           "compare suffixes character "
                                           "by character",
                                           &idxo->sfxstrategy.cmpcharbychar,
                                           false);
  gt_option_is_development_option(idxo->optioncmpcharbychar);
  gt_option_parser_add_option(op, idxo->optioncmpcharbychar);

  idxo->optionnoshortreadsort = gt_option_new_bool("noshortreadsort",
                                           "do not use short read sort",
                                           &idxo->sfxstrategy.noshortreadsort,
                                           false);
  gt_option_is_development_option(idxo->optionnoshortreadsort);
  gt_option_parser_add_option(op, idxo->optionnoshortreadsort);

  idxo->optionmaxwidthrealmedian = gt_option_new_ulong("maxwidthrealmedian",
                                                 "compute real median for "
                                                 "intervals of at most the "
                                                 "given widthprefixes",
                                                 &idxo->sfxstrategy.
                                                      maxwidthrealmedian,
                                                 1UL);
  gt_option_is_development_option(idxo->optionmaxwidthrealmedian);
  gt_option_parser_add_option(op, idxo->optionmaxwidthrealmedian);

  idxo->optionalgbounds
    = gt_option_new_string_array("algbds",
                                 "length boundaries for the different "
                                 "algorithms to sort buckets of suffixes\n"
                                 "first number: maxbound for insertion sort\n"
                                 "second number: maxbound for blindtrie sort\n"
                                 "third number: maxbound for counting sort",
                                 idxo->algbounds);
  gt_option_is_development_option(idxo->optionalgbounds);
  gt_option_parser_add_option(op, idxo->optionalgbounds);

  idxo->optionstorespecialcodes
    = gt_option_new_bool("storespecialcodes",
                         "store special codes (this may speed up the program)",
                         &idxo->sfxstrategy.storespecialcodes,false);

  gt_option_is_development_option(idxo->optionstorespecialcodes);
  gt_option_parser_add_option(op, idxo->optionstorespecialcodes);

  idxo->optionparts
    = gt_option_new_uint_max("parts",
                             "specify number of parts in which the index "
                             "construction is performed",
                             &idxo->numofparts, 1U, (unsigned) ((1 << 22) - 1));
  gt_option_is_development_option(idxo->optionparts);
  gt_option_parser_add_option(op, idxo->optionparts);

  if (idxo->type == GT_INDEX_OPTIONS_ESA)
  {
    idxo->optionspmopt = gt_option_new_uint_min("spmopt",
                                            "optimize esa-construction for "
                                            "suffix-prefix matching",
                                            &idxo->sfxstrategy.spmopt_minlength,
                                            0,1U);
    gt_option_parser_add_option(op, idxo->optionspmopt);
    gt_option_exclude(idxo->optionspmopt, idxo->optiondifferencecover);
    idxo->optionmemlimit = gt_option_new_string("memlimit",
                           "specify maximal amount of memory to be used during "
                           "index construction (in bytes, the keywords 'MB' "
                           "and 'GB' are allowed)",
                           idxo->memlimit, NULL);
    gt_option_parser_add_option(op, idxo->optionmemlimit);
    gt_option_exclude(idxo->optionmemlimit, idxo->optionparts);
  }

  idxo->option = gt_option_new_bool("iterscan",
                                   "use iteratorbased-kmer scanning",
                                   &idxo->sfxstrategy.iteratorbasedkmerscanning,
                                   false);
  gt_option_is_development_option(idxo->option);
  gt_option_parser_add_option(op, idxo->option);

  idxo->option = gt_option_new_bool("samplewithprefixlengthnull",
                                  "sort sample with prefixlength=0",
                                  &idxo->sfxstrategy.samplewithprefixlengthnull,
                                  false);
  gt_option_is_development_option(idxo->option);
  gt_option_parser_add_option(op, idxo->option);

  idxo->option = gt_option_new_bool("suftabuint",
                                    "use uint32_t for suftab",
                                    &idxo->sfxstrategy.suftabuint,
                                    false);
  gt_option_is_development_option(idxo->option);
  gt_option_parser_add_option(op, idxo->option);

  idxo->option = gt_option_new_bool("onlybucketinsertion",
                                    "perform only bucket insertion",
                                    &idxo->sfxstrategy.onlybucketinsertion,
                                    false);
  gt_option_is_development_option(idxo->option);
  gt_option_parser_add_option(op, idxo->option);

  idxo->option = gt_option_new_bool("kmerswithencseqreader",
                               "always perform kmerscanning with encseq-reader",
                               &idxo->sfxstrategy.kmerswithencseqreader,
                               false);
  gt_option_is_development_option(idxo->option);
  gt_option_parser_add_option(op, idxo->option);

  idxo->option = gt_option_new_bool("dccheck",
                               "check intermediate results in difference cover",
                               &idxo->sfxstrategy.dccheck,
                               false);
  gt_option_is_development_option(idxo->option);
  gt_option_parser_add_option(op, idxo->option);

  idxo->option = gt_option_new_bool("withradixsort",
                                    "use radixsort to sort the buckets",
                                    &idxo->sfxstrategy.withradixsort,
                                    false);
  gt_option_is_development_option(idxo->option);
  gt_option_parser_add_option(op, idxo->option);

  gt_option_parser_register_hook(op, gt_index_options_check_set_create_opts,
                                 idxo);
  return idxo;
}

GtIndexOptions* gt_index_options_register_esa(GtOptionParser *op,
                                              GtEncseqOptions *encopts)
{
  GtIndexOptions *idxo;
  gt_assert(op != NULL);

  idxo = gt_index_options_register_generic_create(op,
                                                  GT_INDEX_OPTIONS_ESA);
  return gt_index_options_register_generic_output(op, idxo, NULL, encopts);
}

GtIndexOptions* gt_index_options_register_esa_noout(GtOptionParser *op)
{
  gt_assert(op != NULL);

  return gt_index_options_register_generic_create(op,
                                                  GT_INDEX_OPTIONS_ESA);
}

GtIndexOptions* gt_index_options_register_packedidx(GtOptionParser *op,
                                                    GtStr *indexname,
                                                    GtEncseqOptions *encopts)
{
  GtIndexOptions *idxo;
  gt_assert(op != NULL);
  idxo = gt_index_options_register_generic_create(op,
                                                  GT_INDEX_OPTIONS_PACKED);
  return gt_index_options_register_generic_output(op, idxo, indexname, encopts);
}

void gt_index_options_delete(GtIndexOptions *oi)
{
  if (oi == NULL) return;
  gt_str_delete(oi->kysargumentstring);
  gt_str_delete(oi->indexname);
  gt_str_delete(oi->dir);
  gt_str_delete(oi->memlimit);
  gt_str_array_delete(oi->algbounds);
  gt_free(oi);
}

/* XXX: clean this up */
#ifndef GT_INDEX_OPTS_GETTER_DEFS_DEFINED
#define GT_INDEX_OPTS_GETTER_DEF_OPT(VARNAME) \
GtOption* gt_index_options_##VARNAME##_option(GtIndexOptions *i) \
{ \
  gt_assert(i != NULL); \
  return i->option##VARNAME; \
}
#define GT_INDEX_OPTS_GETTER_DEF_VAL(VARNAME, TYPE) \
TYPE gt_index_options_##VARNAME##_value(GtIndexOptions *i) \
{ \
  gt_assert(i != NULL); \
  return i->VARNAME; \
}
#define GT_INDEX_OPTS_GETTER_DEF(VARNAME,TYPE) \
GT_INDEX_OPTS_GETTER_DEF_OPT(VARNAME) \
GT_INDEX_OPTS_GETTER_DEF_VAL(VARNAME, TYPE)
#define GT_INDEX_OPTS_GETTER_DEFS_DEFINED
#endif

/* these are available as options and values */
GT_INDEX_OPTS_GETTER_DEF(algbounds, GtStrArray*);
GT_INDEX_OPTS_GETTER_DEF(outbcktab, bool);
GT_INDEX_OPTS_GETTER_DEF(outbwttab, bool);
GT_INDEX_OPTS_GETTER_DEF(outlcptab, bool);
GT_INDEX_OPTS_GETTER_DEF(outsuftab, bool);
GT_INDEX_OPTS_GETTER_DEF(prefixlength, unsigned int);
GT_INDEX_OPTS_GETTER_DEF_OPT(spmopt);
/* these are available as values only, set _after_ option processing */
GT_INDEX_OPTS_GETTER_DEF_VAL(lcpdist, bool);
GT_INDEX_OPTS_GETTER_DEF_VAL(maximumspace, unsigned long);
GT_INDEX_OPTS_GETTER_DEF_VAL(numofparts, unsigned int);
GT_INDEX_OPTS_GETTER_DEF_VAL(outkyssort, bool);
GT_INDEX_OPTS_GETTER_DEF_VAL(outkystab, bool);
GT_INDEX_OPTS_GETTER_DEF_VAL(readmode, GtReadmode);
GT_INDEX_OPTS_GETTER_DEF_VAL(sfxstrategy, Sfxstrategy);
GT_INDEX_OPTS_GETTER_DEF_VAL(swallow_tail, bool);
#ifndef S_SPLINT_S
GT_INDEX_OPTS_GETTER_DEF_VAL(bwtIdxParams, struct bwtOptions);
#endif
genometools-1.5.1/src/match/index_options.h000066400000000000000000000064061211610345200207700ustar00rootroot00000000000000/*
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHAciOEVER RESULTING FROM LOSS OF USE, DATA OR PROFIci, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef INDEX_OPTIONS_H
#define INDEX_OPTIONS_H

#include "core/encseq_options.h"
#include "core/option_api.h"
#include "core/readmode.h"
#include "match/sfx-strategy.h"

typedef struct GtIndexOptions GtIndexOptions;

#define GT_PREFIXLENGTH_AUTOMATIC 0
#define GT_MAXDEPTH_AUTOMATIC     0

/* This module encapsulates the registration of options for index generation. */

GtIndexOptions* gt_index_options_register_esa(GtOptionParser *op,
                                              GtEncseqOptions *encopts);
/* this will only options concerning the building of the index, used for
   genomediff, for example, where no output is produced. */
GtIndexOptions* gt_index_options_register_esa_noout(GtOptionParser *op);
GtIndexOptions* gt_index_options_register_packedidx(GtOptionParser *op,
                                                    GtStr *indexname,
                                                    GtEncseqOptions *encopts);

void            gt_index_options_delete(GtIndexOptions *oi);

int             gt_parse_algbounds(Sfxstrategy *sfxstrategy,
                                   const GtStrArray *algbounds,
                                   GtError *err);

/* XXX: clean this up */
#ifndef GT_INDEX_OPTS_GETTER_DECLS_DEFINED
#define GT_INDEX_OPTS_GETTER_DECL_OPT(VARNAME) \
GtOption* gt_index_options_##VARNAME##_option(GtIndexOptions *i);
#define GT_INDEX_OPTS_GETTER_DECL_VAL(VARNAME, TYPE) \
TYPE gt_index_options_##VARNAME##_value(GtIndexOptions *i);
#define GT_INDEX_OPTS_GETTER_DECL(VARNAME,TYPE) \
GT_INDEX_OPTS_GETTER_DECL_OPT(VARNAME) \
GT_INDEX_OPTS_GETTER_DECL_VAL(VARNAME, TYPE)
#define GT_INDEX_OPTS_GETTER_DECLS_DEFINED
#endif

GT_INDEX_OPTS_GETTER_DECL(algbounds, GtStrArray*);
GT_INDEX_OPTS_GETTER_DECL(outbcktab, bool);
GT_INDEX_OPTS_GETTER_DECL(outbwttab, bool);
GT_INDEX_OPTS_GETTER_DECL(outkystab, bool);
GT_INDEX_OPTS_GETTER_DECL(outlcptab, bool);
GT_INDEX_OPTS_GETTER_DECL(outsuftab, bool);
GT_INDEX_OPTS_GETTER_DECL(prefixlength, unsigned int);
GT_INDEX_OPTS_GETTER_DECL_OPT(spmopt);
GT_INDEX_OPTS_GETTER_DECL_VAL(bwtIdxParams, struct bwtOptions);
GT_INDEX_OPTS_GETTER_DECL_VAL(lcpdist, bool);
GT_INDEX_OPTS_GETTER_DECL_VAL(maximumspace, unsigned long);
GT_INDEX_OPTS_GETTER_DECL_VAL(numofparts, unsigned int);
GT_INDEX_OPTS_GETTER_DECL_VAL(outkyssort, bool);
GT_INDEX_OPTS_GETTER_DECL_VAL(readmode, GtReadmode);
GT_INDEX_OPTS_GETTER_DECL_VAL(sfxstrategy, Sfxstrategy);
GT_INDEX_OPTS_GETTER_DECL_VAL(swallow_tail, bool);

#endif
genometools-1.5.1/src/match/initbasepower.c000066400000000000000000000061401211610345200207470ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/array2dim_api.h"
#include "core/assert_api.h"
#include "core/codetype.h"
#include "core/unused_api.h"

unsigned int gt_maxbasepower(unsigned int numofchars)
{
  GtCodetype minfailure, thepower = (GtCodetype) 1;
  unsigned int i;

  minfailure = (~(GtCodetype) 0)/(GtCodetype) numofchars;
  for (i=0; thepower < minfailure; i++)
  {
    thepower *= numofchars;
  }
  return i;
}

GtCodetype *gt_initbasepower(unsigned int numofchars,unsigned int prefixlength)
{
  GtCodetype thepower = (GtCodetype) 1, *basepower;
  unsigned int i;

  basepower = gt_malloc(sizeof *basepower * (prefixlength+1));
  for (i=0; /* Nothing */; i++)
  {
    basepower[i] = thepower;
    if (i == prefixlength)
    {
      break;
    }
    gt_assert(thepower < ((~(GtCodetype) 0)/(GtCodetype) numofchars));
    thepower *= numofchars;
  }
  return basepower;
}

GtCodetype *gt_filllargestchartable(unsigned int numofchars,
                               unsigned int kmersize)
{
  GtCodetype code, *ptr, *filltable;

  filltable = gt_malloc(sizeof *filltable * kmersize);
  code = (GtCodetype) numofchars;
  for (ptr = filltable + kmersize - 1; ptr >= filltable; ptr--)
  {
    *ptr = code-1;
    code *= numofchars;
  }
  return filltable;
}

GtCodetype *gt_initfilltable(unsigned int numofchars,unsigned int prefixlength)
{
  unsigned int i;
  GtCodetype *filltable, *basepower;

  basepower = gt_initbasepower(numofchars,prefixlength);
  filltable = gt_malloc(sizeof *filltable * prefixlength);
  for (i=0; i=0; offset--)
  {
    mmptr = multimappower[offset];
    mmptr[0] = 0;
    for (mapindex = 1U; mapindex < numofchars; mapindex++)
    {
      mmptr[mapindex] = mmptr[mapindex-1] + thepower;
    }
    thepower *= numofchars;
  }
  return multimappower;
}

void gt_multimappower_delete(GtCodetype **multimappower)
{
  if (multimappower != NULL)
  {
    gt_array2dim_delete(multimappower);
  }
}
genometools-1.5.1/src/match/initbasepower.h000066400000000000000000000026131211610345200207550ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef INITBASEPOWER_H
#define INITBASEPOWER_H

#include "core/codetype.h"

unsigned int gt_maxbasepower(unsigned int numofchars);

GtCodetype *gt_initbasepower(unsigned int numofchars,unsigned int prefixlength);

GtCodetype *gt_filllargestchartable(unsigned int numofchars,
                                    unsigned int kmersize);

GtCodetype *gt_initfilltable(unsigned int numofchars,unsigned int prefixlength);

GtCodetype **gt_initmultimappower(unsigned int numofchars,unsigned int qvalue);

void gt_multimappower_delete(GtCodetype **multimappower);

#endif
genometools-1.5.1/src/match/initeqsvec.c000066400000000000000000000045231211610345200202510ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/assert_api.h"
#include "core/chardef.h"
#include "initeqsvec.h"

void gt_initeqsvector(unsigned long *eqsvector,
                   unsigned long eqslen,
                   const GtUchar *pattern,
                   unsigned long patternlength)
{
  unsigned long *eptr, shiftmask;
  const GtUchar *pptr;

  gt_assert(patternlength <=
            (unsigned long) (CHAR_BIT * sizeof (unsigned long)));
  for (eptr = eqsvector; eptr < eqsvector + eqslen; eptr++)
  {
    *eptr = 0;
  }
  for (pptr = pattern, shiftmask = 1UL;
       pptr < pattern + patternlength && shiftmask != 0;
       pptr++, shiftmask <<= 1)
  {
    gt_assert(*pptr != (GtUchar) SEPARATOR);
    if (*pptr != (GtUchar) WILDCARD)
    {
      eqsvector[(unsigned long) *pptr] |= shiftmask;
    }
  }
}

void gt_initeqsvectorrev(unsigned long *eqsvectorrev,
                      unsigned long eqslen,
                      const GtUchar *pattern,
                      unsigned long patternlength)
{
  unsigned long *eptr, shiftmask;
  const GtUchar *pptr;

  gt_assert(patternlength <=
            (unsigned long) (CHAR_BIT * sizeof (unsigned long)));
  for (eptr = eqsvectorrev; eptr < eqsvectorrev + eqslen; eptr++)
  {
    *eptr = 0;
  }
  for (pptr = pattern+patternlength-1, shiftmask = 1UL;
       pptr >= pattern && shiftmask != 0;
       pptr--, shiftmask <<= 1)
  {
    gt_assert(*pptr != (GtUchar) SEPARATOR);
    if (*pptr != (GtUchar) WILDCARD)
    {
      eqsvectorrev[(unsigned long) *pptr] |= shiftmask;
    }
  }
}
genometools-1.5.1/src/match/initeqsvec.h000066400000000000000000000024371211610345200202600ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef INITEQSVEC_H
#define INITEQSVEC_H

#include "core/types_api.h"

void gt_initeqsvector(unsigned long *eqsvector,
                   unsigned long eqslen,
                   const GtUchar *pattern,
                   unsigned long patternlength);

void gt_initeqsvectorrev(unsigned long *eqsvectorrev,
                      unsigned long eqslen,
                      const GtUchar *pattern,
                      unsigned long patternlength);

#endif
genometools-1.5.1/src/match/intcode-def.h000066400000000000000000000023441211610345200202640ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef INTCODE_DEF_H
#define INTCODE_DEF_H

#define PREFIXLENBITS   4
#define CODEBITS        (32-PREFIXLENBITS)
#define MAXPREFIXLENGTH (CODEBITS>>1)
#define MAXCODEVALUE    ((1U << CODEBITS) - 1)

typedef struct
{
  unsigned int maxprefixindex:PREFIXLENBITS;
  unsigned int code:CODEBITS;
  unsigned long position; /* get rid of this by using information from encseq */
} Codeatposition;

#endif
genometools-1.5.1/src/match/iter-window.c000066400000000000000000000142401211610345200203440ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/encseq.h"
#include "iter-window.h"

struct Windowiterator
{
  GtUchar *buffer;
  unsigned long firstpos, bufsize, windowsize;
  unsigned long currentpos, endpos;
  const GtEncseq *encseq;
  GtEncseqReader *esr;
};

Windowiterator *gt_windowiterator_new(const GtEncseq *encseq,
                                   unsigned long windowsize,
                                   unsigned long startpos,
                                   unsigned long endpos)
{
  Windowiterator *wit;

  gt_assert(encseq != NULL);
  gt_assert(endpos <= gt_encseq_total_length(encseq));
  wit = gt_malloc(sizeof (*wit));
  wit->buffer = gt_malloc(sizeof (GtUchar) * windowsize);
  wit->firstpos = wit->bufsize = 0;
  wit->windowsize = windowsize;
  wit->currentpos = startpos;
  wit->endpos = endpos;
  wit->esr = gt_encseq_create_reader_with_readmode(encseq,
                                                   GT_READMODE_FORWARD,
                                                   startpos);
  wit->encseq = encseq;
  return wit;
}

void gt_windowiterator_delete(Windowiterator *wit)
{
  gt_free(wit->buffer);
  gt_free(wit);
}

const GtUchar *gt_windowiterator_next(unsigned long *currentpos,
                                      unsigned long *firstpos,
                                      Windowiterator *wit)
{
  GtUchar currentchar;

  while (wit->currentpos < wit->endpos)
  {
    currentchar = gt_encseq_reader_next_encoded_char(wit->esr);
    if (ISSPECIAL(currentchar))
    {
      wit->bufsize = wit->firstpos = 0;
    } else
    {
      if (wit->bufsize < wit->windowsize)
      {
        wit->buffer[wit->bufsize++] = currentchar;
      } else
      {
        wit->buffer[wit->firstpos++] = currentchar;
        if (wit->firstpos == wit->windowsize)
        {
          wit->firstpos = 0;
        }
      }
    }
    if (wit->bufsize == wit->windowsize)
    {
      gt_assert(wit->currentpos >= (unsigned long) (wit->windowsize-1));
      gt_assert(wit->firstpos < wit->windowsize);
      *currentpos = wit->currentpos++;
      *firstpos = wit->firstpos;
      return wit->buffer;
    }
    wit->currentpos++;
  }
  return NULL;
}

#ifdef  WITHWINDOWCHECK
static void checkcurrentwindow(const GtEncseq *encseq,
                               const GtUchar *buffer,
                               unsigned long windowsize,
                               unsigned long firstpos,
                               unsigned long currentpos)
{
  unsigned long idx, bufpos, bfbufpos;
  GtUchar cc1, cc2;

  bufpos = firstpos;
  for (idx= 0; idx
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef ITER_WINDOW_H
#define ITER_WINDOW_H

#include "core/encseq.h"

typedef struct Windowiterator Windowiterator;

Windowiterator *gt_windowiterator_new(const GtEncseq *encseq,
                                   unsigned long windowsize,
                                   unsigned long startpos,
                                   unsigned long endpos);

void gt_windowiterator_delete(Windowiterator *wit);

const GtUchar *gt_windowiterator_next(unsigned long *currentpos,
                                   unsigned long *firstpos,
                                   Windowiterator *wit);

#endif
genometools-1.5.1/src/match/kmer2string.c000066400000000000000000000025431211610345200203460ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/codetype.h"

void gt_fromkmercode2string(char *buffer,
                         GtCodetype code,
                         unsigned int numofchars,
                         unsigned int kmersize,
                         const char *characters)
{
  int i;
  unsigned int cc;
  GtCodetype tmpcode = code;

  buffer[kmersize] = '\0';
  for (i=(int) (kmersize-1); i>=0; i--)
  {
    cc = (unsigned int) (tmpcode % numofchars);
    buffer[i] = (char) characters[cc];
    tmpcode = (tmpcode - cc) / numofchars;
  }
}
genometools-1.5.1/src/match/kmer2string.h000066400000000000000000000022161211610345200203500ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef KMER2STRING_H
#define KMER2STRING_H

#include "core/codetype.h"

void gt_fromkmercode2string(char *buffer,
                         GtCodetype code,
                         unsigned int numofchars,
                         unsigned int kmersize,
                         const char *characters);

#endif
genometools-1.5.1/src/match/kmercodes.h000066400000000000000000000351631211610345200200640ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef KMERCODES_H
#define KMERCODES_H
#include "core/intbits.h"
#include "core/codetype.h"
#include "core/divmodmul.h"

static inline GtCodetype gt_kmercode_at_position(
                                   const GtTwobitencoding *twobitencoding,
                                   unsigned long pos,
                                   unsigned int kmersize)
{
  const unsigned int unitoffset = (unsigned int) GT_MODBYUNITSIN2BITENC(pos);
  const unsigned long unitindex = GT_DIVBYUNITSIN2BITENC(pos);
  const GtCodetype maskright = GT_MASKRIGHT(kmersize);

  if (unitoffset <= (unsigned int) GT_UNITSIN2BITENC - kmersize)
  {
    return (GtCodetype) (twobitencoding[unitindex]
            >> GT_MULT2(GT_UNITSIN2BITENC - kmersize - unitoffset))
           & maskright;
  } else
  {
    unsigned int shiftleft = GT_MULT2(unitoffset+kmersize-GT_UNITSIN2BITENC);
    return (GtCodetype)
           ((twobitencoding[unitindex] << shiftleft) |
            (twobitencoding[unitindex+1] >> (GT_MULT2(GT_UNITSIN2BITENC) -
                                             shiftleft)))
           & maskright;
  }
}

static inline GtCodetype gt_kmercode_complement(GtCodetype kmer,
                                                GtCodetype maskright)
{
  return kmer ^ maskright;
}

#define GT_SWAPBITPAIRS(KMER,L1,L2,D) (((KMER) & (3UL << L1)) >> D) |\
                                      (((KMER) & (3UL << L2)) << D)

static inline GtCodetype gt_kmercode_reverse(GtCodetype kmer,
                                             unsigned int kmersize)
{
  switch (kmersize)
  {
    case 2:
      return GT_SWAPBITPAIRS(kmer,2,0,2);
    case 3:
      return GT_SWAPBITPAIRS(kmer,4,0,4) |
             (kmer & (3U << 2));
    case 4:
      /* 4 shifts, 4 &, 2 |, 1 assignment = 11 ops */
      kmer = (kmer & 0xF0) >> 4 | (kmer & 0x0F) << 4;
      return (kmer & 0xCC) >> 2 | (kmer & 0x33) << 2;
    case 5:
      return GT_SWAPBITPAIRS(kmer,8,0,8) |
             GT_SWAPBITPAIRS(kmer,6,2,4) |
             (kmer & (3U << 4));
    case 6:
      return GT_SWAPBITPAIRS(kmer,10,0,10) |
             GT_SWAPBITPAIRS(kmer,8,2,6) |
             GT_SWAPBITPAIRS(kmer,6,4,2);
    case 7:
      return GT_SWAPBITPAIRS(kmer,12,0,12) |
             GT_SWAPBITPAIRS(kmer,10,2,8) |
             GT_SWAPBITPAIRS(kmer,8,4,4) |
             (kmer & (3U << 6));
    case 8:
      /* 6 shifts, 6 &, 3 |, 2 assignments = 17 */
      kmer = (kmer & 0xFF00) >> 8 | (kmer & 0xFF) << 8;
      kmer = (kmer & 0XF0F0) >> 4 | (kmer & 0x0F0F) << 4;
      return (kmer & 0xCCCC) >> 2 | (kmer & 0x3333) << 2;
    case 9:
      return GT_SWAPBITPAIRS(kmer,16,0,16) |
             GT_SWAPBITPAIRS(kmer,14,2,12) |
             GT_SWAPBITPAIRS(kmer,12,4,8) |
             GT_SWAPBITPAIRS(kmer,10,6,4) |
             (kmer & (3U << 8));
    case 10:
      return GT_SWAPBITPAIRS(kmer,18,0,18) |
             GT_SWAPBITPAIRS(kmer,16,2,14) |
             GT_SWAPBITPAIRS(kmer,14,4,10) |
             GT_SWAPBITPAIRS(kmer,12,6,6) |
             GT_SWAPBITPAIRS(kmer,10,8,2);
    case 11:
      return GT_SWAPBITPAIRS(kmer,20,0,20) |
             GT_SWAPBITPAIRS(kmer,18,2,16) |
             GT_SWAPBITPAIRS(kmer,16,4,12) |
             GT_SWAPBITPAIRS(kmer,14,6,8) |
             GT_SWAPBITPAIRS(kmer,12,8,4) |
             (kmer & (3U << 10));
    case 12:
      return GT_SWAPBITPAIRS(kmer,22,0,22) |
             GT_SWAPBITPAIRS(kmer,20,2,18) |
             GT_SWAPBITPAIRS(kmer,18,4,14) |
             GT_SWAPBITPAIRS(kmer,16,6,10) |
             GT_SWAPBITPAIRS(kmer,14,8,6) |
             GT_SWAPBITPAIRS(kmer,12,10,2);
    case 13:
      return GT_SWAPBITPAIRS(kmer,24,0,24) |
             GT_SWAPBITPAIRS(kmer,22,2,20) |
             GT_SWAPBITPAIRS(kmer,20,4,16) |
             GT_SWAPBITPAIRS(kmer,18,6,12) |
             GT_SWAPBITPAIRS(kmer,16,8,8) |
             GT_SWAPBITPAIRS(kmer,14,10,4) |
             (kmer & (3U << 12));
    case 14:
      return GT_SWAPBITPAIRS(kmer,26,0,26) |
             GT_SWAPBITPAIRS(kmer,24,2,22) |
             GT_SWAPBITPAIRS(kmer,22,4,18) |
             GT_SWAPBITPAIRS(kmer,20,6,14) |
             GT_SWAPBITPAIRS(kmer,18,8,10) |
             GT_SWAPBITPAIRS(kmer,16,10,6) |
             GT_SWAPBITPAIRS(kmer,14,12,2);
    case 15:
      return GT_SWAPBITPAIRS(kmer,28,0,28) |
             GT_SWAPBITPAIRS(kmer,26,2,24) |
             GT_SWAPBITPAIRS(kmer,24,4,20) |
             GT_SWAPBITPAIRS(kmer,22,6,16) |
             GT_SWAPBITPAIRS(kmer,20,8,12) |
             GT_SWAPBITPAIRS(kmer,18,10,8) |
             GT_SWAPBITPAIRS(kmer,16,12,4) |
             (kmer & (3U << 14));
    case 16:
             /* 8 shifts, 8 &, 4 |, 3 assignments = 23 ops */
             kmer = (kmer & 0xFFFF0000) >> 16 | (kmer & 0x0000FFFF) << 16;
             kmer = (kmer & 0xFF00FF00) >> 8 |  (kmer & 0x00FF00FF) << 8;
             kmer = (kmer & 0XF0F0F0F0) >> 4 |  (kmer & 0x0F0F0F0F) << 4;
             return (kmer & 0xCCCCCCCC) >> 2 |  (kmer & 0x33333333) << 2;
#ifdef _LP64
    case 17:
      return GT_SWAPBITPAIRS(kmer,32,0,32) |
             GT_SWAPBITPAIRS(kmer,30,2,28) |
             GT_SWAPBITPAIRS(kmer,28,4,24) |
             GT_SWAPBITPAIRS(kmer,26,6,20) |
             GT_SWAPBITPAIRS(kmer,24,8,16) |
             GT_SWAPBITPAIRS(kmer,22,10,12) |
             GT_SWAPBITPAIRS(kmer,20,12,8) |
             GT_SWAPBITPAIRS(kmer,18,14,4) |
             (kmer & (3U << 16));
    case 18:
      return GT_SWAPBITPAIRS(kmer,34,0,34) |
             GT_SWAPBITPAIRS(kmer,32,2,30) |
             GT_SWAPBITPAIRS(kmer,30,4,26) |
             GT_SWAPBITPAIRS(kmer,28,6,22) |
             GT_SWAPBITPAIRS(kmer,26,8,18) |
             GT_SWAPBITPAIRS(kmer,24,10,14) |
             GT_SWAPBITPAIRS(kmer,22,12,10) |
             GT_SWAPBITPAIRS(kmer,20,14,6) |
             GT_SWAPBITPAIRS(kmer,18,16,2);
    case 19:
      return GT_SWAPBITPAIRS(kmer,36,0,36) |
             GT_SWAPBITPAIRS(kmer,34,2,32) |
             GT_SWAPBITPAIRS(kmer,32,4,28) |
             GT_SWAPBITPAIRS(kmer,30,6,24) |
             GT_SWAPBITPAIRS(kmer,28,8,20) |
             GT_SWAPBITPAIRS(kmer,26,10,16) |
             GT_SWAPBITPAIRS(kmer,24,12,12) |
             GT_SWAPBITPAIRS(kmer,22,14,8) |
             GT_SWAPBITPAIRS(kmer,20,16,4) |
             (kmer & (3U << 18));
    case 20:
      return GT_SWAPBITPAIRS(kmer,38,0,38) |
             GT_SWAPBITPAIRS(kmer,36,2,34) |
             GT_SWAPBITPAIRS(kmer,34,4,30) |
             GT_SWAPBITPAIRS(kmer,32,6,26) |
             GT_SWAPBITPAIRS(kmer,30,8,22) |
             GT_SWAPBITPAIRS(kmer,28,10,18) |
             GT_SWAPBITPAIRS(kmer,26,12,14) |
             GT_SWAPBITPAIRS(kmer,24,14,10) |
             GT_SWAPBITPAIRS(kmer,22,16,6) |
             GT_SWAPBITPAIRS(kmer,20,18,2);
    case 21:
      return GT_SWAPBITPAIRS(kmer,40,0,40) |
             GT_SWAPBITPAIRS(kmer,38,2,36) |
             GT_SWAPBITPAIRS(kmer,36,4,32) |
             GT_SWAPBITPAIRS(kmer,34,6,28) |
             GT_SWAPBITPAIRS(kmer,32,8,24) |
             GT_SWAPBITPAIRS(kmer,30,10,20) |
             GT_SWAPBITPAIRS(kmer,28,12,16) |
             GT_SWAPBITPAIRS(kmer,26,14,12) |
             GT_SWAPBITPAIRS(kmer,24,16,8) |
             GT_SWAPBITPAIRS(kmer,22,18,4) |
             (kmer & (3U << 20));
    case 22:
      return GT_SWAPBITPAIRS(kmer,42,0,42) |
             GT_SWAPBITPAIRS(kmer,40,2,38) |
             GT_SWAPBITPAIRS(kmer,38,4,34) |
             GT_SWAPBITPAIRS(kmer,36,6,30) |
             GT_SWAPBITPAIRS(kmer,34,8,26) |
             GT_SWAPBITPAIRS(kmer,32,10,22) |
             GT_SWAPBITPAIRS(kmer,30,12,18) |
             GT_SWAPBITPAIRS(kmer,28,14,14) |
             GT_SWAPBITPAIRS(kmer,26,16,10) |
             GT_SWAPBITPAIRS(kmer,24,18,6) |
             GT_SWAPBITPAIRS(kmer,22,20,2);
    case 23:
      return GT_SWAPBITPAIRS(kmer,44,0,44) |
             GT_SWAPBITPAIRS(kmer,42,2,40) |
             GT_SWAPBITPAIRS(kmer,40,4,36) |
             GT_SWAPBITPAIRS(kmer,38,6,32) |
             GT_SWAPBITPAIRS(kmer,36,8,28) |
             GT_SWAPBITPAIRS(kmer,34,10,24) |
             GT_SWAPBITPAIRS(kmer,32,12,20) |
             GT_SWAPBITPAIRS(kmer,30,14,16) |
             GT_SWAPBITPAIRS(kmer,28,16,12) |
             GT_SWAPBITPAIRS(kmer,26,18,8) |
             GT_SWAPBITPAIRS(kmer,24,20,4) |
             (kmer & (3U << 22));
    case 24:
      return GT_SWAPBITPAIRS(kmer,46,0,46) |
             GT_SWAPBITPAIRS(kmer,44,2,42) |
             GT_SWAPBITPAIRS(kmer,42,4,38) |
             GT_SWAPBITPAIRS(kmer,40,6,34) |
             GT_SWAPBITPAIRS(kmer,38,8,30) |
             GT_SWAPBITPAIRS(kmer,36,10,26) |
             GT_SWAPBITPAIRS(kmer,34,12,22) |
             GT_SWAPBITPAIRS(kmer,32,14,18) |
             GT_SWAPBITPAIRS(kmer,30,16,14) |
             GT_SWAPBITPAIRS(kmer,28,18,10) |
             GT_SWAPBITPAIRS(kmer,26,20,6) |
             GT_SWAPBITPAIRS(kmer,24,22,2);
    case 25:
      return GT_SWAPBITPAIRS(kmer,48,0,48) |
             GT_SWAPBITPAIRS(kmer,46,2,44) |
             GT_SWAPBITPAIRS(kmer,44,4,40) |
             GT_SWAPBITPAIRS(kmer,42,6,36) |
             GT_SWAPBITPAIRS(kmer,40,8,32) |
             GT_SWAPBITPAIRS(kmer,38,10,28) |
             GT_SWAPBITPAIRS(kmer,36,12,24) |
             GT_SWAPBITPAIRS(kmer,34,14,20) |
             GT_SWAPBITPAIRS(kmer,32,16,16) |
             GT_SWAPBITPAIRS(kmer,30,18,12) |
             GT_SWAPBITPAIRS(kmer,28,20,8) |
             GT_SWAPBITPAIRS(kmer,26,22,4) |
             (kmer & (3U << 24));
    case 26:
      return GT_SWAPBITPAIRS(kmer,50,0,50) |
             GT_SWAPBITPAIRS(kmer,48,2,46) |
             GT_SWAPBITPAIRS(kmer,46,4,42) |
             GT_SWAPBITPAIRS(kmer,44,6,38) |
             GT_SWAPBITPAIRS(kmer,42,8,34) |
             GT_SWAPBITPAIRS(kmer,40,10,30) |
             GT_SWAPBITPAIRS(kmer,38,12,26) |
             GT_SWAPBITPAIRS(kmer,36,14,22) |
             GT_SWAPBITPAIRS(kmer,34,16,18) |
             GT_SWAPBITPAIRS(kmer,32,18,14) |
             GT_SWAPBITPAIRS(kmer,30,20,10) |
             GT_SWAPBITPAIRS(kmer,28,22,6) |
             GT_SWAPBITPAIRS(kmer,26,24,2);
    case 27:
      return GT_SWAPBITPAIRS(kmer,52,0,52) |
             GT_SWAPBITPAIRS(kmer,50,2,48) |
             GT_SWAPBITPAIRS(kmer,48,4,44) |
             GT_SWAPBITPAIRS(kmer,46,6,40) |
             GT_SWAPBITPAIRS(kmer,44,8,36) |
             GT_SWAPBITPAIRS(kmer,42,10,32) |
             GT_SWAPBITPAIRS(kmer,40,12,28) |
             GT_SWAPBITPAIRS(kmer,38,14,24) |
             GT_SWAPBITPAIRS(kmer,36,16,20) |
             GT_SWAPBITPAIRS(kmer,34,18,16) |
             GT_SWAPBITPAIRS(kmer,32,20,12) |
             GT_SWAPBITPAIRS(kmer,30,22,8) |
             GT_SWAPBITPAIRS(kmer,28,24,4) |
             (kmer & (3U << 26));
    case 28:
      return GT_SWAPBITPAIRS(kmer,54,0,54) |
             GT_SWAPBITPAIRS(kmer,52,2,50) |
             GT_SWAPBITPAIRS(kmer,50,4,46) |
             GT_SWAPBITPAIRS(kmer,48,6,42) |
             GT_SWAPBITPAIRS(kmer,46,8,38) |
             GT_SWAPBITPAIRS(kmer,44,10,34) |
             GT_SWAPBITPAIRS(kmer,42,12,30) |
             GT_SWAPBITPAIRS(kmer,40,14,26) |
             GT_SWAPBITPAIRS(kmer,38,16,22) |
             GT_SWAPBITPAIRS(kmer,36,18,18) |
             GT_SWAPBITPAIRS(kmer,34,20,14) |
             GT_SWAPBITPAIRS(kmer,32,22,10) |
             GT_SWAPBITPAIRS(kmer,30,24,6) |
             GT_SWAPBITPAIRS(kmer,28,26,2);
    case 29:
      return GT_SWAPBITPAIRS(kmer,56,0,56) |
             GT_SWAPBITPAIRS(kmer,54,2,52) |
             GT_SWAPBITPAIRS(kmer,52,4,48) |
             GT_SWAPBITPAIRS(kmer,50,6,44) |
             GT_SWAPBITPAIRS(kmer,48,8,40) |
             GT_SWAPBITPAIRS(kmer,46,10,36) |
             GT_SWAPBITPAIRS(kmer,44,12,32) |
             GT_SWAPBITPAIRS(kmer,42,14,28) |
             GT_SWAPBITPAIRS(kmer,40,16,24) |
             GT_SWAPBITPAIRS(kmer,38,18,20) |
             GT_SWAPBITPAIRS(kmer,36,20,16) |
             GT_SWAPBITPAIRS(kmer,34,22,12) |
             GT_SWAPBITPAIRS(kmer,32,24,8) |
             GT_SWAPBITPAIRS(kmer,30,26,4) |
             (kmer & (3U << 28));
    case 30:
      return GT_SWAPBITPAIRS(kmer,58,0,58) |
             GT_SWAPBITPAIRS(kmer,56,2,54) |
             GT_SWAPBITPAIRS(kmer,54,4,50) |
             GT_SWAPBITPAIRS(kmer,52,6,46) |
             GT_SWAPBITPAIRS(kmer,50,8,42) |
             GT_SWAPBITPAIRS(kmer,48,10,38) |
             GT_SWAPBITPAIRS(kmer,46,12,34) |
             GT_SWAPBITPAIRS(kmer,44,14,30) |
             GT_SWAPBITPAIRS(kmer,42,16,26) |
             GT_SWAPBITPAIRS(kmer,40,18,22) |
             GT_SWAPBITPAIRS(kmer,38,20,18) |
             GT_SWAPBITPAIRS(kmer,36,22,14) |
             GT_SWAPBITPAIRS(kmer,34,24,10) |
             GT_SWAPBITPAIRS(kmer,32,26,6) |
             GT_SWAPBITPAIRS(kmer,30,28,2);
    case 31:
      return GT_SWAPBITPAIRS(kmer,60,0,60) |
             GT_SWAPBITPAIRS(kmer,58,2,56) |
             GT_SWAPBITPAIRS(kmer,56,4,52) |
             GT_SWAPBITPAIRS(kmer,54,6,48) |
             GT_SWAPBITPAIRS(kmer,52,8,44) |
             GT_SWAPBITPAIRS(kmer,50,10,40) |
             GT_SWAPBITPAIRS(kmer,48,12,36) |
             GT_SWAPBITPAIRS(kmer,46,14,32) |
             GT_SWAPBITPAIRS(kmer,44,16,28) |
             GT_SWAPBITPAIRS(kmer,42,18,24) |
             GT_SWAPBITPAIRS(kmer,40,20,20) |
             GT_SWAPBITPAIRS(kmer,38,22,16) |
             GT_SWAPBITPAIRS(kmer,36,24,12) |
             GT_SWAPBITPAIRS(kmer,34,26,8) |
             GT_SWAPBITPAIRS(kmer,32,28,4) |
             (kmer & (3U << 30));
    case 32:
             kmer = (kmer & 0xFFFFFFFF00000000) >> 32 |
                    (kmer & 0x00000000FFFFFFFF) << 32;
             kmer = (kmer & 0xFFFF0000FFFF0000) >> 16 |
                    (kmer & 0x0000FFFF0000FFFF) << 16;
             kmer = (kmer & 0xFF00FF00FF00FF00) >> 8 |
                    (kmer & 0x00FF00FF00FF00FF) << 8;
             kmer = (kmer & 0XF0F0F0F0F0F0F0F0) >> 4 |
                    (kmer & 0x0F0F0F0F0F0F0F0F) << 4;
             return (kmer & 0xCCCCCCCCCCCCCCCC) >> 2 |
                    (kmer & 0x3333333333333333) << 2;
#endif
    default: fprintf(stderr,"illegal kmersize=%u\n",kmersize);
             exit(GT_EXIT_PROGRAMMING_ERROR);
  }
}

#endif
genometools-1.5.1/src/match/lcpinterval.h000066400000000000000000000017571211610345200204350ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LCPINTERVAL_H
#define LCPINTERVAL_H

typedef struct
{
  unsigned long offset,
                left,
                right;
} Lcpinterval;

#endif
genometools-1.5.1/src/match/lcpoverflow.h000066400000000000000000000020631211610345200204430ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LCPOVERFLOW_H
#define LCPOVERFLOW_H

#include 
#include 

#define LCPOVERFLOW ((uint8_t) UCHAR_MAX)

typedef struct
{
  unsigned long position,
                value;
} Largelcpvalue;

#endif
genometools-1.5.1/src/match/lua_tools.c000066400000000000000000000032321211610345200200740ustar00rootroot00000000000000/*
  Copyright (c) 2011 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "lua.h"
#include "lualib.h"

#include "match/lua_tools.h"

void gt_lua_stack_dump(lua_State *L) {
  int i;
  int top = lua_gettop(L);
  for (i = 1; i <= top; i++)
  { /* repeat for each level */
    int t = lua_type(L, i);
    switch (t) {

      case LUA_TSTRING:  /* strings */
        fprintf(stderr, "`%s'", lua_tostring(L, i));
        break;

      case LUA_TBOOLEAN:  /* booleans */
        lua_toboolean(L, i) ? fprintf(stderr,"true") : fprintf(stderr,"false");
        break;

      case LUA_TNUMBER:  /* numbers */
        fprintf(stderr, "%g", lua_tonumber(L, i));
        break;

      default:  /* other values */
        fprintf(stderr, "%s", lua_typename(L, t));
        break;
    }
    fprintf(stderr, "  ");  /* put a separator */
  }
  fprintf(stderr, "\n");  /* end the listing */
}
genometools-1.5.1/src/match/lua_tools.h000066400000000000000000000017531211610345200201070ustar00rootroot00000000000000/*
  Copyright (c) 2011 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef LUA_TOOLS_H
#define LUA_TOOLS_H

#include "lauxlib.h"
#include "lua.h"
#include "lualib.h"

void gt_lua_stack_dump(lua_State *L);

#endif
genometools-1.5.1/src/match/marksubstring.c000066400000000000000000000056621211610345200207770ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/mathsupport.h"
#include "core/unused_api.h"
#include "marksubstring.h"

Gtmarksubstring *gt_marksubstring_new(unsigned int numofchars,
                                      unsigned int kmersize,
                                      bool usesuffix,
                                      unsigned int units)
{
  Gtmarksubstring *mark;

  mark = gt_malloc(sizeof (*mark));
  gt_assert(kmersize >= units);
  mark->units = units;
  mark->entries = gt_power_for_small_exponents(numofchars,units);
  if (usesuffix)
  {
    mark->shiftright = 0;
    mark->mask = (GtCodetype) (mark->entries-1);
  } else
  {
    mark->shiftright = GT_MULT2(kmersize - units);
    mark->mask = ~(GtCodetype) 0;
  }
  GT_INITBITTAB(mark->bits,mark->entries);
  mark->size = sizeof (GtBitsequence) * GT_NUMOFINTSFORBITS(mark->entries);
  return mark;
}

void gt_marksubstring_delete(Gtmarksubstring *mark,bool withbits)
{
  if (mark != NULL)
  {
    if (withbits)
    {
      gt_free(mark->bits);
    }
    gt_free(mark);
  }
}

void gt_marksubstring_mark(Gtmarksubstring *mark,GtCodetype code)
{
  code = (code >> (GtCodetype) mark->shiftright) & mark->mask;

  gt_assert(code < mark->entries);
  if (!GT_ISIBITSET(mark->bits,code))
  {
    GT_SETIBIT(mark->bits,code);
  }
}

bool gt_marksubstring_checkmark(const Gtmarksubstring *mark,GtCodetype code)
{
  code = (code >> (GtCodetype) mark->shiftright) & mark->mask;

  return GT_ISIBITSET(mark->bits,code) ? true : false;
}

unsigned int gt_marksubstring_shiftright(const Gtmarksubstring *mark)
{
  return mark->shiftright;
}

unsigned long gt_marksubstring_entries(const Gtmarksubstring *mark)
{
  return mark->entries;
}

size_t gt_marksubstring_size(const Gtmarksubstring *mark)
{
  return mark->size;
}

void gt_marksubstring_bits_null(GT_UNUSED const Gtmarksubstring *mark,bool null)
{
  if (null)
  {
    gt_assert(mark->bits == NULL);
  } else
  {
    gt_assert(mark->bits != NULL);
  }
}

GtBitsequence** gt_marksubstring_bits_address(Gtmarksubstring *mark)
{
  return &mark->bits;
}

void gt_marksubstring_bits_map(Gtmarksubstring *mark,GtBitsequence *bitsmap)
{
  mark->bits = bitsmap;
}
genometools-1.5.1/src/match/marksubstring.h000066400000000000000000000043161211610345200207770ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef MARKSUBSTRING_H
#define MARKSUBSTRING_H

#include "core/codetype.h"
#include "core/intbits.h"

typedef struct Gtmarksubstring Gtmarksubstring;

struct Gtmarksubstring
{
  size_t size;
  unsigned int units, shiftright;
  unsigned long entries;
  GtCodetype mask;
  GtBitsequence *bits;
};

#define GT_MARKSUBSTRING_CHECKMARK(MARK,CODE)\
        (marksubstringtmpcode\
           = ((CODE) >> (GtCodetype) (MARK)->shiftright) & (MARK)->mask,\
        GT_ISIBITSET((MARK)->bits,marksubstringtmpcode) ? true : false)

Gtmarksubstring *gt_marksubstring_new(unsigned int numofchars,
                                      unsigned int kmersize, bool usesuffix,
                                      unsigned int units);

void gt_marksubstring_delete(Gtmarksubstring *mark,bool withbits);

void gt_marksubstring_mark(Gtmarksubstring *mark,GtCodetype code);

bool gt_marksubstring_checkmark(const Gtmarksubstring *mark,GtCodetype code);

unsigned int gt_marksubstring_shiftright(const Gtmarksubstring *mark);

unsigned long gt_marksubstring_entries(const Gtmarksubstring *mark);

size_t gt_marksubstring_size(const Gtmarksubstring *mark);

void gt_marksubstring_bits_null(const Gtmarksubstring *mark,bool null);

GtBitsequence** gt_marksubstring_bits_address(Gtmarksubstring *mark);

void gt_marksubstring_bits_map(Gtmarksubstring *mark,
                               GtBitsequence *bitsmap);

#endif
genometools-1.5.1/src/match/merger-trie.c000066400000000000000000000462261211610345200203270ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/assert_api.h"
#include "core/arraydef.h"
#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/format64.h"
#include "core/intbits.h"
#include "core/encseq.h"
#include "core/ma_api.h"
#include "merger-trie.h"

#define MTRIE_ISLEAF(NODE) ((NODE)->firstchild == NULL)
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
#define SHOWNODERELATIONS(NODE)\
        shownoderelations(__LINE__,#NODE,NODE)
#else
#define SHOWNODERELATIONS(NODE) /* Nothing */
#endif
#else
#define SHOWNODERELATIONS(NODE) /* Nothing */
#endif

#define SETFIRSTCHILD(NODE,VALUE)\
        (NODE)->firstchild = VALUE;\
        if ((VALUE) != NULL)\
        {\
          (VALUE)->parent = NODE;\
        }

#define SETFIRSTCHILDNULL(NODE)\
        (NODE)->firstchild = NULL

typedef struct
{
  Mergertrienode *previous,
           *current;
} Nodepair;

static GtUchar getfirstedgechar(const Mergertrierep *trierep,
                              const Mergertrienode *node,
                              unsigned long prevdepth)
{
  Encseqreadinfo *eri = trierep->encseqreadinfo + node->suffixinfo.idx;

  if (MTRIE_ISLEAF(node) &&
      node->suffixinfo.startpos + prevdepth >=
      gt_encseq_total_length(eri->encseqptr))
  {
    return (GtUchar) SEPARATOR;
  }
  return gt_encseq_get_encoded_char(eri->encseqptr, /* Random access */
                        node->suffixinfo.startpos + prevdepth,
                        eri->readmode);
}

static int mtrie_comparecharacters(GtUchar cc1,unsigned int idx1,
                                   GtUchar cc2,unsigned int idx2)
{
  if (ISSPECIAL(cc1))
  {
    if (ISSPECIAL(cc2))
    {
      if (idx1 <= idx2)
      {
        return -1;  /* cc1 < cc2 */
      } else
      {
        return 1;  /* cc1 > cc2 */
      }
    } else
    {
      return 1; /* cc1 > cc2 */
    }
  } else
  {
    if (ISSPECIAL(cc2))
    {
      return -1;  /* cc1 < cc2 */
    } else
    {
      if (cc1 < cc2)
      {
        return -1;  /* cc1 < cc2 */
      } else
      {
        if (cc1 > cc2)
        {
          return 1;  /* cc1 > cc2 */
        } else
        {
          return 0; /* cc1 == cc2 */
        }
      }
    }
  }
}

#ifdef WITHTRIEIDENT
static void showmergertrie2(const Mergertrierep *trierep,
                            const GtUchar *characters,
                            unsigned int level,
                            const Mergertrienode *node)
{
  GtUchar cc = 0;
  unsigned long pos, endpos;
  Mergertrienode *current;

  for (current = node->firstchild;
       current != NULL;
       current = current->rightsibling)
  {
    printf("%*.*s",(int) (6 * level),(int) (6 * level)," ");
    if (MTRIE_ISLEAF(current))
    {
      endpos = gt_encseq_total_length(
                                 trierep->encseqtable[current->suffixinfo.idx]);
    } else
    {
      endpos = current->suffixinfo.startpos + current->depth;
    }
    for (pos = current->suffixinfo.startpos + node->depth;
         pos < endpos; pos++)
    {
      cc = gt_encseq_get_encoded_char( /* just for testing */
              trierep->enseqreadinfo[current->suffixinfo.idx].encseqptr,
              pos,
              trierep->enseqreadinfo[current->suffixinfo.idx].readmode);
      if (ISSPECIAL(cc))
      {
        printf("#\n");
        break;
      }
      printf("%c",characters[(int) cc]);
    }
    if (MTRIE_ISLEAF(current))
    {
      if (!ISSPECIAL(cc))
      {
        printf("~\n");
      }
    } else
    {
      printf(" d=%lu,i=" Formatuint64_t "\n",
            current->depth,
            PRINTuint64_tcast(current->suffixinfo.ident));
      showmergertrie2(trierep,characters,level+1,current);
    }
  }
}

void mergertrie_show(const Mergertrierep *trierep,
                     const GtUchar *characters)
{
  if (trierep->root != NULL)
  {
    showmergertrie2(trierep,characters,0,trierep->root);
  }
}

/*
   Check the following:
   (1) for each branching node there exist at least 2 DONE
   (2) for each branching node the list of successors is strictly ordered
       according to the first character of the edge label DONE
   (3) there are no empty edge labels DONE
   (4) there are \(n+1\) leaves and for each leaf there is exactly one
       incoming edge DONE
*/

static void checkmergertrie2(Mergertrierep *trierep,
                             Mergertrienode *node,
                             Mergertrienode *father,
                             Bitsequence *leafused,
                             unsigned int *numberofbitsset)
{
  Mergertrienode *current, *previous;

  if (MTRIE_ISLEAF(node))
  {
    unsigned long start = node->suffixinfo.startpos;
#ifndef NDEBUG
    if (ISIBITSET(leafused,start))
    {
      fprintf(stderr,"leaf %lu already found\n",start);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
#endif
    SETIBIT(leafused,start);
    (*numberofbitsset)++;
  } else
  {
    gt_assert(node->depth == 0 || node->firstchild->rightsibling != NULL);
    if (father != NULL)
    {
      gt_assert(!MTRIE_ISLEAF(father));
#ifndef NDEBUG
      if (father->depth >= node->depth)
      {
        fprintf(stderr,"father.depth = %lu >= %lu = node.depth\n",
                       father->depth,
                       node->depth);
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
#endif
    }
    previous = NULL;
    for (current = node->firstchild; current != NULL;
        current = current->rightsibling)
    {
#ifndef NDEBUG
      if (previous != NULL)
      {
        if (mtrie_comparecharacters(
              getfirstedgechar(trierep,previous,node->depth),
              previous->suffixinfo.idx,
              getfirstedgechar(trierep,current,node->depth),
              current->suffixinfo.idx) >= 0)
        {
          fprintf(stderr,"nodes not correctly ordered\n");
          exit(GT_EXIT_PROGRAMMING_ERROR);
        }
      }
#endif
      checkmergertrie2(trierep,current,node,leafused,numberofbitsset);
      previous = current;
    }
  }
}

void mergertrie_check(Mergertrierep *trierep,unsigned int numberofleaves,
                      unsigned int maxleafnum,GtError *err)
{
  gt_error_check(err);
  if (trierep->root != NULL)
  {
    Bitsequence *leafused;
    unsigned int numberofbitsset = 0;

    INITBITTAB(leafused,maxleafnum+1);
    checkmergertrie2(trierep,trierep->root,NULL,leafused,&numberofbitsset);
#ifndef NDEBUG
    if (numberofbitsset != numberofleaves)
    {
      fprintf(stderr,"numberofbitsset = %u != %u = numberofleaves\n",
                      numberofbitsset,
                      numberofleaves);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
#endif
    gt_free(leafused);
  }
}

#ifdef WITHTRIESHOW
static void shownode(const Mergertrienode *node)
{
  if (node == NULL)
  {
    printf("NULL");
  } else
  {
    printf("%s " Formatuint64_t,MTRIE_ISLEAF(node) ? "leaf" : "branch",
                   PRINTuint64_tcast(node->suffixinfo.ident));
  }
}

static void showsimplenoderelations(const Mergertrienode *node)
{
  shownode(node);
  printf(".firstchild=");
  shownode(node->firstchild);
  printf("; ");
  shownode(node);
  printf(".rightsibling=");
  shownode(node->rightsibling);
  printf("\n");
}

static void shownoderelations(int line,char *nodestring,
                              const Mergertrienode *node)
{
  printf("l. %d: %s: ",line,nodestring);
  showsimplenoderelations(node);
}

void merertrie_showallnoderelations(const Mergertrienode *node)
{
  Mergertrienode *tmp;

  showsimplenoderelations(node);
  for (tmp = node->firstchild; tmp != NULL; tmp = tmp->rightsibling)
  {
    if (tmp->firstchild == NULL)
    {
      showsimplenoderelations(tmp);
    } else
    {
      showallnoderelations(tmp);
    }
  }
}
#endif
#endif

static Mergertrienode *newMergertrienode(Mergertrierep *trierep)
{
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
  printf("# available trie nodes: %u; ",
          trierep->allocatedMergertrienode - trierep->nextfreeMergertrienode);
  printf("unused trie nodes: %u\n",trierep->nextunused);
#endif
#endif
  if (trierep->nextfreeMergertrienode >= trierep->allocatedMergertrienode)
  {
    gt_assert(trierep->nextunused > 0);
    trierep->nextunused--;
    return trierep->unusedMergertrienodes[trierep->nextunused];
  }
  return trierep->nodetable + trierep->nextfreeMergertrienode++;
}

static Mergertrienode *mtrie_makenewleaf(Mergertrierep *trierep,
                                   Suffixinfo *suffixinfo)
{
  Mergertrienode *newleaf;

#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
  printf("makenewleaf(" Formatuint64_t ")\n",
         PRINTuint64_tcast(suffixinfo->ident));
#endif
#endif
  newleaf = newMergertrienode(trierep);
  newleaf->suffixinfo = *suffixinfo;
  SETFIRSTCHILDNULL(newleaf);
  newleaf->rightsibling = NULL;
  SHOWNODERELATIONS(newleaf);
  return newleaf;
}

static Mergertrienode *mtrie_makeroot(Mergertrierep *trierep,
                                      Suffixinfo *suffixinfo)
{
  Mergertrienode *root, *newleaf;

#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
  printf("makeroot(" Formatuint64_t ")\n",PRINTuint64_tcast(suffixinfo->ident));
#endif
#endif
  root = newMergertrienode(trierep);
  root->parent = NULL;
  root->suffixinfo = *suffixinfo;
  root->depth = 0;
  root->rightsibling = NULL;
  newleaf = mtrie_makenewleaf(trierep,suffixinfo);
  SETFIRSTCHILD(root,newleaf);
  SHOWNODERELATIONS(root);
  return root;
}

static void makesuccs(Mergertrienode *newbranch,Mergertrienode *first,
                      Mergertrienode *second)
{
  second->rightsibling = NULL;
  first->rightsibling = second;
  SETFIRSTCHILD(newbranch,first);
  SHOWNODERELATIONS(second);
  SHOWNODERELATIONS(first);
  SHOWNODERELATIONS(newbranch);
}

static Mergertrienode *mtrie_makenewbranch(Mergertrierep *trierep,
                                     Suffixinfo *suffixinfo,
                                     unsigned long currentdepth,
                                     Mergertrienode *oldnode)
{
  Mergertrienode *newbranch, *newleaf;
  GtUchar cc1, cc2;
  Encseqreadinfo *eri = trierep->encseqreadinfo + suffixinfo->idx;

#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
  printf("makenewbranch(ident=" Formatuint64_t ")\n",
          PRINTuint64_tcast(suffixinfo->ident));
#endif
#endif
  newbranch = newMergertrienode(trierep);
  newbranch->suffixinfo = *suffixinfo;
  newbranch->rightsibling = oldnode->rightsibling;
  cc1 = getfirstedgechar(trierep,oldnode,currentdepth);
  if (suffixinfo->startpos + currentdepth >=
      gt_encseq_total_length(eri->encseqptr))
  {
    cc2 = (GtUchar) SEPARATOR;
  } else
  {
    cc2 = gt_encseq_get_encoded_char(eri->encseqptr,
                         suffixinfo->startpos + currentdepth,
                         eri->readmode);
  }
  newleaf = mtrie_makenewleaf(trierep,suffixinfo);
  if (mtrie_comparecharacters(cc1,oldnode->suffixinfo.idx,
                        cc2,suffixinfo->idx) <= 0)
  {
    makesuccs(newbranch,oldnode,newleaf);
  } else
  {
    makesuccs(newbranch,newleaf,oldnode);
  }
  newbranch->depth = currentdepth;
  return newbranch;
}

static unsigned long getlcp(const GtEncseq *encseq1,
                            GtReadmode readmode1,
                            unsigned long start1, unsigned long end1,
                            const GtEncseq *encseq2,
                            GtReadmode readmode2,
                            unsigned long start2, unsigned long end2)
{
  unsigned long i1, i2;
  GtUchar cc1;

  for (i1=start1, i2=start2; i1 <= end1 && i2 <= end2; i1++, i2++)
  {
    cc1 = gt_encseq_get_encoded_char(/*XXX*/ encseq1,i1,readmode1);
    if (cc1 != gt_encseq_get_encoded_char(/*XXX*/ encseq2,i2,readmode2)
          || ISSPECIAL(cc1))
    {
      break;
    }
  }
  return i1 - start1;
}

static bool hassuccessor(const Mergertrierep *trierep,
                         Nodepair *np,
                         unsigned long prevdepth,
                         const Mergertrienode *node,
                         GtUchar cc2,
                         unsigned int idx2)
{
  GtUchar cc1;
  int cmpresult;

  for (np->previous = NULL, np->current = node->firstchild;
      np->current != NULL;
      np->current = np->current->rightsibling)
  {
    cc1 = getfirstedgechar(trierep,np->current,prevdepth);
    cmpresult = mtrie_comparecharacters(cc1,np->current->suffixinfo.idx,cc2,
                                        idx2);
    if (cmpresult == 1)
    {
      return false;
    }
    if (cmpresult == 0)
    {
      return true;
    }
    np->previous = np->current;
  }
  return false;
}

void gt_mergertrie_insertsuffix(Mergertrierep *trierep,
                             Mergertrienode *node,
                             Suffixinfo *suffixinfo)
{
  if (trierep->root == NULL)
  {
    trierep->root = mtrie_makeroot(trierep,suffixinfo);
  } else
  {
    unsigned long currentdepth, lcpvalue, totallength;
    Mergertrienode *currentnode, *newleaf, *newbranch, *succ;
    Nodepair np;
    GtUchar cc;
    Encseqreadinfo *eri = trierep->encseqreadinfo + suffixinfo->idx;

    gt_assert(!MTRIE_ISLEAF(node));
    currentnode = node;
    currentdepth = node->depth;
    totallength = gt_encseq_total_length(eri->encseqptr);
    while (true)
    {
      if (suffixinfo->startpos + currentdepth >= totallength)
      {
        cc = (GtUchar) SEPARATOR;
      } else
      {
        /* Random access */
        cc = gt_encseq_get_encoded_char(eri->encseqptr,
                                            suffixinfo->startpos + currentdepth,
                                            eri->readmode);
      }
      gt_assert(currentnode != NULL);
      gt_assert(!MTRIE_ISLEAF(currentnode));
      if (!hassuccessor(trierep,&np,currentdepth,currentnode,cc,
                        suffixinfo->idx))
      {
        newleaf = mtrie_makenewleaf(trierep,suffixinfo);
        newleaf->rightsibling = np.current;
        SHOWNODERELATIONS(newleaf);
        if (np.previous == NULL)
        {
          SETFIRSTCHILD(currentnode,newleaf);
          SHOWNODERELATIONS(currentnode);
        } else
        {
          np.previous->rightsibling = newleaf;
          SHOWNODERELATIONS(np.previous);
        }
        return;
      }
      succ = np.current;
      if (MTRIE_ISLEAF(succ))
      {
        lcpvalue = getlcp(eri->encseqptr,
                          eri->readmode,
                          suffixinfo->startpos + currentdepth + 1,
                          gt_encseq_total_length(eri->encseqptr) - 1,
                          trierep->encseqreadinfo[succ->suffixinfo.idx].
                                encseqptr,
                          trierep->encseqreadinfo[succ->suffixinfo.idx].
                                readmode,
                          succ->suffixinfo.startpos + currentdepth + 1,
                          gt_encseq_total_length(
                              trierep->encseqreadinfo[succ->suffixinfo.idx].
                                        encseqptr) - 1);
        newbranch = mtrie_makenewbranch(trierep,
                                  suffixinfo,
                                  currentdepth + lcpvalue + 1,
                                  succ);
        if (np.previous == NULL)
        {
          SETFIRSTCHILD(currentnode,newbranch);
          SHOWNODERELATIONS(currentnode);
        } else
        {
          np.previous->rightsibling = newbranch;
          SHOWNODERELATIONS(np.previous);
        }
        return;
      }
      lcpvalue = getlcp(eri->encseqptr,
                        eri->readmode,
                        suffixinfo->startpos + currentdepth + 1,
                        gt_encseq_total_length(eri->encseqptr) - 1,
                        trierep->encseqreadinfo[succ->suffixinfo.idx].encseqptr,
                        trierep->encseqreadinfo[succ->suffixinfo.idx].readmode,
                        succ->suffixinfo.startpos + currentdepth + 1,
                        succ->suffixinfo.startpos + succ->depth - 1);
      if (currentdepth + lcpvalue + 1 < succ->depth)
      {
        newbranch = mtrie_makenewbranch(trierep,
                                  suffixinfo,
                                  currentdepth + lcpvalue + 1,
                                  succ);
        if (np.previous == NULL)
        {
          SETFIRSTCHILD(currentnode,newbranch);
          SHOWNODERELATIONS(currentnode);
        } else
        {
          np.previous->rightsibling = newbranch;
          SHOWNODERELATIONS(np.previous);
        }
        return;
      }
      currentnode = succ;
      currentdepth = currentnode->depth;
    }
  }
}

Mergertrienode *gt_mergertrie_findsmallestnode(const Mergertrierep *trierep)
{
  Mergertrienode *node;

  gt_assert(trierep->root != NULL);
  for (node = trierep->root; node->firstchild != NULL; node = node->firstchild)
    /* Nothing */ ;
  return node;
}

void gt_mergertrie_deletesmallestpath(Mergertrienode *smallest,
                                   Mergertrierep *trierep)
{
  Mergertrienode *father, *son;

  for (son = smallest; son->parent != NULL; son = son->parent)
  {
    father = son->parent;
    if (son->firstchild == NULL)
    {
      SETFIRSTCHILD(father,son->rightsibling);
      SHOWNODERELATIONS(father);
      son->rightsibling = NULL;
    } else
    {
      if (son->firstchild->rightsibling != NULL)
      {
        break;
      }
      son->firstchild->rightsibling = father->firstchild->rightsibling;
      SETFIRSTCHILD(father,son->firstchild);
      SHOWNODERELATIONS(father);
      son->rightsibling = NULL;
      SETFIRSTCHILDNULL(son);
    }
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
    printf("delete %s " Formatuint64_t "\n",
             MTRIE_ISLEAF(son) ? "leaf" : "branch",
             PRINTuint64_tcast(son->suffixinfo.ident));
#endif
#endif
    trierep->unusedMergertrienodes[trierep->nextunused++] = son;
  }
  if (trierep->root->firstchild == NULL)
  {
    trierep->unusedMergertrienodes[trierep->nextunused++] = trierep->root;
    trierep->root = NULL;
  }
}

void gt_mergertrie_initnodetable(Mergertrierep *trierep,
                              unsigned long numofsuffixes,
                              unsigned int numofindexes)
{
  trierep->numofindexes = numofindexes;
  trierep->allocatedMergertrienode
    = (unsigned int) GT_MULT2(numofsuffixes + 1) + 1;
  trierep->nodetable = gt_malloc(sizeof *trierep->nodetable
                                 * trierep->allocatedMergertrienode);
  trierep->nextfreeMergertrienode = 0;
  trierep->root = NULL;
  trierep->nextunused = 0;
  trierep->unusedMergertrienodes
    = gt_malloc(sizeof *trierep->unusedMergertrienodes
                * trierep->allocatedMergertrienode);
}

void gt_mergertrie_delete(Mergertrierep *trierep)
{
  if (trierep != NULL)
  {
    gt_free(trierep->nodetable);
    gt_free(trierep->unusedMergertrienodes);
    gt_free(trierep->encseqreadinfo);
    trierep->encseqreadinfo = NULL;
  }
}
genometools-1.5.1/src/match/merger-trie.h000066400000000000000000000051351211610345200203260ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef MERGER_TRIE_H
#define MERGER_TRIE_H

#include "core/arraydef.h"

#include "core/encseq.h"

typedef struct
{
  unsigned int idx;
  unsigned long startpos;
#ifdef WITHTRIEIDENT
  uint64_t  ident;
#endif
} Suffixinfo;

typedef struct Mergertrienode
{
  Suffixinfo suffixinfo;
  struct Mergertrienode *firstchild,
                        *rightsibling,
                        *parent;
  unsigned long depth;
} Mergertrienode;

typedef Mergertrienode * Mergertrienodeptr;

GT_DECLAREARRAYSTRUCT(Mergertrienodeptr);

typedef struct
{
  GtEncseq *encseqptr;
  GtReadmode readmode;
} Encseqreadinfo;

typedef struct
{
  Encseqreadinfo *encseqreadinfo;
  Mergertrienode *nodetable,
           *root;
  Mergertrienodeptr *unusedMergertrienodes;
  unsigned int numofindexes,
               nextunused,
               allocatedMergertrienode,
               nextfreeMergertrienode;
} Mergertrierep;

void mergertrie_show(const Mergertrierep *trierep,
                     const GtUchar *characters);

void mergertrie_check(Mergertrierep *trierep,unsigned int numberofleaves,
                     unsigned int maxleafnum,GtError *err);

void mergertrie_showallnoderelations(const Mergertrienode *node);

void gt_mergertrie_insertsuffix(Mergertrierep *trierep,
                             Mergertrienode *node,
                             Suffixinfo *suffixinfo);

Mergertrienode *gt_mergertrie_findsmallestnode(const Mergertrierep *trierep);

void gt_mergertrie_deletesmallestpath(Mergertrienode *smallest,
                                   Mergertrierep *trierep);

void gt_mergertrie_initnodetable(Mergertrierep *trierep,
                              unsigned long numofsuffixes,
                              unsigned int numofindexes);

void gt_mergertrie_delete(Mergertrierep *trierep);

#endif
genometools-1.5.1/src/match/merger-trie.pr000066400000000000000000000015361211610345200205210ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
void showmergertrie(const Mergertrierep *trierep,
                    const GtUchar *characters);

void checkmergertrie(Mergertrierep *trierep,unsigned int numberofleaves,
                     unsigned int maxleafnum,GtError *err);

void showallnoderelations(const Mergertrienode *node);

void insertsuffixintomergertrie(Mergertrierep *trierep,
                                Mergertrienode *node,
                                Suffixinfo *suffixinfo);

Mergertrienode *findsmallestnodeintrie(const Mergertrierep *trierep);

void deletesmallesttriepath(Mergertrienode *smallest,Mergertrierep *trierep);

void initmergertrienodetable(Mergertrierep *trierep,unsigned long numofsuffixes,
                             unsigned int numofindexes);

void freemergertrierep(Mergertrierep *trierep);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/mssufpat.c000066400000000000000000000251421211610345200177410ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/assert_api.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/chardef.h"
#include "core/ma_api.h"
#include "core/intbits.h"

#include "absdfstrans-imp.h"
#include "initeqsvec.h"

typedef struct
{
  unsigned long prefixofsuffixbits;
} GtMssufpatLimdfsstate;

typedef struct
{
  unsigned long patternlength,
                mstatlength[GT_INTWORDSIZE],
                *eqsvector;
  unsigned long mstatwitnessleftbound[GT_INTWORDSIZE],
         mstatwitnessrightbound[GT_INTWORDSIZE];
} GtMssufpatLimdfsconstinfo;

#ifdef SKDEBUG

static void pms_showLimdfsstate(const DECLAREPTRDFSSTATE(aliascol),
                                unsigned long currentdepth,
                                const Limdfsconstinfo *mti)
{
  const GtMssufpatLimdfsstate *col = (const GtMssufpatLimdfsstate *) aliascol;
  bool first = true;

  unsigned long idx, backmask;

  printf("at depth %lu: [",currentdepth);
  for (idx=0, backmask = 1UL; idxpatternlength; idx++, backmask <<= 1)
  {
    if (col->prefixofsuffixbits & backmask)
    {
      if (first)
      {
        printf("%lu",idx);
        first = false;
      } else
      {
        printf(",%lu",idx);
      }
    }
  }
  printf("]\n");
}

#endif

static Limdfsconstinfo *pms_allocatedfsconstinfo(unsigned int alphasize)
{
  GtMssufpatLimdfsconstinfo *mti =
                                  gt_malloc(sizeof (GtMssufpatLimdfsconstinfo));

  mti->eqsvector = gt_malloc(sizeof (*mti->eqsvector) * alphasize);
  return (Limdfsconstinfo*) mti;
}

static void pms_initdfsconstinfo(Limdfsconstinfo *mt,
                                 unsigned int alphasize,
                                 ...)
                                 /* Variable argument list is as follows:
                                    unsigned int alphasize
                                    const GtUchar *pattern,
                                    unsigned long patternlength
                                 */
{
  va_list ap;
  GtMssufpatLimdfsconstinfo *mti = (GtMssufpatLimdfsconstinfo*) mt;
  const GtUchar *pattern;

  va_start(ap,alphasize);
  pattern = va_arg(ap, const GtUchar *);
  mti->patternlength = va_arg(ap, unsigned long);
  va_end(ap);
  gt_initeqsvector(mti->eqsvector,(unsigned long) alphasize,
                pattern,mti->patternlength);
}

static void pms_extractdfsconstinfo(Processresult processresult,
                                    void *processinfo,
                                    const void *patterninfo,
                                    Limdfsconstinfo *mt)
{
  unsigned long idx;
  GtMssufpatLimdfsconstinfo *mti = (GtMssufpatLimdfsconstinfo*) mt;

  for (idx=0; idxpatternlength; idx++)
  {
    processresult(processinfo,patterninfo,idx,mti->mstatlength[idx],
                                              mti->mstatwitnessleftbound[idx],
                                              mti->mstatwitnessrightbound[idx]);
  }
}

static void pms_freedfsconstinfo(Limdfsconstinfo **mtptr)
{
  GtMssufpatLimdfsconstinfo **mtiptr = (GtMssufpatLimdfsconstinfo**) mtptr;
  gt_free((*mtiptr)->eqsvector);
  gt_free((*mtiptr));
  *mtiptr = NULL;
}

static unsigned long zerosontheright(unsigned long v)
{
  unsigned long c;     /* c will be the number of zero bits on the right,
                         so if v is 1101000 (base 2), then c will be 3 */
  gt_assert(v > 0);
  if (v & 0x1)
  {
    c = 0; /* special case for odd v (assumed to happen half of the time) */
  } else
  {
    c = 1UL;
#ifdef _LP64
    if ((v & 0xffffffff) == 0)
    {
      v >>= 32;
      c+= 32UL;
    }
#endif
    if ((v & 0xffff) == 0)
    {
      v >>= 16;
      c += 16UL;
    }
    if ((v & 0xff) == 0)
    {
      v >>= 8;
      c += 8UL;
    }
    if ((v & 0xf) == 0)
    {
      v >>= 4;
      c += 4UL;
    }
    if ((v & 0x3) == 0)
    {
      v >>= 2;
      c += 2UL;
    }
    c -= v & 0x1;
  }
  return c;
}

static void pms_initLimdfsstate(DECLAREPTRDFSSTATE(aliascolumn),
                                Limdfsconstinfo *mt)
{
  GtMssufpatLimdfsstate *column = (GtMssufpatLimdfsstate *) aliascolumn;
  GtMssufpatLimdfsconstinfo *mti = (GtMssufpatLimdfsconstinfo*) mt;
  unsigned long idx;

  column->prefixofsuffixbits = ~0UL;
  gt_assert(mti->patternlength <= (unsigned long) GT_INTWORDSIZE);
  for (idx = 0; idxpatternlength; idx++)
  {
    mti->mstatlength[idx] = 0;
    mti->mstatwitnessleftbound[idx] = 0;
    mti->mstatwitnessrightbound[idx] = 0;
  }
}

static void pms_fullmatchLimdfsstate(Limdfsresult *limdfsresult,
                                     DECLAREPTRDFSSTATE(aliascolumn),
                                     unsigned long leftbound,
                                     unsigned long rightbound,
                                     GT_UNUSED unsigned long width,
                                     unsigned long currentdepth,
                                     Limdfsconstinfo *mt)
{
  GtMssufpatLimdfsstate *limdfsstate = (GtMssufpatLimdfsstate *) aliascolumn;
  GtMssufpatLimdfsconstinfo *mti = (GtMssufpatLimdfsconstinfo*) mt;

  if (limdfsstate->prefixofsuffixbits > 0)
  {
    unsigned long bitindex = 0,
                  first1,
                  tmp = limdfsstate->prefixofsuffixbits;
    do
    {
      first1 = zerosontheright(tmp);
      gt_assert(bitindex + first1 < mti->patternlength);
      if (mti->mstatlength[bitindex+first1] < currentdepth)
      {
        /*
        printf("set mstatlength[%lu]=%lu\n",bitindex+first1,currentdepth);
        printf("set mstatwitnessleftbound[%lu]=%lu\n",bitindex+first1,
                                                 (unsigned long) leftbound);
        */
        mti->mstatlength[bitindex+first1] = currentdepth;
        mti->mstatwitnessleftbound[bitindex+first1] = leftbound;
        mti->mstatwitnessrightbound[bitindex+first1] = rightbound;
      }
      tmp >>= (first1+1);
      bitindex += (first1+1);
    } while (tmp != 0);
    limdfsresult->status = Limdfscontinue;
  } else
  {
    limdfsresult->status = Limdfsstop;
  }
}

static void pms_nextLimdfsstate(const Limdfsconstinfo *mt,
                                DECLAREPTRDFSSTATE(aliasoutcol),
                                unsigned long currentdepth,
                                GtUchar currentchar,
                                const DECLAREPTRDFSSTATE(aliasincol))
{
#ifdef SKDEBUG
  char buffer1[GT_INTWORDSIZE+1], buffer2[GT_INTWORDSIZE+1];
#endif
  GtMssufpatLimdfsstate *outcol = (GtMssufpatLimdfsstate *) aliasoutcol;
  GtMssufpatLimdfsconstinfo *mti = (GtMssufpatLimdfsconstinfo*) mt;
  const GtMssufpatLimdfsstate *incol =
                                     (const GtMssufpatLimdfsstate *) aliasincol;

  gt_assert(ISNOTSPECIAL(currentchar));
  gt_assert(currentdepth > 0);

  if (currentdepth > 1UL)
  {
    outcol->prefixofsuffixbits
      = incol->prefixofsuffixbits &
        (mti->eqsvector[currentchar] >> (currentdepth-1));
  } else
  {
    outcol->prefixofsuffixbits = mti->eqsvector[currentchar];
  }
#ifdef SKDEBUG
  bitsequence2string(buffer1,(Bitsequence) incol->prefixofsuffixbits);
  bitsequence2string(buffer2,(Bitsequence) outcol->prefixofsuffixbits);
  printf("next(%s,%u,depth=%lu)->%s\n",buffer1,(unsigned int) currentchar,
                                       currentdepth,buffer2);
#endif
}

static void pms_inplacenextLimdfsstate(const Limdfsconstinfo *mt,
                                       DECLAREPTRDFSSTATE(aliascol),
                                       unsigned long currentdepth,
                                       GtUchar currentchar)
{
#ifdef SKDEBUG
  char buffer1[INTWORDSIZE+1], buffer2[INTWORDSIZE+1];
  unsigned long tmp;
#endif
  GtMssufpatLimdfsstate *col = (GtMssufpatLimdfsstate *) aliascol;
  GtMssufpatLimdfsconstinfo *mti = (GtMssufpatLimdfsconstinfo*) mt;

  gt_assert(ISNOTSPECIAL(currentchar));
#ifdef SKDEBUG
  tmp = col->prefixofsuffixbits;
#endif
  col->prefixofsuffixbits &= (mti->eqsvector[currentchar] >> (currentdepth-1));
#ifdef SKDEBUG
  bitsequence2string(buffer1,(uint32_t) tmp);
  bitsequence2string(buffer2,(uint32_t) col->prefixofsuffixbits);
  printf("inplacenext(%s,%u,%lu)->%s\n",buffer1,(unsigned int) currentchar,
                                        currentdepth,buffer2);
#endif
}

const AbstractDfstransformer *gt_pms_AbstractDfstransformer(void)
{
  static const AbstractDfstransformer pms_adfst =
  {
    sizeof (GtMssufpatLimdfsstate),
    pms_allocatedfsconstinfo,
    pms_initdfsconstinfo,
    pms_extractdfsconstinfo,
    pms_freedfsconstinfo,
    pms_initLimdfsstate,
    NULL,
    NULL,
    NULL,
    pms_fullmatchLimdfsstate,
    pms_nextLimdfsstate,
    pms_inplacenextLimdfsstate,
#ifdef SKDEBUG
    pms_showLimdfsstate,
#endif
  };
  return &pms_adfst;
}

/*
  define bitvector prefixofsuffixbits_{d} such that after processing a
  sequence v of length d we have: for all i\in[0,m-1]
  prefixofsuffixbits_{d}[i] is 1 iff P[i..i+d-1] = v[0..d-1]

  Let eqsvector_{a} be a vector of size m such that
  eqsvector_{a}[i]=1 if P[i]=a

  Let d=0 (i.e. at the root). Then
  P[i..i+d-1]=P[i..i-1]=\varepsilon=v[0..-1]=v[0..d-1] for all i \in[0..m-1]
  and hence prefixofsuffixbits_{d}[i]=1. In other words
  prefixofsuffixbits_{d} = 1^{m}.

  Now suppose d > 0 and assume we have computed
  prefixofsuffixbits_{d-1}. Then by definition
  prefixofsuffixbits_{d}[i]
    iff P[i..i+d-1] = v[0..d-1]
    iff P[i..i+d-2] = v[0..d-2] && P[i+d-1]=v[d-1]
    iff prefixofsuffixbits_{d-1][i]=1 && eqsvector_{v[d-1]}[i+d-1]=1
    iff prefixofsuffixbits_{d-1][i] & eqsvector_{v[d-1]}[i+d-1]

  All values in prefixofsuffixbits_{d} are independent and can be computed
  in parallel by

  prefixofsuffixbits_{d} = prefixofsuffixbits_{d-1} & (eqsvector_{a} << (d-1))
  where a=v[d-1]

  prefixofsuffixbits_{d] = 0 and
  prefixofsuffixbits_{d-1} != 0 then  for all i satisfying
  prefixofsuffixbits_{d-1][i] = 1 do:
    if mstats[i]
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef MSSUFPAT_H
#define MSSUFPAT_H
#include "absdfstrans-def.h"

const AbstractDfstransformer *gt_pms_AbstractDfstransformer(void);

#endif
genometools-1.5.1/src/match/myersapm.c000066400000000000000000000131621211610345200177330ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/chardef.h"
#include "core/types_api.h"
#include "core/encseq.h"
#include "core/defined-types.h"
#include "core/ma_api.h"
#include "myersapm.h"
#include "procmatch.h"
#include "dist-short.h"
#include "initeqsvec.h"

struct Myersonlineresources
{
  GtEncseqReader *esr;
  const GtEncseq *encseq;
  unsigned long totallength;
  unsigned long *eqsvectorrev,
                *eqsvector;
  unsigned int alphasize;
  bool nowildcards;
  ProcessIdxMatch processmatch;
  void *processmatchinfo;
};

Myersonlineresources *gt_newMyersonlineresources(unsigned int numofchars,
                                                 bool nowildcards,
                                                 const GtEncseq *encseq,
                                                 ProcessIdxMatch processmatch,
                                                 void *processmatchinfo)
{
  Myersonlineresources *mor;

  mor = gt_malloc(sizeof *mor);
  mor->eqsvectorrev = gt_malloc(sizeof *mor->eqsvectorrev * numofchars);
  mor->eqsvector = gt_malloc(sizeof *mor->eqsvector * numofchars);
  mor->encseq = encseq;
  mor->esr = gt_encseq_create_reader_with_readmode(encseq, GT_READMODE_REVERSE,
                                                   0);
  gt_assert(numofchars <= GT_MAXALPHABETCHARACTER);
  mor->alphasize = numofchars;
  mor->totallength = gt_encseq_total_length(encseq);
  mor->nowildcards = nowildcards;
  mor->processmatch = processmatch;
  mor->processmatchinfo = processmatchinfo;
  return mor;
}

void gt_freeMyersonlineresources(Myersonlineresources *ptrmyersonlineresources)
{
  if (ptrmyersonlineresources != NULL)
  {
    gt_free(ptrmyersonlineresources->eqsvectorrev);
    gt_free(ptrmyersonlineresources->eqsvector);
    gt_encseq_reader_delete(ptrmyersonlineresources->esr);
    gt_free(ptrmyersonlineresources);
  }
}

void gt_edistmyersbitvectorAPM(Myersonlineresources *mor,
                               const GtUchar *pattern,
                               unsigned long patternlength,
                               unsigned long maxdistance)
{
  unsigned long Pv = ~0UL,
                Mv = 0UL,
                Eq,
                Xv,
                Xh,
                Ph,
                Mh,
                score;
  const unsigned long Ebit = 1UL << (patternlength-1);
  GtUchar cc;
  unsigned long pos;
  const GtReadmode readmode = GT_READMODE_REVERSE;
  GtIdxMatch match;

  gt_initeqsvectorrev(mor->eqsvectorrev,
                   (unsigned long) mor->alphasize,
                   pattern,patternlength);
  score = patternlength;
  gt_encseq_reader_reinit_with_readmode(mor->esr, mor->encseq, readmode, 0);
  match.dbabsolute = NULL;
  match.dbsubstring = NULL;
  match.querystartpos = 0;
  match.querylen = patternlength;
  match.alignment = NULL;
  for (pos = 0; pos < mor->totallength; pos++)
  {
    cc = gt_encseq_reader_next_encoded_char(mor->esr);
    if (cc == (GtUchar) SEPARATOR)
    {
      Pv = ~0UL;
      Mv = 0UL;
      score = patternlength;
    } else
    {
      if (cc == (GtUchar) WILDCARD)
      {
        Eq = 0;
      } else
      {
        Eq = mor->eqsvectorrev[(unsigned long) cc];   /*  6 */
      }
      Xv = Eq | Mv;                                   /*  7 */
      Xh = (((Eq & Pv) + Pv) ^ Pv) | Eq;              /*  8 */

      Ph = Mv | ~ (Xh | Pv);                          /*  9 */
      Mh = Pv & Xh;                                   /* 10 */

      if (Ph & Ebit)
      {
        score++;
      } else
      {
        if (Mh & Ebit)
        {
          gt_assert(score > 0);
          score--;
        }
      }

      Ph <<= 1;                                       /* 15 */
      Pv = (Mh << 1) | ~ (Xv | Ph);                   /* 17 */
      Mv = Ph & Xv;                                   /* 18 */
      if (score <= maxdistance)
      {
        unsigned long dbstartpos = GT_REVERSEPOS(mor->totallength,pos);
        Definedunsignedlong matchlength;

        if (maxdistance > 0)
        {
          matchlength = gt_forwardprefixmatch(mor->encseq,
                                           mor->alphasize,
                                           dbstartpos,
                                           mor->nowildcards,
                                           mor->eqsvector,
                                           pattern,
                                           patternlength,
                                           maxdistance);
        } else
        {
          matchlength.defined = true;
          matchlength.valueunsignedlong = patternlength;
        }
        gt_assert(matchlength.defined || mor->nowildcards);
        if (matchlength.defined)
        {
          match.dbstartpos = dbstartpos;
          match.dblen = (unsigned long) matchlength.valueunsignedlong;
          match.distance = score;
          mor->processmatch(mor->processmatchinfo,&match);
        }
      }
    }
  }
}
genometools-1.5.1/src/match/myersapm.h000066400000000000000000000031471211610345200177420ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef MYERSAPM_H
#define MYERSAPM_H

#include "core/encseq.h"
#include "procmatch.h"

typedef struct Myersonlineresources Myersonlineresources;

Myersonlineresources *gt_newMyersonlineresources(
                        unsigned int numofchars,
                        bool nowildcards,
                        const GtEncseq *encseq,
                        ProcessIdxMatch processmatch,
                        void *processmatchinfo);

void gt_freeMyersonlineresources(
                                Myersonlineresources *ptrmyersonlineresources);

void gt_edistmyersbitvectorAPM(Myersonlineresources *mor,
                            const GtUchar *pattern,
                            unsigned long patternlength,
                            unsigned long maxdistance);

#endif
genometools-1.5.1/src/match/nullcols.c000066400000000000000000000051721211610345200177330ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/types_api.h"
#include "core/ma_api.h"

typedef struct
{
  unsigned long *endindex,
                *positions;
} Charatpos;

Charatpos *gt_newCharatpos(unsigned long patternlength,unsigned int alphasize)
{
  Charatpos *catpos;

  catpos = gt_malloc(sizeof (*catpos));
  catpos->endindex = gt_malloc(sizeof (unsigned long) * alphasize);
  catpos->positions = gt_malloc(sizeof (unsigned long) * patternlength);
  return catpos;
}

Charatpos *gt_reinitCharatpos(Charatpos *catpos,
                           const GtUchar *pattern,unsigned long patternlength,
                           unsigned int alphasize)
{
  const GtUchar *pptr;
  unsigned long partialsum, tmp;
  unsigned int idx;

  for (idx=0; idxendindex[idx] = 0;
  }
  for (pptr=pattern; pptrendindex[(int) *pptr]++;
  }
  partialsum = catpos->endindex[0];
  catpos->endindex[0] = 0;
  for (idx=1U; idxendindex[idx];
    catpos->endindex[idx] = partialsum;
    partialsum += tmp;
  }
  for (pptr=pattern; pptrpositions[catpos->endindex[*pptr]++]
      = (unsigned long) (pptr - pattern);
  }
  return catpos;
}

void gt_wrapCharatpos(Charatpos **catposptr)
{
  Charatpos *catpos = *catposptr;
  gt_free(catpos->endindex);
  gt_free(catpos->positions);
  gt_free(catpos);
  *catposptr = NULL;
}

void gt_maintainnullcols(const Charatpos *catpos,
                      unsigned long *front0,GtUchar cc,unsigned long depth)
{
  unsigned long idx;

  for (idx = (cc == 0) ? 0 : catpos->endindex[cc-1];
       idx < catpos->endindex[cc]; idx++)
  {
    unsigned long pos = catpos->positions[idx];
    if (front0[pos] == depth)
    {
      front0[pos]++;
    }
  }
}
genometools-1.5.1/src/match/optionargmode.c000066400000000000000000000076101211610345200207460ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "optionargmode.h"
#include "core/unused_api.h"

int gt_optionargaddbitmask(const Optionargmodedesc *modedesc,
                           size_t numberofentries,
                           unsigned int *mode,
                           const char *optname,
                           const char *optionargument,
                           GtError *err)
{
  size_t modecount;

  gt_error_check(err);
  for (modecount=0; modecount < numberofentries; modecount++)
  {
    if (strcmp(optionargument,modedesc[modecount].name) == 0)
    {
      if (*mode & modedesc[modecount].bitmask)
      {
        gt_error_set(err,"argument \"%s\" to option %s already specified",
                      modedesc[modecount].name,optname);
        return -1;
      }
      *mode |= modedesc[modecount].bitmask;
      return 0;
    }
  }
  gt_error_set(err,"illegal argument \"%s\" to option %s",
                optionargument,optname);
  return -2;
}

int gt_optionargsetsingle(const Optionargmodedesc *modedesc,
                          size_t numberofentries,
                          const char *optname,
                          const char *optionargument,
                          GtError *err)
{
  size_t modecount;

  gt_error_check(err);
  for (modecount=0; modecount < numberofentries; modecount++)
  {
    if (strcmp(optionargument,modedesc[modecount].name) == 0)
    {
      return (int) modedesc[modecount].bitmask;
    }
  }
  gt_error_set(err,"illegal argument \"%s\" to option %s",
                optionargument,optname);
  return -1;
}

GtStr *gt_getargmodekeywords(const Optionargmodedesc *modedesc,
                             size_t numberofentries,
                             const char *what)
{
  GtStr *helpstring;
  size_t idx, modecount, len, maxlen = 0;
  GT_UNUSED size_t spacelen;
  const char *space = "    ";

  for (modecount=0; modecount < numberofentries; modecount++)
  {
    len = strlen(modedesc[modecount].name);
    if (maxlen < len)
    {
      maxlen = len;
    }
  }
  helpstring = gt_str_new_cstr("use combination of the following keywords "
                               "to specify ");
  gt_str_append_cstr(helpstring,what);
  gt_str_append_cstr(helpstring,"\n");
  spacelen = strlen(space);
  for (modecount=0; modecount < numberofentries; modecount++)
  {
    gt_str_append_cstr(helpstring,modedesc[modecount].name);
    gt_str_append_cstr(helpstring,space);
    len = strlen(modedesc[modecount].name);
    for (idx=0; idx
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef OPTIONARGMODE_H
#define OPTIONARGMODE_H
#include "core/str_api.h"
#include "core/error_api.h"

typedef struct
{
  const char *name,
             *desc;
  unsigned int bitmask;
} Optionargmodedesc;

int gt_optionargaddbitmask(const Optionargmodedesc *modedesc,
                           size_t numberofentries,
                           unsigned int *mode,
                           const char *optname,
                           const char *optionargument,
                           GtError *err);

int gt_optionargsetsingle(const Optionargmodedesc *modedesc,
                          size_t numberofentries,
                          const char *optname,
                          const char *optionargument,
                          GtError *err);

GtStr *gt_getargmodekeywords(const Optionargmodedesc *modedesc,
                             size_t numberofentries,
                             const char *what);

void gt_getsetargmodekeywords(const Optionargmodedesc *modedesc,
                              size_t numberofentries,
                              unsigned int bitfield);

#endif
genometools-1.5.1/src/match/pck-count-nodes.c000066400000000000000000000113611211610345200211060ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 

#include "core/array2dim_api.h"
#include "core/divmodmul.h"
#include "core/log_api.h"
#include "core/logger.h"
#include "core/stack-inlined.h"
#include "core/unused_api.h"

#include "match/eis-voiditf.h"

#include "match/pck-count-nodes.h"

static void visit_count_children(const FMindex *index,
                           Nodecount *parent,
                           GtStackNodecount *stack,
                           Mbtab *tmpmbtab,
                           unsigned long *rangeOccs,
                           GT_UNUSED unsigned int numofchars)
{
  unsigned long rangesize, idx, num_special;
  unsigned int offset;
  Nodecount child;

  gt_assert(parent->lower < parent->upper);
  rangesize = gt_bwtrangesplitallwithoutspecial(tmpmbtab,
                                             rangeOccs,
                                             index,
                                             parent->lower,
                                             parent->upper);
  gt_assert(rangesize <= (unsigned long) numofchars);

  offset = 0U;
  num_special = parent->upper - parent->lower;
  for (idx = 0; idx < rangesize; idx++)
  {
    child.lower = tmpmbtab[idx].lowerbound;
    child.upper = tmpmbtab[idx].upperbound;
    child.leaves = 0UL;
    child.branching = 1UL;
    child.parentOffset = offset + 1U;
    child.visited = false;
    child.on_branch = false;

    /* check if child is part of a branch */
    if (child.upper - child.lower == parent->upper - parent->lower)
    {
      /* XXX do sth with non branching nodes */
      child.on_branch = true;
      parent->branching--;
      GT_STACK_PUSH(stack, child);
      num_special = 0UL;
      offset++;
    }
    else
    {
      /* we found a leave on parent*/
      if (child.lower + 1 == child.upper)
      {
        parent->leaves++;
        num_special--;
      }
      else
        /* child is a branch of parent node */
      {
        if (child.lower == child.upper)
        {
          /* do nothing, this is no node, this is a missing char */
        }
        else
        {
          GT_STACK_PUSH(stack, child);
          offset++;
          num_special -= (child.upper - child.lower);
        }
      }
    }
  }
  parent->leaves += num_special;
}

static void process_count_node(GtStackNodecount *stack,
                         Nodecount *current)
{
  Nodecount *parent;

  parent = &(stack->space[stack->nextfree - current->parentOffset]);
  parent->leaves += current->leaves;
  parent->branching += current->branching;
}

void gt_pck_count_nodes_dfs(const FMindex *index,
                        unsigned long totallength,
                        unsigned int numofchars)
{
  GtStackNodecount stack;
  Nodecount root;
  Nodecount *current;
  Mbtab *tmpmbtab;
  unsigned long *rangeOccs;
  unsigned long resize = 128UL; /* XXX make this user definable, or dependable
                                 * on input data */

  GT_STACK_INIT(&stack, resize);
  rangeOccs = gt_malloc(sizeof (*rangeOccs) * GT_MULT2(numofchars));
  tmpmbtab = gt_malloc(sizeof (*tmpmbtab) * numofchars);

  root.lower = 0UL;
  root.upper = totallength + 1;
  root.leaves = 0UL;
  root.branching = 1UL;
  root.parentOffset = 0U;
  root.visited = false;
  root.on_branch = false;

  GT_STACK_PUSH(&stack, root);

  while (!GT_STACK_ISEMPTY(&stack))
  {
    current = &(stack.space[stack.nextfree -1]);
    if (current->visited)
    {
      current = &(GT_STACK_POP(&stack));
      if GT_STACK_ISEMPTY(&stack)
      {
        /* XXX change to gt_loger_log */
        gt_log_log("on root:\n %lu branching nodes\n %lu leaves\n",
           current->branching, current->leaves);
      }
      else
      {
        process_count_node(&stack, current);
      }
    }
    else
    {
      visit_count_children(index, current, &stack,
                     tmpmbtab, rangeOccs, numofchars);
      current->visited = true;
    }
  }
  gt_free(rangeOccs);
  gt_free(tmpmbtab);
  GT_STACK_DELETE(&stack);
}
genometools-1.5.1/src/match/pck-count-nodes.h000066400000000000000000000025051211610345200211130ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef PCK_COUNT_NODES_H
#define PCK_COUNT_NODES_H

#include 

#include "core/stack-inlined.h"

#include "match/eis-voiditf.h"

typedef struct Nodecount_tag {
  unsigned long leaves, branching, lower, upper;
  unsigned int parentOffset;
  bool visited, on_branch;
} Nodecount;

GT_STACK_DECLARESTRUCT(Nodecount, 256UL);

void gt_pck_count_nodes_dfs(const FMindex *index,
                        unsigned long totallength,
                        unsigned int numofchars);

#endif
genometools-1.5.1/src/match/pckbucket.c000066400000000000000000000221251211610345200200500ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/fa.h"
#include "core/divmodmul.h"
#include "core/xansi_api.h"
#include "core/fileutils_api.h"
#include "core/chardef.h"
#include "eis-voiditf.h"
#include "pckbucket.h"
#include "initbasepower.h"

typedef struct
{
  unsigned long lowerbound,
                upperbound;
  unsigned int depth;
  GtCodetype code;
} Pckbck_Boundsatdepth;

GT_DECLAREARRAYSTRUCT(Pckbck_Boundsatdepth);

struct Pckbuckettable
{
  unsigned int numofchars, maxdepth;
  unsigned long numofvalues, maxnumofvalues;
  Mbtab **mbtab;
  void *mapptr;
  GtCodetype *basepower;
};

static void pckbuckettable_settaboffsets(Pckbuckettable *pckbt)
{
  unsigned int idx;

  gt_assert(pckbt != NULL);
  for (idx=0; idxmaxdepth; idx++)
  {
    pckbt->mbtab[idx+1] = pckbt->mbtab[idx] + pckbt->basepower[idx];
  }
}

static Pckbuckettable *pckbuckettable_allocandinittable(unsigned int numofchars,
                                                        unsigned int maxdepth,
                                                        bool writemode)
{
  Mbtab *cptr;
  unsigned int idx;
  Pckbuckettable *pckbt;

  pckbt = gt_malloc(sizeof (Pckbuckettable));
  pckbt->basepower = gt_initbasepower(numofchars,maxdepth);
  pckbt->numofchars = numofchars;
  pckbt->maxdepth = maxdepth;
  pckbt->maxnumofvalues = pckbt->numofvalues = 0;
  for (idx=0; idx <= maxdepth; idx++)
  {
    /*printf("basepower[%u]=%lu\n",idx,pckbt->basepower[idx]); */
    pckbt->maxnumofvalues += pckbt->basepower[idx];
  }
  pckbt->mbtab = gt_malloc(sizeof (Mbtab *) * (maxdepth+1));
  if (writemode)
  {
    pckbt->mapptr = NULL;
    pckbt->mbtab[0] = gt_malloc(sizeof (Mbtab) * pckbt->maxnumofvalues);
    /*
    printf("allocated = %u * %lu\n",sizeof (Mbtab),pckbt->maxnumofvalues);
    */
    for (cptr = pckbt->mbtab[0];
         cptr < pckbt->mbtab[0] + pckbt->maxnumofvalues; cptr++)
    {
      cptr->lowerbound = cptr->upperbound = 0;
    }
    pckbuckettable_settaboffsets(pckbt);
  }
  return pckbt;
}

void gt_pckbuckettable_delete(Pckbuckettable *pckbt)
{
  gt_assert(pckbt != NULL);
  if (pckbt->mapptr == NULL)
  {
    gt_free(pckbt->mbtab[0]);
  } else
  {
    gt_fa_xmunmap(pckbt->mapptr);
  }
  pckbt->mbtab[0] = NULL;
  gt_free(pckbt->mbtab);
  pckbt->mbtab = NULL;
  gt_free(pckbt->basepower);
  pckbt->basepower = NULL;
  gt_free(pckbt);
}

static void pckbuckettable_storeBoundsatdepth(Pckbuckettable *pckbt,
                                              const Pckbck_Boundsatdepth *bd)
{
  gt_assert(bd != NULL && pckbt != NULL);
  gt_assert(bd->depth <= pckbt->maxdepth);
  gt_assert(bd->code <= pckbt->basepower[bd->depth]);
  /*
  printf("bd->depth=%u,bd->code=%lu\n",bd->depth,bd->code);
  */
  gt_assert(pckbt->mbtab[bd->depth][bd->code].lowerbound == 0 &&
            pckbt->mbtab[bd->depth][bd->code].upperbound == 0);
  gt_assert(pckbt->numofvalues < pckbt->maxnumofvalues);
  pckbt->numofvalues++;
  pckbt->mbtab[bd->depth][bd->code].lowerbound = bd->lowerbound;
  pckbt->mbtab[bd->depth][bd->code].upperbound = bd->upperbound;
}

static void pckbuckettable_followleafedge(Pckbuckettable *pckbt,
                                          const FMindex *fmindex,
                                          const Pckbck_Boundsatdepth *bd)
{
  Bwtseqcontextiterator *bsci;
  GtUchar cc;
  Pckbck_Boundsatdepth bdleaf;

  gt_assert(bd != NULL);
  bdleaf.code = bd->code;
  bdleaf.depth = bd->depth;
  bdleaf.lowerbound = bd->lowerbound;
  bsci = gt_Bwtseqcontextiterator_new(fmindex,bdleaf.lowerbound);
  while (bdleaf.depth < pckbt->maxdepth)
  {
    bdleaf.depth++;
    cc = gt_Bwtseqcontextiterator_next(&bdleaf.lowerbound,bsci);
    if (ISSPECIAL(cc))
    {
      break;
    }
    bdleaf.code = bdleaf.code * pckbt->numofchars + cc;
    bdleaf.upperbound = bdleaf.lowerbound+1;
    pckbuckettable_storeBoundsatdepth(pckbt,&bdleaf);
  }
  gt_Bwtseqcontextiterator_delete(bsci);
  bsci = NULL;
}

Pckbuckettable *gt_pckbuckettable_new(const FMindex *fmindex,
                                      unsigned int numofchars,
                                      unsigned long totallength,
                                      unsigned int maxdepth)
{
  GtArrayPckbck_Boundsatdepth stack;
  Pckbck_Boundsatdepth parent, child;
  unsigned long rangesize, idx, *rangeOccs;
  Pckbuckettable *pckbt;
  Mbtab *tmpmbtab;

  GT_INITARRAY(&stack,Pckbck_Boundsatdepth);
  child.lowerbound = 0;
  child.upperbound = totallength+1;
  child.depth = 0;
  child.code = (GtCodetype) 0;
  GT_STOREINARRAY(&stack,Pckbck_Boundsatdepth,128,child);
  rangeOccs = gt_malloc(sizeof (*rangeOccs) * GT_MULT2(numofchars));
  tmpmbtab = gt_malloc(sizeof (*tmpmbtab) * numofchars);
  pckbt = pckbuckettable_allocandinittable(numofchars,maxdepth,true);
  while (stack.nextfreePckbck_Boundsatdepth > 0)
  {
    parent
      = stack.spacePckbck_Boundsatdepth[--stack.nextfreePckbck_Boundsatdepth];
    gt_assert(parent.lowerbound < parent.upperbound);
    rangesize = gt_bwtrangesplitallwithoutspecial(tmpmbtab,
                                                  rangeOccs,
                                                  fmindex,
                                                  parent.lowerbound,
                                                  parent.upperbound);
    gt_assert(rangesize <= (unsigned long) numofchars);
    for (idx = 0; idx < rangesize; idx++)
    {
      child.lowerbound = tmpmbtab[idx].lowerbound;
      child.upperbound = tmpmbtab[idx].upperbound;
      child.depth = parent.depth + 1;
      gt_assert(child.depth <= maxdepth);
      child.code = parent.code * numofchars + idx;
      pckbuckettable_storeBoundsatdepth(pckbt,&child);
      if (child.depth < maxdepth)
      {
        if (child.lowerbound + 1 < child.upperbound)
        {
          GT_STOREINARRAY(&stack,Pckbck_Boundsatdepth,128,child);
        } else
        {
          pckbuckettable_followleafedge(pckbt,fmindex,&child);
        }
      }
    }
  }
  GT_FREEARRAY(&stack,Pckbck_Boundsatdepth);
  gt_free(rangeOccs);
  gt_free(tmpmbtab);
  printf("filled: %lu (%.2f)\n",pckbt->numofvalues,
                        (double) pckbt->numofvalues/pckbt->maxnumofvalues);
  return pckbt;
}

#define PCKBUCKETTABLE ".pbt"

int gt_pckbuckettable_2file(const char *indexname,
                            const Pckbuckettable *pckbuckettable,
                            GtError *err)
{
  FILE *fp;
  unsigned long seqposmaxdepth;

  gt_error_check(err);
  fp = gt_fa_fopen_with_suffix(indexname,PCKBUCKETTABLE,"wb",err);
  if (fp == NULL)
  {
    return -1;
  }
  seqposmaxdepth = (unsigned long) pckbuckettable->maxdepth;
  gt_xfwrite(&seqposmaxdepth,sizeof (unsigned long),(size_t) 1,fp);
  gt_xfwrite(pckbuckettable->mbtab[0],sizeof (Mbtab),
             (size_t) pckbuckettable->maxnumofvalues,fp);
  gt_fa_fclose(fp);
  return 0;
}

bool gt_pckbuckettable_exists(const char *indexname)
{
  GtStr *tmpfilename;
  bool retval;

  tmpfilename = gt_str_new_cstr(indexname);
  gt_str_append_cstr(tmpfilename,PCKBUCKETTABLE);
  retval = gt_file_exists(gt_str_get(tmpfilename));
  gt_str_delete(tmpfilename);
  return retval;
}

Pckbuckettable *gt_pckbuckettable_map(const char *indexname,
                                      unsigned int numofchars,
                                      GtError *err)
{
  size_t numofbytes;
  void *mapptr;
  unsigned int maxdepth;
  Pckbuckettable *pckbt;

  gt_error_check(err);
  mapptr = gt_fa_mmap_read_with_suffix(indexname,PCKBUCKETTABLE,
                                       &numofbytes,err);
  if (mapptr == NULL)
  {
    return NULL;
  }
  maxdepth = (unsigned int) ((unsigned long *) mapptr)[0];
  pckbt = pckbuckettable_allocandinittable(numofchars,maxdepth,false);
  pckbt->mapptr = mapptr;
  pckbt->mbtab[0] = (Mbtab *) (((unsigned long *) mapptr) + 1);
  pckbuckettable_settaboffsets(pckbt);
  gt_assert(numofbytes ==
            sizeof (unsigned long) + sizeof (Mbtab) * pckbt->maxnumofvalues);
  return pckbt;
}

unsigned int gt_pckbuckettable_maxdepth_get(
                       const Pckbuckettable *pckbuckettable)
{
  gt_assert(pckbuckettable != NULL);
  return pckbuckettable->maxdepth;
}

unsigned int gt_pckbuckettable_numofchars_get(
                       const Pckbuckettable *pckbuckettable)
{
  gt_assert(pckbuckettable != NULL);
  return pckbuckettable->numofchars;
}

const void *gt_pckbuckettable_mbtab_get(const Pckbuckettable *pckbuckettable)
{
  gt_assert(pckbuckettable != NULL);
  return (const void *) pckbuckettable->mbtab;
}
genometools-1.5.1/src/match/pckbucket.h000066400000000000000000000040521211610345200200540ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef PCKBUCKET_H
#define PCKBUCKET_H

#include "core/str.h"
#include "core/error.h"
#include "core/codetype.h"
#include "eis-voiditf.h"
#include "splititv.h"

typedef struct Pckbuckettable Pckbuckettable;

void gt_pckbuckettable_delete(Pckbuckettable *pckbt);

Pckbuckettable *gt_pckbuckettable_new(const FMindex *fmindex,
                                      unsigned int numofchars,
                                      unsigned long totallength,
                                      unsigned int maxdepth);

int gt_pckbuckettable_2file(const char *indexname,
                            const Pckbuckettable *pckbuckettable,
                            GtError *err);

bool gt_pckbuckettable_exists(const char *indexname);

Pckbuckettable *gt_pckbuckettable_map(const char *indexname,
                                      unsigned int numofchars,
                                      GtError *err);

unsigned int gt_pckbuckettable_maxdepth_get(const Pckbuckettable
                                             *pckbuckettable);

const void *gt_pckbuckettable_mbtab_get(const Pckbuckettable *pckbuckettable);

unsigned int gt_pckbuckettable_numofchars_get(
                       const Pckbuckettable *pckbuckettable);

#endif
genometools-1.5.1/src/match/pckdfs.c000066400000000000000000000177051211610345200173570ustar00rootroot00000000000000/*
  Copyright (c) 2010 Stefan Kurtz 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/divmodmul.h"
#include "eis-voiditf.h"
#include "pckdfs.h"

typedef struct
{
  union
  {
    struct
    {
      unsigned long lowerbound,
                    upperbound;
      GtUchar inchar;
    } pckitv;
    unsigned long remainingspecial;
  } either;
  unsigned long depth,
                lcpnodedepth;
  bool isinterval;
} Dfs_Boundsatdepth;

GT_DECLAREARRAYSTRUCT(Dfs_Boundsatdepth);

static unsigned long dfsnonspecialwidth(const GtArrayBoundswithchar *bwci)
{
  unsigned long idx, addwidth = 0;

  for (idx = 0; idx < bwci->nextfreeBoundswithchar; idx++)
  {
    addwidth += bwci->spaceBoundswithchar[idx].rbound -
                bwci->spaceBoundswithchar[idx].lbound;
  }
  return addwidth;
}

#undef SKDEBUG
#ifdef SKDEBUG
static void showcurrentpath(const GtArrayGtUchar *currentpath)
{
  unsigned long idx;

  printf("path=");
  for (idx = 0; idx < currentpath->nextfreeGtUchar; idx++)
  {
    printf("%u ",(unsigned int) currentpath->spaceGtUchar[idx]);
  }
  printf("\n");
}

static void showDfs_Boundsatdepth(const char *kind,const Dfs_Boundsatdepth *bd)
{
  printf("%s ",kind);
  if (bd->isinterval)
  {
    printf("l=%lu u=%lu i=%u d=%lu\n",bd->either.pckitv.lowerbound,
                                      bd->either.pckitv.upperbound,
                                      (unsigned int)
                                      bd->either.pckitv.inchar,
                                      bd->depth);
  } else
  {
    printf("w=%lu d=%lu\n",bd->either.remainingspecial,bd->depth);
  }
}
#endif

int gt_fmindex_dfstraverse(const FMindex *fmindex,
                           unsigned int numofchars,
                           unsigned long totallength,
                           Processlcp processlcp,
                           void *processlcpdata,
                           GtError *err)
{
  GtArrayDfs_Boundsatdepth stack;
  GtArrayBoundswithchar bwci;
  Boundswithchar *bwciptr;
  Dfs_Boundsatdepth parent, child;
  GtArrayGtUchar currentpath;
  unsigned long nonspecialwidth, parentwidth, *rangeOccs;
  bool haserr = false, firstleaf = true;

  GT_INITARRAY(&stack,Dfs_Boundsatdepth);
  GT_INITARRAY(¤tpath,GtUchar);
  bwci.spaceBoundswithchar = gt_malloc(sizeof (*bwci.spaceBoundswithchar) *
                                       (numofchars+1));
  bwci.nextfreeBoundswithchar = 0;
  bwci.allocatedBoundswithchar = (unsigned long) (numofchars+1);
  child.isinterval = true;
  child.depth = 0;
  child.lcpnodedepth = 0;
  child.either.pckitv.lowerbound = 0;
  child.either.pckitv.upperbound = totallength+1;
  child.either.pckitv.inchar = (GtUchar) numofchars; /* undefined */
#ifdef SKDEBUG
  showDfs_Boundsatdepth("push",&child);
#endif
  GT_STOREINARRAY(&stack,Dfs_Boundsatdepth,128,child);
  rangeOccs = gt_malloc(sizeof (*rangeOccs) * GT_MULT2(numofchars));
  while (!haserr && stack.nextfreeDfs_Boundsatdepth > 0)
  {
    parent = stack.spaceDfs_Boundsatdepth[--stack.nextfreeDfs_Boundsatdepth];
#ifdef SKDEBUG
    showDfs_Boundsatdepth("pop",&parent);
#endif
    if (!parent.isinterval)
    {

      gt_assert(parent.depth > 0);
      if (processlcp != NULL)
      {
        unsigned long idx;

        for (idx = 0; idx 0)
      {
        gt_assert(parent.either.pckitv.inchar < (GtUchar) numofchars);
        if (parent.depth - 1 >= currentpath.allocatedGtUchar)
        {
          currentpath.allocatedGtUchar += 32UL;
          currentpath.spaceGtUchar
            = gt_realloc(currentpath.spaceGtUchar,
                         sizeof (*currentpath.spaceGtUchar) *
                         currentpath.allocatedGtUchar);
        }
        gt_assert(currentpath.spaceGtUchar != NULL);
        currentpath.spaceGtUchar[parent.depth - 1]
          = parent.either.pckitv.inchar;
        currentpath.nextfreeGtUchar = parent.depth;
#ifdef SKDEBUG
        showcurrentpath(¤tpath);
#endif
      }
      parentwidth = parent.either.pckitv.upperbound -
                    parent.either.pckitv.lowerbound;
      if (parentwidth == 1UL)
      {
        if (!firstleaf)
        {
          if (processlcp != NULL)
          {
            if (processlcp(processlcpdata,parent.lcpnodedepth,err) != 0)
            {
              haserr = true;
            }
          }
        } else
        {
          firstleaf = false;
        }
      } else
      {
        gt_assert(parentwidth >= 2UL);
        gt_bwtrangesplitwithoutspecial(&bwci,rangeOccs,fmindex,
                                       parent.either.pckitv.lowerbound,
                                       parent.either.pckitv.upperbound);
        nonspecialwidth = dfsnonspecialwidth(&bwci);
#ifdef SKDEBUG
        printf("split %lu %lu into %lu intervals of width %lu\n",
               parent.either.pckitv.lowerbound,
               parent.either.pckitv.upperbound,
               bwci.nextfreeBoundswithchar,
               nonspecialwidth);
#endif
        gt_assert(nonspecialwidth <= parentwidth);
        if (nonspecialwidth < parentwidth)
        {
          child.isinterval = false;
          child.depth = parent.depth + 1;
          child.either.remainingspecial = parentwidth - nonspecialwidth;
          if (bwci.nextfreeBoundswithchar > 0)
          {
            child.lcpnodedepth = parent.depth;
          } else
          {
            child.lcpnodedepth = parent.lcpnodedepth;
          }
#ifdef SKDEBUG
          showDfs_Boundsatdepth("special push",&child);
#endif
          GT_STOREINARRAY(&stack,Dfs_Boundsatdepth,128,child);
        }
        gt_assert(bwci.spaceBoundswithchar != NULL);
        for (bwciptr = bwci.spaceBoundswithchar+bwci.nextfreeBoundswithchar-1;
             bwciptr >= bwci.spaceBoundswithchar;
             bwciptr--)
        {
          child.isinterval = true;
          child.depth = parent.depth + 1;
          child.either.pckitv.lowerbound = bwciptr->lbound;
          child.either.pckitv.upperbound = bwciptr->rbound;
          if (bwciptr > bwci.spaceBoundswithchar)
          {
            child.lcpnodedepth = parent.depth;
          } else
          {
            child.lcpnodedepth = parent.lcpnodedepth;
          }
          gt_assert(bwciptr->inchar < (GtUchar) numofchars);
          child.either.pckitv.inchar = bwciptr->inchar;
          gt_assert(child.either.pckitv.lowerbound <
                    child.either.pckitv.upperbound);
#ifdef SKDEBUG
          showDfs_Boundsatdepth("push",&child);
#endif
          GT_STOREINARRAY(&stack,Dfs_Boundsatdepth,128,child);
        }
      }
    }
  }
  GT_FREEARRAY(&stack,Dfs_Boundsatdepth);
  GT_FREEARRAY(&bwci,Boundswithchar);
  GT_FREEARRAY(¤tpath,GtUchar);
  gt_free(rangeOccs);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/pckdfs.h000066400000000000000000000024261211610345200173560ustar00rootroot00000000000000/*
  Copyright (c) 2010 Stefan Kurtz 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef PCKDFS_H
#define PCKDFS_H
#include "eis-voiditf.h"

typedef int (*Processlcp)(void *processinfo,unsigned long lcp,GtError *err);

int gt_fmindex_dfstraverse(const FMindex *fmindex,
                            unsigned int numofchars,
                            unsigned long totallength,
                            Processlcp processlcp,
                            void *processlcpdata,
                            GtError *err);

#endif
genometools-1.5.1/src/match/procmatch.h000066400000000000000000000030301211610345200200540ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef PROCMATCH_H
#define PROCMATCH_H

#include "core/types_api.h"

typedef struct
{
  bool dbabsolute;
  unsigned long dbseqnum;
  unsigned long dbstartpos,
         dblen;
  const GtUchar *dbsubstring;
  unsigned long querystartpos,
                querylen,
                distance;
  const void *alignment;
} GtIdxMatch;

typedef void (*ProcessIdxMatch)(void *processinfo,
                             const GtIdxMatch *match);

typedef void (*Processresult)(void *,
                              const void *,
                              unsigned long,
                              unsigned long,
                              unsigned long,
                              unsigned long);

#endif
genometools-1.5.1/src/match/prsqualint.c000066400000000000000000000062511211610345200203010ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#endif
#include 
#include 
#include 
#include 
#include "core/ma_api.h"
#include "core/error_api.h"
#include "prsqualint.h"

#define ERRORMSG\
        "argument \"%s\" of option %s must be positive number "\
        "possibly followed by character %c or %c; if the "\
        "number is followed by character %c, then it must be "\
        " <= 100"

#define ERRORLPARAM\
        if (err != NULL)\
        {\
          gt_error_set(err,ERRORMSG,lparam,option,BESTCHARACTER,\
                       PERCENTAWAYCHARACTER,\
                       PERCENTAWAYCHARACTER);\
        } else\
        {\
          fprintf(stderr,ERRORMSG,lparam,option,BESTCHARACTER,\
                         PERCENTAWAYCHARACTER,\
                         PERCENTAWAYCHARACTER);\
        }

Qualifiedinteger *gt_parsequalifiedinteger(const char *option,
                                        const char *lparam,
                                        GtError *err)
{
  long readint;
  size_t i;
  char *lparamcopy;
  bool haserr = false;
  Qualifiedinteger *qualint;

  lparamcopy = gt_malloc(sizeof (char) * (strlen(lparam)+1));
  qualint = gt_malloc(sizeof (*qualint));
  strcpy(lparamcopy,lparam);
  for (i=0; lparamcopy[i] != '\0'; i++)
  {
    if (!isdigit((int) lparamcopy[i]) &&
        lparamcopy[i] != BESTCHARACTER &&
        lparamcopy[i] != PERCENTAWAYCHARACTER)
    {
      ERRORLPARAM;
      haserr = true;
      break;
    }
  }
  if (!haserr && i == 0)
  {
    ERRORLPARAM;
    haserr = true;
  }
  if (!haserr)
  {
    if (lparamcopy[i-1] == BESTCHARACTER)
    {
      lparamcopy[i-1] = '\0';
      qualint->qualtag = Qualbestof;
    } else
    {
      if (lparamcopy[i-1] == PERCENTAWAYCHARACTER)
      {
        lparamcopy[i-1] = '\0';
        qualint->qualtag = Qualpercentaway;
      } else
      {
        qualint->qualtag = Qualabsolute;
      }
    }
    if (sscanf(lparamcopy,"%ld",&readint) != 1 || readint <= 0)
    {
      ERRORLPARAM;
      haserr = true;
    }
  }
  if (!haserr &&
      (qualint->qualtag == Qualpercentaway || qualint->qualtag == Qualbestof))
  {
    if (readint > 100L)
    {
      ERRORLPARAM;
      haserr = true;
    }
  }
  qualint->integervalue = (unsigned long) readint;
  gt_free(lparamcopy);
  if (haserr)
  {
    gt_free (qualint);
    return NULL;
  }
  return qualint;
}
genometools-1.5.1/src/match/prsqualint.h000066400000000000000000000025241211610345200203050ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef PRSQUALINT_H
#define PRSQUALINT_H

#include "core/error_api.h"

#define BESTCHARACTER        'b'
#define PERCENTAWAYCHARACTER 'p'

typedef enum
{
  Qualabsolute,
  Qualpercentaway,
  Qualbestof
} Qualificationtag;

typedef struct
{
  Qualificationtag qualtag;
  unsigned long integervalue;
} Qualifiedinteger;

Qualifiedinteger *gt_parsequalifiedinteger(const char *option,
                                           const char *lparam,
                                           GtError *err);

#endif
genometools-1.5.1/src/match/pssm.c000066400000000000000000000076521211610345200170670ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/assert_api.h"
#include "core/types_api.h"
#include "core/chardef.h"
#include "core/ma_api.h"
#include "core/arraydef.h"
#include "core/encseq.h"
#include "absdfstrans-imp.h"

typedef int ProfScore;
#define SHOWProfScore(FP,VAL) fprintf(FP,"%d",VAL)

#define GETPROFSCORE(S,A,D)   (S)->scoretab[A][D]

typedef struct
{
  unsigned long dimension,
                numofcharacters;
  ProfScore *itmthreshold,  /* intermediate thresholds */
            maxtotalscore,  /* the maximum score */
            mintotalscore,  /* the minimum score */
            **scoretab;     /* the scores */
} Profilematrix;

void gt_showProfilematrix(const Profilematrix *prof,
                              const GtUchar *characters)
{
  unsigned long d, a;

  printf("# %lu x %lu matrix\n",prof->numofcharacters,
                                prof->dimension);
  printf("# mintotalscore=");
  SHOWProfScore(stdout,prof->mintotalscore);
  printf("\n");
  printf("# maxtotalscore=");
  SHOWProfScore(stdout,prof->maxtotalscore);
  printf("\n");
  printf("   ");
  for (a = 0; a < prof->numofcharacters; a++)
  {
    printf("%c",(int) characters[a]);
    printf("%s",(a < prof->numofcharacters - 1) ? "   " : "\n");
  }
  for (d = 0; d < prof->dimension; d++)
  {
    for (a = 0; a < prof->numofcharacters; a++)
    {
      SHOWProfScore(stdout,GETPROFSCORE(prof,a,d));
      printf("%s",(a < prof->numofcharacters - 1) ? " " : " \n");
    }
  }
}

void gt_makeitmthresholds(Profilematrix *prof,
                              ProfScore minscore)
{
  unsigned long d, a;
  long ddown;
  ProfScore partsum,
            score,
            *maxscore;

  maxscore = gt_malloc(sizeof *maxscore * prof->dimension);
  for (d=0; ddimension; d++)
  {
    for (a=0; anumofcharacters; a++)
    {
      score = GETPROFSCORE(prof,a,d);
      if (a == 0 || maxscore[d] < score)
      {
        maxscore[d] = score;
      }
    }
  }
  partsum = (ProfScore) 0;
  gt_assert(prof->itmthreshold != NULL);
  for (ddown = (long) (prof->dimension-1); ddown>=0; ddown--)
  {
    prof->itmthreshold[ddown] = minscore - partsum;
    partsum += maxscore[ddown];
  }
  gt_free(maxscore);
}

void gt_lookaheadsearchPSSM(const GtEncseq *encseq,
                            const Profilematrix *prof)
{
  unsigned long firstpos, bufsize;
  GtUchar currentchar;
  unsigned long pos;
  GtEncseqReader *esr;
  unsigned long totallength = gt_encseq_total_length(encseq);
  GtUchar *buffer;

  esr = gt_encseq_create_reader_with_readmode(encseq,GT_READMODE_FORWARD,0);
  buffer = gt_malloc(sizeof *buffer * prof->dimension);
  firstpos = bufsize = 0;
  for (pos=0; pos < totallength; pos++)
  {
    currentchar = gt_encseq_reader_next_encoded_char(esr);
    if (ISSPECIAL(currentchar))
    {
      bufsize = firstpos = 0;
    } else
    {
      if (bufsize < prof->dimension)
      {
        buffer[bufsize++] = currentchar;
      } else
      {
        buffer[firstpos++] = currentchar;
        if (firstpos == prof->dimension)
        {
          firstpos = 0;
        }
      }
    }
  }
  gt_encseq_reader_delete(esr);
  gt_free(buffer);
}
genometools-1.5.1/src/match/qgram2code.h000066400000000000000000000027171211610345200201330ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef QGRAM2CODE_H
#define QGRAM2CODE_H

#include "core/types_api.h"
#include "core/chardef.h"
#include "core/codetype.h"

static inline unsigned int qgram2code(GtCodetype *code,
                                      const GtCodetype **multimappower,
                                      unsigned int qvalue,
                                      const GtUchar *qgram)
{
  int i;
  GtCodetype tmpcode = 0;
  GtUchar a;

  for (i=(int) (qvalue-1); i>=0; i--)
  {
    a = qgram[i];
    if (ISSPECIAL(a))
    {
      return (unsigned int) i;
    }
    tmpcode += multimappower[i][a];
  }
  *code = tmpcode;
  return qvalue;
}

#endif
genometools-1.5.1/src/match/qsort-array.gen000066400000000000000000000142511211610345200207110ustar00rootroot00000000000000#include 
#include "core/minmax.h"
#include "core/divmodmul.h"
#include "core/stack-inlined.h"

/*
 * Qsort routine from Bentley & McIlroy's ``Engineering a Sort Function''.
 */

#ifndef GT_QSORT_ARR_SWAP
#define GT_QSORT_ARR_SWAP(ARR,A,B)\
        if ((A) != (B))\
        {\
          tmp = QSORTNAME(ARRAY_GET)(ARR,A);\
          QSORTNAME(ARRAY_SET)(ARR,A,QSORTNAME(ARRAY_GET)(ARR,B));\
          QSORTNAME(ARRAY_SET)(ARR,B,tmp);\
        }
#endif

#ifndef GT_QSORT_ARR_VECSWAP
#define GT_QSORT_ARR_VECSWAP(ARR,A,B,N)\
        aidx = A;\
        bidx = B;\
        while ((N)-- > 0)\
        {\
          tmp = QSORTNAME(ARRAY_GET)(ARR,aidx);\
          QSORTNAME(ARRAY_SET)(ARR,aidx,QSORTNAME(ARRAY_GET)(ARR,bidx));\
          QSORTNAME(ARRAY_SET)(ARR,bidx,tmp);\
          aidx++;\
          bidx++;\
        }
#endif

static inline unsigned long QSORTNAME(gt_inlined_qsort_arr_r_med3)
                     (const QSORTNAME(Sorttype) *arr,unsigned long a,
                      unsigned long b, unsigned long c,
                      QSORTNAME(Datatype) data)
{
  return QSORTNAME(qsortcmparr) (arr, a, b, data) < 0
           ? (QSORTNAME(qsortcmparr) (arr, b, c, data) < 0
                ? b
                : (QSORTNAME(qsortcmparr) (arr, a, c, data) < 0
                     ? c : a))
           : (QSORTNAME(qsortcmparr) (arr, b, c, data) > 0
                ? b
                : (QSORTNAME(qsortcmparr) (arr, a, c, data) < 0
                     ? a
                     : c));
}

#ifndef GT_STACK_INTERVALARRAYTOBESORTED_DEFINED
typedef struct
{
  unsigned long startindex,
                len;
} Intervalarrtobesorted;

GT_STACK_DECLARESTRUCT(Intervalarrtobesorted,32UL);
#define GT_STACK_INTERVALARRAYTOBESORTED_DEFINED
#endif

static void QSORTNAME(gt_inlinedarr_qsort_r) (
                                   unsigned long insertionsortthreshold,
                                   bool handlenotswapped,
                                   QSORTNAME(Sorttype) *arr,
                                   unsigned long len,
                                   QSORTNAME(Datatype) data)
{
  unsigned long tmp, pa, pb, pc, pd, pl, pm, pn, aidx, bidx, s;
  int r;
  bool swapped;
  GtStackIntervalarrtobesorted intervalstack;
  Intervalarrtobesorted current;

  GT_STACK_INIT(&intervalstack,32UL);
  current.startindex = 0;
  current.len = len;
  GT_STACK_PUSH(&intervalstack,current);
  if (insertionsortthreshold <= 2UL)
  {
    insertionsortthreshold = 6UL;
  }
  while (!GT_STACK_ISEMPTY(&intervalstack))
  {
    swapped = false;
    current = GT_STACK_POP(&intervalstack);
    if (current.len <= insertionsortthreshold)
    {
      for (pm = current.startindex + 1;
           pm < current.startindex + current.len; pm++)
      {
        for (pl = pm; pl > current.startindex &&
                      QSORTNAME(qsortcmparr) (arr, pl - 1, pl, data) > 0;
             pl--)
        {
          GT_QSORT_ARR_SWAP (arr, pl, pl - 1);
        }
      }
      continue;
    }
    pm = current.startindex + GT_DIV2 (current.len);
    if (current.len > 7UL)
    {
      pl = current.startindex;
      pn = current.startindex + current.len - 1;
      if (current.len > 40UL)
      {
        s = GT_DIV8 (current.len);
        pl = QSORTNAME(gt_inlined_qsort_arr_r_med3) (arr, pl, pl + s,
                                                     pl + GT_MULT2 (s), data);
        gt_assert(pm >= s);
        pm = QSORTNAME(gt_inlined_qsort_arr_r_med3) (arr, pm - s, pm,
                                                     pm + s, data);
        gt_assert(pn >= GT_MULT2(s));
        pn = QSORTNAME(gt_inlined_qsort_arr_r_med3) (arr, pn - GT_MULT2 (s),
                                                     pn - s, pn, data);
      }
      pm = QSORTNAME(gt_inlined_qsort_arr_r_med3) (arr, pl, pm, pn, data);
    }
    GT_QSORT_ARR_SWAP (arr, current.startindex, pm);
    pa = pb = current.startindex + 1;
    pc = pd = current.startindex + current.len - 1;
    while (1)
    {
      while (pb <= pc &&
             (r = QSORTNAME(qsortcmparr) (arr, pb,
                                          current.startindex, data)) <= 0)
      {
        if (r == 0)
        {
          swapped = true;
          GT_QSORT_ARR_SWAP (arr, pa, pb);
          pa++;
        }
        pb++;
      }
      while (pb <= pc &&
             (r = QSORTNAME(qsortcmparr) (arr, pc,
                                          current.startindex, data)) >= 0)
      {
        if (r == 0)
        {
          swapped = true;
          GT_QSORT_ARR_SWAP (arr, pc, pd);
          gt_assert(pd > 0);
          pd--;
        }
        gt_assert(pc > 0);
        pc--;
      }
      if (pb > pc)
      {
        break;
      }
      GT_QSORT_ARR_SWAP (arr, pb, pc);
      swapped = true;
      pb++;
      gt_assert(pc > 0);
      pc--;
    }
    /* The following switch is not explained in the above mentioned
       paper and therefore we ignore it. */
    if (handlenotswapped && !swapped)
    {                                  /* Switch to insertion sort */
      gt_assert(current.len <= 40UL);
      for (pm = current.startindex + 1;
           pm < current.startindex + current.len; pm++)
      {
        for (pl = pm; pl > current.startindex &&
                      QSORTNAME(qsortcmparr) (arr, pl - 1, pl, data) > 0;
             pl--)
        {
          GT_QSORT_ARR_SWAP (arr, pl, pl - 1);
        }
      }
      continue;
    }
    pn = current.startindex + current.len;
    gt_assert(pa >= current.startindex);
    gt_assert(pb >= pa);
    s = MIN ((unsigned long) (pa - current.startindex),
             (unsigned long) (pb - pa));
    gt_assert(pb >= s);
    GT_QSORT_ARR_VECSWAP (arr, current.startindex, pb - s, s);
    gt_assert(pd >= pc);
    gt_assert(pn > pd);
    s = MIN ((unsigned long) (pd - pc), (unsigned long) (pn - pd - 1));
    gt_assert(pn > s);
    GT_QSORT_ARR_VECSWAP (arr, pb, pn - s, s);
    gt_assert(pb >= pa);
    if ((s = (unsigned long) (pb - pa)) > 1UL)
    {
      current.len = s;
      GT_STACK_PUSH(&intervalstack,current);
    }
    gt_assert(pd >= pc);
    if ((s = (unsigned long) (pd - pc)) > 1UL)
    {
      gt_assert(pn >= s);
      current.startindex = pn - s;
      current.len = s;
      GT_STACK_PUSH(&intervalstack,current);
    }
  }
  GT_STACK_DELETE(&intervalstack);
}
genometools-1.5.1/src/match/qsort-inplace.gen000066400000000000000000000102371211610345200212060ustar00rootroot00000000000000#include 
#include "core/minmax.h"
#include "core/divmodmul.h"
#include "core/stack-inlined.h"

/*
 * Qsort routine from Bentley & McIlroy's "Engineering a Sort Function".
 */

#define GT_QSORT_SWAP(A,B)\
        if ((A) != (B))\
        {\
          tmp = *(A);\
          *(A) = *(B);\
          *(B) = tmp;\
        }

#define GT_QSORT_VECSWAP(A,B,N)\
        aptr = A;\
        bptr = B;\
        while ((N)-- > 0)\
        {\
          tmp = *aptr;\
          *aptr++ = *bptr;\
          *bptr++ = tmp;\
        }

static inline Sorttype *gt_inlined_qsort_r_med3 (Sorttype *a, Sorttype *b,
                                                 Sorttype *c, void *data)
{
  return qsortcmp (a, b, data) < 0
           ? (qsortcmp (b, c, data) < 0
                ? b
                : (qsortcmp (a, c, data) < 0
                     ? c : a))
           : (qsortcmp (b, c, data) > 0
                ? b
                : (qsortcmp (a, c, data) < 0
                     ? a
                     : c));
}

typedef struct
{
  Sorttype *startptr;
  unsigned long len;
} Intervaltobesorted;

GT_STACK_DECLARESTRUCT(Intervaltobesorted,32UL);

static void gt_inlined_qsort_r (Sorttype *arr,unsigned long len,void *data)
{
  Sorttype tmp, *pa, *pb, *pc, *pd, *pl, *pm, *pn, *aptr, *bptr;
  unsigned long d, minval;
  int r;
  bool swapped;
  GtStackIntervaltobesorted intervalstack;
  Intervaltobesorted current;

  GT_STACK_INIT(&intervalstack,16UL);
  current.startptr = arr;
  current.len = len;
  GT_STACK_PUSH(&intervalstack,current);
  while (!GT_STACK_ISEMPTY(&intervalstack))
  {
    swapped = false;
    current = GT_STACK_POP(&intervalstack);
    if (current.len < 7UL)
    {
      for (pm = current.startptr + 1; pm < current.startptr + current.len; pm++)
      {
        for (pl = pm; pl > current.startptr && qsortcmp (pl - 1, pl, data) > 0;
             pl--)
        {
          GT_QSORT_SWAP (pl, pl - 1);
        }
      }
      continue;
    }
    pm = current.startptr + GT_DIV2 (current.len);
    if (current.len > 7UL)
    {
      pl = current.startptr;
      pn = current.startptr + current.len - 1;
      if (current.len > 40UL)
      {
        d = GT_DIV8 (current.len);
        pl = gt_inlined_qsort_r_med3 (pl, pl + d, pl + GT_MULT2 (d), data);
        pm = gt_inlined_qsort_r_med3 (pm - d, pm, pm + d, data);
        pn = gt_inlined_qsort_r_med3 (pn - GT_MULT2 (d), pn - d, pn, data);
      }
      pm = gt_inlined_qsort_r_med3 (pl, pm, pn, data);
    }
    GT_QSORT_SWAP (current.startptr, pm);
    pa = pb = current.startptr + 1;
    pc = pd = current.startptr + current.len - 1;
    while (1)
    {
      while (pb <= pc && (r = qsortcmp (pb, current.startptr, data)) <= 0)
      {
        if (r == 0)
        {
          swapped = true;
          GT_QSORT_SWAP (pa, pb);
          pa++;
        }
        pb++;
      }
      while (pb <= pc && (r = qsortcmp (pc, current.startptr, data)) >= 0)
      {
        if (r == 0)
        {
          swapped = true;
          GT_QSORT_SWAP (pc, pd);
          pd--;
        }
        pc--;
      }
      if (pb > pc)
      {
        break;
      }
      GT_QSORT_SWAP (pb, pc);
      swapped = true;
      pb++;
      pc--;
    }
    if (!swapped)
    {                                  /* Switch to insertion sort */
      for (pm = current.startptr + 1; pm < current.startptr + current.len; pm++)
      {
        for (pl = pm; pl > current.startptr && qsortcmp (pl - 1, pl, data) > 0;
             pl--)
        {
          GT_QSORT_SWAP (pl, pl - 1);
        }
      }
      continue;
    }
    pn = current.startptr + current.len;
    minval = MIN ((unsigned long) (pa - current.startptr),
                  (unsigned long) (pb - pa));
    GT_QSORT_VECSWAP (current.startptr, pb - minval, minval);
    minval = MIN ((unsigned long) (pd - pc), (unsigned long) (pn - pd - 1));
    GT_QSORT_VECSWAP (pb, pn - minval, minval);
    if ((minval = (unsigned long) (pb - pa)) > 1UL)
    {
      current.len = minval;
      GT_STACK_PUSH(&intervalstack,current);
    }
    if ((minval = (unsigned long) (pd - pc)) > 1UL)
    {
      current.startptr = pn - minval;
      current.len = minval;
      GT_STACK_PUSH(&intervalstack,current);
    }
  }
  GT_STACK_DELETE(&intervalstack);
}
genometools-1.5.1/src/match/querymatch.c000066400000000000000000000154741211610345200202700ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009 Stefan Kurtz 
  Copyright (c) 2007-2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/unused_api.h"
#include "core/types_api.h"
#include "core/readmode.h"
#include "core/format64.h"
#include "core/minmax.h"
#include "querymatch.h"

struct GtQuerymatch
{
   unsigned long
      dblen, /* length of match in dbsequence */
      querylen, /* same as dblen for exact matches */
      dbstart, /* absolute start position of match in database seq */
      querystart, /* start of match in query, relative to start of query */
      edist; /* 0 for exact match */
   long score; /* 0 for exact match */
   uint64_t queryseqnum; /* ordinal number of match in query */
   GtReadmode readmode; /* readmode by which reference sequence was accessed */
   bool selfmatch,       /* true if both instances of the match refer to the
                            same sequence */
        query_as_reversecopy; /* matched the reverse copy of the query */
};

GtQuerymatch *gt_querymatch_new(void)
{
  return gt_malloc(sizeof (GtQuerymatch));
}

void gt_querymatch_fill(GtQuerymatch *querymatch,
                        unsigned long dblen,
                        unsigned long dbstart,
                        GtReadmode readmode,
                        bool query_as_reversecopy,
                        long score,
                        unsigned long edist,
                        bool selfmatch,
                        uint64_t queryseqnum,
                        unsigned long querylen,
                        unsigned long querystart)
{
  querymatch->dblen = dblen;
  querymatch->dbstart = dbstart;
  querymatch->readmode = readmode;
  querymatch->query_as_reversecopy = query_as_reversecopy;
  querymatch->score = score;
  querymatch->edist = edist;
  querymatch->selfmatch = selfmatch;
  querymatch->queryseqnum = queryseqnum;
  querymatch->querylen = querylen;
  querymatch->querystart = querystart;
}

void gt_querymatch_delete(GtQuerymatch *querymatch)
{
  if (querymatch != NULL)
  {
    gt_free(querymatch);
  }
}

#ifdef VERIFY
static void verifymatch(const GtEncseq *encseq,
                        unsigned long len,
                        unsigned long pos1,
                        uint64_t seqnum2,
                        unsigned long pos2,
                        GtReadmode readmode)
{
  if (readmode == GT_READMODE_REVERSE)
  {
    unsigned long offset,
                  seqstartpos,
                  totallength = gt_encseq_total_length(encseq);
    GtUchar cc1, cc2;

    seqstartpos = gt_encseq_seqstartpos(encseq, seqnum2);
    pos2 += seqstartpos;
    for (offset = 0; offset < len; offset++)
    {
      gt_assert(pos1 + len - 1 < totallength);
      gt_assert(pos2 + len - 1 < totallength);
      cc1 = gt_encseq_get_encoded_char(encseq,pos1+offset,GT_READMODE_FORWARD);
      cc2 = gt_encseq_get_encoded_char(encseq,pos2+len-1-offset,
                                       GT_READMODE_FORWARD);
      gt_assert(cc1 == cc2 && ISNOTSPECIAL(cc1));
    }
    if (pos1 + len < totallength)
    {
      cc1 = gt_encseq_get_encoded_char(encseq,pos1+len,GT_READMODE_FORWARD);
    } else
    {
      cc1 = SEPARATOR;
    }
    if (pos2 > 0)
    {
      cc2 = gt_encseq_get_encoded_char(encseq,pos2-1,GT_READMODE_FORWARD);
    } else
    {
      cc2 = SEPARATOR;
    }
    gt_assert(cc1 != cc2 || ISSPECIAL(cc1));
  }
}
#endif

unsigned long gt_querymatch_dbseqnum(const GtEncseq *encseq,
                                     const GtQuerymatch *querymatch)
{
  return gt_encseq_seqnum(encseq,querymatch->dbstart);
}

int gt_querymatch_output(GT_UNUSED void *info,
                         const GtEncseq *encseq,
                         const GtQuerymatch *querymatch,
                         GT_UNUSED const GtUchar *query,
                         unsigned long query_totallength,
                         GT_UNUSED GtError *err)
{
  const char *outflag = "FRCP";
  unsigned long dbseqnum, querystart, dbstart_relative, seqstartpos;

  gt_assert(encseq != NULL);
  dbseqnum = gt_querymatch_dbseqnum(encseq,querymatch);
  seqstartpos = gt_encseq_seqstartpos(encseq, dbseqnum);
  gt_assert((int) querymatch->readmode < 4);
  if (querymatch->readmode == GT_READMODE_REVERSE ||
      querymatch->readmode == GT_READMODE_REVCOMPL)
  {
    gt_assert(querymatch->querystart + querymatch->querylen <=
              query_totallength);
    querystart = query_totallength -
                 querymatch->querystart - querymatch->querylen;
  } else
  {
    querystart = querymatch->querystart;
  }
  gt_assert(querymatch->dbstart >= seqstartpos);
  dbstart_relative = querymatch->dbstart - seqstartpos;
  if (!querymatch->selfmatch ||
      (uint64_t) dbseqnum != querymatch->queryseqnum ||
      dbstart_relative <= querystart)
  {
#ifdef VERIFY
    verifymatch(encseq,
                querymatch->len,
                querymatch->dbstart,
                querymatch->queryseqnum,
                querystart,
                querymatch->readmode);
#endif
    printf("%lu %lu %lu %c %lu " Formatuint64_t " %lu",
           querymatch->dblen,
           dbseqnum,
           dbstart_relative,
           outflag[querymatch->readmode],
           querymatch->querylen,
           PRINTuint64_tcast(querymatch->queryseqnum),
           querystart);
    if (querymatch->score > 0)
    {
      double similarity = querymatch->edist == 0
        ? 100.0
        : 100.0 * (1.0 - querymatch->edist/
                         (double) MIN(querymatch->dblen,querymatch->querylen));
      printf(" %ld %lu %.2f\n",querymatch->score,querymatch->edist,similarity);
    } else
    {
      printf("\n");
    }
  }
  return 0;
}

unsigned long gt_querymatch_querylen(const GtQuerymatch *querymatch)
{
  return querymatch->querylen;
}

unsigned long gt_querymatch_dbstart(const GtQuerymatch *querymatch)
{
  return querymatch->dbstart;
}

unsigned long gt_querymatch_querystart(const GtQuerymatch *querymatch)
{
  return querymatch->querystart;
}

uint64_t gt_querymatch_queryseqnum(const GtQuerymatch *querymatch)
{
  return querymatch->queryseqnum;
}

bool gt_querymatch_queryreverse(const GtQuerymatch *querymatch)
{
  return querymatch->query_as_reversecopy;
}
genometools-1.5.1/src/match/querymatch.h000066400000000000000000000050301211610345200202600ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009 Stefan Kurtz 
  Copyright (c) 2007-2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef QUERYMATCH_H
#define QUERYMATCH_H

#include 
#include "core/error_api.h"
#include "core/readmode.h"
#include "core/encseq.h"

typedef struct GtQuerymatch GtQuerymatch;

GtQuerymatch *gt_querymatch_new(void);

void gt_querymatch_fill(GtQuerymatch *querymatch,
                        unsigned long dblen,
                        unsigned long dbstart,
                        GtReadmode readmode,
                        bool query_as_reversecopy,
                        long score,
                        unsigned long edist,
                        bool selfmatch,
                        uint64_t queryseqnum,
                        unsigned long querylen,
                        unsigned long querystart);

void gt_querymatch_delete(GtQuerymatch *querymatch);

int gt_querymatch_output(void *info,
                         const GtEncseq *encseq,
                         const GtQuerymatch *querymatch,
                         const GtUchar *query,
                         unsigned long query_totallength,
                         GtError *err);

unsigned long gt_querymatch_querylen(const GtQuerymatch *querymatch);

unsigned long gt_querymatch_dbstart(const GtQuerymatch *querymatch);

unsigned long gt_querymatch_querystart(const GtQuerymatch *querymatch);

uint64_t gt_querymatch_queryseqnum(const GtQuerymatch *querymatch);

const GtUchar *gt_querymatch_querysequence(const GtQuerymatch *querymatch);

unsigned long gt_querymatch_querytotallength(const GtQuerymatch *querymatch);

unsigned long gt_querymatch_dbseqnum(const GtEncseq *encseq,
                                     const GtQuerymatch *querymatch);

bool gt_querymatch_queryreverse(const GtQuerymatch *querymatch);

#endif
genometools-1.5.1/src/match/queue-inline.h000066400000000000000000000137541211610345200205120ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef QUEUE_INLINE_H
#define QUEUE_INLINE_H

#include 
#include 
#include "core/assert_api.h"
#include "core/divmodmul.h"

typedef struct
{
 GtInl_Queueelem *queuespace;  /* the space to store the queue elements */
 unsigned long enqueueindex, /* entry into which element is to be enqued */
               dequeueindex, /* last element of queue */
               queuesize,    /* size of the queue */
               noofelements; /* no ofelements between enqueueindex+1
                                and dequeindex */
} GtInl_Queue;

typedef int (*GtInl_Queueprocessor)(GtInl_Queueelem *,void *info);

/*
  The following function delivers an empty queue with a reservoir of
  \texttt{size} elements to be stored in the queue. The
  reservoir can, if necessary, be enlarged.
*/

static inline GtInl_Queue *gt_inl_queue_new(unsigned long queuesize)
{
  GtInl_Queue *q;

  q = gt_malloc(sizeof (*q));
  gt_assert(queuesize > 0);
  q->queuespace = gt_malloc(sizeof (*q->queuespace) * queuesize);
  q->noofelements = 0;
  q->queuesize = queuesize;
  q->dequeueindex = q->enqueueindex = queuesize - 1;
  return q;
}

/*
  The following function frees the space required for the queue.
*/

static inline void gt_inl_queue_delete(GtInl_Queue *q)
{
  if (q != NULL)
  {
    gt_free(q->queuespace);
    gt_free(q);
  }
}

/*
  The following function returns true iff the queue is empty.
*/

static inline bool gt_inl_queue_isempty(const GtInl_Queue *q)
{
  gt_assert(q != NULL);
  return (q->noofelements == 0) ? true : false;
}

/*
  The following function resizes the queue by doubling the
  space reservoir.
*/

static inline void extendqueuesize(GtInl_Queue *q,bool doublesize)
{
  unsigned long addconst, idx, newsize;

  gt_assert(q != NULL);
  if (doublesize)
  {
    addconst = q->queuesize;
  } else
  {
    addconst = MIN(1024UL,q->queuesize);
  }
  newsize = q->queuesize + addconst;
  q->queuespace = gt_realloc(q->queuespace,sizeof (*q->queuespace) * newsize);
  gt_assert(q->enqueueindex == q->dequeueindex);
  gt_assert(addconst > 0);
  for (idx=q->queuesize-1; idx>q->enqueueindex; idx--)
  {
    q->queuespace[idx+addconst] = q->queuespace[idx];
  }
  q->enqueueindex += addconst;
  /*
  printf("from queue of size %lu to queue of size %lu\n",q->queuesize,newsize);
  printf("now enqueindex=%lu,dequeuindex=%lu\n",
         q->enqueueindex,q->dequeueindex);
  */
  q->queuesize = newsize;
}

/*
  The following function adds an element \texttt{elem} to the end of
  the queue.
*/

static inline void gt_inl_queue_add(GtInl_Queue *q, GtInl_Queueelem elem,
                                    bool doublesize)
{
  gt_assert(q != NULL);
  if (q->noofelements == q->queuesize)
  {
    extendqueuesize(q,doublesize);
  }
  q->noofelements++;
  q->queuespace[q->enqueueindex] = elem;
  if (q->enqueueindex > 0)
  {
    q->enqueueindex--;
  } else
  {
    q->enqueueindex = q->queuesize - 1; /* dequeuindex < queuesize-1 */
  }
}

/*
  The following function removes the element \texttt{elem} from the
  start of the queue.
*/

static inline GtInl_Queueelem gt_inl_queue_get(GtInl_Queue *q)
{
  GtInl_Queueelem value;

  gt_assert(q != NULL && q->noofelements > 0);
  q->noofelements--;
  value = q->queuespace[q->dequeueindex];
  if (q->dequeueindex > 0)
  {
    q->dequeueindex--;
  } else
  {
    q->dequeueindex = q->queuesize - 1;  /* != enqueueindex, since at least
                                            one elem */
  }
  return value;
}

/*@unused@*/ static inline GtInl_Queueelem *gt_inl_queue_head(
                                                     const GtInl_Queue *q)
{
  gt_assert(q != NULL && q->noofelements > 0);
  return q->queuespace + q->dequeueindex;
}

/*@unused@*/ static inline GtInl_Queueelem *gt_inl_queue_tail(
                                                      const GtInl_Queue *q)
{
  gt_assert(q != NULL && q->noofelements > 0);
  if (q->enqueueindex == q->queuesize-1)
  {
    return q->queuespace;
  }
  return q->queuespace + q->enqueueindex + 1;
}

/*@unused@*/ static inline void gt_inl_queue_deletehead(GtInl_Queue *q)
{
  gt_assert(q != NULL && q->noofelements > 0);
  q->noofelements--;
  if (q->dequeueindex > 0)
  {
    q->dequeueindex--;
  } else
  {
    q->dequeueindex = q->queuesize - 1; /* != enqueueindex, since at least
                                           one elem */
  }
}

/*@unused@*/ static inline int gt_inl_queue_iterate(const GtInl_Queue *q,
                                           GtInl_Queueprocessor queueprocessor,
                                           void *info)
{
  gt_assert(q != NULL);
  if (q->noofelements > 0)
  {
    unsigned long idx;

    if (q->enqueueindex < q->dequeueindex)
    {
      for (idx=q->enqueueindex+1; idx<=q->dequeueindex; idx++)
      {
        if (queueprocessor(q->queuespace + idx,info) != 0)
        {
          return -1;
        }
      }
    } else
    {
      for (idx=q->enqueueindex+1; idx<=q->queuesize-1; idx++)
      {
        if (queueprocessor(q->queuespace + idx,info) != 0)
        {
          return -1;
        }
      }
      for (idx=0; idx<=q->dequeueindex; idx++)
      {
        if (queueprocessor(q->queuespace + idx,info) != 0)
        {
          return -1;
        }
      }
    }
  }
  return 0;
}
#endif
genometools-1.5.1/src/match/radixsort_str.c000066400000000000000000000434611211610345200210120ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/intbits.h"
#include "core/ma.h"
#include "core/minmax.h"
#include "core/stack-inlined.h"
#include "core/qsort-ulong.h"
#include "sfx-lcpvalues.h"
#include "radixsort_str.h"

typedef uint8_t gt_radixsort_str_kmercode_t;
/* note: if kmercode_t size is changed, then the RADIXSORT_STR_REVCOMPL
 * macro must be changed to handle the new size too */

typedef uint16_t gt_radixsort_str_bucketnum_t;

#define GT_RADIXSORT_STR_UINT8_REVCOMPL(CODE)\
  (GT_RADIXSORT_STR_KMERCODE_MAX ^\
   (((((CODE) & (3 << 6)) >> 6) | (((CODE) & 3) << 6)) |\
    ((((CODE) & (3 << 4)) >> 2) | (((CODE) & (3 << 2)) << 2))))

#define GT_RADIXSORT_STR_REVCOMPL(CODE) GT_RADIXSORT_STR_UINT8_REVCOMPL(CODE)

#define GT_RADIXSORT_STR_KMERCODE_BITS\
        (sizeof (gt_radixsort_str_kmercode_t) * CHAR_BIT)
#define GT_RADIXSORT_STR_KMERSIZE         (GT_RADIXSORT_STR_KMERCODE_BITS >> 1)
#define GT_RADIXSORT_STR_KMERSIZELOG      2
#define GT_RADIXSORT_STR_NOFKMERCODES     (1 << GT_RADIXSORT_STR_KMERCODE_BITS)
#define GT_RADIXSORT_STR_KMERCODE_MAX\
        ((gt_radixsort_str_kmercode_t)(GT_RADIXSORT_STR_NOFKMERCODES - 1))

#define GT_RADIXSORT_STR_OVERFLOW_MASK ((1 << GT_RADIXSORT_STR_KMERSIZELOG) - 1)

#define GT_RADIXSORT_STR_NOFBUCKETS\
        (size_t)(((1 << (GT_RADIXSORT_STR_KMERSIZE << 1)) *\
                  GT_RADIXSORT_STR_KMERSIZE) + 1)

#define GT_RADIXSORT_STR_SPECIAL_BUCKET\
        ((gt_radixsort_str_bucketnum_t)(GT_RADIXSORT_STR_NOFBUCKETS - 1))

#define GT_RADIXSORT_STR_SPECIAL_BUCKET_BIT\
        (1 << (GT_RADIXSORT_STR_KMERCODE_BITS + GT_RADIXSORT_STR_KMERSIZELOG))

#define GT_RADIXSORT_STR_HAS_OVERFLOW(BUCKETNUM)\
        (((BUCKETNUM) & GT_RADIXSORT_STR_OVERFLOW_MASK) ||\
         ((BUCKETNUM) == GT_RADIXSORT_STR_SPECIAL_BUCKET))

#define GT_RADIXSORT_STR_BUCKETNUM(CODE, OVERFLOW)\
        (((gt_radixsort_str_bucketnum_t)\
            (CODE) << GT_RADIXSORT_STR_KMERSIZELOG) + (OVERFLOW))

#define GT_RADIXSORT_STR_OVERFLOW_NONSPECIAL(BUCKETNUM)\
        ((BUCKETNUM) & GT_RADIXSORT_STR_OVERFLOW_MASK)

#define GT_RADIXSORT_STR_OVERFLOW(BUCKETNUM)\
        (((BUCKETNUM) == GT_RADIXSORT_STR_SPECIAL_BUCKET)\
          ? GT_RADIXSORT_STR_KMERSIZE\
          : GT_RADIXSORT_STR_OVERFLOW_NONSPECIAL(BUCKETNUM))

typedef struct
{
  unsigned long *suffixes;
  unsigned long width;
  unsigned long depth;
  unsigned long lcp;
} GtRadixsortStrBucketInfo;

GT_STACK_DECLARESTRUCT(GtRadixsortStrBucketInfo, 1024);

struct GtRadixsortstringinfo
{
  const GtTwobitencoding *twobitencoding;
  size_t bytesinsizesofbuckets;
  unsigned long equallengthplus1,
                realtotallength,
                maxwidth,
                *sizesofbuckets,
                *sorted;
  gt_radixsort_str_bucketnum_t *oracle;
  uint8_t *xorvalue2lcp;
  GtStackGtRadixsortStrBucketInfo stack;
};

static uint8_t *gt_radixsort_str_init_xorvalue2lcp(void)
{
  const unsigned long nofcodes
    = (unsigned long) GT_POW2(GT_MULT2(GT_RADIXSORT_STR_KMERSIZE));
  uint8_t *xorvalue2lcp, lcp = GT_RADIXSORT_STR_KMERSIZE;
  unsigned long i, j = 0, j_bound = 1UL;

  xorvalue2lcp = gt_malloc(sizeof (*xorvalue2lcp) * nofcodes);
  for (i = 0; i < (unsigned long) GT_RADIXSORT_STR_KMERSIZE; i++)
  {
    if (i > 0)
    {
      j_bound = GT_POW2(GT_MULT2(i));
      gt_assert(lcp > 0);
      lcp--;
    }
    while (j < j_bound)
    {
      xorvalue2lcp[j++] = lcp;
    }
  }
  while (j < nofcodes)
  {
    xorvalue2lcp[j++] = 0;
  }
  return xorvalue2lcp;
}

GtRadixsortstringinfo *gt_radixsort_str_new(const GtTwobitencoding
                                             *twobitencoding,
                                            unsigned long realtotallength,
                                            unsigned long equallengthplus1,
                                            unsigned long maxwidth)
{
  GtRadixsortstringinfo *rsi = gt_malloc(sizeof(*rsi));

  rsi->twobitencoding = twobitencoding;
  rsi->equallengthplus1 = equallengthplus1;
  rsi->realtotallength = realtotallength;
  rsi->maxwidth = maxwidth/2;
  rsi->bytesinsizesofbuckets = sizeof (*rsi->sizesofbuckets) *
                               GT_RADIXSORT_STR_NOFBUCKETS;
  rsi->sizesofbuckets = gt_malloc(rsi->bytesinsizesofbuckets);
  rsi->sorted = gt_malloc(sizeof (*rsi->sorted) * rsi->maxwidth);
  rsi->oracle = gt_malloc(sizeof (*rsi->oracle) * rsi->maxwidth);
  rsi->xorvalue2lcp = gt_radixsort_str_init_xorvalue2lcp();
  GT_STACK_INIT(&rsi->stack, 1024UL);
  return rsi;
}

void gt_radixsort_str_delete(GtRadixsortstringinfo *rsi)
{
  if (rsi != NULL)
  {
    gt_free(rsi->sizesofbuckets);
    gt_free(rsi->sorted);
    gt_free(rsi->oracle);
    gt_free(rsi->xorvalue2lcp);
    GT_STACK_DELETE(&rsi->stack);
    gt_free(rsi);
  }
}

static inline gt_radixsort_str_kmercode_t gt_radixsort_str_code_at_position(
    const GtTwobitencoding *twobitencoding, unsigned long pos)
{
  unsigned int unitoffset = (unsigned int) GT_MODBYUNITSIN2BITENC(pos);
  unsigned long unitindex = GT_DIVBYUNITSIN2BITENC(pos);

  if (unitoffset <=
      (unsigned int) (GT_UNITSIN2BITENC - GT_RADIXSORT_STR_KMERSIZE))
  {
    return (gt_radixsort_str_kmercode_t)
      (twobitencoding[unitindex] >>
       GT_MULT2(GT_UNITSIN2BITENC - GT_RADIXSORT_STR_KMERSIZE - unitoffset))
       & GT_RADIXSORT_STR_KMERCODE_MAX;
  } else
  {
    unsigned int shiftleft =
      GT_MULT2(unitoffset + (unsigned int) GT_RADIXSORT_STR_KMERSIZE -
               GT_UNITSIN2BITENC);
    return (gt_radixsort_str_kmercode_t)
                  ((twobitencoding[unitindex] << shiftleft) |
                   (twobitencoding[unitindex + 1] >>
                       (GT_MULT2(GT_UNITSIN2BITENC) - shiftleft)))
                  & GT_RADIXSORT_STR_KMERCODE_MAX;
  }
}

static inline gt_radixsort_str_bucketnum_t gt_radixsort_str_get_code(
    const GtTwobitencoding *twobitencoding, unsigned long suffixnum,
    unsigned long depth, unsigned long equallengthplus1,
    unsigned long realtotallength)
{
  unsigned long relpos = suffixnum % equallengthplus1 + depth;

  if (relpos >= equallengthplus1 - 1) /* suffix starts on separator position */
  {
    return GT_RADIXSORT_STR_SPECIAL_BUCKET;
  } else
  {
    uint8_t overflow = 0;
    gt_radixsort_str_kmercode_t code;
    unsigned long remaining, pos = suffixnum + depth;

    remaining = equallengthplus1 - 1 - relpos;
    if (suffixnum <= realtotallength)
    {
      code = gt_radixsort_str_code_at_position(twobitencoding, pos);
      if (remaining < (unsigned long) GT_RADIXSORT_STR_KMERSIZE)
      {
        overflow = GT_RADIXSORT_STR_KMERSIZE - remaining;
        code |= (1 << GT_MULT2(overflow)) - 1;
      }
    } else
    {
      gt_assert(pos < GT_MULT2(realtotallength + 1));
      pos = GT_MULT2(realtotallength + 1) - pos - 1;
      pos -= (remaining > (unsigned long) GT_RADIXSORT_STR_KMERSIZE)
               ? (unsigned long) GT_RADIXSORT_STR_KMERSIZE
               : remaining;
      gt_assert(pos < realtotallength);
      code = GT_RADIXSORT_STR_REVCOMPL(gt_radixsort_str_code_at_position(
                                       twobitencoding, pos));
      if (remaining < (unsigned long) GT_RADIXSORT_STR_KMERSIZE)
      {
        overflow = GT_RADIXSORT_STR_KMERSIZE - remaining;
        code = (code << GT_MULT2(overflow)) | ((1 << GT_MULT2(overflow)) - 1);
      }
    }
    return GT_RADIXSORT_STR_BUCKETNUM(code, overflow);
  }
}

/* the following calculates the lcp of two buckets */
static inline gt_radixsort_str_bucketnum_t
        gt_radixsort_str_codeslcp(GtRadixsortstringinfo *rsi,
            gt_radixsort_str_bucketnum_t a, gt_radixsort_str_bucketnum_t b)
{
  if (a != GT_RADIXSORT_STR_SPECIAL_BUCKET &&
      b != GT_RADIXSORT_STR_SPECIAL_BUCKET)
  {
    gt_radixsort_str_bucketnum_t codeslcp, maxcodeslcp, ova, ovb;

    codeslcp = rsi->xorvalue2lcp[GT_DIV4(a ^ b)];
    /* now take the overflow into account */
    ova = GT_RADIXSORT_STR_OVERFLOW_NONSPECIAL(a);
    ovb = GT_RADIXSORT_STR_OVERFLOW_NONSPECIAL(b);
    maxcodeslcp = GT_RADIXSORT_STR_KMERSIZE - MAX(ova, ovb);
    return MIN(codeslcp, maxcodeslcp);
  }
  return 0;
}

unsigned long gt_radixsort_str_minwidth(void)
{
  return (unsigned long) GT_RADIXSORT_STR_NOFBUCKETS;
}

unsigned long gt_radixsort_str_maxwidth(const GtRadixsortstringinfo *rsi)
{
  return rsi->maxwidth;
}

static void gt_radixsort_str_insertionsort(GtRadixsortstringinfo *rsi,
                                           unsigned long *suffixes,
                                           unsigned long subbucketleft,
                                           unsigned long width,
                                           unsigned long depth,
                                           GtLcpvalues *lcpvalues,
                                           unsigned long sortmaxdepth)
{
  unsigned long pm, pl, u, v, lcpvalue;

  for (pm = 1UL; pm < width; pm++)
  {
    for (pl = pm; pl > 0; pl--)
    {
      gt_radixsort_str_bucketnum_t codeslcp, unk = 0, vnk = 0;
      int uvcmp = 0;

      u = suffixes[pl-1];
      v = suffixes[pl];
      for (lcpvalue = depth;
           (sortmaxdepth == 0 || lcpvalue <= sortmaxdepth) && uvcmp == 0;
           /* Nothing */)
      {
        unk = gt_radixsort_str_get_code(rsi->twobitencoding, u, lcpvalue,
                                        rsi->equallengthplus1,
                                        rsi->realtotallength);
        vnk = gt_radixsort_str_get_code(rsi->twobitencoding, v, lcpvalue,
                                        rsi->equallengthplus1,
                                        rsi->realtotallength);
        codeslcp = gt_radixsort_str_codeslcp(rsi, unk, vnk);
        lcpvalue += codeslcp;
        if (unk == vnk)
        {
          if (!GT_RADIXSORT_STR_HAS_OVERFLOW(unk))
          {
            if (!GT_RADIXSORT_STR_HAS_OVERFLOW(vnk))
            {
              uvcmp = 0;
            } else
            {
              uvcmp = -1;
            }
          } else
          {
            if (!GT_RADIXSORT_STR_HAS_OVERFLOW(vnk))
            {
              uvcmp = 1;
            } else
            {
              uvcmp = (u < v) ? -1 : 1;
            }
          }
        } else
        {
          if (unk < vnk)
          {
            uvcmp = -1;
          } else
          {
            uvcmp = 1;
          }
        }
        gt_assert((uvcmp == 0 && codeslcp == GT_RADIXSORT_STR_KMERSIZE) ||
                   (uvcmp != 0 && codeslcp < GT_RADIXSORT_STR_KMERSIZE));
      }
      if (lcpvalues != NULL)
      {
        if (pl < pm && uvcmp > 0)
        {
          gt_lcptab_update(lcpvalues,subbucketleft,pl+1,
                           gt_lcptab_getvalue(lcpvalues,subbucketleft,pl));
        }
        gt_lcptab_update(lcpvalues,subbucketleft,pl,
                         sortmaxdepth == 0 ? lcpvalue
                                           : MIN(lcpvalue,sortmaxdepth));
      }
      if (uvcmp < 0)
      {
        break;
      }
      suffixes[pl-1] = v;
      suffixes[pl] = u;
    }
  }
}

void gt_radixsort_str_eqlen(GtRadixsortstringinfo *rsi,
                            unsigned long *suffixes,
                            GtLcpvalues *lcpvalues,
                            unsigned long subbucketleft,
                            unsigned long depth,
                            unsigned long sortmaxdepth,
                            unsigned long width)
{
  unsigned long idx, previousbucketsize,
                *bucketindex; /* overlay with sizesofbuckets */
  GtRadixsortStrBucketInfo bucket;

  gt_assert(width <= rsi->maxwidth &&
            (sortmaxdepth == 0 ||
            (depth <= sortmaxdepth && sortmaxdepth <= rsi->equallengthplus1)));

  bucket.suffixes = suffixes;
  bucket.width = width;
  bucket.depth = depth;
  bucket.lcp = depth;
  gt_assert(GT_STACK_ISEMPTY(&rsi->stack));
  GT_STACK_PUSH(&rsi->stack, bucket);

  bucketindex = rsi->sizesofbuckets;
  while (!GT_STACK_ISEMPTY(&rsi->stack))
  {
    gt_radixsort_str_bucketnum_t prevbucketnum
      = GT_RADIXSORT_STR_SPECIAL_BUCKET; /* = undefined */
    bucket = GT_STACK_POP(&rsi->stack);
    memset(rsi->sizesofbuckets, 0, rsi->bytesinsizesofbuckets);

    /* Loop A */
    for (idx = 0; idx < bucket.width; idx++)
    {
      rsi->oracle[idx] = gt_radixsort_str_get_code(rsi->twobitencoding,
                                                   bucket.suffixes[idx],
                                                   bucket.depth,
                                                   rsi->equallengthplus1,
                                                   rsi->realtotallength);
    }
    for (idx = 0; idx < bucket.width; idx++)
    {
      rsi->sizesofbuckets[rsi->oracle[idx]]++;
    }
    previousbucketsize = rsi->sizesofbuckets[0];
    bucketindex[0] = 0;
    for (idx = 1UL; idx < (unsigned long) GT_RADIXSORT_STR_NOFBUCKETS; idx++)
    {
      unsigned long tmp;

      tmp = bucketindex[idx-1] + previousbucketsize;
      previousbucketsize = rsi->sizesofbuckets[idx];
      bucketindex[idx] = tmp;
    }

    /* Loop B */
    gt_assert(width > 1UL);
    if (bucket.suffixes[0] > bucket.suffixes[1])
    {
      for (idx = bucket.width; idx > 0; /* Nothing */)
      {
        idx--;
        rsi->sorted[bucketindex[rsi->oracle[idx]]++] = bucket.suffixes[idx];
      }
    } else
    {
      for (idx = 0; idx < bucket.width; idx++)
      {
        rsi->sorted[bucketindex[rsi->oracle[idx]]++] = bucket.suffixes[idx];
      }
    }

    memcpy(bucket.suffixes, rsi->sorted, sizeof (*rsi->sorted) * bucket.width);

    if (bucket.depth < rsi->equallengthplus1)
    {
      gt_radixsort_str_bucketnum_t bucketnum;
      GtRadixsortStrBucketInfo subbucket;

      subbucket.suffixes = bucket.suffixes;
      subbucket.depth = bucket.depth + GT_RADIXSORT_STR_KMERSIZE;
      subbucket.lcp = bucket.lcp;
      for (bucketnum = 0;
           bucketnum < (gt_radixsort_str_bucketnum_t)
                       GT_RADIXSORT_STR_NOFBUCKETS;
           bucketnum++)
      {
        subbucket.width
          = bucketnum > 0 ? (bucketindex[bucketnum] - bucketindex[bucketnum-1])
                          : bucketindex[bucketnum];
        if (subbucket.width > 0)
        {
          unsigned long offset
            = (unsigned long) (subbucket.suffixes - suffixes);
          if (lcpvalues != NULL)
          {
            if (prevbucketnum != GT_RADIXSORT_STR_SPECIAL_BUCKET)
            {
              subbucket.lcp = bucket.depth +
                              gt_radixsort_str_codeslcp(rsi,prevbucketnum,
                                                        bucketnum);
            }
            if (offset > 0)
            {
              gt_lcptab_update(lcpvalues,subbucketleft,offset,
                               sortmaxdepth == 0
                                 ? subbucket.lcp
                                 : MIN(subbucket.lcp,sortmaxdepth));
            }
          }
          if (GT_RADIXSORT_STR_HAS_OVERFLOW(bucketnum))
          {
            if (subbucket.width > 1UL)
            {
              gt_direct_qsort_ulong (6UL, false, subbucket.suffixes,
                                     subbucket.width);
            }
            if (lcpvalues != NULL)
            {
              unsigned long j,
                            lcpvalue = bucket.depth
                                       + GT_RADIXSORT_STR_KMERSIZE
                                       - GT_RADIXSORT_STR_OVERFLOW(bucketnum);

              if (sortmaxdepth > 0 && lcpvalue > sortmaxdepth)
              {
                lcpvalue = sortmaxdepth;
              }
              for (j = 1UL; j < subbucket.width; j++)
              {
                gt_lcptab_update(lcpvalues,subbucketleft,offset+j,lcpvalue);
              }
            }
          } else
          {
            if (subbucket.width > 1UL)
            {
              if (sortmaxdepth == 0 || subbucket.depth <= sortmaxdepth)
              {
                const unsigned long radixsort_str_insertion_sort_max = 31UL;

                if (subbucket.width <= radixsort_str_insertion_sort_max)
                {
                  gt_radixsort_str_insertionsort(rsi,
                                                 subbucket.suffixes,
                                                 subbucketleft + offset,
                                                 subbucket.width,
                                                 subbucket.depth,
                                                 lcpvalues,
                                                 sortmaxdepth);
                } else
                {
                  GT_STACK_PUSH(&rsi->stack, subbucket);
                }
              } else
              {
                if (lcpvalues != NULL)
                {
                  unsigned long j;
                  for (j = 1UL; j < subbucket.width; j++)
                  {
                    gt_lcptab_update(lcpvalues,subbucketleft,offset+j,
                                     sortmaxdepth);
                  }
                }
              }
            }
          }
          subbucket.suffixes += subbucket.width;
          gt_assert(subbucket.suffixes <= bucket.suffixes + bucket.width);
          prevbucketnum = bucketnum;
        }
      }
      gt_assert(bucket.suffixes + bucket.width == subbucket.suffixes);
    }
  }
}
genometools-1.5.1/src/match/radixsort_str.h000066400000000000000000000043371211610345200210160ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RADIXSORT_STR_H
#define RADIXSORT_STR_H
#include "core/intbits.h"
#include "sfx-lcpvalues.h"

/*
 * suffixes = array of suffixes to be sorted
 * width = number of suffixes to sort
 * depth = start sorting at given depth
 * sortmaxdepth = stop sorting at given depth (0 means infinite)
 *
 * realtotallength = "real" length (not the mirror logical length)
 * equallengthplus1 = sequence length, including the separator
 *
 * */

typedef struct GtRadixsortstringinfo GtRadixsortstringinfo;

unsigned long gt_radixsort_str_minwidth(void);

unsigned long gt_radixsort_str_maxwidth(const GtRadixsortstringinfo *rsi);

GtRadixsortstringinfo *gt_radixsort_str_new(const GtTwobitencoding
                                             *twobitencoding,
                                            unsigned long realtotallength,
                                            unsigned long equallengthplus1,
                                            unsigned long maxwidth);

void gt_radixsort_str_delete(GtRadixsortstringinfo *rsi);

void gt_radixsort_str_eqlen(GtRadixsortstringinfo *rsi,
                            unsigned long *suffixes,
                            GtLcpvalues *lcpvalues,
                            unsigned long subbucketleft,
                            unsigned long depth,
                            unsigned long sortmaxdepth,
                            unsigned long width);

#endif
genometools-1.5.1/src/match/randomcodes-correct.c000066400000000000000000000166141211610345200220400ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/fa.h"
#include "core/log_api.h"
#include "core/xansi_api.h"
#include "match/randomcodes-correct.h"

struct GtRandomcodesCorrectData {
  const GtEncseq *encseq;
  unsigned int alphasize;
  unsigned long firstmirrorpos;
  unsigned long totallength;

  unsigned int k;
  unsigned int c;
  unsigned int *count;
  unsigned long *kpositions;
  FILE *outfile;

  unsigned int currentchar;
  bool seprange;
  bool alltrusted;

  /* stats */
  unsigned long nofkmergroups,
                nofkmeritvs,
                nofkmers,
                nofcorrections;
};

static inline void gt_randomcodes_correct_data_reset(
    GtRandomcodesCorrectData *data)
{
  unsigned int i;
  data->seprange = false;
  data->alltrusted = true;
  data->currentchar = 0;
  for (i = 0; i < data->alphasize; i++)
    data->count[i] = 0;
}

static inline void gt_randomcodes_correct_process_kmer_itv(
    const unsigned long *suffixes,
    unsigned long nofsuffixes,
    GtRandomcodesCorrectData *cdata)
{
  unsigned int i, c = cdata->c;
  cdata->nofkmeritvs++;
  cdata->nofkmers += nofsuffixes;
  if (nofsuffixes < (unsigned long)cdata->c)
  {
    cdata->alltrusted = false;
    c = (unsigned int)nofsuffixes;
  }
  for (i = 0; i < c; i++)
  {
    (cdata->kpositions + cdata->currentchar * cdata->c)[i] = suffixes[i];
  }
  cdata->count[cdata->currentchar] = (unsigned int)nofsuffixes;
  cdata->currentchar++;
}

static inline void gt_randomcodes_correct_process_kmergroup_end(
    const GtSeqnumrelpos *snrp, GtRandomcodesCorrectData *cdata)
{
  cdata->nofkmergroups++;
  if (!cdata->alltrusted)
  {
    unsigned int i, max_count = 0, countpos = 0;
    for (i = 0; i < cdata->alphasize; i++)
    {
      if (cdata->count[i] > max_count)
      {
        max_count = cdata->count[i];
        countpos = i;
      }
    }
    if (max_count >= cdata->c)
    {
      const unsigned long trusted_char_seqnumrelpos =
        (cdata->kpositions + countpos * cdata->c)[0];
      GtUchar trusted_char = gt_encseq_get_encoded_char_nospecial(cdata->encseq,
          gt_encseq_seqstartpos(cdata->encseq, gt_seqnumrelpos_decode_seqnum(
              snrp,trusted_char_seqnumrelpos)) + gt_seqnumrelpos_decode_relpos(
              snrp,trusted_char_seqnumrelpos) + cdata->k - 1,
          GT_READMODE_FORWARD);
      for (i = 0; i < cdata->alphasize; i++)
      {
        unsigned int j;
        if (cdata->count[i] < cdata->c)
        {
          for (j = 0; j < cdata->count[i]; j++)
          {
            GtUchar newchar = trusted_char;
            const unsigned long
              seqnumrelpos = (cdata->kpositions + i * cdata->c)[j];
            unsigned long abspos;
            abspos = gt_encseq_seqstartpos(cdata->encseq,
                gt_seqnumrelpos_decode_seqnum(snrp,seqnumrelpos)) +
              gt_seqnumrelpos_decode_relpos(snrp,seqnumrelpos) + cdata->k - 1;
            if (abspos >= cdata->firstmirrorpos)
            {
              abspos = cdata->totallength - 1UL - abspos;
              newchar = (GtUchar)3 - newchar;
            }
            gt_assert(abspos <= (ULONG_MAX >> 2));
            gt_assert(newchar < (GtUchar)4);
            abspos <<= 2;
            abspos += newchar;
            gt_xfwrite(&abspos, sizeof (abspos), (size_t)1, cdata->outfile);
            cdata->nofcorrections++;
          }
        }
      }
    }
  }
  gt_randomcodes_correct_data_reset(cdata);
}

int gt_randomcodes_correct_process_bucket(void *data,
    const unsigned long *bucketofsuffixes, const GtSeqnumrelpos *snrp,
    const uint16_t *lcptab_bucket, unsigned long numberofsuffixes,
    unsigned int correction_kmersize, GT_UNUSED GtError *err)
{
  unsigned long itvstart, next_itvstart;
  unsigned int lcpvalue;
  bool haserr = false;

  for (itvstart = 0, next_itvstart = 1UL; next_itvstart < numberofsuffixes;
      next_itvstart++)
  {
    lcpvalue = (unsigned int) lcptab_bucket[next_itvstart];
    if (lcpvalue < correction_kmersize)
    {
      gt_randomcodes_correct_process_kmer_itv(bucketofsuffixes + itvstart,
          next_itvstart - itvstart, data);
      itvstart = next_itvstart;
      if (lcpvalue < correction_kmersize - 1)
      {
        gt_randomcodes_correct_process_kmergroup_end(snrp, data);
      }
    }
  }
  gt_randomcodes_correct_process_kmer_itv(bucketofsuffixes + itvstart,
      numberofsuffixes - itvstart, data);
  gt_randomcodes_correct_process_kmergroup_end(snrp, data);
  return haserr ? -1 : 0;
}

GtRandomcodesCorrectData *gt_randomcodes_correct_data_new(GtEncseq *encseq,
    unsigned int k, unsigned int c, const char *indexname, const char *suffix,
    unsigned int threadnum, GtError *err)
{
  bool haserr = false;
  GtRandomcodesCorrectData *cdata = gt_malloc(sizeof *cdata);
  GtStr *path = gt_str_new_cstr(indexname);
  gt_str_append_char(path, '.');
  gt_str_append_uint(path, threadnum);
  gt_str_append_cstr(path, suffix);
  cdata->k = k;
  cdata->c = c;
  cdata->encseq = encseq;
  cdata->alphasize = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
  cdata->totallength = gt_encseq_total_length(encseq);
  cdata->firstmirrorpos = cdata->totallength;
  if (gt_encseq_is_mirrored(encseq))
    cdata->firstmirrorpos >>= 1;
  cdata->kpositions = gt_malloc(sizeof (*cdata->kpositions) *
      cdata->alphasize * c);
  cdata->count = gt_malloc(sizeof (*cdata->count) * cdata->alphasize);
  gt_randomcodes_correct_data_reset(cdata);
  /* stats */
  cdata->nofkmergroups = 0;
  cdata->nofkmeritvs = 0;
  cdata->nofkmers = 0;
  cdata->nofcorrections = 0;
  cdata->outfile = gt_fa_fopen(gt_str_get(path), "wb", err);
  if (cdata->outfile == NULL)
  {
    haserr = true;
  }
  if (!haserr && cdata->totallength > (ULONG_MAX >> 2))
  {
    gt_error_set(err, "totallength %lu larger than %lu", cdata->totallength,
        ULONG_MAX >> 2);
    haserr = true;
  }
  gt_str_delete(path);
  if (haserr)
    gt_randomcodes_correct_data_delete(cdata);
  return cdata;
}

#define GT_RANDOMCODES_COLLECT_STAT(S)\
  gt_log_log("thread %u: " #S " %lu", threadnum, cdata->S);\
  if (S != NULL)\
    *S += cdata->S;

void gt_randomcodes_correct_data_collect_stats(GtRandomcodesCorrectData *cdata,
    unsigned int threadnum, unsigned long *nofkmergroups,
    unsigned long *nofkmeritvs, unsigned long *nofkmers,
    unsigned long *nofcorrections)
{
  GT_RANDOMCODES_COLLECT_STAT(nofkmergroups);
  GT_RANDOMCODES_COLLECT_STAT(nofkmeritvs);
  GT_RANDOMCODES_COLLECT_STAT(nofkmers);
  GT_RANDOMCODES_COLLECT_STAT(nofcorrections);
}

void gt_randomcodes_correct_data_delete(GtRandomcodesCorrectData *cdata)
{
  if (cdata == NULL)
    return;
  if (cdata->outfile != NULL)
    gt_fa_fclose(cdata->outfile);
  gt_free(cdata->kpositions);
  gt_free(cdata->count);
  gt_free(cdata);
}
genometools-1.5.1/src/match/randomcodes-correct.h000066400000000000000000000034371211610345200220440ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RANDOMCODES_CORRECT_H
#define RANDOMCODES_CORRECT_H

#include 
#include "core/encseq.h"
#include "match/seqnumrelpos.h"

int gt_randomcodes_correct_process_bucket(void *data,
    const unsigned long *bucketofsuffixes, const GtSeqnumrelpos *snrp,
    const uint16_t *lcptab_bucket, unsigned long numberofsuffixes,
    unsigned int correction_kmersize, GtError *err);

typedef struct GtRandomcodesCorrectData GtRandomcodesCorrectData;

GtRandomcodesCorrectData *gt_randomcodes_correct_data_new(GtEncseq *encseq,
    unsigned int k, unsigned int c, const char *indexname, const char *suffix,
    unsigned int threadnum, GtError *err);
void gt_randomcodes_correct_data_collect_stats(GtRandomcodesCorrectData *cdata,
    unsigned int threadnum, unsigned long *nofkmergroups,
    unsigned long *nofkmeritvs, unsigned long *nofkmers,
    unsigned long *nofcorrections);
void gt_randomcodes_correct_data_delete(GtRandomcodesCorrectData *cdata);

#endif
genometools-1.5.1/src/match/randomcodes-insert.c000066400000000000000000000223041211610345200216740ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/intbits.h"
#include "core/types_api.h"
#include "core/codetype.h"
#include "core/divmodmul.h"
#include "core/encseq.h"
#include "kmercodes.h"
#include "firstcodes-buf.h"
#include "randomcodes-insert.h"

#define GT_RANDOMCODES_INSERTSUFFIXES(BUF,CODE,SEQNUM,RELPOS)\
        {\
          if (\
              ((BUF)->currentmincode == 0 ||\
               (BUF)->currentmincode < (CODE)) &&\
               (CODE) <= (BUF)->currentmaxcode)\
          {\
            if ((BUF)->nextfree == (BUF)->allocated)\
            {\
              (BUF)->flush_function((BUF)->fciptr);\
            }\
            gt_assert ((BUF)->nextfree < (BUF)->allocated);\
            (BUF)->spaceGtUlongPair[(BUF)->nextfree].a = CODE;\
            (BUF)->spaceGtUlongPair[(BUF)->nextfree++].b\
              = gt_seqnumrelpos_encode((BUF)->snrp,SEQNUM,RELPOS);\
          }\
        }

static void gt_randomcodes_insert_kmerscan_range(
                                         const GtBitsequence *twobitencoding,
                                         unsigned int kmersize,
                                         unsigned int minmatchlength,
                                         unsigned long startpos,
                                         unsigned long length,
                                         unsigned long fseqnum,
                                         unsigned long rseqnum,
                                         unsigned long maxunitindex,
                                         GtCodeposbuffer *buf)
{
  const unsigned long maskright = GT_MASKRIGHT(kmersize);
  const unsigned long lastpossiblepos = length - minmatchlength;
  const unsigned long lastfrelpos = length - kmersize;
  const unsigned int shiftleft = GT_MULT2(kmersize-1);
  unsigned int shiftright;
  unsigned long unitindex, frelpos;
  GtTwobitencoding currentencoding;
  GtCodetype cc, fcode, rccode;

  gt_assert(kmersize <= (unsigned int) GT_UNITSIN2BITENC);
  fcode = gt_kmercode_at_position(twobitencoding, startpos, kmersize);
  rccode = gt_kmercode_complement(gt_kmercode_reverse(fcode,kmersize),
                                  maskright);
  GT_RANDOMCODES_INSERTSUFFIXES(buf,fcode,fseqnum,0UL);
  if (kmersize == minmatchlength)
  {
    GT_RANDOMCODES_INSERTSUFFIXES(buf,rccode,rseqnum,lastfrelpos);
  }
  unitindex = GT_DIVBYUNITSIN2BITENC(startpos + kmersize);
  currentencoding = twobitencoding[unitindex];
  shiftright = (unsigned int)
               GT_MULT2(GT_UNITSIN2BITENC - 1 -
                        GT_MODBYUNITSIN2BITENC(startpos + kmersize));
  for (frelpos = 1UL; frelpos <= lastfrelpos; frelpos++)
  {
    cc = (GtCodetype) (currentencoding >> shiftright) & 3;
    fcode = ((fcode << 2) | cc) & maskright;
    rccode = (rccode >> 2) | ((cc ^ 3UL) << shiftleft);
    if (frelpos <= lastpossiblepos)
    {
      GT_RANDOMCODES_INSERTSUFFIXES(buf,fcode,fseqnum,frelpos);
    }
    if (lastfrelpos - frelpos <= lastpossiblepos)
    {
      GT_RANDOMCODES_INSERTSUFFIXES(buf,rccode,rseqnum,lastfrelpos - frelpos);
    }
    if (shiftright > 0)
    {
      shiftright -= 2;
    } else
    {
      gt_assert(unitindex < maxunitindex-1 || frelpos == lastfrelpos);
      if (unitindex < maxunitindex-1)
      {
        currentencoding = twobitencoding[++unitindex];
        shiftright = (unsigned int) (GT_INTWORDSIZE-2);
      }
    }
  }
}

static void gt_randomcodes_insert_kmerscan_eqlen(
                                     const GtBitsequence *twobitencoding,
                                     unsigned long equallength,
                                     unsigned long totallength,
                                     unsigned long numofsequences,
                                     unsigned long maxunitindex,
                                     unsigned int kmersize,
                                     unsigned int minmatchlength,
                                     GtCodeposbuffer *buf)
{
  unsigned long startpos, fseqnum;

  if (equallength >= (unsigned long) kmersize)
  {
    for (startpos = 0, fseqnum = 0; startpos < totallength;
         startpos += equallength+1, fseqnum++)
    {
      gt_randomcodes_insert_kmerscan_range(twobitencoding,
                                          kmersize,
                                          minmatchlength,
                                          startpos,
                                          equallength,
                                          fseqnum,
                                          numofsequences - 1 - fseqnum,
                                          maxunitindex,
                                          buf);
    }
  }
}

static void gt_randomcodes_insert_kmerscan(const GtEncseq *encseq,
                                          const GtBitsequence *twobitencoding,
                                          unsigned long totallength,
                                          unsigned long numofsequences,
                                          unsigned long maxunitindex,
                                          unsigned int kmersize,
                                          unsigned int minmatchlength,
                                          GtCodeposbuffer *buf)
{
  unsigned long laststart = 0, fseqnum = 0;

  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;

    sri = gt_specialrangeiterator_new(encseq,true);
    while (gt_specialrangeiterator_next(sri,&range)
           && range.start < totallength)
    {
      gt_assert(range.start >= laststart);
      if (range.start - laststart >= (unsigned long) minmatchlength)
      {
        gt_randomcodes_insert_kmerscan_range(twobitencoding,
                                            kmersize,
                                            minmatchlength,
                                            laststart,
                                            range.start - laststart,
                                            fseqnum,
                                            numofsequences - 1 - fseqnum,
                                            maxunitindex,
                                            buf);
      }
      laststart = range.end;
      fseqnum++;
    }
    gt_specialrangeiterator_delete(sri);
  }
  if (totallength - laststart >= (unsigned long) minmatchlength)
  {
    gt_randomcodes_insert_kmerscan_range(twobitencoding,
                                        kmersize,
                                        minmatchlength,
                                        laststart,
                                        totallength - laststart,
                                        fseqnum,
                                        numofsequences - 1 - fseqnum,
                                        maxunitindex,
                                        buf);
  }
}

void gt_randomcodes_insert_runkmerscan(const GtEncseq *encseq,
                                      unsigned int kmersize,
                                      unsigned int minmatchlength,
                                      GtCodeposbuffer *buf)
{
  const GtTwobitencoding *twobitencoding
    = gt_encseq_twobitencoding_export(encseq);
  unsigned long totallength, maxunitindex, numofsequences;

  gt_assert(minmatchlength>=kmersize);
  if (gt_encseq_is_mirrored(encseq))
  {
    totallength = (gt_encseq_total_length(encseq)-1)/2;
  } else
  {
    totallength = gt_encseq_total_length(encseq);
  }
  numofsequences = gt_encseq_num_of_sequences(encseq);
  maxunitindex = gt_unitsoftwobitencoding(totallength) - 1;
  if (gt_encseq_accesstype_get(encseq) == GT_ACCESS_TYPE_EQUALLENGTH)
  {
    unsigned long equallength = gt_encseq_equallength(encseq);

    gt_assert(equallength >= (unsigned long) kmersize);
    gt_randomcodes_insert_kmerscan_eqlen(twobitencoding,
                                        equallength,
                                        totallength,
                                        numofsequences,
                                        maxunitindex,
                                        kmersize,
                                        minmatchlength,
                                        buf);
  } else
  {
    gt_randomcodes_insert_kmerscan(encseq,
                                  twobitencoding,
                                  totallength,
                                  numofsequences,
                                  maxunitindex,
                                  kmersize,
                                  minmatchlength,
                                  buf);
  }
}
genometools-1.5.1/src/match/randomcodes-insert.h000066400000000000000000000023241211610345200217010ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RANDOMCODES_INSERT_H
#define RANDOMCODES_INSERT_H

#include "core/encseq_api.h"
#include "match/firstcodes-buf.h"

void gt_randomcodes_insert_runkmerscan(const GtEncseq *encseq,
                                      unsigned int kmersize,
                                      unsigned int minmatchlength,
                                      GtCodeposbuffer *buf);

#endif
genometools-1.5.1/src/match/randomcodes-sfx-partssuf.c000066400000000000000000000401461211610345200230410ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/assert_api.h"
#include "core/ma_api.h"
#include "core/codetype.h"
#include "core/spacecalc.h"
#include "core/log.h"
#include "bcktab.h"
#include "sfx-suffixgetset.h"
#include "spmsuftab.h"
#include "randomcodes-sfx-partssuf.h"
#include "randomcodes-tab.h"

typedef struct
{
  unsigned long nextidx,
                widthofpart,
                suftaboffset,
                sumofwidth,
                minindex,
                maxindex;
} GtSuftabpartcomponent_rc;

struct GtSuftabparts_rc
{
  GtSuftabpartcomponent_rc *components;
  bool indexrange_available;
  unsigned int numofparts;
  unsigned long largestsizemappedpartwise,
                largestsuftabwidth;
  const GtRandomcodestab *fct;
};

void gt_suftabparts_rc_showallrecords(const GtSuftabparts_rc *suftabparts_rc,
                                   bool withminmaxindex)
{
  unsigned int part;
  unsigned long totalwidth;

  gt_assert(suftabparts_rc != NULL);
  gt_assert(suftabparts_rc->numofparts >= 1U);
  totalwidth =
    suftabparts_rc->components[suftabparts_rc->numofparts - 1].sumofwidth;
  for (part = 0; part < suftabparts_rc->numofparts; part++)
  {
    if (withminmaxindex)
    {
      gt_log_log("part %u: width=%lu (%.2f%%) offset=%lu nextidx=%lu "
                 "minindex=%lu maxindex=%lu ",
                 part,
                 suftabparts_rc->components[part].widthofpart,
                 100.00 * (double) suftabparts_rc->components[part].widthofpart/
                                   totalwidth,
                 suftabparts_rc->components[part].suftaboffset,
                 suftabparts_rc->components[part].nextidx,
                 gt_suftabparts_rc_minindex(part,suftabparts_rc),
                 gt_suftabparts_rc_maxindex(part,suftabparts_rc));
    } else
    {
      gt_log_log("part %u: width=%lu (%.2f%%) offset=%lu nextidx=%lu",
                 part,
                 suftabparts_rc->components[part].widthofpart,
                 100.00 * (double) suftabparts_rc->components[part].widthofpart/
                                   totalwidth,
                 suftabparts_rc->components[part].nextidx,
                 suftabparts_rc->components[part].suftaboffset);
    }
  }
  gt_log_log("variance %.0f",gt_suftabparts_rc_variance(suftabparts_rc));
}

static GtCodetype gt_suftabparts_rc_minindex_raw(
    unsigned int part, const GtSuftabparts_rc *suftabparts_rc)
{
  GtCodetype minindex;
  gt_assert(suftabparts_rc != NULL && part < suftabparts_rc->numofparts);

  minindex = (part == 0) ? 0 : suftabparts_rc->components[part-1].nextidx + 1;
  if (suftabparts_rc->fct != NULL)
  {
    return gt_randomcodes_sample2full(suftabparts_rc->fct,minindex);
  }
  return minindex;
}

static GtCodetype gt_suftabparts_rc_maxindex_raw(
    unsigned int part, const GtSuftabparts_rc *suftabparts_rc)
{
  GtCodetype maxindex;

  gt_assert(suftabparts_rc != NULL && part < suftabparts_rc->numofparts);
  if (suftabparts_rc->fct != NULL)
  {
    maxindex = suftabparts_rc->components[part].nextidx;
    return gt_randomcodes_sample2full(suftabparts_rc->fct,maxindex);
  }
  maxindex = (part == suftabparts_rc->numofparts - 1)
               ? suftabparts_rc->components[part].nextidx - 1
               : suftabparts_rc->components[part].nextidx;
  return maxindex;
}

static void gt_suftabparts_rc_removeemptyparts(GtSuftabparts_rc *suftabparts_rc,
                                            GT_UNUSED unsigned long totalwidth,
                                            GtLogger *logger)
{
#undef SKDEBUG
#ifdef SKDEBUG
  gt_log_log("before removal");
  gt_suftabparts_rc_showallrecords(suftabparts_rc,false);
#endif
  gt_assert(suftabparts_rc != NULL);
  if (suftabparts_rc->numofparts > 0)
  {
    unsigned int destpart, srcpart;
    unsigned long sumwidth = 0;

    for (destpart = 0, srcpart = 0; srcpart < suftabparts_rc->numofparts;
         srcpart++)
    {
      if (suftabparts_rc->components[srcpart].widthofpart > 0)
      {
        if (destpart < srcpart)
        {
          suftabparts_rc->components[destpart] =
            suftabparts_rc->components[srcpart];
        }
        destpart++;
      }
    }
    if (destpart < srcpart)
    {
      suftabparts_rc->components[destpart-1].nextidx
        = suftabparts_rc->components[suftabparts_rc->numofparts-1].nextidx;
      suftabparts_rc->numofparts -= (srcpart - destpart);
      gt_assert(suftabparts_rc->numofparts == destpart);
    }
    for (srcpart = 0; srcpart < suftabparts_rc->numofparts; srcpart++)
    {
      gt_assert(suftabparts_rc->components[srcpart].widthofpart > 0);
      sumwidth+=suftabparts_rc->components[srcpart].widthofpart;
      gt_logger_log(logger,"widthofpart[%u]=%lu",
                    srcpart,
                    suftabparts_rc->components[srcpart].widthofpart);
    }
    gt_assert(sumwidth == totalwidth);
  }
#ifdef SKDEBUG
  gt_log_log("after removal");
  gt_suftabparts_rc_showallrecords(suftabparts_rc,true);
#endif
}

GtSuftabparts_rc *gt_suftabparts_rc_new(unsigned int numofparts,
                                  const GtBcktab *bcktab,
                                  const GtRandomcodestab *fct,
                                  const GtSfxmappedrangelist *sfxmrlist,
                                  unsigned long numofsuffixestoinsert,
                                  unsigned long fullspecials,
                                  GtLogger *logger)
{
  GtSuftabparts_rc *suftabparts_rc;
  unsigned long size_mapped;
  unsigned int part;

  gt_assert((bcktab == NULL && fct != NULL) ||
            (bcktab != NULL && fct == NULL));
  suftabparts_rc = gt_malloc(sizeof *suftabparts_rc);
  suftabparts_rc->largestsizemappedpartwise = 0;
  suftabparts_rc->fct = fct;
  gt_assert(suftabparts_rc != NULL);
  if (numofsuffixestoinsert == 0)
  {
    suftabparts_rc->numofparts = 0;
  } else
  {
    if (numofsuffixestoinsert < (unsigned long) numofparts ||
        (bcktab != NULL && gt_bcktab_prefixlength(bcktab) == 1U))
    {
      suftabparts_rc->numofparts = 1U;
    } else
    {
      suftabparts_rc->numofparts = numofparts;
    }
  }
  if (suftabparts_rc->numofparts == 0)
  {
    suftabparts_rc->largestsuftabwidth = fullspecials/numofparts+1;
    suftabparts_rc->largestsizemappedpartwise
      = gt_Sfxmappedrangelist_size_entire(sfxmrlist);
    suftabparts_rc->components = NULL;
  } else
  {
    unsigned int remainder;
    unsigned long secondidx, randombound = 0, secondbound,
                  suftaboffset = 0, sumofwidth = 0;
    const unsigned long widthofsuftabpart
      = numofsuffixestoinsert/suftabparts_rc->numofparts;

    suftabparts_rc->components
      = gt_malloc(sizeof (*suftabparts_rc->components) *
          suftabparts_rc->numofparts);
    remainder = (unsigned int) (numofsuffixestoinsert %
                                (unsigned long) suftabparts_rc->numofparts);
    suftabparts_rc->largestsuftabwidth = 0;
    for (part=0; part < suftabparts_rc->numofparts; part++)
    {
      if (remainder > 0)
      {
        suftaboffset += widthofsuftabpart + 1;
        remainder--;
      } else
      {
        suftaboffset += widthofsuftabpart;
      }
      if (part == suftabparts_rc->numofparts - 1)
      {
        secondidx = bcktab != NULL ? gt_bcktab_numofallcodes(bcktab)
                                   : gt_randomcodes_numofsamples(fct);
      } else
      {
        secondidx = bcktab != NULL
                      ? gt_bcktab_findfirstlarger(bcktab,suftaboffset)
                      : gt_randomcodes_findfirstsamplelarger(fct,suftaboffset);
      }
      suftabparts_rc->components[part].nextidx = secondidx;
      secondbound = bcktab != NULL
                      ? gt_bcktab_get_leftborder(bcktab,secondidx)
                      : gt_randomcodes_get_sample(fct,secondidx);
      if (part == 0)
      {
        suftabparts_rc->components[part].widthofpart = secondbound;
        suftabparts_rc->components[part].suftaboffset = 0;
      } else
      {
        gt_assert(secondbound >= randombound);
        suftabparts_rc->components[part].widthofpart = secondbound -
          randombound;
        suftabparts_rc->components[part].suftaboffset = randombound;
      }
      if (suftabparts_rc->largestsuftabwidth <
          suftabparts_rc->components[part].widthofpart)
      {
        suftabparts_rc->largestsuftabwidth
          = suftabparts_rc->components[part].widthofpart;
      }
      sumofwidth += suftabparts_rc->components[part].widthofpart;
      suftabparts_rc->components[part].sumofwidth = sumofwidth;
      randombound = secondbound;
    }
    gt_assert(sumofwidth == numofsuffixestoinsert);
  }
  gt_suftabparts_rc_removeemptyparts(suftabparts_rc,numofsuffixestoinsert,
      logger);
  if (suftabparts_rc->numofparts > 0)
  {
    gt_assert(suftabparts_rc->components != NULL);
    for (part=0; part < suftabparts_rc->numofparts; part++)
    {
      suftabparts_rc->components[part].minindex
        = gt_suftabparts_rc_minindex_raw(part,suftabparts_rc);
      suftabparts_rc->components[part].maxindex
        = gt_suftabparts_rc_maxindex_raw(part,suftabparts_rc);
    }
    for (part=1U; part < suftabparts_rc->numofparts; part++)
    {
      if (suftabparts_rc->components[part].minindex !=
            suftabparts_rc->components[part-1].maxindex + 1)
      {
        suftabparts_rc->components[part].minindex
          = suftabparts_rc->components[part-1].maxindex + 1;
      }
    }
    for (part=0; part < suftabparts_rc->numofparts; part++)
    {
      size_mapped = gt_Sfxmappedrangelist_size_mapped(sfxmrlist,
          gt_suftabparts_rc_minindex(part,suftabparts_rc),
          gt_suftabparts_rc_maxindex(part,suftabparts_rc));
      if (suftabparts_rc->largestsizemappedpartwise < size_mapped)
      {
        suftabparts_rc->largestsizemappedpartwise = size_mapped;
      }
    }
  }
  return suftabparts_rc;
}

double gt_suftabparts_rc_variance(const GtSuftabparts_rc *suftabparts_rc)
{

  gt_assert(suftabparts_rc->numofparts > 0);
  if (suftabparts_rc->numofparts == 1U)
  {
    return 0.0;
  } else
  {
    double meanwidth, difference, sum = 0.0;
    unsigned int part;

    meanwidth = (double)
      suftabparts_rc->components[suftabparts_rc->numofparts-1].sumofwidth/
      suftabparts_rc->numofparts;
    for (part = 0; part < suftabparts_rc->numofparts; part++)
    {
      difference = (double) suftabparts_rc->components[part].widthofpart
                   - meanwidth;
      sum += difference * difference;
    }
    return sum/(double) (suftabparts_rc->numofparts-1);
  }
}

void gt_suftabparts_rc_delete(GtSuftabparts_rc *suftabparts_rc)
{
  if (suftabparts_rc != NULL)
  {
    gt_free(suftabparts_rc->components);
    gt_free(suftabparts_rc);
  }
}

GtCodetype gt_suftabparts_rc_minindex(unsigned int part,
                                   const GtSuftabparts_rc *suftabparts_rc)
{
  return suftabparts_rc->components[part].minindex;
}

GtCodetype gt_suftabparts_rc_maxindex(unsigned int part,
                                   const GtSuftabparts_rc *suftabparts_rc)
{
  return suftabparts_rc->components[part].maxindex;
}

GtCodetype gt_suftabparts_rc_maxindex_last(
    const GtSuftabparts_rc *suftabparts_rc)
{
  gt_assert(suftabparts_rc->numofparts > 0);
  return gt_suftabparts_rc_maxindex(suftabparts_rc->numofparts-1,
      suftabparts_rc);
}

unsigned long gt_suftabparts_rc_offset(unsigned int part,
                                    const GtSuftabparts_rc *suftabparts_rc)
{
  gt_assert(suftabparts_rc != NULL && part < suftabparts_rc->numofparts);
  return suftabparts_rc->components[part].suftaboffset;
}

unsigned long gt_suftabparts_rc_sumofwidth(unsigned int part,
                                        const GtSuftabparts_rc *suftabparts_rc)
{
  gt_assert(suftabparts_rc != NULL && part < suftabparts_rc->numofparts);
  return suftabparts_rc->components[part].sumofwidth;
}

unsigned long gt_suftabparts_rc_widthofpart(unsigned int part,
                                         const GtSuftabparts_rc *suftabparts_rc)
{
  gt_assert(suftabparts_rc != NULL && part < suftabparts_rc->numofparts);
  return suftabparts_rc->components[part].widthofpart;
}

unsigned long gt_suftabparts_rc_largest_width(
    const GtSuftabparts_rc *suftabparts_rc)
{
  gt_assert(suftabparts_rc != NULL);
  return suftabparts_rc->largestsuftabwidth;
}

unsigned long gt_suftabparts_rc_largestsizemappedpartwise(
    const GtSuftabparts_rc *suftabparts_rc)
{
  gt_assert(suftabparts_rc != NULL);
  return suftabparts_rc->largestsizemappedpartwise;
}

unsigned int gt_suftabparts_rc_numofparts(
    const GtSuftabparts_rc *suftabparts_rc)
{
  gt_assert(suftabparts_rc != NULL);
  return suftabparts_rc->numofparts;
}

int gt_suftabparts_rc_fit_memlimit(size_t estimatedspace,
                                unsigned long maximumspace,
                                const GtBcktab *bcktab,
                                const GtRandomcodestab *fct,
                                const GtSfxmappedrangelist *sfxmrlist,
                                unsigned long totallength,
                                unsigned int bitsforseqnumrelpos,
                                unsigned long specialcharacters,
                                unsigned long numofsuffixestosort,
                                bool suftabuint,
                                GtError *err)
{
  unsigned int parts;
  GtSuftabparts_rc *suftabparts_rc;
  unsigned long size_mapped = gt_Sfxmappedrangelist_size_entire(sfxmrlist);

  gt_error_check(err);
  for (parts = 1U; parts <= 500U; parts++)
  {
    size_t suftabsize;
    unsigned long numofentries;

    suftabparts_rc = gt_suftabparts_rc_new(parts,
                                     bcktab,
                                     fct,
                                     sfxmrlist,
                                     numofsuffixestosort,
                                     specialcharacters + 1,
                                     NULL);
    gt_assert(suftabparts_rc != NULL);
    numofentries = gt_suftabparts_rc_largest_width(suftabparts_rc);
    if (bcktab != NULL)
    {
      gt_assert(fct == NULL);
      suftabsize = gt_suffixsortspace_requiredspace(numofentries,
                                                    totallength,
                                                    suftabuint);
    } else
    {
      gt_assert(fct != NULL);
      suftabsize = gt_spmsuftab_requiredspace(numofentries,
                                              totallength,
                                              bitsforseqnumrelpos);
    }
    if (parts == 1U)
    {
      if ((unsigned long) (suftabsize + estimatedspace) <= maximumspace)
      {
        gt_suftabparts_rc_delete(suftabparts_rc);
        return (int) parts;
      }
    } else
    {
      unsigned long largest
        = gt_suftabparts_rc_largestsizemappedpartwise(suftabparts_rc);
      if ((unsigned long) (suftabsize + largest + estimatedspace - size_mapped)
                           <= maximumspace)
      {
        gt_log_log("return parts = %u as suftabsize=%.2f +"
                   "largest=%.2f + estimated=%.2f - size_mapped=%2.f <= %.2f",
                    parts,
                    GT_MEGABYTES(suftabsize),
                    GT_MEGABYTES(largest),
                    GT_MEGABYTES(estimatedspace),
                    GT_MEGABYTES(size_mapped),
                    GT_MEGABYTES(maximumspace));
        gt_suftabparts_rc_delete(suftabparts_rc);
        return (int) parts;
      }
    }
    gt_suftabparts_rc_delete(suftabparts_rc);
  }
  gt_error_set(err,"cannot compute enhanced suffix array in at most %lu bytes",
                   maximumspace);
  return -1;
}
genometools-1.5.1/src/match/randomcodes-sfx-partssuf.h000066400000000000000000000070101211610345200230370ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RANDOMCODES_SFX_PARTSSUF_H
#define RANDOMCODES_SFX_PARTSSUF_H

#include "core/logger.h"
#include "core/codetype.h"
#include "core/error_api.h"
#include "sfx-maprange.h"
#include "randomcodes-tab.h"
#include "bcktab.h"

typedef struct GtSuftabparts_rc GtSuftabparts_rc;

void gt_suftabparts_rc_showallrecords(const GtSuftabparts_rc *suftabparts_rc,
                                   bool withminmaxindex);

GtSuftabparts_rc *gt_suftabparts_rc_new(unsigned int numofparts,
                                  const GtBcktab *bcktab,
                                  const GtRandomcodestab *fct,
                                  const GtSfxmappedrangelist *sfxmrlist,
                                  unsigned long numofsuffixestoinsert,
                                  unsigned long fullspecials,
                                  GtLogger *logger);

void gt_suftabparts_rc_delete(GtSuftabparts_rc *suftabparts_rc);

GtCodetype gt_suftabparts_rc_minindex(unsigned int part,
                                   const GtSuftabparts_rc *suftabparts_rc);

GtCodetype gt_suftabparts_rc_maxindex(unsigned int part,
                                   const GtSuftabparts_rc *suftabparts_rc);

GtCodetype gt_suftabparts_rc_maxindex_last(
    const GtSuftabparts_rc *suftabparts_rc);

unsigned long gt_suftabparts_rc_offset(unsigned int part,
                                    const GtSuftabparts_rc *suftabparts_rc);

unsigned long gt_suftabparts_rc_sumofwidth(unsigned int part,
                                        const GtSuftabparts_rc *suftabparts_rc);

unsigned long gt_suftabparts_rc_widthofpart(unsigned int part,
    const GtSuftabparts_rc *suftabparts_rc);

unsigned long gt_suftabparts_rc_largest_width(
    const GtSuftabparts_rc *suftabparts_rc);

unsigned int gt_suftabparts_rc_numofparts(
    const GtSuftabparts_rc *suftabparts_rc);

unsigned long gt_suftabparts_rc_largestsizemappedpartwise(
                                       const GtSuftabparts_rc *suftabparts_rc);

double gt_suftabparts_rc_variance(const GtSuftabparts_rc *suftabparts_rc);

int gt_suftabparts_rc_fit_memlimit(size_t estimatedspace,
                                unsigned long maximumspace,
                                const GtBcktab *bcktab,
                                const GtRandomcodestab *fct,
                                const GtSfxmappedrangelist *sfxmrlist,
                                unsigned long totallength,
                                unsigned int bitsforseqnumrelpos,
                                unsigned long specialcharacters,
                                unsigned long numofsuffixestosort,
                                bool suftabuint,
                                GtError *err);

#endif
genometools-1.5.1/src/match/randomcodes-tab.c000066400000000000000000000374071211610345200211500ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/xansi_api.h"
#include "core/fa.h"
#include "core/assert_api.h"
#include "core/divmodmul.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#ifdef SKDEBUG
#include "core/disc_distri_api.h"
#endif
#include "core/log.h"
#include "core/spacecalc.h"
#include "core/hashmap-generic.h"
#include "core/arraydef.h"
#include "randomcodes-tab.h"
#include "firstcodes-psbuf.h"

void gt_randomcodes_countocc_new(GtFirstcodesspacelog *fcsl,
                                       GtRandomcodestab *rct,
                                       unsigned long numofsequences)
{
  rct->countocc_small = gt_calloc((size_t) (numofsequences+1),
                                  sizeof (*rct->countocc_small));
  GT_FCI_ADDWORKSPACE(fcsl,"countocc_small",
                      sizeof (*rct->countocc_small) *
                      (numofsequences+1));
  rct->countocc_exceptions = ul_u32_gt_hashmap_new();
  gt_assert(rct->countocc_exceptions != NULL);
  rct->outfilenameleftborder = NULL;
  rct->leftborder_samples = NULL;
#ifdef _LP64
  rct->modvaluebits = 32U; /* XXX remove the following later */
  if (rct->modvaluebits == 32U)
  {
    rct->modvaluemask = UINT32_MAX;
  } else
  {
    rct->modvaluemask = (uint32_t) ((1UL << rct->modvaluebits) - 1);
  }
  GT_INITARRAY(&rct->bitchangepoints,GtUlong);
#endif
  rct->differentcodes = numofsequences;
}

void gt_randomcodes_countocc_resize(GtFirstcodesspacelog *fcsl,
                                          GtRandomcodestab *rct,
                                          unsigned long numofdifferentcodes)
{
  rct->countocc_small = gt_realloc(rct->countocc_small,
                                   sizeof (*rct->countocc_small) *
                                           (numofdifferentcodes+1));
  GT_FCI_SUBTRACTADDWORKSPACE(fcsl,"countocc_small",
                              sizeof (*rct->countocc_small) *
                              (numofdifferentcodes+1));
}

#ifdef SKDEBUG

typedef struct
{
  unsigned long smallcount, smallsum,
                largecount, largesum,
                hugecount, hugesum;
} GtCountdistri_info;

static void gt_randomcodes_evaluate_distvalue(unsigned long key,
                                             unsigned long long value,
                                             void *data)
{
  GtCountdistri_info *cdi = (GtCountdistri_info *) data;

  gt_assert(value > 0);
  if (key <= UINT8_MAX)
  {
    cdi->smallcount++;
    cdi->smallsum += value;
  } else
  {
    if (key <= UINT16_MAX)
    {
      cdi->largecount++;
      cdi->largesum += value;
    } else
    {
      cdi->hugecount++;
      cdi->hugesum += value;
    }
  }
}

static void gt_randomcodes_evaluate_countdistri(const GtDiscDistri *countdistri)
{
  GtCountdistri_info cdi;
  unsigned long sum;
  size_t spacenow, spacedirectstore, spaceopt, spacewithhash;;

  cdi.smallcount = 0;
  cdi.smallsum = 0;
  cdi.largecount = 0;
  cdi.largesum = 0;
  cdi.hugecount = 0;
  cdi.hugesum = 0;
  gt_disc_distri_foreach(countdistri,gt_randomcodes_evaluate_distvalue,&cdi);
  sum = cdi.smallsum + cdi.largesum + cdi.hugesum;
  gt_log_log("small=%lu,%lu (%.2f)",cdi.smallcount,cdi.smallsum,
          (double) cdi.smallsum/sum);
  gt_log_log("large=%lu,%lu (%.2f)",cdi.largecount,cdi.largesum,
          (double) cdi.largesum/sum);
  gt_log_log("huge=%lu,%lu (%.2f)",cdi.hugecount,cdi.hugesum,
          (double) cdi.largesum/sum);
  spacenow = sizeof (uint32_t) * sum;
  spaceopt = sizeof (uint8_t) * sum;
  spacedirectstore = sizeof (uint32_t) * cdi.largesum;
  spacewithhash = (2 * sizeof (void *)) * cdi.largecount;
  gt_log_log("spacenow=%.2f, spaceopt (direct)=%2.f spaceopt (hash) =%.2f",
          GT_MEGABYTES(spacenow),
          GT_MEGABYTES(spaceopt+spacedirectstore),
          GT_MEGABYTES(spaceopt+spacewithhash));
}
#endif

#ifdef SKDEBUG
static void checkcodesorder(const unsigned long *tab,unsigned long len,
                            bool allowequal)
{
  unsigned long idx;

  for (idx=1UL; idx < len; idx++)
  {
    gt_assert(tab[idx-1] < tab[idx] || (allowequal && tab[idx-1] == tab[idx]));
  }
}
#endif

unsigned long gt_randomcodes_remdups(unsigned long *allrandomcodes,
    unsigned int codesize, unsigned long numofcodes, GtLogger *logger)
{
  unsigned long numofdifferentcodes = 0,
                shift = (unsigned long)GT_MULT2(GT_UNITSIN2BITENC - codesize);
  if (numofcodes != 0)
  {
    unsigned long *storeptr, *readptr;

    for (storeptr = allrandomcodes, readptr = allrandomcodes+1;
         readptr < allrandomcodes + numofcodes;
         readptr++)
    {
      if ((*storeptr ^ *readptr) << shift)
      {
        storeptr++;
        *storeptr = *readptr;
      }
    }
    numofdifferentcodes = (unsigned long) (storeptr - allrandomcodes + 1);
    if (numofdifferentcodes < numofcodes)
    {
#ifdef SKDEBUG
      checkcodesorder(allrandomcodes,numofdifferentcodes,false);
#endif
    }
  }
  gt_logger_log(logger,"number of different bucket codes=%lu (%.2f%%) "
                       "of %lu sampled codes",
                numofdifferentcodes,
                100.00 * (double) numofdifferentcodes/numofcodes,
                numofcodes);
  return numofdifferentcodes;
}

static uint32_t gt_randomcodes_countocc_get(const GtRandomcodestab *rct,
                                           unsigned long idx)
{
  if (rct->countocc_small[idx] != GT_RANDOMCODES_COUNTOCC_OVERFLOW)
  {
    return (uint32_t) rct->countocc_small[idx];
  } else
  {
    uint32_t *valueptr = ul_u32_gt_hashmap_get(rct->countocc_exceptions,idx);

    gt_assert(valueptr != NULL);
    return *valueptr + (uint32_t) GT_RANDOMCODES_MAXSMALL;
  }
}

#ifdef _LP64
#define GT_RCT_PARTIALSUM_LEFTBORDER_SET(BUF,VALUE)\
        if ((BUF)->nextfree == (BUF)->allocated)\
        {\
          gt_leftborderbuffer_flush(BUF);\
        }\
        (BUF)->spaceuint32_t[(BUF)->nextfree++]\
          = (uint32_t) ((VALUE) & rct->modvaluemask)
#else
#define GT_RCT_PARTIALSUM_LEFTBORDER_SET(BUF,VALUE)\
        if ((BUF)->nextfree == (BUF)->allocated)\
        {\
          gt_leftborderbuffer_flush(BUF);\
        }\
        (BUF)->spaceuint32_t[(BUF)->nextfree++] = (uint32_t) (VALUE)
#endif

#define GT_RANDOMCODES_ADD_SAMPLE(PARTSUM)\
        gt_assert(samplecount < rct->numofsamples);\
        rct->leftborder_samples[samplecount++] = PARTSUM

unsigned long gt_randomcodes_partialsums(GtFirstcodesspacelog *fcsl,
                                        GtRandomcodestab *rct,
                                        GT_UNUSED unsigned long
                                                            expectedlastpartsum)
{
  unsigned long idx, partsum, maxbucketsize, bitmask, samplecount = 0,
                spacewithhashmap = 0, spacewithouthashmap = 0;
  uint32_t currentcount;
  GtLeftborderOutbuffer *leftborderbuffer_all = NULL;
#ifdef _LP64
  const unsigned int btp = gt_determinebitspervalue(expectedlastpartsum);
  unsigned long exceedvalue = 1UL << rct->modvaluebits;
#endif
#ifdef SKDEBUG
  GtDiscDistri *countdistri = gt_disc_distri_new();
#endif

  gt_assert(rct->differentcodes < UINT32_MAX);
  gt_log_log("hashmap_addcount=%lu (%.2f%%)",rct->hashmap_addcount,
                  100.0 * (double) rct->hashmap_addcount/
                                   rct->differentcodes);
  gt_log_log("hashmap_incrementcount=%lu (%.2f%%)",
                  rct->hashmap_incrementcount,
                  100.0 * (double) rct->hashmap_incrementcount/
                                   rct->all_incrementcount);
  gt_log_log("hashmap_getcount=%lu (%.2f%%)",
                  rct->hashmap_getcount,
                  100.0 * (double) rct->hashmap_getcount/
                                   rct->all_incrementcount);

#ifdef _LP64
  if (btp <= rct->modvaluebits)
  {
    rct->bitchangepoints.allocatedGtUlong = 0;
    rct->bitchangepoints.spaceGtUlong = NULL;
  } else
  {
    rct->bitchangepoints.allocatedGtUlong = 1UL << (btp - rct->modvaluebits);
    gt_log_log("lastpartsum=%lu, bitchangepoints.allocated=%lu",
              expectedlastpartsum,rct->bitchangepoints.allocatedGtUlong);
    rct->bitchangepoints.spaceGtUlong
      = gt_malloc(sizeof (*rct->bitchangepoints.spaceGtUlong)
                  * rct->bitchangepoints.allocatedGtUlong);
  }
  rct->bitchangepoints.nextfreeGtUlong = 0;
#endif
  currentcount = gt_randomcodes_countocc_get(rct,0);
  partsum = (unsigned long) currentcount;
  maxbucketsize = (unsigned long) currentcount;
#ifdef SKDEBUG
  gt_disc_distri_add(countdistri,(unsigned long) currentcount);
#endif
  rct->sampleshift = 9U;
  while (true)
  {
    rct->sampledistance = 1UL << rct->sampleshift;
    if (rct->sampledistance < rct->differentcodes)
    {
      break;
    }
    rct->sampleshift--;
  }
  bitmask = rct->sampledistance - 1;
  rct->numofsamples = 1UL + 1UL + rct->differentcodes/rct->sampledistance;
  rct->leftborder_samples = gt_malloc(sizeof (*rct->leftborder_samples) *
                                      rct->numofsamples);
  GT_FCI_ADDWORKSPACE(fcsl,"leftborder_samples",
                      sizeof (*rct->leftborder_samples) * rct->numofsamples);
  GT_RANDOMCODES_ADD_SAMPLE(partsum);
  leftborderbuffer_all = gt_leftborderbuffer_new("leftborder",fcsl);
  GT_RCT_PARTIALSUM_LEFTBORDER_SET(leftborderbuffer_all,partsum);
  for (idx = 1UL; idx < rct->differentcodes; idx++)
  {
    currentcount = gt_randomcodes_countocc_get(rct,idx);
#ifdef _LP64
    gt_assert(currentcount <= rct->modvaluemask);
#endif
#ifdef SKDEBUG
    gt_disc_distri_add(countdistri,(unsigned long) currentcount);
#endif
    if (maxbucketsize < (unsigned long) currentcount)
    {
      maxbucketsize = (unsigned long) currentcount;
    }
    partsum += currentcount;
#ifdef _LP64
    if (rct->bitchangepoints.allocatedGtUlong > 0 && partsum >= exceedvalue)
    {
      gt_assert(idx > 0 && rct->bitchangepoints.nextfreeGtUlong <
                           rct->bitchangepoints.allocatedGtUlong);
      gt_assert(rct->bitchangepoints.spaceGtUlong != NULL);
      rct->bitchangepoints.spaceGtUlong
        [rct->bitchangepoints.nextfreeGtUlong++] = idx-1;
      exceedvalue
        = ((exceedvalue >> rct->modvaluebits) + 1) << rct->modvaluebits;
    }
#endif
    if ((idx & bitmask) == 0)
    {
      GT_RANDOMCODES_ADD_SAMPLE(partsum);
    }
    GT_RCT_PARTIALSUM_LEFTBORDER_SET(leftborderbuffer_all,partsum);
  }
  GT_RCT_PARTIALSUM_LEFTBORDER_SET(leftborderbuffer_all,partsum);
  rct->outfilenameleftborder
      = gt_leftborderbuffer_delete(leftborderbuffer_all,fcsl,
                                   gt_randomcodes_leftborder_entries(rct));
  if (partsum > rct->leftborder_samples[samplecount-1])
  {
    GT_RANDOMCODES_ADD_SAMPLE(partsum);
  } else
  {
    gt_assert(partsum == rct->leftborder_samples[samplecount-1]);
  }
  gt_assert(expectedlastpartsum == partsum);
  rct->numofsamples = samplecount-1;
#ifdef SKDEBUG
  gt_randomcodes_evaluate_countdistri(countdistri);
  gt_disc_distri_delete(countdistri);
#endif
  gt_assert (rct->countocc_small != NULL);
  gt_free(rct->countocc_small);
  GT_FCI_SUBTRACTWORKSPACE(fcsl,"countocc_small");
  rct->countocc_small = NULL;
  if (rct->hashmap_addcount > 0 && gt_ma_bookkeeping_enabled())
  {
    spacewithhashmap = gt_ma_get_space_current() + gt_fa_get_space_current();
  }
  gt_hashtable_delete(rct->countocc_exceptions);
  if (rct->hashmap_addcount > 0 && gt_ma_bookkeeping_enabled())
  {
    unsigned long hashmapspace;

    spacewithouthashmap = gt_ma_get_space_current() + gt_fa_get_space_current();
    gt_assert(spacewithouthashmap < spacewithhashmap);
    hashmapspace = spacewithhashmap - spacewithouthashmap;
    gt_log_log("space for hashmap=%.2f (%lu bytes per entry)",
               GT_MEGABYTES(hashmapspace),hashmapspace/rct->hashmap_addcount);
  }
  rct->countocc_exceptions = NULL;
  return maxbucketsize;
}

unsigned long gt_randomcodes_get_sample(const GtRandomcodestab *rct,
                                       unsigned long idx)
{
  gt_assert(idx <= rct->numofsamples);
  return rct->leftborder_samples[idx];
}

unsigned long gt_randomcodes_get_leftborder(const GtRandomcodestab *rct,
                                           unsigned long idx)
{
#ifdef _LP64
  GT_CHANGEPOINT_GET_RCT(changepoint);

  return (unsigned long) rct->leftborder[idx]
                         + (changepoint << rct->modvaluebits);
#else
  return (unsigned long) rct->leftborder[idx];
#endif
}

unsigned long gt_randomcodes_leftborder_entries(const GtRandomcodestab *rct)
{
  return rct->differentcodes + 1;
}

unsigned long gt_randomcodes_numofsamples(const GtRandomcodestab *rct)
{
  return rct->numofsamples;
}

unsigned long gt_randomcodes_findfirstsamplelarger(const GtRandomcodestab *rct,
                                                  unsigned long suftaboffset)
{
  unsigned long left = 0, right, mid, midval, found;

  right = found = rct->numofsamples;
  while (left+1 < right)
  {
    mid = GT_DIV2(left+right);
    midval = gt_randomcodes_get_sample(rct,mid);
    if (suftaboffset == midval)
    {
      return mid;
    }
    if (suftaboffset < midval)
    {
      found = mid;
      right = mid - 1;
    } else
    {
      left = mid + 1;
    }
  }
  gt_assert(suftaboffset <= gt_randomcodes_get_sample(rct,found));
  return found;
}

unsigned long gt_randomcodes_sample2full(const GtRandomcodestab *rct,
                                        unsigned long idx)
{
  gt_assert(idx <= rct->numofsamples);
  if (idx < rct->numofsamples)
  {
    return idx << rct->sampleshift;
  }
  return rct->differentcodes - 1;
}

void gt_randomcodes_samples_delete(GtFirstcodesspacelog *fcsl,
                                  GtRandomcodestab *rct)
{
  if (rct->leftborder_samples != NULL)
  {
    gt_free(rct->leftborder_samples);
    GT_FCI_SUBTRACTWORKSPACE(fcsl,"leftborder_samples");
    rct->leftborder_samples = NULL;
  }
}

void gt_randomcodes_countocc_delete(GtFirstcodesspacelog *fcsl,
                                   GtRandomcodestab *rct)
{
  if (rct->countocc_small != NULL)
  {
    GT_FCI_SUBTRACTWORKSPACE(fcsl,"countocc_small");
    gt_free(rct->countocc_small);
    rct->countocc_small = NULL;
  }
  gt_hashtable_delete(rct->countocc_exceptions);
  rct->countocc_exceptions = NULL;
}

void gt_randomcodes_tab_delete(GtFirstcodesspacelog *fcsl,GtRandomcodestab *rct)
{
  gt_randomcodes_samples_delete(fcsl,rct);
  gt_str_delete(rct->outfilenameleftborder);
  rct->outfilenameleftborder = NULL;
#ifdef _LP64
  GT_FREEARRAY(&rct->bitchangepoints,GtUlong);
#endif
}

void gt_randomcodes_countocc_setnull(GtRandomcodestab *rct)
{
  rct->leftborder = NULL;
  rct->countocc_small = NULL;
  rct->leftborder_samples = NULL;
  rct->countocc_exceptions = NULL;
  rct->differentcodes = 0;
  rct->lastincremented_idx = 0;
  rct->lastincremented_valueptr = NULL;
  rct->hashmap_addcount = 0;
  rct->hashmap_incrementcount = 0;
  rct->all_incrementcount = 0;
  rct->hashmap_getcount = 0;
  rct->outfilenameleftborder = NULL;
#ifdef _LP64
  GT_INITARRAY(&rct->bitchangepoints,GtUlong);
#endif
}

uint32_t **gt_randomcodes_leftborder_address(GtRandomcodestab *rct)
{
  return &rct->leftborder;
}

void gt_randomcodes_leftborder_remap(GtRandomcodestab *rct,uint32_t *ptr)
{
  rct->leftborder = ptr;
}

const GtStr *gt_randomcodes_outfilenameleftborder(const GtRandomcodestab *rct)
{
  return rct->outfilenameleftborder;
}
genometools-1.5.1/src/match/randomcodes-tab.h000066400000000000000000000146211211610345200211460ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RANDOMCODES_TAB_H
#define RANDOMCODES_TAB_H

#include 
#include "core/unused_api.h"
#include "core/str_api.h"
#include "core/hashmap-generic.h"
#include "core/logger_api.h"
#include "core/arraydef.h"
#include "firstcodes-tab.h"
#include "firstcodes-spacelog.h"

#define GT_RANDOMCODES_MAXSMALL (UINT8_MAX - 1)
#define GT_RANDOMCODES_COUNTOCC_OVERFLOW UINT8_MAX

typedef struct
{
  unsigned long differentcodes,
                numofsamples,
                sampledistance,
                hashmap_addcount,
                hashmap_incrementcount,
                hashmap_getcount,
                all_incrementcount;
  unsigned int sampleshift;
  uint32_t *leftborder;
  uint8_t *countocc_small;
  GtHashtable *countocc_exceptions;
  unsigned long *leftborder_samples;
  GtStr *outfilenameleftborder;
  unsigned long lastincremented_idx;
  uint32_t *lastincremented_valueptr;
#ifdef _LP64
  uint32_t modvaluemask;
  unsigned int modvaluebits;
  GtArrayGtUlong bitchangepoints;
#endif
} GtRandomcodestab;

GT_UNUSED
static inline void gt_randomcodes_countocc_increment(GtRandomcodestab *rct,
                                                    unsigned long idx)
{
  rct->all_incrementcount++;
  if (rct->countocc_small[idx] != GT_RANDOMCODES_COUNTOCC_OVERFLOW)
  {
    if (rct->countocc_small[idx] < GT_RANDOMCODES_MAXSMALL)
    {
      rct->countocc_small[idx]++;
    } else
    {
      gt_assert (rct->countocc_small[idx] == GT_RANDOMCODES_MAXSMALL);
      rct->countocc_small[idx] = GT_RANDOMCODES_COUNTOCC_OVERFLOW;
      rct->lastincremented_valueptr
        = ul_u32_gt_hashmap_add_and_return_storage(rct->countocc_exceptions,
            idx, (uint32_t) 1);
      rct->lastincremented_idx = idx;
      rct->hashmap_addcount++;
    }
  } else
  {
    /* there is already an overflow for this index */
    if (rct->lastincremented_valueptr != NULL &&
        rct->lastincremented_idx == idx)
    {
      /* last index is identical to current index. */
      gt_assert(*rct->lastincremented_valueptr < UINT32_MAX);
      (*rct->lastincremented_valueptr)++;
    } else
    {
      uint32_t *valueptr
        = ul_u32_gt_hashmap_get(rct->countocc_exceptions,idx);

      rct->hashmap_getcount++;
      gt_assert(valueptr != NULL && *valueptr < UINT32_MAX);
      (*valueptr)++;
      rct->lastincremented_idx = idx;
      rct->lastincremented_valueptr = valueptr;
    }
    rct->hashmap_incrementcount++;
  }
}

#ifdef _LP64
#define GT_CHANGEPOINT_GET_RCT(CP)\
        unsigned long CP;\
        for (CP = 0; CP < rct->bitchangepoints.nextfreeGtUlong &&\
                     idx > rct->bitchangepoints.spaceGtUlong[CP]; CP++)\
            /* Nothing */ ;
#endif

GT_UNUSED
static inline unsigned long gt_randomcodes_insertionindex(GtRandomcodestab *rct,
                                                         unsigned long idx)
{
#ifdef _LP64
  GT_CHANGEPOINT_GET_RCT(changepoint);
  gt_assert(idx < rct->differentcodes);
  if (rct->leftborder[idx] > 0)
  {
    return (unsigned long) --rct->leftborder[idx]
                           + (changepoint << rct->modvaluebits);
  } else
  {
    gt_assert(changepoint > 0);
    changepoint--;
    rct->bitchangepoints.spaceGtUlong[changepoint]++;
    rct->leftborder[idx] = rct->modvaluemask;
    return (unsigned long)
           rct->leftborder[idx] + (changepoint << rct->modvaluebits);
  }
#else
  gt_assert(idx < rct->differentcodes && rct->leftborder[idx] > 0);
  return (unsigned long) --rct->leftborder[idx];
#endif
}

unsigned long gt_randomcodes_partialsums(GtFirstcodesspacelog *fcsl,
                                        GtRandomcodestab *rct,
                                        unsigned long expectedlastpartsum);

unsigned long gt_randomcodes_get_leftborder(const GtRandomcodestab *rct,
                                           unsigned long idx);

unsigned long gt_randomcodes_numofsamples(const GtRandomcodestab *rct);

unsigned long gt_randomcodes_findfirstsamplelarger(const GtRandomcodestab *rct,
                                                  unsigned long suftaboffset);

void gt_randomcodes_samples_delete(GtFirstcodesspacelog *fcsl,
                                  GtRandomcodestab *rct);

void gt_randomcodes_countocc_delete(GtFirstcodesspacelog *fcsl,
                                   GtRandomcodestab *rct);

void gt_randomcodes_tab_delete(GtFirstcodesspacelog *fcsl,
                              GtRandomcodestab *rct);

void gt_randomcodes_countocc_new(GtFirstcodesspacelog *fcsl,
                                       GtRandomcodestab *rct,
                                       unsigned long numofsequences);

void gt_randomcodes_countocc_resize(GtFirstcodesspacelog *fcsl,
                                          GtRandomcodestab *rct,
                                          unsigned long numofdifferentcodes);

void gt_randomcodes_countocc_setnull(GtRandomcodestab *rct);

uint32_t **gt_randomcodes_leftborder_address(GtRandomcodestab *rct);

void gt_randomcodes_leftborder_remap(GtRandomcodestab *rct,uint32_t *ptr);

const GtStr *gt_randomcodes_outfilenameleftborder(const GtRandomcodestab *rct);

unsigned long gt_randomcodes_sample2full(const GtRandomcodestab *rct,
                                        unsigned long idx);

unsigned long gt_randomcodes_leftborder_entries(const GtRandomcodestab *rct);

unsigned long gt_randomcodes_leftborder_entries(const GtRandomcodestab *rct);

unsigned long gt_randomcodes_get_sample(const GtRandomcodestab *rct,
                                       unsigned long idx);

unsigned long gt_randomcodes_remdups(unsigned long *allrandomcodes,
    unsigned int codesize, unsigned long numofcodes, GtLogger *logger);

#endif
genometools-1.5.1/src/match/randomcodes.c000066400000000000000000001743431211610345200204050ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Stefan Kurtz 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/fa.h"
#include "core/arraydef.h"
#include "core/codetype.h"
#include "core/encseq.h"
#include "core/error_api.h"
#include "core/logger_api.h"
#include "core/mathsupport.h"
#include "core/radix_sort.h"
#include "core/showtime.h"
#include "core/spacecalc.h"
#include "core/spacepeak.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/minmax.h"
#ifdef GT_THREADS_ENABLED
#include "core/thread_api.h"
#endif
#include "match/firstcodes-buf.h"
#include "match/firstcodes-spacelog.h"
#include "match/randomcodes-tab.h"
#include "match/firstcodes-accum.h"
#include "match/randomcodes-insert.h"
#include "match/randomcodes.h"
#include "match/seqnumrelpos.h"
#include "match/randomcodes-sfx-partssuf.h"
#include "match/randomcodes-correct.h"
#include "match/sfx-shortreadsort.h"
#include "match/sfx-suffixer.h"
#include "match/spmsuftab.h"
#include "match/stamp.h"
#include "match/kmercodes.h"

typedef struct
{
  unsigned long *ptr, code, index;
} GtIndexwithcodeRC;

typedef struct
{
  GtIndexwithcodeRC *spaceGtIndexwithcodeRC;
  unsigned long width, nextfreeGtIndexwithcodeRC, allocatedGtIndexwithcodeRC;
  unsigned int depth;
} GtArrayGtIndexwithcodeRC;

typedef struct
{
  unsigned long total_count,
                total_inserted,
                countcodes,
                numofcodes,
                codebuffer_total,
                currentminindex,
                currentmaxindex,
                differentcodes, /* a copy of the same value as in tab */
                widthofpart;
  GtArrayGtIndexwithcodeRC binsearchcache;
  unsigned int flushcount,
               bitsforposref;
  GtRadixsortinfo *radixsort_code,
                  *radixsort_codepos;
  GtSpmsuftab *spmsuftab;
  GtSfxmappedrange *mappedleftborder,
                   *mappedallrandomcodes;
  unsigned long *allrandomcodes;
  GtFirstcodesspacelog *fcsl;
  GtCodeposbuffer buf;
  GtRandomcodestab tab;
} GtRandomcodesinfo;

static void gt_storerandomcodes(void *processinfo,
                               GT_UNUSED bool firstinrange,
                               GT_UNUSED unsigned long pos,
                               GtCodetype code)
{
  GtRandomcodesinfo *fci = (GtRandomcodesinfo *) processinfo;

  gt_assert(fci != NULL && firstinrange &&
            fci->allrandomcodes != NULL &&
            fci->countcodes < fci->numofcodes);
  fci->allrandomcodes[fci->countcodes++] = code;
}

static void gt_randomcodes_fillbinsearchcache(GtRandomcodesinfo *fci,
                                             unsigned int addbscache_depth)
{
  size_t allocbytes = 0;

  fci->binsearchcache.depth
    = addbscache_depth + (unsigned int) log10((double) fci->differentcodes);
  fci->binsearchcache.nextfreeGtIndexwithcodeRC = 0;
  fci->binsearchcache.allocatedGtIndexwithcodeRC
    = 1UL << (fci->binsearchcache.depth+1);
  fci->binsearchcache.width
    = fci->differentcodes/fci->binsearchcache.allocatedGtIndexwithcodeRC;
  if (fci->binsearchcache.allocatedGtIndexwithcodeRC < fci->differentcodes)
  {
    unsigned long idx, current = fci->binsearchcache.width;

    allocbytes = sizeof (*fci->binsearchcache.spaceGtIndexwithcodeRC)
                 * fci->binsearchcache.allocatedGtIndexwithcodeRC;
    fci->binsearchcache.spaceGtIndexwithcodeRC = gt_malloc(allocbytes);
    for (idx=0; idx < fci->binsearchcache.allocatedGtIndexwithcodeRC; idx++)
    {
      gt_assert(current < fci->differentcodes);
      fci->binsearchcache.
           spaceGtIndexwithcodeRC[fci->binsearchcache.nextfreeGtIndexwithcodeRC]
                               .ptr = fci->allrandomcodes + current;
      fci->binsearchcache.
           spaceGtIndexwithcodeRC[fci->binsearchcache.nextfreeGtIndexwithcodeRC]
                               .index = current;
      fci->binsearchcache.
        spaceGtIndexwithcodeRC[fci->binsearchcache.nextfreeGtIndexwithcodeRC++]
        .code = fci->allrandomcodes[current];
      current += fci->binsearchcache.width;
    }
  }
  gt_log_log("binsearchcache.depth=%u => %lu bytes",
             fci->binsearchcache.depth,
             (unsigned long) allocbytes);
  GT_FCI_ADDWORKSPACE(fci->fcsl,"binsearchcache",allocbytes);
}

#define SHOWFOUND(F)\
        if ((F) == NULL)\
        {\
          fprintf(stderr,"%s = NULL\n",#F);\
        } else\
        {\
          fprintf(stderr,"%s = %lu\n",#F,\
                   (unsigned long) ((F) - fci->allrandomcodes));\
        }

unsigned long gt_randomcodes_find_accu(const GtRandomcodesinfo *fci,
                                       unsigned long code)
{
  const unsigned long *found = NULL, *leftptr = NULL, *midptr, *rightptr = NULL;

  if (code <= fci->allrandomcodes[0])
  {
    return 0;
  }
  if (fci->binsearchcache.spaceGtIndexwithcodeRC != NULL)
  {
    const GtIndexwithcodeRC *leftic, *midic, *rightic;
    unsigned int depth;

    leftic = fci->binsearchcache.spaceGtIndexwithcodeRC;
    rightic = fci->binsearchcache.spaceGtIndexwithcodeRC +
              fci->binsearchcache.nextfreeGtIndexwithcodeRC - 1;
    for (depth = 0; /* Nothing */; depth++)
    {
      midic = leftic + GT_DIV2((unsigned long) (rightic-leftic));
      if (code < midic->code)
      {
        found = midic->ptr;
        if (depth < fci->binsearchcache.depth)
        {
          rightic = midic - 1;
        } else
        {
          gt_assert(leftic->ptr != NULL && rightic->ptr != NULL);
          if (leftic > fci->binsearchcache.spaceGtIndexwithcodeRC)
          {
            leftptr = (leftic-1)->ptr + 1;
          } else
          {
            gt_assert(code > fci->allrandomcodes[0]);
            leftptr = fci->allrandomcodes + 1;
          }
          rightptr = rightic->ptr - 1;
          break;
        }
      } else
      {
        if (code > midic->code)
        {
          if (depth < fci->binsearchcache.depth)
          {
            leftic = midic + 1;
          } else
          {
            gt_assert(leftic->ptr != NULL && rightic->ptr != NULL);
            leftptr = leftic->ptr + 1;
            if (rightic < fci->binsearchcache.spaceGtIndexwithcodeRC +
                          fci->binsearchcache.nextfreeGtIndexwithcodeRC - 1)
            {
              rightptr = (rightic+1)->ptr - 1;
            } else
            {
              rightptr = fci->allrandomcodes + fci->differentcodes - 1;
            }
            break;
          }
        } else
        {
          gt_assert(midic->ptr != NULL);
          return (unsigned long) (midic->ptr - fci->allrandomcodes);
        }
      }
    }
    gt_assert(leftptr != NULL && rightptr != NULL);
  } else
  {
    leftptr = fci->allrandomcodes + 1;
    rightptr = fci->allrandomcodes + fci->differentcodes - 1;
  }
  while (leftptr <= rightptr)
  {
    midptr = leftptr + GT_DIV2((unsigned long) (rightptr-leftptr));
    if (code < *midptr)
    {
      rightptr = midptr - 1;
      if (code > *rightptr)
      {
        return (unsigned long) (midptr - fci->allrandomcodes);
      }
      found = midptr;
    } else
    {
      if (code > *midptr)
      {
        leftptr = midptr + 1;
        if (code <= *leftptr)
        {
          return (unsigned long) (leftptr - fci->allrandomcodes);
        }
      } else
      {
        gt_assert(midptr != NULL);
        return (unsigned long) (midptr - fci->allrandomcodes);
      }
    }
  }
 return (found != NULL) ? (unsigned long) (found - fci->allrandomcodes)
                         : ULONG_MAX;
}

const unsigned long *gt_randomcodes_find_insert(const GtRandomcodesinfo *fci,
                                               unsigned long code)
{
  const unsigned long *found = NULL, *leftptr = NULL, *midptr, *rightptr = NULL;

  leftptr = fci->allrandomcodes + fci->currentminindex;
  rightptr = fci->allrandomcodes + fci->currentmaxindex;
  if (code < *leftptr)
  {
    return leftptr;
  }
  while (leftptr <= rightptr)
  {
    midptr = leftptr + GT_DIV2((unsigned long) (rightptr-leftptr));
    if (code < *midptr)
    {
      rightptr = midptr - 1;
      if (code > *rightptr)
      {
        return midptr;
      }
      found = midptr;
    } else
    {
      if (code > *midptr)
      {
        leftptr = midptr + 1;
        if (code <= *leftptr)
        {
          return leftptr;
        }
      } else
      {
        return midptr;
      }
    }
  }
  return found;
}

static unsigned long gt_randomcodes_accumulatecounts_merge(
                                        GtRandomcodesinfo *fci,
                                        const unsigned long *querystream_fst,
                                        const unsigned long *subjectstream_fst)
{
  unsigned long found = 0;
  const unsigned long *query = querystream_fst,
                      *subject = subjectstream_fst,
                      *querystream_lst = fci->buf.spaceGtUlong
                                         + fci->buf.nextfree - 1,
                      *subjectstream_lst = fci->allrandomcodes
                                           + fci->differentcodes - 1;

  while (query <= querystream_lst && subject <= subjectstream_lst)
  {
    if (*query <= *subject)
    {
      gt_randomcodes_countocc_increment(&fci->tab,(unsigned long)
          (subject - fci->allrandomcodes));
      found++;
      query++;
    } else
    {
      subject++;
    }
  }
  return found;
}

static void gt_randomcodes_accumulatecounts_flush(void *data)
{
  GtRandomcodesinfo *fci = (GtRandomcodesinfo *) data;

  if (fci->buf.nextfree > 0)
  {
    unsigned long foundindex;

    gt_assert(fci->allrandomcodes != NULL);
    fci->codebuffer_total += fci->buf.nextfree;
    gt_radixsort_inplace_sort(fci->radixsort_code,fci->buf.nextfree);
    foundindex = gt_randomcodes_find_accu(fci,fci->buf.spaceGtUlong[0]);
    gt_assert(foundindex != ULONG_MAX);
    fci->total_count += gt_randomcodes_accumulatecounts_merge(fci,
        fci->buf.spaceGtUlong, fci->allrandomcodes + foundindex);
    gt_assert(fci->total_count == fci->codebuffer_total);
    fci->flushcount++;
    fci->buf.nextfree = 0;
  }
}

static unsigned long gt_randomcodes_insertsuffixes_merge(
                                        GtRandomcodesinfo *fci,
                                        const GtUlongPair *querystream_fst,
                                        const unsigned long *subjectstream_fst)
{
  unsigned long found = 0, idx;
  const GtUlongPair *query = querystream_fst,
                    *querystream_lst = fci->buf.spaceGtUlongPair +
                                       fci->buf.nextfree - 1;
  const unsigned long *subject = subjectstream_fst,
                      *subjectstream_lst = fci->allrandomcodes +
                                           fci->currentmaxindex;

  while (query <= querystream_lst && subject <= subjectstream_lst)
  {
    if (query->a <= *subject)
    {
      idx = gt_randomcodes_insertionindex(&fci->tab,
          (unsigned long)(subject - fci->allrandomcodes));
      gt_spmsuftab_set(fci->spmsuftab,idx,
          gt_spmsuftab_usebitsforpositions(fci->spmsuftab)
          ? gt_seqnumrelpos_decode_pos(fci->buf.snrp,query->b)
          : query->b);
      found++;
      query++;
    } else
    {
      subject++;
    }
  }
  return found;
}

static void gt_randomcodes_insertsuffixes_flush(void *data)
{
  GtRandomcodesinfo *fci = (GtRandomcodesinfo *) data;

  if (fci->buf.nextfree > 0)
  {
    const unsigned long *ptr;

    gt_assert(fci->allrandomcodes != NULL);
    fci->codebuffer_total += fci->buf.nextfree;
    gt_radixsort_inplace_sort(fci->radixsort_codepos,fci->buf.nextfree);
    ptr = gt_randomcodes_find_insert(fci,fci->buf.spaceGtUlongPair[0].a);
    gt_assert(ptr != NULL);
    fci->total_inserted += gt_randomcodes_insertsuffixes_merge(fci,
        fci->buf.spaceGtUlongPair, ptr);
    gt_assert(fci->total_inserted == fci->codebuffer_total);
    fci->flushcount++;
    fci->buf.nextfree = 0;
  }
}

static void gt_randomcodes_checksuftab_bucket(const GtEncseq *encseq,
                                             GtReadmode readmode,
                                             GtEncseqReader *esr1,
                                             GtEncseqReader *esr2,
                                             unsigned long previoussuffix,
                                             bool previousdefined,
                                             const unsigned long
                                               *seqnum_relpos_bucket,
                                             const GtSeqnumrelpos *snrp,
                                             GT_UNUSED const uint16_t
                                               *lcptab_bucket,
                                             unsigned long numberofsuffixes)
{
  unsigned long idx, current, maxlcp,
                totallength = gt_encseq_total_length(encseq);
  const unsigned long depth = 0;
  GT_UNUSED int cmp;
  const bool specialsareequal = false, specialsareequalatdepth0 = false;

  gt_assert(!previousdefined || previoussuffix < totallength);
  for (idx = 0; idx < numberofsuffixes; idx++)
  {
    current = gt_seqnumrelpos_decode_pos(snrp,seqnum_relpos_bucket[idx]);
    if (previousdefined && idx < totallength)
    {
      gt_assert(current < totallength);
      cmp = gt_encseq_check_comparetwosuffixes(encseq,
                                               readmode,
                                               &maxlcp,
                                               specialsareequal,
                                               specialsareequalatdepth0,
                                               depth,
                                               previoussuffix,
                                               current,
                                               esr1,
                                               esr2);
      gt_assert(cmp <= 0);
      gt_assert(idx == 0 || maxlcp == (unsigned long) lcptab_bucket[idx]);
    }
    previoussuffix = current;
    previousdefined = true;
  }
}

/* this can be maybe improved by using optimized code for
 * determining the position of the most significant bit */
static unsigned long gt_randomcodes_codelcp(unsigned long a, unsigned long b)
{
  unsigned long lcpvalue = 0;
  unsigned long mask;
  const unsigned long xorvalue = a ^ b;
  for (mask = 3UL << GT_MULT2(GT_UNITSIN2BITENC - 1);
      mask > 0; mask >>= 2, lcpvalue++)
    if (xorvalue & mask)
      return lcpvalue;
  return lcpvalue;
}

static int gt_randomcodes_sortremaining(GtShortreadsortworkinfo *srsw,
                                       const GtEncseq *encseq,
                                       GtReadmode readmode,
                                       const GtSpmsuftab *spmsuftab,
                                       const GtSeqnumrelpos *snrp,
                                       const GtRandomcodestab *rct,
                                       const unsigned long *allrandomcodes,
                                       unsigned long minindex,
                                       unsigned long maxindex,
                                       unsigned long sumofwidth,
                                       unsigned int correction_kmersize,
                                       unsigned int bucketkey_kmersize,
                                       GtRandomcodesintervalprocess itvprocess,
                                       GtRandomcodesintervalprocess_end
                                              itvprocess_end,
                                       void *itvprocessdata,
                                       bool usemaxdepth,
                                       bool withsuftabcheck,
                                       GtError *err)
{
  unsigned long current,
                next = GT_UNDEF_ULONG,
                idx,
                width,
                sumwidth = 0,
                previoussuffix = 0;
  GtShortreadsortresult srsresult;
  bool previousdefined = false, haserr = false;

  gt_assert(allrandomcodes != NULL);
  current = gt_randomcodes_get_leftborder(rct,minindex);
  for (idx = minindex; idx <= maxindex; idx++)
  {
    if (idx < maxindex)
    {
      next = gt_randomcodes_get_leftborder(rct,idx+1);
      gt_assert(current <= next);
      width = next - current;
    } else
    {
      gt_assert(sumofwidth >= current);
      width = sumofwidth - current;
    }
    sumwidth += width;
    gt_assert(sumwidth <= spmsuftab->numofentries);
    if (width >= 2UL)
    {
      unsigned long lcpvalue = 0;
      if (idx > minindex)
      {
        lcpvalue = gt_randomcodes_codelcp(allrandomcodes[idx - 1],
            allrandomcodes[idx]);
        gt_assert(lcpvalue >=
            (unsigned long)(GT_UNITSIN2BITENC - bucketkey_kmersize));
        lcpvalue -= (GT_UNITSIN2BITENC - (unsigned long) bucketkey_kmersize);
      }
      gt_assert(lcpvalue < (unsigned long)GT_UNITSIN2BITENC);
      gt_assert(lcpvalue < (unsigned long)(correction_kmersize - 1U));
      gt_shortreadsort_firstcodes_sort(&srsresult,
                                       srsw,
                                       snrp,
                                       encseq,
                                       spmsuftab,
                                       current,
                                       width,
                                       lcpvalue,
                                       usemaxdepth ?
                                       (unsigned long)correction_kmersize : 0);
      if (withsuftabcheck)
      {
        gt_randomcodes_checksuftab_bucket(encseq,
                                         readmode,
                                         NULL,
                                         NULL,
                                         previoussuffix,
                                         previousdefined,
                                         srsresult.suftab_bucket,
                                         snrp,
                                         srsresult.lcptab_bucket,
                                         width);
        previousdefined = true;
        previoussuffix
          = gt_seqnumrelpos_decode_pos(snrp,srsresult.suftab_bucket[width-1]);
      }
      if (itvprocess != NULL)
      {
        if (itvprocess(itvprocessdata,
                       srsresult.suftab_bucket,
                       snrp,srsresult.lcptab_bucket,width,
                       correction_kmersize,err) != 0)
        {
          haserr = true;
          break;
        }
      }
    }
    else if (width == 1UL)
    {
      if (itvprocess != NULL)
      {
        unsigned long suftab_value = gt_spmsuftab_get(spmsuftab, current);
        const uint16_t lcptab_value = 0;
        if (gt_spmsuftab_usebitsforpositions(spmsuftab))
        {
          unsigned long seqnum, relpos;
          seqnum = gt_encseq_seqnum(encseq, suftab_value);
          relpos = suftab_value - gt_encseq_seqstartpos(encseq, seqnum);
          suftab_value = gt_seqnumrelpos_encode(snrp, seqnum, relpos);
        }
        if (itvprocess(itvprocessdata, &suftab_value, snrp, &lcptab_value, 1UL,
                       correction_kmersize, err) != 0)
        {
          haserr = true;
          break;
        }
      }
    }
    gt_assert((minindex == maxindex) || next != GT_UNDEF_ULONG);
    current = next;
  }
  if (itvprocess_end != NULL)
  {
    itvprocess_end(itvprocessdata);
  }
  return haserr ? -1 : 0;
}

#ifdef GT_THREADS_ENABLED

static unsigned long gt_randomcodes_findfirstlarger(const GtRandomcodestab *rct,
                                                   unsigned long start,
                                                   unsigned long end,
                                                   unsigned long offset)
{
  unsigned long left = start, right = end, found = end, mid, midval;

  while (left+1 < right)
  {
    mid = GT_DIV2(left+right);
    midval = gt_randomcodes_get_leftborder(rct,mid);
    if (offset == midval)
    {
      return mid;
    }
    if (offset < midval)
    {
      found = mid;
      right = mid - 1;
    } else
    {
      left = mid + 1;
    }
  }
  return found;
}

static unsigned long *gt_randomcodes_evenly_divide_part(
    const GtRandomcodestab *rct, unsigned long partminindex,
    unsigned long partmaxindex, unsigned long numofsuffixes,
    unsigned int numofparts)
{
  unsigned long *endindexes, widthofpart, offset;
  unsigned int part, remainder;

  gt_assert(partminindex < partmaxindex && numofparts >= 2U);
  widthofpart = numofsuffixes/numofparts;
  endindexes = gt_malloc(sizeof (*endindexes) * numofparts);
  offset = gt_randomcodes_get_leftborder(rct,partminindex);
  remainder = (unsigned int) (numofsuffixes % (unsigned long) numofparts);
  for (part=0; part < numofparts; part++)
  {
    if (remainder > 0)
    {
      offset += widthofpart + 1;
      remainder--;
    } else
    {
      offset += widthofpart;
    }
    if (part == numofparts - 1)
    {
      endindexes[part] = partmaxindex;
    } else
    {
      unsigned long start = (part == 0) ? partminindex : endindexes[part-1] + 1;

      endindexes[part] = gt_randomcodes_findfirstlarger(rct,start,partmaxindex,
                                                       offset);
      gt_assert(endindexes[part] <= partmaxindex);
    }
  }
  return endindexes;
}

typedef struct
{
  GtShortreadsortworkinfo *srsw;
  const GtEncseq *encseq;
  GtReadmode readmode;
  const GtSpmsuftab *spmsuftab;
  const GtSeqnumrelpos *snrp;
  const GtRandomcodestab *rct;
  const unsigned long *allrandomcodes;
  unsigned long minindex,
                maxindex,
                sumofwidth;
  unsigned int correction_kmersize,
               bucketkey_kmersize;
  bool withsuftabcheck,
       usemaxdepth;
  GtRandomcodesintervalprocess itvprocess;
  GtRandomcodesintervalprocess_end itvprocess_end;
  void *itvprocessdata;
  GtError *err;
  GtThread *thread;
} GtRandomcodesSortRemainingThreadinfo;

static void *gt_randomcodes_thread_caller_sortremaining(void *data)
{
  GtRandomcodesSortRemainingThreadinfo *threadinfo =
    (GtRandomcodesSortRemainingThreadinfo *) data;

  if (gt_randomcodes_sortremaining(threadinfo->srsw,
                                  threadinfo->encseq,
                                  threadinfo->readmode,
                                  threadinfo->spmsuftab,
                                  threadinfo->snrp,
                                  threadinfo->rct,
                                  threadinfo->allrandomcodes,
                                  threadinfo->minindex,
                                  threadinfo->maxindex,
                                  threadinfo->sumofwidth,
                                  threadinfo->correction_kmersize,
                                  threadinfo->bucketkey_kmersize,
                                  threadinfo->itvprocess,
                                  threadinfo->itvprocess_end,
                                  threadinfo->itvprocessdata,
                                  threadinfo->usemaxdepth,
                                  threadinfo->withsuftabcheck,
                                  threadinfo->err) != 0)
  {
    gt_assert(false);
  }
  return NULL;
}

static int gt_randomcodes_thread_sortremaining(
                                       GtShortreadsortworkinfo **srswtab,
                                       const GtEncseq *encseq,
                                       GtReadmode readmode,
                                       const GtSpmsuftab *spmsuftab,
                                       const GtSeqnumrelpos *snrp,
                                       const GtRandomcodestab *rct,
                                       unsigned long *allrandomcodes,
                                       unsigned long partminindex,
                                       unsigned long partmaxindex,
                                       unsigned long widthofpart,
                                       unsigned long sumofwidth,
                                       unsigned int correction_kmersize,
                                       unsigned int bucketkey_kmersize,
                                       GtRandomcodesintervalprocess itvprocess,
                                       GtRandomcodesintervalprocess_end
                                         itvprocess_end,
                                       void *itvprocessdatatab,
                                       bool usemaxdepth,
                                       bool withsuftabcheck,
                                       unsigned int threads,
                                       GtLogger *logger,
                                       GtError *err)
{
  unsigned int t;
  unsigned long sum = 0, *endindexes;
  GtRandomcodesSortRemainingThreadinfo *threadinfo;
  bool haserr = false;

  gt_assert(threads >= 2U);
  endindexes = gt_randomcodes_evenly_divide_part(rct, partminindex,
      partmaxindex, widthofpart, threads);
  threadinfo = gt_malloc(sizeof (*threadinfo) * threads);
  for (t=0; tbinsearchcache.spaceGtIndexwithcodeRC != NULL)
  {
    GT_FCI_SUBTRACTWORKSPACE(fci->fcsl,"binsearchcache");
    GT_FREEARRAY(&fci->binsearchcache,GtIndexwithcodeRC);
  }
  if (fci->radixsort_codepos != NULL)
  {
    gt_radixsort_delete(fci->radixsort_codepos);
    GT_FCI_SUBTRACTWORKSPACE(fci->fcsl,"radixsort_codepos");
    fci->radixsort_codepos = NULL;
  }
}

static unsigned long gt_randomcodes_idx2mincode(const GtRandomcodesinfo *fci,
                                            unsigned long idx)
{
  gt_assert(idx <= fci->differentcodes);
  if (idx == 0)
  {
    return 0;
  }
  else
  {
    return fci->allrandomcodes[idx-1];
  }
}

static unsigned long gt_randomcodes_idx2maxcode(const GtRandomcodesinfo *fci,
                                            unsigned long idx)
{
  gt_assert(idx <= fci->differentcodes);
  if (idx == fci->differentcodes)
  {
    return fci->allrandomcodes[idx-1];
  }
  return fci->allrandomcodes[idx];
}

void gt_rungetencseqkmers_rc(const GtEncseq *encseq,unsigned int kmersize)
{
  const GtReadmode readmode = GT_READMODE_FORWARD;

  getencseqkmers_twobitencoding(encseq,
                                readmode,
                                kmersize,
                                kmersize,
                                false,
                                NULL,
                                NULL,
                                NULL,
                                NULL);
}

static void run_allcodes_distribution(const unsigned long *allrandomcodes,
                                      unsigned long differentcodes)
{
  unsigned long idx, diff, mindiff = 0, maxdiff = 0, distbits[64+1] = {0};

  for (idx = 1UL; idx < differentcodes; idx++)
  {
    gt_assert(allrandomcodes[idx-1] < allrandomcodes[idx]);
    diff = allrandomcodes[idx] - allrandomcodes[idx-1];
    if (idx == 1UL || diff < mindiff)
    {
      mindiff = diff;
    }
    if (diff > maxdiff)
    {
      maxdiff = diff;
    }
    distbits[gt_determinebitspervalue(diff)]++;
  }
  printf("allrandomcodes: mindiff=%lu,maxdiff=%lu(%u bits)\n",
         mindiff,maxdiff,gt_determinebitspervalue(maxdiff));
  for (idx = 0; idx <= 64UL; idx++)
  {
    if (distbits[idx] > 0)
    {
      printf("%lu bits: %lu\n",idx,distbits[idx]);
    }
  }
}

static int gt_randomcodes_init(GtRandomcodesinfo *fci,
                              const GtEncseq *encseq,
                              bool withsuftabcheck,
                              unsigned int correction_kmersize,
                              GtError *err)
{
  unsigned long maxseqlength, maxrelpos, numofsequences;
  unsigned int bitsforrelpos, bitsforseqnum;
  bool haserr = false;

  maxseqlength = gt_encseq_max_seq_length(encseq);
  if (maxseqlength > (unsigned long) correction_kmersize)
  {
    maxrelpos = maxseqlength - (unsigned long) correction_kmersize;
  } else
  {
    maxrelpos = 0;
  }
  bitsforrelpos = gt_determinebitspervalue(maxrelpos);
  fci->buf.snrp = gt_seqnumrelpos_new(bitsforrelpos,encseq);
  fci->buf.markprefix = NULL;
  fci->buf.marksuffix = NULL;
  fci->buf.accum_all = true;
  numofsequences = gt_encseq_num_of_sequences(encseq);
  gt_assert(numofsequences > 0);
  bitsforseqnum = gt_determinebitspervalue(numofsequences - 1);
  if (bitsforseqnum + bitsforrelpos > (unsigned int) GT_INTWORDSIZE)
  {
    gt_seqnumrelpos_delete(fci->buf.snrp);
    fci->buf.snrp = NULL;
    gt_error_set(err,"cannot process encoded sequences with %lu sequences "
                     "of length up to %lu (%u+%u bits)",
                     numofsequences,maxseqlength,bitsforseqnum,
                     bitsforrelpos);
    haserr = true;
  }
  fci->fcsl = gt_firstcodes_spacelog_new();
  fci->spmsuftab = NULL;
  fci->radixsort_code = NULL;
  fci->radixsort_codepos = NULL;
  fci->buf.spaceGtUlongPair = NULL;
  fci->buf.spaceGtUlong = NULL;
  fci->mappedallrandomcodes = NULL;
  fci->mappedleftborder = NULL;
  GT_FCI_ADDWORKSPACE(fci->fcsl,"encseq",(size_t) gt_encseq_sizeofrep(encseq));
  if (withsuftabcheck)
  {
    gt_firstcodes_spacelog_start_diff(fci->fcsl);
  }
  fci->allrandomcodes = NULL;
  gt_randomcodes_countocc_setnull(&fci->tab);
  fci->countcodes = 0;
  fci->total_count = 0;
  fci->total_inserted = 0;
  fci->bitsforposref = bitsforseqnum + bitsforrelpos;
  GT_INITARRAY(&fci->binsearchcache,GtIndexwithcodeRC);
  return haserr ? -1 : 0;
}

#define GT_RANDOMCODES_NOFSAMPLES_MIN 2UL

static inline unsigned long gt_randomcodes_calculate_nofsamples(
    GT_UNUSED const GtEncseq *encseq, unsigned long nofsequences,
    unsigned long totallength, unsigned int keysize,
    unsigned int sampling_factor)
{
  unsigned long nofkmers = totallength,
                nofnonkmers = (keysize + 1) * nofsequences - 1,
                nofsamples;
  gt_log_log("totallength = %lu", nofkmers);
  gt_log_log("nofsequences = %lu", nofsequences);
  if (nofnonkmers < nofkmers)
  {
    nofkmers -= nofnonkmers;
    gt_log_log("nofkmers = %lu", nofkmers);
  }
  else
  {
    gt_assert(gt_encseq_min_seq_length(encseq) <= (unsigned long)keysize);
  }
  nofsamples = nofkmers / sampling_factor;
  return MAX(GT_RANDOMCODES_NOFSAMPLES_MIN, nofsamples);
}

static void gt_randomcodes_generate_sampling_positions(unsigned long *buffer,
    unsigned long numofsamples, const GtEncseq *encseq,
    unsigned long totallength, unsigned int sampling_factor,
    unsigned int keysize, bool sort, GtTimer *timer)
{
  unsigned long i, randmax;
  bool sorted = true;
  randmax = (unsigned long)(GT_MULT2(sampling_factor) -
      GT_DIV16(sampling_factor));
  if (randmax >= totallength)
    randmax = totallength;
  buffer[0] = gt_rand_max(randmax);
  for (i = 1UL; i < numofsamples; i++)
  {
    unsigned long sn, sp, sl, rp;
    buffer[i] = buffer[i-1];
    while (true)
    {
      buffer[i] += (gt_rand_max(randmax) + 1UL);
      if (buffer[i] >= totallength)
      {
        buffer[i] = 0;
        sorted = false;
      }
      if (!gt_encseq_position_is_separator(encseq, buffer[i],
            GT_READMODE_FORWARD))
      {
        sn = gt_encseq_seqnum(encseq, buffer[i]);
        sp = gt_encseq_seqstartpos(encseq, sn);
        sl = gt_encseq_seqlength(encseq, sn);
        rp = buffer[i] - sp;
        if (rp < sl - keysize)
          break;
      }
    }
  }
  if (sort && !sorted)
  {
    if (timer != NULL)
      gt_timer_show_progress(timer, "to sort sampling positions", stdout);
    gt_radixsort_inplace_ulong(buffer, numofsamples);
  }
  if (sorted)
  {
    gt_log_log("range of sampling positions = [%lu, %lu]",
        buffer[0], buffer[numofsamples - 1]);
  }
}

static int gt_randomcodes_collectcodes(GtRandomcodesinfo *fci,
    bool usefirstcodes, unsigned int sampling_factor, const GtEncseq *encseq,
    GtReadmode readmode, unsigned int kmersize,
    unsigned int correction_kmersize, size_t maximumspace,
    GtLogger *logger, GtTimer *timer, GtError *err)
{
  size_t sizeforcodestable;
  unsigned long totallength = gt_encseq_total_length(encseq),
                nofsequences = gt_encseq_num_of_sequences(encseq);
  unsigned long maskright = GT_MASKRIGHT((unsigned long) kmersize);

  if (usefirstcodes)
  {
    fci->numofcodes = nofsequences + 1;
  }
  else
  {
    fci->numofcodes = gt_randomcodes_calculate_nofsamples(encseq,
        nofsequences, totallength, kmersize, sampling_factor) + 1;
  }
  sizeforcodestable = sizeof (*fci->allrandomcodes) * fci->numofcodes;
  if (maximumspace > 0 &&
      gt_firstcodes_spacelog_total(fci->fcsl) + sizeforcodestable >
      maximumspace)
  {
    gt_error_set(err,"already used %.2f MB of memory and require %.2f for the "
        "codes table => cannot compute index in at most %.2f MB",
        GT_MEGABYTES(gt_firstcodes_spacelog_total(fci->fcsl)),
        GT_MEGABYTES(sizeforcodestable),
        GT_MEGABYTES(maximumspace));
    return -1;
  }
  fci->allrandomcodes = gt_malloc(sizeforcodestable);
  GT_FCI_ADDSPLITSPACE(fci->fcsl,"allrandomcodes",sizeforcodestable);

  if (usefirstcodes)
  {
    if (timer != NULL)
      gt_timer_show_progress(timer, "to collect first codes", stdout);
    getencseqkmers_twobitencoding(encseq, readmode, kmersize,
        correction_kmersize, true, gt_storerandomcodes, fci, NULL, NULL);
  }
  else
  {
    unsigned long i;
    const GtTwobitencoding *twobitenc =
        gt_encseq_twobitencoding_export(encseq);
    unsigned long realtotallength = totallength;
    if (gt_encseq_is_mirrored(encseq))
    {
      realtotallength >>= 1;
    }
    if (timer != NULL)
      gt_timer_show_progress(timer, "to generate sampling positions", stdout);
    gt_randomcodes_generate_sampling_positions(fci->allrandomcodes,
        fci->numofcodes - 1, encseq, totallength, sampling_factor,
        kmersize, true, timer);
    if (timer != NULL)
      gt_timer_show_progress(timer, "to collect sample codes", stdout);
    for (i = 0; i < fci->numofcodes - 1; i++)
    {
      unsigned long pos = fci->allrandomcodes[i];
      bool revcompl = false;
      if (pos > realtotallength)
      {
        pos = GT_REVERSEPOS(totallength, pos);
        revcompl = true;
      }
      fci->allrandomcodes[i] = gt_kmercode_at_position(twobitenc,
          pos, kmersize);
      if (revcompl)
      {
        fci->allrandomcodes[i] = gt_kmercode_complement(
            gt_kmercode_reverse(fci->allrandomcodes[i], kmersize), maskright);
      }
    }
    fci->countcodes = fci->numofcodes - 1;
  }
  /* add an artificial last bucket to collect suffixes
   * larger than the last code */
  gt_storerandomcodes(fci, true, /* unused*/ 0, maskright);
  gt_logger_log(logger,"have stored %lu bucket keys",fci->countcodes);
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "to sort bucket keys",stdout);
  }
  gt_radixsort_inplace_ulong(fci->allrandomcodes,fci->numofcodes);
  gt_assert(fci->allrandomcodes != NULL);
  fci->differentcodes = gt_randomcodes_remdups(fci->allrandomcodes,
      kmersize, fci->numofcodes, logger);
  if (fci->differentcodes > 0 && fci->differentcodes < fci->numofcodes)
  {
    fci->allrandomcodes = gt_realloc(fci->allrandomcodes,
                                    sizeof (*fci->allrandomcodes) *
                                    fci->differentcodes);
    GT_FCI_SUBTRACTADDSPLITSPACE(fci->fcsl,"allrandomcodes",
                                 sizeof (*fci->allrandomcodes) *
                                 fci->differentcodes);
  }
  gt_randomcodes_countocc_new(fci->fcsl,&fci->tab,fci->differentcodes);
  return 0;
}

static int gt_randomcodes_allocspace(GtRandomcodesinfo *fci,
                                    unsigned int numofparts,
                                    unsigned long maximumspace,
                                    unsigned long phase2extra,
                                    GtError *err)
{
  if (maximumspace > 0)
  {
    if ((unsigned long) gt_firstcodes_spacelog_total(fci->fcsl) +
                        phase2extra >= maximumspace)
    {
      gt_error_set(err,"already used %.2f MB of memory and need %.2f MB later "
                       "=> cannot compute index in at most %.2f MB",
                       GT_MEGABYTES(gt_firstcodes_spacelog_total(fci->fcsl)),
                       GT_MEGABYTES(phase2extra),
                       GT_MEGABYTES(maximumspace));
      return -1;
    } else
    {
      size_t remainspace = (size_t) maximumspace -
                           (gt_firstcodes_spacelog_total(fci->fcsl) +
                            phase2extra);

      fci->buf.allocated
        = gt_radixsort_max_num_of_entries_ulong(remainspace);
      if (fci->buf.allocated < fci->differentcodes / 16UL)
      {
        fci->buf.allocated = fci->differentcodes / 16UL;
      }
    }
  } else
  {
    if (numofparts == 0)
    {
      fci->buf.allocated = gt_radixsort_max_num_of_entries_ulong(
                                 gt_firstcodes_spacelog_total(fci->fcsl)/7UL);
    } else
    {
      fci->buf.allocated = fci->differentcodes/5;
    }
  }
  if (fci->buf.allocated < 16UL)
  {
    fci->buf.allocated = 16UL;
  }
  return 0;
}

static void gt_randomcodes_accumulatecounts_run(GtRandomcodesinfo *fci,
                                               const GtEncseq *encseq,
                                               unsigned int kmersize,
                                               unsigned int correction_kmersize,
                                               GtLogger *logger,
                                               GtTimer *timer)
{
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "to accumulate counts",stdout);
  }
  gt_assert(fci->buf.allocated > 0);
  fci->radixsort_code = gt_radixsort_new_ulong(fci->buf.allocated);
  fci->buf.spaceGtUlong = gt_radixsort_space_ulong(fci->radixsort_code);
  GT_FCI_ADDWORKSPACE(fci->fcsl,"radixsort_code",
                      gt_radixsort_size(fci->radixsort_code));
  fci->buf.fciptr = fci; /* as we need to give fci to the flush function */
  fci->buf.flush_function = gt_randomcodes_accumulatecounts_flush;
  gt_logger_log(logger,"maximum space for accumulating counts %.2f MB",
                GT_MEGABYTES(gt_firstcodes_spacelog_total(fci->fcsl)));
  gt_firstcodes_accum_runkmerscan(encseq, kmersize, correction_kmersize,
      &fci->buf);
  gt_randomcodes_accumulatecounts_flush(fci);
  gt_logger_log(logger,"codebuffer_total=%lu (%.3f%% of all suffixes)",
                fci->codebuffer_total,
                100.0 * (double) fci->codebuffer_total/
                                 gt_encseq_total_length(encseq));
  gt_assert(fci->total_count == fci->codebuffer_total);
  if (fci->total_count > 0)
  {
    gt_assert(fci->flushcount > 0);
    gt_logger_log(logger,"total count=%lu (%.3f%% of all suffixes), "
                         "%u rounds (avg length %lu)",
                         fci->total_count,
                         100.0 * (double) fci->total_count/
                                          gt_encseq_total_length(encseq),
                         fci->flushcount,
                         fci->codebuffer_total/fci->flushcount);
  }
  gt_radixsort_delete(fci->radixsort_code);
  fci->radixsort_code = NULL;
  GT_FCI_SUBTRACTWORKSPACE(fci->fcsl,"radixsort_code");
  if (timer != NULL)
  {
    gt_timer_show_progress(timer,"to compute partial sums",stdout);
  }
}

static void gt_randomcodes_map_sections(GtRandomcodesinfo *fci,
                                       GtSfxmappedrangelist *sfxmrlist)
{
  if (fci->differentcodes > 0)
  {
    fci->mappedallrandomcodes = gt_Sfxmappedrange_new("allrandomcodes",
                                                    fci->differentcodes,
                                                    GtSfxunsignedlong,
                                                    NULL,
                                                    NULL);
    gt_Sfxmappedrangelist_add(sfxmrlist,fci->mappedallrandomcodes);
    fci->mappedleftborder = gt_Sfxmappedrange_new("leftborder",
                                                 fci->differentcodes+1,
                                                 GtSfxuint32_t,
                                                 NULL,
                                                 NULL);
    gt_Sfxmappedrangelist_add(sfxmrlist,fci->mappedleftborder);
  }
}

static int gt_randomcodes_auto_parts(GtRandomcodesinfo *fci,
                                    GtSfxmappedrangelist *sfxmrlist,
                                    unsigned int numofparts,
                                    unsigned long *maximumspace,
                                    unsigned long maxbucketsize,
                                    unsigned int upper_kmersize,
                                    unsigned long totallength,
                                    unsigned long maxseqlength,
                                    unsigned long suftabentries,
                                    unsigned long phase2extra,
                                    bool usemaxdepth,
                                    GtError *err)
{
  int retval;
  unsigned long leftbordersize_all;

  if (numofparts == 0 && *maximumspace == 0)
  {
    *maximumspace = (unsigned long)
                    (gt_firstcodes_spacelog_peak(fci->fcsl) +
                     phase2extra +
                     gt_shortreadsort_size(true, maxbucketsize,
                       usemaxdepth ?  (unsigned long)upper_kmersize :
                       maxseqlength) +
                     4 * 4096);
  } else
  {
    gt_assert(*maximumspace > 0);
  }
  if (fci->mappedleftborder != NULL)
  {
    leftbordersize_all = gt_Sfxmappedrange_size_mapped(
                             fci->mappedleftborder,0,
                             gt_randomcodes_leftborder_entries(&fci->tab)-1);
  } else
  {
    leftbordersize_all = 0;
  }
  retval = gt_suftabparts_rc_fit_memlimit(
      gt_firstcodes_spacelog_total(fci->fcsl)
      /*as this is subtracted*/
      + leftbordersize_all
      + phase2extra,
      *maximumspace,
      NULL,
      &fci->tab,
      sfxmrlist,
      totallength,
      fci->bitsforposref,
      0, /* special characters not used */
      suftabentries,
      false, /* suftabuint not used */
      err);
  if (retval < 0)
  {
    return -1;
  } else
  {
    gt_assert(retval > 0);
    return retval;
  }
}

static void gt_randomcodes_allocsize_for_insertion(GtRandomcodesinfo *fci,
                                                  unsigned long maximumspace,
                                                  const GtSuftabparts_rc
                                                    *suftabparts_rc,
                                                  unsigned long phase2extra)
{
  if (maximumspace > 0)
  {
    const unsigned long maxrounds = 400UL;
    size_t used = gt_firstcodes_spacelog_workspace(fci->fcsl) +
                  phase2extra +
                  gt_suftabparts_rc_largestsizemappedpartwise(suftabparts_rc);

    if ((unsigned long) used < maximumspace)
    {
      fci->buf.allocated = gt_radixsort_max_num_of_entries_ulongpair(
                                                (size_t) maximumspace - used);
    } else
    {
      fci->buf.allocated /= 4UL;
    }
    if ((unsigned long) (fci->codebuffer_total+fci->numofcodes)/
                        fci->buf.allocated > maxrounds)
    {
      fci->buf.allocated
        = (fci->codebuffer_total+fci->numofcodes)/maxrounds;
    }
  } else
  {
    fci->buf.allocated /= 2UL;
  }
}

static int gt_randomcodes_process_part(GtRandomcodesinfo *fci,
                                      const GtEncseq *encseq,
                                      GtReadmode readmode,
                                      unsigned int kmersize,
                                      unsigned int correction_kmersize,
                                      const GtSuftabparts_rc *suftabparts_rc,
                                      unsigned int part,
                                      unsigned long maximumspace,
#ifndef GT_THREADS_ENABLED
                                      GT_UNUSED
#endif
                                      unsigned int threads,
                                      unsigned long suftabentries,
                                      bool withsuftabcheck,
                                      GtShortreadsortworkinfo **srswtab,
                                      GtRandomcodesintervalprocess itvprocess,
                                      GtRandomcodesintervalprocess_end
                                        itvprocess_end,
                                      void *itvprocessdatatab,
                                      bool usemaxdepth,
                                      GtLogger *logger,
                                      GtTimer *timer,
                                      GtError *err)
{
  unsigned long spaceforbucketprocessing = 0;
  void *mapptr;
  bool haserr = false;

  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "to insert suffixes into buckets",stdout);
  }
  fci->widthofpart = gt_suftabparts_rc_widthofpart(part,suftabparts_rc);
  gt_logger_log(logger,"compute part %u (%.2f%% of all kmers)",part,
               (double) 100.0 * fci->widthofpart/suftabentries);
  fci->currentminindex = gt_suftabparts_rc_minindex(part,suftabparts_rc);
  fci->currentmaxindex = gt_suftabparts_rc_maxindex(part,suftabparts_rc);
  if (fci->mappedallrandomcodes != NULL)
  {
    fci->allrandomcodes
      = (unsigned long *)
        gt_Sfxmappedrange_map(fci->mappedallrandomcodes,
                              fci->currentminindex,
                              fci->currentmaxindex);
    GT_FCI_ADDSPLITSPACE(fci->fcsl,"allrandomcodes",
                         (size_t) gt_Sfxmappedrange_size_mapped(
                                        fci->mappedallrandomcodes,
                                        fci->currentminindex,
                                        fci->currentmaxindex));
  }
  gt_assert(fci->allrandomcodes != NULL);
  gt_assert(fci->mappedleftborder != NULL);
  mapptr = gt_Sfxmappedrange_map(fci->mappedleftborder,
                                 fci->currentminindex,
                                 fci->currentmaxindex);
  gt_randomcodes_leftborder_remap(&fci->tab,(uint32_t *) mapptr);
  GT_FCI_ADDSPLITSPACE(fci->fcsl,"leftborder",
                       (size_t) gt_Sfxmappedrange_size_mapped(
                                               fci->mappedleftborder,
                                               fci->currentminindex,
                                               fci->currentmaxindex));
  gt_logger_log(logger,"maximum space for part %u: %.2f MB",
                part,GT_MEGABYTES(gt_firstcodes_spacelog_total(fci->fcsl)));
  fci->buf.currentmincode = gt_randomcodes_idx2mincode(fci,
      fci->currentminindex);
  fci->buf.currentmaxcode = gt_randomcodes_idx2maxcode(fci,
      fci->currentmaxindex);
  gt_spmsuftab_partoffset(fci->spmsuftab,
                          gt_suftabparts_rc_offset(part,suftabparts_rc));
  gt_randomcodes_insert_runkmerscan(encseq,
                                   kmersize,
                                   correction_kmersize,
                                   &fci->buf);
  gt_randomcodes_insertsuffixes_flush(fci);
  if (part == gt_suftabparts_rc_numofparts(suftabparts_rc) - 1)
  {
    gt_randomcodes_delete_before_end(fci);
  }
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "to sort buckets of suffixes",stdout);
  }
  if (maximumspace > 0)
  {
    if ((unsigned long) gt_firstcodes_spacelog_total(fci->fcsl)
        < maximumspace)
    {
      spaceforbucketprocessing = maximumspace -
                                 (unsigned long)
                                 gt_firstcodes_spacelog_total(fci->fcsl);
      gt_log_log("space left for sortremaining: %.2f",
                 GT_MEGABYTES(spaceforbucketprocessing));
    } else
    {
      spaceforbucketprocessing = 0;
    }
  }
#ifdef GT_THREADS_ENABLED
  if (threads > 1U)
  {
    if (gt_randomcodes_thread_sortremaining(
          srswtab,
          encseq,
          readmode,
          fci->spmsuftab,
          fci->buf.snrp,
          &fci->tab,
          fci->allrandomcodes,
          fci->currentminindex,
          fci->currentmaxindex,
          gt_suftabparts_rc_widthofpart(part,suftabparts_rc),
          gt_suftabparts_rc_sumofwidth(part,suftabparts_rc),
          correction_kmersize,
          kmersize,
          itvprocess,
          itvprocess_end,
          itvprocessdatatab,
          usemaxdepth,
          withsuftabcheck,
          threads,
          logger,
          NULL) != 0)
    {
      haserr = true;
    }
  } else
#endif
  {
    if (gt_randomcodes_sortremaining(srswtab[0],
          encseq,
          readmode,
          fci->spmsuftab,
          fci->buf.snrp,
          &fci->tab,
          fci->allrandomcodes,
          fci->currentminindex,
          fci->currentmaxindex,
          gt_suftabparts_rc_sumofwidth(part,suftabparts_rc),
          correction_kmersize,
          kmersize,
          itvprocess,
          itvprocess_end,
          itvprocessdatatab == NULL
          ? NULL
          : ((void **) itvprocessdatatab)[0],
          usemaxdepth,
          withsuftabcheck,
          err) != 0)
    {
      haserr = true;
    }
  }
  if (fci->mappedallrandomcodes != NULL)
  {
    gt_Sfxmappedrange_unmap(fci->mappedallrandomcodes);
    GT_FCI_SUBTRACTSPLITSPACE(fci->fcsl,"allrandomcodes");
  }
  if (fci->mappedleftborder != NULL)
  {
    gt_Sfxmappedrange_unmap(fci->mappedleftborder);
    GT_FCI_SUBTRACTSPLITSPACE(fci->fcsl,"leftborder");
  }
  return haserr ? -1 : 0;
}

int storerandomcodes_getencseqkmers_twobitencoding(const GtEncseq *encseq,
    unsigned int kmersize,
    unsigned int numofparts,
    unsigned long maximumspace,
    unsigned int correction_kmersize,
    bool usefirstcodes,
    unsigned int sampling_factor,
    bool usemaxdepth,
    bool withsuftabcheck,
    bool onlyaccumulation,
    bool onlyallrandomcodes,
    GT_UNUSED
    unsigned int addbscache_depth,
    unsigned long phase2extra,
    GT_UNUSED bool radixsmall,      /* set to true */
    GT_UNUSED unsigned int radixparts, /* set to 2U */
    GtRandomcodesintervalprocess
    itvprocess,
    GtRandomcodesintervalprocess_end
    itvprocess_end,
    void *itvprocessdatatab,
    GtLogger *logger,
    GtTimer *timer,
    GtError *err)
{
  GtRandomcodesinfo fci;
  size_t suftab_size = 0;
  unsigned int part, threadcount;
  unsigned long maxbucketsize, suftabentries = 0, largest_width,
                totallength = gt_encseq_total_length(encseq),
                maxseqlength = gt_encseq_max_seq_length(encseq);
  GtSfxmappedrangelist *sfxmrlist = NULL;
  GtSuftabparts_rc *suftabparts_rc = NULL;
  GtShortreadsortworkinfo **srswtab = NULL;
  const GtReadmode readmode = GT_READMODE_FORWARD;
  bool haserr = false;
#ifdef GT_THREADS_ENABLED
  const unsigned int threads = gt_jobs;
#else
  const unsigned int threads = 1U;
#endif

  if (maxseqlength < (unsigned long) correction_kmersize)
  {
    return 0;
  }
  if (gt_randomcodes_init(&fci,
                         encseq,
                         withsuftabcheck,
                         correction_kmersize,
                         err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    sfxmrlist = gt_Sfxmappedrangelist_new();
    if (gt_randomcodes_collectcodes(&fci,
                               usefirstcodes,
                               sampling_factor,
                               encseq,
                               readmode,
                               kmersize,
                               correction_kmersize,
                               (size_t)maximumspace,
                               logger,
                               timer,
                               err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    if (fci.differentcodes > 0 && onlyallrandomcodes)
    {
      run_allcodes_distribution(fci.allrandomcodes,fci.differentcodes);
      gt_free(fci.allrandomcodes);
      fci.allrandomcodes = NULL;
      gt_randomcodes_countocc_delete(fci.fcsl,&fci.tab);
      gt_firstcodes_spacelog_delete(fci.fcsl);
      gt_seqnumrelpos_delete(fci.buf.snrp);
      gt_Sfxmappedrangelist_delete(sfxmrlist);
      return 0;
    }
    fci.flushcount = 0;
    fci.codebuffer_total = 0;
    gt_randomcodes_fillbinsearchcache(&fci,addbscache_depth);
    if (gt_randomcodes_allocspace(&fci,
                                 numofparts,
                                 maximumspace,
                                 phase2extra,
                                 err) != 0)
    {
      haserr = true;
    }
  }
  fci.buf.nextfree = 0;
  if (!haserr)
  {
    gt_randomcodes_accumulatecounts_run(&fci,
                                       encseq,
                                       kmersize,
                                       correction_kmersize,
                                       logger,
                                       timer);
    maxbucketsize = gt_randomcodes_partialsums(fci.fcsl,&fci.tab,
        fci.total_count);
    gt_logger_log(logger,"maximum space after computing partial sums: %.2f MB",
                  GT_MEGABYTES(gt_firstcodes_spacelog_total(fci.fcsl)));
    gt_logger_log(logger,"maxbucketsize=%lu",maxbucketsize);
    gt_randomcodes_map_sections(&fci,sfxmrlist);
    if (numofparts == 0 || maximumspace > 0)
    {
      int retval = gt_randomcodes_auto_parts(&fci,
                                            sfxmrlist,
                                            numofparts,
                                            &maximumspace,
                                            maxbucketsize,
                                            correction_kmersize,
                                            totallength,
                                            maxseqlength,
                                            fci.total_count,
                                            phase2extra,
                                            usemaxdepth,
                                            err);
      if (retval < 0)
      {
        haserr = true;
      } else
      {
        numofparts = (unsigned int) retval;
      }
    }
  }
  if (!haserr)
  {
    gt_assert(numofparts > 0);
    suftabparts_rc = gt_suftabparts_rc_new(numofparts,
                                     NULL,
                                     &fci.tab,
                                     sfxmrlist,
                                     fci.total_count,
                                     0,
                                     logger);
    gt_assert(suftabparts_rc != NULL);
    gt_suftabparts_rc_showallrecords(suftabparts_rc,true);
    gt_Sfxmappedrangelist_delete(sfxmrlist);
    sfxmrlist = NULL;
    gt_randomcodes_samples_delete(fci.fcsl,&fci.tab);
    gt_assert(fci.buf.nextfree == 0);
    gt_assert(fci.mappedleftborder != NULL);
    gt_Sfxmappedrange_usetmp(fci.mappedleftborder,
        gt_randomcodes_outfilenameleftborder(&fci.tab),
        (void **)
        gt_randomcodes_leftborder_address(&fci.tab),
        gt_randomcodes_leftborder_entries(&fci.tab),
        true);
    if (gt_suftabparts_rc_numofparts(suftabparts_rc) > 1U)
    {
      gt_assert(fci.allrandomcodes != NULL);
      gt_assert(fci.mappedallrandomcodes != NULL);
      gt_Sfxmappedrange_storetmp_ulong(fci.mappedallrandomcodes,
          &fci.allrandomcodes, false);
      GT_FCI_SUBTRACTSPLITSPACE(fci.fcsl,"allrandomcodes");
      gt_assert(fci.allrandomcodes == NULL);
    } else
    {
      gt_Sfxmappedrange_delete(fci.mappedallrandomcodes);
      fci.mappedallrandomcodes = NULL;
    }
    largest_width = gt_suftabparts_rc_largest_width(suftabparts_rc);
    fci.spmsuftab = gt_spmsuftab_new(largest_width,
                                     totallength,
                                     fci.bitsforposref,
                                     logger);
    suftab_size = gt_spmsuftab_requiredspace(largest_width,totallength,
                                             fci.bitsforposref);
    GT_FCI_ADDWORKSPACE(fci.fcsl,"suftab",suftab_size);
    fci.buf.flush_function = gt_randomcodes_insertsuffixes_flush;
    srswtab = gt_malloc(sizeof (*srswtab) * threads);
    for (threadcount = 0; threadcount < threads; threadcount++)
    {
      srswtab[threadcount]
        = gt_shortreadsort_new(maxbucketsize,maxseqlength - kmersize,
                               readmode,true,false);
    }
    GT_FCI_ADDWORKSPACE(fci.fcsl,"shortreadsort",
                        threads * gt_shortreadsort_size(true,maxbucketsize,
                                                        maxseqlength-kmersize));
    gt_randomcodes_allocsize_for_insertion(&fci,
                                          maximumspace,
                                          suftabparts_rc,
                                          phase2extra);
    if (!onlyaccumulation)
    {
      fci.radixsort_codepos = gt_radixsort_new_ulongpair(fci.buf.allocated);
      GT_FCI_ADDWORKSPACE(fci.fcsl,"radixsort_codepos",
                          gt_radixsort_size(fci.radixsort_codepos));
      fci.buf.spaceGtUlongPair
        = gt_radixsort_space_ulongpair(fci.radixsort_codepos);
    }
    fci.codebuffer_total = 0;
    fci.flushcount = 0;
    for (part = 0; !haserr && !onlyaccumulation &&
                   part < gt_suftabparts_rc_numofparts(suftabparts_rc); part++)
    {
      if (gt_randomcodes_process_part(&fci,
                                     encseq,
                                     readmode,
                                     kmersize,
                                     correction_kmersize,
                                     suftabparts_rc,
                                     part,
                                     maximumspace,
                                     threads,
                                     fci.total_count,
                                     withsuftabcheck,
                                     srswtab,
                                     itvprocess,
                                     itvprocess_end,
                                     itvprocessdatatab,
                                     usemaxdepth,
                                     logger,
                                     timer,
                                     err) != 0)
      {
        haserr = true;
      }
    }
  }
  gt_log_log("suftabentries=%lu",suftabentries);
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "cleaning up",stdout);
  }
  if (!haserr)
  {
    GT_FCI_SUBTRACTWORKSPACE(fci.fcsl,"shortreadsort");
  }
  if (!haserr && !onlyaccumulation && srswtab != NULL)
  {
    unsigned long sumofstoredvalues = 0;

    for (threadcount=0; threadcount
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RANDOMCODES_H
#define RANDOMCODES_H

#include 
#include "core/log_api.h"
#include "core/error_api.h"
#include "core/encseq_api.h"
#include "seqnumrelpos.h"

typedef int (*GtRandomcodesintervalprocess)(void *,
                                           const unsigned long *,
                                           const GtSeqnumrelpos *,
                                           const uint16_t *,
                                           unsigned long,
                                           unsigned int,
                                           GtError *);

typedef void (*GtRandomcodesintervalprocess_end)(void *);

void gt_rungetencseqkmers_rc(const GtEncseq *encseq,unsigned int kmersize);

int storerandomcodes_getencseqkmers_twobitencoding(
                    const GtEncseq *encseq,
                    unsigned int kmersize,
                    unsigned int numofparts,
                    unsigned long maximumspace,
                    unsigned int correction_kmersize,
                    bool usefirstcodes,
                    unsigned int sampling_factor,
                    bool usemaxdepth,
                    bool withsuftabcheck, /* set to false, only for tests */
                    bool onlyaccumulation, /* set to false, only for tests */
                    bool onlyallrandomcodes, /* set to false, only for tests */
                    GT_UNUSED unsigned int addbscache_depth, /* set to 5U */
                    unsigned long phase2extra, /* extra space needed in proc.
                                                  intervals */
                    bool radixsmall,      /* set to true */
                    unsigned int radixparts, /* set to 2U */
                    GtRandomcodesintervalprocess itvprocess,
                    GtRandomcodesintervalprocess_end itvprocess_end,
                    void *itvprocessdatatab,
                    GtLogger *logger,
                    GtTimer *timer,
                    GtError *err);

#endif
genometools-1.5.1/src/match/rdj-cntlist.c000066400000000000000000000201651211610345200203340ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/fa.h"
#include "core/fileutils.h"
#include "core/log.h"
#include "core/xansi_api.h"
#include "match/rdj-cntlist.h"

#define GT_CNTLIST_BIT_HEADER   (int)'\0'
#define GT_CNTLIST_BIN_HEADER   (int)'\1'
#define GT_CNTLIST_ASCII_HEADER (int)'['

static inline void gt_cntlist_show_ascii(GtBitsequence *cntlist,
    unsigned long nofreads, FILE *file)
{
  unsigned long i;
  gt_assert(file != NULL);
  fprintf(file, "[n: %lu]\n", nofreads);
  for (i = 0; i < nofreads; i++)
    if (GT_ISIBITSET(cntlist, i))
      fprintf(file, "%lu\n", i);
}

void gt_cntlist_write_bin_header(unsigned long nofreads, FILE *file)
{
  gt_assert(file != NULL);
  gt_xfputc(GT_CNTLIST_BIN_HEADER, file);
  gt_xfputc((char)sizeof(unsigned long), file);
  gt_xfwrite(&(nofreads), sizeof (unsigned long), (size_t)1, file);
}

static inline void gt_cntlist_show_bit(GtBitsequence *cntlist,
    unsigned long nofreads, FILE *file)
{
  gt_assert(file != NULL);
  gt_xfputc(GT_CNTLIST_BIT_HEADER, file);
  gt_xfputc((char)sizeof(unsigned long), file);
  gt_xfwrite(&(nofreads), sizeof (unsigned long), (size_t)1, file);
  gt_xfwrite(cntlist, sizeof (GtBitsequence), GT_NUMOFINTSFORBITS(nofreads),
      file);
}

int gt_cntlist_show(GtBitsequence *cntlist, unsigned long nofreads,
    const char *path, bool binary, GtError *err)
{
  FILE *file;
  gt_assert(cntlist != NULL);
  if (path == NULL)
    file = stdout;
  else
  {
    file = gt_fa_fopen(path, binary ? "wb" : "w", err);
    if (file == NULL)
      return -1;
  }
  gt_assert(file != NULL);
  (binary ? gt_cntlist_show_bit : gt_cntlist_show_ascii)
    (cntlist, nofreads, file);
  if (path != NULL)
    gt_fa_fclose(file);
  return 0;
}

static int gt_cntlist_parse_bin_or_bit_header(FILE *infp,
    unsigned long *nofreads, GtError *err)
{
  int c;
  size_t n;

  gt_assert(infp != NULL && nofreads != NULL);
  gt_error_check(err);
  c = gt_xfgetc(infp);
  if (c == EOF)
  {
    gt_error_set(err, "contained reads list: unexpected end of file");
    return -1;
  }
  else if (c != (char)sizeof(unsigned long))
  {
    gt_error_set(err, "contained reads list: %dbit version "
        "of GenomeTools required to use this list", c * CHAR_BIT);
    return -1;
  }
  n = fread(nofreads, sizeof (unsigned long), (size_t)1, infp);
  if (n != (size_t)1 || *nofreads == 0)
  {
    gt_error_set(err, "contained reads list: unrecognized format");
    return -1;
  }
  return 0;
}

static int gt_cntlist_parse_bit(FILE *infp, bool alloc_cntlist,
    GtBitsequence **cntlist, unsigned long *nofreads, GtError *err)
{
  int had_err = gt_cntlist_parse_bin_or_bit_header(infp, nofreads, err);
  if (had_err == 0)
  {
    size_t n;
    gt_assert(cntlist != NULL);
    if (alloc_cntlist)
    {
      GT_INITBITTAB(*cntlist, *nofreads);
      n = fread(*cntlist, sizeof (GtBitsequence),
          GT_NUMOFINTSFORBITS(*nofreads), infp);
      if (n != GT_NUMOFINTSFORBITS(*nofreads))
      {
        gt_error_set(err, "contained reads file: unrecognized format");
        had_err = -1;
      }
    }
    else
    {
      /* combine using OR with existing data */
      size_t i;
      for (i = 0; i < GT_NUMOFINTSFORBITS(*nofreads); i++)
      {
        GtBitsequence value;
        n = fread(&value, sizeof (GtBitsequence), (size_t)1, infp);
        if (n != (size_t)1)
        {
          gt_error_set(err, "contained reads file: unrecognized format");
          had_err = -1;
          break;
        }
        *cntlist[i] |= value;
      }
    }
  }
  return had_err;
}

static int gt_cntlist_parse_bin(FILE *infp, bool alloc_cntlist,
    GtBitsequence **cntlist, unsigned long *nofreads, GtError *err)
{
  int had_err = gt_cntlist_parse_bin_or_bit_header(infp, nofreads, err);
  if (had_err == 0)
  {
    size_t n;
    unsigned long seqnum;
    gt_assert(cntlist != NULL);
    if (alloc_cntlist)
      GT_INITBITTAB(*cntlist, *nofreads);
    while (true)
    {
      n = fread(&seqnum, sizeof (unsigned long), (size_t)1, infp);
      if (n != (size_t)1)
      {
        if (!feof(infp))
        {
          gt_error_set(err, "contained reads file: unrecognized format");
          had_err = -1;
        }
        break;
      }
      GT_SETIBIT(*cntlist, seqnum);
    }
  }
  return had_err;
}

static int gt_cntlist_parse_ascii(FILE *infp, bool alloc_cntlist,
    GtBitsequence **cntlist, unsigned long *nofreads, GtError *err)
{
  int n;
  unsigned long seqnum;

  gt_assert(infp != NULL && nofreads != NULL && cntlist != NULL);
  /*@i1@*/ gt_error_check(err);
  n = fscanf(infp, "[n: %lu]\n", nofreads);
  if (n!=1 || *nofreads == 0)
  {
    gt_error_set(err, "contained reads file: unrecognized format");
    return -1;
  }
  if (alloc_cntlist)
    GT_INITBITTAB(*cntlist, *nofreads);
  while (true)
  {
    n = fscanf(infp, "%lu\n", &seqnum);
    if (n == EOF)
      break;
    else if (n != 1)
    {
      gt_error_set(err, "contained reads file: unrecognized format");
      return -1;
    }
    GT_SETIBIT(*cntlist, seqnum);
  }
  return 0;
}

int gt_cntlist_parse(const char *filename, bool alloc_cntlist,
    GtBitsequence **cntlist, unsigned long *nofreads, GtError *err)
{
  int c, retval = 0;
  FILE *infp;

  gt_log_log("parse contained reads list file: %s", filename);
  infp = gt_fa_fopen(filename, "rb", err);

  if (infp == NULL)
    return -1;

  c = gt_xfgetc(infp);
  switch (c)
  {
    case EOF:
      gt_error_set(err, "%s: unexpected end of file", filename);
      retval = 1;
      break;
    case GT_CNTLIST_BIN_HEADER:
      gt_log_log("contained reads list format: BIN");
      retval = gt_cntlist_parse_bin(infp, alloc_cntlist, cntlist, nofreads,
          err);
      break;
    case GT_CNTLIST_BIT_HEADER:
      gt_log_log("contained reads list format: BIT");
      retval = gt_cntlist_parse_bit(infp, alloc_cntlist, cntlist, nofreads,
          err);
      break;
    case GT_CNTLIST_ASCII_HEADER:
      gt_xungetc(c, infp);
      gt_log_log("contained reads list format: ASCII");
      retval = gt_cntlist_parse_ascii(infp, alloc_cntlist, cntlist, nofreads,
          err);
      break;
    default:
      gt_error_set(err, "%s: unrecognized format", filename);
      retval = 1;
      break;
  }
  gt_fa_fclose(infp);

  return retval;
}

unsigned long gt_cntlist_count(const GtBitsequence *cntlist,
    unsigned long nofreads)
{
  unsigned long i, counter = 0;

  for (i = 0; i < nofreads; i++)
    if ((bool)GT_ISIBITSET(cntlist, i))
      counter++;
  return counter;
}

unsigned long gt_cntlist_xload(const char *filename, GtBitsequence **cntlist,
    unsigned long expected_nofreads)
{
  int retval;
  unsigned long found_nofreads;
  GtError *err;

  if (!gt_file_exists(filename))
  {
    fprintf(stderr, "FATAL: error by loading contained reads list: "
        "file %s does not exist\n", filename);
    exit(EXIT_FAILURE);
  }

  err = gt_error_new();
  retval = gt_cntlist_parse(filename, true, cntlist, &found_nofreads, err);
  if (retval != 0)
  {
    fprintf(stderr, "FATAL: error by parsing contained reads list: %s\n",
        gt_error_get(err));
    exit(EXIT_FAILURE);
  }
  gt_error_delete(err);

  if (found_nofreads != expected_nofreads)
  {
    fprintf(stderr, "FATAL: error by parsing contained reads list: "
        "file specifies a wrong number of reads\nexpected %lu, found %lu\n",
        expected_nofreads, found_nofreads);
    exit(EXIT_FAILURE);
  }

  return gt_cntlist_count(*cntlist, found_nofreads);
}
genometools-1.5.1/src/match/rdj-cntlist.h000066400000000000000000000042351211610345200203410ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_CNTLIST_H
#define RDJ_CNTLIST_H

/*
 * Two formats for contained reads lists are defined here.
 * One is a text-based one, while the binary one is a copy
 * of the bitsequence preceded by a short header.
 */

#include "core/intbits.h"           /* GtBitsequence */
#include "core/error_api.h"         /* GtError */

/* writes cntlist to file */
int gt_cntlist_show(GtBitsequence *cntlist, unsigned long nofreads,
    const char *path, bool binary, GtError *err);

/* prepare a file for output of cntlist in bin format */
void gt_cntlist_write_bin_header(unsigned long nofreads, FILE *file);

/* parses a cntlist file, format is automatically recognized;
 * if alloc_cntlist is true, **cntlist is allocated, otherwise
 * **cntlist must be a valid bit sequence with the correct size */
int gt_cntlist_parse(const char *filename, bool alloc_cntlist,
    GtBitsequence **cntlist, unsigned long *nofreads, GtError *err);

/* variant of parse: parses, checks that the number of reads is the one
 * specified, returns number of cnt reads, exits on error */
unsigned long gt_cntlist_xload(const char *filename, GtBitsequence **cntlist,
    unsigned long expected_nofreads);

/* counts the number of bit set in bitsequence cntlist */
unsigned long gt_cntlist_count(const GtBitsequence *cntlist,
    unsigned long nofreads);

#endif
genometools-1.5.1/src/match/rdj-contfind-bottomup.c000066400000000000000000000157161211610345200223350ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/progressbar.h"
#include "match/esa-seqread.h"
#include "match/esa-bottomup.h"
#include "match/rdj-revcompl-def.h"
#include "match/rdj-contfind-bottomup.h"

typedef struct
{
  /* length of the shortest sequence in the array */
  unsigned long shortest;

  unsigned long spacing; /* for eqlen read length mode */

  const GtEncseq *encseq;
  GtBitsequence *sspbittab;

  GtBitsequence *contained;

  unsigned long cmin;
  unsigned long csize;

  /* progressbar */
  bool show_progressbar;
  unsigned long long progress;

  /* revcompl mode */
  unsigned long firstrevcompl;
  unsigned long nofsequences;

  unsigned long counter;
} ContfindBUstate;

typedef ContfindBUstate GtBUstate_rdjce;
typedef ContfindBUstate GtBUstate_rdjcv;
typedef struct {} GtBUinfo_rdjce;
typedef struct {} GtBUinfo_rdjcv;

static void initBUinfo_rdjcv(GT_UNUSED GtBUinfo_rdjcv *info,
    GT_UNUSED GtBUstate_rdjcv *state)
{
  /* nothing to do */
}

static void initBUinfo_rdjce(GT_UNUSED GtBUinfo_rdjce *info,
    GT_UNUSED GtBUstate_rdjce *state)
{
  /* nothing to do */
}

static inline void freeBUinfo_rdjcv(GT_UNUSED GtBUinfo_rdjcv *info,
    GT_UNUSED GtBUstate_rdjcv *state)
{
  /* nothing to do */
}

static inline void freeBUinfo_rdjce(GT_UNUSED GtBUinfo_rdjce *info,
    GT_UNUSED GtBUstate_rdjce *state)
{
  /* nothing to do */
}

static inline void processcontained(unsigned long seqnum,
    ContfindBUstate *state)
{
  if (state->firstrevcompl > 0)
    seqnum = GT_READJOINER_READNUM(seqnum, state->firstrevcompl,
        state->nofsequences);
  if (!GT_ISIBITSET(state->contained, seqnum))
  {
    GT_SETIBIT(state->contained, seqnum);
    state->counter++;
  }
  if (state->csize == 0 || seqnum < state->cmin)
    state->cmin = seqnum;
  state->csize++;
}

static inline int processleafedge_rdjcv(GT_UNUSED bool firstsucc,
    unsigned long fatherdepth,
    GT_UNUSED GtBUinfo_rdjcv *father, unsigned long leafnumber,
    GtBUstate_rdjcv *state, GT_UNUSED GtError *err)
{
  unsigned long seqnum;

  if (fatherdepth >= state->shortest)
  {
    if ((leafnumber == 0 ||
        GT_ISIBITSET(state->sspbittab, leafnumber-1)) &&
        GT_ISIBITSET(state->sspbittab, leafnumber + fatherdepth))
    {
      seqnum = gt_encseq_seqnum(state->encseq, leafnumber);
      processcontained(seqnum, state);
    }
  }
  if (state->show_progressbar) state->progress++;
  return 0;
}

static inline int processleafedge_rdjce(GT_UNUSED bool firstsucc,
    unsigned long fatherdepth,
    GT_UNUSED GtBUinfo_rdjce *father, unsigned long leafnumber,
    GtBUstate_rdjce *state, GT_UNUSED GtError *err)
{
  unsigned long seqnum;

  if (fatherdepth == state->shortest && (leafnumber % state->spacing) == 0)
  {
    seqnum = leafnumber / state->spacing;
    processcontained(seqnum, state);
  }
  if (state->show_progressbar) state->progress++;
  return 0;
}

static inline int processbranchingedge_rdjce(GT_UNUSED bool firstsucc,
    GT_UNUSED unsigned long fatherdepth,
    GT_UNUSED GtBUinfo_rdjce *father, unsigned long sondepth,
    GT_UNUSED unsigned long sonwidth,
    GT_UNUSED GtBUinfo_rdjce *son, GtBUstate_rdjce *state,
    GT_UNUSED GtError *err)
{
  if (sondepth == state->shortest /* == read length */)
  {
    /* keep one copy */
    if (state->csize > 0)
    {
      GT_UNSETIBIT(state->contained, state->cmin);
      state->counter--;
    }
  }
  state->csize = 0;
  return 0;
}

static inline int processbranchingedge_rdjcv(GT_UNUSED bool firstsucc,
    GT_UNUSED unsigned long fatherdepth,
    GT_UNUSED GtBUinfo_rdjcv *father, unsigned long sondepth,
    unsigned long sonwidth, GT_UNUSED GtBUinfo_rdjcv *son,
    GtBUstate_rdjcv *state, GT_UNUSED GtError *err)
{
  if (sondepth >= state->shortest)
  {
    /* keep one copy if several copies of a sequence are present
       and the sequence is not contained in any other */
    if (state->csize == sonwidth)
    {
      gt_assert(state->csize > 0);
      GT_UNSETIBIT(state->contained, state->cmin);
      state->counter--;
    }
  }
  state->csize = 0;
  return 0;
}

#include "match/esa-bottomup-rdjcv.inc"

#include "match/esa-bottomup-rdjce.inc"

/* prepare sspbittab and determine length of shortest sequence */
static void prepare_sspbittab_and_shortest(unsigned long totallength,
    ContfindBUstate *state)
{
  unsigned long length, lastseqstart, i, ssp;

  GT_INITBITTAB(state->sspbittab, totallength + 1);
  lastseqstart = 0;
  state->shortest = totallength;
  for (i = 1UL; i <= state->nofsequences - 1; i++)
  {
    ssp = gt_encseq_seqstartpos(state->encseq, i) - 1;
    GT_SETIBIT(state->sspbittab, ssp);
    length = ssp - lastseqstart;
    lastseqstart = ssp + 1;
    if (length < state->shortest)
      state->shortest = length;
  }
  GT_SETIBIT(state->sspbittab, totallength);
  length = totallength - lastseqstart;
  if (length < state->shortest)
    state->shortest = length;
}

unsigned long gt_contfind_bottomup(Sequentialsuffixarrayreader *ssar,
                     bool show_progressbar, GtBitsequence *contained,
                     unsigned long firstrevcompl,
                     unsigned long read_length /* 0 = variable */)
{
  ContfindBUstate state;
  unsigned long totallength;
  GT_UNUSED int retval;

  gt_assert(ssar != NULL);
  gt_assert(contained != NULL);

  state.contained = contained;
  state.encseq = gt_encseqSequentialsuffixarrayreader(ssar);
  totallength = gt_encseq_total_length(state.encseq);
  state.nofsequences = gt_encseq_num_of_sequences(state.encseq);

  if (read_length == 0)
  {
    prepare_sspbittab_and_shortest(totallength, &state);
  }
  else
  {
    state.shortest = read_length;
    state.spacing = read_length + 1;
  }

  state.show_progressbar = show_progressbar;
  state.csize            = 0;
  state.cmin             = 0;
  state.firstrevcompl    = firstrevcompl;
  state.counter          = 0;

  if (show_progressbar)
  {
    state.progress = 0;
    gt_progressbar_start(&(state.progress),
        (unsigned long long)totallength);
  }

  retval = (read_length == 0)
      ? gt_esa_bottomup_rdjcv(ssar, &state, NULL)
      : gt_esa_bottomup_rdjce(ssar, &state, NULL);
  gt_assert(retval == 0);

  if (show_progressbar)
    gt_progressbar_stop();
  if (read_length == 0)
    gt_free(state.sspbittab);
  return state.counter;
}
genometools-1.5.1/src/match/rdj-contfind-bottomup.h000066400000000000000000000036731211610345200223410ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_CONTFIND_BOTTOMUP_H
#define RDJ_CONTFIND_BOTTOMUP_H

#include "match/esa-seqread.h"
#include "core/intbits.h"

/*
* Bottom-up dfs-based esa algorithm to identify contained reads.
*
* A read r is contained in r' iff:
*   - r is a proper substring of r' or revcompl(r'):
*   - r == r' or r == revcompl(r') and r'.seqnum < r.seqnum
*
* Input:
* - GtBitsequence *contained:
*   - size must be 1 bit/read
*   - should be initialized with 0
* - firstrevcompl:
*   - no mirror, single-strand mode     -> 0
*   - virtual mirror                    -> nofreads
*   - real mirror                       -> nofseqs / 2
* - read_length:
*   - fixed length       -> read length  [modulo operations are used]
*   - variable length    -> 0            [a bit table is created]
*
* Output:
* - return value: number of contained reads
* - GtBitsequence *contained:
*   bits are set for each read respecting the definition
*/
unsigned long gt_contfind_bottomup(Sequentialsuffixarrayreader *ssar,
    bool show_progressbar, GtBitsequence *contained,
    unsigned long firstrevcompl, unsigned long read_length);

#endif
genometools-1.5.1/src/match/rdj-contfind-def.h000066400000000000000000000024001211610345200212110ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_CONTFIND_DEF_H
#define RDJ_CONTFIND_DEF_H

/* type of the return value of the ovlfind functions */

typedef enum
{
  GT_CONTFIND_OFF, /* no search for containments */
  GT_CONTFIND_NO,  /* there is no containment */
  GT_CONTFIND_EQ,  /* u and v are (approx) equal */
  GT_CONTFIND_U,   /* u is (approx) contained in v */
  GT_CONTFIND_V    /* v is (approx) contained in u */
}
GtContfind;

#endif
genometools-1.5.1/src/match/rdj-contfinder.c000066400000000000000000000733211211610345200210110ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Giorgio Gonnella 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#ifndef S_SPLINT_S
#include 
#endif
#include "core/fa.h"
#include "core/error_api.h"
#include "core/compact_ulong_store.h"
#include "core/encseq.h"
#include "core/filelengthvalues.h"
#include "core/fileutils.h"
#include "core/intbits.h"
#include "core/log.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/minmax.h"
#include "core/unused_api.h"
#include "core/stack-inlined.h"
#include "core/str_array_api.h"
#include "core/xansi_api.h"
#include "match/rdj-cntlist.h"
#include "match/rdj-filesuf-def.h"
#include "match/reads2twobit.h"
#include "match/rdj-contfinder.h"

#ifdef GT_READJOINER_LARGE_READSET /* > 2^32 reads */
typedef GtCompactUlongStore GtReadjoinerContfinderSeqnumsType;
typedef uint64_t gt_contfinder_seqnum_t;
#define GT_READJOINER_CONTFINDER_ALLOC_SEQNUMS(ARR, NOFSEQS)\
  (ARR) = gt_compact_ulong_store_new((NOFSEQS),\
      gt_determinebitspervalue(NOFSEQS))
#define GT_READJOINER_CONTFINDER_GET_SEQNUM(ARR, POS)\
  gt_compact_ulong_store_get((ARR), (POS))
#define GT_READJOINER_CONTFINDER_SET_SEQNUM(ARR, POS, VALUE) \
  gt_compact_ulong_store_update((ARR), (POS), (VALUE))
#define GT_READJOINER_CONTFINDER_FREE_SEQNUMS(ARR)\
  gt_compact_ulong_store_delete(ARR)
#else
typedef uint32_t GtReadjoinerContfinderSeqnumsType;
typedef uint32_t gt_contfinder_seqnum_t;
#define GT_READJOINER_CONTFINDER_ALLOC_SEQNUMS(ARR, NOFSEQS)\
  (ARR) = gt_malloc(sizeof (GtReadjoinerContfinderSeqnumsType) * (NOFSEQS))
#define GT_READJOINER_CONTFINDER_GET_SEQNUM(ARR, POS)\
  ((ARR)[POS])
#define GT_READJOINER_CONTFINDER_SET_SEQNUM(ARR, POS, VALUE)\
  ((ARR)[POS]=(VALUE))
#define GT_READJOINER_CONTFINDER_FREE_SEQNUMS(ARR)\
  gt_free(ARR)
#endif

typedef uint8_t gt_contfinder_kmercode_t;
typedef uint8_t gt_contfinder_overflow_t;

typedef uint8_t gt_contfinder_copynum_t;
#define GT_CONTFINDER_COPYNUM_MAX UINT8_MAX
#define GT_CONTFINDER_COPYNUM_INC(VALUE, INC) \
  if ((VALUE) < GT_CONTFINDER_COPYNUM_MAX - INC + 1)\
  {\
    (VALUE) += INC;\
  }\

#define GT_CONTFINDER_CONTAINS(CONTFINDERPTR, CONTAINER, CONTAINED)\
  GT_SETIBIT((CONTFINDERPTR)->contained, (CONTAINED));\
  if ((CONTFINDERPTR)->copynum != NULL)\
  {\
    gt_assert(!GT_ISIBITSET((CONTFINDERPTR)->contained, CONTAINER));\
    GT_CONTFINDER_COPYNUM_INC((CONTFINDERPTR)->copynum[(CONTAINER)],\
        (CONTFINDERPTR)->copynum[(CONTAINED)]);\
    (CONTFINDERPTR)->copynum[(CONTAINED)] = 0;\
  }

typedef struct {
  gt_contfinder_kmercode_t code;
  gt_contfinder_overflow_t overflow;
} GtContfinderKmercodeWithOverflow;

#define GT_CONTFINDER_INSERTION_SORT_MAX (size_t)31

#define GT_CONTFINDER_KMERCODE_BITS    \
  (sizeof (gt_contfinder_kmercode_t) * CHAR_BIT)
#define GT_CONTFINDER_KMERSIZE         (GT_CONTFINDER_KMERCODE_BITS >> 1)
#define GT_CONTFINDER_NOFKMERCODES     (1 << GT_CONTFINDER_KMERCODE_BITS)
#define GT_CONTFINDER_KMERCODE_MAX     \
  ((gt_contfinder_kmercode_t)(GT_CONTFINDER_NOFKMERCODES - 1))

#define GT_CONTFINDER_NOFBUCKETS(LEVEL) \
  (1 << ((GT_CONTFINDER_KMERSIZE - (LEVEL)) << 1))

#define GT_CONTFINDER_CODE_UNDEF     (GtTwobitencoding)ULONG_MAX

#define GT_CONTFINDER_UINT8_REVCOMPL(CODE) \
  (GT_CONTFINDER_KMERCODE_MAX ^ \
   (((((CODE) & (3 << 6)) >> 6) | (((CODE) & 3) << 6)) | \
    ((((CODE) & (3 << 4)) >> 2) | (((CODE) & (3 << 2)) << 2))))

#define GT_CONTFINDER_UINT16_REVCOMPL(CODE) \
  ((gt_contfinder_kmercode_t)\
  (GT_CONTFINDER_KMERCODE_MAX ^ \
    (\
      ((((CODE) & (3UL << 14)) >> 14) | (((CODE) & (3UL      )) << 14)) | \
      ((((CODE) & (3UL << 12)) >> 10) | (((CODE) & (3UL <<  2)) << 10)) | \
      ((((CODE) & (3UL << 10)) >> 6)  | (((CODE) & (3UL <<  4)) << 6 )) | \
      ((((CODE) & (3UL << 8 )) >> 2 ) | (((CODE) & (3UL <<  6)) << 2))   \
    )\
  ))

#define GT_CONTFINDER_REVCOMPL(CODE) GT_CONTFINDER_UINT8_REVCOMPL(CODE)

#define GT_CONTFINDER_SEPARATOR (gt_contfinder_kmercode_t)3

#define GT_CONTFINDER_READBUFFER_SIZE ((size_t)256)

#define GT_CONTFINDER_SEPPOS_INC ((size_t)(1 << 14))

#define GT_CONTFINDER_ALPHASIZE 4

struct GtContfinder {
  GtTwobitencoding *twobitencoding;
  gt_contfinder_seqnum_t logicalnofseqs;
  gt_contfinder_seqnum_t nofseqs;
  GtBitsequence *contained;
  /* eqlen: */
  size_t len;
  /* varlen: */
  size_t *seppos;
  /* temp buffers: */
  gt_contfinder_seqnum_t *sorted;
  gt_contfinder_kmercode_t *oracle;
  gt_contfinder_overflow_t *overflows;
  /* copynum buffer */
  gt_contfinder_copynum_t *copynum;
  /* seqnums to sort */
  GtReadjoinerContfinderSeqnumsType *seqnums;
};

static inline gt_contfinder_kmercode_t gt_contfinder_code_at_position(
    const GtTwobitencoding *twobitencoding, size_t pos)
{
  unsigned int unitoffset = (unsigned int) GT_MODBYUNITSIN2BITENC(pos);
  size_t unitindex = GT_DIVBYUNITSIN2BITENC(pos);

  if (unitoffset <=
      (unsigned int)(GT_UNITSIN2BITENC - GT_CONTFINDER_KMERSIZE))
  {
    return (gt_contfinder_kmercode_t)
      (twobitencoding[unitindex] >>
       GT_MULT2(GT_UNITSIN2BITENC - GT_CONTFINDER_KMERSIZE -
         unitoffset))
      & GT_CONTFINDER_KMERCODE_MAX;
  }
  else
  {
    unsigned int shiftleft = GT_MULT2(unitoffset +
        (unsigned int)GT_CONTFINDER_KMERSIZE -
        (unsigned int)GT_UNITSIN2BITENC);
    return (gt_contfinder_kmercode_t)
      ((twobitencoding[unitindex] << shiftleft) |
       (twobitencoding[unitindex + 1] >>
           (GT_MULT2(GT_UNITSIN2BITENC) - shiftleft)))
      & GT_CONTFINDER_KMERCODE_MAX;
  }
}

static inline GtContfinderKmercodeWithOverflow gt_contfinder_get_code(
    const GtTwobitencoding *twobitencoding, gt_contfinder_seqnum_t seqnum,
    const size_t depth, const gt_contfinder_seqnum_t firstrevcompl, size_t len,
    const size_t *seppos)
{
  GtContfinderKmercodeWithOverflow k;
  size_t remaining, seqstart;

  if (seqnum < firstrevcompl)
  {
    if (len != 0)
    {
      seqstart = seqnum * len;
    }
    else
    {
      seqstart = (seqnum > 0) ? seppos[seqnum - 1] + 1 : 0;
      len = seppos[seqnum] - seqstart + 1;
    }
    if (depth < len - 1)
    {
      k.code = gt_contfinder_code_at_position(twobitencoding, seqstart + depth);
      k.overflow = 0;
      remaining = len - 1 - depth;
      if (remaining < GT_CONTFINDER_KMERSIZE)
      {
        k.overflow = GT_CONTFINDER_KMERSIZE -
          (gt_contfinder_overflow_t)remaining;
        k.code &= (GT_CONTFINDER_KMERCODE_MAX - ((1 << (k.overflow << 1)) - 1));
      }
    }
    else
    {
      k.code = 0;
      k.overflow = GT_CONTFINDER_KMERSIZE;
    }
    return k;
  }
  else
  {
    size_t pos;
    if (len != 0)
    {
      pos = ((firstrevcompl << 1) - seqnum) * len - 1 - depth;
    }
    else
    {
      seqnum = (firstrevcompl << 1) - seqnum - 1;
      pos = seppos[seqnum] - depth;
      seqstart = (seqnum > 0) ? seppos[seqnum - 1] + 1 : 0;
      len = seppos[seqnum] - seqstart + 1;
    }
    if (depth < len - 1)
    {
      remaining = len - 1 - depth;
      pos -= (remaining > GT_CONTFINDER_KMERSIZE) ? GT_CONTFINDER_KMERSIZE :
        remaining;
      k.overflow = 0;
      k.code = GT_CONTFINDER_REVCOMPL(
          gt_contfinder_code_at_position(twobitencoding, pos));
      if (remaining < GT_CONTFINDER_KMERSIZE)
      {
        k.overflow = GT_CONTFINDER_KMERSIZE - remaining;
        k.code <<= (k.overflow << 1);
      }
    }
    else
    {
      k.code = 0;
      k.overflow = GT_CONTFINDER_KMERSIZE;
    }
    return k;
  }
}

typedef struct {
  GtReadjoinerContfinderSeqnumsType *seqnums;
  unsigned long seqnums_offset;
  gt_contfinder_seqnum_t nofseqs;
  size_t depth;
} GtContfinderBucketInfo;

GT_STACK_DECLARESTRUCT(GtContfinderBucketInfo, 1024);

static inline void gt_contfinder_insertion_sort(
    const GtContfinder contfinder, GtContfinderBucketInfo bucket)
{
  size_t i, j;
  gt_contfinder_seqnum_t u, v, container;
  int uvcmp;

  gt_assert(bucket.nofseqs > (gt_contfinder_seqnum_t)1);

  for (i = (size_t)1; i < bucket.nofseqs; i++)
  {
    gt_contfinder_seqnum_t ucorrected;
    size_t ulen = 0;
    u = GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums,
        i + bucket.seqnums_offset);
    ucorrected = u;
    if (ucorrected >= contfinder.nofseqs)
      ucorrected = (contfinder.nofseqs << 1) - 1 - ucorrected;
    if (contfinder.len == 0)
    {
      ulen = (ucorrected > 0) ? contfinder.seppos[ucorrected] -
        contfinder.seppos[ucorrected - 1] : contfinder.seppos[ucorrected] + 1;
    }
    for (j = i; j > 0; j--)
    {
      size_t len = contfinder.len;
      size_t pos;
      size_t vlen = 0;
      gt_contfinder_seqnum_t vcorrected;
      GtContfinderKmercodeWithOverflow unk = {0, 0}, vnk = {0, 0};
      v = GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums, j - 1 +
          bucket.seqnums_offset);
      vcorrected = v;
      if (vcorrected >= contfinder.nofseqs)
        vcorrected = (contfinder.nofseqs << 1) - 1 - vcorrected;
      if (len == 0)
      {
        vlen = (vcorrected > 0) ? contfinder.seppos[vcorrected] -
          contfinder.seppos[vcorrected - 1] : contfinder.seppos[vcorrected] + 1;
        len = MIN(ulen, vlen);
      }
      for (pos = bucket.depth, uvcmp = 0; uvcmp == 0 && pos < len;
          pos += GT_CONTFINDER_KMERSIZE)
      {
        unk = gt_contfinder_get_code(contfinder.twobitencoding, u,
            pos, contfinder.nofseqs, contfinder.len,
            contfinder.seppos);
        vnk = gt_contfinder_get_code(contfinder.twobitencoding, v,
            pos, contfinder.nofseqs, contfinder.len,
            contfinder.seppos);
        uvcmp = (int)vnk.code - (int)unk.code;
      }
      if (ulen > vlen)
      {
        unsigned short shift = (unsigned short)
          ((vnk.overflow - unk.overflow) << 1);
        uvcmp = (int)(vnk.code >> shift) - (int)(unk.code >> shift);
        if (uvcmp == 0)
        {
          /* v is contained in u */
          GT_SETIBIT(contfinder.contained, vcorrected);
          break;
        }
      }
      else if (ulen < vlen)
      {
        unsigned short shift = (unsigned short)
          ((unk.overflow - vnk.overflow) << 1);
        uvcmp = (int)(vnk.code >> shift) - (int)(unk.code >> shift);
        if (uvcmp == 0)
        {
          /* u is contained in v */
          GT_SETIBIT(contfinder.contained, ucorrected);
          break;
        }
      }
      if (uvcmp < 0)
      {
        break;
      }
      if (uvcmp == 0)
      {
        if (ucorrected > vcorrected)
        {
          GT_SETIBIT(contfinder.contained, ucorrected);
          break;
        }
      }
      GT_READJOINER_CONTFINDER_SET_SEQNUM(bucket.seqnums,
          j + bucket.seqnums_offset, v);
    }
    GT_READJOINER_CONTFINDER_SET_SEQNUM(bucket.seqnums,
        j + bucket.seqnums_offset, u);
  }

  container = GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums,
        bucket.seqnums_offset);
  if (container >= contfinder.nofseqs)
    container = (contfinder.nofseqs << 1) - 1 - container;
  for (i = (size_t)1; i < bucket.nofseqs; i++)
  {
    u = GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums,
        i + bucket.seqnums_offset);
    if (u >= contfinder.nofseqs)
      u = (contfinder.nofseqs << 1) - 1 - u;
    if (GT_ISIBITSET(contfinder.contained, u))
    {
      GT_CONTFINDER_CONTAINS(&contfinder, container, u);
    }
    else
    {
      container = u;
    }
  }
}

/* the following assumes the seqnums are sorted in the bucket */
static inline void gt_contfinder_mark_as_contained(
    GtContfinder contfinder, GtContfinderBucketInfo bucket,
    bool except_lowest_seqnum)
{
  size_t i, from = 0, to = bucket.nofseqs;
  gt_contfinder_seqnum_t container = 0;
  gt_assert(bucket.nofseqs > 0);
  if (except_lowest_seqnum)
  {
    gt_contfinder_seqnum_t first, last;
    if (bucket.nofseqs == (gt_contfinder_seqnum_t)1)
      return;
    first = GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums, 0 +
        bucket.seqnums_offset);
    last = GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums, bucket.nofseqs
        - 1 + bucket.seqnums_offset);
    from = (size_t)1;
    if (last >= contfinder.nofseqs)
      last = (contfinder.nofseqs << 1) - last - 1;
    if (first >= contfinder.nofseqs || last < first)
    {
      from--;
      to--;
      container = last;
    }
    else
    {
      container = first;
      if (first == last) /* palindromic */
        to--;
    }
  }
  for (i = from; i < to; i++)
  {
    gt_contfinder_seqnum_t corrected =
      GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums,
          i + bucket.seqnums_offset);
    if (corrected >= contfinder.nofseqs)
      corrected = (contfinder.nofseqs << 1) - corrected - 1;
    GT_CONTFINDER_CONTAINS(&contfinder, container, corrected);
  }
}

static void gt_contfinder_radixsort_eqlen(GtContfinder contfinder,
    GtContfinderBucketInfo all)
{
  size_t i;
  GtStackGtContfinderBucketInfo stack;
  gt_contfinder_seqnum_t bucketindex[GT_CONTFINDER_NOFBUCKETS(0)];
#ifndef S_SPLINT_S
  gt_contfinder_seqnum_t bucketsize[GT_CONTFINDER_NOFBUCKETS(0)] = {};
#endif
  GtContfinderBucketInfo subbucket;

  /* Loop A */
  for (i = 0; i < all.nofseqs; ++i)
    ++bucketsize[gt_contfinder_get_code(contfinder.twobitencoding, i, 0,
        contfinder.nofseqs, contfinder.len, NULL).code];

  bucketindex[0] = 0;
  for (i = (size_t)1; i < GT_CONTFINDER_NOFBUCKETS(0); ++i)
    bucketindex[i] = bucketindex[i - 1] + bucketsize[i - 1];

  /* Loop B */
  for (i = 0; i < all.nofseqs; ++i)
    GT_READJOINER_CONTFINDER_SET_SEQNUM(all.seqnums, (bucketindex[
        gt_contfinder_get_code(contfinder.twobitencoding, i, 0,
          contfinder.nofseqs, contfinder.len, NULL).code]++) +
        all.seqnums_offset, i);

  if (contfinder.len <= GT_CONTFINDER_KMERSIZE)
  {
    subbucket.depth = 0;
    subbucket.seqnums = all.seqnums;
    subbucket.seqnums_offset = all.seqnums_offset;
    for (i = 0; i < GT_CONTFINDER_NOFBUCKETS(0); ++i)
    {
      subbucket.nofseqs = bucketsize[i];
      if (subbucket.nofseqs > (size_t)1)
        gt_contfinder_mark_as_contained(contfinder, subbucket, true);
      subbucket.seqnums_offset += subbucket.nofseqs;
    }
    return;
  }

  /* alloc oracle and sorted */
  {
    gt_contfinder_seqnum_t maxbsize = bucketsize[0];
    for (i = (size_t)1; i < GT_CONTFINDER_NOFBUCKETS(0); ++i)
      if (maxbsize < bucketsize[i])
        maxbsize = bucketsize[i];
    contfinder.oracle = gt_malloc(sizeof (gt_contfinder_kmercode_t) * maxbsize);
    contfinder.sorted = gt_malloc(sizeof (gt_contfinder_seqnum_t) * maxbsize);
  }

  GT_STACK_INIT(&stack, 1024UL);

  subbucket.depth = GT_CONTFINDER_KMERSIZE;
  subbucket.seqnums = all.seqnums;
  subbucket.seqnums_offset = all.seqnums_offset;
  for (i = 0; i < GT_CONTFINDER_NOFBUCKETS(0); ++i)
  {
    subbucket.nofseqs = bucketsize[i];
    if (subbucket.nofseqs > (size_t)1)
    {
      if (subbucket.nofseqs <= GT_CONTFINDER_INSERTION_SORT_MAX)
        gt_contfinder_insertion_sort(contfinder, subbucket);
      else
      {
        GT_STACK_PUSH(&stack, subbucket);
      }
    }
    subbucket.seqnums_offset += subbucket.nofseqs;
  }

  while (!GT_STACK_ISEMPTY(&stack))
  {
    GtContfinderBucketInfo bucket = GT_STACK_POP(&stack);

    memset(bucketsize, 0, sizeof (bucketsize));

    /* Loop A */
    for (i = 0; i < bucket.nofseqs; ++i)
    {
      gt_contfinder_seqnum_t ith_seqnum =
        GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums, i +
            bucket.seqnums_offset);
      contfinder.oracle[i] = gt_contfinder_get_code(contfinder.twobitencoding,
          ith_seqnum, bucket.depth, contfinder.nofseqs, contfinder.len,
          NULL).code;
    }

    for (i = 0; i < bucket.nofseqs; ++i)
      ++bucketsize[contfinder.oracle[i]];

    bucketindex[0] = 0;
    for (i = (size_t)1; i < GT_CONTFINDER_NOFBUCKETS(0); ++i)
      bucketindex[i] = bucketindex[i - 1] + bucketsize[i - 1];

    /* Loop B */
    for (i = 0; i < bucket.nofseqs; ++i)
      contfinder.sorted[bucketindex[contfinder.oracle[i]]++] =
        GT_READJOINER_CONTFINDER_GET_SEQNUM(bucket.seqnums,
            i + bucket.seqnums_offset);
    for (i = 0; i < bucket.nofseqs; ++i)
      GT_READJOINER_CONTFINDER_SET_SEQNUM(bucket.seqnums,
          i + bucket.seqnums_offset,
          contfinder.sorted[i]);

    subbucket.depth = bucket.depth + GT_CONTFINDER_KMERSIZE;
    subbucket.seqnums = bucket.seqnums;
    subbucket.seqnums_offset = bucket.seqnums_offset;
    if (subbucket.depth < contfinder.len)
    {
      for (i = 0; i < GT_CONTFINDER_NOFBUCKETS(0); ++i)
      {
        subbucket.nofseqs = bucketsize[i];
        if (subbucket.nofseqs > (size_t)1)
        {
          if (subbucket.nofseqs <= GT_CONTFINDER_INSERTION_SORT_MAX)
            gt_contfinder_insertion_sort(contfinder, subbucket);
          else
          {
            GT_STACK_PUSH(&stack, subbucket);
          }
        }
        subbucket.seqnums_offset += subbucket.nofseqs;
      }
    }
    else
    {
      for (i = 0; i < GT_CONTFINDER_NOFBUCKETS(0); ++i)
      {
        subbucket.nofseqs = bucketsize[i];
        if (subbucket.nofseqs > (size_t)1)
          gt_contfinder_mark_as_contained(contfinder, subbucket, true);
        subbucket.seqnums_offset += subbucket.nofseqs;
      }
    }
  }

  GT_STACK_DELETE(&stack);
  gt_free(contfinder.sorted);
  gt_free(contfinder.oracle);
}

static inline void gt_contfinder_process_buckets(
    const GtContfinder contfinder, const GtContfinderBucketInfo parentbucket,
    gt_contfinder_seqnum_t **bucketsize,
    GtStackGtContfinderBucketInfo *stackptr, GtBitsequence **bucketcontained)
{
  GtContfinderBucketInfo subbucket;
  gt_contfinder_seqnum_t i;
  gt_contfinder_overflow_t overflow;

  /* process buckets with overflow = 0 */
  subbucket.seqnums = parentbucket.seqnums;
  subbucket.seqnums_offset = parentbucket.seqnums_offset;
  subbucket.depth = parentbucket.depth + GT_CONTFINDER_KMERSIZE;
  for (i = 0; i < GT_CONTFINDER_NOFBUCKETS(0); ++i)
  {
    subbucket.nofseqs = bucketsize[0][i];
    if (subbucket.nofseqs > 0)
    {
      if (subbucket.nofseqs > (size_t)1)
      {
        if (subbucket.nofseqs <= GT_CONTFINDER_INSERTION_SORT_MAX)
          gt_contfinder_insertion_sort(contfinder, subbucket);
        else
        {
          GT_STACK_PUSH(stackptr, subbucket);
        }
      }
      for (overflow = (gt_contfinder_overflow_t)1;
          overflow <= GT_CONTFINDER_KMERSIZE; overflow++)
      {
        GT_SETIBIT(bucketcontained[overflow - 1], i >> (overflow << 1));
      }
    }
    subbucket.seqnums_offset += subbucket.nofseqs;
  }

  /* process buckets with overflow > 0 */
  for (overflow = (gt_contfinder_overflow_t)1;
      overflow <= GT_CONTFINDER_KMERSIZE; overflow++)
  {
    for (i = 0; i < GT_CONTFINDER_NOFBUCKETS(overflow); ++i)
    {
      subbucket.nofseqs = bucketsize[overflow][i];
      if (subbucket.nofseqs > 0)
        gt_contfinder_mark_as_contained(contfinder, subbucket,
            (bool)GT_ISIBITSET(bucketcontained[overflow - 1], i));
      subbucket.seqnums_offset += subbucket.nofseqs;
    }
  }
}

static void gt_contfinder_radixsort(GtContfinder contfinder,
    GtContfinderBucketInfo all)
{
  gt_contfinder_seqnum_t i;
  GtStackGtContfinderBucketInfo stack;
  GtContfinderKmercodeWithOverflow k;
  gt_contfinder_overflow_t overflow;
  GtBitsequence *bucketcontained[GT_CONTFINDER_KMERSIZE];
  gt_contfinder_seqnum_t *bucketindex[GT_CONTFINDER_KMERSIZE + 1];
  gt_contfinder_seqnum_t *bucketsize[GT_CONTFINDER_KMERSIZE + 1];
  size_t baseindex;

  for (overflow = 0; overflow <= GT_CONTFINDER_KMERSIZE; overflow++)
  {
    bucketindex[overflow] =
      gt_malloc(sizeof (gt_contfinder_seqnum_t) *
          GT_CONTFINDER_NOFBUCKETS(overflow));
    bucketsize[overflow] =
      gt_calloc(GT_CONTFINDER_NOFBUCKETS(overflow),
          sizeof (gt_contfinder_seqnum_t));
  }
  for (overflow = (gt_contfinder_overflow_t)1;
      overflow <= GT_CONTFINDER_KMERSIZE; overflow++)
  {
    GT_INITBITTAB(bucketcontained[overflow - 1],
        GT_CONTFINDER_NOFBUCKETS(overflow));
  }

  /* Loop A */
  for (i = 0; i < all.nofseqs; ++i)
  {
    k = gt_contfinder_get_code(contfinder.twobitencoding, i, 0,
        contfinder.nofseqs, contfinder.len, contfinder.seppos);
    ++bucketsize[k.overflow][k.code >> GT_MULT2(k.overflow)];
  }

  baseindex = 0;
  for (overflow = 0; overflow <= GT_CONTFINDER_KMERSIZE; overflow++)
  {
    bucketindex[overflow][0] = baseindex;
    for (i = (size_t)1; i < GT_CONTFINDER_NOFBUCKETS(overflow); ++i)
      bucketindex[overflow][i] = bucketindex[overflow][i - 1] +
        bucketsize[overflow][i - 1];
    baseindex = bucketindex[overflow][GT_CONTFINDER_NOFBUCKETS(overflow) - 1]
      + bucketsize[overflow][GT_CONTFINDER_NOFBUCKETS(overflow) - 1];
  }

  /* Loop B */
  for (i = 0; i < all.nofseqs; ++i)
  {
    k = gt_contfinder_get_code(contfinder.twobitencoding, i, 0,
        contfinder.nofseqs, contfinder.len, contfinder.seppos);
    GT_READJOINER_CONTFINDER_SET_SEQNUM(all.seqnums,
        (bucketindex[k.overflow][k.code >> GT_MULT2(k.overflow)]++)
        + all.seqnums_offset, i);
  }

  /* alloc temp buffers */
  {
    gt_contfinder_seqnum_t maxbucketsize = bucketsize[0][0];
    for (i = (size_t)1; i < GT_CONTFINDER_NOFBUCKETS(0); ++i)
      if (maxbucketsize < bucketsize[0][i])
        maxbucketsize = bucketsize[0][i];
    contfinder.oracle = gt_malloc(sizeof (gt_contfinder_kmercode_t) *
        maxbucketsize);
    contfinder.sorted = gt_malloc(sizeof (gt_contfinder_seqnum_t) *
        maxbucketsize);
    contfinder.overflows = gt_malloc(sizeof (unsigned char) * maxbucketsize);
  }

  GT_STACK_INIT(&stack, 1024UL);

  gt_contfinder_process_buckets(contfinder, all, bucketsize, &stack,
      bucketcontained);

  while (!GT_STACK_ISEMPTY(&stack))
  {
    GtContfinderBucketInfo bucket = GT_STACK_POP(&stack);

    for (overflow = 0; overflow <= GT_CONTFINDER_KMERSIZE; overflow++)
    {
      for (i = 0; i < GT_CONTFINDER_NOFBUCKETS(overflow); ++i)
      {
        bucketsize[overflow][i] = 0;
      }
    }

    /* Loop A */
    for (i = 0; i < bucket.nofseqs; ++i)
    {
      k = gt_contfinder_get_code(
          contfinder.twobitencoding, GT_READJOINER_CONTFINDER_GET_SEQNUM(
            bucket.seqnums, i + bucket.seqnums_offset), bucket.depth,
          contfinder.nofseqs, contfinder.len, contfinder.seppos);
      contfinder.oracle[i] = k.code >> GT_MULT2(k.overflow);
      contfinder.overflows[i] = k.overflow;
    }

    for (i = 0; i < bucket.nofseqs; ++i)
      ++(bucketsize[contfinder.overflows[i]][contfinder.oracle[i]]);

    baseindex = 0;
    for (overflow = 0; overflow <= GT_CONTFINDER_KMERSIZE; overflow++)
    {
      bucketindex[overflow][0] = baseindex;
      for (i = (size_t)1; i < GT_CONTFINDER_NOFBUCKETS(overflow); ++i)
        bucketindex[overflow][i] = bucketindex[overflow][i - 1] +
          bucketsize[overflow][i - 1];
      baseindex = bucketindex[overflow][GT_CONTFINDER_NOFBUCKETS(overflow) - 1];
    }

    /* Loop B */
    for (i = 0; i < bucket.nofseqs; ++i)
      contfinder.sorted[(bucketindex[contfinder.overflows[i]]
        [contfinder.oracle[i]])++] = GT_READJOINER_CONTFINDER_GET_SEQNUM(
            bucket.seqnums, i + bucket.seqnums_offset);
    for (i = 0; i < bucket.nofseqs; ++i)
      GT_READJOINER_CONTFINDER_SET_SEQNUM(bucket.seqnums,
          i + bucket.seqnums_offset, contfinder.sorted[i]);

    gt_contfinder_process_buckets(contfinder, bucket, bucketsize, &stack,
        bucketcontained);
  }

  GT_STACK_DELETE(&stack);
  gt_free(contfinder.sorted);
  gt_free(contfinder.oracle);
  gt_free(contfinder.overflows);
  for (overflow = 0; overflow <= GT_CONTFINDER_KMERSIZE; overflow++)
  {
    gt_free(bucketindex[overflow]);
    gt_free(bucketsize[overflow]);
  }
  for (overflow = 0; overflow < GT_CONTFINDER_KMERSIZE; overflow++)
  {
    gt_free(bucketcontained[overflow]);
  }
}

int gt_contfinder_write_seqnums(GtContfinder *contfinder, bool sorted,
    GtFile *outfp, GT_UNUSED GtError *err)
{
  int had_err = 0;
  gt_contfinder_seqnum_t i;
  if (sorted)
  {
    for (i = 0; i < contfinder->logicalnofseqs; i++)
      if (!GT_ISIBITSET(contfinder->contained,
            GT_READJOINER_CONTFINDER_GET_SEQNUM(contfinder->seqnums, i)))
        gt_file_xprintf(outfp, "%lu\n", (unsigned long)
            GT_READJOINER_CONTFINDER_GET_SEQNUM(contfinder->seqnums, i));
  }
  else
  {
    for (i = 0; i < contfinder->nofseqs; i++)
      if (!GT_ISIBITSET(contfinder->contained, i))
        gt_file_xprintf(outfp, "%lu\n", (unsigned long)i);
  }
  return had_err;
}

int gt_contfinder_write_sorted_seqnums(GtContfinder *contfinder, char* path,
    GtError *err)
{
  int had_err = 0;
  GtFile *file;
  file = gt_file_new(path, "wb", err);
  if (file == NULL)
    had_err = -1;
  if (!had_err)
  {
    had_err = gt_contfinder_write_seqnums(contfinder, true, file, err);
  }
  gt_file_delete(file);
  return had_err;
}

int gt_contfinder_write_cntlist(GtContfinder *contfinder, char* path,
    GtError *err)
{
  int had_err;
  had_err = gt_cntlist_show(contfinder->contained,
      (unsigned long)contfinder->nofseqs, path, true, err);
  return had_err;
}

int gt_contfinder_write_copynum(GtContfinder *contfinder, char* path,
    GtError *err)
{
  int had_err = 0;
  gt_contfinder_seqnum_t i;
  FILE *file;
  file = gt_fa_fopen(path, "wb", err);
  if (file == NULL)
    had_err = -1;
  else
  {
#ifndef NDEBUG
    gt_contfinder_seqnum_t n_noncontained = 0;
    unsigned long cnsum = 0;
    bool had_overflow = false;
#endif
    gt_contfinder_copynum_t cn;
    for (i = 0; i < contfinder->nofseqs; i++)
    {
      cn = contfinder->copynum[i];
      if (cn > 0)
      {
        gt_xfwrite(contfinder->copynum + i, sizeof (*contfinder->copynum),
            (size_t)1, file);
#ifndef NDEBUG
        n_noncontained++;
        if (cn == GT_CONTFINDER_COPYNUM_MAX)
        {
          had_overflow = true;
        }
        cnsum += cn;
#endif
      }
    }
    gt_assert(n_noncontained == contfinder->nofseqs);
    gt_assert(had_overflow || (cnsum == (unsigned long)contfinder->nofseqs));
    gt_fa_fclose(file);
  }
  return had_err;
}

GtBitsequence *gt_contfinder_contained(GtContfinder *contfinder)
{
  gt_assert(contfinder);
  return contfinder->contained;
}

static void gt_contfinder_init_copynum(GtContfinder *contfinder)
{
  gt_contfinder_seqnum_t idx;
  /* the mark_as_contained function is currently not able to set
   * correctly the copynum if sequences have variable length,
   * thus: */
  gt_assert(contfinder->len > 0);
  contfinder->copynum = gt_malloc(sizeof (*contfinder->copynum) *
      contfinder->nofseqs);
  for (idx = 0; idx < contfinder->nofseqs; idx++)
    contfinder->copynum[idx] = (gt_contfinder_seqnum_t)1;
}

void gt_contfinder_run(GtContfinder *contfinder, bool mirrored,
    bool calculate_copynum)
{
  GtContfinderBucketInfo all;

  if (contfinder->nofseqs == 0)
    return;

  GT_INITBITTAB(contfinder->contained, contfinder->logicalnofseqs);

  contfinder->nofseqs = contfinder->logicalnofseqs;

  if (mirrored)
    contfinder->logicalnofseqs <<= 1;

  GT_READJOINER_CONTFINDER_ALLOC_SEQNUMS(contfinder->seqnums,
      contfinder->logicalnofseqs);

  if (calculate_copynum)
    gt_contfinder_init_copynum(contfinder);

  all.nofseqs = contfinder->logicalnofseqs;
  all.seqnums = contfinder->seqnums;
  all.seqnums_offset = 0;
  all.depth = 0;

  if (contfinder->len > 0)
    gt_contfinder_radixsort_eqlen(*contfinder, all);
  else
    gt_contfinder_radixsort(*contfinder, all);
}

void gt_contfinder_delete(GtContfinder *contfinder)
{
  if (contfinder != NULL)
  {
    GT_READJOINER_CONTFINDER_FREE_SEQNUMS(contfinder->seqnums);
    gt_free(contfinder->contained);
    gt_free(contfinder->copynum);
    gt_free(contfinder);
  }
}

unsigned long gt_contfinder_nofcontained(GtContfinder *contfinder)
{
  size_t i;
  GtBitsequence v;
  unsigned long nofcontained;
  const size_t tabsize = GT_NUMOFINTSFORBITS(contfinder->nofseqs);
  if (contfinder->contained == NULL)
    return 0;
  nofcontained = 0;
  for (i = 0; i < tabsize; i++)
  {
    v = contfinder->contained[i];
    for (/**/; v; nofcontained++)
      v &= v - 1;
  }
  return nofcontained;
}

GtContfinder* gt_contfinder_new(GtReads2Twobit *r2t)
{
  GtContfinder *contfinder;
  contfinder = gt_malloc(sizeof (*contfinder));
  contfinder->contained = NULL;
  contfinder->copynum = NULL;
  contfinder->seqnums = NULL;
  contfinder->twobitencoding = gt_reads2twobit_export_twobitencoding(r2t);
  contfinder->seppos = (size_t*)gt_reads2twobit_export_seppos(r2t);
  contfinder->nofseqs = (gt_contfinder_seqnum_t)gt_reads2twobit_nofseqs(r2t);
  contfinder->logicalnofseqs = contfinder->nofseqs;
  contfinder->len = (size_t)gt_reads2twobit_seqlen_eqlen(r2t);
  return contfinder;
}

/* radixsort_str tester */

#include "match/radixsort_str.h"

void gt_contfinder_radixsort_str_eqlen_tester(GtContfinder *contfinder,
    bool mirrored, unsigned long depth,
    unsigned long maxdepth, bool print)
{
  unsigned long *suffixes, totallength, width, i;
  GtRadixsortstringinfo *rsi;

  totallength = (unsigned long) contfinder->nofseqs * contfinder->len - 1;
  width = mirrored ? GT_MULT2(totallength + 1) : (totallength + 1);
  rsi = gt_radixsort_str_new(contfinder->twobitencoding,
                             totallength,
                             (unsigned long) contfinder->len,
                             GT_MULT2(width));
  suffixes = gt_malloc(sizeof (unsigned long) * width);
  for (i = 0; i < width; i++)
  {
    suffixes[i] = i;
  }
  gt_radixsort_str_eqlen(rsi, suffixes, NULL, 0, depth, maxdepth, width);
  if (print)
  {
    for (i = 0; i < width; i++)
    {
      printf("%lu\n", suffixes[i]);
    }
  }
  gt_free(suffixes);
  gt_radixsort_str_delete(rsi);
}
genometools-1.5.1/src/match/rdj-contfinder.h000066400000000000000000000036031211610345200210120ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Giorgio Gonnella 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_CONTFINDER_H
#define RDJ_CONTFINDER_H

#include 
#include "core/file.h"
#include "match/reads2twobit.h"

typedef struct GtContfinder GtContfinder;

GtContfinder* gt_contfinder_new(GtReads2Twobit *r2t);

void gt_contfinder_run(GtContfinder *contfinder, bool mirrored,
    bool calculate_copynum);

GtBitsequence *gt_contfinder_contained(GtContfinder *contfinder);

unsigned long gt_contfinder_nofcontained(GtContfinder *contfinder);

int gt_contfinder_write_seqnums(GtContfinder *contfinder, bool sorted,
    GtFile *outfp, GtError *err);

int gt_contfinder_write_sorted_seqnums(GtContfinder *contfinder, char* path,
    GtError *err);

int gt_contfinder_write_cntlist(GtContfinder *contfinder, char* path,
    GtError *err);

int gt_contfinder_write_copynum(GtContfinder *contfinder, char* path,
    GtError *err);

void gt_contfinder_delete(GtContfinder *contfinder);

void gt_contfinder_radixsort_str_eqlen_tester(GtContfinder *contfinder,
    bool mirrored, unsigned long depth,
    unsigned long maxdepth, bool print);

#endif
genometools-1.5.1/src/match/rdj-contigpaths.c000066400000000000000000000070021211610345200211720ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/arraydef.h"
#include "core/fasta_separator.h"
#include "core/xansi_api.h"
#include "core/str.h"
#include "extended/assembly_stats_calculator.h"
#include "match/rdj-contigs-writer.h"
#include "match/rdj-contigpaths.h"

static GtFile* gt_contigpaths_get_file(const char *indexname,
    const char *suffix, const char* mode, GtError *err)
{
  GtStr *path;
  GtFile *file;

  path = gt_str_new_cstr(indexname);
  gt_str_append_cstr(path, suffix);
  file = gt_file_new(gt_str_get(path), mode, err);
  gt_str_delete(path);
  return file;
}

#define GT_CONTIGPATHS_BUFFERSIZE ((size_t)1 << 16)

int gt_contigpaths_to_fasta(const char *indexname,
    const char *contigpaths_suffix, const char *fasta_suffix,
    const GtEncseq *encseq, unsigned long min_contig_length, bool showpaths,
    size_t buffersize, GtLogger *logger, GtError *err)
{
  unsigned long nofchars, seqnum, contig_length = 0;
  GtFile *infp, *outfp;
  int nvalues, i;
  GtContigsWriter *cw;
  GtContigpathElem *buffer;

  if (buffersize == 0)
    buffersize = GT_CONTIGPATHS_BUFFERSIZE * sizeof (GtContigpathElem);
  else
  {
    size_t bsmod = buffersize % sizeof (GtContigpathElem);
    buffersize -= bsmod;
  }
  gt_assert(buffersize > 0);
  gt_assert(buffersize % sizeof (GtContigpathElem) == 0);
  buffer = gt_malloc(buffersize);

  gt_assert(encseq != NULL);
  gt_error_check(err);
  gt_assert(buffer != NULL);

  infp = gt_contigpaths_get_file(indexname, contigpaths_suffix, "r", err);
  if (infp == NULL)
    return -1;
  outfp = gt_contigpaths_get_file(indexname, fasta_suffix, "w", err);
  if (outfp == NULL)
  {
    gt_file_delete(infp);
    return -1;
  }

  cw = gt_contigs_writer_new(encseq, outfp, showpaths);

  while ((nvalues = gt_file_xread(infp, buffer, buffersize)) > 0)
  {
    gt_assert((size_t)nvalues <= buffersize);
    nvalues /= (sizeof (GtContigpathElem) << 1);
    for (i = 0; i < nvalues; i++)
    {
      nofchars = (unsigned long)buffer[(i << 1)];
      seqnum = (unsigned long)buffer[(i << 1) + 1];
      if (nofchars == 0)
      {
        /* end of contig */
        if (contig_length >= min_contig_length)
          gt_contigs_writer_write(cw);
        else
          gt_contigs_writer_abort(cw);
        gt_contigs_writer_start(cw, seqnum);
        contig_length = gt_encseq_seqlength(encseq, seqnum);
      }
      else
      {
        contig_length += nofchars;
        gt_contigs_writer_append(cw, seqnum, nofchars);
      }
    }
  }

  if (contig_length >= min_contig_length)
    gt_contigs_writer_write(cw);
  else
    gt_contigs_writer_abort(cw);
  gt_contigs_writer_show_stats(cw, logger);
  gt_contigs_writer_delete(cw);
  gt_file_delete(infp);
  gt_file_delete(outfp);
  gt_free(buffer);
  return 0;
}
genometools-1.5.1/src/match/rdj-contigpaths.h000066400000000000000000000025251211610345200212040ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_CONTIGPATHS_H
#define RDJ_CONTIGPATHS_H

#include "core/file.h"
#include "core/encseq.h"
#include "core/logger.h"
#include "core/error_api.h"

typedef uint32_t GtContigpathElem;
#define GT_CONTIGPATH_ELEM_MAX (GtContigpathElem)UINT32_MAX

int gt_contigpaths_to_fasta(const char *indexname,
    const char *contigpaths_suffix, const char *fasta_suffix,
    const GtEncseq *encseq, unsigned long min_contig_length, bool showpaths,
    size_t buffersize, GtLogger *logger, GtError *err);

#endif
genometools-1.5.1/src/match/rdj-contigs-writer.c000066400000000000000000000167441211610345200216440ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/arraydef.h"
#include "core/fasta.h"
#include "core/ma.h"
#include "core/str.h"
#include "extended/assembly_stats_calculator.h"
#include "match/rdj-contigs-writer.h"

struct GtContigsWriter
{
  const GtEncseq *reads;
  GtFile *outfp;
  bool showpaths;
  GtAssemblyStatsCalculator *asc;
  GtEncseqReader *esr;
  GtArraychar contig;
  GtStr *contig_desc, *path_desc;
  unsigned long contignum, contigdepth, lastseqnum, nofseqs;
};

#define GT_CONTIGS_WRITER_CONTIG_INC 16384UL

GtContigsWriter *gt_contigs_writer_new(const GtEncseq *reads, GtFile *outfp,
    bool showpaths)
{
  GtContigsWriter *contigs_writer;

  gt_assert(reads != NULL);

  contigs_writer = gt_malloc(sizeof (GtContigsWriter));
  contigs_writer->reads = reads;
  contigs_writer->outfp = outfp;
  contigs_writer->showpaths = showpaths;
  contigs_writer->nofseqs = gt_encseq_num_of_sequences(contigs_writer->reads);
  contigs_writer->contignum = 0;
  contigs_writer->contigdepth = 0;
  GT_INITARRAY(&contigs_writer->contig, char);
  contigs_writer->contig_desc = gt_str_new();
  contigs_writer->path_desc = gt_str_new();
  contigs_writer->asc = gt_assembly_stats_calculator_new();
  contigs_writer->esr = gt_encseq_create_reader_with_readmode(reads,
      GT_READMODE_FORWARD, 0);
  return contigs_writer;
}

void gt_contigs_writer_delete(GtContigsWriter *contigs_writer)
{
  if (contigs_writer == NULL)
    return;
  GT_FREEARRAY(&contigs_writer->contig, char);
  gt_str_delete(contigs_writer->contig_desc);
  gt_str_delete(contigs_writer->path_desc);
  gt_assembly_stats_calculator_delete(contigs_writer->asc);
  gt_encseq_reader_delete(contigs_writer->esr);
  gt_free(contigs_writer);
}

static void gt_contigs_writer_reset_buffers(GtContigsWriter *contigs_writer)
{
  gt_assert(contigs_writer != NULL);
  contigs_writer->contig.nextfreechar = 0;
  gt_str_reset(contigs_writer->contig_desc);
  gt_str_reset(contigs_writer->path_desc);
  contigs_writer->contigdepth = 0;
}

void gt_contigs_writer_abort(GtContigsWriter *contigs_writer)
{
  gt_assert(contigs_writer != NULL);
  gt_contigs_writer_reset_buffers(contigs_writer);
}

GT_UNUSED
static void gt_contigs_writer_append_chars(GtContigsWriter *contigs_writer,
    unsigned long nofchars)
{
  unsigned long i;
  char *c;

  gt_assert(contigs_writer != NULL);
  for (i = 0; i < nofchars; i++)
  {
    GT_GETNEXTFREEINARRAY(c, &contigs_writer->contig, char,
        GT_CONTIGS_WRITER_CONTIG_INC);
    *c = gt_encseq_reader_next_decoded_char(contigs_writer->esr);
  }
}

#define GT_CONTIGS_WRITER_IS_DIRECT(SEQNUM, NOFSEQS)\
        ((SEQNUM) < ((NOFSEQS) >> 1))
#define GT_CONTIGS_WRITER_READNUM(SEQNUM, NOFSEQS)\
        (GT_CONTIGS_WRITER_IS_DIRECT(SEQNUM, NOFSEQS)\
            ? (SEQNUM)\
            : (NOFSEQS) - (SEQNUM) - 1)
#define GT_CONTIGS_WRITER_LETTER(SEQNUM, NOFSEQS)\
        (GT_CONTIGS_WRITER_IS_DIRECT(SEQNUM, NOFSEQS) ? 'E' : 'B')

void gt_contigs_writer_write(GtContigsWriter *contigs_writer)
{
  gt_assert(contigs_writer != NULL);

  if (contigs_writer->contig.nextfreechar > 0)
  {
    gt_assembly_stats_calculator_add(contigs_writer->asc,
        contigs_writer->contig.nextfreechar);
    /* build description */
    gt_str_append_cstr(contigs_writer->contig_desc, "contig_");
    gt_str_append_ulong(contigs_writer->contig_desc,
        contigs_writer->contignum);
    gt_str_append_cstr(contigs_writer->contig_desc, " length=");
    gt_str_append_ulong(contigs_writer->contig_desc,
        contigs_writer->contig.nextfreechar);
    gt_str_append_cstr(contigs_writer->contig_desc, " depth=");
    gt_str_append_ulong(contigs_writer->contig_desc,
        contigs_writer->contigdepth);
    gt_str_append_cstr(contigs_writer->contig_desc, " ");
    if (!contigs_writer->showpaths)
    {
      /* show path summary only */
      gt_str_append_cstr(contigs_writer->path_desc, "-->...-->");
      gt_str_append_ulong(contigs_writer->path_desc,
          GT_CONTIGS_WRITER_READNUM(contigs_writer->lastseqnum,
              contigs_writer->nofseqs));
      gt_str_append_char(contigs_writer->path_desc,
          GT_CONTIGS_WRITER_LETTER(contigs_writer->lastseqnum,
              contigs_writer->nofseqs));
    }
    gt_str_append_str(contigs_writer->contig_desc, contigs_writer->path_desc);

    gt_fasta_show_entry(gt_str_get(contigs_writer->contig_desc),
        contigs_writer->contig.spacechar, contigs_writer->contig.nextfreechar,
        60UL, contigs_writer->outfp);
    contigs_writer->contignum++;
    gt_contigs_writer_reset_buffers(contigs_writer);
  }
}

void gt_contigs_writer_append(GtContigsWriter *contigs_writer,
    unsigned long seqnum, unsigned long nofchars)
{
  unsigned long pos, i;
  gt_assert(contigs_writer != NULL);
  pos = gt_encseq_seqstartpos(contigs_writer->reads, seqnum) +
      gt_encseq_seqlength(contigs_writer->reads, seqnum) - nofchars;
  for (i = 0; i < nofchars; i++, pos++)
  {
    char *c;
    GT_GETNEXTFREEINARRAY(c, &contigs_writer->contig, char,
        GT_CONTIGS_WRITER_CONTIG_INC);
    *c = gt_encseq_get_encoded_char_nospecial(contigs_writer->reads, pos,
        GT_READMODE_FORWARD)["acgt"];
  }
  contigs_writer->contigdepth++;
  if (contigs_writer->showpaths)
  {
    gt_str_append_cstr(contigs_writer->path_desc, "-(");
    gt_str_append_ulong(contigs_writer->path_desc, nofchars);
    gt_str_append_cstr(contigs_writer->path_desc, ")->");
    gt_str_append_ulong(contigs_writer->path_desc,
        GT_CONTIGS_WRITER_READNUM(seqnum, contigs_writer->nofseqs));
    gt_str_append_char(contigs_writer->path_desc,
        GT_CONTIGS_WRITER_LETTER(seqnum, contigs_writer->nofseqs));
  }
  else
  {
    contigs_writer->lastseqnum = seqnum;
  }
}

void gt_contigs_writer_start(GtContigsWriter *contigs_writer,
    unsigned long seqnum)
{
  unsigned long pos, nofchars, i;
  gt_assert(contigs_writer != NULL);
  pos = gt_encseq_seqstartpos(contigs_writer->reads, seqnum);
  nofchars = gt_encseq_seqlength(contigs_writer->reads, seqnum);
  for (i = 0; i < nofchars; i++, pos++)
  {
    char *c;
    GT_GETNEXTFREEINARRAY(c, &contigs_writer->contig, char,
        GT_CONTIGS_WRITER_CONTIG_INC);
    *c = gt_encseq_get_encoded_char_nospecial(contigs_writer->reads, pos,
        GT_READMODE_FORWARD)["acgt"];
  }
  contigs_writer->contigdepth++;
  gt_str_append_ulong(contigs_writer->path_desc,
      GT_CONTIGS_WRITER_READNUM(seqnum, contigs_writer->nofseqs));
  gt_str_append_char(contigs_writer->path_desc,
      GT_CONTIGS_WRITER_LETTER(seqnum, contigs_writer->nofseqs));
}

void gt_contigs_writer_show_stats(GtContigsWriter *contigs_writer,
    GtLogger *logger)
{
  gt_assert(contigs_writer != NULL);
  if (contigs_writer->contignum > 0)
    gt_assembly_stats_calculator_show(contigs_writer->asc, logger);
  else
    gt_logger_log(logger, "no contigs respect the given cutoff parameters");
}
genometools-1.5.1/src/match/rdj-contigs-writer.h000066400000000000000000000031441211610345200216370ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_CONTIGS_WRITER_H
#define RDJ_CONTIGS_WRITER_H

#include "core/encseq.h"
#include "core/file.h"
#include "core/logger.h"

typedef struct GtContigsWriter GtContigsWriter;

GtContigsWriter *gt_contigs_writer_new(const GtEncseq *reads, GtFile *outfp,
    bool showpaths);
void gt_contigs_writer_delete(GtContigsWriter *contigs_writer);

void gt_contigs_writer_start(GtContigsWriter *contigs_writer,
    unsigned long seqnum);

void gt_contigs_writer_append(GtContigsWriter *contigs_writer,
    unsigned long seqnum, unsigned long nofchars);

void gt_contigs_writer_write(GtContigsWriter *contigs_writer);

void gt_contigs_writer_abort(GtContigsWriter *contigs_writer);

void gt_contigs_writer_show_stats(GtContigsWriter *contigs_writer,
    GtLogger *logger);

#endif
genometools-1.5.1/src/match/rdj-ensure-output.h000066400000000000000000000100061211610345200215110ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_ENSURE_OUTPUT_H
#define RDJ_ENSURE_OUTPUT_H

#include 
#include "core/ensure.h"
#include "core/fa.h"
#include "core/xansi_api.h"

/* defines macros to make easier to test output to a temporary file */

#define GT_ENSURE_OUTPUT_DECLARE(MAXOUTSIZE)                               \
        GtStr *fnamestr;                                                   \
        char *fname;                                                       \
        FILE *handle;                                                      \
        GtFile *outfp;                                                     \
        size_t outsize;                                                    \
        char buffer[MAXOUTSIZE]

#define GT_ENSURE_OUTPUT_GETFILE(GTFILE)                                   \
        fnamestr = gt_str_new();                                           \
        handle = gt_xtmpfp(fnamestr);                                      \
        (GTFILE) = gt_file_new_from_fileptr(handle)

#define GT_ENSURE_OUTPUT_TESTFILE(GTFILE, EXPOUT)                          \
        (void)fflush(handle);                                              \
        gt_file_xrewind(GTFILE);                                           \
        outsize = (size_t)gt_file_xread((GTFILE), buffer, strlen(EXPOUT)); \
        gt_ensure(had_err, outsize == strlen(EXPOUT));                     \
        gt_ensure(had_err, memcmp((EXPOUT), buffer, outsize) == 0);        \
        if (had_err != 0)                                                  \
        {                                                                  \
          fprintf(stderr, "\nExpected file content: \n%s\n",               \
                  EXPOUT);                                                 \
          fprintf(stderr, "\nFile content actually read "                  \
                         "(up to %lu bytes):\n%s\n",                       \
               (unsigned long) strlen(EXPOUT), buffer);                    \
        }

#define GT_ENSURE_OUTPUT_RMFILE(GTFILE)                                    \
        gt_file_delete(GTFILE);                                            \
        fname = gt_str_get(fnamestr);                                      \
        gt_xremove(fname);                                                 \
        gt_str_delete(fnamestr)

#define GT_ENSURE_OUTPUT(FNCALL, EXPOUT)                                   \
        GT_ENSURE_OUTPUT_GETFILE(outfp);                                   \
        FNCALL;                                                            \
        GT_ENSURE_OUTPUT_TESTFILE(outfp, EXPOUT);                          \
        GT_ENSURE_OUTPUT_RMFILE(outfp)

/*
  Compares the output of the function call FNCALL
  to the char* EXPOUT (size and content).

  Usage: GT_ENSURE_OUTPUT_DECLARE in the declarations,
         then GT_ENSURE_OUTPUT to run the test (also multiple times);
         FNCALL should print something to the GtFile* outfp
         or to the FILE* handle

  Assumes:
  - int had_err is the return value variable of the unit test method
  - GtError *err (required by the gt_ensure macro)
  - reserved variables: fnamestr, fname, handle, outfp, outsize, buffer
*/

#endif
genometools-1.5.1/src/match/rdj-errfind.c000066400000000000000000000215211211610345200203020ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/fa.h"
#include "core/unused_api.h"
#include "core/undef_api.h"
#include "core/log.h"
#include "match/rdj-twobitenc-editor.h"
#include "match/rdj-errfind.h"

/*#define RDJ_ERRFIND_DEBUG*/

typedef struct {
  void *stack;

  GtError *err;

  const GtEncseq *encseq;
  unsigned int alphasize;
  unsigned int currentchar;

  /* parameters */
  unsigned long k; /* k-mer length */
  unsigned long c; /* min count for k-mer to be trusted */

  unsigned long *kpositions;
  unsigned long *count;
  bool seprange;

  unsigned long debug_value;
  bool quiet;

  unsigned long firstmirrorpos;
  unsigned long totallength;

  GtTwobitencEditor *editor;

  /* statistics */
  unsigned long ncorrections;
} GtBUstate_errfind;

typedef struct { /* empty */ } GtBUinfo_errfind;

static void initBUinfo_errfind(GT_UNUSED GtBUinfo_errfind *buinfo,
    GT_UNUSED GtBUstate_errfind *state)
{
  /* nothing to do */
}

static void freeBUinfo_errfind(GT_UNUSED GtBUinfo_errfind *buinfo,
    GT_UNUSED GtBUstate_errfind *state)
{
  /* nothing to do */
}

static inline void gt_errfind_reset(GtBUstate_errfind *state)
{
  unsigned int i;
  state->currentchar = 0;
  for (i = 0; i < state->alphasize; i++)
    state->count[i] = 0;
  state->seprange = false;
}

static inline void gt_errfind_process_kmer(unsigned long leafnumber,
    GtBUstate_errfind *state)
{
  unsigned long current_count = ++state->count[state->currentchar];
  if (current_count <= state->c)
  {
    gt_assert(leafnumber + state->k - 1 <
        gt_encseq_total_length(state->encseq));
    state->kpositions[state->currentchar * state->c + current_count - 1] =
      leafnumber + state->k - 1;
  }
}

#define RDJ_ERRFIND_KMINUSITHCHAR(I) \
  ((leafnumber + state->k - I) < gt_encseq_total_length(state->encseq)) \
    ? gt_encseq_get_decoded_char(state->encseq, leafnumber +  state->k - I, \
        GT_READMODE_FORWARD) \
    : '-'
#define RDJ_ERRFIND_SHOW_KMER \
  gt_log_log("ln: %lu; fd: %lu; k-mer: %c...%c%c%c%c%c%c%c%c%c%c%c(%c)",\
    leafnumber, fatherdepth, RDJ_ERRFIND_KMINUSITHCHAR(state->k),\
    RDJ_ERRFIND_KMINUSITHCHAR(11), RDJ_ERRFIND_KMINUSITHCHAR(10),\
    RDJ_ERRFIND_KMINUSITHCHAR(9), RDJ_ERRFIND_KMINUSITHCHAR(8),\
    RDJ_ERRFIND_KMINUSITHCHAR(7), RDJ_ERRFIND_KMINUSITHCHAR(6),\
    RDJ_ERRFIND_KMINUSITHCHAR(5), RDJ_ERRFIND_KMINUSITHCHAR(4),\
    RDJ_ERRFIND_KMINUSITHCHAR(3), RDJ_ERRFIND_KMINUSITHCHAR(2),\
    RDJ_ERRFIND_KMINUSITHCHAR(1), RDJ_ERRFIND_KMINUSITHCHAR(0));

#define RDJ_ERRFIND_IS_SEPRANGE(ENCSEQ, POS)\
  ((POS) == gt_encseq_total_length(ENCSEQ) || \
   gt_encseq_position_is_separator((ENCSEQ), (POS), GT_READMODE_FORWARD))

GT_UNUSED
static inline unsigned long gt_errfind_sfxlength(const GtEncseq *encseq,
    unsigned long pos)
{
  unsigned long seqnum = gt_encseq_seqnum(encseq, pos);
  unsigned long seqstartpos = gt_encseq_seqstartpos(encseq, seqnum);
  unsigned long seqlength = gt_encseq_seqlength(encseq, seqnum);
  return seqstartpos + (seqlength - 1) - pos;
}

static int processleafedge_errfind(GT_UNUSED bool firstsucc,
    unsigned long fatherdepth,
    GT_UNUSED GtBUinfo_errfind *father, unsigned long leafnumber,
    GtBUstate_errfind *state, GT_UNUSED GtError *err)
{
#ifdef RDJ_ERRFIND_DEBUG
  if (leafnumber == state->debug_value)
    gt_log_enable();
  RDJ_ERRFIND_SHOW_KMER;
#endif
  if (fatherdepth < state->k - 1)
  {
    gt_errfind_reset(state);
  }
  else if (!state->seprange)
  {
    if (fatherdepth == state->k - 1 &&
        RDJ_ERRFIND_IS_SEPRANGE(state->encseq, leafnumber + fatherdepth))
    {
      state->seprange = true;
    }
    if (!state->seprange && state->currentchar < state->alphasize)
    {
      gt_errfind_process_kmer(leafnumber, state);
      if (fatherdepth == state->k - 1)
      {
        state->currentchar++;
#ifdef RDJ_ERRFIND_DEBUG
        gt_log_log("currentchar incremented, now is %u", state->currentchar);
#endif
      }
    }
  }
  return 0;
}

static int processbranchingedge_errfind(GT_UNUSED bool firstsucc,
    GT_UNUSED unsigned long fatherdepth,
    GT_UNUSED GtBUinfo_errfind *father, GT_UNUSED unsigned long sondepth,
    GT_UNUSED unsigned long sonwidth,
    GT_UNUSED GtBUinfo_errfind *son, GT_UNUSED GtBUstate_errfind *state,
    GT_UNUSED GtError *err)
{
  if (fatherdepth < state->k - 1)
    gt_errfind_reset(state);
  else if (fatherdepth == state->k - 1)
  {
      state->currentchar++;
#ifdef RDJ_ERRFIND_DEBUG
      gt_log_log("currentchar incremented, now is %u", state->currentchar);
#endif
  }
  return 0;
}

static inline bool gt_errfind_are_all_trusted(const GtBUstate_errfind *state)
{
  unsigned int cnum;
  bool alltrusted = true;
  for (cnum = 0; cnum < state->alphasize && alltrusted; cnum++)
    if (state->count[cnum] < state->c)
      alltrusted = false;
#ifdef RDJ_ERRFIND_DEBUG
  for (cnum = 0; cnum < state->alphasize; cnum++)
    gt_log_log("cnum %u count: %lu", cnum, state->count[cnum]);
#endif
  return alltrusted;
}

static inline GtUchar gt_errfind_trusted_char(const GtBUstate_errfind *state)
{
  unsigned int cnum;
  GtUchar trusted_char = (GtUchar)GT_UNDEF_UCHAR;
  unsigned long trusted_count = 0;
  for (cnum = 0; cnum < state->alphasize &&
      trusted_char == (GtUchar)GT_UNDEF_UCHAR; cnum++)
  {
    if (state->count[cnum] >= state->c && state->count[cnum] > trusted_count)
    {
      trusted_char = gt_encseq_get_encoded_char_nospecial(state->encseq,
         state->kpositions[cnum * state->c], GT_READMODE_FORWARD);
#ifdef RDJ_ERRFIND_DEBUG
      gt_log_log("trusted_char: %c (cnum: %u), count: %lu, pos: %lu",
          "acgt"[trusted_char], cnum, state->count[cnum],
          state->kpositions[cnum * state->c]);
#endif
    }
  }
  return trusted_char;
}

static int processlcpinterval_errfind(unsigned long lcp,
    GT_UNUSED GtBUinfo_errfind *info, GtBUstate_errfind *state,
    GT_UNUSED GtError *err)
{
  if (lcp == state->k - 1 && !gt_errfind_are_all_trusted(state))
  {
    GtUchar trusted_char = gt_errfind_trusted_char(state);
    if (trusted_char != (GtUchar)GT_UNDEF_UCHAR)
    {
      unsigned int cnum;
      for (cnum = 0; cnum < state->alphasize && state->count[cnum] > 0; cnum++)
      {
        if (state->count[cnum] < state->c)
        {
          unsigned long i;
          for (i = 0; i < state->count[cnum]; i++)
          {
            unsigned long pos = state->kpositions[cnum * state->c + i];
            GtUchar newchar = trusted_char;
            if (pos >= state->firstmirrorpos)
            {
              pos = state->totallength - 1UL - pos;
              newchar = (GtUchar)3 - newchar;
            }
            if (state->editor != NULL)
            {
#ifdef RDJ_ERRFIND_DEBUG
              printf("%lu:%u\n", pos, (unsigned int)newchar);
#endif
              gt_twobitenc_editor_edit(state->editor, pos, newchar);
            }
          }
        }
      }
    }
  }
  return 0;
}

#include "match/esa-bottomup-errfind.inc"

int gt_errfind(Sequentialsuffixarrayreader *ssar, const GtEncseq *encseq,
    unsigned long k, unsigned long c, unsigned long debug_value,
    bool edit_twobitencoding, const char *indexname, GtError *err)
{
  GtBUstate_errfind *state;
  int had_err = 0;

  state = gt_malloc(sizeof (*state));
  state->alphasize = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
  state->kpositions = gt_malloc(sizeof (unsigned long) * state->alphasize * c);
  state->count = gt_malloc(sizeof (unsigned long) * state->alphasize);
  state->encseq = encseq;
  state->totallength = gt_encseq_total_length(encseq);
  state->firstmirrorpos = state->totallength;
  if (gt_encseq_is_mirrored(encseq))
    state->firstmirrorpos >>= 1;

  state->editor = NULL;
  if (edit_twobitencoding)
  {
    state->editor = gt_twobitenc_editor_new(encseq, indexname, err);
    if (state->editor == NULL)
      had_err = -1;
  }
  state->k = k;
  state->c = c;
  state->debug_value = debug_value;
  state->quiet = (state->debug_value == GT_UNDEF_ULONG ? false : true);
  gt_errfind_reset(state);

  had_err = gt_esa_bottomup_errfind(ssar, state, err);

  if (state->editor != NULL)
  {
    gt_twobitenc_editor_delete(state->editor);
  }

  gt_free(state->kpositions);
  gt_free(state->count);
  gt_free(state);
  return had_err;
}
genometools-1.5.1/src/match/rdj-errfind.h000066400000000000000000000022651211610345200203130ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_ERRFIND_H
#define RDJ_ERRFIND_H

#include "core/error_api.h"
#include "core/encseq.h"
#include "match/esa-seqread.h"

int gt_errfind(Sequentialsuffixarrayreader *ssar, const GtEncseq *encseq,
    unsigned long k, unsigned long c, unsigned long debug_value,
    bool edit_twobitencoding, const char *indexname, GtError *err);

#endif
genometools-1.5.1/src/match/rdj-filesuf-def.h000066400000000000000000000055361211610345200210570ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_FILESUF_DEF_H
#define RDJ_FILESUF_DEF_H

/*
 * Filename suffices relevant to Readjoiner are defined here
 *
 */

/* -- main output -- */

#define GT_READJOINER_SUFFIX_SPMLIST           ".spm"
#define GT_READJOINER_SUFFIX_CONTIG_PATHS      ".paths"
#define GT_READJOINER_SUFFIX_CONTIGS           ".contigs.fas"

/* -- prefilter -- */

#define GT_READJOINER_SUFFIX_PREFILTERED_FAS   ".pf.fas"
#define GT_READJOINER_SUFFIX_READSCOPYNUM      ".rcn"

/* -- test / debug / development output -- */

#define GT_READJOINER_SUFFIX_CNTLIST           ".cnt"
#define GT_READJOINER_SUFFIX_SPMCOUNTS         ".nofspm"
#define GT_READJOINER_SUFFIX_SPMCOUNTS_DISTRI  ".nofspm.distri"
#define GT_READJOINER_SUFFIX_ELEN_DISTRI       ".elen.distri"
#define GT_READJOINER_SUFFIX_SEPPOS            ".sep"
#define GT_READJOINER_SUFFIX_TWOBIT            ".2bit"
#define GT_READJOINER_SUFFIX_SEQNUMS           ".seqnums"
#define GT_READJOINER_SUFFIX_WSIZE_DISTRI      ".wsize.distri"

/* string graph: */

/* before transitive reduction (u=unreduced) */
#define GT_READJOINER_SUFFIX_U_SG              ".u.sg"
#define GT_READJOINER_SUFFIX_U_SG_DOT          ".u.dot"
#define GT_READJOINER_SUFFIX_U_SG_SPMLIST      ".u.sg.spm"
#define GT_READJOINER_SUFFIX_U_SG_ADJLIST      ".u.adj"

/* without submax edges reduction (m=multigraph) */
#define GT_READJOINER_SUFFIX_M_SG              ".m.sg"
#define GT_READJOINER_SUFFIX_M_SG_DOT          ".m.dot"
#define GT_READJOINER_SUFFIX_M_SG_SPMLIST      ".m.sg.spm"
#define GT_READJOINER_SUFFIX_M_SG_ADJLIST      ".m.adj"

/* reduced graph */
#define GT_READJOINER_SUFFIX_SG                ".sg"
#define GT_READJOINER_SUFFIX_SG_DOT            ".dot"
#define GT_READJOINER_SUFFIX_SG_SPMLIST        ".sg.spm"
#define GT_READJOINER_SUFFIX_SG_ADJLIST        ".adj"

/* after error correction */
#define GT_READJOINER_SUFFIX_C_SG              ".c.sg"
#define GT_READJOINER_SUFFIX_C_SG_DOT          ".c.dot"
#define GT_READJOINER_SUFFIX_C_SG_SPMLIST      ".c.sg.spm"
#define GT_READJOINER_SUFFIX_C_SG_ADJLIST      ".c.adj"

#endif
genometools-1.5.1/src/match/rdj-ovlfind-bf.c000066400000000000000000000253651211610345200207110ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include  /* memcmp */
#include "core/ma.h"
#include "core/assert_api.h"
#include "core/minmax.h"
#include "match/rdj-ovlfind-bf.h"
/* for unit test: */
#include "core/array_api.h"
#include "core/ensure.h"

static inline bool contfind_bf(const char *a, unsigned long alen,
    const char *b, unsigned long blen)
{
  unsigned long offset;
  gt_assert(alen < blen);
  for (offset = 0; offset <= blen-alen; offset++)
    if (memcmp(a, b+offset, (size_t)alen) == 0) return true;
  return false;
}

static inline void spmfind_bf(const char *a, unsigned long alen,
    const char *b, unsigned long blen, unsigned long minlen,
    bool find_nonmaximal, bool self_comparison,
    void(*proc)(unsigned long, bool, void*), bool direction,
    void* procdata)
{
  unsigned long len, from;
  from = MIN(alen, blen);
  if (self_comparison)
    from -= 1;
  for (len = from; len >= minlen; len--)
    if (memcmp(a+alen-len, b, (size_t)len) == 0)
    {
      proc(len, direction, procdata);
      if (!find_nonmaximal) break;
    }
}

GtContfind gt_ovlfind_bf(const char *u, unsigned long u_length,
    const char *v, unsigned long v_length, GtOvlfindMode m,
    unsigned long min_length, bool find_nonmaximal,
    void(*spmproc) (unsigned long /* overlap length */,
        bool /* true if suffix of u == prefix of v;
            false if prefix of u == suffix of v */,
        void* /* spmprocdata */), void* spmprocdata)
{
  GtContfind retval = GT_CONTFIND_OFF;
  bool self_comparison;

  gt_assert(u != NULL);
  gt_assert(u_length > 0);
  self_comparison = (v == NULL);
  gt_assert(self_comparison || v_length > 0);
  gt_assert(!self_comparison || m == GT_OVLFIND_SPM || m == GT_OVLFIND_ALL);

  if (self_comparison && m == GT_OVLFIND_ALL)
    retval = GT_CONTFIND_EQ;
  if (m != GT_OVLFIND_SPM && !self_comparison)
  {
    if (u_length == v_length)
      retval = memcmp(u, v, (size_t)u_length) == 0
               ? GT_CONTFIND_EQ : GT_CONTFIND_NO;
    else if (u_length < v_length)
      retval = contfind_bf(u, u_length, v, v_length)
               ? GT_CONTFIND_U : GT_CONTFIND_NO;
    else /* u_length > v_length */
      retval = contfind_bf(v, v_length, u, u_length)
               ? GT_CONTFIND_V : GT_CONTFIND_NO;
    if (m == GT_OVLFIND_PROPER_SPM && retval != GT_CONTFIND_NO)
      return retval;
  }
  if (m != GT_OVLFIND_CNT)
  {
    if (self_comparison)
    {
      spmfind_bf(u, u_length, u, u_length, min_length, find_nonmaximal,
                 self_comparison, spmproc, true, spmprocdata);
    }
    else
    {
      spmfind_bf(u, u_length, v, v_length, min_length, find_nonmaximal,
                 self_comparison, spmproc, true, spmprocdata);
      spmfind_bf(v, v_length, u, u_length, min_length, find_nonmaximal,
                 self_comparison, spmproc, false, spmprocdata);
    }
  }
  return retval;
}

/*--------------------------   UNIT TEST   --------------------------*/

struct GtOvlfindBfResult { bool u_suffix; unsigned long length; };

static
void ovlfind_bf_test_save(unsigned long length, bool u_suffix, void *a)
{
  struct GtOvlfindBfResult r = {u_suffix, length};
  gt_array_add((GtArray*)a,r);
}

#define GT_OVLFIND_BF_EXPECT_RESULT(N,U_SUF,LEN)        \
        if (!had_err) r = gt_array_get(a, (N));         \
        gt_ensure(had_err, r->u_suffix == (U_SUF));        \
        gt_ensure(had_err, r->length == (LEN))

int gt_ovlfind_bf_unit_test(GtError *err)
{
  int had_err = 0;
  GtArray *a;
  struct GtOvlfindBfResult *r;
  GtContfind retval;

  /*@i1@*/ gt_error_check(err);
  a = gt_array_new(sizeof (struct GtOvlfindBfResult));

  /* u suffix == v prefix */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("aacgcacctg", 10UL, "acctgatttc", 10UL,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_NO);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_BF_EXPECT_RESULT(0UL, true, 5UL);
  }
  /* v suffix == u prefix */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("atccgtgacgtg", 12UL, "aagaagaatccg", 12UL,
                           GT_OVLFIND_ALL, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_NO);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_BF_EXPECT_RESULT(0UL, false, 5UL);
  }
  /* no overlap */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("aac", 3UL, "tgc", 3UL,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_NO);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
  }
  /* u suffix of v */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("acagc", 5UL, "gtacagc", 7UL,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    GT_OVLFIND_BF_EXPECT_RESULT(0UL, false, 5UL);

    gt_array_reset(a);
    retval = gt_ovlfind_bf("acagc", 5UL, "gtacagc", 7UL,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_U);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_array_reset(a);

    retval = gt_ovlfind_bf("acagc", 5UL, "gtacagc", 7UL,
                           GT_OVLFIND_CNT, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_ensure(had_err, retval == GT_CONTFIND_U);

    gt_array_reset(a);
    retval = gt_ovlfind_bf("acagc", 5UL, "gtacagc", 7UL,
                           GT_OVLFIND_ALL, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    gt_ensure(had_err, retval == GT_CONTFIND_U);
    GT_OVLFIND_BF_EXPECT_RESULT(0UL, false, 5UL);
  }
  /* v suffix of u */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("gtacagc", 7UL, "acagc", 5UL,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    GT_OVLFIND_BF_EXPECT_RESULT(0UL, true, 5UL);

    gt_array_reset(a);
    retval = gt_ovlfind_bf("gtacagc", 7UL, "acagc", 5UL,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_V);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
  }
  /* u prefix of v */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("ctat", 4UL, "ctatacagg", 9UL,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_BF_EXPECT_RESULT(0UL, true, 4UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);

    gt_array_reset(a);
    retval = gt_ovlfind_bf("ctat", 4UL, "ctatacagg", 9UL,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_ensure(had_err, retval == GT_CONTFIND_U);
  }
  /* v prefix of u */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("ctatacagg", 9UL, "ctat", 4UL,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_BF_EXPECT_RESULT(0UL, false, 4UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);

    gt_array_reset(a);
    retval = gt_ovlfind_bf("ctatacagg", 9UL, "ctat", 4UL,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_ensure(had_err, retval == GT_CONTFIND_V);
  }
  /* identical sequences */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("acagc", 5UL, "acagc", 5UL,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 2UL);
    GT_OVLFIND_BF_EXPECT_RESULT(0UL, true, 5UL);
    GT_OVLFIND_BF_EXPECT_RESULT(1UL, false, 5UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);

    gt_array_reset(a);
    retval = gt_ovlfind_bf("acagc", 5UL, "acagc", 5UL,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_ensure(had_err, retval == GT_CONTFIND_EQ);
  }
  /* find_nonmaximal */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("aacagtagtagt", 12UL, "agtagtagttaa", 12UL,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 2UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    GT_OVLFIND_BF_EXPECT_RESULT(0UL, true, 9UL);
    GT_OVLFIND_BF_EXPECT_RESULT(1UL, false, 2UL);

    gt_array_reset(a);
    retval = gt_ovlfind_bf("aacagtagtagt", 12UL, "agtagtagttaa", 12UL,
                           GT_OVLFIND_SPM, 1UL, true,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 5UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
  }
  /* min_length */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_bf("aggaccagtagt", 12UL, "agtagttactac", 12UL,
                           GT_OVLFIND_SPM, 1UL, true,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 2UL);

    gt_array_reset(a);
    retval = gt_ovlfind_bf("aggaccagtagt", 12UL, "agtagttactac", 12UL,
                           GT_OVLFIND_SPM, 4UL, true,
                           ovlfind_bf_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
  }
  gt_array_delete(a);
  return had_err;
}
genometools-1.5.1/src/match/rdj-ovlfind-bf.h000066400000000000000000000036061211610345200207100ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#ifndef RDJ_OVLFIND_BF_H
#define RDJ_OVLFIND_BF_H

#include "core/error_api.h"               /* GtError       */
#include "match/rdj-contfind-def.h"       /* GtContfind    */
#include "match/rdj-pairwise.h"           /* GtOvlfindMode */

/* brute force overlap finder */

/*
  known issues:
  - case sensitive (a != A)
  - no notion of wildcards (i.e. n == n)
*/

GtContfind gt_ovlfind_bf(const char *u, unsigned long u_length,
                         const char *v, /* NULL for u vs. u */
                         unsigned long v_length,
                         GtOvlfindMode m, unsigned long min_length,
                         bool find_nonmaximal,
                         void(*spmproc)
                           (unsigned long /* overlap length */,
                            bool /* true if suffix of u == prefix of v
                                    false if prefix of u == suffix of v */,
                            void* /* spmprocdata */),
                         void* spmprocdata);

int gt_ovlfind_bf_unit_test(GtError *err);

#endif
genometools-1.5.1/src/match/rdj-ovlfind-dp.c000066400000000000000000000404641211610345200207220ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/minmax.h"
#include "core/unused_api.h"
#include "core/log.h"
#include "match/rdj-ovlfind-dp.h"
/* unit test: */
#include 
#include "core/ensure.h"
#include "core/array_api.h"

typedef struct
{
  unsigned long edist, start_i, start_j;
} GtOvlfindDpCell;

/* true if u == v (approximatively) */
static inline
bool eqlfind_dp(unsigned long max_edist, GtOvlfindDpCell *mn_cell)
{
  return mn_cell->edist <= max_edist &&
         mn_cell->start_i == 0 &&
         mn_cell->start_j == 0;
}

/* true if u is approximatively contained in v */
static inline
bool u_contfind_dp(unsigned long max_edist, unsigned long n,
                  GtOvlfindDpCell **lastrow)
{
  unsigned long j;
  for (j = 0; j <= n; j++)
    if ((*lastrow)[j].edist <= max_edist &&
        (*lastrow)[j].start_i == 0)
      return true;
  return false;
}

/* true if v is approximatively contained in u */
static inline
bool v_contfind_dp(unsigned long max_edist, unsigned long m,
                  GtOvlfindDpCell **lastcol)
{
  unsigned long i;
  for (i = 0; i <= m; i++)
    if ((*lastcol)[i].edist <= max_edist &&
        (*lastcol)[i].start_j == 0)
      return true;
  return false;
}

/* find approximate suffix-prefix matches, with the suffix coming from u */
static inline void u_smpfind_dp(unsigned long min_length,
    unsigned long max_edist, bool find_submaximal,
    unsigned long m, unsigned long n, GtOvlfindDpCell **lastrow,
    void (*proc)(unsigned long, unsigned long, unsigned long, bool,
    void*), void* procdata)
{
  unsigned long j, suffix_length;

  gt_assert(m > 0);
  gt_assert(n > 0);
  gt_assert(lastrow != NULL);
  for (j = n; j >= min_length; j--)
  {
    if ((*lastrow)[j].edist <= max_edist &&
        (*lastrow)[j].start_j == 0)
    {
      suffix_length = m - (*lastrow)[j].start_i;
      if (suffix_length >= min_length)
        proc(suffix_length, j /* prefix length */,
             (*lastrow)[j].edist, true, procdata);
      if (!find_submaximal) break;
    }
  }
}

/* find approximate suffix-prefix matches, with the suffix coming from v */
static inline
void v_smpfind_dp(unsigned long min_length, unsigned long max_edist,
                  bool find_submaximal, unsigned long m,
                  unsigned long n, GtOvlfindDpCell **lastcol,
                  void (*proc)(unsigned long, unsigned long,
                               unsigned long, bool, void*),
                  void* procdata)
{
  unsigned long i, prefix_length;

  gt_assert(m > 0);
  gt_assert(n > 0);
  gt_assert(lastcol != NULL);
  for (i = m; i >= min_length; i--)
  {
    if ((*lastcol)[i].edist <= max_edist &&
        (*lastcol)[i].start_i == 0)
    {
      prefix_length = n - (*lastcol)[i].start_j;
      if (prefix_length >= min_length)
        proc(i /* suffix length */, prefix_length,
             (*lastcol)[i].edist, false, procdata);
      if (!find_submaximal) break;
    }
  }
}

static inline
void run_dp(const char *u, unsigned long m, const char *v, unsigned long n,
            GtOvlfindDpCell **row, GtOvlfindDpCell **col)
{
  unsigned long i, j, cost_r, cost_d, cost_i;
  GtOvlfindDpCell cell_r, next_cell_r;

  /* first row */
  for (i = 0; i <= m; i++)
  {
    (*col)[i].start_i = i;
    (*col)[i].start_j = 0;
    (*col)[i].edist = 0;
  }
  (*row)[0] = (*col)[m];
  /* following (*row)s */
  for (j = 1UL; j <= n; j++)
  {
    (*col)[0].start_j = j;
    cell_r.start_i = 0;
    cell_r.start_j = j - 1;
    cell_r.edist = 0;
    for (i = 1UL; i <= m; i++)
    {
      next_cell_r = (*col)[i];
      cost_i = (*col)[i].edist + 1; /* cost(e --> v[j]) */
      cost_d = (*col)[i - 1].edist + 1; /* cost(u[i] --> e)*/
      cost_r = cell_r.edist + ((u[i - 1] == v[j - 1]) ? 0 : 1);
      if (cost_r < cost_i && cost_r < cost_d)
      {
        /* replacement */
        (*col)[i].start_i = cell_r.start_i;
        (*col)[i].start_j = cell_r.start_j;
        (*col)[i].edist = cost_r;
      }
      else if (cost_i < cost_d)
      {
        /* insertion */
        /* start_i and start_j already correct */
        (*col)[i].edist = cost_i;
      }
      else
      {
        /* deletion */
        (*col)[i].start_i = (*col)[i-1].start_i;
        (*col)[i].start_j = (*col)[i-1].start_j;
        (*col)[i].edist = cost_d;
      }
      cell_r = next_cell_r;
    }
    (*row)[j] = (*col)[m];
  }
}

GT_UNUSED static void print_row_and_col(GtOvlfindDpCell *row, unsigned long m,
    GtOvlfindDpCell *col, unsigned long n)
{
  unsigned long i, j;

  for (i = 0; i <= m; i++)
    gt_log_log("col[%lu]=((%lu,%lu),%lu)\n", i, col[i].start_i,
        col[i].start_j, col[i].edist);

  for (j = 0; j <= n; j++)
    gt_log_log("row[%lu]=((%lu,%lu),%lu)\n", j, row[j].start_i,
        row[j].start_j, row[j].edist);
}

GtContfind gt_ovlfind_dp(const char *u, unsigned long m,
                         const char *v, unsigned long n,
                         double max_error, GtOvlfindMode mode,
                         unsigned long min_length, bool find_submaximal,
                         void (*smpproc)
                           (unsigned long /* length on u */,
                            unsigned long /* length on v */,
                            unsigned long /* unit edit distance */,
                            bool /* true if suffix comes from u,
                                    false if suffix comes from v */,
                            void* /* procdata */),
                         void* smpprocdata)
{
  GtOvlfindDpCell *row, *col;
  unsigned long max_edist;
  GtContfind retval = GT_CONTFIND_OFF;
  bool self_comparison;

  gt_assert(u != NULL);
  gt_assert(m > 0);
  self_comparison = (v == NULL);
  gt_assert(self_comparison || n > 0);
  gt_assert(!self_comparison || mode == GT_OVLFIND_SPM ||
      mode == GT_OVLFIND_ALL);

  if (self_comparison)
  {
    max_edist = (unsigned long)(max_error * m);
    row = gt_malloc(sizeof (GtOvlfindDpCell) * (m + 1));
    col = gt_malloc(sizeof (GtOvlfindDpCell) * (m + 1));

    run_dp(u, m, u, m, &row, &col);
  }
  else
  {
    max_edist = (unsigned long)(max_error * MAX(m,n));
    row = gt_malloc(sizeof (GtOvlfindDpCell) * (n + 1));
    col = gt_malloc(sizeof (GtOvlfindDpCell) * (m + 1));

    run_dp(u, m, v, n, &row, &col);
    /* decomment to show row and col to debug log: */
    /* print_row_and_col(row, m, col, n); */
  }

  if (self_comparison && mode == GT_OVLFIND_ALL)
    retval = GT_CONTFIND_EQ;
  if (mode != GT_OVLFIND_SPM && !self_comparison)
  {
    if (eqlfind_dp(max_edist, row+n))
      retval = GT_CONTFIND_EQ;
    else if (v_contfind_dp(max_edist, m, &col))
      retval = GT_CONTFIND_V;
    else if (u_contfind_dp(max_edist, n, &row))
      retval = GT_CONTFIND_U;
    else
      retval = GT_CONTFIND_NO;
  }
  if (mode == GT_OVLFIND_SPM || mode == GT_OVLFIND_ALL ||
      (mode == GT_OVLFIND_PROPER_SPM && retval == GT_CONTFIND_NO))
  {
    if (self_comparison)
    {
      u_smpfind_dp(min_length, max_edist, find_submaximal, m, m-1, &row,
                   smpproc, smpprocdata);
    }
    else
    {
      u_smpfind_dp(min_length, max_edist, find_submaximal, m, n, &row,
                   smpproc, smpprocdata);
      v_smpfind_dp(min_length, max_edist, find_submaximal, m, n, &col,
                   smpproc, smpprocdata);
    }
  }

  gt_free(row);
  gt_free(col);
  return retval;
}

/*--------------------------   UNIT TEST   --------------------------*/

struct GtOvlfindDpResult { unsigned long ulen, vlen, edist; bool dir; };

static
void ovlfind_dp_test_save(unsigned long ulen, unsigned long vlen,
                          unsigned long edist, bool dir, void *a)
{
  struct GtOvlfindDpResult r = {ulen, vlen, edist, dir};
  gt_array_add((GtArray*)a,r);
}

#define GT_OVLFIND_DP_EXPECT_RESULT(N,ULEN,VLEN,EDST,DIR)        \
        if (!had_err) r = gt_array_get(a, (N));                  \
        gt_ensure(had_err, r->ulen == (ULEN));                      \
        gt_ensure(had_err, r->vlen == (VLEN));                      \
        gt_ensure(had_err, r->edist == (EDST));                     \
        gt_ensure(had_err, r->dir == (DIR))

int gt_ovlfind_dp_unit_test(GtError *err)
{
  int had_err = 0;
  GtArray *a;
  struct GtOvlfindDpResult *r;
  GtContfind retval;

  /*@i1@*/ gt_error_check(err);
  a = gt_array_new(sizeof (struct GtOvlfindDpResult));

  /* u suffix == v prefix */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_dp("aacgcacctg", 10UL, "acctgatttc", 10UL, 0.0,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_NO);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_DP_EXPECT_RESULT(0UL, 5UL, 5UL, 0UL, true);
  }
  /* v suffix == u prefix */
  if (!had_err)
  {
    gt_array_reset(a);

    retval = gt_ovlfind_dp("atccgtgacgtg", 12UL, "aagaagaatccg", 12UL, 0.0,
                           GT_OVLFIND_ALL, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_NO);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_DP_EXPECT_RESULT(0UL, 5UL, 5UL, 0UL, false);
  }
  /* no overlap */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_dp("aac", 3UL, "tgc", 3UL, 0.0,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_NO);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
  }
  /* u suffix of v */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_dp("acagc", 5UL, "gtacagc", 7UL, 0.0,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_DP_EXPECT_RESULT(0UL, 5UL, 5UL, 0UL, false);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("acagc", 5UL, "gtacagc", 7UL, 0.0,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_U);
    gt_ensure(had_err, gt_array_size(a) == 0UL);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("acagc", 5UL, "gtacagc", 7UL, 0.0,
                           GT_OVLFIND_CNT, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_ensure(had_err, retval == GT_CONTFIND_U);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("acagc", 5UL, "gtacagc", 7UL, 0.0,
                           GT_OVLFIND_ALL, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    gt_ensure(had_err, retval == GT_CONTFIND_U);
    GT_OVLFIND_DP_EXPECT_RESULT(0UL, 5UL, 5UL, 0UL, false);
  }
  /* v suffix of u */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_dp("gtacagc", 7UL, "acagc", 5UL, 0.0,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_DP_EXPECT_RESULT(0UL, 5UL, 5UL, 0UL, true);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("gtacagc", 7UL, "acagc", 5UL, 0.0,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_V);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
  }
  /* u prefix of v */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_dp("ctat", 4UL, "ctatacagg", 9UL, 0.0,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_DP_EXPECT_RESULT(0UL, 4UL, 4UL, 0UL, true);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("ctat", 4UL, "ctatacagg", 9UL, 0.0,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_U);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
  }
  /* v prefix of u */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_dp("ctatacagg", 9UL, "ctat", 4UL, 0.0,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_DP_EXPECT_RESULT(0UL, 4UL, 4UL, 0UL, false);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("ctatacagg", 9UL, "ctat", 4UL, 0.0,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_V);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
  }
  /* identical sequences */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_dp("acagc", 5UL, "acagc", 5UL, 0.0,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 2UL);
    GT_OVLFIND_DP_EXPECT_RESULT(0UL, 5UL, 5UL, 0UL, true);
    GT_OVLFIND_DP_EXPECT_RESULT(1UL, 5UL, 5UL, 0UL, false);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("acagc", 5UL, "acagc", 5UL, 0.0,
                           GT_OVLFIND_PROPER_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_ensure(had_err, retval == GT_CONTFIND_EQ);
  }
  /* find_nonmaximal */
  if (!had_err)
  {
    gt_array_reset(a);

    retval = gt_ovlfind_dp("aacagtagtagt", 12UL, "agtagtagttaa", 12UL, 0.0,
                           GT_OVLFIND_SPM, 1UL, false,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 2UL);
    GT_OVLFIND_DP_EXPECT_RESULT(0UL, 9UL, 9UL, 0UL, true);
    GT_OVLFIND_DP_EXPECT_RESULT(1UL, 2UL, 2UL, 0UL, false);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("aacagtagtagt", 12UL, "agtagtagttaa", 12UL, 0.0,
                           GT_OVLFIND_SPM, 1UL, true,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 5UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
  }
  /* min_length */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_dp("aggaccagtagt", 12UL, "agtagttactac", 12UL, 0.0,
                           GT_OVLFIND_SPM, 1UL, true,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 2UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("aggaccagtagt", 12UL, "agtagttactac", 12UL, 0.0,
                           GT_OVLFIND_SPM, 4UL, true,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
  }
  /* max_error */
  if (!had_err)
  {
    gt_array_reset(a);
    retval = gt_ovlfind_dp("gaccactagt", 10UL, "agtagttact", 10UL, 0.0,
                           GT_OVLFIND_SPM, 6UL, true,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);

    gt_array_reset(a);
    retval = gt_ovlfind_dp("gaccactagt", 10UL, "agtagttact", 10UL, 0.1,
                           GT_OVLFIND_SPM, 6UL, true,
                           ovlfind_dp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
  }
  gt_array_delete(a);
  return had_err;
}
genometools-1.5.1/src/match/rdj-ovlfind-dp.h000066400000000000000000000033571211610345200207270ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_OVLFIND_DP_H
#define RDJ_OVLFIND_DP_H

#include "core/error_api.h"               /* GtError       */
#include "match/rdj-contfind-def.h"       /* GtContfind    */
#include "match/rdj-pairwise.h"           /* GtOvlfindMode */

/* Dynamic programming based overlap finder */

/*
  known issues:
  - case sensitive (a != A)
  - no notion of wildcards (i.e. n == n)
*/

GtContfind gt_ovlfind_dp(const char *u, unsigned long m,
    const char *v /* use NULL for self-comparison of u */, unsigned long n,
    double max_error, GtOvlfindMode mode, unsigned long min_length,
    bool find_submaximal, void (*smpproc) (unsigned long /* length on u */,
    unsigned long /* length on v */, unsigned long /* unit edit distance */,
    bool /* true if suffix comes from u, false if suffix comes from v */,
    void* /* procdata */), void* smpprocdata);

int gt_ovlfind_dp_unit_test(GtError *err);

#endif
genometools-1.5.1/src/match/rdj-ovlfind-gusfield.c000066400000000000000000000277341211610345200221260ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/arraydef.h"
#include "core/assert_api.h"
#include "match/esa-seqread.h"
#include "core/encseq.h"
#include "core/progressbar.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "core/intbits.h"
#include "match/esa-splititv.h"
#include "match/rdj-revcompl-def.h"
#include "match/rdj-ovlfind-gusfield.h"

typedef struct
{
  unsigned long offset, leftbound,
                rightbound, specials_leftbound;
  bool visited;
} RdjGusfieldIndexBounds;

GT_DECLAREARRAYSTRUCT(RdjGusfieldIndexBounds);

static inline
void maximize_child_offset(RdjGusfieldIndexBounds *child,
                           const Suffixarray *sarr)
{
  unsigned long idx, lcp;
  child->offset = lcptable_get(sarr, child->leftbound+1);
  for (idx = child->leftbound+2; idx <= child->rightbound; idx++)
  {
    lcp = lcptable_get(sarr, idx);
    if (lcp < child->offset)
    {
      child->offset = lcp;
    }
  }
}

static inline
void rdj_gusfield_processleafedge(unsigned long leafnumber,
                                  const GtEncseq *encseq,
                                  unsigned long nofsequences,
                                  GtArrayGtUlong *matchlen_stacks,
                                  GtBitsequence *has_match,
                                  GtBitsequence *sspbittab,
                                  bool find_submaximal,
                                  unsigned long firstrevcompl,
                                  GtSpmproc proc,
                                  void* procdata)
{
  unsigned long prefix_seqnum, suffix_seqnum, corrected_suffix_seqnum;
  bool suffixseq_direct = true, prefixseq_direct = true;
  unsigned long *matchlen;
  unsigned long stack_pos;

  if (leafnumber == 0 || (bool)GT_ISIBITSET(sspbittab, leafnumber-1))
  {
    prefix_seqnum = gt_encseq_seqnum(encseq, leafnumber);
    if (firstrevcompl != 0)
    {
      GT_READJOINER_CORRECT_REVCOMPL(prefix_seqnum, firstrevcompl,
        nofsequences, prefixseq_direct);
    }
    for (suffix_seqnum = 0; suffix_seqnum < nofsequences; suffix_seqnum++)
    {
      if ((bool)GT_ISIBITSET(has_match, suffix_seqnum))
      {
        corrected_suffix_seqnum = suffix_seqnum;
        if (firstrevcompl != 0)
        {
          GT_READJOINER_CORRECT_REVCOMPL(corrected_suffix_seqnum,
            firstrevcompl, nofsequences, suffixseq_direct);
          if (!GT_READJOINER_IS_CORRECT_REVCOMPL_CASE(corrected_suffix_seqnum,
            suffixseq_direct, prefix_seqnum, prefixseq_direct))
            continue;
        }
        if (!find_submaximal)
        {
          matchlen = matchlen_stacks[suffix_seqnum].spaceGtUlong +
                     matchlen_stacks[suffix_seqnum].nextfreeGtUlong - 1;
          if (suffix_seqnum == prefix_seqnum)
          {
            if (*matchlen == gt_encseq_seqlength(encseq, suffix_seqnum))
            {
              /* read overlaps with whole itself */
              if (matchlen_stacks[suffix_seqnum].nextfreeGtUlong == 1UL)
              {
                /* no other overlap */
                continue;
              }
              else
              {
                matchlen = matchlen_stacks[suffix_seqnum].spaceGtUlong +
                           matchlen_stacks[suffix_seqnum].nextfreeGtUlong - 2;
              }
            }
          }
          proc(corrected_suffix_seqnum, prefix_seqnum,
               (unsigned long) *matchlen, suffixseq_direct,
               prefixseq_direct, procdata);
        }
        else /* process whole stack, not only the top */
        {
          for (stack_pos = 0;
               stack_pos < matchlen_stacks[suffix_seqnum].nextfreeGtUlong;
               stack_pos++)
          {
            matchlen = matchlen_stacks[suffix_seqnum].spaceGtUlong + stack_pos;
            if (suffix_seqnum == prefix_seqnum)
            {
              if (*matchlen == gt_encseq_seqlength(encseq, suffix_seqnum))
                /* skip ovl of read with whole itself */
                continue;
            }
            proc(corrected_suffix_seqnum, prefix_seqnum,
                 (unsigned long) *matchlen, suffixseq_direct,
                 prefixseq_direct, procdata);
          }
        }
      }
    }
  }
}

/* search terminal edges and push/pop offset value on/from spm stacks */
static inline
void processspecials(unsigned long specials_leftbound,
                     unsigned long rightbound,
                     unsigned long offset,
                     bool visited,
                     const unsigned long *suftab,
                     const GtEncseq *encseq,
                     unsigned long totallength,
                     unsigned long nofsequences,
                     GtArrayGtUlong *matchlen_stacks,
                     GtBitsequence *has_match,
                     GtBitsequence *sspbittab)
{
  unsigned long pos, leafnumber;
  unsigned long seqnum;

  gt_assert(offset>0);

  for (pos = specials_leftbound; pos <= rightbound; pos++)
  {
    leafnumber = suftab[pos];
    if ((bool)GT_ISIBITSET(sspbittab, leafnumber + offset))
    {
      seqnum = (leafnumber == totallength)
               ? nofsequences-1
               : gt_encseq_seqnum(encseq,leafnumber);
      if (!visited)
      {
        GT_SETIBIT(has_match, seqnum);
        GT_STOREINARRAY(&(matchlen_stacks[seqnum]),
                        GtUlong, 1, offset);
      }
      else
      {
        gt_assert(matchlen_stacks[seqnum].nextfreeGtUlong>0);
        matchlen_stacks[seqnum].nextfreeGtUlong--;
        if (matchlen_stacks[seqnum].nextfreeGtUlong == 0)
        {
          GT_UNSETIBIT(has_match, seqnum);
        }
      }
    }
  }
}

void gt_rdj_gusfield(Sequentialsuffixarrayreader *ssar,
    unsigned long min_length, bool find_submaximal, bool show_progressbar,
    unsigned long firstrevcompl, GtSpmproc proc, void* procdata)
{

  /* index */
  const Suffixarray *sarr;
  const GtEncseq *encseq;
  const unsigned long *suftab;
  unsigned long nofsequences;
  GtReadmode readmode;
  unsigned long totallength;
  unsigned int numofchars;
  GtBitsequence *sspbittab;

  /* splitting */
  GtArrayRdjGusfieldIndexBounds stack;
  GtArrayBoundswithchar bwci;
  RdjGusfieldIndexBounds parent, child, *parent_stack_ptr;
  unsigned long seqpos_idx;
  unsigned long idx;

  /* stacks for spm determination */
  GtArrayGtUlong *matchlen_stacks;
  GtBitsequence *has_match;

  /* progressbar */
  unsigned long long progress;

  gt_assert(min_length>0);
  gt_assert(ssar != NULL);

  sarr             = gt_suffixarraySequentialsuffixarrayreader(ssar);
  encseq           = gt_encseqSequentialsuffixarrayreader(ssar);
  suftab           = gt_suftabSequentialsuffixarrayreader(ssar);
  nofsequences     = gt_encseq_num_of_sequences(encseq);
  readmode         = gt_readmodeSequentialsuffixarrayreader(ssar);
  totallength      = gt_encseq_total_length(encseq);
  numofchars       = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));

  /* prepare sspbittab */
  GT_INITBITTAB(sspbittab, totallength+1);
  for (idx = 1UL; idx <= nofsequences - 1; idx++)
  {
    GT_SETIBIT(sspbittab, gt_encseq_seqstartpos(encseq, idx) - 1);
  }
  GT_SETIBIT(sspbittab, totallength);

  matchlen_stacks = gt_malloc(sizeof *matchlen_stacks * nofsequences);
  GT_INITBITTAB(has_match, nofsequences);

  for (idx = 0UL; idx < nofsequences; idx++)
  {
    GT_INITARRAY(&(matchlen_stacks[idx]), GtUlong);
  }

  if (show_progressbar)
  {
    progress = 0ULL;
    gt_progressbar_start(&progress, (unsigned long long)totallength);
  }

  GT_INITARRAY(&stack, RdjGusfieldIndexBounds);

  /* prepare bwci array */
  bwci.spaceBoundswithchar = gt_malloc(sizeof *bwci.spaceBoundswithchar *
                                       (numofchars + 1));
  bwci.nextfreeBoundswithchar = 0UL;
  bwci.allocatedBoundswithchar = (unsigned long) (numofchars + 1);

  /* get rid of compiler warnings */
  parent.specials_leftbound = 0UL;
  child.specials_leftbound = 0UL;

  /* start at [0,n] */
  parent.offset = 0UL;
  parent.leftbound = 0UL;
  parent.rightbound = totallength;
  parent.visited = false;
  GT_STOREINARRAY(&stack, RdjGusfieldIndexBounds, 1UL, parent);

  while (stack.nextfreeRdjGusfieldIndexBounds > 0UL)
  {
    parent_stack_ptr = stack.spaceRdjGusfieldIndexBounds +
                          stack.nextfreeRdjGusfieldIndexBounds - 1;
    parent = *parent_stack_ptr;

    if (parent.visited)
    {
      /* search terminal edges and pop spm stacks */
      if (parent.specials_leftbound <= parent.rightbound &&
           parent.offset >= min_length)
        processspecials(parent.specials_leftbound, parent.rightbound,
                        parent.offset, parent.visited, suftab, encseq,
                        totallength, nofsequences, matchlen_stacks, has_match,
                        sspbittab);
      stack.nextfreeRdjGusfieldIndexBounds--;
      continue;
    }

    parent_stack_ptr->visited = true;

    /* split interval */
    gt_lcpintervalsplitwithoutspecial(&bwci, encseq, readmode,
                                   totallength, suftab,
                                   parent.offset,
                                   parent.leftbound,
                                   parent.rightbound);

    if (bwci.nextfreeBoundswithchar > 0)
    {
      parent.specials_leftbound = bwci.spaceBoundswithchar[
                                    bwci.nextfreeBoundswithchar-1].rbound+1;
    }
    else
    {
      parent.specials_leftbound = parent.leftbound;
    }
    parent_stack_ptr->specials_leftbound = parent.specials_leftbound;

    /* search terminal edges and push on spm stacks */
    if (parent.specials_leftbound <= parent.rightbound &&
         parent.offset >= min_length)
      processspecials(parent.specials_leftbound, parent.rightbound,
                      parent.offset, parent.visited, suftab, encseq,
                      totallength, nofsequences, matchlen_stacks, has_match,
                      sspbittab);

    for (idx = bwci.nextfreeBoundswithchar; idx > 0; idx--)
    {
      child.leftbound = bwci.spaceBoundswithchar[idx-1].lbound;
      child.rightbound = bwci.spaceBoundswithchar[idx-1].rbound;
      child.visited = false;

      if (child.leftbound == child.rightbound)
      {
        if (parent.offset >= min_length)
          rdj_gusfield_processleafedge(suftab[child.leftbound], encseq,
                          nofsequences, matchlen_stacks, has_match, sspbittab,
                          find_submaximal, firstrevcompl, proc, procdata);
        if (show_progressbar) progress++;
      }
      else
      {
        maximize_child_offset(&child, sarr);
        GT_STOREINARRAY(&stack, RdjGusfieldIndexBounds, 1, child);
      }
    }

    for (seqpos_idx = parent.specials_leftbound;
         seqpos_idx <= parent.rightbound;
         seqpos_idx++)
    {
      if (parent.offset >= min_length)
        rdj_gusfield_processleafedge(suftab[seqpos_idx], encseq,
                        nofsequences, matchlen_stacks, has_match, sspbittab,
                        find_submaximal, firstrevcompl, proc, procdata);
      if (show_progressbar) progress++;
    }
  }

  GT_FREEARRAY(&stack, RdjGusfieldIndexBounds);
  GT_FREEARRAY(&bwci,Boundswithchar);

  if (show_progressbar) gt_progressbar_stop();

  for (idx = 0; idx < nofsequences; idx++)
  {
    GT_FREEARRAY(&(matchlen_stacks[idx]), GtUlong);
  }
  gt_free(has_match);
  gt_free(sspbittab);
  gt_free(matchlen_stacks);
}
genometools-1.5.1/src/match/rdj-ovlfind-gusfield.h000066400000000000000000000022221211610345200221140ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_OVLFIND_GUSFIELD_H
#define RDJ_OVLFIND_GUSFIELD_H

#include "match/rdj-spmproc.h"

void gt_rdj_gusfield(Sequentialsuffixarrayreader *ssar,
    unsigned long min_length, bool find_submaximal, bool show_progressbar,
    unsigned long firstrevcompl, GtSpmproc proc, void* procdata);

#endif
genometools-1.5.1/src/match/rdj-ovlfind-kmp.c000066400000000000000000000320671211610345200211060ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/minmax.h"
#include "core/assert_api.h"
#include "match/rdj-ovlfind-kmp.h"
/* for unit test: */
#include "core/array_api.h"
#include "core/ensure.h"

gt_kmp_t* gt_kmp_preproc(const char *seq, unsigned long seqlen)
{
  gt_kmp_t* pi;
  gt_kmp_t k;
  unsigned long q;

  pi = gt_malloc(sizeof (gt_kmp_t) * seqlen);
  pi[0] = 0;
  k = 0;
  for (q = 1UL; q < seqlen; q++)
  {
    while ((k > 0) && (seq[k] != seq[q])) k = pi[k-1];
    if (seq[k] == seq[q]) k++;
    gt_assert(k < GT_KMP_MAX);
    pi[q] = k;
  }
  return pi;
}

static inline gt_kmp_t findnextmatch(const char *a, const char *b,
    unsigned long from, unsigned long to, const gt_kmp_t *pi)
{
  gt_kmp_t q;
  unsigned long i;
  q = 0;
  for (i = from; i <= to; i++)
  {
    while ((q > 0) && (a[i] != b[q]))
      q = pi[q - 1];
    if (a[i] == b[q])
      q++;
  }
  return q;
}

static inline void spmfind_kmp(const char *a, unsigned long alen,
    const char *b, unsigned long blen, const gt_kmp_t *pi,
    unsigned long min_length, bool find_submaximal, bool self_comparison,
    void(*proc)(unsigned long, bool, void*), bool direction,
    void* procdata)
{
  gt_kmp_t q;
  unsigned long max_matchlen;
  max_matchlen = MIN(alen, blen);
  if (self_comparison)
    max_matchlen -= 1;
  q = findnextmatch(a, b, alen - max_matchlen, alen - 1, pi);
  if ((unsigned long)q >= min_length)
    proc((unsigned long)q, direction, procdata);
  if (find_submaximal)
    while (q > 0)
    {
      q = findnextmatch(a, b, alen - q + 1, alen - 1, pi);
      if ((unsigned long)q >= min_length)
        proc((unsigned long)q, direction, procdata);
    }
}

static inline bool contfind_kmp(const char *a, unsigned long alen,
    const gt_kmp_t *pi, const char *b, unsigned long blen)
{
  gt_kmp_t q;
  unsigned long i;
  q = 0;
  gt_assert(alen < blen);
  for (i = 0; i < blen; i++)
  {
    while ((q > 0) && (a[q] != b[i]))
      q = pi[q - 1];
    if (a[q] == b[i])
      q++;
    if ((unsigned long)q == alen)
      return true;
  }
  return false;
}

GtContfind gt_ovlfind_kmp(const char *u, unsigned long u_length,
    const gt_kmp_t *u_pi, const char *v, unsigned long v_length,
    const gt_kmp_t *v_pi, GtOvlfindMode m, unsigned long min_length,
    bool find_nonmaximal, void(*spmproc) (unsigned long /* overlap length */,
    bool /* true if suffix of u == prefix of v, false if prefix of
    u == suffix of v */, void* /* spmprocdata */), void* spmprocdata)
{
  GtContfind retval = GT_CONTFIND_OFF;
  bool self_comparison;

  gt_assert(u != NULL);
  gt_assert(u_length > 0);
  gt_assert(u_pi != NULL);
  self_comparison = (v == NULL);
  gt_assert(self_comparison || v_length > 0);
  gt_assert(self_comparison || v_pi != NULL);
  gt_assert(!self_comparison || m == GT_OVLFIND_SPM || m == GT_OVLFIND_ALL);

  if (self_comparison && m == GT_OVLFIND_ALL)
    retval = GT_CONTFIND_EQ;
  if (m != GT_OVLFIND_SPM && !self_comparison)
  {
    if (u_length == v_length)
      retval = memcmp(u, v, (size_t)u_length) == 0
               ? GT_CONTFIND_EQ : GT_CONTFIND_NO;
    else if (u_length < v_length)
      retval = contfind_kmp(u, u_length, u_pi, v, v_length)
               ? GT_CONTFIND_U : GT_CONTFIND_NO;
    else /* u_length > v_length */
      retval = contfind_kmp(v, v_length, v_pi, u, u_length)
               ? GT_CONTFIND_V : GT_CONTFIND_NO;
    if (m == GT_OVLFIND_PROPER_SPM && retval != GT_CONTFIND_NO)
      return retval;
  }
  if (m != GT_OVLFIND_CNT)
  {
    if (self_comparison)
    {
      spmfind_kmp(u, u_length, u, u_length, u_pi, min_length, find_nonmaximal,
                 self_comparison, spmproc, true, spmprocdata);
    }
    else
    {
      spmfind_kmp(u, u_length, v, v_length, v_pi, min_length, find_nonmaximal,
                 self_comparison, spmproc, true, spmprocdata);
      spmfind_kmp(v, v_length, u, u_length, u_pi, min_length, find_nonmaximal,
                 self_comparison, spmproc, false, spmprocdata);
    }
  }
  return retval;
}

/*--------------------------   UNIT TEST   --------------------------*/

int gt_kmp_preproc_unit_test(GtError *err)
{
  int had_err = 0;
  int i;
  gt_kmp_t *pi, expected_pi[10] = {(gt_kmp_t)0, (gt_kmp_t)0, (gt_kmp_t)1,
    (gt_kmp_t)2, (gt_kmp_t)3, (gt_kmp_t)4, (gt_kmp_t)5, (gt_kmp_t)6,
    (gt_kmp_t)0, (gt_kmp_t)1};
  pi = gt_kmp_preproc("ababababca", 10UL);
  for (i = 0; i < 10; i++)
    gt_ensure(had_err, pi[i] == expected_pi[i]);
  gt_free(pi);
  return had_err;
}

struct GtOvlfindKmpResult { bool u_suffix; unsigned long length; };

static
void ovlfind_kmp_test_save(unsigned long length, bool u_suffix, void *a)
{
  struct GtOvlfindKmpResult r = {u_suffix, length};
  gt_array_add((GtArray*)a,r);
}

#define GT_OVLFIND_KMP_EXPECT_RESULT(N,U_SUF,LEN) \
        if (!had_err) r = gt_array_get(a, (N)); \
        gt_ensure(had_err, r->u_suffix == (U_SUF)); \
        gt_ensure(had_err, r->length == (LEN))

int gt_ovlfind_kmp_unit_test(GtError *err)
{
  int had_err = 0;
  GtArray *a;
  struct GtOvlfindKmpResult *r;
  GtContfind retval;
  gt_kmp_t *u_pi, *v_pi;

  /*@i1@*/ gt_error_check(err);

  had_err = gt_kmp_preproc_unit_test(err);
  if (had_err != 0)
    return had_err;

  a = gt_array_new(sizeof (struct GtOvlfindKmpResult));

  /* u suffix == v prefix */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("aacgcacctg", 10UL);
    v_pi = gt_kmp_preproc("acctgatttc", 10UL);
    retval = gt_ovlfind_kmp("aacgcacctg", 10UL, u_pi, "acctgatttc", 10UL, v_pi,
        GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_NO);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 5UL);
    gt_free(u_pi);
    gt_free(v_pi);
  }
  /* v suffix == u prefix */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("atccgtgacgtg", 12UL);
    v_pi = gt_kmp_preproc("aagaagaatccg", 12UL);
    retval = gt_ovlfind_kmp("atccgtgacgtg", 12UL, u_pi, "aagaagaatccg", 12UL,
        v_pi, GT_OVLFIND_ALL, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_NO);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_KMP_EXPECT_RESULT(0UL, false, 5UL);
    gt_free(u_pi);
    gt_free(v_pi);
  }
  /* no overlap */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("aac", 3UL);
    v_pi = gt_kmp_preproc("tgc", 3UL);
    retval = gt_ovlfind_kmp("aac", 3UL, u_pi, "tgc", 3UL, v_pi,
        GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_NO);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_free(u_pi);
    gt_free(v_pi);
  }
  /* u suffix of v */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("acagc", 5UL);
    v_pi = gt_kmp_preproc("gtacagc", 7UL);
    retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "gtacagc", 7UL, v_pi,
        GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    GT_OVLFIND_KMP_EXPECT_RESULT(0UL, false, 5UL);

    gt_array_reset(a);
    retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "gtacagc", 7UL, v_pi,
        GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_U);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_array_reset(a);

    retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "gtacagc", 7UL, v_pi,
        GT_OVLFIND_CNT, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_ensure(had_err, retval == GT_CONTFIND_U);

    gt_array_reset(a);
    retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "gtacagc", 7UL, v_pi,
        GT_OVLFIND_ALL, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    gt_ensure(had_err, retval == GT_CONTFIND_U);
    GT_OVLFIND_KMP_EXPECT_RESULT(0UL, false, 5UL);
    gt_free(u_pi);
    gt_free(v_pi);
  }
  /* v suffix of u */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("gtacagc", 7UL);
    v_pi = gt_kmp_preproc("acagc", 5UL);

    retval = gt_ovlfind_kmp("gtacagc", 7UL, u_pi, "acagc", 5UL, v_pi,
        GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 5UL);

    gt_array_reset(a);
    retval = gt_ovlfind_kmp("gtacagc", 7UL, u_pi, "acagc", 5UL, v_pi,
        GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_V);
    gt_ensure(had_err, gt_array_size(a) == 0UL);

    gt_free(u_pi);
    gt_free(v_pi);
  }
  /* u prefix of v */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("ctat", 4UL);
    v_pi = gt_kmp_preproc("ctatacagg", 9UL);
    retval = gt_ovlfind_kmp("ctat", 4UL, u_pi, "ctatacagg", 9UL, v_pi,
        GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 4UL);

    gt_array_reset(a);
    retval = gt_ovlfind_kmp("ctat", 4UL, u_pi, "ctatacagg", 9UL, v_pi,
        GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_U);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_free(u_pi);
    gt_free(v_pi);
  }
  /* v prefix of u */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("ctatacagg", 9UL);
    v_pi = gt_kmp_preproc("ctat", 4UL);
    retval = gt_ovlfind_kmp("ctatacagg", 9UL, u_pi, "ctat", 4UL, v_pi,
        GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    GT_OVLFIND_KMP_EXPECT_RESULT(0UL, false, 4UL);

    gt_array_reset(a);
    retval = gt_ovlfind_kmp("ctatacagg", 9UL, u_pi, "ctat", 4UL, v_pi,
        GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_V);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_free(u_pi);
    gt_free(v_pi);
  }
  /* identical sequences */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("acagc", 5UL);
    retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "acagc", 5UL, u_pi,
        GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 2UL);
    GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 5UL);
    GT_OVLFIND_KMP_EXPECT_RESULT(1UL, false, 5UL);

    gt_array_reset(a);
    retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "acagc", 5UL, u_pi,
        GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_EQ);
    gt_ensure(had_err, gt_array_size(a) == 0UL);
    gt_free(u_pi);
  }
  /* find_nonmaximal */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("aacagtagtagt", 12UL);
    v_pi = gt_kmp_preproc("agtagtagttaa", 12UL);
    retval = gt_ovlfind_kmp("aacagtagtagt", 12UL, u_pi, "agtagtagttaa", 12UL,
        v_pi, GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 2UL);
    GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 9UL);
    GT_OVLFIND_KMP_EXPECT_RESULT(1UL, false, 2UL);
    gt_array_reset(a);
    retval = gt_ovlfind_kmp("aacagtagtagt", 12UL, u_pi, "agtagtagttaa", 12UL,
        v_pi, GT_OVLFIND_SPM, 1UL, true, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 5UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_free(u_pi);
    gt_free(v_pi);
  }
  /* min_length */
  if (!had_err)
  {
    gt_array_reset(a);
    u_pi = gt_kmp_preproc("aggaccagtagt", 12UL);
    v_pi = gt_kmp_preproc("agtagttactac", 12UL);
    retval = gt_ovlfind_kmp("aggaccagtagt", 12UL, u_pi, "agtagttactac", 12UL,
        v_pi, GT_OVLFIND_SPM, 1UL, true, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_ensure(had_err, gt_array_size(a) == 2UL);
    gt_array_reset(a);
    retval = gt_ovlfind_kmp("aggaccagtagt", 12UL, u_pi, "agtagttactac", 12UL,
        v_pi, GT_OVLFIND_SPM, 4UL, true, ovlfind_kmp_test_save, a);
    gt_ensure(had_err, gt_array_size(a) == 1UL);
    gt_ensure(had_err, retval == GT_CONTFIND_OFF);
    gt_free(u_pi);
    gt_free(v_pi);
  }
  gt_array_delete(a);
  return had_err;
}
genometools-1.5.1/src/match/rdj-ovlfind-kmp.h000066400000000000000000000042151211610345200211050ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_OVLFIND_KMP_H
#define RDJ_OVLFIND_KMP_H

#include "core/error_api.h"          /* GtError       */
#include "match/rdj-contfind-def.h"  /* GtContfind    */
#include "match/rdj-pairwise.h"      /* GtOvlfindMode */

/* KMP overlap finder */

/*
  - case sensitive (a != A)
  - no notion of wildcards (i.e. n == n)
*/

#include 
#include "core/error.h"

typedef uint16_t gt_kmp_t;
#define GT_KMP_MAX UINT16_MAX

gt_kmp_t* gt_kmp_preproc(const char *seq, unsigned long seqlen);

GtContfind gt_ovlfind_kmp(const char *u, unsigned long u_length,
                          const gt_kmp_t *u_pi,
                          const char *v /* use NULL for u vs. u */,
                          unsigned long v_length, const gt_kmp_t *v_pi,
                          GtOvlfindMode m, unsigned long min_length,
                          bool find_nonmaximal,
                          void(*spmproc)
                            (unsigned long /* overlap length */,
                             bool /* true if suffix of u == prefix of v
                                     false if prefix of u == suffix of v */,
                             void* /* spmprocdata */),
                          void* spmprocdata);

int gt_kmp_preproc_unit_test(GtError *err);
int gt_ovlfind_kmp_unit_test(GtError *err);

#endif
genometools-1.5.1/src/match/rdj-pairwise.c000066400000000000000000000256531211610345200205060ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/encseq.h"
#include "core/progressbar.h"
#include "core/unused_api.h"
#include "match/rdj-ovlfind-bf.h"
#include "match/rdj-ovlfind-dp.h"
#include "match/rdj-ovlfind-kmp.h"
#include "match/rdj-ovlfind-kmp.h"
#include "match/rdj-spmlist.h"
#include "match/rdj-pairwise.h"
/* unit test: */
#include "match/rdj-ensure-output.h"
#include "core/fasta.h"

struct Read {
  char* seq;
  unsigned long len;
  unsigned long seqnum;
  bool direct;
  gt_kmp_t *pi;
};

struct Data {
  GtSpmproc proc;
  GtSpmprocA proc_a;
  void* procdata;
  struct Read *u, *v;
  GtOvlfindMode mode;
};

#define GT_RDJ_PAIRWISE_INIT_STRUCT_DATA(DATA, PROC, PROC_A, PROCDATA, U, V, \
    MODE) \
  {\
    (DATA).proc = (PROC);\
    (DATA).proc_a = (PROC_A);\
    (DATA).procdata = (PROCDATA);\
    (DATA).u = (U);\
    (DATA).v = (V);\
  }

static void call_spmproc(unsigned long length, bool suffix_of_u, void *data)
{
  struct Data *d = data;
  if (suffix_of_u)
    d->proc(d->u->seqnum, d->v->seqnum, length,
        d->u->direct, d->v->direct, d->procdata);
  else
    d->proc(d->v->seqnum, d->u->seqnum, length, d->v->direct,
            d->u->direct, d->procdata);
}

static inline GtContfind find_exact_overlaps(struct Data *d, bool use_kmp,
    unsigned long min_length, bool find_nonmaximal)
{
  GtContfind retval;

  if (d->u->seqnum == d->v->seqnum && d->v->direct)
  {
    if (!(d->mode == GT_OVLFIND_SPM || d->mode == GT_OVLFIND_ALL))
      return GT_CONTFIND_EQ;
    if (use_kmp)
      retval = gt_ovlfind_kmp(d->u->seq, d->u->len, d->u->pi, NULL, 0, NULL,
          d->mode, min_length, find_nonmaximal, call_spmproc, d);
    else
      retval = gt_ovlfind_bf(d->u->seq, d->u->len, NULL, 0, d->mode,
          min_length, find_nonmaximal, call_spmproc, d);
  }
  else
  {
    if (use_kmp)
      retval = gt_ovlfind_kmp(d->u->seq, d->u->len, d->u->pi, d->v->seq,
          d->v->len, d->v->pi, d->mode, min_length, find_nonmaximal,
          call_spmproc, d);
    else
      retval = gt_ovlfind_bf(d->u->seq, d->u->len, d->v->seq, d->v->len,
          d->mode, min_length, find_nonmaximal, call_spmproc, d);
  }
  return retval;
}

static void call_spmproc_a(unsigned long length_on_u, unsigned long length_on_v,
    unsigned long unit_edist, bool suffix_of_u, void *data)
{
  struct Data *d = data;
  if (suffix_of_u)
    d->proc_a(d->u->seqnum, d->v->seqnum, length_on_u, length_on_v,
              unit_edist, d->u->direct, d->v->direct, d->procdata);
  else
    d->proc_a(d->v->seqnum, d->u->seqnum, length_on_v, length_on_u,
              unit_edist, d->v->direct, d->u->direct, d->procdata);
}

static inline GtContfind find_approx_overlaps(struct Data *d, double max_error,
    unsigned long min_length, bool find_nonmaximal)
{
  GtContfind retval;

  if (d->u->seqnum == d->v->seqnum && d->v->direct)
  {
    if (!(d->mode == GT_OVLFIND_SPM || d->mode == GT_OVLFIND_ALL))
      return GT_CONTFIND_EQ;
    retval = gt_ovlfind_dp(d->u->seq, d->u->len, NULL, 0, max_error, d->mode,
        min_length, find_nonmaximal, call_spmproc_a, d);
  }
  else
  {
    retval = gt_ovlfind_dp(d->u->seq, d->u->len, d->v->seq, d->v->len,
        max_error, d->mode, min_length, find_nonmaximal, call_spmproc_a, d);
  }
  return retval;
}

static gt_kmp_t** prepare_kmp_values(const GtEncseq *encseq, unsigned long n)
{
  unsigned long i, len, startpos;
  char *seq;
  gt_kmp_t **kmp_values;

  kmp_values = gt_malloc(sizeof (gt_kmp_t*) * n);
  gt_assert(encseq != NULL);
  for (i = 0; i < n; i++)
  {
    len = gt_encseq_seqlength(encseq, i);
    seq = gt_malloc(sizeof (char) * (len + 1));
    startpos = gt_encseq_seqstartpos(encseq, i);
    gt_encseq_extract_decoded(encseq, seq, startpos, startpos + len - 1);
    seq[len] = '\0';

    kmp_values[i] = gt_kmp_preproc(seq, len);
    gt_free(seq);
  }
  return kmp_values;
}

static void free_kmp_values(gt_kmp_t** kmp_values, unsigned long n)
{
  unsigned long i;
  gt_assert(kmp_values != NULL);
  for (i = 0; i < n; i++) gt_free(kmp_values[i]);
  gt_free(kmp_values);
}

static inline void mark_contained(GtContfind c, unsigned long u_seqnum,
    unsigned long v_seqnum, GtBitsequence *cntreads)
{
  gt_assert(cntreads != NULL);
  switch (c)
  {
    case GT_CONTFIND_U:
      GT_SETIBIT(cntreads, u_seqnum);
      break;
    case GT_CONTFIND_EQ:
      /* convention: skip one with higher seqnum (which is v) */
      if (v_seqnum != u_seqnum)
        GT_SETIBIT(cntreads, v_seqnum);
      break;
    case GT_CONTFIND_V:
      GT_SETIBIT(cntreads, v_seqnum);
      break;
    default:
      /* nothing to do */
      break;
  }
}

static inline void rdj_pairwise_generic(bool use_dp, GtOvlfindMode m,
    GtEncseq *encseq, bool revcompl, bool show_progressbar, bool use_kmp,
    double max_error, unsigned long min_length, bool find_nonmaximal,
    GtSpmproc proc, GtSpmprocA proc_a, void* procdata, bool cntfilter,
    GtBitsequence *cntreads_in, GtBitsequence **cntreads_out,
    unsigned long *nofreads)
{
  GtContfind containment_status;
  GtBitsequence *cntreads = NULL;
  unsigned long long progress = 0;
  unsigned long i, j, startpos, v_seqnum, nofsequences, n;
  struct Read u, v;
  struct Data d;
  gt_kmp_t** kmp_values = NULL;

  GT_RDJ_PAIRWISE_INIT_STRUCT_DATA(d, proc, proc_a, procdata, &u, &v, 0);

  gt_assert(encseq != NULL);

  d.mode = m;
  if ((m == GT_OVLFIND_ALL) && cntfilter)
    d.mode = GT_OVLFIND_PROPER_SPM;

  n = gt_encseq_num_of_sequences(encseq);
  if (use_kmp)
    kmp_values = prepare_kmp_values(encseq, n);
  nofsequences = n;
  if (revcompl)
    n = n >> 1;
  if (cntreads_in != NULL)
    cntreads = cntreads_in;
  else if (m != GT_OVLFIND_SPM)
    GT_INITBITTAB(cntreads, n);
  if (show_progressbar) gt_progressbar_start(&progress, (unsigned long long)n *
      ((unsigned long long)n - 1ULL) / 2ULL);

  for (i = 0; i < n; i++)
  {
    u.seqnum = i;
    u.direct = true;
    u.len = gt_encseq_seqlength(encseq, i);
    u.seq = gt_malloc(sizeof (char) * (u.len + 1));
    startpos = gt_encseq_seqstartpos(encseq, i);
    gt_encseq_extract_decoded(encseq, u.seq, startpos, startpos + u.len - 1);
    u.seq[u.len] = '\0';
    if (use_kmp)
    {
      gt_assert(kmp_values != NULL);
      u.pi = kmp_values[i];
    }

    for (j = i; j < n; j++)
    {
      if (cntfilter)
      {
        gt_assert(cntreads != NULL);
        if ((bool)GT_ISIBITSET(cntreads, i)) break;
        if ((bool)GT_ISIBITSET(cntreads, j)) continue;
      }

      v.seqnum = j;

      /* find overlaps using direct v */
      v.direct = true;
      v.len = gt_encseq_seqlength(encseq, j);
      v.seq = gt_malloc(sizeof (char) * (v.len + 1));
      startpos = gt_encseq_seqstartpos(encseq, j);
      gt_encseq_extract_decoded(encseq, v.seq, startpos,
          startpos + v.len - 1);
      v.seq[v.len] = '\0';
      if (use_kmp)
      {
        gt_assert(kmp_values != NULL);
        v.pi = kmp_values[j];
      }
      containment_status = use_dp
          ? find_approx_overlaps(&d, max_error, min_length, find_nonmaximal)
          : find_exact_overlaps(&d, use_kmp, min_length, find_nonmaximal);
      if (m != GT_OVLFIND_SPM)
        mark_contained(containment_status, u.seqnum, v.seqnum, cntreads);

      /* find overlaps using reverse complement of v */
      if (revcompl)
      {
        v_seqnum =  nofsequences - j - 1;
        v.direct = false;
        gt_assert(gt_encseq_seqlength(encseq, j) ==
            gt_encseq_seqlength(encseq, v_seqnum));
        startpos = gt_encseq_seqstartpos(encseq, v_seqnum);
        gt_encseq_extract_decoded(encseq, v.seq, startpos,
            startpos + v.len - 1);
        if (use_kmp)
        {
          gt_assert(kmp_values != NULL);
          v.pi = kmp_values[v_seqnum];
        }
        containment_status = use_dp
          ? find_approx_overlaps(&d, max_error, min_length, find_nonmaximal)
          : find_exact_overlaps(&d, use_kmp, min_length, find_nonmaximal);
        if (m != GT_OVLFIND_SPM)
          mark_contained(containment_status, u.seqnum, v.seqnum, cntreads);
      }
      gt_free(v.seq);
      progress++;
    }
    gt_free(u.seq);
  }

  if (cntreads_out != NULL)
    *cntreads_out = cntreads;
  else if (cntreads_in == NULL)
    gt_free(cntreads);
  if (nofreads != NULL)
    *nofreads = n;
  if (use_kmp)
    free_kmp_values(kmp_values, revcompl ? n << 1 : n);
  if (show_progressbar)
    gt_progressbar_stop();
}

#ifndef NDEBUG
static inline bool rdj_pairwise_check_arguments(GtOvlfindMode m, void *proc,
    void *procdata, GtBitsequence *cntreads_in, GtBitsequence **cntreads_out,
    bool cntfilter)
{
  gt_assert(m == GT_OVLFIND_CNT || m == GT_OVLFIND_ALL || m == GT_OVLFIND_SPM);
  if (proc == NULL)
  {
    gt_assert(m == GT_OVLFIND_CNT);
    gt_assert(procdata == NULL);
  }
  else
    gt_assert(m == GT_OVLFIND_SPM || m == GT_OVLFIND_ALL);
  if (cntfilter || (cntreads_out != NULL))
    gt_assert((m == GT_OVLFIND_CNT) ||
              (m == GT_OVLFIND_ALL) ||
              (cntreads_in != NULL));
  return true; /* allow to wrap in gt_assert() */
}
#endif

void gt_rdj_pairwise_exact(GtOvlfindMode m, GtEncseq *encseq,
    bool revcompl, bool show_progressbar, bool use_kmp,
    unsigned long min_length, bool find_nonmaximal, GtSpmproc proc,
    void *procdata, bool cntfilter, GtBitsequence *cntreads_in,
    GtBitsequence **cntreads_out, unsigned long *nofreads)
{
  gt_assert(rdj_pairwise_check_arguments(m, proc, procdata, cntreads_in,
                            cntreads_out, cntfilter));
  rdj_pairwise_generic(false, m, encseq, revcompl, show_progressbar, use_kmp,
      0.0, min_length, find_nonmaximal, proc, NULL, procdata, cntfilter,
      cntreads_in, cntreads_out, nofreads);
}

void gt_rdj_pairwise_approx(GtOvlfindMode m,  GtEncseq *encseq, bool revcompl,
    bool show_progressbar, double max_error, unsigned long min_length,
    bool find_nonmaximal, GtSpmprocA proc, void* procdata, bool cntfilter,
    GtBitsequence *cntreads_in, GtBitsequence **cntreads_out,
    unsigned long *nofreads)
{
  gt_assert(rdj_pairwise_check_arguments(m, proc, procdata, cntreads_in,
                            cntreads_out, cntfilter));
  rdj_pairwise_generic(true, m, encseq, revcompl, show_progressbar, false,
      max_error, min_length, find_nonmaximal, NULL, proc, procdata,
      cntfilter, cntreads_in, cntreads_out, nofreads);
}
genometools-1.5.1/src/match/rdj-pairwise.h000066400000000000000000000103451211610345200205030ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_PAIRWISE_H
#define RDJ_PAIRWISE_H

#include "match/rdj-spmproc.h"           /* GtSpmproc and GtSpmprocA */
#include "core/intbits.h"                /* GtBitsequence */
#include "core/encseq.h"                 /* GtEncseq */

typedef enum
{
  GT_OVLFIND_SPM,        /* containments are not determined;
                            suf-pref matches are determined,
                            including the one that are also containments */
  GT_OVLFIND_CNT,        /* containments are determined;
                            suf-pref matches are not determined */
  GT_OVLFIND_ALL,        /* containments are determined;
                            suf-pref matches are detemined,
                            including the one that are also containments */
  GT_OVLFIND_PROPER_SPM  /* containments are determined;
                            suf-pref matches are determined
                            only if there is no containment */
}
GtOvlfindMode;

/*
(1) general arguments

m:          mode, see GtOvlfindMode definition
encseq:     pointer to a GtEncseq
revcompl:   if true, the second half of the fasta file must contain
            the reverse complements of the sequences in the first half
show_progressbar: if true, a progressbar is displayed

use_kmp:    [gt_rdj_pairwise_exact]
            if true, the KMP-based algorithm is used,
            if false, the brute force algorithm is used

max_error:  [gt_rdj_pairwise_approx]
            the maximal error rate allowed for both
            suffix-prefix matches and containments

(2) suffix-prefix matches related

min_length: only suffix-prefix matches over this length are considered
find_nonmaximal: if true, suffix-prefix matches shorter than the maximal
                 one are also considered
proc:       matches are processed using this function;
            it must be set to NULL in gt_rdj_CNT mode
procdata:   generic data pointer passed to proc;
            it must be set to NULL in gt_rdj_CNT mode

(3) containment related

cntfilter:   if true, contained reads are eliminated from the
             search for further suffix-prefix matches once identified;
             it must be set to false in gt_rdj_SPM mode
cntreads_in: if not NULL, this will be used as the contained reads list,
             i.e. any bit already set will prevent matches involving the
             corresponding read; it must be NULL in gt_rdj_SPM mode;
             the list will never be deleted
cntreads_out: if not NULL, the address of the contained reads list
              will be written here; it must be NULL in gt_rdj_SPM mode;
              if this and cntreads_in are both NULL, the list is deleted
nofreads:    if not NULL, the number of direct reads is written here
             (which is also the number of elements of the cntreads list)

*/

void gt_rdj_pairwise_exact(GtOvlfindMode m, GtEncseq *encseq,
    bool revcompl, bool show_progressbar, bool use_kmp,
    unsigned long min_length, bool find_nonmaximal, GtSpmproc proc,
    void *procdata, bool cntfilter, GtBitsequence *cntreads_in,
    GtBitsequence **cntreads_out, unsigned long *nofreads);

void gt_rdj_pairwise_approx(GtOvlfindMode m,  GtEncseq *encseq, bool revcompl,
    bool show_progressbar, double max_error, unsigned long min_length,
    bool find_nonmaximal, GtSpmprocA proc, void* procdata, bool cntfilter,
    GtBitsequence *cntreads_in, GtBitsequence **cntreads_out,
    unsigned long *nofreads);

#endif
genometools-1.5.1/src/match/rdj-revcompl-def.h000066400000000000000000000037371211610345200212520ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_REVCOMPL_DEF_H
#define RDJ_REVCOMPL_DEF_H

/* correct seqnum and seqdirect variables if in revcompl range */
#define GT_READJOINER_CORRECT_REVCOMPL(SEQNUM,FIRSTREVCOMPL,NOFSEQ,SEQDIRECT)\
        if ((FIRSTREVCOMPL) > 0 && (SEQNUM) >= (FIRSTREVCOMPL))\
        {\
          gt_assert((SEQNUM) <= ((NOFSEQ)-1));\
          (SEQNUM) = ((NOFSEQ)-1)-(SEQNUM);\
          (SEQDIRECT) = false;\
        }\
        else (SEQDIRECT) = true

#define GT_READJOINER_READNUM(SEQNUM,FIRSTREVCOMPL,NOFSEQ)\
        (((FIRSTREVCOMPL) > 0 && (SEQNUM) >= (FIRSTREVCOMPL)) \
         ? (((NOFSEQ)-1)-(SEQNUM)) : (SEQNUM))

/* in revcompl mode the data would be output twice without this;
   e.g. 2 revcompl have same overlap that 2 direct sequences;
   convention: either are both direct, or the one with higher seqnum
   is allowed to be revcompl; this macro allows one to skip other cases */

#define GT_READJOINER_IS_CORRECT_REVCOMPL_CASE(SN,SD,PN,PD)\
        (\
          ((SD) && (PD)) ||\
          ((SN) == (PN) && !(!(SD) && !(PD))) ||\
          ((SD) && !(PD) && (PN) > (SN)) ||\
          (!(SD) && (PD) && (PN) < (SN))\
        )

#endif
genometools-1.5.1/src/match/rdj-spmfind.c000066400000000000000000000673541211610345200203270ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/arraydef.h"
#include "core/disc_distri_api.h"
#include "core/fa.h"
#include "core/intbits.h"
#include "core/log_api.h"
#include "core/spacecalc.h"
#include "core/types_api.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "match/esa-bottomup.h"
#include "match/rdj-cntlist.h"
#include "match/rdj-filesuf-def.h"
#include "match/rdj-revcompl-def.h"
#include "match/rdj-spmproc.h"
#include "match/rdj-spmlist.h"
#include "match/sfx-bltrie.h"
#include "match/rdj-spmfind.h"

#define GT_SPMFIND_LSET_ALLOC_INC (1UL << 10)
#define GT_SPMFIND_WSET_ALLOC_INC (1UL << 10)
#define GT_SPMFIND_BLTRIE_ALLOC   (1U << 6)

typedef struct {
  unsigned long seqnum;
  GtBlindtrie *blindtrie;
} WholereadInfo;

typedef struct {
  unsigned long w_left;
} GtBUinfo_spmeq;

typedef GtBUinfo_spmeq GtBUinfo_spmvar;

struct GtBUstate_spm {
  void *stack;

  GtLogger *default_logger;
  GtLogger *verbose_logger;
  GtError *err;

  /* algorithm parameters: */
  unsigned long minmatchlength;
  bool elimtrans;

  /* sequence */
  const char *indexname;
  const GtEncseq *encseq;
  unsigned long totallength;
  unsigned long read_length;
  unsigned long nofreads;
  unsigned long first_revcompl;

  /* terminal edges set */
  unsigned long *l_set;
  unsigned long l_nextfree;
  unsigned long l_allocated;

  /* whole-read leaves set */
  WholereadInfo *w_set;
  unsigned long w_nextfree;
  unsigned long w_allocated;
  unsigned long w_offset;
  unsigned long w_count;
  unsigned long w_maxsize;
  bool w_overflow;

  /* function called when results are found, and its data pointer: */
  GtSpmproc proc;
  void* procdata;
  unsigned long nofvalidspm;
  unsigned long nof_transitive_withrc;
  unsigned long nof_transitive_other;

  /* varlen contained reads detection */
  unsigned long shortest;
  FILE *cntfile;
  unsigned long nof_contained;

  unsigned long spaceforbucketprocessing;
  unsigned int threadnum;

#ifdef GT_READJOINER_STATISTICS
  /* statistics */
  unsigned long nof_terminals;
  unsigned long nof_combinable_terminals; /* where w_set is not empty */
  unsigned long nof_t_w_combinations;
  unsigned long nof_wrong_direction;
  unsigned long nof_w_set_realloc;
  unsigned long nof_l_set_realloc;
  unsigned long nof_subtrees; /* with w_set not empty */
  unsigned long nof_terminals_in_subtree;
  unsigned long max_nof_terminals_in_subtree;
  unsigned long nof_overlaps_in_subtree;
  unsigned long max_nof_overlaps_in_subtree;
  unsigned long max_w_nextfree;
  unsigned long max_l_nextfree;
  unsigned long max_blindtrie_size;
  unsigned long max_total_blindtrie_size;
  GtDiscDistri *w_per_terminal;
  unsigned long initial_l_allocated;
  unsigned long initial_w_allocated;
#endif
};

typedef struct GtBUstate_spm GtBUstate_spm;

static void initwset_spm(GtBUstate_spm *state)
{
  unsigned long i;
  state->w_allocated = GT_SPMFIND_WSET_ALLOC_INC;
  state->w_set = gt_malloc(sizeof (WholereadInfo) * (state->w_allocated));
  state->w_nextfree = 0;
  for (i = 0; i < state->w_allocated; i++)
    (state->w_set + i)->blindtrie = NULL;
}

static inline void expandwset_spm(GtBUstate_spm *state)
{
  unsigned long prevsize, i;
  prevsize = state->w_allocated;
  state->w_allocated += GT_SPMFIND_WSET_ALLOC_INC;
  state->w_set = gt_realloc(state->w_set, sizeof (WholereadInfo) *
      state->w_allocated);
  for (i = prevsize; i < state->w_allocated; i++)
    (state->w_set + i)->blindtrie = NULL;
  gt_assert(state->w_nextfree < state->w_allocated);
#ifdef GT_READJOINER_STATISTICS
  (state->nof_w_set_realloc)++;
#endif
}

static inline void appendtowset_spm(unsigned long seqnum,
  GtBUstate_spm *state)
{
  WholereadInfo *w;

  state->w_count++;
  if (state->w_count <= state->w_offset)
    return;

  if (state->w_count > state->w_offset + state->w_maxsize)
  {
    state->w_overflow = true;
    return;
  }

  /* realloc if necessary */
  if (state->w_nextfree == state->w_allocated)
    expandwset_spm(state);

  /* add element */
#ifdef GT_READJOINER_DEBUG
  gt_log_log("-- add to wset: %lu", seqnum);
  gt_log_log("offset: %lu", state->w_offset);
#endif
  w = state->w_set + state->w_nextfree;
  state->w_nextfree++;

  w->seqnum = seqnum;
  /* get a new blind trie or recycle old one */
  if (w->blindtrie == NULL)
    w->blindtrie = gt_blindtrie_new(NULL, 0,
        GT_SPMFIND_BLTRIE_ALLOC, state->encseq, false, NULL,
        NULL, GT_READMODE_REVERSE);
  else
    gt_blindtrie_reset(w->blindtrie);

#ifdef GT_READJOINER_STATISTICS
  /* statistics */
  if (state->w_nextfree > state->max_w_nextfree)
    state->max_w_nextfree = state->w_nextfree;
#endif
}

static inline void printcurrentspace_spm(const char *label)
{
  unsigned long m, f;
  if (gt_ma_bookkeeping_enabled())
  {
    m = gt_ma_get_space_current();
    f = gt_fa_get_space_current();
    gt_log_log("used space %s: %.2f MB (ma: %.2f MB; fa: %.2f MB)", label,
        GT_MEGABYTES(m + f), GT_MEGABYTES(m), GT_MEGABYTES(f));
  }
}

static inline void resetwsetbt_spm(GtBUstate_spm *state)
{
  unsigned long i, bsize_sum = 0, nofbltries = 0;
  GtBlindtrie *b;
  printcurrentspace_spm("before resizing");
  for (i = 0; i < state->w_allocated; i++)
  {
    b = (state->w_set + i)->blindtrie;
    if (b != NULL)
    {
      bsize_sum += gt_blindtrie_current_size(b);
      gt_blindtrie_resize(b, 1U);
      nofbltries++;
    }
    else
      break;
  }
  gt_log_log("current number of blindtries: %lu", nofbltries);
  gt_log_log("total size of the blindtries: %.2f MB", GT_MEGABYTES(bsize_sum));
  printcurrentspace_spm("after resizing");
}

static void deletewset_spm(WholereadInfo *w_set,
    unsigned long w_allocated)
{
  unsigned long i;
  for (i = 0; i < w_allocated; i++)
    gt_blindtrie_delete(w_set[i].blindtrie);
  gt_free(w_set);
}

static void initlset_spm(GtBUstate_spmeq *state)
{
  state->l_allocated = GT_SPMFIND_LSET_ALLOC_INC;
  state->l_set = gt_malloc(sizeof (state->l_set) * (state->l_allocated));
  state->l_nextfree = 0;
}

static inline void expandlset_spm(GtBUstate_spm *state)
{
  state->l_allocated += GT_SPMFIND_LSET_ALLOC_INC;
  state->l_set = gt_realloc(state->l_set, sizeof (state->l_set) *
      state->l_allocated);
  gt_assert(state->l_nextfree < state->l_allocated);
#ifdef GT_READJOINER_STATISTICS
  (state->nof_l_set_realloc)++;
#endif
}

static inline void appendtolset_spm(unsigned long seqnum,
    GtBUstate_spm *state)
{
  /* realloc if necessary */
  if (state->l_nextfree == state->l_allocated)
    expandlset_spm(state);
  /* add element */
  state->l_set[state->l_nextfree] = seqnum;
  state->l_nextfree++;
#ifdef GT_READJOINER_STATISTICS
  (state->nof_terminals)++;
  (state->nof_terminals_in_subtree)++;
  if (state->l_nextfree > state->max_l_nextfree)
    state->max_l_nextfree = state->l_nextfree;
#endif
}

static void initBUinfo_spmeq(GT_UNUSED GtBUinfo_spmeq *info,
    GT_UNUSED GtBUstate_spmeq *state)
{
  /* nothing to do here */
}

static void initBUinfo_spmvar(GT_UNUSED GtBUinfo_spmvar *info,
    GT_UNUSED GtBUstate_spmvar *state)
{
  /* nothing to do here */
}

static void freeBUinfo_spmeq(GT_UNUSED GtBUinfo_spmeq *info,
    GT_UNUSED GtBUstate_spmeq *state)
{
  /* nothing to do here */
}

static void freeBUinfo_spmvar(GT_UNUSED GtBUinfo_spmvar *info,
    GT_UNUSED GtBUstate_spmvar *state)
{
  /* nothing to do here */
}

#ifdef GT_READJOINER_STATISTICS
static void save_blindtrie_statistics(GtBUstate_spm *state)
{
  unsigned long j, bsize, bsize_sum = 0;
  for (j = 0; j < state->w_nextfree; j++)
  {
    bsize = gt_blindtrie_current_size(state->w_set[j].blindtrie);
    if (bsize > state->max_blindtrie_size)
      state->max_blindtrie_size = bsize;
    bsize_sum += bsize;
  }
  if (bsize_sum > state->max_total_blindtrie_size)
    state->max_total_blindtrie_size = bsize_sum;
}

static void reset_subtree_stats(GtBUstate_spm *state)
{
  if (state->w_nextfree > 0)
  {
    save_blindtrie_statistics(state);
    (state->nof_subtrees)++;

    if (state->nof_terminals_in_subtree > state->max_nof_terminals_in_subtree)
      state->max_nof_terminals_in_subtree = state->nof_terminals_in_subtree;
    state->nof_terminals_in_subtree = 0;

    if (state->nof_overlaps_in_subtree > state->max_nof_overlaps_in_subtree)
      state->max_nof_overlaps_in_subtree = state->nof_overlaps_in_subtree;
    state->nof_overlaps_in_subtree = 0;
  }
}
#endif

static void combine_terminal_with_wset(unsigned long seqnum,
    unsigned long seqstartpos, unsigned long seqlen, unsigned long w_left,
    unsigned long lcp, GtBUstate_spm *state)
{
  unsigned long j, suffix_readnum = seqnum;
  bool suffixseq_direct = true;

  GT_READJOINER_CORRECT_REVCOMPL(suffix_readnum, state->first_revcompl,
      state->nofreads, suffixseq_direct);

#ifdef GT_READJOINER_STATISTICS
  (state->nof_terminals)++;
  (state->nof_terminals_in_subtree)++;
  if (w_left < state->w_nextfree)
  {
    (state->nof_combinable_terminals)++;
    gt_disc_distri_add(state->w_per_terminal, state->w_nextfree - w_left);
    state->nof_t_w_combinations += state->w_nextfree - w_left;
  }
#endif
  for (j = w_left; j < state->w_nextfree; j++)
  {
    bool prefixseq_direct = true;
    WholereadInfo *w = state->w_set + j;
    unsigned long prefix_readnum = w->seqnum;
    GT_READJOINER_CORRECT_REVCOMPL(prefix_readnum, state->first_revcompl,
        state->nofreads, prefixseq_direct);
    if (!state->elimtrans ||
        !gt_blindtrie_retrieve(w->blindtrie, state->totallength -
          (seqstartpos + seqlen - lcp), seqstartpos))
    {
      /* irreducible SPM */
      if (GT_READJOINER_IS_CORRECT_REVCOMPL_CASE(suffix_readnum,
            suffixseq_direct, prefix_readnum, prefixseq_direct))
      {
#ifdef GT_READJOINER_DEBUG
        gt_log_log("%lu %s %lu %s %lu\n", suffix_readnum, suffixseq_direct ? "+"
            : "-", prefix_readnum, prefixseq_direct ? "+" : "-", lcp);
#endif
        state->proc(suffix_readnum, prefix_readnum, lcp, suffixseq_direct,
            prefixseq_direct, state->procdata);
        (state->nofvalidspm)++;
#ifdef GT_READJOINER_STATISTICS
        (state->nof_overlaps_in_subtree)++;
#endif
      }
#ifdef GT_READJOINER_STATISTICS
      else
      {
        (state->nof_wrong_direction)++;
      }
#endif
    }
    else
    {
      /* transitive */
      if (prefix_readnum == suffix_readnum)
        (state->nof_transitive_withrc)++;
      else
        (state->nof_transitive_other)++;
    }
  }
}

static inline int processleafedge_spmeq(bool firstsucc,
    unsigned long fatherdepth,
    GtBUinfo_spmeq *father, unsigned long seqnum, unsigned long relpos,
    GtBUstate_spmeq *state, GT_UNUSED GtError *err)
{
  if (fatherdepth >= state->minmatchlength)
  {
    if (firstsucc)
    {
      gt_assert(father != NULL);
      father->w_left = state->w_nextfree;
    }
    if (relpos == 0)
      appendtowset_spm(seqnum, state);
    gt_assert(fatherdepth != state->read_length);
    if (relpos + fatherdepth == state->read_length)
      combine_terminal_with_wset(seqnum, seqnum * (state->read_length + 1),
         state->read_length, father->w_left, fatherdepth, state);
  }
  else
  {
#ifdef GT_READJOINER_STATISTICS
    reset_subtree_stats(state);
#endif
    state->w_nextfree = 0;
  }
  return 0;
}

static inline int processleafedge_spmvar(bool firstsucc,
    unsigned long fatherdepth,
    GtBUinfo_spmeq *father, unsigned long seqnum, unsigned long relpos,
    GtBUstate_spmeq *state, GT_UNUSED GtError *err)
{
  if (fatherdepth >= state->minmatchlength)
  {
    unsigned long seqlen = gt_encseq_seqlength(state->encseq, seqnum);
    if (firstsucc)
    {
      gt_assert(father != NULL);
      father->w_left = state->w_nextfree;
    }
    if (relpos == 0)
    {
      appendtowset_spm(seqnum, state);
      if (fatherdepth == seqlen)
      {
        unsigned long readnum = GT_READJOINER_READNUM(seqnum,
            state->first_revcompl, state->nofreads);
        (void)fwrite(&(readnum), sizeof (unsigned long), (size_t)1,
            state->cntfile);
        state->nof_contained++;
      }
    }
    if (relpos + fatherdepth == seqlen)
      appendtolset_spm(seqnum, state);
  }
  else
  {
#ifdef GT_READJOINER_STATISTICS
    reset_subtree_stats(state);
#endif
    state->w_nextfree = 0;
  }
  return 0;
}

static inline int processbranchingedge_spmeq(GT_UNUSED bool firstsucc,
    unsigned long fatherdepth,
    GT_UNUSED GtBUinfo_spmeq *afather, GT_UNUSED unsigned long sondepth,
    GT_UNUSED unsigned long sonwidth,
    GT_UNUSED GtBUinfo_spmeq *ason, GT_UNUSED GtBUstate_spmeq *state,
    GT_UNUSED GtError *err)
{
  if (fatherdepth < state->minmatchlength)
  {
#ifdef GT_READJOINER_STATISTICS
    reset_subtree_stats(state);
#endif
    state->w_nextfree = 0;
  }
  return 0;
}

static inline int processbranchingedge_spmvar(GT_UNUSED bool firstsucc,
    unsigned long fatherdepth,
    GT_UNUSED GtBUinfo_spmvar *afather, GT_UNUSED unsigned long sondepth,
    GT_UNUSED unsigned long sonwidth,
    GT_UNUSED GtBUinfo_spmvar *ason, GT_UNUSED GtBUstate_spmvar *state,
    GT_UNUSED GtError *err)
{
  if (fatherdepth < state->minmatchlength)
  {
#ifdef GT_READJOINER_STATISTICS
    reset_subtree_stats(state);
#endif
    state->w_nextfree = 0;
  }
  return 0;
}

static int processlcpinterval_spmvar(unsigned long lcp,
    GtBUinfo_spmvar *info, GtBUstate_spmvar *state, GT_UNUSED GtError *err)
{
  if (lcp >= state->minmatchlength)
  {
    unsigned long i;
    for (i = 0; i < state->l_nextfree; i++)
    {
      combine_terminal_with_wset(state->l_set[i],
          gt_encseq_seqstartpos(state->encseq, state->l_set[i]),
          gt_encseq_seqlength(state->encseq, state->l_set[i]), info->w_left,
          lcp, state);
    }
    state->l_nextfree = 0;
  }
  return 0;
}

#ifdef GT_READJOINER_STATISTICS

static int show_disc_distri_datapoint_spm(unsigned long key,
    unsigned long long value, GtFile *outfile)
{
  gt_file_xprintf(outfile, "%lu %llu\n", key, value);
  return 0;
}

void show_wsize_distri_spm(GtBUstate_spmeq *state)
{
  FILE *outfp = NULL;
  GtFile *gt_outfp = NULL;
  GtStr *filename;

  filename = gt_str_new_cstr(state->indexname);
  gt_str_append_cstr(filename, GT_READJOINER_SUFFIX_WSIZE_DISTRI);
  outfp = gt_fa_xfopen(gt_str_get(filename), "w");
  gt_outfp = gt_file_new_from_fileptr(outfp);
  gt_logger_log(state->verbose_logger, "terminals: w_set size distribution: %s",
      gt_str_get(filename));
  gt_file_xprintf(gt_outfp, "# sizeofwset nofterminals\n");
  gt_disc_distri_foreach(state->w_per_terminal,
    (GtDiscDistriIterFunc) show_disc_distri_datapoint_spm, gt_outfp);
  gt_file_delete(gt_outfp);
  gt_str_delete(filename);
}

static void showstatistics_spm(GtBUstate_spmeq *state)
{
  unsigned long nof_correct_dir_transitive;

  gt_logger_log(state->verbose_logger, "--- statistics for thread %u ---",
      state->threadnum);

  /* encseq */
  gt_logger_log(state->verbose_logger, "encseq: number of reads: %lu",
      gt_encseq_num_of_sequences(state->encseq));
  gt_logger_log(state->verbose_logger, "encseq: total length: %lu",
      state->totallength);

  /* subtrees */
  gt_logger_log(state->verbose_logger, "subtrees: number: %lu",
      state->nof_subtrees);

  /* terminals */
  gt_logger_log(state->verbose_logger, "terminals: all: %lu",
      state->nof_terminals);
  gt_logger_log(state->verbose_logger, "terminals: on w-paths %lu",
      state->nof_combinable_terminals);
  gt_logger_log(state->verbose_logger, "terminals: max in subtree: %lu",
      state->max_nof_terminals_in_subtree);
  gt_logger_log(state->verbose_logger,
      "terminals: combinations with w-paths: %lu", state->nof_t_w_combinations);
  show_wsize_distri_spm(state);

  /* spm */
  gt_logger_log(state->verbose_logger,
      "spm: irreducible - correct-direction: %lu", state->nofvalidspm);
  gt_logger_log(state->verbose_logger,
      "spm: irreducible - wrong-direction: %lu", state->nof_wrong_direction);
  gt_logger_log(state->verbose_logger, "spm: transitive - "
      "derived from own revcompl: %lu", state->nof_transitive_withrc);
  gt_logger_log(state->verbose_logger, "spm: transitive - correct/wrong dir - "
      "derived from other: %lu", state->nof_transitive_other);
  nof_correct_dir_transitive = (unsigned long)(state->nof_transitive_withrc) +
    (unsigned long)(state->nof_transitive_other >> 1);
  gt_logger_log(state->verbose_logger, "spm: transitive - "
      "correct direction: %lu", nof_correct_dir_transitive);
  gt_logger_log(state->verbose_logger, "spm: max in subtree: %lu",
      state->max_nof_overlaps_in_subtree);

  /* l_set */
  gt_logger_log(state->verbose_logger, "l_set: max nextfree: %lu",
      state->max_l_nextfree);
  gt_logger_log(state->verbose_logger, "l_set: sizeof: %lu",
      (unsigned long)(sizeof (state->l_set)));
  gt_logger_log(state->verbose_logger, "l_set: initial alloc: %lu (%lu bytes)",
      state->initial_l_allocated, state->initial_l_allocated *
      sizeof (state->l_set));
  gt_logger_log(state->verbose_logger, "l_set: final alloc: %lu (%lu bytes)",
      state->l_allocated, state->l_allocated * sizeof (state->l_set));
  gt_logger_log(state->verbose_logger, "l_set: reallocs: %lu",
      state->nof_l_set_realloc);

  /* w_set */
  gt_logger_log(state->verbose_logger, "w_set: max nextfree: %lu",
      state->max_w_nextfree);
  gt_logger_log(state->verbose_logger, "w_set: sizeof: %lu",
      (unsigned long)(sizeof (WholereadInfo)));
  gt_logger_log(state->verbose_logger, "w_set: initial alloc: %lu (%lu bytes)",
      state->initial_w_allocated,
      state->initial_w_allocated * sizeof (WholereadInfo));
  gt_logger_log(state->verbose_logger, "w_set: final alloc: %lu (%lu bytes)",
      state->w_allocated, state->w_allocated * sizeof (WholereadInfo));
  gt_logger_log(state->verbose_logger, "w_set: reallocs: %lu",
      state->nof_w_set_realloc);
  gt_logger_log(state->verbose_logger, "w_set: largest blindtrie: %lu bytes",
      state->max_blindtrie_size);
  gt_logger_log(state->verbose_logger, "w_set: sum of blindtrie sizes: "
      "%lu bytes", state->max_total_blindtrie_size);
}
#endif

#include "esa-bottomup-spmeq.inc"

#include "esa-bottomup-spmvar.inc"

static GtBUstate_spm *gt_spmfind_state_new(bool eqlen, const GtEncseq *encseq,
    unsigned long minmatchlength, unsigned long w_maxsize, bool elimtrans,
    bool showspm, const char *indexname, unsigned int threadnum,
    GtLogger *default_logger, GtLogger *verbose_logger, GtError *err)
{
  GtBUstate_spmeq *state = gt_calloc((size_t)1, sizeof (*state));

  state->default_logger = default_logger;
  state->verbose_logger = verbose_logger;
  state->err = err;
  state->indexname = indexname;
  state->encseq = encseq;
  state->nofreads = gt_encseq_num_of_sequences(encseq);
  state->first_revcompl = gt_encseq_is_mirrored(encseq) ?
    state->nofreads >> 1 : 0;
  state->totallength = gt_encseq_total_length(encseq);
  state->minmatchlength = minmatchlength;
  state->elimtrans = elimtrans;
  state->w_maxsize = (w_maxsize == 0) ? ULONG_MAX : w_maxsize;\
  if (eqlen)
  {
    state->read_length = gt_encseq_seqlength(encseq, 0);
  }
  else
  {
    GtStr *suffix = gt_str_new();
    state->read_length = 0;
    gt_str_append_char(suffix, '.');
    gt_str_append_uint(suffix, threadnum);
    gt_str_append_cstr(suffix, GT_READJOINER_SUFFIX_CNTLIST);
    state->cntfile = gt_fa_fopen_with_suffix(indexname, gt_str_get(suffix),
        "wb", NULL);
    gt_cntlist_write_bin_header(gt_encseq_is_mirrored(encseq) ?
        state->nofreads >> 1 : state->nofreads, state->cntfile);
    gt_str_delete(suffix);
    if (!state->cntfile)
      exit(-1);
  }
  state->threadnum = threadnum;

  if (threadnum == 0)
  {
    gt_logger_log(verbose_logger, "readset name = %s", indexname);
    if (state->first_revcompl == 0)
      gt_logger_log(verbose_logger, "single strand mode");
    gt_logger_log(default_logger, "number of reads in filtered readset = %lu",
        state->first_revcompl > 0 ? state->first_revcompl : state->nofreads);
    gt_logger_log(verbose_logger, "total length of filtered readset = %lu",
        gt_encseq_is_mirrored(encseq) ? (state->totallength -
          state->nofreads + 1) >> 1 : (state->totallength -
            state->nofreads + 1));
    if (eqlen)
      gt_logger_log(verbose_logger, "read length = %lu", state->read_length);
    else
      gt_logger_log(verbose_logger, "read length = variable");
    gt_logger_log(verbose_logger, "minimal match length = %lu",
        state->minmatchlength);
    if (w_maxsize == 0)
      gt_logger_log(verbose_logger, "wset size limit = unlimited");
    else
      gt_logger_log(verbose_logger, "wset size limit = %lu",
          state->w_maxsize);
    gt_logger_log(verbose_logger, "eliminate transitive SPM = %s",
        state->elimtrans ? "true" : "false");
  }

  if (showspm)
  {
    state->proc = gt_spmproc_show_ascii;
    state->procdata = NULL;
  }
  else
  {
    GtStr *suffix = gt_str_new();
    gt_str_append_char(suffix, '.');
    gt_str_append_uint(suffix, threadnum);
    gt_str_append_cstr(suffix, GT_READJOINER_SUFFIX_SPMLIST);
    /*@ignore@*/
    state->procdata = gt_fa_fopen_with_suffix(indexname, gt_str_get(suffix),
        "wb", NULL);
    /*@end@*/
    gt_str_delete(suffix);
    if (state->procdata == NULL)
      exit(-1);
    if (state->first_revcompl > UINT32_MAX ||
        (state->first_revcompl == 0 && state->nofreads > UINT32_MAX))
    {
      state->proc = gt_spmproc_show_bin64;
      /*@ignore@*/
      gt_spmlist_write_header_bin64((FILE*)state->procdata);
      /*@end@*/
    }
    else
    {
      state->proc = gt_spmproc_show_bin32;
      /*@ignore@*/
      gt_spmlist_write_header_bin32((FILE*)state->procdata);
      /*@end@*/
    }
  }

  state->nofvalidspm = 0;

  initlset_spm(state);
  initwset_spm(state);

  state->stack = (void *) gt_GtArrayGtBUItvinfo_new();

#ifdef GT_READJOINER_STATISTICS
  if (threadnum == 0)
    gt_logger_log(state->verbose_logger,
        "spmfind: additional statistics output activated");
  state->initial_l_allocated = state->l_allocated;
  state->initial_w_allocated = state->w_allocated;
  state->w_per_terminal = gt_disc_distri_new();
#endif

  return state;
}

GtBUstate_spmeq *gt_spmfind_eqlen_state_new(const GtEncseq *encseq,
    unsigned long minmatchlength, unsigned long w_maxsize, bool elimtrans,
    bool showspm, const char *indexname, unsigned int threadnum,
    GtLogger *default_logger, GtLogger *verbose_logger, GtError *err)
{
  return (GtBUstate_spmeq *)gt_spmfind_state_new(true, encseq, minmatchlength,
      w_maxsize, elimtrans, showspm, indexname, threadnum, default_logger,
      verbose_logger, err);
}

GtBUstate_spmvar *gt_spmfind_varlen_state_new(const GtEncseq *encseq,
    unsigned long minmatchlength, unsigned long w_maxsize, bool elimtrans,
    bool showspm, const char *indexname, unsigned int threadnum,
    GtLogger *default_logger, GtLogger *verbose_logger, GtError *err)
{
  return (GtBUstate_spmvar *)gt_spmfind_state_new(false, encseq, minmatchlength,
      w_maxsize, elimtrans, showspm, indexname, threadnum, default_logger,
      verbose_logger, err);
}

static unsigned long gt_spmfind_nof_trans_spm(GtBUstate_spm *state)
{
  return state->nof_transitive_withrc + (state->nof_transitive_other >> 1);
}

static unsigned long gt_spmfind_nof_irr_spm(GtBUstate_spm *state)
{
  return state->nofvalidspm;
}

unsigned long gt_spmfind_varlen_nof_trans_spm(GtBUstate_spmvar *state)
{
  return gt_spmfind_nof_trans_spm(state);
}

unsigned long gt_spmfind_varlen_nof_irr_spm(GtBUstate_spmvar *state)
{
  return gt_spmfind_nof_irr_spm(state);
}

unsigned long gt_spmfind_eqlen_nof_trans_spm(GtBUstate_spmeq *state)
{
  return gt_spmfind_nof_trans_spm(state);
}

unsigned long gt_spmfind_eqlen_nof_irr_spm(GtBUstate_spmeq *state)
{
  return gt_spmfind_nof_irr_spm(state);
}

static void gt_spmfind_state_delete(bool eqlen, GtBUstate_spm *state)
{
  if (state != NULL)
  {
    gt_logger_log(state->verbose_logger, "number of %ssuffix-prefix matches "
        "[thread %u] = %lu", state->elimtrans ? "irreducible " : "",
        state->threadnum, state->nofvalidspm);
    if (state->elimtrans)
      gt_logger_log(state->verbose_logger, "number of transitive "
          "suffix-prefix matches [thread %u] = %lu",
          state->threadnum, state->nof_transitive_withrc +
          (state->nof_transitive_other >> 1));
#ifdef GT_READJOINER_STATISTICS
    showstatistics_spm(state);
    gt_disc_distri_delete(state->w_per_terminal);
#endif

    gt_free(state->l_set);
    deletewset_spm(state->w_set, state->w_allocated);
    if (eqlen)
      gt_GtArrayGtBUItvinfo_delete_spmeq(
          (GtArrayGtBUItvinfo_spmeq *)state->stack, state);
    else
    {
      GtStr *path = gt_str_new_cstr(state->indexname);
      gt_str_append_cstr(path, GT_READJOINER_SUFFIX_CNTLIST);

      gt_logger_log(state->verbose_logger, "number of internally contained "
          "reads [thread %u] = %lu", state->threadnum, state->nof_contained);

      gt_str_delete(path);
      gt_GtArrayGtBUItvinfo_delete_spmvar(
          (GtArrayGtBUItvinfo_spmvar *)state->stack, state);
      gt_fa_fclose(state->cntfile);
    }
    if (state->procdata != NULL)
      /*@ignore@*/
      gt_fa_fclose((FILE*)state->procdata);
      /*@end@*/
    gt_free(state);
  }
}

void gt_spmfind_eqlen_state_delete(GtBUstate_spmeq *state)
{
  gt_spmfind_state_delete(true, state);
}

void gt_spmfind_varlen_state_delete(GtBUstate_spmeq *state)
{
  gt_spmfind_state_delete(false, state);
}

int gt_spmfind_eqlen_process(void *data,
    const unsigned long *seqnum_relpos_bucket, const GtSeqnumrelpos *snrp,
    const uint16_t *lcptab_bucket, unsigned long nonspecials,
    unsigned long spaceforbucketprocessing, GtError *err)
{
  GtBUstate_spmeq *state = data;
  unsigned int nof_w_parts = 0;
  gt_assert(state != NULL);
  gt_assert(snrp != NULL);
  gt_assert(lcptab_bucket != NULL);
  state->spaceforbucketprocessing = spaceforbucketprocessing;
  state->w_offset = 0;
  do
  {
    state->w_nextfree = 0;
    state->w_overflow = false;
    state->w_count = 0;
    if (gt_esa_bottomup_RAM_spmeq(seqnum_relpos_bucket, lcptab_bucket,
          nonspecials, (GtArrayGtBUItvinfo_spmeq *) state->stack, state,
          snrp, err)
        != 0)
    {
      return -1;
    }
    if (state->w_overflow)
      nof_w_parts++;
    state->w_offset += state->w_maxsize;
  } while (state->w_overflow);
#ifdef GT_READJOINER_DEBUG
  gt_log_log("bucket divided in %u parts", nof_w_parts);
#endif
  return 0;
}

void gt_spmfind_eqlen_process_end(void *data)
{
  GtBUstate_spmeq *state = data;
  resetwsetbt_spm(state);
  return;
}

void gt_spmfind_varlen_process_end(void *data)
{
  GtBUstate_spmvar *state = data;
  resetwsetbt_spm(state);
  return;
}

int gt_spmfind_varlen_process(void *data,
    const unsigned long *seqnum_relpos_bucket, const GtSeqnumrelpos *snrp,
    const uint16_t *lcptab_bucket, unsigned long nonspecials,
    unsigned long spaceforbucketprocessing, GtError *err)
{
  GtBUstate_spmvar *state = data;
  unsigned int nof_w_parts = 0;
  gt_assert(state != NULL);
  gt_assert(snrp != NULL);
  gt_assert(lcptab_bucket != NULL);
  state->spaceforbucketprocessing = spaceforbucketprocessing;
  state->w_offset = 0;
  do
  {
    state->w_nextfree = 0;
    state->w_overflow = false;
    state->w_count = 0;
    if (gt_esa_bottomup_RAM_spmvar(seqnum_relpos_bucket, lcptab_bucket,
          nonspecials, (GtArrayGtBUItvinfo_spmvar *) state->stack, state,
          snrp, err)
        != 0)
    {
      return -1;
    }
    if (state->w_overflow)
      nof_w_parts++;
    state->w_offset += state->w_maxsize;
  } while (state->w_overflow);
  return 0;
}
genometools-1.5.1/src/match/rdj-spmfind.h000066400000000000000000000055431211610345200203240ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_SPMFIND_H
#define RDJ_SPMFIND_H

#include 
#include "core/error_api.h"
#include "core/encseq_api.h"
#include "match/seqnumrelpos.h"

/*
 * elimtrans: if false, the blindtrie are never actually used and
 *            all SPM are output, not only the irreducible ones
 * showspm: if true, SPM are shown on stdout in text format; otherwise
 *          they are saved to file in binary format
 */

typedef struct GtBUstate_spm GtBUstate_spmeq;

GtBUstate_spmeq *gt_spmfind_eqlen_state_new(const GtEncseq *encseq,
    unsigned long minmatchlength, unsigned long w_maxsize, bool elimtrans,
    bool showspm, const char *indexname, unsigned int threadnum,
    GtLogger *default_logger, GtLogger *verbose_logger, GtError *err);

void gt_spmfind_eqlen_state_delete(GtBUstate_spmeq *state);

int gt_spmfind_eqlen_process(void *data,
    const unsigned long *seqnum_relpos_bucket, const GtSeqnumrelpos *snrp,
    const uint16_t *lcptab_bucket, unsigned long nonspecials,
    unsigned long spaceforbucketprocessing, GtError *err);

void gt_spmfind_eqlen_process_end(void *data);

typedef struct GtBUstate_spm GtBUstate_spmvar;

GtBUstate_spmvar *gt_spmfind_varlen_state_new(const GtEncseq *encseq,
    unsigned long minmatchlength, unsigned long w_maxsize, bool elimtrans,
    bool showspm, const char *indexname, unsigned int threadnum,
    GtLogger *default_logger, GtLogger *verbose_logger, GtError *err);

void gt_spmfind_varlen_state_delete(GtBUstate_spmvar *state);

int gt_spmfind_varlen_process(void *data,
    const unsigned long *seqnum_relpos_bucket, const GtSeqnumrelpos *snrp,
    const uint16_t *lcptab_bucket, unsigned long nonspecials,
    unsigned long spaceforbucketprocessing, GtError *err);

void gt_spmfind_varlen_process_end(void *data);

unsigned long gt_spmfind_varlen_nof_trans_spm(GtBUstate_spmvar *state);

unsigned long gt_spmfind_varlen_nof_irr_spm(GtBUstate_spmvar *state);

unsigned long gt_spmfind_eqlen_nof_trans_spm(GtBUstate_spmeq *state);

unsigned long gt_spmfind_eqlen_nof_irr_spm(GtBUstate_spmeq *state);

#endif
genometools-1.5.1/src/match/rdj-spmlist.c000066400000000000000000000374221211610345200203530ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include "core/str.h"
#include "core/assert_api.h"
#include "core/file.h"
#include "core/log_api.h"
#include "core/parseutils.h"
#include "core/splitter.h"
#include "core/ensure.h"
#include "core/minmax.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "match/rdj-spmlist.h"
/* unit test: */
#include "match/rdj-spmproc.h"
#include "match/rdj-ensure-output.h"

/* ---------------- Readjoiner bin format ---------------- */

#ifndef NDEBUG
#define GT_SPMLIST_ASSERT_CAST_SAFE(N, FROM, TO, TOMAX)\
  if (sizeof (FROM) > sizeof (TO)) \
    gt_assert(N < (FROM)TOMAX)
#else
#define GT_SPMLIST_ASSERT_CAST_SAFE(N, FROM, TO, TOMAX)
#endif

/*
 * INT1: suffix_seqnum
 * INT2: prefix_seqnum
 * INT3: length << 2 + suffixseq_direct << 1 + prefixseq_direct
 *
 * */

#if defined(_LP64) || (BITS == 32)
#define GT_RDJ_LENGTHASSERTION(BITS)\
        gt_assert(length <= (UINT ## BITS ## _MAX >> 2))
#else
#define GT_RDJ_LENGTHASSERTION(BITS) /* Nothing */
#endif

#define DEFINE_GT_SPMLIST_BIN_FORMAT(BITS)\
void gt_spmlist_write_header_bin ## BITS(FILE *file)\
{\
  gt_xfputc((int)GT_SPMLIST_BIN ## BITS, file);\
}\
void gt_spmproc_show_bin ## BITS(unsigned long suffix_seqnum,\
    unsigned long prefix_seqnum, unsigned long length, bool suffixseq_direct,\
    bool prefixseq_direct, void *file)\
{\
  uint ## BITS ## _t spmdata[3];\
  length <<= 2;\
  GT_RDJ_LENGTHASSERTION(BITS);\
  if (suffixseq_direct)\
    length |= 2;\
  if (prefixseq_direct)\
    length |= 1;\
  GT_SPMLIST_ASSERT_CAST_SAFE(suffix_seqnum, unsigned long, uint ## BITS ## _t,\
      UINT ## BITS ## _MAX);\
  spmdata[0] = (uint ## BITS ## _t) suffix_seqnum;\
  GT_SPMLIST_ASSERT_CAST_SAFE(prefix_seqnum, unsigned long, uint ## BITS ## _t,\
      UINT ## BITS ## _MAX);\
  spmdata[1] = (uint ## BITS ## _t) prefix_seqnum;\
  spmdata[2] = (uint ## BITS ## _t) length;\
  /*@ignore@*/\
  gt_xfwrite(&spmdata, sizeof (uint ## BITS ## _t), (size_t)3, (FILE*)file);\
  /*@end@*/\
}\
static int gt_spmlist_parse_bin ## BITS(FILE *file, unsigned long min_length,\
    GtSpmproc processoverlap, void *data, GtError *err)\
{\
  int had_err = 0;\
  size_t retval;\
  uint ## BITS ## _t spmdata[3];\
  unsigned long length;\
  bool suffixseq_direct, prefixseq_direct;\
  while (!feof(file))\
  {\
    retval = fread(&spmdata, sizeof (uint ## BITS ## _t), (size_t)3, file);\
    if (retval == 0 && feof(file))\
      break;\
    if (retval != (size_t)3)\
    {\
      had_err = -1;\
      gt_log_log("retval: %lu", (unsigned long)retval);\
      gt_error_set(err, "SPM binary file error: %s", feof(file) ?\
          "premature EOF" : strerror(errno));\
    }\
    GT_SPMLIST_ASSERT_CAST_SAFE(spmdata[2] >> 2, uint ## BITS ## _t,\
        unsigned long, ULONG_MAX);\
    length = (unsigned long)(spmdata[2] >> 2);\
    suffixseq_direct = (spmdata[2] & 2) != 0;\
    prefixseq_direct = (spmdata[2] & 1) != 0;\
    GT_SPMLIST_ASSERT_CAST_SAFE(spmdata[0], uint ## BITS ## _t,\
        unsigned long, ULONG_MAX);\
    GT_SPMLIST_ASSERT_CAST_SAFE(spmdata[1], uint ## BITS ## _t,\
        unsigned long, ULONG_MAX);\
    if (had_err == 0 && length >= min_length)\
      processoverlap((unsigned long)spmdata[0], (unsigned long)spmdata[1],\
          length, suffixseq_direct, prefixseq_direct, data);\
  }\
  return had_err;\
}

DEFINE_GT_SPMLIST_BIN_FORMAT(32);
DEFINE_GT_SPMLIST_BIN_FORMAT(64);

/* ---------------- Plain text format ---------------- */

/*@notfunction@*/
#define GT_SPMLIST_EOFERROR\
  do {\
    gt_error_set(err, "unexpected end of file");\
    return -1;\
  } while (false)

static inline int parse_plusminus(bool *destination, const char *source)
{
  if (strlen(source) != (size_t)1)
    return -1;
  switch (source[0])
  {
    case '+':
      *destination = true;
      return 0;
    case '-':
      *destination = false;
      return 0;
    default:
      return -1;
  }
}

#define GT_SPMLIST_PARSE(NR, F, PTR)\
  if (!had_err) \
  {\
    gt_assert(tokens != NULL);\
    had_err = F((PTR), tokens[NR]);\
    if (had_err) \
      gt_error_set(err, "Token %i unrecognized", NR);\
  }

static inline int parse_line(GtStr *s, unsigned long min_length,
    GtSpmproc proc_e, GtSpmprocA proc_a, void *data, GtError *err)
{
  int had_err = 0;
  GtSplitter *splitter;
  char **tokens = NULL;
  unsigned long suffix_seqnum = 0, prefix_seqnum = 0, suffix_length = 0,
                prefix_length, unit_edist;
  bool suffixseq_direct = true, prefixseq_direct = true, exact;

  exact = (proc_e != NULL) ? true : false;
  splitter = gt_splitter_new();
  gt_splitter_split(splitter, gt_str_get(s), gt_str_length(s), ' ');
  if (gt_splitter_size(splitter) != (exact ? 5UL : 7UL))
  {
    gt_error_set(err, "Wrong number of tokens");
    had_err = -1;
  }
  if (!had_err) tokens = gt_splitter_get_tokens(splitter);
  GT_SPMLIST_PARSE(0, gt_parse_ulong, &suffix_seqnum);
  GT_SPMLIST_PARSE(1, parse_plusminus, &suffixseq_direct);
  GT_SPMLIST_PARSE(2, gt_parse_ulong, &prefix_seqnum);
  GT_SPMLIST_PARSE(3, parse_plusminus, &prefixseq_direct);
  GT_SPMLIST_PARSE(4, gt_parse_ulong, &suffix_length);
  if (!exact)
  {
    GT_SPMLIST_PARSE(5, gt_parse_ulong, &prefix_length);
    GT_SPMLIST_PARSE(6, gt_parse_ulong, &unit_edist);
  }
  if (!had_err)
  {
    if (exact && suffix_length >= min_length)
    {
      gt_assert(proc_e != NULL);
      proc_e(suffix_seqnum, prefix_seqnum, suffix_length,
          suffixseq_direct, prefixseq_direct, data);
    }
    else if (!exact && (suffix_length >= min_length ||
          prefix_length >= min_length))
    {
      gt_assert(proc_a != NULL);
      proc_a(suffix_seqnum, prefix_seqnum, suffix_length, prefix_length,
          unit_edist, suffixseq_direct, prefixseq_direct, data);
    }
  }
  gt_splitter_delete(splitter);
  return had_err;
}

static int gt_spmlist_parse_ascii_generic(GtFile *infp,
    unsigned long min_length, GtSpmproc proc_e, GtSpmprocA proc_a, void *data,
    GtError *err)
{
  int had_err = 0;
  GtStr *line;
  gt_error_check(err);
  line = gt_str_new();
  while (!had_err && gt_str_read_next_line_generic(line, infp) != EOF)
  {
    had_err = parse_line(line, min_length, proc_e, proc_a, data, err);
    gt_str_reset(line);
  }
  gt_str_delete(line);
  return had_err;
}

static inline int gt_spmlist_parse_ascii(GtFile *infp, unsigned long min_length,
    GtSpmproc processoverlap, void *data, GtError *err)
{
  return gt_spmlist_parse_ascii_generic(infp, min_length, processoverlap, NULL,
      data, err);
}

int gt_spmlist_parse_ascii_approx(const char* filename,
    unsigned long min_length, GtSpmprocA processoverlap, void *data,
    GtError *err)
{
  int retval = 0;
  GtFile *infp;

  /*@i1@*/ gt_error_check(err);
  infp = gt_file_new(filename, "r", err);
  if (infp == NULL) return -1;
  retval = gt_spmlist_parse_ascii_generic(infp, min_length, NULL,
      processoverlap, data, err);
  gt_file_delete(infp);
  return retval;
}

int gt_spmlist_parse(const char* filename, unsigned long min_length,
    GtSpmproc processoverlap, void *data, GtError *err)
{
  int c, retval = 0;
  FILE *file;
  GtFile *infp;

  file = gt_fa_fopen(filename, "rb", err);
  if (file == NULL)
    return -1;
  infp = gt_file_new_from_fileptr(file);
  if (infp == NULL)
    return -1;

  c = gt_file_xfgetc(infp);
  switch (c)
  {
    case EOF:
      gt_error_set(err, "%s: file is empty", filename);
      retval = -1;
      break;
    case GT_SPMLIST_BIN32:
      gt_log_log("Spm file %s format: readjoiner-bin32", filename);
      retval = gt_spmlist_parse_bin32(file, min_length, processoverlap, data,
          err);
      break;
    case GT_SPMLIST_BIN64:
      gt_log_log("Spm file %s format: readjoiner-bin64", filename);
      retval = gt_spmlist_parse_bin64(file, min_length, processoverlap, data,
          err);
      break;
    default:
      gt_file_unget_char(infp, c);
      gt_log_log("Spm file %s format: readjoiner-text", filename);
      retval = gt_spmlist_parse_ascii(infp, min_length, processoverlap, data,
          err);
  }
  gt_file_delete(infp);
  return retval;
}

/* -------------------------- unit tests -------------------------- */

static inline int parse_plusminus_unit_test(GtError *err)
{
  int had_err = 0;
  bool destination;
  gt_ensure(had_err, parse_plusminus(&destination, "+") == 0);
  gt_ensure(had_err, destination);
  gt_ensure(had_err, parse_plusminus(&destination, "-") == 0);
  gt_ensure(had_err, !destination);
  gt_ensure(had_err, parse_plusminus(&destination, "xy") != 0);
  gt_ensure(had_err, parse_plusminus(&destination, "x") != 0);
  gt_ensure(had_err, parse_plusminus(&destination, "") != 0);
  return had_err;
}

struct GtSpmParseExactResult
{
  unsigned long suffix_seqnum, prefix_seqnum, length;
  bool suffixseq_direct, prefixseq_direct;
};

struct GtSpmParseApproxResult
{
  unsigned long suffix_seqnum, prefix_seqnum,
                suffix_length, prefix_length, unit_edist;
  bool suffixseq_direct, prefixseq_direct;
};

static void gt_spmlist_test_save(unsigned long suffix_seqnum,
    unsigned long prefix_seqnum, unsigned long length, bool suffixseq_direct,
    bool prefixseq_direct, void* data)
{
  struct GtSpmParseExactResult *r = data;
  r->suffix_seqnum = suffix_seqnum;
  r->prefix_seqnum = prefix_seqnum;
  r->length = length;
  r->suffixseq_direct = suffixseq_direct;
  r->prefixseq_direct = prefixseq_direct;
}

static void gt_spmlist_test_save_a(unsigned long suffix_seqnum,
    unsigned long prefix_seqnum, unsigned long suffix_length,
    unsigned long prefix_length, unsigned long unit_edist,
    bool suffixseq_direct, bool prefixseq_direct, void* data)
{
  struct GtSpmParseApproxResult *r = data;
  r->suffix_seqnum = suffix_seqnum;
  r->prefix_seqnum = prefix_seqnum;
  r->suffix_length = suffix_length;
  r->prefix_length = prefix_length;
  r->unit_edist = unit_edist;
  r->suffixseq_direct = suffixseq_direct;
  r->prefixseq_direct = prefixseq_direct;
}

#define GT_SPMPARSE_TEST_LINE_ERR(LINE)\
  do {\
    line = gt_str_new_cstr(LINE);\
    gt_ensure(had_err, parse_line(line, 0, gt_spmlist_test_save, NULL, &r,\
          parse_err) != 0);\
    gt_ensure(had_err, gt_error_is_set(parse_err));\
    gt_error_unset(parse_err);\
    gt_str_delete(line);\
  } while (false)

#define GT_SPMPARSE_TEST_LINE_OK(LINE,SN,PN,L,SD,PD)\
  do {\
    line = gt_str_new_cstr(LINE);\
    gt_ensure(had_err, parse_line(line, 0, gt_spmlist_test_save, NULL, &r,\
          parse_err) == 0);\
    gt_ensure(had_err, !gt_error_is_set(parse_err));\
    gt_ensure(had_err, r.suffix_seqnum == (SN));\
    gt_ensure(had_err, r.prefix_seqnum == (PN));\
    gt_ensure(had_err, r.length == (L));\
    gt_ensure(had_err, r.suffixseq_direct == (SD));\
    gt_ensure(had_err, r.prefixseq_direct == (PD));\
    gt_str_delete(line);\
  } while (false)

#define GT_SPMPARSE_TEST_LINE_A_ERR(LINE)\
  do {\
    line = gt_str_new_cstr(LINE);\
    gt_ensure(had_err, parse_line(line, 0, NULL, gt_spmlist_test_save_a, &r_a,\
          parse_err) != 0);\
    gt_ensure(had_err, gt_error_is_set(parse_err));\
    gt_error_unset(parse_err);\
    gt_str_delete(line);\
  } while (false)

#define GT_SPMPARSE_TEST_LINE_A_OK(LINE,SN,PN,SL,PL,UE,SD,PD)\
  do {\
    line = gt_str_new_cstr(LINE);\
    gt_ensure(had_err, parse_line(line, 0, NULL, gt_spmlist_test_save_a, &r_a,\
          parse_err) == 0);\
    gt_ensure(had_err, !gt_error_is_set(parse_err));\
    gt_ensure(had_err, r_a.suffix_seqnum == (SN));\
    gt_ensure(had_err, r_a.prefix_seqnum == (PN));\
    gt_ensure(had_err, r_a.suffix_length == (SL));\
    gt_ensure(had_err, r_a.prefix_length == (PL));\
    gt_ensure(had_err, r_a.unit_edist == (UE));\
    gt_ensure(had_err, r_a.suffixseq_direct == (SD));\
    gt_ensure(had_err, r_a.prefixseq_direct == (PD));\
    gt_str_delete(line);\
  } while (false)

static inline int parse_line_unit_test(GtError* err)
{
  int had_err = 0;
  GtStr *line;
  GtError *parse_err;
  struct GtSpmParseExactResult r;
  struct GtSpmParseApproxResult r_a;

  gt_error_check(err);
  parse_err = gt_error_new();
  GT_SPMPARSE_TEST_LINE_ERR("1 2 + 3 4");
  GT_SPMPARSE_TEST_LINE_ERR("4 5 1");
  GT_SPMPARSE_TEST_LINE_ERR("1 1 1 1");
  GT_SPMPARSE_TEST_LINE_ERR("1x 2 + 1");
  GT_SPMPARSE_TEST_LINE_OK("1 + 2 - 3", 1UL, 2UL, 3UL, true, false);
  GT_SPMPARSE_TEST_LINE_OK("2 - 1 + 3", 2UL, 1UL, 3UL, false, true);
  GT_SPMPARSE_TEST_LINE_OK("4 + 5 + 6", 4UL, 5UL, 6UL, true, true);
  GT_SPMPARSE_TEST_LINE_A_ERR("1 + 2 + 3");
  GT_SPMPARSE_TEST_LINE_A_ERR("4 + 5 + 1 5 4 5");
  GT_SPMPARSE_TEST_LINE_A_ERR("1 1 1 1 2 3");
  GT_SPMPARSE_TEST_LINE_A_ERR("1x + 2 + 1 2 3");
  GT_SPMPARSE_TEST_LINE_A_OK("1 + 2 - 3 4 1", 1UL, 2UL, 3UL, 4UL, 1UL, true,
      false);
  GT_SPMPARSE_TEST_LINE_A_OK("2 - 1 + 3 4 1", 2UL, 1UL, 3UL, 4UL, 1UL, false,
      true);
  GT_SPMPARSE_TEST_LINE_A_OK("4 + 5 + 6 7 1", 4UL, 5UL, 6UL, 7UL, 1UL, true,
      true);
  gt_error_delete(parse_err);
  return had_err;
}

static int gt_spmlist_parse_unit_test(GtError *err)
{
  int had_err = 0;
  gt_error_check(err);
  had_err = parse_plusminus_unit_test(err);
  if (!had_err) had_err = parse_line_unit_test(err);
  return had_err;
}

void gt_spmproc_show_ascii(unsigned long suffix_seqnum,
    unsigned long prefix_seqnum,
    unsigned long length,
    bool suffixseq_direct,
    bool prefixseq_direct,
    void *data)
{
  GtFile *file = data;
  gt_file_xprintf(file, "%lu %s %lu %s %lu\n", suffix_seqnum,
      suffixseq_direct ? "+" : "-", prefix_seqnum,
      prefixseq_direct ? "+" : "-", length);
}

void gt_spmproc_a_show_ascii(unsigned long suffix_seqnum,
    unsigned long prefix_seqnum,
    unsigned long suffix_length,
    unsigned long prefix_length,
    unsigned long unit_edist,
    bool suffixseq_direct,
    bool prefixseq_direct,
    void *data)
{
  GtFile *file = data;
  gt_file_xprintf(file, "%lu %s %lu %s %lu %lu %lu\n", suffix_seqnum,
      suffixseq_direct ? "+" : "-", prefix_seqnum,
      prefixseq_direct ? "+" : "-", suffix_length, prefix_length,
      unit_edist);
}

/* ---------------------- Unit Test ---------------------- */

static void spmproc_show_caller(GtSpmproc proc, void *data)
{
  proc(0UL, 1UL, 10UL, true, true, data);
  proc(0UL, 2UL, 10UL, true, false, data);
  proc(2UL, 0UL, 10UL, false, true, data);
  proc(1UL, 0UL, 10UL, false, true, data);
}

static void spmproc_a_show_caller(GtSpmprocA proc, void *data)
{
  proc(0UL, 1UL, 10UL, 11UL, 1UL, true, true, data);
  proc(0UL, 2UL, 10UL, 10UL, 0UL, true, false, data);
  proc(2UL, 0UL, 10UL, 12UL, 2UL, false, true, data);
  proc(1UL, 0UL, 11UL, 11UL, 0UL, false, true, data);
}

static int gt_spmproc_show_unit_test(GtError *err)
{
  int had_err = 0;
  GT_ENSURE_OUTPUT_DECLARE(100);

  gt_error_check(err);

  GT_ENSURE_OUTPUT(
      spmproc_show_caller(gt_spmproc_show_ascii, outfp),
      "0 + 1 + 10\n0 + 2 - 10\n2 - 0 + 10\n1 - 0 + 10\n");

  if (!had_err)
  {
    GT_ENSURE_OUTPUT(
        spmproc_a_show_caller(gt_spmproc_a_show_ascii, outfp),
        "0 + 1 + 10 11 1\n0 + 2 - 10 10 0\n"
        "2 - 0 + 10 12 2\n1 - 0 + 11 11 0\n");
  }

  return had_err;
}

int gt_spmlist_unit_test(GtError *err)
{
  int had_err = 0;
  had_err = gt_spmproc_show_unit_test(err);
  if (had_err == 0)
    had_err = gt_spmlist_parse_unit_test(err);
  return had_err;
}
genometools-1.5.1/src/match/rdj-spmlist.h000066400000000000000000000044671211610345200203630ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_SPMLIST_H
#define RDJ_SPMLIST_H

#include "core/error_api.h"
#include "match/rdj-spmproc.h"

                 /* header byte: */
typedef enum {
  GT_SPMLIST_BIN32      = 2,
  GT_SPMLIST_BIN64      = 3,
  GT_SPMLIST_ASCII   /* = any other value */,
} GtSpmlistFormat;

#define DECLARE_GT_SPMLIST_BIN_FORMAT(BITS)\
void gt_spmlist_write_header_bin ## BITS(FILE *file);\
void gt_spmproc_show_bin ## BITS(unsigned long suffix_seqnum,\
    unsigned long prefix_seqnum, unsigned long length, bool suffixseq_direct,\
    bool prefixseq_direct, void *file)

DECLARE_GT_SPMLIST_BIN_FORMAT(32);
DECLARE_GT_SPMLIST_BIN_FORMAT(64);

/* parse a spmlist file; format is recognized by reading the first byte */
int gt_spmlist_parse(const char* filename, unsigned long min_length,
    GtSpmproc processoverlap, void *data, GtError *err);

void gt_spmproc_show_ascii(unsigned long suffix_seqnum,
    unsigned long prefix_seqnum, unsigned long length, bool suffixseq_direct,
    bool prefixseq_direct, void *data /* GtFile */);

/* approx overlaps: */

int gt_spmlist_approx_parse(const char* filename, unsigned long min_length,
    GtSpmprocA processoverlap, void *data, GtError *err);

void gt_spmproc_a_show_ascii(unsigned long suffix_seqnum,
    unsigned long prefix_seqnum, unsigned long suffix_length,
    unsigned long prefix_length, unsigned long unit_edist,
    bool suffixseq_direct, bool prefixseq_direct, void *data /* GtFile */);

/* tests */

int gt_spmlist_unit_test(GtError *err);

#endif
genometools-1.5.1/src/match/rdj-spmproc.c000066400000000000000000000110711211610345200203330ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "match/rdj-spmproc.h"
/* for unit test: */
#include "core/unused_api.h"
#include "core/ensure.h"

void gt_spmproc_a_e(unsigned long suffix_seqnum, unsigned long prefix_seqnum,
  unsigned long suffix_length, GT_UNUSED unsigned long prefix_length,
  unsigned long unit_edist, bool suffixseq_direct, bool prefixseq_direct,
  void *data)
{
  GtSpmprocWithData* a_e_data = data;
  if (unit_edist == 0)
  {
    a_e_data->proc(suffix_seqnum, prefix_seqnum, suffix_length,
                   suffixseq_direct, prefixseq_direct, a_e_data->data);
  }
}

void gt_spmproc_skip(unsigned long suffix_seqnum, unsigned long prefix_seqnum,
  unsigned long length, bool suffixseq_direct, bool prefixseq_direct,
  void *data)
{
  GtSpmprocSkipData *d = data;

  if (d->to_skip != NULL)
  {
    if ((bool)GT_ISIBITSET(d->to_skip, suffix_seqnum) ||
        (bool)GT_ISIBITSET(d->to_skip, prefix_seqnum))
    {
      d->skipped_counter++;
      return;
    }
  }
  if (d->out.e.proc != NULL)
  {
    d->out.e.proc(suffix_seqnum, prefix_seqnum, length, suffixseq_direct,
                  prefixseq_direct, d->out.e.data);
  }
}

void gt_spmproc_a_skip(unsigned long suffix_seqnum,
                       unsigned long prefix_seqnum,
                       unsigned long suffix_length,
                       unsigned long prefix_length,
                       unsigned long unit_edist,
                       bool suffixseq_direct,
                       bool prefixseq_direct,
                       void *data)
{
  GtSpmprocSkipData *d = data;

  if (d->to_skip != NULL)
  {
    if ((bool)GT_ISIBITSET(d->to_skip, suffix_seqnum) ||
        (bool)GT_ISIBITSET(d->to_skip, prefix_seqnum))
    {
      d->skipped_counter++;
      return;
    }
  }

  if (d->out.a.proc != NULL)
  {
    d->out.a.proc(suffix_seqnum, prefix_seqnum, suffix_length, prefix_length,
                unit_edist, suffixseq_direct, prefixseq_direct, d->out.a.data);
  }
}

/* unit test */

static void outproc(GT_UNUSED unsigned long suffix_seqnum,
  GT_UNUSED unsigned long prefix_seqnum, GT_UNUSED unsigned long length,
  GT_UNUSED bool suffixseq_direct, GT_UNUSED bool prefixseq_direct, void *data)
{
  *(bool *)data = false;
}

static void outproc_a(GT_UNUSED unsigned long suffix_seqnum,
  GT_UNUSED unsigned long prefix_seqnum, GT_UNUSED unsigned long suffix_length,
  GT_UNUSED unsigned long prefix_length, GT_UNUSED unsigned long unit_edist,
  GT_UNUSED bool suffixseq_direct, GT_UNUSED bool prefixseq_direct, void *data)
{
  *(bool *)data = false;
}

#define GT_SPMPROC_SKIP_TEST(SN,PN,EXP)\
        skipped = true;\
        d.out.e.proc = outproc;\
        d.out.e.data = &skipped;\
        gt_spmproc_skip((SN), (PN), 100UL, false, true, &d);\
        if (EXP) gt_ensure(had_err, skipped);\
        else gt_ensure(had_err, !skipped);\
        skipped = true;\
        d.out.a.proc = outproc_a;\
        d.out.a.data = &skipped;\
        gt_spmproc_a_skip((SN), (PN), 100UL, 101UL, 1UL, true, false, &d);\
        if (EXP) gt_ensure(had_err, skipped);\
        else gt_ensure(had_err, !skipped)

int gt_spmproc_skip_unit_test(GtError *err)
{
  int had_err = 0;
  GtSpmprocSkipData d;
  bool skipped;

  gt_error_check(err);
  GT_INITBITTAB(d.to_skip, 4);
  GT_SETIBIT(d.to_skip, 1);
  GT_SETIBIT(d.to_skip, 2);
  GT_SPMPROC_SKIP_TEST(0UL, 1UL, true);
  GT_SPMPROC_SKIP_TEST(1UL, 2UL, true);
  GT_SPMPROC_SKIP_TEST(2UL, 3UL, true);
  GT_SPMPROC_SKIP_TEST(0UL, 3UL, false);

  gt_free(d.to_skip);

  return had_err;
}

void gt_spmproc_show_count(GT_UNUSED unsigned long suffix_seqnum,
  GT_UNUSED unsigned long prefix_seqnum, GT_UNUSED unsigned long length,
  GT_UNUSED bool suffixseq_direct, GT_UNUSED bool prefixseq_direct,
  void *data)
{
  unsigned long long *counter = data;
  (*counter)++;
}
genometools-1.5.1/src/match/rdj-spmproc.h000066400000000000000000000061451211610345200203460ustar00rootroot00000000000000/*
  Copyright (c) 2009-2011 Giorgio Gonnella 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_SPMPROC_H
#define RDJ_SPMPROC_H

#include 
#include "core/intbits.h"            /* GtBitsequence */
#include "core/error_api.h"          /* GtError */

/* Prototype for functions processing exact/approximate overlaps */

/* Exact: */
typedef void(*GtSpmproc)(unsigned long /*suffix_seqnum*/,
  unsigned long /*prefix_seqnum*/, unsigned long /*length*/,
  bool /*suffixseq_direct*/, bool /*prefixseq_direct*/, void* /*data*/);

/* Approximate: */
typedef void(*GtSpmprocA)(unsigned long /*suffix_seqnum*/,
  unsigned long /*prefix_seqnum*/, unsigned long /*suffix_length*/,
  unsigned long /*prefix_length*/, unsigned long /*unit_edist*/,
  bool /*suffixseq_direct*/, bool /*prefixseq_direct*/, void* /*data*/);

/* structs containing an spmproc and its data */
typedef struct {GtSpmproc proc; void *data;} GtSpmprocWithData;
typedef struct {GtSpmprocA proc; void *data;} GtSpmprocAWithData;
typedef union {GtSpmprocWithData e; GtSpmprocAWithData a;} GtSpmprocXWithData;

/* allow to use GtSpmproc where GtSpmprocA is expected skipping overlaps with
   unit edist > 0; data must be a pointer to GtSpmprocWithData */
void gt_spmproc_a_e(unsigned long suffix_seqnum, unsigned long prefix_seqnum,
  unsigned long suffix_length, unsigned long prefix_length,
  unsigned long unit_edist, bool suffixseq_direct, bool prefixseq_direct,
  void *data);

void gt_spmproc_count(unsigned long suffix_seqnum, unsigned long prefix_seqnum,
  unsigned long length, bool suffixseq_direct, bool prefixseq_direct,
  void *data);

/*
Given a GtBitsequence (large as the number of reads), acts as a filter
and calls the Spmproc outproc if the bit for both seqnums is not set.
The void* data must be of type GtSpmprocSkipData.
*/

typedef struct {
  GtBitsequence *to_skip;
  GtSpmprocXWithData out;
  unsigned long skipped_counter;
} GtSpmprocSkipData;

void gt_spmproc_skip(unsigned long suffix_seqnum, unsigned long prefix_seqnum,
  unsigned long length, bool suffixseq_direct, bool prefixseq_direct,
  void *data);

void gt_spmproc_a_skip(unsigned long suffix_seqnum,
  unsigned long prefix_seqnum, unsigned long suffix_length,
  unsigned long prefix_length, unsigned long unit_edist, bool suffixseq_direct,
  bool prefixseq_direct, void *data);

int gt_spmproc_skip_unit_test(GtError *err);

#endif
genometools-1.5.1/src/match/rdj-ssar.c000066400000000000000000000047031211610345200176240ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/fileutils_api.h"
#include "match/rdj-ssar.h"

#define GT_READJOINER_CHECK_FILE(SUFFIX)\
  filename = gt_str_clone(indexname);\
  gt_str_append_cstr(filename, SUFFIX);\
  if (!gt_file_exists(gt_str_get(filename)))\
  {\
    gt_error_set(err, "file \"%s\" does not exist "\
                      "or is not readable", gt_str_get(filename));\
    gt_str_delete(filename);\
    return NULL;\
  }\
  gt_str_delete(filename)

Sequentialsuffixarrayreader* gt_readjoiner_ssar_new(GtStr *indexname,
    bool esqtab, bool mapped, GtLogger *logger, GtError *err)
{
  Sequentialsuffixarrayreader *ssar;
  GtStr *filename;

  /*@i1@*/ gt_error_check(err);

  /* check that necessary files are available */
  GT_READJOINER_CHECK_FILE(".suf");
  GT_READJOINER_CHECK_FILE(".lcp");
  GT_READJOINER_CHECK_FILE(".llv");
  GT_READJOINER_CHECK_FILE(".al1");
  GT_READJOINER_CHECK_FILE(".prj");
  if (esqtab)
  {
    GT_READJOINER_CHECK_FILE(".esq");
  }
  /* ".ssp" is not checked as not present for sat eqlen */
  ssar = gt_newSequentialsuffixarrayreaderfromfile(
           gt_str_get(indexname),
           esqtab
             ? SARR_LCPTAB |SARR_SUFTAB | SARR_SSPTAB | SARR_ESQTAB
             : SARR_LCPTAB |SARR_SUFTAB | SARR_SSPTAB,
           mapped
             ? SEQ_mappedboth
             : SEQ_scan,
           logger,
           err);
  if (gt_error_is_set(err))
  {
    if (ssar != NULL)
      gt_freeSequentialsuffixarrayreader(&ssar);
    return NULL;
  }
  else
  {
    return ssar;
  }
}

void gt_readjoiner_ssar_delete(Sequentialsuffixarrayreader *ssar)
{
  if (ssar != NULL)
    gt_freeSequentialsuffixarrayreader(&ssar);
}
genometools-1.5.1/src/match/rdj-ssar.h000066400000000000000000000023171211610345200176300ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_SSAR_H
#define RDJ_SSAR_H

#include "match/esa-seqread.h"       /* Sequentialsuffixarrayreader */
#include "core/error_api.h"          /* GtError */

Sequentialsuffixarrayreader* gt_readjoiner_ssar_new(GtStr *indexname,
    bool esqtab, bool mapped, GtLogger *logger, GtError *err);

void gt_readjoiner_ssar_delete(Sequentialsuffixarrayreader *ssar);

#endif
genometools-1.5.1/src/match/rdj-strgraph-counts-char-def.h000066400000000000000000000127051211610345200234740ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_COUNTS_CHAR_DEF_H
#define RDJ_STRGRAPH_COUNTS_CHAR_DEF_H

#include 
#include "core/hashmap-generic.h"

/* --- for exclusive use in rdj-strgraph.c (__ = private) --- */

#define GT_STRGRAPH_COUNTS_REPRESENTATION "char array + hash table"

typedef unsigned char GtStrgraphCount__Small;
typedef unsigned long GtStrgraphCount__Large;
typedef GtStrgraphCount__Large GtStrgraphCount;
#define FormatGtStrgraphCount       "%lu"
#define PRINTGtStrgraphCountcast(X) (X)
#define SCANGtStrgraphCountcast(X)  (X)
#define GT_STRGRAPH_COUNT_MAX       ULONG_MAX

/* hash map for large counts: vertex number -> count */
DECLARE_HASHMAP(GtStrgraphVnum, v, GtStrgraphCount__Large, c_,
                static, inline);
DEFINE_HASHMAP(GtStrgraphVnum, v, GtStrgraphCount__Large, c_,
               gt_ht_ul_elem_hash, gt_ht_ul_elem_cmp, NULL_DESTRUCTOR,
               NULL_DESTRUCTOR, static, inline);

#define GT_STRGRAPH_DECLARE_COUNTS\
  GtStrgraphCount__Small *__small_counts;\
  GtHashtable            *__large_counts;\
  GtStrgraphVnum       __n_counts

#define GT_STRGRAPH__COUNT_IS_LARGE ((GtStrgraphCount__Small)255)

#define GT_STRGRAPH_ALLOC_COUNTS(STRGRAPH, NOFVERTICES)\
  (STRGRAPH)->__small_counts = gt_calloc((size_t)(NOFVERTICES),\
      sizeof (*(STRGRAPH)->__small_counts));\
  (STRGRAPH)->__large_counts = v_c__gt_hashmap_new();\
  (STRGRAPH)->__n_counts = (NOFVERTICES)

#define GT_STRGRAPH_FREE_COUNTS(STRGRAPH)\
  gt_free((STRGRAPH)->__small_counts);\
  (STRGRAPH)->__small_counts = NULL;\
  if ((STRGRAPH)->__large_counts != NULL)\
    v_c__gt_hashmap_delete((STRGRAPH)->__large_counts);\
  (STRGRAPH)->__large_counts = NULL

#define GT_STRGRAPH_GET_COUNT(STRGRAPH, POSITION) \
  (((STRGRAPH)->__small_counts[(POSITION)] < GT_STRGRAPH__COUNT_IS_LARGE)\
    ? (GtStrgraphCount)((STRGRAPH)->__small_counts[(POSITION)]) \
    : (GtStrgraphCount)*v_c__gt_hashmap_get((STRGRAPH)->__large_counts,\
      (POSITION)))

#define GT_STRGRAPH__SET_COUNT(STRGRAPH, POSITION, VALUE) \
  if ((VALUE) < (GtStrgraphCount)GT_STRGRAPH__COUNT_IS_LARGE)\
  {\
    ((STRGRAPH)->__small_counts[(POSITION)] = (GtStrgraphCount__Small)(VALUE));\
  }\
  else\
  {\
    ((STRGRAPH)->__small_counts[(POSITION)] = GT_STRGRAPH__COUNT_IS_LARGE);\
    v_c__gt_hashmap_add((STRGRAPH)->__large_counts, (POSITION), (VALUE));\
  }\

#define GT_STRGRAPH_INC_COUNT(STRGRAPH, POSITION) \
  if ((STRGRAPH)->__small_counts[(POSITION)] < GT_STRGRAPH__COUNT_IS_LARGE -\
      (GtStrgraphCount__Small)1)\
    ((STRGRAPH)->__small_counts[(POSITION)])++; \
  else if ((STRGRAPH)->__small_counts[(POSITION)] == \
      GT_STRGRAPH__COUNT_IS_LARGE - (GtStrgraphCount__Small)1) \
  { \
    (STRGRAPH)->__small_counts[(POSITION)] = GT_STRGRAPH__COUNT_IS_LARGE;\
    gt_assert(v_c__gt_hashmap_get((STRGRAPH)->__large_counts,\
          (POSITION)) == NULL);\
    v_c__gt_hashmap_add((STRGRAPH)->__large_counts, (POSITION),\
        (GtStrgraphCount__Large)GT_STRGRAPH__COUNT_IS_LARGE);\
  } \
  else\
  {\
    gt_assert((STRGRAPH)->__small_counts[(POSITION)] == \
        GT_STRGRAPH__COUNT_IS_LARGE);\
    gt_assert(v_c__gt_hashmap_get((STRGRAPH)->__large_counts,\
          (POSITION)) != NULL);\
    (*v_c__gt_hashmap_get((STRGRAPH)->__large_counts, (POSITION)))++;\
  }

enum iterator_op gt_strgraph__save_large_count(GtStrgraphVnum vnum,
   GtStrgraphCount__Large count, GtFile *outfp, GT_UNUSED GtError *err)
{
  gt_file_xwrite(outfp, &vnum, sizeof (GtStrgraphVnum));
  gt_file_xwrite(outfp, &count, sizeof (GtStrgraphCount__Large));
  return CONTINUE_ITERATION;
}

#define GT_STRGRAPH_SERIALIZE_COUNTS(STRGRAPH, FP) \
  GT_STRGRAPH_SERIALIZE_DATA((FP), (STRGRAPH)->__n_counts,\
      (STRGRAPH)->__small_counts);\
  (void)v_c__gt_hashmap_foreach((STRGRAPH)->__large_counts,\
      (v_c__gt_hashmap_iteratorfunc)gt_strgraph__save_large_count,\
      (FP), NULL)

#define GT_STRGRAPH__DESERIALIZE_LARGE_COUNTS(STRGRAPH, FP) \
  {\
    GtStrgraphVnum          __large_count_vnum;\
    GtStrgraphCount__Large  __large_count = 0;\
    GT_UNUSED int           __large_count_read_retval;\
    \
    while (gt_file_xread((FP), &__large_count_vnum,\
        sizeof (__large_count_vnum)) == (int)sizeof (__large_count_vnum))\
    {\
      __large_count_read_retval = gt_file_xread((FP), &__large_count, \
          sizeof (__large_count));\
      gt_assert(__large_count_read_retval == (int)sizeof (__large_count));\
      GT_STRGRAPH__SET_COUNT((STRGRAPH), __large_count_vnum, __large_count);\
    }\
  }

#define GT_STRGRAPH_DESERIALIZE_COUNTS(STRGRAPH, FP) \
  GT_STRGRAPH_DESERIALIZE_DATA((FP), \
      (STRGRAPH)->__n_counts, (STRGRAPH)->__small_counts);\
  GT_STRGRAPH__DESERIALIZE_LARGE_COUNTS(STRGRAPH, FP)

#endif
genometools-1.5.1/src/match/rdj-strgraph-edges-bitfield-def.h000066400000000000000000000135361211610345200241200ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_EDGES_BITFIELD_DEF_H
#define RDJ_STRGRAPH_EDGES_BITFIELD_DEF_H

#define GT_STRGRAPH_EDGES_REPRESENTATION "bitfield"

typedef unsigned long GtStrgraphLength;
#define FormatGtStrgraphLength       "%lu"
#define PRINTGtStrgraphLengthcast(X) (X)
#define SCANGtStrgraphLengthcast(X)  (X)
#define GT_STRGRAPH__LEN_BITS        18
#define GT_STRGRAPH_LENGTH_MAX \
  ((GtStrgraphLength)(1UL << GT_STRGRAPH__LEN_BITS) - 1)

#define GT_STRGRAPH__DEST_BITS 44
#ifndef S_SPLINT_S
#define GT_STRGRAPH__DEST_MAX ((1ULL << GT_STRGRAPH__DEST_BITS) - 1)
#else
#define GT_STRGRAPH__DEST_MAX ULONG_MAX
#endif

#if GT_STRGRAPH__DEST_MAX >= ULONG_MAX
#define GT_STRGRAPH_N_READS_MAX (unsigned long)(GT_STRGRAPH__DEST_MAX >> 1)
#else
#define GT_STRGRAPH_N_READS_MAX (ULONG_MAX >> 1)
#endif

typedef struct {
  GtStrgraphVnum    __dest      :GT_STRGRAPH__DEST_BITS;
  GtStrgraphLength  __len       :GT_STRGRAPH__LEN_BITS;
  bool              __reduced   :1;
  bool              __mark      :1;
} GtStrgraph__Edge;

#define GT_STRGRAPH_DECLARE_EDGES \
  GtStrgraphEdgenum  __n_edges;\
  GtStrgraph__Edge  *__e

#define GT_STRGRAPH__EDGE_NOT_REDUCED   false
#define GT_STRGRAPH__EDGE_REDUCED       true
#define GT_STRGRAPH__EDGE_NOT_MARKED    false
#define GT_STRGRAPH__EDGE_MARKED        true

#define GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, N) \
  ((STRGRAPH)->__e + GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, N))

/* edge accessor macros */

#define GT_STRGRAPH_EDGE_SET_DEST(STRGRAPH, V, EDGENUM, DEST) \
  GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__dest = (DEST)

#define GT_STRGRAPH_EDGE_DEST(STRGRAPH, V, EDGENUM) \
  ((GtStrgraphVnum)(GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__dest))

#define GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, V, EDGENUM, LEN) \
  GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__len = (LEN)

#define GT_STRGRAPH_EDGE_LEN(STRGRAPH, V, EDGENUM) \
  ((GtStrgraphLength)(GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__len))

#define GT_STRGRAPH_EDGE_INIT(STRGRAPH, V, EDGENUM) \
  GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__reduced = \
      GT_STRGRAPH__EDGE_NOT_REDUCED; \
  GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__mark = \
      GT_STRGRAPH__EDGE_NOT_MARKED

#define GT_STRGRAPH_EDGE_SET_MARK(STRGRAPH, V, EDGENUM) \
  GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__mark = \
      GT_STRGRAPH__EDGE_MARKED

#define GT_STRGRAPH_EDGE_HAS_MARK(STRGRAPH, V, EDGENUM) \
  ((GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__mark == \
   GT_STRGRAPH__EDGE_MARKED) ? true : false)

#define GT_STRGRAPH_EDGE_REDUCE(STRGRAPH, V, EDGENUM) \
  (GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__reduced = \
   GT_STRGRAPH__EDGE_REDUCED)

#define GT_STRGRAPH_EDGE_IS_REDUCED(STRGRAPH, V, EDGENUM) \
  (GT_STRGRAPH__V_NTH_EDGE(STRGRAPH, V, EDGENUM)->__reduced == \
   GT_STRGRAPH__EDGE_REDUCED)

#define GT_STRGRAPH_NOFEDGES(STRGRAPH) \
  ((STRGRAPH)->__n_edges)

#define GT_STRGRAPH_SET_NOFEDGES(STRGRAPH, VALUE) \
  (STRGRAPH)->__n_edges = (VALUE)

#define GT_STRGRAPH__SIZEOF_EDGE \
  (sizeof (GtStrgraph__Edge))

#define GT_STRGRAPH_SIZEOF_EDGES(STRGRAPH) \
  (GT_STRGRAPH__SIZEOF_EDGE * GT_STRGRAPH_NOFEDGES(STRGRAPH) +\
   sizeof ((STRGRAPH)->__n_edges))

#define GT_STRGRAPH_ALLOC_EDGES(STRGRAPH)\
  (STRGRAPH)->__e = gt_calloc((size_t)GT_STRGRAPH_NOFEDGES(STRGRAPH),\
      sizeof (*(STRGRAPH)->__e))

#define GT_STRGRAPH_SHRINK_EDGES(STRGRAPH, NEWSIZE)\
  do {\
    gt_assert((NEWSIZE) < GT_STRGRAPH_NOFEDGES(STRGRAPH));\
    GT_STRGRAPH_SET_NOFEDGES(STRGRAPH, NEWSIZE);\
    if ((NEWSIZE) == 0)\
    {\
      GT_STRGRAPH_FREE_EDGES(STRGRAPH);\
    }\
    else\
    {\
      (STRGRAPH)->__e = \
          gt_realloc((STRGRAPH)->__e, GT_STRGRAPH_NOFEDGES(STRGRAPH) * \
          sizeof (*(STRGRAPH)->__e));\
    }\
  } while (false)

#define GT_STRGRAPH_FREE_EDGES(STRGRAPH)\
  gt_free((STRGRAPH)->__e);\
  (STRGRAPH)->__e = NULL

#define GT_STRGRAPH_COPY_EDGE(STRGRAPH, OFFSET_SOURCE, OFFSET_DEST)\
  (STRGRAPH)->__e[OFFSET_DEST] = (STRGRAPH)->__e[OFFSET_SOURCE]

/* order by length from < to > */
int gt_strgraph_edges_compare_by_length(const void *edgea,
    const void *edgeb)
{
  const GtStrgraph__Edge *a = edgea, *b = edgeb;
  return (int)(a->__len > b->__len) - (int)(a->__len < b->__len);
}

#define GT_STRGRAPH_SORT_V_EDGES(STRGRAPH, VNUM)\
  do {\
    GtStrgraphVEdgenum v_nofedges;\
    v_nofedges = GT_STRGRAPH_V_NOFEDGES(STRGRAPH, VNUM);\
    if (v_nofedges > (GtStrgraphVEdgenum)1)\
      qsort((STRGRAPH)->__e + GT_STRGRAPH_V_OFFSET(STRGRAPH, VNUM),\
          (size_t)v_nofedges, sizeof (*(STRGRAPH)->__e),\
          gt_strgraph_edges_compare_by_length);\
  } while (false)

#define GT_STRGRAPH_SERIALIZE_EDGES(STRGRAPH, FP)\
  GT_STRGRAPH_SERIALIZE_DATA((FP), \
      GT_STRGRAPH_NOFEDGES(STRGRAPH), (STRGRAPH)->__e)

#define GT_STRGRAPH_DESERIALIZE_EDGES(STRGRAPH, FP)\
  GT_STRGRAPH_DESERIALIZE_DATA((FP), \
      GT_STRGRAPH_NOFEDGES(STRGRAPH), (STRGRAPH)->__e)

#define GT_STRGRAPH_FIND_LONGEST_EDGE(STRGRAPH, VNUM, LONGEST) \
        LONGEST = GT_STRGRAPH_EDGE_LEN(STRGRAPH, VNUM, \
          GT_STRGRAPH_V_NOFEDGES(STRGRAPH, VNUM) - 1);

#endif
genometools-1.5.1/src/match/rdj-strgraph-edges-bitpack-def.h000066400000000000000000000241051211610345200237450ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_EDGES_BITPACK_DEF_H
#define RDJ_STRGRAPH_EDGES_BITPACK_DEF_H

#include 
#include "core/bitpackarray.h"
#include "core/intbits.h"

#define GT_STRGRAPH_EDGES_REPRESENTATION "bitpack"

typedef uint64_t GtStrgraphLength;
#define FormatGtStrgraphLength        Formatuint64_t
#define PRINTGtStrgraphLengthcast(X)  PRINTuint64_tcast(X)
#define SCANGtStrgraphLengthcast(X)   SCANuint64_tcast(X)

/* LENGTH_MAX is limited by __e_len */
#define GT_STRGRAPH_LENGTH_MAX   (GtStrgraphLength)UINT64_MAX

#if UINT64_MAX >= ULONG_MAX
/* N_READS_MAX is limited by read numbers in the encseq */
#define GT_STRGRAPH_N_READS_MAX ((ULONG_MAX >> 1) - 1)
#else
/* N_READS_MAX is limited by __e_dest */
#define GT_STRGRAPH_N_READS_MAX (unsigned long)((UINT64_MAX >> 1) - 1)
#endif

#define GT_STRGRAPH_DECLARE_EDGES\
  BitPackArray       *__e_len;\
  BitPackArray       *__e_dest;\
  GtBitsequence      *__e_mark;\
  GtStrgraphLength   __len_max;\
  GtStrgraphEdgenum   __n_edges

#define GT_STRGRAPH_SET_NOFEDGES(STRGRAPH, VALUE) \
  (STRGRAPH)->__n_edges = (VALUE)

#define GT_STRGRAPH_NOFEDGES(STRGRAPH) \
  ((STRGRAPH)->__n_edges)

#define GT_STRGRAPH__LEN_BITS(STRGRAPH)\
  (gt_requiredUInt64Bits((STRGRAPH)->__len_max))

#define GT_STRGRAPH__UNDEF_EDGE_LEN(STRGRAPH) \
  ((STRGRAPH)->__len_max)

#define GT_STRGRAPH__EDGE_REDUCED(STRGRAPH) \
  GT_STRGRAPH__UNDEF_EDGE_LEN(STRGRAPH)

#define GT_STRGRAPH__ALLOC_LENGTHSLIST(STRGRAPH)\
  (STRGRAPH)->__len_max = gt_strgraph_longest_read(STRGRAPH) - \
    (STRGRAPH)->minmatchlen + 1;\
  (STRGRAPH)->__e_len = bitpackarray_new(GT_STRGRAPH__LEN_BITS(STRGRAPH),\
      (BitOffset)GT_STRGRAPH_NOFEDGES(STRGRAPH), true)

#define GT_STRGRAPH__DEST_BITS(STRGRAPH)\
  (gt_requiredUInt64Bits(GT_STRGRAPH_NOFVERTICES(STRGRAPH)))

#define GT_STRGRAPH__ALLOC_NEIGHBOURSLIST(STRGRAPH)\
  (STRGRAPH)->__e_dest = bitpackarray_new(GT_STRGRAPH__DEST_BITS(STRGRAPH),\
      (BitOffset)GT_STRGRAPH_NOFEDGES(STRGRAPH), true)

#define GT_STRGRAPH_ALLOC_EDGES(STRGRAPH)\
  GT_STRGRAPH__ALLOC_NEIGHBOURSLIST(STRGRAPH);\
  GT_STRGRAPH__ALLOC_LENGTHSLIST(STRGRAPH);\
  GT_INITBITTAB((STRGRAPH)->__e_mark, GT_STRGRAPH_NOFEDGES(STRGRAPH))

#define GT_STRGRAPH__SIZEOF_LENGTHSLIST(STRGRAPH)\
  (sizeofbitarray(GT_STRGRAPH__LEN_BITS(STRGRAPH),\
                  (BitOffset)GT_STRGRAPH_NOFEDGES(STRGRAPH)))

#define GT_STRGRAPH__SIZEOF_NEIGHBOURSLIST(STRGRAPH)\
  (sizeofbitarray(GT_STRGRAPH__DEST_BITS(STRGRAPH),\
                  (BitOffset)GT_STRGRAPH_NOFEDGES(STRGRAPH)))

#define GT_STRGRAPH__SIZEOF_TOREDUCELIST(STRGRAPH)\
  (sizeof (GtBitsequence) * \
   GT_NUMOFINTSFORBITS(GT_STRGRAPH_NOFEDGES(STRGRAPH)))

#define GT_STRGRAPH_SIZEOF_EDGES(STRGRAPH) \
  (sizeof ((STRGRAPH)->__e_len)+\
      GT_STRGRAPH__SIZEOF_LENGTHSLIST(STRGRAPH) +\
      sizeof ((STRGRAPH)->__len_max)+\
      sizeof ((STRGRAPH)->__e_dest)+\
      GT_STRGRAPH__SIZEOF_NEIGHBOURSLIST(STRGRAPH) +\
      sizeof ((STRGRAPH)->__e_mark)+\
      GT_STRGRAPH__SIZEOF_TOREDUCELIST(STRGRAPH)+\
      sizeof ((STRGRAPH)->__n_edges))

#define GT_STRGRAPH_SERIALIZE_EDGES(STRGRAPH, FP)\
  do {\
    GT_STRGRAPH_SERIALIZE_DATA((FP),\
        bitElemsAllocSize(GT_STRGRAPH__DEST_BITS(STRGRAPH) * \
          GT_STRGRAPH_NOFEDGES(STRGRAPH)), (STRGRAPH)->__e_dest);\
    GT_STRGRAPH_SERIALIZE_DATA((FP), \
        bitElemsAllocSize(GT_STRGRAPH__LEN_BITS(STRGRAPH) * \
          GT_STRGRAPH_NOFEDGES(STRGRAPH)), (STRGRAPH)->__e_len);\
    GT_STRGRAPH_SERIALIZE_DATA((FP),\
        GT_NUMOFINTSFORBITS(GT_STRGRAPH_NOFEDGES(STRGRAPH)),\
        (STRGRAPH)->__e_mark);\
  } while (false)

#define GT_STRGRAPH_DESERIALIZE_EDGES(STRGRAPH, FP)\
  do {\
    GT_STRGRAPH_DESERIALIZE_DATA((FP),\
        bitElemsAllocSize(GT_STRGRAPH__DEST_BITS(STRGRAPH) * \
          GT_STRGRAPH_NOFEDGES(STRGRAPH)), (STRGRAPH)->__e_dest);\
    GT_STRGRAPH_DESERIALIZE_DATA((FP), \
        bitElemsAllocSize(GT_STRGRAPH__LEN_BITS(STRGRAPH) * \
          GT_STRGRAPH_NOFEDGES(STRGRAPH)), (STRGRAPH)->__e_len);\
    GT_STRGRAPH_DESERIALIZE_DATA((FP),\
        GT_NUMOFINTSFORBITS(GT_STRGRAPH_NOFEDGES(STRGRAPH)),\
        (STRGRAPH)->__e_mark);\
  } while (false)

#define GT_STRGRAPH_SHRINK_EDGES(STRGRAPH, NEWSIZE)\
  do {\
    gt_assert((NEWSIZE) < GT_STRGRAPH_NOFEDGES(STRGRAPH));\
    GT_STRGRAPH_SET_NOFEDGES(STRGRAPH, NEWSIZE);\
    if ((NEWSIZE) == 0)\
    {\
      GT_STRGRAPH_FREE_EDGES(STRGRAPH);\
    }\
    else\
    {\
      /* XXX: realloc of __e_dest and __e_len not implemented */\
      (STRGRAPH)->__e_mark = gt_realloc((STRGRAPH)->__e_mark,\
          sizeof (*(STRGRAPH)->__e_mark) * \
          GT_NUMOFINTSFORBITS(GT_STRGRAPH_NOFEDGES(STRGRAPH)));\
    }\
  } while (false)

#define GT_STRGRAPH_FREE_EDGES(STRGRAPH)\
  bitpackarray_delete((STRGRAPH)->__e_dest);\
  bitpackarray_delete((STRGRAPH)->__e_len);\
  gt_free((STRGRAPH)->__e_mark);\
  (STRGRAPH)->__e_dest = NULL;\
  (STRGRAPH)->__e_len = NULL;\
  (STRGRAPH)->__e_mark = NULL

#define GT_STRGRAPH_EDGE_SET_DEST(STRGRAPH, V, EDGENUM, DEST) \
  bitpackarray_store_uint64((STRGRAPH)->__e_dest,\
      (BitOffset)GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM), (DEST))

#define GT_STRGRAPH_EDGE_DEST(STRGRAPH, V, EDGENUM) \
  ((GtStrgraphVnum)(bitpackarray_get_uint64((STRGRAPH)->__e_dest,\
      (BitOffset)GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM))))

#define GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, V, EDGENUM, LEN) \
  bitpackarray_store_uint64((STRGRAPH)->__e_len,\
      (BitOffset)GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM), (LEN))

#define GT_STRGRAPH_EDGE_LEN(STRGRAPH, V, EDGENUM) \
  ((GtStrgraphLength)bitpackarray_get_uint64((STRGRAPH)->__e_len,\
      (BitOffset)GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)))

#define GT_STRGRAPH_EDGE_INIT(STRGRAPH, V, EDGENUM) \
  (GT_UNSETIBIT((STRGRAPH)->__e_mark,\
     GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)))

#define GT_STRGRAPH_EDGE_SET_MARK(STRGRAPH, V, EDGENUM) \
  (GT_SETIBIT((STRGRAPH)->__e_mark,\
     GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)))

#define GT_STRGRAPH_EDGE_HAS_MARK(STRGRAPH, V, EDGENUM) \
  (GT_ISIBITSET((STRGRAPH)->__e_mark,\
     GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM))\
   ? true : false)

#define GT_STRGRAPH_EDGE_REDUCE(STRGRAPH, V, EDGENUM) \
  GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, V, EDGENUM,\
      GT_STRGRAPH__EDGE_REDUCED(STRGRAPH))

#define GT_STRGRAPH_EDGE_IS_REDUCED(STRGRAPH, V, EDGENUM) \
  (GT_STRGRAPH_EDGE_LEN(STRGRAPH, V, EDGENUM) == \
      GT_STRGRAPH__EDGE_REDUCED(STRGRAPH) \
   ? true : false)

#define GT_STRGRAPH_COPY_EDGE(STRGRAPH, OFFSET_SOURCE, OFFSET_DEST)\
  do {\
    bitpackarray_store_uint64((STRGRAPH)->__e_dest,\
        (BitOffset)(OFFSET_DEST), bitpackarray_get_uint64((STRGRAPH->__e_dest),\
          (BitOffset)(OFFSET_SOURCE)));\
    bitpackarray_store_uint64((STRGRAPH)->__e_len,\
        (BitOffset)(OFFSET_DEST), bitpackarray_get_uint64((STRGRAPH->__e_len),\
          (BitOffset)(OFFSET_SOURCE)));\
    if (GT_ISIBITSET((STRGRAPH)->__e_mark, OFFSET_SOURCE))\
    {\
      GT_SETIBIT((STRGRAPH)->__e_mark, OFFSET_DEST);\
    }\
    else\
    {\
      GT_UNSETIBIT((STRGRAPH)->__e_mark, OFFSET_DEST);\
    }\
  } while (false)

/* order by length from < to > */

struct GtStrgraph__EdgeData
{
  GtStrgraphVnum     dest;
  GtStrgraphLength   len;
  bool               to_reduce;
};

int gt_strgraph_edges_compare_by_length(const void *edgea,
    const void *edgeb)
{
  const struct GtStrgraph__EdgeData *a = edgea, *b = edgeb;
  return (int)(a->len > b->len) - (int)(a->len < b->len);
}

#define GT_STRGRAPH_SORT_V_EDGES(STRGRAPH, VNUM)\
  do {\
    GtStrgraphVEdgenum v_nofedges, v_edges_i;\
    struct GtStrgraph__EdgeData *v_edges;\
    v_nofedges = GT_STRGRAPH_V_NOFEDGES(STRGRAPH, VNUM);\
    if (v_nofedges > (GtStrgraphVEdgenum)1)\
    {\
      v_edges = gt_malloc(sizeof (*v_edges) * v_nofedges);\
      for (v_edges_i = 0; v_edges_i < v_nofedges; v_edges_i++)\
      {\
        v_edges[v_edges_i].dest = \
          GT_STRGRAPH_EDGE_DEST(STRGRAPH, VNUM, v_edges_i);\
        v_edges[v_edges_i].len = \
          GT_STRGRAPH_EDGE_LEN(STRGRAPH, VNUM, v_edges_i);\
        v_edges[v_edges_i].to_reduce = \
          GT_STRGRAPH_EDGE_HAS_MARK(STRGRAPH, VNUM, v_edges_i);\
      }\
      qsort(v_edges, v_nofedges, sizeof (*v_edges),\
          gt_strgraph_edges_compare_by_length);\
      for (v_edges_i = 0; v_edges_i < v_nofedges; v_edges_i++)\
      {\
        GT_STRGRAPH_EDGE_SET_DEST(STRGRAPH, VNUM, \
            v_edges_i, v_edges[v_edges_i].dest);\
        GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, VNUM, v_edges_i, \
            v_edges[v_edges_i].len);\
        GT_STRGRAPH_EDGE_INIT(STRGRAPH, VNUM, v_edges_i);\
        if (v_edges[v_edges_i].to_reduce)\
          GT_STRGRAPH_EDGE_SET_MARK(STRGRAPH, VNUM, v_edges_i);\
      }\
      gt_free(v_edges);\
    }\
  } while (false)

#define GT_STRGRAPH_FIND_LONGEST_EDGE(STRGRAPH, VNUM, LONGEST) \
  do {\
    GtStrgraphVEdgenum ith_edge_before_last, vnofedges;\
    vnofedges = GT_STRGRAPH_V_NOFEDGES(STRGRAPH, VNUM);\
    LONGEST = (STRGRAPH)->__len_max;\
    for (ith_edge_before_last = 0; ith_edge_before_last < vnofedges;\
        ith_edge_before_last++)\
    {\
      if (!GT_STRGRAPH_EDGE_IS_REDUCED(STRGRAPH, VNUM, vnofedges -\
            ith_edge_before_last - 1))\
      {\
        LONGEST = GT_STRGRAPH_EDGE_LEN(STRGRAPH, VNUM, vnofedges -\
            ith_edge_before_last - 1);\
        break;\
      }\
    }\
  } while (false)

#endif
genometools-1.5.1/src/match/rdj-strgraph-edges-short-def.h000066400000000000000000000203261211610345200234700ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_EDGES_SHORT_DEF_H
#define RDJ_STRGRAPH_EDGES_SHORT_DEF_H

#include 
#include "core/intbits.h"

/*
 * Representation of string graph edges for reads shorter
 * than 255 and less than 2**31 reads (about 2.1E9).
 */

#define GT_STRGRAPH_EDGES_REPRESENTATION "short"

typedef unsigned char GtStrgraphLength;
#define FormatGtStrgraphLength       "%u"
#define PRINTGtStrgraphLengthcast(X) (X)
#define SCANGtStrgraphLengthcast(X)  (X)
#define GT_STRGRAPH__UNDEF_EDGE_LEN  (GtStrgraphLength)UCHAR_MAX
#define GT_STRGRAPH_LENGTH_MAX       (GtStrgraphLength)(UCHAR_MAX-1)

typedef uint32_t GtStrgraphVnum__Short;
#if ULONG_MAX >= UINT32_MAX
#define GT_STRGRAPH_N_READS_MAX (unsigned long)((UINT32_MAX >> 1) - 1)
#else
#define GT_STRGRAPH_N_READS_MAX ((ULONG_MAX >> 1) - 1)
#endif

#define GT_STRGRAPH_DECLARE_EDGES \
  GtStrgraphLength         *__e_len; \
  GtStrgraphVnum__Short    *__e_dest;\
  GtBitsequence            *__e_mark

#define GT_STRGRAPH__EDGE_REDUCED GT_STRGRAPH__UNDEF_EDGE_LEN

#define GT_STRGRAPH_EDGE_SET_DEST(STRGRAPH, V, EDGENUM, DEST) \
  ((STRGRAPH)->__e_dest[GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)] =\
   (DEST))

#define GT_STRGRAPH_EDGE_DEST(STRGRAPH, V, EDGENUM) \
  ((GtStrgraphVnum)\
   ((STRGRAPH)->__e_dest[GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)]))

#define GT_STRGRAPH_EDGE_LEN(STRGRAPH, V, EDGENUM) \
  ((GtStrgraphLength)\
   ((STRGRAPH)->__e_len[GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)]))

#define GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, V, EDGENUM, LEN) \
  ((STRGRAPH)->__e_len[GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)] =\
   (LEN))

#define GT_STRGRAPH_EDGE_INIT(STRGRAPH, V, EDGENUM) \
  (GT_UNSETIBIT((STRGRAPH)->__e_mark,\
     GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)))

#define GT_STRGRAPH_EDGE_SET_MARK(STRGRAPH, V, EDGENUM) \
  (GT_SETIBIT((STRGRAPH)->__e_mark,\
     GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)))

#define GT_STRGRAPH_EDGE_HAS_MARK(STRGRAPH, V, EDGENUM) \
  (GT_ISIBITSET((STRGRAPH)->__e_mark,\
     GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM)))

#define GT_STRGRAPH_EDGE_REDUCE(STRGRAPH, V, EDGENUM) \
  GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, V, EDGENUM, GT_STRGRAPH__EDGE_REDUCED)

#define GT_STRGRAPH_EDGE_IS_REDUCED(STRGRAPH, V, EDGENUM) \
  (GT_STRGRAPH_EDGE_LEN(STRGRAPH, V, EDGENUM) == GT_STRGRAPH__EDGE_REDUCED)

#define GT_STRGRAPH_NOFEDGES(STRGRAPH) \
  GT_STRGRAPH_V_OFFSET((STRGRAPH), GT_STRGRAPH_NOFVERTICES(STRGRAPH))

#define GT_STRGRAPH_SET_NOFEDGES(STRGRAPH, VALUE) \
  GT_STRGRAPH_V_SET_OFFSET((STRGRAPH),\
      GT_STRGRAPH_NOFVERTICES(STRGRAPH), (VALUE))

#define GT_STRGRAPH_ALLOC_EDGES(STRGRAPH)\
  (STRGRAPH)->__e_dest = gt_calloc(GT_STRGRAPH_NOFEDGES(STRGRAPH),\
      sizeof (*(STRGRAPH)->__e_dest));\
  (STRGRAPH)->__e_len = gt_calloc(GT_STRGRAPH_NOFEDGES(STRGRAPH),\
      sizeof (*(STRGRAPH)->__e_len));\
  GT_INITBITTAB((STRGRAPH)->__e_mark, GT_STRGRAPH_NOFEDGES(STRGRAPH))

#define GT_STRGRAPH_SIZEOF_EDGES(STRGRAPH) \
  (((sizeof (*(STRGRAPH)->__e_len) + sizeof (*(STRGRAPH)->__e_dest)) * \
    GT_STRGRAPH_NOFEDGES(STRGRAPH)) + (sizeof (GtBitsequence) * \
    GT_NUMOFINTSFORBITS(GT_STRGRAPH_NOFEDGES(STRGRAPH))))

#define GT_STRGRAPH_SHRINK_EDGES(STRGRAPH, NEWSIZE)\
  gt_assert((NEWSIZE) < GT_STRGRAPH_NOFEDGES(STRGRAPH));\
  GT_STRGRAPH_SET_NOFEDGES(STRGRAPH, NEWSIZE);\
  if ((NEWSIZE) == 0)\
  {\
    GT_STRGRAPH_FREE_EDGES(STRGRAPH);\
  }\
  else\
  {\
    (STRGRAPH)->__e_dest = gt_realloc((STRGRAPH)->__e_dest,\
        sizeof (*(STRGRAPH)->__e_dest) * GT_STRGRAPH_NOFEDGES(STRGRAPH));\
    (STRGRAPH)->__e_len = gt_realloc((STRGRAPH)->__e_len,\
        sizeof (*(STRGRAPH)->__e_len) * GT_STRGRAPH_NOFEDGES(STRGRAPH));\
    (STRGRAPH)->__e_mark = gt_realloc((STRGRAPH)->__e_mark,\
        sizeof (*(STRGRAPH)->__e_mark) * \
        GT_NUMOFINTSFORBITS(GT_STRGRAPH_NOFEDGES(STRGRAPH)));\
  }

#define GT_STRGRAPH_FREE_EDGES(STRGRAPH)\
  gt_free((STRGRAPH)->__e_dest);\
  gt_free((STRGRAPH)->__e_len);\
  gt_free((STRGRAPH)->__e_mark);\
  (STRGRAPH)->__e_dest = NULL;\
  (STRGRAPH)->__e_len = NULL;\
  (STRGRAPH)->__e_mark = NULL

#define GT_STRGRAPH_COPY_EDGE(STRGRAPH, OFFSET_SOURCE, OFFSET_DEST)\
  (STRGRAPH)->__e_dest[OFFSET_DEST] = (STRGRAPH)->__e_dest[OFFSET_SOURCE];\
  (STRGRAPH)->__e_len[OFFSET_DEST] = (STRGRAPH)->__e_len[OFFSET_SOURCE];\
  if (GT_ISIBITSET((STRGRAPH)->__e_mark, OFFSET_SOURCE))\
  {\
    GT_SETIBIT((STRGRAPH)->__e_mark, OFFSET_DEST);\
  }\
  else\
  {\
    GT_UNSETIBIT((STRGRAPH)->__e_mark, OFFSET_DEST);\
  }

/* order by length from < to > */

struct GtStrgraphEdgeData
{
  GtStrgraphVnum__Short  n;
  GtStrgraphLength         len;
  bool                     to_reduce;
};

int gt_strgraph_edges_compare_by_length(const void *edgea,
    const void *edgeb)
{
  const struct GtStrgraphEdgeData *a = edgea, *b = edgeb;
  return (int)(a->len > b->len) - (int)(a->len < b->len);
}

#define GT_STRGRAPH_SORT_V_EDGES(STRGRAPH, VNUM)\
{\
  uint64_t v_nofedges, v_edges_i;\
  struct GtStrgraphEdgeData *v_edges;\
  v_nofedges = GT_STRGRAPH_V_NOFEDGES(STRGRAPH, VNUM);\
  if (v_nofedges > (uint64_t)1)\
  {\
    v_edges = gt_malloc(sizeof (*v_edges) * v_nofedges);\
    for (v_edges_i = 0; v_edges_i < v_nofedges; v_edges_i++)\
    {\
      v_edges[v_edges_i].n = GT_STRGRAPH_EDGE_DEST(STRGRAPH, VNUM, v_edges_i);\
      v_edges[v_edges_i].len = \
        GT_STRGRAPH_EDGE_LEN(STRGRAPH, VNUM, v_edges_i);\
      v_edges[v_edges_i].to_reduce = \
        GT_STRGRAPH_EDGE_HAS_MARK(STRGRAPH, VNUM, v_edges_i);\
    }\
    qsort(v_edges, v_nofedges, sizeof (*v_edges),\
        gt_strgraph_edges_compare_by_length);\
    for (v_edges_i = 0; v_edges_i < v_nofedges; v_edges_i++)\
    {\
      GT_STRGRAPH_EDGE_SET_DEST(STRGRAPH, VNUM, \
          v_edges_i, v_edges[v_edges_i].n);\
      GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, VNUM, v_edges_i, \
          v_edges[v_edges_i].len);\
      GT_STRGRAPH_EDGE_INIT(STRGRAPH, VNUM, v_edges_i);\
      if (v_edges[v_edges_i].to_reduce)\
        GT_STRGRAPH_EDGE_SET_MARK(STRGRAPH, VNUM, v_edges_i);\
    }\
    gt_free(v_edges);\
  }\
}

#define GT_STRGRAPH_SERIALIZE_EDGES(STRGRAPH, FP)\
  GT_STRGRAPH_SERIALIZE_DATA((FP), \
      GT_STRGRAPH_NOFEDGES(STRGRAPH), (STRGRAPH)->__e_dest);\
  GT_STRGRAPH_SERIALIZE_DATA((FP),\
      GT_STRGRAPH_NOFEDGES(STRGRAPH), (STRGRAPH)->__e_len);\
  GT_STRGRAPH_SERIALIZE_DATA((FP),\
      GT_NUMOFINTSFORBITS(GT_STRGRAPH_NOFEDGES(STRGRAPH)),\
      (STRGRAPH)->__e_mark)

#define GT_STRGRAPH_DESERIALIZE_EDGES(STRGRAPH, FP)\
  GT_STRGRAPH_DESERIALIZE_DATA((FP),\
      GT_STRGRAPH_NOFEDGES(STRGRAPH), (STRGRAPH)->__e_dest);\
  GT_STRGRAPH_DESERIALIZE_DATA((FP),\
      GT_STRGRAPH_NOFEDGES(STRGRAPH), (STRGRAPH)->__e_len);\
  GT_STRGRAPH_DESERIALIZE_DATA((FP),\
      GT_NUMOFINTSFORBITS(GT_STRGRAPH_NOFEDGES(STRGRAPH)),\
      (STRGRAPH)->__e_mark)

#define GT_STRGRAPH_FIND_LONGEST_EDGE(STRGRAPH, VNUM, LONGEST) \
        {\
          unsigned long ith_edge_before_last, vnofedges;\
          vnofedges = GT_STRGRAPH_V_NOFEDGES(STRGRAPH, VNUM);\
          LONGEST = GT_STRGRAPH__UNDEF_EDGE_LEN;\
          for (ith_edge_before_last = 0; ith_edge_before_last < vnofedges;\
              ith_edge_before_last++)\
          {\
            if (!GT_STRGRAPH_EDGE_IS_REDUCED(STRGRAPH, VNUM, vnofedges -\
                  ith_edge_before_last - 1))\
            {\
               LONGEST = GT_STRGRAPH_EDGE_LEN(STRGRAPH, VNUM, vnofedges -\
                   ith_edge_before_last - 1);\
               break;\
            }\
          }\
        }

#endif
genometools-1.5.1/src/match/rdj-strgraph-edges-single-bitpack-def.h000066400000000000000000000223301211610345200252220ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_EDGES_SINGLE_BITPACK_DEF_H
#define RDJ_STRGRAPH_EDGES_SINGLE_BITPACK_DEF_H

#include 
#include "core/bitpackarray.h"
#include "core/intbits.h"

#define GT_STRGRAPH_EDGES_REPRESENTATION "single-bitpack"

typedef uint64_t GtStrgraphLength;
#define FormatGtStrgraphLength        Formatuint64_t
#define PRINTGtStrgraphLengthcast(X)  PRINTuint64_tcast(X)
#define SCANGtStrgraphLengthcast(X)   SCANuint64_tcast(X)

/* LENGTH_MAX is limited by __e_len */
#define GT_STRGRAPH_LENGTH_MAX   (GtStrgraphLength)UINT64_MAX

#if UINT64_MAX >= ULONG_MAX
/* N_READS_MAX is limited by read numbers in the encseq */
#define GT_STRGRAPH_N_READS_MAX ((ULONG_MAX >> 1) - 1)
#else
/* N_READS_MAX is limited by __e_dest */
#define GT_STRGRAPH_N_READS_MAX (unsigned long)((UINT64_MAX >> 1) - 1)
#endif

#define GT_STRGRAPH_DECLARE_EDGES\
  BitPackArray       *__e_info;\
  GtStrgraphLength   __len_max;\
  GtStrgraphEdgenum   __n_edges

#define GT_STRGRAPH_SET_NOFEDGES(STRGRAPH, VALUE) \
  (STRGRAPH)->__n_edges = (VALUE)

#define GT_STRGRAPH_NOFEDGES(STRGRAPH) \
  ((STRGRAPH)->__n_edges)

#define GT_STRGRAPH__UNDEF_EDGE_LEN(STRGRAPH) \
  ((STRGRAPH)->__len_max)

#define GT_STRGRAPH__EDGE_REDUCED(STRGRAPH) \
  GT_STRGRAPH__UNDEF_EDGE_LEN(STRGRAPH)

#define GT_STRGRAPH__LEN_BITS(STRGRAPH)\
  (gt_requiredUInt64Bits((STRGRAPH)->__len_max))

#define GT_STRGRAPH__DEST_BITS(STRGRAPH)\
  (gt_requiredUInt64Bits(GT_STRGRAPH_NOFVERTICES(STRGRAPH)))

#define GT_STRGRAPH__EDGE_BITS(STRGRAPH)\
  (GT_STRGRAPH__LEN_BITS(STRGRAPH) + \
   GT_STRGRAPH__DEST_BITS(STRGRAPH) + \
   1 /* mark */)

#define GT_STRGRAPH_ALLOC_EDGES(STRGRAPH)\
  (STRGRAPH)->__len_max = gt_strgraph_longest_read(STRGRAPH) - \
    (STRGRAPH)->minmatchlen + 1;\
  (STRGRAPH)->__e_info = bitpackarray_new(GT_STRGRAPH__EDGE_BITS(STRGRAPH),\
      (BitOffset)GT_STRGRAPH_NOFEDGES(STRGRAPH), true)

#define GT_STRGRAPH_SIZEOF_EDGES(STRGRAPH) \
  (sizeofbitarray(GT_STRGRAPH__EDGE_BITS(STRGRAPH),\
                  (BitOffset)GT_STRGRAPH_NOFEDGES(STRGRAPH)))

#define GT_STRGRAPH_SERIALIZE_EDGES(STRGRAPH, FP)\
  do {\
    GT_STRGRAPH_SERIALIZE_DATA((FP),\
        bitElemsAllocSize(GT_STRGRAPH__EDGE_BITS(STRGRAPH) * \
          GT_STRGRAPH_NOFEDGES(STRGRAPH)), (STRGRAPH)->__e_info);\
  } while (false)

#define GT_STRGRAPH_DESERIALIZE_EDGES(STRGRAPH, FP)\
  do {\
    GT_STRGRAPH_DESERIALIZE_DATA((FP),\
        bitElemsAllocSize(GT_STRGRAPH__DEST_BITS(STRGRAPH) * \
          GT_STRGRAPH_NOFEDGES(STRGRAPH)), (STRGRAPH)->__e_info);\
  } while (false)

#define GT_STRGRAPH_SHRINK_EDGES(STRGRAPH, NEWSIZE)\
  do {\
    gt_assert((NEWSIZE) < GT_STRGRAPH_NOFEDGES(STRGRAPH));\
    GT_STRGRAPH_SET_NOFEDGES(STRGRAPH, NEWSIZE);\
    if ((NEWSIZE) == 0)\
    {\
      GT_STRGRAPH_FREE_EDGES(STRGRAPH);\
    }\
    else\
    {\
      /* XXX: realloc not implemented */\
    }\
  } while (false)

#define GT_STRGRAPH_FREE_EDGES(STRGRAPH)\
  bitpackarray_delete((STRGRAPH)->__e_info);\
  (STRGRAPH)->__e_info = NULL

#define GT_STRGRAPH_EDGE__INFO(STRGRAPH, V, EDGENUM) \
  ((GtStrgraphVnum)(bitpackarray_get_uint64((STRGRAPH)->__e_info,\
      (BitOffset)GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM))))

#define GT_STRGRAPH_EDGE__SET_INFO(STRGRAPH, V, EDGENUM, VALUE) \
  (bitpackarray_store_uint64((STRGRAPH)->__e_info,\
      (BitOffset)GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, EDGENUM), (VALUE)))

/* bit order: dest... len... mark */

#define GT_STRGRAPH_EDGE__MARK_SHIFT(STRGRAPH) 0
#define GT_STRGRAPH_EDGE__LEN_SHIFT(STRGRAPH)  1
#define GT_STRGRAPH_EDGE__DEST_SHIFT(STRGRAPH) \
  (GT_STRGRAPH_EDGE__LEN_SHIFT(STRGRAPH) + GT_STRGRAPH__LEN_BITS(STRGRAPH))

#define GT_STRGRAPH_EDGE__MARK_MASK(STRGRAPH) 1
#define GT_STRGRAPH_EDGE__LEN_MASK(STRGRAPH) \
 (((1 << GT_STRGRAPH__LEN_BITS(STRGRAPH)) - 1) << \
  GT_STRGRAPH_EDGE__LEN_SHIFT(STRGRAPH))
#define GT_STRGRAPH_EDGE__DEST_MASK(STRGRAPH) \
 (((1 << GT_STRGRAPH__DEST_BITS(STRGRAPH)) - 1) << \
  GT_STRGRAPH_EDGE__DEST_SHIFT(STRGRAPH))

#define GT_STRGRAPH_EDGE_DEST(STRGRAPH, V, EDGENUM) \
  ((GT_STRGRAPH_EDGE__INFO(STRGRAPH, V, EDGENUM) & \
    GT_STRGRAPH_EDGE__DEST_MASK(STRGRAPH)) >> \
   GT_STRGRAPH_EDGE__DEST_SHIFT(STRGRAPH))

#define GT_STRGRAPH_EDGE_LEN(STRGRAPH, V, EDGENUM) \
  ((GT_STRGRAPH_EDGE__INFO(STRGRAPH, V, EDGENUM) & \
    GT_STRGRAPH_EDGE__LEN_MASK(STRGRAPH)) >> \
   GT_STRGRAPH_EDGE__LEN_SHIFT(STRGRAPH))

#define GT_STRGRAPH_EDGE_HAS_MARK(STRGRAPH, V, EDGENUM) \
  (((GT_STRGRAPH_EDGE__INFO(STRGRAPH, V, EDGENUM) & \
    GT_STRGRAPH_EDGE__MARK_MASK(STRGRAPH)) >> \
   GT_STRGRAPH_EDGE__MARK_SHIFT(STRGRAPH)) ? true : false)

#define GT_STRGRAPH_EDGE_SET_DEST(STRGRAPH, V, EDGENUM, VALUE) \
  GT_STRGRAPH_EDGE__SET_INFO(STRGRAPH, V, EDGENUM, \
    (((GT_STRGRAPH_EDGE__DEST_MASK(STRGRAPH) ^ UINT64_MAX) & \
    GT_STRGRAPH_EDGE__INFO(STRGRAPH, V, EDGENUM)) + \
    ((VALUE) << GT_STRGRAPH_EDGE__DEST_SHIFT(STRGRAPH))))

#define GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, V, EDGENUM, VALUE) \
  GT_STRGRAPH_EDGE__SET_INFO(STRGRAPH, V, EDGENUM, \
    (((GT_STRGRAPH_EDGE__LEN_MASK(STRGRAPH) ^ UINT64_MAX) & \
    GT_STRGRAPH_EDGE__INFO(STRGRAPH, V, EDGENUM)) + \
    ((VALUE) << GT_STRGRAPH_EDGE__LEN_SHIFT(STRGRAPH))))

#define GT_STRGRAPH_EDGE__SET_MARK(STRGRAPH, V, EDGENUM, VALUE) \
  GT_STRGRAPH_EDGE__SET_INFO(STRGRAPH, V, EDGENUM, \
    (((GT_STRGRAPH_EDGE__MARK_MASK(STRGRAPH) ^ UINT64_MAX) & \
    GT_STRGRAPH_EDGE__INFO(STRGRAPH, V, EDGENUM)) + \
    ((VALUE) << GT_STRGRAPH_EDGE__MARK_SHIFT(STRGRAPH))))

#define GT_STRGRAPH_EDGE_SET_MARK(STRGRAPH, V, EDGENUM) \
  GT_STRGRAPH_EDGE__SET_MARK(STRGRAPH, V, EDGENUM, 1)

#define GT_STRGRAPH_EDGE_INIT(STRGRAPH, V, EDGENUM) \
  GT_STRGRAPH_EDGE__SET_MARK(STRGRAPH, V, EDGENUM, 0)

#define GT_STRGRAPH_EDGE_REDUCE(STRGRAPH, V, EDGENUM) \
  GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, V, EDGENUM,\
      GT_STRGRAPH__EDGE_REDUCED(STRGRAPH))

#define GT_STRGRAPH_EDGE_IS_REDUCED(STRGRAPH, V, EDGENUM) \
  (GT_STRGRAPH_EDGE_LEN(STRGRAPH, V, EDGENUM) == \
      GT_STRGRAPH__EDGE_REDUCED(STRGRAPH) \
   ? true : false)

#define GT_STRGRAPH_COPY_EDGE(STRGRAPH, OFFSET_SOURCE, OFFSET_DEST)\
  do {\
    bitpackarray_store_uint64((STRGRAPH)->__e_info,\
        (BitOffset)(OFFSET_DEST), bitpackarray_get_uint64((STRGRAPH->__e_info),\
          (BitOffset)(OFFSET_SOURCE)));\
  } while (false)

/* order by length from < to > */

struct GtStrgraph__EdgeData
{
  GtStrgraphVnum     dest;
  GtStrgraphLength   len;
  bool               to_reduce;
};

int gt_strgraph_edges_compare_by_length(const void *edgea,
    const void *edgeb)
{
  const struct GtStrgraph__EdgeData *a = edgea, *b = edgeb;
  return (int)(a->len > b->len) - (int)(a->len < b->len);
}

#define GT_STRGRAPH_SORT_V_EDGES(STRGRAPH, VNUM)\
  do {\
    GtStrgraphVEdgenum v_nofedges, v_edges_i;\
    struct GtStrgraph__EdgeData *v_edges;\
    v_nofedges = GT_STRGRAPH_V_NOFEDGES(STRGRAPH, VNUM);\
    if (v_nofedges > (GtStrgraphVEdgenum)1)\
    {\
      v_edges = gt_malloc(sizeof (*v_edges) * v_nofedges);\
      for (v_edges_i = 0; v_edges_i < v_nofedges; v_edges_i++)\
      {\
        v_edges[v_edges_i].dest = \
          GT_STRGRAPH_EDGE_DEST(STRGRAPH, VNUM, v_edges_i);\
        v_edges[v_edges_i].len = \
          GT_STRGRAPH_EDGE_LEN(STRGRAPH, VNUM, v_edges_i);\
        v_edges[v_edges_i].to_reduce = \
          GT_STRGRAPH_EDGE_HAS_MARK(STRGRAPH, VNUM, v_edges_i);\
      }\
      qsort(v_edges, v_nofedges, sizeof (*v_edges),\
          gt_strgraph_edges_compare_by_length);\
      for (v_edges_i = 0; v_edges_i < v_nofedges; v_edges_i++)\
      {\
        GT_STRGRAPH_EDGE_SET_DEST(STRGRAPH, VNUM, \
            v_edges_i, v_edges[v_edges_i].dest);\
        GT_STRGRAPH_EDGE_SET_LEN(STRGRAPH, VNUM, v_edges_i, \
            v_edges[v_edges_i].len);\
        GT_STRGRAPH_EDGE_INIT(STRGRAPH, VNUM, v_edges_i);\
        if (v_edges[v_edges_i].to_reduce)\
          GT_STRGRAPH_EDGE_SET_MARK(STRGRAPH, VNUM, v_edges_i);\
      }\
      gt_free(v_edges);\
    }\
  } while (false)

#define GT_STRGRAPH_FIND_LONGEST_EDGE(STRGRAPH, VNUM, LONGEST) \
  do {\
    GtStrgraphVEdgenum ith_edge_before_last, vnofedges;\
    vnofedges = GT_STRGRAPH_V_NOFEDGES(STRGRAPH, VNUM);\
    LONGEST = (STRGRAPH)->__len_max;\
    for (ith_edge_before_last = 0; ith_edge_before_last < vnofedges;\
        ith_edge_before_last++)\
    {\
      if (!GT_STRGRAPH_EDGE_IS_REDUCED(STRGRAPH, VNUM, vnofedges -\
            ith_edge_before_last - 1))\
      {\
        LONGEST = GT_STRGRAPH_EDGE_LEN(STRGRAPH, VNUM, vnofedges -\
            ith_edge_before_last - 1);\
        break;\
      }\
    }\
  } while (false)

#endif
genometools-1.5.1/src/match/rdj-strgraph-vertices-bitfield-def.h000066400000000000000000000070241211610345200246500ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_VERTICES_BITFIELD_DEF_H
#define RDJ_STRGRAPH_VERTICES_BITFIELD_DEF_H

/* --- for exclusive use in rdj-strgraph.c (__ = private) --- */

#define GT_STRGRAPH_VERTICES_REPRESENTATION "bitfield"

typedef unsigned long GtStrgraphVEdgenum;
#define FormatGtStrgraphVEdgenum       "%lu"
#define PRINTGtStrgraphVEdgenumcast(X) (X)
#define SCANGtStrgraphVEdgenumcast(X)  (X)
#define GT_STRGRAPH__OUTDEG_BITS       24
#define GT_STRGRAPH_V_EDGENUM_MAX \
  ((GtStrgraphVEdgenum)((1UL << GT_STRGRAPH__OUTDEG_BITS) - 1))

typedef uint64_t GtStrgraphEdgenum;
#define FormatGtStrgraphEdgenum       Formatuint64_t
#define PRINTGtStrgraphEdgenumcast(X) PRINTuint64_tcast(X)
#define SCANGtStrgraphEdgenumcast(X)  SCANuint64_tcast(X)
#define GT_STRGRAPH__OFFSET_BITS      38
#define GT_STRGRAPH_EDGENUM_MAX \
  ((GtStrgraphEdgenum)((1ULL << GT_STRGRAPH__OFFSET_BITS) - 1))

typedef struct {
  GtStrgraphEdgenum  offset :GT_STRGRAPH__OFFSET_BITS;
  GtStrgraphVEdgenum outdeg :GT_STRGRAPH__OUTDEG_BITS;
  GtStrgraphVmark    mark   :GT_STRGRAPH_VMARK_BITS;
} GtStrgraph__Vertex;

#define GT_STRGRAPH_DECLARE_VERTICES\
  GtStrgraphVnum       __n_vertices;\
  GtStrgraph__Vertex   *__v

#define GT_STRGRAPH_SET_NOFVERTICES(STRGRAPH, N) \
  ((STRGRAPH)->__n_vertices = (N))

#define GT_STRGRAPH_NOFVERTICES(STRGRAPH) \
  ((STRGRAPH)->__n_vertices)

#define GT_STRGRAPH_ALLOC_VERTICES(STRGRAPH)\
  (STRGRAPH)->__v = \
      gt_calloc((size_t)((GT_STRGRAPH_NOFVERTICES(STRGRAPH)) + 1),\
          sizeof (GtStrgraph__Vertex))

#define GT_STRGRAPH_SIZEOF_VERTICES(STRGRAPH) \
  ((sizeof (GtStrgraph__Vertex) * (GT_STRGRAPH_NOFVERTICES(STRGRAPH) + 1)) +\
   sizeof ((STRGRAPH)->__n_vertices))

#define GT_STRGRAPH_FREE_VERTICES(STRGRAPH)\
  gt_free((STRGRAPH)->__v);\
  (STRGRAPH)->__v = NULL

#define GT_STRGRAPH_SERIALIZE_VERTICES(STRGRAPH, FP)\
  GT_STRGRAPH_SERIALIZE_DATA((FP),\
      GT_STRGRAPH_NOFVERTICES(STRGRAPH) + 1, (STRGRAPH)->__v)

#define GT_STRGRAPH_DESERIALIZE_VERTICES(STRGRAPH, FP)\
  GT_STRGRAPH_DESERIALIZE_DATA((FP),\
      GT_STRGRAPH_NOFVERTICES(STRGRAPH) + 1, (STRGRAPH)->__v)

#define GT_STRGRAPH_V_SET_OFFSET(STRGRAPH, V, VALUE) \
  ((STRGRAPH)->__v[(V)].offset = (VALUE))

#define GT_STRGRAPH_V_OFFSET(STRGRAPH, V) \
  ((GtStrgraphEdgenum)((STRGRAPH)->__v[(V)].offset))

#define GT_STRGRAPH_V_INC_OUTDEG(STRGRAPH, V) \
  (((STRGRAPH)->__v[(V)].outdeg)++)

#define GT_STRGRAPH_V_DEC_OUTDEG(STRGRAPH, V) \
  (((STRGRAPH)->__v[(V)].outdeg)--)

#define GT_STRGRAPH_V_OUTDEG(STRGRAPH, V) \
  ((GtStrgraphVEdgenum)((STRGRAPH)->__v[(V)].outdeg))

#define GT_STRGRAPH_V_SET_MARK(STRGRAPH, V, VALUE) \
  ((STRGRAPH)->__v[(V)].mark = (VALUE))

#define GT_STRGRAPH_V_MARK(STRGRAPH, V) \
  ((STRGRAPH)->__v[(V)].mark)

#endif
genometools-1.5.1/src/match/rdj-strgraph-vertices-bitpack-def.h000066400000000000000000000153201211610345200245010ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_VERTICES_BITPACK_DEF_H
#define RDJ_STRGRAPH_VERTICES_BITPACK_DEF_H

/* --- for exclusive use in rdj-strgraph.c (__ = private) --- */

#define GT_STRGRAPH_VERTICES_REPRESENTATION "bitpack"

typedef uint64_t GtStrgraphVEdgenum;
#define FormatGtStrgraphVEdgenum       Formatuint64_t
#define PRINTGtStrgraphVEdgenumcast(X) PRINTuint64_tcast(X)
#define SCANGtStrgraphVEdgenumcast(X)  SCANuint64_tcast(X)
#define GT_STRGRAPH_V_EDGENUM_MAX      (UINT64_MAX - 1)
/* - 1 is not necessary, but avoids a compiler warning */

typedef uint64_t GtStrgraphEdgenum;
#define FormatGtStrgraphEdgenum       Formatuint64_t
#define PRINTGtStrgraphEdgenumcast(X) PRINTuint64_tcast(X)
#define SCANGtStrgraphEdgenumcast(X)  SCANuint64_tcast(X)
#define GT_STRGRAPH_EDGENUM_MAX       (UINT64_MAX - 1)
/* - 1 is not necessary, but avoids a compiler warning */

#define GT_STRGRAPH_DECLARE_VERTICES\
  BitPackArray       *__v_mark;\
  BitPackArray       *__v_offset;\
  GtStrgraphEdgenum  __offset_max;\
  BitPackArray       *__v_outdeg;\
  GtStrgraphVEdgenum __outdeg_max;\
  GtStrgraphVnum     __n_vertices

/* vertex accessor macros */

#define GT_STRGRAPH_SET_NOFVERTICES(STRGRAPH, N) \
  ((STRGRAPH)->__n_vertices = (N))

#define GT_STRGRAPH_NOFVERTICES(STRGRAPH) \
  ((STRGRAPH)->__n_vertices)

#define GT_STRGRAPH__ALLOC_VMARKS(STRGRAPH)\
  (STRGRAPH)->__v_mark = bitpackarray_new((unsigned int)GT_STRGRAPH_VMARK_BITS,\
      (BitOffset)(GT_STRGRAPH_NOFVERTICES(STRGRAPH) + (GtStrgraphVnum)1), true)

#define GT_STRGRAPH__OFFSET_BITS(STRGRAPH)\
  (gt_requiredUInt64Bits((STRGRAPH)->__offset_max))

#define GT_STRGRAPH__ALLOC_OFFSETS(STRGRAPH)\
  (STRGRAPH)->__offset_max = gt_strgraph_counts_sum(STRGRAPH);\
  (STRGRAPH)->__v_offset = bitpackarray_new(GT_STRGRAPH__OFFSET_BITS(STRGRAPH),\
      (BitOffset)(GT_STRGRAPH_NOFVERTICES(STRGRAPH) + (GtStrgraphVnum)1), true)

#define GT_STRGRAPH__OUTDEG_BITS(STRGRAPH)\
  (gt_requiredUInt64Bits((STRGRAPH)->__outdeg_max))

#define GT_STRGRAPH__ALLOC_OUTDEGS(STRGRAPH)\
  gt_assert(sizeof (GtStrgraphVEdgenum) >= sizeof (GtStrgraphCount));\
  (STRGRAPH)->__outdeg_max = (GtStrgraphVEdgenum)\
      gt_strgraph_largest_count(STRGRAPH);\
  (STRGRAPH)->__v_outdeg = bitpackarray_new(GT_STRGRAPH__OUTDEG_BITS(STRGRAPH),\
      (BitOffset)(GT_STRGRAPH_NOFVERTICES(STRGRAPH) + (GtStrgraphVnum)1), true)

#define GT_STRGRAPH_ALLOC_VERTICES(STRGRAPH)\
  GT_STRGRAPH__ALLOC_VMARKS(STRGRAPH);\
  GT_STRGRAPH__ALLOC_OFFSETS(STRGRAPH);\
  GT_STRGRAPH__ALLOC_OUTDEGS(STRGRAPH)

#define GT_STRGRAPH__SIZEOF_OUTDEGS(STRGRAPH)\
  (sizeofbitarray(GT_STRGRAPH__OUTDEG_BITS(STRGRAPH),\
                  (BitOffset)(\
                    GT_STRGRAPH_NOFVERTICES(STRGRAPH) + (GtStrgraphVnum)1)))

#define GT_STRGRAPH__SIZEOF_OFFSETS(STRGRAPH)\
  (sizeofbitarray(GT_STRGRAPH__OFFSET_BITS(STRGRAPH),\
                  (BitOffset)(\
                  GT_STRGRAPH_NOFVERTICES(STRGRAPH) + (GtStrgraphVnum)1)))

#define GT_STRGRAPH__SIZEOF_VMARKS(STRGRAPH)\
  (sizeofbitarray(GT_STRGRAPH_VMARK_BITS,\
                  (BitOffset)(\
                  GT_STRGRAPH_NOFVERTICES(STRGRAPH) + (GtStrgraphVnum)1)))

#define GT_STRGRAPH_SIZEOF_VERTICES(STRGRAPH) \
  (sizeof ((STRGRAPH)->__v_mark)+\
  GT_STRGRAPH__SIZEOF_VMARKS(STRGRAPH) +\
  sizeof ((STRGRAPH)->__v_offset)+\
  sizeof ((STRGRAPH)->__offset_max)+\
  GT_STRGRAPH__SIZEOF_OFFSETS(STRGRAPH) +\
  sizeof ((STRGRAPH)->__v_outdeg)+\
  sizeof ((STRGRAPH)->__outdeg_max)+\
  GT_STRGRAPH__SIZEOF_OUTDEGS(STRGRAPH))

#define GT_STRGRAPH_SERIALIZE_VERTICES(STRGRAPH, FP)\
  GT_STRGRAPH_SERIALIZE_DATA((FP),\
      bitElemsAllocSize(GT_STRGRAPH_VMARK_BITS * \
        GT_STRGRAPH_NOFVERTICES(STRGRAPH) + 1), (STRGRAPH)->__v_mark);\
  GT_STRGRAPH_SERIALIZE_DATA((FP), \
      bitElemsAllocSize(GT_STRGRAPH__OUTDEG_BITS(STRGRAPH) * \
        GT_STRGRAPH_NOFVERTICES(STRGRAPH) + 1), (STRGRAPH)->__v_outdeg);\
  GT_STRGRAPH_SERIALIZE_DATA((FP), \
      bitElemsAllocSize(GT_STRGRAPH__OFFSET_BITS(STRGRAPH) * \
        GT_STRGRAPH_NOFVERTICES(STRGRAPH) + 1), (STRGRAPH)->__v_offset)

#define GT_STRGRAPH_DESERIALIZE_VERTICES(STRGRAPH, FP)\
  GT_STRGRAPH_DESERIALIZE_DATA((FP),\
      bitElemsAllocSize(GT_STRGRAPH_VMARK_BITS * \
        GT_STRGRAPH_NOFVERTICES(STRGRAPH) + 1), (STRGRAPH)->__v_mark);\
  GT_STRGRAPH_DESERIALIZE_DATA((FP), \
      bitElemsAllocSize(GT_STRGRAPH__OUTDEG_BITS(STRGRAPH) * \
        GT_STRGRAPH_NOFVERTICES(STRGRAPH) + 1), (STRGRAPH)->__v_outdeg);\
  GT_STRGRAPH_DESERIALIZE_DATA((FP), \
      bitElemsAllocSize(GT_STRGRAPH__OFFSET_BITS(STRGRAPH) * \
        GT_STRGRAPH_NOFVERTICES(STRGRAPH) + 1), (STRGRAPH)->__v_offset)

#define GT_STRGRAPH_FREE_VERTICES(STRGRAPH)\
  bitpackarray_delete((STRGRAPH)->__v_mark);\
  bitpackarray_delete((STRGRAPH)->__v_outdeg);\
  bitpackarray_delete((STRGRAPH)->__v_offset);\
  (STRGRAPH)->__v_mark = NULL;\
  (STRGRAPH)->__v_outdeg = NULL;\
  (STRGRAPH)->__v_offset = NULL

#define GT_STRGRAPH_V_SET_OFFSET(STRGRAPH, V, VALUE) \
  bitpackarray_store_uint64((STRGRAPH)->__v_offset, (BitOffset)(V),\
     (uint64_t)(VALUE))

#define GT_STRGRAPH_V_OFFSET(STRGRAPH, V) \
  ((GtStrgraphEdgenum)\
   bitpackarray_get_uint64((STRGRAPH)->__v_offset, (BitOffset)(V)))

#define GT_STRGRAPH_V_OUTDEG(STRGRAPH, V) \
  ((GtStrgraphVEdgenum)\
   bitpackarray_get_uint64((STRGRAPH)->__v_outdeg, (BitOffset)(V)))

#define GT_STRGRAPH_V_INC_OUTDEG(STRGRAPH, V) \
  bitpackarray_store_uint64((STRGRAPH)->__v_outdeg, (BitOffset)(V), \
    (uint64_t)(GT_STRGRAPH_V_OUTDEG(STRGRAPH, V) + (GtStrgraphVEdgenum)1))

#define GT_STRGRAPH_V_DEC_OUTDEG(STRGRAPH, V) \
  bitpackarray_store_uint64((STRGRAPH)->__v_outdeg, (BitOffset)(V), \
    (uint64_t)(GT_STRGRAPH_V_OUTDEG(STRGRAPH, V) - (GtStrgraphVEdgenum)1))

#define GT_STRGRAPH_V_SET_MARK(STRGRAPH, V, VALUE) \
  bitpackarray_store_uint64((STRGRAPH)->__v_mark, (BitOffset)(V),\
     (uint64_t)(VALUE))

#define GT_STRGRAPH_V_MARK(STRGRAPH, V) \
  ((GtStrgraphVmark)\
   bitpackarray_get_uint64((STRGRAPH)->__v_mark, (BitOffset)(V)))

#endif
genometools-1.5.1/src/match/rdj-strgraph-vertices-common-def.h000066400000000000000000000050151211610345200243540ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_VERTICES_COMMON_DEF_H
#define RDJ_STRGRAPH_VERTICES_COMMON_DEF_H

/* --- for exclusive use in rdj-strgraph.c --- */

#define GT_STRGRAPH_NOFSPM_MAX \
  (GT_STRGRAPH_EDGENUM_MAX >> 1)

#define GT_STRGRAPH_NOFREADS(STRGRAPH) \
  (GT_STRGRAPH_NOFVERTICES(STRGRAPH) >> 1)

#define GT_STRGRAPH_V_NTH_EDGE_OFFSET(STRGRAPH, V, N)\
  (GT_STRGRAPH_V_OFFSET(STRGRAPH, V) + (N))

#define GT_STRGRAPH_V_INDEG(STRGRAPH, V) \
  GT_STRGRAPH_V_OUTDEG(STRGRAPH, GT_STRGRAPH_V_OTHER(V))

#define GT_STRGRAPH_V_IS_INTERNAL(STRGRAPH, V) \
  ((GT_STRGRAPH_V_OUTDEG(STRGRAPH, V) == (GtStrgraphVEdgenum)1) && \
   (GT_STRGRAPH_V_INDEG(STRGRAPH, V) == (GtStrgraphVEdgenum)1))

#define GT_STRGRAPH_V_IS_JUNCTION(STRGRAPH, I) \
  ((GT_STRGRAPH_V_OUTDEG(STRGRAPH, I) > (GtStrgraphVEdgenum)1 && \
    GT_STRGRAPH_V_INDEG(STRGRAPH, I) > 0) || \
   (GT_STRGRAPH_V_OUTDEG(STRGRAPH, I) == (GtStrgraphVEdgenum)1 && \
    GT_STRGRAPH_V_INDEG(STRGRAPH, I) > (GtStrgraphVEdgenum)1))

#define GT_STRGRAPH_V_NOFEDGES(STRGRAPH, V) \
   (GtStrgraphVEdgenum)(GT_STRGRAPH_V_OFFSET(STRGRAPH, (V)+1) \
   - GT_STRGRAPH_V_OFFSET(STRGRAPH, V))

/* begin/end vertices: */

#define GT_STRGRAPH_V_B(READNUM) \
  ((GtStrgraphVnum)(READNUM) << 1)

#define GT_STRGRAPH_V_E(READNUM) \
  (GT_STRGRAPH_V_B(READNUM) + (GtStrgraphVnum)1)

#define GT_STRGRAPH_V_READNUM(V) \
  (unsigned long)((V) >> 1)

#define GT_STRGRAPH_V_IS_E(V) \
  (((V) & (GtStrgraphVnum)1) == (GtStrgraphVnum)1)

#define GT_STRGRAPH_V_IS_B(V) \
  (!(GT_STRGRAPH_V_IS_E(V)))

#define GT_STRGRAPH_V_OTHER(V) \
  (GT_STRGRAPH_V_IS_E(V) ? (V) - (GtStrgraphVnum)1 : (V) + (GtStrgraphVnum)1)

#define GT_STRGRAPH_V_CHAR(V) \
  (GT_STRGRAPH_V_IS_E(V) ? 'E' : 'B')

#endif
genometools-1.5.1/src/match/rdj-strgraph-vmark-def.h000066400000000000000000000021061211610345200223600ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_VMARK_DEF_H
#define RDJ_STRGRAPH_VMARK_DEF_H

typedef enum {
  GT_STRGRAPH_V_VACANT = 0,
  GT_STRGRAPH_V_INPLAY,
  GT_STRGRAPH_V_ELIMINATED,
} GtStrgraphVmark;

#define GT_STRGRAPH_VMARK_BITS 2U

#endif
genometools-1.5.1/src/match/rdj-strgraph.c000066400000000000000000002241251211610345200205100ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/array_api.h"
#include "core/arraydef.h"
#include "core/disc_distri_api.h"
#include "core/ensure.h"
#include "core/fasta.h"
#include "core/fileutils.h"
#include "core/format64.h"
#include "core/hashmap-generic.h"
#include "core/log.h"
#include "core/ma.h"
#include "core/progressbar.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/spacecalc.h"
#include "extended/assembly_stats_calculator.h"
#include "match/asqg_writer.h"
#include "match/rdj-contigpaths.h"
#include "match/rdj-contigs-writer.h"
#include "match/rdj-ensure-output.h"
#include "match/rdj-spmlist.h"
#include "match/rdj-strgraph.h"

/* default representation: */

#ifndef GT_STRGRAPH_SHORT
#ifndef GT_STRGRAPH_BITFIELD
#define GT_STRGRAPH_BITPACK
#endif
#endif

/* Combinations of Edges/Vertices/Counts Representations */

#if defined(GT_STRGRAPH_BITFIELD)
#define GT_STRGRAPH_COUNTS_CHAR
#define GT_STRGRAPH_VERTICES_BITFIELD
#define GT_STRGRAPH_EDGES_BITFIELD
#elif defined(GT_STRGRAPH_SHORT)
#define GT_STRGRAPH_COUNTS_CHAR
#define GT_STRGRAPH_VERTICES_BITFIELD
#define GT_STRGRAPH_EDGES_SHORT
#elif defined(GT_STRGRAPH_BITPACK)
#define GT_STRGRAPH_COUNTS_CHAR
#define GT_STRGRAPH_VERTICES_BITPACK
#define GT_STRGRAPH_EDGES_SINGLE_BITPACK
#endif

/* Type For Vertex numbers */

typedef uint64_t GtStrgraphVnum;
#define FormatGtStrgraphVnum       Formatuint64_t
#define PRINTGtStrgraphVnumcast(X) PRINTuint64_tcast(X)
#define SCANGtStrgraphVnumcast(X)  SCANuint64_tcast(X)
#define GT_STRGRAPH_VNUM_MAX (GtStrgraphVnum)UINT64_MAX

/* Common Helper Macros */

#define GT_STRGRAPH_SERIALIZE_DATA(FP, NOFELEMS, SPACE)\
  gt_file_xwrite((FP), (void*)(SPACE), (sizeof (*(SPACE)) * (NOFELEMS)))

#define GT_STRGRAPH_DESERIALIZE_DATA(FP, NOFELEMS, SPACE)\
  {\
    GT_UNUSED int nofreadbytes;\
    nofreadbytes = gt_file_xread((FP), (void*)(SPACE), (sizeof (*(SPACE))) *\
        (NOFELEMS));\
    gt_assert(nofreadbytes == (int)(sizeof (*(SPACE)) * (NOFELEMS)));\
  }

/* Counts Representation */

/*
 * counts representations define:
 *
 * GtStrgraphCount          a type large at least as the largest count
 * GT_STRGRAPH_COUNT_MAX
 * FormatGtStrgraphCount
 * [PRINT|SCAN]GtStrgraphCountcast
 *
 * GT_STRGRAPH...           type:
 * _COUNTS_REPRESENTATION
 * _DECLARE_COUNTS
 * _(ALLOC|FREE)_COUNTS
 * _(GET|INC)_COUNT         GtStrgraphCount
 * _[DE]SERIALIZE_COUNTS
 *
 */

#include "match/rdj-strgraph-counts-char-def.h"

/* Vertices Representation */

/* GtStrgraphVmark / GT_STRGRAPH_VMARK_BITS  */
#include "match/rdj-strgraph-vmark-def.h"

/*
 * vertices representations define:
 *
 * GtStrgraphVEdgenum        degree / edge number in a vertex
 * GT_STRGRAPH_V_EDGENUM_MAX
 * FormatGtStrgraphVEdgenum
 * [PRINT|SCAN]GtStrgraphVEdgenumcast
 *
 * GtStrgraphEdgenum         edge number in graph, offset value in edges tables
 * GT_STRGRAPH_EDGENUM_MAX
 * FormatGtStrgraphEdgenum
 * [PRINT|SCAN]GtStrgraphEdgenumcast
 *
 * GT_STRGRAPH_..            type:
 * VERTICES_REPRESENTATION   string literal
 * [SET_]NOFVERTICES         GtStrgraphVnum
 * [ALLOC|FREE]_VERTICES
 * SIZEOF_VERTICES           size_t
 * [DE]SERIALIZE_VERTICES
 *
 * GT_STRGRAPH_V_...
 * [INC_|DEC_]OUTDEG         GtStrgraphVEdgenum
 * [SET_]OFFSET              GtStrgraphEdgenum
 * [SET_]MARK                GtStrgraphVmark
 *
 */

#ifdef GT_STRGRAPH_VERTICES_BITPACK
#include "match/rdj-strgraph-vertices-bitpack-def.h"
#else
#include "match/rdj-strgraph-vertices-bitfield-def.h"
#endif

/* macros depending on vertices definitions,
 *  but common to all representations:
 *
 * GT_STRGRAPH...
 * NOFSPM_MAX                GtStrgraphEdgenum
 * NOFREADS                  GtStrgraphVnum
 *
 * GT_STRGRAPH_V_...
 * NOFEDGES                  GtStrgraphVEdgenum
 * NTH_EDGE_OFFSET           GtStrgraphEdgenum
 * INDEG                     GtStrgraphVEdgenum
 * IS_INTERNAL               bool
 * IS_JUNCTION               bool
 * [B|E]                     GtStrgraphVnum
 * READNUM                   unsigned long
 * IS_[E|B]                  bool
 * OTHER                     GtStrgraphVnum
 * CHAR                      char
 */
#include "match/rdj-strgraph-vertices-common-def.h"

/* Edges Representation */

/*
 * edges representations define:
 *
 * GtStrgraphLength           length of an edge
 * FormatGtStrgraphLength
 * GT_STRGRAPH_LENGTH_MAX
 *
 * GT_STRGRAPH_N_READS_MAX     unsigned long
 *
 * GT_STRGRAPH_..
 * EDGES_REPRESENTATION        string literal
 * [SET_]NOFEDGES              GtStrgraphEdgenum
 * SIZEOF_EDGES                size_t
 * [ALLOC|SHRINK|FREE]_EDGES
 * COPY_EDGE
 * [DE_]SERIALIZE_EDGES
 * FIND_LONGEST_EDGE           GtStrgraphLength
 * SORT_EDGES_BY_LENGTH_FROM_VERTEX XXX:rename
 *
 * GT_STRGRAPH_EDGE_...
 * [SET_]DEST                  GtStrgraphVnum
 * [SET_]LEN                   GtStrgraphLength
 * INIT
 * [SET|HAS]_MARK              bool
 * REDUCE
 * IS_REDUCED                  bool
 */

#ifdef GT_STRGRAPH_EDGES_SHORT
#include "match/rdj-strgraph-edges-short-def.h"
#elif defined(GT_STRGRAPH_EDGES_BITPACK)
#include "match/rdj-strgraph-edges-bitpack-def.h"
#elif defined(GT_STRGRAPH_EDGES_SINGLE_BITPACK)
#include "match/rdj-strgraph-edges-single-bitpack-def.h"
#else
#include "match/rdj-strgraph-edges-bitfield-def.h"
#endif

void gt_strgraph_show_limits_debug_log(void)
{
  gt_log_log("string graph representation: vertices=%s edges=%s",
      GT_STRGRAPH_VERTICES_REPRESENTATION, GT_STRGRAPH_EDGES_REPRESENTATION);
}

void gt_strgraph_show_limits(void)
{
  printf("# max number of reads: %lu\n", GT_STRGRAPH_N_READS_MAX);
  printf("# max read length: "FormatGtStrgraphLength"\n",
      PRINTGtStrgraphLengthcast(GT_STRGRAPH_LENGTH_MAX));
  printf("# max degree of a vertex: "FormatGtStrgraphVEdgenum"\n",
      PRINTGtStrgraphVEdgenumcast(GT_STRGRAPH_V_EDGENUM_MAX));
  printf("# max number of spm: "FormatGtStrgraphEdgenum"\n",
      PRINTGtStrgraphEdgenumcast(GT_STRGRAPH_NOFSPM_MAX));
  printf("# compile-time chosen representations\n");
  printf("# - counts: %s\n",   GT_STRGRAPH_COUNTS_REPRESENTATION);
  printf("# - vertices: %s\n", GT_STRGRAPH_VERTICES_REPRESENTATION);
  printf("# - edges: %s\n",    GT_STRGRAPH_EDGES_REPRESENTATION);
}

GT_UNUSED
static inline void gt_strgraph_show_current_space(const char *label)
{
  unsigned long m, f;
  if (gt_ma_bookkeeping_enabled())
  {
    m = gt_ma_get_space_current();
    f = gt_fa_get_space_current();
    gt_log_log("used space %s: %.2f MB (ma: %.2f MB; fa: %.2f MB)",
        label == NULL ? "" : label, GT_MEGABYTES(m + f), GT_MEGABYTES(m),
        GT_MEGABYTES(f));
  }
}

typedef enum {
  GT_STRGRAPH_PREPARATION,
  GT_STRGRAPH_CONSTRUCTION,
  GT_STRGRAPH_SORTED_BY_L,
} GtStrgraphState;

struct GtStrgraph {
  const GtEncseq     *encseq;
  GtStrgraphLength   fixlen;
  GtStrgraphState    state;
  FILE               *spmfile;
  char               *spmfile_buffer;
  bool               load_self_spm;
  bool               binary_spmlist;
  GtStrgraphLength   minmatchlen;
  GT_STRGRAPH_DECLARE_COUNTS;
  GT_STRGRAPH_DECLARE_VERTICES;
  GT_STRGRAPH_DECLARE_EDGES;
};

#ifdef GT_STRGRAPH_RUNTIME_CHECKS
#define GT_STRGRAPH_CHECK_NOFREADS(NOFREADS)\
  if ((NOFREADS) > GT_STRGRAPH_N_READS_MAX)\
  {\
    fprintf(stderr, "fatal: overflow\n");\
    fprintf(stderr, "more than %lu reads (%lu found)\n",\
        GT_STRGRAPH_N_READS_MAX, (NOFREADS));\
    exit(EXIT_FAILURE);\
  }

#define GT_STRGRAPH_CHECK_LEN(FROM, TO, LEN)\
  if ((LEN) > GT_STRGRAPH_LENGTH_MAX)\
  {\
    fprintf(stderr, "fatal: overflow\n");\
    fprintf(stderr, "edge %lu%c -> %lu%c has length > "FormatGtStrgraphLength\
        " ("FormatGtStrgraphLength" found)\n",\
        GT_STRGRAPH_V_READNUM(FROM),\
        GT_STRGRAPH_V_IS_E(FROM) ? 'E' : 'B',\
        GT_STRGRAPH_V_READNUM(TO),\
        GT_STRGRAPH_V_IS_E(TO) ? 'E' : 'B',\
        PRINTGtStrgraphLengthcast(GT_STRGRAPH_LENGTH_MAX),\
        PRINTGtStrgraphLengthcast(LEN));\
    exit(EXIT_FAILURE);\
  }

#define GT_STRGRAPH_CHECK_NOFEDGES(NOFEDGES)\
  if ((NOFEDGES) > GT_STRGRAPH_EDGENUM_MAX)\
  {\
    fprintf(stderr, "fatal: overflow\n");\
    fprintf(stderr, "more than "FormatGtStrgraphEdgenum" spm ("\
        FormatGtStrgraphEdgenum" found)\n",\
        PRINTGtStrgraphEdgenumcast(GT_STRGRAPH_EDGENUM_MAX),\
        PRINTGtStrgraphEdgenumcast(NOFEDGES));\
    exit(EXIT_FAILURE);\
  }

#define GT_STRGRAPH_CHECK_OUTDEG(VNUM, OUTDEG)\
  if ((OUTDEG) > GT_STRGRAPH_V_EDGENUM_MAX)\
  {\
    fprintf(stderr, "fatal: overflow\n");\
    fprintf(stderr, "vertex %lu%c has more than "\
        FormatGtStrgraphVEdgenum" outgoing edges ("FormatGtStrgraphVEdgenum\
        " found)\n", GT_STRGRAPH_V_READNUM(VNUM),\
        GT_STRGRAPH_V_IS_E(VNUM) ? 'E' : 'B',\
        PRINTGtStrgraphVEdgenumcast(GT_STRGRAPH_V_EDGENUM_MAX),\
        PRINTGtStrgraphVEdgenumcast(OUTDEG));\
    exit(EXIT_FAILURE);\
  }
#else
#define GT_STRGRAPH_CHECK_NOFREADS(NOFREADS)
#define GT_STRGRAPH_CHECK_LEN(FROM, TO, LEN)
#define GT_STRGRAPH_CHECK_NOFEDGES(NOFEDGES)
#define GT_STRGRAPH_CHECK_OUTDEG(VNUM, OUTDEG)
#endif

#define GT_STRGRAPH_SEQLEN(STRGRAPH, READNUM)\
  (((STRGRAPH)->fixlen > 0) ? ((STRGRAPH)->fixlen)\
   : (GtStrgraphLength)gt_encseq_seqlength((STRGRAPH)->encseq,\
     (unsigned long)(READNUM)))

GtStrgraphLength gt_strgraph_longest_read(GtStrgraph *strgraph)
{
  if (strgraph->fixlen > 0)
  {
    return strgraph->fixlen;
  }
  else
  {
    GtStrgraphLength seqlen, maxseqlen;
    GtStrgraphVnum i;

    gt_assert(strgraph->encseq != NULL);
    maxseqlen = 0;
    for (i = 0; i < GT_STRGRAPH_NOFREADS(strgraph); i++)
    {
      seqlen = (GtStrgraphLength)gt_encseq_seqlength(strgraph->encseq,
          (unsigned long)i);
      if (seqlen > maxseqlen)
        maxseqlen = seqlen;
    }
    gt_assert(maxseqlen > 0);
    gt_assert(sizeof (GtStrgraphLength) >= sizeof (unsigned long) ||
        maxseqlen <= GT_STRGRAPH_LENGTH_MAX);
    return maxseqlen;
  }
}

GtStrgraphCount gt_strgraph_largest_count(GtStrgraph *strgraph)
{
  GtStrgraphCount count, maxcount;
  GtStrgraphVnum i;
  maxcount = 0;
  for (i = 0; i < (GT_STRGRAPH_NOFVERTICES(strgraph)); i++)
  {
    count = GT_STRGRAPH_GET_COUNT(strgraph, i);
    if (count > maxcount)
      maxcount = count;
  }
  return maxcount;
}

GtStrgraphEdgenum gt_strgraph_counts_sum(GtStrgraph *strgraph)
{
  GtStrgraphEdgenum sum;
  GtStrgraphVnum i;
  sum = 0;
  for (i = 0; i < (GT_STRGRAPH_NOFVERTICES(strgraph)); i++)
  {
    gt_assert(sizeof (GtStrgraphEdgenum) >= sizeof (GtStrgraphVEdgenum));
    sum += GT_STRGRAPH_GET_COUNT(strgraph, i);
  }
  return sum;
}

/* --- initialization / preparation --- */

GtStrgraph* gt_strgraph_new(unsigned long nofreads)
{
  GtStrgraph *strgraph;
  strgraph = gt_calloc((size_t)1, sizeof (GtStrgraph));
  strgraph->state = GT_STRGRAPH_PREPARATION;
  strgraph->load_self_spm = false;
  strgraph->minmatchlen = GT_STRGRAPH_LENGTH_MAX;
  gt_strgraph_show_limits_debug_log();
  GT_STRGRAPH_CHECK_NOFREADS(nofreads);
  GT_STRGRAPH_SET_NOFVERTICES(strgraph, (GtStrgraphVnum)nofreads << 1);
  GT_STRGRAPH_ALLOC_COUNTS(strgraph, GT_STRGRAPH_NOFVERTICES(strgraph));
  return strgraph;
}

static void gt_strgraph_create_vertices(GtStrgraph *strgraph)
{
  GtStrgraphVnum i;
  GtStrgraphCount c;
  GtStrgraphEdgenum offset;

  gt_assert(strgraph != NULL);
  gt_assert(strgraph->state == GT_STRGRAPH_PREPARATION);

  GT_STRGRAPH_ALLOC_VERTICES(strgraph);

  offset = 0;
  for (i = (GtStrgraphVnum)1; i <= GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    c = GT_STRGRAPH_GET_COUNT(strgraph, i - 1);
    gt_assert(sizeof (GtStrgraphVEdgenum) >= sizeof (GtStrgraphCount));
    GT_STRGRAPH_CHECK_OUTDEG(i - 1, (GtStrgraphVEdgenum)c);
    gt_assert(sizeof (GtStrgraphEdgenum) >= sizeof (GtStrgraphCount));
    offset += (GtStrgraphCount)c;
    GT_STRGRAPH_V_SET_OFFSET(strgraph, i, offset);
  }
  GT_STRGRAPH_CHECK_NOFEDGES(offset);
  GT_STRGRAPH_SET_NOFEDGES(strgraph, offset);
  GT_STRGRAPH_FREE_COUNTS(strgraph);
}

void gt_strgraph_allocate_graph(GtStrgraph *strgraph, unsigned long fixlen,
    const GtEncseq *encseq)
{
  gt_assert(strgraph != NULL);
  gt_assert((fixlen == 0 && encseq != NULL)||
            (fixlen > 0 && encseq == NULL));
  gt_assert(sizeof (GtStrgraphLength) >= sizeof (unsigned long) ||
      (fixlen > 0 && fixlen <= (unsigned long)GT_STRGRAPH_LENGTH_MAX) ||
      (encseq != NULL && gt_encseq_max_seq_length(encseq)));
  strgraph->fixlen = (GtStrgraphLength)fixlen;
  strgraph->encseq = encseq;
  gt_log_log("minmatchlen = "FormatGtStrgraphLength, strgraph->minmatchlen);
  gt_strgraph_create_vertices(strgraph);
  GT_STRGRAPH_ALLOC_EDGES(strgraph);
  strgraph->state = GT_STRGRAPH_CONSTRUCTION;
}

void gt_strgraph_delete(GtStrgraph *strgraph)
{
  if (strgraph != NULL)
  {
    GT_STRGRAPH_FREE_VERTICES(strgraph);
    GT_STRGRAPH_FREE_EDGES(strgraph);
    GT_STRGRAPH_FREE_COUNTS(strgraph);
    gt_free(strgraph);
  }
}

static void gt_strgraph_save(const GtStrgraph *strgraph, GtFile *outfp)
{
  gt_assert(strgraph != NULL);
  gt_file_xwrite(outfp, (void*)&(GT_STRGRAPH_NOFVERTICES(strgraph)),
      sizeof (GtStrgraphVnum));
  GT_STRGRAPH_SERIALIZE_VERTICES(strgraph, outfp);
  GT_STRGRAPH_SERIALIZE_EDGES(strgraph, outfp);
}

static void gt_strgraph_load(GtStrgraph *strgraph, GtFile *infp)
{
  GT_UNUSED int read;
  GtStrgraphVnum n_vertices;
  read = gt_file_xread(infp, (void*)&n_vertices, sizeof (GtStrgraphVnum));
  gt_assert(read == (int)sizeof (GtStrgraphVnum));
  GT_STRGRAPH_SET_NOFVERTICES(strgraph, n_vertices);
  GT_STRGRAPH_ALLOC_VERTICES(strgraph);
  GT_STRGRAPH_DESERIALIZE_VERTICES(strgraph, infp);
  GT_STRGRAPH_ALLOC_EDGES(strgraph);
  GT_STRGRAPH_DESERIALIZE_EDGES(strgraph, infp);
}

void gt_strgraph_compact(GtStrgraph *strgraph, bool show_progressbar)
{
  GtStrgraphVnum i;
  GtStrgraphEdgenum old_offset, next_free_edge, new_offset;
  GtStrgraphVEdgenum old_nofedges, j;
  unsigned long long progress = 0;

  gt_assert(strgraph != NULL);

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));

  next_free_edge = 0;
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    new_offset = next_free_edge;
    old_offset = GT_STRGRAPH_V_OFFSET(strgraph, i);
    old_nofedges = GT_STRGRAPH_V_NOFEDGES(strgraph, i);
    for (j = 0; j < old_nofedges; j++)
    {
      if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
      {
        GT_STRGRAPH_COPY_EDGE(strgraph, old_offset + j, next_free_edge);
        next_free_edge++;
      }
    }
    GT_STRGRAPH_V_SET_OFFSET(strgraph, i, new_offset);
    gt_assert(next_free_edge - GT_STRGRAPH_V_OFFSET(strgraph, i) ==
        (GtStrgraphEdgenum)GT_STRGRAPH_V_OUTDEG(strgraph, i));
    if (show_progressbar)
      progress++;
  }
  GT_STRGRAPH_V_SET_OFFSET(strgraph, GT_STRGRAPH_NOFVERTICES(strgraph),
      next_free_edge);
  if (next_free_edge < GT_STRGRAPH_NOFEDGES(strgraph))
  {
    GT_STRGRAPH_SHRINK_EDGES(strgraph, next_free_edge);
  }

  if (show_progressbar)
    gt_progressbar_stop();
}

static GtFile* gt_strgraph_get_file(const char *indexname, const char *suffix,
    bool write, bool gzipped)
{
  GtFile *file;
  GtStr *filename;
  GtError *err;

  err = gt_error_new();
  filename = gt_str_new_cstr(indexname);
  gt_str_append_cstr(filename, suffix);
  if (!write && !gt_file_exists(gt_str_get(filename)))
  {
    fprintf(stderr, "file %s does not exist\n", gt_str_get(filename));
    exit(EXIT_FAILURE);
  }
  file = gt_file_open(gzipped ? GT_FILE_MODE_GZIP : GT_FILE_MODE_UNCOMPRESSED,
      gt_str_get(filename), write ? "w" : "r", err);
  if (file == NULL)
  {
    fprintf(stderr, "%s", gt_error_get(err));
    exit(EXIT_FAILURE);
  }
  gt_str_delete(filename);
  gt_error_delete(err);
  return file;
}

GtStrgraph* gt_strgraph_new_from_file(const GtEncseq *encseq,
    unsigned long fixlen, const char *indexname, const char *suffix)
{
  GtStrgraph *strgraph;
  GtFile *infp;

  gt_assert(encseq != NULL || fixlen > 0);
  strgraph = gt_malloc(sizeof (GtStrgraph));
  strgraph->encseq = encseq;
  gt_assert(sizeof (GtStrgraphLength) >= sizeof (unsigned long) ||
     fixlen <= (unsigned long)GT_STRGRAPH_LENGTH_MAX);
  strgraph->fixlen = (GtStrgraphLength)fixlen;
  infp = gt_strgraph_get_file(indexname, suffix, false, false);
  gt_strgraph_load(strgraph, infp);
  gt_file_delete(infp);
  return strgraph;
}

void gt_spmproc_strgraph_count(unsigned long suffix_readnum,
    unsigned long prefix_readnum, unsigned long length,
    bool suffixseq_direct, bool prefixseq_direct, void *strgraph)
{
  GtStrgraph* g;
  GtStrgraphVnum position;

  gt_assert(strgraph != NULL);
  g = (GtStrgraph*)strgraph;

  gt_assert(g->state == GT_STRGRAPH_PREPARATION);
  position = suffixseq_direct ? GT_STRGRAPH_V_E(suffix_readnum)
    : GT_STRGRAPH_V_B(suffix_readnum);
  GT_STRGRAPH_INC_COUNT(g, position);

  position = prefixseq_direct ? GT_STRGRAPH_V_B(prefix_readnum)
    : GT_STRGRAPH_V_E(prefix_readnum);
  GT_STRGRAPH_INC_COUNT(g, position);

  if (g->minmatchlen > (GtStrgraphLength)length)
    g->minmatchlen = (GtStrgraphLength)length;
}

int gt_strgraph_open_spmlist_file(GtStrgraph *strgraph, const char *indexname,
    const char *suffix, bool binary, unsigned long bufsize, GtError *err)
{
  strgraph->binary_spmlist = binary;
  strgraph->spmfile = gt_fa_fopen_with_suffix(indexname, suffix,
      binary ? "wb" : "w", err);
  if (strgraph->spmfile == NULL)
    return -1;
  if (bufsize > 0)
  {
    strgraph->spmfile_buffer = NULL;
    (void)setvbuf(strgraph->spmfile, strgraph->spmfile_buffer, (int)_IOFBF,
        (size_t)bufsize << 20);
  }
  if (binary)
  {
    if (GT_STRGRAPH_NOFREADS(strgraph) > UINT32_MAX)
      gt_spmlist_write_header_bin64(strgraph->spmfile);
    else
      gt_spmlist_write_header_bin32(strgraph->spmfile);
  }
  return 0;
}

void gt_spmproc_strgraph_count_and_save(unsigned long suffix_readnum,
    unsigned long prefix_readnum, unsigned long length,
    bool suffixseq_direct, bool prefixseq_direct, void *strgraph)
{
  GtStrgraph* g;

  gt_assert(strgraph != NULL);
  g = (GtStrgraph*)strgraph;
  gt_spmproc_strgraph_count(suffix_readnum, prefix_readnum, length,
      suffixseq_direct, prefixseq_direct, strgraph);
  if (g->binary_spmlist)
  {
    if (GT_STRGRAPH_NOFREADS(g) > (GtStrgraphVnum)UINT32_MAX)
    {
      /*@ignore@*/
      gt_spmproc_show_bin64(suffix_readnum, prefix_readnum, length,
          suffixseq_direct, prefixseq_direct, g->spmfile);
      /*@end@*/
    }
    else
    {
      /*@ignore@*/
      gt_spmproc_show_bin32(suffix_readnum, prefix_readnum, length,
          suffixseq_direct, prefixseq_direct, g->spmfile);
      /*@end@*/
    }
  }
  else
  {
    GtFile *gtfile = gt_file_new_from_fileptr(g->spmfile);
    gt_spmproc_show_ascii(suffix_readnum, prefix_readnum, length,
        suffixseq_direct, prefixseq_direct, gtfile);
    gt_file_delete_without_handle(gtfile);
  }
}

int gt_strgraph_save_counts(GtStrgraph *strgraph, const char *indexname,
    const char *suffix, GT_UNUSED GtError *err)
{
  GtFile *outfp;

  gt_assert(strgraph != NULL);
  gt_assert(strgraph->state == GT_STRGRAPH_PREPARATION);
  outfp = gt_strgraph_get_file(indexname, suffix, true, false);
  gt_assert(outfp != NULL);
  GT_STRGRAPH_SERIALIZE_COUNTS(strgraph, outfp);
  gt_file_delete(outfp);
  return 0;
}

int gt_strgraph_load_counts(GtStrgraph *strgraph, const char *indexname,
    const char *suffix, GT_UNUSED GtError *err)
{
  GtFile *infp;

  gt_assert(strgraph != NULL);
  gt_assert(strgraph->state == GT_STRGRAPH_PREPARATION);
  infp = gt_strgraph_get_file(indexname, suffix, false, false);
  gt_assert(infp != NULL);
  GT_STRGRAPH_DESERIALIZE_COUNTS(strgraph, infp);
  gt_file_delete(infp);
  return 0;
}

void gt_strgraph_close_spmlist_file(GtStrgraph *strgraph)
{
  gt_fa_fclose(strgraph->spmfile);
  gt_free(strgraph->spmfile_buffer);
}

static void gt_strgraph_mark_empty_edges(GtStrgraph *strgraph)
{
  GtStrgraphVnum i;
  GtStrgraphVEdgenum j, n_empty;

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    gt_assert(GT_STRGRAPH_V_OUTDEG(strgraph, i)
        <= GT_STRGRAPH_V_NOFEDGES(strgraph, i));
    n_empty = GT_STRGRAPH_V_NOFEDGES(strgraph, i) -
      GT_STRGRAPH_V_OUTDEG(strgraph, i);
    if (n_empty > 0)
    {
      for (j = GT_STRGRAPH_V_OUTDEG(strgraph, i);
           j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        GT_STRGRAPH_EDGE_REDUCE(strgraph, i, j);
      }
    }
  }
}

int gt_strgraph_load_spm_from_file(GtStrgraph *strgraph,
    unsigned long min_length, bool load_self_spm, GtBitsequence *contained,
    const char *indexname, unsigned int nspmfiles, const char *suffix,
    GtError *err)
{
  int had_err = 0;
  GtStr *filename = gt_str_new();
  GtSpmprocSkipData skipdata;
  unsigned int i;

  gt_assert(strgraph != NULL);
  if (contained != NULL)
  {
    skipdata.out.e.proc = gt_spmproc_strgraph_add;
    skipdata.to_skip = contained;
    skipdata.out.e.data = strgraph;
  }
  strgraph->load_self_spm = load_self_spm;
  for (i = 0; i < nspmfiles; i++)
  {
    gt_str_append_cstr(filename, indexname);
    gt_str_append_char(filename, '.');
    gt_str_append_uint(filename, i);
    gt_str_append_cstr(filename, suffix);
    had_err = gt_spmlist_parse(gt_str_get(filename), min_length,
        contained != NULL ? gt_spmproc_skip : gt_spmproc_strgraph_add,
        contained != NULL ? (void*)&skipdata : (void*)strgraph, err);
    gt_str_reset(filename);
  }
  gt_str_delete(filename);
  if (!had_err)
    gt_strgraph_mark_empty_edges(strgraph);
  return had_err;
}

/* --- construction --- */

void gt_strgraph_set_encseq(GtStrgraph *strgraph, const GtEncseq *encseq)
{
  gt_assert(strgraph != NULL);
  strgraph->encseq = encseq;
}

static inline void gt_strgraph_add_edge(GtStrgraph *strgraph,
    GtStrgraphVnum from, GtStrgraphVnum to, GtStrgraphLength spmlen)
{
  GtStrgraphLength edgelen;
  GtStrgraphVEdgenum next_free_edge;

  gt_assert(strgraph != NULL);

  edgelen = GT_STRGRAPH_SEQLEN(strgraph, GT_STRGRAPH_V_READNUM(to)) - spmlen;

  GT_STRGRAPH_CHECK_LEN(from, to, edgelen);
  next_free_edge = GT_STRGRAPH_V_OUTDEG(strgraph, from);
  GT_STRGRAPH_EDGE_INIT(strgraph, from, next_free_edge);
  GT_STRGRAPH_EDGE_SET_DEST(strgraph, from, next_free_edge, to);
  GT_STRGRAPH_EDGE_SET_LEN(strgraph, from, next_free_edge, edgelen);
  GT_STRGRAPH_V_INC_OUTDEG(strgraph, from);
}

void gt_spmproc_strgraph_add(unsigned long suffix_readnum,
    unsigned long prefix_readnum, unsigned long length,
    bool suffixseq_direct, bool prefixseq_direct, void *graph)
{
  GtStrgraph *strgraph = graph;
  GtStrgraphLength edgelen = (GtStrgraphLength)length;
  gt_assert(strgraph != NULL);
  gt_assert(suffixseq_direct || prefixseq_direct);

  if (suffix_readnum == prefix_readnum && !strgraph->load_self_spm)
    return;

  if (suffixseq_direct) {
    if (prefixseq_direct) {
      gt_strgraph_add_edge(strgraph, GT_STRGRAPH_V_E(suffix_readnum),
                         GT_STRGRAPH_V_E(prefix_readnum), edgelen);
      gt_strgraph_add_edge(strgraph, GT_STRGRAPH_V_B(prefix_readnum),
                         GT_STRGRAPH_V_B(suffix_readnum), edgelen);
    } else {
      gt_strgraph_add_edge(strgraph, GT_STRGRAPH_V_E(suffix_readnum),
                         GT_STRGRAPH_V_B(prefix_readnum), edgelen);
      gt_strgraph_add_edge(strgraph, GT_STRGRAPH_V_E(prefix_readnum),
                         GT_STRGRAPH_V_B(suffix_readnum), edgelen);
    }
  } else {
    if (prefixseq_direct) {
      gt_strgraph_add_edge(strgraph, GT_STRGRAPH_V_B(suffix_readnum),
                         GT_STRGRAPH_V_E(prefix_readnum), edgelen);
      gt_strgraph_add_edge(strgraph, GT_STRGRAPH_V_B(prefix_readnum),
                         GT_STRGRAPH_V_E(suffix_readnum), edgelen);
    } else {
      gt_strgraph_add_edge(strgraph, GT_STRGRAPH_V_B(suffix_readnum),
                         GT_STRGRAPH_V_B(prefix_readnum), edgelen);
      gt_strgraph_add_edge(strgraph, GT_STRGRAPH_V_E(prefix_readnum),
                         GT_STRGRAPH_V_E(suffix_readnum), edgelen);
    }
  }
}

void gt_strgraph_sort_edges_by_len(GtStrgraph *strgraph, bool show_progressbar)
{
  GtStrgraphVnum i;
  unsigned long long progress = 0;

  gt_assert(strgraph != NULL);

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    GT_STRGRAPH_SORT_V_EDGES(strgraph, i);
    if (show_progressbar)
      progress++;
  }

  strgraph->state = GT_STRGRAPH_SORTED_BY_L;

  if (show_progressbar)
    gt_progressbar_stop();
}

#ifndef NDEBUG
static void gt_strgraph_check_outdegs(GtStrgraph *strgraph)
{
  GtStrgraphVnum i;
  GtStrgraphVEdgenum j, outdeg;
  for (i = 0UL; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    outdeg = 0;
    for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
        outdeg++;
    gt_assert(outdeg == GT_STRGRAPH_V_OUTDEG(strgraph, i));
  }
}
#endif

static unsigned long gt_strgraph_reduce_marked_edges(GtStrgraph *strgraph)
{
  GtStrgraphVnum i;
  unsigned long counter = 0;
  GtStrgraphVEdgenum j;

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) == 0)
      continue;
    for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
    {
      if (GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
        continue;
      if (GT_STRGRAPH_EDGE_HAS_MARK(strgraph, i, j))
      {
        GT_STRGRAPH_EDGE_REDUCE(strgraph, i, j);
        GT_STRGRAPH_V_DEC_OUTDEG(strgraph, i);
        counter++;
      }
    }
  }
  return counter;
}

/* return value: number of self edges */
unsigned long gt_strgraph_redself(GtStrgraph *strgraph, bool show_progressbar)
{
  GtStrgraphVnum vnum;
  GtStrgraphVEdgenum edgenum;
  unsigned long counter = 0;
  unsigned long long progress = 0;

  gt_assert(strgraph != NULL);

  counter = 0;
  if (show_progressbar)
    gt_progressbar_start(&(progress),
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));
  for (vnum = 0; vnum < GT_STRGRAPH_NOFVERTICES(strgraph); vnum++)
  {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, vnum) > 0)
    {
      for (edgenum = 0; edgenum < GT_STRGRAPH_V_NOFEDGES(strgraph, vnum);
          edgenum++)
      {
        if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, vnum, edgenum) &&
            GT_STRGRAPH_EDGE_DEST(strgraph, vnum, edgenum) == vnum)
        {
          counter++;
          GT_STRGRAPH_EDGE_REDUCE(strgraph, vnum, edgenum);
          GT_STRGRAPH_V_DEC_OUTDEG(strgraph, vnum);
        }
      }
    }
    if (show_progressbar)
      progress++;
  }
  if (show_progressbar)
    gt_progressbar_stop();

  gt_log_log("self-matches counter: %lu", counter);
  /* self matches shoud be found twice, check number is even */
  gt_assert((counter & 1) == 0);
#ifndef NDEBUG
  gt_strgraph_check_outdegs(strgraph);
#endif
  return (counter >> 1);
}

/* return value: number of with-rc edges */
unsigned long gt_strgraph_redwithrc(GtStrgraph *strgraph, bool show_progressbar)
{
  GtStrgraphVnum vnum;
  GtStrgraphVEdgenum edgenum;
  unsigned long counter = 0;
  unsigned long long progress = 0;

  gt_assert(strgraph != NULL);

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));

  counter = 0;
  if (show_progressbar)
    gt_progressbar_start(&(progress),
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));
  for (vnum = 0; vnum < GT_STRGRAPH_NOFVERTICES(strgraph); vnum++)
  {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, vnum) > 0)
    {
      for (edgenum = 0; edgenum < GT_STRGRAPH_V_NOFEDGES(strgraph, vnum);
          edgenum++)
      {
        if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, vnum, edgenum) &&
            GT_STRGRAPH_EDGE_DEST(strgraph, vnum, edgenum) ==
            GT_STRGRAPH_V_OTHER(vnum))
        {
          counter++;
          GT_STRGRAPH_EDGE_REDUCE(strgraph, vnum, edgenum);
          GT_STRGRAPH_V_DEC_OUTDEG(strgraph, vnum);
        }
      }
    }
    if (show_progressbar)
      progress++;
  }
  if (show_progressbar)
    gt_progressbar_stop();

  gt_log_log("withrc-matches counter: %lu", counter);
  /* withrc matches shoud be found twice, check number is even */
  gt_assert((counter & 1) == 0);
#ifndef NDEBUG
  gt_strgraph_check_outdegs(strgraph);
#endif
  return (counter >> 1);
}

/* return value: number of transitive edges */
unsigned long gt_strgraph_redtrans(GtStrgraph *strgraph, bool show_progressbar)
{
  GtStrgraphLength jlen, klen, longest;
  GtStrgraphVEdgenum j, k, l;
  GtStrgraphVnum i, jdest, kdest;
  unsigned long counter;
  unsigned long long progress = 0;

  gt_assert(strgraph != NULL);
  gt_assert(strgraph->state == GT_STRGRAPH_SORTED_BY_L);

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
    GT_STRGRAPH_V_SET_MARK(strgraph, i, GT_STRGRAPH_V_VACANT);

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0)
    {
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        GT_STRGRAPH_V_SET_MARK(strgraph, GT_STRGRAPH_EDGE_DEST(strgraph, i, j),
            GT_STRGRAPH_V_INPLAY);
      }
      GT_STRGRAPH_FIND_LONGEST_EDGE(strgraph, i, longest);
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        jdest = GT_STRGRAPH_EDGE_DEST(strgraph, i, j);
        jlen = GT_STRGRAPH_EDGE_LEN(strgraph, i, j);
        for (k = 0; k < GT_STRGRAPH_V_NOFEDGES(strgraph, jdest) &&
            GT_STRGRAPH_EDGE_LEN(strgraph, jdest, k) + jlen <= longest; k++)
        {
          kdest = GT_STRGRAPH_EDGE_DEST(strgraph, jdest, k);
          klen = GT_STRGRAPH_EDGE_LEN(strgraph, jdest, k);
          if (GT_STRGRAPH_V_MARK(strgraph, kdest) == GT_STRGRAPH_V_INPLAY)
          {
            for (l = 0; l < GT_STRGRAPH_V_NOFEDGES(strgraph, i); l++)
            {
              if (GT_STRGRAPH_EDGE_DEST(strgraph, i, l) == kdest &&
                  GT_STRGRAPH_EDGE_LEN(strgraph, i, l) == jlen + klen)
              {
                GT_STRGRAPH_EDGE_SET_MARK(strgraph, i, l);
              }
            }
          }
        }
      }
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        GT_STRGRAPH_V_SET_MARK(strgraph, GT_STRGRAPH_EDGE_DEST(strgraph, i, j),
            GT_STRGRAPH_V_VACANT);
      }
    }
    if (show_progressbar)
      progress++;
  }
  if (show_progressbar)
    gt_progressbar_stop();

  counter = gt_strgraph_reduce_marked_edges(strgraph);
  gt_log_log("transitive counter: %lu", counter);
  /* trans spm should be found twice, check number is even */
  /*gt_assert((counter & 1) == 0);*/
#ifndef NDEBUG
  gt_strgraph_check_outdegs(strgraph);
#endif
  return (counter >> 1);
}

unsigned long gt_strgraph_redsubmax(GtStrgraph *strgraph, bool show_progressbar)
{
  GtStrgraphVnum i;
  GtStrgraphVEdgenum j;
  unsigned long counter = 0;
  unsigned long long progress = 0;

  gt_assert(strgraph != NULL);
  gt_assert(strgraph->state == GT_STRGRAPH_SORTED_BY_L);

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
    GT_STRGRAPH_V_SET_MARK(strgraph, i, GT_STRGRAPH_V_VACANT);

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0)
    {
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        if (GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
          continue;
        if (GT_STRGRAPH_V_MARK(strgraph, GT_STRGRAPH_EDGE_DEST(strgraph, i, j))
              == GT_STRGRAPH_V_INPLAY)
        {
          counter++;
          GT_STRGRAPH_EDGE_REDUCE(strgraph, i, j);
          GT_STRGRAPH_V_DEC_OUTDEG(strgraph, i);
        }
        GT_STRGRAPH_V_SET_MARK(strgraph, i, GT_STRGRAPH_V_INPLAY);
      }
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        GT_STRGRAPH_V_SET_MARK(strgraph, GT_STRGRAPH_EDGE_DEST(strgraph, i, j),
            GT_STRGRAPH_V_VACANT);
      }
    }
    if (show_progressbar)
      progress++;
  }
  if (show_progressbar)
    gt_progressbar_stop();
  gt_log_log("submaximal counter: %lu", counter);
  /* nonmax spm shoud be found twice, check number is even */
  gt_assert((counter & 1) == 0);
#ifndef NDEBUG
  gt_strgraph_check_outdegs(strgraph);
#endif
  return (counter >> 1);
}

static inline GtStrgraphVEdgenum gt_strgraph_find_only_edge(
    GtStrgraph *strgraph, GtStrgraphVnum from)
{
  GtStrgraphVEdgenum j;
  gt_assert(GT_STRGRAPH_V_OUTDEG(strgraph, from) == (GtStrgraphVEdgenum)1);
  for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, from); j++)
  {
    if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, from, j))
      return j;
  }
  gt_assert(false); /* outdeg error */
  return 0; /* to avoid warnings */
}

typedef struct {
  GtStrgraphVnum vnum;
  GtStrgraphVEdgenum edgenum;
} GtStrgraphEdgeID;

unsigned long gt_strgraph_reddepaths(GtStrgraph *strgraph,
    unsigned long maxdepth, bool show_progressbar)
{
  GtStrgraphVnum i, from, to;
  GtStrgraphVEdgenum j, from_to;
  unsigned long depth, d;
  unsigned long counter = 0, nofdepaths = 0;
  unsigned long long progress = 0;
  bool i_branching;
  GtStrgraphEdgeID *edges;

  gt_assert(strgraph != NULL);

  edges = gt_malloc(sizeof (GtStrgraphEdgeID) * (maxdepth + 1));

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0)
    {
      if (GT_STRGRAPH_V_IS_INTERNAL(strgraph, i))
        continue;
      i_branching =
        (GT_STRGRAPH_V_OUTDEG(strgraph, i) > (GtStrgraphVEdgenum)1 &&
         GT_STRGRAPH_V_INDEG(strgraph, i) > 0) ||
        (GT_STRGRAPH_V_OUTDEG(strgraph, i) == (GtStrgraphVEdgenum)1 &&
         GT_STRGRAPH_V_INDEG(strgraph, i) > (GtStrgraphVEdgenum)1);
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j) &&
            !GT_STRGRAPH_EDGE_HAS_MARK(strgraph, i, j))
        {
          from = i;
          from_to = j;
          to = GT_STRGRAPH_EDGE_DEST(strgraph, from, from_to);
          edges->vnum = from;
          edges->edgenum = from_to;
          depth = 1UL;
          while (GT_STRGRAPH_V_IS_INTERNAL(strgraph, to) &&
              depth <= maxdepth)
          {
            depth++;
            from = to;
            from_to = gt_strgraph_find_only_edge(strgraph, from);
            to = GT_STRGRAPH_EDGE_DEST(strgraph, from, from_to);
            gt_assert(depth >= 1UL);
            gt_assert(depth - 1UL <= maxdepth);
            edges[depth - 1UL].vnum = from;
            edges[depth - 1UL].edgenum = from_to;
          }
          if (depth <= maxdepth &&
              (!i_branching || GT_STRGRAPH_V_OUTDEG(strgraph, to) == 0))
          {
            nofdepaths++;
            for (d = 0; d < depth; d++)
            {
              GT_STRGRAPH_EDGE_SET_MARK(strgraph, edges[d].vnum,
                  edges[d].edgenum);
            }
          }
        }
      }
    }
    if (show_progressbar)
      progress++;
  }
  gt_free(edges);
  counter = gt_strgraph_reduce_marked_edges(strgraph);
  if (show_progressbar)
    gt_progressbar_stop();
  gt_log_log("dead-paths = %lu", nofdepaths);
  gt_log_log("dead-path edges = %lu", counter);
#ifndef NDEBUG
  gt_strgraph_check_outdegs(strgraph);
#endif
  return counter;
}

typedef struct {
  GtStrgraphVEdgenum edgenum;
  GtStrgraphVnum dest;
  unsigned long depth;
  unsigned long width;
} GtStrgraphPathInfo;

static int gt_strgraph_path_info_compare(const void *pi_a, const void *pi_b)
{
  int retv;
  const GtStrgraphPathInfo *a = pi_a, *b = pi_b;
  retv = (int)(a->dest > b->dest) -
    (int)(a->dest < b->dest);
  if (retv == 0)
    retv = (int)(a->width > b->width) - (int)(a->width < b->width);
  return retv;
}

unsigned long gt_strgraph_redpbubbles(GtStrgraph *strgraph,
    unsigned long maxwidth, const unsigned long maxdiff,
    bool show_progressbar)
{
  GtStrgraphVnum i, from, to;
  GtStrgraphVEdgenum j, from_to, p, nofpaths;
  GtStrgraphLength len;
  unsigned long depth, width, counter = 0, nofpbubbles = 0;
  unsigned long long progress = 0;
  GtStrgraphPathInfo *info, *prev;

  gt_assert(strgraph != NULL);

  if (maxwidth == 0)
    maxwidth = (unsigned long)(gt_strgraph_longest_read(strgraph) << 2) -
        (strgraph->minmatchlen << 1) - 1;
  gt_log_log("redpbubbles(maxwidth=%lu, maxdiff=%lu)", maxwidth, maxdiff);

  /* allocate info and set all marks to VACANT */
  {
    unsigned long maxoutdeg = 0;
    for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
    {
      GT_STRGRAPH_V_SET_MARK(strgraph, i, GT_STRGRAPH_V_VACANT);
      if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > (GtStrgraphVEdgenum)maxoutdeg)
        maxoutdeg = (unsigned long)GT_STRGRAPH_V_OUTDEG(strgraph, i);
    }
    gt_log_log("maxoutdeg = %lu", maxoutdeg);
    info = gt_malloc(sizeof (GtStrgraphPathInfo) * maxoutdeg);
  }

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0)
    {
      if (GT_STRGRAPH_V_IS_INTERNAL(strgraph, i))
        continue;
      nofpaths = 0;
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
        {
          from = i;
          from_to = j;
          to = GT_STRGRAPH_EDGE_DEST(strgraph, i, j);
          depth = 1UL;
          len = GT_STRGRAPH_EDGE_LEN(strgraph, i, j);
          gt_assert(sizeof (unsigned long) >= sizeof (GtStrgraphLength) ||
              len <= (GtStrgraphLength)ULONG_MAX);
          width = (unsigned long)len;
          while (GT_STRGRAPH_V_IS_INTERNAL(strgraph, to) && width <= maxwidth)
          {
            depth++;
            from = to;
            from_to = gt_strgraph_find_only_edge(strgraph, from);
            len = GT_STRGRAPH_EDGE_LEN(strgraph, from, from_to);
            gt_assert((sizeof (unsigned long) >= sizeof (GtStrgraphLength) &&
                width <= ULONG_MAX - (unsigned long)len) ||
                (GtStrgraphLength)width + len < (GtStrgraphLength)ULONG_MAX);
            width += (unsigned long)len;
            to = GT_STRGRAPH_EDGE_DEST(strgraph, from, from_to);
          }
          if (width <= maxwidth && depth > 1UL)
          {
            info[nofpaths].edgenum = j;
            info[nofpaths].dest = to;
            info[nofpaths].depth = depth;
            info[nofpaths].width = width;
            nofpaths++;
          }
        }
      }
      if (nofpaths > 0)
      {
        qsort(info, (size_t)nofpaths, sizeof (*info),
            gt_strgraph_path_info_compare);
        prev = info;
        for (p = (GtStrgraphVEdgenum)1; p < nofpaths; p++)
        {
          if (info[p].dest == prev->dest &&
              (info[p].width - prev->width <= maxdiff))
          {
            nofpbubbles++;
            if (info[p].depth <= prev->depth)
            {
              from_to = info[p].edgenum;
            }
            else
            {
              from_to = prev->edgenum;
              prev = info + p;
            }
            GT_STRGRAPH_EDGE_SET_MARK(strgraph, i, from_to);
            to = GT_STRGRAPH_EDGE_DEST(strgraph, i, from_to);
            while (GT_STRGRAPH_V_IS_INTERNAL(strgraph, to))
            {
              from = to;
              from_to = gt_strgraph_find_only_edge(strgraph, from);
              GT_STRGRAPH_EDGE_SET_MARK(strgraph, from, from_to);
              to = GT_STRGRAPH_EDGE_DEST(strgraph, from, from_to);
            }
          }
          else
          {
            prev = info + p;
          }
        }
      }
    }
    if (show_progressbar)
      progress++;
  }
  counter = gt_strgraph_reduce_marked_edges(strgraph);

  if (show_progressbar)
    gt_progressbar_stop();
  gt_free(info);
  gt_log_log("p-bubbles = %lu", nofpbubbles);
  gt_log_log("removed p-bubble edges = %lu", counter);
#ifndef NDEBUG
  gt_strgraph_check_outdegs(strgraph);
#endif
  return counter;
}

#define GT_STRGRAPH_DOT_HEADER     "digraph StringGraph {\n"
#define GT_STRGRAPH_DOT_BI_HEADER  "graph StringGraph {\n"
#define GT_STRGRAPH_DOT_FOOTER     "}\n"

static inline void gt_strgraph_dot_show_edge(GtFile *outfp,
    GtStrgraphVnum from, GtStrgraphVnum to, GtStrgraphLength length)
{
  gt_file_xprintf(outfp,
      " \"%lu%c\" -> \"%lu%c\" "
      "[label="FormatGtStrgraphLength"];\n",
      GT_STRGRAPH_V_READNUM(from),
      GT_STRGRAPH_V_IS_E(from) ? 'E' : 'B',
      GT_STRGRAPH_V_READNUM(to),
      GT_STRGRAPH_V_IS_E(to) ? 'E' : 'B',
      PRINTGtStrgraphLengthcast(length));
}

static void gt_strgraph_dot_show(const GtStrgraph *strgraph, GtFile *outfp,
    bool show_progressbar)
{
  GtStrgraphVnum i;
  GtStrgraphVEdgenum j;
  unsigned long long progress = 0;

  gt_assert(strgraph != NULL);

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));

  gt_file_xprintf(outfp, GT_STRGRAPH_DOT_HEADER);
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++) {
    for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
    {
      if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
      {
        gt_strgraph_dot_show_edge(outfp, i,
            GT_STRGRAPH_EDGE_DEST(strgraph, i, j),
            GT_STRGRAPH_EDGE_LEN(strgraph, i, j));
      }
    }
    if (show_progressbar)
      progress++;
  }
  gt_file_xprintf(outfp, GT_STRGRAPH_DOT_FOOTER);

  if (show_progressbar)
    gt_progressbar_stop();
}

static inline void gt_strgraph_dot_bi_show_edge(GtFile *outfp,
    unsigned long sn1, bool towards1, unsigned long sn2,
    bool towards2)
{
  gt_file_xprintf(outfp, " %lu -- %lu [arrowtail=%s,arrowhead=%s];\n",
      sn1, sn2, towards1 ? "normal" : "inv", towards2 ? "normal" : "inv");
}

static void gt_strgraph_dot_bi_show(const GtStrgraph *strgraph, GtFile *outfp,
    bool show_progressbar)
{
  unsigned long sn1, sn2;
  GtStrgraphVnum i;
  GtStrgraphVEdgenum j;
  bool is_e1, is_e2;
  unsigned long long progress = 0;

  gt_assert(strgraph != NULL);

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));

  gt_file_xprintf(outfp, GT_STRGRAPH_DOT_BI_HEADER);
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++) {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0)
    {
      sn1 = GT_STRGRAPH_V_READNUM(i);
      is_e1 = GT_STRGRAPH_V_IS_E(i);
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
        {
          sn2 = GT_STRGRAPH_V_READNUM(GT_STRGRAPH_EDGE_DEST(strgraph, i, j));
          is_e2 = GT_STRGRAPH_V_IS_E(GT_STRGRAPH_EDGE_DEST(strgraph, i, j));
          if (is_e1 && is_e2) {
            gt_strgraph_dot_bi_show_edge(outfp, sn1, false, sn2, true);
          }
          else if ((is_e1 && !is_e2) && (sn1 < sn2)) {
            gt_strgraph_dot_bi_show_edge(outfp, sn1, false, sn2, false);
          }
          else if ((!is_e1 && is_e2) && (sn1 > sn2)) {
            gt_strgraph_dot_bi_show_edge(outfp, sn1, true, sn2, true);
          }
          /* other E->B / B->E cases, as well as all B-B
             are not considered to avoid double output */
        }
      }
    }
    if (show_progressbar)
      progress++;
  }
  gt_file_xprintf(outfp, GT_STRGRAPH_DOT_FOOTER);

  if (show_progressbar)
    gt_progressbar_stop();
}

typedef struct {
  GtStrgraphVnum v;
  unsigned long d;
} GtStrgraphVnumAndDepth;

static void gt_strgraph_dot_show_context(const GtStrgraph *strgraph,
    GtFile *outfp, unsigned long readnum, unsigned long depth)
{
  GtArray *stack;
  GtStrgraphVnumAndDepth to_add, *current;
  GtStrgraphVnum v;
  GtStrgraphVEdgenum j;
  unsigned long d;

  stack = gt_array_new(sizeof (GtStrgraphVnumAndDepth));
  to_add.v = GT_STRGRAPH_V_B(readnum);
  to_add.d = 1UL;
  gt_array_add(stack, to_add);
  to_add.v = GT_STRGRAPH_V_E(readnum);
  to_add.d = 1UL;
  gt_array_add(stack, to_add);
  while (gt_array_size(stack) > 0)
  {
    current = gt_array_pop(stack);
    v = current->v;
    d = current->d;
    for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, v); j++)
    {
      if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, v, j))
      {
        gt_strgraph_dot_show_edge(outfp, v,
            GT_STRGRAPH_EDGE_DEST(strgraph, v, j),
            GT_STRGRAPH_EDGE_LEN(strgraph, v, j));
        if (d < depth)
        {
          to_add.v = GT_STRGRAPH_EDGE_DEST(strgraph, v, j);
          to_add.d = d + 1;
          gt_array_add(stack, to_add);
        }
      }
    }
  }
  gt_array_delete(stack);
}

/* format: read[E|B] [numofedges]: neighbor1[E|B], neighbor2[E|B]... */
static void gt_strgraph_adjlist_show(const GtStrgraph *strgraph, GtFile *outfp)
{
  GtStrgraphVnum i;
  GtStrgraphVEdgenum j;

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    gt_file_xprintf(outfp, "%lu%c "
        "["FormatGtStrgraphVEdgenum"]",
        GT_STRGRAPH_V_READNUM(i),
        GT_STRGRAPH_V_CHAR(i),
        PRINTGtStrgraphVEdgenumcast(GT_STRGRAPH_V_OUTDEG(strgraph, i)));

    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0)
    {
      gt_file_xprintf(outfp, " --> ");
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
        {
          gt_file_xprintf(outfp, "%lu%c ("FormatGtStrgraphLength");",
              GT_STRGRAPH_V_READNUM(GT_STRGRAPH_EDGE_DEST(strgraph, i, j)),
              GT_STRGRAPH_V_CHAR(GT_STRGRAPH_EDGE_DEST(strgraph, i, j)),
              PRINTGtStrgraphVEdgenumcast(
                GT_STRGRAPH_EDGE_LEN(strgraph, i, j)));
        }
      }
    }
    gt_file_xfputc('\n', outfp);
  }
}

static void gt_strgraph_spm_show(const GtStrgraph *strgraph, GtFile *outfp)
{
  unsigned long sn1, sn2;
  GtStrgraphVnum i, v2;
  GtStrgraphLength spm_len;
  GtStrgraphVEdgenum j;
  bool is_e1, is_e2;

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0)
    {
      sn1 = GT_STRGRAPH_V_READNUM(i);
      is_e1 = GT_STRGRAPH_V_IS_E(i);
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
      {
        if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
        {
          v2 = GT_STRGRAPH_EDGE_DEST(strgraph, i, j);
          sn2 = GT_STRGRAPH_V_READNUM(v2);
          spm_len = GT_STRGRAPH_SEQLEN(strgraph, sn2) -
            GT_STRGRAPH_EDGE_LEN(strgraph, i, j);
          is_e2 = GT_STRGRAPH_V_IS_E(v2);
          if ((is_e1 && is_e2) || (is_e1 && !is_e2 && (sn1 <= sn2)) ||
              (!is_e1 &&  is_e2 && (sn1 >= sn2)))
          {
            /* other E->B / B->E cases, as well as all B-B
               are not considered to avoid double output */
            gt_file_xprintf(outfp, "%lu %s %lu %s "FormatGtStrgraphLength"\n",
                sn1, is_e1 ? "+" : "-",
                sn2, is_e2 ? "+" : "-",
                PRINTGtStrgraphLengthcast(spm_len));
          }
        }
      }
    }
  }
}

static void gt_strgraph_asqg_show(const GtStrgraph *strgraph,
    const char *indexname, GtFile *outfp)
{
  unsigned long sn1, sn2;
  GtStrgraphVnum i, v2;
  unsigned long sl2, spm_len;
  GtStrgraphVEdgenum j;
  bool is_e1, is_e2;
  GtError *err;
  int had_err = 0;
  GtAsqgWriter *aw = NULL;

  err = gt_error_new();
  gt_assert(strgraph->encseq != NULL);
  aw = gt_asqg_writer_new(outfp, strgraph->encseq);
  had_err = gt_asqg_writer_show_header(aw, 0.0, (unsigned long)
      strgraph->minmatchlen, indexname, false, false, err);
  if (!had_err)
    had_err = gt_asqg_writer_show_vertices(aw, err);
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph) && !had_err; i++)
  {
    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0)
    {
      sn1 = GT_STRGRAPH_V_READNUM(i);
      is_e1 = GT_STRGRAPH_V_IS_E(i);
      for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i) && !had_err; j++)
      {
        if (!GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
        {
          v2 = GT_STRGRAPH_EDGE_DEST(strgraph, i, j);
          sn2 = GT_STRGRAPH_V_READNUM(v2);
          sl2 = (unsigned long)GT_STRGRAPH_SEQLEN(strgraph, sn2);
          spm_len = sl2 - (unsigned long)GT_STRGRAPH_EDGE_LEN(strgraph, i, j);
          is_e2 = GT_STRGRAPH_V_IS_E(v2);
          if ((is_e1 && is_e2 && (sn1 >= sn2)) ||
              (!is_e1 && !is_e2 && (sn1 > sn2)) ||
              (is_e1 && !is_e2 && (sn1 >= sn2)) ||
              (!is_e1 &&  is_e2 && (sn1 > sn2)))
          {
            /* other E->B / B->E cases, as well as all B-B
               are not considered to avoid double output */
            gt_spmproc_show_asgq(sn1, sn2, spm_len, is_e1, is_e2, aw);
          }
        }
      }
    }
  }
  if (had_err)
  {
    fprintf(stderr, "%s", gt_error_get(err));
    exit(EXIT_FAILURE);
  }
  gt_asqg_writer_delete(aw);
  gt_error_delete(err);
}

void gt_strgraph_show(const GtStrgraph *strgraph, GtStrgraphFormat format,
    const char *indexname, const char *suffix, bool show_progressbar)
{
  GtFile *outfp = NULL;

  gt_assert(strgraph != NULL);
  outfp = gt_strgraph_get_file(indexname, suffix, true,
      format == GT_STRGRAPH_ASQG_GZ ? true : false);
  switch (format)
  {
    case GT_STRGRAPH_DOT:
      gt_strgraph_dot_show(strgraph, outfp, show_progressbar);
      break;
    case GT_STRGRAPH_DOT_BI:
      gt_strgraph_dot_bi_show(strgraph, outfp, show_progressbar);
      break;
    case GT_STRGRAPH_ADJLIST:
      gt_strgraph_adjlist_show(strgraph, outfp);
      break;
    case GT_STRGRAPH_SPM:
      gt_strgraph_spm_show(strgraph, outfp);
      break;
    case GT_STRGRAPH_ASQG_GZ: /*@ fallthrough @*/
    case GT_STRGRAPH_ASQG:
      gt_strgraph_asqg_show(strgraph, indexname, outfp);
      break;
    case GT_STRGRAPH_BIN:
      gt_strgraph_save(strgraph, outfp);
      break;
    default:
      gt_assert(false);
      break;
  }
  gt_file_delete(outfp);
}

static int gt_strgraph_show_disc_distri_datapoint(unsigned long key,
    unsigned long long value, GtFile *outfile)
{
  gt_file_xprintf(outfile, "%lu "Formatuint64_t"\n", key,
     PRINTuint64_tcast((uint64_t)value));
  return 0;
}

void gt_strgraph_show_edge_lengths_distribution(const GtStrgraph *strgraph,
    const char *indexname, const char *suffix)
{
  GtDiscDistri *d = gt_disc_distri_new();
  GtStrgraphVnum i;
  GtStrgraphVEdgenum j;

  GtFile *outfp = gt_strgraph_get_file(indexname, suffix, true, false);

  gt_assert(strgraph != NULL);
  gt_assert(sizeof (unsigned long) >= sizeof (GtStrgraphLength));
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
    {
      gt_disc_distri_add(d,
          (unsigned long)GT_STRGRAPH_EDGE_LEN(strgraph, i, j));
    }
  }
  gt_file_xprintf(outfp, "# length nofedges\n");
  gt_disc_distri_foreach(d,
     (GtDiscDistriIterFunc) gt_strgraph_show_disc_distri_datapoint, outfp);
  gt_disc_distri_delete(d);
  gt_file_delete(outfp);
}

void gt_strgraph_show_counts_distribution(const GtStrgraph *strgraph,
    const char *indexname, const char *suffix)
{
  GtDiscDistri *d = gt_disc_distri_new();
  GtFile *outfp = gt_strgraph_get_file(indexname, suffix, true, false);
  GtStrgraphVnum i;

  gt_assert(strgraph != NULL);
  gt_assert(sizeof (unsigned long) >= sizeof (GtStrgraphCount));
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
    gt_disc_distri_add(d, (unsigned long)GT_STRGRAPH_GET_COUNT(strgraph, i));
  gt_file_xprintf(outfp, "# count nofvertices\n");
  gt_disc_distri_foreach(d,
     (GtDiscDistriIterFunc) gt_strgraph_show_disc_distri_datapoint, outfp);
  gt_disc_distri_delete(d);
  gt_file_delete(outfp);
}

int gt_strgraph_show_context(const GtStrgraph *strgraph,
    GT_UNUSED /* only in assertions */ GtStrgraphFormat format,
    const char *indexname, const char *suffix, unsigned long *readnums,
    unsigned long nofreadnums, unsigned long depth, GtError *err)
{
  GtStrgraphVnum i;
  int had_err = 0;
  GtFile *outfp = NULL;

  gt_assert(strgraph != NULL);
  gt_assert(format == GT_STRGRAPH_DOT);

  outfp = gt_strgraph_get_file(indexname, suffix, true, false);
  gt_file_xprintf(outfp, GT_STRGRAPH_DOT_HEADER);
  gt_assert(sizeof (GtStrgraphVnum) >= sizeof (unsigned long));
  for (i = 0; i < (GtStrgraphVnum)nofreadnums; i++)
  {
    if (i >= GT_STRGRAPH_NOFREADS(strgraph))
    {
      had_err = -1;
      gt_error_set(err, "Can't show context of read "FormatGtStrgraphVnum" "
          "because the readset has "FormatGtStrgraphVnum" reads", i,
          GT_STRGRAPH_NOFREADS(strgraph));
      break;
    }
    gt_strgraph_dot_show_context(strgraph, outfp, readnums[i], depth);
  }
  gt_file_xprintf(outfp, GT_STRGRAPH_DOT_FOOTER);
  gt_file_delete(outfp);
  return had_err;
}

/* log using for large values */
static void gt_strgraph_log_space_value(const char *prefix, size_t value)
{
  char unit_prefix;
  float float_value;
  if (value < (size_t)1024) {
    gt_log_log("%s = %lu bytes", prefix, (unsigned long)value);
  } else {
    if (value < (size_t)1048576) {
      unit_prefix = 'k';
      float_value = (float)value / 1024.F;
    } else if (value < (size_t)1073741824UL) {
      unit_prefix = 'M';
      float_value = (float)value / 1048576.F;
    } else {
      unit_prefix = 'G';
      float_value = (float)value / 1073741824.F;
    }
    gt_log_log("%s = %lu bytes (%.2f %cb)", prefix, (unsigned long)value,
        float_value, unit_prefix);
  }
}

void gt_strgraph_log_space(const GtStrgraph *strgraph)
{
  size_t space_for_edges, space_for_vertices, total_space;
  gt_assert(strgraph != NULL);
  space_for_edges = GT_STRGRAPH_SIZEOF_EDGES(strgraph);
  space_for_vertices = GT_STRGRAPH_SIZEOF_VERTICES(strgraph);
  total_space = sizeof (GtStrgraph) + space_for_edges + space_for_vertices;
  gt_strgraph_log_space_value("space graph", total_space);
  gt_strgraph_log_space_value("- edges", space_for_edges);
  gt_strgraph_log_space_value("- vertices", space_for_vertices);
}

static inline GtStrgraphVnum gt_strgraph_nofvertices_Vnum(
    const GtStrgraph *strgraph)
{
  GtStrgraphVnum i, connected_vertices;

  gt_assert(strgraph != NULL);

  connected_vertices = 0;
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if ((GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0) ||
        (GT_STRGRAPH_V_INDEG(strgraph, i) > 0))
    {
      connected_vertices++;
    }
  }
  return connected_vertices;
}

unsigned long gt_strgraph_nofvertices(const GtStrgraph *strgraph)
{
  GtStrgraphVnum retval;
  retval = gt_strgraph_nofvertices_Vnum(strgraph);
  gt_assert(sizeof (unsigned long) >= sizeof (GtStrgraphVnum) ||
      retval <= (GtStrgraphVnum)ULONG_MAX);
  return (unsigned long)retval;
}

unsigned long gt_strgraph_nofreads(const GtStrgraph *strgraph)
{
  GtStrgraphVnum i;
  unsigned long connected_reads = 0;
  bool already_counted = false;

  gt_assert(strgraph != NULL);
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if (GT_STRGRAPH_V_IS_B(i))
      already_counted = false;
      /* if IS_E, then the read may already have been counted,
         in the case B was connected*/
    if (GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0)
    {
      if (already_counted == false)
      {
        connected_reads++;
        already_counted = true;
      }
    }
  }
  return connected_reads;
}

static inline GtStrgraphEdgenum gt_strgraph_nofedges_Edgenum(
    const GtStrgraph *strgraph)
{
  GtStrgraphVnum i;
  GtStrgraphEdgenum total_degree = 0;
  gt_assert(strgraph != NULL);
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
    total_degree += GT_STRGRAPH_V_OUTDEG(strgraph, i);
  return total_degree;
}

unsigned long gt_strgraph_nofedges(const GtStrgraph *strgraph)
{
  GtStrgraphEdgenum retval;
  retval = gt_strgraph_nofedges_Edgenum(strgraph);
  gt_assert(sizeof (unsigned long) >= sizeof (GtStrgraphEdgenum) ||
      retval <= (GtStrgraphEdgenum)ULONG_MAX);
  return (unsigned long)retval;
}

unsigned long gt_strgraph_nofspm(const GtStrgraph *strgraph)
{
  unsigned long total_degree;
  gt_assert(strgraph != NULL);
  /* nofspm is half of total degree */
  total_degree = gt_strgraph_nofedges(strgraph);
  /*  gt_assert(!(total_degree & 1)); */
  return ((total_degree >> 1));
}

void gt_strgraph_log_stats(const GtStrgraph *strgraph, GtLogger *logger)
{
  GtStrgraphVnum v = 0;
  GtStrgraphEdgenum e = 0;
  float avg_deg;

  gt_assert(strgraph != NULL);

  v = gt_strgraph_nofvertices_Vnum(strgraph);
  e = gt_strgraph_nofedges_Edgenum(strgraph);

  avg_deg = (v == 0UL) ? (float)0 : (float)(e) / (float)(v);

  gt_logger_log(logger, "vertices: "FormatGtStrgraphVnum
      " (reads: "FormatGtStrgraphVnum") -- edges: "FormatGtStrgraphEdgenum" "
      "(spm: "FormatGtStrgraphEdgenum") -- e/v: %.4f", v, v >> 1, e, e >> 1,
      avg_deg);
}

static inline void gt_strgraph_traverse_simple_path(GtStrgraph *strgraph,
    GtStrgraphVnum i, GtStrgraphVEdgenum j, void(*process_edge)
    (GtStrgraphVnum, GtStrgraphLength, void*), void *data)
{
  GtStrgraphVnum from, to;
  GtStrgraphVEdgenum from_to;

  from = i;
  from_to = j;
  to = GT_STRGRAPH_EDGE_DEST(strgraph, i, j);

  while (GT_STRGRAPH_V_IS_INTERNAL(strgraph, to) && i != to &&
      GT_STRGRAPH_V_MARK(strgraph, to) != GT_STRGRAPH_V_ELIMINATED)
  {
    if (process_edge != NULL)
      process_edge(to, GT_STRGRAPH_EDGE_LEN(strgraph, from, from_to), data);
    GT_STRGRAPH_V_SET_MARK(strgraph, to, GT_STRGRAPH_V_ELIMINATED);
    GT_STRGRAPH_V_SET_MARK(strgraph, GT_STRGRAPH_V_OTHER(to),
        GT_STRGRAPH_V_ELIMINATED);
    from = to;
    from_to = gt_strgraph_find_only_edge(strgraph, from);
    to = GT_STRGRAPH_EDGE_DEST(strgraph, from, from_to);
  }
  if (process_edge != NULL)
    process_edge(to, GT_STRGRAPH_EDGE_LEN(strgraph, from, from_to), data);
}

static inline void gt_strgraph_traverse_from_vertex(GtStrgraph *strgraph,
    GtStrgraphVnum i, void(*process_start) (GtStrgraphVnum, void*),
    void(*process_edge) (GtStrgraphVnum, GtStrgraphLength, void*), void *data)
{
  GtStrgraphVEdgenum j;
  gt_assert(GT_STRGRAPH_V_OUTDEG(strgraph, i) > 0);
  for (j = 0; j < GT_STRGRAPH_V_NOFEDGES(strgraph, i); j++)
  {
    if (GT_STRGRAPH_EDGE_IS_REDUCED(strgraph, i, j))
      continue;
    if (GT_STRGRAPH_V_MARK(strgraph, GT_STRGRAPH_EDGE_DEST(strgraph, i, j))
        == GT_STRGRAPH_V_ELIMINATED)
      continue;
    if (process_start != NULL)
      process_start(i, data);
    gt_strgraph_traverse_simple_path(strgraph, i, j, process_edge, data);
  }
}

static void gt_strgraph_traverse(GtStrgraph *strgraph,
    void(*process_start) (GtStrgraphVnum, void*),
    void(*process_edge) (GtStrgraphVnum, GtStrgraphLength, void*),
    void *data, bool show_progressbar)
{
  GtStrgraphVnum i;
  unsigned long long progress = 0;

  gt_assert(strgraph != NULL);

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
    GT_STRGRAPH_V_SET_MARK(strgraph, i, GT_STRGRAPH_V_VACANT);

  if (show_progressbar)
    gt_progressbar_start(&progress,
        (unsigned long long)GT_STRGRAPH_NOFVERTICES(strgraph));

  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if (GT_STRGRAPH_V_MARK(strgraph, i) != GT_STRGRAPH_V_ELIMINATED)
    {
      if (GT_STRGRAPH_V_OUTDEG(strgraph, i) == 0)
      {
        GT_STRGRAPH_V_SET_MARK(strgraph, i, GT_STRGRAPH_V_ELIMINATED);
      }
      else if (!GT_STRGRAPH_V_IS_INTERNAL(strgraph, i))
      {
        gt_strgraph_traverse_from_vertex(strgraph, i, process_start,
            process_edge, data);
        GT_STRGRAPH_V_SET_MARK(strgraph, i, GT_STRGRAPH_V_ELIMINATED);
      }
    }
    if (show_progressbar)
      progress++;
  }

  if (show_progressbar)
    gt_progressbar_stop();

  /* handle circles of internal vertices only */
  for (i = 0; i < GT_STRGRAPH_NOFVERTICES(strgraph); i++)
  {
    if (GT_STRGRAPH_V_IS_INTERNAL(strgraph, i) &&
        GT_STRGRAPH_V_MARK(strgraph, i) != GT_STRGRAPH_V_ELIMINATED)
      gt_strgraph_traverse_from_vertex(strgraph, i, process_start,
          process_edge, data);
  }
}

#define GT_STRGRAPH_CONTIG_INC 16384UL

/* seqnum where to read label for edge/vertex in mirrored encseq */

#define GT_STRGRAPH_V_SEQNUM(NOFV, V) (GT_STRGRAPH_V_IS_E(V) \
    ? GT_STRGRAPH_V_READNUM(V) \
    : ((unsigned long)NOFV - GT_STRGRAPH_V_READNUM(V) - 1))

/* --- Contig Paths Output --- */

/*
 * File format:
 *
 * ELEM1 ELEM2
 *
 * ELEM1: 0   --> start new contig, from seq with seqnum ELEM2
 *        >0  --> read chars (lastchar - ELEM1 + 1)..lastchar
 *                from seq with seqnum ELEM2
 * ELEM2: seqnum in mirrored sequence
 *
 * */

GT_DECLAREARRAYSTRUCT(GtContigpathElem);

typedef struct {
  unsigned long           total_depth, current_depth, contignum,
                          min_depth;
  GtStrgraphVnum          nof_v, lastnode;
  GtFile                  *outfp;
  GtArrayGtContigpathElem contig;
} GtStrgraphContigpathsData;

static void gt_strgraph_show_contigpath_edge(GtStrgraphVnum v,
    GtStrgraphLength len, void *data)
{
  GtStrgraphContigpathsData *pdata = data;
  GtContigpathElem *value;
  unsigned long seqnum;

  (pdata->current_depth)++;

  /* first element: length */
  GT_GETNEXTFREEINARRAY(value, &pdata->contig, GtContigpathElem,
      GT_STRGRAPH_CONTIG_INC);
  gt_assert(sizeof (GtContigpathElem) >= sizeof (GtStrgraphLength) ||
      len <= (GtStrgraphLength)GT_CONTIGPATH_ELEM_MAX);
  *value = (GtContigpathElem)len;

  /* second element: vertex number */
  GT_GETNEXTFREEINARRAY(value, &pdata->contig, GtContigpathElem,
      GT_STRGRAPH_CONTIG_INC);
  seqnum = GT_STRGRAPH_V_SEQNUM(pdata->nof_v, v);
  gt_assert(sizeof (GtContigpathElem) >= sizeof (GtStrgraphVnum) ||
      seqnum <= (unsigned long)GT_CONTIGPATH_ELEM_MAX);
  *value = (GtContigpathElem)seqnum;

  pdata->lastnode = v;
}

static inline void gt_strgraph_show_contigpath(GtStrgraphContigpathsData *pdata)
{
  gt_file_xwrite(pdata->outfp, pdata->contig.spaceGtContigpathElem,
      sizeof (GtContigpathElem) *
      pdata->contig.nextfreeGtContigpathElem);
  pdata->total_depth += pdata->current_depth;
  (pdata->contignum)++;
}

static void gt_strgraph_show_contigpath_vertex(GtStrgraphVnum firstvertex,
    void *data)
{
  GtStrgraphContigpathsData *pdata = data;
  GtContigpathElem *value;
  unsigned long seqnum;

  if (pdata->current_depth >= pdata->min_depth)
    gt_strgraph_show_contigpath(pdata);

  pdata->current_depth = 1UL;

  /* 0 to start a new contig */
  pdata->contig.nextfreeGtContigpathElem = 0;
  GT_GETNEXTFREEINARRAY(value, &pdata->contig, GtContigpathElem,
      GT_STRGRAPH_CONTIG_INC);
  *value = 0;

  /* seqnum of origin vertex */
  GT_GETNEXTFREEINARRAY(value, &pdata->contig, GtContigpathElem,
      GT_STRGRAPH_CONTIG_INC);
  seqnum = GT_STRGRAPH_V_SEQNUM(pdata->nof_v, firstvertex);
  gt_assert(sizeof (GtContigpathElem) >= sizeof (GtStrgraphVnum) ||
      seqnum <= (unsigned long)GT_CONTIGPATH_ELEM_MAX);
  *value = (GtContigpathElem)seqnum;
}

static void gt_strgraph_show_contigpaths(GtStrgraph *strgraph,
    unsigned long min_path_depth, GtFile *outfp, bool show_progressbar)
{
  GtStrgraphContigpathsData pdata;

  pdata.total_depth = 0;
  pdata.current_depth = 0;
  pdata.contignum = 0;

  pdata.lastnode = 0;
  GT_INITARRAY(&pdata.contig, GtContigpathElem);
  pdata.outfp = outfp;
  pdata.min_depth = min_path_depth;
  pdata.nof_v = GT_STRGRAPH_NOFVERTICES(strgraph);

  gt_strgraph_traverse(strgraph, gt_strgraph_show_contigpath_vertex,
      gt_strgraph_show_contigpath_edge, &pdata, show_progressbar);

  /* show last contig path */
  if (pdata.current_depth > pdata.min_depth)
    gt_strgraph_show_contigpath(&pdata);

  gt_log_log("traversed edges = %lu", pdata.total_depth);
  gt_log_log("numofcontigs = %lu", pdata.contignum);

  GT_FREEARRAY(&pdata.contig, GtContigpathElem);
}

/* --- Direct Contig Output --- */

typedef struct {
  unsigned long total_depth, current_depth, min_depth,
                current_length, min_length, contignum;
  GtStrgraph *strgraph;
  GtContigsWriter *cw;
} GtStrgraphSpellData;

static void gt_strgraph_spell_edge(GtStrgraphVnum v, GtStrgraphLength len,
    void *data)
{

  GtStrgraphSpellData *sdata = data;
  gt_contigs_writer_append(sdata->cw, GT_STRGRAPH_V_SEQNUM(
        GT_STRGRAPH_NOFVERTICES(sdata->strgraph), v), (unsigned long)len);
  (sdata->current_depth)++;
  sdata->current_length += len;
}

static void gt_strgraph_spell_vertex(GtStrgraphVnum firstvertex, void *data)
{
  GtStrgraphSpellData *sdata = data;

  if ((sdata->current_depth >= sdata->min_depth) &&
      (sdata->current_length >= sdata->min_length))
  {
    sdata->total_depth += sdata->current_depth;
    gt_contigs_writer_write(sdata->cw);
    (sdata->contignum)++;
  }
  else
    gt_contigs_writer_abort(sdata->cw);

  gt_contigs_writer_start(sdata->cw,
      GT_STRGRAPH_V_SEQNUM(GT_STRGRAPH_NOFVERTICES(sdata->strgraph),
        firstvertex));
  sdata->current_length = (unsigned long)GT_STRGRAPH_SEQLEN(sdata->strgraph,
      firstvertex);
  sdata->current_depth = 1UL;
}

static void gt_strgraph_show_contigs(GtStrgraph *strgraph,
    unsigned long min_path_depth, unsigned long min_contig_length,
    bool showpaths, GtFile *outfp, const GtEncseq *encseq,
    bool show_progressbar, GtLogger *logger)
{
  GtStrgraphSpellData sdata;

  gt_strgraph_set_encseq(strgraph, encseq);
  sdata.cw = gt_contigs_writer_new(encseq, outfp, showpaths);
  sdata.strgraph = strgraph;
  sdata.total_depth = 0;
  sdata.current_depth = 0;
  sdata.current_length = 0;
  sdata.contignum = 0;
  sdata.min_depth = min_path_depth;
  sdata.min_length = min_contig_length;

  gt_strgraph_traverse(strgraph, gt_strgraph_spell_vertex,
      gt_strgraph_spell_edge, &sdata, show_progressbar);

  /* show last contig */
  if (sdata.current_depth >= min_path_depth &&
      sdata.current_length >= min_contig_length)
    gt_contigs_writer_write(sdata.cw);
  else
    gt_contigs_writer_abort(sdata.cw);

  gt_log_log("traversed edges = %lu", sdata.total_depth);
  gt_log_log("numofcontigs = %lu", sdata.contignum);

  if (sdata.contignum > 0)
    gt_contigs_writer_show_stats(sdata.cw, logger);
  else
    gt_logger_log(logger, "no contigs respect the given cutoff parameters");

  gt_contigs_writer_delete(sdata.cw);
}

void gt_strgraph_spell(GtStrgraph *strgraph, unsigned long min_path_depth,
    unsigned long min_contig_length, bool showpaths, const char *indexname,
    const char *suffix, const GtEncseq *encseq, bool delay_reads_mapping,
    bool show_progressbar, GtLogger *logger)
{
  FILE *outfp = NULL;
  GtFile *gt_outfp = NULL;
  GtStr *filename;

  gt_assert(strgraph != NULL);
  filename = gt_str_new_cstr(indexname);
  gt_str_append_cstr(filename, suffix);

  outfp = gt_fa_xfopen(gt_str_get(filename), "w");
  gt_outfp = gt_file_new_from_fileptr(outfp);

  if (!delay_reads_mapping)
    gt_strgraph_show_contigs(strgraph, min_path_depth, min_contig_length,
        showpaths, gt_outfp, encseq, show_progressbar, logger);
  else
    gt_strgraph_show_contigpaths(strgraph, min_path_depth, gt_outfp,
        show_progressbar);

  gt_str_delete(filename);
  gt_file_delete(gt_outfp);
}

/* --- UNIT TESTS --- */

#define GT_STRGRAPH_UTEST(TEST)  \
  if (!had_err)        \
    had_err = gt_strgraph_ ## TEST ## _unit_test(err)

static int gt_strgraph_new_unit_test(GtError *err)
{
  int had_err = 0;
  GtStrgraph *strgraph = NULL;

  gt_error_check(err);

  /* ordinary number of reads */
  strgraph = gt_strgraph_new(100UL);
  gt_ensure(had_err, strgraph != NULL);
  gt_strgraph_delete(strgraph);

  return had_err;
}

static int gt_strgraph_delete_unit_test(GT_UNUSED /* when compiled without
  assertions */ GtError *err)
{
  GtStrgraph *strgraph;

  gt_error_check(err);

  strgraph = NULL;
  gt_strgraph_delete(strgraph);

  strgraph = gt_strgraph_new(100UL);
  gt_strgraph_delete(strgraph);

  return 0;
}

static int gt_strgraph_creation_unit_test(GtError *err)
{
  int had_err = 0;
  GtStrgraph *strgraph;
  unsigned long nofreads = 2UL;

  gt_error_check(err);
  strgraph = gt_strgraph_new(nofreads);
  gt_spmproc_strgraph_count(0, 1UL, 10UL, true, true, strgraph);
  gt_ensure(had_err, GT_STRGRAPH_GET_COUNT(strgraph, GT_STRGRAPH_V_B(0)) == 0);
  gt_ensure(had_err, GT_STRGRAPH_GET_COUNT(strgraph, GT_STRGRAPH_V_E(0)) ==
      (GtStrgraphCount)1);
  gt_ensure(had_err, GT_STRGRAPH_GET_COUNT(strgraph, GT_STRGRAPH_V_B(1)) ==
      (GtStrgraphCount)1);
  gt_ensure(had_err, GT_STRGRAPH_GET_COUNT(strgraph, GT_STRGRAPH_V_E(1)) == 0);
  gt_strgraph_allocate_graph(strgraph, 100UL, NULL);
  gt_ensure(had_err, GT_STRGRAPH_V_NOFEDGES(strgraph, GT_STRGRAPH_V_B(0)) == 0);
  gt_ensure(had_err, GT_STRGRAPH_V_NOFEDGES(strgraph, GT_STRGRAPH_V_E(0)) ==
      (GtStrgraphVEdgenum)1);
  gt_ensure(had_err, GT_STRGRAPH_V_NOFEDGES(strgraph, GT_STRGRAPH_V_B(1)) ==
      (GtStrgraphVEdgenum)1);
  gt_ensure(had_err, GT_STRGRAPH_V_NOFEDGES(strgraph, GT_STRGRAPH_V_E(1)) == 0);
  gt_strgraph_delete(strgraph);
  return had_err;
}

static int gt_strgraph_add_spm_unit_test(GtError *err)
{
  int had_err = 0;
  GtStrgraph *strgraph;
  unsigned long nofreads = 2UL;

  gt_error_check(err);
  strgraph = gt_strgraph_new(nofreads);
  gt_spmproc_strgraph_count(0, 1UL, 10UL, true, true, strgraph);
  gt_strgraph_allocate_graph(strgraph, 22UL, NULL);
  gt_spmproc_strgraph_add(0, 1UL, 10UL, true, true, strgraph);
  gt_ensure(had_err, GT_STRGRAPH_NOFVERTICES(strgraph) == (GtStrgraphVnum)4);
  gt_ensure(had_err, GT_STRGRAPH_V_OUTDEG(strgraph, GT_STRGRAPH_V_B(0)) == 0);
  gt_ensure(had_err, GT_STRGRAPH_V_OUTDEG(strgraph, GT_STRGRAPH_V_E(0)) ==
      (GtStrgraphVEdgenum)1);
  gt_ensure(had_err, GT_STRGRAPH_EDGE_DEST(strgraph, GT_STRGRAPH_V_E(0), 0) ==
      GT_STRGRAPH_V_E(1));
  gt_ensure(had_err, GT_STRGRAPH_EDGE_LEN(strgraph, GT_STRGRAPH_V_E(0), 0) ==
      (GtStrgraphLength)12);
  gt_ensure(had_err, !GT_STRGRAPH_EDGE_IS_REDUCED(strgraph,
      GT_STRGRAPH_V_E(0), 0));
  gt_ensure(had_err, GT_STRGRAPH_V_OUTDEG(strgraph, GT_STRGRAPH_V_B(1)) ==
      (GtStrgraphVEdgenum)1);
  gt_ensure(had_err, GT_STRGRAPH_V_OUTDEG(strgraph, GT_STRGRAPH_V_E(1)) == 0);
  gt_ensure(had_err, GT_STRGRAPH_EDGE_DEST(strgraph, GT_STRGRAPH_V_B(1), 0) ==
      (GtStrgraphVnum)GT_STRGRAPH_V_B(0));
  gt_ensure(had_err, GT_STRGRAPH_EDGE_LEN(strgraph, GT_STRGRAPH_V_B(1), 0) ==
      (GtStrgraphLength)12);
  gt_ensure(had_err, !GT_STRGRAPH_EDGE_IS_REDUCED(strgraph,
      GT_STRGRAPH_V_B(1), 0));
  gt_strgraph_delete(strgraph);
  return had_err;
}

static int gt_strgraph_redtrans_unit_test(GtError *err)
{
  int had_err = 0;
  GtStrgraph *strgraph;
  unsigned long nofreads = 5UL;
  GT_ENSURE_OUTPUT_DECLARE(2000);

  gt_error_check(err);

  /*
  test case:
                          --------2-------------
                   ----------0-----------
             --------RC(1)---------
          ---------3------------
       -------RC(4)----------
  */

  strgraph = gt_strgraph_new(nofreads);
  gt_spmproc_strgraph_count(4UL, 3UL, 19UL, false, true, strgraph);
  gt_spmproc_strgraph_count(1UL, 4UL, 16UL, true, true, strgraph);
  gt_spmproc_strgraph_count(4UL, 0UL, 10UL, false, true, strgraph);
  gt_spmproc_strgraph_count(4UL, 2UL, 3UL, false, true, strgraph);
  gt_spmproc_strgraph_count(3UL, 1UL, 19UL, true, false, strgraph);
  gt_spmproc_strgraph_count(3UL, 0UL, 13UL, true, true, strgraph);
  gt_spmproc_strgraph_count(3UL, 2UL, 6UL, true, true, strgraph);
  gt_spmproc_strgraph_count(1UL, 0UL, 16UL, false, true, strgraph);
  gt_spmproc_strgraph_count(1UL, 2UL, 9UL, false, true, strgraph);
  gt_spmproc_strgraph_count(0UL, 2UL, 15UL, true, true, strgraph);
  gt_strgraph_allocate_graph(strgraph, 22UL, NULL);
  gt_spmproc_strgraph_add(4UL, 3UL, 19UL, false, true, strgraph);
  gt_spmproc_strgraph_add(1UL, 4UL, 16UL, true, true, strgraph);
  gt_spmproc_strgraph_add(4UL, 0UL, 10UL, false, true, strgraph);
  gt_spmproc_strgraph_add(4UL, 2UL, 3UL, false, true, strgraph);
  gt_spmproc_strgraph_add(3UL, 1UL, 19UL, true, false, strgraph);
  gt_spmproc_strgraph_add(3UL, 0UL, 13UL, true, true, strgraph);
  gt_spmproc_strgraph_add(3UL, 2UL, 6UL, true, true, strgraph);
  gt_spmproc_strgraph_add(1UL, 0UL, 16UL, false, true, strgraph);
  gt_spmproc_strgraph_add(1UL, 2UL, 9UL, false, true, strgraph);
  gt_spmproc_strgraph_add(0UL, 2UL, 15UL, true, true, strgraph);
  GT_ENSURE_OUTPUT(gt_strgraph_dot_show(strgraph, outfp, false),
      "digraph StringGraph {\n"
      " \"0B\" -> \"4E\" [label=12];\n"
      " \"0B\" -> \"3B\" [label=9];\n"
      " \"0B\" -> \"1E\" [label=6];\n"
      " \"0E\" -> \"2E\" [label=7];\n"
      " \"1B\" -> \"0E\" [label=6];\n"
      " \"1B\" -> \"2E\" [label=13];\n"
      " \"1E\" -> \"4E\" [label=6];\n"
      " \"1E\" -> \"3B\" [label=3];\n"
      " \"2B\" -> \"4E\" [label=19];\n"
      " \"2B\" -> \"3B\" [label=16];\n"
      " \"2B\" -> \"1E\" [label=13];\n"
      " \"2B\" -> \"0B\" [label=7];\n"
      " \"3B\" -> \"4E\" [label=3];\n"
      " \"3E\" -> \"1B\" [label=3];\n"
      " \"3E\" -> \"0E\" [label=9];\n"
      " \"3E\" -> \"2E\" [label=16];\n"
      " \"4B\" -> \"3E\" [label=3];\n"
      " \"4B\" -> \"1B\" [label=6];\n"
      " \"4B\" -> \"0E\" [label=12];\n"
      " \"4B\" -> \"2E\" [label=19];\n"
      "}\n"
    );
  gt_strgraph_sort_edges_by_len(strgraph, false);
  GT_ENSURE_OUTPUT(gt_strgraph_dot_show(strgraph, outfp, false),
      "digraph StringGraph {\n"
      " \"0B\" -> \"1E\" [label=6];\n"
      " \"0B\" -> \"3B\" [label=9];\n"
      " \"0B\" -> \"4E\" [label=12];\n"
      " \"0E\" -> \"2E\" [label=7];\n"
      " \"1B\" -> \"0E\" [label=6];\n"
      " \"1B\" -> \"2E\" [label=13];\n"
      " \"1E\" -> \"3B\" [label=3];\n"
      " \"1E\" -> \"4E\" [label=6];\n"
      " \"2B\" -> \"0B\" [label=7];\n"
      " \"2B\" -> \"1E\" [label=13];\n"
      " \"2B\" -> \"3B\" [label=16];\n"
      " \"2B\" -> \"4E\" [label=19];\n"
      " \"3B\" -> \"4E\" [label=3];\n"
      " \"3E\" -> \"1B\" [label=3];\n"
      " \"3E\" -> \"0E\" [label=9];\n"
      " \"3E\" -> \"2E\" [label=16];\n"
      " \"4B\" -> \"3E\" [label=3];\n"
      " \"4B\" -> \"1B\" [label=6];\n"
      " \"4B\" -> \"0E\" [label=12];\n"
      " \"4B\" -> \"2E\" [label=19];\n"
      "}\n"
    );
  (void)gt_strgraph_redtrans(strgraph, false);
  GT_ENSURE_OUTPUT(gt_strgraph_dot_show(strgraph, outfp, false),
      "digraph StringGraph {\n"
      " \"0B\" -> \"1E\" [label=6];\n"
      " \"0E\" -> \"2E\" [label=7];\n"
      " \"1B\" -> \"0E\" [label=6];\n"
      " \"1E\" -> \"3B\" [label=3];\n"
      " \"2B\" -> \"0B\" [label=7];\n"
      " \"3B\" -> \"4E\" [label=3];\n"
      " \"3E\" -> \"1B\" [label=3];\n"
      " \"4B\" -> \"3E\" [label=3];\n"
      "}\n"
    );

  gt_strgraph_delete(strgraph);
  return had_err;
}

int gt_strgraph_unit_test(GtError *err)
{
  int had_err = 0;

  gt_error_check(err);
  GT_STRGRAPH_UTEST(new);
  GT_STRGRAPH_UTEST(delete);
  GT_STRGRAPH_UTEST(creation);
  GT_STRGRAPH_UTEST(add_spm);
  GT_STRGRAPH_UTEST(redtrans);
  return had_err;
}
genometools-1.5.1/src/match/rdj-strgraph.h000066400000000000000000000135571211610345200205220ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_STRGRAPH_H
#define RDJ_STRGRAPH_H

#include 
#include "core/encseq_api.h"
#include "core/logger_api.h"
#include "core/error_api.h"

typedef struct GtStrgraph GtStrgraph;

/* --- preparation --- */

GtStrgraph* gt_strgraph_new(unsigned long nofreads);

void gt_spmproc_strgraph_count(unsigned long suffix_readnum,
    unsigned long prefix_readnum, unsigned long length, bool suffixseq_direct,
    bool prefixseq_direct, void *strgraph);

int gt_strgraph_save_counts(GtStrgraph *strgraph, const char *indexname,
    const char *suffix, GtError *err);

int gt_strgraph_load_counts(GtStrgraph *strgraph, const char *indexname,
    const char *suffix, GtError *err);

/* to reduce the memory requirement, the encseq may be freed during the life of
 * strgraph and later reloaded; this method allows one to communicate the
 * changes to the strgraph object (set to NULL by deletion) */
void gt_strgraph_set_encseq(GtStrgraph *strgraph, const GtEncseq *encseq);

/* --- spmlist file --- */

int gt_strgraph_open_spmlist_file(GtStrgraph *strgraph, const char *indexname,
    const char *suffix, bool binary, unsigned long bufsize, GtError *err);

void gt_strgraph_close_spmlist_file(GtStrgraph *strgraph);

void gt_spmproc_strgraph_count_and_save(unsigned long suffix_readnum,
    unsigned long prefix_readnum, unsigned long length,
    bool suffixseq_direct, bool prefixseq_direct, void *strgraph);

int gt_strgraph_load_spm_from_file(GtStrgraph *strgraph,
    unsigned long min_length, bool load_self_spm, GtBitsequence *contained,
    const char *indexname, unsigned int nspmfiles, const char *suffix,
    GtError *err);

/* --- construction --- */

void gt_strgraph_allocate_graph(GtStrgraph *strgraph, unsigned long fixlen,
    const GtEncseq *encseq);

void gt_spmproc_strgraph_add(unsigned long suffix_readnum,
    unsigned long prefix_readnum, unsigned long length,
    bool suffixseq_direct, bool prefixseq_direct, void *graph);

/* --- log information --- */

void gt_strgraph_show_limits(void);
void gt_strgraph_show_limits_debug_log(void);
void gt_strgraph_log_space(const GtStrgraph *strgraph);
void gt_strgraph_log_stats(const GtStrgraph *strgraph, GtLogger *logger);

unsigned long gt_strgraph_nofreads(const GtStrgraph *strgraph);
unsigned long gt_strgraph_nofspm(const GtStrgraph *strgraph);

void gt_strgraph_show_edge_lengths_distribution(const GtStrgraph *strgraph,
    const char *indexname, const char *suffix);
void gt_strgraph_show_counts_distribution(const GtStrgraph *strgraph,
    const char *indexname, const char *suffix);

/* --- save to file --- */

typedef enum {
  GT_STRGRAPH_DOT,     /* Graphviz, e.g.: dot -Tpdf -o graph.pdf graph.dot */
  GT_STRGRAPH_DOT_BI,  /* as _DOT, but bidirected */
  GT_STRGRAPH_SPM,     /* reoutput spm from graph */
  GT_STRGRAPH_ADJLIST, /* adjacence list of each vertex */
  GT_STRGRAPH_BIN,     /* binary format, for gt_strgraph_new_from_file */
  GT_STRGRAPH_ASQG,    /* sga format, plain text */
  GT_STRGRAPH_ASQG_GZ, /* sga format, gzipped */
} GtStrgraphFormat;

void gt_strgraph_show(const GtStrgraph *strgraph, GtStrgraphFormat format,
    const char *indexname, const char *suffix, bool show_progressbar);

int gt_strgraph_show_context(const GtStrgraph *strgraph,
    GtStrgraphFormat format, const char *indexname, const char *suffix,
    unsigned long *readnums, unsigned long nofreadnums, unsigned long depth,
    GtError *err);

/* --- load from file --- */

GtStrgraph* gt_strgraph_new_from_file(const GtEncseq *encseq,
    unsigned long fixlen, const char *indexname, const char *suffix);

/* --- simplify --- */

void gt_strgraph_sort_edges_by_len(GtStrgraph *strgraph, bool show_progressbar);

/* return value: number of transitive matches */
unsigned long gt_strgraph_redtrans(GtStrgraph *strgraph, bool show_progressbar);

/* return value: number of submaximal matches */
unsigned long gt_strgraph_redsubmax(GtStrgraph *strgraph,
    bool show_progressbar);

/* return value: number of self-match matches */
unsigned long gt_strgraph_redself(GtStrgraph *strgraph, bool show_progressbar);

/* return value: number of matches vs. rc edges */
unsigned long gt_strgraph_redwithrc(GtStrgraph *strgraph,
    bool show_progressbar);

/* return value: number of reduced edges */
unsigned long gt_strgraph_reddepaths(GtStrgraph *strgraph,
    unsigned long maxdepth, bool show_progressbar);

/* return value: number of reduced edges */
unsigned long gt_strgraph_redpbubbles(GtStrgraph *strgraph,
    unsigned long maxwidth, unsigned long maxdiff, bool show_progressbar);

/* remove marked edges and realloc edges list */
void gt_strgraph_compact(GtStrgraph *strgraph, bool show_progressbar);

/* --- spell contigs --- */

void gt_strgraph_spell(GtStrgraph *strgraph, unsigned long min_path_depth,
    unsigned long min_contig_length, bool showpaths, const char *indexname,
    const char *suffix, const GtEncseq *encseq, bool delay_reads_mapping,
    bool show_progressbar, GtLogger *logger);

/* --- delete --- */

void gt_strgraph_delete(GtStrgraph *strgraph);

/* --- unit test --- */

int gt_strgraph_unit_test(GtError *err);

#endif
genometools-1.5.1/src/match/rdj-twobitenc-editor.c000066400000000000000000000067221211610345200221410ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/fa.h"
#include "core/ma.h"
#include "match/rdj-twobitenc-editor.h"

struct GtTwobitencEditor
{
  GtTwobitencoding *twobitencoding;
  unsigned long *charcount;
  unsigned char *mapptr;
};

static int gt_twobitenc_editor_check(const GtEncseq *encseq, GtError *err)
{
  int had_err = 0;
  if (!gt_encseq_has_twobitencoding(encseq))
  {
    gt_error_set(err, "encseq correction is only "
        "possible if the sequence has a twobitencoding");
    had_err = -1;
  }
  else if (gt_encseq_accesstype_get(encseq) != GT_ACCESS_TYPE_EQUALLENGTH)
  {
    gt_error_set(err, "twobitencoding correction is currently only "
        "implemented if the sequence access type is EQUALLENGTH");
    had_err = -1;
  }
  return had_err;
}

GtTwobitencEditor *gt_twobitenc_editor_new(const GtEncseq *encseq,
    const char* indexname, GtError *err)
{
  GtTwobitencEditor *twobitenc_editor;
  size_t t_offset;
  size_t c_offset;
  GtStr *encseqfilename;
  int had_err = 0;

  twobitenc_editor = gt_malloc(sizeof (GtTwobitencEditor));
  had_err = gt_twobitenc_editor_check(encseq, err);
  if (had_err == 0)
  {
    t_offset = gt_encseq_twobitencoding_mapoffset(encseq);
    c_offset = gt_encseq_chardistri_mapoffset(encseq);
    encseqfilename = gt_str_new_cstr(indexname);
    gt_str_append_cstr(encseqfilename, GT_ENCSEQFILESUFFIX);
    twobitenc_editor->mapptr = (unsigned char*)gt_fa_mmap_write(gt_str_get(
          encseqfilename), NULL, err);
    twobitenc_editor->twobitencoding = (GtTwobitencoding*)
      (twobitenc_editor->mapptr + t_offset);
    twobitenc_editor->charcount = (unsigned long*)
      (twobitenc_editor->mapptr + c_offset);
    gt_str_delete(encseqfilename);
  }
  return (had_err == 0) ? twobitenc_editor : NULL;
}

void gt_twobitenc_editor_edit(GtTwobitencEditor *twobitenc_editor,
    unsigned long pos, GtUchar newchar)
{
  size_t codenum, posincode;
  GtTwobitencoding oldcode, newcode;
  GtUchar oldchar;

  gt_assert(twobitenc_editor);
  codenum = (size_t)pos / GT_UNITSIN2BITENC;
  oldcode = twobitenc_editor->twobitencoding[codenum];
  posincode = (GT_UNITSIN2BITENC - 1 -
      ((size_t)pos % GT_UNITSIN2BITENC)) << 1;
  oldchar = (oldcode & ((GtTwobitencoding)3 << posincode)) >> posincode;
  newcode = (oldcode & (~((GtTwobitencoding)3 << posincode)));
  newcode |= ((GtTwobitencoding)newchar << posincode);
  twobitenc_editor->twobitencoding[codenum] = newcode;

  /* fix counts */
  twobitenc_editor->charcount[oldchar]--;
  twobitenc_editor->charcount[newchar]++;
}

void gt_twobitenc_editor_delete(GtTwobitencEditor *twobitenc_editor)
{
  gt_assert(twobitenc_editor);
  gt_fa_xmunmap(twobitenc_editor->mapptr);
  gt_free(twobitenc_editor);
}
genometools-1.5.1/src/match/rdj-twobitenc-editor.h000066400000000000000000000024571211610345200221470ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_TWOBITENC_EDITOR_H
#define RDJ_TWOBITENC_EDITOR_H

#include "core/encseq.h"
#include "core/error_api.h"

typedef struct GtTwobitencEditor GtTwobitencEditor;

GtTwobitencEditor *gt_twobitenc_editor_new(const GtEncseq *encseq,
    const char* indexname, GtError *err);

void gt_twobitenc_editor_edit(GtTwobitencEditor *twobitenc_editor,
    unsigned long pos, GtUchar newchar);

void gt_twobitenc_editor_delete(GtTwobitencEditor *twobitenc_editor);

#endif
genometools-1.5.1/src/match/rdj-version.c000066400000000000000000000031771211610345200203450ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/versionfunc.h"
#include "match/rdj-version.h"

void gt_readjoiner_show_version(const char *progname)
{
  char *clean_progname = NULL;
  size_t pnsize = strlen(progname), rdjsize = strlen(" "GT_READJOINER_CMD);
  printf("Readjoiner: a string graph-based sequence assembler\n\n");
  printf("version "GT_READJOINER_VERSION"\n\n");

  /* rm " readjoiner" from progname if possible, to avoid confusing the user */
  clean_progname = gt_malloc(pnsize);
  (void)strcpy(clean_progname, progname);
  if (pnsize > rdjsize && strcmp(clean_progname + (pnsize - rdjsize),
        " "GT_READJOINER_CMD) == 0)
  {
    clean_progname[pnsize - rdjsize] = '\0';
  }
  printf("GenomeTools version:\n");
  gt_versionfunc(clean_progname);
  gt_free(clean_progname);
}
genometools-1.5.1/src/match/rdj-version.h000066400000000000000000000020301211610345200203350ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef RDJ_VERSION_H
#define RDJ_VERSION_H

#define GT_READJOINER_VERSION "1.2"
#define GT_READJOINER_CMD     "readjoiner"

void gt_readjoiner_show_version(const char *progname);

#endif
genometools-1.5.1/src/match/reads2twobit.c000066400000000000000000001636201211610345200205140ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#endif
#include 
#include 
#include "core/array.h"
#include "core/basename_api.h"
#include "core/encseq.h"
#include "core/fa.h"
#include "core/fileutils.h"
#include "core/filelengthvalues.h"
#include "core/intbits.h"
#include "core/log_api.h"
#include "core/minmax.h"
#include "core/parseutils_api.h"
#include "core/qsort_r_api.h"
#include "core/splitter_api.h"
#include "core/xansi_api.h"
#include "core/undef_api.h"
#include "match/reads_library.h"
#include "match/reads2twobit.h"

#define GT_READS2TWOBIT_ALPHASIZE 4U

typedef struct {
  bool paired;
  GtStr *filename1;
  GtStr *filename2;
  unsigned long insertlength;
  unsigned long stdev; /* 0 if unknown */
  unsigned long total_filelength;
  unsigned long total_seqlength;
  unsigned long first_seqnum;
  unsigned long nofseqs;
} GtReadsLibraryInfo;

struct GtReads2Twobit
{
  GtStr *indexname;
  GtArray *collection;
  GtTwobitencoding *twobitencoding;
  unsigned long chardistri[GT_READS2TWOBIT_ALPHASIZE];
  unsigned long *seppos;
  unsigned long nofseqs;
  unsigned long seqlen_eqlen, seqlen_max, seqlen_min;
  unsigned long total_seqlength;
  GtTwobitencoding current_sepcode;
  unsigned long invalid_sequences, invalid_total_length;
  char phredbase, lowqual;
  unsigned long maxlow;
};

GtReads2Twobit* gt_reads2twobit_new(GtStr *indexname)
{
  GtReads2Twobit *r2t;
  gt_assert(indexname != NULL);
  r2t = gt_malloc(sizeof (*r2t));
  r2t->indexname = indexname;
  r2t->collection = gt_array_new(sizeof (GtReadsLibraryInfo));
  r2t->twobitencoding = NULL;
  r2t->seppos = NULL;
  r2t->invalid_sequences = 0;
  r2t->invalid_total_length = 0;
  r2t->seqlen_eqlen = 0;
  r2t->seqlen_max = 0;
  r2t->seqlen_min = 0;
  r2t->total_seqlength = 0;
  r2t->nofseqs = 0;
  r2t->phredbase = (char)33;
  r2t->maxlow = GT_UNDEF_ULONG;
  r2t->lowqual = 0;
  return r2t;
}

void gt_reads2twobit_delete(GtReads2Twobit *r2t)
{
  if (r2t != NULL)
  {
    unsigned long lnum, noflibs;
    noflibs = gt_array_size(r2t->collection);
    for (lnum = 0; lnum < noflibs; lnum++)
    {
      GtReadsLibraryInfo *rli;
      rli = gt_array_get(r2t->collection, lnum);
      gt_str_delete(rli->filename1);
      if (rli->filename2 != NULL)
        gt_str_delete(rli->filename2);
    }
    gt_array_delete(r2t->collection);
    gt_free(r2t->twobitencoding);
    gt_free(r2t->seppos);
    gt_free(r2t);
  }
}

void gt_reads2twobit_add(GtReads2Twobit *r2t, bool paired,
    const GtStr *filename1, const GtStr *filename2, unsigned long insertlength,
    unsigned long stdev)
{
  GtReadsLibraryInfo rli;
  gt_assert(r2t != NULL);
  gt_assert(filename1 != NULL);
  rli.paired = paired;
  rli.filename1 = gt_str_clone(filename1);
  if (filename2 != NULL)
    rli.filename2 = gt_str_clone(filename2);
  else
    rli.filename2 = NULL;
  rli.insertlength = insertlength;
  rli.stdev = stdev;
  rli.total_seqlength = 0;
  rli.first_seqnum = 0;
  rli.nofseqs = 0;
  rli.total_filelength = (unsigned long)gt_file_size(gt_str_get(filename1));
  if (filename2 != NULL)
    rli.total_filelength += (unsigned long)gt_file_size(gt_str_get(filename2));
  gt_array_add(r2t->collection, rli);
}

int gt_reads2twobit_add_library(GtReads2Twobit *r2t, const GtStr *libspec,
    GtError *err)
{
  GtSplitter *s1, *s2;
  char *libspec_copy;
  int had_err = 0;

  gt_assert(r2t != NULL);
  gt_assert(libspec != NULL);
  gt_assert(gt_str_length(libspec) > 0);
  libspec_copy = gt_malloc(sizeof (*libspec_copy) *
      (gt_str_length(libspec) + 1UL));
  (void)strcpy(libspec_copy, gt_str_get(libspec));
  s1 = gt_splitter_new();
  gt_splitter_split(s1, libspec_copy, gt_str_length(libspec),
      GT_READS2TWOBIT_LIBSPECSEP);
  gt_log_log("reads2twobit add library: %s", gt_str_get(libspec));
  if (gt_splitter_size(s1) == 1UL)
  {
    gt_reads2twobit_add(r2t, false, libspec, NULL, 0, 0);
  }
  else if (gt_splitter_size(s1) < 4UL)
  {
    GtStr *filename1, *filename2;
    unsigned long insertlength = 0, stdev = 0;
    char *insertspec, *insertspec_copy;
    filename1 = gt_str_new_cstr(gt_splitter_get_token(s1, 0));
    if (gt_splitter_size(s1) == 3UL)
    {
      filename2 = gt_str_new_cstr(gt_splitter_get_token(s1, 1UL));
      insertspec = gt_splitter_get_token(s1, 2UL);
    }
    else
    {
      filename2 = NULL;
      insertspec = gt_splitter_get_token(s1, 1UL);
    }
    s2 = gt_splitter_new();
    insertspec_copy = gt_malloc(sizeof (*insertspec_copy) *
        (strlen(insertspec) + 1UL));
    (void)strcpy(insertspec_copy, insertspec);
    gt_splitter_split(s2, insertspec_copy, (unsigned long)strlen(insertspec),
      GT_READS2TWOBIT_INSERTSEP);
    if (gt_splitter_size(s2) <= 2UL)
    {
      had_err = gt_parse_ulong(&insertlength, gt_splitter_get_token(s2, 0));
      if (gt_splitter_size(s2) == 2UL && !had_err)
      {
        had_err = gt_parse_ulong(&stdev, gt_splitter_get_token(s2, 1UL));
      }
    }
    if (gt_splitter_size(s2) > 2UL || had_err)
    {
      gt_error_set(err, "insert specification not valid: %s\nthe correct "
          "syntax is \"insertlength[%cstdev]\"", insertspec,
          GT_READS2TWOBIT_INSERTSEP);
    }
    if (!had_err)
    {
      gt_reads2twobit_add(r2t, true, filename1, filename2, insertlength, stdev);
    }
    gt_str_delete(filename1);
    gt_str_delete(filename2);
    gt_free(insertspec_copy);
    gt_splitter_delete(s2);
  }
  else
  {
    gt_error_set(err, "library specification not valid: %s\nthe correct "
        "syntax is \"filename[[%cfilename2]%cinsertlength[%cstdev]]\"\n"
        "(filenames are not allowed to contain \"%c\"",
        gt_str_get(libspec),
      GT_READS2TWOBIT_LIBSPECSEP, GT_READS2TWOBIT_LIBSPECSEP,
      GT_READS2TWOBIT_INSERTSEP, GT_READS2TWOBIT_LIBSPECSEP);
    had_err = -1;
  }
  gt_free(libspec_copy);
  gt_splitter_delete(s1);
  return had_err;
}

void gt_reads2twobit_use_phred64(GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  r2t->phredbase = (char)64;
}

void gt_reads2twobit_set_quality_filter(GtReads2Twobit *r2t,
    unsigned long maxlow, char lowqual)
{
  r2t->maxlow = maxlow;
  r2t->lowqual = lowqual;
}

#define GT_READS2TWOBIT_CODE_UNDEF ((GtTwobitencoding)ULONG_MAX)

typedef struct {
  GtTwobitencoding *tbe_next;
  GtTwobitencoding kmercode;
  unsigned short codepos;
  unsigned long chardistri[GT_READS2TWOBIT_ALPHASIZE];
  unsigned long globalpos;
  unsigned long nofseqs;
  unsigned long seppos_nextfree;
  unsigned long seqlen_max;
  unsigned long seqlen_min;
} GtReads2TwobitEncodeInfo;

#define GT_READS2TWOBIT_INIT_ENCODE_INFO(EI, TBE)\
  memset(&(EI), 0, sizeof (EI));\
  (EI).tbe_next = (TBE)

#define GT_READS2TWOBIT_COPY_ENCODE_INFO(EISRC, EIDEST)\
  memcpy(&(EIDEST), &(EISRC), sizeof (EISRC))

typedef struct {
  GtTwobitencoding char2code[UCHAR_MAX + 1];
  unsigned long inputfiles_totallength;
  unsigned long seqlen, seqlen_first, seqlen_mate;
  GtReads2TwobitEncodeInfo current, backup;
  bool varlen_mode, invalid_mode;
  unsigned long invalid_sequences, invalid_total_length;
  unsigned long *seppos;
  unsigned long seppos_alloc;
  char phredbase, *qbuf, *qbuf2, lowqual;
  size_t qbuf_size, qbuf2_size;
  unsigned long maxlow;
} GtReads2TwobitEncodeState;

static void gt_reads2twobit_init_encode(GtReads2Twobit *r2t,
    GtReads2TwobitEncodeState *state)
{
  const unsigned long noflibraries = gt_array_size(r2t->collection);
  unsigned long i;
  state->inputfiles_totallength = 0;
  for (i = 0; i < noflibraries; i++)
  {
    const GtReadsLibraryInfo *rli = gt_array_get(r2t->collection, i);
    state->inputfiles_totallength += rli->total_filelength;
  }
  r2t->twobitencoding = gt_malloc(sizeof (*r2t->twobitencoding) *
    GT_DIVBYUNITSIN2BITENC(state->inputfiles_totallength) + 2UL);
  GT_READS2TWOBIT_INIT_ENCODE_INFO(state->current, r2t->twobitencoding);
  GT_READS2TWOBIT_COPY_ENCODE_INFO(state->current, state->backup);
  for (i = 0; i < (unsigned long)(UCHAR_MAX) + 1UL; i++)
    state->char2code[i] = GT_READS2TWOBIT_CODE_UNDEF;
  state->char2code[(unsigned char)'A'] = (GtTwobitencoding)0;
  state->char2code[(unsigned char)'a'] = (GtTwobitencoding)0;
  state->char2code[(unsigned char)'C'] = (GtTwobitencoding)1;
  state->char2code[(unsigned char)'c'] = (GtTwobitencoding)1;
  state->char2code[(unsigned char)'G'] = (GtTwobitencoding)2;
  state->char2code[(unsigned char)'g'] = (GtTwobitencoding)2;
  state->char2code[(unsigned char)'T'] = (GtTwobitencoding)3;
  state->char2code[(unsigned char)'t'] = (GtTwobitencoding)3;
  state->seqlen = 0;
  state->seqlen_mate = 0;
  state->seqlen_first = 0;
  state->varlen_mode = false;
  state->invalid_mode = false;
  state->invalid_sequences = 0;
  state->invalid_total_length = 0;
  gt_assert(r2t->seppos == NULL);
  state->seppos = NULL;
  state->qbuf = NULL;
  state->qbuf_size = 0;
  state->qbuf2 = NULL;
  state->qbuf2_size = 0;
  state->phredbase = r2t->phredbase;
  state->lowqual = r2t->lowqual;
  state->maxlow = r2t->maxlow;
}

#define GT_READS2TWOBIT_READBUFFER_SIZE ((size_t)256)

#define GT_READS2TWOBIT_WRITECODE_NOCOUNT(EI, CODE, LEN) \
  (LEN)++;\
  (EI).kmercode = ((EI).kmercode << 2) | (CODE);\
  if (++(EI).codepos == (unsigned short)GT_UNITSIN2BITENC)\
  {\
    *((EI).tbe_next)++ = (EI).kmercode;\
    (EI).codepos = 0;\
    (EI).kmercode = 0;\
  }

#define GT_READS2TWOBIT_WRITECODE(EI, CODE, LEN)\
  GT_READS2TWOBIT_WRITECODE_NOCOUNT(EI, CODE, LEN);\
  (EI).chardistri[CODE]++

static void gt_reads2twobit_init_seppos(GtReads2TwobitEncodeState *state,
    unsigned long currentpos)
{
  gt_assert(state->seppos == NULL);
  gt_assert(currentpos > 0);
  gt_assert(state->inputfiles_totallength > currentpos);
  state->seppos_alloc = state->inputfiles_totallength / currentpos;
  gt_log_log("rough estimate of nofseqs = %lu", state->seppos_alloc);
  state->seppos = gt_malloc(sizeof (state->seppos) * state->seppos_alloc);
  state->current.seppos_nextfree = 0;
}

#define GT_READS2TWOBIT_SEPPOS_INC ((size_t)(1 << 14))

static void gt_reads2twobit_append_seppos(GtReads2TwobitEncodeState *state)
{
  gt_assert(state->seppos != NULL);
  if (state->current.seppos_nextfree == state->seppos_alloc)
  {
    (state->seppos_alloc) += GT_READS2TWOBIT_SEPPOS_INC;
    state->seppos = gt_realloc(state->seppos,
        sizeof (state->seppos) * state->seppos_alloc);
  }
  gt_assert(state->current.globalpos > 0);
  state->seppos[state->current.seppos_nextfree] =
    state->current.globalpos - 1UL;
  state->current.seppos_nextfree++;
}

static void gt_reads2twobit_switch_to_varlen_mode(
    GtReads2TwobitEncodeState *state)
{
  unsigned long seqnum;
  gt_assert(state->varlen_mode == false);
  state->varlen_mode = true;
  gt_assert(state->current.nofseqs > 1UL);
  gt_assert(state->seqlen_first != state->seqlen);
  gt_assert(state->seqlen > 1UL);
  gt_log_log("readset is varlen: sequences 0..%lu are "
      "%lu bp long, sequence %lu is %lu bp long",
      state->current.nofseqs - 2UL, state->seqlen_first - 1UL,
      state->current.nofseqs - 1UL, state->seqlen - 1UL);
  gt_assert(state->current.globalpos == 0);
  gt_reads2twobit_init_seppos(state,
      state->seqlen_first * (state->current.nofseqs - 2UL) +
      state->seqlen);
  for (seqnum = 0; seqnum < state->current.nofseqs - 1UL; seqnum++)
  {
    state->current.globalpos += state->seqlen_first;
    gt_reads2twobit_append_seppos(state);
  }
  state->current.globalpos += state->seqlen;
  gt_reads2twobit_append_seppos(state);
  gt_assert(state->current.seppos_nextfree == state->current.nofseqs);
  state->current.seqlen_max = MAX(state->seqlen_first, state->seqlen);
  state->current.seqlen_min = MIN(state->seqlen_first, state->seqlen);
  state->seqlen_first = 0;
}

#define GT_READS2TWOBIT_DEFAULT_SEPARATOR (GtTwobitencoding)3

static inline void gt_reads2twobit_process_sequence_end(
    GtReads2TwobitEncodeState *state)
{
  GT_READS2TWOBIT_WRITECODE_NOCOUNT(state->current,
      GT_READS2TWOBIT_DEFAULT_SEPARATOR, state->seqlen);
  gt_assert(!state->invalid_mode);
  if (state->varlen_mode)
  {
    if (state->seqlen > state->current.seqlen_max)
      state->current.seqlen_max = state->seqlen;
    if (state->seqlen < state->current.seqlen_min)
      state->current.seqlen_min = state->seqlen;
    state->current.globalpos += state->seqlen;
    gt_reads2twobit_append_seppos(state);
  }
  else
  {
    if (state->current.nofseqs > 1UL)
    {
      if (state->seqlen != state->seqlen_first)
        gt_reads2twobit_switch_to_varlen_mode(state);
    }
    else
      state->seqlen_first = state->seqlen;
  }
}

static inline void gt_reads2twobit_prepare_for_new_sequence(
    GtReads2TwobitEncodeState *state)
{
  GT_READS2TWOBIT_COPY_ENCODE_INFO(state->current, state->backup);
  state->current.nofseqs++;
  state->seqlen = 0;
  state->seqlen_mate = 0;
  state->invalid_mode = false;
}

#define GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(LINE, FILEPTR, FGETSRETVAL)\
  /* handle the case in which a description is longer than the line buffer: */\
  while (strlen(LINE) == GT_READS2TWOBIT_READBUFFER_SIZE - (size_t) 1 \
      && (LINE)[GT_READS2TWOBIT_READBUFFER_SIZE - 2] != '\n' \
      && (FGETSRETVAL) != NULL) \
  {\
    (FGETSRETVAL) = \
      fgets((LINE), (int)GT_READS2TWOBIT_READBUFFER_SIZE, (FILEPTR));\
  }

static void gt_reads2twobit_switch_to_invalid_mode(
    GtReads2TwobitEncodeState *state)
{
  state->invalid_mode = true;
  state->invalid_sequences++;
  state->invalid_total_length += state->seqlen;
  state->invalid_total_length += state->seqlen_mate;
  GT_READS2TWOBIT_COPY_ENCODE_INFO(state->backup, state->current);
}

static inline int gt_reads2twobit_process_qualities_line(
    GtReads2TwobitEncodeState *state, const char *line,
    char *qbuf, unsigned long *qbuf_next)
{
  unsigned long j = 0;
  char c;
  while ((c = line[j++]) != '\0')
  {
    if (c >= state->phredbase)
    {
      if (*qbuf_next == state->seqlen)
        return -1;
      qbuf[*qbuf_next] = c - state->phredbase;
      (*qbuf_next)++;
    }
  }
  return 0;
}

static void gt_reads2twobit_apply_quality_filter(
    GtReads2TwobitEncodeState *state, const char *qbuf, unsigned long nofq)
{
  unsigned long i, low = 0;
  for (i = 0; i < nofq; i++)
    if (qbuf[i] <= state->lowqual)
      low++;
  if (low > state->maxlow)
    gt_reads2twobit_switch_to_invalid_mode(state);
}

static inline void gt_reads2twobit_process_sequence_line(
    GtReads2TwobitEncodeState *state, const char *line)
{
  unsigned long j = 0;
  GtTwobitencoding nextcode;
  char c;
  while (true)
  {
    c = line[j++];
    if (!state->invalid_mode && (nextcode = state->char2code[(unsigned char)c])
        != GT_READS2TWOBIT_CODE_UNDEF)
    {
      GT_READS2TWOBIT_WRITECODE(state->current, nextcode, state->seqlen);
    }
    else
    {
      if (c == '\0')
        break;
      if (!isspace(c))
      {
        if (!state->invalid_mode)
          gt_reads2twobit_switch_to_invalid_mode(state);
        state->invalid_total_length++;
        state->seqlen++;
      }
    }
  }
}

static int gt_reads2twobit_close_file(FILE *file, GtStr *filename, GtError *err)
{
  int had_err = 0;
  gt_assert(file != NULL);
  if (ferror(file) != 0)
  {
    gt_error_set(err, "Error by reading file %s: %s", gt_str_get(filename),
        strerror(errno));
    had_err = -1;
  }
  gt_fa_fclose(file);
  return had_err;
}

static int gt_reads2twobit_encode_unpaired_fastq_library(
    GtReads2TwobitEncodeState *state, GtReadsLibraryInfo *rli, FILE *file,
    char *line)
{
  int had_err = 0;
  unsigned long qbuf_next = 0;
  bool qmode = false;
  char *fgetsretval = NULL;
  state->seqlen = 0;
  do {
    if (!qmode)
    {
      if (line[0] == '@')
      {
        if (state->current.nofseqs > rli->first_seqnum && !state->invalid_mode)
        {
          gt_reads2twobit_process_sequence_end(state);
        }
        GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line, file, fgetsretval);
        gt_reads2twobit_prepare_for_new_sequence(state);
      }
      else if (line[0] == '+')
      {
        GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line, file, fgetsretval);
        if (state->seqlen + 1UL > (unsigned long)(state->qbuf_size))
        {
          state->qbuf_size = (size_t)state->seqlen + 1;
          state->qbuf = gt_realloc(state->qbuf, state->qbuf_size);
        }
        qmode = true;
      }
      else if (!state->invalid_mode)
      {
        gt_reads2twobit_process_sequence_line(state, line);
      }
    }
    else
    {
      had_err = gt_reads2twobit_process_qualities_line(state, line,
          state->qbuf, &qbuf_next);
      if (qbuf_next == state->seqlen)
      {
        if (state->maxlow != GT_UNDEF_ULONG)
          gt_reads2twobit_apply_quality_filter(state, state->qbuf, qbuf_next);
        qbuf_next = 0;
        qmode = false;
      }
    }
  } while ((fgetsretval = fgets(line, (int)GT_READS2TWOBIT_READBUFFER_SIZE,
            file)) == line && !had_err);
  return had_err;
}

static void gt_reads2twobit_encode_unpaired_fasta_library(
    GtReads2TwobitEncodeState *state, GtReadsLibraryInfo *rli, FILE *file,
    char *line)
{
  char *fgetsretval = NULL;
  do {
    if (line[0] == '>')
    {
      if (state->current.nofseqs > rli->first_seqnum && !state->invalid_mode)
      {
        gt_reads2twobit_process_sequence_end(state);
      }
      GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line, file, fgetsretval);
      gt_reads2twobit_prepare_for_new_sequence(state);
    }
    else if (!state->invalid_mode)
    {
      gt_reads2twobit_process_sequence_line(state, line);
    }
  } while ((fgetsretval = fgets(line, (int)GT_READS2TWOBIT_READBUFFER_SIZE,
            file)) == line);
}

static int gt_reads2twobit_encode_unpaired_library(
    GtReads2TwobitEncodeState *state, GtReadsLibraryInfo *rli, GtError *err)
{
  int had_err = 0;
  FILE *file;
  file = gt_fa_fopen(gt_str_get(rli->filename1), "r", err);
  if (file == NULL)
    had_err = -1;
  if (!had_err)
  {
    const unsigned long invalid_tl_before = state->invalid_total_length,
          invalid_s_before = state->invalid_sequences;
    char line[GT_READS2TWOBIT_READBUFFER_SIZE], *fgetsretval;
    rli->first_seqnum = state->current.nofseqs;
    fgetsretval = fgets(line, (int)GT_READS2TWOBIT_READBUFFER_SIZE, file);
    if (fgetsretval == line)
    {
      if (line[0] == '>')
      {
        gt_reads2twobit_encode_unpaired_fasta_library(state, rli, file, line);
      }
      else if (line[0] == '@')
      {
        had_err = gt_reads2twobit_encode_unpaired_fastq_library(state, rli,
            file, line);
        if (had_err != 0)
          gt_error_set(err, "%s: error in FASTQ format",
              gt_str_get(rli->filename1));
      }
      else
      {
        gt_error_set(err, "%s: unknown format", gt_str_get(rli->filename1));
        had_err = -1;
      }
    }
    else
    {
      /* empty file or error */
      gt_assert(fgetsretval == NULL);
    }
    if (!state->invalid_mode)
      gt_reads2twobit_process_sequence_end(state);
    gt_assert(state->current.nofseqs >= rli->first_seqnum);
    rli->nofseqs = state->current.nofseqs - rli->first_seqnum;
    rli->total_seqlength = state->varlen_mode
      ?  state->seppos[state->current.nofseqs - 1UL] + 1UL -
         ((rli->first_seqnum == 0) ? 0 : state->seppos[rli->first_seqnum - 1UL])
      : state->seqlen_first * rli->nofseqs;
    /* the following is not necessary, but is useful for the tests */
    rli->total_filelength -= (state->invalid_total_length - invalid_tl_before +
        3UL * (state->invalid_sequences - invalid_s_before));
    if (!had_err)
      had_err = gt_reads2twobit_close_file(file, rli->filename1, err);
    else
      gt_fa_fclose(file);
  }
  return had_err;
}

static inline int gt_reads2twobit_process_fastq_mate_pair(
    GtReads2TwobitEncodeState *state, char *line2, FILE *file2, bool *file2new)
{
  int had_err = 0;
  char *fgetsretval = NULL;
  bool was_invalid = state->invalid_mode;
  unsigned long prev_seqlen = state->seqlen;
  unsigned long qbuf2_next = 0;
  bool qmode = false;
  if (*file2new)
  {
    fgetsretval = fgets(line2, (int)GT_READS2TWOBIT_READBUFFER_SIZE, file2);
    gt_assert(fgetsretval == line2);
    *file2new = false;
  }
  GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line2, file2, fgetsretval);
  state->seqlen_mate = state->seqlen;
  state->seqlen = 0;
  if (!state->invalid_mode)
    state->current.nofseqs++;
  else
    state->invalid_sequences++;
  while (!had_err)
  {
    fgetsretval = fgets(line2, (int)GT_READS2TWOBIT_READBUFFER_SIZE, file2);
    if (fgetsretval == NULL)
      break;
    if (!qmode)
    {
      if (line2[0] == '@')
        break;
      else if (line2[0] == '+')
      {
        GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line2, file2, fgetsretval);
        if (state->seqlen + 1UL > (unsigned long)(state->qbuf2_size))
        {
          state->qbuf2_size = (size_t)state->seqlen + 1;
          state->qbuf2 = gt_realloc(state->qbuf2, state->qbuf2_size);
        }
        qmode = true;
      }
      else
      {
        gt_reads2twobit_process_sequence_line(state, line2);
      }
    }
    else
    {
      had_err = gt_reads2twobit_process_qualities_line(state, line2,
          state->qbuf2, &qbuf2_next);
      if (had_err == -1)
        had_err = -2;
      if (!had_err && qbuf2_next == state->seqlen)
      {
        if (state->maxlow != GT_UNDEF_ULONG)
          gt_reads2twobit_apply_quality_filter(state, state->qbuf2, qbuf2_next);
        qbuf2_next = 0;
        qmode = false;
      }
    }
  }
  if (!had_err && !state->invalid_mode)
    gt_reads2twobit_process_sequence_end(state);
  if (!had_err && !was_invalid && state->invalid_mode)
  {
    state->invalid_sequences++;
    state->invalid_total_length += (prev_seqlen - 1UL);
  }
  return had_err;
}

static int gt_reads2twobit_encode_interleaved_paired_fastq_library(
    GtReads2TwobitEncodeState *state, GtReadsLibraryInfo *rli, FILE *file,
    char *line)
{
  int had_err = 0;
  unsigned long qbuf_next = 0;
  bool qmode = false;
  bool processing_mate = true;
  char *fgetsretval = line;
  state->seqlen = 0;
  do {
    if (!qmode)
    {
      if (line[0] == '@')
      {
        if (state->current.nofseqs > rli->first_seqnum && !state->invalid_mode)
        {
          gt_reads2twobit_process_sequence_end(state);
        }
        GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line, file, fgetsretval);
        processing_mate = !processing_mate;
        if (processing_mate)
        {
          if (!state->invalid_mode)
            state->current.nofseqs++;
          state->seqlen_mate = state->seqlen;
          state->seqlen = 0;
        }
        else
        {
          gt_reads2twobit_prepare_for_new_sequence(state);
        }
      }
      else if (line[0] == '+')
      {
        GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line, file, fgetsretval);
        if (state->seqlen + 1UL > (unsigned long)(state->qbuf_size))
        {
          state->qbuf_size = (size_t)state->seqlen + 1;
          state->qbuf = gt_realloc(state->qbuf, state->qbuf_size);
        }
        qmode = true;
      }
      else
      {
        gt_reads2twobit_process_sequence_line(state, line);
      }
    }
    else
    {
      had_err = gt_reads2twobit_process_qualities_line(state, line,
          state->qbuf, &qbuf_next);
      if (qbuf_next == state->seqlen)
      {
        if (state->maxlow != GT_UNDEF_ULONG)
          gt_reads2twobit_apply_quality_filter(state, state->qbuf, qbuf_next);
        qbuf_next = 0;
        qmode = false;
      }
    }
  } while ((fgetsretval = fgets(line, (int)GT_READS2TWOBIT_READBUFFER_SIZE,
            file)) == line && !had_err);
  if (!had_err && !state->invalid_mode)
    gt_reads2twobit_process_sequence_end(state);
  return had_err;
}

static int gt_reads2twobit_encode_twofile_paired_fastq_library(
    GtReads2TwobitEncodeState *state, GtReadsLibraryInfo *rli, FILE *file1,
    FILE *file2, char *line1)
{
  int had_err = 0;
  unsigned long qbuf_next = 0;
  bool qmode = false;
  bool file2new = true;
  char *fgetsretval = NULL,
       line2[GT_READS2TWOBIT_READBUFFER_SIZE];
  line2[0] = '\0';
  state->seqlen = 0;
  do {
    if (!qmode)
    {
      if (line1[0] == '@')
      {
        if (state->current.nofseqs > rli->first_seqnum)
        {
          if (!state->invalid_mode)
            gt_reads2twobit_process_sequence_end(state);
          had_err = gt_reads2twobit_process_fastq_mate_pair(state, line2,
              file2, &file2new);
        }
        else
        {
          if (state->invalid_mode)
            had_err = gt_reads2twobit_process_fastq_mate_pair(state, line2,
                file2, &file2new);
        }
        GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line1, file1, fgetsretval);
        gt_reads2twobit_prepare_for_new_sequence(state);
      }
      else if (line1[0] == '+')
      {
        GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line1, file1, fgetsretval);
        if (state->seqlen + 1UL > (unsigned long)(state->qbuf_size))
        {
          state->qbuf_size = (size_t)state->seqlen + 1;
          state->qbuf = gt_realloc(state->qbuf, state->qbuf_size);
        }
        qmode = true;
      }
      else if (!state->invalid_mode)
      {
        gt_reads2twobit_process_sequence_line(state, line1);
      }
    }
    else
    {
      had_err = gt_reads2twobit_process_qualities_line(state, line1,
          state->qbuf, &qbuf_next);
      if (qbuf_next == state->seqlen)
      {
        if (state->maxlow != GT_UNDEF_ULONG)
          gt_reads2twobit_apply_quality_filter(state, state->qbuf, qbuf_next);
        qbuf_next = 0;
        qmode = false;
      }
    }
  } while ((fgetsretval = fgets(line1, (int)GT_READS2TWOBIT_READBUFFER_SIZE,
            file1)) == line1 && !had_err);
  if (!had_err && !state->invalid_mode)
    gt_reads2twobit_process_sequence_end(state);
  if (!had_err)
    had_err = gt_reads2twobit_process_fastq_mate_pair(state, line2, file2,
        &file2new);
  return had_err;
}

static inline void gt_reads2twobit_process_fasta_mate_pair(
    GtReads2TwobitEncodeState *state, char *line2, FILE *file2)
{
  char *fgetsretval = NULL;
  bool was_invalid = state->invalid_mode;
  unsigned long prev_seqlen = state->seqlen;
  if (line2[0] != '>')
  {
    fgetsretval = fgets(line2, (int)GT_READS2TWOBIT_READBUFFER_SIZE,
        file2);
    gt_assert(fgetsretval == line2);
  }
  gt_assert(line2[0] == '>');
  GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line2, file2, fgetsretval);
  state->seqlen = 0;
  state->seqlen_mate = state->seqlen;
  if (!state->invalid_mode)
    state->current.nofseqs++;
  else
    state->invalid_sequences++;
  while (true)
  {
    fgetsretval = fgets(line2, (int)GT_READS2TWOBIT_READBUFFER_SIZE, file2);
    if (fgetsretval != line2 || line2[0] == '>')
      break;
    gt_reads2twobit_process_sequence_line(state, line2);
  }
  if (!state->invalid_mode)
    gt_reads2twobit_process_sequence_end(state);
  if (!was_invalid && state->invalid_mode)
  {
    state->invalid_sequences++;
    state->invalid_total_length += (prev_seqlen - 1UL);
  }
}

static void gt_reads2twobit_encode_interleaved_paired_fasta_library(
    GtReads2TwobitEncodeState *state, GtReadsLibraryInfo *rli, FILE *file,
    char *line)
{
  char *fgetsretval = NULL;
  bool processing_mate = true;
  do {
    if (line[0] == '>')
    {
      if (state->current.nofseqs > rli->first_seqnum && !state->invalid_mode)
      {
        gt_reads2twobit_process_sequence_end(state);
      }
      GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line, file, fgetsretval);
      processing_mate = !processing_mate;
      if (processing_mate)
      {
        if (!state->invalid_mode)
          state->current.nofseqs++;
        state->seqlen_mate = state->seqlen;
        state->seqlen = 0;
      }
      else
      {
        gt_reads2twobit_prepare_for_new_sequence(state);
      }
    }
    else
    {
      gt_reads2twobit_process_sequence_line(state, line);
    }
  } while ((fgetsretval = fgets(line, (int)GT_READS2TWOBIT_READBUFFER_SIZE,
            file)) == line);
  if (!state->invalid_mode)
    gt_reads2twobit_process_sequence_end(state);
}

static void gt_reads2twobit_encode_twofile_paired_fasta_library(
    GtReads2TwobitEncodeState *state, GtReadsLibraryInfo *rli, FILE *file1,
    FILE *file2, char *line1)
{
  char *fgetsretval = NULL,
       line2[GT_READS2TWOBIT_READBUFFER_SIZE];
  line2[0] = '\0';
  do {
    if (line1[0] == '>')
    {
      if (state->current.nofseqs > rli->first_seqnum)
      {
        if (!state->invalid_mode)
          gt_reads2twobit_process_sequence_end(state);
        gt_reads2twobit_process_fasta_mate_pair(state, line2, file2);
      }
      else
      {
        if (state->invalid_mode)
          gt_reads2twobit_process_fasta_mate_pair(state, line2, file2);
      }
      GT_READS2TWOBIT_SKIP_TO_DESCRIPTION_END(line1, file1, fgetsretval);
      gt_reads2twobit_prepare_for_new_sequence(state);
    }
    else if (!state->invalid_mode)
    {
      gt_reads2twobit_process_sequence_line(state, line1);
    }
  } while ((fgetsretval = fgets(line1, (int)GT_READS2TWOBIT_READBUFFER_SIZE,
            file1)) == line1);
  if (!state->invalid_mode)
    gt_reads2twobit_process_sequence_end(state);
  gt_reads2twobit_process_fasta_mate_pair(state, line2, file2);
}

static int gt_reads2twobit_encode_paired_library(
    GtReads2TwobitEncodeState *state, GtReadsLibraryInfo *rli, GtError *err)
{
  int had_err = 0;
  FILE *file1, *file2 = NULL;
  gt_assert(rli->filename1 != NULL);
  file1 = gt_fa_fopen(gt_str_get(rli->filename1), "r", err);
  if (file1 == NULL)
    had_err = -1;
  if (!had_err && rli->filename2 != NULL)
  {
    file2 = gt_fa_fopen(gt_str_get(rli->filename2), "r", err);
    if (file2 == NULL)
      had_err = -1;
  }
  if (!had_err)
  {
    const unsigned long invalid_tl_before = state->invalid_total_length,
          invalid_s_before = state->invalid_sequences;
    char line1[GT_READS2TWOBIT_READBUFFER_SIZE],
         *fgetsretval;
    rli->first_seqnum = state->current.nofseqs;
    fgetsretval = fgets(line1, (int)GT_READS2TWOBIT_READBUFFER_SIZE, file1);
    if (fgetsretval == line1)
    {
      if (line1[0] == '>')
      {
        if (file2 == NULL)
        {
          gt_log_log("encode interleaved paired fasta library");
          gt_reads2twobit_encode_interleaved_paired_fasta_library(state, rli,
              file1, line1);
        }
        else
        {
          gt_log_log("encode two-file paired fasta library");
          gt_reads2twobit_encode_twofile_paired_fasta_library(state, rli, file1,
              file2, line1);
        }
      }
      else if (line1[0] == '@')
      {
        if (file2 == NULL)
        {
          gt_log_log("encode interleaved paired fastQ library");
          had_err = gt_reads2twobit_encode_interleaved_paired_fastq_library(
              state, rli, file1, line1);
        }
        else
        {
          gt_log_log("encode two-file paired fastQ library");
          had_err = gt_reads2twobit_encode_twofile_paired_fastq_library(
              state, rli, file1, file2, line1);
        }
        if (had_err != 0)
          gt_error_set(err, "%s: error in FASTQ format", had_err == -1 ?
              gt_str_get(rli->filename1) : gt_str_get(rli->filename2));
      }
      else
      {
        gt_error_set(err, "%s: unknown format", gt_str_get(rli->filename1));
        had_err = -1;
      }
    }
    else
    {
      /* empty file or error */
      gt_assert(fgetsretval == NULL);
    }
    gt_assert(state->current.nofseqs >= rli->first_seqnum);
    rli->nofseqs = state->current.nofseqs - rli->first_seqnum;
    rli->total_seqlength = state->varlen_mode
      ?  state->seppos[state->current.nofseqs - 1UL] + 1UL -
         ((rli->first_seqnum == 0) ? 0 : state->seppos[rli->first_seqnum - 1UL])
      : state->seqlen_first * rli->nofseqs;
    /* the following is not necessary, but is useful for the tests */
    rli->total_filelength -= (state->invalid_total_length - invalid_tl_before +
        3UL * (state->invalid_sequences - invalid_s_before));
  }
  if (!had_err)
    had_err = gt_reads2twobit_close_file(file1, rli->filename1, err);
  else if (file1 != NULL)
    gt_fa_fclose(file1);
  if (!had_err && file2 != NULL)
    had_err = gt_reads2twobit_close_file(file2, rli->filename2, err);
  else if (file2 != NULL)
    gt_fa_fclose(file2);
  return had_err;
}

static void gt_reads2twobit_tbe_flush_and_realloc(GtReads2Twobit *r2t,
    GtReads2TwobitEncodeState *state)
{
  if (state->current.codepos > 0)
  {
    unsigned long shift = (GT_UNITSIN2BITENC - state->current.codepos) << 1UL;
    *(state->current.tbe_next++) =
      (GtTwobitencoding)(state->current.kmercode << shift);
  }
  if (state->current.nofseqs > 0)
  {
    gt_log_log("realloc tbe, total_seqlength=%lu", r2t->total_seqlength);
    r2t->twobitencoding = gt_realloc(r2t->twobitencoding,
        sizeof (*r2t->twobitencoding) *
        (GT_DIVBYUNITSIN2BITENC(r2t->total_seqlength) + 2UL));
  }
  else
  {
    gt_free(r2t->twobitencoding);
    r2t->twobitencoding = NULL;
  }
}

static void gt_reads2twobit_finalize_encode(GtReads2Twobit *r2t,
    GtReads2TwobitEncodeState *state)
{
  unsigned int i;
  r2t->nofseqs = state->current.nofseqs;
  r2t->current_sepcode = GT_READS2TWOBIT_DEFAULT_SEPARATOR;
  r2t->invalid_sequences = state->invalid_sequences;
  r2t->invalid_total_length = state->invalid_total_length;
  for (i = 0; i < GT_READS2TWOBIT_ALPHASIZE; i++)
    r2t->chardistri[i] = state->current.chardistri[i];
  if (state->varlen_mode)
  {
    state->seppos = gt_realloc(state->seppos, sizeof (state->seppos) *
        (state->current.nofseqs));
    r2t->seqlen_eqlen = 0;
    r2t->seqlen_max = state->current.seqlen_max;
    r2t->seqlen_min = state->current.seqlen_min;
    r2t->total_seqlength = state->seppos[state->current.nofseqs - 1UL];
    r2t->seppos = state->seppos;
  }
  else
  {
    r2t->seqlen_eqlen = state->seqlen_first;
    r2t->seqlen_max = state->seqlen_first;
    r2t->seqlen_min = state->seqlen_first;
    if (state->seqlen_first > 0)
      r2t->total_seqlength = state->seqlen_first * state->current.nofseqs - 1UL;
    else
      r2t->total_seqlength = 0;
    gt_assert(state->seppos == NULL);
  }
  if (state->qbuf_size > 0)
    gt_free(state->qbuf);
  if (state->qbuf2_size > 0)
    gt_free(state->qbuf2);
  gt_reads2twobit_tbe_flush_and_realloc(r2t, state);
}

int gt_reads2twobit_encode(GtReads2Twobit *r2t, GtError *err)
{
  int had_err = 0;
  const unsigned long noflibraries = gt_array_size(r2t->collection);
  unsigned long libnum;
  GtReads2TwobitEncodeState state;

  gt_error_check(err);
  gt_assert(r2t != NULL);
  gt_assert(r2t->twobitencoding == NULL);
  gt_reads2twobit_init_encode(r2t, &state);
  for (libnum = 0; libnum < noflibraries && !had_err; libnum++)
  {
    GtReadsLibraryInfo *rli = gt_array_get(r2t->collection, libnum);
    if (!rli->paired)
    {
      had_err = gt_reads2twobit_encode_unpaired_library(&state, rli, err);
    }
    else
    {
      had_err = gt_reads2twobit_encode_paired_library(&state, rli, err);
    }
  }
  gt_reads2twobit_finalize_encode(r2t, &state);
  return had_err;
}

static void gt_reads2twobit_collect_fileinfo(const GtReads2Twobit *r2t,
    GtFilelengthvalues **filelengthtab, GtStrArray **filenametab)
{
  unsigned long i, noflibraries;
  noflibraries = gt_array_size(r2t->collection);
  *filenametab = gt_str_array_new();
  if (filelengthtab != NULL)
  {
    *filelengthtab = gt_malloc(sizeof (**filelengthtab) * noflibraries);
  }
  for (i = 0; i < noflibraries; i++)
  {
    GtStr *libname;
    GtReadsLibraryInfo *rli;
    rli = gt_array_get(r2t->collection, i);
    if (filelengthtab != NULL)
    {
      (*filelengthtab)[i].effectivelength =
        (uint64_t)rli->total_seqlength - 1UL;
      if (r2t->seqlen_eqlen == 0 && i == noflibraries - 1UL)
        (*filelengthtab)[i].effectivelength--;
      (*filelengthtab)[i].length = (uint64_t)rli->total_filelength;
    }
    libname = gt_str_clone(rli->filename1);
    if (rli->filename2 != NULL)
    {
      gt_str_append_char(libname, GT_READS2TWOBIT_LIBSPECSEP);
      gt_str_append_str(libname, rli->filename2);
    }
    if (rli->paired)
    {
      gt_str_append_char(libname, GT_READS2TWOBIT_LIBSPECSEP);
      gt_str_append_ulong(libname, rli->insertlength);
      if (rli->stdev > 0)
      {
        gt_str_append_char(libname, GT_READS2TWOBIT_INSERTSEP);
        gt_str_append_ulong(libname, rli->stdev);
      }
    }
    gt_str_array_add(*filenametab, libname);
    gt_str_delete(libname);
  }
}

static inline GtTwobitencoding gt_reads2twobit_less_frequent_char(
    GtReads2Twobit *r2t)
{
  GtTwobitencoding i, code;
  unsigned long lowest_value, value;
  lowest_value = r2t->chardistri[0];
  code = 0;
  for (i = (GtTwobitencoding)1;
      i < (GtTwobitencoding)GT_READS2TWOBIT_ALPHASIZE; i++)
  {
    value = r2t->chardistri[i];
    if (value < lowest_value)
    {
      lowest_value = value;
      code = i;
    }
  }
  gt_log_log("less frequent char code: %lu", (unsigned long)code);
  return code;
}

static void gt_reads2twobit_zeropad_tbe(GtReads2Twobit *r2t)
{
  unsigned long pos, codenum, posincode, shift;
  pos = r2t->total_seqlength - 1UL;
  codenum = GT_DIVBYUNITSIN2BITENC(pos);
  posincode = GT_MODBYUNITSIN2BITENC(pos);
  if (posincode < (unsigned long)GT_UNITSIN2BITENC - 1UL)
  {
    shift = GT_MULT2(GT_UNITSIN2BITENC - 1UL - posincode);
    r2t->twobitencoding[codenum] =
      (GtTwobitencoding)((r2t->twobitencoding[codenum] >> shift) << shift);
  }
  r2t->twobitencoding[codenum + 1UL] = 0;
}

static void gt_reads2twobit_seek_sequence(const GtReads2Twobit *r2t,
    unsigned long seqnum, unsigned long *seqlen, GtTwobitencoding *firstcode,
    unsigned long *charsinfirstcode, GtTwobitencoding **nextcode_ptr)
{
  unsigned long pos;
  *seqlen = r2t->seqlen_eqlen;
  if (*seqlen == 0)
  {
    if (seqnum == 0)
    {
      *seqlen = r2t->seppos[0] + 1UL;
      pos = 0;
    }
    else
    {
      *seqlen = r2t->seppos[seqnum] - r2t->seppos[seqnum - 1UL];
      pos = r2t->seppos[seqnum - 1UL] + 1UL;
    }
  }
  else
  {
    pos = seqnum * (*seqlen);
  }
  *nextcode_ptr = r2t->twobitencoding + GT_DIVBYUNITSIN2BITENC(pos);
  *charsinfirstcode = GT_UNITSIN2BITENC - GT_MODBYUNITSIN2BITENC(pos);
  *firstcode = *((*nextcode_ptr)++);
}

void gt_reads2twobit_decode_sequence(const GtReads2Twobit *r2t,
    unsigned long seqnum, char *decoded)
{
  GtTwobitencoding code;
  unsigned long pos, seqlen, charsincode;
  GtTwobitencoding *nextencoded;
  const char code2char[] = "acgt";
  char *nextdecoded = decoded;

  gt_reads2twobit_seek_sequence(r2t, seqnum, &seqlen, &code, &charsincode,
      &nextencoded);
  *(nextdecoded++) = '>';
  *(nextdecoded++) = '\n';
  for (pos = 0; pos < seqlen - 1UL; pos++)
  {
    if (charsincode == 0)
    {
      code = *(nextencoded++);
      charsincode = (unsigned long)GT_UNITSIN2BITENC;
    }
    *(nextdecoded++) = code2char[code >> ((--charsincode) << 1) & 3];
  }
  *(nextdecoded++) = '\n';
  *(nextdecoded) = '\0';
}

static unsigned long gt_reads2twobit_subtract_from_chardistri(
    GtReads2Twobit *r2t, unsigned long seqnum)
{
  GtTwobitencoding code;
  unsigned long pos, seqlen, charsincode;
  GtTwobitencoding *nextencoded;

  gt_reads2twobit_seek_sequence(r2t, seqnum, &seqlen, &code, &charsincode,
      &nextencoded);
  for (pos = 0; pos < seqlen - 1UL; pos++)
  {
    if (charsincode == 0)
    {
      code = *(nextencoded++);
      charsincode = (unsigned long)GT_UNITSIN2BITENC;
    }
    r2t->chardistri[code >> ((--charsincode) << 1) & 3]--;
  }
  return seqlen;
}

void gt_reads2twobit_decode_range(const GtReads2Twobit *r2t,
    GtFile *outfp, unsigned long seqnum_from, unsigned long nofseqs,
    const GtBitsequence *skip)
{
  GtTwobitencoding code;
  unsigned short charsincode;
  const char code2char[] = "acgt";
  unsigned long seqnum, pos, nextsep, nextdecoded, seqnum_to;
  const GtTwobitencoding *nextencoded = r2t->twobitencoding;
  char *decoded;

  gt_assert(r2t->seqlen_max > 0);
  if (nofseqs == 0)
    return;
  seqnum_to = seqnum_from + nofseqs - 1UL;
  decoded = gt_malloc(sizeof (*decoded) * (r2t->seqlen_max + 3UL));
  decoded[0] = '>';
  decoded[1] = '\n';
  nextdecoded = 2UL;

  seqnum = seqnum_from;
  if (skip != NULL)
    while (GT_ISIBITSET(skip, seqnum))
      seqnum++;

  if (r2t->seqlen_eqlen > 0)
  {
    nextsep = r2t->seqlen_eqlen * (seqnum + 1UL) - 1UL;
    pos = seqnum * r2t->seqlen_eqlen;
  }
  else
  {
    nextsep = r2t->seppos[seqnum];
    pos = (seqnum == 0) ? 0 : r2t->seppos[seqnum - 1UL] + 1UL;
  }

  nextencoded = r2t->twobitencoding + GT_DIVBYUNITSIN2BITENC(pos);
  code = *(nextencoded++);
  charsincode = (unsigned short)GT_UNITSIN2BITENC -
    (unsigned short)GT_MODBYUNITSIN2BITENC(pos);

  while (true)
  {
    if (charsincode == 0)
    {
      code = *(nextencoded++);
      charsincode = (unsigned short)GT_UNITSIN2BITENC;
    }
    if (pos++ < nextsep)
    {
      gt_assert(nextsep - pos <= r2t->seqlen_max);
      decoded[nextdecoded++] = code2char[code >> ((--charsincode) << 1) & 3];
    }
    else
    {
      /* output sequence */
      charsincode--;
      decoded[nextdecoded++] = '\n';
      decoded[nextdecoded] = '\0';
      gt_file_xfputs(decoded, outfp);
      nextdecoded = 2UL;

      seqnum++;
      if (seqnum > seqnum_to)
        break;
      if (skip != NULL && GT_ISIBITSET(skip, seqnum))
      {
        /* jump to next non-contained sequence */
        while (seqnum <= seqnum_to && GT_ISIBITSET(skip, seqnum))
          seqnum++;
        if (seqnum > seqnum_to)
          break;
        pos = r2t->seqlen_eqlen > 0 ? seqnum * r2t->seqlen_eqlen :
          r2t->seppos[seqnum - 1UL] + 1UL;
        nextencoded = r2t->twobitencoding + GT_DIVBYUNITSIN2BITENC(pos);
        code = *(nextencoded++);
        charsincode = (unsigned short)GT_UNITSIN2BITENC -
          (unsigned short)GT_MODBYUNITSIN2BITENC(pos);
      }
      nextsep = (r2t->seqlen_eqlen > 0)
        ? r2t->seqlen_eqlen * (seqnum + 1UL) - 1UL
        : r2t->seppos[seqnum];
    }
  }
  gt_free(decoded);
}

int gt_reads2twobit_write_fasta(const GtReads2Twobit *r2t, char *path,
    GtBitsequence *skip, GtError *err)
{
  GtFile *file;
  file = gt_file_new(path, "w", err);
  if (file == NULL)
    return -1;
  gt_reads2twobit_decode_range(r2t, file, 0, r2t->nofseqs, skip);
  gt_file_delete(file);
  return 0;
}

static void gt_reads2twobit_write_encoded_nocodesshift(GtReads2Twobit *r2t,
    GtTwobitencoding *outputbuffer, GtTwobitencoding offset,
    unsigned long firstcodeidx, unsigned long lastcodeidx)
{
  if (offset == 0)
    outputbuffer[0] = r2t->twobitencoding[firstcodeidx];
  else
  {
    GtTwobitencoding mask;
    mask =
      ((GtTwobitencoding)1 << GT_MULT2(GT_UNITSIN2BITENC - offset)) - 1;
    outputbuffer[0] =
      (r2t->twobitencoding[firstcodeidx] & mask) |
      (outputbuffer[0] & ~mask);
  }
  if (lastcodeidx > firstcodeidx)
    memcpy(outputbuffer + 1, r2t->twobitencoding + firstcodeidx + 1,
        sizeof (GtTwobitencoding) * (lastcodeidx - firstcodeidx));
}

static void gt_reads2twobit_write_encoded_leftcodesshift(
    GtReads2Twobit *r2t, GtTwobitencoding *outputbuffer,
    GtTwobitencoding inputoffset, GtTwobitencoding outputoffset,
    unsigned long firstcodeidx, unsigned long lastcodeidx)
{
  const GtTwobitencoding netoffset = inputoffset - outputoffset;
  const GtTwobitencoding shiftright =
    GT_MULT2(GT_UNITSIN2BITENC - netoffset);
  const GtTwobitencoding shiftleft = GT_MULT2(netoffset);
  unsigned long i;
  GtTwobitencoding *nextinoutputbuffer = outputbuffer;
  if (outputoffset == 0)
    outputbuffer[0] = r2t->twobitencoding[firstcodeidx] << shiftleft;
  else
  {
    GtTwobitencoding mask;
    mask = ((GtTwobitencoding)1 << GT_MULT2(GT_UNITSIN2BITENC -
          outputoffset)) - 1;
    outputbuffer[0] =
      ((r2t->twobitencoding[firstcodeidx] << shiftleft) & mask) |
      (outputbuffer[0] & ~mask);
  }
  for (i = firstcodeidx + 1UL; i <= lastcodeidx; i++)
  {
    *(nextinoutputbuffer) |= (r2t->twobitencoding[i] >> shiftright);
    *(++nextinoutputbuffer) = (r2t->twobitencoding[i] << shiftleft);
  }
}

static void gt_reads2twobit_write_encoded_rightcodesshift(
    GtReads2Twobit *r2t, GtTwobitencoding *outputbuffer,
    GtTwobitencoding inputoffset, GtTwobitencoding outputoffset,
    unsigned long firstcodeidx, unsigned long lastcodeidx)
{
  const GtTwobitencoding netoffset = outputoffset - inputoffset;
  const GtTwobitencoding shiftright = GT_MULT2(netoffset);
  const GtTwobitencoding shiftleft =
    GT_MULT2(GT_UNITSIN2BITENC - netoffset);
  unsigned long i;
  GtTwobitencoding *nextinoutputbuffer = outputbuffer + 1;
  GtTwobitencoding mask;
  mask = ((GtTwobitencoding)1 << GT_MULT2(GT_UNITSIN2BITENC -
        outputoffset)) - 1;
  outputbuffer[0] =
    ((r2t->twobitencoding[firstcodeidx] >> shiftright) & mask) |
    (outputbuffer[0] & ~mask);
  outputbuffer[1] =
    r2t->twobitencoding[firstcodeidx] << shiftleft;
  for (i = firstcodeidx + 1; i <= lastcodeidx; i++)
  {
    *(nextinoutputbuffer) |= (r2t->twobitencoding[i] >> shiftright);
    *(++nextinoutputbuffer) = (r2t->twobitencoding[i] << shiftleft);
  }
}

GtTwobitencoding* gt_reads2twobit_write_encoded(GtReads2Twobit *r2t,
    unsigned long seqnum, GtTwobitencoding *outputbuffer,
    GtTwobitencoding outputoffset, GtTwobitencoding *lastcodeoffsetptr)
{
  unsigned long firstpos, firstcodeidx, lastpos, lastcodeidx, seqlen;
  GtTwobitencoding  inputoffset;

  firstpos = (seqnum == 0)
    ? 0
    : (r2t->seqlen_eqlen > 0)
        ? r2t->seqlen_eqlen * seqnum
        : r2t->seppos[seqnum - 1UL] + 1UL;
  firstcodeidx = GT_DIVBYUNITSIN2BITENC(firstpos);

  lastpos = (r2t->seqlen_eqlen > 0)
    ? r2t->seqlen_eqlen * (seqnum + 1UL) - 1UL
    : r2t->seppos[seqnum];
  lastcodeidx = GT_DIVBYUNITSIN2BITENC(lastpos);

  seqlen = (r2t->seqlen_eqlen > 0)
    ? r2t->seqlen_eqlen
    : lastpos - firstpos + 1UL;

  inputoffset = (GtTwobitencoding)GT_MODBYUNITSIN2BITENC(firstpos);

  if (inputoffset == outputoffset)
  {
    gt_reads2twobit_write_encoded_nocodesshift(r2t, outputbuffer, inputoffset,
        firstcodeidx, lastcodeidx);
    *lastcodeoffsetptr = (GtTwobitencoding)GT_MODBYUNITSIN2BITENC(lastpos + 1);
  }
  else if (inputoffset > outputoffset)
  {
    gt_reads2twobit_write_encoded_leftcodesshift(r2t,
        outputbuffer, inputoffset, outputoffset, firstcodeidx, lastcodeidx);
    *lastcodeoffsetptr = GT_MODBYUNITSIN2BITENC(outputoffset + seqlen);
  }
  else
  {
    gt_reads2twobit_write_encoded_rightcodesshift(r2t,
        outputbuffer, inputoffset, outputoffset, firstcodeidx, lastcodeidx);
    *lastcodeoffsetptr = GT_MODBYUNITSIN2BITENC(outputoffset + seqlen);
  }
  return outputbuffer + GT_DIVBYUNITSIN2BITENC(outputoffset + seqlen);
}

static inline void gt_reads2twobit_handle_deleted_mates(
    GT_UNUSED GtReads2Twobit *r2t, GtReadsLibraryInfo *rli, GtBitsequence *list)
{
  unsigned long seqnum, last_seqnum = rli->first_seqnum + rli->nofseqs - 1UL;
  gt_assert(rli->nofseqs % 2 == 0);
  gt_assert(rli->nofseqs > 0);
  for (seqnum = rli->first_seqnum; seqnum < last_seqnum; seqnum += 2UL)
  {
    if (GT_ISIBITSET(list, seqnum))
    {
      GT_SETIBIT(list, seqnum + 1UL);
    }
    else if (GT_ISIBITSET(list, seqnum + 1UL))
    {
      GT_SETIBIT(list, seqnum);
    }
  }
}

void gt_reads2twobit_delete_sequences(GtReads2Twobit *r2t, GtBitsequence *list)
{
  GtTwobitencoding outputoffset = 0, *outputbuffer;
  unsigned long libnum, seqnum, output_seqnum,
                noflibs = gt_array_size(r2t->collection),
                deleted_sequences = 0, deleted_chars = 0, output_startpos = 0;
  for (libnum = 0; libnum < noflibs; libnum++)
  {
    GtReadsLibraryInfo *rli = gt_array_get(r2t->collection, libnum);
    if (rli->nofseqs > 0)
    {
      unsigned long deleted_sequences_in_lib = 0, deleted_chars_in_lib = 0,
                    last_seqnum = rli->first_seqnum + rli->nofseqs - 1UL;
      if (rli->filename2 != NULL)
        gt_reads2twobit_handle_deleted_mates(r2t, rli, list);
      for (seqnum = rli->first_seqnum; seqnum <= last_seqnum; seqnum++)
      {
        if (!GT_ISIBITSET(list, seqnum))
        {
          if (deleted_sequences > 0)
          {
            gt_assert(seqnum >= deleted_sequences);
            output_seqnum = seqnum - deleted_sequences;
            output_startpos = (r2t->seqlen_eqlen > 0)
              ? r2t->seqlen_eqlen * output_seqnum
              : ((output_seqnum == 0) ? 0 :
              r2t->seppos[output_seqnum - 1UL] + 1UL);
            outputbuffer = r2t->twobitencoding +
              GT_DIVBYUNITSIN2BITENC(output_startpos);
            outputoffset = (GtTwobitencoding)
              GT_MODBYUNITSIN2BITENC(output_startpos);
            (void)gt_reads2twobit_write_encoded(r2t, seqnum, outputbuffer,
                outputoffset, &outputoffset);
            if (r2t->seqlen_eqlen == 0)
            {
              unsigned long seqlen;
              gt_assert(seqnum > 0);
              seqlen = r2t->seppos[seqnum] - r2t->seppos[seqnum - 1UL];
              gt_assert(seqlen <= r2t->seqlen_max);
              gt_assert(output_startpos + seqlen <= r2t->total_seqlength);
              r2t->seppos[output_seqnum] = output_startpos + seqlen - 1UL;
            }
          }
        }
        else
        {
          deleted_chars_in_lib +=
            gt_reads2twobit_subtract_from_chardistri(r2t, seqnum);
          deleted_sequences++;
          deleted_sequences_in_lib++;
        }
      }
      deleted_chars += deleted_chars_in_lib;
      gt_assert(deleted_sequences_in_lib <= rli->nofseqs);
      if (rli->filename2 != NULL)
        gt_assert(deleted_sequences_in_lib % 2 == 0);
      rli->nofseqs -= deleted_sequences_in_lib;
      gt_assert(deleted_chars_in_lib <= rli->total_seqlength);
      rli->total_seqlength -= deleted_chars_in_lib;
    }
  }
  gt_assert(deleted_sequences <= r2t->nofseqs);
  r2t->nofseqs -= deleted_sequences;
  gt_assert(deleted_chars <= r2t->total_seqlength);
  r2t->total_seqlength -= deleted_chars;
  if (deleted_sequences > 0)
  {
    r2t->twobitencoding = gt_realloc(r2t->twobitencoding,
        sizeof (*r2t->twobitencoding) *
        (GT_DIVBYUNITSIN2BITENC(r2t->total_seqlength) + 2UL));
  }
}

static void gt_reads2twobit_set_separators_to_less_frequent_char(
    GtReads2Twobit *r2t)
{
  unsigned long seqnum, pos, codenum, posincode;
  GtTwobitencoding sepcode, code, mask, shift;
  sepcode = gt_reads2twobit_less_frequent_char(r2t);
  if (sepcode != r2t->current_sepcode && r2t->nofseqs > 1UL)
  {
    unsigned long from, to;
    gt_log_log("changing sepcode from %lu to %lu",
                (unsigned long) r2t->current_sepcode,
                (unsigned long) sepcode);
    from = r2t->seqlen_eqlen > 0 ? 1UL : 0;
    to = r2t->seqlen_eqlen > 0 ? r2t->nofseqs - 1UL : r2t->nofseqs - 2UL;
    for (seqnum = from; seqnum <= to; seqnum++)
    {
      pos = r2t->seqlen_eqlen > 0
        ? seqnum * r2t->seqlen_eqlen - 1UL
        : r2t->seppos[seqnum];
      codenum = GT_DIVBYUNITSIN2BITENC(pos);
      posincode = GT_MODBYUNITSIN2BITENC(pos);
      code = r2t->twobitencoding[codenum];
      shift = (GtTwobitencoding)GT_MULT2(GT_UNITSIN2BITENC - 1UL - posincode);
      mask = ~((GtTwobitencoding)(3UL) << shift);
      gt_assert((code & ~mask) >> shift ==
          (GtTwobitencoding)r2t->current_sepcode);
      code = (code & mask) | ((GtTwobitencoding)sepcode << shift);
      r2t->twobitencoding[codenum] = code;
    }
    r2t->current_sepcode = sepcode;
  }
}

static int gt_reads2twobit_write_encseq_eqlen(GtReads2Twobit *r2t,
    GtError *err)
{
  int had_err = 0;
  GtFilelengthvalues *filelengthtab;
  GtStrArray *filenametab;

  gt_assert(r2t->seqlen_eqlen > 0);
  gt_reads2twobit_collect_fileinfo(r2t, &filelengthtab, &filenametab);
  gt_reads2twobit_set_separators_to_less_frequent_char(r2t);
  gt_reads2twobit_zeropad_tbe(r2t);
  had_err = gt_encseq_equallength_write_twobitencoding_to_file(
      gt_str_get(r2t->indexname), r2t->total_seqlength,
      r2t->seqlen_eqlen - 1UL, r2t->twobitencoding, r2t->nofseqs,
      gt_array_size(r2t->collection), filelengthtab, filenametab,
      r2t->chardistri, err);
  gt_free(filelengthtab);
  gt_str_array_delete(filenametab);
  return had_err;
}

#define GT_READS2TWOBIT_SIZEOFREP(SAT)\
  gt_encseq_determine_size(SAT, r2t->total_seqlength, r2t->nofseqs,\
      numofdbfiles, lengthofdbfilenames, 0, 4U, 2U, 0);

static int gt_reads2twobit_write_encseq_varlen(GtReads2Twobit *r2t,
    GtError *err)
{
  int had_err = 0;
  GtFilelengthvalues *filelengthtab;
  GtStrArray *filenametab;
  uint64_t sizeofrep, minsizeofrep;
  unsigned long numofdbfiles = gt_array_size(r2t->collection);
  GtEncseqAccessType sat;
  unsigned long idx, lengthofdbfilenames = 0;

  gt_assert(r2t->seppos != NULL);
  gt_reads2twobit_collect_fileinfo(r2t, &filelengthtab, &filenametab);
  for (idx = 0; idx < gt_str_array_size(filenametab); idx++)
  {
    lengthofdbfilenames += gt_str_length(gt_str_array_get_str(
          filenametab, idx)) + 1UL;
  }
  sat = GT_ACCESS_TYPE_UCHARTABLES;
  minsizeofrep = GT_READS2TWOBIT_SIZEOFREP(sat);
  sizeofrep = GT_READS2TWOBIT_SIZEOFREP(GT_ACCESS_TYPE_USHORTTABLES);
  if (sizeofrep < minsizeofrep)
  {
    sat = GT_ACCESS_TYPE_USHORTTABLES;
    minsizeofrep = sizeofrep;
  }
  sizeofrep = GT_READS2TWOBIT_SIZEOFREP(GT_ACCESS_TYPE_UINT32TABLES);
  if (sizeofrep < minsizeofrep)
    sat = GT_ACCESS_TYPE_UINT32TABLES;
  gt_reads2twobit_set_separators_to_less_frequent_char(r2t);
  gt_reads2twobit_zeropad_tbe(r2t);
  had_err = gt_encseq_seppos2ssptab(gt_str_get(r2t->indexname),
      r2t->total_seqlength, r2t->nofseqs, r2t->seppos, err);
  if (!had_err)
    had_err = gt_encseq_generic_write_twobitencoding_to_file(
        gt_str_get(r2t->indexname), r2t->total_seqlength,
        sat, 0, r2t->seqlen_min - 1UL, r2t->seqlen_max - 1UL, 0, 0,
        r2t->seqlen_max - 1UL, r2t->twobitencoding, r2t->nofseqs,
        numofdbfiles, filelengthtab, filenametab, r2t->chardistri, err);
  gt_free(filelengthtab);
  gt_str_array_delete(filenametab);
  return had_err;
}

int gt_reads2twobit_write_encseq(GtReads2Twobit *r2t, GtError *err)
{
  int had_err = 0;
  gt_error_check(err);
  gt_assert(r2t != NULL);
  if (r2t->nofseqs == 0)
  {
    gt_log_log("read set is empty, no encseq was written");
    return had_err;
  }
  gt_assert(r2t->twobitencoding != NULL);
  gt_log_log("write encseq %s", gt_str_get(r2t->indexname));
  gt_log_log("seqlen_eqlen = %lu", r2t->seqlen_eqlen);
  if (r2t->seqlen_eqlen > 0)
  {
    had_err = gt_reads2twobit_write_encseq_eqlen(r2t, err);
  }
  else
  {
    had_err = gt_reads2twobit_write_encseq_varlen(r2t, err);
  }
  return had_err;
}

void gt_reads2twobit_sort(GtReads2Twobit *r2t, GtCompareWithData cmp,
    void *cmp_data)
{
  GtTwobitencoding *tbe, *tbe_next, offset;
  unsigned long i, *order;

  gt_assert(r2t != NULL);

  order = gt_malloc(sizeof (*order) * r2t->nofseqs);
  for (i = 0; i < r2t->nofseqs; i++)
    order[i] = i;

  gt_qsort_r(order, (size_t)r2t->nofseqs, sizeof *order, cmp_data, cmp);

  tbe = gt_malloc(sizeof (*tbe) *
      GT_DIVBYUNITSIN2BITENC(r2t->total_seqlength) + 2UL);

  offset = 0;
  tbe_next = tbe;
  for (i = 0; i < r2t->nofseqs; i++)
  {
    tbe_next = gt_reads2twobit_write_encoded(r2t, order[i], tbe_next, offset,
        &offset);
    if (r2t->seqlen_eqlen == 0)
    {
      /* recycle order memory to store new seppos */
      order[i] = (order[i] == 0)
        ? r2t->seppos[0]
        : r2t->seppos[order[i]] - (r2t->seppos[order[i] - 1UL] + 1UL);
      if (i > 0)
        order[i] += (order[i - 1UL] + 1UL);
    }
  }

  gt_free(r2t->twobitencoding);
  r2t->twobitencoding = tbe;

  if (r2t->seqlen_eqlen == 0)
  {
    gt_free(r2t->seppos);
    r2t->seppos = order;
  }
  else
  {
    gt_free(order);
  }
}

int gt_reads2twobit_write_seppos(GtReads2Twobit *r2t, char* path,
    GtBitsequence *skip, GtError *err)
{
  int had_err = 0;
  FILE *file;
  unsigned long pos, seqnum;
  if (r2t->seppos == NULL)
    return 0;
  file = gt_fa_fopen(path, "wb", err);
  if (file == NULL)
    had_err = -1;
  if (!had_err)
  {
    if (!GT_ISIBITSET(skip, 0))
    {
      gt_xfwrite(r2t->seppos, sizeof (r2t->seppos), (size_t)1, file);
      pos = r2t->seppos[0] + 1UL;
    }
    else
      pos = 0;
    for (seqnum = 1UL; seqnum < r2t->nofseqs; seqnum++)
    {
      if (!GT_ISIBITSET(skip, seqnum))
      {
        pos += r2t->seppos[seqnum] - r2t->seppos[seqnum - 1UL] - 1UL;
        gt_xfwrite(&pos, sizeof (pos), (size_t)1, file);
        pos++;
      }
    }
    gt_fa_fclose(file);
  }
  return had_err;
}

GtTwobitencoding *gt_reads2twobit_export_twobitencoding(
    const GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  return r2t->twobitencoding;
}

unsigned long *gt_reads2twobit_export_seppos(const GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  return r2t->seppos;
}

unsigned long gt_reads2twobit_nof_invalid_seqs(const GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  return r2t->invalid_sequences;
}

unsigned long gt_reads2twobit_invalid_seqs_totallength(
    const GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  return r2t->invalid_total_length;
}

unsigned long gt_reads2twobit_nofseqs(const GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  return r2t->nofseqs;
}

unsigned long gt_reads2twobit_seqlen_eqlen(const GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  return r2t->seqlen_eqlen;
}

unsigned long gt_reads2twobit_seqlen_max(const GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  return r2t->seqlen_max;
}

unsigned long gt_reads2twobit_seqlen_min(const GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  return r2t->seqlen_min;
}

unsigned long gt_reads2twobit_total_seqlength(const GtReads2Twobit *r2t)
{
  gt_assert(r2t != NULL);
  return r2t->total_seqlength;
}

int gt_reads2twobit_write_libraries_table(const GtReads2Twobit *r2t,
    char *path, GtError *err)
{
  int had_err = 0;
  unsigned long noflibs, lnum;
  GtReadsLibrary *lib_table;
  noflibs = gt_array_size(r2t->collection);
  gt_assert(noflibs > 0);
  lib_table = gt_malloc(sizeof (*lib_table) * noflibs);
  for (lnum = 0; lnum < noflibs; lnum++)
  {
    GtReadsLibraryInfo *rli;
    rli = gt_array_get(r2t->collection, lnum);
    lib_table[lnum].first_seqnum = rli->first_seqnum;
    lib_table[lnum].nofseqs = rli->nofseqs;
    lib_table[lnum].paired = (rli->filename2 != NULL) ? true : false;
    lib_table[lnum].insertlength = rli->insertlength;
  }
  had_err = gt_reads_library_table_write(lib_table, noflibs, path, err);
  gt_free(lib_table);
  return had_err;
}
genometools-1.5.1/src/match/reads2twobit.h000066400000000000000000000164701211610345200205210ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef READS2TWOBIT_H
#define READS2TWOBIT_H

#include "core/fptr_api.h"
#include "core/intbits.h"
#include "core/str.h"

/* The  class is a specialized encoder for large collections of
   sequencing reads in FastQ and Fasta format. After encoding, the information
   is accessible as a GtTwobitencoding representation in memory and can be
   output to disk in a GtEncseq-compatible format.
   It is designed to be fast and memory efficient, and thus has some
   limitations compared to the encoding feature of GtEncseq: the only supported
   input is Fasta/FastQ with a DNA alphabet; reads containing wildchars are
   removed; the descriptions are discarded; the md5 are not calculated.
   Paired-end libraries are supported. The input may consists in sets of two
   files (forward reads and reverse reads, in the same order) or a single file
   with interleaved reads. In paired-end mode, if a sequence is discarded (e.g.
   because it contains ambiguities), then its mate is discarded too.
   Both equal lenght and variable length sequence collections are supported.
   Reads2Twobit automatically switches to variable length mode when the first
   sequence is encoded, whose length is not the same of the previous
   sequences. */

typedef struct GtReads2Twobit GtReads2Twobit;

GtReads2Twobit* gt_reads2twobit_new(GtStr *indexname);

void gt_reads2twobit_delete(GtReads2Twobit *r2t);

#define GT_READS2TWOBIT_LIBSPECSEP ':'
#define GT_READS2TWOBIT_INSERTSEP  ','

/* Adds the library described by  to the collection.
   If  contains at least a ':' is is assumed to be in the
   form "filename1[:filename2]:insertlength[,stdev]" and parsed;
   on success 0 is returned, if a parsing error occurs, -1 is returned.
   If  does not contain any ':', it is assumed to be a filename
   of a single-end library; in this case the function returns 0. */
int gt_reads2twobit_add_library(GtReads2Twobit *r2t,
                                const GtStr *libspec,
                                GtError *err);

/* Use phred64 scores instead of phred33;
   it must be called before . */
void gt_reads2twobit_use_phred64(GtReads2Twobit *r2t);

/* filter those reads which contain more than  positions
   whose quality is no more than . */
void gt_reads2twobit_set_quality_filter(GtReads2Twobit *r2t,
    unsigned long maxlow, char lowqual);

/* Encodes the sequences in the twobit-encoding format in memory;
   can be called only once; returns 0 on success, a negative number on
   error and sets  accordingly. */
int gt_reads2twobit_encode(GtReads2Twobit *r2t, GtError *err);

/* encoding statistics, must be called after  */
unsigned long gt_reads2twobit_nofseqs(const GtReads2Twobit *r2t);
unsigned long gt_reads2twobit_seqlen_eqlen(const GtReads2Twobit *r2t);
unsigned long gt_reads2twobit_seqlen_max(const GtReads2Twobit *r2t);
unsigned long gt_reads2twobit_seqlen_min(const GtReads2Twobit *r2t);
unsigned long gt_reads2twobit_total_seqlength(const GtReads2Twobit *r2t);
unsigned long gt_reads2twobit_nof_invalid_seqs(const GtReads2Twobit *r2t);
unsigned long gt_reads2twobit_invalid_seqs_totallength(
    const GtReads2Twobit *r2t);

/* Writes the sequence collection to disk in a GtEncseq-compatible format;
   sets the separator positions to the less frequent character when needed;
   it must be called after ; returns 0 on success. */
int gt_reads2twobit_write_encseq(GtReads2Twobit *r2t, GtError *err);

/* writes the sequence collection to disk in MultiFasta format;
   it must be called after ; if  is not NULL,
   then skips any sequence for which the corresponding bit is set */
int gt_reads2twobit_write_fasta(const GtReads2Twobit *r2t, char *path,
    GtBitsequence *skip, GtError *err);

/* decodes the specified sequence in Fasta format; the  buffer
   must be large enough */
void gt_reads2twobit_decode_sequence(const GtReads2Twobit *r2t,
    unsigned long seqnum, char *decoded);

/* decodes the sequences  to +-1
   in MultiFasta format and outputs to ; if  is not NULL,
   then skips any sequence for which the corresponding bit is set */
void gt_reads2twobit_decode_range(const GtReads2Twobit *r2t,
    GtFile *outfp, unsigned long seqnum_from, unsigned long nofseqs,
    const GtBitsequence *skip);

/* writes the sequence  to ; starts writing at
  the -th character encoded by the  code;
  returns a pointer to the next buffer position where a code is not complete
  and sets <*lastcodeoffsetptr> to the offset of the last code
  (which can be used as  for subsequent calls to the function)
 */
GtTwobitencoding* gt_reads2twobit_write_encoded(GtReads2Twobit *r2t,
    unsigned long seqnum, GtTwobitencoding *outputbuffer,
    GtTwobitencoding outputoffset, GtTwobitencoding *lastcodeoffsetptr);

/* outputs the seppos array to ;
  if  is not NULL, then skips any position
  for which the corresponding bit is set */
int gt_reads2twobit_write_seppos(GtReads2Twobit *r2t, char* path,
    GtBitsequence *skip, GtError *err);

/* delete the sequences for which a bit is set in the list;
   for paired reads: both members of a pair are deleted */
void gt_reads2twobit_delete_sequences(GtReads2Twobit *r2t, GtBitsequence *list);

/* pointer to the internal twobitencoding representation;
   it must be called after  */
GtTwobitencoding *gt_reads2twobit_export_twobitencoding(
    const GtReads2Twobit *r2t);

/* pointer to the internal seppos array;
   it must be called after  */
unsigned long *gt_reads2twobit_export_seppos(const GtReads2Twobit *r2t);

/* sort the sequences according to the specified comparator function  */
void gt_reads2twobit_sort(GtReads2Twobit *r2t, GtCompareWithData cmp,
    void *cmp_data);

/* write the libraries information to disk */
int gt_reads2twobit_write_libraries_table(const GtReads2Twobit *r2t,
    char *path, GtError *err);

#define GT_READS2TWOBIT_LIBSPEC_HELPMSG \
  "specify a list of input libraries (Fasta/FastQ); for single-end " \
  "libraries use the filename (which is not allowed to contain ':' " \
  "symbols); for paired-end libraries with reads interleaved (f,r,f,r,...) "\
  "in a single file use the notation :[,] " \
  "(stdev may be omitted); for paired-end with reads in two files (f, r) " \
  "use the notation ::[,]"

#endif
genometools-1.5.1/src/match/reads_library.c000066400000000000000000000047531211610345200207260ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/file.h"
#include "match/reads_library.h"

int gt_reads_library_table_write(GtReadsLibrary *lib_table,
    unsigned long noflibs, const char *path, GtError *err)
{
  GtFile *file;
  file = gt_file_new(path, "w", err);
  if (file == NULL)
    return -1;
  else
  {
    gt_file_xwrite(file, &noflibs, sizeof (noflibs));
    gt_file_xwrite(file, lib_table, sizeof (*lib_table) * noflibs);
    gt_file_delete(file);
  }
  return 0;
}

GtReadsLibrary* gt_reads_library_table_read(const char *path, GtError *err,
    unsigned long *noflibs)
{
  GtFile *file;
  GtReadsLibrary *lib_table = NULL;
  file = gt_file_new(path, "r", err);
  if (file != NULL)
  {
    int freadretval;
    gt_assert(noflibs != NULL);
    freadretval = gt_file_xread(file, noflibs, sizeof (noflibs));
    if ((size_t)freadretval != sizeof (noflibs))
    {
      gt_error_set(err, "library file %s: "
          "error by reading number of libraries", path);
    }
    else if (*noflibs == 0)
    {
      gt_error_set(err, "library file %s: "
          "number of libraries is 0", path);
    }
    else
    {
      const size_t lib_table_size = sizeof (*lib_table) * (*noflibs);
      lib_table = gt_malloc(lib_table_size);
      freadretval = gt_file_xread(file, lib_table, lib_table_size);
      if ((size_t)freadretval != lib_table_size)
      {
        gt_error_set(err, "library file %s: "
            "error by reading libraries table "
            "(%lu bytes expected, %d bytes read)",
            path, (unsigned long)lib_table_size, freadretval);
        gt_free(lib_table);
        lib_table = NULL;
      }
    }
    gt_file_delete(file);
  }
  return lib_table;
}
genometools-1.5.1/src/match/reads_library.h000066400000000000000000000025161211610345200207260ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef READS_LIBRARY_H
#define READS_LIBRARY_H

#include "core/error_api.h"

#define GT_READS_LIBRARY_TABLE_FILESUFFIX ".rlt"

typedef struct {
  unsigned long first_seqnum;
  unsigned long nofseqs;
  unsigned long insertlength;
  bool paired;
} GtReadsLibrary;

int gt_reads_library_table_write(GtReadsLibrary *lib_table,
    unsigned long noflibs, const char *path, GtError *err);

GtReadsLibrary* gt_reads_library_table_read(const char *path, GtError *err,
    unsigned long *noflibs);

#endif
genometools-1.5.1/src/match/revcompl.c000066400000000000000000000030051211610345200177200ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/types_api.h"
#include "core/readmode.h"

void gt_inplace_reversecomplement(GtUchar *seq,unsigned long len)
{
  GtUchar tmp, *frontptr, *backptr;

  for (frontptr = seq, backptr = seq + len - 1;
       frontptr < backptr; frontptr++, backptr--)
  {
    tmp = *frontptr;
    *frontptr = GT_COMPLEMENTBASE(*backptr);
    *backptr = GT_COMPLEMENTBASE(tmp);
  }
}

void gt_copy_reversecomplement(GtUchar *dest,const GtUchar *src,
                               unsigned long len)
{
  GtUchar *destptr;
  const GtUchar *srcptr;

  for (destptr = dest, srcptr = src + len - 1;
       destptr < dest + len; destptr++, srcptr--)
  {
    *destptr = GT_COMPLEMENTBASE(*srcptr);
  }
}
genometools-1.5.1/src/match/revcompl.h000066400000000000000000000021301211610345200177230ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef REVCOMPL_H
#define REVCOMPL_H

#include "core/types_api.h"

void gt_inplace_reversecomplement(GtUchar *seq,unsigned long len);
void gt_copy_reversecomplement(GtUchar *dest,const GtUchar *src,
                               unsigned long len);

#endif
genometools-1.5.1/src/match/sarr-def.h000066400000000000000000000122031211610345200176010ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SARR_DEF_H
#define SARR_DEF_H

#include 
#include "core/defined-types.h"
#include "core/encseq.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/codetype.h"

#include "lcpoverflow.h"
#include "bcktab.h"

#define FILEBUFFERSIZE 4096

#define SARR_ESQTAB 1U
#define SARR_SUFTAB (1U << 1)
#define SARR_LCPTAB (1U << 2)
#define SARR_BWTTAB (1U << 3)
#define SARR_DESTAB (1U << 4)
#define SARR_SDSTAB (1U << 5)
#define SARR_BCKTAB (1U << 6)
#define SARR_SSPTAB (1U << 7)

#define SARR_ALLTAB (SARR_ESQTAB |\
                     SARR_SUFTAB |\
                     SARR_LCPTAB |\
                     SARR_BWTTAB |\
                     SARR_DESTAB |\
                     SARR_SSPTAB)

#define DECLAREBufferedfiletype(TYPE)\
        typedef struct\
        {\
          unsigned int nextfree,\
                       nextread;\
          TYPE *bufferedfilespace;\
          FILE *fp;\
        } GtBufferedfile_ ## TYPE

#define DECLAREREADFUNCTION(TYPE)\
        GT_UNUSED static int gt_readnextfromstream_ ## TYPE (TYPE *val,\
                                                  GtBufferedfile_ ## TYPE *buf)\
        {\
          if (buf->nextread >= buf->nextfree)\
          {\
            buf->nextfree = (unsigned int) fread(buf->bufferedfilespace,\
                                                 sizeof (TYPE),\
                                                 (size_t) FILEBUFFERSIZE,\
                                                 buf->fp);\
            if (ferror(buf->fp))\
            {\
              fprintf(stderr,"error when trying to read next %s",#TYPE);\
              exit(GT_EXIT_PROGRAMMING_ERROR);\
            }\
            buf->nextread = 0;\
            if (buf->nextfree == 0)\
            {\
              return 0;\
            }\
          }\
          *val = buf->bufferedfilespace[buf->nextread++];\
          return 1;\
        }

DECLAREBufferedfiletype(GtUlong);
DECLAREREADFUNCTION(GtUlong);

#ifdef _LP64
DECLAREBufferedfiletype(uint32_t);
DECLAREREADFUNCTION(uint32_t);
#endif

DECLAREBufferedfiletype(GtUchar);
DECLAREREADFUNCTION(GtUchar);

DECLAREBufferedfiletype(Largelcpvalue);
DECLAREREADFUNCTION(Largelcpvalue);

typedef unsigned long ESASuffixptr;

#define ESASUFFIXPTRGET(TAB,IDX)     TAB[IDX]

typedef struct
{
  GtEncseq *encseq;
  Definedunsignedlong numoflargelcpvalues; /* only in esa-map.c */
  Defineddouble averagelcp;
  Definedunsignedlong longest; /* for BWT */
  GtReadmode readmode; /* relevant when reading the encoded sequence */
  bool mirroredencseq;
  unsigned long numberofallsortedsuffixes;
  /* either with mapped input */
  const ESASuffixptr *suftab;
  const GtUchar *lcptab;
  const Largelcpvalue *llvtab;
  const GtUchar *bwttab;
  unsigned int prefixlength;
  GtBcktab *bcktab;
  /* or with streams */
#ifdef _LP64
  GtBufferedfile_uint32_t suftabstream_uint32_t;
#endif
  GtBufferedfile_GtUlong suftabstream_GtUlong;
  GtBufferedfile_GtUchar bwttabstream,
                         lcptabstream;
  GtBufferedfile_Largelcpvalue llvtabstream;
} Suffixarray;

/*@unused@*/ static inline const Largelcpvalue *getlargelcpvalue(
                       const Suffixarray *suffixarray,
                       unsigned long pos)
{
  const Largelcpvalue *leftptr, *rightptr, *midptr;
  unsigned long len;

  gt_assert(suffixarray->numoflargelcpvalues.defined);

  leftptr = suffixarray->llvtab;
  rightptr = suffixarray->llvtab +
             suffixarray->numoflargelcpvalues.valueunsignedlong - 1;

  while (leftptr<=rightptr)
  {
    len = (unsigned long) (rightptr-leftptr);
    midptr = leftptr + GT_DIV2(len);
    if (pos < midptr->position)
    {
      rightptr = midptr - 1;
    } else
    {
      if (pos > midptr->position)
      {
        leftptr = midptr + 1;
      } else
      {
        return midptr;
      }
    }
  }
  return NULL;
}

/*@unused@*/ static inline unsigned long lcptable_get(
                       const Suffixarray *suffixarray,
                       unsigned long pos)
{
  GtUchar smalllcpvalue;
  const Largelcpvalue *largelcpvalue;

  gt_assert(pos <= gt_encseq_total_length(suffixarray->encseq));
  smalllcpvalue = suffixarray->lcptab[pos];
  if (smalllcpvalue != LCPOVERFLOW)
  {
    return (unsigned long) smalllcpvalue;
  }
  largelcpvalue = getlargelcpvalue(suffixarray,pos);
  gt_assert(largelcpvalue != NULL);
  return largelcpvalue->value;
}

#endif
genometools-1.5.1/src/match/seqabstract.c000066400000000000000000000226511211610345200204150ustar00rootroot00000000000000/*
  Copyright (c) 2013 Stefan Kurtz 
  Copyright (c) 2013 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/chardef.h"
#include "core/types_api.h"
#include "core/ma_api.h"
#include "core/minmax.h"
#include "core/encseq.h"
#include "stamp.h"
#include "greedyedist.h"

struct GtSeqabstract
{
  bool isptr, cmpcharbychar;
  unsigned long len, offset, totallength;
  GtEncseqReader *esr;
  bool stoppossupport;
  union
  {
    const GtUchar *ptr;
    const GtEncseq *encseq;
  } seq;
};

GtSeqabstract *gt_seqabstract_new_empty(void)
{
  GtSeqabstract *sa = gt_malloc(sizeof *sa);

  sa->cmpcharbychar = false;
  sa->isptr = true;
  sa->len = 0;
  sa->esr = NULL;
  sa->totallength = 0;
  sa->stoppossupport = false;
  sa->offset = 0;
  sa->seq.ptr = NULL;
  return sa;
}

void gt_seqabstract_reinit_ptr(GtSeqabstract *sa,
                               const GtUchar *ptr,
                               unsigned long len,
                               unsigned long offset)
{
  sa->cmpcharbychar = false;
  sa->isptr = true;
  sa->len = len;
  sa->stoppossupport = false;
  sa->totallength = 0;
  sa->offset = offset;
  if (sa->esr != NULL)
  {
    gt_encseq_reader_delete(sa->esr);
    sa->esr = NULL;
  }
  sa->seq.ptr = ptr + offset;
}

GtSeqabstract *gt_seqabstract_new_ptr(const GtUchar *ptr,
                                      unsigned long len,
                                      unsigned long offset)
{
  GtSeqabstract *sa = gt_seqabstract_new_empty();

  gt_seqabstract_reinit_ptr(sa,ptr,len,offset);
  return sa;
}

void gt_seqabstract_reinit_encseq(GtSeqabstract *sa,
                                  const GtEncseq *encseq,
                                  unsigned long len,
                                  unsigned long offset)
{
  sa->cmpcharbychar = gt_encseq_has_twobitencoding(encseq) ? false : true;
  sa->isptr = false;
  sa->len = len;
  if (sa->esr != NULL)
  {
    if (encseq != sa->seq.encseq)
    {
      gt_encseq_reader_delete(sa->esr);
      sa->esr = gt_encseq_create_reader_with_readmode(encseq,
                                                      GT_READMODE_FORWARD,0);
    }
  } else
  {
    sa->esr = gt_encseq_create_reader_with_readmode(encseq,
                                                    GT_READMODE_FORWARD,0);
  }
  sa->stoppossupport = gt_encseq_has_twobitencoding_stoppos_support(encseq);
  sa->offset = offset;
  sa->seq.encseq = encseq;
  sa->totallength = gt_encseq_total_length(encseq);
}

GtSeqabstract *gt_seqabstract_new_encseq(const GtEncseq *encseq,
                                         unsigned long len,
                                         unsigned long offset)
{
  GtSeqabstract *sa = gt_seqabstract_new_empty();

  gt_seqabstract_reinit_encseq(sa, encseq, len, offset);
  return sa;
}

unsigned long gt_seqabstract_length_get(const GtSeqabstract *sa)
{
  return sa->len;
}

void gt_seqabstract_delete(GtSeqabstract *sa)
{
  gt_encseq_reader_delete(sa->esr);
  gt_free(sa);
}

GtUchar gt_seqabstract_encoded_char(const GtSeqabstract *sa,
                                    unsigned long idx)
{
  return sa->isptr
           ? sa->seq.ptr[idx]
           : gt_encseq_get_encoded_char(sa->seq.encseq,
                                        sa->offset + idx,
                                        GT_READMODE_FORWARD);
}

#define GT_SEQABSTRACT_CMPCHAR(VARA,VARB)\
        if ((VARA) != (VARB) || ISSPECIAL(VARA))\
        {\
          break;\
        }

unsigned long gt_seqabstract_lcp(bool forward,
                                 const GtSeqabstract *useq,
                                 const GtSeqabstract *vseq,
                                 unsigned long leftstart,
                                 unsigned long rightstart,
                                 unsigned long minlen)
{
  unsigned long lcp;
  GtUchar a, b;

  if (minlen == 0)
  {
    return 0;
  }
  if (useq->isptr)
  {
    if (vseq->isptr)
    {
      if (useq->seq.ptr == vseq->seq.ptr && useq->offset == vseq->offset &&
          leftstart == rightstart)
      {
        for (lcp = 0; lcp < minlen; lcp++)
        {
          a = useq->seq.ptr[forward ? leftstart + lcp : leftstart - lcp];
          if (ISSPECIAL(a))
          {
            break;
          }
        }
      } else
      {
        for (lcp = 0; lcp < minlen; lcp++)
        {
          a = useq->seq.ptr[forward ? leftstart + lcp : leftstart - lcp];
          b = vseq->seq.ptr[forward ? rightstart + lcp : rightstart - lcp];
          GT_SEQABSTRACT_CMPCHAR(a,b);
        }
      }
    } else
    {
      for (lcp = 0; lcp < minlen; lcp++)
      {
        a = useq->seq.ptr[forward ? leftstart + lcp : leftstart - lcp];
        b = gt_encseq_get_encoded_char(vseq->seq.encseq,
                                       vseq->offset +
                                       (forward ? rightstart + lcp
                                                : rightstart - lcp),
                                       GT_READMODE_FORWARD);
        GT_SEQABSTRACT_CMPCHAR(a,b);
      }
    }
  } else
  {
    if (vseq->isptr)
    {
      for (lcp = 0; lcp < minlen; lcp++)
      {
        a = gt_encseq_get_encoded_char(useq->seq.encseq,
                                       useq->offset +
                                       (forward ? leftstart + lcp
                                                : leftstart - lcp),
                                       GT_READMODE_FORWARD);
        b = vseq->seq.ptr[forward ? rightstart + lcp : rightstart - lcp];
        GT_SEQABSTRACT_CMPCHAR(a,b);
      }
    } else
    {
      if (!useq->cmpcharbychar && !vseq->cmpcharbychar)
      {
        if (useq->seq.encseq == vseq->seq.encseq &&
            useq->offset + leftstart == vseq->offset + rightstart)
        {
          if (useq->stoppossupport)
          {
            unsigned long stoppos;
            const unsigned long startpos
               = forward ? (useq->offset + leftstart)
                         : GT_REVERSEPOS(useq->totallength,
                                         useq->offset + leftstart);

            gt_encseq_reader_reinit_with_readmode(useq->esr,
                                                  useq->seq.encseq,
                                                  forward
                                                    ? GT_READMODE_FORWARD
                                                    : GT_READMODE_REVERSE,
                                                  startpos);
            stoppos = gt_getnexttwobitencodingstoppos(forward,useq->esr);
            if (!forward)
            {
              stoppos = GT_REVERSEPOS(useq->totallength+1,stoppos);
            }
            gt_assert(startpos <= stoppos);
            lcp = MIN(minlen,stoppos - startpos);
          } else
          {
            unsigned long startpos = useq->offset + leftstart;
            for (lcp = 0; lcp < minlen; lcp++)
            {
              a = gt_encseq_get_encoded_char(useq->seq.encseq,
                                             forward ? (startpos + lcp)
                                                     : (startpos - lcp),
                                             GT_READMODE_FORWARD);
              if (ISSPECIAL(a))
              {
                break;
              }
            }
          }
        } else
        {
          for (lcp = 0; lcp < minlen; lcp++)
          {
            a = gt_encseq_get_encoded_char(useq->seq.encseq,
                                           useq->offset +
                                           (forward ? leftstart + lcp
                                                    : leftstart - lcp),
                                           GT_READMODE_FORWARD);
            b = gt_encseq_get_encoded_char(vseq->seq.encseq,
                                           vseq->offset +
                                           (forward ? rightstart + lcp
                                                    : rightstart - lcp),
                                           GT_READMODE_FORWARD);
            GT_SEQABSTRACT_CMPCHAR(a,b);
          }
        }
      } else
      {
        for (lcp = 0; lcp < minlen; lcp++)
        {
          a = gt_encseq_get_encoded_char(useq->seq.encseq,
                                         useq->offset +
                                         (forward ? leftstart + lcp
                                                  : leftstart - lcp),
                                         GT_READMODE_FORWARD);
          b = gt_encseq_get_encoded_char(vseq->seq.encseq,
                                         vseq->offset +
                                         (forward ? rightstart + lcp
                                                  : rightstart - lcp),
                                         GT_READMODE_FORWARD);
          GT_SEQABSTRACT_CMPCHAR(a,b);
        }
      }
    }
  }
  return lcp;
}
genometools-1.5.1/src/match/seqabstract.h000066400000000000000000000047411211610345200204220ustar00rootroot00000000000000/*
  Copyright (c) 2013 Stefan Kurtz 
  Copyright (c) 2013 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SEQABSTRACT_H
#define SEQABSTRACT_H

#include "core/types_api.h"
#include "core/encseq_api.h"

typedef struct GtSeqabstract GtSeqabstract;

GtSeqabstract* gt_seqabstract_new_empty(void);

GtSeqabstract* gt_seqabstract_new_ptr(const GtUchar *ptr,
                                      unsigned long len,
                                      unsigned long offset);

GtSeqabstract* gt_seqabstract_new_encseq(const GtEncseq *encseq,
                                         unsigned long len,
                                         unsigned long offset);

void           gt_seqabstract_reinit_ptr(GtSeqabstract *sa,
                                         const GtUchar *ptr,
                                         unsigned long len,
                                         unsigned long offset);

void           gt_seqabstract_reinit_encseq(GtSeqabstract *sa,
                                            const GtEncseq *encseq,
                                            unsigned long len,
                                            unsigned long offset);

unsigned long  gt_seqabstract_length_get(const GtSeqabstract *sa);

GtUchar        gt_seqabstract_encoded_char(const GtSeqabstract *sa,
                                          unsigned long idx);

void           gt_seqabstract_delete(GtSeqabstract *sa);

unsigned long gt_seqabstract_lcp(bool forward,
                                 const GtSeqabstract *useq,
                                 const GtSeqabstract *vseq,
                                 unsigned long leftstart,
                                 unsigned long rightstart,
                                 unsigned long minlen);

#endif
genometools-1.5.1/src/match/seqnumrelpos.c000066400000000000000000000046041211610345200206340ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq_api.h"
#include "core/ma.h"
#include "seqnumrelpos.h"

struct GtSeqnumrelpos
{
  const GtEncseq *encseq;
  unsigned long relposmask;
  unsigned int bitsforrelpos;
};

GtSeqnumrelpos *gt_seqnumrelpos_new(unsigned int bitsforrelpos,
                                    const GtEncseq *encseq)
{
  GtSeqnumrelpos *snrp;

  snrp = gt_malloc(sizeof (*snrp));
  snrp->bitsforrelpos = bitsforrelpos;
  snrp->relposmask = (1UL << snrp->bitsforrelpos) - 1;
  snrp->encseq = encseq;
  return snrp;
}

void gt_seqnumrelpos_delete(GtSeqnumrelpos *snrp)
{
  gt_free(snrp);
}

unsigned long gt_seqnumrelpos_decode_pos(const GtSeqnumrelpos *snrp,
                                         unsigned long seqnumrelpos)
{
  unsigned long seqnum, relpos;

  seqnum = seqnumrelpos >> snrp->bitsforrelpos;
  relpos = seqnumrelpos & snrp->relposmask;
  return gt_encseq_seqstartpos(snrp->encseq,seqnum) + relpos;
}

unsigned long gt_seqnumrelpos_decode_seqnum(const GtSeqnumrelpos *snrp,
                                            unsigned long seqnumrelpos)
{
  return seqnumrelpos >> snrp->bitsforrelpos;
}

unsigned long gt_seqnumrelpos_decode_relpos(const GtSeqnumrelpos *snrp,
                                            unsigned long seqnumrelpos)
{
  return seqnumrelpos & snrp->relposmask;
}

unsigned long gt_seqnumrelpos_encode(const GtSeqnumrelpos *snrp,
                                     unsigned long seqnum,
                                        unsigned long relpos)
{
  gt_assert(relpos <= snrp->relposmask);
  return (seqnum << snrp->bitsforrelpos) | relpos;
}
genometools-1.5.1/src/match/seqnumrelpos.h000066400000000000000000000033251211610345200206400ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SEQNUMRELPOS_H
#define SEQNUMRELPOS_H

typedef struct GtSeqnumrelpos GtSeqnumrelpos;

GtSeqnumrelpos *gt_seqnumrelpos_new(unsigned int bitsforrelpos,
                                    const GtEncseq *encseq);

void gt_seqnumrelpos_delete(GtSeqnumrelpos *snrp);

unsigned long gt_seqnumrelpos_decode_pos(const GtSeqnumrelpos *snrp,
                                         unsigned long seqnumrelpos);

unsigned long gt_seqnumrelpos_decode_seqnum(const GtSeqnumrelpos *snrp,
                                            unsigned long seqnumrelpos);

unsigned long gt_seqnumrelpos_decode_relpos(const GtSeqnumrelpos *snrp,
                                            unsigned long seqnumrelpos);

unsigned long gt_seqnumrelpos_encode(const GtSeqnumrelpos *snrp,
                                     unsigned long seqnum,
                                     unsigned long relpos);

#endif
genometools-1.5.1/src/match/sfx-apfxlen.c000066400000000000000000000133071211610345200203320ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include "core/error.h"
#include "core/minmax.h"
#include "core/codetype.h"
#include "core/logger.h"
#include "bcktab.h"
#include "sfx-apfxlen.h"
#include "initbasepower.h"

/*
  We need \texttt{prefixlenbits} bits to store the length of
  a matching prefix. So we can store the following maximal value
  in the remaining bits.
*/

#define MAXREMAININGAFTERPREFIXLEN(PFXLENBITS)\
        ((((GtCodetype) 1) << (32-(PFXLENBITS))) - 1)

/*
  We allow to choose the prefixlength \(l\) in such a way that the size of
  table bcktab never exceeds the
  $\texttt{GT_MAXMULTIPLIEROFTOTALLENGTH}\cdot n$,
  where \(n\) is the total length of the input sequence.
*/

#define GT_MAXMULTIPLIEROFTOTALLENGTH   4.0
#define GT_MAXVALUEWITHBITS(BITNUM)     ((1U << (BITNUM)) - 1)

static unsigned int prefixlengthwithmaxspace(unsigned int numofchars,
                                             unsigned long maxbytes,
                                             double factor,
                                             unsigned long maxvalue,
                                             bool withspecialsuffixes)
{
  unsigned int prefixlength;
  uint64_t sizeofrep;

#ifdef WITHINFO
  printf("maxbytes = %lu\n",(unsigned long) (maxbytes * factor));
#endif
  for (prefixlength = 1U; /* Nothing */; prefixlength++)
  {
    sizeofrep = gt_bcktab_sizeoftable(numofchars,prefixlength,
                                      maxvalue,withspecialsuffixes);
#ifdef WITHINFO
    printf("sizeofrep = %lu, after divide %lu\n",(unsigned long) sizeofrep,
                                        (unsigned long) (sizeofrep/factor));
#endif
    if (sizeofrep/factor > (uint64_t) maxbytes)
    {
#ifdef WITHINFO
      printf("prefixlengthwithmaxspace = %u\n",prefixlength-1);
#endif
      return prefixlength-1;
    }
  }
  /*@ignore@*/
  return 1U;
  /*@end@*/
}

unsigned int gt_recommendedprefixlength(unsigned int numofchars,
                                        unsigned long totallength,
                                        double recommendedmultiplier,
                                        bool withspecialsuffixes)
{
  unsigned int prefixlength;

  prefixlength = prefixlengthwithmaxspace(numofchars,totallength,
                                          recommendedmultiplier,
                                          totallength+1,
                                          withspecialsuffixes);
  if (prefixlength == 0)
  {
    return 1U;
  } else
  {
    unsigned int mbp = gt_maxbasepower(numofchars);
    if (mbp >= 1U)
    {
      return MIN(mbp,prefixlength);
    } else
    {
      return prefixlength;
    }
  }
}

unsigned int gt_whatisthemaximalprefixlength(unsigned int numofchars,
                                             unsigned long totallength,
                                             unsigned int prefixlenbits,
                                             bool withspecialsuffixes)
{
  unsigned int maxprefixlen, mbp;

  maxprefixlen = prefixlengthwithmaxspace(numofchars,totallength,
                                          GT_MAXMULTIPLIEROFTOTALLENGTH,
                                          totallength+1,
                                          withspecialsuffixes);
  mbp = gt_maxbasepower(numofchars);
  maxprefixlen = MIN(mbp,maxprefixlen);
  if (prefixlenbits > 0)
  {
    unsigned int tmplength;
    tmplength
      = prefixlengthwithmaxspace(numofchars,
                                 (unsigned long)
                                 MAXREMAININGAFTERPREFIXLEN(prefixlenbits),
                                 GT_RECOMMENDED_MULTIPLIER_DEFAULT,
                                 totallength+1,
                                 withspecialsuffixes);
    if (tmplength > 0 && maxprefixlen > tmplength)
    {
      maxprefixlen = tmplength;
    }
    tmplength = GT_MAXVALUEWITHBITS(prefixlenbits);
    if (tmplength > 0 && maxprefixlen > tmplength)
    {
      maxprefixlen = tmplength;
    }
  }
  if (maxprefixlen == 0)
  {
    return 1U;
  }
  return maxprefixlen;
}

int gt_checkprefixlength(unsigned int maxprefixlen,
                      unsigned int prefixlength,
                      GtError *err)
{
  gt_error_check(err);
  if (maxprefixlen < prefixlength)
  {
    gt_error_set(err,"prefix length %u is too large, maximal prefix length "
                      "for this input size and alphabet size is %u",
                      prefixlength,
                      maxprefixlen);
    return -1;
  }
  return 0;
}

void gt_showmaximalprefixlength(GtLogger *logger,
                             unsigned int maxprefixlen,
                             unsigned int recommended)
{
  gt_logger_log(logger,
              "for this input size and alphabet size, "
              "the maximal prefixlength");
  gt_logger_log(logger,"(argument of option -pl) is %u,",maxprefixlen);
  gt_logger_log(logger,"the recommended prefixlength is %u",recommended);
}
genometools-1.5.1/src/match/sfx-apfxlen.h000066400000000000000000000034651211610345200203430ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_APFXLEN_H
#define SFX_APFXLEN_H

#include "core/error_api.h"

#define GT_RECOMMENDED_MULTIPLIER_DEFAULT 0.25

unsigned int gt_recommendedprefixlength(unsigned int numofchars,
                                        unsigned long totallength,
                                        double recommendedmultiplier,
                                        bool withspecialsuffixes);

unsigned int gt_whatisthemaximalprefixlength(unsigned int numofchars,
                                          unsigned long totallength,
                                          unsigned int prefixlenbits,
                                          bool withspecialsuffixes);

int gt_checkprefixlength(unsigned int maxprefixlen,
                         unsigned int prefixlength,
                         GtError *err);

void gt_showmaximalprefixlength(GtLogger *logger,
                                unsigned int maxprefixlen,
                                unsigned int recommended);

#endif
genometools-1.5.1/src/match/sfx-bentsedg.c000066400000000000000000001566271211610345200205050ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/assert_api.h"
#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/minmax.h"
#include "core/arraydef.h"
#include "core/unused_api.h"
#include "core/types_api.h"
#include "core/encseq.h"
#include "bcktab.h"
#include "kmer2string.h"
#include "sfx-radixsort.h"
#include "sfx-bltrie.h"
#include "sfx-copysort.h"
#include "sfx-bentsedg.h"
#include "sfx-lcpvalues.h"
#include "sfx-suftaborder.h"
#include "sfx-suffixgetset.h"
#include "sfx-shortreadsort.h"

#define ACCESSCHARRAND(POS)    gt_encseq_get_encoded_char(bsr->encseq,\
                                                          POS,bsr->readmode)
#define ACCESSCHARSEQ(ESR)     gt_encseq_reader_next_encoded_char(ESR)
#define ISNOTEND(POS)          ((POS) < bsr->totallength &&\
                                ISNOTSPECIAL(ACCESSCHARRAND(POS)))

#define DEREFSTOPPOSSEQ(VAR,POS,STOPPOS,ESR)\
        (((POS) < (STOPPOS) && ISNOTSPECIAL(VAR = ACCESSCHARSEQ(ESR))) ?\
        ((unsigned long) VAR) : GT_UNIQUEINT(POS))

#define DEREFSEQ(VAR,POS,ESR) DEREFSTOPPOSSEQ(VAR,POS,bsr->totallength,ESR)

#define BS_SWAPARRAY(TMP,SUBBUCKETLEFT,IDX1,IDX2)\
        if ((IDX1) != (IDX2))\
        {\
          TMP = gt_suffixsortspace_get(bsr->sssp,SUBBUCKETLEFT,IDX1);\
          gt_suffixsortspace_set(bsr->sssp,SUBBUCKETLEFT,IDX1,\
                                 gt_suffixsortspace_get(bsr->sssp,\
                                                        SUBBUCKETLEFT,\
                                                        IDX2));\
          gt_suffixsortspace_set(bsr->sssp,SUBBUCKETLEFT,IDX2,TMP);\
        }

#define STACKTOP\
        bsr->mkvauxstack.spaceGtMKVstack[bsr->mkvauxstack.nextfreeGtMKVstack]

#define GT_BSR_UPDATELCP(MINVAL,MAXVAL,LCP)\
        if ((MINVAL) > (LCP))\
        {\
          MINVAL = LCP;\
        }\
        GT_UPDATE_MAX(MAXVAL,LCP)

#define CMPCHARBYCHARPTR2INT(VAR,SUBBUCKETLEFT,TMPVAR,IDX)\
        VAR = (((cptr = gt_suffixsortspace_get(bsr->sssp,SUBBUCKETLEFT,IDX)+\
                        depth)\
                < bsr->totallength &&\
                ISNOTSPECIAL(TMPVAR = ACCESSCHARRAND(cptr)))\
                    ? ((unsigned long) TMPVAR) : GT_UNIQUEINT(cptr))

typedef GtEndofTwobitencoding GtSfxcmp;

#define PTR2INTSTOREPOS(TMPVAR,SUBBUCKETLEFT,IDX,POSASSIGNMENT)\
        {\
          unsigned long pos\
            = gt_suffixsortspace_get(bsr->sssp,SUBBUCKETLEFT,IDX);\
          POSASSIGNMENT;\
          TMPVAR.referstartpos = pos;\
          if (pos + depth < bsr->totallength)\
          {\
            pos += depth;\
            (void) gt_encseq_extract2bitencwithtwobitencodingstoppos(&(TMPVAR),\
                                                                 bsr->esr1,\
                                                                 bsr->encseq,\
                                                                 bsr->readmode,\
                                                                 pos);\
          } else\
          {\
            TMPVAR.tbe = 0;\
            TMPVAR.unitsnotspecial = 0;\
          }\
        }

#define PTR2INT(TMPVAR,SUBBUCKETLEFT,IDX)\
        PTR2INTSTOREPOS(TMPVAR,SUBBUCKETLEFT,IDX,/* Nothing */)

#define Sfxdocompare(COMMONUNITS,X,Y)\
        ret##X##Y = gt_encseq_compare_pairof_twobitencodings(bsr->fwd,\
                                                             bsr->complement,\
                                                             COMMONUNITS,&X,&Y)

#define GtSfxcmpEQUAL(X,Y)      (ret##X##Y == 0)
#define GtSfxcmpSMALLER(X,Y)    (ret##X##Y < 0)
#define GtSfxcmpGREATER(X,Y)    (ret##X##Y > 0)

typedef struct
{
  unsigned long subbucketleft,
                width,
                depth;
} GtMKVstack;

typedef struct
{
  GtEndofTwobitencoding etbe;
  unsigned long suftaboffset;
} GtMedianinfo;

typedef GtMedianinfo GtMedianElem;

typedef struct
{
  unsigned long suffix;
  unsigned char lcpwithpivot;
  char cmpresult;
} GtCountingsortinfo;

GT_DECLAREARRAYSTRUCT(GtMKVstack);

typedef struct
{
  const GtEncseq *encseq;
  GtEncseqReader *esr1, /* XXX be careful with threads */
                 *esr2;
  GtReadmode readmode;
  bool fwd, complement;
  unsigned long totallength;
  GtArrayGtMKVstack mkvauxstack; /* XXX be careful with threads */
  GtLcpvalues *tableoflcpvalues;
  GtMedianinfo *medianinfospace;
  GtCountingsortinfo *countingsortinfo;
  const Sfxstrategy *sfxstrategy;
  unsigned int sortmaxdepth,
               prefixlength;
  GtBlindtrie *blindtrie;
  unsigned long leftlcpdist[GT_UNITSIN2BITENC],
                rightlcpdist[GT_UNITSIN2BITENC];
  GtSuffixsortspace *sssp;
  GtProcessunsortedsuffixrange processunsortedsuffixrange;
  void *processunsortedsuffixrangeinfo;
  bool *equalwithprevious;
  size_t sizeofworkspace;
  unsigned long countinsertionsort,
                counttqsort,
                countshortreadsort,
                countradixsort,
                countcountingsort,
                countbltriesort,
                srs_maxremain; /* only relevant for short read sort */
  unsigned long radixsortminwidth,
                radixsortmaxwidth,
                shortreadsort_maxwidth;
  GtShortreadsortworkinfo *srsw;
  const GtTwobitencoding *twobitencoding;
  GtRadixsortstringinfo *rsi;
} GtBentsedgresources;

#ifdef WITHCHECKSTARTPOINTER
static unsigned int checkstartpointorder(const unsigned long *left,
                                         const unsigned long *right)
{
  const unsigned long *ptr;
  bool ascending;

  gt_assert(left < right);
  gt_assert(*left != *(left+1));
  ascending = (*left < *(left+1)) ? true : false;
  for (ptr = left+1; ptr < right; ptr++)
  {
    gt_assert(*ptr != *(ptr+1));
    if (*ptr < *(ptr+1))
    {
      if (!ascending)
      {
        return 0;
      }
    } else
    {
      if (*ptr > *(ptr+1))
      {
        if (ascending)
        {
          return 0;
        }
      }
    }
  }
  return ascending ? 1U : 2U;
}
#endif

static unsigned long medianof3cmpcharbychar(const GtBentsedgresources *bsr,
                                            unsigned long subbucketleft,
                                            unsigned long depth,
                                            unsigned long a,
                                            unsigned long b,
                                            unsigned long c)
{
  unsigned long vala, valb, valc, cptr;
  GtUchar tmpavar, tmpbvar;

  CMPCHARBYCHARPTR2INT(vala,subbucketleft,tmpavar,a);
  CMPCHARBYCHARPTR2INT(valb,subbucketleft,tmpbvar,b);
  if (vala == valb)
  {
    return a;
  }
  CMPCHARBYCHARPTR2INT(valc,subbucketleft,tmpavar,c);
  if (vala == valc || valb == valc)
  {
    return c;
  }
  return vala < valb ?
        (valb < valc ? b : (vala < valc ? c : a))
      : (valb > valc ? b : (vala < valc ? a : c));
}

static unsigned long medianof3(const GtBentsedgresources *bsr,
                               unsigned long subbucketleft,
                               unsigned long depth,
                               unsigned long a,
                               unsigned long b,
                               unsigned long c)
{
  GtSfxcmp vala, valb, valc;
  GtCommonunits commonunits;
  int retvalavalb, retvalavalc, retvalbvalc;

  PTR2INT(vala,subbucketleft,a);
  PTR2INT(valb,subbucketleft,b);
  Sfxdocompare(&commonunits,vala,valb);
  if (GtSfxcmpEQUAL(vala,valb))
  {
    return a;
  }
  PTR2INT(valc,subbucketleft,c);
  Sfxdocompare(&commonunits,vala,valc);
  if (GtSfxcmpEQUAL(vala,valc))
  {
    return c;
  }
  Sfxdocompare(&commonunits,valb,valc);
  if (GtSfxcmpEQUAL(valb,valc))
  {
    return c;
  }
  return GtSfxcmpSMALLER(vala,valb) ?
        (GtSfxcmpSMALLER(valb,valc) ? b : (GtSfxcmpSMALLER(vala,valc) ? c : a))
      : (GtSfxcmpGREATER(valb,valc) ? b : (GtSfxcmpSMALLER(vala,valc) ? a : c));
}

static void bs_insertionsort(GtBentsedgresources *bsr,
                             unsigned long subbucketleft,
                             unsigned long width,
                             unsigned long offset)
{
  unsigned long sval1, sval2, pm, pl, startpos1, startpos2, lcplen = 0;
  int retval;
  GtCommonunits commonunits;

  bsr->countinsertionsort++;
  for (pm = 1UL; pm < width; pm++)
  {
    for (pl = pm; pl > 0; pl--)
    {
      sval1 = gt_suffixsortspace_get(bsr->sssp,subbucketleft,pl-1);
      sval2 = gt_suffixsortspace_get(bsr->sssp,subbucketleft,pl);
      if (bsr->sfxstrategy->cmpcharbychar)
      {
        startpos1 = sval1 + offset;
        if (startpos1 < bsr->totallength)
        {
          gt_encseq_reader_reinit_with_readmode(bsr->esr1, bsr->encseq,
                                                bsr->readmode, startpos1);
        }
        startpos2 = sval2 + offset;
        if (startpos2 < bsr->totallength)
        {
          gt_encseq_reader_reinit_with_readmode(bsr->esr2, bsr->encseq,
                                                bsr->readmode, startpos2);
        }
        for (;;)
        {
          unsigned long ccs, cct;
          GtUchar tmp1, tmp2;

          ccs = DEREFSEQ(tmp1,startpos1,bsr->esr1);
          cct = DEREFSEQ(tmp2,startpos2,bsr->esr2);
          if (ccs != cct)
          {
            lcplen = startpos2 - sval2;
            retval = (ccs < cct) ? -1 : 1;
            break;
          }
          startpos1++;
          startpos2++;
        }
      } else
      {
#ifdef SKDEBUG
        printf("%s[%lu,%lu] at offset %lu\n",__func__,sval1,sval2,offset);
        gt_encseq_showatstartpos(stdout,
                                 bsr->fwd,
                                 bsr->complement,
                                 bsr->encseq,
                                 sval1);
        gt_encseq_showatstartpos(stdout,
                                 bsr->fwd,
                                 bsr->complement,
                                 bsr->encseq,
                                 sval2);
#endif
        retval = gt_encseq_compare_viatwobitencoding(&commonunits,
                                                     bsr->encseq,
                                                     bsr->encseq,
                                                     bsr->readmode,
                                                     bsr->esr1,
                                                     bsr->esr2,
                                                     sval1,
                                                     sval2,
                                                     offset,
                                                     0);
        lcplen = commonunits.finaldepth;
      }
      gt_assert(retval != 0);
      if (bsr->tableoflcpvalues != NULL)
      {
        if (pl < pm && retval > 0)
        {
          gt_lcptab_update(bsr->tableoflcpvalues,subbucketleft,pl+1,
                           gt_lcptab_getvalue(bsr->tableoflcpvalues,
                                              subbucketleft,pl));
        }
        gt_lcptab_update(bsr->tableoflcpvalues,subbucketleft,pl,lcplen);
      }
      if (retval < 0)
      {
        break;
      }
      gt_suffixsortspace_set(bsr->sssp,subbucketleft,pl-1,sval2);
      gt_suffixsortspace_set(bsr->sssp,subbucketleft,pl,sval1);
    }
  }
}

static void bs_insertionsortmaxdepth(GtBentsedgresources *bsr,
                                     unsigned long subbucketleft,
                                     unsigned long width,
                                     unsigned long offset,
                                     unsigned long sortmaxdepth)
{
  unsigned long sval1, sval2, pm, pl, startpos1, startpos2,
                lcplen = 0, idx = 0;
  int retval;
  bool tempb;
  GtCommonunits commonunits;

  bsr->countinsertionsort++;
  for (pm = 1UL; pm < width; pm++)
  {
    for (pl = pm; pl > 0; pl--)
    {
      sval1 = gt_suffixsortspace_get(bsr->sssp,subbucketleft,pl-1);
      sval2 = gt_suffixsortspace_get(bsr->sssp,subbucketleft,pl);
      if (bsr->sfxstrategy->cmpcharbychar)
      {
        unsigned long endpos1, endpos2;

        endpos1 = sval1+sortmaxdepth;
        if (endpos1 > bsr->totallength)
        {
          endpos1 = bsr->totallength;
        }
        endpos2 = sval2+sortmaxdepth;
        if (endpos2 > bsr->totallength)
        {
          endpos2 = bsr->totallength;
        }
        startpos1 = sval1+offset;
        if (startpos1 < bsr->totallength)
        {
          gt_encseq_reader_reinit_with_readmode(bsr->esr1, bsr->encseq,
                                                bsr->readmode, startpos1);
        }
        startpos2 = sval2+offset;
        if (startpos2 < bsr->totallength)
        {
          gt_encseq_reader_reinit_with_readmode(bsr->esr2, bsr->encseq,
                                                bsr->readmode, startpos2);
        }
        for (;;)
        {
          unsigned long ccs, cct;
          GtUchar tmp1, tmp2;

          ccs = DEREFSTOPPOSSEQ(tmp1,startpos1,endpos1,bsr->esr1);
          cct = DEREFSTOPPOSSEQ(tmp2,startpos2,endpos2,bsr->esr2);
          lcplen = startpos2 - sval2;
          if (lcplen == sortmaxdepth)
          {
            retval = 0;
            break;
          }
          gt_assert(lcplen < sortmaxdepth);
          if (ccs != cct)
          {
            retval = (ccs < cct) ? -1 : 1;
            break;
          }
          startpos1++;
          startpos2++;
        }
      } else
      {
        gt_assert(offset < sortmaxdepth);
        retval = gt_encseq_compare_viatwobitencoding(&commonunits,
                                                     bsr->encseq,
                                                     bsr->encseq,
                                                     bsr->readmode,
                                                     bsr->esr1,
                                                     bsr->esr2,
                                                     sval1,
                                                     sval2,
                                                     offset,
                                                     sortmaxdepth);
        lcplen = commonunits.finaldepth;
        gt_assert(lcplen <= sortmaxdepth);
        if (lcplen == sortmaxdepth)
        {
          gt_assert(retval == 0);
        }
      }
#ifdef SKDEBUG
      printf("cmp %lu and %lu: retval = %d, lcplen = %lu\n",
             sval1, sval2, retval, (unsigned long) lcplen);
#endif
      if (bsr->tableoflcpvalues != NULL)
      {
        if (pl < pm && retval > 0)
        {
          gt_lcptab_update(bsr->tableoflcpvalues,subbucketleft,pl+1,
                           gt_lcptab_getvalue(bsr->tableoflcpvalues,
                                              subbucketleft,pl));
        }
        gt_lcptab_update(bsr->tableoflcpvalues,subbucketleft,pl,lcplen);
      }
      if (retval < 0)
      {
        break;
      }
      idx = pl;
      if (retval == 0)
      {
        gt_assert(idx > 0);
        bsr->equalwithprevious[idx] = true;
        break;
      }
      gt_suffixsortspace_set(bsr->sssp,subbucketleft,pl-1,sval2);
      gt_suffixsortspace_set(bsr->sssp,subbucketleft,pl,sval1);
      tempb = bsr->equalwithprevious[idx-1];
      bsr->equalwithprevious[idx-1] = bsr->equalwithprevious[idx];
      bsr->equalwithprevious[idx] = tempb;
    }
  }
  if (idx > 0)
  {
    unsigned long equalsrangewidth = 0;
    unsigned long bucketleftidx
     = gt_suffixsortspace_bucketleftidx_get(bsr->sssp);
#ifdef SKDEBUG
    printf("ordered suffix %lu\n",gt_suffixsortspace_get(bsr->sssp,
                                                         subbucketleft,0));
#endif
    for (idx = 1UL; idx < width; idx++)
    {
#ifdef SKDEBUG
      printf("ordered suffix %lu, equalwithprevious=%s\n",
              gt_suffixsortspace_get(bsr->sssp,subbucketleft,idx),
              bsr->equalwithprevious[idx] ? "true" : "false");
#endif
      if (bsr->equalwithprevious[idx])
      {
        bsr->equalwithprevious[idx] = false;
        equalsrangewidth++;
      } else
      {
        if (equalsrangewidth > 0)
        {
#ifdef SKDEBUG
          printf("process interval of width %lu\n",
                 equalsrangewidth + 1);
#endif
          if (bsr->processunsortedsuffixrange != NULL)
          {
            bsr->processunsortedsuffixrange(bsr->processunsortedsuffixrangeinfo,
                                            bucketleftidx + subbucketleft
                                                          + idx - 1
                                                          - equalsrangewidth,
                                            equalsrangewidth + 1, sortmaxdepth);
          }
          equalsrangewidth = 0;
        }
      }
    }
    if (equalsrangewidth > 0)
    {
#ifdef SKDEBUG
      printf("process interval of width %lu\n",
             equalsrangewidth + 1);
#endif
      if (bsr->processunsortedsuffixrange != NULL)
      {
        bsr->processunsortedsuffixrange(bsr->processunsortedsuffixrangeinfo,
                                        bucketleftidx + subbucketleft + width
                                                      - 1 - equalsrangewidth,
                                        equalsrangewidth + 1, sortmaxdepth);
      }
    }
  }
}

#define DOMEDIANCOMPARE(A,B)\
        gt_encseq_compare_pairof_twobitencodings(fwd,complement,&commonunits,\
                                                 &((A)->etbe),&((B)->etbe))

#define GT_MedianElemGREATER(A,B)  (DOMEDIANCOMPARE(A,B) > 0)

#define GT_MedianElemSWAP(A,B)     {\
                                     register GtMedianElem tmp = *(A);\
                                                           *(A) = *(B);\
                                                           *(B) = tmp;\
                                   }

/*
 *  This Quickselect routine is based on the algorithm described in
 *  "Numerical recipes in C", Second Edition,
 *  Cambridge University Press, 1992, Section 8.5, ISBN 0-521-43108-5
 *  This code by Nicolas Devillard - 1998. Public domain.
 */

static GtMedianElem *quickmedian (bool fwd,bool complement,
                                  GtMedianElem *arr,unsigned long width)
{
  GtMedianElem *low, *high, *median, *middle, *ll, *hh;
  GtCommonunits commonunits;

  gt_assert(width > 0);
  low = arr;
  high = arr + width - 1;
  median = low + GT_DIV2(width);
  for (;;)
  {
    if (high <= low)                   /* One element only */
    {
      return median;
    }
    if (high == low + 1)
    {                                  /* Two elements only */
      if (GT_MedianElemGREATER(low,high))
      {
        GT_MedianElemSWAP (low, high);
      }
      return median;
    }

    /* Find median of low, middle and high items; swap into position low */
    middle = low + GT_DIV2(high - low + 1);
    if (GT_MedianElemGREATER(middle,high))
    {
      GT_MedianElemSWAP (middle, high);
    }
    if (GT_MedianElemGREATER(low,high))
    {
      GT_MedianElemSWAP (low, high);
    }
    if (GT_MedianElemGREATER(middle,low))
    {
      GT_MedianElemSWAP (middle, low);
    }
    /* Swap low item (now in position middle) into position (low+1) */
    GT_MedianElemSWAP (middle, low + 1);

    /* Nibble from each end towards middle, swapping items when stuck */
    ll = low + 1;
    hh = high;
    for (;;)
    {
      do
      {
        ll++;
      } while (GT_MedianElemGREATER(low,ll));
      do
      {
        hh--;
      } while  (GT_MedianElemGREATER(hh,low));
      if (hh < ll)
      {
        break;
      }
      GT_MedianElemSWAP (ll, hh);
    }

    /* Swap middle item (in position low) back into correct position */
    GT_MedianElemSWAP (low, hh);

    /* Re-set active partition */
    if (hh <= median)
    {
      low = ll;
    }
    if (hh >= median)
    {
      high = hh - 1;
    }
  }
}

#ifdef WITHcheckmedian

static void checkmedian(bool fwd,
                        bool complement,
                        const GtMedianinfo *median,
                        const GtMedianinfo *space,
                        unsigned long width)
{
  unsigned long sum1, sum2, idx, smaller = 0, larger = 0, equal = 0, equalpart;
  unsigned int commonunits;
  int cmp;

  for (idx = 0; idx < width; idx++)
  {
    cmp = DOMEDIANCOMPARE(space + idx,median);
    if (cmp > 0)
    {
     larger++;
    } else
    {
      if (cmp < 0)
      {
        smaller++;
      } else
      {
        equal++;
      }
    }
  }
  if (smaller == larger)
  {
    return;
  }
  for (equalpart = 0; equalpart < equal; equalpart++)
  {
    sum1 = smaller + equalpart;
    sum2 = larger + (equal-1) - equalpart;
    if (sum1 < sum2)
    {
      if (sum1 + 1 == sum2)
      {
        return;
      }
    } else
    {
      if (sum1 > sum2)
      {
        if (sum1 == sum2 + 1)
        {
          return;
        }
      } else
      {
        return;
      }
    }
  }
  fprintf(stderr,"problem with equal=%lu,smaller=%lu,larger=%lu\n",
                  equal,smaller,larger);
  exit(GT_EXIT_PROGRAMMING_ERROR);
}
#endif

static unsigned long realmedian(const GtBentsedgresources *bsr,
                                unsigned long subbucketleft,
                                unsigned long width,
                                unsigned long depth)
{
  GtMedianinfo *medianptr;
  unsigned long idx;

  for (idx = 0; idx < width; idx++)
  {
    bsr->medianinfospace[idx].suftaboffset = idx;
    PTR2INT(bsr->medianinfospace[idx].etbe,subbucketleft,idx);
  }
  medianptr = quickmedian(bsr->fwd,bsr->complement,bsr->medianinfospace,width);
/*
  checkmedian(bsr->fwd,bsr->complement,medianptr,medianinfospace,width);
*/
  gt_assert(medianptr != NULL);
  return medianptr->suftaboffset;
}

#define MINMEDIANOF9WIDTH 31UL

static unsigned long cmpcharbychardelivermedian(const GtBentsedgresources *bsr,
                                                unsigned long subbucketleft,
                                                unsigned long width,
                                                unsigned long depth)
{
  unsigned long pl = 0,
                pm = GT_DIV2(width),
                pr = width - 1;

  if (width >= MINMEDIANOF9WIDTH)
  { /* On big arrays, pseudomedian of 9 */
    unsigned long offset, doubleoffset;
    offset = GT_DIV8(width);
    doubleoffset = GT_MULT2(offset);
    pl = medianof3cmpcharbychar(bsr,subbucketleft,depth,pl,pl+offset,
                                pl+doubleoffset);
    pm = medianof3cmpcharbychar(bsr,subbucketleft,depth,pm-offset,
                                pm,pm+offset);
    pr = medianof3cmpcharbychar(bsr,subbucketleft,depth,
                                pr-doubleoffset,pr-offset,
                                pr);
  }
  return medianof3cmpcharbychar(bsr,subbucketleft,depth,pl,pm,pr);
}

static unsigned long blockcmpdelivermedian(const GtBentsedgresources *bsr,
                                           unsigned long subbucketleft,
                                           unsigned long width,
                                           unsigned long depth,
                                           unsigned long maxwidthrealmedian)
{
  unsigned long pl = 0,
                pm = GT_DIV2(width),
                pr = width - 1;

  if (width >= MINMEDIANOF9WIDTH)
  {
    if (width > maxwidthrealmedian)
    { /* On big arrays, pseudomedian of 9 */
      unsigned long offset, doubleoffset;
      offset = GT_DIV8(width);
      doubleoffset = GT_MULT2(offset);
      pl = medianof3(bsr,subbucketleft,depth,pl,pl+offset,
                     pl+doubleoffset);
      pm = medianof3(bsr,subbucketleft,depth,pm-offset,pm,pm+offset);
      pr = medianof3(bsr,subbucketleft,depth,pr-doubleoffset,
                     pr-offset,pr);
      pm = medianof3(bsr,subbucketleft,depth,pl,pm,pr);
    } else /* width <= maxwidthrealmedian */
    {
      pm = realmedian(bsr, subbucketleft,width, depth);
    }
  } else
  {
    pm = medianof3(bsr,subbucketleft,depth,pl,pm,pr);
  }
  return pm;
}

/*
static void showcountingsortinfo(const GtCountingsortinfo *countingsortinfo,
                              unsigned long idx)
{
  printf("countingsortinfo[%lu]=(%lu,",idx,
          (unsigned long) countingsortinfo[idx].suffix);
  printf("%lu,",(unsigned long) countingsortinfo[idx].lcpwithpivot);
  printf("%d)\n",countingsortinfo[idx].cmpresult);
}
*/

#undef CHECKFORWHOLELEAFS
#ifdef CHECKFORWHOLELEAFS
static bool gt_containswholeleaf(const GtBentsedgresources *bsr,
                                 unsigned long subbucketleft,
                                 unsigned long width)
{
  unsigned long position, idx;

  for (idx = 0;  idx < width; idx++)
  {
    position = gt_suffixsortspace_get(bsr->sssp,subbucketleft,idx);
    if (position == 0 || gt_encseq_position_is_separator(bsr->encseq,
                                                         position - 1,
                                                         bsr->readmode))
    {
      return true;
    }
  }
  return false;
}
static unsigned long saved_intervals = 0, saved_width = 0;
#endif

static bool multistrategysort(GtBentsedgresources *bsr,
                              unsigned long subbucketleft,
                              unsigned long width,
                              unsigned long depth,
                              unsigned long sortmaxdepth)
{
  gt_assert(width > 1UL);
  if (width <= bsr->sfxstrategy->maxinsertionsort)
  {
    if (sortmaxdepth == 0)
    {
      bs_insertionsort(bsr,subbucketleft,width,depth);
    } else
    {
      bs_insertionsortmaxdepth(bsr,subbucketleft,width,depth,sortmaxdepth);
    }
    return true;
  }
  if (width <= bsr->sfxstrategy->maxbltriesort)
  {
    gt_blindtrie_suffixsort(bsr->blindtrie,
                            subbucketleft,
                            bsr->tableoflcpvalues,
                            width,
                            depth,
                            sortmaxdepth,
                            bsr->processunsortedsuffixrangeinfo,
                            bsr->processunsortedsuffixrange);
    bsr->countbltriesort++;
    return true;
  }
  return false;
}

static void subsort_bentleysedgewick(GtBentsedgresources *bsr,
                                     unsigned long subbucketleft,
                                     unsigned long width,
                                     unsigned long depth)
{
  gt_assert(width > 1UL);
  if (width > 1UL)
  {
#ifdef SKDEBUG
    if (depth > 0)
    {
      gt_checkifprefixesareidentical(__FILE__,
                                     __LINE__,
                                     bsr->encseq,
                                     bsr->readmode,
                                     bsr->sssp,
                                     subbucketleft,
                                     width,
                                     depth);
    }
#endif
#ifdef CHECKFORWHOLELEAFS
    if (bsr->sfxstrategy->spmopt > 0 &&
        !gt_containswholeleaf(bsr,subbucketleft,width))
    {
      saved_intervals++;
      saved_width += width;
      return;
    }
#endif
    if (bsr->rsi != NULL && width >= bsr->radixsortminwidth
                         && width <= bsr->radixsortmaxwidth)
    {
      gt_sfx_radixsort_str(bsr->rsi,
                           depth,
                           bsr->sortmaxdepth,
                           subbucketleft,
                           width,
                           bsr->sssp,
                           bsr->tableoflcpvalues);
      bsr->countradixsort++;
      return;
    }
    if (bsr->srsw != NULL &&
        !bsr->sfxstrategy->noshortreadsort &&
        width <= bsr->shortreadsort_maxwidth)
    {
      gt_shortreadsort_sssp_sort(bsr->srsw,
                                 bsr->encseq,
                                 bsr->srs_maxremain,
                                 bsr->readmode,
                                 bsr->esr1,
                                 bsr->sssp,
                                 subbucketleft,
                                 width,
                                 depth,
                                 (unsigned long) bsr->sortmaxdepth);
      if (bsr->sortmaxdepth > 0)
      {
        gt_shortreadsort_sssp_add_unsorted(
                              bsr->srsw,
                              gt_suffixsortspace_bucketleftidx_get(bsr->sssp),
                              subbucketleft,
                              width,
                              (unsigned long) bsr->sortmaxdepth,
                              bsr->processunsortedsuffixrange,
                              bsr->processunsortedsuffixrangeinfo);
      }
      bsr->countshortreadsort++;
      return;
    }
    if (bsr->sortmaxdepth > 0 && depth >= (unsigned long) bsr->sortmaxdepth)
    {
      if (bsr->processunsortedsuffixrange != NULL)
      {
        bsr->processunsortedsuffixrange(
                         bsr->processunsortedsuffixrangeinfo,
                         gt_suffixsortspace_bucketleftidx_get(bsr->sssp) +
                         subbucketleft,
                         width,depth);
      }
      return;
    }
    if (multistrategysort(bsr,subbucketleft,width,depth,
                          (unsigned long) bsr->sortmaxdepth))
    {
      return;
    }
    /* push */
    GT_CHECKARRAYSPACE(&bsr->mkvauxstack,GtMKVstack,1024);
    STACKTOP.subbucketleft = subbucketleft;
    STACKTOP.width = width;
    STACKTOP.depth = depth;
    bsr->mkvauxstack.nextfreeGtMKVstack++;
  }
}

static void sarrcountingsort(GtBentsedgresources *bsr,
                             unsigned long subbucketleft,
                             unsigned long width,
                             const GtSfxcmp *pivotcmpbits,
                             unsigned long pivotidx,
                             unsigned long depth)
{
  int cmp;
  unsigned int maxsmallerwithlcp = 0, maxlargerwithlcp = 0;
  GtCommonunits commonunits;
  GtEndofTwobitencoding etbecurrent;
  unsigned long idx, smaller = 0, larger = 0,
                insertindex, end, equaloffset, currentwidth;
  GtCountingsortinfo *csiptr;
  /* const bool cmpcharbychar = false; */

  bsr->countcountingsort++;
  for (idx = 0; idx < width; idx++)
  {
    if (idx != pivotidx)
    {
      PTR2INTSTOREPOS(etbecurrent,subbucketleft,idx,
                      bsr->countingsortinfo[idx].suffix = pos);
      cmp = gt_encseq_compare_pairof_twobitencodings(bsr->fwd,
                                                     bsr->complement,
                                                     &commonunits,
                                                     &etbecurrent,
                                                     pivotcmpbits);
      gt_assert(commonunits.common <= (unsigned int) GT_UNITSIN2BITENC);
      bsr->countingsortinfo[idx].lcpwithpivot = commonunits.common;
      if (cmp > 0)
      {
        gt_assert(commonunits.common < (unsigned int) GT_UNITSIN2BITENC);
        bsr->rightlcpdist[commonunits.common]++;
        if (maxlargerwithlcp < commonunits.common)
        {
          maxlargerwithlcp = commonunits.common;
        }
        bsr->countingsortinfo[idx].cmpresult = (char) 1;
        larger++;
      } else
      {
        if (cmp < 0)
        {
          gt_assert(commonunits.common < (unsigned int) GT_UNITSIN2BITENC);
          bsr->leftlcpdist[commonunits.common]++;
          if (maxsmallerwithlcp < commonunits.common)
          {
            maxsmallerwithlcp = commonunits.common;
          }
          bsr->countingsortinfo[idx].cmpresult = (char) -1;
          smaller++;
        } else
        {
          gt_assert(commonunits.common == (unsigned int) GT_UNITSIN2BITENC);
          bsr->countingsortinfo[idx].cmpresult = 0;
        }
      }
    } else
    {
      bsr->countingsortinfo[idx].suffix
        = gt_suffixsortspace_get(bsr->sssp,subbucketleft,idx);
      bsr->countingsortinfo[idx].lcpwithpivot = (unsigned char)
                                                GT_UNITSIN2BITENC;
      bsr->countingsortinfo[idx].cmpresult = (char) 0;
    }
  }
  for (idx = 1UL; idx <= (unsigned long) maxsmallerwithlcp; idx++)
  {
    bsr->leftlcpdist[idx] += bsr->leftlcpdist[idx-1];
  }
  for (idx = 1UL; idx <= (unsigned long) maxlargerwithlcp; idx++)
  {
    bsr->rightlcpdist[idx] += bsr->rightlcpdist[idx-1];
  }
  equaloffset = width - larger;
  for (csiptr = bsr->countingsortinfo + width -1;
       csiptr >= bsr->countingsortinfo;
       csiptr--)
  {
    switch (csiptr->cmpresult)
    {
      case -1:
        insertindex = --(bsr->leftlcpdist[csiptr->lcpwithpivot]);
        gt_suffixsortspace_set(bsr->sssp,subbucketleft,insertindex,
                               csiptr->suffix);
        break;
      case 0:
        gt_suffixsortspace_set(bsr->sssp,subbucketleft,--equaloffset,
                               csiptr->suffix);
        break;
      case 1:
        insertindex = --(bsr->rightlcpdist[csiptr->lcpwithpivot]);
        gt_suffixsortspace_set(bsr->sssp,subbucketleft,
                               width - 1 - insertindex,
                               csiptr->suffix);
        break;
    }
  }
  for (idx = 0; idx <= (unsigned long) maxsmallerwithlcp; idx++)
  {
    if (idx < (unsigned long) maxsmallerwithlcp)
    {
      end = bsr->leftlcpdist[idx+1];
    } else
    {
      end = smaller;
    }
    if (bsr->leftlcpdist[idx] + 1 < end) /* at least two elements */
    {
      currentwidth = end - bsr->leftlcpdist[idx];
      subsort_bentleysedgewick(bsr,
                               subbucketleft + bsr->leftlcpdist[idx],
                               currentwidth,
                               depth + idx);
    }
    if (bsr->tableoflcpvalues != NULL && bsr->leftlcpdist[idx] < end)
    { /* at least one element */
      gt_lcptab_update(bsr->tableoflcpvalues,subbucketleft,end,depth + idx);
    }
    bsr->leftlcpdist[idx] = 0;
  }
  if (width - smaller - larger > 1UL)
  {
    currentwidth = width - smaller - larger;
    subsort_bentleysedgewick(bsr,
                             subbucketleft + smaller,
                             currentwidth,
                             depth + GT_UNITSIN2BITENC);
  }
  for (idx = 0; idx <= (unsigned long) maxlargerwithlcp; idx++)
  {
    if (idx < (unsigned long) maxlargerwithlcp)
    {
      end = bsr->rightlcpdist[idx+1];
    } else
    {
      end = larger;
    }
    if (bsr->rightlcpdist[idx] + 1 < end) /* at least two elements */
    {
      currentwidth = end - bsr->rightlcpdist[idx];
      subsort_bentleysedgewick(bsr,
                               /* for largest idx use first bucket */
                               subbucketleft + width - end,
                               currentwidth,
                               depth + idx);
    }
    if (bsr->tableoflcpvalues != NULL && bsr->rightlcpdist[idx] < end)
    { /* at least one element */
      gt_assert(width >= end);
      gt_lcptab_update(bsr->tableoflcpvalues,subbucketleft,width - end,
                    depth + idx);
    }
    bsr->rightlcpdist[idx] = 0;
  }
}

static inline void vectorswap(GtSuffixsortspace *sssp,
                              unsigned long subbucketleft1,
                              unsigned long subbucketleft2,
                              unsigned long width)
{
  unsigned long idx, tmp;

  for (idx = 0; idx < width; idx++)
  {
    tmp = gt_suffixsortspace_get(sssp,subbucketleft1,idx);
    gt_suffixsortspace_set(sssp,subbucketleft1,idx,
                           gt_suffixsortspace_get(sssp,subbucketleft2,idx));
    gt_suffixsortspace_set(sssp,subbucketleft2,idx,tmp);
  }
}

static void gt_sort_bentleysedgewick(GtBentsedgresources *bsr,
                                     unsigned long width,
                                     unsigned long depth)
{
  bsr->mkvauxstack.nextfreeGtMKVstack = 0;
/*#ifndef NDEBUG
  gt_suffixsortspace_checkorder(bsr->sssp,0,width);
#endif*/
  subsort_bentleysedgewick(bsr, 0, width, depth);
  while (bsr->mkvauxstack.nextfreeGtMKVstack > 0)
  {
    unsigned long leftplusw, pa, pb, pc, pd, pm, bucketright,
                  cptr, temp, pivotcmpcharbychar = 0, valcmpcharbychar,
                  wtmp, subbucketleft;
    unsigned int smallermaxlcp, greatermaxlcp, smallerminlcp, greaterminlcp;
    GtSfxcmp pivotcmpbits, val;
    int retvalpivotcmpbits;
    GtUchar tmpvar;
    GtCommonunits commonunits;
    const int commonunitsequal = bsr->sfxstrategy->cmpcharbychar
                                 ? 1
                                 : GT_UNITSIN2BITENC;

    /* pop */
    bsr->mkvauxstack.nextfreeGtMKVstack--;
    subbucketleft = STACKTOP.subbucketleft;
    width = STACKTOP.width;
    depth = STACKTOP.depth;
    bucketright = width - 1;

    if (bsr->sfxstrategy->cmpcharbychar)
    {
      pm = cmpcharbychardelivermedian(bsr, subbucketleft, width, depth);
      BS_SWAPARRAY(temp, subbucketleft, 0, pm);
      CMPCHARBYCHARPTR2INT(pivotcmpcharbychar, subbucketleft,tmpvar,0);
    } else
    {
      pm = blockcmpdelivermedian(bsr,
                                 subbucketleft,
                                 width,
                                 depth,
                                 bsr->sfxstrategy->maxwidthrealmedian);
      if (width <= bsr->sfxstrategy->maxcountingsort &&
          width >= MINMEDIANOF9WIDTH)
      {
        PTR2INT(pivotcmpbits,subbucketleft,pm);
        gt_assert(width >= bsr->sfxstrategy->maxbltriesort);
        sarrcountingsort(bsr,
                         subbucketleft,
                         width,
                         &pivotcmpbits,
                         pm,
                         depth);
        /* new values for subbucketleft, bucketright, depth */
        continue;
      }
      BS_SWAPARRAY(temp, subbucketleft, 0, pm);
      PTR2INT(pivotcmpbits,subbucketleft,0UL);
    }
    bsr->counttqsort++;
    /* now pivot element is at index subbucketleft */
    /* all elements to be compared are between pb and pc */
    /* pa is the position at which the next element smaller than the
       pivot element is inserted at */
    /* pd is the position at which the next element greater than the
       pivot element is inserted at */
    pa = pb = 1UL;
    pc = pd = bucketright;
    if (bsr->sfxstrategy->cmpcharbychar)
    {
      smallerminlcp = greaterminlcp = smallermaxlcp = greatermaxlcp = 0;
      for (;;)
      {
        while (pb <= pc)
        {
          CMPCHARBYCHARPTR2INT(valcmpcharbychar,subbucketleft,tmpvar,pb);
          if (valcmpcharbychar > pivotcmpcharbychar)
          {
            break;
          }
          if (valcmpcharbychar == pivotcmpcharbychar)
          {
            BS_SWAPARRAY(temp, subbucketleft, pa, pb);
            pa++;
          }
          pb++;
        }
        while (pb <= pc)
        {
          CMPCHARBYCHARPTR2INT(valcmpcharbychar,subbucketleft,tmpvar,pc);
          if (valcmpcharbychar < pivotcmpcharbychar)
          { /* stop for elements < pivot */
            break;
          }
          if (valcmpcharbychar == pivotcmpcharbychar)
          {
            /* exchange equal element and element at index pd */
            BS_SWAPARRAY(temp, subbucketleft, pc, pd);
            pd--;
          }
          pc--;
        }
        if (pb > pc)
        { /* no elements to compare to pivot */
          break;
        }
        BS_SWAPARRAY(temp, subbucketleft, pb, pc);
        pb++;
        pc--;
      }
    } else
    {
      smallermaxlcp = greatermaxlcp = 0;
      smallerminlcp = greaterminlcp = (unsigned int) GT_UNITSIN2BITENC;
      for (;;)
      {
        /* look for elements identical or smaller than pivot from left */
        while (pb <= pc)
        {
          PTR2INT(val,subbucketleft,pb);
          Sfxdocompare(&commonunits,val,pivotcmpbits);
          if (GtSfxcmpGREATER(val,pivotcmpbits))
          { /* stop for elements val > pivot */
            GT_BSR_UPDATELCP(greaterminlcp,greatermaxlcp,commonunits.common);
            break;
          }
          if (GtSfxcmpEQUAL(val,pivotcmpbits))
          {
            /* exchange equal element and element at index pa */
            BS_SWAPARRAY(temp, subbucketleft, pa, pb);
            pa++;
          } else /* smaller */
          {
            GT_BSR_UPDATELCP(smallerminlcp,smallermaxlcp,commonunits.common);
          }
          pb++;
        }
        /* look for elements identical or greater than pivot from right */
        while (pb <= pc)
        {
          PTR2INT(val,subbucketleft,pc);
          Sfxdocompare(&commonunits,val,pivotcmpbits);
          if (GtSfxcmpSMALLER(val,pivotcmpbits))
          { /* stop for elements val < pivot */
            GT_BSR_UPDATELCP(smallerminlcp,smallermaxlcp,commonunits.common);
            break;
          }
          if (GtSfxcmpEQUAL(val,pivotcmpbits))
          {
            /* exchange equal element and element at index pa */
            BS_SWAPARRAY(temp, subbucketleft, pc, pd);
            pd--;
          } else /* greater */
          {
            GT_BSR_UPDATELCP(greaterminlcp,greatermaxlcp,commonunits.common);
          }
          pc--;
        }
        if (pb > pc)
        { /* interval is empty */
          break;
        }
        BS_SWAPARRAY(temp, subbucketleft, pb, pc);
        pb++;
        pc--;
      }
    }
    gt_assert(pb >= pa);
    wtmp = MIN(pa,pb-pa);
    /* move w elements at the left to the middle */
    gt_assert(pb >= wtmp && wtmp <= pb - wtmp);
    vectorswap(bsr->sssp, subbucketleft, subbucketleft+pb-wtmp, wtmp);
    gt_assert(pd >= pc);
    gt_assert(bucketright >= pd);
    wtmp = MIN(pd-pc, bucketright-pd);
    /* move w elements at the right to the middle */
    gt_assert(bucketright + 1 >= wtmp && pb + wtmp <= bucketright+1-wtmp);
    vectorswap(bsr->sssp, subbucketleft+pb, subbucketleft+bucketright+1-wtmp,
               wtmp);

    /* all elements equal to the pivot are now in the middle namely in the
       range [subbucketleft + (pb-pa) and bucketright - (pd-pc)] */
    /* hence we have to sort the elements in the intervals
       [subbucketleft..subbucketleft+(pb-pa)-1] and
       [bucketright-(pd-pc)+1..bucketright] */

    gt_assert(pb >= pa);
    if ((wtmp = pb-pa) > 0)
    {
      leftplusw = wtmp;
      if (bsr->tableoflcpvalues != NULL)
      {
        /*
          left part has suffix with lcp up to length smallermaxlcp w.r.t.
          to the pivot. This lcp belongs to a suffix on the left
          which is at a minimum distance to the pivot and thus to an
          element in the final part of the left side.
        */
        gt_lcptab_update(bsr->tableoflcpvalues,subbucketleft,leftplusw,
                         depth + smallermaxlcp);
      }
      if (wtmp > 1UL)
      {
        subsort_bentleysedgewick(bsr,
                                 subbucketleft,
                                 wtmp,
                                 depth + smallerminlcp);
      }
    } else
    {
      leftplusw = 0;
    }

    cptr = gt_suffixsortspace_get(bsr->sssp,subbucketleft,leftplusw) + depth;
    if (ISNOTEND(cptr) && (wtmp = bucketright-(pd-pb)-leftplusw) > 1UL)
    {
      subsort_bentleysedgewick(bsr,
                               subbucketleft + leftplusw,
                               wtmp,
                               depth+commonunitsequal);
    }

    gt_assert(pd >= pc);
    if ((wtmp = (unsigned long) (pd-pc)) > 0)
    {
      if (bsr->tableoflcpvalues != NULL)
      {
        /*
          right part has suffix with lcp up to length largermaxlcp w.r.t.
          to the pivot. This lcp belongs to a suffix on the right
          which is at a minimum distance to the pivot and thus to an
          element in the first part of the right side.
        */
        gt_lcptab_update(bsr->tableoflcpvalues,
                         subbucketleft,bucketright - wtmp + 1,
                         depth + greatermaxlcp);
      }
      if (wtmp > 1UL)
      {
        subsort_bentleysedgewick(bsr,
                                 subbucketleft + bucketright - wtmp + 1,
                                 wtmp,
                                 depth + greaterminlcp);
      }
    }
  }
}

static void bentsedgresources_init(GtBentsedgresources *bsr,
                                   GtSuffixsortspace *suffixsortspace,
                                   const GtEncseq *encseq,
                                   GtReadmode readmode,
                                   unsigned int prefixlength,
                                   unsigned int sortmaxdepth,
                                   const Sfxstrategy *sfxstrategy,
                                   bool withlcps)
{
  unsigned long idx;

  bsr->readmode = readmode;
  bsr->totallength = gt_encseq_total_length(encseq);
  bsr->sfxstrategy = sfxstrategy;
  bsr->sssp = suffixsortspace;
  bsr->rsi = NULL;
  gt_suffixsortspace_bucketleftidx_set(bsr->sssp,0);
  bsr->encseq = encseq;
  bsr->fwd = GT_ISDIRREVERSE(bsr->readmode) ? false : true;
  bsr->complement = GT_ISDIRCOMPLEMENT(bsr->readmode) ? true : false;
  bsr->tableoflcpvalues = NULL;
  bsr->prefixlength = prefixlength;
  bsr->esr1 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  bsr->esr2 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  bsr->radixsortminwidth = gt_radixsort_str_minwidth();
  bsr->radixsortmaxwidth = 0;
  if (gt_encseq_accesstype_get(bsr->encseq) == GT_ACCESS_TYPE_EQUALLENGTH)
  {
    bsr->twobitencoding = gt_encseq_twobitencoding_export(bsr->encseq);
  } else
  {
    bsr->twobitencoding = NULL;
  }
  if (sortmaxdepth > 0)
  {
    if (sortmaxdepth > prefixlength)
    {
      bsr->srs_maxremain = sortmaxdepth - (unsigned long) prefixlength;
    } else
    {
      bsr->srs_maxremain = 0;
    }
  } else
  {
    if (gt_encseq_lengthoflongestnonspecial(encseq) >
        (unsigned long) prefixlength)
    {
      bsr->srs_maxremain = gt_encseq_lengthoflongestnonspecial(encseq) -
                           prefixlength;
    } else
    {
      bsr->srs_maxremain = 0;
    }
  }
  bsr->sizeofworkspace = gt_size_of_sort_workspace (sfxstrategy);
  bsr->shortreadsort_maxwidth = gt_shortreadsort_maxwidth(false,
                                                          bsr->srs_maxremain,
                                                          bsr->sizeofworkspace);
  GT_INITARRAY(&bsr->mkvauxstack,GtMKVstack);
  bsr->countingsortinfo = NULL;
  bsr->medianinfospace = NULL;
  bsr->blindtrie = NULL;
  bsr->equalwithprevious = NULL;
  bsr->srsw = NULL;
  if (!sfxstrategy->cmpcharbychar)
  {
    const bool withmediumsizelcps = (sortmaxdepth > 0 && !withlcps)
                                    ? true : false;
    if (sortmaxdepth == 0 ||
        gt_encseq_has_twobitencoding_stoppos_support(encseq))
    {
      bsr->srsw = gt_shortreadsort_new(0,bsr->srs_maxremain,readmode,false,
                                       withmediumsizelcps);
    }
    for (idx = 0; idx < (unsigned long) GT_UNITSIN2BITENC; idx++)
    {
      bsr->leftlcpdist[idx] = bsr->rightlcpdist[idx] = 0;
    }
    bsr->countingsortinfo = gt_malloc(sizeof (*bsr->countingsortinfo) *
                                      sfxstrategy->maxcountingsort);
    if (sfxstrategy->maxwidthrealmedian >= MINMEDIANOF9WIDTH)
    {
      bsr->medianinfospace = gt_malloc(sizeof (*bsr->medianinfospace) *
                                       sfxstrategy->maxwidthrealmedian);
    } else
    {
      bsr->medianinfospace = NULL;
    }
  }
  bsr->blindtrie = gt_blindtrie_new(bsr->sssp,
                                    sfxstrategy->maxbltriesort,
                                    0, /* the nodenumberincrement */
                                    encseq,
                                    sfxstrategy->cmpcharbychar,
                                    bsr->esr1,
                                    bsr->esr2,
                                    readmode);
  if (sortmaxdepth > 0 && bsr->sfxstrategy->maxinsertionsort >= 2UL)
  {
    bsr->equalwithprevious = gt_malloc(sizeof (*bsr->equalwithprevious) *
                                       bsr->sfxstrategy->maxinsertionsort);
    for (idx=0; idx < bsr->sfxstrategy->maxinsertionsort; idx++)
    {
      bsr->equalwithprevious[idx] = false;
    }
  }
  bsr->sortmaxdepth = sortmaxdepth;
  bsr->processunsortedsuffixrangeinfo = NULL;
  bsr->processunsortedsuffixrange = NULL;
  bsr->countinsertionsort = 0;
  bsr->counttqsort = 0;
  bsr->countcountingsort = 0;
  bsr->countbltriesort = 0;
  bsr->countshortreadsort = 0;
  bsr->countradixsort = 0;
}

size_t gt_size_of_sort_workspace (const Sfxstrategy *sfxstrategy)
{
  size_t sumsize = 0;

  if (!sfxstrategy->cmpcharbychar)
  {
    sumsize += sizeof (GtCountingsortinfo) * sfxstrategy->maxcountingsort;
    if (sfxstrategy->maxwidthrealmedian >= MINMEDIANOF9WIDTH)
    {
      sumsize += sizeof (GtMedianinfo) * sfxstrategy->maxwidthrealmedian;
    }
  }
  sumsize += gt_blindtrie_size(sfxstrategy->maxbltriesort);
  return sumsize;
}

static void bentsedgresources_delete(GtBentsedgresources *bsr, GtLogger *logger)
{
  gt_free(bsr->countingsortinfo);
  bsr->countingsortinfo = NULL;
  gt_free(bsr->medianinfospace);
  bsr->medianinfospace = NULL;
  gt_shortreadsort_delete(bsr->srsw);
  bsr->srsw = NULL;
  gt_blindtrie_delete(bsr->blindtrie);
  gt_encseq_reader_delete(bsr->esr1);
  gt_encseq_reader_delete(bsr->esr2);
  gt_free(bsr->equalwithprevious);
  GT_FREEARRAY(&bsr->mkvauxstack,GtMKVstack);
  gt_radixsort_str_delete(bsr->rsi);
  gt_logger_log(logger,"countinsertionsort=%lu",bsr->countinsertionsort);
  gt_logger_log(logger,"countbltriesort=%lu",bsr->countbltriesort);
  gt_logger_log(logger,"countcountingsort=%lu",bsr->countcountingsort);
  gt_logger_log(logger,"countshortreadsort=%lu",bsr->countshortreadsort);
  gt_logger_log(logger,"countradixsort=%lu",bsr->countradixsort);
  gt_logger_log(logger,"counttqsort=%lu",bsr->counttqsort);
}

/*
  The following function is called in sfx-suffixer.c and sorts all buckets by
  different suffix comparison methods without the help of other sorting
  information. GtSuffixsortspace contains the sortspace which is accessed
  by some negative offset.
*/

void gt_sortallbuckets(GtSuffixsortspace *suffixsortspace,
                       unsigned long numberofsuffixes,
                       GtBucketspec2 *bucketspec2,
                       const GtEncseq *encseq,
                       GtReadmode readmode,
                       GtCodetype mincode,
                       GtCodetype maxcode,
                       GtBcktab *bcktab,
                       unsigned int numofchars,
                       unsigned int prefixlength,
                       GtOutlcpinfo *outlcpinfo,
                       unsigned int sortmaxdepth,
                       const Sfxstrategy *sfxstrategy,
                       GtProcessunsortedsuffixrange processunsortedsuffixrange,
                       void *processunsortedsuffixrangeinfo,
                       unsigned long long *bucketiterstep,
                       GtLogger *logger)
{
  GtCodetype code;
  unsigned int rightchar = (unsigned int) (mincode % numofchars);
  GtBucketspecification bucketspec;
  GtBentsedgresources bsr;

  bentsedgresources_init(&bsr,
                         suffixsortspace,
                         encseq,
                         readmode,
                         prefixlength,
                         sortmaxdepth,
                         sfxstrategy,
                         outlcpinfo != NULL ? true : false);
  gt_bcktab_determinemaxsize(bcktab, mincode, maxcode, numberofsuffixes);
  if (bsr.sfxstrategy->withradixsort &&
      gt_encseq_accesstype_get(bsr.encseq) == GT_ACCESS_TYPE_EQUALLENGTH &&
      bsr.readmode == GT_READMODE_FORWARD)
  {
    bsr.rsi = gt_radixsort_str_new(bsr.twobitencoding,
                                   gt_encseq_is_mirrored(encseq)
                                     ? GT_DIV2(bsr.totallength - 1)
                                     : bsr.totallength,
                                   1 + gt_encseq_equallength(bsr.encseq),
                                   gt_bcktab_nonspecialsmaxsize(bcktab));
    bsr.radixsortmaxwidth = gt_radixsort_str_maxwidth(bsr.rsi);
  }
  if (outlcpinfo != NULL)
  {
    bsr.tableoflcpvalues = gt_Outlcpinfo_resizereservoir(outlcpinfo,bcktab);
    if (bsr.srsw != NULL)
    {
      gt_shortreadsort_assigntableoflcpvalues(bsr.srsw,bsr.tableoflcpvalues);
    }
  }
  bsr.processunsortedsuffixrangeinfo = processunsortedsuffixrangeinfo;
  bsr.processunsortedsuffixrange = processunsortedsuffixrange;
  for (code = mincode; code <= maxcode; code++)
  {
    if (bucketspec2 != NULL)
    {
      if (gt_copysort_checkhardwork(bucketspec2,code))
      {
        rightchar = (unsigned int) (code % numofchars);
      } else
      {
        continue;
      }
    }
    (*bucketiterstep)++;
    rightchar = gt_bcktab_calcboundsparts(&bucketspec,
                                          bcktab,
                                          code,
                                          maxcode,
                                          numberofsuffixes,
                                          rightchar);
    gt_Outlcpinfo_prebucket(outlcpinfo,code,bucketspec.left);
    if (bucketspec.nonspecialsinbucket > 0)
    {
      if (bucketspec.nonspecialsinbucket > 1UL)
      {
        gt_suffixsortspace_bucketleftidx_set(bsr.sssp,bucketspec.left);
        gt_sort_bentleysedgewick(&bsr,bucketspec.nonspecialsinbucket,
                                 (unsigned long) prefixlength);
        gt_suffixsortspace_bucketleftidx_set(bsr.sssp,0);
      }
      gt_Outlcpinfo_nonspecialsbucket(outlcpinfo,
                                      prefixlength,
                                      bsr.sssp,
                                      bsr.tableoflcpvalues,
                                      &bucketspec,
                                      code);
    }
    gt_Outlcpinfo_postbucket(outlcpinfo,
                             prefixlength,
                             bsr.sssp,
                             bcktab,
                             &bucketspec,
                             code);
  }
#ifdef CHECKFORWHOLELEAFS
  printf("saved_intervals=%lu,saved_width=%lu (%.2f)\n",
          saved_intervals,saved_width,100.0 *
                                      (double) saved_width/numberofsuffixes);
  saved_intervals = 0;
  saved_width = 0;
#endif
  bentsedgresources_delete(&bsr, logger);
}

void gt_sortallsuffixesfromstart(GtSuffixsortspace *suffixsortspace,
                                 unsigned long numberofsuffixes,
                                 const GtEncseq *encseq,
                                 GtReadmode readmode,
                                 GtOutlcpinfo *outlcpinfo,
                                 unsigned int sortmaxdepth,
                                 const Sfxstrategy *sfxstrategy,
                                 GtProcessunsortedsuffixrange
                                   processunsortedsuffixrange,
                                 void *processunsortedsuffixrangeinfo,
                                 GtLogger *logger)
{
  GtBentsedgresources bsr;

  if (numberofsuffixes > 1UL)
  {
    bentsedgresources_init(&bsr,
                           suffixsortspace,
                           encseq,
                           readmode,
                           0,
                           sortmaxdepth,
                           sfxstrategy,
                           outlcpinfo != NULL ? true : false);
    if (outlcpinfo != NULL)
    {
      bsr.tableoflcpvalues = gt_Outlcpinfo_resizereservoir(outlcpinfo,NULL);
      if (bsr.srsw != NULL)
      {
        gt_shortreadsort_assigntableoflcpvalues(bsr.srsw,bsr.tableoflcpvalues);
      }
    }
    bsr.processunsortedsuffixrangeinfo = processunsortedsuffixrangeinfo;
    bsr.processunsortedsuffixrange = processunsortedsuffixrange;
    gt_suffixsortspace_bucketleftidx_set(bsr.sssp,0);
    gt_sort_bentleysedgewick(&bsr,numberofsuffixes,0);
    gt_suffixsortspace_bucketleftidx_set(bsr.sssp,0);
    bentsedgresources_delete(&bsr, logger);
  }
}
genometools-1.5.1/src/match/sfx-bentsedg.h000066400000000000000000000060621211610345200204750ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_BENTSEDG_H
#define SFX_BENTSEDG_H
#include 
#include "core/error_api.h"
#include "core/str.h"
#include "core/codetype.h"
#include "core/logger_api.h"
#include "core/encseq.h"
#include "bcktab.h"
#include "sfx-bltrie.h"
#include "sfx-strategy.h"
#include "sfx-copysort.h"
#include "sfx-lcpvalues.h"
#include "sfx-suffixgetset.h"

typedef void (*GtCompletelargelcpvalues) (void *,
                                         const GtSuffixsortspace *,
                                         GtLcpvalues *,
                                         unsigned long,
                                         unsigned long);

void gt_sortallbuckets(GtSuffixsortspace *suffixsortspace,
                       unsigned long numberofsuffixes,
                       GtBucketspec2 *bucketspec2,
                       const GtEncseq *encseq,
                       GtReadmode readmode,
                       GtCodetype mincode,
                       GtCodetype maxcode,
                       GtBcktab *bcktab,
                       unsigned int numofchars,
                       unsigned int prefixlength,
                       GtOutlcpinfo *outlcpinfo,
                       unsigned int sortmaxdepth,
                       const Sfxstrategy *sfxstrategy,
                       GtProcessunsortedsuffixrange processunsortedsuffixrange,
                       void *processunsortedsuffixrangeinfo,
                       unsigned long long *bucketiterstep,
                       GtLogger *logger);

void gt_sortallsuffixesfromstart(GtSuffixsortspace *suffixsortspace,
                                 unsigned long numberofsuffixes,
                                 const GtEncseq *encseq,
                                 GtReadmode readmode,
                                 GtOutlcpinfo *outlcpinfo,
                                 unsigned int sortmaxdepth,
                                 const Sfxstrategy *sfxstrategy,
                                 GtProcessunsortedsuffixrange
                                   processunsortedsuffixrange,
                                 void *processunsortedsuffixrangeinfo,
                                 GtLogger *logger);

size_t gt_size_of_sort_workspace (const Sfxstrategy *sfxstrategy);

#endif
genometools-1.5.1/src/match/sfx-bltrie.c000066400000000000000000001355031211610345200201610ustar00rootroot00000000000000/*
  Copyright (c) 2007/2010 Stefan Kurtz 
  Copyright (c) 2007/2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/unused_api.h"
#include "core/arraydef.h"
#include "core/divmodmul.h"
#include "core/minmax.h"
#include "core/encseq.h"
#include "core/arraydef.h"

#include "lcpoverflow.h"
#include "sfx-bltrie.h"
#include "sfx-suffixgetset.h"

#define GT_BLINDTRIECHAR_ISSPECIAL(X)     ((X) >= (GtBlindtriesymbol) WILDCARD)
#define GT_BLINDTRIE_REFNULL              0
#define GT_BLINDTRIE_BITSFORRIGHTSIBLING  31
#define GT_BLINDTRIE_ROOTIDX              0

typedef unsigned long GtBlindtriesymbol;
typedef unsigned int GtBlindtriesnodeptr;

/*
  For clarity, the two unions either1 and either2 should have been
  combined into one union with a struct for internal nodes and
  struct for leaves, like the following:
  union
  {
    struct
    {
      unsigned long depth;
      GtBlindtriesnodeptr firstchild;
    } internalinfo;
    struct
    {
      unsigned long nodestartpos;
      unsigned int nodestartstopposoffset;
    } leafinfo;
  } either;
  But as unions are also aligned to word boundaries, this means for
  -m64 compilations this union requires 16 bytes, which would result in
  32 bytes for a GtBlindtrienode. Instead, in our solution either1 requires
  8 bytes and either2 requires 4 bytes which leads to 24 bytes for the entire
  GtBlindtrienode.
*/

typedef struct
{
  GtBlindtriesymbol firstchar;
  union
  {
    unsigned long depth; /* for internal nodes */
    unsigned long nodestartpos; /* for leaves */
  } either1;
  union
  {
    GtBlindtriesnodeptr firstchild; /* for internal nodes */
    unsigned int nodestartstopposoffset; /* for leaves */
  } either2;
  unsigned int rightsibling:GT_BLINDTRIE_BITSFORRIGHTSIBLING;
  unsigned int isleafbit:1;
} GtBlindtrienode;

GT_DECLAREARRAYSTRUCT(GtBlindtriesnodeptr);

struct GtBlindtrie
{
  /* The following belongs to the state and is initialized by blindtrie_new */
  GtBlindtriesnodeptr allocatedBlindtrienode,
                   nextfreeBlindtrienode;
  GtBlindtrienode *spaceBlindtrienode;
  GtArrayGtBlindtriesnodeptr stack;
  GtArrayGtUlong overflowsuffixes;

  /* The following needs to be supplied for each insertion */
  const GtEncseq *encseq;
  GtEncseqReader *esr1, *esr2;
  GtReadmode readmode;
  unsigned long totallength,
                logicaltotallength,
                sortmaxdepthminusoffset;
  bool cmpcharbychar,
       hasmirror,
       has_twobitencoding_stoppos_support;
  unsigned int nodenumberincrement;
  GtViatwobitkeyvalues *vtk1, *vtk2;
  GtSuffixsortspace *sssp;
};

static bool blindtrie_isleaf(const GtBlindtrie *blindtrie,
                             const GtBlindtriesnodeptr node)
{
  gt_assert(node < blindtrie->nextfreeBlindtrienode);
  return blindtrie->spaceBlindtrienode[node].isleafbit ? true : false;
}

static void blindtrie_setleaf(GtBlindtrie *blindtrie,
                              const GtBlindtriesnodeptr node,bool isleaf)
{
  gt_assert(node < blindtrie->nextfreeBlindtrienode);
  blindtrie->spaceBlindtrienode[node].isleafbit = isleaf ? 1U : 0;
}

static unsigned long blindtrie_getdepth(const GtBlindtrie *blindtrie,
                                        const GtBlindtriesnodeptr node)
{
  gt_assert(!blindtrie_isleaf(blindtrie,node));
  return blindtrie->spaceBlindtrienode[node].either1.depth;
}

static void blindtrie_setdepth(const GtBlindtrie *blindtrie,
                               const GtBlindtriesnodeptr node,
                               unsigned long depth)
{
  gt_assert(!blindtrie_isleaf(blindtrie,node));
  blindtrie->spaceBlindtrienode[node].either1.depth = depth;
}

static GtBlindtriesymbol blindtrie_firstchar_get(const GtBlindtrie *blindtrie,
                                               const GtBlindtriesnodeptr node)
{
  gt_assert(node < blindtrie->nextfreeBlindtrienode);
  return blindtrie->spaceBlindtrienode[node].firstchar;
}

static void blindtrie_firstchar_set(GtBlindtrie *blindtrie,
                                    GtBlindtriesnodeptr node,bool isleaf,
                                    GtBlindtriesymbol firstchar)
{
  blindtrie_setleaf(blindtrie,node,isleaf);
  gt_assert(isleaf || !GT_ISUNIQUEINT(firstchar));
  blindtrie->spaceBlindtrienode[node].firstchar = firstchar;
}

static GtBlindtriesnodeptr blindtrie_rightsibling_get(
                        const GtBlindtrie *blindtrie,
                        const GtBlindtriesnodeptr node)
{
  gt_assert(node < blindtrie->nextfreeBlindtrienode);
  return blindtrie->spaceBlindtrienode[node].rightsibling;
}

static void blindtrie_rightsibling_set(const GtBlindtrie *blindtrie,
                                       GtBlindtriesnodeptr node,
                                       GtBlindtriesnodeptr rightsibling)
{
  gt_assert(node < blindtrie->nextfreeBlindtrienode);
  blindtrie->spaceBlindtrienode[node].rightsibling = rightsibling;
}

static GtBlindtriesnodeptr blindtrie_firstchild_get(
                     const GtBlindtrie *blindtrie,
                     const GtBlindtriesnodeptr node)
{
  gt_assert(!blindtrie_isleaf(blindtrie,node));
  return blindtrie->spaceBlindtrienode[node].either2.firstchild;
}

static void blindtrie_firstchild_set(const GtBlindtrie *blindtrie,
                                     GtBlindtriesnodeptr node,
                                     GtBlindtriesnodeptr firstchild)
{
  gt_assert(!blindtrie_isleaf(blindtrie,node));
  blindtrie->spaceBlindtrienode[node].either2.firstchild
    = firstchild;
}

#define GT_TWOBITENCODINGSTARTSTOPOFFSETUNDEF UINT_MAX
#define GT_BLTRIESTOPPOSUNDEF(BLTRIE)         ((BLTRIE)->totallength)

static void blindtrie_leafinfo_set(GtBlindtrie *blindtrie,
                                   GtBlindtriesnodeptr node,
                                   unsigned long currentstartpos,
                                   unsigned long currenttwobitencodingstoppos)
{
  GtBlindtrienode *leafptr = blindtrie->spaceBlindtrienode + node;

  gt_assert(node < blindtrie->nextfreeBlindtrienode);
  leafptr->either1.nodestartpos = currentstartpos;
  if (currenttwobitencodingstoppos != GT_BLTRIESTOPPOSUNDEF(blindtrie))
  {
    if (GT_ISDIRREVERSE(blindtrie->readmode))
    {
      gt_assert(GT_REVERSEPOS(blindtrie->totallength,currentstartpos) + 1 >=
                currenttwobitencodingstoppos);
      if (currenttwobitencodingstoppos == 0)
      {
        leafptr->either2.nodestartstopposoffset = 0;
      } else
      {
        unsigned long tmp = GT_REVERSEPOS(blindtrie->totallength,
                                          currentstartpos) + 2
                                          - currenttwobitencodingstoppos;
        gt_assert(tmp > 0 &&
                  tmp < (unsigned long) GT_TWOBITENCODINGSTARTSTOPOFFSETUNDEF);
        leafptr->either2.nodestartstopposoffset = (unsigned int) tmp;
      }
    } else
    {
      gt_assert(currentstartpos <= currenttwobitencodingstoppos);
      if (currenttwobitencodingstoppos == blindtrie->totallength)
      {
        leafptr->either2.nodestartstopposoffset = 0;
      } else
      {
        unsigned long tmp = currenttwobitencodingstoppos - currentstartpos + 1;

        gt_assert(tmp > 0 &&
                  tmp < (unsigned long) GT_TWOBITENCODINGSTARTSTOPOFFSETUNDEF);
        leafptr->either2.nodestartstopposoffset = (unsigned int) tmp;
      }
    }
  } else
  {
    leafptr->either2.nodestartstopposoffset
      = GT_TWOBITENCODINGSTARTSTOPOFFSETUNDEF;
  }
}

static unsigned long blindtrie_nodestartpos_get(const GtBlindtrie *blindtrie,
                                                GtBlindtriesnodeptr node)
{
  gt_assert(blindtrie_isleaf(blindtrie,node));
  return blindtrie->spaceBlindtrienode[node].either1.nodestartpos;
}

static unsigned long blindtrie_nodestoppos_get(const GtBlindtrie *blindtrie,
                                               GtBlindtriesnodeptr node)
{
  const GtBlindtrienode *leafptr = blindtrie->spaceBlindtrienode + node;

  gt_assert(blindtrie_isleaf(blindtrie,node));
  if (leafptr->either2.nodestartstopposoffset
      != GT_TWOBITENCODINGSTARTSTOPOFFSETUNDEF)
  {
    unsigned long nodestoppos;

    if (GT_ISDIRREVERSE(blindtrie->readmode))
    {
      if (leafptr->either2.nodestartstopposoffset == 0)
      {
        nodestoppos = 0;
      } else
      {
        gt_assert(GT_REVERSEPOS(blindtrie->totallength,
                                leafptr->either1.nodestartpos)+2
                  >= (unsigned long) leafptr->either2.nodestartstopposoffset);
        nodestoppos
          = GT_REVERSEPOS(blindtrie->totallength,leafptr->either1.nodestartpos)
            + 2 - (unsigned long) leafptr->either2.nodestartstopposoffset;
      }
    } else
    {
      if (leafptr->either2.nodestartstopposoffset == 0)
      {
        nodestoppos = blindtrie->totallength;
      } else
      {
        nodestoppos = leafptr->either1.nodestartpos +
                      (unsigned long) leafptr->either2.nodestartstopposoffset
                      - 1;
      }
    }
    return nodestoppos;
  }
  return GT_BLTRIESTOPPOSUNDEF(blindtrie);
}

static void blindtrie_copy_either(GtBlindtrie *blindtrie,
                                  GtBlindtriesnodeptr destnode,
                                  GtBlindtriesnodeptr srcnode)
{
  gt_assert(destnode < blindtrie->nextfreeBlindtrienode &&
            srcnode < blindtrie->nextfreeBlindtrienode);
  blindtrie->spaceBlindtrienode[destnode].either1
    = blindtrie->spaceBlindtrienode[srcnode].either1;
  blindtrie->spaceBlindtrienode[destnode].either2
    = blindtrie->spaceBlindtrienode[srcnode].either2;
}

static bool blindtrie_isleftofboundary(const GtBlindtrie *blindtrie,
                                       unsigned long currentstartpos,
                                       unsigned long add)
{
  unsigned long endpos;

  if (blindtrie->sortmaxdepthminusoffset == 0)
  {
    endpos = blindtrie->totallength;
  } else
  {
    endpos = currentstartpos + blindtrie->sortmaxdepthminusoffset;
    if (endpos >= blindtrie->totallength)
    {
      endpos = blindtrie->totallength;
    }
  }
  return (currentstartpos + add < endpos) ? true : false;
}

static GtBlindtriesnodeptr blindtrie_newnode(GtBlindtrie *blindtrie)
{
  if (blindtrie->nextfreeBlindtrienode >= blindtrie->allocatedBlindtrienode)
  {
    gt_assert(blindtrie->nodenumberincrement >= 1U);
    gt_assert(blindtrie->allocatedBlindtrienode +
              blindtrie->nodenumberincrement <=
              (1U << GT_BLINDTRIE_BITSFORRIGHTSIBLING) - 1);
    blindtrie->allocatedBlindtrienode += blindtrie->nodenumberincrement;
    blindtrie->spaceBlindtrienode
      = gt_realloc(blindtrie->spaceBlindtrienode,
                   sizeof (*blindtrie->spaceBlindtrienode) *
                          blindtrie->allocatedBlindtrienode);
  }
  return blindtrie->nextfreeBlindtrienode++;
}

static GtBlindtriesnodeptr blindtrie_newleaf(GtBlindtrie *blindtrie,
                                          unsigned long currentstartpos,
                                          unsigned long
                                            currenttwobitencodingstoppos,
                                          GtBlindtriesymbol firstchar,
                                          GtBlindtriesnodeptr rightsibling)
{
  GtBlindtriesnodeptr newleaf;

  newleaf = blindtrie_newnode(blindtrie);
  blindtrie_firstchar_set(blindtrie,newleaf,true,firstchar);
  blindtrie_leafinfo_set(blindtrie,
                         newleaf,
                         currentstartpos,
                         currenttwobitencodingstoppos);
  blindtrie_rightsibling_set(blindtrie,newleaf,rightsibling);
  return newleaf;
}

static unsigned long blindtrie_currenttwobitencodingstoppos_get(
                                     const GtBlindtrie *blindtrie,
                                     unsigned long currentstartpos)
{
  if (!blindtrie->cmpcharbychar &&
      blindtrie->has_twobitencoding_stoppos_support)
  {
    gt_encseq_reader_reinit_with_readmode(blindtrie->esr1,blindtrie->encseq,
                                          blindtrie->readmode,
                                          currentstartpos);
    return gt_getnexttwobitencodingstoppos(GT_ISDIRREVERSE(blindtrie->readmode)
                                           ? false : true,blindtrie->esr1);
  }
  return GT_BLTRIESTOPPOSUNDEF(blindtrie);
}

static void blindtrie_makeroot(GtBlindtrie *blindtrie,
                               unsigned long currentstartpos,
                               unsigned long currenttwobitencodingstoppos)
{
  GtBlindtriesymbol firstchar;

  gt_assert(blindtrie->nextfreeBlindtrienode == GT_BLINDTRIE_ROOTIDX);
  (void) blindtrie_newnode(blindtrie);
  blindtrie_firstchar_set(blindtrie,GT_BLINDTRIE_ROOTIDX,
                          false,0); /* firstchar of root will never be used */
  blindtrie_setdepth(blindtrie,GT_BLINDTRIE_ROOTIDX,0);
  /*blindtrie_rightsibling_set(blindtrie,root,GT_BLINDTRIE_REFNULL); */
  if (blindtrie_isleftofboundary(blindtrie,currentstartpos,0))
  {
    /* Random access */
    firstchar = (GtBlindtriesymbol)
                gt_encseq_get_encoded_char(blindtrie->encseq,
                                           currentstartpos,
                                           blindtrie->readmode);
    if (GT_BLINDTRIECHAR_ISSPECIAL(firstchar))
    {
      firstchar = GT_UNIQUEINT(currentstartpos);
    }
    if (currenttwobitencodingstoppos == ULONG_MAX)
    {
      currenttwobitencodingstoppos
        = blindtrie_currenttwobitencodingstoppos_get(blindtrie,currentstartpos);
    }
  } else
  {
    firstchar = GT_UNIQUEINT(currentstartpos);
    currenttwobitencodingstoppos = GT_BLTRIESTOPPOSUNDEF(blindtrie);
  }
  blindtrie_firstchild_set(blindtrie,GT_BLINDTRIE_ROOTIDX,
                           blindtrie_newleaf(blindtrie,currentstartpos,
                                             currenttwobitencodingstoppos,
                                             firstchar,GT_BLINDTRIE_REFNULL));
}

static GtBlindtriesnodeptr blindtrie_extractleafnode(GtBlindtrie *blindtrie,
                                                     GtBlindtriesnodeptr head)
{
  gt_assert(!blindtrie_isleaf(blindtrie,head));
  do
  {
    head = blindtrie_firstchild_get(blindtrie,head);
  } while (!blindtrie_isleaf(blindtrie,head));
  return head;
}

static int blindtrie_comparecharacters(GtBlindtriesymbol oldchar,
                                              GtBlindtriesymbol newchar)
{
  return (oldchar > newchar) ? 1 : ((oldchar < newchar) ? -1 : 0);
}

static GtBlindtriesnodeptr blindtrie_findsucc(const GtBlindtrie *blindtrie,
                                           GtBlindtriesnodeptr node,
                                           GtBlindtriesymbol newchar)
{
  int retval;

  for (;;)
  {
    retval = blindtrie_comparecharacters(
                     blindtrie_firstchar_get(blindtrie,node),
                     newchar);
    if (retval == 0)
    {              /* found branch corresponding to newchar */
      return node;
    }
    if (retval == 1)
    {               /* found sibling which is already greater than newchar */
      return GT_BLINDTRIE_REFNULL;
    }
    node = blindtrie_rightsibling_get(blindtrie,node);
    if (node == GT_BLINDTRIE_REFNULL) /* no more siblings: mismatch */
    {
      return GT_BLINDTRIE_REFNULL;
    }
  }
}

static GtBlindtriesnodeptr blindtrie_findcompanion(
                                    GtBlindtrie *blindtrie,
                                    unsigned long currentstartpos,
                                    unsigned long currenttwobitencodingstoppos)
{
  GtBlindtriesymbol newchar;
  GtBlindtriesnodeptr head, succ;
  unsigned long headdepth;

  blindtrie->stack.nextfreeGtBlindtriesnodeptr = 0;
  head = GT_BLINDTRIE_ROOTIDX;
  while (!blindtrie_isleaf(blindtrie,head))
  {
    GT_STOREINARRAY (&blindtrie->stack, GtBlindtriesnodeptr, 128, head);
    headdepth = blindtrie_getdepth(blindtrie,head);
    if (blindtrie_isleftofboundary(blindtrie,currentstartpos,headdepth))
    {
      if (!blindtrie->cmpcharbychar &&
          blindtrie->has_twobitencoding_stoppos_support)
      {
        if ((GT_ISDIRREVERSE(blindtrie->readmode) &&
            GT_REVERSEPOS(blindtrie->totallength,currentstartpos+headdepth)
            >= currenttwobitencodingstoppos) ||
            (!GT_ISDIRREVERSE(blindtrie->readmode) &&
             currentstartpos + headdepth < currenttwobitencodingstoppos))
        {
          newchar = (GtBlindtriesymbol)
                    gt_encseq_get_encoded_char_nospecial(
                                                   blindtrie->encseq,
                                                   currentstartpos + headdepth,
                                                   blindtrie->readmode);
        } else
        {
          newchar = GT_UNIQUEINT(currentstartpos + headdepth);
        }
      } else
      {
        newchar = (GtBlindtriesymbol)
                  gt_encseq_get_encoded_char(blindtrie->encseq,
                                             currentstartpos + headdepth,
                                             blindtrie->readmode);
        if (GT_BLINDTRIECHAR_ISSPECIAL(newchar))
        {
          newchar = GT_UNIQUEINT(currentstartpos + headdepth);
        }
      }
    } else
    {
      newchar = GT_UNIQUEINT(currentstartpos + headdepth);
    }
    if (GT_ISUNIQUEINT(newchar))
    {
      return blindtrie_extractleafnode(blindtrie,head);
    }
    succ = blindtrie_findsucc(blindtrie,
                              blindtrie_firstchild_get(blindtrie,head),
                              newchar);
    if (succ == GT_BLINDTRIE_REFNULL)
    {
      return blindtrie_extractleafnode(blindtrie,head);
    }
    head = succ;
  }
  GT_STOREINARRAY (&blindtrie->stack, GtBlindtriesnodeptr, 128, head);
  return head;
}

static void blindtrie_insertatsplitnode(GtBlindtrie *blindtrie,
                                        GtBlindtriesnodeptr oldnode,
                                        GtBlindtriesymbol mm_oldsuffix,
                                        unsigned long lcp,
                                        GtBlindtriesymbol mm_newsuffix,
                                        unsigned long currentstartpos,
                                        unsigned long
                                           currenttwobitencodingstoppos)
{
  GtBlindtriesnodeptr newleaf, newnode, previousnode, currentnode;

  gt_assert(GT_ISUNIQUEINT(mm_oldsuffix) ||
            GT_ISUNIQUEINT(mm_newsuffix) ||
            mm_oldsuffix != mm_newsuffix ||
            blindtrie_isleaf(blindtrie,oldnode) ||
            blindtrie_getdepth(blindtrie,oldnode) == lcp);

  /* insert a new node before node oldnode if necessary */
  if (blindtrie_isleaf(blindtrie,oldnode))
  {
    gt_assert(lcp > 0);
  }
  if (blindtrie_isleaf(blindtrie,oldnode) ||
      blindtrie_getdepth(blindtrie,oldnode) > lcp)
  {
    newnode = blindtrie_newnode(blindtrie);
    blindtrie_firstchar_set(blindtrie,newnode,
                            blindtrie_isleaf(blindtrie,oldnode),mm_oldsuffix);
    if (!blindtrie_isleaf(blindtrie,oldnode))
    {
      blindtrie_setdepth(blindtrie,newnode,
                         blindtrie_getdepth(blindtrie,oldnode));
      /* newnode inherits depth+children */
    }
    blindtrie_copy_either(blindtrie,newnode,oldnode);
    blindtrie_rightsibling_set(blindtrie,newnode,GT_BLINDTRIE_REFNULL);
    blindtrie_setleaf(blindtrie,oldnode,false);
    gt_assert(!GT_ISUNIQUEINT(blindtrie_firstchar_get(blindtrie,oldnode)));
    gt_assert(lcp > 0);
    blindtrie_setdepth(blindtrie,oldnode,lcp);
    /* oldnode has newnode as only child*/
    blindtrie_firstchild_set(blindtrie,oldnode,newnode);
  }
  gt_assert(blindtrie_isleaf(blindtrie,oldnode) ||
            blindtrie_getdepth(blindtrie,oldnode) == lcp);
  previousnode = GT_BLINDTRIE_REFNULL;
  currentnode = blindtrie_firstchild_get(blindtrie,oldnode);
  while (currentnode != GT_BLINDTRIE_REFNULL &&
         blindtrie_comparecharacters(blindtrie_firstchar_get(blindtrie,
                                                             currentnode),
                                     mm_newsuffix) < 0)
  {
    previousnode = currentnode;
    currentnode = blindtrie_rightsibling_get(blindtrie,currentnode);
  }
  /* insert new leaf with current suffix */
  /* search S[lcp] among the offsprings */
  newleaf = blindtrie_newleaf(blindtrie,currentstartpos,
                              currenttwobitencodingstoppos,mm_newsuffix,
                              currentnode);
  if (previousnode != GT_BLINDTRIE_REFNULL)
  {
    blindtrie_rightsibling_set(blindtrie,previousnode,newleaf);
  } else
  {
    blindtrie_firstchild_set(blindtrie,oldnode,newleaf);
  }
}

static unsigned long blindtrie_cmpcharbychar_getlcp(
                                 GtBlindtriesymbol *mm_oldsuffix,
                                 bool *mm_oldsuffixisseparator,
                                 GtBlindtriesymbol *mm_newsuffix,
                                 const GtBlindtrie *blindtrie,
                                 unsigned long leafpos,
                                 unsigned long currentstartpos)
{
  unsigned long lcp;
  GtBlindtriesymbol cc1, cc2;

  if (blindtrie_isleftofboundary(blindtrie,leafpos,0))
  {
    gt_encseq_reader_reinit_with_readmode(blindtrie->esr1,blindtrie->encseq,
                                          blindtrie->readmode,leafpos);
  }
  if (blindtrie_isleftofboundary(blindtrie,currentstartpos,0))
  {
    gt_encseq_reader_reinit_with_readmode(blindtrie->esr2,blindtrie->encseq,
                                          blindtrie->readmode,currentstartpos);
  }
  for (lcp = 0; /* Nothing */; lcp++)
  {
    if (blindtrie_isleftofboundary(blindtrie,leafpos,lcp))
    {
      cc1 = (GtBlindtriesymbol)
            gt_encseq_reader_next_encoded_char(blindtrie->esr1);
      if (GT_BLINDTRIECHAR_ISSPECIAL(cc1))
      {
        if (mm_oldsuffixisseparator != NULL)
        {
          *mm_oldsuffixisseparator = (cc1 == SEPARATOR) ? true : false;
        }
        cc1 = GT_UNIQUEINT(leafpos + lcp);
      }
    } else
    {
      if (mm_oldsuffixisseparator != NULL)
      {
        *mm_oldsuffixisseparator = true;
      }
      cc1 = GT_UNIQUEINT(leafpos + lcp);
    }
    if (blindtrie_isleftofboundary(blindtrie,currentstartpos,lcp))
    {
      cc2 = (GtBlindtriesymbol)
            gt_encseq_reader_next_encoded_char(blindtrie->esr2);
      if (GT_BLINDTRIECHAR_ISSPECIAL(cc2))
      {
        cc2 = GT_UNIQUEINT(currentstartpos + lcp);
      }
    } else
    {
      cc2 = GT_UNIQUEINT(currentstartpos + lcp);
    }
    if (blindtrie_comparecharacters(cc1,cc2) != 0)
    {
      *mm_oldsuffix = cc1;
      *mm_newsuffix = cc2;
      break;
    }
  }
  gt_assert(blindtrie->sortmaxdepthminusoffset == 0 ||
            lcp <= blindtrie->sortmaxdepthminusoffset);
  return lcp;
}

static unsigned long blindtrie_twobitencoding_getlcp(
                                 GtBlindtriesymbol *mm_oldsuffix,
                                 bool *mm_oldsuffixisseparator,
                                 GtBlindtriesymbol *mm_newsuffix,
                                 const GtBlindtrie *blindtrie,
                                 unsigned long leafpos,
                                 unsigned long leaftwobitencodingstoppos,
                                 unsigned long currentstartpos,
                                 unsigned long currenttwobitencodingstoppos)
{
  GtCommonunits commonunits;
  const unsigned long depth = 0;

  gt_assert(leafpos != currentstartpos);
  gt_Viatwobitkeyvalues_reinit(blindtrie->vtk1,
                               blindtrie->encseq,
                               blindtrie->readmode,
                               NULL, /* esr */
                               leafpos,
                               depth,
                               blindtrie->sortmaxdepthminusoffset,
                               leaftwobitencodingstoppos);
  gt_Viatwobitkeyvalues_reinit(blindtrie->vtk2,
                               blindtrie->encseq,
                               blindtrie->readmode,
                               NULL, /* esr */
                               currentstartpos,
                               depth,
                               blindtrie->sortmaxdepthminusoffset,
                               currenttwobitencodingstoppos);
  (void) gt_encseq_twobitencoding_strcmp(&commonunits,
                                         blindtrie->encseq,
                                         blindtrie->encseq,
                                         blindtrie->readmode,
                                         depth,
                                         blindtrie->sortmaxdepthminusoffset,
                                         blindtrie->vtk1,
                                         blindtrie->vtk2);
  if (blindtrie_isleftofboundary(blindtrie,leafpos,commonunits.finaldepth) &&
      !commonunits.leftspecial)
  {
    *mm_oldsuffix = (GtBlindtriesymbol)
                    gt_encseq_get_encoded_char_nospecial(blindtrie->encseq,
                                                         leafpos +
                                                         commonunits.finaldepth,
                                                         blindtrie->readmode);
  } else
  {
    if (mm_oldsuffixisseparator != NULL)
    {
      if (blindtrie_isleftofboundary(blindtrie,leafpos,commonunits.finaldepth))
      {
        *mm_oldsuffixisseparator = true;
      } else
      {
        gt_assert(commonunits.leftspecial);
        /* be careful: if wildcards occur in the sequence,
           the following statement may be wrong. Please contact stefan
           if program is applied for such sequences. */
        *mm_oldsuffixisseparator = true;
      }
    }
    *mm_oldsuffix = GT_UNIQUEINT(leafpos + commonunits.finaldepth);
  }
  if (blindtrie_isleftofboundary(blindtrie,currentstartpos,
                                 commonunits.finaldepth) &&
      !commonunits.rightspecial)
  {
    *mm_newsuffix = (GtBlindtriesymbol)
                    gt_encseq_get_encoded_char_nospecial(blindtrie->encseq,
                                                         currentstartpos +
                                                         commonunits.finaldepth,
                                                         blindtrie->readmode);
  } else
  {
    *mm_newsuffix = GT_UNIQUEINT(currentstartpos + commonunits.finaldepth);
  }
  return commonunits.finaldepth;
}

static unsigned long blindtrie_getlcp(GtBlindtriesymbol *mm_oldsuffix,
                                      bool *mm_oldsuffixisseparator,
                                      GtBlindtriesymbol *mm_newsuffix,
                                      const GtBlindtrie *blindtrie,
                                      const GtBlindtriesnodeptr lis,
                                      unsigned long currentstartpos,
                                      unsigned long
                                        currenttwobitencodingstoppos)
{
  if (blindtrie->cmpcharbychar)
  {
    return blindtrie_cmpcharbychar_getlcp (mm_oldsuffix,
                                           mm_oldsuffixisseparator,
                                           mm_newsuffix,
                                           blindtrie,
                                           blindtrie_nodestartpos_get(blindtrie,
                                                                      lis),
                                           currentstartpos);
  }
  return blindtrie_twobitencoding_getlcp(mm_oldsuffix,
                                         mm_oldsuffixisseparator,
                                         mm_newsuffix,
                                         blindtrie,
                                         blindtrie_nodestartpos_get(blindtrie,
                                                                    lis),
                                         blindtrie_nodestoppos_get(blindtrie,
                                                                   lis),
                                         currentstartpos,
                                         currenttwobitencodingstoppos);
}

static void blindtrie_suffixout(GtBlindtrie *blindtrie,
                                unsigned long subbucketleft,
                                unsigned long offset,
                                unsigned long nextfree,
                                unsigned long startpos)
{
  gt_suffixsortspace_set(blindtrie->sssp,subbucketleft,nextfree,
                         startpos - offset);
}

#define BLINDTRIE_SETCURRENTNODE(NODEPTR)\
        currentnodeisleaf = blindtrie_isleaf(blindtrie,NODEPTR) ? true : false;\
        currentnode = NODEPTR

static unsigned long blindtrie_enumeratetrieleaves (
                           GtBlindtrie *blindtrie,
                           unsigned long subbucketleft,
                           unsigned long offset,
                           unsigned long sortmaxdepth,
                           GtLcpvalues *tableoflcpvalues,
                           void *voiddcov,
                           GtProcessunsortedsuffixrange
                             processunsortedsuffixrange)
{
  bool readyforpop = false, currentnodeisleaf;
  GtBlindtriesnodeptr currentnode, siblval, lcpnode = GT_BLINDTRIE_ROOTIDX;
  unsigned long nextfree = 0, equalsrangewidth = 0, lcpnodedepth,
                bucketleftidxplussubbucketleft;

  blindtrie->stack.nextfreeGtBlindtriesnodeptr = 0;
  GT_STOREINARRAY (&blindtrie->stack, GtBlindtriesnodeptr, 128,
                  GT_BLINDTRIE_ROOTIDX);
  BLINDTRIE_SETCURRENTNODE(blindtrie_firstchild_get(blindtrie,
                           GT_BLINDTRIE_ROOTIDX));
  bucketleftidxplussubbucketleft
    = gt_suffixsortspace_bucketleftidx_get(blindtrie->sssp) + subbucketleft;
  for (;;)
  {
    lcpnodedepth = blindtrie_getdepth(blindtrie,lcpnode);
    if (currentnodeisleaf)
    {
      if (nextfree > 0)
      {
        if (tableoflcpvalues != NULL)
        {
          gt_lcptab_update(tableoflcpvalues,subbucketleft,nextfree,
                           lcpnodedepth + offset);
        }
        if (sortmaxdepth > 0)
        {
          if (lcpnodedepth + offset == sortmaxdepth)
          {
            equalsrangewidth++;
          } else
          {
            gt_assert(lcpnodedepth + offset < sortmaxdepth);
            if (equalsrangewidth > 0)
            {
              if (processunsortedsuffixrange != NULL)
              {
                processunsortedsuffixrange(
                               voiddcov,
                               bucketleftidxplussubbucketleft
                                 + nextfree - 1 - equalsrangewidth,
                               equalsrangewidth + 1,
                               sortmaxdepth);
              }
              equalsrangewidth = 0;
            }
          }
        }
      }
      blindtrie_suffixout(blindtrie,subbucketleft,offset,nextfree,
                          blindtrie_nodestartpos_get(blindtrie,currentnode));
      nextfree++;
      siblval = blindtrie_rightsibling_get(blindtrie,currentnode);
      if (siblval == GT_BLINDTRIE_REFNULL)
      {
        readyforpop = true;
        currentnodeisleaf = false; /* STATE 1 */
      } else
      {
        BLINDTRIE_SETCURRENTNODE(siblval);  /* current comes from brother */
        lcpnode = blindtrie->stack.spaceGtBlindtriesnodeptr[
                             blindtrie->stack.nextfreeGtBlindtriesnodeptr-1];
      }
    } else
    {
      if (readyforpop)
      {
        if (blindtrie->stack.nextfreeGtBlindtriesnodeptr == 1UL)
        {
          break;
        }
        blindtrie->stack.nextfreeGtBlindtriesnodeptr--;
        siblval = blindtrie_rightsibling_get(blindtrie,
                       blindtrie->stack.spaceGtBlindtriesnodeptr[
                       blindtrie->stack.nextfreeGtBlindtriesnodeptr]);
        if (siblval != GT_BLINDTRIE_REFNULL)
        {
          BLINDTRIE_SETCURRENTNODE(siblval);   /* current comes from brother */
          lcpnode = blindtrie->stack.spaceGtBlindtriesnodeptr[
                             blindtrie->stack.nextfreeGtBlindtriesnodeptr - 1];
          readyforpop = false;
        }
      } else
      {
        GT_STOREINARRAY (&blindtrie->stack, GtBlindtriesnodeptr, 128,
                         currentnode);
        BLINDTRIE_SETCURRENTNODE(blindtrie_firstchild_get(blindtrie,
                                                          currentnode));
      }
    }
  }
  if (nextfree > 0 && equalsrangewidth > 0)
  {
    if (processunsortedsuffixrange != NULL)
    {
      processunsortedsuffixrange(voiddcov,
                                 bucketleftidxplussubbucketleft
                                   + nextfree - 1 - equalsrangewidth,
                                 equalsrangewidth + 1,
                                 sortmaxdepth);
    }
    equalsrangewidth = 0;
  }
  return nextfree;
}

GtBlindtrie *gt_blindtrie_new(GtSuffixsortspace *suffixsortspace,
                              unsigned long maxnumofsuffixes,
                              unsigned int nodenumberincrement,
                              const GtEncseq *encseq,
                              bool cmpcharbychar,
                              GtEncseqReader *esr1,
                              GtEncseqReader *esr2,
                              GtReadmode readmode)
{
  GtBlindtrie *blindtrie;

  if (maxnumofsuffixes == 1UL)
  {
    return NULL;
  }
  blindtrie = gt_malloc(sizeof (*blindtrie));
  if (nodenumberincrement == 0)
  {
    gt_assert(maxnumofsuffixes >= 2UL);
    blindtrie->allocatedBlindtrienode
      = (GtBlindtriesnodeptr) GT_MULT2(maxnumofsuffixes + 1) + 1;
    blindtrie->nodenumberincrement = 0;
  } else
  {
    gt_assert(maxnumofsuffixes == 0);
    blindtrie->allocatedBlindtrienode = 0;
    blindtrie->nodenumberincrement = nodenumberincrement;
  }
  blindtrie->spaceBlindtrienode
    = gt_malloc(sizeof (*blindtrie->spaceBlindtrienode) *
                blindtrie->allocatedBlindtrienode);
  /*
  printf("# sizeof (blindtrie)=%lu\n",
            (unsigned long) (sizeof (GtBlindtrie) +
                             blindtrie->allocatedBlindtrienode *
                             sizeof (GtBlindtrienode)));
  */
  GT_INITARRAY (&blindtrie->overflowsuffixes, GtUlong);
  GT_INITARRAY (&blindtrie->stack, GtBlindtriesnodeptr);
  blindtrie->nextfreeBlindtrienode = 0;
  blindtrie->encseq = encseq;
  blindtrie->has_twobitencoding_stoppos_support
    = gt_encseq_has_twobitencoding_stoppos_support(encseq);
  blindtrie->readmode = readmode;
  blindtrie->esr1 = esr1;
  blindtrie->esr2 = esr2;
  blindtrie->totallength = gt_encseq_total_length(encseq);
  blindtrie->cmpcharbychar = cmpcharbychar;
  blindtrie->sssp = suffixsortspace;
  if (cmpcharbychar)
  {
    blindtrie->vtk1 = blindtrie->vtk2 = NULL;
  } else
  {
    blindtrie->vtk1 = gt_Viatwobitkeyvalues_new();
    blindtrie->vtk2 = gt_Viatwobitkeyvalues_new();
  }
  return blindtrie;
}

void gt_blindtrie_resize(GtBlindtrie *blindtrie,unsigned int maxnumofnodes)
{
  gt_assert(maxnumofnodes > 0);
  if (blindtrie->allocatedBlindtrienode > maxnumofnodes)
  {
    blindtrie->allocatedBlindtrienode = maxnumofnodes;
    blindtrie->spaceBlindtrienode
      = gt_realloc(blindtrie->spaceBlindtrienode,
                   sizeof (*blindtrie->spaceBlindtrienode) *
                   blindtrie->allocatedBlindtrienode);
  }
}

size_t gt_blindtrie_size(unsigned long maxnumofsuffixes)
{
  if (maxnumofsuffixes == 1UL)
  {
    return 0;
  } else
  {
    return sizeof (GtBlindtrie) +
           (GT_MULT2(maxnumofsuffixes + 1) + 1) * sizeof (GtBlindtrienode);
  }
}

size_t gt_blindtrie_current_size(const GtBlindtrie *blindtrie)
{
  return sizeof (GtBlindtrie) +
         sizeof (GtBlindtrienode) * blindtrie->allocatedBlindtrienode;
}

void gt_blindtrie_reset(GtBlindtrie *blindtrie)
{
  blindtrie->nextfreeBlindtrienode = 0;
  blindtrie->stack.nextfreeGtBlindtriesnodeptr = 0;
}

void gt_blindtrie_delete(GtBlindtrie *blindtrie)
{
  if (blindtrie == NULL)
  {
    return;
  }
  gt_Viatwobitkeyvalues_delete(blindtrie->vtk1);
  gt_Viatwobitkeyvalues_delete(blindtrie->vtk2);
  gt_free(blindtrie->spaceBlindtrienode);
  GT_FREEARRAY(&blindtrie->overflowsuffixes, GtUlong);
  GT_FREEARRAY(&blindtrie->stack, GtBlindtriesnodeptr);
  gt_free(blindtrie);
}

#undef SKDEBUG
#ifdef SKDEBUG

#define NODENUM(PTR) PTR

static void gt_blindtrie_showleaf(const GtBlindtrie *blindtrie,
                                  unsigned int level,
                                  GtBlindtriesnodeptr current)
{
  printf("%*.*s",(int) (6 * level),(int) (6 * level)," ");
  gt_assert(current != GT_BLINDTRIE_REFNULL);
  printf("Leaf(%u,firstchar=%u,startpos=%lu,rightsibling=%u)\n",
         NODENUM(current),
         (unsigned int) blindtrie_firstchar_get(blindtrie,current),
         blindtrie_nodestartpos_get(blindtrie,current),
         NODENUM(blindtrie_rightsibling_get(blindtrie,current)));
}

static void gt_blindtrie_showintern(const GtBlindtrie *blindtrie,
                                    unsigned int level,
                                    GtBlindtriesnodeptr current)
{
  printf("%*.*s",(int) (6 * level),(int) (6 * level)," ");
  gt_assert(current != GT_BLINDTRIE_REFNULL);
  printf("Intern(%u,firstchar=%lu,depth=%lu"
         ",firstchild=%u,rightsibling=%u)\n",
          NODENUM(current),
          blindtrie_firstchar_get(blindtrie,current),
          blindtrie_getdepth(blindtrie,current),
          NODENUM(blindtrie_firstchild_get(blindtrie,current)),
          NODENUM(blindtrie_rightsibling_get(blindtrie,current)));
}

static void gt_blindtrie_showrecursive(const GtBlindtrie *blindtrie,
                                       unsigned int level,
                                       GtBlindtriesnodeptr node)
{
  GtBlindtriesnodeptr current;

  for (current = blindtrie_firstchild_get(blindtrie,node);
       current != GT_BLINDTRIE_REFNULL;
       current = blindtrie_rightsibling_get(blindtrie,current))
  {
    if (blindtrie_isleaf(blindtrie,current))
    {
      gt_blindtrie_showleaf(blindtrie,level,current);
    } else
    {
      gt_blindtrie_showintern(blindtrie,level,current);
      gt_blindtrie_showrecursive(blindtrie,level+1,current);
    }
  }
}

static void gt_blindtrie_show(const GtBlindtrie *blindtrie)
{
  gt_blindtrie_showrecursive(blindtrie,0,GT_BLINDTRIE_ROOTIDX);
}

static void blindtrie_showstate(const GtBlindtrie *blindtrie,
                                unsigned long subbucketleft,
                                unsigned long numberofsuffixes,
                                unsigned long offset)
{
  unsigned long idx;

  printf("insert suffixes at offset %lu:\n",offset);
  for (idx=0; idx < numberofsuffixes; idx++)
  {
    printf("%lu ",
           gt_suffixsortspace_get(blindtrie->sssp,subbucketleft,idx) + offset);
  }
  printf("\nstep 0\n");
  gt_blindtrie_show(blindtrie);
}

#endif

static GtBlindtriesnodeptr blindtrie_findsplitnode(const GtBlindtrie *blindtrie,
                                                unsigned long lcp)
{
  GtBlindtriesnodeptr currentnode;
  unsigned long stackidx;

  currentnode = GT_BLINDTRIE_ROOTIDX;
  for (stackidx=0;stackidxstack.nextfreeGtBlindtriesnodeptr;
       stackidx++)
  {
    currentnode = blindtrie->stack.spaceGtBlindtriesnodeptr[stackidx];
    if (blindtrie_isleaf(blindtrie,currentnode) ||
        blindtrie_getdepth(blindtrie,currentnode) >= lcp)
    {
      break;
    }
  }
  return currentnode;
}

static void gt_blindtrie_insertsuffix(GtBlindtrie *blindtrie,
                                      unsigned long offset,
                                      unsigned long sortmaxdepth,
                                      unsigned long currentstartpos)
{

  gt_assert(sortmaxdepth == 0 || sortmaxdepth > offset);
  if (blindtrie->nextfreeBlindtrienode == 0)
  { /* empty tree */
    if (sortmaxdepth == 0)
    {
      blindtrie->sortmaxdepthminusoffset = 0;
    } else
    {
      blindtrie->sortmaxdepthminusoffset = sortmaxdepth - offset;
    }
    blindtrie->overflowsuffixes.nextfreeGtUlong = 0;
    blindtrie_makeroot(blindtrie,currentstartpos,ULONG_MAX);
  } else
  {
    if (blindtrie_isleftofboundary(blindtrie,currentstartpos,0))
    {
      unsigned long lcp, currenttwobitencodingstoppos;
      GtBlindtriesnodeptr leafinsubtrie, splitnode;
      GtBlindtriesymbol mm_oldsuffix, mm_newsuffix;

      currenttwobitencodingstoppos
        = blindtrie_currenttwobitencodingstoppos_get(blindtrie,currentstartpos);
      leafinsubtrie = blindtrie_findcompanion(blindtrie,currentstartpos,
                                              currenttwobitencodingstoppos);
      gt_assert(blindtrie_isleaf(blindtrie,leafinsubtrie));
      lcp = blindtrie_getlcp(&mm_oldsuffix,
                             NULL,
                             &mm_newsuffix,
                             blindtrie,
                             leafinsubtrie,
                             currentstartpos,
                             currenttwobitencodingstoppos);
      splitnode = blindtrie_findsplitnode(blindtrie,lcp);
      blindtrie_insertatsplitnode(blindtrie,
                                  splitnode,
                                  mm_oldsuffix,
                                  lcp,
                                  mm_newsuffix,
                                  currentstartpos,
                                  currenttwobitencodingstoppos);
    } else
    {
      GT_STOREINARRAY(&blindtrie->overflowsuffixes,GtUlong,32,currentstartpos);
    }
  }
}

static int blindtrie_compare_ascending(const void *a,const void *b)
{
  unsigned long *aptr = (unsigned long *) a;
  unsigned long *bptr = (unsigned long *) b;
  gt_assert(*aptr != *bptr);
  return *aptr < *bptr ? -1 : 1;
}

static void processoverflowsuffixes(GtBlindtrie *blindtrie,
                                    unsigned long offset,
                                    GtLcpvalues *tableoflcpvalues,
                                    unsigned long subbucketleft,
                                    unsigned long nextsuffixtooutput)
{
  if (blindtrie->overflowsuffixes.nextfreeGtUlong > 0)
  {
    unsigned long idx;

    if (blindtrie->overflowsuffixes.nextfreeGtUlong > 1UL)
    {
      qsort(blindtrie->overflowsuffixes.spaceGtUlong,
            (size_t) blindtrie->overflowsuffixes.nextfreeGtUlong,
            sizeof (*blindtrie->overflowsuffixes.spaceGtUlong),
            blindtrie_compare_ascending);
    }
    for (idx = 0; idx < blindtrie->overflowsuffixes.nextfreeGtUlong; idx++)
    {
      if (tableoflcpvalues != NULL)
      {
        gt_lcptab_update(tableoflcpvalues,subbucketleft,nextsuffixtooutput,
                         offset);
      }
      blindtrie_suffixout(blindtrie,subbucketleft,offset,nextsuffixtooutput,
                          blindtrie->overflowsuffixes.spaceGtUlong[idx]);
      nextsuffixtooutput++;
    }
  }
}

static void gt_blindtrie2sorting(GtBlindtrie *blindtrie,
                                 unsigned long subbucketleft,
                                 GtLcpvalues *tableoflcpvalues,
                                 unsigned long offset,
                                 unsigned long sortmaxdepth,
                                 void *voiddcov,
                                 GtProcessunsortedsuffixrange
                                   processunsortedsuffixrange)
{
  unsigned long nextsuffixtosort;

  nextsuffixtosort
    = blindtrie_enumeratetrieleaves (blindtrie,subbucketleft,offset,
                                     sortmaxdepth,tableoflcpvalues,
                                     voiddcov,processunsortedsuffixrange);
  processoverflowsuffixes(blindtrie,
                          offset,
                          tableoflcpvalues,
                          subbucketleft,
                          nextsuffixtosort);
}

void gt_blindtrie_suffixsort(GtBlindtrie *blindtrie,
                             unsigned long subbucketleft,
                             GtLcpvalues *tableoflcpvalues,
                             unsigned long numberofsuffixes,
                             unsigned long offset,
                             unsigned long sortmaxdepth,
                             void *voiddcov,
                             GtProcessunsortedsuffixrange
                               processunsortedsuffixrange)
{
  unsigned long idx, currentstartpos;

  gt_blindtrie_reset(blindtrie);
  for (idx=0; idx < numberofsuffixes; idx++)
  {
    currentstartpos = gt_suffixsortspace_get(blindtrie->sssp,subbucketleft,idx);
    gt_blindtrie_insertsuffix(blindtrie,
                              offset,
                              sortmaxdepth,
                              currentstartpos + offset);
#ifdef SKDEBUG
    blindtrie_showstate(blindtrie,
                        subbucketleft,
                        idx+1,
                        offset);
#endif
  }
  gt_blindtrie2sorting(blindtrie,
                       subbucketleft,
                       tableoflcpvalues,
                       offset,
                       sortmaxdepth,
                       voiddcov,
                       processunsortedsuffixrange);
}

bool gt_blindtrie_retrieve(GtBlindtrie *blindtrie,
                           unsigned long currentstartpos,
                           unsigned long currenttwobitencodingstoppos)
{
  gt_assert(!blindtrie->cmpcharbychar);
  if (currenttwobitencodingstoppos != ULONG_MAX)
  {
    gt_assert(blindtrie->esr1 == NULL);
    gt_assert(blindtrie->esr2 == NULL);
  }
  if (blindtrie->nextfreeBlindtrienode == 0)
  {
    blindtrie->sortmaxdepthminusoffset = 0;
    blindtrie_makeroot(blindtrie,currentstartpos,currenttwobitencodingstoppos);
    return false;
  } else
  {
    GtBlindtriesnodeptr leafinsubtrie, splitnode;
    GtBlindtriesymbol mm_oldsuffix, mm_newsuffix;
    bool mm_oldsuffixisseparator;
    unsigned long lcp;

    if (currenttwobitencodingstoppos == ULONG_MAX)
    {
      currenttwobitencodingstoppos
        = blindtrie_currenttwobitencodingstoppos_get(blindtrie,currentstartpos);
    }
    leafinsubtrie = blindtrie_findcompanion(blindtrie,currentstartpos,
                                            currenttwobitencodingstoppos);
    gt_assert(blindtrie_isleaf(blindtrie,leafinsubtrie));
    lcp = blindtrie_getlcp(&mm_oldsuffix,
                           &mm_oldsuffixisseparator,
                           &mm_newsuffix,
                           blindtrie,
                           leafinsubtrie,
                           currentstartpos,
                           currenttwobitencodingstoppos);
    splitnode = blindtrie_findsplitnode(blindtrie,lcp);
    if (blindtrie_isleaf(blindtrie,splitnode) && GT_ISUNIQUEINT(mm_oldsuffix) &&
        mm_oldsuffixisseparator)
    {
      return true;
    }
    blindtrie_insertatsplitnode(blindtrie,
                                splitnode,
                                mm_oldsuffix,
                                lcp,
                                mm_newsuffix,
                                currentstartpos,
                                currenttwobitencodingstoppos);
    return false;
  }
}
genometools-1.5.1/src/match/sfx-bltrie.h000066400000000000000000000047001211610345200201600ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_BLTRIE_H
#define SFX_BLTRIE_H

#include "core/encseq.h"
#include "core/readmode.h"
#include "sfx-suffixgetset.h"
#include "sfx-lcpvalues.h"

typedef struct GtBlindtrie GtBlindtrie;

GtBlindtrie *gt_blindtrie_new(GtSuffixsortspace *suffixsortspace,
                              unsigned long maxnumofsuffixes,
                              unsigned int nodenumberincrement,
                              const GtEncseq *encseq,
                              bool cmpcharbychar,
                              GtEncseqReader *esr1,
                              GtEncseqReader *esr2,
                              GtReadmode readmode);

void gt_blindtrie_resize(GtBlindtrie *blindtrie,unsigned int maxnumofnodes);

size_t gt_blindtrie_size(unsigned long maxnumofsuffixes);

size_t gt_blindtrie_current_size(const GtBlindtrie *blindtrie);

void gt_blindtrie_reset(GtBlindtrie *blindtrie);

void gt_blindtrie_suffixsort(GtBlindtrie *blindtrie,
                             unsigned long subbucketleft,
                             GtLcpvalues *tableoflcpvalues,
                             unsigned long numberofsuffixes,
                             unsigned long offset,
                             unsigned long sortmaxdepth,
                             void *voiddcov,
                             GtProcessunsortedsuffixrange
                               processunsortedsuffixrange);

void gt_blindtrie_delete(GtBlindtrie *blindtrie);

bool gt_blindtrie_retrieve(GtBlindtrie *blindtrie,
                           unsigned long currentstartpos,
                           unsigned long currenttwobitencodingstoppos);

#endif
genometools-1.5.1/src/match/sfx-copysort.c000066400000000000000000000435251211610345200205640ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma_api.h"
#include "core/qsort_r.h"
#include "core/array2dim_api.h"
#include "core/mathsupport.h"
#include "bcktab.h"
#include "kmer2string.h"
#include "core/logger.h"
#include "sfx-copysort.h"

typedef struct
{
  bool hardworktodo,
       sorted;
  unsigned long bucketend;
} Bucketinfo;

struct GtBucketspec2
{
  unsigned long partwidth;
  const GtEncseq *encseq;
  GtReadmode readmode;
  unsigned int numofchars, numofcharssquared, prefixlength, *order;
  GtCodetype expandfactor, expandfillsum;
  Bucketinfo *superbuckettab, **subbuckettab;
};

static unsigned long superbucketsize(const GtBucketspec2 *bucketspec2,
                                     unsigned int bucketnum)
{
  if (bucketnum == 0)
  {
    return bucketspec2->superbuckettab[0].bucketend;
  }
  return bucketspec2->superbuckettab[bucketnum].bucketend -
         bucketspec2->superbuckettab[bucketnum-1].bucketend;
}

static int comparesuperbucketsizes(const void *a,const void *b,void *data)
{
  const GtBucketspec2 *bucketspec2 = (const GtBucketspec2 *) data;
  unsigned long size1 = superbucketsize(bucketspec2, *(const unsigned int *) a);
  unsigned long size2 = superbucketsize(bucketspec2, *(const unsigned int *) b);
  if (size1 < size2)
  {
    return -1;
  }
  if (size1 > size2)
  {
    return 1;
  }
  return 0;
}

static unsigned long getstartidx(const GtBucketspec2 *bucketspec2,
                                 unsigned int first,
                                 unsigned int second)
{
  gt_assert(first < bucketspec2->numofchars);
  gt_assert(second <= bucketspec2->numofchars);
  if (second > 0)
  {
    return bucketspec2->subbuckettab[first][second-1].bucketend;
  }
  if (first > 0)
  {
    return bucketspec2->superbuckettab[first-1].bucketend;
  }
  return 0;
}

static unsigned long getendidx(const GtBucketspec2 *bucketspec2,
                        unsigned int first,
                        unsigned int second)
{
  gt_assert(first < bucketspec2->numofchars);
  gt_assert(second <= bucketspec2->numofchars);
  if (second < bucketspec2->numofchars)
  {
    return bucketspec2->subbuckettab[first][second].bucketend;
  }
  return bucketspec2->superbuckettab[first].bucketend;
}

static void resetsorted(GtBucketspec2 *bucketspec2)
{
  unsigned int idx, idx2;

  for (idx = 0; idxnumofchars; idx++)
  {
    bucketspec2->superbuckettab[idx].sorted = false;
    for (idx2 = 0; idx2numofchars; idx2++)
    {
      unsigned long startidx = getstartidx(bucketspec2,idx,idx2),
             endidx = getendidx(bucketspec2,idx,idx2);
      bucketspec2->subbuckettab[idx][idx2].sorted =
        (startidx < endidx) ? false : true;
    }
  }
}

static void determinehardwork(GtBucketspec2 *bucketspec2)
{
  unsigned int idx, idxsource, source, second;

  for (idxsource = 0; idxsourcenumofchars; idxsource++)
  {
    source = bucketspec2->order[idxsource];
    for (second = 0; second < bucketspec2->numofchars; second++)
    {
      if (!bucketspec2->subbuckettab[source][second].sorted && source != second)
      {
        bucketspec2->subbuckettab[source][second].hardworktodo = true;
        bucketspec2->subbuckettab[source][second].sorted = true;
      } else
      {
        bucketspec2->subbuckettab[source][second].hardworktodo = false;
      }
    }
    bucketspec2->superbuckettab[source].sorted = true;
    for (idx = 0; idx < bucketspec2->numofchars; idx++)
    {
      bucketspec2->subbuckettab[idx][source].sorted = true;
    }
  }
}

static GtCodetype expandtwocharcode(GtCodetype twocharcode,
                                  const GtBucketspec2 *bucketspec2)
{
  gt_assert(twocharcode < (GtCodetype) bucketspec2->numofcharssquared);
  return twocharcode * bucketspec2->expandfactor + bucketspec2->expandfillsum;
}

static unsigned long *leftcontextofspecialchardist(unsigned int numofchars,
                                                   const GtEncseq *encseq,
                                                   GtReadmode readmode)
{
  GtUchar cc;
  unsigned int idx;
  unsigned long *specialchardist,
                totallength = gt_encseq_total_length(encseq);
  GtReadmode convertedreadmode = (readmode == GT_READMODE_REVERSE)
                                      ? GT_READMODE_FORWARD
                                      : GT_READMODE_COMPL;

  specialchardist = gt_malloc(sizeof (*specialchardist) * numofchars);
  for (idx = 0; idx 0)
        {
          cc = gt_encseq_get_encoded_char(encseq,range.start-1,readmode);
          if (ISNOTSPECIAL(cc))
          {
            specialchardist[cc]++;
          }
        }
      }
    }
    gt_specialrangeiterator_delete(sri);
  }
  if (GT_ISDIRREVERSE(readmode))
  {
    if (gt_encseq_lengthofspecialprefix(encseq) == 0)
    {
      cc = gt_encseq_get_encoded_char(encseq,0,convertedreadmode);
      gt_assert(ISNOTSPECIAL(cc));
      specialchardist[cc]++;
    }
  } else
  {
    if (gt_encseq_lengthofspecialsuffix(encseq) == 0)
    {
      cc = gt_encseq_get_encoded_char(encseq,totallength-1,readmode);
      gt_assert(ISNOTSPECIAL(cc));
      specialchardist[cc]++;
    }
  }
  return specialchardist;
}

#undef SHOWBUCKETSPEC2
#ifdef SHOWBUCKETSPEC2
static void showbucketspec2(const GtBucketspec2 *bucketspec2)
{
  unsigned int idx1, idx2;

  for (idx1 = 0; idx1 < bucketspec2->numofchars; idx1++)
  {
    for (idx2 = 0; idx2 < bucketspec2->numofchars; idx2++)
    {
      printf("subbucket[%u][%u]=%lu",idx1,idx2,
              bucketspec2->subbuckettab[idx1][idx2].bucketend);
      if (bucketspec2->subbuckettab[idx1][idx2].sorted)
      {
        printf(" sorted\n");
      } else
      {
        printf("\n");
      }
    }
    printf("superbucket[%u]=%lu\n",idx1,
           bucketspec2->superbuckettab[idx1].bucketend);
  }
}

static void showexpandcode(const GtBucketspec2 *bucketspec2,
                           unsigned int prefixlength)
{
  GtCodetype ecode, code2;
  const GtUchar *characters =
                     gt_encseq_alphabetcharacters(bucketspec2->encseq);

  for (code2 = 0; code2 < (GtCodetype) bucketspec2->numofcharssquared; code2++)
  {
    char buffer[100];

    ecode = expandtwocharcode(code2,bucketspec2);
    gt_fromkmercode2string(buffer,
                        ecode,
                        bucketspec2->numofchars,
                        prefixlength,
                        (const char *) characters);
    printf("code2=%u = %lu %s\n",(unsigned int) code2,ecode,buffer);
  }
}
#endif

static void fill2subbuckets(GtBucketspec2 *bucketspec2,const GtBcktab *bcktab)
{
  GtCodetype code, maxcode;
  unsigned int rightchar = 0, currentchar = 0;
  GtBucketspecification bucketspec;
  unsigned long accubucketsize = 0;

  maxcode = gt_bcktab_numofallcodes(bcktab) - 1;
  for (code = 0; code <= maxcode; code++)
  {
    rightchar = gt_bcktab_calcboundsparts(&bucketspec,
                                          bcktab,
                                          code,
                                          maxcode,
                                          bucketspec2->partwidth,
                                          rightchar);
    accubucketsize += bucketspec.nonspecialsinbucket;
    if (rightchar == 0)
    {
      bucketspec2->subbuckettab[currentchar]
                               [bucketspec2->numofchars-1].bucketend
        = accubucketsize;
      accubucketsize += bucketspec.specialsinbucket;
      bucketspec2->superbuckettab[currentchar].bucketend = accubucketsize;
      currentchar++;
    } else
    {
      gt_assert(bucketspec.specialsinbucket == 0);
      bucketspec2->subbuckettab[currentchar]
                               [rightchar-1].bucketend = accubucketsize;
    }
  }
}

static void fillanysubbuckets(GtBucketspec2 *bucketspec2,
                              const GtBcktab *bcktab)
{
  GtCodetype code2, maxcode;
  unsigned int rightchar = 0, currentchar = 0;
  unsigned long rightbound, *specialchardist;

  maxcode = gt_bcktab_numofallcodes(bcktab) - 1;
  bucketspec2->expandfactor
    = (GtCodetype) gt_power_for_small_exponents(bucketspec2->numofchars,
                                                bucketspec2->prefixlength-2);
  bucketspec2->expandfillsum = gt_bcktab_filltable(bcktab,2U);
#ifdef SHOWBUCKETSPEC2
  showexpandcode(bucketspec2,bucketspec2->prefixlength);
#endif
  specialchardist = leftcontextofspecialchardist(bucketspec2->numofchars,
                                                 bucketspec2->encseq,
                                                 bucketspec2->readmode);
  for (code2 = 0; code2 < (GtCodetype) bucketspec2->numofcharssquared; code2++)
  {
    GtCodetype ecode = expandtwocharcode(code2,bucketspec2);
    gt_assert(ecode / bucketspec2->expandfactor == code2);
    rightbound = gt_bcktab_calcrightbounds(bcktab,
                                           ecode,
                                           maxcode,
                                           bucketspec2->partwidth);
    rightchar = (unsigned int) ((code2+1) % bucketspec2->numofchars);
    gt_assert((GtCodetype) currentchar == code2 / bucketspec2->numofchars);
    if (rightchar == 0)
    {
      gt_assert(rightbound >= specialchardist[currentchar]);
      gt_assert((GtCodetype) (bucketspec2->numofchars-1) ==
                code2 % bucketspec2->numofchars);
      bucketspec2->subbuckettab[currentchar]
                               [bucketspec2->numofchars-1].bucketend
        = rightbound - specialchardist[currentchar];
      bucketspec2->superbuckettab[currentchar].bucketend = rightbound;
      currentchar++;
    } else
    {
      gt_assert((GtCodetype) (rightchar-1) == code2 % bucketspec2->numofchars);
      bucketspec2->subbuckettab[currentchar][rightchar-1].bucketend
        = rightbound;
    }
  }
  gt_free(specialchardist);
}

GtBucketspec2 *gt_copysort_new(const GtBcktab *bcktab,
                               const GtEncseq *encseq,
                               GtReadmode readmode,
                               unsigned long partwidth,
                               unsigned int numofchars)
{
  GtBucketspec2 *bucketspec2;
  unsigned int idx;

  gt_assert(numofchars > 0);
  bucketspec2 = gt_malloc(sizeof (*bucketspec2));
  bucketspec2->partwidth = partwidth;
  bucketspec2->prefixlength = gt_bcktab_prefixlength(bcktab);
  bucketspec2->numofchars = numofchars;
  bucketspec2->numofcharssquared = numofchars * numofchars;
  bucketspec2->encseq = encseq;
  bucketspec2->readmode = readmode;
  bucketspec2->order = gt_malloc(sizeof (*bucketspec2->order) * numofchars);
  bucketspec2->superbuckettab
    = gt_malloc(sizeof (*bucketspec2->superbuckettab) * numofchars);
  gt_array2dim_malloc(bucketspec2->subbuckettab,(unsigned long) numofchars,
                      (unsigned long) numofchars);
  if (bucketspec2->prefixlength == 2U)
  {
    fill2subbuckets(bucketspec2,bcktab);
  } else
  {
    fillanysubbuckets(bucketspec2,bcktab);
  }
  for (idx = 0; idxorder[idx] = idx;
  }
  gt_qsort_r(bucketspec2->order,(size_t) numofchars,
             sizeof (*bucketspec2->order),bucketspec2,
             comparesuperbucketsizes);
  resetsorted(bucketspec2);
#ifdef SHOWBUCKETSPEC2
  showbucketspec2(bucketspec2);
#endif
  determinehardwork(bucketspec2);
  resetsorted(bucketspec2);
  return bucketspec2;
}

static void forwardderive(const GtBucketspec2 *bucketspec2,
                          GtSuffixsortspace *suffixsortspace,
                          unsigned long *targetoffset,
                          unsigned int source,
                          unsigned long idx)
{
  unsigned long startpos;
  GtUchar cc;

  gt_assert (idx < targetoffset[source]);
  for (; idx < targetoffset[source]; idx++)
  {
    startpos = gt_suffixsortspace_getdirect(suffixsortspace,idx);
    if (startpos > 0)
    {
      cc = gt_encseq_get_encoded_char(bucketspec2->encseq,
                                      startpos-1,
                                      bucketspec2->readmode);
      if (ISNOTSPECIAL(cc) && !bucketspec2->superbuckettab[cc].sorted)
      {
        gt_suffixsortspace_setdirect(suffixsortspace,targetoffset[cc],
                                     startpos - 1);
        targetoffset[cc]++;
      }
    }
  }
}

static void backwardderive(const GtBucketspec2 *bucketspec2,
                           GtSuffixsortspace *suffixsortspace,
                           unsigned long *targetoffset,
                           unsigned int source,
                           unsigned long idx)
{
  unsigned long startpos;
  GtUchar cc;

  for (; idx + 1 > targetoffset[source] + 1; idx--)
  {
    startpos = gt_suffixsortspace_getdirect(suffixsortspace,idx);
    if (startpos > 0)
    {
      cc = gt_encseq_get_encoded_char(bucketspec2->encseq,
                                      startpos-1,
                                      bucketspec2->readmode);
      if (ISNOTSPECIAL(cc) && !bucketspec2->superbuckettab[cc].sorted)
      {
        gt_suffixsortspace_setdirect(suffixsortspace,targetoffset[cc],
                                     startpos - 1);
        targetoffset[cc]--;
      }
    }
  }
}

bool gt_copysort_checkhardwork(const GtBucketspec2 *bucketspec2,
                               GtCodetype code)
{
  if (bucketspec2->prefixlength > 2U)
  {
    return bucketspec2->subbuckettab[0][code / bucketspec2->expandfactor].
                                        hardworktodo;
  } else
  {
    return bucketspec2->subbuckettab[0][code].hardworktodo;
  }
}

void gt_copysort_derivesorting(const GtBucketspec2 *bucketspec2,
                               GtSuffixsortspace *suffixsortspace,
                               GtLogger *logger)
{
  unsigned long hardwork = 0,
                *targetoffset;
  unsigned int idx, idxsource, source, second;

#ifdef WITHSUFFIXES
  {
    unsigned long idx;
    for (idx = 0; idx < bucketspec2->partwidth; idx++)
    {
      gt_encseq_showatstartpos(
                            stdout,
                            GT_ISDIRREVERSE(readmode) ? false : true,
                            GT_ISDIRCOMPLEMENT(readmode) ? true : false,
                            encseq,
                            gt_suffixsortspace_getdirect(suffixsortspace,idx));
    }
  }
#endif
  targetoffset = gt_malloc(sizeof (*targetoffset) * bucketspec2->numofchars);
  for (idxsource = 0; idxsourcenumofchars; idxsource++)
  {
    source = bucketspec2->order[idxsource];
    for (second = 0; second < bucketspec2->numofchars; second++)
    {
      if (!bucketspec2->subbuckettab[source][second].sorted && source != second)
      {
        gt_assert(bucketspec2->subbuckettab[source][second].hardworktodo);
        gt_logger_log(logger,"hard work for %u %u",source,second);
        hardwork += getendidx(bucketspec2,source,second) -
                    getstartidx(bucketspec2,source,second);
        bucketspec2->subbuckettab[source][second].sorted = true;
      } else
      {
        gt_assert(!bucketspec2->subbuckettab[source][second].hardworktodo);
      }
    }
    if (getstartidx(bucketspec2,source,0) <
        getstartidx(bucketspec2,source,source))
    {
      for (idx = 0; idx < bucketspec2->numofchars; idx++)
      {
        targetoffset[idx] = getstartidx(bucketspec2,idx,source);
      }
      forwardderive(bucketspec2,
                    suffixsortspace,
                    targetoffset,
                    source,
                    getstartidx(bucketspec2,source,0));
    }
    if (getendidx(bucketspec2,source,source) <
        getendidx(bucketspec2,source,bucketspec2->numofchars))
    {
      for (idx = 0; idx < bucketspec2->numofchars; idx++)
      {
        /* do not need to assert that getendidx(idx,source)  > 0, as later the
           value stored in targetoffset is incremented */
        targetoffset[idx] = getendidx(bucketspec2,idx,source) - 1;
      }
      gt_assert(getendidx(bucketspec2,source,bucketspec2->numofchars) > 0);
      backwardderive(bucketspec2,
                     suffixsortspace,
                     targetoffset,
                     source,
                     getendidx(bucketspec2,source,bucketspec2->numofchars) - 1);
    }
    for (idx = 0; idx < bucketspec2->numofchars; idx++)
    {
      bucketspec2->subbuckettab[idx][source].sorted = true;
    }
    bucketspec2->superbuckettab[source].sorted = true;
  }
  gt_free(targetoffset);
  gt_logger_log(logger,"hardwork = %lu (%.2f)",
                hardwork,
                (double) hardwork/gt_encseq_total_length(bucketspec2->encseq));
}

void gt_copysort_delete(GtBucketspec2 *bucketspec2)
{
  gt_assert(bucketspec2 != NULL);
  gt_array2dim_delete(bucketspec2->subbuckettab);
  gt_free(bucketspec2->superbuckettab);
  gt_free(bucketspec2->order);
  gt_free(bucketspec2);
}
genometools-1.5.1/src/match/sfx-copysort.h000066400000000000000000000032541211610345200205640ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_COPYSORT_H
#define SFX_COPYSORT_H

#include "core/codetype.h"
#include "core/encseq.h"
#include "core/logger.h"
#include "bcktab.h"
#include "sfx-suffixgetset.h"

typedef struct GtBucketspec2 GtBucketspec2;

GtBucketspec2 *gt_copysort_new(const GtBcktab *bcktab,
                               const GtEncseq *encseq,
                               GtReadmode readmode,
                               unsigned long partwidth,
                               unsigned int numofchars);

void gt_copysort_derivesorting(const GtBucketspec2 *bucketspec2,
                               GtSuffixsortspace *suffixsortspace,
                               GtLogger *logger);

bool gt_copysort_checkhardwork(const GtBucketspec2 *bucketspec2,
                               GtCodetype code);

void gt_copysort_delete(GtBucketspec2 *bucketspec2);

#endif
genometools-1.5.1/src/match/sfx-diffcov.c000066400000000000000000002125011211610345200203120ustar00rootroot00000000000000/*
  Copyright (c) 2009-2012 Stefan Kurtz 
  Copyright (c) 2009-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/* This module implements the difference cover based suffix sorting
   method from the following paper:

  @INPROCEEDINGS{BUR:KAER:2003,
  author = {Burkhardt, S. and K{\"a}rkk{\"a}inen, J.},
  title = {{Fast Lightweight Suffix Array Construction and Checking}},
  booktitle = {{Proceedings of the 14th Annual Symposium on Combinatorial
                Pattern Matching (CPM)}},
  year = {2003},
  editor = {{Baeza-Yates, R. and Ch{\'a}vez, E. and Crochemore, M.}},
  volume = {2676},
  series = {LNCS},
  pages = {200-210},
  publisher = {Springer-Verlag}
}

  The computation of the lcp follows the general concept of

  @INPROCEEDINGS{PUG:TUR:2008,
  author = {Puglisi, S.J. and Turpin, A.},
  title = {Space-Time Tradeoffs for Longest-Common-Prefix Array Computation},
  booktitle = {Proceedings of Algorithms and Computation, 19th International
               Symposium, {ISAAC} 2008, Gold Coast, Australia,
               December 15-17, 2008. Proceedings},
  year = {2008},
  editor = {Hong, S.-H. and Nagamochi, H. and Fukunaga, T.},
  volume = {5369},
  series = {Lecture Notes in Computer Science},
  pages = {124--135},
  publisher = {Springer},
  url = {http://dx.doi.org/10.1007/978-3-540-92182-0}
}

  based on the method of BUR:KAER:2003 to map sample positions to
  indexes in the sorted array of suffixes.

*/

#include 
#include 
#include "core/arraydef.h"
#include "core/assert_api.h"
#include "core/error_api.h"
#include "core/divmodmul.h"
#include "core/ma_api.h"
#include "core/minmax.h"
#include "core/mathsupport.h"
#include "core/unused_api.h"
#include "core/intbits.h"
#include "core/encseq.h"
#include "core/logger.h"
#include "core/encseq.h"
#include "core/stack-inlined.h"
#include "core/spacecalc.h"
#include "intcode-def.h"
#include "bcktab.h"
#include "initbasepower.h"
#include "sfx-strategy.h"
#include "sfx-diffcov.h"
#include "sfx-suffixgetset.h"
#include "sfx-bentsedg.h"
#include "sfx-apfxlen.h"
#include "sfx-suftaborder.h"
#include "sfx-enumcodes.h"

typedef unsigned char Diffrank;
#define Diffrankmax ((Diffrank) 255)
typedef unsigned short Diffvalue;
#define Diffvaluemax ((Diffvalue) 65535)

#define GT_MODV(VAL) ((VAL) & dcov->vmodmask)
#define GT_DIVV(VAL) ((VAL) >> dcov->logmod)

typedef struct
{
  unsigned long key,
                suffixstart;
} GtDcItventry;

typedef struct
{
  unsigned long blisbl, /* bucketleftindex + subbucketleft */
                width;
} GtDcPairsuffixptr;

GT_DECLAREARRAYSTRUCT(GtDcPairsuffixptr);

typedef GtDcPairsuffixptr GtInl_Queueelem;

#include "queue-inline.h"

typedef struct
{
  unsigned long blisbl, /* bucketleftindex + subbucketleft */
                width,
                count,
                totalwidth,
                maxwidth,
                depth;
  bool defined;
} GtDcFirstwithnewdepth;

typedef struct
{
  unsigned int offset;
  unsigned long idx1, idx2;
} GtLcptrace;

typedef uint32_t GtDifferencecover_Inversesuftabtype;
#define GT_DIFFERENCECOVER_INVERSESUFTAB_UNDEF UINT32_MAX
#define GT_DIFFERENCECOVER_MAX_SAMPLESIZE      (UINT32_MAX-1)

struct GtDifferencecover
{
  unsigned int vparam,
               logmod,
               size,
               vmodmask,
               hvalue,  /* not necessary */
               numofchars,
               prefixlength;
  unsigned long *coverrank_evaluated;
  GtBitsequence *coverrank_bits;
  Diffvalue *diffvalues,  /* points to the difference cover */
            *diff2pos;    /* table d from BUR:KAER:2003 */
  size_t requiredspace;
  unsigned long totallength;
  GtLeftborder *leftborder; /* points to bcktab->leftborder */
  GtBcktab *bcktab;
  const GtEncseq *encseq;
  GtReadmode readmode;
  unsigned long samplesize, effectivesamplesize, samplesize_upperbound;
  const GtCodetype **multimappower;
  GtCodetype *filltable;
  GtEncseqReader *esr1, *esr2;
  GtDifferencecover_Inversesuftabtype *inversesuftab;
  unsigned long allocateditvinfo,
                currentqueuesize,
                maxqueuesize,
                currentdepth;
  GtCodetype maxcode;
  GtDcFirstwithnewdepth firstwithnewdepth;
  GtInl_Queue *rangestobesorted;
  GtDcItventry *itvinfo;
  GtArrayGtDcPairsuffixptr firstgeneration;
  GtLcpvalues *samplelcpvalues, *sssplcpvalues;
  unsigned long firstgenerationtotalwidth,
                firstgenerationcount;
  GtLogger *logger;
  GtSuffixsortspace *sssp,
                    *sortedsample;
  GtRMQ *rmq;
  unsigned long sortoffset;
};

/* Compute difference cover on the fly */

#define UScast(X) ((Diffvalue) X)
#define UCcast(X) ((Diffrank) X)

#include "tab-diffcover.h"

static unsigned long dc_suffixptrget(const GtDifferencecover *dcov,
                                     unsigned long idx)
{
  gt_suffixsortspace_nooffsets(dcov->sortedsample);
  return gt_suffixsortspace_get(dcov->sortedsample,0,idx);
}

static void dc_suffixptrset(const GtDifferencecover *dcov,
                            unsigned long idx,unsigned long value)
{
  gt_suffixsortspace_nooffsets(dcov->sortedsample);
  gt_suffixsortspace_set(dcov->sortedsample,0,idx,value);
}

static void dc_fillcoverrank(GtDifferencecover *dcov)
{
  unsigned int i;
  Diffrank j;
  const unsigned long step = GT_DIVV(dcov->totallength) + 1;
  unsigned long sum;

  dcov->coverrank_evaluated
    = gt_malloc(sizeof (*dcov->coverrank_evaluated) * dcov->vparam);
  GT_INITBITTAB(dcov->coverrank_bits,dcov->vparam);
  dcov->requiredspace += sizeof (*dcov->coverrank_evaluated) * dcov->vparam;
  gt_assert(dcov->size <= Diffrankmax);
  for (i=0; ivparam; i++)
  {
    dcov->coverrank_evaluated[i] = ULONG_MAX; /* initialize as undefined */
  }
  for (sum = 0, j=0; jsize; j++, sum += step)
  {
    Diffvalue d = dcov->diffvalues[j];
    dcov->coverrank_evaluated[d] = sum; /* jth value from difference cover
                                           gets rank j * step. */
    GT_SETIBIT(dcov->coverrank_bits,d);
  }
}

static bool dc_is_in_differencecover(const GtDifferencecover *dcov,
                                     unsigned long modpos)
{
  return GT_ISIBITSET(dcov->coverrank_bits,modpos) ? true : false;
}

static void dc_filldiff2pos(GtDifferencecover *dcov)
{
  Diffvalue *iptr, *jptr;

  dcov->diff2pos = gt_malloc(sizeof (*dcov->diff2pos) * dcov->vparam);
  dcov->requiredspace += sizeof (*dcov->diff2pos) * dcov->vparam;
  for (iptr=dcov->diffvalues + dcov->size - 1; iptr>=dcov->diffvalues; iptr--)
  {
    for (jptr=dcov->diffvalues; jptrdiffvalues + dcov->size; jptr++)
    {
      dcov->diff2pos[GT_MODV(*jptr - *iptr)] = *iptr;
    }
  }
}

#ifdef WITHcomputehvalue

/* XXX: the following function is currently not used */

static unsigned int cd_computehvalue(const GtDifferencecover *dcov,
                                     unsigned long totallength)
{
  Diffvalue next;
  unsigned int h, nmodv = GT_MODV(totallength);

  for (h = 0; h < dcov->size; h++)
  {
    if (dcov->diffvalues[h] <= (Diffvalue) nmodv)
    {
      if (h + 1 < dcov->size)
      {
        next = dcov->diffvalues[h+1];
      } else
      {
        next = (Diffvalue) dcov->vparam;
      }
      if ((Diffvalue) nmodv < next)
      {
        return h;
      }
    }
  }
  gt_assert(false);
  return 0;
}
#endif

void gt_differencecover_set_sssp_lcp(GtDifferencecover *dcov,
                                     GtSuffixsortspace *sssp,
                                     GtOutlcpinfo *outlcpinfo)
{
  dcov->sssp = sssp;
  if (outlcpinfo != NULL)
  {
    dcov->sssplcpvalues = gt_Outlcpinfo_lcpvalues_ref(outlcpinfo);
  }
}

static int gt_differencecover_vparamverify(const GtDifferencecover *dcov,
                                           GtError *err)
{
  if (dcov->vparam < dcov->prefixlength)
  {
    gt_error_set(err,"difference cover modulo %u is too small, use larger "
                     "parameter for option -dc",dcov->vparam);
    return -1;
  }
  return 0;
}

GtDifferencecover *gt_differencecover_new(unsigned int vparam,
                                          const GtEncseq *encseq,
                                          GtReadmode readmode,
                                          unsigned int outerprefixlength,
                                          GtLogger *logger)
{
  unsigned int offset = 0, v = 1U;
  GtDifferencecover *dcov;
  bool found = false;

  dcov = gt_malloc(sizeof (*dcov));
  dcov->requiredspace = sizeof (*dcov);
  dcov->numofchars = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
  dcov->totallength = gt_encseq_total_length(encseq);
  dcov->logger = logger;
  dcov->samplesize_upperbound = 0;
  dcov->sssp = NULL;
  dcov->rmq = NULL;
  for (dcov->logmod = 0;
       dcov->logmod < (unsigned int) (sizeof (differencecoversizes)/
                                      sizeof (differencecoversizes[0]));
       dcov->logmod++)
  {
    if (v == vparam)
    {
      dcov->size = differencecoversizes[dcov->logmod];
      dcov->samplesize_upperbound
        = (unsigned long) (GT_DIVV(dcov->totallength) + 1) * dcov->size;
      dcov->diffvalues = differencecovertab + offset;
      if (dcov->samplesize_upperbound <= GT_DIFFERENCECOVER_MAX_SAMPLESIZE)
      {
        found = true;
        break;
      }
    }
    offset += differencecoversizes[dcov->logmod];
    v = GT_MULT2(v);
  }
  if (!found)
  {
    gt_free(dcov);
    return NULL;
  }
  if (outerprefixlength == 0)
  {
    dcov->prefixlength = 0;
  } else
  {
    dcov->prefixlength
      = gt_recommendedprefixlength(dcov->numofchars,
                                   dcov->samplesize_upperbound,
                                   GT_RECOMMENDED_MULTIPLIER_DEFAULT,
                                   true);
    if (outerprefixlength > 0 && dcov->prefixlength > outerprefixlength)
    {
      dcov->prefixlength = outerprefixlength;
    }
    gt_assert(dcov->prefixlength > 0);
  }
  dcov->vparam = 1U << (dcov->logmod);
  dcov->vmodmask = dcov->vparam-1;
#ifdef WITHcomputehvalue
  dcov->hvalue = dc_computehvalue(dcov,totallength);
#endif
  dcov->encseq = encseq;
  dcov->readmode = readmode;
  dcov->bcktab = NULL;
  dcov->sortedsample = NULL;
  dcov->filltable = NULL;
  dcov->multimappower = NULL;
  dc_fillcoverrank(dcov);
  dcov->diff2pos = NULL; /* this is later initialized */
  dcov->esr1 = NULL;
  dcov->esr2 = NULL;
  dcov->allocateditvinfo = 0;
  dcov->itvinfo = NULL;
  dcov->currentdepth = 0;
  dcov->firstwithnewdepth.defined = false;
  dcov->firstwithnewdepth.depth = 0;
  dcov->firstwithnewdepth.totalwidth = 0;
  dcov->firstwithnewdepth.count = 0;
  dcov->firstwithnewdepth.blisbl = 0;
  dcov->firstwithnewdepth.width = 0;
  dcov->firstwithnewdepth.maxwidth = 0;
  dcov->currentqueuesize = 0;
  dcov->maxqueuesize = 0;
  dcov->inversesuftab = NULL;
  dcov->samplelcpvalues = NULL;
  dcov->sssplcpvalues = NULL;
  dcov->firstgenerationtotalwidth = 0;
  dcov->firstgenerationcount = 0;
  GT_INITARRAY(&dcov->firstgeneration,GtDcPairsuffixptr);
  return dcov;
}

unsigned long gt_differencecover_samplesize(const GtDifferencecover *dcov)
{
  return dcov->samplesize;
}

size_t gt_differencecover_requiredspace(const GtDifferencecover *dcov)
{
  return dcov->requiredspace;
}

/* The following is the \delta function from BUR:KAER:2003. */

static unsigned int dc_differencecover_delta(const GtDifferencecover *dcov,
                                             unsigned long pos1,
                                             unsigned long pos2)
{
  return (unsigned int) GT_MODV(dcov->diff2pos[GT_MODV(pos2 - pos1)] - pos1);
}

bool gt_differencecover_is_empty(const GtDifferencecover *dcov)
{
  gt_assert(dcov != NULL);
  return dcov->effectivesamplesize == 0 ? true : false;
}

void gt_differencecover_delete(GtDifferencecover *dcov)
{
  if (dcov != NULL)
  {
    gt_assert(dcov->bcktab == NULL);
    gt_assert(dcov->sortedsample == NULL);
    gt_assert(dcov->filltable == NULL);
    gt_assert(dcov->multimappower == NULL);
    gt_assert(dcov->esr1 == NULL);
    gt_assert(dcov->esr2 == NULL);

    gt_free(dcov->coverrank_evaluated);
    dcov->coverrank_evaluated = NULL;
    gt_free(dcov->coverrank_bits);
    dcov->coverrank_bits = NULL;
    gt_free(dcov->diff2pos);
    dcov->diff2pos = NULL;
    gt_free(dcov->inversesuftab);
    dcov->inversesuftab = NULL;
    gt_rmq_delete(dcov->rmq);
    dcov->rmq = NULL;
    gt_free(dcov);
  }
}

/* the following implements the \mu function from BAE:KAER:2003 */

static unsigned long dc_differencecover_packsamplepos(
                                                 const GtDifferencecover *dcov,
                                                 unsigned long pos)
{
  gt_assert(dc_is_in_differencecover(dcov,GT_MODV(pos)));
  return dcov->coverrank_evaluated[GT_MODV(pos)] + GT_DIVV(pos);
}

GT_DECLAREARRAYSTRUCT(Codeatposition);

static unsigned long dc_derivespecialcodesonthefly(GtDifferencecover *dcov,
                                                   const GtArrayCodeatposition
                                                           *codelist)
{
  unsigned int prefixindex, unitsnotspecial;
  Enumcodeatposition *ecp;
  Specialcontext specialcontext;
  unsigned long countderived = 0, pos, sampleindex;
  GtCodetype code;

  for (prefixindex=1U; prefixindex < dcov->prefixlength; prefixindex++)
  {
    /* XXX use one structure and reinit it */
    ecp = gt_Enumcodeatposition_new(dcov->encseq,dcov->readmode,
                                    dcov->prefixlength,
                                    dcov->numofchars);
    while (gt_Enumcodeatposition_next(&specialcontext,ecp))
    {
      if (prefixindex <= specialcontext.maxprefixindex)
      {
        gt_assert(specialcontext.position >= (unsigned long) prefixindex);
        pos = (unsigned long) (specialcontext.position - prefixindex);
        if (dc_is_in_differencecover(dcov,GT_MODV(pos)))
        {
          if (codelist != NULL)
          {
            gt_assert(countderived < codelist->nextfreeCodeatposition);
            gt_assert(codelist->spaceCodeatposition[countderived].maxprefixindex
                      == prefixindex);
            gt_assert(codelist->spaceCodeatposition[countderived].position
                      == pos);
          }
          code = gt_encseq_extractprefixcode(&unitsnotspecial,
                                             dcov->encseq,
                                             dcov->filltable,
                                             dcov->readmode,
                                             dcov->esr1,
                                             dcov->multimappower,
                                             pos,
                                             dcov->prefixlength);
          if (codelist != NULL)
          {
            gt_assert((GtCodetype) codelist->spaceCodeatposition[
                                           countderived].code == code);
          }
          /*
          printf("%u %lu\n",prefixindex,
                            (unsigned long)
                            (specialcontext.position-prefixindex));
          */
          countderived++;
          gt_bcktab_updatespecials(dcov->bcktab,code,prefixindex);
          gt_assert(code > 0);
          sampleindex = gt_bcktab_leftborder_insertionindex(dcov->leftborder,
                                                            code);
          gt_assert(sampleindex < dcov->effectivesamplesize);
          dc_suffixptrset(dcov,sampleindex,pos);
        }
      }
    }
    gt_Enumcodeatposition_delete(ecp);
    ecp = NULL;
  }
  if (codelist != NULL)
  {
    gt_assert(countderived == codelist->nextfreeCodeatposition);
  }
  return countderived;
}

static int dc_compareCodeatpositon(const void *vala,const void *valb)
{
  const Codeatposition *a = (const Codeatposition *) vala;
  const Codeatposition *b = (const Codeatposition *) valb;

  if (a->maxprefixindex < b->maxprefixindex)
  {
    return -1;
  }
  if (a->maxprefixindex > b->maxprefixindex)
  {
    return 1;
  }
  if (a->position < b->position)
  {
    return 1;
  }
  if (a->position > b->position)
  {
    return -1;
  }
  gt_assert(false);
  return 0;
}

static void dc_validate_samplepositons(const GtDifferencecover *dcov)
{
  unsigned long pos;
  unsigned int modvalue;
  Diffvalue *diffptr, *afterend;
  unsigned long idx;
  GtBitsequence *sampleidxused = NULL;

  GT_INITBITTAB(sampleidxused,dcov->samplesize_upperbound);
  diffptr = dcov->diffvalues;
  afterend = dcov->diffvalues + dcov->size;
  for (pos = 0, modvalue = 0; pos <= dcov->totallength; pos++)
  {
    gt_assert((unsigned long) modvalue == GT_MODV(pos));
    gt_assert(diffptr == afterend || *diffptr >= (Diffvalue) modvalue);
    if (diffptr < afterend && (Diffvalue) modvalue == *diffptr)
    {
      idx = dc_differencecover_packsamplepos(dcov,pos);
      gt_assert(sampleidxused != NULL);
      if (GT_ISIBITSET(sampleidxused,idx))
      {
        fprintf(stderr,"sample index %lu for pos %lu already used before\n",
                       idx,(unsigned long) pos);
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
      GT_SETIBIT(sampleidxused,idx);
      diffptr++;
    }
    if (modvalue < dcov->vmodmask)
    {
      modvalue++;
    } else
    {
      modvalue = 0;
      diffptr = dcov->diffvalues;
    }
  }
  gt_free(sampleidxused);
}

static void dc_inversesuftab_set(GtDifferencecover *dcov,
                                 unsigned long pos,
                                 unsigned long sampleindex)
{
  gt_assert (sampleindex < dcov->samplesize);
  dcov->inversesuftab[dc_differencecover_packsamplepos(dcov,pos)]
    = (uint32_t) sampleindex;
}

static unsigned long dc_inversesuftab_get(const GtDifferencecover *dcov,
                                          unsigned long pos)
{
  return (unsigned long)
         dcov->inversesuftab[dc_differencecover_packsamplepos(dcov,pos)];
}

static void dc_initinversesuftabnonspecials(GtDifferencecover *dcov)
{
  unsigned long sampleindex, pos;

  for (sampleindex=0; sampleindex < dcov->effectivesamplesize; sampleindex++)
  {
    pos = dc_suffixptrget(dcov,sampleindex);
    dc_inversesuftab_set(dcov,pos,sampleindex);
  }
}

static unsigned long dc_insertfullspecialrangesample(GtDifferencecover *dcov,
                                                     unsigned long specialidx,
                                                     unsigned long leftpos,
                                                     unsigned long rightpos)
{
  unsigned long pos;

  gt_assert(leftpos < rightpos);
  if (GT_ISDIRREVERSE(dcov->readmode))
  {
    pos = rightpos - 1;
  } else
  {
    pos = leftpos;
  }
  while (true)
  {
    if (GT_ISDIRREVERSE(dcov->readmode))
    {
      unsigned long revpos;

      gt_assert(pos < dcov->totallength);
      revpos = GT_REVERSEPOS(dcov->totallength,pos);
      if (dc_is_in_differencecover(dcov,GT_MODV(revpos)))
      {
        dc_inversesuftab_set(dcov,revpos,specialidx);
        specialidx++;
      }
      if (pos == leftpos)
      {
        break;
      }
      pos--;
    } else
    {
      if (dc_is_in_differencecover(dcov,GT_MODV(pos)))
      {
        dc_inversesuftab_set(dcov,pos,specialidx);
        specialidx++;
      }
      if (pos == rightpos-1)
      {
        break;
      }
      pos++;
    }
  }
  return specialidx;
}

static void dc_initinversesuftabspecials(GtDifferencecover *dcov)
{
  unsigned long idx;

  dcov->inversesuftab = gt_malloc(sizeof (*dcov->inversesuftab) *
                                  dcov->samplesize_upperbound);
  for (idx = 0; idx < dcov->samplesize_upperbound; idx++)
  {
    dcov->inversesuftab[idx] = GT_DIFFERENCECOVER_INVERSESUFTAB_UNDEF;
  }
  dcov->requiredspace += sizeof (*dcov->inversesuftab) *
                         dcov->samplesize_upperbound;
  if (gt_encseq_has_specialranges(dcov->encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;
    unsigned long specialidx;

    sri = gt_specialrangeiterator_new(dcov->encseq,
                                      GT_ISDIRREVERSE(dcov->readmode)
                                      ? false : true);
    specialidx = dcov->effectivesamplesize;
    while (gt_specialrangeiterator_next(sri,&range))
    {
      /*
      printf("specialrange %lu %lu\n",(unsigned long) range.leftpos,
                                      (unsigned long) range.rightpos);
      */
      specialidx = dc_insertfullspecialrangesample(dcov,
                                                   specialidx,
                                                   range.start,
                                                   range.end);
    }
    gt_specialrangeiterator_delete(sri);
    sri = NULL;
  }
  if (dc_is_in_differencecover(dcov,GT_MODV(dcov->totallength)))
  {
    gt_assert(dcov->samplesize > 0);
    dc_inversesuftab_set(dcov,dcov->totallength,dcov->samplesize-1);
  }
}

static void dc_updatewidth (GtDifferencecover *dcov,unsigned long width,
                            unsigned int depth)
{
  if (width > 1UL)
  {
    dcov->firstgenerationtotalwidth += width;
    dcov->firstgenerationcount++;
    if (dcov->allocateditvinfo < width)
    {
      dcov->allocateditvinfo = width;
    }
    if (dcov->currentdepth == 0)
    {
      dcov->currentdepth = (unsigned long) depth;
    } else
    {
      gt_assert(dcov->currentdepth == (unsigned long) depth);
    }
  }
}

static void dc_initinversesuftabnonspecialsadjust(GtDifferencecover *dcov)
{
  GtCodetype code;
  GtBucketspecification bucketspec;
  unsigned long idx = 0;
  const GtCodetype mincode = 0;
  unsigned int rightchar = 0; /* as mincode is 0 */

  for (code = mincode; code <= dcov->maxcode; code++)
  {
    rightchar = gt_bcktab_calcboundsparts(&bucketspec,
                                          dcov->bcktab,
                                          code,
                                          dcov->maxcode,
                                          dcov->effectivesamplesize,
                                          rightchar);
    for (/* Nothing */; idx < bucketspec.left; idx++)
    {
      dc_inversesuftab_set(dcov,dc_suffixptrget(dcov,idx),idx);
    }
    dc_updatewidth (dcov,bucketspec.nonspecialsinbucket,dcov->prefixlength);
    for (/* Nothing */;
         idx < bucketspec.left + bucketspec.nonspecialsinbucket;
         idx++)
    {
      dc_inversesuftab_set(dcov,dc_suffixptrget(dcov,idx),
                           bucketspec.left);
    }
  }
  for (/* Nothing */; idx < dcov->effectivesamplesize; idx++)
  {
    dc_inversesuftab_set(dcov,dc_suffixptrget(dcov,idx),idx);
  }
}

static void dc_anchorleftmost(GtDifferencecover *dcov,
                              unsigned long blisbl,
                              unsigned long width)
{
  unsigned long idx;

  for (idx = blisbl; idx < blisbl + width; idx++)
  {
    dc_inversesuftab_set(dcov,dc_suffixptrget(dcov,idx),blisbl);
  }
}

static void dc_showintervalsizes(unsigned long count,
                                 unsigned long totalwidth,
                                 unsigned long effectivesamplesize,
                                 unsigned long maxwidth,
                                 unsigned long depth,
                                 GtLogger *logger)
{
  gt_logger_log(logger,
              "level %lu"
              ": (intervals=%lu,total=%lu,avg=%.2f,%.2f%% of all,maxwidth=%lu)",
              depth,
              count,
              totalwidth,
              (double) totalwidth/count,
              100.0 * (double) totalwidth/effectivesamplesize,
              maxwidth);
}

static void dc_processunsortedrange(GtDifferencecover *dcov,
                                    unsigned long blisbl,
                                    unsigned long width,
                                    unsigned long depth)
{
  GtDcPairsuffixptr pairelem;

  gt_assert(width >= 2UL && depth > 0);
  gt_assert(!dcov->firstwithnewdepth.defined ||
            (dcov->firstwithnewdepth.depth > 0 &&
             dcov->firstwithnewdepth.depth <= depth));
  if (dcov->firstwithnewdepth.defined &&
      dcov->firstwithnewdepth.depth == depth)
  {
    dcov->firstwithnewdepth.count++;
    dcov->firstwithnewdepth.totalwidth += width;
    if (dcov->firstwithnewdepth.maxwidth < width)
    {
      dcov->firstwithnewdepth.maxwidth = width;
    }
  } else
  {
    if (dcov->firstwithnewdepth.defined)
    {
      dc_showintervalsizes(dcov->firstwithnewdepth.count,
                           dcov->firstwithnewdepth.totalwidth,
                           dcov->effectivesamplesize,
                           dcov->firstwithnewdepth.maxwidth,
                           dcov->firstwithnewdepth.depth,
                           dcov->logger);
    } else
    {
      dcov->firstwithnewdepth.defined = true;
    }
    gt_logger_log(dcov->logger,"enter new level %lu",depth);
    dcov->firstwithnewdepth.blisbl = blisbl;
    dcov->firstwithnewdepth.width = width;
    dcov->firstwithnewdepth.depth = depth;
    dcov->firstwithnewdepth.count = 1UL;
    dcov->firstwithnewdepth.totalwidth = width;
    dcov->firstwithnewdepth.maxwidth = width;
  }
  pairelem.blisbl = blisbl;
  pairelem.width = width;
  gt_inl_queue_add(dcov->rangestobesorted,pairelem,false);
  dcov->currentqueuesize++;
  if (dcov->maxqueuesize < dcov->currentqueuesize)
  {
    dcov->maxqueuesize = dcov->currentqueuesize;
  }
}

static int dc_compareitv(const void *a,const void *b)
{
  const GtDcItventry *itva = (const GtDcItventry *) a,
                     *itvb = (const GtDcItventry *) b;

  if (itva->key < itvb->key)
  {
    return -1;
  }
  if (itva->key > itvb->key)
  {
    return 1;
  }
  return 0;
}

static void dc_setlcpvaluesofrunsortedrange(GtLcpvalues *samplelcpvalues,
                                            unsigned long blisbl,
                                            unsigned long width,
                                            unsigned long lcpvalue)
{
  unsigned long idx;

  for (idx = blisbl+1; idx < blisbl + width; idx++)
  {
    gt_lcptab_update(samplelcpvalues,0,idx,lcpvalue);
  }
}

static void dc_sortsuffixesonthislevel(GtDifferencecover *dcov,
                                       unsigned long blisbl,
                                       unsigned long width)
{
  unsigned long idx, rangestart, startpos;

  if (dcov->itvinfo == NULL)
  {
    dcov->itvinfo = gt_malloc(sizeof (*dcov->itvinfo) *
                              dcov->allocateditvinfo);
  }
  if (dcov->firstwithnewdepth.blisbl == blisbl &&
      dcov->firstwithnewdepth.width == width)
  {
    dcov->currentdepth = dcov->firstwithnewdepth.depth;
  }
  gt_assert(dcov->allocateditvinfo >= width);
  /*
  printf("new interval of width %lu\n",width);
  */
  for (idx=0; idxitvinfo[idx].suffixstart = startpos;
    dcov->itvinfo[idx].key
      = dc_inversesuftab_get(dcov,startpos + dcov->currentdepth);
  }
  qsort(dcov->itvinfo,(size_t) width,sizeof (*dcov->itvinfo),dc_compareitv);
  for (idx=0; idxitvinfo[idx].suffixstart);
  }
  rangestart = 0;
  for (idx=1UL; idxitvinfo[idx-1].key != dcov->itvinfo[idx].key)
    {
      if (rangestart + 1 < idx)
      {
        dc_processunsortedrange(dcov,
                                blisbl + rangestart,
                                idx - rangestart,
                                GT_MULT2(dcov->currentdepth));
        if (dcov->samplelcpvalues != NULL)
        {
          dc_setlcpvaluesofrunsortedrange(dcov->samplelcpvalues,
                                          blisbl + rangestart,
                                          idx - rangestart,
                                          GT_MULT2(dcov->currentdepth));
        }
        dc_anchorleftmost(dcov, blisbl + rangestart, idx - rangestart);
      } else
      {
        unsigned long currentsuftabentry
          = dc_suffixptrget(dcov,blisbl+rangestart);

        gt_assert(rangestart + 1 == idx);
        dc_inversesuftab_set(dcov,currentsuftabentry,
                             blisbl+rangestart);
      }
      if (dcov->samplelcpvalues != NULL)
      {
        gt_lcptab_update(dcov->samplelcpvalues,
                         0,blisbl + idx,dcov->currentdepth);
      }
      rangestart = idx;
    }
  }
  if (rangestart + 1 < width)
  {
    dc_processunsortedrange(dcov,
                            blisbl + rangestart,
                            width - rangestart,
                            GT_MULT2(dcov->currentdepth));
    if (dcov->samplelcpvalues != NULL)
    {
      dc_setlcpvaluesofrunsortedrange(dcov->samplelcpvalues,
                                      blisbl + rangestart,
                                      width - rangestart,
                                      GT_MULT2(dcov->currentdepth));
    }
    dc_anchorleftmost(dcov, blisbl + rangestart, width - rangestart);
  } else
  {
    unsigned long currentsuftabentry
      = dc_suffixptrget(dcov,blisbl+rangestart);
    dc_inversesuftab_set(dcov,currentsuftabentry,blisbl+rangestart);
  }
}

static void dc_bcktab2firstlevelintervals(GtDifferencecover *dcov)
{
  GtCodetype code;
  unsigned int rightchar;
  GtBucketspecification bucketspec;
  const GtCodetype mincode = 0;

  gt_logger_log(dcov->logger,"maxbucketsize=%lu",dcov->allocateditvinfo);
  rightchar = (unsigned int) (mincode % dcov->numofchars);
  for (code = 0; code <= dcov->maxcode; code++)
  {
    rightchar = gt_bcktab_calcboundsparts(&bucketspec,
                                          dcov->bcktab,
                                          code,
                                          dcov->maxcode,
                                          dcov->effectivesamplesize,
                                          rightchar);
    if (bucketspec.nonspecialsinbucket > 1UL)
    {
      dc_sortsuffixesonthislevel(dcov,
                                 bucketspec.left,
                                 bucketspec.nonspecialsinbucket);
    }
  }
}

static void dc_addunsortedrange(void *voiddcov,
                                unsigned long blisbl,
                                unsigned long width,
                                GT_UNUSED unsigned long depth)
{
  GtDifferencecover *dcov = (GtDifferencecover *) voiddcov;
  GtDcPairsuffixptr *ptr;

  gt_assert(dcov->sssp == NULL);
  gt_assert(depth >= (unsigned long) dcov->vparam);
  dc_updatewidth (dcov,width,dcov->vparam);
  GT_GETNEXTFREEINARRAY(ptr,&dcov->firstgeneration,GtDcPairsuffixptr,1024);
  ptr->blisbl = blisbl;
  ptr->width = width;
}

static unsigned long gt_differencecover_eval_lcp(const GtLcptrace *lcptrace,
                                                 const GtDifferencecover *dcov)
{
  if (lcptrace->idx1 < dcov->effectivesamplesize &&
      lcptrace->idx2 < dcov->effectivesamplesize)
  {
    gt_assert(dcov->rmq != NULL);
    return (unsigned long)
            gt_rmq_find_min_value(dcov->rmq,
                                  MIN(lcptrace->idx1,lcptrace->idx2)+1,
                                  MAX(lcptrace->idx1,lcptrace->idx2))
             + lcptrace->offset;
  }
  return (unsigned long) lcptrace->offset;
}

int gt_differencecover_compare (const GtDifferencecover *dcov,
                                GtLcptrace *lcptrace,
                                unsigned long suffixpos1,
                                unsigned long suffixpos2)
{
  gt_assert(suffixpos1 < dcov->totallength);
  gt_assert(suffixpos2 < dcov->totallength);
  lcptrace->offset = dc_differencecover_delta(dcov,suffixpos1,suffixpos2);
  lcptrace->idx1 = dc_inversesuftab_get(dcov,suffixpos1 + lcptrace->offset);
  lcptrace->idx2 = dc_inversesuftab_get(dcov,suffixpos2 + lcptrace->offset);
  gt_assert(lcptrace->idx1 != lcptrace->idx2);
  return lcptrace->idx1 < lcptrace->idx2 ? -1 : 1;
}

#ifdef  QSORTNAME
#undef  QSORTNAME
#endif

#define QSORTNAME(NAME) dc_##NAME

#define dc_ARRAY_GET(ARR,RELIDX)\
        gt_suffixsortspace_get(data->sssp,data->sortoffset,RELIDX)

#define dc_ARRAY_SET(ARR,RELIDX,VALUE)\
        gt_suffixsortspace_set(data->sssp,data->sortoffset,RELIDX,VALUE)

typedef GtDifferencecover * QSORTNAME(Datatype);

static int QSORTNAME(qsortcmparr) (
                  unsigned long a,
                  unsigned long b,
                  GtLcptrace *lcptrace,
                  const QSORTNAME(Datatype) data)
{
  unsigned long suffixpos1, suffixpos2;

  gt_assert(data->sssp != NULL);
  suffixpos1 = dc_ARRAY_GET(NULL,a);
  suffixpos2 = dc_ARRAY_GET(NULL,b);
  return gt_differencecover_compare (data, lcptrace, suffixpos1, suffixpos2);
}

typedef void * QSORTNAME(Sorttype);

/*
 * Qsort routine from Bentley & McIlroy's ``Engineering a Sort Function''.
 */

#ifndef GT_QSORT_ARR_SWAP
#define GT_QSORT_ARR_SWAP(ARR,A,B)\
        if ((A) != (B))\
        {\
          tmp = QSORTNAME(ARRAY_GET)(ARR,A);\
          QSORTNAME(ARRAY_SET)(ARR,A,QSORTNAME(ARRAY_GET)(ARR,B));\
          QSORTNAME(ARRAY_SET)(ARR,B,tmp);\
        }
#endif

#ifndef GT_QSORT_ARR_VECSWAP
#define GT_QSORT_ARR_VECSWAP(ARR,A,B,N)\
        aidx = A;\
        bidx = B;\
        while ((N)-- > 0)\
        {\
          tmp = QSORTNAME(ARRAY_GET)(ARR,aidx);\
          QSORTNAME(ARRAY_SET)(ARR,aidx,QSORTNAME(ARRAY_GET)(ARR,bidx));\
          QSORTNAME(ARRAY_SET)(ARR,bidx,tmp);\
          aidx++;\
          bidx++;\
        }
#endif

static inline unsigned long QSORTNAME(gt_inlined_qsort_arr_r_med3)
                     (unsigned long a, unsigned long b, unsigned long c,
                      GtLcptrace *lcptrace,
                      const QSORTNAME(Datatype) data)
{
  return QSORTNAME(qsortcmparr) (a, b, lcptrace, data) < 0
           ? (QSORTNAME(qsortcmparr) (b, c, lcptrace, data) < 0
                ? b
                : (QSORTNAME(qsortcmparr) (a, c, lcptrace, data) < 0
                     ? c : a))
           : (QSORTNAME(qsortcmparr) (b, c, lcptrace, data) > 0
                ? b
                : (QSORTNAME(qsortcmparr) (a, c, lcptrace, data) < 0
                     ? a
                     : c));
}

#ifndef GT_STACK_INTERVALARRAYTOBESORTED_DEFINED
typedef struct
{
  unsigned long startindex,
                len;
} Intervalarrtobesorted;

GT_STACK_DECLARESTRUCT(Intervalarrtobesorted,32UL);
#define GT_STACK_INTERVALARRAYTOBESORTED_DEFINED
#endif

static void QSORTNAME(gt_inlinedarr_qsort_r) (
                                   unsigned long insertionsortthreshold,
                                   bool handlenotswapped,
                                   unsigned long len,
                                   QSORTNAME(Datatype) data,
                                   unsigned long subbucketleft)
{
  unsigned long tmp, pa, pb, pc, pd, pl, pm, pn, aidx, bidx, s,
                smallermaxlcp, greatermaxlcp;
  int r;
  bool swapped;
  GtStackIntervalarrtobesorted intervalstack;
  Intervalarrtobesorted current;
  GtLcptrace lcptrace;

  GT_STACK_INIT(&intervalstack,32UL);
  current.startindex = 0;
  current.len = len;
  GT_STACK_PUSH(&intervalstack,current);
  if (insertionsortthreshold <= 2UL)
  {
    insertionsortthreshold = 6UL;
  }
  while (!GT_STACK_ISEMPTY(&intervalstack))
  {
    swapped = false;
    current = GT_STACK_POP(&intervalstack);
    if (current.len <= insertionsortthreshold)
    {
      for (pm = current.startindex + 1;
           pm < current.startindex + current.len; pm++)
      {
        for (pl = pm; pl > current.startindex; pl--)
        {
          r = QSORTNAME(qsortcmparr) (pl - 1, pl, &lcptrace, data);
          if (data->sssplcpvalues != NULL)
          {
            if (pl < pm && r > 0)
            {
              gt_lcptab_update(data->sssplcpvalues,subbucketleft,pl+1,
                               gt_lcptab_getvalue(data->sssplcpvalues,
                                                     subbucketleft,pl));
            }
            gt_lcptab_update(data->sssplcpvalues,subbucketleft,pl,
                             gt_differencecover_eval_lcp(&lcptrace, data));
          }
          if (r <= 0)
          {
            break;
          }
          GT_QSORT_ARR_SWAP (arr, pl, pl - 1);
        }
      }
      continue;
    }
    pm = current.startindex + GT_DIV2 (current.len);
    if (current.len > 7UL)
    {
      pl = current.startindex;
      pn = current.startindex + current.len - 1;
      if (current.len > 40UL)
      {
        s = GT_DIV8 (current.len);
        pl = QSORTNAME(gt_inlined_qsort_arr_r_med3) (pl, pl + s,
                                                     pl + GT_MULT2 (s),
                                                     &lcptrace, data);
        gt_assert(pm >= s);
        pm = QSORTNAME(gt_inlined_qsort_arr_r_med3) (pm - s, pm,
                                                     pm + s,
                                                     &lcptrace, data);
        gt_assert(pn >= GT_MULT2(s));
        pn = QSORTNAME(gt_inlined_qsort_arr_r_med3) (pn - GT_MULT2 (s),
                                                     pn - s, pn,
                                                     &lcptrace, data);
      }
      pm = QSORTNAME(gt_inlined_qsort_arr_r_med3) (pl, pm, pn, &lcptrace, data);
    }
    GT_QSORT_ARR_SWAP (arr, current.startindex, pm);
    pa = pb = current.startindex + 1;
    pc = pd = current.startindex + current.len - 1;
    smallermaxlcp = greatermaxlcp = 0;
    while (1)
    {
      while (pb <= pc)
      {
        r = QSORTNAME(qsortcmparr) (pb, current.startindex, &lcptrace, data);
        if (r > 0)
        {
          if (data->sssplcpvalues != NULL)
          {
            unsigned long tmplcplen
              = gt_differencecover_eval_lcp(&lcptrace,data);
            GT_UPDATE_MAX(greatermaxlcp,tmplcplen);
          }
          break;
        }
        if (r == 0)
        {
          swapped = true;
          GT_QSORT_ARR_SWAP (arr, pa, pb);
          pa++;
        } else
        {
          if (data->sssplcpvalues != NULL)
          {
            unsigned long tmplcplen
              = gt_differencecover_eval_lcp(&lcptrace,data);
            GT_UPDATE_MAX(smallermaxlcp,tmplcplen);
          }
        }
        pb++;
      }
      while (pb <= pc)
      {
        r = QSORTNAME(qsortcmparr) (pc, current.startindex, &lcptrace, data);
        if (r < 0)
        {
          if (data->sssplcpvalues != NULL)
          {
            unsigned long tmplcplen
              = gt_differencecover_eval_lcp(&lcptrace,data);
            GT_UPDATE_MAX(smallermaxlcp,tmplcplen);
          }
          break;
        }
        if (r == 0)
        {
          swapped = true;
          GT_QSORT_ARR_SWAP (arr, pc, pd);
          gt_assert(pd > 0);
          pd--;
        } else
        {
          if (data->sssplcpvalues != NULL)
          {
            unsigned long tmplcplen
              = gt_differencecover_eval_lcp(&lcptrace,data);
            GT_UPDATE_MAX(greatermaxlcp,tmplcplen);
          }
        }
        gt_assert(pc > 0);
        pc--;
      }
      if (pb > pc)
      {
        break;
      }
      GT_QSORT_ARR_SWAP (arr, pb, pc);
      swapped = true;
      pb++;
      gt_assert(pc > 0);
      pc--;
    }
    /* The following switch is not explained in the above mentioned
       paper and therefore we ignore it. */
    if (handlenotswapped && !swapped)
    {                                  /* Switch to insertion sort */
      gt_assert(current.len <= 40UL);
      for (pm = current.startindex + 1;
           pm < current.startindex + current.len; pm++)
      {
        for (pl = pm; pl > current.startindex; pl--)
        {
          r = QSORTNAME(qsortcmparr) (pl - 1, pl, &lcptrace, data);
          if (r <= 0)
          {
            break;
          }
          GT_QSORT_ARR_SWAP (arr, pl, pl - 1);
        }
      }
      continue;
    }
    pn = current.startindex + current.len;
    gt_assert(pa >= current.startindex);
    gt_assert(pb >= pa);
    s = MIN ((unsigned long) (pa - current.startindex),
             (unsigned long) (pb - pa));
    gt_assert(pb >= s);
    GT_QSORT_ARR_VECSWAP (arr, current.startindex, pb - s, s);
    gt_assert(pd >= pc);
    gt_assert(pn > pd);
    s = MIN ((unsigned long) (pd - pc), (unsigned long) (pn - pd - 1));
    gt_assert(pn > s);
    GT_QSORT_ARR_VECSWAP (arr, pb, pn - s, s);
    gt_assert(pb >= pa);
    if ((s = (unsigned long) (pb - pa)) > 0)
    {
      if (data->sssplcpvalues != NULL)
      {
        /*
          left part has suffix with lcp up to length smallermaxlcp w.r.t.
          to the pivot. This lcp belongs to a suffix on the left
          which is at a minimum distance to the pivot and thus to an
          element in the final part of the left side.
        */
        gt_lcptab_update(data->sssplcpvalues,
                         subbucketleft,current.startindex + s,
                         smallermaxlcp);
      }
      if (s > 1UL)
      {
        current.len = s;
        GT_STACK_PUSH(&intervalstack,current);
      }
    }
    gt_assert(pd >= pc);
    if ((s = (unsigned long) (pd - pc)) > 0)
    {
      if (data->sssplcpvalues != NULL)
      {
        /*
          right part has suffix with lcp up to length largermaxlcp w.r.t.
          to the pivot. This lcp belongs to a suffix on the right
          which is at a minimum distance to the pivot and thus to an
          element in the first part of the right side.
        */
        gt_assert(pn >= s);
        gt_lcptab_update(data->sssplcpvalues,subbucketleft,pn - s,
                         greatermaxlcp);
      }
      if (s > 1UL)
      {
        gt_assert(pn >= s);
        current.startindex = pn - s;
        current.len = s;
        GT_STACK_PUSH(&intervalstack,current);
      }
    }
  }
  GT_STACK_DELETE(&intervalstack);
}

void gt_differencecover_sortunsortedbucket(void *data,
                                           unsigned long blisbl,
                                           unsigned long width,
                                           GT_UNUSED unsigned long depth)
{
  GtDifferencecover *dcov = (GtDifferencecover *) data;
  const unsigned long bucketleftidx
    = gt_suffixsortspace_bucketleftidx_get(dcov->sssp);

  gt_assert(depth >= (unsigned long) dcov->vparam);
  gt_assert(dcov->diff2pos != NULL);
  gt_assert(width >= 2UL);
  gt_assert(dcov->sssp != NULL);
  gt_assert(blisbl >= bucketleftidx);
  /* blisbl = bucketleftindex + subbucketleft already contains
     bucketleftindex, therefore we cannot use
     gt_suffixsortspace_set or
     gt_suffixsortspace_get as these use the index
     bucketleftindex + subbucketleft + idx - partoffset
     = blisbl - partoffset + idx. Thus, instead we use the functions
     to directly access the suffix sortspace. */
  dcov->sortoffset = blisbl - gt_suffixsortspace_bucketleftidx_get(dcov->sssp);
  QSORTNAME(gt_inlinedarr_qsort_r) (6UL, false, width,data,
                                    blisbl - bucketleftidx);
}

static void dc_sortremainingsamples(GtDifferencecover *dcov)
{
  GtDcPairsuffixptr *pairptr;

  if (dcov->firstgenerationcount > 0)
  {
    dc_showintervalsizes(dcov->firstgenerationcount,
                         dcov->firstgenerationtotalwidth,
                         dcov->effectivesamplesize,
                         dcov->allocateditvinfo,
                         dcov->currentdepth,
                         dcov->logger);
  }
  if (dcov->inversesuftab == NULL)
  { /* now maxdepth > prefixlength */
    dc_initinversesuftabspecials(dcov);
    dc_initinversesuftabnonspecials(dcov);
  } else
  {
    gt_assert(dcov->firstgeneration.nextfreeGtDcPairsuffixptr == 0);
  }
  for (pairptr = dcov->firstgeneration.spaceGtDcPairsuffixptr;
       pairptr < dcov->firstgeneration.spaceGtDcPairsuffixptr +
                 dcov->firstgeneration.nextfreeGtDcPairsuffixptr;
       pairptr++)
  {
    dc_anchorleftmost(dcov,pairptr->blisbl,pairptr->width);
  }
  for (pairptr = dcov->firstgeneration.spaceGtDcPairsuffixptr;
       pairptr < dcov->firstgeneration.spaceGtDcPairsuffixptr +
                 dcov->firstgeneration.nextfreeGtDcPairsuffixptr;
       pairptr++)
  {
    dc_sortsuffixesonthislevel(dcov,pairptr->blisbl, pairptr->width);
  }
  GT_FREEARRAY(&dcov->firstgeneration,GtDcPairsuffixptr);
  while (!gt_inl_queue_isempty(dcov->rangestobesorted))
  {
    GtDcPairsuffixptr thispair;
    thispair = gt_inl_queue_get(dcov->rangestobesorted);
    gt_assert(dcov->currentqueuesize > 0);
    dcov->currentqueuesize--;
    dc_sortsuffixesonthislevel(dcov,thispair.blisbl,thispair.width);
  }
  gt_logger_log(dcov->logger,"maxqueuesize=%lu",dcov->maxqueuesize);
  gt_free(dcov->itvinfo);
  dcov->itvinfo = NULL;
  gt_inl_queue_delete(dcov->rangestobesorted);
  dcov->rangestobesorted = NULL;
}

static void dc_init_sfxstrategy_for_sample(Sfxstrategy *sfxstrategy,
                                           const Sfxstrategy *mainsfxstrategy,
                                           bool bitwise_cmp_ok,
                                           unsigned long effectivesamplesize,
                                           unsigned long totallength,
                                           GtLogger *logger)
{
  if (mainsfxstrategy != NULL)
  {
    double sampledproportion = (double) effectivesamplesize/totallength;

    *sfxstrategy = *mainsfxstrategy;
#define SETMAXCOUNT(COMP)\
    if (mainsfxstrategy->COMP >= 1UL)\
    {\
      sfxstrategy->COMP = MAX(2UL,mainsfxstrategy->COMP * sampledproportion);\
    }
    SETMAXCOUNT(maxcountingsort);
    SETMAXCOUNT(maxbltriesort);
    SETMAXCOUNT(maxinsertionsort);
  } else
  {
    defaultsfxstrategy(sfxstrategy,bitwise_cmp_ok);
  }
  gt_logger_log(logger,"samplesort.maxinsertionsort=%lu",
                sfxstrategy->maxinsertionsort);
  gt_logger_log(logger,"samplesort.maxbltriesort=%lu",
                sfxstrategy->maxbltriesort);
  gt_logger_log(logger,"samplesort.maxcountingsort=%lu",
                sfxstrategy->maxcountingsort);
}

static void dc_fill_samplelcpvalues(bool cmpcharbychar,GtDifferencecover *dcov)
{

  unsigned long suffix, kvalue, lcpinherit, start0, start1, currentlcpvalue;
  GtDifferencecover_Inversesuftabtype *inversesuftabptr = dcov->inversesuftab;
  unsigned int svalue;
  GT_UNUSED int retval;
  GtCommonunits commonunits;
  GtUchar cc1, cc2;

  for (svalue = 0; svalue < dcov->size; svalue++)
  {
    lcpinherit = 0;
    for (kvalue = (unsigned long) svalue; kvalue < dcov->samplesize;
         kvalue += dcov->size)
    {
      do
      {
        if (inversesuftabptr >= dcov->inversesuftab +
                                dcov->samplesize_upperbound)
        {
          suffix = (unsigned long) GT_DIFFERENCECOVER_INVERSESUFTAB_UNDEF;
          break;
        }
        suffix = (unsigned long) *inversesuftabptr;
        inversesuftabptr++;
      } while (suffix == (unsigned long)GT_DIFFERENCECOVER_INVERSESUFTAB_UNDEF);
      if (suffix > 0 && suffix < dcov->effectivesamplesize)
      {
        currentlcpvalue = gt_lcptab_getvalue(dcov->samplelcpvalues,0,suffix);
        if (currentlcpvalue < (unsigned long) dcov->vparam)
        {
          lcpinherit = 0;
        } else
        {
          if (lcpinherit < currentlcpvalue)
          {
            lcpinherit = currentlcpvalue;
          }
          start0 = gt_suffixsortspace_get(dcov->sortedsample,0,suffix-1);
          start1 = gt_suffixsortspace_get(dcov->sortedsample,0,suffix);
          if (cmpcharbychar)
          {
            while (start0 + lcpinherit < dcov->totallength &&
                   start1 + lcpinherit < dcov->totallength)
            {
              cc1 = gt_encseq_get_encoded_char(dcov->encseq,start0+lcpinherit,
                                               dcov->readmode);
              cc2 = gt_encseq_get_encoded_char(dcov->encseq,start1+lcpinherit,
                                               dcov->readmode);
              if (ISSPECIAL(cc1) || ISSPECIAL(cc2) || cc1 != cc2)
              {
                break;
              }
              lcpinherit++;
            }
          } else
          {
            retval = gt_encseq_compare_viatwobitencoding(&commonunits,
                                                         dcov->encseq,
                                                         dcov->encseq,
                                                         dcov->readmode,
                                                         dcov->esr1,
                                                         dcov->esr2,
                                                         start0,
                                                         start1,
                                                         lcpinherit,
                                                         0);
            gt_assert(retval <= 0);
            lcpinherit = commonunits.finaldepth;
          }
          gt_lcptab_update(dcov->samplelcpvalues,0,suffix,lcpinherit);
          lcpinherit = lcpinherit > (unsigned long) dcov->vparam
                         ? (lcpinherit - (unsigned long) dcov->vparam)
                         : 0;
        }
      }
    }
  }
}

void gt_differencecover_completelargelcpvalues(void *data,
                                               const GtSuffixsortspace *sssp,
                                               GtLcpvalues *tableoflcpvalues,
                                               unsigned long width,
                                               unsigned long posoffset)
{
  unsigned long idx, lcpvalue, s0, s1, r0, r1;
  GtDifferencecover *dcov = (GtDifferencecover *) data;

  gt_assert(width > 0 && sssp != NULL && tableoflcpvalues != NULL &&
            dcov->rmq != NULL);
  for (idx = 1UL; idx < width; idx++)
  {
    lcpvalue = gt_lcptab_getvalue(tableoflcpvalues,0,idx);
    if (lcpvalue >= (unsigned long) dcov->vparam)
    {
      s0 = gt_suffixsortspace_get(sssp, posoffset, idx-1);
      s1 = gt_suffixsortspace_get(sssp, posoffset, idx);
      lcpvalue = (unsigned long) dc_differencecover_delta(dcov,s0,s1);
      r0 = dc_inversesuftab_get(dcov,s0 + lcpvalue);
      r1 = dc_inversesuftab_get(dcov,s1 + lcpvalue);
      if (r0 < dcov->effectivesamplesize && r1 < dcov->effectivesamplesize)
      {
        gt_assert(r0 < r1);
        lcpvalue += gt_rmq_find_min_value(dcov->rmq, r0+1, r1);
      }
      gt_lcptab_update(tableoflcpvalues,0,idx,lcpvalue);
    }
  }
}

static void dc_verify_inversesuftab(const GtDifferencecover *dcov)
{
  unsigned long idx;

  for (idx=0; idx < dcov->effectivesamplesize; idx++)
  {
    unsigned long idx2 = dc_inversesuftab_get(dcov,dc_suffixptrget(dcov,idx));
    if (idx != idx2)
    {
      fprintf(stderr,"idx = %lu != %lu = idx2\n",idx,idx2);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  }
}

static void dc_differencecover_sortsample(GtDifferencecover *dcov,
                                          GtOutlcpinfo *outlcpinfosample,
                                          const Sfxstrategy *mainsfxstrategy,
                                          GtTimer *sfxprogress,
                                          bool withcheck)
{
  unsigned long pos, sampleindex, posinserted, fullspecials = 0, specials = 0;
  unsigned int modvalue, unitsnotspecial;
  Diffvalue *diffptr, *afterend;
  GtCodetype code;
  GtArrayCodeatposition codelist;
  Codeatposition *codeptr;

  dcov->samplesize = 0;
  dcov->bcktab = gt_bcktab_new(dcov->numofchars,
                               dcov->prefixlength,
                               dcov->totallength+1,
                               true, /* storespecialcodes */
                               true, /* withspecialsuffixes */
                               NULL,
                               NULL);
  dcov->multimappower = gt_bcktab_multimappower(dcov->bcktab);
  dcov->maxcode = gt_bcktab_numofallcodes(dcov->bcktab) - 1;
  dcov->esr1 = gt_encseq_create_reader_with_readmode(dcov->encseq,
                                                     dcov->readmode,
                                                     0);
  dcov->esr2 = gt_encseq_create_reader_with_readmode(dcov->encseq,
                                                     dcov->readmode,
                                                     0);
  dcov->rangestobesorted = gt_inl_queue_new(MAX(16UL,GT_DIV2(dcov->maxcode)));
  dcov->filltable = gt_filllargestchartable(dcov->numofchars,
                                            dcov->prefixlength);
  gt_assert(dcov->bcktab != NULL);
  dcov->leftborder = gt_bcktab_leftborder(dcov->bcktab);
  GT_INITARRAY(&codelist,Codeatposition);
  diffptr = dcov->diffvalues;
  afterend = dcov->diffvalues + dcov->size;
  for (pos = 0, modvalue = 0; pos <= dcov->totallength; pos++)
  {
    if (diffptr < afterend && (Diffvalue) modvalue == *diffptr)
    {
      if (pos < dcov->totallength)
      {
        code = gt_encseq_extractprefixcode(&unitsnotspecial,
                                           dcov->encseq,
                                           dcov->filltable,
                                           dcov->readmode,
                                           dcov->esr1,
                                           dcov->multimappower,
                                           pos,
                                           dcov->prefixlength);
      } else
      {
        code = 0;
        unitsnotspecial = 0;
      }
      dcov->samplesize++;
      if (unitsnotspecial > 0)
      {
        gt_bcktab_leftborder_addcode(dcov->leftborder,code);
        if (unitsnotspecial < dcov->prefixlength)
        {
          if (withcheck)
          {
            GT_GETNEXTFREEINARRAY(codeptr,&codelist,Codeatposition,128);
            gt_assert(codelist.spaceCodeatposition != NULL);
            codeptr->position = pos;
            gt_assert(code <= (GtCodetype) MAXCODEVALUE);
            codeptr->code = (unsigned int) code;
            gt_assert(unitsnotspecial <= (unsigned int) MAXPREFIXLENGTH);
            codeptr->maxprefixindex = unitsnotspecial;
          }
          specials++;
        }
      } else
      {
        fullspecials++;
      }
      diffptr++;
    }
    if (modvalue < dcov->vmodmask)
    {
      modvalue++;
    } else
    {
      modvalue = 0;
      diffptr = dcov->diffvalues;
    }
  }
  dcov->effectivesamplesize = dcov->samplesize - fullspecials;
  gt_assert(dcov->samplesize <= dcov->samplesize_upperbound);
  (void) gt_bcktab_leftborderpartialsums(NULL,NULL,dcov->bcktab);
  gt_logger_log(dcov->logger,
              "%lu positions are sampled (%.2f%%), pl=%u",
              dcov->samplesize,
              100.0 * (double) dcov->samplesize/(dcov->totallength+1),
              dcov->prefixlength);
  gt_logger_log(dcov->logger,"specials=%lu, fullspecials=%lu",
                specials,fullspecials);
  if (withcheck)
  {
    qsort(codelist.spaceCodeatposition,
          (size_t) codelist.nextfreeCodeatposition,
          sizeof (*codelist.spaceCodeatposition),dc_compareCodeatpositon);
  }
  if (dcov->effectivesamplesize > 0)
  {
    gt_assert(mainsfxstrategy != NULL);
    dcov->sortedsample = gt_suffixsortspace_new(dcov->effectivesamplesize,
                                                dcov->totallength,
                                                mainsfxstrategy->suftabuint,
                                                dcov->logger);
  } else
  {
    gt_assert(dcov->sortedsample == NULL);
  }
  posinserted = dc_derivespecialcodesonthefly(dcov,
                                              withcheck ? &codelist : NULL);
  GT_FREEARRAY(&codelist,Codeatposition);
  diffptr = dcov->diffvalues;
  afterend = dcov->diffvalues + dcov->size;
  for (pos = 0, modvalue = 0; pos < dcov->totallength; pos++)
  {
    if (diffptr < afterend && (Diffvalue) modvalue == *diffptr)
    {
      /* XXX: Use a function to extract the code in constant time for
         twobitencoding. */
      code = gt_encseq_extractprefixcode(&unitsnotspecial,
                                         dcov->encseq,
                                         dcov->filltable,
                                         dcov->readmode,
                                         dcov->esr1,
                                         dcov->multimappower,
                                         pos,
                                         dcov->prefixlength);
      if (unitsnotspecial == dcov->prefixlength)
      {
        sampleindex = gt_bcktab_leftborder_insertionindex(dcov->leftborder,
                                                          code);
        gt_assert(sampleindex < dcov->effectivesamplesize);
        dc_suffixptrset(dcov,sampleindex,pos);
        posinserted++;
      }
      diffptr++;
    }
    if (modvalue < dcov->vmodmask)
    {
      modvalue++;
    } else
    {
      modvalue = 0;
      diffptr = dcov->diffvalues;
    }
  }
  dcov->multimappower = NULL;
  gt_free(dcov->filltable);
  dcov->filltable = NULL;
  gt_assert(posinserted == dcov->effectivesamplesize);
  if (withcheck && dcov->effectivesamplesize > 0)
  {
    gt_checksortedsuffixes(__FILE__,
                           __LINE__,
                           dcov->encseq,
                           dcov->readmode,
                           dcov->sortedsample,
                           0,
                           dcov->effectivesamplesize,
                           false, /* specialsareequal  */
                           false,  /* specialsareequalatdepth0 */
                           (unsigned long) dcov->prefixlength);
  }
  gt_Outlcpinfo_reinit(outlcpinfosample,dcov->numofchars,dcov->prefixlength,
                       dcov->effectivesamplesize);
  if (outlcpinfosample != NULL)
  {
    dcov->requiredspace += gt_Outlcpinfo_size(outlcpinfosample);
    dcov->samplelcpvalues = gt_Outlcpinfo_lcpvalues_ref(outlcpinfosample);
  }
  if (dcov->vparam == dcov->prefixlength)
  {
    dc_initinversesuftabspecials(dcov);
    dc_initinversesuftabnonspecialsadjust(dcov);
    dc_bcktab2firstlevelintervals(dcov);
  } else
  {
    unsigned long long bucketiterstep = 0;
    Sfxstrategy sfxstrategy;

    gt_assert (dcov->vparam > dcov->prefixlength);
    dc_init_sfxstrategy_for_sample(&sfxstrategy,
                                   mainsfxstrategy,
                                   gt_encseq_bitwise_cmp_ok(dcov->encseq)
                                     ? false : true,
                                   dcov->effectivesamplesize,
                                   dcov->totallength,
                                   dcov->logger);
    /* now sort the suffix sample up to a prefix of length vparam */
    if (dcov->effectivesamplesize > 0)
    {
      gt_sortallbuckets(dcov->sortedsample,
                        dcov->effectivesamplesize,
                        NULL,
                        dcov->encseq,
                        dcov->readmode,
                        0, /* mincode */
                        dcov->maxcode,
                        dcov->bcktab,
                        dcov->numofchars,
                        dcov->prefixlength,
                        outlcpinfosample,
                        dcov->vparam,
                        &sfxstrategy,
                        dc_addunsortedrange,
                        (void *) dcov,
                        &bucketiterstep,
                        dcov->logger);
    }
    if (withcheck && dcov->effectivesamplesize > 0)
    {
      gt_checksortedsuffixes(__FILE__,
                             __LINE__,
                             dcov->encseq,
                             dcov->readmode,
                             dcov->sortedsample,
                             0,
                             dcov->effectivesamplesize,
                             false, /* specialsareequal  */
                             false,  /* specialsareequalatdepth0 */
                             (unsigned long) dcov->vparam);
    }
  }
  gt_bcktab_delete(dcov->bcktab);
  dcov->bcktab = NULL;
  dc_sortremainingsamples(dcov);
  if (withcheck && dcov->effectivesamplesize > 0)
  {
    gt_checksortedsuffixes(__FILE__,
                           __LINE__,
                           dcov->encseq,
                           dcov->readmode,
                           dcov->sortedsample,
                           0,
                           dcov->effectivesamplesize,
                           false, /* specialsareequal  */
                           false,  /* specialsareequalatdepth0 */
                           0);
    dc_verify_inversesuftab(dcov);
    if (outlcpinfosample != NULL)
    {
      gt_Outlcpinfo_check_lcpvalues(dcov->encseq,
                                    dcov->readmode,
                                    dcov->sortedsample,
                                    dcov->effectivesamplesize,
                                    outlcpinfosample,
                                    false);
    }
  }
  if (outlcpinfosample != NULL)
  {
    gt_assert(mainsfxstrategy != NULL);
    dc_fill_samplelcpvalues(mainsfxstrategy->cmpcharbychar ||
                            !gt_encseq_bitwise_cmp_ok(dcov->encseq),dcov);
    if (withcheck)
    {
      gt_Outlcpinfo_check_lcpvalues(dcov->encseq,
                                    dcov->readmode,
                                    dcov->sortedsample,
                                    dcov->effectivesamplesize,
                                    outlcpinfosample,
                                    true);
    }
  }
  gt_encseq_reader_delete(dcov->esr1);
  dcov->esr1 = NULL;
  gt_encseq_reader_delete(dcov->esr2);
  dcov->esr2 = NULL;
  gt_suffixsortspace_delete(dcov->sortedsample,false);
  dcov->sortedsample = NULL;
  if (dcov->effectivesamplesize > 0 && outlcpinfosample != NULL)
  {
    size_t rmqsize;

    if (sfxprogress != NULL)
    {
      gt_timer_show_progress(sfxprogress,"preparing the RMQ",stdout);
    }
    dcov->rmq = gt_lcpvalues_rmq_new(dcov->samplelcpvalues);
    rmqsize = gt_rmq_size(dcov->rmq);
    gt_logger_log(dcov->logger,
                  "RMQ requires %.2f MB (%.2f bytes per sample position)",
                  GT_MEGABYTES(rmqsize),
                  (double) rmqsize/dcov->samplesize);
    dcov->requiredspace += rmqsize;
  }
  gt_assert(dcov->diff2pos == NULL);
  dc_filldiff2pos(dcov);
}

static void dc_differencecover_sortsample0(GtDifferencecover *dcov,
                                           GtOutlcpinfo *outlcpinfosample,
                                           const Sfxstrategy *mainsfxstrategy,
                                           GT_UNUSED GtTimer *sfxprogress,
                                           bool withcheck)
{
  unsigned long pos, posinserted, fullspecials = 0;
  unsigned int modvalue;
  Diffvalue *diffptr, *afterend;
  Sfxstrategy sfxstrategy;
  GtUchar cc;

  dcov->samplesize = 0;
  dcov->bcktab = NULL;
  dcov->multimappower = NULL;
  dcov->maxcode = 0;
  dcov->esr1 = NULL;
  dcov->esr2 = NULL;
  dcov->rangestobesorted = gt_inl_queue_new(MAX(16UL,GT_DIV2(dcov->maxcode)));
  dcov->filltable = NULL;
  dcov->leftborder = NULL;
  diffptr = dcov->diffvalues;
  afterend = dcov->diffvalues + dcov->size;
  for (pos = 0, modvalue = 0; pos <= dcov->totallength; pos++)
  {
    if (diffptr < afterend && (Diffvalue) modvalue == *diffptr)
    {
      dcov->samplesize++;
      if (pos < dcov->totallength)
      {
        cc = gt_encseq_get_encoded_char(dcov->encseq,pos,dcov->readmode);
        if (ISSPECIAL(cc))
        {
          fullspecials++;
        }
      } else
      {
        fullspecials++;
      }
      diffptr++;
    }
    if (modvalue < dcov->vmodmask)
    {
      modvalue++;
    } else
    {
      modvalue = 0;
      diffptr = dcov->diffvalues;
    }
  }
  dcov->effectivesamplesize = dcov->samplesize - fullspecials;
  gt_logger_log(dcov->logger,
              "%lu positions are sampled (%.2f) pl=%u",
              dcov->samplesize,
              100.0 * (double) dcov->samplesize/(dcov->totallength+1),
              dcov->prefixlength);
  gt_logger_log(dcov->logger,"fullspecials=%lu",fullspecials);
  dcov->sortedsample = gt_suffixsortspace_new(dcov->effectivesamplesize,
                                              dcov->totallength,
                                              sfxstrategy.suftabuint,
                                              dcov->logger);
  posinserted = 0;
  diffptr = dcov->diffvalues;
  afterend = dcov->diffvalues + dcov->size;
  for (pos = 0, modvalue = 0; pos < dcov->totallength; pos++)
  {
    if (diffptr < afterend && (Diffvalue) modvalue == *diffptr)
    {
      if (pos < dcov->totallength)
      {
        cc = gt_encseq_get_encoded_char(dcov->encseq,pos,dcov->readmode);
        if (ISNOTSPECIAL(cc))
        {
          dc_suffixptrset(dcov,posinserted,pos);
          posinserted++;
        }
      }
      diffptr++;
    }
    if (modvalue < dcov->vmodmask)
    {
      modvalue++;
    } else
    {
      modvalue = 0;
      diffptr = dcov->diffvalues;
    }
  }
  gt_assert(posinserted == dcov->effectivesamplesize);

  dc_init_sfxstrategy_for_sample(&sfxstrategy,
                                 mainsfxstrategy,
                                 gt_encseq_bitwise_cmp_ok(dcov->encseq)
                                   ? false : true,
                                 dcov->effectivesamplesize,
                                 dcov->totallength,
                                 dcov->logger);
  gt_Outlcpinfo_reinit(outlcpinfosample,dcov->numofchars,dcov->prefixlength,
                       dcov->effectivesamplesize);
  gt_sortallsuffixesfromstart(dcov->sortedsample,
                              dcov->effectivesamplesize,
                              dcov->encseq,
                              dcov->readmode,
                              outlcpinfosample,
                              dcov->vparam,
                              &sfxstrategy,
                              dc_addunsortedrange,
                              (void *) dcov,
                              dcov->logger);
  if (withcheck && dcov->effectivesamplesize > 0)
  {
    gt_checksortedsuffixes(__FILE__,
                           __LINE__,
                           dcov->encseq,
                           dcov->readmode,
                           dcov->sortedsample,
                           0,
                           dcov->effectivesamplesize,
                           false, /* specialsareequal  */
                           false,  /* specialsareequalatdepth0 */
                           (unsigned long) dcov->vparam);
  }
  dc_sortremainingsamples(dcov);
  if (withcheck && dcov->effectivesamplesize > 0)
  {
    unsigned long idx;

    gt_checksortedsuffixes(__FILE__,
                           __LINE__,
                           dcov->encseq,
                           dcov->readmode,
                           dcov->sortedsample,
                           0,
                           dcov->effectivesamplesize,
                           false, /* specialsareequal  */
                           false,  /* specialsareequalatdepth0 */
                           0);
    for (idx=0; idx < dcov->effectivesamplesize; idx++)
    {
      unsigned long idx2 = dc_inversesuftab_get(dcov,dc_suffixptrget(dcov,idx));
      if (idx != idx2)
      {
        fprintf(stderr,"idx = %lu != %lu = idx2\n",idx,idx2);
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
    }
  }
  gt_suffixsortspace_delete(dcov->sortedsample,false);
  dcov->sortedsample = NULL;
  gt_assert(dcov->diff2pos == NULL);
  dc_filldiff2pos(dcov);
}

GtDifferencecover *gt_differencecover_prepare_sample(
                                        unsigned int vparam,
                                        const GtEncseq *encseq,
                                        GtReadmode readmode,
                                        unsigned int prefixlength,
                                        const Sfxstrategy *sfxstrategy,
                                        GtOutlcpinfo *outlcpinfosample,
                                        GtLogger *logger,
                                        GtTimer *sfxprogress,
                                        GtError *err)
{
  GtDifferencecover *dcov = NULL;

  gt_assert(vparam > 0);
  if (sfxprogress != NULL)
  {
    gt_timer_show_progress(sfxprogress,
                           (outlcpinfosample == NULL)
                           ? "sorting difference cover sample"
                           : ("sorting difference cover sample "
                             "and determine their lcp values"),
                           stdout);
  }
  dcov = gt_differencecover_new(vparam,encseq,readmode,
                                prefixlength,logger);
  if (dcov == NULL)
  {
    gt_error_set(err,"no difference cover modulo %u found",vparam);
  } else
  {
    if (gt_differencecover_vparamverify(dcov,err) != 0)
    {
      gt_differencecover_delete(dcov);
      dcov = NULL;
    } else
    {
      gt_assert(sfxstrategy != NULL);
      gt_logger_log(logger,"presorting sample suffixes according to "
                           "difference cover modulo %u",vparam);
      (prefixlength > 0 ? dc_differencecover_sortsample
                        : dc_differencecover_sortsample0)
                          (dcov,outlcpinfosample,sfxstrategy,
                           sfxprogress,
                           sfxstrategy->dccheck);
    }
  }
  return dcov;
}

void gt_differencecover_check(const GtEncseq *encseq,GtReadmode readmode)
{
  GtDifferencecover *dcov;
  size_t logmod;
  const size_t startlogmod = (size_t) 4;
  unsigned int vparam;
  bool withcheck = true;

  printf("sizeof (differencecovertab)=%lu\n",
          (unsigned long) sizeof (differencecovertab));
  for (logmod = startlogmod;
       logmod < sizeof (differencecoversizes)/sizeof (differencecoversizes[0]);
       logmod++)
  {
    vparam = 1U << logmod;
    dcov = gt_differencecover_new(vparam,encseq,readmode,0,NULL);
    if (dcov == NULL)
    {
      fprintf(stderr,"no difference cover for v=%u\n",vparam);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    printf("v=%u (size=%u)\n",dcov->vparam,dcov->size);
    if (withcheck)
    {
      dc_validate_samplepositons(dcov);
    }
    dc_differencecover_sortsample(dcov,NULL,NULL,NULL,withcheck);
    gt_differencecover_delete(dcov);
  }
  printf("# %u difference covers checked\n",
          (unsigned int) (logmod - startlogmod));
}
genometools-1.5.1/src/match/sfx-diffcov.h000066400000000000000000000065201211610345200203210ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_DIFFCOV_H
#define SFX_DIFFCOV_H

#include "core/encseq.h"
#include "core/unused_api.h"
#include "core/readmode.h"
#include "core/logger.h"
#include "core/timer_api.h"
#include "core/error_api.h"
#include "sfx-strategy.h"
#include "sfx-lcpvalues.h"
#include "sfx-suffixgetset.h"

typedef struct GtDifferencecover GtDifferencecover;

/* The following function is used for test purposes only */

void gt_differencecover_check(const GtEncseq *encseq,
                               GtReadmode readmode);

GtDifferencecover *gt_differencecover_new(unsigned int vparam,
                                          const GtEncseq *encseq,
                                          GtReadmode readmode,
                                          unsigned int outerprefixlength,
                                          GtLogger *logger);

unsigned long gt_differencecover_samplesize(const GtDifferencecover *dcov);

GtDifferencecover *gt_differencecover_prepare_sample(
                                        unsigned int vparam,
                                        const GtEncseq *encseq,
                                        GtReadmode readmode,
                                        unsigned int prefixlength,
                                        const Sfxstrategy *sfxstrategy,
                                        GtOutlcpinfo *outlcpinfosample,
                                        GtLogger *logger,
                                        GtTimer *sfxprogress,
                                        GtError *err);

bool gt_differencecover_is_empty(const GtDifferencecover *dcov);

void gt_differencecover_delete(GtDifferencecover *dcov);

size_t gt_differencecover_requiredspace(const GtDifferencecover *dcov);

void gt_differencecover_sortunsortedbucket(void *data,
                                           unsigned long blisbl,
                                           unsigned long width,
                                           GT_UNUSED unsigned long depth);

void gt_differencecover_completelargelcpvalues(void *data,
                                               const GtSuffixsortspace *sssp,
                                               GtLcpvalues *tableoflcpvalues,
                                               unsigned long width,
                                               unsigned long posoffset);

void gt_differencecover_set_sssp_lcp(GtDifferencecover *dcov,
                                     GtSuffixsortspace *sssp,
                                     GtOutlcpinfo *outlcpinfo);

#endif
genometools-1.5.1/src/match/sfx-enumcodes.c000066400000000000000000000147051211610345200206620ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/assert_api.h"
#include "core/codetype.h"
#include "core/encseq.h"
#include "sfx-enumcodes.h"
#include "stamp.h"
#include "initbasepower.h"

struct Enumcodeatposition
{
  GtRange previousrange;
  GtSpecialrangeiterator *sri;
  bool moveforward;
  unsigned long totallength;
  bool exhausted;
  const GtEncseq *encseq;
  GtReadmode readmode;
  unsigned int prefixlength;
  GtCodetype **multimappower, *filltable;
};

Enumcodeatposition *gt_Enumcodeatposition_new(const GtEncseq *encseq,
                                              GtReadmode readmode,
                                              unsigned int prefixlength,
                                              unsigned int numofchars)
{
  Enumcodeatposition *ecp;

  ecp = gt_malloc(sizeof *ecp);
  ecp->encseq = encseq;
  ecp->readmode = readmode;
  ecp->multimappower = gt_initmultimappower(numofchars,prefixlength);
  ecp->filltable = gt_initfilltable(numofchars,prefixlength);
  ecp->prefixlength = prefixlength;
  ecp->moveforward = GT_ISDIRREVERSE(readmode) ? true : false;
  ecp->totallength = gt_encseq_total_length(encseq);
  if (ecp->moveforward)
  {
    ecp->previousrange.start = ecp->previousrange.end = 0;
  } else
  {
    ecp->previousrange.start = ecp->previousrange.end = ecp->totallength;
  }
  ecp->exhausted = false;
  if (gt_encseq_has_specialranges(encseq))
  {
    ecp->sri = gt_specialrangeiterator_new(encseq,ecp->moveforward);
  } else
  {
    ecp->sri = NULL;
  }
  return ecp;
}

static bool newcodelistelem(Specialcontext *specialcontext,
                            unsigned long smallerval,
                            unsigned long largerval,
                            const Enumcodeatposition *ecp)
{
  if (smallerval < largerval)
  {
    unsigned long distance = largerval - smallerval;

    if (distance > (unsigned long) (ecp->prefixlength-1))
    {
      distance = (unsigned long) (ecp->prefixlength-1);
    }
    specialcontext->maxprefixindex = (unsigned int) distance;
    if (ecp->moveforward)
    {
      specialcontext->position = ecp->totallength - smallerval;
    } else
    {
      specialcontext->position = largerval;
    }
    gt_assert(specialcontext->position >=
              (unsigned long) specialcontext->maxprefixindex);
    return true;
  }
  return false;
}

bool gt_Enumcodeatposition_next(Specialcontext *specialcontext,
                                Enumcodeatposition *ecp)
{
  GtRange currentrange;
  bool done;

  if (ecp->exhausted)
  {
    return false;
  }
  while (ecp->sri != NULL)
  {
    if (!gt_specialrangeiterator_next(ecp->sri,¤trange))
    {
      gt_specialrangeiterator_delete(ecp->sri);
      ecp->sri = NULL;
      break;
    }
    if (ecp->moveforward)
    {
      if (newcodelistelem(specialcontext,
                          ecp->previousrange.end,
                          currentrange.start,
                          ecp))
      {
        ecp->previousrange = currentrange;
        return true;
      }
    } else
    {
      if (newcodelistelem(specialcontext,
                          currentrange.end,
                          ecp->previousrange.start,
                          ecp))
      {
        ecp->previousrange = currentrange;
        return true;
      }
    }
    ecp->previousrange = currentrange;
  }
  ecp->exhausted = true;
  if (ecp->moveforward)
  {
    done = newcodelistelem(specialcontext,
                           ecp->previousrange.end,
                           ecp->totallength,
                           ecp);
  } else
  {
    done = newcodelistelem(specialcontext,
                           0,
                           ecp->previousrange.start,
                           ecp);
  }
  return done;
}

void gt_Enumcodeatposition_delete(Enumcodeatposition *ecp)
{
  if (ecp != NULL)
  {
    gt_free(ecp->filltable);
    gt_multimappower_delete(ecp->multimappower);
    gt_free(ecp);
  }
}

GtCodetype gt_Enumcodeatposition_filledqgramcode(const Enumcodeatposition *ecp,
                                                 unsigned int prefixindex,
                                                 unsigned long pos)
{
  GtCodetype code;
  unsigned int idx;
  GtUchar cc;

  gt_assert(prefixindex > 0 && prefixindex < ecp->prefixlength);
  code = ecp->filltable[prefixindex];
  for (idx=0; idxtotallength);
    cc = gt_encseq_get_encoded_char_nospecial(ecp->encseq,
                                              pos + idx,
                                              ecp->readmode);
    gt_assert(ISNOTSPECIAL(cc));
    code += ecp->multimappower[idx][cc];
  }
  return code;
}

bool gt_Enumcodeatposition_filledqgramcodestopatmax(
                                        GtCodetype *code,
                                        const Enumcodeatposition *ecp,
                                        unsigned int prefixindex,
                                        unsigned long pos,
                                        GtCodetype stopcode)
{
  GtCodetype tmpcode;
  unsigned int idx;
  GtUchar cc;

  gt_assert(prefixindex > 0 && prefixindex < ecp->prefixlength);
  tmpcode = ecp->filltable[prefixindex];
  if (tmpcode > stopcode)
  {
    return false;
  }
  for (idx=0; idxtotallength);
    cc = gt_encseq_get_encoded_char_nospecial(ecp->encseq,
                                              pos + idx,
                                              ecp->readmode);
    gt_assert(ISNOTSPECIAL(cc));
    tmpcode += ecp->multimappower[idx][cc];
    if (tmpcode > stopcode)
    {
      return false;
    }
  }
  *code = tmpcode;
  return true;
}
genometools-1.5.1/src/match/sfx-enumcodes.h000066400000000000000000000041541211610345200206640ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_ENUMCODES_H
#define SFX_ENUMCODES_H

#include "core/codetype.h"
#include "core/encseq.h"

typedef struct Enumcodeatposition Enumcodeatposition;

typedef struct
{
  unsigned int maxprefixindex;
  unsigned long position;
} Specialcontext;

Enumcodeatposition *gt_Enumcodeatposition_new(const GtEncseq *encseq,
                                              GtReadmode readmode,
                                              unsigned int prefixlength,
                                              unsigned int numofchars);

bool gt_Enumcodeatposition_next(Specialcontext *specialcontext,
                                Enumcodeatposition *ecp);

void gt_Enumcodeatposition_delete(Enumcodeatposition *ecp);

GtCodetype gt_Enumcodeatposition_filledqgramcode(const Enumcodeatposition *ecp,
                                                 unsigned int prefixindex,
                                                 unsigned long pos);

bool gt_Enumcodeatposition_filledqgramcodestopatmax(
                                     GtCodetype *code,
                                     const Enumcodeatposition *ecp,
                                     unsigned int prefixindex,
                                     unsigned long pos,
                                     GtCodetype stopcode);
#endif
genometools-1.5.1/src/match/sfx-lcpvalues.c000066400000000000000000000724131211610345200206760ustar00rootroot00000000000000/*
  Copyright (c) 2007-2012 Stefan Kurtz 
  Copyright (c) 2007-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/arraydef.h"
#include "core/disc_distri_api.h"
#include "core/fa.h"
#include "core/minmax.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "extended/rmq.h"
#include "esa-fileend.h"
#include "sfx-lcpvalues.h"
#include "turnwheels.h"

GT_DECLAREARRAYSTRUCT(Largelcpvalue);

typedef struct
{
  FILE *outfplcptab,
       *outfpllvtab;
  GtArrayLargelcpvalue largelcpvalues;
  unsigned long maxbranchdepth,
                totalnumoflargelcpvalues,
                countoutputlcpvalues;
  void *reservoir;
  size_t sizereservoir;
  uint8_t *smalllcpvalues; /* pointer into reservoir */
} Lcpoutput2file;

typedef struct
{
  GtFinalProcessBucket final_process_bucket;
  void *final_process_bucket_info;
} GtProcesslcpvalues;

typedef struct
{
  GtLcpvalues tableoflcpvalues;
  Lcpoutput2file *lcp2file;
  GtProcesslcpvalues *lcpprocess;
  double lcptabsum;
  GtDiscDistri *distlcpvalues;
} Lcpsubtab;

typedef struct
{
  bool defined;
  GtCodetype code;
  unsigned int prefixindex;
#undef SKDEBUG
#ifdef SKDEBUG
  unsigned long startpos;
#endif
} Suffixwithcode;

struct GtOutlcpinfo
{
  Turningwheel *turnwheel;
  unsigned long numsuffixes2output;
  unsigned int minchanged;
  size_t sizeofinfo;
  Suffixwithcode previoussuffix;
  bool previousbucketwasempty,
       swallow_tail_lcpvalues;
  Lcpsubtab lcpsubtab;
};

const GtLcpvaluetype *gt_lcptab_getptr(const GtLcpvalues *tableoflcpvalues,
                                       unsigned long subbucketleft)
{
  return tableoflcpvalues->bucketoflcpvalues + tableoflcpvalues->lcptaboffset
                                             + subbucketleft;
}

/* Now some functions related to the computation of lcp values follow */

static unsigned long computelocallcpvalue(const Suffixwithcode *previoussuffix,
                                          const Suffixwithcode *currentsuffix,
                                          unsigned int minchanged)
{
  unsigned int lcpvalue;

  if (previoussuffix->code == currentsuffix->code)
  {
    lcpvalue = MIN(previoussuffix->prefixindex,
                   currentsuffix->prefixindex);
  } else
  {
    gt_assert(previoussuffix->code < currentsuffix->code);
    lcpvalue = MIN(previoussuffix->prefixindex,currentsuffix->prefixindex);
    if (minchanged < lcpvalue)
    {
      lcpvalue = minchanged;
    }
  }
  return (unsigned long) lcpvalue;
}

static void outsmalllcpvalues(Lcpoutput2file *lcp2file,
                              unsigned long numoflcps)
{
  gt_assert (lcp2file != NULL);
  lcp2file->countoutputlcpvalues += numoflcps;
  gt_assert(lcp2file->outfplcptab != NULL);
  gt_xfwrite(lcp2file->smalllcpvalues,
             sizeof (*lcp2file->smalllcpvalues),
             (size_t) numoflcps,
             lcp2file->outfplcptab);
}

static unsigned int lcp_bucketends(Lcpsubtab *lcpsubtab,
                                   Suffixwithcode *previoussuffix,
                                   GT_UNUSED unsigned long firstspecialsuffix,
                                   unsigned int minchanged,
                                   unsigned long nonspecialsinbucket,
                                   unsigned long specialsinbucket,
                                   GtCodetype code,
                                   const GtBcktab *bcktab)
{
  unsigned long lcpvalue;
  unsigned int maxprefixindex, minprefixindex;
  Suffixwithcode firstspecialsuffixwithcode;

  /*
     there is at least one element in the bucket. if there is more than
     one element in the bucket, then we insert them using the
     information from the bcktab
  */
  if (specialsinbucket > 1UL)
  {
    if (lcpsubtab->lcp2file != NULL)
    {
      maxprefixindex = gt_bcktab_pfxidx2lcpvalues_uint8(
                          &minprefixindex,
                          lcpsubtab->lcp2file->smalllcpvalues,
                          specialsinbucket,
                          bcktab,
                          code);
      if (lcpsubtab->lcp2file->maxbranchdepth < (unsigned long) maxprefixindex)
      {
        lcpsubtab->lcp2file->maxbranchdepth = (unsigned long) maxprefixindex;
      }
    } else
    {
      unsigned long start = lcpsubtab->tableoflcpvalues.lcptaboffset +
                            nonspecialsinbucket;
      maxprefixindex = gt_bcktab_pfxidx2lcpvalues_Lcpvaluetype(
                          &minprefixindex,
                          lcpsubtab->tableoflcpvalues.bucketoflcpvalues + start,
                          specialsinbucket,
                          bcktab,
                          code);
#ifndef NDEBUG
      {
        unsigned long idx;

        for (idx=start; idxtableoflcpvalues.isset,idx);
        }
      }
#endif
    }
  } else
  {
    minprefixindex = maxprefixindex = gt_bcktab_singletonmaxprefixindex(bcktab,
                                                                        code);
  }
  firstspecialsuffixwithcode.code = code;
  firstspecialsuffixwithcode.prefixindex = maxprefixindex;
#ifdef SKDEBUG
  firstspecialsuffixwithcode.startpos = firstspecialsuffix;
  /*
  gt_bcktab_consistencyofsuffix(__LINE__,
                                encseq,readmode,bcktab,numofchars,
                                &firstspecialsuffixwithcode);
  */
#endif
  lcpvalue = computelocallcpvalue(previoussuffix,
                                  &firstspecialsuffixwithcode,
                                  minchanged);
  if (lcpsubtab->lcp2file != NULL)
  {
    if (lcpsubtab->lcp2file->maxbranchdepth < lcpvalue)
    {
      lcpsubtab->lcp2file->maxbranchdepth = lcpvalue;
    }
    lcpsubtab->lcp2file->smalllcpvalues[0] = (uint8_t) lcpvalue;
  } else
  {
    gt_assert(lcpvalue <= GT_LCPVALUE_MAX);
    lcpsubtab->tableoflcpvalues.bucketoflcpvalues
               [lcpsubtab->tableoflcpvalues.lcptaboffset + nonspecialsinbucket]
               = (GtLcpvaluetype) lcpvalue;
#ifndef NDEBUG
    GT_SETIBIT(lcpsubtab->tableoflcpvalues.isset,
               lcpsubtab->tableoflcpvalues.lcptaboffset + nonspecialsinbucket);
#endif
  }
  return minprefixindex;
}

GtOutlcpinfo *gt_Outlcpinfo_new(const char *indexname,
                                unsigned int numofchars,
                                unsigned int prefixlength,
                                bool withdistribution,
                                bool swallow_tail_lcpvalues,
                                GtFinalProcessBucket final_process_bucket,
                                void *final_process_bucket_info,
                                GtError *err)
{
  bool haserr = false;
  GtOutlcpinfo *outlcpinfo;

  outlcpinfo = gt_malloc(sizeof (*outlcpinfo));
  outlcpinfo->sizeofinfo = sizeof (*outlcpinfo);
  outlcpinfo->lcpsubtab.lcptabsum = 0.0;
  outlcpinfo->swallow_tail_lcpvalues = swallow_tail_lcpvalues;
  if (withdistribution)
  {
    outlcpinfo->lcpsubtab.distlcpvalues = gt_disc_distri_new();
  } else
  {
    outlcpinfo->lcpsubtab.distlcpvalues = NULL;
  }
  if (indexname == NULL)
  {
    outlcpinfo->lcpsubtab.lcp2file = NULL;
    if (final_process_bucket != NULL)
    {
      outlcpinfo->lcpsubtab.lcpprocess
        = gt_malloc(sizeof (*outlcpinfo->lcpsubtab.lcpprocess));
      outlcpinfo->lcpsubtab.lcpprocess->final_process_bucket
        = final_process_bucket;
      outlcpinfo->lcpsubtab.lcpprocess->final_process_bucket_info
        = final_process_bucket_info;
    } else
    {
      outlcpinfo->lcpsubtab.lcpprocess = NULL;
    }
  } else
  {
    outlcpinfo->lcpsubtab.lcpprocess = NULL;
    outlcpinfo->lcpsubtab.lcp2file
      = gt_malloc(sizeof (*outlcpinfo->lcpsubtab.lcp2file));
    outlcpinfo->sizeofinfo += sizeof (*outlcpinfo->lcpsubtab.lcp2file);
    outlcpinfo->lcpsubtab.lcp2file->countoutputlcpvalues = 0;
    outlcpinfo->lcpsubtab.lcp2file->maxbranchdepth = 0;
    outlcpinfo->lcpsubtab.lcp2file->totalnumoflargelcpvalues = 0;
    outlcpinfo->lcpsubtab.lcp2file->reservoir = NULL;
    outlcpinfo->lcpsubtab.lcp2file->sizereservoir = 0;
    outlcpinfo->lcpsubtab.lcp2file->smalllcpvalues = NULL;
    GT_INITARRAY(&outlcpinfo->lcpsubtab.lcp2file->largelcpvalues,
                 Largelcpvalue);
    outlcpinfo->lcpsubtab.lcp2file->outfplcptab
      = gt_fa_fopen_with_suffix(indexname,LCPTABSUFFIX,"wb",err);
    if (outlcpinfo->lcpsubtab.lcp2file->outfplcptab == NULL)
    {
      haserr = true;
    }
    if (!haserr)
    {
      outlcpinfo->lcpsubtab.lcp2file->outfpllvtab
        = gt_fa_fopen_with_suffix(indexname,LARGELCPTABSUFFIX,"wb",err);
      if (outlcpinfo->lcpsubtab.lcp2file->outfpllvtab == NULL)
      {
        haserr = true;
      }
    }
  }
  outlcpinfo->numsuffixes2output = 0;
  outlcpinfo->minchanged = 0;
  if (!haserr && prefixlength > 0)
  {
    outlcpinfo->turnwheel = gt_turningwheel_new(prefixlength,numofchars);
    outlcpinfo->sizeofinfo += gt_turningwheel_size();
  } else
  {
    outlcpinfo->turnwheel = NULL;
  }
#ifdef SKDEBUG
  outlcpinfo->previoussuffix.startpos = 0;
#endif
  outlcpinfo->previoussuffix.code = 0;
  outlcpinfo->previoussuffix.prefixindex = 0;
  outlcpinfo->previoussuffix.defined = false;
  outlcpinfo->previousbucketwasempty = false;
  outlcpinfo->lcpsubtab.tableoflcpvalues.bucketoflcpvalues = NULL;
  outlcpinfo->lcpsubtab.tableoflcpvalues.numofentries = 0;
#ifndef NDEBUG
  outlcpinfo->lcpsubtab.tableoflcpvalues.isset = NULL;
#endif
  if (haserr)
  {
    gt_free(outlcpinfo);
    return NULL;
  }
  return outlcpinfo;
}

size_t gt_Outlcpinfo_size(const GtOutlcpinfo *outlcpinfo)
{
  gt_assert(outlcpinfo != NULL);
  return outlcpinfo->sizeofinfo;
}

static size_t gt_tableoflcpvalues_realloc(GtLcpvalues *tableoflcpvalues,
                                          unsigned long numoflcpvalues)
{
  if (numoflcpvalues > tableoflcpvalues->numofentries)
  {
    size_t sizeofinfo;

    tableoflcpvalues->bucketoflcpvalues
      = gt_realloc(tableoflcpvalues->bucketoflcpvalues,
                   sizeof (*tableoflcpvalues->bucketoflcpvalues) *
                   numoflcpvalues);
    sizeofinfo = sizeof (*tableoflcpvalues->bucketoflcpvalues) *
                         (numoflcpvalues - tableoflcpvalues->numofentries);
#ifndef NDEBUG
    GT_INITBITTABGENERIC(tableoflcpvalues->isset,
                         tableoflcpvalues->isset,
                         numoflcpvalues);
#endif
    sizeofinfo += GT_NUMOFINTSFORBITS(numoflcpvalues -
                                      tableoflcpvalues->numofentries)
                  * sizeof (GtBitsequence);
    tableoflcpvalues->numoflargelcpvalues = 0;
    tableoflcpvalues->numofentries = numoflcpvalues;
    tableoflcpvalues->lcptaboffset = 0;
    return sizeofinfo;
  }
  return 0;
}

void gt_Outlcpinfo_reinit(GtOutlcpinfo *outlcpinfo,
                          unsigned int numofchars,
                          unsigned int prefixlength,
                          unsigned long numoflcpvalues)
{
  if (outlcpinfo != NULL)
  {
    if (prefixlength > 0)
    {
      outlcpinfo->turnwheel = gt_turningwheel_new(prefixlength,numofchars);
      outlcpinfo->sizeofinfo += gt_turningwheel_size();
    } else
    {
      outlcpinfo->turnwheel = NULL;
    }
    outlcpinfo->sizeofinfo
      += gt_tableoflcpvalues_realloc(&outlcpinfo->lcpsubtab.tableoflcpvalues,
                                     numoflcpvalues);
  }
}

static void outlcpvalues(Lcpsubtab *lcpsubtab,
                         unsigned long width,
                         unsigned long posoffset)
{
  unsigned long idx, lcpvalue;
  Largelcpvalue *largelcpvalueptr;

  gt_assert(lcpsubtab != NULL && lcpsubtab->lcp2file != NULL);
  lcpsubtab->lcp2file->largelcpvalues.nextfreeLargelcpvalue = 0;
  if (lcpsubtab->tableoflcpvalues.numoflargelcpvalues > 0 &&
      lcpsubtab->tableoflcpvalues.numoflargelcpvalues >=
      lcpsubtab->lcp2file->largelcpvalues.allocatedLargelcpvalue)
  {
    lcpsubtab->lcp2file->largelcpvalues.spaceLargelcpvalue
      = gt_realloc(lcpsubtab->lcp2file->largelcpvalues.spaceLargelcpvalue,
                   sizeof (*lcpsubtab->lcp2file->largelcpvalues.
                           spaceLargelcpvalue) *
                   lcpsubtab->tableoflcpvalues.numoflargelcpvalues);
    lcpsubtab->lcp2file->largelcpvalues.allocatedLargelcpvalue
      = lcpsubtab->tableoflcpvalues.numoflargelcpvalues;
  }
  for (idx=0; idxtableoflcpvalues,0,idx);
    if (lcpsubtab->lcp2file->maxbranchdepth < lcpvalue)
    {
      lcpsubtab->lcp2file->maxbranchdepth = lcpvalue;
    }
    if (lcpvalue < (unsigned long) LCPOVERFLOW)
    {
      lcpsubtab->lcp2file->smalllcpvalues[idx] = (uint8_t) lcpvalue;
    } else
    {
      gt_assert(lcpsubtab->lcp2file->largelcpvalues.nextfreeLargelcpvalue
                < lcpsubtab->lcp2file->largelcpvalues.
                                             allocatedLargelcpvalue);
      largelcpvalueptr
        = lcpsubtab->lcp2file->largelcpvalues.spaceLargelcpvalue +
          lcpsubtab->lcp2file->largelcpvalues.nextfreeLargelcpvalue++;
      largelcpvalueptr->position = posoffset + idx;
      largelcpvalueptr->value = lcpvalue;
      lcpsubtab->lcp2file->smalllcpvalues[idx] = LCPOVERFLOW;
    }
    lcpsubtab->lcptabsum += (double) lcpvalue;
    if (lcpsubtab->distlcpvalues != NULL)
    {
      gt_disc_distri_add(lcpsubtab->distlcpvalues, lcpvalue);
    }
  }
  outsmalllcpvalues(lcpsubtab->lcp2file,width);
  if (lcpsubtab->lcp2file->largelcpvalues.nextfreeLargelcpvalue > 0)
  {
    lcpsubtab->lcp2file->totalnumoflargelcpvalues
      += lcpsubtab->lcp2file->largelcpvalues.nextfreeLargelcpvalue;
    gt_assert(lcpsubtab->lcp2file->outfpllvtab != NULL);
    gt_xfwrite(lcpsubtab->lcp2file->largelcpvalues.spaceLargelcpvalue,
               sizeof (*lcpsubtab->lcp2file->largelcpvalues.
                                   spaceLargelcpvalue),
               (size_t) lcpsubtab->lcp2file->largelcpvalues.
                                   nextfreeLargelcpvalue,
               lcpsubtab->lcp2file->outfpllvtab);
  }
}

static unsigned long outmany0lcpvalues(unsigned long many,
                                       FILE *outfplcptab)
{
  unsigned long i, countout;
#define GT_LCPBUF_NUMBEROFZEROS 1024
  uint8_t outvalues[GT_LCPBUF_NUMBEROFZEROS] = {0};

  countout = many/GT_LCPBUF_NUMBEROFZEROS;
  for (i=0; iturnwheel);
  if (outlcpinfo->lcpsubtab.lcp2file != NULL)
  {
    if (!outlcpinfo->swallow_tail_lcpvalues &&
        outlcpinfo->lcpsubtab.lcp2file->countoutputlcpvalues <
        outlcpinfo->numsuffixes2output)
    {
      outlcpinfo->lcpsubtab.lcp2file->countoutputlcpvalues
        += outmany0lcpvalues(outlcpinfo->numsuffixes2output -
                             outlcpinfo->lcpsubtab.lcp2file
                                                  ->countoutputlcpvalues,
                             outlcpinfo->lcpsubtab.lcp2file->outfplcptab);
    }
    gt_assert(outlcpinfo->swallow_tail_lcpvalues ||
              outlcpinfo->lcpsubtab.lcp2file->countoutputlcpvalues ==
              outlcpinfo->numsuffixes2output);
    GT_FREEARRAY(&outlcpinfo->lcpsubtab.lcp2file->largelcpvalues,
                 Largelcpvalue);
    gt_fa_fclose(outlcpinfo->lcpsubtab.lcp2file->outfplcptab);
    gt_fa_fclose(outlcpinfo->lcpsubtab.lcp2file->outfpllvtab);
    gt_free(outlcpinfo->lcpsubtab.lcp2file->reservoir);
    outlcpinfo->lcpsubtab.lcp2file->smalllcpvalues = NULL;
    outlcpinfo->lcpsubtab.lcp2file->reservoir = NULL;
    outlcpinfo->lcpsubtab.lcp2file->sizereservoir = 0;
    gt_free(outlcpinfo->lcpsubtab.lcp2file);
  } else
  {
    gt_free(outlcpinfo->lcpsubtab.tableoflcpvalues.bucketoflcpvalues);
#ifndef NDEBUG
    gt_free(outlcpinfo->lcpsubtab.tableoflcpvalues.isset);
#endif
  }
  gt_free(outlcpinfo->lcpsubtab.lcpprocess);
  outlcpinfo->lcpsubtab.tableoflcpvalues.bucketoflcpvalues = NULL;
#ifndef NDEBUG
  outlcpinfo->lcpsubtab.tableoflcpvalues.isset = NULL;
#endif
  outlcpinfo->lcpsubtab.tableoflcpvalues.numofentries = 0;
  if (outlcpinfo->lcpsubtab.distlcpvalues != NULL)
  {
    gt_disc_distri_show(outlcpinfo->lcpsubtab.distlcpvalues,NULL);
    gt_disc_distri_delete(outlcpinfo->lcpsubtab.distlcpvalues);
  }
  gt_free(outlcpinfo);
}

void gt_Outlcpinfo_check_lcpvalues(const GtEncseq *encseq,
                                   GtReadmode readmode,
                                   const GtSuffixsortspace *sortedsample,
                                   unsigned long effectivesamplesize,
                                   const GtOutlcpinfo *outlcpinfosample,
                                   bool checkequality)
{
  GT_UNUSED int cmp;
  unsigned long idx, reallcp, startpos1, startpos2, currentlcp,
                totalcmpmissing = 0;

  if (effectivesamplesize == 0)
  {
    return;
  }
  startpos1 = gt_suffixsortspace_getdirect(sortedsample,0);
  for (idx=1UL; idxlcpsubtab.tableoflcpvalues
                                                      .isset,idx));
    currentlcp = (unsigned long) outlcpinfosample->lcpsubtab.tableoflcpvalues.
                                 bucketoflcpvalues[idx];
    if ((checkequality && currentlcp != reallcp) ||
        (!checkequality && currentlcp > reallcp))
    {
      fprintf(stderr,"idx=%lu,suffixpair=%lu,%lu: "
                     "currentlcp = %lu %s %lu = reallcp\n",
                      idx,startpos1,startpos2,currentlcp,
                      checkequality ? "!=" : ">",reallcp);
      gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,startpos1,50UL);
      fprintf(stderr,"\n");
      gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,startpos2,50UL);
      fprintf(stderr,"\n");
      exit(GT_EXIT_PROGRAMMING_ERROR);
    } else
    {
      totalcmpmissing += (reallcp - currentlcp);
    }
    startpos1 = startpos2;
  }
  /*printf("totalcmpmissing = %lu(avg=%.2f)\n",
         totalcmpmissing,(double) totalcmpmissing/effectivesamplesize);*/
}

unsigned long gt_Outlcpinfo_numoflargelcpvalues(const GtOutlcpinfo *outlcpinfo)
{
  if (outlcpinfo->lcpsubtab.lcp2file != NULL)
  {
    return outlcpinfo->lcpsubtab.lcp2file->totalnumoflargelcpvalues;
  }
  return 0;
}

double gt_Outlcpinfo_lcptabsum(const GtOutlcpinfo *outlcpinfo)
{
  gt_assert(outlcpinfo != NULL);
  return outlcpinfo->lcpsubtab.lcptabsum;
}

void gt_Outlcpinfo_numsuffixes2output_set(GtOutlcpinfo *outlcpinfo,
                                          unsigned long numsuffixes2output)
{
  outlcpinfo->numsuffixes2output = numsuffixes2output;
}

unsigned long gt_Outlcpinfo_maxbranchdepth(const GtOutlcpinfo *outlcpinfo)
{
  if (outlcpinfo->lcpsubtab.lcp2file != NULL)
  {
    return outlcpinfo->lcpsubtab.lcp2file->maxbranchdepth;
  }
  return 0;
}

void gt_Outlcpinfo_prebucket(GtOutlcpinfo *outlcpinfo,
                             GtCodetype code,
                             unsigned long lcptaboffset)
{
  if (outlcpinfo != NULL)
  {
    if (outlcpinfo->lcpsubtab.lcp2file != NULL ||
        outlcpinfo->lcpsubtab.lcpprocess != NULL)
    {
      outlcpinfo->lcpsubtab.tableoflcpvalues.numoflargelcpvalues = 0;
    } else
    {
      outlcpinfo->lcpsubtab.tableoflcpvalues.lcptaboffset = lcptaboffset;
    }
    if (code > 0)
    {
      (void) gt_turningwheel_next(outlcpinfo->turnwheel);
      if (outlcpinfo->previousbucketwasempty)
      {
        outlcpinfo->minchanged
          = MIN(outlcpinfo->minchanged,
                gt_turningwheel_minchanged(outlcpinfo->turnwheel));
      } else
      {
        outlcpinfo->minchanged
          = gt_turningwheel_minchanged(outlcpinfo->turnwheel);
      }
    }
  }
}

void gt_Outlcpinfo_nonspecialsbucket(GtOutlcpinfo *outlcpinfo,
                                     unsigned int prefixlength,
                                     const GtSuffixsortspace *sssp,
                                     GtLcpvalues *tableoflcpvalues,
                                     const GtBucketspecification *bucketspec,
                                     GtCodetype code)
{
  if (outlcpinfo != NULL)
  {
    unsigned long lcpvalue;
    Suffixwithcode firstsuffixofbucket;

    if (outlcpinfo->previoussuffix.defined)
    {

      /* compute lcpvalue of first element of bucket with
         last element of previous bucket */
      firstsuffixofbucket.code = code;
      firstsuffixofbucket.prefixindex = prefixlength;
#ifdef SKDEBUG
      firstsuffixofbucket.startpos
        = gt_suffixsortspace_get(sssp,0,bucketspec->left);
      /*
      gt_bcktab_consistencyofsuffix(__LINE__,
                                    encseq,readmode,bcktab,numofchars,
                                    &firstsuffixofbucket);
      */
#endif
      lcpvalue = computelocallcpvalue(&outlcpinfo->previoussuffix,
                                      &firstsuffixofbucket,
                                      outlcpinfo->minchanged);
    } else
    {
      /* first part first code */
      lcpvalue = 0;
    }
    gt_lcptab_update(tableoflcpvalues,0,0,lcpvalue);
    /* all other lcp-values are computed and they can be output */
    if (outlcpinfo->lcpsubtab.lcp2file != NULL)
    {
      outlcpvalues(&outlcpinfo->lcpsubtab,
                   bucketspec->nonspecialsinbucket,
                   bucketspec->left);
    } else
    {
      if (outlcpinfo->lcpsubtab.lcpprocess != NULL)
      {
        outlcpinfo->lcpsubtab.lcpprocess->final_process_bucket(
            outlcpinfo->lcpsubtab.lcpprocess->final_process_bucket_info,
            sssp,
            tableoflcpvalues,
            0,
            bucketspec->nonspecialsinbucket,
            bucketspec->left);
      }
    }
    /* previoussuffix becomes last nonspecial element in current bucket */
    outlcpinfo->previoussuffix.code = code;
    outlcpinfo->previoussuffix.prefixindex = prefixlength;
#ifdef SKDEBUG
    outlcpinfo->previoussuffix.startpos
      = gt_suffixsortspace_get(sssp,0,
                               bucketspec->left
                                 + bucketspec->nonspecialsinbucket - 1);
    /*
    gt_bcktab_consistencyofsuffix(__LINE__,
                                  encseq,readmode,bcktab,numofchars,
                                  &outlcpinfo->previoussuffix);
    */
#endif
  }
}

void gt_Outlcpinfo_postbucket(GtOutlcpinfo *outlcpinfo,
                              unsigned int prefixlength,
                              const GtSuffixsortspace *sssp,
                              const GtBcktab *bcktab,
                              const GtBucketspecification *bucketspec,
                              GtCodetype code)
{
  if (outlcpinfo != NULL)
  {
    if (bucketspec->specialsinbucket > 0)
    {
      unsigned int minprefixindex;
      unsigned long suffixvalue
        = gt_suffixsortspace_get(sssp,
                                 0,
                                 bucketspec->left
                                   + bucketspec->nonspecialsinbucket);
      minprefixindex = lcp_bucketends(&outlcpinfo->lcpsubtab,
                                      &outlcpinfo->previoussuffix,
                                      /* first special element in bucket */
                                      suffixvalue,
                                      outlcpinfo->minchanged,
                                      bucketspec->nonspecialsinbucket,
                                      bucketspec->specialsinbucket,
                                      code,
                                      bcktab);
      if (outlcpinfo->lcpsubtab.lcp2file != NULL)
      {
        outsmalllcpvalues(outlcpinfo->lcpsubtab.lcp2file,
                          bucketspec->specialsinbucket);
      } else
      {
        if (outlcpinfo->lcpsubtab.lcpprocess != NULL)
        {
          outlcpinfo->lcpsubtab.lcpprocess->final_process_bucket(
              outlcpinfo->lcpsubtab.lcpprocess->final_process_bucket_info,
              sssp,
              &outlcpinfo->lcpsubtab.tableoflcpvalues,
              bucketspec->nonspecialsinbucket,
              bucketspec->specialsinbucket,
              bucketspec->left);
        }
      }
      /* there is at least one special element: this is the last element
         in the bucket, and thus the previoussuffix for the next round */
      outlcpinfo->previoussuffix.defined = true;
      outlcpinfo->previoussuffix.code = code;
      outlcpinfo->previoussuffix.prefixindex = minprefixindex;
#ifdef SKDEBUG
      outlcpinfo->previoussuffix.startpos
        = gt_suffixsortspace_get(sssp,
                                 0,
                                 bucketspec->left
                                   + bucketspec->nonspecialsinbucket +
                                     bucketspec->specialsinbucket - 1);
      /*
        gt_bcktab_consistencyofsuffix(__LINE__,
                                      encseq,readmode,bcktab,numofchars,
                                      &outlcpinfo->previoussuffix);
      */
#endif
    } else
    {
      if (bucketspec->nonspecialsinbucket > 0)
      {
        /* if there is at least one element in the bucket, then the last
           one becomes the next previous suffix */
        outlcpinfo->previoussuffix.defined = true;
        outlcpinfo->previoussuffix.code = code;
        outlcpinfo->previoussuffix.prefixindex = prefixlength;
#ifdef SKDEBUG
        outlcpinfo->previoussuffix.startpos
          = gt_suffixsortspace_get(sssp,
                                   0,
                                   bucketspec.left
                                     + bucketspec.nonspecialsinbucket-1);
        /*
        gt_bcktab_consistencyofsuffix(__LINE__,
                                      encseq,readmode,bcktab,numofchars,
                                      &outlcpinfo->previoussuffix);
        */
#endif
      }
    }
    if (bucketspec->nonspecialsinbucket + bucketspec->specialsinbucket == 0)
    {
      outlcpinfo->previousbucketwasempty = true;
    } else
    {
      outlcpinfo->previousbucketwasempty = false;
    }
    if (outlcpinfo->lcpsubtab.lcp2file != NULL ||
        outlcpinfo->lcpsubtab.lcpprocess != NULL)
    {
      gt_assert(outlcpinfo->lcpsubtab.tableoflcpvalues.lcptaboffset == 0);
    } else
    {
      outlcpinfo->lcpsubtab.tableoflcpvalues.lcptaboffset = 0;
    }
  }
}

GtLcpvalues *gt_Outlcpinfo_resizereservoir(GtOutlcpinfo *outlcpinfo,
                                           const GtBcktab *bcktab)
{
  Lcpsubtab *lcpsubtab;

  gt_assert(outlcpinfo != NULL);
  lcpsubtab = &outlcpinfo->lcpsubtab;
  if (lcpsubtab->lcp2file != NULL)
  {
    size_t sizeforlcpvalues; /* in bytes */

    gt_assert(bcktab != NULL);
    sizeforlcpvalues = gt_bcktab_sizeforlcpvalues(bcktab);
    if (lcpsubtab->lcp2file->sizereservoir < sizeforlcpvalues)
    {
      lcpsubtab->lcp2file->sizereservoir = sizeforlcpvalues;
      lcpsubtab->lcp2file->reservoir
        = gt_realloc(lcpsubtab->lcp2file->reservoir,
                     lcpsubtab->lcp2file->sizereservoir);
          /* point to the same area, since this is not used simultaneously */
          /* be careful for the parallel version */
      lcpsubtab->lcp2file->smalllcpvalues
        = (uint8_t *) lcpsubtab->lcp2file->reservoir;
#ifndef NDEBUG
      lcpsubtab->tableoflcpvalues.isset = NULL;
#endif
      lcpsubtab->tableoflcpvalues.bucketoflcpvalues
        = (GtLcpvaluetype *) lcpsubtab->lcp2file->reservoir;
      lcpsubtab->tableoflcpvalues.lcptaboffset = 0;
      lcpsubtab->tableoflcpvalues.numofentries
        = (unsigned long) lcpsubtab->lcp2file->sizereservoir/
          sizeof (*lcpsubtab->tableoflcpvalues.bucketoflcpvalues);
    }
  } else
  {
    if (lcpsubtab->lcpprocess != NULL)
    {
      outlcpinfo->sizeofinfo
        += gt_tableoflcpvalues_realloc(&lcpsubtab->tableoflcpvalues,
                                       gt_bcktab_maxbucketsize(bcktab));
    }
  }
  return &lcpsubtab->tableoflcpvalues;
}

GtLcpvalues *gt_Outlcpinfo_lcpvalues_ref(GtOutlcpinfo *outlcpinfo)
{
  gt_assert(outlcpinfo != NULL);
  return &outlcpinfo->lcpsubtab.tableoflcpvalues;
}

GtRMQ *gt_lcpvalues_rmq_new(const GtLcpvalues *samplelcpvalues)
{
  return gt_rmq_new(samplelcpvalues->bucketoflcpvalues,
                    samplelcpvalues->numofentries);
}
genometools-1.5.1/src/match/sfx-lcpvalues.h000066400000000000000000000156301211610345200207010ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_LCPVALUES_H
#define SFX_LCPVALUES_H
#include "core/error_api.h"
#include "core/codetype.h"
#include "core/unused_api.h"
#include "core/encseq.h"
#include "extended/rmq.h"
#include "lcpoverflow.h"
#include "bcktab.h"
#include "sfx-suffixgetset.h"

typedef struct GtOutlcpinfo GtOutlcpinfo;

typedef struct
{
#ifndef NDEBUG
  GtBitsequence *isset;
#endif
  GtLcpvaluetype *bucketoflcpvalues;
  unsigned long numofentries,
                numoflargelcpvalues,
                lcptaboffset; /* This can be positive when the lcp-values
                                 for an entire range of suffixes (covering
                                 more than one bucket) must
                                 be sorted, as in the case of the difference
                                 cover. In other cases, only the lcp-values
                                 for a single bucket must be computed, which
                                 means that the value is 0. */
} GtLcpvalues;

typedef void (*GtFinalProcessBucket)(void *,
                                     const GtSuffixsortspace *,
                                     const GtLcpvalues *,
                                     unsigned long,
                                     unsigned long,
                                     unsigned long);

/*@unused@*/ static inline void gt_lcptab_update(GtLcpvalues *tableoflcpvalues,
                                                 unsigned long subbucketleft,
                                                 unsigned long idx,
                                                 unsigned long value)
{
  gt_assert (tableoflcpvalues != NULL &&
             tableoflcpvalues->bucketoflcpvalues != NULL &&
             tableoflcpvalues->lcptaboffset+subbucketleft+idx <
             tableoflcpvalues->numofentries);
#ifndef NDEBUG
  if (tableoflcpvalues->isset != NULL)
  {
    GT_SETIBIT(tableoflcpvalues->isset,
               tableoflcpvalues->lcptaboffset+subbucketleft+idx);
  }
#endif
  gt_assert(value <= GT_LCPVALUE_MAX);
  tableoflcpvalues->bucketoflcpvalues[tableoflcpvalues->lcptaboffset +
                                      subbucketleft + idx]
                                      = (GtLcpvaluetype) value;
  if (value >= (unsigned long) LCPOVERFLOW)
  {
    tableoflcpvalues->numoflargelcpvalues++; /* this may overcount as there may
                                                be some value at index 
                                                which was already overflowing */
  }
}

/*@unused@*/ static inline unsigned long gt_lcptab_getvalue(
                                        const GtLcpvalues *tableoflcpvalues,
                                        unsigned long subbucketleft,
                                        unsigned long idx)
{
  gt_assert (tableoflcpvalues != NULL &&
             tableoflcpvalues->bucketoflcpvalues != NULL &&
             tableoflcpvalues->lcptaboffset+subbucketleft+idx <
             tableoflcpvalues->numofentries);
  gt_assert(tableoflcpvalues->isset == NULL ||
            GT_ISIBITSET(tableoflcpvalues->isset,
                         tableoflcpvalues->lcptaboffset+subbucketleft+idx));
  return (unsigned long) tableoflcpvalues->bucketoflcpvalues
                           [tableoflcpvalues->lcptaboffset+subbucketleft+idx];
}

const GtLcpvaluetype *gt_lcptab_getptr(const GtLcpvalues *tableoflcpvalues,
                                       unsigned long subbucketleft);

GtOutlcpinfo *gt_Outlcpinfo_new(const char *indexname,
                                unsigned int numofchars,
                                unsigned int prefixlength,
                                bool withdistribution,
                                bool swallow_tail_lcpvalues,
                                GtFinalProcessBucket final_process_bucket,
                                void *final_process_bucket_info,
                                GtError *err);

size_t gt_Outlcpinfo_size(const GtOutlcpinfo *outlcpinfo);

void gt_Outlcpinfo_reinit(GtOutlcpinfo *outlcpinfo,
                          unsigned int numofchars,
                          unsigned int prefixlength,
                          unsigned long numoflcpvalues);

void gt_Outlcpinfo_delete(GtOutlcpinfo *outlcpinfo);

unsigned long gt_Outlcpinfo_numoflargelcpvalues(const GtOutlcpinfo *outlcpinfo);

double gt_Outlcpinfo_lcptabsum(const GtOutlcpinfo *outlcpinfo);

void gt_Outlcpinfo_numsuffixes2output_set(GtOutlcpinfo *outlcpinfo,
                                          unsigned long numsuffixes2output);

unsigned long gt_Outlcpinfo_maxbranchdepth(const GtOutlcpinfo *outlcpinfo);

void gt_Outlcpinfo_prebucket(GtOutlcpinfo *outlcpinfo,
                             GtCodetype code,
                             unsigned long lcptaboffset);

void gt_Outlcpinfo_nonspecialsbucket(GtOutlcpinfo *outlcpinfo,
                                     unsigned int prefixlength,
                                     const GtSuffixsortspace *sssp,
                                     GtLcpvalues *tableoflcpvalues,
                                     const GtBucketspecification *bucketspec,
                                     GtCodetype code);

void gt_Outlcpinfo_postbucket(GtOutlcpinfo *outlcpinfo,
                              unsigned int prefixlength,
                              const GtSuffixsortspace *sssp,
                              const GtBcktab *bcktab,
                              const GtBucketspecification *bucketspec,
                              GtCodetype code);

GtLcpvalues *gt_Outlcpinfo_resizereservoir(GtOutlcpinfo *outlcpinfo,
                                           const GtBcktab *bcktab);

GtLcpvalues *gt_Outlcpinfo_lcpvalues_ref(GtOutlcpinfo *outlcpinfo);

void gt_Outlcpinfo_check_lcpvalues(const GtEncseq *encseq,
                                   GtReadmode readmode,
                                   const GtSuffixsortspace *sortedsample,
                                   unsigned long effectivesamplesize,
                                   const GtOutlcpinfo *outlcpinfosample,
                                   bool checkequality);

GtRMQ *gt_lcpvalues_rmq_new(const GtLcpvalues *samplelcpvalues);

#endif
genometools-1.5.1/src/match/sfx-linlcp.c000066400000000000000000000622451211610345200201630ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/chardef.h"
#include "core/ma_api.h"
#include "core/encseq.h"
#include "core/range.h"
#include "core/mathsupport.h"
#include "core/logger.h"
#include "core/compact_ulong_store.h"
#include "esa-seqread.h"
#include "sarr-def.h"
#include "sfx-linlcp.h"

unsigned long *gt_lcp13_manzini(const GtEncseq *encseq,
                                GtReadmode readmode,
                                unsigned long partwidth,
                                unsigned long totallength,
                                const ESASuffixptr *suftab,
                                GtCompactUlongStore *inversesuftab)
{
  unsigned long pos, lcpvalue = 0, *lcptab;

  lcptab = gt_malloc(sizeof (unsigned long) * partwidth);
  lcptab[0] = 0;
  for (pos=0; pos <= totallength; pos++)
  {
    unsigned long fillpos = gt_compact_ulong_store_get(inversesuftab,pos);
    if (fillpos > 0 && fillpos < partwidth)
    {
      unsigned long previousstart = ESASUFFIXPTRGET(suftab,fillpos-1);
      while (pos+lcpvalue < totallength &&
             previousstart+lcpvalue < totallength)
      {
        GtUchar cc1, cc2;

        cc1 = gt_encseq_get_encoded_char(encseq,pos+lcpvalue,readmode);
        cc2 = gt_encseq_get_encoded_char(encseq,previousstart+lcpvalue,
                                                readmode);
        if (cc1 == cc2 && ISNOTSPECIAL(cc1))
        {
          lcpvalue++;
        } else
        {
          break;
        }
      }
      lcptab[fillpos] = lcpvalue;
    }
    if (lcpvalue > 0)
    {
      lcpvalue--;
    }
  }
  return lcptab;
}

static unsigned long *computeocclesstab(const GtEncseq *encseq,
                                        GtReadmode readmode)
{
  unsigned long *occless;
  unsigned int charidx, numofchars;

  numofchars = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
  occless = gt_malloc(sizeof (unsigned long) * numofchars);
  occless[0] = 0;
  for (charidx = 1U; charidx < numofchars; charidx++)
  {
    unsigned long count;

    if (GT_ISDIRCOMPLEMENT(readmode))
    {
      count = gt_encseq_charcount(encseq,
                                  (GtUchar) GT_COMPLEMENTBASE(charidx-1));
    } else
    {
      count = gt_encseq_charcount(encseq,(GtUchar) (charidx-1));
    }
    occless[charidx] = occless[charidx-1] + count;
  }
  return occless;
}

/* for computing the ranknext-values of special positions, we only
   need the values inversesuftab[range.end] in this order,
   where range is a special range
   Now, if range.end = suffixarray[i] for some i, then
   inversesuftab[range.end] = inversesuftab[suffixarray[i]] = i.
   Thus, in case where the inversesuftab is not available,
   we obtain these values by the following function:
*/

static void setrelevantfrominversetab(GtCompactUlongStore *rightposinverse,
                                      const GtEncseq *encseq,
                                      GtReadmode readmode,
                                      const ESASuffixptr *suftab,
                                      unsigned long partwidth)
{
  if (gt_encseq_has_specialranges(encseq))
  {
    unsigned long idx, pos;

    for (idx = 0; idx < partwidth; idx++)
    {
      pos = ESASUFFIXPTRGET(suftab,idx);
      if (pos > 0)
      {
        GtUchar cc = gt_encseq_get_encoded_char(encseq,pos-1,readmode);
        if (ISSPECIAL(cc))
        {
          gt_compact_ulong_store_update(rightposinverse,pos,idx);
        }
      }
    }
  }
}

static unsigned long *fillrightofpartwidth(
                                     const GtCompactUlongStore *rightposinverse,
                                     const GtEncseq *encseq,
                                     GtReadmode readmode,
                                     unsigned long partwidth,
                                     unsigned long totallength)
{
  GtSpecialrangeiterator *sri;
  GtRange range;
  unsigned long countlargeranges, *rightofpartwidth = NULL,
                nextrightofpartwidth = 0;

  countlargeranges = gt_encseq_realspecialranges(encseq);
  sri = gt_specialrangeiterator_new(encseq,
                                    GT_ISDIRREVERSE(readmode) ? false : true);
  while (gt_specialrangeiterator_next(sri,&range))
  {
    if (GT_ISDIRREVERSE(readmode))
    {
      gt_range_reverse(totallength,&range);
    }
    if (range.end < partwidth)
    {
      gt_assert(countlargeranges > 0);
      countlargeranges--;
    } else
    {
      if (rightofpartwidth == NULL)
      {
        size_t allocsize = sizeof (*rightofpartwidth) * countlargeranges;
        rightofpartwidth = gt_malloc(allocsize);
        /*printf("allocated %lu bytes for rightofpartwidth (%.2f)\n",
            (unsigned long) allocsize, (double) allocsize/totallength);*/
      }
      gt_assert(nextrightofpartwidth < countlargeranges);
      rightofpartwidth[nextrightofpartwidth++]
        = gt_compact_ulong_store_get(rightposinverse,range.end);
    }
  }
  gt_specialrangeiterator_delete(sri);
  return rightofpartwidth;
}

static void inversesuffixarray2specialranknext(
                         const GtCompactUlongStore *rightposinverse,
                         GtCompactUlongStore *ranknext,
                         const GtEncseq *encseq,
                         GtReadmode readmode,
                         unsigned long partwidth,
                         unsigned long totallength)
{
  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;
    unsigned long idx, *rightofpartwidth = NULL,
                  specialranklistindex, nextrightofpartwidth = 0;

    rightofpartwidth = fillrightofpartwidth(rightposinverse,
                                            encseq,
                                            readmode,
                                            partwidth,
                                            totallength);
    specialranklistindex = partwidth;
    sri = gt_specialrangeiterator_new(encseq,
                                      GT_ISDIRREVERSE(readmode) ? false : true);
    nextrightofpartwidth = 0;
    while (gt_specialrangeiterator_next(sri,&range))
    {
      if (GT_ISDIRREVERSE(readmode))
      {
        gt_range_reverse(totallength,&range);
      }
      gt_assert(range.end <= totallength);
      for (idx = range.start; idx < range.end-1; idx++)
      {
        gt_assert(specialranklistindex < totallength);
        gt_compact_ulong_store_update(ranknext,specialranklistindex,
                                      specialranklistindex + 1);
        specialranklistindex++;
      }
      gt_assert(specialranklistindex < totallength);
      if (range.end < partwidth)
      {
        gt_compact_ulong_store_update(ranknext,specialranklistindex,
                                      gt_compact_ulong_store_get(
                                             rightposinverse,range.end));
      } else
      {
        gt_compact_ulong_store_update(ranknext,specialranklistindex,
                                      rightofpartwidth[nextrightofpartwidth]);
        nextrightofpartwidth++;
      }
      specialranklistindex++;
    }
    gt_free(rightofpartwidth);
    gt_assert(specialranklistindex == totallength);
    gt_specialrangeiterator_delete(sri);
  }
}

static unsigned long sa2ranknext(GtCompactUlongStore *ranknext,
                                 const GtEncseq *encseq,
                                 GtReadmode readmode,
                                 unsigned long partwidth,
                                 unsigned long totallength,
                                 const ESASuffixptr *suftab)
{
  unsigned long idx, pos, longest = 0, *occless;

  gt_assert(partwidth > 0);

  occless = computeocclesstab(encseq,readmode);
  /* now inveresuftab is not used any more, and thus the
     ranknext array (which points to ranknext can savely be stored */
  for (idx=0; idx < partwidth; idx++)
  {
    pos = ESASUFFIXPTRGET(suftab,idx);
    if (pos > 0)
    {
      GtUchar cc = gt_encseq_get_encoded_char(encseq,pos-1, readmode);
      if (ISNOTSPECIAL(cc))
      {
        gt_assert(occless[cc] < partwidth);
        gt_compact_ulong_store_update(ranknext,occless[cc],idx);
        occless[cc]++;
      }
    } else
    {
      longest = idx;
    }
  }
  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;
    unsigned long specialidx;

    sri = gt_specialrangeiterator_new(encseq,
                                      GT_ISDIRREVERSE(readmode) ? false : true);
    gt_assert(partwidth > 0); /* otherwise all lcps would be 0 */
    specialidx = partwidth;
    while (gt_specialrangeiterator_next(sri,&range))
    {
      if (GT_ISDIRREVERSE(readmode))
      {
        gt_range_reverse(totallength,&range);
      }
      gt_assert(range.start < range.end);
      if (range.start > 0)
      {
        GtUchar cc = gt_encseq_get_encoded_char(encseq,range.start-1,readmode);
        if (ISNOTSPECIAL(cc))
        {
          gt_assert(occless[cc] < partwidth);
          gt_compact_ulong_store_update(ranknext, occless[cc], specialidx);
          occless[cc]++;
        }
      } else
      {
        longest = partwidth;
      }
      specialidx += range.end - range.start;
    }
    if ((GT_ISDIRREVERSE(readmode) &&
         gt_encseq_lengthofspecialprefix(encseq) > 0) ||
        (!GT_ISDIRREVERSE(readmode) &&
         gt_encseq_lengthofspecialsuffix(encseq) > 0))
    {
      gt_compact_ulong_store_update(ranknext,totallength-1,totallength);
    }
    gt_specialrangeiterator_delete(sri);
  }
  gt_free(occless);
  return longest;
}

GtCompactUlongStore *gt_lcp9_manzini(GtCompactUlongStore *spacefortab,
                                 const GtEncseq *encseq,
                                 GtReadmode readmode,
                                 unsigned long partwidth,
                                 unsigned long totallength,
                                 const ESASuffixptr *suftab)
{
  unsigned long pos, previousstart, nextfillpos = 0, fillpos, lcpvalue = 0,
                previouscc1pos, previouscc2pos;
  GtCompactUlongStore *lcptab, *ranknext, *rightposinverse;
  GtUchar cc1, cc2;
  GtEncseqReader *esr1, *esr2;

  if (spacefortab == NULL)
  {
    unsigned int bitsperentry = gt_determinebitspervalue(totallength);
    rightposinverse = ranknext
                    = gt_compact_ulong_store_new(totallength+1,bitsperentry);
    gt_compact_ulong_store_update(ranknext,totallength,totallength);
    setrelevantfrominversetab(rightposinverse,encseq,readmode,suftab,
                              partwidth);
  } else
  {
    rightposinverse = ranknext = spacefortab;
  }
  inversesuffixarray2specialranknext(rightposinverse,ranknext,
                                     encseq,
                                     readmode,
                                     partwidth,
                                     totallength);
  fillpos = sa2ranknext(ranknext,encseq,readmode,partwidth,totallength,
                        suftab);
  lcptab = ranknext;
  /* now ranknext and lcptab point to the same memory area. After reading
     ranknext at position fillpos, the same cell is used for storing
     the determined lcp-value */
  /* exploit the fact, that pos + lcpvalue is monotone */
  esr1 = gt_encseq_create_reader_with_readmode(encseq, readmode,0);
  cc1 = gt_encseq_reader_next_encoded_char(esr1);
  previouscc1pos = 0;
  esr2 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  previouscc2pos = totallength;
  cc2 = 0;
  for (pos = 0; pos < totallength; pos++)
  {
    if (pos < totallength - 1)
    {
      nextfillpos = gt_compact_ulong_store_get(ranknext,fillpos);
    }
    if (fillpos > 0 && fillpos - 1 < partwidth)
    {
      previousstart = ESASUFFIXPTRGET(suftab,fillpos-1);
      while (pos+lcpvalue < totallength &&
             previousstart+lcpvalue < totallength)
      {
        gt_assert(pos + lcpvalue >= previouscc1pos);
        while (previouscc1pos < pos + lcpvalue)
        {
          previouscc1pos++;
          cc1 = gt_encseq_reader_next_encoded_char(esr1);
        }
        if (ISSPECIAL(cc1))
        {
          break;
        }
        if (previousstart+lcpvalue < previouscc2pos ||
            previousstart+lcpvalue > previouscc2pos+1)
        {
          previouscc2pos = previousstart+lcpvalue;
          gt_encseq_reader_reinit_with_readmode(esr2, encseq, readmode,
                                                previouscc2pos);
          cc2 = gt_encseq_reader_next_encoded_char(esr2);
        } else
        {
          if (previousstart+lcpvalue == previouscc2pos+1)
          {
            previouscc2pos++;
            cc2 = gt_encseq_reader_next_encoded_char(esr2);
          } else
          {
            gt_assert(previousstart+lcpvalue == previouscc2pos);
          }
        }
        if (cc1 != cc2)
        {
          break;
        }
        lcpvalue++;
      }
      gt_compact_ulong_store_update(lcptab,fillpos,lcpvalue);
      if (lcpvalue > 0)
      {
        lcpvalue--;
      }
    }
    fillpos = nextfillpos;
  }
  gt_encseq_reader_delete(esr1);
  gt_encseq_reader_delete(esr2);
  return lcptab;
}

static unsigned long gt_check_for_range_occurrence(const ESASuffixptr *suftab,
                                                   unsigned long suffix,
                                                   unsigned long start,
                                                   unsigned long end)
{
  unsigned long idx;

  for (idx = start; idx <= end; idx++)
  {
    unsigned long position = ESASUFFIXPTRGET(suftab,idx);

    if (suffix == position)
    {
      return idx;
    }
  }
  return ULONG_MAX;
}

typedef struct
{
  unsigned long start, end;
  GtUchar firstchar;
} GtRangewithchar;

/* The following funktion implements the linear time algorithm of
   @INPROCEEDINGS{BUR:KAER:2003,
   author = {Burkhardt, S. and K{\"a}rkk{\"a}inen, J.},
   title = {{Fast Lightweight Suffix Array Construction and Checking}},
   booktitle = {{Proceedings of the 14th Annual Symposium on Combinatorial
                 Pattern Matching (CPM)}},
   year = {2003},
   editor = {{Baeza-Yates, R. and Ch{\'a}vez, E. and Crochemore, M.}},
   volume = {2676},
   series = {LNCS},
   pages = {200-210},
   publisher = {Springer-Verlag}
   }
   to check the following suffix-order condition of the sorted suffix array:
   For all characters c, if SA[i,j] contains the suffixes starting
   with charcter c, then SA[i]+1, SA[i+1]+1, \ldots, SA[j]+1 occur
   in SA in this order (but not consecutively in general).
   The running time of the algorithm is independent of the alphabet size.
   The main problem is that it requires random access to the sequence
   which slows it down.
*/

static void gt_suftab_bk_suffixorder(const GtEncseq *encseq,
                                     GtReadmode readmode,
                                     unsigned long totallength,
                                     unsigned int numofchars,
                                     const ESASuffixptr *suftab,
                                     const GtRangewithchar *rangestore,
                                     unsigned int numofranges)
{
  unsigned int rangeidx;
  unsigned long idx, *nexttab = gt_calloc((size_t) numofchars,sizeof(*nexttab));

  for (rangeidx = 0; rangeidx < numofranges; rangeidx++)
  {
    nexttab[rangestore[rangeidx].firstchar] = rangestore[rangeidx].start;
  }
  for (idx = 0; idx < totallength; idx++)
  {
    unsigned long position = ESASUFFIXPTRGET(suftab,idx);

    if (position > 0)
    {
      GtUchar cc = gt_encseq_get_encoded_char(encseq,position - 1,readmode);
      if (ISNOTSPECIAL(cc))
      {
        unsigned long checkpos;

        checkpos = ESASUFFIXPTRGET(suftab,nexttab[(int) cc]) + 1;
        if (checkpos != position)
        {
          fprintf(stderr,"idx=%lu,checkpos=%lu,position=%lu\n",
                          idx,checkpos,position);
          exit(GT_EXIT_PROGRAMMING_ERROR);
        }
        nexttab[(int) cc]++;
      }
    }
  }
  gt_free(nexttab);
}

/* The following function checks the suffix-order condition described
   above using an O(\sigma n) algorithm where \sigma is the alphabet size
   and n is the length of the suffix array. The algorithm does not
   access the sequence and performs \sigma linear scans of the suffix array.
   This makes it faster than the previous method. It is probably possible
   to perform the check in one linear scan.
*/

static void gt_suftab_sk_suffixorder(unsigned long totallength,
                                     unsigned int numofchars,
                                     const ESASuffixptr *suftab,
                                     const GtRangewithchar *rangestore,
                                     unsigned int numofranges)
{
  unsigned int rangeidx;
  unsigned long numofcomparisons = 0;
  double ratio;

  for (rangeidx = 0; rangeidx < numofranges; rangeidx++)
  {
    unsigned long idx, start = 0;

    for (idx = rangestore[rangeidx].start; idx <= rangestore[rangeidx].end;
         idx++)
    {
      unsigned long position = ESASUFFIXPTRGET(suftab,idx);

      if (position + 1 <= totallength)
      {
        unsigned long found = gt_check_for_range_occurrence(suftab,
                                                            position + 1,
                                                            start,
                                                            totallength);
        if (found == ULONG_MAX)
        {
          fprintf(stderr,"Cannot find position+1=%lu in range [%lu,%lu]\n",
                            position+1,start,totallength);
          exit(GT_EXIT_PROGRAMMING_ERROR);
        }
        numofcomparisons += found - start + 1;
        start = found + 1;
      }
    }
  }
  ratio = (double) numofcomparisons/totallength;
  if (gt_double_compare(ratio,(double) numofchars) > 0)
  {
    fprintf(stderr,"gt_double_compare(%.2f,%u) = %d > 0 not exected\n",
                    ratio,numofchars,
                    gt_double_compare(ratio,(double) numofchars));
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
}

void gt_suftab_lightweightcheck(const GtEncseq *encseq,
                               GtReadmode readmode,
                               unsigned long totallength,
                               const ESASuffixptr *suftab,
                               GtLogger *logger)
{
  unsigned long idx, countbitsset = 0, previouspos = 0,
                firstspecial = totallength, rangestart = 0;
  unsigned int numofchars, charidx, rangeidx = 0, numofranges;
  GtBitsequence *startposoccurs;
  GtUchar previouscc = 0;
  GtRangewithchar *rangestore;
  const bool skcheck = true;

  GT_INITBITTAB(startposoccurs,totallength+1);
  numofchars = gt_encseq_alphabetnumofchars(encseq);
  rangestore = gt_malloc(sizeof(*rangestore) * numofchars);
  for (idx = 0; idx < totallength; idx++)
  {
    unsigned long position = ESASUFFIXPTRGET(suftab,idx);
    GtUchar cc;

    if (GT_ISIBITSET(startposoccurs,position))
    {
      fprintf(stderr,"ERROR: suffix with startpos %lu already occurs\n",
              ESASUFFIXPTRGET(suftab,idx));
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    GT_SETIBIT(startposoccurs,position);
    countbitsset++;
    cc = gt_encseq_get_encoded_char(encseq,position,readmode);
    if (idx > 0)
    {
      if (ISSPECIAL(cc))
      {
        if (firstspecial == totallength)
        {
          firstspecial = idx;
          gt_assert(rangeidx < numofchars);
          rangestore[rangeidx].start = rangestart;
          rangestore[rangeidx].end = idx-1;
          rangestore[rangeidx++].firstchar = previouscc;
        }
        if (ISSPECIAL(previouscc))
        {
          if (previouspos > position)
          {
            fprintf(stderr,"incorrect order: %lu = %lu=SPECIAL > SPECIAL=%lu "
                           " = %lu\n",
                      idx-1,position,previouspos,idx);
            exit(GT_EXIT_PROGRAMMING_ERROR);
          }
        }
      } else
      {
        if (ISSPECIAL(previouscc))
        {
          fprintf(stderr,"incorrect order: %lu=%lu=SPECIAL > %u=%lu=%lu\n",
                    idx-1,position,(unsigned int) cc,previouspos,idx);
          exit(GT_EXIT_PROGRAMMING_ERROR);
        } else
        {
          if (previouscc > cc)
          {
            fprintf(stderr,"incorrect order: %lu = %lu=%u > %u=%lu=%lu\n",
                      idx-1,position,(unsigned int) previouscc,
                      (unsigned int) cc,previouspos,idx);
            exit(GT_EXIT_PROGRAMMING_ERROR);
          } else
          {
            if (previouscc < cc)
            {
              gt_assert(rangeidx < numofchars);
              rangestore[rangeidx].start = rangestart;
              rangestore[rangeidx].end = idx-1;
              rangestore[rangeidx++].firstchar = previouscc;
              rangestart = idx;
            }
          }
        }
      }
    } else
    {
      if (ISSPECIAL(cc))
      {
        firstspecial = 0;
      }
    }
    previouscc = cc;
    previouspos = position;
  }
  if (countbitsset != totallength)
  {
    fprintf(stderr,"ERROR: only %lu of %lu suffixes occur\n",countbitsset,
                                totallength);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  gt_free(startposoccurs);
  if (firstspecial == totallength)
  {
    gt_assert(firstspecial > 0 && rangeidx < numofchars);
    rangestore[rangeidx].start = rangestart;
    rangestore[rangeidx].end = firstspecial-1;
    rangestore[rangeidx++].firstchar = previouscc;
  }
  numofranges = rangeidx;
  for (charidx = 0, rangeidx = 0; charidx < numofchars; charidx++)
  {
    unsigned long count;

    if (GT_ISDIRCOMPLEMENT(readmode))
    {
      count = gt_encseq_charcount(encseq,(GtUchar) GT_COMPLEMENTBASE(charidx));
    } else
    {
      count = gt_encseq_charcount(encseq,(GtUchar) charidx);
    }
    if (count != 0)
    {
      gt_assert(rangestore[rangeidx].firstchar == (GtUchar) charidx);
      gt_assert(rangestore[rangeidx].end - rangestore[rangeidx].start + 1
                == count);
      rangeidx++;
    }
  }
  gt_logger_log(logger,"suftab-check, first phase done");
  if (skcheck)
  {
    gt_suftab_sk_suffixorder(totallength,
                             numofchars,
                             suftab,
                             rangestore,
                             numofranges);
    gt_logger_log(logger,"suftab-check, second phase (sk-method) done");
  } else
  {
    gt_suftab_bk_suffixorder(encseq,
                             readmode,
                             totallength,
                             numofchars,
                             suftab,
                             rangestore,
                             numofranges);
    gt_logger_log(logger,"suftab-check, second phase (bk-method) done");
  }
  gt_free(rangestore);
}

int gt_lcptab_lightweightcheck(const char *esaindexname,
                               const GtEncseq *encseq,
                               GtReadmode readmode,
                               const ESASuffixptr *suftab,
                               GtLogger *logger,
                               GtError *err)
{
  bool haserr = false;
  Sequentialsuffixarrayreader *ssar;
  unsigned long partwidth, totallength = gt_encseq_total_length(encseq),
                idx, specials = gt_encseq_specialcharacters(encseq);
  GtCompactUlongStore *lcptab = NULL;

  gt_assert(specials <= totallength);
  partwidth = totallength - specials;
  if (partwidth > 0)
  {
    lcptab = gt_lcp9_manzini(NULL,
                           encseq,
                           readmode,
                           partwidth,
                           totallength,
                           suftab);
    gt_logger_log(logger,"computed reference lcp table with manzini algorithm");
  }
  ssar = gt_newSequentialsuffixarrayreaderfromfile(esaindexname,
                                                   SARR_LCPTAB,
                                                   SEQ_scan,
                                                   logger,
                                                   err);
  if (ssar == NULL)
  {
    haserr = true;
  }
  for (idx = 1UL; /* Nothing */; idx++)
  {
    unsigned long mlcpvalue, lcpvalue;
    int retval = gt_nextSequentiallcpvalue(&lcpvalue,ssar,err);

    if (retval < 0)
    {
      haserr = true;
      break;
    }
    if (retval == 0)
    {
      break;
    }
    if (idx < partwidth)
    {
      mlcpvalue = gt_compact_ulong_store_get(lcptab,idx);
    } else
    {
      mlcpvalue = 0;
    }
    if (mlcpvalue != lcpvalue)
    {
      fprintf(stderr,"%lu: mlcpvalue = %lu != %lu = lcpvalue\n",
                       idx,mlcpvalue,lcpvalue);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  }
  gt_logger_log(logger,"compare lcp-values against reference");
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  gt_compact_ulong_store_delete(lcptab);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/sfx-linlcp.h000066400000000000000000000036451211610345200201670ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_LINLCP_H
#define SFX_LINLCP_H

#include "core/encseq.h"
#include "core/compact_ulong_store.h"
#include "match/sarr-def.h"

GtCompactUlongStore *gt_lcp9_manzini(GtCompactUlongStore *spacefortab,
                                 const GtEncseq *encseq,
                                 GtReadmode readmode,
                                 unsigned long partwidth,
                                 unsigned long totallength,
                                 const ESASuffixptr *suftab);

void gt_suftab_lightweightcheck(const GtEncseq *encseq,
                                GtReadmode readmode,
                                unsigned long totallength,
                                const ESASuffixptr *suftab,
                                GtLogger *logger);

int gt_lcptab_lightweightcheck(const char *esaindexname,
                               const GtEncseq *encseq,
                               GtReadmode readmode,
                               const ESASuffixptr *suftab,
                               GtLogger *logger,
                               GtError *err);

#endif
genometools-1.5.1/src/match/sfx-mapped4.gen000066400000000000000000000330451211610345200205570ustar00rootroot00000000000000/*
  Copyright (c) 2007-2012 Stefan Kurtz 
  Copyright (c) 2007-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

static GtCodetype PROCESSKMERPREFIX(getencseqkmers_nospecialtwobitencoding)(
                                    const GtSfxmapped4constinfo *mapped4info,
                                    GT_UNUSED unsigned long specialfreeunit,
                                    const GtReadmode readmode,
                                    PROCESSKMERTYPE *processkmercodeinfo,
                                    unsigned long startpos,
                                    unsigned long endpos)
{
  unsigned long position, unitindex, relpos = 0;
  GtCodetype code, transcode;
  GtTwobitencoding currentencoding;
  unsigned int shiftright;
  GtUchar cc;

  gt_assert(mapped4info->kmersize > 1U);
  if (GT_ISDIRREVERSE(readmode))
  {
    gt_assert(endpos >= (unsigned long) mapped4info->upperkmersize);
    position = endpos - (unsigned long) mapped4info->kmersize;
    unitindex = (position > 0) ? GT_DIVBYUNITSIN2BITENC(position-1) : 0;
    code
      = gt_kmercode_reverse(gt_kmercode_at_position(mapped4info->twobitencoding,
                                                    position,
                                                    mapped4info->kmersize),
                            mapped4info->kmersize);
    transcode = GT_ISDIRCOMPLEMENT(readmode)
                  ? gt_kmercode_complement(code,mapped4info->maskright)
                  : code;
    GT_ENCSEQ_RELPOS_SEQNUM_CHECK(GT_ADJUSTREVERSEPOS(mapped4info->rightbound,
                                                      position));
    PROCESSKMERCODE(processkmercodeinfo,true,
                    GT_ADJUSTREVERSEPOS(mapped4info->rightbound,position),
                    specialfreeunit,
                    relpos,
                    transcode);
    currentencoding = mapped4info->twobitencoding[unitindex];
    startpos += mapped4info->upperkmersize - mapped4info->kmersize;
    shiftright = (unsigned int)
                 GT_MULT2(GT_UNITSIN2BITENC - 1 -
                          GT_MODBYUNITSIN2BITENC(position-1));
    while (position > startpos)
    {
      position--;
      relpos++;
      cc = (GtUchar) (currentencoding >> shiftright) & 3;
      GT_UPDATEKMER(code,cc,mapped4info->maskright);
      transcode = (readmode == GT_READMODE_REVCOMPL)
                    ? gt_kmercode_complement(code,mapped4info->maskright)
                    : code;
      GT_ENCSEQ_RELPOS_SEQNUM_CHECK(GT_ADJUSTREVERSEPOS(mapped4info->rightbound,
                                                        position));
      PROCESSKMERCODE(processkmercodeinfo, false,
                      GT_ADJUSTREVERSEPOS(mapped4info->rightbound,position),
                      specialfreeunit,
                      relpos,
                      transcode);
      if (shiftright < (unsigned int) (GT_INTWORDSIZE-2))
      {
        shiftright += 2;
      } else
      {
        gt_assert(unitindex > 0 || position == startpos);
        if (unitindex > 0)
        {
          currentencoding = mapped4info->twobitencoding[--unitindex];
        }
        shiftright = 0;
      }
    }
  } else
  {
    position = startpos;
    unitindex = GT_DIVBYUNITSIN2BITENC(startpos + mapped4info->kmersize);
    code = gt_kmercode_at_position(mapped4info->twobitencoding,
                                   position,
                                   mapped4info->kmersize);
    transcode = GT_ISDIRCOMPLEMENT(readmode)
                  ? gt_kmercode_complement(code,mapped4info->maskright)
                  : code;
    GT_ENCSEQ_RELPOS_SEQNUM_CHECK(position);
    PROCESSKMERCODE(processkmercodeinfo, true, position, specialfreeunit,
                    relpos, transcode);
    currentencoding = mapped4info->twobitencoding[unitindex];
    shiftright = (unsigned int)
                 GT_MULT2(GT_UNITSIN2BITENC - 1 -
                          GT_MODBYUNITSIN2BITENC(startpos +
                                                 mapped4info->kmersize));
    gt_assert(endpos >= (unsigned long) mapped4info->upperkmersize);
    endpos -= mapped4info->upperkmersize;
    while (position < endpos)
    {
      position++;
      relpos++;
      cc = (GtUchar) (currentencoding >> shiftright) & 3;
      GT_UPDATEKMER(code,cc,mapped4info->maskright);
      transcode = (readmode == GT_READMODE_COMPL)
                    ? gt_kmercode_complement(code,mapped4info->maskright)
                    : code;
      GT_ENCSEQ_RELPOS_SEQNUM_CHECK(position);
      PROCESSKMERCODE(processkmercodeinfo,false,position,specialfreeunit,relpos,
                      transcode);
      if (shiftright > 0)
      {
        shiftright -= 2;
      } else
      {
        gt_assert(unitindex < mapped4info->maxunitindex-1 ||
                  position == endpos);
        if (unitindex < mapped4info->maxunitindex-1)
        {
          currentencoding = mapped4info->twobitencoding[++unitindex];
        }
        shiftright = (unsigned int) (GT_INTWORDSIZE-2);
      }
    }
  }
  return code;
}

static void PROCESSKMERPREFIX(getencseqkmers_rangetwobitencoding)(
                              const GtSfxmapped4constinfo *mapped4info,
                              unsigned long specialfreeunit,
                              GtReadmode readmode,
                              PROCESSKMERTYPE *processkmercodeinfo,
                              PROCESSKMERSPECIALTYPE *processkmerspecialinfo,
                              unsigned long startpos,
                              unsigned long endpos)
{
  GT_UNUSED GtCodetype lastcode;

  if (mapped4info->mirrored && startpos >= mapped4info->realtotallength)
  {
    gt_readmode_invert(readmode);
    startpos = GT_REVERSEPOS(mapped4info->realtotallength,
                             startpos - mapped4info->realtotallength - 2);
    if (endpos == mapped4info->totallength)
    {
      endpos = 0;
    } else
    {
      endpos = GT_REVERSEPOS(mapped4info->realtotallength,
                             endpos - mapped4info->realtotallength - 2);
    }
    if (startpos > endpos)
    {
      unsigned long tmp = startpos;
      startpos = endpos;
      endpos = tmp;
    }
    gt_assert(startpos <= endpos);
    gt_assert(endpos <= mapped4info->realtotallength);
  }
  if (endpos - startpos >= (unsigned long) mapped4info->upperkmersize)
  {
    gt_assert(endpos > 0);
    lastcode = PROCESSKMERPREFIX(getencseqkmers_nospecialtwobitencoding)(
                                                      mapped4info,
                                                      specialfreeunit,
                                                      readmode,
                                                      processkmercodeinfo,
                                                      startpos,
                                                      endpos);
#ifdef PROCESSKMERCODESPECIAL
    {
      GtCodetype newcode;
      if (GT_ISDIRCOMPLEMENT(readmode))
      {
        lastcode = gt_kmercode_complement(lastcode,mapped4info->maskright);
      }
      newcode = ((lastcode << 2) | 3UL) & mapped4info->maskright;
      PROCESSKMERCODESPECIAL(processkmerspecialinfo,
                             mapped4info->kmersize-1,
                             GT_ISDIRREVERSE(readmode)
                               ? (mapped4info->totallength-startpos)
                               : endpos,
                             (unsigned int) newcode);
    }
#endif
  }
#ifdef PROCESSKMERCODESPECIAL
  else
  {
    if (startpos < endpos)
    {
      GtCodetype newcode;
      unsigned int fillpos;

      fillpos = (unsigned int) (mapped4info->kmersize - (endpos - startpos));
      lastcode = gt_kmercode_at_position(mapped4info->twobitencoding,startpos,
                                         (unsigned int) (endpos - startpos));
      if (GT_ISDIRREVERSE(readmode) && (unsigned int) (endpos - startpos) > 1U)
      {
        lastcode = gt_kmercode_reverse(lastcode,
                                       (unsigned int) (endpos-startpos));
      }
      if (GT_ISDIRCOMPLEMENT(readmode))
      {
        lastcode = gt_kmercode_complement(lastcode,mapped4info->maskright);
      }
      newcode
        = ((lastcode << GT_MULT2(fillpos)) | ((1UL << GT_MULT2(fillpos)) - 1))
           & mapped4info->maskright;
      PROCESSKMERCODESPECIAL(processkmerspecialinfo,
                             (unsigned int) (endpos - startpos),
                             GT_ISDIRREVERSE(readmode)
                               ? (mapped4info->totallength - startpos)
                               : endpos,
                             (unsigned int) newcode);
    }
  }
#endif
}

static void PROCESSKMERPREFIX(getencseqkmers_twobitencoding)(
                               const GtEncseq *encseq,
                               const GtReadmode readmode,
                               unsigned int kmersize,
                               unsigned int upperkmersize,
                               PROCESSKMERTYPE *processkmercodeinfo,
                               PROCESSKMERSPECIALTYPE *processkmerspecialinfo)
{
  unsigned long laststart = 0, lastend, specialfreeunit = 0;
  GtSfxmapped4constinfo mapped4info;

  mapped4info.twobitencoding = gt_encseq_twobitencoding_export(encseq);
  lastend = mapped4info.totallength = gt_encseq_total_length(encseq);
  mapped4info.maxunitindex
    = gt_unitsoftwobitencoding(mapped4info.totallength) - 1;
  mapped4info.maskright = GT_MASKRIGHT(kmersize);
  mapped4info.kmersize = kmersize;
  mapped4info.upperkmersize = upperkmersize;
  mapped4info.mirrored = gt_encseq_is_mirrored(encseq);
  mapped4info.rightbound = mapped4info.totallength - mapped4info.kmersize;
  mapped4info.numofsequences = gt_encseq_num_of_sequences(encseq);
  mapped4info.encseq = encseq;
  if (mapped4info.mirrored)
  {
    gt_assert(GT_MOD2(mapped4info.totallength) == 1UL);
    mapped4info.realtotallength = GT_DIV2(mapped4info.totallength - 1);
  } else
  {
    mapped4info.realtotallength = mapped4info.totallength;
  }
  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;

    if (GT_ISDIRREVERSE(readmode))
    {
      sri = gt_specialrangeiterator_new(encseq,false);
      for (specialfreeunit = 0;
           gt_specialrangeiterator_next(sri,&range); specialfreeunit++)
      {
        gt_assert(range.end <= lastend);
        /*printf("line %d: specialfreeunit=%lu, range %lu %lu\n",
                 __LINE__,specialfreeunit,range.end,lastend);*/
        PROCESSKMERPREFIX(getencseqkmers_rangetwobitencoding)(
                                           &mapped4info,
                                           specialfreeunit,
                                           readmode,
                                           processkmercodeinfo,
                                           processkmerspecialinfo,
                                           range.end,
                                           lastend);
        lastend = range.start;
      }
    } else
    {
      sri = gt_specialrangeiterator_new(encseq,true);
      for (specialfreeunit = 0; gt_specialrangeiterator_next(sri,&range);
           specialfreeunit++)
      {
        gt_assert(range.start >= laststart);
        /*printf("region of length %lu\n",range.start - laststart);*/
        /*printf("line %d: range %lu %lu\n",__LINE__,laststart,range.start);*/
        PROCESSKMERPREFIX(getencseqkmers_rangetwobitencoding)(
                                           &mapped4info,
                                           specialfreeunit,
                                           readmode,
                                           processkmercodeinfo,
                                           processkmerspecialinfo,
                                           laststart,
                                           range.start);
        laststart = range.end;
      }
    }
    gt_assert(mapped4info.totallength >= laststart);
    gt_specialrangeiterator_delete(sri);
  }
  /*
  printf("line %d: specialfreeunit=%lu,range %lu %lu\n",__LINE__,
                                     specialfreeunit,
                                     GT_ISDIRREVERSE(readmode)
                                       ? 0
                                       : laststart,
                                     GT_ISDIRREVERSE(readmode)
                                       ? lastend
                                       : mapped4info.totallength);*/
  PROCESSKMERPREFIX(getencseqkmers_rangetwobitencoding)(
                                     &mapped4info,
                                     specialfreeunit,
                                     readmode,
                                     processkmercodeinfo,
                                     processkmerspecialinfo,
                                     GT_ISDIRREVERSE(readmode)
                                       ? 0
                                       : laststart,
                                     GT_ISDIRREVERSE(readmode)
                                       ? lastend
                                       : mapped4info.totallength);
}
genometools-1.5.1/src/match/sfx-mappedstr.c000066400000000000000000000551551211610345200207030ustar00rootroot00000000000000/*
  Copyright (c) 2007-2010 Stefan Kurtz 
  Copyright (c) 2007-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#include 
#endif
#include 
#include 
#include 
#include "core/assert_api.h"
#include "core/chardef.h"
#include "core/ma_api.h"
#include "core/checkencchar.h"
#include "core/divmodmul.h"
#include "core/alphabet.h"
#include "core/error_api.h"
#include "core/sequence_buffer_fasta.h"
#include "core/sequence_buffer_plain.h"
#include "core/str_array.h"
#include "core/intbits.h"
#include "core/encseq.h"
#include "core/format64.h"
#include "intcode-def.h"
#include "initbasepower.h"
#include "sfx-mappedstr.h"
#undef SKDEBUG
#ifdef SKDEBUG
#include "sfx-nextchar.h"
#endif

#undef SPECIALCASE4
#ifdef SPECIALCASE4
#define SUBTRACTLCHARANDSHIFT(CODE,LCHAR,NUMOFCHARS,MULTIMAPPOWER)\
        if ((NUMOFCHARS) == GT_DNAALPHASIZE)\
        {\
          CODE = GT_MULT4((CODE) - MULTIMAPPOWER[(unsigned int) (LCHAR)]);\
        } else\
        {\
          CODE = ((CODE) - MULTIMAPPOWER[(unsigned int) (LCHAR)])\
                 * (NUMOFCHARS);\
        }

#define SUBTRACTLCHARSHIFTADDNEXT(CODE,LCHAR,NUMOFCHARS,MULTIMAPPOWER,CC)\
        if ((NUMOFCHARS) == GT_DNAALPHASIZE)\
        {\
          CODE = GT_MULT4((CODE) - MULTIMAPPOWER[(unsigned int) (LCHAR)]) |\
                 (CC);\
        } else\
        {\
          CODE = (GtCodetype) ((CODE) - MULTIMAPPOWER[(unsigned int) (LCHAR)])*\
                            (NUMOFCHARS) + (CC);\
        }
#else
#define SUBTRACTLCHARANDSHIFT(CODE,LCHAR,NUMOFCHARS,MULTIMAPPOWER)\
        CODE = ((CODE) - MULTIMAPPOWER[(unsigned int) (LCHAR)]) * (NUMOFCHARS)

#define SUBTRACTLCHARSHIFTADDNEXT(CODE,LCHAR,NUMOFCHARS,MULTIMAPPOWER,CC)\
        CODE = (GtCodetype) (((CODE) - MULTIMAPPOWER[(unsigned int) (LCHAR)])*\
                           (NUMOFCHARS) + (CC))
#endif

#ifdef SKDEBUG
static GtCodetype windowkmer2code(unsigned int numofchars,
                                unsigned int kmersize,
                                const GtUchar *cyclicwindow,
                                unsigned int firstindex)
{
  unsigned int i;
  GtCodetype integercode;
  GtUchar cc;
  bool foundspecial;

  cc = cyclicwindow[firstindex];
  if (ISSPECIAL(cc))
  {
    integercode = (GtCodetype) (numofchars-1);
    foundspecial = true;
  } else
  {
    integercode = (GtCodetype) cc;
    foundspecial = false;
  }
  for (i=1U; i < kmersize; i++)
  {
    if (foundspecial)
    {
      ADDNEXTCHAR(integercode,numofchars-1,numofchars);
    } else
    {
      cc = cyclicwindow[(firstindex+i) % kmersize];
      if (ISSPECIAL(cc))
      {
        ADDNEXTCHAR(integercode,numofchars-1,numofchars);
        foundspecial = true;
      } else
      {
        ADDNEXTCHAR(integercode,cc,numofchars);
      }
    }
  }
  return integercode;
}

static GtCodetype prefixwindowkmer2code(unsigned int firstspecialpos,
                                        unsigned int kmersize,
                                        const GtCodetype **multimappower,
                                        const GtUchar *cyclicwindow,
                                        unsigned int firstindex)
{
  unsigned int i;
  GtCodetype integercode = 0;
  GtUchar cc;

  for (i=0; iqueuespace = gt_malloc(sizeof (*spos->queuespace) * queuesize);
  spos->noofelements = 0;
  spos->queuesize = queuesize;
  spos->dequeueindex = spos->enqueueindex = queuesize - 1;
}

static bool specialqueueisempty(const Specialpositions *spos)
{
  return (spos->noofelements == 0) ? true : false;
}

static Specialitem *specialheadofqueue(const Specialpositions *spos)
{
  return spos->queuespace + spos->dequeueindex;
}

static void specialdeleteheadofqueue(Specialpositions *spos)
{
  spos->noofelements--;
  if (spos->dequeueindex > 0)
  {
    spos->dequeueindex--;
  } else
  {
    spos->dequeueindex = spos->queuesize - 1;
  }
}

static void specialenqueue(Specialpositions *spos,Specialitem elem)
{
  spos->noofelements++;
  spos->queuespace[spos->enqueueindex] = elem;
  if (spos->enqueueindex > 0)
  {
    spos->enqueueindex--;
  } else
  {
    spos->enqueueindex = spos->queuesize - 1;
  }
}

static void specialwrapqueue(Specialpositions *spos)
{
  gt_free(spos->queuespace);
}

static Kmerstream *kmerstream_new(unsigned int numofchars,unsigned int kmersize)
{
  Kmerstream *spwp;

  gt_assert(kmersize <= (unsigned int) MAXPREFIXLENGTH);
  spwp = gt_malloc(sizeof (*spwp));
  spwp->multimappower = gt_initmultimappower(numofchars,kmersize);
  spwp->lengthwithoutspecial = 0;
  spwp->codewithoutspecial = 0;
  spwp->kmersize = kmersize;
  spwp->numofchars = numofchars;
  spwp->windowwidth = 0;
  spwp->firstindex = 0;
  specialemptyqueue(&spwp->spos,kmersize);
  spwp->filltable = gt_filllargestchartable(numofchars,kmersize);
  return spwp;
}

static void updatespecialpositions(Kmerstream *spwp,
                                   GtUchar charcode,
                                   bool doshift,
                                   GtUchar lchar)
{
  if (doshift)
  {
    if (!specialqueueisempty(&spwp->spos))
    {
      Specialitem *head;

      /* only here we add some element to the queue */
      head = specialheadofqueue(&spwp->spos);
      if (head->distvalue > 0)
      {
        SUBTRACTLCHARANDSHIFT(head->codeforleftcontext,lchar,spwp->numofchars,
                              spwp->multimappower[0]);
        head->distvalue--;
      } else
      {
        specialdeleteheadofqueue(&spwp->spos);
        if (!specialqueueisempty(&spwp->spos))
        {
          head = specialheadofqueue(&spwp->spos);
          head->distvalue--;
        }
      }
    }
  }
  if (ISNOTSPECIAL(charcode))
  {
    if (spwp->lengthwithoutspecial == spwp->kmersize)
    {
      SUBTRACTLCHARSHIFTADDNEXT(spwp->codewithoutspecial,
                                lchar,
                                spwp->numofchars,
                                spwp->multimappower[0],
                                charcode);
    } else
    {
      spwp->codewithoutspecial +=
        spwp->multimappower[spwp->lengthwithoutspecial][charcode];
      spwp->lengthwithoutspecial++;
    }
  } else
  {
    /* only here we add some element to the queue */
    Specialitem newelem;

    if (specialqueueisempty(&spwp->spos))
    {
      newelem.distvalue = spwp->windowwidth-1;
    } else
    {
      newelem.distvalue = spwp->lengthwithoutspecial+1;
    }
    if (spwp->lengthwithoutspecial == spwp->kmersize)
    {
      SUBTRACTLCHARANDSHIFT(spwp->codewithoutspecial,lchar,
                            spwp->numofchars,spwp->multimappower[0]);
    }
    newelem.codeforleftcontext = spwp->codewithoutspecial;
    specialenqueue(&spwp->spos,newelem);
    spwp->lengthwithoutspecial = 0;
    spwp->codewithoutspecial = 0;
  }
}

static void kmerstream_newcode(GtKmercode *kmercode, Kmerstream *spwp)
{
#ifdef SKDEBUG
  bool firstspecialbrutedefined;
  unsigned int firstspecialbrute;

  if (!specialqueueisempty(&spwp->spos))
  {
    Specialitem *head = specialheadofqueue(&spwp->spos);
    GtCodetype tmpprefixcode = prefixwindowkmer2code(head->distvalue,
                                                     spwp->kmersize,
                                                     (const GtCodetype **)
                                                       spwp->multimappower,
                                                     spwp->cyclicwindow,
                                                     spwp->firstindex);
    gt_assert(tmpprefixcode == head->codeforleftcontext);
  }
  firstspecialbrutedefined
    = determinefirstspecialposition(&firstspecialbrute,
                                    spwp->windowwidth,
                                    spwp->kmersize,
                                    spwp->cyclicwindow,
                                    spwp->firstindex);
  if (specialqueueisempty(&spwp->spos))
  {
    gt_assert(!firstspecialbrutedefined);
  } else
  {
    Specialitem *head = specialheadofqueue(&spwp->spos);
    gt_assert(firstspecialbrutedefined ? 1 : 0);
    gt_assert(head->distvalue == firstspecialbrute);
  }
#endif
  {
#ifdef SKDEBUG
    GtCodetype wcode;

    wcode = windowkmer2code(spwp->numofchars,
                            spwp->kmersize,
                            spwp->cyclicwindow,
                            spwp->firstindex);
#endif
    if (specialqueueisempty(&spwp->spos))
    {
      kmercode->definedspecialposition = false;
      kmercode->specialposition = 0;
      kmercode->code = spwp->codewithoutspecial;
    } else
    {
      Specialitem *head = specialheadofqueue(&spwp->spos);
      kmercode->code = head->codeforleftcontext +
                       spwp->filltable[head->distvalue];
      kmercode->definedspecialposition = true;
      kmercode->specialposition = head->distvalue;
    }
#ifdef SKDEBUG
    gt_assert(wcode == kmercode->code);
#endif
  }
}

static void shiftrightwithchar(Kmerstream *spwp,GtUchar charcode)
{
  gt_assert(spwp->windowwidth == spwp->kmersize);
  updatespecialpositions(spwp,charcode,true,
                         spwp->cyclicwindow[spwp->firstindex]);
  spwp->cyclicwindow[spwp->firstindex] = charcode;
  if (spwp->firstindex < spwp->kmersize-1)
  {
    spwp->firstindex++;
  } else
  {
    spwp->firstindex = 0;
  }
}

static void kmerstream_delete(Kmerstream *spwp)
{
  gt_free(spwp->filltable);
  gt_multimappower_delete(spwp->multimappower);
  specialwrapqueue(&spwp->spos);
  gt_free(spwp);
}

struct GtKmercodeiterator
{
  unsigned long totallength, startpos;
  const GtEncseq *encseq;
  GtEncseqReader *esr;
  GtReadmode readmode;
  Kmerstream *spwp;
  unsigned long currentposition;
  bool hasprocessedfirst, inputexhausted;
  GtKmercode kmercode;
  GtSequenceBuffer *fb; /* only for generating from file */
};

/*@notnull@*/ GtKmercodeiterator *gt_kmercodeiterator_encseq_new(
                                            const GtEncseq *encseq,
                                            GtReadmode readmode,
                                            unsigned int kmersize,
                                            unsigned long startpos)
{
  GtKmercodeiterator *kmercodeiterator;
  unsigned int numofchars;
  GtUchar charcode;

  gt_assert(!GT_ISDIRREVERSE(readmode) || startpos == 0);
  kmercodeiterator = gt_malloc(sizeof (*kmercodeiterator));
  kmercodeiterator->totallength = gt_encseq_total_length(encseq);
  kmercodeiterator->startpos = startpos;
  gt_assert(startpos < kmercodeiterator->totallength);
  if (kmercodeiterator->totallength - startpos < (unsigned long) kmersize)
  {
    kmercodeiterator->inputexhausted = true;
    kmercodeiterator->fb = NULL;
    kmercodeiterator->encseq = encseq;
    kmercodeiterator->esr = NULL;
    kmercodeiterator->spwp = NULL;
  } else
  {
    kmercodeiterator->inputexhausted = false;
    kmercodeiterator->fb = NULL;
    kmercodeiterator->encseq = encseq;
    kmercodeiterator->readmode = readmode;
    kmercodeiterator->esr = gt_encseq_create_reader_with_readmode(encseq,
                                                                  readmode,
                                                                  startpos);
    numofchars = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
    kmercodeiterator->spwp = kmerstream_new(numofchars,kmersize);
    kmercodeiterator->hasprocessedfirst = false;
    for (kmercodeiterator->currentposition = startpos;
         kmercodeiterator->currentposition < startpos+(unsigned long) kmersize;
         kmercodeiterator->currentposition++)
    {
      charcode = gt_encseq_reader_next_encoded_char(kmercodeiterator->esr);
      kmercodeiterator->spwp->windowwidth++;
      updatespecialpositions(kmercodeiterator->spwp,charcode,false,0);
      kmercodeiterator->spwp->cyclicwindow[kmercodeiterator->
                                           spwp->windowwidth-1] = charcode;
    }
  }
  return kmercodeiterator;
}

const GtKmercode *gt_kmercodeiterator_encseq_next(
                             GtKmercodeiterator *kmercodeiterator)
{
  if (!kmercodeiterator->hasprocessedfirst)
  {
    gt_assert(kmercodeiterator->currentposition
              == kmercodeiterator->startpos +
                   (unsigned long) kmercodeiterator->spwp->kmersize);
    kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
    kmercodeiterator->hasprocessedfirst = true;
    return &kmercodeiterator->kmercode;
  }
  if (kmercodeiterator->currentposition < kmercodeiterator->totallength)
  {
    GtUchar charcode
      = gt_encseq_reader_next_encoded_char(kmercodeiterator->esr);
    shiftrightwithchar(kmercodeiterator->spwp,charcode);
    kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
    kmercodeiterator->currentposition++;
    return &kmercodeiterator->kmercode;
  }
  if (kmercodeiterator->currentposition < kmercodeiterator->totallength +
                                          kmercodeiterator->spwp->kmersize)
  {
    shiftrightwithchar(kmercodeiterator->spwp,(GtUchar) WILDCARD);
    kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
    kmercodeiterator->currentposition++;
    return &kmercodeiterator->kmercode;
  }
  return NULL;
}

const GtKmercode *gt_kmercodeiterator_encseq_nonspecial_next(
                             GtKmercodeiterator *kmercodeiterator)
{
  while (true)
  {
    if (!kmercodeiterator->hasprocessedfirst)
    {
      gt_assert(kmercodeiterator->currentposition
                == kmercodeiterator->startpos +
                     (unsigned long) kmercodeiterator->spwp->kmersize);
      kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
      kmercodeiterator->hasprocessedfirst = true;
      if (!kmercodeiterator->kmercode.definedspecialposition)
      {
        return &kmercodeiterator->kmercode;
      }
    } else
    {
      if (kmercodeiterator->currentposition < kmercodeiterator->totallength)
      {
        GtUchar charcode
          = gt_encseq_reader_next_encoded_char(kmercodeiterator->esr);
        shiftrightwithchar(kmercodeiterator->spwp,charcode);
        kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
        kmercodeiterator->currentposition++;
        if (!kmercodeiterator->kmercode.definedspecialposition)
        {
          return &kmercodeiterator->kmercode;
        }
      } else
      {
        break;
      }
    }
  }
  return NULL;
}

GtKmercodeiterator *gt_kmercodeiterator_filetab_new(
                                                const GtStrArray *filenametab,
                                                unsigned int numofchars,
                                                unsigned int kmersize,
                                                const GtUchar *symbolmap,
                                                bool plainformat,
                                                GtError *err)
{
  GtKmercodeiterator *kmercodeiterator;
  GtUchar charcode;
  bool haserr = false;
  int retval;

  gt_error_check(err);
  kmercodeiterator = gt_malloc(sizeof (*kmercodeiterator));
  kmercodeiterator->esr = NULL;
  kmercodeiterator->hasprocessedfirst = false;
  kmercodeiterator->inputexhausted = false;
  kmercodeiterator->spwp = kmerstream_new(numofchars,kmersize);
  kmercodeiterator->totallength = 0;
  if (plainformat)
  {
    kmercodeiterator->fb = gt_sequence_buffer_plain_new(filenametab);
  } else
  {
    kmercodeiterator->fb = gt_sequence_buffer_new_guess_type(filenametab, err);
  }
  if (kmercodeiterator->fb == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    gt_sequence_buffer_set_symbolmap(kmercodeiterator->fb, symbolmap);
    for (kmercodeiterator->currentposition = 0;
         kmercodeiterator->currentposition < (unsigned long) kmersize;
         kmercodeiterator->currentposition++)
    {
      retval = gt_sequence_buffer_next(kmercodeiterator->fb,&charcode,err);
      if (retval < 0)
      {
        haserr = true;
        break;
      }
      if (retval == 0)
      {
        kmercodeiterator->inputexhausted = true;
        break;
      }
      kmercodeiterator->spwp->windowwidth++;
      updatespecialpositions(kmercodeiterator->spwp,charcode,false,0);
      kmercodeiterator->spwp->cyclicwindow[kmercodeiterator->
                                           spwp->windowwidth-1] = charcode;
    }
  }
  if (haserr)
  {
    gt_kmercodeiterator_delete(kmercodeiterator);
    return NULL;
  }
  return kmercodeiterator;
}

int gt_kmercodeiterator_filetab_next(const GtKmercode **kmercodeptr,
                                     GtKmercodeiterator *kmercodeiterator,
                                     GtError *err)
{
  if (!kmercodeiterator->inputexhausted)
  {
    if (kmercodeiterator->hasprocessedfirst)
    {
      GtUchar charcode;
      int retval;

      retval = gt_sequence_buffer_next(kmercodeiterator->fb,&charcode,err);
      if (retval < 0)
      {
        *kmercodeptr = NULL;
        return -1;
      }
      if (retval != 0)
      {
        shiftrightwithchar(kmercodeiterator->spwp,charcode);
        kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
        kmercodeiterator->currentposition++,
        *kmercodeptr = &kmercodeiterator->kmercode;
        return 0;
      }
      kmercodeiterator->inputexhausted = true;
      kmercodeiterator->totallength = kmercodeiterator->currentposition;
    } else
    {
      kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
      kmercodeiterator->hasprocessedfirst = true;
      *kmercodeptr = &kmercodeiterator->kmercode;
      return 0;
    }
  }
  if (kmercodeiterator->currentposition < kmercodeiterator->totallength +
                                          kmercodeiterator->spwp->kmersize)
  {
    shiftrightwithchar(kmercodeiterator->spwp,(GtUchar) WILDCARD);
    kmerstream_newcode(&kmercodeiterator->kmercode, kmercodeiterator->spwp);
    kmercodeiterator->currentposition++,
    *kmercodeptr = &kmercodeiterator->kmercode;
  } else
  {
    *kmercodeptr = NULL;
  }
  return 0;
}

bool gt_kmercodeiterator_inputexhausted(
                              const GtKmercodeiterator *kmercodeiterator)
{
  return kmercodeiterator->inputexhausted;
}

void gt_kmercodeiterator_delete(GtKmercodeiterator *kmercodeiterator)
{
  if (kmercodeiterator == NULL)
  {
    return;
  }
  gt_encseq_reader_delete(kmercodeiterator->esr);
  kmerstream_delete(kmercodeiterator->spwp);
  gt_sequence_buffer_delete(kmercodeiterator->fb);
  gt_free(kmercodeiterator);
}

void getencseqkmers(const GtEncseq *encseq,
                    GtReadmode readmode,
                    unsigned int kmersize,
                    void(*processkmercode)(void *,
                                           unsigned long,
                                           const GtKmercode *),
                    void *processkmercodeinfo)
{
  unsigned long currentposition = 0, totallength;
  Kmerstream *spwp;
  GtUchar charcode;
  GtEncseqReader *esr;
  unsigned int numofchars, overshoot;

  totallength = gt_encseq_total_length(encseq);
  if (totallength < (unsigned long) kmersize)
  {
    return;
  }
  numofchars = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
  spwp = kmerstream_new(numofchars,kmersize);
  esr = gt_encseq_create_reader_with_readmode(encseq,readmode,0);
  for (currentposition = 0; currentposition < (unsigned long) kmersize;
       currentposition++)
  {
    charcode = gt_encseq_reader_next_encoded_char(esr);
    GT_CHECKENCCHAR(charcode,encseq,currentposition,readmode);
    spwp->windowwidth++;
    updatespecialpositions(spwp,charcode,false,0);
    spwp->cyclicwindow[spwp->windowwidth-1] = charcode;
  }
  kmerstream_newcode(&spwp->currentkmercode,spwp);
  processkmercode(processkmercodeinfo,0,&spwp->currentkmercode);
  for (currentposition = (unsigned long) kmersize; currentpositioncurrentkmercode,spwp);
    processkmercode(processkmercodeinfo,currentposition + 1 - spwp->kmersize,
                    &spwp->currentkmercode);
  }
  gt_encseq_reader_delete(esr);
  for (overshoot=0; overshootcurrentkmercode,spwp);
    processkmercode(processkmercodeinfo,
                    overshoot + currentposition + 1 - spwp->kmersize,
                    &spwp->currentkmercode);
  }
  kmerstream_delete(spwp);
}
genometools-1.5.1/src/match/sfx-mappedstr.h000066400000000000000000000053211211610345200206760ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_MAPPEDSTR_H
#define SFX_MAPPEDSTR_H

#include "core/error_api.h"
#include "core/str_array_api.h"
#include "core/encseq_api.h"
#include "core/codetype.h"
#include "intcode-def.h"

typedef struct
{
  bool definedspecialposition;
  unsigned int specialposition;
  GtCodetype code;
} GtKmercode;

typedef struct GtKmercodeiterator GtKmercodeiterator;

/*@notnull@*/ GtKmercodeiterator *gt_kmercodeiterator_encseq_new(
                                            const GtEncseq *encseq,
                                            GtReadmode readmode,
                                            unsigned int kmersize,
                                            unsigned long startpos);

const GtKmercode *gt_kmercodeiterator_encseq_next(
                       GtKmercodeiterator *kmercodeiterator);

const GtKmercode *gt_kmercodeiterator_encseq_nonspecial_next(
                             GtKmercodeiterator *kmercodeiterator);

GtKmercodeiterator *gt_kmercodeiterator_filetab_new(
        const GtStrArray *filenametab,
        unsigned int numofchars,
        unsigned int kmersize,
        const GtUchar *symbolmap,
        bool plainformat,
        GtError *err);

int gt_kmercodeiterator_filetab_next(const GtKmercode **kmercodeptr,
                                     GtKmercodeiterator *kmercodeiterator,
                                     GtError *err);

bool gt_kmercodeiterator_inputexhausted(
                       const GtKmercodeiterator *kmercodeiterator);

void gt_kmercodeiterator_delete(GtKmercodeiterator *kmercodeiterator);

void getencseqkmers(const GtEncseq *encseq,
                    GtReadmode readmode,
                    unsigned int kmersize,
                    void(*processkmercode)(void *,
                                           unsigned long,
                                           const GtKmercode *),
                    void *processkmercodeinfo);
#endif
genometools-1.5.1/src/match/sfx-maprange.c000066400000000000000000000411601211610345200204650ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#ifndef S_SPLINT_S
#include 
#endif
#include "core/xposix.h"
#include "core/xansi_api.h"
#include "core/fa.h"
#include "core/intbits.h"
#include "core/log.h"
#include "sfx-maprange.h"

static unsigned long gt_multipleofpagesize(unsigned long code,
                                           bool smaller,
                                           size_t sizeofbasetype,
                                           unsigned long pagesize)
{
  if ((code * sizeofbasetype) % pagesize == 0)
  {
    return code * sizeofbasetype;
  }
  if (smaller)
  {
    return ((code * sizeofbasetype)/pagesize) * pagesize;
  }
  return ((code * sizeofbasetype)/pagesize) * pagesize + pagesize;
}

typedef struct
{
  unsigned long mapoffset, mapend;
} GtMappedrange;

static void gt_Sfxmapped_offset_end(GtMappedrange *range,
                                    size_t sizeofbasetype,
                                    unsigned long pagesize,
                                    unsigned long minindex,
                                    unsigned long maxindex)
{
  range->mapoffset = gt_multipleofpagesize(minindex,true,sizeofbasetype,
                                           pagesize);
  range->mapend = gt_multipleofpagesize(maxindex,false,sizeofbasetype,pagesize);
}

struct GtSfxmappedrange
{
  void *ptr, *entire, **usedptrptr;
  GtStr *filename, *tablename;
  unsigned long pagesize;
  size_t numofunits, sizeofunit;
  GtSfxmappedrangetype type;
  unsigned long currentminindex, currentmaxindex;
  bool indexrange_defined;
  GtSfxmappedrangetransformfunc transformfunc;
  const void *transformfunc_data;
  bool writable;
};

size_t gt_Sfxmappedrange_size_entire(const GtSfxmappedrange *sfxmappedrange)
{
  gt_assert(sfxmappedrange != NULL);
  return sfxmappedrange->sizeofunit * sfxmappedrange->numofunits;
}

void *gt_Sfxmappedrange_map_entire(GtSfxmappedrange *sfxmappedrange,
                                   GtError *err)
{
  size_t mappedsize;

  gt_assert(sfxmappedrange != NULL);
  sfxmappedrange->entire = gt_fa_mmap_read(gt_str_get(sfxmappedrange->filename),
                                           &mappedsize,err);
  if (sfxmappedrange->entire == NULL)
  {
    return NULL;
  }
  if (mappedsize != gt_Sfxmappedrange_size_entire(sfxmappedrange))
  {
    gt_error_set(err,"map file %s: mapped size = %lu != %lu = expected size",
                     gt_str_get(sfxmappedrange->filename),
                     (unsigned long) mappedsize,
                     (unsigned long) gt_Sfxmappedrange_size_entire(
                                                      sfxmappedrange));
    gt_fa_xmunmap(sfxmappedrange->entire);
    sfxmappedrange->entire = NULL;
    return NULL;
  }
  gt_log_log("map %s completely (%lu units of size %u)",
              gt_str_get(sfxmappedrange->tablename),
              (unsigned long) sfxmappedrange->numofunits,
              (unsigned int) sfxmappedrange->sizeofunit);
  return sfxmappedrange->entire;
}

GtSfxmappedrange *gt_Sfxmappedrange_new(const char *tablename,
                                        unsigned long numofentries,
                                        GtSfxmappedrangetype type,
                                        GtSfxmappedrangetransformfunc
                                          transformfunc,
                                        const void *transformfunc_data)
{
  GtSfxmappedrange *sfxmappedrange;

  sfxmappedrange = gt_malloc(sizeof (*sfxmappedrange));
  sfxmappedrange->ptr = NULL;
  sfxmappedrange->pagesize = (unsigned long) sysconf((int) _SC_PAGESIZE);
  sfxmappedrange->usedptrptr = NULL;
  sfxmappedrange->filename = NULL;
  sfxmappedrange->writable = false;
  sfxmappedrange->entire = NULL;
  sfxmappedrange->transformfunc = transformfunc;
  sfxmappedrange->transformfunc_data = transformfunc_data;
  sfxmappedrange->type = type;
  sfxmappedrange->tablename = gt_str_new_cstr(tablename);
  sfxmappedrange->currentminindex = sfxmappedrange->currentmaxindex = 0;
  sfxmappedrange->indexrange_defined = false;
  switch (type)
  {
    case GtSfxGtBitsequence:
      sfxmappedrange->sizeofunit = sizeof (GtBitsequence);
      sfxmappedrange->numofunits = GT_NUMOFINTSFORBITS(numofentries);
      break;
    case GtSfxuint32_t:
      sfxmappedrange->sizeofunit = sizeof (uint32_t);
      sfxmappedrange->numofunits = (size_t) numofentries;
      break;
    case GtSfxunsignedlong:
      sfxmappedrange->sizeofunit = sizeof (unsigned long);
      sfxmappedrange->numofunits = (size_t) numofentries;
      break;
    default:
      gt_assert(false);
      break;
  }
  return sfxmappedrange;
}

typedef union {
  GtBitsequence **bs;
  unsigned long **ulong;
  uint32_t **uint32;
} GtSfxStoretype;

static void gt_Sfxmappedrange_storetmp(GtSfxmappedrange *sfxmappedrange,
                                       GtSfxStoretype usedptrptr,
                                       GtSfxmappedrangetype type,
                                       bool writable)
{
  FILE *outfp;

  gt_assert(sfxmappedrange != NULL);
  sfxmappedrange->ptr = NULL;
  sfxmappedrange->filename = gt_str_new();
  sfxmappedrange->writable = writable;
  outfp = gt_xtmpfp(sfxmappedrange->filename);
  gt_assert(outfp != NULL);
  gt_log_log("write %s to file %s (%lu units of %lu bytes)",
             gt_str_get(sfxmappedrange->tablename),
             gt_str_get(sfxmappedrange->filename),
             (unsigned long) sfxmappedrange->numofunits,
             (unsigned long) sfxmappedrange->sizeofunit);
  switch (type) {
    case GtSfxGtBitsequence:
      gt_xfwrite(*(usedptrptr.bs),sfxmappedrange->sizeofunit,
                 sfxmappedrange->numofunits,outfp);
      sfxmappedrange->usedptrptr = (void**) usedptrptr.bs;
      gt_free(*(usedptrptr.bs));
      *(usedptrptr.bs) = NULL;
      break;
    case GtSfxunsignedlong:
      gt_xfwrite(*(usedptrptr.ulong),sfxmappedrange->sizeofunit,
                 sfxmappedrange->numofunits,outfp);
      sfxmappedrange->usedptrptr = (void**) usedptrptr.ulong;
      gt_free(*(usedptrptr.ulong));
      *(usedptrptr.ulong) = NULL;
      break;
    case GtSfxuint32_t:
      gt_xfwrite(*(usedptrptr.uint32),sfxmappedrange->sizeofunit,
                 sfxmappedrange->numofunits,outfp);
      sfxmappedrange->usedptrptr = (void**) usedptrptr.uint32;
      gt_free(*(usedptrptr.uint32));
      *(usedptrptr.uint32) = NULL;
      break;
   }
   gt_fa_fclose(outfp);
}

void gt_Sfxmappedrange_storetmp_ulong(GtSfxmappedrange *sfxmappedrange,
                                      unsigned long **usedptrptr,
                                      bool writable)
{
  GtSfxStoretype st;
  gt_assert(usedptrptr != NULL);

  st.ulong = usedptrptr;
  gt_Sfxmappedrange_storetmp(sfxmappedrange, st, GtSfxunsignedlong, writable);
}

void gt_Sfxmappedrange_storetmp_uint32(GtSfxmappedrange *sfxmappedrange,
                                       uint32_t **usedptrptr,
                                       bool writable)
{
  GtSfxStoretype st;
  gt_assert(usedptrptr != NULL);

  st.uint32 = usedptrptr;
  gt_Sfxmappedrange_storetmp(sfxmappedrange, st, GtSfxuint32_t, writable);
}

void gt_Sfxmappedrange_storetmp_bitsequence(GtSfxmappedrange *sfxmappedrange,
                                            GtBitsequence **usedptrptr,
                                            bool writable)
{
  GtSfxStoretype st;
  gt_assert(usedptrptr != NULL);

  st.bs = usedptrptr;
  gt_Sfxmappedrange_storetmp(sfxmappedrange, st, GtSfxGtBitsequence, writable);
}

void gt_Sfxmappedrange_usetmp(GtSfxmappedrange *sfxmappedrange,
                              const GtStr *tmpfilename,
                              void **usedptrptr,
                              unsigned long numofentries,
                              bool writable)
{
  gt_assert(sfxmappedrange != NULL);
  sfxmappedrange->ptr = NULL;
  /*gt_assert(usedptrptr != NULL && *usedptrptr == NULL);*/
  sfxmappedrange->usedptrptr = usedptrptr;
  sfxmappedrange->filename = gt_str_clone(tmpfilename);
  sfxmappedrange->writable = writable;
  if (sfxmappedrange->type == GtSfxGtBitsequence)
  {
    sfxmappedrange->numofunits = GT_NUMOFINTSFORBITS(numofentries);
  } else
  {
    sfxmappedrange->numofunits = (size_t) numofentries;
  }
  gt_log_log("use file %s for table %s (%lu units of %lu bytes)",
             gt_str_get(sfxmappedrange->filename),
             gt_str_get(sfxmappedrange->tablename),
             (unsigned long) sfxmappedrange->numofunits,
             (unsigned long) sfxmappedrange->sizeofunit);
  gt_free(*sfxmappedrange->usedptrptr);
  *sfxmappedrange->usedptrptr = NULL;
}

unsigned long gt_Sfxmappedrange_size_mapped(const GtSfxmappedrange
                                                      *sfxmappedrange,
                                            unsigned long minindex,
                                            unsigned long maxindex)
{
  gt_assert(sfxmappedrange != NULL);
  if (sfxmappedrange->transformfunc != NULL)
  {
    sfxmappedrange->transformfunc(&minindex,&maxindex,
                                  sfxmappedrange->transformfunc_data);
  }
  if (minindex <= maxindex)
  {
    GtMappedrange lbrange;

    gt_Sfxmapped_offset_end(&lbrange,
                            sfxmappedrange->sizeofunit,
                            sfxmappedrange->pagesize,
                            minindex,
                            maxindex);
    return lbrange.mapend - lbrange.mapoffset + 1;
  }
  return 0;
}

void gt_Sfxmappedrange_unmap(GtSfxmappedrange *sfxmappedrange)
{
  gt_assert(sfxmappedrange != NULL);
  if (sfxmappedrange->ptr != NULL)
  {
    gt_fa_xmunmap(sfxmappedrange->ptr);
  }
  sfxmappedrange->ptr = 0;
}

void *gt_Sfxmappedrange_map(GtSfxmappedrange *sfxmappedrange,
                            unsigned long minindex,
                            unsigned long maxindex)
{
  gt_assert(sfxmappedrange != NULL);
  if (sfxmappedrange->ptr != NULL)
  {
    gt_fa_xmunmap(sfxmappedrange->ptr);
  }
  if (sfxmappedrange->transformfunc != NULL)
  {
    sfxmappedrange->transformfunc(&minindex,&maxindex,
                                  sfxmappedrange->transformfunc_data);
  }
  if (minindex <= maxindex)
  {
    GtMappedrange lbrange;
    unsigned long unitoffset;
    size_t sizeoftable;

    gt_Sfxmapped_offset_end(&lbrange,
                            sfxmappedrange->sizeofunit,
                            sfxmappedrange->pagesize,
                            minindex,
                            maxindex);
    sizeoftable = gt_Sfxmappedrange_size_entire(sfxmappedrange);
    gt_log_log("mapped %s[%lu..%lu] for %s (%.1f%% of all)",
               gt_str_get(sfxmappedrange->tablename),
               lbrange.mapoffset,
               lbrange.mapend,
               sfxmappedrange->writable ? "writing" : "reading",
               (lbrange.mapend - lbrange.mapoffset + 1
                 >= (unsigned long) sizeoftable)
                    ? 100.0
                    : 100.0 * (lbrange.mapend - lbrange.mapoffset + 1)/
                               sizeoftable);
    gt_assert(lbrange.mapoffset <= lbrange.mapend);
    gt_assert(lbrange.mapoffset <= minindex * sfxmappedrange->sizeofunit);
    gt_assert(maxindex * sfxmappedrange->sizeofunit <= lbrange.mapend);
    gt_assert(lbrange.mapoffset % sfxmappedrange->pagesize == 0);
    if (sfxmappedrange->writable)
    {
      sfxmappedrange->ptr
        = gt_fa_xmmap_write_range(gt_str_get(sfxmappedrange->filename),
                                  (size_t) (lbrange.mapend-lbrange.mapoffset+1),
                                  (size_t) lbrange.mapoffset);
    } else
    {
      sfxmappedrange->ptr
        = gt_fa_xmmap_read_range (gt_str_get(sfxmappedrange->filename),
                                  (size_t) (lbrange.mapend-lbrange.mapoffset+1),
                                  (size_t) lbrange.mapoffset);
    }
    sfxmappedrange->indexrange_defined = true;
    sfxmappedrange->currentmaxindex = maxindex;
    sfxmappedrange->currentminindex = minindex;
    unitoffset = lbrange.mapoffset / sfxmappedrange->sizeofunit;
    switch (sfxmappedrange->type)
    {
      case GtSfxGtBitsequence:
        return ((GtBitsequence *) sfxmappedrange->ptr) - unitoffset;
      case GtSfxuint32_t:
        return ((uint32_t *) sfxmappedrange->ptr) - unitoffset;
      case GtSfxunsignedlong:
        return ((unsigned long *) sfxmappedrange->ptr) - unitoffset;
      default:
        gt_assert(false);
        break;
    }
    gt_assert(false);
  }
  sfxmappedrange->ptr = NULL;
  sfxmappedrange->indexrange_defined = true;
  sfxmappedrange->currentmaxindex = maxindex;
  sfxmappedrange->currentminindex = minindex;
  return NULL;
}

void gt_Sfxmappedrange_checkindex(const GtSfxmappedrange *sfxmappedrange,
                                  GT_UNUSED unsigned long idx)
{
  if (sfxmappedrange->indexrange_defined)
  {
    gt_assert(sfxmappedrange->currentminindex <= idx);
    gt_assert(idx <= sfxmappedrange->currentminindex);
  }
}

void gt_Sfxmappedrange_delete(GtSfxmappedrange *sfxmappedrange)
{
  if (sfxmappedrange == NULL)
  {
    return;
  }
  gt_log_log("delete table %s",gt_str_get(sfxmappedrange->tablename));
  gt_fa_xmunmap(sfxmappedrange->ptr);
  sfxmappedrange->ptr = NULL;
  gt_fa_xmunmap(sfxmappedrange->entire);
  sfxmappedrange->entire = NULL;
  if (sfxmappedrange->usedptrptr != NULL)
  {
    *sfxmappedrange->usedptrptr = NULL;
  }
  if (sfxmappedrange->filename != NULL)
  {
    gt_log_log("remove \"%s\"",gt_str_get(sfxmappedrange->filename));
    gt_xunlink(gt_str_get(sfxmappedrange->filename));
  }
  gt_str_delete(sfxmappedrange->tablename);
  gt_str_delete(sfxmappedrange->filename);
  gt_free(sfxmappedrange);
}

struct GtSfxmappedrangelist
{
  GtSfxmappedrange **arr;
  unsigned long nextfree, allocated;
};

GtSfxmappedrangelist *gt_Sfxmappedrangelist_new(void)
{
  GtSfxmappedrangelist *sfxmrlist = gt_malloc(sizeof (*sfxmrlist));

  sfxmrlist->arr = NULL;
  sfxmrlist->nextfree = sfxmrlist->allocated = 0;
  return sfxmrlist;
}

void gt_Sfxmappedrangelist_add(GtSfxmappedrangelist *sfxmrlist,
                               GtSfxmappedrange *sfxmappedrange)
{
  gt_assert(sfxmrlist != NULL);

  if (sfxmrlist->nextfree >= sfxmrlist->allocated)
  {
    sfxmrlist->allocated += 4UL;
    sfxmrlist->arr = gt_realloc(sfxmrlist->arr,sizeof (*sfxmrlist->arr) *
                                               sfxmrlist->allocated);
  }
  sfxmrlist->arr[sfxmrlist->nextfree++] = sfxmappedrange;
}

unsigned long gt_Sfxmappedrangelist_size_mapped(
                                         const GtSfxmappedrangelist *sfxmrlist,
                                         unsigned long minindex,
                                         unsigned long maxindex)
{
  if (sfxmrlist == NULL)
  {
    gt_assert(maxindex >= minindex);
    return maxindex - minindex + 1;
  } else
  {
    unsigned long idx, sumsize = 0;

    for (idx = 0; idx < sfxmrlist->nextfree; idx++)
    {
      GtSfxmappedrange *sfxmappedrange = sfxmrlist->arr[idx];
      if (sfxmappedrange != NULL)
      {
        /*printf("size_mapped %s %lu %lu => %lu\n",
                    gt_str_get(sfxmappedrange->tablename),
                    minindex,maxindex,
                    gt_Sfxmappedrange_size_mapped(sfxmappedrange,minindex,
                                                  maxindex));*/
        sumsize += gt_Sfxmappedrange_size_mapped(sfxmappedrange,
                                                 minindex,
                                                 maxindex);
      }
    }
    return sumsize;
  }
}

unsigned long gt_Sfxmappedrangelist_size_entire(
                                         const GtSfxmappedrangelist *sfxmrlist)
{
  if (sfxmrlist == NULL)
  {
    return 0;
  } else
  {
    unsigned long idx, sumsize = 0;

    for (idx = 0; idx < sfxmrlist->nextfree; idx++)
    {
      GtSfxmappedrange *sfxmappedrange = sfxmrlist->arr[idx];
      if (sfxmappedrange != NULL)
      {
        sumsize += gt_Sfxmappedrange_size_entire(sfxmappedrange);
      }
    }
    return sumsize;
  }
}

void gt_Sfxmappedrangelist_delete(GtSfxmappedrangelist *sfxmrlist)
{
  if (sfxmrlist != NULL)
  {
    gt_free(sfxmrlist->arr);
    gt_free(sfxmrlist);
  }
}
genometools-1.5.1/src/match/sfx-maprange.h000066400000000000000000000102021211610345200204630ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_MAPRANGE_H
#define SFX_MAPRANGE_H

#include 
#include 
#include "core/str_api.h"
#include "core/codetype.h"

typedef enum
{
  GtSfxGtBitsequence,
  GtSfxunsignedlong,
  GtSfxuint32_t
} GtSfxmappedrangetype;

typedef struct GtSfxmappedrange GtSfxmappedrange;

void *gt_Sfxmappedrange_map_entire(GtSfxmappedrange *sfxmappedrange,
                                   GtError *err);

typedef void (*GtSfxmappedrangetransformfunc)(unsigned long *,
                                              unsigned long *,
                                              const void *);

GtSfxmappedrange *gt_Sfxmappedrange_new(const char *tablename,
                                        unsigned long numofentries,
                                        GtSfxmappedrangetype type,
                                        GtSfxmappedrangetransformfunc
                                          transformfunc,
                                        const void *transformfunc_data);

void gt_Sfxmappedrange_storetmp_ulong(GtSfxmappedrange *sfxmappedrange,
                                      unsigned long **usedptrptr,
                                      bool writable);

void gt_Sfxmappedrange_storetmp_uint32(GtSfxmappedrange *sfxmappedrange,
                                       uint32_t **usedptrptr,
                                       bool writable);

void gt_Sfxmappedrange_storetmp_bitsequence(GtSfxmappedrange *sfxmappedrange,
                                            GtBitsequence **usedptrptr,
                                            bool writable);

void gt_Sfxmappedrange_usetmp(GtSfxmappedrange *sfxmappedrange,
                              const GtStr *tmpfilename,
                              void **usedptrptr,
                              unsigned long numofentries,
                              bool writable);

void *gt_Sfxmappedrange_map(GtSfxmappedrange *sfxmappedrange,
                            unsigned long minindex,
                            unsigned long maxindex);

void gt_Sfxmappedrange_unmap(GtSfxmappedrange *sfxmappedrange);

size_t gt_Sfxmappedrange_size_entire(const GtSfxmappedrange *sfxmappedrange);

unsigned long gt_Sfxmappedrange_size_mapped(const GtSfxmappedrange
                                                      *sfxmappedrange,
                                            unsigned long minindex,
                                            unsigned long maxindex);

void gt_Sfxmappedrange_checkindex(const GtSfxmappedrange *sfxmappedrange,
                                  GT_UNUSED unsigned long idx);

void gt_Sfxmappedrange_delete(GtSfxmappedrange *sfxmappedrange);

typedef struct GtSfxmappedrangelist GtSfxmappedrangelist;

GtSfxmappedrangelist *gt_Sfxmappedrangelist_new(void);

void gt_Sfxmappedrangelist_add(GtSfxmappedrangelist *sfxmrlist,
                               GtSfxmappedrange *sfxmappedrange);

unsigned long gt_Sfxmappedrangelist_size_mapped(
                                         const GtSfxmappedrangelist *sfxmrlist,
                                         unsigned long minindex,
                                         unsigned long maxindex);

void gt_Sfxmappedrangelist_delete(GtSfxmappedrangelist *sfxmrlist);

unsigned long gt_Sfxmappedrangelist_size_entire(
                                       const GtSfxmappedrangelist *sfxmrlist);

#endif
genometools-1.5.1/src/match/sfx-nextchar.h000066400000000000000000000022471211610345200205170ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_NEXTCHAR_H
#define SFX_NEXTCHAR_H

#include "core/divmodmul.h"

#define ADDNEXTCHAR(CODE,CC,NUMOFCHARS)\
        if ((NUMOFCHARS) == GT_DNAALPHASIZE)\
        {\
          CODE = GT_MULT4(CODE) | ((GtCodetype) (CC));\
        } else\
        {\
          CODE = ((CODE) * (NUMOFCHARS)) + (GtCodetype) (CC);\
        }

#endif
genometools-1.5.1/src/match/sfx-opt.c000066400000000000000000000231361211610345200175000ustar00rootroot00000000000000/*
  Copyright (c) 2007      Stefan Kurtz 
  Copyright (c)      2010 Sascha Steinbiss 
  Copyright (c) 2007-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/basename_api.h"
#include "core/error.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "core/option_api.h"
#include "core/readmode.h"
#include "core/spacecalc.h"
#include "core/str.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "match/sfx-opt.h"
#include "match/sfx-strategy.h"
#include "match/stamp.h"

static GtOPrval parse_options(int *parsed_args,
                              bool doesa,
                              Suffixeratoroptions *so,
                              int argc, const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOption *option,
           *optionshowprogress,
           *optiongenomediff,
           *optionii;
  GtOPrval oprval;
  gt_error_check(err);

  op = gt_option_parser_new("[option ...] (-db file [...] | -ii index)",
                            doesa ? "Compute enhanced suffix array."
                                  : "Compute packed index.");
  gt_option_parser_set_mail_address(op, "");

  /* input info */
  so->indexname = gt_str_new();
  so->inputindex = gt_str_new();
  so->db = gt_str_array_new();

  /* register options for encoded sequence handling */
  so->encopts = gt_encseq_options_register_encoding(op, so->indexname, so->db);
  so->loadopts = gt_encseq_options_register_loading(op, so->indexname);

  /* register options for index handling */
  if (doesa)
    so->idxopts = gt_index_options_register_esa(op, so->encopts);
  else
    so->idxopts = gt_index_options_register_packedidx(op, so->indexname,
                                                      so->encopts);

  /* verbosity */
  option = gt_option_new_verbose(&so->beverbose);
  gt_option_parser_add_option(op, option);

  optionshowprogress = gt_option_new_bool("showprogress",
                                          "show a progress bar",
                                          &so->showprogress,
                                          false);
  gt_option_parser_add_option(op, optionshowprogress);

  optionii = gt_option_new_filename("ii", "specify existing encoded sequence",
                                    so->inputindex);
  gt_option_parser_add_option(op, optionii);
  gt_option_is_mandatory_either(gt_encseq_options_db_option(so->encopts),
                                optionii);
  gt_option_exclude(gt_encseq_options_db_option(so->encopts), optionii);
  gt_option_exclude(optionii, gt_encseq_options_smap_option(so->encopts));
  gt_option_exclude(optionii, gt_encseq_options_dna_option(so->encopts));
  gt_option_exclude(optionii, gt_encseq_options_protein_option(so->encopts));
  gt_option_exclude(optionii, gt_encseq_options_plain_option(so->encopts));
  gt_option_exclude(optionii, gt_encseq_options_sat_option(so->encopts));

  optiongenomediff = gt_option_new_bool("genomediff",
                                   "directly process the lcp intervals using "
                                   "the genomediff algorithm (suffix array and "
                                   "lcp-tables are not output)",
                                   &so->genomediff,
                                   false);
  gt_option_is_extended_option(optiongenomediff);
  if (gt_index_options_outsuftab_option(so->idxopts) != NULL) {
    gt_option_exclude(optiongenomediff,
                      gt_index_options_outsuftab_option(so->idxopts));
  }
  gt_option_parser_add_option(op, optiongenomediff);

  /* suffixerator and friends do not take arguments */
  gt_option_parser_set_min_max_args(op, 0U, 0U);

  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);

  if (gt_str_length(so->indexname) == 0UL) {
    /* we do not have an indexname yet, so there was none given in the
       -indexname option and it could not be derived from the input filenames.
       So it must be in the -ii parameter. */
    char *basenameptr;
    basenameptr = gt_basename(gt_str_get(so->inputindex));
    gt_str_set(so->indexname, basenameptr);
    gt_free(basenameptr);
  }

  gt_option_parser_delete(op);

  return oprval;
}

static void showoptions(const Suffixeratoroptions *so)
{
  unsigned long i;
  Sfxstrategy sfxtrategy;
  GtLogger *logger = gt_logger_new(true, GT_LOGGER_DEFLT_PREFIX, stdout);

  if (gt_str_length(gt_encseq_options_smap_value(so->encopts)) > 0)
  {
    gt_logger_log_force(logger, "smap=\"%s\"",
                        gt_str_get(gt_encseq_options_smap_value(so->encopts)));
  }
  if (gt_encseq_options_dna_value(so->encopts))
  {
    gt_logger_log_force(logger, "dna=yes");
  }
  if (gt_encseq_options_protein_value(so->encopts))
  {
    gt_logger_log_force(logger, "protein=yes");
  }
  if (gt_encseq_options_plain_value(so->encopts))
  {
    gt_logger_log_force(logger, "plain=yes");
  }
  gt_logger_log_force(logger, "indexname=\"%s\"",
                    gt_str_get(so->indexname));

  if (gt_index_options_prefixlength_value(so->idxopts)
                                                   == GT_PREFIXLENGTH_AUTOMATIC)
  {
    gt_logger_log_force(logger, "prefixlength=automatic");
  } else
  {
    gt_logger_log_force(logger, "prefixlength=%u",
                        gt_index_options_prefixlength_value(so->idxopts));
  }
  sfxtrategy = gt_index_options_sfxstrategy_value(so->idxopts);
  gt_logger_log_force(logger, "storespecialcodes=%s",
                        sfxtrategy.storespecialcodes ? "true" : "false");
  for (i=0; idb); i++)
  {
    gt_logger_log_force(logger, "inputfile[%lu]=%s", i,
                   gt_str_array_get(so->db, i));
  }
  if (gt_str_length(so->inputindex) > 0)
  {
    gt_logger_log_force(logger, "inputindex=%s",
                        gt_str_get(so->inputindex));
  }
  gt_assert(gt_str_length(so->indexname) > 0);
  gt_logger_log_force(logger, "indexname=%s",
                    gt_str_get(so->indexname));
  gt_logger_log_force(logger, "outtistab=%s,outsuftab=%s,outlcptab=%s,"
                              "outbwttab=%s,outbcktab=%s,outdestab=%s,"
                              "outsdstab=%s,outssptab=%s,outkystab=%s",
          gt_encseq_options_tis_value(so->encopts) ? "true" : "false",
          gt_index_options_outsuftab_value(so->idxopts) ? "true" : "false",
          gt_index_options_outlcptab_value(so->idxopts) ? "true" : "false",
          gt_index_options_outbwttab_value(so->idxopts) ? "true" : "false",
          gt_index_options_outbcktab_value(so->idxopts) ? "true" : "false",
          gt_encseq_options_des_value(so->encopts) ? "true" : "false",
          gt_encseq_options_sds_value(so->encopts) ? "true" : "false",
          gt_encseq_options_ssp_value(so->encopts) ? "true" : "false",
          gt_index_options_outkystab_value(so->idxopts) ?
             (gt_index_options_outkyssort_value(so->idxopts) ?
                              "true with sort" : "true") :
                              "false");

  if (gt_index_options_maximumspace_value(so->idxopts) > 0)
  {
    gt_assert(gt_index_options_numofparts_value(so->idxopts) == 1U);
    gt_logger_log_force(logger, "maximumspace=%.0f MB",
            GT_MEGABYTES(gt_index_options_maximumspace_value(so->idxopts)));
  } else
  {
    gt_logger_log_force(logger, "parts=%u",
                            gt_index_options_numofparts_value(so->idxopts));
  }
  gt_logger_log_force(logger, "maxinsertionsort=%lu",
                        sfxtrategy.maxinsertionsort);
  gt_logger_log_force(logger, "maxbltriesort=%lu",
                        sfxtrategy.maxbltriesort);
  gt_logger_log_force(logger, "maxcountingsort=%lu",
                        sfxtrategy.maxcountingsort);
  gt_logger_log_force(logger, "lcpdist=%s",
                        gt_index_options_lcpdist_value(so->idxopts)
                          ? "true"
                          : "false");
  gt_logger_delete(logger);
}

void gt_sfxoptions_delete(Suffixeratoroptions *so)
{
  /* no checking if error occurs, since errors have been output before */
  gt_index_options_delete(so->idxopts);
  gt_encseq_options_delete(so->encopts);
  gt_encseq_options_delete(so->loadopts);
  gt_str_delete(so->indexname);
  gt_str_delete(so->inputindex);
  gt_str_array_delete(so->db);
}

int gt_suffixeratoroptions(Suffixeratoroptions *so,
                        bool doesa,
                        int argc,
                        const char **argv,
                        GtError *err)
{
  int parsed_args, retval = 0;
  GtOPrval rval;

  gt_error_check(err);
  rval = parse_options(&parsed_args, doesa, so, argc, argv, err);
  if (rval == GT_OPTION_PARSER_ERROR)
  {
    retval = -1;
  } else
  {
    if (rval == GT_OPTION_PARSER_REQUESTS_EXIT)
    {
      retval = 2;
    } else
    {
      if (rval == GT_OPTION_PARSER_OK)
      {
        if (so->beverbose)
        {
          showoptions(so);
        }
      }
    }
  }
  return retval;
}
genometools-1.5.1/src/match/sfx-opt.h000066400000000000000000000030551211610345200175030ustar00rootroot00000000000000/*
  Copyright (c) 2007      Stefan Kurtz 
  Copyright (c)      2010 Sascha Steinbiss 
  Copyright (c) 2007-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_OPT_H
#define SFX_OPT_H

#include 
#include "core/encseq_options.h"
#include "index_options.h"

typedef struct
{
  bool beverbose,
       showprogress,
       genomediff,
       outlcptab;
  GtEncseqOptions *encopts,
                  *loadopts;
  GtIndexOptions *idxopts;
  GtStr *indexname,
        *inputindex;
  GtStrArray *db;
} Suffixeratoroptions;

void gt_sfxoptions_delete(Suffixeratoroptions *so);

int gt_suffixeratoroptions(Suffixeratoroptions *so,
                        bool doesa,
                        int argc,
                        const char **argv,
                        GtError *err);

#endif
genometools-1.5.1/src/match/sfx-outprj.c000066400000000000000000000102361211610345200202160ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include "core/endianess_api.h"
#include "core/fa.h"
#include "core/filelengthvalues.h"
#include "core/str_array.h"
#include "core/str.h"
#include "core/unused_api.h"
#include "core/defined-types.h"
#include "core/format64.h"
#include "core/readmode.h"
#include "core/encseq.h"

#include "esa-fileend.h"
#include "stamp.h"

#define PRJSPECIALOUT(VAL)\
        fprintf(outprj,"%s=%lu\n",#VAL,gt_encseq_##VAL(encseq))

static void showprjinfo(FILE *outprj,
                        GtReadmode readmode,
                        const GtEncseq *encseq,
                        unsigned long numberofallsortedsuffixes,
                        unsigned int prefixlength,
                        unsigned long numoflargelcpvalues,
                        double averagelcp,
                        unsigned long maxbranchdepth,
                        const Definedunsignedlong *longest)
{
  unsigned long totallength;
  unsigned long numofsequences;

  totallength = gt_encseq_total_length(encseq);
  fprintf(outprj,"totallength=%lu\n",totallength);
  PRJSPECIALOUT(specialcharacters);
  PRJSPECIALOUT(specialranges);
  PRJSPECIALOUT(realspecialranges);
  PRJSPECIALOUT(lengthofspecialprefix);
  PRJSPECIALOUT(lengthofspecialsuffix);
  PRJSPECIALOUT(wildcards);
  PRJSPECIALOUT(wildcardranges);
  PRJSPECIALOUT(realwildcardranges);
  PRJSPECIALOUT(lengthofwildcardprefix);
  PRJSPECIALOUT(lengthofwildcardsuffix);
  numofsequences = gt_encseq_num_of_sequences(encseq);
  fprintf(outprj,"numofsequences=%lu\n",numofsequences);
  fprintf(outprj,"numofdbsequences=%lu\n",numofsequences);
  fprintf(outprj,"numofquerysequences=0\n");
  fprintf(outprj,"numberofallsortedsuffixes=%lu\n",numberofallsortedsuffixes);
  if (longest->defined)
  {
    fprintf(outprj,"longest=%lu\n",longest->valueunsignedlong);
  }
  fprintf(outprj,"prefixlength=%u\n",prefixlength);
  fprintf(outprj,"largelcpvalues=%lu\n",numoflargelcpvalues);
  fprintf(outprj,"averagelcp=%.2f\n",averagelcp);
  fprintf(outprj,"maxbranchdepth=%lu\n",maxbranchdepth);
  fprintf(outprj,"integersize=%u\n",
                  (unsigned int) (sizeof (unsigned long) * CHAR_BIT));
  fprintf(outprj,"littleendian=%c\n",gt_is_little_endian() ? '1' : '0');
  fprintf(outprj,"readmode=%u\n",(unsigned int) readmode);
  fprintf(outprj,"mirrored=%c\n", gt_encseq_is_mirrored(encseq) ? '1' : '0');
}

int gt_outprjfile(const char *indexname,
                  GtReadmode readmode,
                  const GtEncseq *encseq,
                  unsigned long numberofallsortedsuffixes,
                  unsigned int prefixlength,
                  unsigned long numoflargelcpvalues,
                  double averagelcp,
                  unsigned long maxbranchdepth,
                  const Definedunsignedlong *longest,
                  GtError *err)
{
  FILE *prjfp;
  bool haserr = false;

  gt_error_check(err);
  prjfp = gt_fa_fopen_with_suffix(indexname,PROJECTFILESUFFIX,"wb",err);
  if (prjfp == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    showprjinfo(prjfp,
                readmode,
                encseq,
                numberofallsortedsuffixes,
                prefixlength,
                numoflargelcpvalues,
                averagelcp,
                maxbranchdepth,
                longest);
    gt_fa_xfclose(prjfp);
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/sfx-outprj.h000066400000000000000000000027031211610345200202230ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_OUTPRJ_H
#define SFX_OUTPRJ_H
#include "core/readmode_api.h"
#include "core/encseq_api.h"
#include "core/defined-types.h"
#include "core/error_api.h"

int gt_outprjfile(const char *indexname,
                  GtReadmode readmode,
                  const GtEncseq *encseq,
                  unsigned long numberofallsortedsuffixes,
                  unsigned int prefixlength,
                  unsigned long numoflargelcpvalues,
                  double averagelcp,
                  unsigned long maxbranchdepth,
                  const Definedunsignedlong *longest,
                  GtError *err);

#endif
genometools-1.5.1/src/match/sfx-partssuf.c000066400000000000000000000373001211610345200205430ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/assert_api.h"
#include "core/ma_api.h"
#include "core/codetype.h"
#include "core/spacecalc.h"
#include "core/format64.h"
#include "core/log.h"
#include "bcktab.h"
#include "sfx-suffixgetset.h"
#include "spmsuftab.h"
#include "sfx-partssuf.h"
#include "firstcodes-tab.h"

typedef struct
{
  unsigned long nextidx,
                widthofpart,
                suftaboffset,
                sumofwidth,
                minindex,
                maxindex;
} GtSuftabpartcomponent;

struct GtSuftabparts
{
  GtSuftabpartcomponent *components;
  bool indexrange_available;
  unsigned int numofparts;
  unsigned long largestsizemappedpartwise,
                largestsuftabwidth;
  const GtFirstcodestab *fct;
};

void gt_suftabparts_showallrecords(const GtSuftabparts *suftabparts,
                                   bool withminmaxindex)
{
  unsigned int part;
  unsigned long totalwidth;

  gt_assert(suftabparts != NULL);
  gt_assert(suftabparts->numofparts >= 1U);
  totalwidth = suftabparts->components[suftabparts->numofparts - 1].sumofwidth;
  for (part = 0; part < suftabparts->numofparts; part++)
  {
    if (withminmaxindex)
    {
      gt_log_log("part %u: width=%lu (%.2f%%) offset=%lu nextidx=%lu "
                 "minindex=%lu maxindex=%lu ",
                 part,
                 suftabparts->components[part].widthofpart,
                 100.00 * (double) suftabparts->components[part].widthofpart/
                                   totalwidth,
                 suftabparts->components[part].suftaboffset,
                 suftabparts->components[part].nextidx,
                 gt_suftabparts_minindex(part,suftabparts),
                 gt_suftabparts_maxindex(part,suftabparts));
    } else
    {
      gt_log_log("part %u: width=%lu (%.2f%%) offset=%lu nextidx=%lu",
                 part,
                 suftabparts->components[part].widthofpart,
                 100.00 * (double) suftabparts->components[part].widthofpart/
                                   totalwidth,
                 suftabparts->components[part].nextidx,
                 suftabparts->components[part].suftaboffset);
    }
  }
  gt_log_log("variance %.0f",gt_suftabparts_variance(suftabparts));
}

static GtCodetype gt_suftabparts_minindex_raw(unsigned int part,
                                              const GtSuftabparts *suftabparts)
{
  GtCodetype minindex;
  gt_assert(suftabparts != NULL && part < suftabparts->numofparts);

  minindex = (part == 0) ? 0 : suftabparts->components[part-1].nextidx + 1;
  if (suftabparts->fct != NULL)
  {
    return gt_firstcodes_sample2full(suftabparts->fct,minindex);
  }
  return minindex;
}

static GtCodetype gt_suftabparts_maxindex_raw(unsigned int part,
                                              const GtSuftabparts *suftabparts)
{
  GtCodetype maxindex;

  gt_assert(suftabparts != NULL && part < suftabparts->numofparts);
  if (suftabparts->fct != NULL)
  {
    maxindex = suftabparts->components[part].nextidx;
    return gt_firstcodes_sample2full(suftabparts->fct,maxindex);
  }
  maxindex = (part == suftabparts->numofparts - 1)
               ? suftabparts->components[part].nextidx - 1
               : suftabparts->components[part].nextidx;
  return maxindex;
}

static void gt_suftabparts_removeemptyparts(GtSuftabparts *suftabparts,
                                            GT_UNUSED unsigned long totalwidth,
                                            GtLogger *logger)
{
#undef SKDEBUG
#ifdef SKDEBUG
  gt_log_log("before removal");
  gt_suftabparts_showallrecords(suftabparts,false);
#endif
  gt_assert(suftabparts != NULL);
  if (suftabparts->numofparts > 0)
  {
    unsigned int destpart, srcpart;
    unsigned long sumwidth = 0;

    for (destpart = 0, srcpart = 0; srcpart < suftabparts->numofparts;
         srcpart++)
    {
      if (suftabparts->components[srcpart].widthofpart > 0)
      {
        if (destpart < srcpart)
        {
          suftabparts->components[destpart] = suftabparts->components[srcpart];
        }
        destpart++;
      }
    }
    if (destpart < srcpart)
    {
      suftabparts->components[destpart-1].nextidx
        = suftabparts->components[suftabparts->numofparts-1].nextidx;
      suftabparts->numofparts -= (srcpart - destpart);
      gt_assert(suftabparts->numofparts == destpart);
    }
    for (srcpart = 0; srcpart < suftabparts->numofparts; srcpart++)
    {
      gt_assert(suftabparts->components[srcpart].widthofpart > 0);
      sumwidth+=suftabparts->components[srcpart].widthofpart;
      gt_logger_log(logger,"widthofpart[%u]=%lu",
                    srcpart,
                    suftabparts->components[srcpart].widthofpart);
    }
    gt_assert(sumwidth == totalwidth);
  }
#ifdef SKDEBUG
  gt_log_log("after removal");
  gt_suftabparts_showallrecords(suftabparts,true);
#endif
}

GtSuftabparts *gt_suftabparts_new(unsigned int numofparts,
                                  const GtBcktab *bcktab,
                                  const GtFirstcodestab *fct,
                                  const GtSfxmappedrangelist *sfxmrlist,
                                  unsigned long numofsuffixestoinsert,
                                  unsigned long fullspecials,
                                  GtLogger *logger)
{
  GtSuftabparts *suftabparts;
  unsigned long size_mapped;
  unsigned int part;

  gt_assert((bcktab == NULL && fct != NULL) ||
            (bcktab != NULL && fct == NULL));
  suftabparts = gt_malloc(sizeof *suftabparts);
  suftabparts->largestsizemappedpartwise = 0;
  suftabparts->fct = fct;
  gt_assert(suftabparts != NULL);
  if (numofsuffixestoinsert == 0)
  {
    suftabparts->numofparts = 0;
  } else
  {
    if (numofsuffixestoinsert < (unsigned long) numofparts ||
        (bcktab != NULL && gt_bcktab_prefixlength(bcktab) == 1U))
    {
      suftabparts->numofparts = 1U;
    } else
    {
      suftabparts->numofparts = numofparts;
    }
  }
  if (suftabparts->numofparts == 0)
  {
    suftabparts->largestsuftabwidth = fullspecials/numofparts+1;
    suftabparts->largestsizemappedpartwise
      = gt_Sfxmappedrangelist_size_entire(sfxmrlist);
    suftabparts->components = NULL;
  } else
  {
    unsigned int remainder;
    unsigned long secondidx, firstbound = 0, secondbound,
                  suftaboffset = 0, sumofwidth = 0;
    const unsigned long widthofsuftabpart
      = numofsuffixestoinsert/suftabparts->numofparts;

    suftabparts->components
      = gt_malloc(sizeof (*suftabparts->components) * suftabparts->numofparts);
    remainder = (unsigned int) (numofsuffixestoinsert %
                                (unsigned long) suftabparts->numofparts);
    suftabparts->largestsuftabwidth = 0;
    for (part=0; part < suftabparts->numofparts; part++)
    {
      if (remainder > 0)
      {
        suftaboffset += widthofsuftabpart + 1;
        remainder--;
      } else
      {
        suftaboffset += widthofsuftabpart;
      }
      if (part == suftabparts->numofparts - 1)
      {
        secondidx = bcktab != NULL ? gt_bcktab_numofallcodes(bcktab)
                                   : gt_firstcodes_numofsamples(fct);
      } else
      {
        secondidx = bcktab != NULL
                      ? gt_bcktab_findfirstlarger(bcktab,suftaboffset)
                      : gt_firstcodes_findfirstsamplelarger(fct,suftaboffset);
      }
      suftabparts->components[part].nextidx = secondidx;
      secondbound = bcktab != NULL
                      ? gt_bcktab_get_leftborder(bcktab,secondidx)
                      : gt_firstcodes_get_sample(fct,secondidx);
      if (part == 0)
      {
        suftabparts->components[part].widthofpart = secondbound;
        suftabparts->components[part].suftaboffset = 0;
      } else
      {
        gt_assert(secondbound >= firstbound);
        suftabparts->components[part].widthofpart = secondbound - firstbound;
        suftabparts->components[part].suftaboffset = firstbound;
      }
      if (suftabparts->largestsuftabwidth <
          suftabparts->components[part].widthofpart)
      {
        suftabparts->largestsuftabwidth
          = suftabparts->components[part].widthofpart;
      }
      sumofwidth += suftabparts->components[part].widthofpart;
      suftabparts->components[part].sumofwidth = sumofwidth;
      firstbound = secondbound;
    }
    gt_assert(sumofwidth == numofsuffixestoinsert);
  }
  gt_suftabparts_removeemptyparts(suftabparts,numofsuffixestoinsert,logger);
  if (suftabparts->numofparts > 0)
  {
    gt_assert(suftabparts->components != NULL);
    for (part=0; part < suftabparts->numofparts; part++)
    {
      suftabparts->components[part].minindex
        = gt_suftabparts_minindex_raw(part,suftabparts);
      suftabparts->components[part].maxindex
        = gt_suftabparts_maxindex_raw(part,suftabparts);
    }
    for (part=1U; part < suftabparts->numofparts; part++)
    {
      if (suftabparts->components[part].minindex !=
            suftabparts->components[part-1].maxindex + 1)
      {
        suftabparts->components[part].minindex
          = suftabparts->components[part-1].maxindex + 1;
      }
    }
    for (part=0; part < suftabparts->numofparts; part++)
    {
      size_mapped = gt_Sfxmappedrangelist_size_mapped(sfxmrlist,
                                    gt_suftabparts_minindex(part,suftabparts),
                                    gt_suftabparts_maxindex(part,suftabparts));
      if (suftabparts->largestsizemappedpartwise < size_mapped)
      {
        suftabparts->largestsizemappedpartwise = size_mapped;
      }
    }
  }
  return suftabparts;
}

double gt_suftabparts_variance(const GtSuftabparts *suftabparts)
{

  gt_assert(suftabparts->numofparts > 0);
  if (suftabparts->numofparts == 1U)
  {
    return 0.0;
  } else
  {
    double meanwidth, difference, sum = 0.0;
    unsigned int part;

    meanwidth = (double)
                suftabparts->components[suftabparts->numofparts-1].sumofwidth/
                suftabparts->numofparts;
    for (part = 0; part < suftabparts->numofparts; part++)
    {
      difference = (double) suftabparts->components[part].widthofpart
                   - meanwidth;
      sum += difference * difference;
    }
    return sum/(double) (suftabparts->numofparts-1);
  }
}

void gt_suftabparts_delete(GtSuftabparts *suftabparts)
{
  if (suftabparts != NULL)
  {
    gt_free(suftabparts->components);
    gt_free(suftabparts);
  }
}

GtCodetype gt_suftabparts_minindex(unsigned int part,
                                   const GtSuftabparts *suftabparts)
{
  return suftabparts->components[part].minindex;
}

GtCodetype gt_suftabparts_maxindex(unsigned int part,
                                   const GtSuftabparts *suftabparts)
{
  return suftabparts->components[part].maxindex;
}

GtCodetype gt_suftabparts_maxindex_last(const GtSuftabparts *suftabparts)
{
  gt_assert(suftabparts->numofparts > 0);
  return gt_suftabparts_maxindex(suftabparts->numofparts-1,suftabparts);
}

unsigned long gt_suftabparts_offset(unsigned int part,
                                    const GtSuftabparts *suftabparts)
{
  gt_assert(suftabparts != NULL && part < suftabparts->numofparts);
  return suftabparts->components[part].suftaboffset;
}

unsigned long gt_suftabparts_sumofwidth(unsigned int part,
                                        const GtSuftabparts *suftabparts)
{
  gt_assert(suftabparts != NULL && part < suftabparts->numofparts);
  return suftabparts->components[part].sumofwidth;
}

unsigned long gt_suftabparts_widthofpart(unsigned int part,
                                         const GtSuftabparts *suftabparts)
{
  gt_assert(suftabparts != NULL && part < suftabparts->numofparts);
  return suftabparts->components[part].widthofpart;
}

unsigned long gt_suftabparts_largest_width(const GtSuftabparts *suftabparts)
{
  gt_assert(suftabparts != NULL);
  return suftabparts->largestsuftabwidth;
}

unsigned long gt_suftabparts_largestsizemappedpartwise(
                                          const GtSuftabparts *suftabparts)
{
  gt_assert(suftabparts != NULL);
  return suftabparts->largestsizemappedpartwise;
}

unsigned int gt_suftabparts_numofparts(const GtSuftabparts *suftabparts)
{
  gt_assert(suftabparts != NULL);
  return suftabparts->numofparts;
}

int gt_suftabparts_fit_memlimit(size_t estimatedspace,
                                unsigned long maximumspace,
                                const GtBcktab *bcktab,
                                const GtFirstcodestab *fct,
                                const GtSfxmappedrangelist *sfxmrlist,
                                unsigned long totallength,
                                unsigned int bitsforseqnumrelpos,
                                unsigned long specialcharacters,
                                unsigned long numofsuffixestosort,
                                bool suftabuint,
                                GtError *err)
{
  unsigned int parts;
  GtSuftabparts *suftabparts;
  unsigned long size_mapped = gt_Sfxmappedrangelist_size_entire(sfxmrlist);

  gt_error_check(err);
  for (parts = 1U; parts <= 500U; parts++)
  {
    uint64_t suftabsize;
    unsigned long numofentries;

    suftabparts = gt_suftabparts_new(parts,
                                     bcktab,
                                     fct,
                                     sfxmrlist,
                                     numofsuffixestosort,
                                     specialcharacters + 1,
                                     NULL);
    gt_assert(suftabparts != NULL);
    numofentries = gt_suftabparts_largest_width(suftabparts);
    if (bcktab != NULL)
    {
      gt_assert(fct == NULL);
      suftabsize = gt_suffixsortspace_requiredspace(numofentries,
                                                    totallength,
                                                    suftabuint);
    } else
    {
      gt_assert(fct != NULL);
      suftabsize = (uint64_t) gt_spmsuftab_requiredspace(numofentries,
                                                         totallength,
                                                         bitsforseqnumrelpos);
    }
    if (parts == 1U)
    {
      if (suftabsize + (uint64_t) estimatedspace <= (uint64_t) maximumspace)
      {
        gt_suftabparts_delete(suftabparts);
        return (int) parts;
      }
    } else
    {
      unsigned long largest
        = gt_suftabparts_largestsizemappedpartwise(suftabparts);
      if (suftabsize
          + (uint64_t) largest
          + (uint64_t) estimatedspace
          - (uint64_t) size_mapped <= (uint64_t) maximumspace)
      {
        gt_log_log("return parts = %u as suftabsize=%.2f +"
                   "largest=%.2f + estimated=%.2f - size_mapped=%2.f <= %.2f",
                    parts,
                    GT_MEGABYTES(suftabsize),
                    GT_MEGABYTES(largest),
                    GT_MEGABYTES(estimatedspace),
                    GT_MEGABYTES(size_mapped),
                    GT_MEGABYTES(maximumspace));
        gt_suftabparts_delete(suftabparts);
        return (int) parts;
      }
    }
    gt_suftabparts_delete(suftabparts);
  }
  gt_error_set(err,"cannot compute enhanced suffix array in at most %lu bytes",
                   maximumspace);
  return -1;
}
genometools-1.5.1/src/match/sfx-partssuf.h000066400000000000000000000066101211610345200205500ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_PARTSSUF_H
#define SFX_PARTSSUF_H

#include "core/logger.h"
#include "core/codetype.h"
#include "core/error_api.h"
#include "sfx-maprange.h"
#include "firstcodes-tab.h"
#include "bcktab.h"

typedef struct GtSuftabparts GtSuftabparts;

void gt_suftabparts_showallrecords(const GtSuftabparts *suftabparts,
                                   bool withminmaxindex);

GtSuftabparts *gt_suftabparts_new(unsigned int numofparts,
                                  const GtBcktab *bcktab,
                                  const GtFirstcodestab *fct,
                                  const GtSfxmappedrangelist *sfxmrlist,
                                  unsigned long numofsuffixestoinsert,
                                  unsigned long fullspecials,
                                  GtLogger *logger);

void gt_suftabparts_delete(GtSuftabparts *suftabparts);

GtCodetype gt_suftabparts_minindex(unsigned int part,
                                   const GtSuftabparts *suftabparts);

GtCodetype gt_suftabparts_maxindex(unsigned int part,
                                   const GtSuftabparts *suftabparts);

GtCodetype gt_suftabparts_maxindex_last(const GtSuftabparts *suftabparts);

unsigned long gt_suftabparts_offset(unsigned int part,
                                    const GtSuftabparts *suftabparts);

unsigned long gt_suftabparts_sumofwidth(unsigned int part,
                                        const GtSuftabparts *suftabparts);

unsigned long gt_suftabparts_widthofpart(unsigned int part,
                                         const GtSuftabparts *suftabparts);

unsigned long gt_suftabparts_largest_width(const GtSuftabparts *suftabparts);

unsigned int gt_suftabparts_numofparts(const GtSuftabparts *suftabparts);

unsigned long gt_suftabparts_largestsizemappedpartwise(
                                       const GtSuftabparts *suftabparts);

double gt_suftabparts_variance(const GtSuftabparts *suftabparts);

int gt_suftabparts_fit_memlimit(size_t estimatedspace,
                                unsigned long maximumspace,
                                const GtBcktab *bcktab,
                                const GtFirstcodestab *fct,
                                const GtSfxmappedrangelist *sfxmrlist,
                                unsigned long totallength,
                                unsigned int bitsforseqnumrelpos,
                                unsigned long specialcharacters,
                                unsigned long numofsuffixestosort,
                                bool suftabuint,
                                GtError *err);

#endif
genometools-1.5.1/src/match/sfx-radixsort.c000066400000000000000000000053161211610345200207150ustar00rootroot00000000000000/*
  Copyright (c) 2012 Stefan Kurtz 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/intbits.h"
#include "sfx-suffixgetset.h"
#include "radixsort_str.h"
#include "sfx-radixsort.h"
#include "sfx-lcpvalues.h"

void gt_sfx_radixsort_str(GtRadixsortstringinfo *rsi,
                          unsigned long depth,
                          unsigned int sortmaxdepth,
                          unsigned long subbucketleft,
                          unsigned long width,
                          GtSuffixsortspace *sssp,
                          GtLcpvalues *lcpvalues)
{
  unsigned long idx, *suffixes;
  GtSuffixsortspace_exportptr *exportptr
    = gt_suffixsortspace_exportptr(subbucketleft, sssp);
  bool allocated = false;

  if (exportptr->ulongtabsectionptr != NULL)
  {
    suffixes = exportptr->ulongtabsectionptr;
  } else
  {
    suffixes = gt_malloc(sizeof (*suffixes) * width);
    allocated = true;
    for (idx = 0; idx < width; idx++)
    {
      suffixes[idx] = (unsigned long) exportptr->uinttabsectionptr[idx];
    }
  }
  gt_radixsort_str_eqlen(rsi,
                         suffixes,
                         lcpvalues,
                         subbucketleft,
                         depth,
                         (unsigned long) sortmaxdepth,
                         width);
  if (allocated)
  {
    gt_assert(exportptr->uinttabsectionptr != NULL);
    for (idx = 0; idx < width; idx++)
    {
      exportptr->uinttabsectionptr[idx] = (uint32_t) suffixes[idx];
      if (exportptr->uinttabsectionptr[idx] == 0)
      {
        gt_suffixsortspace_updatelongest(sssp,subbucketleft + idx);
      }
    }
    gt_free(suffixes);
  } else
  {
    gt_assert(exportptr->ulongtabsectionptr != NULL);
    for (idx = 0; idx < width; idx++)
    {
      if (exportptr->ulongtabsectionptr[idx] == 0)
      {
        gt_suffixsortspace_updatelongest(sssp,subbucketleft + idx);
        break;
      }
    }
  }
  gt_suffixsortspace_export_done(sssp);
}
genometools-1.5.1/src/match/sfx-radixsort.h000066400000000000000000000025431211610345200207210ustar00rootroot00000000000000/*
  Copyright (c) 2012 Stefan Kurtz 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_RADIXSORT_H
#define SFX_RADIXSORT_H

#include "core/intbits.h"
#include "radixsort_str.h"
#include "sfx-lcpvalues.h"
#include "sfx-suffixgetset.h"

void gt_sfx_radixsort_str(GtRadixsortstringinfo *rsi,
                          unsigned long depth,
                          unsigned int sortmaxdepth,
                          unsigned long subbucketleft,
                          unsigned long width,
                          GtSuffixsortspace *sssp,
                          GtLcpvalues *lcpvalues);

#endif
genometools-1.5.1/src/match/sfx-run.c000066400000000000000000000574771211610345200175210ustar00rootroot00000000000000/*
  Copyright (c) 2007      Stefan Kurtz 
  Copyright (c)      2010 Sascha Steinbiss 
  Copyright (c) 2007-2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 
#include "core/alphabet.h"
#include "core/chardef.h"
#include "core/codetype.h"
#include "core/encseq.h"
#include "core/encseq_metadata.h"
#include "core/fa.h"
#include "core/logger.h"
#include "core/readmode.h"
#include "core/showtime.h"
#include "core/timer_api.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "esa-fileend.h"
#include "esa-shulen.h"
#include "giextract.h"
#include "intcode-def.h"
#include "sfx-apfxlen.h"
#include "sfx-lcpvalues.h"
#include "sfx-opt.h"
#include "sfx-outprj.h"
#include "sfx-run.h"
#include "sfx-suffixer.h"
#include "sfx-suffixgetset.h"
#include "stamp.h"

#ifndef S_SPLINT_S
#include "eis-encidxseq.h"
#include "eis-bwtseq-construct.h"
#include "eis-bwtseq-param.h"
#include "eis-suffixerator-interface.h"
#endif

#define INITOUTFILEPTR(PTR,FLAG,SUFFIX)\
        if (!haserr && (FLAG))\
        {\
          PTR = gt_fa_fopen_with_suffix(gt_str_get(so->indexname),\
                                        SUFFIX, "wb",err);\
          if ((PTR) == NULL)\
          {\
            haserr = true;\
          }\
        }

typedef struct
{
  FILE *outfpsuftab,
       *outfpbwttab,
       *outfpbcktab;
  unsigned long numberofallsortedsuffixes;
  const GtEncseq *encseq;
  Definedunsignedlong longest;
  GtOutlcpinfo *outlcpinfo;
  GtBUstate_shulen *bustate_shulen;
} Outfileinfo;

/*
static void gt_suflcptab2genomediff(GT_UNUSED void *data,
                                    const GtSuffixsortspace *sssp,
                                    const GtLcpvalues *tableoflcpvalues,
                                    unsigned long bucketoffset,
                                    unsigned long width,
                                    unsigned long posoffset)
{
  unsigned long idx, lcpvalue, suffix;

  for (idx=0; idx < width; idx++)
  {
    lcpvalue = gt_lcptab_getvalue(tableoflcpvalues,bucketoffset,idx);
    suffix = gt_suffixsortspace_get(sssp,bucketoffset+posoffset,idx);
    printf("%lu %lu\n",suffix,MIN(lcpvalue,LCPOVERFLOW));
  }
}
*/

static void gt_suflcptab2genomediff(void *data,
                                    const GtSuffixsortspace *sssp,
                                    const GtLcpvalues *tableoflcpvalues,
                                    unsigned long bucketoffset,
                                    unsigned long numberofsuffixes,
                                    unsigned long posoffset)
{
  (void) gt_sfx_multiesa2shulengthdist(
                  (GtBUstate_shulen *) data,
                  gt_suffixsortspace_getptr_ulong(sssp,bucketoffset+posoffset),
                  gt_suffixsortspace_getptr_uint32(sssp,bucketoffset+posoffset),
                  gt_lcptab_getptr(tableoflcpvalues,bucketoffset),
                  numberofsuffixes,
                  NULL);
}

static int initoutfileinfo(Outfileinfo *outfileinfo,
                           unsigned int prefixlength,
                           const GtEncseq *encseq,
                           const Suffixeratoroptions *so,
                           GenomediffInfo *gd_info,
                           GtError *err)
{
  bool haserr = false;

  if (so->outlcptab)
  {

    gt_assert(gt_str_get(so->indexname) != NULL || so->genomediff);
    if (so->genomediff)
    {
      outfileinfo->bustate_shulen =
        gt_sfx_multiesashulengthdist_new(encseq,gd_info);
    }
    outfileinfo->outlcpinfo
      = gt_Outlcpinfo_new(so->genomediff ? NULL : gt_str_get(so->indexname),
                          gt_encseq_alphabetnumofchars(encseq),
                          prefixlength,
                          gt_index_options_lcpdist_value(so->idxopts),
                          gt_index_options_swallow_tail_value(so->idxopts),
                          so->genomediff ? gt_suflcptab2genomediff
                                        : NULL,
                          outfileinfo->bustate_shulen,
                          err);
    if (outfileinfo->outlcpinfo == NULL)
    {
      haserr = true;
    }
  } else
  {
    outfileinfo->outlcpinfo = NULL;
  }
  INITOUTFILEPTR(outfileinfo->outfpsuftab,
                 gt_index_options_outsuftab_value(so->idxopts),
                 SUFTABSUFFIX);
  INITOUTFILEPTR(outfileinfo->outfpbwttab,
                 gt_index_options_outbwttab_value(so->idxopts),
                 BWTTABSUFFIX);
  INITOUTFILEPTR(outfileinfo->outfpbcktab,
                 gt_index_options_outbcktab_value(so->idxopts),
                 BCKTABSUFFIX);
  if (gt_index_options_outsuftab_value(so->idxopts)
        || gt_index_options_outbwttab_value(so->idxopts)
        || so->outlcptab
        || gt_index_options_outbcktab_value(so->idxopts))
  {
    outfileinfo->encseq = encseq;
  } else
  {
    outfileinfo->encseq = NULL;
  }
  return haserr  ? -1 : 0;
}

static int bwttab2file(Outfileinfo *outfileinfo,
                       const GtSuffixsortspace *suffixsortspace,
                       GtReadmode readmode,
                       unsigned long numberofsuffixes,
                       GT_UNUSED GtError *err)
{
  bool haserr = false;

  gt_error_check(err);
  if (outfileinfo->outfpbwttab != NULL)
  {
    unsigned long startpos, pos;
    GtUchar cc = 0;

    for (pos=0; pos < numberofsuffixes; pos++)
    {
      startpos = gt_suffixsortspace_getdirect(suffixsortspace,pos);
      if (startpos == 0)
      {
        cc = (GtUchar) UNDEFBWTCHAR;
      } else
      {
        if (outfileinfo->outfpbwttab != NULL)
        {
          /* Random access */
          cc = gt_encseq_get_encoded_char(outfileinfo->encseq,
                                          startpos - 1,
                                          readmode);
        }
      }
      if (outfileinfo->outfpbwttab != NULL)
      {
        gt_xfwrite(&cc,sizeof (GtUchar),(size_t) 1,outfileinfo->outfpbwttab);
      }
    }
  }
  return haserr ? -1 : 0;
}

static int suffixeratorwithoutput(Outfileinfo *outfileinfo,
                                  const GtEncseq *encseq,
                                  GtReadmode readmode,
                                  unsigned int prefixlength,
                                  unsigned int numofparts,
                                  unsigned long maximumspace,
                                  bool swallow_tail,
                                  const Sfxstrategy *sfxstrategy,
                                  GtTimer *sfxprogress,
                                  bool withprogressbar,
                                  GtLogger *logger,
                                  GtError *err)
{
  bool haserr = false;
  Sfxiterator *sfi = NULL;

  sfi = gt_Sfxiterator_new_withadditionalvalues(encseq,
                           readmode,
                           prefixlength,
                           numofparts,
                           maximumspace,
                           outfileinfo->outlcpinfo,
                           outfileinfo->outfpbcktab,
                           sfxstrategy,
                           sfxprogress,
                           withprogressbar,
                           logger,
                           err);
  if (sfi == NULL)
  {
    haserr = true;
  } else
  {
    const GtSuffixsortspace *suffixsortspace;
    unsigned long numberofsuffixes;
    bool specialsuffixes = false;

    while (true)
    {
      suffixsortspace = gt_Sfxiterator_next(&numberofsuffixes,&specialsuffixes,
                                            sfi);
      if (suffixsortspace == NULL)
      {
        break;
      }
      if (outfileinfo->outfpsuftab != NULL &&
          (!specialsuffixes || !swallow_tail))
      {
        if (gt_suffixsortspace_to_file (outfileinfo->outfpsuftab,
                                        suffixsortspace,
                                        numberofsuffixes,
                                        err) != 0)
        {
          haserr = true;
          break;
        }
      }
      if (bwttab2file(outfileinfo,suffixsortspace,readmode,numberofsuffixes,
                      err) != 0)
      {
        haserr = true;
        break;
      }
      outfileinfo->numberofallsortedsuffixes += numberofsuffixes;
    }
  }
  if (haserr)
  {
    outfileinfo->longest.defined = false;
    outfileinfo->longest.valueunsignedlong = 0;
  } else
  {
    outfileinfo->longest.defined = true;
    outfileinfo->longest.valueunsignedlong = gt_Sfxiterator_longest(sfi);
    gt_assert(outfileinfo->longest.valueunsignedlong <
              gt_encseq_total_length(encseq));
    if (outfileinfo->outfpbcktab != NULL)
    {
      if (gt_Sfxiterator_bcktab2file(outfileinfo->outfpbcktab,sfi,err) != 0)
      {
        haserr = true;
      }
      outfileinfo->outfpbcktab = NULL;
    }
  }
  if (gt_Sfxiterator_delete(sfi,err) != 0)
  {
    haserr = true;
  }
  return haserr ? -1 : 0;
}

static int detpfxlen(unsigned int *prefixlength,
                     const Suffixeratoroptions *so,
                     unsigned int numofchars,
                     unsigned long totallength,
                     bool withspecialsuffixes,
                     GtLogger *logger,
                     GtError *err)
{
  bool haserr = false;
  unsigned int recommendedprefixlength;
  Sfxstrategy sfxstrategy = gt_index_options_sfxstrategy_value(so->idxopts);

  recommendedprefixlength
    = gt_recommendedprefixlength(numofchars,
                                 totallength,
                                 sfxstrategy.spmopt_minlength > 0
                                   ? 0.15 : GT_RECOMMENDED_MULTIPLIER_DEFAULT,
                                 withspecialsuffixes);
  if (gt_index_options_prefixlength_value(so->idxopts)
                                                   == GT_PREFIXLENGTH_AUTOMATIC)
  {
    *prefixlength = recommendedprefixlength;
    gt_logger_log(logger,
                "automatically determined prefixlength=%u",
                *prefixlength);
  } else
  {
    unsigned int maxprefixlen;

    *prefixlength = gt_index_options_prefixlength_value(so->idxopts);
    maxprefixlen
      = gt_whatisthemaximalprefixlength(numofchars,
                                        totallength,
                                        sfxstrategy.storespecialcodes
                                          ? (unsigned int) PREFIXLENBITS
                                          : 0,
                                        withspecialsuffixes);
    if (gt_checkprefixlength(maxprefixlen,*prefixlength,err) != 0)
    {
      haserr = true;
    } else
    {
      gt_showmaximalprefixlength(logger,
                                 maxprefixlen,
                                 recommendedprefixlength);
    }
  }
  return haserr ? -1 : 0;
}

#ifndef S_SPLINT_S
static int run_packedindexconstruction(GtLogger *logger,
                                       GtTimer *sfxprogress,
                                       bool withprogressbar,
                                       const Suffixeratoroptions *so,
                                       unsigned int prefixlength,
                                       const GtEncseq *encseq,
                                       const Sfxstrategy *sfxstrategy,
                                       GtError *err)
{
  sfxInterface *si;
  BWTSeq *bwtSeq;
  bool haserr = false;
  struct bwtParam finalcopy;
  struct bwtOptions bwtIdxParams =
                               gt_index_options_bwtIdxParams_value(so->idxopts);
  unsigned int numofchars
    = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));

  finalcopy = bwtIdxParams.final;
  if (numofchars > 10U && finalcopy.seqParams.encParams.blockEnc.blockSize > 3U)
  {
    finalcopy.seqParams.encParams.blockEnc.blockSize = 3U;
  }
  gt_logger_log(logger, "run construction of packed index for: "
                        "blocksize=%u, blocks-per-bucket=%u, locfreq=%u",
                finalcopy.seqParams.encParams.blockEnc.blockSize,
                finalcopy.seqParams.encParams.blockEnc.bucketBlocks,
                finalcopy.locateInterval);
  si = gt_newSfxInterface(gt_index_options_readmode_value(so->idxopts),
                          prefixlength,
                          gt_index_options_numofparts_value(so->idxopts),
                          gt_index_options_maximumspace_value(so->idxopts),
                          sfxstrategy,
                          encseq,
                          sfxprogress,
                          withprogressbar,
                          gt_encseq_total_length(encseq) + 1,
                          logger,
                          err);
  if (si == NULL)
  {
    haserr = true;
  } else
  {
    bwtSeq = gt_createBWTSeqFromSfxI(&finalcopy, si, err);
    if (bwtSeq == NULL)
    {
      haserr = true;
    } else
    {
      gt_deleteBWTSeq(bwtSeq); /**< the actual object is not * used here */
    }
    gt_deleteSfxInterface(si);
  }
  return haserr ? -1 : 0;
}
#endif

int runsuffixerator(bool doesa,
                    Suffixeratoroptions *so,
                    GenomediffInfo *gd_info,
                    GtLogger *logger,
                    GtError *err)
{
  GtTimer *sfxprogress = NULL;
  Outfileinfo outfileinfo;
  bool haserr = false;
  unsigned int prefixlength;
  Sfxstrategy sfxstrategy;
  GtEncseq *encseq = NULL;
  GtReadmode readmode = gt_index_options_readmode_value(so->idxopts);

  gt_error_check(err);

  so->outlcptab = so->genomediff
    ? true
    : gt_index_options_outlcptab_value(so->idxopts);

  if (gt_showtime_enabled())
  {
    sfxprogress = gt_timer_new_with_progress_description("determining sequence "
                                        "length and number of special symbols");
    gt_timer_start(sfxprogress);
  }

  if (gt_str_length(so->inputindex) > 0)
  {
    GtEncseqLoader *el;
    el = gt_encseq_loader_new_from_options(so->loadopts, err);
    if (!gt_encseq_options_ssp_value(so->loadopts))
    {
      GtEncseqMetadata* emd = gt_encseq_metadata_new(gt_str_get(so->inputindex),
                                                     err);
      if (emd == NULL)
      {
        haserr = true;
      } else
      {
        GtEncseqAccessType at = gt_encseq_metadata_accesstype(emd);
        if (!gt_encseq_access_type_isviautables(at))
        {
          gt_encseq_loader_do_not_require_ssp_tab(el);
        }
      }
      gt_encseq_metadata_delete(emd);
    }
    if (!haserr) {
      gt_encseq_loader_set_logger(el, logger);
      /* as we only construct the des, sds, and ssptable, but do not
         need it later during the construction of the enhanced suffix
         array, we do not load it again: we just load the information
         stored in the .esq file. It would be better to use the
         in memory constructed encseq rather than the one mapped into
         memory. This would require to free the des, sds, and ssptable. */
      gt_encseq_loader_disable_autosupport(el);
      gt_encseq_loader_do_not_require_des_tab(el);
      gt_encseq_loader_do_not_require_sds_tab(el);
      gt_encseq_loader_do_not_require_ssp_tab(el);
      encseq = gt_encseq_loader_load(el, gt_str_get(so->inputindex), err);
    }
    gt_encseq_loader_delete(el);
    if (encseq == NULL)
    {
      haserr = true;
    }
  } else
  {
    GtEncseqEncoder *ee = NULL;
    ee = gt_encseq_encoder_new_from_options(so->encopts, err);
    /* '-plain' implies no description support */
    if (gt_encseq_options_plain_value(so->loadopts)) {
      gt_encseq_encoder_do_not_create_des_tab(ee);
      gt_encseq_encoder_do_not_create_sds_tab(ee);
    }
    if (ee == NULL)
      haserr = true;
    if (!haserr) {
      int rval;
      gt_encseq_encoder_set_timer(ee, sfxprogress);
      gt_encseq_encoder_set_logger(ee, logger);
      rval = gt_encseq_encoder_encode(ee, so->db, gt_str_get(so->indexname),
                                      err);
      if (rval != 0)
        haserr = true;
      if (!haserr) {
        GtEncseqLoader *el = gt_encseq_loader_new_from_options(so->loadopts,
                                                               err);
        /* as we only construct the des, sds, and ssptable, but do not
           need it later during the construction of the enhanced suffix
           array, we do not load it again: we just load the information
           stored in the .esq file. It would be better to use the
           in memory constructed encseq rather than the one mapped into
           memory. This would require to free the des, sds, and ssptable. */
        gt_encseq_loader_disable_autosupport(el);
        gt_encseq_loader_do_not_require_des_tab(el);
        gt_encseq_loader_do_not_require_sds_tab(el);
        gt_encseq_loader_do_not_require_ssp_tab(el);
        encseq = gt_encseq_loader_load(el, gt_str_get(so->indexname), err);
        if (!encseq)
          haserr = true;
        gt_encseq_loader_delete(el);
      }
    }
    if (encseq == NULL)
    {
      haserr = true;
    }
    gt_encseq_encoder_delete(ee);
  }
  if (!haserr)
  {
    gt_encseq_show_features(encseq,logger,false);
    if (readmode == GT_READMODE_COMPL ||
        readmode == GT_READMODE_REVCOMPL)
    {
      if (!gt_alphabet_is_dna(gt_encseq_alphabet(encseq)))
      {
        gt_error_set(err,"option -%s only can be used for DNA alphabets",
                          readmode == GT_READMODE_COMPL ? "cpl" : "rcl");
        haserr = true;
      }
    }
  }
  if (!haserr
        && gt_index_options_outkystab_value(so->idxopts)
        && !gt_index_options_outkyssort_value(so->idxopts))
  {
    if (gt_extractkeysfromdesfile(gt_str_get(so->indexname),
                                  false, logger, err) != 0)
    {
      haserr = true;
    }
  }
  prefixlength = gt_index_options_prefixlength_value(so->idxopts);
  sfxstrategy = gt_index_options_sfxstrategy_value(so->idxopts);
  if (!haserr)
  {
    if (gt_index_options_outsuftab_value(so->idxopts)
        || gt_index_options_outbwttab_value(so->idxopts)
        || so->outlcptab
        || gt_index_options_outbcktab_value(so->idxopts)
        || !doesa)
    {
      unsigned int numofchars = gt_alphabet_num_of_chars(
                                          gt_encseq_alphabet(encseq));

      if (detpfxlen(&prefixlength,
                    so,
                    numofchars,
                    gt_encseq_total_length(encseq),
                    sfxstrategy.spmopt_minlength == 0 ? true : false,
                    logger,
                    err) != 0)
      {
        haserr = true;
      }
    } else
    {
      if (readmode != GT_READMODE_FORWARD)
      {
        gt_error_set(err,"option '-dir %s' only makes sense in combination "
                          "with at least one of the options -suf, -lcp, or "
                          "-bwt",
                          gt_readmode_show(readmode));
        haserr = true;
      }
    }
  }
  outfileinfo.outfpsuftab = NULL;
  outfileinfo.outfpbwttab = NULL;
  outfileinfo.outlcpinfo = NULL;
  outfileinfo.outfpbcktab = NULL;
  outfileinfo.numberofallsortedsuffixes = 0;
  outfileinfo.longest.defined = false;
  outfileinfo.longest.valueunsignedlong = 0;
  outfileinfo.bustate_shulen = NULL;
  outfileinfo.encseq = NULL;
  if (!haserr)
  {
    if (initoutfileinfo(&outfileinfo,prefixlength,encseq,so,gd_info,err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    if (gt_index_options_outsuftab_value(so->idxopts)
        || gt_index_options_outbwttab_value(so->idxopts)
        || so->outlcptab
        || !doesa)
    {
      if (doesa)
      {
        if (suffixeratorwithoutput(
                               &outfileinfo,
                               encseq,
                               readmode,
                               prefixlength,
                               gt_index_options_numofparts_value(so->idxopts),
                               gt_index_options_maximumspace_value(so->idxopts),
                               gt_index_options_swallow_tail_value(so->idxopts),
                               &sfxstrategy,
                               sfxprogress,
                               so->showprogress,
                               logger,
                               err) != 0)
        {
          haserr = true;
        }
      } else
      {
#ifndef S_SPLINT_S
        sfxstrategy.outsuftabonfile = false;
        if (run_packedindexconstruction(logger,
                                        sfxprogress,
                                        so->showprogress,
                                        so,
                                        prefixlength,
                                        encseq,
                                        &sfxstrategy,
                                        err) != 0)
        {
          haserr = true;
        }
#endif
      }
    }
  }
  if (!haserr && outfileinfo.bustate_shulen != NULL &&
      gt_sfx_multiesa2shulengthdist_last(outfileinfo.bustate_shulen,err) != 0)
  {
    haserr = true;
  }
  gt_fa_fclose(outfileinfo.outfpsuftab);
  gt_fa_fclose(outfileinfo.outfpbwttab);
  gt_fa_fclose(outfileinfo.outfpbcktab);
  if (!haserr)
  {
    unsigned long numoflargelcpvalues, maxbranchdepth;
    double averagelcp;

    if (outfileinfo.outlcpinfo == NULL)
    {
      numoflargelcpvalues = maxbranchdepth = 0;
      averagelcp = 0.0;
    } else
    {
      numoflargelcpvalues
        = gt_Outlcpinfo_numoflargelcpvalues(outfileinfo.outlcpinfo);
      maxbranchdepth = gt_Outlcpinfo_maxbranchdepth(outfileinfo.outlcpinfo);
      averagelcp = gt_Outlcpinfo_lcptabsum(outfileinfo.outlcpinfo)/
                   outfileinfo.numberofallsortedsuffixes;
    }
    if (gt_outprjfile(gt_str_get(so->indexname),
                      readmode,
                      encseq,
                      outfileinfo.numberofallsortedsuffixes,
                      prefixlength,
                      numoflargelcpvalues,
                      averagelcp,
                      maxbranchdepth,
                      &outfileinfo.longest,
                      err) != 0)
    {
      haserr = true;
    }
  }
  gt_Outlcpinfo_delete(outfileinfo.outlcpinfo);
  gt_sfx_multiesashulengthdist_delete(outfileinfo.bustate_shulen,gd_info);
  gt_encseq_delete(encseq);
  encseq = NULL;
  if (!haserr
        && gt_index_options_outkystab_value(so->idxopts)
        && gt_index_options_outkyssort_value(so->idxopts))
  {
    if (gt_extractkeysfromdesfile(gt_str_get(so->indexname),
                                  true,
                                  logger, err) != 0)
    {
      haserr = true;
    }
  }
  if (sfxprogress != NULL)
  {
    gt_timer_show_progress_final(sfxprogress, stdout);
    gt_timer_delete(sfxprogress);
  }
  return haserr ? -1 : 0;
}

int gt_parseargsandcallsuffixerator(bool doesa,int argc,
                                    const char **argv,GtError *err)
{
  Suffixeratoroptions so;
  int retval;
  bool haserr = false;

  gt_error_check(err);
  retval = gt_suffixeratoroptions(&so,doesa,argc,argv,err);
  if (retval == 0)
  {
    GtLogger *logger = gt_logger_new(so.beverbose,
                                     GT_LOGGER_DEFLT_PREFIX, stdout);

    gt_logger_log(logger,"sizeof (unsigned long)=%lu",
                  (unsigned long) (sizeof (unsigned long) * CHAR_BIT));
    if (runsuffixerator(doesa,&so,NULL,logger,err) < 0)
    {
      haserr = true;
    }
    gt_logger_delete(logger);
    logger = NULL;
  } else
  {
    if (retval < 0)
    {
      haserr = true;
    }
  }
  gt_sfxoptions_delete(&so);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/sfx-run.h000066400000000000000000000024361211610345200175070ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_RUN_H
#define SFX_RUN_H
#include 
#include "core/error.h"
#include "core/logger.h"
#include "match/sfx-opt.h"
#include "match/genomediff_opt.h"

int gt_parseargsandcallsuffixerator(bool doesa,int argc,
                                    const char **argv,GtError *err);

int runsuffixerator(bool doesa, Suffixeratoroptions *so,
                    GenomediffInfo *gd_info,
                    GtLogger *logger, GtError *err);
#endif
genometools-1.5.1/src/match/sfx-sain.c000066400000000000000000001311621211610345200176270ustar00rootroot00000000000000/*
  Copyright (c) 2012 Stefan Kurtz 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/minmax.h"
#include "core/unused_api.h"
#include "core/timer_api.h"
#include "core/mathsupport.h"
#include "sfx-linlcp.h"
#include "sfx-sain.h"

#define GT_SAIN_SHOWTIMER(DESC)\
        if (timer != NULL && gt_logger_enabled(logger))\
        {\
          gt_timer_show_progress(timer,DESC,stdout);\
        }

typedef enum
{
  GT_SAIN_PLAINSEQ,
  GT_SAIN_INTSEQ,
  GT_SAIN_ENCSEQ
} GtSainSeqtype;

typedef struct
{
  unsigned long totallength,
                numofchars,
                currentround,
                *bucketsize,
                *bucketfillptr,
                *sstarfirstcharcount,
                *roundtable;
  union
  {
    const GtEncseq *encseq;
    const GtUchar *plainseq;
    const unsigned long *array;
  } seq;
  GtReadmode readmode; /* only relevant for encseq */
  GtSainSeqtype seqtype;
  bool bucketfillptrpoints2suftab,
       bucketsizepoints2suftab,
       roundtablepoints2suftab;
} GtSainseq;

static bool gt_sain_decideforfastmethod(unsigned long maxvalue,
                                        unsigned long len)
{
  return maxvalue < (unsigned long) GT_FIRSTTWOBITS && len > 1024UL
         ? true : false;
}

static GtSainseq *gt_sainseq_new_from_encseq(const GtEncseq *encseq,
                                             GtReadmode readmode)
{
  unsigned long idx;
  GtSainseq *sainseq = gt_malloc(sizeof *sainseq);

  sainseq->seqtype = GT_SAIN_ENCSEQ;
  sainseq->seq.encseq = encseq;
  sainseq->readmode = readmode;
  sainseq->totallength = gt_encseq_total_length(encseq);
  sainseq->numofchars = (unsigned long) gt_encseq_alphabetnumofchars(encseq);
  sainseq->bucketsize = gt_malloc(sizeof (*sainseq->bucketsize) *
                                  sainseq->numofchars);
  sainseq->bucketfillptr = gt_malloc(sizeof (*sainseq->bucketfillptr) *
                                     sainseq->numofchars);
  if (gt_sain_decideforfastmethod(sainseq->totallength+GT_COMPAREOFFSET,
                                  sainseq->totallength))
  {
    sainseq->roundtable = gt_malloc(sizeof (*sainseq->roundtable) *
                                    (size_t) GT_MULT2(sainseq->numofchars));
  } else
  {
    sainseq->roundtable = NULL;
  }
  sainseq->sstarfirstcharcount
    = gt_calloc((size_t) sainseq->numofchars,
                sizeof (*sainseq->sstarfirstcharcount));
  sainseq->bucketfillptrpoints2suftab = false;
  sainseq->bucketsizepoints2suftab = false;
  sainseq->roundtablepoints2suftab = false;
  for (idx = 0; idxnumofchars; idx++)
  {
    if (GT_ISDIRCOMPLEMENT(readmode))
    {
      sainseq->bucketsize[idx]
        = gt_encseq_charcount(encseq,(GtUchar) GT_COMPLEMENTBASE(idx));
    } else
    {
      sainseq->bucketsize[idx] = gt_encseq_charcount(encseq,(GtUchar) idx);
    }
  }
  return sainseq;
}

static GtSainseq *gt_sainseq_new_from_plainseq(const GtUchar *plainseq,
                                               unsigned long len)
{
  const GtUchar *cptr;
  GtSainseq *sainseq = gt_malloc(sizeof *sainseq);

  sainseq->seqtype = GT_SAIN_PLAINSEQ;
  sainseq->seq.plainseq = plainseq;
  sainseq->totallength = len;
  sainseq->numofchars = UCHAR_MAX+1;
  sainseq->bucketsize = gt_calloc((size_t) sainseq->numofchars,
                                  sizeof (*sainseq->bucketsize));
  sainseq->bucketfillptr = gt_malloc(sizeof (*sainseq->bucketfillptr) *
                                     sainseq->numofchars);
  if (gt_sain_decideforfastmethod(len+1,len))
  {
    sainseq->roundtable = gt_malloc(sizeof (*sainseq->roundtable) *
                                    (size_t) GT_MULT2(sainseq->numofchars));
  } else
  {
    sainseq->roundtable = NULL;
  }
  sainseq->sstarfirstcharcount
    = gt_calloc((size_t) sainseq->numofchars,
                sizeof (*sainseq->sstarfirstcharcount));
  sainseq->bucketfillptrpoints2suftab = false;
  sainseq->bucketsizepoints2suftab = false;
  sainseq->roundtablepoints2suftab = false;
  for (cptr = sainseq->seq.plainseq; cptr < sainseq->seq.plainseq + len; cptr++)
  {
    sainseq->bucketsize[*cptr]++;
  }
  return sainseq;
}

static GtSainseq *gt_sainseq_new_from_array(unsigned long *arr,
                                            unsigned long len,
                                            unsigned long numofchars,
                                            unsigned long *suftab,
                                            unsigned long firstusable,
                                            unsigned long suftabentries)
{
  unsigned long charidx, *cptr;
  GtSainseq *sainseq = gt_malloc(sizeof *sainseq);

  sainseq->seqtype = GT_SAIN_INTSEQ;
  sainseq->seq.array = arr;
  sainseq->totallength = len;
  sainseq->numofchars = numofchars;
  gt_assert(firstusable < suftabentries);
  if (suftabentries - firstusable >= numofchars)
  {
    /*printf("bucketsize: reclaim suftab[%lu,%lu]\n",
            suftabentries - numofchars,suftabentries-1);*/
    sainseq->bucketsize = suftab + suftabentries - numofchars;
    sainseq->bucketsizepoints2suftab = true;
  } else
  {
    printf("bucketsize requires %lu entries and only %lu are left\n",
           numofchars,suftabentries - firstusable);
    sainseq->bucketsizepoints2suftab = false;
    sainseq->bucketsize = gt_malloc(sizeof (*sainseq->bucketsize) * numofchars);
  }
  if (suftabentries - firstusable >= GT_MULT2(numofchars))
  {
    /*printf("bucketfillptr: reclaim suftab[%lu,%lu]\n",
            suftabentries - GT_MULT2(numofchars),
            suftabentries - numofchars -1);*/
    sainseq->bucketfillptr = suftab + suftabentries - GT_MULT2(numofchars);
    sainseq->bucketfillptrpoints2suftab = true;
  } else
  {
    /*printf("bucketfillptr requires %lu entries and only %lu are left\n",
           numofchars,suftabentries - firstusable);*/
    sainseq->bucketfillptrpoints2suftab = false;
    sainseq->bucketfillptr = gt_malloc(sizeof (*sainseq->bucketfillptr) *
                                       numofchars);
  }
  if (gt_sain_decideforfastmethod(len+1,len))
  {
    if (suftabentries - firstusable >= GT_MULT4(numofchars))
    {
      /*printf("roundtable: reclaim suftab[%lu,%lu]\n",
              suftabentries - GT_MULT4(numofchars),
              suftabentries - GT_MULT2(numofchars) - 1);*/
      sainseq->roundtable = suftab + suftabentries - GT_MULT4(numofchars);
      sainseq->roundtablepoints2suftab = true;
    } else
    {
      sainseq->roundtablepoints2suftab = false;
      sainseq->roundtable = gt_malloc(sizeof (*sainseq->roundtable) *
                                      GT_MULT2(numofchars));
    }
  } else
  {
    sainseq->roundtablepoints2suftab = false;
    sainseq->roundtable = NULL;
  }
  sainseq->sstarfirstcharcount = NULL;
  for (charidx = 0; charidx < sainseq->numofchars; charidx++)
  {
    sainseq->bucketsize[charidx] = 0;
  }
  for (cptr = arr; cptr < arr + sainseq->totallength; cptr++)
  {
    sainseq->bucketsize[*cptr]++;
  }
  return sainseq;
}

static void gt_sainseq_delete(GtSainseq *sainseq)
{
  if (sainseq != NULL)
  {
    if (!sainseq->bucketfillptrpoints2suftab)
    {
      gt_free(sainseq->bucketfillptr);
    }
    if (!sainseq->bucketsizepoints2suftab)
    {
      gt_free(sainseq->bucketsize);
    }
    if (!sainseq->roundtablepoints2suftab)
    {
      gt_free(sainseq->roundtable);
    }
    if (sainseq->seqtype != GT_SAIN_INTSEQ)
    {
      gt_free(sainseq->sstarfirstcharcount);
    }
    gt_free(sainseq);
  }
}

#ifdef GT_SAIN_WITHCOUNTS
static unsigned long gt_sain_countcharaccess = 0;
#endif

static unsigned long gt_sainseq_getchar(const GtSainseq *sainseq,
                                        unsigned long position)
{
  GtUchar cc;

  gt_assert(position < sainseq->totallength);
#ifdef GT_SAIN_WITHCOUNTS
  gt_sain_countcharaccess++;
#endif
  return (sainseq->seqtype == GT_SAIN_PLAINSEQ)
         ? (unsigned long) sainseq->seq.plainseq[position]
         : ((sainseq->seqtype == GT_SAIN_INTSEQ)
            ? sainseq->seq.array[position]
            : ISSPECIAL(cc = gt_encseq_get_encoded_char(sainseq->seq.encseq,
                                                        position,
                                                        sainseq->readmode))
               ? GT_UNIQUEINT(position) : (unsigned long) cc);
}

static void gt_sain_endbuckets(GtSainseq *sainseq)
{
  unsigned long charidx, previous;

  previous = sainseq->bucketfillptr[0] = sainseq->bucketsize[0];
  for (charidx = 1UL; charidx < sainseq->numofchars; charidx++)
  {
    previous += sainseq->bucketsize[charidx];
    sainseq->bucketfillptr[charidx] = previous;
  }
}

static void gt_sain_startbuckets(GtSainseq *sainseq)
{
  unsigned long charidx, previous;

  previous = sainseq->bucketfillptr[0] = 0;
  for (charidx = 1UL; charidx < sainseq->numofchars; charidx++)
  {
    previous += sainseq->bucketsize[charidx-1];
    sainseq->bucketfillptr[charidx] = previous;
  }
}

typedef struct
{
  unsigned long buf_size, numofchars, cachesize, *values, *fillptr, *suftab;
  uint16_t *nextidx;
  int log_bufsize;
  size_t size;
} GtSainbuffer;

static GtSainbuffer *gt_sainbuffer_new(unsigned long *suftab,
                                       unsigned long *fillptr,
                                       unsigned long numofchars,
                                       GtLogger *logger)
{
  if (numofchars <= UCHAR_MAX+1)
  {
    GtSainbuffer *buf = gt_malloc(sizeof (*buf));

    buf->size = sizeof (*buf);
    buf->fillptr = fillptr;
    buf->suftab = suftab;
    buf->log_bufsize = 18 - (sizeof (unsigned long) == (size_t) 4 ? 1 : 2) -
                             (int) gt_determinebitspervalue(numofchars);
    buf->buf_size = 1UL << buf->log_bufsize;
    buf->numofchars = numofchars;
    gt_assert(buf->buf_size <= UINT16_MAX);
    buf->cachesize = numofchars << buf->log_bufsize;
    buf->values = gt_malloc(sizeof (*buf->values) * buf->cachesize);
    buf->size += sizeof (*buf->values) * buf->cachesize;
    buf->nextidx = gt_calloc((size_t) numofchars,sizeof (*buf->nextidx));
    buf->size += sizeof (*buf->nextidx) * numofchars;
    gt_logger_log(logger,"used buffer of %lu bytes (bufsize=%lu)",
                         (unsigned long) buf->size,buf->buf_size);
    return buf;
  } else
  {
    return NULL;
  }
}

static void gt_sainbuffer_update(GtSainbuffer *buf,
                                 unsigned long charidx,
                                 unsigned long value)
{
  const unsigned long offset = charidx << buf->log_bufsize;

  buf->values[offset + (unsigned long) buf->nextidx[charidx]] = value;
  if ((unsigned long) buf->nextidx[charidx] < buf->buf_size - 1)
  {
    buf->nextidx[charidx]++;
  } else
  {
    unsigned long *writeptr = buf->suftab + buf->fillptr[charidx] - 1,
                  *readptr = buf->values + offset;
    const unsigned long *readend = readptr + buf->buf_size;

    while (readptr < readend)
    {
      *(writeptr--) = *(readptr++);
    }
    buf->nextidx[charidx] = 0;
    buf->fillptr[charidx] -= buf->buf_size;
  }
}

static void gt_sainbuffer_flushall(GtSainbuffer *buf)
{
  unsigned long charidx;

  if (buf == NULL)
  {
    return;
  }
  for (charidx = 0; charidx < buf->numofchars; charidx++)
  {
    const unsigned long bufleft = (unsigned long) buf->nextidx[charidx];

    if (bufleft > 0)
    {
      unsigned long *writeptr = buf->suftab + buf->fillptr[charidx] - 1,
                    *readptr = buf->values + (charidx << buf->log_bufsize);
      const unsigned long *readend = readptr + bufleft;

      while (readptr < readend)
      {
        *(writeptr--) = *(readptr++);
      }
      buf->nextidx[charidx] = 0;
      buf->fillptr[charidx] -= bufleft;
    }
  }
}

static void gt_sainbuffer_delete(GtSainbuffer *buf)
{
  if (buf != NULL)
  {
    gt_free(buf->values);
    gt_free(buf->nextidx);
    gt_free(buf);
  }
}

#define GT_SAINUPDATEBUCKETPTR(CURRENTCC)\
        if (bucketptr != NULL)\
        {\
          if ((CURRENTCC) != lastupdatecc)\
          {\
            fillptr[lastupdatecc] = (unsigned long) (bucketptr - suftab);\
            bucketptr = suftab + fillptr[CURRENTCC];\
            lastupdatecc = CURRENTCC;\
          }\
        } else\
        {\
          bucketptr = suftab + fillptr[CURRENTCC];\
          lastupdatecc = CURRENTCC;\
        }

static void gt_sain_special_singleSinduction1(GtSainseq *sainseq,
                                              long *suftab,
                                              long position);

static void gt_sain_induceStypes1fromspecialranges(GtSainseq *sainseq,
                                                   const GtEncseq *encseq,
                                                   long *suftab);

static void gt_sain_special_singleSinduction2(const GtSainseq *sainseq,
                                              long *suftab,
                                              long position,
                                              GT_UNUSED unsigned long
                                                nonspecialentries);

static void gt_sain_induceStypes2fromspecialranges(
                                   const GtSainseq *sainseq,
                                   const GtEncseq *encseq,
                                   long *suftab,
                                   unsigned long nonspecialentries);

#include "match/sfx-sain.inc"

static unsigned long gt_sain_insertSstarsuffixes(GtSainseq *sainseq,
                                                 unsigned long *suftab,
                                                 GtLogger *logger)
{
  switch (sainseq->seqtype)
  {
    case GT_SAIN_PLAINSEQ:
      return gt_sain_PLAINSEQ_insertSstarsuffixes(sainseq,sainseq->seq.plainseq,
                                                  suftab,logger);
    case GT_SAIN_ENCSEQ:
      return gt_sain_ENCSEQ_insertSstarsuffixes(sainseq,sainseq->seq.encseq,
                                                suftab,logger);
    case GT_SAIN_INTSEQ:
      return gt_sain_INTSEQ_insertSstarsuffixes(sainseq,sainseq->seq.array,
                                                suftab,logger);
  }
  /*@ignore@*/
  return 0;
  /*@end@*/
}

static void gt_sain_incrementfirstSstar(GtSainseq *sainseq,
                                        unsigned long *suftab)
{
  unsigned long charidx, sum = 0;

  for (charidx = 0; charidx < sainseq->numofchars; charidx++)
  {
    sum += sainseq->bucketsize[charidx];
    gt_assert(sainseq->bucketfillptr[charidx] <= sum);
    if (sainseq->bucketfillptr[charidx] < sum)
    {
      suftab[sainseq->bucketfillptr[charidx]] += sainseq->totallength;
    }
    sainseq->roundtable[charidx] = 0;
    sainseq->roundtable[charidx+sainseq->numofchars] = 0;
  }
}

static void gt_sain_induceLtypesuffixes1(GtSainseq *sainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  switch (sainseq->seqtype)
  {
    case GT_SAIN_PLAINSEQ:
      (sainseq->roundtable == NULL
        ? gt_sain_PLAINSEQ_induceLtypesuffixes1
        : gt_sain_PLAINSEQ_fast_induceLtypesuffixes1)
           (sainseq,sainseq->seq.plainseq,suftab,nonspecialentries);
      break;
    case GT_SAIN_ENCSEQ:
      (sainseq->roundtable == NULL
        ? gt_sain_ENCSEQ_induceLtypesuffixes1
        : gt_sain_ENCSEQ_fast_induceLtypesuffixes1)
           (sainseq,sainseq->seq.encseq,suftab,nonspecialentries);
      break;
    case GT_SAIN_INTSEQ:
      (sainseq->roundtable == NULL
        ? gt_sain_INTSEQ_induceLtypesuffixes1
        : gt_sain_INTSEQ_fast_induceLtypesuffixes1)
           (sainseq,sainseq->seq.array,suftab,nonspecialentries);
      break;
  }
}

static void gt_sain_adjustsuftab(unsigned long totallength,long *suftab,
                                 unsigned long nonspecialentries)
{
  long *suftabptr;

  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if (*suftabptr > 0 && *suftabptr < (long) totallength)
    {
      long *nextgteq;

      *suftabptr += (long) totallength;
      nextgteq = suftabptr - 1;
      while (nextgteq >= suftab && *nextgteq < (long) totallength)
      {
        nextgteq--;
      }
      if (*nextgteq >= (long) totallength)
      {
        *nextgteq -= (long) totallength;
      }
      suftabptr = nextgteq;
    }
  }
}

static void gt_sain_special_singleSinduction1(GtSainseq *sainseq,
                                              long *suftab,
                                              long position)
{
  unsigned long currentcc = gt_sainseq_getchar(sainseq,
                                               (unsigned long) position);

  if (currentcc < sainseq->numofchars)
  {
    unsigned long leftcontextcc,
                  putidx = --sainseq->bucketfillptr[currentcc];

    gt_assert(position > 0);
    position--;
    leftcontextcc = gt_sainseq_getchar(sainseq,(unsigned long) position);
    if (sainseq->roundtable != NULL)
    {
      unsigned long t = (currentcc << 1) |
                        (leftcontextcc > currentcc ? 1UL : 0);

      gt_assert (sainseq->roundtable[t] <= sainseq->currentround);
      if (sainseq->roundtable[t] < sainseq->currentround)
      {
        position += sainseq->totallength;
        sainseq->roundtable[t] = sainseq->currentround;
      } else
      {
        position += sainseq->totallength;
      }
    }
    suftab[putidx] = (leftcontextcc > currentcc) ? ~(position+1) : position;
#ifdef SAINSHOWSTATE
    printf("end S-induce: suftab[%lu]=%ld\n",putidx,suftab[putidx]);
#endif
  }
}

static void gt_sain_induceStypes1fromspecialranges(GtSainseq *sainseq,
                                                   const GtEncseq *encseq,
                                                   long *suftab)
{
  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;
    sri = gt_specialrangeiterator_new(encseq,
                                      GT_ISDIRREVERSE(sainseq->readmode)
                                        ? true : false);
    while (gt_specialrangeiterator_next(sri,&range))
    {
      if (GT_ISDIRREVERSE(sainseq->readmode))
      {
        gt_range_reverse(sainseq->totallength,&range);
      }
      if (range.start > 1UL)
      {
        gt_sain_special_singleSinduction1(sainseq,
                                          suftab,
                                          (long) (range.start - 1));
      }
    }
    gt_specialrangeiterator_delete(sri);
  }
}

static void gt_sain_induceStypesuffixes1(GtSainseq *sainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  switch (sainseq->seqtype)
  {
    case GT_SAIN_PLAINSEQ:
      (sainseq->roundtable == NULL
        ? gt_sain_PLAINSEQ_induceStypesuffixes1
        : gt_sain_PLAINSEQ_fast_induceStypesuffixes1)
           (sainseq,sainseq->seq.plainseq,suftab,nonspecialentries);
      break;
    case GT_SAIN_ENCSEQ:
      (sainseq->roundtable == NULL
        ? gt_sain_ENCSEQ_induceStypesuffixes1
        : gt_sain_ENCSEQ_fast_induceStypesuffixes1)
           (sainseq,sainseq->seq.encseq,suftab,nonspecialentries);
      break;
    case GT_SAIN_INTSEQ:
      (sainseq->roundtable == NULL
        ? gt_sain_INTSEQ_induceStypesuffixes1
        : gt_sain_INTSEQ_fast_induceStypesuffixes1)
           (sainseq,sainseq->seq.array,suftab,nonspecialentries);
      break;
  }
}

static void gt_sain_moveSstar2front(unsigned long countSstartype,
                                    long *suftab,
                                    GT_UNUSED unsigned long nonspecialentries)
{
  unsigned long readidx, writeidx = 0;
  long position;

  for (readidx = 0; (position = suftab[readidx]) < 0; readidx++)
  {
    position = ~position;
    suftab[readidx] = position;
    gt_assert ((readidx + 1) < nonspecialentries);
  }
  if (readidx < countSstartype)
  {
    for (writeidx = readidx, readidx++; /* Nothing */; readidx++)
    {
      gt_assert (readidx < nonspecialentries);
      if ((position = suftab[readidx]) < 0)
      {
        position = ~position;
        gt_assert(writeidx < readidx);
        suftab[writeidx++] = position;
        suftab[readidx] = 0;
        if (writeidx == countSstartype)
        {
          break;
        }
      } else
      {
        suftab[readidx] = 0;
      }
    }
  } else
  {
    writeidx = readidx;
  }
  gt_assert(writeidx == countSstartype);
}

static unsigned long gt_sain_fast_moveSstar2front(
                                      unsigned long totallength,
                                      unsigned long countSstartype,
                                      long *suftab,
                                      GT_UNUSED unsigned long nonspecialentries)
{
  unsigned long readidx, namecount = 0, writeidx = 0;
  long position;

  for (readidx = 0; (position = suftab[readidx]) < 0; readidx++)
  {
    position = ~position;
    if (position >= (long) totallength)
    {
      namecount++;
    }
    suftab[readidx] = position;
    gt_assert ((readidx + 1) < nonspecialentries);
  }
  if (readidx < countSstartype)
  {
    for (writeidx = readidx, readidx++; /* Nothing */; readidx++)
    {
      gt_assert (readidx < nonspecialentries);
      if ((position = suftab[readidx]) < 0)
      {
        position = ~position;
        if (position >= (long) totallength)
        {
          namecount++;
        }
        gt_assert(writeidx < readidx);
        suftab[writeidx++] = position;
        suftab[readidx] = 0;
        if (writeidx == countSstartype)
        {
          break;
        }
      } else
      {
        suftab[readidx] = 0;
      }
    }
  } else
  {
    writeidx = readidx;
  }
  gt_assert(writeidx == countSstartype);
  return namecount;
}

static void gt_sain_fast_assignSstarnames(unsigned long totallength,
                                          unsigned long countSstartype,
                                          unsigned long *suftab,
                                          unsigned long numberofnames,
                                          unsigned long nonspecialentries)
{
  unsigned long *suftabptr, *secondhalf = suftab + countSstartype;

  if (numberofnames < countSstartype)
  {
    unsigned long currentname = numberofnames + 1;

    for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
         suftabptr--)
    {
      unsigned long position;

      if ((position = *suftabptr) >= totallength)
      {
        position -= totallength;
        gt_assert(currentname > 0);
        currentname--;
      }
      if (currentname <= numberofnames)
      {
        secondhalf[GT_DIV2(position)] = currentname;
      }
    }
  } else
  {
    for (suftabptr = suftab; suftabptr < suftab + nonspecialentries;
         suftabptr++)
    {
      if (*suftabptr >= totallength)
      {
        *suftabptr -= totallength;
      }
    }
  }
}

static void gt_sain_induceLtypesuffixes2(const GtSainseq *sainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  switch (sainseq->seqtype)
  {
    case GT_SAIN_PLAINSEQ:
      gt_sain_PLAINSEQ_induceLtypesuffixes2(sainseq,sainseq->seq.plainseq,
                                            suftab,nonspecialentries);
      break;
    case GT_SAIN_ENCSEQ:
      gt_sain_ENCSEQ_induceLtypesuffixes2(sainseq,sainseq->seq.encseq,suftab,
                                          nonspecialentries);
      break;
    case GT_SAIN_INTSEQ:
      gt_sain_INTSEQ_induceLtypesuffixes2(sainseq,sainseq->seq.array,
                                          suftab,nonspecialentries);
      break;
  }
}

static void gt_sain_special_singleSinduction2(const GtSainseq *sainseq,
                                              long *suftab,
                                              long position,
                                              GT_UNUSED unsigned long
                                                nonspecialentries)
{
  unsigned long currentcc;

  position--;
  currentcc = gt_sainseq_getchar(sainseq,(unsigned long) position);
  if (currentcc < sainseq->numofchars)
  {
    unsigned long putidx = --sainseq->bucketfillptr[currentcc];

    gt_assert(putidx < nonspecialentries);
    suftab[putidx] = (position == 0 ||
                      gt_sainseq_getchar(sainseq,
                                         (unsigned long)
                                         (position-1)) > currentcc)
                      ? ~position : position;
#ifdef SAINSHOWSTATE
    printf("end S-induce: suftab[%lu]=%ld\n",putidx,suftab[putidx]);
#endif
  }
}

static void gt_sain_induceStypes2fromspecialranges(
                                   const GtSainseq *sainseq,
                                   const GtEncseq *encseq,
                                   long *suftab,
                                   unsigned long nonspecialentries)
{
  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;
    sri = gt_specialrangeiterator_new(encseq,
                                      GT_ISDIRREVERSE(sainseq->readmode)
                                        ? true : false);
    while (gt_specialrangeiterator_next(sri,&range))
    {
      if (GT_ISDIRREVERSE(sainseq->readmode))
      {
        gt_range_reverse(sainseq->totallength,&range);
      }
      if (range.start > 0)
      {
        gt_sain_special_singleSinduction2(sainseq,
                                          suftab,
                                          (long) range.start,
                                          nonspecialentries);
      }
    }
    gt_specialrangeiterator_delete(sri);
  }
}

static void gt_sain_induceStypesuffixes2(const GtSainseq *sainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  switch (sainseq->seqtype)
  {
    case GT_SAIN_PLAINSEQ:
      gt_sain_PLAINSEQ_induceStypesuffixes2(sainseq,sainseq->seq.plainseq,
                                            suftab,nonspecialentries);
      break;
    case GT_SAIN_ENCSEQ:
      gt_sain_ENCSEQ_induceStypesuffixes2(sainseq,sainseq->seq.encseq,suftab,
                                          nonspecialentries);
      break;
    case GT_SAIN_INTSEQ:
      gt_sain_INTSEQ_induceStypesuffixes2(sainseq,sainseq->seq.array,
                                          suftab,nonspecialentries);
      break;
  }
}

static int gt_sain_compare_Sstarstrings(const GtSainseq *sainseq,
                                        unsigned long start1,
                                        unsigned long start2,
                                        unsigned long len)
{
  unsigned long end1 = start1 + len;

  gt_assert(start1 <= sainseq->totallength &&
            start2 <= sainseq->totallength &&
            start1 != start2);

  while (start1 < end1)
  {
    unsigned long cc1, cc2;

    if (start1 == sainseq->totallength)
    {
      gt_assert(start1 > start2);
      return 1;
    }
    if (start2 == sainseq->totallength)
    {
      gt_assert(start1 < start2);
      return -1;
    }
    cc1 = gt_sainseq_getchar(sainseq,start1);
    cc2 = gt_sainseq_getchar(sainseq,start2);
    if (cc1 < cc2)
    {
      return -1;
    }
    if (cc1 > cc2)
    {
      return 1;
    }
    start1++;
    start2++;
  }
  return 0;
}

static int gt_sain_compare_suffixes(const GtSainseq *sainseq,
                                    unsigned long start1,
                                    unsigned long start2)
{
  gt_assert(start1 <= sainseq->totallength &&
            start2 <= sainseq->totallength &&
            start1 != start2);

  while (true)
  {
    unsigned long cc1, cc2;

    if (start1 == sainseq->totallength)
    {
      gt_assert(start1 > start2);
      return 1;
    }
    if (start2 == sainseq->totallength)
    {
      gt_assert(start1 < start2);
      return -1;
    }
    cc1 = gt_sainseq_getchar(sainseq,start1);
    cc2 = gt_sainseq_getchar(sainseq,start2);
    if (cc1 < cc2)
    {
      return -1;
    }
    if (cc1 > cc2)
    {
      return 1;
    }
    start1++;
    start2++;
  }
}

static void gt_sain_setundefined(bool fwd,unsigned long *suftab,
                                 unsigned long start, unsigned long end)
{
  unsigned long *ptr;

  if (fwd)
  {
    for (ptr = suftab + start; ptr <= suftab + end; ptr++)
    {
      *ptr = 0;
    }
  } else
  {
    for (ptr = suftab + end; ptr >= suftab + start; ptr--)
    {
      *ptr = 0;
    }
  }
}

static void gt_sain_assignSstarlength(GtSainseq *sainseq,
                                      unsigned long *lentab)
{
  bool nextisStype = true;
  unsigned long position,
                nextSstartypepos = sainseq->totallength,
                nextcc = GT_UNIQUEINT(sainseq->totallength);

  for (position = sainseq->totallength-1; /* Nothing */; position--)
  {
    unsigned long currentcc = gt_sainseq_getchar(sainseq,position);
    bool currentisStype = (currentcc < nextcc ||
                           (currentcc == nextcc && nextisStype)) ? true : false;
    if (!currentisStype && nextisStype)
    {
      gt_assert(position < nextSstartypepos);
      lentab[GT_DIV2(position+1)] = nextSstartypepos - position;
      nextSstartypepos = position + 1;
    }
    nextisStype = currentisStype;
    nextcc = currentcc;
    if (position == 0)
    {
      break;
    }
  }
}

static unsigned long gt_sain_assignSstarnames(const GtSainseq *sainseq,
                                              unsigned long countSstartype,
                                              unsigned long *suftab)
{
  unsigned long *suftabptr, *secondhalf = suftab + countSstartype,
                previouspos, previouslen, currentname = 1UL;

  previouspos = suftab[0];
  previouslen = secondhalf[GT_DIV2(previouspos)];
  secondhalf[GT_DIV2(previouspos)] = currentname;
  for (suftabptr = suftab + 1UL; suftabptr < suftab + countSstartype;
       suftabptr++)
  {
    int cmp;
    unsigned long currentlen = 0, position = *suftabptr;

    currentlen = secondhalf[GT_DIV2(position)];
    if (previouslen == currentlen)
    {
      cmp = gt_sain_compare_Sstarstrings(sainseq,previouspos,position,
                                         currentlen);
      gt_assert(cmp != 1);
    } else
    {
      cmp = -1;
    }
    if (cmp == -1)
    {
      currentname++;
    }
    /* write the names in order of positions. As the positions of
       the Sstar suffixes differ by at least 2, the used address
       is unique */
    previouslen = currentlen;
    secondhalf[GT_DIV2(position)] = currentname;
    previouspos = position;
  }
  return currentname;
}

static void gt_sain_movenames2front(unsigned long *suftab,
                                    unsigned long numberofsuffixes,
                                    unsigned long totallength)
{
  unsigned long *rptr, *wptr;
  const unsigned long *maxrptr = suftab + numberofsuffixes +
                                 GT_DIV2(totallength);

  for (rptr = wptr = suftab + numberofsuffixes; rptr <= maxrptr; rptr++)
  {
    if (*rptr > 0)
    {
      *(wptr++) = *rptr - 1UL; /* As we have used names with
                                  offset 1 to distinguish them
                                  from the undefined values
                                  signified by 0 */
    }
  }
  gt_assert(wptr == suftab + GT_MULT2(numberofsuffixes));
}

static void gt_sain_checkorder(const GtSainseq *sainseq,
                               const unsigned long *suftab,
                               unsigned long start,
                               unsigned long end)
{
  unsigned long idx;

  for (idx = start+1; idx <= end; idx++)
  {
    int cmp
      = gt_sain_compare_suffixes(sainseq,suftab[idx-1],suftab[idx]);

    if (cmp != -1)
    {
      fprintf(stderr,"%s: check interval [%lu,%lu] at idx=%lu: suffix "
                     "%lu >= %lu\n",__func__,start,end,idx,suftab[idx-1],
                     suftab[idx]);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  }
}

static void gt_sain_expandorder2original(GtSainseq *sainseq,
                                         unsigned long numberofsuffixes,
                                         unsigned long *suftab)
{
  switch (sainseq->seqtype)
  {
    case GT_SAIN_PLAINSEQ:
      gt_sain_PLAINSEQ_expandorder2original(sainseq,sainseq->seq.plainseq,
                                            numberofsuffixes,suftab);
      break;
    case GT_SAIN_ENCSEQ:
      gt_sain_ENCSEQ_expandorder2original(sainseq,sainseq->seq.encseq,
                                          numberofsuffixes,suftab);
      break;
    case GT_SAIN_INTSEQ:
      gt_sain_INTSEQ_expandorder2original(sainseq,sainseq->seq.array,
                                          numberofsuffixes,suftab);
      break;
  }
}

static void gt_sain_determineSstarfirstchardist(GtSainseq *sainseq)
{
  const unsigned long *seqptr;
  unsigned long nextcc = GT_UNIQUEINT(sainseq->totallength);
  bool nextisStype = true;

  gt_assert(sainseq->seqtype == GT_SAIN_INTSEQ);
  for (seqptr = sainseq->seq.array + sainseq->totallength - 1;
       seqptr >= sainseq->seq.array; seqptr--)
  {
    unsigned long currentcc = *seqptr;
    bool currentisStype = (currentcc < nextcc ||
                           (currentcc == nextcc && nextisStype)) ? true : false;
    if (!currentisStype && nextisStype)
    {
      sainseq->sstarfirstcharcount[nextcc]++;
    }
    sainseq->bucketsize[currentcc]++;
    nextisStype = currentisStype;
    nextcc = currentcc;
  }
}

static void gt_sain_insertsortedSstarsuffixes(const GtSainseq *sainseq,
                                              unsigned long *suftab,
                                              unsigned long readidx,
                                              unsigned long nonspecialentries)
{
  unsigned long cc, fillidx = nonspecialentries;

  for (cc = sainseq->numofchars - 1; /* Nothing */; cc--)
  {
    if (sainseq->sstarfirstcharcount[cc] > 0)
    {
      unsigned long putidx = fillidx - 1;

      gt_assert(readidx <= putidx);
      if (readidx < putidx)
      {
        unsigned long offset;

        for (offset = 0; offset < sainseq->sstarfirstcharcount[cc]; offset++)
        {
          suftab[putidx - offset] = suftab[readidx - offset];
          suftab[readidx - offset] = 0;
#ifdef SAINSHOWSTATE
          printf("insertsorted: suftab[%lu]=%lu\n",putidx-offset,
                                                   suftab[putidx-offset]);
          printf("insertsorted: suftab[%lu]=undef\n",readidx-offset);
#endif
        }
      }
    }
    gt_assert(fillidx >= sainseq->bucketsize[cc]);
    fillidx -= sainseq->bucketsize[cc];
    gt_assert(sainseq->bucketsize[cc] >=
              sainseq->sstarfirstcharcount[cc]);
    if (sainseq->bucketsize[cc] > sainseq->sstarfirstcharcount[cc])
    {
      gt_sain_setundefined(false,suftab,fillidx,
                           fillidx + sainseq->bucketsize[cc] -
                           sainseq->sstarfirstcharcount[cc] - 1);
    }
    readidx -= sainseq->sstarfirstcharcount[cc];
    if (cc == 0)
    {
      break;
    }
  }
}

static void gt_sain_filltailsuffixes(unsigned long *suftabtail,
                                     const GtEncseq *encseq,
                                     GtReadmode readmode)
{
  unsigned long specialcharacters = gt_encseq_specialcharacters(encseq),
                totallength = gt_encseq_total_length(encseq);

  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;
    unsigned long countspecial = 0;

    sri = gt_specialrangeiterator_new(encseq,
                                      GT_ISDIRREVERSE(readmode) ? false : true);
    while (gt_specialrangeiterator_next(sri,&range))
    {
      unsigned long idx;

      if (GT_ISDIRREVERSE(readmode))
      {
        gt_range_reverse(totallength,&range);
      }
      for (idx = range.start; idx < range.end; idx++)
      {
        gt_assert(countspecial < specialcharacters && idx < totallength);
        suftabtail[countspecial++] = idx;
      }
    }
    gt_assert(countspecial == specialcharacters);
    gt_specialrangeiterator_delete(sri);
  }
  suftabtail[specialcharacters] = totallength;
}

static void gt_sain_rec_sortsuffixes(unsigned int level,
                                     GtSainseq *sainseq,
                                     unsigned long *suftab,
                                     unsigned long firstusable,
                                     unsigned long nonspecialentries,
                                     unsigned long suftabentries,
                                     bool intermediatecheck,
                                     bool finalcheck,
                                     GtLogger *logger,
                                     GtTimer *timer)
{
  unsigned long countSstartype;

  GT_SAIN_SHOWTIMER("insert Sstar suffixes");
  countSstartype = gt_sain_insertSstarsuffixes(sainseq,suftab,logger);
  gt_logger_log(logger,"level %u: sort sequence of length %lu over "
                       "%lu symbols (%.2f)",
          level,sainseq->totallength,sainseq->numofchars,
          (double) sainseq->numofchars/sainseq->totallength);
  gt_logger_log(logger,"Sstar-type: %lu (%.2f)",countSstartype,
                 (double) countSstartype/sainseq->totallength);
  if (countSstartype > 0)
  {
    unsigned long numberofnames;

    if (sainseq->roundtable != NULL)
    {
      gt_sain_incrementfirstSstar(sainseq,suftab);
    }
    gt_sain_startbuckets(sainseq);
    GT_SAIN_SHOWTIMER(sainseq->roundtable == NULL
                      ? "induce L suffixes" : "fast induce L suffixes");

    gt_sain_induceLtypesuffixes1(sainseq,(long *) suftab,nonspecialentries);
    if (sainseq->roundtable != NULL)
    {
      gt_sain_adjustsuftab(sainseq->totallength,(long *) suftab,
                           nonspecialentries);
    }
    gt_sain_endbuckets(sainseq);
    GT_SAIN_SHOWTIMER(sainseq->roundtable == NULL
                      ? "induce S suffixes" : "fast induce S suffixes");
    gt_sain_induceStypesuffixes1(sainseq,(long *) suftab,nonspecialentries);
    if (sainseq->roundtable == NULL)
    {
      GT_SAIN_SHOWTIMER("simple moverSstar2front");
      gt_sain_moveSstar2front(countSstartype,(long *) suftab,nonspecialentries);
      GT_SAIN_SHOWTIMER("simple assignSstarlength");
      gt_sain_assignSstarlength(sainseq,suftab + countSstartype);
      GT_SAIN_SHOWTIMER("simple assignSstarnames");
      numberofnames = gt_sain_assignSstarnames(sainseq,countSstartype,suftab);
    } else
    {
      GT_SAIN_SHOWTIMER("fast moveSstar2front");
      numberofnames = gt_sain_fast_moveSstar2front(sainseq->totallength,
                                                   countSstartype,
                                                   (long *) suftab,
                                                   nonspecialentries);
      if (!sainseq->roundtablepoints2suftab)
      {
        gt_free(sainseq->roundtable);
        sainseq->roundtable = NULL;
      }
      GT_SAIN_SHOWTIMER("fast assignSstarnames");
      gt_sain_fast_assignSstarnames(sainseq->totallength,countSstartype,
                                    suftab,numberofnames,nonspecialentries);
    }
    gt_assert(numberofnames <= countSstartype);
    if (numberofnames < countSstartype)
    {
    /* Now the name sequence is in the range from
       countSstartype .. 2 * countSstartype - 1 */
      unsigned long *subseq = suftab + countSstartype;
      GtSainseq *sainseq_rec;

      GT_SAIN_SHOWTIMER("movenames2front");
      gt_sain_setundefined(true,suftab,0,countSstartype-1);
      gt_sain_movenames2front(suftab,countSstartype,sainseq->totallength);
      if (level == 0)
      {
        firstusable = GT_MULT2(countSstartype);
      }
      sainseq_rec = gt_sainseq_new_from_array(subseq,countSstartype,
                                              numberofnames,
                                              suftab,
                                              firstusable,
                                              suftabentries);
      gt_sain_rec_sortsuffixes(level+1,
                               sainseq_rec,
                               suftab,
                               firstusable,
                               countSstartype,
                               suftabentries,
                               intermediatecheck,
                               finalcheck,
                               logger,
                               timer);
      gt_sainseq_delete(sainseq_rec);
      GT_SAIN_SHOWTIMER("expandorder2original");
      gt_sain_expandorder2original(sainseq,countSstartype,
                                   suftab);
    } else
    {
      if (sainseq->seqtype == GT_SAIN_INTSEQ)
      {
        unsigned long charidx;
        gt_assert(sainseq->sstarfirstcharcount == NULL);
        sainseq->sstarfirstcharcount = sainseq->bucketfillptr;

        for (charidx = 0; charidx < sainseq->numofchars; charidx++)
        {
          sainseq->sstarfirstcharcount[charidx] = 0;
          sainseq->bucketsize[charidx] = 0;
        }
        gt_sain_determineSstarfirstchardist(sainseq);
      }
    }
  }
  if (intermediatecheck && countSstartype > 0)
  {
    gt_sain_checkorder(sainseq,suftab,0,countSstartype-1);
  }
  GT_SAIN_SHOWTIMER("insert sorted Sstar suffixes");
  if (countSstartype > 0)
  {
    gt_sain_insertsortedSstarsuffixes (sainseq, suftab, countSstartype - 1,
                                       nonspecialentries);
  }
  gt_sain_startbuckets(sainseq);
  GT_SAIN_SHOWTIMER("final induce L suffixes");
  gt_sain_induceLtypesuffixes2(sainseq,(long *) suftab,nonspecialentries);
  gt_sain_endbuckets(sainseq);
  GT_SAIN_SHOWTIMER("final induce S suffixes");
  gt_sain_induceStypesuffixes2(sainseq,(long *) suftab,nonspecialentries);
  if (nonspecialentries > 0)
  {
    if (intermediatecheck)
    {
      gt_sain_checkorder(sainseq,suftab,0,nonspecialentries-1);
    }
    if (sainseq->seqtype == GT_SAIN_ENCSEQ && finalcheck)
    {
      GT_SAIN_SHOWTIMER("fill tail suffixes");
      gt_sain_filltailsuffixes(suftab + nonspecialentries,
                               sainseq->seq.encseq,
                               sainseq->readmode);
      GT_SAIN_SHOWTIMER("check suffix order");
      gt_suftab_lightweightcheck(sainseq->seq.encseq,
                                 sainseq->readmode,
                                 sainseq->totallength,
                                 suftab,
                                 NULL);
    }
  }
}

void gt_sain_encseq_sortsuffixes(const GtEncseq *encseq,
                                 GtReadmode readmode,
                                 bool intermediatecheck,
                                 bool finalcheck,
                                 GtLogger *logger,
                                 GtTimer *timer)
{
  unsigned long nonspecialentries, suftabentries, totallength, *suftab;
  GtSainseq *sainseq;

  totallength = gt_encseq_total_length(encseq);
  nonspecialentries = totallength - gt_encseq_specialcharacters(encseq);
  suftabentries = totallength+1;
  suftab = gt_calloc((size_t) suftabentries,sizeof (*suftab));
  sainseq = gt_sainseq_new_from_encseq(encseq,readmode);
  gt_sain_rec_sortsuffixes(0,
                           sainseq,
                           suftab,
                           0,
                           nonspecialentries,
                           suftabentries,
                           intermediatecheck,
                           finalcheck,
                           logger,
                           timer);
#ifdef GT_SAIN_WITHCOUNTS
  printf("countcharaccess=%lu (%.2f)\n",gt_sain_countcharaccess,
          (double) gt_sain_countcharaccess/sainseq->totallength);
#endif
  gt_sainseq_delete(sainseq);
  gt_free(suftab);
}

void gt_sain_plain_sortsuffixes(const GtUchar *plainseq,
                                unsigned long len,
                                bool intermediatecheck,
                                GtLogger *logger,
                                GtTimer *timer)
{
  unsigned long suftabentries, *suftab;
  GtSainseq *sainseq;

  suftabentries = len+1;
  suftab = gt_calloc((size_t) suftabentries,sizeof (*suftab));
  sainseq = gt_sainseq_new_from_plainseq(plainseq,len);
  gt_sain_rec_sortsuffixes(0,
                           sainseq,
                           suftab,
                           0,
                           sainseq->totallength,
                           suftabentries,
                           intermediatecheck,
                           false,
                           logger,
                           timer);
#ifdef GT_SAIN_WITHCOUNTS
  printf("countcharaccess=%lu (%.2f)\n",gt_sain_countcharaccess,
          (double) gt_sain_countcharaccess/sainseq->totallength);
#endif
  gt_sainseq_delete(sainseq);
  gt_free(suftab);
}
genometools-1.5.1/src/match/sfx-sain.h000066400000000000000000000030361211610345200176320ustar00rootroot00000000000000/*
  Copyright (c) 2012 Stefan Kurtz 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_SAIN_H
#define SFX_SAIN_H

#include "core/timer_api.h"
#include "core/logger_api.h"
#include "core/encseq.h"

void gt_sain_encseq_sortsuffixes(const GtEncseq *encseq,
                                 GtReadmode readmode,
                                 bool intermediatecheck,
                                 bool finalcheck,
                                 GtLogger *logger,
                                 GtTimer *timer);

void gt_sain_plain_sortsuffixes(const GtUchar *plainseq,
                                unsigned long len,
                                bool intermediatecheck,
                                GtLogger *logger,
                                GtTimer *timer);

#endif
genometools-1.5.1/src/match/sfx-sain.inc000066400000000000000000001253621211610345200201630ustar00rootroot00000000000000static unsigned long gt_sain_PLAINSEQ_insertSstarsuffixes(GtSainseq *sainseq,
                                                 const GtUchar *plainseq,
                                                 unsigned long *suftab,
                                                 GtLogger *logger)
{
  unsigned long position,
                nextcc = GT_UNIQUEINT(sainseq->totallength),
                countSstartype = 0,
                *fillptr = sainseq->bucketfillptr;
  GtSainbuffer *sainbuffer = gt_sainbuffer_new(suftab,fillptr,
                                               sainseq->numofchars,logger);
  bool nextisStype = true;

  gt_sain_endbuckets(sainseq);
  for (position = sainseq->totallength-1; /* Nothing */; position--)
  {
    unsigned long currentcc = (unsigned long)
plainseq[position];
    bool currentisStype = (currentcc < nextcc ||
                           (currentcc == nextcc && nextisStype)) ? true : false;
    if (!currentisStype && nextisStype)
    {
      countSstartype++;
      if (sainseq->sstarfirstcharcount != NULL)
      {
        sainseq->sstarfirstcharcount[nextcc]++;
      }
      if (sainbuffer != NULL)
      {
        gt_sainbuffer_update(sainbuffer,nextcc,position);
      } else
      {
        suftab[--fillptr[nextcc]] = position;
      }
#undef SAINSHOWSTATE
#ifdef SAINSHOWSTATE
      printf("Sstar.suftab[%lu]=%lu\n",fillptr[nextcc],position+1);
#endif
    }
    nextisStype = currentisStype;
    nextcc = currentcc;
    if (position == 0)
    {
      break;
    }
  }
  gt_sainbuffer_flushall(sainbuffer);
  gt_sainbuffer_delete(sainbuffer);
  gt_assert(GT_MULT2(countSstartype) <= sainseq->totallength);
  return countSstartype;
}

static void gt_sain_PLAINSEQ_fast_induceLtypesuffixes1(GtSainseq *sainseq,
                                                 const GtUchar *plainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_assert(sainseq->roundtable != NULL);
  for (suftabptr = suftab, sainseq->currentround = 0;
       suftabptr < suftab + nonspecialentries; suftabptr++)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc;

      if (position >= (long) sainseq->totallength)
      {
        sainseq->currentround++;
        position -= (long) sainseq->totallength;
      }
      currentcc = (unsigned long)
plainseq[(unsigned long) position];
      if (currentcc < sainseq->numofchars)
      {
        if (position > 0)
        {
          unsigned long t, leftcontextcc;

          gt_assert(position > 0);
          position--;
          leftcontextcc = (unsigned long)
plainseq[(unsigned long) position];
          t = (currentcc << 1) | (leftcontextcc < currentcc ? 1UL : 0);
          gt_assert(currentcc > 0 &&
                    sainseq->roundtable[t] <= sainseq->currentround);
          if (sainseq->roundtable[t] < sainseq->currentround)
          {
            position += (long) sainseq->totallength;
            sainseq->roundtable[t] = sainseq->currentround;
          }
          GT_SAINUPDATEBUCKETPTR(currentcc);
          /* negative => position does not derive L-suffix
             positive => position may derive L-suffix */
          gt_assert(suftabptr < bucketptr);
          *bucketptr++ = (t & 1UL) ? ~position : position;
          *suftabptr = 0;
#ifdef SAINSHOWSTATE
          gt_assert(bucketptr != NULL);
          printf("L-induce: suftab[%lu]=%ld\n",
                  (unsigned long) (bucketptr-1-suftab),*(bucketptr-1));
#endif
        }
      } else
      {
        *suftabptr = 0;
      }
    } else
    {
      if (position < 0)
      {
        *suftabptr = ~position;
      }
    }
  }
}

static void gt_sain_PLAINSEQ_induceLtypesuffixes1(GtSainseq *sainseq,
                                                 const GtUchar *plainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_assert(sainseq->roundtable == NULL);
  for (suftabptr = suftab; suftabptr < suftab + nonspecialentries; suftabptr++)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc = (unsigned long)
plainseq[(unsigned long) position];
      if (currentcc < sainseq->numofchars)
      {
        if (position > 0)
        {
          unsigned long leftcontextcc;

          gt_assert(position > 0);
          position--;
          leftcontextcc = (unsigned long)
plainseq[(unsigned long) position];
          GT_SAINUPDATEBUCKETPTR(currentcc);
          /* negative => position does not derive L-suffix
             positive => position may derive L-suffix */
          gt_assert(suftabptr < bucketptr);
          *bucketptr++ = (leftcontextcc < currentcc) ? ~position : position;
          *suftabptr = 0;
#ifdef SAINSHOWSTATE
          gt_assert(bucketptr != NULL);
          printf("L-induce: suftab[%lu]=%ld\n",
                  (unsigned long) (bucketptr-1-suftab),*(bucketptr-1));
#endif
        }
      } else
      {
        *suftabptr = 0;
      }
    } else
    {
      if (position < 0)
      {
        *suftabptr = ~position;
      }
    }
  }
}

static void gt_sain_PLAINSEQ_fast_induceStypesuffixes1(GtSainseq *sainseq,
                                                 const GtUchar *plainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_assert(sainseq->roundtable != NULL);
  gt_sain_special_singleSinduction1(sainseq,
                                    suftab,
                                    (long) (sainseq->totallength-1));
  if (sainseq->seqtype == GT_SAIN_ENCSEQ)
  {
    gt_sain_induceStypes1fromspecialranges(sainseq,
                                           sainseq->seq.encseq,
                                           suftab);
  }
  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if ((position = *suftabptr) > 0)
    {
      if (position >= (long) sainseq->totallength)
      {
        sainseq->currentround++;
        position -= (long) sainseq->totallength;
      }
      if (position > 0)
      {
        unsigned long currentcc = (unsigned long)
plainseq[(unsigned long) position];

        if (currentcc < sainseq->numofchars)
        {
          unsigned long t, leftcontextcc;

          position--;
          leftcontextcc = (unsigned long)
plainseq[(unsigned long) position];
          t = (currentcc << 1) | (leftcontextcc > currentcc ? 1UL : 0);
          gt_assert(sainseq->roundtable[t] <= sainseq->currentround);
          if (sainseq->roundtable[t] < sainseq->currentround)
          {
            position += sainseq->totallength;
            sainseq->roundtable[t] = sainseq->currentround;
          }
          GT_SAINUPDATEBUCKETPTR(currentcc);
          gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
          *(--bucketptr) = (t & 1UL) ? ~(position+1) : position;
#ifdef SAINSHOWSTATE
          printf("S-induce: suftab[%lu]=%ld\n",
                  (unsigned long) (bucketptr - suftab),*bucketptr);
#endif
        }
      }
      *suftabptr = 0;
    }
  }
}

static void gt_sain_PLAINSEQ_induceStypesuffixes1(GtSainseq *sainseq,
                                                 const GtUchar *plainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_assert(sainseq->roundtable == NULL);
  gt_sain_special_singleSinduction1(sainseq,
                                    suftab,
                                    (long) (sainseq->totallength-1));
  if (sainseq->seqtype == GT_SAIN_ENCSEQ)
  {
    gt_sain_induceStypes1fromspecialranges(sainseq,
                                           sainseq->seq.encseq,
                                           suftab);
  }
  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc = (unsigned long)
plainseq[(unsigned long) position];

      if (currentcc < sainseq->numofchars)
      {
        unsigned long leftcontextcc;

        position--;
        leftcontextcc = (unsigned long)
plainseq[(unsigned long) position];
        GT_SAINUPDATEBUCKETPTR(currentcc);
        gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
        *(--bucketptr) = (leftcontextcc > currentcc)
                          ? ~(position+1) : position;
#ifdef SAINSHOWSTATE
        printf("S-induce: suftab[%lu]=%ld\n",
               (unsigned long) (bucketptr - suftab),*bucketptr);
#endif
      }
      *suftabptr = 0;
    }
  }
}

static void gt_sain_PLAINSEQ_induceLtypesuffixes2(const GtSainseq *sainseq,
                                                 const GtUchar *plainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  for (suftabptr = suftab; suftabptr < suftab + nonspecialentries; suftabptr++)
  {
    position = *suftabptr;
    *suftabptr = ~position;
    if (position > 0)
    {
      unsigned long currentcc;

      position--;
      currentcc = (unsigned long)
plainseq[(unsigned long) position];
      if (currentcc < sainseq->numofchars)
      {
        gt_assert(currentcc > 0);
        GT_SAINUPDATEBUCKETPTR(currentcc);
        gt_assert(bucketptr != NULL && suftabptr < bucketptr);
        *bucketptr++ = (position > 0 &&
                        ((unsigned long)
plainseq[(unsigned long) (position-1)])
                                            < currentcc)
                        ? ~position : position;
#ifdef SAINSHOWSTATE
        gt_assert(bucketptr != NULL);
        printf("L-induce: suftab[%lu]=%ld\n",
               (unsigned long) (bucketptr-1-suftab),*(bucketptr-1));
#endif
      }
    }
  }
}

static void gt_sain_PLAINSEQ_induceStypesuffixes2(const GtSainseq *sainseq,
                                                 const GtUchar *plainseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_sain_special_singleSinduction2(sainseq,
                                    suftab,
                                    (long) sainseq->totallength,
                                    nonspecialentries);
  if (sainseq->seqtype == GT_SAIN_ENCSEQ)
  {
    gt_sain_induceStypes2fromspecialranges(sainseq,
                                           sainseq->seq.encseq,
                                           suftab,
                                           nonspecialentries);
  }
  if (nonspecialentries == 0)
  {
    return;
  }
  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc;

      position--;
      currentcc = (unsigned long)
plainseq[(unsigned long) position];
      if (currentcc < sainseq->numofchars)
      {
        GT_SAINUPDATEBUCKETPTR(currentcc);
        gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
        *(--bucketptr) = (position == 0 ||
                          ((unsigned long)
plainseq[(unsigned long) (position-1)])
                                             > currentcc)
                         ? ~position : position;
#ifdef SAINSHOWSTATE
        gt_assert(bucketptr != NULL);
        printf("S-induce: suftab[%lu]=%ld\n",
                (unsigned long) (bucketptr-suftab),*bucketptr);
#endif
      }
    } else
    {
      *suftabptr = ~position;
    }
  }
}

static void gt_sain_PLAINSEQ_expandorder2original(GtSainseq *sainseq,
                                                 const GtUchar *plainseq,
                                         unsigned long numberofsuffixes,
                                         unsigned long *suftab)
{
  unsigned long *suftabptr, position,
                writeidx = numberofsuffixes - 1,
                nextcc = GT_UNIQUEINT(sainseq->totallength),
                *sstarsuffixes = suftab + numberofsuffixes;
  unsigned long *sstarfirstcharcount = NULL, *bucketsize = NULL;
  bool nextisStype = true;

  if (sainseq->seqtype == GT_SAIN_INTSEQ)
  {
    unsigned long charidx;

    gt_assert(sainseq->sstarfirstcharcount == NULL);
    sstarfirstcharcount = sainseq->sstarfirstcharcount
                        = sainseq->bucketfillptr;
    bucketsize = sainseq->bucketsize;
    for (charidx = 0; charidx < sainseq->numofchars; charidx++)
    {
      sstarfirstcharcount[charidx] = 0;
      bucketsize[charidx] = 0;
    }
  }
  for (position = sainseq->totallength-1; /* Nothing */; position--)
  {
    unsigned long currentcc = (unsigned long)
plainseq[position];
    bool currentisStype = (currentcc < nextcc ||
                           (currentcc == nextcc && nextisStype)) ? true : false;

    if (!currentisStype && nextisStype)
    {
      if (sstarfirstcharcount != NULL)
      {
        sstarfirstcharcount[nextcc]++;
      }
      sstarsuffixes[writeidx--] = position+1;
    }
    if (bucketsize != NULL)
    {
      bucketsize[currentcc]++;
    }
    nextisStype = currentisStype;
    nextcc = currentcc;
    if (position == 0)
    {
      break;
    }
  }
  for (suftabptr = suftab; suftabptr < suftab + numberofsuffixes; suftabptr++)
  {
    *suftabptr = sstarsuffixes[*suftabptr];
  }
}
static unsigned long gt_sain_ENCSEQ_insertSstarsuffixes(GtSainseq *sainseq,
                                                 const GtEncseq *encseq,
                                                 unsigned long *suftab,
                                                 GtLogger *logger)
{
  unsigned long position,
                nextcc = GT_UNIQUEINT(sainseq->totallength),
                countSstartype = 0,
                *fillptr = sainseq->bucketfillptr;
  GtSainbuffer *sainbuffer = gt_sainbuffer_new(suftab,fillptr,
                                               sainseq->numofchars,logger);
  GtUchar tmpcc;
bool nextisStype = true;

  gt_sain_endbuckets(sainseq);
  for (position = sainseq->totallength-1; /* Nothing */; position--)
  {
    unsigned long currentcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
position,
sainseq->readmode))
  ? GT_UNIQUEINT(position) : (unsigned long) tmpcc;
    bool currentisStype = (currentcc < nextcc ||
                           (currentcc == nextcc && nextisStype)) ? true : false;
    if (!currentisStype && nextisStype)
    {
      countSstartype++;
      if (sainseq->sstarfirstcharcount != NULL)
      {
        sainseq->sstarfirstcharcount[nextcc]++;
      }
      if (sainbuffer != NULL)
      {
        gt_sainbuffer_update(sainbuffer,nextcc,position);
      } else
      {
        suftab[--fillptr[nextcc]] = position;
      }
#undef SAINSHOWSTATE
#ifdef SAINSHOWSTATE
      printf("Sstar.suftab[%lu]=%lu\n",fillptr[nextcc],position+1);
#endif
    }
    nextisStype = currentisStype;
    nextcc = currentcc;
    if (position == 0)
    {
      break;
    }
  }
  gt_sainbuffer_flushall(sainbuffer);
  gt_sainbuffer_delete(sainbuffer);
  gt_assert(GT_MULT2(countSstartype) <= sainseq->totallength);
  return countSstartype;
}

static void gt_sain_ENCSEQ_fast_induceLtypesuffixes1(GtSainseq *sainseq,
                                                 const GtEncseq *encseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  GtUchar tmpcc;
long position;

  gt_assert(sainseq->roundtable != NULL);
  for (suftabptr = suftab, sainseq->currentround = 0;
       suftabptr < suftab + nonspecialentries; suftabptr++)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc;

      if (position >= (long) sainseq->totallength)
      {
        sainseq->currentround++;
        position -= (long) sainseq->totallength;
      }
      currentcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;
      if (currentcc < sainseq->numofchars)
      {
        if (position > 0)
        {
          unsigned long t, leftcontextcc;

          gt_assert(position > 0);
          position--;
          leftcontextcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;
          t = (currentcc << 1) | (leftcontextcc < currentcc ? 1UL : 0);
          gt_assert(currentcc > 0 &&
                    sainseq->roundtable[t] <= sainseq->currentround);
          if (sainseq->roundtable[t] < sainseq->currentround)
          {
            position += (long) sainseq->totallength;
            sainseq->roundtable[t] = sainseq->currentround;
          }
          GT_SAINUPDATEBUCKETPTR(currentcc);
          /* negative => position does not derive L-suffix
             positive => position may derive L-suffix */
          gt_assert(suftabptr < bucketptr);
          *bucketptr++ = (t & 1UL) ? ~position : position;
          *suftabptr = 0;
#ifdef SAINSHOWSTATE
          gt_assert(bucketptr != NULL);
          printf("L-induce: suftab[%lu]=%ld\n",
                  (unsigned long) (bucketptr-1-suftab),*(bucketptr-1));
#endif
        }
      } else
      {
        *suftabptr = 0;
      }
    } else
    {
      if (position < 0)
      {
        *suftabptr = ~position;
      }
    }
  }
}

static void gt_sain_ENCSEQ_induceLtypesuffixes1(GtSainseq *sainseq,
                                                 const GtEncseq *encseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  GtUchar tmpcc;
long position;

  gt_assert(sainseq->roundtable == NULL);
  for (suftabptr = suftab; suftabptr < suftab + nonspecialentries; suftabptr++)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;
      if (currentcc < sainseq->numofchars)
      {
        if (position > 0)
        {
          unsigned long leftcontextcc;

          gt_assert(position > 0);
          position--;
          leftcontextcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;
          GT_SAINUPDATEBUCKETPTR(currentcc);
          /* negative => position does not derive L-suffix
             positive => position may derive L-suffix */
          gt_assert(suftabptr < bucketptr);
          *bucketptr++ = (leftcontextcc < currentcc) ? ~position : position;
          *suftabptr = 0;
#ifdef SAINSHOWSTATE
          gt_assert(bucketptr != NULL);
          printf("L-induce: suftab[%lu]=%ld\n",
                  (unsigned long) (bucketptr-1-suftab),*(bucketptr-1));
#endif
        }
      } else
      {
        *suftabptr = 0;
      }
    } else
    {
      if (position < 0)
      {
        *suftabptr = ~position;
      }
    }
  }
}

static void gt_sain_ENCSEQ_fast_induceStypesuffixes1(GtSainseq *sainseq,
                                                 const GtEncseq *encseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  GtUchar tmpcc;
long position;

  gt_assert(sainseq->roundtable != NULL);
  gt_sain_special_singleSinduction1(sainseq,
                                    suftab,
                                    (long) (sainseq->totallength-1));
  if (sainseq->seqtype == GT_SAIN_ENCSEQ)
  {
    gt_sain_induceStypes1fromspecialranges(sainseq,
                                           sainseq->seq.encseq,
                                           suftab);
  }
  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if ((position = *suftabptr) > 0)
    {
      if (position >= (long) sainseq->totallength)
      {
        sainseq->currentround++;
        position -= (long) sainseq->totallength;
      }
      if (position > 0)
      {
        unsigned long currentcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;

        if (currentcc < sainseq->numofchars)
        {
          unsigned long t, leftcontextcc;

          position--;
          leftcontextcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;
          t = (currentcc << 1) | (leftcontextcc > currentcc ? 1UL : 0);
          gt_assert(sainseq->roundtable[t] <= sainseq->currentround);
          if (sainseq->roundtable[t] < sainseq->currentround)
          {
            position += sainseq->totallength;
            sainseq->roundtable[t] = sainseq->currentround;
          }
          GT_SAINUPDATEBUCKETPTR(currentcc);
          gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
          *(--bucketptr) = (t & 1UL) ? ~(position+1) : position;
#ifdef SAINSHOWSTATE
          printf("S-induce: suftab[%lu]=%ld\n",
                  (unsigned long) (bucketptr - suftab),*bucketptr);
#endif
        }
      }
      *suftabptr = 0;
    }
  }
}

static void gt_sain_ENCSEQ_induceStypesuffixes1(GtSainseq *sainseq,
                                                 const GtEncseq *encseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  GtUchar tmpcc;
long position;

  gt_assert(sainseq->roundtable == NULL);
  gt_sain_special_singleSinduction1(sainseq,
                                    suftab,
                                    (long) (sainseq->totallength-1));
  if (sainseq->seqtype == GT_SAIN_ENCSEQ)
  {
    gt_sain_induceStypes1fromspecialranges(sainseq,
                                           sainseq->seq.encseq,
                                           suftab);
  }
  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;

      if (currentcc < sainseq->numofchars)
      {
        unsigned long leftcontextcc;

        position--;
        leftcontextcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;
        GT_SAINUPDATEBUCKETPTR(currentcc);
        gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
        *(--bucketptr) = (leftcontextcc > currentcc)
                          ? ~(position+1) : position;
#ifdef SAINSHOWSTATE
        printf("S-induce: suftab[%lu]=%ld\n",
               (unsigned long) (bucketptr - suftab),*bucketptr);
#endif
      }
      *suftabptr = 0;
    }
  }
}

static void gt_sain_ENCSEQ_induceLtypesuffixes2(const GtSainseq *sainseq,
                                                 const GtEncseq *encseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  GtUchar tmpcc;
long position;

  for (suftabptr = suftab; suftabptr < suftab + nonspecialentries; suftabptr++)
  {
    position = *suftabptr;
    *suftabptr = ~position;
    if (position > 0)
    {
      unsigned long currentcc;

      position--;
      currentcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;
      if (currentcc < sainseq->numofchars)
      {
        gt_assert(currentcc > 0);
        GT_SAINUPDATEBUCKETPTR(currentcc);
        gt_assert(bucketptr != NULL && suftabptr < bucketptr);
        *bucketptr++ = (position > 0 &&
                        (ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) (position-1),
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) (position-1)) : (unsigned long) tmpcc)
                                            < currentcc)
                        ? ~position : position;
#ifdef SAINSHOWSTATE
        gt_assert(bucketptr != NULL);
        printf("L-induce: suftab[%lu]=%ld\n",
               (unsigned long) (bucketptr-1-suftab),*(bucketptr-1));
#endif
      }
    }
  }
}

static void gt_sain_ENCSEQ_induceStypesuffixes2(const GtSainseq *sainseq,
                                                 const GtEncseq *encseq,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  GtUchar tmpcc;
long position;

  gt_sain_special_singleSinduction2(sainseq,
                                    suftab,
                                    (long) sainseq->totallength,
                                    nonspecialentries);
  if (sainseq->seqtype == GT_SAIN_ENCSEQ)
  {
    gt_sain_induceStypes2fromspecialranges(sainseq,
                                           sainseq->seq.encseq,
                                           suftab,
                                           nonspecialentries);
  }
  if (nonspecialentries == 0)
  {
    return;
  }
  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc;

      position--;
      currentcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) position,
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) position) : (unsigned long) tmpcc;
      if (currentcc < sainseq->numofchars)
      {
        GT_SAINUPDATEBUCKETPTR(currentcc);
        gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
        *(--bucketptr) = (position == 0 ||
                          (ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
(unsigned long) (position-1),
sainseq->readmode))
  ? GT_UNIQUEINT((unsigned long) (position-1)) : (unsigned long) tmpcc)
                                             > currentcc)
                         ? ~position : position;
#ifdef SAINSHOWSTATE
        gt_assert(bucketptr != NULL);
        printf("S-induce: suftab[%lu]=%ld\n",
                (unsigned long) (bucketptr-suftab),*bucketptr);
#endif
      }
    } else
    {
      *suftabptr = ~position;
    }
  }
}

static void gt_sain_ENCSEQ_expandorder2original(GtSainseq *sainseq,
                                                 const GtEncseq *encseq,
                                         unsigned long numberofsuffixes,
                                         unsigned long *suftab)
{
  unsigned long *suftabptr, position,
                writeidx = numberofsuffixes - 1,
                nextcc = GT_UNIQUEINT(sainseq->totallength),
                *sstarsuffixes = suftab + numberofsuffixes;
  unsigned long *sstarfirstcharcount = NULL, *bucketsize = NULL;
  GtUchar tmpcc;
bool nextisStype = true;

  if (sainseq->seqtype == GT_SAIN_INTSEQ)
  {
    unsigned long charidx;

    gt_assert(sainseq->sstarfirstcharcount == NULL);
    sstarfirstcharcount = sainseq->sstarfirstcharcount
                        = sainseq->bucketfillptr;
    bucketsize = sainseq->bucketsize;
    for (charidx = 0; charidx < sainseq->numofchars; charidx++)
    {
      sstarfirstcharcount[charidx] = 0;
      bucketsize[charidx] = 0;
    }
  }
  for (position = sainseq->totallength-1; /* Nothing */; position--)
  {
    unsigned long currentcc = ISSPECIAL(tmpcc = gt_encseq_get_encoded_char(
encseq,
position,
sainseq->readmode))
  ? GT_UNIQUEINT(position) : (unsigned long) tmpcc;
    bool currentisStype = (currentcc < nextcc ||
                           (currentcc == nextcc && nextisStype)) ? true : false;

    if (!currentisStype && nextisStype)
    {
      if (sstarfirstcharcount != NULL)
      {
        sstarfirstcharcount[nextcc]++;
      }
      sstarsuffixes[writeidx--] = position+1;
    }
    if (bucketsize != NULL)
    {
      bucketsize[currentcc]++;
    }
    nextisStype = currentisStype;
    nextcc = currentcc;
    if (position == 0)
    {
      break;
    }
  }
  for (suftabptr = suftab; suftabptr < suftab + numberofsuffixes; suftabptr++)
  {
    *suftabptr = sstarsuffixes[*suftabptr];
  }
}
static unsigned long gt_sain_INTSEQ_insertSstarsuffixes(GtSainseq *sainseq,
                                                 const unsigned long *array,
                                                 unsigned long *suftab,
                                                 GtLogger *logger)
{
  unsigned long position,
                nextcc = GT_UNIQUEINT(sainseq->totallength),
                countSstartype = 0,
                *fillptr = sainseq->bucketfillptr;
  GtSainbuffer *sainbuffer = gt_sainbuffer_new(suftab,fillptr,
                                               sainseq->numofchars,logger);
  bool nextisStype = true;

  gt_sain_endbuckets(sainseq);
  for (position = sainseq->totallength-1; /* Nothing */; position--)
  {
    unsigned long currentcc = array[position];
    bool currentisStype = (currentcc < nextcc ||
                           (currentcc == nextcc && nextisStype)) ? true : false;
    if (!currentisStype && nextisStype)
    {
      countSstartype++;
      if (sainseq->sstarfirstcharcount != NULL)
      {
        sainseq->sstarfirstcharcount[nextcc]++;
      }
      if (sainbuffer != NULL)
      {
        gt_sainbuffer_update(sainbuffer,nextcc,position);
      } else
      {
        suftab[--fillptr[nextcc]] = position;
      }
#undef SAINSHOWSTATE
#ifdef SAINSHOWSTATE
      printf("Sstar.suftab[%lu]=%lu\n",fillptr[nextcc],position+1);
#endif
    }
    nextisStype = currentisStype;
    nextcc = currentcc;
    if (position == 0)
    {
      break;
    }
  }
  gt_sainbuffer_flushall(sainbuffer);
  gt_sainbuffer_delete(sainbuffer);
  gt_assert(GT_MULT2(countSstartype) <= sainseq->totallength);
  return countSstartype;
}

static void gt_sain_INTSEQ_fast_induceLtypesuffixes1(GtSainseq *sainseq,
                                                 const unsigned long *array,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_assert(sainseq->roundtable != NULL);
  for (suftabptr = suftab, sainseq->currentround = 0;
       suftabptr < suftab + nonspecialentries; suftabptr++)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc;

      if (position >= (long) sainseq->totallength)
      {
        sainseq->currentround++;
        position -= (long) sainseq->totallength;
      }
      currentcc = array[(unsigned long) position];
      if (currentcc < sainseq->numofchars)
      {
        if (position > 0)
        {
          unsigned long t, leftcontextcc;

          gt_assert(position > 0);
          position--;
          leftcontextcc = array[(unsigned long) position];
          t = (currentcc << 1) | (leftcontextcc < currentcc ? 1UL : 0);
          gt_assert(currentcc > 0 &&
                    sainseq->roundtable[t] <= sainseq->currentround);
          if (sainseq->roundtable[t] < sainseq->currentround)
          {
            position += (long) sainseq->totallength;
            sainseq->roundtable[t] = sainseq->currentround;
          }
          GT_SAINUPDATEBUCKETPTR(currentcc);
          /* negative => position does not derive L-suffix
             positive => position may derive L-suffix */
          gt_assert(suftabptr < bucketptr);
          *bucketptr++ = (t & 1UL) ? ~position : position;
          *suftabptr = 0;
#ifdef SAINSHOWSTATE
          gt_assert(bucketptr != NULL);
          printf("L-induce: suftab[%lu]=%ld\n",
                  (unsigned long) (bucketptr-1-suftab),*(bucketptr-1));
#endif
        }
      } else
      {
        *suftabptr = 0;
      }
    } else
    {
      if (position < 0)
      {
        *suftabptr = ~position;
      }
    }
  }
}

static void gt_sain_INTSEQ_induceLtypesuffixes1(GtSainseq *sainseq,
                                                 const unsigned long *array,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_assert(sainseq->roundtable == NULL);
  for (suftabptr = suftab; suftabptr < suftab + nonspecialentries; suftabptr++)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc = array[(unsigned long) position];
      if (currentcc < sainseq->numofchars)
      {
        if (position > 0)
        {
          unsigned long leftcontextcc;

          gt_assert(position > 0);
          position--;
          leftcontextcc = array[(unsigned long) position];
          GT_SAINUPDATEBUCKETPTR(currentcc);
          /* negative => position does not derive L-suffix
             positive => position may derive L-suffix */
          gt_assert(suftabptr < bucketptr);
          *bucketptr++ = (leftcontextcc < currentcc) ? ~position : position;
          *suftabptr = 0;
#ifdef SAINSHOWSTATE
          gt_assert(bucketptr != NULL);
          printf("L-induce: suftab[%lu]=%ld\n",
                  (unsigned long) (bucketptr-1-suftab),*(bucketptr-1));
#endif
        }
      } else
      {
        *suftabptr = 0;
      }
    } else
    {
      if (position < 0)
      {
        *suftabptr = ~position;
      }
    }
  }
}

static void gt_sain_INTSEQ_fast_induceStypesuffixes1(GtSainseq *sainseq,
                                                 const unsigned long *array,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_assert(sainseq->roundtable != NULL);
  gt_sain_special_singleSinduction1(sainseq,
                                    suftab,
                                    (long) (sainseq->totallength-1));
  if (sainseq->seqtype == GT_SAIN_ENCSEQ)
  {
    gt_sain_induceStypes1fromspecialranges(sainseq,
                                           sainseq->seq.encseq,
                                           suftab);
  }
  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if ((position = *suftabptr) > 0)
    {
      if (position >= (long) sainseq->totallength)
      {
        sainseq->currentround++;
        position -= (long) sainseq->totallength;
      }
      if (position > 0)
      {
        unsigned long currentcc = array[(unsigned long) position];

        if (currentcc < sainseq->numofchars)
        {
          unsigned long t, leftcontextcc;

          position--;
          leftcontextcc = array[(unsigned long) position];
          t = (currentcc << 1) | (leftcontextcc > currentcc ? 1UL : 0);
          gt_assert(sainseq->roundtable[t] <= sainseq->currentround);
          if (sainseq->roundtable[t] < sainseq->currentround)
          {
            position += sainseq->totallength;
            sainseq->roundtable[t] = sainseq->currentround;
          }
          GT_SAINUPDATEBUCKETPTR(currentcc);
          gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
          *(--bucketptr) = (t & 1UL) ? ~(position+1) : position;
#ifdef SAINSHOWSTATE
          printf("S-induce: suftab[%lu]=%ld\n",
                  (unsigned long) (bucketptr - suftab),*bucketptr);
#endif
        }
      }
      *suftabptr = 0;
    }
  }
}

static void gt_sain_INTSEQ_induceStypesuffixes1(GtSainseq *sainseq,
                                                 const unsigned long *array,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_assert(sainseq->roundtable == NULL);
  gt_sain_special_singleSinduction1(sainseq,
                                    suftab,
                                    (long) (sainseq->totallength-1));
  if (sainseq->seqtype == GT_SAIN_ENCSEQ)
  {
    gt_sain_induceStypes1fromspecialranges(sainseq,
                                           sainseq->seq.encseq,
                                           suftab);
  }
  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc = array[(unsigned long) position];

      if (currentcc < sainseq->numofchars)
      {
        unsigned long leftcontextcc;

        position--;
        leftcontextcc = array[(unsigned long) position];
        GT_SAINUPDATEBUCKETPTR(currentcc);
        gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
        *(--bucketptr) = (leftcontextcc > currentcc)
                          ? ~(position+1) : position;
#ifdef SAINSHOWSTATE
        printf("S-induce: suftab[%lu]=%ld\n",
               (unsigned long) (bucketptr - suftab),*bucketptr);
#endif
      }
      *suftabptr = 0;
    }
  }
}

static void gt_sain_INTSEQ_induceLtypesuffixes2(const GtSainseq *sainseq,
                                                 const unsigned long *array,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  for (suftabptr = suftab; suftabptr < suftab + nonspecialentries; suftabptr++)
  {
    position = *suftabptr;
    *suftabptr = ~position;
    if (position > 0)
    {
      unsigned long currentcc;

      position--;
      currentcc = array[(unsigned long) position];
      if (currentcc < sainseq->numofchars)
      {
        gt_assert(currentcc > 0);
        GT_SAINUPDATEBUCKETPTR(currentcc);
        gt_assert(bucketptr != NULL && suftabptr < bucketptr);
        *bucketptr++ = (position > 0 &&
                        (array[(unsigned long) (position-1)])
                                            < currentcc)
                        ? ~position : position;
#ifdef SAINSHOWSTATE
        gt_assert(bucketptr != NULL);
        printf("L-induce: suftab[%lu]=%ld\n",
               (unsigned long) (bucketptr-1-suftab),*(bucketptr-1));
#endif
      }
    }
  }
}

static void gt_sain_INTSEQ_induceStypesuffixes2(const GtSainseq *sainseq,
                                                 const unsigned long *array,
                                         long *suftab,
                                         unsigned long nonspecialentries)
{
  unsigned long lastupdatecc = 0, *fillptr = sainseq->bucketfillptr;
  long *suftabptr, *bucketptr = NULL;
  long position;

  gt_sain_special_singleSinduction2(sainseq,
                                    suftab,
                                    (long) sainseq->totallength,
                                    nonspecialentries);
  if (sainseq->seqtype == GT_SAIN_ENCSEQ)
  {
    gt_sain_induceStypes2fromspecialranges(sainseq,
                                           sainseq->seq.encseq,
                                           suftab,
                                           nonspecialentries);
  }
  if (nonspecialentries == 0)
  {
    return;
  }
  for (suftabptr = suftab + nonspecialentries - 1; suftabptr >= suftab;
       suftabptr--)
  {
    if ((position = *suftabptr) > 0)
    {
      unsigned long currentcc;

      position--;
      currentcc = array[(unsigned long) position];
      if (currentcc < sainseq->numofchars)
      {
        GT_SAINUPDATEBUCKETPTR(currentcc);
        gt_assert(bucketptr != NULL && bucketptr - 1 < suftabptr);
        *(--bucketptr) = (position == 0 ||
                          (array[(unsigned long) (position-1)])
                                             > currentcc)
                         ? ~position : position;
#ifdef SAINSHOWSTATE
        gt_assert(bucketptr != NULL);
        printf("S-induce: suftab[%lu]=%ld\n",
                (unsigned long) (bucketptr-suftab),*bucketptr);
#endif
      }
    } else
    {
      *suftabptr = ~position;
    }
  }
}

static void gt_sain_INTSEQ_expandorder2original(GtSainseq *sainseq,
                                                 const unsigned long *array,
                                         unsigned long numberofsuffixes,
                                         unsigned long *suftab)
{
  unsigned long *suftabptr, position,
                writeidx = numberofsuffixes - 1,
                nextcc = GT_UNIQUEINT(sainseq->totallength),
                *sstarsuffixes = suftab + numberofsuffixes;
  unsigned long *sstarfirstcharcount = NULL, *bucketsize = NULL;
  bool nextisStype = true;

  if (sainseq->seqtype == GT_SAIN_INTSEQ)
  {
    unsigned long charidx;

    gt_assert(sainseq->sstarfirstcharcount == NULL);
    sstarfirstcharcount = sainseq->sstarfirstcharcount
                        = sainseq->bucketfillptr;
    bucketsize = sainseq->bucketsize;
    for (charidx = 0; charidx < sainseq->numofchars; charidx++)
    {
      sstarfirstcharcount[charidx] = 0;
      bucketsize[charidx] = 0;
    }
  }
  for (position = sainseq->totallength-1; /* Nothing */; position--)
  {
    unsigned long currentcc = array[position];
    bool currentisStype = (currentcc < nextcc ||
                           (currentcc == nextcc && nextisStype)) ? true : false;

    if (!currentisStype && nextisStype)
    {
      if (sstarfirstcharcount != NULL)
      {
        sstarfirstcharcount[nextcc]++;
      }
      sstarsuffixes[writeidx--] = position+1;
    }
    if (bucketsize != NULL)
    {
      bucketsize[currentcc]++;
    }
    nextisStype = currentisStype;
    nextcc = currentcc;
    if (position == 0)
    {
      break;
    }
  }
  for (suftabptr = suftab; suftabptr < suftab + numberofsuffixes; suftabptr++)
  {
    *suftabptr = sstarsuffixes[*suftabptr];
  }
}
genometools-1.5.1/src/match/sfx-shortreadsort.c000066400000000000000000000623651211610345200216100ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/intbits.h"
#include "core/stack-inlined.h"
#include "core/minmax.h"
#include "core/assert_api.h"
#include "sfx-lcpvalues.h"
#include "sfx-shortreadsort.h"
#include "spmsuftab.h"
#include "seqnumrelpos.h"

typedef struct
{
  unsigned long suffixrepresentation;
  uint32_t tbeidx;
  unsigned int unitsnotspecial;
} GtShortreadsort;

struct GtShortreadsortworkinfo
{
  GtShortreadsort *shortreadsorttable;
  GtLcpvalues *sssplcpvalues;    /* always NULL in the context of
                                    firstcodes; otherwise: NULL iff
                                    lcpvalues are not required. */
  uint16_t *mediumsizelcpvalues; /* always NULL for firstcodes;
                                    otherwise: NULL if lcpvalues are
                                    not required */
  unsigned long *seqnum_relpos_bucket; /* only for firstcodes */
  GtArrayGtTwobitencoding tbereservoir;
  unsigned long tmplcplen, currentbucketsize, sumofstoredvalues;
  bool fwd, complement, withmediumsizelcps;
};

static double gt_shortreadsort_encoding_factor(unsigned long maxremain)
{
  double factor = 1.0;

  if (maxremain > (2UL * (unsigned long) GT_UNITSIN2BITENC))
  {
    factor += maxremain/(2UL * (unsigned long) GT_UNITSIN2BITENC);
  } else
  {
    factor = 1.0;
  }
  return factor;
}

static unsigned long gt_shortreadsort_encoding_size(unsigned long bucketsize,
                                                    unsigned long maxremain)
{
  return (unsigned long) (bucketsize *
                          gt_shortreadsort_encoding_factor(maxremain));
}

static size_t gt_shortreadsort_size_perbucketentry(bool firstcodes,
                                                   unsigned long maxremain)
{
  return (firstcodes ? sizeof (uint16_t) : 0) +
         sizeof (GtShortreadsort) + sizeof (unsigned long) +
         sizeof (GtTwobitencoding) *
         gt_shortreadsort_encoding_factor(maxremain);
}

size_t gt_shortreadsort_size(bool firstcodes,unsigned long bucketsize,
                             unsigned long maxremain)
{
  return (size_t) bucketsize *
         gt_shortreadsort_size_perbucketentry(firstcodes,maxremain);
}

unsigned long gt_shortreadsort_maxwidth(bool firstcodes,
                                        unsigned long maxremain,
                                        size_t sizeofworkspace)
{
  return (unsigned long) sizeofworkspace/
         gt_shortreadsort_size_perbucketentry(firstcodes,maxremain);
}

static void gt_shortreadsort_resize(GtShortreadsortworkinfo *srsw,
                                    bool firstcodes,
                                    unsigned long bucketsize,
                                    unsigned long maxremain)
{
  gt_assert(!firstcodes || !srsw->withmediumsizelcps);
  gt_assert(bucketsize <= (unsigned long) UINT32_MAX);
  if (srsw->currentbucketsize < bucketsize)
  {
    srsw->shortreadsorttable = gt_realloc(srsw->shortreadsorttable,
                                          sizeof (*srsw->shortreadsorttable) *
                                          bucketsize);
  }
  if (firstcodes && srsw->currentbucketsize < bucketsize)
  {
    srsw->seqnum_relpos_bucket
      = gt_realloc(srsw->seqnum_relpos_bucket,
                   sizeof (*srsw->seqnum_relpos_bucket) * bucketsize);
  }
  if ((firstcodes || srsw->withmediumsizelcps) &&
      srsw->currentbucketsize < bucketsize)
  {
    srsw->mediumsizelcpvalues
      = gt_realloc(srsw->mediumsizelcpvalues,
                   sizeof (*srsw->mediumsizelcpvalues) * bucketsize);
    srsw->mediumsizelcpvalues[0] = 0; /* since it is not set otherwise */
  }
  srsw->tbereservoir.nextfreeGtTwobitencoding = 0;
  if (srsw->currentbucketsize < bucketsize)
  {
    srsw->tbereservoir.allocatedGtTwobitencoding
      = gt_shortreadsort_encoding_size(bucketsize,maxremain);
    srsw->tbereservoir.spaceGtTwobitencoding
      = gt_realloc(srsw->tbereservoir.spaceGtTwobitencoding,
                   sizeof (GtTwobitencoding) *
                   srsw->tbereservoir.allocatedGtTwobitencoding);
    srsw->currentbucketsize = bucketsize;
  }
}

GtShortreadsortworkinfo *gt_shortreadsort_new(unsigned long maxwidth,
                                              unsigned long maxremain,
                                              GtReadmode readmode,
                                              bool firstcodes,
                                              bool withmediumsizelcps)
{
  GtShortreadsortworkinfo *srsw;

  srsw = gt_malloc(sizeof (*srsw));
  srsw->fwd = GT_ISDIRREVERSE(readmode) ? false : true;
  srsw->complement = GT_ISDIRCOMPLEMENT(readmode) ? true : false;
  srsw->sssplcpvalues = NULL;
  srsw->sumofstoredvalues = 0;
  srsw->currentbucketsize = 0;
  srsw->shortreadsorttable = NULL;
  srsw->mediumsizelcpvalues = NULL;
  srsw->withmediumsizelcps = withmediumsizelcps;
  srsw->seqnum_relpos_bucket = NULL;
  GT_INITARRAY(&srsw->tbereservoir,GtTwobitencoding);
  if (maxwidth > 0)
  {
    gt_shortreadsort_resize(srsw,firstcodes,maxwidth,maxremain);
  }
  return srsw;
}

unsigned long gt_shortreadsort_sumofstoredvalues(const GtShortreadsortworkinfo
                                                       *srsw)
{
  return srsw->sumofstoredvalues;
}

void gt_shortreadsort_delete(GtShortreadsortworkinfo *srsw)
{
  if (srsw != NULL)
  {
    gt_free(srsw->shortreadsorttable);
    srsw->shortreadsorttable = NULL;
    gt_free(srsw->mediumsizelcpvalues);
    srsw->mediumsizelcpvalues = NULL;
    gt_free(srsw->seqnum_relpos_bucket);
    srsw->seqnum_relpos_bucket = NULL;
    GT_FREEARRAY(&srsw->tbereservoir,GtTwobitencoding);
    gt_free(srsw);
  }
}

void gt_shortreadsort_assigntableoflcpvalues(GtShortreadsortworkinfo *srsw,
                                             GtLcpvalues *tableoflcpvalues)
{
  if (srsw != NULL)
  {
    srsw->sssplcpvalues = tableoflcpvalues;
  }
}

static int gt_shortreadsort_compare(const GtShortreadsort *aq,
                                    const GtShortreadsort *bq,
                                    GtShortreadsortworkinfo *srsw)
{
  unsigned int maxprefix;
  GtTwobitencoding *aptr, *bptr;

  aptr = srsw->tbereservoir.spaceGtTwobitencoding + aq->tbeidx;
  bptr = srsw->tbereservoir.spaceGtTwobitencoding + bq->tbeidx;
  for (maxprefix = (unsigned int) GT_UNITSIN2BITENC;
       /* Nothing */;
       maxprefix += (unsigned int) GT_UNITSIN2BITENC, aptr++, bptr++)
  {
    int retval;
    GtCommonunits commonunits;

    if (aq->unitsnotspecial >= maxprefix &&
        bq->unitsnotspecial >= maxprefix)
    {
      GtTwobitencoding aval = *aptr, bval = *bptr;

      if (aval != bval)
      {
        retval = gt_encseq_compare_pairof_different_twobitencodings(
                              srsw->fwd,
                              srsw->complement,
                              &commonunits,
                              aval,bval);
        srsw->tmplcplen = (unsigned long) (maxprefix - GT_UNITSIN2BITENC +
                                           commonunits.common);
        return retval;
      }
    } else
    {
      GtEndofTwobitencoding tbe_a, tbe_b;

      tbe_a.referstartpos = aq->suffixrepresentation;
      tbe_b.referstartpos = bq->suffixrepresentation;
      tbe_a.unitsnotspecial
        = aq->unitsnotspecial >= maxprefix
           ? maxprefix
           : aq->unitsnotspecial + GT_UNITSIN2BITENC - maxprefix;
      tbe_a.tbe = tbe_a.unitsnotspecial > 0 ? *aptr : 0;
      tbe_b.unitsnotspecial
        = bq->unitsnotspecial >= maxprefix
           ? maxprefix
           : bq->unitsnotspecial + GT_UNITSIN2BITENC - maxprefix;
      tbe_b.tbe = tbe_b.unitsnotspecial > 0 ? *bptr : 0;
      retval = gt_encseq_compare_pairof_twobitencodings(srsw->fwd,
                                                        srsw->complement,
                                                        &commonunits,
                                                        &tbe_a,
                                                        &tbe_b);
      srsw->tmplcplen = (unsigned long) (maxprefix - GT_UNITSIN2BITENC +
                                         commonunits.common);
      return retval;
    }
  }
  /*@ignore@*/
  return 0;
  /*@end@*/
}

#ifdef QSORTNAME
#undef QSORTNAME
#endif

#define QSORTNAME(NAME)                    shortread_##NAME
#define shortread_ARRAY_GET(ARR,IDX)       data->shortreadsorttable[IDX]
#define shortread_ARRAY_SET(ARR,IDX,VALUE) data->shortreadsorttable[IDX] = VALUE

typedef GtShortreadsortworkinfo * QSORTNAME(Datatype);

static int QSORTNAME(qsortcmparr) (unsigned long a,
                                   unsigned long b,
                                   const QSORTNAME(Datatype) data)
{
  return gt_shortreadsort_compare(&QSORTNAME(ARRAY_GET)(NULL,a),
                                  &QSORTNAME(ARRAY_GET)(NULL,b),
                                  data);
}

typedef unsigned long QSORTNAME(Sorttype);

/*
 * Qsort routine from Bentley & McIlroy's ``Engineering a Sort Function''.
 */

#ifndef GT_QSORT_ARR_SWAP
#define GT_QSORT_ARR_SWAP(ARR,A,B)\
        if ((A) != (B))\
        {\
          tmp = QSORTNAME(ARRAY_GET)(ARR,A);\
          QSORTNAME(ARRAY_SET)(ARR,A,QSORTNAME(ARRAY_GET)(ARR,B));\
          QSORTNAME(ARRAY_SET)(ARR,B,tmp);\
        }
#endif

#ifndef GT_QSORT_ARR_VECSWAP
#define GT_QSORT_ARR_VECSWAP(ARR,A,B,N)\
        aidx = A;\
        bidx = B;\
        while ((N)-- > 0)\
        {\
          tmp = QSORTNAME(ARRAY_GET)(ARR,aidx);\
          QSORTNAME(ARRAY_SET)(ARR,aidx,QSORTNAME(ARRAY_GET)(ARR,bidx));\
          QSORTNAME(ARRAY_SET)(ARR,bidx,tmp);\
          aidx++;\
          bidx++;\
        }
#endif

static inline unsigned long QSORTNAME(gt_inlined_qsort_arr_r_med3)
                     (unsigned long a, unsigned long b, unsigned long c,
                      QSORTNAME(Datatype) data)
{
  return QSORTNAME(qsortcmparr) (a, b, data) < 0
           ? (QSORTNAME(qsortcmparr) (b, c, data) < 0
                ? b
                : (QSORTNAME(qsortcmparr) (a, c, data) < 0 ? c : a))
           : (QSORTNAME(qsortcmparr) (b, c, data) > 0
                ? b
                : (QSORTNAME(qsortcmparr) (a, c, data) < 0 ? a : c));
}

#ifndef GT_STACK_INTERVALARRAYTOBESORTED_DEFINED
typedef struct
{
  unsigned long startindex,
                len;
} Intervalarrtobesorted;

GT_STACK_DECLARESTRUCT(Intervalarrtobesorted,32UL);
#define GT_STACK_INTERVALARRAYTOBESORTED_DEFINED
#endif

static void QSORTNAME(gt_inlinedarr_qsort_r) (
                                   unsigned long insertionsortthreshold,
                                   bool handlenotswapped,
                                   unsigned long len,
                                   QSORTNAME(Datatype) data,
                                   unsigned long depth,
                                   unsigned long subbucketleft)
{
  unsigned long pa, pb, pc, pd, pl, pm, pn, aidx, bidx, s,
                smallermaxlcp, greatermaxlcp;
  GtShortreadsort tmp;
  int r;
  bool swapped;
  GtStackIntervalarrtobesorted intervalstack;
  Intervalarrtobesorted current;

  GT_STACK_INIT(&intervalstack,32UL);
  current.startindex = 0;
  current.len = len;
  GT_STACK_PUSH(&intervalstack,current);
  if (insertionsortthreshold <= 2UL)
  {
    insertionsortthreshold = 6UL;
  }
  while (!GT_STACK_ISEMPTY(&intervalstack))
  {
    swapped = false;
    current = GT_STACK_POP(&intervalstack);
    if (current.len <= insertionsortthreshold)
    {
      for (pm = current.startindex + 1;
           pm < current.startindex + current.len; pm++)
      {
        for (pl = pm; pl > current.startindex; pl--)
        {
          r = QSORTNAME(qsortcmparr) (pl - 1, pl, data);
          if (data->mediumsizelcpvalues != NULL)
          {
            if (pl < pm && r > 0)
            {
              data->mediumsizelcpvalues[pl+1] = data->mediumsizelcpvalues[pl];
            }
            gt_assert(depth + data->tmplcplen <= UINT16_MAX);
            data->mediumsizelcpvalues[pl]
              = (uint16_t) (depth + data->tmplcplen);
          } else
          {
            if (data->sssplcpvalues != NULL)
            {
              if (pl < pm && r > 0)
              {
                gt_lcptab_update(data->sssplcpvalues,subbucketleft,pl+1,
                                 gt_lcptab_getvalue(data->sssplcpvalues,
                                                       subbucketleft,pl));
              }
              gt_lcptab_update(data->sssplcpvalues,subbucketleft,pl,
                               depth + data->tmplcplen);
            }
          }
          if (r <= 0)
          {
            break;
          }
          GT_QSORT_ARR_SWAP (arr, pl, pl - 1);
        }
      }
      continue;
    }
    pm = current.startindex + GT_DIV2 (current.len);
    if (current.len > 7UL)
    {
      pl = current.startindex;
      pn = current.startindex + current.len - 1;
      if (current.len > 40UL)
      {
        s = GT_DIV8 (current.len);
        pl = QSORTNAME(gt_inlined_qsort_arr_r_med3) (pl, pl + s,
                                                     pl + GT_MULT2 (s), data);
        gt_assert(pm >= s);
        pm = QSORTNAME(gt_inlined_qsort_arr_r_med3) (pm - s, pm,
                                                     pm + s, data);
        gt_assert(pn >= GT_MULT2(s));
        pn = QSORTNAME(gt_inlined_qsort_arr_r_med3) (pn - GT_MULT2 (s),
                                                     pn - s, pn, data);
      }
      pm = QSORTNAME(gt_inlined_qsort_arr_r_med3) (pl, pm, pn, data);
    }
    GT_QSORT_ARR_SWAP (arr, current.startindex, pm);
    pa = pb = current.startindex + 1;
    pc = pd = current.startindex + current.len - 1;
    smallermaxlcp = greatermaxlcp = 0;
    while (1)
    {
      while (pb <= pc)
      {
        r = QSORTNAME(qsortcmparr) (pb, current.startindex, data);
        if (r > 0)
        {
          GT_UPDATE_MAX(greatermaxlcp,data->tmplcplen);
          break;
        }
        if (r == 0)
        {
          swapped = true;
          GT_QSORT_ARR_SWAP (arr, pa, pb);
          pa++;
        } else
        {
          GT_UPDATE_MAX(smallermaxlcp,data->tmplcplen);
        }
        pb++;
      }
      while (pb <= pc)
      {
        r = QSORTNAME(qsortcmparr) (pc, current.startindex, data);
        if (r < 0)
        {
          GT_UPDATE_MAX(smallermaxlcp,data->tmplcplen);
          break;
        }
        if (r == 0)
        {
          swapped = true;
          GT_QSORT_ARR_SWAP (arr, pc, pd);
          gt_assert(pd > 0);
          pd--;
        } else
        {
          GT_UPDATE_MAX(greatermaxlcp,data->tmplcplen);
        }
        gt_assert(pc > 0);
        pc--;
      }
      if (pb > pc)
      {
        break;
      }
      GT_QSORT_ARR_SWAP (arr, pb, pc);
      swapped = true;
      pb++;
      gt_assert(pc > 0);
      pc--;
    }
    /* The following switch is not explained in the above mentioned
       paper and therefore we ignore it. */
    if (handlenotswapped && !swapped)
    {                                  /* Switch to insertion sort */
      gt_assert(current.len <= 40UL);
      for (pm = current.startindex + 1;
           pm < current.startindex + current.len; pm++)
      {
        for (pl = pm; pl > current.startindex; pl--)
        {
          r = QSORTNAME(qsortcmparr) (pl - 1, pl, data);
          if (r <= 0)
          {
            break;
          }
          GT_QSORT_ARR_SWAP (arr, pl, pl - 1);
        }
      }
      continue;
    }
    pn = current.startindex + current.len;
    gt_assert(pa >= current.startindex && pb >= pa);
    s = MIN ((unsigned long) (pa - current.startindex),
             (unsigned long) (pb - pa));
    gt_assert(pb >= s);
    GT_QSORT_ARR_VECSWAP (arr, current.startindex, pb - s, s);
    gt_assert(pd >= pc && pn > pd);
    s = MIN ((unsigned long) (pd - pc), (unsigned long) (pn - pd - 1));
    gt_assert(pn > s);
    GT_QSORT_ARR_VECSWAP (arr, pb, pn - s, s);
    gt_assert(pb >= pa);
    if ((s = (unsigned long) (pb - pa)) > 0)
    {
      if (data->mediumsizelcpvalues != NULL)
      {
        gt_assert(depth + smallermaxlcp <= UINT16_MAX);
        data->mediumsizelcpvalues[current.startindex + s]
          = (uint16_t) (depth + smallermaxlcp);
      } else
      {
        if (data->sssplcpvalues != NULL)
        {
          /*
            left part has suffix with lcp up to length smallermaxlcp w.r.t.
            to the pivot. This lcp belongs to a suffix on the left
            which is at a minimum distance to the pivot and thus to an
            element in the final part of the left side.
          */
          gt_lcptab_update(data->sssplcpvalues,
                           subbucketleft,current.startindex + s,
                           depth + smallermaxlcp);
        }
      }
      if (s > 1UL)
      {
        current.len = s;
        GT_STACK_PUSH(&intervalstack,current);
      }
    }
    gt_assert(pd >= pc);
    if ((s = (unsigned long) (pd - pc)) > 0)
    {
      if (data->mediumsizelcpvalues != NULL)
      {
        gt_assert (depth + greatermaxlcp <= UINT16_MAX);
        data->mediumsizelcpvalues[pn - s] = (uint16_t) (depth + greatermaxlcp);
      } else
      {
        if (data->sssplcpvalues != NULL)
        {
          /*
            right part has suffix with lcp up to length largermaxlcp w.r.t.
            to the pivot. This lcp belongs to a suffix on the right
            which is at a minimum distance to the pivot and thus to an
            element in the first part of the right side.
          */
          gt_assert(pn >= s);
          gt_lcptab_update(data->sssplcpvalues,subbucketleft,pn - s,
                           depth + greatermaxlcp);
        }
      }
      if (s > 1UL)
      {
        gt_assert(pn >= s);
        current.startindex = pn - s;
        current.len = s;
        GT_STACK_PUSH(&intervalstack,current);
      }
    }
  }
  GT_STACK_DELETE(&intervalstack);
}

void gt_shortreadsort_sssp_sort(GtShortreadsortworkinfo *srsw,
                                const GtEncseq *encseq,
                                unsigned long maxremain,
                                GtReadmode readmode,
                                GtEncseqReader *esr,
                                GtSuffixsortspace *sssp,
                                unsigned long subbucketleft,
                                unsigned long width,
                                unsigned long depth,
                                unsigned long maxdepth)
{
  unsigned long idx, pos;
  GtSuffixsortspace_exportptr *exportptr;

  gt_shortreadsort_resize(srsw, false, width, maxremain);
  exportptr = gt_suffixsortspace_exportptr(subbucketleft, sssp);
  srsw->tbereservoir.nextfreeGtTwobitencoding = 0;
  if (exportptr->ulongtabsectionptr != NULL)
  {
    for (idx = 0; idx < width; idx++)
    {
      pos = exportptr->ulongtabsectionptr[idx];
      srsw->shortreadsorttable[idx].suffixrepresentation = pos;
      srsw->shortreadsorttable[idx].tbeidx
        = (uint32_t) srsw->tbereservoir.nextfreeGtTwobitencoding;
      srsw->shortreadsorttable[idx].unitsnotspecial
        = gt_encseq_extract2bitencvector(&srsw->tbereservoir,
                                         encseq,
                                         esr,
                                         readmode,
                                         pos+depth,
                                         maxdepth > 0 ? true : false,
                                         pos + maxdepth);
    }
  } else
  {
    for (idx = 0; idx < width; idx++)
    {
      pos = (unsigned long) exportptr->uinttabsectionptr[idx];
      srsw->shortreadsorttable[idx].suffixrepresentation = pos;
      srsw->shortreadsorttable[idx].tbeidx
        = (uint32_t) srsw->tbereservoir.nextfreeGtTwobitencoding;
      srsw->shortreadsorttable[idx].unitsnotspecial
        = gt_encseq_extract2bitencvector(&srsw->tbereservoir,
                                         encseq,
                                         esr,
                                         readmode,
                                         pos+depth,
                                         maxdepth > 0 ? true : false,
                                         pos + maxdepth);
    }
  }
  QSORTNAME(gt_inlinedarr_qsort_r) (6UL, false, width, srsw, depth,
                                    subbucketleft);
  if (exportptr->ulongtabsectionptr != NULL)
  {
    for (idx = 0; idx < width; idx++)
    {
      exportptr->ulongtabsectionptr[idx]
        = srsw->shortreadsorttable[idx].suffixrepresentation;
      if (exportptr->ulongtabsectionptr[idx] == 0)
      {
        gt_suffixsortspace_updatelongest(sssp,subbucketleft + idx);
      }
    }
  } else
  {
    for (idx = 0; idx < width; idx++)
    {
      exportptr->uinttabsectionptr[idx]
        = (uint32_t) srsw->shortreadsorttable[idx].suffixrepresentation;
      if (exportptr->uinttabsectionptr[idx] == 0)
      {
        gt_suffixsortspace_updatelongest(sssp,subbucketleft + idx);
      }
    }
  }
  gt_suffixsortspace_export_done(sssp);
}

void gt_shortreadsort_sssp_add_unsorted(const GtShortreadsortworkinfo *srsw,
                                        unsigned long bucketleftidx,
                                        unsigned long subbucketleft,
                                        unsigned long width,
                                        unsigned long maxdepth,
                                        GtProcessunsortedsuffixrange
                                          processunsortedsuffixrange,
                                        void *processunsortedsuffixrangeinfo)
{
  unsigned long idx, lcpvalue, laststart = 0;

  gt_assert(srsw->mediumsizelcpvalues != NULL || srsw->sssplcpvalues != NULL);
  for (idx = 1UL; idx < width; idx++)
  {
    lcpvalue = srsw->mediumsizelcpvalues != NULL
                 ? (unsigned long) srsw->mediumsizelcpvalues[idx]
                 : gt_lcptab_getvalue(srsw->sssplcpvalues,subbucketleft,idx);
    if (lcpvalue < maxdepth)
    {
      if (laststart < idx-1)
      {
        if (processunsortedsuffixrange != NULL)
        {
          processunsortedsuffixrange(processunsortedsuffixrangeinfo,
                                     bucketleftidx + subbucketleft + laststart,
                                     idx - laststart,maxdepth);
        }
      }
      laststart = idx;
    }
  }
  if (laststart < width-1)
  {
    if (processunsortedsuffixrange != NULL)
    {
      processunsortedsuffixrange(processunsortedsuffixrangeinfo,
                                 bucketleftidx + subbucketleft + laststart,
                                 width - laststart,maxdepth);
    }
  }
}

void gt_shortreadsort_firstcodes_sort(GtShortreadsortresult *srsresult,
                                      GtShortreadsortworkinfo *srsw,
                                      const GtSeqnumrelpos *snrp,
                                      const GtEncseq *encseq,
                                      const GtSpmsuftab *spmsuftab,
                                      unsigned long subbucketleft,
                                      unsigned long width,
                                      unsigned long depth,
                                      unsigned long maxdepth)
{
  unsigned long idx, pos, seqnum, relpos, seqnum_relpos;
  gt_assert(maxdepth == 0 || maxdepth > depth);

  srsw->tbereservoir.nextfreeGtTwobitencoding = 0;
  for (idx = 0; idx < width; idx++)
  {
    if (gt_spmsuftab_usebitsforpositions(spmsuftab))
    {
      pos = gt_spmsuftab_get(spmsuftab,subbucketleft + idx);
      seqnum = gt_encseq_seqnum(encseq,pos);
      relpos = pos - gt_encseq_seqstartpos(encseq,seqnum);
      srsw->shortreadsorttable[idx].suffixrepresentation
        = gt_seqnumrelpos_encode(snrp, seqnum, relpos);
    } else
    {
      seqnum_relpos = gt_spmsuftab_get(spmsuftab,subbucketleft + idx);
      seqnum = gt_seqnumrelpos_decode_seqnum(snrp,seqnum_relpos);
      relpos = gt_seqnumrelpos_decode_relpos(snrp,seqnum_relpos);
      srsw->shortreadsorttable[idx].suffixrepresentation = seqnum_relpos;
    }
    srsw->shortreadsorttable[idx].tbeidx
      = (uint32_t) srsw->tbereservoir.nextfreeGtTwobitencoding;
    srsw->shortreadsorttable[idx].unitsnotspecial
      = gt_encseq_relpos_extract2bitencvector(&srsw->tbereservoir,
                                              encseq,
                                              seqnum,
                                              relpos + depth,
                                              (maxdepth > 0) ?
                                              maxdepth - depth : 0);
  }
  srsw->sumofstoredvalues += srsw->tbereservoir.nextfreeGtTwobitencoding;
  QSORTNAME(gt_inlinedarr_qsort_r) (6UL, false, width, srsw, depth,
                                    subbucketleft);
  for (idx = 0; idx < width; idx++)
  {
    srsw->seqnum_relpos_bucket[idx]
      = srsw->shortreadsorttable[idx].suffixrepresentation;
  }
  srsresult->suftab_bucket = srsw->seqnum_relpos_bucket;
  srsresult->lcptab_bucket = srsw->mediumsizelcpvalues;
}
genometools-1.5.1/src/match/sfx-shortreadsort.h000066400000000000000000000075641211610345200216150ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_SHORTREADSORT_H
#define SFX_SHORTREADSORT_H

#include "core/readmode_api.h"
#include "core/encseq_api.h"
#include "core/unused_api.h"
#include "sfx-lcpvalues.h"
#include "sfx-suffixgetset.h"
#include "spmsuftab.h"
#include "seqnumrelpos.h"

typedef struct GtShortreadsortworkinfo GtShortreadsortworkinfo;

typedef struct
{
  unsigned long *suftab_bucket;
  uint16_t *lcptab_bucket;
} GtShortreadsortresult;

size_t gt_shortreadsort_size(bool firstcodes,unsigned long bucketsize,
                             unsigned long maxremain);

GtShortreadsortworkinfo *gt_shortreadsort_new(unsigned long maxwidth,
                                              unsigned long maxremain,
                                              GtReadmode readmode,
                                              bool firstcodes,
                                              bool withmediumsizelcps);

unsigned long gt_shortreadsort_sumofstoredvalues(
                                      const GtShortreadsortworkinfo *srsw);

void gt_shortreadsort_delete(GtShortreadsortworkinfo *srsw);

void gt_shortreadsort_assigntableoflcpvalues(
          GtShortreadsortworkinfo *srsw,GtLcpvalues *tableoflcpvalues);

void gt_shortreadsort_sssp_sort(GtShortreadsortworkinfo *srsw,
                                const GtEncseq *encseq,
                                unsigned long maxremain,
                                GtReadmode readmode,
                                GtEncseqReader *esr,
                                GtSuffixsortspace *sssp,
                                unsigned long subbucketleft,
                                unsigned long width,
                                unsigned long depth,
                                unsigned long maxdepth);

void gt_shortreadsort_firstcodes_sort(GtShortreadsortresult *srsresult,
                                      GtShortreadsortworkinfo *srsw,
                                      const GtSeqnumrelpos *snrp,
                                      const GtEncseq *encseq,
                                      const GtSpmsuftab *spmsuftab,
                                      unsigned long subbucketleft,
                                      unsigned long width,
                                      unsigned long depth,
                                      unsigned long maxdepth);

void gt_shortreadsort_sssp_add_unsorted(const GtShortreadsortworkinfo *srsw,
                                        unsigned long bucketleftidx,
                                        unsigned long subbucketleft,
                                        unsigned long width,
                                        unsigned long maxdepth,
                                        GtProcessunsortedsuffixrange
                                          processunsortedsuffixrange,
                                        void *processunsortedsuffixrangeinfo);

unsigned long gt_shortreadsort_maxwidth(bool firstcodes,
                                        unsigned long maxremain,
                                        size_t sizeofworkspace);

#endif
genometools-1.5.1/src/match/sfx-strategy.h000066400000000000000000000052441211610345200205450ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_STRATEGY_H
#define SFX_STRATEGY_H

#include 
#include 

#define MAXINSERTIONSORTDEFAULT  3UL
#define MAXBLTRIESORTDEFAULT     1000UL
#define MAXCOUNTINGSORTDEFAULT   4000UL

typedef struct
{
  unsigned long maxwidthrealmedian,
                maxinsertionsort,
                maxbltriesort,
                maxcountingsort;
  unsigned int differencecover,
               userdefinedsortmaxdepth,
               spmopt_minlength;
  bool cmpcharbychar, /* compare suffixes character by character instead
                         of comparing entire words (only for two bit
                         encoding) */
       storespecialcodes,
       iteratorbasedkmerscanning,
       suftabuint,
       onlybucketinsertion,
       kmerswithencseqreader,
       dccheck,
       samplewithprefixlengthnull,
       noshortreadsort,
       outsuftabonfile,
       withradixsort;
} Sfxstrategy;

 /*@unused@*/ static inline void defaultsfxstrategy(Sfxstrategy *sfxstrategy,
                                                    bool cmpcharbychar)
{
  sfxstrategy->maxwidthrealmedian = 1UL;
  sfxstrategy->maxinsertionsort = MAXINSERTIONSORTDEFAULT;
  sfxstrategy->maxbltriesort = MAXBLTRIESORTDEFAULT;
  sfxstrategy->maxcountingsort = MAXCOUNTINGSORTDEFAULT;
  sfxstrategy->differencecover = 0;
  sfxstrategy->cmpcharbychar = cmpcharbychar;
  sfxstrategy->spmopt_minlength = 0;
  sfxstrategy->storespecialcodes = false;
  sfxstrategy->iteratorbasedkmerscanning = false;
  sfxstrategy->suftabuint = false;
  sfxstrategy->onlybucketinsertion = false;
  sfxstrategy->kmerswithencseqreader = false;
  sfxstrategy->dccheck = false;
  sfxstrategy->samplewithprefixlengthnull = false;
  sfxstrategy->outsuftabonfile = true;
  sfxstrategy->noshortreadsort = false;
  sfxstrategy->withradixsort = false;
  sfxstrategy->userdefinedsortmaxdepth = 0;
}

#endif
genometools-1.5.1/src/match/sfx-suffixer.c000066400000000000000000002303021211610345200205240ustar00rootroot00000000000000/*
  Copyright (c) 2007-2011 Stefan Kurtz 
  Copyright (c) 2007-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 
#ifndef S_SPLINT_S
#include 
#include 
#include 
#endif
#include "core/arraydef.h"
#include "core/assert_api.h"
#include "core/chardef.h"
#include "core/error_api.h"
#include "core/unused_api.h"
#include "core/progressbar.h"
#include "core/minmax.h"
#include "core/fa.h"
#include "core/timer_api.h"
#include "core/encseq.h"
#include "core/safecast-gen.h"
#include "core/log_api.h"
#include "core/mathsupport.h"
#include "core/spacecalc.h"
#include "core/divmodmul.h"
#include "core/format64.h"
#include "core/fileutils.h"
#include "intcode-def.h"
#include "firstcodes-buf.h"
#include "esa-fileend.h"
#include "kmercodes.h"
#include "sfx-diffcov.h"
#include "sfx-partssuf.h"
#include "sfx-suffixer.h"
#include "sfx-enumcodes.h"
#include "sfx-strategy.h"
#include "sfx-copysort.h"
#include "sfx-mappedstr.h"
#include "sfx-bentsedg.h"
#include "sfx-suffixgetset.h"
#include "sfx-maprange.h"
#include "stamp.h"

typedef struct
{
  unsigned long allocatedSuffixptr, nextfreeSuffixptr;
  GtSuffixsortspace *sssp;
} GtSuffixposbuffer;

struct Sfxiterator
{
  /* globally constant */
  const GtEncseq *encseq;
  GtReadmode readmode;
  unsigned long specialcharacters,
                totallength;
  unsigned int numofchars,
               prefixlength;
  Sfxstrategy sfxstrategy;
  bool withprogressbar;

  /* invariant for each part */
  GtSuftabparts *suftabparts;
  GtOutlcpinfo *outlcpinfoforsample;
  GtBcktab *bcktab;
  GtLeftborder *leftborder; /* points to bcktab->leftborder */
  GtDifferencecover *dcov;

  /* changed in each part */
  GtSuffixsortspace *suffixsortspace;
  GtCodetype currentmincode,
             currentmaxcode;
  unsigned long widthofpart;
  unsigned int part;
  GtOutlcpinfo *outlcpinfo;
  GtSuffixposbuffer fusp;
  GtRange overhang;
  bool exhausted;
  unsigned long long bucketiterstep; /* for progressbar */
  GtLogger *logger;
  GtTimer *sfxprogress;
  GtSpecialrangeiterator *sri; /* refers to space used in each part */

  /* use for generating k-mer codes */
  FILE *outfpbcktab;
  bool storespecials;
  unsigned long nextfreeCodeatposition;
  Codeatposition *spaceCodeatposition;
  unsigned int kmerfastmaskright;
  GtSuffixsortspace_exportptr *exportptr;
  unsigned int spmopt_kmerscansize,
               spmopt_kmerscancodeshift2bckcode,
               spmopt_kmerscancodeshift2prefixcode,
               spmopt_additionalprefixchars;
  GtBitsequence *markprefixbuckets,
                *marksuffixbuckets;
  GtCodetype spmopt_kmerscancodesuffixmask;
  unsigned long spmopt_numofallprefixcodes,
                spmopt_numofallsuffixcodes;
  GtSfxmappedrange *mappedmarkprefixbuckets;
};

#ifdef SKDEBUG
static unsigned long iterproduceCodeatposition(Codeatposition *codelist,
                                               const  GtEncseq *encseq,
                                               GtReadmode readmode,
                                               unsigned int prefixlength,
                                               unsigned int numofchars)
{
  if (prefixlength > 1U)
  {
    Enumcodeatposition *ecp;
    unsigned long insertindex;
    Specialcontext specialcontext;

    ecp = gt_Enumcodeatposition_new(encseq,
                                    readmode,
                                    prefixlength,
                                    numofchars);
    for (insertindex = 0; gt_Enumcodeatposition_next(&specialcontext,ecp);
         insertindex++)
    {
      codelist[insertindex].maxprefixindex = specialcontext.maxprefixindex;
      codelist[insertindex].position = specialcontext.position;
      codelist[insertindex].code
        = gt_Enumcodeatposition_filledqgramcode(ecp,
                                                specialcontext.maxprefixindex,
                                                specialcontext.position -
                                                specialcontext.maxprefixindex);
    }
    gt_Enumcodeatposition_delete(ecp);
    ecp = NULL;
    return insertindex;
  }
  return 0;
}

static void compareCodeatpositionlists(const Codeatposition *codelist1,
                                       unsigned long len1,
                                       const Codeatposition *codelist2,
                                       unsigned long len2)
{
  unsigned long idx;

  if (len1 != len2)
  {
    fprintf(stderr,"%s: len1 = %lu != %lu = len2\n",__func__,len1,len2);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  for (idx=0; idx= nextfreeCodeatposition2);
  compareCodeatpositionlists(spaceCodeatposition1,
                             nextfreeCodeatposition1,
                             spaceCodeatposition2,
                             nextfreeCodeatposition2);
  gt_free(spaceCodeatposition2);
}

static GtCodetype getencseqcode(const GtEncseq *encseq,
                                GtReadmode readmode,
                                unsigned long totallength,
                                const GtCodetype **multimappower,
                                unsigned int prefixlength,
                                unsigned long pos)
{
  GtCodetype code = 0;
  unsigned int idx;
  GtUchar cc;

  for (idx=0; idxsfxstrategy.spmopt_minlength == 0);
  if (kmercode->definedspecialposition)
  {
    if (sfi->storespecials)
    {
      if (kmercode->specialposition > 0)
      {
        if (sfi->sfxstrategy.storespecialcodes)
        {
          Codeatposition *cp;

          cp = sfi->spaceCodeatposition + sfi->nextfreeCodeatposition++;
          gt_assert(kmercode->code <= (GtCodetype) MAXCODEVALUE);
          cp->code = (unsigned int) kmercode->code;
          gt_assert(kmercode->specialposition
                    <= (unsigned int) MAXPREFIXLENGTH);
          cp->maxprefixindex = kmercode->specialposition;
          cp->position = position + kmercode->specialposition;
          /*
          printf("store(code=%u,maxprefixindex=%u,pos=%lu)\n",
                  cp->code,cp->maxprefixindex,cp->position);
          */
        }
        sfi->storespecials = false;
        gt_assert(kmercode->code > 0);
        gt_bcktab_leftborder_addcode(sfi->leftborder,kmercode->code);
      }
    } else
    {
      if (kmercode->specialposition > 0)
      {
        gt_assert(kmercode->code > 0);
        gt_bcktab_leftborder_addcode(sfi->leftborder,kmercode->code);
      } else
      {
        sfi->storespecials = true;
      }
    }
  } else
  {
#ifdef SKDEBUG
    if (kmercode->code == 0)
    {
      GtCodetype code2 = getencseqcode(sfi->encseq,
                                       sfi->readmode,
                                       gt_encseq_total_length(sfi->encseq),
                                       gt_bcktab_multimappower(sfi->bcktab),
                                       sfi->prefixlength,
                                       position);
      if (code2 != 0)
      {
        fprintf(stderr,"%s: ### position %lu, code2 = %lu != 0\n",__func__,
                       position,code2);
        fprintf(stderr,"previouscode = " FormatGtCodetype "\n",previouscode);
        if (previouskmercodedefined)
        {
          fprintf(stderr,"previouskmercodedefined = true\n");
          fprintf(stderr,"previousstorespecials = %s\n",
                  previousstorespecials ? "true" : "false");
          fprintf(stderr,"previousspecialpos = %u\n",previousspecialpos);
        }
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
    }
#endif
    gt_bcktab_leftborder_addcode(sfi->leftborder,kmercode->code);
  }
#ifdef SKDEBUG
  previouscode = kmercode->code;
  previouskmercodedefined = kmercode->defined;
  previousstorespecials = sfi->storespecials;
  previousspecialpos = kmercode->specialposition;
#endif
}

#define GT_SCANCODE_TO_BCKCODE(SFI,CODE)\
        (GtCodetype) ((CODE) >> (SFI)->spmopt_kmerscancodeshift2bckcode)

#define GT_SCANCODE_TO_PREFIXCODE(SFI,CODE)\
        (GtCodetype) ((CODE) >> (SFI)->spmopt_kmerscancodeshift2prefixcode)

#ifdef _LP64
#define GT_SCANCODE_TO_SUFFIXCODE(SFI,CODE)\
        (GtCodetype) ((CODE) & (SFI)->spmopt_kmerscancodesuffixmask)

static bool gt_checksuffixprefixbuckets(const Sfxiterator *sfi,
                                        GtCodetype scancode)
{
  GtCodetype prefixcode = GT_SCANCODE_TO_PREFIXCODE(sfi,scancode);
  GtCodetype suffixcode = GT_SCANCODE_TO_SUFFIXCODE(sfi,scancode);

  gt_assert(prefixcode < sfi->spmopt_numofallprefixcodes);
  gt_assert(suffixcode < sfi->spmopt_numofallsuffixcodes);
  return (GT_ISIBITSET(sfi->markprefixbuckets,prefixcode) &&
          GT_ISIBITSET(sfi->marksuffixbuckets,suffixcode)) ? true : false;
}
#else
static bool gt_checksuffixprefixbuckets(const Sfxiterator *sfi,
                                        GtCodetype scancode)
{
  GtCodetype prefixcode = GT_SCANCODE_TO_PREFIXCODE(sfi,scancode);

  gt_assert(prefixcode < sfi->spmopt_numofallprefixcodes);
  return GT_ISIBITSET(sfi->markprefixbuckets,prefixcode) ? true : false;
}
#endif

#define GT_INSERTKMERWITHOUTSPECIAL1(SFI,FIRSTINRANGE,POSITION,SEQNUM,RELPOS,\
                                     SCANCODE)\
        if ((SFI)->markprefixbuckets == NULL)\
        {\
          if ((SCANCODE) >= (SFI)->currentmincode &&\
              (SCANCODE) <= (SFI)->currentmaxcode)\
          {\
            unsigned long stidx;\
            stidx = gt_bcktab_leftborder_insertionindex((SFI)->leftborder,\
                                                        SCANCODE);\
            /* from right to left */\
            GT_SUFFIXSORTSPACE_EXPORT_SET((SFI)->suffixsortspace,\
                                          (SFI)->exportptr,stidx,POSITION);\
          }\
        } else\
        {\
          GtCodetype bcktabcode = GT_SCANCODE_TO_BCKCODE((SFI),SCANCODE);\
          if (bcktabcode >= (SFI)->currentmincode &&\
              bcktabcode <= (SFI)->currentmaxcode &&\
              (FIRSTINRANGE || gt_checksuffixprefixbuckets(SFI,SCANCODE)))\
          {\
            unsigned long stidx;\
            stidx = gt_bcktab_leftborder_insertionindex((SFI)->leftborder,\
                                                        bcktabcode);\
            /* from right to left */\
            GT_SUFFIXSORTSPACE_EXPORT_SET((SFI)->suffixsortspace,\
                                          (SFI)->exportptr,stidx,POSITION);\
          }\
        }

static void gt_insertkmerwithoutspecial(void *processinfo,
                                        unsigned long position,
                                        const GtKmercode *kmercode)
{
  if (!kmercode->definedspecialposition)
  {
    GT_INSERTKMERWITHOUTSPECIAL1((Sfxiterator *) processinfo, false,
                                 position, 0, 0, kmercode->code);
  }
}

static void gt_reversespecialcodes(Codeatposition *spaceCodeatposition,
                                   unsigned long nextfreeCodeatposition)
{
  Codeatposition *front, *back, tmp;

  for (front = spaceCodeatposition,
       back = spaceCodeatposition + nextfreeCodeatposition - 1;
       front < back; front++, back--)
  {
    tmp = *front;
    *front = *back;
    *back = tmp;
  }
}

static void sfx_derivespecialcodesfromtable(Sfxiterator *sfi,bool deletevalues)
{
  GtCodetype code;
  unsigned int prefixindex;
  unsigned long insertindex, j, stidx;

  for (prefixindex=1U; prefixindex < sfi->prefixlength; prefixindex++)
  {
    for (j=0, insertindex = 0; j < sfi->nextfreeCodeatposition; j++)
    {
      if (prefixindex <= sfi->spaceCodeatposition[j].maxprefixindex)
      {
        code = gt_bcktab_codedownscale(sfi->bcktab,
                                       (GtCodetype)
                                       sfi->spaceCodeatposition[j].code,
                                       prefixindex,
                                       sfi->spaceCodeatposition[j].
                                            maxprefixindex);
        if (code >= sfi->currentmincode && code <= sfi->currentmaxcode)
        {
          gt_bcktab_updatespecials(sfi->bcktab,code,prefixindex);
          stidx = gt_bcktab_leftborder_insertionindex(sfi->leftborder,code);
          /* from right to left */
          gt_suffixsortspace_set(sfi->suffixsortspace,0,stidx,
                                 sfi->spaceCodeatposition[j].position
                                 - prefixindex);
        }
      }
      if (deletevalues)
      {
        if (prefixindex < sfi->prefixlength - 1 &&
            prefixindex < sfi->spaceCodeatposition[j].maxprefixindex)
        {
          if (insertindex < j)
          {
            sfi->spaceCodeatposition[insertindex] =
              sfi->spaceCodeatposition[j];
          }
          insertindex++;
        }
      }
    }
    if (deletevalues)
    {
      sfi->nextfreeCodeatposition = insertindex;
    }
  }
}

static void sfx_derivespecialcodesonthefly(Sfxiterator *sfi)
{
  GtCodetype code;
  unsigned int prefixindex;
  unsigned long stidx;
  Enumcodeatposition *ecp;
  Specialcontext specialcontext;

  for (prefixindex=1U; prefixindex < sfi->prefixlength; prefixindex++)
  {
    ecp = gt_Enumcodeatposition_new(sfi->encseq,sfi->readmode,
                                    sfi->prefixlength,
                                    sfi->numofchars);
    while (gt_Enumcodeatposition_next(&specialcontext,ecp))
    {
      if (prefixindex <= specialcontext.maxprefixindex)
      {
        if (gt_Enumcodeatposition_filledqgramcodestopatmax(
                                            &code,
                                            ecp,
                                            prefixindex,
                                            specialcontext.position-prefixindex,
                                            sfi->currentmaxcode))
        {
          gt_assert(code <= sfi->currentmaxcode);
          if (code >= sfi->currentmincode)
          {
            gt_bcktab_updatespecials(sfi->bcktab,code,prefixindex);
            gt_assert(code > 0);
            stidx = gt_bcktab_leftborder_insertionindex(sfi->leftborder,code);
            /* from right to left */
            gt_suffixsortspace_set(sfi->suffixsortspace,0,stidx,
                                   specialcontext.position - prefixindex);
          }
        }
      }
    }
    gt_Enumcodeatposition_delete(ecp);
    ecp = NULL;
  }
}

int gt_Sfxiterator_delete(Sfxiterator *sfi,GtError *err)
{
  bool haserr = false;

  if (sfi == NULL)
  {
    return 0;
  }
#ifdef SKDEBUG
  if (sfi->bcktab != NULL)
  {
    gt_bcktab_checkcountspecialcodes(sfi->bcktab);
  }
#endif
  if (sfi->sri != NULL)
  {
    gt_specialrangeiterator_delete(sfi->sri);
  }
  gt_free(sfi->spaceCodeatposition);
  sfi->spaceCodeatposition = NULL;
  gt_suffixsortspace_delete(sfi->suffixsortspace,
                            sfi->sfxstrategy.spmopt_minlength == 0
                              ? true : false);
  if (sfi->suftabparts != NULL &&
      gt_suftabparts_numofparts(sfi->suftabparts) > 1U &&
      sfi->outfpbcktab != NULL)
  {
    if (gt_bcktab_remap_all(sfi->bcktab,err) != 0)
    {
      haserr = true;
    } else
    {
      int ret = gt_bcktab_flush_to_file(sfi->outfpbcktab,sfi->bcktab,err);
      gt_fa_fclose(sfi->outfpbcktab);
      if (ret != 0)
      {
        haserr = true;
      }
    }
  }
  gt_bcktab_delete(sfi->bcktab);
  gt_suftabparts_delete(sfi->suftabparts);
  gt_Outlcpinfo_delete(sfi->outlcpinfoforsample);
  if (sfi->mappedmarkprefixbuckets == NULL)
  {
    gt_free(sfi->markprefixbuckets);
  }
  gt_Sfxmappedrange_delete(sfi->mappedmarkprefixbuckets);
  sfi->mappedmarkprefixbuckets = NULL;
  gt_free(sfi->marksuffixbuckets);
  gt_differencecover_delete(sfi->dcov);
  gt_free(sfi);
  return haserr ? -1 : 0;
}

static void getencseqkmersupdatekmercount(const GtEncseq *encseq,
                                          GtReadmode readmode,
                                          unsigned int kmersize,
                                          Sfxiterator *sfi)
{
  GtKmercodeiterator *kmercodeiterator;
  const GtKmercode *kmercodeptr;

  kmercodeiterator = gt_kmercodeiterator_encseq_new(encseq,readmode,kmersize,0);
  if (!gt_kmercodeiterator_inputexhausted(kmercodeiterator))
  {
    unsigned long position = 0;

    while ((kmercodeptr = gt_kmercodeiterator_encseq_next(kmercodeiterator))
                          != NULL)
    {
      updatekmercount(sfi,position++,kmercodeptr);
    }
  }
  gt_kmercodeiterator_delete(kmercodeiterator);
}

void getencseqkmersinsertkmerwithoutspecial(const GtEncseq *encseq,
                                            GtReadmode readmode,
                                            unsigned int kmersize,
                                            Sfxiterator *sfi)
{
  GtKmercodeiterator *kmercodeiterator;
  const GtKmercode *kmercodeptr;

  kmercodeiterator = gt_kmercodeiterator_encseq_new(encseq,readmode,kmersize,0);
  if (!gt_kmercodeiterator_inputexhausted(kmercodeiterator))
  {
    unsigned long position = 0;

    while ((kmercodeptr = gt_kmercodeiterator_encseq_next(kmercodeiterator))
                          != NULL)
    {
      gt_insertkmerwithoutspecial(sfi,position++,kmercodeptr);
    }
    gt_kmercodeiterator_delete(kmercodeiterator);
  }
}

#undef DEBUGSIZEESTIMATION
#ifdef DEBUGSIZEESTIMATION
static void verifyestimatedspace(size_t estimatedspace)
{
  unsigned long usedspace_ma_fa = gt_ma_get_space_current() +
                                  gt_fa_get_space_current();
  if (usedspace_ma_fa > 0)
  {
    double relativedifference;

    if (usedspace_ma_fa >= (unsigned long) estimatedspace)
    {
      relativedifference
        = (double) (usedspace_ma_fa - estimatedspace)/usedspace_ma_fa;
    } else
    {
      relativedifference
        = (double) (estimatedspace - usedspace_ma_fa)/estimatedspace;
    }
    if (usedspace_ma_fa > 100000UL &&
        gt_double_larger_double(relativedifference,0.1))
    {
      fprintf(stderr, "%s: relativedifference %.4f too large: "
                      "estimatedspace=%.4f, usedspace_ma_fa=%.4f\n",
                      __func__,relativedifference,
                      GT_MEGABYTES(estimatedspace),
                      GT_MEGABYTES(usedspace_ma_fa));
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  }
}
#endif

GtCodetype gt_kmercode_at_firstpos(const GtTwobitencoding *twobitencoding,
                                   unsigned int kmersize)
{
  const GtCodetype maskright = GT_MASKRIGHT(kmersize);
  return (GtCodetype) (twobitencoding[0] >>
                       GT_MULT2(GT_UNITSIN2BITENC - kmersize)) & maskright;
}

#ifdef SKDEBUG

static void checkallreversebitpairs(void)
{
  unsigned int kmersize, code, coderev, coderevrev, maxcode;

  for (kmersize = 2U; kmersize <= 14U; kmersize++)
  {
    maxcode = (1U << 2 * kmersize)-1;
    printf("kmsize=%u,maxcode=%u\n",kmersize,maxcode);
    for (code = 0; code <= maxcode; code++)
    {
      coderev = gt_kmercode_reverse(code,kmersize);
      coderevrev = gt_kmercode_reverse(coderev,kmersize);
      gt_assert(coderevrev != code);
    }
  }
}
#endif

#define GT_UPDATEKMER(KMER,CC,MASKRIGHT)\
        KMER <<= 2;\
        KMER |= CC;\
        KMER &= MASKRIGHT

#define GT_ADJUSTREVERSEPOS(RB,POS) ((RB) - (POS))

static GtCodetype getencseqkmers_nospecialtwobitencoding(
                                    const GtTwobitencoding *twobitencoding,
                                    unsigned long totallength,
                                    GtCodetype maskright,
                                    GtReadmode readmode,
                                    unsigned int kmersize,
                                    unsigned int upperkmersize,
                                    void(*processkmercode)(void *,
                                                           bool,
                                                           unsigned long,
                                                           GtCodetype),
                                    void *processkmercodeinfo,
                                    bool onlyfirst,
                                    unsigned long startpos,
                                    unsigned long endpos)
{
  unsigned long pos, unitindex, rightbound = totallength - kmersize;
  unsigned int shiftright;
  GtCodetype code;
  GtUchar cc;
  GtTwobitencoding currentencoding;

  gt_assert(kmersize > 1U);
  if (GT_ISDIRREVERSE(readmode))
  {
    unsigned long startpos2;

    gt_assert(endpos >= (unsigned long) upperkmersize);
    pos = endpos - (unsigned long) kmersize;
    unitindex = (pos > 0) ? GT_DIVBYUNITSIN2BITENC(pos-1) : 0;
    code = gt_kmercode_reverse(gt_kmercode_at_position(twobitencoding,pos,
                                                       kmersize),
                               kmersize);
    if (processkmercode != NULL)
    {
      processkmercode(processkmercodeinfo,
                      true,
                      GT_ADJUSTREVERSEPOS(rightbound,pos),
                      GT_ISDIRCOMPLEMENT(readmode)
                        ? gt_kmercode_complement(code,maskright)
                        : code);
    }
    if (onlyfirst)
    {
      return code;
    }
    currentencoding = twobitencoding[unitindex];
    startpos2 = startpos + (upperkmersize - kmersize);
    shiftright = (unsigned int)
                 GT_MULT2(GT_UNITSIN2BITENC - 1 -
                          GT_MODBYUNITSIN2BITENC(pos-1));
    while (pos > startpos2)
    {
      pos--;
      cc = (GtUchar) (currentencoding >> shiftright) & 3;
      GT_UPDATEKMER(code,cc,maskright);
      if (processkmercode != NULL)
      {
        processkmercode(processkmercodeinfo,false,
                        GT_ADJUSTREVERSEPOS(rightbound,pos),
                         (readmode == GT_READMODE_REVCOMPL)
                          ? gt_kmercode_complement(code,maskright)
                          : code);
      }
      if (shiftright < (unsigned int) (GT_INTWORDSIZE-2))
      {
        shiftright += 2;
      } else
      {
        gt_assert(unitindex > 0 || pos == startpos2);
        if (unitindex > 0)
        {
          currentencoding = twobitencoding[--unitindex];
        }
        shiftright = 0;
      }
    }
  } else
  {
    unsigned long maxunitindex = gt_unitsoftwobitencoding(totallength) - 1;

    pos = startpos;
    unitindex = GT_DIVBYUNITSIN2BITENC(startpos+kmersize);
    code = gt_kmercode_at_position(twobitencoding,pos,kmersize);
    if (processkmercode != NULL)
    {
      processkmercode(processkmercodeinfo,true,pos,
                      GT_ISDIRCOMPLEMENT(readmode)
                        ? gt_kmercode_complement(code,maskright)
                        : code);
    }
    if (onlyfirst)
    {
      return code;
    }
    currentencoding = twobitencoding[unitindex];
    shiftright = (unsigned int)
                 GT_MULT2(GT_UNITSIN2BITENC - 1 -
                          GT_MODBYUNITSIN2BITENC(startpos+kmersize));
    while (pos < endpos - (unsigned long) upperkmersize)
    {
      pos++;
      cc = (GtUchar) (currentencoding >> shiftright) & 3;
      GT_UPDATEKMER(code,cc,maskright);
      if (processkmercode != NULL)
      {
        processkmercode(processkmercodeinfo,false,pos,
                          (readmode == GT_READMODE_COMPL)
                            ? gt_kmercode_complement(code,maskright)
                            : code);
      }
      if (shiftright > 0)
      {
        shiftright -= 2;
      } else
      {
        gt_assert(unitindex < maxunitindex-1 ||
                  pos == endpos - (unsigned long) upperkmersize);
        if (unitindex < maxunitindex-1)
        {
          currentencoding = twobitencoding[++unitindex];
        }
        shiftright = (unsigned int) (GT_INTWORDSIZE-2);
      }
    }
  }
  return code;
}

static void getencseqkmers_rangetwobitencoding(
                                      const GtTwobitencoding *twobitencoding,
                                      unsigned long totallength,
                                      unsigned long realtotallength,
                                      bool mirrored,
                                      GtCodetype maskright,
                                      GtReadmode readmode,
                                      unsigned int kmersize,
                                      unsigned int upperkmersize,
                                      bool onlyfirst,
                                      void(*processkmercode)(void *,
                                                             bool,
                                                             unsigned long,
                                                             GtCodetype),
                                      void *processkmercodeinfo,
                                      void(*processkmerspecial)(void *,
                                                                unsigned int,
                                                                unsigned int,
                                                                unsigned long),
                                      void *processkmerspecialinfo,
                                      unsigned long startpos,
                                      unsigned long endpos)
{
  GtCodetype lastcode, newcode;

  if (mirrored && startpos >= realtotallength) {
    gt_readmode_invert(readmode);
    startpos = GT_REVERSEPOS(realtotallength, startpos - realtotallength - 2);
    if (endpos == totallength)
      endpos = 0;
    else
      endpos = GT_REVERSEPOS(realtotallength, endpos - realtotallength - 2);
    if (startpos > endpos) {
      unsigned long tmp = startpos;
      startpos = endpos;
      endpos = tmp;
    }
    gt_assert(startpos <= endpos);
    gt_assert(endpos <= realtotallength);
  }
  if (endpos - startpos >= (unsigned long) upperkmersize)
  {
    gt_assert(endpos > 0);
    lastcode = getencseqkmers_nospecialtwobitencoding(twobitencoding,
                                                      totallength,
                                                      maskright,
                                                      readmode,
                                                      kmersize,
                                                      upperkmersize,
                                                      processkmercode,
                                                      processkmercodeinfo,
                                                      onlyfirst,
                                                      startpos,
                                                      endpos);
    if (processkmerspecial != NULL)
    {
      if (GT_ISDIRCOMPLEMENT(readmode))
      {
        lastcode = gt_kmercode_complement(lastcode,maskright);
      }
      newcode = ((lastcode << 2) | 3UL) & maskright;
      processkmerspecial(processkmerspecialinfo,
                         kmersize-1,
                         (unsigned int) newcode,
                         GT_ISDIRREVERSE(readmode) ? (totallength - startpos)
                                                   : endpos);
    }
  } else
  {
    if (processkmerspecial != NULL && startpos < endpos)
    {
      unsigned int fillpos;

      gt_assert((unsigned long) kmersize > endpos - startpos);
      fillpos = (unsigned int) (kmersize - (endpos - startpos));
      lastcode = gt_kmercode_at_position(twobitencoding,startpos,
                                         (unsigned int) (endpos - startpos));
      if (GT_ISDIRREVERSE(readmode) && (unsigned int) (endpos - startpos) > 1U)
      {
        lastcode = gt_kmercode_reverse(lastcode,
                                       (unsigned int) (endpos-startpos));
      }
      if (GT_ISDIRCOMPLEMENT(readmode))
      {
        lastcode = gt_kmercode_complement(lastcode,maskright);
      }
      newcode
        = ((lastcode << GT_MULT2(fillpos)) | ((1UL << GT_MULT2(fillpos)) - 1))
           & maskright;
      processkmerspecial(processkmerspecialinfo,
                         (unsigned int) (endpos - startpos),
                         (unsigned int) newcode,
                         GT_ISDIRREVERSE(readmode) ? (totallength - startpos)
                                                   : endpos);
    }
  }
}

void getencseqkmers_twobitencoding(const GtEncseq *encseq,
                                   GtReadmode readmode,
                                   unsigned int kmersize,
                                   unsigned int upperkmersize,
                                   bool onlyfirst,
                                   void(*processkmercode)(void *,
                                                          bool,
                                                          unsigned long,
                                                          GtCodetype),
                                   void *processkmercodeinfo,
                                   void(*processkmerspecial)(void *,
                                                             unsigned int,
                                                             unsigned int,
                                                             unsigned long),
                                   void *processkmerspecialinfo)
{
  unsigned long laststart = 0, lastend,
                totallength,
                realtotallength;
  const GtTwobitencoding *twobitencoding
    = gt_encseq_twobitencoding_export(encseq);
  const GtCodetype maskright = GT_MASKRIGHT(kmersize);
  bool mirrored = gt_encseq_is_mirrored(encseq);

  lastend = totallength = realtotallength = gt_encseq_total_length(encseq);
  if (mirrored) {
    gt_assert((totallength & 1) == 1UL);
    realtotallength = ((realtotallength - 1) / 2);
  }
  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;

    if (GT_ISDIRREVERSE(readmode))
    {
      sri = gt_specialrangeiterator_new(encseq,false);
      while (gt_specialrangeiterator_next(sri,&range))
      {
        gt_assert(range.end <= lastend);
        getencseqkmers_rangetwobitencoding(twobitencoding,
                                           totallength,
                                           realtotallength,
                                           mirrored,
                                           maskright,
                                           readmode,
                                           kmersize,
                                           upperkmersize,
                                           onlyfirst,
                                           processkmercode,
                                           processkmercodeinfo,
                                           processkmerspecial,
                                           processkmerspecialinfo,
                                           range.end,
                                           lastend);
        lastend = range.start;
      }
    } else
    {
      sri = gt_specialrangeiterator_new(encseq,true);
      while (gt_specialrangeiterator_next(sri,&range))
      {
        gt_assert(range.start >= laststart);
        getencseqkmers_rangetwobitencoding(twobitencoding,
                                           totallength,
                                           realtotallength,
                                           mirrored,
                                           maskright,
                                           readmode,
                                           kmersize,
                                           upperkmersize,
                                           onlyfirst,
                                           processkmercode,
                                           processkmercodeinfo,
                                           processkmerspecial,
                                           processkmerspecialinfo,
                                           laststart,
                                           range.start);
        laststart = range.end;
      }
    }
    gt_assert(totallength >= laststart);
    gt_specialrangeiterator_delete(sri);
  }
  getencseqkmers_rangetwobitencoding(twobitencoding,
                                     totallength,
                                     realtotallength,
                                     mirrored,
                                     maskright,
                                     readmode,
                                     kmersize,
                                     upperkmersize,
                                     onlyfirst,
                                     processkmercode,
                                     processkmercodeinfo,
                                     processkmerspecial,
                                     processkmerspecialinfo,
                                     GT_ISDIRREVERSE(readmode) ? 0
                                                               : laststart,
                                     GT_ISDIRREVERSE(readmode) ? lastend
                                                               : totallength);
}

static void gt_updateleftborderforkmer(Sfxiterator *sfi,
                                       GT_UNUSED bool firstinrange,
                                       GT_UNUSED unsigned long position,
                                       GT_UNUSED unsigned long seqnum,
                                       GT_UNUSED unsigned long relpos,
                                       GtCodetype code)
{
  gt_assert(sfi->sfxstrategy.spmopt_minlength == 0);
  gt_bcktab_leftborder_addcode(sfi->leftborder,code);
}

static void gt_updateleftborderforspecialkmer(Sfxiterator *sfi,
                                              unsigned int maxprefixindex,
                                              unsigned long position,
                                              unsigned int code)
{
  unsigned int idx;

  gt_assert(sfi->sfxstrategy.spmopt_minlength == 0);
  if (sfi->sfxstrategy.storespecialcodes)
  {
    Codeatposition *spcaptr;
    spcaptr = sfi->spaceCodeatposition + sfi->nextfreeCodeatposition++;
    spcaptr->maxprefixindex = maxprefixindex;
    spcaptr->code = code;
    spcaptr->position = position;
  }
  for (idx=maxprefixindex; idx>=1U; idx--)
  {
    gt_bcktab_leftborder_addcode(sfi->leftborder,(GtCodetype) code);
    code = ((code << 2) | 3U) & sfi->kmerfastmaskright;
  }
}

#define GT_SPMOPT_UPDATELEFTBORDERFORKMER(SFI,FIRSTINRANGE,POSITION,SEQNUM,\
                                          RELPOS,SCANCODE)\
        gt_assert((SFI)->sfxstrategy.spmopt_minlength > 0);\
        if (FIRSTINRANGE || gt_checksuffixprefixbuckets(SFI,SCANCODE))\
        {\
          gt_bcktab_leftborder_addcode((SFI)->leftborder,\
                                       GT_SCANCODE_TO_BCKCODE(SFI,SCANCODE));\
        }

typedef struct
{
  const GtTwobitencoding *twobitencoding;
  unsigned long totallength, maxunitindex, realtotallength, rightbound,
                numofsequences;
  GtCodetype maskright;
  unsigned int kmersize, upperkmersize;
  bool mirrored;
  const GtEncseq *encseq; /* XXX remove later */
} GtSfxmapped4constinfo;

/* This is for checking only
#define GT_ENCSEQ_RELPOS_SEQNUM_CHECK(POS)\
        gt_encseq_relpos_seqnum_check(__FILE__,__LINE__,\
                                      mapped4info->encseq,relpos,\
                                      specialfreeunit,POS)
*/
#define GT_ENCSEQ_RELPOS_SEQNUM_CHECK(POS) /* Nothing */

#define PROCESSKMERPREFIX(FUN) updateleftborder_##FUN
#define PROCESSKMERTYPE        Sfxiterator
#define PROCESSKMERSPECIALTYPE GT_UNUSED Sfxiterator
#define PROCESSKMERCODE        gt_updateleftborderforkmer
#define PROCESSKMERCODESPECIAL gt_updateleftborderforspecialkmer

#include "sfx-mapped4.gen"

#undef PROCESSKMERPREFIX
#undef PROCESSKMERTYPE
#undef PROCESSKMERSPECIALTYPE
#undef PROCESSKMERCODE
#undef PROCESSKMERCODESPECIAL

/* start with next inling */

#define PROCESSKMERPREFIX(FUN) spmopt_updateleftborder_##FUN
#define PROCESSKMERTYPE        Sfxiterator
#define PROCESSKMERSPECIALTYPE GT_UNUSED Sfxiterator
#define PROCESSKMERCODE        GT_SPMOPT_UPDATELEFTBORDERFORKMER
#define GT_IGNORERIGHTBOUND

#include "sfx-mapped4.gen"
#undef GT_IGNORERIGHTBOUND

/* start with next inling */

#undef PROCESSKMERPREFIX
#undef PROCESSKMERTYPE
#undef PROCESSKMERSPECIALTYPE
#undef PROCESSKMERCODE

#define PROCESSKMERPREFIX(FUN)          insertsuffix_##FUN
#define PROCESSKMERTYPE                 Sfxiterator
#define PROCESSKMERSPECIALTYPE          GT_UNUSED Sfxiterator
#define PROCESSKMERCODE                 GT_INSERTKMERWITHOUTSPECIAL1

#include "sfx-mapped4.gen"

#undef PROCESSKMERPREFIX
#undef PROCESSKMERTYPE
#undef PROCESSKMERSPECIALTYPE
#undef PROCESSKMERCODE

/*
#define SHOWCURRENTSPACE\
        printf("spacepeak at line %d: %.2f\n",__LINE__,\
          GT_MEGABYTES(gt_ma_get_space_current() + gt_fa_get_space_current()))
*/

#define SHOWCURRENTSPACE /* Nothing */

static void gt_sfimarkprefixsuffixbuckets(void *processinfo,
                                          GT_UNUSED bool firstinrange,
                                          GT_UNUSED unsigned long pos,
                                          GtCodetype scancode)
{
  Sfxiterator *sfi = (Sfxiterator *) processinfo;
  GtCodetype checkcode = GT_SCANCODE_TO_PREFIXCODE(sfi,scancode);

  gt_assert(firstinrange);
  if (!GT_ISIBITSET(sfi->markprefixbuckets,checkcode))
  {
    GT_SETIBIT(sfi->markprefixbuckets,checkcode);
  }
#ifdef _LP64
  checkcode = GT_SCANCODE_TO_SUFFIXCODE(sfi,scancode);
  if (!GT_ISIBITSET(sfi->marksuffixbuckets,checkcode))
  {
    GT_SETIBIT(sfi->marksuffixbuckets,checkcode);
  }
#endif
}

static size_t gt_sizeforbittable(unsigned int numofchars,
                                 unsigned int prefixlength)
{
  unsigned long numofcodes;

  numofcodes = gt_power_for_small_exponents(numofchars,prefixlength);
  return sizeof (GtBitsequence) * GT_NUMOFINTSFORBITS(numofcodes);
}

static void gt_determineaddionalsuffixprefixchars(
                                   unsigned int *additionalprefixchars,
                                   unsigned int *additionalsuffixchars,
                                   unsigned int numofchars,
                                   unsigned int prefixlength,
                                   size_t estimatedspace,
                                   unsigned long maximumspace)
{
  unsigned int prefixchars;
  size_t sizeofprefixmarks;

  for (prefixchars = 1U;
       prefixlength + prefixchars <= (unsigned int) GT_UNITSIN2BITENC;
       prefixchars++)
  {
    sizeofprefixmarks = gt_sizeforbittable(numofchars,prefixlength+prefixchars);
    if (estimatedspace + sizeofprefixmarks > (size_t) maximumspace)
    {
      prefixchars--;
      break;
    }
  }
  *additionalprefixchars = prefixchars;
#ifdef _LP64
  {
    unsigned int suffixchars;
    size_t sizeofsuffixmarks;
    sizeofprefixmarks = gt_sizeforbittable(numofchars,prefixlength+prefixchars);
    for (suffixchars = 1U;
         prefixlength+prefixchars+prefixlength+suffixchars <=
           (unsigned) GT_UNITSIN2BITENC;
         suffixchars++)
    {
      sizeofsuffixmarks = gt_sizeforbittable(numofchars,
                                             prefixlength+suffixchars);
      if (estimatedspace + sizeofprefixmarks + sizeofsuffixmarks
          > (size_t) maximumspace)
      {
        suffixchars--;
        break;
      }
    }
    if (prefixchars <= suffixchars)
    {
      suffixchars = prefixchars - 1;
    }
    *additionalsuffixchars = suffixchars;
  }
#else
  *additionalsuffixchars = 0;
#endif
}

static unsigned long gt_bcktab_code_to_prefix_index(unsigned long code,
                                                    const void *data)
{
  unsigned int additionalprefixchars, *ptr = (unsigned int *) data;

  additionalprefixchars = *ptr;
  if (GT_MULT2(additionalprefixchars) > (unsigned int) GT_LOGWORDSIZE)
  {
    return (unsigned long) (code << (GT_MULT2(additionalprefixchars) -
                                 GT_LOGWORDSIZE));
  }
  return (unsigned long) (code >> (GT_LOGWORDSIZE -
                                GT_MULT2(additionalprefixchars)));
}

static void gt_bcktab_code_to_minmax_prefix_index(unsigned long *mincode,
                                                  unsigned long *maxcode,
                                                  const void *data)
{
  *mincode = gt_bcktab_code_to_prefix_index(*mincode,data);
  *maxcode = gt_bcktab_code_to_prefix_index(*maxcode,data);
}

Sfxiterator *gt_Sfxiterator_new_withadditionalvalues(
                                const GtEncseq *encseq,
                                GtReadmode readmode,
                                unsigned int prefixlength,
                                unsigned int numofparts,
                                unsigned long maximumspace,
                                void *voidoutlcpinfo,
                                FILE *outfpbcktab,
                                const Sfxstrategy *sfxstrategy,
                                GtTimer *sfxprogress,
                                bool withprogressbar,
                                GtLogger *logger,
                                GtError *err)
{
  Sfxiterator *sfi = NULL;
  unsigned long realspecialranges, specialcharacters, numofsuffixestosort = 0;
  bool haserr = false;
  GtSfxmappedrangelist *sfxmrlist = gt_Sfxmappedrangelist_new();
#ifdef _LP64
  size_t estimatedspace = (size_t) 13131;
#else
  size_t estimatedspace = (size_t) 7968;
#endif

  gt_error_check(err);
  SHOWCURRENTSPACE;
  gt_assert(encseq != NULL);
  estimatedspace += (size_t) gt_encseq_sizeofrep(encseq) +
                             gt_encseq_sizeofstructure();
  realspecialranges = gt_encseq_realspecialranges(encseq);
  specialcharacters = gt_encseq_specialcharacters(encseq);
  gt_assert(prefixlength > 0);
  if (sfxstrategy != NULL)
  {
    if (sfxstrategy->storespecialcodes &&
        prefixlength > (unsigned int) MAXPREFIXLENGTH)
    {
      gt_error_set(err,"argument for option -pl must be in the range [1,%u]",
                    MAXPREFIXLENGTH);
      haserr = true;
    } else
    {
      if (sfxstrategy->spmopt_minlength > 0 &&
          prefixlength > sfxstrategy->spmopt_minlength)
      {
        gt_error_set(err,"argument for option -pl must not be larger "
                         "than argument to option -spmopt");
        haserr = true;
      }
    }
  }
  if (!haserr)
  {
    sfi = gt_malloc(sizeof (*sfi));
    estimatedspace += sizeof (*sfi);
    if (sfxstrategy != NULL && sfxstrategy->storespecialcodes &&
        sfxstrategy->spmopt_minlength == 0)
    {
      sfi->spaceCodeatposition
        = gt_malloc(sizeof (*sfi->spaceCodeatposition) * (realspecialranges+1));
      gt_logger_log(logger,"sizeof (spaceCodeatposition)=%lu bytes",
                 (unsigned long) (sizeof (*sfi->spaceCodeatposition) *
                                          (realspecialranges+1)));
      estimatedspace += sizeof (*sfi->spaceCodeatposition) *
                        (realspecialranges+1);
    } else
    {
      sfi->spaceCodeatposition = NULL;
    }
    sfi->bcktab = NULL;
    sfi->nextfreeCodeatposition = 0;
    sfi->suffixsortspace = NULL;
    sfi->suftabparts = NULL;
    sfi->encseq = encseq;
    sfi->readmode = readmode;
    sfi->numofchars = gt_encseq_alphabetnumofchars(encseq);
    sfi->prefixlength = prefixlength;
    sfi->kmerfastmaskright = (1U << GT_MULT2(prefixlength))-1;
    sfi->mappedmarkprefixbuckets = NULL;
    sfi->markprefixbuckets = NULL;
    sfi->marksuffixbuckets = NULL;
    sfi->outfpbcktab = outfpbcktab;
    sfi->spmopt_kmerscansize = 0;
    sfi->spmopt_numofallprefixcodes = 0;
    sfi->spmopt_numofallsuffixcodes = 0;
    sfi->spmopt_kmerscancodeshift2bckcode = 0;
    sfi->spmopt_kmerscancodeshift2prefixcode = 0;
    sfi->spmopt_kmerscancodesuffixmask = 0;
    sfi->spmopt_additionalprefixchars = 3U;
    sfi->dcov = NULL;
    sfi->withprogressbar = withprogressbar;
    if (sfxstrategy != NULL)
    {
      sfi->sfxstrategy = *sfxstrategy;
      if (sfxstrategy->cmpcharbychar || !gt_encseq_bitwise_cmp_ok(encseq))
      {
        sfi->sfxstrategy.cmpcharbychar = true;
      } else
      {
        sfi->sfxstrategy.cmpcharbychar = false;
      }
    } else
    {
      defaultsfxstrategy(&sfi->sfxstrategy,
                         gt_encseq_bitwise_cmp_ok(encseq) ? false : true);
    }
    gt_logger_log(logger,"maxinsertionsort=%lu",
                  sfi->sfxstrategy.maxinsertionsort);
    gt_logger_log(logger,"maxbltriesort=%lu",
                  sfi->sfxstrategy.maxbltriesort);
    gt_logger_log(logger,"maxcountingsort=%lu",
                  sfi->sfxstrategy.maxcountingsort);
    gt_logger_log(logger,"storespecialcodes=%s",
                  sfi->sfxstrategy.storespecialcodes ? "true" : "false");
    gt_logger_log(logger,"cmpcharbychar=%s",
                  sfi->sfxstrategy.cmpcharbychar ? "true" : "false");
    sfi->totallength = gt_encseq_total_length(encseq);
    gt_logger_log(logger,"totallength=%lu",sfi->totallength);
    sfi->specialcharacters = specialcharacters;
    sfi->outlcpinfo = (GtOutlcpinfo *) voidoutlcpinfo;
    sfi->outlcpinfoforsample = NULL;
    sfi->sri = NULL;
    sfi->part = 0;
    sfi->exhausted = false;
    sfi->bucketiterstep = 0;
    sfi->logger = logger;
    sfi->sfxprogress = sfxprogress;
    if (sfi->sfxstrategy.differencecover > 0 &&
        specialcharacters < sfi->totallength)
    {
      if (sfi->outlcpinfo != NULL)
      {
        sfi->outlcpinfoforsample
          = gt_Outlcpinfo_new(NULL,sfi->numofchars,0,false,false,NULL,NULL,err);
        if (sfi->outlcpinfoforsample == NULL)
        {
          haserr = true;
        }
      }
      if (!haserr)
      {
        /* the following function only has an effect for differencecover > 0 */
        sfi->dcov = gt_differencecover_prepare_sample(
                                     sfi->sfxstrategy.differencecover,
                                     sfi->encseq,
                                     sfi->readmode,
                                     sfi->sfxstrategy.samplewithprefixlengthnull
                                       ? 0 : sfi->prefixlength,
                                     &sfi->sfxstrategy,
                                     sfi->outlcpinfoforsample,
                                     sfi->logger,
                                     sfi->sfxprogress,
                                     err);
        if (sfi->dcov == NULL)
        {
          haserr = true;
        } else
        {
          if (gt_differencecover_is_empty(sfi->dcov))
          {
            gt_differencecover_delete(sfi->dcov);
            sfi->dcov = NULL;
          } else
          {
            size_t dcovspace = gt_differencecover_requiredspace(sfi->dcov);
            gt_logger_log(sfi->logger,"difference cover%srequires %.2f MB"
                           " (%.2f bytes/sample position)",
                          sfi->outlcpinfoforsample != NULL
                            ? " (including RMQ) "
                            : " ",
                          GT_MEGABYTES(dcovspace),
                          (double) dcovspace/
                                   gt_differencecover_samplesize(sfi->dcov));
            estimatedspace += dcovspace;
          }
        }
      }
    }
  }
  if (!haserr)
  {
    bool withspecialsuffixes;
    gt_assert(sfi != NULL);
    withspecialsuffixes = sfi->sfxstrategy.spmopt_minlength == 0 ? true : false;
    sfi->bcktab = gt_bcktab_new(sfi->numofchars,
                                prefixlength,
                                sfi->totallength+1,
                                sfi->sfxstrategy.storespecialcodes,
                                withspecialsuffixes,
                                sfi->logger,
                                err);
    if (sfi->bcktab == NULL)
    {
      sfi->leftborder = NULL;
      haserr = true;
    } else
    {
      uint64_t sizeofbcktab;

      sfi->leftborder = gt_bcktab_leftborder(sfi->bcktab);
      sizeofbcktab
        = gt_bcktab_sizeoftable(sfi->numofchars,prefixlength,
                                sfi->totallength+1,
                                sfi->sfxstrategy.spmopt_minlength == 0 ? true
                                                                       : false);
      estimatedspace += (size_t) sizeofbcktab +
                        gt_bcktab_sizeofworkspace(prefixlength);
    }
    SHOWCURRENTSPACE;
    if (prefixlength > 1U && gt_encseq_has_twobitencoding(sfi->encseq) &&
        sfi->sfxstrategy.spmopt_minlength > 0)
    {
      unsigned int suffixchars = 0, additionalsuffixchars = 2U;
      size_t sizeofprefixmarks, intsforbits;
#ifdef _LP64
      size_t sizeofsuffixmarks;
#endif
      if (maximumspace > 0)
      {
        gt_determineaddionalsuffixprefixchars(
                               &sfi->spmopt_additionalprefixchars,
                               &additionalsuffixchars,
                               sfi->numofchars,
                               prefixlength,
                               estimatedspace,
                               maximumspace);
      }
#ifdef _LP64
      if (sfi->prefixlength + sfi->spmopt_additionalprefixchars +
          sfi->prefixlength + additionalsuffixchars >
          (unsigned int) GT_UNITSIN2BITENC)
      {
        suffixchars = (unsigned int) (GT_UNITSIN2BITENC -
                      (sfi->prefixlength + sfi->spmopt_additionalprefixchars));
      } else
      {
        suffixchars = sfi->prefixlength + additionalsuffixchars;
      }
#endif
      sfi->spmopt_kmerscansize = sfi->prefixlength +
                                 sfi->spmopt_additionalprefixchars +
                                 suffixchars;
      gt_assert(sfi->spmopt_kmerscansize <= (unsigned int) GT_UNITSIN2BITENC);
      sfi->spmopt_kmerscancodeshift2bckcode
        = GT_MULT2(sfi->spmopt_additionalprefixchars + suffixchars);
      sfi->spmopt_kmerscancodeshift2prefixcode
        = GT_MULT2(suffixchars);
      sfi->spmopt_kmerscancodesuffixmask
        = (GtCodetype) ((1UL << GT_MULT2(suffixchars)) - 1);
      sfi->spmopt_numofallprefixcodes
        = gt_power_for_small_exponents(sfi->numofchars,
                                       sfi->prefixlength +
                                       sfi->spmopt_additionalprefixchars);
      GT_INITBITTAB(sfi->markprefixbuckets,
                    sfi->spmopt_numofallprefixcodes);
      intsforbits = GT_NUMOFINTSFORBITS(sfi->spmopt_numofallprefixcodes);
      sizeofprefixmarks = sizeof (*sfi->markprefixbuckets) * intsforbits;
      estimatedspace += sizeofprefixmarks;
      gt_logger_log(sfi->logger,"for all sequences, keep track of "
                                "%u-mers starting at position 0 using a "
                                "table of %lu bytes",
                                sfi->prefixlength +
                                sfi->spmopt_additionalprefixchars,
                                (unsigned long) sizeofprefixmarks);
      sfi->mappedmarkprefixbuckets
        = gt_Sfxmappedrange_new("markprefixbuckets",
                                sfi->spmopt_numofallprefixcodes,
                                GtSfxGtBitsequence,
                                gt_bcktab_code_to_minmax_prefix_index,
                                &sfi->spmopt_additionalprefixchars);
      gt_Sfxmappedrangelist_add(sfxmrlist,sfi->mappedmarkprefixbuckets);
      sfi->spmopt_numofallsuffixcodes
        = gt_power_for_small_exponents(sfi->numofchars,suffixchars);
#ifdef _LP64
      GT_INITBITTAB(sfi->marksuffixbuckets,
                    sfi->spmopt_numofallsuffixcodes);
      sizeofsuffixmarks
        = sizeof (*sfi->marksuffixbuckets) *
                  GT_NUMOFINTSFORBITS(sfi->spmopt_numofallsuffixcodes);
      estimatedspace += sizeofsuffixmarks;
      gt_logger_log(sfi->logger,"for all sequences, keep track of "
                                "%u-mers starting at position %u "
                                "using a table of %lu bytes",
                                suffixchars,
                                sfi->prefixlength +
                                sfi->spmopt_additionalprefixchars,
                                (unsigned long) sizeofsuffixmarks);
#endif
      getencseqkmers_twobitencoding(encseq,
                                    sfi->readmode,
                                    sfi->spmopt_kmerscansize,
                                    sfi->spmopt_kmerscansize,
                                    true,
                                    gt_sfimarkprefixsuffixbuckets,
                                    sfi,
                                    NULL,
                                    NULL);
      if (maximumspace > 0)
      {
        gt_assert(estimatedspace <= (size_t) maximumspace);
      }
      /*printf("estimated space %.2f\n",GT_MEGABYTES(estimatedspace));*/
    }
  }
  SHOWCURRENTSPACE;
  if (!haserr)
  {
    unsigned long largestbucketsize,
                  saved_bucketswithoutwholeleaf;
    gt_assert(sfi != NULL);
    sfi->storespecials = true;
    if (sfxprogress != NULL)
    {
      gt_timer_show_progress(sfxprogress, "counting prefix distribution",
                             stdout);
    }
    if (prefixlength == 1U)
    {
      unsigned int charidx;

      for (charidx=0; charidxnumofchars; charidx++)
      {
        unsigned int updateindex = GT_ISDIRCOMPLEMENT(readmode) ?
                                        GT_COMPLEMENTBASE(charidx) :
                                        charidx;
        gt_bcktab_leftborder_assign(sfi->leftborder,(GtCodetype) updateindex,
                                    gt_encseq_charcount(encseq,
                                                        (GtUchar) charidx));
      }
    } else
    {
      if (gt_encseq_has_twobitencoding(encseq) &&
          !sfi->sfxstrategy.kmerswithencseqreader)
      {
        if (sfi->sfxstrategy.spmopt_minlength == 0)
        {
          updateleftborder_getencseqkmers_twobitencoding(encseq,
                                                         readmode,
                                                         prefixlength,
                                                         prefixlength,
                                                         sfi,
                                                         sfi);
        } else
        {
          gt_assert(sfi->spmopt_kmerscansize > prefixlength);
          spmopt_updateleftborder_getencseqkmers_twobitencoding(
                                            encseq,
                                            readmode,
                                            sfi->spmopt_kmerscansize,
                                            sfi->sfxstrategy.spmopt_minlength,
                                            sfi,
                                            NULL);
        }
      } else
      {
        if (sfi->sfxstrategy.iteratorbasedkmerscanning)
        {
          getencseqkmersupdatekmercount(encseq, readmode, prefixlength, sfi);
        } else
        {
          getencseqkmers(encseq,readmode,prefixlength,updatekmercount,sfi);
        }
      }
      if (sfi->sfxstrategy.storespecialcodes &&
          sfi->sfxstrategy.spmopt_minlength == 0)
      {
        gt_assert(realspecialranges+1 >= sfi->nextfreeCodeatposition);
        gt_reversespecialcodes(sfi->spaceCodeatposition,
                               sfi->nextfreeCodeatposition);
#ifdef SKDEBUG
        verifycodelistcomputation(encseq,
                                  readmode,
                                  realspecialranges,
                                  prefixlength,
                                  sfi->numofchars,
                                  sfi->nextfreeCodeatposition,
                                  sfi->spaceCodeatposition);
#endif
      }
    }
#ifdef SKDEBUG
    gt_bcktab_leftborder_show(sfi->bcktab);
#endif
    largestbucketsize
      = gt_bcktab_leftborderpartialsums(&saved_bucketswithoutwholeleaf,
                                        &numofsuffixestosort,
                                        sfi->bcktab);
    gt_logger_log(sfi->logger, "largest bucket size=%lu",largestbucketsize);
    if (sfi->sfxstrategy.spmopt_minlength > 0)
    {
      gt_logger_log(sfi->logger, "relevant suffixes=%.2f%%",100.0 *
                                        (double) numofsuffixestosort/
                                        (sfi->totallength+1));
      gt_logger_log(sfi->logger,"saved_bucketswithoutwholeleaf=%lu",
                                   saved_bucketswithoutwholeleaf);
      /*
      gt_assert(saved_bucketswithoutwholeleaf +
                numofsuffixestosort ==
                sfi->totallength - specialcharacters);
      */
    }
    if (sfi->outlcpinfo != NULL)
    {
      gt_Outlcpinfo_numsuffixes2output_set(
                                      sfi->outlcpinfo,
                                      sfi->sfxstrategy.spmopt_minlength == 0
                                        ? sfi->totallength + 1
                                        : numofsuffixestosort);
    }
    estimatedspace += sizeof (uint8_t) * largestbucketsize;
    SHOWCURRENTSPACE;
#ifdef DEBUGSIZEESTIMATION
    if (sfi->sfxstrategy.outsuftabonfile)
    {
      verifyestimatedspace(estimatedspace);
    }
#endif
    gt_bcktab_maprange_lb_cs(sfxmrlist,sfi->bcktab);
    if (maximumspace > 0)
    {
      int retval;

      gt_assert(numofparts == 1U);
      retval = gt_suftabparts_fit_memlimit(estimatedspace,
                                           maximumspace,
                                           sfi->bcktab,
                                           NULL,
                                           sfxmrlist,
                                           sfi->totallength,
                                           0, /* bitsforseqnumrelpos not
                                                 needed */
                                           specialcharacters,
                                           numofsuffixestosort,
                                           sfi->sfxstrategy.suftabuint,
                                           err);
      if (retval < 0)
      {
        haserr = true;
      } else
      {
        gt_assert(retval > 0);
        numofparts = (unsigned int) retval;
        gt_logger_log(logger, "derived parts=%u",numofparts);
      }
    }
  }
/*
#define SHOWACTUALSPACE printf("line %d,realspace=heap=%.2f,map=%.2f\n",\
                              __LINE__,\
                              GT_MEGABYTES(gt_ma_get_space_current()),\
                              GT_MEGABYTES(gt_fa_get_space_current()))
*/
#define SHOWACTUALSPACE /* Nothing */
  SHOWACTUALSPACE;
  if (!haserr)
  {
    gt_assert(sfi != NULL);
    sfi->suftabparts = gt_suftabparts_new(numofparts,
                                         sfi->bcktab,
                                         NULL,
                                         sfxmrlist,
                                         numofsuffixestosort,
                                         specialcharacters + 1,
                                         logger);
    gt_assert(sfi->suftabparts != NULL);
    if (gt_suftabparts_numofparts(sfi->suftabparts) > 1U)
    {
      gt_bcktab_storetmp(sfi->bcktab);
    }
    SHOWACTUALSPACE;
    gt_assert(sfi != NULL && sfi->suftabparts != NULL);
    if (gt_suftabparts_numofparts(sfi->suftabparts) > 1U &&
        sfi->sfxstrategy.spmopt_minlength > 0)
    {
      gt_assert(sfi->markprefixbuckets != NULL);
      gt_assert(sfi->mappedmarkprefixbuckets != NULL);
      gt_Sfxmappedrange_storetmp_bitsequence(sfi->mappedmarkprefixbuckets,
                                             &sfi->markprefixbuckets,
                                             false);
      gt_assert(sfi->markprefixbuckets == NULL);
    } else
    {
      gt_Sfxmappedrange_delete(sfi->mappedmarkprefixbuckets);
      sfi->mappedmarkprefixbuckets = NULL;
    }
  }
  SHOWACTUALSPACE;
  if (!haserr)
  {
    gt_assert(sfi != NULL);
    sfi->suffixsortspace
      = gt_suffixsortspace_new(gt_suftabparts_largest_width(sfi->suftabparts),
                               sfi->totallength,
                               sfi->sfxstrategy.suftabuint,
                               logger);
    gt_assert(sfi->suffixsortspace);
    if (gt_encseq_has_specialranges(sfi->encseq))
    {
      sfi->sri = gt_specialrangeiterator_new(sfi->encseq,
                                             GT_ISDIRREVERSE(sfi->readmode)
                                               ? false : true);
    } else
    {
      sfi->sri = NULL;
    }
    sfi->fusp.sssp = sfi->suffixsortspace;
    sfi->fusp.allocatedSuffixptr
      = gt_suftabparts_largest_width(sfi->suftabparts);
    sfi->overhang.start = sfi->overhang.end = 0;
  }
  SHOWACTUALSPACE;
  gt_Sfxmappedrangelist_delete(sfxmrlist);
  if (haserr)
  {
    (void) gt_Sfxiterator_delete(sfi,NULL);
    return NULL;
  }
  return sfi;
}

Sfxiterator *gt_Sfxiterator_new(const GtEncseq *encseq,
                                GtReadmode readmode,
                                unsigned int prefixlength,
                                unsigned int numofparts,
                                unsigned long maximumspace,
                                const Sfxstrategy *sfxstrategy,
                                GtTimer *sfxprogress,
                                bool withprogressbar,
                                GtLogger *logger,
                                GtError *err)
{
  return gt_Sfxiterator_new_withadditionalvalues(
                                encseq,
                                readmode,
                                prefixlength,
                                numofparts,
                                maximumspace,
                                NULL,
                                NULL,
                                sfxstrategy,
                                sfxprogress,
                                withprogressbar,
                                logger,
                                err);
}

static void gt_sfxiterator_preparethispart(Sfxiterator *sfi)
{
  unsigned long sumofwidthforpart;
  GtBucketspec2 *bucketspec2 = NULL;

  if (sfi->part == 0 && sfi->withprogressbar)
  {
    gt_assert(sfi->bcktab != NULL);
    gt_progressbar_start(&sfi->bucketiterstep,
                         (unsigned long long)
                         gt_bcktab_numofallcodes(sfi->bcktab));
  }
  sfi->currentmincode = gt_suftabparts_minindex(sfi->part,sfi->suftabparts);
  sfi->currentmaxcode = gt_suftabparts_maxindex(sfi->part,sfi->suftabparts);
  sfi->widthofpart = gt_suftabparts_widthofpart(sfi->part,sfi->suftabparts);
  if (sfi->sfxprogress != NULL)
  {
    gt_timer_show_progress(sfi->sfxprogress, "inserting suffixes into buckets",
                           stdout);
  }
  if (gt_suftabparts_numofparts(sfi->suftabparts) > 1U)
  {
    gt_logger_log(sfi->logger,"compute part %u: "
                              "%lu suffixes,%lu buckets from "
                              "%lu..%lu",
                  sfi->part,
                  gt_suftabparts_widthofpart(sfi->part,sfi->suftabparts),
                  sfi->currentmaxcode - sfi->currentmincode + 1,
                  sfi->currentmincode,
                  sfi->currentmaxcode);
    gt_bcktab_assignboundsforpart(sfi->bcktab,
                                  sfi->currentmincode,
                                  sfi->currentmaxcode);
    if (sfi->mappedmarkprefixbuckets != NULL)
    {
      sfi->markprefixbuckets
        = (GtBitsequence *)
          gt_Sfxmappedrange_map(sfi->mappedmarkprefixbuckets,
                                sfi->currentmincode,
                                sfi->currentmaxcode);
    }
  }
  SHOWACTUALSPACE;
  gt_suffixsortspace_partoffset_set(sfi->suffixsortspace,
                                    gt_suftabparts_offset(sfi->part,
                                                             sfi->suftabparts));
  if (sfi->sfxstrategy.spmopt_minlength == 0)
  {
    if (sfi->sfxstrategy.storespecialcodes)
    {
      sfx_derivespecialcodesfromtable(sfi,
                          gt_suftabparts_numofparts(sfi->suftabparts) == 1U
                            ? true
                            : false);
    } else
    {
      sfx_derivespecialcodesonthefly(sfi);
    }
  }
  SHOWACTUALSPACE;
  sfi->exportptr = gt_suffixsortspace_exportptr(0,sfi->suffixsortspace);
  if (sfi->prefixlength > 1U
      && gt_encseq_has_twobitencoding(sfi->encseq)
      && !sfi->sfxstrategy.kmerswithencseqreader)
  {
    insertsuffix_getencseqkmers_twobitencoding(
                                     sfi->encseq,
                                     sfi->readmode,
                                     sfi->sfxstrategy.spmopt_minlength == 0
                                       ? sfi->prefixlength
                                       : sfi->spmopt_kmerscansize,
                                     sfi->sfxstrategy.spmopt_minlength == 0
                                       ? sfi->prefixlength
                                       : sfi->sfxstrategy.spmopt_minlength,
                                     sfi,
                                     NULL);
  } else
  {
    if (sfi->sfxstrategy.iteratorbasedkmerscanning)
    {
      getencseqkmersinsertkmerwithoutspecial(sfi->encseq,
                                             sfi->readmode,
                                             sfi->prefixlength,
                                             sfi);
    } else
    {
      getencseqkmers(sfi->encseq,sfi->readmode,sfi->prefixlength,
                     gt_insertkmerwithoutspecial,sfi);
    }
  }
  SHOWACTUALSPACE;
  gt_suffixsortspace_export_done(sfi->suffixsortspace);
  if (sfi->sfxprogress != NULL)
  {
    gt_timer_show_progress(sfi->sfxprogress, "sorting the buckets", stdout);
  }
  /* exit(0); just for testing */
  sumofwidthforpart = gt_suftabparts_sumofwidth(sfi->part,sfi->suftabparts);

  if (gt_suftabparts_numofparts(sfi->suftabparts) == 1U &&
      sfi->outlcpinfo == NULL &&
      sfi->prefixlength >= 2U && sfi->sfxstrategy.spmopt_minlength == 0)
  {
    bucketspec2 = gt_copysort_new(sfi->bcktab,sfi->encseq,sfi->readmode,
                                  sumofwidthforpart,sfi->numofchars);
  }
  SHOWACTUALSPACE;
  if (sfi->sfxstrategy.differencecover > 0 && sfi->dcov != NULL)
  {
    gt_differencecover_set_sssp_lcp(sfi->dcov,sfi->suffixsortspace,
                                    sfi->outlcpinfo);
  }
  if (sfi->part == 0)
  {
    gt_logger_log(sfi->logger,"used workspace for sorting: %.2f MB",
                  GT_MEGABYTES(gt_size_of_sort_workspace (&sfi->sfxstrategy)));
  }
  if (!sfi->sfxstrategy.onlybucketinsertion)
  {
    unsigned int sortmaxdepth;
    GtProcessunsortedsuffixrange processunsortedsuffixrange;

    if (sfi->dcov == NULL)
    {
      if (sfi->sfxstrategy.userdefinedsortmaxdepth == 0)
      {
        sortmaxdepth = 0;
      } else
      {
        sortmaxdepth = sfi->sfxstrategy.userdefinedsortmaxdepth;
      }
      processunsortedsuffixrange = NULL;
    } else
    {
      gt_assert(sfi->sfxstrategy.userdefinedsortmaxdepth == 0);
      sortmaxdepth = sfi->sfxstrategy.differencecover;
      processunsortedsuffixrange = gt_differencecover_sortunsortedbucket;
    }
    gt_assert(sortmaxdepth != 0 || processunsortedsuffixrange == NULL);
    gt_sortallbuckets(sfi->suffixsortspace,
                      sumofwidthforpart,
                      bucketspec2,
                      sfi->encseq,
                      sfi->readmode,
                      sfi->currentmincode,
                      sfi->currentmaxcode,
                      sfi->bcktab,
                      sfi->numofchars,
                      sfi->prefixlength,
                      sfi->outlcpinfo,
                      sortmaxdepth,
                      &sfi->sfxstrategy,
                      processunsortedsuffixrange,
                      (void *) sfi->dcov,
                      &sfi->bucketiterstep,
                      sfi->logger);
  }
  if (bucketspec2 != NULL)
  {
    gt_copysort_derivesorting(bucketspec2,sfi->suffixsortspace,sfi->logger);
    gt_copysort_delete(bucketspec2);
    bucketspec2 = NULL;
  }
  SHOWACTUALSPACE;
  sfi->part++;
}

static void insertfullspecialrange(Sfxiterator *sfi,
                                   unsigned long leftpos,
                                   unsigned long rightpos)
{
  unsigned long pos;

  gt_assert(leftpos < rightpos);
  if (GT_ISDIRREVERSE(sfi->readmode))
  {
    pos = rightpos - 1;
  } else
  {
    pos = leftpos;
  }
  while (true)
  {
    if (GT_ISDIRREVERSE(sfi->readmode))
    {
      gt_assert(pos < sfi->totallength);
      gt_suffixsortspace_setdirect(sfi->fusp.sssp,
                                   sfi->fusp.nextfreeSuffixptr,
                                   GT_REVERSEPOS(sfi->totallength,pos));
      sfi->fusp.nextfreeSuffixptr++;
      if (pos == leftpos)
      {
        break;
      }
      pos--;
    } else
    {
      gt_suffixsortspace_setdirect(sfi->fusp.sssp,
                                   sfi->fusp.nextfreeSuffixptr,
                                   pos);
      sfi->fusp.nextfreeSuffixptr++;
      if (pos == rightpos-1)
      {
        break;
      }
      pos++;
    }
  }
}

static void fillspecialnextpage(Sfxiterator *sfi)
{
  GtRange range;
  unsigned long width;

  while (true)
  {
    if (sfi->overhang.start < sfi->overhang.end)
    {
      width = sfi->overhang.end - sfi->overhang.start;
      if (sfi->fusp.nextfreeSuffixptr + width > sfi->fusp.allocatedSuffixptr)
      {
        /* does not fit into the buffer, so only output a part */
        unsigned long rest = sfi->fusp.nextfreeSuffixptr +
                             width - sfi->fusp.allocatedSuffixptr;
        gt_assert(rest > 0);
        if (GT_ISDIRREVERSE(sfi->readmode))
        {
          insertfullspecialrange(sfi,sfi->overhang.start + rest,
                                 sfi->overhang.end);
          sfi->overhang.end = sfi->overhang.start + rest;
        } else
        {
          insertfullspecialrange(sfi,sfi->overhang.start,
                                 sfi->overhang.end - rest);
          sfi->overhang.start = sfi->overhang.end - rest;
        }
        break;
      }
      if (sfi->fusp.nextfreeSuffixptr + width == sfi->fusp.allocatedSuffixptr)
      { /* overhang fits into the buffer and buffer is full */
        insertfullspecialrange(sfi,sfi->overhang.start,sfi->overhang.end);
        sfi->overhang.start = sfi->overhang.end = 0;
        break;
      }
      /* overhang fits into the buffer and buffer is not full */
      insertfullspecialrange(sfi,sfi->overhang.start,sfi->overhang.end);
      sfi->overhang.start = sfi->overhang.end = 0;
    } else
    {
      if (sfi->sri != NULL && gt_specialrangeiterator_next(sfi->sri,&range))
      {
        width = range.end - range.start;
        gt_assert(width > 0);
        if (sfi->fusp.nextfreeSuffixptr + width > sfi->fusp.allocatedSuffixptr)
        { /* does not fit into the buffer, so only output a part */
          unsigned long rest = sfi->fusp.nextfreeSuffixptr +
                               width - sfi->fusp.allocatedSuffixptr;
          if (GT_ISDIRREVERSE(sfi->readmode))
          {
            insertfullspecialrange(sfi,range.start + rest, range.end);
            sfi->overhang.start = range.start;
            sfi->overhang.end = range.start + rest;
          } else
          {
            insertfullspecialrange(sfi,range.start,range.end - rest);
            sfi->overhang.start = range.end - rest;
            sfi->overhang.end = range.end;
          }
          break;
        }
        if (sfi->fusp.nextfreeSuffixptr + width == sfi->fusp.allocatedSuffixptr)
        { /* overhang fits into the buffer and buffer is full */
          insertfullspecialrange(sfi,range.start,range.end);
          sfi->overhang.start = sfi->overhang.end = 0;
          break;
        }
        insertfullspecialrange(sfi,range.start,range.end);
        sfi->overhang.start = sfi->overhang.end = 0;
      } else
      {
        if (sfi->fusp.nextfreeSuffixptr < sfi->fusp.allocatedSuffixptr)
        {
          gt_suffixsortspace_setdirect(sfi->fusp.sssp,
                                       sfi->fusp.nextfreeSuffixptr,
                                       sfi->totallength);
          sfi->fusp.nextfreeSuffixptr++;
          sfi->exhausted = true;
        }
        break;
      }
    }
  }
}

const GtSuffixsortspace *gt_Sfxiterator_next(unsigned long *numberofsuffixes,
                                             bool *specialsuffixes,
                                             Sfxiterator *sfi)
{
  if (sfi->part < gt_suftabparts_numofparts(sfi->suftabparts))
  {
    gt_sfxiterator_preparethispart(sfi);
    *numberofsuffixes = sfi->widthofpart;
    if (specialsuffixes != NULL)
    {
      *specialsuffixes = false;
    }
    return sfi->suffixsortspace;
  }
  if (sfi->exhausted)
  {
    if (sfi->withprogressbar)
    {
      gt_progressbar_stop();
    }
    return NULL;
  }
  sfi->fusp.nextfreeSuffixptr = 0;
  if (sfi->sfxstrategy.spmopt_minlength == 0)
  {
    gt_suffixsortspace_partoffset_set(sfi->suffixsortspace,
                                      sfi->totallength-sfi->specialcharacters);
    fillspecialnextpage(sfi);
    gt_assert(sfi->fusp.nextfreeSuffixptr > 0);
  } else
  {
    sfi->exhausted = true;
  }
  *numberofsuffixes = sfi->fusp.nextfreeSuffixptr;
  if (specialsuffixes != NULL)
  {
    *specialsuffixes = true;
  }
  return sfi->suffixsortspace;
}

int gt_Sfxiterator_bcktab2file(FILE *fp, Sfxiterator *sfi, GtError *err)
{
  gt_error_check(err);
  gt_assert(sfi != NULL && sfi->bcktab != NULL);
  if (gt_suftabparts_numofparts(sfi->suftabparts) <= 1U)
  {
    int ret = gt_bcktab_flush_to_file(fp,sfi->bcktab,err);
    gt_fa_fclose(fp);
    return ret;
  }
  return 0;
}

unsigned long gt_Sfxiterator_longest(const Sfxiterator *sfi)
{
  gt_assert(sfi != NULL);
  if (sfi->sfxstrategy.spmopt_minlength == 0)
  {
    return gt_suffixsortspace_longest(sfi->suffixsortspace);
  } else
  {
    return 0;
  }
}
genometools-1.5.1/src/match/sfx-suffixer.h000066400000000000000000000102011211610345200205230ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_SUFFIXER_H
#define SFX_SUFFIXER_H

#include "core/encseq_api.h"
#include "core/error.h"
#include "core/logger.h"
#include "core/readmode.h"
#include "core/timer_api.h"
#include "core/intbits.h"
#include "core/codetype.h"
#include "extended/uint64hashtable.h"
#include "firstcodes-buf.h"
#include "sfx-suffixgetset.h"
#include "sfx-strategy.h"

typedef struct Sfxiterator Sfxiterator;

int gt_Sfxiterator_delete(Sfxiterator *sfi,GtError *err);

Sfxiterator *gt_Sfxiterator_new(const GtEncseq *encseq,
                                GtReadmode readmode,
                                unsigned int prefixlength,
                                unsigned int numofparts,
                                unsigned long maximumspace,
                                const Sfxstrategy *sfxstrategy,
                                GtTimer *sfxprogress,
                                bool withprogressbar,
                                GtLogger *logger,
                                GtError *err);

Sfxiterator *gt_Sfxiterator_new_withadditionalvalues(
                                const GtEncseq *encseq,
                                GtReadmode readmode,
                                unsigned int prefixlength,
                                unsigned int numofparts,
                                unsigned long maximumspace,
                                void *voidoutlcpinfo,
                                FILE *outfpbcktab,
                                const Sfxstrategy *sfxstrategy,
                                GtTimer *sfxprogress,
                                bool withprogressbar,
                                GtLogger *logger,
                                GtError *err);

const GtSuffixsortspace *gt_Sfxiterator_next(unsigned long *numberofsuffixes,
                                             bool *specialsuffixes,
                                             Sfxiterator *sfi);

int gt_Sfxiterator_postsortfromstream(Sfxiterator *sfi,
                                      const GtStr *indexname,
                                      GtError *err);

int gt_Sfxiterator_bcktab2file(FILE *fp,Sfxiterator *sfi,GtError *err);

unsigned long gt_Sfxiterator_longest(const Sfxiterator *sfi);

GtCodetype gt_kmercode_at_firstpos(const GtTwobitencoding *twobitencoding,
                                   unsigned int kmersize);

void getencseqkmers_twobitencoding(const GtEncseq *encseq,
                                   GtReadmode readmode,
                                   unsigned int kmersize,
                                   unsigned int upperkmersize,
                                   bool onlyfirst,
                                   void(*processkmercode)(void *,
                                                          bool,
                                                          unsigned long,
                                                          GtCodetype),
                                   void *processkmercodeinfo,
                                   void(*processkmerspecial)(void *,
                                                             unsigned int,
                                                             unsigned int,
                                                             unsigned long),
                                   void *processkmerspecialinfo);

#endif
genometools-1.5.1/src/match/sfx-suffixgetset.c000066400000000000000000000334731211610345200214230ustar00rootroot00000000000000/*
  Copyright (c) 2010 Stefan Kurtz 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include "core/assert_api.h"
#include "core/defined-types.h"
#include "core/fa.h"
#include "core/log_api.h"
#include "core/logger_api.h"
#include "core/ma_api.h"
#include "core/mathsupport.h"
#include "core/safearith.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "sfx-suffixgetset.h"

struct GtSuffixsortspace
{
  bool unmapsortspace, currentexport;
  Definedunsignedlong longestidx;
  uint32_t *uinttab;
  size_t basesize;
  GtSuffixsortspace_exportptr exportptr;
  unsigned long maxindex,
                maxvalue,
                partoffset,
                bucketleftidx,
                *ulongtab;
};

static bool gt_decide_to_use_uint(bool useuint,unsigned long maxvalue)
{
  if (useuint && maxvalue <= (unsigned long) UINT_MAX)
  {
    return true;
  }
  return false;
}

uint64_t gt_suffixsortspace_requiredspace(unsigned long numofentries,
                                          unsigned long maxvalue,
                                          bool useuint)
{
  uint64_t requiredspace = (uint64_t) sizeof (GtSuffixsortspace);

  if (gt_decide_to_use_uint(useuint,maxvalue))
  {
    gt_assert(maxvalue <= (unsigned long) UINT_MAX);
    requiredspace += (uint64_t) numofentries * (uint64_t) sizeof (uint32_t);
  } else
  {
    requiredspace += (uint64_t) numofentries *
                     (uint64_t) sizeof (unsigned long);
  }
  return requiredspace;
}

static void gt_suffixsortspace_overflow_abort(GT_UNUSED const char *f,
                                              GT_UNUSED int l,
                                              void *data)
{
  fprintf(stderr, "error: overflow detected while calculating size of "
                  "suffix sorting space: %lu * %lu bytes is too large for "
                  "the current platform, please recompile GenomeTools with "
                  "support for a larger address space to prevent this (e.g. "
                  "64 bit instead of 32 bit) or use the `-parts' option.\n",
                  (unsigned long) sizeof (unsigned long),
                  *(unsigned long*) data);
  exit(GT_EXIT_PROGRAMMING_ERROR);
}

GtSuffixsortspace *gt_suffixsortspace_new(unsigned long numofentries,
                                          unsigned long maxvalue,
                                          bool useuint,
                                          GT_UNUSED GtLogger *logger)
{
  GtSuffixsortspace *suffixsortspace;
  unsigned long sufspacesize;

  gt_assert(numofentries > 0);
  suffixsortspace = gt_malloc(sizeof (*suffixsortspace));
  suffixsortspace->maxindex = numofentries-1;
  suffixsortspace->maxvalue = maxvalue;
  suffixsortspace->longestidx.defined = false;
  suffixsortspace->longestidx.valueunsignedlong = 0;
  suffixsortspace->exportptr.ulongtabsectionptr = NULL;
  suffixsortspace->exportptr.uinttabsectionptr = NULL;
  suffixsortspace->currentexport = false;
#ifdef _LP64
  gt_logger_log(logger,"suftab uses %dbit values: "
                         "maxvalue=%lu,numofentries=%lu",
                         gt_decide_to_use_uint(useuint,maxvalue) ? 32 : 64,
                         maxvalue,numofentries);
#endif
  suffixsortspace->basesize = gt_decide_to_use_uint(useuint,maxvalue)
                                ? sizeof (*suffixsortspace->uinttab)
                                : sizeof (*suffixsortspace->ulongtab);
  sufspacesize
    = gt_safe_mult_ulong_check((unsigned long) suffixsortspace->basesize,
                               numofentries,
                               gt_suffixsortspace_overflow_abort,
                               &numofentries);
  gt_log_log("sizeof (suftab)=%lu bytes",sufspacesize);
  if (gt_decide_to_use_uint(useuint,maxvalue))
  {
    suffixsortspace->ulongtab = NULL;
    suffixsortspace->uinttab = gt_malloc((size_t) sufspacesize);
  } else
  {
    suffixsortspace->uinttab = NULL;
    suffixsortspace->ulongtab = gt_malloc((size_t) sufspacesize);
  }
  suffixsortspace->partoffset = 0;
  suffixsortspace->bucketleftidx = 0;
  suffixsortspace->unmapsortspace = false;
  return suffixsortspace;
}

GtSuffixsortspace *gt_suffixsortspace_new_fromfile(int filedesc,
                                                   const char *filename,
                                                   unsigned long numofentries,
                                                   unsigned long maxvalue,
                                                   bool useuint)
{
  GtSuffixsortspace *suffixsortspace;
  void *ptr;

  suffixsortspace = gt_malloc(sizeof (*suffixsortspace));
  suffixsortspace->basesize = gt_decide_to_use_uint(useuint,maxvalue)
                                ? sizeof (*suffixsortspace->uinttab)
                                : sizeof (*suffixsortspace->ulongtab);
  ptr = gt_fa_mmap_generic_fd(filedesc,filename,
                              (size_t) numofentries * suffixsortspace->basesize,
                              (size_t) 0,false,false,NULL);
  if (gt_decide_to_use_uint(useuint,maxvalue))
  {
    suffixsortspace->uinttab = ptr;
    suffixsortspace->ulongtab = NULL;
  } else
  {
    suffixsortspace->ulongtab = ptr;
    suffixsortspace->uinttab = NULL;
  }
  suffixsortspace->partoffset = 0;
  suffixsortspace->bucketleftidx = 0;
  suffixsortspace->unmapsortspace = true;
  suffixsortspace->maxindex = numofentries - 1;
  suffixsortspace->maxvalue = maxvalue;
  suffixsortspace->longestidx.defined = false;
  suffixsortspace->longestidx.valueunsignedlong = 0;
  suffixsortspace->exportptr.ulongtabsectionptr = NULL;
  suffixsortspace->exportptr.uinttabsectionptr = NULL;
  suffixsortspace->currentexport = false;
  return suffixsortspace;
}

void gt_suffixsortspace_delete(GtSuffixsortspace *suffixsortspace,
                               GT_UNUSED bool checklongestdefined)
{
  if (suffixsortspace != NULL)
  {
    gt_assert(!checklongestdefined || suffixsortspace->longestidx.defined);
    if (suffixsortspace->unmapsortspace)
    {
      gt_fa_xmunmap(suffixsortspace->ulongtab);
      gt_fa_xmunmap(suffixsortspace->uinttab);
    } else
    {
      gt_free(suffixsortspace->uinttab);
      gt_free(suffixsortspace->ulongtab);
    }
    gt_free(suffixsortspace);
  }
}

void gt_suffixsortspace_nooffsets(GT_UNUSED const GtSuffixsortspace *sssp)
{
  gt_assert(sssp->partoffset == 0);
  gt_assert(sssp->bucketleftidx == 0);
}

unsigned long gt_suffixsortspace_getdirect(const GtSuffixsortspace *sssp,
                                           unsigned long idx)
{
  gt_assert(idx <= sssp->maxindex);
  if (sssp->ulongtab != NULL)
  {
    return sssp->ulongtab[idx];
  }
  gt_assert(sssp->uinttab != NULL);
  return (unsigned long) sssp->uinttab[idx];
}

void gt_suffixsortspace_updatelongest(GtSuffixsortspace *sssp,unsigned long idx)
{
  sssp->longestidx.defined = true;
  sssp->longestidx.valueunsignedlong = sssp->bucketleftidx + idx;
}

void gt_suffixsortspace_setdirect(GtSuffixsortspace *sssp,
                                  unsigned long idx,
                                  unsigned long value)
{
  gt_assert(idx <= sssp->maxindex && value <= sssp->maxvalue);
  if (value == 0)
  {
    sssp->longestidx.defined = true;
    sssp->longestidx.valueunsignedlong = sssp->partoffset + idx;
  }
  if (sssp->ulongtab != NULL)
  {
    sssp->ulongtab[idx] = value;
  } else
  {
    gt_assert (sssp->uinttab != NULL);
    gt_assert (value <= (unsigned long) UINT_MAX);
    sssp->uinttab[idx] = (uint32_t) value;
  }
}

void gt_suffixsortspace_showrange(const GtSuffixsortspace *sssp,
                                  unsigned long subbucketleft,
                                  unsigned long width)
{
  unsigned long idx;

  printf("%lu,%lu=",sssp->bucketleftidx+subbucketleft-sssp->partoffset,
                    sssp->bucketleftidx+subbucketleft+width-1-sssp->partoffset);
  for (idx=sssp->bucketleftidx+subbucketleft-sssp->partoffset;
       idxbucketleftidx+subbucketleft+width-sssp->partoffset;
       idx++)
  {
    printf(" %lu", gt_suffixsortspace_getdirect(sssp,idx));
  }
}

void gt_suffixsortspace_checkorder(const GtSuffixsortspace *sssp,
                                   unsigned long subbucketleft,
                                   unsigned long width)
{
  unsigned long idx, currentpos;
  GT_UNUSED unsigned long prevpos;

  gt_assert(width > 0);
  prevpos = gt_suffixsortspace_getdirect(sssp,
                                         sssp->bucketleftidx+subbucketleft -
                                         sssp->partoffset);
  for (idx=sssp->bucketleftidx+subbucketleft - sssp->partoffset + 1;
       idxbucketleftidx+subbucketleft + width - sssp->partoffset;
       idx++)
  {
    currentpos = gt_suffixsortspace_getdirect(sssp,idx);
    gt_assert(prevpos > currentpos);
    prevpos = currentpos;
  }
}

GtSuffixsortspace_exportptr *gt_suffixsortspace_exportptr(
                                  unsigned long subbucketleft,
                                  GtSuffixsortspace *sssp)
{
  if (sssp->ulongtab != NULL)
  {
    sssp->exportptr.ulongtabsectionptr = sssp->ulongtab + sssp->bucketleftidx
                                                        + subbucketleft
                                                        - sssp->partoffset;
    sssp->exportptr.uinttabsectionptr = NULL;
  } else
  {
    gt_assert(sssp->uinttab != NULL);
    sssp->exportptr.uinttabsectionptr = sssp->uinttab + sssp->bucketleftidx
                                                      + subbucketleft
                                                      - sssp->partoffset;
    sssp->exportptr.ulongtabsectionptr = NULL;
  }
  sssp->currentexport = true;
  return &sssp->exportptr;
}

void gt_suffixsortspace_export_done(GtSuffixsortspace *sssp)
{
  sssp->exportptr.ulongtabsectionptr = NULL;
  sssp->exportptr.uinttabsectionptr = NULL;
  sssp->currentexport = false;
}

unsigned long gt_suffixsortspace_get(const GtSuffixsortspace *sssp,
                                     unsigned long subbucketleft,
                                     unsigned long idx)
{
  return gt_suffixsortspace_getdirect(sssp, sssp->bucketleftidx
                                              + subbucketleft
                                              + idx
                                              - sssp->partoffset);
}

const unsigned long *gt_suffixsortspace_getptr_ulong(
                                               const GtSuffixsortspace *sssp,
                                               unsigned long subbucketleft)
{
  if (sssp->ulongtab != NULL)
  {
    return sssp->ulongtab + sssp->bucketleftidx + subbucketleft
                          - sssp->partoffset;
  } else
  {
    return NULL;
  }
}

const uint32_t *gt_suffixsortspace_getptr_uint32(const GtSuffixsortspace *sssp,
                                                 unsigned long subbucketleft)
{
  if (sssp->uinttab != NULL)
  {
    return sssp->uinttab + sssp->bucketleftidx + subbucketleft
                         - sssp->partoffset;
  } else
  {
    return NULL;
  }
}

void gt_suffixsortspace_set(GtSuffixsortspace *sssp,
                            unsigned long subbucketleft,
                            unsigned long idx,
                            unsigned long value)
{
  gt_suffixsortspace_setdirect(sssp, sssp->bucketleftidx
                                       + subbucketleft
                                       + idx
                                       - sssp->partoffset,value);
}

unsigned long gt_suffixsortspace_bucketleftidx_get(const GtSuffixsortspace
                                                   *sssp)
{
  gt_assert(sssp != NULL);
  return sssp->bucketleftidx;
}

void gt_suffixsortspace_bucketleftidx_set(GtSuffixsortspace *sssp,
                                          unsigned long value)
{
  gt_assert(sssp->bucketleftidx == value || !sssp->currentexport);
  sssp->bucketleftidx = value;
}

void gt_suffixsortspace_partoffset_set(GtSuffixsortspace *sssp,
                                       unsigned long partoffset)
{
  gt_assert(sssp->partoffset == partoffset || !sssp->currentexport);
  sssp->partoffset = partoffset;
}

void gt_suffixsortspace_sortspace_delete(GtSuffixsortspace *sssp)
{
  gt_free(sssp->ulongtab);
  sssp->ulongtab = NULL;
  gt_free(sssp->uinttab);
  sssp->uinttab = NULL;
}

unsigned long *gt_suffixsortspace_ulong_get(const GtSuffixsortspace *sssp)
{
  gt_assert(sssp->ulongtab != NULL);
  return (unsigned long *) sssp->ulongtab; /* XXX constrain the type cast */
}

unsigned long gt_suffixsortspace_longest(const GtSuffixsortspace *sssp)
{
  gt_assert(sssp->longestidx.defined);
  return sssp->longestidx.valueunsignedlong;
}

int gt_suffixsortspace_to_file (FILE *outfpsuftab,
                                const GtSuffixsortspace *sssp,
                                unsigned long numberofsuffixes,
                                GT_UNUSED GtError *err)
{
  bool haserr = false;
  size_t basesize = sssp->ulongtab != NULL ? sizeof (*sssp->ulongtab)
                                           : sizeof (*sssp->uinttab);

  gt_xfwrite(sssp->ulongtab != NULL ? (void *) sssp->ulongtab
                                    : (void *) sssp->uinttab,
             basesize,
             (size_t) numberofsuffixes,
             outfpsuftab);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/sfx-suffixgetset.h000066400000000000000000000127511211610345200214240ustar00rootroot00000000000000/*
  Copyright (c) 2010 Stefan Kurtz 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_SUFFIXGETSET_H
#define SFX_SUFFIXGETSET_H

#include 
#include 
#include "core/unused_api.h"
#include "core/logger_api.h"
#include "core/error_api.h"

#define GT_SUFFIXSORTSPACE_EXPORT_SET(SSSP,EXPORTPTR,INDEX,POS)\
        if ((EXPORTPTR)->ulongtabsectionptr != NULL)\
        {\
          (EXPORTPTR)->ulongtabsectionptr[INDEX] = POS;\
        } else\
        {\
          gt_assert((EXPORTPTR)->uinttabsectionptr != NULL);\
          gt_assert(POS <= (unsigned long) UINT_MAX);\
          (EXPORTPTR)->uinttabsectionptr[INDEX] = (uint32_t) POS;\
        }\
        if (POS == 0)\
        {\
          gt_suffixsortspace_updatelongest(SSSP,INDEX);\
        }

typedef struct GtSuffixsortspace GtSuffixsortspace;

typedef struct
{
  uint32_t *uinttabsectionptr;
  unsigned long *ulongtabsectionptr;
} GtSuffixsortspace_exportptr;

typedef void (*GtProcessunsortedsuffixrange)(void *,
                                             unsigned long,
                                             unsigned long,
                                             unsigned long);

GtSuffixsortspace *gt_suffixsortspace_new(unsigned long numofentries,
                                          unsigned long maxvalue,
                                          bool useuint,
                                          GtLogger *logger);

GtSuffixsortspace *gt_suffixsortspace_new_fromfile(int filedesc,
                                                   const char *filename,
                                                   unsigned long numofentries,
                                                   unsigned long maxvalue,
                                                   bool useuint);

void gt_suffixsortspace_delete(GT_UNUSED GtSuffixsortspace *suffixsortspace,
                               GT_UNUSED bool checklongestdefined);

void gt_suffixsortspace_showrange(const GtSuffixsortspace *sssp,
                                  unsigned long subbucketleft,
                                  unsigned long width);

void gt_suffixsortspace_checkorder(const GtSuffixsortspace *sssp,
                                   unsigned long subbucketleft,
                                   unsigned long width);

unsigned long gt_suffixsortspace_getdirect(const GtSuffixsortspace *sssp,
                                           unsigned long idx);

void gt_suffixsortspace_nooffsets(const GtSuffixsortspace *sssp);

void gt_suffixsortspace_updatelongest(GtSuffixsortspace *sssp,
                                      unsigned long idx);

void gt_suffixsortspace_setdirect(GtSuffixsortspace *sssp,
                                  unsigned long idx,
                                  unsigned long value);

GtSuffixsortspace_exportptr *gt_suffixsortspace_exportptr(
                                  unsigned long subbucketleft,
                                  GtSuffixsortspace *sssp);

void gt_suffixsortspace_export_done(GtSuffixsortspace *sssp);

unsigned long gt_suffixsortspace_get(const GtSuffixsortspace *sssp,
                                     unsigned long subbucketleft,
                                     unsigned long idx);

const unsigned long *gt_suffixsortspace_getptr_ulong(
                                               const GtSuffixsortspace *sssp,
                                               unsigned long subbucketleft);

const uint32_t *gt_suffixsortspace_getptr_uint32(const GtSuffixsortspace *sssp,
                                                 unsigned long subbucketleft);

void gt_suffixsortspace_set(GtSuffixsortspace *sssp,
                            unsigned long subbucketleft,
                            unsigned long idx,
                            unsigned long value);

unsigned long gt_suffixsortspace_bucketleftidx_get(
                    const GtSuffixsortspace *sssp);

void gt_suffixsortspace_bucketleftidx_set(GtSuffixsortspace *sssp,
                                          unsigned long value);

void gt_suffixsortspace_sortspace_delete(GtSuffixsortspace *sssp);

void gt_suffixsortspace_partoffset_set(GtSuffixsortspace *sssp,
                                       unsigned long partoffset);

unsigned long *gt_suffixsortspace_ulong_get(const GtSuffixsortspace *sssp);

unsigned long gt_suffixsortspace_longest(const GtSuffixsortspace *sssp);

uint64_t gt_suffixsortspace_requiredspace(unsigned long numofentries,
                                          unsigned long maxvalue,
                                          bool useuint);

int gt_suffixsortspace_to_file (FILE *outfpsuftab,
                                const GtSuffixsortspace *sssp,
                                unsigned long numberofsuffixes,
                                GtError *err);
#endif
genometools-1.5.1/src/match/sfx-suftaborder.c000066400000000000000000000164331211610345200212200ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/unused_api.h"
#include "core/chardef.h"
#include "core/minmax.h"
#include "core/encseq.h"
#include "sfx-suftaborder.h"
#include "sfx-suffixgetset.h"

static void showcomparisonfailure(const char *filename,
                                  int line,
                                  const char *where,
                                  const GtEncseq *encseq,
                                  GtReadmode readmode,
                                  const GtSuffixsortspace *suffixsortspace,
                                  unsigned long subbucketleft,
                                  unsigned long depth,
                                  unsigned long idx1,
                                  unsigned long idx2,
                                  int cmp,
                                  unsigned long maxlcp)
{
  unsigned long pos1, pos2;

  pos1 = gt_suffixsortspace_get(suffixsortspace,subbucketleft,idx1);
  pos2 = gt_suffixsortspace_get(suffixsortspace,subbucketleft,idx2);
  fprintf(stderr,"ERROR: file \"%s\", line %d: ",filename,line);
  fprintf(stderr,"%s(%lu vs %lu"
                 " %lu=\"",
                       where,
                       idx1,
                       idx2,
                       pos1);
  gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,pos1,depth);
  fprintf(stderr,"\",\"");
  gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,pos2,depth);
  fprintf(stderr,"\"=%lu)=%d with maxlcp %lu,depth=%lu\n",pos2,cmp,
          maxlcp,depth);
}

void gt_checkifprefixesareidentical(const char *filename,
                                    int line,
                                    const GtEncseq *encseq,
                                    GtReadmode readmode,
                                    const GtSuffixsortspace *suffixsortspace,
                                    unsigned long subbucketleft,
                                    unsigned long width,
                                    unsigned long depth)
{
  unsigned long idx, maxlcp, pos1, pos2;
  int cmp;
  GtEncseqReader *esr1, *esr2;

  esr1 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  esr2 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  gt_assert(depth > 0);
  for (idx = 0; idx < width-1; idx++)
  {
    pos1 = gt_suffixsortspace_get(suffixsortspace,subbucketleft,idx);
    pos2 = gt_suffixsortspace_get(suffixsortspace,subbucketleft,idx+1);
    cmp = gt_encseq_check_comparetwosuffixes(encseq,
                                             readmode,
                                             &maxlcp,
                                             false, /* specialsareequal */
                                             true,/* specialsareequalatdepth0 */
                                             depth,pos1,
                                             pos2,
                                             esr1,
                                             esr2);
    gt_assert(maxlcp <= depth);
    if (cmp != 0 || maxlcp < depth)
    {
      showcomparisonfailure(filename,
                            line,
                            "checkifprefixesareidentical",
                            encseq,
                            readmode,
                            suffixsortspace,
                            subbucketleft,
                            depth,
                            idx,idx+1,cmp,maxlcp);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  }
  gt_encseq_reader_delete(esr1);
  gt_encseq_reader_delete(esr2);
}

void gt_showentiresuftab(const GtEncseq *encseq,
                         GtReadmode readmode,
                         const GtSuffixsortspace *suffixsortspace,
                         unsigned long subbucketleft,
                         unsigned long depth)
{
  unsigned long idx, pos, totallength = gt_encseq_total_length(encseq);

  for (idx = 0; idx <= totallength; idx++)
  {
    pos = gt_suffixsortspace_get(suffixsortspace,subbucketleft,idx);
    printf("suftab[%lu]=%lu ",idx,pos);
    gt_encseq_showatstartposwithdepth(stdout,encseq,readmode,pos,depth);
    printf("\n");
  }
}

void gt_checksortedsuffixes(const char *filename,
                            int line,
                            const GtEncseq *encseq,
                            GtReadmode readmode,
                            const GtSuffixsortspace *suffixsortspace,
                            unsigned long subbucketleft,
                            unsigned long numberofsuffixes,
                            bool specialsareequal,
                            bool specialsareequalatdepth0,
                            unsigned long depth)
{
  unsigned long idx, pos1, pos2, maxlcp,
                totallength = gt_encseq_total_length(encseq);
  GtEncseqReader *esr1, *esr2;
  int cmp;

  gt_assert(!specialsareequal || specialsareequalatdepth0);
  esr1 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  esr2 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  gt_assert(numberofsuffixes > 0);
  pos1 = gt_suffixsortspace_get(suffixsortspace,subbucketleft,0);
  gt_assert(pos1 < totallength);
  for (idx = 1UL; idx < numberofsuffixes; idx++)
  {
    pos2 = gt_suffixsortspace_get(suffixsortspace,subbucketleft,idx);
    if (pos2 < totallength)
    {
      cmp = gt_encseq_check_comparetwosuffixes(encseq,
                                               readmode,
                                               &maxlcp,
                                               specialsareequal,
                                               specialsareequalatdepth0,
                                               depth,
                                               pos1,
                                               pos2,
                                               esr1,
                                               esr2);
      if (cmp > 0)
      {
        showcomparisonfailure(filename,
                              line,
                              "checksortedsuffixes",
                              encseq,
                              readmode,
                              suffixsortspace,
                              subbucketleft,
                              depth,
                              idx-1,
                              idx,
                              cmp,
                              maxlcp);
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
      gt_assert(depth == 0 || maxlcp <= depth);
    }
    pos1 = pos2;
  }
  gt_encseq_reader_delete(esr1);
  gt_encseq_reader_delete(esr2);
}
genometools-1.5.1/src/match/sfx-suftaborder.h000066400000000000000000000037701211610345200212250ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SFX_SUFTABORDER_H
#define SFX_SUFTABORDER_H

#include "core/error_api.h"
#include "core/encseq.h"
#include "core/readmode.h"
#include "sfx-suffixgetset.h"

void gt_checksortedsuffixes(const char *filename,
                            int line,
                            const GtEncseq *encseq,
                            GtReadmode readmode,
                            const GtSuffixsortspace *suffixsortspace,
                            unsigned long subbucketleft,
                            unsigned long numberofsuffixes,
                            bool specialsareequal,
                            bool specialsareequalatdepth0,
                            unsigned long depth);

void gt_checkifprefixesareidentical(const char *filename,
                                    int line,
                                    const GtEncseq *encseq,
                                    GtReadmode readmode,
                                    const GtSuffixsortspace *suffixsortspace,
                                    unsigned long subbucketleft,
                                    unsigned long width,
                                    unsigned long depth);
#endif
genometools-1.5.1/src/match/shu-dfs.c000066400000000000000000000375561211610345200174640ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 

#include "core/array2dim_api.h"
#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/format64.h"
#include "core/log_api.h"
#include "core/logger.h"
#include "core/safearith.h"
#include "core/stack-inlined.h"
#include "core/unused_api.h"

#include "match/eis-voiditf.h"
#include "match/shu_unitfile.h"

#include "match/shu-dfs.h"

static inline void add_filenum_count(unsigned long lower,
                                     unsigned long upper,
                                     ShuNode *parent,
                                     BwtSeqpositionextractor *pos_extractor,
                                     unsigned long total_length,
                                     const GtShuUnitFileInfo *unit_info,
                                     const GtEncseq *encseq)
{
  long unsigned row;

  for (row = lower; row < upper; row++)
  {
    unsigned long filenum, position;

    position = gt_BwtSeqpositionextractor_extract(pos_extractor, row);
    if (total_length <= position)
    {
      filenum = unit_info->num_of_files - 1;
    }
    else
    {
      gt_assert((position + 1) <= total_length);
      position = total_length - (position + 1);
      filenum = gt_encseq_filenum(encseq, position);
    }
    /*mapping to genome_num*/
    if (unit_info->map_files != NULL)
    {
      parent->countTermSubtree[0][unit_info->map_files[filenum]]++;
    }
    else
    {
      parent->countTermSubtree[0][filenum]++;
    }
  }
}

static inline unsigned long **get_special_pos(const FMindex *index,
                                         BwtSeqpositionextractor *pos_extractor,
                                         unsigned long num_of_specials)
{
  unsigned long row_idx, special_idx = 0,
                **special_char_rows_and_pos,
                first_special_row;
  GtUchar cc;

  first_special_row = gt_pck_get_nonspecial_count(index);

  gt_array2dim_calloc(special_char_rows_and_pos,
                      2UL,
                      num_of_specials);

  for (row_idx = 0; row_idx < first_special_row; row_idx ++)
  {
    cc = gt_bwtseqgetsymbol(row_idx, index);
    if (ISSPECIAL(cc))
    {
      special_char_rows_and_pos[0][special_idx] = row_idx;
      special_char_rows_and_pos[1][special_idx] =
        gt_BwtSeqpositionextractor_extract(pos_extractor, row_idx);
      special_idx++;
    }
  }
  gt_assert(special_idx == num_of_specials);
  return special_char_rows_and_pos;
}

static inline unsigned long get_start_idx_binary_search(ShuNode *parent,
                                                  unsigned long **special_pos,
                                                  unsigned long max_idx)
{
  unsigned long start_idx = 0;

  if (parent->lower <= special_pos[0][0])
  {
    start_idx = 0;
  }
  else
  {
    if (special_pos[0][max_idx - 1] < parent->lower)
    {
      start_idx = max_idx;
    }
    else
    {
      unsigned long left, mid, right, len;
      left = 0;
      right = max_idx - 1;
      while (left<=right)
      {
        len = (unsigned long) (right - left);
        mid = left + GT_DIV2(len);
        if (special_pos[0][mid] < parent->lower)
        {
          if (parent->lower <= special_pos[0][mid+1])
          {
            start_idx = mid + 1;
            break;
          }
          left = mid + 1;
        }
        else
        {
          if (special_pos[0][mid - 1] < parent->lower)
          {
            start_idx = mid;
            break;
          }
          right = mid - 1;
        }
      }
    }
  }
  return start_idx;
}

static int visit_shu_children(const FMindex *index,
                              ShuNode *parent,
                              GtStackShuNode *stack,
                              const GtEncseq *encseq,
                              Mbtab *tmpmbtab,
                              BwtSeqpositionextractor *pos_extractor,
                              unsigned long *rangeOccs,
                              unsigned long **special_pos,
                              GT_UNUSED unsigned long numofchars,
                              const GtShuUnitFileInfo *unit_info,
                              unsigned long total_length,
                              unsigned long max_idx,
                              GT_UNUSED GtLogger *logger,
                              GT_UNUSED GtError *err)
{
  unsigned long rangesize, idx, num_of_rows;
  unsigned int offset;

  gt_assert(parent->lower < parent->upper);
  num_of_rows = parent->upper - parent->lower;

  rangesize = gt_bwtrangesplitallwithoutspecial(tmpmbtab,
                                                rangeOccs,
                                                index,
                                                parent->lower,
                                                parent->upper);
  gt_assert(rangesize <= numofchars);

  offset = 1U;
  for (idx = 0; idx < rangesize; idx++)
  {
    gt_assert (tmpmbtab[idx].lowerbound <= tmpmbtab[idx].upperbound);
    gt_assert ((tmpmbtab[idx].upperbound - tmpmbtab[idx].lowerbound) <=
              num_of_rows);
    num_of_rows -= (tmpmbtab[idx].upperbound - tmpmbtab[idx].lowerbound);

    if (tmpmbtab[idx].lowerbound != tmpmbtab[idx].upperbound)
    {
      if (tmpmbtab[idx].lowerbound + 1 ==
          tmpmbtab[idx].upperbound)
      { /* we found a leaf on parent */
        add_filenum_count(tmpmbtab[idx].lowerbound,
                          tmpmbtab[idx].upperbound,
                          parent,
                          pos_extractor,
                          total_length,
                          unit_info,
                          encseq);
      }
      else
      {
        if (tmpmbtab[idx].upperbound - tmpmbtab[idx].lowerbound ==
            parent->upper - parent->lower)
        { /* tmpmbtab[idx] is part of a branch and no actual node */
          parent->lower = tmpmbtab[idx].lowerbound;
          parent->upper = tmpmbtab[idx].upperbound;
          parent->depth++;
          return 0;
        }
        else
        { /* tmpmbtab[idx] is a branch of parent node */
          ShuNode *child = NULL;

          GT_STACK_NEXT_FREE(stack,child);
          if (child->countTermSubtree == NULL)
          {
            gt_array2dim_calloc(child->countTermSubtree,
                                numofchars+1UL,
                                unit_info->num_of_genomes);
          }
          else
          {
            unsigned long y_idx, file_idx;
            for (y_idx = 0; y_idx < numofchars+1UL; y_idx++)
            {
              for (file_idx = 0;
                   file_idx < unit_info->num_of_genomes;
                   file_idx++)
              {
                child->countTermSubtree[y_idx][file_idx] = 0;
              }
            }
          }
          child->process = false;
          child->lower = tmpmbtab[idx].lowerbound;
          child->upper = tmpmbtab[idx].upperbound;
          child->parentOffset = offset;
          child->depth = parent->depth + 1;
          offset++;
        }
      }
    }
  }
  if (parent->depth > 0 && num_of_rows > 0) {
    unsigned long start_idx;
    /* unsigned long max_idx - already determined*/

    gt_assert(num_of_rows <= max_idx + 1);
    gt_assert(parent->lower <= special_pos[0][max_idx]);
    gt_assert(special_pos[0][0] <= parent->upper);

    start_idx = get_start_idx_binary_search(parent,
                                            special_pos,
                                            max_idx);
    for (idx = start_idx;
        special_pos[0][idx] < parent->upper && idx <= max_idx;
        idx++)
    {
      unsigned long filenum,
                    position = special_pos[1][idx];

      gt_assert(1UL <= num_of_rows);

      num_of_rows--;

      if (total_length <= position)
      {
        filenum = unit_info->num_of_files - 1;
      }
      else
      {
        gt_assert((position + 1) <= total_length);
        position = total_length - (position + 1);
        filenum = gt_encseq_filenum(encseq, position);
      }
      /*mapping to genome_num*/
      if (unit_info->map_files != NULL)
      {
        parent->countTermSubtree[0][unit_info->map_files[filenum]]++;
      }
      else
      {
        parent->countTermSubtree[0][filenum]++;
      }
    }
    gt_assert(num_of_rows==0);
  }
  parent->process = true;
  return 0;
}

static int process_shu_node(ShuNode *node,
                            GtStackShuNode *stack,
                            uint64_t **shulen,
                            unsigned long num_of_genomes,
                            unsigned long numofchars,
                            GT_UNUSED GtLogger *logger,
                            GT_UNUSED GtError *err)
{
  int had_err = 0;
  uint64_t old;
  unsigned long idx_i, idx_j, termChild_x_i, idx_char;
  unsigned child_c;
  ShuNode *parent = NULL;

  gt_assert(node->process);

  if (node->parentOffset > 0)
  {
    parent = stack->space + stack->nextfree - node->parentOffset;
  }

  for (idx_i = 0; idx_i < num_of_genomes; idx_i++)
  {
    if (!had_err && node->countTermSubtree[0][idx_i] > 0)
    {
      /* scan term */
      termChild_x_i = node->countTermSubtree[0][idx_i];
      for (idx_char = 1UL; idx_char <= numofchars; idx_char++)
      {
        gt_assert(node->countTermSubtree[idx_char][idx_i] <= termChild_x_i);
        termChild_x_i -= node->countTermSubtree[idx_char][idx_i];
      }
      if (termChild_x_i > 0)
      {
        for (idx_j = 0; idx_j < num_of_genomes; idx_j++)
        {
          if (node->countTermSubtree[0][idx_j] > 0 &&
                 idx_j != idx_i)
          {
            old = shulen[idx_i][idx_j];
            shulen[idx_i][idx_j] += ((node->depth + 1) * termChild_x_i);
            if (shulen[idx_i][idx_j] < old)
            {
              had_err = -1;
              gt_error_set(err, "overflow in addition of shuSums! "
                                Formatuint64_t "+ %lu ="
                                Formatuint64_t "\n",
                  PRINTuint64_tcast(old),
                  (node->depth + 1) * termChild_x_i,
                  PRINTuint64_tcast(shulen[idx_i][idx_j]));
            }
          }
        }
      }
      /* scan branch */
      for (child_c = 1U; (unsigned long) child_c <= numofchars; child_c++)
      {
        if (!had_err && node->countTermSubtree[child_c][idx_i] > 0)
        {
          for (idx_j = 0; idx_j < num_of_genomes; idx_j++)
          {
            /* idx_j elem seqIds[x] \ seqIds[child_c] */
            if (node->countTermSubtree[0][idx_j] > 0 &&
                node->countTermSubtree[child_c][idx_j] == 0)
            {
              old = shulen[idx_i][idx_j];
              shulen[idx_i][idx_j] += ((node->depth + 1) *
                                       node->countTermSubtree[child_c][idx_i]);
              if (shulen[idx_i][idx_j] < old)
              {
                had_err = -1;
                gt_error_set(err, "overflow in addition of shuSums! "
                                  Formatuint64_t "+ %lu ="
                                  Formatuint64_t "\n",
                    PRINTuint64_tcast(old),
                    (node->depth + 1) * termChild_x_i,
                    PRINTuint64_tcast(shulen[idx_i][idx_j]));
              }
            }
          }
        }
      }
      if (node->parentOffset > 0)
      {
        gt_assert(parent && parent->countTermSubtree);
        parent->countTermSubtree[0][idx_i] += node->countTermSubtree[0][idx_i];
        parent->countTermSubtree[node->parentOffset][idx_i] =
                                              node->countTermSubtree[0][idx_i];
      }
    }
  }
  return had_err;
}

static int initialise_node(void *node)
{
  int had_err = 0;
  ShuNode *tobeinitialised;
  tobeinitialised = (ShuNode *) node;
  tobeinitialised->countTermSubtree = NULL;
  return had_err;
}

int gt_pck_calculate_shulen(const FMindex *index,
                            const GtShuUnitFileInfo *unit_info,
                            uint64_t **shulen,
                            unsigned long numofchars,
                            unsigned long total_length,
                            GtTimer *timer,
                            GtLogger *logger,
                            GtError *err)
{
  int had_err = 0;
  GtStackShuNode stack;
  ShuNode *root;
  Mbtab *tmpmbtab;
  const unsigned long resize = 64UL;
  unsigned long *rangeOccs,
                **special_char_rows_and_pos,
                depth_idx,
                processed_nodes,
                max_idx = gt_pck_special_occ_in_nonspecial_intervals(index) - 1;
  BwtSeqpositionextractor *pos_extractor;
  const GtEncseq *encseq = unit_info->encseq;

  gt_assert(max_idx < total_length);
  rangeOccs = gt_calloc((size_t) GT_MULT2(numofchars), sizeof (*rangeOccs));
  tmpmbtab = gt_calloc((size_t) (numofchars + 3), sizeof (*tmpmbtab ));
  GT_STACK_INIT_WITH_INITFUNC(&stack, resize, initialise_node);
  pos_extractor = gt_newBwtSeqpositionextractor(index, total_length + 1);
  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "obtain special pos", stdout);
  }
  special_char_rows_and_pos = get_special_pos(index,
                                              pos_extractor,
                                              max_idx + 1);
  GT_STACK_NEXT_FREE(&stack,root);
  gt_array2dim_calloc(root->countTermSubtree,
                      numofchars+1UL,
                      unit_info->num_of_genomes);
  root->process = false;
  root->parentOffset = 0;
  root->depth = 0;
  root->lower = 0;
  root->upper = total_length + 1;

  if (timer != NULL)
  {
    gt_timer_show_progress(timer, "traverse virtual tree", stdout);
  }
  processed_nodes = 0;
  while (!had_err && !GT_STACK_ISEMPTY(&stack))
  {
    ShuNode *current;

    gt_assert(stack.nextfree > 0);
    current = stack.space + stack.nextfree -1;
    if (current->process)
    {
      GT_STACK_DECREMENTTOP(&stack);
        had_err = process_shu_node(current,
                                   &stack,
                                   shulen,
                                   unit_info->num_of_genomes,
                                   numofchars,
                                   logger,
                                   err);
      processed_nodes++;
    }
    else
    {
      had_err = visit_shu_children(index,
                                   current,
                                   &stack,
                                   encseq,
                                   tmpmbtab,
                                   pos_extractor,
                                   rangeOccs,
                                   special_char_rows_and_pos,
                                   numofchars,
                                   unit_info,
                                   total_length,
                                   max_idx,
                                   logger,
                                   err);
    }
  }
  gt_logger_log(logger, "max stack depth = %lu", GT_STACK_MAXSIZE(&stack));
  gt_log_log("processed nodes= %lu", processed_nodes);
  for (depth_idx = 0; depth_idx < GT_STACK_MAXSIZE(&stack); depth_idx++)
  {
    gt_array2dim_delete(stack.space[depth_idx].countTermSubtree);
  }
  GT_STACK_DELETE(&stack);
  gt_free(rangeOccs);
  gt_free(tmpmbtab);
  gt_freeBwtSeqpositionextractor(pos_extractor);
  gt_array2dim_delete(special_char_rows_and_pos);
  return had_err;
}
genometools-1.5.1/src/match/shu-dfs.h000066400000000000000000000032041211610345200174500ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SHU_DFS_H
#define SHU_DFS_H

#include 
#include "core/stack-inlined.h"

#include "match/eis-voiditf.h"
#include "match/shu_unitfile.h"

typedef struct ShuNode {
  bool process;
  unsigned parentOffset;
  unsigned long **countTermSubtree;
  unsigned long depth,
                lower,
                upper;
} ShuNode;

GT_STACK_DECLARESTRUCT(ShuNode, 256UL);

int gt_pck_calculate_shulen(const FMindex *index,
                            const GtShuUnitFileInfo *unit_info,
                            uint64_t **shulen,
                            unsigned long numofchars,
                            unsigned long total_length,
                            GtTimer *timer,
                            GT_UNUSED GtLogger *logger,
                            GT_UNUSED GtError *err);

#endif
genometools-1.5.1/src/match/shu-divergence.c000066400000000000000000000130221211610345200210010ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 

#include "core/array2dim_api.h"
#include "core/assert_api.h"
#include "core/log_api.h"
#include "core/mathsupport.h"
#include "match/shu-divergence.h"

static double pmax(double M, /* M value should be explored by simulation ??? */
            unsigned long x,
            double p,
            unsigned long subjectLength,
            int *thresholdReached,
            double *ln_n_fac,
            double *s1,
            unsigned long n_s)
{

  unsigned long k;
  double s = 0.0, ln_x_choose_k;
  double ln, ln1, m1, m, delta;

  if (x > n_s) {
    /* change this to standard GT-behaviour XXX*/
    printf("Error: x = %lu."
           " The maximum number of elements in the array"
           " s1 should be increased!\n", x);
  }
  gt_assert(x <= n_s);
  if (s1[x] != 0.0)
    return s1[x];

  for (k = 0; k <= x; k++) {
    double m_a, m_b, m_c, m_d, m_e;
    if (x == k)
      ln_x_choose_k = 0.0;
    else
      ln_x_choose_k =  ln_n_fac[x] - ln_n_fac[k] - ln_n_fac[x-k];

    m_a = pow (2.0, (double) x);
    m_b = pow (p, (double) k);
    m_c = pow (0.5 - p, (double) x - k);
    m_d = pow (p, (double) k);
    m_e = pow (0.5 - p, (double) x -k);
    m = (m_a * m_b * m_c * pow (1.0 - m_d * m_e, (double) subjectLength));
    /* this is ok even with double, because of next if!*/
    if (m == 0.0)
      delta = 0.0;
    else if (M <= m) {
      ln = log(m);
      if (ln == -HUGE_VAL)
        delta = 0.0;
      else
        delta = exp (ln + ln_x_choose_k);
    }
    else {
      double delta_a, delta_b;
      m1 = 1 + m;  /* for small values of m - to avoid overflow (-INF) */
      ln1 = log(m1);
      delta_a = exp (ln1 + ln_x_choose_k);
      delta_b = exp (ln_x_choose_k);
      delta = delta_a - delta_b;
    }
    s += delta;
    if (s >= 1.0) {
      s = 1.0;
      *thresholdReached = 1;
      break;
    }
  }  /* end for */
  s1[x] = s;
  return s;
}

static double expShulen(double T, /* absolute error */
                 double M, /* min logarithm */
                 double d,
                 double p,
                 unsigned long subjectLength,
                 double *ln_n_fac,
                 double *s1,
                 unsigned long n_s)
{
  unsigned long i;
  int thresholdReached = 0;

  double prob_i, probOld, delta, factor;

  double e = 0.0;    /* expectation */
  double t = 1.0 - d;
  double p_t = t;

  probOld  = 0.0;

  /*since for i = 0, the whole expression is 0*/
  for (i = 1LU; i < subjectLength; i++) {
    factor = 1.0 - p_t;
    if (!thresholdReached) {
      prob_i = factor * pmax(M, i, p,
                             subjectLength,
                             &thresholdReached,
                             ln_n_fac,
                             s1,
                             n_s);
    }
    else
      prob_i = factor;  /* prob_i = factor * s, where s = 1 */
    delta = (prob_i - probOld) * i;  /* delta should always be positive */
    gt_assert(gt_double_equals_double(delta, 0.0) ||
              gt_double_larger_double(delta, 0.0));
    e += delta;    /* expectation of avg shulen length(Q, S) */
    /* check error */
    if (1.0 <= e && delta / e <= T)
      break;
    p_t *= t;
    probOld = prob_i;
  }
  return e;
}

/* calculate divergence */
double gt_divergence(double E, /* relative error for divergence calculation */
                   double T, /* absolute error for exp shulen*/
                   double M, /* minimum for logarithm */
                   double threshold, /* abs error for divergence */
                   double shulen,
                   unsigned long subjectLength,
                   double gc,
                   double *ln_n_fac,
                   unsigned long n_s)
{
  double p, q,
         du, dl, dm, d, exp_shulen;
  double *s1;
  s1 = gt_calloc((size_t) n_s + 1, sizeof (double));

  p = gc / 2;
  q = (1.0 - gc) / 2.0;
  du = 0.0;
  dl = 1.0 - (2 * p * p + 2 * q * q);  /* dl < 0.75 */

  while (gt_double_smaller_double(threshold, (dl - du) / 2.0)) {
    dm = (du + dl) / 2.0;
    exp_shulen = expShulen(T, M, dm, p, subjectLength, ln_n_fac, s1, n_s);
    if (gt_double_smaller_double(shulen, exp_shulen))
      du = dm;
    else
      dl = dm;
    /* test the relative error between du and dl; if it is smaller than some
     * threshold, then break !! */
    if (fabs (dl - du) / dl <= E)
      break;
  }
  d = (du + dl) / 2.0;
  gt_free(s1);
  return d;
}

double *gt_get_ln_n_fac(unsigned long n)
{
  unsigned long i;
  double *ln_n_fac;

  ln_n_fac = gt_calloc((size_t) n + 1, sizeof (double));

  ln_n_fac[0] = log(1.0);
  for (i = 1UL; i <= n; i++) {
    ln_n_fac[i] = log((double) i) + ln_n_fac[i-1];
  }
  return ln_n_fac;
}

double gt_calculateKr(double d)
{
  double kr = -0.75 * log (1 - 4.0 / 3.0 * d);
  return kr;
}
genometools-1.5.1/src/match/shu-divergence.h000066400000000000000000000031471211610345200210150ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SHU_DIVERGENCE_H
#define SHU_DIVERGENCE_H

/* calculates the divergence from the shulength */
double gt_divergence (double E, /* relative error for shulen length */
                   double T, /* absolute error */
                   double M,
                   double threshold, /* break criteria for pmax calculation */
                   double shulen, /*avg shulength*/
                   unsigned long subjectLength, /*subjectlength*/
                   double gc, /*combined gc-content*/
                   double *ln_n_fac,
                   unsigned long n_s /*length of s-array*/);

/* Jukes-Cantor transform of divergence: Kr */
double gt_calculateKr(double d);

/* Calculates ln(n!) for numbers 0 to given n */
double *gt_get_ln_n_fac(unsigned long n);

#endif
genometools-1.5.1/src/match/shu-encseq-gc.c000066400000000000000000000120121211610345200205310ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/alphabet_api.h"
#include "core/divmodmul.h"
#include "core/encseq_api.h"
#include "core/ensure.h"
#include "core/ma_api.h"
#include "core/mathsupport.h"
#include "core/safearith.h"
#include "core/unused_api.h"

#include "match/shu-encseq-gc.h"

static inline void calculate_rel_gc(const GtEncseq *encseq,
                                    double *gc_content,
                                    unsigned long seq_idx,
                                    unsigned long gc_count)
{
  unsigned long length;
  gt_assert(seq_idx < gt_encseq_num_of_sequences(encseq));
  length = gt_encseq_seqlength(encseq, seq_idx);
  gt_assert(gc_count <= length);
  gc_content[seq_idx] = (double) gc_count / (double) length;
  gt_assert(gt_double_compare(gc_content[seq_idx], 0.0) != -1);
  gt_assert(gt_double_compare(gc_content[seq_idx], 1.0) != 1);
}

unsigned long *gt_encseq_gc_count(const GtEncseq *encseq)
{
  GtEncseqReader *reader;
  GtAlphabet *alphabet;
  unsigned long *gc_count_per_seq,
                char_idx, totallength, max_unit,
                seq_idx = 0,
                nextsep = 0;
  bool is_mirrored_encseq;
  GtUchar cCgG_encoded[4], current_c;

  alphabet = gt_encseq_alphabet(encseq);
  gt_assert(gt_alphabet_is_dna(alphabet));
  gt_alphabet_encode_seq(alphabet, cCgG_encoded, "cCgG", 4UL);
  totallength = gt_encseq_total_length(encseq);
  reader = gt_encseq_create_reader_with_readmode(encseq,
                                                 GT_READMODE_FORWARD,
                                                 0);
  is_mirrored_encseq = gt_encseq_is_mirrored(encseq);
  if (is_mirrored_encseq) {
    max_unit = GT_DIV2(gt_encseq_num_of_sequences(encseq));
    gc_count_per_seq = gt_calloc((size_t) GT_MULT2(max_unit),
                                 sizeof (*gc_count_per_seq));
  }
  else {
    max_unit = gt_encseq_num_of_sequences(encseq);
    gc_count_per_seq = gt_calloc((size_t) max_unit, sizeof (*gc_count_per_seq));
  }

  nextsep = gt_encseq_seqstartpos(encseq, seq_idx) +
            gt_encseq_seqlength(encseq, seq_idx);

  for (char_idx = 0; char_idx < totallength; char_idx++)
  {
    if (nextsep == char_idx)
    {
      gt_assert(gc_count_per_seq[seq_idx] <=
                gt_encseq_seqlength(encseq, seq_idx));
      seq_idx++;

      nextsep = gt_encseq_seqstartpos(encseq, seq_idx) +
                gt_encseq_seqlength(encseq, seq_idx);

      gt_encseq_reader_reinit_with_readmode(reader,
                                            encseq,
                                            GT_READMODE_FORWARD,
                                            char_idx + 1UL);
      char_idx++;
    }
    current_c = gt_encseq_reader_next_encoded_char(reader);
    if (current_c == cCgG_encoded[0] || current_c == cCgG_encoded[1] ||
        current_c == cCgG_encoded[2] || current_c == cCgG_encoded[3]) {
       gc_count_per_seq[seq_idx]++;
       gt_assert(gc_count_per_seq[seq_idx] != 0);
    }
  }
  gt_encseq_reader_delete(reader);
  return gc_count_per_seq;
}

double *gt_encseq_get_rel_gc(const GtEncseq *encseq,
                             GT_UNUSED GtError *err)
{
  double *gc_content;
  unsigned long *gc_count_per_seq,
                max_unit,
                seq_idx = 0;
  bool is_mirrored_encseq;

  is_mirrored_encseq = gt_encseq_is_mirrored(encseq);
  if (is_mirrored_encseq)
  {
    max_unit = GT_DIV2(gt_encseq_num_of_sequences(encseq));
    gc_content = gt_calloc((size_t) GT_MULT2(max_unit), sizeof (double));
  }
  else
  {
    max_unit = gt_encseq_num_of_sequences(encseq);
    gc_content = gt_calloc((size_t) max_unit, sizeof (double));
  }

  gc_count_per_seq = gt_encseq_gc_count(encseq);
  for (seq_idx = 0; seq_idx < max_unit; seq_idx++) {
    calculate_rel_gc(encseq,
                     gc_content,
                     seq_idx,
                     gc_count_per_seq[seq_idx]);
  }
  if (is_mirrored_encseq)
  {
    unsigned long double_max_unit = GT_MULT2(max_unit);
    for (seq_idx = 0; seq_idx < max_unit; seq_idx++)
    {
      gc_content[double_max_unit - seq_idx - 1] = gc_content[seq_idx];
    }
  }
  return gc_content;
}

int gt_encseq_gc_unit_test(GT_UNUSED GtError *err)
{
  int had_err = 0;
  /* XXX write new tests for the new functions */
  return had_err;
}
genometools-1.5.1/src/match/shu-encseq-gc.h000066400000000000000000000024611211610345200205450ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SHU_ENCSEQ_GC_H
#define SHU_ENCSEQ_GC_H

#include 

#include "core/encseq_api.h"
#include "core/unused_api.h"

/* returns the count of g's and c's per sequence. */
unsigned long *gt_encseq_gc_count(const GtEncseq *encseq);

/* returns the per sequence relative gc-content of encseq (#gc / totallength) */
double *gt_encseq_get_rel_gc(const GtEncseq *encseq,
                             GtError *err);

int gt_encseq_gc_unit_test(GtError *err);

#endif
genometools-1.5.1/src/match/shu-genomediff.c000066400000000000000000000424731211610345200210050ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/array2dim_api.h"
#include "core/encseq_api.h"
#include "core/format64.h"
#include "core/log_api.h"
#include "core/logger.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/safearith.h"
#include "match/eis-voiditf.h"
#include "match/esa-seqread.h"
#include "match/esa-shulen.h"
#include "match/idx-limdfs.h"
#include "match/sarr-def.h"
#include "match/shu-dfs.h"
#include "match/shu-divergence.h"
#include "match/shu-encseq-gc.h"
#include "match/shu-genomediff.h"
#include "match/shu_unitfile.h"

/* static inline int genomediff_parse_unit(GtShuUnitFileInfo *unit_info,
                                        const GtStr *filename,
                                        GtTimer *timer, GtLogger *logger,
                                        GtError *err)
{
  int had_err = 0;

  if (timer != NULL)
    gt_timer_show_progress(timer, "parse unitfile", stdout);
  had_err = gt_shu_unit_file_info_read(filename, unit_info, logger, err);
  if (!had_err)
    gt_logger_log(logger, "successfully loaded unitfile");
  return had_err;
} */

static unsigned long*
genomediff_calculate_genome_lengths(GtShuUnitFileInfo *unit_info)
{
  bool mirrored = gt_encseq_is_mirrored(unit_info->encseq);
  unsigned long eff_file_length,
                filestart,
                sep_per_file = 0,
                seqs_passed = 0,
                seqs_upto_fileend,
                i_idx;
  unsigned long *genome_lengths = gt_calloc((size_t) unit_info->num_of_genomes,
                                           sizeof (*genome_lengths));
  for (i_idx = 0UL; i_idx < unit_info->num_of_files; i_idx++) {
    eff_file_length = gt_safe_cast2ulong_64(
        gt_encseq_effective_filelength(unit_info->encseq, i_idx));
    filestart = gt_encseq_filestartpos(unit_info->encseq, i_idx);
    if (i_idx == unit_info->num_of_files - 1) {
      if (mirrored) {
        sep_per_file = GT_DIV2(gt_encseq_num_of_sequences(unit_info->encseq))
                       - seqs_passed - 1;
      }
      else {
        sep_per_file = gt_encseq_num_of_sequences(unit_info->encseq)
                       - seqs_passed - 1;
      }
    }
    else {
      seqs_upto_fileend = gt_encseq_seqnum(unit_info->encseq,
                                           filestart +
                                           eff_file_length - 1)
                          + 1;

      sep_per_file = seqs_upto_fileend - seqs_passed - 1;
      seqs_passed = seqs_upto_fileend;
    }
    if (unit_info->map_files != NULL) {
      genome_lengths[unit_info->map_files[i_idx]] +=
        eff_file_length - sep_per_file;
    }
    else {
      genome_lengths[i_idx] = eff_file_length - sep_per_file;
    }
  }
  if (mirrored) {
    for (i_idx = 0UL; i_idx < unit_info->num_of_genomes; i_idx++) {
      genome_lengths[i_idx] += genome_lengths[i_idx];
    }
  }
  if (gt_log_enabled()) {
    for  (i_idx = 0UL; i_idx < unit_info->num_of_genomes; i_idx++) {
      gt_log_log("file/genome %lu has length %lu",
          i_idx, genome_lengths[i_idx]);
    }
  }
  return genome_lengths;
}

static double *genomediff_calculate_gc(unsigned long *genome_lengths,
                                       GtShuUnitFileInfo *unit_info,
                                       GT_UNUSED GtError *err)
{
  unsigned long file_idx = 0UL,
                genome_idx,
                idx,
                *seq_gc_content = NULL,
                num_of_seq,
                *genome_gc_content;
  double *gc_content;

  gt_assert(genome_lengths != NULL);
  gt_assert(unit_info != NULL);

  gt_assert(genome_lengths != NULL);
  gt_assert(unit_info != NULL);

  /*count gc, do not calculate ratio*/
  seq_gc_content = gt_encseq_gc_count(unit_info->encseq);

  if (seq_gc_content == NULL)
    return NULL;

  gc_content = gt_calloc((size_t)unit_info->num_of_genomes,
                         sizeof (*gc_content));
  genome_gc_content = gt_calloc((size_t)unit_info->num_of_genomes,
                                sizeof (*genome_gc_content));
  num_of_seq = gt_encseq_num_of_sequences(unit_info->encseq);

  for (idx = 0; idx < num_of_seq; idx++) {
    file_idx = gt_encseq_filenum(unit_info->encseq,
                                 gt_encseq_seqstartpos(unit_info->encseq, idx));
    if (unit_info->map_files != NULL)
      genome_idx = unit_info->map_files[file_idx];
    else
      genome_idx = file_idx;
    gt_safe_add(genome_gc_content[genome_idx],
                genome_gc_content[genome_idx],
                seq_gc_content[idx]);
  }
  for (idx = 0; idx < unit_info->num_of_genomes; idx++) {
    gt_log_log("file/genome %lu has gc %lu", idx, genome_gc_content[idx]);
  }

  for (idx = 0; idx < unit_info->num_of_genomes; idx++) {
    gt_assert(genome_gc_content[idx] <= genome_lengths[idx]);
    gc_content[idx] = (double) genome_gc_content[idx] /
                      (double) genome_lengths[idx];
  }
  gt_free(seq_gc_content);
  gt_free(genome_gc_content);
  return gc_content;
}

static void genomediff_calculate_div(GtShuUnitFileInfo *unit_info,
                                     double **div, double *gc_content,
                                     unsigned long *genome_lengths,
                                     const GtGenomediffArguments *arguments,
                                     GtTimer *timer)
{
  double query_gc,
         query_shulen,
         *ln_n_fac;
  unsigned long subject_len,
                i_idx, j_idx,
                subject, query;

  if (timer != NULL)
    gt_timer_show_progress(timer, "pre calculate ln_n_fac", stdout);

  ln_n_fac = gt_get_ln_n_fac(arguments->max_ln_n_fac);
  if (timer != NULL)
    gt_timer_show_progress(timer, "calculate divergence", stdout);
  for (i_idx = 0; i_idx < unit_info->num_of_genomes; i_idx++) {
    for (j_idx = i_idx+1; j_idx < unit_info->num_of_genomes; j_idx++) {
      /* query is the one with smaller avg shulen */
      if (gt_double_smaller_double(div[i_idx][j_idx], div[j_idx][i_idx])) {
        subject = j_idx;
        query = i_idx;
      }
      else if (gt_double_smaller_double(div[j_idx][i_idx], div[i_idx][j_idx])) {
          subject = i_idx;
          query = j_idx;
      }
      /* if avg shulen is equal, choose query with gc content farther from .5 */
      else {
        if (gt_double_smaller_double(fabs(gc_content[i_idx]-0.5),
                                     fabs(gc_content[j_idx]-0.5))) {
          subject = i_idx;
          query = j_idx;
        }
        else {
          subject = j_idx;
          query = i_idx;
        }
      }
      query_gc = gc_content[query];
      query_shulen = div[query][subject];
      subject_len = genome_lengths[subject];

      div[i_idx][j_idx] = gt_divergence(arguments->divergence_rel_err,
                                        arguments->divergence_abs_err,
                                        arguments->divergence_m,
                                        arguments->divergence_threshold,
                                        query_shulen,
                                        subject_len,
                                        query_gc,
                                        ln_n_fac,
                                        arguments->max_ln_n_fac);
      div[j_idx][i_idx] = div[i_idx][j_idx];
    }
  }
  gt_free(ln_n_fac);
}

uint64_t **gt_genomediff_shulen_sum(const GtGenomediffArguments *arguments,
                                    GtShuUnitFileInfo *unit_info,
                                    GtLogger *logger,
                                    GtTimer *timer,
                                    GtError *err)
{
  int had_err = 0;
  unsigned long i_idx, j_idx;
  uint64_t **shulensums = NULL;
  const GtEncseq *encseq = NULL;
  Genericindex *generic_index_subject = NULL;
  Sequentialsuffixarrayreader *ssar = NULL;

  gt_error_check(err);
  gt_assert(unit_info != NULL);

  /* prepare index */
  if (arguments->with_esa) {
    if (timer != NULL)
      gt_timer_show_progress(timer, "load sequential sa reader", stdout);

    ssar = gt_newSequentialsuffixarrayreaderfromfile(
                                    gt_str_array_get(arguments->filenames, 0),
                                    SARR_LCPTAB | SARR_SUFTAB | SARR_ESQTAB |
                                      SARR_SSPTAB,
                                    arguments->scan ? SEQ_scan : SEQ_mappedboth,
                                    logger, err);
    if (ssar == NULL)
      had_err = -1;

    if (!had_err) {
      encseq = gt_encseqSequentialsuffixarrayreader(ssar);
    }
  }
  else {
    gt_assert(arguments->with_pck);

    if (timer != NULL)
      gt_timer_show_progress(timer, "map generic index", stdout);

    generic_index_subject =
      genericindex_new(gt_str_array_get(arguments->filenames, 0),
                       false, true, false, true,
                       arguments->user_max_depth,
                       logger, err);
    if (generic_index_subject == NULL) {
      had_err = -1;
    }
    /*get num of genomes from unitfile or encseq and allocate shulen-matrix*/
    if (!had_err) {
      encseq = genericindex_getencseq(generic_index_subject);
    }
  }

  /*calculate sums of shulens*/
  if (!had_err) {
    gt_array2dim_calloc(shulensums,
                        unit_info->num_of_genomes,
                        unit_info->num_of_genomes);

    if (arguments->with_esa) {
      if (timer != NULL)
        gt_timer_show_progress(timer, "dfs esa index", stdout);

      had_err = gt_multiesa2shulengthdist(ssar, encseq, shulensums,
                                          unit_info, err);
    }
    else {
      const FMindex *subjectindex = NULL;
      unsigned long num_of_chars,
                    total_length;
      const GtAlphabet *alphabet = gt_encseq_alphabet(unit_info->encseq);

      num_of_chars = (unsigned long) gt_alphabet_num_of_chars(alphabet);
      total_length = genericindex_get_totallength(generic_index_subject);

      subjectindex = genericindex_get_packedindex(generic_index_subject);
      gt_assert(subjectindex != NULL);

      had_err = gt_pck_calculate_shulen(subjectindex,
                                        unit_info,
                                        shulensums,
                                        num_of_chars,
                                        total_length,
                                        timer,
                                        logger,
                                        err);
    }
  }

  if (arguments->with_esa) {
    if (ssar != NULL)
      gt_freeSequentialsuffixarrayreader(&ssar);
  }
  else
    genericindex_delete(generic_index_subject);

  if (had_err) {
    gt_log_log("foo");
    if (shulensums != NULL)
      gt_array2dim_delete(shulensums);
    shulensums = NULL;
  }
  else {
    gt_assert(shulensums != NULL);
    gt_log_log("sum of shulens");
    if (gt_log_enabled()) {
      for (i_idx = 0; i_idx < unit_info->num_of_genomes; i_idx++) {
        fprintf(stderr, "debug: %s\t",
                gt_str_array_get(unit_info->genome_names, i_idx));
        for (j_idx = 0; j_idx < unit_info->num_of_genomes; j_idx++) {
          if (i_idx == j_idx)
            fprintf(stderr, "0");
          else
            fprintf(stderr, Formatuint64_t"\t",
                    PRINTuint64_tcast(shulensums[i_idx][j_idx]));
        }
        fprintf(stderr, "\n");
      }
    }
  }
  return shulensums;
}

static void genomediff_print_table(double **tab,
                                   GtShuUnitFileInfo *unit_info)
{
  unsigned long i_idx, j_idx;

  for (i_idx = 0; i_idx < unit_info->num_of_genomes; i_idx++) {
    printf("# %s\t", gt_str_array_get(unit_info->genome_names, i_idx));
    for (j_idx = 0; j_idx < unit_info->num_of_genomes; j_idx++) {
      if (i_idx == j_idx)
        printf("%.6f\t",0.0);
      else
        printf("%f\t", tab[i_idx][j_idx]);
    }
    printf("\n");
  }
}

int gt_genomediff_calculate_div_from_avg(double **avgshu,
                                         const GtGenomediffArguments *arguments,
                                         GtShuUnitFileInfo *unit_info,
                                         GtLogger *logger,
                                         GtTimer *timer,
                                         GtError *err)
{
  int had_err = 0;
  const GtAlphabet *alphabet;
  double *gc_content = NULL;
  unsigned long i_idx, j_idx;
  unsigned long *genome_lengths = NULL;

  genome_lengths = genomediff_calculate_genome_lengths(unit_info);

  /*get alphabet and check if alphabet is dna, which is presumed for
    gc-calculation*/
  alphabet = gt_encseq_alphabet(unit_info->encseq);
  if (!gt_alphabet_is_dna(alphabet)) {
    gt_error_set(err,"error: sequences need to be dna to calculate gc!");
    had_err = -1;
  }

  if (!had_err && timer != NULL)
    gt_timer_show_progress(timer, "calculate gc", stdout);
  if (!had_err) {
    gc_content = genomediff_calculate_gc(genome_lengths, unit_info, err);
    if (gc_content == NULL)
      had_err = -1;
  }

    /* calculation of divergence */
  if (!had_err) {
    genomediff_calculate_div(unit_info, avgshu, gc_content, genome_lengths,
                             arguments, timer);

    if (gt_logger_enabled(logger)) {
      gt_logger_log(logger, "table of divergences");
      genomediff_print_table(avgshu, unit_info);
    }
  }

  if (!had_err && timer != NULL)
    gt_timer_show_progress(timer, "calculate kr", stdout);

  if (!had_err) {
    gt_logger_log(logger, "# Table of Kr");
    printf("%lu\n", unit_info->num_of_genomes);
    for (i_idx = 0; i_idx < unit_info->num_of_genomes; i_idx++) {
      printf("%s\t", gt_str_array_get(unit_info->genome_names, i_idx));
      for (j_idx = 0; j_idx < unit_info->num_of_genomes; j_idx++) {
        if ( i_idx == j_idx )
          printf("%.6f\t",0.0);
        else
          printf("%f\t", gt_calculateKr(avgshu[i_idx][j_idx]));
      }
      printf("\n");
    }
  }
  gt_free(gc_content);
  return had_err;
}

int gt_genomediff_kr_calc(uint64_t **shulensums,
                          const GtGenomediffArguments *arguments,
                          GtShuUnitFileInfo *unit_info,
                          bool pcktable,
                          GtLogger *logger,
                          GtTimer *timer,
                          GtError *err)
{
  int had_err = 0;
  double **div = NULL,
         *gc_content = NULL;
  unsigned long *genome_lengths = NULL,
                i_idx, j_idx;
  const GtAlphabet *alphabet;

  gt_assert(shulensums != NULL);
  gt_assert(unit_info != NULL);

  genome_lengths =
    genomediff_calculate_genome_lengths(unit_info);

  if (timer != NULL)
    gt_timer_show_progress(timer, "calculate avg shulen", stdout);

  gt_array2dim_calloc(div,
                      unit_info->num_of_genomes,
                      unit_info->num_of_genomes);

  for (i_idx = 0; i_idx < unit_info->num_of_genomes; i_idx++) {
    unsigned long length_i;
    length_i = genome_lengths[i_idx];

    for (j_idx = 0; j_idx < unit_info->num_of_genomes; j_idx++) {
      div[i_idx][j_idx] = pcktable ?
                            ((double) shulensums[i_idx][j_idx]) / length_i :
                            ((double) shulensums[j_idx][i_idx]) / length_i;
    }
  }
  if (gt_logger_enabled(logger)) {
    gt_logger_log(logger, "table of avg shulens");
    genomediff_print_table(div, unit_info);
  }

  /*get alphabet and check if alphabet is dna, which is presumed for
    gc-calculation*/
  alphabet = gt_encseq_alphabet(unit_info->encseq);
  if (!gt_alphabet_is_dna(alphabet)) {
    gt_error_set(err,"error: sequences need to be dna to calculate gc!");
    had_err = -1;
  }

  if (!had_err && timer != NULL)
    gt_timer_show_progress(timer, "calculate gc", stdout);
  if (!had_err) {
    gc_content = genomediff_calculate_gc(genome_lengths, unit_info, err);
    if (gc_content == NULL)
      had_err = -1;
  }

    /* calculation of divergence */
  if (!had_err) {
    genomediff_calculate_div(unit_info, div, gc_content, genome_lengths,
                             arguments, timer);

    if (gt_logger_enabled(logger)) {
      gt_logger_log(logger, "table of divergences");
      genomediff_print_table(div, unit_info);
    }
  }

  if (!had_err && timer != NULL)
    gt_timer_show_progress(timer, "calculate kr", stdout);

  if (!had_err) {
    gt_logger_log(logger, "# Table of Kr");
    printf("%lu\n", unit_info->num_of_genomes);
    for (i_idx = 0; i_idx < unit_info->num_of_genomes; i_idx++) {
      printf("%s\t", gt_str_array_get(unit_info->genome_names, i_idx));
      for (j_idx = 0; j_idx < unit_info->num_of_genomes; j_idx++) {
        if ( i_idx == j_idx )
          printf("%.6f\t",0.0);
        else
          printf("%f\t", gt_calculateKr(div[i_idx][j_idx]));
      }
      printf("\n");
    }
  }

  gt_free(genome_lengths);
  gt_free(gc_content);
  if (div != NULL)
    gt_array2dim_delete(div);
  return had_err;
}
genometools-1.5.1/src/match/shu-genomediff.h000066400000000000000000000037221211610345200210040ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SHU_GENOMEDIFF_H
#define SHU_GENOMEDIFF_H

#include "match/genomediff_opt.h"
#include "match/idx-limdfs.h"

uint64_t **gt_genomediff_shulen_sum(const GtGenomediffArguments *arguments,
                                    GtShuUnitFileInfo *unit_info,
                                    GtLogger *logger,
                                    GtTimer *timer,
                                    GtError *err);

int gt_genomediff_calculate_div_from_avg(double **avgshu,
                                         const GtGenomediffArguments *arguments,
                                         GtShuUnitFileInfo *unit_info,
                                         GtLogger *logger,
                                         GtTimer *timer,
                                         GtError *err);

int gt_genomediff_kr_calc(uint64_t **shulensums,
                          const GtGenomediffArguments *arguments,
                          GtShuUnitFileInfo *unit_info,
                          bool pcktable,
                          GtLogger *logger,
                          GtTimer *timer,
                          GtError *err);
#endif
genometools-1.5.1/src/match/shu_unitfile.c000066400000000000000000000167331211610345200206030ustar00rootroot00000000000000/*
  Copyright (c) 2011 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "lauxlib.h"
#include "lua.h"
#include "lualib.h"

#include "core/assert_api.h"
#include "core/basename_api.h"
#include "core/encseq_api.h"
#include "core/fileutils_api.h"
#include "core/log_api.h"
#include "core/ma_api.h"
#include "core/str_api.h"
#include "core/str_array.h"
#include "core/str_array_api.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"

#include "match/lua_tools.h"

#include "match/shu_unitfile.h"

static int shu_unitfile_load(lua_State *L,
                             const char *unitfile,
                             GtError *err)
{
  int had_err = 0;
  if (luaL_loadfile(L, unitfile) ||
      lua_pcall(L, 0, 0, 0)) {
    had_err = -1;
    gt_error_set(err, "Lua could not load file '%s'!", lua_tostring(L, -1));
  }
  if (!had_err) {
    lua_getglobal(L, "units");
    if (!lua_istable(L, -1)) {
      had_err = -1;
      gt_error_set(err, "Somethings wrong with the unitfile.");
    }
  }
  return had_err;
}

static int shu_unitfile_compare_inner_key_filenames(lua_State *L,
                                                   GtShuUnitFileInfo *unit_info,
                                                   bool *file_set,
                                                   GtStr *mapping_filename,
                                                   unsigned long genome_idx,
                                                   GtError *err)
{
  bool found = false;
  int had_err = 0;
  unsigned long file_idx;
  GtStr *encseq_filename;

  gt_str_reset(mapping_filename);
  gt_str_append_cstr(mapping_filename, lua_tostring(L, -1));

  for (file_idx = 0;
       file_idx < unit_info->num_of_files && !had_err && !found;
       file_idx++) {

    encseq_filename = gt_str_array_get_str(unit_info->file_names, file_idx);
    if (gt_str_cmp(encseq_filename, mapping_filename) == 0) {
      if (file_set[file_idx] != false) {
        gt_error_set(err, "file %s double entry",
                     gt_str_get(mapping_filename));
        had_err = -1;
      }
      else {
        file_set[file_idx] = true;
        unit_info->map_files[file_idx] = genome_idx;
        found = true;
      }
    }
  }
  if (!found && !had_err) {
    gt_error_set(err, "file %s not found in index, part of genome %s",
                 gt_str_get(mapping_filename),
                 gt_str_get(gt_str_array_get_str(unit_info->genome_names,
                                                 genome_idx)));
    had_err = -1;
  }
  return had_err;
}

static int shu_unitfile_traverse_inner_keys(lua_State *L,
                                            GtShuUnitFileInfo *unit_info,
                                            bool *file_set,
                                            GtStr *mapping_filename,
                                            unsigned long genome_idx,
                                            unsigned long *files_added,
                                            GtError *err)
{
  int had_err = 0;

  gt_str_array_add_cstr(unit_info->genome_names, lua_tostring(L, -2));

  lua_pushnil(L); /* the first inner key */
  while (lua_next(L, -2) != 0 && !had_err) {
    had_err = shu_unitfile_compare_inner_key_filenames(L, unit_info, file_set,
                                                       mapping_filename,
                                                       genome_idx,
                                                       err);
    if (!had_err)
      (*files_added)++;
    lua_pop(L, 1);
  }
  return had_err;
}

static int traverse_units(lua_State *L,
                          GtShuUnitFileInfo *unit_info,
                          GtError *err)
{
  int had_err = 0;
  unsigned long genome_idx = 0,
                files_added = 0;
  bool *file_set;
  GtStr *mapping_filename = gt_str_new();

  gt_assert(unit_info->file_names);

  file_set = gt_calloc((size_t) unit_info->num_of_files,
                       sizeof (file_set));

  unit_info->map_files = gt_calloc((size_t) unit_info->num_of_files,
                                   sizeof (unit_info->map_files));

  gt_str_array_reset(unit_info->genome_names);

  lua_pushnil(L); /*the first outer key*/
  while (lua_next(L, -2) != 0 && !had_err) {
    had_err = shu_unitfile_traverse_inner_keys(L, unit_info, file_set,
                                               mapping_filename,
                                               genome_idx, &files_added, err);
    lua_pop(L, 1);
    genome_idx++;
  }
  lua_pop(L, 1);

  gt_free(file_set);

  if (!had_err) {
    unit_info->num_of_genomes = genome_idx;
    gt_assert(unit_info->num_of_genomes ==
        gt_str_array_size(unit_info->genome_names));
  }
  if (!had_err && files_added != unit_info->num_of_files) {
    had_err = -1;
    gt_error_set(err, "number of files in index (%lu) and unitfile (%lu)! "
                 "differ!", unit_info->num_of_files, files_added);
  }
  if (!had_err) {
    unsigned long file_idx;
    for (file_idx = 0; file_idx < unit_info->num_of_files; file_idx++) {
      gt_log_log("file: %lu belongs to genome: %s",
                 file_idx,
                 gt_str_array_get(unit_info->genome_names,
                                  unit_info->map_files[file_idx]));
    }
  }
  gt_str_delete(mapping_filename);
  return had_err;
}

int gt_shu_unit_file_info_read(const GtStr *unitfile,
                               GtShuUnitFileInfo *unit_info,
                               GT_UNUSED GtLogger *logger,
                               GtError *err)
{
  int had_err = 0;
  /* open Lua */
  lua_State *L = luaL_newstate();
  /* library needed?
  lua_openlibs(L); */

  had_err = shu_unitfile_load(L, gt_str_get(unitfile), err);
  if (!had_err)
    had_err = traverse_units(L, unit_info, err);

  lua_close(L);
  return had_err;
}

void gt_shu_unit_info_delete(GtShuUnitFileInfo *unit_info) {
  if (unit_info != NULL) {
    gt_free(unit_info->map_files);
    gt_str_array_delete(unit_info->genome_names);
    gt_free(unit_info);
  }
}

static void gt_shu_unit_info_files_as_units(GtShuUnitFileInfo *unit_info)
{
  unsigned long i_idx;

  unit_info->num_of_genomes = unit_info->num_of_files;
  unit_info->genome_names = gt_str_array_new();
  for (i_idx = 0; i_idx < unit_info->num_of_files; i_idx++)
  {
    gt_str_array_add(unit_info->genome_names,
                     gt_str_array_get_str(unit_info->file_names, i_idx));
  }
}

GtShuUnitFileInfo *gt_shu_unit_info_new(const GtEncseq *encseq)
{
  GtShuUnitFileInfo *unit_info = gt_malloc(sizeof (*unit_info));

  unit_info->map_files = NULL;
  unit_info->genome_names = NULL;
  unit_info->num_of_genomes = 0;
  unit_info->num_of_files = gt_encseq_num_of_files(encseq);
  unit_info->file_names = gt_encseq_filenames(encseq);
  unit_info->encseq = encseq;
  gt_shu_unit_info_files_as_units(unit_info);
  return unit_info;
}
genometools-1.5.1/src/match/shu_unitfile.h000066400000000000000000000040501211610345200205750ustar00rootroot00000000000000/*
  Copyright (c) 2011 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SHU_UNITFILE_H
#define SHU_UNITFILE_H

#include "core/encseq_api.h"
#include "core/str_array_api.h"
#include "core/unused_api.h"

typedef struct GtShuUnitFileInfo {
  unsigned long num_of_genomes,
                num_of_files;
  GtStrArray *genome_names;
  const GtStrArray *file_names;
  /*array holding the mapping of file to genome*/
  unsigned long *map_files;
  const GtEncseq *encseq;
} GtShuUnitFileInfo;

/* Reads the lua  and collects the names of the genomes, and mapping
   of file number within the associated  to the genomes. Sets 
   and returns -1 on error. */
int                gt_shu_unit_file_info_read(const GtStr *unitfile,
                                              GtShuUnitFileInfo *unit_info,
                                              GT_UNUSED GtLogger *logger,
                                              GtError *err);

/* Initialize and malloc , will use filenames as units per
   default, call gt_shu_unit_file_info_read() to combine files to units. */
GtShuUnitFileInfo* gt_shu_unit_info_new(const GtEncseq *encseq);

/* frees memory of unit_info struct */
void               gt_shu_unit_info_delete(GtShuUnitFileInfo *unit_info);

#endif
genometools-1.5.1/src/match/spaced-seeds.c000066400000000000000000000142341211610345200204370ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/assert_api.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/chardef.h"
#include "core/ma_api.h"
#include "core/intbits.h"

#include "absdfstrans-imp.h"

typedef struct
{
  bool pathmatches;
} SpseLimdfsstate;

typedef struct
{
  GtBitsequence seedbitvector;
  unsigned long seedweight;
  const GtUchar *pattern;
} SpseLimdfsconstinfo;

#ifdef SKDEBUG

static void spse_showLimdfsstate(const DECLAREPTRDFSSTATE(aliascol),
                                unsigned long currentdepth,
                                GT_UNUSED const Limdfsconstinfo *mti)
{
  const SpseLimdfsstate *col = (const SpseLimdfsstate *) aliascol;

  printf("at depth %lu (pathmatches=%s)\n",currentdepth,
                                           col->pathmatches ? "true" : "false");
}

#endif

static Limdfsconstinfo *spse_allocatedfsconstinfo(
                               GT_UNUSED unsigned int alphasize)
{
  SpseLimdfsconstinfo *mti = gt_malloc(sizeof (SpseLimdfsconstinfo));
  return (Limdfsconstinfo*) mti;
}

static void spse_initdfsconstinfo(Limdfsconstinfo *mt,
                                  unsigned int alphasize,
                                  ...)
                                 /* Variable argument list is as follows:
                                    const GtUchar *pattern,
                                    Bitsequence seedbitvector,
                                    unsigned long seedweight
                                 */
{
  va_list ap;
  SpseLimdfsconstinfo *mti = (SpseLimdfsconstinfo*) mt;

  va_start(ap,alphasize);
  mti->pattern = va_arg(ap, const GtUchar *);
  mti->seedbitvector = va_arg(ap, GtBitsequence);
  mti->seedweight = va_arg(ap, unsigned long);
  va_end(ap);
}

static void spse_freedfsconstinfo(Limdfsconstinfo **mtiptr)
{
  gt_free(*mtiptr);
  *mtiptr = NULL;
}

static void spse_initLimdfsstate(DECLAREPTRDFSSTATE(aliascolumn),
                                 GT_UNUSED Limdfsconstinfo *mti)
{
  SpseLimdfsstate *column = (SpseLimdfsstate *) aliascolumn;

  column->pathmatches = true;
}

static void spse_fullmatchLimdfsstate(Limdfsresult *limdfsresult,
                                      DECLAREPTRDFSSTATE(aliascolumn),
                                      GT_UNUSED unsigned long leftbound,
                                      GT_UNUSED unsigned long rightbound,
                                      GT_UNUSED unsigned long width,
                                      unsigned long currentdepth,
                                      Limdfsconstinfo *mt)
{
  SpseLimdfsstate *limdfsstate = (SpseLimdfsstate *) aliascolumn;
  SpseLimdfsconstinfo *mti = (SpseLimdfsconstinfo*) mt;

  if (limdfsstate->pathmatches)
  {
    if (currentdepth == mti->seedweight)
    {
      limdfsresult->status = Limdfssuccess;
      limdfsresult->pprefixlen = mti->seedweight;
      limdfsresult->distance = 0;
      return;
    }
    if (currentdepth < mti->seedweight)
    {
      limdfsresult->status = Limdfscontinue;
      return;
    }
  }
  limdfsresult->status = Limdfsstop;
}

static bool setpathmatch(GtBitsequence seedbitvector,
                         const GtUchar *pattern,
                         unsigned long currentdepth,
                         GtUchar currentchar)
{
  return (!GT_ISBITSET(seedbitvector,currentdepth-1) ||
          currentchar == pattern[currentdepth-1]) ? true : false;
}

static void spse_nextLimdfsstate(const Limdfsconstinfo *mt,
                                 DECLAREPTRDFSSTATE(aliasoutcol),
                                 unsigned long currentdepth,
                                 GtUchar currentchar,
                                 GT_UNUSED const DECLAREPTRDFSSTATE(aliasincol))
{
  SpseLimdfsstate *outcol = (SpseLimdfsstate *) aliasoutcol;
#ifndef NDEBUG
  const SpseLimdfsstate *incol = (const SpseLimdfsstate *) aliasincol;
#endif
  SpseLimdfsconstinfo *mti = (SpseLimdfsconstinfo*) mt;

  gt_assert(ISNOTSPECIAL(currentchar));
  gt_assert(currentdepth > 0);
  gt_assert(incol->pathmatches);

  outcol->pathmatches = setpathmatch(mti->seedbitvector,
                                     mti->pattern,
                                     currentdepth,
                                     currentchar);
}

static void spse_inplacenextLimdfsstate(const Limdfsconstinfo *mt,
                                        DECLAREPTRDFSSTATE(aliascol),
                                        unsigned long currentdepth,
                                        GtUchar currentchar)
{
  SpseLimdfsstate *col = (SpseLimdfsstate *) aliascol;
  const SpseLimdfsconstinfo *mti = (const SpseLimdfsconstinfo*) mt;

  gt_assert(ISNOTSPECIAL(currentchar));
  gt_assert(currentdepth > 0);
  col->pathmatches = setpathmatch(mti->seedbitvector,
                                  mti->pattern,
                                  currentdepth,
                                  currentchar);
}

const AbstractDfstransformer *gt_spse_AbstractDfstransformer(void)
{
  static const AbstractDfstransformer spse_adfst =
  {
    sizeof (SpseLimdfsstate),
    spse_allocatedfsconstinfo,
    spse_initdfsconstinfo,
    NULL, /* no extractdfsconstinfo */
    spse_freedfsconstinfo,
    spse_initLimdfsstate,
    NULL,
    NULL,
    NULL,
    spse_fullmatchLimdfsstate,
    spse_nextLimdfsstate,
    spse_inplacenextLimdfsstate,
#ifdef SKDEBUG
    spse_showLimdfsstate,
#endif
  };
  return &spse_adfst;
}
genometools-1.5.1/src/match/spaced-seeds.h000066400000000000000000000017551211610345200204500ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SPACED_SEEDS_H
#define SPACED_SEEDS_H
#include "absdfstrans-def.h"

const AbstractDfstransformer *gt_spse_AbstractDfstransformer(void);

#endif
genometools-1.5.1/src/match/specialrank.c000066400000000000000000000125021211610345200203670ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/encseq.h"
#include "core/ma_api.h"
#include "core/unused_api.h"

typedef struct
{
  unsigned long lowerbound,
         upperbound,
         rank;
} Rankedbounds;

Rankedbounds *gt_fillrankbounds(const GtEncseq *encseq,
                             GtReadmode readmode)
{
  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;
    unsigned long currentrank = 0, realspecialranges;
    Rankedbounds *rankedbounds, *rbptr;

    realspecialranges = gt_encseq_realspecialranges(encseq);
    rankedbounds = gt_malloc(sizeof (Rankedbounds) * realspecialranges);
    sri = gt_specialrangeiterator_new(encseq,
                                      GT_ISDIRREVERSE(readmode)
                                      ? false : true);
    for (rbptr = rankedbounds;
         gt_specialrangeiterator_next(sri,&range);
         rbptr++)
    {
      rbptr->lowerbound = range.start;
      rbptr->upperbound = range.end;
      rbptr->rank = currentrank;
      currentrank += rbptr->upperbound - rbptr->lowerbound;
    }
    gt_assert(rbptr == rankedbounds + realspecialranges);
    gt_specialrangeiterator_delete(sri);
    return rankedbounds;
  }
  return NULL;
}

unsigned long gt_frompos2rank(const Rankedbounds *leftptr,
                              const Rankedbounds *rightptr,
                              unsigned long specialpos)
{
  const Rankedbounds *midptr;

  while (leftptr <= rightptr)
  {
    midptr = leftptr + GT_DIV2((unsigned long) (rightptr-leftptr));
    if (specialpos < midptr->lowerbound)
    {
      rightptr = midptr-1;
    } else
    {
      if (specialpos >= midptr->upperbound)
      {
        leftptr = midptr + 1;
      } else
      {
        return midptr->rank + specialpos - midptr->lowerbound;
      }
    }
  }
  fprintf(stderr,"frompos2rank: cannot find pos %lu"
                 " in ranges",specialpos);
  exit(GT_EXIT_PROGRAMMING_ERROR);
  /*@ignore@*/
  return 0;
  /*@end@*/
}

unsigned long gt_fromrank2pos(const Rankedbounds *leftptr,
                              const Rankedbounds *rightptr,
                              unsigned long rank)
{
  const Rankedbounds *midptr;

  while (leftptr <= rightptr)
  {
    midptr = leftptr + GT_DIV2((unsigned long) (rightptr-leftptr));
    if (rank < midptr->rank)
    {
      rightptr = midptr-1;
    } else
    {
      if (rank >= midptr->rank + (midptr->upperbound - midptr->lowerbound))
      {
        leftptr = midptr + 1;
      } else
      {
        return midptr->lowerbound + (rank - midptr->rank);
      }
    }
  }
  fprintf(stderr,"fromrank2rank: cannot find rank %lu"
                 " in ranges",rank);
  exit(GT_EXIT_PROGRAMMING_ERROR);
  /*@ignore@*/
  return 0;
  /*@end@*/
}

typedef struct
{
  unsigned long specialrank,
         key;
} Specialrank;

static int compareSpecialrank(const void *a,const void *b)
{
  const Specialrank *aptr = (const Specialrank *) a,
                    *bptr = (const Specialrank *) b;

  if (aptr->key < bptr->key)
  {
    return -1;
  }
  if (aptr->key > bptr->key)
  {
    return 1;
  }
  gt_assert(false);
  return 0;
}

Specialrank *gt_fillspecialranklist(const GtEncseq *encseq,
                                 GtReadmode readmode,
                                 const unsigned long *inversesuftab)
{
  if (gt_encseq_has_specialranges(encseq))
  {
    GtSpecialrangeiterator *sri;
    GtRange range;
    unsigned long realspecialranges, specialrank;
    GT_UNUSED unsigned long totallength;
    Specialrank *specialranklist, *rbptr;

    totallength = gt_encseq_total_length(encseq);
    realspecialranges = gt_encseq_realspecialranges(encseq);
    specialranklist = gt_malloc(sizeof (Specialrank) * realspecialranges);
    sri = gt_specialrangeiterator_new(encseq,
                                  GT_ISDIRREVERSE(readmode)
                                  ? false : true);
    rbptr = specialranklist;
    specialrank = 0;
    while (gt_specialrangeiterator_next(sri,&range))
    {
      gt_assert(rbptr < specialranklist + realspecialranges);
      gt_assert(range.end<=totallength);
      specialrank += range.end - range.start;
      rbptr->specialrank = specialrank - 1;
      rbptr->key = inversesuftab[range.end];
      rbptr++;
    }
    gt_assert(rbptr == specialranklist + realspecialranges);
    gt_specialrangeiterator_delete(sri);
    qsort(specialranklist,(size_t) realspecialranges,
          sizeof (Specialrank),compareSpecialrank);
    return specialranklist;
  }
  return NULL;
}
genometools-1.5.1/src/match/splititv.h000066400000000000000000000021021211610345200177510ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SPLITITV_H
#define SPLITITV_H

#include "core/types_api.h"
#include "core/arraydef.h"

typedef struct
{
  unsigned long lbound,
         rbound;
  GtUchar inchar;
} Boundswithchar;

GT_DECLAREARRAYSTRUCT(Boundswithchar);

#endif
genometools-1.5.1/src/match/spmsuftab.c000066400000000000000000000064351211610345200201070ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/minmax.h"
#include "spmsuftab.h"

GtSpmsuftab *gt_spmsuftab_new(unsigned long numofentries,
                              unsigned long maxvalue,
                              unsigned int bitsforseqnumrelpos,
                              GtLogger *logger)
{
  GtSpmsuftab *spmsuftab;
  unsigned int bitsforpositions;
  unsigned long required;

  spmsuftab = gt_malloc(sizeof (*spmsuftab));
  required = (unsigned long) gt_spmsuftab_requiredspace(numofentries,
                                                        maxvalue,
                                                        bitsforseqnumrelpos);
  bitsforpositions = gt_determinebitspervalue(maxvalue);
  if (bitsforpositions < bitsforseqnumrelpos)
  {
    gt_logger_log(logger,"use %lu bitpackarray-entries for all positions "
                         "(%u bits each,%lu bytes total)",
                         numofentries,bitsforpositions,required);
    spmsuftab->bitpackarray
      = gt_compact_ulong_store_new(numofentries,bitsforpositions);
    spmsuftab->usebitsforpositions = true;
    spmsuftab->maxvalue = maxvalue;
  } else
  {
    gt_logger_log(logger,"use %lu bitpackarray-entries for all "
                         "seqnum/relpos-pairs (%u bits each,%lu bytes total)",
                         numofentries,bitsforseqnumrelpos,required);
    spmsuftab->bitpackarray
      = gt_compact_ulong_store_new(numofentries,bitsforseqnumrelpos);
    spmsuftab->usebitsforpositions = false;
    spmsuftab->maxvalue = (1UL << bitsforseqnumrelpos) - 1;
  }
  spmsuftab->partoffset = 0;
  spmsuftab->numofentries = numofentries;
  return spmsuftab;
}

void gt_spmsuftab_delete(GtSpmsuftab *spmsuftab)
{
  if (spmsuftab != NULL)
  {
    gt_compact_ulong_store_delete(spmsuftab->bitpackarray);
    gt_free(spmsuftab);
  }
}

bool gt_spmsuftab_usebitsforpositions(const GtSpmsuftab *spmsuftab)
{
  return spmsuftab->usebitsforpositions;
}

void gt_spmsuftab_partoffset(GtSpmsuftab *spmsuftab,unsigned long offset)
{
  spmsuftab->partoffset = offset;
}

size_t gt_spmsuftab_requiredspace(unsigned long numofentries,
                                  unsigned long maxvalue,
                                  unsigned int bitsforseqnumrelpos)
{
  unsigned int bitsforpositions = gt_determinebitspervalue(maxvalue);

  return sizeof (GtSpmsuftab) +
         gt_compact_ulong_store_size(numofentries,
                                     MIN(bitsforpositions,bitsforseqnumrelpos));
}
genometools-1.5.1/src/match/spmsuftab.h000066400000000000000000000051121211610345200201030ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SPMSUFTAB_H
#define SPMSUFTAB_H

#include "core/unused_api.h"
#include "core/logger_api.h"
#include "core/compact_ulong_store.h"

typedef struct
{
  unsigned long partoffset, numofentries, maxvalue;
  bool usebitsforpositions;
  GtCompactUlongStore *bitpackarray;
} GtSpmsuftab;

GT_UNUSED static inline void gt_spmsuftab_set(GtSpmsuftab *spmsuftab,
                                              unsigned long idx,
                                              unsigned long value)
{
  gt_assert(idx >= spmsuftab->partoffset);
  idx -= spmsuftab->partoffset;
  gt_assert(idx < spmsuftab->numofentries && value <= spmsuftab->maxvalue);
  gt_assert(spmsuftab->bitpackarray != NULL);
  gt_compact_ulong_store_update(spmsuftab->bitpackarray,idx,value);
}

GT_UNUSED static inline unsigned long gt_spmsuftab_get(
                                      const GtSpmsuftab *spmsuftab,
                                      unsigned long idx)
{
  gt_assert(idx >= spmsuftab->partoffset);
  idx -= spmsuftab->partoffset;
  gt_assert(idx < spmsuftab->numofentries);
  return gt_compact_ulong_store_get(spmsuftab->bitpackarray,idx);
}

GtSpmsuftab *gt_spmsuftab_new(unsigned long numofentries,
                              unsigned long maxvalue,
                              unsigned int bitsforseqnumrelpos,
                              GtLogger *logger);

bool gt_spmsuftab_usebitsforpositions(const GtSpmsuftab *spmsuftab);

void gt_spmsuftab_delete(GtSpmsuftab *spmsuftab);

size_t gt_spmsuftab_requiredspace(unsigned long numofentries,
                                  unsigned long maxvalue,
                                  unsigned int bitsforseqnumrelpos);

void gt_spmsuftab_partoffset(GtSpmsuftab *spmsuftab,
                             unsigned long offset);

#endif
genometools-1.5.1/src/match/squarededist.c000066400000000000000000000040751211610345200205760ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/types_api.h"
#include "core/ma_api.h"
#include "squarededist.h"

static unsigned long gt_squarededistunit2 (const GtUchar *u, unsigned long m,
                                        const GtUchar *v, unsigned long n)
{
  unsigned long val, we, nw, *ecol, *ecolptr;
  const GtUchar *uptr, *vptr;

  ecol = gt_malloc(sizeof *ecol * (m+1));
  for (*ecol = 0, ecolptr = ecol+1, uptr = u; uptr < u + m; ecolptr++, uptr++)
  {
    *ecolptr = *(ecolptr-1) + 1;
  }
  for (vptr = v; vptr < v + n; vptr++)
  {
    nw = *ecol;
    *ecol = nw + 1;
    for (ecolptr = ecol+1, uptr = u; uptr < u + m; ecolptr++, uptr++)
    {
      we = *ecolptr;
      *ecolptr = *(ecolptr-1) + 1;
      if (*uptr == *vptr)
      {
        val = nw;
      } else
      {
        val = nw + 1;
      }
      if (val < *ecolptr)
      {
        *ecolptr = val;
      }
      if ((val = we + 1) < *ecolptr)
      {
        *ecolptr = val;
      }
      nw = we;
    }
  }
  val = *(ecolptr-1);
  gt_free(ecol);
  return val;
}

unsigned long gt_squarededistunit (const GtUchar *u, unsigned long m,
                                const GtUchar *v, unsigned long n)
{
  if (m < n)
  {
    return gt_squarededistunit2(u,m,v,n);
  }
  return gt_squarededistunit2(v,n,u,m);
}
genometools-1.5.1/src/match/squarededist.h000066400000000000000000000020631211610345200205760ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SQUAREDEDIST_H
#define SQUAREDEDIST_H

#include "core/types_api.h"

unsigned long gt_squarededistunit (const GtUchar *u, unsigned long m,
                                const GtUchar *v, unsigned long n);

#endif
genometools-1.5.1/src/match/stamp.h000066400000000000000000000020041211610345200172200ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef STAMP_H
#define STAMP_H

#define STAMP\
        printf("STAMP(%d,%s)\n",__LINE__,__FILE__);\
        (void) fflush(stdout)

#ifndef STAMP
#define STAMP
#endif

#endif
genometools-1.5.1/src/match/substriter.c000066400000000000000000000054051211610345200203050ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/str_array.h"
#include "core/seq_iterator_api.h"
#include "core/chardef.h"
#include "core/codetype.h"
#include "core/ma_api.h"
#include "substriter.h"
#include "qgram2code.h"
#include "initbasepower.h"

struct Substriter
{
  const GtUchar *currentptr, *start;
  unsigned long remaining;
  GtCodetype currentcode;
  unsigned int qvalue,
               numofchars;
  GtCodetype **multimappower;
};

Substriter *gt_substriter_new(const GtAlphabet *alphabet,unsigned int qvalue)
{
  Substriter *substriter;

  substriter = gt_malloc(sizeof *substriter);
  substriter->qvalue = qvalue;
  substriter->numofchars = gt_alphabet_num_of_chars(alphabet);
  substriter->multimappower = gt_initmultimappower(substriter->numofchars,
                                                   qvalue);
  return substriter;
}

void gt_substriter_init(Substriter *substriter,const GtUchar *start,
                    unsigned long len)
{
  substriter->start = substriter->currentptr = start;
  substriter->remaining = len;
  gt_assert(substriter->remaining > 0);
}

int gt_substriter_next(Substriter *substriter)
{
  unsigned int firstspecial;

  while (true)
  {
    if (substriter->remaining >= (unsigned long) substriter->qvalue)
    {
      firstspecial = qgram2code(&substriter->currentcode,
                                (const GtCodetype **) substriter->multimappower,
                                substriter->qvalue,
                                substriter->currentptr);
      if (firstspecial == substriter->qvalue)
      {
        substriter->remaining--;
        substriter->currentptr++;
        break;
      }
      substriter->remaining -= firstspecial + 1;
      substriter->currentptr += firstspecial + 1;
    } else
    {
      return 0;
    }
  }
  return 1;
}

void gt_substriter_delete(Substriter *substriter)
{
  if (substriter != NULL)
  {
    gt_multimappower_delete(substriter->multimappower);
    gt_free(substriter);
  }
}
genometools-1.5.1/src/match/substriter.h000066400000000000000000000025211211610345200203060ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef SUBSTRITER_H
#define SUBSTRITER_H

#include 
#include 
#include "core/alphabet.h"
#include "core/str_array.h"
#include "core/types_api.h"

typedef struct Substriter Substriter;

Substriter *gt_substriter_new(const GtAlphabet *alphabet,unsigned int qvalue);

void gt_substriter_init(Substriter *substriter,const GtUchar *start,
                     unsigned long len);

int gt_substriter_next(Substriter *substriter);

void gt_substriter_delete(Substriter *substriter);

#endif
genometools-1.5.1/src/match/tab-diffcover.h000066400000000000000000000323031211610345200206140ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#ifndef TAB_DIFFCOVER_H
#define TAB_DIFFCOVER_H

static Diffvalue differencecovertab[] = {
  /*
     1
   */ UScast (0),
  /*
     2
   */ UScast (0), UScast (1),
  /*
     4
   */ UScast (0), UScast (1), UScast (2),
  /*
     8
   */ UScast (0), UScast (1), UScast (2), UScast (4),
  /*
     16
   */ UScast (0), UScast (1), UScast (2), UScast (5), UScast (8),
  /*
     32
   */ UScast (0), UScast (1), UScast (2), UScast (3), UScast (7),
    UScast (11), UScast (19),
  /*
     64
   */ UScast (0), UScast (1), UScast (2), UScast (5),
    UScast (14), UScast (16), UScast (34), UScast (42),
    UScast (59),
  /*
     128
   */ UScast (0), UScast (1), UScast (3), UScast (7),
    UScast (17), UScast (40), UScast (55), UScast (64),
    UScast (75), UScast (85), UScast (104), UScast (109),
    UScast (117),
  /*
     256
   */ UScast (0), UScast (1), UScast (3), UScast (7),
    UScast (12), UScast (20), UScast (30), UScast (44),
    UScast (65), UScast (80), UScast (89), UScast (96),
    UScast (114), UScast (122), UScast (128), UScast (150),
    UScast (196), UScast (197), UScast (201), UScast (219),
  /*
     512
   */ UScast (0), UScast (1), UScast (2), UScast (3), UScast (4),
    UScast (9), UScast (18), UScast (27), UScast (36),
    UScast (45), UScast (64), UScast (83), UScast (102),
    UScast (121), UScast (140), UScast (159), UScast (178),
    UScast (197), UScast (216), UScast (226), UScast (236),
    UScast (246), UScast (256), UScast (266), UScast (267),
    UScast (268), UScast (269), UScast (270),
  /*
     1024
   */ UScast (0), UScast (1), UScast (2), UScast (3), UScast (4),
    UScast (5), UScast (6), UScast (13), UScast (26),
    UScast (39), UScast (52), UScast (65), UScast (78),
    UScast (91), UScast (118), UScast (145), UScast (172),
    UScast (199), UScast (226), UScast (253), UScast (280),
    UScast (307), UScast (334), UScast (361), UScast (388),
    UScast (415), UScast (442), UScast (456), UScast (470),
    UScast (484), UScast (498), UScast (512), UScast (526),
    UScast (540), UScast (541), UScast (542), UScast (543),
    UScast (544), UScast (545), UScast (546),
  /*
     2048
   */ UScast (0), UScast (1), UScast (2), UScast (3), UScast (4),
    UScast (5), UScast (6), UScast (7), UScast (8), UScast (9),
    UScast (19), UScast (38), UScast (57), UScast (76),
    UScast (95), UScast (114), UScast (133), UScast (152),
    UScast (171), UScast (190), UScast (229), UScast (268),
    UScast (307), UScast (346), UScast (385), UScast (424),
    UScast (463), UScast (502), UScast (541), UScast (580),
    UScast (619), UScast (658), UScast (697), UScast (736),
    UScast (775), UScast (814), UScast (853), UScast (892),
    UScast (931), UScast (951), UScast (971), UScast (991),
    UScast (1011), UScast (1031), UScast (1051), UScast (1071),
    UScast (1091), UScast (1111), UScast (1131), UScast (1132),
    UScast (1133), UScast (1134), UScast (1135), UScast (1136),
    UScast (1137), UScast (1138), UScast (1139), UScast (1140),
  /*
     4096
   */ UScast (0), UScast (1), UScast (2), UScast (3), UScast (4),
    UScast (5), UScast (6), UScast (7), UScast (8), UScast (9),
    UScast (10), UScast (11), UScast (12), UScast (13),
    UScast (27), UScast (54), UScast (81), UScast (108),
    UScast (135), UScast (162), UScast (189), UScast (216),
    UScast (243), UScast (270), UScast (297), UScast (324),
    UScast (351), UScast (378), UScast (433), UScast (488),
    UScast (543), UScast (598), UScast (653), UScast (708),
    UScast (763), UScast (818), UScast (873), UScast (928),
    UScast (983), UScast (1038), UScast (1093), UScast (1148),
    UScast (1203), UScast (1258), UScast (1313), UScast (1368),
    UScast (1423), UScast (1478), UScast (1533), UScast (1588),
    UScast (1643), UScast (1698), UScast (1753), UScast (1808),
    UScast (1863), UScast (1891), UScast (1919), UScast (1947),
    UScast (1975), UScast (2003), UScast (2031), UScast (2059),
    UScast (2087), UScast (2115), UScast (2143), UScast (2171),
    UScast (2199), UScast (2227), UScast (2255), UScast (2256),
    UScast (2257), UScast (2258), UScast (2259), UScast (2260),
    UScast (2261), UScast (2262), UScast (2263), UScast (2264),
    UScast (2265), UScast (2266), UScast (2267), UScast (2268),
  /*
     8192
   */ UScast (0), UScast (1), UScast (2), UScast (3), UScast (4),
    UScast (5), UScast (6), UScast (7), UScast (8), UScast (9),
    UScast (10), UScast (11), UScast (12), UScast (13),
    UScast (14), UScast (15), UScast (16), UScast (17),
    UScast (18), UScast (37), UScast (74), UScast (111),
    UScast (148), UScast (185), UScast (222), UScast (259),
    UScast (296), UScast (333), UScast (370), UScast (407),
    UScast (444), UScast (481), UScast (518), UScast (555),
    UScast (592), UScast (629), UScast (666), UScast (703),
    UScast (778), UScast (853), UScast (928), UScast (1003),
    UScast (1078), UScast (1153), UScast (1228), UScast (1303),
    UScast (1378), UScast (1453), UScast (1528), UScast (1603),
    UScast (1678), UScast (1753), UScast (1828), UScast (1903),
    UScast (1978), UScast (2053), UScast (2128), UScast (2203),
    UScast (2278), UScast (2353), UScast (2428), UScast (2503),
    UScast (2578), UScast (2653), UScast (2728), UScast (2803),
    UScast (2878), UScast (2953), UScast (3028), UScast (3103),
    UScast (3178), UScast (3253), UScast (3328), UScast (3403),
    UScast (3478), UScast (3516), UScast (3554), UScast (3592),
    UScast (3630), UScast (3668), UScast (3706), UScast (3744),
    UScast (3782), UScast (3820), UScast (3858), UScast (3896),
    UScast (3934), UScast (3972), UScast (4010), UScast (4048),
    UScast (4086), UScast (4124), UScast (4162), UScast (4200),
    UScast (4201), UScast (4202), UScast (4203), UScast (4204),
    UScast (4205), UScast (4206), UScast (4207), UScast (4208),
    UScast (4209), UScast (4210), UScast (4211), UScast (4212),
    UScast (4213), UScast (4214), UScast (4215), UScast (4216),
    UScast (4217), UScast (4218),
  /*
     16384
   */ UScast (0), UScast (1), UScast (2), UScast (3), UScast (4),
    UScast (5), UScast (6), UScast (7), UScast (8), UScast (9),
    UScast (10), UScast (11), UScast (12), UScast (13),
    UScast (14), UScast (15), UScast (16), UScast (17),
    UScast (18), UScast (19), UScast (20), UScast (21),
    UScast (22), UScast (23), UScast (24), UScast (25),
    UScast (26), UScast (53), UScast (106), UScast (159),
    UScast (212), UScast (265), UScast (318), UScast (371),
    UScast (424), UScast (477), UScast (530), UScast (583),
    UScast (636), UScast (689), UScast (742), UScast (795),
    UScast (848), UScast (901), UScast (954), UScast (1007),
    UScast (1060), UScast (1113), UScast (1166), UScast (1219),
    UScast (1272), UScast (1325), UScast (1378), UScast (1431),
    UScast (1538), UScast (1645), UScast (1752), UScast (1859),
    UScast (1966), UScast (2073), UScast (2180), UScast (2287),
    UScast (2394), UScast (2501), UScast (2608), UScast (2715),
    UScast (2822), UScast (2929), UScast (3036), UScast (3143),
    UScast (3250), UScast (3357), UScast (3464), UScast (3571),
    UScast (3678), UScast (3785), UScast (3892), UScast (3999),
    UScast (4106), UScast (4213), UScast (4320), UScast (4427),
    UScast (4534), UScast (4641), UScast (4748), UScast (4855),
    UScast (4962), UScast (5069), UScast (5176), UScast (5283),
    UScast (5390), UScast (5497), UScast (5604), UScast (5711),
    UScast (5818), UScast (5925), UScast (6032), UScast (6139),
    UScast (6246), UScast (6353), UScast (6460), UScast (6567),
    UScast (6674), UScast (6781), UScast (6888), UScast (6995),
    UScast (7102), UScast (7156), UScast (7210), UScast (7264),
    UScast (7318), UScast (7372), UScast (7426), UScast (7480),
    UScast (7534), UScast (7588), UScast (7642), UScast (7696),
    UScast (7750), UScast (7804), UScast (7858), UScast (7912),
    UScast (7966), UScast (8020), UScast (8074), UScast (8128),
    UScast (8182), UScast (8236), UScast (8290), UScast (8344),
    UScast (8398), UScast (8452), UScast (8506), UScast (8560),
    UScast (8561), UScast (8562), UScast (8563), UScast (8564),
    UScast (8565), UScast (8566), UScast (8567), UScast (8568),
    UScast (8569), UScast (8570), UScast (8571), UScast (8572),
    UScast (8573), UScast (8574), UScast (8575), UScast (8576),
    UScast (8577), UScast (8578), UScast (8579), UScast (8580),
    UScast (8581), UScast (8582), UScast (8583), UScast (8584),
    UScast (8585), UScast (8586),
  /*
     32768
   */ UScast (0), UScast (1), UScast (2), UScast (3), UScast (4),
    UScast (5), UScast (6), UScast (7), UScast (8), UScast (9),
    UScast (10), UScast (11), UScast (12), UScast (13),
    UScast (14), UScast (15), UScast (16), UScast (17),
    UScast (18), UScast (19), UScast (20), UScast (21),
    UScast (22), UScast (23), UScast (24), UScast (25),
    UScast (26), UScast (27), UScast (28), UScast (29),
    UScast (30), UScast (31), UScast (32), UScast (33),
    UScast (34), UScast (35), UScast (36), UScast (37),
    UScast (75), UScast (150), UScast (225), UScast (300),
    UScast (375), UScast (450), UScast (525), UScast (600),
    UScast (675), UScast (750), UScast (825), UScast (900),
    UScast (975), UScast (1050), UScast (1125), UScast (1200),
    UScast (1275), UScast (1350), UScast (1425), UScast (1500),
    UScast (1575), UScast (1650), UScast (1725), UScast (1800),
    UScast (1875), UScast (1950), UScast (2025), UScast (2100),
    UScast (2175), UScast (2250), UScast (2325), UScast (2400),
    UScast (2475), UScast (2550), UScast (2625), UScast (2700),
    UScast (2775), UScast (2850), UScast (3001), UScast (3152),
    UScast (3303), UScast (3454), UScast (3605), UScast (3756),
    UScast (3907), UScast (4058), UScast (4209), UScast (4360),
    UScast (4511), UScast (4662), UScast (4813), UScast (4964),
    UScast (5115), UScast (5266), UScast (5417), UScast (5568),
    UScast (5719), UScast (5870), UScast (6021), UScast (6172),
    UScast (6323), UScast (6474), UScast (6625), UScast (6776),
    UScast (6927), UScast (7078), UScast (7229), UScast (7380),
    UScast (7531), UScast (7682), UScast (7833), UScast (7984),
    UScast (8135), UScast (8286), UScast (8437), UScast (8588),
    UScast (8739), UScast (8890), UScast (9041), UScast (9192),
    UScast (9343), UScast (9494), UScast (9645), UScast (9796),
    UScast (9947), UScast (10098), UScast (10249),
    UScast (10400), UScast (10551), UScast (10702),
    UScast (10853), UScast (11004), UScast (11155),
    UScast (11306), UScast (11457), UScast (11608),
    UScast (11759), UScast (11910), UScast (12061),
    UScast (12212), UScast (12363), UScast (12514),
    UScast (12665), UScast (12816), UScast (12967),
    UScast (13118), UScast (13269), UScast (13420),
    UScast (13571), UScast (13722), UScast (13873),
    UScast (14024), UScast (14175), UScast (14251),
    UScast (14327), UScast (14403), UScast (14479),
    UScast (14555), UScast (14631), UScast (14707),
    UScast (14783), UScast (14859), UScast (14935),
    UScast (15011), UScast (15087), UScast (15163),
    UScast (15239), UScast (15315), UScast (15391),
    UScast (15467), UScast (15543), UScast (15619),
    UScast (15695), UScast (15771), UScast (15847),
    UScast (15923), UScast (15999), UScast (16075),
    UScast (16151), UScast (16227), UScast (16303),
    UScast (16379), UScast (16455), UScast (16531),
    UScast (16607), UScast (16683), UScast (16759),
    UScast (16835), UScast (16911), UScast (16987),
    UScast (17063), UScast (17064), UScast (17065),
    UScast (17066), UScast (17067), UScast (17068),
    UScast (17069), UScast (17070), UScast (17071),
    UScast (17072), UScast (17073), UScast (17074),
    UScast (17075), UScast (17076), UScast (17077),
    UScast (17078), UScast (17079), UScast (17080),
    UScast (17081), UScast (17082), UScast (17083),
    UScast (17084), UScast (17085), UScast (17086),
    UScast (17087), UScast (17088), UScast (17089),
    UScast (17090), UScast (17091), UScast (17092),
    UScast (17093), UScast (17094), UScast (17095),
    UScast (17096), UScast (17097), UScast (17098),
    UScast (17099), UScast (17100)
};

static Diffrank differencecoversizes[] = {
    UCcast (1), /* 2^0 */
    UCcast (2), /* 2^1 */
    UCcast (3), /* 2^2 */
    UCcast (4), /* 2^3 */
    UCcast (5), /* 2^4 */
    UCcast (7), /* 2^5 */
    UCcast (9), /* 2^6 */
    UCcast (13), /* 2^7 */
    UCcast (20), /* 2^8 */
    UCcast (28), /* 2^9 */
    UCcast (40), /* 2^10 */
    UCcast (58), /* 2^11 */
    UCcast (82), /* 2^12 */
    UCcast (112), /* 2^13 */
    UCcast (160), /* 2^14 */
    UCcast (226) /* 2^15 */
};

#endif
genometools-1.5.1/src/match/tagerator.c000066400000000000000000000635741211610345200201020ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/alphabet.h"
#include "core/arraydef.h"
#include "core/error.h"
#include "core/fileutils_api.h"
#include "core/format64.h"
#include "core/intbits.h"
#include "core/ma_api.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "core/str_array.h"
#include "core/unused_api.h"
#include "apmeoveridx.h"
#include "dist-short.h"
#include "echoseq.h"
#include "esa-map.h"
#include "idx-limdfs.h"
#include "mssufpat.h"
#include "myersapm.h"
#include "revcompl.h"
#include "sarr-def.h"
#include "stamp.h"
#include "tagerator.h"

#define MAXTAGSIZE GT_INTWORDSIZE

#define ISRCDIR(TWL)  (((TWL)->tagptr == (TWL)->transformedtag)\
                        ? false\
                        : true)

typedef struct
{
  unsigned long dbstartpos,
         matchlength;
  bool rcmatch;
} TgrSimplematch;

typedef struct
{
  const GtUchar *tagptr;
  GtUchar transformedtag[MAXTAGSIZE],
        rctransformedtag[MAXTAGSIZE];
  unsigned long taglen;
} TgrTagwithlength;

typedef struct
{
  const TageratorOptions *tageratoroptions;
  unsigned int alphasize;
  const GtUchar *tagptr;
  const GtAlphabet *alpha;
  unsigned long *eqsvector;
  const TgrTagwithlength *twlptr;
  const GtEncseq *encseq;
} TgrShowmatchinfo;

#define ADDTABULATOR\
        if (firstitem)\
        {\
          firstitem = false;\
        } else\
        {\
          (void) putchar('\t');\
        }

static void tgr_showmatch(void *processinfo,const GtIdxMatch *match)
{
  TgrShowmatchinfo *showmatchinfo = (TgrShowmatchinfo *) processinfo;
  bool firstitem = true;

  gt_assert(showmatchinfo->tageratoroptions != NULL);
  if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_DBLENGTH)
  {
    printf("%lu",match->dblen);
    firstitem = false;
  }
  if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_DBSTARTPOS)
  {
    ADDTABULATOR;
    if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_DBABSPOS)
    {
      printf("%lu",match->dbstartpos);
    } else
    {
      unsigned long seqstartpos,
                    seqnum = gt_encseq_seqnum(showmatchinfo->encseq,
                                                  match->dbstartpos);
      seqstartpos = gt_encseq_seqstartpos(showmatchinfo->encseq, seqnum);
      gt_assert(seqstartpos <= match->dbstartpos);
      printf("%lu\t%lu",seqnum, match->dbstartpos - seqstartpos);
    }
  }
  if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_DBSEQUENCE)
  {
    ADDTABULATOR;
    gt_assert(match->dbsubstring != NULL);
    gt_alphabet_decode_seq_to_fp(showmatchinfo->alpha,
                                 stdout,
                                 match->dbsubstring,
                                 (unsigned long) match->dblen);
  }
  if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_STRAND)
  {
    ADDTABULATOR;
    printf("%c",ISRCDIR(showmatchinfo->twlptr) ? '-' : '+');
  }
  if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_EDIST)
  {
    ADDTABULATOR;
    printf("%lu",match->distance);
  }
  if (showmatchinfo->tageratoroptions->maxintervalwidth > 0)
  {
    if (showmatchinfo->tageratoroptions->skpp)
    {
      if (showmatchinfo->tageratoroptions->outputmode &
          (TAGOUT_TAGSTARTPOS | TAGOUT_TAGLENGTH | TAGOUT_TAGSUFFIXSEQ))
      {
        unsigned long suffixlength
          = gt_reversesuffixmatch(showmatchinfo->eqsvector,
                               showmatchinfo->alphasize,
                               match->dbsubstring,
                               (unsigned long) match->dblen,
                               showmatchinfo->tagptr,
                               match->querylen,
                               (unsigned long) showmatchinfo->tageratoroptions->
                                                        userdefinedmaxdistance);
        gt_assert(match->querylen >= suffixlength);
        if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_TAGSTARTPOS)
        {
          ADDTABULATOR;
          printf("%lu",match->querylen - suffixlength);
        }
        if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_TAGLENGTH)
        {
          ADDTABULATOR;
          printf("%lu",suffixlength);
        }
        if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_TAGSUFFIXSEQ)
        {
          ADDTABULATOR;
          gt_alphabet_decode_seq_to_fp(NULL,
                                       stdout,showmatchinfo->tagptr +
                                       (match->querylen - suffixlength),
                                       suffixlength);
        }
      }
    } else
    {
      if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_TAGSTARTPOS)
      {
        ADDTABULATOR;
        printf("0");
      }
      if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_TAGLENGTH)
      {
        ADDTABULATOR;
        printf("%lu",match->querylen);
      }
      if (showmatchinfo->tageratoroptions->outputmode & TAGOUT_TAGSUFFIXSEQ)
      {
        ADDTABULATOR;
        gt_alphabet_decode_seq_to_fp(NULL,
                                     stdout,
                                     showmatchinfo->tagptr,
                                     match->querylen);
      }
    }
  }
  if (!firstitem)
  {
    printf("\n");
  }
}

typedef struct
{
  TgrSimplematch *spaceTgrSimplematch;
  unsigned long nextfreeTgrSimplematch, allocatedTgrSimplematch;
  const TgrTagwithlength *twlptr;
} ArrayTgrSimplematch;

static void tgr_storematch(void *processinfo,const GtIdxMatch *match)
{
  ArrayTgrSimplematch *storetab = (ArrayTgrSimplematch *) processinfo;
  TgrSimplematch *simplematch;

  GT_GETNEXTFREEINARRAY(simplematch,storetab,TgrSimplematch,32);
  simplematch->dbstartpos = match->dbstartpos;
  simplematch->matchlength = match->dblen;
  simplematch->rcmatch = ISRCDIR(storetab->twlptr);
}

static void checkmstats(void *processinfo,
                        const void *patterninfo,
                        unsigned long patternstartpos,
                        unsigned long mstatlength,
                        unsigned long leftbound,
                        unsigned long rightbound)
{
  GT_UNUSED unsigned long realmstatlength;
  TgrTagwithlength *twl = (TgrTagwithlength *) patterninfo;

  realmstatlength = genericmstats((const Limdfsresources *) processinfo,
                                  twl->tagptr + patternstartpos,
                                  twl->tagptr + twl->taglen);
#ifndef NDEBUG
  if (mstatlength != realmstatlength)
  {
    fprintf(stderr,"patternstartpos = %lu: mstatlength = %lu != %lu "
                   " = realmstatlength\n",
                    patternstartpos,mstatlength,realmstatlength);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
#endif
  if (gt_intervalwidthleq((const Limdfsresources *) processinfo,leftbound,
                       rightbound))
  {
    GtUchar cc;
    unsigned long *sptr, witnessposition;
    unsigned long idx;
    GtArrayGtUlong *mstatspos = gt_fromitv2sortedmatchpositions(
                                  (Limdfsresources *) processinfo,
                                  leftbound,
                                  rightbound,
                                  mstatlength);
    for (sptr = mstatspos->spaceGtUlong; sptr < mstatspos->spaceGtUlong +
                                               mstatspos->nextfreeGtUlong;
         sptr++)
    {
      witnessposition = *sptr;
      for (idx = patternstartpos; idx < patternstartpos + mstatlength; idx++)
      {
        cc = gt_limdfs_getencodedchar((const Limdfsresources *) processinfo,
                                  witnessposition + idx - patternstartpos,
                                  GT_READMODE_FORWARD);
        if (twl->tagptr[idx] != cc)
        {
          fprintf(stderr,"patternstartpos = %lu: pattern[%lu] = %u != %u = "
                         "sequence[%lu]\n",
                          patternstartpos,
                          idx,
                          (unsigned int) twl->tagptr[idx],
                          (unsigned int) cc,
                          (unsigned long)
                          (witnessposition+idx-patternstartpos));
          exit(GT_EXIT_PROGRAMMING_ERROR);
        }
      }
    }
  }
}

static void showmstats(void *processinfo,
                       const void *patterninfo,
                       GT_UNUSED unsigned long patternstartpos,
                       unsigned long mstatlength,
                       unsigned long leftbound,
                       unsigned long rightbound)
{
  TgrTagwithlength *twl = (TgrTagwithlength *) patterninfo;

  printf("%lu %c",mstatlength,ISRCDIR(twl) ? '-' : '+');
  if (gt_intervalwidthleq((const Limdfsresources *) processinfo,leftbound,
                       rightbound))
  {
    unsigned long idx;
    GtArrayGtUlong *mstatspos = gt_fromitv2sortedmatchpositions(
                                  (Limdfsresources *) processinfo,
                                  leftbound,
                                  rightbound,
                                  mstatlength);
    for (idx = 0; idxnextfreeGtUlong; idx++)
    {
      printf(" %lu",mstatspos->spaceGtUlong[idx]);
    }
  }
  printf("\n");
}

static int cmpdescend(const void *a,const void *b)
{
  TgrSimplematch *valuea = (TgrSimplematch *) a;
  TgrSimplematch *valueb = (TgrSimplematch *) b;

  if (!valuea->rcmatch && valueb->rcmatch)
  {
    return -1;
  }
  if (valuea->rcmatch && !valueb->rcmatch)
  {
    return 1;
  }
  if (valuea->dbstartpos < valueb->dbstartpos)
  {
    return 1;
  }
  if (valuea->dbstartpos > valueb->dbstartpos)
  {
    return -1;
  }
  return 0;
}

static int dotransformtag(GtUchar *transformedtag,
                          const GtUchar *symbolmap,
                          const GtUchar *currenttag,
                          unsigned long taglen,
                          uint64_t tagnumber,
                          bool replacewildcard,
                          GtError *err)
{
  unsigned long idx;
  GtUchar charcode;

  if (taglen > (unsigned long) MAXTAGSIZE)
  {
    gt_error_set(err,"tag \"%*.*s\" of length %lu; "
                  "tags must not be longer than %lu",
                   (int) taglen,(int) taglen,currenttag,taglen,
                   (unsigned long) MAXTAGSIZE);
    return -1;
  }
  for (idx = 0; idx < taglen; idx++)
  {
    charcode = symbolmap[currenttag[idx]];
    if (charcode == (GtUchar) UNDEFCHAR)
    {
      gt_error_set(err,"undefined character '%c' in tag number " Formatuint64_t,
                currenttag[idx],
                PRINTuint64_tcast(tagnumber));
      return -1;
    }
    if (charcode == (GtUchar) WILDCARD)
    {
      if (replacewildcard)
      {
        charcode = 0;
      } else
      {
        gt_error_set(err,"wildcard in tag number " Formatuint64_t,
                  PRINTuint64_tcast(tagnumber));
        return -1;
      }
    }
    transformedtag[idx] = charcode;
  }
  return 0;
}

static bool performpatternsearch(const AbstractDfstransformer *dfst,
                                 bool domstats,
                                 unsigned long maxdistance,
                                 bool doonline,
                                 bool docompare,
                                 unsigned long maxintervalwidth,
                                 bool skpp,
                                 Myersonlineresources *mor,
                                 Limdfsresources *limdfsresources,
                                 const GtUchar *tagptr,
                                 unsigned long taglen)
{
  if (doonline || (!domstats && docompare))
  {
    gt_assert(mor != NULL);
    gt_edistmyersbitvectorAPM(mor,tagptr,taglen,maxdistance);
  }
  if (!doonline || docompare)
  {
    if (domstats)
    {
      gt_indexbasedmstats(limdfsresources,tagptr,taglen,dfst);
      return false;
    }
    if (maxdistance == 0)
    {
      return gt_indexbasedexactpatternmatching(limdfsresources,tagptr,taglen);
    } else
    {
      return gt_indexbasedapproxpatternmatching(limdfsresources,tagptr,taglen,
                                             maxdistance,
                                             maxintervalwidth,
                                             skpp,
                                             dfst);
    }
  }
  return false;
}

static void compareresults(const ArrayTgrSimplematch *storeonline,
                           const ArrayTgrSimplematch *storeoffline)
{
  unsigned long ss;

  if (storeonline->nextfreeTgrSimplematch
        != storeoffline->nextfreeTgrSimplematch)
  {
    fprintf(stderr,"nextfreeTgrSimplematch: storeonline = %lu != %lu "
                   "storeoffline\n",
                   storeonline->nextfreeTgrSimplematch,
                   storeoffline->nextfreeTgrSimplematch);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  gt_assert(storeonline->nextfreeTgrSimplematch ==
            storeoffline->nextfreeTgrSimplematch);
  if (storeoffline->nextfreeTgrSimplematch > 1UL)
  {
    qsort(storeoffline->spaceTgrSimplematch,(size_t)
          storeoffline->nextfreeTgrSimplematch,
          sizeof (TgrSimplematch),
          cmpdescend);
  }
  for (ss=0; ss < storeoffline->nextfreeTgrSimplematch; ss++)
  {
    gt_assert(storeonline->spaceTgrSimplematch != NULL &&
           storeoffline->spaceTgrSimplematch != NULL);
    if (storeonline->spaceTgrSimplematch[ss].rcmatch &&
        !storeoffline->spaceTgrSimplematch[ss].rcmatch)
    {
      fprintf(stderr,"rcmatch: storeonline[%lu] = p != d "
                     "= storeoffline[%lu]\n",ss,ss);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    if (!storeonline->spaceTgrSimplematch[ss].rcmatch &&
        storeoffline->spaceTgrSimplematch[ss].rcmatch)
    {
      fprintf(stderr,"rcmatch: storeonline[%lu] = d != p "
                     "= storeoffline[%lu]\n",ss,ss);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    if (storeonline->spaceTgrSimplematch[ss].matchlength !=
        storeoffline->spaceTgrSimplematch[ss].matchlength)
    {
      fprintf(stderr,"matchlength: storeonline[%lu] = %lu"
                     " != %lu = storeoffline[%lu]\n",
                     ss,
                     storeonline->spaceTgrSimplematch[ss].matchlength,
                     storeoffline->spaceTgrSimplematch[ss].matchlength,
                     ss);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    if (storeonline->spaceTgrSimplematch[ss].dbstartpos !=
        storeoffline->spaceTgrSimplematch[ss].dbstartpos)
    {
      fprintf(stderr,"dbstartpos: storeonline[%lu] = %lu"
                     " != %lu = storeoffline[%lu]\n",
                     ss,
                     storeonline->spaceTgrSimplematch[ss].dbstartpos,
                     storeoffline->spaceTgrSimplematch[ss].dbstartpos,
                     ss);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  }
}

static void searchoverstrands(const TageratorOptions *tageratoroptions,
                              TgrTagwithlength *twl,
                              const AbstractDfstransformer *dfst,
                              Myersonlineresources *mor,
                              Limdfsresources *limdfsresources,
                              TgrShowmatchinfo *showmatchinfo,
                              ArrayTgrSimplematch *storeonline,
                              ArrayTgrSimplematch *storeoffline)
{
  int try;
  bool domstats, matchfound;
  unsigned long maxdistance, mindistance, distance;

  if (tageratoroptions->userdefinedmaxdistance < 0)
  {
    domstats = true;
    mindistance = maxdistance = 0;
  } else
  {
    domstats = false;
    gt_assert(tageratoroptions->userdefinedmaxdistance >= 0);
    maxdistance = (unsigned long) tageratoroptions->userdefinedmaxdistance;
    if (tageratoroptions->best)
    {
      mindistance = 0;
    } else
    {
      mindistance = maxdistance;
    }
  }
  matchfound = false;
  for (distance = mindistance; distance <= maxdistance; distance++)
  {
    showmatchinfo->tagptr = twl->tagptr = twl->transformedtag;
    for (try=0 ; try < 2; try++)
    {
      if ((try == 0 && !tageratoroptions->nofwdmatch) ||
          (try == 1 && !tageratoroptions->norcmatch))
      {
        if (try == 1 && !tageratoroptions->norcmatch)
        {
          showmatchinfo->tagptr = twl->tagptr = twl->rctransformedtag;
        }
        if (performpatternsearch(dfst,
                                 domstats,
                                 distance,
                                 tageratoroptions->doonline,
                                 tageratoroptions->docompare,
                                 tageratoroptions->maxintervalwidth,
                                 tageratoroptions->skpp,
                                 mor,
                                 limdfsresources,
                                 twl->tagptr,
                                 twl->taglen) && !matchfound)
        {
          matchfound = true;
        }
        if (tageratoroptions->docompare)
        {
          compareresults(storeonline,storeoffline);
        }
      }
    }
    if (tageratoroptions->best && matchfound)
    {
      break;
    }
  }
}

int gt_runtagerator(const TageratorOptions *tageratoroptions,GtError *err)
{
  bool haserr = false, firstitem;
  int retval;
  Myersonlineresources *mor = NULL;
  Genericindex *genericindex = NULL;
  const GtEncseq *encseq = NULL;
  GtLogger *logger;

  logger = gt_logger_new(tageratoroptions->verbose,
                         GT_LOGGER_DEFLT_PREFIX, stdout);
  if (tageratoroptions->doonline)
  {
    GtEncseqLoader *el;
    el = gt_encseq_loader_new();
    gt_encseq_loader_do_not_require_des_tab(el);
    gt_encseq_loader_do_not_require_ssp_tab(el);
    gt_encseq_loader_do_not_require_sds_tab(el);
    gt_encseq_loader_set_logger(el, logger);
    encseq = gt_encseq_loader_load(el, gt_str_get(tageratoroptions->indexname),
                                   err);
    gt_encseq_loader_delete(el);
    if (encseq == NULL)
    {
      haserr = true;
    }
  } else
  {
    genericindex = genericindex_new(gt_str_get(tageratoroptions->indexname),
                                    tageratoroptions->withesa,
                                    tageratoroptions->withesa ||
                                    tageratoroptions->docompare,
                                    false,
                                    (tageratoroptions->outputmode &
                                     TAGOUT_DBABSPOS) ? false : true,
                                    tageratoroptions->userdefinedmaxdepth,
                                    logger,
                                    err);
    if (genericindex == NULL)
    {
      haserr = true;
    } else
    {
      encseq = genericindex_getencseq(genericindex);
    }
  }
  if (!haserr)
  {
    TgrTagwithlength twl;
    uint64_t tagnumber;
    unsigned int numofchars;
    const GtUchar *symbolmap, *currenttag;
    char *desc = NULL;
    ProcessIdxMatch processmatch;
    TgrShowmatchinfo showmatchinfo;
    void *processmatchinfoonline, *processmatchinfooffline;
    Limdfsresources *limdfsresources = NULL;
    const GtAlphabet *alpha;
    ArrayTgrSimplematch storeonline, storeoffline;
    const AbstractDfstransformer *dfst;
    GtSeqIterator *seqit = NULL;

    if (tageratoroptions->userdefinedmaxdistance >= 0)
    {
      dfst = gt_apme_AbstractDfstransformer();
    } else
    {
      dfst = gt_pms_AbstractDfstransformer();
    }
    GT_INITARRAY(&storeonline,TgrSimplematch);
    GT_INITARRAY(&storeoffline,TgrSimplematch);
    storeonline.twlptr = storeoffline.twlptr = &twl;
    alpha = gt_encseq_alphabet(encseq);
    symbolmap = gt_alphabet_symbolmap(alpha);
    numofchars = gt_alphabet_num_of_chars(alpha);
    if (tageratoroptions->docompare)
    {
      processmatch = tgr_storematch;
      processmatchinfoonline = &storeonline;
      processmatchinfooffline = &storeoffline;
      showmatchinfo.eqsvector = NULL;
      showmatchinfo.encseq = encseq;
    } else
    {
      processmatch = tgr_showmatch;
      showmatchinfo.twlptr = &twl;
      showmatchinfo.tageratoroptions = tageratoroptions;
      showmatchinfo.alphasize = (unsigned int) numofchars;
      showmatchinfo.alpha = alpha;
      showmatchinfo.eqsvector = gt_malloc(sizeof (*showmatchinfo.eqsvector) *
                                          showmatchinfo.alphasize);
      showmatchinfo.encseq = encseq;
      processmatchinfooffline = &showmatchinfo;
      processmatchinfoonline = &showmatchinfo;
    }
    if (tageratoroptions->doonline || tageratoroptions->docompare)
    {
      gt_assert(encseq != NULL);
      mor = gt_newMyersonlineresources(numofchars,
                                    tageratoroptions->nowildcards,
                                    encseq,
                                    processmatch,
                                    processmatchinfoonline);
    }
    if (!tageratoroptions->doonline || tageratoroptions->docompare)
    {
      unsigned long maxpathlength;

      if (tageratoroptions->userdefinedmaxdistance >= 0)
      {
        maxpathlength = (unsigned long) (1+ MAXTAGSIZE +
                                         tageratoroptions->
                                         userdefinedmaxdistance);
      } else
      {
        maxpathlength = (unsigned long) (1+MAXTAGSIZE);
      }
      limdfsresources = gt_newLimdfsresources(genericindex,
                                           tageratoroptions->nowildcards,
                                           tageratoroptions->maxintervalwidth,
                                           maxpathlength,
                                           false, /* keepexpandedonstack */
                                           processmatch,
                                           processmatchinfooffline,
                                           tageratoroptions->docompare
                                             ? checkmstats
                                             : showmstats,
                                           &twl, /* refer to uninit structure */
                                           dfst);
    }
    printf("# for each match show: ");
    gt_getsetargmodekeywords(tageratoroptions->modedesc,
                             tageratoroptions->numberofmodedescentries,
                             tageratoroptions->outputmode);
    seqit = gt_seq_iterator_sequence_buffer_new(tageratoroptions->tagfiles,
                                                err);
    if (!seqit)
    {
      haserr = true;
    }
    if (!haserr)
    {
      for (tagnumber = 0; !haserr; tagnumber++)
      {
        retval = gt_seq_iterator_next(seqit, ¤ttag, &twl.taglen, &desc,
                                     err);
        if (retval != 1)
        {
          break;
        }
        if (dotransformtag(twl.transformedtag,
                           symbolmap,
                           currenttag,
                           twl.taglen,
                           tagnumber,
                           tageratoroptions->replacewildcard,
                           err) != 0)
        {
          haserr = true;
          gt_free(desc);
          break;
        }
        gt_copy_reversecomplement(twl.rctransformedtag,twl.transformedtag,
                               twl.taglen);
        twl.tagptr = twl.transformedtag;
        firstitem = true;
        printf("#");
        if (tageratoroptions->outputmode & TAGOUT_TAGNUM)
        {
          printf("\t" Formatuint64_t,PRINTuint64_tcast(tagnumber));
          firstitem = false;
        }
        if (tageratoroptions->outputmode & TAGOUT_TAGLENGTH)
        {
          ADDTABULATOR;
          printf("%lu",twl.taglen);
        }
        if (tageratoroptions->outputmode & TAGOUT_TAGSEQ)
        {
          ADDTABULATOR;
          gt_alphabet_decode_seq_to_fp(alpha,stdout,twl.transformedtag,
                                       twl.taglen);
        }
        printf("\n");
        storeoffline.nextfreeTgrSimplematch = 0;
        storeonline.nextfreeTgrSimplematch = 0;
        if (tageratoroptions->userdefinedmaxdistance > 0 &&
            twl.taglen <= (unsigned long)
                          tageratoroptions->userdefinedmaxdistance)
        {
          gt_error_set(err,"tag \"%*.*s\" of length %lu; "
                       "tags must be longer than the allowed number of errors "
                       "(which is %ld)",
                       (int) twl.taglen,
                       (int) twl.taglen,currenttag,
                       twl.taglen,
                       tageratoroptions->userdefinedmaxdistance);
          haserr = true;
          gt_free(desc);
          break;
        }
        gt_assert(tageratoroptions->userdefinedmaxdistance < 0 ||
                  twl.taglen > (unsigned long)
                               tageratoroptions->userdefinedmaxdistance);
        searchoverstrands(tageratoroptions,
                          &twl,
                          dfst,
                          mor,
                          limdfsresources,
                          &showmatchinfo,
                          &storeonline,
                          &storeoffline);
      }
      gt_seq_iterator_delete(seqit);
    }
    GT_FREEARRAY(&storeonline,TgrSimplematch);
    GT_FREEARRAY(&storeoffline,TgrSimplematch);
    gt_free(showmatchinfo.eqsvector);
    if (limdfsresources != NULL)
    {
      gt_freeLimdfsresources(&limdfsresources,dfst);
    }
  }
  gt_freeMyersonlineresources(mor);
  if (genericindex == NULL)
  {
    if (encseq != NULL)
    {
      gt_encseq_delete((GtEncseq *) encseq);
      encseq = NULL;
    }
  } else
  {
    genericindex_delete(genericindex);
  }
  gt_logger_delete(logger);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/tagerator.h000066400000000000000000000050411211610345200200700ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TAGERATOR_H
#define TAGERATOR_H

#include 
#include "core/str_array.h"
#include "core/error.h"
#include "core/option_api.h"
#include "match/optionargmode.h"

#define TAGOUT_TAGNUM       1U
#define TAGOUT_TAGSEQ       (1U << 1)
#define TAGOUT_DBLENGTH     (1U << 2)
#define TAGOUT_DBSTARTPOS   (1U << 3)
#define TAGOUT_DBABSPOS     (1U << 4)
#define TAGOUT_DBSEQUENCE   (1U << 5)
#define TAGOUT_STRAND       (1U << 6)
#define TAGOUT_EDIST        (1U << 7)
#define TAGOUT_TAGSTARTPOS  (1U << 8)
#define TAGOUT_TAGLENGTH    (1U << 9)
#define TAGOUT_TAGSUFFIXSEQ (1U << 10)

typedef struct
{
  GtStrArray *tagfiles, *outputspec;
  GtStr *indexname, *outputhelp;
  GtOption *refoptionesaindex,
           *refoptionpckindex;
  const Optionargmodedesc *modedesc;
  bool verbose,
       withesa,
       doonline,  /* perform online search, for testing */
       docompare, /* compare results with online search */
       replacewildcard, /* replace wildcards by random symbol */
       nofwdmatch, /* do not perform matching on forward strand */
       norcmatch, /* do not perform matching on reverse complemented strand */
       nowildcards, /* ignore matches containing wildcards */
       skpp, /* Skip prefix of pattern without counting errors */
       best; /* use best match mode, only for edit distance */
  long userdefinedmaxdistance; /* maximal number of allowed differences */
  int userdefinedmaxdepth;   /* use pckbuckets only up to this depth */
  unsigned int outputmode;  /* mode of output of tag matches */
  unsigned long maxintervalwidth; /* max width of interval */
  size_t numberofmodedescentries;
} TageratorOptions;

int gt_runtagerator(const TageratorOptions *tageratoroptions,GtError *err);

#endif
genometools-1.5.1/src/match/test-mappedstr.c000066400000000000000000000220041211610345200210450ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include "core/arraydef.h"
#include "core/chardef.h"
#include "core/error.h"
#include "core/unused_api.h"
#include "core/encseq.h"
#include "sfx-nextchar.h"
#include "kmer2string.h"
#include "sfx-mappedstr.h"

static GtCodetype qgram2codefillspecial(unsigned int numofchars,
                                      unsigned int kmersize,
                                      const GtEncseq *encseq,
                                      GtReadmode readmode,
                                      unsigned long startpos,
                                      unsigned long totallength)
{
  GtCodetype integercode;
  unsigned long pos;
  bool foundspecial;
  GtUchar cc;

  if (startpos >= totallength)
  {
    integercode = (GtCodetype) (numofchars - 1);
    foundspecial = true;
  } else
  {
    /* for testing */
    cc = gt_encseq_get_encoded_char(encseq,startpos,readmode);
    if (ISSPECIAL(cc))
    {
      integercode = (GtCodetype) (numofchars - 1);
      foundspecial = true;
    } else
    {
      integercode = (GtCodetype) cc;
      foundspecial = false;
    }
  }
  for (pos = startpos + 1; pos < startpos + kmersize; pos++)
  {
    if (foundspecial)
    {
      ADDNEXTCHAR(integercode,numofchars-1,numofchars);
    } else
    {
      if (pos >= totallength)
      {
        ADDNEXTCHAR(integercode,numofchars-1,numofchars);
        foundspecial = true;
      } else
      {
        /* for testing */
        cc = gt_encseq_get_encoded_char(encseq,pos,readmode);
        if (ISSPECIAL(cc))
        {
          ADDNEXTCHAR(integercode,numofchars-1,numofchars);
          foundspecial = true;
        } else
        {
          ADDNEXTCHAR(integercode,cc,numofchars);
        }
      }
    }
  }
  return integercode;
}

GT_DECLAREARRAYSTRUCT(GtCodetype);

static void outkmeroccurrence(void *processinfo,
                              const GtKmercode *kmercode)
{
  GtArrayGtCodetype *codelist = (GtArrayGtCodetype *) processinfo;

  GT_STOREINARRAY(codelist,GtCodetype,1024,kmercode->code);
}

/*
   The function to collect the code from a stream of fasta files
   can only produce the sequence of code in forward mode.
   Hence we compute the corresponding sequence also in GT_READMODE_FORWARD.
   Thus we restrict the call for gt_verifymappedstr to the case where
   the suffix array is in readmode = GT_READMODE_FORWARD.
*/

static void collectkmercode(GtArrayGtCodetype *codelist,
                            const GtEncseq *encseq,
                            unsigned int kmersize,
                            unsigned int numofchars,
                            unsigned long stringtotallength)
{
  unsigned long offset;
  GtCodetype code;

  for (offset=0; offset<=stringtotallength; offset++)
  {
    code = qgram2codefillspecial(numofchars,
                                 kmersize,
                                 encseq,
                                 GT_READMODE_FORWARD,
                                 offset,
                                 stringtotallength);
    GT_STOREINARRAY(codelist,GtCodetype,1024,code);
  }
}

static int comparecodelists(const GtArrayGtCodetype *codeliststream,
                            const GtArrayGtCodetype *codeliststring,
                            unsigned int kmersize,
                            unsigned int numofchars,
                            const char *characters,
                            GtError *err)
{
  unsigned long i;
  char buffer1[64+1], buffer2[64+1];

  gt_error_check(err);
  if (codeliststream->nextfreeGtCodetype != codeliststring->nextfreeGtCodetype)
  {
    gt_error_set(err,"length codeliststream= %lu != %lu =length codeliststring",
                  (unsigned long) codeliststream->nextfreeGtCodetype,
                  (unsigned long) codeliststring->nextfreeGtCodetype);
    return -1;
  }
  for (i=0; inextfreeGtCodetype; i++)
  {
    if (codeliststream->spaceGtCodetype[i] !=
          codeliststring->spaceGtCodetype[i])
    {
      gt_fromkmercode2string(buffer1,
                          codeliststream->spaceGtCodetype[i],
                          numofchars,
                          kmersize,
                          characters);
      gt_fromkmercode2string(buffer2,
                          codeliststring->spaceGtCodetype[i],
                          numofchars,
                          kmersize,
                          characters);
      gt_error_set(err,"codeliststream[%lu] = " FormatGtCodetype " != "
                    FormatGtCodetype " = codeliststring[%lu]\n%s != %s",
                    i,
                    codeliststream->spaceGtCodetype[i],
                    codeliststring->spaceGtCodetype[i],
                    i,
                    buffer1,
                    buffer2);
      return -1;
    }
  }
  return 0;
}

static int getfastastreamkmers(const GtStrArray *filenametab,
                               unsigned int numofchars,
                               unsigned int kmersize,
                               const GtUchar *symbolmap,
                               bool plainformat,
                               GtArrayGtCodetype *codeliststream,
                               GtError *err)
{
  GtKmercodeiterator *kmercodeiterator;
  const GtKmercode *kmercodeptr;
  bool haserr = false;

  kmercodeiterator = gt_kmercodeiterator_filetab_new(
                                filenametab,
                                numofchars,
                                kmersize,
                                symbolmap,
                                plainformat,
                                err);
  if (!gt_kmercodeiterator_inputexhausted(kmercodeiterator))
  {
    while (!haserr)
    {
      int retval = gt_kmercodeiterator_filetab_next(&kmercodeptr,
                                                    kmercodeiterator,
                                                    err);
      if (retval < 0)
      {
        haserr = true;
      } else
      {
        if (kmercodeptr != NULL)
        {
          outkmeroccurrence(codeliststream,kmercodeptr);
        } else
        {
          break;
        }
      }
    }
  }
  gt_kmercodeiterator_delete(kmercodeiterator);
  return haserr ? -1 : 0;
}

static int verifycodelists(const GtEncseq *encseq,
                           unsigned int kmersize,
                           unsigned int numofchars,
                           const GtArrayGtCodetype *codeliststream,
                           GtError *err)
{
  bool haserr = false;
  GtArrayGtCodetype codeliststring;
  const GtUchar *characters;
  unsigned long stringtotallength;

  gt_error_check(err);
  stringtotallength = gt_encseq_total_length(encseq);
  characters = gt_alphabet_characters(gt_encseq_alphabet(encseq));
  GT_INITARRAY(&codeliststring,GtCodetype);
  collectkmercode(&codeliststring,
                  encseq,
                  kmersize,
                  numofchars,
                  stringtotallength);
  if (comparecodelists(codeliststream,
                       &codeliststring,
                       kmersize,
                       numofchars,
                       (const char *) characters,
                       err) != 0)
  {
    haserr = true;
  }
  GT_FREEARRAY(&codeliststring,GtCodetype);
  return haserr ? -1 : 0;
}

int gt_verifymappedstr(const GtEncseq *encseq,
                       unsigned int prefixlength,
                       GtError *err)
{
  unsigned int numofchars;
  GtArrayGtCodetype codeliststream;
  bool haserr = false;

  gt_error_check(err);
  numofchars = gt_alphabet_num_of_chars(gt_encseq_alphabet(encseq));
  GT_INITARRAY(&codeliststream,GtCodetype);
  if (getfastastreamkmers(gt_encseq_filenames(encseq),
                          numofchars,
                          prefixlength,
                          gt_alphabet_symbolmap(
                                gt_encseq_alphabet(encseq)),
                          false,
                          &codeliststream,
                          err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (verifycodelists(encseq,
                        prefixlength,
                        numofchars,
                        &codeliststream,
                        err) != 0)
    {
      haserr = true;
    }
  }
  GT_FREEARRAY(&codeliststream,GtCodetype);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/test-mappedstr.pr000066400000000000000000000003131211610345200212430ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
int gt_verifymappedstr(const GtEncseq *encseq,
                       unsigned int prefixlength,
                       GtError *err);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/test-maxpairs.c000066400000000000000000000360111211610345200206750ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/alphabet.h"
#include "core/array.h"
#include "core/arraydef.h"
#include "core/divmodmul.h"
#include "core/encseq.h"
#include "core/format64.h"
#include "core/logger.h"
#include "core/timer_api.h"
#include "core/unused_api.h"
#include "core/ma_api.h"
#include "esa-mmsearch.h"
#include "echoseq.h"
#include "sfx-suffixer.h"
#include "sfx-apfxlen.h"
#include "esa-maxpairs.h"
#include "esa-seqread.h"

typedef struct
{
  unsigned int minlength;
  GtEncseq *encseq;
  Processmaxpairs processmaxpairs;
  void *processmaxpairsinfo;
} Substringmatchinfo;

static int constructsarrandrunmaxpairs(
                 Substringmatchinfo *ssi,
                 GtReadmode readmode,
                 unsigned int prefixlength,
                 unsigned int numofparts,
                 unsigned long maximumspace,
                 GtTimer *sfxprogress,
                 bool withprogressbar,
                 GT_UNUSED GtLogger *logger,
                 GtError *err)
{
  const GtSuffixsortspace *suffixsortspace;
  unsigned long numberofsuffixes;
  bool haserr = false;
  Sfxiterator *sfi;
  bool specialsuffixes = false;

  Sfxstrategy sfxstrategy;

  defaultsfxstrategy(&sfxstrategy,
                     gt_encseq_bitwise_cmp_ok(ssi->encseq) ? false : true);
  sfi = gt_Sfxiterator_new(ssi->encseq,
                           readmode,
                           prefixlength,
                           numofparts,
                           maximumspace,
                           &sfxstrategy,
                           sfxprogress,
                           withprogressbar,
                           NULL, /* logger */
                           err);
  if (sfi == NULL)
  {
    haserr = true;
  } else
  {
    Sequentialsuffixarrayreader *ssar = NULL;
    bool firstpage = true;

    ssar = gt_newSequentialsuffixarrayreaderfromRAM(ssi->encseq,
                                                    readmode);
    while (true)
    {
      suffixsortspace = gt_Sfxiterator_next(&numberofsuffixes,&specialsuffixes,
                                            sfi);
      if (suffixsortspace == NULL || specialsuffixes)
      {
        break;
      }
      gt_updateSequentialsuffixarrayreaderfromRAM(
               ssar,
               (const ESASuffixptr *)
               gt_suffixsortspace_ulong_get(suffixsortspace),
               firstpage,
               numberofsuffixes);
      firstpage = false;
      if (gt_enumeratemaxpairs(ssar,
                               ssi->encseq,
                               readmode,
                               ssi->minlength,
                               ssi->processmaxpairs,
                               ssi->processmaxpairsinfo,
                               err) != 0)
      {
        haserr = true;
      }
    }
    if (ssar != NULL)
    {
      gt_freeSequentialsuffixarrayreader(&ssar);
    }
  }
  if (gt_Sfxiterator_delete(sfi,err) != 0)
  {
    haserr = true;
  }
  return haserr ? -1 : 0;
}

static int sarrselfsubstringmatch(const GtUchar *dbseq,
                                  unsigned long dblen,
                                  const GtUchar *query,
                                  unsigned long querylen,
                                  unsigned int minlength,
                                  GtAlphabet *alpha,
                                  Processmaxpairs processmaxpairs,
                                  void *processmaxpairsinfo,
                                  GtLogger *logger,
                                  GtError *err)
{
  Substringmatchinfo ssi;
  unsigned int numofchars, recommendedprefixlength;
  GtEncseqBuilder *eb;
  bool haserr = false;

  eb = gt_encseq_builder_new(alpha);
  gt_encseq_builder_disable_multiseq_support(eb);
  gt_encseq_builder_disable_description_support(eb);
  gt_encseq_builder_set_logger(eb, logger);
  gt_encseq_builder_add_encoded(eb, dbseq, dblen, NULL);
  gt_encseq_builder_add_encoded(eb, query, querylen, NULL);
  ssi.encseq = gt_encseq_builder_build(eb, err);
  gt_encseq_builder_delete(eb);

  ssi.minlength = minlength;
  ssi.processmaxpairs = processmaxpairs;
  ssi.processmaxpairsinfo = processmaxpairsinfo;
  numofchars = gt_alphabet_num_of_chars(alpha);
  recommendedprefixlength
    = gt_recommendedprefixlength(numofchars,
                                 dblen+querylen+1,
                                 GT_RECOMMENDED_MULTIPLIER_DEFAULT,
                                 true);
  if (constructsarrandrunmaxpairs(&ssi,
                                  GT_READMODE_FORWARD,
                                  recommendedprefixlength,
                                  1U, /* parts */
                                  0, /* maximumspace */
                                  NULL,
                                  false,
                                  logger,
                                  err) != 0)
  {
    haserr = true;
  }
  gt_encseq_delete(ssi.encseq);
  ssi.encseq = NULL;
  return haserr ? -1 : 0;
}

static unsigned long samplesubstring(GtUchar *seqspace,
                              const GtEncseq *encseq,
                              unsigned long substringlength)
{
  unsigned long start, totallength;

  totallength = gt_encseq_total_length(encseq);
  start = (unsigned long) (random() % totallength);
  if (start + substringlength > totallength)
  {
    substringlength = totallength - start;
  }
  gt_assert(substringlength > 0);
  gt_encseq_extract_encoded(encseq,seqspace,start,
                                       start+substringlength-1);
  return substringlength;
}

typedef struct
{
  unsigned long len,
         dbstart,
         querystart;
  uint64_t queryseqnum;
} Substringmatch;

static int storemaxmatchquery(void *info,
                              GT_UNUSED const GtEncseq *encseq,
                              const GtQuerymatch *querymatch,
                              GT_UNUSED const GtUchar *query,
                              GT_UNUSED unsigned long query_totallength,
                              GT_UNUSED GtError *err)
{
  GtArray *tab = (GtArray *) info;
  Substringmatch subm;

  subm.len = gt_querymatch_querylen(querymatch);
  subm.dbstart = gt_querymatch_dbstart(querymatch);
  subm.querystart = gt_querymatch_querystart(querymatch);
  subm.queryseqnum = gt_querymatch_queryseqnum(querymatch);
  gt_array_add(tab,subm);
  return 0;
}

typedef struct
{
  GtArray *results;
  unsigned long dblen, *querymarkpos, querylen;
  unsigned long numofquerysequences;
} Maxmatchselfinfo;

static int storemaxmatchself(void *info,
                             GT_UNUSED const GtEncseq *encseq,
                             unsigned long len,
                             unsigned long pos1,
                             unsigned long pos2,
                             GT_UNUSED GtError *err)
{
  Maxmatchselfinfo *maxmatchselfinfo = (Maxmatchselfinfo *) info;
  unsigned long dbstart, querystart;

  if (pos1 < pos2)
  {
    dbstart = pos1;
    querystart = pos2;
  } else
  {
    dbstart = pos2;
    querystart = pos1;
  }
  if (dbstart < maxmatchselfinfo->dblen &&
      maxmatchselfinfo->dblen < querystart)
  {
    Substringmatch subm;
    unsigned long pos;

    subm.len = len;
    subm.dbstart = dbstart;
    pos = querystart - (maxmatchselfinfo->dblen + 1);
    if (maxmatchselfinfo->querymarkpos == NULL)
    {
      subm.queryseqnum = 0;
      subm.querystart = pos;
    } else
    {
      unsigned long queryseqnum
        = gt_encseq_sep2seqnum(maxmatchselfinfo->querymarkpos,
                                        maxmatchselfinfo->numofquerysequences,
                                        maxmatchselfinfo->querylen,
                                        pos);
      if (queryseqnum == maxmatchselfinfo->numofquerysequences)
      {
        return -1;
      }
      if (queryseqnum == 0)
      {
        subm.querystart = pos;
      } else
      {
        subm.querystart = pos -
                          (maxmatchselfinfo->querymarkpos[queryseqnum-1] + 1);
      }
      subm.queryseqnum = (uint64_t) queryseqnum;
    }
    gt_array_add(maxmatchselfinfo->results,subm);
  }
  return 0;
}

static int orderSubstringmatch(const void *a,const void *b)
{
  Substringmatch *m1 = (Substringmatch *) a,
                 *m2 = (Substringmatch *) b;

  if (m1->queryseqnum < m2->queryseqnum)
  {
    return -1;
  }
  if (m1->queryseqnum > m2->queryseqnum)
  {
    return 1;
  }
  if (m1->querystart < m2->querystart)
  {
    return -1;
  }
  if (m1->querystart > m2->querystart)
  {
    return 1;
  }
  if (m1->dbstart < m2->dbstart)
  {
    return -1;
  }
  if (m1->dbstart > m2->dbstart)
  {
    return 1;
  }
  if (m1->len < m2->len)
  {
    return -1;
  }
  if (m1->len > m2->len)
  {
    return 1;
  }
  return 0;
}

static int showSubstringmatch(void *a, GT_UNUSED void *info,
                              GT_UNUSED GtError *err)
{
  Substringmatch *m = (Substringmatch *) a;

  printf("%lu %lu " Formatuint64_t " %lu\n",
           m->len,
           m->dbstart,
           PRINTuint64_tcast(m->queryseqnum),
           m->querystart);
  return 0;
}

static unsigned long *sequence2markpositions(unsigned long *numofsequences,
                                      const GtUchar *seq,
                                      unsigned long seqlen)
{
  unsigned long *spacemarkpos, idx;
  unsigned long allocatedmarkpos, nextfreemarkpos;

  *numofsequences = 1UL;
  for (idx=0; idx totallength/2)
    {
      substringlength = totallength/2;
    }
    dbseq = gt_malloc(sizeof *dbseq * substringlength);
    query = gt_malloc(sizeof *query * substringlength);
  }
  for (s=0; s
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include "core/fa.h"
#include "core/logger.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "core/ma_api.h"
#include "sarr-def.h"
#include "emimergeesa.h"
#include "esa-fileend.h"
#include "lcpoverflow.h"

#include "encseq2offset.pr"

typedef struct
{
  GtStr *outfilename;
  FILE *fp;
} NameandFILE;

typedef struct
{
  NameandFILE outsuf,
              outlcp,
              outllv;
  unsigned long currentlcpindex,
         absstartpostable[SIZEOFMERGERESULTBUFFER];
} Mergeoutinfo;

static int initNameandFILE(NameandFILE *nf,
                            const GtStr *outindex,
                            const char *suffix,
                            GtError *err)
{
  gt_error_check(err);
  nf->outfilename = gt_str_clone(outindex);
  gt_str_append_cstr(nf->outfilename,suffix);
  nf->fp = gt_fa_fopen(gt_str_get(nf->outfilename),"wb",err);
  if (nf->fp == NULL)
  {
    return -1;
  }
  return 0;
}

static void freeNameandFILE(NameandFILE *nf)
{
  gt_fa_xfclose(nf->fp);
  gt_str_delete(nf->outfilename);
}

static int outputsuflcpllv(void *processinfo,
                           const unsigned long *sequenceoffsettable,
                           const Suflcpbuffer *buf,
                           GT_UNUSED GtError *err)
{
  Mergeoutinfo *mergeoutinfo = (Mergeoutinfo *) processinfo;

  unsigned int i, lastindex;
  unsigned long lcpvalue;
  Largelcpvalue currentexception;
  GtUchar smallvalue;
  bool haserr = false;

  gt_error_check(err);
  for (i=0; inextstoreidx; i++)
  {
    mergeoutinfo->absstartpostable[i]
      = sequenceoffsettable[buf->suftabstore[i].idx] +
        buf->suftabstore[i].startpos;
  }
  gt_xfwrite(mergeoutinfo->absstartpostable, sizeof (unsigned long),
            (size_t) buf->nextstoreidx, mergeoutinfo->outsuf.fp);
  if (!haserr)
  {
    if (buf->lastpage)
    {
      lastindex = buf->nextstoreidx - 1;
    } else
    {
      lastindex = buf->nextstoreidx;
    }
    for (i=0; ilcptabstore[i];
      if (lcpvalue < (unsigned long) LCPOVERFLOW)
      {
        smallvalue = (GtUchar) lcpvalue;
      } else
      {
        currentexception.position = mergeoutinfo->currentlcpindex;
        currentexception.value = lcpvalue;
        gt_xfwrite(¤texception,sizeof (Largelcpvalue), (size_t) 1,
                   mergeoutinfo->outllv.fp);
        smallvalue = LCPOVERFLOW;
      }
      gt_xfwrite(&smallvalue,sizeof (GtUchar),(size_t) 1,
                 mergeoutinfo->outlcp.fp);
      mergeoutinfo->currentlcpindex++;
    }
  }
  return haserr ? -1 : 0;
}

static int mergeandstoreindex(const GtStr *storeindex,
                              Emissionmergedesa *emmesa,
                              GtError *err)
{
  Mergeoutinfo mergeoutinfo;
  GtUchar smalllcpvalue;
  GtSpecialcharinfo specialcharinfo;
  unsigned long *sequenceoffsettable, totallength;
  bool haserr = false;

  gt_error_check(err);
  if (initNameandFILE(&mergeoutinfo.outsuf,storeindex,SUFTABSUFFIX,err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (initNameandFILE(&mergeoutinfo.outlcp,storeindex,LCPTABSUFFIX,err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    if (initNameandFILE(&mergeoutinfo.outllv,storeindex,LARGELCPTABSUFFIX,
                       err) != 0)
    {
      haserr = true;
    }
  }
  smalllcpvalue = 0;
  if (!haserr) {
    gt_xfwrite(&smalllcpvalue,sizeof (GtUchar),(size_t) 1,
               mergeoutinfo.outlcp.fp);
  }
  if (!haserr)
  {
    mergeoutinfo.currentlcpindex = (unsigned long) 1;
    sequenceoffsettable = gt_encseqtable2sequenceoffsets(&totallength,
                                                      &specialcharinfo,
                                                      emmesa->suffixarraytable,
                                                      emmesa->numofindexes);
    gt_assert(sequenceoffsettable != NULL);
    while (emmesa->numofentries > 0)
    {
      if (gt_emissionmergedesa_stepdeleteandinsertothersuffixes(emmesa,
                                                                err) != 0)
      {
        haserr = true;
        break;
      }
      if (outputsuflcpllv(&mergeoutinfo,
                         sequenceoffsettable,
                         &emmesa->buf,
                         err) != 0)
      {
        haserr = true;
        break;
      }
    }
    gt_free(sequenceoffsettable);
  }
  freeNameandFILE(&mergeoutinfo.outsuf);
  freeNameandFILE(&mergeoutinfo.outlcp);
  freeNameandFILE(&mergeoutinfo.outllv);
  return haserr ? -1 : 0;
}

int gt_performtheindexmerging(const GtStr *storeindex,
                           const GtStrArray *indexnametab,
                           GtLogger *logger,
                           GtError *err)
{
  Emissionmergedesa emmesa;
  unsigned int demand = SARR_ESQTAB | SARR_SUFTAB | SARR_LCPTAB;
  bool haserr = false;

  gt_error_check(err);
  if (gt_emissionmergedesa_init(&emmesa,
                             indexnametab,
                             demand,
                             logger,
                             err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (gt_str_array_size(indexnametab) > 1UL)
    {
      if (mergeandstoreindex(storeindex,&emmesa,err) != 0)
      {
        haserr = true;
      }
    } else
    {
      gt_error_set(err,"merging requires more than one index");
      haserr = true;
    }
  }
  gt_emissionmergedesa_wrap(&emmesa);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/test-mergeesa.pr000066400000000000000000000004151211610345200210370ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
int gt_performtheindexmerging(const GtStr *storeindex,
                           const GtStrArray *indexnametab,
                           GtLogger *logger,
                           GtError *err);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/test-mtrieins.c000066400000000000000000000072371211610345200207130ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/alphabet.h"
#include "core/unused_api.h"
#include "core/encseq.h"
#include "core/ma_api.h"
#include "sarr-def.h"
#include "merger-trie.h"
#include "esa-map.h"

static void maketrie(Mergertrierep *trierep,
                     GT_UNUSED const GtUchar *characters,
                     unsigned long len)
{
  Suffixinfo suffixinfo;

  suffixinfo.idx = 0;
#ifdef WITHTRIEIDENT
  suffixinfo.ident = 0;
#endif
  for (suffixinfo.startpos = 0;
       suffixinfo.startpos <= len;
       suffixinfo.startpos++)
  {
    gt_mergertrie_insertsuffix(trierep,trierep->root,&suffixinfo);
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
    showtrie(trierep,characters);
#endif
    suffixinfo.ident++;
#endif
  }
}

static void successivelydeletesmallest(Mergertrierep *trierep,
                                       GT_UNUSED unsigned long seqlen,
                                       GT_UNUSED const GtUchar *characters,
                                       GT_UNUSED GtError *err)
{
  Mergertrienode *smallest;
#ifdef WITHTRIEIDENT
  unsigned int numberofleaves = (unsigned int) seqlen+1;
  unsigned int maxleafnum = (unsigned int) seqlen;
#endif

  while (trierep->root != NULL && trierep->root->firstchild != NULL)
  {
    smallest = gt_mergertrie_findsmallestnode(trierep);
    gt_mergertrie_deletesmallestpath(smallest,trierep);
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
    showtrie(trierep,characters);
#endif
    numberofleaves--;
    checktrie(trierep,numberofleaves,maxleafnum,err);
#endif
  }
}

int gt_test_trieins(bool onlyins,const char *indexname,GtError *err)
{
  Suffixarray suffixarray;
  bool haserr = false;
  unsigned long totallength = 0;

  gt_error_check(err);
  if (streamsuffixarray(&suffixarray,
                        SARR_ESQTAB,
                        indexname,
                        NULL,
                        err) != 0)
  {
    haserr = true;
  } else
  {
    totallength = gt_encseq_total_length(suffixarray.encseq);
  }
  if (!haserr)
  {
    Mergertrierep trierep;
    const GtUchar *characters;

    trierep.encseqreadinfo = gt_malloc(sizeof *trierep.encseqreadinfo);
    trierep.encseqreadinfo->encseqptr = suffixarray.encseq;
    trierep.encseqreadinfo->readmode = suffixarray.readmode;
    characters
      = gt_alphabet_characters(gt_encseq_alphabet(suffixarray.encseq));
    gt_mergertrie_initnodetable(&trierep,totallength,1U);
    maketrie(&trierep,characters,totallength);
    if (onlyins)
    {
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
      showtrie(&trierep,characters);
#endif
      checktrie(&trierep,totallength+1,totallength,err);
#endif
    } else
    {
#ifdef WITHTRIEIDENT
#ifdef WITHTRIESHOW
      showallnoderelations(trierep.root);
#endif
#endif
      successivelydeletesmallest(&trierep,totallength,characters,err);
    }
    gt_mergertrie_delete(&trierep);
  }
  gt_freesuffixarray(&suffixarray);
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/test-mtrieins.pr000066400000000000000000000002121211610345200210740ustar00rootroot00000000000000#ifdef __cplusplus
extern "C" {
#endif
int gt_test_trieins(bool onlyins,const char *indexname,GtError *err);

#ifdef __cplusplus
}
#endif
genometools-1.5.1/src/match/test-pairwise.c000066400000000000000000000123431211610345200206760ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include "core/fa.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/ma_api.h"
#include "test-pairwise.h"
#include "greedyedist.h"
#include "squarededist.h"

void gt_runcheckfunctionontwofiles(Checkcmppairfuntype checkfunction,
                                const char *file1,
                                const char *file2)
{
  const GtUchar *useq = NULL, *vseq = NULL;
  size_t ulen, vlen;
  bool forward = true;
  GtError *err;

  err = gt_error_new();
  useq = (const GtUchar *) gt_fa_mmap_read(file1,&ulen,err);
  if (useq == NULL)
  {
    fprintf(stderr, "error: %s\n", gt_error_get(err));
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  vseq = (const GtUchar *) gt_fa_mmap_read(file2,&vlen,err);
  if (vseq == NULL)
  {
    fprintf(stderr, "error: %s\n", gt_error_get(err));
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  gt_error_delete(err);
  while (true)
  {
    checkfunction(forward,useq,(unsigned long) ulen,
                          vseq,(unsigned long) vlen);
    if (!forward)
    {
      break;
    }
    forward = false;
  }
  gt_fa_xmunmap((void *) useq);
  gt_fa_xmunmap((void *) vseq);
}

unsigned long gt_runcheckfunctionontext(Checkcmppairfuntype checkfunction,
                                     const char *text)
{
  unsigned long i, len;

  len = (unsigned long) strlen(text);
  for (i=1UL; i<=len/2; i++)
  {
    checkfunction(true,
                  (const GtUchar *) text,
                  i,
                  (const GtUchar *) (text+i),
                  len-i);
  }
  return len/2;
}

unsigned long gt_applycheckfunctiontotext(const GtUchar *text,
                                       unsigned long textlen,
                                       void *info)
{
  unsigned long i;
  Checkcmppairfuntype checkfunction = (Checkcmppairfuntype) info;

#ifdef SKDEBUG
  printf("%s\n",(char *) text);
#endif
  for (i=0; i<=textlen/2; i++)
  {
    checkfunction(true,text,i,text+i,textlen-i);
  }
  return textlen/2+1;
}

static unsigned long applyall(const char *alpha,
                              unsigned long textlen,void *info,
                              unsigned long (*apply)(const GtUchar *,
                                                     unsigned long,
                                                     void *))
{
  unsigned long i, *w, z = textlen-1,
                testcases = 0,
                asize = (unsigned long) strlen(alpha);
  GtUchar *text;
  bool stop = false;

  w = gt_malloc(sizeof *w * (textlen+1));
  text = gt_malloc(sizeof *text * (textlen+1));
  for (i=0; i<=textlen; i++)
  {
    w[i] = 0;
  }
  text[textlen] = (GtUchar) '\0';
  while (!stop)
  {
    for (i = 0; i
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TEST_PAIRWISE_H
#define TEST_PAIRWISE_H

#include 
#include "core/types_api.h"

typedef void (*Checkcmppairfuntype)(bool,
                                    const GtUchar *,unsigned long,
                                    const GtUchar *,unsigned long);

void gt_runcheckfunctionontwofiles(Checkcmppairfuntype checkfunction,
                               const char *file1,
                               const char *file2);

unsigned long gt_runcheckfunctionontext(Checkcmppairfuntype checkfunction,
                                     const char *text);

unsigned long gt_applycheckfunctiontotext(const GtUchar *text,
                                       unsigned long textlen,
                                       void *info);

unsigned long gt_runcheckfunctiononalphalen(Checkcmppairfuntype checkfunction,
                                         const char *charlist,
                                         unsigned long len);

void gt_checkgreedyunitedist(bool forward,
                          const GtUchar *useq,
                          unsigned long ulen,
                          const GtUchar *vseq,
                          unsigned long vlen);

#endif
genometools-1.5.1/src/match/turnwheels.c000066400000000000000000000045121211610345200202750ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "turnwheels.h"

#define MAXNUMOFWHEELS 18

struct Turningwheel
{
  unsigned int wheelspace[MAXNUMOFWHEELS],
               numofwheels,
               asize,
               idx,
               minchanged;
};

Turningwheel *gt_turningwheel_new(unsigned int numofwheels,
                                  unsigned int asize)
{
  unsigned int i;
  Turningwheel *tw;

  tw = gt_malloc(sizeof (*tw));
  gt_assert(numofwheels < (unsigned int) MAXNUMOFWHEELS);
  gt_assert(numofwheels > 0);
  gt_assert(asize > 0);
  for (i=0; iwheelspace[i] = 0;
  }
  tw->numofwheels = numofwheels;
  tw->asize = asize;
  tw->idx = numofwheels - 1;
  tw->minchanged = 0;
  return tw;
}

size_t gt_turningwheel_size(void)
{
  return sizeof (Turningwheel);
}

bool gt_turningwheel_next(Turningwheel *tw)
{
  while (true)
  {
    tw->wheelspace[tw->idx]++;
    tw->minchanged = tw->idx;
    if (tw->wheelspace[tw->idx] == tw->asize)
    {
      tw->wheelspace[tw->idx] = 0;
      if (tw->idx == 0)
      {
        return false;
      }
      tw->idx--;
    } else
    {
      tw->idx = tw->numofwheels-1;
      break;
    }
  }
  return true;
}

unsigned int gt_turningwheel_minchanged(const Turningwheel *tw)
{
  return tw->minchanged;
}

void gt_turningwheel_output(const Turningwheel *tw)
{
  unsigned int i;

  for (i=0; inumofwheels; i++)
  {
    printf("%u",tw->wheelspace[i]);
  }
}

void gt_turningwheel_delete(Turningwheel *tw)
{
  if (tw != NULL)
  {
    gt_free(tw);
  }
}
genometools-1.5.1/src/match/turnwheels.h000066400000000000000000000024401211610345200203000ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TURNWHEELS_H
#define TURNWHEELS_H

typedef struct Turningwheel Turningwheel;

Turningwheel *gt_turningwheel_new(unsigned int numofwheels,
                                  unsigned int asize);

size_t gt_turningwheel_size(void);

bool gt_turningwheel_next(Turningwheel *tw);

unsigned int gt_turningwheel_minchanged(const Turningwheel *tw);

void gt_turningwheel_output(const Turningwheel *tw);

void gt_turningwheel_delete(Turningwheel *tw);

#endif
genometools-1.5.1/src/match/twobits2kmers.c000066400000000000000000000251651211610345200207230ustar00rootroot00000000000000/*
  Copyright (c) 2007-2011 Stefan Kurtz 
  Copyright (c) 2007-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/arraydef.h"
#include "core/codetype.h"
#include "core/encseq.h"
#include "core/encseq_api.h"
#include "core/format64.h"
#include "core/intbits.h"
#include "core/unused_api.h"
#include "hashfirstcodes.h"
#include "sfx-mappedstr.h"
#include "sfx-suffixer.h"
#include "stamp.h"
#include "twobits2kmers.h"

#define READNEXTCODEANDCHECKIGNORESPECIAL(POS)\
        gt_assert(kmercodeiterator != NULL);\
        kmercodeptr = gt_kmercodeiterator_encseq_next(kmercodeiterator);\
        gt_assert(kmercodeptr != NULL);\
        if (!kmercodeptr->definedspecialposition && kmer != kmercodeptr->code)\
        {\
          showdifferentkmers(__LINE__,POS,kmer,kmercodeptr->code);\
          exit(GT_EXIT_PROGRAMMING_ERROR);\
        }

typedef struct
{
  int shiftright;
  const GtTwobitencoding *tbptr;
  GtTwobitencoding currentencoding;
} Singlecharacterbitstreamstate;

static void showdifferentkmers(int line,unsigned long pos,GtCodetype kmer1,
                               GtCodetype kmer2)
{
  char buffer[2*GT_INTWORDSIZE+1];

  fprintf(stderr,"line %d: pos=%lu\n",line,pos);
  gt_bitsequence_tostring_units(buffer,(GtBitsequence) kmer1,2U);
  fprintf(stderr,"kmer1=%s\n",buffer);
  gt_bitsequence_tostring_units(buffer,(GtBitsequence) kmer2,2U);
  fprintf(stderr,"kmer2=%s\n",buffer);
  fprintf(stderr,"kmer1=%lu != %lu= kmer2\n",kmer1,kmer2);
}

static void scbs_init(Singlecharacterbitstreamstate *scbs,
                      const GtTwobitencoding *twobitencoding,
                      unsigned int kmersize)
{
  scbs->tbptr = twobitencoding;
  if (kmersize == 0)
  {
    scbs->currentencoding = 0;
    scbs->shiftright = 0;
  } else
  {
    scbs->currentencoding = *(scbs->tbptr++);
    gt_assert(2U * kmersize < (unsigned int) GT_INTWORDSIZE);
    scbs->shiftright = GT_INTWORDSIZE - GT_MULT2(kmersize);
  }
}

static inline GtUchar scbs_next(Singlecharacterbitstreamstate *scbs)
{
  if (scbs->shiftright > 0)
  {
    scbs->shiftright -= 2;
  } else
  {
    scbs->currentencoding = *(scbs->tbptr++);
    scbs->shiftright = GT_INTWORDSIZE-2;
  }
  return (GtUchar) (scbs->currentencoding >> scbs->shiftright) & 3;
}

typedef struct
{
  const GtTwobitencoding *tbptr;
  GtTwobitencoding currentencoding;
  unsigned int unitoffset, shiftleft, shiftright;
  GtCodetype maskright;
} Multicharacterbitstreamstate;

static void mcbs_init(Multicharacterbitstreamstate *mcbs,
                      const GtTwobitencoding *twobitencoding,
                      unsigned int kmersize)
{
  mcbs->tbptr = twobitencoding;
  mcbs->unitoffset = 0;
  mcbs->shiftleft = 2U;
  mcbs->shiftright = (unsigned int) GT_MULT2(GT_UNITSIN2BITENC - kmersize);
  mcbs->maskright = (GtCodetype) (1 << GT_MULT2(kmersize))-1;
  mcbs->currentencoding = *(mcbs->tbptr++);
}

static inline GtCodetype mcbs_next(Multicharacterbitstreamstate *mcbs,
                                   unsigned int kmersize)
{
  GtCodetype kmer;

  if (mcbs->unitoffset <= (unsigned int) GT_UNITSIN2BITENC - kmersize)
  {
    kmer = (GtCodetype) (mcbs->currentencoding >> mcbs->shiftright)
                        & mcbs->maskright;
    mcbs->shiftright-=2U;
  } else
  {
    kmer = (GtCodetype)
             ((mcbs->currentencoding << mcbs->shiftleft) |
              (*(mcbs->tbptr) >>
               (GT_MULT2(GT_UNITSIN2BITENC)-mcbs->shiftleft)))
              & mcbs->maskright;
    mcbs->shiftleft+=2;
  }
  if (mcbs->unitoffset < (unsigned int) GT_UNITSIN2BITENC-1)
  {
    mcbs->unitoffset++;
  } else
  {
    mcbs->unitoffset = 0;
    mcbs->shiftleft = 2U;
    mcbs->shiftright = (unsigned int) GT_MULT2(GT_UNITSIN2BITENC - kmersize);
    mcbs->currentencoding = *(mcbs->tbptr++);
  }
  return kmer;
}

static void gt_checkkmercode(GT_UNUSED void *processinfo,
                             GT_UNUSED bool firstinrange,
                             GT_UNUSED unsigned long pos,
                             GT_UNUSED GtCodetype code)
{
#ifndef NDEBUG
  GtKmercodeiterator *kmercodeiterator = (GtKmercodeiterator *) processinfo;
  const GtKmercode *kmercodeptr;

  gt_assert(kmercodeiterator != NULL);
  kmercodeptr = gt_kmercodeiterator_encseq_nonspecial_next(kmercodeiterator);
  gt_assert(kmercodeptr != NULL && !kmercodeptr->definedspecialposition);
  gt_assert(code == kmercodeptr->code);
#endif
}

static void multireadmode_getencseqkmers_twobitencoding(const GtEncseq *encseq,
                                                        unsigned int kmersize)
{
  GtKmercodeiterator *kmercodeiterator;
  int readmode_int;

  for (readmode_int = 0; readmode_int < 4; readmode_int++)
  {
    printf("getencseqkmers_twobitencoding(kmersize=%u,%s)\n",
                         kmersize,
                         gt_readmode_show((GtReadmode) readmode_int));
    kmercodeiterator = gt_kmercodeiterator_encseq_new(encseq,
                                                      (GtReadmode) readmode_int,
                                                      kmersize,0);
    getencseqkmers_twobitencoding(encseq,
                                  (GtReadmode) readmode_int,
                                  kmersize,
                                  kmersize,
                                  false,
                                  gt_checkkmercode,
                                  kmercodeiterator,
                                  NULL,
                                  NULL);
    gt_kmercodeiterator_delete(kmercodeiterator);
    kmercodeiterator = NULL;
  }
}

static void gt_encseq_faststream_kmers(const GtEncseq *encseq,
                                       Bitstreamreadmode bsrsmode,
                                       unsigned int kmersize)
{
  unsigned long totallength, pos;
  GtCodetype kmer;
  GtKmercodeiterator *kmercodeiterator = NULL;
  const GtKmercode *kmercodeptr;
  const GtTwobitencoding *twobitencoding;
  Multicharacterbitstreamstate mcbs;

  gt_assert(kmersize <= (unsigned int) GT_UNITSIN2BITENC);
  totallength = gt_encseq_total_length(encseq);
  if (totallength < (unsigned long) kmersize)
  {
    return;
  }
  twobitencoding = gt_encseq_twobitencoding_export(encseq);
  if (bsrsmode == BSRS_reader_multi ||
      bsrsmode == BSRS_stream_reader_multi)
  {
    kmercodeiterator = gt_kmercodeiterator_encseq_new(encseq,
                                                      GT_READMODE_FORWARD,
                                                      kmersize,0);
  }
  switch (bsrsmode)
  {
    case BSRS_reader_multi:
      {
        uint64_t kmersum = 0;

        for (pos = 0; pos <= totallength - (unsigned long) kmersize; pos++)
        {
          kmercodeptr = gt_kmercodeiterator_encseq_next(kmercodeiterator);
          gt_assert(kmercodeptr != NULL);
          kmersum += (uint64_t) kmercodeptr->code;
        }
        printf("kmersum=" Formatuint64_t "\n",PRINTuint64_tcast(kmersum));
        break;
      }
    case BSRS_stream_reader_multi:
      mcbs_init(&mcbs,twobitencoding,kmersize);
      for (pos = 0; pos <= totallength - (unsigned long) kmersize; pos++)
      {
        kmer = mcbs_next(&mcbs,kmersize);
        READNEXTCODEANDCHECKIGNORESPECIAL(pos);
      }
      break;
    case BSRS_stream_reader_multi3:
      multireadmode_getencseqkmers_twobitencoding(encseq,kmersize);
      break;
    case BSRS_hashfirstcodes:
      hashfirstcodes_getencseqkmers_twobitencoding(encseq,kmersize);
      break;
    default:
      break;
  }
  gt_kmercodeiterator_delete(kmercodeiterator);
}

void gt_encseq_faststream(const GtEncseq *encseq,
                          Bitstreamreadmode bsrsmode,
                          unsigned int multiarg)
{
  const GtTwobitencoding *twobitencoding;

  twobitencoding = gt_encseq_twobitencoding_export(encseq);
  if (twobitencoding != NULL)
  {
    unsigned long idx, totallength, pos;
    uint64_t pairbitsum = 0, pairbitsumBF;
    GtUchar cc, ccesr;
    GtEncseqReader *esr = NULL;
    Singlecharacterbitstreamstate scbs;

    scbs_init(&scbs,twobitencoding,0);
    if (bsrsmode == BSRS_reader_single ||
        bsrsmode == BSRS_stream_reader_single)
    {
      esr = gt_encseq_create_reader_with_readmode(encseq,
                                                  GT_READMODE_FORWARD,
                                                  0);
    }
    totallength = gt_encseq_total_length(encseq);
    switch (bsrsmode)
    {
      case BSRS_stream_words:
        for (idx = 0; idx < gt_unitsoftwobitencoding(totallength); idx++)
        {
          pairbitsum += twobitencoding[idx];
        }
        break;
      case BSRS_stream_single:
        for (pos = 0; pos < totallength; pos++)
        {
          cc = scbs_next(&scbs);
          pairbitsum += (uint64_t) cc;
        }
        pairbitsumBF = gt_encseq_pairbitsum(encseq);
        if (pairbitsum != pairbitsumBF)
        {
          fprintf(stderr,"pairbitsum=" Formatuint64_t "!=" Formatuint64_t
                         "=pairbitsumBF\n",
                         PRINTuint64_tcast(pairbitsum),
                         PRINTuint64_tcast(pairbitsumBF));
          exit(GT_EXIT_PROGRAMMING_ERROR);
        }
        break;
      case BSRS_reader_single:
        for (pos = 0; pos < totallength; pos++)
        {
          ccesr = gt_encseq_reader_next_encoded_char(esr);
          pairbitsum += (uint64_t) ccesr;
        }
        break;
      case BSRS_stream_reader_single:
        for (pos = 0; pos < totallength; pos++)
        {
          cc = scbs_next(&scbs);
          pairbitsum += (uint64_t) cc;
          ccesr = gt_encseq_reader_next_encoded_char(esr);
          pairbitsum += (uint64_t) ccesr;
          gt_assert(cc == ccesr || ISSPECIAL(ccesr));
        }
        break;
      case BSRS_reader_multi:
      case BSRS_stream_reader_multi:
      case BSRS_stream_reader_multi3:
      case BSRS_hashfirstcodes:
        gt_encseq_faststream_kmers(encseq,bsrsmode,multiarg);
        break;
    }
    if (pairbitsum > 0)
    {
      printf("pairbitsum=" Formatuint64_t "\n",PRINTuint64_tcast(pairbitsum));
    }
    gt_encseq_reader_delete(esr);
  }
}
genometools-1.5.1/src/match/twobits2kmers.h000066400000000000000000000024541211610345200207240ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TWOBITS2KMERS_H
#define TWOBITS2KMERS_H

#include "core/encseq_api.h"

typedef enum
{
  BSRS_stream_words,
  BSRS_stream_single,
  BSRS_reader_single,
  BSRS_stream_reader_single,
  BSRS_reader_multi,
  BSRS_stream_reader_multi,
  BSRS_stream_reader_multi3,
  BSRS_hashfirstcodes
} Bitstreamreadmode;

void gt_encseq_faststream(const GtEncseq *encseq,
                          Bitstreamreadmode bsrsmode,
                          unsigned int multiarg);
#endif
genometools-1.5.1/src/match/tyr-basic.h000066400000000000000000000023061211610345200177760ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TYR_BASIC_H
#define TYR_BASIC_H

#include "core/arraydef.h"
#include "core/divmodmul.h"

#define MERSUFFIX     ".mer"
#define COUNTSSUFFIX  ".mct"
#define EXTRAINTEGERS 2

#define MERBYTES(SL)  (GT_DIV4(SL) + ((GT_MOD4(SL) == 0) ? 0 : 1UL))

typedef struct
{
  unsigned long idx,
                value;
} Largecount;

GT_DECLAREARRAYSTRUCT(Largecount);

#endif
genometools-1.5.1/src/match/tyr-map.c000066400000000000000000000302611211610345200174660ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/defined-types.h"
#include "core/divmodmul.h"
#include "core/encseq.h"
#include "core/fa.h"
#include "core/unused_api.h"
#include "core/ma_api.h"
#include "sfx-apfxlen.h"
#include "tyr-basic.h"
#include "tyr-map.h"

struct Tyrindex
{
  void *mappedfileptr;
  const char *indexfilename;
  unsigned int alphasize;
  size_t numofmers;
  unsigned long mersize,
                merbytes;
  GtUchar *mertable,
        *lastmer;
};

struct Tyrcountinfo
{
  void *mappedmctfileptr;
  const char *indexfilename;
  GtUchar *smallcounts;
  Largecount *largecounts;
  unsigned long numoflargecounts;
};

unsigned long gt_decodesingleinteger(const GtUchar *start)
{
  unsigned long idx, value;

  value = (unsigned long) start[0];
  for (idx=1UL; idx < (unsigned long) sizeof (unsigned long); idx++)
  {
    value |= (((unsigned long) start[idx]) << GT_MULT8(idx));
  }
  return value;
}

Tyrindex *gt_tyrindex_new(const char *tyrindexname,GtError *err)
{
  bool haserr = false;
  size_t numofbytes, rest;
  Tyrindex *tyrindex;

  gt_error_check(err);
  tyrindex = gt_malloc(sizeof *tyrindex);
  tyrindex->indexfilename = tyrindexname;
  tyrindex->mappedfileptr = gt_fa_mmap_read_with_suffix(tyrindexname,MERSUFFIX,
                                                     &numofbytes,err);
  if (tyrindex->mappedfileptr == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    tyrindex->mertable = (GtUchar *) tyrindex->mappedfileptr;
    rest = sizeof (unsigned long) * EXTRAINTEGERS;
    if (rest > numofbytes)
    {
      gt_error_set(err,"index must contain at least %lu bytes",
                        (unsigned long) rest);
      haserr = true;
    }
  }
  if (!haserr)
  {
    gt_assert(tyrindex->mertable != NULL);
    tyrindex->mersize
      = gt_decodesingleinteger(tyrindex->mertable + numofbytes - rest);
    tyrindex->alphasize
      = (unsigned int) gt_decodesingleinteger(tyrindex->mertable +
                                           numofbytes - rest +
                                           sizeof (unsigned long));
    tyrindex->merbytes = MERBYTES(tyrindex->mersize);
    if ((numofbytes - rest) % tyrindex->merbytes != 0)
    {
      gt_error_set(err,"size of index is %lu which is not a multiple of %lu",
                   (unsigned long) (numofbytes - rest),
                   tyrindex->merbytes);
      haserr = true;
    }
  }
  if (!haserr)
  {
    tyrindex->numofmers = (numofbytes - rest) / tyrindex->merbytes;
    gt_assert(tyrindex->mertable != NULL);
    if (tyrindex->numofmers == 0)
    {
      tyrindex->lastmer = tyrindex->mertable - 1;
    } else
    {
      tyrindex->lastmer
        = tyrindex->mertable + numofbytes - rest - tyrindex->merbytes;
    }
  }
  if (haserr)
  {
    if (tyrindex->mappedfileptr != NULL)
    {
      gt_fa_xmunmap(tyrindex->mappedfileptr);
      tyrindex->mappedfileptr = NULL;
    }
    gt_free(tyrindex);
  }
  return haserr ? NULL : tyrindex;
}

void gt_tyrindex_show(const Tyrindex *tyrindex)
{
  printf("# indexfilename = %s\n",tyrindex->indexfilename);
  printf("# alphasize = %u\n",tyrindex->alphasize);
  printf("# mersize = %lu\n",tyrindex->mersize);
  printf("# numofmers = %lu\n",(unsigned long) tyrindex->numofmers);
  printf("# merbytes = %lu\n",tyrindex->merbytes);
}

bool gt_tyrindex_isempty(const Tyrindex *tyrindex)
{
  return tyrindex->numofmers == 0 ? true : false;
}

const GtUchar *gt_tyrindex_mertable(const Tyrindex *tyrindex)
{
  return tyrindex->mertable;
}

const GtUchar *gt_tyrindex_lastmer(const Tyrindex *tyrindex)
{
  return tyrindex->lastmer;
}

unsigned long gt_tyrindex_merbytes(const Tyrindex *tyrindex)
{
  return tyrindex->merbytes;
}

unsigned long gt_tyrindex_mersize(const Tyrindex *tyrindex)
{
  return tyrindex->mersize;
}

unsigned int gt_tyrindex_alphasize(const Tyrindex *tyrindex)
{
  return tyrindex->alphasize;
}

unsigned long gt_tyrindex_ptr2number(const Tyrindex *tyrindex,
                                  const GtUchar *result)
{
  return (unsigned long) (result - tyrindex->mertable)/tyrindex->merbytes;
}

void gt_tyrindex_delete(Tyrindex **tyrindexptr)
{
  Tyrindex *tyrindex = *tyrindexptr;

  gt_fa_xmunmap(tyrindex->mappedfileptr);
  tyrindex->mappedfileptr = NULL;
  gt_free(tyrindex);
  *tyrindexptr = NULL;
}

Tyrcountinfo *gt_tyrcountinfo_new(const Tyrindex *tyrindex,
                                  const char *tyrindexname,
                                  GtError *err)
{
  size_t numofbytes;
  void *tmp;
  bool haserr = false;
  Tyrcountinfo *tyrcountinfo;

  gt_error_check(err);
  tyrcountinfo = gt_malloc(sizeof *tyrcountinfo);
  tyrcountinfo->indexfilename = tyrindexname;
  tyrcountinfo->mappedmctfileptr
    = gt_fa_mmap_read_with_suffix(tyrindexname,COUNTSSUFFIX,&numofbytes,err);
  if (tyrcountinfo->mappedmctfileptr == NULL)
  {
    tyrcountinfo->smallcounts = NULL;
    haserr = true;
  } else
  {
    tyrcountinfo->smallcounts
      = (GtUchar *) tyrcountinfo->mappedmctfileptr;
    tmp = &tyrcountinfo->smallcounts[tyrindex->numofmers];
    tyrcountinfo->largecounts = (Largecount *) tmp;
    if (numofbytes < tyrindex->numofmers)
    {
      gt_error_set(err,"size of file \"%s.%s\" is smaller than minimum size "
                       "%lu",tyrindexname,COUNTSSUFFIX,
                       (unsigned long) tyrindex->numofmers);
      haserr = true;
    }
  }
  if (!haserr && (numofbytes - tyrindex->numofmers) % sizeof (Largecount) != 0)
  {
    gt_error_set(err,"(numofbytes - numofmers) = %lu must be a multiple of %lu",
           (unsigned long) (numofbytes - tyrindex->numofmers),
           (unsigned long) sizeof (Largecount));
    haserr = true;
  }
  if (!haserr)
  {
    tyrcountinfo->numoflargecounts
      = (unsigned long) (numofbytes - tyrindex->numofmers)/
        (unsigned long) sizeof (Largecount);
  }
  if (haserr)
  {
    if (tyrcountinfo->mappedmctfileptr != NULL)
    {
      gt_fa_xmunmap(tyrcountinfo->mappedmctfileptr);
      tyrcountinfo->mappedmctfileptr = NULL;
    }
    gt_free(tyrcountinfo);
  }
  return haserr ? NULL : tyrcountinfo;
}

static /*@null@*/ const Largecount *binsearchLargecount(unsigned long key,
                                                        const Largecount *left,
                                                        const Largecount *right)
{
  const Largecount *leftptr = left, *midptr, *rightptr = right;
  unsigned long len;

  while (leftptr<=rightptr)
  {
    len = (unsigned long) (rightptr-leftptr);
    midptr = leftptr + GT_DIV2(len); /* halve len */
    if (key < midptr->idx)
    {
      rightptr = midptr-1;
    } else
    {
      if (key > midptr->idx)
      {
        leftptr = midptr + 1;
      } else
      {
        return midptr;
      }
    }
  }
  return NULL;
}

unsigned long gt_tyrcountinfo_get(const Tyrcountinfo *tyrcountinfo,
                               unsigned long mernumber)
{
  if (tyrcountinfo->smallcounts[mernumber] == 0)
  {
    const Largecount *lc
      = binsearchLargecount(mernumber,
                            tyrcountinfo->largecounts,
                            tyrcountinfo->largecounts +
                            tyrcountinfo->numoflargecounts-1);
#ifndef NDEBUG
    if (lc == NULL)
    {
      fprintf(stderr,"cannot find count for mer number %lu",mernumber);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
#endif
    gt_assert (lc != NULL);
    return lc->value;
  }
  return (unsigned long) tyrcountinfo->smallcounts[mernumber];
}

void gt_tyrcountinfo_delete(Tyrcountinfo **tyrcountinfoptr)
{
  Tyrcountinfo *tyrcountinfo = *tyrcountinfoptr;

  gt_fa_xmunmap(tyrcountinfo->mappedmctfileptr);
  tyrcountinfo->mappedmctfileptr = NULL;
  gt_free(tyrcountinfo);
  *tyrcountinfoptr = NULL;
}

static int mymemcmp(unsigned long *offset,const GtUchar *s1,const GtUchar *s2,
                    unsigned long len)
{
  unsigned long idx;

  for (idx=*offset; idx s2[idx])
    {
      *offset = idx;
      return 1;
    }
  }
  return 0;
}

/*@null@*/ const GtUchar *gt_tyrindex_binmersearch(const Tyrindex *tyrindex,
                                              unsigned long offset,
                                              const GtUchar *key,
                                              const GtUchar *leftbound,
                                              const GtUchar *rightbound)
{
  const GtUchar *leftptr, *midptr, *rightptr;
  int cmpval;
  unsigned long leftlength = offset, rightlength = offset, len;

  leftptr = leftbound;
  rightptr = rightbound;
  while (leftptr <= rightptr)
  {
    len = (unsigned long) (rightptr-leftptr)/GT_MULT2(tyrindex->merbytes);
    midptr = leftptr + tyrindex->merbytes * len;
    cmpval = mymemcmp(&offset,midptr,key,tyrindex->merbytes);
    if (cmpval < 0)
    {
      leftptr = midptr + tyrindex->merbytes;
      leftlength = offset;
      if (offset > rightlength)
      {
        offset = rightlength;
      }
    } else
    {
      if (cmpval > 0)
      {
        rightptr = midptr - tyrindex->merbytes;
        rightlength = offset;
        if (offset > leftlength)
        {
          offset = leftlength;
        }
      } else
      {
        return midptr;
      }
    }
  }
  return NULL;
}

void gt_tyrindex_check(GT_UNUSED const Tyrindex *tyrindex)
{
#ifndef NDEBUG
  GtUchar *mercodeptr;
  const GtUchar *result;
  unsigned long position;
  GT_UNUSED unsigned long previousposition = 0;

  for (mercodeptr = tyrindex->mertable;
       mercodeptr <= tyrindex->lastmer;
       mercodeptr += tyrindex->merbytes)
  {
    result = gt_tyrindex_binmersearch(tyrindex,0,mercodeptr,
                                   tyrindex->mertable,
                                   tyrindex->lastmer);
    gt_assert(result != NULL);
    if ((result - tyrindex->mertable) % tyrindex->merbytes != 0)
    {
      fprintf(stderr,"result is not multiple of %lu\n",tyrindex->merbytes);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    position = (unsigned long) (result-tyrindex->mertable)/
                               tyrindex->merbytes;
    if (position > 0 && previousposition + 1 != position)
    {
      fprintf(stderr,"position %lu is not increasing\n",position);
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    previousposition = position;
  }
#endif
}

int gt_determinetyrbckpfxlen(unsigned int *prefixlength,
                          const Tyrindex *tyrindex,
                          const Definedunsignedint *callprefixlength,
                          GtError *err)
{
  gt_error_check(err);
  if (callprefixlength->defined)
  {
    unsigned int maxprefixlen
      = gt_whatisthemaximalprefixlength(tyrindex->alphasize,
                                     (unsigned long) tyrindex->numofmers,
                                     0,true);
    if (maxprefixlen > (unsigned int) tyrindex->mersize)
    {
      maxprefixlen = (unsigned int) tyrindex->mersize;
    }
    if (gt_checkprefixlength(maxprefixlen,callprefixlength->valueunsignedint,
                          err) != 0)
    {
      return -1;
    }
    *prefixlength = callprefixlength->valueunsignedint;
  } else
  {
    unsigned int recommendedprefixlength
      = gt_recommendedprefixlength(tyrindex->alphasize,
                                   (unsigned long) tyrindex->numofmers,
                                   GT_RECOMMENDED_MULTIPLIER_DEFAULT,
                                   true);
    if (recommendedprefixlength > (unsigned int) tyrindex->mersize)
    {
      recommendedprefixlength = (unsigned int) tyrindex->mersize;
    }
    *prefixlength = recommendedprefixlength;
  }
  return 0;
}
genometools-1.5.1/src/match/tyr-map.h000066400000000000000000000052401211610345200174720ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TYR_MAP_H
#define TYR_MAP_H

#include "core/str_api.h"
#include "core/error_api.h"
#include "core/types_api.h"
#include "core/defined-types.h"

typedef struct Tyrindex Tyrindex;

Tyrindex *gt_tyrindex_new(const char *tyrindexname,GtError *err);
const GtUchar *gt_tyrindex_mertable(const Tyrindex *tyrindex);
const GtUchar *gt_tyrindex_lastmer(const Tyrindex *tyrindex);
unsigned long gt_tyrindex_merbytes(const Tyrindex *tyrindex);
unsigned int gt_tyrindex_alphasize(const Tyrindex *tyrindex);
unsigned long gt_tyrindex_mersize(const Tyrindex *tyrindex);
bool gt_tyrindex_isempty(const Tyrindex *tyrindex);
void gt_tyrindex_show(const Tyrindex *tyrindex);
void gt_tyrindex_delete(Tyrindex **tyrindexptr);
/*@null@*/ const GtUchar *gt_tyrindex_binmersearch(const Tyrindex *tyrindex,
                                              unsigned long offset,
                                              const GtUchar *key,
                                              const GtUchar *leftbound,
                                              const GtUchar *rightbound);
void gt_tyrindex_check(const Tyrindex *tyrindex);
int gt_determinetyrbckpfxlen(unsigned int *prefixlength,
                          const Tyrindex *tyrindex,
                          const Definedunsignedint *callprefixlength,
                          GtError *err);
unsigned long gt_tyrindex_ptr2number(const Tyrindex *tyrindex,
                                  const GtUchar *result);
typedef struct Tyrcountinfo Tyrcountinfo;

Tyrcountinfo *gt_tyrcountinfo_new(const Tyrindex *tyrindex,
                                  const char *tyrindexname,
                                  GtError *err);
unsigned long gt_tyrcountinfo_get(const Tyrcountinfo *tyrcountinfo,
                               unsigned long mernumber);
void gt_tyrcountinfo_delete(Tyrcountinfo **tyrcountinfoptr);

#endif
genometools-1.5.1/src/match/tyr-mersplit.c000066400000000000000000000343751211610345200205620ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/defined-types.h"
#include "core/divmodmul.h"
#include "core/fa.h"
#include "core/intbits.h"
#include "core/mathsupport.h"
#include "core/minmax.h"
#include "core/str_api.h"
#include "core/types_api.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "core/ma_api.h"
#include "tyr-map.h"
#include "tyr-mersplit.h"

#define BUCKETSUFFIX                     ".mbd"
#define MAXUCHARVALUEWITHBITS(BITNUM)    ((1 << (BITNUM)) - 1)
#define ISBOUNDDEFINED(UDB,IDX)          GT_ISIBITSET(UDB,IDX)
#define SETDEFINEDBOUND(UDB,IDX)         GT_SETIBIT(UDB,IDX)

struct Tyrbckinfo
{
  void *mappedmbdfileptr;
  unsigned int prefixlength;
  unsigned long numofcodes,
                *boundisdefined,
                *bounds;
  GtUchar remainmask;
};

typedef struct
{
  const GtUchar *leftmer,
              *rightmer;
} Merbounds;

static unsigned long extractprefixbytecode(unsigned long merbytes,
                                           unsigned int prefixlength,
                                           const GtUchar *bytecode)
{
  unsigned long idx, code = 0;

  for (idx=0; idx < MIN((unsigned long) sizeof (unsigned long),merbytes); idx++)
  {
    code = (code << 8) | bytecode[idx];
    if (GT_MULT4(idx+1) == (unsigned long) prefixlength)
    {
      break;
    }
    if (GT_MULT4(idx+1) > (unsigned long) prefixlength)
    {
      code >>= GT_MULT2(GT_MULT4(idx+1) - prefixlength);
      break;
    }
  }
  return code;
}

static GtUchar extractremainingbytes(const GtUchar remainmask,
                                   unsigned long byteoffset,
                                   const GtUchar *bytecode)
{
  return bytecode[byteoffset] & remainmask;
}

static const GtUchar *remainingleftmost(unsigned long merbytes,
                                      unsigned long byteoffset,
                                      GtUchar remainmask,
                                      GtUchar code,
                                      const GtUchar *leftptr,
                                      const GtUchar *rightptr)
{
  unsigned long len;
  GtUchar midcode;
  const GtUchar *midptr;

  while (leftptr + merbytes < rightptr)
  {
    len = (unsigned long) (rightptr-leftptr)/GT_MULT2(merbytes);
    midptr = leftptr + merbytes * len;
    midcode = extractremainingbytes(remainmask,byteoffset,midptr);
    if (code <= midcode)
    {
      rightptr = midptr;
    } else
    {
      leftptr = midptr;
    }
  }
  return rightptr;
}

static const GtUchar *remainingrightmost(unsigned long merbytes,
                                       unsigned long byteoffset,
                                       GtUchar remainmask,
                                       GtUchar code,
                                       const GtUchar *leftptr,
                                       const GtUchar *rightptr)
{
  unsigned long len;
  GtUchar midcode;
  const GtUchar *midptr;

  while (leftptr + merbytes < rightptr)
  {
    len = (unsigned long) (rightptr-leftptr)/GT_MULT2(merbytes);
    midptr = leftptr + merbytes * len;
    midcode = extractremainingbytes(remainmask,byteoffset,midptr);
    if (code >= midcode)
    {
      leftptr = midptr;
    } else
    {
      rightptr = midptr;
    }
  }
  return leftptr;
}

static bool remainadvance(Merbounds *merbounds,
                          unsigned long merbytes,
                          unsigned long byteoffset,
                          GtUchar remainmask,
                          const GtUchar *searchbytecode,
                          const GtUchar *leftptr,
                          const GtUchar *rightptr)
{
  GtUchar scode, scodeleft, scoderight;

  scode = extractremainingbytes(remainmask,byteoffset,searchbytecode);
  scodeleft = extractremainingbytes(remainmask,byteoffset,leftptr);
  if (scode > scodeleft)
  {
    scoderight = extractremainingbytes(remainmask,byteoffset,rightptr);
    if (scode > scoderight)
    {
      return false;
    }
    merbounds->leftmer = remainingleftmost(merbytes,
                                           byteoffset,
                                           remainmask,
                                           scode,
                                           leftptr,
                                           rightptr);
  }
  if (scode < scodeleft)
  {
    return false;
  }
  if (scode == scodeleft)
  {
    merbounds->leftmer = leftptr;
  }
  scoderight = extractremainingbytes(remainmask,byteoffset,rightptr);
  if (scode >= scoderight)
  {
    merbounds->rightmer = rightptr;
  } else
  {
    merbounds->rightmer = remainingrightmost(merbytes,
                                             byteoffset,
                                             remainmask,
                                             scode,
                                             leftptr,
                                             rightptr);
  }
  return true;
}

const GtUchar *gt_searchinbuckets(const Tyrindex *tyrindex,
                             const Tyrbckinfo *tyrbckinfo,
                             const GtUchar *bytecode)
{
  const GtUchar *result;
  unsigned long prefixcode, leftbound, merbytes;

  gt_assert(tyrbckinfo != NULL);
  merbytes = gt_tyrindex_merbytes(tyrindex);
  prefixcode = extractprefixbytecode(merbytes,
                                     tyrbckinfo->prefixlength,
                                     bytecode);
  leftbound = tyrbckinfo->bounds[prefixcode];
  if (ISBOUNDDEFINED(tyrbckinfo->boundisdefined,prefixcode))
  {
    const GtUchar *mertable;
    unsigned long rightbound;

    mertable = gt_tyrindex_mertable(tyrindex);
    rightbound = tyrbckinfo->bounds[prefixcode+1] - merbytes;
    if (GT_MOD4(tyrbckinfo->prefixlength) == 0)
    {
      result = gt_tyrindex_binmersearch(tyrindex,
                                     (unsigned long)
                                     GT_DIV4(tyrbckinfo->prefixlength),
                                     bytecode,
                                     mertable + leftbound,
                                     mertable + rightbound);
    } else
    {
      Merbounds merbounds;

      merbounds.leftmer = merbounds.rightmer = NULL;
      if (!remainadvance(&merbounds,
                         merbytes,
                         (unsigned long) GT_DIV4(tyrbckinfo->prefixlength),
                         tyrbckinfo->remainmask,
                         bytecode,
                         mertable + leftbound,
                         mertable + rightbound) ||
         merbounds.leftmer == NULL ||
         merbounds.leftmer > merbounds.rightmer)
      {
        result = NULL;
      } else
      {
        result = gt_tyrindex_binmersearch(tyrindex,
                                       1UL + (unsigned long)
                                             GT_DIV4(tyrbckinfo->prefixlength),
                                       bytecode,
                                       merbounds.leftmer,
                                       merbounds.rightmer);
      }
    }
  } else
  {
    result = NULL;
  }
  return result;
}

static const GtUchar *findrightmostmer(unsigned long merbytes,
                                     unsigned int prefixlength,
                                     unsigned long code,
                                     const GtUchar *leftptr,
                                     const GtUchar *rightptr)
{
  unsigned long len, midcode;
  const GtUchar *midptr;

  while (leftptr + merbytes < rightptr)
  {
    len = (unsigned long) (rightptr-leftptr)/GT_MULT2(merbytes);
    midptr = leftptr + merbytes * len;
    midcode = extractprefixbytecode(merbytes,prefixlength,midptr);
    if (midcode > code)
    {
      rightptr = midptr;
    } else
    {
      leftptr = midptr;
    }
  }
  return leftptr;
}

static void splitmerinterval(Tyrbckinfo *tyrbckinfo,
                             const Tyrindex *tyrindex)

{
  const GtUchar *rightbound, *leftptr, *rightptr, *mertable, *lastmer;
  unsigned long code, leftcode, rightcode, merbytes;

  mertable = gt_tyrindex_mertable(tyrindex);
  lastmer = gt_tyrindex_lastmer(tyrindex);
  merbytes = gt_tyrindex_merbytes(tyrindex);
  leftptr = mertable;
  rightptr = lastmer;
  rightcode = extractprefixbytecode(merbytes,
                                    tyrbckinfo->prefixlength,
                                    rightptr);
  while (true)
  {
    leftcode = extractprefixbytecode(merbytes,
                                     tyrbckinfo->prefixlength,
                                     leftptr);
    tyrbckinfo->bounds[leftcode] = (unsigned long) (leftptr - mertable);
    SETDEFINEDBOUND(tyrbckinfo->boundisdefined,leftcode);
    if (leftcode == rightcode)
    {
      break;
    }
    rightbound = findrightmostmer(merbytes,
                                  tyrbckinfo->prefixlength,
                                  leftcode,leftptr,rightptr);
    leftptr = rightbound + merbytes;
  }
  tyrbckinfo->bounds[tyrbckinfo->numofcodes]
    = (unsigned long) (lastmer + merbytes - mertable);
  SETDEFINEDBOUND(tyrbckinfo->boundisdefined,tyrbckinfo->numofcodes);
  for (code = tyrbckinfo->numofcodes - 1; /* Nothing */ ; code--)
  {
    if (!ISBOUNDDEFINED(tyrbckinfo->boundisdefined,code))
    {
      tyrbckinfo->bounds[code] = tyrbckinfo->bounds[code+1];
    }
    if (code == 0)
    {
      break;
    }
  }
}

int gt_constructmerbuckets(const char *inputindex,
                           const Definedunsignedint *callprefixlength,
                           GtError *err)
{
  Tyrindex *tyrindex;
  Tyrbckinfo tyrbckinfo;
  FILE *bucketfp = NULL;
  bool haserr = false;

  gt_error_check(err);
  tyrbckinfo.bounds = NULL;
  tyrbckinfo.boundisdefined = NULL;
  tyrindex = gt_tyrindex_new(inputindex,err);
  if (tyrindex == NULL)
  {
    haserr = true;
  }
  if (!haserr && tyrindex != NULL && !gt_tyrindex_isempty(tyrindex))
  {
    if (gt_determinetyrbckpfxlen(&tyrbckinfo.prefixlength,
                              tyrindex,
                              callprefixlength,
                              err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr && tyrindex != NULL && !gt_tyrindex_isempty(tyrindex))
  {
    printf("# construct mer buckets for prefixlength %u\n",
            tyrbckinfo.prefixlength);
    tyrbckinfo.numofcodes
      = gt_power_for_small_exponents(gt_tyrindex_alphasize(tyrindex),
                                     tyrbckinfo.prefixlength);
    tyrbckinfo.mappedmbdfileptr = NULL;
    printf("# numofcodes = %lu\n",tyrbckinfo.numofcodes);
    gt_tyrindex_show(tyrindex);
    tyrbckinfo.bounds = gt_malloc(sizeof *tyrbckinfo.bounds
                                  * (tyrbckinfo.numofcodes+1));
    GT_INITBITTAB(tyrbckinfo.boundisdefined,tyrbckinfo.numofcodes+1);
    splitmerinterval(&tyrbckinfo,tyrindex);
    bucketfp = gt_fa_fopen_with_suffix(inputindex,BUCKETSUFFIX,"wb",err);
    if (bucketfp == NULL)
    {
      haserr = true;
    }
  }
  if (!haserr && tyrindex != NULL && !gt_tyrindex_isempty(tyrindex))
  {
    unsigned long pl_long = (unsigned long) tyrbckinfo.prefixlength;
    gt_assert(bucketfp != NULL);
    gt_xfwrite(&pl_long, sizeof (pl_long), (size_t) 1, bucketfp);
  }
  if (!haserr && tyrindex != NULL && !gt_tyrindex_isempty(tyrindex))
  {
    gt_assert(bucketfp != NULL);
    gt_xfwrite(tyrbckinfo.bounds, sizeof (*tyrbckinfo.bounds),
               (size_t) (tyrbckinfo.numofcodes+1), bucketfp);
  }
  if (!haserr && tyrindex != NULL && !gt_tyrindex_isempty(tyrindex))
  {
    gt_assert(bucketfp != NULL);
    gt_xfwrite(tyrbckinfo.boundisdefined, sizeof (*tyrbckinfo.boundisdefined),
               GT_NUMOFINTSFORBITS(tyrbckinfo.numofcodes+1), bucketfp);
  }
  gt_fa_xfclose(bucketfp);
  if (tyrindex != NULL)
  {
    gt_tyrindex_delete(&tyrindex);
  }
  gt_free(tyrbckinfo.bounds);
  gt_free(tyrbckinfo.boundisdefined);
  return haserr ? -1 : 0;
}

Tyrbckinfo *gt_tyrbckinfo_new(const char *tyrindexname,unsigned int alphasize,
                              GtError *err)
{
  size_t numofbytes;
  Tyrbckinfo *tyrbckinfo;
  bool haserr = false;

  tyrbckinfo = gt_malloc(sizeof *tyrbckinfo);
  tyrbckinfo->mappedmbdfileptr = gt_fa_mmap_read_with_suffix(tyrindexname,
                                                          BUCKETSUFFIX,
                                                          &numofbytes,err);
  if (tyrbckinfo->mappedmbdfileptr == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    unsigned long pl_long;

    gt_assert(tyrbckinfo->mappedmbdfileptr != NULL);
    pl_long = *((unsigned long *) tyrbckinfo->mappedmbdfileptr);
    tyrbckinfo->prefixlength = (unsigned int) pl_long;
    tyrbckinfo->numofcodes
      = gt_power_for_small_exponents(alphasize,tyrbckinfo->prefixlength);
    /*check if numofbytes == expected size*/
    gt_assert(numofbytes == sizeof (unsigned long) *
                            (1UL +
                             (tyrbckinfo->numofcodes+1) +
                             GT_NUMOFINTSFORBITS(tyrbckinfo->numofcodes + 1)));
    tyrbckinfo->bounds = ((unsigned long *) tyrbckinfo->mappedmbdfileptr) + 1;
    tyrbckinfo->boundisdefined
      = tyrbckinfo->bounds + tyrbckinfo->numofcodes + 1;
    if (tyrbckinfo->prefixlength > 0 && GT_MOD4(tyrbckinfo->prefixlength) > 0)
    {
      tyrbckinfo->remainmask
        = (GtUchar) MAXUCHARVALUEWITHBITS(GT_MULT2(
                                       4U - GT_MOD4(tyrbckinfo->prefixlength)));
    }
  }
  if (haserr)
  {
    gt_free(tyrbckinfo);
    return NULL;
  }
  return tyrbckinfo;
}

void gt_tyrbckinfo_delete(Tyrbckinfo **tyrbckinfoptr)
{
  Tyrbckinfo *tyrbckinfo = *tyrbckinfoptr;

  gt_fa_xmunmap(tyrbckinfo->mappedmbdfileptr);
  tyrbckinfo->mappedmbdfileptr = NULL;
  gt_free(tyrbckinfo);
  *tyrbckinfoptr = NULL;
}
genometools-1.5.1/src/match/tyr-mersplit.h000066400000000000000000000030611211610345200205530ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TYR_MERSPLIT_H
#define TYR_MERSPLIT_H

#include "core/str_api.h"
#include "core/error_api.h"
#include "core/defined-types.h"
#include "tyr-map.h"

typedef struct Tyrbckinfo Tyrbckinfo;

int gt_constructmerbuckets(const char *inputindex,
                           const Definedunsignedint *callprefixlength,
                           GtError *err);

Tyrbckinfo *gt_tyrbckinfo_new(const char *tyrindexname,unsigned int alphasize,
                              GtError *err);

void gt_tyrbckinfo_delete(Tyrbckinfo **tyrbckinfoptr);

const GtUchar *gt_searchinbuckets(const Tyrindex *tyrindex,
                                  const Tyrbckinfo *tyrbckinfo,
                                  const GtUchar *bytecode);

#endif
genometools-1.5.1/src/match/tyr-mkindex.c000066400000000000000000000545021211610345200203540ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/alphabet.h"
#include "core/divmodmul.h"
#include "core/fa.h"
#include "core/format64.h"
#include "core/logger.h"
#include "core/spacecalc.h"
#include "core/str.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "core/ma_api.h"
#include "esa-seqread.h"
#include "esa-mmsearch.h"
#include "tyr-basic.h"
#include "tyr-mkindex.h"
#include "echoseq.h"

typedef struct /* information stored for each node of the lcp interval tree */
{
  unsigned long leftmostleaf,
                rightmostleaf,
                suftabrightmostleaf,
                lcptabrightmostleafplus1;
} TyrDfsinfo;

typedef int (*Processoccurrencecount)(unsigned long,
                                      unsigned long,
                                      void *,
                                      GtError *);

typedef struct listUlong
{
  unsigned long position;
  struct listUlong *nextptr;
} ListUlong;

typedef struct
{
  unsigned long occcount;
  ListUlong *positionlist;
} Countwithpositions;

GT_DECLAREARRAYSTRUCT(Countwithpositions);

typedef struct /* global information */
{
  unsigned long mersize,
                totallength,
                minocc,
                maxocc;
  const GtEncseq *encseq;
  GtReadmode readmode;
  Processoccurrencecount processoccurrencecount;
  GtArrayCountwithpositions occdistribution;
  FILE *merindexfpout,
       *countsfilefpout;
  GtEncseqReader *esrspace;
  bool performtest;
  bool storecounts;
  GtUchar *bytebuffer;
  unsigned long sizeofbuffer;
  GtArrayLargecount largecounts;
  unsigned long countoutputmers;
  const ESASuffixptr *suftab; /* only necessary for performtest */
  GtUchar *currentmer;    /* only necessary for performtest */
} TyrDfsstate;

#include "esa-dfs.h"

static uint64_t bruteforcecountnumofmers(const TyrDfsstate *state)
{
  unsigned long idx;
  uint64_t numofmers = 0;

  for (idx=0; idx <= state->totallength - state->mersize; idx++)
  {
    if (!gt_encseq_contains_special(state->encseq,
                                    state->readmode,
                                    state->esrspace,
                                    idx,
                                    state->mersize))
    {
      numofmers++;
    }
  }
  return numofmers;
}

static void checknumofmers(const TyrDfsstate *state,
                           uint64_t dnumofmers)
{
  uint64_t bfnumofmers = bruteforcecountnumofmers(state);

  if (dnumofmers != bfnumofmers)
  {
    fprintf(stderr,"numofmers(distribution) = " Formatuint64_t " != "
                   Formatuint64_t,
                   PRINTuint64_tcast(dnumofmers),
                   PRINTuint64_tcast(bfnumofmers));
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
}

static void checknumberofoccurrences(const TyrDfsstate *dfsstate,
                                     unsigned long countocc,
                                     unsigned long position)
{
  GtMMsearchiterator *mmsi;
  unsigned long idx, bfcount;

  for (idx = 0; idx < dfsstate->mersize; idx++)
  {
    dfsstate->currentmer[idx] =
              gt_encseq_get_encoded_char(dfsstate->encseq,position+idx,
                                                dfsstate->readmode);
  }
  mmsi = gt_mmsearchiterator_new_complete_olain(dfsstate->encseq,
                                              dfsstate->suftab,
                                              0,
                                              dfsstate->totallength,
                                              0,
                                              dfsstate->readmode,
                                              dfsstate->currentmer,
                                              dfsstate->mersize);
  bfcount = gt_mmsearchiterator_count(mmsi);
  if (bfcount != countocc)
  {
    fprintf(stderr,"bfcount = %lu != %lu = countocc\n",bfcount,countocc);
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  gt_mmsearchiterator_delete(mmsi);
}

static /*@null@*/ ListUlong *insertListUlong(ListUlong *liststart,
                                             unsigned long position)
{
  ListUlong *newnode;

  newnode = gt_malloc(sizeof *newnode);
  newnode->position = position;
  newnode->nextptr = liststart;
  return newnode;
}

static void wrapListUlong(ListUlong *node)
{
  ListUlong *tmpnext;

  if (node != NULL)
  {
    while (true)
    {
      if (node->nextptr == NULL)
      {
        gt_free(node);
        break;
      }
      tmpnext = node->nextptr;
      gt_free(node);
      node = tmpnext;
    }
  }
}

static void showListUlong(const GtEncseq *encseq,
                          unsigned long mersize,
                          const ListUlong *node)
{
  const ListUlong *tmp;

  for (tmp = node; tmp != NULL; tmp = tmp->nextptr)
  {
    gt_fprintfencseq(stdout,encseq,tmp->position,mersize);
    (void) putchar((int) '\n');
  }
}

static bool decideifocc(const TyrDfsstate *state,unsigned long countocc)
{
  if (state->minocc > 0)
  {
    if (state->maxocc > 0)
    {
      if (countocc >= state->minocc && countocc <= state->maxocc)
      {
        return true;
      }
    } else
    {
      if (countocc >= state->minocc)
      {
        return true;
      }
    }
  } else
  {
    if (state->maxocc > 0)
    {
      if (countocc <= state->maxocc)
      {
        return true;
      }
    }
  }
  return false;
}

static uint64_t addupdistribution(const GtArrayCountwithpositions *distribution)
{
  unsigned long idx;
  uint64_t addcount = 0;

  for (idx=0; idx < distribution->nextfreeCountwithpositions; idx++)
  {
    if (distribution->spaceCountwithpositions[idx].occcount > 0)
    {
      addcount += (uint64_t)
                  (idx * distribution->spaceCountwithpositions[idx].occcount);
    }
  }
  return addcount;
}

static void showmerdistribution(const TyrDfsstate *state)
{
  unsigned long countocc;

  for (countocc = 0;
      countocc < state->occdistribution.nextfreeCountwithpositions;
      countocc++)
  {
    if (state->occdistribution.spaceCountwithpositions[countocc].occcount > 0)
    {
      printf("%lu %lu\n",countocc,
                         state->occdistribution.
                                spaceCountwithpositions[countocc].occcount);
      if (decideifocc(state,countocc))
      {
        showListUlong(state->encseq,
                      state->mersize,
                      state->occdistribution.spaceCountwithpositions[countocc].
                                             positionlist);
        wrapListUlong(state->occdistribution.spaceCountwithpositions[countocc].
                                             positionlist);
      }
    }
  }
}

static void showfinalstatistics(const TyrDfsstate *state,
                                const char *inputindex,
                                GtLogger *logger)
{
  uint64_t dnumofmers = addupdistribution(&state->occdistribution);

  if (state->performtest)
  {
    checknumofmers(state,dnumofmers);
  }
  gt_logger_log(logger,
              "the following output refers to the set of all sequences");
  gt_logger_log(logger,
              "represented by the index \"%s\"",inputindex);
  gt_logger_log(logger,
              "number of %lu-mers in the sequences not containing a "
              "wildcard: " Formatuint64_t,
              (unsigned long) state->mersize,
              PRINTuint64_tcast(dnumofmers));
  gt_logger_log(logger,
              "show the distribution of the number of occurrences of %lu-mers",
               (unsigned long) state->mersize);
  gt_logger_log(logger,"not containing a wildcard as rows of the form "
              "i d where");
  gt_logger_log(logger,
              "d is the number of events that a %lu-mer occurs exactly i times",
              (unsigned long) state->mersize);
  showmerdistribution(state);
}

static void incrementdistribcounts(GtArrayCountwithpositions *occdistribution,
                                   unsigned long countocc,unsigned long value)
{
  if (countocc >= occdistribution->allocatedCountwithpositions)
  {
    const unsigned long addamount = 128UL;
    unsigned long idx;

    occdistribution->spaceCountwithpositions
      = gt_realloc(occdistribution->spaceCountwithpositions,
                   sizeof *occdistribution->spaceCountwithpositions
                   * (countocc+addamount));
    for (idx=occdistribution->allocatedCountwithpositions;
         idxspaceCountwithpositions[idx].occcount = 0;
      occdistribution->spaceCountwithpositions[idx].positionlist = NULL;
    }
    occdistribution->allocatedCountwithpositions = countocc+addamount;
  }
  if (countocc + 1 > occdistribution->nextfreeCountwithpositions)
  {
    occdistribution->nextfreeCountwithpositions = countocc+1;
  }
  occdistribution->spaceCountwithpositions[countocc].occcount += value;
}

static int adddistpos2distribution(unsigned long countocc,
                                   unsigned long position,
                                   void *adddistposinfo,
                                   GT_UNUSED GtError *err)
{
  TyrDfsstate *state = (TyrDfsstate *) adddistposinfo;

  incrementdistribcounts(&state->occdistribution,countocc,1UL);
  if (decideifocc(state,countocc))
  {
    state->occdistribution.spaceCountwithpositions[countocc].positionlist
      = insertListUlong(state->occdistribution.
                               spaceCountwithpositions[countocc].positionlist,
                         position);
  }
  if (state->performtest)
  {
    checknumberofoccurrences(state,countocc,position);
  }
  return 0;
}

#define MAXSMALLMERCOUNT UCHAR_MAX

static int outputsortedstring2indexviafileptr(const GtEncseq *encseq,
                                              unsigned long mersize,
                                              GtUchar *bytebuffer,
                                              unsigned long sizeofbuffer,
                                              FILE *merindexfpout,
                                              FILE *countsfilefpout,
                                              unsigned long position,
                                              unsigned long countocc,
                                              GtArrayLargecount *largecounts,
                                              unsigned long countoutputmers,
                                              GT_UNUSED GtError *err)
{
  gt_encseq_sequence2bytecode(bytebuffer,encseq,position,mersize);
  gt_xfwrite(bytebuffer, sizeof (*bytebuffer), (size_t) sizeofbuffer,
             merindexfpout);
  if (countsfilefpout != NULL)
  {
    GtUchar smallcount;

    if (countocc <= MAXSMALLMERCOUNT)
    {
      smallcount = (GtUchar) countocc;
    } else
    {
      Largecount *lc;

      GT_GETNEXTFREEINARRAY(lc,largecounts,Largecount,32);
      lc->idx = countoutputmers;
      lc->value = countocc;
      smallcount = 0;
    }
    gt_xfwrite(&smallcount, sizeof (smallcount),(size_t) 1,countsfilefpout);
  }
  return 0;
}

static int outputsortedstring2index(unsigned long countocc,
                                    unsigned long position,
                                    void *adddistposinfo,
                                    GtError *err)
{
  TyrDfsstate *state = (TyrDfsstate *) adddistposinfo;

  if (decideifocc(state,countocc))
  {
    if (outputsortedstring2indexviafileptr(state->encseq,
                                           state->mersize,
                                           state->bytebuffer,
                                           state->sizeofbuffer,
                                           state->merindexfpout,
                                           state->countsfilefpout,
                                           position,
                                           countocc,
                                           &state->largecounts,
                                           state->countoutputmers,
                                           err) != 0)
    {
      return -1;
    }
    state->countoutputmers++;
  }
  return 0;
}

static Dfsinfo* tyr_allocateDfsinfo(GT_UNUSED Dfsstate *state)
{
  TyrDfsinfo *dfsinfo;

  dfsinfo = gt_malloc(sizeof *dfsinfo);
  return (Dfsinfo*) dfsinfo;
}

static void tyr_freeDfsinfo(Dfsinfo *adfsinfo, GT_UNUSED Dfsstate *state)
{
  TyrDfsinfo *dfsinfo = (TyrDfsinfo*) adfsinfo;
  gt_free(dfsinfo);
}

static int tyr_processleafedge(GT_UNUSED bool firstsucc,
                           unsigned long fatherdepth,
                           GT_UNUSED Dfsinfo *father,
                           unsigned long leafnumber,
                           Dfsstate *astate,
                           GtError *err)
{
  TyrDfsstate *state = (TyrDfsstate*) astate;
  gt_error_check(err);
  if (fatherdepth < state->mersize &&
      leafnumber + state->mersize <= state->totallength &&
      !gt_encseq_contains_special(state->encseq,
                                  state->readmode,
                                  state->esrspace,
                                  leafnumber + fatherdepth,
                                  state->mersize - fatherdepth))
  {
    if (state->processoccurrencecount(1UL,leafnumber,state,err) != 0)
    {
      return -1;
    }
  }
  return 0;
}

static int tyr_processcompletenode(unsigned long nodeptrdepth,
                               Dfsinfo *anodeptr,
                               unsigned long nodeptrminusonedepth,
                               Dfsstate *astate,
                               GtError *err)
{
  TyrDfsinfo *nodeptr = (TyrDfsinfo*) anodeptr;
  TyrDfsstate *state = (TyrDfsstate*) astate;
  gt_error_check(err);
  if (state->mersize <= nodeptrdepth)
  {
    unsigned long fatherdepth;

    fatherdepth = nodeptr->lcptabrightmostleafplus1;
    if (fatherdepth < nodeptrminusonedepth)
    {
      fatherdepth = nodeptrminusonedepth;
    }
    if (fatherdepth < state->mersize)
    {
      if (state->processoccurrencecount((unsigned long)
                                        (nodeptr->rightmostleaf -
                                         nodeptr->leftmostleaf + 1),
                                        nodeptr->suftabrightmostleaf,
                                        state,
                                        err) != 0)
      {
        return -1;
      }
    }
  }
  return 0;
}

static void tyr_assignleftmostleaf(Dfsinfo *adfsinfo,unsigned long leftmostleaf,
                                   GT_UNUSED Dfsstate *dfsstate)
{
  TyrDfsinfo *dfsinfo = (TyrDfsinfo*) adfsinfo;
  dfsinfo->leftmostleaf = leftmostleaf;
}

static void tyr_assignrightmostleaf(Dfsinfo *adfsinfo,
                                    unsigned long currentindex,
                                    unsigned long previoussuffix,
                                    unsigned long currentlcp,
                                    GT_UNUSED Dfsstate *dfsstate)
{
  TyrDfsinfo *dfsinfo = (TyrDfsinfo*) adfsinfo;
  dfsinfo->rightmostleaf = currentindex;
  dfsinfo->suftabrightmostleaf = previoussuffix;
  dfsinfo->lcptabrightmostleafplus1 = currentlcp;
}

static void outputbytewiseUlongvalue(FILE *fpout,unsigned long value)
{
  size_t i;

  for (i=0; i < sizeof (value); i++)
  {
    (void) putc((int) (value & UCHAR_MAX),fpout);
    value >>= 8;
  }
}

static int enumeratelcpintervals(const char *inputindex,
                                 Sequentialsuffixarrayreader *ssar,
                                 const char *storeindex,
                                 bool storecounts,
                                 unsigned long mersize,
                                 unsigned long minocc,
                                 unsigned long maxocc,
                                 bool performtest,
                                 GtLogger *logger,
                                 GtError *err)
{
  TyrDfsstate *state;
  bool haserr = false;
  unsigned int alphasize;

  gt_error_check(err);
  state = gt_malloc(sizeof (*state));
  GT_INITARRAY(&state->occdistribution,Countwithpositions);
  state->esrspace = gt_encseq_create_reader_with_readmode(
                                   gt_encseqSequentialsuffixarrayreader(ssar),
                                   gt_readmodeSequentialsuffixarrayreader(ssar),
                                   0);
  state->mersize = (unsigned long) mersize;
  state->encseq = gt_encseqSequentialsuffixarrayreader(ssar);
  alphasize = gt_alphabet_num_of_chars(gt_encseq_alphabet(state->encseq));
  state->readmode = gt_readmodeSequentialsuffixarrayreader(ssar);
  state->storecounts = storecounts;
  state->minocc = minocc;
  state->maxocc = maxocc;
  state->totallength = gt_encseq_total_length(state->encseq);
  state->performtest = performtest;
  state->countoutputmers = 0;
  state->merindexfpout = NULL;
  state->countsfilefpout = NULL;
  GT_INITARRAY(&state->largecounts,Largecount);
  if (strlen(storeindex) == 0)
  {
    state->sizeofbuffer = 0;
    state->bytebuffer = NULL;
  } else
  {
    state->sizeofbuffer = MERBYTES(mersize);
    state->bytebuffer = gt_malloc(sizeof *state->bytebuffer
                                  * state->sizeofbuffer);
  }
  if (performtest)
  {
    state->currentmer = gt_malloc(sizeof *state->currentmer
                                  * state->mersize);
    state->suftab = gt_suftabSequentialsuffixarrayreader(ssar);
  } else
  {
    state->currentmer = NULL;
    state->suftab = NULL;
  }
  if (state->mersize > state->totallength)
  {
    gt_error_set(err,"mersize %lu > %lu = totallength not allowed",
                 state->mersize,
                 state->totallength);
    haserr = true;
  } else
  {
    if (strlen(storeindex) == 0)
    {
      state->processoccurrencecount = adddistpos2distribution;
    } else
    {
      state->merindexfpout = gt_fa_fopen_with_suffix(storeindex,MERSUFFIX,
                                                    "wb",err);
      if (state->merindexfpout == NULL)
      {
        haserr = true;
      } else
      {
        if (state->storecounts)
        {
          state->countsfilefpout
            = gt_fa_fopen_with_suffix(storeindex,COUNTSSUFFIX,"wb",err);
          if (state->countsfilefpout == NULL)
          {
            haserr = true;
          }
        }
      }
      state->processoccurrencecount = outputsortedstring2index;
    }
    if (!haserr)
    {
      if (gt_depthfirstesa(ssar,
                          tyr_allocateDfsinfo,
                          tyr_freeDfsinfo,
                          tyr_processleafedge,
                          NULL,
                          tyr_processcompletenode,
                          tyr_assignleftmostleaf,
                          tyr_assignrightmostleaf,
                          (Dfsstate*) state,
                          logger,
                          err) != 0)
      {
        haserr = true;
      }
      if (strlen(storeindex) == 0)
      {
        showfinalstatistics(state,inputindex,logger);
      }
    }
    if (!haserr)
    {
      if (state->countsfilefpout != NULL)
      {
        gt_logger_log(logger,"write %lu mercounts > %lu to file \"%s%s\"",
                    state->largecounts.nextfreeLargecount,
                    (unsigned long) MAXSMALLMERCOUNT,
                    storeindex,
                    COUNTSSUFFIX);
        gt_xfwrite(state->largecounts.spaceLargecount, sizeof (Largecount),
                  (size_t) state->largecounts.nextfreeLargecount,
                  state->countsfilefpout);
      }
    }
    if (!haserr)
    {
      gt_logger_log(logger,"number of %lu-mers in index: %lu",
                  mersize,
                  state->countoutputmers);
      gt_logger_log(logger,"index size: %.2f megabytes\n",
                  GT_MEGABYTES(state->countoutputmers * state->sizeofbuffer +
                               sizeof (unsigned long) * EXTRAINTEGERS));
    }
  }
  /* now out EXTRAINTEGERS integer values */
  if (!haserr && state->merindexfpout != NULL)
  {
    outputbytewiseUlongvalue(state->merindexfpout,
                             (unsigned long) state->mersize);
    outputbytewiseUlongvalue(state->merindexfpout,(unsigned long) alphasize);
  }
  gt_fa_xfclose(state->merindexfpout);
  gt_fa_xfclose(state->countsfilefpout);
  GT_FREEARRAY(&state->occdistribution,Countwithpositions);
  gt_free(state->currentmer);
  gt_free(state->bytebuffer);
  GT_FREEARRAY(&state->largecounts,Largecount);
  gt_encseq_reader_delete(state->esrspace);
  gt_free(state);
  return haserr ? -1 : 0;
}

int gt_merstatistics(const char *inputindex,
                  unsigned long mersize,
                  unsigned long minocc,
                  unsigned long maxocc,
                  const char *storeindex,
                  bool storecounts,
                  bool scanfile,
                  bool performtest,
                  GtLogger *logger,
                  GtError *err)
{
  bool haserr = false;
  Sequentialsuffixarrayreader *ssar;

  gt_error_check(err);
  ssar = gt_newSequentialsuffixarrayreaderfromfile(inputindex,
                                                SARR_LCPTAB |
                                                SARR_SUFTAB |
                                                SARR_ESQTAB,
                                                (scanfile && !performtest)
                                                  ? SEQ_scan : SEQ_mappedboth,
                                                logger,
                                                err);
  if (ssar == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (enumeratelcpintervals(inputindex,
                              ssar,
                              storeindex,
                              storecounts,
                              mersize,
                              minocc,
                              maxocc,
                              performtest,
                              logger,
                              err) != 0)
    {
      haserr = true;
    }
  }
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/tyr-mkindex.h000066400000000000000000000026041211610345200203550ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TYR_MKINDEX_H
#define TYR_MKINDEX_H

#include 
#include "core/str.h"
#include "core/error_api.h"
#include "core/logger.h"

int gt_merstatistics(const char *inputindex,
                     unsigned long mersize,
                     unsigned long minocc,
                     unsigned long maxocc,
                     const char *storeindex,
                     bool storecounts,
                     bool scanfile,
                     bool performtest,
                     GtLogger *logger,
                     GtError *err);

#endif
genometools-1.5.1/src/match/tyr-occratio.c000066400000000000000000000226211211610345200205150ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/str.h"
#include "core/unused_api.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "esa-seqread.h"
#include "tyr-occratio.h"

typedef struct /* information stored for each node of the lcp interval tree */
{
  unsigned long leftmostleaf,
                rightmostleaf,
                lcptabrightmostleafplus1;
} OccDfsinfo;

typedef struct /* global information */
{
  const GtEncseq *encseq;
  GtReadmode readmode;
  unsigned long totallength;
  unsigned long minmersize,
                maxmersize;
  GtArrayuint64_t *uniquedistribution,
                  *nonuniquedistribution,
                  *nonuniquemultidistribution;
} OccDfsstate;

#include "esa-dfs.h"

static Dfsinfo* occ_allocateDfsinfo(GT_UNUSED Dfsstate *state)
{
  OccDfsinfo *dfsinfo;

  dfsinfo = gt_malloc(sizeof *dfsinfo);
  return (Dfsinfo *) dfsinfo;
}

static void occ_freeDfsinfo(Dfsinfo *adfsinfo, GT_UNUSED Dfsstate *state)
{
  OccDfsinfo *dfsinfo = (OccDfsinfo*) adfsinfo;
  gt_free(dfsinfo);
}

static void adddistributionuint64_t(GtArrayuint64_t *occdistribution,
                                    unsigned long countocc,
                                    unsigned long value)
{
  if (countocc >= occdistribution->allocateduint64_t)
  {
    const unsigned long addamount = 128UL;
    unsigned long idx;

    occdistribution->spaceuint64_t
      = gt_realloc(occdistribution->spaceuint64_t,
                   sizeof *occdistribution->spaceuint64_t *
                   (countocc+addamount));
    for (idx=occdistribution->allocateduint64_t;
         idxspaceuint64_t[idx] = 0;
    }
    occdistribution->allocateduint64_t = countocc+addamount;
  }
  if (countocc + 1 > occdistribution->nextfreeuint64_t)
  {
    occdistribution->nextfreeuint64_t = countocc+1;
  }
  occdistribution->spaceuint64_t[countocc] += value;
}

static void iteritvdistribution(GtArrayuint64_t *distribution,
                                const GtEncseq *encseq,
                                GtReadmode readmode,
                                unsigned long totallength,
                                unsigned long minmersize,
                                unsigned long maxmersize,
                                unsigned long length,
                                unsigned long startpos)
{

  if (length <= (unsigned long) maxmersize)
  {
    unsigned long ulen, pos;

    for (ulen = length,
         pos = startpos + length - 1;
         ulen <= (unsigned long) maxmersize &&
         pos < totallength &&
         ISNOTSPECIAL(gt_encseq_get_encoded_char(encseq,pos,readmode));
         pos++, ulen++)
    {
      if (ulen >= (unsigned long) minmersize)
      {
        adddistributionuint64_t(distribution,(unsigned long) ulen,1UL);
      }
    }
  }
}

static int occ_processleafedge(GT_UNUSED bool firstsucc,
                           unsigned long fatherdepth,
                           GT_UNUSED Dfsinfo *father,
                           unsigned long leafnumber,
                           Dfsstate *astate,
                           GT_UNUSED GtError *err)
{
  OccDfsstate *state = (OccDfsstate*) astate;
  iteritvdistribution(state->uniquedistribution,
                      state->encseq,
                      state->readmode,
                      state->totallength,
                      state->minmersize,
                      state->maxmersize,
                      fatherdepth+1,
                      leafnumber);
  return 0;
}

static int occ_processcompletenode(unsigned long nodeptrdepth,
                               Dfsinfo *anodeptr,
                               unsigned long nodeptrminusonedepth,
                               Dfsstate *astate,
                               GT_UNUSED GtError *err)
{
  unsigned long fatherdepth;
  unsigned long startlength, endlength;
  OccDfsinfo *nodeptr = (OccDfsinfo*) anodeptr;
  OccDfsstate *state = (OccDfsstate*) astate;

  fatherdepth = nodeptr->lcptabrightmostleafplus1;
  if (fatherdepth < nodeptrminusonedepth)
  {
    fatherdepth = nodeptrminusonedepth;
  }
  startlength = (unsigned long) (fatherdepth + 1);
  if (startlength < state->minmersize)
  {
    startlength = state->minmersize;
  }
  endlength = (unsigned long) nodeptrdepth;
  if (endlength > state->maxmersize)
  {
    endlength = state->maxmersize;
  }
  if (startlength <= endlength)
  {
    unsigned long lenval;
    unsigned long occcount = nodeptr->rightmostleaf - nodeptr->leftmostleaf + 1;

    for (lenval = startlength; lenval <= endlength; lenval++)
    {
      adddistributionuint64_t(state->nonuniquemultidistribution,
                              lenval,
                              (unsigned long) occcount);
      adddistributionuint64_t(state->nonuniquedistribution,
                              lenval,
                              1UL);
    }
  }
  return 0;
}

static void occ_assignleftmostleaf(Dfsinfo *adfsinfo,unsigned long leftmostleaf,
                                   GT_UNUSED Dfsstate *dfsstate)
{
  OccDfsinfo *dfsinfo = (OccDfsinfo*) adfsinfo;
  dfsinfo->leftmostleaf = leftmostleaf;
}

static void occ_assignrightmostleaf(Dfsinfo *adfsinfo,
                                    unsigned long currentindex,
                                    GT_UNUSED unsigned long previoussuffix,
                                    unsigned long currentlcp,
                                    GT_UNUSED Dfsstate *dfsstate)
{
  OccDfsinfo *dfsinfo = (OccDfsinfo*) adfsinfo;
  dfsinfo->rightmostleaf = currentindex;
  dfsinfo->lcptabrightmostleafplus1 = currentlcp;
}

static int computeoccurrenceratio(Sequentialsuffixarrayreader *ssar,
                                  unsigned long minmersize,
                                  unsigned long maxmersize,
                                  GtArrayuint64_t *uniquedistribution,
                                  GtArrayuint64_t *nonuniquedistribution,
                                  GtArrayuint64_t *nonuniquemultidistribution,
                                  GtLogger *logger,
                                  GtError *err)
{
  OccDfsstate *state;
  bool haserr = false;

  gt_error_check(err);
  state = gt_malloc(sizeof (*state));
  state->encseq = gt_encseqSequentialsuffixarrayreader(ssar);
  state->readmode = gt_readmodeSequentialsuffixarrayreader(ssar);
  state->totallength = gt_encseq_total_length(state->encseq);
  state->minmersize = minmersize;
  state->maxmersize = maxmersize;
  state->uniquedistribution = uniquedistribution;
  state->nonuniquedistribution = nonuniquedistribution;
  state->nonuniquemultidistribution = nonuniquemultidistribution;
  if (gt_depthfirstesa(ssar,
                    occ_allocateDfsinfo,
                    occ_freeDfsinfo,
                    occ_processleafedge,
                    NULL,
                    occ_processcompletenode,
                    occ_assignleftmostleaf,
                    occ_assignrightmostleaf,
                    (Dfsstate*) state,
                    logger,
                    err) != 0)
  {
    haserr = true;
  }
  gt_free(state);
  return haserr ? -1 : 0;
}

int gt_tyr_occratio_func(const char *inputindex,
                         bool scanfile,
                         unsigned long minmersize,
                         unsigned long maxmersize,
                         GtArrayuint64_t *uniquedistribution,
                         GtArrayuint64_t *nonuniquedistribution,
                         GtArrayuint64_t *nonuniquemultidistribution,
                         GtLogger *logger,
                         GtError *err)
{
  bool haserr = false;
  Sequentialsuffixarrayreader *ssar;

  gt_error_check(err);
  ssar = gt_newSequentialsuffixarrayreaderfromfile(inputindex,
                                                SARR_LCPTAB |
                                                SARR_SUFTAB |
                                                SARR_ESQTAB,
                                                scanfile ? SEQ_scan
                                                         : SEQ_mappedboth,
                                                logger,
                                                err);
  if (ssar == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (computeoccurrenceratio(ssar,
                               minmersize,
                               maxmersize,
                               uniquedistribution,
                               nonuniquedistribution,
                               nonuniquemultidistribution,
                               logger,
                               err) != 0)
    {
      haserr = true;
    }
  }
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/tyr-occratio.h000066400000000000000000000027371211610345200205300ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TYR_OCCRATIO_H
#define TYR_OCCRATIO_H

#include 
#include "core/str.h"
#include "core/error_api.h"
#include "core/arraydef.h"
#include "core/logger.h"

int gt_tyr_occratio_func(const char *inputindex,
                         bool scanfile,
                         unsigned long minmersize,
                         unsigned long maxmersize,
                         GtArrayuint64_t *uniquedistribution,
                         GtArrayuint64_t *nonuniquedistribution,
                         GtArrayuint64_t *nonuniquemultidistribution,
                         GtLogger *logger,
                         GtError *err);

#endif
genometools-1.5.1/src/match/tyr-search.c000066400000000000000000000232071211610345200201600ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/alphabet.h"
#include "core/fa.h"
#include "core/unused_api.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "core/chardef.h"
#include "core/format64.h"
#include "core/encseq.h"
#include "core/ma_api.h"
#include "revcompl.h"
#include "tyr-map.h"
#include "tyr-search.h"
#include "tyr-show.h"
#include "tyr-mersplit.h"

typedef struct
{
  GtUchar *bytecode,  /* buffer for encoded word to be searched */
        *rcbuf;
  const GtUchar *mertable, *lastmer;
  unsigned long mersize;
  unsigned int showmode,
               searchstrand;
  GtAlphabet *dnaalpha;
} Tyrsearchinfo;

static void gt_tyrsearchinfo_init(Tyrsearchinfo *tyrsearchinfo,
                               const Tyrindex *tyrindex,
                               unsigned int showmode,
                               unsigned int searchstrand)
{
  unsigned long merbytes;

  merbytes = gt_tyrindex_merbytes(tyrindex);
  tyrsearchinfo->mersize = gt_tyrindex_mersize(tyrindex);
  tyrsearchinfo->mertable = gt_tyrindex_mertable(tyrindex);
  tyrsearchinfo->lastmer = gt_tyrindex_lastmer(tyrindex);
  tyrsearchinfo->showmode = showmode;
  tyrsearchinfo->searchstrand = searchstrand;
  tyrsearchinfo->dnaalpha = gt_alphabet_new_dna();
  tyrsearchinfo->bytecode = gt_malloc(sizeof *tyrsearchinfo->bytecode
                                      * merbytes);
  tyrsearchinfo->rcbuf = gt_malloc(sizeof *tyrsearchinfo->rcbuf
                                   * tyrsearchinfo->mersize);
}

static void gt_tyrsearchinfo_delete(Tyrsearchinfo *tyrsearchinfo)
{
  if (tyrsearchinfo != NULL)
  {
    gt_alphabet_delete(tyrsearchinfo->dnaalpha);
    gt_free(tyrsearchinfo->bytecode);
    gt_free(tyrsearchinfo->rcbuf);
  }
}

/*@null@*/ const GtUchar *gt_searchsinglemer(const GtUchar *qptr,
                                        const Tyrindex *tyrindex,
                                        const Tyrsearchinfo *tyrsearchinfo,
                                        const Tyrbckinfo *tyrbckinfo)
{
  const GtUchar *result;

  gt_encseq_plainseq2bytecode(tyrsearchinfo->bytecode,qptr,
                                       tyrsearchinfo->mersize);
  if (tyrbckinfo == NULL)
  {
    result = gt_tyrindex_binmersearch(tyrindex,0,tyrsearchinfo->bytecode,
                                   tyrsearchinfo->mertable,
                                   tyrsearchinfo->lastmer);
  } else
  {
    result = gt_searchinbuckets(tyrindex,tyrbckinfo,tyrsearchinfo->bytecode);
  }
  return result;
}

#define ADDTABULATOR\
        if (firstitem)\
        {\
          firstitem = false;\
        } else\
        {\
          (void) putchar('\t');\
        }

static void mermatchoutput(const Tyrindex *tyrindex,
                           const Tyrcountinfo *tyrcountinfo,
                           const Tyrsearchinfo *tyrsearchinfo,
                           const GtUchar *result,
                           const GtUchar *query,
                           const GtUchar *qptr,
                           uint64_t unitnum,
                           bool forward)
{
  bool firstitem = true;
  unsigned long queryposition;

  queryposition = (unsigned long) (qptr-query);
  if (tyrsearchinfo->showmode & SHOWQSEQNUM)
  {
    printf(Formatuint64_t,PRINTuint64_tcast(unitnum));
    firstitem = false;
  }
  if (tyrsearchinfo->showmode & SHOWQPOS)
  {
    ADDTABULATOR;
    printf("%c%lu",forward ? '+' : '-',queryposition);
  }
  if (tyrsearchinfo->showmode & SHOWCOUNTS)
  {
    unsigned long mernumber = gt_tyrindex_ptr2number(tyrindex,result);
    ADDTABULATOR;
    printf("%lu",gt_tyrcountinfo_get(tyrcountinfo,mernumber));
  }
  if (tyrsearchinfo->showmode & SHOWSEQUENCE)
  {
    ADDTABULATOR;
    gt_alphabet_decode_seq_to_fp(tyrsearchinfo->dnaalpha,
                                 stdout,
                                 qptr,
                                 tyrsearchinfo->mersize);
  }
  if (tyrsearchinfo->showmode & (SHOWSEQUENCE | SHOWQPOS | SHOWCOUNTS))
  {
    (void) putchar('\n');
  }
}

static void singleseqtyrsearch(const Tyrindex *tyrindex,
                               const Tyrcountinfo *tyrcountinfo,
                               const Tyrsearchinfo *tyrsearchinfo,
                               const Tyrbckinfo *tyrbckinfo,
                               uint64_t unitnum,
                               const GtUchar *query,
                               unsigned long querylen,
                               GT_UNUSED const char *desc)
{
  const GtUchar *qptr, *result;
  unsigned long offset, skipvalue;

  if (tyrsearchinfo->mersize > querylen)
  {
    return;
  }
  qptr = query;
  offset = 0;
  while (qptr <= query + querylen - tyrsearchinfo->mersize)
  {
    skipvalue = containsspecialbytestring(qptr,offset,tyrsearchinfo->mersize);
    if (skipvalue == tyrsearchinfo->mersize)
    {
      offset = tyrsearchinfo->mersize-1;
      if (tyrsearchinfo->searchstrand & STRAND_FORWARD)
      {
        result = gt_searchsinglemer(qptr,tyrindex,tyrsearchinfo,tyrbckinfo);
        if (result != NULL)
        {
          mermatchoutput(tyrindex,
                         tyrcountinfo,
                         tyrsearchinfo,
                         result,
                         query,
                         qptr,
                         unitnum,
                         true);
        }
      }
      if (tyrsearchinfo->searchstrand & STRAND_REVERSE)
      {
        gt_assert(tyrsearchinfo->rcbuf != NULL);
        gt_copy_reversecomplement(tyrsearchinfo->rcbuf,qptr,
                               tyrsearchinfo->mersize);
        result = gt_searchsinglemer(tyrsearchinfo->rcbuf,tyrindex,
                                    tyrsearchinfo,tyrbckinfo);
        if (result != NULL)
        {
          mermatchoutput(tyrindex,
                         tyrcountinfo,
                         tyrsearchinfo,
                         result,
                         query,
                         qptr,
                         unitnum,
                         false);
        }
      }
      qptr++;
    } else
    {
      offset = 0;
      qptr += (skipvalue+1);
    }
  }
}

int gt_tyrsearch(const char *tyrindexname,
                 const GtStrArray *queryfilenames,
                 unsigned int showmode,
                 unsigned int searchstrand,
                 bool verbose,
                 bool performtest,
                 GtError *err)
{
  Tyrindex *tyrindex;
  Tyrcountinfo *tyrcountinfo = NULL;
  Tyrbckinfo *tyrbckinfo = NULL;
  bool haserr = false;

  gt_error_check(err);
  tyrindex = gt_tyrindex_new(tyrindexname,err);
  if (tyrindex == NULL)
  {
    haserr = true;
  } else
  {
    if (verbose)
    {
      gt_tyrindex_show(tyrindex);
    }
    if (performtest)
    {
      gt_tyrindex_check(tyrindex);
    }
  }
  if (!haserr)
  {
    gt_assert(tyrindex != NULL);
    if ((showmode & SHOWCOUNTS) && !gt_tyrindex_isempty(tyrindex))
    {
      tyrcountinfo = gt_tyrcountinfo_new(tyrindex,tyrindexname,err);
      if (tyrcountinfo == NULL)
      {
        haserr = true;
      }
    }
  }
  if (!haserr)
  {
    gt_assert(tyrindex != NULL);
    if (!gt_tyrindex_isempty(tyrindex))
    {
      tyrbckinfo = gt_tyrbckinfo_new(tyrindexname,
                                     gt_tyrindex_alphasize(tyrindex),
                                     err);
      if (tyrbckinfo == NULL)
      {
        haserr = true;
      }
    }
  }
  if (!haserr)
  {
    const GtUchar *query;
    unsigned long querylen;
    char *desc = NULL;
    uint64_t unitnum;
    int retval;
    Tyrsearchinfo tyrsearchinfo;
    GtSeqIterator *seqit;

    gt_assert(tyrindex != NULL);
    gt_tyrsearchinfo_init(&tyrsearchinfo,tyrindex,showmode,searchstrand);
    seqit = gt_seq_iterator_sequence_buffer_new(queryfilenames, err);
    if (!seqit)
      haserr = true;
    if (!haserr)
    {
      gt_seq_iterator_set_symbolmap(seqit,
                                 gt_alphabet_symbolmap(tyrsearchinfo.dnaalpha));
      for (unitnum = 0; /* Nothing */; unitnum++)
      {
        retval = gt_seq_iterator_next(seqit,
                                     &query,
                                     &querylen,
                                     &desc,
                                     err);
        if (retval < 0)
        {
          haserr = true;
          break;
        }
        if (retval == 0)
        {
          break;
        }
        singleseqtyrsearch(tyrindex,
                           tyrcountinfo,
                           &tyrsearchinfo,
                           tyrbckinfo,
                           unitnum,
                           query,
                           querylen,
                           desc);
      }
      gt_seq_iterator_delete(seqit);
    }
    gt_tyrsearchinfo_delete(&tyrsearchinfo);
  }
  if (tyrbckinfo != NULL)
  {
    gt_tyrbckinfo_delete(&tyrbckinfo);
  }
  if (tyrcountinfo != NULL)
  {
    gt_tyrcountinfo_delete(&tyrcountinfo);
  }
  if (tyrindex != NULL)
  {
    gt_tyrindex_delete(&tyrindex);
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/match/tyr-search.h000066400000000000000000000024101211610345200201560ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TYR_SEARCH_H
#define TYR_SEARCH_H

#include 
#include "core/str_api.h"
#include "core/str_array_api.h"
#include "core/error_api.h"

int gt_tyrsearch(const char *tyrindexname,
                 const GtStrArray *queryfilenames,
                 unsigned int showmode,
                 unsigned int searchstrand,
                 bool verbose,
                 bool performtest,
                 GtError *err);

#endif
genometools-1.5.1/src/match/tyr-show.h000066400000000000000000000021341211610345200176740ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef TYR_SHOW_H
#define TYR_SHOW_H

#define STRAND_FORWARD 1U
#define STRAND_REVERSE (STRAND_FORWARD << 1)

#define SHOWQSEQNUM  1U
#define SHOWQPOS     (SHOWQSEQNUM << 1)
#define SHOWCOUNTS   (SHOWQSEQNUM << 2)
#define SHOWSEQUENCE (SHOWQSEQNUM << 3)

#endif
genometools-1.5.1/src/match/xdrop.c000066400000000000000000000352741211610345200172420ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Ellinghaus 
  Copyright (c) 2012-2013 Stefan Kurtz 
  Copyright (c) 2007-2013 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/chardef.h"
#include "core/divmodmul.h"
#include "core/minmax.h"
#include "xdrop.h"

typedef struct
{
  int mis,
      ins,
      del,
      gcd;  /* greatest common divisor */
} GtXdropArbitrarydistances;

typedef struct
{
  long row;
  unsigned char direction; /* one of the bits GT_XDROP_REPLACEMENTBIT,
                                              GT_XDROP_DELETIONBIT,
                                              GT_XDROP_INSERTIONBIT */
} GtXdropfrontvalue;

GT_DECLAREARRAYSTRUCT(GtXdropfrontvalue);

#define GT_XDROP_FRONTIDX(D,K)    ((unsigned long) (D) * (D) + (D) + (K))

/*
  For each entry in the DP-matrix we store a single byte, and
  use the three rightmost bits to mark which edge in the edit distance
  graph to trace back.
*/

#define GT_XDROP_REPLACEMENTBIT   ((unsigned char) 1)
#define GT_XDROP_DELETIONBIT      (((unsigned char) 1) << 1)
#define GT_XDROP_INSERTIONBIT     (((unsigned char) 1) << 2)

/*
 The following function shows the matrix of the calculated fronts.
 */
/* CAUTION: fronts, that run over the matrix boundaries are not shown in
   the printed matrix.
 */
void gt_showfrontvalues(const GtArrayGtXdropfrontvalue *fronts,
                       long distance,
                       const unsigned char *useqptr,
                       const unsigned char *vseqptr,
                       long ulen,
                       long vlen)
{
  unsigned long l;
  long i, j, k, d = distance + 1, filled = 0, integermax = MAX(ulen,vlen),
       integermin = -integermax;

  printf("frontvalues:\n");
  printf("        ");
  printf("%-3c ", vseqptr[0]);
  /* print vseq */
  for (i = 1L; i < vlen; i++)
  {
    printf("%-3c ", vseqptr[i]);
  }
  for (i = 0; i <= ulen; i++)
  {
    printf("\n");
    /* print useq */
    if (i != 0)
    {
      printf("%-3c ", useqptr[i - 1]);
    } else
    {
      printf("    ");
    }
    for (j = 0; j <= vlen; j++)
    {
      d = distance + 1;
      k = i - j;
      for (l = 0; l < fronts->nextfreeGtXdropfrontvalue; l++)
      {
        if (fronts->spaceGtXdropfrontvalue[l].row == integermin)
        {
          continue;
        }
        if (i == fronts->spaceGtXdropfrontvalue[l].row)
        {
          for (d = 0; d <= distance; d++)
          {
            if (k >= -d && k <= d && l == GT_XDROP_FRONTIDX(d, i - j))
            {
              printf("%-3ld ", d);
              l = fronts->nextfreeGtXdropfrontvalue;
              filled++;
              break;
            }
          }
        }
      }
      if (d > distance)
      {
        printf("U   ");
      }
    }
  }
  printf("\n%.2f percent of matrix filled\n",
           (double) filled * 100.00 / ((ulen + 1) * (vlen + 1)));
}

static unsigned int gt_xdrop_gcd(unsigned int m, unsigned int n)
{
  unsigned int r;

  if (m < n)
  {
    r = m;
    m = n;
    n = r;
  }
  do
  {
    gt_assert(m >= n);
    r = m % n;
    m = n;
    n = r;
  } while (r != 0);
  return m;
}

/*
 The following function calculates the distance from the given scores.
 */
static void gt_calculatedistancesfromscores(
                                    const GtXdropArbitraryscores *arbitscores,
                                    GtXdropArbitrarydistances *dist)
{
  int mat, mis, ins, del;

  /* if mat is odd double all scores */
  gt_assert(arbitscores->mat > 0);
  if (GT_MOD2((unsigned int) arbitscores->mat) > 0)
  {
    mat = arbitscores->mat * 2;
    mis = arbitscores->mis * 2;
    ins = arbitscores->ins * 2;
    del = arbitscores->del * 2;
  } else
  {
    mat = arbitscores->mat;
    mis = arbitscores->mis;
    ins = arbitscores->ins;
    del = arbitscores->del;
  }
  gt_assert(mat >= mis && mat/2 >= ins && mat/2 >= del);
  dist->gcd
    = (int) gt_xdrop_gcd(gt_xdrop_gcd((unsigned int) (mat-mis),
                                      (unsigned int) (mat/2-ins)),
                         (unsigned int) (mat/2-del));
  dist->mis = (mat - mis) / dist->gcd;
  dist->ins = (mat/2 - ins) / dist->gcd;
  dist->del = (mat/2 - del) / dist->gcd;
}

struct GtXdropresources
{
  const GtXdropArbitraryscores *arbitscores;
  GtXdropArbitrarydistances arbitdistances;
  GtArrayGtXdropfrontvalue fronts;
  GtArrayGtXdropscore big_t;
};

GtXdropresources *gt_xdrop_resources_new(const GtXdropArbitraryscores *scores)
{
  GtXdropresources *res = gt_malloc(sizeof *res);

  res->arbitscores = scores;
  GT_INITARRAY (&res->fronts, GtXdropfrontvalue);
  GT_INITARRAY (&res->big_t, GtXdropscore);
  gt_calculatedistancesfromscores(scores,&res->arbitdistances);
  return res;
}

void gt_xdrop_resources_delete(GtXdropresources *res)
{
  if (res != NULL)
  {
    GT_FREEARRAY (&res->fronts, GtXdropfrontvalue);
    GT_FREEARRAY (&res->big_t, GtXdropscore);
    gt_free(res);
  }
}

#define GT_XDROP_EVAL(K,D)\
        ((K) * res->arbitscores->mat/2 - (D) * res->arbitdistances.gcd)

#define GT_XDROP_SETDBACK(XDROPBELOWSCORE)\
        (XDROPBELOWSCORE + res->arbitscores->mat/2)/res->arbitdistances.gcd + 1

static long gt_xdrop_frontvalue_get(const GtXdropresources *res,long d,long k)
{
  const unsigned long frontidx = GT_XDROP_FRONTIDX(d,k);
  return res->fronts.spaceGtXdropfrontvalue[frontidx].row;
}

static void gt_xdrop_frontvalue_set(GtXdropresources *res,long d,long k,
                                    GtXdropfrontvalue value)
{
  const unsigned long frontidx = GT_XDROP_FRONTIDX(d,k);

  if (frontidx >= res->fronts.allocatedGtXdropfrontvalue)
  {
    res->fronts.allocatedGtXdropfrontvalue = frontidx + 32UL;
    res->fronts.spaceGtXdropfrontvalue
      = gt_realloc_mem(res->fronts.spaceGtXdropfrontvalue,
                       sizeof (*res->fronts.spaceGtXdropfrontvalue) *
                       res->fronts.allocatedGtXdropfrontvalue,
                       __FILE__, __LINE__);
  }
  res->fronts.spaceGtXdropfrontvalue[frontidx] = value;
  res->fronts.nextfreeGtXdropfrontvalue = frontidx + 1;
}

void gt_evalxdroparbitscoresextend(bool forward,
                                   GtXdropbest *xdropbest,
                                   GtXdropresources *res,
                                   const GtSeqabstract *useq,
                                   const GtSeqabstract *vseq,
                                   unsigned long uoffset,
                                   unsigned long voffset,
                                   GtXdropscore xdropbelowscore)
{
  const long ulen = (long) gt_seqabstract_length_get(useq),
             vlen = (long) gt_seqabstract_length_get(vseq),
             end_k = ulen - vlen, /* diagonal of endpoint (ulen, vlen) */
             integermax = MAX(ulen, vlen),
             integermin = -integermax,
             dback = GT_XDROP_SETDBACK(xdropbelowscore);
  long idx,
       lbound,    /* diagonal lower bound */
       ubound,    /* diagonal upper bound */
       currd = 0; /* distance */
  /*The following function calculates the maximal allowed number of
    generations with all front values equal minus infinity.*/
  const int allowedMININFINITYINTgenerations
              = MAX(MAX(res->arbitdistances.mis,res->arbitdistances.ins),
                    res->arbitdistances.del) - 1;
  int currentMININFINITYINTgeneration = 0;
  GtXdropfrontvalue tmpfront;
  GtXdropscore bigt_tmp;        /* best score T' seen already */
  bool alwaysMININFINITYINT = true;

  res->big_t.nextfreeGtXdropscore = 0;
  res->fronts.nextfreeGtXdropfrontvalue = 0;
  /* phase 0 */
  idx = (long) gt_seqabstract_lcp(forward,
                                  useq,
                                  vseq,
                                  forward ? uoffset : uoffset - 1,
                                  forward ? voffset : voffset - 1,
                                  (unsigned long) MIN(ulen,vlen));
  /* alignment already finished */
  if (idx >= ulen || idx >= vlen)
  {
    lbound =  1L;
    ubound = -1L;
  } else
  {
    lbound = 0;
    ubound = 0;
  }
  tmpfront.row = idx;
  tmpfront.direction = (GtUchar) 0;   /* no predecessor */
  gt_xdrop_frontvalue_set(res,0,0,tmpfront);
  xdropbest->score = bigt_tmp = GT_XDROP_EVAL(idx + idx, 0);
  gt_assert(idx >= 0);
  xdropbest->ivalue = xdropbest->jvalue = (unsigned long) idx;
  GT_STOREINARRAY (&res->big_t, GtXdropscore, 10, bigt_tmp);
  /* phase d > 0 */
  while (lbound <= ubound)
  {
    long k;

    currd++;
    /* calculate fronts */
    for (k = lbound - 1; k <= ubound + 1; k++)
    {
      long i = integermin;
      /* case 1 : DELETION-EDGE  */
      if (lbound < k &&
          currd - res->arbitdistances.del >= 0 &&
          -(currd - res->arbitdistances.del) <= k - 1 &&
          k - 1 <= currd - res->arbitdistances.del)
      {
        i = gt_xdrop_frontvalue_get(res,currd - res->arbitdistances.del,k-1)
            + 1;
        tmpfront.direction = GT_XDROP_DELETIONBIT;
      }
      /* case 2: REPLACEMENT-EDGE */
      if (lbound <= k &&
          k <= ubound &&
          currd - res->arbitdistances.mis >= 0 &&
          -(currd - res->arbitdistances.mis) <= k &&
          k <= currd - res->arbitdistances.mis)
      {
        /* test, if case 1 has happened. */
        long row = gt_xdrop_frontvalue_get(res,
                                           currd - res->arbitdistances.mis,k)
                   + 1;
        if (!(tmpfront.direction & GT_XDROP_DELETIONBIT) || row > i)
        {
          i = row;
          tmpfront.direction = GT_XDROP_REPLACEMENTBIT;
        }
      }
      /* case 3: INSERTION-EDGE */
      if (k < ubound &&
          currd - res->arbitdistances.ins >= 0 &&
          -(currd - res->arbitdistances.ins) <= k + 1 &&
           k + 1 <= currd - res->arbitdistances.ins)
      {
        long row = gt_xdrop_frontvalue_get(res,
                                           currd - res->arbitdistances.ins,k+1);
        if (!(tmpfront.direction & (GT_XDROP_DELETIONBIT |
                                    GT_XDROP_REPLACEMENTBIT)) || row > i)
        {
          i = row;
          tmpfront.direction = GT_XDROP_INSERTIONBIT;
        }
      }
      /* if i = MINUSINFINITYINY or MINUSINFINITYINY + 1 */
      if (i < 0)
      {
        if (tmpfront.direction == (GtUchar) 0)
        {
          alwaysMININFINITYINT = false;
        }
        tmpfront.row = integermin;
      } else
      {
        long j = i - k;
        const long previousd = currd - dback;

        /* alignment score smaller than T - X */
        if (previousd > 0 &&
            res->big_t.spaceGtXdropscore != NULL &&
            GT_XDROP_EVAL (i + j, currd) <
            res->big_t.spaceGtXdropscore[previousd] - xdropbelowscore)
        {
          tmpfront.row = integermin;
        } else
        {
          if (k <= -currd || k >= currd ||
              (gt_xdrop_frontvalue_get(res,currd-1,k) < i &&
               i <= MIN(ulen,vlen + k)))
          {
            if (ulen > i && vlen > j)
            {
              unsigned long lcp;
              gt_assert(forward || (uoffset > (unsigned long) i &&
                                    voffset > (unsigned long) j));
              lcp = gt_seqabstract_lcp(forward,
                                       useq,
                                       vseq,
                                       forward ? uoffset + i : uoffset - i - 1,
                                       forward ? voffset + j : voffset - j - 1,
                                       (unsigned long) MIN(ulen - i,vlen - j));
              i += lcp;
              j += lcp;
            }
            alwaysMININFINITYINT = false;
            tmpfront.row = i;
            if (GT_XDROP_EVAL(i + j, currd) > bigt_tmp)
            {
              xdropbest->score = bigt_tmp = GT_XDROP_EVAL(i + j,currd);
              gt_assert(i >= 0 && j >= 0);
              xdropbest->ivalue = (unsigned long) i;
              xdropbest->jvalue = (unsigned long) j;
            }
          } else
          {
            alwaysMININFINITYINT = false;
            tmpfront.row = gt_xdrop_frontvalue_get(res,currd-1,k);
          }
        }
      }
      gt_xdrop_frontvalue_set(res,currd,k,tmpfront);
    }
    /* if all front values are integermin, aligment prematurely finished if
       allowedMININFINITYINTgenerations exceeded (full front has already ended
       at currd - currentMININFINITYINTgeneration). */
    if (alwaysMININFINITYINT)
    {
      currentMININFINITYINTgeneration++;
      if (currentMININFINITYINTgeneration > allowedMININFINITYINTgenerations)
      {
        currd -= currentMININFINITYINTgeneration;
        break;
      }
    } else
    {
      currentMININFINITYINTgeneration = 0;
      alwaysMININFINITYINT = true;
    }
    GT_STOREINARRAY (&res->big_t, GtXdropscore, 10, bigt_tmp);
    /* fill out of bounds values of integermin
       needed for gt_showfrontvalues function */
    for (k = -currd; k < lbound - 1; k++)
    {
      tmpfront.row = integermin;
      gt_xdrop_frontvalue_set(res,currd,k,tmpfront);
    }
    for (k = ubound + 2; k <= currd; k++)
    {
      tmpfront.row = integermin;
      gt_xdrop_frontvalue_set(res,currd,k,tmpfront);
    }
    /* alignment finished */
    if (-currd <= end_k && end_k <= currd &&
        gt_xdrop_frontvalue_get(res,currd,end_k) == ulen)
    {
      break;
    }
    /* pruning lower bound
       lbound may decrease by one or increase/stays the same */
    for (k = lbound - 1; k <= ubound + 1; k++)
    {
      if (gt_xdrop_frontvalue_get(res,currd,k) > integermin)
      {
        lbound = k;
        break;
      }
    }
    /* pruning upper bound
       ubound may increase by one or decrease/stays the same */
    for (k = ubound + 1; k >= lbound - 1; k--)
    {
      if (gt_xdrop_frontvalue_get(res,currd,k) > integermin)
      {
        ubound = k;
        break;
      }
    }
    /* handling boundaries lower bound */
    for (k = 0; k >= lbound; k--)
    {
      if (gt_xdrop_frontvalue_get(res,currd,k) == vlen + k)
      {
        lbound = k;
        break;
      }
    }
    /* handling boundaries upper bound */
    for (k = 0; k <= ubound; k++)
    {
      if (gt_xdrop_frontvalue_get(res,currd,k) == ulen)
      {
        ubound = k;
        break;
      }
    }
  }
}
genometools-1.5.1/src/match/xdrop.h000066400000000000000000000044551211610345200172440ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Ellinghaus 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef XDROP_H
#define XDROP_H

#include "core/arraydef.h"
#include "match/seqabstract.h"

typedef struct GtXdropresources GtXdropresources;

typedef struct
{
  int mat,
      mis,
      ins,
      del;
} GtXdropArbitraryscores;

/* This is the type for the xdrop scores. */
typedef long GtXdropscore;

typedef struct
{
  unsigned long ivalue, jvalue;
  GtXdropscore score;
} GtXdropbest;

GT_DECLAREARRAYSTRUCT(GtXdropscore);

/*
   The following functions extend seeds to the right (forward = true)
   and to the left (forward = false),
   respectively. GtXdropbest stores information about the best match
   found. useq is the first sequence position and vseq is the
   second sequence position. ulen and vlen are the
   remaining sequence length to align. If an alignment has score smaller than
   xdropbelowscore, then this alignment is not extended
   any more.
*/

GtXdropresources *gt_xdrop_resources_new(const GtXdropArbitraryscores *scores);

void gt_evalxdroparbitscoresextend(bool forward,
                                   GtXdropbest *xdropbest,
                                   GtXdropresources *res,
                                   const GtSeqabstract *useq,
                                   const GtSeqabstract *vseq,
                                   unsigned long uoffset,
                                   unsigned long voffset,
                                   GtXdropscore xdropbelowscore);

void gt_xdrop_resources_delete(GtXdropresources *);

#endif
genometools-1.5.1/src/mgth/000077500000000000000000000000001211610345200155725ustar00rootroot00000000000000genometools-1.5.1/src/mgth/metagenomethreader.c000066400000000000000000000744471211610345200216160ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/fileutils_api.h"
#include "core/file.h"
#include "core/hashmap-generic.h"
#include "core/mathsupport.h"
#include "core/unused_api.h"
#include "match/giextract.h"
#include "mg_xmlparser.h"
#include "metagenomethreader.h"

static GtOPrval mgth_parse_options(int *parsed_args,
                              MetagenomeThreaderArguments
                              *metagenomethreader_arguments, int argc,
                              const char **argv, GtError * err)
{
  GtOptionParser *op;
  GtOPrval oprval;

  /* Definition der optionalen Eingabeparameter */
  GtOption *syn_value_option,
   *nonsyn_value_option,
   *blasthitend_value_option,
   *stopcodon_queryseq_option,
   *stopcodon_hitseq_option,
   *frameshift_span_option,
   *prediction_span_option,
   *curlfcgi_option,
   *leavegene_value_option,
   *resulttextfile_name_option,
   *giexpfile_name_option,
   *hitfile_bool_option,
   *homology_mode_option,
   *extended_mode_option,
   *testmodus_mode_option,
   *outputfile_format_option,
   *codon_mode_option,
   *min_as_option,
   *percent_option;

  /* Check Umgebungsvariablen */
  gt_error_check(err);

  /* init Option-Parser */
  op =
    gt_option_parser_new
    ("[option ...] XML-File Query-FASTA-File Hit-FASTA-File",
     "Metagenomethreader, for predicting genes in metagenomeprojects.");

  /* GtOption zur Eingabe des Scores fuer synonymen Basenaustausch; default:
     1.0 */
  syn_value_option =
    gt_option_new_double("s", "score for synonymic base exchanges",
                      &metagenomethreader_arguments->synonomic_value, 1.0);
  gt_option_parser_add_option(op, syn_value_option);

  /* GtOption zur Eingabe des Scores fuer nicht-synonymen Basenaustausch;
     default: -1.0 */
  nonsyn_value_option =
    gt_option_new_double("n", "score for non-synonymic base exchanges",
                      &metagenomethreader_arguments->nonsynonomic_value,
                      -1.0);
  gt_option_parser_add_option(op, nonsyn_value_option);

  /* GtOption zur Eingabe des Scores fuer das Blast-Hit-Ende; default: -10 */
  blasthitend_value_option =
    gt_option_new_double("b", "score for blast-hit-end within query sequence",
                      &metagenomethreader_arguments->blasthit_end_value,
                      -10.0);
  gt_option_parser_add_option(op, blasthitend_value_option);

  /* GtOption zur Eingabe des Scores zur Bewertung eines Stop-Codons in der
     Query-Sequence; default: -2 */
  stopcodon_queryseq_option =
    gt_option_new_double("q", "score for stop-codon within querysequence",
                      &metagenomethreader_arguments->stopcodon_queryseq,
                      -2.0);
  gt_option_parser_add_option(op, stopcodon_queryseq_option);

  /* GtOption zur Eingabe des Scores zur Bewertung eines Stop-Codons in der
     Hit-Sequence; default: -5 */
  stopcodon_hitseq_option =
    gt_option_new_double("h", "score for stop-codon within hitsequence",
                      &metagenomethreader_arguments->stopcodon_hitseq,
                      -5.0);
  gt_option_parser_add_option(op, stopcodon_hitseq_option);

  /* GtOption zur Eingabe des Scores zur Bewertung des Verlassens oder
     Eintretens eines bzw. in ein Gen ; default: -2 */
  leavegene_value_option =
    gt_option_new_double("l",
                      "score for leaving a gene on forward/reverse strand "
                      "or enter a gene on forward/reverse strand",
                      &metagenomethreader_arguments->leavegene_value,
                      -2.0);
  gt_option_parser_add_option(op, leavegene_value_option);

  /* GtOption zur Eingabe des Wertes innerhalb welches Zwischenbereichs ein
     zusammenhaengender Genbereich vorliegt; default: 400 */
  prediction_span_option =
    gt_option_new_double_min("p",
                          "max. span between coding-regions resume as one "
                          "prediction",
                          &metagenomethreader_arguments->prediction_span,
                          400.0, 0.0);
  gt_option_parser_add_option(op, prediction_span_option);

  /* GtOption zur Eingabe des Wertes innerhalb welches Zwischenbereichs ein
     Frameshift vorliegt; default: 200 */
  frameshift_span_option =
    gt_option_new_double_min("f",
                          "max. span between coding-regions in different "
                          "reading frames resume as coding-regions in the "
                          "optimal reading-frame",
                          &metagenomethreader_arguments->frameshift_span,
                      200.0, 0.0);
  gt_option_parser_add_option(op, frameshift_span_option);

  /* GtOption zur Eingabe der DB, die bei der Verwendung des fcgi-Skriptes
     verwendet wird; default: nucleotide */
  curlfcgi_option =
    gt_option_new_string("c", "db-name for fcgi-db",
                      metagenomethreader_arguments->curl_fcgi_db,
                      "nucleotide");
  gt_option_parser_add_option(op, curlfcgi_option);

  /* GtOption zur Eingabe des Namens der Outputdatei; default: output.txt */
  resulttextfile_name_option =
    gt_option_new_string("o", "name for resulting output-file",
                      metagenomethreader_arguments->outputtextfile_name,
                      "output");
  gt_option_parser_add_option(op, resulttextfile_name_option);

  /* GtOption zur Angabe der Hit-Sequenz-DB  */
  giexpfile_name_option =
    gt_option_new_string("k", "name for the Hit-Sequence-DB",
                         metagenomethreader_arguments->giexpfile_name,
                         "nucleotide database");
  gt_option_parser_add_option(op, giexpfile_name_option);

  /* GtOption zur Angabe, ob ein Hit-FASTA-File exisitiert; default: false */
  hitfile_bool_option =
    gt_option_new_bool("t", "true or false if a Hit-FASTA-File exist",
                    &metagenomethreader_arguments->hitfile_bool, false);
  gt_option_parser_add_option(op, hitfile_bool_option);

  /* GtOption zur Angabe des Formates der Outputdatei; default: 1 -> txt */
  outputfile_format_option =
    gt_option_new_int("r", "format of the output-file",
                   &metagenomethreader_arguments->outputfile_format, 1);
  gt_option_parser_add_option(op, outputfile_format_option);

  /* GtOption zur Angabe der minimalen Laenger der AS-Sequnezen, die in der
     Ausgabedatei aufgefuehrt werden sollen; default: 15; min: 15 */
  min_as_option =
    gt_option_new_ulong_min("a", "minimum length of the as-sequence",
                         &metagenomethreader_arguments->min_as, 15, 15);
  gt_option_parser_add_option(op, min_as_option);

  /* GtOption zur Angabe der minimalen Prozentzahl, ab der Hits-Def. im
     Statistikbereich der Ausgabe angezeigt werden */
  percent_option =
    gt_option_new_double_min_max("d",
                              "minimum percent-value for hit-statistic-output",
                              &metagenomethreader_arguments->percent_value,
                              0.0, 0.0, 1.0);
  gt_option_parser_add_option(op, percent_option);

  /* GtOption zur Angabe, ob alternative Start-Codons verwendet werden
     sollen; default: 1 -> txt */
  codon_mode_option =
    gt_option_new_int("e", "use of alternative start-codons",
                   &metagenomethreader_arguments->codon_mode, 1);
  gt_option_parser_add_option(op, codon_mode_option);

  /* Experimenteller Status dieser GtOption - Funktionsfaehigkeit nicht
     abschliessend geklaert */
  /* GtOption zur Angabe, ob nach Homologien gesucht werden soll, statt nach
     synonymen-Basenaustauschen; default: false */
  homology_mode_option =
    gt_option_new_bool("m", "search for homology",
                    &metagenomethreader_arguments->homology_mode, false);
  gt_option_parser_add_option(op, homology_mode_option);

  /* Testmodus: die Programm-Parameter werden zur Vergleichbarkeit der
     Ergebnisse nicht mit ausgegeben; default: false */
  testmodus_mode_option =
    gt_option_new_bool("g", "testmodus, output without creating date",
                    &metagenomethreader_arguments->testmodus_mode, false);
  gt_option_parser_add_option(op, testmodus_mode_option);

  /* GtOption zur Angabe, ob die EGTs auf den max. ORF erweitert werden
     sollen, default: false */
  extended_mode_option =
    gt_option_new_bool("x", "extend the EGTs to max",
                    &metagenomethreader_arguments->extended_mode, false);
  gt_option_parser_add_option(op, extended_mode_option);

  gt_option_parser_set_min_max_args(op, 3, 3);
  gt_option_parser_refer_to_manual(op);

  /* es werden die Parameter XML-File, Query-Fasta-File und Hit-FASTA-File
     erwartet, Min und Max. der Anzahl an Parametern ist also 3 */
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);

  gt_option_parser_delete(op);
  return oprval;
}

DEFINE_HASHMAP(char *, gt_cstr_nofree, unsigned long *,
               ulp, gt_ht_cstr_elem_hash,
               gt_ht_cstr_elem_cmp, NULL_DESTRUCTOR, NULL_DESTRUCTOR,,)

typedef struct {
  unsigned long *statpos;
  const char *string;
  ParseStruct *parsestruct;
} GtMgthStatsPair;

static int statspair_cmp(const void *y, const void *z)
{
  const GtMgthStatsPair *a = (const GtMgthStatsPair*) y;
  const GtMgthStatsPair *b = (const GtMgthStatsPair*) z;
  double val_a, val_b;
  int ret;
  gt_assert(a && b && a->parsestruct && b->parsestruct);

  /* calculate result values to sort by */
  val_a = (double) (*(a->parsestruct->hits_statistics.hitsnum
                        + *(a->statpos)) /
                   ((double) a->parsestruct->hits_statistics.hitsnumber) * 100);
  val_b = (double) (*(b->parsestruct->hits_statistics.hitsnum
                        + *(b->statpos)) /
                   ((double) b->parsestruct->hits_statistics.hitsnumber) * 100);

  if ((ret = gt_double_compare(val_a, val_b) * -1) == 0) {
    /* tie breaking, we need canonical ordering!
       if two entries have the same numerical value, let strings decide */
    return strcmp(a->string, b->string);
  }
  return ret;
}

static enum iterator_op
insert_into_outlist(char *key, unsigned long *value, void *data,
                    GT_UNUSED GtError *err)
{
  ParseStruct *parsestruct_ptr = (ParseStruct *) data;
  gt_assert(key && parsestruct_ptr && parsestruct_ptr->outlist);
  gt_error_check(err);

  /* create new output entry and store in sorted list */
  GtMgthStatsPair *pair = gt_calloc(1, sizeof (GtMgthStatsPair));
  pair->parsestruct = parsestruct_ptr;
  pair->statpos = value;
  pair->string = key;
  gt_dlist_add(parsestruct_ptr->outlist, pair);

  return CONTINUE_ITERATION;
}

int gt_metagenomethreader(int argc, const char **argv, GtError * err)
{
  int had_err = 0,
      parsed_args = 0;

  /* Variablen/Zeiger zur Erstellung des Hashes fuer die GtBioseq-Strukturen
   */
  unsigned long *querynum,
   *hitnum = NULL,
    nrofseq,
    loop_index;
  char *descr_ptr_hit,
   *descr_ptr_query;

  GtStr *outputfilename;

  /* GtFile Zeiger auf die XML-Datei mit den Blast-Hits */
  GtFile *fp_xmlfile;

  /* Anlegen der Parser-Array-Struktur, ueber den der Austausch von
     Informationen Parsestruct parsestruct; zwischen den
     XML-Parser-Handlern erfolgt Zeiger auf die parser_array-Struktur;
     notwendig, da bei expat nur die Uebergabe eines Zeigers auf die
     UserDaten erfolgen kann und nicht z.B. ein Zeiger auf Zeiger */
  ParseStruct parsestruct;
  ParseStruct *parsestruct_ptr;

  parsestruct_ptr = &parsestruct;

  ARGUMENTS(curl_fcgi_db) = gt_str_new();
  ARGUMENTS(outputtextfile_name) = gt_str_new();
  ARGUMENTS(giexpfile_name) = gt_str_new();

  /* Check der Umgebungsvariablen */
  gt_error_check(err);

  /* option parsing */
  switch (mgth_parse_options(&parsed_args,
                             &parsestruct.metagenomethreader_arguments,
                             argc, argv, err)) {
    case GT_OPTION_PARSER_OK:
      break;
    case GT_OPTION_PARSER_ERROR:
      gt_str_delete(ARGUMENTS(curl_fcgi_db));
      gt_str_delete(ARGUMENTS(outputtextfile_name));
      return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT:
      gt_str_delete(ARGUMENTS(curl_fcgi_db));
      gt_str_delete(ARGUMENTS(outputtextfile_name));
      return 0;
  }

  /* GtBioseqstruktur des Query-DNA-FASTA-File wird erzeugt */
  parsestruct.queryseq = gt_bioseq_new(argv[parsed_args + 1], err);
  /* Erstellung der GtBioseq-Struktur fehlerhaft -> Fehlercode setzen */
  if (!parsestruct.queryseq)
  {
    had_err = -1;
  }

  /* nur wenn die Hitfile-Bool-GtOption auf true gesetzt ist (File
     vorhanden) und der Fehlercode nicht gesetzt ist, muss die
     GtBioseq-Struktur auch fuer die Hits erstellt werden */
  if (ARGUMENTS(hitfile_bool) && !had_err)
  {
    /* GtBioseqstruktur des Hit-DNA-FASTA-File wird erzeugt */
    parsestruct.hitseq = gt_bioseq_new(argv[parsed_args + 2], err);
    /* Erstellung der GtBioseq-Struktur fehlerhaft -> Fehlercode setzen */
    if (!parsestruct.hitseq)
    {
      gt_bioseq_delete(parsestruct.queryseq);
      had_err = -1;
    }
  }

  if (!had_err)
  {
    outputfilename = gt_str_new();

    /* StringArrays zur Aufnahme der einzulesenden XML-Tag Bezeichnungen */
    parsestruct.query_array = gt_str_array_new();
    parsestruct.hit_array = gt_str_array_new();
    parsestruct.hit_hsp_array = gt_str_array_new();
    parsestruct.hits_statistics.hits_statistic = gt_str_array_new();
    parsestruct.key_tmp = gt_str_array_new();

    /* String fuer die Bezeichnung des letzten XML-Tags eines
       Bearbeitunsschrittes */
    parsestruct.xml_tag = gt_str_new();

    /* Zeiger auf den Speicherbereich, wo der aktuelle Text abgespeichert
       wird */
    parsestruct.buf_ptr = gt_str_new();

    /* temp-Variable zum Zwischenspeichern der Hit-GI-Definition */
    parsestruct.gi_def_tmp = gt_str_new();
    parsestruct.gi_acc_tmp = gt_str_new();
    parsestruct.hit_gi_nr_tmp = gt_str_new();
    parsestruct.fasta_row = gt_str_new();

    /* Zeiger auf Query-DNA bzw. Query-Def */
    parsestruct.matrix_info.query_dna = gt_str_new();
    parsestruct.matrix_info.query_def = gt_str_new();

    /* Strings fuer Blast-XML-File und Hit-FASTA-File */
    parsestruct.hit_fastafile = gt_str_new();
    parsestruct.xmlfile = gt_str_new();
    /* String fuer die aktuelle Hit-Def fuer die Statistik */
    parsestruct.result_hits = gt_str_new();

    /* diverse Zeiger auf Informationen aus dem XML-File */
    parsestruct.matrix_info.query_from = gt_array_new(sizeof (unsigned long));
    parsestruct.matrix_info.query_to = gt_array_new(sizeof (unsigned long));
    parsestruct.matrix_info.query_frame = gt_array_new(sizeof (unsigned long));
    parsestruct.matrix_info.hit_frame = gt_array_new(sizeof (unsigned long));
    parsestruct.value_tmp = gt_array_new(sizeof (unsigned long));

    /* mit dem schliessenden Iteration_hits XML-Tag wird im Programmablauf
       der Abschluss eines Query-Eintrages erkannt */
    gt_str_set(parsestruct.xml_tag, "Iteration_stat");

    /* XML-Tags im Query-Def-Bereich */
    gt_str_array_add_cstr(parsestruct.query_array, "Iteration_query-def");

    /* XML-Tags im Hit-Def-Bereich */
    gt_str_array_add_cstr(parsestruct.hit_array, "Hit_id");
    gt_str_array_add_cstr(parsestruct.hit_array, "Hit_def");
    gt_str_array_add_cstr(parsestruct.hit_array, "Hit_accession");

    /* XML-Tags im Hits-Bereich */
    gt_str_array_add_cstr(parsestruct.hit_hsp_array, "Hsp_num");
    gt_str_array_add_cstr(parsestruct.hit_hsp_array, "Hsp_query-from");
    gt_str_array_add_cstr(parsestruct.hit_hsp_array, "Hsp_query-to");
    gt_str_array_add_cstr(parsestruct.hit_hsp_array, "Hsp_hit-from");
    gt_str_array_add_cstr(parsestruct.hit_hsp_array, "Hsp_hit-to");
    gt_str_array_add_cstr(parsestruct.hit_hsp_array, "Hsp_query-frame");
    gt_str_array_add_cstr(parsestruct.hit_hsp_array, "Hsp_hit-frame");
    gt_str_array_add_cstr(parsestruct.hit_hsp_array, "Hsp_qseq");
    gt_str_array_add_cstr(parsestruct.hit_hsp_array, "Hsp_hseq");

    /* 3 Flags, die bei oeffnenden XML-Tags gesetzt und bei schliessenden
       geloescht werden */
    parsestruct.def_flag = MGTH_UNSET;
    parsestruct.hit_flag = MGTH_UNSET;
    parsestruct.hit_hsp_flag = MGTH_UNSET;
    parsestruct.xml_tag_flag = MGTH_UNSET;
    parsestruct.giexp_flag = MGTH_UNSET;
    parsestruct.gi_flag = MGTH_UNSET;

    /* Variablen (Zeilennummer, Fehlercode) zur Fehlerbehandlung waehrend
       des Parsvorganges des XML-Files */
    parsestruct.xml_linenumber = 0;
    parsestruct.had_err = 0;

    /* Zaehlvariablen fuer die Anzahl der Syn- und Nichtsynonymen
       DNA-Austausche */
    parsestruct.syn = 0.0;
    parsestruct.non_syn = 0.0;

    /* hit_counter zum Zaehlen der Hits pro Hit-GI */
    parsestruct.xmlparser_static.hit_counter = 0;

    /* Zaehlvariablen, die Position in den jeweiligen XML-Tag-Bloecken
       angeben */
    parsestruct.xmlparser_static.query_array_index_start = 0;
    parsestruct.xmlparser_static.hit_array_index_start = 0;
    parsestruct.xmlparser_static.hit_hsp_array_index_start = 0;
    parsestruct.xmlparser_static.query_array_index_end = 0;
    parsestruct.xmlparser_static.hit_array_index_end = 0;
    parsestruct.xmlparser_static.hit_hsp_array_index_end = 0;

    /* als "Static" verwendete Variablen in der Struktur */
    parsestruct.geneprediction_static.matrixscore = 0;
    parsestruct.geneprediction_static.matrixscore_before = 0;
    parsestruct.geneprediction_static.current_frame = 0;
    parsestruct.geneprediction_static.frame_before = 0;
    parsestruct.geneprediction_static.function_stop = 0;
    parsestruct.geneprediction_static.noncodingcounter = 0;
    parsestruct.geneprediction_static.codingcounter = 0;
    parsestruct.hits_statistics.hitsnumber = 0;

    /* Speichergroesse fuer die Speicherbereiche der Statistik setzen */
    parsestruct.hits_memory = MGTH_MEMORY_SIZE;

    /* Speicher fuer die Statistik reservieren und zuweisen */
    parsestruct.hits_statistics.hitsnum =
      gt_calloc(MGTH_MEMORY_SIZE, sizeof (unsigned long));
    parsestruct.hits_statistics.memory =
      gt_calloc(MGTH_MEMORY_SIZE, sizeof (unsigned long));

    /* Variable der Umgebungsvariablen - genometools.org */
    parsestruct.err = err;

    /* Abspeichern des XML- und des Hit-Dateinamens in der
       ParseStruct-Struktur */
    gt_str_set(parsestruct.hit_fastafile, argv[parsed_args + 2]);
    gt_str_set(parsestruct.xmlfile, argv[parsed_args]);

    /* Anzahl der Query-DNA-Eintraege */
    nrofseq = gt_bioseq_number_of_sequences(parsestruct.queryseq);
    /* Speicherbereich reservieren fuer Zeiger auf die Indices der
       Query-DNA-Eintraege in der GtBioseq-Struktur */
    querynum = gt_calloc(nrofseq, sizeof (unsigned long));
    /* Hash erzeugen - Eintraege: Key - Query-FASTA-Def; Value - Zeiger
       auf deren Indices in der GtBioseq - Struktur */
    parsestruct.queryhash = gt_cstr_nofree_ulp_gt_hashmap_new();

    for (loop_index = 0; loop_index < nrofseq; loop_index++)
    {
      /* Descriptions der GtBioseq-Struktur werden nacheinander
         abgearbeitet */
      descr_ptr_query =
        (char *) gt_bioseq_get_description(parsestruct.queryseq, loop_index);
      /* Position in der GtBioseq in den Speicher querynum schreiben */
      querynum[loop_index] = loop_index;

      /* Dem aktuellen Schluessel Zeige auf die Position in der GtBioseq
         zuordnen */
      if (!gt_cstr_nofree_ulp_gt_hashmap_get(parsestruct.queryhash,
                                             descr_ptr_query))
        gt_cstr_nofree_ulp_gt_hashmap_add(parsestruct.queryhash,
                                          descr_ptr_query,
                                          querynum + loop_index);
    }

    /* nur wenn die GtOption hitfile_bool auf TRUE gesetzt ist, muss die
       GtBioseq-Struktur bzw. die Hash-Tabelle auch fuer die Hits erzeugt
       werden; Erzeugung inkl. Hash wie beim Query-DNA-FASTA-File */
    if (ARGUMENTS(hitfile_bool))
    {
      /* Anzahl der Hit-DNA-Eintraege */
      nrofseq = gt_bioseq_number_of_sequences(parsestruct.hitseq);
      /* Speicherbereich reservieren fuer Zeiger auf die Indices der
         Hit-DNA-Eintraege in der GtBioseq-Struktur */
      hitnum = gt_calloc(nrofseq, sizeof (unsigned long));
      /* Hash erzeugen - Eintraege: Key - Hit-FASTA-Zeile; Value - Zeiger
         auf deren Indices in der GtBioseq - Struktur */
      parsestruct.hithash = gt_cstr_nofree_ulp_gt_hashmap_new();

      /* Hit-Fasta-File zeilenweise abarbeiten */
      for (loop_index = 0; loop_index < nrofseq; loop_index++)
      {
        /* Der Schluessel ist die Hit-FASTA-Zeile */
        descr_ptr_hit =
          (char *) gt_bioseq_get_description(parsestruct.hitseq, loop_index);
        /* Position in der GtBioseq in den Speicher hitnum schreiben */
        hitnum[loop_index] = loop_index;

        /* Dem aktuellen Schluessel Zeige auf die Position in der GtBioseq
           zuordnen */
        if (!gt_cstr_nofree_ulp_gt_hashmap_get(parsestruct.hithash,
                                               descr_ptr_hit))
          gt_cstr_nofree_ulp_gt_hashmap_add(parsestruct.hithash, descr_ptr_hit,
                                     hitnum + loop_index);
      }
    }

    /* Hashtabelle fuer die Statistik anlegen */
    parsestruct.resulthits = gt_cstr_nofree_ulp_gt_hashmap_new();

    /* konstruieren des Output-Filenames aus angegebenen Filename und dem
       angegebenen Format */
    switch (ARGUMENTS(outputfile_format))
    {
      case 2:
        gt_str_append_str(outputfilename, ARGUMENTS(outputtextfile_name));
        gt_str_append_cstr(outputfilename, ".");
        gt_str_append_cstr(outputfilename, "html");
        break;
      case 3:
        gt_str_append_str(outputfilename, ARGUMENTS(outputtextfile_name));
        gt_str_append_cstr(outputfilename, ".");
        gt_str_append_cstr(outputfilename, "xml");
        break;
      default:
        gt_str_append_str(outputfilename, ARGUMENTS(outputtextfile_name));
        gt_str_append_cstr(outputfilename, ".");
        gt_str_append_cstr(outputfilename, "txt");
    }

    /* Der Name des XML-Files mit den Blast-Hits ist das erste Argument
       nach dem Programmnamen */
    fp_xmlfile = gt_file_xopen(argv[parsed_args], "r");

    if (gt_file_exists(gt_str_get(outputfilename)))
    {
      parsestruct.fp_outputfile = gt_file_xopen(gt_str_get(outputfilename),
                                                   "w+");
      gt_file_delete(parsestruct.fp_outputfile);
    }

    /* Der Name des Outputfiles wird den eingegebenen Optionen entnommen
       oder der default-Wert output.txt verwendet */
    parsestruct.fp_outputfile = gt_file_xopen(gt_str_get(outputfilename),
                                                 "a+");

    if (!ARGUMENTS(hitfile_bool))
    {
      GtStr *gi_numbers_txt;
      gi_numbers_txt = gt_str_new();

      gt_str_set(gi_numbers_txt, "gi_numbers.txt");
      unsigned long row_width = 150;

      if (gt_str_length(ARGUMENTS(giexpfile_name)) == 0 )
      {
        gt_str_set(ARGUMENTS(giexpfile_name), "nt.gz");
      }

      /* Datei fuer die GI-Nr. des XML-Files  */
      parsestruct.fp_giexp_file = gt_file_xopen(gt_str_get(gi_numbers_txt),
                                                   "w+");

      had_err = mg_xmlparser(parsestruct_ptr, fp_xmlfile, err);

      gt_file_delete(parsestruct.fp_giexp_file);
      gt_file_delete(fp_xmlfile);

      if (!had_err)
      {
        parsestruct.giexp_flag = 1;

        GtStrArray *giexpfile_name_array;
        giexpfile_name_array = gt_str_array_new();
        gt_str_array_add_cstr(giexpfile_name_array,
                              gt_str_get(ARGUMENTS(giexpfile_name)));

        /* Die Hit-Datei wird mit dem Modus w+ geoeffnet */
        parsestruct.fp_blasthit_file =
          gt_file_xopen(gt_str_get(parsestruct.hit_fastafile), "w+");

        had_err = gt_extractkeysfromfastafile(true,
                                              parsestruct.fp_blasthit_file,
                                              row_width,
                                              gi_numbers_txt,
                                              giexpfile_name_array,
                                              err);
        gt_file_delete(parsestruct.fp_blasthit_file);
        if (had_err)
        {
          had_err = 0;
        }
        if (!had_err)
        {
          parsestruct.hitseq = gt_bioseq_new(argv[parsed_args + 2], err);

          if (!parsestruct.hitseq)
          {
            had_err = -1;
          }
          if (!had_err)
          {
            /* Anzahl der Hit-DNA-Eintraege */
            nrofseq = gt_bioseq_number_of_sequences(parsestruct.hitseq);
            /* Speicherbereich reservieren fuer Zeiger auf die Indices der
               Hit-DNA-Eintraege in der GtBioseq-Struktur */
            hitnum = gt_calloc(nrofseq, sizeof (unsigned long));
            /* Hash erzeugen - Eintraege: Key - Hit-FASTA-Zeile;
               Value - Zeiger
               auf deren Indices in der GtBioseq - Struktur */
            parsestruct.hithash = gt_cstr_nofree_ulp_gt_hashmap_new();

            /* Hit-Fasta-File zeilenweise abarbeiten */
            for (loop_index = 0; loop_index < nrofseq; loop_index++)
            {
              /* Der Schluessel ist die Hit-FASTA-Zeile */
              descr_ptr_hit =
              (char *) gt_bioseq_get_description(parsestruct.hitseq,
                                                 loop_index);
              /* Position in der GtBioseq in den Speicher hitnum schreiben */
              hitnum[loop_index] = loop_index;

             /* Dem aktuellen Schluessel Zeige auf die Position in der GtBioseq
                zuordnen */
              if (!gt_cstr_nofree_ulp_gt_hashmap_get(parsestruct.hithash,
                                              descr_ptr_hit))
                gt_cstr_nofree_ulp_gt_hashmap_add(parsestruct.hithash,
                                               descr_ptr_hit,
                                               hitnum + loop_index);
            }
          }
        }
      }
    }

    if (!had_err)
    {
      /* Schreiben des Ausgabe-Headers */
      mg_outputwriter(parsestruct_ptr, NULL, NULL, NULL, 't', err);

      if (!ARGUMENTS(hitfile_bool))
      {
        /* Der Name des XML-Files mit den Blast-Hits ist das erste Argument
           nach dem Programmnamen */
        fp_xmlfile = gt_file_xopen(argv[parsed_args], "r");
      }
      parsestruct.giexp_flag = 1;

      /* Aufruf des xmlparsers; uebergeben werden: Zeiger auf die
         parser_array-Struktur der Filepointer auf die XML-Datei Zeiger auf
         die "Programmierumgebung" */
      had_err = mg_xmlparser(parsestruct_ptr, fp_xmlfile, err);
    }

    if (!had_err)
    {
      GtDlistelem *dlistelem;

      /* Schreiben des Ausgabe-Footers */
      mg_outputwriter(parsestruct_ptr, NULL, NULL, NULL, 'v', err);

      parsestruct_ptr->outlist = gt_dlist_new(statspair_cmp);

      /* Erzeugen einer sortierten Liste, indem die Hashtabelle einmal
         vollstaendig durchlaufen wird */
      (void) gt_cstr_nofree_ulp_gt_hashmap_foreach(parsestruct.resulthits,
                                                insert_into_outlist,
                                                &parsestruct, err);

      /* Ausgabe der sortierten Hit-Ergebnisse */
      for (dlistelem = gt_dlist_first(parsestruct_ptr->outlist);
           dlistelem != NULL;
           dlistelem = gt_dlistelem_next(dlistelem))
      {
        GtMgthStatsPair *pair = (GtMgthStatsPair*)
                                  gt_dlistelem_get_data(dlistelem);
        gt_error_check(err);

        HITSTRUCT(stat_pos) = *(pair->statpos);

        /* Ausgabe erfolgt nur, wenn der Anteil des Hits ueber dem Wert des
           Metagenomethreader-Argumentes liegt */
        if ((double)
            (HITSTRUCT(hitsnum)[HITSTRUCT(stat_pos)] /
             (double) HITSTRUCT(hitsnumber)) >= ARGUMENTSSTRUCT(percent_value))
        {
          mg_outputwriter(parsestruct_ptr, NULL, NULL, NULL, 's', err);
        }
        gt_free(pair);
      }
      gt_dlist_delete(parsestruct_ptr->outlist);

      /* Schreiben des Ausgabe-Footers */
      mg_outputwriter(parsestruct_ptr, NULL, NULL, NULL, 'f', err);
    }

    /* Freigabe der verschiedenen reservierten Speicherbereiche */
    gt_str_array_delete(parsestruct.query_array);
    gt_str_array_delete(parsestruct.hit_array);
    gt_str_array_delete(parsestruct.hit_hsp_array);
    gt_str_array_delete(parsestruct.hits_statistics.hits_statistic);
    gt_str_array_delete(parsestruct.key_tmp);

    gt_str_delete(outputfilename);
    gt_str_delete(parsestruct.xml_tag);
    gt_str_delete(parsestruct.buf_ptr);
    gt_str_delete(parsestruct.gi_def_tmp);
    gt_str_delete(parsestruct.gi_acc_tmp);
    gt_str_delete(parsestruct.hit_gi_nr_tmp);
    gt_str_delete(parsestruct.fasta_row);
    gt_str_delete(parsestruct.matrix_info.query_dna);
    gt_str_delete(parsestruct.matrix_info.query_def);
    gt_str_delete(parsestruct.hit_fastafile);
    gt_str_delete(parsestruct.xmlfile);
    gt_str_delete(parsestruct.result_hits);

    gt_array_delete(parsestruct.matrix_info.query_from);
    gt_array_delete(parsestruct.matrix_info.query_to);
    gt_array_delete(parsestruct.matrix_info.query_frame);
    gt_array_delete(parsestruct.matrix_info.hit_frame);
    gt_array_delete(parsestruct.value_tmp);

    gt_free(querynum);
    gt_free(parsestruct.hits_statistics.hitsnum);
    gt_free(parsestruct.hits_statistics.memory);

    /* Schliessen der XML-, Output-Datei und des Hit-Sequenz-Files */
    gt_file_delete(fp_xmlfile);
    gt_file_delete(parsestruct.fp_outputfile);

    /* GtHashtable loeschen */
    gt_hashtable_delete(parsestruct.queryhash);
    gt_hashtable_delete(parsestruct.resulthits);

    gt_hashtable_delete(parsestruct.hithash);
    gt_bioseq_delete(parsestruct.hitseq);
    gt_free(hitnum);

    gt_bioseq_delete(parsestruct.queryseq);
  }

  gt_str_delete(ARGUMENTS(curl_fcgi_db));
  gt_str_delete(ARGUMENTS(outputtextfile_name));
  gt_str_delete(ARGUMENTS(giexpfile_name));

  /* Rueckgabe des Fehlercode */
  return had_err;
}
genometools-1.5.1/src/mgth/metagenomethreader.h000066400000000000000000000175321211610345200216130ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef METAGENOMETHREADER_H
#define METAGENOMETHREADER_H

#include 
#include 
#include 
#include 
#include "core/array.h"
#include "core/array2dim_api.h"
#include "core/bioseq.h"
#include "core/dlist_api.h"
#include "core/error.h"
#include "core/hashmap-generic.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/str.h"
#include "core/str_array.h"
#include "core/versionfunc.h"

/* jeweils die Anzahl der zu betrachtenden XML-Tags; Definitionen werden auch
 * in Schleifenkoepfen verwendet */
#define MGTH_QUERY_SIZE           1
#define MGTH_HIT_SIZE             3
#define MGTH_HIT_TO_QUERY_SIZE    9

#define MGTH_SET             1
#define MGTH_UNSET           0
#define MGTH_MEMORY_SIZE     250

/* Makros zum Zugriff auf die Parsestruct-Strukturen und Substrukturen */
#define ARGUMENTS(PATH)\
             parsestruct.metagenomethreader_arguments.PATH
#define ARGUMENTSSTRUCT(PATH)\
             parsestruct_ptr->metagenomethreader_arguments.PATH
#define MATRIXSTRUCT(PATH)      parsestruct_ptr->matrix_info.PATH
#define XMLPARSERSTRUCT(PATH)   parsestruct_ptr->xmlparser_static.PATH
#define HITSTRUCT(PATH)         parsestruct_ptr->hits_statistics.PATH
#define FILEPOINTEROUT          parsestruct_ptr->fp_outputfile
#define HITFILEOUT              parsestruct_ptr->fp_giexp_file
#define PARSESTRUCT(PATH)       parsestruct_ptr->PATH

/* Strukturdefinition fuer die Eintraege in der Combined-Score-Matrix */
typedef struct
{
  double matrix_score;
  unsigned long count;
  GtArray *hit_number;
} CombinedScoreMatrixEntry;

/* Struktur zur Speicherung der Bereichsgrenzen kodierender Abschnitte */
typedef struct
{
  GtArray *from;
  GtArray *to;
} RegionStruct;

/* Strukturdefinition fuer die Struktur zur Speicherung ausschliesslich
   der Hit-Informationen, die zu einem syn-Score beitragen */
typedef struct
{
  GtStrArray *hit_gi,
   *hit_def,
   *hit_hsp_nr,
   *hit_from,
   *hit_to;
} HitInformation;

/* Strukturdefinition fuer die Eintraege in die Path-Matrix */
typedef struct
{
  double score;
  unsigned short path_frame;
} PathMatrixEntry;

/* Strukturdefinition, die zur Aufnahme der Kommandozeilenargumente
   dient */
typedef struct
{
  double synonomic_value,
    nonsynonomic_value,
    blasthit_end_value,
    stopcodon_queryseq,
    stopcodon_hitseq,
    frameshift_span,
    prediction_span,
    leavegene_value,
    percent_value;
  GtStr *curl_fcgi_db,
   *outputtextfile_name,
   *giexpfile_name;
  int outputfile_format,
    codon_mode;
  bool hitfile_bool,
    homology_mode,
    extended_mode,
    testmodus_mode;
  unsigned long min_as;
} MetagenomeThreaderArguments;

/* Typdefinition der Struktur zur Aufnahme von Informationen aus dem
   XML-File und den DNA-Informationen von Query und Hit */
typedef struct
{
  GtArray *query_frame,
   *hit_frame,
   *query_from,
   *query_to;
  GtStr *query_dna,
   *query_def;
  GtStrArray *hit_gi_nr,
   *hit_num,
   *hit_gi_def,
   *hit_acc,
   *fasta_row,
   *hit_from,
   *hit_to,
   *hit_dna,
   *hsp_qseq,
   *hsp_hseq;
} MatrixMemory;

/* Struktur fuer den Statistikbereich */
typedef struct
{
  GtStrArray *hits_statistic;
  unsigned long *hitsnum,
   *memory,
    hitsnumber,
    stat_pos;
} HitsStatistic;

/* Struktur fuer Variablen in der mg_xmlparser-Datei */
typedef struct
{
  unsigned short query_array_index_start,
    hit_array_index_start,
    hit_hsp_array_index_start,
    query_array_index_end,
    hit_array_index_end,
    hit_hsp_array_index_end;
  unsigned long hit_counter;
} XMLparser_static;

/* Struktur fuer Variablen in der mg_compute_gene_prediction-Datei */
typedef struct
{
  double matrixscore,
    matrixscore_before;
  short current_frame,
    frame_before,
    function_stop;
  unsigned long noncodingcounter,
    codingcounter;
} GenePrediction_static;

/* Typdefinition der Struktur, die als Data an die Expat-Funktionen
   uebergeben werden kann Hauptstruktur, die auch an die wesentlichen
   anderen Funktionen uebergeben wird */

typedef struct
{
  GtStrArray *query_array,
   *hit_array,
   *hit_hsp_array,
   *query_frame_tmp,
   *hit_frame_tmp,
   *key_tmp;
  GtStr *xml_tag,
   *buf_ptr,
   *hit_fastafile,
   *xmlfile,
   *gi_def_tmp,
   *gi_acc_tmp,
   *hit_gi_nr_tmp,
   *fasta_row,
   *result_hits;
  GtArray *value_tmp;
  GtBioseq *queryseq,
   *hitseq;
  GtFile *fp_outputfile,
   *fp_blasthit_file,
   *fp_giexp_file;
  GtHashtable *queryhash,
   *hithash,
   *resulthits;
  GtDlist *outlist;
  GtError *err;
  int had_err;
  unsigned short def_flag,
    hit_flag,
    hit_hsp_flag,
    xml_tag_flag,
    giexp_flag,
    gi_flag;
  unsigned long xml_linenumber,
    hits_memory;
  double syn,
    non_syn;
  MatrixMemory matrix_info;
  MetagenomeThreaderArguments metagenomethreader_arguments;
  HitsStatistic hits_statistics;
  XMLparser_static xmlparser_static;
  GenePrediction_static geneprediction_static;
} ParseStruct;

/* specific access mode of queryhash */
DECLARE_HASHMAP(char *, gt_cstr_nofree, unsigned long *, ulp,,)
DECLARE_SAFE_DEREF(unsigned long *, ulp)

/* Funktion, mit der der Metagenomethreader gestartet wird
   Parameter: Anzahl der Kommandozeilenargumente, Zeiger auf die
              Kommandozeilenargumente, GtError-Variable
   Returnwert: Fehlercode */
int gt_metagenomethreader(int argc, const char **argv, GtError *);

/* Funktion zur Ueberpruefung auf ein Stop-Codon
   Parameter:  Zeiger auf ein Triplet von Zeichen
   Returnwert: 0 = kein Stop-Codon, 1 = Stop-Codon */
short gt_check_stopcodon(char *);

/* Funktion zum Auslesen der Query-DNA Sequenz zu einem GI-Def Eintrag des
   XML-Files
   Parameter:  Zeiger auf StringArray (Sequenzen der Treffer zu einer
               Hit-GI-Nr), String-Zeiger auf die Hit-GI-Nr, String-Zeiger
               auf Hit-From und String-Zeiger auf den Hit-To String,
               GtError-Variable
   Returnwert: void */
int mg_curl(ParseStruct *, unsigned long, GtError *);

/* Funktion zur Berechnung der Combined-Scores
   Parameter: Zeiger auf die Parsestruct; Anzahl der Hits zur betrachteten
              Hit-GI-Nr; GtError-Variable
   Returnwert: void */
int mg_combinedscore(ParseStruct *, unsigned long, GtError *);

/* Funktion zur Ausgabe der berechneten Ergebnisse
   Parameter:  Zeiger auf ParseStruct-Struktur, CombinedScore-Matrix,
               die HitInformation-Struktur, die RegionStruct-Struktur,
               das Char-Zeichen, um welchen Bereich es sich handelt
   Returnwert: void */
void mg_outputwriter(ParseStruct *,
                     CombinedScoreMatrixEntry **,
                     HitInformation *, RegionStruct **, char, GtError *);

/* Funktion zur Bestimmung der zu einem Lesereahmen gehoerigen Matrix-Zeile
   Parameter: aktueller Leserahmen
   Returnwert: Matrixzeile */
short get_matrix_row(long);

/* Funktion zur Bestimmung des Leserahmens zu einer Matrix-Zeile
   Parameter: Matrixzeile
   Returnwert: Leserahmen */
short get_current_frame(long);

/* Funktion zur Berechnung des reversen Komplements
   Parameter: Zeiger auf eine Seq., Seq-Laenge, GtError-Variable
   Returnwert: had_err */
int mg_reverse_complement(char *, unsigned long, GtError *);

#endif
genometools-1.5.1/src/mgth/mg_codon.c000066400000000000000000000053351211610345200175310ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  Copyright (c) 2006 Gordon Gremme 
  Copyright (c) 2006 Center for Bioinformatics, University of Hamburg
  See LICENSE file or http://genometools.org/license.html for license details.
*/

/* This implementation was heavily inspired by code from Stefan Kurtz. */

/* erweitert fuer MG um den Fall unbekannter AS X und den Faellen
   der Degeneration an der dritten Stelle (R/Y/N) */

/*     modified for metagenomethreader; */

#include "mg_codon.h"

#define T_CODE 0
#define C_CODE 1
#define A_CODE 2
#define G_CODE 3
#define X_CODE 4

char mg_codon2amino(char n0, char n1, char n2)
{
  static char aminos[] = "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRR"
    "IIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGX";
  unsigned int code = 0;

  switch (n0)
  {
    case 'A':
    case 'a':
      code = A_CODE << 4;
      break;
    case 'C':
    case 'c':
      code = C_CODE << 4;
      break;
    case 'G':
    case 'g':
      code = G_CODE << 4;
      break;
    case 'T':
    case 't':
    case 'U':
    case 'u':
      code = T_CODE << 4;
      break;
    default:
      code = G_CODE << 4;
  }

  switch (n1)
  {
    case 'A':
    case 'a':
      code += A_CODE << 2;
      break;
    case 'C':
    case 'c':
      code += C_CODE << 2;
      break;
    case 'G':
    case 'g':
      code += G_CODE << 2;
      break;
    case 'T':
    case 't':
    case 'U':
    case 'u':
      /* code += T_CODE << 2; */
      break;
    default:
      code = G_CODE << 2;
  }

  switch (n2)
  {
    case 'A':
    case 'a':
    case 'R':
    case 'r':
      code += A_CODE;
      break;
    case 'C':
    case 'c':
      code += C_CODE;
      break;
    case 'G':
    case 'g':
      code += G_CODE;
      break;
    case 'T':
    case 't':
    case 'U':
    case 'u':
    case 'N':
    case 'n':
    case 'Y':
    case 'y':
      code += T_CODE;
      break;
    default:
      code += X_CODE;
  }

  return aminos[code];
}
genometools-1.5.1/src/mgth/mg_codon.h000066400000000000000000000022711211610345200175320ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  Copyright (c) 2006 Gordon Gremme 
  Copyright (c) 2006 Center for Bioinformatics, University of Hamburg
  See LICENSE file or http://genometools.org/license.html for license details.

    modiefied for metagenomethreader;
*/

#ifndef MG_CODON_H
#define MG_CODON_H

char mg_codon2amino(char, char, char);

#endif
genometools-1.5.1/src/mgth/mg_combinedscore.c000066400000000000000000000522451211610345200212450ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "mg_combinedscore.h"
#include "core/trans_table_api.h"

int mg_combinedscore(ParseStruct *parsestruct_ptr,
                     unsigned long hit_counter, GtError * err)
{
  int had_err = 0;

  unsigned short current_row,
    k;

  unsigned long contig_len = 0,
    contig_seq_diff = 0,
    hit_len = 0,
    hit_seq_diff = 0,
    i = 0,
    j = 0,
    contig_index = 0,
    hit_index = 0,
    gap_len = 0,
    ulhit_from = 0,
    ulhit_to = 0,
    mod = 0,
    *count_row;                        /* Hilfszaehler fuer die
                                          involvierten Hits fuer den jew.
                                          combined-Score */

  /* Matrix der Combined-Scores */
  CombinedScoreMatrixEntry **combinedscore_matrix;

  /* Hit-Informationen der relevanten Blast-Hits (relevant:
     Synonym/Nicht-Synonym Rate >=1) */
  HitInformation hit_information;

  /* Hilfszeile zur Abarbeitungs eines Hit */
  double *matrix_row;

  char contig_triplet[3],              /* Query-Triplet von dem die AS
                                          bestimmt werden soll */
    contig_as,                         /* Aminosaeure des uebergebenen
                                          Query-Triplets */
    hit_triplet[3],                    /* Hit-Triplet von dem die AS
                                          bestimmt werden soll */
    hit_as,                            /* Aminosaeure des uebergebenen
                                          Hit-Triplets */
   *contig_seq = NULL,                 /* Contig-DNA-Sequenz */
    *hit_seq = NULL,                   /* Hit-DNA-Sequenz */
    *contig_seq_tri = NULL,
    *hit_seq_tri = NULL,
    *contig_seq_ptr;

  const char *contig_as_ptr,
   *hit_as_ptr;

  GtTransTable *transtable;           /* Standard-Translationstabelle */

  transtable = gt_trans_table_new_standard(NULL);
  gt_assert(transtable);

  /* Check Umgebungsvariablen */
  gt_error_check(err);

  /* Zeiger auf den vollstaendigen Query-DNA Eintrag */
  contig_seq_ptr = gt_str_get(MATRIXSTRUCT(query_dna));

  /* contig_len legt die Anzahl der Spalten der Matrix fest */
  contig_len = gt_str_length(MATRIXSTRUCT(query_dna));

  /* Speicherplatzreservierung fuer die Combined-Score Matrix */
  gt_array2dim_calloc(combinedscore_matrix, 7, contig_len);

  /* Erstellen der GtArrays fuer die Hit-Nummer fuer jeden Matrix-Eintrag
     Ueber die Hit-Nummer erfolgt die Zuordnung zu den entsprechenden
     Blast-Hits in der Hit-Information-Struktur */
  for (k = 0; k < 7; k++)
  {
    for (j = 0; j < contig_len; j++)
    {
      combinedscore_matrix[k][j].hit_number =
        gt_array_new(sizeof (unsigned long));
    }
  }

  /* String-Arrays der Hit-Information Struktur anlegen */
  hit_information.hit_gi = gt_str_array_new();
  hit_information.hit_def = gt_str_array_new();
  hit_information.hit_hsp_nr = gt_str_array_new();
  hit_information.hit_from = gt_str_array_new();
  hit_information.hit_to = gt_str_array_new();

  /* fuer jeden Hit erfolgt eine Berechnung der Combined-Scores */
  for (i = 0; i < hit_counter; i++)
  {
    /* Speicherplatz fuer die Hilfszeilen wird reserviert */
    matrix_row = gt_calloc(contig_len, sizeof (double));
    count_row = gt_calloc(contig_len, sizeof (unsigned long));
    contig_seq_tri = gt_calloc(4, sizeof (char));
    hit_seq_tri = gt_calloc(4, sizeof (char));

    /* Zeiger auf die Proteinsequenzen von Hit und Query */
    contig_as_ptr = gt_str_array_get(MATRIXSTRUCT(hsp_qseq), i);
    hit_as_ptr = gt_str_array_get(MATRIXSTRUCT(hsp_hseq), i);

    /* Funktion zur Bestimmung der Zeile in der Matrix, die fuer den
       aktuellen Leserahmen steht */
    current_row = get_matrix_row(LONG_VALUE(MATRIXSTRUCT(query_frame), i));

    /* to-from+1 ist die anzahl der zu betrachtenden DNA-Basen,
       zusaetzlich +1 fuer das Stringendezeichen */
    contig_seq_diff =
      LONG_VALUE(MATRIXSTRUCT(query_to), i)
                 - LONG_VALUE(MATRIXSTRUCT(query_from), i) + 2;

    hit_len = strlen(gt_str_array_get(MATRIXSTRUCT(hit_dna), i));

    ulhit_from = atol(gt_str_array_get(MATRIXSTRUCT(hit_from), i));
    ulhit_to = atol(gt_str_array_get(MATRIXSTRUCT(hit_to), i));
    hit_seq_diff = ulhit_to - ulhit_from + 2;

    /* Ueberpruefen der Vereinbarkeit von Query- und Hit-Sequenz
       unterschiedliche Laengen sind nur in 3er Schritten erlaubt -> Gaps
       in der AS-Sequenz */
    if (contig_seq_diff - hit_seq_diff > 0)
    {
      mod = (contig_seq_diff - hit_seq_diff) % 3;
    }
    else
      mod = (hit_seq_diff - contig_seq_diff) % 3;

    if ((LONG_VALUE(MATRIXSTRUCT(query_to), i) > contig_len)
        || (hit_seq_diff - 1 != hit_len))
      mod = 1;

    /* Fehlermeldung bei Unvereinbarkeit */
    if (mod != 0)
    {
      gt_error_set(err,
                "sequences error: matching sequences do not fit in length.\
                 wrong FASTA-files or please delete entry %s!?",
                gt_str_array_get(MATRIXSTRUCT(hit_gi_def), i));
      had_err = -1;
    }

    /* Speicherplatreservierung fuer die Query-DNA-Seq. */
    contig_seq = gt_calloc(contig_seq_diff, sizeof (char));
    /* kopieren von contig_seq_diff-1 Zeichen */
    (void) snprintf(contig_seq, contig_seq_diff, "%s",
                    contig_seq_ptr +
                    (LONG_VALUE(MATRIXSTRUCT(query_from), i) - 1));

    /* die laenge der Hit-Sequenz kann max. der Laenge der QueryDNA Seq
       entsprechen */
    hit_seq = gt_calloc(hit_seq_diff, sizeof (char));
    /* kopieren von hit_seq_diff-1 Zeichen */
    (void) snprintf(hit_seq, hit_seq_diff, "%s",
                    gt_str_array_get(MATRIXSTRUCT(hit_dna), i));

    /* Bei einem negativen Leserahmen muss das Reverse-Komplement der
       Sequenz gebildet werden */
    if ((LONG_VALUE(MATRIXSTRUCT(query_frame), i) < 0) && !had_err)
    {
      /* bestimmen des Reverse-Komplement */
      had_err =
        mg_reverse_complement(contig_seq, contig_seq_diff - 1, err);
    }

    /* Gleiches Vorgehen bei negativen Leserahmen wie bei der Query-DNA */
    if ((LONG_VALUE(MATRIXSTRUCT(hit_frame), i) < 0) && !had_err)
    {
      had_err = mg_reverse_complement(hit_seq, hit_seq_diff - 1, err);
    }

    if (!had_err)
    {
      for (j = 0, contig_index = 0, hit_index = 0; j < hit_len - 2;
           j += 3, contig_index += 3, hit_index += 3)
      {
        if (contig_index < contig_len && hit_index < hit_len)
        {
          contig_as = contig_as_ptr[j / 3];
          hit_as = hit_as_ptr[j / 3];

          if (contig_as == '-')
          {
            gap_len = strspn(contig_as_ptr + j / 3, "-");
            hit_index += 3 * gap_len;
          }
          if (hit_as == '-')
          {
            gap_len = strspn(hit_as_ptr + j / 3, "-");
            contig_index += 3 * gap_len;
          }
          if (hit_as != '-' && contig_as != '-')
          {
            (void) snprintf(contig_seq_tri, 4, "%s",
                            contig_seq + contig_index);
            (void) snprintf(hit_seq_tri, 4, "%s", hit_seq + hit_index);

            if ((strspn(contig_seq_tri, "acgtuACGTU") == 3)
                && (strspn(hit_seq_tri, "acgtuACGTU") == 3))
            {
              /* Aktuelles Hit-Triplet */
              hit_triplet[0] = hit_seq[hit_index];
              hit_triplet[1] = hit_seq[hit_index + 1];
              hit_triplet[2] = hit_seq[hit_index + 2];

              /* Aktuelles Query-Triplet */
              contig_triplet[0] = contig_seq[contig_index];
              contig_triplet[1] = contig_seq[contig_index + 1];
              contig_triplet[2] = contig_seq[contig_index + 2];

              /* Bestimmen der AS der jeweiligen Triplets */
              had_err = gt_trans_table_translate_codon(transtable,
                                                       contig_triplet[0],
                                                       contig_triplet[1],
                                                       contig_triplet[2],
                                                       &contig_as,
                                                       err);
              if (!had_err) {
                had_err = gt_trans_table_translate_codon(transtable,
                                                         hit_triplet[0],
                                                         hit_triplet[1],
                                                         hit_triplet[2],
                                                         &hit_as,
                                                         err);
              }
            }
          }

          /* Aufruf der Funktion fill_matrix; berechnet die
             Combined-Scores uebergeben werden: die Combined-Score-Matrix
             Hit-AS des aktuellen Triplets Query-AS des aktuelen Triplets
             der aktuelle Leserahmen j - hier: die Position in der
             Query-Sequenz hit-len und contig-len i - hier: die aktuell
             betrachtete Hit-Sequenz Zeiger auf die parsestruct die
             Hilfs-Matrix-Zeile Contig- und Hit-Sequenz */
          fill_matrix(combinedscore_matrix,
                      &hit_as,
                      &contig_as,
                      current_row,
                      contig_index,
                      hit_index,
                      hit_len,
                      contig_len,
                      i,
                      parsestruct_ptr,
                      matrix_row,
                      count_row, contig_seq, hit_seq, &hit_information);
        }
      }
      gt_free(contig_seq);
      gt_free(hit_seq);
      gt_free(contig_seq_tri);
      gt_free(hit_seq_tri);
      gt_free(matrix_row);
      gt_free(count_row);
    }
    else
    {
      gt_free(contig_seq);
      gt_free(hit_seq);
      gt_free(contig_seq_tri);
      gt_free(hit_seq_tri);
      gt_free(matrix_row);
      gt_free(count_row);

      break;
    }
  }

  if (!had_err)
  {
    /* nach dem erstellen der Combined-Score Matrix muessen die einzelnen
       Positionen noch mit der Anzahl der beteiligten Hits normalisiert
       werden */
    for (j = 0; j < contig_len; j++)
    {
      for (k = 0; k < 7; k++)
      {
        if (combinedscore_matrix[k][j].count != 0)
        {
          combinedscore_matrix[k][j].
            matrix_score /= combinedscore_matrix[k][j].count;
        }
      }
    }

    /* Aufruf der Funktion computepath - DP-Ansatz uebergeben werden: die
       Combined-Score-Matrix Anzahl Zeilen Anzahl Spalten */
    had_err = mg_computepath(combinedscore_matrix,
                             &hit_information,
                             7, contig_len, parsestruct_ptr, err);
  }

  for (i = 0; i < 7; i++)
  {
    for (j = 0; j < contig_len; j++)
    {
      gt_array_delete(combinedscore_matrix[i][j].hit_number);
    }
  }

  gt_array2dim_delete(combinedscore_matrix);

  gt_trans_table_delete(transtable);

  gt_str_array_delete(hit_information.hit_gi);
  gt_str_array_delete(hit_information.hit_def);
  gt_str_array_delete(hit_information.hit_hsp_nr);
  gt_str_array_delete(hit_information.hit_from);
  gt_str_array_delete(hit_information.hit_to);

  return had_err;
}

/* Funktion zur Bestimmung der dem Leserahmen entsprechenden Matrix-Zeile */
short get_matrix_row(long frame_fct)
{
  gt_assert(frame_fct >= -3 && frame_fct <= 3);
  return 3 - frame_fct;         /* [-3..3] -> [6..0] */
}

/* Umkehrfunktion zu get_matrix_row - aus der Matrix-Zeile wird der Leserahmen
   bestimmt */
short get_current_frame(long row_fct)
{
  gt_assert(row_fct >= 0 && row_fct <= 6);
  return 3 - row_fct;           /* [0..6] -> [3..-3] */
}

static void fill_matrix(CombinedScoreMatrixEntry **combinedscore_matrix,
                        char *hit_amino,
                        char *query_amino,
                        short current_row_fct,
                        unsigned long position_contig,
                        unsigned long position_hit,
                        unsigned long hit_len,
                        unsigned long contig_len,
                        unsigned long hit_number,
                        ParseStruct *parsestruct_ptr,
                        double *matrix_row,
                        unsigned long *count_row_fct,
                        char *contig_seq,
                        char *hit_seq, HitInformation *hit_information)
{
  unsigned long j = 0,
    nr_of_strings = 0;
  unsigned short k = 0;

  unsigned long query_from;
  unsigned long query_to;

  query_from = LONG_VALUE(MATRIXSTRUCT(query_from), hit_number) - 1;
  query_to = LONG_VALUE(MATRIXSTRUCT(query_to), hit_number) - 1;

  /* das Ende von Blast-Hits innerhalb der Query-Sequenz wird mit -10
     bewertet */
  if (position_hit == hit_len - 3
      && *(long *) MATRIXSTRUCT(query_to) != contig_len && k == 3)
  {
    /* Wenn der Leserahmen negativ ist, muessen die Combined-Scores von
       Rechts nach Links in die Combined-Score Matrix eingetragen werden -
       also ausgehend vom Query-to Wert */
    if (current_row_fct > 3)
    {
      matrix_row[POSITION
                 (MATRIXSTRUCT(query_to), hit_number, -position_contig,
                  -k + 1)] += ARGUMENTSSTRUCT(blasthit_end_value);
    }
    else
    {
      matrix_row[POSITION
                 (MATRIXSTRUCT(query_from), hit_number, position_contig,
                  k - 1)] += ARGUMENTSSTRUCT(blasthit_end_value);
    }
  }
  /* Stop-Codon in der Query-Sequenz, kein Stop-Codon in der Hit-Sequenz */
  else if (*hit_amino != '*' && *query_amino == '*')
  {
    /* Berechnung der Combined-Scores immer fuer die 3 DNA-Basen des
       Triplets Stop-Codon in der Query-Sequnez wird mit -2.0 bestraft;
       Anzahl der beteiligten Hits am Combined-Score um 1 erhoeht */
    for (k = 0; k < 3; k++)
    {
      add_scores(parsestruct_ptr, matrix_row, count_row_fct,
                 current_row_fct, hit_number, position_contig, k,
                 ARGUMENTSSTRUCT(stopcodon_hitseq));
    }
  }
  /* Stop-Codon in der Hit-Sequnez, kein Stop-Codon in der Query-Sequenz */
  else if (*hit_amino == '*' || *query_amino == '*')
  {
    /* Berechnung der Combined-Scores immer fuer die 3 DNA-Basen des
       Triplets Stop-Codon in der Hit-Sequnez wird mit -5.0 bestraft;
       Anzahl der beteiligten Hits am Combined-Score um 1 erhoeht */
    for (k = 0; k < 3; k++)
    {
      add_scores(parsestruct_ptr, matrix_row, count_row_fct,
                 current_row_fct, hit_number, position_contig, k,
                 ARGUMENTSSTRUCT(stopcodon_queryseq));
    }
  }
  /* AS von Hit und Query sind identisch */
  else if (*hit_amino == *query_amino)
  {
    /* Berechnung der Combined-Scores immer fuer die 3 DNA-Basen des
       Triplets */
    for (k = 0; k < 3; k++)
    {
      if (!ARGUMENTSSTRUCT(homology_mode))
      {
        /* DNA-Basen stimmen nicht ueberein - synonymer Austausch; hit_seq
           ist Zeiger auf die erste DNA-Base der Sequenz position ist die
           aktuelle Position in der DNA-Sequenz und k die Position im
           aktuellen Triplet */
        if (tolower(hit_seq[position_hit + k]) !=
            tolower(contig_seq[position_contig + k]))
        {
          /* Bei Uebereinstimmung der AS und keiner Basen-Uebereinstimmung
             wird der Zaheler der Synonymen Basen-Austausche erhoeht, der
             aktuellen Position in der Combined-Score-Matrix der Wert 1
             hinzuaddiert und gleichzeitig die Anzahl der beteiligten Hits
             ebenfalls um 1 erhoeht */
          add_scores(parsestruct_ptr, matrix_row, count_row_fct,
                     current_row_fct, hit_number, position_contig, k,
                     ARGUMENTSSTRUCT(synonomic_value));
          parsestruct_ptr->syn++;
        }
      }
      else
      {
        /* Experimenteller Status - Suche nach Homologien statt
           Orieentierung an Synonymen-Basenaustauschen */
        if (tolower(hit_seq[position_hit + k]) ==
            tolower(contig_seq[position_contig + k]))
        {
          /* Bei Uebereinstimmung der AS und keiner Basen-Uebereinstimmung
             wird der Zaheler der Synonymen Basen-Austausche erhoeht, der
             aktuellen Position in der Combined-Score-Matrix der Wert 1
             hinzuaddiert und gleichzeitig die Anzahl der beteiligten Hits
             ebenfalls um 1 erhoeht */
          add_scores(parsestruct_ptr, matrix_row, count_row_fct,
                     current_row_fct, hit_number, position_contig, k,
                     ARGUMENTSSTRUCT(synonomic_value));
          parsestruct_ptr->syn++;
        }
      }
    }
  }
  /* AS stimmen nicht ueberein - nicht synonymer Base-Austausch */
  else if (*hit_amino != *query_amino)
  {
    /* Berechnung der Combined-Scores immer fuer die 3 DNA-Basen des
       Triplets */
    for (k = 0; k < 3; k++)
    {
      /* DNA-Basen stimmen nicht ueberein - nicht-synonymer Austausch;
         hit_seq ist Zeiger auf die erste DNA-Base der Sequenz position
         ist die aktuelle Position in der DNA-Sequenz und k die Position
         im aktuellen Triplet */
      if (tolower(hit_seq[position_hit + k]) !=
          tolower(contig_seq[position_contig + k]))
      {
        /* Bei Nicht-Uebereinstimmung der AS und keiner
           Basen-Uebereinstimmung wird der Zaheler der Nicht-Synonymen
           Basen-Austausche erhoeht, vom Wert der aktuellen Position in
           der Combined-Score-Matrix der Wert 1 subtrahiert und
           gleichzeitig die Anzahl der beteiligten Hits ebenfalls um 1
           erhoeht */
        add_scores(parsestruct_ptr, matrix_row, count_row_fct,
                   current_row_fct, hit_number, position_contig, k,
                   ARGUMENTSSTRUCT(nonsynonomic_value));
        parsestruct_ptr->non_syn++;
      }
    }
  }
  /* Sequenzende und damit Ende der Bearbeitung des aktuellen Hits
     erreicht */
  if (hit_len - 3 == position_hit)
  {
    /* Falls die Non-Syn Anzahl 0 ist wird sie auf 1 gesetzt, um eine
       Division durch 0 zu vermeiden */
    if (parsestruct_ptr->non_syn == 0.0)
      parsestruct_ptr->non_syn = 1.0;
    /* Falls die Rate von Syn zu Non-Syn Austauschen kleiner als 1 ist,
       werden die Ergebnisse nicht betrachtet, da mit hoher WS keine
       codierende Sequenz vorliegt */
    if (parsestruct_ptr->syn / parsestruct_ptr->non_syn < 1.0)
    {
      parsestruct_ptr->syn = 0.0;
      parsestruct_ptr->non_syn = 0.0;
    }
    /* codierende Sequenz liegt mit hoher WS vor, da syn/non_syn >=1 */
    else
    {
      /* Abspeichern der Hit-Informationen */
      gt_str_array_add_cstr(hit_information->hit_gi,
                        gt_str_array_get(MATRIXSTRUCT(hit_gi_nr), hit_number));
      gt_str_array_add_cstr(hit_information->hit_def,
                        gt_str_array_get(MATRIXSTRUCT(hit_gi_def),
                                     hit_number));
      gt_str_array_add_cstr(hit_information->hit_hsp_nr,
                        gt_str_array_get(MATRIXSTRUCT(hit_num), hit_number));
      gt_str_array_add_cstr(hit_information->hit_from,
                        gt_str_array_get(MATRIXSTRUCT(hit_from), hit_number));
      gt_str_array_add_cstr(hit_information->hit_to,
                        gt_str_array_get(MATRIXSTRUCT(hit_to), hit_number));

      nr_of_strings = gt_str_array_size(hit_information->hit_def) - 1;

      /* Uebertragen der Ergebnisse des aktuellen Hits in die
         Combined-Score Matrix */
      for (j = query_from; j < query_to + 1; j++)
      {
        combinedscore_matrix[current_row_fct][j].matrix_score +=
          matrix_row[j];
        combinedscore_matrix[current_row_fct][j].count += count_row_fct[j];
        gt_array_add(combinedscore_matrix[current_row_fct][j].hit_number,
                  nr_of_strings);
      }
      parsestruct_ptr->syn = 0.0;
      parsestruct_ptr->non_syn = 0.0;
    }
  }
}

static void add_scores(ParseStruct *parsestruct_ptr,
                       double *matrix_row,
                       unsigned long *count_row_fct,
                       short current_row_fct,
                       unsigned long hit_number,
                       unsigned long position,
                       unsigned short k, double score)
{
  /* Wenn der Query-Leserahmen negativ ist, muessen die Combined-Scores
     von Rechts nach Links in die Combined-Score Matrix eingetragen werden
     - also ausgehend vom Query-to Wert */
  if (current_row_fct > 3)
  {
    matrix_row[POSITION(MATRIXSTRUCT(query_to), hit_number, -position, -k)]
      += score;
    count_row_fct[POSITION
                  (MATRIXSTRUCT(query_to), hit_number, -position, -k)] +=
      1;
  }
  else
  {
    matrix_row[POSITION(MATRIXSTRUCT(query_from), hit_number, position, k)]
      += score;
    count_row_fct[POSITION
                  (MATRIXSTRUCT(query_from), hit_number, position, k)] +=
      1;
  }
}
genometools-1.5.1/src/mgth/mg_combinedscore.h000066400000000000000000000057311211610345200212500ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef MG_COMBINEDSCORE_H
#define MG_COMBINEDSCORE_H

#include "core/codon_api.h"
#include "metagenomethreader.h"
#include "mg_computepath.h"

#define LONG_VALUE(VALUE, INDEX)\
                *(long*)gt_array_get((VALUE), (INDEX))

#define POSITION(QUERY_FROM, HIT_NUMBER, POSITION, K)\
           LONG_VALUE(QUERY_FROM, HIT_NUMBER)+(POSITION)+(K)-1

/* Funktion zum Eintragen des Scores in die Combined-Score Matrix
   Parameter: Combined-Score-Matrix, Hit-AS, Query-AS, aktueller
              Leserahmen der Query-DNA, Position in der Query-Seq.,
              Position in der Hit-Seq., Laenge des Blast-Hits, Laenge der
              Contig-Seq, Hit-Nr, Zeiger auf die ParseStruct-Struktur,
              Hilfezeile fuer die Combined-Scores, Hilfszeile der Counts,
              Query-DNA-Seq, Hit-DNA-Seq, Zeiger auf die
              HitInformation-Struktur
   Returnwert: void */
static void fill_matrix(CombinedScoreMatrixEntry **,
                        char *,
                        char *,
                        short,
                        unsigned long,
                        unsigned long,
                        unsigned long,
                        unsigned long,
                        unsigned long,
                        ParseStruct *,
                        double *,
                        unsigned long *,
                        char *,
                        char *,
                        HitInformation *);

/* Funktion zur Berechnung des Matrixscore an der entsprechenden Position
   der Combined-Score-Matrix
   Parameter: Zeiger auf ParseStruct, Hilfszeilen matrix_row u. count_row,
              aktuelle Matrix-Zeile, Hit-Number, Position in der Query-DNA,
              Position im Triplet, Score - abh. vom Fall (syn, nonsyn,
              stop-codon in Query- oder Hit-Sequence, Blast-Hit-Ende)
   Returnwert: void */
static void add_scores(ParseStruct *,
                       double *,
                       unsigned long *,
                       short,
                       unsigned long,
                       unsigned long,
                       unsigned short,
                       double);

#endif
genometools-1.5.1/src/mgth/mg_compute_gene_prediction.c000066400000000000000000001204411211610345200233150ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#include 

#include "mg_compute_gene_prediction.h"

#include "core/unused_api.h"

/* Funktion zur Berechnung der Start-Stop Informationen der genkodierenden
   Bereiche sowie deren Leserahmen
   Parameter: row, column, max-Wert der letzten Spalte der Opt-Path-Matrix,
              Path-Matrix, CombinedScore-Matrix, GtArray des opt. Pfades
              (Leserahmen), Hit-Information, Zeiger auf ParseStruct, Zeiger
              auf RegionStruct, Zeiger auf den Speicherbereich zum
              Abspeichern der beteiligten Hits an einem Ergebnis
   Returnwert: void */
static void gene_prediction(unsigned short,
                            unsigned long,
                            double,
                            PathMatrixEntry **,
                            CombinedScoreMatrixEntry **,
                            GtArray *,
                            HitInformation *,
                            ParseStruct *,
                            RegionStruct **, unsigned long *, GtError *);

/* Funktion zur Vereinigung von genkodierenden Bereichen innerhalb des
   selben Leserahmen
   Parameter: Zeiger auf ParseStruct, Zeiger auf RegionStruct,
              der "reale" Leserahmen
   Returnwert: void */
static void genemergeprocessing(ParseStruct *, RegionStruct **, GtError *);

/* Funktion zur Identifizierung von Frameshifts
   Parameter: Zeiger auf ParseStruct, Zeiger auf RegionStruct,
              der "reale" Leserahmen
   Returnwert: void */
static int frameshiftprocessing(ParseStruct *, RegionStruct **, short,
                                GtError *);

/* Funktion zur Ueberpruefung von Sequenzbereichen auf beinhaltende
   Stop-Codons
   Parameter: Zeiger auf ParseStruct, from-Wert, to-Wert,
              aktueller Leserahmen
   Returnwert: 0 - kein Stop-Codon; 1 - Stop-Codon */
static int check_coding(ParseStruct *,
                        unsigned long, unsigned long, short, GtError *);

/* Funktion zum sortierten Einfuegen neuer Bereichsgrenzen kodierender
   Abschnitte in das real-Frame-Array
   Parameter: Zeiger auf RegionStruct-Struktur, GtArrays mit den From- und
              To-Werten des real-Frames,Arrays mit den From- und To-Werten
              der einzufuegenden Abschnitte, Index des Real-Frames,Index
              des tmp-Frames, real-Frame, Zeilenindex;
   Returnwert: void */
static void merge_array(RegionStruct **,
                        GtArray *,
                        GtArray *,
                        GtArray *,
                        GtArray *,
                        unsigned long,
                        unsigned long, short, unsigned short);

/* Funktion zum sortierten der GtArrays mit den neu einzufuegenden
   Bereichsgrenzen
   Parameter: GtArrays der sortierten From- und To-Werte, GtArrays mit den
              From- und To-Werten der zu sortierenden GtArrays;
   Returnwert: void */
static void sort_realtmp(GtArray *, GtArray *, GtArray *, GtArray *);

int mg_compute_gene_prediction(CombinedScoreMatrixEntry
                               **combinedscore_matrix,
                               PathMatrixEntry **path_matrix,
                               unsigned long contig_len,
                               HitInformation *hit_information,
                               ParseStruct *parsestruct_ptr, GtError * err)
{
  int had_err = 0;

  /* Variablen zur Bestimmung des Maximums der letzten Path-Matrix-Spalte */
  double max_lastcolumn = DBL_MIN,
    max_tmp;

  /* Zaehlvariablen fuer die Zeilen */
  unsigned short row_index,
    row_idx,
    real_frame = 0;

  /* Zaehlvariable fuer die Haeufigkeiten der einzelnen Frames sowie
     Variable fuer den Frame-Score */
  unsigned long *frame_counter,
    real_frame_score;

  /* Struktur zur Speicherung der kodierenden Bereiche (from-to - Werte) */
  RegionStruct **regionmatrix;

  /* GtArray fuer das Speichern der Frames des optimalen Pfades */
  GtArray *frame_path_array;
  frame_path_array = gt_array_new(sizeof (unsigned short));

  gt_error_check(err);

  /* Bestimmen des/der Max-Werte(s) der letzten Spalte der path_matrix */
  for (row_index = 0; row_index < 7; row_index++)
  {
    max_tmp = path_matrix[row_index][contig_len - 1].score;

    if (max_tmp > max_lastcolumn)
    {
      max_lastcolumn = max_tmp;
    }
  }

  /* ausgehend von den Max-Werten startet die Vorhersage codierender
     Bereiche */
  for (row_index = 0; row_index < 7; row_index++)
  {
    /* Matrix-Score der aktuellen Zeile entspricht dem Max-Wert */
    if (path_matrix[row_index][contig_len - 1].score == max_lastcolumn)
    {
      gt_array2dim_calloc(regionmatrix, 7, 1);
      /* frame-counter zaehlt die Auftritts-haeufigkeiten der einzelnen
         Frames im opt. Pfad */
      frame_counter = gt_calloc(7, sizeof (unsigned long));
      real_frame_score = 0;

      for (row_idx = 0; row_idx < 7; row_idx++)
      {
        regionmatrix[row_idx][0].from = gt_array_new(sizeof (unsigned long));
        regionmatrix[row_idx][0].to = gt_array_new(sizeof (unsigned long));
      }
      /* Aufruf der Genvorhersagemethode */
      gene_prediction(row_index,
                      contig_len - 1,
                      max_lastcolumn,
                      path_matrix,
                      combinedscore_matrix,
                      frame_path_array,
                      hit_information,
                      parsestruct_ptr, regionmatrix, frame_counter, err);

      /* Falls es fuer Frame X kodierende Abschnitte gibt, werden diese
         von hinten nach vorne in der regionmatrix abgespeichert - hier
         werden sie nun umgedreht, um sie in aufsteigender Form vorliegen
         zu haben */
      for (row_idx = 0; row_idx < 7; row_idx++)
      {
        if (gt_array_size(regionmatrix[row_idx][0].from) > 0)
        {
          gt_array_reverse(regionmatrix[row_idx][0].from);
          gt_array_reverse(regionmatrix[row_idx][0].to);
        }
      }

      /* XXX bestimmen des vermutlich realen Frames - Verbesserung
         moeglich? XXX */
      for (row_idx = 0; row_idx < 7; row_idx++)
      {
        if ((frame_counter[row_idx] > real_frame_score)
            && (gt_array_size(regionmatrix[row_idx][0].from) > 0))
        {
          real_frame_score = frame_counter[row_idx];
          real_frame = row_idx;
        }
      }

      /* Aufruf der Funktion, in der auf moegliche Frame-Shifts geprueft
         wird */
      had_err =
        frameshiftprocessing(parsestruct_ptr, regionmatrix, real_frame,
                             err);

      if (!had_err)
      {
        /* Aufruf der Funktion, in der auf moegliche Vereinbarkeit
           kodierender Bereiche geprueft wird */
        genemergeprocessing(parsestruct_ptr, regionmatrix, err);

        /* Aufruf der Ausgabefunktion und Ausgabe der Ergebnisse */
        mg_outputwriter(parsestruct_ptr, combinedscore_matrix,
                        hit_information, regionmatrix, 'h', err);

        for (row_idx = 0; row_idx < 7; row_idx++)
        {
          gt_array_delete(regionmatrix[row_idx][0].from);
          gt_array_delete(regionmatrix[row_idx][0].to);
        }
      }
      gt_array2dim_delete(regionmatrix);
      gt_free(frame_counter);
    }
  }
  gt_array_delete(frame_path_array);

  return had_err;
}

static void gene_prediction(unsigned short row,
                            unsigned long column,
                            double max_lastcolumn,
                            PathMatrixEntry **path_matrix,
                            CombinedScoreMatrixEntry
                            **combinedscore_matrix,
                            GtArray * frame_path_array,
                            HitInformation *hit_information,
                            ParseStruct *parsestruct_ptr,
                            RegionStruct **regionmatrix,
                            unsigned long *frame_counter, GtError * err)
{
  unsigned long column_from,
    column_to;

  gt_error_check(err);

  /* die ersten beiden Spalten werden gesondert bearbeitet, da immer zwei
     Spalten zur Beurteilung, ob es sich um kodierende oder
     nicht-kodierende Positionen handelt, benoetigt werden. Zudem werden
     erst so die Berechnungen der Sequenzlaengen kodierender Bereiche bei
     Framewechsel und auch bei Wechsel von kodierendem zu
     nicht-kodierendem Bereich */
  if (column == gt_str_length(MATRIXSTRUCT(query_dna)) - 1)
  {
    GENEPREDSTRUCT(matrixscore_before) = path_matrix[row][column].score;
    GENEPREDSTRUCT(frame_before) = path_matrix[row][column].path_frame;

    /* hinzufuegen des aktuellen Leserahmens - als Zeile - in das
       frame_path-Array */
    gt_array_add(frame_path_array, row);
    /* Zaehlen der Frame-Haeufigkeiten */
    frame_counter[row] += 1.0;
  }
  else if (column == gt_str_length(MATRIXSTRUCT(query_dna)) - 2)
  {
    GENEPREDSTRUCT(matrixscore) = path_matrix[row][column].score;
    GENEPREDSTRUCT(current_frame) = path_matrix[row][column].path_frame;

    /* hinzufuegen des aktuellen Leserahmens - als Zeile - in das
       frame_path-Array */
    gt_array_add(frame_path_array, row);
    /* Zaehlen der Frame-Haeufigkeiten */
    frame_counter[row] += 1.0;
  }
  /* ab hier beginnt die eigentliche Bearbeitung des optimalen Pfades in
     der Combined-Score-Matrix - berechnet wird jeweils die Position
     column+2 */
  else
  {
    /* hinzufuegen des aktuellen Leserahmens - als Zeile - in das
       frame_path-Array */
    gt_array_add(frame_path_array, row);
    /* Zaehlen der Frame-Haeufigkeiten */
    frame_counter[row] += 1.0;

    /* nur wenn der vorherige Matrixscore(column+2) hoeher ist als der
       Aktuelle(column+1) ist, handelt es sich bei Position column+2 um
       eine kodierende Position */
    if (GENEPREDSTRUCT(matrixscore_before) - GENEPREDSTRUCT(matrixscore) >
        0)
    {
      /* Laenge des kodierenden Abschnittes um 1 erhoehen */
      ++GENEPREDSTRUCT(codingcounter);

      /* Wechsel des Leserahmens von Position column+2 zu Position
         column+1; kodierender zu kodierender Abschnitt */
      if (GENEPREDSTRUCT(current_frame) != GENEPREDSTRUCT(frame_before)
          && GENEPREDSTRUCT(noncodingcounter) == 0)
      {
        /* Speichern der Grenzen des kodierenden Bereichs vor dem
           Framewechsel */
        column_from = column + 2;
        column_to = column + GENEPREDSTRUCT(codingcounter) + 1;

        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].from,
                  column_from);
        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].to,
                  column_to);

        GENEPREDSTRUCT(codingcounter) = 0;
      }
      /* wenn noncodingcounter > 0 liegt ein Wechsel von nicht-kodierender
         zu kodierender Region vor */
      else if (GENEPREDSTRUCT(noncodingcounter) > 0)
      {
        GENEPREDSTRUCT(noncodingcounter) = 0;
      }
    }
    /* else-Fall: nicht-kodierender Positionen */
    else
    {
      /* Wechsel von kodierendem zu nicht-kodierendem Abschnitt */
      if (GENEPREDSTRUCT(codingcounter) > 0)
      {
        /* Speichern der Grenzen des vorangegangenen kodierenden Bereichs */
        column_from = column + 3;
        column_to = column + GENEPREDSTRUCT(codingcounter) + 2;

        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].from,
                  column_from);
        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].to,
                  column_to);

        GENEPREDSTRUCT(codingcounter) = 0;
      }
      GENEPREDSTRUCT(noncodingcounter)++;
    }

    /* Sichern der Vorgaengerinformationen (column+1) und einlesen der
       aktuellen Informationen (column) */
    GENEPREDSTRUCT(matrixscore_before) = GENEPREDSTRUCT(matrixscore);
    GENEPREDSTRUCT(frame_before) = GENEPREDSTRUCT(current_frame);

    GENEPREDSTRUCT(matrixscore) =
      path_matrix[GENEPREDSTRUCT(current_frame)][column].score;
    GENEPREDSTRUCT(current_frame) =
      path_matrix[GENEPREDSTRUCT(current_frame)][column].path_frame;
  }

  /* die ersten beiden Spalten der Combined-Score-Matrix werden in einem
     Fall bearbeitet */
  if (column == 0)
  {
    /* das Function Stop-Flag wird gesetzt */
    GENEPREDSTRUCT(function_stop) = 1;
    /* if-Fall: kodierende Base an Position 1 */

    if (GENEPREDSTRUCT(matrixscore_before) - GENEPREDSTRUCT(matrixscore) >
        0)
    {
      ++GENEPREDSTRUCT(codingcounter);

      /* Wechsel des Leserahmens - kodierender zu kodierender Abschnitt */
      if (GENEPREDSTRUCT(current_frame) != GENEPREDSTRUCT(frame_before)
          && GENEPREDSTRUCT(noncodingcounter == 0))
      {
        column_from = column + 1;
        column_to = column + GENEPREDSTRUCT(codingcounter);

        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].from,
                  column_from);
        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].to,
                  column_to);

        GENEPREDSTRUCT(codingcounter) = 0;
      }
      if (GENEPREDSTRUCT(noncodingcounter) > 0)
      {
        GENEPREDSTRUCT(noncodingcounter) = 0;
      }
    }
    /* else-Fall: nicht-kodiernde Base an Position 1 */
    else
    {
      /* der Bereich vor der nicht-kodiernden Position 1 ist kodierend */
      if (GENEPREDSTRUCT(codingcounter) > 0)
      {
        column_from = column + 2;
        column_to = column + GENEPREDSTRUCT(codingcounter) + 1;

        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].from,
                  column_from);
        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].to,
                  column_to);

        GENEPREDSTRUCT(codingcounter) = 0;
      }
      GENEPREDSTRUCT(noncodingcounter)++;
    }

    /* Wenn der Wert in der ersten Spalte der Combined-Score-Matrix
       positiv ist, ist die Position 0 kodierend */
    if (GENEPREDSTRUCT(matrixscore) > 0)
    {
      GENEPREDSTRUCT(codingcounter)++;

      /* Falls der noncodingcounter > 0 ist, ist der Bereich vor 0
         nicht-kodierend */
      if (GENEPREDSTRUCT(noncodingcounter) > 0)
      {
        column_from = 0;
        column_to = 0;

        gt_array_add(regionmatrix[GENEPREDSTRUCT(current_frame)][0].from,
                  column_from);
        gt_array_add(regionmatrix[GENEPREDSTRUCT(current_frame)][0].to,
                  column_to);

        GENEPREDSTRUCT(noncodingcounter) = 0;
      }
      else
      {
        /* if-Fall: Wechsel des Leserahmens von kodierendem zu kodierendem
           Abschnitt */
        if (GENEPREDSTRUCT(current_frame) != GENEPREDSTRUCT(frame_before))
        {
          /* Vorgaengerbereich von Position 0 ist kodierend */
          column_from = 1;
          column_to = GENEPREDSTRUCT(codingcounter) - 1;

          gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].from,
                    column_from);
          gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].to,
                    column_to);

          /* Position 0 ist ebenfalls kodierend */
          column_from = 0;
          column_to = 0;

          gt_array_add(regionmatrix[GENEPREDSTRUCT(current_frame)][0].from,
                    column_from);
          gt_array_add(regionmatrix[GENEPREDSTRUCT(current_frame)][0].to,
                    column_to);

          GENEPREDSTRUCT(codingcounter) = 1;
        }
        /* else-Fall: Speichern des kodierenden Bereichs von 0 bis x */
        else
        {
          column_from = 0;
          column_to = GENEPREDSTRUCT(codingcounter) - 1;

          gt_array_add(regionmatrix[GENEPREDSTRUCT(current_frame)][0].from,
                    column_from);
          gt_array_add(regionmatrix[GENEPREDSTRUCT(current_frame)][0].to,
                    column_to);
        }
      }
    }
    /* Position 0 ist nicht-kodierend */
    else
    {
      /* Falls codingcounter > 0, dann ist der vor 0 liegende Bereich
         kodierend */
      if (GENEPREDSTRUCT(codingcounter) > 0)
      {
        column_from = 1;
        column_to = column + GENEPREDSTRUCT(codingcounter);

        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].from,
                  column_from);
        gt_array_add(regionmatrix[GENEPREDSTRUCT(frame_before)][0].to,
                  column_to);

        GENEPREDSTRUCT(codingcounter) = 0;
      }
    }
    GENEPREDSTRUCT(noncodingcounter) = 0;
    GENEPREDSTRUCT(codingcounter) = 0;
  }
  /* solange das Stop-Flag nicht gesetzt ist wird die CombinedScore-Matrix
     rekursiv spaltenweise abgearbeitet */
  if (!GENEPREDSTRUCT(function_stop))
  {
    if (column > 0)
      gene_prediction(path_matrix[row][column].path_frame,
                      column - 1,
                      max_lastcolumn,
                      path_matrix,
                      combinedscore_matrix,
                      frame_path_array,
                      hit_information,
                      parsestruct_ptr, regionmatrix, frame_counter, err);
    else
      gene_prediction(path_matrix[row][column].path_frame,
                      column,
                      max_lastcolumn,
                      path_matrix,
                      combinedscore_matrix,
                      frame_path_array,
                      hit_information,
                      parsestruct_ptr, regionmatrix, frame_counter, err);
  }
  else
    GENEPREDSTRUCT(function_stop) = 0;
}

static int frameshiftprocessing(ParseStruct *parsestruct_ptr,
                                RegionStruct **regionmatrix,
                                short real_frame, GtError * err)
{
  int had_err = 0;

  unsigned short row_index,
    check_bp = 0;

  unsigned long arraysize,
    arraysize_realframe,
    GT_UNUSED arraysize_real,
    arraysize_tmp,
    array_idx,
    arrayreal_idx = 0,
    from_tmp,
    to_tmp,
    from_real,
    to_real,
    from_min = 0,
    to_min = 0;

  long min_value,
    min_value_tmp = LONG_MAX;

  GtArray *tmp_from;
  GtArray *tmp_to;
  GtArray *real_from;
  GtArray *real_to;
  GtArray *real_fromtmp;
  GtArray *real_totmp;
  GtArray *realfrom;
  GtArray *realto;

  gt_error_check(err);

  tmp_from = gt_array_new(sizeof (unsigned long));
  tmp_to = gt_array_new(sizeof (unsigned long));
  real_from = gt_array_new(sizeof (unsigned long));
  real_to = gt_array_new(sizeof (unsigned long));
  real_fromtmp = gt_array_new(sizeof (unsigned long));
  real_totmp = gt_array_new(sizeof (unsigned long));
  realfrom = gt_array_new(sizeof (unsigned long));
  realto = gt_array_new(sizeof (unsigned long));

  /* Vergleich mit allen anderen Frames - Der reale Frame ist der Frame
     mit der hoechsten Haeufigkeit (frame_counter) */
  for (row_index = 0; row_index < 7; row_index++)
  {
    /* Frameshift nur zwischen realem und von diesem verschiedenen Frames
       moeglich */
    if (row_index != real_frame)
    {
      /* Anzahl der kodierenden Bereiche im zu vergleichendem Leserahmen */
      arraysize = gt_array_size(regionmatrix[row_index][0].from);

      if (arraysize > 0)
      {
        /* alle kodierenden Bereiche des zu vergleichenden Frames werden
           betrachtet */
        for (array_idx = 0; array_idx < arraysize; array_idx++)
        {
          /* Grenzen des zu Betrachtenden Abschnitts - Abschnitte liegen
             in aufsteigender Reihenfolge vor */
          from_tmp =
            *(unsigned long *) gt_array_get(regionmatrix[row_index][0].from,
                                            array_idx);
          to_tmp =
            *(unsigned long *) gt_array_get(regionmatrix[row_index][0].to,
                                            array_idx);

          /* Aufruf der Methode zur Ueberpruefung auf Stop-Codons im
             kodierendem Bereich des zu vergleichendem Frames -
             ueberprueft wird der kodierende Abschnitt bezgl. Stop-Codons
             im realen Frame */
          check_bp = check_coding(parsestruct_ptr,
                                  from_tmp, to_tmp, real_frame, err);

          if (check_bp || !check_bp)
          {
            arraysize_realframe =
              gt_array_size(regionmatrix[real_frame][0].from);

            /* alle kodierenden Bereiche des realen Frames werden
               betrachtet */
            for (arrayreal_idx = 0; arrayreal_idx < arraysize_realframe;
                 arrayreal_idx++)
            {
              /* Grenzen des kodierenden Bereichs des realen Frames */
              from_real =
                *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].
                                             from, arrayreal_idx);
              to_real =
                *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].
                                             to, arrayreal_idx);

              /* Bestimmen der Frames von realem und zu vergleichendem
                 Frame mit minimalem Abstand */
              if (from_real > from_tmp)
              {
                min_value = from_real - from_tmp;
              }
              else
                min_value = from_tmp - from_real;

              /* kodierender Bereich mit minimalem Abstand wird
                 gespeichert */
              if (min_value < min_value_tmp)
              {
                min_value_tmp = min_value;
                from_min = from_real =
                  *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].
                                               from, arrayreal_idx);
                to_min = to_real =
                  *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].
                                               to, arrayreal_idx);
              }
            }

            /* Falls der betrachtete Abschnitt des zu vergleichenden
               Frames innerhalb des max. Abstandes liegt (per GtOption bei
               Programmaufruf einstellbar) und der kodierende Bereich kein
               Stop-Codon enthaelt werden die Grenzen des Abschnittes im
               real_fromtmp- bzw. real_totmp-Array abgespeichert */
            if (!check_bp
                && ((to_tmp + ARGUMENTSSTRUCT(frameshift_span) > from_min)
                    || (to_min + ARGUMENTSSTRUCT(frameshift_span) >
                        from_tmp)))
            {
              gt_array_add(real_fromtmp, from_tmp);
              gt_array_add(real_totmp, to_tmp);
            }
            /* ansonsten im from_tmp- bzw. to_tmp-Array */
            else
            {
              gt_array_add(tmp_from, from_tmp);
              gt_array_add(tmp_to, to_tmp);
            }
          }
          else
          {
            had_err = -1;
          }
        }
      }

      if (!had_err)
      {
        /* die from- to-Grenzen des zu vergleichenden GtArrays werden
           aktualisiert */
        gt_array_delete(regionmatrix[row_index][0].from);
        gt_array_delete(regionmatrix[row_index][0].to);

        regionmatrix[row_index][0].from = gt_array_clone(tmp_from);
        regionmatrix[row_index][0].to = gt_array_clone(tmp_to);
        gt_array_reset(tmp_from);
        gt_array_reset(tmp_to);
      }
    }
  }

  if (!had_err)
  {
    /* Anzahl der kodierenden Bereiche im realen- und im
       real_fromtmp-Array werden bestimmt */
    arraysize_real = gt_array_size(regionmatrix[real_frame][0].from);
    arraysize_tmp = gt_array_size(real_fromtmp);

    /* Falls im tmp-Array Eintraege vorhanden sind, sind diese in das
       GtArray der kodierenden Abschnitte der realen-Frames einzutragen */
    if (arraysize_tmp > 0)
    {
      /* sortieren der neu einzutragenden kodierenden Abschnitte anhand
         des From-Wertes */
      sort_realtmp(realfrom, realto, real_fromtmp, real_totmp);

      /* bisher: rueckwaerts von hinten angegebene Bereichsgrenzen -
         danach: Bereichsgrenzen von vorne nach hinten */
      gt_array_reverse(realfrom);
      gt_array_reverse(realto);

      /* sortiertes einfuegen der neuen Bereichsgrenzen in das GtArray
         bestehender kodierender Bereiche des realen Frames */
      merge_array(regionmatrix,
                  real_from,
                  real_to, realfrom, realto, 0, 0, real_frame, row_index);

      /* aktualisieren der Bereichsgrenzen im GtArray des realen-Frames */
      gt_array_delete(regionmatrix[real_frame][0].from);
      gt_array_delete(regionmatrix[real_frame][0].to);

      regionmatrix[real_frame][0].from = gt_array_clone(real_from);
      regionmatrix[real_frame][0].to = gt_array_clone(real_to);
    }
  }

  gt_array_delete(tmp_from);
  gt_array_delete(tmp_to);
  gt_array_delete(real_from);
  gt_array_delete(real_to);
  gt_array_delete(real_fromtmp);
  gt_array_delete(real_totmp);
  gt_array_delete(realfrom);
  gt_array_delete(realto);

  return had_err;
}

static void genemergeprocessing(ParseStruct *parsestruct_ptr,
                                RegionStruct **regionmatrix, GtError * err)
{
  unsigned short row_index;
  short check_bp;
  unsigned long array_idx,
    arraysize,
    from_tmp,
    to_tmp,
    from_tmp_next,
    to_tmp_real,
    function_stop = 0;
  GtArray *tmp_from;
  GtArray *tmp_to;

  gt_error_check(err);

  tmp_from = gt_array_new(sizeof (unsigned long));
  tmp_to = gt_array_new(sizeof (unsigned long));

  /* Frames werden nacheinander abgearbeitet - zeilenkodiert */
  for (row_index = 0; row_index < 7; row_index++)
  {
    /* bestimmen der Anzahl kodierender Bereiche im aktuell betrachteten
       Frame */
    arraysize = gt_array_size(regionmatrix[row_index][0].from);

    gt_array_reset(tmp_from);
    gt_array_reset(tmp_to);

    if (arraysize > 1)
    {
      /* die kodierenden Bereiche werden nacheinander abgearbeitet */
      for (array_idx = 0; array_idx < arraysize - 1;)
      {
        /* ist gt_array_size des tmp-Arrays > 0 wurden bereits Aenderungen
           vorgenommen und die neuen Bereichsgrenzen-Werte muessen
           verwendet werden */
        if (gt_array_size(tmp_from) > 0)
        {
          from_tmp = *(unsigned long *) gt_array_get_last(tmp_from);
          to_tmp = *(unsigned long *) gt_array_get_last(tmp_to);
        }
        /* ansonsten auslesen der Bereichsgrenzen aus dem "original" */
        else
        {
          from_tmp =
            *(unsigned long *) gt_array_get(regionmatrix[row_index][0].from,
                                            array_idx);
          to_tmp =
            *(unsigned long *) gt_array_get(regionmatrix[row_index][0].to,
                                            array_idx);
        }

        ++array_idx;
        function_stop = 0;

        do
        {
          /* auslesen der Grenzen des nachfolgenden kodierenden Bereiches */
          from_tmp_next =
            *(unsigned long *) gt_array_get(regionmatrix[row_index][0].from,
                                            array_idx);
          to_tmp_real =
            *(unsigned long *) gt_array_get(regionmatrix[row_index][0].to,
                                            array_idx);

          /* zusammenlegen kodierender Bereiche nur, wenn diese innerhalb
             der per GtOption angegebenen Spanbreite liegen */
          if (to_tmp + ARGUMENTSSTRUCT(prediction_span) > from_tmp_next)
          {
            /* es wurden noch keine Eintragungen vorgenommen - der erste
               kodierende Abschnitt wird in das tmp-Array eingetragen */
            if (gt_array_size(tmp_from) == 0)
            {
              gt_array_add(tmp_from, from_tmp);
              gt_array_add(tmp_to, to_tmp);
            }

            /* Ueberpruefen, ob zwischen den kodierenden Abschnitten
               Stop-Codons liegen */
            check_bp = check_coding(parsestruct_ptr,
                                    to_tmp, from_tmp_next, row_index, err);

            /* kein Stop-Codon gefunden */
            if (!check_bp)
            {
              /* befindet sich schon ein Eintrag im temp-Array, muss der
                 letzte Eintrag wieder entfernt werden */
              if (gt_array_size(tmp_from) > 0)
              {
                (void) gt_array_pop(tmp_from);
                (void) gt_array_pop(tmp_to);
              }
              /* Speichern der neuen Bereichsgrenzen */
              gt_array_add(tmp_from, from_tmp);
              gt_array_add(tmp_to, to_tmp_real);

              ++array_idx;
            }
            /* Stop-Codon gefunden - der next-Abschnitt wird ebenfalls in
               das tmp-Array eingetragen; die Bearbeitung kann hier
               abgebrochen werden, da das Stop-Codon auch im Vergleich zu
               den anderen Abschnitten eine Vereinigung verhindert */
            else
            {
              gt_array_add(tmp_from, from_tmp_next);
              gt_array_add(tmp_to, to_tmp_real);

              function_stop = 1;
            }
          }
          /* Abstand der kodierenden Bereiche > als angegebene
             Spannbreite, auch hier kann die Bearbeitung beendet werden */
          else
          {
            gt_array_add(tmp_from, from_tmp_next);
            gt_array_add(tmp_to, to_tmp_real);

            function_stop = 1;
          }
          /* Bearbeitung solange, bis keine weiteren Abschnitte vorliegen
             oder das Stop-Flag gesetzt ist */
        } while (array_idx < arraysize && !function_stop);
      }

      /* aktualisieren der Bereichsgrenzen */
      gt_array_delete(regionmatrix[row_index][0].from);
      gt_array_delete(regionmatrix[row_index][0].to);
      regionmatrix[row_index][0].from = gt_array_clone(tmp_from);
      regionmatrix[row_index][0].to = gt_array_clone(tmp_to);
    }
  }
  gt_array_delete(tmp_from);
  gt_array_delete(tmp_to);
}

static int check_coding(ParseStruct *parsestruct_ptr,
                        unsigned long from,
                        unsigned long to, short current_row, GtError * err)
{
  int had_err = 0;

  unsigned long startpoint = 0,
    endpoint = 0,
    contig_len = 0;

  long diff;

  short current_frame = 0,
    found = 0;

  GtStr *query_seq;

  char *contig_seq_ptr = NULL,
    contig_seq_tri[4] = { '\0', '\0', '\0', '\0' };

  gt_error_check(err);

  /* Start- und Endsequenzpositionen der in AS umzuwandelnden Sequenz */
  startpoint = from;
  endpoint = to;

  contig_len = gt_str_length(MATRIXSTRUCT(query_dna));
  query_seq = gt_str_new_cstr(gt_str_get(MATRIXSTRUCT(query_dna)));
  contig_seq_ptr = gt_str_get(query_seq);

  /* Bestimmung des aktuellen Frames aus der Zeilennummer */
  current_frame = get_current_frame(current_row);

  /* Bestimmen der Laenge der umzuwandelnden Sequenz */
  diff = startpoint - endpoint;
  if (diff < 0)
    diff = (-1) * diff;

  /* nur bei 3 oder mehr DNA-Basen ist eine Umwandlung in eine AS-Sequenz
     sinnvoll bzw. machbar */
  if (!(diff < 3))
  {
    /* if: aktueller Leserahmen ist -1, -2 oder -3 */
    if (current_frame < 0)
    {
      /* fuer die weiteren Berechnungen erfolgt eine Multiplikation mit -1
       */
      current_frame *= -1;
      /* das reverse Komplement der Sequenz wird gebildet - erweiterte
         reverse_complement-Funktion beruecksichtigt das erweiterte
         DNA-Alphabet */
      had_err = mg_reverse_complement(contig_seq_ptr, contig_len, err);

      /* Der Startpunkt muss im Fall negativer Leserahmen neu berechnet
         werden */
      startpoint = contig_len - 1 - to;
      endpoint = contig_len - from;
    }

    if (!had_err)
    {
      /* ist der Startpunkt < 3 ist die Startposition 0, 1 oder 2 */
      if (startpoint < 3)
      {
        startpoint = current_frame - 1;
      }
      /* sonst: Berechnung der Startposition anhand der gegebenen Formel */
      else
      {
        startpoint -= (((startpoint) - current_frame) % 3);
        startpoint -= 1;
      }

      /* abschreiten der Sequenz */
      while ((startpoint <= endpoint - 2) && !found)
      {
        /* DNA-Basen-Triplet einlesen */

        contig_seq_tri[0] = tolower(contig_seq_ptr[startpoint]);
        contig_seq_tri[1] =
          tolower(contig_seq_ptr[startpoint + 1]);
        contig_seq_tri[2] =
          tolower(contig_seq_ptr[startpoint + 2]);

        found = gt_check_stopcodon(contig_seq_tri);

        /* Startwert um 3 Basen weitersetzen */
        startpoint += 3;
      }
    }
    else
    {
      found = -1;
    }
  }
  gt_str_delete(query_seq);

  return found;

}

static void merge_array(RegionStruct **regionmatrix,
                        GtArray * real_from_ar,
                        GtArray * real_to_ar,
                        GtArray * real_fromtmp,
                        GtArray * real_totmp,
                        unsigned long real_index,
                        unsigned long tmp_index,
                        short real_frame, unsigned short row_index)
{
  unsigned long real_from,
    real_to,
    tmp_from,
    tmp_to;

  /* Fall 1: Eintraege im GtArray des realen Frames sind abgearbeitet,
     Eintraege im tmp-Array noch nicht */
  if (!(real_index < gt_array_size(regionmatrix[real_frame][0].from))
      && tmp_index < gt_array_size(real_fromtmp))
  {
    /* Bereichsgrenzen des Realtmp-Arrays - from/to-Werte */
    real_from = *(unsigned long *) gt_array_get(real_fromtmp, tmp_index);
    real_to = *(unsigned long *) gt_array_get(real_totmp, tmp_index);

    /* solange sich noch Eintraege im realtmp-Array befinden */
    while (tmp_index < gt_array_size(real_fromtmp))
    {
      /* hinzufuegen der Bereichsgrenzen */
      gt_array_add(real_from_ar, real_from);
      gt_array_add(real_to_ar, real_to);

      tmp_index++;

      /* nur wenn noch weitere Eintraege vorhanden sind, werden die
         naechsten Bereichsgrenzen ausgelesen */
      if (tmp_index < gt_array_size(real_fromtmp))
      {
        real_from = *(unsigned long *) gt_array_get(real_fromtmp, tmp_index);
        real_to = *(unsigned long *) gt_array_get(real_totmp, tmp_index);
      }
    }
  }
  /* Fall 2: Eintraege im GtArray des realen Frames sind noch nicht
     abgearbeitet, Eintraege im tmp-Array abgearbeitet */
  else if (!(tmp_index < gt_array_size(real_fromtmp))
           && real_index < gt_array_size(regionmatrix[real_frame][0].from))
  {
    /* Bereichsgrenzen des Real-Arrays - from/to-Werte */
    tmp_from =
      *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].from,
                                   real_index);
    tmp_to =
      *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].to,
                                   real_index);

    /* solange sich noch Eintraege im real-Array befinden */
    while (real_index < gt_array_size(regionmatrix[real_frame][0].from))
    {
      /* hinzufuegen der Bereichsgrenzen */
      gt_array_add(real_from_ar, tmp_from);
      gt_array_add(real_to_ar, tmp_to);

      real_index++;

      /* nur wenn noch weitere Eintraege vorhanden sind, werden die
         naechsten Bereichsgrenzen ausgelesen */
      if (real_index < gt_array_size(regionmatrix[real_frame][0].from))
      {
        tmp_from =
          *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].from,
                                       real_index);
        tmp_to =
          *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].to,
                                       real_index);
      }
    }
  }
  /* Fall 3: Es sind noch Eintraege in beiden GtArrays vorhanden */
  else if ((tmp_index < gt_array_size(real_fromtmp))
           && real_index < gt_array_size(regionmatrix[real_frame][0].from))
  {
    /* Bereichsgrenzen des Realtmp- und des real-Arrays - from/to-Werte */
    tmp_from =
      *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].from,
                                   real_index);
    tmp_to =
      *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].to,
                                   real_index);
    real_from = *(unsigned long *) gt_array_get(real_fromtmp, tmp_index);
    real_to = *(unsigned long *) gt_array_get(real_totmp, tmp_index);

    /* Fall: realtmp-Abschnitt liegt vor dem real_frame Abschnitt */
    if (real_from < tmp_from)
    {
      /* solange es noch Eintraege gibt, die vor dem real_frame-Abschnitt
         liegen... */
      while (tmp_index < gt_array_size(real_fromtmp) && real_from < tmp_from)
      {
        /* ... werden die bereichsgrenzen Eingetragen... */
        gt_array_add(real_from_ar, real_from);
        gt_array_add(real_to_ar, real_to);

        tmp_index++;

        /* und der naechste realtmp-Eintrag eingelesen */
        if (tmp_index < gt_array_size(real_fromtmp))
        {
          real_from =
            *(unsigned long *) gt_array_get(real_fromtmp, tmp_index);
          real_to = *(unsigned long *) gt_array_get(real_totmp, tmp_index);
        }
      }
      /* rekursiver Aufruf der Sortierfunktion unter Beruecksichtigung der
         neu Eingetragenen Abschnitte */
      merge_array(regionmatrix,
                  real_from_ar,
                  real_to_ar,
                  real_fromtmp,
                  real_totmp,
                  real_index, tmp_index, real_frame, row_index);
    }
    /* real_frame- vor dem realtmp-Abschnitt */
    else if (tmp_from < real_from)
    {
      /* solange es noch Eintraege gibt, die vor dem realtmp-Abschnitt
         liegen... */
      while (real_index < gt_array_size(regionmatrix[real_frame][0].from)
             && tmp_from < real_from)
      {
        /* ... werden die bereichsgrenzen Eingetragen... */
        gt_array_add(real_from_ar, tmp_from);
        gt_array_add(real_to_ar, tmp_to);

        real_index++;

        /* und der naechste real_frame-Eintrag eingelesen */
        if (real_index < gt_array_size(regionmatrix[real_frame][0].from))
        {
          tmp_from =
            *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].from,
                                         real_index);
          tmp_to =
            *(unsigned long *) gt_array_get(regionmatrix[real_frame][0].to,
                                         real_index);
        }
      }
      /* rekursiver Aufruf der Sortierfunktion unter Beruecksichtigung der
         neu Eingetragenen Abschnitte */
      merge_array(regionmatrix,
                  real_from_ar,
                  real_to_ar,
                  real_fromtmp,
                  real_totmp,
                  real_index, tmp_index, real_frame, row_index);
    }
  }
}

static void sort_realtmp(GtArray * realfrom,
                         GtArray * realto,
                         GtArray * real_fromtmp, GtArray * real_totmp)
{
  unsigned long index_outer,
    index_inner,
    max_value = 0,
    from,
    to,
    from_tmp = 0,
    to_tmp = 0;

  /* durchlaufen des GtArrays mit einer aeusseren und einer inneren Schleife
   */
  for (index_outer = 0; index_outer < gt_array_size(real_fromtmp);
       index_outer++)
  {
    /* die innere Schleife bestimmt den naechsten maximalen Wert im GtArray */
    for (index_inner = 0; index_inner < gt_array_size(real_fromtmp);
         index_inner++)
    {
      from = *(unsigned long *) gt_array_get(real_fromtmp, index_inner);
      to = *(unsigned long *) gt_array_get(real_totmp, index_inner);

      /* Fall: es gibt bereits Eintraege im tmp-Array */
      if (gt_array_size(realfrom) > 0)
      {
        /* der aktuelle from-Wert ist groesser als der tmp-Wert und
           kleiner als der letzte max-Wert */
        if ((from > from_tmp) && (from < max_value))
        {
          from_tmp = from;
          to_tmp = to;
        }
      }
      /* Fall: keine Eintraege im tmp-Array */
      else
      {
        /* bestimmen des max-Wertes */
        if (from > from_tmp)
        {
          from_tmp = from;
          to_tmp = to;
        }
      }
    }
    /* Speichern des max-Wertes */
    gt_array_add(realfrom, from_tmp);
    gt_array_add(realto, to_tmp);

    /* merken des letzten max-Wertes */
    max_value = from_tmp;
    from_tmp = 0;
    to_tmp = 0;
  }
}

short gt_check_stopcodon(char *contig_seq_ptrfct)
{
  unsigned short codon_status = 0;

  /* jeder if-Zweig ueberprueft entsprechend des
     Metagenomethreader-Arguments zur Verwendung alternativer Start-Codons
     auf Start-Codons */
  if (!strcmp(contig_seq_ptrfct, "tga")
      || !strcmp(contig_seq_ptrfct, "taa")
      || !strcmp(contig_seq_ptrfct, "tag")
      || !strcmp(contig_seq_ptrfct, "tar")
      || !strcmp(contig_seq_ptrfct, "uga")
      || !strcmp(contig_seq_ptrfct, "uaa")
      || !strcmp(contig_seq_ptrfct, "uag")
      || !strcmp(contig_seq_ptrfct, "uar"))
  {
    codon_status = 1;
  }

  return codon_status;
}
genometools-1.5.1/src/mgth/mg_compute_gene_prediction.h000066400000000000000000000030251211610345200233200ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef MG_COMPUTE_GENE_PREDICTION_H
#define MG_COMPUTE_GENE_PREDICTION_H

#include 
#include 
#include "metagenomethreader.h"

#define GENEPREDSTRUCT(PATH)    parsestruct_ptr->geneprediction_static.PATH

/* Funktion zur Berechnung der Genkodierenden-Sequenzbereiche
   Parameter: CombinedScore-Matrix, Opt-Path-Matrix, column bzw. Laenge
              der Query-Sequenz, Hit-Informationen, ParseStruct-Zeiger
   Returnwert: void */
int mg_compute_gene_prediction(CombinedScoreMatrixEntry **,
                               PathMatrixEntry **,
                               unsigned long,
                               HitInformation *, ParseStruct *, GtError *);
#endif
genometools-1.5.1/src/mgth/mg_computepath.c000066400000000000000000000157311211610345200207610ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "mg_computepath.h"
#include "core/mathsupport.h"

/* Funktion zur Berechnung der erlaubten Vorgaenger-Leserahmen
   Parameter: aktueller Leserahmen, Position in der Query-Sequence,
   (Zeiger auf) GtArray der moeglichen Vorgaenger
   Returnwert: void */
static void compute_precursors(short, unsigned long, short *);

enum {
  NUM_PRECURSORS = 3,
};

int mg_computepath(CombinedScoreMatrixEntry **combinedscore_matrix,
                   HitInformation *hit_information,
                   unsigned long rows,
                   unsigned long contig_len,
                   ParseStruct *parsestruct_ptr, GtError * err)
{
  int had_err = 0;

  /* Initialisieren der Matrix fuer die Pfadberechnung */
  PathMatrixEntry **path_matrix;

  /* i: Zaehlvariable fuer die Matrix-Zeilen; k: Zaehlvariable Precursors
     (von 0 bis max 2) maxpath_frame: Speichern des vorherigen Frames von
     dem der max-Wert berechnet wird */
  unsigned short row_index = 0,
    precursor_index = 0,
    precursors_row = 0,
    maxpath_frame = 0;

  /* Position in der Query-DNA */
  unsigned long column_index = 0;

  /* Variablen fuer den aktuellen Frame, den vorherigen Frame(speichert
     einen Wert aus precursors[], die Zeile des vorherigen Frames, GtArray
     mit den Precursors-Frames */
  short current_frame = 0,
    precursors_frame = 0,
    precursors[NUM_PRECURSORS];

  /* q ist der Wert, der bei Aus- oder Eintreten in ein Gen auf dem
     Forward- bzw. Reverse-Strang berechnet wird */
  double q = ARGUMENTSSTRUCT(leavegene_value),
    max_new = 1,
    max_old = 1;

  /* Speicherreservierung fuer die Path-Matrix - Groesse entsprechend der
     CombinedScore-Matrix */
  gt_array2dim_calloc(path_matrix, 7, contig_len);

  gt_error_check(err);

  /* fuer die erste Spalte der Path-Matrix wird die erste Spalte der
     CombinedScore-Matrix uebernommen */
  for (row_index = 0; row_index < rows; row_index++)
  {
    path_matrix[row_index][0].score =
      combinedscore_matrix[row_index][0].matrix_score;
    path_matrix[row_index][0].path_frame = row_index;
  }

  /* Spaltenweise Berechnung des opt. Pfades */
  for (column_index = 1; column_index < contig_len; column_index++)
  {
    for (row_index = 0; row_index < rows; row_index++)
    {
      /* Zaehlvariable fuer die Zeile wird umgerechnet in den entsprechenden
         Leserahmen */
      current_frame = get_current_frame(row_index);
      /* Aufruf der Methode zum Berechnen der moeglichen Leserahmen anhand von
         aktuellem Leserahmen und der Query-DNA-Sequenz */
      compute_precursors(current_frame,
                         column_index,
                         precursors);

      /* der max-Wert der moeglichen Vorgaenger wird berechnet */
      for (precursor_index = 0;
           precursor_index < NUM_PRECURSORS
             && (precursors[precursor_index] != UNDEFINED);
           ++precursor_index)
      {
        /* aktueller Vorgaengerleserahmen - es gibt max. 3 moegliche
           Vorgaenger */
        precursors_frame = precursors[precursor_index];
        /* Vorgaengerleserahmen wird umgerechnet in die entsprechende
           Matrix-Zeile */
        precursors_row = get_matrix_row(precursors_frame);

        /* der DP-Algo umfasst 3 moegliche Faelle
           1. Fall: Wechsel vom Reversen- auf den Forward-Strang bzw.
           umgekehrt */
        if ((current_frame < 0 && precursors_frame > 0) ||
            (current_frame > 0 && precursors_frame < 0))
        {
            max_new = path_matrix[precursors_row][column_index-1].score +
                      combinedscore_matrix[row_index][column_index].matrix_score
                      + 2*q;
        }
        /* 2. Fall: Einfacher Wechsel des Leserahmens, also von + zu +
           bzw.- zu - */
        else if (current_frame != 0 && precursors_frame != current_frame)
        {
            max_new = path_matrix[precursors_row][column_index-1].score +
                      combinedscore_matrix[row_index][column_index].matrix_score
                      + q;
        }
        /* 3. Fall: Leserahmen wird beibehalten bzw. Wechsel von kodierend zu
           nicht-kodierend oder umgekehrt */
        else
        {
            max_new = path_matrix[precursors_row][column_index-1].score +
                      combinedscore_matrix[row_index][column_index]
                      .matrix_score;
        }

        /* Bestimmen des Max-Wertes der max. 3 Moeglichkeiten und Speichern der
           Zeile, von der der Max-Wert stammt */
        if (gt_double_compare(max_new, max_old) > 0)
        {
            max_old = max_new;
            maxpath_frame = precursors_row;
        }
      }

      /* Speichern des Max-Wertes und der "Vorgaenger"-Zeile;
         zuruecksetzen der Variablen */
      path_matrix[row_index][column_index].score      = max_old;
      path_matrix[row_index][column_index].path_frame = maxpath_frame;

      max_new = DBL_MIN;
      max_old = DBL_MIN;
      maxpath_frame = 0;
    }
  }

  /* Aufruf der Methode zur Genvorhersage */
  had_err = mg_compute_gene_prediction(combinedscore_matrix,
                                       path_matrix,
                                       contig_len,
                                       hit_information,
                                       parsestruct_ptr, err);

  gt_array2dim_delete(path_matrix);

  return had_err;
}

/* Methode zur Berechnung der moeglichen Vorgaengerleserahmen */
static void compute_precursors(short current_frame,
                               unsigned long position,
                               short *precursors_fct)
{
  short j = 0;

  /* Formel zur Bestimmung moeglicher Vorgaengerleserahmen anhand der
     aktuellen Position in der Query-DNA */
  j = (position)%NUM_PRECURSORS + 1;

  /* 3 Faelle zur Bestimmung der Vorgaengermenge */
  if (current_frame == 0)
  {
    precursors_fct[0] = j;
    precursors_fct[1] = 0;
    precursors_fct[2] = (-1)*j;
  }
  else if ((current_frame > 0 ? current_frame : (-1) * current_frame) == j)
  {
    precursors_fct[0] = current_frame;
    precursors_fct[1] = 0;
    precursors_fct[2] = (-1)*current_frame;
  }
  else
  {
    precursors_fct[0] = current_frame;
    precursors_fct[1] = UNDEFINED;
    precursors_fct[2] = UNDEFINED;
  }
}
genometools-1.5.1/src/mgth/mg_computepath.h000066400000000000000000000025401211610345200207600ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef MG_COMPUTEPATH_H
#define MG_COMPUTEPATH_H

#include 
#include "metagenomethreader.h"
#include "mg_compute_gene_prediction.h"

#define UNDEFINED   9

/* Funktion zur DP-Berechnung der Pfade durch die Combined-Score-Matrix
   Parameter: Combined-Score Matrix, Anzahl Zeilen, Anzahl Spalten
   Returnwert: void */
int mg_computepath(CombinedScoreMatrixEntry **,
                   HitInformation *hit_information,
                   unsigned long, unsigned long, ParseStruct *, GtError *);
#endif
genometools-1.5.1/src/mgth/mg_outputwriter.c000066400000000000000000001620541211610345200212260ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#include 

#include "mg_outputwriter.h"

#include "core/hashmap.h"
#include "core/unused_api.h"

/* Funktion, die nacheinander die erforderlichen Funktionen zur Erstellung
   des txt-Dokuments aufruft
   Parameter:  Zeiger auf ParseStruct-Struktur, CombinedScore-Matrix,
               die HitInformation-Struktur, die RegionStruct-Struktur,
               das Char-Zeichen, um welchen Bereich es sich handelt
   Returnwert: void */
static void outputwriter_txt(ParseStruct *,
                             CombinedScoreMatrixEntry **,
                             HitInformation *,
                             RegionStruct **, char, GtError *);

/* Funktion, die nacheinander die erforderlichen Funktionen zur Erstellung
   des html-Dokuments aufruft
   Parameter: Zeiger auf ParseStruct-Struktur, CombinedScore-Matrix,
              die HitInformation-Struktur, die RegionStruct-Struktur,
              das Char-Zeichen, um welchen Bereich es sich handelt
   Returnwert: void */
static void outputwriter_html(ParseStruct *,
                              CombinedScoreMatrixEntry **,
                              HitInformation *,
                              RegionStruct **, char, GtError *);

/* Funktion, die nacheinander die erforderlichen Funktionen zur Erstellung
   des xml-Dokuments aufruft
   Parameter: Zeiger auf ParseStruct-Struktur, CombinedScore-Matrix,
              die HitInformation-Struktur, die RegionStruct-Struktur,
              das Char-Zeichen, um welchen Bereich es sich handelt
   Returnwert: void */
static void outputwriter_xml(ParseStruct *,
                             CombinedScoreMatrixEntry **,
                             HitInformation *,
                             RegionStruct **, char, GtError *);

/* Funktion zum Schreiben des Output-Header der txt-Datei
   Parameter:  Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_header_txt(const ParseStruct *);

/* Funktion zum Schreiben des Output-Header der html-Datei
   Parameter:  Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_header_html(const ParseStruct *);

/* Funktion zum Schreiben des Output-Header der xml-Datei
   Parameter:  Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_header_xml(const ParseStruct *);

/* Funktion zum Schreiben des Query-DNA Abschnittes der txt-Datei
   Parameter:  Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_querydna_txt(const ParseStruct *);

/* Funktion zum Schreiben des Query-DNA Abschnittes der html-Datei
   Parameter:  Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_querydna_html(const ParseStruct *);

/* Funktion zum Schreiben des Query-DNA Abschnittes der xml-Datei
   Parameter:  Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_querydna_xml(const ParseStruct *);

/* Funktion zur Berechnung der Ausgabemenge fuer den Hit-Information
   Abschnittes;
   Parameter: Zeiger auf ParseStruct-Struktur, CombinedScore-Matrix,
              die HitInformation-Struktur, die RegionStruct-Struktur,
              das Char-Zeichen, um welchen Bereich es sich handelt
   Returnwert: void */
static void output_hitdna(ParseStruct *,
                          CombinedScoreMatrixEntry **,
                          HitInformation *, RegionStruct **, GtError *);

/* Funktion zum Schreiben des Coding-DNA-Abschnittes
   Parameter:  Zeiger auf ParseStruct, Zeiger auf die DNA-Seq,
               Str der Protein-Seq, Ausgabe-Format
   Returnwert: void */
static void print_codingheader(const ParseStruct *, const char *, GtStr *);

/* Funktion zum Schreiben des Hit-Information-Abschnittes
   Parameter: Zeiger auf die ParseStruct, Zeiger auf die
              HitInformation-Struktur, Zeiger auf die kodierende-Seq,
              Ausgabeformat, Sequenzposition
   Returnwert: void */
static void print_hitinformation(const ParseStruct *,
                                 const HitInformation *, unsigned long);

/* Funktion zum Schreiben der Metagenomethreader-Statistik der Text-Datei
   Parameter: Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_statistics_txt(const ParseStruct *);

/* Funktion zum Schreiben der Metagenomethreader-Statistik der HTML-Datei
   Parameter: Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_statistics_html(const ParseStruct *);

/* Funktion zum Schreiben der Metagenomethreader-Statistik der XML-Datei
   Parameter: Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_statistics_xml(const ParseStruct *);

/* Funktion zum Schreiben des Output-Footer der HTML-Datei
   Parameter: Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_footer_html(const ParseStruct *);

/* Funktion zum Schreiben des Output-Footer der XML-Datei
   Parameter: Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_footer_xml(const ParseStruct *);

/* Funktion zur Berechnung der AS-Sequenz
   Parameter: Zeiger auf die DNA-Sequnez, Str fuer die Proteinsequenz,
              from-Wert, to-Wert, aktueller Frame
   Returnwert: void */
static int as_coding(const ParseStruct *,
                     char *,
                     GtStr *,
                     unsigned long,
                     unsigned long, unsigned short, GtError *);

static enum iterator_op
newmemory_hash(char *key, unsigned long *value, void *data, GtError * err);

/* Funktion zum Schreiben des Statistic-Headers
   Parameter: Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_statistics_header(const ParseStruct *);

static short check_startcodon(const ParseStruct *, const char *);

/* Funktion zum Abschluss eines Iterations-Bereich im XML-File
   Parameter: Zeiger auf die ParseStruct-Struktur
   Returnwert: void */
static void output_close_iteration_xml(const ParseStruct *);

/* Zeitstruktur liefert die Struktur fuer das aktuelle Datum in der Form
   dd.mm.yyyy */
struct tm *gt_today(void)
{
  static struct tm *tmnow;

  time_t tnow;

  (void) time(&tnow);
  tmnow = localtime(&tnow);

  return tmnow;
}

void mg_outputwriter(ParseStruct *parsestruct_ptr,
                     CombinedScoreMatrixEntry **combinedscore_matrix,
                     HitInformation *hit_information,
                     RegionStruct **regionmatrix, char type, GtError * err)
{
  gt_error_check(err);

  /* je nach dem per GtOption angegebenen Output-Fileformat wird die
     entsprechende Ausgabefunktion aufgerufen */
  switch (ARGUMENTSSTRUCT(outputfile_format))
  {
      /* txt */
    case 1:
      outputwriter_txt(parsestruct_ptr, combinedscore_matrix,
                       hit_information, regionmatrix, type, err);
      break;
      /* html */
    case 2:
      outputwriter_html(parsestruct_ptr, combinedscore_matrix,
                        hit_information, regionmatrix, type, err);
      break;
      /* xml */
    case 3:
      outputwriter_xml(parsestruct_ptr, combinedscore_matrix,
                       hit_information, regionmatrix, type, err);
      break;
  }
}

static void outputwriter_txt(ParseStruct *parsestruct_ptr,
                      CombinedScoreMatrixEntry **combinedscore_matrix,
                      HitInformation *hit_information,
                      RegionStruct **regionmatrix, char type, GtError * err)
{
  gt_error_check(err);

  /* Aufruf der jeweiligen Funtion zum erstellen der Bereiche Header(t),
     Query-DNA(q) und Coding-DNA(h) */
  if (type == 't')
    output_header_txt(parsestruct_ptr);
  else if (type == 'q')
    output_querydna_txt(parsestruct_ptr);
  else if (type == 'h')
    output_hitdna(parsestruct_ptr, combinedscore_matrix, hit_information,
                  regionmatrix, err);
  else if (type == 'v')
    output_statistics_header(parsestruct_ptr);
  else if (type == 's')
    output_statistics_txt(parsestruct_ptr);
}

static void outputwriter_html(ParseStruct *parsestruct_ptr,
                       CombinedScoreMatrixEntry **combinedscore_matrix,
                       HitInformation *hit_information,
                       RegionStruct **regionmatrix, char type, GtError * err)
{
  gt_error_check(err);

  /* Aufruf der jeweiligen Funtion zum erstellen der Bereiche Header(t),
     Query-DNA(q) und Coding-DNA(h) und des Footer(f) */
  if (type == 't')
    output_header_html(parsestruct_ptr);
  else if (type == 'q')
    output_querydna_html(parsestruct_ptr);
  else if (type == 'h')
    output_hitdna(parsestruct_ptr, combinedscore_matrix, hit_information,
                  regionmatrix, err);
  else if (type == 's')
    output_statistics_html(parsestruct_ptr);
  else if (type == 'v')
    output_statistics_header(parsestruct_ptr);
  else if (type == 'f')
    output_footer_html(parsestruct_ptr);
}

static void outputwriter_xml(ParseStruct *parsestruct_ptr,
                      CombinedScoreMatrixEntry **combinedscore_matrix,
                      HitInformation *hit_information,
                      RegionStruct **regionmatrix, char type, GtError * err)
{
  gt_error_check(err);

  /* Aufruf der jeweiligen Funtion zum erstellen der Bereiche Header(t),
     Query-DNA(q) und Coding-DNA(h) und des Footer(f) */
  if (type == 't')
    output_header_xml(parsestruct_ptr);
  else if (type == 'q')
    output_querydna_xml(parsestruct_ptr);
  else if (type == 'h')
    output_hitdna(parsestruct_ptr, combinedscore_matrix, hit_information,
                  regionmatrix, err);
  else if (type == 's')
    output_statistics_xml(parsestruct_ptr);
  else if (type == 'v')
    output_statistics_header(parsestruct_ptr);
  else if (type == 'f')
    output_footer_xml(parsestruct_ptr);
  else if (type == 'x')
    output_close_iteration_xml(parsestruct_ptr);
}

static void output_header_txt(const ParseStruct *parsestruct_ptr)
{
  /* Aktuelle Datum in Variable speichern */
  struct tm *tmstamp;

  tmstamp = gt_today();

  if (!ARGUMENTSSTRUCT(testmodus_mode))
  {
    /* Headerbereich schreiben inkl. Auflistung der Parametereinstellugen */
    gt_file_xprintf(FILEPOINTEROUT,
                    "\nMetagenomethreader Result %d.%d.%d\n\n",
                    tmstamp->tm_mday, tmstamp->tm_mon + 1,
                    tmstamp->tm_year + 1900);
  }
  gt_file_xprintf(FILEPOINTEROUT,
                  "\nParametereinstellungen\n Synonymic Value: %.4f\n ",
                  ARGUMENTSSTRUCT(synonomic_value));
  gt_file_xprintf(FILEPOINTEROUT, "Nonsynonymic Value: %.4f\n ",
                  ARGUMENTSSTRUCT(nonsynonomic_value));
  gt_file_xprintf(FILEPOINTEROUT, "Blasthit-End Value: %.4f\n ",
                  ARGUMENTSSTRUCT(blasthit_end_value));
  gt_file_xprintf(FILEPOINTEROUT, "Query-Stopcodon-Value: %.4f\n ",
                  ARGUMENTSSTRUCT(stopcodon_queryseq));
  gt_file_xprintf(FILEPOINTEROUT, "Hit-Stopcodon-Value: %.4f\n ",
                  ARGUMENTSSTRUCT(stopcodon_hitseq));
  gt_file_xprintf(FILEPOINTEROUT, "Frameshift-Span: %.4f\n ",
                  ARGUMENTSSTRUCT(frameshift_span));
  gt_file_xprintf(FILEPOINTEROUT, "Prediction-Span: %.4f\n ",
                  ARGUMENTSSTRUCT(prediction_span));
  gt_file_xprintf(FILEPOINTEROUT, "Leavegene-Value: %.4f\n ",
                  ARGUMENTSSTRUCT(leavegene_value));
  gt_file_xprintf(FILEPOINTEROUT, "Curl-DB: %s\n ",
                  gt_str_get(ARGUMENTSSTRUCT(curl_fcgi_db)));
  gt_file_xprintf(FILEPOINTEROUT, "Output-Filename: %s\n ",
                  gt_str_get(ARGUMENTSSTRUCT(outputtextfile_name)));
  gt_file_xprintf(FILEPOINTEROUT, "Output-Fileformat: %d\n ",
                  ARGUMENTSSTRUCT(outputfile_format));
  gt_file_xprintf(FILEPOINTEROUT, "Hitfile (yes=1/no=0): %d\n ",
                  ARGUMENTSSTRUCT(hitfile_bool));
  gt_file_xprintf(FILEPOINTEROUT, "Min Protein-Length (>=15): %lu\n ",
                  ARGUMENTSSTRUCT(min_as));
  gt_file_xprintf(FILEPOINTEROUT, "Min Result-Percentage: %.4f\n ",
                  ARGUMENTSSTRUCT(percent_value));
  gt_file_xprintf(FILEPOINTEROUT, "Extended-Modus (yes=1/no=0): %d\n ",
                  ARGUMENTSSTRUCT(extended_mode));
  gt_file_xprintf(FILEPOINTEROUT, "Homology-Modus (yes=1/no=0): %d\n ",
                  ARGUMENTSSTRUCT(homology_mode));
  gt_file_xprintf(FILEPOINTEROUT, "Codon-Modus (yes=1/no=0): %d\n\n",
                  ARGUMENTSSTRUCT(codon_mode));
}

static void output_header_html(const ParseStruct *parsestruct_ptr)
{
  /* Aktuelle Datum in Variable speichern */
  struct tm *tmstamp;

  tmstamp = gt_today();

  /* Headerbereich schreiben inkl. Auflistung der Parametereinstellugen */
  gt_file_xprintf(FILEPOINTEROUT,
                  "\n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "\n");
  gt_file_xprintf(FILEPOINTEROUT, " \n");
  if (!ARGUMENTSSTRUCT(testmodus_mode))
  {
    gt_file_xprintf(FILEPOINTEROUT,
                    "  Metagenomethreader Result %d.%d.%d\n",
                    tmstamp->tm_mday, tmstamp->tm_mon + 1,
                    tmstamp->tm_year + 1900);
  }
    gt_file_xprintf(FILEPOINTEROUT,
                    "  \n");
    gt_file_xprintf(FILEPOINTEROUT,
                    "  \n");
    gt_file_xprintf(FILEPOINTEROUT, " \n");
    gt_file_xprintf(FILEPOINTEROUT, " \n");
    gt_file_xprintf(FILEPOINTEROUT,
                    "  \n");
  if (!ARGUMENTSSTRUCT(testmodus_mode))
  {
    gt_file_xprintf(FILEPOINTEROUT,"   \n");

    gt_file_xprintf(FILEPOINTEROUT,
                    "    \n"
                    "    \n",
                    tmstamp->tm_mday, tmstamp->tm_mon + 1,
                    tmstamp->tm_year + 1900);

    gt_file_xprintf(FILEPOINTEROUT,"   \n");
  }
  gt_file_xprintf(FILEPOINTEROUT,"   \n");

  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(synonomic_value));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(nonsynonomic_value));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(blasthit_end_value));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(stopcodon_queryseq));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(stopcodon_hitseq));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(frameshift_span));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(prediction_span));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(leavegene_value));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  gt_str_get(ARGUMENTSSTRUCT(curl_fcgi_db)));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  gt_str_get(ARGUMENTSSTRUCT(outputtextfile_name)));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(outputfile_format));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(hitfile_bool));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(min_as));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(percent_value));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(extended_mode));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(homology_mode));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  ARGUMENTSSTRUCT(codon_mode));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
}

static void output_header_xml(const ParseStruct *parsestruct_ptr)
{
  /* Aktuelle Datum in Variable speichern */
  struct tm *tmstamp;

  tmstamp = gt_today();

  /* Headerbereich schreiben inkl. Auflistung der Parametereinstellugen */
  gt_file_xprintf(FILEPOINTEROUT, "\n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "\n");
  gt_file_xprintf(FILEPOINTEROUT, "\n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "  Metagenomethreader"
                  "\n");

  if (!ARGUMENTSSTRUCT(testmodus_mode))
  {
    gt_file_xprintf(FILEPOINTEROUT,
                    "  Result %d.%d.%d"
                    "\n",
                    tmstamp->tm_mday, tmstamp->tm_mon + 1,
                    tmstamp->tm_year + 1900);
  }
  gt_file_xprintf(FILEPOINTEROUT, "  \n");
  gt_file_xprintf(FILEPOINTEROUT, "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %.4f\n",
                  ARGUMENTSSTRUCT(synonomic_value));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %.4f\n",
                  ARGUMENTSSTRUCT(nonsynonomic_value));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %.4f"
                  "\n",
                  ARGUMENTSSTRUCT(blasthit_end_value));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %.4f"
                  "\n",
                  ARGUMENTSSTRUCT(stopcodon_queryseq));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %.4f"
                  "\n",
                  ARGUMENTSSTRUCT(stopcodon_hitseq));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %.4f"
                  "\n",
                  ARGUMENTSSTRUCT(frameshift_span));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %.4f"
                  "\n",
                  ARGUMENTSSTRUCT(prediction_span));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %.4f"
                  "\n",
                  ARGUMENTSSTRUCT(leavegene_value));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %s"
                  "\n",
                  gt_str_get(ARGUMENTSSTRUCT(curl_fcgi_db)));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %s"
                  "\n",
                  gt_str_get(ARGUMENTSSTRUCT(outputtextfile_name)));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %d"
                  "\n",
                  ARGUMENTSSTRUCT(outputfile_format));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %d\n",
                  ARGUMENTSSTRUCT(hitfile_bool));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %lu\n",
                  ARGUMENTSSTRUCT(min_as));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %.4f"
                  "\n",
                  ARGUMENTSSTRUCT(percent_value));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %d"
                  "\n",
                  ARGUMENTSSTRUCT(extended_mode));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %d"
                  "\n",
                  ARGUMENTSSTRUCT(homology_mode));
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %d"
                  "\n",
                  ARGUMENTSSTRUCT(codon_mode));
  gt_file_xprintf(FILEPOINTEROUT, "    \n");
  gt_file_xprintf(FILEPOINTEROUT, "  \n");
}

static void output_querydna_txt(const ParseStruct *parsestruct_ptr)
{
  /* schreiben des Query-DNA Headers inkl. Query-Def. und Query-Sequenz */
  gt_file_xprintf(FILEPOINTEROUT, "Query-DNA-Entry-Section\n\n");
  gt_file_xprintf(FILEPOINTEROUT, "Query-DNA-Def: %s\n",
                  gt_str_get(MATRIXSTRUCT(query_def)));
  gt_file_xprintf(FILEPOINTEROUT, "Query_DNA-Sequence:\n%s\n",
                  gt_str_get(MATRIXSTRUCT(query_dna)));
  gt_file_xprintf(FILEPOINTEROUT, "\nCoding-DNA-Entry-Section\n\n");
}

static void output_querydna_html(const ParseStruct *parsestruct_ptr)
{
  /* schreiben des Query-DNA Headers inkl. Query-Def. und Query-Sequenz */
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n"
                  "    \n",
                  gt_str_get(MATRIXSTRUCT(query_def)));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n",
                  gt_str_get(MATRIXSTRUCT(query_dna)));
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
}

static void output_querydna_xml(const ParseStruct *parsestruct_ptr)
{
  /* schreiben des Query-DNA Headers inkl. Query-Def. und Query-Sequenz */
  gt_file_xprintf(FILEPOINTEROUT,
                  "  \n");
  gt_file_xprintf(FILEPOINTEROUT, "  \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "    %s\n",
                  gt_str_get(MATRIXSTRUCT(query_def)));
  gt_file_xprintf(FILEPOINTEROUT,
                  "    %s\n",
                  gt_str_get(MATRIXSTRUCT(query_dna)));
  gt_file_xprintf(FILEPOINTEROUT, "    \n");
}

static void output_hitdna(ParseStruct *parsestruct_ptr,
                   CombinedScoreMatrixEntry **combinedscore_matrix,
                   HitInformation *hit_information,
                   RegionStruct **regionmatrix, GtError * err)
{
  GT_UNUSED int had_err = 0;

  unsigned long arraysize,
    from = 0,
    to = 0,
    contig_seq_diff,
    hit_numbers = 0,
    current,
    *hit_ptr,
    hitcounter = 0,
    gt_array_index,
    seq_index,
    hit_index,
    string_number,
    tmp_var,
    *hitsnum_tmp,
    hit_from,
    hit_to,
    hash_index = 0,
    *memory_tmp;

  unsigned short row_index;

  char *contig_seq,
   *contig_seq_ptr;

  GtStr *as_seq;

  gt_error_check(err);

  hit_ptr = NULL;
  as_seq = gt_str_new();
  hitcounter = gt_str_array_size(hit_information->hit_gi);
  contig_seq_ptr = gt_str_get(MATRIXSTRUCT(query_dna));

  /* in allen Leserahmen nach kodierenden Abschnitten suchen */
  for (row_index = 0; row_index < 7; row_index++)
  {
    if (row_index != 3)
    {
      /* Anzahl kodierender Abschnitte im aktuellen Leserahmen */
      arraysize = gt_array_size(regionmatrix[row_index][0].from);

      for (gt_array_index = 0; gt_array_index < arraysize; gt_array_index++)
      {
        /* Bereichsgrenzen des kodierenden Abschnittes - Werte bereits in
           0- bis X-Kodierung */
        from =
          *(unsigned long *) gt_array_get(regionmatrix[row_index][0].from,
                                       gt_array_index);
        to =
          *(unsigned long *) gt_array_get(regionmatrix[row_index][0].to,
                                       gt_array_index);

        /* nur wenn die Mindestlaenge in Anzahl AS erfuellt ist, erfolgt
           eine Ausgabe */
        if ((to - from + 1) / 3 > ARGUMENTSSTRUCT(min_as))
        {
          /* to-from+1+1 entspricht Anzahl der zu betrachtenden Basen +
             Stringende-Zeichen */
          contig_seq_diff = to - from + 2;

          contig_seq = gt_malloc(contig_seq_diff*sizeof (char));
          /* kopieren von contig_seq_diff-1 Zeichen */
          (void) snprintf(contig_seq, contig_seq_diff, "%s",
                          contig_seq_ptr + from);
          gt_assert(contig_seq);

          had_err = as_coding(parsestruct_ptr,
                              contig_seq_ptr, as_seq, from, to, row_index, err);

          /* je nach Ausgabeformat die entsprechende Ausgabefunktion
             aufrufen */
          switch (ARGUMENTSSTRUCT(outputfile_format))
          {
            case 1:
              print_codingheader(parsestruct_ptr, contig_seq, as_seq);
              break;
            case 2:
              print_codingheader(parsestruct_ptr, contig_seq, as_seq);
              break;
            case 3:
              print_codingheader(parsestruct_ptr, contig_seq, as_seq);
              break;
          }

          /* Sequnezbereich wird genauer betrachtet */
          for (seq_index = from; seq_index < to + 1; seq_index++)
          {
            /* hit_numbers ist die Anzahl der beteiligten Hits an
               Sequenzposition seq_index */
            hit_numbers =
              gt_array_size(combinedscore_matrix[row_index][seq_index].
                         hit_number);

            if (hit_ptr == NULL)
            {
              hit_ptr = gt_calloc(hitcounter, sizeof (unsigned long));
            }
            /* Abfragen aller Hit-Nummern fuer jede Position */
            for (hit_index = 0; hit_index < hit_numbers; hit_index++)
            {
              /* current entspricht der Hit-Nummer */
              current =
                *(unsigned long *)
                gt_array_get(combinedscore_matrix[row_index][seq_index].
                          hit_number, hit_index);
              /* hit_ptr wird an der Stelle current auf 1 gesetzt - so
                 wird eine Mehrfachnennung vermieden */
              hit_ptr[current] |= 1;
            }
          }

          /* hitcounter ist max. Anzahl der Hits */
          for (seq_index = 0; seq_index < hitcounter; seq_index++)
          {

            gt_assert(hit_ptr != NULL);
            /* Wenn an der Position seq_index eine 1 steht, kommt der
               entsprechende Hit(-Eintrag) in der Ergebnismenge vor und
               muss ausgegeben werden */
            if (hit_ptr[seq_index])
            {
              /* Die aktuelle Hit-Definition wird eingelesen */
              gt_str_set(parsestruct_ptr->result_hits,
                      gt_str_array_get(hit_information->hit_def, seq_index));

              hit_from =
                atoi(gt_str_array_get(hit_information->hit_from, seq_index));
              hit_to =
                atoi(gt_str_array_get(hit_information->hit_to, seq_index));

              /* ueberpruefen, ob der aktuelle Hit bereits erfasst wurde */
              if (!gt_cstr_nofree_ulp_gt_hashmap_get
                  (parsestruct_ptr->resulthits,
                   gt_str_get(parsestruct_ptr->result_hits)))
              {
                /* Hit noch nicht erfasst, also in das Statistik-Array
                   einfuegen */
                gt_str_array_add_cstr(HITSTRUCT(hits_statistic),
                                  gt_str_get(parsestruct_ptr->result_hits));
                /* Position der Hit-Def. im Statistik-Array */
                string_number =
                  gt_str_array_size(HITSTRUCT(hits_statistic)) - 1;

                /* Hitscounter: zaehlt , Hitsnumber: zaehlt das Auftreten
                   der Hit-Def. in der Ergebnismenge */
                HITSTRUCT(hitsnumber) =
                  HITSTRUCT(hitsnumber) + hit_to - hit_from + 1;

                /* Bei Bedarf speicher reallokieren */
                if (string_number + 1 > parsestruct_ptr->hits_memory - 20)
                {
                  hitsnum_tmp = HITSTRUCT(hitsnum);
                  memory_tmp = HITSTRUCT(memory);

                  gt_array_reset(parsestruct_ptr->value_tmp);
                  (void) gt_cstr_nofree_ulp_gt_hashmap_foreach(
                    parsestruct_ptr->resulthits,
                    newmemory_hash, parsestruct_ptr, err);

                  /* Speichergroesse erhoehen */
                  parsestruct_ptr->hits_memory =
                    MGTH_MEMORY_SIZE + parsestruct_ptr->hits_memory;

                  HITSTRUCT(hitsnum) =
                    gt_realloc(hitsnum_tmp,
                               parsestruct_ptr->hits_memory *
                               sizeof (unsigned long));
                  HITSTRUCT(memory) =
                    gt_realloc(memory_tmp,
                               parsestruct_ptr->hits_memory *
                               sizeof (unsigned long));

                  gt_hashtable_reset(parsestruct_ptr->resulthits);

                  for (hash_index = 0;
                       hash_index < gt_array_size(parsestruct_ptr->value_tmp);
                       hash_index++)
                  {
                    gt_cstr_nofree_ulp_gt_hashmap_add(
                                   parsestruct_ptr->resulthits,
                                  (char *)
                                  gt_str_array_get(HITSTRUCT(hits_statistic),
                                               *(unsigned long *)
                                               gt_array_get(parsestruct_ptr->
                                                         value_tmp,
                                                         hash_index)),
                                  HITSTRUCT(memory +
                                            *(unsigned long *)
                                            gt_array_get(parsestruct_ptr->
                                                      value_tmp,
                                                      hash_index)));
                  }
                }

                tmp_var = string_number;

                *(HITSTRUCT(memory + tmp_var)) = tmp_var;
                *(HITSTRUCT(hitsnum + tmp_var)) = hit_to - hit_from + 1;

                gt_cstr_nofree_ulp_gt_hashmap_add(parsestruct_ptr->resulthits,
                              (char *)
                              gt_str_array_get(HITSTRUCT(hits_statistic),
                                           string_number),
                              HITSTRUCT(memory + tmp_var));
              }
              else
              {
                HITSTRUCT(hitsnumber) =
                  HITSTRUCT(hitsnumber) + hit_to - hit_from + 1;
                tmp_var =
                  **gt_cstr_nofree_ulp_gt_hashmap_get(
                    parsestruct_ptr->resulthits,
                    gt_str_get(parsestruct_ptr->result_hits));

                *(HITSTRUCT(hitsnum) + tmp_var) =
                  *(HITSTRUCT(hitsnum) + tmp_var) + hit_to - hit_from + 1;;
              }

              /* je nach Ausgabeformat die entsprechende
                 Hit-Information-Ausgabefunktion aufrufen */
              switch (ARGUMENTSSTRUCT(outputfile_format))
              {
                case 1:
                  print_hitinformation(parsestruct_ptr, hit_information,
                                       seq_index);
                  break;
                case 2:
                  print_hitinformation(parsestruct_ptr, hit_information,
                                       seq_index);
                  break;
                case 3:
                  print_hitinformation(parsestruct_ptr, hit_information,
                                       seq_index);
                  break;
              }
              gt_str_reset(parsestruct_ptr->result_hits);
            }
          }

          switch (ARGUMENTSSTRUCT(outputfile_format))
          {
              /* Ausgabe Coding-DNA-Header - txt */
            case 1:
              gt_file_xprintf(FILEPOINTEROUT, "\n\n");
              break;
              /* Ausgabe Coding-DNA-Header - html */
            case 2:
              break;
              /* Ausgabe Coding-DNA-Header - xml */
            case 3:
              gt_file_xprintf(FILEPOINTEROUT, "        \n");
              gt_file_xprintf(FILEPOINTEROUT, "      \n");
              break;
          }

          gt_free(hit_ptr);
          gt_free(contig_seq);
          hit_ptr = NULL;
          gt_str_reset(as_seq);
        }
      }
    }
  }
  gt_str_delete(as_seq);
}

static void print_codingheader(const ParseStruct *parsestruct_ptr,
                               const char *contig_seq, GtStr * as_seq)
{
  gt_assert(contig_seq);

  switch (ARGUMENTSSTRUCT(outputfile_format))
  {
      /* Ausgabe Coding-DNA-Header - txt */
    case 1:
      gt_file_xprintf(FILEPOINTEROUT, "Coding-DNA: \n");
      gt_file_xprintf(FILEPOINTEROUT, "%s\n", contig_seq);
      gt_file_xprintf(FILEPOINTEROUT, "Protein-Seq: ");
      gt_file_xprintf(FILEPOINTEROUT, "%s\n", gt_str_get(as_seq));
      gt_file_xprintf(FILEPOINTEROUT, "Hit-Information Section\n");
      break;
      /* Ausgabe Coding-DNA-Header - html */
    case 2:
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,
                      "    \n");
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,
                      "    \n",
                      contig_seq);
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,
                      "    \n");
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,
                      "    \n", gt_str_get(as_seq));
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,
                      "    \n");
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      break;
      /* Ausgabe Coding-DNA-Header - xml */
    case 3:
      gt_file_xprintf(FILEPOINTEROUT, "      \n");
      gt_file_xprintf(FILEPOINTEROUT, "        %s\n",
                      contig_seq);
      gt_file_xprintf(FILEPOINTEROUT,
                      "        %s\n",
                      gt_str_get(as_seq));
      gt_file_xprintf(FILEPOINTEROUT, "        \n");
      break;
  }
}

static void print_hitinformation(const ParseStruct *parsestruct_ptr,
                                 const HitInformation *hit_information,
                                 unsigned long seq_index)
{
  /* je nach Ausgabeformat schreiben der Hit-Informationen */
  switch (ARGUMENTSSTRUCT(outputfile_format))
  {
      /* txt */
    case 1:
      gt_file_xprintf(FILEPOINTEROUT, "gi-nr: gi|%s ",
                      gt_str_array_get(hit_information->hit_gi, seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "gi_def: %s ",
                      gt_str_array_get(hit_information->hit_def, seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "hsp_num: %s ",
                      gt_str_array_get(hit_information->hit_hsp_nr,
                                   seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "from: %s ",
                      gt_str_array_get(hit_information->hit_from, seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "to: %s\n",
                      gt_str_array_get(hit_information->hit_to, seq_index));
      break;
      /* html */
    case 2:
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      gt_file_xprintf(FILEPOINTEROUT,
                      "    \n",
                      gt_str_array_get(hit_information->hit_to, seq_index));
      gt_file_xprintf(FILEPOINTEROUT,"   \n");
      break;
      /* xml */
    case 3:
      gt_file_xprintf(FILEPOINTEROUT, "          \n");
      gt_file_xprintf(FILEPOINTEROUT,
                      "            gi|%s\n",
                      gt_str_array_get(hit_information->hit_gi, seq_index));
      gt_file_xprintf(FILEPOINTEROUT,
                      "            %s\n",
                      gt_str_array_get(hit_information->hit_def, seq_index));
      gt_file_xprintf(FILEPOINTEROUT,
                      "            %s\n",
                      gt_str_array_get(hit_information->hit_hsp_nr,
                                   seq_index));
      gt_file_xprintf(FILEPOINTEROUT,
                      "            %s\n",
                      gt_str_array_get(hit_information->hit_from, seq_index));
      gt_file_xprintf(FILEPOINTEROUT,
                      "            %s\n",
                      gt_str_array_get(hit_information->hit_to, seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "          \n");
      break;
  }
}

static void output_statistics_txt(const ParseStruct *parsestruct_ptr)
{
  /* schreiben des Query-DNA Headers inkl. Query-Def. und Query-Sequenz */
  gt_file_xprintf(FILEPOINTEROUT, "%-8.4f   ",
                  ((double) *(HITSTRUCT(hitsnum) + HITSTRUCT(stat_pos)) /
                   (double) HITSTRUCT(hitsnumber)) * 100);
  gt_file_xprintf(FILEPOINTEROUT, "%s\n",
                  gt_str_array_get(HITSTRUCT(hits_statistic),
                               *(HITSTRUCT(memory) +
                                 HITSTRUCT(stat_pos))));
}

static void output_statistics_html(const ParseStruct *parsestruct_ptr)
{
  gt_file_xprintf(FILEPOINTEROUT,"      \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "       \n",
                  ((float) *(HITSTRUCT(hitsnum) + HITSTRUCT(stat_pos)) /
                   (float) HITSTRUCT(hitsnumber)) * 100);
  gt_file_xprintf(FILEPOINTEROUT,
                  "       \n",
                  gt_str_array_get(HITSTRUCT(hits_statistic),
                               *(HITSTRUCT(memory) +
                                 HITSTRUCT(stat_pos))));
  gt_file_xprintf(FILEPOINTEROUT,"      \n");
}

static void output_statistics_xml(const ParseStruct *parsestruct_ptr)
{
  gt_file_xprintf(FILEPOINTEROUT, "    \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %-8.4f\n",
                  ((double) *(HITSTRUCT(hitsnum) + HITSTRUCT(stat_pos)) /
                   (double) HITSTRUCT(hitsnumber)) * 100);
  gt_file_xprintf(FILEPOINTEROUT,
                  "      %s\n",
                  gt_str_array_get(HITSTRUCT(hits_statistic),
                               *(HITSTRUCT(memory) +
                                 HITSTRUCT(stat_pos))));
  gt_file_xprintf(FILEPOINTEROUT, "    \n");
}

static void output_footer_html(const ParseStruct *parsestruct_ptr)
{
  /* Schreiben des HTML-Footers */
  gt_file_xprintf(FILEPOINTEROUT,"     
    "
                    "Metagenomethreader Result %d.%d.%d

    "
                  "Parametereinstellungen
    "
                  "Synonymic Value: %.4f
    "
                  "Non-Synonymic Value: %.4f
    "
                  "Blast-Hit-End Value: %.4f
    "
                  "Query Stop-Codon Value: %.4f
    "
                  "Hit Stop-Codon Value: %.4f
    "
                  "Frameshift-Span: %.4f
    "
                  "Prediction-Span: %.4f
    "
                  "Leavegene-Value: %.4f
    cURL-DB: "
                  "%s
    "
                  "Output-Filename: %s
    "
                  "Output-Fileformat
    (1/2/3):     		%d"
                  "
    Hitfile
    "
                  "(yes=1/no=0):     		%d"
                  "
    "
                  "Min-Protein-Length
    (>=15):     		%lu"
                  "
    "
                  "Min-Result-Percentage: %.4f
    "
                  "Extended-Modus
    (yes=1/no=0):     		%d"
                  "
    "
                  "Homology-Modus
    (yes=1/no=0):     		%d"
                  "
    "
                  "Codon-Modus
    (1/2/3):     		%d"
                  "

    "
                  "
    Query-DNA-Entry-Section

    Query-DNA-Def%s
    "
                  "Query_DNA-Sequence
    %s"
                  "

    "
                  "Coding-DNA-Entry-Section

    "
                      "Coding-DNA
    %s"
                      "
    "
                      "Protein-Sequence
    %s"
                      "
    "
                      "Hit-Information Section
    gi-nr: ");
      gt_file_xprintf(FILEPOINTEROUT,
                      "",
                      gt_str_array_get(hit_information->hit_gi, seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "gi|%s  ",
                      gt_str_array_get(hit_information->hit_gi, seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "gi_def: %s ",
                      gt_str_array_get(hit_information->hit_def, seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "hsp_num: %s ",
                      gt_str_array_get(hit_information->hit_hsp_nr,
                                   seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "from: %s ",
                      gt_str_array_get(hit_information->hit_from, seq_index));
      gt_file_xprintf(FILEPOINTEROUT, "to: %s
    %-8.4f  %s
    \n");
  gt_file_xprintf(FILEPOINTEROUT,"    \n");
  gt_file_xprintf(FILEPOINTEROUT,"   \n");
  gt_file_xprintf(FILEPOINTEROUT,"  \n");
  gt_file_xprintf(FILEPOINTEROUT," \n");
  gt_file_xprintf(FILEPOINTEROUT,"\n");
}

static void output_footer_xml(const ParseStruct *parsestruct_ptr)
{
  /* Schreiben des HTML-Footers */
  gt_file_xprintf(FILEPOINTEROUT,
                  "  \n");
  gt_file_xprintf(FILEPOINTEROUT, "\n");
}

static int as_coding(const ParseStruct *parsestruct_ptr,
                     char *contig_seq,
                      GtStr *as_seq,
                      unsigned long from,
                      unsigned long to,
                      unsigned short current_row, GtError * err)
{
  int had_err = 0;

  unsigned long startpoint = from,
    endpoint = to,
    startpoint_start,
    startpoint_atg,
    startpoint_safe,
    contig_len;

  char contig_triplet[3],
   *contig_seq_tri = NULL,
    contig_as;

  short current_frame,
    current_frame_tmp,
    found = 0,
    found_start = 0,
    found_end = 0,
    start_codon = 0;

  gt_error_check(err);
  gt_assert(contig_seq);

  contig_len = strlen(contig_seq);
  current_frame = get_current_frame(current_row);
  current_frame_tmp = current_frame;

  if (current_frame_tmp < 0)
  {
    current_frame_tmp *= -1;

    had_err = mg_reverse_complement(contig_seq, contig_len, err);

    startpoint = contig_len - 1 - to;
    endpoint = contig_len - from;
  }

  if (!had_err)
  {
    if (startpoint < 3)
    {
      startpoint = current_frame_tmp - 1;
      startpoint_start = startpoint;
    }
    else
    {
      startpoint -= (((startpoint) - current_frame_tmp) % 3);
      startpoint -= 1;
      startpoint_start = startpoint;
    }

    startpoint_safe = startpoint;

    while ((startpoint <= endpoint) && (startpoint <= contig_len - 3))
    {
      /* Aktuelles Query-Triplet */
      contig_triplet[0] = contig_seq[startpoint];
      contig_triplet[1] = contig_seq[startpoint + 1];
      contig_triplet[2] = contig_seq[startpoint + 2];
      /* XXX gt_assert(contig_triplet); */

      /* Bestimmen der AS der jeweiligen Triplets */
      contig_as = mg_codon2amino(contig_triplet[0],
                                 contig_triplet[1], contig_triplet[2]);
      gt_assert(contig_as);

      gt_str_append_char(as_seq, contig_as);
      startpoint += 3;
    }

    if (ARGUMENTSSTRUCT(extended_mode))
    {
      GtStr *as_seq_start;

      as_seq_start = gt_str_new();

      contig_seq_tri = gt_malloc(4*sizeof (char));

      /* DNA-Basen-Triplet einlesen */
      contig_seq_tri[0] = tolower(contig_seq[startpoint - 3]);
      contig_seq_tri[1] = tolower(contig_seq[startpoint - 2]);
      contig_seq_tri[2] = tolower(contig_seq[startpoint - 1]);
      contig_seq_tri[3] = '\0';
      gt_assert(contig_seq_tri);

      found = gt_check_stopcodon(contig_seq_tri);

      while (startpoint <= contig_len - 3 && !found_end && found)
      {
        /* DNA-Basen-Triplet einlesen */
        contig_seq_tri[0] = tolower(contig_seq[startpoint - 3]);
        contig_seq_tri[1] = tolower(contig_seq[startpoint - 2]);
        contig_seq_tri[2] = tolower(contig_seq[startpoint - 1]);
        contig_seq_tri[3] = '\0';
        gt_assert(contig_seq_tri);

        found_end = gt_check_stopcodon(contig_seq_tri);

        if (found_end)
        {
          /* Aktuelles Query-Triplet */
          contig_triplet[0] = contig_seq[startpoint];
          contig_triplet[1] = contig_seq[startpoint + 1];
          contig_triplet[2] = contig_seq[startpoint + 2];
          /* XXX gt_assert(contig_triplet); */

          /* Bestimmen der AS der jeweiligen Triplets */
          contig_as = mg_codon2amino(contig_triplet[0],
                                     contig_triplet[1], contig_triplet[2]);
          gt_assert(contig_as);

          gt_str_append_char(as_seq, contig_as);
        }
        /* Startwert um 3 Basen weitersetzen */
        startpoint += 3;
      }

      /* DNA-Basen-Triplet einlesen */
      contig_seq_tri[0] = tolower(contig_seq[startpoint_start]);
      contig_seq_tri[1] = tolower(contig_seq[startpoint_start + 1]);
      contig_seq_tri[2] = tolower(contig_seq[startpoint_start + 2]);
      contig_seq_tri[3] = '\0';
      gt_assert(contig_seq_tri);

      start_codon = check_startcodon(parsestruct_ptr, contig_seq_tri);

      found = 0;

      if (!start_codon)
      {
        while (startpoint_start > 2 && !found)
        {
          /* DNA-Basen-Triplet einlesen */
          contig_seq_tri[0] = tolower(contig_seq[startpoint_start - 3]);
          contig_seq_tri[1] =
            tolower(contig_seq[startpoint_start - 2]);
          contig_seq_tri[2] =
            tolower(contig_seq[startpoint_start - 1]);
          contig_seq_tri[3] = '\0';
          gt_assert(contig_seq_tri);

          found = gt_check_stopcodon(contig_seq_tri);

          startpoint_atg = startpoint_start;

          if (found || startpoint_start < 3)
          {
            while (startpoint_atg <= startpoint_safe - 2)
            {
              if (!found_start)
              {
                /* DNA-Basen-Triplet einlesen */
                contig_seq_tri[0] = tolower(contig_seq[startpoint_atg]);
                contig_seq_tri[1] =
                  tolower(contig_seq[startpoint_atg + 1]);
                contig_seq_tri[2] =
                  tolower(contig_seq[startpoint_atg + 2]);
                contig_seq_tri[3] = '\0';
                gt_assert(contig_seq_tri);

                start_codon = check_startcodon(parsestruct_ptr,
                                               contig_seq_tri);

                /* ueberpruefen auf Start-Codon */
                if (start_codon)
                {
                  gt_str_append_char(as_seq_start, 'M');
                  found_start = 1;
                }
              }
              else
              {
                /* Aktuelles Query-Triplet */
                contig_triplet[0] = contig_seq[startpoint_atg];
                contig_triplet[1] = contig_seq[startpoint_atg + 1];
                contig_triplet[2] = contig_seq[startpoint_atg + 2];
                /* XXX gt_assert(contig_triplet); */

                /* Bestimmen der AS der jeweiligen Triplets */
                contig_as = mg_codon2amino(contig_triplet[0],
                                           contig_triplet[1],
                                           contig_triplet[2]);
                gt_assert(contig_as);

                gt_str_append_char(as_seq_start, contig_as);
              }
              /* Startwert um 3 Basen weitersetzen */
              startpoint_atg += 3;
            }
          }
          startpoint_start -= 3;
        }
        gt_str_append_str(as_seq_start, as_seq);
        gt_str_reset(as_seq);
        gt_str_append_str(as_seq, as_seq_start);
      }
      gt_str_reset(as_seq_start);
      gt_str_delete(as_seq_start);
      gt_free(contig_seq_tri);
    }

    if (current_frame < 0)
    {
      had_err = mg_reverse_complement(contig_seq, contig_len, err);
    }
  }
  return had_err;
}

static enum iterator_op
newmemory_hash(GT_UNUSED char *key, unsigned long *value, void *data,
               GT_UNUSED GtError * err)
{
  /* Parsestruct-Struktur */
  ParseStruct *parsestruct_ptr = (ParseStruct *) data;

  /* Position des aktuell betrachteten Schluessels */
  HITSTRUCT(stat_pos) = *value;

  gt_error_check(err);

  gt_array_add(parsestruct_ptr->value_tmp, HITSTRUCT(stat_pos));

  return 0;
}

static void output_statistics_header(const ParseStruct *parsestruct_ptr)
{
  /* Statistik-Bereich-Header schreiben */
  if (ARGUMENTSSTRUCT(outputfile_format) == 3)
  {
    gt_file_xprintf(FILEPOINTEROUT,
                    "  \n");
  }
  else if (ARGUMENTSSTRUCT(outputfile_format) == 2)
  {
    gt_file_xprintf(FILEPOINTEROUT, "   \n");
    gt_file_xprintf(FILEPOINTEROUT,
                    "    \n");
    gt_file_xprintf(FILEPOINTEROUT, "     \n");
    gt_file_xprintf(FILEPOINTEROUT, "      \n");
    gt_file_xprintf(FILEPOINTEROUT,
                    "       \n");
    gt_file_xprintf(FILEPOINTEROUT, "      \n");
  }
  else
  {
    gt_file_xprintf(FILEPOINTEROUT, "Statistic-Section\n\n");
  }
}

static short check_startcodon(const ParseStruct *parsestruct_ptr,
                              const char *contig_seq_ptrfct)
{
  unsigned short codon_status = 0;

  /* jeder if-Zweig ueberprueft entsprechend des
     Metagenomethreader-Arguments zur Verwendung alternativer Start-Codons
     auf Start-Codons */
  if (ARGUMENTSSTRUCT(codon_mode) == 2)
  {
    if (!strcmp(contig_seq_ptrfct, "atg")
        || !strcmp(contig_seq_ptrfct, "ctg")
        || !strcmp(contig_seq_ptrfct, "gtg")
        || !strcmp(contig_seq_ptrfct, "aug")
        || !strcmp(contig_seq_ptrfct, "cug")
        || !strcmp(contig_seq_ptrfct, "gug"))
    {
      codon_status = 1;
    }
  }
  else if (ARGUMENTSSTRUCT(codon_mode) == 3)
  {
    if (!strcmp(contig_seq_ptrfct, "atg")
        || !strcmp(contig_seq_ptrfct, "ctg")
        || !strcmp(contig_seq_ptrfct, "gtg")
        || !strcmp(contig_seq_ptrfct, "ttg")
        || !strcmp(contig_seq_ptrfct, "aug")
        || !strcmp(contig_seq_ptrfct, "cug")
        || !strcmp(contig_seq_ptrfct, "gug")
        || !strcmp(contig_seq_ptrfct, "uug"))
    {
      codon_status = 1;
    }
  }
  else
  {
    if (!strcmp(contig_seq_ptrfct, "atg")
        || !strcmp(contig_seq_ptrfct, "aug"))
    {
      codon_status = 1;
    }
  }

  return codon_status;
}

static void output_close_iteration_xml(const ParseStruct *parsestruct_ptr)
{
  gt_file_xprintf(FILEPOINTEROUT, "    \n");
  gt_file_xprintf(FILEPOINTEROUT, "  \n");
  gt_file_xprintf(FILEPOINTEROUT,
                  "  \n");
}
genometools-1.5.1/src/mgth/mg_outputwriter.h000066400000000000000000000026171211610345200212310ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef MG_OUTPUTWRITER_H
#define MG_OUTPUTWRITER_H

#include "metagenomethreader.h"
#include "mg_codon.h"

/* Funktion zur Ausgabe der berechneten Ergebnisse
   Parameter:  Zeiger auf ParseStruct-Struktur, CombinedScore-Matrix,
               die HitInformation-Struktur, die RegionStruct-Struktur,
               das Char-Zeichen, um welchen Bereich es sich handelt
   Returnwert: void */
void mg_outputwriter(ParseStruct *,
                     CombinedScoreMatrixEntry **,
                     HitInformation *, RegionStruct **, char, GtError *);
#endif
genometools-1.5.1/src/mgth/mg_reverse.c000066400000000000000000000073321211610345200201010ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  Copyright (c) 2006-2007 Gordon Gremme 
  Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg
  See LICENSE file or http://genometools.org/license.html for license details.

    modiefied for metagenomethreader;

*/

#include "mg_reverse.h"

static int mg_complement(char *reverse_char, char dna_char, GtError * err)
{
  gt_error_check(err);
  switch (dna_char)
  {
    case 'A':
      *reverse_char = 'T';
      return 0;
    case 'C':
      *reverse_char = 'G';
      return 0;
    case 'G':
      *reverse_char = 'C';
      return 0;
    case 'T':
      *reverse_char = 'A';
      return 0;
    case 'U':
      *reverse_char = 'A';
      return 0;
    case 'a':
      *reverse_char = 't';
      return 0;
    case 'c':
      *reverse_char = 'g';
      return 0;
    case 'g':
      *reverse_char = 'c';
      return 0;
    case 't':
      *reverse_char = 'a';
      return 0;
    case 'u':
      *reverse_char = 'a';
      return 0;
    case 'S':
      *reverse_char = 'S';
      return 0;
    case 's':
      *reverse_char = 's';
      return 0;
    case 'N':
      *reverse_char = 'N';
      return 0;
    case 'n':
      *reverse_char = 'n';
      return 0;
    case 'R':
      *reverse_char = 'Y';
      return 0;
    case 'r':
      *reverse_char = 'y';
      return 0;
    case 'Y':
      *reverse_char = 'R';
      return 0;
    case 'y':
      *reverse_char = 'r';
      return 0;
    case 'M':
      *reverse_char = 'K';
      return 0;
    case 'm':
      *reverse_char = 'k';
      return 0;
    case 'K':
      *reverse_char = 'M';
      return 0;
    case 'k':
      *reverse_char = 'm';
      return 0;
    case 'W':
      *reverse_char = 'W';
      return 0;
    case 'w':
      *reverse_char = 'w';
      return 0;
    case 'H':
      *reverse_char = 'D';
      return 0;
    case 'h':
      *reverse_char = 'd';
      return 0;
    case 'D':
      *reverse_char = 'H';
      return 0;
    case 'd':
      *reverse_char = 'h';
      return 0;
    case 'B':
      *reverse_char = 'V';
      return 0;
    case 'b':
      *reverse_char = 'v';
      return 0;
    case 'V':
      *reverse_char = 'B';
      return 0;
    case 'v':
      *reverse_char = 'b';
      return 0;

    default:
      gt_error_set(err, "complement of DNA character '%c' not defined",
                dna_char);
      return -1;
  }
}

int mg_reverse_complement(char *dna_seq, unsigned long seqlen, GtError * err)
{
  char *front_char,
   *back_char,
    tmp_char;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(dna_seq);

  for (front_char = dna_seq, back_char = dna_seq + seqlen - 1;
       front_char <= back_char; front_char++, back_char--)
  {
    had_err = mg_complement(&tmp_char, *front_char, err);
    if (!had_err)
      had_err = mg_complement(front_char, *back_char, err);
    if (!had_err)
      *back_char = tmp_char;
    if (had_err)
      break;
  }
  return had_err;
}
genometools-1.5.1/src/mgth/mg_reverse.h000066400000000000000000000025341211610345200201050ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/*
  Copyright (c) 2006-2007 Gordon Gremme 
  Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg
  See LICENSE file or http://genometools.org/license.html for license details.

  modified for gt_metagenomethreader
*/

#ifndef MG_REVERSE_H
#define MG_REVERSE_H

#include "core/assert_api.h"
#include "metagenomethreader.h"

/* reverse 'dna_seq' of length 'seqlen' in place */
int mg_reverse_complement(char *dna_seq, unsigned long seqlen, GtError *);

#endif
genometools-1.5.1/src/mgth/mg_xmlparser.c000066400000000000000000001045101211610345200204370ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "mg_xmlparser.h"
#include "core/unused_api.h"
#include "metagenomethreader.h"

#ifdef CURLDEF
#ifndef S_SPLINT_S
#include 
#include 
#include 
#endif

/* Expat Hilfs-Struktur zum Abspeichern der Hit-DNA-Sequenz und der
   Hit-DNA-Laenge */
typedef struct
{
  char *memory;
  size_t size;
} MemoryStruct;

/* Expat-Hilfsfunktion zum Abspeichern der empfangenen Daten
   Parameter:  void-Zeiger auf den Anfang des Speicherbereichs,
               Anzahl zu speichernder Elemente, Groesse des zu
               speichernden Datentyps, void-Zeiger auf die zu
               speichernden Daten
   Returnwert: Groesse des neu allokierten Speicherbereichs*/

static size_t WriteMemoryCallback(void *ptr,
                                  size_t size, size_t nmemb, void *data)
{
  size_t realsize = size * nmemb;
  MemoryStruct *mem = (MemoryStruct *) data;

  mem->memory = (char *) realloc(mem->memory, mem->size + realsize + 1);
  if (mem->memory)
  {
    memcpy(&(mem->memory[mem->size]), ptr, realsize);
    mem->size += realsize;
    mem->memory[mem->size] = 0;
  }
  return realsize;
}

int mg_curl(ParseStruct *parsestruct_ptr,
            unsigned long hit_counter, GtError * err)
{
  int had_err = 0,
    curl_errornr = 0;

  /* Laenge der aus dem XML-File stammenden Hit-DNA-Sequenz */
  unsigned long seq_len;
  long numb_from = 0, numb_to = 0, numb_diff = 0;

  GtStr *seq_var,
   *http_adr;

  MemoryStruct memorystruct;

  /* char-Zeiger auf die HTTP-Adresse des cgi-Skriptes efetch von NCBI */
  char *http_adr_ptr,
   *seq_pos;                           /* char-Zeiger, wird benutzt zum
                                          Auslesen der Sequenzinformation
                                          aus dem XML-File, welche
                                          Ergebnis der efetch-Anfrage ist */
  const char *curlerror;

  /* Curl-Handle */
  CURL *curl_handle;

  /* char-Zeiger auf die Daten ist NULL */
  memorystruct.memory = NULL;
  /* noch keine Daten eingetragen bzw. abgespeichert */
  memorystruct.size = 0;

  /* Zwischenspeicher fuer die Sequnezinformation, da die GtStrArray-Klasse
     keine Funktion zum begrenzten Einfuegen eines Strings zur Verfuegung
     stellt; setzen des ersten Teils der HTTP-Adresse */
  seq_var = gt_str_new();
  http_adr =
    gt_str_new_cstr
    ("http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=");

  /* Check der Umgebungsvariablen */
  gt_error_check(err);

  curl_global_init(CURL_GLOBAL_ALL);

  /* initialisieren der curl-session */
  curl_handle = curl_easy_init();

  /* Zusammensetzen der http-Adresse durch Anhaengen der query-GI-Nummer,
     des Hit-from, des Hit-to Wertes und des Rueckgabetyps an den ersten
     Teil der HTTP-Adresse */
  gt_str_append_str(http_adr, ARGUMENTSSTRUCT(curl_fcgi_db));
  gt_str_append_cstr(http_adr, "&id=gi|");
  gt_str_append_str(http_adr, parsestruct_ptr->hit_gi_nr_tmp);
  gt_str_append_cstr(http_adr, "&seq_start=");
  gt_str_append_cstr(http_adr,
                  gt_str_array_get(MATRIXSTRUCT(hit_from), hit_counter));
  gt_str_append_cstr(http_adr, "&seq_stop=");
  gt_str_append_cstr(http_adr,
                  gt_str_array_get(MATRIXSTRUCT(hit_to), hit_counter));
  gt_str_append_cstr(http_adr, "&retmode=xml");

  /* char-Zeiger wird benoetigt, da curl_easy_setopt als 3. Parameter
     einen char-Zeiger erwartet */
  http_adr_ptr = gt_str_get(http_adr);

  /* festlegen, welche HTTP-Adresse aufgerufen werden soll */
  curl_easy_setopt(curl_handle, CURLOPT_URL, http_adr_ptr);

  /* die empfangenen Daten werden an die Funktion WriteMemoryCallback
     gesendet, wo Speicherplatz reserviert und die Daten in diesen
     Speicherbereich kopiert werden */
  curl_easy_setopt(curl_handle, CURLOPT_WRITEFUNCTION,
                   WriteMemoryCallback);

  /* Die Daten werden in die Struktur eingetragen */
  curl_easy_setopt(curl_handle, CURLOPT_WRITEDATA, (void *) &memorystruct);

  /* setzen des user-agent field, da einige Server diesen voraussetzen */
  curl_easy_setopt(curl_handle, CURLOPT_USERAGENT, "libcurl-agent/1.0");

  /* Anfrage wird ausgefuehrt */
  curl_errornr = curl_easy_perform(curl_handle);
  curlerror = curl_easy_strerror(curl_errornr);

  if (curl_errornr)
  {
    gt_error_set(err,
              "an error occurred during curl-processing (error-code %d):\
               \"%s\"", curl_errornr, curlerror);
    had_err = -1;
  }

  if (!had_err)
  {
    /* Die Hit-DNA steht zwischen dem  und dem
        XML-Tag, Zeiger auf das < Zeichen von
        */
    seq_pos = strstr(memorystruct.memory, "");

    if (!seq_pos)
    {
      gt_error_set(err,
                "an error occurred while retrieving sequence-information\
                 with the following request: \"%s\"", http_adr_ptr);
      had_err = -1;
    }

    if (!had_err)
    {
      /* seq_pos+16 zeigt auf das erste Zeichen der Sequence; gezaehlt
         wird die Laenge bis zum naechsten Zeichen das kein g,a,c oder t
         etc. ist */
      gt_assert(seq_pos != NULL);
      seq_len = strspn(seq_pos + 16, "gactrymkswhbvdnu");

      numb_from = atol(gt_str_array_get(MATRIXSTRUCT(hit_from), hit_counter));
      numb_to = atol(gt_str_array_get(MATRIXSTRUCT(hit_to), hit_counter));

      numb_diff = numb_to - numb_from +1;

      if (numb_diff == seq_len)
      {
        /* seq_len Zeichen werden in die Hilfsvariable seq_var kopiert */
        gt_str_append_cstr_nt(seq_var, seq_pos + 16, seq_len);

        /* Die Sequenz in seq_var wird in das GtStrArray hit_dna kopiert */
        gt_str_array_add_cstr(MATRIXSTRUCT(hit_dna), gt_str_get(seq_var));

        /* das Hit-Sequenz-File wird geschrieben; die erste Zeile eines
           Eintrages ist die Hit-GI-Def, an die durch ein Leerzeichen
           getrennt die Hsp-Num des jeweiligen Hits angehaengt wird */
        gt_file_xprintf(parsestruct_ptr->fp_blasthit_file, ">%s ",
                           gt_str_array_get(MATRIXSTRUCT(hit_num),
                                            hit_counter));
        gt_file_xprintf(parsestruct_ptr->fp_blasthit_file, "%s ",
                           gt_str_array_get(MATRIXSTRUCT(hit_from),
                                            hit_counter));
        gt_file_xprintf(parsestruct_ptr->fp_blasthit_file, "%s ",
                           gt_str_array_get(MATRIXSTRUCT(hit_to),
                                            hit_counter));
        gt_file_xprintf(parsestruct_ptr->fp_blasthit_file, "%s ",
                           gt_str_array_get(MATRIXSTRUCT(fasta_row),
                                            hit_counter));
        gt_file_xprintf(parsestruct_ptr->fp_blasthit_file, "%s\n",
                           gt_str_array_get(MATRIXSTRUCT(hit_gi_def),
                                            hit_counter));

        /* nach dem GI-Def Eintrag folgt in der naechsten Zeile die Sequenz */
        gt_file_xprintf(parsestruct_ptr->fp_blasthit_file, "%s\n",
                        gt_str_get(seq_var));
      }
      else
      {
        PARSESTRUCT(gi_flag) = 1;
      }
    }
  }
  /* cleanup des Curl-Handle */
  curl_easy_cleanup(curl_handle);

  if (memorystruct.memory)
    free(memorystruct.memory);

  gt_str_delete(http_adr);
  gt_str_delete(seq_var);

  return had_err;
}

#endif

/* Expat-Funktion zur Verarbeitung des Textes zwischen XML-Tags
   Parameter: void-Zeiger auf die (Nutzer)Daten - hier: parsestruct-Struktur;
              Zeiger auf das erste Zeichen nach einem XML-Tag;
              int-Wert der Laenge des Textes zwischen den XML-Tags
   Returnwert: void */
static void textElement(void *, const XML_Char *, int);

/* Expat-Funktion zur Behandlung oeffnender XML-Tags
   Parameter: void-Zeiger auf die (Nutzer)Daten - hier: parsestruct-Struktur;
              Name des aktuellen XML-Tags;
              Expat XML-Attribute (nicht verwendet)
   Returnwert: void */
static void XMLCALL startElement(void *, const char *, const char **);

/* Expat-Funktion zur Behandlung schliessender XML-Tags
   Parameter: void-Zeiger auf die (Nutzer)Daten - hier: parsestruct-Struktur;
              Name des aktuellen XML-Tags
   Returnwert: void */
static void XMLCALL endElement(void *, const char *);

/* Funktion zum Setzen von Flags, bei Uebereinstimmung von gesuchtem und
   aktuell oeffnendem XML-Tag-Namen
   Parameter: das zu setzende Flag; der Counter, der das zu betrachtende
              XML-Tag bestimmt; ein Zeichen zur Unterscheidung von Query-,
              Hit- und Hsp-XML-Tags
   Returnwert: void */
static void flag_setting(unsigned short *, unsigned short *, char);

/* Funktion zum Loeschen von Flags, bei Uebereinstimmung von gesuchtem und
   aktuell schliessendem XML-Tag-Namen
   Parameter: das zu setzende Flag; der counter, der das zu betrachtende
              XML-Tag bestimmt; ein Zeichen zur Unterscheidung von Query-,
              Hit- und Hsp-XML-Tags
   Returnwert: void */
static void flag_delete(unsigned short *, unsigned short *, char);

/* Funktion, die den Stand der Counter ueberprueft und bei Bedarf auf
   UNSET setzt; stimmt der Counter mit den definierten Grenzen ueberein
   wird er auf UNSET gesetzt
   Parameter: der counter, der das zu betrachtende XML-Tag bestimmt; ein
              Zeichen zur Unterscheidung von Query-, Hit- und Hsp-XML-Tags
   Returnwert: void */
static void check_counter(unsigned short *, char);

int mg_xmlparser(ParseStruct *parsestruct_ptr, GtFile * fp_xmlfile,
                 GtError * err)
{
  int had_err = 0;

  /* Expat XML-Error setzen */
  enum XML_Error error;

  /* Puffer zum zeilenweisen Einlesen des XML-Files, XML_Parser
     deklarieren */
  GtStr *buf;
  XML_Parser parser;

  /* Check Umgebungsvariablen */
  gt_error_check(err);

  /* Puffer-String anlegen */
  buf = gt_str_new();

  /* XML-Parser wird initialisiert */
  parser = XML_ParserCreate(NULL);
  /* Die Struktur parsestruct wird als UserData gesetzt */
  XML_SetUserData(parser, parsestruct_ptr);
  /* Start- und Endelement Handler werden gesetzt */
  XML_SetElementHandler(parser, startElement, endElement);
  /* Text-Handler setzen */
  XML_SetCharacterDataHandler(parser, textElement);

  while ((gt_str_read_next_line_generic(buf, fp_xmlfile) != EOF) && !had_err)
  {
    PARSESTRUCT(xml_linenumber)++;
    if (PARSESTRUCT(had_err))
    {
      had_err = -1;
    }

    if ((XML_Parse(parser, gt_str_get(buf), gt_str_length(buf), false) ==
         XML_STATUS_ERROR) && !had_err)
    {
      error = XML_GetErrorCode(parser);
      gt_error_set(err,
                "an error occurred parsing line %lu of file \"%s\": %s",
                PARSESTRUCT(xml_linenumber), gt_str_get(PARSESTRUCT(xmlfile)),
                XML_ErrorString(error));

      had_err = -1;
    }
    /* reset line buffer */
    gt_str_reset(buf);
  }

  /* finish parsing */
  if ((XML_Parse(parser, NULL, 0, true) == XML_STATUS_ERROR) && !had_err)
  {
    error = XML_GetErrorCode(parser);
    gt_error_set(err,
              "an error occurred while finishing the parsing of file\
               \"%s\": %s",
              gt_str_get(PARSESTRUCT(xmlfile)), XML_ErrorString(error));

    had_err = -1;
  }

  if (PARSESTRUCT(xml_tag_flag) && !(!had_err) && PARSESTRUCT(giexp_flag))
  {
    gt_str_array_delete(MATRIXSTRUCT(hit_gi_nr));
    gt_str_array_delete(MATRIXSTRUCT(hit_num));
    gt_str_array_delete(MATRIXSTRUCT(hit_dna));
    gt_str_array_delete(MATRIXSTRUCT(hit_gi_def));
    gt_str_array_delete(MATRIXSTRUCT(hit_acc));
    gt_str_array_delete(MATRIXSTRUCT(fasta_row));
    gt_str_array_delete(MATRIXSTRUCT(hit_from));
    gt_str_array_delete(MATRIXSTRUCT(hit_to));
    gt_str_array_delete(MATRIXSTRUCT(hsp_qseq));
    gt_str_array_delete(MATRIXSTRUCT(hsp_hseq));
    gt_str_array_delete(PARSESTRUCT(query_frame_tmp));
    gt_str_array_delete(PARSESTRUCT(hit_frame_tmp));
  }

  /* Freigeben des XML-Parser und loeschen des Puffer-Strings */
  XML_ParserFree(parser);
  gt_str_delete(buf);

  return had_err;
}

static void XMLCALL startElement(void *data, const char *name,
                                 GT_UNUSED const char **atts)
{
  ParseStruct *parsestruct_ptr = (ParseStruct *) data;

  if (!PARSESTRUCT(had_err))
  {
    /* Vergleich des aktuellen XML-Tags mit dem aktuellen Tag-Namen im
       jew. GtArray bei Uebereinstimmung wird das jeweilige Flag gesetzt */
    if (strcmp
        (name,
         gt_str_array_get(PARSESTRUCT(query_array),
                      XMLPARSERSTRUCT(query_array_index_start))) == 0)
    {
      flag_setting(&XMLPARSERSTRUCT(query_array_index_start),
                   &PARSESTRUCT(def_flag), 'q');
    }
    else
      if (strcmp
          (name,
           gt_str_array_get(PARSESTRUCT(hit_array),
                        XMLPARSERSTRUCT(hit_array_index_start))) == 0)
    {
      flag_setting(&XMLPARSERSTRUCT(hit_array_index_start),
                   &PARSESTRUCT(hit_flag), 'h');
    }
    else
      if (strcmp
          (name,
           gt_str_array_get(PARSESTRUCT(hit_hsp_array),
                        XMLPARSERSTRUCT(hit_hsp_array_index_start))) == 0)
    {
      flag_setting(&XMLPARSERSTRUCT(hit_hsp_array_index_start),
                   &PARSESTRUCT(hit_hsp_flag), 't');
    }
  }
}

static void XMLCALL endElement(void *data, const char *name)
{
  ParseStruct *parsestruct_ptr = (ParseStruct *) data;

  if (!PARSESTRUCT(had_err))
  {
    GtError *err = PARSESTRUCT(err);

    /* Laenge der GI-Nr in einem GI-Def-XML-Eintrag */
    unsigned short gi_len = 0;

    /* Temp-Variablen zum Zwischenspeichern der Query-Start- bzw.
       -End-Werte sowie der Frame-Informationen */
    unsigned long ulong_numb_buf = 0,
      query_nr = 0, **query_nr_p;
    long numb_buf = 0;

    /* Zeiger auf die erste Zahl der GI-Nr in einem Hit-ID-XML-Eintrag */
    const char *gi_ptr = NULL;

    /* Check Umgebungsvariablen */
    gt_error_check(err);

    /* wurde das Iteration_hits XML-Tag erreicht wird die mg_combinedscore
       Methode aufgerufen und diverse Variablen fuer einen neuen Eintrag
       resetet bzw. geloescht */
    if (strcmp(name, gt_str_get(PARSESTRUCT(xml_tag))) == 0
                             && PARSESTRUCT(giexp_flag))
    {
      if (XMLPARSERSTRUCT(hit_counter) > 0)
      {
        PARSESTRUCT(had_err) =
          mg_combinedscore(parsestruct_ptr, XMLPARSERSTRUCT(hit_counter),
                           err);

        /* Zaehler der Hits pro Hit-GI-Nr */
        XMLPARSERSTRUCT(hit_counter) = 0;
        PARSESTRUCT(gi_flag) = 0;

        gt_array_reset(MATRIXSTRUCT(query_from));
        gt_array_reset(MATRIXSTRUCT(query_to));
        gt_array_reset(MATRIXSTRUCT(hit_frame));
        gt_array_reset(MATRIXSTRUCT(query_frame));
      }

      /* Schreiben der schliessenden XML-Tags nach der Hit-Bearbeitung */
      if (ARGUMENTSSTRUCT(outputfile_format) == 3)
      {
        /* Abschluss des Iteration-Bereichs im XML-File */
        mg_outputwriter(parsestruct_ptr, NULL, NULL, NULL, 'x', err);
      }

      gt_str_array_delete(MATRIXSTRUCT(hit_gi_nr));
      gt_str_array_delete(MATRIXSTRUCT(hit_gi_def));
      gt_str_array_delete(MATRIXSTRUCT(hit_acc));
      gt_str_array_delete(MATRIXSTRUCT(fasta_row));
      gt_str_array_delete(MATRIXSTRUCT(hit_num));

      gt_str_array_delete(MATRIXSTRUCT(hit_dna));
      gt_str_array_delete(MATRIXSTRUCT(hit_from));
      gt_str_array_delete(MATRIXSTRUCT(hit_to));
      gt_str_array_delete(MATRIXSTRUCT(hsp_qseq));
      gt_str_array_delete(MATRIXSTRUCT(hsp_hseq));
      gt_str_array_delete(PARSESTRUCT(query_frame_tmp));
      gt_str_array_delete(PARSESTRUCT(hit_frame_tmp));

      PARSESTRUCT(xml_tag_flag) = MGTH_UNSET;
    }
    /* nur wenn ein Flag gesetzt ist und Text eingelesen wurde, ist eine
       weitere Bearbeitung notwendig */
    if ((PARSESTRUCT(def_flag) == 1 || PARSESTRUCT(hit_flag) == 1
         || PARSESTRUCT(hit_hsp_flag) == 1))
    {
      /* Anhand der Query-GI-Def kann mittels Hash-Table und
         GtBioseq-Struktur die Query-DNA ausgelesen werden */
      if (strcmp(name, gt_str_array_get(PARSESTRUCT(query_array), 0)) == 0
                                    && PARSESTRUCT(giexp_flag))
      {
        /* Query-DNA-Strings fuer die Sequenz und die Definition werden
           geloescht, bevor der neue Eintrag hineinkopiert wird */
        gt_str_reset(MATRIXSTRUCT(query_dna));
        gt_str_reset(MATRIXSTRUCT(query_def));

        /* Abspeichern der Query-Def */
        gt_str_set(MATRIXSTRUCT(query_def), gt_str_get(PARSESTRUCT(buf_ptr)));

        /* Erzeugen von StringArrays zur Aufnahme der
           Hit-DNA-Sequenz-Informationen */
        MATRIXSTRUCT(hit_gi_nr) = gt_str_array_new();
        MATRIXSTRUCT(hit_num) = gt_str_array_new();
        MATRIXSTRUCT(hit_dna) = gt_str_array_new();
        MATRIXSTRUCT(hit_gi_def) = gt_str_array_new();
        MATRIXSTRUCT(hit_acc) = gt_str_array_new();
        MATRIXSTRUCT(fasta_row) = gt_str_array_new();
        MATRIXSTRUCT(hit_from) = gt_str_array_new();
        MATRIXSTRUCT(hit_to) = gt_str_array_new();
        MATRIXSTRUCT(hsp_qseq) = gt_str_array_new();
        MATRIXSTRUCT(hsp_hseq) = gt_str_array_new();
        PARSESTRUCT(query_frame_tmp) = gt_str_array_new();
        PARSESTRUCT(hit_frame_tmp) = gt_str_array_new();

        /* Fuer den Fall eines Parse-Fehlers - Das Flag zeigt an, dass die
           Strings angelegt und nicht geloescht wurden */
        PARSESTRUCT(xml_tag_flag) = MGTH_SET;

        /* Auslesen der Eintrags-Nr aus der Hashtabelle */
        if ((query_nr_p = gt_cstr_nofree_ulp_gt_hashmap_get(
               PARSESTRUCT(queryhash), gt_str_get(PARSESTRUCT(buf_ptr)))))
        {
          char *seq;
          query_nr = **query_nr_p;
          seq = gt_bioseq_get_sequence(PARSESTRUCT(queryseq), query_nr);
          /* Abspeichern der zur Query-Def passenden Query-DNA */
          gt_str_append_cstr_nt(MATRIXSTRUCT(query_dna), seq,
                                gt_bioseq_get_sequence_length(PARSESTRUCT
                                                              (queryseq),
                                                              query_nr));
          gt_free(seq);
          mg_outputwriter(parsestruct_ptr, NULL, NULL, NULL, 'q', err);
        }
        else
        {
          gt_error_set(err,
                    "query-dna entry in xml-file does not exist in\
                     query-hash. wrong query-dna file?");
          PARSESTRUCT(had_err) = -1;
        }
      }
      /* Hit_id liefert die GI-Nummer, die fuer die efetch-NCBI-Abfrage
         benoetigt wird */
      else
        if ((strcmp(name, gt_str_array_get(PARSESTRUCT(hit_array), 0)) == 0))
      {
        /* loeschen des alten hit_gi_nr Eintrages */
        gt_str_reset(PARSESTRUCT(hit_gi_nr_tmp));
        gt_str_reset(PARSESTRUCT(fasta_row));

        gt_str_set(PARSESTRUCT(fasta_row), gt_str_get(PARSESTRUCT(buf_ptr)));

        /* gi_ptr zeigt auf die erste Zahl der Hit-GI-Nummer */
        gi_ptr = strchr(gt_str_get(PARSESTRUCT(buf_ptr)), '|');

        gt_assert(gi_ptr != NULL);
        gi_ptr = gi_ptr + 1;

        if (!isalpha(*gi_ptr))
        {
          /* bestimmen der GI-Nummer Laenge; strspn liest solange Zeichen,
             bis ein Zeichen auftritt, dass nicht im angegebenen String
             auftaucht - hier: '|' */
          gi_len = strspn(gi_ptr + 1, "0123456789") + 1;

          /* Die GI-Nummer der Laenge gi_len wird abgespeichert */
          gt_str_append_cstr_nt(PARSESTRUCT(hit_gi_nr_tmp), gi_ptr, gi_len);
        }
        else
        {
          gt_error_set(err,
                    "incorrect gi-hit-number in xmlfile - required format\
                     is gi|[0-9]");
          PARSESTRUCT(had_err) = -1;
        }
      }
      /* einlesen der hit_gi_def */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_array), 1)) == 0
                                         && PARSESTRUCT(giexp_flag))
      {
        gt_str_set(PARSESTRUCT(gi_def_tmp), gt_str_get(PARSESTRUCT(buf_ptr)));
      }
      /* einlesen der hit_acc_nr */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_array), 2)) == 0
                                         && PARSESTRUCT(giexp_flag))
      {
        gt_str_set(PARSESTRUCT(gi_acc_tmp), gt_str_get(PARSESTRUCT(buf_ptr)));
      }
      /* abspeichern der Hit-GI-Def, Hit-ACC-Nr. und der Hsp-num -
         Kombination ist Bestandteil der eindeutigen Hit-FASTA-Zeile im
         Hit-File und dient der Identifizierung der Hit-DNA-Sequenzen im
         XML-File */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_hsp_array), 0)) ==
               0 && PARSESTRUCT(giexp_flag))
      {
        /* Die GI-Nummer wird entsprechend ihrer Laenge gi_len
           abgespeichert */
        gt_str_array_add_cstr(MATRIXSTRUCT(hit_gi_nr),
                          gt_str_get(PARSESTRUCT(hit_gi_nr_tmp)));
        /* einlesen der aktuellen hit_gi_def */
        gt_str_array_add_cstr(MATRIXSTRUCT(hit_gi_def),
                          gt_str_get(PARSESTRUCT(gi_def_tmp)));
        /* einlesen der aktuellen hit_accession-number */
        gt_str_array_add_cstr(MATRIXSTRUCT(hit_acc),
                          gt_str_get(PARSESTRUCT(gi_acc_tmp)));
        gt_str_array_add_cstr(MATRIXSTRUCT(fasta_row),
                          gt_str_get(PARSESTRUCT(fasta_row)));
        /* einlesen der aktuellen hit_num */
        gt_str_array_add_cstr(MATRIXSTRUCT(hit_num),
                          gt_str_get(PARSESTRUCT(buf_ptr)));
      }
      /* Der Query-Start-Wert wird gespeichert */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_hsp_array), 1)) ==
               0 && PARSESTRUCT(giexp_flag))
      {
        /* Der Query-from Wert wird als Long-Wert gespeichert, dazu
           zunaechst Umwandlung des Strings mittels atol */
        ulong_numb_buf = atol(gt_str_get(PARSESTRUCT(buf_ptr)));
        /* Der Query-from Wert wird zum GtArray query_from hinzugefuegt */
        gt_array_add_elem(MATRIXSTRUCT(query_from), &ulong_numb_buf,
                       sizeof (unsigned long));
      }
      /* Query-Stop-Wert wird gespeichert/Bearbeitung siehe
         Query-Start-Wert */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_hsp_array), 2)) ==
               0 && PARSESTRUCT(giexp_flag))
      {
        ulong_numb_buf = atol(gt_str_get(PARSESTRUCT(buf_ptr)));
        gt_array_add_elem(MATRIXSTRUCT(query_to), &ulong_numb_buf,
                       sizeof (unsigned long));
      }
      /* Hit-from XML-Tag */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_hsp_array), 3)) ==
               0)
      {
        if (PARSESTRUCT(giexp_flag))
        {
          /* Speichern des Hit-from Wertes in der matrix_info Struktur
             innerhalb der parsestruct-Struktur */
          gt_str_array_add_cstr(MATRIXSTRUCT(hit_from),
                               gt_str_get(PARSESTRUCT(buf_ptr)));
        }
        else
        {
          gt_file_xprintf(HITFILEOUT, "%s ",
                             gt_str_get(PARSESTRUCT(hit_gi_nr_tmp)));
          gt_file_xprintf(HITFILEOUT, "%s ",
                             gt_str_get(PARSESTRUCT(buf_ptr)));
        }
      }
      /* Hit-to XML-Tag - Bearbeitung siehe Hit-from-Tag */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_hsp_array), 4)) ==
               0)
      {
        if (PARSESTRUCT(giexp_flag))
        {
          /* Speichern des Hit-from Wertes in der matrix_info Struktur
             innerhalb der parsestruct-Struktur */
          gt_str_array_add_cstr(MATRIXSTRUCT(hit_to),
                            gt_str_get(PARSESTRUCT(buf_ptr)));
        }
        else
        {
          gt_file_xprintf(HITFILEOUT, "%s \n",
                             gt_str_get(PARSESTRUCT(buf_ptr)));
        }
      }
      /* Query-Frame XML-Tag; bei der Berechnung der Combined-Scores
         bilden die Hits Cluster entsprechend der Query-Frames;
         Speicherung der Frames erfolgt als Long-Wert */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_hsp_array), 5)) ==
               0 && PARSESTRUCT(giexp_flag))
      {
        /* abspeichern des query_frames fuer die FASTA-File Zeile im
           Hit-File als String */
        gt_str_array_add_cstr(PARSESTRUCT(query_frame_tmp),
                          gt_str_get(PARSESTRUCT(buf_ptr)));

        /* abspeichern des query_frames fuer spaetere Sequenzberechnnugen
           als long Value */
        numb_buf = atol(gt_str_get(PARSESTRUCT(buf_ptr)));
        gt_array_add_elem(MATRIXSTRUCT(query_frame), &numb_buf, sizeof (long));
      }
      /* Hit-Frame XML-Tag/Bearbeitung siehe Query-Frame XML-Tag als
         String */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_hsp_array), 6)) ==
               0 && PARSESTRUCT(giexp_flag))
      {
        /* abspeichern des hit_frames fuer die FASTA-File Zeile im
           Hit-File */
        gt_str_array_add_cstr(PARSESTRUCT(hit_frame_tmp),
                          gt_str_get(PARSESTRUCT(buf_ptr)));

        /* abspeichern des hit_frames fuer spaetere Sequenzberechnnugen
           als long Value */
        numb_buf = atol(gt_str_get(PARSESTRUCT(buf_ptr)));
        gt_array_add_elem(MATRIXSTRUCT(hit_frame), &numb_buf, sizeof (long));

        /* Wenn ein Hit-FASTA-File vorliegt existiert eine GtBioseq-Struktur
           und eine Hashtabelle, ueber die die Hit-Sequenz-Informationen
           eingelesen werden */

        unsigned long hit_nr = 0;

        GtStr *hit_tmp;
        GtStr *hit_dna_tmp;

        hit_tmp = gt_str_new();
        hit_dna_tmp = gt_str_new();

        /* Die Fasta-Zeile im Hit-File besteht aus der Hit-Gi-Def, der
           Accession-Nr, der Hit-Hsp-Nr, dem Hit-From und Hit-To Wert
           sowie des Query- und Hit-Frames getrennt durch ein
           Leerzeichen; Zeile muss eindeutig sein - durch diese
           Kombination ist dies gewaehrleistet */

        gt_str_set(hit_tmp,
                gt_str_array_get(MATRIXSTRUCT(hit_gi_nr),
                             XMLPARSERSTRUCT(hit_counter)));
        gt_str_append_cstr(hit_tmp, " ");
        gt_str_append_cstr(hit_tmp,
                        gt_str_array_get(MATRIXSTRUCT(hit_from),
                                     XMLPARSERSTRUCT(hit_counter)));
        gt_str_append_cstr(hit_tmp, " ");
        gt_str_append_cstr(hit_tmp,
                        gt_str_array_get(MATRIXSTRUCT(hit_to),
                                     XMLPARSERSTRUCT(hit_counter)));
        gt_str_append_cstr(hit_tmp, " ");
        gt_str_append_cstr(hit_tmp,
                        gt_str_array_get(MATRIXSTRUCT(fasta_row),
                                     XMLPARSERSTRUCT(hit_counter)));
        gt_str_append_cstr(hit_tmp, " ");
        gt_str_append_cstr(hit_tmp,
                        gt_str_array_get(MATRIXSTRUCT(hit_gi_def),
                                     XMLPARSERSTRUCT(hit_counter)));

        /* Hit-Hashtabelle enthaelt den konstruierten Eintrag */
        if ((query_nr_p = gt_cstr_nofree_ulp_gt_hashmap_get(
               PARSESTRUCT(hithash), gt_str_get(hit_tmp))))
        {
          char *seq;
          /* Positionsbestimmung des Eintrages in der GtBioseq-Struktur */
          hit_nr = **query_nr_p;
          seq = gt_bioseq_get_sequence(PARSESTRUCT(hitseq), hit_nr);
          /* auslesen der Sequenzinformation */
          gt_str_append_cstr_nt(hit_dna_tmp, seq,
                                gt_bioseq_get_sequence_length(PARSESTRUCT
                                                              (hitseq),
                                                              hit_nr));
          gt_free(seq);
          /* abspeichern der Hit-DNA in der Matrix-Info Struktur */
          gt_str_array_add_cstr(MATRIXSTRUCT(hit_dna), gt_str_get(hit_dna_tmp));
        }
        /* Falls kein Eintrag in der Hashtabelle gefunden wurde,
           Fehlercode setzen - falsche Hit-DNA-Datei als Parameter bei
           Programmaufruf angegeben ? */
        else
        {
          /* Hit-GI-Nr nicht in der Hashtabelle, also ueber cURL von
             z.B. NCBI nachladen */
#ifdef CURLDEF
          PARSESTRUCT(had_err) =
            mg_curl(parsestruct_ptr, XMLPARSERSTRUCT(hit_counter), err);
#else
          PARSESTRUCT(gi_flag) = 1;
#endif
        }
        gt_str_delete(hit_tmp);
        gt_str_delete(hit_dna_tmp);
      }
      /* Einlesen der translatierten Query-DNA-Sequenz */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_hsp_array), 7)) ==
               0 && PARSESTRUCT(giexp_flag))
      {
        gt_str_array_add_cstr(MATRIXSTRUCT(hsp_qseq),
                          gt_str_get(PARSESTRUCT(buf_ptr)));
      }
      /* Einlesen der translatierten Hit-DNA-Sequenz */
      else if (strcmp(name, gt_str_array_get(PARSESTRUCT(hit_hsp_array), 8)) ==
               0 && PARSESTRUCT(giexp_flag))
      {
        gt_str_array_add_cstr(MATRIXSTRUCT(hsp_hseq),
                          gt_str_get(PARSESTRUCT(buf_ptr)));
        /* Zaehler fuer die Hits pro GI-Nummer wird um 1 erhoeht */
        XMLPARSERSTRUCT(hit_counter)++;

        if (PARSESTRUCT(gi_flag))
        {
           PARSESTRUCT(gi_flag) = 0;

           gt_str_array_set_size(MATRIXSTRUCT(hit_gi_nr),
                             gt_str_array_size(MATRIXSTRUCT(hit_gi_nr))-1);
           gt_str_array_set_size(MATRIXSTRUCT(hit_gi_def),
                             gt_str_array_size(MATRIXSTRUCT(hit_gi_def))-1);
           gt_str_array_set_size(MATRIXSTRUCT(hit_acc),
                             gt_str_array_size(MATRIXSTRUCT(hit_acc))-1);
           gt_str_array_set_size(MATRIXSTRUCT(fasta_row),
                             gt_str_array_size(MATRIXSTRUCT(fasta_row))-1);
           gt_str_array_set_size(MATRIXSTRUCT(hit_num),
                             gt_str_array_size(MATRIXSTRUCT(hit_num))-1);
           gt_array_set_size(MATRIXSTRUCT(query_from),
                          gt_array_size(MATRIXSTRUCT(query_from))-1);
           gt_array_set_size(MATRIXSTRUCT(query_to),
                          gt_array_size(MATRIXSTRUCT(query_to))-1);
           gt_str_array_set_size(MATRIXSTRUCT(hit_from),
                             gt_str_array_size(MATRIXSTRUCT(hit_from))-1);
           gt_str_array_set_size(MATRIXSTRUCT(hit_to),
                             gt_str_array_size(MATRIXSTRUCT(hit_to))-1);
           gt_array_set_size(MATRIXSTRUCT(query_frame),
                          gt_array_size(MATRIXSTRUCT(query_frame))-1);
           gt_array_set_size(MATRIXSTRUCT(hit_frame),
                          gt_array_size(MATRIXSTRUCT(hit_frame))-1);
           gt_str_array_set_size(MATRIXSTRUCT(hsp_qseq),
                             gt_str_array_size(MATRIXSTRUCT(hsp_qseq))-1);
           gt_str_array_set_size(MATRIXSTRUCT(hsp_hseq),
                             gt_str_array_size(MATRIXSTRUCT(hsp_hseq))-1);

           XMLPARSERSTRUCT(hit_counter)--;
        }
      }

      /* Flagberechnungen */
      if (strcmp
          (name,
           gt_str_array_get(PARSESTRUCT(query_array),
                        XMLPARSERSTRUCT(query_array_index_end))) == 0
          && !PARSESTRUCT(had_err))
      {
        flag_delete(&XMLPARSERSTRUCT(query_array_index_end),
                    &PARSESTRUCT(def_flag), 'q');
      }
      else
        if (strcmp
            (name,
             gt_str_array_get(PARSESTRUCT(hit_array),
                          XMLPARSERSTRUCT(hit_array_index_end))) == 0
            && !PARSESTRUCT(had_err))
      {
        flag_delete(&XMLPARSERSTRUCT(hit_array_index_end),
                    &PARSESTRUCT(hit_flag), 'h');
      }
      else
        if (strcmp
            (name,
             gt_str_array_get(PARSESTRUCT(hit_hsp_array),
                          XMLPARSERSTRUCT(hit_hsp_array_index_end))) == 0
            && !PARSESTRUCT(had_err))
      {
        flag_delete(&XMLPARSERSTRUCT(hit_hsp_array_index_end),
                    &PARSESTRUCT(hit_hsp_flag), 't');
      }

      /* Der Lesepuffer fuer den Text zwischen 2 XML-Tags wird resetet */
      gt_str_reset(PARSESTRUCT(buf_ptr));
    }
  }
}

static void textElement(void *data, const XML_Char *txt_element, int len)
{
  ParseStruct *parsestruct_ptr = (ParseStruct *) data;

  if (!PARSESTRUCT(had_err))
  {
    /* falls ein Flag gesetzt ist (relevanter XML-Tag Zwischenbereich),
       wird mit der Bearbeitung der Textpassage begonnen; dazu wird der
       "aktuelle Text" txt_element an den bereits eingelesenen Text angehaengt
     */
    if (PARSESTRUCT(hit_flag) == MGTH_SET || PARSESTRUCT(def_flag) == MGTH_SET
        || PARSESTRUCT(hit_hsp_flag) == MGTH_SET)
    {
      gt_str_append_cstr_nt(PARSESTRUCT(buf_ptr), txt_element, len);
    }
  }
}

static void flag_setting(unsigned short *counter_fct, unsigned short *flag,
                         char flag_sign)
{
  /* das uebergebene Flag wird auf SET gesetzt und der Counter um eine
     Stelle auf den naechsten Tag-Namen in der Struktur weitergesetzt */
  *flag = MGTH_SET;
  (*counter_fct)++;

  /* ueberpruefen, ob der Counter die Grenzen zur naechsten Kategorie
     erreicht hat */
  check_counter(counter_fct, flag_sign);
}

static void flag_delete(unsigned short *counter_fct, unsigned short *flag,
                        char flag_sign)
{
  /* das uebergebene Flag wird auf UNSET gesetzt und der Counter um eine
     Stelle auf den naechsten Tag-Namen in der Struktur weitergesetzt */
  *flag = MGTH_UNSET;
  (*counter_fct)++;

  /* ueberpruefen, ob der Counter die Grenzen zur neachsten Kategorie
     erreicht hat */
  check_counter(counter_fct, flag_sign);
}

static void check_counter(unsigned short *counter_check,
                          char flag_sign_fct)
{
  /* ist das Ende der aktuellen XML-Tag Kategorie erreicht, werden die
     Counter wieder auf den Anfang (0) zurueckgesetzt; das flag_sign zeigt
     an,um welchen counter es sich aktuell handelt */
  if (*counter_check == MGTH_QUERY_SIZE && flag_sign_fct == 'q')
  {
    *counter_check = 0;
  }
  if (*counter_check == MGTH_HIT_SIZE && flag_sign_fct == 'h')
  {
    *counter_check = 0;
  }
  if (*counter_check == MGTH_HIT_TO_QUERY_SIZE && flag_sign_fct == 't')
  {
    *counter_check = 0;
  }
}
genometools-1.5.1/src/mgth/mg_xmlparser.h000066400000000000000000000022031211610345200204400ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#ifndef MG_XMLPARSER_H
#define MG_XMLPARSER_H

#include "metagenomethreader.h"

/* Funktion zum Aufruf des XML-Parsers
   Parameter: Zeiger auf ParseStruct-Struktur, Zeiger auf die XML-Datei,
              Env-Variable
   Returnwert: had_err */
int mg_xmlparser(ParseStruct *, GtFile *, GtError *);

#endif
genometools-1.5.1/src/skproto.c000066400000000000000000000020671211610345200165050ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2001      Stefan Kurtz 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/tooldriver.h"
#include "tools/gt_skproto.h"

int main(int argc, char *argv[])
{
  return gt_toolobjdriver(gt_skproto, argc, argv);
}
genometools-1.5.1/src/tools/000077500000000000000000000000001211610345200157735ustar00rootroot00000000000000genometools-1.5.1/src/tools/gt_bed_to_gff3.c000066400000000000000000000106651211610345200210020ustar00rootroot00000000000000/*
  Copyright (c) 2008-2009, 2011 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "extended/bed_parser.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/bed_in_stream_api.h"
#include "tools/gt_bed_to_gff3.h"

typedef struct {
  GtStr *feature_type,
        *thick_feature_type,
        *block_type;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} BEDToGFF3Arguments;

static void *gt_bed_to_gff3_arguments_new(void)
{
  BEDToGFF3Arguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->feature_type = gt_str_new();
  arguments->thick_feature_type = gt_str_new();
  arguments->block_type = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_bed_to_gff3_arguments_delete(void *tool_arguments)
{
  BEDToGFF3Arguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->block_type);
  gt_str_delete(arguments->thick_feature_type);
  gt_str_delete(arguments->feature_type);
  gt_free(arguments);
}

static GtOptionParser* gt_bed_to_gff3_option_parser_new(void *tool_arguments)
{
  BEDToGFF3Arguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *o;

  op = gt_option_parser_new("[BED_file]",
                            "Parse BED file and convert it to GFF3.");

  o = gt_option_new_string("featuretype", "Set type of parsed BED features",
                           arguments->feature_type, BED_FEATURE_TYPE);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_string("thicktype", "Set type of parsed thick BED features",
                           arguments->thick_feature_type,
                           BED_THICK_FEATURE_TYPE);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_string("blocktype", "Set type of parsed BED blocks",
                           arguments->block_type, BED_BLOCK_TYPE);
  gt_option_parser_add_option(op, o);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_max_args(op, 1);

  return op;
}

static int gt_bed_to_gff3_runner(GT_UNUSED int argc, const char **argv,
                                 int parsed_args, void *tool_arguments,
                                 GtError *err)
{
  GtNodeStream *bed_in_stream = NULL, *gff3_out_stream = NULL;
  BEDToGFF3Arguments *arguments = tool_arguments;
  int had_err;

  gt_error_check(err);

  /* create a BED input stream */
  bed_in_stream = gt_bed_in_stream_new(argv[parsed_args]);
  gt_bed_in_stream_set_feature_type((GtBEDInStream*) bed_in_stream,
                                    gt_str_get(arguments->feature_type));
  gt_bed_in_stream_set_thick_feature_type((GtBEDInStream*) bed_in_stream,
                                          gt_str_get(arguments
                                                     ->thick_feature_type));
  gt_bed_in_stream_set_block_type((GtBEDInStream*) bed_in_stream,
                                  gt_str_get(arguments->block_type));

  /* create a GFF3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(bed_in_stream, arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(bed_in_stream);

  return had_err;
}

GtTool* gt_bed_to_gff3(void)
{
  return gt_tool_new(gt_bed_to_gff3_arguments_new,
                     gt_bed_to_gff3_arguments_delete,
                     gt_bed_to_gff3_option_parser_new,
                     NULL,
                     gt_bed_to_gff3_runner);
}
genometools-1.5.1/src/tools/gt_bed_to_gff3.h000066400000000000000000000016411211610345200210010ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_BED_TO_GFF3_H
#define GT_BED_TO_GFF3_H

#include "core/tool_api.h"

/* the BED to GFF3 tool */
GtTool* gt_bed_to_gff3(void);

#endif
genometools-1.5.1/src/tools/gt_cds.c000066400000000000000000000131241211610345200174030ustar00rootroot00000000000000/*
  Copyright (c) 2006-2011 Gordon Gremme 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "extended/cds_stream_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gtdatahelp.h"
#include "extended/seqid2file.h"
#include "tools/gt_cds.h"

#define GT_CDS_SOURCE_TAG "gt cds"

typedef struct {
  unsigned int minorflen;
  bool start_codon,
       final_stop_codon,
       generic_start_codons,
       verbose;
  GtSeqid2FileInfo *s2fi;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} CDSArguments;

static void* gt_cds_arguments_new(void)
{
  CDSArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_cds_arguments_delete(void *tool_arguments)
{
  CDSArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_free(arguments);
}

static GtOptionParser* gt_cds_option_parser_new(void *tool_arguments)
{
  CDSArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [GFF3_file]",
                            "Add CDS (coding sequence) features to exon "
                            "features given in GFF3 file.");

  /* -minorflen */
  option = gt_option_new_uint_min("minorflen", "set the minimum length an open "
                                  "reading frame (ORF) must have to be added "
                                  "as a CDS feature (measured in amino acids)",
                                  &arguments->minorflen, 64, 1);
  gt_option_parser_add_option(op, option);

  /* -startcodon */
  option = gt_option_new_bool("startcodon", "require than an ORF must begin "
                              "with a start codon", &arguments->start_codon,
                              false);
  gt_option_parser_add_option(op, option);

  /* -finalstopcodon */
  option = gt_option_new_bool("finalstopcodon", "require that the final ORF "
                              "must end with a stop codon",
                              &arguments->final_stop_codon, false);
  gt_option_parser_add_option(op, option);

  /* -genericstartcodons */
  option = gt_option_new_bool("genericstartcodons", "use generic start codons",
                              &arguments->generic_start_codons, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -seqfile, -matchdesc, -usedesc and -regionmapping */
  gt_seqid2file_register_options(op, arguments->s2fi);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_max_args(op, 1);

  return op;
}

static int gt_cds_runner(GT_UNUSED int argc, const char **argv, int parsed_args,
                         void *tool_arguments, GtError *err)
{
  GtNodeStream *gff3_in_stream, *cds_stream = NULL, *gff3_out_stream = NULL;
  CDSArguments *arguments = tool_arguments;
  GtRegionMapping *region_mapping;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  /* create gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);

  /* create region mapping */
  region_mapping = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
  if (!region_mapping)
    had_err = -1;

  if (!had_err) {
    /* create CDS stream */
    cds_stream = gt_cds_stream_new(gff3_in_stream, region_mapping,
                                   arguments->minorflen, GT_CDS_SOURCE_TAG,
                                   arguments->start_codon,
                                   arguments->final_stop_codon,
                                   arguments->generic_start_codons);

    /* create gff3 output stream */
    gff3_out_stream = gt_gff3_out_stream_new(cds_stream, arguments->outfp);

    /* pull the features through the stream and free them afterwards */
    had_err = gt_node_stream_pull(gff3_out_stream, err);
  }

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(cds_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool* gt_cds(void)
{
  return gt_tool_new(gt_cds_arguments_new,
                     gt_cds_arguments_delete,
                     gt_cds_option_parser_new,
                     NULL,
                     gt_cds_runner);
}
genometools-1.5.1/src/tools/gt_cds.h000066400000000000000000000017431211610345200174140ustar00rootroot00000000000000/*
  Copyright (c) 2006-2008 Gordon Gremme 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_CDS_H
#define GT_CDS_H

#include "core/tool_api.h"

/* the coding sequence (CDS) tool */
GtTool* gt_cds(void);

#endif
genometools-1.5.1/src/tools/gt_chain2dim.c000066400000000000000000000260511211610345200204730ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "core/tool_api.h"
#include "gt_chain2dim.h"

static void *gt_chain2dim_arguments_new (void)
{
  return gt_malloc (sizeof (GtChain2dimoptions));
}

static void gt_chain2dim_arguments_delete (void *tool_arguments)
{
  GtChain2dimoptions *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete (arguments->matchfile);
  gt_str_array_delete (arguments->globalargs);
  gt_str_array_delete (arguments->localargs);
  gt_option_delete (arguments->refoptionmaxgap);
  gt_option_delete (arguments->refoptionweightfactor);
  gt_option_delete (arguments->refoptionglobal);
  gt_option_delete (arguments->refoptionlocal);
  gt_free (arguments);
}

static GtOptionParser *gt_chain2dim_option_parser_new (void *tool_arguments)
{
  GtChain2dimoptions *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionglobal, *optionlocal;

  gt_assert (arguments != NULL);
  arguments->matchfile = gt_str_new ();
  arguments->globalargs = gt_str_array_new();
  arguments->localargs = gt_str_array_new();

  op = gt_option_parser_new("[options] -m matchfile",
                            "Chain pairwise matches.");

  gt_option_parser_set_mail_address(op, "");
  option = gt_option_new_filename("m","Specify file containing the matches\n"
                                  "mandatory option",
                                  arguments->matchfile);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  optionglobal = gt_option_new_string_array("global",
                   "perform global chaining\n"
                   "- optional parameter gc switches\n"
                   "  on gap costs (according to L1-model)\n"
                   "- optional parameter ov means\n"
                   "  that overlaps between matches are allowed\n"
                   "- optional parameter all means\n"
                   "  that all optimal chains are processed",
                   arguments->globalargs);
  gt_option_argument_is_optional(optionglobal);
  arguments->refoptionglobal = gt_option_ref (optionglobal);
  gt_option_parser_add_option(op, optionglobal);

  optionlocal = gt_option_new_string_array("local",
                   "perform local chaining\n"
                   "compute local chains (according to L1-model).\n"
                   "- If no parameter is given, compute local chains with\n"
                   "  maximums score.\n"
                   "- If parameter is given, this must be a positive number\n"
                   "  optionally followed by the character b or p.\n"
                   "- If only the number, say k, is given, this is the "
                   "minimum\n"
                   "  score of the chains output.\n"
                   "- If a number is followed by character b, then output all\n"
                   "  chains with the largest k scores.\n"
                   "- If a number is followed by character p, then output all\n"
                   "  chains with scores at most k percent away\n"
                   "  from the best score.",
                   arguments->localargs);
  gt_option_argument_is_optional(optionlocal);
  gt_option_parser_add_option(op, optionlocal);
  arguments->refoptionlocal = gt_option_ref(optionlocal);
  gt_option_exclude(optionlocal,optionglobal);
  option = gt_option_new_double("wf","specify weight factor > 0.0 to obtain "
                                     "score of a fragment\nrequires one of "
                                     "the options\n-local const\n-global "
                                     "gc\n-global ov",
                                     &arguments->weightfactor,1.0);
  arguments->refoptionweightfactor = gt_option_ref (option);
  gt_option_parser_add_option(op, option);
  option = gt_option_new_ulong("maxgap","specify maximal width of gap in chain",
                                         &arguments->maxgap,0);
  arguments->refoptionmaxgap = gt_option_ref(option);
  gt_option_parser_add_option(op, option);
  option = gt_option_new_bool("silent","do not output the chains but only "
                                       "report their lengths and scores",
                                       &arguments->silent,false);
  gt_option_parser_add_option(op, option);
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);
  return op;
}

static int gt_chain2dim_arguments_check (GT_UNUSED int rest_argc,
                                         void *tool_arguments,
                                         GtError * err)
{
  GtChain2dimoptions *arguments = tool_arguments;
  const char *globalargs = NULL, *localargs = NULL;

  if (gt_option_is_set (arguments->refoptionmaxgap))
  {
    if (arguments->maxgap == 0)
    {
      gt_error_set(err,"argument of option -maxgap must be positive integer");
      return -1;
    }
  }
  if (gt_option_is_set (arguments->refoptionweightfactor))
  {
    if (arguments->weightfactor <= 0.0)
    {
      gt_error_set(err,"argument of option -wf must be positive real value");
      return -1;
    }
  }
  gt_assert(arguments->refoptionglobal != NULL);
  gt_assert(arguments->refoptionlocal != NULL);
  if (gt_option_is_set(arguments->refoptionglobal))
  {
    unsigned long globalargsnum = gt_str_array_size(arguments->globalargs);
    if (globalargsnum > 1UL)
    {
      gt_error_set(err,"option -global can only have one optional argument");
      return -1;
    }
    if (globalargsnum == 1UL)
    {
      globalargs = gt_str_array_get(arguments->globalargs,0);
    }
  }
  if (gt_option_is_set(arguments->refoptionlocal))
  {
    unsigned long localargsnum = gt_str_array_size(arguments->localargs);
    if (localargsnum > 1UL)
    {
      gt_error_set(err,"option -local can only have one optional argument");
      return -1;
    }
    if (localargsnum == 1UL)
    {
      localargs = gt_str_array_get(arguments->localargs,0);
    }
  }
  if (gt_option_is_set(arguments->refoptionweightfactor) &&
      !gt_option_is_set(arguments->refoptionlocal) &&
      globalargs == NULL)
  {
    gt_error_set(err,
                 "option wf requires either option -local or option -global "
                 "with argument %s or %s or %s",
                 GT_CHAIN2DIM_GAPCOSTSWITCH,
                 GT_CHAIN2DIM_OVERLAPSWITCH,
                 GT_CHAIN2DIM_ALLSWITCH);
    return -1;
  }
  arguments->gtchainmode
    = gt_chain_chainmode_new(arguments->maxgap,
                             gt_option_is_set(arguments->refoptionglobal),
                             globalargs,
                             gt_option_is_set(arguments->refoptionlocal),
                             localargs,
                             err);
  return (arguments->gtchainmode == NULL) ? -1 : 0;
}

typedef struct
{
  unsigned long chaincounter;
} Counter;

static void gt_outputformatchaingeneric(
                                bool silent,
                                void *data,
                                const GtChain2Dimmatchtable *matchtable,
                                const GtChain2Dim *chain)
{
  unsigned long idx, chainlength;
  Counter *counter = (Counter *) data;

  chainlength = gt_chain_chainlength(chain);
  printf("# chain %lu: length %lu score %ld\n",
         counter->chaincounter,chainlength,gt_chain_chainscore(chain));
  if (!silent)
  {
    GtChain2Dimmatchvalues value;

    if (gt_chain_storedinreverseorder(chain))
    {
      for (idx=chainlength; idx > 0; idx--)
      {
        gt_chain_extractchainelem(&value, matchtable, chain, idx - 1);
        gt_chain_printchainelem(stdout,&value);
      }
    } else
    {
      for (idx=0; idx < chainlength; idx++)
      {
        gt_chain_extractchainelem(&value, matchtable, chain, idx);
        gt_chain_printchainelem(stdout,&value);
      }
    }
  }
  counter->chaincounter++;
}

void gt_outputformatchainsilent(void *data,
                               const GtChain2Dimmatchtable *matchtable,
                               const GtChain2Dim *chain)
{
  gt_outputformatchaingeneric(true,data,matchtable,chain);
}

void gt_outputformatchain(void *data,
                          const GtChain2Dimmatchtable *matchtable,
                          const GtChain2Dim *chain)
{
  gt_outputformatchaingeneric(false,data,matchtable,chain);
}

static int gt_chain2dim_runner (GT_UNUSED int argc,
                                GT_UNUSED const char **argv,
                                GT_UNUSED int parsed_args,
                                void *tool_arguments,
                                GtError * err)
{
  GtChain2dimoptions *arguments = tool_arguments;
  GtChain2Dimmatchtable *matchtable;
  bool haserr = false;
  GtLogger *logger = NULL;

  gt_error_check (err);
  gt_assert (arguments != NULL);
  gt_assert (parsed_args == argc);

  matchtable = gt_chain_analyzeopenformatfile(arguments->weightfactor,
                                              gt_str_get(arguments->
                                                         matchfile),
                                              err);
  if (matchtable == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    unsigned int presortdim = 1U;
    GtChain2Dim *chain;
    Counter counter;

    logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
    gt_chain_possiblysortmatches(logger, matchtable, presortdim);
    chain = gt_chain_chain_new();
    counter.chaincounter = 0;
    gt_chain_fastchaining(arguments->gtchainmode,
                          chain,
                          matchtable,
                          true,
                          presortdim,
                          true,
                          arguments->silent ? gt_outputformatchainsilent
                                            : gt_outputformatchain,
                          &counter,
                          logger);
    gt_chain_chain_delete(chain);
  }
  gt_chain_chainmode_delete(arguments->gtchainmode);
  gt_chain_matchtable_delete(matchtable);
  if (logger != NULL)
  {
    gt_logger_delete(logger);
  }
  return haserr ? -1 : 0;
}

GtTool *gt_chain2dim (void)
{
  return gt_tool_new (gt_chain2dim_arguments_new,
                      gt_chain2dim_arguments_delete,
                      gt_chain2dim_option_parser_new,
                      gt_chain2dim_arguments_check,
                      gt_chain2dim_runner);
}
genometools-1.5.1/src/tools/gt_chain2dim.h000066400000000000000000000026431211610345200205010ustar00rootroot00000000000000/*
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_CHAIN2DIM_H
#define GT_CHAIN2DIM_H

#include 
#include "core/tool_api.h"
#include "core/str_array_api.h"
#include "core/option_api.h"
#include "match/chain2dim.h"

/* the chain2dim tool */

typedef struct
{
  bool silent,
       verbose;
  double weightfactor;
  unsigned long maxgap;
  GtStr *matchfile;
  GtStrArray *globalargs,
             *localargs;
  GtOption *refoptionmaxgap,
           *refoptionweightfactor,
           *refoptionglobal,
           *refoptionlocal;
  GtChain2Dimmode *gtchainmode;
} GtChain2dimoptions;

GtTool* gt_chain2dim(void);

#endif
genometools-1.5.1/src/tools/gt_chseqids.c000066400000000000000000000104371211610345200204410ustar00rootroot00000000000000/*
  Copyright (c) 2007-2011 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/versionfunc.h"
#include "extended/chseqids_stream.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gtdatahelp.h"
#include "extended/sort_stream_api.h"
#include "tools/gt_chseqids.h"

#define DEFAULT_JOINLENGTH 300

typedef struct {
  bool sort,
       verbose;
  GtFile *outfp;
} ChseqidsArguments;

static GtOPrval parse_options(int *parsed_args, ChseqidsArguments *arguments,
                              int argc, const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOutputFileInfo *ofi;
  GtOption *option;
  GtOPrval oprval;
  gt_error_check(err);

  /* init */
  op = gt_option_parser_new("[option ...] mapping_file [GFF3_file]",
                         "Change sequence ids by the mapping given in "
                         "mapping_file.");
  ofi = gt_output_file_info_new();

  /* -sort */
  option = gt_option_new_bool("sort",
                              "sort the GFF3 features after changing the "
                              "sequence ids\n(memory consumption is "
                              "proportional to the input file size)",
                              &arguments->sort, false);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, ofi);

  /* parse options */
  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_min_max_args(op, 1, 2);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);

  /* free */
  gt_output_file_info_delete(ofi);
  gt_option_parser_delete(op);

  return oprval;
}

int gt_chseqids(int argc, const char **argv, GtError *err)
{
  GtNodeStream *gff3_in_stream, *chseqids_stream, *sort_stream = NULL,
               *gff3_out_stream = NULL;
  ChseqidsArguments arguments;
  GtStr *chseqids;
  int parsed_args, had_err = 0;

  gt_error_check(err);

  /* option parsing */
  switch (parse_options(&parsed_args, &arguments, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR: return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }

  /* create the streams */
  gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args + 1]);
  if (arguments.verbose && arguments.outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);
  chseqids = gt_str_new_cstr(argv[parsed_args]);
  chseqids_stream = gt_chseqids_stream_new(gff3_in_stream, chseqids, err);
  if (!chseqids_stream)
    had_err = -1;
  gt_str_delete(chseqids);
  if (!had_err) {
    if (arguments.sort) {
      sort_stream = gt_sort_stream_new(chseqids_stream);
      gff3_out_stream = gt_gff3_out_stream_new(sort_stream, arguments.outfp);
    }
    else {
      gff3_out_stream = gt_gff3_out_stream_new(chseqids_stream,
                                               arguments.outfp);
    }
  }

  /* pull the features through the stream and free them afterwards */
  if (!had_err)
    had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(chseqids_stream);
  gt_node_stream_delete(sort_stream);
  gt_node_stream_delete(gff3_in_stream);
  gt_file_delete(arguments.outfp);

  return had_err;
}
genometools-1.5.1/src/tools/gt_chseqids.h000066400000000000000000000017621211610345200204470ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_CHSEQIDS_H
#define GT_CHSEQIDS_H

/* the change sequence ids (chseqids) tool */
int gt_chseqids(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_clean.c000066400000000000000000000054561211610345200177250ustar00rootroot00000000000000/*
  Copyright (c) 2007-2011 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/bioseq.h"
#include "core/md5_tab.h"
#include "core/option_api.h"
#include "core/versionfunc.h"
#include "core/xposix.h"
#include "tools/gt_clean.h"

static GtOPrval parse_options(int *parsed_args, int argc, const char **argv,
                              GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  gt_error_check(err);
  op = gt_option_parser_new("",
                            "Remove all files in the current directory which "
                            "are automatically created by gt.");
  gt_option_parser_set_max_args(op, 0);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

static void remove_pattern_in_current_dir(const char *pattern)
{
  char **files_to_remove;
  GtStr *path;
  glob_t g;

  path = gt_str_new_cstr("./*");
  gt_str_append_cstr(path, pattern);
  gt_xglob(gt_str_get(path), GLOB_NOCHECK, NULL, &g);

  /* remove found files */
  if (g.gl_pathc) {
    files_to_remove = g.gl_pathv;
    if (strcmp(*files_to_remove, gt_str_get(path))) {
      while (*files_to_remove) {
        gt_xunlink(*files_to_remove);
        files_to_remove++;
      }
    }
  }

  /* free */
  globfree(&g);
  gt_str_delete(path);
}

int gt_clean(int argc, const char **argv, GtError *err)
{
  int parsed_args;
  gt_error_check(err);

  /* option parsing */
  switch (parse_options(&parsed_args, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR: return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }
  gt_assert(parsed_args == 1);

  remove_pattern_in_current_dir(GT_ENCSEQFILESUFFIX);
  remove_pattern_in_current_dir(GT_SSPTABFILESUFFIX);
  remove_pattern_in_current_dir(GT_DESTABFILESUFFIX);
  remove_pattern_in_current_dir(GT_SDSTABFILESUFFIX);
  remove_pattern_in_current_dir(GT_OISTABFILESUFFIX);
  remove_pattern_in_current_dir(GT_MD5TABFILESUFFIX);

  return 0;
}
genometools-1.5.1/src/tools/gt_clean.h000066400000000000000000000017201211610345200177200ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_CLEAN_H
#define GT_CLEAN_H

/* the clean tool */
int gt_clean(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_compreads.c000066400000000000000000000074661211610345200206230ustar00rootroot00000000000000/*
  Copyright (c) 2011 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/cstr_array.h"
#include "core/unused_api.h"
#include "extended/toolbox.h"
#include "tools/gt_compreads.h"
#include "tools/gt_compreads_refcompress.h"
#include "tools/gt_compreads_refdecompress.h"
#include "tools/gt_compreads_compress.h"
#include "tools/gt_compreads_decompress.h"

static void* gt_compreads_arguments_new(void)
{
  GtToolbox *compreads_toolbox = gt_toolbox_new();
  gt_toolbox_add_tool(compreads_toolbox,
      "refcompress", gt_compreads_refcompress());
  gt_toolbox_add_tool(compreads_toolbox,
      "refdecompress", gt_compreads_refdecompress());
  gt_toolbox_add_tool(compreads_toolbox,
      "compress", gt_compreads_compress());
  gt_toolbox_add_tool(compreads_toolbox,
      "decompress", gt_compreads_decompress());
  return compreads_toolbox;
}

static void gt_compreads_arguments_delete(void *tool_arguments)
{
  GtToolbox *compreads_toolbox = tool_arguments;
  if (!compreads_toolbox)
    return;
  gt_toolbox_delete(compreads_toolbox);
}

static GtOptionParser* gt_compreads_option_parser_new(void *tool_arguments)
{
  GtToolbox *compreads_toolbox = tool_arguments;
  GtOptionParser *op;
  gt_assert(compreads_toolbox);
  op = gt_option_parser_new("[option ...] tool [argument ...]",
                            "Call fastq file compression tool .");
  gt_option_parser_set_comment_func(op, gt_toolbox_show, compreads_toolbox);
  gt_option_parser_set_min_args(op, 1U);
  return op;
}

static int gt_compreads_runner(GT_UNUSED int argc,
                         const char **argv,
                         int parsed_args,
                         void *tool_arguments, GtError *err)
{
  GtToolbox *compreads_toolbox = tool_arguments;
  GtToolfunc toolfunc;
  GtTool *tool = NULL;
  int had_err = 0;
  char **nargv = NULL;

  gt_error_check(err);
  gt_assert(compreads_toolbox);
  if (!gt_toolbox_has_tool(compreads_toolbox, argv[parsed_args])) {
    gt_error_set(err, "compreads tool '%s' not found; option -help lists "
                      "possible tools", argv[parsed_args]);
    had_err = -1;
  }

  if (!had_err) {
    if (!(toolfunc = gt_toolbox_get(compreads_toolbox, argv[parsed_args]))) {
      tool = gt_toolbox_get_tool(compreads_toolbox, argv[parsed_args]);
      gt_assert(tool);
    }

    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    if (toolfunc != NULL)
      had_err = toolfunc(argc - parsed_args, (const char**) nargv, err);
    else
      had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv,
                            err);
  }
  gt_cstr_array_delete(nargv);

  return had_err;
}

GtTool* gt_compreads(void)
{
  return gt_tool_new(gt_compreads_arguments_new,
                  gt_compreads_arguments_delete,
                  gt_compreads_option_parser_new,
                  NULL,
                  gt_compreads_runner);
}
genometools-1.5.1/src/tools/gt_compreads.h000066400000000000000000000020641211610345200206150ustar00rootroot00000000000000/*
  Copyright (c) 2011 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_COMPREADS_H
#define GT_COMPREADS_H

#include "core/tool_api.h"

/* the compreads toolbox */
GtTool* gt_compreads(void);

#endif
genometools-1.5.1/src/tools/gt_compreads_compress.c000066400000000000000000000241421211610345200225240ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/alphabet_api.h"
#include "core/basename_api.h"
#include "core/fa.h"
#include "core/fileutils_api.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/safearith.h"
#include "core/showtime.h"
#include "core/splitter_api.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "extended/hcr.h"
#include "extended/sampling.h"
#include "tools/gt_compreads_compress.h"

typedef struct {
  bool descs,
       pagewise,
       regular;
  GtStr  *smap,
         *method,
         *name;
  GtStrArray *files;
  unsigned long srate;
  GtQualRange qrng;
  GtRange arg_range;
} GtCsrHcrEncodeArguments;

static void* gt_compreads_compress_arguments_new(void)
{
  GtCsrHcrEncodeArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->smap = gt_str_new();
  arguments->name = gt_str_new();
  arguments->files = gt_str_array_new();
  arguments->qrng.start = GT_UNDEF_UINT;
  arguments->qrng.end = GT_UNDEF_UINT;
  arguments->arg_range.start = GT_UNDEF_ULONG;
  arguments->arg_range.end = GT_UNDEF_ULONG;
  arguments->method = gt_str_new();
  arguments->pagewise = false;
  arguments->regular = false;
  return arguments;
}

static void gt_compreads_compress_arguments_delete(void *tool_arguments)
{
  GtCsrHcrEncodeArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->name);
  gt_str_array_delete(arguments->files);
  gt_str_delete(arguments->smap);
  gt_str_delete(arguments->method);
  gt_free(arguments);
}

static GtOptionParser*
gt_compreads_compress_option_parser_new(void *tool_arguments)
{
  GtCsrHcrEncodeArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  static const char *methods[] = { "page", "regular", "none" };
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] (-files file [...])",
                         "Generates compact encoding for fastq data.");

  option = gt_option_new_bool("descs","encode descriptions",
                              &arguments->descs, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_filename_array("files", "File(s) containing reads.",
                                        arguments->files);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("name", "specify base name for HCR to be"
                                " generated. Only mandatory, if more than one"
                                " file was given.", arguments->name, NULL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("smap", "file containing alphabet description."
                                " If \"-smap\" is not set, dna alphabet is"
                                " used.",
                                arguments->smap, NULL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_range("qrange", "specify range of quality values."
                               " All values smaller or equal to the lower bound"
                               " will be converted to the lower bound. All"
                               " values equal or larger than the upper bound"
                               " will be converted to the upper bound.",
                               &arguments->arg_range, NULL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("srate", "sampling rate, set to sensible default"
                               " depending on sampling method",
                               &arguments->srate, GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_choice("stype", "type of sampling\n"
                                "one of regular - page - none",
                                arguments->method, "page",
                                methods);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 0U, 0U);
  return op;
}

static int gt_compreads_compress_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments,
                                       GtError *err)
{
  int had_err = 0;
  GtCsrHcrEncodeArguments *arguments = tool_arguments;
  GtSplitter *splitter = NULL;
  GtStr *buffer;
  gt_error_check(err);
  gt_assert(arguments);

  if (gt_str_length(arguments->name) == 0) {
    if (gt_str_array_size(arguments->files) > 1UL) {
      gt_error_set(err, "option \"-name\" needs to be specified if more"
                        " than one file is given");
      had_err = -1;
    }
    else {
      unsigned long i;
      char *basename;
      splitter = gt_splitter_new();
      basename = gt_basename(gt_str_array_get(arguments->files, 0));
      buffer = gt_str_new_cstr(basename);
      gt_splitter_split(splitter, gt_str_get(buffer), gt_str_length(buffer),
                        '.');
      for (i = 0; i < gt_splitter_size(splitter) - 1; i++) {
        gt_str_append_cstr(arguments->name,
                           gt_splitter_get_token(splitter, i));
        if (i < gt_splitter_size(splitter) - 2)
          gt_str_append_char(arguments->name, '.');
      }
      gt_free(basename);
      gt_splitter_delete(splitter);
      gt_str_delete(buffer);
    }
  }

  if (!had_err) {
    char *sampling_type = gt_str_get(arguments->method);
    static const char *methods[] = { "page", "regular", "none" };

    if (!strcmp(methods[0], sampling_type)) {
      arguments->pagewise = true;
      if (arguments->srate == GT_UNDEF_ULONG)
        arguments->srate = GT_SAMPLING_DEFAULT_PAGE_RATE;
      else if (arguments->srate == 0) {
        gt_error_set(err, "page sampling was chosen, but sampling rate was"
                          " set to %lu! this seems wrong.", arguments->srate);
        had_err = -1;
      }
    }
    else if (!strcmp(methods[1], sampling_type)) {
      arguments->regular = true;
      if (arguments->srate == GT_UNDEF_ULONG)
        arguments->srate = GT_SAMPLING_DEFAULT_REGULAR_RATE;
      else if (arguments->srate == 0) {
        gt_error_set(err, "regular sampling was chosen, but sampling rate "
                          " was set to %lu! this seems wrong.",
                     arguments->srate);
        had_err = -1;
      }
    }
    else if (!strcmp(methods[2], sampling_type)) {
      if (arguments->srate == GT_UNDEF_ULONG)
        arguments->srate = 0;
      else if (arguments->srate != 0) {
        gt_error_set(err, "no sampling was chosen, but sampling rate was"
                          " set to %lu! this seems wrong.", arguments->srate);
        had_err = -1;
      }
    }
    else {
      gt_error_set(err, "somethings wrong with the stype option");
      had_err = -1;
    }
  }

  if (!had_err) {
    if (arguments->arg_range.start != GT_UNDEF_ULONG) {
      if (arguments->arg_range.start <= (unsigned long) UINT_MAX) {
        gt_safe_assign(arguments->qrng.start, arguments->arg_range.start);
        if (arguments->arg_range.end <= (unsigned long) UINT_MAX)
          gt_safe_assign(arguments->qrng.end, arguments->arg_range.end);
        else
          had_err = -1;
      }
      else
        had_err = -1;
    }
    if (had_err)
      gt_error_set(err, "Range for qualities: value to large! larger than %u",
                   UINT_MAX);
  }
  return had_err;
}

static int gt_compreads_compress_runner(GT_UNUSED int argc,
                                    GT_UNUSED const char **argv,
                                    GT_UNUSED int parsed_args,
                                    void *tool_arguments, GtError *err)
{
  GtCsrHcrEncodeArguments *arguments = tool_arguments;
  int had_err = 0;
  GtAlphabet *alpha = NULL;
  GtHcrEncoder *hcre = NULL;
  GtTimer *timer = NULL;

  gt_error_check(err);
  gt_assert(arguments);
  if (gt_showtime_enabled()) {
    timer = gt_timer_new_with_progress_description("start");
    gt_timer_start(timer);
    gt_assert(timer);
  }

  if (gt_str_length(arguments->smap) > 0) {
    alpha = gt_alphabet_new_from_file_no_suffix(gt_str_get(arguments->smap),
                                                err);
    if (!alpha)
      had_err = 1;
  }
  else {
    alpha = gt_alphabet_new_dna();
    if (!alpha)
      had_err = 1;
  }
  if (!had_err) {
    if (timer != NULL)
      gt_timer_show_progress(timer, "encoding", stdout);
    hcre = gt_hcr_encoder_new(arguments->files, alpha, arguments->descs,
                              arguments->qrng, timer, err);
    if (!hcre)
      had_err = 1;
    else {
      if (arguments->pagewise)
        gt_hcr_encoder_set_sampling_page(hcre);
      else if (arguments->regular)
        gt_hcr_encoder_set_sampling_regular(hcre);

      gt_hcr_encoder_set_sampling_rate(hcre, arguments->srate);

      if (gt_hcr_encoder_encode(hcre, gt_str_get(arguments->name),
                                timer, err) != 0)
        had_err = 1;
    }
    gt_hcr_encoder_delete(hcre);
  }
  gt_alphabet_delete(alpha);
  if (timer != NULL) {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  return had_err;
}

GtTool* gt_compreads_compress(void)
{
  return gt_tool_new(gt_compreads_compress_arguments_new,
                  gt_compreads_compress_arguments_delete,
                  gt_compreads_compress_option_parser_new,
                  gt_compreads_compress_arguments_check,
                  gt_compreads_compress_runner);
}
genometools-1.5.1/src/tools/gt_compreads_compress.h000066400000000000000000000021301211610345200225220ustar00rootroot00000000000000/*
  Copyright (c) 2011 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_COMPREADS_COMPRESS_H
#define GT_COMPREADS_COMPRESS_H

#include "core/tool_api.h"

/* the compreads_compress toolbox */
GtTool* gt_compreads_compress(void);

#endif
genometools-1.5.1/src/tools/gt_compreads_decompress.c000066400000000000000000000217321211610345200230370ustar00rootroot00000000000000/*
  Copyright (c) 2011-2012 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/alphabet_api.h"
#include "core/basename_api.h"
#include "core/fa.h"
#include "core/fileutils_api.h"
#include "core/log_api.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/range_api.h"
#include "core/showtime.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "extended/hcr.h"
#include "tools/gt_compreads_decompress.h"

typedef struct {
  bool descs,
       verbose;
  unsigned long bench;
  GtStr  *file,
         *smap,
         *alphabet,
         *name;
  GtRange rng;
} GtCsrHcrDecodeArguments;

static void* gt_compreads_decompress_arguments_new(void)
{
  GtCsrHcrDecodeArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->file = gt_str_new();
  arguments->smap = gt_str_new();
  arguments->name = gt_str_new();
  arguments->rng.start = GT_UNDEF_ULONG;
  arguments->rng.end = GT_UNDEF_ULONG;
  arguments->bench = 0;

  return arguments;
}

static void gt_compreads_decompress_arguments_delete(void *tool_arguments)
{
  GtCsrHcrDecodeArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->file);
  gt_str_delete(arguments->name);
  gt_str_delete(arguments->smap);
  gt_free(arguments);
}

static GtOptionParser*
gt_compreads_decompress_option_parser_new(void *tool_arguments)
{
  GtCsrHcrDecodeArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] (-file file)",
                         "Decodes a file of compressed reads.");

  option = gt_option_new_bool("v", "be verbose",
                              &arguments->verbose, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("descs","enable description decoding",
                              &arguments->descs, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("file", "specify base name of files containing"
                                " HCR.",
                                arguments->file, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("name", "specify base name for decoded hcr"
                                " (suffix will be \".fastq\")",
                                arguments->name, NULL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("smap", "specify file containing alphabet"
                                "description (file must be an .al1 file)."
                                " If \"-smap\" is not set, dna alphabet is"
                                " used.",
                                arguments->smap, NULL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_range("range", "decode multiple consecutive reads."
                               " If range is not specified, the "
                               " entire file will be decoded.",
                               &arguments->rng, NULL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("benchmark", "decode given number random reads "
                               "and report the time to do this",
                               &arguments->bench, 0);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 0U, 0U);
  return op;
}

static int gt_compreads_decompress_benchmark(GtHcrDecoder *hcrd,
                                             unsigned long amount,
                                             GtTimer *timer,
                                             GtError *err) {
  char qual[BUFSIZ] = {0},
       seq[BUFSIZ] = {0};
  int had_err = 0;
  unsigned long rand,
                max_rand = gt_hcr_decoder_num_of_reads(hcrd) - 1,
                count;

  GtStr *timer_comment = gt_str_new_cstr("extracting ");
  GtStr *desc = gt_str_new();

  gt_str_append_ulong(timer_comment, amount);
  gt_str_append_cstr(timer_comment, " reads of ");
  gt_str_append_ulong(timer_comment, max_rand + 1);
  gt_str_append_cstr(timer_comment, "!");

  if (timer == NULL) {
    timer = gt_timer_new_with_progress_description("extract random reads");
    gt_timer_start(timer);
  }
  else {
    gt_timer_show_progress(timer, "extract random reads", stdout);
  }

  gt_log_log("%s",gt_str_get(timer_comment));
  for (count = 0; count < amount; count++) {
    if (!had_err) {
      rand = gt_rand_max(max_rand);
      gt_log_log("get read: %lu", rand);
      had_err = gt_hcr_decoder_decode(hcrd, rand, seq, qual, desc, err);
      gt_log_log("%s",gt_str_get(desc));
      gt_log_log("%s",seq);
      gt_log_log("%s",qual);
    }
  }
  gt_str_delete(timer_comment);
  gt_str_delete(desc);
  if (!gt_showtime_enabled())
    gt_timer_delete(timer);
  return had_err;
}

static int gt_compreads_decompress_runner(GT_UNUSED int argc,
                                    GT_UNUSED const char **argv,
                                    GT_UNUSED int parsed_args,
                                    void *tool_arguments, GtError *err)
{
  GtCsrHcrDecodeArguments *arguments = tool_arguments;
  int had_err = 0;
  GtAlphabet *alpha = NULL;
  GtHcrDecoder *hcrd = NULL;
  GtTimer *timer = NULL;
  unsigned long start,
                end;

  gt_error_check(err);
  gt_assert(arguments);

  if (gt_showtime_enabled()) {
    timer = gt_timer_new_with_progress_description("start");
    gt_timer_start(timer);
    gt_assert(timer);
  }

  if (gt_str_length(arguments->smap) > 0) {
    alpha = gt_alphabet_new_from_file_no_suffix(gt_str_get(arguments->smap),
                                                err);
    if (!alpha)
      had_err = -1;
  }
  else {
    alpha = gt_alphabet_new_dna();
    if (!alpha)
      had_err = -1;
  }

  if (!had_err) {
    if (timer != NULL)
      gt_timer_show_progress(timer, "decoding", stdout);

    if (gt_str_length(arguments->name) == 0) {
      char *basenameptr;
      basenameptr = gt_basename(gt_str_get(arguments->file));
      gt_str_set(arguments->name, basenameptr);
      gt_free(basenameptr);
    }
    hcrd = gt_hcr_decoder_new(gt_str_get(arguments->file), alpha,
                              arguments->descs, timer, err);
    if (hcrd == NULL)
      had_err = -1;
    else {
      if (arguments->bench != 0) {
        had_err = gt_compreads_decompress_benchmark(hcrd,
                                                    arguments->bench,
                                                    timer, err);
      }
      else {
        if (arguments->rng.start != GT_UNDEF_ULONG
            && arguments->rng.end != GT_UNDEF_ULONG) {
          if (arguments->rng.start >= gt_hcr_decoder_num_of_reads(hcrd)
                || arguments->rng.end >= gt_hcr_decoder_num_of_reads(hcrd)) {
            gt_error_set(err, "range %lu-%lu includes a read number exceeding "
                              "the total number of reads (%lu)",
                              arguments->rng.start,
                              arguments->rng.end,
                              gt_hcr_decoder_num_of_reads(hcrd));
            had_err = -1;
          }
          start = arguments->rng.start;
          end = arguments->rng.end;
        }
        else {
          start = 0;
          end = gt_hcr_decoder_num_of_reads(hcrd) - 1;
        }
        if (!had_err) {
          gt_log_log("filebasename: %s", gt_str_get(arguments->name));
          if (gt_hcr_decoder_decode_range(hcrd, gt_str_get(arguments->name),
                                          start, end, timer, err)
            != 0)
            had_err = -1;
        }
      }
    }
    gt_hcr_decoder_delete(hcrd);
  }
  gt_alphabet_delete(alpha);
  if (timer != NULL) {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  if (had_err)
    gt_assert(gt_error_is_set(err));
  return had_err;
}

GtTool* gt_compreads_decompress(void)
{
  return gt_tool_new(gt_compreads_decompress_arguments_new,
                     gt_compreads_decompress_arguments_delete,
                     gt_compreads_decompress_option_parser_new,
                     NULL,
                     gt_compreads_decompress_runner);
}
genometools-1.5.1/src/tools/gt_compreads_decompress.h000066400000000000000000000021401211610345200230340ustar00rootroot00000000000000/*
  Copyright (c) 2011 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_COMPREADS_DECOMPRESS_H
#define GT_COMPREADS_DECOMPRESS_H

#include "core/tool_api.h"

/* the compreads_decompress toolbox */
GtTool* gt_compreads_decompress(void);

#endif
genometools-1.5.1/src/tools/gt_compreads_refcompress.c000066400000000000000000000201771211610345200232250ustar00rootroot00000000000000/*
  Copyright (c) 2011 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 

#include "core/alphabet_api.h"
#include "core/basename_api.h"
#include "core/encseq_api.h"
#include "core/fa.h"
#include "core/fileutils_api.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/range_api.h"
#include "core/showtime.h"
#include "core/splitter_api.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "extended/rcr.h"
#include "tools/gt_compreads_refcompress.h"

typedef struct {
  bool verbose,
       vquals,
       mquals,
       quals,
       ureads,
       descs;
  GtStr *name,
        *ref,
        *align;
  unsigned long srate;
  GtRange qrng;
} GtCsrRcrEncodeArguments;

static void* gt_compreads_refcompress_arguments_new(void)
{
  GtCsrRcrEncodeArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->name = gt_str_new();
  arguments->ref = gt_str_new();
  arguments->align = gt_str_new();
  arguments->qrng.start = GT_UNDEF_ULONG;
  arguments->qrng.end = GT_UNDEF_ULONG;

  return arguments;
}

static void gt_compreads_refcompress_arguments_delete(void *tool_arguments)
{
  GtCsrRcrEncodeArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->name);
  gt_str_delete(arguments->ref);
  gt_str_delete(arguments->align);
  gt_free(arguments);
}

static GtOptionParser*
gt_compreads_refcompress_option_parser_new(void *tool_arguments)
{
  GtCsrRcrEncodeArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option,
           *option1;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] (-bam file -ref file)",
                         "Generates compact encoding for fastq data using"
                         " Reference Compressed Reads (RCR).");

  option = gt_option_new_bool("v", "be verbose",
                              &arguments->verbose, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("mquals", "store mapping quality for each read",
                              &arguments->mquals, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("quals", "store all quality values for each read,"
                                        " this implies enabling of option"
                                        " \"vquals\"",
                              &arguments->quals, false);

  option1 = gt_option_new_bool("vquals", "store quality values of read"
                               " positions having variations compared to"
                               " reference",
                              &arguments->vquals, false);

  gt_option_exclude(option, option1);

  gt_option_parser_add_option(op, option);
  gt_option_parser_add_option(op, option1);

  option = gt_option_new_bool("descs", "store read name for each read",
                              &arguments->descs, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("ureads", "store unmapped reads in a separated"
                              " fastq file (base name will be the value given"
                              " in name and suffix will be"
                              " \" _unmapped.fastq\"",
                              &arguments->ureads, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("ref", "Index file (generated by the gt encseq"
                                " tool) for reference genome.",
                                arguments->ref, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("bam", "File containing alignment of reads to"
                                " genome (sorted \".bam\" file).",
                                arguments->align, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("name", "specify base name for RCR to be"
                                " generated. If not set, base name will be set"
                                " to base name of value given for option"
                                " \"bam\"",
                                arguments->name, NULL);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 0U, 0U);
  return op;
}

static int gt_compreads_refcompress_runner(GT_UNUSED int argc,
                                    GT_UNUSED const char **argv,
                                    GT_UNUSED int parsed_args,
                                    void *tool_arguments, GtError *err)
{
  GtCsrRcrEncodeArguments *arguments = tool_arguments;
  int had_err = 0;
  GtTimer *timer = NULL;
  GtEncseq *encseq = NULL;
  GtRcrEncoder *rcre = NULL;
  GtEncseqLoader *el = NULL;
  GtSplitter *splitter = NULL;
  GtStr *buffer;
  unsigned long i;
  gt_error_check(err);
  gt_assert(arguments);
  if (gt_showtime_enabled()) {
    timer = gt_timer_new_with_progress_description("start");
    gt_timer_start(timer);
    gt_assert(timer);
  }
  if (!had_err) {
    if (timer != NULL)
      gt_timer_show_progress(timer, "encoding", stdout);

    if (gt_str_length(arguments->name) == 0) {
      splitter = gt_splitter_new();
      buffer = gt_str_clone(arguments->align);
      gt_splitter_split(splitter, gt_str_get(buffer), gt_str_length(buffer),
                        '.');
      for (i = 0; i < gt_splitter_size(splitter) - 1; i++) {
        gt_str_append_cstr(arguments->name,
                           gt_splitter_get_token(splitter, i));
        if (i < gt_splitter_size(splitter) - 2)
          gt_str_append_char(arguments->name, '.');
      }
      gt_splitter_delete(splitter);
      gt_str_delete(buffer);
    }
    el = gt_encseq_loader_new();
    gt_encseq_loader_enable_autosupport(el);
    gt_encseq_loader_require_description_support(el);
    encseq = gt_encseq_loader_load(el, gt_str_get(arguments->ref), err);
    gt_encseq_loader_delete(el);
    if (!encseq) {
      gt_error_set(err, "could not load GtEncseq %s",
                   gt_str_get(arguments->ref));
      had_err = -1;
    }

    if (!had_err) {
      if (!gt_alphabet_is_dna(gt_encseq_alphabet(encseq))) {
        gt_error_set(err, "alphabet in %s has to be DNA",
                     gt_str_get(arguments->ref));
        had_err = -1;
      }
      if (!had_err) {

        rcre = gt_rcr_encoder_new(encseq, gt_str_get(arguments->align),
                                  arguments->vquals, arguments->mquals,
                                  arguments->quals, arguments->ureads,
                                  arguments->descs, timer, err);
        if (!rcre)
          had_err = -1;
        else {
          if (arguments->verbose)
            gt_rcr_encoder_enable_verbosity(rcre);
          had_err = gt_rcr_encoder_encode(rcre, gt_str_get(arguments->name),
                                          timer, err);
        }
        gt_rcr_encoder_delete(rcre);
      }
    }
    gt_encseq_delete(encseq);
  }
  if (timer != NULL) {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  return had_err;
}

GtTool* gt_compreads_refcompress(void)
{
  return gt_tool_new(gt_compreads_refcompress_arguments_new,
                  gt_compreads_refcompress_arguments_delete,
                  gt_compreads_refcompress_option_parser_new,
                  NULL,
                  gt_compreads_refcompress_runner);
}
genometools-1.5.1/src/tools/gt_compreads_refcompress.h000066400000000000000000000021441211610345200232240ustar00rootroot00000000000000/*
  Copyright (c) 2011 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_COMPREADS_REFCOMPRESS_H
#define GT_COMPREADS_REFCOMPRESS_H

#include "core/tool_api.h"

/* the compreads_refcompress toolbox */
GtTool* gt_compreads_refcompress(void);

#endif
genometools-1.5.1/src/tools/gt_compreads_refdecompress.c000066400000000000000000000136061211610345200235350ustar00rootroot00000000000000/*
  Copyright (c) 2011 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/alphabet_api.h"
#include "core/basename_api.h"
#include "core/fa.h"
#include "core/fileutils_api.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/range_api.h"
#include "core/showtime.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "extended/rcr.h"
#include "tools/gt_compreads_refdecompress.h"

typedef struct {
  GtStr  *file,
         *ref,
         *name;
  bool verbose,
       qnames;
} GtCsrRcrDecodeArguments;

static void* gt_compreads_refdecompress_arguments_new(void)
{
  GtCsrRcrDecodeArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->file = gt_str_new();
  arguments->ref = gt_str_new();
  arguments->name = gt_str_new();

  return arguments;
}

static void gt_compreads_refdecompress_arguments_delete(void *tool_arguments)
{
  GtCsrRcrDecodeArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->file);
  gt_str_delete(arguments->name);
  gt_str_delete(arguments->ref);
  gt_free(arguments);
}

static GtOptionParser* gt_compreads_refdecompress_option_parser_new(
                                void *tool_arguments)
{
  GtCsrRcrDecodeArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] (-file file)",
                         "Decodes a given RCR (Reference Compressed Reads).");

  option = gt_option_new_bool("v", "be verbose",
                              &arguments->verbose, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("qnames", "decode read names, default is "
                              "to just number them",
                              &arguments->qnames, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("ref", "Index file (generated by the gt encseq"
                                " tool) for reference genome.",
                                arguments->ref, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("rcr", "specify base name of file containing"
                                " RCR.",
                                arguments->file, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("name", "specify base name for decoded RCR"
                                " (suffix will be \".rcr.decoded\")",
                                arguments->name, NULL);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 0U, 0U);
  return op;
}

static int gt_compreads_refdecompress_runner(GT_UNUSED int argc,
                                    GT_UNUSED const char **argv,
                                    GT_UNUSED int parsed_args,
                                    void *tool_arguments, GtError *err)
{
  GtCsrRcrDecodeArguments *arguments = tool_arguments;
  int had_err = 0;
  GtRcrDecoder *rcrd = NULL;
  GtTimer *timer = NULL;
  GtEncseq *encseq = NULL;
  GtEncseqLoader *el = NULL;

  gt_error_check(err);
  gt_assert(arguments);

  if (gt_showtime_enabled()) {
    timer = gt_timer_new_with_progress_description("start");
    gt_timer_start(timer);
    gt_assert(timer);
  }

  if (gt_str_length(arguments->name) == 0) {
    char *basename = gt_basename(gt_str_get(arguments->file));
    gt_str_set(arguments->name, basename);
    gt_free(basename);
  }
  if (timer != NULL)
    gt_timer_show_progress(timer, "load encseq", stdout);
  el = gt_encseq_loader_new();
  gt_encseq_loader_enable_autosupport(el);
  gt_encseq_loader_require_description_support(el);
  encseq = gt_encseq_loader_load(el, gt_str_get(arguments->ref), err);
  gt_encseq_loader_delete(el);
  if (!encseq) {
    gt_error_set(err, "Could not load GtEncseq %s", gt_str_get(arguments->ref));
    had_err = -1;
  }

  if (!had_err) {
    if (!gt_alphabet_is_dna(gt_encseq_alphabet(encseq))) {
      gt_error_set(err, "Alphabet in %s has to be DNA",
                   gt_str_get(arguments->ref));
      had_err = -1;
    }
  }

  if (!had_err) {
    rcrd = gt_rcr_decoder_new(gt_str_get(arguments->file), encseq, timer,
                              err);
    if (rcrd == NULL)
      had_err = -1;
  }
  if (!had_err &&
      arguments->qnames)
    had_err = gt_rcr_decoder_enable_description_support(rcrd, err);
  if (!had_err)
    had_err = gt_rcr_decoder_decode(rcrd,
                                    gt_str_get(arguments->name), timer, err);
  if (timer != NULL) {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  gt_rcr_decoder_delete(rcrd);
  gt_encseq_delete(encseq);
  return had_err;
}

GtTool* gt_compreads_refdecompress(void)
{
  return gt_tool_new(gt_compreads_refdecompress_arguments_new,
                     gt_compreads_refdecompress_arguments_delete,
                     gt_compreads_refdecompress_option_parser_new,
                     NULL,
                     gt_compreads_refdecompress_runner);
}
genometools-1.5.1/src/tools/gt_compreads_refdecompress.h000066400000000000000000000021541211610345200235360ustar00rootroot00000000000000/*
  Copyright (c) 2011 Joachim Bonnet 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_COMPREADS_REFDECOMPRESS_H
#define GT_COMPREADS_REFDECOMPRESS_H

#include "core/tool_api.h"

/* the compreads_refdecompress toolbox */
GtTool* gt_compreads_refdecompress(void);

#endif
genometools-1.5.1/src/tools/gt_congruence.c000066400000000000000000000203571211610345200207700ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/cstr_array.h"
#include "core/error.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "core/option_api.h"
#include "core/str.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "extended/toolbox.h"
#include "match/cgr_spacedseed.h"
#include "tools/gt_congruence.h"

typedef struct
{
  bool withesa, docompare, verbose;
  GtStr *str_inputindex;
  GtStrArray *queryfilenames;
  GtOption *refoptionesaindex, *refoptionpckindex;
} Cge_spacedseed_options;

static void *gt_cge_spacedseed_arguments_new(void)
{
  Cge_spacedseed_options *arguments
    = gt_malloc(sizeof (Cge_spacedseed_options));
  arguments->str_inputindex = gt_str_new();
  arguments->queryfilenames = gt_str_array_new();
  return arguments;
}

static void gt_cge_spacedseed_arguments_delete(void *tool_arguments)
{
  Cge_spacedseed_options *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->str_inputindex);
  gt_str_array_delete(arguments->queryfilenames);
  gt_option_delete(arguments->refoptionpckindex);
  gt_option_delete(arguments->refoptionesaindex);
  gt_free(arguments);
}

static GtOptionParser
            *gt_cge_spacedseed_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GtOption *option,
           *optionesaindex,
           *optionpckindex;
  Cge_spacedseed_options *arguments = tool_arguments;

  op = gt_option_parser_new("[options]",
                            "Match spaced seeds.");
  gt_option_parser_set_mail_address(op,"");

  optionesaindex = gt_option_new_string("esa",
                                     "Specify index (enhanced suffix array)",
                                     arguments->str_inputindex, NULL);
  gt_option_parser_add_option(op, optionesaindex);
  arguments->refoptionesaindex = gt_option_ref(optionesaindex);

  optionpckindex = gt_option_new_string("pck",
                                     "Specify index (packed index)",
                                     arguments->str_inputindex, NULL);
  gt_option_parser_add_option(op, optionpckindex);
  arguments->refoptionpckindex = gt_option_ref(optionpckindex);
  gt_option_exclude(optionesaindex,optionpckindex);
  gt_option_is_mandatory_either(optionesaindex,optionpckindex);

  option = gt_option_new_filename_array("q",
                                    "Specify files containing the "
                                    "query sequences",
                                    arguments->queryfilenames);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  option = gt_option_new_bool("cmp","compare results of offline and online "
                              "searches",&arguments->docompare,false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  return op;
}

static int gt_cge_spacedseed_arguments_check(int rest_argc,
                                             void *tool_arguments,
                                             GtError *err)
{
  Cge_spacedseed_options *arguments = tool_arguments;

  if (gt_str_length(arguments->str_inputindex) == 0)
  {
    gt_error_set(err,"missing indexname");
    return -1;
  }
  if (gt_option_is_set(arguments->refoptionesaindex))
  {
    arguments->withesa = true;
  } else
  {
    gt_assert(gt_option_is_set(arguments->refoptionpckindex));
    arguments->withesa = false;
  }
  if (rest_argc != 0)
  {
    gt_error_set(err,"superfluous file arguments");
    return -1;
  }
  return 0;
}

static int gt_cge_spacedseed_runner(GT_UNUSED int argc,
                                    GT_UNUSED const char **argv,
                                    GT_UNUSED int parsed_args,
                                    void *tool_arguments,
                                    GtError *err)
{
  Cge_spacedseed_options *arguments = tool_arguments;
  GtLogger *logger = NULL;
  bool haserr = false;

  gt_assert(parsed_args == argc);
  logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  if (arguments->verbose)
  {
    unsigned long idx;

    printf("# %sindex=%s\n",arguments->withesa ? "esa" : "pck",
                            gt_str_get(arguments->str_inputindex));
    for (idx = 0; idx < gt_str_array_size(arguments->queryfilenames); idx++)
    {
      printf("# queryfile=%s\n",
             gt_str_array_get(arguments->queryfilenames,idx));
    }
  }
  if (gt_matchspacedseed(arguments->withesa,
                      arguments->docompare,
                      gt_str_get(arguments->str_inputindex),
                      arguments->queryfilenames,
                      arguments->verbose,
                      err) != 0)
  {
    haserr = true;
  }
  gt_logger_delete(logger);
  return haserr ? - 1 : 0;
}

static GtTool* gt_cge_spacedseed(void)
{
  return gt_tool_new(gt_cge_spacedseed_arguments_new,
                     gt_cge_spacedseed_arguments_delete,
                     gt_cge_spacedseed_option_parser_new,
                     gt_cge_spacedseed_arguments_check,
                     gt_cge_spacedseed_runner);
}

static void *gt_cge_arguments_new(void)
{
  GtToolbox *cge_toolbox = gt_toolbox_new();
  gt_toolbox_add_tool(cge_toolbox, "spacedseed", gt_cge_spacedseed());
  return cge_toolbox;
}

static void gt_cge_arguments_delete(void *tool_arguments)
{
  GtToolbox *index_toolbox = tool_arguments;
  if (!index_toolbox) return;
  gt_toolbox_delete(index_toolbox);
}

static GtOptionParser* gt_cge_option_parser_new(void *tool_arguments)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtOptionParser *op;

  gt_assert(index_toolbox != NULL);
  op = gt_option_parser_new(
                    "[option ...] congruence_tool [argument ...]",
                    "Call congruence tool with name congruence_tool and pass "
                    "argument(s) to it.");
  gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
  gt_option_parser_set_min_args(op, 1U);
  gt_option_parser_refer_to_manual(op);
  return op;
}

static int gt_cge_runner(int argc, const char **argv, int parsed_args,
                                 void *tool_arguments, GtError *err)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtToolfunc toolfunc;
  GtTool *tool = NULL;
  char **nargv = NULL;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(index_toolbox != NULL);

  /* determine tool */
  if (!gt_toolbox_has_tool(index_toolbox, argv[parsed_args]))
  {
    gt_error_set(err, "congruence tool '%s' not found; option -help lists "
                   "possible tools", argv[parsed_args]);
    had_err = -1;
  }

  /* call sub-tool */
  if (!had_err)
  {
    if (!(toolfunc = gt_toolbox_get(index_toolbox, argv[parsed_args])))
    {
      tool = gt_toolbox_get_tool(index_toolbox, argv[parsed_args]);
      gt_assert(tool != NULL);
    }
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    if (toolfunc != NULL)
      had_err = toolfunc(argc - parsed_args, (const char**) nargv, err);
    else
      had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv,
                            err);
  }
  gt_cstr_array_delete(nargv);
  return had_err;
}

GtTool* gt_congruence(void)
{
  return gt_tool_new(gt_cge_arguments_new,
                     gt_cge_arguments_delete,
                     gt_cge_option_parser_new,
                     NULL,
                     gt_cge_runner);
}
genometools-1.5.1/src/tools/gt_congruence.h000066400000000000000000000017071211610345200207730ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_CONGRUENCE_H
#define GT_CONGRUENCE_H

#include "core/tool_api.h"

GtTool* gt_congruence(void);

#endif
genometools-1.5.1/src/tools/gt_consensus_sa.c000066400000000000000000000107161211610345200213410ustar00rootroot00000000000000/*
  Copyright (c) 2005-2008 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/fptr_api.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "extended/consensus_sa.h"
#include "extended/sspliced_alignment.h"
#include "extended/sspliced_alignment_parsing.h"
#include "tools/gt_consensus_sa.h"

static GtRange get_genomic_range(const void *sa)
{
  GtSSplicedAlignment *alignment = *(GtSSplicedAlignment**) sa;
  gt_assert(alignment);
  return gt_sspliced_alignment_genomic_range(alignment);
}

static GtStrand get_strand(const void *sa)
{
  GtSSplicedAlignment *alignment = *(GtSSplicedAlignment**) sa;
  if (gt_sspliced_alignment_is_forward(alignment))
    return GT_STRAND_FORWARD;
  return GT_STRAND_REVERSE;
}

static void get_exons(GtArray *exon_ranges, const void *sa)
{
  GtSSplicedAlignment *alignment = *(GtSSplicedAlignment**) sa;
  GtRange exon;
  unsigned long i;
  gt_assert(alignment);
  for (i = 0; i < gt_sspliced_alignment_num_of_exons(alignment); i++) {
    exon = gt_sspliced_alignment_get_exon(alignment, i);
    gt_array_add(exon_ranges, exon);
  }
}

static void process_splice_form(GtArray *spliced_alignments_in_form,
                                GT_UNUSED const void *set_of_sas,
                                GT_UNUSED unsigned long number_of_sas,
                                GT_UNUSED size_t size_of_sa,
                                GT_UNUSED void *userdata)
{
  unsigned long i;

  printf("contains [");
  for (i = 0; i < gt_array_size(spliced_alignments_in_form); i++) {
    if (i)
      gt_xputchar(',');
    printf("%lu",
           *((unsigned long*) gt_array_get(spliced_alignments_in_form, i)));
  }
  printf("]\n");
}

static GtOptionParser* gt_consensus_sa_option_parser_new(GT_UNUSED
                                                       void *tool_arguments)
{
  GtOptionParser *op;
  op = gt_option_parser_new("spliced_alignment_file", "Read file containing "
                         "spliced alingments, compute consensus spliced "
                         "alignments,\nand print them to stdout.");
  gt_option_parser_set_min_max_args(op, 1, 1);
  return op;
}

static int gt_consensus_sa_runner(GT_UNUSED int argc, const char **argv,
                                  int parsed_args,
                                  GT_UNUSED void *tool_arguments, GtError *err)
{
  GtArray *spliced_alignments;
  GtSSplicedAlignment *sa;
  unsigned long i;
  int had_err = 0;
  gt_error_check(err);

  /* parse input file and store resuilts in the spliced alignment array */
  spliced_alignments = gt_array_new(sizeof (GtSSplicedAlignment*));
  had_err = gt_sspliced_alignment_parse(spliced_alignments, argv[parsed_args],
                                     err);

  if (!had_err) {
    /* sort spliced alignments */
    qsort(gt_array_get_space(spliced_alignments),
          gt_array_size(spliced_alignments),
          gt_array_elem_size(spliced_alignments),
          (GtCompare) gt_sspliced_alignment_compare_ptr);

    /* compute the consensus spliced alignments */
    gt_consensus_sa(gt_array_get_space(spliced_alignments),
                    gt_array_size(spliced_alignments),
                    gt_array_elem_size(spliced_alignments), get_genomic_range,
                    get_strand, get_exons, process_splice_form, NULL);
  }

  /* free */
  for (i = 0; i < gt_array_size(spliced_alignments); i++) {
    sa = *(GtSSplicedAlignment**) gt_array_get(spliced_alignments, i);
    gt_sspliced_alignment_delete(sa);
  }
  gt_array_delete(spliced_alignments);

  return had_err;
}

GtTool* gt_consensus_sa_tool(void)
{
  return gt_tool_new(NULL,
                  NULL,
                  gt_consensus_sa_option_parser_new,
                  NULL,
                  gt_consensus_sa_runner);
}
genometools-1.5.1/src/tools/gt_consensus_sa.h000066400000000000000000000020301211610345200213340ustar00rootroot00000000000000/*
  Copyright (c) 2005-2008 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_CONSENSUS_SA_H
#define GT_CONSENSUS_SA_H

#include "core/tool_api.h"

/* the exercise consensus spliced alignment (csa) tool */
GtTool* gt_consensus_sa_tool(void);

#endif
genometools-1.5.1/src/tools/gt_convertseq.c000066400000000000000000000204251211610345200210250ustar00rootroot00000000000000/*
  Copyright (c) 2009 Sascha Steinbiss 
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2009-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#else
#ifndef GT_ISUPPER_DEFINED
#define GT_ISUPPER_DEFINED
int isupper(int c);
#endif
#endif
#include 
#include "core/fileutils_api.h"
#include "core/filelengthvalues.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/sequence_buffer.h"
#include "core/seq_iterator_sequence_buffer.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "core/progressbar.h"
#include "extended/reverse_api.h"
#include "tools/gt_convertseq.h"

typedef struct
{
  bool reduce_wc_dna,
       reduce_wc_prot,
       revcomp,
       showflv,
       showseq,
       verbose;
  unsigned long fastawidth;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} ConvertseqOptions;

static GtOPrval parse_options(ConvertseqOptions *opts, int *parsed_args,
                              int argc, const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOption *optionverbose, *o;
  GtOPrval oprval;

  gt_error_check(err);

  op = gt_option_parser_new("[options] file [...]",
                            "Parse and convert sequence file formats.");

  optionverbose = gt_option_new_bool("v","be verbose",
                                     &opts->verbose, false);
  gt_option_parser_add_option(op, optionverbose);

  optionverbose = gt_option_new_bool("r","reverse complement sequences",
                                     &opts->revcomp, false);
  gt_option_parser_add_option(op, optionverbose);

  o = gt_option_new_bool("showfilelengthvalues","show filelengths",
                         &opts->showflv, false);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_bool("noseq","do not show sequences",
                         &opts->showseq, false);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_ulong("fastawidth","FASTA output line width",
                         &opts->fastawidth, 60UL);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_bool("contractdnawc", "replace stretches of DNA wildcards "
                                          "with a single 'N'",
                         &opts->reduce_wc_dna, false);
  gt_option_parser_add_option(op, o);

  o = gt_option_new_bool("contractproteinwc", "replace stretches of protein "
                                              "wildcards with a single 'X'",
                         &opts->reduce_wc_prot, false);
  gt_option_parser_add_option(op, o);

  gt_output_file_register_options(op, &opts->outfp, opts->ofi);

  gt_option_parser_set_min_args(op, 1U);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

int gt_convertseq(int argc, const char **argv, GtError *err)
{
  GtStrArray *files;
  const GtUchar *sequence;
  char *desc;
  unsigned long len, j;
  int i, parsed_args, had_err = 0;
  off_t totalsize;
  ConvertseqOptions opts;
  GtFilelengthvalues *flv;
  GtSeqIterator *seqit;
  GtSequenceBuffer *sb = NULL;
  opts.ofi = gt_output_file_info_new();
  opts.outfp = NULL;

  gt_error_check(err);

  /* option parsing */
  switch (parse_options(&opts,&parsed_args, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR:
        gt_file_delete(opts.outfp);
        gt_output_file_info_delete(opts.ofi);
        return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT:
        gt_file_delete(opts.outfp);
        gt_output_file_info_delete(opts.ofi);
        return 0;
  }

  files = gt_str_array_new();
  for (i = parsed_args; i < argc; i++)
  {
    gt_str_array_add_cstr(files, argv[i]);
  }
  totalsize = gt_files_estimate_total_size(files);

  flv = gt_calloc((size_t) gt_str_array_size(files),
                  sizeof (GtFilelengthvalues));

  sb = gt_sequence_buffer_new_guess_type(files, err);
  if (!sb) {
    had_err = -1;
  }
  if (!had_err) {
    gt_sequence_buffer_set_filelengthtab(sb, flv);
    /* read input using seqiterator */
    seqit = gt_seq_iterator_sequence_buffer_new_with_buffer(sb);
    if (opts.verbose)
    {
      gt_progressbar_start(gt_seq_iterator_getcurrentcounter(seqit,
                                                           (unsigned long long)
                                                           totalsize),
                           (unsigned long long) totalsize);
    }
    while (true)
    {
      GtUchar *seq = NULL;
      desc = NULL;
      i = 0; j = 0UL;
      had_err = gt_seq_iterator_next(seqit, &sequence, &len, &desc, err);
      if (had_err != 1)
        break;
      if (opts.revcomp) {
        GtUchar *newseq = gt_calloc((size_t) len+1, sizeof (GtUchar));
        memcpy(newseq, sequence, (size_t) len*sizeof (GtUchar));
        had_err = gt_reverse_complement((char*) newseq, len, err);
        if (had_err)
          break;
        seq = newseq;
      } else seq = (GtUchar*) sequence;

      if (!opts.showseq) {
        bool in_wildcard = false;
        gt_file_xprintf(opts.outfp, ">%s\n", desc);
        for (i = 0; (unsigned long) i < len; i++) {
          if (opts.reduce_wc_dna) {
            switch (seq[i]) {
              case 'a':
              case 'A':
              case 'c':
              case 'C':
              case 'g':
              case 'G':
              case 't':
              case 'u':
              case 'T':
              case 'U':
                in_wildcard = false;
                gt_file_xfputc((int) seq[i], opts.outfp);
                j++;
                break;
              default:
                if (!in_wildcard) {
                  in_wildcard = true;
                  if (isupper((int) seq[i]))
                    gt_file_xfputc((int) 'N', opts.outfp);
                  else
                    gt_file_xfputc((int) 'n', opts.outfp);
                  j++;
                }
            }
          }
          else if (opts.reduce_wc_prot) {
            switch (seq[i]) {
              case 'X':
              case 'B':
              case 'Z':
                if (!in_wildcard) {
                  in_wildcard = true;
                  gt_file_xfputc((int) 'N', opts.outfp);
                  j++;
                }
                break;
              case 'x':
              case 'b':
              case 'z':
                if (!in_wildcard) {
                  in_wildcard = true;
                  gt_file_xfputc((int) 'n', opts.outfp);
                  j++;
                }
                break;
              default:
                in_wildcard = false;
                gt_file_xfputc((int) seq[i], opts.outfp);
                j++;
            }
          }
          else {
            gt_file_xfputc((int) seq[i], opts.outfp);
            j++;
          }
          if ((j % opts.fastawidth) == 0) {
            j = 0;
            gt_file_xprintf(opts.outfp, "\n");
          }
        }
        gt_file_xprintf(opts.outfp, "\n");
      }
      if (opts.revcomp) {
        gt_free(seq);
      }
    }
    if (opts.showflv) {
      for (j=0;j
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_CONVERTSEQ_H
#define GT_CONVERTSEQ_H

/* the *-to-FASTA conversion tool */
int gt_convertseq(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_csa.c000066400000000000000000000075251211610345200174100ustar00rootroot00000000000000/*
  Copyright (c) 2005-2011 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "extended/csa_stream_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gtdatahelp.h"
#include "tools/gt_csa.h"

typedef struct {
  bool verbose;
  unsigned long join_length;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} CSAArguments;

static void* gt_csa_arguments_new(void)
{
  CSAArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_csa_arguments_delete(void *tool_arguments)
{
  CSAArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_csa_option_parser_new(void *tool_arguments)
{
  CSAArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file]",
                            "Transform spliced alignments from GFF3 file into "
                            "consensus spliced alignments.");

  /* -join-length */
  option = gt_option_new_ulong("join-length", "set join length for the spliced "
                               "alignment clustering", &arguments->join_length,
                               GT_DEFAULT_JOIN_LENGTH);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_max_args(op, 1);

  return op;
}

static int gt_csa_runner(GT_UNUSED int argc, const char **argv, int parsed_args,
                         void *tool_arguments, GtError *err)
{
  GtNodeStream *gff3_in_stream, *csa_stream, *gff3_out_stream;
  CSAArguments *arguments = tool_arguments;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create the streams */
  gff3_in_stream  = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);
  csa_stream      = gt_csa_stream_new(gff3_in_stream, arguments->join_length);
  gff3_out_stream = gt_gff3_out_stream_new(csa_stream, arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(csa_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool* gt_csa(void)
{
  return gt_tool_new(gt_csa_arguments_new,
                     gt_csa_arguments_delete,
                     gt_csa_option_parser_new,
                     NULL,
                     gt_csa_runner);
}
genometools-1.5.1/src/tools/gt_csa.h000066400000000000000000000017571211610345200174160ustar00rootroot00000000000000/*
  Copyright (c) 2005-2008 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_CSA_H
#define GT_CSA_H

#include "core/tool_api.h"

/* the consensus spliced alignment (csa) tool */
GtTool* gt_csa(void);

#endif
genometools-1.5.1/src/tools/gt_dev.c000066400000000000000000000122401211610345200174060ustar00rootroot00000000000000/*
  Copyright (c) 2007-2010 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/cstr_array.h"
#include "core/option_api.h"
#include "core/versionfunc.h"
#include "extended/toolbox.h"
#include "gth/gt_gthmkbssmfiles.h"
#include "tools/gt_consensus_sa.h"
#include "tools/gt_dev.h"
#include "tools/gt_extracttarget.h"
#include "tools/gt_gdiffcalc.h"
#include "tools/gt_guessprot.h"
#include "tools/gt_idxlocali.h"
#include "tools/gt_magicmatch.h"
#include "tools/gt_mergeesa.h"
#include "tools/gt_paircmp.h"
#include "tools/gt_patternmatch.h"
#include "tools/gt_readreads.h"
#include "tools/gt_regioncov.h"
#include "tools/gt_sain.h"
#include "tools/gt_sam_interface.h"
#include "tools/gt_seqcorrect.h"
#include "tools/gt_seqlensort.h"
#include "tools/gt_sfxmap.h"
#include "tools/gt_skproto.h"
#include "tools/gt_sortbench.h"
#include "tools/gt_trieins.h"

static void* gt_dev_arguments_new(void)
{
  GtToolbox *dev_toolbox = gt_toolbox_new();
  /* add development tools here with a function call like this:
     gt_toolbox_add(dev_toolbox, "devtool", gt_devtool); */
  gt_toolbox_add(dev_toolbox, "gthmkbssmfiles", gt_gthmkbssmfiles);
  gt_toolbox_add(dev_toolbox, "guessprot", gt_guessprot);
  gt_toolbox_add(dev_toolbox, "mergeesa", gt_mergeesa);
  gt_toolbox_add(dev_toolbox, "paircmp", gt_paircmp);
  gt_toolbox_add(dev_toolbox, "patternmatch", gt_patternmatch);
  gt_toolbox_add(dev_toolbox, "regioncov", gt_regioncov);
  gt_toolbox_add(dev_toolbox, "trieins", gt_trieins);
  gt_toolbox_add_tool(dev_toolbox, "consensus_sa", gt_consensus_sa_tool());
  gt_toolbox_add_tool(dev_toolbox, "extracttarget", gt_extracttarget());
  gt_toolbox_add_tool(dev_toolbox, "gdiffcalc", gt_gdiffcalc());
  gt_toolbox_add_tool(dev_toolbox, "idxlocali", gt_idxlocali());
  gt_toolbox_add_tool(dev_toolbox, "magicmatch", gt_magicmatch());
  gt_toolbox_add_tool(dev_toolbox, "readreads", gt_readreads());
  gt_toolbox_add_tool(dev_toolbox, "sain", gt_sain());
  gt_toolbox_add_tool(dev_toolbox, "sambam", gt_sam_interface());
  gt_toolbox_add_tool(dev_toolbox, "seqcorrect", gt_seqcorrect());
  gt_toolbox_add_tool(dev_toolbox, "seqlensort", gt_seqlensort());
  gt_toolbox_add_tool(dev_toolbox, "sfxmap", gt_sfxmap());
  gt_toolbox_add_tool(dev_toolbox, "skproto", gt_skproto());
  gt_toolbox_add_tool(dev_toolbox, "sortbench", gt_sortbench());
  return dev_toolbox;
}

static void gt_dev_arguments_delete(void *tool_arguments)
{
  GtToolbox *dev_toolbox = tool_arguments;
  if (!dev_toolbox) return;
  gt_toolbox_delete(dev_toolbox);
}

static GtOptionParser* gt_dev_option_parser_new(void *tool_arguments)
{
  GtToolbox *dev_toolbox = tool_arguments;
  GtOptionParser *op;
  gt_assert(dev_toolbox);
  op = gt_option_parser_new("[option ...] dev_tool_name [argument ...]",
                            "Call development tool with name dev_tool_name and "
                            "pass argument(s) to it.");
  gt_option_parser_set_comment_func(op, gt_toolbox_show, dev_toolbox);
  gt_option_parser_set_min_args(op, 1);
  return op;
}

static int gt_dev_runner(int argc, const char **argv, int parsed_args,
                         void *tool_arguments, GtError *err)
{
  GtToolbox *dev_toolbox = tool_arguments;
  GtToolfunc toolfunc;
  GtTool *tool = NULL;
  int had_err = 0;
  char **nargv = NULL;

  gt_error_check(err);
  gt_assert(dev_toolbox);

  /* get development tools */
  if (!gt_toolbox_has_tool(dev_toolbox, argv[parsed_args])) {
    gt_error_set(err, "development tool '%s' not found; option -help lists "
                      "possible tools", argv[parsed_args]);
    had_err = -1;
  }

  /* call development tool */
  if (!had_err) {
    if (!(toolfunc = gt_toolbox_get(dev_toolbox, argv[parsed_args]))) {
      tool = gt_toolbox_get_tool(dev_toolbox, argv[parsed_args]);
      gt_assert(tool);
    }
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    if (toolfunc)
      had_err = toolfunc(argc - parsed_args, (const char**) nargv, err);
    else
      had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv,
                            err);
  }

  /* free */
  gt_cstr_array_delete(nargv);

  return had_err;
}

GtTool* gt_dev(void)
{
  return gt_tool_new(gt_dev_arguments_new,
                     gt_dev_arguments_delete,
                     gt_dev_option_parser_new,
                     NULL,
                     gt_dev_runner);
}
genometools-1.5.1/src/tools/gt_dev.h000066400000000000000000000017311211610345200174160ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_DEV_H
#define GT_DEV_H

#include "core/tool_api.h"

/* the development tool */
GtTool* gt_dev(void);

#endif
genometools-1.5.1/src/tools/gt_dot.c000066400000000000000000000050351211610345200174220ustar00rootroot00000000000000/*
  Copyright (c) 2013 Sascha Steinbiss 
  Copyright (c) 2013 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/unused_api.h"
#include "extended/dot_visitor.h"
#include "extended/gff3_in_stream.h"
#include "extended/visitor_stream.h"
#include "tools/gt_dot.h"

typedef struct {
} GtDotArguments;

static void* gt_dot_arguments_new(void)
{
  GtDotArguments *arguments = gt_calloc(1, sizeof *arguments);
  return arguments;
}

static void gt_dot_arguments_delete(void *tool_arguments)
{
  GtDotArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_free(arguments);
}

static GtOptionParser* gt_dot_option_parser_new(void *tool_arguments)
{
  GT_UNUSED GtDotArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GT_UNUSED GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [files]",
                            "Prints feature graphs in dotfile format.");

  return op;
}

static int gt_dot_runner(int argc, const char **argv, int parsed_args,
                         void *tool_arguments, GtError *err)
{
  GT_UNUSED GtDotArguments *arguments = tool_arguments;
  GtNodeStream *vs = NULL, *ins = NULL;
  GtNodeVisitor *dv = NULL;
  int had_err = 0;
  gt_error_check(err);

  ins = gt_gff3_in_stream_new_unsorted(argc - parsed_args, argv + parsed_args);
  if (ins) {
    vs = gt_visitor_stream_new(ins, (dv = gt_dot_visitor_new()));
  }
  if (vs) {
    had_err = gt_node_stream_pull(vs, err);
    gt_dot_visitor_finalize(dv);
  }
  gt_node_stream_delete(ins);
  gt_node_stream_delete(vs);
  return had_err;
}

GtTool* gt_dot(void)
{
  return gt_tool_new(gt_dot_arguments_new,
                     gt_dot_arguments_delete,
                     gt_dot_option_parser_new,
                     NULL,
                     gt_dot_runner);
}
genometools-1.5.1/src/tools/gt_dot.h000066400000000000000000000017151211610345200174300ustar00rootroot00000000000000/*
  Copyright (c) 2013 Sascha Steinbiss 
  Copyright (c) 2013 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_DOT_H
#define GT_DOT_H

#include "core/tool_api.h"

/* the dot tool */
GtTool* gt_dot(void);

#endif
genometools-1.5.1/src/tools/gt_dupfeat.c000066400000000000000000000077601211610345200202730ustar00rootroot00000000000000/*
  Copyright (c) 2009 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/output_file_api.h"
#include "extended/dup_feature_stream.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "tools/gt_interfeat.h"

typedef struct {
  GtStr *dest_type,
        *source_type;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} InterFeatArguments;

static void* gt_interfeat_arguments_new(void)
{
  InterFeatArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->dest_type = gt_str_new();
  arguments->source_type = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_interfeat_arguments_delete(void *tool_arguments)
{
  InterFeatArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->source_type);
  gt_str_delete(arguments->dest_type);
  gt_free(arguments);
}

static GtOptionParser* gt_interfeat_option_parser_new(void *tool_arguments)
{
  InterFeatArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Duplicate "
                            "internal feature nodes in given GFF3_file(s).");

  /* -outside */
  option = gt_option_new_string("dest", "set destination type",
                                arguments->dest_type, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  /* -inter */
  option = gt_option_new_string("source", "set source type",
                                arguments->source_type, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  return op;
}

static int gt_interfeat_runner(int argc, const char **argv, int parsed_args,
                          void *tool_arguments, GtError *err)
{
  InterFeatArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream,
               *dup_feature_stream,
               *gff3_out_stream;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);

  /* create intermediary feature stream */
  dup_feature_stream =
    gt_dup_feature_stream_new(gff3_in_stream, gt_str_get(arguments->dest_type),
                              gt_str_get(arguments->source_type));

  /* create gff3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(dup_feature_stream,
                                           arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(dup_feature_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool* gt_dupfeat(void)
{
  return gt_tool_new(gt_interfeat_arguments_new,
                     gt_interfeat_arguments_delete,
                     gt_interfeat_option_parser_new,
                     NULL,
                     gt_interfeat_runner);
}
genometools-1.5.1/src/tools/gt_dupfeat.h000066400000000000000000000016331211610345200202710ustar00rootroot00000000000000/*
  Copyright (c) 2009 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_DUPFEAT_H
#define GT_DUPFEAT_H

#include "core/tool_api.h"

/* the duplicate feature tool */
GtTool* gt_dupfeat(void);

#endif
genometools-1.5.1/src/tools/gt_encseq.c000066400000000000000000000072151211610345200201140ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/cstr_array.h"
#include "core/error.h"
#include "core/option_api.h"
#include "core/versionfunc.h"
#include "extended/toolbox_api.h"
#include "tools/gt_encseq_bitextract.h"
#include "tools/gt_encseq_check.h"
#include "tools/gt_encseq_decode.h"
#include "tools/gt_encseq_encode.h"
#include "tools/gt_encseq_info.h"
#include "tools/gt_encseq_md5.h"
#include "tools/gt_encseq_bench.h"

static void* gt_encseq_arguments_new(void)
{
  GtToolbox *encseq_toolbox = gt_toolbox_new();
  gt_toolbox_add_tool(encseq_toolbox, "bitextract", gt_encseq_bitextract());
  gt_toolbox_add_tool(encseq_toolbox, "check", gt_encseq_check());
  gt_toolbox_add_tool(encseq_toolbox, "info", gt_encseq_info());
  gt_toolbox_add_tool(encseq_toolbox, "md5", gt_encseq_md5());
  gt_toolbox_add_tool(encseq_toolbox, "decode", gt_encseq_decode());
  gt_toolbox_add_tool(encseq_toolbox, "encode", gt_encseq_encode());
  gt_toolbox_add_tool(encseq_toolbox, "bench", gt_encseq_bench());
  return encseq_toolbox;
}

static void gt_encseq_arguments_delete(void *tool_arguments)
{
  GtToolbox *encseq_toolbox = tool_arguments;
  if (!encseq_toolbox) return;
  gt_toolbox_delete(encseq_toolbox);
}

static GtOptionParser* gt_encseq_option_parser_new(void *tool_arguments)
{
  GtToolbox *encseq_toolbox = tool_arguments;
  GtOptionParser *op;
  gt_assert(encseq_toolbox);
  op = gt_option_parser_new("[option ...] tool [argument ...]",
                            "Call encoded sequence manipulation tool  "
                            "and pass argument(s) to it.");
  gt_option_parser_set_comment_func(op, gt_toolbox_show, encseq_toolbox);
  gt_option_parser_set_min_args(op, 1);
  return op;
}

static int gt_encseq_runner(int argc, const char **argv, int parsed_args,
                         void *tool_arguments, GtError *err)
{
  GtToolbox *encseq_toolbox = tool_arguments;
  GtTool *tool = NULL;
  int had_err = 0;
  char **nargv = NULL;

  gt_error_check(err);
  gt_assert(encseq_toolbox);

  /* get encseq tools */
  tool = gt_toolbox_get_tool(encseq_toolbox, argv[parsed_args]);
  if (!tool) {
    gt_error_set(err, "encseq tool '%s' not found; option -help lists "
                      "possible tools", argv[parsed_args]);
    had_err = -1;
  }

  /* call encseq tool */
  if (!had_err) {
    gt_assert(tool);
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv, err);
  }

  /* free */
  gt_cstr_array_delete(nargv);

  return had_err;
}

GtTool* gt_encseq(void)
{
  return gt_tool_new(gt_encseq_arguments_new,
                     gt_encseq_arguments_delete,
                     gt_encseq_option_parser_new,
                     NULL,
                     gt_encseq_runner);
}
genometools-1.5.1/src/tools/gt_encseq.h000066400000000000000000000017341211610345200201210ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ENCSEQ_H
#define GT_ENCSEQ_H

#include "core/tool_api.h"

/* the encseq toolbox */
GtTool* gt_encseq(void);

#endif
genometools-1.5.1/src/tools/gt_encseq2spm.c000066400000000000000000000404101211610345200207100ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/unused_api.h"
#include "core/option_api.h"
#include "core/encseq_api.h"
#include "core/logger.h"
#include "core/intbits.h"
#include "core/minmax.h"
#include "core/showtime.h"
#ifdef GT_THREADS_ENABLED
#include "core/thread_api.h"
#endif
#include "tools/gt_encseq2spm.h"
#include "match/firstcodes.h"
#include "match/firstcodes-scan.h"
#include "match/esa-spmsk.h"

typedef struct
{
  bool checksuftab,
       singlestrand,
       verbose,
       outputspms,
       onlyaccum,
       onlyallfirstcodes,
       radixlarge,
       countspms;
  unsigned int minmatchlength,
               numofparts,
               radixparts,
               singlescan,
               addbscache_depth,
               forcek;
  unsigned long maximumspace,
                phase2extra;
  GtStr *encseqinput,
        *spmspec,
        *memlimitarg,
        *phase2extraarg;
  GtOption *refoptionmemlimit,
           *refoptionphase2extra;
} GtEncseq2spmArguments;

static void* gt_encseq2spm_arguments_new(void)
{
  GtEncseq2spmArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->outputspms = false;
  arguments->countspms = false;
  arguments->radixlarge = false;
  arguments->singlescan = 0;
  arguments->numofparts = 0;
  arguments->radixparts = 1U;
  arguments->encseqinput = gt_str_new();
  arguments->spmspec = gt_str_new();
  arguments->memlimitarg = gt_str_new();
  arguments->phase2extraarg = gt_str_new();
  arguments->phase2extra = 0UL; /* in bytes */
  arguments->maximumspace = 0UL; /* in bytes */
  return arguments;
}

static void gt_encseq2spm_arguments_delete(void *tool_arguments)
{
  GtEncseq2spmArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->encseqinput);
  gt_str_delete(arguments->spmspec);
  gt_option_delete(arguments->refoptionmemlimit);
  gt_option_delete(arguments->refoptionphase2extra);
  gt_str_delete(arguments->memlimitarg);
  gt_str_delete(arguments->phase2extraarg);
  gt_free(arguments);
}

static GtOptionParser* gt_encseq2spm_option_parser_new(void *tool_arguments)
{
  GtEncseq2spmArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionparts, *optionmemlimit;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [file]",
                            "Compute suffix prefix matches "
                            "from encoded sequence.");

  /* -l */
  option = gt_option_new_uint_min("l", "specify the minimum length",
                                  &arguments->minmatchlength, 0, 1U);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -parts */
  optionparts = gt_option_new_uint("parts", "specify the number of parts",
                                  &arguments->numofparts, 0U);
  gt_option_parser_add_option(op, optionparts);

  /* -memlimit */
  optionmemlimit = gt_option_new_string("memlimit",
                       "specify maximal amount of memory to be used during "
                       "index construction (in bytes, the keywords 'MB' "
                       "and 'GB' are allowed)",
                       arguments->memlimitarg, NULL);
  gt_option_parser_add_option(op, optionmemlimit);
  gt_option_exclude(optionmemlimit, optionparts);
  arguments->refoptionmemlimit = gt_option_ref(optionmemlimit);

  /* -checksuftab */
  option = gt_option_new_bool("checksuftab", "check the suffix table",
                             &arguments->checksuftab, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -singlestrand */
  option = gt_option_new_bool("singlestrand", "use only the forward strand "
                              "of the sequence",
                              &arguments->singlestrand, false);
  gt_option_parser_add_option(op, option);

  /* -spm */
  option = gt_option_new_string("spm", "specify output for spms",
                                arguments->spmspec, NULL);
  gt_option_parser_add_option(op, option);

  /* -ii */
  option = gt_option_new_string("ii", "specify the input sequence",
                                arguments->encseqinput, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -onlyaccum */
  option = gt_option_new_bool("onlyaccum", "only accumulate codes",
                             &arguments->onlyaccum, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -onlyallfirstcodes */
  option = gt_option_new_bool("onlyallfirstcodes", "only determines allcodes",
                              &arguments->onlyallfirstcodes, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -addbscachedepth */
  option = gt_option_new_uint("addbscachedepth", "only determines allcodes",
                              &arguments->addbscache_depth, 5U);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -phase2extra */
  option = gt_option_new_string("phase2extra",
                       "specify  amount of additional space required for "
                       "the second phase of the computation involving the "
                       "processing of the intervals (in bytes, "
                       "the keywords 'MB' and 'GB' are allowed)",
                       arguments->phase2extraarg, NULL);
  gt_option_parser_add_option(op, option);
  arguments->refoptionphase2extra = gt_option_ref(option);
  gt_option_is_development_option(option);

  /* -radixlarge */
  option = gt_option_new_bool("radixlarge", "use large tables for radixsort",
                              &arguments->radixlarge, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -radixparts */
  option = gt_option_new_uint("radixparts", "specify the number of parts "
                              "for radixsort",
                              &arguments->radixparts, 1U);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -singlescan */
  option = gt_option_new_uint("singlescan", "run a single scan: 1=fast; "
                              "2=fast with check; 3=fast with output; "
                              "4=sfx-mapped4-version",
                              &arguments->singlescan, 0);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -forcek */
  option = gt_option_new_uint("forcek", "specify the value of k",
                              &arguments->forcek, 0);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  return op;
}

static bool gt_encseq2spm_kmersize(GtEncseq2spmArguments *arguments,
    unsigned int *kmersize, GtError *err)
{
  bool haserr = false;
  gt_assert(kmersize != NULL);
  if (arguments->forcek > 0)
  {
    *kmersize = arguments->forcek;
    if (*kmersize > arguments->minmatchlength)
    {
      gt_error_set(err,"argument %u to option -forcek > l",
          *kmersize);
      haserr = true;
    }
    else if (*kmersize > (unsigned int)GT_UNITSIN2BITENC)
    {
      gt_error_set(err,
          "argument %u to option -forcek > %u (machine word size/2)",
          *kmersize, (unsigned int)GT_UNITSIN2BITENC);
      haserr = true;
    }
  }
  else
  {
    *kmersize = MIN((unsigned int) GT_UNITSIN2BITENC,
        arguments->minmatchlength);
  }
  gt_log_log("kmersize=%u", *kmersize);
  gt_assert(*kmersize > 0);
  return haserr;
}

static int gt_encseq2spm_arguments_check(int rest_argc,
                                         void *tool_arguments,
                                         GtError *err)
{
  GtEncseq2spmArguments *arguments = tool_arguments;
  bool haserr = false;

  gt_error_check(err);
  if (rest_argc != 0)
  {
    gt_error_set(err,"unnecessary arguments");
    haserr = true;
  }
  if (!haserr && gt_str_length(arguments->spmspec) > 0)
  {
    const char *spmspecstring = gt_str_get(arguments->spmspec);
    if (strcmp(spmspecstring,"show") == 0)
    {
      arguments->outputspms = true;
    } else
    {
      if (strcmp(spmspecstring,"count") == 0)
      {
        arguments->countspms = true;
      } else
      {
        gt_error_set(err,"illegal argument \"%s\" to option -spm",
                     spmspecstring);
        haserr = true;
      }
    }
  }
  if (!haserr && gt_option_is_set(arguments->refoptionmemlimit))
  {
    if (gt_option_parse_spacespec(&arguments->maximumspace,
                                  "memlimit",
                                  arguments->memlimitarg,
                                  err) != 0)
    {
      haserr = true;
    }
    if (!haserr && !gt_ma_bookkeeping_enabled()) {
      gt_error_set(err, "option '-memlimit' requires "
                        "GT_MEM_BOOKKEEPING=on");
      haserr = true;
    }
  }
  if (!haserr && gt_option_is_set(arguments->refoptionphase2extra))
  {
    if (gt_option_parse_spacespec(&arguments->phase2extra,
                                  "phase2extra",
                                  arguments->phase2extraarg,
                                  err) != 0)
    {
      haserr = true;
    }
  }
#ifdef GT_THREADS_ENABLED
  if (!haserr) {
    if (gt_jobs > 1 && gt_ma_bookkeeping_enabled()) {
      gt_error_set(err, "gt option '-j' and GT_MEM_BOOKKEEPING=on "
                        "are incompatible");
      haserr = true;
    }
  }
#endif
  return haserr ? -1 : 0;
}

static int gt_encseq2spm_runner(GT_UNUSED int argc,
                                GT_UNUSED const char **argv,
                                GT_UNUSED int parsed_args,
                                void *tool_arguments,
                                GtError *err)
{
  GtEncseq2spmArguments *arguments = tool_arguments;
  GtEncseqLoader *el = NULL;
  GtEncseq *encseq = NULL;
  bool haserr = false;

  gt_error_check(err);
  gt_assert(arguments);
  el = gt_encseq_loader_new();
  gt_encseq_loader_drop_description_support(el);
  gt_encseq_loader_disable_autosupport(el);
  encseq = gt_encseq_loader_load(el, gt_str_get(arguments->encseqinput),
                                 err);
  if (encseq == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (arguments->singlestrand)
    {
      gt_error_set(err,"option -singlestand is not implemented");
      haserr = true;
    } else
    {
      if (gt_encseq_mirror(encseq, err) != 0)
      {
        haserr = true;
      }
    }
  }

  if (!haserr && arguments->singlescan > 0)
  {
    GtTimer *timer = NULL;

    if (gt_showtime_enabled())
    {
      char *outmsg;

      switch (arguments->singlescan)
      {
        case 1:
          outmsg = "to run fast scanning";
          break;
        case 2:
          outmsg = "to run fast scanning with check";
          break;
        case 3:
          outmsg = "to run fast scanning with output";
          break;
        case 4:
          outmsg = "to run old scanning code";
          break;
        default:
          gt_error_set(err,"argument %u to option -singlescan not allowed",
                       arguments->singlescan);
          haserr = true;
      }
      if (!haserr)
      {
        timer = gt_timer_new_with_progress_description(outmsg);
        gt_timer_start(timer);
      }
    }
    if (!haserr)
    {
      unsigned int kmersize = 0;
      haserr = gt_encseq2spm_kmersize(arguments, &kmersize, err);
      if (!haserr)
      {
        if (arguments->singlescan == 4U)
        {
          gt_rungetencseqkmers(encseq,kmersize);
        } else
        {
          if (arguments->singlescan > 0)
          {
            gt_firstcode_runkmerscan(encseq,arguments->singlescan - 1,kmersize,
                arguments->minmatchlength);
          }
        }
      }
    }
    if (timer != NULL)
    {
      gt_timer_show_progress_final(timer, stdout);
      gt_timer_delete(timer);
    }
  }
  if (!haserr && arguments->singlescan == 0)
  {
    GtLogger *logger;
    const GtReadmode readmode = GT_READMODE_FORWARD;
    GtBUstate_spmsk **spmsk_states = NULL;
    unsigned int kmersize, threadcount;

#ifdef GT_THREADS_ENABLED
    const unsigned int threads = gt_jobs;
#else
    const unsigned int threads = 1U;
#endif

    if (arguments->countspms || arguments->outputspms)
    {
      spmsk_states = gt_malloc(sizeof (*spmsk_states) * threads);
      for (threadcount = 0; threadcount < threads; threadcount++)
      {
        spmsk_states[threadcount]
          = gt_spmsk_inl_new(encseq,
                             readmode,
                             (unsigned long) arguments->minmatchlength,
                             arguments->countspms,
                             arguments->outputspms,
                             gt_str_get(arguments->encseqinput));
      }
    }
    logger = gt_logger_new(arguments->verbose,GT_LOGGER_DEFLT_PREFIX, stdout);
    haserr = gt_encseq2spm_kmersize(arguments, &kmersize, err);
    if (!haserr)
    {
      if (storefirstcodes_getencseqkmers_twobitencoding(encseq,
                                                      kmersize,
                                                      arguments->numofparts,
                                                      arguments->maximumspace,
                                                      arguments->minmatchlength,
                                     /* use false */  arguments->checksuftab,
                                     /* use false */  arguments->onlyaccum,
                                     /* use false */  arguments->
                                                            onlyallfirstcodes,
                                     /* use 5U */     arguments->
                                                            addbscache_depth,
                                     /* specify the extra space needed for
                                        the function processing the interval */
                                                      arguments->phase2extra,
                                     /* use true */   arguments->radixlarge ?
                                                        false : true,
                                     /* use 2 without threads and
                                        use 1 with threads */
                                                      arguments->radixparts,
                                                      spmsk_states != NULL
                                                        ? gt_spmsk_inl_process
                                                        : NULL,
                                                      gt_spmsk_inl_process_end,
                                                      spmsk_states,
                                                      logger,
                                                      err) != 0)
      {
        haserr = true;
      }
    }
    if (spmsk_states != NULL)
    {
      unsigned long countmatches = 0;

      for (threadcount = 0; threadcount < threads; threadcount++)
      {
        countmatches += gt_spmsk_inl_delete(spmsk_states[threadcount]);
      }
      if (arguments->countspms)
      {
        printf("number of suffix-prefix matches=%lu\n",countmatches);
      }
      gt_free(spmsk_states);
    }
    gt_logger_delete(logger);
  }
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(el);
  return haserr ? -1 : 0;
}

GtTool* gt_encseq2spm(void)
{
  return gt_tool_new(gt_encseq2spm_arguments_new,
                     gt_encseq2spm_arguments_delete,
                     gt_encseq2spm_option_parser_new,
                     gt_encseq2spm_arguments_check,
                     gt_encseq2spm_runner);
}
genometools-1.5.1/src/tools/gt_encseq2spm.h000066400000000000000000000017411211610345200207210ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ENCSEQ2SPM_H
#define GT_ENCSEQ2SPM_H

#include "core/tool_api.h"

/* the encseq2spm tool */
GtTool* gt_encseq2spm(void);

#endif
genometools-1.5.1/src/tools/gt_encseq_bench.c000066400000000000000000000277411211610345200212610ustar00rootroot00000000000000/*
  Copyright (c) 2012 Stefan Kurtz 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/unused_api.h"
#include "core/encseq.h"
#include "core/encseq_metadata.h"
#include "core/mathsupport.h"
#include "core/showtime.h"
#include "core/logger.h"
#include "tools/gt_encseq_bench.h"

typedef struct
{
  unsigned long ccext;
  bool sortlenprepare, verbose;
} GtEncseqBenchArguments;

static void* gt_encseq_bench_arguments_new(void)
{
  GtEncseqBenchArguments *arguments = gt_malloc(sizeof *arguments);
  return arguments;
}

static void gt_encseq_bench_arguments_delete(void *tool_arguments)
{
  GtEncseqBenchArguments *arguments = tool_arguments;

  if (arguments != NULL)
  {
    gt_free(arguments);
  }
}

static GtOptionParser* gt_encseq_bench_option_parser_new(void *tool_arguments)
{
  GtEncseqBenchArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] indexname",
                            "Perform benchmark on extractions from encseq.");

  option = gt_option_new_ulong("ccext", "specify number of random character "
                                        "extractions",
                               &arguments->ccext, 0UL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("solepr", "prepare data structure for sequences "
                                         "ordered by their length",
                               &arguments->sortlenprepare, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 1U, 1U);
  return op;
}

static void gt_bench_character_extractions(const GtEncseq *encseq,
                                           unsigned long ccext)
{
  unsigned long idx, ccsum = 0,
                totallength = gt_encseq_total_length(encseq);
  GtTimer *timer = NULL;

  if (gt_showtime_enabled())
  {
    timer = gt_timer_new_with_progress_description("run character "
                                                   "extractions");
    gt_timer_start(timer);
  }
  for (idx = 0; idx < ccext; idx++)
  {
    GtUchar cc;
    unsigned long pos = gt_rand_max(totallength-1);

    cc = gt_encseq_get_encoded_char(encseq,pos,GT_READMODE_FORWARD);
    ccsum += (unsigned long) cc;
  }
  printf("ccsum=%lu\n",ccsum);
  if (timer != NULL)
  {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
}

typedef struct
{
  unsigned long minlength, maxlength, numofdifferentseqlen, *seqlenseppos,
                *seqlencount, *seqlentab;
} GtSortedlengthinfo;

void gt_sortedlengthinfo_delete(GtSortedlengthinfo *sortedlengthinfo)
{
  if (sortedlengthinfo != NULL)
  {
    gt_free(sortedlengthinfo->seqlentab);
    gt_free(sortedlengthinfo->seqlenseppos);
    gt_free(sortedlengthinfo->seqlencount);
    gt_free(sortedlengthinfo);
  }
}

GtSortedlengthinfo *gt_sortedlengthinfo_new(const GtEncseq *encseq,
                                            const char *indexname,
                                            GtError *err)
{
  GtEncseqMetadata *emd;
  GtSortedlengthinfo *sortedlengthinfo = NULL;
  int had_err = 0;

  emd = gt_encseq_metadata_new(indexname, err);
  if (emd == NULL)
  {
    had_err = -1;
  } else
  {
    unsigned long seqlen, previousseqlen = 0, seqnum,
                  countdifferentlength = 1UL, currentpos = 0;

    sortedlengthinfo = gt_malloc(sizeof *sortedlengthinfo);
    sortedlengthinfo->minlength = gt_encseq_metadata_min_seq_length(emd);
    sortedlengthinfo->maxlength = gt_encseq_metadata_max_seq_length(emd);
    gt_assert(sortedlengthinfo->minlength > 0 &&
              sortedlengthinfo->minlength <= sortedlengthinfo->maxlength);
    for (seqnum = 0; seqnum < gt_encseq_num_of_sequences(encseq); seqnum++)
    {
      seqlen = gt_encseq_seqlength(encseq,seqnum);

      if (seqnum > 0)
      {
        if (previousseqlen > seqlen)
        {
          gt_error_set(err,"sequence %lu of length %lu is longer than "
                           "sequence %lu of length %lu",
                           seqnum-1,previousseqlen,seqnum,seqlen);
          had_err = -1;
          break;
        }
        if (previousseqlen < seqlen)
        {
          countdifferentlength++;
        }
      }
      previousseqlen = seqlen;
    }
    if (!had_err)
    {
      sortedlengthinfo->seqlentab
        = gt_calloc((size_t) countdifferentlength,
                    sizeof (*sortedlengthinfo->seqlentab));
    } else
    {
      sortedlengthinfo->seqlentab = NULL;
    }
    if (!had_err && countdifferentlength >= 2UL)
    {
      sortedlengthinfo->seqlenseppos
        = gt_malloc(sizeof (*sortedlengthinfo->seqlenseppos) *
                    (countdifferentlength-1));
      sortedlengthinfo->seqlencount
        = gt_malloc(sizeof (*sortedlengthinfo->seqlencount) *
                    (countdifferentlength-1));
    } else
    {
      sortedlengthinfo->seqlenseppos = NULL;
      sortedlengthinfo->seqlencount = NULL;
    }
    sortedlengthinfo->numofdifferentseqlen = 0;
    if (!had_err)
    {
      gt_assert(sortedlengthinfo->seqlenseppos != NULL &&
                sortedlengthinfo->seqlencount != NULL &&
                sortedlengthinfo->seqlentab != NULL);
      for (seqnum = 0; seqnum < gt_encseq_num_of_sequences(encseq); seqnum++)
      {
        seqlen = gt_encseq_seqlength(encseq,seqnum);

        if (seqnum > 0)
        {
          if (previousseqlen < seqlen)
          {
            gt_assert(sortedlengthinfo->numofdifferentseqlen <
                      countdifferentlength-1);
            sortedlengthinfo->seqlencount[
              sortedlengthinfo->numofdifferentseqlen] = seqnum;
            sortedlengthinfo->seqlenseppos[
              sortedlengthinfo->numofdifferentseqlen++] = currentpos;
            sortedlengthinfo->seqlentab[
               sortedlengthinfo->numofdifferentseqlen] = seqlen;
            gt_assert(gt_encseq_get_encoded_char(encseq,currentpos,
                                                 GT_READMODE_FORWARD)
                      == (GtUchar) SEPARATOR);
          }
          currentpos += 1UL + seqlen;
        } else
        {
          sortedlengthinfo->seqlentab[0] = seqlen;
          currentpos = seqlen;
        }
        previousseqlen = seqlen;
      }
      sortedlengthinfo->numofdifferentseqlen++;
    }
  }
  gt_encseq_metadata_delete(emd);
  if (!had_err)
  {
    return sortedlengthinfo;
  }
  gt_sortedlengthinfo_delete(sortedlengthinfo);
  return NULL;
}

unsigned long gt_sortedlengthinfo_seqnum(const GtEncseq *encseq,
                                   const GtSortedlengthinfo *sortedlengthinfo,
                                   unsigned long position)
{
  unsigned long recordnum, totallength = gt_encseq_total_length(encseq);

  gt_assert(position < totallength);
  if (gt_encseq_get_encoded_char(encseq,position,GT_READMODE_FORWARD)
                    == (GtUchar) SEPARATOR)
  {
    return ULONG_MAX;
  }
  recordnum = gt_encseq_sep2seqnum(sortedlengthinfo->seqlenseppos,
                                   sortedlengthinfo->numofdifferentseqlen,
                                   totallength,
                                   position);
  if (recordnum == 0)
  {
    return position/(sortedlengthinfo->seqlentab[0]+1);
  } else
  {
    return sortedlengthinfo->seqlencount[recordnum-1] +
           (position - sortedlengthinfo->seqlenseppos[recordnum-1])/
           (sortedlengthinfo->seqlentab[recordnum]+1);
  }
}

unsigned long gt_sortedlengthinfo_seqstart(const GtEncseq *encseq,
                                   const GtSortedlengthinfo *sortedlengthinfo,
                                   unsigned long seqnum)
{
  if (seqnum == 0)
  {
    return 0;
  } else
  {
    unsigned long numberofsequences = gt_encseq_num_of_sequences(encseq),
                  recordnum;

    gt_assert(seqnum < numberofsequences);
    recordnum = gt_encseq_sep2seqnum(sortedlengthinfo->seqlencount,
                                     sortedlengthinfo->numofdifferentseqlen,
                                     numberofsequences,
                                     seqnum);
    if (recordnum == 0)
    {
      return (sortedlengthinfo->seqlentab[0] + 1) * seqnum;
    }
    gt_assert(seqnum >= sortedlengthinfo->seqlencount[recordnum-1]);
    return sortedlengthinfo->seqlenseppos[recordnum-1] +
           (sortedlengthinfo->seqlentab[recordnum] + 1) *
           (seqnum - sortedlengthinfo->seqlencount[recordnum-1]) + 1;
  }
}

static int gt_encseq_bench_runner(GT_UNUSED int argc, const char **argv,
                                  int parsed_args, void *tool_arguments,
                                  GtError *err)
{
  GtEncseqBenchArguments *arguments = tool_arguments;
  GtEncseqLoader *encseq_loader;
  GtEncseq *encseq;
  GtLogger *logger = NULL;
  const char *indexname;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments != NULL);
  encseq_loader = gt_encseq_loader_new();
  indexname = argv[parsed_args];
  encseq = gt_encseq_loader_load(encseq_loader, indexname, err);
  if (encseq == NULL)
  {
    had_err = -1;
  } else
  {
    if (arguments->sortlenprepare)
    {
      unsigned long seqnum, position;
      GtSortedlengthinfo *sortedlengthinfo
        = gt_sortedlengthinfo_new(encseq,indexname,err);

      if (sortedlengthinfo == NULL)
      {
        had_err = -1;
      } else
      {
        logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX,
                               stdout);
      }
      gt_logger_log(logger,"prepare sorted length info");
      for (position = 0; !had_err && position < gt_encseq_total_length(encseq);
           position++)
      {
        seqnum = gt_sortedlengthinfo_seqnum(encseq,sortedlengthinfo,position);
        if (seqnum != ULONG_MAX)
        {
          unsigned long seqnum2 = gt_encseq_seqnum(encseq,position);
          if (seqnum2 != seqnum)
          {
            fprintf(stderr,"position %lu: seqnum2 = %lu != %lu = seqnum\n",
                    position,seqnum,seqnum2);
            exit(GT_EXIT_PROGRAMMING_ERROR);
          }
        }
      }
      gt_logger_log(logger,"perform seqnum check");
      for (seqnum = 0; !had_err && seqnum < gt_encseq_num_of_sequences(encseq);
           seqnum++)
      {
        unsigned long seqstart = gt_encseq_seqstartpos(encseq,seqnum);
        unsigned long seqstart2 = gt_sortedlengthinfo_seqstart(encseq,
                                   sortedlengthinfo,seqnum);
        if (seqstart != seqstart2)
        {
          fprintf(stderr,"seqnum=%lu: seqstart = %lu != %lu = seqstart2\n",
                          seqnum,seqstart,seqstart2);
          exit(GT_EXIT_PROGRAMMING_ERROR);
        }
      }
      gt_logger_log(logger,"perform seqstart check");
      gt_sortedlengthinfo_delete(sortedlengthinfo);
    }
    if (!had_err && arguments->ccext > 0)
    {
      gt_logger_log(logger,"perform character extractions");
      gt_bench_character_extractions(encseq,arguments->ccext);
    }
  }
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(encseq_loader);
  gt_logger_delete(logger);
  return had_err;
}

GtTool* gt_encseq_bench(void)
{
  return gt_tool_new(gt_encseq_bench_arguments_new,
                  gt_encseq_bench_arguments_delete,
                  gt_encseq_bench_option_parser_new,
                  NULL,
                  gt_encseq_bench_runner);
}
genometools-1.5.1/src/tools/gt_encseq_bench.h000066400000000000000000000017511211610345200212570ustar00rootroot00000000000000/*
  Copyright (c) 2012 Stefan Kurtz 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ENCSEQ_BENCH_H
#define GT_ENCSEQ_BENCH_H

#include "core/tool_api.h"

/* the encseq_bench tool */
GtTool* gt_encseq_bench(void);

#endif
genometools-1.5.1/src/tools/gt_encseq_bitextract.c000066400000000000000000000145201211610345200223420ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/parseutils_api.h"
#include "core/readmode_api.h"
#include "core/unused_api.h"
#include "core/undef_api.h"
#include "tools/gt_encseq_bitextract.h"

typedef struct {
  bool mirror,
       specialranges;
  GtStr *readmode;
  unsigned long bitpos,
                stoppos;
} GtEncseqBitextractArguments;

static void* gt_encseq_bitextract_arguments_new(void)
{
  GtEncseqBitextractArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->readmode = gt_str_new();
  return arguments;
}

static void gt_encseq_bitextract_arguments_delete(void *tool_arguments)
{
  GtEncseqBitextractArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->readmode);
  gt_free(arguments);
}

static GtOptionParser* gt_encseq_bitextract_option_parser_new(void
                                                                *tool_arguments)
{
  GtEncseqBitextractArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [indexname]",
                            "Extracts internal data from encoded sequences.");

  option = gt_option_new_bool("mirrored", "mirror sequence",
                               &arguments->mirror, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("stoppos", "output stop positions",
                               &arguments->stoppos, GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("specialranges", "output special ranges",
                               &arguments->specialranges, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("bitpos", "extract and display "
                                         "two bit encoding for position",
                               &arguments->bitpos, GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, option);

  gt_encseq_options_add_readmode_option(op, arguments->readmode);

  gt_option_parser_set_min_args(op, 1U);

  return op;
}

static int gt_encseq_bitextract_runner(GT_UNUSED int argc, const char **argv,
                                       GT_UNUSED int parsed_args,
                                       void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  GtEncseqBitextractArguments *arguments = tool_arguments;
  GtEncseqLoader *el;
  GtEncseq *encseq;
  int had_err = 0;
  bool fwd, it1, GT_UNUSED it2;
  char buffer[BUFSIZ];
  GtEndofTwobitencoding etbe;
  GtEncseqReader *esr;
  GtSpecialrangeiterator *sri;
  GtRange srng;
  GtReadmode rm;

  gt_error_check(err);
  gt_assert(arguments);

  el = gt_encseq_loader_new();
  encseq = gt_encseq_loader_load(el, argv[parsed_args], err);
  if (!encseq)
    had_err = -1;

  if (!had_err && arguments->mirror) {
    had_err = gt_encseq_mirror(encseq, err);
  }

  if (!had_err) {
    rm = gt_readmode_parse(gt_str_get(arguments->readmode), NULL);
    fwd = GT_ISDIRREVERSE(rm) ? false : true;
  }

  if (!had_err && arguments->bitpos != GT_UNDEF_ULONG) {
    if (arguments->bitpos >= gt_encseq_total_length(encseq)) {
      gt_error_set(err, "position %lu exceeds encoded sequence length of %lu",
                   arguments->bitpos, gt_encseq_total_length(encseq));
      had_err = -1;
    }

    if (!had_err) {
      unsigned long ret;
      esr = gt_encseq_create_reader_with_readmode(encseq, rm,
                                                  arguments->bitpos);
      ret = gt_encseq_extract2bitencwithtwobitencodingstoppos(&etbe, esr,
                                                        encseq,
                                                        rm, arguments->bitpos);
      gt_bitsequence_tostring(buffer, etbe.tbe);
      printf("Twobitencoding   %s\n"
             "unitsnotspecial  %u\n"
             "position         %lu\n"
             "returnvalue      %lu\n",
             buffer,
             etbe.unitsnotspecial,
             arguments->bitpos,
             ret);
      gt_encseq_reader_delete(esr);
    }
  }

  if (!had_err && arguments->stoppos != GT_UNDEF_ULONG) {
    if (arguments->stoppos >= gt_encseq_total_length(encseq)) {
      gt_error_set(err, "position %lu exceeds encoded sequence length of %lu",
                   arguments->stoppos, gt_encseq_total_length(encseq));
      had_err = -1;
    }
    if (!had_err) {
      esr = gt_encseq_create_reader_with_readmode(encseq, rm, 0);
      /* check stoppos stuff */
      gt_encseq_reader_reinit_with_readmode(esr, encseq, rm,
                                            arguments->stoppos);
      printf("%lu: %lu\n", arguments->stoppos,
                           gt_getnexttwobitencodingstoppos(fwd, esr));
      gt_encseq_reader_delete(esr);
    }
  }

  if (!had_err && arguments->specialranges) {
    /* check specialrangeiterator stuff */
    if (gt_encseq_has_specialranges(encseq)) {
      sri = gt_specialrangeiterator_new(encseq, fwd);
      while (true) {
        it1 = gt_specialrangeiterator_next(sri, &srng);
        if (it1)
          printf("%lu:%lu\n", srng.start, srng.end);
        else break;
      }
      gt_specialrangeiterator_delete(sri);
    }
  }

  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(el);
  return had_err;
}

GtTool* gt_encseq_bitextract(void)
{
  return gt_tool_new(gt_encseq_bitextract_arguments_new,
                  gt_encseq_bitextract_arguments_delete,
                  gt_encseq_bitextract_option_parser_new,
                  NULL,
                  gt_encseq_bitextract_runner);
}
genometools-1.5.1/src/tools/gt_encseq_bitextract.h000066400000000000000000000020051211610345200223420ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ENCSEQ_BITEXTRACT_H
#define GT_ENCSEQ_BITEXTRACT_H

#include "core/tool_api.h"

/* the encseq bitextract tool */
GtTool* gt_encseq_bitextract(void);

#endif
genometools-1.5.1/src/tools/gt_encseq_check.c000066400000000000000000000125511211610345200212500ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "core/logger.h"
#include "match/intcode-def.h"  /* XXX */
#include "match/test-mappedstr.pr"  /* XXX */
#include "tools/gt_encseq_check.h"

typedef struct {
  unsigned long scantrials,
                multicharcmptrials,
                prefixlength;
  bool verbose,
       nocheckunit;
} GtEncseqCheckArguments;

static void* gt_encseq_check_arguments_new(void)
{
  GtEncseqCheckArguments *arguments = gt_calloc(1, sizeof *arguments);
  return arguments;
}

static void gt_encseq_check_arguments_delete(void *tool_arguments)
{
  GtEncseqCheckArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_free(arguments);
}

static GtOptionParser* gt_encseq_check_option_parser_new(void *tool_arguments)
{
  GtEncseqCheckArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GT_UNUSED GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [file]",
                            "Check the consistency of an encoded "
                            "sequence file.");

  option = gt_option_new_ulong("scantrials", "specify number of scan trials",
                               &arguments->scantrials, 0);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("multicharcmptrials",
                               "specify number of multicharacter trials",
                               &arguments->multicharcmptrials, 0);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong_min_max("prefixlength",
                                       "prefix length",
                                       &arguments->prefixlength, 0,
                                       0, MAXPREFIXLENGTH);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("nocheckunit","do not run checkextractunitatpos",
                              &arguments->nocheckunit, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_args(op, 1);

  return op;
}

static int gt_encseq_check_runner(GT_UNUSED int argc, const char **argv,
                                  int parsed_args, void *tool_arguments,
                                  GtError *err)
{
  GtEncseqCheckArguments *arguments = tool_arguments;
  int had_err = 0;
  GtEncseqLoader *encseq_loader;
  GtEncseq *encseq;
  GtLogger *logger = NULL;

  gt_error_check(err);
  gt_assert(arguments);

  logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  encseq_loader = gt_encseq_loader_new();
  if (!(encseq = gt_encseq_loader_load(encseq_loader, argv[parsed_args], err)))
    had_err = -1;
  if (!had_err) {
    int readmode;

    gt_encseq_check_startpositions(encseq,logger);
    for (readmode = 0; readmode < 4; readmode++)
    {
      if (gt_alphabet_is_dna(gt_encseq_alphabet(encseq)) ||
           ((GtReadmode) readmode) == GT_READMODE_FORWARD ||
           ((GtReadmode) readmode) == GT_READMODE_REVERSE)
      {
        gt_logger_log(logger,"check consistency for readmode %s",
                      gt_readmode_show((GtReadmode) readmode));
        if (gt_encseq_check_consistency(encseq,
                           gt_encseq_filenames(encseq),
                           (GtReadmode) readmode,
                           arguments->scantrials,
                           arguments->multicharcmptrials,
                           gt_encseq_has_multiseq_support(encseq),
                           !arguments->nocheckunit,
                           logger,
                           err) != 0)
        {
          had_err = -1;
          break;
        }
      }
    }
    if (!had_err)
    {
      gt_encseq_check_specialranges(encseq);
    }
    if (!had_err)
    {
      gt_encseq_check_markpos(encseq);
    }
    if (!had_err)
    {
      had_err = gt_encseq_check_minmax(encseq, err);
    }
    if (!had_err &&
           arguments->prefixlength > 0)
    {
      if (gt_verifymappedstr(encseq,
                             arguments->prefixlength,
                             err) != 0)
      {
        had_err = -1;
      }
    }
  }
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(encseq_loader);
  gt_logger_delete(logger);
  return had_err;
}

GtTool* gt_encseq_check(void)
{
  return gt_tool_new(gt_encseq_check_arguments_new,
                     gt_encseq_check_arguments_delete,
                     gt_encseq_check_option_parser_new,
                     NULL,
                     gt_encseq_check_runner);
}
genometools-1.5.1/src/tools/gt_encseq_check.h000066400000000000000000000017611211610345200212560ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ENCSEQ_CHECK_H
#define GT_ENCSEQ_CHECK_H

#include "core/tool_api.h"

/* the encseq check tool */
GtTool* gt_encseq_check(void);

#endif
genometools-1.5.1/src/tools/gt_encseq_decode.c000066400000000000000000000315561211610345200214240ustar00rootroot00000000000000/*
  Copyright (c) 2010      Gordon Gremme 
  Copyright (c) 2010-2012 Sascha Steinbiss 
  Copyright (c) 2010-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/chardef.h"
#include "core/encseq_api.h"
#include "core/encseq_options.h"
#include "core/fasta_separator.h"
#include "core/log_api.h"
#include "core/readmode.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/warning_api.h"
#include "core/xansi_api.h"
#include "tools/gt_encseq_decode.h"

typedef struct {
  bool singlechars;
  GtStr *mode,
        *sepchar;
  GtRange rng,
          seqrng;
  GtEncseqOptions *eopts;
  GtReadmode rm;
  GtStr *dir;
  unsigned long seq;
} GtEncseqDecodeArguments;

static void* gt_encseq_decode_arguments_new(void)
{
  GtEncseqDecodeArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->mode = gt_str_new();
  arguments->sepchar = gt_str_new();
  arguments->dir = gt_str_new();
  arguments->seqrng.start = arguments->seqrng.end = GT_UNDEF_ULONG;
  arguments->rng.start = arguments->rng.end = GT_UNDEF_ULONG;
  return arguments;
}

static void gt_encseq_decode_arguments_delete(void *tool_arguments)
{
  GtEncseqDecodeArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->mode);
  gt_str_delete(arguments->sepchar);
  gt_str_delete(arguments->dir);
  gt_encseq_options_delete(arguments->eopts);
  gt_free(arguments);
}

static GtOptionParser* gt_encseq_decode_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GtOption *option,
           *optionsep,
           *optionseq,
           *optionseqrange,
           *optionmode;
  GtEncseqDecodeArguments *arguments =
                                      (GtEncseqDecodeArguments*) tool_arguments;
  static const char *modes[] = {"fasta", "concat", NULL};

  /* init */
  op = gt_option_parser_new("(sequence_file|indexname)",
                            "Decode/extract encoded sequences.");

  /* encseq options */
  arguments->eopts = gt_encseq_options_register_loading(op, NULL);
  gt_encseq_options_add_readmode_option(op, arguments->dir);

  /* -singlechars */
  option = gt_option_new_bool("singlechars",
                              "do not use a GtEncseqReader but access each "
                              "sequence character separately",
                              &arguments->singlechars,
                              false);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -seq */
  optionseq = gt_option_new_ulong("seq",
                                  "extract sequence identified by its number",
                                  &arguments->seq,
                                  GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, optionseq);

  /* -seqrange */
  optionseqrange = gt_option_new_range("seqrange",
                                       "extract multiple consecutive sequences",
                                       &arguments->seqrng,
                                       NULL);
  gt_option_parser_add_option(op, optionseqrange);
  gt_option_exclude(optionseqrange, optionseq);
  gt_option_exclude(optionseq, optionseqrange);

  /* -output */
  optionmode = gt_option_new_choice("output",
                                    "specify output format "
                                    "(choose from fasta|concat)",
                                    arguments->mode,
                                    modes[0],
                                    modes);
  gt_option_parser_add_option(op, optionmode);

  /* -range */
  option = gt_option_new_range("range",
                               "concatenated range to extract "
                               "(implies '-output concat')",
                               &arguments->rng,
                               NULL);
  gt_option_parser_add_option(op, option);
  gt_option_imply(option, optionmode);

  /* -sepchar */
  optionsep = gt_option_new_string("sepchar",
                                   "specify character to print as SEPARATOR",
                                   arguments->sepchar, "|");
  gt_option_parser_add_option(op, optionsep);
  gt_option_imply(optionsep, optionmode);

  gt_option_parser_set_min_max_args(op, 1, 1);

  return op;
}

int gt_encseq_decode_arguments_check(GT_UNUSED int rest_argc,
                                     void *tool_arguments,
                                     GtError* err)
{
  GtEncseqDecodeArguments *args = (GtEncseqDecodeArguments*) tool_arguments;
  int had_err = 0;
  int rval;

  if (gt_str_length(args->dir) > 0) {
    rval = gt_readmode_parse(gt_str_get(args->dir), err);
    if (rval < 0)
      had_err = -1;
    else
      args->rm = (GtReadmode) rval;
  }
  if (!had_err && args->seqrng.start != GT_UNDEF_ULONG &&
        args->seqrng.end != GT_UNDEF_ULONG && args->seq != GT_UNDEF_ULONG) {
    gt_error_set(err, "'-seq' and '-seqrange' cannot be used together");
    had_err = -1;
  }
  if (!had_err && (args->seqrng.start != GT_UNDEF_ULONG ||
        args->seqrng.end != GT_UNDEF_ULONG || args->seq != GT_UNDEF_ULONG)
        && strcmp(gt_str_get(args->mode), "fasta") != 0) {
    gt_error_set(err, "'-seq' and '-seqrange' can only be used with the "
                      "'-output fasta' option");
    had_err = -1;
  }
  if (!had_err && (args->rng.start != GT_UNDEF_ULONG ||
        args->rng.end != GT_UNDEF_ULONG)
        && strcmp(gt_str_get(args->mode), "concat") != 0) {
    gt_error_set(err, "'-range' can only be used with the "
                      "'-output concat' option");
    had_err = -1;
  }
  return had_err;
}

static int output_sequence(GtEncseq *encseq, GtEncseqDecodeArguments *args,
                           const char *filename, GtError *err)
{
  unsigned long i, j, sfrom, sto;
  int had_err = 0;
  bool has_desc;
  GtEncseqReader *esr;
  gt_assert(encseq);

  if (!(has_desc = gt_encseq_has_description_support(encseq)))
    gt_warning("Missing description support for file %s", filename);

  if (strcmp(gt_str_get(args->mode), "fasta") == 0) {
    /* specify a single sequence to extract */
    if (args->seq != GT_UNDEF_ULONG) {
      if (args->seq >= gt_encseq_num_of_sequences(encseq)) {
        gt_error_set(err, "requested sequence %lu exceeds number of sequences "
                          "(%lu)", args->seq,
                          gt_encseq_num_of_sequences(encseq));
        return -1;
      }
      sfrom = args->seq;
      sto = args->seq + 1;
    } else if (args->seqrng.start != GT_UNDEF_ULONG
                 && args->seqrng.end != GT_UNDEF_ULONG) {
      /* specify a sequence range to extract */
      if (args->seqrng.start >= gt_encseq_num_of_sequences(encseq)
            || args->seqrng.end >= gt_encseq_num_of_sequences(encseq)) {
        gt_error_set(err, "range %lu-%lu includes a sequence number exceeding "
                          "the total number of sequences (%lu)",
                          args->seqrng.start,
                          args->seqrng.end,
                          gt_encseq_num_of_sequences(encseq));
        return -1;
      }
      sfrom = args->seqrng.start;
      sto = args->seqrng.end + 1;
    } else {
      /* extract all sequences */
      sfrom = 0;
      sto = gt_encseq_num_of_sequences(encseq);
    }
    for (i = sfrom; i < sto; i++) {
      unsigned long desclen, startpos, len;
      char buf[BUFSIZ];
      const char *desc = NULL;
      /* XXX: maybe make this distinction in the functions via readmode? */
      if (!GT_ISDIRREVERSE(args->rm)) {
        startpos = gt_encseq_seqstartpos(encseq, i);
        len = gt_encseq_seqlength(encseq, i);
        if (has_desc) {
          desc = gt_encseq_description(encseq, &desclen, i);
        } else {
          (void) snprintf(buf, BUFSIZ, "sequence %lu", i);
          desclen = strlen(buf);
          desc = buf;
        }
      } else {
        startpos = gt_encseq_seqstartpos(encseq, i);
        len = gt_encseq_seqlength(encseq,
                                  gt_encseq_num_of_sequences(encseq)-1-i);
        startpos = gt_encseq_total_length(encseq)
                     - (gt_encseq_seqstartpos(encseq,
                                              gt_encseq_num_of_sequences(
                                                encseq)-1-i) + len);
        if (has_desc) {
          desc = gt_encseq_description(encseq,
                                       &desclen,
                                       gt_encseq_num_of_sequences(encseq)-1-i);
        } else {
          (void) snprintf(buf, BUFSIZ, "sequence %lu", i);
          desclen = strlen(buf);
          desc = buf;
        }
      }
      gt_assert(desc);
      /* output description */
      gt_xfputc(GT_FASTA_SEPARATOR, stdout);
      gt_xfwrite(desc, 1, desclen, stdout);
      gt_xfputc('\n', stdout);
      /* XXX: make this more efficient by writing in a buffer first and then
         showing the result */
      if (args->singlechars) {
        for (j = 0; j < len; j++) {
           gt_xfputc(gt_encseq_get_decoded_char(encseq,
                                                startpos + j,
                                                args->rm),
                     stdout);
        }
      } else {
        esr = gt_encseq_create_reader_with_readmode(encseq, args->rm, startpos);
        for (j = 0; j < len; j++) {
           gt_xfputc(gt_encseq_reader_next_decoded_char(esr), stdout);
        }
        gt_encseq_reader_delete(esr);
      }
      gt_xfputc('\n', stdout);
    }
  }

  if (strcmp(gt_str_get(args->mode), "concat") == 0) {
    unsigned long from = 0,
                  to = gt_encseq_total_length(encseq) - 1;
    if (args->rng.start != GT_UNDEF_ULONG && args->rng.end != GT_UNDEF_ULONG) {
      if (args->rng.end > to) {
        had_err = -1;
        gt_error_set(err, "end of range (%lu) exceeds encoded sequence length "
                          "(%lu)", args->rng.end, to);
      }
      if (!had_err) {
        from = args->rng.start;
        to = args->rng.end;
      }
    }
    if (!had_err) {
      if (args->singlechars) {
        for (j = from; j <= to; j++) {
          char cc = gt_encseq_get_decoded_char(encseq, j, args->rm);
          if (cc == (char) SEPARATOR)
            cc = gt_str_get(args->sepchar)[0];
          gt_xfputc(cc, stdout);
        }
      } else {
        esr = gt_encseq_create_reader_with_readmode(encseq, args->rm, from);
        if (esr) {
          for (j = from; j <= to; j++) {
            char cc = gt_encseq_reader_next_decoded_char(esr);
            if (cc == (char) SEPARATOR)
              cc = gt_str_get(args->sepchar)[0];
            gt_xfputc(cc, stdout);
          }
          gt_encseq_reader_delete(esr);
        }
      }
      gt_xfputc('\n', stdout);
    }
  }
  return had_err;
}

static int decode_sequence_file(const char *seqfile,
                                GtEncseqDecodeArguments *args,
                                GtError *err)
{
  GtEncseqLoader *encseq_loader;
  GtEncseq *encseq;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(seqfile);
  encseq_loader = gt_encseq_loader_new();
  if (!had_err && gt_encseq_options_lossless_value(args->eopts)) {
    gt_encseq_loader_require_lossless_support(encseq_loader);
  }
  if (!(encseq = gt_encseq_loader_load(encseq_loader, seqfile, err)))
    had_err = -1;
  if (!had_err && gt_encseq_options_mirrored_value(args->eopts)) {
    if (!gt_alphabet_is_dna(gt_encseq_alphabet(encseq))) {
      gt_error_set(err, "mirroring is only defined on DNA sequences");
      had_err = -1;
    }
    if (!had_err)
      had_err = gt_encseq_mirror(encseq, err);
  }
  if (!had_err)
    had_err = output_sequence(encseq, args, seqfile, err);
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(encseq_loader);
  return had_err;
}

static int gt_encseq_decode_runner(GT_UNUSED int argc, const char **argv,
                               int parsed_args, void *tool_arguments,
                               GtError *err)
{
  gt_error_check(err);
  return decode_sequence_file(argv[parsed_args], tool_arguments, err);
}

GtTool* gt_encseq_decode(void)
{
  return gt_tool_new(gt_encseq_decode_arguments_new,
                     gt_encseq_decode_arguments_delete,
                     gt_encseq_decode_option_parser_new,
                     gt_encseq_decode_arguments_check,
                     gt_encseq_decode_runner);
}
genometools-1.5.1/src/tools/gt_encseq_decode.h000066400000000000000000000016511211610345200214220ustar00rootroot00000000000000/*
  Copyright (c) 2010 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ENCSEQ_DECODE_H
#define GT_ENCSEQ_DECODE_H

#include "core/tool_api.h"

/* the encseq decode tool */
GtTool* gt_encseq_decode(void);

#endif
genometools-1.5.1/src/tools/gt_encseq_encode.c000066400000000000000000000156121211610345200214310ustar00rootroot00000000000000/*
  Copyright (c) 2010 Gordon Gremme 
  Copyright (c) 2010 Sascha Steinbiss 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/alphabet.h"
#include "core/basename_api.h"
#include "core/ma.h"
#include "core/encseq.h"
#include "core/encseq_options.h"
#include "core/fileutils.h"
#include "core/logger_api.h"
#include "core/str_array_api.h"
#include "core/unused_api.h"
#include "tools/gt_encseq_encode.h"

typedef struct {
  GtEncseqOptions *eopts;
  bool showstats,
       no_esq_header,
       verbose;
  GtStr *indexname;
} GtEncseqEncodeArguments;

static void* gt_encseq_encode_arguments_new(void)
{
  GtEncseqEncodeArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->indexname = gt_str_new();
  return arguments;
}

static void gt_encseq_encode_arguments_delete(void *tool_arguments)
{
  GtEncseqEncodeArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_encseq_options_delete(arguments->eopts);
  gt_str_delete(arguments->indexname);
  gt_free(arguments);
}

static GtOptionParser* gt_encseq_encode_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GtOption *option;
  GtEncseqEncodeArguments *arguments =
                                      (GtEncseqEncodeArguments*) tool_arguments;

  /* init */
  op = gt_option_parser_new("sequence_file [sequence_file "
                            "[sequence_file ...]]",
                            "Encode sequence files efficiently.");

  /* -showstats */
  option = gt_option_new_bool("showstats",
                              "show compression results",
                              &arguments->showstats,
                              false);
  gt_option_parser_add_option(op, option);

  /* -no_esq_header */
  option = gt_option_new_bool("no_esq_header",
                              "omit the header in the .esq file",
                              &arguments->no_esq_header,
                              false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* encoded sequence options */
  arguments->eopts = gt_encseq_options_register_encoding(op,
                                                         arguments->indexname,
                                                         NULL);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_args(op, 1);

  return op;
}

static int encode_sequence_files(GtStrArray *infiles, GtEncseqOptions *opts,
                                 const char *indexname, bool verbose,
                                 bool esq_no_header,
                                 GtError *err)
{
  GtEncseqEncoder *encseq_encoder;
  GtLogger *logger;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(infiles && gt_str_array_size(infiles) > 0 && opts);
  logger = gt_logger_new(verbose, "# ", stderr);
  encseq_encoder = gt_encseq_encoder_new_from_options(opts, err);
  if (!encseq_encoder)
    had_err = -1;
  if (!had_err) {
    gt_encseq_encoder_set_logger(encseq_encoder, logger);
    if (esq_no_header)
    {
      gt_encseq_encoder_disable_esq_header(encseq_encoder);
    }
    had_err = gt_encseq_encoder_encode(encseq_encoder, infiles, indexname, err);
  }
  gt_encseq_encoder_delete(encseq_encoder);
  gt_logger_delete(logger);
  return had_err;
}

static off_t index_size(const char *prefix, const char *suffix)
{
 off_t size = 0;
 GtStr *index_name = gt_str_new_cstr(prefix);
 gt_str_append_cstr(index_name, suffix);
 if (gt_file_exists(gt_str_get(index_name))) {
   size = gt_file_size(gt_str_get(index_name));
 }
 gt_str_delete(index_name);
 return size;
}

static void show_encoded_statistics(GtStrArray *infiles, const char *indexname)
{
  int i;
  off_t orig_size = 0, enc_size = 0;
  const char *seqfile;
  gt_assert(infiles);
  for (i=0; i < gt_str_array_size(infiles);i ++) {
    seqfile = gt_str_array_get(infiles, i);
    orig_size += gt_file_size(seqfile);
  }
  enc_size += index_size(indexname, GT_ALPHABETFILESUFFIX);
  enc_size += index_size(indexname, GT_ENCSEQFILESUFFIX);
  enc_size += index_size(indexname, GT_SSPTABFILESUFFIX);
  enc_size += index_size(indexname, GT_DESTABFILESUFFIX);
  enc_size += index_size(indexname, GT_SDSTABFILESUFFIX);
  enc_size += index_size(indexname, GT_OISTABFILESUFFIX);
  printf("encoded sequence file(s) are %.1f%% of original file size\n",
         ((double) enc_size / orig_size) * 100.0);
}

static int gt_encseq_encode_runner(GT_UNUSED int argc, const char **argv,
                               int parsed_args, GT_UNUSED void *tool_arguments,
                               GtError *err)
{
  int had_err = 0,
      i;
  GtEncseqEncodeArguments *arguments =
                                      (GtEncseqEncodeArguments*) tool_arguments;
  GtStrArray *infiles;
  gt_error_check(err);

  infiles = gt_str_array_new();
  for (i = parsed_args; i < argc; i++) {
    gt_str_array_add_cstr(infiles, argv[i]);
  }

  if (gt_str_length(arguments->indexname) == 0UL) {
    if (gt_str_array_size(infiles) > 1UL) {
      gt_error_set(err,"if more than one input file is given, then "
                       "option -indexname is mandatory");
      had_err = -1;
    } else {
      char *basenameptr;
      basenameptr = gt_basename(gt_str_array_get(infiles, 0UL));
      gt_str_set(arguments->indexname, basenameptr);
      gt_free(basenameptr);
    }
  }

  if (!had_err) {
    gt_assert(gt_str_length(arguments->indexname) > 0UL);
    had_err = encode_sequence_files(infiles,
                                    arguments->eopts,
                                    gt_str_get(arguments->indexname),
                                    arguments->verbose,
                                    arguments->no_esq_header,
                                    err);
  }

  if (!had_err && arguments->showstats)
    show_encoded_statistics(infiles, gt_str_get(arguments->indexname));

  gt_str_array_delete(infiles);
  return had_err;
}

GtTool* gt_encseq_encode(void)
{
  return gt_tool_new(gt_encseq_encode_arguments_new,
                     gt_encseq_encode_arguments_delete,
                     gt_encseq_encode_option_parser_new,
                     NULL,
                     gt_encseq_encode_runner);
}
genometools-1.5.1/src/tools/gt_encseq_encode.h000066400000000000000000000016511211610345200214340ustar00rootroot00000000000000/*
  Copyright (c) 2010 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ENCSEQ_ENCODE_H
#define GT_ENCSEQ_ENCODE_H

#include "core/tool_api.h"

/* the encseq encode tool */
GtTool* gt_encseq_encode(void);

#endif
genometools-1.5.1/src/tools/gt_encseq_info.c000066400000000000000000000313201211610345200211210ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/encseq_metadata.h"
#include "core/ma.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "tools/gt_encseq_info.h"

typedef struct {
  bool nomap,
       mirror,
       noindexname,
       show_alphabet;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} GtEncseqInfoArguments;

static void* gt_encseq_info_arguments_new(void)
{
  GtEncseqInfoArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_encseq_info_arguments_delete(void *tool_arguments)
{
  GtEncseqInfoArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_encseq_info_option_parser_new(void *tool_arguments)
{
  GtEncseqInfoArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionnomap;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] indexname",
                            "Display meta-information about an "
                            "encoded sequence.");

  optionnomap = gt_option_new_bool("nomap", "do not map encoded sequence "
                                            "(gives less information)",
                                   &arguments->nomap, false);
  gt_option_parser_add_option(op, optionnomap);

  option = gt_option_new_bool("mirrored", "use mirrored encoded sequence "
                                          "(DNA only)",
                              &arguments->mirror, false);
  gt_option_parser_add_option(op, option);
  gt_option_exclude(optionnomap, option);

  option = gt_option_new_bool("noindexname", "do not output index name",
                              &arguments->noindexname, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("show_alphabet", "output alphabet definition",
                              &arguments->show_alphabet, false);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_min_max_args(op, 1, 1);
  return op;
}

static int gt_encseq_info_runner(GT_UNUSED int argc, const char **argv,
                           int parsed_args, void *tool_arguments,
                           GtError *err)
{
  GtEncseqInfoArguments *arguments = tool_arguments;
  int had_err = 0;
  GtAlphabet *alpha;
  const GtUchar *chars;
  gt_error_check(err);
  gt_assert(arguments);

  if (arguments->nomap) {
    GtEncseqMetadata *emd = gt_encseq_metadata_new(argv[parsed_args], err);
    if (!emd)
      had_err = -1;

    if (!had_err) {
      if (!arguments->noindexname) {
        gt_file_xprintf(arguments->outfp, "index name: ");
        gt_file_xprintf(arguments->outfp, "%s\n", argv[parsed_args]);
      }

      gt_file_xprintf(arguments->outfp, "file format version: ");
      gt_file_xprintf(arguments->outfp, "%lu\n",
                                          gt_encseq_metadata_version(emd));

      gt_file_xprintf(arguments->outfp, "64-bit file: ");
      gt_file_xprintf(arguments->outfp, "%s\n", gt_encseq_metadata_is64bit(emd)
                                                  ? "yes"
                                                  : "no");

      gt_file_xprintf(arguments->outfp, "total length: ");
      gt_file_xprintf(arguments->outfp, "%lu\n",
                                        gt_encseq_metadata_total_length(emd));

      gt_file_xprintf(arguments->outfp, "number of sequences: ");
      gt_file_xprintf(arguments->outfp, "%lu\n",
                                      gt_encseq_metadata_num_of_sequences(emd));

      gt_file_xprintf(arguments->outfp, "number of files: ");
      gt_file_xprintf(arguments->outfp, "%lu\n",
                                        gt_encseq_metadata_num_of_files(emd));

      gt_file_xprintf(arguments->outfp, "length of shortest/longest "
                                        "sequence: ");
      gt_file_xprintf(arguments->outfp, "%lu/%lu\n",
                                        gt_encseq_metadata_min_seq_length(emd),
                                        gt_encseq_metadata_max_seq_length(emd));

      gt_file_xprintf(arguments->outfp, "accesstype: ");
      gt_file_xprintf(arguments->outfp, "%s\n",
                 gt_encseq_access_type_str(gt_encseq_metadata_accesstype(emd)));

      alpha = gt_encseq_metadata_alphabet(emd);
      chars = gt_alphabet_characters(alpha);
      gt_file_xprintf(arguments->outfp, "alphabet size: ");
      gt_file_xprintf(arguments->outfp, "%u\n",
                                        gt_alphabet_num_of_chars(alpha));
      gt_file_xprintf(arguments->outfp, "alphabet characters: ");
      gt_file_xprintf(arguments->outfp, "%.*s", gt_alphabet_num_of_chars(alpha),
                                        (char*) chars);
      if (gt_alphabet_is_dna(alpha))
        gt_file_xprintf(arguments->outfp, " (DNA)");
      if (gt_alphabet_is_protein(alpha))
        gt_file_xprintf(arguments->outfp, " (Protein)");
      gt_file_xprintf(arguments->outfp, "\n");
      if (arguments->show_alphabet) {
        GtStr *out = gt_str_new();
        gt_alphabet_to_str(alpha, out);
        gt_file_xprintf(arguments->outfp, "alphabet definition:\n");
        gt_file_xprintf(arguments->outfp, "%s\n", gt_str_get(out));
        gt_str_delete(out);
      }

    }
    gt_encseq_metadata_delete(emd);
  } else {
    GtEncseqLoader *encseq_loader;
    GtEncseq *encseq;

    encseq_loader = gt_encseq_loader_new();
    if (arguments->mirror)
      gt_encseq_loader_mirror(encseq_loader);
    if (!(encseq = gt_encseq_loader_load(encseq_loader,
                                         argv[parsed_args], err)))
      had_err = -1;

    if (!had_err) {
      const GtStrArray *filenames;
      unsigned long i;

      if (!arguments->noindexname) {
        gt_file_xprintf(arguments->outfp, "index name: ");
        gt_file_xprintf(arguments->outfp, "%s\n", argv[parsed_args]);
      }

      gt_file_xprintf(arguments->outfp, "file format version: ");
      gt_file_xprintf(arguments->outfp, "%lu\n", gt_encseq_version(encseq));

      gt_file_xprintf(arguments->outfp, "64-bit file: ");
      gt_file_xprintf(arguments->outfp, "%s\n", gt_encseq_is_64_bit(encseq)
                                                   ? "yes"
                                                   : "no");

      gt_file_xprintf(arguments->outfp, "total length: ");
      gt_file_xprintf(arguments->outfp, "%lu\n",
                                        gt_encseq_total_length(encseq));

      gt_file_xprintf(arguments->outfp, "compressed size: ");
      gt_file_xprintf(arguments->outfp, "%lu bytes\n",
                                        gt_encseq_sizeofrep(encseq));

      gt_file_xprintf(arguments->outfp, "number of sequences: ");
      gt_file_xprintf(arguments->outfp, "%lu\n",
                                        gt_encseq_num_of_sequences(encseq));

      gt_file_xprintf(arguments->outfp, "number of files: ");
      gt_file_xprintf(arguments->outfp, "%lu\n",
                                        gt_encseq_num_of_files(encseq));

      gt_file_xprintf(arguments->outfp, "length of shortest/longest "
                                        "sequence: ");
      gt_file_xprintf(arguments->outfp, "%lu/%lu\n",
                                      gt_encseq_min_seq_length(encseq),
                                      gt_encseq_max_seq_length(encseq));

      filenames = gt_encseq_filenames(encseq);
      gt_file_xprintf(arguments->outfp, "original filenames:\n");
      for (i = 0; i < gt_str_array_size(filenames); i++) {
        gt_file_xprintf(arguments->outfp, "\t%s (%lu characters)\n",
                                          gt_str_array_get(filenames, i),
                                          (unsigned long)
                                     gt_encseq_effective_filelength(encseq, i));
      }

      alpha = gt_encseq_alphabet(encseq);
      chars = gt_alphabet_characters(alpha);
      gt_file_xprintf(arguments->outfp, "alphabet size: ");
      gt_file_xprintf(arguments->outfp, "%u\n",
                                        gt_alphabet_num_of_chars(alpha));
      gt_file_xprintf(arguments->outfp, "alphabet characters: ");
      gt_file_xprintf(arguments->outfp, "%.*s", gt_alphabet_num_of_chars(alpha),
                                        (char*) chars);
      if (gt_alphabet_is_dna(alpha))
        gt_file_xprintf(arguments->outfp, " (DNA)");
      if (gt_alphabet_is_protein(alpha))
        gt_file_xprintf(arguments->outfp, " (Protein)");
      gt_file_xprintf(arguments->outfp, "\n");
      if (arguments->show_alphabet) {
        GtStr *out = gt_str_new();
        gt_alphabet_to_str(alpha, out);
        gt_file_xprintf(arguments->outfp, "alphabet definition:\n");
        gt_file_xprintf(arguments->outfp, "%s\n", gt_str_get(out));
        gt_str_delete(out);
      }

      gt_file_xprintf(arguments->outfp, "character distribution:\n");
      for (i = 0; i < gt_alphabet_num_of_chars(alpha); i++) {
        unsigned long cc;
        cc = gt_encseq_charcount(encseq, gt_alphabet_encode(alpha, chars[i]));
        gt_file_xprintf(arguments->outfp, "\t%c: %lu (%.2f%%)\n",
                                          (char) chars[i],
                                          cc,
                             (cc /(double) (gt_encseq_total_length(encseq)
                                  - gt_encseq_num_of_sequences(encseq)+1))*100);
      }

      gt_file_xprintf(arguments->outfp, "number of wildcards: ");
      gt_file_xprintf(arguments->outfp, "%lu (%lu range(s))\n",
                                        gt_encseq_wildcards(encseq),
                                        gt_encseq_realwildcardranges(encseq));

      gt_file_xprintf(arguments->outfp, "number of special characters: ");
      gt_file_xprintf(arguments->outfp, "%lu (%lu range(s))\n",
                                        gt_encseq_specialcharacters(encseq),
                                        gt_encseq_realspecialranges(encseq));

      gt_file_xprintf(arguments->outfp, "length of longest non-special "
                                        "character stretch: ");
      gt_file_xprintf(arguments->outfp, "%lu\n",
                                   gt_encseq_lengthoflongestnonspecial(encseq));

      gt_file_xprintf(arguments->outfp, "accesstype: ");
      gt_file_xprintf(arguments->outfp, "%s\n",
                   gt_encseq_access_type_str(gt_encseq_accesstype_get(encseq)));

      gt_file_xprintf(arguments->outfp, "bits used per character: ");
      gt_file_xprintf(arguments->outfp, "%f\n",
        (double) ((uint64_t) CHAR_BIT *
                  (uint64_t) gt_encseq_sizeofrep(encseq)) /
        (double) gt_encseq_total_length(encseq));

      gt_file_xprintf(arguments->outfp, "has special ranges: ");
      gt_file_xprintf(arguments->outfp, "%s\n",
                                        gt_encseq_has_specialranges(encseq)
                                          ? "yes"
                                          : "no");

      gt_file_xprintf(arguments->outfp, "has description support: ");
      gt_file_xprintf(arguments->outfp, "%s\n",
                                       gt_encseq_has_description_support(encseq)
                                          ? "yes"
                                          : "no");

      gt_file_xprintf(arguments->outfp, "has multiple sequence support: ");
      gt_file_xprintf(arguments->outfp, "%s\n",
                                        gt_encseq_has_multiseq_support(encseq)
                                          ? "yes"
                                          : "no");
    }
    gt_encseq_delete(encseq);
    gt_encseq_loader_delete(encseq_loader);
  }

  return had_err;
}

GtTool* gt_encseq_info(void)
{
  return gt_tool_new(gt_encseq_info_arguments_new,
                  gt_encseq_info_arguments_delete,
                  gt_encseq_info_option_parser_new,
                  NULL,
                  gt_encseq_info_runner);
}
genometools-1.5.1/src/tools/gt_encseq_info.h000066400000000000000000000017551211610345200211370ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ENCSEQ_INFO_H
#define GT_ENCSEQ_INFO_H

#include "core/tool_api.h"

/* the encseq info tool */
GtTool* gt_encseq_info(void);

#endif
genometools-1.5.1/src/tools/gt_encseq_md5.c000066400000000000000000000104651211610345200206620ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Steinbiss 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/ma.h"
#include "core/md5_fingerprint_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "tools/gt_encseq_md5.h"

typedef struct {
  GtOutputFileInfo *ofi;
  GtFile *outfp;
  bool fromindex;
} GtEncseqInfoArguments;

static void* gt_encseq_md5_arguments_new(void)
{
  GtEncseqInfoArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_encseq_md5_arguments_delete(void *tool_arguments)
{
  GtEncseqInfoArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_encseq_md5_option_parser_new(void *tool_arguments)
{
  GtEncseqInfoArguments *arguments = tool_arguments;
  GtOption *option;
  GtOptionParser *op;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] indexname",
                            "Display MD5 sums for an encoded sequence.");

  /* -fromindex */
  option = gt_option_new_bool("fromindex", "use MD5 table from .md5 file",
                              &arguments->fromindex, true);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_min_max_args(op, 1, 1);
  return op;
}

static int gt_encseq_md5_runner(GT_UNUSED int argc, const char **argv,
                           int parsed_args, void *tool_arguments,
                           GtError *err)
{
  GtEncseqInfoArguments *arguments = tool_arguments;
  int had_err = 0;
  GtEncseqLoader *encseq_loader;
  GtEncseq *encseq;
  gt_error_check(err);
  gt_assert(arguments);

  encseq_loader = gt_encseq_loader_new();
  if (!(encseq = gt_encseq_loader_load(encseq_loader,
                                       argv[parsed_args], err)))
    had_err = -1;

  if (!had_err) {
    unsigned long i;

    if (arguments->fromindex) {
      GtMD5Tab *tab;

      if (!gt_encseq_has_md5_support(encseq)) {
        gt_error_set(err, "encoded sequence given by indexname \"%s\" does not "
                          "have MD5 support", argv[parsed_args]);
        had_err = -1;
      }
      if (!had_err) {
        tab = gt_encseq_get_md5_tab(encseq, err);
        if (tab) {
          for (i = 0; i < gt_encseq_num_of_sequences(encseq); i++) {
            gt_file_xprintf(arguments->outfp,
                            "%lu: %s\n", i, gt_md5_tab_get(tab, i));
          }
          gt_md5_tab_delete(tab);
        } else had_err = -1;
      }
    } else {
      char *seq,
           *md5str;
      for (i = 0; i < gt_encseq_num_of_sequences(encseq); i++) {
        unsigned long len, start, end;
        len = gt_encseq_seqlength(encseq, i);
        start = gt_encseq_seqstartpos(encseq, i);
        end = len + start -1;
        seq = gt_malloc(len * sizeof (char));
        gt_encseq_extract_decoded(encseq, seq, start, end);
        md5str = gt_md5_fingerprint(seq, len);
        gt_file_xprintf(arguments->outfp, "%lu: %s\n", i, md5str);
        gt_free(seq);
        gt_free(md5str);
      }
    }
  }
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(encseq_loader);
  return had_err;
}

GtTool* gt_encseq_md5(void)
{
  return gt_tool_new(gt_encseq_md5_arguments_new,
                  gt_encseq_md5_arguments_delete,
                  gt_encseq_md5_option_parser_new,
                  NULL,
                  gt_encseq_md5_runner);
}
genometools-1.5.1/src/tools/gt_encseq_md5.h000066400000000000000000000017511211610345200206650ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Steinbiss 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ENCSEQ_MD5_H
#define GT_ENCSEQ_MD5_H

#include "core/tool_api.h"

/* the encseq md5 tool */
GtTool* gt_encseq_md5(void);

#endif
genometools-1.5.1/src/tools/gt_eval.c000066400000000000000000000136371211610345200175720ustar00rootroot00000000000000/*
  Copyright (c) 2006-2011 Gordon Gremme 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "extended/gff3_in_stream.h"
#include "extended/gtdatahelp.h"
#include "extended/stream_evaluator.h"
#include "tools/gt_eval.h"

typedef struct {
  bool verbose,
       exondiff,
       exondiffcollapsed,
       nuceval,
       evalLTR;
  unsigned long LTRdelta;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} EvalArguments;

static void* gt_eval_arguments_new(void)
{
  EvalArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_eval_arguments_delete(void *tool_arguments)
{
  EvalArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_eval_option_parser_new(void *tool_arguments)
{
  EvalArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *ltroption, *ltrdeltaoption;
  gt_assert(arguments);

  op = gt_option_parser_new("reference_file prediction_file ",
                            "Compare annotation files and show "
                            "accuracy measures (prediction vs. reference).");

  /* -exondiff */
  option = gt_option_new_bool("exondiff", "show a diff for the exons",
                              &arguments->exondiff, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -exondiffcollapsed */
  option = gt_option_new_bool("exondiffcollapsed", "show a diff for the "
                              "collapsed exons", &arguments->exondiffcollapsed,
                              false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -nuc */
  option = gt_option_new_bool("nuc",
                              "evaluate nucleotide level (memory consumption "
                              "is proportional to the input file sizes)",
                              &arguments->nuceval, true);
  gt_option_parser_add_option(op, option);

  /* -ltr */
  ltroption = gt_option_new_bool("ltr", "evaluate a LTR retrotransposon "
                                 "prediction instead of a gene prediction\n"
                                 "(all LTR_retrotransposon elements are "
                                 "considered to have an undetermined strand)",
                                 &arguments->evalLTR, false);
  gt_option_parser_add_option(op, ltroption);

  /* -ltrdelta */
  ltrdeltaoption = gt_option_new_ulong("ltrdelta", "set allowed delta for LTR "
                                       "borders to be considered equal",
                                       &arguments->LTRdelta, 20);
  gt_option_parser_add_option(op, ltrdeltaoption);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  /* option implications */
  gt_option_imply(ltrdeltaoption, ltroption);

  /* set comment function */
  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);

  /* set minimum and maximum number of arguments */
  gt_option_parser_set_min_max_args(op, 2, 2);

  return op;
}

int gt_eval_runner(GT_UNUSED int argc, const char **argv, int parsed_args,
                   void *tool_arguments, GtError *err)
{
  EvalArguments *arguments = tool_arguments;
  GtNodeStream *reference_stream,
               *prediction_stream;
  GtStreamEvaluator *evaluator;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create the reference stream */
  reference_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
  if (arguments->verbose)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) reference_stream);

  /* create the prediction stream */
  prediction_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args + 1]);
  if (arguments->verbose)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) prediction_stream);

  /* create the stream evaluator */
  evaluator = gt_stream_evaluator_new(reference_stream, prediction_stream,
                                      arguments->nuceval, arguments->evalLTR,
                                      arguments->LTRdelta);

  /* compute the evaluation */
  had_err = gt_stream_evaluator_evaluate(evaluator, arguments->verbose,
                                         arguments->exondiff,
                                         arguments->exondiffcollapsed, NULL,
                                         err);

  /* show the evaluation */
  if (!had_err)
    gt_stream_evaluator_show(evaluator, arguments->outfp);

  /* free */
  gt_stream_evaluator_delete(evaluator);
  gt_node_stream_delete(prediction_stream);
  gt_node_stream_delete(reference_stream);

  return had_err;
}

GtTool* gt_eval(void)
{
  return gt_tool_new(gt_eval_arguments_new,
                     gt_eval_arguments_delete,
                     gt_eval_option_parser_new,
                     NULL,
                     gt_eval_runner);
}
genometools-1.5.1/src/tools/gt_eval.h000066400000000000000000000017471211610345200175760ustar00rootroot00000000000000/*
  Copyright (c) 2006-2007, 2011 Gordon Gremme 
  Copyright (c) 2006-2007       Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_EVAL_H
#define GT_EVAL_H

#include "core/tool_api.h"

/* the evaluation tool */
GtTool* gt_eval(void);

#endif
genometools-1.5.1/src/tools/gt_extractfeat.c000066400000000000000000000137651211610345200211570ustar00rootroot00000000000000/*
  Copyright (c) 2006-2011 Gordon Gremme 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "extended/extract_feature_stream_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/gtdatahelp.h"
#include "extended/seqid2file.h"
#include "tools/gt_extractfeat.h"

typedef struct {
  bool join,
       translate,
       seqid,
       target,
       verbose;
  GtStr *type;
  GtSeqid2FileInfo *s2fi;
  unsigned long width;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} GtExtractFeatArguments;

static void* gt_extractfeat_arguments_new(void)
{
  GtExtractFeatArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->type = gt_str_new();
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_extractfeat_arguments_delete(void *tool_arguments)
{
  GtExtractFeatArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_str_delete(arguments->type);
  gt_free(arguments);
}

static GtOptionParser* gt_extractfeat_option_parser_new(void *tool_arguments)
{
  GtExtractFeatArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [GFF3_file]",
                            "Extract features given in GFF3 file from "
                            "sequence file.");

  /* -type */
  option = gt_option_new_string("type", "set type of features to extract",
                                arguments->type, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  /* -join */
  option = gt_option_new_bool("join", "join feature sequences in the same "
                              "subgraph into a single one", &arguments->join,
                              false);
  gt_option_parser_add_option(op, option);

  /* -translate */
  option = gt_option_new_bool("translate", "translate the features (of a DNA "
                              "sequence) into protein", &arguments->translate,
                              false);
  gt_option_parser_add_option(op, option);

  /* -seqid */
  option = gt_option_new_bool("seqid", "add sequence ID of extracted features "
                              "to FASTA descriptions", &arguments->seqid,
                              false);
  gt_option_parser_add_option(op, option);

  /* -target */
  option = gt_option_new_bool("target", "add target ID(s) of extracted "
                              "features to FASTA descriptions",
                              &arguments->target, false);
  gt_option_parser_add_option(op, option);

  /* -seqfile, -matchdesc, -usedesc and -regionmapping */
  gt_seqid2file_register_options(op, arguments->s2fi);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* -width */
  option = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_max_args(op, 1);

  return op;
}

static int gt_extractfeat_runner(GT_UNUSED int argc, const char **argv,
                                 int parsed_args, void *tool_arguments,
                                 GtError *err)
{
  GtNodeStream *gff3_in_stream = NULL, *extract_feature_stream = NULL;
  GtExtractFeatArguments *arguments = tool_arguments;
  GtRegionMapping *region_mapping;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (!had_err) {
    /* create gff3 input stream */
    gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
    if (arguments->verbose)
      gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);

    /* create region mapping */
    region_mapping = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
    if (!region_mapping)
      had_err = -1;
  }

  if (!had_err) {
    /* create extract feature stream */
    extract_feature_stream =
      gt_extract_feature_stream_new(gff3_in_stream,
                                    region_mapping,
                                    gt_str_get(arguments->type),
                                    arguments->join,
                                    arguments->translate,
                                    arguments->seqid,
                                    arguments->target,
                                    arguments->width,
                                    arguments->outfp);

    /* pull the features through the stream and free them afterwards */
    had_err = gt_node_stream_pull(extract_feature_stream, err);
  }

  /* free */
  gt_node_stream_delete(extract_feature_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool* gt_extractfeat(void)
{
  return gt_tool_new(gt_extractfeat_arguments_new,
                     gt_extractfeat_arguments_delete,
                     gt_extractfeat_option_parser_new,
                     NULL,
                     gt_extractfeat_runner);
}
genometools-1.5.1/src/tools/gt_extractfeat.h000066400000000000000000000017651211610345200211610ustar00rootroot00000000000000/*
  Copyright (c) 2006-2008 Gordon Gremme 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_EXTRACTFEAT_H
#define GT_EXTRACTFEAT_H

#include "core/tool_api.h"

/* the extract feature tool */
GtTool* gt_extractfeat(void);

#endif
genometools-1.5.1/src/tools/gt_extractseq.c000066400000000000000000000257511211610345200210260ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009 Gordon Gremme 
  Copyright (c) 2007-2009 Stefan Kurtz 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/bioseq_iterator.h"
#include "core/fasta.h"
#include "core/grep_api.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "match/giextract.h"
#include "extended/gtdatahelp.h"
#include "tools/gt_extractseq.h"

#define FROMPOS_OPTION_STR  "frompos"
#define TOPOS_OPTION_STR    "topos"

typedef struct {
  GtStr *pattern,
        *fastakeyfile;
  unsigned long frompos,
                topos,
                width;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} ExtractSeqArguments;

static void* gt_extractseq_arguments_new(void)
{
  ExtractSeqArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->pattern = gt_str_new();
  arguments->fastakeyfile = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_extractseq_arguments_delete(void *tool_arguments)
{
  ExtractSeqArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->fastakeyfile);
  gt_str_delete(arguments->pattern);
  gt_free(arguments);
}

static GtOptionParser* gt_extractseq_option_parser_new(void *tool_arguments)
{
  ExtractSeqArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *frompos_option, *topos_option, *match_option, *width_option,
         *fastakeyfile_option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [sequence_file(s)] | fastaindex",
                            "Extract sequences from given sequence file(s) or "
                            "fastaindex.");

  /* -frompos */
  frompos_option = gt_option_new_ulong_min(FROMPOS_OPTION_STR,
                                        "extract sequence from this position\n"
                                        "counting from 1 on",
                                        &arguments->frompos, 0, 1UL);
  gt_option_parser_add_option(op, frompos_option);

  /* -topos */
  topos_option = gt_option_new_ulong_min(TOPOS_OPTION_STR,
                                      "extract sequence up to this position\n"
                                      "counting from 1 on",
                                      &arguments->topos, 0, 1UL);
  gt_option_parser_add_option(op, topos_option);

  /* -match */
  match_option = gt_option_new_string("match", "extract all sequences whose "
                                   "description matches the given pattern.\n"
                                   "The given pattern must be a valid extended "
                                   "regular expression.", arguments->pattern,
                                   NULL);
  gt_option_parser_add_option(op, match_option);

  /* -keys */
  fastakeyfile_option = gt_option_new_filename("keys",
                                               "extract substrings for keys "
                                               "in specified file",
                                     arguments->fastakeyfile);
  gt_option_parser_add_option(op, fastakeyfile_option);

  /* -width */
  width_option = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, width_option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  /* option implications */
  gt_option_imply(frompos_option, topos_option);
  gt_option_imply(topos_option, frompos_option);

  /* option exclusions */
  gt_option_exclude(frompos_option, match_option);
  gt_option_exclude(topos_option, match_option);
  gt_option_exclude(frompos_option, fastakeyfile_option);
  gt_option_exclude(match_option, fastakeyfile_option);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  return op;
}

static int gt_extractseq_arguments_check(GT_UNUSED int argc,
                                         void *tool_arguments, GtError *err)
{
  ExtractSeqArguments *arguments = tool_arguments;
  gt_error_check(err);
  gt_assert(arguments);
  if (arguments->frompos > arguments->topos) {
    gt_error_set(err,
              "argument to option '-%s' must be <= argument to option '-%s'",
              FROMPOS_OPTION_STR, TOPOS_OPTION_STR);
    return -1;
  }
  return 0;
}

static int extractseq_pos(GtFile *outfp, GtBioseq *bs,
                          unsigned long frompos, unsigned long topos,
                          unsigned long width, GtError *err)
{
  int had_err = 0;
  GtStr *buf;
  char *out = NULL;
  unsigned long accupos = 0,
                newstartpos = 0,
                len = topos - frompos + 1,
                i = 0;
  gt_assert(bs);
  gt_error_check(err);

  if (frompos > gt_bioseq_get_total_length(bs)
        || topos > gt_bioseq_get_total_length(bs)) {
    gt_error_set(err, "invalid position pair %lu-%lu one value is larger than "
                      "sequence length %lu", frompos, topos,
                      gt_bioseq_get_total_length(bs));
    return -1;
  }
  frompos--; topos--;
  buf = gt_str_new();

  /* look for beginning of sequence */
  while (accupos + gt_bioseq_get_sequence_length(bs, i) <= frompos
            && i < gt_bioseq_number_of_sequences(bs)) {
    accupos += gt_bioseq_get_sequence_length(bs, i);
    i++;
  }
  if (i == 0) {
    newstartpos = frompos;
    accupos = frompos;
  } else {
    gt_assert(accupos > 0);
    newstartpos = frompos - accupos;
  }

  /* do we need to cross a sequence boundary to print the full output? */
  if (len <= gt_bioseq_get_sequence_length(bs, i) - newstartpos) {
    /* no, just print */
    out = gt_bioseq_get_sequence_range(bs, i, newstartpos,
                                       newstartpos + len - 1);
    gt_str_append_cstr_nt(buf, out, len);
    gt_free(out);
  } else {
    /* yes, first output the part on this sequence... */
    unsigned long restlen = gt_bioseq_get_sequence_length(bs, i) - newstartpos,
                  restfulllen = topos - accupos + 1;
    out = gt_bioseq_get_sequence_range(bs, i, newstartpos,
                                       newstartpos + restlen - 1);
    restfulllen -= restlen;
    gt_str_append_cstr_nt(buf, out, restlen);
    gt_free(out);

    i++;
    /* ...then determine whether we need to output full seqs in between... */
    while (restfulllen > gt_bioseq_get_sequence_length(bs, i)
             && i < gt_bioseq_number_of_sequences(bs) - 1) {
      unsigned long thislen = gt_bioseq_get_sequence_length(bs, i);
      out = gt_bioseq_get_sequence_range(bs, i, 0, thislen - 1);
      gt_str_append_cstr_nt(buf, out, thislen);
      gt_free(out);
      restfulllen -= thislen;
      i++;
    }

    /* ...then output the last sequence */
    if (restfulllen > 0) {
      out = gt_bioseq_get_sequence_range(bs, i, 0, restfulllen - 1);
      gt_str_append_cstr_nt(buf, out, restfulllen);
      gt_free(out);
    }
  }

  gt_fasta_show_entry(NULL, gt_str_get(buf), gt_str_length(buf), width, outfp);
  gt_str_delete(buf);
  return had_err;
}

static int extractseq_match(GtFile *outfp, GtBioseq *bs,
                            const char *pattern, unsigned long width,
                            GtError *err)
{
  const char *desc;
  unsigned long i;
  bool match;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(bs && pattern);

  for (i = 0; !had_err && i < gt_bioseq_number_of_sequences(bs); i++) {
    desc = gt_bioseq_get_description(bs, i);
    gt_assert(desc);
    had_err = gt_grep(&match, pattern, desc, err);
    if (!had_err && match) {
      char *out = gt_bioseq_get_sequence(bs, i);
      gt_fasta_show_entry(desc, out, gt_bioseq_get_sequence_length(bs, i),
                          width, outfp);
      gt_free(out);
    }
  }

  return had_err;
}

static int process_fastakeyfile(GtStr *fastakeyfile, int argc,
                                const char **argv, unsigned long width,
                                GtFile *outfp, GtError *err)
{
  int had_err = 0;
  gt_error_check(err);
  gt_assert(gt_str_length(fastakeyfile));

  if (argc == 0) {
    gt_error_set(err,"option -keys requires at least one file argument");
    had_err = -1;
  }

  if (!had_err)
  {
    const char *indexname = argv[0];

    if (argc == 1 && gt_deskeysfileexists(indexname))
    {
      if (gt_extractkeysfromfastaindex(indexname,fastakeyfile,width,err) != 0)
      {
        had_err = -1;
      }
    } else
    {
      GtStrArray *referencefiletab;
      int i;

      referencefiletab = gt_str_array_new();
      for (i = 0; i < argc; i++)
      {
        gt_str_array_add_cstr(referencefiletab, argv[i]);
      }
      if (gt_extractkeysfromfastafile(true, outfp, width, fastakeyfile,
                                      referencefiletab, err) != 1)
      {
        had_err = -1;
      }
      gt_str_array_delete(referencefiletab);
    }
  }
  return had_err;
}

static int gt_extractseq_runner(int argc, const char **argv, int parsed_args,
                                void *tool_arguments, GtError *err)
{
  ExtractSeqArguments *arguments = tool_arguments;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);
  if (gt_str_length(arguments->fastakeyfile)) {
    had_err = process_fastakeyfile(arguments->fastakeyfile, argc - parsed_args,
                            argv + parsed_args, arguments->width,
                            arguments->outfp, err);
  }
  else {
    GtBioseqIterator *bsi;
    GtBioseq *bs;
    bsi = gt_bioseq_iterator_new(argc - parsed_args, argv + parsed_args);
    while (!had_err &&
           !(had_err = gt_bioseq_iterator_next(bsi, &bs, err)) && bs) {
      if (arguments->frompos) {
        had_err = extractseq_pos(arguments->outfp, bs, arguments->frompos,
                                 arguments->topos, arguments->width, err);
      }
      else {
        had_err = extractseq_match(arguments->outfp, bs,
                                   gt_str_get(arguments->pattern),
                                   arguments->width, err);
      }
      gt_bioseq_delete(bs);
    }
    gt_bioseq_iterator_delete(bsi);
  }
  return had_err;
}

GtTool* gt_extractseq(void)
{
  return gt_tool_new(gt_extractseq_arguments_new,
                     gt_extractseq_arguments_delete,
                     gt_extractseq_option_parser_new,
                     gt_extractseq_arguments_check,
                     gt_extractseq_runner);
}
genometools-1.5.1/src/tools/gt_extractseq.h000066400000000000000000000017631211610345200210300ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_EXTRACTSEQ_H
#define GT_EXTRACTSEQ_H

#include "core/tool_api.h"

/* the extract sequence tool */
GtTool* gt_extractseq(void);

#endif
genometools-1.5.1/src/tools/gt_extracttarget.c000066400000000000000000000152331211610345200215160ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/bioseq.h"
#include "core/cstr_api.h"
#include "core/fasta.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/splitter.h"
#include "core/unused_api.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_escaping.h"
#include "extended/gff3_in_stream.h"
#include "extended/string_matching.h"
#include "tools/gt_extracttarget.h"

typedef struct {
  GtStrArray *seqfiles;
} ExtractTargetArguments;

static void* gt_extracttarget_arguments_new(void)
{
  ExtractTargetArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->seqfiles = gt_str_array_new();
  return arguments;
}

static void gt_extracttarget_arguments_delete(void *tool_arguments)
{
  ExtractTargetArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_array_delete(arguments->seqfiles);
  gt_free(arguments);
}

static GtOptionParser* gt_extracttarget_option_parser_new(void *tool_arguments)
{
  ExtractTargetArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *o;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] -seqfile sequence_file GFF3_file",
                         "Extract target sequences given in GFF3_file from "
                         "sequence_file.");

  /* -seqfile */
  o = gt_option_new_filename_array("seqfiles",
                                   "set the sequence file from which "
                                   "to extract the features",
                                   arguments->seqfiles);
  gt_option_is_mandatory(o);
  gt_option_parser_add_option(op, o);

  gt_option_parser_set_min_max_args(op, 1, 1);

  return op;
}

typedef struct {
  GtBioseq *bioseq;
  unsigned long seqnum;
} TargetInfo;

static bool show_target(GT_UNUSED unsigned long pos, void *data)
{
  TargetInfo *ti = data;
  char *seq;
  gt_assert(ti);
  seq = gt_bioseq_get_sequence(ti->bioseq, ti->seqnum);
  gt_fasta_show_entry(gt_bioseq_get_description(ti->bioseq, ti->seqnum),
                      seq,
                      gt_bioseq_get_sequence_length(ti->bioseq, ti->seqnum), 0,
                      NULL);
  gt_free(seq);
  return true;
}

static int extracttarget_from_seqfiles(const char *target,
                                       GtStrArray *seqfiles,
                                       GtError *err)
{
  GtStr *unescaped_target;
  char *escaped_target;
  GtSplitter *splitter;
  unsigned long i;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(target && seqfiles);
  splitter = gt_splitter_new();
  unescaped_target = gt_str_new();
  escaped_target = gt_cstr_dup(target);
  gt_splitter_split(splitter, escaped_target, strlen(escaped_target), ',');
  for (i = 0; !had_err && i < gt_splitter_size(splitter); i++) {
    GtSplitter *blank_splitter;
    char *token = gt_splitter_get_token(splitter, i);
    blank_splitter = gt_splitter_new();
    gt_splitter_split(blank_splitter, token, strlen(token), ' ');
    had_err = gt_gff3_unescape(unescaped_target,
                               gt_splitter_get_token(blank_splitter, 0),
                               strlen(gt_splitter_get_token(blank_splitter, 0)),
                               err);
    if (!had_err) {
      unsigned long j;
      for (j = 0; j < gt_str_array_size(seqfiles); j++) {
        unsigned long k;
        GtBioseq *bioseq;
        if (!(bioseq =  gt_bioseq_new(gt_str_array_get(seqfiles, j), err))) {
          had_err = -1;
          break;
        }
        for (k = 0; k < gt_bioseq_number_of_sequences(bioseq); k++) {
          TargetInfo target_info;
          const char *desc = gt_bioseq_get_description(bioseq, k);
          target_info.bioseq = bioseq;
          target_info.seqnum = k;
          gt_string_matching_bmh(desc, strlen(desc),
                                 gt_str_get(unescaped_target),
                                 gt_str_length(unescaped_target), show_target,
                                 &target_info);
        }
        gt_bioseq_delete(bioseq);
      }
    }
    gt_splitter_delete(blank_splitter);
  }
  gt_free(escaped_target);
  gt_str_delete(unescaped_target);
  gt_splitter_delete(splitter);
  return had_err;
}

static int extracttarget_from_node(GtGenomeNode *gn, GtStrArray *seqfiles,
                                   GtError *err)
{
  GtFeatureNodeIterator *fni;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(gn && seqfiles);
  /* XXX */
  if (gt_genome_node_cast(gt_feature_node_class(), gn)) {
    const char *target;
    GtFeatureNode *child;
    fni = gt_feature_node_iterator_new(gt_feature_node_cast(gn));
    while (!had_err && /* XXX remove cast */
           (child = (GtFeatureNode*) gt_feature_node_iterator_next(fni))) {
      if ((target = gt_feature_node_get_attribute(child, "Target")))
        had_err = extracttarget_from_seqfiles(target, seqfiles, err);
    }
    gt_feature_node_iterator_delete(fni);
  }
  return had_err;
}

static int gt_extracttarget_runner(GT_UNUSED int argc, const char **argv,
                                   int parsed_args, void *tool_arguments,
                                   GtError *err)
{
  ExtractTargetArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream;
  GtGenomeNode *gn;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  gff3_in_stream = gt_gff3_in_stream_new_unsorted(1, argv + parsed_args);

  while (!(had_err = gt_node_stream_next(gff3_in_stream, &gn, err)) && gn) {
    had_err = extracttarget_from_node(gn, arguments->seqfiles, err);
    gt_genome_node_delete(gn);
  }

  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool* gt_extracttarget(void)
{
  return gt_tool_new(gt_extracttarget_arguments_new,
                     gt_extracttarget_arguments_delete,
                     gt_extracttarget_option_parser_new,
                     NULL,
                     gt_extracttarget_runner);
}
genometools-1.5.1/src/tools/gt_extracttarget.h000066400000000000000000000017601211610345200215230ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_EXTRACTTARGET_H
#define GT_EXTRACTTARGET_H

#include "core/tool_api.h"

/* the extract target tool */
GtTool* gt_extracttarget(void);

#endif
genometools-1.5.1/src/tools/gt_featureindex.c000066400000000000000000000264641211610345200213300ustar00rootroot00000000000000/*
  Copyright (c) 2009 Sascha Steinbiss 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/fileutils_api.h"
#include "core/ma.h"
#include "core/password_entry.h"
#include "core/str_api.h"
#include "core/unused_api.h"
#include "extended/anno_db_gfflike_api.h"
#include "extended/anno_db_schema_api.h"
#include "extended/feature_index_api.h"
#include "extended/feature_node.h"
#include "extended/feature_stream_api.h"
#include "extended/gff3_visitor.h"
#include "extended/rdb_api.h"
#ifdef HAVE_MYSQL
#include "extended/rdb_mysql_api.h"
#endif
#ifdef HAVE_SQLITE
#include "extended/rdb_sqlite_api.h"
#endif
#include "tools/gt_featureindex.h"

#define GT_SQLITE_BACKEND_STRING "sqlite"
#define GT_MYSQL_BACKEND_STRING  "mysql"

typedef struct {
  GtRange qry_rng;
  GtStr *seqid;
  GtStr *backend,
        *filename,
        *host,
        *user,
        *pass,
        *database;
  int port;
  bool verbose,
       retain,
       child_callback_check,
       attributes_callback_check;
  GtOption *rngopt;
} GtFeatureindexArguments;

static void* gt_featureindex_arguments_new(void)
{
  GtFeatureindexArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->seqid = gt_str_new();
  arguments->backend = gt_str_new();
  arguments->filename = gt_str_new();
  arguments->host = gt_str_new();
  arguments->user = gt_str_new();
  arguments->database = gt_str_new();
  return arguments;
}

static void gt_featureindex_arguments_delete(void *tool_arguments)
{
  GtFeatureindexArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->seqid);
  gt_str_delete(arguments->backend);
  gt_str_delete(arguments->filename);
  gt_str_delete(arguments->host);
  gt_str_delete(arguments->user);
  gt_str_delete(arguments->pass);
  gt_str_delete(arguments->database);
  gt_option_delete(arguments->rngopt);
  gt_free(arguments);
}

static GtOptionParser* gt_featureindex_option_parser_new(void *tool_arguments)
{
  GtFeatureindexArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *backend_option, *filenameoption;
  static const char *backends[] = {
#ifdef HAVE_SQLITE
    GT_SQLITE_BACKEND_STRING,
#endif
#ifdef HAVE_MYSQL
    GT_MYSQL_BACKEND_STRING,
#endif
    NULL
  };
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] indexfilename",
                            "Retrieve annotations from a persistent "
                            "feature index as GFF3 output.");

  arguments->rngopt = gt_option_new_range("range",
                                          "range constraint for index query",
                                          &arguments->qry_rng, NULL);
  gt_option_parser_add_option(op, gt_option_ref(arguments->rngopt));

  option = gt_option_new_string("seqid", "sequence region",
                                arguments->seqid, NULL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("retain", "retain attributes",
                              &arguments->retain, true);
  gt_option_parser_add_option(op, option);

  /* -backend */
  backend_option = gt_option_new_choice("backend", "database backend to use\n"
                                        "choose from ["
#ifdef HAVE_SQLITE
                                         GT_SQLITE_BACKEND_STRING
#endif
#ifdef HAVE_MYSQL
                                        "|" GT_MYSQL_BACKEND_STRING
#endif
                                        "]",
                                        arguments->backend, backends[0],
                                        backends);
  gt_option_parser_add_option(op, backend_option);

  /* -filename */
  filenameoption = gt_option_new_string("filename",
                                        "filename for feature database "
                                        "(sqlite backend only)",
                                        arguments->filename, NULL);
  gt_option_parser_add_option(op, filenameoption);

#ifdef HAVE_MYSQL
  /* -host */
  option = gt_option_new_string("host", "hostname for database connection",
                                arguments->host, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory_either(option, filenameoption);

  /* -user */
  option = gt_option_new_string("user", "username for database connection",
                                arguments->user, NULL);
  gt_option_parser_add_option(op, option);

  /* -database */
  option = gt_option_new_string("database",
                                "database name for database connection",
                                arguments->database, NULL);
  gt_option_parser_add_option(op, option);

  /* -port */
  option = gt_option_new_int_max("port", "port for database connection",
                                 &arguments->port, 3333, 65534);
  gt_option_parser_add_option(op, option);
#else
  gt_option_is_mandatory(filenameoption);
#endif

  option = gt_option_new_bool("child_check", "test callbacks for "
                                             "child node addition",
                              &arguments->child_callback_check, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  option = gt_option_new_bool("attributes_check", "test callbacks for "
                                                  "attribute modification",
                              &arguments->attributes_callback_check, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  return op;
}

static int gt_featureindex_arguments_check(GT_UNUSED int rest_argc,
                                           GT_UNUSED void *tool_arguments,
                                           GT_UNUSED GtError *err)
{
  GT_UNUSED GtFeatureindexArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  return had_err;
}

static int gt_featureindex_runner(GT_UNUSED int argc,
                                  GT_UNUSED const char **argv,
                                  GT_UNUSED int parsed_args,
                                  void *tool_arguments,
                                  GtError *err)
{
  GtFeatureindexArguments *arguments = tool_arguments;
  GtFeatureIndex *fi = NULL;
  GtArray *results = NULL;
  GtRange rng;
  GtRDB *rdb = NULL;
  GtAnnoDBSchema *adbs = NULL;
  GtNodeVisitor *gff3visitor = NULL;
  GtGenomeNode *regn = NULL;
  unsigned long i = 0;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

#ifdef HAVE_SQLITE
  if (!had_err) {
    if (strcmp(gt_str_get(arguments->backend),
               GT_SQLITE_BACKEND_STRING) == 0) {
      if (!gt_file_exists(gt_str_get(arguments->filename))) {
        gt_error_set(err, "file '%s' does not exist",
                     gt_str_get(arguments->filename));
        had_err = -1;
      }
      if (!had_err) {
        rdb = gt_rdb_sqlite_new(gt_str_get(arguments->filename), err);
        if (!rdb)
          had_err = -1;
      }
    }
  }
#endif
#ifdef HAVE_MYSQL
  if (!had_err) {
    if (strcmp(gt_str_get(arguments->backend),
                      GT_MYSQL_BACKEND_STRING) == 0) {
      arguments->pass = gt_get_password("password: ", err);
      rdb = gt_rdb_mysql_new(gt_str_get(arguments->host),
                             arguments->port,
                             gt_str_get(arguments->database),
                             gt_str_get(arguments->user),
                             gt_str_get(arguments->pass),
                             err);
      if (!rdb)
        had_err = -1;
    }
  }
#endif
  if (!had_err)
    adbs = gt_anno_db_gfflike_new();

  if (!had_err && !adbs)
    had_err = -1;

  if (!had_err) {
    fi = gt_anno_db_schema_get_feature_index(adbs, rdb, err);
    had_err = fi ? 0 : -1;
  }

  if (!had_err && gt_str_length(arguments->seqid) == 0) {
    char *firstseqid = gt_feature_index_get_first_seqid(fi, err);
    if (firstseqid == NULL)
      had_err = -1;
    else {
      gt_str_append_cstr(arguments->seqid, firstseqid);
      gt_free(firstseqid);
    }
  }

  if (!had_err && !gt_option_is_set(arguments->rngopt)) {
    had_err = gt_feature_index_get_range_for_seqid(fi, &arguments->qry_rng,
                                                   gt_str_get(arguments->seqid),
                                                   err);
  }

  if (!had_err) {
    results = gt_array_new(sizeof (GtFeatureNode*));
    had_err = gt_feature_index_get_features_for_range(fi, results,
                                                   gt_str_get(arguments->seqid),
                                                   &arguments->qry_rng, err);
  }
  if (!had_err) {
    gff3visitor = gt_gff3_visitor_new(NULL);
    if (arguments->retain)
      gt_gff3_visitor_retain_id_attributes((GtGFF3Visitor*) gff3visitor);

    had_err = gt_feature_index_get_range_for_seqid(fi, &rng,
                                                   gt_str_get(arguments->seqid),
                                                   err);
  }
  if (!had_err) {
    regn = gt_region_node_new(arguments->seqid, rng.start, rng.end);
    gt_genome_node_accept(regn, gff3visitor, err);
    gt_genome_node_delete(regn);

    for (i=0; ichild_callback_check) {
          GtFeatureNode *fn;
          fn = (GtFeatureNode*) gt_feature_node_new(arguments->seqid, "test",
                                                    nrng.start, nrng.end,
                                                    GT_STRAND_FORWARD);
          gt_feature_node_add_child((GtFeatureNode*) gn, fn);
        }
        if (arguments->attributes_callback_check) {
          if (gt_feature_node_get_attribute(fgn, "foo")) {
            gt_feature_node_set_attribute(fgn, "foo", "boooo");
            gt_feature_node_remove_attribute(fgn, "foo");
          }
          gt_feature_node_add_attribute(fgn, "foo", "bar");
        }
      }
      gt_genome_node_accept(gn, gff3visitor, err);
      gt_genome_node_delete(gn);
    }
  }

  gt_array_delete(results);
  gt_node_visitor_delete(gff3visitor);
  gt_rdb_delete(rdb);
  gt_anno_db_schema_delete(adbs);

  gt_feature_index_delete(fi);
  return had_err;
}

GtTool* gt_featureindex(void)
{
  return gt_tool_new(gt_featureindex_arguments_new,
                  gt_featureindex_arguments_delete,
                  gt_featureindex_option_parser_new,
                  gt_featureindex_arguments_check,
                  gt_featureindex_runner);
}
genometools-1.5.1/src/tools/gt_featureindex.h000066400000000000000000000017611211610345200213260ustar00rootroot00000000000000/*
  Copyright (c) 2009 Sascha Steinbiss 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_FEATUREINDEX_H
#define GT_FEATUREINDEX_H

#include "core/tool_api.h"

/* the featureindex tool */
GtTool* gt_featureindex(void);

#endif
genometools-1.5.1/src/tools/gt_fingerprint.c000066400000000000000000000312001211610345200211540ustar00rootroot00000000000000/*
  Copyright (c) 2008-2012 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/bioseq.h"
#include "core/bioseq_col.h"
#include "core/fa.h"
#include "core/fasta.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/seq_info_cache.h"
#include "core/string_distri.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "extended/gtdatahelp.h"
#include "tools/gt_fingerprint.h"

typedef struct {
  bool show_duplicates,
       detect_collisions;
  GtStr *checklist,
        *extract;
  unsigned long width;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} FingerprintArguments;

static void* gt_fingerprint_arguments_new(void)
{
  FingerprintArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->checklist = gt_str_new();
  arguments->extract = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_fingerprint_arguments_delete(void *tool_arguments)
{
  FingerprintArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->extract);
  gt_str_delete(arguments->checklist);
  gt_free(arguments);
}

static GtOptionParser* gt_fingerprint_option_parser_new(GT_UNUSED
                                                        void *tool_arguments)
{
  FingerprintArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *check_option, *collisions_option, *duplicates_option,
           *extract_option, *width_option;
  gt_assert(arguments);
  op = gt_option_parser_new("[option ...] sequence_file [...] ",
                            "Compute MD5 fingerprints for each sequence given "
                            "in sequence_file(s).");

  /* -check */
  check_option = gt_option_new_filename("check", "compare all fingerprints "
                                        "contained in the given checklist file "
                                        "with checksums in given "
                                        "sequence_files(s). The comparison is "
                                        "successful, if all fingerprints given "
                                        "in checkfile can be found in the "
                                        "sequence_file(s) in the exact same "
                                        "quantity and vice versa.",
                                        arguments->checklist);
  gt_option_parser_add_option(op, check_option);

  /* -duplicates */
  duplicates_option = gt_option_new_bool("duplicates", "show duplicate "
                                         "fingerprints from given "
                                         "sequence_file(s).",
                                         &arguments->show_duplicates, false);
  gt_option_parser_add_option(op, duplicates_option);

  /* -collisions */
  collisions_option = gt_option_new_bool("collisions", "detect hash collisions",
                                         &arguments->detect_collisions, false);
  gt_option_is_development_option(collisions_option);
  gt_option_parser_add_option(op, collisions_option);

  /* -extract */
  extract_option = gt_option_new_string("extract",
                                        "extract the sequence(s) with "
                                        "the given fingerprint from "
                                        "sequence_file(s) and show them on "
                                        "stdout.", arguments->extract, NULL);
  gt_option_parser_add_option(op, extract_option);

  /* -width */
  width_option = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, width_option);

  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  /* option exclusions */
  gt_option_exclude(check_option, duplicates_option);
  gt_option_exclude(extract_option, check_option);
  gt_option_exclude(extract_option, duplicates_option);
  gt_option_exclude(collisions_option, check_option);
  gt_option_exclude(collisions_option, duplicates_option);
  gt_option_exclude(collisions_option, extract_option);

  /* option implications */
  gt_option_imply(width_option, extract_option);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_min_args(op, 1);
  return op;
}

static void proc_superfluous_sequence(const char *string,
                                      GT_UNUSED unsigned long occurrences,
                                      GT_UNUSED double probability, void *data)
{
  bool *comparisons_failed = data;
  gt_assert(string && occurrences && comparisons_failed);
  printf("%s only in sequence_file(s)\n", string);
  *comparisons_failed = true;
}

static int compare_fingerprints(GtStringDistri *sd, const char *checklist,
                                GtError *err)
{
  bool comparisons_failed = false, use_stdin = false;
  FILE *checkfile;
  GtStr *line;
  gt_error_check(err);
  gt_assert(sd && checklist);
  if (!strcmp(checklist, "-"))
    use_stdin = true;
  checkfile = use_stdin ? stdin : gt_fa_xfopen(checklist, "r");
  line = gt_str_new();
  /* process checklist */
  while (gt_str_read_next_line(line, checkfile) != EOF) {
    if (gt_string_distri_get(sd, gt_str_get(line)))
      gt_string_distri_sub(sd, gt_str_get(line));
    else {
      printf("%s only in checklist\n", gt_str_get(line));
      comparisons_failed = true;
    }
    gt_str_reset(line);
  }
  gt_str_delete(line);
  if (!use_stdin)
    gt_fa_xfclose(checkfile);
  /* process remaining sequence_file(s) fingerprints */
  gt_string_distri_foreach(sd, proc_superfluous_sequence, &comparisons_failed);
  if (comparisons_failed) {
    gt_error_set(err, "fingerprint comparison failed");
    return -1;
  }
  return 0;
}

typedef struct {
  unsigned long long duplicates,
                     num_of_sequences;
} FingerprintInfo;

static void show_duplicate(const char *fingerprint, unsigned long occurrences,
                           GT_UNUSED double probability, void *data)
{
  FingerprintInfo *info = data;
  if (occurrences > 1) {
    printf("%s\t%lu\n", fingerprint, occurrences);
    info->duplicates += occurrences - 1;
  }
  info->num_of_sequences += occurrences;
}

static int show_duplicates(GtStringDistri *sd, GtError *err)
{
  FingerprintInfo info;
  gt_error_check(err);
  gt_assert(sd);
  info.duplicates = 0;
  info.num_of_sequences = 0;
  gt_string_distri_foreach(sd, show_duplicate, &info);
  if (info.duplicates) {
    gt_error_set(err, "duplicates found: %llu out of %llu (%.3f%%)",
                 info.duplicates, info.num_of_sequences,
                 (((double) info.duplicates / info.num_of_sequences) * 100.0));
    return -1;
  }
  return 0;
}

static int compare_md5s(GtBioseqCol *bsc, const GtSeqInfo *si,
                        unsigned long filenum, unsigned long seqnum,
                        const char *md5, GtError *err)
{
  unsigned long i, seq_a_len, seq_b_len;
  char *seq_a_upper, *seq_b_upper;
  char *seq_a, *seq_b;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(bsc && si && md5);
  seq_a_len = gt_seq_col_get_sequence_length((GtSeqCol*) bsc, si->filenum,
                                             si->seqnum);
  seq_b_len = gt_seq_col_get_sequence_length((GtSeqCol*) bsc, filenum, seqnum);
  seq_a = gt_seq_col_get_sequence((GtSeqCol*) bsc, si->filenum, si->seqnum, 0,
                                  seq_a_len - 1);
  seq_b = gt_seq_col_get_sequence((GtSeqCol*) bsc, filenum, seqnum, 0,
                                  seq_b_len - 1);
  seq_a_upper = gt_malloc((seq_a_len + 1) * sizeof (char));
  seq_b_upper = gt_malloc((seq_b_len + 1) * sizeof (char));
  for (i = 0; i < seq_a_len; i++)
    seq_a_upper[i] = toupper(seq_a[i]);
  for (i = 0; i < seq_b_len; i++)
    seq_b_upper[i] = toupper(seq_b[i]);
  gt_free(seq_a);
  gt_free(seq_b);
  seq_a_upper[seq_a_len] = '\0';
  seq_b_upper[seq_b_len] = '\0';
  if (strcmp(seq_a_upper, seq_b_upper)) {
    gt_error_set(err, "sequence collision detected for fingerprint '%s'", md5);
    had_err = -1;
  }
  gt_free(seq_b_upper);
  gt_free(seq_a_upper);
  return had_err;
}

static int detect_collisions_on_bsc(GtBioseqCol *bsc, GtError *err)
{
  unsigned long filenum, seqnum;
  GtSeqInfoCache *sic;
  gt_error_check(err);
  gt_assert(bsc);
  int had_err = 0;
  sic = gt_seq_info_cache_new();
  for (filenum = 0;
       !had_err && filenum < gt_seq_col_num_of_files((GtSeqCol*) bsc);
       filenum++) {
    for (seqnum = 0;
         !had_err && seqnum < gt_seq_col_num_of_seqs((GtSeqCol*) bsc, filenum);
         seqnum++) {
      const GtSeqInfo *si_ptr;
      const char *md5;
      md5 = gt_seq_col_get_md5_fingerprint((GtSeqCol*) bsc, filenum, seqnum);
      if ((si_ptr = gt_seq_info_cache_get(sic, md5)))
        had_err = compare_md5s(bsc, si_ptr, filenum, seqnum, md5, err);
      else {
        GtSeqInfo si;
        si.filenum = filenum;
        si.seqnum = seqnum;
        gt_seq_info_cache_add(sic, md5, &si);
      }
    }
  }
  gt_seq_info_cache_delete(sic);
  return had_err;
}

static int detect_collisions(int num_of_seqfiles, const char **seqfiles,
                             GtError *err)
{
  GtStrArray *sequence_files;
  GtSeqCol *sc;
  unsigned long i;
  int had_err = 0;
  gt_error_check(err);
  sequence_files = gt_str_array_new();
  for (i = 0; i < num_of_seqfiles; i++)
    gt_str_array_add_cstr(sequence_files, seqfiles[i]);
  if (!(sc = gt_bioseq_col_new(sequence_files, err)))
    had_err = -1;
  if (!had_err)
    had_err = detect_collisions_on_bsc((GtBioseqCol*) sc, err);
  gt_seq_col_delete(sc);
  gt_str_array_delete(sequence_files);
  return had_err;
}

static int gt_fingerprint_runner(int argc, const char **argv, int parsed_args,
                                 void *tool_arguments, GtError *err)
{
  FingerprintArguments *arguments = tool_arguments;
  bool extract_found = true;
  GtBioseq *bs;
  GtStringDistri *sd;
  unsigned long i, j;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);
  sd = gt_string_distri_new();

  if (gt_str_length(arguments->extract))
    extract_found = false;

  /* process sequence files */
  for (i = parsed_args; !had_err && i < argc; i++) {
    if (!(bs = gt_bioseq_new(argv[i], err)))
      had_err = -1;
    if (!had_err) {
      for (j = 0; j < gt_bioseq_number_of_sequences(bs); j++) {
        if (gt_str_length(arguments->checklist) || arguments->show_duplicates)
          gt_string_distri_add(sd, gt_bioseq_get_md5_fingerprint(bs, j));
        else if (gt_str_length(arguments->extract)) {
          if (!strcmp(gt_bioseq_get_md5_fingerprint(bs, j),
                      gt_str_get(arguments->extract))) {
            char *seq = gt_bioseq_get_sequence(bs, j);
            gt_fasta_show_entry(gt_bioseq_get_description(bs, j),
                                seq,
                                gt_bioseq_get_sequence_length(bs, j),
                                arguments->width, arguments->outfp);
            gt_free(seq);
            extract_found = true;
          }
        }
        else if (!arguments->detect_collisions)
          gt_xputs(gt_bioseq_get_md5_fingerprint(bs, j));
      }
    }
    gt_bioseq_delete(bs);
  }

  if (!had_err && !extract_found) {
    gt_error_set(err, "could not find sequence with fingerprint '%s' in given "
                      "sequence file(s)", gt_str_get(arguments->extract));
    had_err = -1;
  }

  if (!had_err) {
    if (gt_str_length(arguments->checklist))
      had_err = compare_fingerprints(sd, gt_str_get(arguments->checklist), err);
    else if (arguments->show_duplicates)
      had_err = show_duplicates(sd, err);
    else if (arguments->detect_collisions)
      had_err = detect_collisions(argc - parsed_args, argv + parsed_args, err);
  }

  gt_string_distri_delete(sd);

  return had_err;
}

GtTool* gt_fingerprint(void)
{
  return gt_tool_new(gt_fingerprint_arguments_new,
                     gt_fingerprint_arguments_delete,
                     gt_fingerprint_option_parser_new,
                     NULL,
                     gt_fingerprint_runner);
}
genometools-1.5.1/src/tools/gt_fingerprint.h000066400000000000000000000017471211610345200211760ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_FINGERPRINT_H
#define GT_FINGERPRINT_H

#include "core/tool_api.h"

/* the fingerprint tool */
GtTool* gt_fingerprint(void);

#endif
genometools-1.5.1/src/tools/gt_gdiffcalc.c000066400000000000000000000254721211610345200205450ustar00rootroot00000000000000/*
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 

#include "core/array2dim_api.h"
#include "core/cstr_api.h"
#include "core/encseq.h"
#include "core/encseq_options.h"
#include "core/fa.h"
#include "core/log_api.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "core/showtime.h"
#include "core/warning_api.h"
#include "core/tokenizer.h"
#include "core/io.h"
#include "extended/gtdatahelp.h"
#include "match/esa-fileend.h"
#include "match/genomediff_opt.h"
#include "match/index_options.h"
#include "match/sfx-opt.h"
#include "match/sfx-run.h"
#include "match/shu-genomediff.h"
#include "tools/gt_gdiffcalc.h"

static void* gt_gdiffcalc_arguments_new(void)
{
  GtGenomediffArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->indexname = gt_str_new();
  arguments->unitfile = gt_str_new();
  arguments->indextype = gt_str_new();
  arguments->filenames = gt_str_array_new();
  arguments->with_esa = arguments->with_pck = false;
  return arguments;
}

static void gt_gdiffcalc_arguments_delete(void *tool_arguments)
{
  GtGenomediffArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->indexname);
  gt_str_delete(arguments->unitfile);
  gt_str_delete(arguments->indextype);
  gt_str_array_delete(arguments->filenames);
  gt_option_delete(arguments->ref_unitfile);
  gt_encseq_options_delete(arguments->loadopts);
  gt_index_options_delete(arguments->idxopts);
  gt_free(arguments);
}

static GtOptionParser* gt_gdiffcalc_option_parser_new(void *tool_arguments)
{
  GtGenomediffArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *option_unitfile;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] "
                          "-indexname NAME AVGSHULEN) ",
                          "Calculates Kr: pairwise distances between genomes.");

  /* options */
  option = gt_option_new_string("indexname", "Basename of encseq to construct.",
                                arguments->indexname, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  /*-unitfile*/
  option_unitfile =
    gt_option_new_filename("unitfile",
                           "specifies genomic units, see below for description",
                           arguments->unitfile);
  gt_option_parser_add_option(op, option_unitfile);
  arguments->ref_unitfile = gt_option_ref(option_unitfile);

  /* encseq options */
  arguments->loadopts =
    gt_encseq_options_register_loading(op, arguments->indexname);

  gt_option_is_development_option(
                        gt_encseq_options_lossless_option(arguments->loadopts));

  /* dev options */
  /* -max_n */
  option = gt_option_new_ulong("max_n", "Number of precalculated values "
                               "for ln(n!) and pmax(x)",
                               &arguments->max_ln_n_fac, 1000UL);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* thresholds */
  /* divergence error */
  option = gt_option_new_double("thr",
                                "Threshold for difference (du, dl) in "
                                "divergence calculation.\n"
                                "default: 1e-9",
                                &arguments->divergence_threshold,
                                1e-9);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* expected shulen error */
  option = gt_option_new_double("abs_err",
                                "absolute error for expected shulen "
                                "calculation.\n"
                                "default: 1e-5",
                                &arguments->divergence_abs_err,
                                1e-5);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* relative expected shulen error */
  option = gt_option_new_double("rel_err",
                                "relative error for expected shulen "
                                "calculation.\n"
                                "default: 1e-3",
                                &arguments->divergence_rel_err,
                                1e-3);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* M */
  option = gt_option_new_double("M",
                                "threshold for minimum logarithm.\n"
                                "default: DBL_MIN",
                                &arguments->divergence_m,
                                DBL_MIN);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* mail */
  gt_option_parser_set_mail_address(op, "");
  /* doc */
  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  return op;
}

static int gt_gdiffcalc_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  GtGenomediffArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  gt_assert(rest_argc == 1);
  if (!had_err)
    arguments->with_units = gt_option_is_set(arguments->ref_unitfile);

  return had_err;
}

static int gt_gdiffcalc_runner(int argc, const char **argv, int parsed_args,
                              void *tool_arguments, GT_UNUSED GtError *err)
{
  GtGenomediffArguments *arguments = tool_arguments;
  int had_err = 0, i;
  unsigned long lcounter = 0, zcounter = 0;
  double **shusums = NULL;
  GtEncseq              *encseq = NULL;
  GtLogger              *logger;
  GtShuUnitFileInfo     *unit_info = NULL;
  GtTimer               *timer = NULL;

  gt_error_check(err);
  gt_assert(arguments);

  logger = gt_logger_new(arguments->verbose,
                         GT_LOGGER_DEFLT_PREFIX,
                         stdout);
  gt_assert(logger);

  for (i = parsed_args; i < argc; i++) {
    gt_str_array_add_cstr(arguments->filenames, argv[i]);
  }

  if (gt_showtime_enabled()) {
    timer = gt_timer_new_with_progress_description("load encseq");
    gt_timer_start(timer);
    gt_assert(timer);
  }

  if (arguments->with_units) {
    gt_logger_log(logger, "unitfile option set, filename is %s\n",
                  gt_str_get(arguments->unitfile));
  }

  if (!had_err) {
    GtEncseqLoader *el = gt_encseq_loader_new_from_options(arguments->loadopts,
                                                           err);
    encseq =
      gt_encseq_loader_load(el, gt_str_get(arguments->indexname), err);
    gt_encseq_loader_delete(el);
  }
  if (encseq == NULL)
    had_err = -1;

  if (timer != NULL)
    gt_timer_show_progress(timer, "load units", stdout);

  if (!had_err) {
    unit_info = gt_shu_unit_info_new(encseq);
    if (arguments->with_units)
      had_err = gt_shu_unit_file_info_read(arguments->unitfile, unit_info,
                                           logger, err);
  }

  if (timer != NULL)
    gt_timer_show_progress(timer, "read table", stdout);

  if (!had_err) {
    GtIO *table_file = NULL;
    GtTokenizer *tokenizer = NULL;
    GtStr *line = NULL;

    gt_assert(unit_info != NULL);
    gt_array2dim_calloc(shusums, unit_info->num_of_genomes,
                        unit_info->num_of_genomes);

    table_file = gt_io_new(gt_str_array_get(arguments->filenames, 0), "r");
    tokenizer = gt_tokenizer_new(table_file);
    line = gt_tokenizer_get_token(tokenizer);
    while (line != NULL && !had_err) {
      char *cline = gt_str_get(line);
      char *elem = strtok(cline, ";");
      zcounter = 0;
      while (elem != NULL && !had_err) {
        if (*elem != '#') {
          if (1 != sscanf(elem, "%lf",
                          &shusums[lcounter][zcounter])) {
            had_err = 1;
            gt_error_set(err, "couldn't scan");
            break;
          }
          gt_logger_log(logger,"wert: %lf", shusums[lcounter][zcounter]);
          zcounter++;
        }
        else {
          gt_logger_log(logger, "name: %s", elem++);
        }
        elem = strtok(NULL, ";");
      }
      gt_tokenizer_next_token(tokenizer);
      gt_str_delete(line);
      line = gt_tokenizer_get_token(tokenizer);
      lcounter++;
      gt_logger_log(logger, "line %ld", lcounter);
    }
  }
  if (!had_err) {
    unsigned long num_of_seq, file_idx, seq_idx, startpos;
    GT_UNUSED unsigned long oldpos = 0;

    gt_assert(unit_info != NULL);
    gt_assert(lcounter == zcounter);
    gt_assert(lcounter == unit_info->num_of_genomes);

    num_of_seq = gt_encseq_num_of_sequences(unit_info->encseq);

    for (seq_idx = 0; seq_idx < num_of_seq; seq_idx++) {
      startpos = gt_encseq_seqstartpos(unit_info->encseq, seq_idx);
      file_idx = gt_encseq_filenum(unit_info->encseq, startpos);
      gt_log_log("seq: %lu starts at: %lu\n"
                 "belonges to file: %lu which is part of genome: %s",
                 seq_idx, startpos, file_idx,
                 gt_str_array_get(unit_info->genome_names,
                                  unit_info->map_files[file_idx]));
      gt_assert(oldpos <= startpos);
      oldpos = startpos;
    }
  }
  if (!had_err && shusums != NULL) {
    had_err = gt_genomediff_calculate_div_from_avg(shusums, arguments,
                                                   unit_info,
                                                   logger, timer, err);
    gt_array2dim_delete(shusums);
  }

  if (timer != NULL) {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  gt_logger_delete(logger);
  gt_encseq_delete(encseq);
  gt_shu_unit_info_delete(unit_info);
  return had_err;
}

GtTool* gt_gdiffcalc(void)
{
  return gt_tool_new(gt_gdiffcalc_arguments_new,
                  gt_gdiffcalc_arguments_delete,
                  gt_gdiffcalc_option_parser_new,
                  gt_gdiffcalc_arguments_check,
                  gt_gdiffcalc_runner);
}
genometools-1.5.1/src/tools/gt_gdiffcalc.h000066400000000000000000000017331211610345200205440ustar00rootroot00000000000000/*
  Copyright (c) 2012 Dirk Willrodt 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_GDIFFCALC_H
#define GT_GDIFFCALC_H

#include "core/tool_api.h"

/* the foo tool */
GtTool* gt_gdiffcalc(void);

#endif
genometools-1.5.1/src/tools/gt_genomediff.c000066400000000000000000000336721211610345200207470ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include 

#include "core/array2dim_api.h"
#include "core/cstr_api.h"
#include "core/encseq.h"
#include "core/encseq_options.h"
#include "core/fa.h"
#include "core/log_api.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "core/showtime.h"
#include "core/warning_api.h"
#include "extended/gtdatahelp.h"
#include "match/esa-fileend.h"
#include "match/genomediff_opt.h"
#include "match/index_options.h"
#include "match/sfx-opt.h"
#include "match/sfx-run.h"
#include "match/shu-genomediff.h"
#include "tools/gt_genomediff.h"

static void* gt_genomediff_arguments_new(void)
{
  GtGenomediffArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->indexname = gt_str_new();
  arguments->unitfile = gt_str_new();
  arguments->indextype = gt_str_new();
  arguments->filenames = gt_str_array_new();
  arguments->with_esa = arguments->with_pck = false;
  return arguments;
}

static void gt_genomediff_arguments_delete(void *tool_arguments)
{
  GtGenomediffArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->indexname);
  gt_str_delete(arguments->unitfile);
  gt_str_delete(arguments->indextype);
  gt_str_array_delete(arguments->filenames);
  gt_option_delete(arguments->ref_unitfile);
  gt_encseq_options_delete(arguments->loadopts);
  gt_index_options_delete(arguments->idxopts);
  gt_free(arguments);
}

static GtOptionParser* gt_genomediff_option_parser_new(void *tool_arguments)
{
  GtGenomediffArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *option_unitfile;
  static const char *indextypes[] = { "esa", "pck", "encseq", NULL };

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] "
                          "(INDEX | -indexname NAME SEQFILE SEQFILE [...]) ",
                          "Calculates Kr: pairwise distances between genomes.");

  /* options */
  option = gt_option_new_choice("indextype", "specify type of index, one of: "
                                "esa|pck|encseq. Where encseq is an encoded "
                                "sequence and an enhanced suffix array will be "
                                "constructed only in memory.",
                                arguments->indextype, indextypes[2],
                                indextypes);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("indexname", "Basename of encseq to construct.",
                                arguments->indexname, NULL);
  gt_option_parser_add_option(op, option);

  /*-unitfile*/
  option_unitfile =
    gt_option_new_filename("unitfile",
                           "specifies genomic units, "
                           "see below for description.",
                           arguments->unitfile);
  gt_option_parser_add_option(op, option_unitfile);
  arguments->ref_unitfile = gt_option_ref(option_unitfile);

  /* encseq options */
  arguments->loadopts =
    gt_encseq_options_register_loading(op, arguments->indexname);

  gt_option_is_development_option(
                        gt_encseq_options_lossless_option(arguments->loadopts));
  /* esa options */
  arguments->idxopts =
    gt_index_options_register_esa_noout(op);
  gt_option_is_development_option(
                            gt_index_options_spmopt_option(arguments->idxopts));

  /* scan */
  option = gt_option_new_bool("scan", "do not load esa index but scan "
                              "it sequentially.", &arguments->scan, true);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* dev options */
  /* -max_n */
  option = gt_option_new_ulong("max_n", "Number of precalculated values "
                               "for ln(n!) and pmax(x).",
                               &arguments->max_ln_n_fac, 1000UL);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -maxdepth */
  option =  gt_option_new_int("maxdepth", "max depth of .pbi-file, use with "
                              "-indextype pck.",
                              &arguments->user_max_depth, -1);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* thresholds */
  /* divergence error */
  option = gt_option_new_double("thr",
                                "Threshold for difference (du, dl) in "
                                "divergence calculation.\n"
                                "default: 1e-9",
                                &arguments->divergence_threshold,
                                1e-9);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* expected shulen error */
  option = gt_option_new_double("abs_err",
                                "absolute error for expected shulen "
                                "calculation.\n"
                                "default: 1e-5",
                                &arguments->divergence_abs_err,
                                1e-5);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* relative expected shulen error */
  option = gt_option_new_double("rel_err",
                                "relative error for expected shulen "
                                "calculation.\n"
                                "default: 1e-3",
                                &arguments->divergence_rel_err,
                                1e-3);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* M */
  option = gt_option_new_double("M",
                                "threshold for minimum logarithm.\n"
                                "default: DBL_MIN",
                                &arguments->divergence_m,
                                DBL_MIN);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* mail */
  gt_option_parser_set_mail_address(op, "");
  /* doc */
  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  return op;
}

static int gt_genomediff_arguments_check(int rest_argc,
                                         void *tool_arguments,
                                         GtError *err)
{
  GtGenomediffArguments *arguments = tool_arguments;
  bool prepared_index;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  if (rest_argc == 0) {
    gt_error_set(err, "give at least one file (base)name!");
    had_err = -1;
  }
  if (!had_err) {
    if (strcmp("esa", gt_str_get(arguments->indextype)) == 0)
      arguments->with_esa = true;
    else if (strcmp("pck", gt_str_get(arguments->indextype)) == 0)
      arguments->with_pck = true;
  }
  prepared_index = (arguments->with_esa || arguments->with_pck);

  if (!had_err && arguments->user_max_depth != -1 && !arguments->with_pck)
    gt_warning("option -maxdepth does only apply to -indextype pck");

  if (!had_err &&
      prepared_index && gt_encseq_options_mirrored_value(arguments->loadopts))
    gt_warning("option -mirrored is ignored with esa and pck index");

  if (!had_err && prepared_index && rest_argc > 1) {
    gt_error_set(err, "there should be only one basename argument with "
                 "-indextype esa|pck");
    had_err = -1;
  }
  if (rest_argc == 1 && gt_str_length(arguments->indexname) != 0) {
    gt_error_set(err, "Option -indexname is only needed with sequence files, "
                 "if one file is given as argument, this should be an index.");
    had_err = -1;
  }
  if (!had_err && rest_argc > 1 && gt_str_length(arguments->indexname) == 0) {
    gt_error_set(err, "use -indexname for basename of encseq");
    had_err = -1;
  }

  if (!had_err)
    arguments->with_units = gt_option_is_set(arguments->ref_unitfile);

  return had_err;
}

static int gt_genomediff_runner(int argc, const char **argv,
                                int parsed_args, void *tool_arguments,
                                GtError *err)
{
  bool mirrored = false;
  int had_err = 0,
      i;
  GtEncseq              *encseq = NULL;
  GtGenomediffArguments *arguments = tool_arguments;
  GtLogger              *logger;
  GtShuUnitFileInfo     *unit_info = NULL;
  GtTimer               *timer = NULL;

  gt_error_check(err);
  gt_assert(arguments);

  logger = gt_logger_new(arguments->verbose,
                         GT_LOGGER_DEFLT_PREFIX,
                         stdout);
  gt_assert(logger);

  for (i = parsed_args; i < argc; i++) {
    gt_str_array_add_cstr(arguments->filenames, argv[i]);
  }

  if (gt_showtime_enabled()) {
    timer = gt_timer_new_with_progress_description("start");
    gt_timer_start(timer);
    gt_assert(timer);
  }

  if (arguments->with_units) {
    gt_logger_log(logger, "unitfile option set, filename is %s\n",
                  gt_str_get(arguments->unitfile));
  }

  if (timer != NULL)
    gt_timer_show_progress(timer, "start shu search", stdout);

  if (gt_str_array_size(arguments->filenames) > 1UL) {
    GtEncseqEncoder *ee = gt_encseq_encoder_new();
    gt_encseq_encoder_set_timer(ee, timer);
    gt_encseq_encoder_set_logger(ee, logger);
    /* kr only makes sense for dna, so we can check this already with ee */
    gt_encseq_encoder_set_input_dna(ee);
    had_err = gt_encseq_encoder_encode(ee, arguments->filenames,
                                       gt_str_get(arguments->indexname), err);
    gt_encseq_encoder_delete(ee);
  }
  else {
    gt_str_append_str(arguments->indexname,
                      gt_str_array_get_str(arguments->filenames, 0));
    if (arguments->with_esa || arguments->with_pck) {
      GtStr *current_line = gt_str_new();
      FILE *prj_fp;
      const char *buffer;
      char **elements = NULL;

      prj_fp = gt_fa_fopen_with_suffix(gt_str_get(arguments->indexname),
                                       PROJECTFILESUFFIX,"rb",err);
      if (prj_fp == NULL)
        had_err = -1;
      while (!had_err && gt_str_read_next_line(current_line, prj_fp) != EOF) {
        buffer = gt_str_get(current_line);
        if (elements != NULL) {
          gt_free(elements[0]);
          gt_free(elements[1]);
        }
        gt_free(elements);
        elements = gt_cstr_split(buffer, '=');
        gt_log_log("%s", elements[0]);
        if (strcmp("mirrored", elements[0]) == 0) {
          gt_log_log("%s", elements[1]);
          if (strcmp("1", elements[1]) == 0) {
            mirrored = true;
            gt_log_log("sequences are treated as mirrored");
          }
        }
        gt_str_reset(current_line);
      }
      gt_str_delete(current_line);
      if (elements != NULL) {
        gt_free(elements[0]);
        gt_free(elements[1]);
      }
      gt_free(elements);
      gt_fa_xfclose(prj_fp);
    }
  }

  if (!had_err) {
    GtEncseqLoader *el = gt_encseq_loader_new_from_options(arguments->loadopts,
                                                           err);
    if (mirrored)
      gt_encseq_loader_mirror(el);
    encseq =
      gt_encseq_loader_load(el, gt_str_get(arguments->indexname), err);
    gt_encseq_loader_delete(el);
  }
  if (encseq == NULL)
    had_err = -1;
  if (!had_err) {
    unit_info = gt_shu_unit_info_new(encseq);
    if (arguments->with_units)
      had_err = gt_shu_unit_file_info_read(arguments->unitfile, unit_info,
                                           logger, err);
  }

  if (!had_err) {
    uint64_t **shusums = NULL;
    if (arguments->with_esa || arguments->with_pck) {
      shusums = gt_genomediff_shulen_sum(arguments, unit_info,
                                         logger, timer, err);
      if (shusums == NULL)
        had_err = -1;
    }
    else {
      const bool doesa = true;
      GenomediffInfo gd_info;
      Suffixeratoroptions sopts;
      sopts.beverbose = arguments->verbose;
      sopts.indexname = arguments->indexname;
      sopts.db = NULL;
      sopts.encopts = NULL;
      sopts.genomediff = true;
      sopts.inputindex = arguments->indexname;
      sopts.loadopts = arguments->loadopts;
      sopts.showprogress = false;
      sopts.idxopts = arguments->idxopts;

      gt_assert(unit_info != NULL);
      gt_array2dim_calloc(shusums, unit_info->num_of_genomes,
                          unit_info->num_of_genomes);
      gd_info.shulensums = shusums;
      gd_info.unit_info = unit_info;
      had_err = runsuffixerator(doesa, &sopts, &gd_info, logger, err);
    }
    if (!had_err && shusums != NULL) {
      had_err = gt_genomediff_kr_calc(shusums, arguments, unit_info,
                                      arguments->with_pck, logger, timer, err);
      gt_array2dim_delete(shusums);
    }
  }

  if (timer != NULL) {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  gt_logger_delete(logger);
  gt_encseq_delete(encseq);
  gt_shu_unit_info_delete(unit_info);

  return had_err;
}

GtTool* gt_genomediff(void)
{
  return gt_tool_new(gt_genomediff_arguments_new,
                     gt_genomediff_arguments_delete,
                     gt_genomediff_option_parser_new,
                     gt_genomediff_arguments_check,
                     gt_genomediff_runner);
}
genometools-1.5.1/src/tools/gt_genomediff.h000066400000000000000000000017451211610345200207500ustar00rootroot00000000000000/*
  Copyright (c) 2010 Dirk Willrodt 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_GENOMEDIFF_H
#define GT_GENOMEDIFF_H

#include "core/tool_api.h"

/* the genomediff tool */
GtTool* gt_genomediff(void);

#endif
genometools-1.5.1/src/tools/gt_gff3.c000066400000000000000000000273471211610345200174730ustar00rootroot00000000000000/*
  Copyright (c) 2005-2013 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/undef_api.h"
#include "core/versionfunc.h"
#include "extended/add_introns_stream_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_defines.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gff3_parser.h"
#include "extended/gtdatahelp.h"
#include "extended/load_stream.h"
#include "extended/merge_feature_stream_api.h"
#include "extended/sort_stream_api.h"
#include "extended/typecheck_info.h"
#include "tools/gt_gff3.h"

typedef struct {
  bool sort,
       load,
       retainids,
       checkids,
       addids,
       mergefeat,
       addintrons,
       verbose,
       strict,
       tidy,
       show,
       fixboundaries;
  long offset;
  GtStr *offsetfile;
  unsigned long width;
  GtTypecheckInfo *tci;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} GFF3Arguments;

static void* gt_gff3_arguments_new(void)
{
  GFF3Arguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->offsetfile = gt_str_new();
  arguments->tci = gt_typecheck_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_gff3_arguments_delete(void *tool_arguments)
{
  GFF3Arguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_typecheck_info_delete(arguments->tci);
  gt_str_delete(arguments->offsetfile);
  gt_free(arguments);
}

static GtOptionParser* gt_gff3_option_parser_new(void *tool_arguments)
{
  GFF3Arguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *sort_option, *load_option, *strict_option, *tidy_option,
           *mergefeat_option, *addintrons_option, *offset_option,
           *offsetfile_option, *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Parse, possibly "
                            "transform, and output GFF3 files.");

  /* -sort */
  sort_option = gt_option_new_bool("sort", "sort the GFF3 features (memory "
                                   "consumption is proportional to the input "
                                   "file size(s))",
                                   &arguments->sort, false);
  gt_option_parser_add_option(op, sort_option);

  /* -strict */
  strict_option = gt_option_new_bool("strict", "be very strict during GFF3 "
                                     "parsing (stricter than the specification "
                                     "requires)", &arguments->strict, false);
  gt_option_is_development_option(strict_option);
  gt_option_parser_add_option(op, strict_option);

  /* -tidy */
  tidy_option = gt_option_new_bool("tidy", "try to tidy the GFF3 files up "
                                   "during parsing", &arguments->tidy, false);
  gt_option_parser_add_option(op, tidy_option);
  gt_option_exclude(strict_option, tidy_option);

  /* -retainids */
  option = gt_option_new_bool("retainids",
                              "when available, use the original IDs provided "
                              "in the source file\n"
                              "(memory consumption is proportional to the "
                              "input file size(s))", &arguments->retainids,
                              false);
  gt_option_parser_add_option(op, option);

  /* -checkids */
  option = gt_option_new_bool("checkids",
                              "make sure the ID attributes are unique "
                              "within the scope of each GFF3_file, as required "
                              "by GFF3 specification\n"
                              "(memory consumption is proportional to the "
                              "input file size(s))", &arguments->checkids,
                              false);
  gt_option_parser_add_option(op, option);

  /* -addids */
  option = gt_option_new_bool("addids", "add missing \""
                              GT_GFF_SEQUENCE_REGION"\" lines automatically",
                              &arguments->addids, true);
  gt_option_parser_add_option(op, option);

  /* -fixregionboundaries */
  option = gt_option_new_bool("fixregionboundaries", "automatically adjust \""
                              GT_GFF_SEQUENCE_REGION"\" lines to contain all "
                              "their features (memory consumption is "
                              "proportional to the input file size(s))",
                              &arguments->fixboundaries, false);
  gt_option_parser_add_option(op, option);

  /* -mergefeat */
  mergefeat_option = gt_option_new_bool("mergefeat",
                                        "merge adjacent features of the same "
                                        "type", &arguments->mergefeat, false);
  gt_option_is_development_option(mergefeat_option);
  gt_option_imply(mergefeat_option, sort_option);
  gt_option_parser_add_option(op, mergefeat_option);

  /* -load */
  load_option = gt_option_new_bool("load", "load the GFF3 features into memory "
                                   "(requires space proportional to the input "
                                   "file size(s))",
                                   &arguments->load, false);
  gt_option_is_development_option(load_option);
  gt_option_parser_add_option(op, load_option);

  /* -addintrons */
  addintrons_option = gt_option_new_bool("addintrons", "add intron features "
                                         "between existing exon features",
                                         &arguments->addintrons, false);
  gt_option_parser_add_option(op, addintrons_option);

  /* -offset */
  offset_option = gt_option_new_long("offset", "transform all features by the "
                                     "given offset", &arguments->offset,
                                     GT_UNDEF_LONG);
  gt_option_parser_add_option(op, offset_option);

  /* -offsetfile */
  offsetfile_option = gt_option_new_filename("offsetfile", "transform all "
                                             "features by the offsets given in "
                                             "file", arguments->offsetfile);
  gt_option_parser_add_option(op, offsetfile_option);
  gt_option_exclude(offset_option, offsetfile_option);

  /* typecheck options */
  gt_typecheck_info_register_options(arguments->tci, op);

  /* -show */
  option = gt_option_new_bool("show", "show GFF3 output", &arguments->show,
                              true);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* -width */
  option = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  /* set comment function */
  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);

  return op;
}

static int gt_gff3_runner(int argc, const char **argv, int parsed_args,
                          void *tool_arguments, GtError *err)
{
  GFF3Arguments *arguments = tool_arguments;
  GtTypeChecker *type_checker = NULL;
  GtNodeStream *gff3_in_stream,
               *sort_stream = NULL,
               *load_stream = NULL,
               *merge_feature_stream = NULL,
               *add_introns_stream = NULL,
               *gff3_out_stream = NULL,
               *last_stream;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);
  if (arguments->checkids)
    gt_gff3_in_stream_check_id_attributes((GtGFF3InStream*) gff3_in_stream);
  if (!arguments->addids)
    gt_gff3_in_stream_disable_add_ids(gff3_in_stream);

  last_stream = gff3_in_stream;

  /* set different type checker if necessary */
  if (gt_typecheck_info_option_used(arguments->tci)) {
    type_checker = gt_typecheck_info_create_type_checker(arguments->tci, err);
    if (!type_checker)
      had_err = -1;
    if (!had_err)
      gt_gff3_in_stream_set_type_checker(gff3_in_stream, type_checker);
  }

  /* set offset (if necessary) */
  if (!had_err && arguments->offset != GT_UNDEF_LONG)
    gt_gff3_in_stream_set_offset(gff3_in_stream, arguments->offset);

  /* set offsetfile (if necessary) */
  if (!had_err && gt_str_length(arguments->offsetfile)) {
    had_err = gt_gff3_in_stream_set_offsetfile(gff3_in_stream,
                                               arguments->offsetfile, err);
  }

  /* enable strict mode (if necessary) */
  if (!had_err && arguments->strict)
    gt_gff3_in_stream_enable_strict_mode((GtGFF3InStream*) gff3_in_stream);
  /* enable tidy mode (if necessary) */
  if (!had_err && arguments->tidy)
    gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream*) gff3_in_stream);

  if (!had_err && arguments->fixboundaries)
    gt_gff3_in_stream_fix_region_boundaries((GtGFF3InStream*) gff3_in_stream);

  /* create load stream (if necessary) */
  if (!had_err && arguments->load) {
    load_stream = gt_load_stream_new(last_stream);
    last_stream = load_stream;
  }

  /* create sort stream (if necessary) */
  if (!had_err && arguments->sort) {
    sort_stream = gt_sort_stream_new(last_stream);
    last_stream = sort_stream;
  }

  /* create merge feature stream (if necessary) */
  if (!had_err && arguments->mergefeat) {
    gt_assert(sort_stream);
    merge_feature_stream = gt_merge_feature_stream_new(sort_stream);
    last_stream = merge_feature_stream;
  }

  /* create addintrons stream (if necessary) */
  if (!had_err && arguments->addintrons) {
    gt_assert(last_stream);
    add_introns_stream = gt_add_introns_stream_new(last_stream);
    last_stream = add_introns_stream;
  }

  /* create gff3 output stream */
  if (!had_err && arguments->show) {
    gff3_out_stream = gt_gff3_out_stream_new(last_stream, arguments->outfp);
    last_stream = gff3_out_stream;
    gt_gff3_out_stream_set_fasta_width((GtGFF3OutStream*) last_stream,
                                       arguments->width);
    if (arguments->retainids)
      gt_gff3_out_stream_retain_id_attributes((GtGFF3OutStream*) last_stream);
  }

  /* pull the features through the stream and free them afterwards */
  if (!had_err)
    had_err = gt_node_stream_pull(last_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(sort_stream);
  gt_node_stream_delete(load_stream);
  gt_node_stream_delete(merge_feature_stream);
  gt_node_stream_delete(add_introns_stream);
  gt_node_stream_delete(gff3_in_stream);
  gt_type_checker_delete(type_checker);

  return had_err;
}

GtTool* gt_gff3(void)
{
  return gt_tool_new(gt_gff3_arguments_new,
                     gt_gff3_arguments_delete,
                     gt_gff3_option_parser_new,
                     NULL,
                     gt_gff3_runner);
}
genometools-1.5.1/src/tools/gt_gff3.h000066400000000000000000000017251211610345200174700ustar00rootroot00000000000000/*
  Copyright (c) 2005-2008 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_GFF3_H
#define GT_GFF3_H

#include "core/tool_api.h"

/* the GFF3 tool */
GtTool* gt_gff3(void);

#endif
genometools-1.5.1/src/tools/gt_gff3_to_gtf.c000066400000000000000000000060531211610345200210240ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009, 2011 Gordon Gremme 
  Copyright (c) 2007-2008       Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/gtf_out_stream_api.h"
#include "tools/gt_gff3_to_gtf.h"

typedef struct {
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} GFF3ToGTFArguments;

static void* gt_gff3_to_gtf_arguments_new(void)
{
  GFF3ToGTFArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_gff3_to_gtf_arguments_delete(void *tool_arguments)
{
  GFF3ToGTFArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_gff3_to_gtf_option_parser_new(void *tool_arguments)
{
  GFF3ToGTFArguments *arguments = tool_arguments;
  GtOptionParser *op;
  op = gt_option_parser_new("[GFF3_file ...]",
                            "Parse GFF3 file(s) and show them as GTF2.2.");
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);
  return op;
}

static int gt_gff3_to_gtf_runner(int argc, const char **argv, int parsed_args,
                                 void *tool_arguments, GtError *err)
{
  GFF3ToGTFArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream = NULL, *gtf_out_stream = NULL;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);

  /* create a gtf output stream */
  gtf_out_stream = gt_gtf_out_stream_new(gff3_in_stream, arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gtf_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_in_stream);
  gt_node_stream_delete(gtf_out_stream);

  return had_err;
}

GtTool* gt_gff3_to_gtf(void)
{
  return gt_tool_new(gt_gff3_to_gtf_arguments_new,
                     gt_gff3_to_gtf_arguments_delete,
                     gt_gff3_to_gtf_option_parser_new,
                     NULL,
                     gt_gff3_to_gtf_runner);
}
genometools-1.5.1/src/tools/gt_gff3_to_gtf.h000066400000000000000000000017631211610345200210340ustar00rootroot00000000000000/*
  Copyright (c) 2007, 2001 Gordon Gremme 
  Copyright (c) 2007       Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_GFF3_TO_GTF_H
#define GT_GFF3_TO_GTF_H

#include "core/tool_api.h"

/* the GFF3 to GTF tool */
GtTool* gt_gff3_to_gtf(void);

#endif
genometools-1.5.1/src/tools/gt_gff3validator.c000066400000000000000000000075331211610345200213740ustar00rootroot00000000000000/*
  Copyright (c) 2008-2013 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/typecheck_info.h"
#include "tools/gt_gff3validator.h"

typedef struct {
  GtTypecheckInfo *tci;
  bool strict;
} GFF3ValidatorArguments;

static void* gt_gff3validator_arguments_new(void)
{
  GFF3ValidatorArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->tci = gt_typecheck_info_new();
  return arguments;
}

static void gt_gff3validator_arguments_delete(void *tool_arguments)
{
  GFF3ValidatorArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_typecheck_info_delete(arguments->tci);
  gt_free(arguments);
}

static GtOptionParser* gt_gff3validator_option_parser_new(void *tool_arguments)
{
  GFF3ValidatorArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                         "Strictly validate given GFF3 files.");

  /* typecheck options */
  gt_typecheck_info_register_options(arguments->tci, op);

  /* -strict */
  option = gt_option_new_bool("strict", "be very strict during GFF3 parsing "
                              "(stricter than the specification requires)",
                              &arguments->strict, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  return op;
}

static int gt_gff3validator_runner(int argc, const char **argv, int parsed_args,
                                   void *tool_arguments, GtError *err)
{
  GFF3ValidatorArguments *arguments = tool_arguments;
  GtTypeChecker *type_checker = NULL;
  GtNodeStream *gff3_in_stream;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a GFF3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);
  gt_gff3_in_stream_check_id_attributes((GtGFF3InStream*) gff3_in_stream);

  /* set different type checker if necessary */
  if (gt_typecheck_info_option_used(arguments->tci)) {
    type_checker = gt_typecheck_info_create_type_checker(arguments->tci, err);
    if (!type_checker)
      had_err = -1;
    if (!had_err)
      gt_gff3_in_stream_set_type_checker(gff3_in_stream, type_checker);
  }

  /* enable strict mode (if necessary) */
  if (!had_err && arguments->strict)
    gt_gff3_in_stream_enable_strict_mode((GtGFF3InStream*) gff3_in_stream);

  /* pull the features through the stream and free them afterwards */
  if (!had_err)
    had_err = gt_node_stream_pull(gff3_in_stream, err);

  if (!had_err)
    printf("input is valid GFF3\n");

  /* free */
  gt_node_stream_delete(gff3_in_stream);
  gt_type_checker_delete(type_checker);

  return had_err;
}

GtTool* gt_gff3validator(void)
{
  return gt_tool_new(gt_gff3validator_arguments_new,
                  gt_gff3validator_arguments_delete,
                  gt_gff3validator_option_parser_new,
                  NULL,
                  gt_gff3validator_runner);
}
genometools-1.5.1/src/tools/gt_gff3validator.h000066400000000000000000000017601211610345200213750ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_GFF3VALIDATOR_H
#define GT_GFF3VALIDATOR_H

#include "core/tool_api.h"

/* the GFF3 validator tool */
GtTool* gt_gff3validator(void);

#endif
genometools-1.5.1/src/tools/gt_gtf_to_gff3.c000066400000000000000000000067211211610345200210260ustar00rootroot00000000000000/*
  Copyright (c) 2006-2009, 2011 Gordon Gremme 
  Copyright (c) 2006-2008       Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "extended/genome_node.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gtf_in_stream.h"
#include "tools/gt_gtf_to_gff3.h"

typedef struct {
  bool tidy;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} GTFToGFF3Arguments;

static void* gt_gtf_to_gff3_arguments_new(void)
{
  GTFToGFF3Arguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_gtf_to_gff3_arguments_delete(void *tool_arguments)
{
  GTFToGFF3Arguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_gtf_to_gff3_option_parser_new(void *tool_arguments)
{
  GTFToGFF3Arguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[GTF_file]",
                            "Parse GTF2.2 file and convert it to GFF3.");

  /* -tidy */
  option = gt_option_new_bool("tidy", "try to tidy the GTF file up during "
                              "parsing", &arguments->tidy, false);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_max_args(op, 1);

  return op;
}

static int gt_gtf_to_gff3_runner(GT_UNUSED int argc, const char **argv,
                                 int parsed_args, void *tool_arguments,
                                 GtError *err)
{
  GTFToGFF3Arguments *arguments = tool_arguments;
  GtNodeStream *gtf_in_stream = NULL, *gff3_out_stream = NULL;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a GTF input stream */
  gtf_in_stream = gt_gtf_in_stream_new(argv[parsed_args]);
  if (arguments->tidy)
    gt_gtf_in_stream_enable_tidy_mode(gtf_in_stream);

  /* create a GFF3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(gtf_in_stream, arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(gtf_in_stream);

  return had_err;
}

GtTool* gt_gtf_to_gff3(void)
{
  return gt_tool_new(gt_gtf_to_gff3_arguments_new,
                     gt_gtf_to_gff3_arguments_delete,
                     gt_gtf_to_gff3_option_parser_new,
                     NULL,
                     gt_gtf_to_gff3_runner);
}
genometools-1.5.1/src/tools/gt_gtf_to_gff3.h000066400000000000000000000017611211610345200210320ustar00rootroot00000000000000/*
  Copyright (c) 2006-2008 Gordon Gremme 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_GTF_TO_GFF3_H
#define GT_GTF_TO_GFF3_H

#include "core/tool_api.h"

/* the GTF to GFF3 tool */
GtTool* gt_gtf_to_gff3(void);

#endif
genometools-1.5.1/src/tools/gt_guessprot.c000066400000000000000000000043421211610345200206670ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/fileutils_api.h"
#include "core/option_api.h"
#include "core/versionfunc.h"
#include "tools/gt_guessprot.h"

static GtOPrval parse_options(int *parsed_args, int argc, const char **argv,
                              GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  gt_error_check(err);
  op = gt_option_parser_new("filenames",
                         "Guess if sequence in filenames is protein or DNA.");
  gt_option_parser_set_min_args(op, 1U);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

int gt_guessprot(int argc, const char **argv, GtError *err)
{
  int i, parsed_args, retval;
  GtStrArray *filenametab;

  gt_error_check(err);

  switch (parse_options(&parsed_args, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR: return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }

  filenametab = gt_str_array_new();
  for (i=parsed_args; i < argc; i++)
  {
    gt_str_array_add_cstr(filenametab,argv[i]);
  }
  retval = gt_files_guess_if_protein_sequences(filenametab,err);
  gt_str_array_delete(filenametab);
  if (retval < 0)
  {
    return -1;
  }
  if (retval == 1)
  {
    /*@ignore@*/
    exit(EXIT_FAILURE); /* guess it is a protein sequence */
    /*@end@*/

  } else
  {
    return 0;
  }
}
genometools-1.5.1/src/tools/gt_guessprot.h000066400000000000000000000017361211610345200207000ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_GUESSPROT_H
#define GT_GUESSPROT_H

/* the guessprot tool */
int gt_guessprot(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_hop.c000066400000000000000000000466151211610345200174330ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/basename_api.h"
#include "core/ma.h"
#include "core/undef_api.h"
#include "core/seq_iterator_fastq_api.h"
#include "core/unused_api.h"
#include "extended/feature_type.h"
#include "extended/gtdatahelp.h"
#include "extended/hpol_processor.h"
#include "tools/gt_hop.h"

typedef struct {
  GtStr  *encseqinput, *annotation, *map, *outfilename, *atype, *outprefix;
  unsigned long hmin, clenmax, read_hmin, covmin, mapqmin;
  bool verbose, map_is_sam, rchk, stats, allow_partial, allow_multiple,
       aggressive, moderate, conservative, expert, state_of_truth;
  double altmax, refmin;
  GtStrArray *readset;
} GtHopArguments;

static void* gt_hop_arguments_new(void)
{
  GtHopArguments *arguments = gt_malloc(sizeof (*arguments));
  arguments->encseqinput = gt_str_new();
  arguments->annotation = gt_str_new();
  arguments->atype = gt_str_new();
  arguments->map = gt_str_new();
  arguments->outfilename = gt_str_new();
  arguments->outprefix = gt_str_new();
  arguments->readset = gt_str_array_new();
  return arguments;
}

static void gt_hop_arguments_delete(void *tool_arguments)
{
  GtHopArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->encseqinput);
  gt_str_delete(arguments->annotation);
  gt_str_delete(arguments->atype);
  gt_str_delete(arguments->map);
  gt_str_delete(arguments->outfilename);
  gt_str_delete(arguments->outprefix);
  gt_str_array_delete(arguments->readset);
  gt_free(arguments);
}

static GtOptionParser* gt_hop_option_parser_new(void *tool_arguments)
{
  GtHopArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *ann_option, *aggressive_option, *conservative_option,
           *moderate_option, *expert_option, *o_option, *reads_option,
           *stats_option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("- -ref  -map  "
      "-reads  [options...]",
      "Reference-based homopolymer error correction.");

  /* -ref */
  option = gt_option_new_string("ref",
      "reference sequence in GtEncseq format\n"
      "(can be prepared using gt encseq encode)",
      arguments->encseqinput, NULL);
  gt_option_is_mandatory(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* -map */
  option = gt_option_new_string("map",
      "mapping of reads to reference\n"
      "it must be in SAM/BAM format, and sorted by coordinate\n"
      "(can be prepared e.g. using: samtools sort)",
      arguments->map, NULL);
  gt_option_is_mandatory(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* -sam */
  option = gt_option_new_bool("sam",
      "mapping file is SAM\ndefault: BAM",
      &arguments->map_is_sam, false);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* -aggressive */
  aggressive_option = gt_option_new_bool("aggressive",
      "correct as much as possible",
       &arguments->aggressive, false);
  gt_option_hide_default(aggressive_option);
  gt_option_parser_add_option(op, aggressive_option);

  /* -moderate */
  moderate_option = gt_option_new_bool("moderate",
      "mediate between sensitivity and precision",
      &arguments->moderate, false);
  gt_option_hide_default(moderate_option);
  gt_option_exclude(moderate_option, aggressive_option);
  gt_option_parser_add_option(op, moderate_option);

  /* -conservative */
  conservative_option = gt_option_new_bool("conservative",
      "correct only most likely errors",
      &arguments->conservative, false);
  gt_option_hide_default(conservative_option);
  gt_option_exclude(conservative_option, aggressive_option);
  gt_option_exclude(conservative_option, moderate_option);
  gt_option_parser_add_option(op, conservative_option);

  /* -expert */
  expert_option = gt_option_new_bool("expert",
      "manually select correction criteria",
      &arguments->expert, false);
  gt_option_hide_default(expert_option);
  gt_option_exclude(expert_option, aggressive_option);
  gt_option_exclude(expert_option, moderate_option);
  gt_option_exclude(expert_option, conservative_option);
  gt_option_parser_add_option(op, expert_option);

  /* -reads */
  reads_option = gt_option_new_filename_array("reads",
      "uncorrected read file(s) in FastQ format;\n"
      "the corrected reads are output in the currect working directory "
      "in files which are named as the input files, each prepended "
      "by a prefix (see -outprefix option)\n"
      "-reads allows one to output the reads in the same order as in the input "
      "and is mandatory if the SAM contains more than a single primary "
      "alignment for each read (e.g. output of bwasw)\n"
      "see also -o option as an alternative",
      arguments->readset);
  gt_option_parser_add_option(op, reads_option);

  /* -outprefix */
  option = gt_option_new_string("outprefix",
      "prefix for output filenames (corrected reads)"
      "when -reads is specified\n"
      "the prefix is prepended to each input filename",
      arguments->outprefix, "hop_");
  gt_option_imply(option, reads_option);
  gt_option_parser_add_option(op, option);

  /* -o */
  o_option = gt_option_new_string("o", "output file for corrected reads\n"
      "(see also -reads/-outprefix) if -o is used, reads are output "
      "in a single file in the order they are found in the SAM file "
      "(which usually differ from the original order)\n"
      "this will only work if the reads were aligned with a software which "
      "only includes 1 alignment for each read (e.g. bwa)",
      arguments->outfilename, NULL);
  gt_option_exclude(reads_option, o_option);
  gt_option_is_mandatory_either(reads_option, o_option);
  gt_option_parser_add_option(op, o_option);

  /* -hmin */
  option = gt_option_new_ulong_min("hmin",
      "minimal homopolymer length in reference\n"
      "minimal number of consecutive identical symbols on the reference",
      &arguments->hmin, 3UL, 2UL);
  gt_option_is_extended_option(option);
  gt_option_imply(option, expert_option);
  gt_option_parser_add_option(op, option);

  /* -read-hmin */
  option = gt_option_new_ulong_min("read-hmin",
      "minimal homopolymer length in reads",
      &arguments->read_hmin, 2UL, 1UL);
  gt_option_is_extended_option(option);
  gt_option_imply(option, expert_option);
  gt_option_parser_add_option(op, option);

  /* -altmax */
  option = gt_option_new_double_min_max("altmax",
      "max support of alternate homopol. length;\n"
      "e.g. 0.8 means: do not correct any read if homop. length in more than "
      "80\% of the reads has the same value, different from the reference\n"
      "if altmax is set to 1.0 reads are always corrected",
      &arguments->altmax, (double) 0.8, 0.0, (double) 1.0);
  gt_option_is_extended_option(option);
  gt_option_imply(option, expert_option);
  gt_option_parser_add_option(op, option);

  /* -refmin */
  option = gt_option_new_double_min_max("refmin",
      "min support of reference homopol. length;\n"
      "e.g. 0.1 means: do not correct any read if ref. homop. length "
      "is not present in at least 10\% of the reads\n"
      "if refmin is set to 0.0 reads are always corrected",
      &arguments->refmin, (double) 0.1, 0.0, (double) 1.0);
  gt_option_hide_default(option);
  gt_option_is_extended_option(option);
  gt_option_imply(option, expert_option);
  gt_option_parser_add_option(op, option);

  /* -mapqmin */
  option = gt_option_new_ulong("mapqmin",
      "minimal mapping quality",
      &arguments->mapqmin, 21UL);
  gt_option_is_extended_option(option);
  gt_option_imply(option, expert_option);
  gt_option_parser_add_option(op, option);

  /* -covmin */
  option = gt_option_new_ulong_min("covmin",
      "minimal coverage;\n"
      "e.g. 5 means: do not correct any read if coverage "
      "(number of reads mapped over whole homopolymer) "
      "is less than 5\n"
      "if covmin is set to 1 reads are always corrected",
      &arguments->covmin, 1UL, 1UL);
  gt_option_is_extended_option(option);
  gt_option_imply(option, expert_option);
  gt_option_parser_add_option(op, option);

  /* -allow-multiple */
  option = gt_option_new_bool("allow-muliple",
      "allow multiple corrections in a read",
      &arguments->allow_multiple, false);
  gt_option_is_extended_option(option);
  gt_option_imply(option, expert_option);
  gt_option_parser_add_option(op, option);

  /* -clenmax */
  option = gt_option_new_ulong("clenmax", "maximal correction length\n"
      "default: unlimited", &arguments->clenmax, GT_UNDEF_ULONG);
  gt_option_hide_default(option);
  gt_option_is_extended_option(option);
  gt_option_imply(option, expert_option);
  gt_option_parser_add_option(op, option);

  /* -ann */
  ann_option = gt_option_new_string("ann",
      "annotation of reference sequence\n"
      "it must be sorted by coordinates on the reference sequence\n"
      "(this can be e.g. done using: gt gff3 -sort)\n"
      "if -ann is used, corrections will be limited to homopolymers starting"
      "or ending inside the feature type indicated by -ft option"
      "format: sorted GFF3",
      arguments->annotation, NULL);
  gt_option_is_extended_option(ann_option);
  gt_option_parser_add_option(op, ann_option);

  /* -ft */
  option = gt_option_new_string("ft", "feature type to use when -ann option "
      "is specified",
      arguments->atype, gt_ft_CDS);
  gt_option_is_extended_option(option);
  gt_option_imply(option, ann_option);
  gt_option_parser_add_option(op, option);

  /* -stats */
  stats_option = gt_option_new_bool("stats", "output statistics for each "
      "correction position", &arguments->stats, false);
  gt_option_is_development_option(stats_option);
  gt_option_parser_add_option(op, stats_option);

  /* -state-of-truth */
  option = gt_option_new_bool("state-of-truth",
      "similar to -stats in -aggressive "
      "mode, but used to determine the \"state of truth\" set of corrections "
      "for evaluation; currently the only difference is that if multiple hits "
      "are present for a read, they are used all independently for "
      "correction (-reads must be set)",
      &arguments->state_of_truth, false);
  gt_option_is_development_option(option);
  gt_option_exclude(option, stats_option);
  gt_option_exclude(option, aggressive_option);
  gt_option_exclude(option, moderate_option);
  gt_option_exclude(option, conservative_option);
  gt_option_exclude(option, expert_option);
  gt_option_parser_add_option(op, option);

  /* -rchk */
  option = gt_option_new_bool("rchk", "debug option; check that ref region "
      "of aligned segments is compatible with encseq data",
      &arguments->rchk, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -allow-partial */
  option = gt_option_new_bool("allow-partial",
      "allow insertions also if there are less gaps in read homopolymer "
      "than the difference in length with the reference\n"
      "(at most as many symbols as the gaps will be inserted)",
      &arguments->allow_partial, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);

  gt_option_parser_set_min_max_args(op, 0, 0);

  return op;
}

int gt_hop_arguments_check(GT_UNUSED int rest_argc, void *tool_arguments,
    GtError* err)
{
  GtHopArguments *args = (GtHopArguments*) tool_arguments;
  int had_err = 0;

  if (!args->aggressive &&
      !args->moderate &&
      !args->conservative &&
      !args->expert &&
      !args->state_of_truth)
  {
    gt_error_set(err, "Select correction mode: "
        "-aggressive, -moderate, -conservative or -expert");
    had_err = -1;
  }
  else if (args->aggressive || args->state_of_truth)
  {
    args->hmin = 3UL;
    args->read_hmin = 1UL;
    args->altmax = (double) 1.00;
    args->refmin = (double) 0.00;
    args->mapqmin = 0UL;
    args->covmin = 1UL;
    args->clenmax = ULONG_MAX;
    args->allow_multiple = true;
  }
  else if (args->moderate)
  {
    args->hmin = 3UL;
    args->read_hmin = 1UL;
    args->altmax = (double) 0.99;
    args->refmin = (double) 0.00;
    args->mapqmin = 10UL;
    args->covmin = 1UL;
    args->clenmax = ULONG_MAX;
    args->allow_multiple = true;
  }
  else if (args->conservative)
  {
    args->hmin = 3UL;
    args->read_hmin = 2UL;
    args->altmax = (double) 0.80;
    args->refmin = (double) 0.10;
    args->mapqmin = 21UL;
    args->covmin = 1UL;
    args->clenmax = ULONG_MAX;
    args->allow_multiple = false;
  }

  if (gt_str_length(args->outprefix) == 0)
  {
    gt_error_set(err, "outprefix cannot be an empty string");
    had_err = -1;
  }
  return had_err;
}

static int gt_hop_runner(GT_UNUSED int argc, GT_UNUSED const char **argv,
    GT_UNUSED int parsed_args, void *tool_arguments, GtError *err)
{
  GtHopArguments *arguments = tool_arguments;
  GtEncseq *encseq;
  GtEncseqLoader *el;
  GtLogger *v_logger;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);
  v_logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  gt_logger_log(v_logger, "Correction parameters:");
  gt_logger_log(v_logger, "hmin = %lu", arguments->hmin);
  gt_logger_log(v_logger, "read-hmin = %lu", arguments->read_hmin);
  gt_logger_log(v_logger, "altmax = %.2f", arguments->altmax);
  gt_logger_log(v_logger, "refmin = %.2f", arguments->refmin);
  gt_logger_log(v_logger, "mapqmin = %lu", arguments->mapqmin);
  gt_logger_log(v_logger, "covmin = %lu", arguments->covmin);
  if (arguments->clenmax == ULONG_MAX)
    gt_logger_log(v_logger, "clenmax = unlimited");
  else
    gt_logger_log(v_logger, "clenmax = %lu", arguments->clenmax);
  gt_logger_log(v_logger, "allow-multiple = %s", arguments->allow_multiple
      ? "yes" : "no");
  if (gt_str_length(arguments->annotation) > 0)
    gt_logger_log(v_logger, "restrict to %s feature in annotation %s",
        gt_str_get(arguments->atype), gt_str_get(arguments->annotation));
  gt_assert(gt_str_length(arguments->encseqinput) > 0);
  el = gt_encseq_loader_new();
  encseq = gt_encseq_loader_load(el, gt_str_get(arguments->encseqinput), err);
  if (encseq == NULL)
  {
    had_err = -1;
  }
  if (!had_err)
  {
    GtHpolProcessor *hpp;
    GtSeqposClassifier *spc = NULL;
    GtSamfileIterator *sfi = NULL;
    GtSamfileEncseqMapping *sem = NULL;
    GtAlignedSegmentsPile *asp = NULL;
    GtFile *outfile = NULL;
    GtAlphabet *dna = gt_alphabet_new_dna();
    GtSeqIterator **readset_iters = NULL;
    GtStrArray **infiles = NULL;
    GtFile **outfiles = NULL;
    unsigned long nfiles = 0, i;
    hpp = gt_hpol_processor_new(encseq, arguments->hmin);
    if (gt_str_length(arguments->map) > 0)
    {
      if (!arguments->map_is_sam)
        sfi = gt_samfile_iterator_new_bam(gt_str_get(arguments->map), dna, err);
      else
        sfi = gt_samfile_iterator_new_sam(gt_str_get(arguments->map), dna,
            NULL, err);
      if (sfi == NULL)
        had_err = -1;
      sem = gt_samfile_encseq_mapping_new(sfi, encseq, err);
      if (sem == NULL)
        had_err = -1;
      if (!had_err)
      {
        asp = gt_aligned_segments_pile_new(sfi, sem);
        if (!arguments->rchk)
          gt_hpol_processor_enable_segments_hlen_adjustment(hpp, asp,
              arguments->read_hmin, arguments->altmax, arguments->refmin,
              arguments->mapqmin, arguments->covmin, arguments->allow_partial,
              arguments->allow_multiple, arguments->clenmax);
        else
          gt_hpol_processor_enable_aligned_segments_refregionscheck(hpp, asp);
        if (arguments->stats || arguments->state_of_truth)
          gt_hpol_processor_enable_statistics_output(hpp,
              arguments->state_of_truth, NULL);
        if (!had_err && gt_str_length(arguments->outfilename) > 0)
        {
          outfile = gt_file_new(gt_str_get(arguments->outfilename), "w", err);
          if (outfile == NULL)
            had_err = -1;
          else
            gt_hpol_processor_enable_direct_segments_output(hpp, outfile);
        }
        else if (!had_err)
        {
          nfiles = gt_str_array_size(arguments->readset);
          if (!had_err && nfiles > 0)
          {
            GtStr *outfn = gt_str_new();
            infiles = gt_calloc((size_t)nfiles, sizeof (*infiles));
            outfiles = gt_calloc((size_t)nfiles, sizeof (*outfiles));
            readset_iters = gt_malloc(sizeof (*readset_iters) * nfiles);
            for (i = 0; i < nfiles && !had_err; i++)
            {
              char *bn;
              gt_str_set(outfn, gt_str_get(arguments->outprefix));
              infiles[i] = gt_str_array_new();
              gt_str_array_add_cstr(infiles[i],
                  gt_str_array_get(arguments->readset, i));
              bn = gt_basename(gt_str_array_get(arguments->readset, i));
              gt_str_append_cstr(outfn, bn);
              outfiles[i] = gt_file_new(gt_str_get(outfn), "w", err);
              if (outfiles[i] == NULL)
                had_err = -1;
              readset_iters[i] =
                gt_seq_iterator_fastq_new(infiles[i], err);
              if (readset_iters[i] == NULL)
                had_err = -1;
              gt_seq_iterator_fastq_relax_check_of_quality_description(
                  (GtSeqIteratorFastQ*)readset_iters[i]);
              gt_free(bn);
            }
            if (!had_err)
              gt_hpol_processor_enable_sorted_segments_output(hpp, nfiles,
                  readset_iters, outfiles);
            gt_str_delete(outfn);
          }
        }
      }
    }
    if (!had_err && gt_str_length(arguments->annotation) > 0)
    {
      spc = gt_seqpos_classifier_new(gt_str_get(arguments->annotation),
          gt_str_get(arguments->atype));
      gt_hpol_processor_restrict_to_feature_type(hpp, spc);
    }
    if (!had_err)
      had_err = gt_hpol_processor_run(hpp, v_logger, err);
    gt_aligned_segments_pile_delete(asp);
    gt_samfile_iterator_delete(sfi);
    gt_samfile_encseq_mapping_delete(sem);
    gt_seqpos_classifier_delete(spc);
    gt_file_delete(outfile);
    gt_hpol_processor_delete(hpp);
    for (i = 0; i < nfiles; i++)
    {
      gt_assert(infiles != NULL);
      gt_assert(readset_iters != NULL);
      gt_assert(outfiles != NULL);
      gt_str_array_delete(infiles[i]);
      gt_seq_iterator_delete(readset_iters[i]);
      gt_file_delete(outfiles[i]);
    }
    gt_free(infiles);
    gt_free(outfiles);
    gt_free(readset_iters);
    gt_alphabet_delete(dna);
  }
  gt_logger_delete(v_logger);
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(el);
  return had_err;
}

GtTool* gt_hop(void)
{
  return gt_tool_new(gt_hop_arguments_new,
                  gt_hop_arguments_delete,
                  gt_hop_option_parser_new,
                  gt_hop_arguments_check,
                  gt_hop_runner);
}
genometools-1.5.1/src/tools/gt_hop.h000066400000000000000000000017141211610345200174270ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_HOP_H
#define GT_HOP_H

#include "core/tool_api.h"

/* the hop tool */
GtTool* gt_hop(void);

#endif
genometools-1.5.1/src/tools/gt_id_to_md5.c000066400000000000000000000116331211610345200205000ustar00rootroot00000000000000/*
  Copyright (c) 2010-2012 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "extended/add_ids_stream.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gtdatahelp.h"
#include "extended/seqid2file.h"
#include "extended/id_to_md5_stream_api.h"
#include "tools/gt_id_to_md5.h"

typedef struct {
  bool verbose,
       substitute_target_ids;
  GtSeqid2FileInfo *s2fi;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} SeqidsToMD5Arguments;

static void *gt_id_to_md5_arguments_new(void)
{
  SeqidsToMD5Arguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_id_to_md5_arguments_delete(void *tool_arguments)
{
  SeqidsToMD5Arguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_free(arguments);
}

static GtOptionParser* gt_id_to_md5_option_parser_new(void *tool_arguments)
{
  SeqidsToMD5Arguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                            "Change sequence IDs in given GFF3 files to MD5 "
                            "fingerprints of the corresponding sequences.");

  /* -seqfile, -matchdesc, -usedesc and -regionmapping */
  gt_seqid2file_register_options(op, arguments->s2fi);

  /* -subtargetids */
  option = gt_option_new_bool("subtargetids", "substitute the target IDs with "
                              "MD5 sums", &arguments->substitute_target_ids,
                              true);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);

  return op;
}

static int gt_id_to_md5_runner(GT_UNUSED int argc, const char **argv,
                                   int parsed_args, void *tool_arguments,
                                   GtError *err)
{
  GtNodeStream *gff3_in_stream, *id_to_md5_stream = NULL,
               *add_ids_stream = NULL, *gff3_out_stream = NULL;
  SeqidsToMD5Arguments *arguments = tool_arguments;
  GtRegionMapping *region_mapping;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);
  /* add automatically generated sequence IDs later to avoid collisions */
  gt_gff3_in_stream_disable_add_ids(gff3_in_stream);

  /* create region mapping */
  region_mapping = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
  if (!region_mapping)
    had_err = -1;

  if (!had_err) {
    /* create seqid to md5 stream */
    id_to_md5_stream =
      gt_id_to_md5_stream_new(gff3_in_stream, region_mapping,
                              arguments->substitute_target_ids);

    /* create add IDs stream */
    add_ids_stream = gt_add_ids_stream_new(id_to_md5_stream);

    /* create gff3 output stream */
    gff3_out_stream = gt_gff3_out_stream_new(add_ids_stream, arguments->outfp);

    /* pull the features through the stream and free them afterwards */
    had_err = gt_node_stream_pull(gff3_out_stream, err);
  }

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(add_ids_stream);
  gt_node_stream_delete(id_to_md5_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool *gt_id_to_md5(void)
{
  return gt_tool_new(gt_id_to_md5_arguments_new,
                     gt_id_to_md5_arguments_delete,
                     gt_id_to_md5_option_parser_new,
                     NULL,
                     gt_id_to_md5_runner);
}
genometools-1.5.1/src/tools/gt_id_to_md5.h000066400000000000000000000016361211610345200205070ustar00rootroot00000000000000/*
  Copyright (c) 2010 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ID_TO_MD5_H
#define GT_ID_TO_MD5_H

#include "core/tool_api.h"

/* the seqids to MD5s tool */
GtTool* gt_id_to_md5(void);

#endif
genometools-1.5.1/src/tools/gt_idxlocali.c000066400000000000000000000150121211610345200206000ustar00rootroot00000000000000/*
  Copyright (c) 2009 Z. Tang 
  Copyright (c) 2009 Stefan Kurtz 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "core/ma.h"
#include "core/str_array.h"
#include "core/unused_api.h"
#include "core/tool_api.h"
#include "match/idxlocali.h"
#include "tools/gt_idxlocali.h"

static void *gt_idxlocali_arguments_new(void)
{
  return gt_malloc(sizeof (IdxlocaliOptions));
}

static void gt_idxlocali_arguments_delete(void *tool_arguments)
{
  IdxlocaliOptions *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->indexname);
  gt_str_array_delete(arguments->queryfiles);
  gt_option_delete(arguments->refoptionesaindex);
  gt_option_delete(arguments->refoptionpckindex);
  gt_free(arguments);
}

static GtOptionParser *gt_idxlocali_option_parser_new(void *tool_arguments)
{
  IdxlocaliOptions *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionesaindex, *optionpckindex, *optiononline, *optioncmp;

  gt_assert(arguments != NULL);
  arguments->indexname = gt_str_new ();
  arguments->queryfiles = gt_str_array_new ();

  op = gt_option_parser_new
    ("[options] -q query-file-names [-esa|-pck] indexname",
     "Find all local alignments using suffix tree.");

  gt_option_parser_set_mail_address(op, "");
  option = gt_option_new_filename_array("q","Specify files containing the "
                                            "query sequences",
                                        arguments->queryfiles);
  gt_option_parser_add_option (op, option);

  option = gt_option_new_long("match",
                              "Specify match score",
                              &arguments->matchscore, 1L);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_long("mismatch",
                              "Specify mismatch score",
                              &arguments->mismatchscore, -3L);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_long("gapstart",
                              "Specify gap start score",
                              &arguments->gapstart, -5L);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_long("gapextend",
                              "Specify gap extension score",
                              &arguments->gapextend, -2L);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong_min("th",
                                   "Specify the threshold",
                                    &arguments->threshold, 0, 1UL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  optionesaindex = gt_option_new_string("esa",
                                        "Specify index "
                                        "(enhanced suffix array)",
                                        arguments->indexname, NULL);
  gt_option_parser_add_option(op, optionesaindex);
  arguments->refoptionesaindex = gt_option_ref(optionesaindex);

  optionpckindex = gt_option_new_string("pck",
                                        "Specify index (packed index)",
                                        arguments->indexname, NULL);
  gt_option_parser_add_option(op, optionpckindex);
  arguments->refoptionpckindex = gt_option_ref (optionpckindex);
  gt_option_exclude (optionesaindex, optionpckindex);
  gt_option_is_mandatory_either(optionesaindex, optionpckindex);

  optiononline = gt_option_new_bool("online","Perform online searches",
                                    &arguments->doonline, false);
  gt_option_parser_add_option(op, optiononline);
  gt_option_is_development_option(optiononline);

  optioncmp = gt_option_new_bool("cmp","Compare results of offline and online "
                                 "searches",
                                 &arguments->docompare, false);
  gt_option_parser_add_option(op,optioncmp);
  gt_option_exclude(optiononline,optioncmp);

  option = gt_option_new_bool("s",
                              "Show alignments",
                              &arguments->showalignment, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);
  return op;
}

static int gt_idxlocali_arguments_check(GT_UNUSED int rest_argc,
                                        void *tool_arguments,
                                        GT_UNUSED GtError * err)
{
  IdxlocaliOptions *arguments = tool_arguments;

  if (gt_option_is_set(arguments->refoptionesaindex))
  {
    arguments->withesa = true;
  } else
  {
    gt_assert(gt_option_is_set(arguments->refoptionpckindex));
    arguments->withesa = false;
  }
  return 0;
}

static int gt_idxlocali_runner(GT_UNUSED int argc,
                               GT_UNUSED const char **argv,
                               GT_UNUSED int parsed_args,
                               void *tool_arguments,
                               GtError * err)
{
  IdxlocaliOptions *arguments = tool_arguments;
  bool haserr = false;
  unsigned long idx;

  gt_error_check(err);
  gt_assert(arguments != NULL);

  gt_assert(parsed_args == argc);
  printf("# indexname(%s)=%s\n", arguments->withesa ? "esa" : "pck",
         gt_str_get(arguments->indexname));
  for (idx = 0; idx < gt_str_array_size (arguments->queryfiles); idx++)
  {
    printf("# queryfile=%s\n",gt_str_array_get (arguments->queryfiles, idx));
  }
  printf("# threshold=%lu\n", arguments->threshold);
  if (!haserr && gt_runidxlocali (arguments, err) != 0)
  {
    haserr = true;
  }
  return haserr ? -1 : 0;
}

GtTool *gt_idxlocali(void)
{
  return gt_tool_new(gt_idxlocali_arguments_new,
                     gt_idxlocali_arguments_delete,
                     gt_idxlocali_option_parser_new,
                     gt_idxlocali_arguments_check,
                     gt_idxlocali_runner);
}
genometools-1.5.1/src/tools/gt_idxlocali.h000066400000000000000000000017361211610345200206150ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_IDXLOCALI_H
#define GT_IDXLOCALI_H

#include "core/tool_api.h"

/* the idxlocali tool */

GtTool* gt_idxlocali(void);

#endif
genometools-1.5.1/src/tools/gt_interfeat.c000066400000000000000000000101201211610345200206040ustar00rootroot00000000000000/*
  Copyright (c) 2009 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/output_file_api.h"
#include "extended/feature_type.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/inter_feature_stream_api.h"
#include "tools/gt_interfeat.h"

typedef struct {
  GtStr *outside_type,
        *inter_type;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} InterFeatArguments;

static void* gt_interfeat_arguments_new(void)
{
  InterFeatArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->outside_type = gt_str_new();
  arguments->inter_type = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_interfeat_arguments_delete(void *tool_arguments)
{
  InterFeatArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->inter_type);
  gt_str_delete(arguments->outside_type);
  gt_free(arguments);
}

static GtOptionParser* gt_interfeat_option_parser_new(void *tool_arguments)
{
  InterFeatArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Add intermediary "
                            "features between outside features in given "
                            "GFF3 file(s).");

  /* -outside */
  option = gt_option_new_string("outside", "set outside type",
                                arguments->outside_type, gt_ft_exon);
  gt_option_parser_add_option(op, option);

  /* -inter */
  option = gt_option_new_string("inter", "set intermediary type",
                                arguments->inter_type, gt_ft_intron);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  return op;
}

static int gt_interfeat_runner(int argc, const char **argv, int parsed_args,
                          void *tool_arguments, GtError *err)
{
  InterFeatArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream,
               *inter_feature_stream,
               *gff3_out_stream;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);

  /* create intermediary feature stream */
  inter_feature_stream =
    gt_inter_feature_stream_new(gff3_in_stream,
                                gt_str_get(arguments->outside_type),
                                gt_str_get(arguments->inter_type));

  /* create gff3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(inter_feature_stream,
                                           arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(inter_feature_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool* gt_interfeat(void)
{
  return gt_tool_new(gt_interfeat_arguments_new,
                     gt_interfeat_arguments_delete,
                     gt_interfeat_option_parser_new,
                     NULL,
                     gt_interfeat_runner);
}
genometools-1.5.1/src/tools/gt_interfeat.h000066400000000000000000000016441211610345200206240ustar00rootroot00000000000000/*
  Copyright (c) 2009 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_INTERFEAT_H
#define GT_INTERFEAT_H

#include "core/tool_api.h"

/* the intermediary feature tool */
GtTool* gt_interfeat(void);

#endif
genometools-1.5.1/src/tools/gt_magicmatch.c000066400000000000000000000072741211610345200207400ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/bioseq.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/unused_api.h"
#include "extended/gtdatahelp.h"
#include "tools/gt_magicmatch.h"

typedef struct {
  GtStrArray *seqfiles;
  bool translate;
} MagicMatchArguments;

static void* gt_magicmatch_arguments_new(void)
{
  MagicMatchArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->seqfiles = gt_str_array_new();
  return arguments;
}

static void gt_magicmatch_arguments_delete(void *tool_arguments)
{
  MagicMatchArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_array_delete(arguments->seqfiles);
  gt_free(arguments);
}

static GtOptionParser* gt_magicmatch_option_parser_new(void *tool_arguments)
{
  MagicMatchArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *o;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] -f sequence_file [...] -t",
                         "Compute MD5 fingerprints for each sequence given in "
                         "sequence_file(s).");

  /* -f */
  o = gt_option_new_filename_array("f", "fasta file names (at least one file "
                                   "is required)", arguments->seqfiles);
  gt_option_is_mandatory(o);
  gt_option_parser_add_option(op, o);

  /* -t */
  o = gt_option_new_bool("t", "translate the sequences of the files",
                         &arguments->translate, false);
  gt_option_is_mandatory(o);
  gt_option_parser_add_option(op, o);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_min_max_args(op, 0, 0);

  return op;
}

static void translate_sequence_file(GtBioseq *bs)
{
  unsigned long i;
  gt_assert(bs);
  for (i = 0; i < gt_bioseq_number_of_sequences(bs); i++) {
    printf("%s\t%s\n", gt_bioseq_get_md5_fingerprint(bs, i),
                       gt_bioseq_get_description(bs, i));
  }
}

static int gt_magicmatch_runner(GT_UNUSED int argc, GT_UNUSED const char **argv,
                                GT_UNUSED int parsed_args, void *tool_arguments,
                                GtError *err)
{
  MagicMatchArguments *arguments = tool_arguments;
  GtBioseq *bioseq;
  unsigned long i;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (arguments->translate) {
    for (i = 0; !had_err && i < gt_str_array_size(arguments->seqfiles); i++) {
      if (!(bioseq = gt_bioseq_new(gt_str_array_get(arguments->seqfiles, i),
                                   err))) {
        had_err = -1;
      }
      if (!had_err)
        translate_sequence_file(bioseq);
      gt_bioseq_delete(bioseq);
    }
  }

  return had_err;
}

GtTool* gt_magicmatch(void)
{
  return gt_tool_new(gt_magicmatch_arguments_new,
                  gt_magicmatch_arguments_delete,
                  gt_magicmatch_option_parser_new,
                  NULL,
                  gt_magicmatch_runner);
}
genometools-1.5.1/src/tools/gt_magicmatch.h000066400000000000000000000017431211610345200207400ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MAGICMATCH_H
#define GT_MAGICMATCH_H

#include "core/tool_api.h"

/* the MagicMatch tool */
GtTool* gt_magicmatch(void);

#endif
genometools-1.5.1/src/tools/gt_matchtool.c000066400000000000000000000406321211610345200206300ustar00rootroot00000000000000/*
  Copyright (c) 2011      Sascha Kastens 
  Copyright (c) 2011-2012 Sascha Steinbiss 
  Copyright (c) 2011-2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/encseq.h"
#include "core/ma.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "extended/match.h"
#include "extended/match_blast.h"
#include "extended/match_last.h"
#include "extended/match_open.h"
#include "extended/match_sw.h"
#include "extended/match_iterator_api.h"
#include "extended/match_iterator_blast.h"
#include "extended/match_iterator_last.h"
#include "extended/match_iterator_open.h"
#include "extended/match_iterator_sw.h"
#include "tools/gt_matchtool.h"

typedef struct {
  GtStr *type,
        *matchfile,
        *query,
        *db;
  unsigned long minlen,
                maxedist;
} GtMatchtoolArguments;

static void* gt_matchtool_arguments_new(void)
{
  GtMatchtoolArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->type = gt_str_new();
  arguments->matchfile = gt_str_new();
  arguments->query = gt_str_new();
  arguments->db = gt_str_new();
  return arguments;
}

static void gt_matchtool_arguments_delete(void *tool_arguments)
{
  GtMatchtoolArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->type);
  gt_str_delete(arguments->matchfile);
  gt_str_delete(arguments->query);
  gt_str_delete(arguments->db);
  gt_free(arguments);
}

static GtOptionParser* gt_matchtool_option_parser_new(void *tool_arguments)
{
  GtMatchtoolArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionfile, *optiondb, *optionquery, *optionminlen,
           *optionmaxedist;
  gt_assert(arguments);

  static const char *type[] = {
    "OPENMATCH",
    "BLASTOUT",
    "BLASTALLP",
    "BLASTALLN",
    "BLASTP",
    "BLASTN",
    "LAST",
    "SW",
    NULL
  };

  /* init */
  op = gt_option_parser_new("[option ...]",
                            "Parse match formats and/or invoke matching "
                            "tools.");

  /* -type */
  option = gt_option_new_choice("type", "choose match file format:\n"
                                        "OPENMATCH: 'open match' format, e.g. "
                                        "vmatch\n"
                                        "BLASTOUT : tabular BLAST output "
                                        "(-m 8)\n"
                                        "BLASTALLP: invoke BLASTALL with "
                                        "blastp\n"
                                        "BLASTALLN: invoke BLASTALL with "
                                        "blastn\n"
                                        "BLASTP   : invoke blastp\n"
                                        "BLASTN   : invoke blastn\n"
                                        "LAST     : invoke LAST\n"
                                        "SW       : use Smith-Waterman",
                                arguments->type, type[0],
                                type);
  gt_option_parser_add_option(op, option);

  /* -matchfile */
  optionfile = gt_option_new_filename("matchfile", "set input file name",
                                      arguments->matchfile);
  gt_option_parser_add_option(op, optionfile);

  /* -db */
  optiondb = gt_option_new_filename("db", "set database file name",
                                    arguments->db);
  gt_option_parser_add_option(op, optiondb);

  /* -swminlen */
  optionminlen = gt_option_new_ulong("swminlen",
                                     "set minimum required alignment length "
                                     "(for Smith-Waterman alignment)",
                                     &arguments->minlen,
                                     10);
  gt_option_parser_add_option(op, optionminlen);

  /* -swmaxedist */
  optionmaxedist = gt_option_new_ulong("swmaxedist",
                                       "set maximum allowed edit distance "
                                       "(for Smith-Waterman alignment)",
                                       &arguments->maxedist,
                                       0);
  gt_option_parser_add_option(op, optionmaxedist);

  /* -query */
  optionquery = gt_option_new_filename("query", "set query file name",
                                       arguments->query);
  gt_option_parser_add_option(op, optionquery);

  gt_option_imply(optiondb, optionquery);
  gt_option_imply(optionquery, optiondb);

  gt_option_is_mandatory_either(optiondb, optionfile);

  gt_option_parser_set_min_max_args(op, 0, 0);

  return op;
}

static int gt_matchtool_arguments_check(GT_UNUSED int rest_argc,
                                          void *tool_arguments,
                                          GtError *err)
{
  GtMatchtoolArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  if (strcmp(gt_str_get(arguments->type), "OPENMATCH") == 0 ||
      strcmp(gt_str_get(arguments->type), "BLASTOUT") == 0) {
    if (gt_str_length(arguments->matchfile) == 0) {
      gt_error_set(err, "types OPENMATCH and BLASTOUT require the "
                        "option -matchfile");
      had_err = -1;
    }
  }
  if (strcmp(gt_str_get(arguments->type), "BLASTALLP") == 0 ||
      strcmp(gt_str_get(arguments->type), "BLASTALLN") == 0 ||
      strcmp(gt_str_get(arguments->type), "BLASTP") == 0 ||
      strcmp(gt_str_get(arguments->type), "SW") == 0 ||
      strcmp(gt_str_get(arguments->type), "LAST") == 0 ||
      strcmp(gt_str_get(arguments->type), "BLASTN") == 0) {
    if (gt_str_length(arguments->db) == 0
        || gt_str_length(arguments->query) == 0) {
      gt_error_set(err, "types BLASTALLP, BLASTALLN, BLASTP, BLASTN, LAST, SW "
                        "require the options -db and -query");
      had_err = -1;
    }
  }

  return had_err;
}

static int gt_matchtool_runner(GT_UNUSED int argc,
                               GT_UNUSED const char **argv,
                               GT_UNUSED int parsed_args,
                               void *tool_arguments, GtError *err)
{
  GtMatchtoolArguments *arguments = tool_arguments;
  GtMatchIterator *mp = NULL;
  GtMatch *match = NULL;

  int status, had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (strcmp(gt_str_get(arguments->type), "OPENMATCH") == 0) {
    mp = gt_match_iterator_open_new(gt_str_get(arguments->matchfile), err);
    if (!mp)
      had_err = -1;
  } else if (strcmp(gt_str_get(arguments->type), "BLASTOUT") == 0) {
    mp = gt_match_iterator_blast_file_new(gt_str_get(arguments->matchfile),
                                          err);
    if (!mp)
      had_err = -1;
  } else if (strcmp(gt_str_get(arguments->type), "BLASTALLP") == 0) {
    mp = gt_match_iterator_blastallp_process_new(gt_str_get(arguments->query),
                                          gt_str_get(arguments->db),
                                          GT_UNDEF_DOUBLE, GT_UNDEF_INT,
                                          GT_UNDEF_INT, GT_UNDEF_INT,
                                          GT_UNDEF_INT, err);
    if (!mp)
      had_err = -1;
  } else if (strcmp(gt_str_get(arguments->type), "BLASTALLN") == 0) {
    mp = gt_match_iterator_blastalln_process_new(gt_str_get(arguments->query),
                                          gt_str_get(arguments->db),
                                          GT_UNDEF_DOUBLE, false, GT_UNDEF_INT,
                                          GT_UNDEF_INT, GT_UNDEF_INT,
                                          GT_UNDEF_INT, GT_UNDEF_INT,
                                          GT_UNDEF_DOUBLE, GT_UNDEF_INT,
                                          GT_UNDEF_INT, err);
    if (!mp)
      had_err = -1;
  } else if (strcmp(gt_str_get(arguments->type), "BLASTP") == 0) {
    mp = gt_match_iterator_blastp_process_new(gt_str_get(arguments->query),
                                       gt_str_get(arguments->db),
                                       GT_UNDEF_DOUBLE, GT_UNDEF_INT,
                                       GT_UNDEF_INT, GT_UNDEF_INT,
                                       GT_UNDEF_INT, GT_UNDEF_DOUBLE, err);
    if (!mp)
      had_err = -1;
  } else if (strcmp(gt_str_get(arguments->type), "BLASTN") == 0) {
    mp = gt_match_iterator_blastn_process_new(gt_str_get(arguments->query),
                                       gt_str_get(arguments->db),
                                       GT_UNDEF_DOUBLE, false, GT_UNDEF_INT,
                                       GT_UNDEF_INT, GT_UNDEF_INT,
                                       GT_UNDEF_INT, GT_UNDEF_INT,
                                       GT_UNDEF_DOUBLE, GT_UNDEF_INT,
                                       GT_UNDEF_DOUBLE, NULL, err);
    if (!mp)
      had_err = -1;
  } else if (strcmp(gt_str_get(arguments->type), "SW") == 0) {
    GtEncseqLoader *el = NULL;
    GtEncseq *es1 = NULL, *es2 = NULL;
    GtScoreMatrix *sm = NULL;
    GtScoreFunction *sf = NULL;
    el = gt_encseq_loader_new();
    es1 = gt_encseq_loader_load(el, gt_str_get(arguments->db), err);
    if (!es1)
      had_err = -1;
    if (!had_err) {
      es2 = gt_encseq_loader_load(el, gt_str_get(arguments->query), err);
      if (!es2)
        had_err = -1;
    }
    gt_encseq_loader_delete(el);
    if (!had_err) {
      unsigned long i, j;
      GtAlphabet *a;
      gt_assert(es1 && es2);
      a = gt_encseq_alphabet(es1);
      sm = gt_score_matrix_new(a);
      for (i = 0; i < gt_alphabet_num_of_chars(a); i++)
        for (j = 0; j < gt_alphabet_num_of_chars(a); j++)
          gt_score_matrix_set_score(sm, i, j, (i == j) ? 1 : -1);
      sf = gt_score_function_new(sm, -1, -1);
      mp = gt_match_iterator_sw_new(es1, es2, sf, arguments->minlen,
                                    arguments->maxedist, err);
      if (!mp)
        had_err = -1;
    }
    gt_encseq_delete(es1);
    gt_encseq_delete(es2);
    gt_score_function_delete(sf);
  } else if (strcmp(gt_str_get(arguments->type), "LAST") == 0) {
    GtEncseqLoader *el = NULL;
    GtEncseq *es1 = NULL, *es2 = NULL;
    el = gt_encseq_loader_new();
    es1 = gt_encseq_loader_load(el, gt_str_get(arguments->db), err);
    if (!es1)
      had_err = -1;
    if (!had_err) {
      es2 = gt_encseq_loader_load(el, gt_str_get(arguments->query), err);
      if (!es2)
        had_err = -1;
    }
    gt_encseq_loader_delete(el);
    if (!had_err) {
      mp = gt_match_iterator_last_new(es1, es2,
                                      GT_UNDEF_INT,
                                      GT_UNDEF_INT,
                                      GT_UNDEF_INT,
                                      GT_UNDEF_INT,
                                      GT_UNDEF_INT,
                                      GT_UNDEF_INT,
                                      GT_UNDEF_INT,
                                      10,
                                      GT_UNDEF_INT,
                                      GT_UNDEF_INT,
                                      err);
      if (!mp)
        had_err = -1;
    }
    gt_encseq_delete(es1);
    gt_encseq_delete(es2);
  } else {
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }

  if ((!had_err) && (strcmp(gt_str_get(arguments->type), "OPENMATCH") == 0)) {
    fprintf(stdout, "seqid1\tseqid2\tstartpos1\tstartpos2\tendpos1\tendpos2\t"
                    "weight\n");
    while ((status = gt_match_iterator_next(mp, &match, err))
                                                     != GT_MATCHER_STATUS_END) {
      if (status == GT_MATCHER_STATUS_OK) {
        GtMatchOpen *matcho = (GtMatchOpen*) match;
        GtRange range_seq1;
        GtRange range_seq2;
        gt_match_get_range_seq1(match, &range_seq1);
        gt_match_get_range_seq2(match, &range_seq2);
        fprintf(stdout, "%s\t%s\t%lu\t%lu\t%lu\t%lu\t%lu\n",
                gt_match_get_seqid1(match),
                gt_match_get_seqid2(match),
                range_seq1.start,
                range_seq2.start,
                range_seq1.end,
                range_seq2.end,
                gt_match_open_get_weight(matcho));
        gt_match_delete(match);
      } else if (status == GT_MATCHER_STATUS_ERROR) {
        had_err =-1;
        break;
      }
    }
    gt_match_iterator_delete(mp);
  } else if ((!had_err) && (strcmp(gt_str_get(arguments->type), "SW") == 0)) {
    fprintf(stdout, "seqid1\tseqid2\tstartpos1\tstartpos2\tendpos1\tendpos2\t"
                    "alilen\tedist\n");
    while ((status = gt_match_iterator_next(mp, &match, err))
                                                     != GT_MATCHER_STATUS_END) {
      if (status == GT_MATCHER_STATUS_OK) {
        GtMatchSW *matchs = gt_match_sw_cast(match);
        GtRange range_seq1;
        GtRange range_seq2;
        gt_match_get_range_seq1(match, &range_seq1);
        gt_match_get_range_seq2(match, &range_seq2);
        fprintf(stdout, "%s\t%s\t%lu\t%lu\t%lu\t%lu\t%lu\t%lu\n",
                gt_match_get_seqid1(match),
                gt_match_get_seqid2(match),
                range_seq1.start,
                range_seq2.start,
                range_seq1.end,
                range_seq2.end,
                gt_match_sw_get_alignment_length(matchs),
                gt_match_sw_get_edist(matchs));
        gt_match_delete(match);
      } else if (status == GT_MATCHER_STATUS_ERROR) {
        had_err =-1;
        break;
      }
    }
    gt_match_iterator_delete(mp);
  } else if ((!had_err) && (strcmp(gt_str_get(arguments->type), "LAST") == 0)) {
    fprintf(stdout, "seqid1\tseqid2\tstartpos1\tstartpos2\tendpos1\tendpos2\t"
                    "score\n");
    while ((status = gt_match_iterator_next(mp, &match, err))
                                                     != GT_MATCHER_STATUS_END) {
      if (status == GT_MATCHER_STATUS_OK) {
        GtMatchLAST *matchl = gt_match_last_cast(match);
        GtRange range_seq1;
        GtRange range_seq2;
        gt_match_get_range_seq1(match, &range_seq1);
        gt_match_get_range_seq2(match, &range_seq2);
        fprintf(stdout, "%lu\t%lu\t%lu\t%lu\t%lu\t%lu\t%lu\n",
                gt_match_last_get_seqno1(matchl),
                gt_match_last_get_seqno2(matchl),
                range_seq1.start,
                range_seq2.start,
                range_seq1.end,
                range_seq2.end,
                gt_match_last_get_score(matchl));
        gt_match_delete(match);
      } else if (status == GT_MATCHER_STATUS_ERROR) {
        had_err =-1;
        break;
      }
    }
    gt_match_iterator_delete(mp);
  } else if (!had_err) {
    fprintf(stdout, "query\tdbname2\tq.startpos\td.startpos\tq.endpos\t"
                    "d.endpos\tbit score\tevalue\tali length\n");
    while ((status = gt_match_iterator_next(mp, &match, err)) !=
                                          GT_MATCHER_STATUS_END) {
      if (status == GT_MATCHER_STATUS_OK) {
        GtMatchBlast *matchb = (GtMatchBlast*) match;
        GtRange range_seq1;
        GtRange range_seq2;
        gt_match_get_range_seq1(match, &range_seq1);
        gt_match_get_range_seq2(match, &range_seq2);
        fprintf(stdout, "%s\t%s\t%lu\t%lu\t%lu\t%lu\t%.3f\t%Lg\t%lu\n",
                gt_match_get_seqid1(match),
                gt_match_get_seqid2(match),
                range_seq1.start,
                range_seq2.start,
                range_seq1.end,
                range_seq2.end,
                gt_match_blast_get_bitscore(matchb),
                gt_match_blast_get_evalue(matchb),
                gt_match_blast_get_align_length(matchb));
        gt_match_delete(match);
      } else if (status == GT_MATCHER_STATUS_ERROR) {
        had_err =-1;
        break;
      }
    }
    gt_match_iterator_delete(mp);
  }

  return had_err;
}

GtTool* gt_matchtool(void)
{
  return gt_tool_new(gt_matchtool_arguments_new,
                     gt_matchtool_arguments_delete,
                     gt_matchtool_option_parser_new,
                     gt_matchtool_arguments_check,
                     gt_matchtool_runner);
}
genometools-1.5.1/src/tools/gt_matchtool.h000066400000000000000000000017541211610345200206370ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Kastens 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MATCHTOOL_H
#define GT_MATCHTOOL_H

#include "core/tool_api.h"

/* the matchtool tool */
GtTool* gt_matchtool(void);

#endif
genometools-1.5.1/src/tools/gt_matstat.c000066400000000000000000000354651211610345200203230ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/defined-types.h"
#include "core/error.h"
#include "core/option_api.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "match/eis-voiditf.h"
#include "match/esa-map.h"
#include "match/fmindex.h"
#include "match/greedyfwdmat.h"
#include "match/optionargmode.h"
#include "match/sarr-def.h"
#include "match/stamp.h"
#include "tools/gt_matstat.h"
#include "tools/gt_uniquesub.h"
#include "match/esa-minunique.h"

#include "match/fmi-fwduni.pr"
#include "match/fmi-map.pr"

#define SHOWSEQUENCE   1U
#define SHOWQUERYPOS   (SHOWSEQUENCE << 1)
#define SHOWSUBJECTPOS (SHOWSEQUENCE << 2)

typedef enum
{
  Fmindextype,
  Esaindextype,
  Packedindextype
} Indextype;

typedef struct
{
  Definedunsignedlong minlength,
                      maxlength;
  unsigned int showmode;
  bool verifywitnesspos;
  GtStr *indexname;
  GtStrArray *queryfilenames;
  Indextype indextype;
} Gfmsubcallinfo;

static GtOPrval parsegfmsub(bool doms,
                            Gfmsubcallinfo *gfmsubcallinfo,
                            int argc,
                            const char **argv,
                            GtError *err)
{
  GtOptionParser *op;
  GtOption *optionmin, *optionmax, *optionoutput, *optionfmindex,
         *optionesaindex, *optionpckindex, *optionquery, *optionverify;
  GtOPrval oprval;
  GtStrArray *flagsoutputoption;
  int parsed_args;
  const Optionargmodedesc msgfmsubmodedesctable[] =
  {
    {"sequence","matching sequence",SHOWSEQUENCE},
    {"querypos","position in query sequence",SHOWQUERYPOS},
    {"subjectpos","position in subject sequence",SHOWSUBJECTPOS}
  };
  const Optionargmodedesc gfmsubmodedesctable[] =
  {
    {"sequence","matching sequence",SHOWSEQUENCE},
    {"querypos","position in query sequence",SHOWQUERYPOS}
  };

  gt_error_check(err);
  gfmsubcallinfo->minlength.defined = false;
  gfmsubcallinfo->maxlength.defined = false;
  gfmsubcallinfo->showmode = 0;
  gfmsubcallinfo->indexname = gt_str_new();
  gfmsubcallinfo->queryfilenames = gt_str_array_new();
  flagsoutputoption = gt_str_array_new();

  op = gt_option_parser_new("[options ...] -query queryfile [...]",
                         doms
                         ? "Compute matching statistics."
                         : "Compute length of minumum unique prefixes."
                         );
  gt_option_parser_set_mail_address(op,"");

  optionfmindex = gt_option_new_string("fmi", "specify fmindex",
                                    gfmsubcallinfo->indexname,NULL);
  gt_option_parser_add_option(op, optionfmindex);

  optionesaindex = gt_option_new_string("esa", "specify suffix array",
                                     gfmsubcallinfo->indexname,NULL);
  gt_option_parser_add_option(op, optionesaindex);

  optionpckindex = gt_option_new_string("pck", "specify packed index",
                                     gfmsubcallinfo->indexname,NULL);
  gt_option_parser_add_option(op, optionpckindex);

  gt_option_exclude(optionfmindex,optionesaindex);
  gt_option_exclude(optionpckindex,optionesaindex);
  gt_option_exclude(optionpckindex,optionfmindex);

  optionquery = gt_option_new_filename_array("query", "specify queryfiles",
                                             gfmsubcallinfo->queryfilenames);
  gt_option_is_mandatory(optionquery);
  gt_option_parser_add_option(op, optionquery);

  optionmin = gt_option_new_ulong_min("min",
                                   "only output length "
                                   "if >= given minimum length",
                                   &gfmsubcallinfo->minlength.
                                          valueunsignedlong,
                                   0,(unsigned long) 1);
  gt_option_parser_add_option(op, optionmin);

  optionmax = gt_option_new_ulong_min("max",
                                   "only output length "
                                   "if <= given maximum length",
                                   &gfmsubcallinfo->maxlength.
                                          valueunsignedlong,
                                   0,(unsigned long) 1);
  gt_option_parser_add_option(op, optionmax);

  optionoutput = gt_option_new_string_array("output",
                   doms
                     ? "set output flags (sequence, querypos, subjectpos)"
                     : "set output flags (sequence, querypos)",
                   flagsoutputoption);
  gt_option_parser_add_option(op, optionoutput);

  if (doms)
  {
    optionverify = gt_option_new_bool("verify","verify witness positions",
                                   &gfmsubcallinfo->verifywitnesspos,
                                   false);
    gt_option_is_development_option(optionverify);
    gt_option_parser_add_option(op, optionverify);
  } else
  {
    gfmsubcallinfo->verifywitnesspos = false;
  }

  gt_option_parser_refer_to_manual(op);
  oprval = gt_option_parser_parse(op, &parsed_args, argc, argv,
                               gt_versionfunc,err);

  if (oprval == GT_OPTION_PARSER_OK)
  {
    if (gt_option_is_set(optionfmindex))
    {
      gfmsubcallinfo->indextype = Fmindextype;
    } else
    {
      if (gt_option_is_set(optionesaindex))
      {
        gfmsubcallinfo->indextype = Esaindextype;
      } else
      {
        if (gt_option_is_set(optionpckindex))
        {
          gfmsubcallinfo->indextype = Packedindextype;
        } else
        {
          gt_error_set(err,"one of the options -esa, -pck must be used");
          oprval = GT_OPTION_PARSER_ERROR;
        }
      }
    }
    if (oprval != GT_OPTION_PARSER_ERROR)
    {
      if (gt_option_is_set(optionmin))
      {
         gfmsubcallinfo->minlength.defined = true;
      }
      if (gt_option_is_set(optionmax))
      {
         gfmsubcallinfo->maxlength.defined = true;
      }
      if (!gt_option_is_set(optionmin) && !gt_option_is_set(optionmax))
      {
        gt_error_set(err,"one of the options -min or -max must be set");
        oprval = GT_OPTION_PARSER_ERROR;
      }
    }
    if (oprval != GT_OPTION_PARSER_ERROR)
    {
      if (gfmsubcallinfo->minlength.defined &&
          gfmsubcallinfo->maxlength.defined)
      {
        if (gfmsubcallinfo->maxlength.valueunsignedlong <
            gfmsubcallinfo->minlength.valueunsignedlong)
        {
          gt_error_set(err,"minvalue must be smaller or equal than maxvalue");
          oprval = GT_OPTION_PARSER_ERROR;
        }
      }
    }
    if (oprval != GT_OPTION_PARSER_ERROR && gt_option_is_set(optionoutput))
    {
      if (gt_str_array_size(flagsoutputoption) == 0)
      {
        gt_error_set(err,"missing arguments to option -output");
        oprval = GT_OPTION_PARSER_ERROR;
      } else
      {
        unsigned long i;

        for (i=0; ishowmode,
                                 "-output",
                                 gt_str_array_get(flagsoutputoption,i),
                                 err) != 0)
            {
              oprval = GT_OPTION_PARSER_ERROR;
              break;
            }
          } else
          {
            if (gt_optionargaddbitmask(gfmsubmodedesctable,
                                    sizeof (gfmsubmodedesctable)/
                                    sizeof (gfmsubmodedesctable[0]),
                                    &gfmsubcallinfo->showmode,
                                    "-output",
                                    gt_str_array_get(flagsoutputoption,i),
                                    err) != 0)
            {
              oprval = GT_OPTION_PARSER_ERROR;
              break;
            }
          }
        }
      }
    }
  }
  gt_str_array_delete(flagsoutputoption);
  gt_option_parser_delete(op);
  if (oprval == GT_OPTION_PARSER_OK && parsed_args != argc)
  {
    gt_error_set(err,"superfluous program parameters");
    oprval = GT_OPTION_PARSER_ERROR;
  }
  return oprval;
}

static bool dotestsequence(bool doms,const Gfmsubcallinfo *gfmsubcallinfo)
{
  if (gfmsubcallinfo->indextype == Packedindextype &&
      gfmsubcallinfo->verifywitnesspos &&
      doms)
  {
    return true;
  }
  return false;
}

static int gt_greedyfwdmat(bool doms,int argc, const char **argv,GtError *err)
{
  Gfmsubcallinfo gfmsubcallinfo;
  Fmindex fmindex;
  Suffixarray suffixarray;
  void *packedindex = NULL;
  GtLogger *logger = NULL;
  bool haserr = false;
  const GtAlphabet *alphabet = NULL;
#ifdef WITHBCKTAB
  unsigned int prefixlength = 0;
#endif
  unsigned long totallength;
  bool gt_mapfmindexfail = false;

  gt_error_check(err);
  switch (parsegfmsub(doms,&gfmsubcallinfo, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR:
      gt_str_delete(gfmsubcallinfo.indexname);
      gt_str_array_delete(gfmsubcallinfo.queryfilenames);
      return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT:
      gt_str_delete(gfmsubcallinfo.indexname);
      gt_str_array_delete(gfmsubcallinfo.queryfilenames);
      return 0;
  }
  logger = gt_logger_new(false, GT_LOGGER_DEFLT_PREFIX, stdout);
  if (gfmsubcallinfo.indextype == Fmindextype)
  {
    if (gt_mapfmindex(&fmindex,gt_str_get(gfmsubcallinfo.indexname),
                      logger, err) != 0)
    {
      haserr = true;
      gt_mapfmindexfail = true;
    } else
    {
      alphabet = fmindex.alphabet;
    }
    totallength = fmindex.bwtlength-1;
  } else
  {
    unsigned int mappedbits;

    if (gfmsubcallinfo.indextype == Esaindextype)
    {
      mappedbits = SARR_ESQTAB | SARR_SUFTAB
#undef WITHBCKTAB
#ifdef WITHBCKTAB
                   | SARR_BCKTAB
#endif
                   ;
    } else
    {
      if (dotestsequence(doms,&gfmsubcallinfo))
      {
        mappedbits = SARR_ESQTAB;
      } else
      {
        mappedbits = 0;
      }
    }
    if (gt_mapsuffixarray(&suffixarray,
                       mappedbits,
                       gt_str_get(gfmsubcallinfo.indexname),
                       logger,
                       err) != 0)
    {
      haserr = true;
      totallength = 0;
    } else
    {
      alphabet = gt_encseq_alphabet(suffixarray.encseq);
#ifdef WITHBCKTAB
      prefixlength = suffixarray.prefixlength;
#endif
      totallength = gt_encseq_total_length(suffixarray.encseq);
    }
    if (!haserr)
    {
      if (gfmsubcallinfo.indextype == Packedindextype)
      {
        packedindex =
          gt_loadvoidBWTSeqForSA(gt_str_get(gfmsubcallinfo.indexname),
                                 false,
                                 err);
        if (packedindex == NULL)
        {
          haserr = true;
        }
      }
    }
  }
  if (!haserr)
  {
    const void *theindex;
    Greedygmatchforwardfunction gmatchforwardfunction;

    if (gfmsubcallinfo.indextype == Fmindextype)
    {
      theindex = (const void *) &fmindex;
      if (doms)
      {
        gmatchforwardfunction = gt_skfmmstats;
      } else
      {
        gmatchforwardfunction = gt_skfmuniqueforward;
      }
    } else
    {
      if (gfmsubcallinfo.indextype == Esaindextype)
      {
        theindex = (const void *) &suffixarray;
        if (doms)
        {
          gmatchforwardfunction = gt_suffixarraymstats;
        } else
        {
          gmatchforwardfunction = gt_suffixarrayuniqueforward;
        }
      } else
      {
        gt_assert(gfmsubcallinfo.indextype == Packedindextype);
        theindex = (const void *) packedindex;
        if (doms)
        {
          gmatchforwardfunction = gt_voidpackedindexmstatsforward;
        } else
        {
          gmatchforwardfunction = gt_voidpackedindexuniqueforward;
        }
      }
    }
    if (!haserr)
    {
#ifdef WITHBCKTAB
      if (prefixlength > 0 &&
          gfmsubcallinfo.indextype == Esaindextype &&
          runsubstringiteration(gmatchforwardfunction,
                                theindex,
                                totallength,
                                suffixarray.bcktab,
                                suffixarray.countspecialcodes,
                                alphabet,
                                prefixlength,
                                gfmsubcallinfo.queryfilenames,
                                err) != 0)

      {
        haserr = true;
      }
#endif
      if (!haserr &&
          gt_findsubquerygmatchforward(dotestsequence(doms,&gfmsubcallinfo)
                                      ? suffixarray.encseq
                                      : NULL,
                                      theindex,
                                      totallength,
                                      gmatchforwardfunction,
                                      alphabet,
                                      gfmsubcallinfo.queryfilenames,
                                      gfmsubcallinfo.minlength,
                                      gfmsubcallinfo.maxlength,
                                      (gfmsubcallinfo.showmode & SHOWSEQUENCE)
                                             ? true : false,
                                      (gfmsubcallinfo.showmode & SHOWQUERYPOS)
                                             ? true : false,
                                      (gfmsubcallinfo.showmode & SHOWSUBJECTPOS)
                                             ? true : false,
                                      err) != 0)
      {
        haserr = true;
      }
    }
  }
  if (gfmsubcallinfo.indextype == Fmindextype)
  {
    if (!gt_mapfmindexfail)
    {
      gt_freefmindex(&fmindex);
    }
  } else
  {
    if (gfmsubcallinfo.indextype == Packedindextype && packedindex != NULL)
    {
      gt_deletevoidBWTSeq(packedindex);
    }
    gt_freesuffixarray(&suffixarray);
  }
  gt_logger_delete(logger);
  gt_str_delete(gfmsubcallinfo.indexname);
  gt_str_array_delete(gfmsubcallinfo.queryfilenames);
  return haserr ? -1 : 0;
}

int gt_uniquesub(int argc, const char **argv, GtError *err)
{
  return gt_greedyfwdmat(false,argc, argv, err);
}

int gt_matstat(int argc, const char **argv, GtError *err)
{
  return gt_greedyfwdmat(true,argc, argv, err);
}
genometools-1.5.1/src/tools/gt_matstat.h000066400000000000000000000017261211610345200203210ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MATSTAT_H
#define GT_MATSTAT_H

/* the matstat tool */
int gt_matstat(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_maxpairs.c000066400000000000000000000601311211610345200204560ustar00rootroot00000000000000/*
  Copyright (c) 2007-2013 Stefan Kurtz 
  Copyright (c) 2007-2013 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/error_api.h"
#include "core/str_api.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "core/unused_api.h"
#include "core/option_api.h"
#include "core/tool_api.h"
#include "core/versionfunc.h"
#include "core/format64.h"
#include "match/esa-seqread.h"
#include "match/esa-mmsearch.h"
#include "match/esa-maxpairs.h"
#include "match/test-maxpairs.pr"
#include "match/querymatch.h"
#include "match/greedyedist.h"
#include "match/xdrop.h"
#include "tools/gt_maxpairs.h"

typedef struct
{
  unsigned int userdefinedleastlength;
  unsigned long samples;
  bool scanfile, beverbose, forward, reverse, searchspm, extendseed;
  GtStr *indexname;
  GtStrArray *queryfiles;
  GtOption *refforwardoption;
} Maxpairsoptions;

static int gt_simpleexactselfmatchoutput(void *info,
                                         const GtEncseq *encseq,
                                         unsigned long len,
                                         unsigned long pos1,
                                         unsigned long pos2,
                                         GT_UNUSED GtError *err)
{
  unsigned long queryseqnum, seqstartpos, seqlength;
  GtQuerymatch *querymatch = (GtQuerymatch *) info;

  if (pos1 > pos2)
  {
    unsigned long tmp = pos1;
    pos1 = pos2;
    pos2 = tmp;
  }
  queryseqnum = gt_encseq_seqnum(encseq,pos2);
  seqstartpos = gt_encseq_seqstartpos(encseq, queryseqnum);
  seqlength = gt_encseq_seqlength(encseq, queryseqnum);
  gt_assert(pos2 >= seqstartpos);
  gt_querymatch_fill(querymatch,
                     len,
                     pos1,
                     GT_READMODE_FORWARD,
                     false,
                     0,
                     0,
                     true,
                     (uint64_t) queryseqnum,
                     len,
                     pos2 - seqstartpos);
  return gt_querymatch_output(info, encseq, querymatch, NULL, seqlength, err);
}

typedef struct
{
  GtQuerymatch *querymatchspaceptr;
  GtXdropArbitraryscores arbitscores;
  GtXdropresources *res;
  GtFrontResource *frontresource;
  GtXdropbest best_left;
  GtXdropbest best_right;
  GtXdropscore belowscore;
  GtSeqabstract *useq, *vseq;
  const GtUchar *query_sequence;
  unsigned long query_totallength;
} GtXdropmatchinfo;

static int gt_simplexdropselfmatchoutput(void *info,
                                         const GtEncseq *encseq,
                                         unsigned long len,
                                         unsigned long pos1,
                                         unsigned long pos2,
                                         GtError *err)
{
  GtXdropmatchinfo *xdropmatchinfo = (GtXdropmatchinfo *) info;
  GtXdropscore score;
  unsigned long dbseqnum, dbseqstartpos, dbseqlength, dbstart, dblen,
                querystart, queryseqnum, querylen, queryseqlength,
                queryseqstartpos;
  const unsigned long dbtotallength = gt_encseq_total_length(encseq);

  if (pos1 > pos2)
  {
    unsigned long tmp = pos1;
    pos1 = pos2;
    pos2 = tmp;
  }
  dbseqnum = gt_encseq_seqnum(encseq,pos1),
  dbseqstartpos = gt_encseq_seqstartpos(encseq,dbseqnum),
  dbseqlength = gt_encseq_seqlength(encseq,dbseqnum);

  if (pos2 < dbseqstartpos + dbseqlength)
  {
    queryseqnum = dbseqnum;
    queryseqstartpos = dbseqstartpos;
    queryseqlength = dbseqlength;
  } else
  {
    queryseqnum = gt_encseq_seqnum(encseq,pos2);
    gt_assert(dbseqnum < queryseqnum);
    queryseqstartpos = gt_encseq_seqstartpos(encseq,queryseqnum);
    queryseqlength = gt_encseq_seqlength(encseq,queryseqnum);
  }
  if (pos1 > 0 && pos2 > 0)
  {
    gt_assert(pos1 >= dbseqstartpos && pos2 >= queryseqstartpos);
    gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,encseq,
                                 pos1 - dbseqstartpos,0);
    gt_seqabstract_reinit_encseq(xdropmatchinfo->vseq,encseq,
                                 pos2 - queryseqstartpos,0);
    gt_evalxdroparbitscoresextend(false,
                                  &xdropmatchinfo->best_left,
                                  xdropmatchinfo->res,
                                  xdropmatchinfo->useq,
                                  xdropmatchinfo->vseq,
                                  pos1,
                                  pos2,
                                  xdropmatchinfo->belowscore);
  } else
  {
    xdropmatchinfo->best_left.ivalue = 0;
    xdropmatchinfo->best_left.jvalue = 0;
    xdropmatchinfo->best_left.score = 0;
  }
  if (pos1 + len < dbtotallength && pos2 + len < dbtotallength)
  {
    const unsigned long seqend1 = dbseqstartpos + dbseqlength;
    const unsigned long seqend2 = queryseqstartpos + queryseqlength;

    gt_assert(seqend1 >= pos1 + len && seqend2 >= pos2 + len);
    gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,
                                 encseq,seqend1 - (pos1 + len),0);
    gt_seqabstract_reinit_encseq(xdropmatchinfo->vseq,
                                 encseq,seqend2 - (pos2 + len),0);
    gt_evalxdroparbitscoresextend(true,
                                  &xdropmatchinfo->best_right,
                                  xdropmatchinfo->res,
                                  xdropmatchinfo->useq,
                                  xdropmatchinfo->vseq,
                                  pos1 + len,
                                  pos2 + len,
                                  xdropmatchinfo->belowscore);
  } else
  {
    xdropmatchinfo->best_right.ivalue = 0;
    xdropmatchinfo->best_right.jvalue = 0;
    xdropmatchinfo->best_right.score = 0;
  }
  gt_assert(pos1 >= (unsigned long) xdropmatchinfo->best_left.ivalue &&
            pos2 >= (unsigned long) xdropmatchinfo->best_left.jvalue);
  querystart = pos2 - xdropmatchinfo->best_left.jvalue;
  gt_assert(querystart >= queryseqstartpos);
  dblen = len + xdropmatchinfo->best_left.ivalue
              + xdropmatchinfo->best_right.ivalue;
  dbstart = pos1 - xdropmatchinfo->best_left.ivalue;
  querylen = len + xdropmatchinfo->best_left.jvalue
                 + xdropmatchinfo->best_right.jvalue,
  score = (GtXdropscore) len * xdropmatchinfo->arbitscores.mat +
          xdropmatchinfo->best_left.score +
          xdropmatchinfo->best_right.score;
  gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,
                               encseq,
                               dblen,
                               dbstart);
  gt_seqabstract_reinit_encseq(xdropmatchinfo->vseq,
                               encseq,
                               querylen,
                               querystart);
  gt_querymatch_fill(xdropmatchinfo->querymatchspaceptr,
                     dblen,
                     dbstart,
                     GT_READMODE_FORWARD,
                     false,
                     score,
                     greedyunitedist(xdropmatchinfo->frontresource,
                                     xdropmatchinfo->useq,xdropmatchinfo->vseq),
                     true,
                     (uint64_t) queryseqnum,
                     querylen,
                     querystart - queryseqstartpos);
  return gt_querymatch_output(info, encseq, xdropmatchinfo->querymatchspaceptr,
                              NULL, gt_encseq_seqlength(encseq, queryseqnum),
                              err);
}

static int gt_processxdropquerymatches(void *info,
                                       const GtEncseq *encseq,
                                       const GtQuerymatch *querymatch,
                                       const GtUchar *query,
                                       unsigned long query_totallength,
                                       GtError *err)
{
  GtXdropmatchinfo *xdropmatchinfo = (GtXdropmatchinfo *) info;
  GtXdropscore score;
  unsigned long querystart, dblen, dbstart, querylen;
  unsigned long pos1 = gt_querymatch_dbstart(querymatch);
  unsigned long pos2 = gt_querymatch_querystart(querymatch);
  unsigned long len = gt_querymatch_querylen(querymatch);
  const unsigned long dbtotallength = gt_encseq_total_length(encseq);
  uint64_t queryseqnum;
  unsigned long dbseqnum, dbseqstartpos, dbseqlength;

  dbseqnum = gt_encseq_seqnum(encseq,pos1);
  dbseqstartpos = gt_encseq_seqstartpos(encseq,dbseqnum);
  dbseqlength = gt_encseq_seqlength(encseq,dbseqnum);
  if (pos1 > 0 && pos2 > 0)
  {
    gt_assert(dbseqstartpos < pos1);
    gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,encseq,
                                 pos1 - dbseqstartpos,0);
    gt_seqabstract_reinit_ptr(xdropmatchinfo->vseq,query,pos2,0);
    gt_evalxdroparbitscoresextend(false,
                                  &xdropmatchinfo->best_left,
                                  xdropmatchinfo->res,
                                  xdropmatchinfo->useq,
                                  xdropmatchinfo->vseq,
                                  pos1,
                                  pos2,
                                  xdropmatchinfo->belowscore);
  } else
  {
    xdropmatchinfo->best_left.ivalue = 0;
    xdropmatchinfo->best_left.jvalue = 0;
    xdropmatchinfo->best_left.score = 0;
  }
  if (pos1 + len < dbtotallength && pos2 + len < query_totallength)
  {
    gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,
                                 encseq,dbseqstartpos + dbseqlength -
                                        (pos1 + len),0);
    gt_seqabstract_reinit_ptr(xdropmatchinfo->vseq,
                              query,query_totallength - (pos2 + len),0);
    gt_evalxdroparbitscoresextend(true,
                                  &xdropmatchinfo->best_right,
                                  xdropmatchinfo->res,
                                  xdropmatchinfo->useq,
                                  xdropmatchinfo->vseq,
                                  pos1 + len,
                                  pos2 + len,
                                  xdropmatchinfo->belowscore);
  } else
  {
    xdropmatchinfo->best_right.ivalue = 0;
    xdropmatchinfo->best_right.jvalue = 0;
    xdropmatchinfo->best_right.score = 0;
  }
  gt_assert(pos1 >= (unsigned long) xdropmatchinfo->best_left.ivalue &&
            pos2 >= (unsigned long) xdropmatchinfo->best_left.jvalue);
  querystart = pos2 - xdropmatchinfo->best_left.jvalue;
  queryseqnum = gt_querymatch_queryseqnum(querymatch);
  dblen = len + xdropmatchinfo->best_left.ivalue
              + xdropmatchinfo->best_right.ivalue;
  dbstart = pos1 - xdropmatchinfo->best_left.ivalue;
  querylen = len + xdropmatchinfo->best_left.jvalue
                 + xdropmatchinfo->best_right.jvalue,
  score = (GtXdropscore) len * xdropmatchinfo->arbitscores.mat +
          xdropmatchinfo->best_left.score +
          xdropmatchinfo->best_right.score;
  gt_seqabstract_reinit_encseq(xdropmatchinfo->useq,
                               encseq,
                               dblen,
                               dbstart);
  gt_seqabstract_reinit_ptr(xdropmatchinfo->vseq,
                            query,
                            querylen,
                            querystart);
  gt_querymatch_fill(xdropmatchinfo->querymatchspaceptr,
                     dblen,
                     dbstart,
                     GT_READMODE_FORWARD,
                     false,
                     score,
                     greedyunitedist(xdropmatchinfo->frontresource,
                                     xdropmatchinfo->useq,xdropmatchinfo->vseq),
                     false,
                     queryseqnum,
                     querylen,
                     querystart);
  return gt_querymatch_output(info, encseq, xdropmatchinfo->querymatchspaceptr,
                              query, query_totallength,
                              err);
}

static int gt_simplesuffixprefixmatchoutput(GT_UNUSED void *info,
                                            const GtEncseq *encseq,
                                            unsigned long matchlen,
                                            unsigned long pos1,
                                            unsigned long pos2,
                                            GT_UNUSED GtError *err)
{
  unsigned long seqnum1, relpos1, seqnum2, relpos2, seqstartpos;

  if (pos1 > pos2)
  {
    unsigned long tmp = pos1;
    pos1 = pos2;
    pos2 = tmp;
  }
  seqnum1 = gt_encseq_seqnum(encseq,pos1);
  seqstartpos = gt_encseq_seqstartpos(encseq, seqnum1);
  gt_assert(seqstartpos <= pos1);
  relpos1 = pos1 - seqstartpos;
  seqnum2 = gt_encseq_seqnum(encseq,pos2);
  seqstartpos = gt_encseq_seqstartpos(encseq, seqnum2);
  gt_assert(seqstartpos <= pos2);
  relpos2 = pos2 - seqstartpos;
  if (relpos1 == 0)
  {
    unsigned long seqlen2 = gt_encseq_seqlength(encseq,seqnum2);

    if (relpos2 + matchlen == seqlen2)
    {
      printf("%lu %lu %lu\n",seqnum2,seqnum1,matchlen);
    }
  } else
  {
    if (relpos2 == 0)
    {
      unsigned long seqlen1 = gt_encseq_seqlength(encseq,seqnum1);

      if (relpos1 + matchlen == seqlen1)
      {
        printf("%lu %lu %lu\n",seqnum1,seqnum2,matchlen);
      }
    }
  }
  return 0;
}

static int callenummaxpairs(const char *indexname,
                            unsigned int userdefinedleastlength,
                            bool scanfile,
                            Processmaxpairs processmaxpairs,
                            void *processmaxpairsinfo,
                            GtLogger *logger,
                            GtError *err)
{
  bool haserr = false;
  Sequentialsuffixarrayreader *ssar;

  gt_error_check(err);
  ssar = gt_newSequentialsuffixarrayreaderfromfile(indexname,
                                                   SARR_LCPTAB |
                                                   SARR_SUFTAB |
                                                   SARR_ESQTAB |
                                                   SARR_SSPTAB,
                                                   scanfile ? SEQ_scan
                                                            : SEQ_mappedboth,
                                                   logger,
                                                   err);
  if (ssar == NULL)
  {
    haserr = true;
  }
  if (!haserr &&
      gt_enumeratemaxpairs(ssar,
                           gt_encseqSequentialsuffixarrayreader(ssar),
                           gt_readmodeSequentialsuffixarrayreader(ssar),
                           userdefinedleastlength,
                           processmaxpairs,
                           processmaxpairsinfo,
                           err) != 0)
  {
    haserr = true;
  }
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  return haserr ? -1 : 0;
}

static void *gt_repfind_arguments_new(void)
{
  Maxpairsoptions *arguments;

  arguments = gt_malloc(sizeof (*arguments));
  arguments->indexname = gt_str_new();
  arguments->queryfiles = gt_str_array_new();
  return arguments;
}

static void gt_repfind_arguments_delete(void *tool_arguments)
{
  Maxpairsoptions *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->indexname);
  gt_str_array_delete(arguments->queryfiles);
  gt_option_delete(arguments->refforwardoption);
  gt_free(arguments);
}

static GtOptionParser *gt_repfind_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GtOption *option, *reverseoption, *queryoption, *extendseedoption,
           *scanoption, *sampleoption, *forwardoption, *spmoption;
  Maxpairsoptions *arguments = tool_arguments;

  op = gt_option_parser_new("[options] -ii indexname",
                            "Compute maximal repeats.");
  gt_option_parser_set_mail_address(op,"");

  option = gt_option_new_uint_min("l","Specify minimum length of repeats",
                                  &arguments->userdefinedleastlength,
                                  20U,
                                  1U);
  gt_option_parser_add_option(op, option);

  forwardoption = gt_option_new_bool("f","Compute maximal forward repeats",
                                     &arguments->forward,
                                     true);
  gt_option_parser_add_option(op, forwardoption);
  arguments->refforwardoption = gt_option_ref(forwardoption);

  reverseoption = gt_option_new_bool("r","Compute maximal reverse matches",
                                     &arguments->reverse,
                                     false);
  gt_option_parser_add_option(op, reverseoption);

  sampleoption = gt_option_new_ulong_min("samples","Specify number of samples",
                                         &arguments->samples,
                                         0,
                                         1UL);
  gt_option_is_development_option(sampleoption);
  gt_option_parser_add_option(op, sampleoption);

  spmoption = gt_option_new_bool("spm","Search for suffix prefix matches",
                                       &arguments->searchspm,
                                       false);
  gt_option_is_development_option(spmoption);
  gt_option_parser_add_option(op, spmoption);

  extendseedoption = gt_option_new_bool("extend","Extend seed to both sides",
                                        &arguments->extendseed,
                                    false);
  gt_option_is_development_option(extendseedoption);
  gt_option_parser_add_option(op, extendseedoption);

  scanoption = gt_option_new_bool("scan","scan index rather than mapping "
                                         "it to main memory",
                                  &arguments->scanfile,
                                  false);
  gt_option_parser_add_option(op, scanoption);

  option = gt_option_new_string("ii",
                                "Specify input index",
                                arguments->indexname, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  queryoption = gt_option_new_filename_array("q",
                                             "Specify query files",
                                             arguments->queryfiles);
  gt_option_is_development_option(queryoption);
  gt_option_parser_add_option(op, queryoption);

  option = gt_option_new_bool("v",
                              "be verbose ",
                              &arguments->beverbose,
                              false);
  gt_option_parser_add_option(op, option);

  gt_option_exclude(queryoption,sampleoption);
  gt_option_exclude(queryoption,scanoption);
  gt_option_exclude(queryoption,reverseoption);
  gt_option_exclude(queryoption,spmoption);
  gt_option_exclude(reverseoption,spmoption);
  gt_option_exclude(queryoption,spmoption);
  gt_option_exclude(sampleoption,spmoption);
  return op;
}

static int gt_repfind_arguments_check(GT_UNUSED int rest_argc,
                                      void *tool_arguments,
                                      GT_UNUSED GtError *err)
{
  Maxpairsoptions *arguments = tool_arguments;

  if (!gt_option_is_set(arguments->refforwardoption) && arguments->reverse)
  {
    arguments->forward = false;
  }
  return 0;
}

static int gt_repfind_runner(GT_UNUSED int argc,
                             GT_UNUSED const char **argv,
                             GT_UNUSED int parsed_args,
                             void *tool_arguments, GtError *err)
{
  bool haserr = false;
  Maxpairsoptions *arguments = tool_arguments;
  GtLogger *logger = NULL;
  GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
  GtXdropmatchinfo xdropmatchinfo;

  gt_error_check(err);
  xdropmatchinfo.querymatchspaceptr = querymatchspaceptr;
  xdropmatchinfo.useq = gt_seqabstract_new_empty();
  xdropmatchinfo.vseq = gt_seqabstract_new_empty();
  xdropmatchinfo.arbitscores.mat = 2;
  xdropmatchinfo.arbitscores.mis = -2;
  xdropmatchinfo.arbitscores.ins = -3;
  xdropmatchinfo.arbitscores.del = -3;
  xdropmatchinfo.frontresource = gt_frontresource_new(100UL);
  xdropmatchinfo.res = gt_xdrop_resources_new(&xdropmatchinfo.arbitscores);
  xdropmatchinfo.belowscore = 5L;
  logger = gt_logger_new(arguments->beverbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  if (parsed_args < argc)
  {
    gt_error_set(err,"superfluous arguments: \"%s\"",argv[argc-1]);
    haserr = true;
  }
  if (!haserr)
  {
    if (gt_str_array_size(arguments->queryfiles) == 0)
    {
      if (arguments->samples == 0)
      {
        if (arguments->forward)
        {
          if (callenummaxpairs(gt_str_get(arguments->indexname),
                               arguments->userdefinedleastlength,
                               arguments->scanfile,
                               arguments->searchspm
                                 ? gt_simplesuffixprefixmatchoutput
                                 : (arguments->extendseed
                                     ? gt_simplexdropselfmatchoutput
                                     : gt_simpleexactselfmatchoutput),
                               arguments->extendseed
                                 ? (void *) &xdropmatchinfo
                                 : (void *) querymatchspaceptr,
                               logger,
                               err) != 0)
          {
            haserr = true;
          }
        }
        if (!haserr && arguments->reverse)
        {
          if (gt_callenumselfmatches(gt_str_get(arguments->indexname),
                                     GT_READMODE_REVERSE,
                                     arguments->userdefinedleastlength,
                                     /*arguments->extendseed
                                       ? gt_processxdropquerymatches
                                       :*/ gt_querymatch_output,
                                     /*arguments->extendseed
                                       ? (void *) &xdropmatchinfo
                                       :*/ NULL,
                                     logger,
                                     err) != 0)
          {
            haserr = true;
          }
        }
      } else
      {
        if (gt_testmaxpairs(gt_str_get(arguments->indexname),
                            arguments->samples,
                            arguments->userdefinedleastlength,
                            (unsigned long)
                            (100 * arguments->userdefinedleastlength),
                            logger,
                            err) != 0)
        {
          haserr = true;
        }
      }
    } else
    {
      if (gt_callenumquerymatches(gt_str_get(arguments->indexname),
                                  arguments->queryfiles,
                                  false,
                                  true,
                                  false,
                                  arguments->userdefinedleastlength,
                                  NULL,
                                  arguments->extendseed
                                    ? gt_processxdropquerymatches
                                    : gt_querymatch_output,
                                  arguments->extendseed
                                    ? (void *) &xdropmatchinfo
                                    : NULL,
                                  logger,
                                  err) != 0)
      {
        haserr = true;
      }
    }
  }
  gt_querymatch_delete(querymatchspaceptr);
  gt_seqabstract_delete(xdropmatchinfo.useq);
  gt_seqabstract_delete(xdropmatchinfo.vseq);
  gt_xdrop_resources_delete(xdropmatchinfo.res);
  gt_frontresource_delete(xdropmatchinfo.frontresource);
  gt_logger_delete(logger);
  return haserr ? -1 : 0;
}

GtTool* gt_repfind(void)
{
  return gt_tool_new(gt_repfind_arguments_new,
                     gt_repfind_arguments_delete,
                     gt_repfind_option_parser_new,
                     gt_repfind_arguments_check,
                     gt_repfind_runner);
}
genometools-1.5.1/src/tools/gt_maxpairs.h000066400000000000000000000016731211610345200204710ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MAXPAIRS_H
#define GT_MAXPAIRS_H

/* the repfind tool */
GtTool* gt_repfind(void);

#endif
genometools-1.5.1/src/tools/gt_md5_to_id.c000066400000000000000000000104501211610345200204740ustar00rootroot00000000000000/*
  Copyright (c) 2010-2012 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gtdatahelp.h"
#include "extended/seqid2file.h"
#include "extended/md5_to_id_stream_api.h"
#include "tools/gt_md5_to_id.h"

typedef struct {
  bool verbose;
  GtSeqid2FileInfo *s2fi;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} MD5ToSeqidsArguments;

static void *gt_md5_to_id_arguments_new(void)
{
  MD5ToSeqidsArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_md5_to_id_arguments_delete(void *tool_arguments)
{
  MD5ToSeqidsArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_free(arguments);
}

static GtOptionParser* gt_md5_to_id_option_parser_new(void *tool_arguments)
{
  MD5ToSeqidsArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                            "Change MD5 fingerprints used as sequence IDs in "
                            "given GFF3 files to ``regular'' ones.");

  /* -seqfile, -matchdesc, -usedesc and -regionmapping */
  gt_seqid2file_register_options_ext(op, arguments->s2fi, false, true);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  return op;
}

static int gt_md5_to_id_runner(GT_UNUSED int argc, const char **argv,
                                   int parsed_args, void *tool_arguments,
                                   GtError *err)
{
  GtNodeStream *gff3_in_stream, *md5_to_id_stream = NULL,
               *gff3_out_stream = NULL;
  MD5ToSeqidsArguments *arguments = tool_arguments;
  GtRegionMapping *region_mapping = NULL;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);

  /* create region mapping */
  if (gt_seqid2file_option_used(arguments->s2fi)) {
    region_mapping = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
    if (!region_mapping)
      had_err = -1;
  }

  if (!had_err) {
    /* create seqid to md5 stream */
    md5_to_id_stream = gt_md5_to_id_stream_new(gff3_in_stream, region_mapping);

    /* create gff3 output stream */
    gff3_out_stream = gt_gff3_out_stream_new(md5_to_id_stream,
                                             arguments->outfp);

    /* pull the features through the stream and free them afterwards */
    had_err = gt_node_stream_pull(gff3_out_stream, err);
  }

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(md5_to_id_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool *gt_md5_to_id(void)
{
  return gt_tool_new(gt_md5_to_id_arguments_new,
                     gt_md5_to_id_arguments_delete,
                     gt_md5_to_id_option_parser_new,
                     NULL,
                     gt_md5_to_id_runner);
}
genometools-1.5.1/src/tools/gt_md5_to_id.h000066400000000000000000000016361211610345200205070ustar00rootroot00000000000000/*
  Copyright (c) 2010 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MD5_TO_ID_H
#define GT_MD5_TO_ID_H

#include "core/tool_api.h"

/* the MD5s to seqids tool */
GtTool* gt_md5_to_id(void);

#endif
genometools-1.5.1/src/tools/gt_merge.c000066400000000000000000000065561211610345200177440ustar00rootroot00000000000000/*
  Copyright (c) 2006-2011 Gordon Gremme 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/versionfunc.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/merge_stream_api.h"
#include "tools/gt_merge.h"

static GtOPrval parse_options(int *parsed_args, GtFile **outfp, int argc,
                              const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOutputFileInfo *ofi;
  GtOPrval oprval;
  gt_error_check(err);
  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                         "Merge sorted GFF3 files in sorted fashion.");
  ofi = gt_output_file_info_new();
  gt_output_file_register_options(op, outfp, ofi);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_output_file_info_delete(ofi);
  gt_option_parser_delete(op);
  return oprval;
}

int gt_merge(int argc, const char **argv, GtError *err)
{
  GtNodeStream *gff3_in_stream,
                *merge_stream,
                *gff3_out_stream;
  GtArray *genome_streams;
  unsigned long i;
  int parsed_args, had_err;
  GtFile *outfp;

  /* option parsing */
  switch (parse_options(&parsed_args, &outfp, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR: return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }

  /* alloc */
  genome_streams = gt_array_new(sizeof (GtNodeStream*));

  /* XXX: check for multiple specification of '-' */

  /* create an gff3 input stream for each given file */
  if (parsed_args < argc) {
    /* we got files to open */
    for (i = parsed_args; i < argc; i++) {
      gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[i]);
      gt_array_add(genome_streams, gff3_in_stream);
    }
   }
   else {
     /* use stdin */
     gff3_in_stream = gt_gff3_in_stream_new_sorted(NULL);
     gt_array_add(genome_streams, gff3_in_stream);
   }

  /* create a merge stream */
  merge_stream = gt_merge_stream_new(genome_streams);

  /* create a gff3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(merge_stream, outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(merge_stream);
  for (i = 0; i < gt_array_size(genome_streams); i++)
    gt_node_stream_delete(*(GtNodeStream**) gt_array_get(genome_streams, i));
  gt_array_delete(genome_streams);
  gt_file_delete(outfp);

  return had_err;
}
genometools-1.5.1/src/tools/gt_merge.h000066400000000000000000000017321211610345200177400ustar00rootroot00000000000000/*
  Copyright (c) 2006-2007 Gordon Gremme 
  Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MERGE_H
#define GT_MERGE_H

/* the merge tool */
int gt_merge(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_mergeesa.c000066400000000000000000000063601211610345200204260ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/error.h"
#include "core/logger.h"
#include "core/option_api.h"
#include "core/versionfunc.h"
#include "match/test-mergeesa.pr"
#include "tools/gt_mergeesa.h"

static GtOPrval parse_options(GtStr *indexname,GtStrArray *indexnametab,
                              int *parsed_args, int argc,
                              const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  GtOption *option;

  gt_error_check(err);
  op = gt_option_parser_new("storeindex   ...",
                         "Merge indexes into one index.");
  gt_option_parser_set_mail_address(op,"");
  option = gt_option_new_filename_array("ii",
                                    "specify input index files (mandatory)",
                                    indexnametab);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("indexname",
                             "specify index to be created",
                             indexname, NULL);

  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

int gt_mergeesa(int argc, const char **argv, GtError *err)
{
  GtStr *storeindex;
  GtStrArray *indexnametab;
  bool haserr = false;
  int parsed_args;

  gt_error_check(err);

  storeindex = gt_str_new();
  indexnametab = gt_str_array_new();
  switch (parse_options(storeindex, indexnametab, &parsed_args, argc, argv,
                        err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR:
         haserr = true; break;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }
  if (!haserr)
  {
    unsigned long i;
    GtLogger *logger;

    printf("# storeindex=%s\n",gt_str_get(storeindex));
    for (i=0; i
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MERGEESA_H
#define GT_MERGEESA_H

/* the mergeesa tool */
int gt_mergeesa(int argc, const char **argv, GtError *err);

#endif
genometools-1.5.1/src/tools/gt_mergefeat.c000066400000000000000000000065331211610345200205770ustar00rootroot00000000000000/*
  Copyright (c) 2009 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/output_file_api.h"
#include "extended/feature_type.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/merge_feature_stream_api.h"
#include "tools/gt_mergefeat.h"

typedef struct {
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} InterFeatArguments;

static void* gt_mergefeat_arguments_new(void)
{
  InterFeatArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_mergefeat_arguments_delete(void *tool_arguments)
{
  InterFeatArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_mergefeat_option_parser_new(void *tool_arguments)
{
  InterFeatArguments *arguments = tool_arguments;
  GtOptionParser *op;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Merge adjacent "
                            "features without children of the same type in "
                            "given GFF3 file(s).");

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  return op;
}

static int gt_mergefeat_runner(int argc, const char **argv, int parsed_args,
                          void *tool_arguments, GtError *err)
{
  InterFeatArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream,
               *merge_feature_stream,
               *gff3_out_stream;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);

  /* create merge feature stream */
  merge_feature_stream = gt_merge_feature_stream_new(gff3_in_stream);

  /* create gff3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(merge_feature_stream,
                                           arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(merge_feature_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool* gt_mergefeat(void)
{
  return gt_tool_new(gt_mergefeat_arguments_new,
                     gt_mergefeat_arguments_delete,
                     gt_mergefeat_option_parser_new,
                     NULL,
                     gt_mergefeat_runner);
}
genometools-1.5.1/src/tools/gt_mergefeat.h000066400000000000000000000016351211610345200206020ustar00rootroot00000000000000/*
  Copyright (c) 2009 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MERGEFEAT_H
#define GT_MERGEFEAT_H

#include "core/tool_api.h"

/* the merge feature tool */
GtTool* gt_mergefeat(void);

#endif
genometools-1.5.1/src/tools/gt_mgth.c000066400000000000000000000020451211610345200175710ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "mgth/metagenomethreader.h"
#include "tools/gt_mgth.h"

int gt_mgth(int argc, const char **argv, GtError *err)
{
  gt_error_check(err);
  return gt_metagenomethreader(argc, argv, err);
}
genometools-1.5.1/src/tools/gt_mgth.h000066400000000000000000000017441211610345200176030ustar00rootroot00000000000000/*
  Copyright (c) 2007 David Schmitz-Huebsch 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MGTH_H
#define GT_MGTH_H

/* the MetaGenomeThreader tool */
int gt_mgth(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_mkfeatureindex.c000066400000000000000000000217641211610345200216560ustar00rootroot00000000000000/*
  Copyright (c) 2009 Sascha Steinbiss 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/fileutils_api.h"
#include "core/ma.h"
#include "core/str_array_api.h"
#include "core/unused_api.h"
#include "core/xposix.h"
#include "extended/anno_db_gfflike_api.h"
#include "extended/bed_in_stream.h"
#include "extended/feature_index_api.h"
#include "extended/feature_stream_api.h"
#include "extended/gff3_in_stream.h"
#include "extended/gtf_in_stream.h"
#include "extended/rdb_api.h"
#ifdef HAVE_MYSQL
#include "core/password_entry.h"
#include "extended/rdb_mysql_api.h"
#endif
#include "extended/rdb_sqlite_api.h"
#include "tools/gt_mkfeatureindex.h"

#define GT_SQLITE_BACKEND_STRING "sqlite"
#define GT_MYSQL_BACKEND_STRING  "mysql"

typedef struct {
  GtStr *backend,
        *filename,
        *host,
        *user,
        *pass,
        *database,
        *input;
  int port;
  bool verbose,
       force;
} GtMkfeatureindexArguments;

static void* gt_mkfeatureindex_arguments_new(void)
{
  GtMkfeatureindexArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->backend = gt_str_new();
  arguments->filename = gt_str_new();
  arguments->host = gt_str_new();
  arguments->user = gt_str_new();
  arguments->pass = gt_str_new();
  arguments->database = gt_str_new();
  arguments->input = gt_str_new();
  return arguments;
}

static void gt_mkfeatureindex_arguments_delete(void *tool_arguments)
{
  GtMkfeatureindexArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->backend);
  gt_str_delete(arguments->filename);
  gt_str_delete(arguments->host);
  gt_str_delete(arguments->user);
  gt_str_delete(arguments->pass);
  gt_str_delete(arguments->database);
  gt_str_delete(arguments->input);
  gt_free(arguments);
}

static GtOptionParser* gt_mkfeatureindex_option_parser_new(void *tool_arguments)
{
  GtMkfeatureindexArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *backend_option, *filenameoption;
  static const char *backends[] = {
    GT_SQLITE_BACKEND_STRING,
#ifdef HAVE_MYSQL
    GT_MYSQL_BACKEND_STRING,
#endif
    NULL
  };
  static const char *inputs[] = {
    "gff",
    "bed",
    "gtf",
    NULL
  };
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] ",
                            "Creates a new FeatureIndex from annotation data.");

  /* -force */
  option = gt_option_new_bool("force", "force writing to output file",
                              &arguments->force, false);
  gt_option_parser_add_option(op, option);

  /* -backend */
  backend_option = gt_option_new_choice("backend", "database backend to use\n"
                                        "choose from ["
#ifdef HAVE_SQLITE
                                        GT_SQLITE_BACKEND_STRING
#endif
#ifdef HAVE_MYSQL
                                        "|" GT_MYSQL_BACKEND_STRING
#endif
                                        "]",
                                        arguments->backend, backends[0],
                                        backends);
  gt_option_parser_add_option(op, backend_option);

  /* -input */
  option = gt_option_new_choice("input", "input data format\n"
                                       "choose from gff|bed|gtf",
                             arguments->input, inputs[0], inputs);
  gt_option_parser_add_option(op, option);

  /* -filename */
  filenameoption = gt_option_new_string("filename",
                                        "filename for feature database "
                                        "(sqlite backend only)",
                                        arguments->filename, NULL);
  gt_option_parser_add_option(op, filenameoption);

#ifdef HAVE_MYSQL
  /* -host */
  option = gt_option_new_string("host", "hostname for database connection",
                                arguments->host, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory_either(option, filenameoption);

  /* -user */
  option = gt_option_new_string("user", "username for database connection",
                                arguments->user, NULL);
  gt_option_parser_add_option(op, option);

  /* -database */
  option = gt_option_new_string("database",
                                "database name for database connection",
                                arguments->database, NULL);
  gt_option_parser_add_option(op, option);

  /* -port */
  option = gt_option_new_int_max("port", "port for database connection",
                                 &arguments->port, 3333, 65534);
  gt_option_parser_add_option(op, option);
#else
  gt_option_is_mandatory(filenameoption);
#endif

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  return op;
}

static int gt_mkfeatureindex_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  GT_UNUSED GtMkfeatureindexArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  return had_err;
}

static int gt_mkfeatureindex_runner(int argc,
                                    const char **argv,
                                    int parsed_args,
                                    void *tool_arguments,
                                    GtError *err)
{
  GtMkfeatureindexArguments *arguments = tool_arguments;
  GtNodeStream *in_stream = NULL,
              *feature_stream = NULL;
  GtRDB *rdb = NULL;
  GtAnnoDBSchema *adb = NULL;
  GtFeatureIndex *fis = NULL;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

#ifdef HAVE_SQLITE
  if (strcmp(gt_str_get(arguments->backend),
             GT_SQLITE_BACKEND_STRING) == 0) {
    if (gt_file_exists(gt_str_get(arguments->filename))) {
      if (arguments->force) {
        gt_xunlink(gt_str_get(arguments->filename));
      } else {
        gt_error_set(err, "file \"%s\" exists already. use option -force to "
                     "overwrite", gt_str_get(arguments->filename));
        had_err = -1;
      }
    }
    if (!had_err) {
      rdb = gt_rdb_sqlite_new(gt_str_get(arguments->filename), err);
      if (!rdb)
        had_err = -1;
    }
  }
#endif
#ifdef HAVE_MYSQL
  if (strcmp(gt_str_get(arguments->backend),
                    GT_MYSQL_BACKEND_STRING) == 0) {
    arguments->pass = gt_get_password("password: ", err);
    rdb = gt_rdb_mysql_new(gt_str_get(arguments->host),
                           arguments->port,
                           gt_str_get(arguments->database),
                           gt_str_get(arguments->user),
                           gt_str_get(arguments->pass),
                           err);
    if (!rdb)
      had_err = -1;
  }
#endif

  adb = gt_anno_db_gfflike_new();
  if (!had_err && !adb)
    had_err = -1;

  if (!had_err) {
    fis = gt_anno_db_schema_get_feature_index(adb, rdb, err);
    if (!fis)
      had_err = -1;
  }

  if (!had_err) {
    if (strcmp(gt_str_get(arguments->input), "gff") == 0)
    {
      in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                 argv + parsed_args);
      if (arguments->verbose)
        gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) in_stream);
    } else if (strcmp(gt_str_get(arguments->input), "bed") == 0)
    {
      if (argc - parsed_args == 0)
        in_stream = gt_bed_in_stream_new(NULL);
      else
        in_stream = gt_bed_in_stream_new(argv[parsed_args]);
    } else if (strcmp(gt_str_get(arguments->input), "gtf") == 0)
    {
      if (argc - parsed_args == 0)
        in_stream = gt_gtf_in_stream_new(NULL);
      else
        in_stream = gt_gtf_in_stream_new(argv[parsed_args]);
    }
    gt_assert(in_stream);

    feature_stream = gt_feature_stream_new(in_stream, fis);
    had_err = gt_node_stream_pull(feature_stream, err);
  }
  gt_node_stream_delete(feature_stream);
  gt_node_stream_delete(in_stream);
  gt_feature_index_delete(fis);
  gt_anno_db_schema_delete(adb);
  gt_rdb_delete(rdb);
  return had_err;
}

GtTool* gt_mkfeatureindex(void)
{
  return gt_tool_new(gt_mkfeatureindex_arguments_new,
                     gt_mkfeatureindex_arguments_delete,
                     gt_mkfeatureindex_option_parser_new,
                     gt_mkfeatureindex_arguments_check,
                     gt_mkfeatureindex_runner);
}
genometools-1.5.1/src/tools/gt_mkfeatureindex.h000066400000000000000000000017711211610345200216570ustar00rootroot00000000000000/*
  Copyright (c) 2009 Sascha Steinbiss 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MKFEATUREINDEX_H
#define GT_MKFEATUREINDEX_H

#include "core/tool_api.h"

/* the mkfeatureindex tool */
GtTool* gt_mkfeatureindex(void);

#endif
genometools-1.5.1/src/tools/gt_mkfmindex.c000066400000000000000000000020751211610345200206170ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/error.h"
#include "match/fmi-mkindex.pr"
#include "tools/gt_mkfmindex.h"

int gt_mkfmindex(int argc, const char **argv, GtError *err)
{
  gt_error_check(err);
  return gt_parseargsandcallmkfmindex(argc, argv, err);
}
genometools-1.5.1/src/tools/gt_mkfmindex.h000066400000000000000000000017361211610345200206270ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MKFMINDEX_H
#define GT_MKFMINDEX_H

/* the mkfmindex tool */
int gt_mkfmindex(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_mmapandread.c000066400000000000000000000056561211610345200211160ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/error.h"
#include "core/option_api.h"
#include "core/progressbar.h"
#include "core/versionfunc.h"
#include "core/xposix.h"
#include "tools/gt_mmapandread.h"

static GtOPrval parse_options(int *parsed_args, int argc, const char **argv,
                              GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  gt_error_check(err);
  op = gt_option_parser_new("file [...]",
                            "Map the supplied files into memory and "
                            "read them once.");
  gt_option_parser_set_min_args(op, 1);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

int gt_mmapandread(int argc, const char **argv, GtError *err)
{
  int i, fd, parsed_args;
  void *map;
  struct stat sb;
  unsigned long long j;
  unsigned int byte = 0;
  gt_error_check(err);

  /* option parsing */
  switch (parse_options(&parsed_args, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR: return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }

  /* iterate over all files */
  for (i = parsed_args; i < argc; i++) {
    /* open file */
    fd = gt_xopen(argv[i], O_RDONLY, 0);

    /* get file statistics */
    gt_xfstat(fd, &sb);

    if (sb.st_size == 0)
      printf("file \"%s\" is empty\n", argv[i]);
    else if (!(sb.st_mode & S_IFREG))
      printf("\"%s\" is not a regular file\n", argv[i]);
    else {
      /* map file */
      map = gt_xmmap(0, sb.st_size, PROT_READ, MAP_PRIVATE, fd, 0);

      /* read file */
      printf("reading file \"%s\"\n", argv[i]);
      j = 0;
      gt_progressbar_start(&j, (unsigned long long) sb.st_size);
      for (; j < (unsigned long long) sb.st_size; j++)
        byte |= (unsigned int) ((char*) map)[j];
      gt_progressbar_stop();

      /* unmap file */
      gt_xmunmap(map, sb.st_size);
    }

    /* close file */
    gt_xclose(fd);
  }

  if (!byte)
    printf("all read files contained only null characters\n");

  return 0;
}
genometools-1.5.1/src/tools/gt_mmapandread.h000066400000000000000000000017671211610345200211220ustar00rootroot00000000000000/*
  Copyright (c) 2006-2007 Gordon Gremme 
  Copyright (c) 2006-2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_MMAPANDREAD_H
#define GT_MMAPANDREAD_H

/* the mmap(2) and read tool */
int gt_mmapandread(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_orffinder.c000066400000000000000000000163501211610345200206140ustar00rootroot00000000000000  /*
  Copyright (c) 2010      Sascha Kastens 
  Copyright (c)      2011 Sascha Steinbiss 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/codon_iterator_encseq_api.h"
#include "core/encseq.h"
#include "core/fileutils_api.h"
#include "core/hashmap.h"
#include "core/log.h"
#include "core/logger.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/str_array.h"
#include "core/output_file_api.h"
#include "core/safearith.h"
#include "core/str_array.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/warning_api.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/orf_finder_stream.h"
#include "gt_orffinder.h"

typedef struct {
  GtFile *outfp;
  unsigned int min,
               max;
  GtStrArray *types;
  GtOutputFileInfo *ofi;
  bool allorfs,
       verbose;
} GtOrffinderArguments;

static void* gt_orffinder_arguments_new(void)
{
  GtOrffinderArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  arguments->types = gt_str_array_new();
  return arguments;
}

static void gt_orffinder_arguments_delete(void *tool_arguments)
{
  GtOrffinderArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_array_delete(arguments->types);
  gt_free(arguments);
}

static GtOptionParser* gt_orffinder_option_parser_new(void *tool_arguments)
{
  GtOrffinderArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optiontypes;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] indexname [GFF3_file ...]",
                            "Identifies ORFs (open reading frames) in "
                            "sequences.");

  /* types */
  optiontypes = gt_option_new_string_array("types",
                                           "Specify regions which should be "
                                           "searched for open reading frames,\n"
                                           "e.g. 'LTR_retrotransposon'",
                                           arguments->types);
  gt_option_parser_add_option(op, optiontypes);

  /* -allorfs */
  option = gt_option_new_bool("allorfs", "search for all ORFs "
                              "instead of only the longest",
                              &arguments->allorfs, false);
  gt_option_parser_add_option(op, option);

  /* -min */
  option = gt_option_new_uint_min("min", "minimum length of ORF",
                                  &arguments->min, 30, 30);
  gt_option_parser_add_option(op, option);

  /* -max */
  option = gt_option_new_uint_max("max", "maximum length of ORF",
                                  &arguments->max, 10000, 1000000);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_min_args(op, 1U);

  return op;
}

static int gt_orffinder_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments, GtError *err)
{
  GtOrffinderArguments *arguments = tool_arguments;
  int had_err = 0;
  int diff;

  gt_error_check(err);
  gt_assert(arguments);

  diff = (arguments->max - arguments->min);
  if (diff < 0) {
    gt_error_set(err, "Value for -min must be larger than -max");
    had_err = -1;
  }

  return had_err;
}

static int gt_orffinder_runner(int argc, const char **argv,
                               int parsed_args, void *tool_arguments,
                               GtError *err)
{
  GtOrffinderArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream   = NULL,
               *last_stream      = NULL,
               *orffinder_stream = NULL,
               *gff3_out_stream  = NULL;
  int had_err = 0, i = 0, arg = parsed_args;
  const char *indexname = argv[arg];
  GtLogger *logger = gt_logger_new(arguments->verbose,
                                   GT_LOGGER_DEFLT_PREFIX, stderr);
  GtHashmap *types;
  GtEncseqLoader *el;
  GtEncseq *encseq;

  gt_error_check(err);
  gt_assert(arguments);
  arg++;

  types = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);

  if (gt_str_array_size(arguments->types) == 0) {
    gt_hashmap_add(types, (void*) "all", (void*) 1);
  } else {
    for (i = 0; i < gt_str_array_size(arguments->types); i++) {
      gt_hashmap_add(types,
                     (void*) gt_str_array_get(arguments->types, i),
                     (void*) 1);
      gt_hashmap_add(types, (void*) "all", (void*) 0);
    }
  }

  /* Set sequence encoder options. */
  el = gt_encseq_loader_new();
  gt_encseq_loader_set_logger(el, logger);

  /* Open sequence file */
  encseq = gt_encseq_loader_load(el, indexname, err);
  if (!encseq)
    had_err = -1;

  if (!had_err) {
    last_stream = gff3_in_stream  = gt_gff3_in_stream_new_unsorted(argc - arg,
                                                                  argv + arg);
    last_stream = orffinder_stream = gt_orf_finder_stream_new(last_stream,
                                                             encseq,
                                                             types,
                                                             arguments->min,
                                                             arguments->max,
                                                             arguments->allorfs,
                                                             err);
    if (!orffinder_stream)
      had_err = -1;

    if (!had_err)  {
      last_stream = gff3_out_stream = gt_gff3_out_stream_new(last_stream,
                                                             arguments->outfp);

      /* pull the features through the stream and free them afterwards */
      had_err = gt_node_stream_pull(last_stream, err);
    }

    gt_node_stream_delete(orffinder_stream);
    gt_node_stream_delete(gff3_in_stream);
    gt_node_stream_delete(gff3_out_stream);
  }
  gt_encseq_loader_delete(el);
  gt_encseq_delete(encseq);
  encseq = NULL;
  gt_hashmap_delete(types);
  types = NULL;
  gt_logger_delete(logger);

  return had_err;
}

GtTool* gt_orffinder(void)
{
  return gt_tool_new(gt_orffinder_arguments_new,
                     gt_orffinder_arguments_delete,
                     gt_orffinder_option_parser_new,
                     gt_orffinder_arguments_check,
                     gt_orffinder_runner);
}
genometools-1.5.1/src/tools/gt_orffinder.h000066400000000000000000000021011211610345200206060ustar00rootroot00000000000000/*
  Copyright (c) 2010      Sascha Kastens 
  Copyright (c)      2011 Sascha Steinbiss 
  Copyright (c) 2010-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_ORFFINDER_H
#define GT_ORFFINDER_H

#include "core/tool_api.h"

/* the ORF finder tool */
GtTool* gt_orffinder(void);

#endif
genometools-1.5.1/src/tools/gt_packedindex.c000066400000000000000000000101541211610345200211110ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/cstr_array.h"
#include "core/error.h"
#include "core/option_api.h"
#include "core/str.h"
#include "extended/toolbox.h"
#include "core/versionfunc.h"
#include "match/sfx-run.h"
#include "tools/gt_packedindex.h"
#include "tools/gt_packedindex_mkctxmap.h"
#include "tools/gt_packedindex_trsuftab.h"
#include "tools/gt_packedindex_chk_integrity.h"
#include "tools/gt_packedindex_chk_search.h"

/* rely on suffixerator for on the fly index construction */
static int gt_packedindex_make(int argc, const char *argv[], GtError *err)
{
  return gt_parseargsandcallsuffixerator(false, argc, argv, err);
}

static void* gt_packedindex_arguments_new(void)
{
  GtToolbox *packedindex_toolbox = gt_toolbox_new();
  gt_toolbox_add(packedindex_toolbox, "mkindex", gt_packedindex_make);
  gt_toolbox_add(packedindex_toolbox, "mkctxmap", gt_packedindex_mkctxmap);
  gt_toolbox_add(packedindex_toolbox, "trsuftab", gt_packedindex_trsuftab);
  gt_toolbox_add(packedindex_toolbox, "chkintegrity",
              gt_packedindex_chk_integrity );
  gt_toolbox_add(packedindex_toolbox, "chksearch", gt_packedindex_chk_search);
  return packedindex_toolbox;
}

static void gt_packedindex_arguments_delete(void *tool_arguments)
{
  GtToolbox *index_toolbox = tool_arguments;
  if (!index_toolbox) return;
  gt_toolbox_delete(index_toolbox);
}

static GtOptionParser* gt_packedindex_option_parser_new(void *tool_arguments)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtOptionParser *op;
  gt_assert(index_toolbox);
  op = gt_option_parser_new("[option ...] index_tool [argument ...]",
                         "Call packed index tool with name index_tool and "
                         "pass argument(s) to it.");
  gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
  gt_option_parser_set_min_args(op, 1);
  gt_option_parser_refer_to_manual(op);
  return op;
}

static int gt_packedindex_runner(int argc, const char **argv, int parsed_args,
                                 void *tool_arguments, GtError *err)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtToolfunc toolfunc;
  GtTool *tool = NULL;
  char **nargv = NULL;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(index_toolbox);

  /* determine tool */
  if (!gt_toolbox_has_tool(index_toolbox, argv[parsed_args])) {
    gt_error_set(err, "packedindex tool '%s' not found; option -help lists "
                   "possible tools", argv[parsed_args]);
    had_err = -1;
  }

  /* call sub-tool */
  if (!had_err) {
    if (!(toolfunc = gt_toolbox_get(index_toolbox, argv[parsed_args]))) {
      tool = gt_toolbox_get_tool(index_toolbox, argv[parsed_args]);
      gt_assert(tool);
    }
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    if (toolfunc)
      had_err = toolfunc(argc - parsed_args, (const char**) nargv, err);
    else
      had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv,
                            err);
  }

  gt_cstr_array_delete(nargv);
  return had_err;
}

GtTool* gt_packedindex(void)
{
  return gt_tool_new(gt_packedindex_arguments_new,
                  gt_packedindex_arguments_delete,
                  gt_packedindex_option_parser_new,
                  NULL,
                  gt_packedindex_runner);
}
genometools-1.5.1/src/tools/gt_packedindex.h000066400000000000000000000017411211610345200211200ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_PACKEDINDEX_H
#define GT_PACKEDINDEX_H

#include "core/tool_api.h"

/* the packedindex tool */
GtTool* gt_packedindex(void);

#endif
genometools-1.5.1/src/tools/gt_packedindex_chk_integrity.c000066400000000000000000000112371211610345200240370ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

/**
 * \file gt_packedindex_chk_integrity
 * calls routines to validate basic index integrity
 */

#include "gt_packedindex_chk_integrity.h"
#include "core/error.h"
#include "core/logger.h"
#include "core/option_api.h"
#include "core/versionfunc.h"
#include "match/eis-encidxseq.h"
#include "match/eis-encidxseq-param.h"
#include "match/eis-encidxseq-construct.h"
#include "tools/gt_packedindex_chk_integrity.h"

#define DEFAULT_PROGRESS_INTERVAL  100000UL

struct chkIndexOptions
{
  unsigned long skipCount;
  unsigned long progressInterval;
  int checkFlags;
  bool verboseOutput;
  enum seqBaseEncoding encType;
  int EISFeatureSet;
};

static GtOPrval
parseChkIndexOptions(int *parsed_args, int argc, const char *argv[],
                     struct chkIndexOptions *param, GtError *err);

extern int
gt_packedindex_chk_integrity(int argc, const char *argv[], GtError *err)
{
  struct encIdxSeq *seq;
  struct chkIndexOptions params;
  const char *inputProject;
  int parsedArgs;
  int had_err = 0;
  GtLogger *logger = NULL;
  gt_error_check(err);

  switch (parseChkIndexOptions(&parsedArgs, argc, argv, ¶ms, err))
  {
    case GT_OPTION_PARSER_OK:
      break;
    case GT_OPTION_PARSER_ERROR:
      return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT:
      return 0;
  }

  inputProject = argv[parsedArgs];

  logger = gt_logger_new(params.verboseOutput, GT_LOGGER_DEFLT_PREFIX, stdout);

  seq = gt_loadEncIdxSeq(inputProject, params.encType, params.EISFeatureSet,
                      logger, err);
  if ((had_err = seq == NULL))
  {
    gt_error_set(err, "Failed to load index: %s", inputProject);
  }
  else
  {
    fprintf(stderr, "# Using index over sequence %lu"
            " symbols long.\n", EISLength(seq));
    {
      int corrupt
        = gt_EISVerifyIntegrity(seq, inputProject, params.skipCount,
                             params.progressInterval, stderr,
                             params.checkFlags, logger, err);
      if ((had_err = corrupt != 0))
      {
        fputs(gt_error_get(err), stderr); fputs("\n", stderr);
        gt_error_set(err, "Integrity check failed for index: %s",
                  EISIntegrityCheckResultStrings[corrupt]);
      }
    }
  }
  if (seq) gt_deleteEncIdxSeq(seq);
  if (logger) gt_logger_delete(logger);
  return had_err?-1:0;
}

static GtOPrval
parseChkIndexOptions(int *parsed_args, int argc, const char *argv[],
                     struct chkIndexOptions *params, GtError *err)
{
  GtOptionParser *op;
  GtOption *option;
  GtOPrval oprval;
  bool extRankCheck;

  gt_error_check(err);
  op = gt_option_parser_new("indexname",
                         "Map  block composition index"
                         "and bwt and check index integrity.");

  option = gt_option_new_bool("v",
                           "print verbose progress information",
                           ¶ms->verboseOutput,
                           false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("skip", "number of symbols to skip",
                            ¶ms->skipCount, 0);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("ticks", "print dot after this many symbols"
                            " tested okay", ¶ms->progressInterval,
                            DEFAULT_PROGRESS_INTERVAL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("ext-rank-check",
                           "do additional checks of rank query results",
                           &extRankCheck, false);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 1, 1);
  oprval = gt_option_parser_parse(op, parsed_args, argc, (const char**) argv,
                               gt_versionfunc, err);
  gt_option_parser_delete(op);
  params->checkFlags = EIS_VERIFY_BASIC | (extRankCheck?EIS_VERIFY_EXT_RANK:0);
  params->EISFeatureSet = EIS_FEATURE_REGION_SUMS;
  params->encType = BWT_ON_BLOCK_ENC;
  return oprval;
}
genometools-1.5.1/src/tools/gt_packedindex_chk_integrity.h000066400000000000000000000017171211610345200240460ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#ifndef GT_PACKEDINDEX_CHK_INTEGRITY_H
#define GT_PACKEDINDEX_CHK_INTEGRITY_H

#include "core/error.h"

extern int
gt_packedindex_chk_integrity(int argc, const char *argv[], GtError *err);

#endif
genometools-1.5.1/src/tools/gt_packedindex_chk_search.c000066400000000000000000000311671211610345200232720ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/error.h"
#include "core/logger.h"
#include "core/minmax.h"
#include "core/option_api.h"
#include "core/str.h"
#include "core/versionfunc.h"
#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-param.h"
#include "core/encseq.h"
#include "match/enum-patt.h"
#include "match/esa-mmsearch.h"
#include "match/sarr-def.h"
#include "match/esa-map.h"
#include "tools/gt_packedindex_chk_search.h"
#include "match/sfx-apfxlen.h"

#define DEFAULT_PROGRESS_INTERVAL  100000UL

struct chkSearchOptions
{
  struct bwtOptions idx;
  long minPatLen, maxPatLen;
  unsigned long numOfSamples, progressInterval;
  int flags;
  bool verboseOutput;
};

static GtOPrval
parseChkBWTOptions(int *parsed_args, int argc, const char **argv,
                   struct chkSearchOptions *params, const GtStr *projectName,
                   GtError *err);

extern int
gt_packedindex_chk_search(int argc, const char *argv[], GtError *err)
{
  struct chkSearchOptions params;
  Suffixarray suffixarray;
  Enumpatterniterator *epi = NULL;
  bool saIsLoaded = false;
  BWTSeq *bwtSeq = NULL;
  GtStr *inputProject = NULL;
  int parsedArgs;
  bool had_err = false;
  BWTSeqExactMatchesIterator EMIter;
  bool EMIterInitialized = false;
  GtLogger *logger = NULL;
  inputProject = gt_str_new();

  do {
    gt_error_check(err);
    {
      bool exitNow = false;
      switch (parseChkBWTOptions(&parsedArgs, argc, argv, ¶ms,
                                 inputProject, err))
      {
      case GT_OPTION_PARSER_OK:
        break;
      case GT_OPTION_PARSER_ERROR:
        had_err = true;
        exitNow = true;
        break;
      case GT_OPTION_PARSER_REQUESTS_EXIT:
        exitNow = true;
        break;
      }
      if (exitNow)
        break;
    }
    gt_str_set(inputProject, argv[parsedArgs]);

    logger = gt_logger_new(params.verboseOutput,
                           GT_LOGGER_DEFLT_PREFIX, stdout);

    bwtSeq = gt_availBWTSeq(¶ms.idx.final, logger, err);
    if ((had_err = bwtSeq == NULL))
      break;

    {
      enum verifyBWTSeqErrCode retval =
        gt_BWTSeqVerifyIntegrity(bwtSeq, gt_str_get(inputProject), params.flags,
                              params.progressInterval, stderr, logger, err);
      if ((had_err = (retval != VERIFY_BWTSEQ_NO_ERROR)))
      {
        fprintf(stderr, "index integrity check failed: %s\n",
                gt_error_get(err));
        gt_error_set(err, "aborted because of index integrity check fail");
        break;
      }
    }
    if (BWTSeqHasLocateInformation(bwtSeq))
    {
      if ((had_err = !gt_initEmptyEMIterator(&EMIter, bwtSeq)))
      {
        gt_error_set(err, "Cannot create matches iterator for sequence index.");
        break;
      }
      EMIterInitialized = true;
    }
    {
      unsigned long totalLen, dbstart;
      unsigned long trial, patternLen;

      if ((had_err =
           gt_mapsuffixarray(&suffixarray, SARR_SUFTAB | SARR_ESQTAB,
                             gt_str_get(inputProject), NULL, err) != 0))
      {
        gt_error_set(err, "Can't load suffix array project with"
                  " demand for encoded sequence and suffix table files\n");
        break;
      }
      totalLen = gt_encseq_total_length(suffixarray.encseq);
      saIsLoaded = true;
      if ((had_err = (params.minPatLen >= 0L && params.maxPatLen >= 0L
                      && params.minPatLen > params.maxPatLen)))
      {
        gt_error_set(err, "Invalid pattern lengths selected: min=%ld, max=%ld;"
                  " min <= max is required.", params.minPatLen,
                  params.maxPatLen);
        break;
      }
      if (params.minPatLen < 0 || params.maxPatLen < 0)
      {
        unsigned int numofchars
          = gt_alphabet_num_of_chars(
                               gt_encseq_alphabet(suffixarray.encseq));
        if (params.minPatLen < 0)
          params.minPatLen
            = gt_recommendedprefixlength(numofchars,
                                         totalLen,
                                         GT_RECOMMENDED_MULTIPLIER_DEFAULT,
                                         true);
        if (params.maxPatLen < 0)
          params.maxPatLen =
            MAX(params.minPatLen,
                125 * gt_recommendedprefixlength(numofchars,totalLen,
                                         GT_RECOMMENDED_MULTIPLIER_DEFAULT,
                                         true)/100);
        else
          params.maxPatLen = MAX(params.maxPatLen, params.minPatLen);
      }
      fprintf(stderr, "Using patterns of lengths %lu to %lu\n",
              params.minPatLen, params.maxPatLen);
      if ((had_err = totalLen + 1 != BWTSeqLength(bwtSeq)))
      {
        gt_error_set(err, "base suffix array and index have diferrent lengths!"
                          "%lu vs. %lu",  totalLen + 1,
                  BWTSeqLength(bwtSeq));
        break;
      }
      if ((had_err =
           (epi = gt_newenumpatterniterator(params.minPatLen, params.maxPatLen,
                                         suffixarray.encseq,
                                         err)) == NULL))
      {
        fputs("Creation of pattern iterator failed!\n", stderr);
        break;
      }
      for (trial = 0; !had_err && trial < params.numOfSamples; ++trial)
      {
        const GtUchar *pptr = gt_nextEnumpatterniterator(&patternLen, epi);
        GtMMsearchiterator *mmsi =
          gt_mmsearchiterator_new_complete_olain(suffixarray.encseq,
                                            suffixarray.suftab,
                                            0,  /* leftbound */
                                            totalLen, /* rightbound */
                                            0, /* offset */
                                            suffixarray.readmode,
                                            pptr,
                                            patternLen);
        if (BWTSeqHasLocateInformation(bwtSeq))
        {
          if ((had_err = !gt_reinitEMIterator(&EMIter, bwtSeq, pptr, patternLen,
                                           false)))
          {
            fputs("Internal error: failed to reinitialize pattern match"
                  " iterator", stderr);
            abort();
          }
          gt_assert(gt_EMINumMatchesTotal(&EMIter) ==
                    gt_BWTSeqMatchCount(bwtSeq, pptr, patternLen,
                                        false));
          gt_assert(gt_EMINumMatchesTotal(&EMIter)
                      == gt_mmsearchiterator_count(mmsi));
          while (gt_mmsearchiterator_next(&dbstart,mmsi))
          {
            unsigned long matchPos = 0;
            bool match = EMIGetNextMatch(&EMIter, &matchPos, bwtSeq);
            if ((had_err = !match))
            {
              gt_error_set(err,
                           "matches of packedindex expired before mmsearch!");
              break;
            }
            if ((had_err = matchPos != dbstart))
            {
              gt_error_set(err, "packedindex match doesn't equal mmsearch "
                           "match result!\n%lu vs. %lu\n",
                           matchPos, dbstart);
            }
          }
          if (!had_err)
          {
            unsigned long matchPos;
            bool trailingMatch = EMIGetNextMatch(&EMIter, &matchPos, bwtSeq);
            if ((had_err = trailingMatch))
            {
              gt_error_set(err, "matches of mmsearch expired before fmindex!");
              break;
            }
          }
        }
        else
        {
          unsigned long numFMIMatches = gt_BWTSeqMatchCount(bwtSeq, pptr,
                                                         patternLen,
                                                         false),
            numMMSearchMatches = gt_mmsearchiterator_count(mmsi);
          if ((had_err = numFMIMatches != numMMSearchMatches))
          {
            gt_error_set(err, "Number of matches not equal for suffix array ("
                              "%lu) and fmindex (%lu).\n",
                      numFMIMatches, numMMSearchMatches);
          }
        }
        gt_mmsearchiterator_delete(mmsi);
        mmsi = NULL;
        if (params.progressInterval && !((trial + 1) % params.progressInterval))
          putc('.', stderr);
      }
      if (params.progressInterval)
        putc('\n', stderr);
      fprintf(stderr, "Finished %lu of %lu matchings successfully.\n",
              trial, params.numOfSamples);
    }
  } while (0);
  if (EMIterInitialized) gt_destructEMIterator(&EMIter);
  if (saIsLoaded) gt_freesuffixarray(&suffixarray);
  gt_freeEnumpatterniterator(epi);
  if (bwtSeq) gt_deleteBWTSeq(bwtSeq);
  if (logger) gt_logger_delete(logger);
  if (inputProject) gt_str_delete(inputProject);
  return had_err?-1:0;
}

static GtOPrval
parseChkBWTOptions(int *parsed_args, int argc, const char **argv,
                   struct chkSearchOptions *params, const GtStr *projectName,
                   GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  GtOption *option, *optionProgress;
  bool checkSuffixArrayValues, tryContextRetrieve, tryFullRegen;

  gt_error_check(err);
  op = gt_option_parser_new("indexname",
                         "Load (or build if necessary) BWT index for project"
                         "  and perform verification of search"
                         " results.");

  gt_registerPackedIndexOptions(op, ¶ms->idx, BWTDEFOPT_MULTI_QUERY,
                             projectName);

  option = gt_option_new_long("minpatlen",
                           "minimum length of patterns searched for, -1 "
                           "implies automatic choice based on index "
                           "properties", ¶ms->minPatLen, -1);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_long("maxpatlen",
                           "maximum length of patterns searched for, -1 "
                           "implies automatic choice based on index "
                           "properties", ¶ms->maxPatLen, -1);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("nsamples",
                            "number of sequences to search for",
                            ¶ms->numOfSamples, 1000);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("chksfxarray",
                           "verify integrity of stored suffix array positions",
                           &checkSuffixArrayValues, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("full-lfmap",
                           "verify complete backwards regeneration of "
                           "original sequence", &tryFullRegen, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("chkcontext",
                           "verify integrity of regenerated sequence context",
                           &tryContextRetrieve, false);
  gt_option_parser_add_option(op, option);

  optionProgress = gt_option_new_ulong("ticks",
                                    "print dot after this many symbols "
                                    "tested okay", ¶ms->progressInterval,
                                    DEFAULT_PROGRESS_INTERVAL);
  gt_option_parser_add_option(op, optionProgress);

  option = gt_option_new_bool("v",
                           "print verbose progress information",
                           ¶ms->verboseOutput,
                           false);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 1, 1);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);

  /* condense boolean options to flags field */
  params->flags = (checkSuffixArrayValues?VERIFY_BWTSEQ_SUFVAL:0)
    | (tryFullRegen?VERIFY_BWTSEQ_LFMAPWALK:0)
    | (tryContextRetrieve?VERIFY_BWTSEQ_CONTEXT:0);
  /* compute parameters currently not set from command-line or
   * determined indirectly */
  gt_computePackedIndexDefaults(¶ms->idx, BWTBaseFeatures);

  gt_option_parser_delete(op);

  return oprval;
}
genometools-1.5.1/src/tools/gt_packedindex_chk_search.h000066400000000000000000000020161211610345200232660ustar00rootroot00000000000000/*
  Copyright (c) 2007 Thomas Jahns 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#ifndef GT_PACKEDINDEX_CHK_SEARCH_H
#define GT_PACKEDINDEX_CHK_SEARCH_H

#include "core/error.h"

extern int
gt_packedindex_chk_search(int argc, const char *argv[], GtError *error);

#endif
genometools-1.5.1/src/tools/gt_packedindex_mkctxmap.c000066400000000000000000000123051211610345200230150ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/error.h"
#include "core/logger.h"
#include "core/option_api.h"
#include "core/str.h"
#include "core/versionfunc.h"
#include "match/eis-bwtseq.h"
#include "match/eis-bwtseq-construct.h"
#include "match/eis-bwtseq-context-param.h"
#include "match/eis-bwtseq-sass.h"

#include "match/sarr-def.h"
#include "match/esa-map.h"
#include "tools/gt_packedindex_mkctxmap.h"

struct mkCtxMapOptions
{
  int mapIntervalLog2;
  bool verboseOutput;
};

static GtOPrval
parseMkCtxMapOptions(int *parsed_args, int argc, const char **argv,
                     struct mkCtxMapOptions *params, GtError *err);

extern int
gt_packedindex_mkctxmap(int argc, const char *argv[], GtError *err)
{
  struct mkCtxMapOptions params;
  const char *projectName;
  GtLogger *logger = NULL;
  BWTSeq *bwtSeq = NULL;
  SASeqSrc *src;
  int parsedArgs;
  bool had_err = false;
  bool saInitialized = false, saiInitialized = false;
  Suffixarray sa;
  SuffixarrayFileInterface sai;

  do {
    gt_error_check(err);
    {
      bool exitNow = false;
      switch (parseMkCtxMapOptions(&parsedArgs, argc, argv, ¶ms, err))
      {
      case GT_OPTION_PARSER_OK:
        break;
      case GT_OPTION_PARSER_ERROR:
        had_err = true;
        exitNow = true;
        break;
      case GT_OPTION_PARSER_REQUESTS_EXIT:
        exitNow = true;
        break;
      }
      if (exitNow)
        break;
    }
    projectName = argv[parsedArgs];
    logger = gt_logger_new(params.verboseOutput,
                           GT_LOGGER_DEFLT_PREFIX, stdout);
    /* try to find appropriate suffix source */
    {
      unsigned long len;
      if (streamsuffixarray(&sa, SARR_SUFTAB, projectName, logger, err))
      {
        gt_error_unset(err);
        if (streamsuffixarray(&sa, 0, projectName, logger, err))
        {
          had_err = true;
          break;
        }
        len = gt_encseq_total_length(sa.encseq) + 1;
        saInitialized = true;
        bwtSeq = gt_loadBWTSeqForSA(projectName, BWT_ON_BLOCK_ENC,
                                 BWTDEFOPT_MULTI_QUERY,
                                 gt_encseq_alphabet(sa.encseq), err);
        if (!(src = gt_BWTSeqNewSASeqSrc(bwtSeq, NULL)))
        {
          gt_error_set(err, "The project %s does not contain sufficient"
                       " information to regenerate the suffix array.",
                       projectName);
          had_err = true;
          break;
        }
      }
      else
      {
        len = gt_encseq_total_length(sa.encseq) + 1;
        saInitialized = true;
        gt_initSuffixarrayFileInterface(&sai, len, &sa);
        src = SAI2SASS(&sai);
        saiInitialized = true;
      }
      {
        SeqDataReader readSfxIdx = SASSCreateReader(src, SFX_REQUEST_SUFTAB);
        BWTSeqContextRetriever *bwtSeqCR;
        BWTSeqContextRetrieverFactory *bwtSeqCRF
          = gt_newBWTSeqContextRetrieverFactory(len, params.mapIntervalLog2);
        if (gt_BWTSCRFReadAdvance(bwtSeqCRF, len, readSfxIdx)
            != len)
        {
          gt_error_set(err, "Creation of context map unsuccessful: %s",
                    gt_error_get(err));
          had_err = true;
          gt_deleteBWTSeqContextRetrieverFactory(bwtSeqCRF);
          break;
        }
        bwtSeqCR = gt_BWTSCRFGet(bwtSeqCRF, bwtSeq, projectName);
        gt_deleteBWTSeqCR(bwtSeqCR);
        gt_deleteBWTSeqContextRetrieverFactory(bwtSeqCRF);
      }
    }
  } while (0);
  if (bwtSeq)
  {
    SASSDelete(src);
    gt_deleteBWTSeq(bwtSeq);
  }
  if (saiInitialized) gt_destructSuffixarrayFileInterface(&sai);;
  if (saInitialized) gt_freesuffixarray(&sa);
  if (logger) gt_logger_delete(logger);
  return had_err?-1:0;
}

static GtOPrval
parseMkCtxMapOptions(int *parsed_args, int argc, const char **argv,
                     struct mkCtxMapOptions *params, GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  GtOption *option;

  gt_error_check(err);
  op = gt_option_parser_new("indexname",
                         "Build BWT packedindex for project .");
  gt_registerCtxMapOptions(op, ¶ms->mapIntervalLog2);

  option = gt_option_new_bool("v",
                           "print verbose progress information",
                           ¶ms->verboseOutput,
                           false);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 1, 1);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);

  gt_option_parser_delete(op);

  return oprval;
}
genometools-1.5.1/src/tools/gt_packedindex_mkctxmap.h000066400000000000000000000020111211610345200230130ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_PACKEDINDEX_MKCTXMAP_H
#define GT_PACKEDINDEX_MKCTXMAP_H

#include "core/error.h"

extern int
gt_packedindex_mkctxmap(int argc, const char *argv[], GtError *error);

#endif
genometools-1.5.1/src/tools/gt_packedindex_trsuftab.c000066400000000000000000000072471211610345200230340ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/error.h"
#include "core/logger.h"
#include "core/option_api.h"
#include "core/str.h"
#include "core/versionfunc.h"
#include "match/eis-bwtseq.h"
#include "core/encseq.h"
#include "match/sarr-def.h"
#include "match/eis-bwtseq-param.h"
#include "tools/gt_packedindex_trsuftab.h"

#define DEFAULT_PROGRESS_INTERVAL  100000UL

struct trSufTabOptions
{
  struct bwtOptions idx;
  bool verboseOutput;
};

static GtOPrval
parseTrSufTabOptions(int *parsed_args, int argc, const char **argv,
                     struct trSufTabOptions *params, const GtStr *projectName,
                     GtError *err);

extern int
gt_packedindex_trsuftab(int argc, const char *argv[], GtError *err)
{
  struct trSufTabOptions params;
  BWTSeq *bwtSeq = NULL;
  GtStr *inputProject = NULL;
  int parsedArgs;
  bool had_err = false;
  GtLogger *logger = NULL;
  inputProject = gt_str_new();

  do {
    gt_error_check(err);
    {
      bool exitNow = false;
      switch (parseTrSufTabOptions(&parsedArgs, argc, argv, ¶ms,
                                   inputProject, err))
      {
      case GT_OPTION_PARSER_OK:
        break;
      case GT_OPTION_PARSER_ERROR:
        had_err = true;
        exitNow = true;
        break;
      case GT_OPTION_PARSER_REQUESTS_EXIT:
        exitNow = true;
        break;
      }
      if (exitNow)
        break;
    }
    gt_str_set(inputProject, argv[parsedArgs]);
    logger = gt_logger_new(params.verboseOutput,
                           GT_LOGGER_DEFLT_PREFIX, stdout);
    bwtSeq = gt_trSuftab2BWTSeq(¶ms.idx.final, logger, err);
    had_err = bwtSeq == NULL;
    if (had_err)
      break;
  } while (0);
  if (bwtSeq) gt_deleteBWTSeq(bwtSeq);
  if (logger) gt_logger_delete(logger);
  if (inputProject) gt_str_delete(inputProject);
  return had_err?-1:0;
}

static GtOPrval
parseTrSufTabOptions(int *parsed_args, int argc, const char **argv,
                     struct trSufTabOptions *params, const GtStr *projectName,
                     GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  GtOption *option;

  gt_error_check(err);
  op = gt_option_parser_new("indexname",
                         "Build BWT packedindex for project .");

  gt_registerPackedIndexOptions(op, ¶ms->idx, BWTDEFOPT_MULTI_QUERY,
                             projectName);

  option = gt_option_new_bool("v",
                           "print verbose progress information",
                           ¶ms->verboseOutput,
                           false);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 1, 1);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  /* compute parameters currently not set from command-line or
   * determined indirectly */
  gt_computePackedIndexDefaults(¶ms->idx, BWTBaseFeatures);

  gt_option_parser_delete(op);

  return oprval;
}
genometools-1.5.1/src/tools/gt_packedindex_trsuftab.h000066400000000000000000000020101211610345200230200ustar00rootroot00000000000000/*
  Copyright (c) 2008 Thomas Jahns 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/
#ifndef GT_PACKEDINDEX_TRSUFTAB_H
#define GT_PACKEDINDEX_TRSUFTAB_H

#include "core/error.h"

extern int
gt_packedindex_trsuftab(int argc, const char *argv[], GtError *error);

#endif
genometools-1.5.1/src/tools/gt_paircmp.c000066400000000000000000000202101211610345200202570ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include "core/error.h"
#include "core/ma_api.h"
#include "core/versionfunc.h"
#include "core/option_api.h"
#include "core/str.h"
#include "core/str_array.h"
#include "core/types_api.h"
#include "match/test-pairwise.h"
#include "tools/gt_paircmp.h"

typedef struct
{
  GtStr *charlist;
  unsigned long len;
} Charlistlen;

typedef struct
{
  GtStrArray *strings,
           *files;
  Charlistlen *charlistlen;
  GtStr *text;
} Cmppairwiseopt;

static void showsimpleoptions(const Cmppairwiseopt *opt)
{
  if (gt_str_array_size(opt->strings) > 0)
  {
    printf("# two strings \"%s\" \"%s\"\n",gt_str_array_get(opt->strings,0),
                                           gt_str_array_get(opt->strings,1UL));
    return;
  }
  if (gt_str_array_size(opt->files) > 0)
  {
    printf("# two files \"%s\" \"%s\"\n",gt_str_array_get(opt->files,0),
                                         gt_str_array_get(opt->files,1UL));
    return;
  }
  if (opt->charlistlen != NULL)
  {
    printf("# alphalen \"%s\" %lu\n",
             gt_str_get(opt->charlistlen->charlist),
             opt->charlistlen->len);
    return;
  }
  if (gt_str_length(opt->text) > 0)
  {
    printf("# text \"%s\"\n",gt_str_get(opt->text));
    return;
  }
}

static GtOPrval parse_options(int *parsed_args,
                              Cmppairwiseopt *pw,
                              int argc, const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOption *optionstrings,
         *optionfiles,
         *optioncharlistlen,
         *optiontext;
  GtStrArray *charlistlen;
  GtOPrval oprval;

  gt_error_check(err);
  charlistlen = gt_str_array_new();
  pw->strings = gt_str_array_new();
  pw->files = gt_str_array_new();
  pw->text = gt_str_new();
  pw->charlistlen = NULL;
  op = gt_option_parser_new("options","Apply function to pairs of strings.");
  gt_option_parser_set_mail_address(op,"");

  optionstrings = gt_option_new_string_array("ss","use two strings",
                                             pw->strings);
  gt_option_parser_add_option(op, optionstrings);

  optionfiles = gt_option_new_filename_array("ff","use two files",
                                             pw->files);
  gt_option_parser_add_option(op, optionfiles);

  optioncharlistlen = gt_option_new_string_array("a",
                                             "use character list and length",
                                             charlistlen);
  gt_option_parser_add_option(op, optioncharlistlen);

  optiontext = gt_option_new_string("t","use text",pw->text, NULL);
  gt_option_parser_add_option(op, optiontext);

  gt_option_exclude(optionstrings, optionfiles);
  gt_option_exclude(optionstrings, optioncharlistlen);
  gt_option_exclude(optionstrings, optiontext);
  gt_option_exclude(optionfiles, optioncharlistlen);
  gt_option_exclude(optionfiles, optiontext);
  gt_option_exclude(optioncharlistlen, optiontext);

  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  if (oprval == GT_OPTION_PARSER_OK)
  {
    if (gt_option_is_set(optionstrings))
    {
      if (gt_str_array_size(pw->strings) != 2UL)
      {
        gt_error_set(err, "option -ss requires two string arguments");
        oprval = GT_OPTION_PARSER_ERROR;
      }
    } else
    {
      if (gt_option_is_set(optionfiles))
      {
        if (gt_str_array_size(pw->files) != 2UL)
        {
          gt_error_set(err, "option -ff requires two filename arguments");
          oprval = GT_OPTION_PARSER_ERROR;
        }
      } else
      {
        if (gt_option_is_set(optioncharlistlen))
        {
          long readint;

          if (gt_str_array_size(charlistlen) != 2UL)
          {
            gt_error_set(err,
                         "option -a requires charlist and length argument");
            oprval = GT_OPTION_PARSER_ERROR;
          }
          pw->charlistlen = gt_malloc(sizeof *pw->charlistlen);
          pw->charlistlen->charlist =
            gt_str_ref(gt_str_array_get_str(charlistlen,
                                                                  0));
          if (sscanf(gt_str_array_get(charlistlen,1UL),"%ld",&readint) != 1 ||
              readint < 1L)
          {
            gt_error_set(err,
                         "option -a requires charlist and length argument");
            oprval = GT_OPTION_PARSER_ERROR;
          }
          pw->charlistlen->len = (unsigned long) readint;
        } else
        {
          if (!gt_option_is_set(optiontext))
          {
            gt_error_set(err,
                         "use exactly one of the options -ss, -ff, -a, -t");
            oprval = GT_OPTION_PARSER_ERROR;
          }
        }
      }
    }
  }
  gt_option_parser_delete(op);
  if (oprval == GT_OPTION_PARSER_OK && *parsed_args != argc)
  {
    gt_error_set(err, "superfluous program parameters");
    oprval = GT_OPTION_PARSER_ERROR;
  }
  gt_str_array_delete(charlistlen);
  return oprval;
}

static void freesimpleoption(Cmppairwiseopt *cmppairwise)
{
  gt_str_array_delete(cmppairwise->strings);
  gt_str_array_delete(cmppairwise->files);
  gt_str_delete(cmppairwise->text);
  if (cmppairwise->charlistlen != NULL)
  {
    gt_str_delete(cmppairwise->charlistlen->charlist);
    gt_free(cmppairwise->charlistlen);
  }
}

static unsigned long applycheckfunctiontosimpleoptions(
                                  Checkcmppairfuntype checkfunction,
                                  const Cmppairwiseopt *opt)
{
  if (gt_str_array_size(opt->strings) > 0)
  {
    bool forward = true;
    while (true)
    {
      checkfunction(forward,
                    (const GtUchar *) gt_str_array_get(opt->strings,0),
                    (unsigned long) strlen(gt_str_array_get(opt->strings,0)),
                    (const GtUchar *) gt_str_array_get(opt->strings,1UL),
                    (unsigned long) strlen(gt_str_array_get(opt->strings,1UL)));
      if (!forward)
      {
        break;
      }
      forward = false;
    }
    return 2UL; /* number of testcases */
  }
  if (gt_str_array_size(opt->files) > 0)
  {
    gt_runcheckfunctionontwofiles(checkfunction,
                               gt_str_array_get(opt->files,0),
                               gt_str_array_get(opt->files,1UL));
    return 2UL;
  }
  if (opt->charlistlen != NULL)
  {
    return gt_runcheckfunctiononalphalen(checkfunction,
                                      gt_str_get(opt->charlistlen->charlist),
                                      opt->charlistlen->len);
  }
  if (gt_str_length(opt->text) > 0)
  {
    return gt_runcheckfunctionontext(checkfunction,gt_str_get(opt->text));
  }
  gt_assert(false);
  return 0;
}

int gt_paircmp(int argc, const char **argv, GtError *err)
{
  int parsed_args;
  Cmppairwiseopt cmppairwise;
  GtOPrval oprval;

  gt_error_check(err);

  oprval = parse_options(&parsed_args,&cmppairwise,argc, argv, err);
  if (oprval == GT_OPTION_PARSER_OK)
  {
    unsigned long testcases;

    gt_assert(parsed_args == argc);
    showsimpleoptions(&cmppairwise);
    testcases = applycheckfunctiontosimpleoptions(gt_checkgreedyunitedist,
                                                  &cmppairwise);
    printf("# number of testcases: %lu\n",testcases);
  }
  freesimpleoption(&cmppairwise);
  if (oprval == GT_OPTION_PARSER_REQUESTS_EXIT)
  {
    return 0;
  }
  if (oprval == GT_OPTION_PARSER_ERROR)
  {
    return -1;
  }
  return 0;
}
genometools-1.5.1/src/tools/gt_paircmp.h000066400000000000000000000017321211610345200202740ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_PAIRCMP_H
#define GT_PAIRCMP_H

/* the paircmp tool */
int gt_paircmp(int argc, const char **argv, GtError *err);

#endif
genometools-1.5.1/src/tools/gt_patternmatch.c000066400000000000000000000253401211610345200213270ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/encseq.h"
#include "core/error.h"
#include "core/option_api.h"
#include "core/str.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "match/cutendpfx.h"
#include "match/enum-patt.h"
#include "match/esa-map.h"
#include "match/esa-mmsearch.h"
#include "match/qgram2code.h"
#include "match/sarr-def.h"
#include "tools/gt_patternmatch.h"

typedef struct
{
  unsigned long minpatternlen, maxpatternlen, numofsamples;
  bool showpatt, usebcktab, immediate;
  GtStr *indexname;
} Pmatchoptions;

static void comparemmsis(const GtMMsearchiterator *mmsi1,
                         const GtMMsearchiterator *mmsi2)
{
  if (gt_mmsearchiterator_isempty(mmsi1))
  {
    if (!gt_mmsearchiterator_isempty(mmsi2))
    {
      fprintf(stderr,"mmsi1 is empty but mmsi2 not\n");
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  } else
  {
    if (gt_mmsearchiterator_isempty(mmsi2))
    {
      fprintf(stderr,"mmsi2 is empty but mmsi1 not\n");
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    if (!gt_mmsearchiterator_identical(mmsi1,mmsi2))
    {
      fprintf(stderr,"mmsi1 and mmsi2 are different\n");
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
  }
}

#define UNDEFREFSTART totallength

static int callpatternmatcher(const Pmatchoptions *pmopt, GtError *err)
{
  Suffixarray suffixarray;
  unsigned long totallength = 0;
  bool haserr = false;
  const GtUchar *pptr;
  unsigned long patternlen;
  unsigned int demand = SARR_SUFTAB | SARR_ESQTAB;

  if (pmopt->usebcktab)
  {
    demand |= SARR_BCKTAB;
  }
  if (gt_mapsuffixarray(&suffixarray,
                     demand,
                     gt_str_get(pmopt->indexname),
                     NULL,
                     err) != 0)
  {
    haserr = true;
  } else
  {
    totallength = gt_encseq_total_length(suffixarray.encseq);
  }
  if (!haserr)
  {
    unsigned long trial;
    unsigned long dbstart;
    Enumpatterniterator *epi;
    GT_UNUSED unsigned int firstspecial;
    GtMMsearchiterator *mmsibck = NULL, *mmsiimm = NULL;
    GtBucketspecification bucketspec;
    Bucketenumerator *bucketenumerator;
    Lcpinterval itv;
    unsigned long refstart;
    GtEncseqReader *esr1, *esr2;
    GT_UNUSED int retval;
    unsigned long idx, maxlcp;
    GtCodetype code = 0;
    const GtCodetype **multimappower;
    const GtAlphabet *alpha;

    if (pmopt->usebcktab)
    {
      multimappower = gt_bcktab_multimappower(suffixarray.bcktab);
    } else
    {
      multimappower = NULL;
    }
    epi = gt_newenumpatterniterator(pmopt->minpatternlen,
                                    pmopt->maxpatternlen,
                                    suffixarray.encseq,
                                    err);
    esr1 = gt_encseq_create_reader_with_readmode(suffixarray.encseq,
                                                 suffixarray.readmode, 0);
    esr2 = gt_encseq_create_reader_with_readmode(suffixarray.encseq,
                                                 suffixarray.readmode, 0);
    alpha = gt_encseq_alphabet(suffixarray.encseq);
    for (trial = 0; trial < pmopt->numofsamples; trial++)
    {
      pptr = gt_nextEnumpatterniterator(&patternlen,epi);
      if (pmopt->showpatt)
      {
        gt_alphabet_decode_seq_to_fp(alpha,stdout,pptr,patternlen);
        printf("\n");
      }
      if (pmopt->usebcktab)
      {
        if (patternlen < (unsigned long) suffixarray.prefixlength)
        {
          mmsibck = NULL;
          bucketenumerator
            = gt_newbucketenumerator(suffixarray.bcktab,
                                  suffixarray.prefixlength,
                                  pptr,
                                  (unsigned int) patternlen);
          refstart = UNDEFREFSTART;
          while (gt_nextbucketenumerator(&itv,bucketenumerator))
          {
            if (refstart == UNDEFREFSTART)
            {
              refstart = ESASUFFIXPTRGET(suffixarray.suftab,itv.left);
            } else
            {
              for (idx=itv.left; idx<=itv.right; idx++)
              {
                retval = gt_encseq_check_comparetwosuffixes(
                                        suffixarray.encseq,
                                        suffixarray.readmode,
                                        &maxlcp,
                                        false,
                                        false,
                                        patternlen,
                                        refstart,
                                        ESASUFFIXPTRGET(suffixarray.suftab,idx),
                                        esr1,
                                        esr2);
                gt_assert(retval == 0 && maxlcp == patternlen);
              }
            }
          }
          gt_freebucketenumerator(bucketenumerator);
        } else
        {
          firstspecial = qgram2code(&code,
                                    multimappower,
                                    suffixarray.prefixlength,
                                    pptr);
          gt_assert(firstspecial == suffixarray.prefixlength);
          gt_bcktab_calcboundaries(&bucketspec,
                                   suffixarray.bcktab,
                                   code);
          if (bucketspec.nonspecialsinbucket == 0)
          {
            mmsibck = NULL;
          } else
          {
            mmsibck
              = gt_mmsearchiterator_new_complete_olain(
                                       suffixarray.encseq,
                                       suffixarray.suftab,
                                       bucketspec.left,
                                       bucketspec.left +
                                         bucketspec.nonspecialsinbucket-1,
                                       (unsigned long) suffixarray.prefixlength,
                                       suffixarray.readmode,
                                       pptr,
                                       patternlen);
          }
        }
      }
      if (pmopt->immediate)
      {
        mmsiimm = gt_mmsearchiterator_new_complete_olain(
                                            suffixarray.encseq,
                                            suffixarray.suftab,
                                            0,  /* leftbound */
                                            totallength, /* rightbound */
                                            0, /* offset */
                                            suffixarray.readmode,
                                            pptr,
                                            patternlen);
      }
      if (pmopt->immediate && pmopt->usebcktab)
      {
        comparemmsis(mmsibck,mmsiimm);
      }
      if (pmopt->usebcktab && mmsibck != NULL)
      {
        while (gt_mmsearchiterator_next(&dbstart,mmsibck))
        {
          /* Nothing */;
        }
        gt_mmsearchiterator_delete(mmsibck);
        mmsibck = NULL;
      }
      if (pmopt->immediate)
      {
        while (gt_mmsearchiterator_next(&dbstart,mmsiimm))
        {
          /* Nothing */;
        }
        gt_mmsearchiterator_delete(mmsiimm);
        mmsiimm = NULL;
      }
    }
    gt_encseq_reader_delete(esr1);
    gt_encseq_reader_delete(esr2);
    if (pmopt->showpatt)
    {
      gt_showPatterndistribution(epi);
    }
    gt_freeEnumpatterniterator(epi);
  }
  gt_freesuffixarray(&suffixarray);
  return haserr ? -1 : 0;
}

static GtOPrval parse_options(Pmatchoptions *pmopt,
                              int *parsed_args,
                              int argc, const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOption *option, *optionimm, *optionbck;
  GtOPrval oprval;

  gt_error_check(err);
  op = gt_option_parser_new("[options] -ii indexname",
                         "Perform pattern matches.");
  gt_option_parser_set_mail_address(op, "");

  option = gt_option_new_ulong("minpl","Specify minimum length of pattern",
                           &pmopt->minpatternlen,
                           (unsigned long) 20);
  gt_option_parser_add_option(op, option);
  option = gt_option_new_ulong("maxpl","Specify maximum length of pattern",
                            &pmopt->maxpatternlen,
                            (unsigned long) 30);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("samples","Specify number of samples",
                            &pmopt->numofsamples,
                           (unsigned long) 100000);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("s","Show generated pattern",
                            &pmopt->showpatt,
                            false);
  gt_option_parser_add_option(op, option);

  optionbck = gt_option_new_bool("bck","Use the bucket boundaries",
                              &pmopt->usebcktab,
                              false);
  gt_option_parser_add_option(op, optionbck);

  optionimm = gt_option_new_bool("imm","Start with offset 0",
                              &pmopt->immediate,
                              false);
  gt_option_parser_add_option(op, optionimm);

  option = gt_option_new_string("ii",
                             "Specify input index",
                             pmopt->indexname, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  oprval = gt_option_parser_parse(op, parsed_args, argc, argv,
                               gt_versionfunc, err);
  gt_option_parser_delete(op);

  return oprval;
}

int gt_patternmatch(int argc, const char **argv, GtError *err)
{
  bool haserr = false;
  int parsed_args;
  Pmatchoptions pmopt;
  GtOPrval oprval;

  gt_error_check(err);

  pmopt.indexname = gt_str_new();
  oprval = parse_options(&pmopt,&parsed_args, argc, argv, err);
  if (oprval == GT_OPTION_PARSER_OK)
  {
    gt_assert(parsed_args == argc);
    if (callpatternmatcher(&pmopt,err) != 0)
    {
      haserr = true;
    }
  }
  gt_str_delete(pmopt.indexname);
  if (oprval == GT_OPTION_PARSER_REQUESTS_EXIT)
  {
    return 0;
  }
  if (oprval == GT_OPTION_PARSER_ERROR)
  {
    return -1;
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/tools/gt_patternmatch.h000066400000000000000000000017561211610345200213410ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_PATTERNMATCH_H
#define GT_PATTERNMATCH_H

/* the patternmatch tool */
int gt_patternmatch(int argc, const char **argv, GtError *err);

#endif
genometools-1.5.1/src/tools/gt_prebwt.c000066400000000000000000000077721211610345200201510ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/alphabet_api.h"
#include "core/encseq_metadata.h"
#include "core/ma.h"
#include "core/str.h"
#include "core/tool_api.h"
#include "match/pckbucket.h"
#include "match/eis-voiditf.h"

typedef struct
{
  GtStr *indexname;
  unsigned int maxdepth;
} Prebwtoptions;

static void *gt_prebwt_arguments_new(void)
{
  return gt_malloc(sizeof (Prebwtoptions));
}

static void gt_prebwt_arguments_delete(void *tool_arguments)
{
  Prebwtoptions *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->indexname);
  gt_free(arguments);
}

static GtOptionParser* gt_prebwt_option_parser_new(void *tool_arguments)
{
  Prebwtoptions *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionpck;

  gt_assert(arguments != NULL);
  arguments->indexname = gt_str_new();
  op = gt_option_parser_new("[options] -pck indexname",
                            "Precompute bwt-bounds for some prefix length.");
  gt_option_parser_set_mail_address(op, "");

  optionpck = gt_option_new_string("pck","Specify index (packed index)",
                             arguments->indexname, NULL);
  gt_option_parser_add_option(op, optionpck);
  gt_option_is_mandatory(optionpck);

  option = gt_option_new_uint_min("maxdepth",
                                  "specify maximum depth (value > 0)",
                                  &arguments->maxdepth,0,1U);
  gt_option_parser_add_option(op, option);
  return op;
}

static int gt_prebwt_runner(GT_UNUSED int argc,
                            GT_UNUSED const char **argv,
                            GT_UNUSED int parsed_args,
                            void *tool_arguments, GtError *err)
{
  unsigned long totallength = 0;
  FMindex *fmindex = NULL;
  bool haserr = false;
  GtEncseqMetadata *emd = NULL;
  Prebwtoptions *prebwtoptions = (Prebwtoptions *) tool_arguments;
  GtAlphabet *alphabet;
  const char *indexname = gt_str_get(prebwtoptions->indexname);

  emd = gt_encseq_metadata_new(indexname, err);
  if (emd == NULL) {
    haserr = true;
  }
  if (!haserr) {
    alphabet = gt_encseq_metadata_alphabet(emd);
    if (alphabet == NULL)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    fmindex = gt_loadvoidBWTSeqForSA(indexname,false, err);
    if (fmindex == NULL)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    unsigned int numofchars = gt_alphabet_num_of_chars(alphabet);
    Pckbuckettable *pckbt;
    totallength = gt_voidpackedindex_totallength_get(fmindex);

    pckbt = gt_pckbuckettable_new((const void *) fmindex,
                                  numofchars,
                                  totallength,
                                  prebwtoptions->maxdepth);
    if (gt_pckbuckettable_2file(indexname,pckbt,err) != 0)
    {
      haserr = true;
    }
    gt_pckbuckettable_delete(pckbt);
  }
  gt_encseq_metadata_delete(emd);
  if (fmindex != NULL)
  {
    gt_deletevoidBWTSeq(fmindex);
  }
  return haserr ? -1 : 0;
}

GtTool* gt_prebwt(void)
{
  return gt_tool_new(gt_prebwt_arguments_new,
                  gt_prebwt_arguments_delete,
                  gt_prebwt_option_parser_new,
                  NULL,
                  gt_prebwt_runner);
}
genometools-1.5.1/src/tools/gt_prebwt.h000066400000000000000000000017241211610345200201450ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_PREBWT_H
#define GT_PREBWT_H

#include "core/tool_api.h"

/* the tagerator tool */
GtTool* gt_prebwt(void);

#endif
genometools-1.5.1/src/tools/gt_readjoiner.c000066400000000000000000000102221211610345200207500ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/cstr_array.h"
#include "core/option_api.h"
#include "core/unused_api.h"
#include "extended/toolbox.h"
#include "extended/gtdatahelp.h"
#include "match/rdj-version.h"
#include "tools/gt_readjoiner_prefilter.h"
#include "tools/gt_readjoiner_overlap.h"
#include "tools/gt_readjoiner_assembly.h"
#include "tools/gt_readjoiner_asqg.h"
#include "tools/gt_readjoiner_cnttest.h"
#include "tools/gt_readjoiner_spmtest.h"
#include "tools/gt_readjoiner_correct.h"

static void* gt_readjoiner_arguments_new(void)
{
  GtToolbox *readjoiner_toolbox = gt_toolbox_new();
  gt_toolbox_add_tool(readjoiner_toolbox, "prefilter",
      gt_readjoiner_prefilter());
  gt_toolbox_add_tool(readjoiner_toolbox, "overlap", gt_readjoiner_overlap());
  gt_toolbox_add_tool(readjoiner_toolbox, "assembly", gt_readjoiner_assembly());
  gt_toolbox_add_hidden_tool(readjoiner_toolbox, "asqg", gt_readjoiner_asqg());
  gt_toolbox_add_hidden_tool(readjoiner_toolbox, "cnttest",
      gt_readjoiner_cnttest());
  gt_toolbox_add_hidden_tool(readjoiner_toolbox, "spmtest",
      gt_readjoiner_spmtest());
  gt_toolbox_add_hidden_tool(readjoiner_toolbox, "correct",
      gt_readjoiner_correct());
  return readjoiner_toolbox;
}

static void gt_readjoiner_arguments_delete(void *tool_arguments)
{
  GtToolbox *readjoiner_toolbox = tool_arguments;
  if (!readjoiner_toolbox) return;
  gt_toolbox_delete(readjoiner_toolbox);
}

static GtOptionParser* gt_readjoiner_option_parser_new(GT_UNUSED
    void *tool_arguments)
{
  GtOptionParser *op;
  op = gt_option_parser_new("[option ...] tool [argument ...]",
                 "Readjoiner: a string graph-based sequence assembler.");
  gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_min_args(op, 1);
  return op;
}

static int gt_readjoiner_runner(int argc, const char **argv, int parsed_args,
                         void *tool_arguments, GtError *err)
{
  GtToolbox *readjoiner_toolbox = tool_arguments;
  GtToolfunc toolfunc;
  GtTool *tool = NULL;
  int had_err = 0;
  char **nargv = NULL;

  gt_error_check(err);
  gt_assert(readjoiner_toolbox);

  /* get readjoiner tools */
  if (!gt_toolbox_has_tool(readjoiner_toolbox, argv[parsed_args])) {
    gt_error_set(err, "readjoiner tool '%s' not found; option -help lists "
                      "possible tools", argv[parsed_args]);
    had_err = -1;
  }

  /* call readjoiner tool */
  if (!had_err) {
    if (!(toolfunc = gt_toolbox_get(readjoiner_toolbox, argv[parsed_args]))) {
      tool = gt_toolbox_get_tool(readjoiner_toolbox, argv[parsed_args]);
      gt_assert(tool);
    }
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    if (toolfunc)
      had_err = toolfunc(argc - parsed_args, (const char**) nargv, err);
    else
      had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv,
                            err);
  }

  /* free */
  gt_cstr_array_delete(nargv);

  return had_err;
}

GtTool* gt_readjoiner(void)
{
  return gt_tool_new(gt_readjoiner_arguments_new,
                     gt_readjoiner_arguments_delete,
                     gt_readjoiner_option_parser_new,
                     NULL,
                     gt_readjoiner_runner);
}
genometools-1.5.1/src/tools/gt_readjoiner.h000066400000000000000000000017541211610345200207670ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_READJOINER_H
#define GT_READJOINER_H

#include "core/tool_api.h"

/* the readjoiner toolbox */
GtTool* gt_readjoiner(void);

#endif
genometools-1.5.1/src/tools/gt_readjoiner_asqg.c000066400000000000000000000277031211610345200217770ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/log_api.h"
#include "core/logger.h"
#include "core/fa.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "core/showtime.h"
#include "core/spacecalc.h"
#include "match/asqg_writer.h"
#include "match/rdj-contigpaths.h"
#include "match/rdj-cntlist.h"
#include "match/rdj-spmlist.h"
#include "match/rdj-strgraph.h"
#include "match/rdj-filesuf-def.h"
#include "match/rdj-version.h"
#include "tools/gt_readjoiner_asqg.h"

typedef struct {
  bool verbose, quiet;
  unsigned int minmatchlength;
  GtStr  *readset;
  bool gz, sg;
  unsigned int nspmfiles;
} GtReadjoinerAsqgArguments;

static void* gt_readjoiner_asqg_arguments_new(void)
{
  GtReadjoinerAsqgArguments *arguments = gt_calloc((size_t)1,
      sizeof *arguments);
  arguments->readset = gt_str_new();
  return arguments;
}

static void gt_readjoiner_asqg_arguments_delete(void *tool_arguments)
{
  GtReadjoinerAsqgArguments *arguments = tool_arguments;
  if (!arguments)
    return;
  gt_str_delete(arguments->readset);
  gt_free(arguments);
}

static GtOptionParser* gt_readjoiner_asqg_option_parser_new(
    void *tool_arguments)
{
  GtReadjoinerAsqgArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *v_option;
  gt_assert(arguments != NULL);

  /* init */
  op = gt_option_parser_new("[option ...]",
      "Output string graph in SGA asqg format.");

  /* -readset */
  option = gt_option_new_string("readset", "specify the readset name",
      arguments->readset, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -spmfiles */
  option = gt_option_new_uint_min("spmfiles", "number of SPM files to read\n"
      "this must be equal to the value of -j for the overlap phase",
      &arguments->nspmfiles, 1U, 1U);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -l */
  option = gt_option_new_uint_min("l", "specify the minimum SPM length",
      &arguments->minmatchlength, 0, 2U);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -gz */
  option = gt_option_new_bool("gz", "output gzipped file",
      &arguments->gz, false);
  gt_option_parser_add_option(op, option);

  /* -sg */
  option = gt_option_new_bool("sg", "first construct a Readjoiner string "
      "graph, then convert it into SGA format",
      &arguments->sg, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -v */
  v_option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, v_option);

  /* -q */
  option = gt_option_new_bool("q", "suppress standard output messages",
      &arguments->quiet, false);
  gt_option_exclude(option, v_option);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
  gt_option_parser_set_max_args(op, 0);

  return op;
}

#define GT_READJOINER_ASQG_MSG_INIT \
  "initialization"
#define GT_READJOINER_ASQG_MSG_CNT \
  "parse lists of contained reads"

/* encseq + spm -> asqg */
#define GT_READJOINER_ASQG_MSG_VERTICES \
  "output vertices in asqg format"
#define GT_READJOINER_ASQG_MSG_EDGES \
  "output edges in asqg format"

/* encseq + sg -> asqg */
#define GT_READJOINER_ASQG_MSG_COUNT \
  "build string graph (counting phase)"
#define GT_READJOINER_ASQG_MSG_INSERT \
  "build string graph (insertion phase)"
#define GT_READJOINER_ASQG_MSG_OUTPUT \
  "output string graph in asqg format"

static int gt_readjoiner_asqg_use_spmfiles(GtSpmproc proc, void *procdata,
    const char *readset, unsigned int minmatchlength, unsigned int nspmfiles,
    GtBitsequence *contained, GtError *err)
{
  int had_err = 0;
  GtSpmprocSkipData skipdata;
  unsigned int i;
  GtStr *filename = gt_str_new();
  if (contained != NULL)
  {
    skipdata.to_skip = contained;
    skipdata.out.e.proc = proc;
    skipdata.out.e.data = procdata;
  }
  for (i = 0; i < nspmfiles; i++)
  {
    gt_str_append_cstr(filename, readset);
    gt_str_append_char(filename, '.');
    gt_str_append_uint(filename, i);
    gt_str_append_cstr(filename, GT_READJOINER_SUFFIX_SPMLIST);
    had_err = gt_spmlist_parse(gt_str_get(filename),
        (unsigned long)minmatchlength,
        contained == NULL ? proc : gt_spmproc_skip,
        contained == NULL ? (void*)procdata : (void*)&skipdata, err);
    gt_str_reset(filename);
  }
  gt_str_delete(filename);
  return had_err;
}

static inline void gt_readjoiner_asqg_show_current_space(const char *label)
{
  unsigned long m, f;
  if (gt_ma_bookkeeping_enabled())
  {
    m = gt_ma_get_space_current();
    f = gt_fa_get_space_current();
    gt_log_log("used space after %s: %.2f MB (ma: %.2f MB; fa: %.2f MB)",
        label == NULL ? "" : label, GT_MEGABYTES(m + f), GT_MEGABYTES(m),
        GT_MEGABYTES(f));
  }
}

static int gt_readjoiner_asqg_runner(GT_UNUSED int argc,
    GT_UNUSED const char **argv, GT_UNUSED int parsed_args,
    void *tool_arguments, GtError *err)
{
  GtReadjoinerAsqgArguments *arguments = tool_arguments;
  GtLogger *verbose_logger, *default_logger;
  GtEncseqLoader *el;
  GtEncseq *reads;
  GtTimer *timer = NULL;
  GtStrgraph *strgraph = NULL;
  GtBitsequence *contained = NULL;
  const char *readset = gt_str_get(arguments->readset);
  bool eqlen;
  unsigned long nreads;
  int had_err = 0;

  if (gt_showtime_enabled())
  {
    timer = gt_timer_new_with_progress_description(
        GT_READJOINER_ASQG_MSG_INIT);
    gt_timer_start(timer);
    gt_timer_show_cpu_time_by_progress(timer);
  }
  gt_assert(arguments);
  gt_error_check(err);
  default_logger = gt_logger_new(!arguments->quiet, GT_LOGGER_DEFLT_PREFIX,
      stdout);
  gt_logger_log(default_logger, "gt readjoiner asqg");
  verbose_logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX,
      stdout);
  gt_logger_log(verbose_logger, "verbose output activated");
  gt_logger_log(verbose_logger, "readset name = %s", readset);
  if (arguments->minmatchlength > 0)
    gt_logger_log(verbose_logger, "SPM length cutoff = %u",
        arguments->minmatchlength);

  el = gt_encseq_loader_new();
  gt_encseq_loader_drop_description_support(el);
  gt_encseq_loader_disable_autosupport(el);
  reads = gt_encseq_loader_load(el, readset, err);
  nreads = gt_encseq_num_of_sequences(reads);
  gt_assert(reads != NULL);
  eqlen = gt_encseq_accesstype_get(reads) == GT_ACCESS_TYPE_EQUALLENGTH;
  gt_readjoiner_asqg_show_current_space(GT_READJOINER_ASQG_MSG_INIT);
  if (!eqlen)
  {
    unsigned int i;
    unsigned long nofreads;
    GtStr *filename = gt_str_clone(arguments->readset);
    if (gt_showtime_enabled())
      gt_timer_show_progress(timer, GT_READJOINER_ASQG_MSG_CNT, stdout);
    gt_logger_log(default_logger, GT_READJOINER_ASQG_MSG_CNT);
    gt_str_append_cstr(filename, ".0" GT_READJOINER_SUFFIX_CNTLIST);
    had_err = gt_cntlist_parse(gt_str_get(filename), true, &contained,
        &nofreads, err);
    for (i = 1U; i < arguments->nspmfiles && had_err == 0; i++)
    {
      unsigned long nofreads_i;
      gt_str_reset(filename);
      gt_str_append_str(filename, arguments->readset);
      gt_str_append_char(filename, '.');
      gt_str_append_uint(filename, i);
      gt_str_append_cstr(filename, GT_READJOINER_SUFFIX_CNTLIST);
      had_err = gt_cntlist_parse(gt_str_get(filename), false, &contained,
          &nofreads_i, err);
      gt_assert(nofreads == nofreads_i);
    }
    gt_str_delete(filename);
    gt_readjoiner_asqg_show_current_space(GT_READJOINER_ASQG_MSG_CNT);
  }
  if (!arguments->sg)
  {
    GtStr *filename = NULL;
    GtFile *file = NULL;
    GtAsqgWriter *aw = NULL;
    if (had_err == 0)
    {
      filename = gt_str_clone(arguments->readset);
      gt_str_append_cstr(filename, arguments->gz ? ".asqg.gz" : ".asqg");
      file = gt_file_open(arguments->gz ? GT_FILE_MODE_GZIP :
          GT_FILE_MODE_UNCOMPRESSED, gt_str_get(filename), "w", err);
      if (file == NULL)
        had_err = -1;
    }
    if (had_err == 0)
    {
      aw = gt_asqg_writer_new(file, reads);
      if (gt_showtime_enabled())
        gt_timer_show_progress(timer, GT_READJOINER_ASQG_MSG_VERTICES,
            stdout);
      gt_logger_log(default_logger, GT_READJOINER_ASQG_MSG_VERTICES);
      had_err = gt_asqg_writer_show_header(aw, 0.0,
          (unsigned long)arguments->minmatchlength,
          gt_str_get(arguments->readset), false, false, err);
    }
    if (had_err == 0)
    {
      had_err = gt_asqg_writer_show_vertices(aw, err);
      gt_readjoiner_asqg_show_current_space(GT_READJOINER_ASQG_MSG_VERTICES);
    }
    if (had_err == 0)
    {
      if (gt_showtime_enabled())
        gt_timer_show_progress(timer, GT_READJOINER_ASQG_MSG_EDGES, stdout);
      gt_logger_log(default_logger, GT_READJOINER_ASQG_MSG_EDGES);
      had_err = gt_readjoiner_asqg_use_spmfiles(gt_spmproc_show_asgq,
          aw, readset, arguments->minmatchlength, arguments->nspmfiles,
          contained, err);
      gt_readjoiner_asqg_show_current_space(GT_READJOINER_ASQG_MSG_EDGES);
    }
    gt_str_delete(filename);
    gt_file_delete(file);
    gt_asqg_writer_delete(aw);
  }
  else
  {
    if (had_err == 0)
    {
      if (gt_showtime_enabled())
        gt_timer_show_progress(timer, GT_READJOINER_ASQG_MSG_COUNT, stdout);
      gt_logger_log(default_logger, GT_READJOINER_ASQG_MSG_COUNT);
      strgraph = gt_strgraph_new(nreads);
      had_err = gt_readjoiner_asqg_use_spmfiles(gt_spmproc_strgraph_count,
          strgraph, readset, arguments->minmatchlength, arguments->nspmfiles,
          contained, err);
      gt_readjoiner_asqg_show_current_space(GT_READJOINER_ASQG_MSG_COUNT);
    }
    if (had_err == 0)
    {
      if (gt_showtime_enabled())
        gt_timer_show_progress(timer, GT_READJOINER_ASQG_MSG_INSERT, stdout);
      gt_logger_log(default_logger, GT_READJOINER_ASQG_MSG_INSERT);
      gt_strgraph_allocate_graph(strgraph,
          eqlen ? gt_encseq_seqlength(reads, 0) : 0,
          eqlen ? NULL : reads);
      had_err = gt_strgraph_load_spm_from_file(strgraph,
          (unsigned long)arguments->minmatchlength, false,
          contained, readset, arguments->nspmfiles,
          GT_READJOINER_SUFFIX_SPMLIST, err);
      gt_readjoiner_asqg_show_current_space(GT_READJOINER_ASQG_MSG_INSERT);
    }
    if (had_err == 0)
    {
      if (gt_showtime_enabled())
        gt_timer_show_progress(timer, GT_READJOINER_ASQG_MSG_OUTPUT, stdout);
      gt_logger_log(default_logger, GT_READJOINER_ASQG_MSG_OUTPUT);
      gt_strgraph_set_encseq(strgraph, reads);
      gt_strgraph_show(strgraph, arguments->gz ? GT_STRGRAPH_ASQG_GZ :
          GT_STRGRAPH_ASQG, gt_str_get(arguments->readset),
          arguments->gz ? ".asqg.gz" : ".asqg", false);
      gt_readjoiner_asqg_show_current_space(GT_READJOINER_ASQG_MSG_OUTPUT);
    }
  }
  if (gt_showtime_enabled())
  {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  gt_free(contained);
  gt_strgraph_delete(strgraph);
  gt_encseq_loader_delete(el);
  gt_encseq_delete(reads);
  gt_logger_delete(default_logger);
  gt_logger_delete(verbose_logger);
  return had_err;
}

GtTool* gt_readjoiner_asqg(void)
{
  return gt_tool_new(gt_readjoiner_asqg_arguments_new,
                  gt_readjoiner_asqg_arguments_delete,
                  gt_readjoiner_asqg_option_parser_new,
                  NULL, gt_readjoiner_asqg_runner);
}
genometools-1.5.1/src/tools/gt_readjoiner_asqg.h000066400000000000000000000017741211610345200220040ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_READJOINER_ASQG_H
#define GT_READJOINER_ASQG_H

#include "core/tool_api.h"

/* the readjoiner_asqg tool */
GtTool* gt_readjoiner_asqg(void);

#endif
genometools-1.5.1/src/tools/gt_readjoiner_assembly.c000066400000000000000000000462231211610345200226610ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/log_api.h"
#include "core/logger.h"
#include "core/fa.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "core/showtime.h"
#include "core/spacecalc.h"
#include "match/rdj-contigpaths.h"
#include "match/rdj-cntlist.h"
#include "match/rdj-spmlist.h"
#include "match/rdj-strgraph.h"
#include "match/rdj-filesuf-def.h"
#include "match/rdj-version.h"
#include "tools/gt_readjoiner_assembly.h"

typedef struct {
  bool verbose, quiet;
  unsigned int minmatchlength;
  unsigned int lengthcutoff, depthcutoff;
  GtStr  *readset, *buffersizearg;
  bool errors, paths2seq, redtrans, elendistri;
  unsigned int deadend, bubble, deadend_depth;
  GtOption *refoptionbuffersize;
  unsigned long buffersize;
  unsigned int nspmfiles;
} GtReadjoinerAssemblyArguments;

static void* gt_readjoiner_assembly_arguments_new(void)
{
  GtReadjoinerAssemblyArguments *arguments = gt_calloc((size_t)1,
      sizeof *arguments);
  arguments->readset = gt_str_new();
  arguments->buffersizearg = gt_str_new();
  arguments->buffersize = 0UL; /* in bytes */
  return arguments;
}

static void gt_readjoiner_assembly_arguments_delete(void *tool_arguments)
{
  GtReadjoinerAssemblyArguments *arguments = tool_arguments;
  if (!arguments)
    return;
  gt_str_delete(arguments->readset);
  gt_str_delete(arguments->buffersizearg);
  gt_option_delete(arguments->refoptionbuffersize);
  gt_free(arguments);
}

static GtOptionParser* gt_readjoiner_assembly_option_parser_new(
    void *tool_arguments)
{
  GtReadjoinerAssemblyArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *errors_option, *deadend_option, *v_option,
           *q_option, *bubble_option, *deadend_depth_option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...]",
      "Construct string graph and output contigs.");

  /* -readset */
  option = gt_option_new_string("readset", "specify the readset name",
      arguments->readset, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -spmfiles */
  option = gt_option_new_uint_min("spmfiles", "number of SPM files to read\n"
      "this must be equal to the value of -j for the overlap phase",
      &arguments->nspmfiles, 1U, 1U);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -l */
  option = gt_option_new_uint_min("l", "specify the minimum SPM length",
      &arguments->minmatchlength, 0, 2U);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -depthcutoff */
  option = gt_option_new_uint_min("depthcutoff", "specify the minimal "
      "number of nodes in a contig",
      &arguments->depthcutoff, 3U, 1U);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -lengthcutoff */
  option = gt_option_new_uint_min("lengthcutoff", "specify the minimal "
      "length of a contig",
      &arguments->lengthcutoff, 100U, 1U);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -redtrans */
  option = gt_option_new_bool("redtrans", "reduce transitive edges",
      &arguments->redtrans, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -errors */
  errors_option = gt_option_new_bool("errors", "search graph features which "
      "may originate from sequencing errors and remove them",
      &arguments->errors, false);
  gt_option_is_extended_option(errors_option);
  gt_option_parser_add_option(op, errors_option);

  /* -bubble */
  bubble_option = gt_option_new_uint("bubble", "number of rounds of p-bubble "
      "removal to perform", &arguments->bubble, 3U);
  gt_option_is_extended_option(bubble_option);
  gt_option_imply(bubble_option, errors_option);
  gt_option_parser_add_option(op, bubble_option);

  /* -deadend */
  deadend_option = gt_option_new_uint("deadend", "number of rounds of "
      "dead end removal to perform a dead end",
      &arguments->deadend, 10U);
  gt_option_is_extended_option(deadend_option);
  gt_option_imply(deadend_option, errors_option);
  gt_option_parser_add_option(op, deadend_option);

  /* -deadend-depth */
  deadend_depth_option = gt_option_new_uint_min("deadend-depth", "specify the "
      "maximal depth of a path to an end-vertex by which the path shall be "
      "considered a dead end",
      &arguments->deadend_depth, 10U, 1U);
  gt_option_is_extended_option(deadend_depth_option);
  gt_option_imply(deadend_depth_option, errors_option);
  gt_option_parser_add_option(op, deadend_depth_option);

  /* -paths2seq */
  option = gt_option_new_bool("paths2seq", "read "
      GT_READJOINER_SUFFIX_CONTIG_PATHS " and write "
      "" GT_READJOINER_SUFFIX_CONTIGS,
      &arguments->paths2seq, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -buffersize */
  option = gt_option_new_string("buffersize", "specify size for read buffer"
      " of paths2seq phase (in bytes, the keywords 'MB' and 'GB' are allowed)",
                       arguments->buffersizearg, NULL);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);
  arguments->refoptionbuffersize = gt_option_ref(option);

  /* -v */
  v_option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, v_option);

  /* -q */
  q_option = gt_option_new_bool("q", "suppress standard output messages",
      &arguments->quiet, false);
  gt_option_parser_add_option(op, q_option);
  gt_option_exclude(q_option, v_option);

  /* -elendistri */
  option = gt_option_new_bool("elendistri", "output edges lenght"
      "distribution to " GT_READJOINER_SUFFIX_ELEN_DISTRI,
      &arguments->elendistri, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
  gt_option_parser_set_max_args(op, 0);

  return op;
}

static int gt_readjoiner_assembly_arguments_check(GT_UNUSED int rest_argc,
    void *tool_arguments, GtError *err)
{
  GtReadjoinerAssemblyArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  if (had_err == 0 && gt_option_is_set(arguments->refoptionbuffersize))
    if (gt_option_parse_spacespec(&arguments->buffersize,
          "buffersize", arguments->buffersizearg, err) != 0)
      had_err = -1;
  return had_err;
}

#define GT_READJOINER_MSG_COUNTSPM \
  "calculate edges space for each vertex"
#define GT_READJOINER_MSG_BUILDSG \
  "build string graph"
#define GT_READJOINER_MSG_REDTRANS \
  "reduce transitive edges"
#define GT_READJOINER_MSG_CLEANSG \
  "correct sequencing errors"
#define GT_READJOINER_MSG_TRAVERSESG \
  "save contig paths"
#define GT_READJOINER_MSG_PUMPENCSEQ \
  "pump encseq through cache"
#define GT_READJOINER_MSG_OUTPUTCONTIGS \
  "save contig sequences"

static int gt_readjoiner_assembly_count_spm(const char *readset, bool eqlen,
    unsigned int minmatchlength, unsigned int nspmfiles, GtStrgraph *strgraph,
    GtBitsequence *contained, GtLogger *default_logger, GtError *err)
{
  GtSpmprocSkipData skipdata;
  int had_err = 0;
  unsigned int i;
  GtStr *filename = gt_str_new();
  gt_logger_log(default_logger, GT_READJOINER_MSG_COUNTSPM);
  if (!eqlen)
  {
    skipdata.out.e.proc = gt_spmproc_strgraph_count;
    skipdata.to_skip = contained;
    skipdata.out.e.data = strgraph;
  }
  for (i = 0; i < nspmfiles; i++)
  {
    gt_str_append_cstr(filename, readset);
    gt_str_append_char(filename, '.');
    gt_str_append_uint(filename, i);
    gt_str_append_cstr(filename, GT_READJOINER_SUFFIX_SPMLIST);
    had_err = gt_spmlist_parse(gt_str_get(filename),
        (unsigned long)minmatchlength,
        eqlen ? gt_spmproc_strgraph_count : gt_spmproc_skip,
        eqlen ? (void*)strgraph : (void*)&skipdata, err);
    gt_str_reset(filename);
  }
  gt_str_delete(filename);
  return had_err;
}

static int gt_readjoiner_assembly_error_correction(GtStrgraph *strgraph,
    unsigned int bubble, unsigned int deadend, unsigned int deadend_depth,
    GtLogger *verbose_logger)
{
  unsigned int i;
  unsigned long retval, retval_sum;
  gt_logger_log(verbose_logger, "remove p-bubbles");

  retval_sum = 0;
  retval = 1UL;
  for (i = 0; i < bubble && retval > 0; i++)
  {
    retval = gt_strgraph_redpbubbles(strgraph, 0, 1UL, false);
    retval_sum += retval;
    gt_logger_log(verbose_logger, "removed p-bubble edges [round %u] = %lu",
        i + 1, retval);
  }
  gt_logger_log(verbose_logger, "removed p-bubble edges [%u rounds] = %lu", i,
      retval_sum);
  gt_logger_log(verbose_logger, "remove dead-end paths");

  retval_sum = 0;
  retval = 1UL;
  for (i = 0; i < deadend && retval > 0; i++)
  {
    retval = gt_strgraph_reddepaths(strgraph, (unsigned long)deadend_depth,
        false);
    retval_sum += retval;
    gt_logger_log(verbose_logger, "removed dead-end path edges [round %u] = "
        "%lu", i + 1, retval);
  }
  gt_logger_log(verbose_logger,
      "removed dead-end path edges [%u rounds] = %lu", i, retval);
  return 0;
}

static void gt_readjoiner_assembly_pump_encseq_through_cache(
    const GtEncseq *encseq)
{
  const GtTwobitencoding *twobitencoding = gt_encseq_twobitencoding_export(
      encseq);
  uint64_t sum = 0; /* compute the sum, so that the compiler does no remove the
                       code accessing twobitencoding during optimization */
  unsigned long idx, totallength = gt_encseq_total_length(encseq),
                numofunits = ! gt_encseq_is_mirrored(encseq)
                  ? gt_unitsoftwobitencoding(totallength)
                  : gt_unitsoftwobitencoding((totallength - 1)/2);
  for (idx = 0; idx < numofunits; idx++)
    sum += twobitencoding[idx];
  gt_assert(sum > 0);
#ifndef S_SPLINT_S
  gt_log_log("encseq codes-sum: %"PRIu64, sum);
#endif
}

static int gt_readjoiner_assembly_paths2seq(const char *readset,
    unsigned long lengthcutoff, unsigned long buffersize,
    GtLogger *default_logger, GtTimer **timer, GtError *err)
{
  int had_err;
  GtEncseqLoader *el = gt_encseq_loader_new();
  GtEncseq *reads;

  if (gt_showtime_enabled())
  {
    gt_assert(timer != NULL);
    if (*timer == NULL) /* paths2seq */
    {
      *timer = gt_timer_new_with_progress_description(
          GT_READJOINER_MSG_PUMPENCSEQ);
      gt_timer_show_cpu_time_by_progress(*timer);
      gt_timer_start(*timer);
    }
    else
      gt_timer_show_progress(*timer, GT_READJOINER_MSG_PUMPENCSEQ, stdout);
  }
  gt_logger_log(default_logger, GT_READJOINER_MSG_PUMPENCSEQ);
  gt_encseq_loader_drop_description_support(el);
  gt_encseq_loader_disable_autosupport(el);
  gt_encseq_loader_mirror(el);
  reads = gt_encseq_loader_load(el, readset, err);
  gt_assert(reads != NULL);
  gt_readjoiner_assembly_pump_encseq_through_cache(reads);
  if (gt_showtime_enabled())
    gt_timer_show_progress(*timer, GT_READJOINER_MSG_OUTPUTCONTIGS, stdout);
  gt_logger_log(default_logger, GT_READJOINER_MSG_OUTPUTCONTIGS);
  had_err = gt_contigpaths_to_fasta(readset, GT_READJOINER_SUFFIX_CONTIG_PATHS,
      GT_READJOINER_SUFFIX_CONTIGS, reads, lengthcutoff, false,
      (size_t)buffersize, default_logger, err);
  gt_encseq_delete(reads);
  gt_encseq_loader_delete(el);
  return had_err;
}

static inline void gt_readjoiner_assembly_show_current_space(const char *label)
{
  unsigned long m, f;
  if (gt_ma_bookkeeping_enabled())
  {
    m = gt_ma_get_space_current();
    f = gt_fa_get_space_current();
    gt_log_log("used space %s: %.2f MB (ma: %.2f MB; fa: %.2f MB)",
        label == NULL ? "" : label, GT_MEGABYTES(m + f), GT_MEGABYTES(m),
        GT_MEGABYTES(f));
  }
}

static int gt_readjoiner_assembly_runner(GT_UNUSED int argc,
    GT_UNUSED const char **argv, GT_UNUSED int parsed_args,
    void *tool_arguments, GtError *err)
{
  GtReadjoinerAssemblyArguments *arguments = tool_arguments;
  GtLogger *verbose_logger, *default_logger;
  GtEncseqLoader *el;
  GtEncseq *reads;
  GtTimer *timer = NULL;
  GtStrgraph *strgraph = NULL;
  GtBitsequence *contained = NULL;
  const char *readset = gt_str_get(arguments->readset);
  bool eqlen;
  unsigned long nreads, tlen, rlen;
  int had_err = 0;

  gt_assert(arguments);
  gt_error_check(err);
  default_logger = gt_logger_new(!arguments->quiet, GT_LOGGER_DEFLT_PREFIX,
      stdout);
  gt_logger_log(default_logger,
      "gt readjoiner assembly (version "GT_READJOINER_VERSION")");
  verbose_logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX,
      stdout);
  gt_logger_log(verbose_logger, "verbose output activated");
  gt_logger_log(verbose_logger, "readset name = %s", readset);

  if (!arguments->paths2seq)
  {
    el = gt_encseq_loader_new();
    gt_encseq_loader_drop_description_support(el);
    gt_encseq_loader_disable_autosupport(el);
    reads = gt_encseq_loader_load(el, readset, err);
    gt_assert(reads != NULL);
    eqlen = gt_encseq_accesstype_get(reads) == GT_ACCESS_TYPE_EQUALLENGTH;
    nreads = gt_encseq_num_of_sequences(reads);
    gt_logger_log(default_logger, "number of reads in filtered readset = %lu",
        nreads);
    tlen = gt_encseq_total_length(reads) - nreads + 1;
    gt_logger_log(verbose_logger, "total length of filtered readset = %lu",
        tlen);

    if (eqlen)
    {
      rlen = gt_encseq_seqlength(reads, 0);
      gt_logger_log(verbose_logger, "read length = %lu", rlen);
      gt_encseq_delete(reads);
      reads = NULL;
    }
    else
    {
      unsigned int i;
      unsigned long nofreads;
      GtStr *filename = gt_str_clone(arguments->readset);
      gt_str_append_cstr(filename, ".0" GT_READJOINER_SUFFIX_CNTLIST);
      had_err = gt_cntlist_parse(gt_str_get(filename), true, &contained,
          &nofreads, err);
      for (i = 1U; i < arguments->nspmfiles && had_err == 0; i++)
      {
        unsigned long nofreads_i;
        gt_str_reset(filename);
        gt_str_append_str(filename, arguments->readset);
        gt_str_append_char(filename, '.');
        gt_str_append_uint(filename, i);
        gt_str_append_cstr(filename, GT_READJOINER_SUFFIX_CNTLIST);
        had_err = gt_cntlist_parse(gt_str_get(filename), false, &contained,
            &nofreads_i, err);
        gt_assert(nofreads == nofreads_i);
      }
      gt_str_delete(filename);
      rlen = 0;
      gt_logger_log(verbose_logger, "read length = variable");
      gt_assert(reads != NULL);
    }

    if (had_err == 0)
    {
      if (arguments->minmatchlength > 0)
        gt_logger_log(verbose_logger, "SPM length cutoff = %u",
            arguments->minmatchlength);

      strgraph = gt_strgraph_new(nreads);
      if (gt_showtime_enabled())
      {
        timer = gt_timer_new_with_progress_description(
            GT_READJOINER_MSG_COUNTSPM);
        gt_timer_start(timer);
        gt_timer_show_cpu_time_by_progress(timer);
      }
      had_err = gt_readjoiner_assembly_count_spm(readset, eqlen,
         arguments->minmatchlength, arguments->nspmfiles, strgraph, contained,
         default_logger, err);
      gt_readjoiner_assembly_show_current_space("(edges counted)");
      if (gt_showtime_enabled())
        gt_timer_show_progress(timer, GT_READJOINER_MSG_BUILDSG, stdout);
      gt_logger_log(default_logger, GT_READJOINER_MSG_BUILDSG);
    }
    if (had_err == 0)
    {
      gt_assert((eqlen && rlen > 0 && reads == NULL) ||
          (!eqlen && rlen == 0 && reads != NULL));
      gt_strgraph_allocate_graph(strgraph, rlen, reads);
      gt_readjoiner_assembly_show_current_space("(graph allocated)");
      had_err = gt_strgraph_load_spm_from_file(strgraph,
            (unsigned long)arguments->minmatchlength, arguments->redtrans,
            contained, readset, arguments->nspmfiles,
            GT_READJOINER_SUFFIX_SPMLIST, err);
    }
    if (had_err == 0)
    {
      if (arguments->elendistri)
        gt_strgraph_show_edge_lengths_distribution(strgraph, readset,
            GT_READJOINER_SUFFIX_ELEN_DISTRI);
      gt_strgraph_log_stats(strgraph, verbose_logger);
      gt_strgraph_log_space(strgraph);
    }

    if (!eqlen && reads != NULL && !arguments->errors)
    {
      gt_encseq_delete(reads);
      reads = NULL;
      if (had_err == 0)
        gt_strgraph_set_encseq(strgraph, NULL);
    }

    if (had_err == 0 && arguments->redtrans)
    {
      if (gt_showtime_enabled())
        gt_timer_show_progress(timer, GT_READJOINER_MSG_REDTRANS, stdout);
      gt_strgraph_sort_edges_by_len(strgraph, false);
      (void)gt_strgraph_redtrans(strgraph, false);
      (void)gt_strgraph_redself(strgraph, false);
      (void)gt_strgraph_redwithrc(strgraph, false);
      gt_strgraph_log_stats(strgraph, verbose_logger);
    }

    if (had_err == 0 && arguments->errors)
    {
      if (gt_showtime_enabled())
        gt_timer_show_progress(timer, GT_READJOINER_MSG_CLEANSG, stdout);
      gt_logger_log(default_logger, GT_READJOINER_MSG_CLEANSG);
      had_err = gt_readjoiner_assembly_error_correction(strgraph,
          arguments->bubble, arguments->deadend, arguments->deadend_depth,
          verbose_logger);
    }

    if (!eqlen && reads != NULL)
    {
      gt_encseq_delete(reads);
      reads = NULL;
      if (had_err == 0)
        gt_strgraph_set_encseq(strgraph, NULL);
    }

    if (had_err == 0)
    {
      if (gt_showtime_enabled())
        gt_timer_show_progress(timer, GT_READJOINER_MSG_TRAVERSESG, stdout);
      gt_logger_log(default_logger, GT_READJOINER_MSG_TRAVERSESG);
      gt_readjoiner_assembly_show_current_space("(before traversal)");
      gt_strgraph_spell(strgraph, (unsigned long)arguments->depthcutoff,
          (unsigned long)arguments->lengthcutoff, false, readset,
          GT_READJOINER_SUFFIX_CONTIG_PATHS, NULL, true, false,
          verbose_logger);
    }

    if (contained != NULL)
      gt_free(contained);
    gt_strgraph_delete(strgraph);
    strgraph = NULL;
    gt_assert(reads == NULL);
    gt_encseq_loader_delete(el);
  }

  if (had_err == 0)
  {
    gt_readjoiner_assembly_show_current_space("(before paths2seq)");
    had_err = gt_readjoiner_assembly_paths2seq(readset,
        (unsigned long)arguments->lengthcutoff,
        arguments->buffersize, default_logger, &timer, err);
  }

  if (gt_showtime_enabled())
  {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  gt_logger_delete(default_logger);
  gt_logger_delete(verbose_logger);
  return had_err;
}

GtTool* gt_readjoiner_assembly(void)
{
  return gt_tool_new(gt_readjoiner_assembly_arguments_new,
                  gt_readjoiner_assembly_arguments_delete,
                  gt_readjoiner_assembly_option_parser_new,
                  gt_readjoiner_assembly_arguments_check,
                  gt_readjoiner_assembly_runner);
}
genometools-1.5.1/src/tools/gt_readjoiner_assembly.h000066400000000000000000000020141211610345200226540ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_READJOINER_ASSEMBLY_H
#define GT_READJOINER_ASSEMBLY_H

#include "core/tool_api.h"

/* the readjoiner_assembly tool */
GtTool* gt_readjoiner_assembly(void);

#endif
genometools-1.5.1/src/tools/gt_readjoiner_cnttest.c000066400000000000000000000163521211610345200225260ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/logger.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "match/esa-seqread.h"
#include "match/rdj-contfind-bottomup.h"
#include "match/rdj-filesuf-def.h"
#include "match/rdj-ovlfind-gusfield.h"
#include "match/rdj-pairwise.h"
#include "match/rdj-cntlist.h"
#include "match/rdj-version.h"
#include "tools/gt_readjoiner_cnttest.h"

typedef enum {
  GT_READJOINER_CNTTEST_SHOWLIST,
  GT_READJOINER_CNTTEST_BRUTEFORCE,
  GT_READJOINER_CNTTEST_KMP,
  GT_READJOINER_CNTTEST_ESA,
} GtReadjoinerCnttestTestspec;

typedef struct {
  GtStr *readset, *teststr;
  GtReadjoinerCnttestTestspec test;
  bool singlestrand;
  bool verbose;
} GtReadjoinerCnttestArguments;

static void* gt_readjoiner_cnttest_arguments_new(void)
{
  GtReadjoinerCnttestArguments *arguments = gt_calloc((size_t)1,
      sizeof *arguments);
  arguments->readset = gt_str_new();
  arguments->teststr = gt_str_new();
  return arguments;
}

static void gt_readjoiner_cnttest_arguments_delete(void *tool_arguments)
{
  GtReadjoinerCnttestArguments *arguments = tool_arguments;
  if (arguments == NULL)
    return;
  gt_str_delete(arguments->readset);
  gt_str_delete(arguments->teststr);
  gt_free(arguments);
}

static GtOptionParser* gt_readjoiner_cnttest_option_parser_new(
    void *tool_arguments)
{
  GtReadjoinerCnttestArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("-readset [option ...]",
      "Test/development tool for readjoiner containments filtering.");

  /* -readset */
  option = gt_option_new_string("readset", "specify the readset name",
      arguments->readset, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -test */
  option = gt_option_new_string("test",
      "select among the available tests:\n"
      "showlist: show content of an cnt list (input: cntlist)\n"
      "bruteforce: memcmp reads vs all suffixes and prefixes (input: encseq)\n"
      "kmp: variant of Knuth-Morris-Pratt (input: encseq)\n"
      "esa: own esa-based algorithm (input: esa)",
      arguments->teststr, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -singlestrand */
  option = gt_option_new_bool("singlestrand", "do not use reads "
      "reverse complements", &arguments->singlestrand, false);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
  gt_option_parser_set_max_args(op, 0);

  return op;
}

static int gt_readjoiner_cnttest_arguments_check(GT_UNUSED int rest_argc,
    void *tool_arguments, GT_UNUSED GtError *err)
{
  GtReadjoinerCnttestArguments *arguments = tool_arguments;
  const char *teststr = gt_str_get(arguments->teststr);
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (strcmp(teststr, "showlist") == 0)
    arguments->test = GT_READJOINER_CNTTEST_SHOWLIST;
  else if (strcmp(teststr, "bruteforce") == 0)
    arguments->test = GT_READJOINER_CNTTEST_BRUTEFORCE;
  else if (strcmp(teststr, "kmp") == 0)
    arguments->test = GT_READJOINER_CNTTEST_KMP;
  else if (strcmp(teststr, "esa") == 0)
    arguments->test = GT_READJOINER_CNTTEST_ESA;
  else
  {
    gt_error_set(err, "illegal argument \"%s\" to option -test", teststr);
    had_err = -1;
  }
  return had_err;
}

static int gt_readjoiner_cnttest_runner(GT_UNUSED int argc,
    GT_UNUSED const char **argv, GT_UNUSED int parsed_args,
    void *tool_arguments, GT_UNUSED GtError *err)
{
  GtReadjoinerCnttestArguments *arguments = tool_arguments;
  GtEncseqLoader *el = NULL;
  GtEncseq *reads = NULL;
  GtBitsequence *bits = NULL;
  unsigned long nofreads;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (arguments->test == GT_READJOINER_CNTTEST_SHOWLIST)
  {
    GtStr *fn = NULL;
    fn = gt_str_clone(arguments->readset);
    gt_str_append_cstr(fn, GT_READJOINER_SUFFIX_CNTLIST);
    had_err = gt_cntlist_parse(gt_str_get(fn), true, &bits, &nofreads, err);
    gt_str_delete(fn);
  }
  else if (arguments->test == GT_READJOINER_CNTTEST_BRUTEFORCE ||
      arguments->test == GT_READJOINER_CNTTEST_KMP)
  {
    el = gt_encseq_loader_new();
    gt_encseq_loader_drop_description_support(el);
    gt_encseq_loader_disable_autosupport(el);
    if (!arguments->singlestrand)
      gt_encseq_loader_mirror(el);
    reads = gt_encseq_loader_load(el, gt_str_get(arguments->readset), err);
    if (reads == NULL)
      had_err = -1;
    else
    {
      gt_rdj_pairwise_exact(GT_OVLFIND_CNT, reads, !arguments->singlestrand,
          false, arguments->test == GT_READJOINER_CNTTEST_KMP, 1UL, true,
          NULL, NULL, false, NULL, &bits, &nofreads);
    }
    gt_encseq_delete(reads);
    gt_encseq_loader_delete(el);
  }
  else if (arguments->test == GT_READJOINER_CNTTEST_ESA)
  {
    Sequentialsuffixarrayreader *ssar = NULL;
    unsigned long readlength = 0, firstrevcompl = 0;
    GtLogger *verbose_logger = gt_logger_new(arguments->verbose,
        GT_LOGGER_DEFLT_PREFIX, stderr);
    ssar = gt_newSequentialsuffixarrayreaderfromfile(gt_str_get(
          arguments->readset), SARR_LCPTAB | SARR_SUFTAB | SARR_SSPTAB,
        SEQ_scan, verbose_logger, err);
    if (gt_error_is_set(err))
      had_err = -1;
    else
    {
      nofreads = gt_encseq_num_of_sequences(ssar->encseq);
      if (!arguments->singlestrand)
      {
        nofreads = GT_DIV2(nofreads);
        firstrevcompl = nofreads;
      }
      GT_INITBITTAB(bits, nofreads);
      if (!arguments->singlestrand)
      if (gt_encseq_accesstype_get(ssar->encseq) == GT_ACCESS_TYPE_EQUALLENGTH)
        readlength = gt_encseq_seqlength(ssar->encseq, 0);
      (void)gt_contfind_bottomup(ssar, false, bits, arguments->singlestrand ? 0
          : firstrevcompl, readlength);
    }
    if (ssar != NULL)
      gt_freeSequentialsuffixarrayreader(&ssar);
    gt_logger_delete(verbose_logger);
  }
  else
  {
    gt_assert(false);
  }
  if (!had_err)
    had_err = gt_cntlist_show(bits, nofreads, NULL, false, err);
  gt_free(bits);
  return had_err;
}

GtTool* gt_readjoiner_cnttest(void)
{
  return gt_tool_new(gt_readjoiner_cnttest_arguments_new,
                  gt_readjoiner_cnttest_arguments_delete,
                  gt_readjoiner_cnttest_option_parser_new,
                  gt_readjoiner_cnttest_arguments_check,
                  gt_readjoiner_cnttest_runner);
}
genometools-1.5.1/src/tools/gt_readjoiner_cnttest.h000066400000000000000000000020101211610345200225150ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_READJOINER_CNTTEST_H
#define GT_READJOINER_CNTTEST_H

#include "core/tool_api.h"

/* the readjoiner_cnttest tool */
GtTool* gt_readjoiner_cnttest(void);

#endif
genometools-1.5.1/src/tools/gt_readjoiner_correct.c000066400000000000000000000107331211610345200225000ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/logger.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "match/esa-seqread.h"
#include "match/rdj-errfind.h"
#include "match/rdj-version.h"
#include "tools/gt_readjoiner_correct.h"

#define GT_READJOINER_CORRECT_TAG ".corrected"

typedef struct {
  unsigned long k, c;
  GtStr *indexname;
  unsigned long debug_value;
  bool edit_twobitencoding;
} GtReadjoinerCorrectArguments;

static void* gt_readjoiner_correct_arguments_new(void)
{
  GtReadjoinerCorrectArguments *arguments = gt_calloc((size_t)1,
      sizeof *arguments);
  arguments->indexname = gt_str_new();
  return arguments;
}

static void gt_readjoiner_correct_arguments_delete(void *tool_arguments)
{
  GtReadjoinerCorrectArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->indexname);
  gt_free(arguments);
}

static GtOptionParser* gt_readjoiner_correct_option_parser_new(
    void *tool_arguments)
{
  GtReadjoinerCorrectArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[options] -ii indexname",
      "Readjoiner k-mer based error correction.");

  option = gt_option_new_ulong_min("k","k-mer length",
                                  &arguments->k, 31UL, 1UL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong_min("c","minimal trusted count",
                                  &arguments->c, 3UL, 1UL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("encseq","correct encoded sequence",
      &arguments->edit_twobitencoding, true);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("ii", "input index",
                                arguments->indexname, NULL);
  gt_option_is_mandatory(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("dbg","(debug value) "
      "see code for current meaning", &arguments->debug_value, GT_UNDEF_ULONG);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
  gt_option_parser_set_max_args(op, 0);

  return op;
}

static int gt_readjoiner_correct_runner(GT_UNUSED int argc,
    GT_UNUSED const char **argv, GT_UNUSED int parsed_args,
    void *tool_arguments, GT_UNUSED GtError *err)
{
  GtReadjoinerCorrectArguments *arguments = tool_arguments;
  Sequentialsuffixarrayreader *ssar;
  GtLogger *logger;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);
  logger = gt_logger_new(true, GT_LOGGER_DEFLT_PREFIX, stderr);

  ssar = gt_newSequentialsuffixarrayreaderfromfile(
      gt_str_get(arguments->indexname), SARR_LCPTAB | SARR_SUFTAB |
      SARR_ESQTAB | SARR_SSPTAB, SEQ_scan, logger, err);
  if (ssar == NULL)
    had_err = -1;
  else
  {
    GtStr *indexname_corrected = gt_str_clone(arguments->indexname);
    gt_str_append_cstr(arguments->indexname, GT_READJOINER_CORRECT_TAG);
    had_err = gt_errfind(ssar, gt_encseqSequentialsuffixarrayreader(ssar),
           arguments->k, arguments->c, arguments->debug_value,
           arguments->edit_twobitencoding, gt_str_get(indexname_corrected),
           err);
    gt_freeSequentialsuffixarrayreader(&ssar);
    gt_str_delete(indexname_corrected);
  }
  gt_logger_delete(logger);
  return had_err;
}

GtTool* gt_readjoiner_correct(void)
{
  return gt_tool_new(gt_readjoiner_correct_arguments_new,
                  gt_readjoiner_correct_arguments_delete,
                  gt_readjoiner_correct_option_parser_new,
                  NULL,
                  gt_readjoiner_correct_runner);
}
genometools-1.5.1/src/tools/gt_readjoiner_correct.h000066400000000000000000000020101211610345200224720ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_READJOINER_CORRECT_H
#define GT_READJOINER_CORRECT_H

#include "core/tool_api.h"

/* the readjoiner_correct tool */
GtTool* gt_readjoiner_correct(void);

#endif
genometools-1.5.1/src/tools/gt_readjoiner_overlap.c000066400000000000000000000324021211610345200225040ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/unused_api.h"
#include "core/option_api.h"
#include "core/encseq.h"
#include "core/intbits.h"
#include "core/logger.h"
#include "core/minmax.h"
#ifdef GT_THREADS_ENABLED
#include "core/thread_api.h"
#endif
#include "match/rdj-spmfind.h"
#include "match/rdj-version.h"
#include "match/firstcodes.h"
#include "tools/gt_readjoiner_overlap.h"

typedef struct {
  bool singlestrand,
       elimtrans,
       verbose,
       quiet,
       showspm;
  unsigned int minmatchlength,
               numofparts,
               w_maxsize;
  unsigned long maximumspace,
                phase2extra;
  GtStr *encseqinput,
        *memlimitarg,
        *phase2extraarg;
  GtOption *refoptionmemlimit,
           *refoptionphase2extra;
  bool radixsmall;
  unsigned int radixparts;
  bool onlyallfirstcodes;
} GtReadjoinerOverlapArguments;

static void* gt_readjoiner_overlap_arguments_new(void)
{
  GtReadjoinerOverlapArguments *arguments = gt_calloc((size_t) 1,
      sizeof *arguments);
  arguments->encseqinput = gt_str_new();
  arguments->numofparts = 0;
  arguments->memlimitarg = gt_str_new();
  arguments->phase2extraarg = gt_str_new();
  arguments->phase2extra = 0UL; /* in bytes */
  arguments->maximumspace = 0UL; /* in bytes */
  return arguments;
}

static void gt_readjoiner_overlap_arguments_delete(void *tool_arguments)
{
  GtReadjoinerOverlapArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->encseqinput);
  gt_option_delete(arguments->refoptionmemlimit);
  gt_option_delete(arguments->refoptionphase2extra);
  gt_str_delete(arguments->memlimitarg);
  gt_str_delete(arguments->phase2extraarg);
  gt_free(arguments);
}

static GtOptionParser* gt_readjoiner_overlap_option_parser_new(
    void *tool_arguments)
{
  GtReadjoinerOverlapArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionparts, *optionmemlimit, *q_option, *v_option;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [file]",
                            "Compute suffix prefix matches "
                            "from encoded sequence.");

  /* -readset */
  option = gt_option_new_string("readset", "specify the readset name",
                                arguments->encseqinput, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -l */
  option = gt_option_new_uint_min("l", "specify the minimum SPM length",
                                  &arguments->minmatchlength, 0, 2U);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -parts */
  optionparts = gt_option_new_uint("parts", "specify the number of parts",
                                  &arguments->numofparts, 0U);
  gt_option_parser_add_option(op, optionparts);

  /* -memlimit */
  optionmemlimit = gt_option_new_string("memlimit",
                       "specify maximal amount of memory to be used during "
                       "index construction (in bytes, the keywords 'MB' "
                       "and 'GB' are allowed)",
                       arguments->memlimitarg, NULL);
  gt_option_parser_add_option(op, optionmemlimit);
  gt_option_exclude(optionmemlimit, optionparts);
  arguments->refoptionmemlimit = gt_option_ref(optionmemlimit);

  /* -singlestrand */
  option = gt_option_new_bool("singlestrand", "do not use reverse complements "
      "of the reads", &arguments->singlestrand, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -elimtrans */
  option = gt_option_new_bool("elimtrans", "output only irreducible SPMs",
      &arguments->elimtrans, true);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -wmax */
  option = gt_option_new_uint("wmax", "specify the maximum width of w set;\n"
                              "use 0 to disable w set partitioning",
                              &arguments->w_maxsize, 32U);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -showspm */
  option = gt_option_new_bool("showspm", "show textual SPMs list on stdout",
      &arguments->showspm, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -phase2extra */
  option = gt_option_new_string("phase2extra",
                       "specify amount of additional space required for "
                       "the second phase of the computation involving the "
                       "processing of the intervals (in bytes, "
                       "the keywords 'MB' and 'GB' are allowed)",
                       arguments->phase2extraarg, NULL);
  gt_option_parser_add_option(op, option);
  arguments->refoptionphase2extra = gt_option_ref(option);
  gt_option_is_development_option(option);

  /* -v */
  v_option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, v_option);

  /* -q */
  q_option = gt_option_new_bool("q", "suppress standard output messages",
                             &arguments->quiet, false);
  gt_option_parser_add_option(op, q_option);
  gt_option_exclude(q_option, v_option);

  /* -radixparts */
  option = gt_option_new_uint("radixparts", "specify the radixpart parameter",
      &arguments->radixparts, 1U);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -radixsmall */
  option = gt_option_new_bool("radixsmall", "specify the radixsmall parameter",
      &arguments->radixsmall, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -onlyallfirstcodes */
  option = gt_option_new_bool("onlyallfirstcodes", "only determines allcodes",
                              &arguments->onlyallfirstcodes, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
  return op;
}

static int gt_readjoiner_overlap_arguments_check(int rest_argc,
                                         void *tool_arguments,
                                         GtError *err)
{
  GtReadjoinerOverlapArguments *arguments = tool_arguments;
  bool haserr = false;

  gt_error_check(err);
  if (rest_argc != 0)
  {
    gt_error_set(err,"unnecessary arguments");
    haserr = true;
  }
  if (!haserr && gt_option_is_set(arguments->refoptionmemlimit))
  {
    if (gt_option_parse_spacespec(&arguments->maximumspace,
          "memlimit",
          arguments->memlimitarg,
          err) != 0)
    {
      haserr = true;
    }
    if (!haserr && !gt_ma_bookkeeping_enabled()) {
      gt_error_set(err, "option '-memlimit' requires "
                        "GT_MEM_BOOKKEEPING=on");
      haserr = true;
    }
  }
  if (!haserr && gt_option_is_set(arguments->refoptionphase2extra))
  {
    if (gt_option_parse_spacespec(&arguments->phase2extra,
          "phase2extra",
          arguments->phase2extraarg,
          err) != 0)
    {
      haserr = true;
    }
  }
#ifdef GT_THREADS_ENABLED
  if (!haserr) {
    if (gt_jobs > 1 && gt_ma_bookkeeping_enabled()) {
      gt_error_set(err, "gt option '-j' and GT_MEM_BOOKKEEPING=on "
                        "are incompatible");
      haserr = true;
    }
  }
#endif
  return haserr ? -1 : 0;
}

static int gt_readjoiner_overlap_runner(GT_UNUSED int argc,
                                GT_UNUSED const char **argv,
                                GT_UNUSED int parsed_args,
                                void *tool_arguments,
                                GtError *err)
{
  GtReadjoinerOverlapArguments *arguments = tool_arguments;
  GtEncseqLoader *el = NULL;
  GtEncseq *encseq = NULL;
  GtLogger *default_logger, *verbose_logger;
  unsigned int kmersize;
  bool haserr = false;
  bool eqlen;
  unsigned long total_nof_irr_spm = 0, total_nof_trans_spm = 0;

  gt_error_check(err);
  gt_assert(arguments);

  default_logger = gt_logger_new(!arguments->quiet, GT_LOGGER_DEFLT_PREFIX,
      stdout);
  gt_logger_log(default_logger,
      "gt readjoiner overlap (version "GT_READJOINER_VERSION")");
  verbose_logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX,
      stdout);
  gt_logger_log(verbose_logger, "verbose output activated");
  kmersize = MIN((unsigned int) GT_UNITSIN2BITENC, arguments->minmatchlength);

  el = gt_encseq_loader_new();
  gt_encseq_loader_drop_description_support(el);
  gt_encseq_loader_disable_autosupport(el);
  encseq = gt_encseq_loader_load(el, gt_str_get(arguments->encseqinput),
                                 err);
  eqlen = gt_encseq_accesstype_get(encseq) == GT_ACCESS_TYPE_EQUALLENGTH;

  if (encseq == NULL)
    haserr = true;
  if (!haserr && !arguments->singlestrand)
  {
    if (gt_encseq_mirror(encseq, err) != 0)
      haserr = true;
  }
  if (!haserr)
  {
    unsigned int threadcount;
#ifdef GT_THREADS_ENABLED
    const unsigned int threads = gt_jobs;
#else
    const unsigned int threads = 1U;
#endif
    if (eqlen)
    {
      GtBUstate_spmeq **state_table
        = gt_malloc(sizeof (*state_table) * threads);

      for (threadcount = 0; threadcount < threads; threadcount++)
      {
        state_table[threadcount]
          = gt_spmfind_eqlen_state_new(encseq,
                (unsigned long)arguments->minmatchlength,
                (unsigned long)arguments->w_maxsize, arguments->elimtrans,
                arguments->showspm, gt_str_get(arguments->encseqinput),
                threadcount, default_logger, verbose_logger, err);
      }
      if (storefirstcodes_getencseqkmers_twobitencoding(encseq, kmersize,
            arguments->numofparts, arguments->maximumspace,
            arguments->minmatchlength, false, false,
            arguments->onlyallfirstcodes, 5U, arguments->phase2extra,
            arguments->radixsmall, arguments->radixparts,
            gt_spmfind_eqlen_process, gt_spmfind_eqlen_process_end,
            state_table, verbose_logger, err)
            != 0)
      {
        haserr = true;
      }
      for (threadcount = 0; threadcount < threads; threadcount++)
      {
        total_nof_irr_spm +=
          gt_spmfind_eqlen_nof_irr_spm(state_table[threadcount]);
        total_nof_trans_spm +=
          gt_spmfind_eqlen_nof_irr_spm(state_table[threadcount]);
        gt_spmfind_eqlen_state_delete(state_table[threadcount]);
      }
      gt_free(state_table);
    }
    else
    {
      GtBUstate_spmvar **state_table
        = gt_malloc(sizeof (*state_table) * threads);

      for (threadcount = 0; threadcount < threads; threadcount++)
      {
        state_table[threadcount]
           = gt_spmfind_varlen_state_new(encseq,
                  (unsigned long)arguments->minmatchlength,
                  (unsigned long)arguments->w_maxsize, arguments->elimtrans,
                  arguments->showspm, gt_str_get(arguments->encseqinput),
                  threadcount, default_logger, verbose_logger, err);
      }
      if (storefirstcodes_getencseqkmers_twobitencoding(encseq, kmersize,
            arguments->numofparts, arguments->maximumspace,
            arguments->minmatchlength, false, false,
            arguments->onlyallfirstcodes, 5U, arguments->phase2extra,
            arguments->radixsmall, arguments->radixparts,
            gt_spmfind_varlen_process, gt_spmfind_varlen_process_end,
            state_table, verbose_logger, err)
          != 0)
      {
        haserr = true;
      }
      for (threadcount = 0; threadcount < threads; threadcount++)
      {
        gt_spmfind_varlen_state_delete(state_table[threadcount]);
        total_nof_irr_spm +=
          gt_spmfind_eqlen_nof_irr_spm(state_table[threadcount]);
        total_nof_trans_spm +=
          gt_spmfind_eqlen_nof_irr_spm(state_table[threadcount]);
      }
      gt_free(state_table);
    }
  }
  if (!haserr)
  {
    gt_logger_log(default_logger, "number of %ssuffix-prefix matches = %lu",
        arguments->elimtrans ? "irreducible " : "", total_nof_irr_spm);
    if (arguments->elimtrans)
      gt_logger_log(default_logger, "number of transitive suffix-prefix "
          "matches = %lu", total_nof_trans_spm);
  }
  gt_logger_delete(default_logger);
  gt_logger_delete(verbose_logger);
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(el);
  return haserr ? -1 : 0;
}

GtTool* gt_readjoiner_overlap(void)
{
  return gt_tool_new(gt_readjoiner_overlap_arguments_new,
                     gt_readjoiner_overlap_arguments_delete,
                     gt_readjoiner_overlap_option_parser_new,
                     gt_readjoiner_overlap_arguments_check,
                     gt_readjoiner_overlap_runner);
}
genometools-1.5.1/src/tools/gt_readjoiner_overlap.h000066400000000000000000000021051211610345200225060ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_READJOINER_OVERLAP_H
#define GT_READJOINER_OVERLAP_H

#include "core/tool_api.h"

/* the readjoiner overlap tool */
GtTool* gt_readjoiner_overlap(void);

#endif
genometools-1.5.1/src/tools/gt_readjoiner_prefilter.c000066400000000000000000000373301211610345200230350ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/log.h"
#include "core/logger.h"
#include "core/encseq.h"
#include "core/fa.h"
#include "core/ma.h"
#include "core/output_file_api.h"
#include "core/option_api.h"
#include "core/unused_api.h"
#include "core/undef_api.h"
#include "match/rdj-contfinder.h"
#include "match/rdj-filesuf-def.h"
#include "match/rdj-version.h"
#include "match/reads_library.h"
#include "match/reads2twobit.h"
#include "tools/gt_readjoiner_prefilter.h"

typedef struct {
  bool verbose, quiet;
  bool singlestrand, encodeonly, cntlist, encseq, seqnums, fasta, copynum,
       libtable, phred64;
  GtStr *readset;
  GtStrArray *db;
  /* rdj-radixsort test */
  bool testrs, testrs_print;
  unsigned long testrs_depth, testrs_maxdepth, maxlow;
  unsigned int lowqual;
} GtReadjoinerPrefilterArguments;

static void* gt_readjoiner_prefilter_arguments_new(void)
{
  GtReadjoinerPrefilterArguments *arguments = gt_calloc((size_t)1,
      sizeof *arguments);
  arguments->readset = gt_str_new();
  arguments->db = gt_str_array_new();
  return arguments;
}

static void gt_readjoiner_prefilter_arguments_delete(void *tool_arguments)
{
  GtReadjoinerPrefilterArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->readset);
  gt_str_array_delete(arguments->db);
  gt_free(arguments);
}

static GtOptionParser* gt_readjoiner_prefilter_option_parser_new(
    void *tool_arguments)
{
  GtReadjoinerPrefilterArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *singlestrand_option, *encodeonly_option, *cntlist_option,
           *fasta_option, *seqnums_option, *encseq_option, *readset_option,
           *v_option, *q_option, *db_option, *copynum_option, *libtable_option,
           *testrs_option, *testrs_depth_option, *testrs_print_option,
           *testrs_maxdepth_option, *phred64_option, *maxlow_option,
           *lowqual_option;

  gt_assert(arguments);

  op = gt_option_parser_new("[option ...]",
                            "Remove contained and low-quality reads "
                            "and encode read set in GtEncseq format.");

  /* -readset */
  readset_option = gt_option_new_string("readset",
      "specify the readset name\n"
      "default: filename of first input sequence_file",
      arguments->readset, NULL);
  gt_option_hide_default(readset_option);
  gt_option_parser_add_option(op, readset_option);

  /* -db */
  db_option = gt_option_new_filename_array("db",
      GT_READS2TWOBIT_LIBSPEC_HELPMSG, arguments->db);
  gt_option_hide_default(db_option);
  gt_option_is_mandatory(db_option);
  gt_option_parser_add_option(op, db_option);

  /* -v */
  v_option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, v_option);

  /* -q */
  q_option = gt_option_new_bool("q",
      "suppress standard output messages",
      &arguments->quiet, false);
  gt_option_exclude(q_option, v_option);
  gt_option_parser_add_option(op, q_option);

  /* -maxlow */
  maxlow_option = gt_option_new_ulong("maxlow",
      "maximal number of low-quality positions in a read\n"
      "default: infinite",
      &arguments->maxlow, GT_UNDEF_ULONG);
  gt_option_hide_default(maxlow_option);
  gt_option_is_extended_option(maxlow_option);
  gt_option_parser_add_option(op, maxlow_option);

  /* -lowqual */
  lowqual_option = gt_option_new_uint_max("lowqual",
      "maximal quality for a position to be considered low-quality",
      &arguments->lowqual, 3U, 127U);
  gt_option_is_extended_option(lowqual_option);
  gt_option_imply(lowqual_option, maxlow_option);
  gt_option_parser_add_option(op, lowqual_option);

  /* -phred64 */
  phred64_option = gt_option_new_bool("phred64",
      "use phred64 scores for FastQ format",
      &arguments->phred64, false);
  gt_option_is_extended_option(phred64_option);
  gt_option_parser_add_option(op, phred64_option);

  /* -singlestrand */
  singlestrand_option = gt_option_new_bool("singlestrand",
      "do not use reverse complements of the reads",
      &arguments->singlestrand, false);
  gt_option_is_development_option(singlestrand_option);
  gt_option_parser_add_option(op, singlestrand_option);

  /* -encodeonly */
  encodeonly_option = gt_option_new_bool("encodeonly",
      "do not remove contained reads",
      &arguments->encodeonly, false);
  gt_option_is_development_option(encodeonly_option);
  gt_option_parser_add_option(op, encodeonly_option);

  /* -encseq */
  encseq_option = gt_option_new_bool("encseq",
      "output reads in GtEncseq format",
      &arguments->encseq, true);
  gt_option_is_development_option(encseq_option);
  gt_option_parser_add_option(op, encseq_option);

  /* -libtable */
  libtable_option = gt_option_new_bool("libtable",
      "output reads libraries table",
      &arguments->libtable, true);
  gt_option_is_development_option(libtable_option);
  gt_option_parser_add_option(op, libtable_option);

  /* -fasta */
  fasta_option = gt_option_new_bool("fasta",
      "output reads in MultiFasta format",
      &arguments->fasta, false);
  gt_option_is_development_option(fasta_option);
  gt_option_parser_add_option(op, fasta_option);

  /* -cnt */
  cntlist_option = gt_option_new_bool("cnt",
      "output contained reads list",
      &arguments->cntlist, false);
  gt_option_is_development_option(cntlist_option);
  gt_option_exclude(encodeonly_option, cntlist_option);
  gt_option_parser_add_option(op, cntlist_option);

  /* -seqnums */
  seqnums_option = gt_option_new_bool("seqnums",
      "output sorted sequence numbers",
      &arguments->seqnums, false);
  gt_option_is_development_option(seqnums_option);
  gt_option_exclude(encodeonly_option, seqnums_option);
  gt_option_parser_add_option(op, seqnums_option);

  /* -copynum */
  copynum_option = gt_option_new_bool("copynum",
      "[eqlen only] output reads copy number to "
      GT_READJOINER_SUFFIX_READSCOPYNUM,
      &arguments->copynum, false);
  gt_option_is_development_option(copynum_option);
  gt_option_exclude(encodeonly_option, copynum_option);
  gt_option_parser_add_option(op, copynum_option);

  /* -testrs */
  testrs_option = gt_option_new_bool("testrs",
      "run gt_radixsort_str test (match/radixsort_str.[ch])",
      &arguments->testrs, false);
  gt_option_is_development_option(testrs_option);
  gt_option_parser_add_option(op, testrs_option);

  /* -testrs-print */
  testrs_print_option = gt_option_new_bool("testrs-print",
      "printf gt_radixsort_str test results",
      &arguments->testrs_print, true);
  gt_option_is_development_option(testrs_print_option);
  gt_option_parser_add_option(op, testrs_print_option);

  /* -testrs-depth */
  testrs_depth_option = gt_option_new_ulong("testrs-depth",
      "depth for gt_radixsort_str test",
      &arguments->testrs_depth, 0);
  gt_option_is_development_option(testrs_depth_option);
  gt_option_parser_add_option(op, testrs_depth_option);

  /* -testrs-maxdepth */
  testrs_maxdepth_option = gt_option_new_ulong("testrs-maxdepth",
      "depth for gt_radixsort_str test",
      &arguments->testrs_maxdepth, 0);
  gt_option_is_development_option(testrs_maxdepth_option);
  gt_option_parser_add_option(op, testrs_maxdepth_option);

  gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
  gt_option_parser_set_max_args(op, 0U);
  return op;
}

static void gt_readjoiner_prefilter_list_input_files(
    GtReadjoinerPrefilterArguments *arguments, GtLogger *verbose_logger)
{
  unsigned long i;
  GtStr *inputfileslist = gt_str_new();
  for (i = 0; i < gt_str_array_size(arguments->db); i++)
  {
    gt_str_append_cstr(inputfileslist, gt_str_array_get(arguments->db, i));
    if (i + 1 < gt_str_array_size(arguments->db))
      gt_str_append_cstr(inputfileslist, ", ");
  }
  gt_logger_log(verbose_logger, "input files = %s", gt_str_get(inputfileslist));
  gt_str_delete(inputfileslist);
}

#define GT_READJOINER_PREFILTER_CF_OUTPUT(FUNC, FILESUF, MSG)\
{\
  GtStr *fn;\
  fn = gt_str_new_cstr(gt_str_get(arguments->readset));\
  gt_str_append_cstr(fn, (FILESUF));\
  had_err = (FUNC)(contfinder, gt_str_get(fn), err);\
  gt_logger_log(verbose_logger, MSG": %s", gt_str_get(fn));\
  gt_str_delete(fn);\
}

static int gt_readjoiner_prefilter_runner(GT_UNUSED int argc,
    GT_UNUSED const char **argv, GT_UNUSED int parsed_args,
    void *tool_arguments, GtError *err)
{
  GtReadjoinerPrefilterArguments *arguments = tool_arguments;
  int had_err = 0;
  bool varlen;
  unsigned long i;
  unsigned long nofreads_valid, nofreads_invalid, nofreads_input,
                nofreads_output,
                tlen_valid, tlen_invalid, tlen_input;
  GtLogger *default_logger, *verbose_logger;
  GtReads2Twobit *r2t;

  default_logger =
    gt_logger_new(!arguments->quiet, GT_LOGGER_DEFLT_PREFIX, stdout);
  verbose_logger =
    gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);

  gt_logger_log(default_logger,
      "gt readjoiner prefilter (version "GT_READJOINER_VERSION")");

  /* default readset name: first db argument */
  if (gt_str_length(arguments->readset) == 0)
    gt_str_append_cstr(arguments->readset, gt_str_array_get(arguments->db, 0));
  gt_logger_log(verbose_logger, "readset name = %s",
      gt_str_get(arguments->readset));

  if (arguments->verbose)
    gt_readjoiner_prefilter_list_input_files(arguments, verbose_logger);

  r2t = gt_reads2twobit_new(arguments->readset);

  if (arguments->phred64)
    gt_reads2twobit_use_phred64(r2t);

  if (arguments->maxlow != GT_UNDEF_ULONG)
    gt_reads2twobit_set_quality_filter(r2t, arguments->maxlow,
        (char)arguments->lowqual);

  for (i = 0; i < gt_str_array_size(arguments->db) && !had_err; i++)
  {
    GtStr *dbentry = gt_str_array_get_str(arguments->db, i);
    had_err = gt_reads2twobit_add_library(r2t, dbentry, err);
  }

  if (!had_err)
    had_err = gt_reads2twobit_encode(r2t, err);

  if (!had_err)
  {
    nofreads_valid = gt_reads2twobit_nofseqs(r2t);
    nofreads_invalid = gt_reads2twobit_nof_invalid_seqs(r2t);
    nofreads_input = nofreads_valid + nofreads_invalid;
    tlen_valid = gt_reads2twobit_total_seqlength(r2t) -
      gt_reads2twobit_nofseqs(r2t);
    tlen_invalid = gt_reads2twobit_invalid_seqs_totallength(r2t);
    tlen_input = tlen_valid + tlen_invalid;

    gt_logger_log(default_logger, "number of reads in complete readset = %lu",
        nofreads_input);

    varlen = (gt_reads2twobit_seqlen_eqlen(r2t) == 0);
    if (varlen)
      gt_logger_log(verbose_logger, "read length = variable [%lu..%lu]",
          gt_reads2twobit_seqlen_min(r2t), gt_reads2twobit_seqlen_max(r2t));
    else
      gt_logger_log(verbose_logger, "read length = %lu",
          gt_reads2twobit_seqlen_eqlen(r2t) - 1UL);

    gt_logger_log(verbose_logger, "total length of complete readset = %lu",
        tlen_input);
    gt_logger_log(verbose_logger, "low-quality reads = %lu "
        "[%.2f %% of input]", nofreads_invalid, (float)nofreads_invalid * 100 /
        (float)nofreads_input);
    if (!arguments->verbose)
      gt_logger_log(default_logger, "low-quality reads = %lu",
          nofreads_invalid);
    nofreads_output = nofreads_valid;
    if (arguments->encodeonly)
    {
      if (!had_err && arguments->fasta)
      {
        GtStr *fn;
        fn = gt_str_new_cstr(gt_str_get(arguments->readset));
        gt_str_append_cstr(fn, GT_READJOINER_SUFFIX_PREFILTERED_FAS);
        had_err = gt_reads2twobit_write_fasta(r2t, gt_str_get(fn), NULL, err);
        gt_logger_log(verbose_logger, "readset saved: %s", gt_str_get(fn));
        gt_str_delete(fn);
      }
      if (!had_err && arguments->encseq)
      {
        had_err = gt_reads2twobit_write_encseq(r2t, err);
        gt_logger_log(verbose_logger, "readset saved: %s.%s",
            gt_str_get(arguments->readset), varlen ? "(esq|ssp)" : "esq");
      }
      gt_logger_log(default_logger, "number of reads in output readset = %lu",
          nofreads_output);
    }
    else
    {
      GtContfinder *contfinder;
      unsigned long nofreads_contained;
      contfinder = gt_contfinder_new(r2t);
      gt_contfinder_run(contfinder, !arguments->singlestrand,
          arguments->copynum);

      nofreads_contained = gt_contfinder_nofcontained(contfinder);
      nofreads_output -= nofreads_contained;

      gt_logger_log(verbose_logger, "contained reads = %lu [%.2f %% of input]",
          nofreads_contained, (float)nofreads_contained * 100 /
          (float)nofreads_input);
      if (!arguments->verbose)
        gt_logger_log(default_logger, "contained reads = %lu",
            nofreads_contained);

      gt_logger_log(default_logger, "number of reads in filtered readset = %lu",
          nofreads_output);

      if (!had_err && arguments->cntlist)
      {
        GT_READJOINER_PREFILTER_CF_OUTPUT(gt_contfinder_write_cntlist,
            GT_READJOINER_SUFFIX_CNTLIST, "contained reads list saved");
      }
      if (!had_err && arguments->copynum)
      {
        GT_READJOINER_PREFILTER_CF_OUTPUT(gt_contfinder_write_copynum,
            GT_READJOINER_SUFFIX_READSCOPYNUM, "reads copy number saved");
      }
      if (!had_err && arguments->seqnums)
      {
        GT_READJOINER_PREFILTER_CF_OUTPUT(gt_contfinder_write_sorted_seqnums,
            GT_READJOINER_SUFFIX_SEQNUMS, "sorted sequence numbers "
            "saved");
      }
      if (!had_err && arguments->fasta)
      {
        GtStr *fn;
        fn = gt_str_new_cstr(gt_str_get(arguments->readset));
        gt_str_append_cstr(fn, GT_READJOINER_SUFFIX_PREFILTERED_FAS);
        had_err = gt_reads2twobit_write_fasta(r2t, gt_str_get(fn),
            gt_contfinder_contained(contfinder), err);
        gt_logger_log(verbose_logger, "suffix-prefix-free readset saved: %s",
            gt_str_get(fn));
        gt_str_delete(fn);
      }
      if (!had_err && arguments->encseq)
      {
        gt_reads2twobit_delete_sequences(r2t,
            gt_contfinder_contained(contfinder));
        had_err = gt_reads2twobit_write_encseq(r2t, err);
        gt_logger_log(verbose_logger, "suffix-prefix-free readset saved: %s.%s",
            gt_str_get(arguments->readset),
            varlen ? "(esq|ssp)" : "esq");
      }
      if (arguments->testrs)
      {
        gt_contfinder_radixsort_str_eqlen_tester(contfinder,
            !arguments->singlestrand,
            arguments->testrs_depth, arguments->testrs_maxdepth,
            arguments->testrs_print);
      }
      gt_contfinder_delete(contfinder);
    }
    if (!had_err && arguments->libtable) {
      GtStr *fn;
      fn = gt_str_new_cstr(gt_str_get(arguments->readset));
      gt_str_append_cstr(fn, GT_READS_LIBRARY_TABLE_FILESUFFIX);
      had_err = gt_reads2twobit_write_libraries_table(r2t, gt_str_get(fn), err);
      gt_logger_log(verbose_logger, "reads library table saved: %s",
          gt_str_get(fn));
      gt_str_delete(fn);
    }
  }
  gt_reads2twobit_delete(r2t);
  gt_logger_delete(verbose_logger);
  gt_logger_delete(default_logger);
  return had_err;
}

GtTool* gt_readjoiner_prefilter(void)
{
  return gt_tool_new(gt_readjoiner_prefilter_arguments_new,
                     gt_readjoiner_prefilter_arguments_delete,
                     gt_readjoiner_prefilter_option_parser_new,
                     NULL,
                     gt_readjoiner_prefilter_runner);
}
genometools-1.5.1/src/tools/gt_readjoiner_prefilter.h000066400000000000000000000020201211610345200230260ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_READJOINER_PREFILTER_H
#define GT_READJOINER_PREFILTER_H

#include "core/tool_api.h"

/* the readjoiner prefilter tool */
GtTool* gt_readjoiner_prefilter(void);

#endif
genometools-1.5.1/src/tools/gt_readjoiner_spmtest.c000066400000000000000000000163561211610345200225450ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/logger.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "match/esa-seqread.h"
#include "match/rdj-filesuf-def.h"
#include "match/rdj-ovlfind-gusfield.h"
#include "match/rdj-pairwise.h"
#include "match/rdj-spmlist.h"
#include "match/rdj-version.h"
#include "tools/gt_readjoiner_spmtest.h"

typedef enum {
  GT_READJOINER_SPMTEST_SHOWLIST,
  GT_READJOINER_SPMTEST_BRUTEFORCE,
  GT_READJOINER_SPMTEST_KMP,
  GT_READJOINER_SPMTEST_GUSFIELD,
} GtReadjoinerSpmtestTestspec;

typedef struct {
  GtStr *readset, *teststr;
  GtReadjoinerSpmtestTestspec test;
  unsigned int minmatchlength;
  bool singlestrand;
  bool verbose;
} GtReadjoinerSpmtestArguments;

static void* gt_readjoiner_spmtest_arguments_new(void)
{
  GtReadjoinerSpmtestArguments *arguments = gt_calloc((size_t)1,
      sizeof *arguments);
  arguments->readset = gt_str_new();
  arguments->teststr = gt_str_new();
  return arguments;
}

static void gt_readjoiner_spmtest_arguments_delete(void *tool_arguments)
{
  GtReadjoinerSpmtestArguments *arguments = tool_arguments;
  if (arguments == NULL)
    return;
  gt_str_delete(arguments->readset);
  gt_str_delete(arguments->teststr);
  gt_free(arguments);
}

static GtOptionParser* gt_readjoiner_spmtest_option_parser_new(
    void *tool_arguments)
{
  GtReadjoinerSpmtestArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("-readset [option ...]",
      "Test/development tool for readjoiner overlap phase.");

  /* -readset */
  option = gt_option_new_string("readset", "specify the readset name",
      arguments->readset, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -l */
  option = gt_option_new_uint_min("l", "specify the minimum spm length",
      &arguments->minmatchlength, 0, 1U);
  gt_option_parser_add_option(op, option);

  /* -test */
  option = gt_option_new_string("test",
      "select among the available tests:\n"
      "showlist: show content of an spm list (input: spmlist)\n"
      "bruteforce: memcmp all suffixes and prefixes (input: encseq)\n"
      "kmp: variant of Knuth-Morris-Pratt (input: encseq)\n"
      "gusfield: Gusfield all pairs suffix-prefix (input: esa)",
      arguments->teststr, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -singlestrand */
  option = gt_option_new_bool("singlestrand", "do not use reads "
      "reverse complements", &arguments->singlestrand, false);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
  gt_option_parser_set_max_args(op, 0);

  return op;
}

static int gt_readjoiner_spmtest_arguments_check(GT_UNUSED int rest_argc,
    void *tool_arguments, GT_UNUSED GtError *err)
{
  GtReadjoinerSpmtestArguments *arguments = tool_arguments;
  const char *teststr = gt_str_get(arguments->teststr);
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (strcmp(teststr, "showlist") == 0)
    arguments->test = GT_READJOINER_SPMTEST_SHOWLIST;
  else if (strcmp(teststr, "bruteforce") == 0)
    arguments->test = GT_READJOINER_SPMTEST_BRUTEFORCE;
  else if (strcmp(teststr, "kmp") == 0)
    arguments->test = GT_READJOINER_SPMTEST_KMP;
  else if (strcmp(teststr, "gusfield") == 0)
    arguments->test = GT_READJOINER_SPMTEST_GUSFIELD;
  else
  {
    gt_error_set(err, "illegal argument \"%s\" to option -test", teststr);
    had_err = -1;
  }
  return had_err;
}

static int gt_readjoiner_spmtest_runner(GT_UNUSED int argc,
    GT_UNUSED const char **argv, GT_UNUSED int parsed_args,
    void *tool_arguments, GT_UNUSED GtError *err)
{
  GtReadjoinerSpmtestArguments *arguments = tool_arguments;
  GtEncseqLoader *el = NULL;
  GtEncseq *reads = NULL;
  GtLogger *verbose_logger;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (arguments->test == GT_READJOINER_SPMTEST_SHOWLIST)
  {
    GtStr *fn = NULL;
    fn = gt_str_clone(arguments->readset);
    gt_str_append_cstr(fn, GT_READJOINER_SUFFIX_SPMLIST);
    had_err = gt_spmlist_parse(gt_str_get(fn), 0, gt_spmproc_show_ascii,
        NULL, err);
    gt_str_delete(fn);
    return had_err;
  }
  verbose_logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX,
      stderr);
  el = gt_encseq_loader_new();
  gt_encseq_loader_drop_description_support(el);
  gt_encseq_loader_disable_autosupport(el);
  if (!arguments->singlestrand)
    gt_encseq_loader_mirror(el);
  reads = gt_encseq_loader_load(el, gt_str_get(arguments->readset), err);
  if (reads == NULL)
    had_err = -1;
  else
  {
    Sequentialsuffixarrayreader *ssar = NULL;
    switch (arguments->test)
    {
      case GT_READJOINER_SPMTEST_BRUTEFORCE:
        gt_rdj_pairwise_exact(GT_OVLFIND_SPM, reads, !arguments->singlestrand,
            false, false, (unsigned long)arguments->minmatchlength, true,
            gt_spmproc_show_ascii, NULL, false, NULL, NULL, NULL);
        break;
      case GT_READJOINER_SPMTEST_KMP:
        gt_rdj_pairwise_exact(GT_OVLFIND_SPM, reads, !arguments->singlestrand,
            false, true, (unsigned long)arguments->minmatchlength, true,
            gt_spmproc_show_ascii, NULL, false, NULL, NULL, NULL);
        break;
      case GT_READJOINER_SPMTEST_GUSFIELD:
        ssar = gt_newSequentialsuffixarrayreaderfromfile(gt_str_get(
              arguments->readset), SARR_LCPTAB | SARR_SUFTAB | SARR_SSPTAB |
            SARR_ESQTAB, SEQ_mappedboth, verbose_logger, err);
        if (gt_error_is_set(err))
          had_err = -1;
        else
          gt_rdj_gusfield(ssar, (unsigned long)arguments->minmatchlength, true,
              true, arguments->singlestrand ? 0 :
              GT_DIV2(gt_encseq_num_of_sequences(reads)), gt_spmproc_show_ascii,
              NULL);
        if (ssar != NULL)
          gt_freeSequentialsuffixarrayreader(&ssar);
        break;
      default:
        gt_assert(false);
    }
    gt_encseq_delete(reads);
  }
  gt_encseq_loader_delete(el);
  gt_logger_delete(verbose_logger);
  return had_err;
}

GtTool* gt_readjoiner_spmtest(void)
{
  return gt_tool_new(gt_readjoiner_spmtest_arguments_new,
                  gt_readjoiner_spmtest_arguments_delete,
                  gt_readjoiner_spmtest_option_parser_new,
                  gt_readjoiner_spmtest_arguments_check,
                  gt_readjoiner_spmtest_runner);
}
genometools-1.5.1/src/tools/gt_readjoiner_spmtest.h000066400000000000000000000020101211610345200225300ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_READJOINER_SPMTEST_H
#define GT_READJOINER_SPMTEST_H

#include "core/tool_api.h"

/* the readjoiner_spmtest tool */
GtTool* gt_readjoiner_spmtest(void);

#endif
genometools-1.5.1/src/tools/gt_readreads.c000066400000000000000000000153241211610345200205700ustar00rootroot00000000000000/*
  Copyright (c) 2009      Sascha Steinbiss 
  Copyright (c)      2011 Dirk Willrodt 
  Copyright (c) 2009-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/fileutils_api.h"
#include "core/ma.h"
#include "core/progressbar.h"
#include "core/quality.h"
#include "core/seq_iterator_fastq_api.h"
#include "core/str_array_api.h"
#include "core/unused_api.h"
#include "core/fasta.h"
#include "tools/gt_readreads.h"

#define SEQUENCE_CHAR_SEPARATOR '|'

typedef struct {
  bool verbose,
       showseq,
       fasta,
       colorspace;
  GtStr *qualformat;
  unsigned long fastawidth;
} GtReadreads;

static void* gt_readreads_arguments_new(void)
{
  GtReadreads *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->qualformat = gt_str_new();
  return arguments;
}

static void gt_readreads_arguments_delete(void *tool_arguments)
{
  GtReadreads *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->qualformat);
  gt_free(arguments);
}

static GtOptionParser* gt_readreads_option_parser_new(void *tool_arguments)
{
  GtReadreads *opts = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *fasta;
  gt_assert(opts);

#ifndef S_SPLINT_S
  static const char *qualformats[] = {
    "phred",
    "solexa",
    NULL
  };
#endif

  /* init */
  op = gt_option_parser_new("[option ...] file [...]",
                            "Read in FASTQ reads with PHRED or Solexa "
                            "qualities and print them.");

  option = gt_option_new_bool("v","be verbose",
                              &opts->verbose, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("showseq","show sequences",
                              &opts->showseq, false);
  gt_option_parser_add_option(op, option);

  fasta = gt_option_new_bool("fasta","output reads in fasta format",
                              &opts->fasta, false);
  gt_option_exclude(fasta, option);
  gt_option_parser_add_option(op, fasta);

  option = gt_option_new_ulong("fastawidth","fasta output line width",
                               &opts->fastawidth, 60UL);
  gt_option_imply(option, fasta);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_choice("format", "quality score scale\n"
                                          "can be 'phred' or 'solexa'",
                                opts->qualformat,
                                qualformats[0],
                                qualformats);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("colorspace", "reads are color space coded",
                              &opts->colorspace,
                              false);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_args(op, 1U);
  return op;
}

static int gt_readreads_arguments_check(GT_UNUSED int rest_argc,
                                        GT_UNUSED void *tool_arguments,
                                        GT_UNUSED GtError *err)
{
  GT_UNUSED GtReadreads *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  return had_err;
}

static int gt_readreads_runner(int argc, const char **argv, int parsed_args,
                               void *tool_arguments, GT_UNUSED GtError *err)
{
  GtReadreads *opts = tool_arguments;
  GtStrArray *files;
  GtSeqIterator *siq;
  int had_err = 0;
  unsigned long i,
                totalsize,
                len;
  const GtUchar *seq,
                *qual = NULL;
  char *desc;
  GtStr *scores = gt_str_new();

  gt_error_check(err);
  gt_assert(opts);

  files = gt_str_array_new();
  for (i = (unsigned long) parsed_args; i < (unsigned long) argc; i++)
  {
    gt_str_array_add_cstr(files, argv[i]);
  }
  totalsize = (unsigned long) gt_files_estimate_total_size(files);

  if (opts->colorspace)
  {
    siq = gt_seq_iterator_colorspace_fastq_new(files, err);
  }
  else
  {
    siq = gt_seq_iterator_fastq_new(files, err);
  }
  gt_seq_iterator_set_quality_buffer(siq, &qual);

  if (opts->verbose)
  {
    gt_progressbar_start(gt_seq_iterator_getcurrentcounter(siq,
                                                         (unsigned long long)
                                                         totalsize),
                         (unsigned long long) totalsize);
  }

  while (true)
  {
    had_err = gt_seq_iterator_next(siq, &seq, &len, &desc, err);
    if (had_err != 1)
      break;
    if (opts->fasta) {
      gt_fasta_show_entry((char*)desc, (char*)seq, len, opts->fastawidth, NULL);
    }
    else if (opts->showseq) {
      unsigned long *lens = gt_malloc(sizeof (unsigned long)*len);
      gt_str_reset(scores);
      for (i=0;iqualformat), "phred") == 0) {
          l = gt_str_length(scores);
          gt_assert(qual);
          gt_str_append_uint(scores,
                             gt_quality_fastq_to_phred(qual[i]));
          lens[i] = gt_str_length(scores) - l;
        } else if (strcmp(gt_str_get(opts->qualformat), "solexa") == 0) {
          l = gt_str_length(scores);
          gt_assert(qual);
          gt_str_append_int(scores,
                            gt_quality_fastq_to_solexa(qual[i]));
          lens[i] = gt_str_length(scores) - l;
        }
        if (i != len-1)
          gt_str_append_char(scores, SEQUENCE_CHAR_SEPARATOR);
      }
      for (i=0;iverbose)
    gt_progressbar_stop();
  gt_str_array_delete(files);
  gt_str_delete(scores);
  gt_seq_iterator_delete(siq);
  return had_err;
}

GtTool* gt_readreads(void)
{
  return gt_tool_new(gt_readreads_arguments_new,
                     gt_readreads_arguments_delete,
                     gt_readreads_option_parser_new,
                     gt_readreads_arguments_check,
                     gt_readreads_runner);
}
genometools-1.5.1/src/tools/gt_readreads.h000066400000000000000000000017451211610345200205770ustar00rootroot00000000000000/*
  Copyright (c) 2009 Sascha Steinbiss 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_READREADS_H
#define GT_READREADS_H

#include "core/tool_api.h"

/* the readreads tool */
GtTool* gt_readreads(void);

#endif
genometools-1.5.1/src/tools/gt_regioncov.c000066400000000000000000000066501211610345200206330ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "core/versionfunc.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/regioncov_visitor.h"
#include "tools/gt_regioncov.h"

typedef struct {
  unsigned long max_feature_dist;
  bool verbose;
} RegionCovArguments;

static GtOPrval parse_options(int *parsed_args, RegionCovArguments *arguments,
                              int argc, const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOption *o;
  GtOPrval oprval;
  gt_error_check(err);
  op = gt_option_parser_new("[option ...] GFF3_file",
                         "Show which parts of the given sequence regions are "
                         "covered by features.");
  /* -maxfeaturedist */
  o = gt_option_new_ulong("maxfeaturedist", "set the maximum distance two "
                       "features can have while still being in the same "
                       "``cluster''", &arguments->max_feature_dist, 0);
  gt_option_parser_add_option(op, o);
  /* -v */
  o = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, o);
  /* parse */
  gt_option_parser_set_min_max_args(op, 1, 1);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

int gt_regioncov(int argc, const char **argv, GtError *err)
{
  GtNodeVisitor *regioncov_visitor;
  GtNodeStream *gff3_in_stream;
  GtGenomeNode *gn;
  RegionCovArguments arguments;
  int parsed_args, had_err = 0;
  gt_error_check(err);

  /* option parsing */
  switch (parse_options(&parsed_args, &arguments, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR:
      return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT:
      return 0;
  }

  /* create gff3 input stream */
  gt_assert(parsed_args < argc);
  gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
  if (arguments.verbose)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);

  /* create region coverage visitor */
  regioncov_visitor = gt_regioncov_visitor_new(arguments.max_feature_dist);

  /* pull the features through the stream and free them afterwards */
  while (!(had_err = gt_node_stream_next(gff3_in_stream, &gn, err)) && gn) {
      had_err = gt_genome_node_accept(gn, regioncov_visitor, err);
      gt_genome_node_delete(gn);
  }

  /* show region coverage */
  if (!had_err)
    gt_regioncov_visitor_show_coverage(regioncov_visitor);

  /* free */
  gt_node_visitor_delete(regioncov_visitor);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}
genometools-1.5.1/src/tools/gt_regioncov.h000066400000000000000000000017461211610345200206410ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_REGIONCOV_H
#define GT_REGIONCOV_H

/* the region coverage tool */
int gt_regioncov(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_sain.c000066400000000000000000000206751211610345200175750ustar00rootroot00000000000000/*
  Copyright (c) 2012 Stefan Kurtz 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/unused_api.h"
#include "core/fa.h"
#include "core/timer_api.h"
#include "core/showtime.h"
#include "core/logger.h"
#include "tools/gt_sain.h"
#include "match/sfx-sain.h"

typedef struct
{
  bool icheck, fcheck, verbose;
  GtStr *encseqfile, *plainseqfile, *dir;
  GtReadmode readmode;
} GtSainArguments;

static void* gt_sain_arguments_new(void)
{
  GtSainArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->encseqfile = gt_str_new();
  arguments->plainseqfile = gt_str_new();
  arguments->dir = gt_str_new_cstr("fwd");
  arguments->readmode = GT_READMODE_FORWARD;
  return arguments;
}

static void gt_sain_arguments_delete(void *tool_arguments)
{
  GtSainArguments *arguments = tool_arguments;

  if (arguments != NULL)
  {
    gt_str_delete(arguments->encseqfile);
    gt_str_delete(arguments->plainseqfile);
    gt_str_delete(arguments->dir);
    gt_free(arguments);
  }
}

static GtOptionParser* gt_sain_option_parser_new(void *tool_arguments)
{
  GtSainArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionfcheck, *optionesq, *optionfile;

  gt_assert(arguments != NULL);

  /* init */
  op = gt_option_parser_new("[option ...] [file]", /* XXX */
                            "Compute suffix array using induced "
                            "suffix sorting.");
  gt_option_parser_set_mail_address(op,"");

  /* -esq */
  optionesq = gt_option_new_string("esq", "specify encseq file",
                             arguments->encseqfile, NULL);
  gt_option_parser_add_option(op, optionesq);

  /* -dir */
  gt_encseq_options_add_readmode_option(op, arguments->dir);

  /* -file */
  optionfile = gt_option_new_string("file", "specify filename",
                                   arguments->plainseqfile, NULL);
  gt_option_parser_add_option(op, optionfile);

  /* -icheck */
  option = gt_option_new_bool("icheck",
                              "intermediate check of all sorted arrays",
                              &arguments->icheck, false);
  gt_option_parser_add_option(op, option);

  /* -fcheck */
  optionfcheck = gt_option_new_bool("fcheck", "final check of suffix array",
                                    &arguments->fcheck, false);
  gt_option_parser_add_option(op, optionfcheck);
  gt_option_imply(optionfcheck, optionesq);
  gt_option_exclude(optionesq,optionfile);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  return op;
}

static int gt_sain_option_parser_check(int rest_argc,
                                       void *tool_arguments, GtError *err)
{
  int retval;
  GtSainArguments *arguments = tool_arguments;

  if (rest_argc > 0)
  {
    gt_error_set(err,"%d superfluous argument%s",
                 rest_argc,rest_argc > 1 ? "s" : "");
    return -1;
  }
  retval = gt_readmode_parse(gt_str_get(arguments->dir), err);
  if (retval < 0)
  {
    return -1;
  } else
  {
    arguments->readmode = (GtReadmode) retval;
    return 0;
  }
}

static int gt_sain_checkmaxsequencelength(unsigned long len,bool forencseq,
                                          GtError *err)
{
  unsigned long maxsequencelength;

  if (forencseq)
  {
    maxsequencelength = (unsigned long) (~GT_FIRSTBIT) - 1 - GT_COMPAREOFFSET;
  } else
  {
    maxsequencelength = (unsigned long) (~GT_FIRSTBIT) - 1;
  }
  if (len > maxsequencelength)
  {
    gt_error_set(err,"sequence of size %lu is too long: sain algorithm "
                     "can only compute sequence of length up to %lu",
                     len,maxsequencelength);
    return -1;
  }
  return 0;
}

typedef struct
{
  GtTimer *timer;
  GtLogger *logger;
} GtSainTimerandLogger;

static GtSainTimerandLogger *gt_sain_timer_logger_new(bool verbose)
{
  GtSainTimerandLogger *tl = gt_malloc(sizeof (*tl));

  tl->timer = NULL;
  tl->logger = gt_logger_new(verbose,GT_LOGGER_DEFLT_PREFIX,stdout);
  if (gt_showtime_enabled())
  {
    if (verbose)
    {
      tl->timer = gt_timer_new_with_progress_description(
                                       "allocate suftab and undef entries");
    } else
    {
      tl->timer = gt_timer_new();
      gt_timer_omit_last_stage(tl->timer);
    }
    gt_timer_start(tl->timer);
  }
  return tl;
}

static void gt_sain_timer_logger_delete(GtSainTimerandLogger *tl)
{
  if (tl->timer != NULL)
  {
    gt_timer_show_progress_final(tl->timer, stdout);
    gt_timer_stop(tl->timer);
    gt_timer_delete(tl->timer);
  }
  gt_logger_delete(tl->logger);
  gt_free(tl);
}

static int gt_sain_runner(int argc, GT_UNUSED const char **argv,
                          int parsed_args, void *tool_arguments, GtError *err)
{
  GtSainArguments *arguments = tool_arguments;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments != NULL);

  gt_assert (argc >= parsed_args);
  if (parsed_args < argc)
  {
    gt_error_set(err,"superfluous arguments");
    had_err = -1;
  } else
  {
    if (gt_str_length(arguments->encseqfile) > 0)
    {
      GtEncseqLoader *el = gt_encseq_loader_new();
      GtEncseq *encseq
        = gt_encseq_loader_load(el,gt_str_get(arguments->encseqfile),err);
      if (encseq == NULL)
      {
        had_err = -1;
      } else
      {
        if (gt_sain_checkmaxsequencelength(gt_encseq_total_length(encseq),true,
                                           err)
                       != 0)
        {
          had_err = -1;
        } else
        {
          if (!gt_alphabet_is_dna(gt_encseq_alphabet(encseq)) &&
              (arguments->readmode == GT_READMODE_COMPL ||
               arguments->readmode == GT_READMODE_REVCOMPL))
          {
            gt_error_set(err,"option -dir cpl and -dir rcl is only "
                             "possible for DNA sequences");
            had_err = -1;
          }
        }
        if (!had_err)
        {
          GtSainTimerandLogger *tl
            = gt_sain_timer_logger_new(arguments->verbose);
          gt_sain_encseq_sortsuffixes(encseq,
                                      arguments->readmode,
                                      arguments->icheck,
                                      arguments->fcheck,
                                      tl->logger,
                                      tl->timer);
          gt_sain_timer_logger_delete(tl);
        }
      }
      gt_encseq_delete(encseq);
      gt_encseq_loader_delete(el);
    }
    if (gt_str_length(arguments->plainseqfile) > 0)
    {
      GtUchar *plainseq;
      size_t len;

      plainseq = gt_fa_mmap_read(gt_str_get(arguments->plainseqfile),&len,err);
      if (plainseq == NULL)
      {
        had_err = -1;
      } else
      {
        if (gt_sain_checkmaxsequencelength((unsigned long) len,false,err) != 0)
        {
          had_err = -1;
        } else
        {
          if (arguments->readmode != GT_READMODE_FORWARD)
          {
            gt_error_set(err,"option -dir and -file exclude each other");
            had_err = -1;
          }
        }
        if (!had_err)
        {
          GtSainTimerandLogger *tl
            = gt_sain_timer_logger_new(arguments->verbose);
          gt_sain_plain_sortsuffixes(plainseq,
                                     (unsigned long) len,
                                     arguments->icheck,
                                     tl->logger,
                                     tl->timer);
          gt_sain_timer_logger_delete(tl);
        }
      }
      gt_fa_xmunmap(plainseq);
    }
  }
  return had_err;
}

GtTool* gt_sain(void)
{
  return gt_tool_new(gt_sain_arguments_new,
                     gt_sain_arguments_delete,
                     gt_sain_option_parser_new,
                     gt_sain_option_parser_check,
                     gt_sain_runner);
}
genometools-1.5.1/src/tools/gt_sain.h000066400000000000000000000017111211610345200175700ustar00rootroot00000000000000/*
  Copyright (c) 2012 Stefan Kurtz 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SAIN_H
#define GT_SAIN_H

#include "core/tool_api.h"

/* the sain tool */
GtTool* gt_sain(void);

#endif
genometools-1.5.1/src/tools/gt_sam_interface.c000066400000000000000000000130011211610345200214240ustar00rootroot00000000000000/*
  Copyright (c) 2011 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/alphabet_api.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "extended/sam_alignment.h"
#include "extended/samfile_iterator.h"
#include "tools/gt_sam_interface.h"

typedef struct {
  bool bool_is_sam;
  int lines;
  GtOption *ref_idxfile;
  GtStr *indexfilename;
} GtSamInterfaceArguments;

static void* gt_sam_interface_arguments_new(void)
{
  GtSamInterfaceArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->indexfilename = gt_str_new();
  return arguments;
}

static void gt_sam_interface_arguments_delete(void *tool_arguments)
{
  GtSamInterfaceArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_option_delete(arguments->ref_idxfile);
  gt_str_delete(arguments->indexfilename);
  gt_free(arguments);
}

static GtOptionParser* gt_sam_interface_option_parser_new(void *tool_arguments)
{
  GtSamInterfaceArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);
  /* init */
  op = gt_option_parser_new("[options] filename",
                         "This tool exists solely as an "
                         "test for the interface.");

  /* -sam */
  option = gt_option_new_bool("sam",
                              "filetype is sam, default is bam",
                              &arguments->bool_is_sam, false);
  gt_option_parser_add_option(op, option);

  /* -idxfile */
  option = gt_option_new_filename("idxfile",
                                  "file containing reference info",
                                  arguments->indexfilename);
  gt_option_parser_add_option(op, option);
  arguments->ref_idxfile = gt_option_ref(option);

  /* -lines */
  option = gt_option_new_int("lines", "number of lines to print"
                             " leave undefined for all",
                             &arguments->lines, -1);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 1U, 1U);
  return op;
}

static int gt_sam_interface_arguments_check(GT_UNUSED int rest_argc,
                                       GT_UNUSED void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  GT_UNUSED GtSamInterfaceArguments *arguments = tool_arguments;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);
  gt_assert(rest_argc == 1);

  return had_err;
}

static int gt_sam_interface_runner(GT_UNUSED int argc,
                                   GT_UNUSED const char **argv,
                                   GT_UNUSED int parsed_args,
                                   void *tool_arguments, GtError *err)
{
  GtSamInterfaceArguments *arguments = tool_arguments;
  int had_err = 0, count_out = 0;
  GtSamfileIterator *sa_iter;
  GtSamAlignment *sa_align;
  GtAlphabet *alpha = gt_alphabet_new_dna();

  gt_error_check(err);
  gt_assert(arguments);

  if (arguments->bool_is_sam) {
    if (gt_option_is_set(arguments->ref_idxfile))
      sa_iter = gt_samfile_iterator_new_sam(argv[parsed_args], alpha,
                                        gt_str_get(arguments->indexfilename),
                                        err);
    else
      sa_iter  = gt_samfile_iterator_new_sam(argv[parsed_args], alpha,
                                        NULL,
                                        err);

  }
  else {
    sa_iter = gt_samfile_iterator_new_bam(argv[parsed_args], alpha, err);
  }
  while (gt_samfile_iterator_next(sa_iter, &sa_align) > 0 &&
         arguments->lines - count_out) {
    uint16_t cig_len, idx;

    cig_len = gt_sam_alignment_cigar_length(sa_align);

    printf("%s\t%d\t%s\t",
           gt_sam_alignment_identifier(sa_align),
           (int) gt_sam_alignment_flag(sa_align),
           gt_samfile_iterator_reference_name(sa_iter,
                                         gt_sam_alignment_ref_num(sa_align)));
    if (gt_sam_alignment_is_unmapped(sa_align))
      printf("*");
    else {
      for (idx = 0; idx < cig_len; idx++) {
        printf("%d%c",
               (int) gt_sam_alignment_cigar_i_length(sa_align, idx),
               gt_sam_alignment_cigar_i_operation(sa_align, idx));
      }
    }
    printf("\t");
    gt_alphabet_decode_seq_to_fp(alpha, stdout,
        gt_sam_alignment_sequence(sa_align),
        gt_sam_alignment_read_length(sa_align));
    printf("\t%s\n",
           (char *) gt_sam_alignment_qualitystring(sa_align));
    count_out++;
  }
  gt_samfile_iterator_delete(sa_iter);
  gt_alphabet_delete(alpha);
  return had_err;
}

GtTool* gt_sam_interface(void)
{
  return gt_tool_new(gt_sam_interface_arguments_new,
                  gt_sam_interface_arguments_delete,
                  gt_sam_interface_option_parser_new,
                  gt_sam_interface_arguments_check,
                  gt_sam_interface_runner);
}
genometools-1.5.1/src/tools/gt_sam_interface.h000066400000000000000000000017611211610345200214430ustar00rootroot00000000000000/*
  Copyright (c) 2011 Dirk Willrodt 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SAM_INTERFACE_H
#define GT_SAM_INTERFACE_H

#include "core/tool_api.h"

/* the sam_interface tool */
GtTool* gt_sam_interface(void);

#endif
genometools-1.5.1/src/tools/gt_script_filter.c000066400000000000000000000131561211610345200215100ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/unused_api.h"
#include "extended/script_filter.h"
#include "tools/gt_script_filter.h"

typedef struct {
  bool oneline,
       showinfo,
       scriptname,
       validate;
} GtScriptFilterArguments;

static void* gt_script_filter_arguments_new(void)
{
  GtScriptFilterArguments *arguments = gt_calloc(1, sizeof *arguments);
  return arguments;
}

static void gt_script_filter_arguments_delete(void *tool_arguments)
{
  GtScriptFilterArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_free(arguments);
}

static GtOptionParser* gt_script_filter_option_parser_new(void *tool_arguments)
{
  GtScriptFilterArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [script file(s)]",
                            "Get info about and validate Lua script filters.");

  /* -showinfo */
  option = gt_option_new_bool("showinfo", "show information about filter",
                              &arguments->showinfo, true);
  gt_option_parser_add_option(op, option);

  /* -validate */
  option = gt_option_new_bool("validate", "validate filter function",
                              &arguments->validate, true);
  gt_option_parser_add_option(op, option);

  /* -oneline */
  option = gt_option_new_bool("oneline", "show compact information on one line",
                             &arguments->oneline, false);
  gt_option_parser_add_option(op, option);

  /* -scriptname */
  option = gt_option_new_bool("scriptname", "show script name",
                             &arguments->scriptname, true);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_args(op, 1);

  return op;
}

static int gt_script_filter_runner(int argc, const char **argv, int parsed_args,
                                   void *tool_arguments, GT_UNUSED GtError *err)
{
  GtScriptFilterArguments *arguments = tool_arguments;
  int had_err = 0;
  unsigned long i;

  gt_error_check(err);
  gt_assert(arguments);

  for (i = parsed_args; !had_err && i < argc; i++) {
    GtScriptFilter *sf = NULL;
    sf = gt_script_filter_new(argv[i], err);
    if (!sf) {
      had_err = -1;
      break;
    } else {
      if (arguments->showinfo) {
        if (arguments->oneline) {
          const char *name,
                     *version,
                     *author;

          if (!(name = gt_script_filter_get_name(sf, err)))
            had_err = -1;

          if (!had_err) {
            if (!(version = gt_script_filter_get_version(sf, err)))
              had_err = -1;
          }

          if (!had_err) {
            if (!(author = gt_script_filter_get_author(sf, err)))
              had_err = -1;
          }

          if (!had_err) {
            printf("%s v%s (by %s)\n", name, version, author);
          }
        } else {
          const char *out;

          if (arguments->scriptname)
            printf("script name:\t%s\n", argv[i]);

          out = gt_script_filter_get_name(sf, err);
          if (out)
            printf("filter name:\t%s\n", out);
          else
            had_err = -1;

          if (!had_err) {
            out = gt_script_filter_get_version(sf, err);
            if (out)
              printf("version:\t%s\n", out);
            else
              had_err = -1;
          }

          if (!had_err) {
            out = gt_script_filter_get_author(sf, err);
            if (out)
              printf("author:\t\t%s\n", out);
            else
              had_err = -1;
          }

          if (!had_err) {
            out = gt_script_filter_get_email(sf, err);
            if (out)
              printf("email:\t\t%s\n", out);
            else
              had_err = -1;
          }

          if (!had_err) {
            out = gt_script_filter_get_description(sf, err);
            if (out)
              printf("description:\t%s\n", out);
            else
              had_err = -1;
          }

          if (i != argc-1)
            printf("\n");
        }
      }
      if (arguments->validate) {
        GT_UNUSED bool select;
        GtStr *seqid = gt_str_new_cstr("foo");
        GtFeatureNode *fn = (GtFeatureNode*) gt_feature_node_new(seqid, "gene",
                                                             23, 42,
                                                             GT_STRAND_FORWARD);
        had_err = gt_script_filter_run(sf, fn, &select, err);
        gt_genome_node_delete((GtGenomeNode*) fn);
        gt_str_delete(seqid);
      }
      gt_script_filter_delete(sf);
    }
  }

  return had_err;
}

GtTool* gt_script_filter(void)
{
  return gt_tool_new(gt_script_filter_arguments_new,
                  gt_script_filter_arguments_delete,
                  gt_script_filter_option_parser_new,
                  NULL,
                  gt_script_filter_runner);
}
genometools-1.5.1/src/tools/gt_script_filter.h000066400000000000000000000017651211610345200215200ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SCRIPT_FILTER_H
#define GT_SCRIPT_FILTER_H

#include "core/tool_api.h"

/* the script_filter tool */
GtTool* gt_script_filter(void);

#endif
genometools-1.5.1/src/tools/gt_select.c000066400000000000000000000370521211610345200201170ustar00rootroot00000000000000/*
  Copyright (c) 2005-2012 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_defines.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gff3_output.h"
#include "extended/gff3_parser.h"
#include "extended/gff3_visitor.h"
#include "extended/gtdatahelp.h"
#include "extended/select_stream.h"
#include "extended/targetbest_select_stream.h"
#include "tools/gt_select.h"

#define GT_STRAND_OPT  "strand"
#define TARGETGT_STRAND_OPT  "targetstrand"

typedef struct {
  bool verbose,
       has_CDS,
       targetbest;
  GtStr *seqid,
        *source,
        *gt_strand_char,
        *targetgt_strand_char;
  GtRange contain_range,
          overlap_range;
  GtStrand strand,
           targetstrand;
  unsigned long max_gene_length,
                max_gene_num,
                feature_num;
  double min_gene_score,
         max_gene_score,
         min_average_splice_site_prob,
         single_intron_factor;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
  GtStrArray  *filter_files;
  GtStr *filter_logic;
  GtStr *dropped_file;
} SelectArguments;

static void* gt_select_arguments_new(void)
{
  SelectArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->seqid = gt_str_new();
  arguments->source = gt_str_new();
  arguments->gt_strand_char = gt_str_new();
  arguments->strand = GT_NUM_OF_STRAND_TYPES;
  arguments->targetgt_strand_char = gt_str_new();
  arguments->targetstrand = GT_NUM_OF_STRAND_TYPES;
  arguments->ofi = gt_output_file_info_new();
  arguments->filter_files = gt_str_array_new();
  arguments->filter_logic = gt_str_new();
  arguments->dropped_file = gt_str_new();
  return arguments;
}

static void gt_select_arguments_delete(void *tool_arguments)
{
  SelectArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->targetgt_strand_char);
  gt_str_delete(arguments->gt_strand_char);
  gt_str_delete(arguments->source);
  gt_str_delete(arguments->seqid);
  gt_str_array_delete(arguments->filter_files);
  gt_str_delete(arguments->filter_logic);
  gt_str_delete(arguments->dropped_file);
  gt_free(arguments);
}

static GtOptionParser* gt_select_option_parser_new(void *tool_arguments)
{
  SelectArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *contain_option, *overlap_option, *minaveragessp_option,
           *singleintron_option, *optiondroppedfile;
  gt_assert(arguments);

  static const char *filter_logic[] = {
    "AND",
    "OR",
    NULL
  };

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                            "Select certain features (specified by the used "
                            "options) from given GFF3 file(s).");

  /* -seqid */
  option = gt_option_new_string("seqid", "select feature with the given "
                                "sequence ID (all comments are selected). ",
                                arguments->seqid, NULL);
  gt_option_parser_add_option(op, option);

  /* -source */
  option = gt_option_new_string("source", "select feature with the given "
                                "source (the source is column 2 in regular "
                                "GFF3 lines)" , arguments->source, NULL);
  gt_option_parser_add_option(op, option);

  /* -contain */
  contain_option = gt_option_new_range("contain", "select all features which "
                                       "are contained in the given range",
                                       &arguments->contain_range, NULL);
  gt_option_parser_add_option(op, contain_option);

  /* -overlap */
  overlap_option = gt_option_new_range("overlap", "select all features which "
                                       "do overlap with the given range",
                                       &arguments->overlap_range, NULL);
  gt_option_parser_add_option(op, overlap_option);

  /* -strand */
  option = gt_option_new_string(GT_STRAND_OPT, "select all top-level features"
                                "(i.e., features without parents) whose strand "
                                "equals the given one (must be one of '"
                                GT_STRAND_CHARS"')", arguments->gt_strand_char,
                                NULL);
  gt_option_parser_add_option(op, option);

  /* -targetstrand */
  option = gt_option_new_string(TARGETGT_STRAND_OPT, "select all top-level "
                                "features (i.e., features without parents) "
                                "which have exactly one target attribute whose "
                                "strand equals the given one (must be one of '"
                                GT_STRAND_CHARS"')",
                                arguments->targetgt_strand_char, NULL);
  gt_option_parser_add_option(op, option);

  /* -targetbest */
  option = gt_option_new_bool("targetbest", "if multiple top-level features "
                             "(i.e., features without parents) with exactly "
                             "one target attribute have the same target_id, "
                             "keep only the feature with the best score. If "
                             "-"TARGETGT_STRAND_OPT" is used at the same time, "
                             "this option is applied after "
                             "-"TARGETGT_STRAND_OPT".\n"
                             "Memory consumption is proportional to the input "
                             "file size(s).", &arguments->targetbest, false);
  gt_option_parser_add_option(op, option);

  /* -hascds */
  option = gt_option_new_bool("hascds", "select all top-level features which "
                              "do have a CDS child", &arguments->has_CDS,
                              false);
  gt_option_parser_add_option(op, option);

  /* -maxgenelength */
  option = gt_option_new_ulong_min("maxgenelength", "select genes up to the "
                                   "given maximum length",
                                   &arguments->max_gene_length, GT_UNDEF_ULONG,
                                   1);
  gt_option_parser_add_option(op, option);

  /* -maxgenenum */
  option = gt_option_new_ulong("maxgenenum", "select the first genes up to the "
                               "given maximum number", &arguments->max_gene_num,
                               GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, option);

  /* -mingenescore */
  option = gt_option_new_double("mingenescore", "select genes with the given "
                                "minimum score", &arguments->min_gene_score,
                                GT_UNDEF_DOUBLE);
  gt_option_parser_add_option(op, option);

  /* -maxgenescore */
  option = gt_option_new_double("maxgenescore", "select genes with the given "
                                "maximum score", &arguments->max_gene_score,
                                GT_UNDEF_DOUBLE);
  gt_option_parser_add_option(op, option);

  /* -minaveragessp */
  minaveragessp_option =
    gt_option_new_probability("minaveragessp",
                              "set the minimum average splice site probability",
                              &arguments->min_average_splice_site_prob,
                              GT_UNDEF_DOUBLE);
  gt_option_parser_add_option(op, minaveragessp_option);

  /* -singleintronfactor */
  singleintron_option =
    gt_option_new_double_min("singleintronfactor",
                             "factor to multiplicate the average splice site "
                             "probability with for single introns before "
                             "comparing it to the minimum average splice site "
                             "probability", &arguments->single_intron_factor,
                             1.0, 1.0);
  gt_option_is_development_option(singleintron_option);
  gt_option_parser_add_option(op, singleintron_option);

  /* -featurenum */
  option = gt_option_new_ulong_min("featurenum",
                                   "select feature tree occurring "
                                   "at given position in input",
                                   &arguments->feature_num, GT_UNDEF_ULONG, 1);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -filter_files */
  option = gt_option_new_filename_array("rule_files",
                                        "specify Lua files to be used "
                                        "for selection",
                                        arguments->filter_files);
  gt_option_parser_add_option(op, option);

  /* -filter_logic */
  option = gt_option_new_choice("rule_logic", "select how multiple Lua "
                                "files should be combined\nchoose from AND|OR",
                                arguments->filter_logic, filter_logic[0],
                                filter_logic);
  gt_option_parser_add_option(op, option);

  /* -nh_file */
  optiondroppedfile = gt_option_new_filename("dropped_file",
                                             "save non-selected features to "
                                             "file",
                                             arguments->dropped_file);
  gt_option_parser_add_option(op, optiondroppedfile);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* option exclusions */
  gt_option_exclude(contain_option, overlap_option);

  /* option implications */
  gt_option_imply(singleintron_option, minaveragessp_option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);

  return op;
}

static int process_gt_strand_arg(GtStr *gt_strand_char, GtStrand *strand,
                                 const char *optstr, GtError *err)
{
  int had_err = 0;
  gt_error_check(err);
  if (gt_str_length(gt_strand_char)) {
    GtStrand tmpstrand = gt_strand_get(gt_str_get(gt_strand_char)[0]);
    if ((gt_str_length(gt_strand_char) > 1) ||
        (tmpstrand == GT_NUM_OF_STRAND_TYPES)) {
      gt_error_set(err, "argument to option -%s must be one of '"
                        GT_STRAND_CHARS"'", optstr);
      had_err = -1;
    }
    if (!had_err)
      *strand = tmpstrand;
  }
  return had_err;
}

static int gt_select_arguments_check(GT_UNUSED int rest_argc,
                                     void *tool_arguments, GtError *err)
{
  SelectArguments *arguments = tool_arguments;
  int had_err;
  gt_error_check(err);
  gt_assert(arguments);
  had_err = process_gt_strand_arg(arguments->gt_strand_char, &arguments->strand,
                                  GT_STRAND_OPT, err);
  if (!had_err) {
    had_err = process_gt_strand_arg(arguments->targetgt_strand_char,
                                    &arguments->targetstrand,
                                    TARGETGT_STRAND_OPT, err);
  }

  return had_err;
}

static int print_to_file_drophandler(GtGenomeNode *gn, void *data,
                                     GtError *err)
{
  GtNodeVisitor *v;
  gt_assert(gn && data);
  v = (GtNodeVisitor*) data;
  return gt_genome_node_accept(gn, v, err);
}

static int default_drophandler(GT_UNUSED GtGenomeNode *gn, GT_UNUSED void *data,
                               GT_UNUSED GtError *err)
{
  gt_assert(gn);
  return 0;
}

static int gt_select_runner(int argc, const char **argv, int parsed_args,
                            void *tool_arguments, GtError *err)
{
  SelectArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream, *select_stream,
               *targetbest_select_stream = NULL, *gff3_out_stream;
  int had_err;
  GtFile *drop_file = NULL;
  GtNodeVisitor *gff3outvis = NULL;
  gt_error_check(err);
  gt_assert(arguments);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);

  /* create a filter stream */
  select_stream = gt_select_stream_new(gff3_in_stream, arguments->seqid,
                                       arguments->source,
                                       &arguments->contain_range,
                                       &arguments->overlap_range,
                                       arguments->strand,
                                       arguments->targetstrand,
                                       arguments->has_CDS,
                                       arguments->max_gene_length,
                                       arguments->max_gene_num,
                                       arguments->min_gene_score,
                                       arguments->max_gene_score,
                                       arguments->min_average_splice_site_prob,
                                       arguments->feature_num,
                                       arguments->filter_files,
                                       arguments->filter_logic,
                                       err);

  if (select_stream) {
    GtSelectStream *fs = (GtSelectStream*) select_stream;

    if (gt_str_length(arguments->dropped_file) > 0) {
      drop_file = gt_file_new(gt_str_get(arguments->dropped_file), "w", err);
      gff3outvis = gt_gff3_visitor_new(drop_file);
      gt_select_stream_set_drophandler(fs, print_to_file_drophandler,
                                       (void*) gff3outvis);
    } else {
      gt_select_stream_set_drophandler(fs, default_drophandler, NULL);
    }

    gt_select_stream_set_single_intron_factor(select_stream,
                                              arguments->single_intron_factor);

    if (arguments->targetbest)
      targetbest_select_stream = gt_targetbest_select_stream_new(select_stream);

    /* create a gff3 output stream */
    gff3_out_stream = gt_gff3_out_stream_new(arguments->targetbest
                                             ? targetbest_select_stream
                                             : select_stream,
                                             arguments->outfp);

    /* pull the features through the stream and free them afterwards */
    had_err = gt_node_stream_pull(gff3_out_stream, err);

    /* free */
    gt_node_stream_delete(gff3_out_stream);
    gt_node_stream_delete(select_stream);
    gt_node_stream_delete(targetbest_select_stream);
  } else {
    had_err = -1;
  }
  gt_file_delete(drop_file);
  gt_node_visitor_delete(gff3outvis);
  gt_node_stream_delete(gff3_in_stream);
  return had_err;
}

GtTool* gt_select(void)
{
  return gt_tool_new(gt_select_arguments_new,
                     gt_select_arguments_delete,
                     gt_select_option_parser_new,
                     gt_select_arguments_check,
                     gt_select_runner);
}
genometools-1.5.1/src/tools/gt_select.h000066400000000000000000000017351211610345200201230ustar00rootroot00000000000000/*
  Copyright (c) 2005-2011 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SELECT_H
#define GT_SELECT_H

#include "core/tool_api.h"

/* the select tool */
GtTool* gt_select(void);

#endif
genometools-1.5.1/src/tools/gt_seq.c000066400000000000000000000153431211610345200174270ustar00rootroot00000000000000/*
  Copyright (c) 2006-2010 Gordon Gremme 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/bioseq.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/undef_api.h"
#include "tools/gt_seq.h"

typedef struct {
  bool recreate,
       showfasta,
       gc_content,
       stat,
       seqlengthdistri;
  unsigned long showseqnum,
                width;
  GtStr *reader;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} SeqArguments;

static void* gt_seq_arguments_new(void)
{
  SeqArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->reader = gt_str_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_seq_arguments_delete(void *tool_arguments)
{
  SeqArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_str_delete(arguments->reader);
  gt_free(arguments);
}

static GtOptionParser* gt_seq_option_parser_new(void *tool_arguments)
{
  SeqArguments *arguments = tool_arguments;
  GtOption *option, *option_recreate, *option_showfasta, *option_showseqnum,
           *option_width, *option_stat;
  GtOptionParser *op;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] sequence_file [...]",
                            "Parse the given sequence file(s) and construct "
                            "the corresponding index files.");

  /* -recreate */
  option_recreate = gt_option_new_bool("recreate", "recreate index files, even "
                                       "if they exist already",
                                       &arguments->recreate, false);
  gt_option_parser_add_option(op, option_recreate);

  /* -showfasta */
  option_showfasta = gt_option_new_bool("showfasta", "show all sequences (in "
                                        "FASTA format)", &arguments->showfasta,
                                        false);
  gt_option_parser_add_option(op, option_showfasta);

  /* -showseqnum */
  option_showseqnum = gt_option_new_ulong_min("showseqnum", "show sequence "
                                              "with given number (in FASTA "
                                              "format)", &arguments->showseqnum,
                                              GT_UNDEF_ULONG, 1);
  gt_option_parser_add_option(op, option_showseqnum);

  /* -gc-content */
  option = gt_option_new_bool("gc-content", "print GC-content (for DNA files)",
                              &arguments->gc_content, false);
  gt_option_parser_add_option(op, option);

  /* -stat */
  option_stat = gt_option_new_bool("stat", "show sequence statistics",
                                   &arguments->stat, false);
  gt_option_parser_add_option(op, option_stat);

  /* -seqlengthdistri */
  option = gt_option_new_bool("seqlengthdistri", "show sequence length "
                              "distribution", &arguments->seqlengthdistri,
                              false);
  gt_option_parser_add_option(op, option);

  /* -width */
  option_width = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, option_width);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  /* option implications */
  gt_option_imply_either_2(option_width, option_showfasta, option_showseqnum);

  /* option exclusions */
  gt_option_exclude(option_showfasta, option_stat);
  gt_option_exclude(option_showfasta, option_showseqnum);
  gt_option_exclude(option_showseqnum, option_stat);

  /* set minimal arguments */
  gt_option_parser_set_min_args(op, 1);

  return op;
}

static int gt_seq_arguments_check(int rest_argc, void *tool_arguments,
                                  GtError *err)
{
  SeqArguments *arguments = tool_arguments;
  gt_error_check(err);
  gt_assert(arguments);
  /* option -showseqnum makes only sense if we got a single sequence file */
  if (arguments->showseqnum != GT_UNDEF_ULONG && rest_argc > 1) {
    gt_error_set(err, "option '-showseqnum' makes only sense with a single "
                      "sequence_file");
    return -1;
  }
  return 0;
}

static int gt_seq_runner(int argc, const char **argv, int parsed_args,
                         void *tool_arguments, GtError *err)
{
  SeqArguments *arguments = tool_arguments;
  GtBioseq *bioseq;
  int arg = parsed_args, had_err = 0;
  gt_error_check(err);
  gt_assert(tool_arguments);

  while (!had_err && arg < argc) {
    /* bioseq construction */
    if (arguments->recreate)
      bioseq = gt_bioseq_new_recreate(argv[arg], err);
    else
      bioseq = gt_bioseq_new(argv[arg], err);
    if (!bioseq)
      had_err = -1;

    /* output */
    if (!had_err && arguments->showfasta)
      gt_bioseq_show_as_fasta(bioseq, arguments->width, arguments->outfp);

    if (!had_err && arguments->showseqnum != GT_UNDEF_ULONG) {
      if (arguments->showseqnum > gt_bioseq_number_of_sequences(bioseq)) {
        gt_error_set(err, "argument '%lu' to option '-showseqnum' is too "
                     "large. The sequence index contains only '%lu' sequences.",
                     arguments->showseqnum,
                     gt_bioseq_number_of_sequences(bioseq));
        had_err = -1;
      }
      if (!had_err) {
        gt_bioseq_show_sequence_as_fasta(bioseq, arguments->showseqnum - 1,
                                         arguments->width, arguments->outfp);
      }
    }

    if (!had_err && arguments->gc_content)
      gt_bioseq_show_gc_content(bioseq, arguments->outfp);

    if (!had_err && arguments->stat)
      gt_bioseq_show_stat(bioseq, arguments->outfp);

    if (!had_err && arguments->seqlengthdistri)
      gt_bioseq_show_seqlengthdistri(bioseq, arguments->outfp);

    /* free */
    gt_bioseq_delete(bioseq);

    arg++;
  }

  return had_err;
}

GtTool* gt_seq(void)
{
  return gt_tool_new(gt_seq_arguments_new,
                     gt_seq_arguments_delete,
                     gt_seq_option_parser_new,
                     gt_seq_arguments_check,
                     gt_seq_runner);
}
genometools-1.5.1/src/tools/gt_seq.h000066400000000000000000000017261211610345200174340ustar00rootroot00000000000000/*
  Copyright (c) 2006-2010 Gordon Gremme 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQ_H
#define GT_SEQ_H

#include "core/tool_api.h"

/* the sequence tool */
GtTool* gt_seq(void);

#endif
genometools-1.5.1/src/tools/gt_seqcorrect.c000066400000000000000000000511251211610345200210070ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/fa.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "core/option_api.h"
#include "core/encseq_api.h"
#include "core/log_api.h"
#include "core/logger.h"
#include "core/intbits.h"
#include "core/minmax.h"
#include "core/showtime.h"
#include "core/undef_api.h"
#ifdef GT_THREADS_ENABLED
#include "core/thread_api.h"
#endif
#include "core/warning_api.h"
#include "core/xposix.h"
#include "tools/gt_seqcorrect.h"
#include "match/reads2twobit.h"
#include "match/rdj-contfinder.h"
#include "match/rdj-twobitenc-editor.h"
#include "match/randomcodes.h"
#include "match/randomcodes-correct.h"
#include "tools/gt_seqcorrect.h"

#define GT_SEQCORRECT_FILESUFFIX ".cor"

typedef struct
{
  bool usefirstcodes,
       verbose,
       quiet,
       onlyaccum,
       onlyallrandomcodes,
       radixlarge,
       checksuftab,
       usemaxdepth;
  unsigned int correction_kmersize,
               samplingfactor,
               trusted_count,
               numofparts,
               radixparts,
               addbscache_depth,
               forcek;
  unsigned long maximumspace;
  GtStr *encseqinput,
        *memlimitarg,
        *indexname;
  GtOption *refoptionmemlimit;
  GtStrArray *db;
  bool phred64;
  unsigned long maxlow;
  unsigned int lowqual;
} GtSeqcorrectArguments;

static void* gt_seqcorrect_arguments_new(void)
{
  GtSeqcorrectArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->radixlarge = false;
  arguments->numofparts = 0;
  arguments->radixparts = 1U;
  arguments->encseqinput = gt_str_new();
  arguments->indexname = gt_str_new();
  arguments->memlimitarg = gt_str_new();
  arguments->maximumspace = 0UL; /* in bytes */
  arguments->db = gt_str_array_new();
  return arguments;
}

static void gt_seqcorrect_arguments_delete(void *tool_arguments)
{
  GtSeqcorrectArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->encseqinput);
  gt_str_delete(arguments->indexname);
  gt_option_delete(arguments->refoptionmemlimit);
  gt_str_delete(arguments->memlimitarg);
  gt_str_array_delete(arguments->db);
  gt_free(arguments);
}

static GtOptionParser* gt_seqcorrect_option_parser_new(void *tool_arguments)
{
  GtSeqcorrectArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionparts, *optionmemlimit, *q_option, *v_option,
           *db_option, *maxlow_option;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("(-ii |-db ) "
      "-k  [option ...]", "K-mer based sequence correction.");

  /* -db */
  db_option = gt_option_new_filename_array("db",
      GT_READS2TWOBIT_LIBSPEC_HELPMSG, arguments->db);
  gt_option_hide_default(db_option);
  gt_option_parser_add_option(op, db_option);

  /* -indexname */
  option = gt_option_new_string("indexname", "specify the indexname to use "
      "for the input\ndefault: first argument of the -db option",
      arguments->indexname, NULL);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* -ii */
  option = gt_option_new_string("ii", "specify the input enseq index",
                                arguments->encseqinput, NULL);
  gt_option_is_mandatory_either(option, db_option);
  gt_option_exclude(option, db_option);
  gt_option_parser_add_option(op, option);

  /* -k */
  option = gt_option_new_uint_min("k", "specify the kmer size for the "
      "correction algorithm", &arguments->correction_kmersize, 31U, 2U);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -c */
  option = gt_option_new_uint_min("c", "specify the trusted count threshold",
      &arguments->trusted_count, 3U, 2U);
  gt_option_parser_add_option(op, option);

  /* -sf */
  option = gt_option_new_uint_min("sf", "specify the sampling factor",
                                  &arguments->samplingfactor, 50U, 1U);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -parts */
  optionparts = gt_option_new_uint("parts", "specify the number of parts",
                                  &arguments->numofparts, 0U);
  gt_option_parser_add_option(op, optionparts);

  /* -memlimit */
  optionmemlimit = gt_option_new_string("memlimit",
                       "specify maximal amount of memory to be used during "
                       "index construction (in bytes, the keywords 'MB' "
                       "and 'GB' are allowed)",
                       arguments->memlimitarg, NULL);
  gt_option_parser_add_option(op, optionmemlimit);
  gt_option_exclude(optionmemlimit, optionparts);
  arguments->refoptionmemlimit = gt_option_ref(optionmemlimit);

  /* -forcek */
  option = gt_option_new_uint("forcek", "specify the kmersize for the bucket "
      "keys", &arguments->forcek, 0);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -usefirstcodes */
  option = gt_option_new_bool("usefirstcodes", "use first codes instead of "
      "random sampled codes", &arguments->usefirstcodes, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -v */
  v_option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, v_option);

  /* -q */
  q_option = gt_option_new_bool("q",
      "suppress standard output messages",
      &arguments->quiet, false);
  gt_option_exclude(q_option, v_option);
  gt_option_parser_add_option(op, q_option);

  /* -maxlow */
  maxlow_option = gt_option_new_ulong("maxlow",
      "maximal number of low-quality positions in a read\n"
      "default: infinite",
      &arguments->maxlow, GT_UNDEF_ULONG);
  gt_option_hide_default(maxlow_option);
  gt_option_is_extended_option(maxlow_option);
  gt_option_parser_add_option(op, maxlow_option);

  /* -lowqual */
  option = gt_option_new_uint_max("lowqual",
      "maximal quality for a position to be considered low-quality",
      &arguments->lowqual, 3U, 127U);
  gt_option_is_extended_option(option);
  gt_option_imply(option, maxlow_option);
  gt_option_parser_add_option(op, option);

  /* -phred64 */
  option = gt_option_new_bool("phred64", "use phred64 scores for FastQ format",
      &arguments->phred64, false);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -usemaxdepth */
  option = gt_option_new_bool("usemaxdepth", "use maxdepth in sortremaining",
                             &arguments->usemaxdepth, true);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -checksuftab */
  option = gt_option_new_bool("checksuftab", "check the suffix table",
                             &arguments->checksuftab, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -onlyaccum */
  option = gt_option_new_bool("onlyaccum", "only accumulate codes",
                             &arguments->onlyaccum, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -onlyallrandomcodes */
  option = gt_option_new_bool("onlyallrandomcodes", "only determines allcodes",
                              &arguments->onlyallrandomcodes, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -addbscachedepth */
  option = gt_option_new_uint("addbscachedepth", "only determines allcodes",
                              &arguments->addbscache_depth, 5U);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -radixlarge */
  option = gt_option_new_bool("radixlarge", "use large tables for radixsort",
                              &arguments->radixlarge, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -radixparts */
  option = gt_option_new_uint("radixparts", "specify the number of parts "
                              "for radixsort",
                              &arguments->radixparts, 1U);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  gt_option_parser_set_max_args(op, 0);

  return op;
}

static bool gt_seqcorrect_bucketkey_kmersize(GtSeqcorrectArguments *arguments,
    unsigned int *kmersize, GtError *err)
{
  bool haserr = false;
  gt_assert(kmersize != NULL);
  if (arguments->forcek > 0)
  {
    *kmersize = arguments->forcek;
    if (*kmersize >= arguments->correction_kmersize)
    {
      gt_error_set(err,"argument %u to option -forcek must be < "
          "correction kmersize (-k)", *kmersize);
      haserr = true;
    }
    else if (*kmersize > (unsigned int)GT_UNITSIN2BITENC)
    {
      gt_error_set(err,
          "argument %u to option -forcek > %u (machine word size/2)",
          *kmersize, (unsigned int)GT_UNITSIN2BITENC);
      haserr = true;
    }
  }
  else
  {
    gt_assert(arguments->correction_kmersize > 1U);
    *kmersize = MIN((unsigned int) GT_UNITSIN2BITENC,
        arguments->correction_kmersize - 1);
  }
  gt_log_log("bucketkey kmersize=%u", *kmersize);
  gt_assert(*kmersize > 0);
  return haserr;
}

static int gt_seqcorrect_arguments_check(GT_UNUSED int rest_argc,
                                         void *tool_arguments,
                                         GtError *err)
{
  GtSeqcorrectArguments *arguments = tool_arguments;
  bool haserr = false;

  gt_error_check(err);
  if (!haserr && gt_option_is_set(arguments->refoptionmemlimit))
  {
    if (gt_option_parse_spacespec(&arguments->maximumspace,
                                  "memlimit",
                                  arguments->memlimitarg,
                                  err) != 0)
    {
      haserr = true;
    }
    if (!haserr && !gt_ma_bookkeeping_enabled()) {
      gt_error_set(err, "option '-memlimit' requires "
                        "GT_MEM_BOOKKEEPING=on");
      haserr = true;
    }
  }
#ifdef GT_THREADS_ENABLED
  if (!haserr) {
    if (gt_jobs > 1 && gt_ma_bookkeeping_enabled()) {
      gt_error_set(err, "gt option '-j' and GT_MEM_BOOKKEEPING=on "
                        "are incompatible");
      haserr = true;
    }
  }
#endif
  return haserr ? -1 : 0;
}

static int gt_seqcorrect_apply_corrections(GtEncseq *encseq,
    const char *indexname, const unsigned int threads,
    GtError *err)
{
  bool haserr = false;
  GtTwobitencEditor *editor;
  unsigned int threadcount;
  editor = gt_twobitenc_editor_new(encseq, indexname, err);
  if (editor == NULL)
    haserr = true;
  gt_log_log("number of correction lists: %u", threads);
  for (threadcount = 0; !haserr && threadcount < threads; threadcount++)
  {
    FILE *corrections;
    GtStr *filename;
    filename = gt_str_new_cstr(indexname);
    gt_str_append_char(filename, '.');
    gt_str_append_uint(filename, threadcount);
    gt_str_append_cstr(filename, GT_SEQCORRECT_FILESUFFIX);
    corrections = gt_fa_fopen(gt_str_get(filename), "r", err);
    gt_log_log("apply corrections list %s.%u.%s", indexname, threadcount,
        GT_SEQCORRECT_FILESUFFIX);
    if (corrections == NULL)
      haserr = true;
    else
    {
      unsigned long pos;
      GtUchar newchar;
      size_t retval;
      while ((retval = fread(&pos, sizeof (pos), (size_t)1, corrections))
          == (size_t)1)
      {
        newchar = (GtUchar)(pos & 3UL);
        pos >>= 2;
        gt_twobitenc_editor_edit(editor, pos, newchar);
      }
      if (ferror(corrections) != 0)
      {
        gt_error_set(err, "error by reading file %s", gt_str_get(filename));
        haserr = true;
      }
      gt_fa_fclose(corrections);
    }
    gt_str_delete(filename);
  }
  gt_twobitenc_editor_delete(editor);
  return haserr ? -1 : 0;
}

static int gt_seqcorrect_runner(GT_UNUSED int argc,
                                GT_UNUSED const char **argv,
                                GT_UNUSED int parsed_args,
                                void *tool_arguments,
                                GtError *err)
{
  GtSeqcorrectArguments *arguments = tool_arguments;
  GtEncseqLoader *el = NULL;
  GtEncseq *encseq = NULL;
  GtTimer *timer = NULL;
  GtLogger *default_logger, *verbose_logger;
  bool haserr = false;

  gt_error_check(err);
  gt_assert(arguments);

  if (gt_showtime_enabled())
  {
    timer = gt_timer_new_with_progress_description("for initialization");
    gt_timer_show_cpu_time_by_progress(timer);
    gt_timer_start(timer);
  }
  default_logger =
    gt_logger_new(!arguments->quiet, GT_LOGGER_DEFLT_PREFIX, stdout);
  gt_logger_log(default_logger, "gt seqcorrect");
  verbose_logger =
    gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  gt_logger_log(verbose_logger, "verbose output enabled");

  if (gt_str_array_size(arguments->db) != 0)
  {
    GtReads2Twobit *r2t;
    unsigned long i;
    bool autoindexname = false;
    gt_logger_log(verbose_logger, "input is a list of libraries");
    if (gt_str_length(arguments->indexname) == 0)
    {
      autoindexname = true;
      gt_str_append_cstr(arguments->indexname,
          gt_str_array_get(arguments->db, 0));
    }
    gt_logger_log(verbose_logger, "indexname: %s [%s]",
          gt_str_get(arguments->indexname), autoindexname ?
          "first input library" : "user-specified");

    r2t = gt_reads2twobit_new(arguments->indexname);

    if (arguments->phred64)
      gt_reads2twobit_use_phred64(r2t);

    if (arguments->maxlow != GT_UNDEF_ULONG)
      gt_reads2twobit_set_quality_filter(r2t, arguments->maxlow,
          (char)arguments->lowqual);

    for (i = 0; i < gt_str_array_size(arguments->db) && !haserr; i++)
    {
      GtStr *dbentry = gt_str_array_get_str(arguments->db, i);
      if (gt_reads2twobit_add_library(r2t, dbentry, err) != 0)
        haserr = true;
    }
    if (!haserr)
    {
      if (gt_reads2twobit_encode(r2t, err) != 0)
        haserr = true;
    }
    gt_assert(gt_str_length(arguments->encseqinput) == 0);
    gt_str_append_cstr(arguments->encseqinput,
        gt_str_get(arguments->indexname));
    if (!haserr)
    {
      unsigned long nofreads_valid, nofreads_invalid, nofreads_input,
                    tlen_valid;
      bool varlen;
      nofreads_valid = gt_reads2twobit_nofseqs(r2t);
      nofreads_invalid = gt_reads2twobit_nof_invalid_seqs(r2t);
      nofreads_input = nofreads_valid + nofreads_invalid;
      tlen_valid = gt_reads2twobit_total_seqlength(r2t) -
        gt_reads2twobit_nofseqs(r2t);

      gt_logger_log(default_logger, "number of reads in original read set "
          "= %lu", nofreads_input);

      varlen = (gt_reads2twobit_seqlen_eqlen(r2t) == 0);
      if (varlen)
        gt_logger_log(verbose_logger, "read length = variable [%lu..%lu]",
            gt_reads2twobit_seqlen_min(r2t), gt_reads2twobit_seqlen_max(r2t));
      else
        gt_logger_log(verbose_logger, "read length = %lu",
            gt_reads2twobit_seqlen_eqlen(r2t) - 1UL);

      gt_logger_log(verbose_logger, "total length of original read set = %lu",
          tlen_valid + gt_reads2twobit_invalid_seqs_totallength(r2t));
      gt_logger_log(verbose_logger, "low-quality reads = %lu "
          "[%.2f %% of input]", nofreads_invalid, (float)nofreads_invalid *
          100 / (float)nofreads_input);
      if (!arguments->verbose)
        gt_logger_log(default_logger, "low-quality reads = %lu",
            nofreads_invalid);
      if (!haserr)
      {
        if (gt_reads2twobit_write_encseq(r2t, err) != 0)
          haserr = true;
        if (!haserr)
        {
          gt_logger_log(verbose_logger,
              "number of reads in output read set = %lu", nofreads_valid);
          gt_logger_log(verbose_logger,
              "total length of output read set = %lu", tlen_valid);
          gt_logger_log(verbose_logger, "read set saved as GtEncseq: %s.%s",
              gt_str_get(arguments->indexname), varlen ?
              "(esq|ssp)" : "esq");
        }
      }
    }
    gt_reads2twobit_delete(r2t);
  }
  else
  {
    gt_logger_log(verbose_logger, "input is an encseq: %s",
        gt_str_get(arguments->encseqinput));
  }
  if (!haserr)
  {
    el = gt_encseq_loader_new();
    gt_encseq_loader_drop_description_support(el);
    gt_encseq_loader_disable_autosupport(el);
    encseq = gt_encseq_loader_load(el, gt_str_get(arguments->encseqinput),
        err);
    if (encseq == NULL)
    {
      haserr = true;
    }
    if (!haserr)
    {
      if (gt_encseq_mirror(encseq, err) != 0)
      {
        haserr = true;
      }
      if (!haserr && gt_encseq_has_md5_support(encseq))
      {
        GtStr *md5path = gt_str_clone(arguments->encseqinput);
        gt_str_append_cstr(md5path, GT_MD5TABFILESUFFIX);
        gt_xunlink(gt_str_get(md5path));
        gt_warning("MD5 support detected -- sequence correction will "
                   "invalidate MD5 table, permanently disabling MD5 support "
                   "in index %s", gt_str_get(arguments->encseqinput));
        gt_str_delete(md5path);
      }
    }
  }
  if (!haserr)
  {
    GtRandomcodesCorrectData **data_array = NULL;
    unsigned int bucketkey_kmersize, threadcount;
    unsigned long nofkmergroups = 0, nofkmeritvs = 0, nofcorrections = 0,
                  nofkmers = 0;

#ifdef GT_THREADS_ENABLED
    const unsigned int threads = gt_jobs;
#else
    const unsigned int threads = 1U;
#endif

    data_array = gt_malloc(sizeof (*data_array) * threads);
    for (threadcount = 0; !haserr && threadcount < threads; threadcount++)
    {
      data_array[threadcount] = gt_randomcodes_correct_data_new(encseq,
          arguments->correction_kmersize, arguments->trusted_count,
          gt_str_get(arguments->encseqinput), GT_SEQCORRECT_FILESUFFIX,
          threadcount, err);
      if ((data_array[threadcount]) == NULL)
      {
        haserr = true;
      }
    }
    gt_log_log("correction kmersize=%u", arguments->correction_kmersize);
    haserr = gt_seqcorrect_bucketkey_kmersize(arguments,
        &bucketkey_kmersize, err);
    if (!haserr)
    {
      if (storerandomcodes_getencseqkmers_twobitencoding(encseq,
            bucketkey_kmersize,
            arguments->numofparts,
            arguments->maximumspace,
            arguments->correction_kmersize,
            arguments->usefirstcodes,
            arguments->samplingfactor,
            arguments->usemaxdepth,
            arguments->checksuftab,
            arguments->onlyaccum,
            arguments->onlyallrandomcodes,
            arguments->addbscache_depth,
            0,
            arguments->radixlarge ? false : true,
            arguments->radixparts,
            gt_randomcodes_correct_process_bucket,
            NULL,
            data_array,
            verbose_logger,
            timer,
            err) != 0)
            {
              haserr = true;
            }
    }
    for (threadcount = 0; threadcount < threads; threadcount++)
    {
      if (!haserr) {
        gt_randomcodes_correct_data_collect_stats(data_array[threadcount],
            threadcount, &nofkmergroups, &nofkmeritvs, &nofkmers,
            &nofcorrections);
      }
      gt_randomcodes_correct_data_delete(data_array[threadcount]);
    }
    gt_logger_log(verbose_logger, "total number of k-mers: %lu",
        nofkmers);
    gt_logger_log(verbose_logger, "number of different k-mers: %lu",
        nofkmeritvs);
    gt_logger_log(verbose_logger, "number of different k-1-mers: %lu",
        nofkmergroups);
    gt_logger_log(verbose_logger, "number of kmer corrections: %lu",
        nofcorrections);
    gt_free(data_array);
    if (!haserr) {
      if (gt_seqcorrect_apply_corrections(encseq,
          gt_str_get(arguments->encseqinput), threads, err) != 0) {
        haserr = true;
      }
    }
  }
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(el);
  if (timer != NULL)
  {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  gt_logger_delete(default_logger);
  gt_logger_delete(verbose_logger);
  return haserr ? -1 : 0;
}

GtTool* gt_seqcorrect(void)
{
  return gt_tool_new(gt_seqcorrect_arguments_new,
                     gt_seqcorrect_arguments_delete,
                     gt_seqcorrect_option_parser_new,
                     gt_seqcorrect_arguments_check,
                     gt_seqcorrect_runner);
}
genometools-1.5.1/src/tools/gt_seqcorrect.h000066400000000000000000000017411211610345200210130ustar00rootroot00000000000000/*
  Copyright (c) 2011 Stefan Kurtz 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQCORRECT_H
#define GT_SEQCORRECT_H

#include "core/tool_api.h"

/* the seqcorrect tool */
GtTool* gt_seqcorrect(void);

#endif
genometools-1.5.1/src/tools/gt_seqfilter.c000066400000000000000000000120741211610345200206330ustar00rootroot00000000000000/*
  Copyright (c) 2008-2010 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include "core/bioseq_iterator.h"
#include "core/fasta.h"
#include "core/ma.h"
#include "core/output_file_api.h"
#include "core/option_api.h"
#include "core/undef_api.h"
#include "tools/gt_seqfilter.h"

typedef struct {
  unsigned long minlength,
                maxlength,
                maxseqnum,
                width;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} SeqFilterArguments;

static void* gt_seqfilter_arguments_new(void)
{
  SeqFilterArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_seqfilter_arguments_delete(void *tool_arguments)
{
  SeqFilterArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_seqfilter_option_parser_new(void *tool_arguments)
{
  SeqFilterArguments *arguments = tool_arguments;
  GtOption *option;
  GtOptionParser *op;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [sequence_file ...]",
                            "Filter the given sequence_file(s) and show the "
                            "results on stdout.");

  /* -minlength */
  option = gt_option_new_ulong("minlength",
                               "set minimum length a sequence must "
                               "have to pass the filter", &arguments->minlength,
                               GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, option);

  /* -maxlength */
  option = gt_option_new_ulong("maxlength", "set maximum length a sequence can "
                               "have to pass the filter", &arguments->maxlength,
                               GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, option);

  /* -maxseqnum */
  option = gt_option_new_ulong("maxseqnum", "set the maximum number of "
                               "sequences which can pass the filter",
                               &arguments->maxseqnum, GT_UNDEF_ULONG);
  gt_option_parser_add_option(op, option);

  /* -width */
  option = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, option);

  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  return op;
}

static int gt_seqfilter_runner(int argc, const char **argv, int parsed_args,
                               void *tool_arguments, GtError *err)
{
  SeqFilterArguments *arguments = tool_arguments;
  GtBioseqIterator *bsi;
  GtBioseq *bioseq;
  unsigned long i;
  unsigned long long passed = 0, filtered = 0, num_of_sequences = 0;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(tool_arguments);

  bsi = gt_bioseq_iterator_new(argc - parsed_args, argv + parsed_args);

  while (!(had_err = gt_bioseq_iterator_next(bsi, &bioseq, err)) && bioseq) {
    for (i = 0; i < gt_bioseq_number_of_sequences(bioseq); i++) {
      char *seq;
      if ((arguments->minlength == GT_UNDEF_ULONG ||
           gt_bioseq_get_sequence_length(bioseq, i) >= arguments->minlength) &&
          (arguments->maxlength == GT_UNDEF_ULONG ||
           gt_bioseq_get_sequence_length(bioseq, i) <= arguments->maxlength) &&
          (arguments->maxseqnum == GT_UNDEF_ULONG ||
           passed + 1 <= arguments->maxseqnum)) {
        seq = gt_bioseq_get_sequence(bioseq, i);
        gt_fasta_show_entry(gt_bioseq_get_description(bioseq, i),
                            seq,
                            gt_bioseq_get_sequence_length(bioseq, i),
                            arguments->width, arguments->outfp);
        gt_free(seq);
        passed++;
      }
      else
        filtered++;
      num_of_sequences++;
    }
    gt_bioseq_delete(bioseq);
  }

  /* show statistics */
  if (!had_err) {
    gt_assert(passed + filtered == num_of_sequences);
    fprintf(stderr, "# %llu out of %llu sequences have been removed (%.3f%%)\n",
            filtered, num_of_sequences,
            ((double) filtered / num_of_sequences) * 100.0);
  }

  gt_bioseq_iterator_delete(bsi);

  return had_err;
}

GtTool* gt_seqfilter(void)
{
  return gt_tool_new(gt_seqfilter_arguments_new,
                     gt_seqfilter_arguments_delete,
                     gt_seqfilter_option_parser_new,
                     NULL,
                     gt_seqfilter_runner);
}
genometools-1.5.1/src/tools/gt_seqfilter.h000066400000000000000000000017371211610345200206440ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQFILTER_H
#define GT_SEQFILTER_H

#include "core/tool_api.h"

/* the seqfilter tool */
GtTool* gt_seqfilter(void);

#endif
genometools-1.5.1/src/tools/gt_seqids.c000066400000000000000000000047741211610345200201350ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Steinbiss 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "core/unused_api.h"
#include "extended/collect_ids_visitor.h"
#include "extended/gff3_in_stream.h"
#include "extended/visitor_stream.h"
#include "tools/gt_seqids.h"

static GtOptionParser* gt_seqids_option_parser_new(GT_UNUSED
                                                       void *tool_arguments)
{
  GtOptionParser *op;
  op = gt_option_parser_new("[GFF3_file]",
                            "Show sequence IDs from annotation file.");
  gt_option_parser_set_min_max_args(op, 1, 1);
  return op;
}

static int gt_seqids_runner(GT_UNUSED int argc, const char **argv,
                                  int parsed_args,
                                  GT_UNUSED void *tool_arguments, GtError *err)
{
  GtNodeStream *in_stream, *v_stream;
  GtCstrTable *cst;
  int had_err = 0;
  gt_error_check(err);

  cst = gt_cstr_table_new();
  in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                             argv + parsed_args);
  v_stream = gt_visitor_stream_new(in_stream, gt_collect_ids_visitor_new(cst));

  had_err = gt_node_stream_pull(v_stream, err);
  if (!had_err) {
    GtStrArray *seqids;
    unsigned long i;
    seqids = gt_cstr_table_get_all(cst);
    for (i = 0; i < gt_str_array_size(seqids); i++) {
      printf("%s\n", gt_str_array_get(seqids, i));
    }
    gt_str_array_delete(seqids);
  }

  gt_node_stream_delete(v_stream);
  gt_node_stream_delete(in_stream);
  gt_cstr_table_delete(cst);
  return had_err;
}

GtTool* gt_seqids(void)
{
  return gt_tool_new(NULL,
                  NULL,
                  gt_seqids_option_parser_new,
                  NULL,
                  gt_seqids_runner);
}
genometools-1.5.1/src/tools/gt_seqids.h000066400000000000000000000017561211610345200201370ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Steinbiss 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQIDS_H
#define GT_SEQIDS_H

#include "core/tool_api.h"

/* the print sequence ids (seqids) tool */
GtTool* gt_seqids(void);

#endif
genometools-1.5.1/src/tools/gt_seqlensort.c000066400000000000000000000105571211610345200210400ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/str_array.h"
#include "core/unused_api.h"
#include "match/reads2twobit.h"
#include "tools/gt_seqlensort.h"

typedef struct {
  GtStr  *indexname;
  GtStrArray  *db;
} GtSeqlensortArguments;

static void* gt_seqlensort_arguments_new(void)
{
  GtSeqlensortArguments *arguments = gt_malloc(sizeof (*arguments));
  arguments->indexname = gt_str_new();
  arguments->db = gt_str_array_new();
  return arguments;
}

static void gt_seqlensort_arguments_delete(void *tool_arguments)
{
  GtSeqlensortArguments *arguments = tool_arguments;
  gt_str_delete(arguments->indexname);
  gt_str_array_delete(arguments->db);
  gt_free(arguments);
}

static GtOptionParser* gt_seqlensort_option_parser_new(void *tool_arguments)
{
  GtSeqlensortArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *indexname_option, *db_option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("-db  [-indexname ...]",
      "Encode DNA MultiFasta sequences (with no wildcards) "
      "in GtEncseq format, sorting the sequences by length.");

  /* -indexname */
  indexname_option = gt_option_new_string("indexname",
      "specify the indexname to use\n"
      "default: first argument of -db option",
      arguments->indexname, NULL);
  gt_option_hide_default(indexname_option);
  gt_option_parser_add_option(op, indexname_option);

  /* -db */
  db_option = gt_option_new_filename_array("db",
      "name of input MultiFasta file(s)", arguments->db);
  gt_option_hide_default(db_option);
  gt_option_is_mandatory(db_option);
  gt_option_parser_add_option(op, db_option);

  return op;
}

#define GT_SEQLENSORT_SEQLEN(SEQNUM, SEPPOS) \
  ((SEQNUM) == 0 \
    ? ((SEPPOS)[SEQNUM]) \
    : ((SEPPOS)[SEQNUM] - ((SEPPOS)[(SEQNUM) - 1UL] + 1UL)))

static int gt_seqlensort_cmp(const void *a, const void *b, void *data)
{
  const unsigned long seqnum_a = *(const unsigned long*)a,
                      seqnum_b = *(const unsigned long*)b;
  unsigned long seqlen_a = GT_SEQLENSORT_SEQLEN(seqnum_a, (unsigned long*)data),
                seqlen_b = GT_SEQLENSORT_SEQLEN(seqnum_b, (unsigned long*)data);
  if (seqlen_a == seqlen_b)
    return (int)((seqnum_a > seqnum_b) - (seqnum_a < seqnum_b));
  return (int)((seqlen_a > seqlen_b) - (seqlen_a < seqlen_b));
}

static int gt_seqlensort_runner(GT_UNUSED int argc,
    GT_UNUSED const char **argv, GT_UNUSED int parsed_args,
    void *tool_arguments, GtError *err)
{
  GtSeqlensortArguments *arguments = tool_arguments;
  int had_err = 0;
  unsigned long i;
  GtReads2Twobit *r2t = NULL;

  gt_error_check(err);
  gt_assert(arguments);

  if (gt_str_length(arguments->indexname) == 0)
  {
    gt_str_append_cstr(arguments->indexname,
        gt_str_array_get(arguments->db, 0));
  }

  r2t = gt_reads2twobit_new(arguments->indexname);

  for (i = 0; i < gt_str_array_size(arguments->db) && !had_err; i++)
    had_err = gt_reads2twobit_add_library(r2t, gt_str_array_get_str(
          arguments->db, i), err);

  if (!had_err)
    had_err = gt_reads2twobit_encode(r2t, err);

  if (!had_err)
  {
    if (gt_reads2twobit_seqlen_eqlen(r2t) == 0)
    {
      gt_reads2twobit_sort(r2t, gt_seqlensort_cmp,
          gt_reads2twobit_export_seppos(r2t));
    }
    had_err = gt_reads2twobit_write_encseq(r2t, err);
  }

  gt_reads2twobit_delete(r2t);
  return had_err;
}

GtTool* gt_seqlensort(void)
{
  return gt_tool_new(gt_seqlensort_arguments_new,
                  gt_seqlensort_arguments_delete,
                  gt_seqlensort_option_parser_new,
                  NULL,
                  gt_seqlensort_runner);
}
genometools-1.5.1/src/tools/gt_seqlensort.h000066400000000000000000000017501211610345200210400ustar00rootroot00000000000000/*
  Copyright (c) 2012 Giorgio Gonnella 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQLENSORT_H
#define GT_SEQLENSORT_H

#include "core/tool_api.h"

/* the seqlensort tool */
GtTool* gt_seqlensort(void);

#endif
genometools-1.5.1/src/tools/gt_seqmutate.c000066400000000000000000000077041211610345200206510ustar00rootroot00000000000000/*
  Copyright (c) 2007-2010 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/bioseq_iterator.h"
#include "core/fasta.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "extended/gtdatahelp.h"
#include "extended/mutate.h"
#include "tools/gt_seqmutate.h"

typedef struct {
  unsigned int rate; /* the mutate rate */
  unsigned long width;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} MutateArguments;

static void* gt_seqmutate_arguments_new(void)
{
  MutateArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_seqmutate_arguments_delete(void *tool_arguments)
{
  MutateArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_seqmutate_option_parser_new(void *tool_arguments)
{
  MutateArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *o;
  gt_assert(arguments);
  op = gt_option_parser_new("[option ...] [sequence_file ...]",
                            "Mutate the sequences of the given sequence "
                            "file(s).");
  /* -rate */
  o = gt_option_new_uint_max("rate", "set the mutation rate", &arguments->rate,
                             1, 100);
  gt_option_parser_add_option(op, o);

  /* -width */
  o = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, o);

  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);

  return op;
}

static int gt_seqmutate_runner(int argc, const char **argv, int parsed_args,
                            void *tool_arguments, GtError *err)
{
  MutateArguments *arguments = tool_arguments;
  GtBioseqIterator *bsi;
  unsigned long i;
  GtBioseq *bioseq;
  GtSeq *mutated_seq;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  bsi = gt_bioseq_iterator_new(argc - parsed_args, argv + parsed_args);

  while (!(had_err = gt_bioseq_iterator_next(bsi, &bioseq, err)) && bioseq) {
    char *seq;
    for (i = 0; i < gt_bioseq_number_of_sequences(bioseq); i++) {
      seq = gt_bioseq_get_sequence(bioseq, i);
      mutated_seq = gt_mutate_seq(gt_bioseq_get_description(bioseq, i),
                                  seq,
                                  gt_bioseq_get_sequence_length(bioseq, i),
                                  gt_bioseq_get_alphabet(bioseq),
                                  arguments->rate);
      gt_fasta_show_entry(gt_seq_get_description(mutated_seq),
                          gt_seq_get_orig(mutated_seq),
                          gt_seq_length(mutated_seq),
                          arguments->width, arguments->outfp);
      gt_free(seq);
      gt_seq_delete(mutated_seq);
    }
    gt_bioseq_delete(bioseq);
  }

  gt_bioseq_iterator_delete(bsi);

  return had_err;
}

GtTool* gt_seqmutate(void)
{
  return gt_tool_new(gt_seqmutate_arguments_new,
                     gt_seqmutate_arguments_delete,
                     gt_seqmutate_option_parser_new,
                     NULL,
                     gt_seqmutate_runner);
}
genometools-1.5.1/src/tools/gt_seqmutate.h000066400000000000000000000017511211610345200206520ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQMUTATE_H
#define GT_SEQMUTATE_H

#include "core/tool_api.h"

/* the seqmutate tool */
GtTool* gt_seqmutate(void);

#endif
genometools-1.5.1/src/tools/gt_seqorder.c000066400000000000000000000171001211610345200204540ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq.h"
#include "core/fasta_separator.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/unused_api.h"
#include "core/warning_api.h"
#include "core/xansi_api.h"
#include "match/sfx-bentsedg.h"
#include "match/sfx-suffixgetset.h"
#include "match/sfx-strategy.h"
#include "tools/gt_seqorder.h"

typedef struct {
  bool invert, sort, revsort, shuffle;
} GtSeqorderArguments;

static void* gt_seqorder_arguments_new(void)
{
  GtSeqorderArguments *arguments = gt_calloc((size_t)1, sizeof *arguments);
  return arguments;
}

static void gt_seqorder_arguments_delete(void *tool_arguments)
{
  GtSeqorderArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_free(arguments);
}

static GtOptionParser* gt_seqorder_option_parser_new(void *tool_arguments)
{
  GtSeqorderArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *invert_option, *sort_option, *revsort_option, *shuffle_option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("(-invert|-sort|-revsort|-shuffle) encseq",
                            "Output sequences as MultiFasta in specified "
                            "order.");

  /* -invert */
  invert_option = gt_option_new_bool("invert", "invert order of sequences",
                           &arguments->invert, false);
  gt_option_parser_add_option(op, invert_option);

  /* -sort */
  sort_option = gt_option_new_bool("sort", "sort sequences lexicographically",
                           &arguments->sort, false);
  gt_option_exclude(sort_option, invert_option);
  gt_option_parser_add_option(op, sort_option);

  /* -revsort */
  revsort_option = gt_option_new_bool("revsort", "sort sequences in reverse "
                           "lexicographic order", &arguments->revsort, false);
  gt_option_exclude(revsort_option, invert_option);
  gt_option_exclude(revsort_option, sort_option);
  gt_option_parser_add_option(op, revsort_option);

  /* -shuffle */
  shuffle_option = gt_option_new_bool("shuffle", "shuffle sequences "
                           "pseudo-randomly", &arguments->shuffle, false);
  gt_option_exclude(shuffle_option, invert_option);
  gt_option_exclude(shuffle_option, sort_option);
  gt_option_exclude(shuffle_option, revsort_option);
  gt_option_parser_add_option(op, shuffle_option);

  gt_option_parser_set_min_max_args(op, 1U, 1U);

  return op;
}

static int gt_seqorder_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  GtSeqorderArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments != NULL);

  if (!(arguments->invert || arguments->sort || arguments->revsort ||
      arguments->shuffle))
  {
    had_err = 1;
    gt_error_set(err, "order option needed: -invert|-sort|-revsort|-shuffle");
  }

  return had_err;
}

static void gt_seqorder_sort(GtSuffixsortspace *suffixsortspace,
    GtEncseq *encseq)
{
  unsigned long i;
  Sfxstrategy sfxstrategy;

  defaultsfxstrategy(&sfxstrategy, false);
  for (i = 0; i < gt_encseq_num_of_sequences(encseq); i++)
    gt_suffixsortspace_setdirect(suffixsortspace, i,
        gt_encseq_seqstartpos(encseq, i));
  gt_sortallsuffixesfromstart(suffixsortspace,
      gt_encseq_num_of_sequences(encseq), encseq, GT_READMODE_FORWARD, NULL, 0,
      &sfxstrategy, NULL, NULL, NULL);
}

static void gt_seqorder_get_shuffled_seqnums(unsigned long nofseqs,
    unsigned long *seqnums)
{
  unsigned long i, j;

  gt_assert(seqnums != NULL);
  seqnums[0] = 0;
  for (i = 1UL; i < nofseqs; i++)
  {
    j = gt_rand_max(i);
    seqnums[i] = seqnums[j];
    seqnums[j] = i;
  }
}

static void gt_seqorder_output(unsigned long seqnum, GtEncseq *encseq)
{
  GtEncseqReader *esr;
  unsigned long startpos, len, desclen = 0;
  const char *desc = NULL;
  unsigned long i;

  startpos = gt_encseq_seqstartpos(encseq, seqnum);
  len = gt_encseq_seqlength(encseq, seqnum);
  gt_xfputc(GT_FASTA_SEPARATOR, stdout);
  if (gt_encseq_has_description_support(encseq))
  {
    desc = gt_encseq_description(encseq, &desclen, seqnum);
    gt_xfwrite(desc, (size_t)1, (size_t)desclen, stdout);
  }
  gt_xfputc('\n', stdout);
  esr = gt_encseq_create_reader_with_readmode(encseq, GT_READMODE_FORWARD,
      startpos);
  for (i = 0; i < len; i++)
  {
    gt_xfputc(gt_encseq_reader_next_decoded_char(esr), stdout);
  }
  gt_encseq_reader_delete(esr);
  gt_xfputc('\n', stdout);
}

static int gt_seqorder_runner(GT_UNUSED int argc, const char **argv,
    int parsed_args, void *tool_arguments, GtError *err)
{
  GtSeqorderArguments *arguments = tool_arguments;
  int had_err = 0;
  GtEncseq *encseq;
  GtEncseqLoader *loader;
  unsigned long i, nofseqs;

  gt_error_check(err);
  gt_assert(arguments != NULL);

  /* load encseq */
  loader = gt_encseq_loader_new();
  encseq = gt_encseq_loader_load(loader, argv[parsed_args], err);
  if (encseq == NULL)
    had_err = -1;
  if (had_err == 0 && !gt_encseq_has_description_support(encseq))
    gt_warning("%s has no description support", argv[parsed_args]);
  if (!had_err)
  {
    nofseqs = gt_encseq_num_of_sequences(encseq);
    if (arguments->invert)
    {
      for (i = nofseqs; i > 0; i--)
        gt_seqorder_output(i - 1, encseq);
    }
    else if (arguments->shuffle)
    {
      unsigned long *seqnums;
      seqnums = gt_malloc(sizeof (unsigned long) * nofseqs);
      gt_seqorder_get_shuffled_seqnums(nofseqs, seqnums);
      for (i = 0; i < nofseqs; i++)
        gt_seqorder_output(seqnums[i], encseq);
      gt_free(seqnums);
    }
    else
    {
      GtSuffixsortspace *suffixsortspace;
      gt_assert(arguments->sort || arguments->revsort);
      suffixsortspace
        = gt_suffixsortspace_new(nofseqs,
                                 /* Use iterator over sequence separators:
                                    saves a lot of binary searches */
                                 gt_encseq_seqstartpos(encseq, nofseqs-1),
                                 false,NULL);
      gt_seqorder_sort(suffixsortspace, encseq);
      if (arguments->sort)
        for (i = 0; i < nofseqs; i++)
          gt_seqorder_output(gt_encseq_seqnum(encseq,
                gt_suffixsortspace_getdirect(suffixsortspace, i)), encseq);
      else
        for (i = nofseqs; i > 0; i--)
          gt_seqorder_output(gt_encseq_seqnum(encseq,
                gt_suffixsortspace_getdirect(suffixsortspace, i - 1)), encseq);
      gt_suffixsortspace_delete(suffixsortspace, false);
    }
  }

  gt_encseq_loader_delete(loader);
  gt_encseq_delete(encseq);
  return had_err;
}

GtTool* gt_seqorder(void)
{
  return gt_tool_new(gt_seqorder_arguments_new,
                  gt_seqorder_arguments_delete,
                  gt_seqorder_option_parser_new,
                  gt_seqorder_arguments_check,
                  gt_seqorder_runner);
}
genometools-1.5.1/src/tools/gt_seqorder.h000066400000000000000000000017401211610345200204640ustar00rootroot00000000000000/*
  Copyright (c) 2011 Giorgio Gonnella 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQORDER_H
#define GT_SEQORDER_H

#include "core/tool_api.h"

/* the seqorder tool */
GtTool* gt_seqorder(void);

#endif
genometools-1.5.1/src/tools/gt_seqstat.c000066400000000000000000000320531211610345200203200ustar00rootroot00000000000000/*
  Copyright (c) 2007      Stefan Kurtz 
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2010-2011 Giorgio Gonnella 
  Copyright (c) 2007-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#ifndef S_SPLINT_S
#include 
#endif
#include "core/fileutils_api.h"
#include "core/xposix.h"
#include "core/fa.h"
#include "core/ma.h"
#include "core/versionfunc.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "core/seq_iterator_fastq_api.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "core/xansi_api.h"
#include "core/progressbar.h"
#include "core/format64.h"
#include "core/unused_api.h"
#include "core/types_api.h"
#include "core/disc_distri_api.h"
#include "core/option_api.h"
#include "core/error_api.h"
#include "core/logger.h"
#include "extended/assembly_stats_calculator.h"
#include "match/stamp.h"
#include "tools/gt_seqstat.h"

typedef struct
{
  bool verbose,
       dodistlen,
       binarydistlen,
       doastretch,
       docstats,
       showestimsize;
  unsigned int bucketsize;
  unsigned long genome_length;
} SeqstatArguments;

#define GT_SEQSTAT_BINARY_DISTLEN_SUFFIX ".distlen"

static GtOPrval parse_options(SeqstatArguments *arguments,
                              int *parsed_args,int argc,
                              const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOption *optionverbose, *optiondistlen, *optionbucketsize,
           *optioncontigs, *optionastretch, *optionestimsize,
           *optionbinarydistlen, *optiongenome;
  GtOPrval oprval;

  gt_error_check(err);

  op = gt_option_parser_new("[options] file [...]",
                            "Calculate statistics for fasta file(s).");

  optionverbose = gt_option_new_bool("v","be verbose",
                                  &arguments->verbose,false);
  gt_option_parser_add_option(op, optionverbose);

  optiondistlen = gt_option_new_bool("distlen",
                                  "show distribution of sequence length",
                                  &arguments->dodistlen,false);
  gt_option_parser_add_option(op, optiondistlen);

  optionbucketsize = gt_option_new_uint_min("b",
                                "bucket size for distlen option",
                                &arguments->bucketsize, 100U, 1U);
  gt_option_imply(optionbucketsize, optiondistlen);
  gt_option_parser_add_option(op, optionbucketsize);

  optionbinarydistlen = gt_option_new_bool("binary",
                                  "use a binary format for distlen output\n"
                                  "output filename: "
                                  GT_SEQSTAT_BINARY_DISTLEN_SUFFIX "\n"
                                  "bucketsize: 1",
                                  &arguments->binarydistlen,false);
  gt_option_imply(optionbinarydistlen, optiondistlen);
  gt_option_exclude(optionbinarydistlen, optionbucketsize);
  gt_option_parser_add_option(op, optionbinarydistlen);

  optioncontigs = gt_option_new_bool("contigs",
                                   "summary of contigs set statistics",
                                   &arguments->docstats,false);
  gt_option_parser_add_option(op, optioncontigs);

  optionastretch = gt_option_new_bool("astretch",
                                   "show distribution of A-substrings",
                                   &arguments->doastretch,false);
  gt_option_exclude(optiondistlen, optionastretch);
  gt_option_parser_add_option(op, optionastretch);
  gt_option_is_extended_option(optionastretch);

  optionestimsize = gt_option_new_bool("estimsize",
                                   "show estimated size",
                                   &arguments->showestimsize,false);
  gt_option_parser_add_option(op, optionestimsize);
  gt_option_is_development_option(optionestimsize);

  optiongenome = gt_option_new_ulong_min("genome",
                                "set genome length for NG50/NG80 calculation",
                                &arguments->genome_length, 0, 1UL);
  gt_option_imply(optiongenome, optioncontigs);
  gt_option_parser_add_option(op, optiongenome);

  gt_option_parser_set_min_args(op, 1U);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

static void showdistseqlen(unsigned long key, unsigned long long value,
                            void *data)
{
  unsigned long distvalue;
  unsigned int *bucketsize = data;

  gt_assert(value <= (unsigned long long) ULONG_MAX);
  distvalue = (unsigned long) value;
  printf("%lu--%lu %lu\n",
         (*bucketsize) * key,
         (*bucketsize) * (key+1) - 1,
         distvalue);
}

static void showdistseqlenbinary(unsigned long key, unsigned long long value,
                            void *data)
{
  unsigned long value_ul;
  /*@ignore@*/
  FILE *file = data;
  /*@end@*/

  gt_assert(value <= (unsigned long long) ULONG_MAX);
  value_ul = (unsigned long) value;
  gt_xfwrite(&key, sizeof (key), (size_t)1, file);
  gt_xfwrite(&value_ul, sizeof (value_ul), (size_t)1, file);
}

typedef struct
{
  unsigned long long sumA, *mmercount;
  unsigned long maxvalue, minkey;
} Astretchinfo;

static void showastretches(unsigned long key, unsigned long long value,
                           void *data)
{
  Astretchinfo *astretchinfo = (Astretchinfo *) data;

  astretchinfo->sumA += value * (unsigned long long) key;
  if (key > astretchinfo->maxvalue)
  {
    astretchinfo->maxvalue = key;
  }
  /*@ignore@*/
  printf("%lu %llu\n", key,value);
  /*@end@*/
}

static void showmeroccurrence(unsigned long key, unsigned long long value,
                              void *data)
{
  unsigned long len;
  Astretchinfo *astretchinfo = (Astretchinfo *) data;

  for (len=astretchinfo->minkey; len<= key; len++)
  {
    gt_assert(len <= astretchinfo->maxvalue);
    astretchinfo->mmercount[len] += value * (unsigned long long) (key-len+1);
  }
}

static unsigned long long accumulateastretch(GtDiscDistri *distastretch,
                                             const GtUchar *sequence,
                                             unsigned long len)
{
  unsigned long i, lenofastretch = 0;
  unsigned long long countA = 0;

  for (i=0; i 0)
      {
        gt_disc_distri_add(distastretch,lenofastretch);
        lenofastretch = 0;
      }
    }
  }
  if (lenofastretch > 0)
  {
    gt_disc_distri_add(distastretch,lenofastretch);
  }
  return countA;
}

static void processastretches(const GtDiscDistri *distastretch,
                              GT_UNUSED unsigned long long countA)
{
  Astretchinfo astretchinfo;
  unsigned long len;

  astretchinfo.sumA = 0;
  astretchinfo.maxvalue = 0;
  astretchinfo.minkey = 10UL;
  gt_disc_distri_foreach(distastretch,showastretches,&astretchinfo);
  astretchinfo.mmercount = gt_malloc(sizeof (*astretchinfo.mmercount) *
                                    (astretchinfo.maxvalue+1));
  memset(astretchinfo.mmercount,0,sizeof (*astretchinfo.mmercount) *
                                  (astretchinfo.maxvalue+1));
  gt_disc_distri_foreach(distastretch,showmeroccurrence,&astretchinfo);
  for (len=astretchinfo.minkey; len<=astretchinfo.maxvalue; len++)
  {
    /*@ignore@*/
    printf("a^{%lu} occurs %llu times\n", len,astretchinfo.mmercount[len]);
    /*@end@*/
  }
  gt_assert(astretchinfo.sumA == countA);
  gt_free(astretchinfo.mmercount);
}

int gt_seqstat(int argc, const char **argv, GtError *err)
{
  GtStrArray *files;
  GtSeqIterator *seqit;
  const GtUchar *sequence;
  char *desc;
  unsigned long len;
  int i, parsed_args, had_err = 0;
  off_t totalsize;
  GtDiscDistri *distseqlen = NULL;
  GtAssemblyStatsCalculator *asc = NULL;
  GtLogger *asc_logger = NULL;
  GtDiscDistri *distastretch = NULL;
  uint64_t numofseq = 0, sumlength = 0;
  unsigned long minlength = 0, maxlength = 0;
  unsigned long long countA = 0;
  bool minlengthdefined = false;
  SeqstatArguments arguments;

  gt_error_check(err);

  /* option parsing */
  switch (parse_options(&arguments,&parsed_args, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR:
        return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT:
        return 0;
  }

  files = gt_str_array_new();
  for (i = parsed_args; i < argc; i++)
  {
    gt_str_array_add_cstr(files, argv[i]);
  }
  totalsize = gt_files_estimate_total_size(files);
  if (arguments.showestimsize)
  {
    printf("# estimated total size is " Formatuint64_t "\n",
              PRINTuint64_tcast(totalsize));
  }
  if (!had_err) {
    /* read input using seqiterator */
    seqit = gt_seq_iterator_sequence_buffer_new(files, err);
    if (!seqit)
      had_err = -1;
    if (!had_err)
    {
      if (arguments.dodistlen)
      {
        distseqlen = gt_disc_distri_new();
        if (arguments.binarydistlen)
          arguments.bucketsize = 1U;
      }
      if (arguments.docstats)
      {
        asc = gt_assembly_stats_calculator_new();
        gt_assembly_stats_calculator_set_genome_length(asc,
            arguments.genome_length);
      }
      if (arguments.doastretch)
      {
        distastretch = gt_disc_distri_new();
      }
      if (arguments.verbose)
      {
        gt_progressbar_start(gt_seq_iterator_getcurrentcounter(seqit,
                                                            (unsigned long long)
                                                            totalsize),
                             (unsigned long long) totalsize);
      }
      while (true)
      {
        desc = NULL;
        had_err = gt_seq_iterator_next(seqit, &sequence, &len, &desc, err);
        if (had_err != 1) break; /* 0: finished; 1: error */
        if (arguments.dodistlen || arguments.docstats)
        {
          if (!minlengthdefined || minlength > len)
          {
            minlength = len;
            minlengthdefined = true;
          }
          if (maxlength < len)
          {
            maxlength = len;
          }
          sumlength += (uint64_t) len;
          numofseq++;
          if (arguments.dodistlen)
          {
            gt_disc_distri_add(distseqlen,len/arguments.bucketsize);
          }
          if (arguments.docstats)
          {
            gt_assembly_stats_calculator_add(asc, len);
          }
        }
        if (arguments.doastretch)
        {
          countA += accumulateastretch(distastretch,sequence,len);
        }
      }
      if (arguments.verbose)
      {
        gt_progressbar_stop();
      }
      gt_seq_iterator_delete(seqit);
    }
  }
  gt_str_array_delete(files);
  if (!had_err && arguments.dodistlen)
  {
    printf("# " Formatuint64_t " sequences of average length %.2f\n",
             PRINTuint64_tcast(numofseq),(double) sumlength/numofseq);
    printf("# total length " Formatuint64_t "\n",
             PRINTuint64_tcast(sumlength));
    printf("# minimum length %lu\n",minlength);
    printf("# maximum length %lu\n",maxlength);
    if (arguments.binarydistlen)
    {
      FILE *distlenoutfile;
      GtStr *distlenoutfilename = gt_str_new_cstr(argv[parsed_args]);
      gt_str_append_cstr(distlenoutfilename, GT_SEQSTAT_BINARY_DISTLEN_SUFFIX);
      distlenoutfile = gt_fa_fopen(gt_str_get(distlenoutfilename), "wb", err);
      if (distlenoutfile == NULL)
        had_err = -1;
      else
      {
        /*@ignore@*/
        gt_disc_distri_foreach(distseqlen, showdistseqlenbinary,
            distlenoutfile);
        /*@end@*/
        printf("# distribution of sequence length written to file: %s\n",
          gt_str_get(distlenoutfilename));
        gt_fa_fclose(distlenoutfile);
      }
      gt_str_delete(distlenoutfilename);
    }
    else
    {
      printf("# distribution of sequence length in buckets of size %u\n",
          arguments.bucketsize);
      gt_disc_distri_foreach(distseqlen, showdistseqlen,
          &(arguments.bucketsize));
    }
    gt_disc_distri_delete(distseqlen);
  }
  if (!had_err && arguments.docstats)
  {
    asc_logger = gt_logger_new(true, GT_LOGGER_DEFLT_PREFIX, stdout);
    gt_assembly_stats_calculator_show(asc, asc_logger);
    gt_logger_delete(asc_logger);
  }
  if (asc != NULL)
    gt_assembly_stats_calculator_delete(asc);
  if (!had_err && arguments.doastretch)
  {
    processastretches(distastretch,countA);
    gt_disc_distri_delete(distastretch);
  }
  return had_err;
}
genometools-1.5.1/src/tools/gt_seqstat.h000066400000000000000000000017441211610345200203300ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQSTAT_H
#define GT_SEQSTAT_H

/* the sequence statistics tool */
int gt_seqstat(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_seqtransform.c000066400000000000000000000077501211610345200213660ustar00rootroot00000000000000/*
  Copyright (c) 2010 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/bioseq_iterator.h"
#include "core/fasta.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/trans_table.h"
#include "tools/gt_seqtransform.h"

typedef struct {
  bool addstopaminos;
  unsigned long width;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} SeqtransformArguments;

static void* gt_seqtransform_arguments_new(void)
{
  SeqtransformArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_seqtransform_arguments_delete(void *tool_arguments)
{
  SeqtransformArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_seqtransform_option_parser_new(void *tool_arguments)
{
  SeqtransformArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *o;
  gt_assert(arguments);
  op = gt_option_parser_new("[option ...] [sequence_file ...]",
                            "Perform simple transformations on the given "
                            "sequence file(s).");

  /* -addstopaminos */
  o = gt_option_new_bool("addstopaminos", "append stop amino acids ('"
                         GT_STOP_AMINO_CSTR"') to given protein sequences, if "
                         "not already present", &arguments->addstopaminos,
                         false);
  gt_option_parser_add_option(op, o);

  /* -width */
  o = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, o);

  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  return op;
}

static int gt_seqtransform_runner(int argc, const char **argv, int parsed_args,
                            void *tool_arguments, GtError *err)
{
  SeqtransformArguments *arguments = tool_arguments;
  GtBioseqIterator *bsi;
  unsigned long i;
  GtBioseq *bioseq;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  bsi = gt_bioseq_iterator_new(argc - parsed_args, argv + parsed_args);

  while (!(had_err = gt_bioseq_iterator_next(bsi, &bioseq, err)) && bioseq) {
    GtAlphabet *alphabet;
    bool is_protein;
    alphabet = gt_bioseq_get_alphabet(bioseq);
    is_protein = gt_alphabet_is_protein(alphabet);
    for (i = 0; i < gt_bioseq_number_of_sequences(bioseq); i++) {
      const char *desc, *suffix = NULL;
      char *seq;
      unsigned long seqlen;
      desc = gt_bioseq_get_description(bioseq, i);
      seq = gt_bioseq_get_sequence(bioseq, i);
      seqlen = gt_bioseq_get_sequence_length(bioseq, i);
      if (arguments->addstopaminos && is_protein && seqlen &&
          seq[seqlen-1] != GT_STOP_AMINO) {
        suffix = GT_STOP_AMINO_CSTR;
      }
      gt_fasta_show_entry_with_suffix(desc, seq, seqlen, suffix,
                                      arguments->width, arguments->outfp);
      gt_free(seq);
    }
    gt_bioseq_delete(bioseq);
  }

  gt_bioseq_iterator_delete(bsi);

  return had_err;
}

GtTool* gt_seqtransform(void)
{
  return gt_tool_new(gt_seqtransform_arguments_new,
                     gt_seqtransform_arguments_delete,
                     gt_seqtransform_option_parser_new,
                     NULL,
                     gt_seqtransform_runner);
}
genometools-1.5.1/src/tools/gt_seqtransform.h000066400000000000000000000016451211610345200213700ustar00rootroot00000000000000/*
  Copyright (c) 2010 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQTRANSFORM_H
#define GT_SEQTRANSFORM_H

#include "core/tool_api.h"

/* the seqtransform tool */
GtTool* gt_seqtransform(void);

#endif
genometools-1.5.1/src/tools/gt_seqtranslate.c000066400000000000000000000161231211610345200213420ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/codon_api.h"
#include "core/codon_iterator_simple_api.h"
#include "core/cstr_api.h"
#include "core/fasta.h"
#include "core/ma.h"
#include "core/output_file_api.h"
#include "core/seq_iterator_sequence_buffer.h"
#include "core/sequence_buffer.h"
#include "core/translator.h"
#include "core/unused_api.h"
#include "core/warning_api.h"
#include "extended/reverse_api.h"
#include "tools/gt_seqtranslate.h"

typedef struct {
  GtOutputFileInfo *ofi;
  GtFile *outfp;
  unsigned long fasta_width;
  bool reverse;
} GtTranslateArguments;

static void* gt_seqtranslate_arguments_new(void)
{
  GtTranslateArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_seqtranslate_arguments_delete(void *tool_arguments)
{
  GtTranslateArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_output_file_info_delete(arguments->ofi);
  gt_file_delete(arguments->outfp);
  gt_free(arguments);
}

static GtOptionParser* gt_seqtranslate_option_parser_new(void *tool_arguments)
{
  GtTranslateArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [files]",
                            "Translates a nucleotide sequence into a protein "
                            "sequence.");

  option = gt_option_new_bool("reverse", "also translate reverse complements",
                              &arguments->reverse, true);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("fastawidth", "width of the FASTA output",
                              &arguments->fasta_width, 60);
  gt_option_parser_add_option(op, option);

  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);
  gt_option_parser_set_min_args(op, 1);

  return op;
}

static int gt_seqtranslate_arguments_check(GT_UNUSED int rest_argc,
                                        GT_UNUSED void *tool_arguments,
                                        GT_UNUSED GtError *err)
{
  GT_UNUSED GtTranslateArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  return had_err;
}

static int gt_seqtranslate_do_translation(GtTranslateArguments *arguments,
                                       const char *sequence,
                                       unsigned long length,
                                       const char *desc,
                                       GtStr **translations,
                                       bool rev,
                                       GtError *err)
{
  GtTranslator *tr;
  GT_UNUSED GtTranslatorStatus trst;
  GtCodonIterator *ci;
  char translated;
  int had_err = 0;
  GtStr *str;
  unsigned int frame,
               i;

  ci = gt_codon_iterator_simple_new(sequence, length, err);
  tr = gt_translator_new(ci);
  trst = gt_translator_next(tr, &translated, &frame, err);
  while (trst == GT_TRANSLATOR_OK) {
    gt_str_append_char(translations[frame], translated);
    trst = gt_translator_next(tr, &translated, &frame, err);
  }
  gt_codon_iterator_delete(ci);
  gt_translator_delete(tr);
  if (trst == GT_TRANSLATOR_ERROR)
    return -1;
  str = gt_str_new();
  for (i = 0; i < 3; i++) {
    if (gt_str_length(translations[i]) > 0) {
      gt_str_append_cstr(str, desc);
      gt_str_append_cstr(str, " (");
      gt_str_append_ulong(str, i+1);
      gt_str_append_cstr(str, rev ? "-" : "+");
      gt_str_append_cstr(str, ")");
      gt_fasta_show_entry(gt_str_get(str), gt_str_get(translations[i]),
                          gt_str_length(translations[i]),
                          arguments->fasta_width, arguments->outfp);
      gt_str_reset(translations[i]);
      gt_str_reset(str);
    }
  }
  gt_str_delete(str);
  return had_err;
}

static int gt_seqtranslate_runner(int argc, const char **argv, int parsed_args,
                              void *tool_arguments, GT_UNUSED GtError *err)
{
  GtTranslateArguments *arguments = tool_arguments;
  GtSeqIterator *si = NULL;
  GtSequenceBuffer *sb = NULL;
  GtStrArray *infiles;
  int had_err = 0,
      rval,
      i;
  GtStr *translations[3];
  translations[0] = gt_str_new();
  translations[1] = gt_str_new();
  translations[2] = gt_str_new();

  gt_error_check(err);
  gt_assert(arguments);

  infiles = gt_str_array_new();
  for (i = parsed_args; i < argc; i++) {
    gt_str_array_add_cstr(infiles, argv[i]);
  }
  sb = gt_sequence_buffer_new_guess_type(infiles, err);
  if (!sb)
    had_err = -1;
  if (!had_err) {
    si = gt_seq_iterator_sequence_buffer_new_with_buffer(sb);
    if (!si)
      had_err = -1;
  }
  if (!had_err) {
    char *desc;
    const GtUchar *sequence;
    unsigned long len;
    while (!had_err && (rval = gt_seq_iterator_next(si,
                                                   &sequence,
                                                   &len, &desc, err))) {
      if (rval < 0) {
        had_err = -1;
        break;
      }
      if (len < GT_CODON_LENGTH) {
        gt_warning("sequence '%s' is shorter than codon length of %d, skipping",
                   desc, GT_CODON_LENGTH);
      } else {
        had_err = gt_seqtranslate_do_translation(arguments, (char*) sequence,
                                                 len, desc,
                                                 translations, false, err);
        if (!had_err && arguments->reverse) {
          char *revseq = gt_cstr_dup_nt((char*) sequence, len);
          had_err = gt_reverse_complement(revseq, len, err);
          if (!had_err) {
            had_err = gt_seqtranslate_do_translation(arguments, revseq, len,
                                                  desc, translations, true,
                                                  err);
          }
          gt_free(revseq);
        }
      }
    }
  }
  gt_str_delete(translations[0]);
  gt_str_delete(translations[1]);
  gt_str_delete(translations[2]);
  gt_str_array_delete(infiles);
  gt_seq_iterator_delete(si);
  gt_sequence_buffer_delete(sb);
  return had_err;
}

GtTool* gt_seqtranslate(void)
{
  return gt_tool_new(gt_seqtranslate_arguments_new,
                     gt_seqtranslate_arguments_delete,
                     gt_seqtranslate_option_parser_new,
                     gt_seqtranslate_arguments_check,
                     gt_seqtranslate_runner);
}
genometools-1.5.1/src/tools/gt_seqtranslate.h000066400000000000000000000017611211610345200213510ustar00rootroot00000000000000/*
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQTRANSLATE_H
#define GT_SEQTRANSLATE_H

#include "core/tool_api.h"

/* the seqtranslate tool */
GtTool* gt_seqtranslate(void);

#endif
genometools-1.5.1/src/tools/gt_sequniq.c000066400000000000000000000156711211610345200203300ustar00rootroot00000000000000/*
  Copyright (c) 2008-2011 Gordon Gremme 
  Copyright (c) 2011      Giorgio Gonnella 
  Copyright (c) 2008-2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/bioseq.h"
#include "core/fasta.h"
#include "core/fileutils_api.h"
#include "core/ma.h"
#include "core/output_file_api.h"
#include "core/option_api.h"
#include "core/progressbar.h"
#include "core/seq_iterator_sequence_buffer_api.h"
#include "core/string_distri.h"
#include "core/unused_api.h"
#include "extended/md5set.h"
#include "tools/gt_sequniq.h"

typedef struct {
  bool seqit, verbose, rev;
  unsigned long width, nofseqs;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} GtSequniqArguments;

static void* gt_sequniq_arguments_new(void)
{
  GtSequniqArguments *arguments = gt_calloc((size_t)1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_sequniq_arguments_delete(void *tool_arguments)
{
  GtSequniqArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_sequniq_option_parser_new(void *tool_arguments)
{
  GtSequniqArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *seqit_option, *verbose_option, *width_option, *rev_option,
           *nofseqs_option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] sequence_file [...] ",
                            "Filter out repeated sequences in given in given "
                            "sequence_file(s).");

  /* -seqit */
  seqit_option = gt_option_new_bool("seqit", "use sequence iterator",
                                    &arguments->seqit, false);
  gt_option_is_development_option(seqit_option);
  gt_option_parser_add_option(op, seqit_option);

  /* -nofseqs */
  nofseqs_option = gt_option_new_ulong("nofseqs", "number of sequences "
      "(improves efficiency)\ndefault: unspecified",
      &arguments->nofseqs, 0);
  gt_option_is_development_option(nofseqs_option);
  gt_option_hide_default(nofseqs_option);
  gt_option_parser_add_option(op, nofseqs_option);

  /* -rev */
  rev_option = gt_option_new_bool("rev", "filter out also sequences whose "
      "reverse complement is identical to a sequence already output",
      &arguments->rev, false);
  gt_option_parser_add_option(op, rev_option);

  /* -v */
  verbose_option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, verbose_option);

  /* -width */
  width_option = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, width_option);

  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  /* option implications */
  gt_option_imply(verbose_option, seqit_option);

  gt_option_parser_set_min_args(op, 1U);
  return op;
}

static int gt_sequniq_runner(int argc, const char **argv, int parsed_args,
                             void *tool_arguments, GtError *err)
{
  GtSequniqArguments *arguments = tool_arguments;
  unsigned long long duplicates = 0, num_of_sequences = 0;
  int i, had_err = 0;
  GtMD5Set *md5set;

  gt_error_check(err);
  gt_assert(arguments);
  md5set = gt_md5set_new(arguments->nofseqs);
  if (!arguments->seqit) {
    unsigned long j;
    GtBioseq *bs;

    for (i = parsed_args; !had_err && i < argc; i++) {
      if (!(bs = gt_bioseq_new(argv[i], err)))
        had_err = -1;
      if (!had_err) {
        GtMD5SetStatus retval;
        for (j = 0; j < gt_bioseq_number_of_sequences(bs) && !had_err; j++) {
          char *seq = gt_bioseq_get_sequence(bs, j);
          retval = gt_md5set_add_sequence(md5set, seq,
                                          gt_bioseq_get_sequence_length(bs, j),
                                          arguments->rev, err);
          if (retval == GT_MD5SET_NOT_FOUND)
            gt_fasta_show_entry(gt_bioseq_get_description(bs, j), seq,
                                gt_bioseq_get_sequence_length(bs, j),
                                arguments->width, arguments->outfp);
          else if (retval != GT_MD5SET_ERROR)
            duplicates++;
          else
            had_err = -1;
          num_of_sequences++;
          gt_free(seq);
        }
        gt_bioseq_delete(bs);
      }
    }
  }
  else {
    GtSeqIterator *seqit;
    GtStrArray *files;
    off_t totalsize;
    const GtUchar *sequence;
    char *desc;
    unsigned long len;

    files = gt_str_array_new();
    for (i = parsed_args; i < argc; i++)
      gt_str_array_add_cstr(files, argv[i]);
    totalsize = gt_files_estimate_total_size(files);
    seqit = gt_seq_iterator_sequence_buffer_new(files, err);
    if (!seqit)
      had_err = -1;
    if (!had_err) {
      if (arguments->verbose) {
        gt_progressbar_start(gt_seq_iterator_getcurrentcounter(seqit,
                                                            (unsigned long long)
                                                            totalsize),
                             (unsigned long long) totalsize);
      }
      while (!had_err) {
        GtMD5SetStatus retval;
        if ((gt_seq_iterator_next(seqit, &sequence, &len, &desc, err)) != 1)
          break;

        retval = gt_md5set_add_sequence(md5set, (const char*) sequence, len,
            arguments->rev, err);
        if (retval == GT_MD5SET_NOT_FOUND)
          gt_fasta_show_entry(desc, (const char*) sequence, len,
                              arguments->width, arguments->outfp);
        else if (retval != GT_MD5SET_ERROR)
          duplicates++;
        else
          had_err = -1;
        num_of_sequences++;
      }
      if (arguments->verbose)
        gt_progressbar_stop();
      gt_seq_iterator_delete(seqit);
    }
    gt_str_array_delete(files);
  }

  /* show statistics */
  if (!had_err) {
    fprintf(stderr, "# %lu out of %lu sequences have been removed (%.3f%%)\n",
            (unsigned long)duplicates, (unsigned long)num_of_sequences,
            ((double) duplicates / (double)num_of_sequences) * 100.0);
  }

  gt_md5set_delete(md5set);
  return had_err;
}

GtTool* gt_sequniq(void)
{
  return gt_tool_new(gt_sequniq_arguments_new,
                     gt_sequniq_arguments_delete,
                     gt_sequniq_option_parser_new,
                     NULL,
                     gt_sequniq_runner);
}
genometools-1.5.1/src/tools/gt_sequniq.h000066400000000000000000000017271211610345200203320ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SEQUNIQ_H
#define GT_SEQUNIQ_H

#include "core/tool_api.h"

/* the sequniq tool */
GtTool* gt_sequniq(void);

#endif
genometools-1.5.1/src/tools/gt_sfxmap.c000066400000000000000000001234271211610345200201400ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/encseq_metadata.h"
#include "core/error.h"
#include "core/logger.h"
#include "core/option_api.h"
#include "core/str_array_api.h"
#include "core/unused_api.h"
#include "match/echoseq.h"
#include "match/eis-voiditf.h"
#include "match/esa-lcpintervals.h"
#include "match/esa-map.h"
#include "match/esa-seqread.h"
#include "match/esa-spmitvs.h"
#include "match/index_options.h"
#include "match/optionargmode.h"
#include "match/pckdfs.h"
#include "match/sfx-bentsedg.h"
#include "match/sfx-diffcov.h"
#include "match/sfx-strategy.h"
#include "match/sfx-suffixgetset.h"
#include "match/sfx-suftaborder.h"
#include "match/stamp.h"
#include "match/test-mappedstr.pr"
#include "match/twobits2kmers.h"
#include "match/sfx-linlcp.h"
#include "tools/gt_sfxmap.h"

typedef struct
{
  bool usestream,
       bfcheck,
       verbose,
       cmpsuf,
       cmplcp,
       inputtis,
       inputsuf,
       inputdes,
       inputsds,
       inputbwt,
       inputlcp,
       inputbck,
       inputssp,
       enumlcpitvs,
       enumlcpitvtree,
       enumlcpitvtreeBU,
       diffcovercheck,
       wholeleafcheck,
       spmitv,
       ownencseq2file;
  unsigned long delspranges;
  GtStr *esaindexname,
        *pckindexname;
  unsigned int sortmaxdepth,
               scanesa;
  GtStrArray *algbounds,
             *streamesq;
} Sfxmapoptions;

static void deletethespranges(const GtEncseq *encseq,
                              unsigned long delspranges)
{
  GtSpecialrangeiterator *sri;
  GtRange range;
  unsigned long rangewidth, nextpos = 0, totallength;
  const unsigned long fastawidth = 70UL;

  sri = gt_specialrangeiterator_new(encseq,true);
  printf(">\n");
  while (gt_specialrangeiterator_next(sri,&range))
  {
    gt_assert(range.end > range.start);
    rangewidth = range.end - range.start;
    if (rangewidth > (unsigned long) delspranges)
    {
      if (range.start == 0)
      {
        nextpos = range.end;
      } else
      {
        if (range.start > nextpos)
        {
          gt_encseq2symbolstring(stdout,
                              encseq,
                              GT_READMODE_FORWARD,
                              nextpos,
                              range.start + delspranges - nextpos,
                              fastawidth);
          nextpos = range.end;
        }
      }
    }
  }
  totallength = gt_encseq_total_length(encseq);
  if (nextpos < totallength-1)
  {
    gt_encseq2symbolstring(stdout,
                        encseq,
                        GT_READMODE_FORWARD,
                        nextpos,
                        totallength - nextpos,
                        fastawidth);
  }
  gt_specialrangeiterator_delete(sri);
}

static void *gt_sfxmap_arguments_new(void)
{
  Sfxmapoptions *arguments;

  arguments = gt_malloc(sizeof (*arguments));
  arguments->esaindexname = gt_str_new();
  arguments->pckindexname = gt_str_new();
  arguments->streamesq = gt_str_array_new();
  arguments->algbounds = gt_str_array_new();
  return arguments;
}

static void gt_sfxmap_arguments_delete(void *tool_arguments)
{
  Sfxmapoptions *arguments = tool_arguments;

  if (arguments != NULL)
  {
    gt_str_delete(arguments->esaindexname);
    gt_str_delete(arguments->pckindexname);
    gt_str_array_delete(arguments->streamesq);
    gt_str_array_delete(arguments->algbounds);
    gt_free(arguments);
  }
}

static GtOptionParser* gt_sfxmap_option_parser_new(void *tool_arguments)
{
  Sfxmapoptions *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *optionstream, *optionverbose, *optionbck, *optionsuf,
         *optiondes, *optionsds, *optionbwt, *optionlcp, *optiontis, *optionssp,
         *optiondelspranges, *optionpckindex, *optionesaindex,
         *optioncmpsuf, *optioncmplcp, *optionstreamesq,
         *optionsortmaxdepth, *optionalgbounds, *optiondiffcov,
         *optionwholeleafcheck,
         *optionenumlcpitvs, *optionenumlcpitvtree, *optionenumlcpitvtreeBU,
         *optionscanesa, *optionspmitv, *optionownencseq2file,
         *optionbfcheck;

  gt_assert(arguments != NULL);
  op = gt_option_parser_new("[options]",
                            "Map or Stream  and check consistency.");
  gt_option_parser_set_mail_address(op,"");

  optionesaindex = gt_option_new_string("esa",
                                        "Specify index (enhanced suffix array)",
                                        arguments->esaindexname, NULL);
  gt_option_parser_add_option(op, optionesaindex);

  optionpckindex = gt_option_new_string("pck",
                                        "Specify index (packed index)",
                                        arguments->pckindexname, NULL);
  gt_option_parser_add_option(op, optionpckindex);

  optionstreamesq = gt_option_new_string_array("stream-esq",
                                               "Stream the encoded sequence",
                                               arguments->streamesq);
  gt_option_parser_add_option(op, optionstreamesq);

  optionsortmaxdepth = gt_option_new_uint("sortmaxdepth",
                                          "sort suffixes up to some depth",
                                          &arguments->sortmaxdepth,0);
  gt_option_parser_add_option(op, optionsortmaxdepth);

  optionalgbounds = gt_option_new_string_array("algbds",
                                "length boundaries for the different "
                                "algorithms to sort buckets of suffixes\n"
                                "first number: maxbound for insertion sort\n"
                                "second number: maxbound for blindtrie sort\n"
                                "third number: maxbound for counting sort",
                                arguments->algbounds);
  gt_option_parser_add_option(op, optionalgbounds);

  gt_option_is_mandatory_either_3(optionesaindex,optionpckindex,
                                  optionstreamesq);

  optionstream = gt_option_new_bool("stream","stream the index",
                                    &arguments->usestream,false);
  gt_option_parser_add_option(op, optionstream);

  optionbfcheck = gt_option_new_bool("bfcheck",
                                     "perform check by brute force algorithm "
                                     "(this can be slow if lcps are long)",
                                     &arguments->bfcheck,false);
  gt_option_parser_add_option(op, optionbfcheck);

  optiondelspranges = gt_option_new_ulong("delspranges",
                                          "delete ranges of special values",
                                           &arguments->delspranges,
                                           0);
  gt_option_parser_add_option(op, optiondelspranges);

  optiontis = gt_option_new_bool("tis","input the transformed input sequence",
                                 &arguments->inputtis,
                                 false);
  gt_option_parser_add_option(op, optiontis);

  optiondes = gt_option_new_bool("des","input the descriptions",
                                 &arguments->inputdes,
                                 false);
  gt_option_parser_add_option(op, optiondes);

  optionsds = gt_option_new_bool("sds","input the description end positions",
                                 &arguments->inputsds,
                                 false);
  gt_option_parser_add_option(op, optionsds);

  optionsuf = gt_option_new_bool("suf","input the suffix array",
                                 &arguments->inputsuf,
                                 false);
  gt_option_parser_add_option(op, optionsuf);

  optionlcp = gt_option_new_bool("lcp","input the lcp-table",
                                 &arguments->inputlcp,
                                 false);
  gt_option_parser_add_option(op, optionlcp);

  optionbwt = gt_option_new_bool("bwt",
                                 "input the Burrows-Wheeler Transformation",
                                 &arguments->inputbwt,
                                 false);
  gt_option_parser_add_option(op, optionbwt);

  optionbck = gt_option_new_bool("bck","input the bucket table",
                                 &arguments->inputbck,
                                 false);
  gt_option_parser_add_option(op, optionbck);

  optioncmpsuf = gt_option_new_bool("cmpsuf","compare pck derived suftab with "
                                    "esa-suftab",
                                    &arguments->cmpsuf,
                                    false);
  gt_option_parser_add_option(op, optioncmpsuf);

  optioncmplcp = gt_option_new_bool("cmplcp","compare pck derived lcptab with "
                                    "esa-lcptab",
                                    &arguments->cmplcp,
                                    false);
  gt_option_parser_add_option(op, optioncmplcp);
  gt_option_exclude(optioncmpsuf,optioncmplcp);

  optionssp = gt_option_new_bool("ssp","input the sequence separator table",
                                 &arguments->inputssp,
                                 false);
  gt_option_parser_add_option(op, optionssp);

  optiondiffcov = gt_option_new_bool("diffcover","check difference covers",
                                     &arguments->diffcovercheck,false);
  gt_option_parser_add_option(op, optiondiffcov);

  optionwholeleafcheck = gt_option_new_bool("wholeleafcheck",
                                            "check if all whole leaves are "
                                            "present",
                                            &arguments->wholeleafcheck,false);
  gt_option_parser_add_option(op, optionwholeleafcheck);

  optionenumlcpitvs = gt_option_new_bool("enumlcpitvs",
                                         "enumerate the lcp-intervals",
                                         &arguments->enumlcpitvs,false);
  gt_option_parser_add_option(op, optionenumlcpitvs);

  optionenumlcpitvtree = gt_option_new_bool("enumlcpitvtree",
                                            "enumerate the lcp-interval tree",
                                            &arguments->enumlcpitvtree,false);
  gt_option_parser_add_option(op, optionenumlcpitvtree);

  optionenumlcpitvtreeBU = gt_option_new_bool("enumlcpitvtreeBU",
                                      "enumerate the lcp-interval tree "
                                      "(using a bottom-up strategy)",
                                       &arguments->enumlcpitvtreeBU,false);
  gt_option_parser_add_option(op, optionenumlcpitvtreeBU);

  optionscanesa = gt_option_new_uint("scanesa",
                                     "scan suftab and lcptab",
                                     &arguments->scanesa,0);
  gt_option_parser_add_option(op, optionscanesa);

  optionspmitv = gt_option_new_bool("spmitv",
                                    "determine distribution of intervals "
                                    "with whole leaves",
                                    &arguments->spmitv,false);
  gt_option_parser_add_option(op, optionspmitv);

  optionownencseq2file = gt_option_new_bool("ownencseq2file",
                                            "write own encseq to file",
                                            &arguments->ownencseq2file,false);
  gt_option_parser_add_option(op, optionownencseq2file);
  gt_option_imply(optionownencseq2file, optionesaindex);

  optionverbose = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, optionverbose);

  gt_option_exclude(optionenumlcpitvs,optionenumlcpitvtree);
  gt_option_exclude(optionenumlcpitvs,optionenumlcpitvtreeBU);
  gt_option_exclude(optionenumlcpitvtree,optionenumlcpitvtreeBU);
  gt_option_imply(optionlcp,optionsuf);
  gt_option_imply(optionenumlcpitvs,optionesaindex);
  gt_option_imply(optionsortmaxdepth,optionesaindex);
  gt_option_imply(optionalgbounds,optionsortmaxdepth);
  return op;
}

static int gt_sfxmap_arguments_check(GT_UNUSED int rest_argc,
                                     GT_UNUSED void *tool_arguments,
                                     GT_UNUSED GtError *err)
{
  return 0;
}

static void showcomparisonfailureESA(const char *filename,
                                     int line,
                                     const char *where,
                                     const GtEncseq *encseq,
                                     GtReadmode readmode,
                                     const ESASuffixptr *suftab,
                                     unsigned long depth,
                                     unsigned long idx1,
                                     unsigned long idx2,
                                     int cmp,
                                     unsigned long maxlcp)
{
  fprintf(stderr,"ERROR: file \"%s\", line %d: ",filename,line);
  fprintf(stderr,"%s(%lu vs %lu"
                 " %lu=\"",
                       where,
                       idx1,
                       idx2,
                       ESASUFFIXPTRGET(suftab,idx1));
  gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,
                                    ESASUFFIXPTRGET(suftab,idx1),depth);
  fprintf(stderr,"\",\"");
  gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,
                                    ESASUFFIXPTRGET(suftab,idx2),depth);
  fprintf(stderr,"\"=%lu)=%d with maxlcp %lu\n",ESASUFFIXPTRGET(suftab,idx2),
                                                cmp,
                                                maxlcp);
}

static unsigned long determinenumberofwholeleaves(const GtEncseq *encseq,
                                                  GtReadmode readmode)
{
  unsigned long idx, wholeleafcount = 0, totallength;
  GtEncseqReader* esr;
  GtUchar cc;
  bool sequencestart = true;

  esr = gt_encseq_create_reader_with_readmode(encseq,readmode,0);
  totallength = gt_encseq_total_length(encseq);
  for (idx = 0; idx < totallength; idx++)
  {
    cc = gt_encseq_reader_next_encoded_char(esr);
    if (cc == (GtUchar) SEPARATOR)
    {
      sequencestart = true;
    } else
    {
      if (sequencestart)
      {
        if (cc != (GtUchar) WILDCARD)
        {
          wholeleafcount++;
        }
        sequencestart = false;
      }
    }
  }
  gt_encseq_reader_delete(esr);
  return wholeleafcount;
}

static int gt_encseq_check_comparefullsuffixes(const GtEncseq *encseq,
                                               GtReadmode readmode,
                                               unsigned long *maxlcp,
                                               unsigned long start1,
                                               unsigned long start2,
                                               GtEncseqReader *esr1,
                                               GtEncseqReader *esr2)
{
  GtUchar cc1, cc2;
  unsigned long pos1, pos2, totallength;
  int retval;

  totallength = gt_encseq_total_length(encseq);
  if (esr1 != NULL && esr2 != NULL)
  {
    gt_encseq_reader_reinit_with_readmode(esr1,encseq,readmode,start1);
    gt_encseq_reader_reinit_with_readmode(esr2,encseq,readmode,start2);
  } else
  {
    gt_assert(esr1 == NULL && esr2 == NULL);
  }
  for (pos1=start1, pos2=start2; /* Nothing */; pos1++, pos2++)
  {
    if (pos1 >= totallength)
    {
      cc1 = (GtUchar) SEPARATOR;
    } else
    {
      cc1 = (esr1 != NULL) ? gt_encseq_reader_next_encoded_char(esr1)
                           : gt_encseq_get_encoded_char(encseq,pos1,readmode);
    }
    if (pos2 >= totallength)
    {
      cc2 = (GtUchar) SEPARATOR;
    } else
    {
      cc2 = (esr2 != NULL) ? gt_encseq_reader_next_encoded_char(esr2)
                           : gt_encseq_get_encoded_char(encseq,pos2,readmode);
    }
    if (ISSPECIAL(cc1))
    {
      if (ISSPECIAL(cc2))
      {
        if (pos1 < pos2)
        {
          *maxlcp = pos1  - start1;
          retval = -1; /* a < b */
          break;
        }
        if (pos1 > pos2)
        {
          *maxlcp = pos1 - start1;
          retval = 1; /* a > b */
          break;
        }
        *maxlcp = pos1 - start1 + 1;
        retval = 0; /* a = b */
        break;
      }
      *maxlcp = pos1 - start1;
      retval = 1; /* a > b */
      break;
    } else
    {
      if (ISSPECIAL(cc2))
      {
        *maxlcp = pos1 - start1;
        retval = -1; /* a < b */
        break;
      }
      if (cc1 < cc2)
      {
        *maxlcp = pos1 - start1;
        retval = -1; /* a < b */
        break;
      }
      if (cc1 > cc2)
      {
        *maxlcp = pos1 - start1;
        retval = 1; /* a > b */
        break;
      }
    }
  }
  return retval;
}

static int gt_checkentiresuftab(const char *filename,
                                int line,
                                const GtEncseq *encseq,
                                GtReadmode readmode,
                                const ESASuffixptr *suftab,
                                unsigned long numberofsuffixes,
                                bool wholeleafcheck,
                                Sequentialsuffixarrayreader *ssar,
                                GT_UNUSED bool specialsareequal,
                                GT_UNUSED bool specialsareequalatdepth0,
                                unsigned long depth,
                                GT_UNUSED GtError *err)
{
  unsigned long idx, maxlcp,
                currentlcp = 0,
                countbitsset = 0,
                wholeleafcount = 0,
                totallength = gt_encseq_total_length(encseq);
  int cmp;
  GtEncseqReader *esr1, *esr2;
  bool haserr = false;
  GtBitsequence *startposoccurs;
  GtEncseqReader *esr;
  /*
#define MAXDIST 100
  unsigned long countdist[MAXDIST+1] = {0};
  */

  gt_error_check(err);
  gt_assert(!specialsareequal || specialsareequalatdepth0);
  if (numberofsuffixes == 0)
  {
    return 0;
  }
  GT_INITBITTAB(startposoccurs,totallength+1);
  esr = gt_encseq_create_reader_with_readmode(encseq,readmode,0);
  for (idx = 0; idx < numberofsuffixes; idx++)
  {
    unsigned long position = ESASUFFIXPTRGET(suftab,idx);
    if (GT_ISIBITSET(startposoccurs,position))
    {
      fprintf(stderr,"ERROR: suffix with startpos %lu already occurs\n",
              ESASUFFIXPTRGET(suftab,idx));
      exit(GT_EXIT_PROGRAMMING_ERROR);
    }
    GT_SETIBIT(startposoccurs,position);
    countbitsset++;
    if (wholeleafcheck)
    {
      if (position == 0 || gt_encseq_position_is_separator(encseq,
                                                           position - 1,
                                                           readmode))
      {
        /*printf("whole %lu\n",position);*/
        wholeleafcount++;
      }
    }
  }
  gt_encseq_reader_delete(esr);
  gt_free(startposoccurs);
  if (wholeleafcheck)
  {
    unsigned long expectednumofwholeleaves
      = determinenumberofwholeleaves(encseq,readmode);
    if (wholeleafcount != expectednumofwholeleaves)
    {
      fprintf(stderr,"wholeleafcount=%lu != %lu=expectednumofwholeleaves\n",
                      wholeleafcount,expectednumofwholeleaves);
      exit(EXIT_FAILURE);
    }
  }
  if (numberofsuffixes == totallength + 1 && countbitsset != numberofsuffixes)
  {
    fprintf(stderr,"ERROR: not all bits are set\n");
    exit(GT_EXIT_PROGRAMMING_ERROR);
  }
  esr1 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  esr2 = gt_encseq_create_reader_with_readmode(encseq, readmode, 0);
  gt_assert(numberofsuffixes > 0);
  gt_assert(ESASUFFIXPTRGET(suftab,0) < totallength);
  for (idx = 1UL; !haserr && idx < numberofsuffixes; idx++)
  {
    if (idx < totallength)
    {
      gt_assert(ESASUFFIXPTRGET(suftab,idx) < totallength);
      cmp = gt_encseq_check_comparefullsuffixes(encseq,
                                                readmode,
                                                &maxlcp,
                                                ESASUFFIXPTRGET(suftab,idx-1),
                                                ESASUFFIXPTRGET(suftab,idx),
                                                esr1,
                                                esr2);
      if (cmp >= 0)
      {
        showcomparisonfailureESA(filename,
                                 line,
                                 "checkentiresuftab",
                                 encseq,
                                 readmode,
                                 suftab,
                                 depth,
                                 idx-1,
                                 idx,
                                 cmp,
                                 maxlcp);
        haserr = true;
        break;
      }
    } else
    {
      maxlcp = 0;
      if (numberofsuffixes == totallength+1)
      {
        gt_assert(ESASUFFIXPTRGET(suftab,idx) == totallength);
      }
    }
    if (ssar != NULL)
    {
      NEXTSEQUENTIALLCPTABVALUE(currentlcp,ssar);
      if (maxlcp != currentlcp)
      {
        fprintf(stderr,"%lu: startpos=%lu, firstchar=%u, "
                "startpos=%lu,firstchar=%u",
                idx,
                ESASUFFIXPTRGET(suftab,idx-1),
                (unsigned int)
                gt_encseq_get_encoded_char(encseq,
                                           ESASUFFIXPTRGET(suftab,idx-1),
                                           readmode),
                ESASUFFIXPTRGET(suftab,idx),
                (ESASUFFIXPTRGET(suftab,idx) < totallength)
                   ? (unsigned int) gt_encseq_get_encoded_char(encseq,
                                                     ESASUFFIXPTRGET(suftab,
                                                                     idx),
                                                     readmode)
                   : SEPARATOR);
        fprintf(stderr,", maxlcp(bruteforce) = %lu != %lu(fast)\n",
                          maxlcp, currentlcp);
        exit(GT_EXIT_PROGRAMMING_ERROR);
      }
    }
  }
  gt_encseq_reader_delete(esr1);
  gt_encseq_reader_delete(esr2);
  return haserr ? -1 : 0;
  /*
  printf("# gt_checkentiresuftab with mode 'specials are %s'\n",
               specialsareequal ? "equal" : "different");
  */
}

static int sfxmap_esa(const Sfxmapoptions *arguments, GtLogger *logger,
                      GtError *err)
{
  bool haserr = false;
  Suffixarray suffixarray;
  unsigned int demand = 0;

  if (arguments->inputtis || arguments->delspranges > 0 || arguments->inputsuf)
  {
    demand |= SARR_ESQTAB;
  }
  if (arguments->inputdes)
  {
    demand |= SARR_DESTAB;
  }
  if (arguments->inputsds)
  {
    demand |= SARR_SDSTAB;
  }
  if (arguments->inputsuf)
  {
    demand |= SARR_SUFTAB;
  }
  if (arguments->inputlcp)
  {
    demand |= SARR_LCPTAB;
  }
  if (arguments->inputbwt)
  {
    demand |= SARR_BWTTAB;
  }
  if (arguments->inputbck)
  {
    demand |= SARR_BCKTAB;
  }
  if (arguments->inputssp)
  {
    demand |= SARR_SSPTAB;
  }
  if ((arguments->usestream
         ? streamsuffixarray
         : gt_mapsuffixarray)(&suffixarray,
                              demand,
                              gt_str_get(arguments->esaindexname),
                              logger,
                              err) != 0)
  {
    haserr = true;
  }
  if (!haserr && suffixarray.encseq != NULL)
  {
    if (arguments->delspranges > 0)
    {
      deletethespranges(suffixarray.encseq,arguments->delspranges);
    } else
    {
      unsigned long totallength = gt_encseq_total_length(suffixarray.encseq);
      if (!haserr && arguments->inputsuf && !arguments->usestream)
      {
        if (suffixarray.numberofallsortedsuffixes != totallength + 1 ||
            arguments->bfcheck)
        {
          Sequentialsuffixarrayreader *ssar;

          if (arguments->inputlcp)
          {
            ssar = gt_newSequentialsuffixarrayreaderfromfile(
                                          gt_str_get(arguments->esaindexname),
                                          SARR_LCPTAB | SARR_ESQTAB,
                                          SEQ_scan,
                                          logger,
                                          err);
          } else
          {
            ssar = NULL;
          }
          gt_logger_log(logger, "checkentiresuftab");
          if (gt_checkentiresuftab(__FILE__,
                                   __LINE__,
                                   suffixarray.encseq,
                                   suffixarray.readmode,
                                   suffixarray.suftab,
                                   suffixarray.numberofallsortedsuffixes,
                                   arguments->wholeleafcheck,
                                   ssar,
                                   false, /* specialsareequal  */
                                   false,  /* specialsareequalatdepth0 */
                                   0,
                                   err) != 0)
          {
            fprintf(stderr,"gt_checkentiresuftab failed\n");
            exit(GT_EXIT_PROGRAMMING_ERROR);
          }
          if (ssar != NULL)
          {
            gt_freeSequentialsuffixarrayreader(&ssar);
          }
        } else
        {
          if (suffixarray.numberofallsortedsuffixes == totallength + 1)
          {
            gt_suftab_lightweightcheck(suffixarray.encseq, suffixarray.readmode,
                                       totallength,suffixarray.suftab,
                                       logger);
            if (arguments->inputlcp)
            {
              if (gt_lcptab_lightweightcheck(
                                      gt_str_get(arguments->esaindexname),
                                      suffixarray.encseq,
                                      suffixarray.readmode,
                                      suffixarray.suftab,
                                      logger,err) != 0)
              {
                haserr = true;
              }
            }
          }
        }
        if (!haserr)
        {
          gt_logger_log(logger, "okay");
        }
      }
      if (!haserr && arguments->inputbwt)
      {
        unsigned long bwtdifferentconsecutive = 0, idx;
        GT_UNUSED unsigned long longest;

        gt_assert(suffixarray.longest.defined);
        longest = suffixarray.longest.valueunsignedlong;
        if (!haserr && arguments->inputsuf && !arguments->usestream)
        {
          gt_assert(suffixarray.numberofallsortedsuffixes == totallength+1);
          gt_assert(longest < totallength);
          gt_assert(suffixarray.suftab != NULL);
          gt_assert(ESASUFFIXPTRGET(suffixarray.suftab,longest) == 0);
        }
        if (!arguments->usestream)
        {
          for (idx = (unsigned long) 1; idxinputdes && arguments->inputsds)
  {
    gt_logger_log(logger, "checkallsequencedescriptions");
    gt_encseq_check_descriptions(suffixarray.encseq);
  }
  gt_freesuffixarray(&suffixarray);
  return haserr ? -1 : 0;
}

static int comparelcpvalue(void *info,unsigned long lcp,GtError *err)
{
  unsigned long currentlcpvalue;
  Sequentialsuffixarrayreader *ssar = (Sequentialsuffixarrayreader *) info;
  bool haserr = false;

  do /* fake loop to allow for the use of a break statement */
  {
    NEXTSEQUENTIALLCPTABVALUE(currentlcpvalue,ssar);
    if (lcp != currentlcpvalue)
    {
      gt_error_set(err,"lcp=%lu != %lu=currentlcpvalue",lcp,currentlcpvalue);
      haserr = true;
      break;
    }
    break;
  } while (true);
  return haserr ? -1 : 0;
}

static int sfxmap_pck(const Sfxmapoptions *arguments,GtLogger *logger,
                      GtError *err)
{
  bool haserr = false;
  FMindex *fmindex;
  unsigned long totallength = 0;
  unsigned int numofchars = 0;
  GtEncseqMetadata *encseqmetadata = NULL;
  Sequentialsuffixarrayreader *ssar;

  gt_assert(gt_str_length(arguments->pckindexname) > 0);
  fmindex = gt_loadvoidBWTSeqForSA(gt_str_get(arguments->pckindexname),false,
                                   err);
  if (fmindex == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    encseqmetadata = gt_encseq_metadata_new(gt_str_get(arguments->pckindexname),
                                            err);
    if (encseqmetadata == NULL)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    if (gt_str_length(arguments->esaindexname) > 0 &&
        (arguments->cmpsuf || arguments->cmplcp))
    {
      ssar = gt_newSequentialsuffixarrayreaderfromfile(
                                          gt_str_get(arguments->esaindexname),
                                          arguments->cmpsuf ? SARR_SUFTAB
                                                            : SARR_LCPTAB,
                                          SEQ_scan,
                                          logger,
                                          err);
      if (ssar == NULL)
      {
        haserr = true;
      }
    } else
    {
      ssar = NULL;
    }
  }
  if (!haserr)
  {
    unsigned long idx, pos, numofnonspecials;
    GT_UNUSED unsigned long currentsuffix = 0;
    GtSpecialcharinfo specialcharinfo;
    Bwtseqpositioniterator *bspi;

    gt_assert(encseqmetadata != NULL);
    totallength = gt_encseq_metadata_total_length(encseqmetadata);
    specialcharinfo = gt_encseq_metadata_specialcharinfo(encseqmetadata);
    gt_assert(totallength >= specialcharinfo.specialcharacters);
    numofnonspecials = totallength - specialcharinfo.specialcharacters;
    bspi = gt_Bwtseqpositioniterator_new(fmindex,0,totallength);
    gt_logger_log(logger, "iterate over all suftab values");
    for (idx = 0; idx < numofnonspecials; idx++)
    {
      if (!gt_Bwtseqpositioniterator_next(&pos,bspi))
      {
        gt_error_set(err,"cannot decode enough symbols");
        haserr = true;
        break;
      }
      if (arguments->cmpsuf && ssar != NULL)
      {
        NEXTSEQUENTIALSUFTABVALUE(currentsuffix,ssar);
        gt_assert(pos == currentsuffix);
      }
      /*printf("%lu: pos = %lu\n",idx,pos);*/
    }
    gt_assert(idx == numofnonspecials);
    gt_Bwtseqpositioniterator_delete(bspi);
  }
  if (!haserr)
  {
    GtAlphabet *alphabet;

    alphabet = gt_encseq_metadata_alphabet(encseqmetadata);
    if (alphabet == NULL)
    {
      haserr = true;
    }
    numofchars = gt_alphabet_num_of_chars(alphabet);
  }
  if (!haserr)
  {
    if (arguments->cmplcp && ssar != NULL)
    {
      gt_logger_log(logger,"perform dfs traversal");
      if (gt_fmindex_dfstraverse(fmindex,
                                 numofchars,
                                 totallength,
                                 comparelcpvalue,
                                 (void *) ssar,
                                 err) != 0)
      {
        haserr = true;
      }
    }
  }
  gt_deletevoidBWTSeq(fmindex);
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  gt_encseq_metadata_delete(encseqmetadata);
  return haserr ? -1 : 0;
}

static const Optionargmodedesc stream_esq_operation[] =
{
  {"stream_words","read words from stream",(unsigned int) BSRS_stream_words},
  {"stream_single","read single characters from word stream",
                   (unsigned int) BSRS_stream_single},
  {"reader_single","read single characters with encseq reader",
                   (unsigned int) BSRS_reader_single},
  {"stream_reader_single","read single characters with encseq reader and "
                          "from word stream",
                   (unsigned int) BSRS_stream_reader_single},
  {"reader_multi","read kmers with encseq reader",
                   (unsigned int) BSRS_reader_multi},
  {"stream_reader_multi","read kmers with encseq reader and from word stream",
                   (unsigned int) BSRS_stream_reader_multi},
  {"stream_reader_multi3","read kmers with encseq reader and from word stream",
                   (unsigned int) BSRS_stream_reader_multi3},
  {"hashfirstcodes","hash first codes of each sequence in the encseq",
                   (unsigned int) BSRS_hashfirstcodes}
};

static int stream_esq(const Sfxmapoptions *arguments,GtError *err)
{
  GtEncseqLoader *el = NULL;
  GtEncseq *encseq = NULL;
  bool haserr = false;
  Bitstreamreadmode brsmode = BSRS_stream_single;
  int multiarg = 0;
  unsigned long streamesq_size = gt_str_array_size(arguments->streamesq);

  if (streamesq_size == 2UL || streamesq_size == 3UL)
  {
    int mode;

    mode = gt_optionargsetsingle(stream_esq_operation,
                                 sizeof stream_esq_operation/
                                 sizeof stream_esq_operation[0],
                                 "stream-esq",
                                 gt_str_array_get(arguments->streamesq,1UL),
                                 err);
    if (mode < 0)
    {
      haserr = true;
    } else
    {
      brsmode = (Bitstreamreadmode) mode;
      if ((brsmode == BSRS_stream_words ||
           brsmode == BSRS_stream_single ||
           brsmode == BSRS_reader_single ||
           brsmode == BSRS_stream_reader_single) &&
           streamesq_size != 2UL)
      {
        gt_error_set(err,"if option -streamesq has one of the arguments "
                         "stream_words stream_single reader_single "
                         "stream_reader_single then no other argument "
                         "is allowed");
        haserr = true;
      } else
      {
        if ((brsmode == BSRS_reader_multi ||
             brsmode == BSRS_stream_reader_multi ||
             brsmode == BSRS_stream_reader_multi3 ||
             brsmode == BSRS_hashfirstcodes) &&
             streamesq_size != 3UL)
        {
          gt_error_set(err,"if option -streamesq has one of the arguments "
                           "stream_multi reader_multi "
                           "stream_reader_multi then one more argument "
                           "is required");
          haserr = true;
        }
      }
    }
    if (!haserr && streamesq_size == 3UL)
    {
      if (sscanf(gt_str_array_get(arguments->streamesq,2UL),"%d",&multiarg)
          != 1 || multiarg < 1)
      {
        gt_error_set(err,"if option -streamesq has three arguments, "
                         "then third argument must be positive integer");
        haserr = true;
      }
    }
  } else
  {
    gt_error_set(err,"option -streamesq must have two or three arguments");
    haserr = true;
  }
  if (!haserr)
  {
    el = gt_encseq_loader_new();
    encseq = gt_encseq_loader_load(el, gt_str_array_get(arguments->streamesq,0),
                                   err);
    if (encseq == NULL)
    {
      haserr = true;
    }
  }
  if (!haserr && brsmode == BSRS_hashfirstcodes)
  {
    if (gt_encseq_mirror(encseq, err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    gt_assert(multiarg >= 0);
    gt_encseq_faststream(encseq,brsmode,(unsigned int) multiarg);
  }
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(el);
  return haserr ? -1 : 0;
}

typedef struct
{
  GtEncseq *encseq;
  GtReadmode readmode;
  unsigned int sortmaxdepth;
  GtSuffixsortspace *sssp;
} Checkunsortedrangeinfo;

static void sortmaxdepth_processunsortedrange(void *voiddcov,
                                              unsigned long subbucketleft,
                                              unsigned long width,
                                              GT_UNUSED unsigned long depth)
{
  Checkunsortedrangeinfo *curi = voiddcov;

  gt_checkifprefixesareidentical(__FILE__,
                                 __LINE__,
                                 curi->encseq,
                                 curi->readmode,
                                 curi->sssp,
                                 subbucketleft,
                                 width,
                                 (unsigned long) curi->sortmaxdepth);
}

static int performsortmaxdepth(const Sfxmapoptions *arguments,
                               GtLogger *logger,GtError *err)
{
  bool haserr = false;
  GtEncseqLoader *el = NULL;
  Checkunsortedrangeinfo curi;
  Sfxstrategy sfxstrategy;
  const char *indexname;

  indexname = gt_str_get(arguments->esaindexname);
  el = gt_encseq_loader_new();
  curi.encseq = gt_encseq_loader_load(el, indexname, err);
  if (curi.encseq == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    gt_logger_log(logger,"performsortmaxdepth(%s,%u)",
                  indexname,arguments->sortmaxdepth);
    defaultsfxstrategy(&sfxstrategy,
                       gt_encseq_bitwise_cmp_ok(curi.encseq) ? false : true);
    if (gt_str_array_size(arguments->algbounds) > 0 &&
        gt_parse_algbounds(&sfxstrategy,arguments->algbounds,err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr)
  {
    unsigned long idx, totallength = gt_encseq_total_length(curi.encseq);

    curi.sssp = gt_suffixsortspace_new(totallength+1, totallength, true,
                                       logger);
    for (idx=0; idx<=totallength; idx++)
    {
      gt_suffixsortspace_setdirect(curi.sssp,idx,idx);
    }
    curi.readmode = GT_READMODE_FORWARD;
    curi.sortmaxdepth = arguments->sortmaxdepth;
    gt_sortallsuffixesfromstart(curi.sssp,
                                totallength+1,
                                curi.encseq,
                                curi.readmode,
                                NULL,
                                arguments->sortmaxdepth,
                                &sfxstrategy,
                                sortmaxdepth_processunsortedrange,
                                &curi, /* voiddcov */
                                logger);
    gt_checksortedsuffixes(__FILE__,
                           __LINE__,
                           curi.encseq,
                           curi.readmode,
                           curi.sssp,
                           0,
                           totallength+1,
                           false, /* specialsareequal  */
                           false,  /* specialsareequalatdepth0 */
                           (unsigned long) curi.sortmaxdepth);
    gt_suffixsortspace_delete(curi.sssp,false);
  }
  gt_encseq_delete(curi.encseq);
  gt_encseq_loader_delete(el);
  return haserr ? -1 : 0;
}

static int run_diffcover_check(const Sfxmapoptions *arguments, GtError *err)
{
  int had_err = 0;
  GtEncseqLoader *el = NULL;
  GtEncseq *encseq = NULL;
  const char *indexname;

  indexname = gt_str_get(arguments->esaindexname);
  el = gt_encseq_loader_new();
  encseq = gt_encseq_loader_load(el, indexname, err);
  if (!encseq)
    had_err = -1;

  if (!had_err) {
    GtReadmode readmode;
    for (readmode = GT_READMODE_FORWARD;
         readmode <= GT_READMODE_REVCOMPL; readmode++) {
      gt_differencecover_check(encseq, readmode);
    }
  }
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(el);
  return had_err;
}

static int gt_sfxmap_runner(GT_UNUSED int argc,
                            GT_UNUSED const char **argv,
                            GT_UNUSED int parsed_args,
                            void *tool_arguments, GtError *err)
{
  bool haserr = false;
  Sfxmapoptions *arguments = tool_arguments;
  GtLogger *logger;

  gt_error_check(err);
  logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  if (gt_str_length(arguments->esaindexname) > 0)
  {
    if (sfxmap_esa(arguments,logger,err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr && gt_str_length(arguments->pckindexname) > 0)
  {
    if (sfxmap_pck(arguments,logger,err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr && gt_str_array_size(arguments->streamesq) > 0)
  {
    if (stream_esq(arguments,err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr && arguments->sortmaxdepth > 0)
  {
    if (performsortmaxdepth(arguments,logger,err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr && arguments->diffcovercheck)
  {
    if (run_diffcover_check(arguments, err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr && (arguments->enumlcpitvs || arguments->enumlcpitvtree ||
                  arguments->enumlcpitvtreeBU))
  {
    if (gt_runenumlcpvalues(gt_str_get(arguments->esaindexname),
                            arguments->enumlcpitvs ? false : true,
                            arguments->enumlcpitvtreeBU,
                            logger, err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr && arguments->scanesa > 0)
  {
    if (gt_runscanesa(gt_str_get(arguments->esaindexname),arguments->scanesa,
                      logger,err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr && arguments->spmitv)
  {
    if (gt_process_spmitv(gt_str_get(arguments->esaindexname),logger,err) != 0)
    {
      haserr = true;
    }
  }
  if (!haserr && arguments->ownencseq2file)
  {
    if (gt_encseq_check_external_twobitencoding_to_file(
                                 gt_str_get(arguments->esaindexname), err) != 0)
    {
      haserr = true;
    }
  }
  gt_logger_delete(logger);
  return haserr ? -1 : 0;
}

GtTool* gt_sfxmap(void)
{
  return gt_tool_new(gt_sfxmap_arguments_new,
                     gt_sfxmap_arguments_delete,
                     gt_sfxmap_option_parser_new,
                     gt_sfxmap_arguments_check,
                     gt_sfxmap_runner);
}
genometools-1.5.1/src/tools/gt_sfxmap.h000066400000000000000000000017211211610345200201350ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SFXMAP_H
#define GT_SFXMAP_H

#include "core/tool_api.h"

/* the sfxmap tool */
GtTool* gt_sfxmap(void);

#endif
genometools-1.5.1/src/tools/gt_shredder.c000066400000000000000000000130611211610345200204320ustar00rootroot00000000000000/*
  Copyright (c) 2008-2010 Gordon Gremme 
  Copyright (c) 2008      Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/bioseq_iterator.h"
#include "core/fasta.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/ma.h"
#include "core/unused_api.h"
#include "extended/gtdatahelp.h"
#include "extended/shredder.h"
#include "tools/gt_shredder.h"

typedef struct {
  unsigned long coverage,
                minlength,
                maxlength,
                overlap,
                width;
  double sample_probability;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} ShredderArguments;

static void* gt_shredder_arguments_new(void)
{
  ShredderArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_shredder_arguments_delete(void *tool_arguments)
{
  ShredderArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_shredder_option_parser_new(void *tool_arguments)
{
  ShredderArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *o;
  gt_assert(arguments);
  op = gt_option_parser_new("[option ...] [sequence_file ...]",
                            "Shredder sequence file(s) into consecutive pieces "
                            "of random length.");
  o = gt_option_new_ulong_min("coverage", "set the number of times the "
                              "sequence_file is shreddered",
                              &arguments->coverage, 1, 1);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_ulong("minlength",
                          "set the minimum length of the shreddered "
                          "fragments", &arguments->minlength, 300);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_ulong("maxlength",
                          "set the maximum length of the shreddered "
                          "fragments", &arguments->maxlength, 700);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_ulong("overlap", "set the overlap between consecutive "
                          "pieces", &arguments->overlap, 0);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_probability("sample", "take samples of the generated "
                                "sequences pieces with the given probability",
                                &arguments->sample_probability, 1.0);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, o);
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);
  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  return op;
}

static int gt_shredder_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments, GtError *err)
{
  ShredderArguments *arguments = tool_arguments;
  gt_error_check(err);
  gt_assert(arguments);
  if (arguments->minlength > arguments->maxlength) {
    gt_error_set(err, "-minlength must be <= than -maxlength");
    return -1;
  }
  return 0;
}

static int gt_shredder_runner(GT_UNUSED int argc, const char **argv,
                              int parsed_args, void *tool_arguments,
                              GtError *err)
{
  ShredderArguments *arguments = tool_arguments;
  GtBioseqIterator *bsi;
  unsigned long i;
  GtBioseq *bioseq;
  int had_err;
  GtStr *desc;

  gt_error_check(err);
  gt_assert(arguments);

  /* init */
  desc = gt_str_new();
  bsi = gt_bioseq_iterator_new(argc - parsed_args, argv + parsed_args);

  /* shredder */
  while (!(had_err = gt_bioseq_iterator_next(bsi, &bioseq, err)) && bioseq) {
    for (i = 0; i < arguments->coverage; i++) {
      GtShredder *shredder;
      unsigned long fragment_length;
      char *fragment;
      shredder = gt_shredder_new(bioseq, arguments->minlength,
                              arguments->maxlength);
      gt_shredder_set_overlap(shredder, arguments->overlap);
      gt_shredder_set_sample_probability(shredder,
                                         arguments->sample_probability);
      while ((fragment = gt_shredder_shred(shredder, &fragment_length, desc))) {
        gt_str_append_cstr(desc, " [shreddered fragment]");
        gt_fasta_show_entry(gt_str_get(desc), fragment, fragment_length,
                            arguments->width, arguments->outfp);
        gt_free(fragment);
      }
      gt_shredder_delete(shredder);
    }
    gt_bioseq_delete(bioseq);
  }

  /* free */
  gt_bioseq_iterator_delete(bsi);
  gt_str_delete(desc);

  return had_err;
}

GtTool* gt_shredder(void)
{
  return gt_tool_new(gt_shredder_arguments_new,
                     gt_shredder_arguments_delete,
                     gt_shredder_option_parser_new,
                     gt_shredder_arguments_check,
                     gt_shredder_runner);
}
genometools-1.5.1/src/tools/gt_shredder.h000066400000000000000000000017331211610345200204420ustar00rootroot00000000000000/*
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SHREDDER_H
#define GT_SHREDDER_H

#include "core/tool_api.h"

/* the shredder tool */
GtTool* gt_shredder(void);

#endif
genometools-1.5.1/src/tools/gt_shulen.c000066400000000000000000000161551211610345200201370ustar00rootroot00000000000000/*
  Copyright (c) 2010 Stefan Kurtz 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/error_api.h"
#include "core/str_api.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "core/unused_api.h"
#include "core/option_api.h"
#include "core/tool_api.h"
#include "core/versionfunc.h"
#include "match/esa-seqread.h"
#include "match/esa-shulen.h"
#include "match/esa-map.h"
#include "tools/gt_shulen.h"

typedef struct
{
  bool scanfile, beverbose;
  GtStr *indexname;
  GtStrArray *queryfilenames;
} Shulengthoptions;

static int callmultishulengthdist(const char *indexname,
                                  bool scanfile,
                                  GtLogger *logger,
                                  GtError *err)
{
  bool haserr = false;
  Sequentialsuffixarrayreader *ssar;

  gt_error_check(err);
  ssar = gt_newSequentialsuffixarrayreaderfromfile(indexname,
                                                   SARR_LCPTAB |
                                                   SARR_SUFTAB |
                                                   SARR_ESQTAB,
                                                   scanfile
                                                    ? SEQ_scan : SEQ_mappedboth,
                                                   logger,
                                                   err);
  if (ssar == NULL)
  {
    haserr = true;
  }
  if (!haserr)
  {
    if (gt_multiesa2shulengthdist_print(ssar,
                                  gt_encseqSequentialsuffixarrayreader(ssar),
                                  err) != 0)
    {
      haserr = true;
    }
  }
  if (ssar != NULL)
  {
    gt_freeSequentialsuffixarrayreader(&ssar);
  }
  return haserr ? -1 : 0;
}

static int callpairswisesshulendistdist(const char *indexname,
                                        const GtStrArray *queryfilenames,
                                        GtLogger *logger,
                                        GtError *err)
{
  bool haserr = false;
  Suffixarray suffixarray;

  if (gt_mapsuffixarray(&suffixarray,
                        SARR_SUFTAB |
                        SARR_ESQTAB,
                        indexname,
                        logger,
                        err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    unsigned long totalgmatchlength = 0;

    if (gt_esa2shulengthqueryfiles(&totalgmatchlength,
                                   &suffixarray,
                                   queryfilenames,
                                   err) != 0)
    {
      haserr = true;
    } else
    {
      printf("%lu\n",totalgmatchlength);
    }
  }
  gt_freesuffixarray(&suffixarray);
  return haserr ? -1 : 0;
}

static void *gt_shulengthdist_arguments_new(void)
{
  Shulengthoptions *arguments;

  arguments = gt_malloc(sizeof (*arguments));
  arguments->indexname = gt_str_new();
  arguments->queryfilenames = gt_str_array_new();
  return arguments;
}

static void gt_shulengthdist_arguments_delete(void *tool_arguments)
{
  Shulengthoptions *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->indexname);
  gt_str_array_delete(arguments->queryfilenames);
  gt_free(arguments);
}

static GtOptionParser *gt_shulengthdist_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GtOption *option, *queryoption, *scanoption;
  Shulengthoptions *arguments = tool_arguments;

  op = gt_option_parser_new("[options] -ii indexname",
                            "Compute distribution of pairwise "
                            "shustring lengths.");
  gt_option_parser_set_mail_address(op,"");

  option = gt_option_new_string("ii",
                                "Specify input index",
                                arguments->indexname, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  scanoption = gt_option_new_bool("scan","scan index rather than mapping "
                                  "it to main memory",
                                  &arguments->scanfile,
                                  false);
  gt_option_parser_add_option(op, scanoption);

  queryoption = gt_option_new_filename_array("q",
                                             "Specify query files",
                                             arguments->queryfilenames);
  gt_option_is_development_option(queryoption);
  gt_option_parser_add_option(op, queryoption);

  option = gt_option_new_bool("v",
                              "be verbose ",
                              &arguments->beverbose,
                              false);
  gt_option_parser_add_option(op, option);

  gt_option_exclude(queryoption,scanoption);
  return op;
}

static int gt_shulengthdist_arguments_check(GT_UNUSED int rest_argc,
                                            GT_UNUSED void *tool_arguments,
                                            GT_UNUSED GtError *err)
{
  return 0;
}

static int gt_shulengthdist_runner(GT_UNUSED int argc,
                                   GT_UNUSED const char **argv,
                                   GT_UNUSED int parsed_args,
                                   void *tool_arguments, GtError *err)
{
  bool haserr = false;
  Shulengthoptions *arguments = tool_arguments;
  GtLogger *logger = NULL;

  gt_error_check(err);
  logger = gt_logger_new(arguments->beverbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  if (parsed_args < argc)
  {
    gt_error_set(err,"superfluous arguments: \"%s\"",argv[argc-1]);
    haserr = true;
  }
  if (!haserr)
  {
    if (gt_str_array_size(arguments->queryfilenames) == 0)
    {
      if (callmultishulengthdist(gt_str_get(arguments->indexname),
                                 arguments->scanfile,
                                 logger,
                                 err) != 0)
      {
        haserr = true;
      }
    } else
    {
      if (callpairswisesshulendistdist(gt_str_get(arguments->indexname),
                                       arguments->queryfilenames,
                                       logger,
                                       err) != 0)
      {
        haserr = true;
      }
    }
  }
  gt_logger_delete(logger);
  return haserr ? -1 : 0;
}

GtTool* gt_shulengthdist(void)
{
  return gt_tool_new(gt_shulengthdist_arguments_new,
                     gt_shulengthdist_arguments_delete,
                     gt_shulengthdist_option_parser_new,
                     gt_shulengthdist_arguments_check,
                     gt_shulengthdist_runner);
}
genometools-1.5.1/src/tools/gt_shulen.h000066400000000000000000000016751211610345200201450ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SHULEN_H
#define GT_SHULEN_H

/* the repfind tool */
GtTool* gt_shulengthdist(void);

#endif
genometools-1.5.1/src/tools/gt_simreads.c000066400000000000000000000420001211610345200204340ustar00rootroot00000000000000/*
  Copyright (c) 2009-2010 Giorgio Gonnella 
  Copyright (c) 2010 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/str.h"
#include "core/disc_distri_api.h"
#include "core/encseq.h"
#include "core/fasta.h"
#include "core/fa.h"
#include "core/file_api.h"
#include "core/fileutils.h"
#include "core/logger.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/progressbar.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "tools/gt_simreads.h"

typedef struct {
  unsigned long num, minlen, maxlen, coverage;
  bool show_progressbar, verbose, ds, dl, singlestrand;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
  GtStr *dsfilename, *dlfilename, *distlen_filename;
  FILE *distlen_file;
} GtSimreadsArguments;

static void* gt_simreads_arguments_new(void)
{
  GtSimreadsArguments *arguments = gt_calloc((size_t)1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  arguments->distlen_filename = gt_str_new();
  arguments->distlen_file = NULL;
  arguments->dsfilename = gt_str_new();
  arguments->dlfilename = gt_str_new();
  return arguments;
}

static void gt_simreads_arguments_delete(void *tool_arguments)
{
  GtSimreadsArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  if (arguments->distlen_file != NULL)
    gt_fa_fclose(arguments->distlen_file);
  gt_str_delete(arguments->distlen_filename);
  gt_str_delete(arguments->dsfilename);
  gt_str_delete(arguments->dlfilename);
  gt_free(arguments);
}

static GtOptionParser* gt_simreads_option_parser_new(void *tool_arguments)
{
  GtSimreadsArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *num_option, *coverage_option, *len_option,
           *minlen_option, *maxlen_option, *p_option, *v_option,
           *dl_option, *ds_option, *ss_option, *distlen_option;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] ",
                         "Simulate sequencing reads from "
                         "random positions in the input sequence(s).");

  /* -num */
  num_option = gt_option_new_ulong_min("num", "desired number of reads",
                                       &arguments->num, GT_UNDEF_ULONG, 1UL);
  gt_option_parser_add_option(op, num_option);

  /* -coverage */
  coverage_option = gt_option_new_ulong_min("coverage",
                                            "desired coverage of the reads",
                                            &arguments->coverage,
                                            GT_UNDEF_ULONG, 1UL);
  gt_option_parser_add_option(op, coverage_option);

  /* -len */
  len_option = gt_option_new_ulong_min("len", "fixed read length",
                                               &arguments->minlen,
                                               GT_UNDEF_ULONG, 1UL);
  gt_option_parser_add_option(op, len_option);

  /* -minlen */
  minlen_option = gt_option_new_ulong_min("minlen",
                                          "minimal read length",
                                          &arguments->minlen,
                                          GT_UNDEF_ULONG, 1UL);
  gt_option_parser_add_option(op, minlen_option);

  /* -maxlen */
  maxlen_option = gt_option_new_ulong_min("maxlen",
                                          "maximal read length",
                                          &arguments->maxlen,
                                          GT_UNDEF_ULONG, 1UL);
  gt_option_parser_add_option(op, maxlen_option);

  /* -distlen */
  distlen_option = gt_option_new_string("distlen",
      "use read length distribution file\n"
      "(in the output format of the seqstat tool)",
      arguments->distlen_filename, NULL);
  gt_option_parser_add_option(op, distlen_option);

  /* output file options */;
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  /* -p */
  p_option = gt_option_new_bool("p", "show a progress bar",
                                &arguments->show_progressbar, false);
  gt_option_parser_add_option(op, p_option);

  /* -v */
  v_option = gt_option_new_bool("v", "be verbose",
                                &arguments->verbose, false);
  gt_option_parser_add_option(op, v_option);

  /* -ds */
  ds_option = gt_option_new_string("ds", "output distribution of starting"
                                       " positions to specified file",
                                   arguments->dsfilename, NULL);
  gt_option_parser_add_option(op, ds_option);
  gt_option_is_extended_option(ds_option);

  /* -dl */
  dl_option = gt_option_new_string("dl", "output distribution of read lengths"
                                       " to specified file",
                                   arguments->dlfilename, NULL);
  gt_option_parser_add_option(op, dl_option);
  gt_option_is_extended_option(dl_option);

  /* -ss */
  ss_option = gt_option_new_bool("ss", "simulate reads in forward direction "
                                 "only", &arguments->singlestrand, false);
  gt_option_parser_add_option(op, ss_option);

  gt_option_is_mandatory_either(num_option, coverage_option);
  gt_option_is_mandatory_either_3(len_option, minlen_option, distlen_option);
  gt_option_imply(minlen_option, maxlen_option);
  gt_option_imply(maxlen_option, minlen_option);
  gt_option_exclude(maxlen_option, len_option);
  gt_option_exclude(maxlen_option, distlen_option);
  gt_option_exclude(minlen_option, len_option);
  gt_option_exclude(minlen_option, distlen_option);
  gt_option_exclude(len_option, distlen_option);
  gt_option_exclude(len_option, dl_option);

  gt_option_parser_set_min_max_args(op, 1U, 1U);

  gt_option_parser_set_mail_address(op,"");

  return op;
}

static int gt_simreads_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments, GtError *err)
{
  GtSimreadsArguments *arguments = tool_arguments;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  arguments->dl = (gt_str_length(arguments->dlfilename) > 0);
  arguments->ds = (gt_str_length(arguments->dsfilename) > 0);

  if ((arguments->maxlen != GT_UNDEF_ULONG) &&
      (arguments->minlen > arguments->maxlen)) {
    gt_error_set(err,
      "argument to option '-minlen' must be <= argument to option '-maxlen'");
    had_err = -1;
  }

  /* cannot use imply with outputfile_register_options registered options: */
  if (!had_err && arguments->show_progressbar && !arguments->outfp)
  {
    gt_error_set(err, "option \"-p\" requires option \"-o\"");
    had_err = -1;
  }

  if (!had_err && gt_str_length(arguments->distlen_filename) > 0)
  {
    if (gt_file_exists(gt_str_get(arguments->distlen_filename)))
    {
      arguments->distlen_file =
        gt_fa_fopen(gt_str_get(arguments->distlen_filename), "rb", err);
      if (arguments->distlen_file == NULL)
        had_err = -1;
    }
    else
    {
      gt_error_set(err, "file %s not found",
          gt_str_get(arguments->distlen_filename));
      had_err = -1;
    }
  }

  if (had_err != 0)
    gt_file_delete(arguments->outfp);

  return had_err;
}

static int gt_simreads_plot_disc_distri(unsigned long key,
                                        unsigned long long value,
                                        GtFile *outfile)
{
  gt_file_xprintf(outfile, "%lu %llu\n", key, value);
  return 0;
}

static int gt_simreads_write_dist_file(const char *title, GtDiscDistri *dist,
                                       GtStr *filename, GtError *err)
{
  int had_err = 0;
  GtFile *dfile;

  gt_assert(filename);
  gt_assert(dist);
  gt_error_check(err);
  dfile = gt_file_new(gt_str_get(filename), "w", err);
  if (!dfile)
  {
    had_err = -1;
  }
  else
  {
    gt_file_xprintf(dfile, "%s", title);
    gt_disc_distri_foreach(dist,
     (GtDiscDistriIterFunc) gt_simreads_plot_disc_distri, dfile);
    gt_file_delete(dfile);
  }
  return had_err;
}

typedef struct {
  unsigned long value;
  unsigned long length;
} GtSimreadsDistvalue;

static unsigned long gt_simreads_readlen_from_dist(
    const GtSimreadsDistvalue *dist, const unsigned long value,
    const unsigned long nofvalues)
{
  unsigned long l = 0, r = nofvalues - 1, m = r >> 1;
  while (value != dist[m].value)
  {
    if (value < dist[m].value)
    {
      gt_assert(l <= r);
      if (m == 0 || value > dist[m - 1].value)
        return dist[m].length;
      else
        r = m - 1;
    }
    else
    {
      gt_assert(m < nofvalues - 1);
      l = m + 1;
    }
    m = l + ((r - l) >> 1);
  }
  return dist[m].length;
}

static int gt_simreads_runner(GT_UNUSED int argc,
                              const char **argv, int parsed_args,
                              void *tool_arguments, GtError *err)
{
  GtSimreadsArguments *arguments = tool_arguments;
  GtEncseq *target = NULL;
  GtEncseqLoader *target_loader = NULL;
  GtEncseqReader *target_reader = NULL;
  GtReadmode readmode;
  GtStr *read = NULL, *description = NULL;
  unsigned long output_bases = 0, output_reads = 0,
                output_rcmode_reads = 0,
                required_output_bases = 0,
                target_total_length,
                startpos, readlen, i;
  unsigned long long progress = 0;
  bool fixed_readlen;
  int had_err = 0;
  GtUchar ch;
  GtLogger *logger = NULL;
  GtDiscDistri *lengths = NULL, *starts = NULL;
  GtSimreadsDistvalue *input_distlen = NULL;
  off_t j, nofvalues = 0;

  gt_error_check(err);
  gt_assert(arguments);

  logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stderr);
  fixed_readlen = (arguments->maxlen == GT_UNDEF_ULONG &&
      arguments->minlen != GT_UNDEF_ULONG);
  if (arguments->ds)
    starts = gt_disc_distri_new();
  if (arguments->dl)
    lengths = gt_disc_distri_new();
  readlen = arguments->minlen;

  /* load encseq */
  target_loader = gt_encseq_loader_new();
  target = gt_encseq_loader_load(target_loader, argv[parsed_args], err);
  if (target == NULL)
    had_err = -1;
  if (!had_err) {
    target_reader = gt_encseq_create_reader_with_readmode(target,
                                                          GT_READMODE_FORWARD,
                                                          0);
  }

  if (!had_err)
  {
    target_total_length = gt_encseq_total_length(target);
    gt_logger_log(logger, "number of templates: %lu",
                  gt_encseq_num_of_sequences(target));
    gt_logger_log(logger, "total template length: %lu",
                  target_total_length);
    if (arguments->coverage != GT_UNDEF_ULONG)
    {
      gt_logger_log(logger, "required coverage: %lu",
                            arguments->coverage);
      required_output_bases = arguments->coverage * target_total_length;
      if (arguments->show_progressbar)
        gt_progressbar_start(&progress,
            (unsigned long long)required_output_bases);
    }
    else
    {
      gt_assert(arguments->num != GT_UNDEF_ULONG);
      gt_logger_log(logger, "required number of reads: %lu",
                            arguments->num);
      if (arguments->show_progressbar)
        gt_progressbar_start(&progress, (unsigned long long)arguments->num);
    }
    read = gt_str_new();
    description = gt_str_new();
    if (arguments->distlen_file != NULL)
    {
      gt_logger_log(logger, "read length distribution file: %s",
          gt_str_get(arguments->distlen_filename));
      nofvalues = gt_file_size(gt_str_get(arguments->distlen_filename)) /
                       (off_t) (sizeof (unsigned long) << 1);
      input_distlen = gt_malloc(sizeof(GtSimreadsDistvalue) * nofvalues);
      for (j = 0; j < nofvalues; j++)
      {
        (void)gt_xfread(&(input_distlen[j].length), sizeof (unsigned long),
            (size_t)1, arguments->distlen_file);
        (void)gt_xfread(&(input_distlen[j].value), sizeof (unsigned long),
            (size_t)1, arguments->distlen_file);
      }
      for (j = (off_t)1; j < nofvalues; j++)
      {
        input_distlen[j].value += input_distlen[j - 1].value;
      }
    }
    else if (fixed_readlen)
      gt_logger_log(logger, "required read length (fixed): %lu",
                    arguments->minlen);
    else
      gt_logger_log(logger, "required read length range: %lu-%lu",
                    arguments->minlen, arguments->maxlen);
  }

  while (!had_err)
  {
    gt_str_reset(read);
    if (!fixed_readlen)
    {
      if (arguments->distlen_file != NULL)
      {
        gt_assert(input_distlen != NULL);
        readlen = gt_simreads_readlen_from_dist(input_distlen,
            gt_rand_max(input_distlen[nofvalues - 1].value),
            (unsigned long)nofvalues);
        gt_assert(readlen <= input_distlen[nofvalues - 1].value);
      }
      else
      {
        readlen = gt_rand_max(arguments->maxlen -
            arguments->minlen) + arguments->minlen;
      }
      if (arguments->dl)
        gt_disc_distri_add(lengths, readlen);
    }
    gt_assert(target_total_length > readlen);
    startpos = gt_rand_max(target_total_length - readlen);
    readmode = (arguments->singlestrand || gt_rand_max(1UL)
      ? GT_READMODE_FORWARD : GT_READMODE_REVCOMPL);
    gt_encseq_reader_reinit_with_readmode(target_reader, target,
                                          readmode, startpos);
    for (i = 0; i < readlen; i++)
    {
      ch = gt_encseq_reader_next_encoded_char(target_reader);
      if (ch == (GtUchar)SEPARATOR)
      {
        break;
      }
      else
      {
        gt_str_append_char(read, gt_alphabet_decode(
                             gt_encseq_alphabet(target), ch));
      }
    }
    if (i < readlen)
    {
      /* a separator was found, discard read and restart */
      continue;
    }
    else
    {
      gt_str_reset(description);
      gt_str_append_cstr(description, "read_");
      gt_str_append_ulong(description, output_reads);
      gt_fasta_show_entry(gt_str_get(description),
                          gt_str_get(read),
                          gt_str_length(read),
                          60UL,
                          arguments->outfp);
      output_bases += gt_str_length(read);
      output_reads++;
      if (arguments->verbose && readmode == GT_READMODE_FORWARD)
        output_rcmode_reads++;
      if (arguments->ds)
      {
        if (readmode == GT_READMODE_FORWARD)
          gt_disc_distri_add(starts, startpos);
        else
          gt_disc_distri_add(starts, target_total_length - 1 - startpos);
      }
    }

    /* test break conditions and update progressbar */
    if (arguments->coverage != GT_UNDEF_ULONG)
    {
      if (arguments->show_progressbar)
        progress = (unsigned long long)output_bases;
      if (output_bases >= required_output_bases)
        break;
    }
    else
    {
      gt_assert(arguments->num != GT_UNDEF_ULONG);
      if (arguments->show_progressbar)
        progress = (unsigned long long)output_reads;
      if (output_reads == arguments->num)
        break;
    }
  }

  if (!had_err)
  {
    gt_logger_log(logger, "coverage: %.3f",
                  (float) output_bases / target_total_length);
    gt_logger_log(logger, "total reads length: %lu", output_bases);
    if (!fixed_readlen)
      gt_logger_log(logger, "average reads length: %.1f",
                    (float) output_bases / output_reads);
    gt_logger_log(logger, "number of reads: %lu", output_reads);
    gt_logger_log(logger, "- forward: %lu", output_reads-output_rcmode_reads);
    gt_logger_log(logger, "- revcompl: %lu", output_rcmode_reads);
  }

  if (!had_err && arguments->dl)
    had_err = gt_simreads_write_dist_file(
                   "# distribution of read lengths:\n", lengths,
                   arguments->dlfilename, err);
  if (!had_err && arguments->ds)
    had_err = gt_simreads_write_dist_file(
                   "# distribution of start positions:\n", starts,
                   arguments->dsfilename, err);

  if (arguments->show_progressbar)
    gt_progressbar_stop();
  gt_free(input_distlen);
  gt_str_delete(read);
  gt_str_delete(description);
  gt_encseq_reader_delete(target_reader);
  gt_encseq_loader_delete(target_loader);
  gt_encseq_delete(target);
  gt_logger_delete(logger);
  if (arguments->dl)
    gt_disc_distri_delete(lengths);
  if (arguments->ds)
    gt_disc_distri_delete(starts);
  return had_err;
}

GtTool* gt_simreads(void)
{
  return gt_tool_new(gt_simreads_arguments_new,
                     gt_simreads_arguments_delete,
                     gt_simreads_option_parser_new,
                     gt_simreads_arguments_check,
                     gt_simreads_runner);
}
genometools-1.5.1/src/tools/gt_simreads.h000066400000000000000000000017261211610345200204530ustar00rootroot00000000000000/*
  Copyright (c) 2009 Giorgio Gonnella 
  Copyright (c) 2009 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SIMREADS_H
#define GT_SIMREADS_H

#include "core/tool_api.h"

/* the simreads tool */
GtTool* gt_simreads(void);

#endif
genometools-1.5.1/src/tools/gt_skproto.c000066400000000000000000000125411211610345200203350ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009 Gordon Gremme 
  Copyright (c) 2001      Stefan Kurtz 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef S_SPLINT_S
#include 
#endif
#include 
#include "core/fa.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "core/warning_api.h"
#include "tools/gt_skproto.h"

#define MAX_LINE_LENGTH  80

static GtOptionParser* gt_skproto_option_parser_new(GT_UNUSED
                                                  void *tool_arguments)
{
  return gt_option_parser_new("[C-file ...]",
                           "Extract Header-File from C-file(s).");
}

static char *forbid[] = {
  "static ",
  "typedef ",
  "int main",
  "DECLAREARRAYSTRUCT(",
  "GT_DECLAREARRAYSTRUCT(",
  "/*@null@*/ static",
  "/*@unused@*/ static"
};

static unsigned char forbiddenstring(GtStr *line)
{
  size_t slen, i;
  for (i = 0; i < sizeof (forbid) / sizeof (forbid[0]); i++) {
    slen = strlen(forbid[i]);
    if (slen <= (size_t) gt_str_length(line) &&
       !strncmp(forbid[i], gt_str_get(line), slen)) {
      return (unsigned char) 1;
    }
  }
  return 0;
}

static void removecomments(GtStr *line, int *incomment)
{
  unsigned char *buffer;
  unsigned long pos=0, bufpos=0;

  if (!line || !gt_str_length(line))
    return;

  buffer = gt_malloc((size_t) gt_str_length(line) + 1);

  /* remove comments, except for those used for splint: */
  while (pos < gt_str_length(line)) {
    if (*incomment) {
      if (!strncmp(gt_str_get(line) + pos, "*/", (size_t) 2)) {
        *incomment=0;
        pos+=2;
      }
      else
        pos++;
    }
    else {
      if (gt_str_length(line)     >  (unsigned long) 2   &&
          gt_str_get(line)[pos]   == '/' &&
          gt_str_get(line)[pos+1] == '/') {
        break;
      }
      else if (!strncmp(gt_str_get(line) + pos, "/*", (size_t) 2) &&
               (pos + 2 >= gt_str_length(line) ||
                gt_str_get(line)[pos+2] != '@')) {
        *incomment=1;
        pos+=2;
      }
      else
        buffer[bufpos++] = (unsigned char) gt_str_get(line)[pos++];
    }
  }

  /* remove white spaces */
  while (bufpos && buffer[bufpos-1] == ' ')
    bufpos--;
  buffer[bufpos]='\0';

  /* copy back into line */
  memcpy(gt_str_get(line), buffer, (size_t) (bufpos + 1));
  gt_str_set_length(line, bufpos);
  gt_free(buffer);
}

static void skproto(const char *filename, FILE *fpin)
{
  int linenum = 0, startfunction = 1, incomment = 0;
  GtStr *line;

  gt_assert(filename && fpin);

  line = gt_str_new();

  while (gt_str_read_next_line(line, fpin) != EOF) {
    linenum++;
    removecomments(line, &incomment);
    if (gt_str_length(line)) {
      if (startfunction) {
        if (isalpha((int) (gt_str_get(line)[0])) ||
            (gt_str_length(line) >= (unsigned long) 3 &&
             strncmp(gt_str_get(line), "/*@", (size_t) 3) == 0)) {
          if (!forbiddenstring(line)) {
            if (gt_str_length(line) >= (unsigned long) MAX_LINE_LENGTH)
              gt_warning("file %s, line %d too long\n", filename, linenum);
            printf("%s", gt_str_get(line));
            if (gt_str_get(line)[gt_str_length(line)-1] == ')') {
              (void) putchar(';');
              (void) putchar('\n');
            }
            else
              startfunction = 0;
            (void) putchar('\n');
          }
        }
      }
      else {
        if (gt_str_length(line) >= (unsigned long) MAX_LINE_LENGTH)
          gt_warning("file %s, line %d too long\n", filename, linenum);
        printf("%s", gt_str_get(line));
        if (gt_str_get(line)[gt_str_length(line)-1] == ')') {
          (void) putchar(';');
          (void) putchar('\n');
          startfunction = 1;
        }
        (void) putchar('\n');
      }
    }
    gt_str_reset(line);
  }

  gt_str_delete(line);
}

static int gt_skproto_runner(int argc, const char **argv, int parsed_args,
                             GT_UNUSED void *tool_arguments,
                             GT_UNUSED GtError *err)
{
  FILE *fpin;
  int i;

  gt_error_check(err);

  printf("#ifdef __cplusplus\n");
  printf("extern \"C\" {\n");
  printf("#endif\n");

  if (!argc)
    skproto("(stdout)", stdin);
  else {
    for (i = parsed_args; i < argc; i++) {
      fpin = gt_fa_xfopen(argv[i], "r");
      skproto(argv[i], fpin);
      gt_fa_xfclose(fpin);
    }
  }

  printf("#ifdef __cplusplus\n");
  printf("}\n");
  printf("#endif\n");

  return 0;
}

GtTool* gt_skproto(void)
{
  return gt_tool_new(NULL,
                  NULL,
                  gt_skproto_option_parser_new,
                  NULL,
                  gt_skproto_runner);
}
genometools-1.5.1/src/tools/gt_skproto.h000066400000000000000000000020431211610345200203360ustar00rootroot00000000000000/*
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2001      Stefan Kurtz 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SKPROTO_H
#define GT_SKPROTO_H

#include "core/tool_api.h"

/* the skproto tool */
GtTool* gt_skproto(void);

#endif
genometools-1.5.1/src/tools/gt_snpper.c000066400000000000000000000131671211610345200201500ustar00rootroot00000000000000/*
  Copyright (c) 2012-2013 Sascha Steinbiss 
  Copyright (c) 2012-2013 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/trans_table_api.h"
#include "core/unused_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gtdatahelp.h"
#include "extended/seqid2file.h"
#include "extended/snp_annotator_stream.h"
#include "tools/gt_snpper.h"

typedef struct {
  GtSeqid2FileInfo *s2fi;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
  unsigned int ttable;
  GtStr *desc;
} GtSnpperArguments;

static void* gt_snpper_arguments_new(void)
{
  GtStrArray *descs;
  unsigned long i;
  GtSnpperArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  arguments->desc = gt_str_new_cstr("NCBI translation table number, "
                                    "choose from:\n");
  descs = gt_trans_table_get_scheme_descriptions();
  for (i = 0; i < gt_str_array_size(descs); i++) {
    gt_str_append_cstr(arguments->desc, gt_str_array_get(descs, i));
    if (i != gt_str_array_size(descs)-1)
      gt_str_append_cstr(arguments->desc, "\n");
  }
  gt_str_array_delete(descs);
  return arguments;
}

static void gt_snpper_arguments_delete(void *tool_arguments)
{
  GtSnpperArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_str_delete(arguments->desc);
  gt_output_file_info_delete(arguments->ofi);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_free(arguments);
}

static GtOptionParser* gt_snpper_option_parser_new(void *tool_arguments)
{
  GtSnpperArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] GFF3_file [GVF_file]",
                            "Annotates SNPs according to their effect on "
                            "the genome as given by a genomic annotation.");

  /* -trans_table */
  option = gt_option_new_uint("trans_table", gt_str_get(arguments->desc),
                              &arguments->ttable, 1);
  gt_option_parser_add_option(op, option);

  /* -seqfile, -encseq, -matchdesc, -usedesc and -regionmapping */
  gt_seqid2file_register_options(op, arguments->s2fi);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_min_max_args(op, 1, 2);

  return op;
}

static int gt_snpper_runner(GT_UNUSED int argc, const char **argv,
                                 int parsed_args, void *tool_arguments,
                                 GtError *err)
{
  GtNodeStream *gff3_in_stream = NULL,
               *gvf_in_stream = NULL,
               *gvf_out_stream = NULL,
               *snp_annotator_stream = NULL;
  GtSnpperArguments *arguments = tool_arguments;
  GtRegionMapping *region_mapping = NULL;
  GtTransTable *tt = NULL;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (!(tt = gt_trans_table_new(arguments->ttable, err)))
    had_err = -1;

  if (!had_err) {
    /* create GFF3 input stream */
    gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
    if (!gff3_in_stream)
      had_err = -1;
  }

  if (!had_err) {
    /* create GVF input stream */
    gvf_in_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args+1]);
    if (!gvf_in_stream)
      had_err = -1;
  }

  if (!had_err) {
    /* create region mapping */
    region_mapping = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
    if (!region_mapping)
      had_err = -1;
  }

  if (!had_err) {
    gt_assert(tt);
    snp_annotator_stream = gt_snp_annotator_stream_new(gvf_in_stream,
                                                       gff3_in_stream,
                                                       tt,
                                                       region_mapping);
    if (!snp_annotator_stream)
      had_err = -1;
  }

  if (!had_err) {
    gvf_out_stream = gt_gff3_out_stream_new(snp_annotator_stream,
                                            arguments->outfp);
    if (!gvf_out_stream)
      had_err = -1;
  }

  if (!had_err) {
    /* pull the features through the stream and free them afterwards */
    had_err = gt_node_stream_pull(gvf_out_stream, err);
  }

  /* free */
  gt_node_stream_delete(snp_annotator_stream);
  gt_node_stream_delete(gff3_in_stream);
  gt_node_stream_delete(gvf_in_stream);
  gt_node_stream_delete(gvf_out_stream);
  gt_trans_table_delete(tt);
  gt_region_mapping_delete(region_mapping);

  return had_err;
}

GtTool* gt_snpper(void)
{
  return gt_tool_new(gt_snpper_arguments_new,
                     gt_snpper_arguments_delete,
                     gt_snpper_option_parser_new,
                     NULL,
                     gt_snpper_runner);
}
genometools-1.5.1/src/tools/gt_snpper.h000066400000000000000000000017311211610345200201470ustar00rootroot00000000000000/*
  Copyright (c) 2012 Sascha Steinbiss 
  Copyright (c) 2012 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SNPPER_H
#define GT_SNPPER_H

#include "core/tool_api.h"

/* the SNPPER tool */
GtTool* gt_snpper(void);

#endif
genometools-1.5.1/src/tools/gt_sortbench.c000066400000000000000000000260441211610345200206260ustar00rootroot00000000000000/*
  Copyright (c) 2010-2011 Sascha Steinbiss 
  Copyright (c) 2010-2011 Stefan Kurtz 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include 
#include 
#include 
#include "core/assert_api.h"
#include "core/ma.h"
#include "core/mathsupport.h"
#include "core/qsort_r.h"
#include "core/str.h"
#include "core/timer.h"
#include "core/radix_sort.h"
#include "core/unused_api.h"
#include "core/qsort-ulong.h"
#include "tools/gt_sortbench.h"
#ifdef GT_THREADS_ENABLED
#include "core/thread_api.h"
#endif

typedef struct {
  GtStr *impl;
  unsigned long num_values,
                maxvalue;
  bool use_aqsort,
       use_permute,
       verbose;
} QSortBenchArguments;

static void *gt_sortbench_arguments_new(void)
{
  QSortBenchArguments *arguments = gt_calloc((size_t) 1, sizeof *arguments);
  arguments->impl = gt_str_new();
  return arguments;
}

static void gt_sortbench_arguments_delete(void *tool_arguments)
{
  QSortBenchArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->impl);
  gt_free(arguments);
}

static const char *gt_sort_implementation_names[]
    = {"thomas","system","inlinedptr","inlinedarr","direct",
       "radixinplace","radixlsb",NULL};

static GtOptionParser* gt_sortbench_option_parser_new(void *tool_arguments)
{
  QSortBenchArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...]",
                            "Benchmarks quicksort implementations.");

  option = gt_option_new_choice(
                 "impl", "implementation\nchoose from "
                 "thomas|system|inlinedptr|inlinedarr|direct|\n"
                 "radixinplace|radixlsb",
                  arguments->impl,
                  gt_sort_implementation_names[0],
                  gt_sort_implementation_names);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("size", "number of integers to sort",
                               &arguments->num_values, 1000000UL);
  gt_option_parser_add_option(op, option);

  /* default set to ULONG_MAX-1 to facilitate proper testing of the
     radixsort implementations (make sure that higher order bits are set) */
  option = gt_option_new_ulong("maxval", "maximal integer to sort",
                               &arguments->maxvalue, ULONG_MAX-1);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("aqsort", "prepare bad input array using the "
                                        "'aqsort' anti-quicksort algorithm",
                               &arguments->use_aqsort, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("permute", "prepare bad input array by "
                                         "permutation of unique items",
                               &arguments->use_permute, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);
  return op;
}

static int gt_sortbench_arguments_check(GT_UNUSED int rest_argc,
                                        void *tool_arguments,
                                        GT_UNUSED GtError *err)
{
  GT_UNUSED QSortBenchArguments *arguments = tool_arguments;
  int had_err = 0;

  gt_assert(arguments != NULL);
  return had_err;
}

static void gt_qbenchsort_permute_ulong_array (unsigned long *arr,
                                               unsigned long size)
{
  unsigned long i, j, c;

  for (i = 0; i < size; ++i)
  {
    j = gt_rand_max(size-1);
    c = arr[i];
    arr[i] = arr[j];
    arr[j] = c;
  }
}

unsigned long *val;         /* array, solidified on the fly */
unsigned long ncmp;         /* number of comparisons */
unsigned long nsolid;       /* number of solid items */
unsigned long candidate;    /* pivot candidate */
unsigned long gas;          /* gas value = highest sorted value */
#define freeze(x) val[x] = nsolid++

static int gt_sortbench_cmp(const void *px, const void *py)
{
  const unsigned long x = *(const unsigned long*)px;
  const unsigned long y = *(const unsigned long*)py;
  ncmp++;
  if (val[x]==gas && val[y]==gas) {
    if (x == candidate) {
      freeze(x);
    } else {
      freeze(y);
    }
  }
  if (val[x] == gas)
    candidate = x;
  else if (val[y] == gas)
    candidate = y;
  if (val[x] < val[y])
  {
    return -1;
  }
  if (val[x] > val[y])
  {
    return 1;
  }
  return 0;
}

static void gt_sortbench_aqsort(unsigned long n, unsigned long *a)
{
  unsigned long i;
  unsigned long *ptr = gt_malloc(sizeof (*ptr) * n);

  val = a;
  gas = n-1;
  nsolid = ncmp = candidate = 0;
  for (i=0; i (*b))
  {
    return 1;
  }
  return 0;
}

#ifdef  QSORTNAME
#undef  QSORTNAME
#endif

#define QSORTNAME(NAME) sortbench_##NAME

#define sortbench_ARRAY_GET(ARR,RELIDX) ARR[RELIDX]

#define sortbench_ARRAY_SET(ARR,RELIDX,VALUE) ARR[RELIDX] = VALUE

typedef void * QSORTNAME(Datatype);

typedef unsigned long QSORTNAME(Sorttype);

static int QSORTNAME(qsortcmparr)(const QSORTNAME(Sorttype) *arr,
                                  unsigned long a,
                                  unsigned long b,
                                  const GT_UNUSED void *data)
{
  cmpcount++;
  if (arr[a] < arr[b])
  {
    return -1;
  }
  if (arr[a] > arr[b])
  {
    return 1;
  }
  return 0;
}

static void gt_sortbench_verify(GT_UNUSED const unsigned long *arr,
                                 unsigned long len)
{
  unsigned long idx;

  for (idx = 1UL; idx < len; idx++)
  {
    gt_assert(arr[idx-1] <= arr[idx]);
  }
  printf("verified\n");
}

#include "match/qsort-array.gen"

static void check_inlinedarr_qsort(unsigned long *arr, unsigned long len)
{
  QSORTNAME(gt_inlinedarr_qsort_r) (6UL, false, arr, len, NULL);
  gt_sortbench_verify(arr,len);
}

static void check_direct_qsort(unsigned long *arr, unsigned long len)
{
  gt_direct_qsort_ulong (6UL, false, arr, len);
  gt_sortbench_verify(arr,len);
}

static int sortcmpwithdata(const void *a,const void *b, GT_UNUSED void *data)
{
  cmpcount++;
  if (*(Sorttype*)a < *((Sorttype*)b))
  {
    return -1;
  }
  if (*(Sorttype*)a > *(Sorttype*)b)
  {
    return 1;
  }
  return 0;
}

#include "match/qsort-inplace.gen"

static void check_thomas_qsort(unsigned long *arr, unsigned long len)
{
  gt_qsort_r(arr,(size_t) len,sizeof (Sorttype),NULL, sortcmpwithdata);
  gt_sortbench_verify(arr,len);
}

static int sortcmpnodata(const void *a,const void *b)
{
  cmpcount++;
  if (*(Sorttype*)a < *((Sorttype*)b))
  {
    return -1;
  }
  if (*(Sorttype*)a > *(Sorttype*)b)
  {
    return 1;
  }
  return 0;
}

static void check_gnu_qsort(unsigned long *arr, unsigned long len)
{
  qsort(arr,(size_t) len, sizeof (Sorttype), sortcmpnodata);
  gt_sortbench_verify(arr,len);
}

static void check_inlinedptr_qsort(unsigned long *arr, unsigned long len)
{
  gt_inlined_qsort_r(arr, len, NULL);
  gt_sortbench_verify(arr,len);
}

static void check_radixsort_lsb(unsigned long *arr, unsigned long len)
{
  /* note that lsb_linear allocates extra temp space of size equal to
     the area to be sorted */
  gt_radixsort_lsb_linear(arr,len);
  gt_sortbench_verify(arr,len);
}

static void check_radixsort_inplace(unsigned long *arr, unsigned long len)
{
  gt_radixsort_inplace_ulong(arr,len);
  gt_sortbench_verify(arr,len);
}

typedef void (*GtQsortimplementationfunc)(unsigned long *,unsigned long);

static GtQsortimplementationfunc gt_sort_implementation_funcs[] =
{
  check_thomas_qsort,
  check_gnu_qsort,
  check_inlinedptr_qsort,
  check_inlinedarr_qsort,
  check_direct_qsort,
  check_radixsort_inplace,
  check_radixsort_lsb
};

#define GT_NUM_OF_SORT_IMPLEMENTATIONS\
        (sizeof (gt_sort_implementation_funcs)/\
         sizeof (gt_sort_implementation_funcs[0]))

static int gt_sortbench_runner(GT_UNUSED int argc, GT_UNUSED const char **argv,
                                GT_UNUSED int parsed_args,
                                void *tool_arguments, GT_UNUSED GtError *err)
{
  QSortBenchArguments *arguments = tool_arguments;
  int had_err = 0;
  size_t method;
  GtTimer *timer;
  unsigned long *array, idx;

  gt_error_check(err);
  gt_assert(arguments);
  if (arguments->verbose) {
    printf("# number of items = %lu\n", arguments->num_values);
    printf("# max value items = %lu\n", arguments->maxvalue);
    printf("# implementation = %s\n", gt_str_get(arguments->impl));
  }

  /* prepare benchmark input data */
  array = gt_malloc(sizeof (*array) * arguments->num_values );
  if (arguments->use_aqsort) {
    if (arguments->verbose)
      printf("# using aqsort\n");
    gt_sortbench_aqsort(arguments->num_values, array);
  } else if (arguments->use_permute) {
    if (arguments->verbose)
      printf("# using permuted array\n");
    for (idx = 0; idx < arguments->num_values; idx++) {
      array[idx] = idx;
    }
    gt_qbenchsort_permute_ulong_array(array, arguments->num_values);
  } else {
    if (arguments->verbose)
      printf("# using simple array of random numbers\n");
    /* use seed initialization to make array deterministic */
    srand48(366292341);
    for (idx = 0; idx < arguments->num_values; idx++) {
      array[idx] = drand48() * arguments->maxvalue;
    }
  }

  timer = gt_timer_new();
  gt_timer_start(timer);
  /* run implementation */
  for (method = 0; method < GT_NUM_OF_SORT_IMPLEMENTATIONS; method++)
  {
    if (strcmp(gt_str_get(arguments->impl),
               gt_sort_implementation_names[method]) == 0)
    {
      gt_sort_implementation_funcs[method](array, arguments->num_values);
      break;
    }
  }
  gt_timer_show(timer, stdout);
  gt_timer_delete(timer);
  gt_free(array);
  if (cmpcount > 0)
  {
    printf("cmpcount = %lu\n",cmpcount);
  }
  return had_err;
}

GtTool* gt_sortbench(void)
{
  return gt_tool_new(gt_sortbench_arguments_new,
                     gt_sortbench_arguments_delete,
                     gt_sortbench_option_parser_new,
                     gt_sortbench_arguments_check,
                     gt_sortbench_runner);
}
genometools-1.5.1/src/tools/gt_sortbench.h000066400000000000000000000017301211610345200206260ustar00rootroot00000000000000/*
  Copyright (c) CCYY YOUR NAME HERE 
  Copyright (c) CCYY Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SORTBENCH_H
#define GT_SORTBENCH_H

#include "core/tool_api.h"

/* the sortbench tool */
GtTool* gt_sortbench(void);

#endif
genometools-1.5.1/src/tools/gt_splicesiteinfo.c000066400000000000000000000122011211610345200216450ustar00rootroot00000000000000/*
  Copyright (c) 2007-2011 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/versionfunc.h"
#include "core/warning_api.h"
#include "extended/add_introns_stream_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/splice_site_info_stream.h"
#include "extended/gtdatahelp.h"
#include "extended/seqid2file.h"
#include "tools/gt_splicesiteinfo.h"

typedef struct {
  bool addintrons;
  GtSeqid2FileInfo *s2fi;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} SpliceSiteInfoArguments;

static void* gt_splicesiteinfo_arguments_new(void)
{
  SpliceSiteInfoArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->s2fi = gt_seqid2file_info_new();
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_splicesiteinfo_arguments_delete(void *tool_arguments)
{
  SpliceSiteInfoArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_seqid2file_info_delete(arguments->s2fi);
  gt_free(arguments);
}

static GtOptionParser* gt_splicesiteinfo_option_parser_new(void *tool_arguments)
{
  SpliceSiteInfoArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  op = gt_option_parser_new("[option ...] [GFF3_file ...]", "Show information "
                            "about splice sites given in GFF3 files.");

  /* -seqfile, -matchdesc, -usedesc and -regionmapping */
  gt_seqid2file_register_options(op, arguments->s2fi);

  /* -addintrons */
  option = gt_option_new_bool("addintrons", "add intron features between "
                              "existing exon features\n(before computing the "
                              "information to be shown)",
                              &arguments->addintrons, false);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);

  return op;
}

static int gt_splicesiteinfo_runner(int argc, const char **argv,
                                    int parsed_args, void *tool_arguments,
                                    GtError *err)
{
  SpliceSiteInfoArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream = NULL,
               *add_introns_stream = NULL,
               *splice_site_info_stream = NULL;
  GtRegionMapping *region_mapping;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  if (!had_err) {
    /* create gff3 input stream */
    gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                    argv + parsed_args);

    /* create region mapping */
    region_mapping = gt_seqid2file_region_mapping_new(arguments->s2fi, err);
    if (!region_mapping)
      had_err = -1;
  }

  if (!had_err) {
    /* create addintrons stream (if necessary) */
    if (arguments->addintrons)
      add_introns_stream = gt_add_introns_stream_new(gff3_in_stream);

    /* create extract feature stream */
    splice_site_info_stream = gt_splice_site_info_stream_new(
                                                          arguments->addintrons
                                                          ? add_introns_stream
                                                          : gff3_in_stream,
                                                          region_mapping);

    /* pull the features through the stream and free them afterwards */
    had_err = gt_node_stream_pull(splice_site_info_stream, err);
  }

  if (!had_err) {
    if (!gt_splice_site_info_stream_show(splice_site_info_stream,
                                         arguments->outfp)) {
      gt_warning("input file(s) contained no intron, use option -addintrons to "
                 "add introns automatically");
    }
  }

  /* free */
  gt_node_stream_delete(splice_site_info_stream);
  gt_node_stream_delete(add_introns_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool* gt_splicesiteinfo(void)
{
  return gt_tool_new(gt_splicesiteinfo_arguments_new,
                     gt_splicesiteinfo_arguments_delete,
                     gt_splicesiteinfo_option_parser_new,
                     NULL,
                     gt_splicesiteinfo_runner);
}
genometools-1.5.1/src/tools/gt_splicesiteinfo.h000066400000000000000000000017651211610345200216670ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SPLICESITEINFO_H
#define GT_SPLICESITEINFO_H

#include "core/tool_api.h"

/* the splice site info tool */
GtTool* gt_splicesiteinfo(void);

#endif
genometools-1.5.1/src/tools/gt_splitfasta.c000066400000000000000000000227541211610345200210150ustar00rootroot00000000000000/*
  Copyright (c) 2003-2010 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/bioseq.h"
#include "core/fa.h"
#include "core/fasta.h"
#include "core/fileutils_api.h"
#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file.h"
#include "core/unused_api.h"
#include "core/xansi_api.h"
#include "tools/gt_splitfasta.h"

typedef struct {
  unsigned long max_filesize_in_MB, width;
  unsigned int num_files;
  GtStr *splitdesc;
  bool force;
} SplitfastaArguments;

static void* gt_splitfasta_arguments_new(void)
{
  SplitfastaArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->splitdesc = gt_str_new();
  return arguments;
}

void gt_splitfasta_arguments_delete(void *tool_arguments)
{
  SplitfastaArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->splitdesc);
  gt_free(arguments);
}

static GtOptionParser* gt_splitfasta_option_parser_new(void *tool_arguments)
{
  SplitfastaArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *targetsize_option, *splitdesc_option, *o, *numfiles_option;
  gt_assert(arguments);
  op = gt_option_parser_new("[option ...] fastafile","Split the supplied fasta "
                         "file.");

  numfiles_option = gt_option_new_uint_min("numfiles",
                                           "set the number of target files "
                                           "",
                                           &arguments->num_files, 0,
                                           1);
  gt_option_parser_add_option(op, numfiles_option);

  targetsize_option = gt_option_new_ulong_min("targetsize",
                                              "set the target file "
                                              "size in MB",
                                              &arguments->max_filesize_in_MB,
                                              50, 1);
  gt_option_parser_add_option(op, targetsize_option);
  splitdesc_option = gt_option_new_string("splitdesc",
                                          "put every fasta entry in "
                                          "a separate file named by its "
                                          "description in the given directory",
                                          arguments->splitdesc, NULL);
  gt_option_parser_add_option(op, splitdesc_option);
  gt_option_exclude(targetsize_option, splitdesc_option);
  gt_option_exclude(numfiles_option, splitdesc_option);
  gt_option_exclude(numfiles_option, targetsize_option);
  o = gt_option_new_width(&arguments->width);
  gt_option_parser_add_option(op, o);
  o = gt_option_new_bool(GT_FORCE_OPT_CSTR, "force writing to output file",
                         &arguments->force, false);
  gt_option_parser_add_option(op, o);
  gt_option_parser_set_min_max_args(op, 1, 1);
  return op;
}

static unsigned long buf_contains_separator(char *buf, int offset,
                                            int read_bytes)
{
  char *cc;
  gt_assert(buf && offset < read_bytes);
  for (cc = buf + offset; cc < buf + read_bytes; cc++) {
    if (*cc == '>')
      return cc - buf + 1;
  }
  return 0;
}

static int split_description(const char *filename, GtStr *splitdesc,
                             unsigned long width, bool force, GtError *err)
{
  unsigned long i;
  GtBioseq *bioseq;
  GtStr *descname;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(filename && splitdesc && gt_str_length(splitdesc));

  descname = gt_str_new();
  if (!(bioseq = gt_bioseq_new(filename, err)))
    had_err = -1;

  for (i = 0; !had_err && i < gt_bioseq_number_of_sequences(bioseq); i++) {
    GtFile *outfp;
    char *seq;
    gt_str_reset(descname);
    gt_str_append_str(descname, splitdesc);
    gt_str_append_char(descname, '/');
    gt_str_append_cstr(descname, gt_bioseq_get_description(bioseq, i));
    gt_str_append_cstr(descname, gt_file_suffix(filename));
    if (!(outfp = gt_output_file_xopen_forcecheck(gt_str_get(descname), "w",
                                                 force, err))) {
      had_err = -1;
      break;
    }
    seq = gt_bioseq_get_sequence(bioseq, i);
    gt_fasta_show_entry(gt_bioseq_get_description(bioseq, i), seq,
                        gt_bioseq_get_sequence_length(bioseq, i), width,
                        outfp);
    gt_free(seq);
    gt_file_delete(outfp);
  }

  gt_bioseq_delete(bioseq);
  gt_str_delete(descname);

  return had_err;
}

static int split_fasta_file(const char *filename, unsigned long max_filesize,
                            bool force, GtError *err)
{
  GtFile *srcfp = NULL, *destfp = NULL;
  GtStr *destfilename = NULL;
  unsigned long filenum = 0, bytecount = 0, separator_pos;
  int read_bytes, had_err = 0;
  char buf[BUFSIZ];

  gt_error_check(err);
  gt_assert(filename && max_filesize);

  /* open source file */
  srcfp = gt_file_xopen(filename, "r");
  gt_assert(srcfp);

  /* read start characters */
  if ((read_bytes = gt_file_xread(srcfp, buf, BUFSIZ)) == 0) {
    gt_error_set(err, "file \"%s\" is empty", filename);
    had_err = -1;
  }
  bytecount += read_bytes;

  /* make sure the file is in fasta format */
  if (!had_err && buf[0] != '>') {
    gt_error_set(err, "file is not in FASTA format");
    had_err = -1;
  }

  if (!had_err) {
    /* open destination file */
    destfilename = gt_str_new();
    gt_str_append_cstr_nt(destfilename, filename,
                          gt_file_basename_length(filename));
    gt_str_append_char(destfilename, '.');
    gt_str_append_ulong(destfilename, ++filenum);
    gt_str_append_cstr(destfilename,
                       gt_file_mode_suffix(gt_file_mode(srcfp)));
    if (!(destfp = gt_output_file_xopen_forcecheck(gt_str_get(destfilename),
                                                  "w",
                                                  force, err))) {
      had_err = -1;
    }
    if (!had_err)
      gt_file_xwrite(destfp, buf, read_bytes);

    while (!had_err &&
           (read_bytes = gt_file_xread(srcfp, buf, BUFSIZ)) != 0) {
      if (bytecount + read_bytes > max_filesize) {
        int offset = bytecount < max_filesize ? max_filesize - bytecount : 0;
        if ((separator_pos = buf_contains_separator(buf, offset, read_bytes))) {
          separator_pos--;
          gt_assert(separator_pos < read_bytes);
          if (separator_pos)
            gt_file_xwrite(destfp, buf, separator_pos);
          /* close current file */
          gt_file_delete(destfp);
          /* open new file */
          gt_str_reset(destfilename);
          gt_str_append_cstr_nt(destfilename, filename,
                                gt_file_basename_length(filename));
          gt_str_append_char(destfilename, '.');
          gt_str_append_ulong(destfilename, ++filenum);
          gt_str_append_cstr(destfilename,
                             gt_file_mode_suffix(gt_file_mode(srcfp)));
          if (!(destfp =
                  gt_output_file_xopen_forcecheck(gt_str_get(destfilename), "w",
                                                 force, err))) {
            had_err = -1;
            break;
          }
          bytecount = read_bytes - separator_pos; /* reset */
          gt_assert(buf[separator_pos] == '>');
          gt_file_xwrite(destfp, buf + separator_pos,
                         read_bytes - separator_pos);
          continue;
        }
      }
      bytecount += read_bytes;
      gt_file_xwrite(destfp, buf, read_bytes);
    }
  }

  /* free */
  gt_str_delete(destfilename);

  /* close current file */
  gt_file_delete(destfp);

  /* close source file */
  gt_file_delete(srcfp);

  return had_err;
}

static int gt_splitfasta_runner(GT_UNUSED int argc, const char **argv,
                                int parsed_args, void *tool_arguments,
                                GtError *err)
{
  SplitfastaArguments *arguments = tool_arguments;
  unsigned int num_files;
  int had_err;
  off_t file_size;
  const char* filename;
  gt_error_check(err);
  gt_assert(arguments);

  num_files = arguments->num_files;
  filename = argv[parsed_args];

  if (gt_str_length(arguments->splitdesc)) {
    had_err = split_description(filename, arguments->splitdesc,
                                arguments->width, arguments->force, err);
  }
  else {
    unsigned long max_filesize;
    if (num_files) {
      /* set the maxfile size based on requested number of files */
      file_size = gt_file_estimate_size(filename);
      max_filesize= file_size / num_files ;
    }
    else
      max_filesize= arguments->max_filesize_in_MB << 20;
    had_err = split_fasta_file(filename, max_filesize, arguments->force, err);
  }

  return had_err;
}

GtTool* gt_splitfasta(void)
{
  return gt_tool_new(gt_splitfasta_arguments_new,
                     gt_splitfasta_arguments_delete,
                     gt_splitfasta_option_parser_new,
                     NULL,
                     gt_splitfasta_runner);
}
genometools-1.5.1/src/tools/gt_splitfasta.h000066400000000000000000000017551211610345200210200ustar00rootroot00000000000000/*
  Copyright (c) 2003-2008 Gordon Gremme 
  Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SPLITFASTA_H
#define GT_SPLITFASTA_H

#include "core/tool_api.h"

/* the splitfasta tool */
GtTool* gt_splitfasta(void);

#endif
genometools-1.5.1/src/tools/gt_stat.c000066400000000000000000000150151211610345200176060ustar00rootroot00000000000000/*
  Copyright (c) 2005-2011 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "extended/add_introns_stream_api.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream.h"
#include "extended/sort_stream_api.h"
#include "extended/stat_stream_api.h"
#include "tools/gt_stat.h"

typedef struct {
  bool gene_length_distribution,
       gene_score_distribution,
       exon_number_distribution,
       exon_length_distribution,
       intron_length_distribution,
       cds_length_distribution,
       used_sources,
       addintrons,
       verbose;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} StatArguments;

static void* gt_stat_argument_new(void)
{
  StatArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_stat_arguments_delete(void *tool_arguments)
{
  StatArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_stat_option_parser_new(void *tool_arguments)
{
  StatArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;

  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                            "Show statistics about features contained in GFF3 "
                            "files.");

  /* -genelengthdistri */
  option = gt_option_new_bool("genelengthdistri",
                              "show gene length distribution",
                              &arguments->gene_length_distribution, false);
  gt_option_parser_add_option(op, option);

  /* -genescoresdistri */
  option = gt_option_new_bool("genescoredistri", "show gene score distribution",
                              &arguments->gene_score_distribution, false);
  gt_option_parser_add_option(op, option);

  /* -exonlengthdistri */
  option = gt_option_new_bool("exonlengthdistri",
                              "show exon length distribution",
                              &arguments->exon_length_distribution, false);
  gt_option_parser_add_option(op, option);

  /* -exonnumberdistri */
  option = gt_option_new_bool("exonnumberdistri",
                              "show exon number distribution",
                              &arguments->exon_number_distribution, false);
  gt_option_parser_add_option(op, option);

  /* -intronlengthdistri */
  option = gt_option_new_bool("intronlengthdistri",
                              "show intron length distribution",
                              &arguments->intron_length_distribution, false);
  gt_option_parser_add_option(op, option);

  /* -cdslengthdistri */
  option = gt_option_new_bool("cdslengthdistri", "show CDS length distribution "
                              "(measured in amino acids)",
                              &arguments->cds_length_distribution, false);
  gt_option_parser_add_option(op, option);

  /* -source */
  option = gt_option_new_bool("source", "show the set of used source tags "
                              "(column 2 in regular GFF3 lines)",
                              &arguments->used_sources, false);
  gt_option_parser_add_option(op, option);

  /* -addintrons */
  option = gt_option_new_bool("addintrons", "add intron features between "
                              "existing exon features (before computing stats)",
                              &arguments->addintrons, false);
  gt_option_parser_add_option(op, option);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  return op;
}

static int gt_stat_runner(int argc, const char **argv, int parsed_args,
                          void *tool_arguments, GtError *err)
{
  StatArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream, *sort_stream, *add_introns_stream = NULL,
               *stat_stream;
  int had_err;
  gt_error_check(err);

  /* create a gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_unsorted(argc - parsed_args,
                                                  argv + parsed_args);
  if (arguments->verbose)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);

  /* create add introns stream if -addintrons was used */
  if (arguments->addintrons) {
    sort_stream = gt_sort_stream_new(gff3_in_stream);
    add_introns_stream = gt_add_introns_stream_new(sort_stream);
  }

  /* create s status stream */
  stat_stream = gt_stat_stream_new(arguments->addintrons
                                   ? add_introns_stream : gff3_in_stream,
                                   arguments->gene_length_distribution,
                                   arguments->gene_score_distribution,
                                   arguments->exon_length_distribution,
                                   arguments->exon_number_distribution,
                                   arguments->intron_length_distribution,
                                   arguments->cds_length_distribution,
                                   arguments->used_sources);

  /* pull the features through the stream , compute the statistics, and free
     them afterwards */
  had_err = gt_node_stream_pull(stat_stream, err);

  /* show statistics */
  if (!had_err)
    gt_stat_stream_show_stats((GtStatStream*) stat_stream, arguments->outfp);

  /* free */
  gt_node_stream_delete(stat_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool *gt_stat(void)
{
  return gt_tool_new(gt_stat_argument_new,
                     gt_stat_arguments_delete,
                     gt_stat_option_parser_new,
                     NULL,
                     gt_stat_runner);
}
genometools-1.5.1/src/tools/gt_stat.h000066400000000000000000000017251211610345200176160ustar00rootroot00000000000000/*
  Copyright (c) 2005-2010 Gordon Gremme 
  Copyright (c) 2005-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_STAT_H
#define GT_STAT_H

#include "core/tool_api.h"

/* the stat tool */
GtTool* gt_stat(void);

#endif
genometools-1.5.1/src/tools/gt_suffixerator.c000066400000000000000000000021061211610345200213510ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/error.h"
#include "match/sfx-run.h"
#include "tools/gt_suffixerator.h"

int gt_suffixerator(int argc, const char **argv, GtError *err)
{
  gt_error_check(err);
  return gt_parseargsandcallsuffixerator(true,argc, argv, err);
}
genometools-1.5.1/src/tools/gt_suffixerator.h000066400000000000000000000017521211610345200213640ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_SUFFIXERATOR_H
#define GT_SUFFIXERATOR_H

/* the suffixerator tool */
int gt_suffixerator(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/src/tools/gt_tagerator.c000066400000000000000000000270061211610345200206260ustar00rootroot00000000000000/*
  Copyright (c) 2006-2008 Stefan Kurtz 
  Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/option_api.h"
#include "core/ma.h"
#include "core/str_array.h"
#include "core/unused_api.h"
#include "core/tool_api.h"
#include "match/tagerator.h"
#include "match/optionargmode.h"
#include "tools/gt_tagerator.h"

static const Optionargmodedesc outputmodedesctable[] =
{
  {"tagnum","ordinal number of tag",TAGOUT_TAGNUM},
  {"tagseq","tag sequence",TAGOUT_TAGSEQ},
  {"dblength","length of match in database",TAGOUT_DBLENGTH},
  {"dbstartpos","start position of match in database",TAGOUT_DBSTARTPOS},
  {"abspos","absolute value of dbstartpos",TAGOUT_DBABSPOS},
  {"dbsequence","sequence of match",TAGOUT_DBSEQUENCE},
  {"strand","strand",TAGOUT_STRAND},
  {"edist","edit distance",TAGOUT_EDIST},
  {"tagstartpos","start position of match in tag (only for -maxocc)",
                 TAGOUT_TAGSTARTPOS},
  {"taglength","length of match in tag (only for -maxocc)",TAGOUT_TAGLENGTH},
  {"tagsuffixseq","suffix tag involved in match (only for -maxocc)",
                  TAGOUT_TAGSUFFIXSEQ}
};

static void *gt_tagerator_arguments_new(void)
{
  TageratorOptions *arguments;

  arguments = gt_malloc(sizeof (TageratorOptions));
  arguments->indexname = gt_str_new();
  arguments->tagfiles = gt_str_array_new();
  arguments->outputspec = gt_str_array_new();
  arguments->outputmode = 0;
  arguments->numberofmodedescentries = sizeof (outputmodedesctable)/
                                       sizeof (outputmodedesctable[0]);
  arguments->outputhelp
    = gt_getargmodekeywords(outputmodedesctable,
                            arguments->numberofmodedescentries,
                            "output");
  arguments->modedesc = outputmodedesctable;
  return arguments;
}

static void gt_tagerator_arguments_delete(void *tool_arguments)
{
  TageratorOptions *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->indexname);
  gt_str_delete(arguments->outputhelp);
  gt_str_array_delete(arguments->tagfiles);
  gt_str_array_delete(arguments->outputspec);
  gt_option_delete(arguments->refoptionesaindex);
  gt_option_delete(arguments->refoptionpckindex);
  gt_free(arguments);
}

static GtOptionParser* gt_tagerator_option_parser_new(void *tool_arguments)
{
  TageratorOptions *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionrw, *optiononline, *optioncmp, *optionesaindex,
           *optionpckindex, *optionmaxdepth, *optionbest;

  gt_assert(arguments != NULL);
  op = gt_option_parser_new("[options] -q tagfile [-esa|-pck] indexname",
                         "Map short sequence tags in given index.");
  gt_option_parser_set_mail_address(op,"");
  option = gt_option_new_filename_array("q",
                                    "Specify files containing the short "
                                    "sequence tags",
                                    arguments->tagfiles);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  option = gt_option_new_long("e",
                           "Specify the allowed number of differences "
                           "(replacements/insertions/deletions)",
                           &arguments->userdefinedmaxdistance,
                           -1L);
  gt_option_parser_add_option(op, option);

  optionesaindex = gt_option_new_string("esa",
                                     "Specify index (enhanced suffix array)",
                                     arguments->indexname, NULL);
  gt_option_parser_add_option(op, optionesaindex);
  arguments->refoptionesaindex = gt_option_ref(optionesaindex);

  optionpckindex = gt_option_new_string("pck",
                                     "Specify index (packed index)",
                                     arguments->indexname, NULL);
  gt_option_parser_add_option(op, optionpckindex);
  arguments->refoptionpckindex = gt_option_ref(optionpckindex);
  gt_option_exclude(optionesaindex,optionpckindex);
  gt_option_is_mandatory_either(optionesaindex,optionpckindex);

  optionmaxdepth = gt_option_new_int("maxdepth",
                                  "Use the data in the .pbt file only up to "
                                  "this depth (only relevant with option -pck)",
                                  &arguments->userdefinedmaxdepth,
                                  -1);
  gt_option_parser_add_option(op, optionmaxdepth);
  gt_option_is_development_option(optionmaxdepth);

  optiononline = gt_option_new_bool("online","Perform online searches",
                                    &arguments->doonline, false);
  gt_option_parser_add_option(op, optiononline);
  gt_option_is_development_option(optiononline);

  optioncmp = gt_option_new_bool("cmp","compare results of offline and online "
                                 "searches",
                                 &arguments->docompare, false);
  gt_option_parser_add_option(op, optioncmp);
  gt_option_exclude(optiononline,optioncmp);
  gt_option_is_development_option(optioncmp);

  optionrw = gt_option_new_bool("rw","Replace wildcard in tag by random char",
                             &arguments->replacewildcard, false);
  gt_option_parser_add_option(op, optionrw);
  gt_option_is_development_option(optionrw);

  option = gt_option_new_bool("nod","Do not compute direct matches",
                           &arguments->nofwdmatch, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("nop","Do not compute palindromic matches "
                           "(i.e. no reverse complemented matches.)",
                             &arguments->norcmatch, false);
  gt_option_parser_add_option(op, option);

  optionbest = gt_option_new_bool("best","Compute only best matches, i.e. only "
                                  "for smallest edit distance with matches",
                                  &arguments->best, false);
  gt_option_parser_add_option(op, optionbest);
  gt_option_exclude(optiononline,optionbest);
  gt_option_exclude(optioncmp,optionbest);

  option = gt_option_new_ulong_min("maxocc",
                                   "specify max number of match-occurrences",
                                   &arguments->maxintervalwidth,0,1UL);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("skpp",
                           "Skip prefix of pattern (only in pdiff mode)",
                           &arguments->skpp, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("withwildcards","output matches containing "
                              "wildcard characters (e.g. N); only relevant for "
                              "approximate matching",
                              &arguments->nowildcards, true);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string_array("output",
                                      gt_str_get(arguments->outputhelp),
                                      arguments->outputspec);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  return op;
}

static int gt_tagerator_arguments_check(GT_UNUSED int rest_argc,
                                        void *tool_arguments,
                                        GtError *err)
{
  TageratorOptions *arguments = tool_arguments;
  unsigned long idx;

  if (!arguments->nowildcards && arguments->userdefinedmaxdistance <= 0)
  {
    arguments->nowildcards = true;
  }
  if (gt_option_is_set(arguments->refoptionesaindex))
  {
    arguments->withesa = true;
  } else
  {
    gt_assert(gt_option_is_set(arguments->refoptionpckindex));
    arguments->withesa = false;
  }
  if (arguments->userdefinedmaxdistance < 0)
  {
    if (arguments->doonline)
    {
      gt_error_set(err,"option -online requires option -e");
      return -1;
    }
    if (arguments->maxintervalwidth == 0)
    {
      gt_error_set(err,
                   "if option -e is not used then option -maxocc is required");
      return -1;
    }
    if (arguments->best)
    {
      gt_error_set(err,"option -best requires option -e");
      return -1;
    }
  } else
  {
    if (arguments->skpp &&
        (arguments->userdefinedmaxdistance == 0 ||
         arguments->maxintervalwidth == 0))
    {
      gt_error_set(err,"option -skpp only works in pdiff mode");
      return -1;
    }
  }
  for (idx=0; idxoutputspec); idx++)
  {
    if (gt_optionargaddbitmask(outputmodedesctable,
                            sizeof (outputmodedesctable)/
                            sizeof (outputmodedesctable[0]),
                            &arguments->outputmode,
                            "-output",
                            gt_str_array_get(arguments->outputspec,idx),
                            err) != 0)
    {
      return -1;
    }
  }
  if (arguments->outputmode == 0)
  {
    arguments->outputmode = TAGOUT_TAGNUM | TAGOUT_TAGSEQ |
                            TAGOUT_DBLENGTH | TAGOUT_DBSTARTPOS |
                            TAGOUT_STRAND;
    if (arguments->maxintervalwidth > 0)
    {
      arguments->outputmode |= TAGOUT_TAGLENGTH;
    }
  }
  return 0;
}

static int gt_tagerator_runner(GT_UNUSED int argc,
                               GT_UNUSED const char **argv,
                               GT_UNUSED int parsed_args,
                               void *tool_arguments, GtError *err)
{
  TageratorOptions *arguments = tool_arguments;
  bool haserr = false;
  unsigned long idx;

  gt_error_check(err);
  gt_assert(arguments != NULL);

  gt_assert(parsed_args == argc);
  if (arguments->userdefinedmaxdistance == -1L)
  {
    printf("# computing matching statistics\n");
  } else
  {
    if (arguments->maxintervalwidth == 0)
    {
      printf("# computing complete matches");
    } else
    {
      printf("# computing prefix matches");
    }
    if (arguments->userdefinedmaxdistance == 0)
    {
      printf(" without differences (exact matches)");
    } else
    {
      printf(" with up to %ld differences",arguments->userdefinedmaxdistance);
    }
    if (arguments->maxintervalwidth > 0)
    {
      printf(" and at most %lu occurrences in the subject sequences",
             arguments->maxintervalwidth);
    }
    printf("\n");
  }
  printf("# indexname(%s)=%s\n",arguments->withesa ? "esa" : "pck",
                                gt_str_get(arguments->indexname));
  for (idx=0; idxtagfiles); idx++)
  {
    printf("# queryfile=%s\n",gt_str_array_get(arguments->tagfiles,idx));
  }
  if (gt_runtagerator(arguments,err) != 0)
  {
    haserr = true;
  }
  return haserr ? -1 : 0;
}

GtTool* gt_tagerator(void)
{
  return gt_tool_new(gt_tagerator_arguments_new,
                     gt_tagerator_arguments_delete,
                     gt_tagerator_option_parser_new,
                     gt_tagerator_arguments_check,
                     gt_tagerator_runner);
}
genometools-1.5.1/src/tools/gt_tagerator.h000066400000000000000000000017351211610345200206340ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_TAGERATOR_H
#define GT_TAGERATOR_H

#include "core/tool_api.h"

/* the tagerator tool */
GtTool* gt_tagerator(void);

#endif
genometools-1.5.1/src/tools/gt_tallymer.c000066400000000000000000001024701211610345200204660ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/cstr_array.h"
#include "core/defined-types.h"
#include "core/error.h"
#include "core/format64.h"
#include "core/intbits.h"
#include "core/logger.h"
#include "core/ma_api.h"
#include "core/option_api.h"
#include "core/str.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "core/minmax.h"
#include "extended/toolbox.h"
#include "match/optionargmode.h"
#include "match/tyr-mkindex.h"
#include "match/tyr-show.h"
#include "match/tyr-search.h"
#include "match/tyr-mersplit.h"
#include "match/tyr-occratio.h"
#include "tools/gt_tallymer.h"

typedef enum
{
  Autoprefixlength,
  Undeterminedprefixlength,
  Determinedprefixlength
} Prefixlengthflag;

typedef struct
{
  unsigned int value;
  Prefixlengthflag flag;
} Prefixlengthvalue;

typedef struct
{
  unsigned long mersize,
                userdefinedminocc,
                userdefinedmaxocc;
  unsigned int userdefinedprefixlength;
  Prefixlengthvalue prefixlength;
  GtOption *refoptionpl;
  GtStr *str_storeindex,
        *str_inputindex;
  bool storecounts,
       performtest,
       verbose,
       scanfile;
} Tyr_mkindex_options;

static void *gt_tyr_mkindex_arguments_new(void)
{
  Tyr_mkindex_options *arguments
    = gt_malloc(sizeof (Tyr_mkindex_options));
  arguments->str_storeindex = gt_str_new();
  arguments->str_inputindex = gt_str_new();
  return arguments;
}

static void gt_tyr_mkindex_arguments_delete(void *tool_arguments)
{
  Tyr_mkindex_options *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->str_storeindex);
  gt_str_delete(arguments->str_inputindex);
  gt_option_delete(arguments->refoptionpl);
  gt_free(arguments);
}

static GtOptionParser *gt_tyr_mkindex_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GtOption *option,
           *optionminocc,
           *optionmaxocc,
           *optionpl,
           *optionstoreindex,
           *optionstorecounts,
           *optionscan,
           *optionesa;
  Tyr_mkindex_options *arguments = tool_arguments;

  op = gt_option_parser_new("[options] -esa suffixerator-index [options]",
                            "Count and index k-mers in the given enhanced "
                            "suffix array for a fixed value of k.");
  gt_option_parser_set_mail_address(op, "");

  optionesa = gt_option_new_string("esa","specify suffixerator-index\n"
                                   "(mandatory option)",
                                   arguments->str_inputindex,
                                   NULL);
  gt_option_is_mandatory(optionesa);
  gt_option_parser_add_option(op, optionesa);

  option = gt_option_new_ulong("mersize",
                               "Specify the mer size.",
                               &arguments->mersize,
                               20UL);
  gt_option_parser_add_option(op, option);

  optionminocc
    = gt_option_new_ulong("minocc",
                          "Specify the minimum occurrence number for "
                          "the mers to output/index",
                          &arguments->userdefinedminocc,
                          0);
  gt_option_parser_add_option(op, optionminocc);

  optionmaxocc
    = gt_option_new_ulong("maxocc",
                          "Specify the maximum occurrence number for "
                          "the mers to output/index",
                          &arguments->userdefinedmaxocc,
                          0);
  gt_option_parser_add_option(op, optionmaxocc);

  optionpl = gt_option_new_uint_min("pl",
                 "specify prefix length for bucket boundary construction\n"
                 "recommendation: use without argument;\n"
                 "then a reasonable prefix length is automatically determined",
                 &arguments->userdefinedprefixlength,
                 0,
                 1U);
  gt_option_argument_is_optional(optionpl);
  gt_option_parser_add_option(op, optionpl);
  arguments->refoptionpl = gt_option_ref(optionpl);

  optionstoreindex = gt_option_new_string("indexname",
                                          "store the mers specified by options "
                                          "-maxocc and -minocc in an index",
                                          arguments->str_storeindex, NULL);
  gt_option_parser_add_option(op, optionstoreindex);

  optionstorecounts = gt_option_new_bool("counts", "store counts of the mers",
                                         &arguments->storecounts,false);
  gt_option_parser_add_option(op, optionstorecounts);

  option = gt_option_new_bool("test", "perform tests to verify program "
                                      "correctness", &arguments->performtest,
                                      false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  optionscan = gt_option_new_bool("scan",
                                  "read enhanced suffix array sequentially "
                                  "instead of mapping it to memory",
                                  &arguments->scanfile,
                                  false);
  gt_option_parser_add_option(op, optionscan);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  gt_option_imply(optionpl, optionstoreindex);
  gt_option_imply(optionstorecounts, optionstoreindex);
  gt_option_imply_either_2(optionstoreindex,optionminocc,optionmaxocc);
  return op;
}

static int gt_tyr_mkindex_arguments_check(int rest_argc,
                                          void *tool_arguments,
                                          GtError *err)
{
  Tyr_mkindex_options *arguments = tool_arguments;

  if (rest_argc != 0)
  {
    gt_error_set(err,"superfluous arguments");
    return -1;
  }
  if (gt_option_is_set(arguments->refoptionpl))
  {
    if (arguments->userdefinedprefixlength == 0)
    {
      arguments->prefixlength.flag = Autoprefixlength;
      arguments->prefixlength.value = 0;
    } else
    {
      arguments->prefixlength.flag = Determinedprefixlength;
      arguments->prefixlength.value = arguments->userdefinedprefixlength;
    }
  } else
  {
    arguments->prefixlength.flag = Undeterminedprefixlength;
    arguments->prefixlength.value = 0;
  }
  return 0;
}

static int gt_tyr_mkindex_runner(GT_UNUSED int argc,
                                 GT_UNUSED const char **argv,
                                 GT_UNUSED int parsed_args,
                                 void *tool_arguments,
                                 GtError *err)
{
  Tyr_mkindex_options *arguments = tool_arguments;
  GtLogger *logger;
  bool haserr = false;

  logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  if (arguments->verbose)
  {
    printf("# mersize=%lu\n",arguments->mersize);
    if (arguments->userdefinedminocc > 0)
    {
      printf("# minocc=%lu\n",arguments->userdefinedminocc);
    } else
    {
      printf("# minocc=undefined\n");
    }
    if (arguments->userdefinedmaxocc > 0)
    {
      printf("# maxocc=%lu\n",arguments->userdefinedmaxocc);
    } else
    {
      printf("# maxocc=undefined\n");
    }
    printf("# prefixlength=");
    if (arguments->prefixlength.flag == Autoprefixlength)
    {
      printf("automatic");
    } else
    {
      if (arguments->prefixlength.flag == Determinedprefixlength)
      {
        printf("%u",arguments->prefixlength.value);
      } else
      {
        printf("undefined");
      }
    }
    printf("\n");
    if (gt_str_length(arguments->str_storeindex) > 0)
    {
      printf("# storeindex=%s\n",gt_str_get(arguments->str_storeindex));
    }
    printf("# inputindex=%s\n",gt_str_get(arguments->str_inputindex));
  }
  if (gt_merstatistics(gt_str_get(arguments->str_inputindex),
                    arguments->mersize,
                    arguments->userdefinedminocc,
                    arguments->userdefinedmaxocc,
                    gt_str_get(arguments->str_storeindex),
                    arguments->storecounts,
                    arguments->scanfile,
                    arguments->performtest,
                    logger,
                    err) != 0)
  {
    haserr = true;
  }
  if (!haserr &&
      gt_str_length(arguments->str_storeindex) > 0 &&
      arguments->prefixlength.flag != Undeterminedprefixlength)
  {
    Definedunsignedint callprefixlength;

    if (arguments->prefixlength.flag == Determinedprefixlength)
    {
      callprefixlength.defined = true;
      callprefixlength.valueunsignedint = arguments->prefixlength.value;
    } else
    {
      callprefixlength.defined = false;
    }
    if (gt_constructmerbuckets(gt_str_get(arguments->str_storeindex),
                               &callprefixlength,err) != 0)
    {
      haserr = true;
    }
  }
  gt_logger_delete(logger);
  return haserr ? - 1 : 0;
}

static GtTool *gt_tyr_mkindex(void)
{
  return gt_tool_new(gt_tyr_mkindex_arguments_new,
                     gt_tyr_mkindex_arguments_delete,
                     gt_tyr_mkindex_option_parser_new,
                     gt_tyr_mkindex_arguments_check,
                     gt_tyr_mkindex_runner);
}

typedef struct
{
  GtStrArray *mersizesstrings, *outputspec;
  GtStr *str_inputindex;
  GtOption *refoptionmersizes;
  unsigned long minmersize, maxmersize, stepmersize;
  GtBitsequence *outputvector;
  unsigned int outputmode;
  bool scanfile,
       verbose;
} Tyr_occratio_options;

static void *gt_tyr_occratio_arguments_new(void)
{
  Tyr_occratio_options *arguments
    = gt_malloc(sizeof (Tyr_occratio_options));
  arguments->mersizesstrings = gt_str_array_new();
  arguments->outputspec = gt_str_array_new();
  arguments->str_inputindex = gt_str_new();
  arguments->outputvector = NULL;
  arguments->outputmode = 0;
  return arguments;
}

static void gt_tyr_occratio_arguments_delete(void *tool_arguments)
{
  Tyr_occratio_options *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_array_delete(arguments->mersizesstrings);
  gt_str_array_delete(arguments->outputspec);
  gt_str_delete(arguments->str_inputindex);
  gt_option_delete(arguments->refoptionmersizes);
  gt_free(arguments->outputvector);
  gt_free(arguments);
}

static GtOptionParser *gt_tyr_occratio_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GtOption *optionmersizes, *optionesa, *optionminmersize, *optionmaxmersize,
           *optionstep, *optionoutput, *option;
  Tyr_occratio_options *arguments = tool_arguments;

  op = gt_option_parser_new("[options] -esa suffixerator-index [options]",
                            "Compute occurrence ratio for a set of sequences "
                            "represented by an enhanced suffix array.");
  gt_option_parser_set_mail_address(op, "");

  optionesa = gt_option_new_string("esa","specify suffixerator-index\n"
                                   "(mandatory option)",
                                   arguments->str_inputindex,
                                   NULL);
  gt_option_is_mandatory(optionesa);
  gt_option_parser_add_option(op, optionesa);

  optionminmersize
    = gt_option_new_ulong_min("minmersize",
                              "specify minimum mer size for which "
                              "to compute the occurrence distribution",
                              &arguments->minmersize,0,1UL);
  gt_option_parser_add_option(op, optionminmersize);

  optionmaxmersize
    = gt_option_new_ulong_min("maxmersize",
                              "specify maximum mer size for which "
                              "to compute the occurrence distribution",
                              &arguments->maxmersize,0,1UL);
  gt_option_parser_add_option(op, optionmaxmersize);

  optionstep
    = gt_option_new_ulong_min("step",
                              "specify step size when specifying mer sizes",
                              &arguments->stepmersize,1UL,1UL);
  gt_option_parser_add_option(op, optionstep);

  optionmersizes = gt_option_new_string_array(
                          "mersizes",
                          "specify mer sizes as non-empty sequence of "
                          "non decreasing positive integers",
                          arguments->mersizesstrings);
  arguments->refoptionmersizes = gt_option_ref(optionmersizes);
  gt_option_parser_add_option(op, optionmersizes);

  optionoutput = gt_option_new_string_array(
                          "output",
                          "use combination of the following keywords: "
                          "unique nonunique nonuniquemulti relative total "
                          "to specify kind of output",
                          arguments->outputspec);
  gt_option_parser_add_option(op, optionoutput);

  option = gt_option_new_bool("scan",
                              "read suffixerator-index sequentially "
                              "instead of mapping it to memory",
                              &arguments->scanfile,
                              false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  gt_option_exclude(optionmersizes,optionminmersize);
  gt_option_exclude(optionmersizes,optionmaxmersize);
  gt_option_exclude(optionmersizes,optionstep);
  return op;
}

#define TYROCC_OUTPUTUNIQUE          1U
#define TYROCC_OUTPUTNONUNIQUE       (1U << 1)
#define TYROCC_OUTPUTNONUNIQUEMULTI  (1U << 2)
#define TYROCC_OUTPUTRELATIVE        (1U << 3)
#define TYROCC_OUTPUTTOTAL           (1U << 4)

static int gt_tyr_occratio_arguments_check(int rest_argc,
                                           void *tool_arguments,
                                           GtError *err)
{
  Tyr_occratio_options *arguments = tool_arguments;
  bool haserr = false;

  Optionargmodedesc outputmodedesctable[] =
  {
    {"unique","number of unique mers",TYROCC_OUTPUTUNIQUE},
    {"nonunique","number of nonunique mers (single count)",
                 TYROCC_OUTPUTNONUNIQUE},
    {"nonuniquemulti","number of nonunique mers (multi count)",
                 TYROCC_OUTPUTNONUNIQUEMULTI},
    {"relative","fraction of unique/non-unique mers relative to all mers",
                 TYROCC_OUTPUTRELATIVE},
    {"total","number of all mers",TYROCC_OUTPUTTOTAL}
  };
  if (rest_argc != 0)
  {
    gt_error_set(err,"superfluous arguments");
    return -1;
  }
  if (gt_option_is_set(arguments->refoptionmersizes))
  {
    unsigned long *mersizes = NULL;
    unsigned long idx,
                  numofmersizes = gt_str_array_size(arguments->mersizesstrings);
    if (numofmersizes == 0)
    {
      gt_error_set(err,"missing argument to option -mersizes:");
      haserr = true;
    } else
    {
      mersizes = gt_malloc(sizeof (*mersizes) * numofmersizes);
      for (idx=0; idxmersizesstrings,idx),
                   "%ld",&readnum) != 1 || readnum <= 0)
        {
          gt_error_set(err,"invalid argument \"%s\" of option -mersizes: "
                       "must be a positive integer",
                       gt_str_array_get(arguments->mersizesstrings,idx));
          haserr = true;
          break;
        }
        mersizes[idx] = (unsigned long) readnum;
        if (idx > 0 && mersizes[idx-1] >= mersizes[idx])
        {
          gt_error_set(err,"invalid argumnt %s to option -mersizes: "
                       "positive numbers must be strictly increasing",
                       gt_str_array_get(arguments->mersizesstrings,idx));
          haserr = true;
          break;
        }
      }
    }
    if (!haserr)
    {
      gt_assert(mersizes != NULL);
      arguments->minmersize = mersizes[0];
      arguments->maxmersize = mersizes[numofmersizes-1];
      GT_INITBITTAB(arguments->outputvector,arguments->maxmersize+1);
      for (idx=0; idxoutputvector,mersizes[idx]);
      }
    }
    gt_free(mersizes);
  } else
  {
    if (arguments->minmersize == 0)
    {
      gt_error_set(err,"if option -mersizes is not used, then option "
                       "-minmersize is mandatory");
      haserr = true;
    }
    if (!haserr)
    {
      if (arguments->maxmersize == 0)
      {
        gt_error_set(err,"if option -mersizes is not used, then option "
                         "-maxmersize is mandatory");
        haserr = true;
      }
    }
    if (!haserr)
    {
      if (arguments->minmersize > arguments->maxmersize)
      {
        gt_error_set(err,"minimum mer size must not be larger than "
                         "maximum mer size");
        haserr = true;
      }
    }
    if (!haserr)
    {
      if (arguments->minmersize+arguments->stepmersize > arguments->maxmersize)
      {
        gt_error_set(err,"minimum mer size + step value must be smaller or "
                         "equal to maximum mersize");
        haserr = true;
      }
    }
    if (!haserr)
    {
      unsigned long outputval;

      GT_INITBITTAB(arguments->outputvector,arguments->maxmersize+1);
      for (outputval = arguments->minmersize;
           outputval <= arguments->maxmersize;
           outputval += arguments->stepmersize)
      {
        GT_SETIBIT(arguments->outputvector,outputval);
      }
    }
  }
  if (!haserr)
  {
    unsigned long idx;
    for (idx=0; idxoutputspec); idx++)
    {
      if (gt_optionargaddbitmask(outputmodedesctable,
                           sizeof (outputmodedesctable)/
                           sizeof (outputmodedesctable[0]),
                           &arguments->outputmode,
                           "-output",
                           gt_str_array_get(arguments->outputspec,idx),
                           err) != 0)
      {
        haserr = true;
        break;
      }
    }
  }
  if (!haserr)
  {
    if ((arguments->outputmode & TYROCC_OUTPUTRELATIVE) &&
        !(arguments->outputmode &
            (TYROCC_OUTPUTUNIQUE | TYROCC_OUTPUTNONUNIQUE |
                                   TYROCC_OUTPUTNONUNIQUEMULTI)))
    {
      gt_error_set(err,"argument relative to option -output requires that one "
                   "of the arguments unique, nonunique, or nonuniquemulti "
                   "is used");
      haserr = true;
    }
  }
  return haserr ? - 1: 0;
}

static void showitvdistribution(const GtArrayuint64_t *dist,
                                const GtBitsequence *outputvector)
{
  unsigned long idx;

  gt_assert(outputvector != NULL);
  for (idx=0; idx < dist->nextfreeuint64_t; idx++)
  {
    if (GT_ISIBITSET(outputvector,idx) && dist->spaceuint64_t[idx] > 0)
    {
      /*@ignore@*/
      printf("%lu " Formatuint64_t "\n",
              idx,
              PRINTuint64_tcast(dist->spaceuint64_t[idx]));
      /*@end@*/
    }
  }
}

typedef enum
{
  Onlyshowsum,
  Showfirst,
  Showsecond
} Summode;

static void showitvsumdistributionoftwo(Summode mode,
                                        const GtArrayuint64_t *dist1,
                                        const GtArrayuint64_t *dist2,
                                        const GtBitsequence *outputvector)
{
  unsigned long idx;
  uint64_t sumoftwo, tmp;

  gt_assert(outputvector != NULL);
  for (idx=0; /* Nothing */; idx++)
  {
    if (GT_ISIBITSET(outputvector,idx))
    {
      if (idx < dist1->nextfreeuint64_t)
      {
        if (idx < dist2->nextfreeuint64_t)
        {
          sumoftwo = dist1->spaceuint64_t[idx] + dist2->spaceuint64_t[idx];
        } else
        {
          sumoftwo = dist1->spaceuint64_t[idx];
        }
      } else
      {
        if (idx < dist2->nextfreeuint64_t)
        {
          sumoftwo = dist2->spaceuint64_t[idx];
        } else
        {
          break;
        }
      }
      if (sumoftwo > 0)
      {
        if (mode == Onlyshowsum)
        {
          /*@ignore@*/
          printf("%lu " Formatuint64_t "\n",
                  idx,
                  PRINTuint64_tcast(sumoftwo));
          /*@end@*/
        } else
        {
          if (mode == Showfirst)
          {
            tmp = (idx < dist1->nextfreeuint64_t)
                     ? dist1->spaceuint64_t[idx]
                     : 0;
          } else
          {
            tmp = (idx < dist2->nextfreeuint64_t)
                     ? dist2->spaceuint64_t[idx]
                     : 0;
          }
          if (tmp > 0)
          {
            /*@ignore@*/
            printf("%lu " Formatuint64_t " %.3f\n",
                  idx,
                  PRINTuint64_tcast(tmp),
                  (double) tmp/(double) sumoftwo);
            /*@end@*/
          }
        }
      }
    }
  }
}

#define ONLYONCE     "(counting each non unique mer only once)"
#define MORETHANONCE "(counting each non unique mer more than once)"

static void showoccratios(const GtArrayuint64_t *uniquedistribution,
                          const GtArrayuint64_t *nonuniquedistribution,
                          const GtArrayuint64_t *nonuniquemultidistribution,
                          unsigned int outputmode,
                          const GtBitsequence *outputvector)
{
  if (outputmode & TYROCC_OUTPUTUNIQUE)
  {
    printf("# distribution of unique mers\n");
    if (outputmode & TYROCC_OUTPUTRELATIVE)
    {
      showitvsumdistributionoftwo(Showfirst,
                                  uniquedistribution,
                                  nonuniquedistribution,
                                  outputvector);
    } else
    {
      showitvdistribution(uniquedistribution,outputvector);
    }
  }
  if (outputmode & TYROCC_OUTPUTNONUNIQUE)
  {
    printf("# distribution of non unique mers " ONLYONCE "\n");
    if (outputmode & TYROCC_OUTPUTRELATIVE)
    {
      showitvsumdistributionoftwo(Showsecond,
                                  uniquedistribution,
                                  nonuniquedistribution,
                                  outputvector);
    } else
    {
      showitvdistribution(nonuniquedistribution,outputvector);
    }
  }
  if (outputmode & TYROCC_OUTPUTNONUNIQUEMULTI)
  {
    printf("# distribution of non unique mers " MORETHANONCE "\n");
    if (outputmode & TYROCC_OUTPUTRELATIVE)
    {
      showitvsumdistributionoftwo(Showsecond,
                                  uniquedistribution,
                                  nonuniquemultidistribution,
                                  outputvector);
    } else
    {
      showitvdistribution(nonuniquemultidistribution,outputvector);
    }
  }
  if (outputmode & TYROCC_OUTPUTTOTAL)
  {
    printf("# distribution of all mers " ONLYONCE "\n");
    showitvsumdistributionoftwo(Onlyshowsum,
                                uniquedistribution,
                                nonuniquedistribution,
                                outputvector);
    printf("# distribution of all mers " MORETHANONCE "\n");
    showitvsumdistributionoftwo(Onlyshowsum,
                                uniquedistribution,
                                nonuniquemultidistribution,
                                outputvector);
  }
}

static int gt_tyr_occratio_runner(GT_UNUSED int argc,
                                  GT_UNUSED const char **argv,
                                  GT_UNUSED int parsed_args,
                                  void *tool_arguments,
                                  GtError *err)
{
  GtLogger *logger;
  Tyr_occratio_options *arguments = tool_arguments;
  bool haserr = false;
  GtArrayuint64_t uniquedistribution,
                  nonuniquedistribution,
                  nonuniquemultidistribution;

  logger = gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  GT_INITARRAY(&uniquedistribution,uint64_t);
  GT_INITARRAY(&nonuniquedistribution,uint64_t);
  GT_INITARRAY(&nonuniquemultidistribution,uint64_t);
  if (gt_tyr_occratio_func(gt_str_get(arguments->str_inputindex),
                           arguments->scanfile,
                           arguments->minmersize,
                           arguments->maxmersize,
                           &uniquedistribution,
                           &nonuniquedistribution,
                           &nonuniquemultidistribution,
                           logger,
                           err) != 0)
  {
    haserr = true;
  }
  if (!haserr)
  {
    showoccratios(&uniquedistribution,
                  &nonuniquedistribution,
                  &nonuniquemultidistribution,
                  arguments->outputmode,
                  arguments->outputvector);
  }
  gt_logger_delete(logger);
  GT_FREEARRAY(&uniquedistribution,uint64_t);
  GT_FREEARRAY(&nonuniquedistribution,uint64_t);
  GT_FREEARRAY(&nonuniquemultidistribution,uint64_t);
  return haserr ? -1 : 0;
}

static GtTool *gt_tyr_occratio(void)
{
  return gt_tool_new(gt_tyr_occratio_arguments_new,
                     gt_tyr_occratio_arguments_delete,
                     gt_tyr_occratio_option_parser_new,
                     gt_tyr_occratio_arguments_check,
                     gt_tyr_occratio_runner);
}

typedef struct
{
  GtStr *str_inputindex;
  GtStrArray *queryfilenames;
  GtStr *strandspec;
  GtStrArray *showmodespec;
  unsigned int strand,
               showmode;
  bool verbose,
       performtest;
} Tyr_search_options;

static void *gt_tyr_search_arguments_new(void)
{
  Tyr_search_options *arguments
    = gt_malloc(sizeof (Tyr_search_options));
  arguments->str_inputindex = gt_str_new();
  arguments->strandspec = gt_str_new();
  arguments->queryfilenames = gt_str_array_new();
  arguments->showmodespec = gt_str_array_new();
  arguments->showmode = 0;
  arguments->strand = 0;
  return arguments;
}

static void gt_tyr_search_arguments_delete(void *tool_arguments)
{
  Tyr_search_options *arguments = tool_arguments;

  if (!arguments)
  {
    return;
  }
  gt_str_delete(arguments->str_inputindex);
  gt_str_delete(arguments->strandspec);
  gt_str_array_delete(arguments->queryfilenames);
  gt_str_array_delete(arguments->showmodespec);
  gt_free(arguments);
}

static GtOptionParser *gt_tyr_search_option_parser_new(void *tool_arguments)
{
  GtOptionParser *op;
  GtOption *option, *optiontyr, *optionqueries;
  Tyr_search_options *arguments = tool_arguments;

  op = gt_option_parser_new("[options] -tyr tallymer-index -q queryfile0 "
                            "[queryfile1..] [options]",
                            "Search a set of k-mers in an index constructed "
                            "by \"gt tyr mkindex\".");
  gt_option_parser_set_mail_address(op, "");

  optiontyr = gt_option_new_string("tyr","specify tallymer-index",
                                   arguments->str_inputindex,
                                   NULL);
  gt_option_is_mandatory(optiontyr);
  gt_option_parser_add_option(op, optiontyr);

  optionqueries = gt_option_new_filename_array("q","specify query file names",
                                               arguments->queryfilenames);
  gt_option_is_mandatory(optionqueries);
  gt_option_parser_add_option(op, optionqueries);

  option = gt_option_new_string("strand",
                                "specify the strand to be searched: "
                                "use f (for forward strand) or "
                                "p (for reverse complemented strand) or "
                                "fp (for both); default is f",
                                arguments->strandspec,
                                "f");
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string_array("output",
                                      "specify output flags "
                                      "(qseqnum, qpos, counts, sequence)",
                                      arguments->showmodespec);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("test", "perform tests to verify program "
                                      "correctness", &arguments->performtest,
                                      false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  return op;
}

static int gt_tyr_search_arguments_check(int rest_argc,
                                         void *tool_arguments,
                                         GtError *err)
{
  Optionargmodedesc showmodedesctable[] =
  {
    {"qseqnum","query sequence number",SHOWQSEQNUM},
    {"qpos","query position",SHOWQPOS},
    {"counts","number of occurrence counts",SHOWCOUNTS},
    {"sequence","mer-sequence",SHOWSEQUENCE}
  };

  Optionargmodedesc stranddesctable[] =
  {
    {"f","forward strand",STRAND_FORWARD},
    {"p","reverse strand",STRAND_REVERSE},
    {"fp","forward and reverse strand",STRAND_FORWARD | STRAND_REVERSE}
  };
  unsigned long idx;
  Tyr_search_options *arguments = tool_arguments;

  if (rest_argc != 0)
  {
    gt_error_set(err,"superfluous arguments");
    return -1;
  }
  for (idx=0; idxshowmodespec); idx++)
  {
    if (gt_optionargaddbitmask(showmodedesctable,
                         sizeof (showmodedesctable)/
                         sizeof (showmodedesctable[0]),
                         &arguments->showmode,
                         "-output",
                         gt_str_array_get(arguments->showmodespec,idx),
                         err) != 0)
    {
      return -1;
    }
  }
  if (gt_optionargaddbitmask(stranddesctable,
                          sizeof (stranddesctable)/
                          sizeof (stranddesctable[0]),
                          &arguments->strand,
                          "-output",
                          gt_str_get(arguments->strandspec),err) != 0)
  {
    return -1;
  }
  return 0;
}

static int gt_tyr_search_runner(GT_UNUSED int argc,
                                GT_UNUSED const char **argv,
                                GT_UNUSED int parsed_args,
                                void *tool_arguments,
                                GtError *err)
{
  Tyr_search_options *arguments = tool_arguments;

  if (gt_tyrsearch(gt_str_get(arguments->str_inputindex),
                   arguments->queryfilenames,
                   arguments->showmode,
                   arguments->strand,
                   arguments->verbose,
                   arguments->performtest,
                   err) != 0)
  {
    return -1;
  }
  return 0;
}

static GtTool *gt_tyr_search(void)
{
  return gt_tool_new(gt_tyr_search_arguments_new,
                     gt_tyr_search_arguments_delete,
                     gt_tyr_search_option_parser_new,
                     gt_tyr_search_arguments_check,
                     gt_tyr_search_runner);
}

static void *gt_tyr_arguments_new(void)
{
  GtToolbox *tyr_toolbox = gt_toolbox_new();
  gt_toolbox_add_tool(tyr_toolbox, "mkindex", gt_tyr_mkindex());
  gt_toolbox_add_tool(tyr_toolbox, "occratio", gt_tyr_occratio());
  gt_toolbox_add_tool(tyr_toolbox, "search", gt_tyr_search());
  return tyr_toolbox;
}

static void gt_tyr_arguments_delete(void *tool_arguments)
{
  GtToolbox *index_toolbox = tool_arguments;
  if (!index_toolbox) return;
  gt_toolbox_delete(index_toolbox);
}

static GtOptionParser* gt_tyr_option_parser_new(void *tool_arguments)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtOptionParser *op;

  gt_assert(index_toolbox != NULL);
  op = gt_option_parser_new(
                    "[option ...] tallymer_tool [argument ...]",
                    "Call tallymer tool with name tallymer_tool and pass "
                    "argument(s) to it.");
  gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
  gt_option_parser_set_min_args(op, 1U);
  gt_option_parser_refer_to_manual(op);
  return op;
}

static int gt_tyr_runner(int argc, const char **argv, int parsed_args,
                         void *tool_arguments, GtError *err)
{
  GtToolbox *index_toolbox = tool_arguments;
  GtToolfunc toolfunc;
  GtTool *tool = NULL;
  char **nargv = NULL;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(index_toolbox != NULL);

  if (!had_err && !gt_toolbox_has_tool(index_toolbox, argv[parsed_args]))
  {
    gt_error_set(err, "tallymer tool '%s' not found; option -help lists "
                      "possible tools", argv[parsed_args]);
    had_err = -1;
  }

  /* call sub-tool */
  if (!had_err)
  {
    if (!(toolfunc = gt_toolbox_get(index_toolbox, argv[parsed_args])))
    {
      tool = gt_toolbox_get_tool(index_toolbox, argv[parsed_args]);
      gt_assert(tool != NULL);
    }
    nargv = gt_cstr_array_prefix_first(argv + parsed_args,
                                       gt_error_get_progname(err));
    gt_error_set_progname(err, nargv[0]);
    if (toolfunc != NULL)
      had_err = toolfunc(argc - parsed_args, (const char**) nargv, err);
    else
      had_err = gt_tool_run(tool, argc - parsed_args, (const char**) nargv,
                            err);
  }
  gt_cstr_array_delete(nargv);
  return had_err;
}

GtTool* gt_tallymer(void)
{
  return gt_tool_new(gt_tyr_arguments_new,
                     gt_tyr_arguments_delete,
                     gt_tyr_option_parser_new,
                     NULL,
                     gt_tyr_runner);
}
genometools-1.5.1/src/tools/gt_tallymer.h000066400000000000000000000017011211610345200204660ustar00rootroot00000000000000/*
  Copyright (c) 2008 Stefan Kurtz 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_TALLYMER_H
#define GT_TALLYMER_H

#include "core/tool_api.h"

GtTool* gt_tallymer(void);

#endif
genometools-1.5.1/src/tools/gt_template.c000066400000000000000000000066231211610345200204530ustar00rootroot00000000000000/*
  Copyright (c) CCYY YOUR NAME HERE 
  Copyright (c) CCYY Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma.h"
#include "core/unused_api.h"
#include "tools/gt_template.h"

typedef struct {
  bool bool_option_template;
  GtStr  *str_option_template;
} TemplateArguments;

static void* gt_template_arguments_new(void)
{
  TemplateArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->str_option_template = gt_str_new();
  return arguments;
}

static void gt_template_arguments_delete(void *tool_arguments)
{
  TemplateArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_str_delete(arguments->str_option_template);
  gt_free(arguments);
}

static GtOptionParser* gt_template_option_parser_new(void *tool_arguments)
{
  TemplateArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [file]", /* XXX */
                            "DESCRIBE YOUR TOOL IN ONE LINE HERE."); /* XXX */

  /* -bool */
  option = gt_option_new_bool("bool", "bool option template",
                              &arguments->bool_option_template, false);
  gt_option_parser_add_option(op, option);

  /* -str */
  option = gt_option_new_string("str", "str option template",
                                arguments->str_option_template, NULL);
  gt_option_parser_add_option(op, option);

  return op;
}

static int gt_template_arguments_check(GT_UNUSED int rest_argc,
                                       void *tool_arguments,
                                       GT_UNUSED GtError *err)
{
  TemplateArguments *arguments = tool_arguments;
  int had_err = 0;
  gt_error_check(err);
  gt_assert(arguments);

  /* XXX: do some checking after the option have been parsed (usally this is not
     necessary and this function can be removed completely). */
  if (gt_str_length(arguments->str_option_template))
    printf("%s\n", gt_str_get(arguments->str_option_template));

  return had_err;
}

static int gt_template_runner(int argc, const char **argv, int parsed_args,
                              void *tool_arguments, GT_UNUSED GtError *err)
{
  TemplateArguments *arguments = tool_arguments;
  int had_err = 0;

  gt_error_check(err);
  gt_assert(arguments);

  /* XXX */
  if (arguments->bool_option_template)
    printf("argc=%d, parsed_args=%d\n", argc, parsed_args);
  printf("argv[0]=%s\n", argv[0]);

  return had_err;
}

GtTool* gt_template(void)
{
  return gt_tool_new(gt_template_arguments_new,
                     gt_template_arguments_delete,
                     gt_template_option_parser_new,
                     gt_template_arguments_check,
                     gt_template_runner);
}
genometools-1.5.1/src/tools/gt_template.h000066400000000000000000000017241211610345200204550ustar00rootroot00000000000000/*
  Copyright (c) CCYY YOUR NAME HERE 
  Copyright (c) CCYY Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_TEMPLATE_H
#define GT_TEMPLATE_H

#include "core/tool_api.h"

/* the template tool */
GtTool* gt_template(void);

#endif
genometools-1.5.1/src/tools/gt_trieins.c000066400000000000000000000043241211610345200203110ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/error.h"
#include "core/option_api.h"
#include "core/versionfunc.h"
#include "match/test-mtrieins.pr"
#include "tools/gt_trieins.h"

static GtOPrval parse_options(bool *onlyins,int *parsed_args,
                              int argc, const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOption *option;
  GtOPrval oprval;

  gt_error_check(err);
  op = gt_option_parser_new("[options] indexname",
                         "Perform trie insertions and check consistency.");
  gt_option_parser_set_mail_address(op, "");
  option= gt_option_new_bool("ins","perform only insertions",onlyins,false);
  gt_option_parser_add_option(op, option);
  gt_option_parser_set_min_max_args(op, 1U, 1U);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  gt_option_parser_delete(op);
  return oprval;
}

int gt_trieins(int argc, const char **argv, GtError *err)
{
  bool haserr = false;
  int parsed_args;
  bool onlyins = false;

  gt_error_check(err);

  switch (parse_options(&onlyins,&parsed_args, argc, argv, err)) {
    case GT_OPTION_PARSER_OK: break;
    case GT_OPTION_PARSER_ERROR: return -1;
    case GT_OPTION_PARSER_REQUESTS_EXIT: return 0;
  }
  gt_assert(parsed_args == 1);

  if (gt_test_trieins(onlyins,argv[parsed_args],err) != 0)
  {
    haserr = true;
  }
  return haserr ? -1 : 0;
}
genometools-1.5.1/src/tools/gt_trieins.h000066400000000000000000000017321211610345200203160ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_TRIEINS_H
#define GT_TRIEINS_H

/* the trieins tool */
int gt_trieins(int argc, const char **argv, GtError *err);

#endif
genometools-1.5.1/src/tools/gt_uniq.c000066400000000000000000000072151211610345200176120ustar00rootroot00000000000000/*
  Copyright (c) 2007-2009, 2011 Gordon Gremme 
  Copyright (c) 2007-2008       Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#include "core/ma_api.h"
#include "core/option_api.h"
#include "core/output_file_api.h"
#include "core/unused_api.h"
#include "core/versionfunc.h"
#include "extended/genome_node.h"
#include "extended/gff3_in_stream_api.h"
#include "extended/gff3_out_stream_api.h"
#include "extended/gtdatahelp.h"
#include "extended/uniq_stream_api.h"
#include "tools/gt_uniq.h"

typedef struct {
  bool verbose;
  GtOutputFileInfo *ofi;
  GtFile *outfp;
} UniqArguments;

static void* gt_uniq_arguments_new(void)
{
  UniqArguments *arguments = gt_calloc(1, sizeof *arguments);
  arguments->ofi = gt_output_file_info_new();
  return arguments;
}

static void gt_uniq_arguments_delete(void *tool_arguments)
{
  UniqArguments *arguments = tool_arguments;
  if (!arguments) return;
  gt_file_delete(arguments->outfp);
  gt_output_file_info_delete(arguments->ofi);
  gt_free(arguments);
}

static GtOptionParser* gt_uniq_option_parser_new(void *tool_arguments)
{
  UniqArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file]", "Filter out repeated "
                            "feature node graphs in a sorted GFF3 file.");

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* output file options */
  gt_output_file_register_options(op, &arguments->outfp, arguments->ofi);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  gt_option_parser_set_max_args(op, 1);

  return op;
}

static int gt_uniq_runner(GT_UNUSED int argc, const char **argv,
                          int parsed_args, void *tool_arguments, GtError *err)
{
  UniqArguments *arguments = tool_arguments;
  GtNodeStream *gff3_in_stream,
               *uniq_stream = NULL,
               *gff3_out_stream = NULL;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  /* create gff3 input stream */
  gff3_in_stream = gt_gff3_in_stream_new_sorted(argv[parsed_args]);
  if (arguments->verbose && arguments->outfp)
    gt_gff3_in_stream_show_progress_bar((GtGFF3InStream*) gff3_in_stream);

  /* create uniq stream */
  uniq_stream = gt_uniq_stream_new(gff3_in_stream);

  /* create gff3 output stream */
  gff3_out_stream = gt_gff3_out_stream_new(uniq_stream, arguments->outfp);

  /* pull the features through the stream and free them afterwards */
  had_err = gt_node_stream_pull(gff3_out_stream, err);

  /* free */
  gt_node_stream_delete(gff3_out_stream);
  gt_node_stream_delete(uniq_stream);
  gt_node_stream_delete(gff3_in_stream);

  return had_err;
}

GtTool* gt_uniq(void)
{
  return gt_tool_new(gt_uniq_arguments_new,
                     gt_uniq_arguments_delete,
                     gt_uniq_option_parser_new,
                     NULL,
                     gt_uniq_runner);
}
genometools-1.5.1/src/tools/gt_uniq.h000066400000000000000000000017131211610345200176140ustar00rootroot00000000000000/*
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_UNIQ_H
#define GT_UNIQ_H

#include "core/tool_api.h"

/* the uniq tool */
GtTool* gt_uniq(void);

#endif
genometools-1.5.1/src/tools/gt_uniquesub.h000066400000000000000000000017361211610345200206650ustar00rootroot00000000000000/*
  Copyright (c) 2007 Stefan Kurtz 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

#ifndef GT_UNIQUESUB_H
#define GT_UNIQUESUB_H

/* the uniquesub tool */
int gt_uniquesub(int argc, const char **argv, GtError*);

#endif
genometools-1.5.1/testdata/000077500000000000000000000000001211610345200156555ustar00rootroot00000000000000genometools-1.5.1/testdata/Arabidopsis-C99826.embl000066400000000000000000000007351211610345200215650ustar00rootroot00000000000000ID   C99826
XX
DE   gi|3719183|dbj|C99826.1|C99826 C99826 YAC clone CIC8B11 region-specific 
DE   cDNA Arabidopsis thaliana cDNA, mRNA sequence
XX
SQ
     AGCCATTGGGGGCAAAAGGAGCAGCAGCAGATGTTGAGCAAGGGACAGTTCAGGTGAGCG
     ATAAGGTGAAGAAAATGGCTGAGGAGTGTAGAGATGGAGTTGGGAAGATCTCTCAGAGGT
     TCAAGACCTAAAGTAACAGTCTTTTAACTTTTTTGTATCTTGTTTCTACATGATAAAAAT
     AAAAGAGAATAATGGGATGGCCATTACATTTACAGTATTGGTCAGTGATGTTCAGAATTC
     ATAATTGTATCATTTTGTAATCTTTGTTATGTGGTTTACTAATACTTACACTTT
//
genometools-1.5.1/testdata/Arabidopsis-C99826.fna000066400000000000000000000006421211610345200214070ustar00rootroot00000000000000>gi|3719183|dbj|C99826.1|C99826 C99826 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AGCCATTGGGGGCAAAAGGAGCAGCAGCAGATGTTGAGCAAGGGACAGTTCAGGTGAGCG
ATAAGGTGAAGAAAATGGCTGAGGAGTGTAGAGATGGAGTTGGGAAGATCTCTCAGAGGT
TCAAGACCTAAAGTAACAGTCTTTTAACTTTTTTGTATCTTGTTTCTACATGATAAAAAT
AAAAGAGAATAATGGGATGGCCATTACATTTACAGTATTGGTCAGTGATGTTCAGAATTC
ATAATTGTATCATTTTGTAATCTTTGTTATGTGGTTTACTAATACTTACACTTT
genometools-1.5.1/testdata/Arabidopsis-C99826.gbk000066400000000000000000000010731211610345200214050ustar00rootroot00000000000000LOCUS       C99826
DEFINITION  gi|3719183|dbj|C99826.1|C99826 C99826 YAC clone CIC8B11
            region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ACCESSION   atC99826
ORIGIN
              1 AGCCATTGGGGGCAAAAGGAGCAGCAGCAGATGTTGAGCAAGGGACAGTTCAGGTGAGCG
             61 ATAAGGTGAAGAAAATGGCTGAGGAGTGTAGAGATGGAGTTGGGAAGATCTCTCAGAGGT
            121 TCAAGACCTAAAGTAACAGTCTTTTAACTTTTTTGTATCTTGTTTCTACATGATAAAAAT
            181 AAAAGAGAATAATGGGATGGCCATTACATTTACAGTATTGGTCAGTGATGTTCAGAATTC
            241 ATAATTGTATCATTTTGTAATCTTTGTTATGTGGTTTACTAATACTTACACTTT
//
genometools-1.5.1/testdata/Atinsert.embl000066400000000000000000001324171211610345200203170ustar00rootroot00000000000000ID   AF078689; SV 1; linear; mRNA; EST; PLN; 275 BP.
XX
AC   AF078689;
XX
DT   28-JUL-1999 (Rel. 60, Created)
DT   03-MAR-2000 (Rel. 62, Last updated, Version 2)
XX
DE   AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana cDNA
DE   clone IFA2, mRNA sequence.
XX
KW   EST.
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-275
RA   Zhao D., Chen D., Yang C., Zhai Z.;
RT   "Isolation of intermediate filament-like genes from Arabidopsis";
RL   Unpublished.
XX
DR   UNILIB; 6039; 1974.
XX
CC   On Dec 20, 1995 this sequence version replaced gi:1130836.
CC   Contact: Tan K
CC   Plant Development Biology
CC   Institute of Botany
CC   20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..275
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /clone_lib="Arabidopsis thaliana library (Tan K)"
FT                   /clone="IFA2"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:6039"
XX
SQ   Sequence 275 BP; 80 A; 55 C; 70 G; 70 T; 0 other;
     antnnctacn ncnncnntnn cnncnatnna antanacnna tnntnntann aatnaaannc        60
     tanaancnnc nnanaantat ntnnataana aataacaaaa actnannnna tcatnaantt       120
     cttcnttata ttatantttt caatctnaat ttcaattccn ccnctcncct ttttcctctc       180
     cnccttttcc ntctctccna tctnctcccn ccnccnacct tntnatnatt atanctctna       240
     anntccatac aannatataa aaaaaaaaaa aaaaa                                  275
//
ID   C99932; SV 1; linear; mRNA; EST; PLN; 852 BP.
XX
AC   C99932;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 88.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-852
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-852
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..852
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 852 BP; 251 A; 167 C; 160 G; 231 T; 43 other;
     atnrayamtc aaaaatnnan tmtanntttc atatctctcn cttttctctt catcacttcc        60
     tcttcanctn anttcatcat tcaacanntc acaaannnca rannaatana ntacaacant       120
     tcttacantc tcnannanaa tcttnnantn acrananant tnananaana ncnaccatcn       180
     antaanatan tnacaataac aancttctca ntnattaaan ncanannana accctatnaa       240
     tcctctnttt ttnannctnc tnnttacaaa tnnanattnn ttttntacnt naatnntaat       300
     aaaaacnacn ntnnaaatna tcatatttcc ctttacncaa nnatcnaana nacaaactct       360
     cttccattan nttnnnaant naatnttnat ctcaaactct ttntccataa tnnnaancta       420
     cacaaatatt tnactnttac anatnnctta rttnaancna tataacaatn csaaaaaana       480
     atnnnntttc nnacaattna ttcctcnatc aacattctac aacncnaacn aannttacct       540
     ttnaccaann acactnnttc cttttnnntn ncynnaaaan cctttattnt ttaaaccnns       600
     tccaccaacm aaraaaawwa ytttctwtym mtyytccaac aysytycccw wcsaatnttt       660
     tttcccttnn naaaaanacc tncntttcct cctacctttn nnaaaaanaa anttcntttt       720
     tactcccnaa tnaattttcc ccctttnnaa aaaccnaatn cctnnttnna cttannaatt       780
     ttaacccccn aaannnnnaa tnnaannaaa naaaaaaccc ctttncccnt tcccaatcct       840
     tccctanttt nc                                                           852
//
ID   C99931; SV 1; linear; mRNA; EST; PLN; 719 BP.
XX
AC   C99931;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 87-1.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-719
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-719
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..719
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 719 BP; 216 A; 140 C; 132 G; 215 T; 16 other;
     ntnartnttn atctcaaact ctttntccat aatnnnaanc tacacaaata tttnactntt        60
     acanatnnct tantnaancn atataacaat ncnaaaaaan aatnnnnttt cnnacaattn       120
     attcctcnat caacattcta caacncnaac naannttacc ttnaccanna cactnnttct       180
     tttnntnctn anatctttat tnttaaaccn nctcaacaac aananaaant tacattcata       240
     tcaaaccctc caaacaatnt tttcacttnn aanatacttc ntttctctac cttnnaanat       300
     aaattctatt actccnatna ttttctcntt naanaccnat actnnanact annatttaac       360
     ccnaaannnn atnnannann aanaccacat ncacttccaa tcttcctatt tnctcaannc       420
     cataanncaa atncanttnc tacaaacact tnnnnancnn ttaatctncn nttaaanaat       480
     caacnaartt ctaaccatan acaatatwtc tncacttnnt acccattnna aacnttatnn       540
     tktnnnakta acatatctac tnttnctnat taacnancat ccaaannatt ttnntnatna       600
     nccytatctt naactnaatn nttaankcct ataccactct ctccctwaat tctccttctt       660
     ntcwcnacat cncyttrata aaaaatttat tnataatttt ttaraaactt atttttkta        719
//
ID   C99930; SV 1; linear; mRNA; EST; PLN; 746 BP.
XX
AC   C99930;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 86.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-746
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-746
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..746
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 746 BP; 227 A; 151 C; 138 G; 220 T; 10 other;
     ntnaancnat acaacnatnc aaaaaaanan tnnnnattca cacaattnat ttctcttcca        60
     acattctaca acncnaacna annntacytt ntncannaca cancttcttt tnntnctnan       120
     atcttcatcn ttaacccnac anaaaaacaa nanaaantca cattcatatc aaaccctccn       180
     aacaatnttt tcacttnnaa natacttcnt ttctctacct tnnaanataa attctattac       240
     tctnatnatt ttctcnttna anaccnatac tnnanattan natttaaccc naaannatct       300
     nntnnannna naccacatnc acttccaatc ttcctatatn ctcaanncca taanncaaac       360
     ncanttntta caaacacttn nnnancnntt aatctncnnt taaanaatca acnaanctcc       420
     aaccacaaac aattatattc tncancttnn taccccnatt cnaancnatt atnntntnnn       480
     antnaacaat atcatattna tntcanaanc taaaanatnc atcmaaannn tatatnntna       540
     atnatnccat tatcttttna aactnaaatn nttaanntct ctntnaacaa catartctcc       600
     scttaaatat atntcactac ttctttatcc cccnnaataa ccttacaaan aaaaattnat       660
     natttaattt nttatacnac actttattna tncctntnan ntaaccttnt ttccnctccc       720
     cnaatttcct tttttttcct nttttt                                            746
//
ID   C99929; SV 1; linear; mRNA; EST; PLN; 668 BP.
XX
AC   C99929;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 85.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-668
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-668
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..668
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 668 BP; 215 A; 138 C; 138 G; 173 T; 4 other;
     tcaaaatatn natantcaca aatnnantct anntttcaca ttacttnctt tcctcttcat        60
     cacttcctct tccnctnanc tcatcattaa acanntcaca cannncanan naatananta       120
     caacaactct tacantctca cntcnaatct tnnantnacn acaananant tnananacna       180
     ncnaccatca antaanatan tnacaatcac aancttctct ntnattaann acanannana       240
     accctatnaa tcatctattt ttnannctnc cnnttacaaa tnnanattan ttttntacnt       300
     naannntaat ccnaaanncn ntataaataa tcatatttca ctttacncna nnatanaana       360
     nacanaaact cttccaanan nntnnnaant naatnttnat ctcaaactct ttntccacaa       420
     tcnnaaktta aanaaatatt tntctnttac anatnnaaca ntnaancnat acaacnatnc       480
     aaaaaaanan tnnnnattcn cacaattnat ttctcttcca acattctaca acncnaacna       540
     annnttcctt ntnccannac acarcttcct ttnnntnctn araacttcat cnttaacccn       600
     accnaaaaac canaaaaaat ccctttcttt tcaaaccccc cnaaacatnt ttttcccttt       660
     nnaaaaaa                                                                668
//
ID   C99928; SV 1; linear; mRNA; EST; PLN; 800 BP.
XX
AC   C99928;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 84.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-800
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-800
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..800
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 800 BP; 255 A; 145 C; 162 G; 238 T; 0 other;
     nnaanttaaa naaatatttn tctnttacan atnnaacant naancnatac aacnatncaa        60
     aaaaanantn nnnattcaca caattnattt ctcttccaac attctacaac ncnaacnaan       120
     nntaccttnt ncannacaca ncttcttttn ntnctnanat cttcatcntt aacccnacan       180
     aaaaacaana naaantcaca ttcatatcaa accctccana caatnttttc acttnnaana       240
     tacttcnttt ctctaccttn naanataaat tctattactc cnatnatttt ctcnttnaan       300
     accnatactn nanactanna tttaacccna aannnnatnn annannaana ccacatncac       360
     ttccaatctt cctatttnct caannccata anncaaacnc anttnctaca aacacttnnn       420
     nancnnttaa tctncnntta aanaatcaac naantactaa ccatanacaa atatattctn       480
     cancttnnta cccnattnna ancnnttatn ntntnnnant naacaatatc atactnttan       540
     ctnatttaaa cnatncatca aaannatatt tnntnaatna tnccattatc tttnaanctn       600
     aaatnnttaa nntctctata accaacatcn tctccnctta aatatctnca cttctttntc       660
     tacnatcaat caaccttatn aataaanana tatttnatna ntttntaata anaaaacntt       720
     aatntttntn aattntnaan ttattacttc tnttcttctn anttttttta tttcaatnaa       780
     aataaaactc ttaccnnttt                                                   800
//
ID   C99927; SV 1; linear; mRNA; EST; PLN; 797 BP.
XX
AC   C99927;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 83.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-797
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-797
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..797
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 797 BP; 220 A; 140 C; 151 G; 241 T; 45 other;
     ntnaancnat mcmwcnatnm wmaaaamkar tnknnattyr cayratwnat ytctcttcyw        60
     myattctwsw mcncnaayna annntacctt ntnyasnacr mwscttcttt ynntnctnak       120
     atcttcatnc nwtamcccna canaaamacm mkakawantc wcattcatat cmwaccctcc       180
     raacaatntt ttcacttnna anatacttcn tttctctacc ttnnaanata aattctatta       240
     ctctnatnat tttctcnttn aanaccnata ctnnanatta nnatttaacc cnaaannatc       300
     tnntnnannn anaccacatn cacttccaat cttcctatat nctcaanncc ataanncaaa       360
     cncanttntt acaaacactt nnnnancnnt taatctncnn ttaaanaatc aacnaanctc       420
     caaccacaaa caattatatt ctncancttn ntacccnatt cnaancnatt atnntntnnn       480
     antnaacaat ataatattna tntcananct aaaanatnca tccaaaannn tatatnntna       540
     atnatnccat tatctttnaa nctnaaatnn ttaanntctc tntnacaaac atantctccn       600
     tttaaatatc actacttctt tttcaacaac aaccttacna ataaantnna ctttnatnan       660
     tttaatttnt tatacnacaa cnttnttnat ncttntnatn taatcnttnt ttctnctctc       720
     cnanttttcn ttttactttt tttttcatnt tttnctatca atnaaataaa nntataaaac       780
     tctcttnntt ttaaant                                                      797
//
ID   C99926; SV 1; linear; mRNA; EST; PLN; 371 BP.
XX
AC   C99926;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 82.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-371
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-371
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..371
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 371 BP; 115 A; 83 C; 60 G; 101 T; 12 other;
     nnaanttaaa naaatatttn tctnttacan atnnaacant naancnatac aacnatncaa        60
     aaaaanantn nnnattcaca caattnattt ctcttccaac attctacaac ncnaacnaan       120
     nntaccttnt ncannacaca ncttcttttn ntnctnanat cttcatcntt aacccnacan       180
     aaaaacaana naaantcaca ttcatatcaa accmtsswrm cmrkrtyytc acttnnaana       240
     tacttcnttt ctctaccttn tcacctaaat tcaattcatc ntacccnnat cctcnattct       300
     tttncttttt accctnnaan aaatactcat aanccacctc tnttatttac ccccaatctt       360
     cacaanaaaa a                                                            371
//
ID   C99925; SV 1; linear; mRNA; EST; PLN; 565 BP.
XX
AC   C99925;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 81.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-565
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-565
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..565
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 565 BP; 151 A; 117 C; 122 G; 174 T; 1 other;
     cntctccata cnttnttccc naanacatnt ccttnacaaa nntatacaat cttttccnnc        60
     aacttnnntt ncnacatcta ttcnttnttc cccntccttc ccntntnata nncttnatca       120
     ccanaaanna tttactnatt nannaaaatn nnnaatcatc ancantnnaa ctccaacant       180
     caactantan ntcnntacan tnanacanca acncnnatnn acnctncacn accncttcta       240
     nacnatcttt tannttaata aaacanacca aacatataca ancanttnaa nctnntanct       300
     aanatcttta ntcnnnccaa ttcttcntcc atacaannat acaancttnt tccncatntt       360
     nccacccaaa tccnntatnn annatatatn atcntctctt nanatnnnat tntnttnttc       420
     nctaaccnat ctcattctcc nttcacanan antanaaana ttatatatnt ttaanncttt       480
     tnattnttnt aattntncaa tctttnawta ttttcttnnt ccctntaaaa taatccacct       540
     tttnatatat ttacttnatt aactt                                             565
//
ID   C99923; SV 1; linear; mRNA; EST; PLN; 110 BP.
XX
AC   C99923;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 79.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-110
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-110
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..110
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 110 BP; 20 A; 24 C; 23 G; 31 T; 12 other;
     tctnntccnt ctnanacatc nnatcanntn nnnnntacaa tcatctcncc nttcantann        60
     tntttacnna tttcnncnnt cntatanctn ncntnactaa nnctttaacc                  110
//
ID   C99922; SV 1; linear; mRNA; EST; PLN; 815 BP.
XX
AC   C99922;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 78.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-815
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-815
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..815
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 815 BP; 179 A; 125 C; 299 G; 202 T; 10 other;
     nntranatct acsttnctnn anntnntnnt nnttcnnakn ttncnncnnc nntnnaasta        60
     ntatnatccn nanttnaatc nntnnnaant tntnactcaa tcnncsanna asanatacnn       120
     ttncatcnna ncanccnttn acnnantttt ttatntnatc nntnnattna aaattnnnaa       180
     tnanacctca cncncnntnn cnncncntnc ttatncnanc tctatnnatc ttttcnatnt       240
     nnantcncnt cantnnttaa nnantcnttc nnttcctnnc nntnnatntn tantnncnnc       300
     ntntncnncn nttnnatatn tntatntnct aaccantcac ncnntnnanc tttcnttttt       360
     nncnatttna tncncntcnt cntnntnnaa acaccnnntt tnnaaaaatn ncanaanctn       420
     aaaantcccc cnttaccnnc acaanntncs nnttaanatn naaccnntna anntttaacc       480
     tncntcnnan tnnaanataa antnncnntn nttcanntnn tnnnatncat tnacnatttn       540
     cttcnncnna ntnnnannnn tnananannn attananaaa nccttntntt nctntatnat       600
     acnacnnann nanantnnan nanancnncn natttacctn anatnattac acncnccncc       660
     tntncntntn tnnantnnta anannnnana ccacnncnca nnattatnnn tacnanaant       720
     tnnaanatnc tavcntacnc annatatatt aaantnnnca aaaacaatat cattatnatt       780
     nntncacatn tttactntmt naaaancaat ancnt                                  815
//
ID   C99921; SV 1; linear; mRNA; EST; PLN; 602 BP.
XX
AC   C99921;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 77.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-602
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-602
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..602
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 602 BP; 157 A; 119 C; 123 G; 164 T; 39 other;
     cnnnncttct raaanacnca atctnatnta ctcntacatn ctanntncta tctcttctat        60
     aatntctnat cctttctncc ctcccacwcn ttnccntanc ckcaaawtct cctktnayat       120
     ttmcctnmtc anaytntcct natnnatnsn naynttcacm tanataccaa ancacaanaa       180
     attcnaannt nctnnanaaa anncnaccac tttcactaan ancatttnnc tcnannaanc       240
     tnatncnany nccatatccn ttnntnanna antaactttn atnnattnnn naaatnctat       300
     cntaaannaa atcmcmaakn acnannannn tcntntcact nccttatctn ntntcttnaa       360
     tctccaannt tctntwaana ctacaaanct naanctnaca tnncttcctn atactaatna       420
     attnntccat ctcrcmttaa canantttna ttatctaatc cccmanaana aactnnaana       480
     tnatnatnaa atttnctnat tttnctnaat ccymmcccna aaaannaana cmtttnncmc       540
     ttknntnnat tcccaatatt nananaatct tnaaattntt nnaaaatntt tattccccct       600
     tt                                                                      602
//
ID   C99920; SV 1; linear; mRNA; EST; PLN; 92 BP.
XX
AC   C99920;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 76.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-92
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-92
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..92
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 92 BP; 17 A; 19 C; 13 G; 43 T; 0 other;
     tcanctnttt cnttcaacna tctaaactat ctcaatnctt ctttnaatct attntcnntt        60
     tccttntact cntcaatttc atnttttttt tn                                      92
//
ID   C99919; SV 1; linear; mRNA; EST; PLN; 461 BP.
XX
AC   C99919;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 75.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-461
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-461
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..461
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 461 BP; 85 A; 111 C; 84 G; 120 T; 61 other;
     ccctcccnct cctnntttct anttnnnttc nnnttctntt atcnnntttt tcncnnnnnt        60
     cttttntcnn nnccctnnac cnnaattcnc nnntcnacca actcntcana tntnntnctn       120
     cnctacaatn aancaaannn antcacactc tcnnactnan nctctcccct ccncttctnt       180
     aaccatancn nctcnacntc tatntctccn atctaaccan ctctnnnnnt tcnannanan       240
     ataannanaa aantannnan nnacnantat ncttncccnt tctntncana ctattttnat       300
     ntcntctctc tnnncnntca cattnatnaa natcntccta tnnatnctta aantnnnntn       360
     tntcccntcc tntncnntna aantnanctc nnnatatnat tncntcntat anccccncnn       420
     cncnnccnat atnttcaann tnacccnnat cannaaatca a                           461
//
ID   C99918; SV 1; linear; mRNA; EST; PLN; 556 BP.
XX
AC   C99918;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 74.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-556
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-556
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..556
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 556 BP; 147 A; 119 C; 132 G; 150 T; 8 other;
     ntttatcacn ccttncattn atcanaascc cttnctacnn cattnancca knctnccnaa        60
     nctntttctt cnnnaaattc anatncaant natnccactn caaaanctnn aatcattttn       120
     ttncccanca cacatcaact tnacnaanan nttactnmnn aacatantna nnannaaatn       180
     actnaanann aaccaactct tctcaantnn ccaaataanc ccnnnattcc anattctnat       240
     ttntttnacc ntnatcaatc ntnntttnat nnacctccan annncttcaa tctcacatta       300
     tcaaatttcn ctntnatntn nnattcactn tttnnctnnn tatcatcntc ctctctnnca       360
     tacatatatn nnaannaana atctnctcat narnanttct tattnnttaa cnnnaannan       420
     tacccccnna nnattatcat nntanatnnn ctttcctcan aratcaanca nacaattnct       480
     nnnttncctt nccanaactt taccnaaaat cntcactcat ctcannnctn ccaatancna       540
     tatccrattt taaaaa                                                       556
//
ID   C99917; SV 1; linear; mRNA; EST; PLN; 476 BP.
XX
AC   C99917;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 73.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-476
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-476
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..476
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 476 BP; 86 A; 111 C; 98 G; 106 T; 75 other;
     atanncnana tcccccccaa annattncct natntnanna acatnnnnan atcatcntnn        60
     aatcnancnc nnnnantcnc cnntnaantn nntnnntnna cantcncncc cnnacnnacn       120
     cnncatnacc ncttcactac nanctnttan ntttntnnna ctnntcctac natataccnt       180
     ctcttnntnn tnnnnccncn aaactcnnct cannactnnn ctcctcnaaa ttcnnatnaa       240
     nnntntcccn cctntnacna cnnnnttcnn nattnnancn atctannann nnacactctn       300
     anaatntnat cnntnattnn tcnntncnct nnatcacatt nctcnccttn ccantaccac       360
     ttttnacana nttccccttc tttttcncaa cnnncnatnc tnnnanaann natnnntaac       420
     tcnnntnccn nctctnnatc nnanatancn tnntcctctc nnnnttccan annntc           476
//
ID   C99916; SV 1; linear; mRNA; EST; PLN; 865 BP.
XX
AC   C99916;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 72.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-865
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-865
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..865
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 865 BP; 278 A; 157 C; 171 G; 254 T; 5 other;
     nntaataaaa acnacnntnn aaatnatcat atttcccttt acncaannat cnaananaca        60
     aactctcttc cattannttn nnaantnaat nttnatctca aactctttnt ccataatnnn       120
     aanctacaca aatatttnac tnttacanat nncttantna ancnatataa caatncnaaa       180
     aaanaatnnn ntttcnnaca attnattcct cnatcaacat tctacaacnc naacnaannt       240
     taccttnacc annacactnn ttcttttnnt nctnanatct ttattnttaa accnnctcaa       300
     caacaanana aanttacatt catatcaaac cctccaaaca atnttttcac ttnnaanata       360
     cttcntttct ctaccttnna anataaattc tattactccn atnatwttct cnttnaanac       420
     cnatactnna nactannatt taacccnaaa nnnnatnnan nannaanacc acatncactt       480
     ccaatcttcc tatttnctca annccataan ncaaatncan ttnctacaaa cacttnnnna       540
     ncnnttaatc tncnnttaaa naatcaacna antactaacc atanacaaat atattctnca       600
     ncttnntacc cnattnnaaa cnnttatnnt ntnnnantna acaatatcat actnttanct       660
     natttaaacn atncatccaa annatatttn ntnaatnatn ccattatctt tnaanctnaa       720
     atnnttaann tctctataac caacatcntc tccncttaaa tatctncmct tctttntcta       780
     craycaatcc accttatnaa taaaaaaatt ttaatttnat naatttntta taanaaaact       840
     ttaatntttn ttaaatntna aattt                                             865
//
ID   C99914; SV 1; linear; mRNA; EST; PLN; 628 BP.
XX
AC   C99914;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 70.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-628
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-628
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..628
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 628 BP; 148 A; 161 C; 150 G; 162 T; 7 other;
     nnnacnaacc nntntaccac natttnnttc ntcactntct nncctaccca aaancnnatn        60
     naatcttnnt naatacatnn naananatnn ancccaaatc attaaantcc cttcaanacc       120
     cnaaactttt nnnccnnntc nctcntntac cnntttatcc nnttnntccn ttatncanac       180
     cnatacaatc atccacnacc natcacccnn tttttnattn nttaaacaaa caaccaaacn       240
     antcnnttct ctacatttcc ttcnnnantn ntnnttctct aacnnctcaa canttaaccn       300
     aattnncntn nnnnctcnan nananccanc aacnntttat atnnntnntt cnaccncccn       360
     ttnacnnctc ntcttncant nattatttct cnnctaaann cnntntaacc aaanacaaca       420
     cnccanaata tctaccaaaa annnttcntn actcstactt tncnataaaa ntttcatnat       480
     cccatcatnn ncaccncaan ctnaaatcct aacccatcca nnccnttnnt nnntttttaa       540
     cacatttntt nntttnnaac tccactttnn raaaccttcc ttttnccnnc nttcccawtr       600
     anaaccttkn cccccttttc ccccaacc                                          628
//
ID   C99913; SV 1; linear; mRNA; EST; PLN; 497 BP.
XX
AC   C99913;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 69.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-497
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-497
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..497
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 497 BP; 114 A; 82 C; 148 G; 148 T; 5 other;
     cctntcccat cnnnccnttr ntnnnttttt nacccattnc nnttnnanct cnacnttsna        60
     aancntcntt nncnncnttc cnatsatcnc atnnccactt tttnccnanc anaatatnaa       120
     tncnncnttn ctcancnacn aactnnnaat cncantcana ttnnatnatc caaannanna       180
     tatttctann tnnaanattn anncnttnnt nannaanntt atnactnana annaanntna       240
     ancnatnana annaaantna anaanttnan anactcnncn nanatntcac tnancattna       300
     cnntnntnnt ttnncncacn antcnctttn canantcacc aannantntc aacnnttttt       360
     nnaacntntc ntnnacttnt cacntnntnc ttaaaaattn ttaccntttt ctaactcttt       420
     tattattart tnnttnaatt atacntntcn ttcctctntt anttnttata atataataaa       480
     tcnatttact ctttntt                                                      497
//
ID   C99911; SV 1; linear; mRNA; EST; PLN; 661 BP.
XX
AC   C99911;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 67.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-661
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-661
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..661
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 661 BP; 186 A; 117 C; 149 G; 206 T; 3 other;
     cntttctncc acattaaaac anaanantnc aacaattnaa nncatanaaa antnncctta        60
     tnaancanct nccattnctt tcnannctat tccacntacc ctnnctcaaa actntnnnnt       120
     taacntnatc cntactatna ctncattnca annnaancat ncaaatnntn aaaacncatn       180
     nactnntatt nacnnnaaca ctnntncaat anctnatatn aaanananca anatatnnna       240
     ttcntacaat ntnaanncnc aaactttcaa nacnnctata naancancnt ntatncttct       300
     aannnatcna tnatatantn antnnaatca anaanaanca anctcctnna tctnnacctt       360
     caaancctac cattnanaca naannanatn canacaacna acaaattctt cccnactaan       420
     cnaannnana aacactttnn tctcancata actcaatctc tnttttcact tntttaatnn       480
     ttncactctt ttnnctatta tcttcccttn acatatcttt ttaattctnc anttttnact       540
     tnnntnanat aaaattttcc caanntnntt tttttttntt tnttttnnna atattaactt       600
     ttttnaattt tcntantccc tttnttnntt tttaaaattc caattnttat tnttcttttt       660
     n                                                                       661
//
ID   C99910; SV 1; linear; mRNA; EST; PLN; 241 BP.
XX
AC   C99910;
XX
DT   09-APR-1999 (Rel. 59, Created)
DT   09-APR-1999 (Rel. 59, Last updated, Version 1)
XX
DE   Arabidopsis thaliana YAC CIC3B1 region specific cDNA, clone 66.
XX
KW   EST(expressed sequence tag).
XX
OS   Arabidopsis thaliana (thale cress)
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids;
OC   eurosids II; Brassicales; Brassicaceae; Arabidopsis.
XX
RN   [1]
RP   1-241
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   ;
RL   Submitted (08-OCT-1998) to the EMBL/GenBank/DDBJ databases.
RL   Reiko Motohashi, Institute of Physical and Chemical Research(RIKEN),
RL   Laboratory of Plant Molecular Biology; 3-1-1, Koyadai, Tsukuba 305-0074,
RL   Japan (E-mail:motohasi@rtc.riken.go.jp, Tel:+81-298-36-4359)
XX
RN   [2]
RP   1-241
RA   Motohashi R., Shinozaki K., Yamaguchi-Shinozaki K.;
RT   "Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2";
RL   Unpublished.
XX
DR   UNILIB; 1782; 1741.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..241
FT                   /organism="Arabidopsis thaliana"
FT                   /mol_type="mRNA"
FT                   /db_xref="taxon:3702"
FT                   /db_xref="UNILIB:1782"
XX
SQ   Sequence 241 BP; 79 A; 29 C; 50 G; 82 T; 1 other;
     cncscctaan aannaaaana tnanaanaan aanaanaana aaactnannt ctnaananac        60
     ctttaatatt tttncntnnt ctantttact ttnttatcan aaacaaanaa aatcttttnt       120
     nncnttannt nttaantaan ntttttnttt tntttnaaac ttaaaaaaaa naactactct       180
     tcnttttnta annttataat atntttnntt tantccttat cccaaaaact tncattttnc       240
     c                                                                       241
//
genometools-1.5.1/testdata/Atinsert.fna000066400000000000000000000346371211610345200201510ustar00rootroot00000000000000>gi|5587835|gb|AF078689.1|AF078689 AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana cDNA clone IFA2, mRNA sequence
ANTNNCTACNNCNNCNNTNNCNNCNATNNAANTANACNNATNNTNNTANNAATNAAANNCTANAANCNNC
NNANAANTATNTNNATAANAAATAACAAAAACTNANNNNATCATNAANTTCTTCNTTATATTATANTTTT
CAATCTNAATTTCAATTCCNCCNCTCNCCTTTTTCCTCTCCNCCTTTTCCNTCTCTCCNATCTNCTCCCN
CCNCCNACCTTNTNATNATTATANCTCTNAANNTCCATACAANNATATAAAAAAAAAAAAAAAAA
>gi|4714049|dbj|C99932.1|C99932 C99932 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 88, mRNA sequence
ATNRAYAMTCAAAAATNNANTMTANNTTTCATATCTCTCNCTTTTCTCTTCATCACTTCCTCTTCANCTN
ANTTCATCATTCAACANNTCACAAANNNCARANNAATANANTACAACANTTCTTACANTCTCNANNANAA
TCTTNNANTNACRANANANTTNANANAANANCNACCATCNANTAANATANTNACAATAACAANCTTCTCA
NTNATTAAANNCANANNANAACCCTATNAATCCTCTNTTTTTNANNCTNCTNNTTACAAATNNANATTNN
TTTTNTACNTNAATNNTAATAAAAACNACNNTNNAAATNATCATATTTCCCTTTACNCAANNATCNAANA
NACAAACTCTCTTCCATTANNTTNNNAANTNAATNTTNATCTCAAACTCTTTNTCCATAATNNNAANCTA
CACAAATATTTNACTNTTACANATNNCTTARTTNAANCNATATAACAATNCSAAAAAANAATNNNNTTTC
NNACAATTNATTCCTCNATCAACATTCTACAACNCNAACNAANNTTACCTTTNACCAANNACACTNNTTC
CTTTTNNNTNNCYNNAAAANCCTTTATTNTTTAAACCNNSTCCACCAACMAARAAAAWWAYTTTCTWTYM
MTYYTCCAACAYSYTYCCCWWCSAATNTTTTTTCCCTTNNNAAAAANACCTNCNTTTCCTCCTACCTTTN
NNAAAAANAAANTTCNTTTTTACTCCCNAATNAATTTTCCCCCTTTNNAAAAACCNAATNCCTNNTTNNA
CTTANNAATTTTAACCCCCNAAANNNNNAATNNAANNAAANAAAAAACCCCTTTNCCCNTTCCCAATCCT
TCCCTANTTTNC
>gi|4714048|dbj|C99931.1|C99931 C99931 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 87-1, mRNA sequence
NTNARTNTTNATCTCAAACTCTTTNTCCATAATNNNAANCTACACAAATATTTNACTNTTACANATNNCT
TANTNAANCNATATAACAATNCNAAAAAANAATNNNNTTTCNNACAATTNATTCCTCNATCAACATTCTA
CAACNCNAACNAANNTTACCTTNACCANNACACTNNTTCTTTTNNTNCTNANATCTTTATTNTTAAACCN
NCTCAACAACAANANAAANTTACATTCATATCAAACCCTCCAAACAATNTTTTCACTTNNAANATACTTC
NTTTCTCTACCTTNNAANATAAATTCTATTACTCCNATNATTTTCTCNTTNAANACCNATACTNNANACT
ANNATTTAACCCNAAANNNNATNNANNANNAANACCACATNCACTTCCAATCTTCCTATTTNCTCAANNC
CATAANNCAAATNCANTTNCTACAAACACTTNNNNANCNNTTAATCTNCNNTTAAANAATCAACNAARTT
CTAACCATANACAATATWTCTNCACTTNNTACCCATTNNAAACNTTATNNTKTNNNAKTAACATATCTAC
TNTTNCTNATTAACNANCATCCAAANNATTTTNNTNATNANCCYTATCTTNAACTNAATNNTTAANKCCT
ATACCACTCTCTCCCTWAATTCTCCTTCTTNTCWCNACATCNCYTTRATAAAAAATTTATTNATAATTTT
TTARAAACTTATTTTTKTA
>gi|4714047|dbj|C99930.1|C99930 C99930 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 86, mRNA sequence
NTNAANCNATACAACNATNCAAAAAAANANTNNNNATTCACACAATTNATTTCTCTTCCAACATTCTACA
ACNCNAACNAANNNTACYTTNTNCANNACACANCTTCTTTTNNTNCTNANATCTTCATCNTTAACCCNAC
ANAAAAACAANANAAANTCACATTCATATCAAACCCTCCNAACAATNTTTTCACTTNNAANATACTTCNT
TTCTCTACCTTNNAANATAAATTCTATTACTCTNATNATTTTCTCNTTNAANACCNATACTNNANATTAN
NATTTAACCCNAAANNATCTNNTNNANNNANACCACATNCACTTCCAATCTTCCTATATNCTCAANNCCA
TAANNCAAACNCANTTNTTACAAACACTTNNNNANCNNTTAATCTNCNNTTAAANAATCAACNAANCTCC
AACCACAAACAATTATATTCTNCANCTTNNTACCCCNATTCNAANCNATTATNNTNTNNNANTNAACAAT
ATCATATTNATNTCANAANCTAAAANATNCATCMAAANNNTATATNNTNAATNATNCCATTATCTTTTNA
AACTNAAATNNTTAANNTCTCTNTNAACAACATARTCTCCSCTTAAATATATNTCACTACTTCTTTATCC
CCCNNAATAACCTTACAAANAAAAATTNATNATTTAATTTNTTATACNACACTTTATTNATNCCTNTNAN
NTAACCTTNTTTCCNCTCCCCNAATTTCCTTTTTTTTCCTNTTTTT
>gi|4714046|dbj|C99929.1|C99929 C99929 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 85, mRNA sequence
TCAAAATATNNATANTCACAAATNNANTCTANNTTTCACATTACTTNCTTTCCTCTTCATCACTTCCTCT
TCCNCTNANCTCATCATTAAACANNTCACACANNNCANANNAATANANTACAACAACTCTTACANTCTCA
CNTCNAATCTTNNANTNACNACAANANANTTNANANACNANCNACCATCAANTAANATANTNACAATCAC
AANCTTCTCTNTNATTAANNACANANNANAACCCTATNAATCATCTATTTTTNANNCTNCCNNTTACAAA
TNNANATTANTTTTNTACNTNAANNNTAATCCNAAANNCNNTATAAATAATCATATTTCACTTTACNCNA
NNATANAANANACANAAACTCTTCCAANANNNTNNNAANTNAATNTTNATCTCAAACTCTTTNTCCACAA
TCNNAAKTTAAANAAATATTTNTCTNTTACANATNNAACANTNAANCNATACAACNATNCAAAAAAANAN
TNNNNATTCNCACAATTNATTTCTCTTCCAACATTCTACAACNCNAACNAANNNTTCCTTNTNCCANNAC
ACARCTTCCTTTNNNTNCTNARAACTTCATCNTTAACCCNACCNAAAAACCANAAAAAATCCCTTTCTTT
TCAAACCCCCCNAAACATNTTTTTCCCTTTNNAAAAAA
>gi|4714045|dbj|C99928.1|C99928 C99928 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 84, mRNA sequence
NNAANTTAAANAAATATTTNTCTNTTACANATNNAACANTNAANCNATACAACNATNCAAAAAAANANTN
NNNATTCACACAATTNATTTCTCTTCCAACATTCTACAACNCNAACNAANNNTACCTTNTNCANNACACA
NCTTCTTTTNNTNCTNANATCTTCATCNTTAACCCNACANAAAAACAANANAAANTCACATTCATATCAA
ACCCTCCANACAATNTTTTCACTTNNAANATACTTCNTTTCTCTACCTTNNAANATAAATTCTATTACTC
CNATNATTTTCTCNTTNAANACCNATACTNNANACTANNATTTAACCCNAAANNNNATNNANNANNAANA
CCACATNCACTTCCAATCTTCCTATTTNCTCAANNCCATAANNCAAACNCANTTNCTACAAACACTTNNN
NANCNNTTAATCTNCNNTTAAANAATCAACNAANTACTAACCATANACAAATATATTCTNCANCTTNNTA
CCCNATTNNAANCNNTTATNNTNTNNNANTNAACAATATCATACTNTTANCTNATTTAAACNATNCATCA
AAANNATATTTNNTNAATNATNCCATTATCTTTNAANCTNAAATNNTTAANNTCTCTATAACCAACATCN
TCTCCNCTTAAATATCTNCACTTCTTTNTCTACNATCAATCAACCTTATNAATAAANANATATTTNATNA
NTTTNTAATAANAAAACNTTAATNTTTNTNAATTNTNAANTTATTACTTCTNTTCTTCTNANTTTTTTTA
TTTCAATNAAAATAAAACTCTTACCNNTTT
>gi|4714044|dbj|C99927.1|C99927 C99927 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 83, mRNA sequence
NTNAANCNATMCMWCNATNMWMAAAAMKARTNKNNATTYRCAYRATWNATYTCTCTTCYWMYATTCTWSW
MCNCNAAYNAANNNTACCTTNTNYASNACRMWSCTTCTTTYNNTNCTNAKATCTTCATNCNWTAMCCCNA
CANAAAMACMMKAKAWANTCWCATTCATATCMWACCCTCCRAACAATNTTTTCACTTNNAANATACTTCN
TTTCTCTACCTTNNAANATAAATTCTATTACTCTNATNATTTTCTCNTTNAANACCNATACTNNANATTA
NNATTTAACCCNAAANNATCTNNTNNANNNANACCACATNCACTTCCAATCTTCCTATATNCTCAANNCC
ATAANNCAAACNCANTTNTTACAAACACTTNNNNANCNNTTAATCTNCNNTTAAANAATCAACNAANCTC
CAACCACAAACAATTATATTCTNCANCTTNNTACCCNATTCNAANCNATTATNNTNTNNNANTNAACAAT
ATAATATTNATNTCANANCTAAAANATNCATCCAAAANNNTATATNNTNAATNATNCCATTATCTTTNAA
NCTNAAATNNTTAANNTCTCTNTNACAAACATANTCTCCNTTTAAATATCACTACTTCTTTTTCAACAAC
AACCTTACNAATAAANTNNACTTTNATNANTTTAATTTNTTATACNACAACNTTNTTNATNCTTNTNATN
TAATCNTTNTTTCTNCTCTCCNANTTTTCNTTTTACTTTTTTTTTCATNTTTTNCTATCAATNAAATAAA
NNTATAAAACTCTCTTNNTTTTAAANT
>gi|4714043|dbj|C99926.1|C99926 C99926 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 82, mRNA sequence
NNAANTTAAANAAATATTTNTCTNTTACANATNNAACANTNAANCNATACAACNATNCAAAAAAANANTN
NNNATTCACACAATTNATTTCTCTTCCAACATTCTACAACNCNAACNAANNNTACCTTNTNCANNACACA
NCTTCTTTTNNTNCTNANATCTTCATCNTTAACCCNACANAAAAACAANANAAANTCACATTCATATCAA
ACCMTSSWRMCMRKRTYYTCACTTNNAANATACTTCNTTTCTCTACCTTNTCACCTAAATTCAATTCATC
NTACCCNNATCCTCNATTCTTTTNCTTTTTACCCTNNAANAAATACTCATAANCCACCTCTNTTATTTAC
CCCCAATCTTCACAANAAAAA
>gi|4714042|dbj|C99925.1|C99925 C99925 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 81, mRNA sequence
CNTCTCCATACNTTNTTCCCNAANACATNTCCTTNACAAANNTATACAATCTTTTCCNNCAACTTNNNTT
NCNACATCTATTCNTTNTTCCCCNTCCTTCCCNTNTNATANNCTTNATCACCANAAANNATTTACTNATT
NANNAAAATNNNNAATCATCANCANTNNAACTCCAACANTCAACTANTANNTCNNTACANTNANACANCA
ACNCNNATNNACNCTNCACNACCNCTTCTANACNATCTTTTANNTTAATAAAACANACCAAACATATACA
ANCANTTNAANCTNNTANCTAANATCTTTANTCNNNCCAATTCTTCNTCCATACAANNATACAANCTTNT
TCCNCATNTTNCCACCCAAATCCNNTATNNANNATATATNATCNTCTCTTNANATNNNATTNTNTTNTTC
NCTAACCNATCTCATTCTCCNTTCACANANANTANAAANATTATATATNTTTAANNCTTTTNATTNTTNT
AATTNTNCAATCTTTNAWTATTTTCTTNNTCCCTNTAAAATAATCCACCTTTTNATATATTTACTTNATT
AACTT
>gi|4714041|dbj|C99923.1|C99923 C99923 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 79, mRNA sequence
TCTNNTCCNTCTNANACATCNNATCANNTNNNNNNTACAATCATCTCNCCNTTCANTANNTNTTTACNNA
TTTCNNCNNTCNTATANCTNNCNTNACTAANNCTTTAACC
>gi|4714040|dbj|C99922.1|C99922 C99922 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 78, mRNA sequence
NNTRANATCTACSTTNCTNNANNTNNTNNTNNTTCNNAKNTTNCNNCNNCNNTNNAASTANTATNATCCN
NANTTNAATCNNTNNNAANTTNTNACTCAATCNNCSANNAASANATACNNTTNCATCNNANCANCCNTTN
ACNNANTTTTTTATNTNATCNNTNNATTNAAAATTNNNAATNANACCTCACNCNCNNTNNCNNCNCNTNC
TTATNCNANCTCTATNNATCTTTTCNATNTNNANTCNCNTCANTNNTTAANNANTCNTTCNNTTCCTNNC
NNTNNATNTNTANTNNCNNCNTNTNCNNCNNTTNNATATNTNTATNTNCTAACCANTCACNCNNTNNANC
TTTCNTTTTTNNCNATTTNATNCNCNTCNTCNTNNTNNAAACACCNNNTTTNNAAAAATNNCANAANCTN
AAAANTCCCCCNTTACCNNCACAANNTNCSNNTTAANATNNAACCNNTNAANNTTTAACCTNCNTCNNAN
TNNAANATAAANTNNCNNTNNTTCANNTNNTNNNATNCATTNACNATTTNCTTCNNCNNANTNNNANNNN
TNANANANNNATTANANAAANCCTTNTNTTNCTNTATNATACNACNNANNNANANTNNANNANANCNNCN
NATTTACCTNANATNATTACACNCNCCNCCTNTNCNTNTNTNNANTNNTAANANNNNANACCACNNCNCA
NNATTATNNNTACNANAANTTNNAANATNCTAVCNTACNCANNATATATTAAANTNNNCAAAAACAATAT
CATTATNATTNNTNCACATNTTTACTNTMTNAAAANCAATANCNT
>gi|4714039|dbj|C99921.1|C99921 C99921 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 77, mRNA sequence
CNNNNCTTCTRAAANACNCAATCTNATNTACTCNTACATNCTANNTNCTATCTCTTCTATAATNTCTNAT
CCTTTCTNCCCTCCCACWCNTTNCCNTANCCKCAAAWTCTCCTKTNAYATTTMCCTNMTCANAYTNTCCT
NATNNATNSNNAYNTTCACMTANATACCAAANCACAANAAATTCNAANNTNCTNNANAAAANNCNACCAC
TTTCACTAANANCATTTNNCTCNANNAANCTNATNCNANYNCCATATCCNTTNNTNANNAANTAACTTTN
ATNNATTNNNNAAATNCTATCNTAAANNAAATCMCMAAKNACNANNANNNTCNTNTCACTNCCTTATCTN
NTNTCTTNAATCTCCAANNTTCTNTWAANACTACAAANCTNAANCTNACATNNCTTCCTNATACTAATNA
ATTNNTCCATCTCRCMTTAACANANTTTNATTATCTAATCCCCMANAANAAACTNNAANATNATNATNAA
ATTTNCTNATTTTNCTNAATCCYMMCCCNAAAAANNAANACMTTTNNCMCTTKNNTNNATTCCCAATATT
NANANAATCTTNAAATTNTTNNAAAATNTTTATTCCCCCTTT
>gi|4714038|dbj|C99920.1|C99920 C99920 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 76, mRNA sequence
TCANCTNTTTCNTTCAACNATCTAAACTATCTCAATNCTTCTTTNAATCTATTNTCNNTTTCCTTNTACT
CNTCAATTTCATNTTTTTTTTN
>gi|4714037|dbj|C99919.1|C99919 C99919 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 75, mRNA sequence
CCCTCCCNCTCCTNNTTTCTANTTNNNTTCNNNTTCTNTTATCNNNTTTTTCNCNNNNNTCTTTTNTCNN
NNCCCTNNACCNNAATTCNCNNNTCNACCAACTCNTCANATNTNNTNCTNCNCTACAATNAANCAAANNN
ANTCACACTCTCNNACTNANNCTCTCCCCTCCNCTTCTNTAACCATANCNNCTCNACNTCTATNTCTCCN
ATCTAACCANCTCTNNNNNTTCNANNANANATAANNANAAAANTANNNANNNACNANTATNCTTNCCCNT
TCTNTNCANACTATTTTNATNTCNTCTCTCTNNNCNNTCACATTNATNAANATCNTCCTATNNATNCTTA
AANTNNNNTNTNTCCCNTCCTNTNCNNTNAAANTNANCTCNNNATATNATTNCNTCNTATANCCCCNCNN
CNCNNCCNATATNTTCAANNTNACCCNNATCANNAAATCAA
>gi|4714036|dbj|C99918.1|C99918 C99918 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 74, mRNA sequence
NTTTATCACNCCTTNCATTNATCANAASCCCTTNCTACNNCATTNANCCAKNCTNCCNAANCTNTTTCTT
CNNNAAATTCANATNCAANTNATNCCACTNCAAAANCTNNAATCATTTTNTTNCCCANCACACATCAACT
TNACNAANANNTTACTNMNNAACATANTNANNANNAAATNACTNAANANNAACCAACTCTTCTCAANTNN
CCAAATAANCCCNNNATTCCANATTCTNATTTNTTTNACCNTNATCAATCNTNNTTTNATNNACCTCCAN
ANNNCTTCAATCTCACATTATCAAATTTCNCTNTNATNTNNNATTCACTNTTTNNCTNNNTATCATCNTC
CTCTCTNNCATACATATATNNNAANNAANAATCTNCTCATNARNANTTCTTATTNNTTAACNNNAANNAN
TACCCCCNNANNATTATCATNNTANATNNNCTTTCCTCANARATCAANCANACAATTNCTNNNTTNCCTT
NCCANAACTTTACCNAAAATCNTCACTCATCTCANNNCTNCCAATANCNATATCCRATTTTAAAAA
>gi|4714035|dbj|C99917.1|C99917 C99917 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 73, mRNA sequence
ATANNCNANATCCCCCCCAAANNATTNCCTNATNTNANNAACATNNNNANATCATCNTNNAATCNANCNC
NNNNANTCNCCNNTNAANTNNNTNNNTNNACANTCNCNCCCNNACNNACNCNNCATNACCNCTTCACTAC
NANCTNTTANNTTTNTNNNACTNNTCCTACNATATACCNTCTCTTNNTNNTNNNNCCNCNAAACTCNNCT
CANNACTNNNCTCCTCNAAATTCNNATNAANNNTNTCCCNCCTNTNACNACNNNNTTCNNNATTNNANCN
ATCTANNANNNNACACTCTNANAATNTNATCNNTNATTNNTCNNTNCNCTNNATCACATTNCTCNCCTTN
CCANTACCACTTTTNACANANTTCCCCTTCTTTTTCNCAACNNNCNATNCTNNNANAANNNATNNNTAAC
TCNNNTNCCNNCTCTNNATCNNANATANCNTNNTCCTCTCNNNNTTCCANANNNTC
>gi|4714034|dbj|C99916.1|C99916 C99916 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 72, mRNA sequence
NNTAATAAAAACNACNNTNNAAATNATCATATTTCCCTTTACNCAANNATCNAANANACAAACTCTCTTC
CATTANNTTNNNAANTNAATNTTNATCTCAAACTCTTTNTCCATAATNNNAANCTACACAAATATTTNAC
TNTTACANATNNCTTANTNAANCNATATAACAATNCNAAAAAANAATNNNNTTTCNNACAATTNATTCCT
CNATCAACATTCTACAACNCNAACNAANNTTACCTTNACCANNACACTNNTTCTTTTNNTNCTNANATCT
TTATTNTTAAACCNNCTCAACAACAANANAAANTTACATTCATATCAAACCCTCCAAACAATNTTTTCAC
TTNNAANATACTTCNTTTCTCTACCTTNNAANATAAATTCTATTACTCCNATNATWTTCTCNTTNAANAC
CNATACTNNANACTANNATTTAACCCNAAANNNNATNNANNANNAANACCACATNCACTTCCAATCTTCC
TATTTNCTCAANNCCATAANNCAAATNCANTTNCTACAAACACTTNNNNANCNNTTAATCTNCNNTTAAA
NAATCAACNAANTACTAACCATANACAAATATATTCTNCANCTTNNTACCCNATTNNAAACNNTTATNNT
NTNNNANTNAACAATATCATACTNTTANCTNATTTAAACNATNCATCCAAANNATATTTNNTNAATNATN
CCATTATCTTTNAANCTNAAATNNTTAANNTCTCTATAACCAACATCNTCTCCNCTTAAATATCTNCMCT
TCTTTNTCTACRAYCAATCCACCTTATNAATAAAAAAATTTTAATTTNATNAATTTNTTATAANAAAACT
TTAATNTTTNTTAAATNTNAAATTT
>gi|4714033|dbj|C99914.1|C99914 C99914 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 70, mRNA sequence
NNNACNAACCNNTNTACCACNATTTNNTTCNTCACTNTCTNNCCTACCCAAAANCNNATNNAATCTTNNT
NAATACATNNNAANANATNNANCCCAAATCATTAAANTCCCTTCAANACCCNAAACTTTTNNNCCNNNTC
NCTCNTNTACCNNTTTATCCNNTTNNTCCNTTATNCANACCNATACAATCATCCACNACCNATCACCCNN
TTTTTNATTNNTTAAACAAACAACCAAACNANTCNNTTCTCTACATTTCCTTCNNNANTNNTNNTTCTCT
AACNNCTCAACANTTAACCNAATTNNCNTNNNNNCTCNANNANANCCANCAACNNTTTATATNNNTNNTT
CNACCNCCCNTTNACNNCTCNTCTTNCANTNATTATTTCTCNNCTAAANNCNNTNTAACCAAANACAACA
CNCCANAATATCTACCAAAAANNNTTCNTNACTCSTACTTTNCNATAAAANTTTCATNATCCCATCATNN
NCACCNCAANCTNAAATCCTAACCCATCCANNCCNTTNNTNNNTTTTTAACACATTTNTTNNTTTNNAAC
TCCACTTTNNRAAACCTTCCTTTTNCCNNCNTTCCCAWTRANAACCTTKNCCCCCTTTTCCCCCAACC
>gi|4714032|dbj|C99913.1|C99913 C99913 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 69, mRNA sequence
CCTNTCCCATCNNNCCNTTRNTNNNTTTTTNACCCATTNCNNTTNNANCTCNACNTTSNAAANCNTCNTT
NNCNNCNTTCCNATSATCNCATNNCCACTTTTTNCCNANCANAATATNAATNCNNCNTTNCTCANCNACN
AACTNNNAATCNCANTCANATTNNATNATCCAAANNANNATATTTCTANNTNNAANATTNANNCNTTNNT
NANNAANNTTATNACTNANAANNAANNTNAANCNATNANAANNAAANTNAANAANTTNANANACTCNNCN
NANATNTCACTNANCATTNACNNTNNTNNTTTNNCNCACNANTCNCTTTNCANANTCACCAANNANTNTC
AACNNTTTTTNNAACNTNTCNTNNACTTNTCACNTNNTNCTTAAAAATTNTTACCNTTTTCTAACTCTTT
TATTATTARTTNNTTNAATTATACNTNTCNTTCCTCTNTTANTTNTTATAATATAATAAATCNATTTACT
CTTTNTT
>gi|4714031|dbj|C99911.1|C99911 C99911 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 67, mRNA sequence
CNTTTCTNCCACATTAAAACANAANANTNCAACAATTNAANNCATANAAAANTNNCCTTATNAANCANCT
NCCATTNCTTTCNANNCTATTCCACNTACCCTNNCTCAAAACTNTNNNNTTAACNTNATCCNTACTATNA
CTNCATTNCAANNNAANCATNCAAATNNTNAAAACNCATNNACTNNTATTNACNNNAACACTNNTNCAAT
ANCTNATATNAAANANANCAANATATNNNATTCNTACAATNTNAANNCNCAAACTTTCAANACNNCTATA
NAANCANCNTNTATNCTTCTAANNNATCNATNATATANTNANTNNAATCAANAANAANCAANCTCCTNNA
TCTNNACCTTCAAANCCTACCATTNANACANAANNANATNCANACAACNAACAAATTCTTCCCNACTAAN
CNAANNNANAAACACTTTNNTCTCANCATAACTCAATCTCTNTTTTCACTTNTTTAATNNTTNCACTCTT
TTNNCTATTATCTTCCCTTNACATATCTTTTTAATTCTNCANTTTTNACTTNNNTNANATAAAATTTTCC
CAANNTNNTTTTTTTTTNTTTNTTTTNNNAATATTAACTTTTTTNAATTTTCNTANTCCCTTTNTTNNTT
TTTAAAATTCCAATTNTTATTNTTCTTTTTN
>gi|4714030|dbj|C99910.1|C99910 C99910 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 66, mRNA sequence
CNCSCCTAANAANNAAAANATNANAANAANAANAANAANAAAACTNANNTCTNAANANACCTTTAATATT
TTTNCNTNNTCTANTTTACTTTNTTATCANAAACAAANAAAATCTTTTNTNNCNTTANNTNTTAANTAAN
NTTTTTNTTTTNTTTNAAACTTAAAAAAAANAACTACTCTTCNTTTTNTAANNTTATAATATNTTTNNTT
TANTCCTTATCCCAAAAACTTNCATTTTNCC
genometools-1.5.1/testdata/Atinsert.gbk000066400000000000000000001233061211610345200201400ustar00rootroot00000000000000LOCUS       AF078689                 275 bp    mRNA    linear   EST 26-JUL-1999
DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
ORIGIN      
        1 antnnctacn ncnncnntnn cnncnatnna antanacnna tnntnntann aatnaaannc
       61 tanaancnnc nnanaantat ntnnataana aataacaaaa actnannnna tcatnaantt
      121 cttcnttata ttatantttt caatctnaat ttcaattccn ccnctcncct ttttcctctc
      181 cnccttttcc ntctctccna tctnctcccn ccnccnacct tntnatnatt atanctctna
      241 anntccatac aannatataa aaaaaaaaaa aaaaa
//

LOCUS       C99932                   852 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99932 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 88, mRNA sequence.
ACCESSION   C99932
VERSION     C99932.1  GI:4714049
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 852)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..852
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="88"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 atnrayamtc aaaaatnnan tmtanntttc atatctctcn cttttctctt catcacttcc
       61 tcttcanctn anttcatcat tcaacanntc acaaannnca rannaatana ntacaacant
      121 tcttacantc tcnannanaa tcttnnantn acrananant tnananaana ncnaccatcn
      181 antaanatan tnacaataac aancttctca ntnattaaan ncanannana accctatnaa
      241 tcctctnttt ttnannctnc tnnttacaaa tnnanattnn ttttntacnt naatnntaat
      301 aaaaacnacn ntnnaaatna tcatatttcc ctttacncaa nnatcnaana nacaaactct
      361 cttccattan nttnnnaant naatnttnat ctcaaactct ttntccataa tnnnaancta
      421 cacaaatatt tnactnttac anatnnctta rttnaancna tataacaatn csaaaaaana
      481 atnnnntttc nnacaattna ttcctcnatc aacattctac aacncnaacn aannttacct
      541 ttnaccaann acactnnttc cttttnnntn ncynnaaaan cctttattnt ttaaaccnns
      601 tccaccaacm aaraaaawwa ytttctwtym mtyytccaac aysytycccw wcsaatnttt
      661 tttcccttnn naaaaanacc tncntttcct cctacctttn nnaaaaanaa anttcntttt
      721 tactcccnaa tnaattttcc ccctttnnaa aaaccnaatn cctnnttnna cttannaatt
      781 ttaacccccn aaannnnnaa tnnaannaaa naaaaaaccc ctttncccnt tcccaatcct
      841 tccctanttt nc
//

LOCUS       C99931                   719 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99931 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 87-1, mRNA sequence.
ACCESSION   C99931
VERSION     C99931.1  GI:4714048
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 719)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..719
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="87-1"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 ntnartnttn atctcaaact ctttntccat aatnnnaanc tacacaaata tttnactntt
       61 acanatnnct tantnaancn atataacaat ncnaaaaaan aatnnnnttt cnnacaattn
      121 attcctcnat caacattcta caacncnaac naannttacc ttnaccanna cactnnttct
      181 tttnntnctn anatctttat tnttaaaccn nctcaacaac aananaaant tacattcata
      241 tcaaaccctc caaacaatnt tttcacttnn aanatacttc ntttctctac cttnnaanat
      301 aaattctatt actccnatna ttttctcntt naanaccnat actnnanact annatttaac
      361 ccnaaannnn atnnannann aanaccacat ncacttccaa tcttcctatt tnctcaannc
      421 cataanncaa atncanttnc tacaaacact tnnnnancnn ttaatctncn nttaaanaat
      481 caacnaartt ctaaccatan acaatatwtc tncacttnnt acccattnna aacnttatnn
      541 tktnnnakta acatatctac tnttnctnat taacnancat ccaaannatt ttnntnatna
      601 nccytatctt naactnaatn nttaankcct ataccactct ctccctwaat tctccttctt
      661 ntcwcnacat cncyttrata aaaaatttat tnataatttt ttaraaactt atttttkta
//

LOCUS       C99930                   746 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99930 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 86, mRNA sequence.
ACCESSION   C99930
VERSION     C99930.1  GI:4714047
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 746)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..746
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="86"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 ntnaancnat acaacnatnc aaaaaaanan tnnnnattca cacaattnat ttctcttcca
       61 acattctaca acncnaacna annntacytt ntncannaca cancttcttt tnntnctnan
      121 atcttcatcn ttaacccnac anaaaaacaa nanaaantca cattcatatc aaaccctccn
      181 aacaatnttt tcacttnnaa natacttcnt ttctctacct tnnaanataa attctattac
      241 tctnatnatt ttctcnttna anaccnatac tnnanattan natttaaccc naaannatct
      301 nntnnannna naccacatnc acttccaatc ttcctatatn ctcaanncca taanncaaac
      361 ncanttntta caaacacttn nnnancnntt aatctncnnt taaanaatca acnaanctcc
      421 aaccacaaac aattatattc tncancttnn taccccnatt cnaancnatt atnntntnnn
      481 antnaacaat atcatattna tntcanaanc taaaanatnc atcmaaannn tatatnntna
      541 atnatnccat tatcttttna aactnaaatn nttaanntct ctntnaacaa catartctcc
      601 scttaaatat atntcactac ttctttatcc cccnnaataa ccttacaaan aaaaattnat
      661 natttaattt nttatacnac actttattna tncctntnan ntaaccttnt ttccnctccc
      721 cnaatttcct tttttttcct nttttt
//

LOCUS       C99929                   668 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99929 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 85, mRNA sequence.
ACCESSION   C99929
VERSION     C99929.1  GI:4714046
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 668)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..668
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="85"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 tcaaaatatn natantcaca aatnnantct anntttcaca ttacttnctt tcctcttcat
       61 cacttcctct tccnctnanc tcatcattaa acanntcaca cannncanan naatananta
      121 caacaactct tacantctca cntcnaatct tnnantnacn acaananant tnananacna
      181 ncnaccatca antaanatan tnacaatcac aancttctct ntnattaann acanannana
      241 accctatnaa tcatctattt ttnannctnc cnnttacaaa tnnanattan ttttntacnt
      301 naannntaat ccnaaanncn ntataaataa tcatatttca ctttacncna nnatanaana
      361 nacanaaact cttccaanan nntnnnaant naatnttnat ctcaaactct ttntccacaa
      421 tcnnaaktta aanaaatatt tntctnttac anatnnaaca ntnaancnat acaacnatnc
      481 aaaaaaanan tnnnnattcn cacaattnat ttctcttcca acattctaca acncnaacna
      541 annnttcctt ntnccannac acarcttcct ttnnntnctn araacttcat cnttaacccn
      601 accnaaaaac canaaaaaat ccctttcttt tcaaaccccc cnaaacatnt ttttcccttt
      661 nnaaaaaa
//

LOCUS       C99928                   800 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99928 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 84, mRNA sequence.
ACCESSION   C99928
VERSION     C99928.1  GI:4714045
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 800)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..800
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="84"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 nnaanttaaa naaatatttn tctnttacan atnnaacant naancnatac aacnatncaa
       61 aaaaanantn nnnattcaca caattnattt ctcttccaac attctacaac ncnaacnaan
      121 nntaccttnt ncannacaca ncttcttttn ntnctnanat cttcatcntt aacccnacan
      181 aaaaacaana naaantcaca ttcatatcaa accctccana caatnttttc acttnnaana
      241 tacttcnttt ctctaccttn naanataaat tctattactc cnatnatttt ctcnttnaan
      301 accnatactn nanactanna tttaacccna aannnnatnn annannaana ccacatncac
      361 ttccaatctt cctatttnct caannccata anncaaacnc anttnctaca aacacttnnn
      421 nancnnttaa tctncnntta aanaatcaac naantactaa ccatanacaa atatattctn
      481 cancttnnta cccnattnna ancnnttatn ntntnnnant naacaatatc atactnttan
      541 ctnatttaaa cnatncatca aaannatatt tnntnaatna tnccattatc tttnaanctn
      601 aaatnnttaa nntctctata accaacatcn tctccnctta aatatctnca cttctttntc
      661 tacnatcaat caaccttatn aataaanana tatttnatna ntttntaata anaaaacntt
      721 aatntttntn aattntnaan ttattacttc tnttcttctn anttttttta tttcaatnaa
      781 aataaaactc ttaccnnttt
//

LOCUS       C99927                   797 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99927 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 83, mRNA sequence.
ACCESSION   C99927
VERSION     C99927.1  GI:4714044
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 797)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..797
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="83"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 ntnaancnat mcmwcnatnm wmaaaamkar tnknnattyr cayratwnat ytctcttcyw
       61 myattctwsw mcncnaayna annntacctt ntnyasnacr mwscttcttt ynntnctnak
      121 atcttcatnc nwtamcccna canaaamacm mkakawantc wcattcatat cmwaccctcc
      181 raacaatntt ttcacttnna anatacttcn tttctctacc ttnnaanata aattctatta
      241 ctctnatnat tttctcnttn aanaccnata ctnnanatta nnatttaacc cnaaannatc
      301 tnntnnannn anaccacatn cacttccaat cttcctatat nctcaanncc ataanncaaa
      361 cncanttntt acaaacactt nnnnancnnt taatctncnn ttaaanaatc aacnaanctc
      421 caaccacaaa caattatatt ctncancttn ntacccnatt cnaancnatt atnntntnnn
      481 antnaacaat ataatattna tntcananct aaaanatnca tccaaaannn tatatnntna
      541 atnatnccat tatctttnaa nctnaaatnn ttaanntctc tntnacaaac atantctccn
      601 tttaaatatc actacttctt tttcaacaac aaccttacna ataaantnna ctttnatnan
      661 tttaatttnt tatacnacaa cnttnttnat ncttntnatn taatcnttnt ttctnctctc
      721 cnanttttcn ttttactttt tttttcatnt tttnctatca atnaaataaa nntataaaac
      781 tctcttnntt ttaaant
//

LOCUS       C99926                   371 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99926 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 82, mRNA sequence.
ACCESSION   C99926
VERSION     C99926.1  GI:4714043
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 371)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..371
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="82"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 nnaanttaaa naaatatttn tctnttacan atnnaacant naancnatac aacnatncaa
       61 aaaaanantn nnnattcaca caattnattt ctcttccaac attctacaac ncnaacnaan
      121 nntaccttnt ncannacaca ncttcttttn ntnctnanat cttcatcntt aacccnacan
      181 aaaaacaana naaantcaca ttcatatcaa accmtsswrm cmrkrtyytc acttnnaana
      241 tacttcnttt ctctaccttn tcacctaaat tcaattcatc ntacccnnat cctcnattct
      301 tttncttttt accctnnaan aaatactcat aanccacctc tnttatttac ccccaatctt
      361 cacaanaaaa a
//

LOCUS       C99925                   565 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99925 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 81, mRNA sequence.
ACCESSION   C99925
VERSION     C99925.1  GI:4714042
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 565)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..565
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="81"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 cntctccata cnttnttccc naanacatnt ccttnacaaa nntatacaat cttttccnnc
       61 aacttnnntt ncnacatcta ttcnttnttc cccntccttc ccntntnata nncttnatca
      121 ccanaaanna tttactnatt nannaaaatn nnnaatcatc ancantnnaa ctccaacant
      181 caactantan ntcnntacan tnanacanca acncnnatnn acnctncacn accncttcta
      241 nacnatcttt tannttaata aaacanacca aacatataca ancanttnaa nctnntanct
      301 aanatcttta ntcnnnccaa ttcttcntcc atacaannat acaancttnt tccncatntt
      361 nccacccaaa tccnntatnn annatatatn atcntctctt nanatnnnat tntnttnttc
      421 nctaaccnat ctcattctcc nttcacanan antanaaana ttatatatnt ttaanncttt
      481 tnattnttnt aattntncaa tctttnawta ttttcttnnt ccctntaaaa taatccacct
      541 tttnatatat ttacttnatt aactt
//

LOCUS       C99923                   110 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99923 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 79, mRNA sequence.
ACCESSION   C99923
VERSION     C99923.1  GI:4714041
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 110)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..110
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="79"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 tctnntccnt ctnanacatc nnatcanntn nnnnntacaa tcatctcncc nttcantann
       61 tntttacnna tttcnncnnt cntatanctn ncntnactaa nnctttaacc
//

LOCUS       C99922                   815 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99922 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 78, mRNA sequence.
ACCESSION   C99922
VERSION     C99922.1  GI:4714040
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 815)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..815
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="78"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 nntranatct acsttnctnn anntnntnnt nnttcnnakn ttncnncnnc nntnnaasta
       61 ntatnatccn nanttnaatc nntnnnaant tntnactcaa tcnncsanna asanatacnn
      121 ttncatcnna ncanccnttn acnnantttt ttatntnatc nntnnattna aaattnnnaa
      181 tnanacctca cncncnntnn cnncncntnc ttatncnanc tctatnnatc ttttcnatnt
      241 nnantcncnt cantnnttaa nnantcnttc nnttcctnnc nntnnatntn tantnncnnc
      301 ntntncnncn nttnnatatn tntatntnct aaccantcac ncnntnnanc tttcnttttt
      361 nncnatttna tncncntcnt cntnntnnaa acaccnnntt tnnaaaaatn ncanaanctn
      421 aaaantcccc cnttaccnnc acaanntncs nnttaanatn naaccnntna anntttaacc
      481 tncntcnnan tnnaanataa antnncnntn nttcanntnn tnnnatncat tnacnatttn
      541 cttcnncnna ntnnnannnn tnananannn attananaaa nccttntntt nctntatnat
      601 acnacnnann nanantnnan nanancnncn natttacctn anatnattac acncnccncc
      661 tntncntntn tnnantnnta anannnnana ccacnncnca nnattatnnn tacnanaant
      721 tnnaanatnc tavcntacnc annatatatt aaantnnnca aaaacaatat cattatnatt
      781 nntncacatn tttactntmt naaaancaat ancnt
//

LOCUS       C99921                   602 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99921 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 77, mRNA sequence.
ACCESSION   C99921
VERSION     C99921.1  GI:4714039
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 602)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..602
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="77"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 cnnnncttct raaanacnca atctnatnta ctcntacatn ctanntncta tctcttctat
       61 aatntctnat cctttctncc ctcccacwcn ttnccntanc ckcaaawtct cctktnayat
      121 ttmcctnmtc anaytntcct natnnatnsn naynttcacm tanataccaa ancacaanaa
      181 attcnaannt nctnnanaaa anncnaccac tttcactaan ancatttnnc tcnannaanc
      241 tnatncnany nccatatccn ttnntnanna antaactttn atnnattnnn naaatnctat
      301 cntaaannaa atcmcmaakn acnannannn tcntntcact nccttatctn ntntcttnaa
      361 tctccaannt tctntwaana ctacaaanct naanctnaca tnncttcctn atactaatna
      421 attnntccat ctcrcmttaa canantttna ttatctaatc cccmanaana aactnnaana
      481 tnatnatnaa atttnctnat tttnctnaat ccymmcccna aaaannaana cmtttnncmc
      541 ttknntnnat tcccaatatt nananaatct tnaaattntt nnaaaatntt tattccccct
      601 tt
//

LOCUS       C99920                    92 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99920 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 76, mRNA sequence.
ACCESSION   C99920
VERSION     C99920.1  GI:4714038
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 92)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..92
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="76"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 tcanctnttt cnttcaacna tctaaactat ctcaatnctt ctttnaatct attntcnntt
       61 tccttntact cntcaatttc atnttttttt tn
//

LOCUS       C99919                   461 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99919 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 75, mRNA sequence.
ACCESSION   C99919
VERSION     C99919.1  GI:4714037
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 461)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..461
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="75"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 ccctcccnct cctnntttct anttnnnttc nnnttctntt atcnnntttt tcncnnnnnt
       61 cttttntcnn nnccctnnac cnnaattcnc nnntcnacca actcntcana tntnntnctn
      121 cnctacaatn aancaaannn antcacactc tcnnactnan nctctcccct ccncttctnt
      181 aaccatancn nctcnacntc tatntctccn atctaaccan ctctnnnnnt tcnannanan
      241 ataannanaa aantannnan nnacnantat ncttncccnt tctntncana ctattttnat
      301 ntcntctctc tnnncnntca cattnatnaa natcntccta tnnatnctta aantnnnntn
      361 tntcccntcc tntncnntna aantnanctc nnnatatnat tncntcntat anccccncnn
      421 cncnnccnat atnttcaann tnacccnnat cannaaatca a
//

LOCUS       C99918                   556 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99918 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 74, mRNA sequence.
ACCESSION   C99918
VERSION     C99918.1  GI:4714036
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 556)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..556
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="74"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 ntttatcacn ccttncattn atcanaascc cttnctacnn cattnancca knctnccnaa
       61 nctntttctt cnnnaaattc anatncaant natnccactn caaaanctnn aatcattttn
      121 ttncccanca cacatcaact tnacnaanan nttactnmnn aacatantna nnannaaatn
      181 actnaanann aaccaactct tctcaantnn ccaaataanc ccnnnattcc anattctnat
      241 ttntttnacc ntnatcaatc ntnntttnat nnacctccan annncttcaa tctcacatta
      301 tcaaatttcn ctntnatntn nnattcactn tttnnctnnn tatcatcntc ctctctnnca
      361 tacatatatn nnaannaana atctnctcat narnanttct tattnnttaa cnnnaannan
      421 tacccccnna nnattatcat nntanatnnn ctttcctcan aratcaanca nacaattnct
      481 nnnttncctt nccanaactt taccnaaaat cntcactcat ctcannnctn ccaatancna
      541 tatccrattt taaaaa
//

LOCUS       C99917                   476 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99917 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 73, mRNA sequence.
ACCESSION   C99917
VERSION     C99917.1  GI:4714035
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 476)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..476
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="73"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 atanncnana tcccccccaa annattncct natntnanna acatnnnnan atcatcntnn
       61 aatcnancnc nnnnantcnc cnntnaantn nntnnntnna cantcncncc cnnacnnacn
      121 cnncatnacc ncttcactac nanctnttan ntttntnnna ctnntcctac natataccnt
      181 ctcttnntnn tnnnnccncn aaactcnnct cannactnnn ctcctcnaaa ttcnnatnaa
      241 nnntntcccn cctntnacna cnnnnttcnn nattnnancn atctannann nnacactctn
      301 anaatntnat cnntnattnn tcnntncnct nnatcacatt nctcnccttn ccantaccac
      361 ttttnacana nttccccttc tttttcncaa cnnncnatnc tnnnanaann natnnntaac
      421 tcnnntnccn nctctnnatc nnanatancn tnntcctctc nnnnttccan annntc
//

LOCUS       C99916                   865 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99916 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 72, mRNA sequence.
ACCESSION   C99916
VERSION     C99916.1  GI:4714034
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 865)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..865
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="72"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 nntaataaaa acnacnntnn aaatnatcat atttcccttt acncaannat cnaananaca
       61 aactctcttc cattannttn nnaantnaat nttnatctca aactctttnt ccataatnnn
      121 aanctacaca aatatttnac tnttacanat nncttantna ancnatataa caatncnaaa
      181 aaanaatnnn ntttcnnaca attnattcct cnatcaacat tctacaacnc naacnaannt
      241 taccttnacc annacactnn ttcttttnnt nctnanatct ttattnttaa accnnctcaa
      301 caacaanana aanttacatt catatcaaac cctccaaaca atnttttcac ttnnaanata
      361 cttcntttct ctaccttnna anataaattc tattactccn atnatwttct cnttnaanac
      421 cnatactnna nactannatt taacccnaaa nnnnatnnan nannaanacc acatncactt
      481 ccaatcttcc tatttnctca annccataan ncaaatncan ttnctacaaa cacttnnnna
      541 ncnnttaatc tncnnttaaa naatcaacna antactaacc atanacaaat atattctnca
      601 ncttnntacc cnattnnaaa cnnttatnnt ntnnnantna acaatatcat actnttanct
      661 natttaaacn atncatccaa annatatttn ntnaatnatn ccattatctt tnaanctnaa
      721 atnnttaann tctctataac caacatcntc tccncttaaa tatctncmct tctttntcta
      781 craycaatcc accttatnaa taaaaaaatt ttaatttnat naatttntta taanaaaact
      841 ttaatntttn ttaaatntna aattt
//

LOCUS       C99914                   628 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99914 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 70, mRNA sequence.
ACCESSION   C99914
VERSION     C99914.1  GI:4714033
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 628)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..628
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="70"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 nnnacnaacc nntntaccac natttnnttc ntcactntct nncctaccca aaancnnatn
       61 naatcttnnt naatacatnn naananatnn ancccaaatc attaaantcc cttcaanacc
      121 cnaaactttt nnnccnnntc nctcntntac cnntttatcc nnttnntccn ttatncanac
      181 cnatacaatc atccacnacc natcacccnn tttttnattn nttaaacaaa caaccaaacn
      241 antcnnttct ctacatttcc ttcnnnantn ntnnttctct aacnnctcaa canttaaccn
      301 aattnncntn nnnnctcnan nananccanc aacnntttat atnnntnntt cnaccncccn
      361 ttnacnnctc ntcttncant nattatttct cnnctaaann cnntntaacc aaanacaaca
      421 cnccanaata tctaccaaaa annnttcntn actcstactt tncnataaaa ntttcatnat
      481 cccatcatnn ncaccncaan ctnaaatcct aacccatcca nnccnttnnt nnntttttaa
      541 cacatttntt nntttnnaac tccactttnn raaaccttcc ttttnccnnc nttcccawtr
      601 anaaccttkn cccccttttc ccccaacc
//

LOCUS       C99913                   497 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99913 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 69, mRNA sequence.
ACCESSION   C99913
VERSION     C99913.1  GI:4714032
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 497)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..497
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="69"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 cctntcccat cnnnccnttr ntnnnttttt nacccattnc nnttnnanct cnacnttsna
       61 aancntcntt nncnncnttc cnatsatcnc atnnccactt tttnccnanc anaatatnaa
      121 tncnncnttn ctcancnacn aactnnnaat cncantcana ttnnatnatc caaannanna
      181 tatttctann tnnaanattn anncnttnnt nannaanntt atnactnana annaanntna
      241 ancnatnana annaaantna anaanttnan anactcnncn nanatntcac tnancattna
      301 cnntnntnnt ttnncncacn antcnctttn canantcacc aannantntc aacnnttttt
      361 nnaacntntc ntnnacttnt cacntnntnc ttaaaaattn ttaccntttt ctaactcttt
      421 tattattart tnnttnaatt atacntntcn ttcctctntt anttnttata atataataaa
      481 tcnatttact ctttntt
//

LOCUS       C99911                   661 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99911 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 67, mRNA sequence.
ACCESSION   C99911
VERSION     C99911.1  GI:4714031
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 661)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..661
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="67"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 cntttctncc acattaaaac anaanantnc aacaattnaa nncatanaaa antnncctta
       61 tnaancanct nccattnctt tcnannctat tccacntacc ctnnctcaaa actntnnnnt
      121 taacntnatc cntactatna ctncattnca annnaancat ncaaatnntn aaaacncatn
      181 nactnntatt nacnnnaaca ctnntncaat anctnatatn aaanananca anatatnnna
      241 ttcntacaat ntnaanncnc aaactttcaa nacnnctata naancancnt ntatncttct
      301 aannnatcna tnatatantn antnnaatca anaanaanca anctcctnna tctnnacctt
      361 caaancctac cattnanaca naannanatn canacaacna acaaattctt cccnactaan
      421 cnaannnana aacactttnn tctcancata actcaatctc tnttttcact tntttaatnn
      481 ttncactctt ttnnctatta tcttcccttn acatatcttt ttaattctnc anttttnact
      541 tnnntnanat aaaattttcc caanntnntt tttttttntt tnttttnnna atattaactt
      601 ttttnaattt tcntantccc tttnttnntt tttaaaattc caattnttat tnttcttttt
      661 n
//

LOCUS       C99910                   241 bp    mRNA    linear   EST 21-SEP-1999
DEFINITION  C99910 Arabidopsis thaliana library (Motohashi R) Arabidopsis
            thaliana cDNA clone 66, mRNA sequence.
ACCESSION   C99910
VERSION     C99910.1  GI:4714030
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 241)
  AUTHORS   Motohashi,R., Shinozaki,K. and Yamaguchi-Shinozaki,K.
  TITLE     Arabidopsis thaliana YAC CIC3B1 region specific cDNA,clone 2
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Motohashi R
            Laboratory of Plant Molecular Biology
            Institute of Physical and Chemical Research(RIKEN)
            3-1-1, Koyadai, Tsukuba 305-0074, Japan.
FEATURES             Location/Qualifiers
     source          1..241
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="66"
                     /clone_lib="Arabidopsis thaliana library (Motohashi R)"
ORIGIN      
        1 cncscctaan aannaaaana tnanaanaan aanaanaana aaactnannt ctnaananac
       61 ctttaatatt tttncntnnt ctantttact ttnttatcan aaacaaanaa aatcttttnt
      121 nncnttannt nttaantaan ntttttnttt tntttnaaac ttaaaaaaaa naactactct
      181 tcnttttnta annttataat atntttnntt tantccttat cccaaaaact tncattttnc
      241 c
//

genometools-1.5.1/testdata/Atinsert_seqrange_13-17_rev.fna000066400000000000000000000077171211610345200234410ustar00rootroot00000000000000>gi|4714043|dbj|C99926.1|C99926 C99926 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 82, mRNA sequence
aaaaanaacacttctaacccccatttattntctccaccnaatactcataaanaanntcccatttttcnttttcttanctcctanncccatnctacttaacttaaatccactnttccatctctttncttcatanaannttcactnntnnnncnnnnntnccaaactatacttacactnaaananaacaaaaanacancccaattnctacttctanantcntnnttttcttcnacacannacntnttccatnnnaancaancncaacatcttacaaccttctctttanttaacacacttannnntnanaaaaaaacntancaacatancnaantnacaanntanacattntctntttataaanaaattnaann
>gi|4714044|dbj|C99927.1|C99927 C99927 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 83, mRNA sequence
tnaaattttnnttctctcaaaatatnnaaataaantaactatcnttttntactttttttttcattttncttttnancctctcntctttnttnctaatntantnttcntanttnttncaacancatattntttaatttnantantttcanntnaaataancattccaacaacaactttttcttcatcactataaatttncctctnatacaaacantntctctnnaattnntaaantcnaantttctattaccntantaantnntatatnnnaaaacctacntanaaaatcnanactntanttataatataacaantnannntntnntattancnaancttancccatnnttcnacntcttatattaacaaacaccaacctcnaancaactaanaaattnncntctaattnncnannnnttcacaaacattnttnacncaaacnnaataccnnaactcntatatccttctaaccttcacntacaccanannnanntnntctannaaancccaatttannattananntcatanccanaanttnctcttttantantctcattatcttaaatanaannttccatctctttncttcatanaannttcacttttntaacaancctcccannctatacttacnctnananannncanaaanacancccnatnncntacttctanantcntnnntttcttcnnnncannanntnttccatnnnaannaancncnnnntcttannnncttctctntanntannacnnttannnntnannaaaannnntancnncntancnaantn
>gi|4714045|dbj|C99928.1|C99928 C99928 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 84, mRNA sequence
tttnnccattctcaaaataaaantaactttatttttttnantcttcttntcttcattattnaantnttaantntttntaattncaaaanaataatntttnantantttatananaaataantattccaactaactancatctntttcttcacntctataaattcncctctnctacaaccaatatctctnnaattnntaaantcnaantttctattaccntantaantnntttatannaaaactacntancaaatttantcnattntcatactataacaantnannntntnntattnncnaannttancccatnnttcnacntcttatataaacanataccaatcatnaancaactaanaaattnncntctaattnncnannnnttcacaaacatcnttnacncaaacnnaataccnnaactcntttatccttctaaccttcacntacaccanaannannanntannnnaaancccaatttannatcananntcatanccanaanttnctcttttantancctcattatcttaaatanaannttccatctctttncttcatanaannttcacttttntaacanacctcccaaactatacttacactnaaananaacaaaaanacancccaattnctacttctanantcntnnttttcttcnacacannacntnttccatnnnaancaancncaacatcttacaaccttctctttanttaacacacttannnntnanaaaaaaacntancaacatancnaantnacaanntanacattntctntttataaanaaattnaann
>gi|4714046|dbj|C99929.1|C99929 C99929 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 85, mRNA sequence
aaaaaanntttccctttttntacaaanccccccaaacttttctttccctaaaaaanaccaaaaanccancccaattnctacttcaanantcntnnntttccttcnacacannaccntnttccttnnnaancaancncaacatcttacaaccttctctttanttaacacncttannnntnanaaaaaaacntancaacatancnaantnacaanntanacattntctntttataaanaaattnaannctaacacctntttctcaaactctanttntaantnaannntnnnanaaccttctcaaanacananaanatannancncatttcactttatactaataaatatnncnnaaancctaatnnnaantncatnttttnattananntaaacattnnccntcnnantttttatctactaantatcccaanannanacannaattantntctcttcnaacactaacantnatanaatnaactaccancnancanananttnananaacancantnannttctaanctncactctnacattctcaacaacatnanataannanacnnnacacactnnacaaattactactcnantcnccttctccttcactacttctcctttcnttcattacactttnnatctnanntaaacactnatanntataaaact
>gi|4714047|dbj|C99930.1|C99930 C99930 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 86, mRNA sequence
tttttntccttttttttcctttaancccctcncctttnttccaatnnantntccntanttatttcacancatattntttaatttantanttaaaaanaaacattccaataannccccctatttcttcatcactntatataaattcncctctnatacaacaantntctctnnaattnntaaantcaaanttttctattaccntantaantnntatatnnnaaanctacntanaaaatcnaanactntanttatactataacaantnannntntnntattancnaancttanccccatnnttcnacntcttatattaacaaacaccaacctcnaancaactaanaaattnncntctaattnncnannnnttcacaaacattnttnacncaaacnnaataccnnaactcntatatccttctaaccttcacntacaccanannnanntnntctannaaancccaatttannattananntcatanccanaanttnctcttttantantctcattatcttaaatanaannttccatctctttncttcatanaannttcacttttntaacaancctcccaaactatacttacactnaaananaacaaaaanacancccaattnctacttctanantcntnnttttcttcnacacannacntnttncatnnnaancaancncaacatcttacaaccttctctttanttaacacacttannnntnanaaaaaaacntancaacatancnaantn
genometools-1.5.1/testdata/Atinsert_seqrange_3-7.fna000066400000000000000000000077171211610345200224230ustar00rootroot00000000000000>gi|4714047|dbj|C99930.1|C99930 C99930 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 86, mRNA sequence
ntnaancnatacaacnatncaaaaaaanantnnnnattcacacaattnatttctcttccaacattctacaacncnaacnaannntacnttntncannacacancttcttttnntnctnanatcttcatcnttaacccnacanaaaaacaananaaantcacattcatatcaaaccctccnaacaatnttttcacttnnaanatacttcntttctctaccttnnaanataaattctattactctnatnattttctcnttnaanaccnatactnnanattannatttaacccnaaannatctnntnnannnanaccacatncacttccaatcttcctatatnctcaannccataanncaaacncanttnttacaaacacttnnnnancnnttaatctncnnttaaanaatcaacnaanctccaaccacaaacaattatattctncancttnntaccccnattcnaancnattatnntntnnnantnaacaatatcatattnatntcanaanctaaaanatncatcnaaannntatatnntnaatnatnccattatcttttnaaactnaaatnnttaanntctctntnaacaacatantctccncttaaatatatntcactacttctttatcccccnnaataaccttacaaanaaaaattnatnatttaatttnttatacnacactttattnatncctntnanntaaccttntttccnctccccnaatttccttttttttcctnttttt
>gi|4714046|dbj|C99929.1|C99929 C99929 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 85, mRNA sequence
tcaaaatatnnatantcacaaatnnantctanntttcacattacttnctttcctcttcatcacttcctcttccnctnanctcatcattaaacanntcacacannncanannaatanantacaacaactcttacantctcacntcnaatcttnnantnacnacaanananttnananacnancnaccatcaantaanatantnacaatcacaancttctctntnattaannacanannanaaccctatnaatcatctatttttnannctnccnnttacaaatnnanattanttttntacntnaannntaatccnaaanncnntataaataatcatatttcactttacncnannatanaananacanaaactcttccaanannntnnnaantnaatnttnatctcaaactctttntccacaatcnnaanttaaanaaatatttntctnttacanatnnaacantnaancnatacaacnatncaaaaaaanantnnnnattcncacaattnatttctcttccaacattctacaacncnaacnaannnttccttntnccannacacancttcctttnnntnctnanaacttcatcnttaacccnaccnaaaaaccanaaaaaatccctttcttttcaaaccccccnaaacatntttttccctttnnaaaaaa
>gi|4714045|dbj|C99928.1|C99928 C99928 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 84, mRNA sequence
nnaanttaaanaaatatttntctnttacanatnnaacantnaancnatacaacnatncaaaaaaanantnnnnattcacacaattnatttctcttccaacattctacaacncnaacnaannntaccttntncannacacancttcttttnntnctnanatcttcatcnttaacccnacanaaaaacaananaaantcacattcatatcaaaccctccanacaatnttttcacttnnaanatacttcntttctctaccttnnaanataaattctattactccnatnattttctcnttnaanaccnatactnnanactannatttaacccnaaannnnatnnannannaanaccacatncacttccaatcttcctatttnctcaannccataanncaaacncanttnctacaaacacttnnnnancnnttaatctncnnttaaanaatcaacnaantactaaccatanacaaatatattctncancttnntacccnattnnaancnnttatnntntnnnantnaacaatatcatactnttanctnatttaaacnatncatcaaaannatatttnntnaatnatnccattatctttnaanctnaaatnnttaanntctctataaccaacatcntctccncttaaatatctncacttctttntctacnatcaatcaaccttatnaataaananatatttnatnantttntaataanaaaacnttaatntttntnaattntnaanttattacttctnttcttctnantttttttatttcaatnaaaataaaactcttaccnnttt
>gi|4714044|dbj|C99927.1|C99927 C99927 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 83, mRNA sequence
ntnaancnatncnncnatnnnnaaaannantnnnnattnncannatnnatntctcttcnnnnattctnnnncncnaannaannntaccttntnnannacnnnncttctttnnntnctnanatcttcatncnntancccnacanaaanacnnnananantcncattcatatcnnaccctccnaacaatnttttcacttnnaanatacttcntttctctaccttnnaanataaattctattactctnatnattttctcnttnaanaccnatactnnanattannatttaacccnaaannatctnntnnannnanaccacatncacttccaatcttcctatatnctcaannccataanncaaacncanttnttacaaacacttnnnnancnnttaatctncnnttaaanaatcaacnaanctccaaccacaaacaattatattctncancttnntacccnattcnaancnattatnntntnnnantnaacaatataatattnatntcananctaaaanatncatccaaaannntatatnntnaatnatnccattatctttnaanctnaaatnnttaanntctctntnacaaacatantctccntttaaatatcactacttctttttcaacaacaaccttacnaataaantnnactttnatnantttaatttnttatacnacaacnttnttnatncttntnatntaatcnttntttctnctctccnanttttcnttttactttttttttcatnttttnctatcaatnaaataaanntataaaactctcttnnttttaaant
>gi|4714043|dbj|C99926.1|C99926 C99926 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 82, mRNA sequence
nnaanttaaanaaatatttntctnttacanatnnaacantnaancnatacaacnatncaaaaaaanantnnnnattcacacaattnatttctcttccaacattctacaacncnaacnaannntaccttntncannacacancttcttttnntnctnanatcttcatcnttaacccnacanaaaaacaananaaantcacattcatatcaaaccntnnnnncnnnntnntcacttnnaanatacttcntttctctaccttntcacctaaattcaattcatcntacccnnatcctcnattcttttnctttttaccctnnaanaaatactcataanccacctctnttatttacccccaatcttcacaanaaaaa
genometools-1.5.1/testdata/Atinsert_single_3.fna000066400000000000000000000015571211610345200217270ustar00rootroot00000000000000>gi|4714047|dbj|C99930.1|C99930 C99930 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 86, mRNA sequence
ntnaancnatacaacnatncaaaaaaanantnnnnattcacacaattnatttctcttccaacattctacaacncnaacnaannntacnttntncannacacancttcttttnntnctnanatcttcatcnttaacccnacanaaaaacaananaaantcacattcatatcaaaccctccnaacaatnttttcacttnnaanatacttcntttctctaccttnnaanataaattctattactctnatnattttctcnttnaanaccnatactnnanattannatttaacccnaaannatctnntnnannnanaccacatncacttccaatcttcctatatnctcaannccataanncaaacncanttnttacaaacacttnnnnancnnttaatctncnnttaaanaatcaacnaanctccaaccacaaacaattatattctncancttnntaccccnattcnaancnattatnntntnnnantnaacaatatcatattnatntcanaanctaaaanatncatcnaaannntatatnntnaatnatnccattatcttttnaaactnaaatnnttaanntctctntnaacaacatantctccncttaaatatatntcactacttctttatcccccnnaataaccttacaaanaaaaattnatnatttaatttnttatacnacactttattnatncctntnanntaaccttntttccnctccccnaatttccttttttttcctnttttt
genometools-1.5.1/testdata/Atinsert_single_3_rev.fna000066400000000000000000000015571211610345200226030ustar00rootroot00000000000000>gi|4714047|dbj|C99930.1|C99930 C99930 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 86, mRNA sequence
tttttntccttttttttcctttaancccctcncctttnttccaatnnantntccntanttatttcacancatattntttaatttantanttaaaaanaaacattccaataannccccctatttcttcatcactntatataaattcncctctnatacaacaantntctctnnaattnntaaantcaaanttttctattaccntantaantnntatatnnnaaanctacntanaaaatcnaanactntanttatactataacaantnannntntnntattancnaancttanccccatnnttcnacntcttatattaacaaacaccaacctcnaancaactaanaaattnncntctaattnncnannnnttcacaaacattnttnacncaaacnnaataccnnaactcntatatccttctaaccttcacntacaccanannnanntnntctannaaancccaatttannattananntcatanccanaanttnctcttttantantctcattatcttaaatanaannttccatctctttncttcatanaannttcacttttntaacaancctcccaaactatacttacactnaaananaacaaaaanacancccaattnctacttctanantcntnnttttcttcnacacannacntnttncatnnnaancaancncaacatcttacaaccttctctttanttaacacacttannnntnanaaaaaaacntancaacatancnaantn
genometools-1.5.1/testdata/BLOSUM62000066400000000000000000000032501211610345200167510ustar00rootroot00000000000000   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X
A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0
R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1
N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1
D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1
C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2
Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1
E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1
G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1
H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1
I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1
L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1
K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1
M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1
F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2
S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0
T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2
Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1
V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1
B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1
Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1
X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1
genometools-1.5.1/testdata/BLOSUM62.gth000066400000000000000000000041121211610345200175300ustar00rootroot00000000000000#  Matrix made by matblas from blosum62.iij
#  * column uses minimum score
#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
#  Blocks Database = /data/blocks_5.0/blocks.dat
#  Cluster Percentage: >= 62
#  Entropy =   0.6979, Expected =  -0.5209
   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4 
R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4 
N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4 
D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4 
C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 
Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4 
E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4 
H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4 
I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4 
L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4 
K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4 
M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4 
F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4 
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4 
S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4 
T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4 
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4 
Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4 
V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4 
B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4 
Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4 
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1 
genometools-1.5.1/testdata/BLOSUM62.out000066400000000000000000000034721211610345200175650ustar00rootroot00000000000000   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4
R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4
N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4
D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4
C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4
E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4
G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4
H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4
I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4
L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4
K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4
M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4
F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4
S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4
T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4
Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4
V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4
B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4
Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4
X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1
genometools-1.5.1/testdata/Copysorttest.embl000066400000000000000000000011311211610345200212340ustar00rootroot00000000000000ID   sequence0
XX
DE   
XX
SQ
     ngtgttngtn tnnntggntg tgngtnngnn ttntttgntg gngnggnggg nnnngtntgg        60
     gtgntnngng ttnngntngn gntnnttggg ggnggttgtn ggtgngtgng ttngggntnn       120
     gngggngnng nttnnttntt ngntgtnngt ntttnntntt ttggggntgt tgtnggngtn       180
     tggttnttnt gntggggnnt nntngnntgg ttgnnggtgg ngngtntttt ggggtntgng       240
     ggtgnnttnn gntngntngt tntttgntng gtggntnggn ntntnttgnt gnttngtgnn       300
     ggnntnggnt nggttnnttn ntgnggtngg ttgtngtnnt gnngttgttg tggggtggtt       360
     ggt                                                                     363
//

genometools-1.5.1/testdata/Copysorttest.fna000066400000000000000000000005631211610345200210710ustar00rootroot00000000000000>
ngtgttngtntnnntggntgtgngtnngnnttntttgntggngnggngggn
nnngtntgggtgntnngngttnngntngngntnnttgggggnggttgtnggtgngtgngttngggntnng
ngggngnngnttnnttnttngntgtnngtntttnntnttttggggntgttgtnggngtntggttnttntg
ntggggnntnntngnntggttgnnggtggngngtnttttggggtntgngggtgnnttnngntngntngtt
ntttgntnggtggntnggnntntnttgntgnttngtgnnggnntnggntnggttnnttnntgnggtnggt
tgtngtnntgnngttgttgtggggtggttggt
genometools-1.5.1/testdata/Copysorttest.gbk000066400000000000000000000010171211610345200210630ustar00rootroot00000000000000LOCUS       sequence0
DEFINITION  
ORIGIN      
        1 ngtgttngtn tnnntggntg tgngtnngnn ttntttgntg gngnggnggg nnnngtntgg 
       61 gtgntnngng ttnngntngn gntnnttggg ggnggttgtn ggtgngtgng ttngggntnn 
      121 gngggngnng nttnnttntt ngntgtnngt ntttnntntt ttggggntgt tgtnggngtn 
      181 tggttnttnt gntggggnnt nntngnntgg ttgnnggtgg ngngtntttt ggggtntgng 
      241 ggtgnnttnn gntngntngt tntttgntng gtggntnggn ntntnttgnt gnttngtgnn 
      301 ggnntnggnt nggttnnttn ntgnggtngg ttgtngtnnt gnngttgttg tggggtggtt 
      361 ggt
//
genometools-1.5.1/testdata/Duplicate.embl000066400000000000000000000050761211610345200204400ustar00rootroot00000000000000ID   Duplicate1
XX
DE   gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome
XX
SQ
     AGCTTTTCAT TCTGACTGCA ACGGGCAATA TGTCTCTGTG TGGATTAAAA AAAGAGTGTC        60
     TGATAGCAGC TTCTGAACTG GTTACCTGCC GTGAGTAAAT TAAAATTTTA TTGACTTAGG       120
     TCACTAAATA CTTTAACCAA TATAGGCATA GCGCACAGAC AGATAAAAAT TACAGAGTAC       180
     ACAACATCCA TGAAACGCAT TAGCACCACC ATTACCACCA CCATCACCAT TACCACAGGT       240
     AACGGTGCGG GCTGACGCGT ACAGGAAACA CAGAAAAAAG CCCGCACCTG ACAGTGCGGG       300
     CTTTTTTTTT CGACCAAAGG TAACGAGGTA ACAACCATGC GAGTGTTGAA GTTCGGCGGT       360
     ACATCAGTGG CAAATGCAGA ACGTTTTCTG CGTGTTGCCG ATATTCTGGA AAGCAATGCC       420
     AGGCAGGGGC AGGTGGCCAC CGTCCTCTCT GCCCCCGCCA AAATCACCAA CCACCTGGTG       480
     GCGATGATTG AAAAAACCAT TAGCGGCCAG GATGCTTTAC CCAATATCAG CGATGCCGAA       540
     CGTATTTTTG CCGAACTTTT GACGGGACTC GCCGCCGCCC AGCCGGGGTT CCCGCTGGCG       600
     CAATTGAAAA CTTTCGTCGA TCAGGAATTT GCCCAAATAA AACATGTCCT GCATGGCATT       660
     AGTTTGTTGG GGCAGTGCCC GGATAGCATC AACGCTGCGC TGATTTGCCG TGGCGAGAAA       720
     ATGTCGATCG CCATTATGGC CGGCGTATTA GAAGCGCGCG GTCACAACGT TACTGTTATC       780
     GATCCGGTCG AAAAACTGCT GGCAGTGGGG CATTACCTCG AATCTACCGT CGATATTGCT       840
//

ID   Duplicate1
XX
DE   gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome
XX
SQ 
     AGCTTTTCAT TCTGACTGCA ACGGGCAATA TGTCTCTGTG TGGATTAAAA AAAGAGTGTC        60
     TGATAGCAGC TTCTGAACTG GTTACCTGCC GTGAGTAAAT TAAAATTTTA TTGACTTAGG       120
     TCACTAAATA CTTTAACCAA TATAGGCATA GCGCACAGAC AGATAAAAAT TACAGAGTAC       180
     ACAACATCCA TGAAACGCAT TAGCACCACC ATTACCACCA CCATCACCAT TACCACAGGT       240
     AACGGTGCGG GCTGACGCGT ACAGGAAACA CAGAAAAAAG CCCGCACCTG ACAGTGCGGG       300
     CTTTTTTTTT CGACCAAAGG TAACGAGGTA ACAACCATGC GAGTGTTGAA GTTCGGCGGT       360
     ACATCAGTGG CAAATGCAGA ACGTTTTCTG CGTGTTGCCG ATATTCTGGA AAGCAATGCC       420
     AGGCAGGGGC AGGTGGCCAC CGTCCTCTCT GCCCCCGCCA AAATCACCAA CCACCTGGTG       480
     GCGATGATTG AAAAAACCAT TAGCGGCCAG GATGCTTTAC CCAATATCAG CGATGCCGAA       540
     CGTATTTTTG CCGAACTTTT GACGGGACTC GCCGCCGCCC AGCCGGGGTT CCCGCTGGCG       600
     CAATTGAAAA CTTTCGTCGA TCAGGAATTT GCCCAAATAA AACATGTCCT GCATGGCATT       660
     AGTTTGTTGG GGCAGTGCCC GGATAGCATC AACGCTGCGC TGATTTGCCG TGGCGAGAAA       720
     ATGTCGATCG CCATTATGGC CGGCGTATTA GAAGCGCGCG GTCACAACGT TACTGTTATC       780
     GATCCGGTCG AAAAACTGCT GGCAGTGGGG CATTACCTCG AATCTACCGT CGATATTGCT       840
     GAGTCCACCC GCCGTATTGC GGCAAGCCGC ATTCCGGCTG ATCACATGGT GCTGATGGCA       900
     GGTTTCACCG                                                              910
//
genometools-1.5.1/testdata/Duplicate.fna000066400000000000000000000035551211610345200202650ustar00rootroot00000000000000>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
genometools-1.5.1/testdata/Duplicate.gbk000066400000000000000000001076611211610345200202670ustar00rootroot00000000000000LOCUS       U00096                   840 bp    DNA     linear   BCT 11-MAR-2009
DEFINITION  Escherichia coli str. K-12 substr. MG1655, complete genome.
ACCESSION   U00096 REGION: 1..840
VERSION     U00096.2  GI:48994873
PROJECT     GenomeProject:225
DBLINK      Project:225
KEYWORDS    .
SOURCE      Escherichia coli str. K-12 substr. MG1655
  ORGANISM  Escherichia coli str. K-12 substr. MG1655
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (sites)
  AUTHORS   Kang,W.K., Icho,T., Isono,S., Kitakawa,M. and Isono,K.
  TITLE     Characterization of the gene rimK responsible for the addition of
            glutamic acid residues to the C-terminus of ribosomal protein S6 in
            Escherichia coli K12
  JOURNAL   Mol. Gen. Genet. 217 (2-3), 281-288 (1989)
   PUBMED   2570347
REFERENCE   2  (bases 1 to 840)
  AUTHORS   Blattner,F.R., Plunkett,G., Bloch,C.A., Perna,N.T., Burland,V.,
            Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F.,
            Gregor,J., Davis,N.W., Kirkpatrick,H.A., Goeden,M.A., Rose,D.J.,
            Mau,B. and Shao,Y.
  TITLE     The complete genome sequence of Escherichia coli K-12
  JOURNAL   Science 277 (5331), 1453-1474 (1997)
   PUBMED   9278503
REFERENCE   3  (bases 1 to 840)
  AUTHORS   Riley,M., Abe,T., Arnaud,M.B., Berlyn,M.K., Blattner,F.R.,
            Chaudhuri,R.R., Glasner,J.D., Horiuchi,T., Keseler,I.M., Kosuge,T.,
            Mori,H., Perna,N.T., Plunkett,G. III, Rudd,K.E., Serres,M.H.,
            Thomas,G.H., Thomson,N.R., Wishart,D. and Wanner,B.L.
  TITLE     Escherichia coli K-12: a cooperatively developed annotation
            snapshot--2005
  JOURNAL   Nucleic Acids Res. 34 (1), 1-9 (2006)
   PUBMED   16397293
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 840)
  AUTHORS   Arnaud,M., Berlyn,M.K.B., Blattner,F.R., Galperin,M.Y.,
            Glasner,J.D., Horiuchi,T., Kosuge,T., Mori,H., Perna,N.T.,
            Plunkett,G. III, Riley,M., Rudd,K.E., Serres,M.H., Thomas,G.H. and
            Wanner,B.L.
  TITLE     Workshop on Annotation of Escherichia coli K-12
  JOURNAL   Unpublished
  REMARK    Woods Hole, Mass., on 14-18 November 2003 (sequence corrections)
REFERENCE   5  (bases 1 to 840)
  AUTHORS   Glasner,J.D., Perna,N.T., Plunkett,G. III, Anderson,B.D.,
            Bockhorst,J., Hu,J.C., Riley,M., Rudd,K.E. and Serres,M.H.
  TITLE     ASAP: Escherichia coli K-12 strain MG1655 version m56
  JOURNAL   Unpublished
  REMARK    ASAP download 10 June 2004 (annotation updates)
REFERENCE   6  (bases 1 to 840)
  AUTHORS   Hayashi,K., Morooka,N., Mori,H. and Horiuchi,T.
  TITLE     A more accurate sequence comparison between genomes of Escherichia
            coli K12 W3110 and MG1655 strains
  JOURNAL   Unpublished
  REMARK    GenBank accessions AG613214 to AG613378 (sequence corrections)
REFERENCE   7  (bases 1 to 840)
  AUTHORS   Perna,N.T.
  TITLE     Escherichia coli K-12 MG1655 yqiK-rfaE intergenic region, genomic
            sequence correction
  JOURNAL   Unpublished
  REMARK    GenBank accession AY605712 (sequence corrections)
REFERENCE   8  (bases 1 to 840)
  AUTHORS   Rudd,K.E.
  TITLE     A manual approach to accurate translation start site annotation: an
            E. coli K-12 case study
  JOURNAL   Unpublished
REFERENCE   9  (bases 1 to 840)
  AUTHORS   Blattner,F.R. and Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-JAN-1997) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
REFERENCE   10 (bases 1 to 840)
  AUTHORS   Blattner,F.R. and Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-SEP-1997) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
REFERENCE   11 (bases 1 to 840)
  AUTHORS   Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-OCT-1998) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
REFERENCE   12 (bases 1 to 840)
  AUTHORS   Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2004) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
  REMARK    Sequence update by submitter
REFERENCE   13 (bases 1 to 840)
  AUTHORS   Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-FEB-2006) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
  REMARK    Protein updates by submitter
REFERENCE   14 (bases 1 to 840)
  AUTHORS   Rudd,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-APR-2007) Department of Biochemistry and Molecular
            Biology, University of Miami Miller School of Medicine, 118 Gautier
            Bldg., Miami, FL 33136, USA
  REMARK    Annotation update from ecogene.org as a multi-database
            collaboration
REFERENCE   15 (bases 1 to 840)
  AUTHORS   Rudd,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-SEP-2007) Department of Biochemistry and Molecular
            Biology, University of Miami Miller School of Medicine, 118 Gautier
            Bldg., Miami, FL 33136, USA
  REMARK    Annotation update from ecogene.org as a multi-database
            collaboration
REFERENCE   16 (bases 1 to 840)
  AUTHORS   Rudd,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-MAR-2008) Department of Biochemistry and Molecular
            Biology, University of Miami Miller School of Medicine, 118 Gautier
            Bldg., Miami, FL 33136, USA
  REMARK    Annotation update from ecogene.org as a multi-database
            collaboration
REFERENCE   17 (bases 1 to 840)
  AUTHORS   Rudd,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-DEC-2008) Department of Biochemistry and Molecular
            Biology, University of Miami Miller School of Medicine, 118 Gautier
            Bldg., Miami, FL 33136, USA
  REMARK    Annotation update from ecogene.org as a multi-database
            collaboration
COMMENT     On or before Jun 21, 2004 this sequence version replaced
            gi:1786181, gi:1786192, gi:2367095, gi:1786217, gi:1786230,
            gi:1786240, gi:1786250, gi:1786262, gi:1786283, gi:1786298,
            gi:1786306, gi:1786315, gi:1786327, gi:1786339, gi:1786348,
            gi:1786358, gi:1786370, gi:1786383, gi:1786395, gi:1786402,
            gi:1786415, gi:2367098, gi:2367099, gi:1786454, gi:1786465,
            gi:2367103, gi:2367108, gi:1786501, gi:1786510, gi:1786520,
            gi:1786532, gi:1786542, gi:1786554, gi:1786568, gi:1786580,
            gi:1786596, gi:1786603, gi:1786614, gi:1786628, gi:1786639,
            gi:1786649, gi:1786660, gi:1786671, gi:1786683, gi:1786692,
            gi:1786705, gi:1786716, gi:1786728, gi:1786739, gi:1786751,
            gi:1786766, gi:1786782, gi:1786790, gi:1786800, gi:1786808,
            gi:1786819, gi:1786836, gi:1786849, gi:1786862, gi:1786875,
            gi:1786888, gi:1786896, gi:1786910, gi:1786920, gi:1786934,
            gi:1786947, gi:1786955, gi:1786967, gi:1786978, gi:1786988,
            gi:1786998, gi:1787015, gi:1787025, gi:1787036, gi:1787047,
            gi:1787058, gi:1787070, gi:1787084, gi:1787097, gi:1787106,
            gi:1787115, gi:1787125, gi:1787134, gi:1787148, gi:1787156,
            gi:1787169, gi:1787180, gi:1787189, gi:1787202, gi:2367111,
            gi:2367113, gi:1787233, gi:1787248, gi:1787256, gi:1787265,
            gi:1787282, gi:1787293, gi:1787308, gi:1787322, gi:1787332,
            gi:1787345, gi:1787358, gi:1787371, gi:1787382, gi:1787405,
            gi:1787417, gi:1787434, gi:1787444, gi:1787453, gi:1787467,
            gi:1787476, gi:1787486, gi:1787496, gi:1787509, gi:1787523,
            gi:2367115, gi:1787543, gi:2367117, gi:1787566, gi:1787578,
            gi:1787588, gi:1787600, gi:1787613, gi:1787633, gi:1787643,
            gi:1787652, gi:1787665, gi:1787673, gi:1787682, gi:1787695,
            gi:1787706, gi:1787720, gi:1787730, gi:1787742, gi:1787752,
            gi:1787764, gi:1787773, gi:1787783, gi:1787790, gi:1787801,
            gi:1787814, gi:2367119, gi:1787841, gi:1787862, gi:1787875,
            gi:1787888, gi:1787898, gi:2367121, gi:1787921, gi:1787935,
            gi:1787945, gi:1787955, gi:1787966, gi:1787978, gi:2367122,
            gi:1787997, gi:1788011, gi:1788022, gi:1788033, gi:1788045,
            gi:1788058, gi:1788067, gi:1788078, gi:1788089, gi:1788106,
            gi:1788117, gi:1788129, gi:1788139, gi:1788154, gi:1788163,
            gi:1788179, gi:1788189, gi:1788200, gi:1788214, gi:1788229,
            gi:1788241, gi:1788257, gi:2367124, gi:1788285, gi:2367125,
            gi:1788298, gi:1788310, gi:2367127, gi:1788338, gi:1788354,
            gi:1788373, gi:1788382, gi:1788395, gi:1788413, gi:1788425,
            gi:2367129, gi:1788447, gi:1788456, gi:1788470, gi:1788479,
            gi:1788489, gi:1788498, gi:1788508, gi:1788520, gi:2367131,
            gi:1788547, gi:1788555, gi:2367132, gi:1788570, gi:1788582,
            gi:1788594, gi:1788605, gi:1788623, gi:1788634, gi:1788647,
            gi:1788659, gi:1788672, gi:1788684, gi:1788694, gi:1788709,
            gi:1788718, gi:1788731, gi:2367135, gi:2367137, gi:1788763,
            gi:1788775, gi:1788789, gi:1788805, gi:1788813, gi:1788821,
            gi:1788839, gi:1788850, gi:1788862, gi:1788870, gi:1788883,
            gi:1788899, gi:1788907, gi:2367139, gi:1788927, gi:1788939,
            gi:2367141, gi:2367142, gi:1788975, gi:2367143, gi:2367147,
            gi:1789011, gi:1789024, gi:1789037, gi:2367149, gi:2367151,
            gi:2367153, gi:2367155, gi:2367156, gi:1789110, gi:2367157,
            gi:2367160, gi:1789143, gi:1789153, gi:2367162, gi:2367163,
            gi:1789185, gi:1789195, gi:2367165, gi:2367168, gi:2367170,
            gi:1789239, gi:2367171, gi:2367173, gi:1789270, gi:1789282,
            gi:2367176, gi:2367178, gi:1789319, gi:2367179, gi:1789344,
            gi:2367181, gi:2367182, gi:2367184, gi:2367186, gi:1789405,
            gi:2367187, gi:1789431, gi:1789441, gi:1789451, gi:2367189,
            gi:2367191, gi:2367194, gi:1789499, gi:2367197, gi:1789524,
            gi:1789536, gi:2367199, gi:1789562, gi:2367201, gi:2367203,
            gi:1789607, gi:1789619, gi:2367205, gi:2367207, gi:1789659,
            gi:2367209, gi:2367211, gi:1789694, gi:1789718, gi:1789734,
            gi:2367213, gi:1789758, gi:2367215, gi:1789783, gi:1789798,
            gi:2367219, gi:2367220, gi:2367222, gi:2367227, gi:1789840,
            gi:1789854, gi:1789868, gi:1789880, gi:2367230, gi:2367232,
            gi:1789910, gi:1789919, gi:1789931, gi:2367235, gi:2367238,
            gi:1789957, gi:2367241, gi:1789977, gi:1789989, gi:2367244,
            gi:2367246, gi:2367249, gi:2367251, gi:1790036, gi:2367252,
            gi:1790063, gi:2367253, gi:2367255, gi:2367258, gi:1790105,
            gi:2367261, gi:2367266, gi:1790142, gi:2367269, gi:1790166,
            gi:2367272, gi:1790188, gi:2367276, gi:2367278, gi:2367282,
            gi:2367291, gi:2367294, gi:2367299, gi:2367306, gi:2367315,
            gi:2367318, gi:1790295, gi:2367320, gi:2367324, gi:2367326,
            gi:2367328, gi:1790356, gi:1790374, gi:1790385, gi:2367332,
            gi:1790404, gi:2367333, gi:2367336, gi:1790440, gi:1790448,
            gi:1790456, gi:2367338, gi:2367339, gi:2367340, gi:2367344,
            gi:2367346, gi:2367349, gi:2367351, gi:2367352, gi:1790563,
            gi:1790574, gi:1790582, gi:2367354, gi:1790607, gi:2367356,
            gi:2367357, gi:1790649, gi:2367360, gi:1790670, gi:2367361,
            gi:2367366, gi:1790711, gi:2367368, gi:1790732, gi:2367369,
            gi:2367372, gi:2367374, gi:1790777, gi:1790789, gi:2367375,
            gi:2367377, gi:2367380, gi:2367382, gi:2367383, gi:1790858,
            gi:6626251.
            Current U00096 annotation updates are derived from EcoGene
            http://ecogene.org. Suggestions for updates can be sent to Dr.
            Kenneth Rudd (krudd@miami.edu). These updates are being generated
            from a collaboration that also includes ASAP/ERIC, the Coli Genetic
            Stock Center, EcoliHub, EcoCyc, RegulonDB and UniProtKB/Swiss-Prot.
FEATURES             Location/Qualifiers
     source          1..840
                     /organism="Escherichia coli str. K-12 substr. MG1655"
                     /mol_type="genomic DNA"
                     /strain="K-12"
                     /sub_strain="MG1655"
                     /db_xref="taxon:511145"
     gene            190..255
                     /gene="thrL"
                     /locus_tag="b0001"
                     /gene_synonym="ECK0001"
                     /gene_synonym="JW4367"
                     /db_xref="EcoGene:EG11277"
     CDS             190..255
                     /gene="thrL"
                     /locus_tag="b0001"
                     /gene_synonym="ECK0001"
                     /gene_synonym="JW4367"
                     /function="leader; Amino acid biosynthesis: Threonine"
                     /function="1.5.1.8 metabolism; building block
                     biosynthesis; amino acids; threonine"
                     /note="GO_process: GO:0009088 - threonine biosynthetic
                     process"
                     /codon_start=1
                     /transl_table=11
                     /product="thr operon leader peptide"
                     /protein_id="AAC73112.1"
                     /db_xref="GI:1786182"
                     /db_xref="ASAP:ABE-0000006"
                     /db_xref="UniProtKB/Swiss-Prot:P0AD86"
                     /db_xref="EcoGene:EG11277"
                     /translation="MKRISTTITTTITITTGNGAG"
     gene            337..>840
                     /gene="thrA"
                     /locus_tag="b0002"
                     /gene_synonym="ECK0002"
                     /gene_synonym="Hs"
                     /gene_synonym="JW0001"
                     /gene_synonym="thrA1"
                     /gene_synonym="thrA2"
                     /gene_synonym="thrD"
                     /db_xref="EcoGene:EG10998"
     CDS             337..>840
                     /gene="thrA"
                     /locus_tag="b0002"
                     /gene_synonym="ECK0002"
                     /gene_synonym="Hs"
                     /gene_synonym="JW0001"
                     /gene_synonym="thrA1"
                     /gene_synonym="thrA2"
                     /gene_synonym="thrD"
                     /EC_number="2.7.2.4"
                     /EC_number="1.1.1.3"
                     /function="enzyme; Amino acid biosynthesis: Threonine"
                     /function="1.5.1.8 metabolism; building block
                     biosynthesis; amino acids; threonine"
                     /function="1.5.1.21 metabolism; building block
                     biosynthesis; amino acids; homoserine"
                     /function="7.1 location of gene products; cytoplasm"
                     /experiment="N-terminus verified by Edman degradation:
                     PMID 354697,4562989"
                     /note="bifunctional: aspartokinase I (N-terminal);
                     homoserine dehydrogenase I (C-terminal);
                     GO_component: GO:0005737 - cytoplasm;
                     GO_process: GO:0009088 - threonine biosynthetic process;
                     GO_process: GO:0009086 - methionine biosynthetic process;
                     GO_process: GO:0009090 - homoserine biosynthetic process"
                     /codon_start=1
                     /transl_table=11
                     /product="fused aspartokinase I and homoserine
                     dehydrogenase I"
                     /protein_id="AAC73113.1"
                     /db_xref="GI:1786183"
                     /db_xref="ASAP:ABE-0000008"
                     /db_xref="UniProtKB/Swiss-Prot:P00561"
                     /db_xref="EcoGene:EG10998"
                     /translation="MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKIT
                     NHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIK
                     HVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHY
                     LESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACL
                     RADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQF
                     QIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAAR
                     VFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAV
                     TERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATT
                     GVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKA
                     LLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYAD
                     FLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLN
                     AGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARK
                     LLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEG
                     KVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAG
                     NDVTAAGVFADLLRTLSWKLGV"
ORIGIN      
        1 agcttttcat tctgactgca acgggcaata tgtctctgtg tggattaaaa aaagagtgtc
       61 tgatagcagc ttctgaactg gttacctgcc gtgagtaaat taaaatttta ttgacttagg
      121 tcactaaata ctttaaccaa tataggcata gcgcacagac agataaaaat tacagagtac
      181 acaacatcca tgaaacgcat tagcaccacc attaccacca ccatcaccat taccacaggt
      241 aacggtgcgg gctgacgcgt acaggaaaca cagaaaaaag cccgcacctg acagtgcggg
      301 cttttttttt cgaccaaagg taacgaggta acaaccatgc gagtgttgaa gttcggcggt
      361 acatcagtgg caaatgcaga acgttttctg cgtgttgccg atattctgga aagcaatgcc
      421 aggcaggggc aggtggccac cgtcctctct gcccccgcca aaatcaccaa ccacctggtg
      481 gcgatgattg aaaaaaccat tagcggccag gatgctttac ccaatatcag cgatgccgaa
      541 cgtatttttg ccgaactttt gacgggactc gccgccgccc agccggggtt cccgctggcg
      601 caattgaaaa ctttcgtcga tcaggaattt gcccaaataa aacatgtcct gcatggcatt
      661 agtttgttgg ggcagtgccc ggatagcatc aacgctgcgc tgatttgccg tggcgagaaa
      721 atgtcgatcg ccattatggc cggcgtatta gaagcgcgcg gtcacaacgt tactgttatc
      781 gatccggtcg aaaaactgct ggcagtgggg cattacctcg aatctaccgt cgatattgct
//
LOCUS       U00096                   910 bp    DNA     linear   BCT 11-MAR-2009
DEFINITION  Escherichia coli str. K-12 substr. MG1655, complete genome.
ACCESSION   U00096 REGION: 1..910
VERSION     U00096.2  GI:48994873
PROJECT     GenomeProject:225
DBLINK      Project:225
KEYWORDS    .
SOURCE      Escherichia coli str. K-12 substr. MG1655
  ORGANISM  Escherichia coli str. K-12 substr. MG1655
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (sites)
  AUTHORS   Kang,W.K., Icho,T., Isono,S., Kitakawa,M. and Isono,K.
  TITLE     Characterization of the gene rimK responsible for the addition of
            glutamic acid residues to the C-terminus of ribosomal protein S6 in
            Escherichia coli K12
  JOURNAL   Mol. Gen. Genet. 217 (2-3), 281-288 (1989)
   PUBMED   2570347
REFERENCE   2  (bases 1 to 910)
  AUTHORS   Blattner,F.R., Plunkett,G., Bloch,C.A., Perna,N.T., Burland,V.,
            Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K., Mayhew,G.F.,
            Gregor,J., Davis,N.W., Kirkpatrick,H.A., Goeden,M.A., Rose,D.J.,
            Mau,B. and Shao,Y.
  TITLE     The complete genome sequence of Escherichia coli K-12
  JOURNAL   Science 277 (5331), 1453-1474 (1997)
   PUBMED   9278503
REFERENCE   3  (bases 1 to 910)
  AUTHORS   Riley,M., Abe,T., Arnaud,M.B., Berlyn,M.K., Blattner,F.R.,
            Chaudhuri,R.R., Glasner,J.D., Horiuchi,T., Keseler,I.M., Kosuge,T.,
            Mori,H., Perna,N.T., Plunkett,G. III, Rudd,K.E., Serres,M.H.,
            Thomas,G.H., Thomson,N.R., Wishart,D. and Wanner,B.L.
  TITLE     Escherichia coli K-12: a cooperatively developed annotation
            snapshot--2005
  JOURNAL   Nucleic Acids Res. 34 (1), 1-9 (2006)
   PUBMED   16397293
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 910)
  AUTHORS   Arnaud,M., Berlyn,M.K.B., Blattner,F.R., Galperin,M.Y.,
            Glasner,J.D., Horiuchi,T., Kosuge,T., Mori,H., Perna,N.T.,
            Plunkett,G. III, Riley,M., Rudd,K.E., Serres,M.H., Thomas,G.H. and
            Wanner,B.L.
  TITLE     Workshop on Annotation of Escherichia coli K-12
  JOURNAL   Unpublished
  REMARK    Woods Hole, Mass., on 14-18 November 2003 (sequence corrections)
REFERENCE   5  (bases 1 to 910)
  AUTHORS   Glasner,J.D., Perna,N.T., Plunkett,G. III, Anderson,B.D.,
            Bockhorst,J., Hu,J.C., Riley,M., Rudd,K.E. and Serres,M.H.
  TITLE     ASAP: Escherichia coli K-12 strain MG1655 version m56
  JOURNAL   Unpublished
  REMARK    ASAP download 10 June 2004 (annotation updates)
REFERENCE   6  (bases 1 to 910)
  AUTHORS   Hayashi,K., Morooka,N., Mori,H. and Horiuchi,T.
  TITLE     A more accurate sequence comparison between genomes of Escherichia
            coli K12 W3110 and MG1655 strains
  JOURNAL   Unpublished
  REMARK    GenBank accessions AG613214 to AG613378 (sequence corrections)
REFERENCE   7  (bases 1 to 910)
  AUTHORS   Perna,N.T.
  TITLE     Escherichia coli K-12 MG1655 yqiK-rfaE intergenic region, genomic
            sequence correction
  JOURNAL   Unpublished
  REMARK    GenBank accession AY605712 (sequence corrections)
REFERENCE   8  (bases 1 to 910)
  AUTHORS   Rudd,K.E.
  TITLE     A manual approach to accurate translation start site annotation: an
            E. coli K-12 case study
  JOURNAL   Unpublished
REFERENCE   9  (bases 1 to 910)
  AUTHORS   Blattner,F.R. and Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-JAN-1997) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
REFERENCE   10 (bases 1 to 910)
  AUTHORS   Blattner,F.R. and Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-SEP-1997) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
REFERENCE   11 (bases 1 to 910)
  AUTHORS   Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-OCT-1998) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
REFERENCE   12 (bases 1 to 910)
  AUTHORS   Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2004) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
  REMARK    Sequence update by submitter
REFERENCE   13 (bases 1 to 910)
  AUTHORS   Plunkett,G. III.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-FEB-2006) Laboratory of Genetics, University of
            Wisconsin, 425G Henry Mall, Madison, WI 53706-1580, USA
  REMARK    Protein updates by submitter
REFERENCE   14 (bases 1 to 910)
  AUTHORS   Rudd,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-APR-2007) Department of Biochemistry and Molecular
            Biology, University of Miami Miller School of Medicine, 118 Gautier
            Bldg., Miami, FL 33136, USA
  REMARK    Annotation update from ecogene.org as a multi-database
            collaboration
REFERENCE   15 (bases 1 to 910)
  AUTHORS   Rudd,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-SEP-2007) Department of Biochemistry and Molecular
            Biology, University of Miami Miller School of Medicine, 118 Gautier
            Bldg., Miami, FL 33136, USA
  REMARK    Annotation update from ecogene.org as a multi-database
            collaboration
REFERENCE   16 (bases 1 to 910)
  AUTHORS   Rudd,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-MAR-2008) Department of Biochemistry and Molecular
            Biology, University of Miami Miller School of Medicine, 118 Gautier
            Bldg., Miami, FL 33136, USA
  REMARK    Annotation update from ecogene.org as a multi-database
            collaboration
REFERENCE   17 (bases 1 to 910)
  AUTHORS   Rudd,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-DEC-2008) Department of Biochemistry and Molecular
            Biology, University of Miami Miller School of Medicine, 118 Gautier
            Bldg., Miami, FL 33136, USA
  REMARK    Annotation update from ecogene.org as a multi-database
            collaboration
COMMENT     On or before Jun 21, 2004 this sequence version replaced
            gi:1786181, gi:1786192, gi:2367095, gi:1786217, gi:1786230,
            gi:1786240, gi:1786250, gi:1786262, gi:1786283, gi:1786298,
            gi:1786306, gi:1786315, gi:1786327, gi:1786339, gi:1786348,
            gi:1786358, gi:1786370, gi:1786383, gi:1786395, gi:1786402,
            gi:1786415, gi:2367098, gi:2367099, gi:1786454, gi:1786465,
            gi:2367103, gi:2367108, gi:1786501, gi:1786510, gi:1786520,
            gi:1786532, gi:1786542, gi:1786554, gi:1786568, gi:1786580,
            gi:1786596, gi:1786603, gi:1786614, gi:1786628, gi:1786639,
            gi:1786649, gi:1786660, gi:1786671, gi:1786683, gi:1786692,
            gi:1786705, gi:1786716, gi:1786728, gi:1786739, gi:1786751,
            gi:1786766, gi:1786782, gi:1786790, gi:1786800, gi:1786808,
            gi:1786819, gi:1786836, gi:1786849, gi:1786862, gi:1786875,
            gi:1786888, gi:1786896, gi:1786910, gi:1786920, gi:1786934,
            gi:1786947, gi:1786955, gi:1786967, gi:1786978, gi:1786988,
            gi:1786998, gi:1787015, gi:1787025, gi:1787036, gi:1787047,
            gi:1787058, gi:1787070, gi:1787084, gi:1787097, gi:1787106,
            gi:1787115, gi:1787125, gi:1787134, gi:1787148, gi:1787156,
            gi:1787169, gi:1787180, gi:1787189, gi:1787202, gi:2367111,
            gi:2367113, gi:1787233, gi:1787248, gi:1787256, gi:1787265,
            gi:1787282, gi:1787293, gi:1787308, gi:1787322, gi:1787332,
            gi:1787345, gi:1787358, gi:1787371, gi:1787382, gi:1787405,
            gi:1787417, gi:1787434, gi:1787444, gi:1787453, gi:1787467,
            gi:1787476, gi:1787486, gi:1787496, gi:1787509, gi:1787523,
            gi:2367115, gi:1787543, gi:2367117, gi:1787566, gi:1787578,
            gi:1787588, gi:1787600, gi:1787613, gi:1787633, gi:1787643,
            gi:1787652, gi:1787665, gi:1787673, gi:1787682, gi:1787695,
            gi:1787706, gi:1787720, gi:1787730, gi:1787742, gi:1787752,
            gi:1787764, gi:1787773, gi:1787783, gi:1787790, gi:1787801,
            gi:1787814, gi:2367119, gi:1787841, gi:1787862, gi:1787875,
            gi:1787888, gi:1787898, gi:2367121, gi:1787921, gi:1787935,
            gi:1787945, gi:1787955, gi:1787966, gi:1787978, gi:2367122,
            gi:1787997, gi:1788011, gi:1788022, gi:1788033, gi:1788045,
            gi:1788058, gi:1788067, gi:1788078, gi:1788089, gi:1788106,
            gi:1788117, gi:1788129, gi:1788139, gi:1788154, gi:1788163,
            gi:1788179, gi:1788189, gi:1788200, gi:1788214, gi:1788229,
            gi:1788241, gi:1788257, gi:2367124, gi:1788285, gi:2367125,
            gi:1788298, gi:1788310, gi:2367127, gi:1788338, gi:1788354,
            gi:1788373, gi:1788382, gi:1788395, gi:1788413, gi:1788425,
            gi:2367129, gi:1788447, gi:1788456, gi:1788470, gi:1788479,
            gi:1788489, gi:1788498, gi:1788508, gi:1788520, gi:2367131,
            gi:1788547, gi:1788555, gi:2367132, gi:1788570, gi:1788582,
            gi:1788594, gi:1788605, gi:1788623, gi:1788634, gi:1788647,
            gi:1788659, gi:1788672, gi:1788684, gi:1788694, gi:1788709,
            gi:1788718, gi:1788731, gi:2367135, gi:2367137, gi:1788763,
            gi:1788775, gi:1788789, gi:1788805, gi:1788813, gi:1788821,
            gi:1788839, gi:1788850, gi:1788862, gi:1788870, gi:1788883,
            gi:1788899, gi:1788907, gi:2367139, gi:1788927, gi:1788939,
            gi:2367141, gi:2367142, gi:1788975, gi:2367143, gi:2367147,
            gi:1789011, gi:1789024, gi:1789037, gi:2367149, gi:2367151,
            gi:2367153, gi:2367155, gi:2367156, gi:1789110, gi:2367157,
            gi:2367160, gi:1789143, gi:1789153, gi:2367162, gi:2367163,
            gi:1789185, gi:1789195, gi:2367165, gi:2367168, gi:2367170,
            gi:1789239, gi:2367171, gi:2367173, gi:1789270, gi:1789282,
            gi:2367176, gi:2367178, gi:1789319, gi:2367179, gi:1789344,
            gi:2367181, gi:2367182, gi:2367184, gi:2367186, gi:1789405,
            gi:2367187, gi:1789431, gi:1789441, gi:1789451, gi:2367189,
            gi:2367191, gi:2367194, gi:1789499, gi:2367197, gi:1789524,
            gi:1789536, gi:2367199, gi:1789562, gi:2367201, gi:2367203,
            gi:1789607, gi:1789619, gi:2367205, gi:2367207, gi:1789659,
            gi:2367209, gi:2367211, gi:1789694, gi:1789718, gi:1789734,
            gi:2367213, gi:1789758, gi:2367215, gi:1789783, gi:1789798,
            gi:2367219, gi:2367220, gi:2367222, gi:2367227, gi:1789840,
            gi:1789854, gi:1789868, gi:1789880, gi:2367230, gi:2367232,
            gi:1789910, gi:1789919, gi:1789931, gi:2367235, gi:2367238,
            gi:1789957, gi:2367241, gi:1789977, gi:1789989, gi:2367244,
            gi:2367246, gi:2367249, gi:2367251, gi:1790036, gi:2367252,
            gi:1790063, gi:2367253, gi:2367255, gi:2367258, gi:1790105,
            gi:2367261, gi:2367266, gi:1790142, gi:2367269, gi:1790166,
            gi:2367272, gi:1790188, gi:2367276, gi:2367278, gi:2367282,
            gi:2367291, gi:2367294, gi:2367299, gi:2367306, gi:2367315,
            gi:2367318, gi:1790295, gi:2367320, gi:2367324, gi:2367326,
            gi:2367328, gi:1790356, gi:1790374, gi:1790385, gi:2367332,
            gi:1790404, gi:2367333, gi:2367336, gi:1790440, gi:1790448,
            gi:1790456, gi:2367338, gi:2367339, gi:2367340, gi:2367344,
            gi:2367346, gi:2367349, gi:2367351, gi:2367352, gi:1790563,
            gi:1790574, gi:1790582, gi:2367354, gi:1790607, gi:2367356,
            gi:2367357, gi:1790649, gi:2367360, gi:1790670, gi:2367361,
            gi:2367366, gi:1790711, gi:2367368, gi:1790732, gi:2367369,
            gi:2367372, gi:2367374, gi:1790777, gi:1790789, gi:2367375,
            gi:2367377, gi:2367380, gi:2367382, gi:2367383, gi:1790858,
            gi:6626251.
            Current U00096 annotation updates are derived from EcoGene
            http://ecogene.org. Suggestions for updates can be sent to Dr.
            Kenneth Rudd (krudd@miami.edu). These updates are being generated
            from a collaboration that also includes ASAP/ERIC, the Coli Genetic
            Stock Center, EcoliHub, EcoCyc, RegulonDB and UniProtKB/Swiss-Prot.
FEATURES             Location/Qualifiers
     source          1..910
                     /organism="Escherichia coli str. K-12 substr. MG1655"
                     /mol_type="genomic DNA"
                     /strain="K-12"
                     /sub_strain="MG1655"
                     /db_xref="taxon:511145"
     gene            190..255
                     /gene="thrL"
                     /locus_tag="b0001"
                     /gene_synonym="ECK0001"
                     /gene_synonym="JW4367"
                     /db_xref="EcoGene:EG11277"
     CDS             190..255
                     /gene="thrL"
                     /locus_tag="b0001"
                     /gene_synonym="ECK0001"
                     /gene_synonym="JW4367"
                     /function="leader; Amino acid biosynthesis: Threonine"
                     /function="1.5.1.8 metabolism; building block
                     biosynthesis; amino acids; threonine"
                     /note="GO_process: GO:0009088 - threonine biosynthetic
                     process"
                     /codon_start=1
                     /transl_table=11
                     /product="thr operon leader peptide"
                     /protein_id="AAC73112.1"
                     /db_xref="GI:1786182"
                     /db_xref="ASAP:ABE-0000006"
                     /db_xref="UniProtKB/Swiss-Prot:P0AD86"
                     /db_xref="EcoGene:EG11277"
                     /translation="MKRISTTITTTITITTGNGAG"
     gene            337..>910
                     /gene="thrA"
                     /locus_tag="b0002"
                     /gene_synonym="ECK0002"
                     /gene_synonym="Hs"
                     /gene_synonym="JW0001"
                     /gene_synonym="thrA1"
                     /gene_synonym="thrA2"
                     /gene_synonym="thrD"
                     /db_xref="EcoGene:EG10998"
     CDS             337..>910
                     /gene="thrA"
                     /locus_tag="b0002"
                     /gene_synonym="ECK0002"
                     /gene_synonym="Hs"
                     /gene_synonym="JW0001"
                     /gene_synonym="thrA1"
                     /gene_synonym="thrA2"
                     /gene_synonym="thrD"
                     /EC_number="2.7.2.4"
                     /EC_number="1.1.1.3"
                     /function="enzyme; Amino acid biosynthesis: Threonine"
                     /function="1.5.1.8 metabolism; building block
                     biosynthesis; amino acids; threonine"
                     /function="1.5.1.21 metabolism; building block
                     biosynthesis; amino acids; homoserine"
                     /function="7.1 location of gene products; cytoplasm"
                     /experiment="N-terminus verified by Edman degradation:
                     PMID 354697,4562989"
                     /note="bifunctional: aspartokinase I (N-terminal);
                     homoserine dehydrogenase I (C-terminal);
                     GO_component: GO:0005737 - cytoplasm;
                     GO_process: GO:0009088 - threonine biosynthetic process;
                     GO_process: GO:0009086 - methionine biosynthetic process;
                     GO_process: GO:0009090 - homoserine biosynthetic process"
                     /codon_start=1
                     /transl_table=11
                     /product="fused aspartokinase I and homoserine
                     dehydrogenase I"
                     /protein_id="AAC73113.1"
                     /db_xref="GI:1786183"
                     /db_xref="ASAP:ABE-0000008"
                     /db_xref="UniProtKB/Swiss-Prot:P00561"
                     /db_xref="EcoGene:EG10998"
                     /translation="MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKIT
                     NHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIK
                     HVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHY
                     LESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACL
                     RADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQF
                     QIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAAR
                     VFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAV
                     TERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATT
                     GVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKA
                     LLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYAD
                     FLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLN
                     AGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARK
                     LLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEG
                     KVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAG
                     NDVTAAGVFADLLRTLSWKLGV"
ORIGIN      
        1 agcttttcat tctgactgca acgggcaata tgtctctgtg tggattaaaa aaagagtgtc
       61 tgatagcagc ttctgaactg gttacctgcc gtgagtaaat taaaatttta ttgacttagg
      121 tcactaaata ctttaaccaa tataggcata gcgcacagac agataaaaat tacagagtac
      181 acaacatcca tgaaacgcat tagcaccacc attaccacca ccatcaccat taccacaggt
      241 aacggtgcgg gctgacgcgt acaggaaaca cagaaaaaag cccgcacctg acagtgcggg
      301 cttttttttt cgaccaaagg taacgaggta acaaccatgc gagtgttgaa gttcggcggt
      361 acatcagtgg caaatgcaga acgttttctg cgtgttgccg atattctgga aagcaatgcc
      421 aggcaggggc aggtggccac cgtcctctct gcccccgcca aaatcaccaa ccacctggtg
      481 gcgatgattg aaaaaaccat tagcggccag gatgctttac ccaatatcag cgatgccgaa
      541 cgtatttttg ccgaactttt gacgggactc gccgccgccc agccggggtt cccgctggcg
      601 caattgaaaa ctttcgtcga tcaggaattt gcccaaataa aacatgtcct gcatggcatt
      661 agtttgttgg ggcagtgccc ggatagcatc aacgctgcgc tgatttgccg tggcgagaaa
      721 atgtcgatcg ccattatggc cggcgtatta gaagcgcgcg gtcacaacgt tactgttatc
      781 gatccggtcg aaaaactgct ggcagtgggg cattacctcg aatctaccgt cgatattgct
      841 gagtccaccc gccgtattgc ggcaagccgc attccggctg atcacatggt gctgatggca
      901 ggtttcaccg
//
genometools-1.5.1/testdata/Duplicate.shreddered000066400000000000000000000152501211610345200216250ustar00rootroot00000000000000>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AGCTTTTCATTCTGACTGCAACGGGCAATA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
TGTCTCTGTGTGGATTAAAAAAAGAGTGTC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
TGATAGCAGCTTCTGAACTGGTTACCTGCC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GTGAGTAAATTAAAATTTTATTGACTTAGG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
TCACTAAATACTTTAACCAATATAGGCATA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCGCACAGACAGATAAAAATTACAGAGTAC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ACAACATCCATGAAACGCATTAGCACCACC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ATTACCACCACCATCACCATTACCACAGGT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AACGGTGCGGGCTGACGCGTACAGGAAACA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CAGAAAAAAGCCCGCACCTGACAGTGCGGG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CTTTTTTTTTCGACCAAAGGTAACGAGGTA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ACAACCATGCGAGTGTTGAAGTTCGGCGGT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ACATCAGTGGCAAATGCAGAACGTTTTCTG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CGTGTTGCCGATATTCTGGAAAGCAATGCC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AGGCAGGGGCAGGTGGCCACCGTCCTCTCT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCCCCCGCCAAAATCACCAACCACCTGGTG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCGATGATTGAAAAAACCATTAGCGGCCAG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GATGCTTTACCCAATATCAGCGATGCCGAA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CGTATTTTTGCCGAACTTTTGACGGGACTC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CAATTGAAAACTTTCGTCGATCAGGAATTT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCCCAAATAAAACATGTCCTGCATGGCATT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AGTTTGTTGGGGCAGTGCCCGGATAGCATC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AACGCTGCGCTGATTTGCCGTGGCGAGAAA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ATGTCGATCGCCATTATGGCCGGCGTATTA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GAAGCGCGCGGTCACAACGTTACTGTTATC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GATCCGGTCGAAAAACTGCTGGCAGTGGGG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CATTACCTCGAATCTACCGTCGATATTGCT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AGCTTTTCATTCTGACTGCAACGGGCAATA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
TGTCTCTGTGTGGATTAAAAAAAGAGTGTC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
TGATAGCAGCTTCTGAACTGGTTACCTGCC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GTGAGTAAATTAAAATTTTATTGACTTAGG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
TCACTAAATACTTTAACCAATATAGGCATA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCGCACAGACAGATAAAAATTACAGAGTAC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ACAACATCCATGAAACGCATTAGCACCACC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ATTACCACCACCATCACCATTACCACAGGT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AACGGTGCGGGCTGACGCGTACAGGAAACA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CAGAAAAAAGCCCGCACCTGACAGTGCGGG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CTTTTTTTTTCGACCAAAGGTAACGAGGTA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ACAACCATGCGAGTGTTGAAGTTCGGCGGT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ACATCAGTGGCAAATGCAGAACGTTTTCTG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CGTGTTGCCGATATTCTGGAAAGCAATGCC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AGGCAGGGGCAGGTGGCCACCGTCCTCTCT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCCCCCGCCAAAATCACCAACCACCTGGTG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCGATGATTGAAAAAACCATTAGCGGCCAG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GATGCTTTACCCAATATCAGCGATGCCGAA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CGTATTTTTGCCGAACTTTTGACGGGACTC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CAATTGAAAACTTTCGTCGATCAGGAATTT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GCCCAAATAAAACATGTCCTGCATGGCATT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AGTTTGTTGGGGCAGTGCCCGGATAGCATC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
AACGCTGCGCTGATTTGCCGTGGCGAGAAA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ATGTCGATCGCCATTATGGCCGGCGTATTA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GAAGCGCGCGGTCACAACGTTACTGTTATC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GATCCGGTCGAAAAACTGCTGGCAGTGGGG
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
CATTACCTCGAATCTACCGTCGATATTGCT
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GAGTCCACCCGCCGTATTGCGGCAAGCCGC
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
ATTCCGGCTGATCACATGGTGCTGATGGCA
>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome [shreddered fragment]
GGTTTCACCG
genometools-1.5.1/testdata/Ecoli-section1.fna000066400000000000000000000005451211610345200211250ustar00rootroot00000000000000>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
>
NTTTTNC
genometools-1.5.1/testdata/Ecoli-section2.fna000066400000000000000000000005411211610345200211220ustar00rootroot00000000000000>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome
TTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
>
NTTTTN
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CAATACGATATCCATTTTAAAA
genometools-1.5.1/testdata/Query3000066400000000000000000000000361211610345200167670ustar00rootroot00000000000000>
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genometools-1.5.1/testdata/Random-Small.embl000066400000000000000000000001651211610345200210060ustar00rootroot00000000000000ID   Random-small
XX
DE   
XX
SQ
     acnnnnanan abn                                                           13
//
genometools-1.5.1/testdata/Random-Small.fna000066400000000000000000000000201211610345200206210ustar00rootroot00000000000000>
acnnnnananabn
genometools-1.5.1/testdata/Random-Small.gbk000066400000000000000000000001251211610345200206260ustar00rootroot00000000000000LOCUS       Random-small
DEFINITION  Random-small
ORIGIN
       13 acnnnnanan abn
//
genometools-1.5.1/testdata/Random.embl000066400000000000000000000323661211610345200177500ustar00rootroot00000000000000ID   Random
XX
DE   
XX
SQ
     nnacancaaa cncaccaaac caanancnca cncnanaccc anccnnanna ancccnaacn        60
     aacnaaaaan ncnncnanan accnacanaa cannnnncnn caanacnacc nnaaccnaac       120
     ncanccancc naaaacacac caaccaannc cnaanccccn ccnnccacna ncccnnnnnc       180
     nnacacaann acncacnnnc cnananacan nnccnnnanc acancaacna cacancaaca       240
     aacaaaccac caaccacccc acaacaacnn cannacnaca accnaccnca nnaannaacc       300
     nanccnannc cnncacnaan cancaanana nnccnancca ccnancaaan aacnancnan       360
     cnnaanncac ccncanaccc caaaanacnc nccaccnnca accanncnan nannccccan       420
     canaanaacc anacnccnac aacancccca aaanannaaa nacnnacanc naanaannaa       480
     ncnncncccn cnnancccna acncacncac cnacaaccnc ccccaannan cncnancnna       540
     acncnnanca cccanacnnn annaannaan annnncccnc cncnccanca aanaanncnn       600
     acncacancc annnanacna aaaaacacna acccanccan ccncaccann acnnaaanac       660
     cnnananann acnnccnanc accaacacaa cacnaacccc cnnacacnna aaacnaaccc       720
     anncncannn nncnncaacn acnccacacc aacnanacnc ncnncaanca acaaanccnc       780
     ncnnaaacca anancnnana caannanaca nnaaacccnc cnanaacnan aanancaaca       840
     nccanacacc aannaaaacc aaaaccanac aancaaaann anannacccc acnacnaann       900
     annccnnnnc cnnnaaannc cccaaanncn ncanncnacc cccacacaaa ccncnnanaa       960
     naaccanann acnncanaca acncncanaa anacnancna acaaccccnn nnccncccnn      1020
     nccancnnaa cancaccnnn cancccnncn aanaacccna cnncnncanc ccccncncaa      1080
     anaacccnaa cccnnacnac canancncaa aancnaanaa ccnccnacnn acaancaanc      1140
     ncnnnnanca cncncnaann ncancnanac naancnnnaa aanacaccac acnnnannca      1200
     naaannnann anaccacnnc ncnaancncn cancccacaa cncccaccnc cnccaannnn      1260
     nnnnacccca ncnnncncaa anacancncc acacncacnn accnnanaaa canccccaaa      1320
     nancccccnc acnnnannan acaancccna aacaccccac naannacana aaaannaacc      1380
     aaacaananc nnnnccnanc cncaananaa cannaannca acncccnncn nnncccaacc      1440
     cnncaacann cnnanncacn ncaccnaaac ncannncacn naacnnnaaa cacancaacn      1500
     caaaaacacn ccnanaacnc nnaccaaanc cnccannaan nnnnaccaaa nanaancnaa      1560
     cacnacccan cccaccaana ccnncacncn canncanaac nnacnnnanc accnaccccc      1620
     acanccaaac ccaaaaaaaa acaacnnana ananaacacn ncncnnacnc caacanccaa      1680
     naanaccacn anacacnnnn nacnaacanc ncananaaaa nnacncaanc aanaacnncn      1740
     ncannnccnn nnacnanncn cacaannnac aanancacca nnaaaananc nnaccnccnc      1800
     aaaacccaan ncccncccnc nncnaaaaaa acaaaccaaa cnnaannaac acnancaaca      1860
     ccaaanaanc cncanananc nccnncnnaa acanccnaaa acaacnncan cnaanaannc      1920
     nncncaanca accaacaaan acacncnacn annnnnnnca ccacancnaa caacnnccaa      1980
     caaacccccc acanaaaann aaaaaccaac nanncanaac cccnacccaa acancaccac      2040
     nnanccacnn aacnncncna nncaaaaccc cnncaccnnn nnnncaacca ccacccnncc      2100
     nnanacccnc caaancanca anccaacanc annannacaa anaancncan ncaaccccca      2160
     nacnacacca anacncnncc acncacaaaa ccaannaana nannacccac nancnccccc      2220
     nannncacac cacnccacca aaccnnaccc ncacnnacna caccnannnc ccccacnnnc      2280
     ccannnnnna accnaanann ncacanacnc aaccacaaaa aacaanncaa nacnccccna      2340
     cnannaaanc anaaccncna cncacaannn acaaacacac nacaccacnc caacanccnn      2400
     caccnnncan aannnaanna ccccccnnna ccanacancc acncccaacn accnaaaann      2460
     naannancan aanacanaan nnaaaancnc nnnccacncn ccccccaana ccnaananan      2520
     nncnancaaa nacnnnccaa ncacacannc aancnaacan ccacnaanca cccncanacc      2580
     accnannccc ncacncannn nannncccca ncacaaccca naaanncncn ccaaccnanc      2640
     cncnanaacc nnncancana nnannaccca ancnacnaca anncaaaaac ccccncacaa      2700
     nacnnaccac accanccccn nanncanncn ncacaacaca nnncncaann ccccccnaan      2760
     ccncnncaca ccaaanacca nnncnccann ncaccaanca ccnccnacnc acccaacann      2820
     nccnannacc aaananccaa aacancaaac cncncacanc cananncnnc accanncnnc      2880
     caaccnaann acnancnncc aacacancca aaccnnaaaa acccncaaan naccacnnnn      2940
     cnncccanaa cnnncccaac ncnncnacac naaancnaac nnnanannac cnnncnnacn      3000
     nccnccnanc ananaccncc ncnaaacann anaaaancan cnccanacnc aannccaccn      3060
     cnccacacnn ccnaccaaac cacaanncnc ccanncnccn acacnccanc cnncancccn      3120
     ncnncaccan cnanncaanc nnaancnanc ccccncnanc ncaccccacc nanaaccana      3180
     naanncccna anccccnnan ncaaaannca cnncaaacac ncancnanaa aacnncccan      3240
     nnnnnncccn naanacnnna aanccncaaa caanaaccna nnccanaacn acnnaannaa      3300
     cnaacnnaca acnaacacnn ncncnncnnc ncacncaanc ccnanacanc acnncaccaa      3360
     ancnnaannc nccaacncna nncncanaca accanncncn nnncnccnnc cnacccacnn      3420
     naancaccnc nanncaacnn naaacannna cnnnaaannc cnaannaana cnnnnccnnn      3480
     annaanacac aaccacacaa ncacanncnn caacnncncn naaaancnac ccccancncn      3540
     ccnaanncan ncaaaacnnc cnncncccnc nacnncncnc nnnaacnana nnnnaanaca      3600
     aaacaccaac nannancaac nancnanacc cnaacanaaa cannnccnaa cnnnaanncn      3660
     nnanaccnan nnacnannaa cnannannnn cncnncannn ncacacaanc acancananc      3720
     annnaanana ncnnaccnaa aacanannnc caccnnannc nnccacnnac nccnnancnc      3780
     nncncanccn ncaancnnnn cnaaccnnaa acccacnaca nccacacnaa nccncnnnan      3840
     cacnnacnan ncncacannn cacnnnaann cncaannnaa ananancanc aancaaacna      3900
     acaancaaaa naancnnnaa cnacaaccnc nnaannnnna ncccacaana nnnaccaccn      3960
     aanaaccaaa nacnccnacn accccancnc ccnnnnnncc naaccnccaa aanncancaa      4020
     nannccnaac nacncnncaa nannnnncan cnncaaaccn acnncncccc ccaaccnnna      4080
     annacnccac nacaacacna cccacnncca anaanacaca naacanncaa nncaacacnn      4140
     ancacananc nannnncacn acacnaacca cananacaac cnaaccccna aacnnaaaca      4200
     aaanannnna annancncac nanacaacca caacaaccaa aaccacnnac ccacacccnn      4260
     nacacncccc nncaacnaan nnancnnnac nacnaaaann annanannnc acaaannana      4320
     nnaaccccac canaannccn cnacncnnna ccnnacnacc anaannaann cnancccnna      4380
     nnaannaccc ccannccaac caaccnnnnn ccncnccncn ncnacacnna aaaancnacc      4440
     aaanacannc nancanccac acccanacnc cnnanannca nnnnnaancc aacaacacca      4500
     annaancnna nanannncca nacaccaaan cancancnac naancaancc cccccaaaan      4560
     aaaaancnna cnccaaacnn nccncaanan cnananaaca cacaanncnc cacanaaanc      4620
     cancnaanca ccnnaannaa ncnaccccac ancncnaacc ancaaananc naaaaanaac      4680
     accnccnnaa accaacnnnn cnanacncac acacnaancn cccncnaaaa cnnacncaca      4740
     ncnnacanaa naaanaannn anancncnna cnncacaana acnncnnann cccaannncn      4800
     ccanacaann cccncnnncc ccaacaacna anacanaccc aaaannnaac acccccanna      4860
     nncnacnana cacnananaa nnnaannaan ccnanaaaac aanccaccna cacanncnnc      4920
     nccaanccan cncnnccncn aacaaancca nnnaaccncc ncnaacncan acacncncac      4980
     nacnnancaa canccnacnc ccacncaann nnnccaaccc nanannnccc anccccaaac      5040
     acaannaccc aacncnncac cnacancccn canccanncc nnacnnaacn cnnancaana      5100
     cacnnaanna nnncaaacan nacaccnccc ccaccnnana annnananan ccacacacnc      5160
     canncnaccn ncacccnnaa aancnnancc nnaaccanca cacnccnanc ncaccnccac      5220
     ccnaanacaa ncaacccnna aaacanannn accaanccan ccncaanccc ncncananac      5280
     aaacncnnaa acnaacaanc ccaaaaanca anaancncnn anacnccnan anccnncccc      5340
     cnnnacannn cnannncncn caaaacccna anaaaacnnn nancannaac aacaccaann      5400
     cacnaanacn aanccanccn cacaacnnca aaccncnncn caanccanan aanccacaca      5460
     cccanaccna ancacnaccc nnccaanaca ccnannnana nncccacncn aaacnacanc      5520
     acnannnacc ncnncnnacn caacccnnnc acancaaccn nacncannan ncaaacnnca      5580
     ncnncncccc nnncncanac cccnnanaca nncacnccca caacaccaac accaannanc      5640
     naacnanana ccacanccca anannccaca annaaaacan nccnaaaccn ncacanaaaa      5700
     acncaacann ccacanaccc nnccccnnnc nannnnaacc cacccnnaan ccncnnnnan      5760
     ncnncannnc ncccannnac nnnaacaacc nccaanncnc ccncnncaca nacaccnnan      5820
     nnaacacanc ancnnnanac cccccnaana aaaanncnnn aacncnnaaa nncnnnnacn      5880
     nnaaacanna ccccacaacc caaannaana accnnannan naccaaaaan cnaacacacn      5940
     ncaanncanc cnnacaanna cnnanaanaa acancnnnnn acccnannna nnanannnan      6000
     nacnccccnc naacnnanna accnccacca nccnnccaaa ccacnccnan aacnaccnnn      6060
     ncncaacanc caccaccacc ccncncanaa cacnncccan cnaccnacna nnccncncnn      6120
     cannacnaan cncaancnna acacacnnna ccaaaanncn aacnncnanc nccnaaacca      6180
     cannanccnc nacancnaaa aanaccnncc ancanacacc accnncccca cccanncnca      6240
     cnnccnccnc anannacncn aacncanacc aannnnaccn cnnncccaaa acnaccanac      6300
     ncnncnnnnc ccncancaac aanacnacan ccnnnnncac aaacnaaacn cnaanncaan      6360
     accaaccaac anncnanacc cnacanacan acanaacnnc canccaacac aanacanaaa      6420
     acnaannncn nnaacaaanc naacnacacn ncnnnnccnc acaanccaan anaanannnn      6480
     cancaaanaa nacanccaac cacancnccn caacacanaa cncaccnaan accnnacnaa      6540
     cnccacacan acnaaanacn ccaccacccc nacnanaccc ccccnaacca acccaacccc      6600
     aancncccca nnncaanncn anccacnanc aaaaanannc cnncncnnna aanaaaanac      6660
     cnacacccaa ncncacaacn nananancnc cnnaaancnn ncnnannnca ncannacanc      6720
     naacnnaaan cnaancnnnn aanncacnaa cnaccacanc nnaaccnnnn cancaacaan      6780
     acnanaacca annnnccaac acaccaanna cancannacc cccnacacaa cnnnanacnc      6840
     cnnacaanaa ccnacccccc nanccncanc cnancaccca nncannnaan ccacnccncc      6900
     canaanaaan cncccnnnna anancnccna ncnncnacnc annnnanncn cnccacccaa      6960
     nacnannacc cnaaacaacc ccncaannna accaannacc canaanannc nnanacccca      7020
     caacnanncc cannnnacan cnaanancca anannccann nacccnccan acnanccaaa      7080
     nacccacaca nnccncnnna nccnnnncan aacacaccca aacaacccna accncannan      7140
     acnccacccc aaaaacnncn aacnccncnn cannaaanca nnnnncnnaa ncannanncc      7200
     anaaaaannc cacnaacnnc nncccnncca annccccaaa anccccccna ccncncacan      7260
     naaaccannc caccaccccn nacaaccncc acancccann aanncnannn ccancannaa      7320
     caccnanacn cacnncncac aacnnacana ccaannacaa cnacaaaccc nccnccaaca      7380
     acananacnn ccacaancaa cannccccna acncccaacc cncannanac naacnnccca      7440
     nannnnnacn aaccccaaac ncnnccnanc nanncacanc aaaaaaacan caaccccaan      7500
     naaacannna annacacnaa nnancccnca ccnaanacaa canncnaaaa cccnancccc      7560
     cnncnnnncn cacaccancc aancncaccn acncanaacn cnnanncacn cnnacaaaan      7620
     ncanaaaacc acancncccc annnnaancn cccncccaac ancacnnnac accccacann      7680
     ccnnaananc annccnacaa cncccacccc anaccnnnna cnccancncc nnacanncca      7740
     cccaacnncn acaacnncna naacaccnan nnaaaaancn aaanacnacn cancncnanc      7800
     cananannna nanacnnnnc nacanaacan caacnnncac ancancnanc cnnccccann      7860
     nncncncnca aanaacnnnc nncacannna nncnacnaca acaanccnnn cccanaaaaa      7920
     aancncnnnc annnancccn ccacanccna ncnnnnncaa acncacnaac naanacacna      7980
     nnccaccacn ncccnncnnn ncaacnaacc cncnnannac nnnannccan aannanncna      8040
     aaanncnncc cananncccn nnanacnncn nacncacccc nanaaanann nacnccnaan      8100
     ancncanacc ncancncnac ccacncacnn ccaaaaaccn cnanaaanac aannnnancc      8160
     nacncnnann cnccanannn nnccnnaccn ncacannanc cccnncaaan nnccancnna      8220
     nncnccancc anaccnncna nacanncann acnaacnaac ncacnccacn nacanaccnn      8280
     ccnaaacacc ncaanaccac nnaacaaccc anacnnnacn anacncannn nnnccannnc      8340
     cncccaannc ccnaaccncn aancccaaaa cnccccnacc nccacacacn canncncana      8400
     aacanannnn cnaaanncan aaacacaaan nncnncaaac anccncacaa acaananacn      8460
     ncnacnccca acnaaaaacn annncccacn nccannncac anccccccna cnacnnccca      8520
     nnnaccccaa nannccncan annaaccnnc aacnccacnc ccacaacacc aancaaaccn      8580
     cnncaccnna nanccnaanc cnacacncac caaaaacaan anncaanacn naacnaaana      8640
     acccccnncn ccccaaanca ncanaacann anaacaaaac aacnananac acaaancacc      8700
     aannannann ncaanncaac ccaacnnaaa nanaananan nnncnaaanc cnccnacnna      8760
     caaaccnacn cncnccnanc acaaanaccc nnnnncnacn nnanaaanan aaacncaaan      8820
     aaacacnnca ccaancacnn ccacncncac cacanaancc acnnaaacan ncccaccncc      8880
     aaanncncna cacaanaccn aaaannaann acanaanaca nnacanaacn aaaanaaaan      8940
     acccanaaaa nncncacaca anccnnnann aanacccccn nnaannancc annacacnac      9000
     cnnnncaacn nnnnnaaanc ccncannnac nnaacnccac ncncanncnn aaannanacc      9060
     nccacanccc acncnnnaca canaccacaa cccaccccan ancanncncn annnnncaca      9120
     cncacncnnn ccnncacacc cnccnnancc ccnnccnaca ncncacaaca acnanccaac      9180
     canacaacac aaaanccccc acacaccccn acnnnanccc cnaacncnaa acaacnaacn      9240
     acaccnaccc naaccnancn nancancanc nncnnacnna cnnnacacan caaccnanca      9300
     acncaanncc anccccnccc acacaannac ccccnaanna caannnacac naaannannn      9360
     aancccnnna nccacnancn nncaaanann caaacaacac ncannnccnn nncaanncac      9420
     nnncanaaac canannccac nannnnaana cccanacnna naananacnn nanaaacncn      9480
     ccccnanana acnnacannn ancncccnan ccnccancna cannncaaaa ancanccccc      9540
     naaacancnn ncanncaanc naacnncanc annannccac ncnnaccncc anancacccn      9600
     nnacaanana acccnancan nncnncacna acacccnnan nnanacancn nncnaacccn      9660
     caanancaan ccacncnnca nnnnnncnca cnnnnnccan annaanaacn nnacccncnn      9720
     ancnccnnnn ccnaancaaa cacnaannaa ncnacaacac annncnnnna caccanncnn      9780
     ncncnacccc acaacaccac ncanncacnn aannnacnaa caccccaaaa naccnccccn      9840
     nnacnancnn nacccannna ncnncnaccn nccccccana ccccnaaana cccaaacncn      9900
     ncnanacnna nccccncnca nncnccacca nacccaccaa naccaccaan acnacnannc      9960
     cnnnanaanc caccaannan caancancan naaaccncac nnn                       10003
// 
genometools-1.5.1/testdata/Random.fna000066400000000000000000000236441211610345200175740ustar00rootroot00000000000000>
nnacancaaacncaccaaaccaanancncacncnanacccanccnnannaancccnaacnaacnaaaaan
ncnncnananaccnacanaacannnnncnncaanacnaccnnaaccnaacncanccanccnaaaacacac
caaccaannccnaanccccnccnnccacnancccnnnnncnnacacaannacncacnnnccnananacan
nnccnnnancacancaacnacacancaacaaacaaaccaccaaccaccccacaacaacnncannacnaca
accnaccncannaannaaccnanccnannccnncacnaancancaananannccnanccaccnancaaan
aacnancnancnnaanncacccncanaccccaaaanacncnccaccnncaaccanncnannannccccan
canaanaaccanacnccnacaacanccccaaaanannaaanacnnacancnaanaannaancnncncccn
cnnancccnaacncacncaccnacaaccncccccaannancncnancnnaacncnnancacccanacnnn
annaannaanannnncccnccncnccancaaanaanncnnacncacanccannnanacnaaaaaacacna
acccanccanccncaccannacnnaaanaccnnananannacnnccnancaccaacacaacacnaacccc
cnnacacnnaaaacnaacccanncncannnnncnncaacnacnccacaccaacnanacncncnncaanca
acaaanccncncnnaaaccaanancnnanacaannanacannaaacccnccnanaacnanaanancaaca
nccanacaccaannaaaaccaaaaccanacaancaaaannanannaccccacnacnaannannccnnnnc
cnnnaaannccccaaanncnncanncnacccccacacaaaccncnnanaanaaccanannacnncanaca
acncncanaaanacnancnaacaaccccnnnnccncccnnnccancnnaacancaccnnncancccnncn
aanaacccnacnncnncancccccncncaaanaacccnaacccnnacnaccanancncaaaancnaanaa
ccnccnacnnacaancaancncnnnnancacncncnaannncancnanacnaancnnnaaaanacaccac
acnnnanncanaaannnannanaccacnncncnaancncncancccacaacncccaccnccnccaannnn
nnnnaccccancnnncncaaanacancnccacacncacnnaccnnanaaacanccccaaanancccccnc
acnnnannanacaancccnaaacaccccacnaannacanaaaaannaaccaaacaanancnnnnccnanc
cncaananaacannaanncaacncccnncnnnncccaacccnncaacanncnnanncacnncaccnaaac
ncannncacnnaacnnnaaacacancaacncaaaaacacnccnanaacncnnaccaaanccnccannaan
nnnnaccaaananaancnaacacnacccancccaccaanaccnncacncncanncanaacnnacnnnanc
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naanaccacnanacacnnnnnacnaacancncananaaaannacncaancaanaacnncnncannnccnn
nnacnanncncacaannnacaanancaccannaaaanancnnaccnccncaaaacccaanncccncccnc
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acanccnaaaacaacnncancnaanaanncnncncaancaaccaacaaanacacncnacnannnnnnnca
ccacancnaacaacnnccaacaaaccccccacanaaaannaaaaaccaacnanncanaaccccnacccaa
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nnanacccnccaaancancaanccaacancannannacaaanaancncanncaacccccanacnacacca
anacncnnccacncacaaaaccaannaananannacccacnancncccccnannncacaccacnccacca
aaccnnacccncacnnacnacaccnannncccccacnnncccannnnnnaaccnaanannncacanacnc
aaccacaaaaaacaanncaanacnccccnacnannaaancanaaccncnacncacaannnacaaacacac
nacaccacnccaacanccnncaccnnncanaannnaannaccccccnnnaccanacanccacncccaacn
accnaaaannnaannancanaanacanaannnaaaancncnnnccacncnccccccaanaccnaananan
nncnancaaanacnnnccaancacacanncaancnaacanccacnaancacccncanaccaccnannccc
ncacncannnnannnccccancacaacccanaaanncncnccaaccnanccncnanaaccnnncancana
nnannacccaancnacnacaanncaaaaacccccncacaanacnnaccacaccanccccnnanncanncn
ncacaacacannncncaannccccccnaanccncnncacaccaaanaccannncnccannncaccaanca
ccnccnacncacccaacannnccnannaccaaananccaaaacancaaaccncncacanccananncnnc
accanncnnccaaccnaannacnancnnccaacacanccaaaccnnaaaaacccncaaannaccacnnnn
cnncccanaacnnncccaacncnncnacacnaaancnaacnnnanannaccnnncnnacnnccnccnanc
ananaccnccncnaaacannanaaaancancnccanacncaannccaccncnccacacnnccnaccaaac
cacaanncncccanncnccnacacnccanccnncancccnncnncaccancnanncaancnnaancnanc
ccccncnancncaccccaccnanaaccananaanncccnaanccccnnanncaaaanncacnncaaacac
ncancnanaaaacnncccannnnnnncccnnaanacnnnaaanccncaaacaanaaccnannccanaacn
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nanncaacnnnaaacannnacnnnaaannccnaannaanacnnnnccnnnannaanacacaaccacacaa
ncacanncnncaacnncncnnaaaancnacccccancncnccnaanncanncaaaacnnccnncncccnc
nacnncncncnnnaacnanannnnaanacaaaacaccaacnannancaacnancnanacccnaacanaaa
cannnccnaacnnnaanncnnnanaccnannnacnannaacnannannnncncnncannnncacacaanc
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ncncacannncacnnnaanncncaannnaaananancancaancaaacnaacaancaaaanaancnnnaa
cnacaaccncnnaannnnnancccacaanannnaccaccnaanaaccaaanacnccnacnaccccancnc
ccnnnnnnccnaaccnccaaaanncancaanannccnaacnacncnncaanannnnncancnncaaaccn
acnncnccccccaaccnnnaannacnccacnacaacacnacccacnnccaanaanacacanaacanncaa
nncaacacnnancacanancnannnncacnacacnaaccacananacaaccnaaccccnaaacnnaaaca
aaanannnnaannancncacnanacaaccacaacaaccaaaaccacnnacccacacccnnnacacncccc
nncaacnaannnancnnnacnacnaaaannannanannncacaaannanannaaccccaccanaannccn
cnacncnnnaccnnacnaccanaannaanncnancccnnannaannacccccannccaaccaaccnnnnn
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nnnnnaanccaacaacaccaannaancnnananannnccanacaccaaancancancnacnaancaancc
cccccaaaanaaaaancnnacnccaaacnnnccncaanancnananaacacacaanncnccacanaaanc
cancnaancaccnnaannaancnaccccacancncnaaccancaaanancnaaaaanaacaccnccnnaa
accaacnnnncnanacncacacacnaancncccncnaaaacnnacncacancnnacanaanaaanaannn
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anacanacccaaaannnaacacccccannanncnacnanacacnananaannnaannaanccnanaaaac
aanccaccnacacanncnncnccaanccancncnnccncnaacaaanccannnaaccnccncnaacncan
acacncncacnacnnancaacanccnacncccacncaannnnnccaacccnanannncccanccccaaac
acaannacccaacncnncaccnacancccncanccannccnnacnnaacncnnancaanacacnnaanna
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aancnnanccnnaaccancacacnccnancncaccnccacccnaanacaancaacccnnaaaacanannn
accaanccanccncaancccncncananacaaacncnnaaacnaacaancccaaaaancaanaancncnn
anacnccnananccnncccccnnnacannncnannncncncaaaacccnaanaaaacnnnnancannaac
aacaccaanncacnaanacnaanccanccncacaacnncaaaccncnncncaanccananaanccacaca
cccanaccnaancacnacccnnccaanacaccnannnananncccacncnaaacnacancacnannnacc
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cccnnanacanncacncccacaacaccaacaccaannancnaacnananaccacancccaanannccaca
annaaaacannccnaaaccnncacanaaaaacncaacannccacanacccnnccccnnncnannnnaacc
cacccnnaanccncnnnnanncnncannncncccannnacnnnaacaaccnccaanncncccncnncaca
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nnaaacannaccccacaacccaaannaanaaccnnannannaccaaaaancnaacacacnncaanncanc
cnnacaannacnnanaanaaacancnnnnnacccnannnannanannnannacnccccncnaacnnanna
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cacnncccancnaccnacnannccncncnncannacnaancncaancnnaacacacnnnaccaaaanncn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-1.5.1/testdata/Random.gbk000066400000000000000000000306701211610345200175700ustar00rootroot00000000000000LOCUS       Random
DEFINITION  Random
ORIGIN      
        1 nnacancaaa cncaccaaac caanancnca cncnanaccc anccnnanna ancccnaacn
       61 aacnaaaaan ncnncnanan accnacanaa cannnnncnn caanacnacc nnaaccnaac
      121 ncanccancc naaaacacac caaccaannc cnaanccccn ccnnccacna ncccnnnnnc
      181 nnacacaann acncacnnnc cnananacan nnccnnnanc acancaacna cacancaaca
      241 aacaaaccac caaccacccc acaacaacnn cannacnaca accnaccnca nnaannaacc
      301 nanccnannc cnncacnaan cancaanana nnccnancca ccnancaaan aacnancnan
      361 cnnaanncac ccncanaccc caaaanacnc nccaccnnca accanncnan nannccccan
      421 canaanaacc anacnccnac aacancccca aaanannaaa nacnnacanc naanaannaa
      481 ncnncncccn cnnancccna acncacncac cnacaaccnc ccccaannan cncnancnna
      541 acncnnanca cccanacnnn annaannaan annnncccnc cncnccanca aanaanncnn
      601 acncacancc annnanacna aaaaacacna acccanccan ccncaccann acnnaaanac
      661 cnnananann acnnccnanc accaacacaa cacnaacccc cnnacacnna aaacnaaccc
      721 anncncannn nncnncaacn acnccacacc aacnanacnc ncnncaanca acaaanccnc
      781 ncnnaaacca anancnnana caannanaca nnaaacccnc cnanaacnan aanancaaca
      841 nccanacacc aannaaaacc aaaaccanac aancaaaann anannacccc acnacnaann
      901 annccnnnnc cnnnaaannc cccaaanncn ncanncnacc cccacacaaa ccncnnanaa
      961 naaccanann acnncanaca acncncanaa anacnancna acaaccccnn nnccncccnn
     1021 nccancnnaa cancaccnnn cancccnncn aanaacccna cnncnncanc ccccncncaa
     1081 anaacccnaa cccnnacnac canancncaa aancnaanaa ccnccnacnn acaancaanc
     1141 ncnnnnanca cncncnaann ncancnanac naancnnnaa aanacaccac acnnnannca
     1201 naaannnann anaccacnnc ncnaancncn cancccacaa cncccaccnc cnccaannnn
     1261 nnnnacccca ncnnncncaa anacancncc acacncacnn accnnanaaa canccccaaa
     1321 nancccccnc acnnnannan acaancccna aacaccccac naannacana aaaannaacc
     1381 aaacaananc nnnnccnanc cncaananaa cannaannca acncccnncn nnncccaacc
     1441 cnncaacann cnnanncacn ncaccnaaac ncannncacn naacnnnaaa cacancaacn
     1501 caaaaacacn ccnanaacnc nnaccaaanc cnccannaan nnnnaccaaa nanaancnaa
     1561 cacnacccan cccaccaana ccnncacncn canncanaac nnacnnnanc accnaccccc
     1621 acanccaaac ccaaaaaaaa acaacnnana ananaacacn ncncnnacnc caacanccaa
     1681 naanaccacn anacacnnnn nacnaacanc ncananaaaa nnacncaanc aanaacnncn
     1741 ncannnccnn nnacnanncn cacaannnac aanancacca nnaaaananc nnaccnccnc
     1801 aaaacccaan ncccncccnc nncnaaaaaa acaaaccaaa cnnaannaac acnancaaca
     1861 ccaaanaanc cncanananc nccnncnnaa acanccnaaa acaacnncan cnaanaannc
     1921 nncncaanca accaacaaan acacncnacn annnnnnnca ccacancnaa caacnnccaa
     1981 caaacccccc acanaaaann aaaaaccaac nanncanaac cccnacccaa acancaccac
     2041 nnanccacnn aacnncncna nncaaaaccc cnncaccnnn nnnncaacca ccacccnncc
     2101 nnanacccnc caaancanca anccaacanc annannacaa anaancncan ncaaccccca
     2161 nacnacacca anacncnncc acncacaaaa ccaannaana nannacccac nancnccccc
     2221 nannncacac cacnccacca aaccnnaccc ncacnnacna caccnannnc ccccacnnnc
     2281 ccannnnnna accnaanann ncacanacnc aaccacaaaa aacaanncaa nacnccccna
     2341 cnannaaanc anaaccncna cncacaannn acaaacacac nacaccacnc caacanccnn
     2401 caccnnncan aannnaanna ccccccnnna ccanacancc acncccaacn accnaaaann
     2461 naannancan aanacanaan nnaaaancnc nnnccacncn ccccccaana ccnaananan
     2521 nncnancaaa nacnnnccaa ncacacannc aancnaacan ccacnaanca cccncanacc
     2581 accnannccc ncacncannn nannncccca ncacaaccca naaanncncn ccaaccnanc
     2641 cncnanaacc nnncancana nnannaccca ancnacnaca anncaaaaac ccccncacaa
     2701 nacnnaccac accanccccn nanncanncn ncacaacaca nnncncaann ccccccnaan
     2761 ccncnncaca ccaaanacca nnncnccann ncaccaanca ccnccnacnc acccaacann
     2821 nccnannacc aaananccaa aacancaaac cncncacanc cananncnnc accanncnnc
     2881 caaccnaann acnancnncc aacacancca aaccnnaaaa acccncaaan naccacnnnn
     2941 cnncccanaa cnnncccaac ncnncnacac naaancnaac nnnanannac cnnncnnacn
     3001 nccnccnanc ananaccncc ncnaaacann anaaaancan cnccanacnc aannccaccn
     3061 cnccacacnn ccnaccaaac cacaanncnc ccanncnccn acacnccanc cnncancccn
     3121 ncnncaccan cnanncaanc nnaancnanc ccccncnanc ncaccccacc nanaaccana
     3181 naanncccna anccccnnan ncaaaannca cnncaaacac ncancnanaa aacnncccan
     3241 nnnnnncccn naanacnnna aanccncaaa caanaaccna nnccanaacn acnnaannaa
     3301 cnaacnnaca acnaacacnn ncncnncnnc ncacncaanc ccnanacanc acnncaccaa
     3361 ancnnaannc nccaacncna nncncanaca accanncncn nnncnccnnc cnacccacnn
     3421 naancaccnc nanncaacnn naaacannna cnnnaaannc cnaannaana cnnnnccnnn
     3481 annaanacac aaccacacaa ncacanncnn caacnncncn naaaancnac ccccancncn
     3541 ccnaanncan ncaaaacnnc cnncncccnc nacnncncnc nnnaacnana nnnnaanaca
     3601 aaacaccaac nannancaac nancnanacc cnaacanaaa cannnccnaa cnnnaanncn
     3661 nnanaccnan nnacnannaa cnannannnn cncnncannn ncacacaanc acancananc
     3721 annnaanana ncnnaccnaa aacanannnc caccnnannc nnccacnnac nccnnancnc
     3781 nncncanccn ncaancnnnn cnaaccnnaa acccacnaca nccacacnaa nccncnnnan
     3841 cacnnacnan ncncacannn cacnnnaann cncaannnaa ananancanc aancaaacna
     3901 acaancaaaa naancnnnaa cnacaaccnc nnaannnnna ncccacaana nnnaccaccn
     3961 aanaaccaaa nacnccnacn accccancnc ccnnnnnncc naaccnccaa aanncancaa
     4021 nannccnaac nacncnncaa nannnnncan cnncaaaccn acnncncccc ccaaccnnna
     4081 annacnccac nacaacacna cccacnncca anaanacaca naacanncaa nncaacacnn
     4141 ancacananc nannnncacn acacnaacca cananacaac cnaaccccna aacnnaaaca
     4201 aaanannnna annancncac nanacaacca caacaaccaa aaccacnnac ccacacccnn
     4261 nacacncccc nncaacnaan nnancnnnac nacnaaaann annanannnc acaaannana
     4321 nnaaccccac canaannccn cnacncnnna ccnnacnacc anaannaann cnancccnna
     4381 nnaannaccc ccannccaac caaccnnnnn ccncnccncn ncnacacnna aaaancnacc
     4441 aaanacannc nancanccac acccanacnc cnnanannca nnnnnaancc aacaacacca
     4501 annaancnna nanannncca nacaccaaan cancancnac naancaancc cccccaaaan
     4561 aaaaancnna cnccaaacnn nccncaanan cnananaaca cacaanncnc cacanaaanc
     4621 cancnaanca ccnnaannaa ncnaccccac ancncnaacc ancaaananc naaaaanaac
     4681 accnccnnaa accaacnnnn cnanacncac acacnaancn cccncnaaaa cnnacncaca
     4741 ncnnacanaa naaanaannn anancncnna cnncacaana acnncnnann cccaannncn
     4801 ccanacaann cccncnnncc ccaacaacna anacanaccc aaaannnaac acccccanna
     4861 nncnacnana cacnananaa nnnaannaan ccnanaaaac aanccaccna cacanncnnc
     4921 nccaanccan cncnnccncn aacaaancca nnnaaccncc ncnaacncan acacncncac
     4981 nacnnancaa canccnacnc ccacncaann nnnccaaccc nanannnccc anccccaaac
     5041 acaannaccc aacncnncac cnacancccn canccanncc nnacnnaacn cnnancaana
     5101 cacnnaanna nnncaaacan nacaccnccc ccaccnnana annnananan ccacacacnc
     5161 canncnaccn ncacccnnaa aancnnancc nnaaccanca cacnccnanc ncaccnccac
     5221 ccnaanacaa ncaacccnna aaacanannn accaanccan ccncaanccc ncncananac
     5281 aaacncnnaa acnaacaanc ccaaaaanca anaancncnn anacnccnan anccnncccc
     5341 cnnnacannn cnannncncn caaaacccna anaaaacnnn nancannaac aacaccaann
     5401 cacnaanacn aanccanccn cacaacnnca aaccncnncn caanccanan aanccacaca
     5461 cccanaccna ancacnaccc nnccaanaca ccnannnana nncccacncn aaacnacanc
     5521 acnannnacc ncnncnnacn caacccnnnc acancaaccn nacncannan ncaaacnnca
     5581 ncnncncccc nnncncanac cccnnanaca nncacnccca caacaccaac accaannanc
     5641 naacnanana ccacanccca anannccaca annaaaacan nccnaaaccn ncacanaaaa
     5701 acncaacann ccacanaccc nnccccnnnc nannnnaacc cacccnnaan ccncnnnnan
     5761 ncnncannnc ncccannnac nnnaacaacc nccaanncnc ccncnncaca nacaccnnan
     5821 nnaacacanc ancnnnanac cccccnaana aaaanncnnn aacncnnaaa nncnnnnacn
     5881 nnaaacanna ccccacaacc caaannaana accnnannan naccaaaaan cnaacacacn
     5941 ncaanncanc cnnacaanna cnnanaanaa acancnnnnn acccnannna nnanannnan
     6001 nacnccccnc naacnnanna accnccacca nccnnccaaa ccacnccnan aacnaccnnn
     6061 ncncaacanc caccaccacc ccncncanaa cacnncccan cnaccnacna nnccncncnn
     6121 cannacnaan cncaancnna acacacnnna ccaaaanncn aacnncnanc nccnaaacca
     6181 cannanccnc nacancnaaa aanaccnncc ancanacacc accnncccca cccanncnca
     6241 cnnccnccnc anannacncn aacncanacc aannnnaccn cnnncccaaa acnaccanac
     6301 ncnncnnnnc ccncancaac aanacnacan ccnnnnncac aaacnaaacn cnaanncaan
     6361 accaaccaac anncnanacc cnacanacan acanaacnnc canccaacac aanacanaaa
     6421 acnaannncn nnaacaaanc naacnacacn ncnnnnccnc acaanccaan anaanannnn
     6481 cancaaanaa nacanccaac cacancnccn caacacanaa cncaccnaan accnnacnaa
     6541 cnccacacan acnaaanacn ccaccacccc nacnanaccc ccccnaacca acccaacccc
     6601 aancncccca nnncaanncn anccacnanc aaaaanannc cnncncnnna aanaaaanac
     6661 cnacacccaa ncncacaacn nananancnc cnnaaancnn ncnnannnca ncannacanc
     6721 naacnnaaan cnaancnnnn aanncacnaa cnaccacanc nnaaccnnnn cancaacaan
     6781 acnanaacca annnnccaac acaccaanna cancannacc cccnacacaa cnnnanacnc
     6841 cnnacaanaa ccnacccccc nanccncanc cnancaccca nncannnaan ccacnccncc
     6901 canaanaaan cncccnnnna anancnccna ncnncnacnc annnnanncn cnccacccaa
     6961 nacnannacc cnaaacaacc ccncaannna accaannacc canaanannc nnanacccca
     7021 caacnanncc cannnnacan cnaanancca anannccann nacccnccan acnanccaaa
     7081 nacccacaca nnccncnnna nccnnnncan aacacaccca aacaacccna accncannan
     7141 acnccacccc aaaaacnncn aacnccncnn cannaaanca nnnnncnnaa ncannanncc
     7201 anaaaaannc cacnaacnnc nncccnncca annccccaaa anccccccna ccncncacan
     7261 naaaccannc caccaccccn nacaaccncc acancccann aanncnannn ccancannaa
     7321 caccnanacn cacnncncac aacnnacana ccaannacaa cnacaaaccc nccnccaaca
     7381 acananacnn ccacaancaa cannccccna acncccaacc cncannanac naacnnccca
     7441 nannnnnacn aaccccaaac ncnnccnanc nanncacanc aaaaaaacan caaccccaan
     7501 naaacannna annacacnaa nnancccnca ccnaanacaa canncnaaaa cccnancccc
     7561 cnncnnnncn cacaccancc aancncaccn acncanaacn cnnanncacn cnnacaaaan
     7621 ncanaaaacc acancncccc annnnaancn cccncccaac ancacnnnac accccacann
     7681 ccnnaananc annccnacaa cncccacccc anaccnnnna cnccancncc nnacanncca
     7741 cccaacnncn acaacnncna naacaccnan nnaaaaancn aaanacnacn cancncnanc
     7801 cananannna nanacnnnnc nacanaacan caacnnncac ancancnanc cnnccccann
     7861 nncncncnca aanaacnnnc nncacannna nncnacnaca acaanccnnn cccanaaaaa
     7921 aancncnnnc annnancccn ccacanccna ncnnnnncaa acncacnaac naanacacna
     7981 nnccaccacn ncccnncnnn ncaacnaacc cncnnannac nnnannccan aannanncna
     8041 aaanncnncc cananncccn nnanacnncn nacncacccc nanaaanann nacnccnaan
     8101 ancncanacc ncancncnac ccacncacnn ccaaaaaccn cnanaaanac aannnnancc
     8161 nacncnnann cnccanannn nnccnnaccn ncacannanc cccnncaaan nnccancnna
     8221 nncnccancc anaccnncna nacanncann acnaacnaac ncacnccacn nacanaccnn
     8281 ccnaaacacc ncaanaccac nnaacaaccc anacnnnacn anacncannn nnnccannnc
     8341 cncccaannc ccnaaccncn aancccaaaa cnccccnacc nccacacacn canncncana
     8401 aacanannnn cnaaanncan aaacacaaan nncnncaaac anccncacaa acaananacn
     8461 ncnacnccca acnaaaaacn annncccacn nccannncac anccccccna cnacnnccca
     8521 nnnaccccaa nannccncan annaaccnnc aacnccacnc ccacaacacc aancaaaccn
     8581 cnncaccnna nanccnaanc cnacacncac caaaaacaan anncaanacn naacnaaana
     8641 acccccnncn ccccaaanca ncanaacann anaacaaaac aacnananac acaaancacc
     8701 aannannann ncaanncaac ccaacnnaaa nanaananan nnncnaaanc cnccnacnna
     8761 caaaccnacn cncnccnanc acaaanaccc nnnnncnacn nnanaaanan aaacncaaan
     8821 aaacacnnca ccaancacnn ccacncncac cacanaancc acnnaaacan ncccaccncc
     8881 aaanncncna cacaanaccn aaaannaann acanaanaca nnacanaacn aaaanaaaan
     8941 acccanaaaa nncncacaca anccnnnann aanacccccn nnaannancc annacacnac
     9001 cnnnncaacn nnnnnaaanc ccncannnac nnaacnccac ncncanncnn aaannanacc
     9061 nccacanccc acncnnnaca canaccacaa cccaccccan ancanncncn annnnncaca
     9121 cncacncnnn ccnncacacc cnccnnancc ccnnccnaca ncncacaaca acnanccaac
     9181 canacaacac aaaanccccc acacaccccn acnnnanccc cnaacncnaa acaacnaacn
     9241 acaccnaccc naaccnancn nancancanc nncnnacnna cnnnacacan caaccnanca
     9301 acncaanncc anccccnccc acacaannac ccccnaanna caannnacac naaannannn
     9361 aancccnnna nccacnancn nncaaanann caaacaacac ncannnccnn nncaanncac
     9421 nnncanaaac canannccac nannnnaana cccanacnna naananacnn nanaaacncn
     9481 ccccnanana acnnacannn ancncccnan ccnccancna cannncaaaa ancanccccc
     9541 naaacancnn ncanncaanc naacnncanc annannccac ncnnaccncc anancacccn
     9601 nnacaanana acccnancan nncnncacna acacccnnan nnanacancn nncnaacccn
     9661 caanancaan ccacncnnca nnnnnncnca cnnnnnccan annaanaacn nnacccncnn
     9721 ancnccnnnn ccnaancaaa cacnaannaa ncnacaacac annncnnnna caccanncnn
     9781 ncncnacccc acaacaccac ncanncacnn aannnacnaa caccccaaaa naccnccccn
     9841 nnacnancnn nacccannna ncnncnaccn nccccccana ccccnaaana cccaaacncn
     9901 ncnanacnna nccccncnca nncnccacca nacccaccaa naccaccaan acnacnannc
     9961 cnnnanaanc caccaannan caancancan naaaccncac nnn
//
genometools-1.5.1/testdata/Random.magicmatch000066400000000000000000000000421211610345200211100ustar00rootroot000000000000005142f1ea8ce4a265f8dc4640e5bb9799	
genometools-1.5.1/testdata/Random159.embl000066400000000000000000000006151211610345200201770ustar00rootroot00000000000000ID   Random140
XX
DE   n140
XX
SQ
     nnacancaaa cncaccaaac caanancnca cncnanaccc anccnnanna ancccnaacn        60
     aacnaaaaan ncnncnanan accnacanaa cannnnncnn caanacnacc nnaaccnaac       120
     ncanccancc naaaacaca                                                    139
//

ID   Random18
XX
DE   n18
XX
SQ
     caaccaannc cnaanccc                                                      18
//
genometools-1.5.1/testdata/Random159.fna000066400000000000000000000002541211610345200200230ustar00rootroot00000000000000>n140
nnacancaaacncaccaaaccaanancncacncnanacccanccnnannaancccnaacnaacnaaaaan
ncnncnananaccnacanaacannnnncnncaanacnaccnnaaccnaacncanccanccnaaaacaca

>n18
caaccaannccnaanccc
genometools-1.5.1/testdata/Random159.gbk000066400000000000000000000005521211610345200200230ustar00rootroot00000000000000LOCUS      Random140
DEFINITION  n140
ORIGIN     
      60 nnacancaaa cncaccaaac caanancnca cncnanaccc anccnnanna ancccnaacn
     120 aacnaaaaan ncnncnanan accnacanaa cannnnncnn caanacnacc nnaaccnaac
     140 ncanccancc naaaacaca                                             
//

LOCUS       Random18
DEFINITION  n18
ORIGIN      
       18 caaccaannc cnaanccc
//
genometools-1.5.1/testdata/Random160.embl000066400000000000000000000006151211610345200201670ustar00rootroot00000000000000ID   Random140
XX
DE   n140
XX
SQ
     nnacancaaa cncaccaaac caanancnca cncnanaccc anccnnanna ancccnaacn        60
     aacnaaaaan ncnncnanan accnacanaa cannnnncnn caanacnacc nnaaccnaac       120
     ncanccancc naaaacacac                                                   140
//

ID   Random18
XX
DE   n18
XX
SQ
     caaccaannc cnaanccc                                                      18
//
genometools-1.5.1/testdata/Random160.fna000066400000000000000000000002551211610345200200140ustar00rootroot00000000000000>n140
nnacancaaacncaccaaaccaanancncacncnanacccanccnnannaancccnaacnaacnaaaaan
ncnncnananaccnacanaacannnnncnncaanacnaccnnaaccnaacncanccanccnaaaacacac

>n18
caaccaannccnaanccc
genometools-1.5.1/testdata/Random160.gbk000066400000000000000000000005531211610345200200140ustar00rootroot00000000000000LOCUS      Random140
DEFINITION  n140
ORIGIN     
      60 nnacancaaa cncaccaaac caanancnca cncnanaccc anccnnanna ancccnaacn
     120 aacnaaaaan ncnncnanan accnacanaa cannnnncnn caanacnacc nnaaccnaac
     140 ncanccancc naaaacacac                                             
//

LOCUS       Random18
DEFINITION  n18
ORIGIN      
       18 caaccaannc cnaanccc
//
genometools-1.5.1/testdata/Random80.fna000066400000000000000000000001351211610345200177320ustar00rootroot00000000000000>n140
nnacancaaacncaccaaaccaanancncacncnanacccanccnnannaancccnaacnaacnaaaaan

>n18 
cnaanccc
genometools-1.5.1/testdata/RandomN.embl000066400000000000000000000323661211610345200200660ustar00rootroot00000000000000ID   RandomN
XX
DE   
XX
SQ
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn        60
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       120
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       180
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       240
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       300
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       360
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       420
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       480
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       540
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       600
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       660
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       720
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       780
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       840
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       900
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn       960
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      1020
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      1080
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      1140
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      1260
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      2040
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      2160
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      3000
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      3120
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      3180
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      3240
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      3660
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      3720
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      3780
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      3840
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      3900
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      4260
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      4380
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      4440
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      4500
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      4560
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      4620
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      4680
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      4800
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9000
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9060
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9120
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9180
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9240
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9300
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9600
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9720
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9780
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     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9900
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn      9960
     nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn                           10000
//
genometools-1.5.1/testdata/RandomN.fna000066400000000000000000000236411211610345200177070ustar00rootroot00000000000000>
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
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genometools-1.5.1/testdata/RandomN.gbk000066400000000000000000000311341211610345200177020ustar00rootroot00000000000000LOCUS       RandomN
DEFINITION  RandomN
ORIGIN      
        1 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
       61 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      121 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      181 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      241 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      301 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      361 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      421 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      481 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      541 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      601 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      661 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      721 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      781 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      841 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      901 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
      961 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1021 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1081 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
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     1321 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1381 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1441 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1501 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1561 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1621 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1681 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
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     1801 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1861 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1921 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     1981 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
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     2221 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     2281 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     2341 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     2401 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     2461 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     2521 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     2581 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     2641 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     2701 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
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     2881 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     2941 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3001 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3061 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3121 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3181 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3241 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3301 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3361 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3421 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3481 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3541 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3601 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3661 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3721 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3781 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3841 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3901 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     3961 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4021 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4081 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4141 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4201 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4261 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4321 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4381 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4441 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4501 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4561 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4621 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4681 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4741 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4801 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4861 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4921 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     4981 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5041 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5101 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5161 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5221 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5281 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5341 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5401 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5461 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5521 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5581 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5641 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5701 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5761 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5821 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5881 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     5941 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6001 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6061 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6121 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6181 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6241 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6301 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6361 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6421 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6481 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6541 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6601 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6661 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6721 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6781 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6841 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6901 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     6961 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7021 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7081 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7141 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7201 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7261 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7321 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7381 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7441 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7501 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7561 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7621 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7681 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7741 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7801 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7861 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7921 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     7981 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8041 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8101 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8161 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8221 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8281 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8341 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8401 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8461 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8521 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8581 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8641 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8701 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8761 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8821 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8881 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     8941 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9001 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9061 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9121 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9181 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9241 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9301 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9361 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9421 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9481 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9541 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9601 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9661 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9721 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9781 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9841 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9901 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn 
     9961 nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
//
genometools-1.5.1/testdata/RandomN.magicmatch000066400000000000000000000000421211610345200212260ustar00rootroot000000000000005259f373a3b672b7d9b631a8d2b3a11e	
genometools-1.5.1/testdata/Reads1.fna000066400000000000000000000134041211610345200174640ustar00rootroot00000000000000>L1_S1
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S2
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S3
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S4
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S5
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S6
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S7
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S8
CCCGTCTCTTCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S9
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S10
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S11
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S12
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S13
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S14
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S15
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S16
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S17
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S18
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S19
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S20
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S21
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S22
ACCGTCTGTCCTTCGATCTGTCCGACTCCTACACTCAGTCACACTGACCC
>L1_S23
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S24
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S25
ACCGTCTGTCCTTCGATCTGTCCGACTCCTACACTCAGTCACACTGACCC
>L1_S26
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S27
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACAGTGACCC
>L1_S28
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S29
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S30
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S31
ACCGTCTGTCCTTCGATCTGTCCGACTCCTACACTCAGTCACACTGACCC
>L1_S32
CCCGTCTCTTCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S33
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S34
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S35
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S36
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S37
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S38
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S39
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S40
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S41
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S42
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S43
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S44
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S45
ACCGTCTGTCCTTCGATCTGTCCGACTCCTACACTCAGTCACACTGACCC
>L1_S46
ACCGTCTGTCCTTCGATCTGTCCGACTCCTACACTCAGTCACACTGACCC
>L1_S47
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S48
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S49
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S50
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACAGTGACCC
>L1_S51
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACAGTGACCC
>L1_S52
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S53
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S54
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S55
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S56
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S57
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S58
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S59
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S60
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S61
ACCGTCTGTCCTTCGATCTGTCCGACTCCTACACTCAGTCACACTGACCC
>L1_S62
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S63
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S64
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S65
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S66
ACCGTCTGTCCTTCGATCTGTCCGACTCCTACACTCAGTCACACTGACCC
>L1_S67
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S68
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S69
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACAGTGACCC
>L1_S70
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S71
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACAGTGACCC
>L1_S72
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S73
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S74
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S75
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S76
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S77
CCCGTCTCTTCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S78
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S79
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S80
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACAGTGACCC
>L1_S81
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S82
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S83
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S84
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S85
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S86
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S87
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACAGTGACCC
>L1_S88
CCCGTCTCTTCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S89
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S90
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S91
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S92
ACCGTCTGTCCTTCGATCTGTCCGACTCCTACACTCAGTCACACTGACCC
>L1_S93
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S94
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S95
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACAGTGACCC
>L1_S96
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S97
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S98
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S99
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
>L1_S100
CCCGTCTGTCCTTCGATCTGTCCGACTCCTACAGTCAGTCACACTGACCC
genometools-1.5.1/testdata/Reads2-spmitv.txt000066400000000000000000000043351211610345200210630ustar00rootroot00000000000000unnecessaryleaves=47 (0.01)
wholeleaf[1]:num=1 (0.25), width=1393 (0.27)
wholeleaf[2]:num=1 (0.07), width=200 (0.04)
wholeleaf[3]:num=1 (0.03), width=200 (0.04)
wholeleaf[4]:num=1 (0.02), width=100 (0.02)
wholeleaf[5]:num=1 (0.02), width=100 (0.02)
wholeleaf[6]:num=1 (0.01), width=100 (0.02)
wholeleaf[7]:num=1 (0.01), width=100 (0.02)
wholeleaf[8]:num=1 (0.01), width=100 (0.02)
wholeleaf[9]:num=1 (0.01), width=100 (0.02)
wholeleaf[10]:num=1 (0.01), width=100 (0.02)
wholeleaf[11]:num=1 (0.01), width=100 (0.02)
wholeleaf[12]:num=1 (0.01), width=100 (0.02)
wholeleaf[13]:num=1 (0.01), width=100 (0.02)
wholeleaf[14]:num=1 (0.01), width=100 (0.02)
wholeleaf[15]:num=1 (0.01), width=100 (0.02)
wholeleaf[16]:num=1 (0.01), width=100 (0.02)
wholeleaf[17]:num=1 (0.01), width=100 (0.02)
wholeleaf[18]:num=1 (0.01), width=100 (0.02)
wholeleaf[19]:num=1 (0.01), width=100 (0.02)
wholeleaf[20]:num=1 (0.01), width=100 (0.02)
wholeleaf[21]:num=1 (0.01), width=100 (0.02)
wholeleaf[22]:num=1 (0.01), width=100 (0.02)
wholeleaf[23]:num=1 (0.01), width=100 (0.02)
wholeleaf[24]:num=1 (0.01), width=100 (0.02)
wholeleaf[25]:num=1 (0.01), width=100 (0.02)
wholeleaf[26]:num=2 (0.02), width=100 (0.02)
wholeleaf[27]:num=2 (0.02), width=100 (0.02)
wholeleaf[28]:num=3 (0.03), width=100 (0.02)
wholeleaf[29]:num=4 (0.04), width=100 (0.02)
wholeleaf[30]:num=4 (0.04), width=100 (0.02)
wholeleaf[31]:num=4 (0.04), width=100 (0.02)
wholeleaf[32]:num=4 (0.04), width=100 (0.02)
wholeleaf[33]:num=4 (0.05), width=100 (0.02)
wholeleaf[34]:num=4 (0.05), width=100 (0.02)
wholeleaf[35]:num=5 (0.06), width=100 (0.02)
wholeleaf[36]:num=5 (0.07), width=100 (0.02)
wholeleaf[37]:num=5 (0.07), width=100 (0.02)
wholeleaf[38]:num=5 (0.08), width=100 (0.02)
wholeleaf[39]:num=5 (0.08), width=100 (0.02)
wholeleaf[40]:num=5 (0.09), width=100 (0.02)
wholeleaf[41]:num=5 (0.10), width=100 (0.02)
wholeleaf[42]:num=5 (0.11), width=100 (0.02)
wholeleaf[43]:num=5 (0.12), width=100 (0.02)
wholeleaf[44]:num=5 (0.14), width=100 (0.02)
wholeleaf[45]:num=5 (0.17), width=100 (0.02)
wholeleaf[46]:num=5 (0.20), width=100 (0.02)
wholeleaf[47]:num=5 (0.25), width=100 (0.02)
wholeleaf[48]:num=5 (0.33), width=100 (0.02)
wholeleaf[49]:num=5 (0.50), width=100 (0.02)
wholeleaf[50]:num=5 (1.00), width=99 (0.02)
genometools-1.5.1/testdata/Reads2.fna000066400000000000000000000134041211610345200174650ustar00rootroot00000000000000>L6_S1
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S2
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S3
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S4
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S5
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S6
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S7
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S8
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S9
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S10
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S11
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S12
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S13
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S14
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S15
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S16
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S17
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCACGCTCTATCGCCTGC
>L6_S18
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S19
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S20
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S21
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S22
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S23
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S24
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S25
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S26
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S27
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S28
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S29
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S30
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S31
TTCTAGACGGCCTCAGTTCGCTAGTCGTGCCACCTCGCTCTATCGCCTGC
>L6_S32
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S33
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S34
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S35
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S36
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S37
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCACGCTCTATCGCCTGC
>L6_S38
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S39
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGA
>L6_S40
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S41
TTCTAGACGGCCTCAGTTCGCTAGTGGCCCCACCTCGCTCTATCGCCTGC
>L6_S42
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S43
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCACGCTCTATCGCCTGC
>L6_S44
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S45
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S46
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S47
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S48
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S49
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S50
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S51
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S52
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S53
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCACGCTCTATCGCCTGC
>L6_S54
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S55
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S56
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S57
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S58
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S59
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S60
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S61
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S62
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S63
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S64
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S65
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCACGCTCTATCGCCTGC
>L6_S66
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S67
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S68
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S69
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S70
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S71
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S72
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S73
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S74
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S75
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S76
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S77
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S78
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S79
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S80
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S81
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S82
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S83
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S84
TTCTAGACGGCCTCAGTTCGCTAGTGGCCCCACCTCGCTCTATCGCCTGC
>L6_S85
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S86
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S87
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S88
TTCTAGACGGCCTCAGTTCGCTAGTCGTGCCACCTCGCTCTATCGCCTGC
>L6_S89
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S90
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S91
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S92
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S93
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S94
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S95
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S96
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S97
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S98
TTCTAGACGGCCTCAGTTCGCTAGTGGTCCCACCTCGCTCTATCGCCTGC
>L6_S99
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
>L6_S100
TTCTAGACGGCCTCAGTTCGCTAGTCGTCCCACCTCGCTCTATCGCCTGC
genometools-1.5.1/testdata/Reads3.fna000066400000000000000000000134041211610345200174660ustar00rootroot00000000000000>L3_S1
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S2
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S3
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S4
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S5
TCCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S6
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S7
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S8
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S9
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S10
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S11
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTTGCCACCTGGGCGCCGG
>L3_S12
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S13
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S14
TGCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S15
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S16
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S17
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S18
TCCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S19
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S20
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S21
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S22
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S23
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S24
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S25
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S26
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S27
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S28
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S29
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S30
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S31
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S32
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S33
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S34
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S35
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S36
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S37
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S38
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S39
TGCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S40
TGCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S41
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S42
TCCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S43
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S44
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S45
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S46
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S47
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S48
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S49
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S50
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S51
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S52
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S53
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S54
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S55
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S56
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S57
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S58
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S59
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S60
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S61
TCCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S62
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S63
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S64
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S65
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S66
TCCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S67
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S68
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S69
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S70
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S71
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S72
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S73
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S74
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S75
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S76
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S77
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S78
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S79
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S80
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S81
TCCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S82
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S83
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S84
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S85
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S86
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S87
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S88
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S89
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S90
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S91
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S92
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S93
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S94
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S95
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S96
TCCTCGGAGGGATCGGCTTGGTTCTATCTCCGTAGCCACCTGAGCGCCGG
>L3_S97
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S98
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S99
TGCTCGGAGGGATCGGCTAGGTTCTATCTCCGTAGCCACCTGGGCGCCGG
>L3_S100
TGCTCGGAGGGATCGGCTTGGTGCTATCTCCGTAGCCACCTGAGCGCCGG
genometools-1.5.1/testdata/Reference1000066400000000000000000000000261211610345200175550ustar00rootroot00000000000000>
CCNCTCNCCTTTTTCCTCT
genometools-1.5.1/testdata/Reference2000066400000000000000000000000151211610345200175540ustar00rootroot00000000000000>
acaaacatat
genometools-1.5.1/testdata/Repfind-example.fna000066400000000000000000000001461211610345200213640ustar00rootroot00000000000000>sample sequence for repfind
gagctcgagcgctgct
>another sample sequence for repfind
cttaaggaattccccggc
genometools-1.5.1/testdata/SKsplintoptions000066400000000000000000000013701211610345200207640ustar00rootroot00000000000000-checks
+enumindex
-onlyunqglobaltrans
-looploopbreak
-readonlytrans
-retalias
-infloopsuncon
-declundef
-redecl
-namechecks
-exportheader
-exportlocal
+charint
-warnposix
-mustfreefresh
-boolops
-usereleased
-mustfreeonly
-compmempass
-compdef
-kepttrans
-predboolint
-unrecog
-usedef
-compdestroy
-statictrans
-branchstate
-temptrans
-globstate
-dependenttrans
-noeffect
-nullstate
-realcompare
-initallelements
-aliasunique
-nullassign
-nullpass
-unqualifiedtrans
-maintype
-observertrans
-immediatetrans
-castfcnptr
-onlytrans
-bufferoverflowhigh
-uniondef
-sefuncon
-nullret
-sysunrecog
-shiftnegative
-shiftimplementation
+posixlib
-duplicatequals
-exitarg
# added to inhibit system errors on Ubuntu lucid, 20100618
-incondefs
-fixedformalarray
-mustmod
genometools-1.5.1/testdata/Small.embl000066400000000000000000000012621211610345200175670ustar00rootroot00000000000000ID   sequence0
XX
DE   
XX
SQ
     naatatcgac atan                                                          14
//

ID   sequence1
XX
DE   
XX
SQ
     agatctatcc agagcatact acnnnnnnna tatcgtnnnn nnn                          43
//

ID   sequence2
XX
DE   
XX
SQ
     nnnagtacta gcatactcag gactcatcac gac                                     33
//

ID   sequence3
XX
DE   
XX
SQ
     nnnnnnnnnn nnnnnnnnnn nnnn                                               24
//

ID   sequence4
XX
DE   
XX
SQ
     ntatacgacc atactacgac nnnn                                               24
//

ID   sequence5
XX
DE   
XX
SQ
     aagactca                                                                  8
//

genometools-1.5.1/testdata/Small.fna000066400000000000000000000002441211610345200174130ustar00rootroot00000000000000>
naatatcgacatan
>
agatctatccagagcatactacnnnnnnnatatcgtnnnnnnn
>
nnnagtactagcatactcaggactcatcacgac
>
nnnnnnnnnnnnnnnnnnnnnnnn
>
ntatacgaccatactacgacnnnn
>
aagactca
genometools-1.5.1/testdata/Small.gbk000066400000000000000000000010221211610345200174050ustar00rootroot00000000000000LOCUS       sequence0
DEFINITION  
ORIGIN      
        1 naatatcgac atan
//
LOCUS       sequence1
DEFINITION  
ORIGIN      
        1 agatctatcc agagcatact acnnnnnnna tatcgtnnnn nnn
//
LOCUS       sequence2
DEFINITION  
ORIGIN      
        1 nnnagtacta gcatactcag gactcatcac gac
//
LOCUS       sequence3
DEFINITION  
ORIGIN      
        1 nnnnnnnnnn nnnnnnnnnn nnnn
//
LOCUS       sequence4
DEFINITION  
ORIGIN      
        1 ntatacgacc atactacgac nnnn
//
LOCUS       sequence5
DEFINITION  
ORIGIN      
        1 aagactca
//
genometools-1.5.1/testdata/Smalldup.fna000066400000000000000000000000411211610345200201170ustar00rootroot00000000000000>
acctcgaatctac
>
acctcgaatctacg
genometools-1.5.1/testdata/Splintoptions000066400000000000000000000013731211610345200204710ustar00rootroot00000000000000-aliasunique
+boolint
-boolops
-branchstate
-bufferoverflowhigh
-castfcnptr
+charint
-checks
-compdef
-compdestroy
-compmempass
-declundef
-dependenttrans
+enumindex
-evalorder
-exitarg
-exportheader
-exportlocal
-fcnuse
-globstate
-immediatetrans
-incompletetype
-infloops
-infloopsuncon
-kepttrans
-looploopbreak
-maintype
+matchanyintegral
-mayaliasunique
-mustfreefresh
-mustmod
-mustfreeonly
-namechecks
-noeffect
-nullassign
-nullpass
-nullret
-nullstate
-observertrans
-onlytrans
-onlyunqglobaltrans
-predboolint
-predboolothers
-predboolptr
-readonlytrans
-realcompare
-redecl
-redef
-retalias
-sefuncon
-shiftimplementation
-shiftnegative
-statictrans
-temptrans
-type
-unqualifiedtrans
-unrecog
-usedef
-usereleased
+voidabstract
-warnposix
-whileempty
genometools-1.5.1/testdata/TTT-small.embl000066400000000000000000000001621211610345200202760ustar00rootroot00000000000000ID   TTT-small
XX
DE   
XX
SQ
     NTTTTNC                                                                   7
//
genometools-1.5.1/testdata/TTT-small.fna000066400000000000000000000000121211610345200201150ustar00rootroot00000000000000>
NTTTTNC
genometools-1.5.1/testdata/TTT-small.gbk000066400000000000000000000001161211610345200201210ustar00rootroot00000000000000LOCUS       TTT-small
DEFINITION  TTT-small
ORIGIN      
        7 NTTTTNC
//
genometools-1.5.1/testdata/TTTN.fna000066400000000000000000000000161211610345200171310ustar00rootroot00000000000000>
TTT
>
NTTTN
genometools-1.5.1/testdata/U89959_cds.fas000066400000000000000000000237141211610345200200440ustar00rootroot00000000000000>CDS_1 (joined) (translated)
DTGLRDLGQLEQDLVFGDAGAKDVINFLRTNQDTNPENKLRLLMIYATVYPEKFEGDKGVKLMQLARLSPVDMKVISNMQLIAGSPENKAKSGSFSLKFD
>CDS_2 (joined) (translated)
AKGLSCHQDIAGDGCFSLGMIARFEPALREKGSWMYPRLFWETGVVGQVLYLEAHAMGISATGIGCYFDDPVHEVLGINDSSFQSLYHFTVGGPVVDKRIMTLPAYPGPTTTVA*
>CDS_3 (joined) (translated)
IAVELFPKSQREITGNFGYPLTGPSISEPSRYKDPLVSGFEMSNPRQRKGEAMMNPTISWRFASSTSLLSIPRTPKSAFIFAMTFSSSSSSSSSSSSVENPNKDDSSSSLELVLKYHNQTKHSLNGYARGPRGLDWANQPNPFRRYLSAPLLPLQHPNHDIDDDSDSPLYSTLFDSLPPPKPISLPTISHLFYHSL
>CDS_4 (joined) (translated)
AKSPLLCCVTFLLQLISHILHHIQYRVAAHVPVIHQRPSAALQLLFLQLQFCLQTVQNRRSSWMNSPEHVIELHRLIASLSHQLLAELFYVLLYLLREVSSKLEVYAFLSQPPLDHVLCPRQELLNRIVQLHERSFTLSRVSSDDHSS
>CDS_5 (joined) (translated)
AVLVFHDMLSRGLKPNAVTYNTLIKGLSEAHRYDEIKDILIGGNDAFTTFAPDACTFNILIKAHCDAGHLDAAMKVFQEMLNMKLHPDSASYSVLIRTLCMRNEFDRAETLFNELFEKEVLLGKDECKPLAAAYNPMFEYLCANGKTKQAEKVFRQLMKRGVQDPPSYKTLI
>CDS_6 (joined) (translated)
HISRQLSSAMVSSVPKLHALFVSKSQPVLRAAKVTNEERSTKSKLARSLARAVNSNPWSDELESSLSSLHPSQTISRTTVLQTLRLIKVPADGLRFFDWVSNKGFSHKEQSFFLMLEFLGRARNLNVARNFLFSIERRSNGCVKLQDRYF
>CDS_7 (joined) (translated)
FYKQKKERERDLPRDCNMLDYEWDNPSSIVLSGDERNPDSDPTRSSFSFFDPISHYNNDHRHITISPPLLSSFSNQQQQHHLTLYGQTNSNNQFLHHHHHHHSLYGSTTTTTPYGASDPIYHPHSSAPPASLFSYDQTGPGSGSGSSYNFLIPKTEVDFTSNRIGLNLGGRTYFSAADDDFVSRLYRRSRPGESGMANSLSTPRCQAEGCNADL
>CDS_8 (joined) (translated)
LTITAAAVNVTNQPPPPKTPAPARLLQSHRTIRVLKRHRHRRPTRRLRYHWSASGKGSSKRQRLHPRQRLRLQIQCFSPADSYKLYSYDILCLK*
>CDS_9 (joined) (translated)
TVALGSCIPTELPTPRSWNVDILVDTIKQLQAPGISWRKVIENLDHDGFDIPNMESFSFFMRIYKAACKEPFPLDAVCGSVWKNMDGQLSFLKHAISAPPEVFTFMHSPRKLVYIDNMHSQEQQLGLSNHAWLSLDLLDVLCQLAERGHAVLVSSLLQYPLTQCPRTLLLGMT
>CDS_10 (joined) (translated)
VIEQALSRISSGNLESDASVSHPGPSQSFPGNGELSGSGIGQPALQLSSPLQLQQKNEVPSVPSNEAKPLLPSLSTTSVDVSVNPKNPGIPTSSSTSTGFVRPARATTSTRFGSALNIETLVAAAERRENAIEAPPSDVQDKVSFIINNISTTNIESKGKEFAEI
>CDS_11 (joined) (translated)
PQQYYPWFAQYMVMKRASIEPNFHDLYLKFLDKVDSKLLFKEILQNTYENCKVLLGSELIKSSSEERSLLKNLGSWLGRLTIGRNYVLRAREIDPKSLIVEAYEKGLMIAVIPFTSKVLEPCQNSIAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFD
>CDS_12 (joined) (translated)
TNTLMDEEKVATLGLPEQLPSPQGLFQSTPSPLFSISQLSAALPNIGNHVVINQKLSAFGMHFPFQRVVPLAMDRAIKEIVSGIVQRSVCIACQTTKELVLKDYALEPDESRIYNAAHLMVASLAGSLAHVTCKEPLRTSISGHLRNSLQGLNISNDALEQIVQLVTNDNLDLGCAAIEQAATEKAIQTIDADIAQQLLLRRKHRDGAGSSFFDPNILSQNSVSFIPESLRPKPGHLSLSQQRVYEDFVQHPWQK
>CDS_13 (joined) (translated)
SSSSGDVALGSGYGPVSGKVASEFLSNAGNARMDMVSRPSDISVDGFESSPVSLLSSQVDPAGDSSSLQFTKSLPTSELNLAESSDAATKETGTSLQTLTSAATMERLGAS
>CDS_14 (joined) (translated)
RVVKELTSWVIYSEEDRKLNKDITIGLIQRELLSLAEYNVHMAKHLDGGRNKTATDFAISLLQSLVTEESSVISELHSLVDALAKLASKSGSSESLQQLIDIIRNPVTNTAGLSDSSTGNDNNDRQKDEKVACNTTNTEESTSLDYVESDPAGFQNRVSTLFKNWYQICELPGANETACSQYVLHL
>CDS_15 (joined) (translated)
GWPYVQRLLVDLLQFLEPFLRNAELGGPVHFLYKGTLRVLLVLLHDFPEFLCDYHFTFCDVIPSSCIQMRNIILSSFPRNMRLPDPSTPNLKIDLLPEIVEAPCILSEVDAALKAKQMKNDVDEYLTSRQQNSTFLSELKTKLLLSSSEASSAGTRYSVPLINSLVLYTGMQAIQQLQAGETQAQNVVALQMFKYLSMELDTEGRYLFLNAIANQLRYPNNHTHYFSFIMLYLFFESDQEIIQEQITRVLLERLIVNRPHPWGLLITFIELIKNPRYSFWKQAFIRCAPEIEKLFESVARSCGGLKPVDEGMVSGGWVSDNSH*
>CDS_16 (joined) (translated)
ELSETQPPETIPSSTGFRPPQDLATDSNSFSISGAHLMKACFQKLYLGFFISSMNVIRSPHGCGLFTISRSNSTLVICSCMISC
>CDS_17 (joined) (translated)
TTGNRFVWKMDIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDSVYLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELDVSNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGNMLHTLSNWLNTSENLLISIQDKIKWADNMSEMDKKHRKEAEEGVEEVKKSLSMKGDVDIRGNKEMFGEPSGVMDYEEDGIRPKRRRHPVTR*
>CDS_18 (joined) (translated)
EEPVKQPHQDPNGKEHSDHVTTSSDCYKTKLVVRHKNLKEILDAVQDYFDKAASAGDQVSAMLEIGRAELDRSFSKLRKTVYHSSSVFSNLSASWTSKPPLAVKYKLDASTLNDEQGGLKSLCSTLDRLLAWEKKLYEDV
>CDS_19 (joined) (translated)
QQLCKVTSDNTLHTYMHISIRILHKQRVGCSKFTVCCGGGGVPNGGTEPSRRHGLVASSANDPQPSSSLPSGNAFSSLTTPKSPRLHCTRRTSHDTPLAPLLLFSVAPLS
>CDS_20 (joined) (translated)
EKRERDLWLCIARCSSSHRSKTMNPEYDYLFKLLLIGDSGVGKSCLLLRFSDDSYVESYISTIGVDFKIRTVEQDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDEESFNNVKQWLSEIDRYASDNVNKLLVGNKSDLTENRAIPYETAKAFADEIGIPFMETSAKDATNVEQAFMAMSASIKERMASQPAGNNARPPTVQIRGQPVAQKNGCCST*
>CDS_21 (joined) (translated)
SRSRERKKKREGMAAEEATEFYLRYYVGHKGKFGHEFLEFEFREDGKLRYANNSNYKNDTIIRKEVFLTPAVLKECKRIVSESEILKEDDNNWPEPDRVGKQELEIVLGNEHISFATSKIGSLVDCQSSNDPEGLRIFYYLVQDLKCLVFSLISLHFKIKPI*
>CDS_22 (joined) (translated)
FRFPDTETMPTDSKMAKFLQSYGYDLILGSVAAIYVVMAPYTKVEESFNVQSMHDILYHRHHLDSYDHLEFPGVVPRTFIGAFIVSVFASPVVSIISCLGFPKVYSLVAARLVLGCIILSTLRFFRIQIKKKFGNQVETFFVLFTSLQFHFLFYCTRPLPNILALGLVNLAYGNWLKGNFYPALSFLIFATVIFRCDTMLLLGPIGLELLLTKSISF
>CDS_23 (joined) (translated)
PANVAGEEWVHIDTFGAMNGISRFCEDDFPWRYSKEEEIVVEELRNRNFTYLVNEHSSVDGYKCLFYEEGFERLELRRGFPPIVLVKKAKVYLHREMKKEDPFHKKWPGC*
>CDS_24 (joined) (translated)
RREMLLQAAVQNRNVPLASSASYSRLLRCRSPVVSVAALSKKTAAIVCSISQVYGYGTVDYERRPIVQWNAIYKKISLMEKPELGAASVLNQWEKAGRKLTKWELCRVVKELRKYKRANQALEVYDWMNNRGERFRLSASDAAIQLDLIGKVRGIPDAEEFFLQLPENFKDRRVYGSLLNAYVRAKSREKAEALLNTMRDKGYALHPLPFNVMMTLYMNLREYDKVDAMVFEMKQKDIRLDIYSYN
>CDS_25 (joined) (translated)
LLSLYGSLGNKKELYRVWHVYKSVVPSIPNLGYHALVSSLVRMGDIEGAEKVYEEWLPVKSSYDPRIPNLLMNAYVKNDQLETAEGLFDHMVEMGGKP
>CDS_26 (joined) (translated)
GKCRRKARRRRTLARLGYLILHVIFSTLLLSNVLKNLDQTRVNARIILMCTRNARRKRGKLDWNAIRHGRCSRECRSSNTNDVSEHHLASSILLFHLQWLCLYDLSK*
>CDS_27 (joined) (translated)
CIVVFLTRFGNPIRLHLIPSLPRIIMYPPPPSSIYAPPMLVNCSGCRTPLQLPSGARSIRCALCQAVTHIADPRTAPPPQPSSAPSPPPQIHAPPGQLPHPHGRKRAVICGISYRFSRHELKGCINDAKCMRHLLINKFKFSPDSILMLT
>CDS_28 (joined) (translated)
DLSSRSPDCLNNSKTASLLVTSDSSSQSLKKPDSINTLGLQLLDPSAEKAFLRQVKASEIHLFLV*
>CDS_29 (joined) (translated)
LHSIIDACHSGTVLDLPFLCRMNRAGQYVWEDHRPRSGLWKGTAGGEAISISGCDDDQTSADTSALSKITSTGAMTFCFIQAIERSAQGTTYGSLLNSMRTTIRNTGNDGGGSGGVVTTVLSMLLTGGSAIGGLRQEPQLTACQTFDVYAKPFTL*
>CDS_30 (joined) (translated)
SGTSQHLHQAHLLSKTFSFSVFCFSRFFENPPARAITLGIQRIKHDMKNEISILELILLFLSLSSVLASSKLHGNSAHEMVSILNQNRTARKLGKLNESPGLGCMALQYVELCEGNCNVNNTLSCEHPEDDFTQVFAPNCGVELPTFGTITGHILGCSSKYAAPEVAFSDILFRDSSALSVLRNRSHTEVGVGMARLHKGTFFWCLLFSD
>CDS_31 (joined) (translated)
LKYLWMASRPGALTEWPWSPLGSFKYLLVAPLVMASMHSYVTAVDEEKDLSRLMIVVLMLWRIVHSQIWISVSRQRTAKGTNKIVDKPIEFEQVDRERTWDDQVIFNTLLMYLANIKLPGASHLPPWRLDGAILMALLHAGPVEFLYYWFHRALHHHFLYSRYHSHHHSSIVTEPITSVVHPFAEH
>CDS_32 (joined) (translated)
LNGSGEMYVQKYPKLKIRLVDGSSMAATVVINNIPKEATEIVFRGNLTKVASAVVFALCQKGVKVVVLREEEHSKLIKSGVDKNLVLSTSNSYYSPKVWLVGDGIENEEQMKAKEGTLFVPFSHFPPNKLRKDCFYQSTPAMRVPKSAQNIDSCENWLGRRVMSAWKIGGIVHALEGWEEHDCGNTCNVLRLHAIWEAALRHDFQPLPPSPL*
>CDS_33 (joined) (translated)
RHKHITFDGIMATKPGVLTDWPWTPLGSFKYIVIAPWAVHSTYRFVTDDPEKRDLGYFLVFPFLLFRILHNQVWISLSRYYTSSGKRRIVDKGIDFNQVDRETNWDDQILFNGVLFYIGINLLPEAKQLPWWRTDGVLMAALIHTGPVEFLYYWLHKALHHHFLYSRYHSHHHSSIVTEPITCNYCFLP*
>CDS_34 (joined) (translated)
DGIMATKPGVLTDWPWTPLGSFKYIVIAPWAVHSTYRFVTDDPEKRDLGYFLVFPFLLFRILHNQVWISLSRYYTSSGKRRIVDKGIDFNQVDRETNWDDQILFNGVLFYIGINLLPEAKQLPWWRTDGVLMAALIHTGPVEFLYYCGDT
>CDS_35 (joined) (translated)
EKAILEADKKGVKVLSLGLMNQGEELNRNGEVYIHNHPDMKVRLVDGSRLAAAVVINSVPKATTSVVMTGNLTKVAYTIASALCQRGVQVSTLRLDEYEKIRSCVPQECRDHLVYLTSEAL
>CDS_36 (joined) (translated)
KDGKCMSVAHPFFSRIWTKYGKPVSATASSLSSFHIIKTPTLEDFRRMRATRSVLLFLMIQLFHAQMNYETYIKRTHIFMHIKLLVIMVLIESN*
>CDS_37 (joined) (translated)
EGTTREEQEKATKGTLFIPFSQFPLKQLRRDCIYHTTPALIVPKSLVNVHSCENWLPRKAMSATRVAGILHALEGWEMHECGTSLLLSDLDQVWEACLSHGFQPLLLPHH*
>CDS_38 (joined) (translated)
FICAWKSWIIRKRSTERVALILLKSSKVGVLMMWKEERLEAVAETGFPYLVQIREKKGCATLMHFPSF*
>CDS_39 (joined) (translated)
FICAWKSWIIRKRSTERVALILLKSSKVGVLMMWKEERLEAVAETGFPYLVQIREKKGCATLMHFPSF*
>CDS_40 (joined) (translated)
FICAWKSWIIRKRSTERVALILLKSSKVGVLMMWKEERLEAVAETGFPYLVQIREKKGCATLMHFPSF*
>CDS_41 (joined) (translated)
INLVSLTQEVSQALITSIDTAEKKKNPYDDAQGTEIGEHKLGQETIKKKRAGFFHRMIQKFVKKIHLCSSISRT*
>CDS_42 (joined) (translated)
KMANPVGFRFRPTDGEIVDIYLRPKNLESNTSHVDEVISTVDICSFDPWDLPSHSRMKTRDQVWYFFGRKENKYGKGDRQIRKTKSGFWKKTGVTMDIMRKTGDREKIGEKRVLVFKNHGGSKSDWAMHEYHATFSSPNQMMTYTVCKVEFKGEETEISSSSTG
>CDS_43 (joined) (translated)
VSYSLLIFFCGMFITVDGFNKTGIPTALWDLMEPYAKIDQAKGIAVLAVVILVLSNVASNVPTVLLLGARVAASAMGREEEKKAWLLLAWVSTVAGNLTLLGSAANLIVCEQARRAVSHGYTLTFTKHFKFGLPSTLIVTAIGLFLIK*
>CDS_44 (joined) (translated)
CLALQKVNLTGIPHGLSFEETKELWVRADLDGNGVFDYEELKKIWNMTMVNQPGNCKESVMESKKEEGEDEAIGLKVNKAILFPQEAEKGLWPENYNISDHACLTVQFSPVKMLCS*
>CDS_45 (joined) (translated)
LREFERKTQMQSHQNRSRLSLILRSRFIPSFSSPLSLFVVLAAVPLPIYFSGLLSGRNNKPLSVMRLNSNLASSMVESNISCTTFNILAPIYKRVDQKNHSTRESDFRTLWLARNQRILDLLLHQRSSVICLQEVWVGNEELVNMYHHQLSSSGYTIYQLARTNSRGDGLLTAIHKDHFKVVNYRELLFNDFGDRVAQLLHVKTVIPFPLNGKQDVQQEVIIVNTHLLFPHDSSLSIVRLHQVYKILEYLEAYQKENKLNHMPIILCGDWNGSKRGHVYKFLRSQGFISSYDDAHQYTDSDAHRWVSHRNHRGNICGVDFIWLCNP
>CDS_46 (joined) (translated)
RNTSRELLPKTSNAPHTTGLGVMGSLVREWVGFQQFPAATQEKLIEFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIGEQVVRVSPFQAEGLRPVMVSRTMGGFTINIIDTPGLVEAGYVNHQALELIKGFLVNRTIDVLLYVDRLDVYRVDELDKQVVIAITQTFGKEIWCKTLLVLTHAQFSPPDELSYETFSSKRSDSLLKTIRAGSKMRKQEFEDSAIAVVYAENSGRCSKNDKDEKALPNGEAWIPNLVKAITDVATNQRKAIHVDKKMVDGSYSDDKGKKLIPLIIGAQYLIVKMIQGAIRNDIKTSGKPL*
>CDS_47 (joined) (translated)
HCVDSGILCGNEKFVQGRFIMADSCCIRLHLLASVFLLLFSSFNLQGIAAENLSKQKLTSLILQNEIVKEVNENPNAGWKAAFNDRFANATVAEFKRLLGVIQTPKTAYLGVPIVRHDLSLKLPKEFDARTAWSHCTSIRRILGRGHCGSCWAFGAVESLSDRFCIKYNLNVSLSANDVIACCGLLCGFGCNGGFPMGAWLYFKYHGVVTQECDPYFDNTGCSHPGCEPTYPTPKCERKCVSRNQLWGESKHYGVGAYRINPDPQDIMAEVYKNGPVEVAFTVYEDFAHYKSGVYKYITGTKIGGHAVKLIGWGTSDDGEDYWLLANQWNRSWGDDGYFKIRRGTNECGIEQSVVAGLPSEKNVFKGITTSDDLLVSSV*
>CDS_48 (joined) (translated)
VGYILNNVLLWSTITLWFWFLLGHCGSCWAFGAVESLSDRFCIKYNLNVSLSANDVIACCGLLCGFGCNGGFPMGAWLYFKYHGVVTQECDPYFDNTGCSHPGCEPTYPTPKCERKCVSRNQLWGESKHYGVGAYRINPDPQDIMAEVYKNGPVEVAFTVYEDFAHYKSGVYKYITGTKIGGHAVKLIGWGTSDDGEDYWLLANQWNRSWGDDGYFKIRRGTNECGIEQSVVAGLPSEKNVFKGITTSDDLLVSSV*
>CDS_49 (joined) (translated)
LLASVFLLLSICWTLELQGIAAENLSKQKLTSLILQNEIVKEVNENPNAGWKAAFNDRFANATVAEFKRLLGVIQTPKTAYLGVPIVRHDLSLKLPKEFDARTAWSHCTSIRRILGRGHCGSCWAFGAVESLSDRFCIKYNLNVSLSANDVIACCGLLCGFGCNGGFPMGAWLYFKYHGVVTQECDPYFDNTGCSHPGCEPTYPTPKCERKCVSRNQLWGESKHYGVGAYRINPDPQDIMAEVYKNGPVEVAFTVYEDFAHYKSGVYKYITGTKIGGHAVKLIGWGTSDDGEDYWLLANQWNRSWGDDGYFKIRRGTNECGIEQSVVAGLPSEKNVFKGITTSDDLLVSSV*
>CDS_50 (joined) (translated)
CDPYFDNTGCSHPGCEPTYPTPKCERKCVSRNQLWGESKHYGVGAYRINPDPQDIMAEVYKNGPVEVAFTVYEDFAHYKSGVYKYITGTKIGGHAVKLIGWGTSDDGEDYWLLANQWNRSWGDDGYFKIRRGTNECGIEQSVVAGLPSEKNVFKGITTSDDLLVSSV*
>CDS_51 (joined) (translated)
GIEKKIIRRERSMADNCIRLLHSASVFFCLGLLISSFNLLQGIAAENLSKQKLTSWILQNEIVKEVNENPNAGWKASFNDRFANATVAEFKRLLGVKPTPKTEFLGVPIVSHDISLKL
genometools-1.5.1/testdata/U89959_cds.gff3000066400000000000000000000773671211610345200201350ustar00rootroot00000000000000##gff-version   3
##sequence-region   1877523 1 106973
1877523	gt csa	gene	1074	1540	.	+	.	ID=gene1
1877523	gt csa	mRNA	1074	1540	.	+	.	ID=mRNA1;Parent=gene1;Target=8721428 1 303 +
1877523	gt csa	exon	1074	1171	1	+	.	Parent=mRNA1
1877523	gt cds	CDS	1076	1171	.	+	0	ID=CDS1;Parent=mRNA1
1877523	gt csa	exon	1259	1354	1	+	.	Parent=mRNA1
1877523	gt cds	CDS	1259	1354	.	+	0	ID=CDS1;Parent=mRNA1
1877523	gt cds	CDS	1432	1539	.	+	0	ID=CDS1;Parent=mRNA1
1877523	gt csa	exon	1432	1540	1	+	.	Parent=mRNA1
###
1877523	gt csa	gene	2779	3506	.	+	.	ID=gene2
1877523	gt csa	mRNA	2779	3506	.	+	.	ID=mRNA2;Parent=gene2;Target=8732738 1 337 +,19843099 1 426 +
1877523	gt csa	exon	2779	2801	0.696	+	.	Parent=mRNA2
1877523	gt csa	exon	3043	3506	0.974	+	.	Parent=mRNA2
1877523	gt csa	mRNA	3025	3506	.	+	.	ID=mRNA3;Parent=gene2;Target=19837778 1 327 +,19843099 1 426 +
1877523	gt csa	exon	3025	3506	0.974	+	.	Parent=mRNA3
###
1877523	gt csa	gene	3041	3651	.	-	.	ID=gene3
1877523	gt csa	mRNA	3041	3651	.	-	.	ID=mRNA4;Parent=gene3;Target=8732878 1 536 -
1877523	gt csa	exon	3041	3550	0.996	-	.	Parent=mRNA4
1877523	gt cds	CDS	3230	3550	.	-	0	ID=CDS2;Parent=mRNA4
1877523	gt cds	CDS	3626	3649	.	-	0	ID=CDS2;Parent=mRNA4
1877523	gt csa	exon	3626	3651	1	-	.	Parent=mRNA4
###
1877523	gt csa	gene	4768	5357	.	-	.	ID=gene4
1877523	gt csa	mRNA	4768	5357	.	-	.	ID=mRNA5;Parent=gene4;Target=19871046 1 591 +
1877523	gt csa	exon	4768	5357	0.987	-	.	Parent=mRNA5
1877523	gt cds	CDS	4769	5356	.	-	0	ID=CDS3;Parent=mRNA5
###
1877523	gt csa	gene	9505	10058	.	+	.	ID=gene5
1877523	gt csa	mRNA	9505	10058	.	+	.	ID=mRNA6;Parent=gene5;Target=8682455 1 554 +
1877523	gt csa	exon	9505	10058	1	+	.	Parent=mRNA6
1877523	gt cds	CDS	9615	10058	.	+	0	ID=CDS4;Parent=mRNA6
###
1877523	gt csa	gene	12024	12542	.	-	.	ID=gene6
1877523	gt csa	mRNA	12024	12542	.	-	.	ID=mRNA7;Parent=gene6;Target=8688760 1 519 +
1877523	gt csa	exon	12024	12542	1	-	.	Parent=mRNA7
1877523	gt cds	CDS	12026	12541	.	-	0	ID=CDS5;Parent=mRNA7
###
1877523	gt csa	gene	13014	13465	.	-	.	ID=gene7
1877523	gt csa	mRNA	13014	13465	.	-	.	ID=mRNA8;Parent=gene7;Target=2748705 1 459 +
1877523	gt csa	exon	13014	13465	0.881	-	.	Parent=mRNA8
1877523	gt cds	CDS	13016	13465	.	-	0	ID=CDS6;Parent=mRNA8
###
1877523	gt csa	gene	15955	16603	.	+	.	ID=gene8
1877523	gt csa	mRNA	15955	16603	.	+	.	ID=mRNA9;Parent=gene8;Target=19878194 1 649 +
1877523	gt csa	exon	15955	16603	0.997	+	.	Parent=mRNA9
1877523	gt cds	CDS	15962	16603	.	+	0	ID=CDS7;Parent=mRNA9
###
1877523	gt csa	gene	17165	17684	.	+	.	ID=gene9
1877523	gt csa	mRNA	17165	17684	.	+	.	ID=mRNA10;Parent=gene9;Target=19798999 1 396 -
1877523	gt csa	exon	17165	17247	0.97	+	.	Parent=mRNA10
1877523	gt cds	CDS	17167	17247	.	+	0	ID=CDS8;Parent=mRNA10
1877523	gt cds	CDS	17374	17577	.	+	0	ID=CDS8;Parent=mRNA10
1877523	gt csa	exon	17374	17684	0.989	+	.	Parent=mRNA10
###
1877523	gt csa	gene	25221	26100	.	+	.	ID=gene10
1877523	gt csa	mRNA	25221	26100	.	+	.	ID=mRNA11;Parent=gene10;Target=8690053 1 521 +
1877523	gt csa	exon	25221	25310	1	+	.	Parent=mRNA11
1877523	gt cds	CDS	25221	25310	.	+	0	ID=CDS9;Parent=mRNA11
1877523	gt csa	exon	25510	25626	1	+	.	Parent=mRNA11
1877523	gt cds	CDS	25510	25626	.	+	0	ID=CDS9;Parent=mRNA11
1877523	gt csa	exon	25713	25841	1	+	.	Parent=mRNA11
1877523	gt cds	CDS	25713	25841	.	+	0	ID=CDS9;Parent=mRNA11
1877523	gt cds	CDS	25916	26098	.	+	0	ID=CDS9;Parent=mRNA11
1877523	gt csa	exon	25916	26100	1	+	.	Parent=mRNA11
###
1877523	gt csa	gene	27900	29817	.	+	.	ID=gene11
1877523	gt csa	mRNA	27900	28989	.	+	.	ID=mRNA12;Parent=gene11;Target=8726341 1 499 +
1877523	gt csa	exon	27900	28003	1	+	.	Parent=mRNA12
1877523	gt cds	CDS	27902	28003	.	+	0	ID=CDS10;Parent=mRNA12
1877523	gt csa	exon	28269	28424	1	+	.	Parent=mRNA12
1877523	gt cds	CDS	28269	28424	.	+	0	ID=CDS10;Parent=mRNA12
1877523	gt csa	exon	28507	28579	1	+	.	Parent=mRNA12
1877523	gt cds	CDS	28507	28579	.	+	0	ID=CDS10;Parent=mRNA12
1877523	gt csa	exon	28686	28753	1	+	.	Parent=mRNA12
1877523	gt cds	CDS	28686	28753	.	+	2	ID=CDS10;Parent=mRNA12
1877523	gt cds	CDS	28892	28987	.	+	0	ID=CDS10;Parent=mRNA12
1877523	gt csa	exon	28892	28989	1	+	.	Parent=mRNA12
1877523	gt csa	mRNA	28990	29817	.	+	.	ID=mRNA13;Parent=gene11;Target=8726286 1 477 +
1877523	gt csa	exon	28990	29037	1	+	.	Parent=mRNA13
1877523	gt cds	CDS	28991	29037	.	+	0	ID=CDS11;Parent=mRNA13
1877523	gt csa	exon	29134	29242	1	+	.	Parent=mRNA13
1877523	gt cds	CDS	29134	29242	.	+	1	ID=CDS11;Parent=mRNA13
1877523	gt csa	exon	29331	29477	1	+	.	Parent=mRNA13
1877523	gt cds	CDS	29331	29477	.	+	0	ID=CDS11;Parent=mRNA13
1877523	gt csa	exon	29571	29618	1	+	.	Parent=mRNA13
1877523	gt cds	CDS	29571	29618	.	+	0	ID=CDS11;Parent=mRNA13
1877523	gt cds	CDS	29693	29815	.	+	0	ID=CDS11;Parent=mRNA13
1877523	gt csa	exon	29693	29817	1	+	.	Parent=mRNA13
###
1877523	gt csa	gene	30278	32362	.	+	.	ID=gene12
1877523	gt csa	mRNA	30278	31820	.	+	.	ID=mRNA14;Parent=gene12;Target=8690080 1 524 +,8689616 1 333 +
1877523	gt csa	exon	30278	30391	1	+	.	Parent=mRNA14
1877523	gt cds	CDS	30278	30391	.	+	0	ID=CDS12;Parent=mRNA14
1877523	gt csa	exon	30477	30562	1	+	.	Parent=mRNA14
1877523	gt cds	CDS	30477	30562	.	+	0	ID=CDS12;Parent=mRNA14
1877523	gt csa	exon	30658	30763	1	+	.	Parent=mRNA14
1877523	gt cds	CDS	30658	30763	.	+	1	ID=CDS12;Parent=mRNA14
1877523	gt csa	exon	30990	31085	1	+	.	Parent=mRNA14
1877523	gt cds	CDS	30990	31085	.	+	0	ID=CDS12;Parent=mRNA14
1877523	gt csa	exon	31234	31386	1	+	.	Parent=mRNA14
1877523	gt cds	CDS	31234	31386	.	+	0	ID=CDS12;Parent=mRNA14
1877523	gt csa	exon	31538	31720	1	+	.	Parent=mRNA14
1877523	gt cds	CDS	31538	31720	.	+	0	ID=CDS12;Parent=mRNA14
1877523	gt cds	CDS	31793	31819	.	+	0	ID=CDS12;Parent=mRNA14
1877523	gt csa	exon	31793	31820	1	+	.	Parent=mRNA14
1877523	gt csa	mRNA	31855	32362	.	+	.	ID=mRNA15;Parent=gene12;Target=8689215 1 334 +,9784594 1 269 +
1877523	gt csa	exon	31855	32022	1	+	.	Parent=mRNA15
1877523	gt cds	CDS	31856	32022	.	+	0	ID=CDS13;Parent=mRNA15
1877523	gt csa	exon	32118	32220	1	+	.	Parent=mRNA15
1877523	gt cds	CDS	32118	32220	.	+	1	ID=CDS13;Parent=mRNA15
1877523	gt csa	exon	32300	32362	1	+	.	Parent=mRNA15
1877523	gt cds	CDS	32300	32362	.	+	0	ID=CDS13;Parent=mRNA15
###
1877523	gt csa	gene	32928	34560	.	+	.	ID=gene13
1877523	gt csa	mRNA	32928	34560	.	+	.	ID=mRNA16;Parent=gene13;Target=19875482 1 227 +,9782568 1 427 +
1877523	gt csa	exon	32928	32955	1	+	.	Parent=mRNA16
1877523	gt cds	CDS	32929	32955	.	+	0	ID=CDS14;Parent=mRNA16
1877523	gt csa	exon	33191	33317	0.98	+	.	Parent=mRNA16
1877523	gt cds	CDS	33191	33317	.	+	0	ID=CDS14;Parent=mRNA16
1877523	gt csa	exon	33418	33518	1	+	.	Parent=mRNA16
1877523	gt cds	CDS	33418	33518	.	+	2	ID=CDS14;Parent=mRNA16
1877523	gt csa	exon	33783	33917	1	+	.	Parent=mRNA16
1877523	gt cds	CDS	33783	33917	.	+	0	ID=CDS14;Parent=mRNA16
1877523	gt csa	exon	33996	34076	1	+	.	Parent=mRNA16
1877523	gt cds	CDS	33996	34076	.	+	0	ID=CDS14;Parent=mRNA16
1877523	gt cds	CDS	34472	34558	.	+	0	ID=CDS14;Parent=mRNA16
1877523	gt csa	exon	34472	34560	1	+	.	Parent=mRNA16
###
1877523	gt csa	gene	35628	37208	.	+	.	ID=gene14
1877523	gt csa	mRNA	35628	37208	.	+	.	ID=mRNA17;Parent=gene14;Target=2759121 1 451 +,5841805 1 479 +,8683519 1 604 -,8682814 1 522 -,8690927 1 566 -,5845530 1 547 -,8717375 1 521 -,2048630 53 438 +
1877523	gt csa	exon	35628	35712	1	+	.	Parent=mRNA17
1877523	gt cds	CDS	35629	35712	.	+	0	ID=CDS15;Parent=mRNA17
1877523	gt csa	exon	35820	36011	1	+	.	Parent=mRNA17
1877523	gt cds	CDS	35820	36011	.	+	0	ID=CDS15;Parent=mRNA17
1877523	gt csa	exon	36101	36205	1	+	.	Parent=mRNA17
1877523	gt cds	CDS	36101	36205	.	+	0	ID=CDS15;Parent=mRNA17
1877523	gt csa	exon	36297	36431	1	+	.	Parent=mRNA17
1877523	gt cds	CDS	36297	36431	.	+	0	ID=CDS15;Parent=mRNA17
1877523	gt csa	exon	36521	36721	1	+	.	Parent=mRNA17
1877523	gt cds	CDS	36521	36721	.	+	0	ID=CDS15;Parent=mRNA17
1877523	gt cds	CDS	36816	37070	.	+	0	ID=CDS15;Parent=mRNA17
1877523	gt csa	exon	36816	37208	1	+	.	Parent=mRNA17
###
1877523	gt csa	gene	36812	37235	.	-	.	ID=gene15
1877523	gt csa	mRNA	36812	37235	.	-	.	ID=mRNA18;Parent=gene15;Target=8735393 1 424 +,19741846 1 380 +,8738747 1 395 +,8679389 1 133 +
1877523	gt cds	CDS	36812	37063	.	-	0	ID=CDS16;Parent=mRNA18
1877523	gt csa	exon	36812	37235	0.998	-	.	Parent=mRNA18
###
1877523	gt csa	gene	37669	40032	.	-	.	ID=gene16
1877523	gt csa	mRNA	37669	40032	.	-	.	ID=mRNA19;Parent=gene16;Target=8738841 1 588 -,19831991 1 401 -,19840745 1 390 -,5843191 1 490 -,19869427 1 606 +,8722075 1 568 +
1877523	gt csa	exon	37669	37891	1	-	.	Parent=mRNA19
1877523	gt cds	CDS	37867	37891	.	-	1	ID=CDS17;Parent=mRNA19
1877523	gt csa	exon	37972	38060	1	-	.	Parent=mRNA19
1877523	gt cds	CDS	37972	38060	.	-	0	ID=CDS17;Parent=mRNA19
1877523	gt csa	exon	38656	38794	1	-	.	Parent=mRNA19
1877523	gt cds	CDS	38656	38794	.	-	1	ID=CDS17;Parent=mRNA19
1877523	gt csa	exon	38927	38997	1	-	.	Parent=mRNA19
1877523	gt cds	CDS	38927	38997	.	-	0	ID=CDS17;Parent=mRNA19
1877523	gt csa	exon	39104	39148	1	-	.	Parent=mRNA19
1877523	gt cds	CDS	39104	39148	.	-	0	ID=CDS17;Parent=mRNA19
1877523	gt csa	exon	39239	39328	1	-	.	Parent=mRNA19
1877523	gt cds	CDS	39239	39328	.	-	0	ID=CDS17;Parent=mRNA19
1877523	gt csa	exon	39438	39526	1	-	.	Parent=mRNA19
1877523	gt cds	CDS	39438	39526	.	-	2	ID=CDS17;Parent=mRNA19
1877523	gt csa	exon	39614	39689	1	-	.	Parent=mRNA19
1877523	gt cds	CDS	39614	39689	.	-	0	ID=CDS17;Parent=mRNA19
1877523	gt cds	CDS	39798	39983	.	-	0	ID=CDS17;Parent=mRNA19
1877523	gt csa	exon	39798	40032	0.996	-	.	Parent=mRNA19
###
1877523	gt csa	gene	42783	43204	.	-	.	ID=gene17
1877523	gt csa	mRNA	42783	43204	.	-	.	ID=mRNA20;Parent=gene17;Target=19858773 1 422 +
1877523	gt csa	exon	42783	43204	1	-	.	Parent=mRNA20
###
1877523	gt csa	gene	44029	44540	.	+	.	ID=gene18
1877523	gt csa	mRNA	44029	44540	.	+	.	ID=mRNA21;Parent=gene18;Target=402959 1 423 +
1877523	gt csa	exon	44029	44263	0.991	+	.	Parent=mRNA21
1877523	gt cds	CDS	44029	44263	.	+	0	ID=CDS18;Parent=mRNA21
1877523	gt cds	CDS	44354	44538	.	+	2	ID=CDS18;Parent=mRNA21
1877523	gt csa	exon	44354	44540	0.947	+	.	Parent=mRNA21
###
1877523	gt csa	gene	45542	45941	.	-	.	ID=gene19
1877523	gt csa	mRNA	45542	45941	.	-	.	ID=mRNA22;Parent=gene19;Target=8682693 1 322 +,402964 1 388 +
1877523	gt csa	exon	45542	45941	0.924	-	.	Parent=mRNA22
###
1877523	gt csa	gene	45843	45920	.	+	.	ID=gene20
1877523	gt csa	mRNA	45843	45920	.	+	.	ID=mRNA23;Parent=gene20;Target=8720010 1 78 -
1877523	gt csa	exon	45843	45920	0.949	+	.	Parent=mRNA23
###
1877523	gt csa	gene	49874	52242	.	-	.	ID=gene21
1877523	gt csa	mRNA	49874	50547	.	-	.	ID=mRNA24;Parent=gene21;Target=19837290 1 412 +
1877523	gt csa	exon	49874	50284	1	-	.	Parent=mRNA24
1877523	gt cds	CDS	49876	50205	.	-	0	ID=CDS19;Parent=mRNA24
1877523	gt csa	exon	50547	50547	1	-	.	Parent=mRNA24
1877523	gt csa	mRNA	50433	52242	.	-	.	ID=mRNA25;Parent=gene21;Target=19807151 1 426 -,8731976 1 441 -,19805724 1 385 -,19866668 1 647 +,2747604 1 362 +,2596256 1 446 +,2596953 1 336 +,5839790 1 404 +,403229 1 350 +,9785390 1 263 +
1877523	gt csa	exon	50433	50834	0.978	-	.	Parent=mRNA25
1877523	gt cds	CDS	50738	50834	.	-	1	ID=CDS20;Parent=mRNA25
1877523	gt csa	exon	51113	51216	1	-	.	Parent=mRNA25
1877523	gt cds	CDS	51113	51216	.	-	0	ID=CDS20;Parent=mRNA25
1877523	gt csa	exon	51319	51474	1	-	.	Parent=mRNA25
1877523	gt cds	CDS	51319	51474	.	-	0	ID=CDS20;Parent=mRNA25
1877523	gt csa	exon	51552	51623	1	-	.	Parent=mRNA25
1877523	gt cds	CDS	51552	51623	.	-	0	ID=CDS20;Parent=mRNA25
1877523	gt csa	exon	51711	51758	1	-	.	Parent=mRNA25
1877523	gt cds	CDS	51711	51758	.	-	0	ID=CDS20;Parent=mRNA25
1877523	gt csa	exon	51849	51896	1	-	.	Parent=mRNA25
1877523	gt cds	CDS	51849	51896	.	-	0	ID=CDS20;Parent=mRNA25
1877523	gt csa	exon	51983	52055	1	-	.	Parent=mRNA25
1877523	gt cds	CDS	51983	52055	.	-	1	ID=CDS20;Parent=mRNA25
1877523	gt csa	exon	52163	52242	1	-	.	Parent=mRNA25
1877523	gt cds	CDS	52163	52242	.	-	0	ID=CDS20;Parent=mRNA25
###
1877523	gt csa	gene	50475	50702	.	+	.	ID=gene22
1877523	gt csa	mRNA	50475	50702	.	+	.	ID=mRNA26;Parent=gene22;Target=8727457 1 228 +
1877523	gt csa	exon	50475	50702	1	+	.	Parent=mRNA26
###
1877523	gt csa	gene	53602	54829	.	-	.	ID=gene23
1877523	gt csa	mRNA	53602	54829	.	-	.	ID=mRNA27;Parent=gene23;Target=8697180 1 427 -,19803773 1 627 -,19840006 1 413 -,19823046 1 417 -,2393553 57 528 +,19843722 1 431 -,8696505 49 568 +,5839694 1 477 +,9778953 1 365 +,19865963 1 414 +,9784661 1 248 +,933584 1 311 +,8696543 49 319 +
1877523	gt csa	exon	53602	53914	0.994	-	.	Parent=mRNA27
1877523	gt cds	CDS	53855	53914	.	-	0	ID=CDS21;Parent=mRNA27
1877523	gt csa	exon	54159	54335	1	-	.	Parent=mRNA27
1877523	gt cds	CDS	54159	54335	.	-	0	ID=CDS21;Parent=mRNA27
1877523	gt cds	CDS	54574	54825	.	-	0	ID=CDS21;Parent=mRNA27
1877523	gt csa	exon	54574	54829	0.992	-	.	Parent=mRNA27
###
1877523	gt csa	gene	53632	56652	.	+	.	ID=gene24
1877523	gt csa	mRNA	53632	53909	.	+	.	ID=mRNA28;Parent=gene24;Target=8697126 1 279 +
1877523	gt csa	exon	53632	53909	0.991	+	.	Parent=mRNA28
1877523	gt csa	mRNA	54991	56652	.	+	.	ID=mRNA29;Parent=gene24;Target=19874826 1 651 +
1877523	gt csa	exon	54991	55057	0.985	+	.	Parent=mRNA29
1877523	gt cds	CDS	54991	55057	.	+	0	ID=CDS22;Parent=mRNA29
1877523	gt csa	exon	55145	55230	1	+	.	Parent=mRNA29
1877523	gt cds	CDS	55145	55230	.	+	2	ID=CDS22;Parent=mRNA29
1877523	gt csa	exon	55300	55341	1	+	.	Parent=mRNA29
1877523	gt cds	CDS	55300	55341	.	+	0	ID=CDS22;Parent=mRNA29
1877523	gt csa	exon	55453	55498	1	+	.	Parent=mRNA29
1877523	gt cds	CDS	55453	55498	.	+	0	ID=CDS22;Parent=mRNA29
1877523	gt csa	exon	55618	55704	1	+	.	Parent=mRNA29
1877523	gt cds	CDS	55618	55704	.	+	2	ID=CDS22;Parent=mRNA29
1877523	gt csa	exon	55818	55873	1	+	.	Parent=mRNA29
1877523	gt cds	CDS	55818	55873	.	+	2	ID=CDS22;Parent=mRNA29
1877523	gt csa	exon	56036	56153	1	+	.	Parent=mRNA29
1877523	gt cds	CDS	56036	56153	.	+	0	ID=CDS22;Parent=mRNA29
1877523	gt csa	exon	56281	56339	1	+	.	Parent=mRNA29
1877523	gt cds	CDS	56281	56339	.	+	2	ID=CDS22;Parent=mRNA29
1877523	gt csa	exon	56449	56520	1	+	.	Parent=mRNA29
1877523	gt cds	CDS	56449	56520	.	+	0	ID=CDS22;Parent=mRNA29
1877523	gt csa	exon	56635	56652	1	+	.	Parent=mRNA29
1877523	gt cds	CDS	56635	56652	.	+	0	ID=CDS22;Parent=mRNA29
###
1877523	gt csa	gene	58115	62646	.	+	.	ID=gene25
1877523	gt csa	mRNA	58115	59001	.	+	.	ID=mRNA30;Parent=gene25;Target=19741042 1 460 -
1877523	gt csa	exon	58115	58209	0.958	+	.	Parent=mRNA30
1877523	gt cds	CDS	58115	58209	.	+	0	ID=CDS23;Parent=mRNA30
1877523	gt csa	exon	58461	58526	1	+	.	Parent=mRNA30
1877523	gt cds	CDS	58461	58526	.	+	1	ID=CDS23;Parent=mRNA30
1877523	gt csa	exon	58624	58717	1	+	.	Parent=mRNA30
1877523	gt cds	CDS	58624	58717	.	+	1	ID=CDS23;Parent=mRNA30
1877523	gt cds	CDS	58796	58873	.	+	0	ID=CDS23;Parent=mRNA30
1877523	gt csa	exon	58796	59001	0.983	+	.	Parent=mRNA30
1877523	gt csa	mRNA	59010	59976	.	+	.	ID=mRNA31;Parent=gene25;Target=8715845 1 475 +,19864079 1 653 +,9787190 1 255 +,397215 1 333 +
1877523	gt csa	exon	59010	59526	0.989	+	.	Parent=mRNA31
1877523	gt cds	CDS	59158	59526	.	+	0	ID=CDS24;Parent=mRNA31
1877523	gt cds	CDS	59607	59975	.	+	0	ID=CDS24;Parent=mRNA31
1877523	gt csa	exon	59607	59976	0.991	+	.	Parent=mRNA31
1877523	gt csa	mRNA	60190	60487	.	+	.	ID=mRNA32;Parent=gene25;Target=398270 1 298 +
1877523	gt csa	exon	60190	60487	0.987	+	.	Parent=mRNA32
1877523	gt cds	CDS	60192	60485	.	+	0	ID=CDS25;Parent=mRNA32
1877523	gt csa	mRNA	61186	61974	.	+	.	ID=mRNA33;Parent=gene25;Target=2722481 1 371 +,19837990 1 398 -
1877523	gt csa	exon	61186	61281	0.99	+	.	Parent=mRNA33
1877523	gt cds	CDS	61186	61281	.	+	0	ID=CDS26;Parent=mRNA33
1877523	gt csa	exon	61565	61641	1	+	.	Parent=mRNA33
1877523	gt cds	CDS	61565	61641	.	+	0	ID=CDS26;Parent=mRNA33
1877523	gt cds	CDS	61724	61874	.	+	1	ID=CDS26;Parent=mRNA33
1877523	gt csa	exon	61724	61974	1	+	.	Parent=mRNA33
1877523	gt csa	mRNA	62196	62646	.	+	.	ID=mRNA34;Parent=gene25;Target=2747645 1 448 +
1877523	gt cds	CDS	62196	62645	.	+	0	ID=CDS27;Parent=mRNA34
1877523	gt csa	exon	62196	62646	0.921	+	.	Parent=mRNA34
###
1877523	gt csa	gene	60319	61000	.	-	.	ID=gene26
1877523	gt csa	mRNA	60319	61000	.	-	.	ID=mRNA35;Parent=gene26;Target=19801463 1 682 +,8692149 1 559 +,19827386 1 453 +,7610825 1 500 +,8736724 1 496 +,19828552 1 452 +,19838343 1 409 +,397216 1 390 +
1877523	gt csa	exon	60319	61000	0.997	-	.	Parent=mRNA35
1877523	gt cds	CDS	60518	60715	.	-	0	ID=CDS28;Parent=mRNA35
###
1877523	gt csa	gene	63106	64320	.	+	.	ID=gene27
1877523	gt csa	mRNA	63106	64320	.	+	.	ID=mRNA36;Parent=gene27;Target=8701755 1 598 -,8735505 1 490 -,19798134 1 412 +,5846657 1 345 +
1877523	gt csa	exon	63106	63178	1	+	.	Parent=mRNA36
1877523	gt cds	CDS	63108	63178	.	+	0	ID=CDS29;Parent=mRNA36
1877523	gt csa	exon	63271	63391	1	+	.	Parent=mRNA36
1877523	gt cds	CDS	63271	63391	.	+	1	ID=CDS29;Parent=mRNA36
1877523	gt csa	exon	63468	63683	1	+	.	Parent=mRNA36
1877523	gt cds	CDS	63468	63683	.	+	0	ID=CDS29;Parent=mRNA36
1877523	gt cds	CDS	63755	63814	.	+	0	ID=CDS29;Parent=mRNA36
1877523	gt csa	exon	63755	64320	0.979	+	.	Parent=mRNA36
###
1877523	gt csa	gene	64196	65033	.	-	.	ID=gene28
1877523	gt csa	mRNA	64196	65033	.	-	.	ID=mRNA37;Parent=gene28;Target=19877649 1 632 +
1877523	gt csa	exon	64196	64605	1	-	.	Parent=mRNA37
1877523	gt cds	CDS	64196	64605	.	-	2	ID=CDS30;Parent=mRNA37
1877523	gt cds	CDS	64812	65031	.	-	0	ID=CDS30;Parent=mRNA37
1877523	gt csa	exon	64812	65033	0.995	-	.	Parent=mRNA37
###
1877523	gt csa	gene	65467	66157	.	+	.	ID=gene29
1877523	gt csa	mRNA	65467	66157	.	+	.	ID=mRNA38;Parent=gene29;Target=19875812 1 621 +
1877523	gt csa	exon	65467	66058	0.992	+	.	Parent=mRNA38
1877523	gt cds	CDS	65527	66058	.	+	0	ID=CDS31;Parent=mRNA38
1877523	gt cds	CDS	66130	66155	.	+	2	ID=CDS31;Parent=mRNA38
1877523	gt csa	exon	66130	66157	0.964	+	.	Parent=mRNA38
###
1877523	gt csa	gene	67358	68396	.	+	.	ID=gene30
1877523	gt csa	mRNA	67358	68396	.	+	.	ID=mRNA39;Parent=gene30;Target=396603 1 749 +,19742246 1 423 -
1877523	gt csa	exon	67358	67550	1	+	.	Parent=mRNA39
1877523	gt cds	CDS	67359	67550	.	+	0	ID=CDS32;Parent=mRNA39
1877523	gt csa	exon	67636	67908	0.969	+	.	Parent=mRNA39
1877523	gt cds	CDS	67636	67908	.	+	0	ID=CDS32;Parent=mRNA39
1877523	gt cds	CDS	68011	68184	.	+	0	ID=CDS32;Parent=mRNA39
1877523	gt csa	exon	68011	68396	0.99	+	.	Parent=mRNA39
###
1877523	gt csa	gene	69163	70072	.	+	.	ID=gene31
1877523	gt csa	mRNA	69163	69968	.	+	.	ID=mRNA40;Parent=gene31;Target=19872996 1 536 +,19869130 1 603 +,19870921 1 486 +,7612059 1 362 +
1877523	gt csa	exon	69163	69265	0.971	+	.	Parent=mRNA40
1877523	gt cds	CDS	69176	69265	.	+	0	ID=CDS33;Parent=mRNA40
1877523	gt csa	exon	69375	69598	1	+	.	Parent=mRNA40
1877523	gt cds	CDS	69375	69598	.	+	0	ID=CDS33;Parent=mRNA40
1877523	gt cds	CDS	69685	69940	.	+	1	ID=CDS33;Parent=mRNA40
1877523	gt csa	exon	69685	69968	0.996	+	.	Parent=mRNA40
1877523	gt csa	mRNA	69196	70072	.	+	.	ID=mRNA41;Parent=gene31;Target=905849 1 455 +,7612059 1 362 +
1877523	gt csa	exon	69196	69265	0.986	+	.	Parent=mRNA41
1877523	gt cds	CDS	69197	69265	.	+	0	ID=CDS34;Parent=mRNA41
1877523	gt csa	exon	69375	69598	1	+	.	Parent=mRNA41
1877523	gt cds	CDS	69375	69598	.	+	0	ID=CDS34;Parent=mRNA41
1877523	gt csa	exon	69685	69831	0.816	+	.	Parent=mRNA41
1877523	gt cds	CDS	69685	69831	.	+	1	ID=CDS34;Parent=mRNA41
1877523	gt csa	exon	70063	70072	0.4	+	.	Parent=mRNA41
1877523	gt cds	CDS	70063	70072	.	+	1	ID=CDS34;Parent=mRNA41
###
1877523	gt csa	gene	71414	72803	.	+	.	ID=gene32
1877523	gt csa	mRNA	71414	72009	.	+	.	ID=mRNA42;Parent=gene32;Target=17520 1 168 +,8734707 1 319 +
1877523	gt csa	exon	71414	71479	1	+	.	Parent=mRNA42
1877523	gt cds	CDS	71414	71479	.	+	0	ID=CDS35;Parent=mRNA42
1877523	gt csa	exon	71579	71779	0.985	+	.	Parent=mRNA42
1877523	gt cds	CDS	71579	71779	.	+	0	ID=CDS35;Parent=mRNA42
1877523	gt csa	exon	71914	72009	1	+	.	Parent=mRNA42
1877523	gt cds	CDS	71914	72009	.	+	0	ID=CDS35;Parent=mRNA42
1877523	gt csa	mRNA	72121	72753	.	+	.	ID=mRNA43;Parent=gene32;Target=2597031 1 221 +,958004 1 484 +,3449674 1 333 +
1877523	gt csa	exon	72121	72753	0.929	+	.	Parent=mRNA43
1877523	gt cds	CDS	72430	72714	.	+	0	ID=CDS36;Parent=mRNA43
1877523	gt csa	mRNA	72137	72803	.	+	.	ID=mRNA44;Parent=gene32;Target=1159193 1 351 +,8737761 1 497 -,2749490 79 466 +,7610337 1 466 -,19829297 1 429 -,19829716 1 434 -,19831127 1 431 -,8731753 1 480 -,19839622 1 421 -,2762921 1 237 +,2762922 1 337 +,19825274 1 460 -,19855736 1 420 -,8695920 1 405 -,3449674 1 333 +
1877523	gt csa	exon	72137	72296	1	+	.	Parent=mRNA44
1877523	gt cds	CDS	72138	72296	.	+	0	ID=CDS37;Parent=mRNA44
1877523	gt cds	CDS	72369	72542	.	+	0	ID=CDS37;Parent=mRNA44
1877523	gt csa	exon	72369	72803	1	+	.	Parent=mRNA44
###
1877523	gt csa	gene	72359	74920	.	-	.	ID=gene33
1877523	gt csa	mRNA	72359	72827	.	-	.	ID=mRNA45;Parent=gene33;Target=19841232 1 443 +,19826275 1 444 +,19834843 1 430 +,19828253 1 431 +,19825742 1 430 +,19828054 1 455 +,19844666 1 418 +,19829934 1 418 +,19842362 1 417 +,19837074 1 417 +,8728304 1 365 +,19827775 1 416 +,19855995 1 403 +,8694120 1 354 +,19831839 1 401 +,19833332 1 405 +,8732348 1 369 +,8695842 1 280 +
1877523	gt csa	exon	72359	72827	0.992	-	.	Parent=mRNA45
1877523	gt cds	CDS	72426	72632	.	-	0	ID=CDS38;Parent=mRNA45
1877523	gt csa	mRNA	72390	74046	.	-	.	ID=mRNA46;Parent=gene33;Target=8728304 1 365 +,8694120 1 354 +,2597485 1 163 -
1877523	gt csa	exon	72390	72789	0.978	-	.	Parent=mRNA46
1877523	gt cds	CDS	72426	72632	.	-	0	ID=CDS39;Parent=mRNA46
1877523	gt csa	exon	74021	74046	0.615	-	.	Parent=mRNA46
1877523	gt csa	mRNA	72390	74920	.	-	.	ID=mRNA47;Parent=gene33;Target=8728304 1 365 +,8694120 1 354 +,3450080 1 166 -
1877523	gt csa	exon	72390	72800	0.919	-	.	Parent=mRNA47
1877523	gt cds	CDS	72426	72632	.	-	0	ID=CDS40;Parent=mRNA47
1877523	gt csa	exon	74901	74920	0.75	-	.	Parent=mRNA47
###
1877523	gt csa	gene	79098	79663	.	-	.	ID=gene34
1877523	gt csa	mRNA	79098	79663	.	-	.	ID=mRNA48;Parent=gene34;Target=19857409 11 314 -
1877523	gt csa	exon	79098	79127	0.767	-	.	Parent=mRNA48
1877523	gt csa	exon	79241	79487	0.866	-	.	Parent=mRNA48
1877523	gt cds	CDS	79290	79487	.	-	0	ID=CDS41;Parent=mRNA48
1877523	gt cds	CDS	79636	79662	.	-	0	ID=CDS41;Parent=mRNA48
1877523	gt csa	exon	79636	79663	1	-	.	Parent=mRNA48
###
1877523	gt csa	gene	86444	89957	.	-	.	ID=gene35
1877523	gt csa	mRNA	86444	89957	.	-	.	ID=mRNA49;Parent=gene35;Target=19873300 87 582 +
1877523	gt csa	exon	86444	86516	0.767	-	.	Parent=mRNA49
1877523	gt cds	CDS	86445	86516	.	-	0	ID=CDS42;Parent=mRNA49
1877523	gt csa	exon	89440	89702	0.683	-	.	Parent=mRNA49
1877523	gt cds	CDS	89440	89702	.	-	2	ID=CDS42;Parent=mRNA49
1877523	gt cds	CDS	89794	89950	.	-	0	ID=CDS42;Parent=mRNA49
1877523	gt csa	exon	89794	89957	0.823	-	.	Parent=mRNA49
###
1877523	gt csa	gene	90829	91133	.	+	.	ID=gene36
1877523	gt csa	mRNA	90829	91133	.	+	.	ID=mRNA50;Parent=gene36;Target=5845361 1 307 +
1877523	gt csa	exon	90829	91133	0.948	+	.	Parent=mRNA50
###
1877523	gt csa	gene	91050	91786	.	-	.	ID=gene37
1877523	gt csa	mRNA	91050	91786	.	-	.	ID=mRNA51;Parent=gene37;Target=8735154 1 543 -
1877523	gt csa	exon	91050	91401	1	-	.	Parent=mRNA51
1877523	gt cds	CDS	91145	91401	.	-	2	ID=CDS43;Parent=mRNA51
1877523	gt csa	exon	91524	91713	1	-	.	Parent=mRNA51
1877523	gt cds	CDS	91524	91713	.	-	0	ID=CDS43;Parent=mRNA51
1877523	gt csa	exon	91786	91786	1	-	.	Parent=mRNA51
###
1877523	gt csa	gene	92903	94384	.	-	.	ID=gene38
1877523	gt csa	mRNA	92903	93265	.	-	.	ID=mRNA52;Parent=gene38;Target=9786193 1 266 +
1877523	gt csa	exon	92903	93008	1	-	.	Parent=mRNA52
1877523	gt csa	exon	93106	93265	1	-	.	Parent=mRNA52
1877523	gt csa	mRNA	93551	94384	.	-	.	ID=mRNA53;Parent=gene38;Target=19806050 1 401 -,2047981 81 377 +,19857902 1 407 -
1877523	gt csa	exon	93551	93913	0.957	-	.	Parent=mRNA53
1877523	gt cds	CDS	93689	93913	.	-	0	ID=CDS44;Parent=mRNA53
1877523	gt csa	exon	94017	94124	1	-	.	Parent=mRNA53
1877523	gt cds	CDS	94017	94124	.	-	0	ID=CDS44;Parent=mRNA53
1877523	gt csa	exon	94367	94384	1	-	.	Parent=mRNA53
1877523	gt cds	CDS	94367	94384	.	-	0	ID=CDS44;Parent=mRNA53
###
1877523	gt csa	gene	94706	96614	.	-	.	ID=gene39
1877523	gt csa	mRNA	94706	96614	.	-	.	ID=mRNA54;Parent=gene39;Target=9782167 1 392 +,19866748 1 646 +,9778306 1 422 +,9778321 1 398 +
1877523	gt csa	exon	94706	94771	0.871	-	.	Parent=mRNA54
1877523	gt cds	CDS	94706	94771	.	-	0	ID=CDS45;Parent=mRNA54
1877523	gt csa	exon	94877	94985	0.954	-	.	Parent=mRNA54
1877523	gt cds	CDS	94877	94985	.	-	1	ID=CDS45;Parent=mRNA54
1877523	gt csa	exon	95071	95147	1	-	.	Parent=mRNA54
1877523	gt cds	CDS	95071	95147	.	-	0	ID=CDS45;Parent=mRNA54
1877523	gt csa	exon	95234	95454	1	-	.	Parent=mRNA54
1877523	gt cds	CDS	95234	95454	.	-	2	ID=CDS45;Parent=mRNA54
1877523	gt csa	exon	95842	95947	0.991	-	.	Parent=mRNA54
1877523	gt cds	CDS	95842	95947	.	-	0	ID=CDS45;Parent=mRNA54
1877523	gt csa	exon	96036	96140	1	-	.	Parent=mRNA54
1877523	gt cds	CDS	96036	96140	.	-	0	ID=CDS45;Parent=mRNA54
1877523	gt csa	exon	96232	96330	1	-	.	Parent=mRNA54
1877523	gt cds	CDS	96232	96330	.	-	0	ID=CDS45;Parent=mRNA54
1877523	gt cds	CDS	96418	96612	.	-	0	ID=CDS45;Parent=mRNA54
1877523	gt csa	exon	96418	96614	0.987	-	.	Parent=mRNA54
###
1877523	gt csa	gene	98857	100804	.	-	.	ID=gene40
1877523	gt csa	mRNA	98857	100804	.	-	.	ID=mRNA55;Parent=gene40;Target=19836538 1 392 -,8737545 1 333 -,2446000 47 535 +,5846455 1 525 -,8734273 1 383 -,397246 1 362 +,19863867 1 661 +,19870774 1 577 +,958152 1 437 +,8732177 1 326 +
1877523	gt csa	exon	98857	99121	1	-	.	Parent=mRNA55
1877523	gt cds	CDS	99053	99121	.	-	0	ID=CDS46;Parent=mRNA55
1877523	gt csa	exon	99200	99361	1	-	.	Parent=mRNA55
1877523	gt cds	CDS	99200	99361	.	-	0	ID=CDS46;Parent=mRNA55
1877523	gt csa	exon	99443	99511	1	-	.	Parent=mRNA55
1877523	gt cds	CDS	99443	99511	.	-	0	ID=CDS46;Parent=mRNA55
1877523	gt csa	exon	99613	99877	1	-	.	Parent=mRNA55
1877523	gt cds	CDS	99613	99877	.	-	1	ID=CDS46;Parent=mRNA55
1877523	gt csa	exon	100102	100226	1	-	.	Parent=mRNA55
1877523	gt cds	CDS	100102	100226	.	-	0	ID=CDS46;Parent=mRNA55
1877523	gt csa	exon	100327	100434	1	-	.	Parent=mRNA55
1877523	gt cds	CDS	100327	100434	.	-	0	ID=CDS46;Parent=mRNA55
1877523	gt csa	exon	100539	100646	1	-	.	Parent=mRNA55
1877523	gt cds	CDS	100539	100646	.	-	0	ID=CDS46;Parent=mRNA55
1877523	gt cds	CDS	100749	100802	.	-	0	ID=CDS46;Parent=mRNA55
1877523	gt csa	exon	100749	100804	0.982	-	.	Parent=mRNA55
###
1877523	gt csa	gene	103616	106973	.	+	.	ID=gene41
1877523	gt csa	mRNA	103616	105860	.	+	.	ID=mRNA56;Parent=gene41;Target=2580948 1 435 +,8722221 103 366 +,623629 87 375 +,9778203 71 401 +,8731408 68 518 +,937871 1 457 +,9781141 22 358 +,7611662 1 549 -,19801855 1 495 -,8695006 1 452 -,8702125 1 452 -,19825204 1 402 -,2748033 88 460 -,19835442 1 367 -,8734878 1 354 -,19823987 1 352 -,19841468 39 385 -,2747682 1 302 +,2412846 1 302 +,17325 1 277 -,3449578 65 370 +,19859011 1 296 -
1877523	gt csa	exon	103616	103753	0.975	+	.	Parent=mRNA56
1877523	gt cds	CDS	103616	103753	.	+	0	ID=CDS47;Parent=mRNA56
1877523	gt csa	exon	103982	104035	0.981	+	.	Parent=mRNA56
1877523	gt cds	CDS	103982	104035	.	+	0	ID=CDS47;Parent=mRNA56
1877523	gt csa	exon	104118	104198	0.975	+	.	Parent=mRNA56
1877523	gt cds	CDS	104118	104198	.	+	0	ID=CDS47;Parent=mRNA56
1877523	gt csa	exon	104295	104455	0.932	+	.	Parent=mRNA56
1877523	gt cds	CDS	104295	104455	.	+	0	ID=CDS47;Parent=mRNA56
1877523	gt csa	exon	104649	104724	0.934	+	.	Parent=mRNA56
1877523	gt cds	CDS	104649	104724	.	+	1	ID=CDS47;Parent=mRNA56
1877523	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA56
1877523	gt cds	CDS	104803	104928	.	+	0	ID=CDS47;Parent=mRNA56
1877523	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA56
1877523	gt cds	CDS	105010	105228	.	+	0	ID=CDS47;Parent=mRNA56
1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA56
1877523	gt cds	CDS	105315	105428	.	+	0	ID=CDS47;Parent=mRNA56
1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA56
1877523	gt cds	CDS	105500	105535	.	+	0	ID=CDS47;Parent=mRNA56
1877523	gt cds	CDS	105630	105764	.	+	0	ID=CDS47;Parent=mRNA56
1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA56
1877523	gt csa	mRNA	103616	105860	.	+	.	ID=mRNA57;Parent=gene41;Target=2580948 1 435 +,2759743 1 460 +,5840051 1 700 +,8722221 103 366 +,623629 87 375 +,9781141 22 358 +,7611662 1 549 -,19801855 1 495 -,8695006 1 452 -,8702125 1 452 -,19825204 1 402 -,2748033 88 460 -,19835442 1 367 -,8734878 1 354 -,19823987 1 352 -,19841468 39 385 -,2747682 1 302 +,2412846 1 302 +,17325 1 277 -,3449578 65 370 +,19859011 1 296 -
1877523	gt csa	exon	103616	103753	1	+	.	Parent=mRNA57
1877523	gt csa	exon	103982	104035	1	+	.	Parent=mRNA57
1877523	gt csa	exon	104118	104198	1	+	.	Parent=mRNA57
1877523	gt csa	exon	104295	104724	0.921	+	.	Parent=mRNA57
1877523	gt cds	CDS	104584	104724	.	+	0	ID=CDS48;Parent=mRNA57
1877523	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA57
1877523	gt cds	CDS	104803	104928	.	+	0	ID=CDS48;Parent=mRNA57
1877523	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA57
1877523	gt cds	CDS	105010	105228	.	+	0	ID=CDS48;Parent=mRNA57
1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA57
1877523	gt cds	CDS	105315	105428	.	+	0	ID=CDS48;Parent=mRNA57
1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA57
1877523	gt cds	CDS	105500	105535	.	+	0	ID=CDS48;Parent=mRNA57
1877523	gt cds	CDS	105630	105764	.	+	0	ID=CDS48;Parent=mRNA57
1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA57
1877523	gt csa	mRNA	103706	105860	.	+	.	ID=mRNA58;Parent=gene41;Target=8686177 99 409 +,453733 78 357 +,9778203 71 401 +,8731408 68 518 +,937871 1 457 +,9781141 22 358 +,7611662 1 549 -,19801855 1 495 -,8695006 1 452 -,8702125 1 452 -,19825204 1 402 -,2748033 88 460 -,19835442 1 367 -,8734878 1 354 -,19823987 1 352 -,19841468 39 385 -,2747682 1 302 +,2412846 1 302 +,17325 1 277 -,3449578 65 370 +,19859011 1 296 -
1877523	gt csa	exon	103706	103731	0.885	+	.	Parent=mRNA58
1877523	gt cds	CDS	103706	103731	.	+	0	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	103799	103826	0.518	+	.	Parent=mRNA58
1877523	gt cds	CDS	103799	103826	.	+	1	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	103982	104035	0.944	+	.	Parent=mRNA58
1877523	gt cds	CDS	103982	104035	.	+	0	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	104118	104198	0.951	+	.	Parent=mRNA58
1877523	gt cds	CDS	104118	104198	.	+	0	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	104295	104455	0.888	+	.	Parent=mRNA58
1877523	gt cds	CDS	104295	104455	.	+	0	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	104649	104724	0.934	+	.	Parent=mRNA58
1877523	gt cds	CDS	104649	104724	.	+	1	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA58
1877523	gt cds	CDS	104803	104928	.	+	0	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA58
1877523	gt cds	CDS	105010	105228	.	+	0	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA58
1877523	gt cds	CDS	105315	105428	.	+	0	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA58
1877523	gt cds	CDS	105500	105535	.	+	0	ID=CDS49;Parent=mRNA58
1877523	gt cds	CDS	105630	105764	.	+	0	ID=CDS49;Parent=mRNA58
1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA58
1877523	gt csa	mRNA	105009	105860	.	+	.	ID=mRNA59;Parent=gene41;Target=8734901 1 533 -,19801855 1 495 -,8695006 1 452 -,8702125 1 452 -,19825204 1 402 -,2748033 88 460 -,19835442 1 367 -,8734878 1 354 -,19823987 1 352 -,19841468 39 385 -,2747682 1 302 +,2412846 1 302 +,17325 1 277 -,3449578 65 370 +,19859011 1 296 -
1877523	gt csa	exon	105009	105228	0.864	+	.	Parent=mRNA59
1877523	gt cds	CDS	105010	105228	.	+	0	ID=CDS50;Parent=mRNA59
1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA59
1877523	gt cds	CDS	105315	105428	.	+	0	ID=CDS50;Parent=mRNA59
1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA59
1877523	gt cds	CDS	105500	105535	.	+	0	ID=CDS50;Parent=mRNA59
1877523	gt cds	CDS	105630	105764	.	+	0	ID=CDS50;Parent=mRNA59
1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA59
1877523	gt csa	mRNA	106097	106973	.	+	.	ID=mRNA60;Parent=gene41;Target=19871766 1 425 +,17300 1 350 +,7612621 1 248 +,935362 1 377 +,936803 1 374 +,7612394 1 366 +,2733258 26 261 +,8729681 1 298 +,2759942 1 130 +,9778889 1 162 +
1877523	gt csa	exon	106097	106290	0.995	+	.	Parent=mRNA60
1877523	gt cds	CDS	106168	106290	.	+	0	ID=CDS51;Parent=mRNA60
1877523	gt csa	exon	106566	106619	1	+	.	Parent=mRNA60
1877523	gt cds	CDS	106566	106619	.	+	0	ID=CDS51;Parent=mRNA60
1877523	gt csa	exon	106702	106782	1	+	.	Parent=mRNA60
1877523	gt cds	CDS	106702	106782	.	+	0	ID=CDS51;Parent=mRNA60
1877523	gt csa	exon	106878	106973	1	+	.	Parent=mRNA60
1877523	gt cds	CDS	106878	106973	.	+	0	ID=CDS51;Parent=mRNA60
###
1877523	gt csa	gene	105662	105806	.	-	.	ID=gene42
1877523	gt csa	mRNA	105662	105806	.	-	.	ID=mRNA61;Parent=gene42;Target=8735385 30 173 +
1877523	gt csa	exon	105662	105806	0.855	-	.	Parent=mRNA61
###
genometools-1.5.1/testdata/U89959_csas.gff3000066400000000000000000000520501211610345200202730ustar00rootroot00000000000000##gff-version   3
##sequence-region   1877523 1 106973
1877523	gt csa	gene	1074	1540	.	+	.	ID=gene1
1877523	gt csa	mRNA	1074	1540	.	+	.	ID=mRNA1;Parent=gene1;Target=8721428 1 303 +
1877523	gt csa	exon	1074	1171	1	+	.	Parent=mRNA1
1877523	gt csa	exon	1259	1354	1	+	.	Parent=mRNA1
1877523	gt csa	exon	1432	1540	1	+	.	Parent=mRNA1
###
1877523	gt csa	gene	2779	3506	.	+	.	ID=gene2
1877523	gt csa	mRNA	2779	3506	.	+	.	ID=mRNA2;Parent=gene2;Target=8732738 1 337 +,19843099 1 426 +
1877523	gt csa	exon	2779	2801	0.696	+	.	Parent=mRNA2
1877523	gt csa	exon	3043	3506	0.974	+	.	Parent=mRNA2
1877523	gt csa	mRNA	3025	3506	.	+	.	ID=mRNA3;Parent=gene2;Target=19837778 1 327 +,19843099 1 426 +
1877523	gt csa	exon	3025	3506	0.974	+	.	Parent=mRNA3
###
1877523	gt csa	gene	3041	3651	.	-	.	ID=gene3
1877523	gt csa	mRNA	3041	3651	.	-	.	ID=mRNA4;Parent=gene3;Target=8732878 1 536 -
1877523	gt csa	exon	3041	3550	0.996	-	.	Parent=mRNA4
1877523	gt csa	exon	3626	3651	1	-	.	Parent=mRNA4
###
1877523	gt csa	gene	4768	5357	.	-	.	ID=gene4
1877523	gt csa	mRNA	4768	5357	.	-	.	ID=mRNA5;Parent=gene4;Target=19871046 1 591 +
1877523	gt csa	exon	4768	5357	0.987	-	.	Parent=mRNA5
###
1877523	gt csa	gene	9505	10058	.	+	.	ID=gene5
1877523	gt csa	mRNA	9505	10058	.	+	.	ID=mRNA6;Parent=gene5;Target=8682455 1 554 +
1877523	gt csa	exon	9505	10058	1	+	.	Parent=mRNA6
###
1877523	gt csa	gene	12024	12542	.	-	.	ID=gene6
1877523	gt csa	mRNA	12024	12542	.	-	.	ID=mRNA7;Parent=gene6;Target=8688760 1 519 +
1877523	gt csa	exon	12024	12542	1	-	.	Parent=mRNA7
###
1877523	gt csa	gene	13014	13465	.	-	.	ID=gene7
1877523	gt csa	mRNA	13014	13465	.	-	.	ID=mRNA8;Parent=gene7;Target=2748705 1 459 +
1877523	gt csa	exon	13014	13465	0.881	-	.	Parent=mRNA8
###
1877523	gt csa	gene	15955	16603	.	+	.	ID=gene8
1877523	gt csa	mRNA	15955	16603	.	+	.	ID=mRNA9;Parent=gene8;Target=19878194 1 649 +
1877523	gt csa	exon	15955	16603	0.997	+	.	Parent=mRNA9
###
1877523	gt csa	gene	17165	17684	.	+	.	ID=gene9
1877523	gt csa	mRNA	17165	17684	.	+	.	ID=mRNA10;Parent=gene9;Target=19798999 1 396 -
1877523	gt csa	exon	17165	17247	0.97	+	.	Parent=mRNA10
1877523	gt csa	exon	17374	17684	0.989	+	.	Parent=mRNA10
###
1877523	gt csa	gene	25221	26100	.	+	.	ID=gene10
1877523	gt csa	mRNA	25221	26100	.	+	.	ID=mRNA11;Parent=gene10;Target=8690053 1 521 +
1877523	gt csa	exon	25221	25310	1	+	.	Parent=mRNA11
1877523	gt csa	exon	25510	25626	1	+	.	Parent=mRNA11
1877523	gt csa	exon	25713	25841	1	+	.	Parent=mRNA11
1877523	gt csa	exon	25916	26100	1	+	.	Parent=mRNA11
###
1877523	gt csa	gene	27900	29817	.	+	.	ID=gene11
1877523	gt csa	mRNA	27900	28989	.	+	.	ID=mRNA12;Parent=gene11;Target=8726341 1 499 +
1877523	gt csa	exon	27900	28003	1	+	.	Parent=mRNA12
1877523	gt csa	exon	28269	28424	1	+	.	Parent=mRNA12
1877523	gt csa	exon	28507	28579	1	+	.	Parent=mRNA12
1877523	gt csa	exon	28686	28753	1	+	.	Parent=mRNA12
1877523	gt csa	exon	28892	28989	1	+	.	Parent=mRNA12
1877523	gt csa	mRNA	28990	29817	.	+	.	ID=mRNA13;Parent=gene11;Target=8726286 1 477 +
1877523	gt csa	exon	28990	29037	1	+	.	Parent=mRNA13
1877523	gt csa	exon	29134	29242	1	+	.	Parent=mRNA13
1877523	gt csa	exon	29331	29477	1	+	.	Parent=mRNA13
1877523	gt csa	exon	29571	29618	1	+	.	Parent=mRNA13
1877523	gt csa	exon	29693	29817	1	+	.	Parent=mRNA13
###
1877523	gt csa	gene	30278	32362	.	+	.	ID=gene12
1877523	gt csa	mRNA	30278	31820	.	+	.	ID=mRNA14;Parent=gene12;Target=8690080 1 524 +,8689616 1 333 +
1877523	gt csa	exon	30278	30391	1	+	.	Parent=mRNA14
1877523	gt csa	exon	30477	30562	1	+	.	Parent=mRNA14
1877523	gt csa	exon	30658	30763	1	+	.	Parent=mRNA14
1877523	gt csa	exon	30990	31085	1	+	.	Parent=mRNA14
1877523	gt csa	exon	31234	31386	1	+	.	Parent=mRNA14
1877523	gt csa	exon	31538	31720	1	+	.	Parent=mRNA14
1877523	gt csa	exon	31793	31820	1	+	.	Parent=mRNA14
1877523	gt csa	mRNA	31855	32362	.	+	.	ID=mRNA15;Parent=gene12;Target=8689215 1 334 +,9784594 1 269 +
1877523	gt csa	exon	31855	32022	1	+	.	Parent=mRNA15
1877523	gt csa	exon	32118	32220	1	+	.	Parent=mRNA15
1877523	gt csa	exon	32300	32362	1	+	.	Parent=mRNA15
###
1877523	gt csa	gene	32928	34560	.	+	.	ID=gene13
1877523	gt csa	mRNA	32928	34560	.	+	.	ID=mRNA16;Parent=gene13;Target=19875482 1 227 +,9782568 1 427 +
1877523	gt csa	exon	32928	32955	1	+	.	Parent=mRNA16
1877523	gt csa	exon	33191	33317	0.98	+	.	Parent=mRNA16
1877523	gt csa	exon	33418	33518	1	+	.	Parent=mRNA16
1877523	gt csa	exon	33783	33917	1	+	.	Parent=mRNA16
1877523	gt csa	exon	33996	34076	1	+	.	Parent=mRNA16
1877523	gt csa	exon	34472	34560	1	+	.	Parent=mRNA16
###
1877523	gt csa	gene	35628	37208	.	+	.	ID=gene14
1877523	gt csa	mRNA	35628	37208	.	+	.	ID=mRNA17;Parent=gene14;Target=2759121 1 451 +,5841805 1 479 +,8683519 1 604 -,8682814 1 522 -,8690927 1 566 -,5845530 1 547 -,8717375 1 521 -,2048630 53 438 +
1877523	gt csa	exon	35628	35712	1	+	.	Parent=mRNA17
1877523	gt csa	exon	35820	36011	1	+	.	Parent=mRNA17
1877523	gt csa	exon	36101	36205	1	+	.	Parent=mRNA17
1877523	gt csa	exon	36297	36431	1	+	.	Parent=mRNA17
1877523	gt csa	exon	36521	36721	1	+	.	Parent=mRNA17
1877523	gt csa	exon	36816	37208	1	+	.	Parent=mRNA17
###
1877523	gt csa	gene	36812	37235	.	-	.	ID=gene15
1877523	gt csa	mRNA	36812	37235	.	-	.	ID=mRNA18;Parent=gene15;Target=8735393 1 424 +,19741846 1 380 +,8738747 1 395 +,8679389 1 133 +
1877523	gt csa	exon	36812	37235	0.998	-	.	Parent=mRNA18
###
1877523	gt csa	gene	37669	40032	.	-	.	ID=gene16
1877523	gt csa	mRNA	37669	40032	.	-	.	ID=mRNA19;Parent=gene16;Target=8738841 1 588 -,19831991 1 401 -,19840745 1 390 -,5843191 1 490 -,19869427 1 606 +,8722075 1 568 +
1877523	gt csa	exon	37669	37891	1	-	.	Parent=mRNA19
1877523	gt csa	exon	37972	38060	1	-	.	Parent=mRNA19
1877523	gt csa	exon	38656	38794	1	-	.	Parent=mRNA19
1877523	gt csa	exon	38927	38997	1	-	.	Parent=mRNA19
1877523	gt csa	exon	39104	39148	1	-	.	Parent=mRNA19
1877523	gt csa	exon	39239	39328	1	-	.	Parent=mRNA19
1877523	gt csa	exon	39438	39526	1	-	.	Parent=mRNA19
1877523	gt csa	exon	39614	39689	1	-	.	Parent=mRNA19
1877523	gt csa	exon	39798	40032	0.996	-	.	Parent=mRNA19
###
1877523	gt csa	gene	42783	43204	.	-	.	ID=gene17
1877523	gt csa	mRNA	42783	43204	.	-	.	ID=mRNA20;Parent=gene17;Target=19858773 1 422 +
1877523	gt csa	exon	42783	43204	1	-	.	Parent=mRNA20
###
1877523	gt csa	gene	44029	44540	.	+	.	ID=gene18
1877523	gt csa	mRNA	44029	44540	.	+	.	ID=mRNA21;Parent=gene18;Target=402959 1 423 +
1877523	gt csa	exon	44029	44263	0.991	+	.	Parent=mRNA21
1877523	gt csa	exon	44354	44540	0.947	+	.	Parent=mRNA21
###
1877523	gt csa	gene	45542	45941	.	-	.	ID=gene19
1877523	gt csa	mRNA	45542	45941	.	-	.	ID=mRNA22;Parent=gene19;Target=8682693 1 322 +,402964 1 388 +
1877523	gt csa	exon	45542	45941	0.924	-	.	Parent=mRNA22
###
1877523	gt csa	gene	45843	45920	.	+	.	ID=gene20
1877523	gt csa	mRNA	45843	45920	.	+	.	ID=mRNA23;Parent=gene20;Target=8720010 1 78 -
1877523	gt csa	exon	45843	45920	0.949	+	.	Parent=mRNA23
###
1877523	gt csa	gene	49874	52242	.	-	.	ID=gene21
1877523	gt csa	mRNA	49874	50547	.	-	.	ID=mRNA24;Parent=gene21;Target=19837290 1 412 +
1877523	gt csa	exon	49874	50284	1	-	.	Parent=mRNA24
1877523	gt csa	exon	50547	50547	1	-	.	Parent=mRNA24
1877523	gt csa	mRNA	50433	52242	.	-	.	ID=mRNA25;Parent=gene21;Target=19807151 1 426 -,8731976 1 441 -,19805724 1 385 -,19866668 1 647 +,2747604 1 362 +,2596256 1 446 +,2596953 1 336 +,5839790 1 404 +,403229 1 350 +,9785390 1 263 +
1877523	gt csa	exon	50433	50834	0.978	-	.	Parent=mRNA25
1877523	gt csa	exon	51113	51216	1	-	.	Parent=mRNA25
1877523	gt csa	exon	51319	51474	1	-	.	Parent=mRNA25
1877523	gt csa	exon	51552	51623	1	-	.	Parent=mRNA25
1877523	gt csa	exon	51711	51758	1	-	.	Parent=mRNA25
1877523	gt csa	exon	51849	51896	1	-	.	Parent=mRNA25
1877523	gt csa	exon	51983	52055	1	-	.	Parent=mRNA25
1877523	gt csa	exon	52163	52242	1	-	.	Parent=mRNA25
###
1877523	gt csa	gene	50475	50702	.	+	.	ID=gene22
1877523	gt csa	mRNA	50475	50702	.	+	.	ID=mRNA26;Parent=gene22;Target=8727457 1 228 +
1877523	gt csa	exon	50475	50702	1	+	.	Parent=mRNA26
###
1877523	gt csa	gene	53602	54829	.	-	.	ID=gene23
1877523	gt csa	mRNA	53602	54829	.	-	.	ID=mRNA27;Parent=gene23;Target=8697180 1 427 -,19803773 1 627 -,19840006 1 413 -,19823046 1 417 -,2393553 57 528 +,19843722 1 431 -,8696505 49 568 +,5839694 1 477 +,9778953 1 365 +,19865963 1 414 +,9784661 1 248 +,933584 1 311 +,8696543 49 319 +
1877523	gt csa	exon	53602	53914	0.994	-	.	Parent=mRNA27
1877523	gt csa	exon	54159	54335	1	-	.	Parent=mRNA27
1877523	gt csa	exon	54574	54829	0.992	-	.	Parent=mRNA27
###
1877523	gt csa	gene	53632	56652	.	+	.	ID=gene24
1877523	gt csa	mRNA	53632	53909	.	+	.	ID=mRNA28;Parent=gene24;Target=8697126 1 279 +
1877523	gt csa	exon	53632	53909	0.991	+	.	Parent=mRNA28
1877523	gt csa	mRNA	54991	56652	.	+	.	ID=mRNA29;Parent=gene24;Target=19874826 1 651 +
1877523	gt csa	exon	54991	55057	0.985	+	.	Parent=mRNA29
1877523	gt csa	exon	55145	55230	1	+	.	Parent=mRNA29
1877523	gt csa	exon	55300	55341	1	+	.	Parent=mRNA29
1877523	gt csa	exon	55453	55498	1	+	.	Parent=mRNA29
1877523	gt csa	exon	55618	55704	1	+	.	Parent=mRNA29
1877523	gt csa	exon	55818	55873	1	+	.	Parent=mRNA29
1877523	gt csa	exon	56036	56153	1	+	.	Parent=mRNA29
1877523	gt csa	exon	56281	56339	1	+	.	Parent=mRNA29
1877523	gt csa	exon	56449	56520	1	+	.	Parent=mRNA29
1877523	gt csa	exon	56635	56652	1	+	.	Parent=mRNA29
###
1877523	gt csa	gene	58115	62646	.	+	.	ID=gene25
1877523	gt csa	mRNA	58115	59001	.	+	.	ID=mRNA30;Parent=gene25;Target=19741042 1 460 -
1877523	gt csa	exon	58115	58209	0.958	+	.	Parent=mRNA30
1877523	gt csa	exon	58461	58526	1	+	.	Parent=mRNA30
1877523	gt csa	exon	58624	58717	1	+	.	Parent=mRNA30
1877523	gt csa	exon	58796	59001	0.983	+	.	Parent=mRNA30
1877523	gt csa	mRNA	59010	59976	.	+	.	ID=mRNA31;Parent=gene25;Target=8715845 1 475 +,19864079 1 653 +,9787190 1 255 +,397215 1 333 +
1877523	gt csa	exon	59010	59526	0.989	+	.	Parent=mRNA31
1877523	gt csa	exon	59607	59976	0.991	+	.	Parent=mRNA31
1877523	gt csa	mRNA	60190	60487	.	+	.	ID=mRNA32;Parent=gene25;Target=398270 1 298 +
1877523	gt csa	exon	60190	60487	0.987	+	.	Parent=mRNA32
1877523	gt csa	mRNA	61186	61974	.	+	.	ID=mRNA33;Parent=gene25;Target=2722481 1 371 +,19837990 1 398 -
1877523	gt csa	exon	61186	61281	0.99	+	.	Parent=mRNA33
1877523	gt csa	exon	61565	61641	1	+	.	Parent=mRNA33
1877523	gt csa	exon	61724	61974	1	+	.	Parent=mRNA33
1877523	gt csa	mRNA	62196	62646	.	+	.	ID=mRNA34;Parent=gene25;Target=2747645 1 448 +
1877523	gt csa	exon	62196	62646	0.921	+	.	Parent=mRNA34
###
1877523	gt csa	gene	60319	61000	.	-	.	ID=gene26
1877523	gt csa	mRNA	60319	61000	.	-	.	ID=mRNA35;Parent=gene26;Target=19801463 1 682 +,8692149 1 559 +,19827386 1 453 +,7610825 1 500 +,8736724 1 496 +,19828552 1 452 +,19838343 1 409 +,397216 1 390 +
1877523	gt csa	exon	60319	61000	0.997	-	.	Parent=mRNA35
###
1877523	gt csa	gene	63106	64320	.	+	.	ID=gene27
1877523	gt csa	mRNA	63106	64320	.	+	.	ID=mRNA36;Parent=gene27;Target=8701755 1 598 -,8735505 1 490 -,19798134 1 412 +,5846657 1 345 +
1877523	gt csa	exon	63106	63178	1	+	.	Parent=mRNA36
1877523	gt csa	exon	63271	63391	1	+	.	Parent=mRNA36
1877523	gt csa	exon	63468	63683	1	+	.	Parent=mRNA36
1877523	gt csa	exon	63755	64320	0.979	+	.	Parent=mRNA36
###
1877523	gt csa	gene	64196	65033	.	-	.	ID=gene28
1877523	gt csa	mRNA	64196	65033	.	-	.	ID=mRNA37;Parent=gene28;Target=19877649 1 632 +
1877523	gt csa	exon	64196	64605	1	-	.	Parent=mRNA37
1877523	gt csa	exon	64812	65033	0.995	-	.	Parent=mRNA37
###
1877523	gt csa	gene	65467	66157	.	+	.	ID=gene29
1877523	gt csa	mRNA	65467	66157	.	+	.	ID=mRNA38;Parent=gene29;Target=19875812 1 621 +
1877523	gt csa	exon	65467	66058	0.992	+	.	Parent=mRNA38
1877523	gt csa	exon	66130	66157	0.964	+	.	Parent=mRNA38
###
1877523	gt csa	gene	67358	68396	.	+	.	ID=gene30
1877523	gt csa	mRNA	67358	68396	.	+	.	ID=mRNA39;Parent=gene30;Target=396603 1 749 +,19742246 1 423 -
1877523	gt csa	exon	67358	67550	1	+	.	Parent=mRNA39
1877523	gt csa	exon	67636	67908	0.969	+	.	Parent=mRNA39
1877523	gt csa	exon	68011	68396	0.99	+	.	Parent=mRNA39
###
1877523	gt csa	gene	69163	70072	.	+	.	ID=gene31
1877523	gt csa	mRNA	69163	69968	.	+	.	ID=mRNA40;Parent=gene31;Target=19872996 1 536 +,19869130 1 603 +,19870921 1 486 +,7612059 1 362 +
1877523	gt csa	exon	69163	69265	0.971	+	.	Parent=mRNA40
1877523	gt csa	exon	69375	69598	1	+	.	Parent=mRNA40
1877523	gt csa	exon	69685	69968	0.996	+	.	Parent=mRNA40
1877523	gt csa	mRNA	69196	70072	.	+	.	ID=mRNA41;Parent=gene31;Target=905849 1 455 +,7612059 1 362 +
1877523	gt csa	exon	69196	69265	0.986	+	.	Parent=mRNA41
1877523	gt csa	exon	69375	69598	1	+	.	Parent=mRNA41
1877523	gt csa	exon	69685	69831	0.816	+	.	Parent=mRNA41
1877523	gt csa	exon	70063	70072	0.4	+	.	Parent=mRNA41
###
1877523	gt csa	gene	71414	72803	.	+	.	ID=gene32
1877523	gt csa	mRNA	71414	72009	.	+	.	ID=mRNA42;Parent=gene32;Target=17520 1 168 +,8734707 1 319 +
1877523	gt csa	exon	71414	71479	1	+	.	Parent=mRNA42
1877523	gt csa	exon	71579	71779	0.985	+	.	Parent=mRNA42
1877523	gt csa	exon	71914	72009	1	+	.	Parent=mRNA42
1877523	gt csa	mRNA	72121	72753	.	+	.	ID=mRNA43;Parent=gene32;Target=2597031 1 221 +,958004 1 484 +,3449674 1 333 +
1877523	gt csa	exon	72121	72753	0.929	+	.	Parent=mRNA43
1877523	gt csa	mRNA	72137	72803	.	+	.	ID=mRNA44;Parent=gene32;Target=1159193 1 351 +,8737761 1 497 -,2749490 79 466 +,7610337 1 466 -,19829297 1 429 -,19829716 1 434 -,19831127 1 431 -,8731753 1 480 -,19839622 1 421 -,2762921 1 237 +,2762922 1 337 +,19825274 1 460 -,19855736 1 420 -,8695920 1 405 -,3449674 1 333 +
1877523	gt csa	exon	72137	72296	1	+	.	Parent=mRNA44
1877523	gt csa	exon	72369	72803	1	+	.	Parent=mRNA44
###
1877523	gt csa	gene	72359	74920	.	-	.	ID=gene33
1877523	gt csa	mRNA	72359	72827	.	-	.	ID=mRNA45;Parent=gene33;Target=19841232 1 443 +,19826275 1 444 +,19834843 1 430 +,19828253 1 431 +,19825742 1 430 +,19828054 1 455 +,19844666 1 418 +,19829934 1 418 +,19842362 1 417 +,19837074 1 417 +,8728304 1 365 +,19827775 1 416 +,19855995 1 403 +,8694120 1 354 +,19831839 1 401 +,19833332 1 405 +,8732348 1 369 +,8695842 1 280 +
1877523	gt csa	exon	72359	72827	0.992	-	.	Parent=mRNA45
1877523	gt csa	mRNA	72390	74046	.	-	.	ID=mRNA46;Parent=gene33;Target=8728304 1 365 +,8694120 1 354 +,2597485 1 163 -
1877523	gt csa	exon	72390	72789	0.978	-	.	Parent=mRNA46
1877523	gt csa	exon	74021	74046	0.615	-	.	Parent=mRNA46
1877523	gt csa	mRNA	72390	74920	.	-	.	ID=mRNA47;Parent=gene33;Target=8728304 1 365 +,8694120 1 354 +,3450080 1 166 -
1877523	gt csa	exon	72390	72800	0.919	-	.	Parent=mRNA47
1877523	gt csa	exon	74901	74920	0.75	-	.	Parent=mRNA47
###
1877523	gt csa	gene	79098	79663	.	-	.	ID=gene34
1877523	gt csa	mRNA	79098	79663	.	-	.	ID=mRNA48;Parent=gene34;Target=19857409 11 314 -
1877523	gt csa	exon	79098	79127	0.767	-	.	Parent=mRNA48
1877523	gt csa	exon	79241	79487	0.866	-	.	Parent=mRNA48
1877523	gt csa	exon	79636	79663	1	-	.	Parent=mRNA48
###
1877523	gt csa	gene	86444	89957	.	-	.	ID=gene35
1877523	gt csa	mRNA	86444	89957	.	-	.	ID=mRNA49;Parent=gene35;Target=19873300 87 582 +
1877523	gt csa	exon	86444	86516	0.767	-	.	Parent=mRNA49
1877523	gt csa	exon	89440	89702	0.683	-	.	Parent=mRNA49
1877523	gt csa	exon	89794	89957	0.823	-	.	Parent=mRNA49
###
1877523	gt csa	gene	90829	91133	.	+	.	ID=gene36
1877523	gt csa	mRNA	90829	91133	.	+	.	ID=mRNA50;Parent=gene36;Target=5845361 1 307 +
1877523	gt csa	exon	90829	91133	0.948	+	.	Parent=mRNA50
###
1877523	gt csa	gene	91050	91786	.	-	.	ID=gene37
1877523	gt csa	mRNA	91050	91786	.	-	.	ID=mRNA51;Parent=gene37;Target=8735154 1 543 -
1877523	gt csa	exon	91050	91401	1	-	.	Parent=mRNA51
1877523	gt csa	exon	91524	91713	1	-	.	Parent=mRNA51
1877523	gt csa	exon	91786	91786	1	-	.	Parent=mRNA51
###
1877523	gt csa	gene	92903	94384	.	-	.	ID=gene38
1877523	gt csa	mRNA	92903	93265	.	-	.	ID=mRNA52;Parent=gene38;Target=9786193 1 266 +
1877523	gt csa	exon	92903	93008	1	-	.	Parent=mRNA52
1877523	gt csa	exon	93106	93265	1	-	.	Parent=mRNA52
1877523	gt csa	mRNA	93551	94384	.	-	.	ID=mRNA53;Parent=gene38;Target=19806050 1 401 -,2047981 81 377 +,19857902 1 407 -
1877523	gt csa	exon	93551	93913	0.957	-	.	Parent=mRNA53
1877523	gt csa	exon	94017	94124	1	-	.	Parent=mRNA53
1877523	gt csa	exon	94367	94384	1	-	.	Parent=mRNA53
###
1877523	gt csa	gene	94706	96614	.	-	.	ID=gene39
1877523	gt csa	mRNA	94706	96614	.	-	.	ID=mRNA54;Parent=gene39;Target=9782167 1 392 +,19866748 1 646 +,9778306 1 422 +,9778321 1 398 +
1877523	gt csa	exon	94706	94771	0.871	-	.	Parent=mRNA54
1877523	gt csa	exon	94877	94985	0.954	-	.	Parent=mRNA54
1877523	gt csa	exon	95071	95147	1	-	.	Parent=mRNA54
1877523	gt csa	exon	95234	95454	1	-	.	Parent=mRNA54
1877523	gt csa	exon	95842	95947	0.991	-	.	Parent=mRNA54
1877523	gt csa	exon	96036	96140	1	-	.	Parent=mRNA54
1877523	gt csa	exon	96232	96330	1	-	.	Parent=mRNA54
1877523	gt csa	exon	96418	96614	0.987	-	.	Parent=mRNA54
###
1877523	gt csa	gene	98857	100804	.	-	.	ID=gene40
1877523	gt csa	mRNA	98857	100804	.	-	.	ID=mRNA55;Parent=gene40;Target=19836538 1 392 -,8737545 1 333 -,2446000 47 535 +,5846455 1 525 -,8734273 1 383 -,397246 1 362 +,19863867 1 661 +,19870774 1 577 +,958152 1 437 +,8732177 1 326 +
1877523	gt csa	exon	98857	99121	1	-	.	Parent=mRNA55
1877523	gt csa	exon	99200	99361	1	-	.	Parent=mRNA55
1877523	gt csa	exon	99443	99511	1	-	.	Parent=mRNA55
1877523	gt csa	exon	99613	99877	1	-	.	Parent=mRNA55
1877523	gt csa	exon	100102	100226	1	-	.	Parent=mRNA55
1877523	gt csa	exon	100327	100434	1	-	.	Parent=mRNA55
1877523	gt csa	exon	100539	100646	1	-	.	Parent=mRNA55
1877523	gt csa	exon	100749	100804	0.982	-	.	Parent=mRNA55
###
1877523	gt csa	gene	103616	106973	.	+	.	ID=gene41
1877523	gt csa	mRNA	103616	105860	.	+	.	ID=mRNA56;Parent=gene41;Target=2580948 1 435 +,8722221 103 366 +,623629 87 375 +,9778203 71 401 +,8731408 68 518 +,937871 1 457 +,9781141 22 358 +,7611662 1 549 -,19801855 1 495 -,8695006 1 452 -,8702125 1 452 -,19825204 1 402 -,2748033 88 460 -,19835442 1 367 -,8734878 1 354 -,19823987 1 352 -,19841468 39 385 -,2747682 1 302 +,2412846 1 302 +,17325 1 277 -,3449578 65 370 +,19859011 1 296 -
1877523	gt csa	exon	103616	103753	0.975	+	.	Parent=mRNA56
1877523	gt csa	exon	103982	104035	0.981	+	.	Parent=mRNA56
1877523	gt csa	exon	104118	104198	0.975	+	.	Parent=mRNA56
1877523	gt csa	exon	104295	104455	0.932	+	.	Parent=mRNA56
1877523	gt csa	exon	104649	104724	0.934	+	.	Parent=mRNA56
1877523	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA56
1877523	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA56
1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA56
1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA56
1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA56
1877523	gt csa	mRNA	103616	105860	.	+	.	ID=mRNA57;Parent=gene41;Target=2580948 1 435 +,2759743 1 460 +,5840051 1 700 +,8722221 103 366 +,623629 87 375 +,9781141 22 358 +,7611662 1 549 -,19801855 1 495 -,8695006 1 452 -,8702125 1 452 -,19825204 1 402 -,2748033 88 460 -,19835442 1 367 -,8734878 1 354 -,19823987 1 352 -,19841468 39 385 -,2747682 1 302 +,2412846 1 302 +,17325 1 277 -,3449578 65 370 +,19859011 1 296 -
1877523	gt csa	exon	103616	103753	1	+	.	Parent=mRNA57
1877523	gt csa	exon	103982	104035	1	+	.	Parent=mRNA57
1877523	gt csa	exon	104118	104198	1	+	.	Parent=mRNA57
1877523	gt csa	exon	104295	104724	0.921	+	.	Parent=mRNA57
1877523	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA57
1877523	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA57
1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA57
1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA57
1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA57
1877523	gt csa	mRNA	103706	105860	.	+	.	ID=mRNA58;Parent=gene41;Target=8686177 99 409 +,453733 78 357 +,9778203 71 401 +,8731408 68 518 +,937871 1 457 +,9781141 22 358 +,7611662 1 549 -,19801855 1 495 -,8695006 1 452 -,8702125 1 452 -,19825204 1 402 -,2748033 88 460 -,19835442 1 367 -,8734878 1 354 -,19823987 1 352 -,19841468 39 385 -,2747682 1 302 +,2412846 1 302 +,17325 1 277 -,3449578 65 370 +,19859011 1 296 -
1877523	gt csa	exon	103706	103731	0.885	+	.	Parent=mRNA58
1877523	gt csa	exon	103799	103826	0.518	+	.	Parent=mRNA58
1877523	gt csa	exon	103982	104035	0.944	+	.	Parent=mRNA58
1877523	gt csa	exon	104118	104198	0.951	+	.	Parent=mRNA58
1877523	gt csa	exon	104295	104455	0.888	+	.	Parent=mRNA58
1877523	gt csa	exon	104649	104724	0.934	+	.	Parent=mRNA58
1877523	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA58
1877523	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA58
1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA58
1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA58
1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA58
1877523	gt csa	mRNA	105009	105860	.	+	.	ID=mRNA59;Parent=gene41;Target=8734901 1 533 -,19801855 1 495 -,8695006 1 452 -,8702125 1 452 -,19825204 1 402 -,2748033 88 460 -,19835442 1 367 -,8734878 1 354 -,19823987 1 352 -,19841468 39 385 -,2747682 1 302 +,2412846 1 302 +,17325 1 277 -,3449578 65 370 +,19859011 1 296 -
1877523	gt csa	exon	105009	105228	0.864	+	.	Parent=mRNA59
1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA59
1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA59
1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA59
1877523	gt csa	mRNA	106097	106973	.	+	.	ID=mRNA60;Parent=gene41;Target=19871766 1 425 +,17300 1 350 +,7612621 1 248 +,935362 1 377 +,936803 1 374 +,7612394 1 366 +,2733258 26 261 +,8729681 1 298 +,2759942 1 130 +,9778889 1 162 +
1877523	gt csa	exon	106097	106290	0.995	+	.	Parent=mRNA60
1877523	gt csa	exon	106566	106619	1	+	.	Parent=mRNA60
1877523	gt csa	exon	106702	106782	1	+	.	Parent=mRNA60
1877523	gt csa	exon	106878	106973	1	+	.	Parent=mRNA60
###
1877523	gt csa	gene	105662	105806	.	-	.	ID=gene42
1877523	gt csa	mRNA	105662	105806	.	-	.	ID=mRNA61;Parent=gene42;Target=8735385 30 173 +
1877523	gt csa	exon	105662	105806	0.855	-	.	Parent=mRNA61
###
genometools-1.5.1/testdata/U89959_csas.gff3md5000066400000000000000000001226541211610345200207110ustar00rootroot00000000000000##gff-version   3
##sequence-region   md5:063b1024d68e26716b7f38caf958316f:1877523 1 106973
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	1074	1540	.	+	.	ID=gene1
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	1074	1540	.	+	.	ID=mRNA1;Parent=gene1;Target=md5:14c0ff5e76ef8ac009fdcc923f701356:8721428 1 303 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	1074	1171	1	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	1259	1354	1	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	1432	1540	1	+	.	Parent=mRNA1
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	2779	3506	.	+	.	ID=gene2
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	2779	3506	.	+	.	ID=mRNA2;Parent=gene2;Target=md5:527995da853a37f9c47e616ce237d523:8732738 1 337 +,md5:a9dcd316817972a94c0af505715b10bc:19843099 1 426 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	2779	2801	0.696	+	.	Parent=mRNA2
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	3043	3506	0.974	+	.	Parent=mRNA2
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	3025	3506	.	+	.	ID=mRNA3;Parent=gene2;Target=md5:f1a0d426e93585553b21aa1a47aa2970:19837778 1 327 +,md5:a9dcd316817972a94c0af505715b10bc:19843099 1 426 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	3025	3506	0.974	+	.	Parent=mRNA3
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	3041	3651	.	-	.	ID=gene3
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	3041	3651	.	-	.	ID=mRNA4;Parent=gene3;Target=md5:cabe5b677d534fb65e0d2245f61e2bd1:8732878 1 536 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	3041	3550	0.996	-	.	Parent=mRNA4
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	3626	3651	1	-	.	Parent=mRNA4
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	4768	5357	.	-	.	ID=gene4
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	4768	5357	.	-	.	ID=mRNA5;Parent=gene4;Target=md5:e40253c45f8d96170d6af32f8d8e3e05:19871046 1 591 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	4768	5357	0.987	-	.	Parent=mRNA5
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	9505	10058	.	+	.	ID=gene5
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	9505	10058	.	+	.	ID=mRNA6;Parent=gene5;Target=md5:f28eda487869903339de7a431f00fccd:8682455 1 554 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	9505	10058	1	+	.	Parent=mRNA6
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	12024	12542	.	-	.	ID=gene6
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	12024	12542	.	-	.	ID=mRNA7;Parent=gene6;Target=md5:300d9c80d9f566412745a6bda32e3e12:8688760 1 519 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	12024	12542	1	-	.	Parent=mRNA7
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	13014	13465	.	-	.	ID=gene7
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	13014	13465	.	-	.	ID=mRNA8;Parent=gene7;Target=md5:c6826f50615c7fb2eb70e294bb7202cb:2748705 1 459 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	13014	13465	0.881	-	.	Parent=mRNA8
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	15955	16603	.	+	.	ID=gene8
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	15955	16603	.	+	.	ID=mRNA9;Parent=gene8;Target=md5:bceada3d0ee38c76dafe93fd74e71dfe:19878194 1 649 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	15955	16603	0.997	+	.	Parent=mRNA9
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	17165	17684	.	+	.	ID=gene9
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	17165	17684	.	+	.	ID=mRNA10;Parent=gene9;Target=md5:8bbc72e5847196327c25661544c6bdf9:19798999 1 396 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	17165	17247	0.97	+	.	Parent=mRNA10
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	17374	17684	0.989	+	.	Parent=mRNA10
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	25221	26100	.	+	.	ID=gene10
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	25221	26100	.	+	.	ID=mRNA11;Parent=gene10;Target=md5:ff7357d7a1877d31d94543a13d64fa0e:8690053 1 521 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	25221	25310	1	+	.	Parent=mRNA11
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	25510	25626	1	+	.	Parent=mRNA11
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	25713	25841	1	+	.	Parent=mRNA11
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	25916	26100	1	+	.	Parent=mRNA11
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	27900	29817	.	+	.	ID=gene11
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	27900	28989	.	+	.	ID=mRNA12;Parent=gene11;Target=md5:c69c15ebe466171a13ee5aa610e90e61:8726341 1 499 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	27900	28003	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	28269	28424	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	28507	28579	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	28686	28753	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	28892	28989	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	28990	29817	.	+	.	ID=mRNA13;Parent=gene11;Target=md5:0870e7d5d9d76766ebd3dce1758b733f:8726286 1 477 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	28990	29037	1	+	.	Parent=mRNA13
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	29134	29242	1	+	.	Parent=mRNA13
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	29331	29477	1	+	.	Parent=mRNA13
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	29571	29618	1	+	.	Parent=mRNA13
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	29693	29817	1	+	.	Parent=mRNA13
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	30278	32362	.	+	.	ID=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	30278	31820	.	+	.	ID=mRNA14;Parent=gene12;Target=md5:97350772e29b7881b149afbedf09290d:8690080 1 524 +,md5:cc954bf1761c4c9f05f8822afb1079e3:8689616 1 333 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	30278	30391	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	30477	30562	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	30658	30763	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	30990	31085	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	31234	31386	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	31538	31720	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	31793	31820	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	31855	32362	.	+	.	ID=mRNA15;Parent=gene12;Target=md5:70facb44682374068ef43fd0a6e116b5:8689215 1 334 +,md5:c7084aa0f01934072f9e244363059ca0:9784594 1 269 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	31855	32022	1	+	.	Parent=mRNA15
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	32118	32220	1	+	.	Parent=mRNA15
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	32300	32362	1	+	.	Parent=mRNA15
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	32928	34560	.	+	.	ID=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	32928	34560	.	+	.	ID=mRNA16;Parent=gene13;Target=md5:4e8ae3a74fefacbbb8650ba892c2b2da:19875482 1 227 +,md5:f53ad09e45a4038f2261b9ee90353658:9782568 1 427 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	32928	32955	1	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	33191	33317	0.98	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	33418	33518	1	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	33783	33917	1	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	33996	34076	1	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	34472	34560	1	+	.	Parent=mRNA16
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	35628	37208	.	+	.	ID=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	35628	37208	.	+	.	ID=mRNA17;Parent=gene14;Target=md5:a7fa97bc84c3aebaea34e169b73094c9:2759121 1 451 +,md5:cdced248d13c7c0f89e7e889cc30164a:5841805 1 479 +,md5:0d914f8b8fdfef05d05e32a617ce8737:8683519 1 604 -,md5:634e9a3d54562a834a900edb41abe7d4:8682814 1 522 -,md5:e24a612b49c52c8aca23eb196c1ebe06:8690927 1 566 -,md5:835eb4298c428885b3d16d0e4514c30b:5845530 1 547 -,md5:b280ddc383280ca975eeaa3329e34c14:8717375 1 521 -,md5:3ff6374febf91a5f28c3f7bcc4ccd774:2048630 53 438 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	35628	35712	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	35820	36011	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	36101	36205	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	36297	36431	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	36521	36721	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	36816	37208	1	+	.	Parent=mRNA17
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	36812	37235	.	-	.	ID=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	36812	37235	.	-	.	ID=mRNA18;Parent=gene15;Target=md5:26ebd521c00f7b4d595086f162ab00e1:8735393 1 424 +,md5:7f0facaa45cacec8ffaa0c98a51edf56:19741846 1 380 +,md5:275dc2512038a6501b7d27e38165bec7:8738747 1 395 +,md5:af2486ba93823b9389100222c0ddffdb:8679389 1 133 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	36812	37235	0.998	-	.	Parent=mRNA18
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	37669	40032	.	-	.	ID=gene16
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	37669	40032	.	-	.	ID=mRNA19;Parent=gene16;Target=md5:b1da76b1bfdf36225429a5be70ff88a2:8738841 1 588 -,md5:354c93700a73d01ea73f641c62c593cd:19831991 1 401 -,md5:f42df1d200fb31e1bed322fab31540d6:19840745 1 390 -,md5:f55d7bcc44b78111563b02f8a19805ee:5843191 1 490 -,md5:a3f1555a0375aea877145c8c372ae4af:19869427 1 606 +,md5:a5f947d297585356da9380d22ac8c974:8722075 1 568 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	37669	37891	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	37972	38060	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	38656	38794	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	38927	38997	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	39104	39148	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	39239	39328	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	39438	39526	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	39614	39689	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	39798	40032	0.996	-	.	Parent=mRNA19
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	42783	43204	.	-	.	ID=gene17
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	42783	43204	.	-	.	ID=mRNA20;Parent=gene17;Target=md5:bdc426cd84a477b9b48d7e7d1538fc85:19858773 1 422 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	42783	43204	1	-	.	Parent=mRNA20
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	44029	44540	.	+	.	ID=gene18
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	44029	44540	.	+	.	ID=mRNA21;Parent=gene18;Target=md5:0f6d1e4ce29d042b5804f8ae8bd9c43a:402959 1 423 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	44029	44263	0.991	+	.	Parent=mRNA21
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	44354	44540	0.947	+	.	Parent=mRNA21
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	45542	45941	.	-	.	ID=gene19
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	45542	45941	.	-	.	ID=mRNA22;Parent=gene19;Target=md5:7ba0b8c1bb50abf3c5a844abacf9fe67:8682693 1 322 +,md5:38229ac075d9c6d15fd1152c4eccc834:402964 1 388 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	45542	45941	0.924	-	.	Parent=mRNA22
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	45843	45920	.	+	.	ID=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	45843	45920	.	+	.	ID=mRNA23;Parent=gene20;Target=md5:6d3b4b9db4531cda588528f2c69c0a57:8720010 1 78 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	45843	45920	0.949	+	.	Parent=mRNA23
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	49874	52242	.	-	.	ID=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	49874	50547	.	-	.	ID=mRNA24;Parent=gene21;Target=md5:494051ed1147d22a2b2967b64c329678:19837290 1 412 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	49874	50284	1	-	.	Parent=mRNA24
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	50547	50547	1	-	.	Parent=mRNA24
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	50433	52242	.	-	.	ID=mRNA25;Parent=gene21;Target=md5:634ef96163dc4d4f8a585fe8059d867b:19807151 1 426 -,md5:754b35896aef0625da39ee42e61db715:8731976 1 441 -,md5:741ff4d6dd193d77cc75fb61f373ca5b:19805724 1 385 -,md5:597ada174987f3f2f0b2e4046f09247d:19866668 1 647 +,md5:8fdc30d821ff25b48b6182936cf72cd5:2747604 1 362 +,md5:26e5980fbaaefb58d84de6755d521845:2596256 1 446 +,md5:d342e4ee66b1c4db3e83e076c5dd7d44:2596953 1 336 +,md5:7f11e59ff50ce68b25c6120418df3d51:5839790 1 404 +,md5:b0183ab4aa646b9e8f95f61daf0e23a3:403229 1 350 +,md5:8ed84d5653334535562a21058880db81:9785390 1 263 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	50433	50834	0.978	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	51113	51216	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	51319	51474	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	51552	51623	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	51711	51758	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	51849	51896	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	51983	52055	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	52163	52242	1	-	.	Parent=mRNA25
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	50475	50702	.	+	.	ID=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	50475	50702	.	+	.	ID=mRNA26;Parent=gene22;Target=md5:950b7715ab6cc030a8c810a0dba2dd33:8727457 1 228 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	50475	50702	1	+	.	Parent=mRNA26
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	53602	54829	.	-	.	ID=gene23
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	53602	54829	.	-	.	ID=mRNA27;Parent=gene23;Target=md5:16258f1ad08d9c0c91c627eefad05949:8697180 1 427 -,md5:2642a22855698a3125c99a9759f9147c:19803773 1 627 -,md5:752fa8c75ecef45cfa9cf0c5a59afe49:19840006 1 413 -,md5:0743a82e324754dfc94ed4c0cd8a8816:19823046 1 417 -,md5:198a4aa7626135303d0e996d4e2775ef:2393553 57 528 +,md5:f692730f2bd8700f690f8a231d2e446b:19843722 1 431 -,md5:18fb5ebf5d11ec1db0d36de3ea2a049d:8696505 49 568 +,md5:ed9e14d2b83e7ea606c9d1d5fdbeb857:5839694 1 477 +,md5:7db3e698f27f19f0343e6b23af07a5b3:9778953 1 365 +,md5:6021387359d7e25495b6b804ebbbb0aa:19865963 1 414 +,md5:72f3e9cbd94835f59aa0a43b22a01b0f:9784661 1 248 +,md5:2fa0ef57b1f4391f7a2ae4283410311c:933584 1 311 +,md5:215d14a53287c2aca2d8bd12b09aca14:8696543 49 319 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	53602	53914	0.994	-	.	Parent=mRNA27
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	54159	54335	1	-	.	Parent=mRNA27
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	54574	54829	0.992	-	.	Parent=mRNA27
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	53632	56652	.	+	.	ID=gene24
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	53632	53909	.	+	.	ID=mRNA28;Parent=gene24;Target=md5:5a03dd7605925c94812a9550acc2d354:8697126 1 279 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	53632	53909	0.991	+	.	Parent=mRNA28
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	54991	56652	.	+	.	ID=mRNA29;Parent=gene24;Target=md5:dd287e28fe668e94028c1a241a6a1c7d:19874826 1 651 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	54991	55057	0.985	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	55145	55230	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	55300	55341	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	55453	55498	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	55618	55704	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	55818	55873	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	56036	56153	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	56281	56339	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	56449	56520	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	56635	56652	1	+	.	Parent=mRNA29
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	58115	62646	.	+	.	ID=gene25
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	58115	59001	.	+	.	ID=mRNA30;Parent=gene25;Target=md5:a12796a152e829b54f2f56b4910d701c:19741042 1 460 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	58115	58209	0.958	+	.	Parent=mRNA30
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	58461	58526	1	+	.	Parent=mRNA30
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	58624	58717	1	+	.	Parent=mRNA30
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	58796	59001	0.983	+	.	Parent=mRNA30
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	59010	59976	.	+	.	ID=mRNA31;Parent=gene25;Target=md5:cc404517a12f1a399ab48b948f4e71ff:8715845 1 475 +,md5:33eefc92073ab38229f0ce775746b219:19864079 1 653 +,md5:cdbabc0602366c37167aba18498d8232:9787190 1 255 +,md5:e72969c46cd2e7d078d339cda62260a8:397215 1 333 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	59010	59526	0.989	+	.	Parent=mRNA31
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	59607	59976	0.991	+	.	Parent=mRNA31
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	60190	60487	.	+	.	ID=mRNA32;Parent=gene25;Target=md5:322e03bbf0f0ddac43d4ca12dd0cc795:398270 1 298 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	60190	60487	0.987	+	.	Parent=mRNA32
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	61186	61974	.	+	.	ID=mRNA33;Parent=gene25;Target=md5:3ab44e284886cca199c6a4d221725734:2722481 1 371 +,md5:f63fe9c59e53d9587766136a15864412:19837990 1 398 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	61186	61281	0.99	+	.	Parent=mRNA33
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	61565	61641	1	+	.	Parent=mRNA33
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	61724	61974	1	+	.	Parent=mRNA33
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	62196	62646	.	+	.	ID=mRNA34;Parent=gene25;Target=md5:77ba8b822b44308184b4dcab6ecfa75e:2747645 1 448 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	62196	62646	0.921	+	.	Parent=mRNA34
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	60319	61000	.	-	.	ID=gene26
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	60319	61000	.	-	.	ID=mRNA35;Parent=gene26;Target=md5:c94289917098254e5d5b7c3ed48e81b7:19801463 1 682 +,md5:48f4c66f41d3805c7213639bcb949d6a:8692149 1 559 +,md5:1b775af1ef6f8f8b80ba60a8245cba0b:19827386 1 453 +,md5:2acbf49eaca817b303d60c7c22dfdd15:7610825 1 500 +,md5:9b6924737e47f2eed133a565b35dd804:8736724 1 496 +,md5:653662b06e7e300256655269264f4004:19828552 1 452 +,md5:81a8f87434a337a21077462e2a1cb5c9:19838343 1 409 +,md5:1634572862a7fc3d7dcb1ca5950cf137:397216 1 390 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	60319	61000	0.997	-	.	Parent=mRNA35
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	63106	64320	.	+	.	ID=gene27
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	63106	64320	.	+	.	ID=mRNA36;Parent=gene27;Target=md5:c4e23aeca494361878d3407ae5c05e3d:8701755 1 598 -,md5:bbbbef70abd153db9376c364e9fafbae:8735505 1 490 -,md5:67e8b62becffff524bac4f51bfa344e1:19798134 1 412 +,md5:3b10d6f56bfea7b6b57a41146f6c140b:5846657 1 345 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	63106	63178	1	+	.	Parent=mRNA36
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	63271	63391	1	+	.	Parent=mRNA36
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	63468	63683	1	+	.	Parent=mRNA36
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	63755	64320	0.979	+	.	Parent=mRNA36
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	64196	65033	.	-	.	ID=gene28
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	64196	65033	.	-	.	ID=mRNA37;Parent=gene28;Target=md5:e5089d2bdb42934617cd38749662eb21:19877649 1 632 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	64196	64605	1	-	.	Parent=mRNA37
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	64812	65033	0.995	-	.	Parent=mRNA37
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	65467	66157	.	+	.	ID=gene29
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	65467	66157	.	+	.	ID=mRNA38;Parent=gene29;Target=md5:f19b5223816de3060184fb9250936fce:19875812 1 621 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	65467	66058	0.992	+	.	Parent=mRNA38
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	66130	66157	0.964	+	.	Parent=mRNA38
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	67358	68396	.	+	.	ID=gene30
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	67358	68396	.	+	.	ID=mRNA39;Parent=gene30;Target=md5:893d07af699d973ed4e8e3423fc87165:396603 1 749 +,md5:3b9295d3ee44af4cf4f79b2e27003f1b:19742246 1 423 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	67358	67550	1	+	.	Parent=mRNA39
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	67636	67908	0.969	+	.	Parent=mRNA39
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	68011	68396	0.99	+	.	Parent=mRNA39
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	69163	70072	.	+	.	ID=gene31
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	69163	69968	.	+	.	ID=mRNA40;Parent=gene31;Target=md5:79435902b3753af094ba24f8a4847978:19872996 1 536 +,md5:811cb37790973c1b417241d62fe2a569:19869130 1 603 +,md5:bce4ec40fb993e1733ea6d2d16398ed0:19870921 1 486 +,md5:979a4ec86ab17d2a4625c90ed575c145:7612059 1 362 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	69163	69265	0.971	+	.	Parent=mRNA40
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	69375	69598	1	+	.	Parent=mRNA40
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	69685	69968	0.996	+	.	Parent=mRNA40
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	69196	70072	.	+	.	ID=mRNA41;Parent=gene31;Target=md5:49b16de93b5b34374e7e2a7e71253124:905849 1 455 +,md5:979a4ec86ab17d2a4625c90ed575c145:7612059 1 362 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	69196	69265	0.986	+	.	Parent=mRNA41
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	69375	69598	1	+	.	Parent=mRNA41
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	69685	69831	0.816	+	.	Parent=mRNA41
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	70063	70072	0.4	+	.	Parent=mRNA41
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	71414	72803	.	+	.	ID=gene32
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	71414	72009	.	+	.	ID=mRNA42;Parent=gene32;Target=md5:e311a17e67c458d42ed86de05242f87b:17520 1 168 +,md5:1f44f865b53e6414d5296a088f0a75e7:8734707 1 319 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	71414	71479	1	+	.	Parent=mRNA42
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	71579	71779	0.985	+	.	Parent=mRNA42
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	71914	72009	1	+	.	Parent=mRNA42
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	72121	72753	.	+	.	ID=mRNA43;Parent=gene32;Target=md5:7d5ceada204939fc948a837d482fe57c:2597031 1 221 +,md5:a8b76267e5f1749ca29c5465c631ab8e:958004 1 484 +,md5:b7056f0f128b406b094ebf5cb33fb74f:3449674 1 333 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	72121	72753	0.929	+	.	Parent=mRNA43
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	72137	72803	.	+	.	ID=mRNA44;Parent=gene32;Target=md5:7882e88f260382672a97918b652cad4a:1159193 1 351 +,md5:fa15dcef7c84118ca9ee3f95600132c8:8737761 1 497 -,md5:03636fa4a9e17baae04ad57d13cdc386:2749490 79 466 +,md5:9a5ec5d4597ac1be9d10ba63ecc457c1:7610337 1 466 -,md5:df066a65ac8236486c7d59f90157d43e:19829297 1 429 -,md5:ace313cc0542136c91ac52da3c676d77:19829716 1 434 -,md5:2d0e152a577c91a47f0b5781e67cd3b0:19831127 1 431 -,md5:6db92a6a61672ceedb192c31b975e370:8731753 1 480 -,md5:14f58b2b12e291455a69d48e56728992:19839622 1 421 -,md5:1c07f0f3b1115fb653b7f47df5b1344b:2762921 1 237 +,md5:061cac88caefa5d8bba4a1ff47031dc3:2762922 1 337 +,md5:9b19d8ea196896df9be4cf56b285abf2:19825274 1 460 -,md5:a179a430866ce2f2826fec132cd9e71f:19855736 1 420 -,md5:b2925aa2103833c4c0e3e2ba4e27e66f:8695920 1 405 -,md5:b7056f0f128b406b094ebf5cb33fb74f:3449674 1 333 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	72137	72296	1	+	.	Parent=mRNA44
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	72369	72803	1	+	.	Parent=mRNA44
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	72359	74920	.	-	.	ID=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	72359	72827	.	-	.	ID=mRNA45;Parent=gene33;Target=md5:80d8c2289eb0b45dd9ab395572f44eae:19841232 1 443 +,md5:3c0dc775fc37af77e71cd10a45d4723c:19826275 1 444 +,md5:f2f65df067412c3be8da37366e71763f:19834843 1 430 +,md5:faf314d3fa8ba5d3d99734b83ebb7f7b:19828253 1 431 +,md5:897eae7810009eb141a5f887289d95c8:19825742 1 430 +,md5:e252994eb503f22fdc871a97738a525a:19828054 1 455 +,md5:11f83a01fda0f6e2061e6e17dc9cc0fe:19844666 1 418 +,md5:8e8cf2914e87c5de17ca1cea5185961d:19829934 1 418 +,md5:c39b7a42d0e463287ec636842fe38b67:19842362 1 417 +,md5:dc0b347c18391d65d897b1c1f14bc31f:19837074 1 417 +,md5:5a9fcf1a7370455e62e2701803939c8e:8728304 1 365 +,md5:3f342edcab14d21711f3d75e3ff81743:19827775 1 416 +,md5:a3891b57fd37552bdad1be4e20266a5a:19855995 1 403 +,md5:cc7281740fd5e50cb1f19a22a728e790:8694120 1 354 +,md5:b9d8ea84787a6573a7bd2acdb795af44:19831839 1 401 +,md5:d056310e74cdfca4f2f5de040aabc6c6:19833332 1 405 +,md5:fd4ec29ab7c96a341ad546c954b7f557:8732348 1 369 +,md5:fd65d023d2d6b71c478da3cfa418cbbc:8695842 1 280 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	72359	72827	0.992	-	.	Parent=mRNA45
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	72390	74046	.	-	.	ID=mRNA46;Parent=gene33;Target=md5:5a9fcf1a7370455e62e2701803939c8e:8728304 1 365 +,md5:cc7281740fd5e50cb1f19a22a728e790:8694120 1 354 +,md5:2c08f2fc011c03e5aa709690db242c3b:2597485 1 163 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	72390	72789	0.978	-	.	Parent=mRNA46
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	74021	74046	0.615	-	.	Parent=mRNA46
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	72390	74920	.	-	.	ID=mRNA47;Parent=gene33;Target=md5:5a9fcf1a7370455e62e2701803939c8e:8728304 1 365 +,md5:cc7281740fd5e50cb1f19a22a728e790:8694120 1 354 +,md5:44f49124e83c2c61713d3c50b3a9a47c:3450080 1 166 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	72390	72800	0.919	-	.	Parent=mRNA47
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	74901	74920	0.75	-	.	Parent=mRNA47
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	79098	79663	.	-	.	ID=gene34
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	79098	79663	.	-	.	ID=mRNA48;Parent=gene34;Target=md5:e7ffec1ba9f35a3e29c9946f86b8fe72:19857409 11 314 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	79098	79127	0.767	-	.	Parent=mRNA48
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	79241	79487	0.866	-	.	Parent=mRNA48
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	79636	79663	1	-	.	Parent=mRNA48
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	86444	89957	.	-	.	ID=gene35
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	86444	89957	.	-	.	ID=mRNA49;Parent=gene35;Target=md5:2276b4a96eb715159638ed0f90239b89:19873300 87 582 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	86444	86516	0.767	-	.	Parent=mRNA49
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	89440	89702	0.683	-	.	Parent=mRNA49
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	89794	89957	0.823	-	.	Parent=mRNA49
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	90829	91133	.	+	.	ID=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	90829	91133	.	+	.	ID=mRNA50;Parent=gene36;Target=md5:88e24a075574a85734a081b57a7ec852:5845361 1 307 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	90829	91133	0.948	+	.	Parent=mRNA50
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	91050	91786	.	-	.	ID=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	91050	91786	.	-	.	ID=mRNA51;Parent=gene37;Target=md5:b18a91dba09f9ffefbe7b4a6aed19945:8735154 1 543 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	91050	91401	1	-	.	Parent=mRNA51
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	91524	91713	1	-	.	Parent=mRNA51
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	91786	91786	1	-	.	Parent=mRNA51
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	92903	94384	.	-	.	ID=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	92903	93265	.	-	.	ID=mRNA52;Parent=gene38;Target=md5:ddbfcce4683cac59087c5f26e674349b:9786193 1 266 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	92903	93008	1	-	.	Parent=mRNA52
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	93106	93265	1	-	.	Parent=mRNA52
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	93551	94384	.	-	.	ID=mRNA53;Parent=gene38;Target=md5:d9d61048b8d25d868bda7f00a0831100:19806050 1 401 -,md5:a0d33d57c705a829d80c318c595fcccb:2047981 81 377 +,md5:41d17c6950c12d0d8ec2b305108f08ac:19857902 1 407 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	93551	93913	0.957	-	.	Parent=mRNA53
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	94017	94124	1	-	.	Parent=mRNA53
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	94367	94384	1	-	.	Parent=mRNA53
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	94706	96614	.	-	.	ID=gene39
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	94706	96614	.	-	.	ID=mRNA54;Parent=gene39;Target=md5:da4c1ce6a2ee20bb9c4c5d9462be98de:9782167 1 392 +,md5:c9a4247a29baa59833607fc71f58bb40:19866748 1 646 +,md5:e6343ecf374a95dd0356831650af82f1:9778306 1 422 +,md5:29b2d16dd6ee3e8669ae77b4e053ee20:9778321 1 398 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	94706	94771	0.871	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	94877	94985	0.954	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	95071	95147	1	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	95234	95454	1	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	95842	95947	0.991	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	96036	96140	1	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	96232	96330	1	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	96418	96614	0.987	-	.	Parent=mRNA54
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	98857	100804	.	-	.	ID=gene40
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	98857	100804	.	-	.	ID=mRNA55;Parent=gene40;Target=md5:4a2861ff4a54b0b8a099c7ca178c113f:19836538 1 392 -,md5:432d83294aa0f2f3fc1b7673977ea4d1:8737545 1 333 -,md5:50590ee6555b56ad95151d25d300c6fe:2446000 47 535 +,md5:08f77d13c4ad88c1c44c0314426f2218:5846455 1 525 -,md5:d75212b190b11adfcbc1b62e6d392ed1:8734273 1 383 -,md5:dd3ace06137c29bf383632984aadf8af:397246 1 362 +,md5:eaca300e106a2e1c1897455c6a2cb618:19863867 1 661 +,md5:1fd1b5316d6ec8962be7986ceebf3ce6:19870774 1 577 +,md5:8bfbb0491705b51d42ef6d8ba0c3e2ef:958152 1 437 +,md5:8e46b5509ea749211c8c5cacdc1e2500:8732177 1 326 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	98857	99121	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	99200	99361	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	99443	99511	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	99613	99877	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	100102	100226	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	100327	100434	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	100539	100646	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	100749	100804	0.982	-	.	Parent=mRNA55
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	103616	106973	.	+	.	ID=gene41
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	103616	105860	.	+	.	ID=mRNA56;Parent=gene41;Target=md5:0c4c41ad6668fd55d5f1140088f1064d:2580948 1 435 +,md5:b9155494bf5b0de513f322e685542888:8722221 103 366 +,md5:0e851efbbe2bfb244a388865f785495d:623629 87 375 +,md5:f1cb6a33be382d29ff291be589f1ed70:9778203 71 401 +,md5:b289385ff9ca374ceb056d5950d090b5:8731408 68 518 +,md5:ddab1d6f7c76a6508e85423cd56d46e5:937871 1 457 +,md5:257d2dc2f7c0bb730fe685a8052aaa63:9781141 22 358 +,md5:649b4501a3ba1d922dce7b623c7f6de9:7611662 1 549 -,md5:c24d4bd4c7cae864049bd096522750b1:19801855 1 495 -,md5:52b0aff6e54274ccb35b371b7630b68a:8695006 1 452 -,md5:085f029e3f483828cb30f70b141fa58a:8702125 1 452 -,md5:174d324a9dca8baddcdcd0dbef55f969:19825204 1 402 -,md5:0920b24475a189fbfc148593eec03cb6:2748033 88 460 -,md5:15ed737c8deffb63f79d93a8fecb5a93:19835442 1 367 -,md5:f8e9d021f04423c2ad6499f4ce6eca57:8734878 1 354 -,md5:a45d1a65f8024adcc2ce8bdcdfb36569:19823987 1 352 -,md5:07c4180bd9082b53416a778fee66e3f3:19841468 39 385 -,md5:15adef11b8ee98d85e7a5e3106495193:2747682 1 302 +,md5:f74aca5cee266c7bc442898be20363ae:2412846 1 302 +,md5:5db2b668ce1df476a932c078b6e77122:17325 1 277 -,md5:e6338114b6c0dcc78811d3be5b36ff63:3449578 65 370 +,md5:940e92280507db531e4654cc1f1054ef:19859011 1 296 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	103616	103753	0.975	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	103982	104035	0.981	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104118	104198	0.975	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104295	104455	0.932	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104649	104724	0.934	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	103616	105860	.	+	.	ID=mRNA57;Parent=gene41;Target=md5:0c4c41ad6668fd55d5f1140088f1064d:2580948 1 435 +,md5:d4793f2935cfa07221be201386cb079b:2759743 1 460 +,md5:e47b883ccda180d280195029954ea7f5:5840051 1 700 +,md5:b9155494bf5b0de513f322e685542888:8722221 103 366 +,md5:0e851efbbe2bfb244a388865f785495d:623629 87 375 +,md5:257d2dc2f7c0bb730fe685a8052aaa63:9781141 22 358 +,md5:649b4501a3ba1d922dce7b623c7f6de9:7611662 1 549 -,md5:c24d4bd4c7cae864049bd096522750b1:19801855 1 495 -,md5:52b0aff6e54274ccb35b371b7630b68a:8695006 1 452 -,md5:085f029e3f483828cb30f70b141fa58a:8702125 1 452 -,md5:174d324a9dca8baddcdcd0dbef55f969:19825204 1 402 -,md5:0920b24475a189fbfc148593eec03cb6:2748033 88 460 -,md5:15ed737c8deffb63f79d93a8fecb5a93:19835442 1 367 -,md5:f8e9d021f04423c2ad6499f4ce6eca57:8734878 1 354 -,md5:a45d1a65f8024adcc2ce8bdcdfb36569:19823987 1 352 -,md5:07c4180bd9082b53416a778fee66e3f3:19841468 39 385 -,md5:15adef11b8ee98d85e7a5e3106495193:2747682 1 302 +,md5:f74aca5cee266c7bc442898be20363ae:2412846 1 302 +,md5:5db2b668ce1df476a932c078b6e77122:17325 1 277 -,md5:e6338114b6c0dcc78811d3be5b36ff63:3449578 65 370 +,md5:940e92280507db531e4654cc1f1054ef:19859011 1 296 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	103616	103753	1	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	103982	104035	1	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104118	104198	1	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104295	104724	0.921	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	103706	105860	.	+	.	ID=mRNA58;Parent=gene41;Target=md5:41ccefe046c76c005c6f83a09aac40de:8686177 99 409 +,md5:556ae7f08b7cc887b54786f0bc100dd4:453733 78 357 +,md5:f1cb6a33be382d29ff291be589f1ed70:9778203 71 401 +,md5:b289385ff9ca374ceb056d5950d090b5:8731408 68 518 +,md5:ddab1d6f7c76a6508e85423cd56d46e5:937871 1 457 +,md5:257d2dc2f7c0bb730fe685a8052aaa63:9781141 22 358 +,md5:649b4501a3ba1d922dce7b623c7f6de9:7611662 1 549 -,md5:c24d4bd4c7cae864049bd096522750b1:19801855 1 495 -,md5:52b0aff6e54274ccb35b371b7630b68a:8695006 1 452 -,md5:085f029e3f483828cb30f70b141fa58a:8702125 1 452 -,md5:174d324a9dca8baddcdcd0dbef55f969:19825204 1 402 -,md5:0920b24475a189fbfc148593eec03cb6:2748033 88 460 -,md5:15ed737c8deffb63f79d93a8fecb5a93:19835442 1 367 -,md5:f8e9d021f04423c2ad6499f4ce6eca57:8734878 1 354 -,md5:a45d1a65f8024adcc2ce8bdcdfb36569:19823987 1 352 -,md5:07c4180bd9082b53416a778fee66e3f3:19841468 39 385 -,md5:15adef11b8ee98d85e7a5e3106495193:2747682 1 302 +,md5:f74aca5cee266c7bc442898be20363ae:2412846 1 302 +,md5:5db2b668ce1df476a932c078b6e77122:17325 1 277 -,md5:e6338114b6c0dcc78811d3be5b36ff63:3449578 65 370 +,md5:940e92280507db531e4654cc1f1054ef:19859011 1 296 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	103706	103731	0.885	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	103799	103826	0.518	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	103982	104035	0.944	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104118	104198	0.951	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104295	104455	0.888	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104649	104724	0.934	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	105009	105860	.	+	.	ID=mRNA59;Parent=gene41;Target=md5:c6730817f9a41f80296421e6b7da6f25:8734901 1 533 -,md5:c24d4bd4c7cae864049bd096522750b1:19801855 1 495 -,md5:52b0aff6e54274ccb35b371b7630b68a:8695006 1 452 -,md5:085f029e3f483828cb30f70b141fa58a:8702125 1 452 -,md5:174d324a9dca8baddcdcd0dbef55f969:19825204 1 402 -,md5:0920b24475a189fbfc148593eec03cb6:2748033 88 460 -,md5:15ed737c8deffb63f79d93a8fecb5a93:19835442 1 367 -,md5:f8e9d021f04423c2ad6499f4ce6eca57:8734878 1 354 -,md5:a45d1a65f8024adcc2ce8bdcdfb36569:19823987 1 352 -,md5:07c4180bd9082b53416a778fee66e3f3:19841468 39 385 -,md5:15adef11b8ee98d85e7a5e3106495193:2747682 1 302 +,md5:f74aca5cee266c7bc442898be20363ae:2412846 1 302 +,md5:5db2b668ce1df476a932c078b6e77122:17325 1 277 -,md5:e6338114b6c0dcc78811d3be5b36ff63:3449578 65 370 +,md5:940e92280507db531e4654cc1f1054ef:19859011 1 296 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105009	105228	0.864	+	.	Parent=mRNA59
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA59
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105500	105535	1	+	.	Parent=mRNA59
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA59
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	106097	106973	.	+	.	ID=mRNA60;Parent=gene41;Target=md5:1adc4b78b212af1a83a6460bd27222f0:19871766 1 425 +,md5:21c1b9817f74d01695e650726543cfbc:17300 1 350 +,md5:c446b7e0b708aafe5473ef397e104ae3:7612621 1 248 +,md5:5b0a1904c2c8e69fe643091fee181037:935362 1 377 +,md5:11a2689b92ee76c83cd57591ae940971:936803 1 374 +,md5:d1a97200c69d88855784612802e7c024:7612394 1 366 +,md5:5ae608a9518c5417787d0da5f4dc93b7:2733258 26 261 +,md5:7be43cab2c3d57b779ea0f8ceeacfc0c:8729681 1 298 +,md5:802e6347770300a7bbc0064a90f1f061:2759942 1 130 +,md5:e5c6d7f52bae4b6b57c6320ef95f9b66:9778889 1 162 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	106097	106290	0.995	+	.	Parent=mRNA60
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	106566	106619	1	+	.	Parent=mRNA60
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	106702	106782	1	+	.	Parent=mRNA60
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	106878	106973	1	+	.	Parent=mRNA60
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	gene	105662	105806	.	-	.	ID=gene42
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	mRNA	105662	105806	.	-	.	ID=mRNA61;Parent=gene42;Target=md5:816e83d74c3a633c3ccc005f1c14d55a:8735385 30 173 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gt csa	exon	105662	105806	0.855	-	.	Parent=mRNA61
###
genometools-1.5.1/testdata/U89959_csas.gff3md5old000066400000000000000000001117221211610345200214020ustar00rootroot00000000000000##gff-version   3
##sequence-region   md5:063b1024d68e26716b7f38caf958316f 1 106973
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	1074	1540	.	+	.	ID=gene1
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	1074	1540	.	+	.	ID=mRNA1;Parent=gene1;Target=md5:14c0ff5e76ef8ac009fdcc923f701356 1 303 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	1074	1171	1	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	1259	1354	1	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	1432	1540	1	+	.	Parent=mRNA1
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	2779	3506	.	+	.	ID=gene2
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	2779	3506	.	+	.	ID=mRNA2;Parent=gene2;Target=md5:527995da853a37f9c47e616ce237d523 1 337 +,md5:a9dcd316817972a94c0af505715b10bc 1 426 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	2779	2801	0.696	+	.	Parent=mRNA2
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	3043	3506	0.974	+	.	Parent=mRNA2
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	3025	3506	.	+	.	ID=mRNA3;Parent=gene2;Target=md5:f1a0d426e93585553b21aa1a47aa2970 1 327 +,md5:a9dcd316817972a94c0af505715b10bc 1 426 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	3025	3506	0.974	+	.	Parent=mRNA3
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	3041	3651	.	-	.	ID=gene3
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	3041	3651	.	-	.	ID=mRNA4;Parent=gene3;Target=md5:cabe5b677d534fb65e0d2245f61e2bd1 1 536 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	3041	3550	0.996	-	.	Parent=mRNA4
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	3626	3651	1	-	.	Parent=mRNA4
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	4768	5357	.	-	.	ID=gene4
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	4768	5357	.	-	.	ID=mRNA5;Parent=gene4;Target=md5:e40253c45f8d96170d6af32f8d8e3e05 1 591 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	4768	5357	0.987	-	.	Parent=mRNA5
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	9505	10058	.	+	.	ID=gene5
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	9505	10058	.	+	.	ID=mRNA6;Parent=gene5;Target=md5:f28eda487869903339de7a431f00fccd 1 554 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	9505	10058	1	+	.	Parent=mRNA6
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	12024	12542	.	-	.	ID=gene6
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	12024	12542	.	-	.	ID=mRNA7;Parent=gene6;Target=md5:300d9c80d9f566412745a6bda32e3e12 1 519 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	12024	12542	1	-	.	Parent=mRNA7
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	13014	13465	.	-	.	ID=gene7
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	13014	13465	.	-	.	ID=mRNA8;Parent=gene7;Target=md5:c6826f50615c7fb2eb70e294bb7202cb 1 459 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	13014	13465	0.881	-	.	Parent=mRNA8
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	15955	16603	.	+	.	ID=gene8
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	15955	16603	.	+	.	ID=mRNA9;Parent=gene8;Target=md5:bceada3d0ee38c76dafe93fd74e71dfe 1 649 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	15955	16603	0.997	+	.	Parent=mRNA9
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	17165	17684	.	+	.	ID=gene9
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	17165	17684	.	+	.	ID=mRNA10;Parent=gene9;Target=md5:8bbc72e5847196327c25661544c6bdf9 1 396 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	17165	17247	0.97	+	.	Parent=mRNA10
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	17374	17684	0.989	+	.	Parent=mRNA10
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	25221	26100	.	+	.	ID=gene10
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	25221	26100	.	+	.	ID=mRNA11;Parent=gene10;Target=md5:ff7357d7a1877d31d94543a13d64fa0e 1 521 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	25221	25310	1	+	.	Parent=mRNA11
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	25510	25626	1	+	.	Parent=mRNA11
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	25713	25841	1	+	.	Parent=mRNA11
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	25916	26100	1	+	.	Parent=mRNA11
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	27900	29817	.	+	.	ID=gene11
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	27900	28989	.	+	.	ID=mRNA12;Parent=gene11;Target=md5:c69c15ebe466171a13ee5aa610e90e61 1 499 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	27900	28003	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	28269	28424	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	28507	28579	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	28686	28753	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	28892	28989	1	+	.	Parent=mRNA12
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	28990	29817	.	+	.	ID=mRNA13;Parent=gene11;Target=md5:0870e7d5d9d76766ebd3dce1758b733f 1 477 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	28990	29037	1	+	.	Parent=mRNA13
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	29134	29242	1	+	.	Parent=mRNA13
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	29331	29477	1	+	.	Parent=mRNA13
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	29571	29618	1	+	.	Parent=mRNA13
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	29693	29817	1	+	.	Parent=mRNA13
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	30278	32362	.	+	.	ID=gene12
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	30278	31820	.	+	.	ID=mRNA14;Parent=gene12;Target=md5:97350772e29b7881b149afbedf09290d 1 524 +,md5:cc954bf1761c4c9f05f8822afb1079e3 1 333 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	30278	30391	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	30477	30562	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	30658	30763	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	30990	31085	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	31234	31386	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	31538	31720	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	31793	31820	1	+	.	Parent=mRNA14
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	31855	32362	.	+	.	ID=mRNA15;Parent=gene12;Target=md5:70facb44682374068ef43fd0a6e116b5 1 334 +,md5:c7084aa0f01934072f9e244363059ca0 1 269 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	31855	32022	1	+	.	Parent=mRNA15
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	32118	32220	1	+	.	Parent=mRNA15
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	32300	32362	1	+	.	Parent=mRNA15
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	32928	34560	.	+	.	ID=gene13
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	32928	34560	.	+	.	ID=mRNA16;Parent=gene13;Target=md5:4e8ae3a74fefacbbb8650ba892c2b2da 1 227 +,md5:f53ad09e45a4038f2261b9ee90353658 1 427 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	32928	32955	1	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	33191	33317	0.98	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	33418	33518	1	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	33783	33917	1	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	33996	34076	1	+	.	Parent=mRNA16
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	34472	34560	1	+	.	Parent=mRNA16
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	35628	37208	.	+	.	ID=gene14
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	35628	37208	.	+	.	ID=mRNA17;Parent=gene14;Target=md5:a7fa97bc84c3aebaea34e169b73094c9 1 451 +,md5:cdced248d13c7c0f89e7e889cc30164a 1 479 +,md5:0d914f8b8fdfef05d05e32a617ce8737 1 604 -,md5:634e9a3d54562a834a900edb41abe7d4 1 522 -,md5:e24a612b49c52c8aca23eb196c1ebe06 1 566 -,md5:835eb4298c428885b3d16d0e4514c30b 1 547 -,md5:b280ddc383280ca975eeaa3329e34c14 1 521 -,md5:3ff6374febf91a5f28c3f7bcc4ccd774 53 438 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	35628	35712	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	35820	36011	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	36101	36205	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	36297	36431	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	36521	36721	1	+	.	Parent=mRNA17
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	36816	37208	1	+	.	Parent=mRNA17
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	36812	37235	.	-	.	ID=gene15
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	36812	37235	.	-	.	ID=mRNA18;Parent=gene15;Target=md5:26ebd521c00f7b4d595086f162ab00e1 1 424 +,md5:7f0facaa45cacec8ffaa0c98a51edf56 1 380 +,md5:275dc2512038a6501b7d27e38165bec7 1 395 +,md5:af2486ba93823b9389100222c0ddffdb 1 133 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	36812	37235	0.998	-	.	Parent=mRNA18
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	37669	40032	.	-	.	ID=gene16
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	37669	40032	.	-	.	ID=mRNA19;Parent=gene16;Target=md5:b1da76b1bfdf36225429a5be70ff88a2 1 588 -,md5:354c93700a73d01ea73f641c62c593cd 1 401 -,md5:f42df1d200fb31e1bed322fab31540d6 1 390 -,md5:f55d7bcc44b78111563b02f8a19805ee 1 490 -,md5:a3f1555a0375aea877145c8c372ae4af 1 606 +,md5:a5f947d297585356da9380d22ac8c974 1 568 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	37669	37891	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	37972	38060	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	38656	38794	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	38927	38997	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	39104	39148	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	39239	39328	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	39438	39526	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	39614	39689	1	-	.	Parent=mRNA19
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	39798	40032	0.996	-	.	Parent=mRNA19
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	42783	43204	.	-	.	ID=gene17
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	42783	43204	.	-	.	ID=mRNA20;Parent=gene17;Target=md5:bdc426cd84a477b9b48d7e7d1538fc85 1 422 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	42783	43204	1	-	.	Parent=mRNA20
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	44029	44540	.	+	.	ID=gene18
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	44029	44540	.	+	.	ID=mRNA21;Parent=gene18;Target=md5:0f6d1e4ce29d042b5804f8ae8bd9c43a 1 423 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	44029	44263	0.991	+	.	Parent=mRNA21
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	44354	44540	0.947	+	.	Parent=mRNA21
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	45542	45941	.	-	.	ID=gene19
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	45542	45941	.	-	.	ID=mRNA22;Parent=gene19;Target=md5:7ba0b8c1bb50abf3c5a844abacf9fe67 1 322 +,md5:38229ac075d9c6d15fd1152c4eccc834 1 388 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	45542	45941	0.924	-	.	Parent=mRNA22
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	45843	45920	.	+	.	ID=gene20
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	45843	45920	.	+	.	ID=mRNA23;Parent=gene20;Target=md5:6d3b4b9db4531cda588528f2c69c0a57 1 78 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	45843	45920	0.949	+	.	Parent=mRNA23
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	49874	52242	.	-	.	ID=gene21
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	49874	50547	.	-	.	ID=mRNA24;Parent=gene21;Target=md5:494051ed1147d22a2b2967b64c329678 1 412 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	49874	50284	1	-	.	Parent=mRNA24
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	50547	50547	1	-	.	Parent=mRNA24
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	50433	52242	.	-	.	ID=mRNA25;Parent=gene21;Target=md5:634ef96163dc4d4f8a585fe8059d867b 1 426 -,md5:754b35896aef0625da39ee42e61db715 1 441 -,md5:741ff4d6dd193d77cc75fb61f373ca5b 1 385 -,md5:597ada174987f3f2f0b2e4046f09247d 1 647 +,md5:8fdc30d821ff25b48b6182936cf72cd5 1 362 +,md5:26e5980fbaaefb58d84de6755d521845 1 446 +,md5:d342e4ee66b1c4db3e83e076c5dd7d44 1 336 +,md5:7f11e59ff50ce68b25c6120418df3d51 1 404 +,md5:b0183ab4aa646b9e8f95f61daf0e23a3 1 350 +,md5:8ed84d5653334535562a21058880db81 1 263 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	50433	50834	0.978	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	51113	51216	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	51319	51474	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	51552	51623	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	51711	51758	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	51849	51896	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	51983	52055	1	-	.	Parent=mRNA25
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	52163	52242	1	-	.	Parent=mRNA25
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	50475	50702	.	+	.	ID=gene22
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	50475	50702	.	+	.	ID=mRNA26;Parent=gene22;Target=md5:950b7715ab6cc030a8c810a0dba2dd33 1 228 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	50475	50702	1	+	.	Parent=mRNA26
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	53602	54829	.	-	.	ID=gene23
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	53602	54829	.	-	.	ID=mRNA27;Parent=gene23;Target=md5:16258f1ad08d9c0c91c627eefad05949 1 427 -,md5:2642a22855698a3125c99a9759f9147c 1 627 -,md5:752fa8c75ecef45cfa9cf0c5a59afe49 1 413 -,md5:0743a82e324754dfc94ed4c0cd8a8816 1 417 -,md5:198a4aa7626135303d0e996d4e2775ef 57 528 +,md5:f692730f2bd8700f690f8a231d2e446b 1 431 -,md5:18fb5ebf5d11ec1db0d36de3ea2a049d 49 568 +,md5:ed9e14d2b83e7ea606c9d1d5fdbeb857 1 477 +,md5:7db3e698f27f19f0343e6b23af07a5b3 1 365 +,md5:6021387359d7e25495b6b804ebbbb0aa 1 414 +,md5:72f3e9cbd94835f59aa0a43b22a01b0f 1 248 +,md5:2fa0ef57b1f4391f7a2ae4283410311c 1 311 +,md5:215d14a53287c2aca2d8bd12b09aca14 49 319 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	53602	53914	0.994	-	.	Parent=mRNA27
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	54159	54335	1	-	.	Parent=mRNA27
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	54574	54829	0.992	-	.	Parent=mRNA27
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	53632	56652	.	+	.	ID=gene24
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	53632	53909	.	+	.	ID=mRNA28;Parent=gene24;Target=md5:5a03dd7605925c94812a9550acc2d354 1 279 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	53632	53909	0.991	+	.	Parent=mRNA28
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	54991	56652	.	+	.	ID=mRNA29;Parent=gene24;Target=md5:dd287e28fe668e94028c1a241a6a1c7d 1 651 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	54991	55057	0.985	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	55145	55230	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	55300	55341	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	55453	55498	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	55618	55704	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	55818	55873	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	56036	56153	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	56281	56339	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	56449	56520	1	+	.	Parent=mRNA29
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	56635	56652	1	+	.	Parent=mRNA29
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	58115	62646	.	+	.	ID=gene25
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	58115	59001	.	+	.	ID=mRNA30;Parent=gene25;Target=md5:a12796a152e829b54f2f56b4910d701c 1 460 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	58115	58209	0.958	+	.	Parent=mRNA30
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	58461	58526	1	+	.	Parent=mRNA30
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	58624	58717	1	+	.	Parent=mRNA30
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	58796	59001	0.983	+	.	Parent=mRNA30
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	59010	59976	.	+	.	ID=mRNA31;Parent=gene25;Target=md5:cc404517a12f1a399ab48b948f4e71ff 1 475 +,md5:33eefc92073ab38229f0ce775746b219 1 653 +,md5:cdbabc0602366c37167aba18498d8232 1 255 +,md5:e72969c46cd2e7d078d339cda62260a8 1 333 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	59010	59526	0.989	+	.	Parent=mRNA31
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	59607	59976	0.991	+	.	Parent=mRNA31
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	60190	60487	.	+	.	ID=mRNA32;Parent=gene25;Target=md5:322e03bbf0f0ddac43d4ca12dd0cc795 1 298 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	60190	60487	0.987	+	.	Parent=mRNA32
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	61186	61974	.	+	.	ID=mRNA33;Parent=gene25;Target=md5:3ab44e284886cca199c6a4d221725734 1 371 +,md5:f63fe9c59e53d9587766136a15864412 1 398 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	61186	61281	0.99	+	.	Parent=mRNA33
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	61565	61641	1	+	.	Parent=mRNA33
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	61724	61974	1	+	.	Parent=mRNA33
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	62196	62646	.	+	.	ID=mRNA34;Parent=gene25;Target=md5:77ba8b822b44308184b4dcab6ecfa75e 1 448 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	62196	62646	0.921	+	.	Parent=mRNA34
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	60319	61000	.	-	.	ID=gene26
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	60319	61000	.	-	.	ID=mRNA35;Parent=gene26;Target=md5:c94289917098254e5d5b7c3ed48e81b7 1 682 +,md5:48f4c66f41d3805c7213639bcb949d6a 1 559 +,md5:1b775af1ef6f8f8b80ba60a8245cba0b 1 453 +,md5:2acbf49eaca817b303d60c7c22dfdd15 1 500 +,md5:9b6924737e47f2eed133a565b35dd804 1 496 +,md5:653662b06e7e300256655269264f4004 1 452 +,md5:81a8f87434a337a21077462e2a1cb5c9 1 409 +,md5:1634572862a7fc3d7dcb1ca5950cf137 1 390 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	60319	61000	0.997	-	.	Parent=mRNA35
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	63106	64320	.	+	.	ID=gene27
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	63106	64320	.	+	.	ID=mRNA36;Parent=gene27;Target=md5:c4e23aeca494361878d3407ae5c05e3d 1 598 -,md5:bbbbef70abd153db9376c364e9fafbae 1 490 -,md5:67e8b62becffff524bac4f51bfa344e1 1 412 +,md5:3b10d6f56bfea7b6b57a41146f6c140b 1 345 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	63106	63178	1	+	.	Parent=mRNA36
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	63271	63391	1	+	.	Parent=mRNA36
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	63468	63683	1	+	.	Parent=mRNA36
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	63755	64320	0.979	+	.	Parent=mRNA36
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	64196	65033	.	-	.	ID=gene28
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	64196	65033	.	-	.	ID=mRNA37;Parent=gene28;Target=md5:e5089d2bdb42934617cd38749662eb21 1 632 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	64196	64605	1	-	.	Parent=mRNA37
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	64812	65033	0.995	-	.	Parent=mRNA37
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	65467	66157	.	+	.	ID=gene29
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	65467	66157	.	+	.	ID=mRNA38;Parent=gene29;Target=md5:f19b5223816de3060184fb9250936fce 1 621 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	65467	66058	0.992	+	.	Parent=mRNA38
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	66130	66157	0.964	+	.	Parent=mRNA38
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	67358	68396	.	+	.	ID=gene30
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	67358	68396	.	+	.	ID=mRNA39;Parent=gene30;Target=md5:893d07af699d973ed4e8e3423fc87165 1 749 +,md5:3b9295d3ee44af4cf4f79b2e27003f1b 1 423 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	67358	67550	1	+	.	Parent=mRNA39
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	67636	67908	0.969	+	.	Parent=mRNA39
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	68011	68396	0.99	+	.	Parent=mRNA39
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	69163	70072	.	+	.	ID=gene31
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	69163	69968	.	+	.	ID=mRNA40;Parent=gene31;Target=md5:79435902b3753af094ba24f8a4847978 1 536 +,md5:811cb37790973c1b417241d62fe2a569 1 603 +,md5:bce4ec40fb993e1733ea6d2d16398ed0 1 486 +,md5:979a4ec86ab17d2a4625c90ed575c145 1 362 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	69163	69265	0.971	+	.	Parent=mRNA40
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	69375	69598	1	+	.	Parent=mRNA40
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	69685	69968	0.996	+	.	Parent=mRNA40
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	69196	70072	.	+	.	ID=mRNA41;Parent=gene31;Target=md5:49b16de93b5b34374e7e2a7e71253124 1 455 +,md5:979a4ec86ab17d2a4625c90ed575c145 1 362 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	69196	69265	0.986	+	.	Parent=mRNA41
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	69375	69598	1	+	.	Parent=mRNA41
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	69685	69831	0.816	+	.	Parent=mRNA41
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	70063	70072	0.4	+	.	Parent=mRNA41
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	71414	72803	.	+	.	ID=gene32
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	71414	72009	.	+	.	ID=mRNA42;Parent=gene32;Target=md5:e311a17e67c458d42ed86de05242f87b 1 168 +,md5:1f44f865b53e6414d5296a088f0a75e7 1 319 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	71414	71479	1	+	.	Parent=mRNA42
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	71579	71779	0.985	+	.	Parent=mRNA42
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	71914	72009	1	+	.	Parent=mRNA42
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	72121	72753	.	+	.	ID=mRNA43;Parent=gene32;Target=md5:7d5ceada204939fc948a837d482fe57c 1 221 +,md5:a8b76267e5f1749ca29c5465c631ab8e 1 484 +,md5:b7056f0f128b406b094ebf5cb33fb74f 1 333 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	72121	72753	0.929	+	.	Parent=mRNA43
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	72137	72803	.	+	.	ID=mRNA44;Parent=gene32;Target=md5:7882e88f260382672a97918b652cad4a 1 351 +,md5:fa15dcef7c84118ca9ee3f95600132c8 1 497 -,md5:03636fa4a9e17baae04ad57d13cdc386 79 466 +,md5:9a5ec5d4597ac1be9d10ba63ecc457c1 1 466 -,md5:df066a65ac8236486c7d59f90157d43e 1 429 -,md5:ace313cc0542136c91ac52da3c676d77 1 434 -,md5:2d0e152a577c91a47f0b5781e67cd3b0 1 431 -,md5:6db92a6a61672ceedb192c31b975e370 1 480 -,md5:14f58b2b12e291455a69d48e56728992 1 421 -,md5:1c07f0f3b1115fb653b7f47df5b1344b 1 237 +,md5:061cac88caefa5d8bba4a1ff47031dc3 1 337 +,md5:9b19d8ea196896df9be4cf56b285abf2 1 460 -,md5:a179a430866ce2f2826fec132cd9e71f 1 420 -,md5:b2925aa2103833c4c0e3e2ba4e27e66f 1 405 -,md5:b7056f0f128b406b094ebf5cb33fb74f 1 333 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	72137	72296	1	+	.	Parent=mRNA44
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	72369	72803	1	+	.	Parent=mRNA44
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	72359	74920	.	-	.	ID=gene33
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	72359	72827	.	-	.	ID=mRNA45;Parent=gene33;Target=md5:80d8c2289eb0b45dd9ab395572f44eae 1 443 +,md5:3c0dc775fc37af77e71cd10a45d4723c 1 444 +,md5:f2f65df067412c3be8da37366e71763f 1 430 +,md5:faf314d3fa8ba5d3d99734b83ebb7f7b 1 431 +,md5:897eae7810009eb141a5f887289d95c8 1 430 +,md5:e252994eb503f22fdc871a97738a525a 1 455 +,md5:11f83a01fda0f6e2061e6e17dc9cc0fe 1 418 +,md5:8e8cf2914e87c5de17ca1cea5185961d 1 418 +,md5:c39b7a42d0e463287ec636842fe38b67 1 417 +,md5:dc0b347c18391d65d897b1c1f14bc31f 1 417 +,md5:5a9fcf1a7370455e62e2701803939c8e 1 365 +,md5:3f342edcab14d21711f3d75e3ff81743 1 416 +,md5:a3891b57fd37552bdad1be4e20266a5a 1 403 +,md5:cc7281740fd5e50cb1f19a22a728e790 1 354 +,md5:b9d8ea84787a6573a7bd2acdb795af44 1 401 +,md5:d056310e74cdfca4f2f5de040aabc6c6 1 405 +,md5:fd4ec29ab7c96a341ad546c954b7f557 1 369 +,md5:fd65d023d2d6b71c478da3cfa418cbbc 1 280 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	72359	72827	0.992	-	.	Parent=mRNA45
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	72390	74046	.	-	.	ID=mRNA46;Parent=gene33;Target=md5:5a9fcf1a7370455e62e2701803939c8e 1 365 +,md5:cc7281740fd5e50cb1f19a22a728e790 1 354 +,md5:2c08f2fc011c03e5aa709690db242c3b 1 163 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	72390	72789	0.978	-	.	Parent=mRNA46
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	74021	74046	0.615	-	.	Parent=mRNA46
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	72390	74920	.	-	.	ID=mRNA47;Parent=gene33;Target=md5:5a9fcf1a7370455e62e2701803939c8e 1 365 +,md5:cc7281740fd5e50cb1f19a22a728e790 1 354 +,md5:44f49124e83c2c61713d3c50b3a9a47c 1 166 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	72390	72800	0.919	-	.	Parent=mRNA47
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	74901	74920	0.75	-	.	Parent=mRNA47
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	79098	79663	.	-	.	ID=gene34
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	79098	79663	.	-	.	ID=mRNA48;Parent=gene34;Target=md5:e7ffec1ba9f35a3e29c9946f86b8fe72 11 314 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	79098	79127	0.767	-	.	Parent=mRNA48
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	79241	79487	0.866	-	.	Parent=mRNA48
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	79636	79663	1	-	.	Parent=mRNA48
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	86444	89957	.	-	.	ID=gene35
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	86444	89957	.	-	.	ID=mRNA49;Parent=gene35;Target=md5:2276b4a96eb715159638ed0f90239b89 87 582 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	86444	86516	0.767	-	.	Parent=mRNA49
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	89440	89702	0.683	-	.	Parent=mRNA49
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	89794	89957	0.823	-	.	Parent=mRNA49
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	90829	91133	.	+	.	ID=gene36
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	90829	91133	.	+	.	ID=mRNA50;Parent=gene36;Target=md5:88e24a075574a85734a081b57a7ec852 1 307 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	90829	91133	0.948	+	.	Parent=mRNA50
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	91050	91786	.	-	.	ID=gene37
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	91050	91786	.	-	.	ID=mRNA51;Parent=gene37;Target=md5:b18a91dba09f9ffefbe7b4a6aed19945 1 543 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	91050	91401	1	-	.	Parent=mRNA51
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	91524	91713	1	-	.	Parent=mRNA51
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	91786	91786	1	-	.	Parent=mRNA51
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	92903	94384	.	-	.	ID=gene38
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	92903	93265	.	-	.	ID=mRNA52;Parent=gene38;Target=md5:ddbfcce4683cac59087c5f26e674349b 1 266 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	92903	93008	1	-	.	Parent=mRNA52
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	93106	93265	1	-	.	Parent=mRNA52
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	93551	94384	.	-	.	ID=mRNA53;Parent=gene38;Target=md5:d9d61048b8d25d868bda7f00a0831100 1 401 -,md5:a0d33d57c705a829d80c318c595fcccb 81 377 +,md5:41d17c6950c12d0d8ec2b305108f08ac 1 407 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	93551	93913	0.957	-	.	Parent=mRNA53
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	94017	94124	1	-	.	Parent=mRNA53
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	94367	94384	1	-	.	Parent=mRNA53
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	94706	96614	.	-	.	ID=gene39
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	94706	96614	.	-	.	ID=mRNA54;Parent=gene39;Target=md5:da4c1ce6a2ee20bb9c4c5d9462be98de 1 392 +,md5:c9a4247a29baa59833607fc71f58bb40 1 646 +,md5:e6343ecf374a95dd0356831650af82f1 1 422 +,md5:29b2d16dd6ee3e8669ae77b4e053ee20 1 398 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	94706	94771	0.871	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	94877	94985	0.954	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	95071	95147	1	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	95234	95454	1	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	95842	95947	0.991	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	96036	96140	1	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	96232	96330	1	-	.	Parent=mRNA54
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	96418	96614	0.987	-	.	Parent=mRNA54
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	98857	100804	.	-	.	ID=gene40
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	98857	100804	.	-	.	ID=mRNA55;Parent=gene40;Target=md5:4a2861ff4a54b0b8a099c7ca178c113f 1 392 -,md5:432d83294aa0f2f3fc1b7673977ea4d1 1 333 -,md5:50590ee6555b56ad95151d25d300c6fe 47 535 +,md5:08f77d13c4ad88c1c44c0314426f2218 1 525 -,md5:d75212b190b11adfcbc1b62e6d392ed1 1 383 -,md5:dd3ace06137c29bf383632984aadf8af 1 362 +,md5:eaca300e106a2e1c1897455c6a2cb618 1 661 +,md5:1fd1b5316d6ec8962be7986ceebf3ce6 1 577 +,md5:8bfbb0491705b51d42ef6d8ba0c3e2ef 1 437 +,md5:8e46b5509ea749211c8c5cacdc1e2500 1 326 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	98857	99121	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	99200	99361	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	99443	99511	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	99613	99877	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	100102	100226	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	100327	100434	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	100539	100646	1	-	.	Parent=mRNA55
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	100749	100804	0.982	-	.	Parent=mRNA55
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	103616	106973	.	+	.	ID=gene41
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	103616	105860	.	+	.	ID=mRNA56;Parent=gene41;Target=md5:0c4c41ad6668fd55d5f1140088f1064d 1 435 +,md5:b9155494bf5b0de513f322e685542888 103 366 +,md5:0e851efbbe2bfb244a388865f785495d 87 375 +,md5:f1cb6a33be382d29ff291be589f1ed70 71 401 +,md5:b289385ff9ca374ceb056d5950d090b5 68 518 +,md5:ddab1d6f7c76a6508e85423cd56d46e5 1 457 +,md5:257d2dc2f7c0bb730fe685a8052aaa63 22 358 +,md5:649b4501a3ba1d922dce7b623c7f6de9 1 549 -,md5:c24d4bd4c7cae864049bd096522750b1 1 495 -,md5:52b0aff6e54274ccb35b371b7630b68a 1 452 -,md5:085f029e3f483828cb30f70b141fa58a 1 452 -,md5:174d324a9dca8baddcdcd0dbef55f969 1 402 -,md5:0920b24475a189fbfc148593eec03cb6 88 460 -,md5:15ed737c8deffb63f79d93a8fecb5a93 1 367 -,md5:f8e9d021f04423c2ad6499f4ce6eca57 1 354 -,md5:a45d1a65f8024adcc2ce8bdcdfb36569 1 352 -,md5:07c4180bd9082b53416a778fee66e3f3 39 385 -,md5:15adef11b8ee98d85e7a5e3106495193 1 302 +,md5:f74aca5cee266c7bc442898be20363ae 1 302 +,md5:5db2b668ce1df476a932c078b6e77122 1 277 -,md5:e6338114b6c0dcc78811d3be5b36ff63 65 370 +,md5:940e92280507db531e4654cc1f1054ef 1 296 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	103616	103753	0.975	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	103982	104035	0.981	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104118	104198	0.975	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104295	104455	0.932	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104649	104724	0.934	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105500	105535	1	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA56
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	103616	105860	.	+	.	ID=mRNA57;Parent=gene41;Target=md5:0c4c41ad6668fd55d5f1140088f1064d 1 435 +,md5:d4793f2935cfa07221be201386cb079b 1 460 +,md5:e47b883ccda180d280195029954ea7f5 1 700 +,md5:b9155494bf5b0de513f322e685542888 103 366 +,md5:0e851efbbe2bfb244a388865f785495d 87 375 +,md5:257d2dc2f7c0bb730fe685a8052aaa63 22 358 +,md5:649b4501a3ba1d922dce7b623c7f6de9 1 549 -,md5:c24d4bd4c7cae864049bd096522750b1 1 495 -,md5:52b0aff6e54274ccb35b371b7630b68a 1 452 -,md5:085f029e3f483828cb30f70b141fa58a 1 452 -,md5:174d324a9dca8baddcdcd0dbef55f969 1 402 -,md5:0920b24475a189fbfc148593eec03cb6 88 460 -,md5:15ed737c8deffb63f79d93a8fecb5a93 1 367 -,md5:f8e9d021f04423c2ad6499f4ce6eca57 1 354 -,md5:a45d1a65f8024adcc2ce8bdcdfb36569 1 352 -,md5:07c4180bd9082b53416a778fee66e3f3 39 385 -,md5:15adef11b8ee98d85e7a5e3106495193 1 302 +,md5:f74aca5cee266c7bc442898be20363ae 1 302 +,md5:5db2b668ce1df476a932c078b6e77122 1 277 -,md5:e6338114b6c0dcc78811d3be5b36ff63 65 370 +,md5:940e92280507db531e4654cc1f1054ef 1 296 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	103616	103753	1	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	103982	104035	1	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104118	104198	1	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104295	104724	0.921	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105500	105535	1	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA57
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	103706	105860	.	+	.	ID=mRNA58;Parent=gene41;Target=md5:41ccefe046c76c005c6f83a09aac40de 99 409 +,md5:556ae7f08b7cc887b54786f0bc100dd4 78 357 +,md5:f1cb6a33be382d29ff291be589f1ed70 71 401 +,md5:b289385ff9ca374ceb056d5950d090b5 68 518 +,md5:ddab1d6f7c76a6508e85423cd56d46e5 1 457 +,md5:257d2dc2f7c0bb730fe685a8052aaa63 22 358 +,md5:649b4501a3ba1d922dce7b623c7f6de9 1 549 -,md5:c24d4bd4c7cae864049bd096522750b1 1 495 -,md5:52b0aff6e54274ccb35b371b7630b68a 1 452 -,md5:085f029e3f483828cb30f70b141fa58a 1 452 -,md5:174d324a9dca8baddcdcd0dbef55f969 1 402 -,md5:0920b24475a189fbfc148593eec03cb6 88 460 -,md5:15ed737c8deffb63f79d93a8fecb5a93 1 367 -,md5:f8e9d021f04423c2ad6499f4ce6eca57 1 354 -,md5:a45d1a65f8024adcc2ce8bdcdfb36569 1 352 -,md5:07c4180bd9082b53416a778fee66e3f3 39 385 -,md5:15adef11b8ee98d85e7a5e3106495193 1 302 +,md5:f74aca5cee266c7bc442898be20363ae 1 302 +,md5:5db2b668ce1df476a932c078b6e77122 1 277 -,md5:e6338114b6c0dcc78811d3be5b36ff63 65 370 +,md5:940e92280507db531e4654cc1f1054ef 1 296 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	103706	103731	0.885	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	103799	103826	0.518	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	103982	104035	0.944	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104118	104198	0.951	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104295	104455	0.888	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104649	104724	0.934	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	104803	104928	0.841	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105010	105228	0.863	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105500	105535	1	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA58
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	105009	105860	.	+	.	ID=mRNA59;Parent=gene41;Target=md5:c6730817f9a41f80296421e6b7da6f25 1 533 -,md5:c24d4bd4c7cae864049bd096522750b1 1 495 -,md5:52b0aff6e54274ccb35b371b7630b68a 1 452 -,md5:085f029e3f483828cb30f70b141fa58a 1 452 -,md5:174d324a9dca8baddcdcd0dbef55f969 1 402 -,md5:0920b24475a189fbfc148593eec03cb6 88 460 -,md5:15ed737c8deffb63f79d93a8fecb5a93 1 367 -,md5:f8e9d021f04423c2ad6499f4ce6eca57 1 354 -,md5:a45d1a65f8024adcc2ce8bdcdfb36569 1 352 -,md5:07c4180bd9082b53416a778fee66e3f3 39 385 -,md5:15adef11b8ee98d85e7a5e3106495193 1 302 +,md5:f74aca5cee266c7bc442898be20363ae 1 302 +,md5:5db2b668ce1df476a932c078b6e77122 1 277 -,md5:e6338114b6c0dcc78811d3be5b36ff63 65 370 +,md5:940e92280507db531e4654cc1f1054ef 1 296 -
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105009	105228	0.864	+	.	Parent=mRNA59
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105315	105428	0.912	+	.	Parent=mRNA59
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105500	105535	1	+	.	Parent=mRNA59
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105630	105860	0.827	+	.	Parent=mRNA59
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	106097	106973	.	+	.	ID=mRNA60;Parent=gene41;Target=md5:1adc4b78b212af1a83a6460bd27222f0 1 425 +,md5:21c1b9817f74d01695e650726543cfbc 1 350 +,md5:c446b7e0b708aafe5473ef397e104ae3 1 248 +,md5:5b0a1904c2c8e69fe643091fee181037 1 377 +,md5:11a2689b92ee76c83cd57591ae940971 1 374 +,md5:d1a97200c69d88855784612802e7c024 1 366 +,md5:5ae608a9518c5417787d0da5f4dc93b7 26 261 +,md5:7be43cab2c3d57b779ea0f8ceeacfc0c 1 298 +,md5:802e6347770300a7bbc0064a90f1f061 1 130 +,md5:e5c6d7f52bae4b6b57c6320ef95f9b66 1 162 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	106097	106290	0.995	+	.	Parent=mRNA60
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	106566	106619	1	+	.	Parent=mRNA60
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	106702	106782	1	+	.	Parent=mRNA60
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	106878	106973	1	+	.	Parent=mRNA60
###
md5:063b1024d68e26716b7f38caf958316f	gt csa	gene	105662	105806	.	-	.	ID=gene42
md5:063b1024d68e26716b7f38caf958316f	gt csa	mRNA	105662	105806	.	-	.	ID=mRNA61;Parent=gene42;Target=md5:816e83d74c3a633c3ccc005f1c14d55a 30 173 +
md5:063b1024d68e26716b7f38caf958316f	gt csa	exon	105662	105806	0.855	-	.	Parent=mRNA61
###
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897eae7810009eb141a5f887289d95c8
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8bfbb0491705b51d42ef6d8ba0c3e2ef
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9a5ec5d4597ac1be9d10ba63ecc457c1
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ff7357d7a1877d31d94543a13d64fa0e
genometools-1.5.1/testdata/U89959_ests.fas000066400000000000000000002775411211610345200202620ustar00rootroot00000000000000>gi|8690080|dbj|AV529797.1|AV529797 AV529797 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL48c08R 5', mRNA sequence
ACTAATACTTTGATGGATGAGGAGAAAGTAGCAACTCTTGGCTTGCCAGAACAGCTCCCG
TCACCTCAAGGACTGTTCCAGTCAACTCCATCGCCATTGTTTTCTATTAGTCAGCTGTCA
GCAGCACTTCCCAATATTGGAAATCATGTTGTTATCAATCAGAAATTAAGCGCATTTGGT
ATGCACTTTCCATTTCAAAGAGTGGTACCACTTGCCATGGACAGAGCTATCAAGGAGATT
GTGTCTGGTATTGTTCAGCGAAGTGTTTGTATTGCATGCCAAACAACAAAGGAGCTTGTG
CTAAAGGATTACGCCCTGGAACCCGATGAGTCACGTATTTATAATGCAGCTCACTTGATG
GTTGCGAGTTTAGCTGGGAGTTTGGCTCATGTGACTTGCAAGGAACCCCTGCGCACTTCA
ATATCCGGTCATCTACGGAATTCGCTTCAGGGTCTGAATATTTCAAATGATGCTCTTGAA
CAAATTGTGCAACTTGTCACCAATGACAACCTGGATTTGGGTTG
>gi|8690053|dbj|AV529770.1|AV529770 AV529770 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL47a02R 5', mRNA sequence
ACTGTAGCCCTTGGTTCCTGCATTCCAACTGAACTTCCCACGCCAAGGTCGTGGAATGTT
GATATTCTAGTTGACACAATCAAGCAGCTTCAGGCTCCTGGCATAAGCTGGAGGAAAGTA
ATTGAGAATCTCGATCATGACGGATTTGACATCCCTAATATGGAGTCTTTCTCATTTTTT
ATGCGGATCTATAAAGCTGCTTGCAAGGAGCCATTTCCTCTTGATGCTGTATGTGGTTCT
GTCTGGAAAAATATGGATGGTCAATTATCCTTTCTTAAGCACGCAATATCTGCTCCACCA
GAAGTATTCACCTTTATGCATTCTCCAAGGAAGCTGGTATATATTGATAACATGCACAGC
CAAGAGCAACAGTTAGGACTATCCAATCATGCATGGCTGTCGCTCGATCTCTTGGATGTA
CTGTGCCAATTGGCCGAGAGAGGTCATGCTGTTTTAGTTAGTTCGTTACTCCAGTATCCA
CTCACACAGTGTCCTAGAACCTTGCTTCTTGGAATGACACA
>gi|8689616|dbj|AV529333.1|AV529333 AV529333 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL34a01R 5', mRNA sequence
TACGGAATTCGCTTCAGGGTCTGAATATTTCAAATGATGCTCTTGAACAAATTGTGCAAC
TTGTCACCAATGACAACCTGGATTTGGGTTGTGCTGCTATTGAACAGGCTGCTACAGAAA
AGGCAATACAAACAATTGATGCGGACATTGCTCAACAATTGTTGTTACGGAGAAAGCATA
GAGATGGTGCTGGATCCTCCTTTTTCGATCCAAACATTCTATCACAGAATTCCGTCAGTT
TTATACCCGAATCCCTCCGTCCAAAACCTGGACACCTCTCCCTGTCTCAGCAGAGAGTTT
ATGAGGACTTTGTTCAACATCCTTGGCAAAAGC
>gi|8689215|dbj|AV528932.1|AV528932 AV528932 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL23a03R 5', mRNA sequence
ATCAAGCTCATCTGGTGATGTTGCGCTTGGTAGTGGTTATGGTCCAGTATCAGGAAAAGT
TGCTTCTGAATTTTTGTCTAATGCTGGAAACGCTCGGATGGACATGGTCTCCCGGCCATC
AGATATTTCTGTGGATGGTTTTGAATCTTCTCCAGTCTCACTTTTGAGCTCACAAGTCGA
TCCAGCTGGTGACTCATCCAGTCTTCAATTTACTAAGTCACTACCAACCTCTGAATTGAA
TCTGGCTGAATCCTCTGACGCTGCTACGAAAGAAACTGGAACATCACTGCAGACATTGAC
TTCAGCTGCTACCATGGAACGACTTGGTGCTAGT
>gi|8688760|dbj|AV528477.1|AV528477 AV528477 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL10c02R 5', mRNA sequence
AGCAGTGCTTGTGTTTCATGACATGCTGAGTAGAGGGCTGAAACCCAATGCTGTTACTTA
CAATACTCTGATCAAGGGGCTCTCTGAGGCTCACAGATATGATGAGATCAAAGATATCTT
GATTGGAGGGAACGACGCATTTACCACTTTCGCTCCAGATGCCTGCACTTTTAATATTTT
GATCAAAGCCCACTGCGATGCTGGTCATTTGGATGCAGCGATGAAGGTGTTCCAAGAAAT
GCTGAATATGAAGTTGCATCCTGATTCAGCTTCTTATAGTGTTTTGATTCGTACTCTGTG
CATGAGAAACGAATTTGATAGAGCTGAGACATTGTTCAATGAGTTATTTGAGAAGGAAGT
ATTGTTAGGTAAGGATGAATGCAAGCCTCTCGCTGCAGCTTATAACCCAATGTTTGAATA
CTTATGTGCCAATGGGAAAACAAAACAAGCGGAGAAAGTTTTCAGGCAGCTGATGAAAAG
AGGAGTGCAAGATCCGCCCTCTTACAAGACTTTGATAAC
>gi|8686177|dbj|AV526649.1|AV526649 AV526649 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZ18c11R 5', mRNA sequence
CCACCATTGAGGTTTAACTTATACAAACAGATCTTTTTGAAATTGGATTCATCTAAGAAG
CAGACTCTGTTTTCATGGCTGTTTACAATACCAAACTCTGTTTGGCCTCTGTTTTCTTGC
TCTTAGGGCTTCTCTTGGCTTTTGACTTGAAGGGTATAGAAGCAGAAAGTCTTACCAAAC
AGAAACTGGACTCGAAGATACTTCAGGATGAGATTGTGAAGAAAGTCAACGAAAACCCAA
ACGCTGGATGGAAAGCTGCTATAAATGATCGATTTTCAAACGCCACTGTTGCAGAGTTTA
AGCGTCTTCTCGGTGTTAAACCAACACCAAAGAAGCATTTCTTAGGTGTTCCTATTGTGA
GCCATGATCCATCTTTGAAGCTACCTAAAGCTTTTGATGCTAGAACTGC
>gi|8683519|dbj|AV523991.1|AV523991 AV523991 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL47e02F 3', mRNA sequence
TCCTAAAATCTCTCCTACTGTATGTATAATTGTTACAACATAATATCAAAATACGCATAC
ATATATACAAGTTGAAAGCTAAAGAGCTAGTGAGAATTGTCTGAGACCCAACCTCCCGAA
ACCATTCCCTCGTCGACAGGCTTCAGGCCACCACAGGATCTGGCTACCGATTCAAACAGC
TTCTCAATCTCAGGCGCACATCTGATGAAGGCTTGTTTCCAGAAGCTATATCTTGGGTTC
TTTATTAGCTCAATGAATGTGATTAGAAGTCCCCATGGATGTGGCCTGTTCACAATTAGC
CGTTCCAACAGCACTCTAGTTATTTGCTCCTGTATGATCTCCTGATCAGATTCGAAGAAT
AGATAGAGCATGATGAAAGAAAAGTAATGAGTGTGGTTGTTGGGGTATCGAAGCTGATTG
GCGATTGCATTAAGGAACAGATACCGCCCTTCCGTATCAAGTTCCATACTTAAATACTTG
AACATCTGCAAGGCCACAACATTTTGAGCCTGTGTCTCACCGGCCTGAAGCTGCTGAATA
GCCTGCATTCCAGTATATAGCACAAGCGAGTTGATCAATGGTACACTGTAACGGGTTCCA
GCTG
>gi|8682814|dbj|AV523286.1|AV523286 AV523286 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL23a03F 3', mRNA sequence
ATACGCATACATATATACAAGTTGAAAGCTAAAGAGCTAGTGAGAATTGTCTGAGACCCA
ACCTCCCGAAACCATTCCCTCGTCGACAGGCTTCAGGCCACCACAGGATCTGGCTACCGA
TTCAAACAGCTTCTCAATCTCAGGCGCACATCTGATGAAGGCTTGTTTCCAGAAGCTATA
TCTTGGGTTCTTTATTAGCTCAATGAATGTGATTAGAAGTCCCCATGGATGTGGCCTGTT
CACAATTAGCCGTTCCAACAGCACTCTAGTTATTTGCTCCTGTATGATCTCCTGATCAGA
TTCGAAGAATAGATAGAGCATGATGAAAGAAAAGTAATGAGTGTGGTTGTTGGGGTATCG
AAGCTGATTGGCGATTGCATTAAGGAACAGATACCGCCCTTCCGTATCAAGTTCCATACT
TAAATACTTGAACATCTGCAAGGCCACAACATTTTGAGCCTGTGTCTCACCGGCCTGAAG
CTGCTGAATAGCCTGCATTCCAGTATATAGCACAAGCGAGTT
>gi|8682693|dbj|AV523166.1|AV523166 AV523166 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL18h09F 3', mRNA sequence
CAACGTAATGAGAGCTTAAAAATAAATGAGAAACTTGGACATAATCAGTTGATGGAGTAG
GAACGAGAACAGACAGTCTGGAGAGATTCAGTGAAGAGAGATGAGAAGCTGGTCAAGGCC
TGGAATACATTGGGCAGGCCGGTTTGTAGATTGTTGAGAGTCATAGCTCGTGTCACCTCC
ACAGCCTTCACGTGCCTCATTACCTCATCCTCCACCTGCCTCTGACATGCCGCCAGCTCA
CATTTCTTAGATAGCGGGTCCCGTGAGTCCAACACCTCCGGTCCAGGGCCTATCCCAACC
GTCGAGTATGCCTGGTAGTACT
>gi|8682455|dbj|AV522928.1|AV522928 AV522928 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL10c02F 3', mRNA sequence
ATTTCATGCTTACAATATGTTTATAACCCAAATGTAAATTATAACAATTAGGAAGAGGTG
AGGCTGCGGATGAGAAGGCCTTCGAAGGTGATTCCAGGTCCGAAAGCTAAGCCAAGTCCC
CACTCTTGTGCTGCGTCACCTTTCTTCTTCAGCTCATCTCTCATATACTCCATCACATAC
AGTATCGTGTTGCTGCTCACGTTCCCGTAATCCACCAACGCCCTTCTGCTGCTCTCCAGC
TTCTCTTTCTCCAGCTTCAGTTTTGTCTCCAGACGGTTCAGAATCGCAGGTCCTCCTGGA
TGAACAGCCCAGAACATGTCATTGAACTCCATCGACTCATCGCCAGCCTTTCCCATCAGC
TTCTTGCAGAACTCTTCTATGTTCTCCTCTATCTTCTGCGGGAGGTCTCGTCCAAGCTTG
AAGTTTATGCCTTCCTCAGTCAACCTCCCCTCGATCACGTTCTGTGTCCCCGGCAAGAAC
TGCTGAACCGCATAGTGCAGCTCCATGAAAGGAGCTTCACACTCTCTCGGGTCAGCTCCG
ATGATCACAGCAGC
>gi|8679389|dbj|AV519862.1|AV519862 AV519862 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APD69d04F 3', mRNA sequence
TAGAAAACATGTTTGTGAATCTTGAAGTTAAATAAATAAACTAAGACTCCTAAAATCTCT
CCTACTGTATGTATAATTGTTACAACATAATATCAAAATACGCATACATATATACAAGTT
GAAAGCTAAAGAG
>gi|7612621|dbj|AV442217.1|AV442217 AV442217 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APZ38e01_r 5', mRNA sequence
TGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCACTACGAGAAAGATCCATG
GCTGATAATTGTATCAGACTTCTTCACTCATCCTCTGTTCTCTTCTGTTTAGGGCTTCTA
ATTTCATCCTTCAACTTGTAGCAGGGTATTGCAGCTGAAAATCTTTCCAAGCAGAAACTG
ACCTCATGGATTCTTCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTCGA
TGGAAAGC
>gi|7612394|dbj|AV441995.1|AV441995 AV441995 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APD19b11_r 5', mRNA sequence
GGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAAT
TGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTCATCC
TTCAACTTGTTGCAGGGTATTGCAGCTGAAAATCTTTCCAAGCAGAAACTGACCTCATGG
ATTCTTCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGATGGAAAGCT
TCTTTCAATGATCGGTTTGCAAACGCCACTGTTGCAGAGTTTAAGCGCCTTCTTGGTGTT
AAACCAACACCAAAGACGGAATTTTTGGGTGTGCCTATTGTAAGCCATGATATATCTTTG
AAGCTTCCAAAAGAATTTGATGCTAGAACCGCTTGGTCACAGTGCACCAGTATTGGAAGG
ATC
>gi|7612059|dbj|AV441666.1|AV441666 AV441666 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APD33a12_r 5', mRNA sequence
CAGGAGTCCTCACCGATTGGCCTTGGACACCCCTCGGAAGTTTCAAGTACATCGTAATAG
CACCATGGGCTGTCCATAGCACATACAGGTTTGTGACAGATGATCCAGAGAAGAGGGATC
TCGGGTACTTCCTTGTGTTCCCATTCTTGCTCTTCAGAATTCTGCACAACCAGGTTTGGA
TCTCTCTGTCCCGTTACTATACGTCCTCGGGAAAGAGACGCATCGTCGACAAGGGAATCG
ACTTCAATCAGGTCGACAGGGAGACCAACTGGGATGACCAAATATTGTTCAACGGAGTGC
TGTTCTATATAGGCATCAACCTATTGCCGGAGGCCAAACAACTTCCCTGGTGGAGAACTG
AC
>gi|7611662|dbj|AV441278.1|AV441278 AV441278 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APZ38e01_f 3', mRNA sequence
CTAAATGGTATATACAATAGACTTCTTTTTGGGTTGAAAGTCGTTTTATTTCATTGGTAA
CAACAACACAGTGGGAAATTATGTATTACAGAGTAGAGACACATATTCCTGTTTAAAATG
AGGAAACAAGAAGATCATCTGAAGTAGTAATACCTTTAACTACGTTCCTGTCTGAAGGTA
AACCAGCTACAACACCATGTTCAATGCCACATTCGTTTGTTCCTCTCCTGATCTTGAAGT
ACCCATCATCACCCCAGCTTCGGTTCCATTGATTTGCAAGCAACCAATAATCTTCACCGT
CATCAGAAGTTCCCCAGCCAATAAGTTTAACAGCATGACCTCCAATGTTAGTACCTGTTA
TGTGCTTGTACACTCCAGATTTGTAATGCGCAAAGTCCTCGTAAACAGTGAAGGCAACCT
CAACAGGTCCATTTTTGTAAACTTCTGCCATAATGTCATCAGGGTGAGATCTGACCTTGT
ACGCACTAACACCATAATGTTTTGATTCACGCCAAAGCTGGTTTCCGCTAACACATTTCC
TTGCACATTTTGGTGTAGGGTAAGCGGGTTCACATCCCGGGTGCGAGCAACCAGTATTGT
CGAAGTATGGATCACACTCTTCAGTGACTACAC
>gi|7610825|dbj|AV440461.1|AV440461 AV440461 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APD64c02_f 3', mRNA sequence
GGCACAAAAAGGGACACAGCTCTTACATTCATGTTTCACTAGGCAGTCTCTTGTGTACAT
TATACATATTTCGCATTTCCTCAGTTGACTCCGGTTACAAGATTCGTTTTTTAAAGCAAA
GATCTAGGACTATCAGATTACAAATCATCTTGTAGCTGTGTTAGAAGCGCATCGGTCTCA
TGGGCATCGATTTCACTGTTGGTTACTGTTCTGTTTTCGTCCACATCAATAAGAGCTAGG
TAAGATTTGTCTTCAAGATCCCCCGACTGCCTTAACAATTCCAAAACGGCCTCTTTACTG
GTAACATCCGATTCCTCTTCACAGAGCTTGAAGAAACCAGACAGCATCAACACCTTGGGC
CTCCAATTGCTGGACCCTTCAGCCGAAAAAGCATTTCTAAGACAAGTCAAAGCCTCTGAA
ATACACCTCTTTCTGGTATGACCAACAGCTAGAATCTCCCACGTACTTGAACTTGGTTTT
CCTCCCATTTCAACCATGTG
>gi|7610337|dbj|AV439986.1|AV439986 AV439986 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APD33a12_f 3', mRNA sequence
GGAAATAGTACTCTTATTAATACCATAGTCATCGTTCTTAATTTGACTCTATCAATACCA
TAATCGCCAAAAGTTTGATATGCATAAATATATGCGTGCGCTTTATATATGTTTCATAGT
TCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCA
TTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAG
CCGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCA
CACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTC
ATCGCCTTTCTCGGTAACCAGTTCTCACAGGAGTGGACATTCACCAGAGATTTTGGAACT
ATCAATGCTGGTGTGGTATGATAGATACAATCTCTACGTAACTGCT
>gi|5846657|gb|AI999752.1|AI999752 701557284 A. thaliana, Columbia Col-0, rosette-3 Arabidopsis thaliana cDNA clone 701557284, mRNA sequence
GATCTNTAACAAAATGTGCCATCTATTCTTTAGTCTTTACAAACAAGCAGCAAATGGTTT
GCCTTTCAGAATCAAAATTTAAGGTGTTTCTCGAATAGACAGAAGGAAGAGAAGAGAAGT
CCCAGAAAGCTGTTCAGAAGGCGCATACAAATCATGTGTGCGTTGCTGCTGCAAGGAAAA
NCACTTCCGCTGTAGCAGCCTGTTCTTTGTTTGATACCCCGGNCGTTATCTTCCAGTACA
AAGGAGGAGTTTTTCACACCATCGCTAAAGAGAAGACACCAAAAGAAGGTACCTTTATGC
AACCTAGCCATTCCCACTCCAACCTCGGTATGCGACCTGTTTCTG
>gi|5846455|gb|AI999550.1|AI999550 701556366 A. thaliana, Columbia Col-0, rosette-3 Arabidopsis thaliana cDNA clone 701556366, mRNA sequence
TTTAACNAGAAAGCATGGCAATCTTTTCTTTGAACAAATCTCCATAAATTACAGACAAAG
ATAAAGCCGGAAACAAGAAAATGTTGCAGATAAAATCTAACAAAAGAAAGAACAATCGAA
AAACTCTTCTTCTCCTTGTAATTTGCTCACAACAAAACCTCTTCTTCAGAGCCTCTTAAA
GTGGCTTTCCACTTGTCTTGATATCATTTCTGATTGCTCCTTGAATCATCTTAACGATCA
AATACTGAGCGCCTATGATAAGAGGGATGAGTTTCTTTCCTTTATCATCAGAGTAAGATC
CATCTACCATCTTCTTGTCTACATGAATTGCTTTCCTCTGGTTTGTTGCTACATCAGTTA
TCGCCTTAACCAAGTTCGGGATCCACGCTTCACCATTTGGAAGAGCCTTTTCGTCCTTAT
CGTTCTTGCTGCATCTTCCGCTGTTCTCTGCATAGACTACCGCGATTGCAGAATCCTCAA
ACTCTGTTTTCGCATCTATTTAACAGCCCGGATAGTTTTGAGGAG
>gi|5845530|gb|AI998625.1|AI998625 701546353 A. thaliana, Columbia Col-0, rosette-2 Arabidopsis thaliana cDNA clone 701546353, mRNA sequence
AATCTTGAAGTTAAATAAATAAACTAAGACTCCTAAAATCTCTCCTACTGTATGTATAAT
TGTTACAACATAATATCAAAATACGCATACATATATACAAGTTGAAAGCTAAAGAGCTAG
TGAGAATTGTCTGAGACCCAACCTCCCGAAACCATTCCCTCGTCGACAGGCTTCAGGCCA
CCACAGGATCTGGCTACCGATTCAAACAGCTTCTCAATCTCAGGCGCACATCTGATGAAG
GCTTGTTTCCAGAAGCTATATCTTGGGTTCTTTATTAGCTCAATGAATGTGATTAGAAGT
CCCCATGGATGTGGCCTGTTCACAATTAGCCGTTCCAACAGCACTCTAGTTATTTGCTCC
TGTATGATCTCCTGATCAGATTCGAAGAATAGATAGAGCATGATGAAAGAAAAGTAATGA
GTGTGGTTGTTGGGGTATCGAAGCTGATTGGCGATTGCATTAAGGAACAGATACCGCCCT
TCCGTATCAAGTTCCATACTTAAATACTTGAACATCTGCNAGGGCCACAACATTTGAGNC
TGTGTCT
>gi|5845361|gb|AI998456.1|AI998456 701545753 A. thaliana, Columbia Col-0, rosette-2 Arabidopsis thaliana cDNA clone 701545753, mRNA sequence
GCNTTTTGAAGAATTGGGAAGAAACAAAACCAATTACTTTTTATTGCTTTTTGAAGAATT
GGGAAGAAACAAAACCAATTACTTTTTATCTGACTGGTTACATTTAAGTACAACACAGAA
GAATTCTTTNCACAAANTTACTATTTTTCTTCTATAGAAGACTACCAGTCAGACCCATAG
TTGTGATACTGTTTGTTTTTCAATGATGCAAATATGGATATTATAACTATTATTAAATTA
CATAAGTGTGGAAATAAAACCTAGCTATAAACACTGGNTCNTGAAAAAAGAAAGCNTNTA
TGCAGAG
>gi|5843191|gb|AI996286.1|AI996286 701551019 A. thaliana, Columbia Col-0, inflorescence-2 Arabidopsis thaliana cDNA clone 701551019, mRNA sequence
GCTAATGAGGGAAATCAAACATAACAAGGGGTTATTGTGAGAGAGAACANAGGATCTTAT
ACAAGTTGAAAATCCGCAACCANATAATCATAATCTACTCTCGGTAAATGGAATGTCAAT
CCGCACTGACCATTTGCTCTCTCTTGCTCCTCTACCTTGTTANAGGATGNCTCCTCCTCT
TTGGTCGGATCCCATCTTCTTCGTAGTCCATCACTCCACTTGGTTCCCCAAACATCTCCT
TATTCCCTCTGATGTCAACATCCCCCTNCATGNACAGAGACTTCTTCACTTCTTCCACCC
CTTCTTCTGCTTCCTTACGATGTTNTNTTGTCCATCTCACTCATATTGTCCGCCCATTTG
ATCTTGTCTTGAATTGAAATGAGCAGATTTTCTGACGTGTTCAACCAGTTGGACAATGTG
TGTAACATATTCCCTAGTTGNCCTGGGCTTAGATNCCTACCAGCTGNGAACGGAACTCAA
AACATCTTTT
>gi|5841805|gb|AI994900.1|AI994900 701500362 A. thaliana, Ohio State clone set Arabidopsis thaliana cDNA clone 701500362, mRNA sequence
GGGTTGGCCATATGTTCAGCGCCTGCTGGTGGACTTGCTTCAGTTTCTTGAGCCATTTTT
AAGAAATGCTGAACTCGGAGGACCGGTTCATTTCCTATACAAAGGGACATTGAGAGTATT
ACTGGTTCTGCTTCATGATTTCCCAGAGTTCCTATGTGATTATCATTTTACTTTCTGTGA
TGTGATTCCTTCAAGTTGCATACAAATGCGGAATATTATCCTCAGTTCTTTTCCACGGAA
CATGAGGCTTCCTGATCCTTCTACCCCAAATTTAAAGATTGATTTGTTACCTGAGATAGT
AGAAGCTCCCTGTATCCTTTCTGAGGTTGATGCTGCGCTAAAGGCAAAGCAAATGAAGAA
TGACGTGGATGAGTATCTTACGTCGAGGCAGCAAAATTCAACTTTCTCAAGTGAGTTGAA
GACAAAGTTACCTCTATCGTCCAGCGGGGCTAATTCCAGCTGGAACCCGTTACAGTGTA
>gi|5840051|gb|AI993146.1|AI993146 701495464 A. thaliana, Ohio State clone set Arabidopsis thaliana cDNA clone 701495464, mRNA sequence
CATTGTGTTGATTCTGGAATTCTTTGTGGGAACGAGAAATTTGTACAAGGGAGATTCATC
ATGGCTGATAGTTGTTGTATCAGACTTCACTTATTAGCCTCTGTTTTCTTGCTCTTATTT
TCATCCTTCAACTTGCAGGGTATTGCAGCGGAAAATCTTTCCAAGCAGAAACTGACCTCA
CTGATTCTTCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGTTGGAAA
GCTGCTTTCAATGATCGGTTTGCAAATGCCACCGTTGCAGAGTTTAAGCGACTCCTCGGT
GTTATACAAACACCAAAGACGGCATACTTAGGTGTACCTATTGTAAGACATGATTTACGT
TGAACTTCCTAAAGAATTTGATGCTAGAACCGCTTGGTCACATTGCACCAGTATTCGAAG
GATCTTAGGTCGGTTTTAATCTCTTAGCTTCCACTATCTCTGTCATTAACCCAATGATTT
ACTGACTCTTCTTATGTCTTGTTCAAATTATCTCCTCTTTAGTGCACTAAAGATCAGGTG
AACATCATTCCATTGAGTGGGTATATATTGACAATGTGTACTCTGGTNACNGATAGCTTA
TGGTTTGGGTTCTTTTGGGTCATGTGGTCTTGCTGGCGATTGGTGCTGTGATCACTGCCG
GCAGTTCTGCATCGAGTATACTTNGATGTTCCGTATCTCC
>gi|5839790|gb|AI992885.1|AI992885 701493873 A. thaliana, Ohio State clone set Arabidopsis thaliana cDNA clone 701493873, mRNA sequence
CTCTAGGCTCTGTATCGCTCGCTGCTCTTCCTGCCACAGATCGATAACCATGAATCCTGA
GTACGACTATCTTTTCAAGCTCCTGCTTATCGGGGATTCTAGCGTAGGCAAGTCTTGTCT
TCTCTTGAGATTCTCCGATGATTCTTATGTAGCGAGTTACATTAGCACTATTGGAGTCGA
TTTTAAACATCAGGACTGTGGATCAAGATGGCACTACAACTAAGCTCCATATTTGGGCCA
CTGCTGGTCAAGACCGGTTCAGGACTATTACCCGCAGTTGCTACCGTGGGGCACATGGAA
TTATTATTGTCTACGATGTCACCGATGATGAATGCTTCAATAATGTCAACCACTGGTTGG
GTGAAATTGGCCGCTACGCTACCGACAATGTCAACTAACCCGTTCCTGGGGACAATTCTT
GACCTAGGGGAAACCAAGGGCCTTCCCTTTCGAAACTGCCCGGCCT
>gi|5839694|gb|AI992789.1|AI992789 701493549 A. thaliana, Ohio State clone set Arabidopsis thaliana cDNA clone 701493549, mRNA sequence
AAGAAAAAAAGACAAGGCATGGCCGCGGAAGAAGCGACGGAGTTCTACCTGAGATACTAT
GTCGGTCACAAAGGGAAATTTGGACACGAGTTCCTGGAGTTCGAGTTTAGAGAGGACGGT
AAGCTCCGTTACGCCAATAACTCTAACTACAAGAACGCTACTATTATCCGCAAGGAGGTA
TTTCTCACCCCCGCCGTGCTCAAGGAGTGCAAGCGTATCGGCTCCGACAGCGAGATTCTG
ACAGAAGCCGACAGCAATTGGCCGGAACCTGCACGTGTTGGCCAGCAAGAGCTCGAGATC
GACTTGGGTAATGAGCATATCTCATTCGCTGCATCTAAGACTGGACCTCATGTTGCTTGC
CAGCGCAGTAAAGATCCTGGAGGGCTTCGCATCTTCTACTATCTGGTTCAAGACCTGTGA
TGGCATGATTTGGCGCTCATCTCACAGCACTTCCGAAATCAAGCCTCTCTAGGGGAGGAA
ATCAGCTTCGTCACAAGC
>gi|3450080|gb|AI100119.1|AI100119 34494 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105B20XP 3', mRNA sequence
GTGCTTNTTTTCCTTATGATCCAGCTCTTCCACGCNCNCATGAACTATGAAACATATATA
ANGCGCNCNCATTTTATGTTTCCNCGCNCACATATATTTATGCATATCAAGCTTTTGGTG
ATTATGGTATTGATAGAGTCAAATTAAGCTCGGTGACTATGGTATTAATAAGAGTACTAT
TTCCTTATCTCTTTGTGAACTAAGANNCATATATATATATATATATATATAAAGCAAACA
TGTTCCAGAAT
>gi|3449674|gb|AI099935.1|AI099935 34088 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138J5XP 3', mRNA sequence
CCTTAGANGGTGGGAAATTGCATGAGTTTGGCACATCCCTTNTTCTNNCGGATTTNGGAT
CNNAGTATGGGAAGCCCTGTCTCAGCCTNNGCTTCCAGCNTCTCCTCCTTCCACATCNTT
AAAACTCCAACCTTGGAAGATTTTAGGAGAATGAGAGCGACACGCTCTGTGCTTCTTTTC
CTTATGATCCAGCTCTTCCACGCACAAATGAACTATGAAACATATATAAAGCGCACACAT
ATATTTATGCATATCAAGCTTTTGGTGATTATGGTATTGATAGAGTCAAATTAAGCTCGG
TGACTATGGTATTAATAAGAGTACTATTTCCTT
>gi|3449578|gb|AI099839.1|AI099839 33992 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127K5XP 3', mRNA sequence
TTTCCAANTCGGGGNGTTTTACAANTTCCATANCGGGTACTTAAGNTTTGGNGGTNCATG
CCANTTAANCTCATTGGCTGGGGAACTTCTGATGACGGCGAAGATTATTGGTTGCTTGCA
AATCAAATGGANCCGAAGCTGGGGTGATGATGGTTACTTCAAGATCAGGNGAGGAACGAA
CGAATGTGGCATTGAACAGAGTNTTGTAGCTGGTTTACCTTCAGNGAAGAACGTATTTAA
AGGTATTACCACTTCAGATGATCTTCTGGTTTCCTCAGTCTAAACAAGACGATGTGTCCC
TACTTCTGTAATATATCATTTGCAACTGTGTTGTAAGTTTAATATACCATTGAAAGAATC
ACCTTCAATC
>gi|2762922|gb|T46227.1|T46227 9490 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138J5T7, mRNA sequence
CCAAAATCTCTGGTGAATGTCCACTCCTGTNAGAACTGGTTACCGAGAAAGGCGATGAGT
GCAACTAGAGTGGCCGGCATATTGCACGCCTTAGAAGGATGGGAAATGCATGAGTGTGGC
ACATCCCTTCTTCTCTCGGATTTGGACCAAGTATGGGAAGCCTGTCTCAGCCACGGCTTC
CAGCCTCTCCTCCTTCCACATCATTAAAACTCCAACCTTGGAAGATTTTAGGAGAATNAG
AGCGACACGNTCTGTGCTTCTTTTCCTTATGATCCAGCTCTTNCACGGACAAATGNACTA
TGNAACATNTTNTAAAGGNGNACACATNTNTTTTNTG
>gi|2762921|gb|T46226.1|T46226 9489 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138J4T7, mRNA sequence
CCAAAANCTCTGGTGAATGTCCACTCCTGTNAGAACTGGTTACCGAGAAAGGCGATGAGT
GCAACTAGAGTGGCCGGCATATTGCACGCNTTAGAAGGATGGGAAATGCATGANTNTGGC
ACATCCCTTCTNCTCTCGGATTTGGACCAAGTATGGGAAGCCTNTCTCAGCCACGGCTTC
CAGCCTCTCCTNCTTCCACATCATTAAAACTCCAACCTTGGANGATTTTAGGAGAAT
>gi|2759942|gb|T42274.1|T42274 5537 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111I3T7, mRNA sequence
ACTTCTTCACTCAGCCTCTGTTTTNTNCTGTTTAGGGCTTCTAATTTNATCCNTCAACTT
GTTGCAGGGTATTGCAGCTGAAAATCTTTCCAAGCAGAAACNGACCTCATGGATTCTTCA
GAATGAGATT
>gi|2759743|gb|T44958.1|T44958 8221 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127K5T7, mRNA sequence
CATTGTGTTGATTCTGGAATTCTTTGTGGGAACGAGAAATTTGTACAAGGGAGATTCATC
ATGGCTGATAGTTGTTGTATCAGACTTCACTTATTAGCCTCTGTTTTCTTGCTCTTATTT
TCATCCTTCAACTTGCAGGGTATTGCAGCGGAAAATCTTTCCAAGCAGAAACTGACCTCA
CTGATTCTNCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGTTGGAAA
GCTGCTTTCAATGATCGGTTTGCAAATGCCACCGTTGCAGAGTTTAAGCGGCTCCTCGGT
GTTATACAAACACCAAAGACGGGATACTTAGGGNGTACCNATTGTAAAGACATGATTTAN
CGTTTNAAGNTTCCCAAAAGAATTTAATNCTAGGACCCGCTNGGNCANANNGCACCNGTT
TTCGAGGGTCTTAGGGCGGNTTTAANCNNTNGGTTCCACT
>gi|2759121|gb|T44328.1|T44328 7591 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124H12T7, mRNA sequence
GGGTTGGCCATATGTTCCAGCGCCTGCTGGTGGACTTGCTTCAGTTTCTTGAGCCATTTT
TAAGAAATNCTGAACTCGGAGGACCGGTTCATTTCCTATACAAAGGGACATTGAGAGTAT
TACTGGTTCTNCTTCATGATTTCCCAGAGTTCCTATGTNATTATNATTTTACTTTCTGTN
ATGTGATTCCTTCAAGTTGCATACAAATGCGGAATATTATCCTCAGTTCTTTTCCACGGA
ACATGAGGCTTCCTGATCCTTCTACCCCAAATTTAAAGATTGATTTGTTACCTGAGATAG
TAGAAGCTCCCTGTATCCTTTCTNAGGTTGATGCTGCGCTAAAGGCAAAGCAAAATTNAA
GGATGACGTGGATGAGTATCTTACGGCGNGGCAGGAAANTTCAACCTTTCNAAGGTNGGT
TNAGGCAAAGGTACTTCTTTTGGCCNGCGGGGGTNGTTCAANTTGGACCCNGTNNAAGGG
NCCCCTTGG
>gi|2749490|gb|AA651247.1|AA651247 31361 Lambda-PRL2 Arabidopsis thaliana cDNA clone 178C3XP 3', mRNA sequence
CCCAAACAGGTTTCCTTNGGGNAGGNCCCCAGGGGNGGCCGGNAAACCCCNAAGGGGNNN
TTTTTTCCCCNTTTCCCANGCCCCCCNAAGGGGTTTCCGTGCGGNTTTNCTTTCNTCCCC
CCCCGCCNTTGTTGNTCCCAAATCTCCGGGGAATTCCCACCCCTGGGAGAACTGGTTCCC
GGGAAAGGCNGATGGAGTGCAACTAGAGTGGCCNGGCATATTGCACGCCTTAGAAGGATG
GGGAAACGCATGGAGTGTGGCACATCCCTTCTTCTCTCGGATTTGGACAAAGTATGGGAA
GCCTGTCTCAGCCAACGNTTCCAGCCTCTCCTCCTTCCACATCATTAAAACTCCAACCTT
GGAAGATTTTTGGAGAATGAGAGCGACACGCTCTGTGCTTCTTTTCCTTATGATCCAGCT
CTTCCACGCACACATGAACTATGAAACATATATAAAGCGCACACATTTTATGTTTTACGC
ACACATATATTTATGCATATCAAGCTTTTGGTGATTATGGTATTGATAGAGTCAAATTAA
GCTCGGTGACTATGGTATTAATAAGAGTACTATTTCCTT
>gi|2748705|gb|N95878.1|N95878 21603 CD4-16 Arabidopsis thaliana cDNA clone H1B11T7, mRNA sequence
CATATTTCGCGGCAACTTTCTTCTGCAATGGTATCTNCTGTACCTAAACTCCATGCTTTG
TTTGTCTCCAAGTCTCAACCAGTTCTCCGAGCCGCCAAAGTTACCAATGAAGAAAGGTCC
ACCAAATCAAAACTCGCCAGGTCCTTGGCCCGTNCCGTGAACTCTAACCCGTGGTCGGAC
GAACTCGAGTCTTCACTATCATCTCTTCATCCGTCCCAAACCATCTCCAGAACCACCGTT
CTCCAAACCCTGCGTCTCATCAAGGTCCCTGCGGATGGTCTCCGGTTCTTTNACTGGGTT
TCCAACAAGGGGTTTTCTTAACAAAGNGNAAGTCTTTCTTNCCTCATGTTAGAGTTCCTC
GGGTNGAGCTNGGNAATNTCAAATGTGGGTTGGAAATNCCTTTGTNCTCCATNGNNGGGA
GGTTAATTGGTTGNGTAAGGTCAAGGGTNGNTATTTTAA
>gi|2748033|gb|N95955.1|N95955 21140 CD4-14 Arabidopsis thaliana cDNA clone F3F3T7, mRNA sequence
CGTTTTATTTCATTGGTAACAACAACACAGTGGGAAATTATGTATTACAGAGTAGAGACA
CATATTCCTGTTTAAAATGAGGAAACAAGAAGATCATCTGAAGTAGTAATACCTTTAACT
ACGTTCCTGTCTGANGGTAAACCAGCTACAACACCATGTTCAATGCCACATTCGTTTGTT
CCTCTCCTGATCTTGAAGTACCCATCATCACCCCAGCTTCGGTTCCATTGATTTGCAAGC
AACCAATAATCTTCACCGTCATCAGAAGTTCCCCAGCCAATAAGTTTAACAGCATGACCT
CCAATGTTAGTACCTGTTATGTGCTTGTACACTCCAGATTTGTAATGCGNAAAGTCCTCG
TAAACAGTGNAGGNANCCTCAACAGGNNCNTTTTTGTAAAACTTCTGCCNNAATGNATCA
GGGGNGGGTCTGNCCTGTTCGGGCTNACANCNTAAGTTTTGTTACGCCAANNGGTTCCGT
NAAAAATTCTTGACATTTNGGTG
>gi|1159193|gb|N38051.1|N38051 19278 Lambda-PRL2 Arabidopsis thaliana cDNA clone 217D15T7, mRNA sequence
AGAAGGAACAACAAGAGAAGAGCAGGAAAAAGCCACAAAAGGGACATTGTTTATACCATT
CTCACAGTTCCCCCTCAAGCAGTTACGTAGAGATTGTATCTATCATACCACACCAGCATT
GATAGTTCCAAAATCTCTGGTGAATGTCCACTCCTGTGAGAACTGGTTACCGAGAAAGGC
GATGAGTGCAACTAGAGTGGCCGGCATATTGCACGCCTTAGAAGGATGGGAAATGCATGA
GTNTGGCACATCCCTTCTTCTCTCGGATTTGGACCAAGTATTGGGGAGCCTGTNTTAAGC
CACGGTTTCCAGCNTTTTCCTNCTTTCCANAATNTTTNAAAACNTCCAACCCTTTGGANG
GTTTTTGGGGGGATTTGNGGGCCCACACGCTTTTGNGTTTTTTTCCCCTTANNGNCCCAN
TTTTTTNCGGGGNAAAA
>gi|2747682|gb|H76955.1|H76955 17386 Lambda-PRL2 Arabidopsis thaliana cDNA clone 199P18T7, mRNA sequence
CACATAACAGGTACTAACATTGGAGGTCATGCTGTTAAACTTATTGGCTGGGGAACTTCT
GATGACGGTGAAGATTATTGGTTGCTTGCAAATCAATGGAACCGAAGCTGGGGTGATGAT
GGGTACTTCAAGATCAGGAGAGGAACAAACGAATGTGGCATTGAACATGGTGTTGTAGCT
GGTTTACCTTCAGACAGGAACGTAGTTAAAGGTATTACTACTTCAGATGATCTTCTTGTT
TCCTCATTTTAAACAGGAATATGTGTCTCTACTCTGTAATACATAATTNCCCACTGTGTT
GTTGTTACCAATGAAATAAAACGGCTTTCAACCCAAAAAGGAAGTCTATTGTATATACCA
TTTAGGCTTTTNGTTCATATTCAATTATAATGTGTTGTTGTTNCCATGNAAGATCCAANG
GCATTCANCTNTTNCTNCATATNAA
>gi|2747645|gb|H76651.1|H76651 17082 Lambda-PRL2 Arabidopsis thaliana cDNA clone 199N11T7, mRNA sequence
TGCATCGTCGTCTTCCTCACGCNATTTGGTAATCCNATTCGTCTTCATCTAATTCCCTCC
CTTCCNAGAATAATAATGTACCCGCNACCTCCCTCAAGCATCTACGCTCCTCCAATGCTG
GTNAATTGCTCCGGTTGCCGGACGCCTCTCCAGCTCCCATCCGGCGCCCGANCTATTCGC
TGCGCTCTCTGCCAGGCTGTNACTCATATCGCCGACCCTCGCACCGCCCCTCCTCCGCAA
CCTTCCTCCGCCCCTTCTNCGCCTCCCCAAATCCACGTGGCTCCCGGTCAGCTGCCTCAC
CCCCATGGCAGGAAGAGGGCCGTNATCTGTGGCATCTGGTATCGTTTCTTTTNGNCACGA
GCTCAAAGGCTGCATCAACGGCGGCAAGTGCATGNGTAACTTCTTATNAACAAANTNAAT
TNNTCCCAGATTNATTCTATGCTTACCGGGGAGAACT
>gi|2747604|gb|H76393.1|H76393 18098 Lambda-PRL2 Arabidopsis thaliana cDNA clone 194B12T7, mRNA sequence
TTTTAAAATTAGGACTGTGGAACAAGATGGCAAAACANTTAAGCTCCAAATTTGGGACAC
TGCTGGTCAAGAACGGTTCAGGACTATTACTAGCAGTTACTACCGTGGGGCACATGGAAT
TATTATTGTNTACGATGTCACAGATGAAGAAAGCTTCAATAATGTCAAGCAATGGTTGAG
TGAAATTNATCGTTATGCTAGTGACAATGTCAACAAACTCCTTGTTGGAAACANGTCTGA
TCTTACTGAAAACAGAGCCATTCCTTATGAAACTNCCAAGGCTTTTGCCGNTGAAATCGG
GGTTCCCTTTTATGGGGGCTNGGTGCAAAANATGCTNCAAAACGGTNGNCCAGGGTTTCA
TNGGCAATGTNTNNA
>gi|2733258|gb|H37487.1|H37487 15616 Lambda-PRL2 Arabidopsis thaliana cDNA clone 182E10T7, mRNA sequence
GGGCAGCCCACTGAGCCTGGGAACANNGTTGAGGGATTGAANAAAAAATAATCAGAAGAG
AAAGATCCATNGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTT
TAGGGCTTCTAATTTCATCCTTCAACTTGTTGCAGGGTATTGCAGCTGAAAATNTTTCCA
AGCAGAAACTGACCTCATGGATTCTTCAGAATGAGATTNTAAAGGAAGTCAAATGAGNAT
TCNAACGGCTGGNNTGGAAAA
>gi|2722481|gb|AA712564.1|AA712564 31697 Lambda-PRL2 Arabidopsis thaliana cDNA clone 172P13T7, mRNA sequence
GGGAAATGTCGACGAAAGGCGCGGCGGCGGCGTACCCTAGCGCGGCTCGGATATCTGATT
CTCCATGTTATCTTCAGTACTCTGCTTCTNTCAAATGTNTTGAAGAATTTGGATCAGACA
AGAGTAAATNCCAGGTTCATTTTNATGTGTACAAGGAATGCAAGAAGAAAGAGAGGGAAG
CTCGACTGGAACGCAATAAGACACGGTCGTTGTTCTCGTGAATNCAGATCCTCGAATACC
AATGATGTCTCAGAACATCACCTAGCTAGTAGTATCCTGTTGTTTCATTTGCAATGGCTG
TGTTTGNATGANCTATCTAAGTAAACAAGTGGGAAGTTTTTNTNAATGTTACTTTTTACC
CCCCTTGGNGG
>gi|2597485|gb|R82906.1|R82906 5044 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109D5T7, mRNA sequence
AGCTCTTCCACGCACACATGAACTATGAAACATATATAAAGCGCACACATTTTATGTTTT
ACGCACACATATATTTATGCATATCAAGCTTTTGGTGATTATGGTATTGATAGAGTCAAA
TTAAGCTCGGTGACTATGGTATTAATAAGAGTACTATTTCCTTATCTCTTTGTGAACTAA
GAAACATATATATATATATATATATATAANGNAAACATGTTCCAG
>gi|2597031|gb|T22420.1|T22420 4428 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105B20T7, mRNA sequence
AGGTATGGCTGGTGGGAGAAGGAACAACAAGAGAAGAGCAGGAAAAAGCCACAAAAGGGA
CATTGTTTATACCATTCTCACAGTTCCCCCTCAAGCAGTTACGTAGCGATTGTATCTATC
ATACCACACCAGCATTGATAGTTCCAAAATCTCTGGTGAATGTCCACTCCTGTNAGGTAA
GTNTTCAAAGCTACCCAATCCAACTAAATTTNTTAGAAGAGGTNGGCCNTATTTATAAAA
AAAAACATCTTGCAGAACCTNGTTNCCCCGGAAANGCGNTNNAGTG
>gi|2596953|gb|T22318.1|T22318 4326 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103P9T7, mRNA sequence
CTTTTCAAGCTCCTGCTTATCGGGGATTCTGGCGTAGGCAAGTCTTGTCTTCTTTTGAGA
TTCTCTGATGATTCTNATGTAGAAAGTTACATTAGCACTATTGGAGTCGATTTTAAAATT
AGGACTGTGGAACAAGATGGCAAAACAATTAAGCTCCAAATTTGGGACACTGCTGGTCAA
GAACGGTTCAGGACTATTACTAGCAGTTACTACCGTGGGGCACATGGAATTATTATTGTC
TACGATGTCACAGATGNNGGAAGCTTCAATAATGTCAAGCAAATGGTTGAGTGNAATTNA
TCCGTTATGCTAGTGNCAATGTCAACCAAACTCCCTGTTTGGGAACAAGTCCNGATCCTT
CTTNNAAAACAAGAGCCCNTCCCTTTTGAAANNTNCCAAGGNTTTTTCCCNNTGG
>gi|2596256|gb|T21132.1|T21132 3140 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90H7T7, mRNA sequence
CTGGCTCTGTATCGCTCGCTGCTCTTCCTCCCACAGATCGAAAACCATGAATCCTGAGTA
CGACTATCTTTTCAAGCTCCTGCTTATCGGGGATTCTGGCGTAGGCAAGTCTTGTCTTCT
TTTGAGATTCTCTGATGATTCTAATGTAGAAAGTTACATTAGCACTATTGGAGTCGATTT
TAAAATTAGGACTGTGGAACAAGATGGCAAAACAATTAAGCTCCAAATTTGGGACACTGC
TGGTCAAGAACGGTTCAGGACTATTACTAGCAGTTACTACCGTGGGGCACATGGAATTAT
TATTGTCTACGNTGGTCACAGATGANGAAAGCTTCAATAATGTCANGCAATGNNTTGAGT
GNAATTAATCGTNATGCTAGTGNCAATNTCAACAAAACTCCTNNTTGGGAACAAGTTTTN
TNCTTNCTTNAAACAANGGCCTTNCT
>gi|2580948|gb|AA650856.1|AA650856 30970 Lambda-PRL2 Arabidopsis thaliana cDNA clone 288E9T7, mRNA sequence
CATTGTGTTGATTCATGGAATTCTTTGTGGGAACGAGAAATTTGTACAAGGGAGATTCAT
CATGGCTGATAGTTGTTGTATCAGACTTCACTTATNAGCCTCTGTTTTCTTGCTCTTATT
TTCATCCTTCAACTTGCAGGGTATTGCAGCGGAAAATCTTTCCAAGCAGAAACNGACCTC
ACTGATTCTTCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGTTGGAA
AGCNGCTTTCAATGATCGGTTTGCAAATNCCACCGTTGCAGAGTTTAAGCGACTCCTCGG
TGTTATACAAACACCAAAGACGGCATACNNAGGTGTACCTATTGTAAGACATGATTTATC
GTTGAAGCTTCCNAAAGAATTTGATGCAAGAACCGCTTGGGCACATTGGACCAGNATCCG
AAGGACCTAAGGCCGGGTTAACCCCTANNTCCANAACCCCGGCANNAACCCANNGNTNCC
GGGCCCCCCAAGGNTNGGNCAAAAAACCCCCCCT
>gi|2048630|gb|AA395265.1|AA395265 27216 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124H12XP 3', mRNA sequence
TGNNCCCANACCCNCCATCTTCTTCATCAGCCTNCTATTCTCGATCTGATCNGGGATNTN
CAGGGCAATACTAGAGTCTGTTGGACCGGCTATTGTGACAGGCCACATCCATGGGGACTT
CTAATCACATTCATTGAGCTNATAAAGACCCCAAGATATAGCTTCTGGAAACAAGCCTTC
ATCAGATGTGCGCCTGAGATTGAGAAGCTGTTTGAATCGGTAGCCAGATCCTGTGGTGGC
CTGAAGCCTGTCGACGAGGGAATGGTTTCGGGAGGTTGGGTCTCAGACAATTCTCACTAG
CTCTTTAGCTTTCAACTTGTATATATGTATGCGTATTTTGATATTATGTTGTAACAATTA
TACATACAGTAGGAGAGATTTTAGGNGTCTTAGTTTATTTATTTAACTTCAAGATTCACA
AACATGTTTTCTAATTAC
>gi|2047981|gb|AA394770.1|AA394770 26567 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165D3XP 3', mRNA sequence
TTNGGGACCTTGCCNGTGGNAAACCCACCCTGGNAACCTCCAAGGGGNTTTTTGNTGGNN
GNTTTAGGAAGGGAGGAGGGGGGANGTTGAGNCAACCGGNTTGGAAGGTGATTAAGGCAT
TTTTGGTTCCCACCAAGGAAGCNGGAGGAAAGGATTGTTGCCCGGGGATTTACCATATAA
CCCGATCCATGCTTGTCTCCCCGTACAAATCTNCNCCAGTCAAAATGCTTTTGTAGCTAA
ATTTTGTTTAATTACGGCTCTTGTAAATGTAAAGAAGCAATGAGATTGAGATTTGCAATG
AGACATCTTTACGAACCTTATGGAGTGTGCTGTATAGTTTTGTCTGTTTAAAGATTTTTT
ATTTATTTTCATGAATC
>gi|2446000|gb|AA605472.1|AA605472 30508 Lambda-PRL2 Arabidopsis thaliana cDNA clone 190I17XP 3', mRNA sequence
CGGTCCCCCCAACTTCCGGCTGTNTAAGTCCGAAACCAGGGTTGNGGATCNCCATCCCGG
TAGCTNNCCNNNGACCNCGGAANTCCCNCNAGACNGTTAGGNCCGAAAGGCNCTCCCAAA
TGGTGAAGCGTGGANCCCGACTTGGTTAAGGCCGATAACTGATGTGGCAACCAACCCAGA
GGAANGCCAATTCCATGTAGCCAAGAAGATGGTAGATGGATCTTACTCTGATGATAAAGG
AAAGAAACTCATCCCTCTTATCATAGGCGCTCNGTATTTGATCGTTAAGATGATTCAAGG
AGCAATCAGAAATGATATCAAGACAAGTGGAAAGCCACTTTAAGAGGCTCTGAAGAAGNG
GTTTTGTTGTGAGCAAATTACAAGGAGAAGAAGNGTTTTTCGATTGTTCTTTCTTTTGTT
AGATTTTATCTGCAACATTTTCTTGTTTCCGGCTTTATCTTTGTCTGTAATTTATGGAGA
TTTGTTCAAAGAAAAGATTGCCATGCTTTCTGGTTAAATGAAATGGATGTTTCCC
>gi|2412846|gb|AA597423.1|AA597423 29694 Lambda-PRL2 Arabidopsis thaliana cDNA clone 197P18T7, mRNA sequence
CACATAACAGGTACTAACATTGGAGGTCATGCTGTTAAACTTATTGGCTGGGGAACTTCT
GATGACGGTGAAGATTATTGGTTGCTTGCAAATCAATGGAACCGAAGCTGGGGTGATGAT
GGGTACTTCAAGATCAGGAGAGGAACAAACGAATGTGGCATTGAACATGGTGTTGTAGCT
GGTTTACCTTCAGACAGGAACGTAGTTAAAGGTATTACTACTTCAGATGATCTTCTTGTT
TCCTCATTTTAAACAGGAATATGTGTCTCTACTCTGTAATACATAATTTCCCACTGTGTT
GTTGTTACCAATGAAATAAAACGGCTTTCAACCCAAAAAGGAAGTCTATTGTATATACCA
TTTAGCTTTTTTGTNCATATTCAATATAATGGGGTTGGTGGTTCCCATGGAAGGATCCAA
AGGCATTCCACCTNTCTTCCATTTCG
>gi|2393553|gb|AA586141.1|AA586141 28790 Lambda-PRL2 Arabidopsis thaliana cDNA clone 80B1XP 3', mRNA sequence
CAGGGGTNTNCCCCCCCCCCCCGTCNAGNATCCAAGCGTNCCCTCCCGNGNCCGGGNTTT
TNAAAGAANGCCGTAACCAATGGCCCGGGACCCTGCCCGNTTGGAAANCAAGNGCNCCGG
AAANCNCTGGGGTAATGGNGCATATCCCCATCCGCNAACATCNTAAGATGGGATCNCTTG
GTGGATNGCCCAGAGCAGTAATGACCCTGAAGGGACTTCGCATCTTCTACTATCTTGTTC
CAGGACTTGAAATGTCTTGTTTTTTCGCTCATCTCTCTGCACTTCAAAATCAAGCCTATC
TAGAGAAGAAAATCAGTTTGTGACATGTCAAGACGCGATGAATTTGTTGGGAACATGAGG
ACTTTGTGACTGAAGTTTGGTTGTTTTTATGTCTCTGGTTCTCTGTTTTTTTTTTTTTGT
TGGATTTGGGTGAAAGTGGGTATGTAAGATGTTCTACCTCAACTTTTGGTCCTTTTTTGT
GTCAACATCCCATGTGAAGAACCTTTCATGAACCACAACCTATCTTCT
>gi|623629|emb|Z47590.1|Z47590 ATTS4446 Strasbourg-A Arabidopsis thaliana cDNA clone FAI255 5', mRNA sequence
AGCAGACTCTGTTTTCATGGCTGTTTACAATACCAAACTCTGTTTGGCCTCTGTTTTCTT
GCTCTTAGGGCTTCTCTTGGCTTTTGACTTGAAGGGTATAGAAGCAGAAAGTCTTACCAA
ACAGAAACTGGACTCGAAGATACTTCAGGATGAGATTGTGAAGAAAGTCAACGAAAACCC
AAACGCTGGATGGAAAGCTGCTATAAATGATCGATTTTCAAACGCCACTGTTGCAGAGTT
TAAGCGTCTTCTCGGTGTTAAACCAACACCAAAGAAGCATTTCTTAGGTGTTCCTATTGT
GAGCCATGATCCATCTTTGAAGCTACCTAAAGCTTTTGATGCTAGAACTGCTTGGCCACA
GTGCACTAGTATTGG
>gi|453733|emb|Z29751.1|Z29751 ATTS2195 Ors-A Arabidopsis thaliana cDNA clone OAO139 5', mRNA sequence
CAGATCTTTTTGAAATTGGATTCATCTAAGAAGCAGACTCTGTTTTCATGGCTGTTTACA
ATACCAAACTCTGTTTGCCTCTGTTTTCTTGCTCTTAGGGCTTCTCTTGGCTTTTGACTT
GAAGGGTATAGAAGCAGAAAGTCTTACCAAACAGAAACTGGACTCGAAGATACTTCAGGA
TGAGATTGTGAAGAAAGTCAACGAAAACCCAAACGCTGGATGGAAAGCTGCTATAAATGA
TCGATTTTCAAACGCCACTGTTGCAGAGTTTAAGCGTCTTCTCGGTGTTAAACCAACACC
AAAGAAGCATTTCTTAGGTGTTCCTATTGTGAGCCATGATCCCATCTTTGAAGCTAC
>gi|402964|emb|Z26362.1|Z26362 ATTS1481 Gif-SeedA Arabidopsis thaliana cDNA clone YAY048 3', mRNA sequence
TTTAAATGAGAAAGATTGTGAGTCCTCACAAAACCACAAGACTCAATTTAATCAATCCTC
AAATTTACATGATACCAACGTAATGAGAGCTTAAAANTAAATGAGAAACTTGGACATAAT
CAGTTGATGGAGTAGGAACGAGAACAGACAGTCTGGAGAGATTCAGTGAAGAGAGATGAG
AAGCTGGTCAAGGCCTGGAATACATTGGGCAGGCCGGTTTGTAGATTGTTGAGAGTCATA
GCTCGTGTCACCTTCCACAGCCTTCACGTGCCTCATTACCTCATCCTTCCACCTGGCCTT
TGACATGCCGGCAGTCACATTTTCTTCTCAGATAGGGGGGTCCCGTGAGTTCCACAACTT
CGGTTCCAGGGGCTATTCCAACCGTTGGGGTATTGCCT
>gi|402959|emb|Z26361.1|Z26361 ATTS1480 Gif-SeedA Arabidopsis thaliana cDNA clone YAY048 5', mRNA sequence
GAAGAGCCTGTTAACAACCACATCAAGACCCAAATGGCAAAGAGCACTCTGACCATGTTA
CCACTTCTTCCGACTGCTACAAGACCAAATTGGTGGTAAGGCACAAGAATTTGAAGGAGA
TCCTTGACGCCGTTCAAGACTACTTCGACAAGGCTGCCTCCGCTGGGGACCAGGTCTCCG
CCATGCTTGAGATCGGCCGGGCTGAGCTCGACCGCAGCTTCAGCAAGCTGAGGAAGACGG
TGTATCATTCAAGCAGTGTGTTCAGCAACTTGAGCGCAAGCTGGGACCTCAAAACCCCCA
TTGGCAGTCAAATACAAGCTCGATGCATCTACCCTGAATGATGAACAAGGCGGCCTCAAG
AGCCTCTTGTTCACTCTAGACCGACTTCTCGCTTGGGAAAAGAAGCTTTATTGAGGATGT
AAA
>gi|403229|emb|Z26415.1|Z26415 ATTS1541 AC16H Arabidopsis thaliana cDNA clone TAI278 5' similar to A.Thaliana mRNA for ara-5,partail sequence, mRNA sequence
GAAAAGAGAGAGAGAGATCTCTGGCTCTGTATCGCTCGCTGCTCTTCCTCCCACAGATCG
AAAACCATGAATCCTGAGTACGACTATCTTTTCAAGCTCCTGCTTATGGGGGATTCTGGC
GTAGGCAAGTCTTGTCTTCTTTTGAGATTCTCTGATGATTCTTATGTAGAAAGTTACATT
AGCACTATTGGAGTCGATTTTAAAATTAGGACTGTGGAACAAGATGGCAAAACAATTAAG
CTCCAAATTTGGGACACTGCTGGTCAAGAACGGTTCAGGACTATTACTAGCAGTTACTAC
CGTGGGGCACATGGAATTATTATTGTCTACGATGTCACAGATGAAGAAAA
>gi|398270|emb|Z25982.1|Z25982 ATTS1259 Versailles-VB Arabidopsis thaliana cDNA clone VBV38-10992, mRNA sequence
ACCTCTTGAGTTTGTATGGCAGCCTTGGTAACAAGAAAGAGCTGTACCGAGTCTGGCACG
TCTACAAATCTGTTGTCCCGAGCATTCCCAATTTGGGTTACCATGCCTTGGTCTCGTCGC
TGGTNAGGATGGGAGACATTGAAGGGGCCNAGAAGGTATATGAGGAATGGCTTCCAGTCA
AGTCTTCTTATGACCCCAGGATACCAAATCTTCTGATGAATGCGTATGTCAAAAACGACC
AACTAGAGACAGCTGAGGGGTTGTTCGNCCACATGGTTGAAATNGGAGGAAAACCAAG
>gi|397246|emb|Z25655.1|Z25655 ATTS1120 Versailles-VB Arabidopsis thaliana cDNA clone VBVYA12, mRNA sequence
CAATCGCGGTAGTCTATGCAGAGAACAGCGGAAGATGCAGCAAGAACGATAAGGACGAAA
AGGCTCTTCCAAATGGTGAAGCGTGGATCCCGAACTTGGTTAAGGCGATAACTGATGTAG
CAACAAACCAGAGGAAAGCAATTCATGTAGACAAGAAGATGGTAGATGGATCTTACTCTG
ATGATAAAGGAAAGAAACTCATCCCTCTTATCATAGGCGCTCAGTATTTGATCGTTAAGA
TGATTCAAGGNGCAATCAGAAATGNTATCAAGACAAGTGGAAAGCCACTTTAAGAGGCTC
TGAAGAAGAGGTTTTTGTTGTGAGCAAATTTCCAAGGNGGAAGAAGAGTTTTTCGATTGC
CC
>gi|397216|emb|Z25629.1|Z25629 ATTS1092 Versailles-VB Arabidopsis thaliana cDNA clone VBVID01, mRNA sequence
GGACACAGCTCTTACATTCATGTTTCACTAGGCAGTCTCTTGTGTACATTATACATATTT
CGCATTTCCTCAGTTGACTCCGGTTACAAGATTCGTTTTTTAAAGCAAAGATCTAGGACT
ATCAGATTACAAATCATCTTGTAGCTGTGTTAGAAGCGCATCGGTCTCATGGGCATCGAT
TTCACTGTTGTTTACTGTTCTGTTTTCGTCCACATCAATAAGAGCTAGGTAAGATTTGTC
TTCAAGATCCCCCGACTGCCTTAACAATTCCAAAACGGCCTCTTTACTGGTAACATCCGA
TTCCTCTTCACAGAGCTTGAAGAAACCAGACAGCATCAACACCTTGGGNCTCCAATTGCT
GGNCCCTTCAGCCGAAAAAGCATTTCTAAG
>gi|397215|emb|Z25628.1|Z25628 ATTS1091 Versailles-VB Arabidopsis thaliana cDNA clone VBVID01, mRNA sequence
CGGTTGTCTGCAAGTGATGCTGCAATCCAGCTCGACTTAATCGGCAAAGTGCGTGGCATT
CCAGACGCCGAAGAGTTCTTCCTCCAGCTCCCTGAGAATTTTAAGGACCGGAGAGTTTAT
GGTTCCCTCCTCAATGCCTATGTGAGGGCCAAGTCGAGAGAAAAGGCTGAAGCCTGCTCA
ACACCATGAGGGACAAAGGTTACGCCCTGCACCCGCTTCCCTTCAACGTCATGNTGACTC
TCTACATGAACCTCAGGGAGTATGACAAAGTCGACGCTATGGTCTTCGAGATGAAGCAGA
AAGNTATACGTCTCGACATTTACTCCTACAACA
>gi|396603|emb|Z25487.1|Z25487 ATTS1001 Grenoble-B Arabidopsis thaliana cDNA clone GBGe40, mRNA sequence
ACTAAACGGGTCTGGAGAAATGTACGTGCAAAAGTATCCGAAGTTGAAGATAAGACTAGT
GGACGGGAGCAGCATGGCAGCTACGGTGGTTATCAACAATATTCCAAAGGAAGCCACGGA
AATTGTCTTTAGAGGAAATCTCACAAAGGTGGCTTCGGCTGTTGTCTTTGCTCTGTGCCA
AAAGGGCGTCAAGGTGGTCGTGTTACGCGAGGAGGAACACAGCAAACTCATCAAATCTGG
GGTTGACAAGAATCTGGTACTGTCTACAAGCAATAGTTATTACTCCCCAAAGGTGTGGTT
GGTGGGGGATGGAATAGAGAACGAAAGAGCAGATGAAAGCAAAGAAGGACCTCTTTGTTC
CCTTTTCTCACTTTCGCCCAACAAACTCGCAAGACTGTTTCTACCAGTCCACTCCAGCTA
TGCGTGTTCCCAAGTCTGCCCAAAACATCGACTCCTGTGAGAACTGGCTGGGGAGGAGGG
TGATGAGTGCATGGAAAATAGGAGGTATAGTGCATGCACTTGAGGGTTGGGAGGAGCATG
ACTGCGGCAACACTTGCAACGTCCTCCGTCTCCACGCCATATGGGAAGCTGCTCTTCGCC
ATGATTTCCAACCTCTCCCACCATCTCCTCTATGTGCTTTTTTCATATTGATATATCTAT
GTCCCCTTTCTTGATTATATCTACTTCCCTTCCATCATTGTTTCCTGTTTACTATGTTTT
TCTATCGACTATATATAAGTACCCTTGTT
>gi|17325|emb|Z18783.1|Z18783 ATTS0641 Versailles-VB Arabidopsis thaliana cDNA clone VBV12-30792 3' similar to cathepsin B-like cysteine proteinase precursor (EC 3.4.22.-). Swiss-Prot entry P05689, mRNA sequence
TGAATATGAACAAAAAGCTAAATGGTATATACAATAGACTTCTTTTTGGGTTGAAAGTCG
TTTTATTTCATTGGTAACAACAACACAGTGGGAAATTATGTATTACAGAGTAGAGACACA
TATTCCTGTTTAAAATGAGGAAACAAGAAGATCATCTGAAGTAGTAATACCTTTAACTAC
GTTCCTGTCTGAAGGTAAACCAGCTACAACACCATGTTCAATGCCACATTCGTTTGTNCC
TCTCCTGATCTTGAAGTACCCATCATCACCCCAGCTTCGGTTCCNTTGATTTGCAAGCAA
CCAATAATCTTCACCGTCATCAGAAGTTCCCCAGCCAATAAGTTTAACAGCATGACCT
>gi|17300|emb|Z18780.1|Z18780 ATTS0623 Versailles-VB Arabidopsis thaliana cDNA clone VBV12-30792 5' similar to Cathepsin B-like cysteine proteinase precursor. Swiss-Prot entry P25792, mRNA sequence
GCAAATCATTGTNNTTNATTACTGGAACTCGTTGAGGGATTGAGAAAAAANTAATCAGAA
GAGAAAGATCCATGGCTGATAATTGTATCAGACTTCNTCACTCAGCCTCTGTTTTCTTCT
GTTTAGGGCTTCTAATTTCATCCTTCAACTTNTTGCAGGGTATTGCAGCTGANAATCTTT
CCAAGCAGAAACTGACCTCATGGATTCTTCAGAATGAGATTGTAAAGGAAGTCAATGAGA
ATCCAAACGCTGGATGGAAAGCTTCTTTCAATGATCGGTTTGCAAACGCCACTNTTGCAG
AGTTTAAGCGNNTTCTTGGNGTTAAACCANCACCAAAGACGGAATTTTTG
>gi|17520|emb|Z18418.1|Z18418 ATTS0793 Grenoble-B Arabidopsis thaliana cDNA clone GBGa464 5', mRNA sequence
GAGAAAGCGATACTGGAGGCAGATAAGAAAGGAGTGAAGGTGCTTAGTCTGGGTCTCATG
AACCAAGGGGAGGAGCTTAACAGGAACNAGAGGTGTATATCCACAACCATCCAGTATATG
AAAGTGAGACTGGTCGACCGGCAGTAGATTAGCAGCAGCTGTTGTGAT
>SQ;19741042
GGATGAATTTGTTGAATCCATTAAAGTAAGTCAGTAACAAGCATCTCCGTTGTTACATTA
CATCATGTCCTCTCTGAGGAATGCTACATTACATCGACCCAAAACATTGTCTCTATTTGT
AGGATTACCTAACATCCAGGCCATTTCTTATGAAAAGGATCTTCCTTCTTCATCTCCCGG
CTGCAAGTATACTTTGGCTTTTTTTACCAAGACAATGGGAGGGAAACCTCGCCGCAGCTC
AAGTCTCTCAAAGCCTTCTTCATAAAATAAGCACTTGTATCCATCTACAGAGGAATGCTC
GTTCACCAGGTACGTGAAATTTCGGTTTCGCAACTCCTCCACTACTATCTCTTCTTCTTT
GGAATATCTCCACGGAAAATCATCTTCACAAAAGCGAGATATCCATTCATCGCACCAAAA
GTGTCTATGTGAACCCACTCTTCCCAGCTAGATTTGGAGG
>SQ;19741846
AATTAGAAAACATGTTTGTGAATCTTGAAGTTAAATAAATAAACTAAGACTCCTAAAATC
TCTCCTACTGTATGTATAATTGTTACAACATAATATCAAAATACGCATACATATATACAA
GTTGAAAGCTAAAGAGCTAGTGAGAATTGTCTGAGACCCAACCTCCCGAAACCATTCCCT
CGTCGAAAGGCTTCAGGCCACCACAGGATCTGGCTACCGATTCAAACAGCTTCTCAATCT
CAGGCGCACATCTGATGAAGGCTTGTTTCCAGAAGCTATATCTTGGGTTCTTTATTAGCT
CAATGAATGTGATTAGAAGTCCCCATGGATGTGGCCTGTTCACAATTAGCCGTTCCAACA
GCACTCTAGTTATTTGCTCC
>SQ;19742246
GAAGATTTTTATTGAGTTTTATAAAATTTAACTAAGCATATCATACGACGAATTTTTTTG
CCCTTTCTAACATATATGAAGCACGTGGCACCAAGGGTAACAAGGGTACTTATATATTGT
CGATAGAAAAACATAGTAAACAGCAAACAATGATGGAAGGGAAGTAGATATAATCAAGAA
AGGGGACATAGATGTATGAATATGAAAAAAGCTCATAGAGGAGATGGTGGGAGAGGTTGG
AAATCATGGGGAAGAGCAGCTTCCATATGGCGTGGAGACGGAGGACGTTGCAAGTGTTGC
CGCAGTCATGCTCCTCCCAAACCTCAAGTGCATGGACTATACCTCCTATTTTCCATGCAC
TCATCACCCTCCTCCCCAGCCAGTTCTCACAGGAGTCGATGTTTTGGGGAGACTTGGGAA
CAG
>SQ;19798134
GGATAAAGGAAAACATTGATTTGGTGATTCGATAACAAAATGTGCCATCTATTCTTTAGC
TCTTTACAAACAAGCAGCAAATGGTTTGCCTTTCAGAATCAAAATTTAAGGTGTTTCTCG
AATAGACAGAAGGAAGAGAAGAGAAGTCCCAGAAAGCTGTTCAGAAGGCGCATACAAATC
ATGTGTGCGTTGCTGCTGCAAGGAAAAGCACTTCCGCTGTAGCAGCCTGTTCTTTGTTTG
ATACCCCGGCCGTTATCTTCCAGTAAAAAGGAGGAGTTTTTCAAACCATCGCTAAAGAGA
AGAAACCAAAAGAAGGTACCTTTATGCAACCTAGCCATTCCCACTCCAACCTCGGTATGG
GACCTGTTTCTGAGCACCGACAAGGCACTGCTATCTCTAAAGAGAATGTCTG
>SQ;19798999
ACGACAAACGAAACGAGAGACATGAAATAAAACGTTACACATTACCGACTAATTCAGATG
ATAGACAGCTAGCATTAACTAGCTGATATTGAAGAGTCCTTTGATTTCTCATTTTAAGCA
TAATATATCATATGAGTAAAGCTTATAACTATCCGCTGGAGAAAAACATTGAATTTGAAG
ACGAAGACGCTGACGTGGATGAAGACGCTGTCGTTTGGAACCGCCTTTGCCGGAAGCACT
CCAGTGATATCGTAGGCGGCGCGTTGGACGACGGTGACGATGACGCTTTAACACCCGAAT
CGTTCGGTGACTTTGGAGTAGTCTTGCCGGTGCCGGCTGTCTTGGGTGGCGGAGGCTGAT
TGGTGACATTTACGGCGGCGGCGGTTATGGTCAGCA
>SQ;19801463
CGGCTAATCCAGTTCCCTAAGCAACACTAATTCCAAATAGCTGTCACAAAAAGGGACACA
GCTCTTACATTCATGTTTCACTAGGCAGTCTCTTGTGTACATTATACATATTTCGCATTT
CCTCAGTTGACTCCGGTTACAAGATTCGTTTTTTAAAGCAAAGATCTAGGACTATCAGAT
TACAAATCATCTTGTAGCTGTGTTAGAAGCGCATCGGTCTCATGGGCATCGATTTCACTG
TTGTTTACTGTTCTGTTTTCGTCCACATCAATAAGAGCTAGGTAAGATTTGTCTTCAAGA
TCCCCCGACTGCCTTAACAATTCCAAAACGGCCTCTTTACTGGTAACATCCGATTCCTCT
TCACAGAGCTTGAAGAAACCAGACAGCATCAACACCTTGGGCCTCCAATTGCTGGACCCT
TCAGCCGAAAAAGCATTTCTAAGACAAGTCAAAGCCTCTGAAATACACCTCTTTCTGGTA
TGACCAACAGCTAGAATCTCCCACGTACTTGAACTTGGTTTTCCTCCCATTTCAACCATG
TGGTCGAACAACCCCTCAGCTGTCTCTAGTTGGTCGTTTTTGACATACGCATTCATCAGA
AGATTTGGTATCCTGGGGTCATAAGAAGACTTGACTGGAAGCCATTCCTCATATACCTTC
TCGGCCCCTTCAATGTCTCCCT
>SQ;19801855
GAAAACAACAACACATTATATTGAATATGAACAAAAAGCTAAATGGTATATACAATAGAC
TTCTTTTTGGGTTGAAAGTCGTTTTATTTCATTGGTAACAACAACACAGTGGGAAATTAT
GTATTACAGAGTAGAGACACATATTCCTGTTTAAAATGAGGAAACAAGAAGATCATCTGA
AGTAGTAATACCTTTAACTACGTTCCTGTCTGAAGGTAAACCAGCTACAACACCATGTTC
AATGCCACATTCGTTTGTTCCTCTCCTGATCTTGAAGTACCCATCATCACCCCAGCTTCG
GTTCCATTGATTTGCAAGCAACCAATAATCTTCACCGTCATCAGAAGTTCCCCAGCCAAT
AAGTTTAACAGCATGACCTCCAATGTTAGTACCTGTTATGTGCTTGTACACTCCAGATTT
GTAATGCGCAAAGTCCTCGTAAACAGTGAAGGCAACCTCAACAGGTCCATTTTTGTAAAC
TTCTGCCATAATGTCATCAGGGTGAGATCTGACCTTGTACGCACTAACACCATAATGTTT
TGATTCACGCCAAAGCTGGTTTCCGCTAACACATTTCCTTGCACATTTTGGTGTA
>SQ;19803773
GGTAAGAAAACAGCAAGTATATGGTTTTTAGAAGATAGGTTGTGGTTCATGAAAGGTTCT
TCACATGGGATGTTGACACAAAAAAGGACTAAAAGTTGAGGTAGAACATCTTACATACCC
ACTTTCACCCAAATCCAACAAAAAAAAAAAACAGAGAACCAGAGACATAAAAACAACCAA
ACTTCAGTCACAAAGTCCTCATGTTCCCAACAAATTCATCGCGTCTTGACATGTCACAAA
CTGATTTTCTTCTCTAGATAGGCTTGATTTTGAAGTGCAGAGAGATGAGCGAAAAAACAA
GACATTTCAAGTCCTGAACAAGATAGTAGAAGATGCGAAGTCCTTCAGGATCATTACTGC
TCTGGCAATCAACAAGAGATCCAATCTTAGATGTAGCGAATGAGATATGCTCATTACCCA
AGACGATCTCGAGCTCTTGCTTTCCAACACGGTCAGGTTCCGGCCAATTGTTATCGTCTT
CTTTCAGAATCTCGCTCTCGGAGACGATACGCTTGCATTCCTTGAGCACGGCGGGGGTGA
GAAATACCTCCTTGCGGATAATAGTATCGTTCTTGTAGTTAGAGGTATTGGCGTAACGGA
GCTTACCGTCCTCTCTAAACTCGAACT
>SQ;19805724
AATAACCAACCAAAGGAGCTTAATTACAGACAAGACAGATTTGGGGGGATGTTGTGTAAA
AACCAAGTAGTAGTGAATTGGAGCCTAGTCAAAAGAAGGAACACGTGTTCTAAGATTGGA
AAGGATATTGCTAGGCTGGTCACGTCAATCAAGTTGAGCAGCAGCCGTTCTTCTGTGCCA
CAGGCTGTCCTCTGATCTGCACGGTCGGTGGTCTTGCATTATTCCCAGCTGGTTGGCTAG
CCATTCTCTCTTTGATGGATGCAGACATTGCCATGAAAGCCTGTTCTACGTTTGTAGCAT
CTTTTGCACTAGTCTCCATAAAAGGAATCCCGATTTCATCGGCAAAAGCCTTGGCAGTTT
CATAAGGAATGGCTCTGTTTTCAGT
>SQ;19806050
AGATTCATGAAAATAAATAAAAAATCTTTAAACAGACAAAACTATACAGCACACTCCATA
AGGTTCGTAAAGATGTCTCATTGCAAATGTCAATCTCATTGCTTGCTTTACATTTACAAG
AGCCGTAATTAAACAAAATTTAGCTACAAAGCATTTTGACTGGAGAGAATTGTACGGTGA
GACAAGCATGATCGGATATATTGTAATTCTCCGGGCAAAATCCTTTCTCTGCTTCTTGTG
GAAACAAAATTGCTTTATTCACTTTAAATCCGATTGGTTAATCTTCTACTTCTTCTTTCT
TACTCTCCATAAAACTCTCTTTGCAGTTTAAAGGTTGATTTACCATCGTCATGTTCAAAA
TTTTGTTAAGTTCTTCATAGTCGAAGAAACCATTTCGATCA
>SQ;19807151
GAAAAAACAATTTGTGGGTTTTAAATCGAGTCGTAAAACATTGTTATGCGAAGAAACCCA
TAGAAAACCACTAAAGGCAGAAATGAAAAACAAGAATGTTGGAAAGATGAGGACCTCATC
ATGAGGTAAAGCAAATAGGAAACGTGAAAAACAGAATAATAACCAACCAAAGGAGCTTAG
TTACAGACAAGACAGATTTGGGGGGATGTTGTGTAAAAACCAAGTAGTAGTGAATTGGAG
CCTAGTCAAAAGAAGGAACACGTGTTCTAAGATTGGAAAGGATATTGCTAGGCTGGTCAG
GTCAATCAAGTTGAGCAGCAGACCGTTCTTCTGTGCCACAGGCTGTCCTCTGATCTGCAC
GGTCGGTGGTCTTGCATTATTCCCAGACTGGTTGGCTAGCCATTCTCTCTTTGATGGATG
CAGACA
>SQ;19823046
CGGTTTTTAGAAGATAGGTTGTGGTTCATGAAAGGTTCTTCACATGGGATGTTGACACAA
AAAAGGACCAAAAGTTGAGGTAGAACATCTTACATACCCACTTTCACCCAAATCCAACAA
AAAAAAAAAAACAGAGAACCAGAGACATAAAAACAACCAAACTTCAGTCACAAAGTCCTC
ATGTTCCCAACAAATTCATCGCGTCTTGACATGTCACAAACTGATTTCCTTCTCTAGATA
GGCTTGATTTTGAAGTGCAGAGAGATGAGCGAAAAAACAAGACATTTCAAGTCCTGAACA
AGATAGTAGAAGATGCGAAGTCCTTCAGGATCATTACTGCTCTGGCAATCAACAAGAGAT
CCAATCTTAGATGTAGCGAATGAGATATGCTCATTACCCAAGACGATCTCGAGCTCTT
>SQ;19823987
TGTGGGTTGAAAGTCGTTTTATTTCATTGGTAACAACAACACAGTGGGAAATTATGTATT
ACAGAGTAGAGACACATATTCCTGTTTAAAATGAGGAAACAAGAAGATCATCTGAAGTAG
TAATACCTTTAACTACGTTCCTGTCTGAAGGTAAACCAGCTACAACACCATGTTCAATGC
CACATTCGTTTGTTCCTCTCCTGATCTTGAAGTACCCATCATCACCCCAGCTTCGGTTCC
ATTGATTTGCAAGCAACCAATAATCTTCACCGTCATCAGAAGTTCCCCAGCCAATAAGTT
TAACAGCATGACCTCCAATGTTAGTACCTGTTATGTGCTTGTACACTCCAGATTTGTAAT
GCGCAAAGTCCTCGTAAACAGTGAAGGCAACCTCAACAGGTCCATTTTT
>SQ;19825204
CGGTTGAAAGTCGTTTTATTTCATTGGTAACAACAACACAGTGGGAAATTATGTATTACA
GAGTAGAGACACATATTCCTGTTTAAAATGAGGAAACAAGAAGATCATCTGAAGTAGTAA
TACCTTTAACTACGTTCCTGTCTGAAGGTAAACCAGCTACAACACCATGTTCAATGCCAC
ATTCGTTTGTTCCTCTCCTGATCTTGAAGTACCCATCATCACCCCAGCTTCGGTTCCATT
GATTTGCAAGCAACCAATAATCTTCACCGTCATCAGAAGTTCCCCAGCCAATAAGTTTAA
CAGCATGACCTCCAATGTTAGTACCTGTTATGTGCTTGTACACTCCAGATTTGTAATGCG
CAAAGTCCTCGTAAACAGTGAAGGCAACCTCAACAGGTCCATTTTTGTAAACTTCTGCCA
TAATGTCATCAGGGTGAGATCTGACCTTGTACGCAC
>SQ;19825274
GGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAGTA
CTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCAA
AAGCTTGATATGCATAAATATATGTGTGGGCTTTATATATGTTTCATAGTTCATTTGTGC
GTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAAA
ATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTGA
GACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGCA
TTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTCATCGCCTTTC
TCGGTAACCAGTTCTCACAGGAGTGGAAATTCACCAGAGA
>SQ;19825742
GGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAGTA
CTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCAA
AAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGTGC
GTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAAA
ATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTGA
GACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGCA
TTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTCATCGCCTTTC
TCGGTAACCAGTTCTCACAGGAGTG
>SQ;19826275
AGATATTCTGGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAG
GAAATAGTACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCAT
AATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTT
CATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCAT
TCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGC
CGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCAC
ACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTCA
TCGCCTTTCTCGGTAACCAGTTCT
>SQ;19827386
GCATTATACATATTTCGCATTTCCTCAGTTGACTCCGGTTACAAGATTCGTTTTTTAAAG
CAAAGATCTAGGACTATCAGATTACAAATCATCTTGTAGCTGTGTTAGAAGCGCATCGGT
CTCATGGGCATCGATTTCACTGTTGTTTACTGTTCTGTTTTCGTCCACATCAATAAGAGC
TAGGTAAGATTTGTCTTCAAGATCCCCCGACTGCCTTAACAATTCCAAAACGGCCTCTTT
ACTGGTAACATCCGATTCCTCTTCACAGAGCTTGAAGAAACCAGACAGCATCAACACCTT
GGGCCTCCAATTGCTGGACCCTTCAGCCGAAAAAGCATTTCTAAGACAAGTCAAAGCCTC
TGAAATACACCTCTTTCTGGTATGACCAACAGCTAGAATCTCCCACGTACTTGAACTTGG
TTTTCCTCCCATTTCAACCATGTGGTCGAACAA
>SQ;19827775
GCTGGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATA
GTACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCAC
CAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTG
TGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCTTTCTCCT
AAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGT
TGAGACAGGCTTCCCATACTTGGTCCAAATCCGATAGAAGAAGGGATGTGCCCCACTCAT
GCTATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCAGTCAT
>SQ;19828054
CGGGAGAAGAAAAACTTAGATATTCTGGAACATGTTTGCTTTATATATATATGTTTCTTA
GTTCACAAAGAGAAAAGGAAATAGTACTCTTATTAATACCATAGTCACCGAGCTTAATTT
GACTCTATCAATACCATAATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTT
ATATATGTTTCATAGTTCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACA
GAGCGTGTCGCCTCTCATTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAA
GGAGGAGAGGCTGGAAGCCGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGA
GAAGAAGGGATGTGCCACACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGG
CCACTCTAGTTGCACTCATCGCCTTTCTCGGTAAC
>SQ;19828253
GGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAGTA
CTCTTATTAATACCATAGTCACCGAGCCTTAATTTGACTCTATCAATACCATAATCACCA
CAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGTG
CGTGGAAGAGCTGGATCATAAGGAAAAGAAGGACAGAGCGTGTCGCTCTCATTCTCCTAA
AATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTG
AGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGC
ATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTCATCGCCTTT
CTCGGTAACCAGTTCTCACAGGAGTGG
>SQ;19828552
CGTCACAAAAAGGGACACAGCTCTTACATTCATGTTTCACTAGGCAGTCTCTTGTGTACA
TTATACATATTTCGCATTTCCTCAGTTGACTCCGGTTACAAGATTCGTTTTTTAAAGCAA
AGATCTAGGACTATCAGATTACAAATCATCTTGTAGCTGTGTTAGAAGCGCATCGGTCTC
ATGGGCATCGATTTCACTGTTGTTTACTGTTCTGTTTTCGTCCAAATCAATAAGAGCTAG
GTAAGATTTGTCTTCAAGATCCCCCGACTGGCTTAACAATTCCAAAAGGGCCTCTTTACT
GGTAACATCCGATTCCTCTTCACAGAGCTTGAAGAAAACCAGACAGCATCAACACCTTGG
GCCTCCAATTGCTGGACCCTTCAGCCGAAAAAGCATTTCTAAGACAAGTCAAAGCCTCTG
AAATACACCTCTTTCTGGTATGACAACAGCTA
>SQ;19829297
CACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCAAAAGCTTGATA
TGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGTGCGTGGAAGAGC
TGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAAAATCTTCCAAG
GTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTGAGACAGGCTTC
CCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGCATTTCCCATCC
TTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTCATCGCCTTTCTCGGTAACCA
GTTCTCACAGGAGTGGACATTCACCAGAGATTTTGGAACTATCAATGCTGGTGTGGTATG
ATAGATACA
>SQ;19829716
AAGGAAATAGTACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATAC
CATAATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATA
GTTCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCT
CATTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGA
AGCCGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGC
CACACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCAC
TCATCGCCTTTCTCGGTAACAGTTCTCACAGGAGTGGACATTACCAGAGATTTTGGAACT
ATCAATGCTGGTGT
>SQ;19829934
GGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAGTA
CTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCAA
AAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGTGC
GTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAAA
ATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTGA
GACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGCA
TTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTCATCGCCTT
>SQ;19831127
AAGGAAATAGTACTCTTATTAATACCATAGCTCACCGAGCTTAATTTGACTCTATCAATA
CCATAATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCAT
AGTTCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTC
TCATTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGG
AAGCCGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTG
CCACACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTACTTGCA
CTCATCGCCTTTCTCGGTAAACAGTTCTCACAGGAGTGGACATTCACCAGAGATTTTGGA
ACTATCAATGC
>SQ;19831839
ACTGGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATA
GTACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCAC
CAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTG
TGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCT
AAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGC
TGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCAT
GCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACT
>SQ;19831991
AAGTGGGCAGAGAGACACCAAATTTGCTAATGAGGGAAATCAAACATAACAAGGGGTTAT
TGTGAGAGAGAACAGAGGATCTTATACAAGTTGAAAATCCGCAACCAAATAATCATAATC
TACTCTCGGTAAATGGAATGTCAATCCGCACTGACCATTTGCTCTCTCTTGCTCCTCTAC
CTTGTTACAGGATGCCTCCTCCTCTTTGGTCGGATCCCATCTTCTTCGTAGTCCATCACT
CCACTTGGTTCCCCAAACATCTCCTTATTCCCTCTGATGTCAACATCCCCCTTCATGGAC
AGAGACTTCTTCACTTCTTCCACCCCTTCTTCTGCTTCCTTACGATGTTTTTTGTCCATC
TCACTCATATTGTCCGCCCATTTGATCTTGTCTTGAATTGA
>SQ;19833332
GAGAGAAGAAAAACTTAGATATTCTGGAACATGTTTGCTTTATATATATATGTTTCTTAG
TTCACAAAGAGAAAAGGAAATAGTACTCTTATTAATACCATAGTCACCGAGCTTAATTTG
ACTCTATCAATACCATAATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTA
TATATGTTTCATAGTTCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAG
AGCGTGTCGCTCTCATTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGG
AGGAGAGGCTGGAAGCCGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGA
AGAAGGGATGTGCCACACTCATGCATTTCCCATCCTTCTAAGGCG
>SQ;19834843
GGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAGTA
CTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCAA
AAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGTGC
GTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAAA
ATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTGA
GAAAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGCA
TTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTCATCGCCTTTT
CGGTAACCAG
>SQ;19835442
GGGTTGAAAGTCGTTTTATTTCATTGGTAACAACAACACAGTGGGGAATTATGTATTACA
GAGTAGAGACACATATTCCTGTTTAAAATGAGGAAACAAGAAGATCATCTGAAGTAGTAA
TACCTTTAACTACGTTCCTGTCTGAAGGTAAACCAGCTACAACACCATGTTCAATGCCAC
ATTCGTTTGTTCCTCTCCTGATCTTGAAGTACCCATCATCACCCCAGCTTCGGTTCCATT
GATTTGCAAGCAACCAATAATCTTCACCGTCATCAGAAGTTCCCCAGCCAATAAGTTTAA
CAGCATGACCTCCAATGTTAGTACCTGTTATGTGCTTGTACACTCCAGATTTGTAATGCG
CAAAGTCCTCGTAAACAGTGAAGGCAACCTCAACAGGTCCATTTTTGTAAACTTCTGCCA
T
>SQ;19836538
GATTGGGAAACATCCATTTCATTTAACCAGAAAGCATGGCAATCTTTTCTTTGAACAAAT
CTCCATAAATTACAGACAAAGATAAAGCCGGAAACAAGAAAATGTTGCAGATAAAATCTA
ACAAAAGAAAGAACAATCGAAAAACTCTTCTTCTCCTTGTAATTTGCTCACAACAAAACC
TCTTCTTCAGAGCCTCTTAAAGTGGCTTTCCACTTGTCTTGATATCATTTCTGATTGCTC
CTTGAATCATCTTAACGATCAAATACTGAGCGCCTATGATAAGAGGGATGAGTTTCTTTC
CTTTATCATCAGAGTAAGATCCATCTACCATCTTCTTGTCTACATGAATTGCTTTCCTCT
GGTTTGTTGCTACATCAGTTATCGCCTTAACC
>SQ;19837074
ATGGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAG
TACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACC
AAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGT
GCGTGGAAGAGCTGGATAATAAGGAAAAGAAGCCCAGAGCGTGTCGCTCTCATTCTCCTA
AAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCT
GAGACAGGCTTCCCATACTTGGTCCAAATCGAGAGAAGAAGGGATGTGCCATACTCATGG
CTTTCCCATCCTTCTAAGGGGTGCAATATGCGGGCAACTCTAGTTGCCCTCATCGCC
>SQ;19837290
GGTGCAACACGAATACAATTGATTACATCATTTCGTTTAACAGAGTCTCTGCTCATATTC
ATATGAGTAGGTAGGTATAACAACAACTTTGCAAAGTAACGTCCGATAATACATTACATA
CATACATGCATATATCCATCCGCATTCTGCACAAACAGAGAGTAGGGTGTAGCAAATTTA
CTGTTTGTTGCGGCGGAGGAGGCGTTCCAAATGGTGGAACTGAGCCTTCAAGGCGGCATG
GTCTTGTCGCATCCTCTGCAAACGATCCTCAACCATCATCATCTCTTCCCTCAGGAAATG
CATTCTCTTCTCTAACCACCCCAAAGTCTCCCCGTTTACACTGTACTCGTCGTACCTCTC
ATGATACTCCACTTGCCCCCCTCCTCCTTTTTTCAGTAGCACCACTATCGTC
>SQ;19837778
GGACAACAAAACGCAAATATGATAGAGCGGAAGCTCATTAAAAAATCGTTTTAGAGCAAT
GTCACCAAACAAAGAAAATCCATTTCCCAATAAAAAAACAACGAATATAAAATTCGATTA
TATATTTACCATCAACCACTTAACAGACCACAAAATGAAGGCTGTTTACGGATTCAACAC
AGATTAACGGGTATGTATGTATGATCTAGGCAACGGTGGTGGTGGGACCAGGATAAGCAG
GAAGAGTCATGATCCGCTTGTCTACAACTGGACCTCCCACAGTGAAATGGTACAGACTCT
GAAAGCTAGAGTCATTAATCCCCAGAA
>SQ;19837990
AACTAAATAAATAACCACTTGCTCTCAAAGTTTAACAGGTATACACCATGATTCACCAAT
GGGGAGTAAAAAGTAACATTAACAAACACTTTCCACTTGTTTACTTAGATAGATCATACA
AACACAGCCATTGCAAATGAAACAACAGGATACTACTAGCTAGGTGATGTTCTGAGACAT
CATTGGTATTCGAGGATCTGCATTCACGAGAACAACGACCGTGTCTTATTGCGTTCCAGT
CGAGCTTCCCTCTCTTTCTTCTTGCATTCCTTGTACACATCAAAATGATCCTGGCATTTA
CTCTTGTCTGATCCAAATTCTTCAAGACATTTGAGAGAAGCAGAGTACTGAAGATAACAT
GGAGAATCAGATATCCGAGCCGCGCTAGGGTACGCCGC
>SQ;19838343
AAGGGACACAGCTCTTACATTCATGTTTCACTAGGCAGTCTCTTGTGTACATTATACATA
TTTCGCATTTCCTCAGTTGACTCCGGTTACAAGATTCGTTTTTTAAAGCAAAGATCTAGG
ACTATCAGATTACAAATCATCTTGTAGCTGTGTTAGAAGCGCATCGGTCTCATGGGCATC
GATTTCACTGTTGTTTACTGTTCTGTTTTCGTCCACATCAATAAGAGCTAGGTAAGATTT
GTCTTCAAGATCCCCCGACTGCCTTAACAATTCCAAAACGGCCTCTTTACTGGTAACATC
CGATTCCTCTTCACAGAGCTTGAAGAAACCAGACAGCATCAACACCTTGGGCCTCCAATT
GCTGGACCCTTCAGCCGAAAAAGCATTTCTAAGACAAGTCAAAGCCTCT
>SQ;19839622
AAAGGAAATAGTACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATA
CCATAATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCAT
AGTTCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTC
TCATTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGG
AAGCCGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTG
CCACACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCA
CTCATCGCCTTTCTCGGTAACCAGTTCTCACAGGAGTGGACATTCACCAGAGATTTTGGA
A
>SQ;19840006
GGTTTTTAGAAGATAGGTTGTGGTTCATGAAAGGTTCTTCACATGGGATGTTGACACAAA
AAAGGACCAAAAGTTGAGGTAGAACATCTTACATACCCACTTTCACCCAAATCCAACAAA
AAAAAAAAAACAGAGAACCAGAGACATAAAAACAACCAAACTTCAGTCACAAAGTCCTCA
TGTTCCCAACAAATTCATCGCGTCTTGACATGTCACAAACTGATTTTCTTCTCTAGATAG
GCTTGATTTTGAAGTGCAGAGAGATGAGCGAGAAAACAAGACATTTCAAGTCCTGAACAA
GATAGTAGAAGATGCGAAGTCCTTCAGGATCATTACTGCTCTGGCAATCAACAAGAGATC
CAATCTTAGATGTAGCGAATGAGATATGCTCATTACCCAAGAGGATCTCGAGC
>SQ;19840745
AATGGGCAGAGAGACACCAAATTTGCTAATGAGGGAAATCAAACATAACAAGGGGTTATT
GTGAGAGAGAACAGAGGATCTTATACAAGTTGAAAATCCGCAACCAAATAATCATAATCT
ACTCTCGGTAAATGGAATGTCAATCCGCACTGACCATTTGCTCTCTCTTGCTCCTCTACC
TTGTTACAGGATGCCTCCTCCTCTTTGGTCGGATCCCATCTTCTTCGTAGTCCATCACTC
CACTTGGTTCCCCAAACATCTCCTTATTCCCTCTGATGTCAACATCCCCCTTCATGGACA
GAGACTTCTTCACTTCTTCCACCCCTTCTTCTGCTTCCTTACGATGTTTTTTGTCCATCT
CACTCATATTGTCCGCCCATTTGATCTTGT
>SQ;19841232
GGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAGTA
CTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCAA
AAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGTGC
GTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAAA
ATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTGA
GACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGCA
TTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTTCTAGTTGCACTCATCGCCTTT
CTCGGTAACCAGTTCTCACAGGA
>SQ;19841468
GAGTTGAAAGTCGTTTTATTTCATTGGTAACAACAACACAGTGGGAAATTATGTATTACA
GAGTAGAGACACATATTCCCTGTTTAAAATGAGGAAACAAGAAAGATCATCTGAAAGTAG
TAATACCTTTAAACTACGTTTCCTGTCTGAAGGTAAACCAGCTACAACACCATGTTCAAT
GCCACATTCGTTTGTTCCTCTCCTGATTTTGAAAGTACCCATAATCACCCCAGCTTCGGT
TCCATTGATTGCAAGCAACCAATAATCTTCACCGTCATCGGAAGTTCCCCAGCCAATAAG
TTTAACAGCATGACCTCCAATGTTAGTACCTGTTATGTGCTTGTACACTCCAGATTTGTA
ATGCGCAAAGTCTCGTAAACAGTGAAGGCAACCTCAACAGGTCCATTTTTGTAAACTTCT
GCCATAATGTCATCAGGGG
>SQ;19842362
AGGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAGT
ACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCA
AAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGTG
CGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAA
AATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTG
AGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGC
ATTTCCCATCCTTCTAAGGGGTGCAATATGCCGGCCACTCTAGTTGCACTCATCGGC
>SQ;19843099
AGAGCAATGTCACCAAACAAAGAAAATCCATTTCCCAACTAAAAAAACAACGAATATAAA
ATTCGATTATATATTTACCATCAACCACTTAACAGACCACAAAATGAAGGCTGTTTACGG
ATTCAACACAGATTAACGGGTATGTATGTATGATCTAGGCAACGGTGGTGGTGGGACCAG
GATAAGCAGGAAGAGTCATGATCCGCTTGTCTACAACCTGGACCTCCCACAGTGAAATGG
TACAGACTCTGAAAGCTAGAGTCATTAATCCCCAGAACCTCGTGCACTGGATCATCGAAA
TAGCACCCAATCCCGGTTGCTGAGATCCCATTGCGTGTGCTTCAGGTAAAAACTGTCAAC
AACACCGTCTCCCAGAACAGTCGAGGGTACATCCATGAGCCCTTCTCCCGCAGTGCTGGT
TCAAAC
>SQ;19843722
GGTTCATGAAAGGTTCTTCACATGGGATGTTGACACAAAAAAAGGACCAAAAGTTGAGGT
AGAACATCTTACATACCCACTTTCACCCAAATCCAACAAAAAAAAAAAACAGAGAACCAG
AGACATAAAAACAACCAAACTTCAGTCACAAAGTCCTCATGTTCCCAACAAATTCATCGC
GTCTTGACATGTCACAAACTGATTTTCTTCTCTAGATAGGCTTGATTTTGAAGTGCAGAG
AGATGAGCGAAAAAACAAGACATTTCAAGTCCTGAACAAGATAGTAGAAGATGCGAAGTC
CTTCAGGATCATTACTGCTCTGGCAATCAACAAGAGATCCAATCTTAGATGTAGCGAATG
AGATATGCTCATTACCCAAGACGATCTCGAGCTCTTGCTTTCAACACGGTCAGGTTCGGC
CAATTGTTATC
>SQ;19844666
GGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAGTA
CTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCAA
AAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGTGC
GTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAAA
ATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTGA
GACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGCA
TTTCCCATCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTCATCGCCCTTTG
TGGG
>SQ;19855736
GGGAAATAGTACTCTTATAATACCATAGTCACCGAGCTTAATTTGACTCTATAATACCAT
AATCACCAAAAGCTTGATATGCATAAATATTATGTGTGCGCTTTATATATGTTTCATAGT
TCATTTGTGCGTGGAAGAGCTGGGATCATAAGGAAAAGAAACACAGAGCGTGTCGCTCTC
ATTCTCCTAAAAATTTTTAAGGGTTGGGAGTTTTAAATGATGTGGGAAGGAGGGAGAGGC
TGGAAAGCCGTGGGCTGAGAACAGGGCTTTCCCCATACTTGGGTCCAAAATCCGAGAGAA
GAAGGGATGTGCCACACTCATGCATTTCCCATCCTTCTAACGCGTGCAATATGCCGGCCA
CCTCTAGTTGCACTCATCGCCTTTCTCGGTAACCAGTTCTCACAGGAGTGGACATTCACC
>SQ;19855995
GGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAGTA
CTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCAA
AAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGTGC
GTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAAA
ATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCTGA
GACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATGCA
TTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGT
>SQ;19857409
AAGTCAACTGATACAAATTTGTCTTCTCTAACCACTTTCTTATCACAGTTTCACCATCTT
TATATATTAAGACACACATACAGTTATGGAAAAGTTACAAAACAAGATATACATAGCAAA
AAAAGATTTTGGAAAGTAAAATGGTGTTTTTGATCTCATTTACTGCTATTATGTTCTTGA
GATAGAAGAACATTGGTGAATTTTCTTGACGAATATTTGTATCATCCTGTGAAAGAAACC
AGCTCGTTTCTTCTCTCGAGTCTCTTGACCCAATTTTTGCCCTCCAGCCCCAGTCCCTTG
TGCATCATCATAAGGACTCTTAATCTTCTCGGGTGTATCAATACTGGTTATCAGAGCTTG
GCTCACCTCTTGAGTTAGTGACACTAAGTTGATTTGGTCTGAGC
>SQ;19857902
GCAAATCTCAATCTCATTGCTTCTTTACATTTACAAGAGCCGTAATTAAACAAAATTTAG
CTACAAAGCATTTTGACTGGAGAGAATTGTACGGTGAGACAAGCATGATCGGATATATTG
TAATTCTCCGGCCACAATCCTTTCTCTGCTTCTTGTGGAAACAAAATTGCTTTATTCACT
TTCAATCCGATTGCTTCATCTTCTCCTTCTTCTTTCTTACTCTCCATCACACTCTCTTTG
CAGTTTCCAGGTTGATTTACCATCGTCATGTTCCAAATTTTCTTAAGTTCTTCATAGTCG
AAGACACCATTTCCATCAAGATCAGCTCGGACCCATAGCTCTTTTGTCTCTTCGAAGCTA
AGTCCATGTGGAATACCCGTTAGATTTACCTTTTGAAGTGCTAGGCA
>SQ;19858773
AACAACCTTCAGAGTTCAGATTTCAGAGCGTTTCTTGACCGAGGTGAGGTTTCTTTGTTT
TGCACAATTATTAGAAAATACAACCAAAAATAAAACAAGGGGAGGCCCGGCCCACATATC
TCGACCATGAGCCTAAACTAAATCAAAAGCACAGATAACGCAGACAAGTTCGTGTTTCCT
TCGTTTTCTGCTCAGCACCCAGAGAAAGGCCTTTCTAACTTTGTGCAATCAATCATCATT
CCTTACAAATTAGGTAAACCAAGCACTATCAGATTCTACCCACCACCAGGGGTTTTCCTC
CAACTGTATTAACTAACGTACCAGTTGCAAGTTCCGGGGATTCAATGCAATACAAACCCT
CCTCCTTTTCAAGGTGATGACGCTGATGAGCTCATTCTTTCACCGCCCCCTTCTCTTGTG
AA
>SQ;19859011
AGTTGAATGTCTTTTGATTCTTTCATTGGAAACAACAACACATTATATTGAATATGAACA
AAAAGCTAAATGGTATATACAATAGACTTCTTTTTGGGTTGAAAGTCGTTTTATTTCATT
GGTAAAAACAACACAGTGGGAAATTATGTATTACAGAGTAGAGACACATATTCCTGTTTA
AAATGAGGAAACAAGAAGATCATCTGAAGTAGTAATACCTTTAACTACGTTCCTGTCTGA
AGGTAAACCAGCTACAACACCATGTTCAATGCCACATTCGTTTGTTCCTCTCCTGATCTT
GAAGTACCCATCATCACCCCAGCTTCGGTTCCATTGATTTGCAAGCAACCAATAATCTTC
ACCGTCATCAGAAGTTCCCCAGC
>SQ;19863867
TGGGAACACATCGAGAGAGCTTCTTCCAAAAACCTCAAACGCTCCTCACACAACGGGTTT
AGGAGTGATGGGGTCTCTCGTTCGTGAATGGGTTGGGTTTCAGCAATTTCCAGCAGCTAC
CCAGGAAAAGCTGATTGAATTCTTCGGAAAATTGAAGCAAAAGGATATGAACTCAATGAC
AGTTCTTGTTCTGGGTAAAGGCGGTGTCGGAAAATCATCCACTGTCAATTCTCTTATCGG
CGAACAAGTCGTCCGTGTCAGTCCTTTCCAAGCTGAAGGATTGAGACCAGTGATGGTTTC
AAGAACAATGGGAGGGTTCACTATCAACATTATTGACACCCCTGGACTTGTGGAAGCTGG
ATATGTCAATCACCAAGCTCTCGAGTTAATCAAAGGGTTTCTTGTGAACAGAACAATAGA
TGTCTTGCTCTATGTTGATCGTTTGGATGTGTATAGAGTCGATGAGCTAGATAAGCAAGT
TGTTATAGCAATCACCCAAACCTTTGGAAAAGAGATATGGTGCAAAACCTTGCTTGTTCT
GACTCATGCTCAATTTTCCCCTCCCGATGAACTTTCCTACGAAACTTTTTCCTCCAAGAG
ATCAGATTCTCTCCTCAAAACTATCCGGGCTGGTTCTAAGATGCGAAAACAAGAGTTTGA
GGATT
>SQ;19864079
GAACGAGTAACGACGAGAGATGCTTCTTCAGGCGGCGGTGCAGAACCGCAATGTTCCACT
GGCTTCTTCCGCCTCCTACTCTCGTCTCCTTCGCTGCAGATCTCCTGTCGTTTTCGTAGC
TGCTCTCTCGAAGAAGACGGCAGCAATCGTGTGCTCCATCTCCCAGGTTTATGGCTACGG
CACGGTGGACTACGAGAGAAGGCCGATTGTCCAGTGGAATGCCATCTACAAGAAGATTTC
GCTGATGGAGAAGCCAGAGCTTGGCGCTGCTTCCGTCTTGAATCAGTGGGAGAAAGCCGG
CCGCAAGCTTACCAAGTGGGAGCTCTGTCGGGTCGTCAAGGAGCTTCGCAAGTACAAGCG
TGCCAACCAAGCTATCGAGGTGTACGACTGGATGAACAACAGAGGCGAAAGGTTTCGGTT
GTCTGCAAGTGATGCTGCAATCCAGCTCGACTTAATCGGCAAAGTGCGTGGCATTCCAGA
CGCCGAAGAGTTCTTCCTCCAGCTCCCTGAGAATTTTAAGGACCGGAGAGTTTATGGTTC
CCTCCTCAATGCCTATGTGAGGGCCAAGTCGAGAGAAAAGGCTGAAGCCCTGCTCAACAC
CATGAGGGACAAAGGTTACGCCCTGCACCCGCTTNCCTTCAACGNCATGATGA
>SQ;19865963
GAATCTCGATCTCGAGAAAGAAAGAAAAAAAGAGAAGGCATGGCCGCGGAAGAAGCGACG
GAGTTCTACCTGAGATACTATGTCGGTCACAAAGGGAAATTTGGACACGAGTTCCTGGAG
TTCGAGTTTAGAGAGGACGGTAAGCTCCGTTACGCCAATAACTCTAACTACAAGAACGAT
ACTATTATCCGCAAGGAGGTATTTCTCACCCCCGCCGTGCTCAAGGAATGCAAGCGTATC
GTCTCCGAGAGCGAGATTCTGAAAGAAGACGATAACAATTGGCCGGAACCTGACCGTGTT
GGAAAGCAAGAGCTCGAGATCGTCTTGGGTAATGAGCATATCTCATTCGCTACATCTAAN
AATGGATCTCTTGGTNGATTGGCAGAGCAGTAATGATCCTGAAGGACTTNGCAT
>SQ;19866668
GGAGAGATCTCTGGCTCTGTATCGCTCGCTGCTCTTCCTCCCACAGATCGAAAACCATGA
ATCCTGAGTACGACTATCTTTTCAAGCTCCTGCTTATCGGGGATTCTGGCGTAGGCAAGT
CTTGTCTTCTTTTGAGATTCTCTGATGATTCTTATGTAGAAAGTTACATTAGCACTATTG
GAGTCGATTTTAAAATTAGGACTGTGGAACAAGATGGCAAAACAATTAAGCTCCAAATTT
GGGACACTGCTGGTCAAGAACGGTTCAGGACTATTACTAGCAGTTACTACCGTGGGGCAC
ATGGAATTATTATTGTCTACGATGTCACAGATGAAGAAAGCTTCAATAATGTCAAGCAAT
GGTTGAGTGAAATTGATCGTTATGCTAGTGACAATGTCAACAAACTCCTTGTTGGAAACA
AGTCTGATCTTACTGAAAACAGAGCCATTCCTTATGAAACTGCCAAGGCTTTTGCCGATG
AAATCGGGATTCCTTTTATGGAGACTAGTGCAAAAGATGCTACAAACGTAGAACAGGCTT
TCATGGCAATGTCTGCATCCATCAAAGAGAGAATGGCTAGCCAACCAGCTGGGAATAATG
CAAGACCACCGACCGTGCAGATCAGAGGACAGNCTGTGGCCAAAANA
>SQ;19866748
TGTTGAGAGAATTCGAAAGAAAAACTCAAATGCAAAGCCATCAGAATCGAAGCAGGCTGA
GCCTTGATTCTACGGTCTAGATTCATCCCTTCCTTCTCTTCACCACTCTCCCTCTTCGTC
GTCCTCGCTGCTGTTCCTCTTCCGATCTACTTTTCCGGTCTACTCTCCGGCAGAAACAAC
AAGCCGCTTTCAGTTATGAGACTCAACTCCAACTTAGCTTCTTCAATGGTGGAATCGAAT
ATTTCTTGTACCACTTTCAATATCTTGGCTCCGATTTATAAACGCGTTGATCAAAAGAAT
CATAGCACTCGAGAGAGCGATTTCCGCACGCTTTGGTTAGCTCGTAACCAGAGGATTTTA
GATTTGTTACTCCATCAACGCTCTTCAGTTATCTGTCTCCAGGAAGTTTGGGTTGGGAAT
GAGGAATTAGTGAACATGTACCACCACCAGCTTTCATCTTCAGGCTACACTATTTATCAG
TTGGCTAGAACAAACAGTCGTGGNGATGGTCTTTTAACAGCCATTCATAAGGACCATTTT
AAAGTTGTAAATTACCGGGAGCTGCTCTTTAACGATTTTGGAGACCGTGTTGCTCAGCTC
TTACATGTCAAAACAGTTATTCCCTTTCCGCTTAATGGAAAGCAAG
>SQ;19869130
GGTGACGACACAAACATATTACATTCGACGGTATAATGGCCACAAAACCAGGAGTCCTCA
CCGATTGGCCTTGGACACCCCTCGGAAGTTTCAAGTACATCGTAATAGCACCATGGGCTG
TCCATAGCACATACAGGTTTGTGACAGATGATCCAGAGAAGAGGGATCTCGGGTACTTCC
TTGTGTTCCCATTCTTGCTCTTCAGAATTCTGCACAACCAGGTTTGGATCTCTCTGTCCC
GTTACTATACGTCCTCGGGAAAGAGACGCATCGTCGACAAGGGAATCGACTTCAATCAGG
TCGACAGGGAGACCAACTGGGATGACCAAATATTGTTCAACGGAGTGCTGTTCTATATAG
GCATCAACCTATTGCCGGAGGCCAAACAACTTCCCTGGTGGAGAACTGACGGAGTGTTGA
TGGCAGCGCTTATTCACACCGGACCGGTGGAGTTCCTCTATTATTGGCTCCACAAAGCTC
TCCACCATCACTTTCTTTATTCCCGCTACCATTCCCACCACCACTCCTCTATCGTCACTG
AGCCCATCACTTGTAACTATTGGTTCTTACCTTGATTTTTACGCTGCCTATATTTCCGTT
TTT
>SQ;19869427
GAGTTTGGGATTTTATTCGTTATTAGTGTGGTAAGAAAGAAAACCCTAAACCACCGGAAA
TCGATTTGTTTGGAAGATGGATATCGAGCAGAAGCAAGCCGAGATCATTGATCAGCTCGT
GAAGCGAGCTTCTACTTGCAAATCCGAGGCTCTGGGCCCGCTCATCATCGAAGCCACATC
GCATCCTTCTCTCTTCGCCTTCTCCGAGATTTTGGCTCTACCCAATGTTGCCCAGCTTGA
AGGAACCACAGATTCTGTGTACCTGGATCTACTACGCTTGTTTGCCCATGGCACCTGGGG
AGACTACAAATGCAATGCCACCCGTCTTCCGCACTTGTCCCCTGACCAAATTCTTAAGCT
TAAGCAGCTCACTGTCCTCACCCTTGCTGAGTCTAACAAGGTATTGCCCTATGATACACT
AATGGTCGAGTTAGATGTTTCCAATGTTCGCGAACTCGAGGACTTTCTTATCAATGAATG
CATGTATGCGGGTATAGTTAGGGGAAAACTGGATCAGTTAAAAAGATGTTTTGAGGTTCC
GTTTGCAGCTGGTANGGATCTAAGGCCAGGTCAACTAGGGAATATGTTACACACATTGTC
CAACTG
>SQ;19870774
GGCGGAACACATCGAGAGAGCTTCTTCCAAAAACCTCAAACGCTCCTCACACAACGGGTT
TAGGAGTGATGGGGTCTCTCGTTCGTGAATGGGTTGGGTTTCAGCAATTTCCAGCAGCTA
CCCAGGAAAAGCTGATTGAATTCTTCGGAAAATTGAAGCAAAAGGATATGAACTCAATGA
CAGTTCTTGTTCTGGGTAAAGGCGGTGTCGGAAAATCATCCACTGTCAATTCTCTTATCG
GCGAACAAGTCGTCCGTGTCAGTCCTTTCCAAGCTGAAGGATTGAGACCAGTGATGGTTT
CAAGAACAATGGGAGGGTTCACTATCAACATTATTGACACCCCTGGACTTGTGGAAGCTG
GATATGTCAATCACCAAGCTCTCGAGTTAATCAAAGGGTTTCTTGTGAACAGAACAATAG
ATGTCTTGCTCTATGTTGATCGTTTGGATGTGTATAGAGTCGATGAGCTAGATAAGCAAG
TTGTTATAGCAATCACCCAAACCTTTGGAAAAGAGATATGGGGCAAAACCTTGCTTGTTC
TGACTCATGCTCAATTTTCCCCTCCCGATGAACTTTC
>SQ;19870921
GGACGACACAAACATATTACATTCGACGGTATAATGGCCACAAAACCAGGAGTCCTCACC
GATTGGCCTTGGACACCCCTCGGAAGTTTCAAGTACATCGTAATAGCACCATGGGCTGTC
CATAGCACATACAGGTTTGTGACAGATGATCCAGAGAAGAGGGATCTCGGGTACTTCCTT
GTGTTCCCATTCTTGCTCTTCAGAATTCTGCACAACCAGGTTTGGATCTCTCTGTCCCGT
TACTATACGTCCTCGGGAAAGAGACGCATCGTCGACAAGGGAATCGACTTCAATCAGGTC
GACAGGGAGACCAACTGGGATGACCAAATATTGTTCAACGGAGTGCTGTTCTATATAGGC
ATCAACCTATTGCCGGAGGCCAAACAACTTCCCTGGTGGAGAACTGACGGAGTGTTGATG
GCAGCGCTTATTCACACCGGACCGGNGGAGTTCCTCTATTATTGGCTCCACAAAGCTNTN
CACCAT
>SQ;19871046
AATTGCAGTGGAGTTGTTCCCCAAGTCACAGAGAGAAATCACAGGCAATTTTGGTTATCC
CTTAACCGGTCCATCCATATCTGAACCGTCCCGGTACAAAGATCCGTTGGTTTCTGGTTT
TGAGATGTCGAATCCCAGACAGAGGAAAGGAGAAGCAATGATGAATCCGACGATTTCGTG
GAGGTTCGCGTCTTCGACCTCTCTTCTCTCCATTCCTCGAACACCAAAAAGTGCCTTTAT
CTTCGCCATGACCTTCTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTGTGGAAAA
CCCTAACAAGGACGATTCCTCCTCTTCGCTTGAATTGGTCCTCAAGTACCACAACCAGAC
GAAGCACTCCTTGAACGGTTACGCGAGAGGTCCTCGTGGTCTCGACTGGGCCAATCAGCC
TAATCCCTTCCGCCGGTACCTCTCTGCTCCTCTTCTTCCTTTCCAACACCCCAATCACGA
CATCGACGACGACTCCGACTCTCCTCTCTACTCTACTNTATTCGACTCGCTTCCTNCGCC
CAAACCCATCTCTCTTCCTACAATCTCTTACCTTTTNTACCATTTCTCTCG
>SQ;19871766
GAGAAAAGAAAACTTTGTACCTTTTCCAAAGTCTAAGCAAATCATTGTTTTTGATTACTG
GAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATT
GTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAATTTCATCCT
TCAACTTGTTGCAGGGTATTGCAGCTGAAAATCTTTCCAAGCAGAAACTGACCTCATGGA
TTCTTCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGATGGAAAGCTT
CTTTCAATGATCGGTTTGCAAACGCCACTGTTGCAGAGTTTAAGCGCCTTCTTGGTGTTA
AACCAACACCAAAGACGGAATTTTTGGGTGTGCCTATTGTAAGCCATGATATATCTTTGA
AGCTTCCAAAAGAATTTGATGCTAGAACCGCTTGGTCACAGTGCACCAGTATTGGAAGGA
TCTTAGATCAGGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTG
ACAGATTCTGCATCAAATATAACATGAATGTTTCTTTATCTGGCAATGATCTTT
>SQ;19872996
TTGGACACAGTGACGACACAAACATATTACATTCGACGGTATAATGGCCACAAAACCAGG
AGTCCTCACCGATTGGCCTTGGACACCCCTCGGAAGTTTCAAGTACATCGTAATAGCACC
ATGGGCTGTCCATAGCACATACAGGTTTGTGACAGATGATCCAGAGAAGAGGGATCTCGG
GTACTTCCTTGTGTTCCCATTCTTGCTCTTCAGAATTCTGCACAACCAGGTTTGGATCTC
TCTGTCCCGTTACTATACGTCCTCGGGAAAGAGACGCATCGTCGACAAGGGAATCGACTT
CAATCAGGTCGACAGGGAGACCAACTGGGATGACCAAATATTGTTCAACGGAGTGCTGTT
CTATATAGGCATCAACCTATTGCCGGAGGCCAAACAACTTNCCTGGTGGAGAACTGACGG
AGTGTTGATGGCAGCGCTTATTCACACCGGACCGGTGGAGTTCCTCTATTATTGGCTCCA
CAAAGCTCTCCACCATCACTTTTCTTTNTTCCCGCTACCATTTCCACANCACTCCT
>SQ;19873300
GAATCTAAGTTGCAGAACCATGGCCAAAACTCTCTACTGCAATTTTTTTTGATCTTTTCT
TTTACTTTTTCTCTTCGTAATCGCTGGTTCGAGAAATGGAGAATCCGGTGGGTTTAAGAT
TCCGTCCGACCGACAAGGAGATCGTCGTCGATTACCTCCGACCAAAAAACTCCGATAGGG
ACACGAGTCATGTTGATCGAGTCATTAGCACAGTCACTATCCGTAGCTTCGACCCTTGGG
AGTTACCTTGCCAGTCTAGGATCAAACTGAAAGATGAGTCTTGGTGTTTCTTCAGCCCTA
AGGAGAACAAATATGGCAGAGGTGATCAACAAATTAGAAAAACGAAATCTGGTTACTGGA
AGATTACTGGCAAACCAAAGCCTATCTTGCGTAACCGCCAAGAGATCGGTGAGAAAAAGG
TTTTGATGTTTTACATGAGTAAGGAACTTGGTGGATCCAAATCCGACTGGGTTATGCACG
AGTACCATGCTTTCTCTCCTACTCAGATGATGATGACATATACAATATGTAAAGGTTTGT
TTAAGGGTGACGTGAGAGAGATTTCTTCTTCTTCTGNTTCCT
>SQ;19874826
CTCCGATTCCCCGATACAGAGACGATGCCGACGGATTCGAAAATGGCCAAGTTTCTTCAA
TCCTATGGATATGATTTGATTCTGGGATCTGTAGCTGCAATCTATGTGGTCATGGCACCA
TATACTAAGGTGGAAGAGAGCTTCAACGTTCAGTCAATGCACGACATTCTTTACCATCGC
CATCATTTGGACTCTTATGATCATTTGGAGTTCCCCGGTGTTGTCCCTCGAACTTTTATT
GGAGCCTTCATAGTCTCTGTTTTTGCATCACCTGTTGTATCAATTATCAGCTGCCTTGGC
TTCCCCAAGGTTTATAGCCTTGTTGCAGCTCGTTTGGTGTTGGGCTGCATCATATTGTCC
ACACTAAGATTTTTCCGGATTCAGATAAAAAAAAAGTTTGGAAATCAAGTGGAAACTTTC
TTTGTACTTTTCACCAGTCTTCAGTTTCATTTTCTTTTCTACTGCACTCGTCCTCTTCCT
AATATTCTAGCTTTGGGATTAGTCAATCTGGCATATGGTAATTGGTTAAAGGGAAATTTT
TATCCAGCTTTGAGTTTCCTGATTTTTGCCACTGTAATCTTCAGATGCGATACGATGTTA
CTGCTTGGGCCTATTGGTCTTGAACTTTTATTGACCAAATCGATCTCCTTC
>SQ;19875482
GCGTGTTGTTAAAGAGCTCACTAGTTGGGTGATTTATTCAGAGGAGGATCCGGAAGCTCA
ACAAAGATATTACTATTGGTCTTATCCAGCGTGAGTTGCTTAGCCTAGCGGAGTACAATG
TCCACATGGCGAAGCATCTTGATGGAGGGAGAAACAAGACCGCAACTGACTTTGCTATTT
CTCTACTCCAATCCTTGGTCACTGAGGAGTCNAGTGTCATTTNNTAG
>SQ;19875812
ACATTATAAACAAGTACCTCCAAATTGCACTTCCTTCAAACTTATTCGACAGTAGACTAG
CTCAAGTACCTTTGGATGGCGTCGAGGCCCGGAGCTCTTACGGAGTGGCCATGGAGTCCC
CTTGGTAGCTTCAAGTACCTCTTGGTGGCCCCGTTGGTGATGGCGAGCATGCACTCGTAC
GTGACGGCTGTGGATGAGGAGAAAGACCTCAGCAGACTTATGATAGTCGTGTTGATGCTG
TGGAGAATAGTTCACAGCCAGATATGGATCAGCGTGTCTCGCCAGAGGACGGCTAAGGGA
ACGAACAAGATCGTGGACAAGCCCATTGAGTTTGAGCAAGTGGACCGAGAGCGCACTTGG
GACGACCAAGTCATCTTCAACACTCTCCTCATGTATCTCGCAAACATCAAGCTCCCAGGC
GCCTCCCACCTTCCCCCATGGAGGCTAGACGGGGCCATCCTCATGGCTCTACTTCACGCT
GGTCCCGTCGAGTTTCTCTACTACTGGTTTCACAGAGCTCTNCACCACCATTTTCCTCTA
CTCTCGCTACCATTCTCACCACCACTCCTNCATTGTCACCGAGCCCATCACGTNTGTGGT
GCACCCCTTCGCCGAGCACAT
>SQ;19877649
ATTCTGGGACCAGTCAACATCTCCATCAAGCTCATCTCCTTTCAAAAACTTTCTCCTTTT
CTGTTTTTTGTTTTTCTCGATTTTTCGAAAATCCGCCAGCTCGAGCTATTACGCTGGGAA
TTCAGAGGATAAAACACGATATGAAGAACGAAATCAGCATTTTGGAGTTGATTTTACTGT
TTCTGTCACTCTCATCAGTGCTAGCTAGCTCCAAATTGCACGGAAACTCAGCTCATGAAA
TGGTGAGCATCTTGAACCAGAACAGAACAGCTCGGAAACTAGGCAAACTAAATGAGAGTC
CCGGTCTTGGCTGCATGGCCCTCCAGTATGTTGAGCTCTGCGAGGGGAATTGCAATGTCA
ACAACACTCTCAGCTGTGAACACCCTGAAGACGACTTCACTCAGGTGTTTGCCCCAAACT
GTGGTGTAGAACTCCCCACTTTTGGTACCATAACTGGCCATATCCTCGGCTGCAGCTCTA
AGTATGCAGCACCAGAAGTCGCTTTCTCAGACATTCTCTTTAGAGATAGCAGTGCGTTGT
CGGTGCTCAGAAACAGGTCGCATACCGAGGTTGGAGTGGGAATGGCTAGGTTGCATAAAG
GTACCTTCTTTTGGTGTCTTCTCTTTAGCGAT
>SQ;19878194
GTCTTGATTTTATAAACAAAAGAAAGAAAGAGAGAGAGATCTTCCTCGGGATTGCAACAT
GTTGGACTACGAATGGGATAATCCTTCCTCCATCGTTCTCTCCGGAGATGAAAGAAACCC
GGACTCTGACCCGACCCGGTCATCCTTCTCCTTTTTCGACCCCATCTCCCATTACAACAA
CGACCACCGTCACATCACCATTTCTCCTCCCCTCCTCTCTTCCTTCTCTAACCAACAACA
ACAGCAACACCTCACCCTCTACGGTCAGACCAACAGCAACAACCAGTTTCTTCATCATCA
CCATCACCACCACTCCTTGTACGGGTCCACCACCACCACCACTCCTTACGGCGCCTCCGA
TCCCATCTACCATCCCCACTCTTCCGCTCCGCCAGCCTCCTTGTTCTCCTACGACCAGAC
AGGACCGGGCTCGGGATCCGGATCTTCCTACAACTTCCTCATCCCCAAGACAGAAGTGGA
TTTCACGTCCAACAGGATCGGGCTGAACCTGGGAGGCCGTACGTACTTCTCAGCGGCGGA
CGACGACTTCGTGAGCAGGCTATACAGGAGGTCTCGACCAGGTGAGTCAGGGATGGCGAA
CTCGCTGAGCACGCCGCGGTGCCAAGCANAGGGATGCAACGCGGATCTG
>SQ;8690927
TGTGAATCTTGAAGTTAAATAAATAAACTAAGACTCCTAAAATCTCTCCTACTGTATGTA
TAATTGTTACAACATAATATCAAAATACGCATACATATATACAAGTTGAAAGCTAAAGAG
CTAGTGAGAATTGTCTGAGACCCAACCTCCCGAAACCATTCCCTCGTCGACAGGCTTCAG
GCCACCACAGGATCTGGCTACCGATTCAAACAGCTTCTCAATCTCAGGCGCACATCTGAT
GAAGGCTTGTTTCCAGAAGCTATATCTTGGGTTCTTTATTAGCTCAATGAATGTGATTAG
AAGTCCCCATGGATGTGGCCTGTTCACAATTAGCCGTTCCAACAGCACTCTAGTTATTTG
CTCCTGTATGATCTCCTGATCAGATTCGAAGAATAGATAGAGCATGATGAAAGAAAAGTA
ATGAGTGTGGTTGTTGGGGTATCGAAGCTGATTGGCGATTGCATTAAGGAACAGATACCG
CCCTTCCGTATCAAGTTCCATACTTAAATACTTGAACATCTGCAAGGCCACAACATTTTG
AGCCTGTGTCTCACCGGCCTGAAGCT
>SQ;8692149
CCAAATAGCTGTCACAAAAAGGGACACAGCTCTTACATTCATGTTTCACTAGGCAGTCTC
TTGTGTACATTATACATATTTCGCATTTCCTCAGTTGACTCCGGTTACAAGATTCGTTTT
TTAAAGCAAAGATCTAGGACTATCAGATTACAAATCATCTTGTAGCTGTGTTAGAAGCGC
ATCGGTCTCATGGGCATCGATTTCACTGTTGTTTACTGTTCTGTTTTCGTCCACATCAAT
AAGAGCTAGGTAAGATTTGTCTTCAAGATCCCCCGACTGCCTTAACAATTCCAAAACGGC
CTCTTTACTGGTAACATCCGATTCCTCTTCACAGAGCTTGAAGAAACCAGACAGCATCAA
CACCTTGGGCCTCCAATTGCTGGACCCTTCAGCCGAAAAAGCATTTCTAAGACAAGTCAA
AGCCTCTGAAATACACCTCTTTCTGGTATGACCAACAGCTAGAATCTCCCACGTACTTGA
ACTTGGTTTTCCTCCCATTTCAACCATGTGGTCGAACAACCCCTCAGCTGTCTCTAGTTG
GTCGTTTTTGACATACGCA
>SQ;8694120
AAGGAAATAGTACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATAC
CATAATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATA
GTTCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCT
CATTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGA
AGCCGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGC
CACACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAG
>SQ;8695006
TATACAATAGACTTCTTTTTGGGTTGAAAGTCGTTTTATTTCATTGGTAACAACAACACA
GTGGGAAATTATGTATTACAGAGTAGAGACACATATTCCTGTTTAAAATGAGGAAACAAG
AAGATCATCTGAAGTAGTAATACCTTTAACTACGTTCCTGTCTGAAGGTAAACCAGCTAC
AACACCATGTTCAATGCCACATTCGTTTGTTCCTCTCCTGATCTTGAAGTACCCATCATC
ACCCCAGCTTCGGTTCCATTGATTTGCAGGCAACCAATAATCTTCACCGTCATCAGAAGT
TCCCCAGCCAATAAGTTTAACAGCATGACCTCCAATGTTAGTACCTGTTATGTGCTTGTA
CACTCCAGATTTGTAATGCGCAAAGTCCTCGTAAACAGTGAAGGCAACCTCAACAGGTCC
ATTTTTGTAAACTTCTGCCATAATGTCATCAGGGTGAGATCTGACCTTGTACGCACTAAC
ACCATAATGTTTTGATTCACGCCAAAGCTGGTTTCCGCTAACACAT
>SQ;8695842
GGAACATGTTTGCTTTATATATATATGGTTTTTTTTTCACAAAGAGAAAAGGAAATAGAA
CTGTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACCAA
AAGCTTGATATGCATAAATATATGTGAGCGCTTTATATATGTTTCATAGTTCATTTGTGC
GTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTAAA
ATCTTCCAAGGCTGGAGTTTTAATGATGTGGAAGGAGGAG
>SQ;8695920
AAGGAAATAGTACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATAC
CATAATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATA
GTTCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCT
CATTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGA
AGCCGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGC
CACACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCAC
TCATCGCCTTTCTCGGTAACCAGTTCTCACAGGAGTGGACATTCA
>SQ;8696505
GAATTCCCGGGCCCGGGCCCGGGACGGCTGCGAGAAGACGACAGAAGGGGAATCTCGATC
TCGAGAAAGAAAGAAAAAAAGAGAAGGCATGGCCGCGGAAGAAGCGACGGAGTTCTACCT
GAGATACTATGTCGGTCACAAAGGGAAATTTGGACACGAGTTCCTGGAGTTCGAGTTTAG
AGAGGACGGTAAGCTCCGTTACGCCAATAACTCTAACTACAAGAACGATACTATTATCCG
CAAGGAGGCATTTCTCACCCCCGCCGTGCTCAAGGAATGCAAGCGTATCGTCTCCGAGAG
CGAGATTCTGAAAGAAGACGATAACAATTGGCCGGAACCTGACCGTGTTGGAAAGCAAGA
GCTCGAGATCGTCTTGGGTAATGAGCATATCTCATTCGCTACATCTAAGATTGGATCTCT
TGTTGATTGCCAGAGCAGTAATGATCCTGAAGGACTTCGCATCTTCTACTATCTTGTTCA
GGACTTGAAATGTCTTGTTTTTTTCGCTCATCTCTCTGCACTTCAAAATCAAGCCTATCT
AGAGAAGAAAATCAGTTTGTGACATGTC
>SQ;8696543
GAATTCCCGGGCCCGGGCCCGGGACGGCTGCGAGAAGACGACAGAAGGGGAATCTCGATC
TCGAGAAAGAAAGAAAAAAAGAGAAGGCATGGCCGCGGAAGAAGCGACGGAGTTCTACCT
GAGATACTATGTCGGTCACAAAGGGAAATTTGGACACGAGTTCCTGGAGTTCGAGTTTAG
AGAGGACGGTAAGCTCCGTTACGCCAATAACTCTAACTACAAGAACGATACTATTATCCG
CAAGGAGGCATTTCTCACCCCCGCCGTGCTCAAGGAATGCAAGCGTATCGTCTCCGAGAG
CGAGATTCTGAAAGAAGAC
>SQ;8697126
GAAGATAGGTTGTGGTTCATGAAAGGTTCTTCACATGGGATGTTGACACAAAAAAGGACC
AAAAGTTGAGGTAGAACATCTTACATACCCACTTTCACCCAAATCCAACAAAAAAAAAAA
ACAGAGAACCAGAGACATAAAAACAACCAAACTTCAGTCACAAAGTCCTCATGTTCCCAA
CAAATTCATCGCGTCTTGACATGTCACAAACTGATTTTCTTCTCTAGATAGGCTTGATTT
TGAAGTGCAGAGAGATGAGCGAAAAAAACAAGACATTTC
>SQ;8697180
GATAAGAAAACAGCAAGTATATGGTTTTTAGAAGATAGGTTGTGGTTCATGAAAGGTTCT
TCACATGGGATGTTGACACAAAAAAGGACCAAAAGTTGAGGTAGAACATCTTACATACCC
ACTTTCACCCAAATCCAACAAAAAAAAAAAACAGAGAACCAGAGACATAAAAACAACCAA
ACTTCAGTCACAAAGTCCTCATGTTCCCAACAAATTCATCGCGTCTTGACATGTCACAAA
CTGATTTTCTTCTCTAGATAGGCTTGATTTTGAAGTGCAGAGAGATGAGCGAAAAAAACA
AGACATTTCAAGTCCTGAACAAGATAGTAGAAGATGCGAAGTCCTTCAGGATCATTACTG
CTCTGGCAATCAACAAGAGATCCAATCTTAGATGTAGCGAATGAGATATGCTCATTACCC
AAGACGA
>SQ;8701755
ATCGAATCACCAAATCAATGTTTTCCTTTATTCTTTTGAAAGAAAAATAAAAATAAGAAA
CAAAAGGTGGTTATATGGACGGATTCTCAAATCACACTCGCTATACATAAAAAGTGACTT
GTCCTTTACTAGAGAGTGAAAGGCTTTGCATAGACATCGAATGTTTGGCAAGCAGTCAGT
TGAGGCTCCTGTCTTAATCCCCCAATCGCACTTCCCCCTGTCAGAAGCATGCTCAGCACA
GTCGTCACAACTCCACCACTACCACCACCATCATTCCCTGTATTCCTTATTGTGGTGCGC
ATAGAATTCAGAAGGCTTCCATAGGTTGTGCCTTGTGCGCTGCGTTCAATTGCTTGAATA
AAACAGAAAGTCATAGCACCCGTAGACGTGATCTTCGACAGCGCTGATGTGTCGGCCGAA
GTCTGATCATCATCACATCCACTAATTGAAATGGCTTCTCCACCAGCAGTTCCTTTCCAC
AAACCTGACCTAGGCCGATGATCCTCCCACACATACTGCCCAGCTCTGTTCATTCTGCAT
AGGAAGGGTAAATCCAGAACGGTACCACTATGGCAAGCATCGATAATTGAATGGAGCT
>SQ;8702125
TTTTTTTTTTTGGGTTGAAAGTTGCTTTATTTCATTGGTAACAACAACACAGTGGGAAAT
TATGTATTACAGAGTATAGACACATATTCCTGTTTAAAATGAGGAAACAAGAAGATCATC
TGAAGTAGTAATACCTTTAACTACGTTCCTGTCTGAAGGTAAACCAGCTACAACACCATG
TTCAATGCCACATTCGTTTGTTCCTCTCCTGATCTTGAAGTACCCATCATTACCCCAGCT
TCGGTTCCATTGATTTGCAAGCAACCAATAATCTTAACCGTCATCAGAAGTTCCCTAGCC
AATAAGTTTAACAGCATGACCTCCAATGTTAGTACCTGGTATGTGCTTGTACACTCCAGA
TTTGTAATGCGCAAAGTCCTCGTAAACAGTGAAGGCAACCTCAACAGGTCCATTTTTGTA
AACTTCTGCCATAATGTCATCAGGGTGAGATCTGACCTTGTACGCACTAACACCATAATG
CTTTGATTCACCGCCAAAGCTGGCTTCCGGTAACACA
>SQ;8715845
CATCGGCCTTTGGGCTTTGAGTTACGCGTCACAATTGAATCAATTGGTCCTTTTAATTAG
TTTTACCAATATACCCCTCCGTCTTTTCCCCCTTCTCGTTTAGGAAAAAAAATCATTAGC
TTCGACTTATCCGAAACCTAACGAGTAACGACGAGAGATGCTTCTTCAGGCGGCGGTGCA
GAACCGCAATGTTCCACTGGCTTCTTCCGCCTCCTACTCTCGTCTCCTTCGCTGCAGATC
TCCTGTCGTCTCCGTAGCTGCTCTCTCGAAGAAGACGGCAGCAATCGTGTGCTCCATCTC
CCAGGTTTATGGCTACGGCACGGTGGACTACGAGAGAAGGCCGATTGTCCAGTGGAATGC
CATCTACAAGAAGATTTCGCTGATGGAGAAGCCAGAGCTTGGCGCTGCTTCCGTCTTGAA
TCAGTGGGAGAAAGCCGGCCGCAAGCTTACCAAGTGGGAGCTCTGTCGGGTCGTC
>SQ;8717375
GTAATTAGAAAACATGTTTGTGAATCTTGAAGTTAAATAAATAAACTAAGACTCCTAAAA
TCTCTCCTACTGTATGTATAATTGTTACAACATAATATCAAAATACGCATACATATATAC
AAGTTGAAAGCTAAAGAGCTAGTGAGAATTGTCTGAGACCCAACCTCCCGAAACCATTCC
CTCGTCGACAGGCTTCAGGCCACCACAGGATCTGGCTACCGATTCAAACAGCTTCTCAAT
CTCAGGCGCACATCTGATGAAGGCTTGTTTCCAGAAGCTATATCTTGGGTTCTTTATTAG
CTCAATGAATGTGATTAGAAGTCCCCATGGATGTGGCCTGTTCACAATTAGCCGTTCCAA
CAGCACTCTAGTTATTTGCTCCTGTATGATCTCCTGATCAGATTCGAAGAATAGATAGAG
CATGATGAAAGAAAAGTAATGAGTGTGGTTGTTGGGGTATCGAAGCTGATTGGCGATTGC
ATTAAGGAACAGATACCGCCCTTCCGTATCAAGTTCCATAC
>SQ;8720010
TTTTTTTTTTTTTTTTTCCTGACAAAACCCCAAGACTCAATTTAATCAATCCTCAAATTT
ACATGATACCAACGTAATGGGAGCTTAAAAATA
>SQ;8721428
GAGACACAGGACTTCGGGATCTTGGGCAGCTGGAACAAGATCTTGTTTTTGGAGATGCAG
GTGCCAAGGACGTTATCAACTTTCTGAGGACGAATCAGGACACAAACCCGGAAAACAAAT
TACGGCTTTTGATGATTTATGCAACAGTGTACCCCGAGAAGTTTGAAGGTGACAAGGGTG
TGAAGCTAATGCAGCTTGCTAGATTATCACCTGTGGATATGAAGGTTATAAGCAACATGC
AATTGATAGCTGGATCCCCAGAAAACAAAGCTAAGTCCGGTAGTTTCTCCCTCAAATTTG
ACG
>SQ;8722075
TGTGGTAAGAAAGAAAACCCTAAACCACCGGAAATCGATTTGTTTGGAAGATGGATATCG
AGCAGAAGCAAGCCGAGATCATTGATCAGCTCGTGAAGCGACTTCTACTTGCAAATCCGA
GGCTCTGGGCCCGCTCATCATCGAAGCCACATCGCATCCTTCTCTCTTCGCCTTCTCCGA
GATTTTGGCTCTACCCAATGTTGCCCAGCTTGAAGGAACCACAGATTCTGTGTACCTGGA
TCTACTACGCTTGTTTGCCCATGGCACCTGGGGAGACTACAAATGCAATGCCACCCGTCT
TCCGCACTTGTCCCCTGACCAAATTCTTAAGCTTAAGCAGCTCACTGTCCTCACCCTTGC
TGAGTCTAACAAGGTATTGCCCTATGATACACTAATGGTCGAGTTAGATGTTTCCAATGT
TCGCGAACTCGAGGACTTTCTTATCAATGAATGCATGTATGCGGGTATAGTTAGGGGAAA
ACTGGATCAGTTAAAAAGATGTTTTGAGGTTCCGTTTGCAGCTGGTAGGGATCTAAGGCC
AGGTCAACTAGGGAATATGTTACACACA
>SQ;8722221
TTGGATTCATCTAAGAAGCAGACTCTGTTTTCATGGCTGTTTACAATACCAAACTCTGTT
TGGCCTCTGTTTTCTTGCTCTTAGGGCTTCTCTTGGCTTTTGACTTGAAGGGTATAGAAG
CAGAAAGTCTTACCAAACAGAAACTGGACTCGAAGATACTTCAGGATGAGATTGTGAAGA
AAGTCAACGAAAACCCAAACGCTGGATGGAAAGCTGCTATAAATGATCGATTTTCAAACG
CCACTGTTGCAGAGTTGAAGCGTCTTCTCGGTGTTAAACCAACACCAAAGAAGCATTTCT
TAGGTGTGCCTATTGTGAGCCATGATCCATCTTTGAAGCTACCTAAAGCGTTTGATGCTA
GAACTG
>SQ;8726286
GCCCCAACAGTATTATCCTTGGTTTGCACAGTACATGGTTATGAAAAGAGCGAGCATCGA
GCCGAATTTTCATGATCTGTACCTGAAGTTCTTGGACAAAGTTGATTCCAAGCTGCTGTT
TAAGGAGATACTTCAAAATACTTACGAAAATTGCAAGGTTCTTTTGGGCTCAGAGCTCAT
AAAGTCGAGTTCTGAAGAGCGTTCTCTTCTTAAAAATTTAGGCAGTTGGCTTGGAAGGTT
GACCATTGGAAGGAATTATGTTTTAAGGGCGCGAGAAATAGATCCAAAATCCTTGATTGT
GGAGGCCTATGAAAAAGGGTTGATGATAGCAGTCATTCCGTTCACTTCAAAGGTTCTGGA
GCCATGCCAAAACAGTATTGCTTATCAACCTCCCAATCCTTGGACGATGGCTATACTAGG
GTTGCTTGCTGAGATCTATTCAATGCCAAACCTAAAAATGAATCTGAAGTTTGACAT
>SQ;8726341
CTGTTATTGAACAAGCACTTTCAAGGATATCATCTGGTAATTTAGAATCAGATGCCTCTG
TTTCACACCCTGGTCCCTCACAATCTTTCCCTGGAAATGGCGAGTTGAGTGGTTCTGGAA
TTGGCCAACCTGCATTACAGCTTTCTTCTCCCCTACAGCTTCAACAGAAAAATGAAGTGC
CAAGTGTGCCATCTAACGAGGCAAAGCCACTTCTGCCATCGTTATCAACTACTTCCGTTG
ATGTTTCTGTCAATCCTAAGAATCCTGGCATTCCAACTTCTTCATCAACCTCAACTGGTT
TTGTTCGTCCAGCTCGTGCAACCACTTCAACAAGGTTTGGCTCGGCTTTGAACATAGAAA
CCTTGGTTGCAGCAGCAGAAAGAAGGGAAAACGCAATCGAGGCTCCACCTTCAGATGTTC
AGGACAAAGTTTCGTTCATAATCAATAATATCTCTACAACAAACATTGAATCTAAAGGGA
AAGAGTTTGCTGAAATTTT
>SQ;8727457
GTTATGCAAAGAAACCCATAGAAAACCACTAAAGGCAGAAATGAAAAACAAGAATGTTGG
AAAGATGAGGACCTCATCATGAGGTAAAGCAAATAGGAAACGTGAAAAACAGAATAATAA
CCAACCAAAGGAGCTTAATTACAGACAAGACAGATTTGGGGGGATGTTGTGTAAAAACCA
AGTAGTAGTGAATTGGAGCCTAGTCAAAAGAAGGAACACGTGTTCTAA
>SQ;8728304
AAAGGAAATAGTACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATA
CCATAATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCAT
AGTTCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTC
TCATTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGG
AAGCCGTGGCTGATACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTG
CCACACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCA
CTCAT
>SQ;8729681
GGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAATTGTATCAGACTT
CTTCACTCAGCCTCTGATTTCTTCTGTTTAGGGCTTCTAATTTCATCCTTCAACTTGGTG
CACGGTATCGCAGCTGAAAATCTTTCCAAGCAGAAACTGACCTCATGGATTCTTCAGAAC
GAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGATGGAAAGCTTCTTTCAATGAT
CGGTTTGCAAACGCCACTGTAGCAGAGTTTAAGCGCCTTCTTGGAGTTAAACCAACAC
>SQ;8731408
ACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGTCTTCTAATTTCATCCTTCAACTT
GTTGCAGGGTATTGCAGCTGAAAATCTTTCCAAGCAGAAACTGACCTCATGGATTCTTCA
GAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGATGGAAAGCTTCTTTCAA
TGATCGGTTTGCAAACGCCACTGTTGCAGAGTTTAAGCGCCTTCTTGGTGTTAAACCAAC
ACCAAAGACGGAATTTTTGGGTGTGCCTATTGTAAGCCATGATATATCTTTGAAGCTTCC
AAAAGAATTTGATGCTAGAACCGCTTGGTCACAGTGCACCAGTATTGGAAGGATCTTAGA
TCAGGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTCTGACAGATT
CTGCATCAAATATAACATGAATGTTTCTTTATCTGTCAATGATCTTTTAGCATGTTGTGG
ATTCCTTTGCGGTCAAGGTTGTAATGGTGGATACCCAA
>SQ;8731753
CTGGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAATAG
TACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCACC
AAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATAGTTCATTTGT
GCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCCTA
AAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGGCT
GAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGCCACACTCATG
CATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCACTCATCGCCTT
TCTCGGTAACCAGTTCTCACAGGAGTGGACATTCACCAGAGATTTTGGAACTATCAATGC
>SQ;8731976
GTTATGCAAAGAAACCCATAGAAAACCACTAAAGGCAGAAATGAAAAACAAGAATGTTGG
AAAGATGAGGACCTCATCATGAGGTAAAGCAAATAGGAAACGTGAAAAACAGAATAATAA
CCAACCAAAGGAGCTTAATTACAGACAAGACAGATTTGGGGGGATGTTGTGTAAAAACCA
AGTAGTAGTGAATTGGAGCCTAGTCAAAAGAAGGAACACGTGTTCTAAGATTGGAAAGGA
TATTGCTAGGCTGGTCACGTCAATCAAGTTGAGCAGCAGCCGTTCTTCTGTGCCACAGGC
TGTCCTCTGATCTGCACGGTCGGTGGTCTTGCATTATTCCCAGCTGGTTGGCTAGCCATT
CTCTCTTTGATGGATGCAGACATTGCCATGAAAGCCTGTTCTACGTTTGTAGCATCTTTT
GCACTAGTCTCCATAAAAGGA
>SQ;8732177
ATGGGGTCTCTCGTTCGTGAATGGGTTGGGTTTCAGCAATTTCCAGCAGCTACCCAGGAA
AAGCTGATTGAATTCTTCGGAAAATTGAAGCAAAAGGATATGAACTCAATGACAGTTCTT
GTTCTGGGTAAAGGCGGTGTCGGAAAATCATCCACTGTCAATTCTCTTATCGGCGAACAA
GTCGTCCGTGTCAGTCCTTTCCAAGCTGAAGGATTGAGACCAGTGATGGTTTCAAGAACA
ATGGGAGGGTTCACTATCAACATTATTGACACCCCTGGACTTGTGGAAGCTGGATATGTC
AATCACCAAGCTCTCGAGTTAATCAA
>SQ;8732348
TTCTGGAACATGTTTGCTTTATATATATATGTTTCTTAGTTCACAAAGAGAAAAGGAAAT
AGTTCTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATACCATAATCA
CCAAAAGCTTGATATGCATAAATATATGTGGGCGCTTTATATATGTTTCATAGTTCATTT
GGGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCTCATTCTCC
TAAAATCTTCCAAGGGTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGAAGCCGTGG
CTGAAACAGGCTTCCCATACTTGGTCCAAATCCGAAAGAAAAAGGGATGTGCCACACTCA
TGCATTTCC
>SQ;8732738
AGTTTTTTTTTTTTTTTATTTGAATGATAGAGCGGTTGCTCATTAAAAAATCGTTTTAGA
GCAATGTCACCAAACAAAGAAAATCCATTTGCCGATGAAAAAACACCGAATATAAAATTC
GATTATATATTGACCATTAACCATGTTACTGACCGGGAACTGAGGGGTGGTGACGGGTTC
AACACAGATTCCACAAAGGGAGAGAATGACCTACGCAACGGGGGAGGTGGGACTTCCATA
ACTTACGAAGAGTCATGATCCGCTAGACTACAACTGGACCTCCCACAGAGAAATGGTACA
GACTCTGAAAGCTAGAGTCATTAATCCCCAGAACCTC
>SQ;8732878
GTATGATAGAGCGGAAGCTTATTAAAAAATCGTTTTAGAGCAATGTCACCAAACAAAGAA
AATCCATTTCCCAATAAAAAAACAACGAATATAAAATTCGATTATATATTTACCATCAAC
CACTTAACAGACCACAAAATGAAGGCTGTTTACGGATTCAACACAGATTAACGGGTATGT
ATGTATGATCTAGGCAACGGTGGTGGTGGGACCAGGATAAGCAGGAAGAGTCATGATCCG
CTTGTCTACAACTGGACCTCCCACAGTGAAATGGTACAGACTCTGAAAGCTAGAGTCATT
AATCCCCAGAACCTCGTGCACTGGATCATCGAAATAGCACCCAATCCCGGTTGCTGAGAT
CCCCATTGCGTGTGCTTCCAGGTACAAAACTTGTCCAACAACACCCGTCTCCCAGAACAG
TCGAGGGTACATCCATGAGCCCTTCTCCCGCAGTGCTGGTTCAAACCGAGCTATCATGCC
TAAGCTGAAGCATCCATCCCCTGCAATGTCCTGATGACATGATAGCCCTTTTGCCA
>SQ;8734273
GAACAAATCTCCATAAATTACAGACAAAGATAAAGCCGGAAACAAGAAAATGTTGCAGAT
AAAATCTAACAAAAGAAAGAACAATCGAAAAACTCTTCTTCTCCTTGTAATTTGCTCACA
ACAAAACCTCTTCTTCAGAGCCTCTTAAAGTGGCTTTCCACTTGTCTTGATATCATTTCT
GATTGCTCCTTGAATCATCTTAACGATCAAATACTGAGCGCCTATGATAAGAGGGATGAG
TTTCTTTCCTTTATCATCAGAGTAAGATCCATCTACCATCTTCTTGTCTACATGAATTGC
TTTCCTCTGGTTTGTTGCTACATCAGTTATCGCCTTAACCAAGTTCGGGATCCACGCTTC
ACCATTTGGAAGAGCCTTTTCGT
>SQ;8734707
TAGTCTGGGTCTCATGAACCAAGGGGAGGAGCTTAACAGGATCGGTGAGGTGTATATCCA
CAACCATCCAGATATGAAAGTGAGACTGGTCGACGGCAGTAGATTAGCAGCAGCTGTTGT
GATCAACAGTGTACCCAAAGCAACTACAAGCGTCGTGATGACAGGCAATCTCACTAAGGT
TGCCTACACCATCGTCTCTGCTCTCTGCCAGAGAGGCGTTCAGGTCTCCACTCTGCGCCT
AGACGAGTATGAGAAAATAAGATCATGCGTTCCACAAGAATGCAGAGACCATTTGGTCTA
TTTAACCTCTGAAGCACTC
>SQ;8734878
GGGTTGAAAGTCGTTTTATTTCATTGGTAACAACAACACAGTGGGAAATTATGTATTAGC
AGAGTAGAGACACATATTCCTGTTTAAAATGAGGAAACAAGAAGATCATCTGAAGTAGTA
ATACCTTTAACTACGTTCCTGTCTGAAGGTAAACCAGCTACAACACCATGTTCAATGCCA
CATTCGTTTGTTCCTCTCCTGATCTTGAAGTACCCATCATCACCCCAGCTTCGGTTCCAT
TGATTTGCAAGCAACCAATAATCTTCACCGTCATCAGAAGTTCCCCAGCCAATAAGTTTA
ACAGCATGACCTCCAATGTTAGTACCTGTTATGTGCTTGTACACTCCAGATTTGTAATGC
GCAAAGTCCTCGTAAACAGTGAAGGCAACCTCAACAGGTCCATTTTTG
>SQ;8734901
GGGTTGAAAGTCGTTTTATTTCATTGGTAACAACAACACAGTGGGAAATTATGTATGGCA
GAGTAGAGACACATATTCCTGTTTAAAATGAGGAAACAAGAAGATCATCTGAAGTAGTAA
TACCTTTAACTACGTTCCTGTCTGAAGGTAAACCAGCTACAACACCATGTTCAATGCCAC
ATTCGTTTGTTCCTCTCCTGATCTTGAAGTACCCATCATCACCCCAGCTTCGGTTCCATT
GATTTGCAAGCAACCAATAATCTTCACCGTCATCAGAAGTTCCCCAGCCAATAAGTTTAA
CAGCATGACCTCCAATGTTAGTACCTGTTATGTGCTTGTACACTCCAGATTTGTAATGCG
CAAAGTCCTCGTAAACAGTGAAGGCAACCTCAACAGGTCCATTTTTGTAAACTTCTGCCA
TAATGTCATCAGGGTGAGATCTGACCTTGTACGCACTAACACCATAATGTTTTGATTCAC
GCCAAAGCTGGTTTCCGCTAACACATTTCCTTGCACATTTTGGTGTAGGGTAAGCGGGTT
CACATCCCGGGTGCGAGCAACCAGTATTGTCGAAGTATGGATCACAC
>SQ;8735154
TAACTATTATTAAATTACATAAGTGTGGAAATAAAACCTAGCTATAAACACTGGTTCTTG
AAAAAAGAAAGCATATATGCAGAGTGAGCTATGATTTACTTGATAAGGAAGAGACCAATC
GCAGTGACGATGAGTGTTGAAGGCAAACCGAATTTGAAATGTTTAGTGAAAGTGAGAGTG
TATCCATGGCTCACTGCTCTACGAGCTTGCTCACACACTATCAGGTTTGCTGCTGAACCA
AGCAACGTCAAGTTTCCAGCCACTGTGCTCACCCACGCCAGCAACAACCACGCCTTCTTC
TCCTCCTCCCTCCCCATCGCTGATGCCGCCACTCTTGCTCCCAACAAAAGCACGGTTGGT
ACATTAGAGGCTACATTGGAGAGGACAAGAATCACAACTGCTAGAACCGCGATTCCTTTG
GCTTGATCAATTTTGGCATATGGCTCCATTAGGTCCCATAGAGCGGTAGGGATACCAGTT
TTGTTGAATCCATCAACGGTTATGAACATCCCGCAGAAAAAGATCAAAAGCGAATACGAT
ACC
>SQ;8735385
GTTTTATTTCATTGGTAACAACAACACAGGGGGAAATTATGTATTACAGAGTAGAGACAC
ATATTCCTGTTTAAAATGAGGAAACAAGAAGATCATTTGAAGTAGTAATACCTTTAACTA
CGTTCCTGGCTGAAGGTAAACCAGCTACAACACCATGTTCAATGCCACATTCG
>SQ;8735393
AAAGGAATAATAGTGTTTTTTTTTTTTGTAATTAGAAAACATGTTTGTGAATCTTGAAGT
TAAATAAATAAACTAAGACTCCTAAAATCTCTCCTACTGTATGTATAATTGTTACAACAT
AATATCAAAATACGCATACATATATACAAGTTGAAAGCTAAAGAGCTAGTGAGAATTGTC
TGAGACCCAACCTCCCGAAACCATTCCCTCGTCGACAGGCTTCAGGCCACCACAGGATCT
GGCTACCGATTCAAACAGCTTCTCAATCTCAGGCGCACATCTGATGAAGGCTTGTTTCCA
GAAGCTATATCTTGGGTTCTTTATTAGCTCAATGAATGTGATTAGAAGTCCCCATGGATG
TGGCCTGTTCACAATTAGCCGTTCCAACAGCACTCTAGTTATTTGCTCCTGTATGATCTC
CTGA
>SQ;8735505
ATCGAATCACCAAATCAATGTTTTCCTTTATTCTTTTGAAAGAAAAATAAAAATAAGAAA
CAAAAGGTGGTTATATGGACGGATTCTCAAATCACACTCGCTATACATAAAAAGTGACTT
GTCCTTTACTAGAGAGTGAAAGGCTTTGCATAGACATCGAATGTTTGGCAAGCAGTCAGT
TGAGGCTCCTGTCTTAATCCCCCAATCGCACTTCCCCCTGTCAGAAGCATGCTCAGCACA
GTCGTCACAACTCCACCACTACCACCACCATCATTCCCTGTATTCCTTATTGTGGTGCGC
ATAGAATTCAGAAGGCTTCCATAGGTTGTGCCTTGTGCGCTGCGTTCAATTGCTTGAATA
AAACAGAAAGTCATAGCACCCGTAGACGTGATCTTCGACAGCGCTGATGTGTCGGCCGAA
GTCTGATCATCATCACATCCACTAATTGAAATGGCTTCTCCACCAGCAGTTCCTTTCCAC
AAACCTGACC
>SQ;8736724
GTCACAAAAAGGGACACAGCTTTTTCATTCATGTTTCACTAGGCAGTCTCTTGTGTACAT
TATACATATTTCGCATTTCCTCAGTTGACTCCGGTTACAAGATTCGTTTTTTAAAGCAAA
GATCTAGGACTATCAGATTACAAATCATCTTGTAGCTGTGTTAGAAGCGCATCGGTCTCA
TGGGCATCGATTTCACTGTTGTTTACTGTTCTGTTTTCGTCCACATCAATAAGAGCTAGG
TAAGATTTGTCTTCAAGATCCCCCGACTGCCTTAACAATTCCAAAACGGCCTCTTTACTG
GTAACATCCGATTCCTCTTCACAGAGCTTGAAGAAACCAGACAGCATCAACACCTTGGGC
CTCCAATTGCTGGACCCTTCAGCCGAAAAAGCATTTCTAAGACAAGTCAAAGCCTCTGAA
ATACACCTCTTTCTGGTATGACCAACAGCTAGAATCTCCCACGTACTTGAACTTGGTTTT
CCTCCCATTTCAACCA
>SQ;8737545
GGGAAACATCCATTTCATTTAACCAGAAAGCATGGCAATCTTTTCTTTGAACAAATCTCC
ATAAATTACAGACAAAGATAAAGCCGGAAACAAGAAAATGTTGCAGATAAAATCTAACAA
AAGAAAGAACAATCGAAAAACTCTTCTTCTCCTTGTAATTTGCTCACAACAAAACCTCTT
CTTCAGAGCCTCTTAAAGTGGCTTTCCACTTGTCTTGATATCATTTCTGATTGCTCCTTG
AATCATCTTAACGATCAAATACTGAGCGCCTATGATAAGAGGGATGAGTTTCTTTCCTTT
ATCATCAGAGTAAGATCCATCTACCATCTTCTT
>SQ;8737761
AAGGAAATAGTACTCTTATTAATACCATAGTCACCGAGCTTAATTTGACTCTATCAATAC
CATAATCACCAAAAGCTTGATATGCATAAATATATGTGTGCGCTTTATATATGTTTCATA
GTTCATTTGTGCGTGGAAGAGCTGGATCATAAGGAAAAGAAGCACAGAGCGTGTCGCTCT
CATTCTCCTAAAATCTTCCAAGGTTGGAGTTTTAATGATGTGGAAGGAGGAGAGGCTGGA
AGCCGTGGCTGAGACAGGCTTCCCATACTTGGTCCAAATCCGAGAGAAGAAGGGATGTGC
CACACTCATGCATTTCCCATCCTTCTAAGGCGTGCAATATGCCGGCCACTCTAGTTGCAC
TCATCGCCTTTCTCGGTAACCAGTTCTCACAGGAGTGGACATTCACCAGAGATTTTGGAA
CTATCAATGCTGGTGTGGTATGATAGATACAATCTCTACGTAACTGCTTGAGGGGGAACT
GTGAGAATGGTATAAAC
>SQ;8738747
AAGGAATAATAGTGTTTTTTTTTTTTGTAATTAGAAAACATGTTTGTGAATCTTGAAGTT
AAATAAATAAACTAAGACTCCTAAAATCTCTCCTACTGTATGTATAATTGTTACAACATA
ATATCAAAATACGCATACATATATACAAGTTGAAAGCTAAAGAGCTAGTGAGAATTGTCT
GAGACCCAACCTCCCGAAACCATTCCCTCGTCGACAGGCTTCAGGCCACCACAGGATCTG
GCTACCGATTCAAACAGCTTCTCAATCTCAGGCGCACATCTGATGAAGGCTTGTTTCCAG
AAGCTATATCTTGGGTTCTTTATTAGCTCAATGAATGTGATTAGAAGTCCCCATGGATGT
GGCCTGTTCACAATTAGCCGTTCCAACAGCACTCT
>SQ;8738841
AAATTCAAAGCCATTTTTCTTTTAATGGGCAGAGAGACACCAAATTTGCTAATGAGGGAA
ATCAAACATAACAAGGGGTTATTGTGAGAGAGAACAGAGGATCTTATACAAGTTGAAAAT
CCGCAACCAAATAATCATAATCTACTCTCGGTAAATGGAATGTCAATCCGCACTGACCAT
TTGCTCTCTCTTGCTCCTCTACCTTGTTACAGGATGCCTCCTCCTCTTTGGTCGGATCCC
ATCTTCTTCGTAGTCCATCACTCCACTTGGTTCCCCAAACATCTCCTTATTCCCTCTGAT
GTCAACATCCCCCTTCATGGACAGAGACTTCTTCACTTCTTCCACCCCTTCTTCTGCTTC
CTTACGATGTTTTTTGTCCATCTCACTCATATTGTCCGCCCATTTGATCTTGTCTTGAAT
TGAAATGAGCAGATTCTCTGACGTGTTCAACCAGTTGGACAATGTGTGTAACATATTCCC
TAGTTGACCTGGCCTTAGATCCCTACCAGCTGCAAACGGAACCTCAAAACATCTTTTTAA
CTGATCCAGTTTTCCCCTAACTATACCCGCATACATGCATTCATTGAT
>SQ;905849
CNACGGTATAATGGCCACAAAACCAGGAGTCCTCACCGATTGGCCTTGGACACCCCTCGG
AAGTTTCAAGTACATCGTAATAGCACCATGGGCTGTCCATAGCACATACAGGTTTGTGAC
AGATGATCCAGAGAAGAGGGATCTCGGGTACTTCCTTGTGTTCCCCTTCTTGCTCTTCAG
AATTCTGCACAACCAGGTTTGGNTCTCTCTGTCCCGTTACTATACGTCCTCGGGAAAGAG
ACGCATCGTCGACAAGGGAATCGACTTCAATCAGGTCGACAGGGAGACCAACTGGGATGA
CCAAATATTGTTCAACGGAGTGCTTGTTCTATATAGGCATCAAACCTATTNCCGGAGGCA
AACAACTTTCCCTGGGTGGAGAACTTNACGGAGTGTTTNATGGAAGCGCTTTTTNAAAAC
GGACCCGTGGAGTTCCNCTANTATTGGTTCNNAAAGGTTTCANCATAACTTTNTTNATTC
CGNTNCCATTCCACAACAATCTTTNTNGGNNTTGGCCATAATTGGNGA
>SQ;933584
AAGTAAAAAAAGACAAGGCATGGCCGCGGAAGAAGCGACGGAGTTCTACCTGAGATACTA
TGTCGGTCACAAAGGGAAATTTGGACACGAGTTCCTGGAGTTCGAGTTTAGAGAGGACGG
TAAGCTCCNTTACGCCAATAACTCTAACTACAAGANCGATACTATTATCCGCAAGGAGGT
ATTTCTCACCCCCGACGTGCTCAAGGAATGCAAGCGTATCNTCTCCGNGAGCGAGATTCT
GAANGANGNCGATAACAATTGGCCGGAACCTGACCGTNTTGGAAAGCANGNAGCTTCGAG
ATCGGTCTTTGGGTAAATATGCATATCTCATTCCGCTACANCCTAAAGATTGGGTNCTCC
TTGTCGANTNNCCAGAGCNGNNATG
>SQ;935362
GATTACNGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAGAAGAGAAAGATCCATGGC
TGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGGCTTCTAAT
TTNATCCNTCAACTTGTTGCAGGGTATNGCAGCTGAAAATCTTTCCAAGCAGAAACNGAC
CTCATGGNTTCTTCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGATG
GAAAGCNTCTTTCAATGATCGGTTTGCAAACGGCACTGTTGCAGAGTTTAAGCGCCTTCT
TTGGTGTTAAACCAACACCAAAGGNCGGANTTTTTNGGGTGTGCTATTGTAAGCCATTGA
TAATANCTTTTNANGTTTCNAAANGAATTTAATGCTAGAACCGTTNGGTCACAGTGGANC
AGTATTT
>SQ;936803
GGAACTCGTTGAGGGATTGANAAAAAAATAATCAGAAGAGAAAGATCCATGGCTGATAAT
TGTATCANACTTCTTCACTCAGCCTCTGTTTTCTNCTGTTTAGGGCTTCTAATTTNATCC
TTCAACTTGTTGCAGGGTATTGCAGCTGAAAATCTTTCCAAGCAGAAACTGACCTCATGG
ATTCTNCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGATGGAAAGCT
TCTTTCAATGATCGGTTTGCAAACGCCACTGTTGCAGAGTTTAAGCGCCTTCTTGGTGTT
AAACCAACACCAAAGNCGGGGATTTTTTGGGGTGTGCCCTATTTGTAAGGCCATGGTNAT
NTCCTTTNAAGGTTTCCCAAAAGNATTTTNATNCNNGGACCCCCTTTGGGCAAAGGGGCN
CCCCTNTTTTGGAGGGCCCTTTNGGTC
>SQ;937871
AAAGANTTTNATGCTAGAACCGCTTGGTCACAGTGCACCAGTATTGGAAGGNTCTTAGAT
CAGGGTCACTGTGGTTCTTGCTGGGCCTTTGGTGCTGTTGAATCACTGTNTGACAGATTC
TGCATCAAATATAACATGAATGTTTCTTTATCTGTCAATGATCTTTTAGCATGTTGTGGA
TTCCTTTGCGGTCAAGGTTGTAATGGTGGATACCCAATTGCTGCGTGGCGGTACTTTAAG
CACCACGGTGTAGTCACTGAAGAGTGTGATCCATACTTCGACAATACTGGTTTGNTCGCA
CCCGGGATGTGAACCCGCTTACCCTACANCAAAATGTGCAAGGAAATGTNTTAGCGGAAA
CCCAGCTTTGGNGTGAATCAAAACAATTATGGTGTAGTGCGGTCAAGGTCAGATCTCACC
CTGNTGCAATATGGCAGAAGGTTNCAAAAATGGGCCTTTTAGGTTCCTCACTNNTTNNNG
GCNTTTCGGATTAAAATCTGGGGTTC
>SQ;958004
AGGTATGGCTGGTGGGAGAAGGAACAACAAGAGAAGAGCAGGAAAAAGCCACAAAAGGGA
CATTGTTTATACCATTCTCACAGTTCCCCCTCAAGCAGTTACGTAGCGATTGTATCTATC
ATACCACACCAGCATTGATAGTTCCAAAATCTCTGGTGAATGTCCACTCCTGTGAGGTAA
GTATTCAAAGCTACCCAATCCAACTAATTTATTAGAAGAGGTAGTCCTTATTATAAAAAA
AACATCTGCAGAACTGGTTACCGAGAAAGGCGATGAGTGCAACTAGAGTGGCCGGCATAT
TGCACGCCTTAGAAGGATGGGAAACGCATGAGTNTGGCACATCCCTTCTTCTCTCGGATT
TTGACAAAGTATTGGAAGCCTGTNTCAGCCACGGGTTTCAGCTTTTCCTCCTTCCACATC
ATTAAACTCCAACCTTGGGAGGTTTTTTGGGGATNAGAGNGNCACGGTTTGTGCTTTTTT
CCTATNTCCAGTTTTCACGGCACATGACTTTGACATTTTAAGGGGCAAATTTTGGTTCGC
AAATTC
>SQ;958152
AACGCTCCTCACACAACGGGTTTAGGAGTNATGGGGTCTCTCGTTCGTNAATGGGTTGGG
TTTCAGCAATTTCCAGCAGCTACCCAGGAAAAGCTGATTGANTTCTTCGGAAAATTGAAG
CAAAAGGATATGAACTCAATGACAGTTCTTGTTCTGGGTAAAGGCGGTGTCGGAAAATCA
TCCACTGTCAATTCTCTTATCGGCGAACAAGTCGTCCGTGTCAGTCCTTTCCAAGCTGAA
GGATTGAGACCAGTGATGGTTTCAAGAACAATGGGAGGGTTCACTATCAACATTATTGAC
ANCCCTGGNCTTGTGGAAGCTGGNTATGTCAATCACCAAGCTCTCGGGTTAATCAAAGGG
GGTTCTTGTGANCAGGACAATAGNTGTNTTTGCNCTATGTTGANCGTTTGGTTGTNTATA
GNGCCGTTGGCTGGTAANAAANTTGTTTTGNATTCCCCAACCTTTGGAAAGGGTTTTGGG
AAAACCTGTTNTCTNCNANGCCAATTCCCCCCGT
>SQ;9778203
TTACTATACCAAACTCTGTTTGGCCTCTGTTTTCTTGCTCTTAGGGCTTCTCTTGGCTTT
TGACTTGAAGGGTATANAAGCAGAAAGTCTTACCAAACAGAAACTGGACTCGAAGATACT
TCAGGATGAGATTGTGAAGAAAGTCAACGAAAACCCAAACGCTGGATGGAAAGCTGCTAT
AAATGATCGATTTTCAAACGCCACTGTTGCAGAGTTTAAGCGTCTTCTCGGTGTTAAACC
AACACCAAAGAAGCATTTCTTAGGTGTTCCTATTGTGAGCCATGATCCATCTTTGAAGCT
ACCTAAAGCTTTTGATGCTAGAACTGCTTGGCCACAGTGCACTAGTATTGGAAACATCTT
AAATCAGGGACATTGTGGTTCTTGCTGGGCATTTGGTGCTG
>SQ;9778306
ACGAGAAATGCAAAGCCATCAGAATCGAAGCAGGCTGAGCTTGATTCTACGGTCTAGATT
CATCCCTTCCTTCTCTTCACCACTCTCCCTCTTCGTCGTCCTCGCTGCTGTTCCTCTTCC
GATCTACTTTTCCGGTCTACTCTCCGGCAGAAACAACAAGCCGCTTTCAGTTATGAGACT
CAACTCCAACTTAGCTTCTTCAATGGTGGAATCGAATATTTCTTGTACCACTTTCAATAT
CTTGGCTCCGATTTATAAACGCGTTGATCAAAAGAATCATAGCACTCGAGAGAGCGATTT
CCGCACGCTTTGGTTAGCTCGTAACCAGAGGATTTTAGATTTGTTACTCCATCAACGCTC
TTCAGTTATCTGTCTCCAGGAAGTTTGGGTTGGGAATGANGAATTAGTGAACATGTTACA
CA
>SQ;9778321
ACGAGAAATGCAAAGCCATCAGAATCGAAGCAGGCTGAGCTTGATTCTACGGTCTAGATT
CATCCCTTCCTTCTCTTCACCACTCTCCCTCTTCGTCGTCCTCGCTGCTGTTCCTCTTCC
GATCTACTTTTCCGGTCTACTCTCCGGCAGAAACAACAAGCCGCTTTCAGTTATGAGACT
CAACTCCAACTTAGCTTCTTCAATGGTGGAATCGAATATTTCTTGTACCACTTTCAATAT
CTTGGCTCCGATTTATAAACGCGTTGATCAAAAGAATCATAGCACTCGAGAGAGCGATTT
CCGCACGCTTTGGTTAGCTCGTAACCAGAAGATTTTAGATTTGTTACTCCATCAACGCTC
TTCAGTTATCTGTCTCCANGAAATTTGGGTTGGGAATG
>SQ;9778889
ACTAGTCTCGAAAACCCAAACGCTGGATGGAAAGCTGCTATAAATGATCGATTTTCAAAC
GCCACTGTTGCAGAGTTTAAGCGTCTTCTCGGTGTTAAACCAACACCAAAGAAGCATTTC
TTAGGTGTTCCTATTGTGAGCCATGATCCATCTTTGAAGCTACCTAAAGCTTTTGATGCT
AGAACTGCTTGGCCACAGTGCACTAGTATTGGAAACATCTTAGATCAGGGACATTGTGGT
TCTTGCTGGGCATTTGGTGCTGTTGAATCACTATCAGATAGATTCTGTATCCAATTTGGG
CA
>SQ;9778953
GGAGTTCTACCTGAGATACTATGTCGGTCACAAAGGGAAATTTGGACACGAGTTCCTGGA
GTTCGAGTTTAGAGAGGACGGTAAGCTCCGTTACGCCAATAACTCTAACTACAAGAACGA
TACTATTATCCGCAAGGAGGTATTTCTCACCCCCGCCGTGCTCAAGGAATGCAAGCGTAT
CGTCTCCGAGAGCGAGATTCTGAAAGAAGACGATAACAATTGGCCGGAACCTGACCGTGT
TGGAAAGCAAGAGCTCGAGATCGTCTTGGGTAATGAGCATATCTCATTCGCTACATCTAA
GATTGGATCTCTTGTTGATTGCCAGAGCAGTAATGATCCTGAAAGACTTCGCATCTTCTA
CTATC
>SQ;9781141
CAGGAATGCCGCACGAGCATGAATGTTTCTTTATCTGTCAATGATCTTTTAGCATGTTGT
GGATTCCTTTGCGGTCAAGGTTGTAATGGTGGATACCCAATTGCTGCGTGGCGGTACTTT
AAGCACCACGGTGTAGTCACTGAAGAGTGTGATCCATACTTCGACAATACTGGTTGCTCG
CACCCGGGATGTGAACCCGCTTACCCTACACCAAAATGTGCAAGGAAATGTGTTAGCGGA
AACCAGCTTTGGCGTGAATCAAAACATTATGGTGTTAGTGCGTACAAAGTCAGATCTCAC
CCTGATGACATTATGGCAGAAGTTTACAAAAATGGACCTGTTGAAGTTGCCTTCACTG
>SQ;9782167
ACGAGCTTACATGACAAAACAGTTATTCCCTTTCCGCTTAATGGAAAGCAAGACGTCCAA
CAAGAAGTTATTATAGTGAACACTCACCTCTTGTTTCCTCACGATTCTAGTTTGTCTATT
GTAAGACTGCATCAGGTTTACAAAATTCTTGAATATCTGGAAGCTTACCAAAAGGAAAAT
AAACTTAATCACATGCCCATTATTCTCTGCGGTGACTGGAATGGAAGCAAACGCGGGCAT
GTTCTACAAATTTTTGAGATCTCAAGGGTTTTATTTCATCATACGATGATGCTCATCAGT
ATACCGACAGTGATGCTCATAGGTGGGTTTAGCCACAGAAACCACAGGGGGAAATATTTG
CGGAATTTGATTTCATATGGCTCTGTAACCCT
>SQ;9782568
AATTCGGCACGAGGAGAAACAAGACCGCAACTGACTTTGCTATTTCTCTACTCCAATCCT
TGGTCACTGAGGAGTCGAGTGTCATTTCAGAGCTCCACAGTCTTGTTGATGCGCTGGCAA
AGCTTGCCTCAAAATCCGGATCTTCTGAGTCATTGCAACAGCTAATTGACATCATACGAA
ATCCAGTTACTAACACAGCTGGCCTCTCTGATAGTTCAACCGGAAATGATAACAACGATA
GGCAAAAGGATGAGAAGGTTGCGTGCAACACCACTAACACAGAAGAGAGTACCAGCTTGG
ATTATGTGGAATCAGATCCTGCGGGTTTCCAGAATCGGGTGTCCACGCTATTTAAAAACT
GGTATCAAATCTGCGAACTTCCTGGTGCAAATGAAACCGCATGTTCACAATATGTCCTGC
ATTTGCA
>SQ;9784594
GGAAAAGTTGCTTCTGAATTTTTGTCTAATGCTGGAAACGCTCGGATGGACATGGTCTCC
CGGCCATCAGATATTTCTGTGGATGGTTTTGAATCTTCTCCAGTCTCACTTTTGAGCTCA
CAAGTCGATCCAGCTGGTGACTCATCCAGTCTTCAATTTACTAAGTCACTACCAACCTCT
GAATTGAATCTGGCTGAATCCTCTGACGCTGCTACGAAAGAAACTGGAACATCACTGCAG
ACATTGACTTCAGCTGCTACCATGGAACG
>SQ;9784661
ANANGACGGTAAGCNCCGTTACGNNAATAACTCTAACTACAAGAACGANACTATTATCCG
CAANGAGGTATTTCTCACCCCCGCCGTGCTCAAGGAATGCAAGCGTATCGTCTCCGAGAG
CGAGATTCTGAAAGAAGACGATAACAATTGGCCGGAACCTGACCGTGTTGGAAAGCAAGA
GCTCGAGATCGGCTTGGGTAATGNGCATATCTCANNCGCTACATCTAAGATTGGATCTCT
TGCTGATT
>SQ;9785390
GAGAGACCTCTGGCTCTGTATCGCTCGCTGCTCTTCCTCCCACAGATCGAAAACCATGAA
TCCTGAGTACGACTATCTTTTCAAGCTCCTGCTTATCGGGGATTCTGGCGTAGGCAAGTC
TTGTCTTCTTTTGAGATTCTCTGATGATTCTTATGTAGAAAGTTACATTAGCACTATTGG
AGTCGATTTTAAAATTAGGACTGTGGAACAAGATGGCAAAACAATTAAGCTCCAAATTTG
GGACACTGCTGGTCAAGAACGGT
>SQ;9786193
AAGAAAATTGGAAAAGGGCTGACTTTTTTGGTTTGGTGAAGTTCGTCGTGGGGACTCGGG
ACAATATAATAAAGATGAGTCCTCGCTTACTCTGAGTGTTATCTATGTAGTTGCTTCAAT
TTTTGTCACTCATTTGCCTTCGATTCCTCCTTAAGAAACTGACGATTCTTCTATTGGGAA
TCGGTCAACGTCCTCAAGTTTATCAGAGATCTTAGGGTTTCTAATCAGATATTTGATTCA
TCAAAATCACCAACTAGGGTTTACAA
>SQ;9787190
GAGATGCTTCTTCAGGCGGCGGTGCAGAACCGCAATGTTCCNCTGGCTTCTTCCGCCTCC
TACTCTCGTCTCCTTCGCTGCAGATCTCCTGTCGTCTCCGTAGCTGCTCTCTCGAAGAAG
ACGGCAGCAATCGTGTGCTCCATCTCCCAGGTTTATGGCTACGGCACGGTGGACTACGAG
AGAAGGCCGATTGTCCAGTGGAATGCCATCTACAAGAAGATTTCGCTGATGGAGAAGCCA
GAGCTTGGCGCTGCT
>SQ;8727457
GTTATGCAAAGAAACCCATAGAAAACCACTAAAGGCAGAAATGAAAAACAAGAATGTTGG
AAAGATGAGGACCTCATCATGAGGTAAAGCAAATAGGAAACGTGAAAAACAGAATAATAA
CCAACCAAAGGAGCTTAATTACAGACAAGACAGATTTGGGGGGATGTTGTGTAAAAACCA
AGTAGTAGTGAATTGGAGCCTAGTCAAAAGAAGGAACACGTGTTCTAA
genometools-1.5.1/testdata/U89959_ests.magicmatch000066400000000000000000000404231211610345200215710ustar00rootroot0000000000000097350772e29b7881b149afbedf09290d	gi|8690080|dbj|AV529797.1|AV529797 AV529797 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL48c08R 5', mRNA sequence
ff7357d7a1877d31d94543a13d64fa0e	gi|8690053|dbj|AV529770.1|AV529770 AV529770 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL47a02R 5', mRNA sequence
cc954bf1761c4c9f05f8822afb1079e3	gi|8689616|dbj|AV529333.1|AV529333 AV529333 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL34a01R 5', mRNA sequence
70facb44682374068ef43fd0a6e116b5	gi|8689215|dbj|AV528932.1|AV528932 AV528932 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL23a03R 5', mRNA sequence
300d9c80d9f566412745a6bda32e3e12	gi|8688760|dbj|AV528477.1|AV528477 AV528477 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL10c02R 5', mRNA sequence
41ccefe046c76c005c6f83a09aac40de	gi|8686177|dbj|AV526649.1|AV526649 AV526649 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZ18c11R 5', mRNA sequence
0d914f8b8fdfef05d05e32a617ce8737	gi|8683519|dbj|AV523991.1|AV523991 AV523991 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL47e02F 3', mRNA sequence
634e9a3d54562a834a900edb41abe7d4	gi|8682814|dbj|AV523286.1|AV523286 AV523286 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL23a03F 3', mRNA sequence
7ba0b8c1bb50abf3c5a844abacf9fe67	gi|8682693|dbj|AV523166.1|AV523166 AV523166 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL18h09F 3', mRNA sequence
f28eda487869903339de7a431f00fccd	gi|8682455|dbj|AV522928.1|AV522928 AV522928 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL10c02F 3', mRNA sequence
af2486ba93823b9389100222c0ddffdb	gi|8679389|dbj|AV519862.1|AV519862 AV519862 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APD69d04F 3', mRNA sequence
c446b7e0b708aafe5473ef397e104ae3	gi|7612621|dbj|AV442217.1|AV442217 AV442217 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APZ38e01_r 5', mRNA sequence
d1a97200c69d88855784612802e7c024	gi|7612394|dbj|AV441995.1|AV441995 AV441995 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APD19b11_r 5', mRNA sequence
979a4ec86ab17d2a4625c90ed575c145	gi|7612059|dbj|AV441666.1|AV441666 AV441666 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APD33a12_r 5', mRNA sequence
649b4501a3ba1d922dce7b623c7f6de9	gi|7611662|dbj|AV441278.1|AV441278 AV441278 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APZ38e01_f 3', mRNA sequence
2acbf49eaca817b303d60c7c22dfdd15	gi|7610825|dbj|AV440461.1|AV440461 AV440461 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APD64c02_f 3', mRNA sequence
9a5ec5d4597ac1be9d10ba63ecc457c1	gi|7610337|dbj|AV439986.1|AV439986 AV439986 Arabidopsis thaliana above-ground organ two to six-week old Arabidopsis thaliana cDNA clone APD33a12_f 3', mRNA sequence
3b10d6f56bfea7b6b57a41146f6c140b	gi|5846657|gb|AI999752.1|AI999752 701557284 A. thaliana, Columbia Col-0, rosette-3 Arabidopsis thaliana cDNA clone 701557284, mRNA sequence
08f77d13c4ad88c1c44c0314426f2218	gi|5846455|gb|AI999550.1|AI999550 701556366 A. thaliana, Columbia Col-0, rosette-3 Arabidopsis thaliana cDNA clone 701556366, mRNA sequence
835eb4298c428885b3d16d0e4514c30b	gi|5845530|gb|AI998625.1|AI998625 701546353 A. thaliana, Columbia Col-0, rosette-2 Arabidopsis thaliana cDNA clone 701546353, mRNA sequence
88e24a075574a85734a081b57a7ec852	gi|5845361|gb|AI998456.1|AI998456 701545753 A. thaliana, Columbia Col-0, rosette-2 Arabidopsis thaliana cDNA clone 701545753, mRNA sequence
f55d7bcc44b78111563b02f8a19805ee	gi|5843191|gb|AI996286.1|AI996286 701551019 A. thaliana, Columbia Col-0, inflorescence-2 Arabidopsis thaliana cDNA clone 701551019, mRNA sequence
cdced248d13c7c0f89e7e889cc30164a	gi|5841805|gb|AI994900.1|AI994900 701500362 A. thaliana, Ohio State clone set Arabidopsis thaliana cDNA clone 701500362, mRNA sequence
e47b883ccda180d280195029954ea7f5	gi|5840051|gb|AI993146.1|AI993146 701495464 A. thaliana, Ohio State clone set Arabidopsis thaliana cDNA clone 701495464, mRNA sequence
7f11e59ff50ce68b25c6120418df3d51	gi|5839790|gb|AI992885.1|AI992885 701493873 A. thaliana, Ohio State clone set Arabidopsis thaliana cDNA clone 701493873, mRNA sequence
ed9e14d2b83e7ea606c9d1d5fdbeb857	gi|5839694|gb|AI992789.1|AI992789 701493549 A. thaliana, Ohio State clone set Arabidopsis thaliana cDNA clone 701493549, mRNA sequence
44f49124e83c2c61713d3c50b3a9a47c	gi|3450080|gb|AI100119.1|AI100119 34494 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105B20XP 3', mRNA sequence
b7056f0f128b406b094ebf5cb33fb74f	gi|3449674|gb|AI099935.1|AI099935 34088 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138J5XP 3', mRNA sequence
e6338114b6c0dcc78811d3be5b36ff63	gi|3449578|gb|AI099839.1|AI099839 33992 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127K5XP 3', mRNA sequence
061cac88caefa5d8bba4a1ff47031dc3	gi|2762922|gb|T46227.1|T46227 9490 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138J5T7, mRNA sequence
1c07f0f3b1115fb653b7f47df5b1344b	gi|2762921|gb|T46226.1|T46226 9489 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138J4T7, mRNA sequence
802e6347770300a7bbc0064a90f1f061	gi|2759942|gb|T42274.1|T42274 5537 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111I3T7, mRNA sequence
d4793f2935cfa07221be201386cb079b	gi|2759743|gb|T44958.1|T44958 8221 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127K5T7, mRNA sequence
a7fa97bc84c3aebaea34e169b73094c9	gi|2759121|gb|T44328.1|T44328 7591 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124H12T7, mRNA sequence
03636fa4a9e17baae04ad57d13cdc386	gi|2749490|gb|AA651247.1|AA651247 31361 Lambda-PRL2 Arabidopsis thaliana cDNA clone 178C3XP 3', mRNA sequence
c6826f50615c7fb2eb70e294bb7202cb	gi|2748705|gb|N95878.1|N95878 21603 CD4-16 Arabidopsis thaliana cDNA clone H1B11T7, mRNA sequence
0920b24475a189fbfc148593eec03cb6	gi|2748033|gb|N95955.1|N95955 21140 CD4-14 Arabidopsis thaliana cDNA clone F3F3T7, mRNA sequence
7882e88f260382672a97918b652cad4a	gi|1159193|gb|N38051.1|N38051 19278 Lambda-PRL2 Arabidopsis thaliana cDNA clone 217D15T7, mRNA sequence
15adef11b8ee98d85e7a5e3106495193	gi|2747682|gb|H76955.1|H76955 17386 Lambda-PRL2 Arabidopsis thaliana cDNA clone 199P18T7, mRNA sequence
77ba8b822b44308184b4dcab6ecfa75e	gi|2747645|gb|H76651.1|H76651 17082 Lambda-PRL2 Arabidopsis thaliana cDNA clone 199N11T7, mRNA sequence
8fdc30d821ff25b48b6182936cf72cd5	gi|2747604|gb|H76393.1|H76393 18098 Lambda-PRL2 Arabidopsis thaliana cDNA clone 194B12T7, mRNA sequence
5ae608a9518c5417787d0da5f4dc93b7	gi|2733258|gb|H37487.1|H37487 15616 Lambda-PRL2 Arabidopsis thaliana cDNA clone 182E10T7, mRNA sequence
3ab44e284886cca199c6a4d221725734	gi|2722481|gb|AA712564.1|AA712564 31697 Lambda-PRL2 Arabidopsis thaliana cDNA clone 172P13T7, mRNA sequence
2c08f2fc011c03e5aa709690db242c3b	gi|2597485|gb|R82906.1|R82906 5044 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109D5T7, mRNA sequence
7d5ceada204939fc948a837d482fe57c	gi|2597031|gb|T22420.1|T22420 4428 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105B20T7, mRNA sequence
d342e4ee66b1c4db3e83e076c5dd7d44	gi|2596953|gb|T22318.1|T22318 4326 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103P9T7, mRNA sequence
26e5980fbaaefb58d84de6755d521845	gi|2596256|gb|T21132.1|T21132 3140 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90H7T7, mRNA sequence
0c4c41ad6668fd55d5f1140088f1064d	gi|2580948|gb|AA650856.1|AA650856 30970 Lambda-PRL2 Arabidopsis thaliana cDNA clone 288E9T7, mRNA sequence
3ff6374febf91a5f28c3f7bcc4ccd774	gi|2048630|gb|AA395265.1|AA395265 27216 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124H12XP 3', mRNA sequence
a0d33d57c705a829d80c318c595fcccb	gi|2047981|gb|AA394770.1|AA394770 26567 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165D3XP 3', mRNA sequence
50590ee6555b56ad95151d25d300c6fe	gi|2446000|gb|AA605472.1|AA605472 30508 Lambda-PRL2 Arabidopsis thaliana cDNA clone 190I17XP 3', mRNA sequence
f74aca5cee266c7bc442898be20363ae	gi|2412846|gb|AA597423.1|AA597423 29694 Lambda-PRL2 Arabidopsis thaliana cDNA clone 197P18T7, mRNA sequence
198a4aa7626135303d0e996d4e2775ef	gi|2393553|gb|AA586141.1|AA586141 28790 Lambda-PRL2 Arabidopsis thaliana cDNA clone 80B1XP 3', mRNA sequence
0e851efbbe2bfb244a388865f785495d	gi|623629|emb|Z47590.1|Z47590 ATTS4446 Strasbourg-A Arabidopsis thaliana cDNA clone FAI255 5', mRNA sequence
556ae7f08b7cc887b54786f0bc100dd4	gi|453733|emb|Z29751.1|Z29751 ATTS2195 Ors-A Arabidopsis thaliana cDNA clone OAO139 5', mRNA sequence
38229ac075d9c6d15fd1152c4eccc834	gi|402964|emb|Z26362.1|Z26362 ATTS1481 Gif-SeedA Arabidopsis thaliana cDNA clone YAY048 3', mRNA sequence
0f6d1e4ce29d042b5804f8ae8bd9c43a	gi|402959|emb|Z26361.1|Z26361 ATTS1480 Gif-SeedA Arabidopsis thaliana cDNA clone YAY048 5', mRNA sequence
b0183ab4aa646b9e8f95f61daf0e23a3	gi|403229|emb|Z26415.1|Z26415 ATTS1541 AC16H Arabidopsis thaliana cDNA clone TAI278 5' similar to A.Thaliana mRNA for ara-5,partail sequence, mRNA sequence
322e03bbf0f0ddac43d4ca12dd0cc795	gi|398270|emb|Z25982.1|Z25982 ATTS1259 Versailles-VB Arabidopsis thaliana cDNA clone VBV38-10992, mRNA sequence
dd3ace06137c29bf383632984aadf8af	gi|397246|emb|Z25655.1|Z25655 ATTS1120 Versailles-VB Arabidopsis thaliana cDNA clone VBVYA12, mRNA sequence
1634572862a7fc3d7dcb1ca5950cf137	gi|397216|emb|Z25629.1|Z25629 ATTS1092 Versailles-VB Arabidopsis thaliana cDNA clone VBVID01, mRNA sequence
e72969c46cd2e7d078d339cda62260a8	gi|397215|emb|Z25628.1|Z25628 ATTS1091 Versailles-VB Arabidopsis thaliana cDNA clone VBVID01, mRNA sequence
893d07af699d973ed4e8e3423fc87165	gi|396603|emb|Z25487.1|Z25487 ATTS1001 Grenoble-B Arabidopsis thaliana cDNA clone GBGe40, mRNA sequence
5db2b668ce1df476a932c078b6e77122	gi|17325|emb|Z18783.1|Z18783 ATTS0641 Versailles-VB Arabidopsis thaliana cDNA clone VBV12-30792 3' similar to cathepsin B-like cysteine proteinase precursor (EC 3.4.22.-). Swiss-Prot entry P05689, mRNA sequence
21c1b9817f74d01695e650726543cfbc	gi|17300|emb|Z18780.1|Z18780 ATTS0623 Versailles-VB Arabidopsis thaliana cDNA clone VBV12-30792 5' similar to Cathepsin B-like cysteine proteinase precursor. Swiss-Prot entry P25792, mRNA sequence
e311a17e67c458d42ed86de05242f87b	gi|17520|emb|Z18418.1|Z18418 ATTS0793 Grenoble-B Arabidopsis thaliana cDNA clone GBGa464 5', mRNA sequence
a12796a152e829b54f2f56b4910d701c	SQ;19741042
7f0facaa45cacec8ffaa0c98a51edf56	SQ;19741846
3b9295d3ee44af4cf4f79b2e27003f1b	SQ;19742246
67e8b62becffff524bac4f51bfa344e1	SQ;19798134
8bbc72e5847196327c25661544c6bdf9	SQ;19798999
c94289917098254e5d5b7c3ed48e81b7	SQ;19801463
c24d4bd4c7cae864049bd096522750b1	SQ;19801855
2642a22855698a3125c99a9759f9147c	SQ;19803773
741ff4d6dd193d77cc75fb61f373ca5b	SQ;19805724
d9d61048b8d25d868bda7f00a0831100	SQ;19806050
634ef96163dc4d4f8a585fe8059d867b	SQ;19807151
0743a82e324754dfc94ed4c0cd8a8816	SQ;19823046
a45d1a65f8024adcc2ce8bdcdfb36569	SQ;19823987
174d324a9dca8baddcdcd0dbef55f969	SQ;19825204
9b19d8ea196896df9be4cf56b285abf2	SQ;19825274
897eae7810009eb141a5f887289d95c8	SQ;19825742
3c0dc775fc37af77e71cd10a45d4723c	SQ;19826275
1b775af1ef6f8f8b80ba60a8245cba0b	SQ;19827386
3f342edcab14d21711f3d75e3ff81743	SQ;19827775
e252994eb503f22fdc871a97738a525a	SQ;19828054
faf314d3fa8ba5d3d99734b83ebb7f7b	SQ;19828253
653662b06e7e300256655269264f4004	SQ;19828552
df066a65ac8236486c7d59f90157d43e	SQ;19829297
ace313cc0542136c91ac52da3c676d77	SQ;19829716
8e8cf2914e87c5de17ca1cea5185961d	SQ;19829934
2d0e152a577c91a47f0b5781e67cd3b0	SQ;19831127
b9d8ea84787a6573a7bd2acdb795af44	SQ;19831839
354c93700a73d01ea73f641c62c593cd	SQ;19831991
d056310e74cdfca4f2f5de040aabc6c6	SQ;19833332
f2f65df067412c3be8da37366e71763f	SQ;19834843
15ed737c8deffb63f79d93a8fecb5a93	SQ;19835442
4a2861ff4a54b0b8a099c7ca178c113f	SQ;19836538
dc0b347c18391d65d897b1c1f14bc31f	SQ;19837074
494051ed1147d22a2b2967b64c329678	SQ;19837290
f1a0d426e93585553b21aa1a47aa2970	SQ;19837778
f63fe9c59e53d9587766136a15864412	SQ;19837990
81a8f87434a337a21077462e2a1cb5c9	SQ;19838343
14f58b2b12e291455a69d48e56728992	SQ;19839622
752fa8c75ecef45cfa9cf0c5a59afe49	SQ;19840006
f42df1d200fb31e1bed322fab31540d6	SQ;19840745
80d8c2289eb0b45dd9ab395572f44eae	SQ;19841232
07c4180bd9082b53416a778fee66e3f3	SQ;19841468
c39b7a42d0e463287ec636842fe38b67	SQ;19842362
a9dcd316817972a94c0af505715b10bc	SQ;19843099
f692730f2bd8700f690f8a231d2e446b	SQ;19843722
11f83a01fda0f6e2061e6e17dc9cc0fe	SQ;19844666
a179a430866ce2f2826fec132cd9e71f	SQ;19855736
a3891b57fd37552bdad1be4e20266a5a	SQ;19855995
e7ffec1ba9f35a3e29c9946f86b8fe72	SQ;19857409
41d17c6950c12d0d8ec2b305108f08ac	SQ;19857902
bdc426cd84a477b9b48d7e7d1538fc85	SQ;19858773
940e92280507db531e4654cc1f1054ef	SQ;19859011
eaca300e106a2e1c1897455c6a2cb618	SQ;19863867
33eefc92073ab38229f0ce775746b219	SQ;19864079
6021387359d7e25495b6b804ebbbb0aa	SQ;19865963
597ada174987f3f2f0b2e4046f09247d	SQ;19866668
c9a4247a29baa59833607fc71f58bb40	SQ;19866748
811cb37790973c1b417241d62fe2a569	SQ;19869130
a3f1555a0375aea877145c8c372ae4af	SQ;19869427
1fd1b5316d6ec8962be7986ceebf3ce6	SQ;19870774
bce4ec40fb993e1733ea6d2d16398ed0	SQ;19870921
e40253c45f8d96170d6af32f8d8e3e05	SQ;19871046
1adc4b78b212af1a83a6460bd27222f0	SQ;19871766
79435902b3753af094ba24f8a4847978	SQ;19872996
2276b4a96eb715159638ed0f90239b89	SQ;19873300
dd287e28fe668e94028c1a241a6a1c7d	SQ;19874826
4e8ae3a74fefacbbb8650ba892c2b2da	SQ;19875482
f19b5223816de3060184fb9250936fce	SQ;19875812
e5089d2bdb42934617cd38749662eb21	SQ;19877649
bceada3d0ee38c76dafe93fd74e71dfe	SQ;19878194
e24a612b49c52c8aca23eb196c1ebe06	SQ;8690927
48f4c66f41d3805c7213639bcb949d6a	SQ;8692149
cc7281740fd5e50cb1f19a22a728e790	SQ;8694120
52b0aff6e54274ccb35b371b7630b68a	SQ;8695006
fd65d023d2d6b71c478da3cfa418cbbc	SQ;8695842
b2925aa2103833c4c0e3e2ba4e27e66f	SQ;8695920
18fb5ebf5d11ec1db0d36de3ea2a049d	SQ;8696505
215d14a53287c2aca2d8bd12b09aca14	SQ;8696543
5a03dd7605925c94812a9550acc2d354	SQ;8697126
16258f1ad08d9c0c91c627eefad05949	SQ;8697180
c4e23aeca494361878d3407ae5c05e3d	SQ;8701755
085f029e3f483828cb30f70b141fa58a	SQ;8702125
cc404517a12f1a399ab48b948f4e71ff	SQ;8715845
b280ddc383280ca975eeaa3329e34c14	SQ;8717375
6d3b4b9db4531cda588528f2c69c0a57	SQ;8720010
14c0ff5e76ef8ac009fdcc923f701356	SQ;8721428
a5f947d297585356da9380d22ac8c974	SQ;8722075
b9155494bf5b0de513f322e685542888	SQ;8722221
0870e7d5d9d76766ebd3dce1758b733f	SQ;8726286
c69c15ebe466171a13ee5aa610e90e61	SQ;8726341
950b7715ab6cc030a8c810a0dba2dd33	SQ;8727457
5a9fcf1a7370455e62e2701803939c8e	SQ;8728304
7be43cab2c3d57b779ea0f8ceeacfc0c	SQ;8729681
b289385ff9ca374ceb056d5950d090b5	SQ;8731408
6db92a6a61672ceedb192c31b975e370	SQ;8731753
754b35896aef0625da39ee42e61db715	SQ;8731976
8e46b5509ea749211c8c5cacdc1e2500	SQ;8732177
fd4ec29ab7c96a341ad546c954b7f557	SQ;8732348
527995da853a37f9c47e616ce237d523	SQ;8732738
cabe5b677d534fb65e0d2245f61e2bd1	SQ;8732878
d75212b190b11adfcbc1b62e6d392ed1	SQ;8734273
1f44f865b53e6414d5296a088f0a75e7	SQ;8734707
f8e9d021f04423c2ad6499f4ce6eca57	SQ;8734878
c6730817f9a41f80296421e6b7da6f25	SQ;8734901
b18a91dba09f9ffefbe7b4a6aed19945	SQ;8735154
816e83d74c3a633c3ccc005f1c14d55a	SQ;8735385
26ebd521c00f7b4d595086f162ab00e1	SQ;8735393
bbbbef70abd153db9376c364e9fafbae	SQ;8735505
9b6924737e47f2eed133a565b35dd804	SQ;8736724
432d83294aa0f2f3fc1b7673977ea4d1	SQ;8737545
fa15dcef7c84118ca9ee3f95600132c8	SQ;8737761
275dc2512038a6501b7d27e38165bec7	SQ;8738747
b1da76b1bfdf36225429a5be70ff88a2	SQ;8738841
49b16de93b5b34374e7e2a7e71253124	SQ;905849
2fa0ef57b1f4391f7a2ae4283410311c	SQ;933584
5b0a1904c2c8e69fe643091fee181037	SQ;935362
11a2689b92ee76c83cd57591ae940971	SQ;936803
ddab1d6f7c76a6508e85423cd56d46e5	SQ;937871
a8b76267e5f1749ca29c5465c631ab8e	SQ;958004
8bfbb0491705b51d42ef6d8ba0c3e2ef	SQ;958152
f1cb6a33be382d29ff291be589f1ed70	SQ;9778203
e6343ecf374a95dd0356831650af82f1	SQ;9778306
29b2d16dd6ee3e8669ae77b4e053ee20	SQ;9778321
e5c6d7f52bae4b6b57c6320ef95f9b66	SQ;9778889
7db3e698f27f19f0343e6b23af07a5b3	SQ;9778953
257d2dc2f7c0bb730fe685a8052aaa63	SQ;9781141
da4c1ce6a2ee20bb9c4c5d9462be98de	SQ;9782167
f53ad09e45a4038f2261b9ee90353658	SQ;9782568
c7084aa0f01934072f9e244363059ca0	SQ;9784594
72f3e9cbd94835f59aa0a43b22a01b0f	SQ;9784661
8ed84d5653334535562a21058880db81	SQ;9785390
ddbfcce4683cac59087c5f26e674349b	SQ;9786193
cdbabc0602366c37167aba18498d8232	SQ;9787190
950b7715ab6cc030a8c810a0dba2dd33	SQ;8727457
genometools-1.5.1/testdata/U89959_genomic.fas000066400000000000000000003240411211610345200207110ustar00rootroot00000000000000>gi|1877523|gb|U89959.1| Arabidopsis thaliana BAC T7I23, complete sequence
AAGCTTGCTGCTGCAATTTGGGACTGTATCTCAAAATATAAAGCCATTCCCAACTTCCCCCAGACCGAAA
CATGTGAGCTGCTCATTGTGGATAGATCAGTGGATCAGGTTTTAAGGCTCATCTACTACATTTACTCCTC
AAGTCCATATTGATAGTTTATTTCTCTAAACGATTGAGGTGTAACTGTAGATCGCTCCTATCATACACGA
ATGGACCTATGATGCTATGTGCCATGATTTGCTTGACATGGAGGGGAATAAACATGTCATTGAGGTAATT
CTATTTTTCTTTCTTATCCTTCAACTTTTTTCCGTTTCTGAAAGGCCCCGATCCGGACTGCCTAAAGTCC
GGTCGAGAGAAGTCCTAGCCAACGATCCTATTGAGGATCGCGGGCGTTACAGTTTCTCTCTTCCTAATCT
CTCTACCATATGCTAGGTTCCCAGTAAAACTGGTGGGCCTCCGGAGAAAAAGGAGATAGTGCTTGAAGAT
CATGATCCAGTGTGGCTTGAGCTTCGACACACACATATAGCAGATGTATAACACAATTATATACATCATC
TTTTCACTGAATAGCTCACCATGTTGACACCATCATTTTTGGTTTATAAATAGGCTAGCGAGCGTTTGCA
TGAGAAAATGACCAACTTTGCTTCAAAAAACAAAGCCGCACAAATGAGATCAAGGTCAGCGCTAAGAACT
TATCTTTCTGTCTTCATAACCGAGTGCTTAGACAATGGAACAGTTGCCTAAGTTTGATATCTGGAAGACT
TTAAGTTTCTTGTTATCCTCGATATGGATTCGTGATCCCTCACAGACTTTTTTGATATGTATTGCTAACA
TCTTTGGCTAATGTGACGCAGGGACGGTAGCGAGTTGTCTACACGAGATCTACAGAAAATAGTTCAGGCT
TTGCCGCAATATGGAGAACAAGTTGACAAACTCTCCACTCATGTAGAGGTTTGTCTCACCATTAAATTAT
CTCAAAATTCAATGTTAGATGTGGTTGCTGACAGTTTTTTTTTTTTACTTTATAATCAAATTCAGCTAGC
TGGAAAAATTAATAGAATAATCAGAGACACAGGACTTCGGGATCTTGGGCAGCTGGAACAAGATCTTGTT
TTTGGAGATGCAGGTGCCAAGGACGTTATCAACTTTCTGAGGACGAATCAGGTGAATAAGTTTGAAACAT
GACAAAAAAAACTTGATAGCCGCATTGATTTAGTGTTTGAAATGACACATCATGTATTTAAAATGCAGGA
CACAAACCCGGAAAACAAATTACGGCTTTTGATGATTTATGCAACAGTGTACCCCGAGAAGTTTGAAGGT
GACAAGGGTGTGAAGCTAATGCAGGTAGCTTTTCGTGTGATAGAGACCCCTTGTAATGCATGGAACAACT
TGCTAAACAAATACTGCATTTATGTTATCAGCTTGCTAGATTATCACCTGTGGATATGAAGGTTATAAGC
AACATGCAATTGATAGCTGGATCCCCAGAAAACAAAGCTAAGTCCGGTAGTTTCTCCCTCAAATTTGACG
CTGGAAAGGTAACAGATTCAGTTTAATTATGAAAAATCAACACTAGTTACCGAGAATAAGAAGAAGAATC
TGACGGATATGTATACTCTTTTGCTATAGACAAAACAAGCAAACAGGAAAGATCGATCTGGTGAAGAAGA
AACATGGCAACTGTTCCGGTTTTATCCCATGATCGAGGTAGATGAACACCCCGGCTTATAAGCTACATAT
CCACTATGTAAACATGAAGTGGCTGAGATACATCTTTGTTATGTTGCAGGAGCTGCTTGAGAAACTCGTG
AAAGGCGATCTATCTAAAAGCGACTATCTATGTATGAACCAATCAAGTCATAAGGAGGAGAGTGAAGCAA
GAACAGGATCTGTCAGGAAGAGTTCTGCTCCTACAGCGGTTCCAGAGAGAAAAGCCACCCCTCATTCTAT
GAGATCAAGACGAACTGCAACTTGGGCGCGTCCTCATTCTTCTGACGATGGATATTCCAGGCATTCTATT
TTACATAATGATTTCTTATTTTTTGGTCCATTTGAGAGGAGCTTGGATTTTTTCTAAGAGTAGTTCATAT
CTTTCTTCACACCCAGTGACTCAGTGTTGAAAAGTGCTTCTACGGAGTTCAAGAAGCTGGGGCAACGCAT
CTTTGTATTCATAATTGGTGGGGCAACTCGATCCGAGGTATACATTCAAACAAATCCGACCTTAAATGAA
TGCTATATATGTTTCTTTTTGTCAAAGCTTGTGTCAACATTGGCATAACTTTTTGACAGCTCCGAGTTTG
CCACAAGTTGACAAGCAGTTTGAGGAGAGAAGTGGTACTAGGCTCCACTAGTTTCGATGATCCCCCACAG
TACATCACGGTAACACAACATATCCCTTTTAAGAGTTGCTGATTGCTAAATACAAAAAAAAATACCATGG
AACCTCAAAGACTGGTGACTGATTTAAATTCTTAATCCAACTGTGTTTTAAATGTTGTCGCAGAAGCTGA
AATTGCTGTCGGAAAAAGACATACAAGGGGCTCCTGCTCAGCCCTTCAAACCACAATACTGGTGAATTTG
ACACAGCTTGAGTCTCAAAAATGTATTTAGGAGAAGTAAAAAAAAAGGCTAATAATTTTGCAATTGAAAG
AAGAGTGGATAAGTAAACCTTGTCCAGAGACAAGACTTGGGATCAGGTTAGTAGAAACGTTATGGTGAAG
ACTTATTTTTTGTTCTTGCTTCTCCTTGACCCCAAACCGTCGCCTTTCCCTTATTTTTTTTCTTCATATG
GGTCATTTGGTTCATACTCTATATACTTTTGTGTCACAATTTAACTCTATATATTAGTCTCTACGTCGAC
TTAATGGAAAAAGTGAAGATGATAGCTTCTAATTTGCTTTATTTATTTATAAACTTTTGGCTATTATTGA
TTCTTCTGATGTAAGTTAATTTTAAGTTTCGAGTTATATAGCAATCGTTAAGTTGGCAAAAGATTTTAAC
CCTCGAGACTTTTTGGACAACAAAACGCAAATATGATAGAGCGGAAGCTCATTAAAAAATCGTTTTAGAG
CAATGTCACCAAACAAAGAAAATCCATTTCCCAATAAAAAAACAACGAATATAAAATTCGATTATATATT
TACCATCAACCACTTAACAGACCACAAAATGAAGGCTGTTTACGGATTCAACACAGATTAACGGGTATGT
ATGTATGATCTAGGCAACGGTGGTGGTGGGACCAGGATAAGCAGGAAGAGTCATGATCCGCTTGTCTACA
ACTGGACCTCCCACAGTGAAATGGTACAGACTCTGAAAGCTAGAGTCATTAATCCCCAGAACCTCGTGCA
CTGGATCATCGAAATAGCACCCAATCCCGGTTGCTGAGATCCCCATTGCGTGTGCTTCCAGGTACAAAAC
TTGTCCAACAACACCCGTCTCCCAGAACAGTCGAGGGTACATCCATGAGCCCTTCTCCCGCAGTGCTGGT
TCAAACCGAGCTATCATGCCTAAGCTGAAGCATCCATCCCCTGCAATGTCCTGCATCCATCAACCACAAT
GATTCAGTAACCAAGTGAAATATATTGTTAATTACAACTCTATCCGACTCTGTACCTGATGACATGATAG
CCCTTTTGCCAGCCTCTGGCAATCACCCTCGGCGAGCTTGTACAGAGGAAGATTGTCCGGACATCCATCT
GGTTTAGTCCACTCAAATTCAGGCCTCGTAGCTGTCTTGAGATCACTGAGATGATCCTCGTTTCTGACTA
GGAGATACAGTCCCTTAGGCAAACCCGAAACTCTGTGAACAAACAAGGCAAGATGAACCTCAGCAGTATC
CCAAGGAAGAGCTCGAAACGGCAGCGCAAGTTGCTCTTTTTGGGACTCGCCTGTGGAAGGAAGACAGTGC
ATCAGCATCTGGTAAAACGAAGACATGTCTATACAAGTAACAGCGTCCATATCAACAGCACTTCTTCTCG
TCCTTACAACTTGCCTCACCGTTAACTTATTATATGAACTGTGGCTAAACAGAGCACGACTGCTTGTGAA
GGAAGCAACATCAATTGAAGAAGAAGAGGTGGAGTAGATCAATGGAGGCTTTTCTACAGCCTTGGCTGTC
CTGTAGATGATATCCCAACACAAATGCTCTTTGCTCAGAGTATTGGGGTTTCCAGTCCATTCTAGGCTTG
GGAAGTCTCTAAGGGCAGAGCTAATTGCGAGGTAGTCTAAGTTGAGATGTTCTCTACTAGTTCCGTTGGG
GAAAACAAGGAGTAAGCAGTCAGGATGCTCGAATTCAATCTCAGGGAGCTCAGCTTTACCTTTACCTTCA
GGTAACTGAAATTCGGGGAGACCCATAAGCCTCTTGAGATCATCAGCTCCGAAAGCGTCGAGAAGCTTCA
AGTCCCAGCCTAGGTCTGCGGCTGCAATGGAGAGAGCGGCAATGGCGTGGCCGACGTCGTGGTTACAGTA
ACGAAACGCTCGTTCTCCGTACTTCCAAGCTTCACGCCAGAAAATTGAAGAAATTCCGATGAGAAAAGAA
TTCTCCGGGAAGAAGTTGGGGAAAAAGGAAGAGGGGATGTGAGCTCTAACCTCCAAAGAATGCTCTTTGG
GAGCATAGTGGGAGACGAAAGCGGATTGGGAGAGGGAAGGGATGGGAGGAGCAATGAGATAGGCCTCGGT
GGGATGCAAGTTACCGCTGCTGGGGTTGACGCGGAGGGGCCACGTGGAGGATCCGGTGGTCTTCCAGGCG
GAGAGAGCGAGAGAATGGTAGAAAAGGTGAGAGATTGTAGGAAGAGAGATGGGTTTGGGCGGAGGAAGCG
AGTCGAATAGAGTAGAGTAGAGAGGAGAGTCGGAGTCGTCGTCGATGTCGTGATTGGGGTGTTGGAGAGG
AAGAAGAGGAGCAGAGAGGTACCGGCGGAAGGGATTAGGCTGATTGGCCCAGTCGAGACCACGAGGACCT
CTCGCGTAACCGTTCAAGGAGTGCTTCGTCTGGTTGTGGTACTTGAGGACCAATTCAAGCGAAGAGGAGG
AATCGTCCTTGTTAGGGTTTTCCACAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGAAGGTCAT
GGCGAAGATAAAGGCACTTTTTGGTGTTCGAGGAATGGAGAGAAGAGAGGTCGAAGACGCGAACCTCCAC
GAAATCGTCGGATTCATCATTGCTTCTCCTTTCCTCTGTCTGGGATTCGACATCTCAAAACCAGAAACCA
ACGGATCTTTGTACCGGGACGGTTCAGATATGGATGGACCGGTTAAGGGATAACCAAAATTGCCTGTGAT
TTCTCTCTGTGACTTGGGGAACAACTCCACTGCAATTACACCTTTGTTTTCTTTCCTTTTTTTAAAGAAG
AAGAAGAAAGTGCAATCTAAAGGCGTGACTCGTTAGAGCTTTTTTGTTGTCCAAAAGTTACGGTGGTCTC
TCTGTCTCTTAGTCGGCAAAATTCCCTCTTTAAGAGTATATAAGTAATTTTGGGTATTCTTTTTTTATTT
CATTGGCATAACGAAACACACGACTTGAGCAACAACAAACCACGTCACTCGATCACGCTTTCATGCTTTA
CCATTTTCCCACACAAATCGACTACTATCACATGATTTCCCTCATTACCTAACTCACTTGTGTTCTTTGA
CCACATCAAAATTTGTCCTCAATACGTACACTTGGAGAATTTTACTACATTACTTGGAATCAAAGGTGGT
AATTACTATAGTTTGACCAATCTGATCAAGCATTAAAAAACCGACGAGGCCATCTCTTCCTCCTCCGATG
GCGCTGGGAGATTTAGATCTATCAAGCTAATTATTATTCCTGATCTTCTCGTGAATTCATTATTAGCGGA
AGCGTGAGATCTTTTGTGACCTCCGAGAGCTTGACCAGATGTGAAGACTTTGGCACAGATTGGACATTCA
TGGTGACTACTAGTACTCTTCTTCTTCTTCTTCTTCAACTCATCTGAGCCTAATTGATCTGTTTCTGCTA
TCTTCTTCTTGTGGCTTGCTCTGTGTCCCCCTAACGCCTGATACGACTTAAACACTTTCTCGCAAGTCTC
GCACTCGAACCACTTATTCCTCTTCTTCTTCCATCTCTCTTCATCACTTTCCTCTTCCTCCTTCTCCCAC
TTGTCTCTCGACAGCAACATGAGACTCAAGGCCACGTCTTCTTCCGTTGTTGCAGCGTCCGACACCGAAC
TCATCGGTTCCTGCTCCGTACACGACTCACTGAGTTCTTGAACCCCGATCTTGATATCTGCTGCTCTTGC
GGTTTCACTTTTCCCTTCTTCGTTGGATTGTTGATGACGTAATGATGAGATGGATCTCCGGTTAAGTCTG
GATCGTTTGCGGGAGGGCTTCTTGGACGACTCGGTTTCACTCTCTCTGTCCTGAAGAACAAACCCTGGAT
CAGCCATGGAAGACGAATATGACTCGGGCTGACTGGGGAGAGGGTGAATGAGCATGTGAGACCTCATGTG
ACCTCCCAAAGCCCTTCCATTAGCGAAGCTCTTCCAACATAACTTGCACTTATGCCTCTCTTCCATTTCC
TCAATTTACCAAAACAGAGCAGAAATAGAAGAAAAAGGAGAGAGAGAGAGAGGGAGAATATAAGAAGAAG
AAGAAGAAGAAGTCGGAGTAGGTTACAAGCACTCTTCCACCAACACTTAAGCTAATATACGAAGTCCCAA
CAACAAGTTAATGTTTTCTTTTTAAGGAAAAGAATTAATGGGATACTTAAGAATATCAACGAAAGCAGTT
TACTTTCTTTTTTAATATCAGAAACGGCTAAATAAAAGACCTGTCTGTTGTGTAAACATAAATACAAATA
AGCCTCTAAATATATATAATTATCAGTTATGTTTTTCTTATTTTATTGACAGATTGAGCCAAAAAAAAAG
AAAAAAAAAAGAGTATTGAATGATGAAGTGAAGAGCCGTTGATCAAACATGTAACATGCGATCTCACACC
TTTATTCCTCCACGCTGACTTTTTTTCTCCTCTAATTTTTCAAATACACTCTTCTACTAGCCCAAAAATA
CTAGTATGTAAATAGTAAATACTAGTATGTAACTGAAAATTTCAATACTTTGTTGATTAGAAAAGAGTTT
GTGGATGAGGGTATTCATTTTGGTAAAGTTGCAAACAAAAACCGTTGAGGTTTTGTTGTAACGACTAAAC
AACACTAGCACTGGCCCCTCTATTTCTAACTTTACCAAATTTTAATGATTCTGTGACAAATACACCAACT
CTCCTTAAATCATAGGTTGACACGTGTGACTAAACTGCTGACTTCCCGCATCGTATAGTTAGTGCTATCT
TTGACTCTCATACTCACACGCCCTTTTGGTGTTGACTCACCTCTTGTCATTTATTTGGATGAAATTTCAA
TATAAGAATCTAAATTTCATTACTCTACAAATTTCTACTAACAAAAATATTTTCCCAAGCATGTCTAAAT
AATTTTAACCTTATCTCGTTGAGACGTTATTACCTCATACTAGACCAAAATTTCCTTGTATCAATAGCGT
GCAACTCTTGTACGTGTCTATATGTGTCAATTGTTGTTAAAGTACATGTCCTCAAGTTAATTGATTAAAG
ATCTTTTGAGTGGCCCAAAGAGTCATATACTTTGCTTGAGCTTTTCTCAAAGAGAAATTGGAGGATATCA
GTTGACATTAATCAAATTCCCCCCGCTAATCCTAGTTTTCAGCTGATGGTTGGTGGGCTTCCTAAAGTCA
AAAGTTCATAACTTGTAATGGCAACCACTCATTAATAACATATATGCGAGATAAAAATGACTCTTTTCTT
GTAATCGTATTGAGAGAAATGACCCTTTCCTTGCAATCGGTGCTTAATTAAGAACCACCAAAATTATCAA
TTCCGTTGAGGCGTTGACTCATGTTCATGTGTTTTCAGTGTAGTAAGAGCCTTTTGATTATTAACATGAT
TAAAATATATATGGGCATATCACGAGAGTTATTTGATACGTGATATTCGTTTATTTATTTGATATTTTTC
TTCTTTGTGATTTCTTAATTTCGAATTTACAATTTCTTTTCTGGAAAACTTCAAAATTATATCTCCTTCT
TGATGGCTTAACAAGTAAATTATATCACTCTGTAAGATTACAAACATGAAATTAAAACATTTGCGCTTAT
ATGAGCAAGGAGCCCTTGGTTATCTTACTTTATTCTCAACGTATATAATAATAAAAAATGATACAATTAT
CTATCTTGTATATTAACTAGTTGTGAAACTTAATTTCTTACTTATATCTTTGTATATATTGGACTAGAAC
TCCTTATGGCTCTCTAAATCTGCAGAAGACGCCAAGTGTAATTCATATAAATCCATAAACTCTATATATA
AACTCATGCACTTAATTGTATATATGTAAAGAATATAAACGAATGAAAGTTAAAAGAATATAATTAGCAA
CTTAATTAAATTAGTCAGTCGTCAAGACCAATCACCACTTGCGAGTTTTAACCACGAAGATGAAGTAGCG
TTGTGATTATTGCCACCACCATCTCTCTCGATCATCCCTACGCTCATGGCCGTTGGATCGACGGAATATT
CTTGGCAAGCTAAGTTGAGATCGAGAGATGGTTGATCTAACGGCTGCGGTCTGCCGACGGAATGATGATG
ATCGTGGAGCGACGTCATACGAAGATAATTGGAAGGTGTTAGCCAATGGCATCGCTTGTGGCCTCCTAAG
GCCTGTCCCGAAGAGAAGACGCGATGGCAGATGGTGCATTCGTGAGCGTTGGATCTCTTTCTTGCGATAT
GAGCCGTTGATTTGTCTTCCTCATCCTCCTCCTCATCTTCGTCCTCGTCGTTGTCGTCGTCGTCTTCTTT
GTATTCCTCTTCCTCTTCCTCTTCTTTATCTTGAGAGGCAAAACAACCCTTCACTTTCTTGTGGCTTGCC
CTGTGTCCACCCAATGCCTGATGCGACGTGAACACCTTCTTGCAAGCTTTGCATTGGAAAACCTGGGCGG
TTTTTTGCTTTTTGACGGTTTTGCCCTTACCATGTCCATGTTGTTTATGCTGATCACCACCATGCGCATC
CCCTGAATTGGACAACAAGACAAGACAGTTGGCAAGCTCTTCGTCTTCGTTTGGAGACAAGTTAAGATGA
TGATGCTGAGTGGACATCGATCTCTCCCTCTTCCACGGAGGACGACGTGACATGTTGTCCTCATCGTGTT
GTCCACGACTGAACATTACGAAATCAATGCATGGTGAGTTCATGGCTCCATGCATGTGTGTGTTCAAAGT
GTTTTGGTGTGAATTAAAAAGAAGAAAGCCCTTGTTTTTAGTGGAAGTAACGGGTTTGGTGTCTTCTTGT
TCATGTGGTTCCAAGTAGCTAAGCACTTGCTTTAACGACACGTGGTGCAACTTTTGACTTTTTCCAACAT
TCCTAGTCACATGCATCTATTCTATATAGATGTTGTTTAACAAATAATACTCTCATTTCATGCTTACAAT
ATGTTTATAACCCAAATGTAAATTATAACAATTAGGAAGAGGTGAGGCTGCGGATGAGAAGGCCTTCGAA
GGTGATTCCAGGTCCGAAAGCTAAGCCAAGTCCCCACTCTTGTGCTGCGTCACCTTTCTTCTTCAGCTCA
TCTCTCATATACTCCATCACATACAGTATCGTGTTGCTGCTCACGTTCCCGTAATCCACCAACGCCCTTC
TGCTGCTCTCCAGCTTCTCTTTCTCCAGCTTCAGTTTTGTCTCCAGACGGTTCAGAATCGCAGGTCCTCC
TGGATGAACAGCCCAGAACATGTCATTGAACTCCATCGACTCATCGCCAGCCTTTCCCATCAGCTTCTTG
CAGAACTCTTCTATGTTCTCCTCTATCTTCTGCGGGAGGTCTCGTCCAAGCTTGAAGTTTATGCCTTCCT
CAGTCAACCTCCCCTCGATCACGTTCTGTGTCCCCGGCAAGAACTGCTGAACCGCATAGTGCAGCTCCAT
GAAAGGAGCTTCACACTCTCTCGGGTCAGCTCCGATGATCACAGCAGCTGCACCATCTCCAAACAGAGCA
GCTCCAACTAGGTCGTACGGACGCGCTTTGTTTGGTGGCCGAAATCCGAGAATGGTGGTTTCAGAGGTTG
TGAGCAGAACACGGCTTCCGGGGTTGTTCTCAGCAATGTCTTTGGCCACACGGAGGCCAGTCACACCTCC
GTAGCATCCCAGAAAATACAGCATCACTCTGTTCACGTCATTCCTCAGGCCTAGCTTTGCTGAGAGGTAA
AGGTCACCACCGGGTAAACGGATCTCGCTTGAGGAAACGTAGACAATGTGAGTGATGTCTTCCACTGGCC
TTCCCCATTCCTTGATGCAACCTAAACTGGCTTCCAATGCCATTTCCACAACCGCCTCGTTTGCAATTTC
AAGTCTTTGCTTGATTGTTGGTGAACCCTCTGTTGTTAGCTCAGGGTATTTAGCCAGTATCTCTCGCGTC
AACACAGTGTATCGCGTCTTCACGGTTGTCGTTTTGCCTAAACAACAGCACAAAACATTAGAAAGCTTTC
AGCATTTCACAAGAGAGCATAGCTGTCTGAAAAAAATATAAAGAGACTGAGGCTTACACAAGTGTTCCAG
CTTTTCTTTGATAAACGCGTCATCACATTTGGTGTCTCGTAGAAATCCTTCCACTAGATTCTCCTGAGGA
ACGACTTGGCTTGGGAAGGCTTTGCCAAGAGCAAGCAGTGTTGCCTTTCCGGCATTTGCGACACGCCTTG
TGGATTTGCTGCTTAGCTTCTCAACACCATTCATCCTAGAATTCGACATTTCTTTTCAAGCGCAGAAGGA
AAAAACTCAATTAGATATTGGGAAGAAAGATGGTGGATGCAGAATATCAGCAAATGGCAAAGGATTATAA
AGGAAGGGTTGAGGGTTTTCTTGGGGAGAGTTTGGTGCTGAAGAGTGAAGATCATGTAAAGAGAGAAACG
GTTATTTTATTAGGGTTTGGTGATTCTTTGGCCTGTGTTGGTTAGAAATGCAAAAAACACCATGAAACCT
ATTTTCCCGGGATAAGTAATATAAGCCTAATCTACTTAGGAAATAGGTACCATGAAGGTGAAAGTTAGGA
ACAGAGAGTTGCAACGTCCATAGAGACCTGTAACAGACACGATGAATACAAACTTGCTTAATTGCTGAGG
GCCAAAAATTTTACAATTGCCAATGGATAATTTTAGACACAGAATTGAAAACGGAACAAAGAGAGAGGAT
CCTGTTTACCAGAAACCAGATGCACGGTCTATCCTTCATTCTAATACAGAGCAATCATCTGATTCTCTCA
ATGTAGCCATCCTCTTTGACACAAACTGAAGTTCTTCCCACTTTCCAGCAGCCTCTAAGGCATTCCTCAA
AACCACGTGGCAGCTAAGCTGTTGGTGGTTTCCTAGTTCTACTAATTCATTGTACAAACTAAACGCTTCA
GAGTGTCTCTTATGCTTACAGAGTCCTTCTATGACCGTGTTGCATGTGTCGATATCTACCATTTGACTTT
TTTCCAGACAAAACAGAACAAGTGTATGTGCATCAAGTAGTTTTCTATTCTCGCAGAGGTAACCAAGTAA
TTCCTCCATCTTAACCAAATACCCGTTATCATAAAGCAACCTAACAATCAGAAATGCCTTCTCTTTCTGT
GCACTACTAAAAAGCAATCTGACAACCTGCGTTGAAAGATCAATGTTCTGTCTTATTCGTTTTTCCAACA
TTAGCGTTACCAAGCAGAAAGACTCGTTAGCAAATTTCCTTTTCGCAAGTTCTGCAAGTACAGAATGGAA
AGTGGTTGCAACAGGAAGATAAGAGCTCCTTAGCATCCTTTGTAGGGTATCGTGAGCAAGAAGAGCTTCA
CCTATCTTCAACAGTCCATCAATCAATAACTCGTAAGTTTCAAGATCAGGTACAAATTCCCGCCTGAGCA
TTAGAACCAACAGCTCATAAGCAGGCTTGAATTTACCTTCTCTGCAGTGACCCGTTATCAAAGTCTTGTA
AGAGGGCGGATCTTGCACTCCTCTTTTCATCAGCTGCCTGAAAACTTTCTCCGCTTGTTTTGTTTTCCCA
TTGGCACATAAGTATTCAAACATTGGGTTATAAGCTGCAGCGAGAGGCTTGCATTCATCCTTACCTAACA
ATACTTCCTTCTCAAATAACTCATTGAACAATGTCTCAGCTCTATCAAATTCGTTTCTCATGCACAGAGT
ACGAATCAAAACACTATAAGAAGCTGAATCAGGATGCAACTTCATATTCAGCATTTCTTGGAACACCTTC
ATCGCTGCATCCAAATGACCAGCATCGCAGTGGGCTTTGATCAAAATATTAAAAGTGCAGGCATCTGGAG
CGAAAGTGGTAAATGCGTCGTTCCCTCCAATCAAGATATCTTTGATCTCATCATATCTGTGAGCCTCAGA
GAGCCCCTTGATCAGAGTATTGTAAGTAACAGCATTGGGTTTCAGCCCTCTACTCAGCATGTCATGAAAC
ACAAGCACTGCTTCATCAATTTCCTGCTTCATACAATAGCCTCGCACCAGAGTAGTGTAACTAACAACGT
TGGGATGCACATCGGTTGCTTTCTTCAACATTCCACTCAAAACATTATGTGCAATCTTGACCTTGCCGGC
TCTGCATAACCCATCGATGATCGTGTTATATGTAACAACGTCAGGATTGCAATGATACAGCTCCATATCC
TTAAAAATCCTAAAGGCTTCATCGACCATGGAGTTCTTACAAAACCCATTTATCAATGTATTGAAAGTAT
AGGAGTCTGGGGTAACCCCGTAGGTACGACGCATTTCGTCGAACAAGTCATGGGCCATTCCAGTTCTGCC
ACGCTTGAGCAAAATGGAGAGAAGACTGTTGAAGGTAAGAACGGAAGGGGAGATGCCCATCTGCTTCATG
GTCTGGAACAGCTTCACTGACTCCTGGAAGAGCCCAGCGTTCCCGTAGCTCCTAATCAAGCTGTTGAAGT
AGCGATCCTGGAGCTTGACGCAGCCATTAGACCTTCTCTCGATGGAGAACAAGAAATTGCGAGCCACATT
GAGATTGCGAGCTCGACCGAGGAACTCTAACATGAGGAAGAAAGACTGCTCTTTGTGAGAAAACCCCTTG
TTGGAAACCCAGTCAAAGAACCGGAGACCATCCGCAGGGACCTTGATGAGACGCAGGGTTTGGAGAACGG
TGGTTCTGGAGATGGTTTGGGACGGATGAAGAGATGATAGTGAAGACTCGAGTTCGTCCGACCACGGGTT
AGAGTTCACGGCACGGGCCAAGGACCTGGCGAGTTTTGATTTGGTGGACCTTTCTTCATTGGTAACTTTG
GCGGCTCGGAGAACTGGTTGAGACTTGGAGACAAACAAAGCATGGAGTTTAGGTACAGAAGATACCATTG
CAGAAGAAAGTTGCCGCGAAATATGGCGGCACACGTCCGCCGCTCCTCCACCCCTTCCGGCGGACCAAGA
GAACAAACCCTTTCTTCTTCATTCTATAACTCTCTAAGGCCCAATCTAAATGGGCTCCTCTTTGTTCTAG
ATAACTTTACTTTAGGCCCAATTATAGAGGTGGCCCCGACACAATATTTTGTTTTGTTTTAAACTTTAAA
AAAAAAAGGAGAAGAAGCAACAGCATATAATTAAGTCCTAGCTATTAATCATCATCCATAGCATATCAGT
AAGTTTTTGAAGATAGATTGTTTGATTGCATACAGATTTTAAAATAATGTTAAACCCTGAAGTAAACTTG
TAACTGCACCAACACAAGACGTGGTGTATGGATGATCTACTACATTCCGTTTCCCTTTCATTGGGAATCA
ATTTGCGGACTAGTTTAAAACAATCGCATATGCATAATACTTGCGCAGTAATTAGGGAAGAAAGGAGGTG
GGGGTAATGAGTGAGAAAGTGCAATAAGTGGGTATCTCTCAAATTAAGAGAGAGATGTTGACAAGGCAAC
AAGTTTGGTGTAACATTATCCTCCTCCTTTTATTTTGCCTTTTTCTCTATTTTTATATATATGCACAGTC
TTTTTTACTCTTAATAAAATACACTGTTAATTCCTCGGATACCAACGGAATCGGTTGAATAAATTATGGA
TGTTACAGTATACACACTATGTAGGGACTTCTTAATTTATTTTGGTATAGTTAGAAAGATAGCTTATCGT
TAGAGCGATTGAGAGCTTTTCATTATAATTAGGAGTTAGTTTACTTTAATTGTGATAACTGCCTTAGTAG
ATACATAAGTACACTATCAATTGACTACTTTGAGTGAATTAAAAAAGCCTCCTAACAGCGTACTATATGT
ACATCAGAATAAGTTGTAGTAGGAGCAGCATTCCTATTTTCAATATTGTACACTGTATTAAAACAAAAAC
AAAAAAGTAGAAGACAGGATTATGCATATAAATATATATCCCAGAACCAAATATGAAAATAGAAAATTTG
GTTTTCGGGTTTATAATTTGTTTTAGAAAAAAAAAAAAGAGAGAGAGAGAGGGGCAAGGATAATAGAGAC
AGGAGTCCGTACGGTTTCGGGGGTCAACGTCGATGGCAGCCTTTGAGCACCTAAAAATAGGGGACCCACG
CCATTACCAATTACAAAACCTCACTCTCTCGTCTATGCTCAGCTAACCCTACTCTCTTCCCTGTGCTGCC
ACGTGATCACCATCCGATTAATCGGGACCGTTCGATTAAGTAGAGATAGCAGCGCGTGAGGTAGAGAAAG
AAGAGAGAGAGAGAGTTGGCGAATAATAGTAATTTGTTGTTTGGGGGTGAGTGGGTGTACGTTAGCAAGA
TACGATCGGTCATTCTGTCTTCCCTAAAACGATCAACCTCCAACTTGCTACCTATTTACACTTTTGCCAT
CCTGTCTTTCGAAACCCCAACACCGTTTTTGCCTCTTATCTCTCTCTCTTTTTTGGCCTTTTCCTCCTTT
TTTTTTTGTGGTTAATTGAAATAGATATTTTATTTCTCTCTATTCTTAAAAAAAACCACGTATAAACTTG
TAACTGACTACGATGATTTATCTCATTCTCATATCTTATTTATCGCTAGTAAAAAAGAAAACAAATGTAA
GAGAGAGGCCCAGCAGGGGAACAGAAGCGGGTCCCGACATAATTAAATAAGTGTAGAACAAACGCGTTTT
TTACTCTTCTTTTTCCTTAACCACACGATCACCACCAATACTAGCTAGACCCTTTTCTTTCTTTTTTTTT
AAAGTCCTGCGGGGGCTATATATGTATCATCCATATATACAATACGCTGTTAAAAAATAACATAGTAAGA
GTCTGTCTATACATACTTGTGTGTTTAATTTGTTTGTCAAACAAAAGTTCAATTAGAGGCTCCATCAACA
GTTGCTAAGTAGTGAGTTACGTTTTTTCGATATTCAAATTAATCCTACGTAGGTACTACTAAGATTACAA
ATTAGAAAGCTTTGAAAAATACTAGTAGTAAAAAGGGGCAGATGATTGGTAAATAATAATTTAAATTGTT
TTTAGTAAAAAAGGGCACAGACACTCACACACACACTGCTTTCACGACCCATGTGAGTTTTCTTTCTTCT
CCATCTTCACTTTTTTAAGTAGCTAGATGACAAGACAGACAGCTATCTCTCTTTTTTTTTTACGAAGAAG
AAGATCAAAAAAAAAATGAATTTTAAAAAGGGACCTTTAAGAGAGATGGTGGGAGAGAGAGCAATAGAGA
GAGAAGGAAATCCACCCCCACAAATAGAAAGTTAGGGTTTATTGGAAAAAAAGAAAGAGAGTGTGTCTCT
GTGTGTGATTCTAATAGAGGTGTAGTACGTCGCTTTGCTTTCAGTCCATTAAAACCATTCCATAACCTAT
TCCGCACCGACATGTCTCCTCCCCCTTTCCTTTATTAGCCTCTCTCTCTCTTTTTCACTACTCCGTCTTG
ATTTTATAAACAAAAGAAAGAAAGAGAGAGAGATCTTCCTCGGGATTGCAACATGTTGGACTACGAATGG
GATAATCCTTCCTCCATCGTTCTCTCCGGAGATGAAAGAAACCCGGACTCTGACCCGACCCGGTCATCCT
TCTCCTTTTTCGACCCCATCTCCCATTACAACAACGACCACCGTCACATCACCATTTCTCCTCCCCTCCT
CTCTTCCTTCTCTAACCAACAACAACAGCATCACCTCACCCTCTACGGTCAGACCAACAGCAACAACCAG
TTTCTTCATCATCACCATCACCACCACTCCTTGTACGGGTCCACCACCACCACCACTCCTTACGGCGCCT
CCGATCCCATCTACCATCCCCACTCTTCCGCTCCGCCAGCCTCCTTGTTCTCCTACGACCAGACAGGACC
GGGCTCGGGATCCGGATCTTCCTACAACTTCCTCATCCCCAAGACAGAAGTGGATTTCACGTCCAACAGG
ATCGGGCTGAACCTGGGAGGCCGTACGTACTTCTCAGCGGCGGACGACGACTTCGTGAGCAGGCTATACA
GGAGGTCTCGACCAGGTGAGTCAGGGATGGCGAACTCGCTGAGCACGCCGCGGTGCCAAGCAGAGGGATG
CAACGCGGATCTGAGCCACGCGAAACACTACCACAGAAGGCACAAAGTGTGCGAATTCCACTCAAAAGCA
TCGACGGTTGTAGCCGCCGGACTAAGCCAAAGGTTTTGCCAGCAATGCAGCAGGTTTGTGCCCCCTAAAG
TTGCCACCTTTGACCTTTTTTAAATAAATAAAAAAATACTATAGCTGTGGGGTTTCGGCTATCTTCTCTT
CTCTTCGTCCGTACATCCTTAATCTTGTTCTATCTTAGTTTTTAGATCTTCTTTGGATCTCCTTTTTTTT
CATTAGTTAGTTAGCTTCCCTTTTTGTTTATTAATTAATTTACAATCACTGCTAAAGGATCGACACAATC
ATTGAGAGGGTTCGTACTGTGTGGTGTGGGGGATCCCGATATGGCTTTCTCTCGTCCTTTCCAACCAAAT
CATTTTAGCCCTAACTAACCAACCAAACTCTTATCACTAATTCTCCATCTCATCATCATCATCTGATTTA
TACATATATATATCGAAATAATCAATACAGGTTCCATTTGCTGTCGGAATTCGACAACGGGAAACGGAGC
TGCCGTAAGCGACTTGCTGACCATAACCGCCGCCGCCGTAAATGTCACCAATCAGCCTCCGCCACCCAAG
ACACCGGCACCGGCAAGACTACTCCAAGTACGTACTTAATTCTCTTATCATATATATATATATATATATA
TCCTCTTTCAAATTAAGATAATCTCTAGATATATGTGTGCATTTAATTAATAAATGGGAATATGTGATGA
TGATGATGACCAGAGTCACCGAACGATTCGGGTGTTAAAGCGTCATCGTCACCGTCGTCCAACGCGCCGC
CTACGATATCACTGGAGTGCTTCCGGCAAAGGCAGTTCCAAACGACAGCGTCTTCATCCACGTCAGCGTC
TTCGTCTTCAAATTCAATGTTTTTCTCCAGCGGATAGTTATAAGCTTTACTCATATGATATATTATGCTT
AAAATGAGAAATCAAAGGACTCTTCAATATCACTAGTTAATGCTAGCTGTCTATCATCTGAATTAGTCGG
TAATGTGTAACGTTTTATTTCATGTCTCTCGTTTCGTTTGTCGTTTTCATATTGTTTTTGACTTAGTAGA
GGTTTATTTAATTAACCAACAACATATCAGATTTCTGATTCTATTATCAATATCTCCTTACAAAAATAAC
AATTTTCAAAAGATGTCTTCAAAAGAAAAAAAGAAAGAAATTGAAAGTGTGATTGATATATTATTGCTGG
TAAAAGCAAAGACCGGGGAGAGTACTCGTGCATGGTGGTTCGTTCATCGTTTATTCATTTCGGGGAACTG
AATTATTGACTCTCTCTCTCTCTCTCTGTCTGCTGTCTGATGCTGAGCTGCTGGAATTTTCCTATAAAAC
TACAAGAAACCAATATTTTAGAAAGTGACCGATCAATGTACGTCCACGTGGTTTTACCGTCTTTTAAAAA
CAAAATAATATAAAGAAATACAGTAGTATTAGGTTGTTGTTGTCCCCCATTTTGAAGCTAAAAATCATAC
AATTTTTTTGTCAAATTAAATCAGTATCCCCACCGAGATTAATAATTTGCACTTTGATCGGTTGTGATAT
TAGTAAATGCTTGTCTACCCCACAACGGATGGATGATATAGGAGACGTTGACAAAATTAAGCGATTTTCC
AAGCTAGTACCAAGTAGTAGTATATATGCTCCGCGTTACTTGATTTTTGTTACTTGCCAAAATTCATGAT
AAAACAATTGCTATGATGAAATAAAAAGAGCCGATCTGAGTATTGTTTGTTGCATATGTATATTCATTCC
TCCCCTTGCTATTGTTATGCCGTAAGAACTCAACGAGGACTTTGCCATTGGTTCCCCTGATTCCAGCTGG
GTGGGTCCATCGTTTTGCACACGTGTCATATTTGGGTTGGATTTTTTGGCAAAGTGGTTGGGTCTGCGAG
CTAATTTTCATCAGAGCGCTGCACCCACACGTGATCATTTTCTGGCACTAACCTCCCGGTACGGTGTGGT
GGGGATGCATCAAAATAAAGGCCCAAATGCATGGCCCAACCATTTATAACACTACACACACTCGTATACT
ATCTATTTATTATCCCTTCCTTTTCACTAATTAGGCCACGGATCAAATTGATGAATGATATTCCGAAGAC
TAGGGCTCTCTGATTATGGACCGCCCCACTCGCATCTCCTATGTAGTTTACGTATTAGTAGATTTATGTC
AATTATATGTGTATGCATATGTCGCTGTTACATAAAGTCCTATGTTTTATTATACAACCTAAGTTATCTA
ACTCTTTGCCGTGACAGGGATCGGACTGTCCACATTCATGTAATTTATTCATGTCCCGCCCTATTTATTT
TTGTTAATTGAATTGAACCAACTCATTTTTATTTCTATATATCCACTAAATAAATAAAATGAACAGACAA
GAAAGAAAAAGCGTTGTGGTGCTGAAAAGTCAATGATTACAGACAAATGTGGAGGAGACTTGTATCATTT
TATTTATCATCCAAGGACTTTGGGAAGAGAGTATCCAAAGTCTTAGCATTATACAACTGCTTCAATCATT
ACGTCACCACGTGTACGACTATATATTATCACTTTCTCATTTCATCTCATGTGTATATCTCAATCTTATT
ATAAGAATCACGACACAAAATAAAAAGTTTAGCAATAGCCTATATATACAAGTAAAAAATGTTCTAACAA
ATGCAAAGCATAGTGTTATGTAGAAAAGATGATCAAATCAATAGTTTGATGTGTCCCTCGAGGACTTGAC
TTCAGTAAAATATATGAATTTTATTCAGTCTAATTTTTGTGGATGTTCGATAACATTTACATGCATTTTT
AAAGGAACGCCTAAAAAAAGATTGTTACAAAATAAATGTGCAAGCTTTTAAGTTGTTACACCTAGTATTT
GCGAGCATTAAATCCGTAGTTTCATTATAAAACTATACATCAAATAACCATAGTATATAACAATATAATG
GTGATGGATGATATACTACTTTCTTACATTTTAAAAATTGATTACTATATTATGCTGAGTTGGTGGAATA
AACTTTTCAAAAGATAATATTACATAAGGTGTATTTAATTTTATGGGACAATATAAGTTACGTTGATGCA
AAAAAAGTTCTTCTAAACTTGCTGTGATTATATGGGCCAGTATCAGTGTTGAGGAACCCAAACAAGTTAA
TTTTCGAGCCCACTATGATTTAAATCCCATTGTTTCTTCCCTACTAACTTACTACGAAATATATTTTTCT
GTTGGCATATCACATATGTATGTGAATGGCCTAATGGGATTATATAACTCTTTTTGATGCCCGTTATGGA
TTCCATTTTTCAAGATCAAAAAAAAAAAAAAAAACGGCTGTGTCATTTAATTACTGGACAAGGAGCTGGC
TATTTGTCTGTATTCATAAACAGTGTTTGTATCATTATTTAACGAATATTGTTTCCATAAGTACACACGA
ATATATTCTTATACATACGGGATATTTAGACAGGATTGGTACGATTCGTAGTCGATACACCATACTAATT
TAGACCGACCCTTATTATTATTACATGTACTAAGTGCTTCTAGTACTAGCTAGCTATTACCCCCACTTCT
TCTTTTCATTCTAGTATATGTTTTTCCCCACCGTTCGTATTTATATACAAAAAATATATATATATAATAT
TCCTTTGGTCCACATATTAATTCCCGTATCAAATTGTAAATCACGTACTTGTTGATTTTGTGAATGTACA
CGCGTACGCCTCCCTAACATTTGTTGACAATTAGGGTTTGCGGATATGTATCTTGATTTATACGATTTTA
CACGAATCACGATGACTTCCGATTGTACTCGCATTATTAATGGTATTTAACGACGAAACCTAAAGGAACC
CAGACCTATATTTATATATACGTGGATGTTAAGTTTAATAAAGATCTTTACGAAAGGTTTTAAAGAAAAA
GGAGTCTTTTACGCAAATTGCAGTTATTAATAGCTTATATGGTGATTAAGAAAACACAAGCTCACGCCAA
ACACACATTCATTTCATATATATAAACACAAAGTAAAAAGGAAAAAAGGATGAAAACAAACAACGACGTT
TTCTTTTTTAATTTGCTCTCTCCGTAGTCTAATTATACATAATTTAATCACACAGTCTCGAAAGAGTAGT
ATGATTATAGTAAGTCTTCTAATACCTCTCGTTTAGGTGGAACTAACACATGACATCTTTGAGAAGCTTG
TACCTTCGTGTGGCCGTCTTAGGCGACGTAACTCCGCCTCCATCTCCAGCAACGCCCTTGGCTACTTGAT
CGTGACGGTTATTGTTATGCTTGATCCGGTGGCCGGGCGAATATTCCGATCTGTTTGAGAAGTCATTTTC
ATATTTAACCGAAGAAGAAGGCTTCTTTGAAGAAGAACCGCCATGTCTAGCAACGTTGCTCAGCTTCCGG
TCGTCGCTGCGGCACCAGTCGCAAATCTCGGTAGGCTCCGCAAACTGGCCGTAGTAGTTGCTACAATAAC
TATATATATATATACACACATATATGATCAATTAAGAAACCCATTAATAGCCGTGAATGGTCACTCTGAT
ATACATATGCATGAATGATGAAGGAGGACTACTTACGAGTGTTGGAAGCGGCAGCGGCAGTGACCGCAGC
TGAAGAGCTTGTCGGAGAAACCGACATCACCGCACATGCAACACACTCTCTCCATGATATATCTTCACAA
TCTTTATTATTTATATATATCGACCCTTGTATATATATGTTAGGCCGTGATGTTTAAAGTAATTATACAA
CTATGCGTGTTAGTAAAAATGTACAGGTAGACTAGAGAGTTTGCTTGCCGTCGTTTTCACTTTTCGGTTT
TAGAGAGAAAGCCAACCTTAAAATGGGGAGTTTTTCGGAAATGACTGTTTTCTCCTTCCTTTTGTGTTTT
TCCCCTGTCTTGTCATTTTCTAGTTTTTTCACTCTTCGTGCACATATGGTGGATGGATCCTTCTCCATGC
CTACGGAAAGCGCAATGCAGTGACTTGTGGTCTTTTCTTTCTTTCAAATTATAGGCTTTCAAATAAAATA
AATGTTGTATATCACGTATCATCAAATTCATTAGAACTCGATCGACCATCAGTTTTTTTAACTTTATAAC
GATGTTGACGTGACGAAACGCATGCTGCTGTGCGAGTGAGAGAGTGTTAAGCGATGTGAACAACAGAACA
AACAGTTTGCGACAATAATTAACAACACCAATTTTTTCATCCAACTTAGTAGTAGTGCTGCTTTTTCTCC
CTTTTCACATAAAGCGGAAAAAATATATTGGGATTATCTCTTGGTGGTGATGTATAGATCGCACACTAAC
ATGTAAGTTAGTGGGAGTTCAGGCTTGAAGATCTAGTTCTTTAGCGAGTCTTCGTTGGTCCGGCGGCTTA
TTATCAACGTACGTGTACATGATGAGCTCTAGCTATAGTAGGGTCCAACTTGTCGCCAAGACTGATTAAT
TCGTCATATACTAGTTAATTACTCTAAACGTATAGCTAAAGAAGAACATTATATATAGAATATTTTGTTA
ACTATGATTTGTTTATGGTGTTAGACATATAAGTTTGTTTAATGTAACTTCAAATTATGTTGATGGATAG
AGATGGATTTAATGAGGAGGGTTAGGTTATATACAATTTGGTACCCATTTATTGTTTGCTTTCCCAATAT
TTATTGCGGTTTGCATGTTTTATAAAAACTGGTTAATATATTTTTCGGGAGATTAAATATAAGGAAACTT
TGATGCGACTCGACGACTTTGAGTGTAAAATTGATTAAACGCACCAGTCACATGATATGGAGGCAATCGG
AGGGGAAACAAAACCGACGGCGATGTGAAGTTCCCGGTGGTTTCGCTAACTTGGAACCTAAACGGTCGGA
GAGGGATCCACGTGGCAGAATTCAGGAGATATTTTTGGAGTTTGGTTGGCCATGTTAAGCACATGCCCTG
TCTTCTTCTCCCTATCTCTCATCCTTTGCGTTGCTTCCTCTTTTCACTGATACTATATTTTTTATTTCCA
CCTATCAGTCATTTACCATGTACATTAGTACGCAACGCACAATTCGGTGCCAAATTAGAGTTTCAGGGTC
TCACCTCTCTCTAATCTGTTTGTATAAACTTTGAATGGAGGGAGACTTAGACCATGTACATGGGTGATAT
TTTTAGAGTATCATCAGTTTAAAAATTATTTTTATATTAACCAAACAATTAGAATGAGCTTGATTAGTAT
CATTCCAATGATTTTTTTGATATTACTATCATTTACGTGGCATCTCCTGATTGGTCGCATTTGTCAAAAA
TAAGAAAAAAATATTTATCTATTAAACAAATATTATAAATAATACTAAAATTTTTTAATGATAGTTTGTT
AGTATCACCTATAACCATGCTCTTAATAATTAGGATATAAAACATGTGAATGAGAGAAGTGGACCCTAGT
GATCTTTGTTTGTAGTGGCCTCAAGATTTTACTTTAGTCCCAAATTCGGAGGAAATTATTTTTGTTAATT
AATCATTTATTCTTTCTTTTGTTCTACCTCATTCCAACTTACAAATTCAGTATCCAATTCATAAGTTGAA
CCAAAAGGAAAGACATCATTCAACCCAAGATTAGACCAACTGTCTTTCGTGACACACTTGCAATTAATAT
GATTCTTAAAAAATGTTAATGATTTTGTTTGGAACCAAAAGACAATAAGTTAGCAGTCAAAAAAGCAGTA
AATGTAATTAGAAAGAAGAGACATGGTAATATAATAGATATTATGGATGGTGTGACGAATAATTGATCTA
ATAATCATTTCAGACAAGTGGACAACCCTACCTCCTGAGATGATCTTTTTAGCATTCTATGTATGTACTG
GTTAAAAAAAGGTTTCAGAATCAAAATGATGATGATCGTATATTTGAAAAGAAGCCAATGATCTCTACTT
TGAAAGAAGAGAAGATGAAAAGAAGCCAATTATGAAGATGAAGAAAGGGCATAACAGAAGATTGAGTGTT
ATCCTTTGTTGAGGAGTGCCCAACACAAATTAAAGAATGCTTCTTTTCCTTTGTTGGATATAATGTATTC
AAAGACAATTGAAAATCCAGACGAGACGAGTCCACGAATAATGTGGGCCTTAAAAAGAGTCAGGTAAGGG
AAGGCCCAATAACGAAAATAATGGGCTTATTATTAGCAGCGGCGGTGAGTTATTATATGTGTGGAAAGAA
GGGCCAAAATCACAACTCACAACCCCCAAAACGCAAAAAACGCAAAATCGCAGAAAGAAACTTTGCAATC
AAATCTCTCTCTCGGATCTCTGAGAGAGCGTTCTCGTAAATCCCTAACTATAGCTACTCTCGTGGATCCA
CCGAAAACCCTAGAAGGAAGAGCCCCTCTCCCGTCGTCCCTGGCATTTCGGATCTCGGATTTCCTTACCT
CATGACTCCCTCCAAGGTCGCCGGTCATACCCGGTTCTTGCTCCACAGCTTTCATGATTCCGATGTCGAC
TCCATCGCCCTCCAGCTTTCTCAGGTACTTCGTTTTCTGTCTCTCACTTGCCGTCTAGTTCGGAGATCAG
CATACGAAGAAATTTGGTTGGGTTTCTGATTTTTTTTAAAAAAAAATCAATTTGGGCAGTTTGTTGATTT
TGGAGTCGAGACTAGTATTCCAGTTCTCAAGACCTGCCTGGATTGCTTCACCGCCCGGAGAAGCCATCCT
AATTCGTTGCAGCTTGAGAAAGTTGTATCCTTGCTCTTTAAACATGTGCTCAAGTTGTCAAACCTTGCCA
CCCTGCTTCCTCACGCCCTCAATGATTTTGAGCTCACTCAAGAATCCGTGGATGATTTGACTACTACTTT
GAATTTTTCAATCTCTGAGAATATTGGCTTTGCTCTCGCCCTGACCGATTTTGAAAGATTAGATGCAAAG
ACCACTGGTAAGACTGTCTCTTACTAGTTCTCTCATCTCTCTTTCGCTTTATCTACCATTTGATGACATT
TTGCTCTTTCCTTTTCTAGGACGGAACTTACTGTTGGCTCAGATTGAGCAACTCTGTGCCAATACTGGCC
AGATTCTTTCATCTGAGCTAATCCATTCTGTTCTTTCGTTTCTCCGCAAATCTGAGGATCTTTCCATGCA
TTTGGATTCCTTCTTACAGTTTTTGTCTTCTGCTCAACCTAGAGATGACTTCTCTTTTGCTCTAACACCT
ATGCTTGCTCAACAAGTTCATGAAGCTCCTGTTTTCAGGTGCTGCTTATGAGTTGCTTTCTTCTCTTATC
CCTTATGTTCCGAATGCGTTTCTCAACAAAATTTTCCTCTTCTCCTGCAGGAGCATGGATTTTCACACTG
ATTCTGCTGATAACGACCTTGATGCTATCTTAGCTGAAATCGATAAGGAAGTCAGCGTTGGAGATCTCAT
GGGAGAATTAGGTTGTGGATTCACTGCTGATGCCCAACAATGCAAAGAAATCTTGTCTAGTTTTGCTCCA
CTAGGAGAGGCTACTATCTCAAGAATTGTTGGCAATGTTTCTCGGACCTGTGCTGATCTTGAAGATAATC
AAACCACCTTTTCAACGTTTACTGTAGCCCTTGGTTCCTGCATTCCAACTGAACTTCCCACGCCAAGGTC
GTGGAATGTTGATATTCTAGTTGACACAATCAAGCAGCTTGTAAGTCATCTGAAACTCTTATTACTTTGT
CTAATCAATATCGTTGATAGTTTCAAAACTTCAGTTAGCCTTTTTTTGTGTGTATGTGTGTCTCACTAGC
ATGCATGATTATGTTTCTTTTACCAATGGAGCTGTGAAGACGCATCTAGCTTATTGTTAAGTGTTATGTG
GTTCATGCTCTTAAGATTTTATGCTAAAGCAGGCTCCTGGCATAAGCTGGAGGAAAGTAATTGAGAATCT
CGATCATGACGGATTTGACATCCCTAATATGGAGTCTTTCTCATTTTTTATGCGGATCTATAAAGCTGCT
TGCAAGGTGTGTTCTCATACTCTCTAATTTGACTGTTTAAAAATATGTTTACTTCATTTTGTTGTTTGAG
GGTGTTAATCTGATTCTTGCAGGAGCCATTTCCTCTTGATGCTGTATGTGGTTCTGTCTGGAAAAATATG
GATGGTCAATTATCCTTTCTTAAGCACGCAATATCTGCTCCACCAGAAGTATTCACCTTTATGCATTCTC
CAAGGAAGCTGGTGAGATACCACACATCTGTGCTTAGAGCTGTTCTTCCTTGTCCCAGTCACTATTCTGA
CCAGTTGTATTTCAGGTATATATTGATAACATGCACAGCCAAGAGCAACAGTTAGGACTATCCAATCATG
CATGGCTGTCGCTCGATCTCTTGGATGTACTGTGCCAATTGGCCGAGAGAGGTCATGCTGTTTTAGTTAG
TTCGTTACTCCAGTATCCACTCACACAGTGTCCTAGAACCTTGCTTCTTGGAATGACACACATCAAAGTA
TTTCTCCTCGACTGGTCTTTGGTGATATATGCTTGTAATCTTGCTTCTTTTTGTTTGGCTAAGTATGTCA
ATCCTCTTATTGCAGACTGCCTATAACCTCATACAGCGTGAAGTGGTTTCTGCTATTCTGCCAGTGATAA
TAACGAGTCCCCAGGATAGTGGTTTTATCCATAATCTCTGGCATCAAAATGCAGAACTCGTTCTGTGGGG
GATTATAGATGCCCAACATCTCAAAGCAGACAGCATGCTCCGAATAATTGAAATCTGCCATGAGCTAAAG
GTGAATAGAAAAATGCGTGGCAGTGGCTCAAATTATCTCATTATACTGTTTTTCTCTTTCTTACAGCAGC
CTCTCTGTGTCTATGTACTAATCATGGCTTATTTATTTCAGATTCTCTCTGTTGTCTTAGAATCAGTTCC
AGTCTCATCCAGTATCAGATTGGCAGTCCTTGCCTCATTGAGAGGTCTTTTGGACATTGAGAACTGGTTG
CCTAACTGCTTGTATATGTATAAGGATCTCTTTGCTGAGGTAACATATCGTTTCACAATCATAGTTCTAT
TTCTAATTTTCTAGAGTTGAGAAGATGCTAATCTAACATTTTTTTTTCTTTTTCTTTTTCATATTTCAGG
AGTGCCTCAAATTTGTCAAAAATGTGCATTTTAGCGAATCAGACGATTTCAGGGCCAAAATTTTTCATCC
TTCTGATCCATTATCAGATCTTCATTTGGAAGCAACAACTTCCCTTTTAAAAGTTAGTTAGTTTCCCTTT
TTGGTTTGGTTTTCGGCTCGTCCTTAACTTCATATCTACTGAATTATTTTGTTTGATAATGTATTAAAGG
TTTTGAAAGCTCATGATAATGCGATTACTTCATCTCAACTGGTCGAGGAGATTGAAAAAGTCAATGCAGC
TATTTTGGATTGTAATCCTAAGCTGCAGAATGGTGAGGCTAAAGATTCATCAGCTCCCAATGCATATGGA
GATGATGTTGAGGCAGAGGCAAACGCATATTTTCATCAAATGTTTTCTAGTCATTTGAGTGTTGACGCAA
TGGTTCAAATGCTTTCCCGATACAAGGAATCTTTGGTTCCAAGGTTTGATATTGACAAACTATACATATT
TGAGAATTTTAATTTTTCTCGTCATGTTTGTCATGCTCCTCATGCATAATGAAAATAACGAGATTGTTTT
TTTTTTGGGCAGGGAAAAATTAATTTTTGAATGCATGATTGCTAATCTGTTTGAAGAATATCGGTTTTTC
CCCAAGTATCCTGAGAGACAGCTGAAAATAGCCTCCATACTCTTTGGTGAGTAGGATATTTTACTTTGAT
ATAGCGGGTGGTTTTTGTTGGGGAGGGGGAGACCATCATATCTTCTATGCTATTGTGTAGCCCCCAACAT
TTCTTACTGTACTATTTGAGCGTCTCTTCAGATTTGTATTGTTGTCGTGACATTCTCTTGAATCTACTGC
GACTTATACAAATTTCAGGTTCTGTTATAAAACACCAGCTTATAAGTTCGCTCACTCTGGGGATGGCCCT
GCGTCTAGTGTTGGATTCTTTGCGTAAACCTGCAGATTCAAAAGTATGGATTCTTTTGTAATTTATTTCT
GTCTCCCGGCTTTTCCTGTGAGAGATCTGTCATCTTCTTTCTTTCCTGATTCGTGCAGATGTTTCTGTTT
GGAAGCAAAGCTCTGGAACAGTTTGTGAATCGTCTGGTTGAATTGCCTCAATACTGTAACCATATTTTGC
AAATATCTCATCTGCGTAGTACTCACCCGGAGTTAGTCACTGTTATTGAACAAGCACTTTCAAGGATATC
ATCTGGTAATTTAGAATCAGATGCCTCTGTTTCACACCCTGGTCCCTCACAATCTTTCCCTGGAAATGGC
GAGGTAGGATTTGGTTTATTAGTTTTCTTTTGATTGAATGTTCTAATTGTCTCAATTTTGATCAACAATC
TGTTTCAAACATGAGATCATATAGCTAGAGTTATCTATTGAAAAGGGAAAGAAAATTGATTGATCATTTC
TGTTTCTAGTGTCATGCCTTTCATTTTTAGCCCTTTAGCCATAATGGGGAATTACTGTAAGCTGTAAATC
GGTTTTTTGGATTTTTATGGTGAGATGAAATTAAAACTCTTTTTGTTTCCGTTGACAGTTGAGTGGTTCT
GGAATTGGCCAACCTGCATTACAGCTTTCTTCTCCCCTACAGCTTCAACAGAAAAATGAAGTGCCAAGTG
TGCCATCTAACGAGGCAAAGCCACTTCTGCCATCGTTATCAACTACTTCCGTTGATGTTTCTGTCAATCC
TAAGGTGATGAATTTCTCTTGTTTTTCTTTTATAGACGTGTGTGGATGGAAGGGTTTTCATTTCATCTTG
CTAGTTATTCCTGCAGAATCCTGGCATTCCAACTTCTTCATCAACCTCAACTGGTTTTGTTCGTCCAGCT
CGTGCAACCACTTCAACAAGTAATCTCCAGTCAACTTAGTTTTATAACTGTTTTTTGAAATATAATAGGG
ACTATAGTTCTTTCCTATCAAGAGAAGAAATGTTATTAAAATTCGATTTTCACAGGGTTTGGCTCGGCTT
TGAACATAGAAACCTTGGTTGCAGCAGCAGAAAGAAGGGAAAACGCAATCGAGGTACTTTACTATTTTAC
TACTGTCTATGCACATTCAGAATTATTTGCTTTTGGTTTTACATTGCATAAGGAATTGTCAGTATGCCAA
ATGTCTACTTTTTAGTATAAGTGACAATAATAATGTATTTTTTTTTTCCAGGCTCCACCTTCAGATGTTC
AGGACAAAGTTTCGTTCATAATCAATAATATCTCTACAACAAACATTGAATCTAAAGGGAAAGAGTTTGC
TGAAATTTTGCCCCAACAGTATTATCCTTGGTTTGCACAGTACATGGTTATGAAAAGGTACTGATAGTTG
TATTCTTCATGCAAGGTTTCTTTCTTATTTTTTCCCTCCAAGTGTGTAATACCTGATAGAGCGATGTGTT
TAATACCTGATAGAGCGAGCATCGAGCCGAATTTTCATGATCTGTACCTGAAGTTCTTGGACAAAGTTGA
TTCCAAGCTGCTGTTTAAGGAGATACTTCAAAATACTTACGAAAATTGCAAGGTTATTTTTCTTCACACA
AGTGATTTGCGGTGATAAGTGTACTTTTTTTCAGCAAATTTTTCTCTTCTTAATTTCTTTTGTTTTGCAG
GTTCTTTTGGGCTCAGAGCTCATAAAGTCGAGTTCTGAAGAGCGTTCTCTTCTTAAAAATTTAGGCAGTT
GGCTTGGAAGGTTGACCATTGGAAGGAATTATGTTTTAAGGGCGCGAGAAATAGATCCAAAATCCTTGAT
TGTGGAGGTAATTGCTGCTATTTCCTTTAAATTGATCTCGTTCATTTGTAATACACAGTCAAATTGTAGA
TATGAACTTTGTTTTCGCATCCTTTGACAGGCCTATGAAAAAGGGTTGATGATAGCAGTCATTCCGTTCA
CTTCAAAGGTTGGTGATGGTTGATTGGCGTTCATAGCTGTTCTAGGGTTGATTTCCTGAGTTCTAATTTA
CTGTTTATTCAGGTTCTGGAGCCATGCCAAAACAGTATTGCTTATCAACCTCCCAATCCTTGGACGATGG
CTATACTAGGGTTGCTTGCTGAGATCTATTCAATGCCAAACCTAAAAATGAATCTGAAGTTTGACATAGA
GGTATCTGATAGTTCCTATTGAGCATCACGAGTTATTTTACATCACTTTTATTTGTGTATTTTATGTGTT
GTTCTCATTTCGTCTTTCTCTTCAGGTTTTATTCAAGAACCTTGGTGTTGAAATGAAGGAAGTAGTGCCA
ACTTCCCTTCTAAAGGATCGGAAGAGAGAAATAGATGGCAATCCTGATTTTAGTAACAAAGATCCTGGAG
TAACACAGATATCTCAGCCACAGATGATTCCAGAGCCTAAAACAATTTCTCCTCTTAAACAAATTGACCT
ACCTCTTGATGTTGCAAATTCGCCTAATACAGATGTTCCCTCGAAGTTATTATCACAGGTTATTTTATGT
GTAGTCTTTTTTTTCTCTTTCTTTAAGCTATAATGTCTGTTTTACTTATCAATGATAATTATCCCCTTGG
TTTTCCTTTTCAGTATGTAGCCCCACAACGTGTTTATACTAATACTTTGATGGATGAGGAGAAAGTAGCA
ACTCTTGGCTTGCCAGAACAGCTCCCGTCACCTCAAGGACTGTTCCAGTCAACTCCATCGCCATTGTTTT
CTATTAGTCAGGTACGATTTTCATAGGAATGTAGATTAAAGTTATTATATAGATGATTGCTCAAATCCTT
TCTACTTTTAATGTGATGGCCAGCAGCTGTCAGCAGCACTTCCCAATATTGGAAATCATGTTGTTATCAA
TCAGAAATTAAGCGCATTTGGTATGCACTTTCCATTTCAAAGGTTTGTGACTAATGGTCTCCTACTGGTG
AAATCATTATGATTGTAGAGCATTGAAGCTATATTCTATTACACACTAAACTATTATCCATTGTCAGAGT
GGTACCACTTGCCATGGACAGAGCTATCAAGGAGATTGTGTCTGGTATTGTTCAGCGAAGTGTTTGTATT
GCATGCCAAACAACAAAGGAGCTTGTGCTAAAGGTTGGCCAATCTAAACCTTTCTGCTTTTTTTTTTTGT
TCTTTTCCTTTATTACTTTTACGTAACTTGTTTTTTAGTTTCGTGCCTCAAAATTTTCCTTAACCCCCAT
TCGATTTCCATTGCTTTTGACTCCACAACTAAATTTTTTTATTTCCATTTATCACAAACATCTTCAGGGT
TTTGATCTTATTTATTTATCGTTAATTGTTGTTTCTTTTTTGACTCCAGGATTACGCCCTGGAACCCGAT
GAGTCACGTATTTATAATGCAGCTCACTTGATGGTTGCGAGTTTAGCTGGGAGTTTGGCTCATGTGACTT
GCAAGGTTTTTCCTTCTTATAAGGCCTTGGATTCTGAAGATTCTTTAGCTTTTTGTTTACACATTTACAA
TAATGCTATTATATCTCGGCCCTGTTACCCTAAACCAACAAGATCTATTTTTTCTCTGGTTTTTAATGCT
CTTGTATTTTTAGGAACCCCTGCGCACTTCAATATCCGGTCATCTACGGAATTCGCTTCAGGGTCTGAAT
ATTTCAAATGATGCTCTTGAACAAATTGTGCAACTTGTCACCAATGACAACCTGGATTTGGGTTGTGCTG
CTATTGAACAGGCTGCTACAGAAAAGGTTTGTGTCAGATATTAGATCTCGGACTTTATTTCTGTTTCAGC
TGATTGAATCAAATAACCGAAGTAGGTTTCCCTGGAGTGTAGGCACTTCCGTTTACCAGAGGGTTAATTT
CTTCTAGTTACTAATTTTTATGTCCGTGTCACTACAGGCAATACAAACAATTGATGCGGACATTGCTCAA
CAATTGTTGTTACGGAGAAAGCATAGAGATGGTGCTGGATCCTCCTTTTTCGATCCAAACATTCTATCAC
AGAATTCCGTCAGTTTTATACCCGAATCCCTCCGTCCAAAACCTGGACACCTCTCCCTGTCTCAGCAGAG
AGTTTATGAGGTACTGTTTTTAACAGGTAGCCTCTGGTATGTTCTGTGTTTGTATGACTAAACAAGATGT
GTGCATTTTCAGGACTTTGTTCAACATCCTTGGCAAAAGCAGTCGACCCAAACTTCACACGGTTTATCTG
CTGCATCAAGCTCATCTGGTGATGTTGCGCTTGGTAGTGGTTATGGTCCAGTATCAGGAAAAGTTGCTTC
TGAATTTTTGTCTAATGCTGGAAACGCTCGGATGGACATGGTCTCCCGGCCATCAGATATTTCTGTGGAT
GGTTTTGAATCTTCTCCAGTCTCACTTTTGAGGTGCTTAGTTGTAAAGCAGATCGATAAAACTGCTCTCA
TTTCTATTCGTATATTTCACAGCTGAATGTTGACATATCATTTTACCTGTCTTAAAGCTCACAAGTCGAT
CCAGCTGGTGACTCATCCAGTCTTCAATTTACTAAGTCACTACCAACCTCTGAATTGAATCTGGCTGAAT
CCTCTGACGCTGCTACGAAAGTGAGATATACTGTGTTTTCAAATGATTACTCGCTTAGGTTTATAATGAA
TTACTAAGCTGTGCTTATTTATATACAAGGAAACTGGAACATCACTGCAGACATTGACTTCAGCTGCTAC
CATGGAACGACTTGGTGCTAGTAATATTACACAGCCTTCACTGTCCACGAGAGATGCACTGGATAAATGT
CAAATTGTTACTCAGAAGGTTACTAAAGTGGTTATCCTGTGTTTTCCTTGCTGCATTTTTTTTTTGCTGC
TTTATATGTGAGAAACTTCTTGAAACTGTTTCAGATGGAGGAATTAGTGGCTAATAATGCAGGAGATGAT
GAAATCCAGGTATTTGATTTCCTAGTGCCTAGGTGGTTATAGTGCAGAATTGTTATCCATTTACGTGCAC
CTAGAATAAATGAAATTAGAAGTTAATTTTGAAAACCTTCTCTAACTTTTGGAAATGGTTTCTGTGTTTT
CCAATTGATGCCTATTTTCTTCTATCCAGTATGAATTCAATAACTAATGCAGATCTCATTGATTTTTCAG
GCCGTAATTTCTGAAGTTCCTGAAATCATCCTCAGATGTATAAGCAGAGATGAAGCCGCTTTTGCTGTCG
CTCAAAAAGCTTTCAAGGCTCTTTACGAGAATGCATCAAGTAACCTTCACGTCAGTGCTAACCTAGCAAT
ACTTGTTGCTATCCGTGATGTTTGCAAGCGTGTTGTTAAAGAGCTCACTAGTTGGGTATGTTTACAACCT
TTTCAAGATTTCACTTCGCTGATGTGCTTTGTTCAGTTACTTCTCCATTAATTTGTCACTATTTCTGTCA
GAACACATAGGATAACACATATCATATAAGTGCTAGGTCGAGTCTGTTTCCTGTAGTTGGAGCCTATCCT
CAACTGGTTATAGATACTAGATTTGTTTCTTTGGTATTTTTAGTTATAATTAATTATCTTTCTTCAAACT
TTTGACACAGGTGATTTATTCAGAGGAGGATCGGAAGCTCAACAAAGATATTACTATTGGTCTTATCCAG
CGTGAGTTGCTTAGCCTAGCGGAGTACAATGTCCACATGGCGAAGCATCTTGATGGAGGGAGAAACAGTA
TGCTGAATTGCTTAACCTTTGTTGATGTCCTTGTGTGGTAACATTCTTTTTTTGTTTTGGCTAGTGAACT
TGTTTTAACAAGTTGTTTGTTACGCAGAGACCGCAACTGACTTTGCTATTTCTCTACTCCAATCCTTGGT
CACTGAGGAGTCGAGTGTCATTTCAGAGCTCCACAGTCTTGTTGATGCGCTGGCAAAGGTTGCAATTTTA
ACATTCTTCTGCGTTTGTTGTTGCAGTCGCATATTCTTGTTCTATTATATAAAAAAACAGTTAATAGGTG
TGAAAACATACAACTAGGGAAGGGATAGGTTCAATTTTTTTTTTTTGTGGTTAAATCTACTGCATAACAC
TGTTTATCATATAATGCCAACTGACAAGTATTGTGGTTAGGTTCAAATATTATGAAATTTGGCATTGTTA
TATTTGGTGACGCTGCAATTTGTATTCTTGTTTTGGTTGTAGCTTGCCTCAAAATCCGGATCTTCTGAGT
CATTGCAACAGCTAATTGACATCATACGAAATCCAGTTACTAACACAGCTGGCCTCTCTGATAGTTCAAC
CGGAAATGATAACAACGATAGGCAAAAGGATGAGAAGGTGTCAGATGTCTTCATTACCGAATGTTGCCTG
TAATCAGACTGTAAATGTATATTTGACATGTTAGCTTTTTCTTAGGTTGCGTGCAACACCACTAACACAG
AAGAGAGTACCAGCTTGGATTATGTGGAATCAGATCCTGCGGGTTTCCAGAATCGGGTAATTGTCTGCAT
GTTATTAGCGTTTATGAACTTCTATATTGATTTAGAGCTCTACCTTTTCTTTTTTAAAAGTTGATTGGGA
ATTGCATATATCTAAATTTTTCACTTGCAAAAGAGTAAATCAAAAGCTAAAATGTTTGTATCAGCACAAT
GAATTTGCAAGCTACAAAAAGGATTTCAAAACAAACGTTTCTATGAAGCTATTTTCGTTCAGTATGCATG
TTTTTTTCCTTATTTTTGTCTTGTAGATGGATTTTAAATTTTCACTTTAATTCGATGTATTTAGATACAT
GTGTTTGTAGTTTGTTATCTCTTCAGTTTTATGTTTGAACATACATCTCTCGTACTTCTTGTTTATATCT
TGTTTTTGTCTTCCTCTGTATGGTTTGGCAGGTGTCCACGCTATTTAAAAACTGGTATCAAATCTGCGAA
CTTCCTGGTGCAAATGAAACCGCATGTTCACAATATGTCCTGCATTTGCACCAGACTGGATTACTTAAGG
GAGATGATACAACAGAGAGTTTTTTCCGAATTCTTCTGGTGATTTTACCTTTTAAGAATGTTTTAGCATC
AGCACTTTCAAATCTTGAGAGGCATCATTATTGATTTTGGCTTTCCTTTCTGTAGGAACTTTCTGTTGCT
CATTGTATATCTTCTGAAGATATTAATTCCGGTGCTGTGCAATCTCCTCAGCAACCTCAGAGTCCATCAT
TCCTTATCATTGATATGTATGCAAAGCTTGTTTTTTCAATATTGAAGGTAGAGTGCTCATTTTTTTTTTT
GCATTCTTCGTGGATAATTATACCCAAAATACATTGCCGGCTAAGCTTTTTTTGTTTTGTTTGTTTCTTA
TGACAATCTGTTCAGTATTTCCCTGAGCAGGAGTCTAGCAGTAGGTTATTTCTTCTTTCAGAGGTAAGGG
GACACATACTCTTATTGGAAATAAATCTAACTTCTACTATAATGGATGGAAAAGGTGAGTGGTATTGATT
ACCTGTTTCAGATCATGGCTGACACAGTGAGATTTATTCAAAAGGACGCAGAAGATAAAAAGACATCACT
CAATTCTAAACCATATTTCCGATTGTTCATCAACTGGCTACTGGACTTGTGTTCCCTGGATCCTGGGACG
GATGGTGCAAACTTTCAGGTGCATTTTGTTGTCCTTGAAGTAGCTGCTATTAATTGTTATCACTTTAATT
AATCTTTTGTTGCAGGTTCTCACAGCTTTTGCCAACGCCTTCCACGCATTGCAGCCTCTTAAGATTCCTG
CTTTCAGGTTAGGACACAAACCTATTTCTCACCGTGCTTCTATTAAAACTTAAAAATTTGAATCTCTCAG
GAAATTTGAGGGCAGTCAAATACCTATGTTGTCAAACATTTCATGTTGTTGACATATGTATCTTCTTTTC
TTTGATCTGTGATCCGTGTTTTATACATTTTTTTTCTTCTCCACTGAGGTTTTTATAAATTTTTCCAGTT
TTGCATGGCTAGAACTTGTCAGCCACAGAAGCTTCATGCCCAAACTACTTACAGTAAATGGCCAGAAGGG
TTGGCCATATGTTCAGCGCCTGCTGGTGGACTTGCTTCAGTTTCTTGAGCCATTTTTAAGAAATGCTGAA
CTCGGAGGACCGGTTTGTGCCTTTTTCTCTTCTGTAATTGTTTTGCATTGGACACTAAAGGATATAGTCG
ATGGTAACTTAAAGTGGTCTCTTTTTTGGTGTGTTTATTAATTGCGTAGGTTCATTTCCTATACAAAGGG
ACATTGAGAGTATTACTGGTTCTGCTTCATGATTTCCCAGAGTTCCTATGTGATTATCATTTTACTTTCT
GTGATGTGATTCCTTCAAGTTGCATACAAATGCGGAATATTATCCTCAGTTCTTTTCCACGGAACATGAG
GCTTCCTGATCCTTCTACCCCAAATTTAAAGGTACGAGATGATAGTGGAGATTCCAGCATGTTCAACATA
TTTTAAAGAAAATATATTCCTTGTAGGCTGAATTATCGTGTTCATTGCAGATTGATTTGTTACCTGAGAT
AGTAGAAGCTCCCTGTATCCTTTCTGAGGTTGATGCTGCGCTAAAGGCAAAGCAAATGAAGAATGACGTG
GATGAGTATCTTACGGTAATGGGAACACCTGATTCTTCAATTTACTTATATTCACTTTGGTATTCTTGAG
ATTATATCAAGAGATACTCATATAATTTTTCTGCAGTCGAGGCAGCAAAATTCAACTTTCCTAAGTGAGT
TGAAGACAAAGTTACTTCTATCGTCCAGCGAGGCTAGTTCAGCTGGAACCCGTTACAGTGTACCATTGAT
CAACTCGCTTGTGCTATATACTGGAATGCAGGTATGGGTCTAATTTCTATACAGCCTTTTCTTTTGATTT
CTAGTTTATTATATATATATATATGCAAATAACCGACATTGCGATAACAGGCTATTCAGCAGCTTCAGGC
CGGTGAGACACAGGCTCAAAATGTTGTGGCCTTGCAGATGTTCAAGTATTTAAGTATGGAACTTGATACG
GAAGGGCGGTATCTGTTCCTTAATGCAATCGCCAATCAGCTTCGATACCCCAACAACCACACTCATTACT
TTTCTTTCATCATGCTCTATCTATTCTTCGAATCTGATCAGGTGAGTTTGCTTTGCTTGTCAAGAGTTGT
GTGGAAAAATTAGTGAGCATGGAAATCTGATTTTTTTTTTCTTTTTCTTGGGATGAATGAAACAGGAGAT
CATACAGGAGCAAATAACTAGAGTGCTGTTGGAACGGCTAATTGTGAACAGGCCACATCCATGGGGACTT
CTAATCACATTCATTGAGCTAATAAAGAACCCAAGATATAGCTTCTGGAAACAAGCCTTCATCAGATGTG
CGCCTGAGATTGAGAAGCTGTTTGAATCGGTAGCCAGATCCTGTGGTGGCCTGAAGCCTGTCGACGAGGG
AATGGTTTCGGGAGGTTGGGTCTCAGACAATTCTCACTAGCTCTTTAGCTTTCAACTTGTATATATGTAT
GCGTATTTTGATATTATGTTGTAACAATTATACATACAGTAGGAGAGATTTTAGGAGTCTTAGTTTATTT
ATTTAACTTCAAGATTCACAAACATGTTTTCTAATTACAAAAAAAAAAAACACTATTATTCCTTTATCCT
TGCTCTTAAGGGTCTGTTTGAGAATTAGTTAGGTGAAAACATGTTTGAGAAATCGGCGGGGATTGTGTTT
TCATGGTCATAAAACATGACCATAAACACTGAAAGAGATTATGATTATGCTGAGGGAGTGTGAGAAATCG
GCAGGGATTGTCATCATATAGTACTAGACTACTAGTACTTTGTATAACGTTCTCAGGAACATGTTTCGGT
CAGAATTCCGATGGTGGGATCTAGTCGATGACGTAATAAACAACACTTTCATGCCCGCCTAAGAGGCAGC
TGTCGCAGACTAAGCAGGTTTCAACATGTGAGGGGCCAAGGCGCTGGCTAGTGGTCAAAAGACGGAACAC
TGAGAATATCTGTATCATTCCATATGATCCAAGCGCCTAGCTTTGCTCAAGTGTCAAGACTATTGATTAC
TGAATACTAAATTCAAAGCCATTTTTCTTTTAATGGGCAGAGAGACACCAAATTTGCTAATGAGGGAAAT
CAAACATAACAAGGGGTTATTGTGAGAGAGAACAGAGGATCTTATACAAGTTGAAAATCCGCAACCAAAT
AATCATAATCTACTCTCGGTAAATGGAATGTCAATCCGCACTGACCATTTGCTCTCTCTTGCTCCTCTAC
CTTGTTACAGGATGCCTCCTCCTGCGTTCCAAAGTTGAATGTGTGTATGTTATATCATCTCCTTTGTACT
TATCATCTCACTCATATCTAATATTCGTTACCTCTTTGGTCGGATCCCATCTTCTTCGTAGTCCATCACT
CCACTTGGTTCCCCAAACATCTCCTTATTCCCTCTGATGTCAACATCCCCCTGCCCACAACGTAAGTAAG
ACTATATCGACCACCACCCTTCCCAATCATATTTCAGACACAAAAAACCAAACGAACCTTGTTTCATTTC
ATTTAACAATCAGACAATAACCAAGTACTACCATTCCAAACAATTCATGTCCTCTAATGACTTTAACACT
TCACTAACAGCCGTTGTGATTGCGTTCCTTGTTTGTTTTTAATTAAAGAAAACTTCATAATATATGTTTA
CATCCAACATGTAAGATTTCTTGTTCCACGAAAGAACGGTTAAAAAAGCCCGCCACAGTTGGCTGATCGA
TTCGTTTGTTATTAAGAAACATAACTTTTTAATCTATGATAGGACTGGACTTGGAAAGCTCAAAGACCTA
GAAAGATTTTTTTATCAAGTCTCTCCCATCCCCGCTTACATAGACCTAAGCTATTAATAAGAAGAAACCC
ACTACAATTCTCTGAAGAAATATAAGACAGAATAGCTGACTGGACTCTAACTCATGGTCACAAGACAGTA
ACCAAGAAAGAATGTAACCAATATTAGTTACATAATATACTTAGTAGGGAAAAGTGAAGCCAATAGGACT
CCAAGCGCGACTGACCTTCATGGACAGAGACTTCTTCACTTCTTCCACCCCTTCTTCTGCTTCCTTACGA
TGTTTTTTGTCCATCTCACTCATATTGTCCGCCCATTTGATCTTGTCTTGAATTGAAATGAGCAGATTCT
CTGACGTGTTCAACCTAGACATCAATTTGGGCCAACACATAAAAGAGTAGGACGTCATTAGCCATGTATT
CTAACATCACGTACAAGTTCTTATAATTAGATATAGAAGGCAAAAAATCCTGGATCTAAGGGAAGAAGAA
AACTACCAGTTGGACAATGTGTGTAACATATTCCCTAGTTGACCTGGCCTTAGATCCCTACCAGCTGCAA
ACGGAACCTGCATGGTTGCAAGAGATATATGATGTTTAGAAGGGGGGGCTCGTACGTTTAGAAACAAAGC
ACAATGGTTAAAATAGGAAAAGGAGGCCCAAACCAAAACACACCTCAAAACATCTTTTTAACTGATCCAG
TTTTCCCCTAACTATACCCTGCAAAGTGTAAAAGAAAAAAAATGAGCACCATGCGTTGTCACAGTTAGTT
GTCAAATAGAGATTAGAAGACTGCTAAAGAGTACTCACCGCATACATGCATTCATTGATAAGAAAGTCCT
CGAGTTCGCGAACATTGGAAACATCTAACTCGACCATTAGTGTATCATAGGGCAATACCTATAACAAGCA
GAGTGAGAGAGACATTCAGTTAGGCAAACAGCAGGGGAAAAAGATAATGGAACAGAGTAGATAGCAGGAG
CAAATCATGAACCTAAGACAAATATACCTTGTTAGACTCAGCAAGGGTGAGGACAGTGAGCTGCTTAAGC
TTAAGAATTTGGTCAGGGGACAAGTGCGGAAGACGGGTGGCATTGCCTAGTGTTTCGATGAAAGCAAGTC
AAGAGGAGAGAATATGACAAAAGGGAAAACGAATTGAAATAGCATATGACAAAGGGGTCATACATTTGTA
GTCTCCCCAGGTGCCATGGGCAAACAAGCGTAGTAGATCCAGGTACACAGAATCTGTGGTTCCTTCAAGC
TGCACAATTACGATTAATCAGCTACTAGTATCTATCAAGTTGTTATGATCAGCGAAGAACAAAAGCATGT
AAAACCCTAGATCGTGAAAAGCATAAAGTAGTAGTACCTGGGCAACATTGGGTAGAGCCAAAATCTCGGA
GAAGGCGAAGAGAGAAGGATGCGATGTGGCTTCGATGATGAGCGGGCCCAGAGCCTCGGATTTGCAAGTA
GAAGCTCGCTTCACGAGCTGATCAATGATCTCGGCTTGCTTCTGCTCGATATCCATCTTCCAAACAAATC
GATTTCCGGTGGTTTAGGGTTTTCTTTCTTACCACACTAATAACGAATAAAATCCCAAACTTCTTCTCTC
TGCTCCTTCCTTCTTCCGTTTTTATATTACTGTTTTTTTTATGTGACCGACCGAATTCTTCTAGAATCTT
GTTTAATAATTGGGCTCAAATTTCGTAGTTTCTGGGCCAAGGCCTACTAAGAGAAATATTAGAAACCGCG
TCTGGTGAGCCCAAACAATCCCGGGGAAGAGAGAGACTATTGAATATTCTTCTTCCTTCATTTTGGCTGA
GAGAGCGACGACGATGGCGGAATCTCGCAGCAACAGAGCGGCGGTTCAGGCTACTAACGACGATGCATCC
GCCAGTAAATTGTACGCCTACCTCTTTCTCTCTTCTTTAATTAGGGCTCTTCTTTTTTTTTTGTTGTTGT
TGTGGATCTTTGAGCCTAGATAATATTTTTAAAGGTCTTGTGTCAAAAAGGGATATATGAAAGACGACTA
TGTTCATCTCTTTGTGAAAAGACCTGTTCGAAGATCTCCCATCATTAATCGAGGTTACTTTTCCCGTTGG
GCTGCCTTCCGAAAGCTTATGTCTCAGTTTCTTCTAAGCGGGACAAGTTCTAAGAAACAGATACTGTCTC
TCGGAGCTGGCTTTGATACTACCTATTTTCAGTTGCTGGTGCGTCTTCTTTTTCTTCTCCTTTTTGTTAG
CTTTTACCAAATTCACCATTCTTCGGCTTATTCCAGGGATCTCTCGCTTCTTCTCTTCTCATTTTGTAGG
ATGAGGGGAATGGGCCCAATCTCTATGTGGAACTTGATTTTAAGGAGGTACTACTGGATGAGCGTGCTGA
CAAAAGTATCCATCATGTGTTTTGAGTCTAATGCCTAAATGGATTTGCTTCTTACGTTAGGTGACTAGCA
AGAAGGCTGCTGTTATACAAAACTCCAGCCAACTCAGGGACAAACTAGGAGCCAATGCATCTATTTCTAT
TGGTAAGAGCCTTTTTTCCCCCCATGTATTATTATGTAGAATGATCCTTTTCATTATGATGCATTTCAGC
TTGTGCACTCATATTTTTCTTCATTCCGCTTCTACTAGCTACTAACTCAACCACCCCCTTTTACTTTGTA
CCGTTAGCGTCTAGTTTCAGTTGCTTACTCTTAACTCGTTGGGCTGTTTATCTCTACAGACGAAGGACAA
GTTCTCAGTGATCATTACAAGTTACTTCCAGTTGACCTGCGCGATATACCAAAATTAAGAGATGTTATAT
CCTTTGCAGATATGGATCTAAGGTATCCATGAATAATTTTTATTTATTTTACACACTGTTATCTTGAACC
TTCAACCCTCTTCTTCTACCCGGGTTTAAGATATATGGTAACAGATACTTACTGGTGATAGACCTACTTG
ATCCCTAATATCATTATCAGTCTGCCGACGTTTATTATTGCAGAATGTGTTTTGATTTATCTGGACCCCG
ATTCAAGCCGTGCCATCGTCAATTGGTCGTCAAAAACGTTTTCAACTGCAGTATTTTTCTTATATGAGCA
GGTTAGCTCAACTGTGATTTTCCTTGTCTGCATAATATTGCAGATACGAATCTTATTGCTTATGTGTCTA
ACCCGTTGGGTTTCTGTTTGCAGATCCATCCAGATGATGCATTTGGGCATCAAATGATTAGAAATTTGGA
GGTAAGAACGTGTACTCTACTACTCTAGTTACAGCGACATCTTCATTAGTAAAGCTTTTTTGAGATTTTT
GTCAAAATATGGATACTAGTATGACACTAAAATATTCTAGTATTGCCACATGGGTTCATGTTGTACTGAT
CAATTACCTTCATTTAAACTTGTTCTGAAAGCTTAACGGTGTTTCTGTTCTTCAGAGTCGGGGATGTGCA
CTCTTAAGCATTGATGCATCACCAACTTTACTTGCAAAGGAGAGATTGTTTCTTGATAATGGATGGCAGG
TTCGTTTTGCAGTTAGAATATTATGATTAAAGCAGGGCTAACTTTCATGTATAATTTCTGATATAAGGAC
TCTCATTTCTTTACCCTCTTCTTTATTCTGGTGTTTCAGAGAGCTGTTGCCTGGGACATGCTAAAAGTGT
ATGGTAGTTTTGTTGATACTCAAGAAAAACGCAGGTCAGTACTGTACGTTTTGTTAAAACTGTGTAAGGG
CGTTATGTTATTCATACCTAGTATCTGGCTGAACTCTGTCAAGAAATATCTAAAAAATGCTGTTGCCCGT
GACTTTTGAGCTTTCCAATGTTTTTTAGATGAACCTCTTACAGTCTTACTATATATATCCTGTTTTTTGT
TTTTTCTTCTCTCTCACTCTCTCTCTCACTATCCTGTTTTGGCTCTCTTGTTTCTTCAATTCATGAGCTT
TCATTAGAAAGCCTACTTCTCTTGGAATATATCTTAAATGAGAATGTCGTGTTTCTAGGATCGAGCGATT
GGAGTTGTTTGACGAATTTGAAGAGTGGCACATGATGCAGGCAAGTCTGTCTATACCTCATTAACTAGAT
GTTGCACCTCTATGTATGTATGGGAAAGCATAAAAAGACCAAAAGATGATTGGTGTTGAATATCAACGGT
ATCCATTATATATTTTTGATGATGCATGCGTCAGATCTTGTTCTAGTGTGTAGGTAGTTGAGCATTATTT
AACCGTTTATATTCAACAGGAACATTACTGTGTCACATATGCTGTCAATGATGCAATGGTACGTACATGA
GTCTCTACAAGTCATTGTACTTTTTAGATTCTGGAATGTTTTTTTGATTAAAAAAATGCAGGGAATATTT
GGTGATTTCGGTTTCACAAGAGAAGGGGGCGGTGAAAGAATGAGCTCATCAGCGTCATCACCTTGAAAAG
GAGGAGGGTTTGTATTGCATTGAATCCCCGGAACTTGCAACTGGTACGTTAGTTAATACAGTTGGAGGAA
AACCCCTGGTGGTGGGTAGAATCTGATAGTGCTTGGTTTACCTAATTTGTAAGGAATGATGATTGATTGC
ACAAAGTTAGAAAGGCCTTTCTCTGGGTGCTGAGCAGAAAACGAAGGAAACACGAACTTGTCTGCGTTAT
CTGTGCTTTTGATTTAGTTTAGGCTCATGGTCGAGATATGTGGGCCGGGCCTCCCCTTGTTTTATTTTTG
GTTGTATTTTCTAATAATTGTGCAAAACAAAGAAACCTCACCTCGGTCAAGAAACGCTCTGAAATCTGAA
CTCTGAAGGTTGTTTTTCTTCTTCTTTCGGTGGTGAAAAAATTATCTTTATGAAAAGACAAAAAAGTTTT
TGAAAAAAGGAAATTTTTTTCAAAAAAACAGACTGAGAGAGAGAGAGAGAGAGTGTGTTGTTGGCCATGG
GATGCACGGCCTCCAAGCTCGACAGTGAGGATGCTGTCCGTCGCTGCAAGGAGCGGCGCCGTCTTATGAA
GGACGCCGTCTACGCTCGTCACCATCTCGCCGCCGCTCACTCTGACTACTGCCGCTCCCTTCGTCTCACT
GGCTCTGCCCTCTCCTCCTTCGCCGCCGGCGAGCCCCTCTCCGTCTCCGAGAATACTCCCGCTGTTTTTC
TCCGCCCTTCCTCCAGTCAGGACGCGCCACGTGTCCCTTCTTCCCATTCCCCAGAACCCCCTCCTCCGCC
CATCCGCAGCAAGCCTAAGCCTACTAGGCCTAGGAGGCTTCCACACATTCTCTCCGACTCCTCTCCTTCT
TCCTCTCCTGCCACCAGTTTCTATCCCACTGCTCACCAGAACTCTACTTACTCTCGCTCTCCATCTCAAG
CTTCCTCTGTCTGGAACTGGGAGAATTTCTACCCTCCCTCTCCCCCCGACTCCGAGTACTTCGAACGCAA
AGCTCGCCAGAACCACAAGCACCGTCCTCCTTCCGACTACGACGCCGAAACTGAAAGATCCGACCACGAT
TACTGCCACTCACGGAGAGATGCCGCCGAGGAAGTTCACTGCAGCGAGTGGGGCGACGACCACGACCGTT
TCACTGCCACCTCTTCGTCCGACGGAGATGGGGAGGTCGAAACTCACGTTTCCAGATCCGGTATTGAAGA
AGAGCCTGTGAAACAACCACATCAAGACCCAAATGGCAAAGAGCACTCTGACCATGTTACCACTTCTTCC
GACTGCTACAAGACCAAATTGGTGGTAAGGCACAAGAATTTGAAGGAGATCCTTGACGCCGTTCAAGACT
ACTTCGACAAGGCTGCCTCCGCTGGGGACCAGGTCTCCGCCATGCTTGAGATCGGCCGGGCTGAGCTCGA
CCGCAGCTTCAGCAAGCTGAGGAGTAAGTCTCACACTCTACTAACTAGATGTAGATGATGATGCATTGAA
ACCCATCTCATTCTCTTACTCTCTCTATATTTGTTGTCTGCAGAGACGGTGTATCATTCAAGCAGTGTGT
TCAGCAACTTGAGCGCAAGCTGGACCTCAAAACCCCCATTGGCAGTCAAATACAAGCTCGATGCATCTAC
CCTGAATGATGAACAAGGCGGCCTCAAGAGCCTCTGCTCCACTCTAGACCGACTCCTCGCTTGGGAAAAG
AAGCTTTATGAGGATGTCAAGGTACATTCCCTGTTTTTGTTTTCGGTTTTCGGCTTACCAACGGTTACGA
AATAAACTTGTGAATTCGAATTTAGGCAAGAGAAGGAGTTAAGATTGAGCACGAGAAGAAGCTGTCTGCG
CTGCAGAGTCAGGAGTATAAGGGAGGTGATGAATCCAAGCTAGACAAGACTAAAACTTCCATAACCAGAC
TGCAATCACTCATCATTGTTTCTTCAGAAGCTGTTTTAACCACGTCTAATGCCATTCTCCGCCTCCGGGA
CACTGACCTTGTCCCTCAGCTTGTTGAACTCTGCCACGGGTCAGTCTTTTTTTTGTAGTTGTGTTTGTGT
TTCATTGTTCCTTGAGGGCTGCTGGTTCGGTCTAGGCTTGTTTATATGCTTCTGCAAACTCATGTGAACC
CGAATTAGGCATATGTAATACCAAACCCATTGCTGTTCTGCCAGTGGGGGATTTTATAGGTAAGTTCGAA
ATAAAAGTAGGGAGGATTTGTATGTGTCTCTAACCACCTTGAAATGCAGATTAATGTACATGTGGAAGTC
AATGCACGAGTATCACGAAATCCAGAACAACATCGTGCAACAAGTCCGTGGCCTGATCAACCAAACAGAG
AGAGGTGAGTCAACATCAGAGGTACACCGGCAGGTGACGCGGGACCTAGAGTCAGCTGTGTCCTTGTGGC
ATTCGAGCTTCTGTCGCATCATTAAATTCCAGAGGGAGTTCATATGCTCTCTCCACGCATGGTTCAAGCT
GAGCCTGGTTCCCCTGAGCAACGGAGACCCAAAGAAACAGCGGCCAGACTCATTTGCCTTGTGCGAGGAG
TGGAAGCAGAGCCTGGAACGGGTGCCTGACACAGTGGCGTCAGAAGCCATAAAGAGCTTTGTAAACGTGG
TACATGTGATATCAATAAAGCAGGCGGAAGAGGTGAAGATGAAGAAACGCACGGAGAGTGCAGGAAAGGA
GCTGGAGAAGAAAGCATCCTCACTGAGGAGCATAGAGAGGAAGTACTACCAGGCATACTCGACGGTTGGG
ATAGGCCCTGGACCGGAGGTGTTGGACTCACGGGACCCGCTATCTGAGAAGAAATGTGAGCTGGCGGCAT
GTCAGAGGCAGGTGGAGGATGAGGTAATGAGGCACGTGAAGGCTGTGGAGGTGACACGAGCTATGACTCT
CAACAATCTACAAACCGGCCTGCCCAATGTATTCCAGGCCTTGACCAGCTTCTCATCTCTCTTCACTGAA
TCTCTCCAGACTGTCTGTTCTCGTTCCTACTCCATCAACTGATTATGTCCAAGTTTCTCATTTATTTTTA
AGCTCTCATTACGTTGGTATCATGTAAATTTGAGGATTGATTAAATTGAGTCTTGTGGTTTTGTGAGGAC
TCACAATCTTTCTCATTTAATACATGAGCAGACACGGCACCTAACTAATGGCCCAAAGGTGGCCCGCCAA
ATTGAATACAAGGGTAAGAAATGGGCCAAGAAAGTGAGAGCCCAAAAGAGGCCGATCGTTCGTTTTTGAC
TCAATGGCCGTTGACGTTGACATCGTACGCCGCACCCAACGACCGCCAAACAGCAAACAACAACACTTTC
CCCTTTCTCTCTCTAAACATGGCGATGCTTTCTACTGCTTCCGTTTCGGGGAGCGTCGACCTTCCTCGAG
GAACCATGAAGGTTGACTCGTCTGCGTCTCCGGAGGTCGTATCCGATCTCCCACCATCTTCCCCAAAGGG
CTCACCTGATCGCCATGACCCTTCCACTTCTTCTCCGAGCCCCAGTCGTGGTGGTGACAATCAGGTATCT
GATGAATTCTCTCTGCTTCGATCTATTCGTTTCCTTGGTTTATGACCTGGATTTCTTCTTACTTATTCTC
CTCTAGTCTGAAGTCATATCCAAGAGTGAAGAGTATCGGCAATTGTTTCGGCTTCCAGCTGACGAAGTAA
GTATTGCCTCTCTCGTCTTGAAATTCCATCAATGAGAGAAGTACTGACTCCACCATTGCTTCCGAATTGT
GTAGATCCTTGTTCAAGATTTTAACTGTGCTTGTCAGGAGAGTATTCTTATGCAGGTTAGGTACTTTTAT
CTTTCTCTCTTTGCGAATACTTACCTTATCTTTTAATCATCTTTACTTTTTGTTGCAGGGTCATATGTAC
CTCTTCATCCATTATATCTGCTTTTACTCCAACATCTTTGGTTATGAGACCAAGGTGCCGCCATTGTTGC
TCTCCTCCACTCACTTTTGTTTCTTCCCTTTTTCCTCTTCAATATTGATCGGAACTCTCTTTGCAGAAAA
TTATCCCATTTGCTGAAATATCTTGTGTTAAACGAGCCAAGACTGCTGGTATTTTTCCTAATGCCATTGA
GATTTTAGCTGGAGGGAAGAAGGTACCACTAGTTCCCTCTTTACTCGATATTGGTTGGTGCGTCTGTCCT
GATCTTTGAACCGCATTCTCTCCCAGTACTTTTTTGCATCGTTTCTTTCCCGCGATGAAGCTTTCAAGCT
TATCCATGATGGATGGTTGGAATATGGTAGTGCTGTCAAATCAGAAGGCGAGATTCTGGTGACCGAACCG
CAGGTGGGTGCAACACACACTCTTATTTTACTGCTTAATCCTTGTTTCCTTATCTGAGTCCAAAATCCAG
GTAAGCGATGGAGTTGTTAAAAGGGCACGCAGTTCCATGGATTTGGCCAATGAACTAGATATTCCAGTAA
GGTGCGTTTATCTCTTCCATATGGTGTTCCATCTTTCTGTTTCTTACTGCTTTATCGCTCACTATACTTC
CTTCTCAGGGATGAAACTCTTCATCTTTCCAGCAGTTCCAGTCTTCCTGTCATTAGTCAGAATGGCGTTC
CACCTTCATCCGTTCAGCGGCACGCTGAACCAGATGTAGATGTTGTGGCGGCCAATACTTTCAACTGGAA
GCCTGAAGATACAGATGCACCTAAATGTAGTTAAACTCCTTCCTCGCTTTTACCTTAGTTCTTTTTGGTT
GGTTTGGGTAGTGTGGTAGATTATCTTTTTCAAGTCAACTGTTTAAGGATGTGAATGCTAGTGTTTTCAG
TAAATTCAACGGGTTTTTTTTTTTTTGCTGGGGTCAGGTCAACCTGTTGGTAAAGAGTATTAAAAATGCA
GACGCTTGGGTTTCTCCTAACTCCTTTAAAGTTCCTTTAAAGTGGACAATCAGTTAACTTCTTACTGTTT
CTAGGTATATGTCATTATGTGTCTATCTTTTAGCTTGTTTTCTTTGCAATATAAATTGTTTGAAATTTAA
ATGGTCAATGGGAAACGGTCTCTTAATGGTTTTGCTAAATAAGGCCTATCAGGATGGGGTAGCTTAGCTT
TATGATCTTGTCTTTTGGTGCTACTTCACAAGTTGCACTAGTTCTCAGTTTGTCCCAACGAGCTTGCACT
CAGTATGGAGATCCTATATTACTGAACCGGTTATTTCGTTTTTGCATACATGATCTCTCATCTATTTCTT
TTGGTTATCGTGATCTCTTTTCTTGTTCTCATTTGTATTCACCACACAAATTTGTGTTCCTTGCACGCAG
TGTCATCTGACTTTACAAAGGTAGCAGAGGCAAAGTTTTCGGTAATGTCTCGTTCTTTGTCTTATCAGCT
AGAGGAAATTATGGAACCATTCTCATTCAAATTTATGAGAATATAAGCATTGACTGGATGCAGAAGTTTC
ATATACCTAAATAGACTTTAGTTTATATTTGCAGATTCCAGTAGAAGAGTTCTTTAGATTGTTTTTTTCA
GATGGTGCTGTCAGTTTTGTTGAATCTTTCCATAAAAATTGTGGAGACAAAGGTAAAGCTATAAGTGATG
GAATCATTTTGCTCCTGTGTTTAGCTGTTTTCTCTCTCTTTCTCGGTGTTCTTTTAACCAGAAGAGATAT
TTGTACTTGCAGAGTTTAGGTGTACCTCTTGGCAACCTCATGAAAAGCTTGGACACACCCGCAATGTCTC
ATTTCAACATCCGATAAAAATTTATTTTGGTAATATTTTTTCTTTCCTATAGATAAACAGTACTAGATTA
CGGTTTATATCAAATATATATTTTTTTGGTGTAATTATATAAAATAGATTACGGTTTATATCAAATATAT
GTATGCATGACTCTGGCTTTCGTTTAAAGGTGCAAAGTTTGGTGGCTGCCAGGAGTCACAGAAATTTCGG
ATGTACAGAAATAGGTACAGAAATTTTGTAATGTTTTTTGGTTTTATTCTATATCGTCAAAGCAAAGCTA
GTCTGAACTCATGCATGCTTATCCTCTGTTAGCTAATATTGTAATTTCCTATGCTAGCCATCTGGTTATT
GAAACATCACAGGAGATCAGCGATGTGCCTTATGCAGATTATTTTACGGTAGAGGTAGGGGAAATTTACA
TCAAATGCTATCAATATTTTGTTGTTTGATGTGTGTTACATGTGAAAAATTTTACCTTTGGCTGATCCCA
GGGAGTCTGGGACTTGAAAAGAGATTGCAGAGACTCGGTAGAAGGTTGTATATTGGATGTTTATGTCAAT
GTGGCCTTCTCTAAAAGAACAGTGTGGAAAGGTTTGTTAAGCCTAATTTACTCTTCTTTATCCTTGATTT
TTTTCACTCTTGCCTCCTATCAATGAAGAAATTTCAATTAATAGTTCAAGAGTGTTTGCTGCGGATTCTC
GTTCTTATAGATTTGGAAATCTTTCAGCTTTGTTGAATTTGATGGTTCTTGAATCTGGCTTGACGTCTAT
GAATTTTTACAGGGAAAATAGTGCAGTCTACTTTAGAAGAATGTAGAGAAGCTTATGCACATTGGATAAG
AATGGTACTTGATCAGGGGCCATTGGGTCAACATTTTTTTTTTTTTAGTTTCTGCAGGAATTTAAACAAG
TTTATATATATTTTTCTTCATTATTATCTTTGGAGGCACATGAACTGTTGAAGCAGAAGAAGCTGGAGAA
CCAAGAAGGTTAGTGTTGTAGACTGATGATTAACAGAAGCTTTTCCCCGAAGAAAGCTGGCTGACACCAT
ATTCTACAGGGAATAAGTTGATTGAGGATGGTGAACCGCTAGCAGCAAGGGAAGAAAGAGTATCTGAATG
TGACGAGGAGGGGAAGGTGGAAATGGTGGGCGAAGGGGTAGTTAAAAAAAGCTTAAAGGAAGCATGGGTG
AATCTGACTTCATTTGTGAAGAGGCAAAGCGGGACAAGGCAGGTTATAGTATTAGCGTTTGCAGTAATCT
TACTGATGCAGGTATGTGTATTTTGGATAAATTGGTAGTGAAAGAGAGAGAGAGGGAGATAGAGAAAAAA
AAAAGCTAACAATAGGTGGAAGTGTGGACAGGTGACGATAGTGGTGCTACTGAAAAAAGGAGGAGGGGGG
CAAGTGGAGTATCATGAGAGGTACGACGAGTACAGTGTAAACGGGGAGACTTTGGGGTGGTTAGAGAAGA
GAATGCATTTCCTGAGGGAAGAGATGATGATGGTTGAGGATCGTTTGCAGAGGATGCGACAAGACCATGC
CGCCTTGAAGGCTCAGTTCCACCATTTGGAACGCCTCCTCCGCCGCAACAAACAGTAAATTTGCTACACC
CTACTCTCTGTTTGTGCAGAATGCGGATGGATATATGCATGTATGTATGTAATGTATTATCGGACGTTAC
TTTGCAAAGTTGTTGTTATACCTACCTACTCATATGAATATGAGCAGAGACTCTGTTAAACGAAATGATG
TAATCAATTGTATTCGTGTTGCACCTGTATCAAAGATTAAATTCACACTGGTGACTCCACTTTCTCGCTA
TTGGATTCTCTCAATGTCTCAATCAAACAAACAAAAGTTGATTCTAATTTAAATTCCCGAGACGATTATC
TTTGTTTTCAATGATGATCACGTTTGATATAGGAAAAAACAATTTGTGGGTTTTAAATCGAGTCGTAGAA
CATTGTTATGCAAAGAAACCCATAGAAAACCACTAAAGGCAGAAATGAAAAACAAGAATGTTGGAAAGAT
GAGGACCTCATCATGAGGTAAAGCAAATAGGAAACGTGAAAAACAGAATAATAACCAACCAAAGGAGCTT
AATTACAGACAAGACAGATTTGGGGGGATGTTGTGTAAAAACCAAGTAGTAGTGAATTGGAGCCTAGTCA
AAAGAAGGAACACGTGTTCTAAGATTGGAAAGGATATTGCTAGGCTGGTCACGTCAATCAAGTTGAGCAG
CAGCCGTTCTTCTGTGCCACAGGCTGTCCTCTGATCTGCACGGTCGGTGGTCTTGCATTATTCCCAGCTG
GTTGGCTAGCCATTCTGCATCCAAACCACAGAGATCAATTTCTCTCATATATCACACGAACGCACACTCT
CTGCAAATTGATTAAGTACAACTACTTGAATTTTCAATTTGAACACTGCAAGGTCAACATCAGTCATTTA
TTTATTTCACTCCAAGGTCACTTACACAGTGACACTTTCTGAGATCTATATAAACACTTACAAAAATGAG
ATTATGGCTTCGCAAAAGTTCCATCAGGTATGATGAGTATATTAACCGCAGTTACTTAAAAAGAACGATG
TAAGATAAATACCTCTCTTTGATGGATGCAGACATTGCCATGAAAGCCTGTTCTACGTTTGTAGCATCTT
TTGCACTAGTCTCCATAAAAGGAATCCCGATTTCATCGGCAAAAGCCTATGAATGTTTCGAAGTAATCAG
GAAAGTAATAATAGCCTTAGAGTTTGATGATTTTCAAAACTTGAGAAGAAAGAATTGGTTCAAGTGGCAT
ATATATACCTTGGCAGTTTCATAAGGAATGGCTCTGTTTTCAGTAAGATCAGACTTGTTTCCAACAAGGA
GTTTGTTGACATTGTCACTAGCATAACGATCAATTTCACTCAACCATTGCTTGACATTATTGAAGCTTTC
TTCATCTGTGACATCGTAGACAATCTACCAGGTGCAAGAACTAAATTAGGACATAAACTTAAAGGAGTCA
ACAGAAAGAACCTAGATAAGATGTTGCTTACAATAATTCCATGTGCCCCACGGTAGTAACTGCTAGTAAT
AGTCCTGAACCGTTCTTGACCAGCAGTGTCCCACTGAAAATAAGTGAAGAGGGAAAAATATGAATTAAGG
GAAAGAGACGTAGAGCTATTAACTTGACAAGTGTGAAAATAGTTACATACAATTTGGAGCTTAATTGTTT
TGCCATCTTGTTCCACAGTCCTAATTTTCTGAACAAGAGATATATAAGAAAAAAAAAAAGGTCAGATCAA
AGCATCGTCATCAGTAGCAAGAAGAAAAAAAAGAAAACATCAACTTACAAAATCGACTCCAATAGTGCTA
ATGTAACTTTCTACATAAGAATCATCCTGCAGCAGAACAACAAACATGAACAAATGTAGAAAGCTACAGT
GTTTGATCTCTGAGAAAGAAAAAGACAAAAAAAAAAACTTACAGAGAATCTCAAAAGAAGACAAGACTTG
CCTACGCCAGAATCCCCGATAAGCAGGAGCTTGAAAAGATAGTCGCTGCAAATCCCAAAACGCTAATTAA
ACCCTAGGAACCACCCGGAGAATCAAATATATAACAGAGGTAATTTCGACCCAAGTATGTGTCGATGGAG
AAAGGAACTTACTACTCAGGATTCATGGTTTTCGATCTGTGGGAGGAAGAGCAGCGAGCGATACAGAGCC
AGAGATCTCTCTCTCTCTTTTCTGATTTTCTCTCGCGATTTACAAGAGGAGGAGATTCAGTGTTTGGGCC
TTGAATAATAATATGAGCGAAGGCCCAATAATGCAAAAGATTAAAATTCATTCTTCTTTCACAAGTTTAG
GGTTCCTACGATCCACTCAGCAACGAAAATGGATCAAGCCCGACAGAGTCCAGAGGAGCGGAGGCCCAAT
AACGCCAAGATTAAAATTCATTCTTCTTTCACAAGTTTAGGGTTGTAAATTGGCCCTTCCTACGATCCAC
TCAGCAATTGGAGATTGTTTTGTGGTTCCCAGATGTTGGATCTATACTAGTCTTCTTGATTCATTTTTCC
AATTGTTGCTTGCTTTTTGATTGACATCTATATTTTAAGTTGGGAGATATACTCTAACTCTTTCTGGAGG
AGGAGGTTAAAACAAGGTAAGGCTTGGACTCGGGTCCCATCTTCCAGTAGAAGCTCTCTCTCCAGTTGAT
GCCTTGTCGATTTCAGCACCGTCTGCCAAACAAACACAAATTTACTTACACTCAGTCTCTGAAGACTGAG
TTGATCTCTTAAAGTCAAAGCTATATGGAGGAGAAAGGCTACGTTAAAATCCATGTAAAAAAAAAAAAAA
AAAAATCCATGTAGGAATCCCGCATTGTGAGCCACTTATCATCCATCACCTTGAACGCAATGCAATATCG
AATATCAAATGCGGACTCGTTTTCTAACAATAAATTATACACCATCCAATTGTCAATATATATGGCTTCG
CGTTTATCTCTCTTAACCCAAAGCTGCTGTAACTAACTAACTAACCAGCTACTAATGTTTCCCCGACCAT
CTTAAAAGGTAACTAACTAACTAGCTGATGCTAGTTGGTGCCTGAGCAGGGGTGAGATCAAAGGAATAAC
GAGAGTGGTGATCCCTTTTCTGTGCACAAACACAAGCCAGTCCCCGCCCTAACCATGCACCTGATCCTGC
CACAAGATGAAATATGCATGTGACTCTCTGCAACACACTACAACAAGGTAAAGGAGACTAGTGCGTGCTT
AACCTGAGGATGAATGGCAGGTGCGTCCTCTGTCTAGGCTGTGAGTAATCCGCCTGACACTGACAAATGA
ATCCTCCATTGTTCTTCCCGATTCATAAAAAGCTACTCTTGATATCTTCAATGCAAAACCAGATTTACGG
GTTTTGGAGGAGCAGTTTGAATGGTCCGAGGGCGTTTTTTTAGAATGGAAACAATCCTAATTATCGACTA
ATCCAGCTAGTTTTTGATACTTTGTATTTTAGATAGATCACATTCCTTAGTTTAAATTGGCTTGAGGGAA
AAGAAACATGCATCATATGTAGATGTACATTAGGGAGAGTGAATGATTTGTGATAAGAAAACAGCAAGTA
TATGGTTTTTAGAAGATAGGTTGTGGTTCATGAAAGGTTCTTCACATGGGATGTTGACACAAAAAAGGAC
CAAAAGTTGAGGTAGAACATCTTACATACCCACTTTCACCCAAATCCAACAAAAAAAAAAAACAGAGAAC
CAGAGACATAAAAACAACCAAACTTCAGTCACAAAGTCCTCATGTTCCCAACAAATTCATCGCGTCTTGA
CATGTCACAAACTGATTTTCTTCTCTAGATAGGCTTGATTTTGAAGTGCAGAGAGATGAGCGAAAAAACA
AGACATTTCAAGTCCTGCAACCATGAAAGTTTCAAAAGGAATATGTTAGAGCACAAATAAATACAGAAAC
TAAAAAAAAAAAAACTACAGAACCATGTAAGGGATGAGTGTTAACAGCCAAACCCTAAATGTTAAAGTTT
GAGACAGTGAATACGTTAAAAGGCAGAGTCCTAAATATATAATCGAGTCCAATAGAGTTAAGGGATTAGG
TAAAAGAAAAGATGGTAAGGCAAGGGGTGGAAGAAAAAGAGAGGAGACCTGAACAAGATAGTAGAAGATG
CGAAGTCCTTCAGGATCATTACTGCTCTGGCAATCAACAAGAGATCCAATCTTAGATGTAGCGAATGAGA
TATGCTCATTACCCAAGACGATCTCGAGCTCTTGCTTTCCAACACGGTCAGGTTCCGGCCAATTGTTATC
GTCTTCTTTCAGAATCTACCCGCAGACAAATAATCACATGTCAGGTTGTACAAAATCATCCATTATTCCT
AGATAATAGCATTAACAACGAAGAGGGTTCTAAACCTACAACACTAGTCAGGAAAGATGCCCTAGATCGA
CAAAAATCGAAGCAAAATCACTAAAACCCTAATTGGCTATTATAGCGTCGATTGACCAAAACGCGGACAA
TTAACAAGAGAGAAGCAAATCGGAAGAGAGAGAGAAAAAGGACCTCGCTCTCGGAGACGATACGCTTGCA
TTCCTTGAGCACGGCGGGGGTGAGAAATACCTCCTTGCGGATAATAGTATCGTTCTTGTAGTTAGAGTTA
TTGGCGTAACGGAGCTTACCGTCCTCTCTAAACTCGAACTCCAGGAACTCGTGTCCAAATTTCCCTTTGT
GACCGACATAGTATCTCAGGTAGAACTCCGTCGCTTCTTCCGCGGCCATGCCTTCTCTTTTTTTCTTTCT
TTCTCGAGATCGAGATTACCTCTCCGTGTCCTTTGCCCTTCTTTAAGTCCGTCCCCGCAAAAGAAAAAAG
GTAATGGGCTTACATATTGGGCCAGAACCCATTTGTAACCCGAAAAGTTAAGGCCCAGTTTTAGTTTTTC
TGTTTCCATCGAAATTGTGTGTGTATCCGGGCTGCCTGATTTCCGATTCCCCGATACAGAGACGATGCCG
ACGGATTCGAAAATGGCCAAGTTTCTTCAATCCTATGGTAATTTCTTCGTTTCGTCTTCTTAGGCGGCCA
GATGATCTCTTTTTCTTTTTTTATATAACTGAAACTTTCGATTGGTGGGAGCAGGATATGATTTGATTCT
GGGATCTGTAGCTGCAATCTATGTGGTCATGGCACCATATACTAAGGTGGAAGAGAGCTTCAACGTTCAG
GTAGGTTTTCAAAGTATTTAGAGTCACACTCTTTCTCCGTTTTACTGAAACCGTTTCACTCGTCTCAAGT
CAATGCACGACATTCTTTACCATCGCCATCATTTGGACTCTGTGAGTGACCTCTCTTTTTACTTCTTCTC
TGAAGCTTTACTCTTTTTTTTTTTATCTCTAGAGTGATGTCAATTTTTACCGACTTCTGTCTTTTTATTT
TTTTCCTATCAGTATGATCATTTGGAGTTCCCCGGTGTTGTCCCTCGAACTTTTATTGGTAAGGAGGGCT
GTTGAATTTCGCTCTCTGTTTTTGCATCACCTGTTGATGGTTTTTTTTTTATCATTATACATTAGTGGAT
GGTTTTTTTTTTATTCCACTCTGATTTGTTCTTGCAGGAGCCTTCATAGTCTCTGTTTTTGCATCACCTG
TTGTATCAATTATCAGCTGCCTTGGCTTCCCCAAGGTTTATAGCCTTGTTGCAGGTTTCTCTTCTGTTTC
TCCCTCCCTATATAATTCCTTAATGAATCGCTAACTATTTTCCCCTAAACACAGACAAAACCAATTCACA
TCATAGTTTTATCATTTTGTCTTGCAGCTCGTTTGGTGTTGGGCTGCATCATATTGTCCACACTAAGATT
TTTCCGGATTCAGGTATGAAGTTCCTTTAGTGCTTCTTTCCATACCACACTTCTGACTCCCCTATCTGAT
TCTTTGTCCCTTCCCATGTCCTTGGAATTGGGATCTCTTACATGCATCTTGTTGGCTGTTTTTCTCCTAT
ATACTGCCACTGACCAAAATCTACTGGTTTGTCAGATAAAAAAAAAGTTTGGAAATCAAGTGGAAACTTT
CTTTGTACTTTTCACCAGTCTTCAGTTTCATTTTCTTTTCTACTGCACTCGTCCTCTTCCTAATATTCTA
GCTTTGGGATTAGGTAATTACTTCTATTCATCTTACTCTACTAGTAGTGGTCCTTCAGATGTCCTAGCAA
TCTTTCCCATGACCCATCTAGCGTAGGCCTTACTAGGTTCTGCTTATGTTTTTAAATTTTGATTTTGCAG
TCAATCTGGCATATGGTAATTGGTTAAAGGGAAATTTTTATCCAGCTTTGAGTTTCCTGGTATGTATTAT
CTTTGTGGTGACATATTTTCTCGATTATAGATTTAGAAAATCGGTCATGCTATCCAGAACTATGGGGTTT
GCTGACATCTCTGTTATCCGATAATCAGATTTTTGCCACTGTAATCTTCAGATGCGATACGATGTTACTG
CTTGGGCCTATTGGTCTTGAACTTTTATTGGTGAGCTGGTGACGAATATTAAATAGTTTGGGTTCTCAAC
TTCTGTATATGTATAATTGGCCGTATACTTTACCGTTCCATCTGATGCGGGTGCTTTATGTTTGTCAATG
ACAGACCAAATCGATCTCCTTCTGGAAAGCACTTAAGTATTGTGTTGGAACCGCTCTGTTGGCCGTAGGT
TGGTTAAAATTCCTCTTCTTTCTGTGATCTATTTTGCTTTTTCCCTTCAGACACTAATTCCCGAGTCTAT
TTTCTGTGGTCATGGAATAATCCTTAGCACAGGTCTTACCATTTTCGTTGACTCTATCATGTGGAAGAAG
TTTGTCTGGCCAGAATTTGAAGTTTTCTGGTTTAACTCCATTCTAAACCGGAGTTCTGATTGGGGTGTAT
CCTTCAAAAAAATTGTTTCCTCAATTGATTTATTTTTCATATGATGCATAATGTTCTAGCATTTTTCTAC
TGCCTGATTAAAGGATTGCGTTCTGTACAATGATAACCGTTTGGAATTTCCAATTCAAAGTTTAATATTG
TGGCACTTGCATTTGTATGAAATGATGTGTTGTCCTTGAAAATTAGTTGCTAAACTAGACACATTCCATA
CATTGGTACTTCACCTCAGCACTCCCACGGTCTTTACTTGTAGCTTATCCACTTTCATTGGTAAATACCA
GACTTCCTAACATCTGTGATAGTGTTTGTCTTGTTCCTTTCTAGTTAGGATCGCTAATTGTATCTCTACA
AATTTTCTTATTTGGTTTCTTTTTATGCAGCTTGGTACTTTAGTTGACAGAAGGGTTCCATTCTTTATAG
TTCCAGTTTTATCGTTCGTTATACTATACTCTAAACTTCCACACAAGGTATTCAGATGGATTACTTATCT
CAGTAGCCATCAACGTTTCTTAACCATTTTCTGACATCGGCTTACCTATCTTTCTTGATTTATGAAGGAA
CTCCGATTTATCATTAGTTCAGTGCCAATGTTCAACTTGTCTGCTGCAGTTGCTGCTAGCAGAATGTATG
AGTTCTATCAGATGTTTGCTAGCTAAGCTTTCAATCATAGCTAGGACGTTCTTTGATTCTGTATCTTAAG
AGCTCTTTGGAGTTTGGATACACATAATTTCTGTATGCCACTTTAAATTACTACCAATGCGGGCCGACCT
CTTAATATAATCCGATTTTGTTGTACAGCTACAATAATAGGAAGAAAACGATTTGGAAACTGGTGAATAT
GGTTATGCTAGCGTTTTTTGCAATCAGGTAGAAATAGTAAACAATTATCTTTGCTATGTAAGAGAAGGAA
AGAGATTTGCTAGTCTACTAAACCTGGTTCTATAGTGCAGGGTGCACGGTTGTAACATTCATGGCATCTT
ACTACAATTATCCTAGCGGCTATGCTTTAAAGCGCTTGCATCAGATTGGTGAGTGACTTATTCTGTTATT
GGGGTTTGTTATTAATGCAGCAGCATTGACTTGGCTATCAAACAAGAAACATCTGCTGGTCAGCGTTTGT
TTTGTGGTGTCTATCTACCTCTGGTTGATAATTTGCCTACAATATGATTAATTGACTTGGTGCCTTCCAT
GGTTCTCAGGCCATCCTGCAAATGTAGCTGGGGAAGAGTGGGTTCACATAGACACTTTTGGTGCGATGAA
TGGAATATCTCGCTTTTGTGAAGATGATTTTCCGTGGAGGTATGTTAGCTGTACTACCTCGTTTTAGGGT
TGGTAAAAGTAAAGGAAATATCAATGTACATGGAAAAAAGTTGCCACTCGGAAGCACCCATTTGTGCGAG
ATGAGGCATCTGTTTGTTTTTCATGTTCATTTTCTTGGATACGAATATCACTTTGTTGGAAAAGGGATCA
TTCTACATTGCCTTTGAATACATAGAAGAGGTATCTGTTTATCTATTTAGGAGGATATAAAATTTTGTTG
TGCAATGCAGATATTCCAAAGAAGAAGAGATAGTAGTGGAGGAGTTGCGAAACCGAAATTTCACGTACCT
GGTGAAGTGAGTATTTCATCATATAGTAGAAAGCAATTCATAGTAAATAAAAAAAGATACCACTGGTGGT
CAACATGTAACACTGTTGTCATGCTTGGTGCAGCGAGCATTCCTCTGTAGATGGATACAAGTGCTTATTT
TATGAAGAAGGCTTTGAGAGACTTGAGCTGCGGCGAGGTTTCCCTCCCATTGTCTTGGTAAATCGGTGGG
CGTGGGGCTAGTATTTCATCAAAATAGGTGCATGGAATGTAATGTAATGTAATGTTGAATTGCAGGTAAA
AAAAGCCAAAGTATACTTGCACCGGGAGATGAAGAAGGAAGATCCTTTTCATAAGAAATGGCCTGGATGT
TAGGTAATCCTACAAATAGAGACAATGTTTTGGGTCGATGTAATGTAGCATTCCTCAGAGAGGACATGAT
GTAATGTAACAACGGAGATGCTTGTTACTGACTTACTGTAATGGATTCAACAAATTCATCCAGAAGCATC
ATCGGCCTTTGGGCTTTGAGTTACGCGTCACAATTGAATCAATTGGTCCTTTTAATTAGTTTTACCAATA
TACCCCTCCGTCTTTTCCCCCTTCTCGTTTAGGAAAAAAAATCATTAGCTTCGACTTATCCGAAACCTAA
CGAGTAACGACGAGAGATGCTTCTTCAGGCGGCGGTGCAGAACCGCAATGTTCCACTGGCTTCTTCCGCC
TCCTACTCTCGTCTCCTTCGCTGCAGATCTCCTGTCGTCTCCGTAGCTGCTCTCTCGAAGAAGACGGCAG
CAATCGTGTGCTCCATCTCCCAGGTTTATGGCTACGGCACGGTGGACTACGAGAGAAGGCCGATTGTCCA
GTGGAATGCCATCTACAAGAAGATTTCGCTGATGGAGAAGCCAGAGCTTGGCGCTGCTTCCGTCTTGAAT
CAGTGGGAGAAAGCCGGCCGCAAGCTTACCAAGTGGGAGCTCTGTCGGGTCGTCAAGGAGCTTCGCAAGT
ACAAGCGTGCCAACCAAGCTCTCGAGGTCCGTGTCCTCCTTGTATTTGCCCTCGCTTTATTTTGTATCTT
TAACACTACTTACTTGATCGCGTATCGTTTTCATAGGTGTACGACTGGATGAACAACAGAGGCGAAAGGT
TTCGGTTGTCTGCAAGTGATGCTGCAATCCAGCTCGACTTAATCGGCAAAGTGCGTGGCATTCCAGACGC
CGAAGAGTTCTTCCTCCAGCTCCCTGAGAATTTTAAGGACCGGAGAGTTTATGGTTCCCTCCTCAATGCC
TATGTGAGGGCCAAGTCGAGAGAAAAGGCTGAAGCCCTGCTCAACACCATGAGGGACAAAGGTTACGCCC
TGCACCCGCTTCCCTTCAACGTCATGATGACTCTCTACATGAACCTCAGGGAGTATGACAAAGTCGACGC
TATGGTCTTCGAGATGAAGCAGAAAGATATACGTCTCGACATTTACTCCTACAACATCTGGCTCTCCTCT
TGCGGCTCCTTAGGATCAGTTGAGAAAATGGAACTAGTGTATCAGCAGATGAAATCGGATGTTTCCATTT
ATCCCAACTGGACCACGTTTAGCACAATGGCCACAATGTACATAAAGATGGGTGAAACTGAGAAAGCCGA
AGATGCACTGAGGAAGGTTGAAGCAAGGATTACTGGTCGTAATCGCATTCCGTATCACTACCTCTTGAGT
TTGTATGGCAGCCTTGGTAACAAGAAAGAGCTGTACCGAGTCTGGCACGTCTACAAATCTGTTGTCCCGA
GCATTCCCAATTTGGGTTACCATGCCTTGGTCTCGTCGCTGGTGAGGATGGGAGACATTGAAGGGGCCGA
GAAGGTATATGAGGAATGGCTTCCAGTCAAGTCTTCTTATGACCCCAGGATACCAAATCTTCTGATGAAT
GCGTATGTCAAAAACGACCAACTAGAGACAGCTGAGGGGTTGTTCGACCACATGGTTGAAATGGGAGGAA
AACCAAGTTCAAGTACGTGGGAGATTCTAGCTGTTGGTCATACCAGAAAGAGGTGTATTTCAGAGGCTTT
GACTTGTCTTAGAAATGCTTTTTCGGCTGAAGGGTCCAGCAATTGGAGGCCCAAGGTGTTGATGCTGTCT
GGTTTCTTCAAGCTCTGTGAAGAGGAATCGGATGTTACCAGTAAAGAGGCCGTTTTGGAATTGTTAAGGC
AGTCGGGGGATCTTGAAGACAAATCTTACCTAGCTCTTATTGATGTGGACGAAAACAGAACAGTAAACAA
CAGTGAAATCGATGCCCATGAGACCGATGCGCTTCTAACACAGCTACAAGATGATTTGTAATCTGATAGT
CCTAGATCTTTGCTTTAAAAAACGAATCTTGTAACCGGAGTCAACTGAGGAAATGCGAAATATGTATAAT
GTACACAAGAGACTGCCTAGTGAAACATGAATGTAAGAGCTGTGTCCCTTTTTGTGACAGCTATTTGGAA
TTAGTGTTGCTTAGGGAACTGGATTAGCCTTTGTTCTCTTGTTTGATTGTTGTTACTTGTTAAGACTAAT
ATTGGAGAGGTTAGGTTGTGCTCTTTTATTTTGGGCCGGACGGATAAAAGGCCCGATATTGAATATATAA
GTCTGAGAGTCTCAAAGGCCCATCTCCATTAAGATATCTTCGCGGAATCGGTTGTGAGAGAGAGAGACGG
TGATCGGGAAATGTCGACGAAAGGCGCGGCGGCGGCGTACCCTAGCGCGGCTCGGATATCTGATTCTCCA
TGTTATCTTCAGTACTCTGCTTCTCTCAAATGTGAGTCATGCTCCTGATCTCACCCTTTGTGATTGTTTC
TTCGAGGATAGGATTTGACATGTTATCTTCAGTACTGTCAAGTTCCATAACGAATTAGCATTGATTAGAT
CTCATCTATTTCATTATGCTTCCTCAAGGTGATTAGATTAGTGGGTTGAATCCCATGTCAGTGATTCGAT
TTAGGTCCCATCAATTGATAACGTCGGGTTTGATTCCTGATTGTTTATGTGTTTCCGTTTTCATTAGTTA
TGCCTCTTAGCTTGACCCCTTGATTTCTTATCAGGTCTTGAAGAATTTGGATCAGACAAGAGTAAATGCC
AGGATCATTTTGATGTGTACAAGGAATGCAAGAAGAAAGAGGTTGTTGTTGTGAATGAATATTTAGGCTT
TTGGCGTTTCCAACTTCTTTGCTGCTTTACCTATGTGTTATTTTGTTTCTCAGAGGGAAGCTCGACTGGA
ACGCAATAAGACACGGTCGTTGTTCTCGTGAATGCAGATCCTCGAATACCAATGATGTCTCAGAACATCA
CCTAGCTAGTAGTATCCTGTTGTTTCATTTGCAATGGCTGTGTTTGTATGATCTATCTAAGTAAACAAGT
GGAAAGTGTTTGTTAATGTTACTTTTTACTCCCCATTGGTGAATCATGGTGTATACCTGTTAAACTTTGA
GAGCAAGTGGTTATTTATTTAGTTAGAGAGTTAGAGCTTCTCCACCACCATATTGAATAAGAAGATCTTT
CTCTCATTCTTTTACTTTACTCTGGCGTCTGAAACAGATCCAGGGATTCCAGTAGTGAATTGGGCTTAAA
AACTGTTATATGGGCTTTCGAAAGTAAAAGGTTCGGTGAGCTGCCAAAGAAAAGTCAGATGCCTTTAATC
GCATTTGACGACGATTCTTTACGTGCGCCATTGACTGCATCGTCGTCTTCCTCACGCGATTTGGTAATCC
GATTCGTCTTCATCTGATTCCCTCCCTTCCGAGAATAATAATGTACCCGCCACCTCCCTCAAGCATCTAC
GCTCCTCCGATGCTGGTGAATTGCTCCGGTTGCCGGACGCCTCTCCAGCTCCCATCCGGCGCCCGATCTA
TTCGCTGCGCTCTCTGCCAGGCTGTTACTCATATCGCCGACCCTCGCACCGCCCCTCCTCCGCAACCTTC
CTCCGCCCCTTCTCCGCCTCCCCAAATCCACGCGCCTCCCGGTCAGCTGCCTCACCCCCATGGCAGGAAG
AGGGCCGTGATCTGTGGCATCTCGTATCGTTTCTCTCGCCACGAGCTCAAAGGCTGCATCAACGACGCCA
AGTGCATGCGTCACCTTCTCATCAACAAATTCAAATTCTCCCCAGATTCAATTCTCATGCTTACCGGTAC
AGAGTATTTCTATCTTTTCAAATGCCTATGTTTGCTACTATACTACTATTCCTTGGATTTTGAATACAAT
TTTCCTTGGCCTCTTCAATCTGATAAACACACATTCCAAGTTACCATTTCGAACCACTTTGATAAAAATG
TGTTGCATTCCATAGCTGACTAACTAATTGTTCATCATGGATGGTTTTCATTCTCAGAGGAAGAAACTGA
TCCATATCGTATCCCGACCAAGCAAAACATGAGGATGGCATTGTATTGGCTCGTACAGGGATGCACAGCA
GGCGACTCACTTGTCTTCCACTACTCTGGTCATGGTTCGCGTCAAAGAAACTACAACGGTGATGAAGTTG
ATGGCTATGATGAAACACTCTGTCCTCTGGATTTTGAAACTCAGGGGATGATTGTAGACGATGAGATCAA
CGCAACCATTGTACGCCCTCTTCCACATGGTGTCAAGCTCCATTCAATTATCGATGCTTGCCATAGTGGT
ACCGTTCTGGATTTACCCTTCCTATGCAGAATGAACAGGTTATTAGTCCCTCAACCGCTTCTAAAAGGGA
TGTTGCTTACCTCTCTCGTTATATTTAACATACATCCATTTTTTTTTTTAATTGAAACAGAGCTGGGCAG
TATGTGTGGGAGGATCATCGGCCTAGGTCAGGTTTGTGGAAAGGAACTGCTGGTGGAGAAGCCATTTCAA
TTAGTGGATGTGATGATGATCAGACTTCGGCCGACACATCAGTAAGTAGAACGACTCTAATCATACGTCT
TGCTGTTGTAGTTGGTTCCTCCTCTCATGATTAAAACACATACACAGGCGCTGTCGAAGATCACGTCTAC
GGGTGCTATGACTTTCTGTTTTATTCAAGCAATTGAACGCAGCGCACAAGGCACAACCTATGGAAGCCTT
CTGAATTCTATGCGCACCACAATAAGGAATACAGGGAATGATGGTGGTGGTAGTGGTGGAGTTGTGACGA
CTGTGCTGAGCATGCTTCTGACAGGGGGAAGTGCGATTGGGGGATTAAGACAGGTAAAATTCTTTCTTGC
TCTCTTGTGTTGATACAGATCGATAAATGTTTTCTTAAATCTGTTTTTTGACAGGAGCCTCAACTGACTG
CTTGCCAAACATTCGATGTCTATGCAAAGCCTTTCACTCTCTAGTAAAGGACAAGTCACTTTTTATGTAT
AGCGAGTGTGATTTGAGAATCCGTCCATATAACCACCTTTTGTTTCTTATTTTTATTTTTCTTTCAAAAG
AATAAAGGAAAACATTGATTTGGTGATTCGATAACAAAATGTGCCATCTATTCTTTAGTCTTTACAAACA
AGCAGCAAATGGTTTGCCTTTCAGAATCAAAATTTAAGGTGTTTCTCGAATAGACAGAAGGAAGAGAAGA
GAAGTCCCAGAAAGCTGTTCAGAAGGCGCATACAAATCATGTGTGCGTTGCTGCTGCAAGGAAAAGCACT
TCCGCTGTAGCAGCCTGTTCTTTGTTTGATACCCCGGCCGTTATCTTCCAGTACAAAGGAGGAGTTTTTC
ACACCATCGCTAAAGAGAAGACACCAAAAGAAGGTACCTTTATGCAACCTAGCCATTCCCACTCCAACCT
CGGTATGCGACCTGTTTCTGAGCACCGACAACGCACTGCTATCTCTAAAGAGAATGTCTGAGAAAGCGAC
TTCTGGTGCTGCATACTTAGAGCTGCAGCCGAGGATATGGCCAGTTATGGTACCAAAAGTGGGGAGTTCT
ACACCACAGTTTGGGGCAAACACCTGAGTGAAGTCGTCTTCAGGGTGTTCACAGCTGAGAGTGTTGTTGA
CATTGCAATTCCCCTCGCAGAGCTCAACATACTGGAGGGCCATGCAGCCAAGACCGGGACTCTCATTTAG
TTTGCCTAGTTTCCGAGCTGTTCTGTTCTGGTTCAAGATGCTCACCATTTCATGAGCTGAGTTTCCTGCA
ACCATTCTAACTAACACTTAGTCCGCCTAAAACGAATCAACATAATATAAACTGTCGAATCTGGTTCTGA
CTAAAGAAAGCGAACTCGAGATTAAATCAGAGGGAGTGGCTGTAAATTCAAAATAAAGCCTGGCCAAATG
CTGAACGAGAAATCCAAGTCTATATTCGCATATGTTATGAGGGGATAAAGCAAGGAGTTACCGTGCAATT
TGGAGCTAGCTAGCACTGATGAGAGTGACAGAAACAGTAAAATCAACTCCAAAATGCTGATTTCGTTCTT
CATATCGTGTTTTATCCTCTGAATTCCCAGCGTAATAGCTCGAGCTGGCGGATTTTCGAAAAATCGAGAA
AAACAAAAAACAGAAAAGGAGAAAGTTTTTGAAAGGAGATGAGCTTGATGGAGATGTTGACTGGTCCCTG
AATAAATGAAAAATGTGTTGCATTATTTCTATTATTGAGAAGAAAAAAACCAGGCATTTTGGTTATTGGG
CTTTGATTTGATGTTGGGCTCTCAACCATTGAAATTGAATGAAGAAAGAAGGAAAGTACGTGACTTGAAT
TTCATTTACTTCATTAAATGGGCGGCGTTGGGGCCGGTGGAGGTGGGCCAATGACATTGATGTGTAAACA
GAGGTAAAGCCGAATTTTGGCTAAGGCGAATCAATGCCCATTGGCTCCTCTCCTTACATATTTGAAGTTT
GAGGTTTCCTTCCTTTTCTTAAATTAAATGTTGCTGTAACATTTCTACTATTGTAAACCGGGGCTCCACC
ACCATGTGCTTCTTCAACACTGTATCATCAGAGCCCACATGGTCATGCCTCTATATAATACTTTGTATTA
TTATTATTCTTATGTCACATTATAAACAAGTACCTCCAAATTGCACTTCCTTCAAACTTATTCGACAGTA
GACTAGCTCAAGTACCTTTGGATGGCGTCGAGGCCCGGAGCTCTTACGGAGTGGCCATGGAGTCCCCTTG
GTAGCTTCAAGTACCTCTTGGTGGCCCCGTTGGTGATGGCGAGCATGCACTCGTACGTGACGGCTGTGGA
TGAGGAGAAAGACCTCAGCAGACTTATGATAGTCGTGTTGATGCTGTGGAGAATAGTTCACAGCCAGATA
TGGATCAGCGTGTCTCGCCAGAGGACGGCTAAGGGAACGAACAAGATCGTGGACAAGCCCATTGAGTTTG
AGCAAGTGGACCGAGAGCGCACTTGGGACGACCAAGTCATCTTCAACACTCTCCTCATGTATCTCGCAAA
CATCAAGCTCCCAGGCGCCTCCCACCTTCCCCCATGGAGGCTAGACGGGGCCATCCTCATGGCTCTACTT
CACGCTGGTCCCGTCGAGTTTCTCTACTACTGGTTTCACAGAGCTCTCCACCACCATTTCCTCTACTCTC
GCTACCATTCTCACCACCACTCCTCCATTGTCACCGAGCCCATCACGTGTACGTACCTTTATCCACCATT
TGCTTCTATTCTATATACATTCATTCATATCTTTAATCAAACTTGGCAGCTGTGGTGCACCCCTTCGCCG
AGCACATCGCCTACACACTACTCTTTGCCATACCTATGGTAACGGCGTCCCTGTGTGGGATCCTCTCCAT
CGTTTCCATCATGGGATACATTACTTACATTGACTTCATGAACAACATGGGACATTGCAACTTCGAGCTT
TTCCCTAAGCGTCTCTTCCACCTCTTCCCTCCCCTCAAGTTCCTCTGTTACACCCCCTCGTACGTCGTTT
GTAAAAACACTACTATTTATTTGGATTTGAATATATGCATGCATTTATAACATGGCATCAAATATGTTGA
AGGTTTCACTCGCTCCACCACACGCAGTTCCGGACCAACTACTCTCTGTTCATGCCAATATACGACTTCA
TCTACGGGACGACTGATAATTTGACCGACTCACTATACGAGAGGTCGTTGGAGATAGAGGAAGAATCACC
CGACGTCATCCACCTCACTCACCTCACCACACACAACTCCATCTACCAAATGCGCCTTGGTTTCCCGTCC
CTCTCCTCTTGCCCCTTGTGGTCTCGACCCCCATGGTACCTCACATGCTTCATGTGGCCCTTCACTCTCC
TCTGCTCATTTGCCCTCACTTCAGCTATCCCTTTGCGCACCTTTGTCTTTGAGCGAAACCGTCTCCGTGA
CCTCACCGTTCACTCTCACCTCCTTCCCAAGTTTTCCTTTCACGTAAGCATTTTACACGCATGCATATGC
ACTTTCCCTCTCTCTCGCTCTCTTGACACAAACGGGTTTACTTATTATGTTGTACTTCACACCACTATTT
TCCAAACTTTCACACACAAAAAAAACATTGATTCTCACTTAACTTGTACGTACTACGTAGGAAGGACATA
ACCTTTTATACAAAAAGAAAATTAAAACAACCTAAAAATGAACAATGAACATTTTCTTGTGGGTATACCT
TTTGTAAGTTGCATCTAAAGTTTATTAATAATTTTGCCTCATAAACATGCGGCGGTAGTATAAATCACAG
CGCCACCATGAGTCCATCAACACTATCATAGAGGAAGCTATCCTTGAAGCAGATGAAAAGGGTGTGAAAG
TAATGAGTCTTGGCCTGATGAACAATGTAAGTTTATTTACTTCAAATCCCCCTAAATATATATGAATCAC
TATTGGATAAGTACTGTAACTAATTACACACGCTGGCAAAAGAAAAAAGTAACTAATCAACACACAATTA
ATTAATGAGAGGGAGGAACTAAACGGGTCTGGAGAAATGTACGTGCAAAAGTATCCGAAGTTGAAGATAA
GACTAGTGGACGGGAGCAGCATGGCAGCTACGGTGGTTATCAACAATATTCCAAAGGAAGCCACGGAAAT
TGTCTTTAGAGGAAATCTCACAAAGGTGGCTTCGGCTGTTGTCTTTGCTCTGTGCCAAAAGGGCGTCAAG
GTTTGTGAATATATGAGGGAATTGGAATATATATACTCAGCTTCTCATATCAAACAAAAAATAATGTAGT
AATGTGTATATATAGGTGGTCGTGTTACGCGAGGAGGAACACAGCAAACTCATCAAATCTGGGGTTGACA
AGAATCTGGTACTGTCTACAAGCAATAGTTATTACTCCCCAAAGGTGTGGTTGGTGGGGGATGGAATAGA
GAACGAAGAGCAGATGAAAGCAAAAGAAGGAACCCTCTTTGTTCCCTTTTCTCACTTTCCGCCCAACAAA
CTCCGCAAGGACTGTTTCTACCAGTCCACTCCAGCTATGCGTGTTCCCAAGTCTGCCCAAAACATCGACT
CCTGTGAGGTACATCTTTGAATTCTTATAGATATATCTGTAACTTTTATATTATATAAGCTGATAGATGT
GTTCATCTATAATGAATGAATGGTTGTTATATATATATAGAACTGGCTGGGGAGGAGGGTGATGAGTGCA
TGGAAAATAGGAGGTATAGTGCATGCACTTGAGGGTTGGGAGGAGCATGACTGCGGCAACACTTGCAACG
TCCTCCGTCTCCACGCCATATGGGAAGCTGCTCTTCGCCATGATTTCCAACCTCTCCCACCATCTCCTCT
ATGAGCTTTTTTCATATTCATACATCTATGTCCCCTTTCTTGATTATATCTACTTCCCTTCCATCATTGT
TTGCTGTTTACTATGTTTTTCTATCGACAATATATAAGTACCCTTGTTACCCTTGGTGCCACGTGCTTCA
TATATGTTAGAAAGGGCAAAAAAATTCGTCGTATGATATGCTTAGTTAAATTTTATAAAACTCAATAAAA
ATCTTCAGAAACAGTGCTATGATCATTACATCTTAACTAAGTGATATATATCTGCGTGCCTATTTAACAA
AATAAACAAAAAAACAAAACAAAATATATTTGGGTGCATCATCAAATCAAAGTAGTTGCAAAAACTGGAC
GAGGTTTTTACTTAAATGGTCCTTACCCCGCATGGTCCACTTGCTACCTAATTAAGGATTGGTAGGGTGC
GTATACGTATATAAATTGTGGCGGTGGGAGATGGAGTTACTAAAAACGAAACGTACAAGTATTATTCATA
GCTCTCGTATAAGGGGTTAGTCCTTAGATCTAGATATTTTCACTTTTCTTTCATTTATGTCGGAGCAACA
GACACTAGCTGGCGCTTCAACGTGCATGATCTTGATTGGCTAGTAAATTCCAAGCATCAATACCTAACAC
ATGCCCAACTTGGTTCATTAGTATTCTTTCATTGGTAAAATACCCTTACCTTTCAATAATATCCAGAAAT
AAATATATGAAGCCATCCATCAACCGGTGCATTTCCTCAAGGCATGGATATGATATCAGAACATCGATGA
AGGTGGGAGGGGGTAATTAGCTGAGTGTCATAAATGAGGATCCATGTGGAGATCATCGAATGGTAGTAGT
ACATGTTTGGTCTTAGCTGGCCCCACCACAAGGAATTGGACTGGTGGGAAGATAGGGGTGGTTACGTCAT
TCCACATATCTACCAATTAAGGAGTTTAATATAAACCTTGCTATATAATGTACCTTGGCTCACAAGAGTT
GAAGAGACACAGTGACGACACAAACATATTACATTCGACGGTATAATGGCCACAAAACCAGGAGTCCTCA
CCGATTGGCCTTGGACACCCCTCGGAAGTTTCAAGGTGCACTCTGTTTTCTTGTCCTTTAAATTTAAAAA
AACGCGTGCTTATGATCGAATCCCGTTACGTTACTGATATATATGTTTTTCTTGACATTGAAACAATACA
AAAGTACATCGTAATAGCACCATGGGCTGTCCATAGCACATACAGGTTTGTGACAGATGATCCAGAGAAG
AGGGATCTCGGGTACTTCCTTGTGTTCCCATTCTTGCTCTTCAGAATTCTGCACAACCAGGTTTGGATCT
CTCTGTCCCGTTACTATACGTCCTCGGGAAAGAGACGCATCGTCGACAAGGGAATCGACTTCAATCAGGT
CGACAGGGAGACCAACTGGTGCGCTTTTCTAAATTTTTAACTACCTGCGTGCCTCGTGAGTATATGTAAT
CAACGTAACTAATGAAATCCTGATATATGCGCAGGGATGACCAAATATTGTTCAACGGAGTGCTGTTCTA
TATAGGCATCAACCTATTGCCGGAGGCCAAACAACTTCCCTGGTGGAGAACTGACGGAGTGTTGATGGCA
GCGCTTATTCACACCGGACCGGTGGAGTTCCTCTATTATTGGCTCCACAAAGCTCTCCACCATCACTTTC
TTTATTCCCGCTACCATTCCCACCACCACTCCTCTATCGTCACTGAGCCCATCACTTGTAACTATTGTTT
CTTACCTTGATTTTTACGCTGCCTATATTTCCGTTTTTCTTTTTATAATTATTATACGTAAAATATACAT
CGTTCACGTCCTAACTAGTAGCTTTTATCTGTATATAATGGGATTTGATCAAATGTATGCAGCGGTGATA
CATCCGTTTGCGGAGCACATAGCATACTTCATCCTCTTCGCGATACCACTACTTACCACGTTGCTAACAA
AAACGGCGTCAATAATTTCGTTCGCCGGATACATAATCTACATAGACTTCATGAACAACATGGGACACTG
CAACTTCGAGCTAATCCCTAAGCGCCTTTTCCACCTCTTTCCTCCCCTCAAGTTCCTCTGTTACACCCCC
TCGTAAGTCCTTAATTAACAACTCCTCTTCTGTTTCATACACTACCAATTTGGCGTAGTAAAAGCATTTA
CAAGAAACCATTCTTGATGATCTGATACAAATACCTAGTTAGATCATATTAATTAATCCTCTTATGGTCA
TCATAAAATCTAAGCAAATGATAAATCATACTAATACAGGGGATATATGCTATTATAATAGAATTCCATA
CACGTACTCCATTCCTGTATAAAATAAAGGTGACGTGATACAGTTGTATGCTTAATATGATCGTCAACTA
CTGAATCCCTGGACCACAACAGAAAAAAAAACAATTATTTAATATATCTTACATGGTTCAACTTATCGGC
ACATAATCCAATTTCCCACAACTTTACGCATTGATAGCATCTTTAACCAAACATCCTTTGAGAACTATTT
TAAATATCAAATTCATTAGTCGATATGTAGCAGGTGGTCCCTCTAAACGCTCAAGTTATATTAAACCTTC
TGGATTCATATTTACTTTTAAATATTTGTGACTTTTTTTCCTTCGGTATTAATTTAGCGCAATGTGAAAG
CAAAATTTAATAGTTAAAATACATTAAAGTTTGGATAATAAATGGAGCATGAGAATTGCAGATACCACTC
GCTGCACCACACGCAGTTCCGGACCAACTACTCCCTCTTCATGCCCTTGTATGACTACATCTACGGCACA
ATGGATGAAAGCACGGATACGTTGTACGAGAAAACTCTAGAAAGAGGAGATGATATAGTGGACGTGGTGC
ACTTAACTCACCTGACGACGCCAGAATCCATATACCATTTGCGCATTGGCTTGGCCTCATTTGCCTCCTA
CCCCTTCGCTTATAGATGGTTCATGCGCCTTTTGTGGCCTTTCACCTCTCTCTCCATGATATTCACGCTC
TTCTACGCCCGCCTCTTTGTCGCTGAGAGAAACTCCTTCAACAAGCTCAACTTGCAGTCTTGGGTGATAC
CTAGATATAATCTACAGGTCCTCATCATCATCATCATCATCATCATATATATAGGCTGGTTAACTTGCTG
ATGCATATATATTAATGGTGATATATATATGATGCATGCAGTACTTGTTAAAATGGAGGAAAGAAGCGAT
CAATAACATGATTGAGAAAGCGATACTGGAGGCAGATAAGAAAGGAGTGAAGGTGCTTAGTCTGGGTCTC
ATGAACCAAGTAAAGAAACTATCTCTGACTGTTTTGGTTTTATATTGGGTAGATGCCGTACGTACTACGT
AGTGTATGTTAAAGCTTTAATTTGATGAACTGAAACAGGGGGAGGAGCTTAACAGGAACGGAGAGGTGTA
TATCCACAACCATCCAGATATGAAAGTGAGACTGGTCGACGGCAGTAGATTAGCAGCAGCTGTTGTGATC
AACAGTGTACCCAAAGCAACTACAAGCGTCGTGATGACAGGCAATCTCACTAAGGTTGCCTACACCATCG
CCTCTGCTCTCTGCCAGAGAGGCGTTCAGGTCCTTTGTTTTCCTTTTGCTCCTATGTTGTGATATCAAAT
TGATGATCTCTAGGAGAAAAATAAAATCCAAGCTTTATCTACATGTATTTATGCTCATGACTCGTAACAT
TTTCATGTGAATGTCATCCGCAGGTCTCCACTCTGCGCCTAGACGAGTATGAGAAAATAAGATCATGCGT
TCCACAAGAATGCAGAGACCATTTGGTCTATTTAACCTCTGAAGCACTCTCATCAAACAAGGTAATTCAG
TATACAAAAGAAGCACAATTAATCAAAGAATCAGAAGGAAAATATTCAAAGAGCTTATATAAAGAAAACT
AATGAAGGGATTTTGGGTGAAGGTATGGCTGGTGGGAGAAGGAACAACAAGAGAAGAGCAGGAAAAAGCC
ACAAAAGGGACATTGTTTATACCATTCTCACAGTTCCCCCTCAAGCAGTTACGTAGAGATTGTATCTATC
ATACCACACCAGCATTGATAGTTCCAAAATCTCTGGTGAATGTCCACTCCTGTGAGGTAAGCATTCAAAG
CTACCCAATCCAACTAATTTATTAGAAGAGGTCCTTATTATAAAAAAAACATCTGCAGAACTGGTTACCG
AGAAAGGCGATGAGTGCAACTAGAGTGGCCGGCATATTGCACGCCTTAGAAGGATGGGAAATGCATGAGT
GTGGCACATCCCTTCTTCTCTCGGATTTGGACCAAGTATGGGAAGCCTGTCTCAGCCACGGCTTCCAGCC
TCTCCTCCTTCCACATCATTAAAACTCCAACCTTGGAAGATTTTAGGAGAATGAGAGCGACACGCTCTGT
GCTTCTTTTCCTTATGATCCAGCTCTTCCACGCACAAATGAACTATGAAACATATATAAAGCGCACACAT
ATATTTATGCATATCAAGCTTTTGGTGATTATGGTATTGATAGAGTCAAATTAAGCTCGGTGACTATGGT
ATTAATAAGAGTACTATTTCCTTTTCTCTTTGTGAACTAAGAAACATATATATATAAAGCAAACATGTTC
CAGAATATCTAAGTTTTTCTTCTCCCACTCCTAGACTTTATAGTTCTACAAAATTTAAGTAGCATAGAAC
ATAGCATTTGGATCGCTTGATGCTATTACTAGGACAATTCAAATGGTCTCTCATCACTTATAGGAGAAAC
ACCTATCTTATTCAAATCATTTGGTGGTCAATAACCGTTTTGAATACATTGATTGGTGTTAGTTAGTAGT
TAGTTCTCATACACAGTGGCTAGAGCCGGGCAAAACGGATACCACCACCGTTTTTTAAATTATTTATTGG
TTTTCTTAAATAAACTAACAAATAATTAAATTAGTGATAATGTACTATTTAAAAAATAATTATGTAAATA
AAAATATGAAGTTACGAATAAATTCATGAAATTTAAAAATTTAACACTTATCAAAAACAAAACCTAATAG
AAATATAAAAATATAATTTTAAAAACAATAAAAACAAGTGTTAAAATTAAAAAAATGTGTAAACCGTATT
GAACCTAAGACACCTTTTTGGGGTTTGGATGTTATGTCCAATTAAGTTACACAAAATTTAAAAAATTAAC
ATTTATCAAAAACGAAACTTTATAATTTTTAATAGTAATATAAAAATAGAATTTTAAAAACATTTTTTAA
TAAATAAAAACAAGTGTTAAAAATTTAAATTATGAGTATTGAACCTAGGACAACTCTTTGTGAAATCGTT
AATGACCACGGTTAAATGGCAGGATCAAAAATCCGATTAGATTTCACAACGTCATATTCATTTAGTATTT
ATAAAACCTTCTAAAAAAAAATTAAGAAAAGAGTTGAAAAACTTTTAAGAAAAAATAAAATAAAAATAAA
TGCTAAATATACATAAAGATGTGAAAAACATGTTGGACTTGTGAAATCGCTAATGGCCACGGTTAAATGG
CGGGATCCAAAATCCGGTGAGATTTCACAACGTCATATTAATTTAGTGTTTGTAAATACTTTTTAAAAAA
TAAAAAATAAAGAGTTGAAAACCTTTTAAGAAAATAAAATAAAAATTAAATTATAAATATACATGAAGAT
GAGAAAATATTTTGGATTTGTGGAATCGCTAATGACCACGGTTAAATGGCGGGATCCAAAATCCGGTTAG
ATTTCACAACATCATATTAATTTAACATTTATAAAACCTTTTAAAATAAAATAAAATAAAAAAGTTGGAA
ACCTTTTAAGAAAATAAATGCTACATATACATGAAGATATGAAAAACATGTTGGACTTGTGGAATCGCTA
ATGACCACAGTTAAATGGCGGGATCCAAAATCCGGTTAGATTTCACAACGTCATATTAATTTAGTATTTA
TAAAACCTTTTAAAAATAAAAAATAAAAAGATAACAAAAATCGAAAGAGTTGAATACCTTTTAAGAAAAT
AAAATAAAAAATAAATGCTAAATATATATGAAAATGTGAAAAAACATGTTGGATTTGTGGAATCGCTAAT
GACCACGGCTGAATGGCGGGATCCAAAATCCGATTAGATTTCACAACGTCATATTAATTTAATATTTATA
AAACCTTTTTTAAAAAAAAAAAATTGAAAGAGTTGAAAACCTTTTAAGAAAAAAAATAAAAAAAATAAAT
GCTAAATATATATGAAGATGTGAAAAACATGTTGGATTTATGGAATCGCTAATGACCACGGTTCAATGGC
GGGATCCAAAATCCGGTTAGATTTCACAACGTCATATTAATTTAGTATTTGTAAAACCTTTTGAAAATAA
AATAAAAAAAAAAAGACAAAAAAAATAAAGAATTAAAAACCTTTTAAGAAAATAAAATAAAAAATAAATG
CTAAATATACATGAAGATGTGAAAAACATGTTGGATTTGTGGAATTGCTAATGACCATGGTTAAATGGCG
GGATCCAAAATCCGATTAGATTTTATAACGTCATATTAATTTAGTATTTATAAAAACCTTAAAAATTATT
TATTTAAATGTTTTAGTGAAAGTTTTAAACTAATTAGTTTTAGTTTTGGTTAAAACAATTTTTTAAAGAA
AGGAAGAAAAAAAAGTAGAATGAAGAAAGTAAATACCTTATTGGATTTGGTTGTAAAGAAGGCCTCATAC
AGCAAAGCCCATTCCAAAATCCTAGTGTAGCTCTGTCGTGACATCATCCACCACTTTTAGGTCAATTTTG
TAAGTAAATTACTCATACAAATAAATTAAAAAAGGAAATTGATCACATCAATATTAAAAAGTGACCGTTA
CAAATAAATTAAAAAAGGAACTACATAGAAACAGTATCCCGATAATTGCTTTCATCATAACAGATTCTCA
CACCTTTGCAATTGTGGCTTTAAGAGATTCCAAATTGTTGATTTGAGTTTGAAATATAATTTTAAAATAT
CAATAAAGAAGTAAAGAAAGTATTATACCTGATTGGACCTCGTTTGGGCCGTCACAGGAAAAGCCCATTA
CCAAATTCTTCGTCACTGCTCTGTTCTGTAGTTGATGACATCGATGAAACTCAAACTATCGCACTCGTCG
TCATTACCAAGTCCACTGAACATGATCTGTTCCATCGCCAAGTTATTCTTCGCTGCCACTGAACTGGTCG
TCGTCTTCACTAATCTCATGAGAACGGTGAAATTAGGGTAGACCCGATTGACAGAAAACAGAGGATGGTG
ATCAATCACGAAACGAGATGAAATCGTTTCATAAATCATCGGCATACTCTGAATGGGTCATCTCTTTCAC
GCTCTGGATTCTTTTGTTTTCCTTTTGAAGAAGAAGATGAATGGAGAATTATGATTTCACAAGGGAGAAA
GAGTATTTATAAAACAAACGTTTTCAATAGAAAAATGAAATTTTGGATTGTTTCCTTTTTTTACAACGGT
GTTAAGAAAAAAGGAAATTTCAGTTATACTGCAAAAAATAATGAAAATTTGCTCACAACGGTCATATTTG
TTATTGTGCATAATATTATTTGAGTTTTAATGGGTAACAATTTATCAAGAAAATTATTTGGGTTTTAGTT
CGTAACGGTCATATTTGTTATTTGTGCAAAAAAATTATCTTAGTTCACAACAATTAATCTAGATAAATCA
TTTGAGTTTTCTTATTTGTTAAAACAGAGAATGCGCCGTTGAGATAGAGAGGAGCAAAGTCGGGATCGTG
TGTAGTTACTTATCTTTGGTTACTTTGTAAAAACACAATTACAAACTCAAAACTGTTACAAAAAACAACA
ACTTTTCACTCATTAAAGAACACTAACAATCATCATCCATGATACAAAACAGAACAGAGCATTCTTTAAT
CATCATCCCGGAAGCTTTAGATCTGTGTCTCGCTTCAGACCATACCCTTCACCACCCCCAGGTTATTTAA
TTTACTTACAAAAAGTTCATACTTTAACTTTGTAAACCAAAAATGTTTTATTTATACATTTTCAGTCTTA
ATTATTTTCTTGGAAAAATTATCTATTCATTTATTTATTTTTAAAACAATAATTTTGGTTAATTTTGTTT
GGTCTTTATTACAAGTTGTTCAGATAAAACTGAATTACTGTATTTCCAATTTGGTTTGAGTTTCAAGATC
ACTTTATTTTTAAGTTTCATGTGATTTTAAGTTGAGAAGTTTATAACCAAATTTGAAATATATTTGACTA
TTTTTAGATGCTGAAGGAGAACAAGAACATGGTCGAAGATTAAGGTGGAGATTATTGCAATGGCTTAGAC
GAGCTTCTCCCAATAGTTCACTCTCAGTATTCTCATCAATTCGATTATTTTCATTGGGGTTGTTTCACCG
ATCTAACGCATGTACGCATATAAAATAATATTATGTTTTAAAAGAAAATAATAATCTGGTTATCAAAACG
ACTTTTTCAAATATATAATTTATTCACATATATAAGTTCATATCATAATAGTTATGGTACAAGTTTCCTA
AAACTAAAAAATAAAAACAAATTTTGGCTTCACAGTCATTGGAACAAGGTGAATCCAGCGGTCTCCTTCT
CGGAGAAAATGGCCACGCGGACGGACGATACACCACAGAAAAGTCCAACGTGAGTTAACTCTAAAGAAAA
CATTTTATTTGCCAAATATAACGAATAATTATTTATTATTTTCAGAAAATATTATTATAGTTGTGATTCT
CTGTTTCGCAAGAGTTGGGAGTAGGGAATGTGAAGTAGTAGTGGTGGCCCAAGTTATGTTTCCAAACGCC
AGTAACGACCAAATCTAGGCATGTAGATTTCATTGGGTCACGTGGATGCATCAAATTTAACGCGCCGCAT
TTACTTTTCAACGAATGGCACAGTTTCAACTACCTCGAGAAAAATCCAAAACCAAAAAAGCTATTTGGAA
TCTTTAAAATCTTTTTACAAATTTCTTCTATTATAGTATTGCTTTGTTGTACTATATTTCACGACCTTTC
ATGAATATTTTAAATATAAATAGAAGTGGTAGGCGCATATCTTTTTATATTCAAAAGATTCATATCCAAT
GACACAACTAATCAATGTTCAACCGACCTTAGTAGCCAAGTTCCGTTATGGTCAATACGAGAGGTTGAAG
AGTGATTAAGCTCAATTATACCAGATTTACCACAACGACTAATATCCTTCCTTATCTTCACTTTTGAACT
CTACTTTGCAGACAATATATGCTCTCTGTCGTCAAAGCCCATAAGATATCTCACTAAAACGTTCAAACTC
ACTCTACGTATAAGATCATATACCACACGTAGACAAAAATTGAACCTACTCAGGCTGATCTTTGTTTCAA
GTTTTATTTTTAACAAATTTATAAAGAAAATATACGACATGTATCTTAGTAACCATTGTGTAGAGATATA
TCAGATTGTGATTTGAAGAGGTGGTCCTGATGTTTGAAACACAACACTCTCAGCTTTAGGCAATAGTTTA
ACTAAGATGGATGGTAATTTTTACAAATAACATGCACGTACGATTTGTTTAACTATTTCTCGACAACCTA
AACCAAATAGGATATAATATATGATCGTGTTAATTAAGTAAGATAATATATATATATATATATATATATA
TATATATATATGTACCAAATAACCTAAAATTTGATTGTTTTAGGGCTAATCGGCAGATTCTCTCATAACA
TCGTTGAGAAAAAAGGACACGGTGATTAAACATCATAAATTCGGAATATTACCTGATTAGGAGGCAAAAA
CGTTGGTTGATACACGTGCATTACCCAATCGGATTTGGATCCATTGATGTTTTCATACGATTGGAAAACC
AAAACTTGTTTCTCACCAATTTTAACACCATTACTAGTTATCCACTTGCCAATGATTGGTGTGTTGGATA
CAGTTTCTTTCCAATAACCCGAATTCGTTTTCAATATTTCTTCGTTATATTCATCACAACTAAAGAAGAA
CCATACCATAGTATCAGCCCACTCGCTCTTTGATTTGGCTATAATAATTATTAAAAAAAAAAACCTAAAT
CAGAAATCAGCCTATAATCAATGATTGAATCAGAAAATCATGATCTAGCATTAATTGACCAAAACTTTCA
TGGCACATGCCAAGGATCGTAACTAGAGATTTTAACGGTGGTAATGAAATGATGATATTGCCTTCCTTGA
TGCCGAGATGTTTTAGCAGGAGGTAATATTCGATGATAACGTCATCTGTCGGCCGGAATCTGAAATCCGC
CGGATATTTCATTCTTATCGAATAAACCCATAAAGTTAAAAACAATAGAGAGCGATGAAAAATGCAAAAT
AGGGTTTACAATTTTTATATGTAGGTAATTTAGAAAAACAAAATTCTTTTTTTTTGGGCAACATAAAAAA
ATTCCTTAATTCTGAAGAAGATATAACGAATAAGGTACGTAATTTGATGTATAATAAACGAAAGCAAAGT
CTTTGAACGCCGAAACAGAGGAATTAACAAGAAACAGAATGAAAGTGATGTAGAAGAAAAAGAAAGATTA
CTAAAATTACATGATATAGGATAATGTAAACAAATAAACAATAGTCTAATGGGTTTTGGATTTAGCCATC
AACATGACAACATGCACGTGTACATATATGATGTAGACTTGAAAGTCCAAAAAAAGACTCTTGACATTAC
TGAAATGAAGCATCTTAATTTGAAATTTATTCTTGTTTTCTTTCGTTGAATGGAATTTGTTTATGGGGTT
AGGTAGGACTAGAATAGTACTTCGAGGTTGATTGATACTTGATAGGGTACGTCAAATAAAATTTGAGCAT
TTGGTTAGCTGTATGAGCAGAAATTATACAACTTTGTCTTCACAATGGAGCATACATACAAGATGAGAAA
GTAACAAAACAAGATAGACATTATTATGTCAATGGATACAAATTTGTCTTCACAAATTTACCAGTTTTAT
ACATATCACACATACAGTATGGTAAAGTTACAAACCAAGATAGACATCATAGCATACACTTGTACTGTTG
TAAATAATTTGGAAAGTAGAAAAGGTGTTATTGATCACTTTTATTGTTATCAAGTTCTTGAGATGGAAGA
ACATAGGTGAATTTTCTTGACGAATTTTTGTATCATCCTGTGAAAGAAACCAGCTCTTTTCTTCTTGATC
GTCTCTTGACCCAATTTATGCTCACCAATCTCAGTCCCTTGTGCATCATCATAAGGATTCTTCTTCTTCT
CGGCGGTATCAATACTGGTTATTAGAGCTTGGCTCACCTTGAATCATAACAAAGAAACAAAGTCGTTGTA
ATGAGTGTTGGCACAAAGTAGCATCATTGATTGTTTGTGTTGTTAGTAGTGATGGCACAAAGTAGCATTA
AGGATTGTTTGCCTCAGTGAAAGATAGAGAGATAAGAAAGCTCACCTCTTGAGTTAGTGACACTAAGTTG
ATTGTTGAGGTAGGAGATTCTTGCAGGTCTTTGATCTGGTCTATGCGATGATTTGAGCTACCAAAACTAT
CACAAGTGCTCGAAGTTTGAATAGAGTTCTGTCAAATGAATGAAACAAAAACTTGAGCTTTGTAAGGTGA
AATACGAAAACAGAGGATTATAAAGGTACAAAAGTAGAAATTTGCTTACTGTTTTTGGAGTTAGCAAATC
AGAATCATTATCATCACTGCTAACATCATCACTGAAGACACCAGTTAATGAGTTTGGAGGTCTGTAATCA
CTTCGATTATCATGCATAAACATGATACTCTTCTCCTTAGCATCATCAATATCATTCAACCATGTTTCCC
ATTCCTCAATCGGTATAGCATCCTCGATTTGAGCATCATCCTCATCATTCATCAGCCATTTTACCAATTC
CTCGGTCAGTTTAGCATCCTCGATTGGAGCTTCTTGCAGCACATCACCAAACTGACTTGGATCTTCTCTG
TGAAGTGAGGATCCCTGAAAAAGGGGGAGAACGCAAAAGAAGTCGTTGTCAGATTTAAAACAGAAAAGAA
GTTTTGAGATGAACCCACCTCAGAATTGTTGACAAGCTGAGGGATTAAAGAGTCACGACGACTCTGCTCA
ATTCCACTAACACCAGAAGAAGAAGGAGAAGAGGAAGACTTCTCTCTCATGCCACCATTAAACATAACTT
TACAGAGTGTGTATGTCATCATCATCTGCAAAAATTCGATAAAAAAACTCAGAATCGCAGCAATAGTAAG
TAACACAAAAAAAAAACAGAGAGTACCTGGTTATGAGAGAAACCGTGGTACTCGTGTATAACCCAATCGG
ATTTGGATTCCTTACTCGTGTAAAACATCAAAATCTTTTTCTCACCGATCTGTTGGCGATTACGCATGAT
AGGCTTTGGTCTGCCAGTACTCTTCCAAAACCCAGATTTCGTTTTTCTCATCTGCTGATCACCTCTGCCA
TATTTGTTCTCCTTAGGTCTGAAGAAACACCAAGCCACATCTTTCAGTTTGATCCTTGACTGGCCTACCA
TACCAAAACGAGAAAACGCTAAAATCAGAAAGTAGCGGATGATTCGATTGAACAGTGAGAAGGACGACAC
TCGGTGATATGAATGACTTACAAGGTAACTCCCAAGGATCGAGTCTACAGACAGGGACTGTGTTAATGAA
TCGATCGACATGGCTCGTGTCTCTATCGGAATTTTTCGGCCAAAGGTAATCGACGACGATCTCCTCGTCG
GTCGGACAGAATCTTAAACCCACAGGAGTTTCCATTTCTCTGCAGCGATCAAAAAAGAAGGGAAAAGGAA
AAGATCAAAAAAATATGCATTGGAGAGCTTTCGCCATGGTTGATGTTCTTCTGCAACTTAAAATGATGGA
GAAGAAAGACGTATAGGGTTTTGTATTTATGCGGAAATTCTCAAATTCAAAAAAATAAAAAAAATAATAC
AACAATAAAAGAGTAAAAATATTAAATAGTCATGACGGTATACTTGTCGAATTCGATTACGCTAAGACAG
GACATTCAAAGGGTTAAGTTTCGGAATGGTAAATACGTGGTGCGTTTGTTTATCACTTGTCTTATAAATT
TTGTAATTATTTTTTCCATACGACCATACCAATCTTCAATCCATGAAATTGAAAATATTCCCCATAAATT
CTCTTACATTGTGTGACTTGTTAAAAAAATATCAATCAGAAAAGGAGGGTGGAAAAAGAGGATTTGCAAG
CTGCAAGTTTGCATAAATTTAATCAGATAGTGACATATCTTTTCATCATGGGACGGTAGTTTCGCCCAAC
ACGTAACGACGAAATTACATTTCTTTCTTGAACTTGTTTGATGTTTCTCTTTATTATATTTTGTTGGCCC
ATTTGGAAATTATATAATGATTAACGTTGCCCACAAAAAAAATAAATATAATGATTAACGTTAACGTCGA
TCGTCCGTTATCTATGTAGAAACAGAAACATAGATACGATGACAAAAAGTATCTCTATATGCTATTATGC
TAATAGGTAGAGCTGTCAATTAGACAGGCGGCTCATGAACTTGCCCAGTCCAAATGCATATGGACGAACT
ATATTCTGGACCATAAAACAAATGGTCCAATTGGGCATATAACCAGTTTTGTCCACGAATAATATGAGTT
TGACCATATGGACAATGGGCTGCCCATGGGCATGAATTGAGGGAAAAATACAATTTCTCCGATTTTACGA
TTTTGACGGAAAAACGTAATTCTGCAAATTTCCTCTAAAACGCGATTTTATTATTTTGGCGAGAACACAA
TTTTACAGTTTCGACGGGAAAACGCAATTCTCCGATTTTACGGTTTTGGCGGGAAAACGCAATTTTTCTA
CCAAAATCGTGATTTTATTATATTGGCGAAAAACACAATTTTACAGTTTTGGTGAGAAAACACAATTCTA
CGTTTTGGCGAGAAAAAACAATTTTACGATTCTACCGTTTTGGCGAAAAAAAACAATTTCATAATTTTTC
CGCCAAAATCGTGATTTTATTGTATTGGTAAGAAAAACACAATTTTACCGTTTTGTCGGAAAAATGCAAA
ATGCAAAAACATAATTCTTTAAAATCATGATTTTTGATTTATCAATAATAAAATGGGCTATACATGGGCT
TGCCCATATGGACATGGTCTTTATTGGGCATGGACATTTTTCGGACCATTGTCCATTATGGACCGTCCAA
CTTGACCCATAAAAAGAATTGTCCCTACGGACACGCCCAATGGTCCCTGGACGGATCATTTGACAGTTAT
ACTAATAGGAAGCTTCGTAGAAGCCGTAAGCCGAAATAATCTAAAGCCCTTTTAAGATTTGGGGATAAAT
ATTTATATATAAGGCTAGACATGGGGAAAAAAAATTAAATATTTATAGACATGCATGCTATATACCAGAT
TACCAGGTCCAGAAATAATCTAAAGAGAGCATACAAAGTGAATATTAAATTGCAAAAATGGGGGAAAATA
AAAACAAGAATAGACATGCATGCTATATACGCATATGCAGAGTGAGCGATCACTTGATGAGAATTTTTTG
TAAAACGATTATCGCAATTTGAGCATCTTTATTGATGAAATACTTATAGAAAGTTTCTCAAATAAAATAC
TACTAATATATTTATTTATTTTTTGTTTTGAGAGTTTTACATATATAGGGTTCTCATATATAGATTCTCA
ATTATGAACCTTTTGTACTAAAAACTCTACTATTCTAGAAACTTACCTTTTTTTTAAAAAAAATGTGTGA
ATACTATGGATGGAAATGTCTTTAGTTGCTATGAAAACTAATTTGTGTTATTTATACGGTTATACCTAAC
GTTTCTAGTTATCACAAAAATTAATGGTGTATTAATGTATTTAATAAAGTAAGTTAAGTTGTTGCACAGA
AAAGAAAGTGTAAGTTGGGTAAATTGTGTGAGCCAAAAAAGATTGTAAATTGTGAGTTTGTGACGCTGAA
GAGTGAAGACAATTCAAAAGGTTATATCTTATATGCGACGGCGTAGGTCAGTTTTGGAATGGTAAACACG
CGGCAAGTTTGGTTATCATCATTTGTCACAATCATATATATTTACTCATATAACATACATACATTGCTTT
ATCGTCATCTTTGGTTCATGAATAAGAAAAATGTTCTCCCACAAAATATCTTTACCCTTTGGTTTATATT
TTAGTTTTTTTTTTTTTTTTTTTTTTGTCAACCGATATAAATTAAACCTCAAAAGAGCCAATCCCGAGGG
ATATTGTTTACATACGTGACATGATGCGGTACGGTACGAATCTTTCGTGCCAACTTATCCGCTTTTACAT
TTGCACTACGAGAAATTAAAGATAAAGAGAAATTTGTGAATTCTTCCCTATCACTTTGCAACTCCTCCAA
ATACACTGAAAACGCCGGCCATTCGGTTGGAGAAGACACCATCTTCACCAAGTCTGAACAGTCTGTAAAG
AAAGCTACGTTCTGATTATCTGCTCCAATCATGCACTTCATCGCCCAAAGAAGAGCTTCCATTTCGGTAT
GTAGAGGAGATAGACTTCTACGAACGTTGGCGGCTCCCATGGTTGGCGACTCTCCAAGAGATGATAGACA
GAACCATCCTGTTCCTGAGAACTGGTCACTTGCTTTCCAAGATCCATCAATAAAACACCGAAAGCCAGAA
AAAGTTGTATCTTGTGATACATCCCTCACCCGAATTCGACTATCTATAGACAAGGAACCATGTTTTTCAC
TATGGAGCTCGACTTGAGCTTCCTGCCACGATTGAGCCTCTTTTACCGATAAGAGCAATATTTCCATTGG
ATCTTTATCCACATTTTCAAAAACTTTTTCATTTCTTGCTTTCCATATATACCAAATTATCCATGGGTAA
GAAGCCGAATCGACGCCTGAAGGAATTCTCCAAAACAAATGATCCAAATTCGTAAAAATTGAATTCGAAG
GAAAAATCCTTGGGGCCGTAGGAATTTGTGATAGTGCCCAAATCTGCCTTGCAGGATGGCATAGAAAAGG
TTTATATTTTAGTTTTAATATAAAAAAGAGGGGAAAAGAGTATTTGCAAGTTGCAAGTTTTTAAAATATA
CATTAATCAAAAGACTGACATATAATTATTGCACTTATCATGTGACAGTTACGCTGTTAATCCCACATTT
TTTTTTCTATTTTTGCTCTGTTAAATTCGATAGTTCATTATTTATGTCGAAGCAAACGATGTAAAAATGT
AAACCACATATAATGATTTTGTATATAGGAAACTTCGTAGGAGGCGTAGATAAAAGAACTAGACAGCTCC
AACCAAATACTCCTCCTCCTACTTAGTAATTTTTTTTGCTAAATACAGCTTATTAGTTCGTTATAAGAGT
TACCAAGGAGTAGTAAAGCTAAAGTATTAGCAAGTTGCAATTTAGGATTTTCATTAATTAATTGAACAGT
GAAGTAGTGGTGGGCCAGGACATGTTACCAAACACCAACAACGACCAAATCTAAAATATGTGAGCTAATT
GGGCCACGTGGAAGCATTTTAATTACACGCGCCGTGCATACTTTTCAACCAAGGCACAGTTTCAACTTTC
AACTAAGGCCATAATATTTTCTGGCCATAAAATATTCTTTCAGATTTAGAGAAAATGTTTTTTTTTTTGT
TTTTTTTTTAAATTTTAGAGAAATGTTTGGTAACAGTTTGCTGAAATGATTTTGATTTGGATTGGTTGTA
TTTAGCCAAAGAATCTTGTTCATTATTTGTTAATAAAATAAAAAATCTCAAAATGAGGAAGAAAACAAAA
AGTTAGCATCAGTCAAATGGGGTTTGGACTCAAAGATAAAAGTGACAATATGCTGCACGTAAGATGTAGA
CTAAAAGTCTTATAGAAAACTCTTGACATTATTAAAATCGAAGCATCTTGATTTGATATTATCCTTGTTT
CCTTTTGTTGAGAACCTGACATCTTTTGTGGGGATTAGGTAGGACTATAGCCTCAAGGTTGATTGTGATC
ATTTTCATCTTTTGTCAAAGAAAGTGACCATTTTATTAGTTGTATCGTGTATGAATTGAAAATTATCCAA
CTTTCTCTTCTCGGACTTCTCATCACAAATTTACCGTTTTTATATATTGGACCAACATAAAATAGGGAAA
TTTTACACAAAAAAGGATAGACATAACATTTTGGTAGTTGTATTAATTGAATTCATACAACTTTATCTTC
TCTAACAACTTCGTATCACAAATCCACCCTTTTTATATAGAGAGAGTACATACATGAAGTCACACAATCT
GATCAAAGTTTACAAAACAAGATAGACATAACTTATATTTCTACAAATTTGGAAAAGTACTAAAAGGTGT
TCTTGGTCTCATCTATTGTTATCATGTTCTTGAGATAGAATAACATTGGTGAATTTTCTTGACTAATCTG
TGTATCATCCTGTAAACGAAACTAGCTCTTTTCTTCTTGACAGACTCTTCACCCAATTTATGCTCTCGAA
TCACAGTCACTTGACCCGGACCTTGGCTCACCTGCAAAATATATTAAAGAACCAACCATTTAAATAATTT
CTCTAATCTGGTCTCAATGTTGTGAGTGGTGAAATTAACAAAGTAACATGATTAGCATTTAGAGTTAAAT
GAGATAATAAATCTCACCTCTTGAGTTAATGACACTAGCTGGACTGTTGAGTCAGGAGAATGTTGAGTTT
GGTCTATCTGATGATTTGAGCTAGCAAAACTAGCACAAGTGCTCGAAGTTCCAATAGAATTCTGTCATAT
GAAACAAAAACTTTAGCTTTCTGATGTCAAATCTGAAAACAGAGGATTATCAAGATGCAGAGTAAAATTT
TGCTTACTGTTTTAGGAGATATCAAATCAGAATCATTATCATCACTGCTATCATCACTGAAGACACCAGT
TAACGACTTTAGAGGTGTGTAATCGCTGCGATGATCTTGCATAAACATGATATTCCTCTGCTCATCACCA
TCATTATTCAACCATGTTTTCCATTCCTCCTCAATCGGTGTAGTTGCATCATCGATTTGAGATTCTCCCT
GCACATTAGCAAAGACACCAGACTGACTTGAATTCTGTAATTCTTGGCTGTGAAACGACGAACCCTGAAA
AAGGGGAGGAACACTAATGTCAGATATTTCAAAGTTTCTAAAGACAAAACAGAGAAAGTTTGAGATTCTC
CCACCTCAGATCCTCCAGAACTGTTCACAAGAGGGATTAAAGAGTGAATCTGTTCAATTTCACTACCAGT
AGAAGAAGAAGAGATCTCTGTCTCTTCACCCTTAAACTCAACTTTGCAGACTGTATACGTCATCATCTGT
ACAAATAATCAAATCAAAACACGATCACCACCACAAAACACCAGAATTAGGTCAATTAACAAGAGAGATA
GAAAAAACCCTAGGAATCTGGAATTAGGTCAATCAACAACAAAAAACCCTAAAAGTTTGGAATTGAAAAA
TTACCTGATTAGGAAACAAGGACGTAGCGTGATACTCGTGCATAACCCAGTCGGTCTTTGAACCATCTCG
ATTCTTAAAAACCAAAACCCTTTTCTCACCGATCTTCTCACGATTTCCTCTTTTGCGCATGACAGTCATT
GTTTTTCCAGTTTTCTTCCAAAACCCAGAGTTTGTTCTTCTTCTCTGTTGATCACCTCTGTTATACTTCA
TCTCCTTAACACTAAAGAAATACCAAACCCCATCTCTCGATTTGATCATCGACTTGGCTGTGAAAAAAGA
GGGAGAGGAAATCAGAGCAAATGATTTCGAATTCGATACAACAGTTTGGGAAAAAATAACTCGACTTACA
AGGTAAATCCCAAGGCTCGAAGCTACAGATATCGACTGTGCTAATGACTTCATCGACATGGCTAGTGTCA
CTATCGAGATTTTTTGGCCGGAGGTAATGGTCGACGATCTCCTCGTCGTTTGGACGGAATCTGAAACCCA
CCGGATTCATCATTGTCCGAGAGCGACTAAAGTTTCAGATAAAAGACAAAATTGGTGAGAAAAAGTCAAA
ATATGTAGCAGAGAGGTTTCGCCATTAACGATGCTCTGCAAGTTATGTGTGAGTTTTTTTGTTTTTAGGA
GGAAGACGAAGTGTGTGTTTATAATTTTTTATAAAAAGGCTGTGACGGGAGTAAGTGACGTCAACTATGA
CCAGATGATGGGACCCACTAAGTGGATGACGTCATGTATGATGAAAGCAGGACACATCACACCAAGTTCA
CATGGCGGCGGCTGGCACTTATCCTAATGACCCCACCATGATTTTTCCAATCCCCACACACTTGTTTTAT
TTGTTTACACTTTCTGACAAATTCTCTAAATACTCTTTTTCATTCCGTTTTATTTTACCGGATTAATGAC
ATTTTCACATTCCGATTTAGTATAATTTTTAACACGTTTTATAGTAAATACATAGTAAAATCACTTTTTT
TAAAAGTCGGTAACGTGGAAAATAATAAAACAACTGGTAAAGAAAGATAAAATTTATCAAATTGAATGAT
GACGACCGTTAAGACGTTCAAATAAAATAAAAGTTATGATTAGTCTAATGGCGGGTTTTGGGCTTAAACA
TCTAACATGACAAGATATTCGCGTGGCACACATCTATAAAAGTCCAAAAGAGACTCGTGACATTGCTAGA
ATTAAGATTAAAGCATCTTTGATTTGATGATACTGTTATTTTATTTTGTTGAACGAAATCTTTTGTGGGG
TTAAGTAGGACTAGCTGACTAGATGAGTAGAGGTTGATTGCTACGAAAAATTGTCTATTTTGTTAGGTTG
ATTGCTACAGCTTTTGATATCCATATTGTATCTCTAGTTTTCTTCCATTAAAAAGGAGGGAAAATCCGAA
TATTTTTCGGGGATTCTAAAATAAAACAAAACAATACATAATTATGGGAGTTATTATGTCACGTTACTAC
CAAAAAAAAAAAAAAGATGTGGTTTGACCATTTTGTTAGTTGAATCAAATGAAGTGATACATCTTTCTTT
CCTCTAACCACATCTTATCACAAATTCACCATTATATTTTAATATATCTCAGGGCACACATACAATGTGT
AAAAGTTACAAAACCAGATAGACACATATTACATACTACTACAGATTTTGGAAAGTACAAAATTGATATC
ATGTTCTTAGGTGAATTTTCTTGACGAATTTTTGTATCATCCTGTGAAAGAAACCAGCTCTTTTGTTCTT
GATCGTCTCTTGACCCAATTTATGCTCACCAATCTCAGTCCCTTGTGCATCATTATCAATACCGGTTCCC
GGTGTTTTGCTCACCTTAAATCACATCATAGAACCCAAAATGCTGTGAGTACTGGCACAAAGTAGCTTGG
TTAATTAGCAGTTTAGAATGGTTGGTCTTTAAGAAAAGGAGATGATAAAGCTCACCTCTTGAGCTAATGA
CACTAACTTGATTGAGTTAGGAGATTCCTGCAAGTCAGTGATTTGGTATAGAGGATTTGAGCTACCAAAA
CTAGGACAAGTGCTTAAAGTTTGAATGGAAATCTGTCGTATTAAACAAAACTATAGCTTTGTGAGAAAAA
ACTGAAAACAGAGGAGATAGTAAAGGTAAAATAGGAAAATTTTGCTTACAGTTGTTGCAGAAATCGGATC
AGAATCACTACCATCGGTGCTATGATCACTGAAGACACCGGTCAATGGCTTTTGAGGTGTGTGGTTGTTG
CGATCATCTTGCATAGAAACAATCTTACTCTGCTCATCGTCATCATTAAAGAAGCCTTTGAAATCATCAC
TCAAAATATTGCAGAAGTCCCTATCTAGTGCATCCACATCAAGAAAGCCAGAAAACTGACTTGGATTCTG
TGATTCTTGGCTGTGAAACAACGATCCCTGAAAAAAGGAACAACGTAACACAGATGAAAAAACTATGTGT
ACGAGATATGATTTTGAAGATTTAAAAGAGAAACAGGGAAAGTTTTTGAGATTGACTCACCTCTGTCTCT
ACACTCAAAACTCCAGAATTGTTGGTAGGAGGGATTAAAGAGTGAGTATGCTTAATTCCACTACCAGTAG
CAACTGAAAATTCTCTCCTTTCACCCTTAAACTTAACTTTGCAGAGTGTGTATGTCATTATCTACAGATC
AACTCAGCATAAATGATTACCATAAACTCAGATTTTTCCCGTTTACGAGAAATAAAATCACGGTAAGAAA
ACAACAACAACAAGTTAAAGAAGCCTAAACAAGAGAATCGAAAAATGACCTGATTAGGAGACGAGAACGT
AGCGTGATACTCATGCATAGCCCAATCGGACTTGGAACCACCGTGATTCTTAAACACCAAAACCCTTTTC
TCACCGATCTTCTCACGATCTCCCGTTTTGCGCATTATATCCATGGTAACGCCAGTTTTCTTCCAAAAAC
CAGACTTGGTTTTTCTTATCTGTCGATCACCTTTACCATATTTGTTCTCCTTACGGCCGAAGAAATACCA
AACCTGATCTCTTGTTTTCATCCTAGAATGGGCTGGGAAAGACAGAACATGATCAGAAATTACCGGGATG
ATACAACAGTTGGGAACCAAAGAAAAACAAACACTCGCGTTAGAAAGACTTACAAGGTAAGTCCCAAGGG
TCGAAGCTACAAATATCAACTGTGCTAATGACTTCATCGACATGGCTCGTGTTACTTTCGAGATTTTTCG
GTCGGAGGTAAATGTCGACGATCTCCCCGTCAGTCGGACGGAATCTAAAACCCACCGGATTCGCCATTTT
TCAACAGCTACAAAAAGGTTCAGATCAAAACTAAGAGAGGGAAAGATATCAAAATATGAAGTAGAGAGCT
TTCTCTATGGTCGCTCTTCGCCCGCTCGTCTACAAGTTTATATCATAAGAGCAAGTCCAACAAAGGGATT
TAAAGCATATCTTAACTGTTGAGAACCAAATTTAAAAAACTACCGCTGGTCATGCTCTAAGCAGGCAAGA
TGGGTTTGTGCGCTTATATAAGGCACAATAAAGGAGATCCTAAAAAAAAAAAAAAAAAAAAAAATTGAGA
TCCTTGGTAGATTTCGTCAACTATTTTACGGACAGGTTTTGGACCCCATAATGCAGATGTTGGGTCACAT
AATTTCTTTCCTACCAGATCATCTTCTTGATACCCTACCCACTTAAGTCAAAGTGCGCTTAGTCATGTGA
TGTGACAGTTACTCCTAACGTTAACGTCAATGGTTAATTTATCTTGAAGCTTATATAAGATCACAAAAAG
TAAACCACATTGAAATTTGTATATAGGAAACTTCGTAGAAGTCGTAAATAAAAAGAACCAGCCACAAATA
TAAGGATTTGCCGAGTATGGAACATAGCATACAATACAATGTGAATATTAAATTACAAAAGACAAAAAAA
AAGAGGGGCGCTTACATATACATTCATAAATTCCTCAGCTCTACATACACACATCTGCGGAGTAGAAGAA
CCACTTCAACTTGAAAAATGCTATACCATTTTCTTACTTATATAGGGTGTGACTGATAAAAAATGGACGA
AATGAGATGAAAAATAAACGAAGAAAAGTGAAGAAAAGAAAAAGCAAAAAGCAGAAGAATTTTCTCTCTC
ATGTATTTGAAGTGGGATGAATTCTTCCTTTTCACGTTGCTTTTTGAAGAATTGGGAAGAAACAAAACCA
ATTACTTTTTATTGCTTTTTGAAGAATTGGGAAGAAACAAAACCAATTACTTTTTATCTGACTGGTTACA
TTTAAGTACAACACAGAAGAATTCTTTTTCTTCTCACTATTTTTCTTCTATAGAAGACTACCAGTCAGAC
CCATAGTTGTGATACTGTTTGTTTTTCAATGATGCAAATATGGATATTATAACTATTATTAAATTACATA
AGTGTGGAAATAAAACCTAGCTATAAACACTGGTTCTTGAAAAAAGAAAGCATATATGCAGAGTGAGCTA
TGATTTACTTGATAAGGAAGAGACCAATCGCAGTGACGATGAGTGTTGAAGGCAAACCGAATTTGAAATG
TTTAGTGAAAGTGAGAGTGTATCCATGGCTCACTGCTCTACGAGCTTGCTCACACACTATCAGGTTTGCT
GCTGAACCAAGCAACGTCAAGTTTCCAGCCACTGTGCTCACCCACGCCAGCAACAACCACGCCTTCTTCT
CCTCCTCCCTCCCCATCGCTGATGCCGCCACTCTTGCTCCCAACAAAAGCACTACAAACGATTAAAAAAA
AAAGAAAAAATAATCATTCGCATGGTCTTGTGGTTCCTTTTGAATCAAGAAATTGTTCGTGGAGCCAACC
ATACATGTTTGGCTTTAAAAATAATGACATTACCGGTTGGTACATTAGAGGCTACATTGGAGAGGACAAG
AATCACAACTGCTAGAACCGCGATTCCTTTGGCTTGATCAATTTTGGCATATGGCTCCATTAGGTCCCAT
AGAGCGGTAGGGATACCAGTTTTGTTGAATCCATCAACGGTTATGAACATCCCGCAGAAAAAGATCAAAA
GCGAATACGATACCTGCAAAAGTTACAACTTTGATAAGATCTTTGAATTGTATCTCTAAAGAGTTTAAGA
AAATTTGGTTTTCACCTTCTCGAGAGACGGCCTTGCGTCTTTGAAATCAAGAACCACGAGTGCTAGAGCC
GCGGTAATTGCGGTCCACGACATGTTTAAACCCATAAGCAGAGATATTAGCATTCCTAATGTGATGAAAT
AAACACTTGATTTCCATAAAACTCTTCTCCATCTCTTGGTCTGGAACATATTGTTGGTATTATTGCTCTC
TCCTTGAGACTCTGCGTCGTTGTGTTGTTCTCTCGACGCATTTGAATTGCAGCTTATTAACTCGCTCTCA
CCCGCTGAACCCGCTCTGTTTCTGAGAGTCTCGGCGGCATCCATTCTCAAGTTCGAATCTTCGGATGAGA
CTGGCGAAAATGTAGCTGGCGAGAACCTATGAGATTGGACATCTTCTTGGGCAACAACTTCAGAATCAGC
ATTTTGTACTTCTTCTTCATCCTCTTTATGATCTGACAATAACCGCCAATACATACCGAGAAGAAGCATA
GCGTTAACGGTAATACCAACAATCATCGCAGGAAAAACACCAAGAAGAAACTCCCAAAACGGGATCTTGC
TTTGAACCGCAATAACAAGATTCTGCGGATTCCCAATGGGAGTAGCAGAAGAACCAATATTCGCACTCGT
GGCTAAAGCGAGCAAAAACGGGTGAGGCGGGAGATTCTTTTGCCTAGCGATCTTCAACACAAACTCGGTT
AAAACCACACAAGATGTATCGTTAGTAAACAGAGCGCTTGAAACAGCGGAAACAAGACAGACTCTACATA
GCAAGTCTTTCGGACCTCTGCTTTTCCACGAAAGCAATGTGCCTAAGTACTTGAACATATCAGCTCTCTC
AAGGTATATACTAACAACCATCGTTCCAAAGAGAAGACCGAGTATCGGGAGATCAATGGCTGCATAAGCT
TGTTCCGGGGTTATCACTTGGAAGATAACCATTAGCATTGCACCGAACAGAGAACCGGCGGTTCGACCAA
TTGGTAGGAATGGTACAGAGGGAAACACTGCTAATATCCAGAAAATGGCAAAGGCAACTGAACCTAAGAC
CAGCTTTATTACTGGAGCCATTGCCATTTTCTTGCAAATATTTCTTGAAAGCTCTCTGATCAATGATCGA
AAAGCATGGACTTTGTAAACCCTAGTTGGTGATTTTGATGAATCAAATATCTGATTAGAAACCCTAAGAT
CTCTGATAAACTTGAGGACGTTGACCGATTCCCAATAGAAGAATCGTCCTGTTGAAAAAACAAGAAAAGG
GCAATCAGTTACGAATTCAGAACGACAAGTATTGGATAATCAAACAAACTTGACCAGTTTCATGGTTAAA
CATACAGTTTCTTAAGGAGGAATCGAAGGCAAATGAGTGACAAAAATTGAAGCAACTACATAGATAACAC
TCAGAGTAAGCGAGGACTCATCTTTATTATATTGTCCCGAGTCCCCACGACGAACTTCACCAAACCAAAA
AAGTCAGCCCTTTTCCAATTTTCTTTAGTTTCCAAAAAGTGAAGACAAGATACCGAGAAGAAGTCTCTCT
GTTGTGTTCGCTGTTTCAGATCTTTCTTCTTCCCCTTTTTCAATTTTCATGAAATTAACAATTTGACCTG
CCACGTCCTTTAGATTAATTAAAGTGTTTTCTTTTACATAACAGCCAAAATTGAAGTGTTATAACGAGTC
AACAAATCCTACACGATACTGTATTTTAAAAATAATTAAAATTTAACTTCATCTTATTGGCTTAACATTT
TAAATTTATCACTTTTACTCCACTAAAATTTGATTCATGAAAATAAATAAAAAATCTTTAAACAGACAAA
ACTATACAGCACACTCCATAAGGTTCGTAAAGATGTCTCATTGCAAATCTCAATCTCATTGCTTCTTTAC
ATTTACAAGAGCCGTAATTAAACAAAATTTAGCTACAAAGCATTTTGACTGGAGAGAATTGTACGGTGAG
ACAAGCATGATCGGATATATTGTAATTCTCCGGCCACAATCCTTTCTCTGCTTCTTGTGGAAACAAAATT
GCTTTATTCACTTTCAATCCGATTGCTTCATCTTCTCCTTCTTCTTTCTTACTCTCCATCACACTCTCTT
TGCAGTTTCCAGGTTGATTTACCATCGTCATGTTCCAAATTTTCTGACATTACATAACACAACACATCAG
AGTCTTGATTGACGTTTTAAACAAAGCTACCGGTTTGTGATTTCTGTTATGTACCAATTGGTTTAGTTTT
ATTTACCTTAAGTTCTTCATAGTCGAAGACACCATTTCCATCAAGATCAGCTCGGACCCATAGCTCTTTT
GTCTCTTCGAAGCTAAGTCCATGTGGAATACCCGTTAGATTTACCTACCACACAATATCAAATTTTGTTG
TCAGCATAAAAGTCCATTCGTCTTTGAAAGAATTTGTAAAAATCTGGAAGAACTTATTTGATCCTTATTC
TACTGTTATGATAAGTGAAATCTCTAGATGATCACAAAGTTTTTTCAGAAGTGTCAAATTCCAATTAGAA
TGTGCAAATCTAAGATTTTTTTATCAGCATTTGTGGAAAATTGAGGTCTACTTTTTCCTGAAGAGAATGT
ATTTACCTTTTGAAGTGCTAGGCAAAAGTCAGAGTAGGTTAGTGAATCACTGTGATTTTTTGCCCCAAGA
AAAGTAAAGGCATCGTCCTCGGCTATGGAAGCTTTGTGTAGTTGATACTGGAAGAAACCATCAAGAGAAA
TCAGAAATAGACAAAATGAACATGAAAATATCGTTTAGGAAAAAGTAAATTTGGAAAGAATGAGACAAGA
CATGGTAAGTATGATGTGACTTTAACATTTTGTAAAGGTATAGTGCTTAATATCTTAGTTTTCCGAATAT
CTCACCTTGATAATGCTGAAAACAGCTTCCACCCAACTTGTTCTCAATGGTTTTCTTGAATCACTAGGGT
TACAGAGCCATATGAAATCAACTCCGCAAATATTTCCCCTGTGGTTTCTGTGGCTAACCCACTGAAGAAA
TAAATGGAAGAATGACGGATAAGGATGTGTCTTTTACAATATGAGGCGTTTTAAATAACAGAAGGCTGGA
GGAAGTTTTTTTGAAGAGATGTTTACCCTATGAGCATCACTGTCGGTATACTGATGAGCATCATCGTATG
ATGAAATAAACCCTTGAGATCTCAAAAATTTGTAGACATGCCCGCGTTTGCTTCCATTCCAGTCACTGCA
ATAAGCATAATTCAAAAGTCTGTGATTACATTGAACTGGCGGATGGACACAATATCAAGACTCAAAGACT
AGAAGCTAACCCGCAGAGAATAATGGGCATGTGATTAAGTTTATTTTCCTTTTGGTAAGCTTCCAGATAT
TCAAGAATTTTGTAAACCTGTGAAAAGAAGCAATCAAATTAAACTATCACAAGATTCAAGGTGAACGGTC
TCAAAATGCAAAATGATGGAAAGGATGACCAACCTGATGCAGTCTTACAATAGACAAACTAGAATCGTGA
GGAAACAAGAGGTGAGTGTTCACTATAATAACTTCTTGTTGAACGTCTTGCTTTCCATTAAGCGGAAAGG
GAATAACTGTTTTGACATGTAAGAGCTGAGCAACACGGTCTCCAAAATCGTTAAAGAGCAGCTCCCGGTA
ATTTACAACTTTAAAATGGTCCTTATGAATGGCTGTTAAAAGACCTGTAAGAAAGATATTCAAGTCCACA
AATGAGACATCAAAAGCGAAGAAGCCTATCTTTCATCGCATGCGATCAGCTAGAGGAGTCCAAACATATA
GCATTGACTTTGAATTTTAGACAATATTTCTACTCCATCCATAAGATTGCCTTTTAATACGGCATCCTAC
TAACAACGACGTTAAGATCATATAAACACCAACAAGAACACTTTGACACCAGAAAGATCCTGAACTACCA
GTTTCCAAGTCATGAAAAGGTATAGATTTGGACAACCCTACACTATTTACTGAAGCATATCAAGCAGTAA
CATTGAGCCTCTTAACTTTCTAATGACTCTGGACAGAGACCATATTCAATCAAAAACATGATAAAAAATA
AAGAATCTTACCATCACCACGACTGTTTGTTCTAGCCAACTGATAAATAGTGTAGCCTGAAGATGAAAGC
TGGTGGTGGTACATGTTCACTAATTCCTCATTCCCAACCCAAACTTCCTACGAACAGTCACAATTGCTAA
GAGTCAGCTTAACAAAAAAAAAAAAAAGTCAAAATTTGACTCTTTCTAAGAGACAAAGTGTGTACCTGGA
GACAGATAACTGAAGAGCGTTGATGGAGTAACAAATCTAAAATCCTCTGGTTACGAGCTAACCAAAGCGT
GCGGAAATCGCTCTCTCGAGTGCTATGATTCTGTTAATAACACCCAACACAATCAACCAATGTCGTCGAT
TCCAGAATCAACAAGGTAAAGAGTGAAGAAATCAGAAGAATAGAAGCAAACCTTTTGATCAACGCGTTTA
TAAATCGGAGCCAAGATATTGAAAGTGGTACAAGAAATATTCGATTCCACCATTGAAGAAGCTAAGTTGG
AGTTGAGTCTCTGCACAAACAAACAAACACAATCGGCGAATCAAATCTCAGAACAAACAAAAAAAAGAAG
GAAAGTGGAGGAAGAGCGACGACGAACCATAACTGAAAGCGGCTTGTTGTTTCTGCCGGAGAGTAGACCG
GAAAAGTAGATCGGAAGAGGAACAGCAGCGAGGACGACGAAGAGGGAGAGTGGTGAAGAGAAGGAAGGGA
TGAATCTAGACCGTAGAATCAAGCTCAGCCTGCTTCGATTCTGATGGCTTTGCATTTGAGTTTTTCTTTC
GAATTCTCTCAACAGATCTTTTTTCTCATCTTATAATGAATTTCTATCGGATTTATTCTTTTTGGCAGTA
CTTGATTATTATTATTATTATTATTTTATTCATAAGTTAAAAAAAAATATGAACCGTTGGTTTCGTAAAT
ATCTAATTTCAGTGAAATAAAGACAATGTAATTTCTTCATAATTGCAATGAAATAAAGAAAAATTAGTCT
ATTGACCAATGGTAGATTTTGGTATTTTTGTTTTGGCCATTCATGGAAGTTTACAACGATCATAACGTTT
TAAATCGTACTTGTATTTTTTGTAGATTTATGAGAAAAGGTAAGTACAATAAAGAGTAATTGCAGGGAAG
AAGAGGGATATTAATGATTGGAGAAGGAGAACCGCGTATCAGGCTGGGCTATGTCGGTTTCTCATGACAC
GGTCTTGTTGTATCACACCGATTATATATTATCGTTTTACAGCAATGTTTATATCATGCCTACAAAATAT
AGGGATTCAAATTGCTTAACCACGTTGTATTCTTCTTCTTCTTCTTGTCCAACTTTTTCTACGAAATTAT
AGCAAATCAAATTCATGCTATTTATTGAACGCAAATGTTTAATTTTCAGACAAATCAGATTCTTACTTTT
GCTGTTCAAACCCCAAAATTCAATGAAGAAATTTTATAATATTCATCAGATACTGAGCGGATTTTAAGCA
AAAAACCAAGAGAAGTGATAGATACTGAGCGAGTTTGATATGAAGATTATCTTGGCCGGAGGTTGATTAT
CGTCTTTCCAACGAAGCAACTGCAACACCATTATATGGATATTTGGTGTCTCGTCATCAGAGTCGTGCCA
ATGAATTTTGATGCTATAAACAAAAAAATATAGTTTAATATTTTAATAAATAATGTAAACATAACAAAAA
AATTATTTATTAAAATATACACATAACAAAGAAGACGGAAAGCTCCTCTCTCACAAGCCAGGCTATCTCG
CCACCTGCTATACCTTTGAATATTTCAAAGGTCTTTTTTGAGAAGTATTTCAAAGGTCCGTCTTCTTGAC
ACTACCGGCGACAAGAGACATTTTTACAACGAAAGAGTTCGATAATAGAAAGGTTAGTAAAAAAATAAAA
ATATTCTTTGTCGTAATTATTTCAAAGGTCATTTTTGAGAAGTCAATAAAACTATGTTTTGTTTTGTTAA
CAACATGCATTATACCGTTTGATTGATAACATAATAACGACACTAGCACATTTTACTAGTTTACACATTA
TAATCAACCTAATCGTTTTTGGTCATATTTTTGTTCTAAATTATTTATGTTTTGCTTAAAATTTGCTTAA
TTTATTATTAAACTTTAAATATTAATTATTTTTTTTGTTATGTTTATAATATTTATTAAAATATTAAATC
ATATTTTCGCGTATGGTATCAAATTTTTTTGGCACGTTCTGTTTGGATGTTATGTCACAAAAATTAAAAA
TTTAGTACTTACAAAAAAAACAAAACATGGTTGAAAAAATCTTTCAATCAATTACTAAAAAAAAAAGTAA
ATGAAGAAAGCAATACCTCATGCAGCAGCTTGTGATATGATCCAAAAACAAATCGGGACAGCTAAAGGTC
TTGGCTGGTACAAGCAAAAACTCGGTCTCCTTGAGCCCATCCAGCTTCTTTCAGGTACTACAACATATTA
AAAAGATTGCACATGTCAAAATGACTATTACCATATCCAAATTTCGATTGTTTCCTACTTTCCTTTTATC
TTCAACAGTTGTTTCCTTTTTCTTATTTGAGAACGTTCGAGAAATCTGGACCGTCTATTTTCATCATATT
GCAACTGTGAGATCTGATGGTGATTATCTAATCTAAACGGTAAGTTTGTTAGATTATGTGGGACCGGGAC
GATCTATTTCTTAAACCTCTGTTACAAACAAACACTCATGTCTATTAGTATTAGGAAATAAGAGATGGAT
ATGATGATGATTCCGAACCAATTCTCAATAAACTGTTTATAATGGAACAGAAGCAGCAGTGATTGATGAT
CTAACAGACATTGACATCAGGCTACCAATGCTAGTCTTCCTGTGGGAGATAGAAGCGGCCTTGGTTATGC
CGAGTTTTCTGTTGATCTGTGTTTATGTAATCACCCGAGGATGCAAACAATTAATCCCATCAGCTAAAAG
ACTTGTTTGATTCAAAACAGACTTTAGCAGATCATTTGTTTTTCTTATCTACAGAACATAATATATTCTT
TTTTTGGTGATATTATGATTGGGAAACATCCATTTCATTTAACCAGAAAGCATGGCAATCTTTTCTTTGA
ACAAATCTCCATAAATTACAGACAAAGATAAAGCCGGAAACAAGAAAATGTTGCAGATAAAATCTAACAA
AAGAAAGAACAATCGAAAAACTCTTCTTCTCCTTGTAATTTGCTCACAACAAAACCTCTTCTTCAGAGCC
TCTTAAAGTGGCTTTCCACTTGTCTTGATATCATTTCTGATTGCTCCTTGAATCATCTTAACGATCAAAT
ACTGCAAAGTAGAAGAAAGGATTTCACTTGTTTACCAAATTCGAACAAGACAATAAATCAAACTGTGTCT
CTTTCTTACCTGAGCGCCTATGATAAGAGGGATGAGTTTCTTTCCTTTATCATCAGAGTAAGATCCATCT
ACCATCTTCTTGTCTACATGAATTGCTTTCCTCTGGTTTGTTGCTACATCAGTTATCGCCTTAACCAAGT
TCGGGATCCACGCTTCACCATTTGGAAGAGCCTGAACCGAGAGCAGGTAAGCAACTTTTAACAGTCAGTC
TCTCTCCAAGTCGGATCAAATCAGAGATTCGAAAACACAAACCTTTTCGTCCTTATCGTTCTTGCTGCAT
CTTCCGCTGTTCTCTGCATAGACTACCGCGATTGCAGAATCCTACAAGCCAGTAAAGAATGAAACTGATT
CTTGCTACAATGAACCAAACATACATTGGTATAACAATTTTCGGAGACAGGTATATGTATAAATAACCAT
ACCTCAAACTCTTGTTTTCGCATCTTAGAACCAGCCCGGATAGTTTTGAGGAGAGAATCTGATCTCTTGG
AGGAAAAAGTTTCGTAGGAAAGTTCATCGGGAGGGGAAAATTGAGCATGAGTCAGAACAAGCAAGGTTTT
GCACCATATCTCTTTTCCAAAGGTTTGGGTGATTGCTATAACAACTTGCTTATCTAGCTCATCGACTCTA
TACACATCCAAACGATCAACATAGAGCAAGACATCTATTGTTCTGTTCACAAGAAACCTGTCCAAAATCC
GAGAAACACAACAACTATCGTAAAACTTCCACACACACTCCAATATACAGCTTCAGCGTAAACCAGATAC
TCATAATTCACAATTTCAACAGAAACCCACAAGTAAACATGTTAACCACATATATACTTAGCTTAATTAA
TTCAAAAACGAATGAGATAATCCTATATGCAACAATCAACGAAGAGATATTCCAAAAGAGTAGCTACTGA
CCCTTTGATTAACTCGAGAGCTTGGTGATTGACATATCCAGCTTCCACAAGTCCAGGGGTGTCAATAATG
TTGATAGTGAACCCTCCCATTGTTCTTGAAACCATCACTGGTCTCAATCCTTCAGCCTACAAAATCAACA
AAACAGAGCCATCAAATATCTTGAAATGACTACTCTTTCTTAATCCAAATTAAAAAAATCAAGCTTAGGG
AAACTGAATTACGTACTTGGAAAGGACTGACACGGACGACTTGTTCGCCGATAAGAGAATTGACAGTGGA
TGATTTTCCGACACCGCCTTTACCCAGAACAAGAACTGTCATTGAGTTCATATCCTGCAATTACAAAAAC
CTCCCATCATTATCTCCTAATCACAACGGAGAATCCGAGAAACCGACTTAAGCACCAAAGAAACAGGAAC
AACAACAACAAAACACACCTTTTGCTTCAATTTTCCGAAGAATTCAATCAGCTTTTCCTGGGTAGCTGCT
GGAAATTGCTGAAACCCAACCCATTCACGAACGAGAGACCCCATCACTCCTAAACCCTTCAGCAAAAAAA
TTCTTTTGGTAAATAATCGCTGAGTGATGACGATGATGATAATTAATTTCGAAAGCGATAACGTTTTGGG
AGATTTGGAGGAGCTTACCGTTGTGTGAGGAGCGTTTGAGGTTTTTGGAAGAAGCTCTCTCGATGTGTTC
CGCAGAGAAAAGCTAAAGAATGTGACCTTATCGGTAATTTGTTTAATAGTTCAAATTATTTTCACTTTTA
CTCCTCTATTTCTTTAGTGTTTCTTTTTAGTGCCTTCAAATTTTGAAAACTAACAAACTCAACCCCAAAC
CAAATCCAGTTACCAAGTTGCAGCATTACACTTCATATTTTCATGGAAGACTACATTAGGTGGAACATTG
AATTAGCATAGCGTCACGGGAGCTCAAGCGATTCTCTGAACCTTTCTTCGCTTGTAAGTCAAGGAAAACA
AATGGTCACTATTGGCTTCTCGAGCATGATTGTCTTCGCTCAGGACCCCCAGCGGTTTTCTCAGAGCCTT
GGCTTCCCTCTGAAAGTTATTACTAGACGAAATCCTCTTGCTCTCTGTTGTTTCAGAGCCTCTGTCAACA
GTCCTAGGCTTAAAACCAGGAGACTTCAGGTGGTACCGGACATATTCTTCTTGCTTTAGAGGTATATTCT
GTTCTGTGATGGAGTAATTTGAAACACGGAGAGCACTGGGAACAGTGTGTGTTGGATCATGAAACACCGG
TTCTGTACCTTGGATTGATCTTTGTGTAGTTTCCAAATAGGTTAAGAAAGGGTCTGGGATAGAACAGCCA
AGAGTTCCGTAGGGTGGTTTCTCAAATGTCGTACCTAAGTATGGAGACGCTGCAAATCTAGTACTCTTTG
AACCGGTTTCATGGATTTGCAGGAGATTGTTTCCTGGAGCTACATAGGGTTTCCTGAGGATGGCAGAAGA
AGATTTAGGGACTAATTTGAGAACACCCTTTGGCAAAGTCTGATGATGATGGCCAGCAGAAACTAAGCTG
GAACCTTGATACCGGAATACTCCTTCCTTGGTTATCTTTATCTTGAGACTGTTCTTGGAGCTGCCACTGC
GAGGGAAGGTTAAACTTTTCGATCTATTTCTTTCCACGGGTTTCACTACATTGGGAGTTTTGAATCTACA
TGTAGCACTATCCATTTCCTTAGATGGAACTCTATTGAGGTCCAGTAGCTTGAGATTACCGGTTTGAGTT
CGTCCTGACCAAATGAGGAGCCTTGAGTAATTGCCCAATTTATTTCCATACTGAACCCACACCCTTTGCA
TTTCGGTAAATGTCCTGATCAGCTTTTCATGATAGAACTTTAAAGAGTAGTAATACTTTCTCCTCTTGAC
AAACATAACACCTTCTTTGAAACAAGCTACCTTTGGAGTAAACAATCCACCTAGCAAATTCTTGTAAAAC
TTATCCTCTGGATTCCCAAAATATAAATTGGCACCATCAAGAAGTTCCTGCATCGTCAAACTGAAAGTCT
GTGGATCCATATCTGGCAGAAAACATGAGAGGAAGAATCTTTCTTCTTCAGTCAGAAGTGAGTTCCAAGT
CTCAACAGACAATATTCCCGTTAAATCTGGTAGATCGTAGAGCTCGTATGGTATGTTACAGAGCTGACCT
TCAACCAAAGCTAGCTCACAGTTTACTTGCGCAATGTCGTAATCATCAGAGTCATCATCTTCAGAGTCTA
GCCCAACTGTTTGATTCTTATTCATCTGTAGTTAACCACTTACTACCCTTAAAACACAAGTACTTCAAAT
CTCCAACCACAAACTCAGTAGAAAGGAACACAAGCAGGAGATACCTAGATAGAAAATGTTAAAGACTCAT
CATCAGCAATTCACATTACAAGAATTCTACTACAATACAATGGACAGCGAGAAGCTGAGTATGTTACTAA
TCAGAAATCAAACGAACATAAATAGCATTTTACTCACTGATTTCAGCAACAACAACACTAAAGGCTATAT
AAAACACGAAATATACATTGTGAGATCAATGAAGCACTCAAAAAGAAGAAGATACACAACACCAGAAAAT
CTCCCAGATCGGATCAGCTACAAAGCTTAAACGTAATCGATCGCGAACTCAATCAATAACCAAAATCAAA
AGCTCCAACAAGGCAAATAACTAGAGAGCGAAAACCCTTGGATTTGACAACAAAAATGTGCAGACAATTT
GAATAAAAAACAAGTATCATACAAATCTCAGCACAAATCAGCTCCAATGAGTTTCAAAAACCTACCGGAA
CTAATAAAAAAAAAGAATCTCGAGATATTCAGAGAAATCGATCGGAAAGCGTAAAAGACGAGGAGCTTAC
CGGCTCTAAAGACAGGTGAAATTAGCAGATTAGGGTCGAAGAAACCATATCCCTTTGGCTACAGATACGA
ACTTCATCGCCTTCAAAGATTCTCTGCTTCCTTTCTAGAGATTTCTATGGCTTTTCGATCGATGCGACAG
TAGAGTAGAGACTAGAGAGACTAATTACTGTTACACTTGTATTTTGATTTCTTTAATTAAAGCCGCCTAA
AGTAACTAATGCCTTGATTACTTTAATTAATAATCATTTTTAAATTGTGATTTATAATCAAGTTAGACAT
TACTTCACAAATAGTTTGGGCCTGGAAACGTATAGGCCCATGTAAACTTTAATAAAAGAATCACCTTGCA
GGTAAGTATAATATCCTGATATTATTATTTACTTGATAGAATGGGCCTATAATAAAAGAAATCACCATTA
AAGAATTATAGGCCCATGATATCAAGTAAATATCAAGAAATGATGATTAATGATCAAGTTAGACATCATT
ACTTGATATTTTGGTAAGTAGGATCAATCAACGGTCAGGATCCTTTTAGTAAAATCATGTGTCATTTTCA
GTTTGTCTAAAAGATAAGCCTTTCACTTTCTCTCTCTGTCTTATTAGAAAAGAAAATTTGTACCGTTTCC
AAAGTCTGAGCCAATCATTGTGTTGATTCTGGAATTCTTTGTGGGAACGAGAAATTTGTACAAGGGAGAT
TCATCATGGCTGATAGTTGTTGTATCAGACTTCACTTATTAGCCTCTGTTTTCTTGCTCTTATTTTCATC
CTTCAACTTGCAGGTACTTTAAACTTTCGTAATCTGTGTGTTAAAATTGCTTACTAAGATCGATTTGTTG
GACTCTTGAGCTACAAGTTAAAAAAAAACAAAATAAATCAAACTTTGTGATTTTTTTCTCTGCGTATCAA
TCTAAGACATATGAAGGGGAAATGTATATATGGTTTTTTGTAATTGTTTCTATATCAGTAAAGTTTTAAA
CTTTTGAAGCTGGTTTATCTCTTAATCTCAGGGTATTGCAGCGGAAAATCTTTCCAAGCAGAAACTGACC
TCACTGATTCTTCAGGTTTTGATCTTAATCCACACAATTATCTGTATTGTTTTCGTCTCTTTTAGATTGC
CTAAACGTTGATGATCAACTTTTGCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGTT
GGAAAGCTGCTTTCAATGATCGGTTTGCAAATGCCACCGTGAGTTTATTATCACCTCCATGCTCTTATCT
CTTTAAGAGCTACGTTACTTATCATTGTTCCTGAAAGTTTGTGTTTTTGTGTATGTATGTGCAGGTTGCA
GAGTTTAAGCGACTCCTCGGTGTTATACAAACACCAAAGACGGCATACTTAGGTGTACCTATTGTAAGAC
ATGATTTATCGTTGAAGCTTCCTAAAGAATTTGATGCTAGAACCGCTTGGTCACATTGCACCAGTATTCG
AAGGATCTTAGGTCGGTTTTAATCTCTTAGCTTCCACTATCTCTGTCATTAACCCAATGATTTACTGACT
CTTCTTATGTTTTGTTTCAAATTATCTCCCTCTTTATTGCACTAAAGATCAGGTGAAACATCATTTCATT
TGAGTGGGTTATATATTGAACAATGTGTTACTCTGGTCGACGATAACTTTATGGTTTTGGTTTCTTTTGG
GTCATTGTGGTTCTTGCTGGGCATTTGGTGCTGTTGAATCACTGTCCGACAGGTTCTGCATCAAATATAA
CTTGGTAACACAACTTTCTCCATCAAGCCAAGATTGACGATTGCTACAGCTTTTTAATGTAATTGCTCTT
CTTCCCTTGCAGAATGTTTCCTTATCTGCCAATGATGTCATAGCATGTTGTGGATTACTTTGCGGTTTTG
GTTGTAATGGTGGTTTCCCAATGGGTGCATGGTTGTACTTTAAGTACCACGGTGTAGTAACCCAAGAGGT
AAATTCTCAGCAAAGAACAAATAATAATGGCAATGTGGTCAAAGTGTATTGAACTTTTGTAATGCTGTTG
GTTCTTCAGTGTGATCCATACTTTGACAATACTGGTTGCTCTCACCCGGGATGTGAACCCACTTACCCTA
CACCAAAATGTGAGAGGAAATGTGTAAGCAGAAACCAGCTATGGGGTGAATCAAAACACTATGGTGTCGG
CGCATACAGAATCAATCCTGACCCTCAAGACATTATGGCTGAGGTTTACAAGAATGGACCTGTCGAGGTT
GCTTTTACCGTTTACGAGGTAATGAAAAAGATTTTTGATTGATCAAACCATATTGATTATATCTTGGTGA
AGTCCACATTTTCATGTATCTTTTTGTTCTTCAGGACTTTGCACATTACAAATCAGGAGTATACAAGTAC
ATAACGGGTACTAAGATTGGAGGTCATGCAGTTAAGCTCATTGGCTGGGGAACTTCTGATGACGGCGAAG
ATTATTGGGTATGAATTCTCTGGATTTTGATTCAGATCAAGCTGAAAAAGTAATAACATTTTCTTGTTCG
TTGTTGCAGTTGCTTGCAAATCAATGGAACCGAAGCTGGGGTGATGTAAGTTCTTCTTTTCTCCAATCAA
AACTTTTAAATTAGACCTTCCAAGTAAACAAAAGCACAGAACCTGAGATAGAAAATGTGAAAATCTCAGG
ATGGTTACTTCAAGATCAGGAGAGGAACGAACGAATGTGGCATTGAACAGAGTGTTGTAGCTGGTTTACC
TTCAGAGAAGAACGTATTTAAAGGTATTACCACTTCAGATGATCTTCTGGTTTCCTCAGTCTAAACAAGA
CGATGTGTCCCTACTTCTGTAATATATCATTTGCAACTGTGTTGTAAGTTTAATATACCATTGAAAGAAT
CACCTTCAATCAAAACAAAAGTATGTATAGCTTCTGTTAATATTCAATTTTACATGTTACCATGCAAGAG
GACTGTTACAGTGTTTATTTGGTTTTGGTAAATTATAGCCACCTAAAAGTAACGCCTTAATTAATCATTT
TAAATTATGATTAACAATCAAGTAAGTGGAACAAATCAACGGTCAGGATCTTATCCTCGCAGTAATATGA
TCTGTCATTCTCTAACTAAAAAGATAAGCCTCTCTCTGTCTCTTCCTAGAAAAGAAAACTTTGTACCTTT
TCCAAAGTCTAAGCAAATCATTGTTTTTGATTACTGGAACTCGTTGAGGGATTGAGAAAAAAATAATCAG
AAGAGAAAGATCCATGGCTGATAATTGTATCAGACTTCTTCACTCAGCCTCTGTTTTCTTCTGTTTAGGG
CTTCTAATTTCATCCTTCAACTTGTTGCAGGTACTTGAACCTTCATAATCTGTGTTTGAAATTGCTTACG
AATATTTATGCATGTTAGTGCTTTCTTCTAGTTACGATCTGTTTCGTAGCCTTCTCGGGTTTTTCTGGGT
TTGATCATGTTTGCTTATTTGTTGGACTCTTGAAGCTAGAAGTTTTAAAAAAAAAAATCGAAATTTTCTG
GGTCTTAATCGAATCAATGAACGGGAAACATATTTGTGATATCAGAATTGTTTAAAGTTTTAAACTTTTG
AAGCTGGGTTGTCTCTTAATCTCAGGGTATTGCAGCTGAAAATCTTTCCAAGCAGAAACTGACCTCATGG
ATTCTTCAGGTTTTGATCTTAATCCACCCAATTTTCTGTTTTGTTTTCGTCTCTTTTAGATTGCCTAAGC
GTTGATGATCAACTTTTGCAGAATGAGATTGTAAAGGAAGTCAATGAGAATCCAAACGCTGGATGGAAAG
CTTCTTTCAATGATCGGTTTGCAAACGCCACTGTGAGTTTCTGATTACCTCCACCATTCCTTACATATAT
CCTATCAATGCTTATCACTGTTCCTGAAAACTTGTGTTTTTGTGAATCTATGTGTAGGTTGCAGAGTTTA
AGCGCCTTCTTGGTGTTAAACCAACACCAAAGACGGAATTTTTGGGTGTGCCTATTGTAAGCCATGATAT
ATCTTTGAAGCTT
genometools-1.5.1/testdata/U89959_genomic.magicmatch000066400000000000000000000001531211610345200222300ustar00rootroot00000000000000063b1024d68e26716b7f38caf958316f	gi|1877523|gb|U89959.1| Arabidopsis thaliana BAC T7I23, complete sequence
genometools-1.5.1/testdata/U89959_ginums.corrupt000066400000000000000000000000331211610345200215070ustar00rootroot000000000000008690053 1 10
-8689616 1 10
genometools-1.5.1/testdata/U89959_ginums.out000066400000000000000000000005741211610345200206320ustar00rootroot00000000000000>8690053 1 10 gi|8690053|dbj|AV529770.1|AV529770 AV529770 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL47a02R 5', mRNA sequence
ACTGTAGCCC
>8689616 1 10 gi|8689616|dbj|AV529333.1|AV529333 AV529333 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL34a01R 5', mRNA sequence
TACGGAATTC
genometools-1.5.1/testdata/U89959_ginums.txt000066400000000000000000000000321211610345200206270ustar00rootroot000000000000008690053 1 10
8689616 1 10
genometools-1.5.1/testdata/U89959_sas.gff3000066400000000000000000002667631211610345200201520ustar00rootroot00000000000000##gff-version   3
##sequence-region   1877523 1 106973
1877523	gth	gene	1074	1540	1	+	.	ID=gene1;Target=8721428 1 303 +
1877523	gth	exon	1074	1171	1	+	.	Parent=gene1
1877523	gth	five_prime_cis_splice_site	1172	1173	0.866	+	.	Parent=gene1
1877523	gth	three_prime_cis_splice_site	1257	1258	0.994	+	.	Parent=gene1
1877523	gth	exon	1259	1354	1	+	.	Parent=gene1
1877523	gth	five_prime_cis_splice_site	1355	1356	0	+	.	Parent=gene1
1877523	gth	three_prime_cis_splice_site	1430	1431	0.745	+	.	Parent=gene1
1877523	gth	exon	1432	1540	1	+	.	Parent=gene1
###
1877523	gth	gene	2779	3355	0.84	+	.	ID=gene2;Target=8732738 1 337 +
1877523	gth	exon	2779	2801	0.696	+	.	Parent=gene2
1877523	gth	five_prime_cis_splice_site	2802	2803	0.459	+	.	Parent=gene2
1877523	gth	three_prime_cis_splice_site	3041	3042	0	+	.	Parent=gene2
1877523	gth	exon	3043	3355	0.84	+	.	Parent=gene2
###
1877523	gth	gene	3025	3351	1	+	.	ID=gene3;Target=19837778 1 327 +
1877523	gth	exon	3025	3351	1	+	.	Parent=gene3
###
1877523	gth	gene	3041	3651	0.996	-	.	ID=gene4;Target=8732878 1 536 -
1877523	gth	exon	3041	3550	0.996	-	.	Parent=gene4
1877523	gth	three_prime_cis_splice_site	3550	3551	1	-	.	Parent=gene4
1877523	gth	five_prime_cis_splice_site	3625	3626	0.741	-	.	Parent=gene4
1877523	gth	exon	3626	3651	1	-	.	Parent=gene4
###
1877523	gth	gene	3077	3506	0.974	+	.	ID=gene5;Target=19843099 1 426 +
1877523	gth	exon	3077	3506	0.974	+	.	Parent=gene5
###
1877523	gth	gene	4768	5357	0.987	-	.	ID=gene6;Target=19871046 1 591 +
1877523	gth	exon	4768	5357	0.987	-	.	Parent=gene6
###
1877523	gth	gene	9505	10058	1	+	.	ID=gene7;Target=8682455 1 554 +
1877523	gth	exon	9505	10058	1	+	.	Parent=gene7
###
1877523	gth	gene	12024	12542	1	-	.	ID=gene8;Target=8688760 1 519 +
1877523	gth	exon	12024	12542	1	-	.	Parent=gene8
###
1877523	gth	gene	13014	13465	0.881	-	.	ID=gene9;Target=2748705 1 459 +
1877523	gth	exon	13014	13465	0.881	-	.	Parent=gene9
###
1877523	gth	gene	15955	16603	0.997	+	.	ID=gene10;Target=19878194 1 649 +
1877523	gth	exon	15955	16603	0.997	+	.	Parent=gene10
###
1877523	gth	gene	17165	17684	0.985	+	.	ID=gene11;Target=19798999 1 396 -
1877523	gth	exon	17165	17247	0.97	+	.	Parent=gene11
1877523	gth	five_prime_cis_splice_site	17248	17249	1	+	.	Parent=gene11
1877523	gth	three_prime_cis_splice_site	17372	17373	0.994	+	.	Parent=gene11
1877523	gth	exon	17374	17684	0.989	+	.	Parent=gene11
###
1877523	gth	gene	25221	26100	1	+	.	ID=gene12;Target=8690053 1 521 +
1877523	gth	exon	25221	25310	1	+	.	Parent=gene12
1877523	gth	five_prime_cis_splice_site	25311	25312	0.993	+	.	Parent=gene12
1877523	gth	three_prime_cis_splice_site	25508	25509	0.439	+	.	Parent=gene12
1877523	gth	exon	25510	25626	1	+	.	Parent=gene12
1877523	gth	five_prime_cis_splice_site	25627	25628	0.998	+	.	Parent=gene12
1877523	gth	three_prime_cis_splice_site	25711	25712	0.996	+	.	Parent=gene12
1877523	gth	exon	25713	25841	1	+	.	Parent=gene12
1877523	gth	five_prime_cis_splice_site	25842	25843	0.63	+	.	Parent=gene12
1877523	gth	three_prime_cis_splice_site	25914	25915	0.926	+	.	Parent=gene12
1877523	gth	exon	25916	26100	1	+	.	Parent=gene12
###
1877523	gth	gene	27900	28989	1	+	.	ID=gene13;Target=8726341 1 499 +
1877523	gth	exon	27900	28003	1	+	.	Parent=gene13
1877523	gth	five_prime_cis_splice_site	28004	28005	0.999	+	.	Parent=gene13
1877523	gth	three_prime_cis_splice_site	28267	28268	0.995	+	.	Parent=gene13
1877523	gth	exon	28269	28424	1	+	.	Parent=gene13
1877523	gth	five_prime_cis_splice_site	28425	28426	0.936	+	.	Parent=gene13
1877523	gth	three_prime_cis_splice_site	28505	28506	0	+	.	Parent=gene13
1877523	gth	exon	28507	28579	1	+	.	Parent=gene13
1877523	gth	five_prime_cis_splice_site	28580	28581	0.989	+	.	Parent=gene13
1877523	gth	three_prime_cis_splice_site	28684	28685	0.994	+	.	Parent=gene13
1877523	gth	exon	28686	28753	1	+	.	Parent=gene13
1877523	gth	five_prime_cis_splice_site	28754	28755	0.999	+	.	Parent=gene13
1877523	gth	three_prime_cis_splice_site	28890	28891	0.999	+	.	Parent=gene13
1877523	gth	exon	28892	28989	1	+	.	Parent=gene13
###
1877523	gth	gene	28990	29817	1	+	.	ID=gene14;Target=8726286 1 477 +
1877523	gth	exon	28990	29037	1	+	.	Parent=gene14
1877523	gth	five_prime_cis_splice_site	29038	29039	0.907	+	.	Parent=gene14
1877523	gth	three_prime_cis_splice_site	29132	29133	0	+	.	Parent=gene14
1877523	gth	exon	29134	29242	1	+	.	Parent=gene14
1877523	gth	five_prime_cis_splice_site	29243	29244	0.84	+	.	Parent=gene14
1877523	gth	three_prime_cis_splice_site	29329	29330	1	+	.	Parent=gene14
1877523	gth	exon	29331	29477	1	+	.	Parent=gene14
1877523	gth	five_prime_cis_splice_site	29478	29479	0.983	+	.	Parent=gene14
1877523	gth	three_prime_cis_splice_site	29569	29570	0.998	+	.	Parent=gene14
1877523	gth	exon	29571	29618	1	+	.	Parent=gene14
1877523	gth	five_prime_cis_splice_site	29619	29620	0	+	.	Parent=gene14
1877523	gth	three_prime_cis_splice_site	29691	29692	0.993	+	.	Parent=gene14
1877523	gth	exon	29693	29817	1	+	.	Parent=gene14
###
1877523	gth	gene	30278	31355	1	+	.	ID=gene15;Target=8690080 1 524 +
1877523	gth	exon	30278	30391	1	+	.	Parent=gene15
1877523	gth	five_prime_cis_splice_site	30392	30393	0.985	+	.	Parent=gene15
1877523	gth	three_prime_cis_splice_site	30475	30476	0.918	+	.	Parent=gene15
1877523	gth	exon	30477	30562	1	+	.	Parent=gene15
1877523	gth	five_prime_cis_splice_site	30563	30564	0.938	+	.	Parent=gene15
1877523	gth	three_prime_cis_splice_site	30656	30657	0.973	+	.	Parent=gene15
1877523	gth	exon	30658	30763	1	+	.	Parent=gene15
1877523	gth	five_prime_cis_splice_site	30764	30765	0.996	+	.	Parent=gene15
1877523	gth	three_prime_cis_splice_site	30988	30989	1	+	.	Parent=gene15
1877523	gth	exon	30990	31085	1	+	.	Parent=gene15
1877523	gth	five_prime_cis_splice_site	31086	31087	0.644	+	.	Parent=gene15
1877523	gth	three_prime_cis_splice_site	31232	31233	0.987	+	.	Parent=gene15
1877523	gth	exon	31234	31355	1	+	.	Parent=gene15
###
1877523	gth	gene	31265	31820	1	+	.	ID=gene16;Target=8689616 1 333 +
1877523	gth	exon	31265	31386	1	+	.	Parent=gene16
1877523	gth	five_prime_cis_splice_site	31387	31388	0.996	+	.	Parent=gene16
1877523	gth	three_prime_cis_splice_site	31536	31537	0.99	+	.	Parent=gene16
1877523	gth	exon	31538	31720	1	+	.	Parent=gene16
1877523	gth	five_prime_cis_splice_site	31721	31722	0.994	+	.	Parent=gene16
1877523	gth	three_prime_cis_splice_site	31791	31792	0.995	+	.	Parent=gene16
1877523	gth	exon	31793	31820	1	+	.	Parent=gene16
###
1877523	gth	gene	31855	32362	1	+	.	ID=gene17;Target=8689215 1 334 +
1877523	gth	exon	31855	32022	1	+	.	Parent=gene17
1877523	gth	five_prime_cis_splice_site	32023	32024	0	+	.	Parent=gene17
1877523	gth	three_prime_cis_splice_site	32116	32117	0.558	+	.	Parent=gene17
1877523	gth	exon	32118	32220	1	+	.	Parent=gene17
1877523	gth	five_prime_cis_splice_site	32221	32222	0.912	+	.	Parent=gene17
1877523	gth	three_prime_cis_splice_site	32298	32299	0.895	+	.	Parent=gene17
1877523	gth	exon	32300	32362	1	+	.	Parent=gene17
###
1877523	gth	gene	31907	32349	1	+	.	ID=gene18;Target=9784594 1 269 +
1877523	gth	exon	31907	32022	1	+	.	Parent=gene18
1877523	gth	five_prime_cis_splice_site	32023	32024	0	+	.	Parent=gene18
1877523	gth	three_prime_cis_splice_site	32116	32117	0.558	+	.	Parent=gene18
1877523	gth	exon	32118	32220	1	+	.	Parent=gene18
1877523	gth	five_prime_cis_splice_site	32221	32222	0.912	+	.	Parent=gene18
1877523	gth	three_prime_cis_splice_site	32298	32299	0.895	+	.	Parent=gene18
1877523	gth	exon	32300	32349	1	+	.	Parent=gene18
###
1877523	gth	gene	32928	33488	0.967	+	.	ID=gene19;Target=19875482 1 227 +
1877523	gth	exon	32928	32955	1	+	.	Parent=gene19
1877523	gth	five_prime_cis_splice_site	32956	32957	0.985	+	.	Parent=gene19
1877523	gth	three_prime_cis_splice_site	33189	33190	0.999	+	.	Parent=gene19
1877523	gth	exon	33191	33317	0.98	+	.	Parent=gene19
1877523	gth	five_prime_cis_splice_site	33318	33319	0.956	+	.	Parent=gene19
1877523	gth	three_prime_cis_splice_site	33416	33417	0.983	+	.	Parent=gene19
1877523	gth	exon	33418	33488	0.944	+	.	Parent=gene19
###
1877523	gth	gene	33296	34560	1	+	.	ID=gene20;Target=9782568 1 427 +
1877523	gth	exon	33296	33317	0.636	+	.	Parent=gene20
1877523	gth	five_prime_cis_splice_site	33318	33319	0.956	+	.	Parent=gene20
1877523	gth	three_prime_cis_splice_site	33416	33417	0.983	+	.	Parent=gene20
1877523	gth	exon	33418	33518	1	+	.	Parent=gene20
1877523	gth	five_prime_cis_splice_site	33519	33520	0.993	+	.	Parent=gene20
1877523	gth	three_prime_cis_splice_site	33781	33782	0.99	+	.	Parent=gene20
1877523	gth	exon	33783	33917	1	+	.	Parent=gene20
1877523	gth	five_prime_cis_splice_site	33918	33919	0.705	+	.	Parent=gene20
1877523	gth	three_prime_cis_splice_site	33994	33995	0.988	+	.	Parent=gene20
1877523	gth	exon	33996	34076	1	+	.	Parent=gene20
1877523	gth	five_prime_cis_splice_site	34077	34078	0.961	+	.	Parent=gene20
1877523	gth	three_prime_cis_splice_site	34470	34471	0.999	+	.	Parent=gene20
1877523	gth	exon	34472	34560	1	+	.	Parent=gene20
###
1877523	gth	gene	35628	36362	0.921	+	.	ID=gene21;Target=2759121 1 451 +
1877523	gth	exon	35628	35712	0.959	+	.	Parent=gene21
1877523	gth	five_prime_cis_splice_site	35713	35714	0.988	+	.	Parent=gene21
1877523	gth	three_prime_cis_splice_site	35818	35819	0.971	+	.	Parent=gene21
1877523	gth	exon	35820	36011	0.979	+	.	Parent=gene21
1877523	gth	five_prime_cis_splice_site	36012	36013	0.955	+	.	Parent=gene21
1877523	gth	three_prime_cis_splice_site	36099	36100	0.992	+	.	Parent=gene21
1877523	gth	exon	36101	36205	0.924	+	.	Parent=gene21
1877523	gth	five_prime_cis_splice_site	36206	36207	0.99	+	.	Parent=gene21
1877523	gth	three_prime_cis_splice_site	36295	36296	0.979	+	.	Parent=gene21
1877523	gth	exon	36297	36362	0.697	+	.	Parent=gene21
###
1877523	gth	gene	35628	36392	0.984	+	.	ID=gene22;Target=5841805 1 479 +
1877523	gth	exon	35628	35712	1	+	.	Parent=gene22
1877523	gth	five_prime_cis_splice_site	35713	35714	0.988	+	.	Parent=gene22
1877523	gth	three_prime_cis_splice_site	35818	35819	0.971	+	.	Parent=gene22
1877523	gth	exon	35820	36011	1	+	.	Parent=gene22
1877523	gth	five_prime_cis_splice_site	36012	36013	0.955	+	.	Parent=gene22
1877523	gth	three_prime_cis_splice_site	36099	36100	0.992	+	.	Parent=gene22
1877523	gth	exon	36101	36205	1	+	.	Parent=gene22
1877523	gth	five_prime_cis_splice_site	36206	36207	0.99	+	.	Parent=gene22
1877523	gth	three_prime_cis_splice_site	36295	36296	0.979	+	.	Parent=gene22
1877523	gth	exon	36297	36392	0.922	+	.	Parent=gene22
###
1877523	gth	gene	36370	37156	1	+	.	ID=gene23;Target=8683519 1 604 -
1877523	gth	exon	36370	36431	1	+	.	Parent=gene23
1877523	gth	five_prime_cis_splice_site	36432	36433	0.994	+	.	Parent=gene23
1877523	gth	three_prime_cis_splice_site	36519	36520	1	+	.	Parent=gene23
1877523	gth	exon	36521	36721	1	+	.	Parent=gene23
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene23
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene23
1877523	gth	exon	36816	37156	1	+	.	Parent=gene23
###
1877523	gth	gene	36402	37106	1	+	.	ID=gene24;Target=8682814 1 522 -
1877523	gth	exon	36402	36431	1	+	.	Parent=gene24
1877523	gth	five_prime_cis_splice_site	36432	36433	0.994	+	.	Parent=gene24
1877523	gth	three_prime_cis_splice_site	36519	36520	1	+	.	Parent=gene24
1877523	gth	exon	36521	36721	1	+	.	Parent=gene24
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene24
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene24
1877523	gth	exon	36816	37106	1	+	.	Parent=gene24
###
1877523	gth	gene	36531	37190	1	+	.	ID=gene25;Target=8690927 1 566 -
1877523	gth	exon	36531	36721	1	+	.	Parent=gene25
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene25
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene25
1877523	gth	exon	36816	37190	1	+	.	Parent=gene25
###
1877523	gth	gene	36546	37186	0.99	+	.	ID=gene26;Target=5845530 1 547 -
1877523	gth	exon	36546	36721	0.969	+	.	Parent=gene26
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene26
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene26
1877523	gth	exon	36816	37186	1	+	.	Parent=gene26
###
1877523	gth	gene	36594	37208	1	+	.	ID=gene27;Target=8717375 1 521 -
1877523	gth	exon	36594	36721	1	+	.	Parent=gene27
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene27
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene27
1877523	gth	exon	36816	37208	1	+	.	Parent=gene27
###
1877523	gth	gene	36812	37235	0.998	-	.	ID=gene28;Target=8735393 1 424 +
1877523	gth	exon	36812	37235	0.998	-	.	Parent=gene28
###
1877523	gth	gene	36816	37208	0.964	+	.	ID=gene29;Target=2048630 53 438 +
1877523	gth	exon	36816	37208	0.964	+	.	Parent=gene29
###
1877523	gth	gene	36827	37206	0.997	-	.	ID=gene30;Target=19741846 1 380 +
1877523	gth	exon	36827	37206	0.997	-	.	Parent=gene30
###
1877523	gth	gene	36840	37234	1	-	.	ID=gene31;Target=8738747 1 395 +
1877523	gth	exon	36840	37234	1	-	.	Parent=gene31
###
1877523	gth	gene	37071	37203	1	-	.	ID=gene32;Target=8679389 1 133 +
1877523	gth	exon	37071	37203	1	-	.	Parent=gene32
###
1877523	gth	gene	37669	39259	1	-	.	ID=gene33;Target=8738841 1 588 -
1877523	gth	exon	37669	37891	1	-	.	Parent=gene33
1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene33
1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene33
1877523	gth	exon	37972	38060	1	-	.	Parent=gene33
1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene33
1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene33
1877523	gth	exon	38656	38794	1	-	.	Parent=gene33
1877523	gth	three_prime_cis_splice_site	38794	38795	0.976	-	.	Parent=gene33
1877523	gth	five_prime_cis_splice_site	38926	38927	0.977	-	.	Parent=gene33
1877523	gth	exon	38927	38997	1	-	.	Parent=gene33
1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene33
1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene33
1877523	gth	exon	39104	39148	1	-	.	Parent=gene33
1877523	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene33
1877523	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene33
1877523	gth	exon	39239	39259	1	-	.	Parent=gene33
###
1877523	gth	gene	37691	38766	0.995	-	.	ID=gene34;Target=19831991 1 401 -
1877523	gth	exon	37691	37891	0.99	-	.	Parent=gene34
1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene34
1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene34
1877523	gth	exon	37972	38060	1	-	.	Parent=gene34
1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene34
1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene34
1877523	gth	exon	38656	38766	1	-	.	Parent=gene34
###
1877523	gth	gene	37692	38756	1	-	.	ID=gene35;Target=19840745 1 390 -
1877523	gth	exon	37692	37891	1	-	.	Parent=gene35
1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene35
1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene35
1877523	gth	exon	37972	38060	1	-	.	Parent=gene35
1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene35
1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene35
1877523	gth	exon	38656	38756	1	-	.	Parent=gene35
###
1877523	gth	gene	37716	39118	0.967	-	.	ID=gene36;Target=5843191 1 490 -
1877523	gth	exon	37716	37891	0.977	-	.	Parent=gene36
1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene36
1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene36
1877523	gth	exon	37972	38060	1	-	.	Parent=gene36
1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene36
1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene36
1877523	gth	exon	38656	38794	0.953	-	.	Parent=gene36
1877523	gth	three_prime_cis_splice_site	38794	38795	0.976	-	.	Parent=gene36
1877523	gth	five_prime_cis_splice_site	38926	38927	0.977	-	.	Parent=gene36
1877523	gth	exon	38927	38997	0.93	-	.	Parent=gene36
1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene36
1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene36
1877523	gth	exon	39104	39118	0.933	-	.	Parent=gene36
###
1877523	gth	gene	38927	40032	0.996	-	.	ID=gene37;Target=19869427 1 606 +
1877523	gth	exon	38927	38997	0.986	-	.	Parent=gene37
1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene37
1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene37
1877523	gth	exon	39104	39148	1	-	.	Parent=gene37
1877523	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene37
1877523	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene37
1877523	gth	exon	39239	39328	1	-	.	Parent=gene37
1877523	gth	three_prime_cis_splice_site	39328	39329	0.974	-	.	Parent=gene37
1877523	gth	five_prime_cis_splice_site	39437	39438	0.999	-	.	Parent=gene37
1877523	gth	exon	39438	39526	1	-	.	Parent=gene37
1877523	gth	three_prime_cis_splice_site	39526	39527	0.453	-	.	Parent=gene37
1877523	gth	five_prime_cis_splice_site	39613	39614	0.986	-	.	Parent=gene37
1877523	gth	exon	39614	39689	1	-	.	Parent=gene37
1877523	gth	three_prime_cis_splice_site	39689	39690	0.973	-	.	Parent=gene37
1877523	gth	five_prime_cis_splice_site	39797	39798	0.999	-	.	Parent=gene37
1877523	gth	exon	39798	40032	0.996	-	.	Parent=gene37
###
1877523	gth	gene	38938	40006	0.998	-	.	ID=gene38;Target=8722075 1 568 +
1877523	gth	exon	38938	38997	1	-	.	Parent=gene38
1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene38
1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene38
1877523	gth	exon	39104	39148	1	-	.	Parent=gene38
1877523	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene38
1877523	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene38
1877523	gth	exon	39239	39328	1	-	.	Parent=gene38
1877523	gth	three_prime_cis_splice_site	39328	39329	0.974	-	.	Parent=gene38
1877523	gth	five_prime_cis_splice_site	39437	39438	0.999	-	.	Parent=gene38
1877523	gth	exon	39438	39526	1	-	.	Parent=gene38
1877523	gth	three_prime_cis_splice_site	39526	39527	0.453	-	.	Parent=gene38
1877523	gth	five_prime_cis_splice_site	39613	39614	0.986	-	.	Parent=gene38
1877523	gth	exon	39614	39689	1	-	.	Parent=gene38
1877523	gth	three_prime_cis_splice_site	39689	39690	0.973	-	.	Parent=gene38
1877523	gth	five_prime_cis_splice_site	39797	39798	0.999	-	.	Parent=gene38
1877523	gth	exon	39798	40006	0.995	-	.	Parent=gene38
###
1877523	gth	gene	42783	43204	1	-	.	ID=gene39;Target=19858773 1 422 +
1877523	gth	exon	42783	43204	1	-	.	Parent=gene39
###
1877523	gth	gene	44029	44540	0.972	+	.	ID=gene40;Target=402959 1 423 +
1877523	gth	exon	44029	44263	0.991	+	.	Parent=gene40
1877523	gth	five_prime_cis_splice_site	44264	44265	0.99	+	.	Parent=gene40
1877523	gth	three_prime_cis_splice_site	44352	44353	0.998	+	.	Parent=gene40
1877523	gth	exon	44354	44540	0.947	+	.	Parent=gene40
###
1877523	gth	gene	45542	45866	0.991	-	.	ID=gene41;Target=8682693 1 322 +
1877523	gth	exon	45542	45866	0.991	-	.	Parent=gene41
###
1877523	gth	gene	45559	45941	0.924	-	.	ID=gene42;Target=402964 1 388 +
1877523	gth	exon	45559	45941	0.924	-	.	Parent=gene42
###
1877523	gth	gene	45843	45920	0.949	+	.	ID=gene43;Target=8720010 1 78 -
1877523	gth	exon	45843	45920	0.949	+	.	Parent=gene43
###
1877523	gth	gene	49874	50547	1	-	.	ID=gene44;Target=19837290 1 412 +
1877523	gth	exon	49874	50284	1	-	.	Parent=gene44
1877523	gth	three_prime_cis_splice_site	50284	50285	0.587	-	.	Parent=gene44
1877523	gth	five_prime_cis_splice_site	50546	50547	0.677	-	.	Parent=gene44
1877523	gth	exon	50547	50547	1	-	.	Parent=gene44
###
1877523	gth	gene	50433	51134	0.978	-	.	ID=gene45;Target=19807151 1 426 -
1877523	gth	exon	50433	50834	0.978	-	.	Parent=gene45
1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene45
1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene45
1877523	gth	exon	51113	51134	1	-	.	Parent=gene45
###
1877523	gth	gene	50475	50702	1	+	.	ID=gene46;Target=8727457 1 228 +
1877523	gth	exon	50475	50702	1	+	.	Parent=gene46
###
1877523	gth	gene	50475	51193	1	-	.	ID=gene47;Target=8731976 1 441 -
1877523	gth	exon	50475	50834	1	-	.	Parent=gene47
1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene47
1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene47
1877523	gth	exon	51113	51193	1	-	.	Parent=gene47
###
1877523	gth	gene	50590	51354	1	-	.	ID=gene48;Target=19805724 1 385 -
1877523	gth	exon	50590	50834	1	-	.	Parent=gene48
1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene48
1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene48
1877523	gth	exon	51113	51216	1	-	.	Parent=gene48
1877523	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene48
1877523	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene48
1877523	gth	exon	51319	51354	1	-	.	Parent=gene48
###
1877523	gth	gene	50758	52232	0.991	-	.	ID=gene49;Target=19866668 1 647 +
1877523	gth	exon	50758	50834	0.948	-	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene49
1877523	gth	exon	51113	51216	1	-	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene49
1877523	gth	exon	51319	51474	1	-	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene49
1877523	gth	exon	51552	51623	1	-	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene49
1877523	gth	exon	51711	51758	1	-	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene49
1877523	gth	exon	51849	51896	1	-	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene49
1877523	gth	exon	51983	52055	1	-	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene49
1877523	gth	exon	52163	52232	0.986	-	.	Parent=gene49
###
1877523	gth	gene	51139	51852	0.915	-	.	ID=gene50;Target=2747604 1 362 +
1877523	gth	exon	51139	51216	0.718	-	.	Parent=gene50
1877523	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene50
1877523	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene50
1877523	gth	exon	51319	51474	0.974	-	.	Parent=gene50
1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene50
1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene50
1877523	gth	exon	51552	51623	1	-	.	Parent=gene50
1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene50
1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene50
1877523	gth	exon	51711	51758	0.979	-	.	Parent=gene50
1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene50
1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene50
1877523	gth	exon	51849	51852	1	-	.	Parent=gene50
###
1877523	gth	gene	51334	52222	0.905	-	.	ID=gene51;Target=2596256 1 446 +
1877523	gth	exon	51334	51474	0.766	-	.	Parent=gene51
1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene51
1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene51
1877523	gth	exon	51552	51623	1	-	.	Parent=gene51
1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene51
1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene51
1877523	gth	exon	51711	51758	1	-	.	Parent=gene51
1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene51
1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene51
1877523	gth	exon	51849	51896	0.979	-	.	Parent=gene51
1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene51
1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene51
1877523	gth	exon	51983	52055	1	-	.	Parent=gene51
1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene51
1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene51
1877523	gth	exon	52163	52222	1	-	.	Parent=gene51
###
1877523	gth	gene	51376	52048	0.939	-	.	ID=gene52;Target=2596953 1 336 +
1877523	gth	exon	51376	51474	0.854	-	.	Parent=gene52
1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene52
1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene52
1877523	gth	exon	51552	51623	1	-	.	Parent=gene52
1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene52
1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene52
1877523	gth	exon	51711	51758	1	-	.	Parent=gene52
1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene52
1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene52
1877523	gth	exon	51849	51896	0.979	-	.	Parent=gene52
1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene52
1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene52
1877523	gth	exon	51983	52048	1	-	.	Parent=gene52
###
1877523	gth	gene	51376	52224	0.91	-	.	ID=gene53;Target=5839790 1 404 +
1877523	gth	exon	51376	51474	0.848	-	.	Parent=gene53
1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene53
1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene53
1877523	gth	exon	51552	51623	0.931	-	.	Parent=gene53
1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene53
1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene53
1877523	gth	exon	51711	51758	0.823	-	.	Parent=gene53
1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene53
1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene53
1877523	gth	exon	51849	51896	0.958	-	.	Parent=gene53
1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene53
1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene53
1877523	gth	exon	51983	52055	0.959	-	.	Parent=gene53
1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene53
1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene53
1877523	gth	exon	52163	52224	0.927	-	.	Parent=gene53
###
1877523	gth	gene	51446	52242	0.996	-	.	ID=gene54;Target=403229 1 350 +
1877523	gth	exon	51446	51474	0.966	-	.	Parent=gene54
1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene54
1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene54
1877523	gth	exon	51552	51623	1	-	.	Parent=gene54
1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene54
1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene54
1877523	gth	exon	51711	51758	1	-	.	Parent=gene54
1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene54
1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene54
1877523	gth	exon	51849	51896	1	-	.	Parent=gene54
1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene54
1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene54
1877523	gth	exon	51983	52055	0.986	-	.	Parent=gene54
1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene54
1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene54
1877523	gth	exon	52163	52242	1	-	.	Parent=gene54
###
1877523	gth	gene	51599	52231	0.993	-	.	ID=gene55;Target=9785390 1 263 +
1877523	gth	exon	51599	51623	1	-	.	Parent=gene55
1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene55
1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene55
1877523	gth	exon	51711	51758	1	-	.	Parent=gene55
1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene55
1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene55
1877523	gth	exon	51849	51896	1	-	.	Parent=gene55
1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene55
1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene55
1877523	gth	exon	51983	52055	1	-	.	Parent=gene55
1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene55
1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene55
1877523	gth	exon	52163	52231	0.986	-	.	Parent=gene55
###
1877523	gth	gene	53602	54271	0.994	-	.	ID=gene56;Target=8697180 1 427 -
1877523	gth	exon	53602	53914	0.992	-	.	Parent=gene56
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene56
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene56
1877523	gth	exon	54159	54271	1	-	.	Parent=gene56
###
1877523	gth	gene	53602	54710	0.995	-	.	ID=gene57;Target=19803773 1 627 -
1877523	gth	exon	53602	53914	0.994	-	.	Parent=gene57
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene57
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene57
1877523	gth	exon	54159	54335	1	-	.	Parent=gene57
1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene57
1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene57
1877523	gth	exon	54574	54710	0.993	-	.	Parent=gene57
###
1877523	gth	gene	53624	54279	0.989	-	.	ID=gene58;Target=19840006 1 413 -
1877523	gth	exon	53624	53914	0.988	-	.	Parent=gene58
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene58
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene58
1877523	gth	exon	54159	54279	0.992	-	.	Parent=gene58
###
1877523	gth	gene	53624	54283	0.992	-	.	ID=gene59;Target=19823046 1 417 -
1877523	gth	exon	53624	53914	0.988	-	.	Parent=gene59
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene59
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene59
1877523	gth	exon	54159	54283	1	-	.	Parent=gene59
###
1877523	gth	gene	53631	54335	0.866	-	.	ID=gene60;Target=2393553 57 528 +
1877523	gth	exon	53631	53914	0.991	-	.	Parent=gene60
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene60
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene60
1877523	gth	exon	54159	54335	0.664	-	.	Parent=gene60
###
1877523	gth	gene	53632	53909	0.991	+	.	ID=gene61;Target=8697126 1 279 +
1877523	gth	exon	53632	53909	0.991	+	.	Parent=gene61
###
1877523	gth	gene	53645	54320	0.99	-	.	ID=gene62;Target=19843722 1 431 -
1877523	gth	exon	53645	53914	0.991	-	.	Parent=gene62
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene62
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene62
1877523	gth	exon	54159	54320	0.988	-	.	Parent=gene62
###
1877523	gth	gene	53829	54829	0.991	-	.	ID=gene63;Target=8696505 49 568 +
1877523	gth	exon	53829	53914	0.971	-	.	Parent=gene63
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene63
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene63
1877523	gth	exon	54159	54335	1	-	.	Parent=gene63
1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene63
1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene63
1877523	gth	exon	54574	54829	0.992	-	.	Parent=gene63
###
1877523	gth	gene	53850	54807	0.913	-	.	ID=gene64;Target=5839694 1 477 +
1877523	gth	exon	53850	53914	0.746	-	.	Parent=gene64
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene64
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene64
1877523	gth	exon	54159	54335	0.887	-	.	Parent=gene64
1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene64
1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene64
1877523	gth	exon	54574	54807	0.979	-	.	Parent=gene64
###
1877523	gth	gene	54167	54769	0.997	-	.	ID=gene65;Target=9778953 1 365 +
1877523	gth	exon	54167	54335	0.994	-	.	Parent=gene65
1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene65
1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene65
1877523	gth	exon	54574	54769	1	-	.	Parent=gene65
###
1877523	gth	gene	54178	54828	0.979	-	.	ID=gene66;Target=19865963 1 414 +
1877523	gth	exon	54178	54335	0.953	-	.	Parent=gene66
1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene66
1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene66
1877523	gth	exon	54574	54828	0.996	-	.	Parent=gene66
###
1877523	gth	gene	54212	54697	0.952	-	.	ID=gene67;Target=9784661 1 248 +
1877523	gth	exon	54212	54335	0.96	-	.	Parent=gene67
1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene67
1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene67
1877523	gth	exon	54574	54697	0.944	-	.	Parent=gene67
###
1877523	gth	gene	54263	54808	0.93	-	.	ID=gene68;Target=933584 1 311 +
1877523	gth	exon	54263	54335	0.815	-	.	Parent=gene68
1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene68
1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene68
1877523	gth	exon	54574	54808	0.966	-	.	Parent=gene68
###
1877523	gth	gene	54321	54829	0.992	-	.	ID=gene69;Target=8696543 49 319 +
1877523	gth	exon	54321	54335	1	-	.	Parent=gene69
1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene69
1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene69
1877523	gth	exon	54574	54829	0.992	-	.	Parent=gene69
###
1877523	gth	gene	54991	56652	0.998	+	.	ID=gene70;Target=19874826 1 651 +
1877523	gth	exon	54991	55057	0.985	+	.	Parent=gene70
1877523	gth	five_prime_cis_splice_site	55058	55059	0.896	+	.	Parent=gene70
1877523	gth	three_prime_cis_splice_site	55143	55144	1	+	.	Parent=gene70
1877523	gth	exon	55145	55230	1	+	.	Parent=gene70
1877523	gth	five_prime_cis_splice_site	55231	55232	0.997	+	.	Parent=gene70
1877523	gth	three_prime_cis_splice_site	55298	55299	0	+	.	Parent=gene70
1877523	gth	exon	55300	55341	1	+	.	Parent=gene70
1877523	gth	five_prime_cis_splice_site	55342	55343	0.997	+	.	Parent=gene70
1877523	gth	three_prime_cis_splice_site	55451	55452	0.898	+	.	Parent=gene70
1877523	gth	exon	55453	55498	1	+	.	Parent=gene70
1877523	gth	five_prime_cis_splice_site	55499	55500	0.237	+	.	Parent=gene70
1877523	gth	three_prime_cis_splice_site	55616	55617	0.997	+	.	Parent=gene70
1877523	gth	exon	55618	55704	1	+	.	Parent=gene70
1877523	gth	five_prime_cis_splice_site	55705	55706	0.991	+	.	Parent=gene70
1877523	gth	three_prime_cis_splice_site	55816	55817	0.952	+	.	Parent=gene70
1877523	gth	exon	55818	55873	1	+	.	Parent=gene70
1877523	gth	five_prime_cis_splice_site	55874	55875	0.983	+	.	Parent=gene70
1877523	gth	three_prime_cis_splice_site	56034	56035	0.0357	+	.	Parent=gene70
1877523	gth	exon	56036	56153	1	+	.	Parent=gene70
1877523	gth	five_prime_cis_splice_site	56154	56155	0.99	+	.	Parent=gene70
1877523	gth	three_prime_cis_splice_site	56279	56280	0.703	+	.	Parent=gene70
1877523	gth	exon	56281	56339	1	+	.	Parent=gene70
1877523	gth	five_prime_cis_splice_site	56340	56341	0.464	+	.	Parent=gene70
1877523	gth	three_prime_cis_splice_site	56447	56448	0.287	+	.	Parent=gene70
1877523	gth	exon	56449	56520	1	+	.	Parent=gene70
1877523	gth	five_prime_cis_splice_site	56521	56522	0.187	+	.	Parent=gene70
1877523	gth	three_prime_cis_splice_site	56633	56634	0.791	+	.	Parent=gene70
1877523	gth	exon	56635	56652	1	+	.	Parent=gene70
###
1877523	gth	gene	58115	59001	0.984	+	.	ID=gene71;Target=19741042 1 460 -
1877523	gth	exon	58115	58209	0.958	+	.	Parent=gene71
1877523	gth	five_prime_cis_splice_site	58210	58211	0.856	+	.	Parent=gene71
1877523	gth	three_prime_cis_splice_site	58459	58460	1	+	.	Parent=gene71
1877523	gth	exon	58461	58526	1	+	.	Parent=gene71
1877523	gth	five_prime_cis_splice_site	58527	58528	0.784	+	.	Parent=gene71
1877523	gth	three_prime_cis_splice_site	58622	58623	0.977	+	.	Parent=gene71
1877523	gth	exon	58624	58717	1	+	.	Parent=gene71
1877523	gth	five_prime_cis_splice_site	58718	58719	0	+	.	Parent=gene71
1877523	gth	three_prime_cis_splice_site	58794	58795	1	+	.	Parent=gene71
1877523	gth	exon	58796	59001	0.983	+	.	Parent=gene71
###
1877523	gth	gene	59010	59484	1	+	.	ID=gene72;Target=8715845 1 475 +
1877523	gth	exon	59010	59484	1	+	.	Parent=gene72
###
1877523	gth	gene	59148	59880	0.991	+	.	ID=gene73;Target=19864079 1 653 +
1877523	gth	exon	59148	59526	0.989	+	.	Parent=gene73
1877523	gth	five_prime_cis_splice_site	59527	59528	0.993	+	.	Parent=gene73
1877523	gth	three_prime_cis_splice_site	59605	59606	0.997	+	.	Parent=gene73
1877523	gth	exon	59607	59880	0.993	+	.	Parent=gene73
###
1877523	gth	gene	59164	59418	0.996	+	.	ID=gene74;Target=9787190 1 255 +
1877523	gth	exon	59164	59418	0.996	+	.	Parent=gene74
###
1877523	gth	gene	59643	59976	0.991	+	.	ID=gene75;Target=397215 1 333 +
1877523	gth	exon	59643	59976	0.991	+	.	Parent=gene75
###
1877523	gth	gene	60190	60487	0.987	+	.	ID=gene76;Target=398270 1 298 +
1877523	gth	exon	60190	60487	0.987	+	.	Parent=gene76
###
1877523	gth	gene	60319	61000	0.997	-	.	ID=gene77;Target=19801463 1 682 +
1877523	gth	exon	60319	61000	0.997	-	.	Parent=gene77
###
1877523	gth	gene	60410	60968	1	-	.	ID=gene78;Target=8692149 1 559 +
1877523	gth	exon	60410	60968	1	-	.	Parent=gene78
###
1877523	gth	gene	60450	60902	0.998	-	.	ID=gene79;Target=19827386 1 453 +
1877523	gth	exon	60450	60902	0.998	-	.	Parent=gene79
###
1877523	gth	gene	60459	60958	0.996	-	.	ID=gene80;Target=7610825 1 500 +
1877523	gth	exon	60459	60958	0.996	-	.	Parent=gene80
###
1877523	gth	gene	60463	60958	0.996	-	.	ID=gene81;Target=8736724 1 496 +
1877523	gth	exon	60463	60958	0.996	-	.	Parent=gene81
###
1877523	gth	gene	60508	60959	0.983	-	.	ID=gene82;Target=19828552 1 452 +
1877523	gth	exon	60508	60959	0.983	-	.	Parent=gene82
###
1877523	gth	gene	60542	60950	1	-	.	ID=gene83;Target=19838343 1 409 +
1877523	gth	exon	60542	60950	1	-	.	Parent=gene83
###
1877523	gth	gene	60558	60947	0.995	-	.	ID=gene84;Target=397216 1 390 +
1877523	gth	exon	60558	60947	0.995	-	.	Parent=gene84
###
1877523	gth	gene	61186	61922	0.957	+	.	ID=gene85;Target=2722481 1 371 +
1877523	gth	exon	61186	61281	0.99	+	.	Parent=gene85
1877523	gth	five_prime_cis_splice_site	61282	61283	0.316	+	.	Parent=gene85
1877523	gth	three_prime_cis_splice_site	61563	61564	0.959	+	.	Parent=gene85
1877523	gth	exon	61565	61641	0.948	+	.	Parent=gene85
1877523	gth	five_prime_cis_splice_site	61642	61643	0	+	.	Parent=gene85
1877523	gth	three_prime_cis_splice_site	61722	61723	0.994	+	.	Parent=gene85
1877523	gth	exon	61724	61922	0.945	+	.	Parent=gene85
###
1877523	gth	gene	61212	61974	1	+	.	ID=gene86;Target=19837990 1 398 -
1877523	gth	exon	61212	61281	1	+	.	Parent=gene86
1877523	gth	five_prime_cis_splice_site	61282	61283	0.316	+	.	Parent=gene86
1877523	gth	three_prime_cis_splice_site	61563	61564	0.959	+	.	Parent=gene86
1877523	gth	exon	61565	61641	1	+	.	Parent=gene86
1877523	gth	five_prime_cis_splice_site	61642	61643	0	+	.	Parent=gene86
1877523	gth	three_prime_cis_splice_site	61722	61723	0.994	+	.	Parent=gene86
1877523	gth	exon	61724	61974	1	+	.	Parent=gene86
###
1877523	gth	gene	62196	62646	0.921	+	.	ID=gene87;Target=2747645 1 448 +
1877523	gth	exon	62196	62646	0.921	+	.	Parent=gene87
###
1877523	gth	gene	63106	63942	1	+	.	ID=gene88;Target=8701755 1 598 -
1877523	gth	exon	63106	63178	1	+	.	Parent=gene88
1877523	gth	five_prime_cis_splice_site	63179	63180	0	+	.	Parent=gene88
1877523	gth	three_prime_cis_splice_site	63269	63270	0.999	+	.	Parent=gene88
1877523	gth	exon	63271	63391	1	+	.	Parent=gene88
1877523	gth	five_prime_cis_splice_site	63392	63393	0.823	+	.	Parent=gene88
1877523	gth	three_prime_cis_splice_site	63466	63467	0	+	.	Parent=gene88
1877523	gth	exon	63468	63683	1	+	.	Parent=gene88
1877523	gth	five_prime_cis_splice_site	63684	63685	0.999	+	.	Parent=gene88
1877523	gth	three_prime_cis_splice_site	63753	63754	0.992	+	.	Parent=gene88
1877523	gth	exon	63755	63942	1	+	.	Parent=gene88
###
1877523	gth	gene	63306	63942	1	+	.	ID=gene89;Target=8735505 1 490 -
1877523	gth	exon	63306	63391	1	+	.	Parent=gene89
1877523	gth	five_prime_cis_splice_site	63392	63393	0.823	+	.	Parent=gene89
1877523	gth	three_prime_cis_splice_site	63466	63467	0	+	.	Parent=gene89
1877523	gth	exon	63468	63683	1	+	.	Parent=gene89
1877523	gth	five_prime_cis_splice_site	63684	63685	0.999	+	.	Parent=gene89
1877523	gth	three_prime_cis_splice_site	63753	63754	0.992	+	.	Parent=gene89
1877523	gth	exon	63755	63942	1	+	.	Parent=gene89
###
1877523	gth	gene	63910	64320	0.979	+	.	ID=gene90;Target=19798134 1 412 +
1877523	gth	exon	63910	64320	0.979	+	.	Parent=gene90
###
1877523	gth	gene	63935	64280	0.986	+	.	ID=gene91;Target=5846657 1 345 +
1877523	gth	exon	63935	64280	0.986	+	.	Parent=gene91
###
1877523	gth	gene	64196	65033	0.998	-	.	ID=gene92;Target=19877649 1 632 +
1877523	gth	exon	64196	64605	1	-	.	Parent=gene92
1877523	gth	three_prime_cis_splice_site	64605	64606	0.942	-	.	Parent=gene92
1877523	gth	five_prime_cis_splice_site	64811	64812	0.991	-	.	Parent=gene92
1877523	gth	exon	64812	65033	0.995	-	.	Parent=gene92
###
1877523	gth	gene	65467	66157	0.992	+	.	ID=gene93;Target=19875812 1 621 +
1877523	gth	exon	65467	66058	0.992	+	.	Parent=gene93
1877523	gth	five_prime_cis_splice_site	66059	66060	1	+	.	Parent=gene93
1877523	gth	three_prime_cis_splice_site	66128	66129	0.994	+	.	Parent=gene93
1877523	gth	exon	66130	66157	0.964	+	.	Parent=gene93
###
1877523	gth	gene	67358	68298	0.982	+	.	ID=gene94;Target=396603 1 749 +
1877523	gth	exon	67358	67550	1	+	.	Parent=gene94
1877523	gth	five_prime_cis_splice_site	67551	67552	0.896	+	.	Parent=gene94
1877523	gth	three_prime_cis_splice_site	67634	67635	0.998	+	.	Parent=gene94
1877523	gth	exon	67636	67908	0.969	+	.	Parent=gene94
1877523	gth	five_prime_cis_splice_site	67909	67910	1	+	.	Parent=gene94
1877523	gth	three_prime_cis_splice_site	68009	68010	0.999	+	.	Parent=gene94
1877523	gth	exon	68011	68298	0.983	+	.	Parent=gene94
###
1877523	gth	gene	67871	68396	0.99	+	.	ID=gene95;Target=19742246 1 423 -
1877523	gth	exon	67871	67908	0.947	+	.	Parent=gene95
1877523	gth	five_prime_cis_splice_site	67909	67910	1	+	.	Parent=gene95
1877523	gth	three_prime_cis_splice_site	68009	68010	0.999	+	.	Parent=gene95
1877523	gth	exon	68011	68396	0.99	+	.	Parent=gene95
###
1877523	gth	gene	69163	69893	0.98	+	.	ID=gene96;Target=19872996 1 536 +
1877523	gth	exon	69163	69265	0.971	+	.	Parent=gene96
1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene96
1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene96
1877523	gth	exon	69375	69598	1	+	.	Parent=gene96
1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene96
1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene96
1877523	gth	exon	69685	69893	0.964	+	.	Parent=gene96
###
1877523	gth	gene	69171	69968	0.997	+	.	ID=gene97;Target=19869130 1 603 +
1877523	gth	exon	69171	69265	0.989	+	.	Parent=gene97
1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene97
1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene97
1877523	gth	exon	69375	69598	1	+	.	Parent=gene97
1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene97
1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene97
1877523	gth	exon	69685	69968	0.996	+	.	Parent=gene97
###
1877523	gth	gene	69173	69853	0.992	+	.	ID=gene98;Target=19870921 1 486 +
1877523	gth	exon	69173	69265	0.989	+	.	Parent=gene98
1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene98
1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene98
1877523	gth	exon	69375	69598	1	+	.	Parent=gene98
1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene98
1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene98
1877523	gth	exon	69685	69853	0.982	+	.	Parent=gene98
###
1877523	gth	gene	69196	70072	0.932	+	.	ID=gene99;Target=905849 1 455 +
1877523	gth	exon	69196	69265	0.986	+	.	Parent=gene99
1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene99
1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene99
1877523	gth	exon	69375	69598	0.991	+	.	Parent=gene99
1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene99
1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene99
1877523	gth	exon	69685	69831	0.816	+	.	Parent=gene99
1877523	gth	five_prime_cis_splice_site	69832	69833	0.48	+	.	Parent=gene99
1877523	gth	three_prime_cis_splice_site	70061	70062	0.999	+	.	Parent=gene99
1877523	gth	exon	70063	70072	0.4	+	.	Parent=gene99
###
1877523	gth	gene	69219	69775	1	+	.	ID=gene100;Target=7612059 1 362 +
1877523	gth	exon	69219	69265	1	+	.	Parent=gene100
1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene100
1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene100
1877523	gth	exon	69375	69598	1	+	.	Parent=gene100
1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene100
1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene100
1877523	gth	exon	69685	69775	1	+	.	Parent=gene100
###
1877523	gth	gene	71414	71679	0.958	+	.	ID=gene101;Target=17520 1 168 +
1877523	gth	exon	71414	71479	1	+	.	Parent=gene101
1877523	gth	five_prime_cis_splice_site	71480	71481	0.948	+	.	Parent=gene101
1877523	gth	three_prime_cis_splice_site	71577	71578	0.982	+	.	Parent=gene101
1877523	gth	exon	71579	71679	0.931	+	.	Parent=gene101
###
1877523	gth	gene	71458	72009	0.99	+	.	ID=gene102;Target=8734707 1 319 +
1877523	gth	exon	71458	71479	1	+	.	Parent=gene102
1877523	gth	five_prime_cis_splice_site	71480	71481	0.948	+	.	Parent=gene102
1877523	gth	three_prime_cis_splice_site	71577	71578	0.982	+	.	Parent=gene102
1877523	gth	exon	71579	71779	0.985	+	.	Parent=gene102
1877523	gth	five_prime_cis_splice_site	71780	71781	0.998	+	.	Parent=gene102
1877523	gth	three_prime_cis_splice_site	71912	71913	0.977	+	.	Parent=gene102
1877523	gth	exon	71914	72009	1	+	.	Parent=gene102
###
1877523	gth	gene	72121	72340	0.966	+	.	ID=gene103;Target=2597031 1 221 +
1877523	gth	exon	72121	72340	0.966	+	.	Parent=gene103
###
1877523	gth	gene	72121	72603	0.931	+	.	ID=gene104;Target=958004 1 484 +
1877523	gth	exon	72121	72603	0.931	+	.	Parent=gene104
###
1877523	gth	gene	72137	72552	0.917	+	.	ID=gene105;Target=1159193 1 351 +
1877523	gth	exon	72137	72296	1	+	.	Parent=gene105
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene105
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene105
1877523	gth	exon	72369	72552	0.845	+	.	Parent=gene105
###
1877523	gth	gene	72185	72753	1	+	.	ID=gene106;Target=8737761 1 497 -
1877523	gth	exon	72185	72296	1	+	.	Parent=gene106
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene106
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene106
1877523	gth	exon	72369	72753	1	+	.	Parent=gene106
###
1877523	gth	gene	72204	72660	0.856	+	.	ID=gene107;Target=2749490 79 466 +
1877523	gth	exon	72204	72296	0.634	+	.	Parent=gene107
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene107
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene107
1877523	gth	exon	72369	72660	0.926	+	.	Parent=gene107
###
1877523	gth	gene	72214	72751	0.987	+	.	ID=gene108;Target=7610337 1 466 -
1877523	gth	exon	72214	72296	1	+	.	Parent=gene108
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene108
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene108
1877523	gth	exon	72369	72751	0.984	+	.	Parent=gene108
###
1877523	gth	gene	72231	72731	0.998	+	.	ID=gene109;Target=19829297 1 429 -
1877523	gth	exon	72231	72296	1	+	.	Parent=gene109
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene109
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene109
1877523	gth	exon	72369	72731	0.997	+	.	Parent=gene109
###
1877523	gth	gene	72246	72753	0.995	+	.	ID=gene110;Target=19829716 1 434 -
1877523	gth	exon	72246	72296	0.98	+	.	Parent=gene110
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene110
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene110
1877523	gth	exon	72369	72753	0.997	+	.	Parent=gene110
###
1877523	gth	gene	72252	72753	0.988	+	.	ID=gene111;Target=19831127 1 431 -
1877523	gth	exon	72252	72296	1	+	.	Parent=gene111
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene111
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene111
1877523	gth	exon	72369	72753	0.988	+	.	Parent=gene111
###
1877523	gth	gene	72252	72803	1	+	.	ID=gene112;Target=8731753 1 480 -
1877523	gth	exon	72252	72296	1	+	.	Parent=gene112
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene112
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene112
1877523	gth	exon	72369	72803	1	+	.	Parent=gene112
###
1877523	gth	gene	72262	72754	1	+	.	ID=gene113;Target=19839622 1 421 -
1877523	gth	exon	72262	72296	1	+	.	Parent=gene113
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene113
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene113
1877523	gth	exon	72369	72754	1	+	.	Parent=gene113
###
1877523	gth	gene	72264	72572	0.966	+	.	ID=gene114;Target=2762921 1 237 +
1877523	gth	exon	72264	72296	0.939	+	.	Parent=gene114
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene114
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene114
1877523	gth	exon	72369	72572	0.966	+	.	Parent=gene114
###
1877523	gth	gene	72264	72670	0.93	+	.	ID=gene115;Target=2762922 1 337 +
1877523	gth	exon	72264	72296	0.97	+	.	Parent=gene115
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene115
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene115
1877523	gth	exon	72369	72670	0.93	+	.	Parent=gene115
###
1877523	gth	gene	72270	72801	0.998	+	.	ID=gene116;Target=19825274 1 460 -
1877523	gth	exon	72270	72296	0.963	+	.	Parent=gene116
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene116
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene116
1877523	gth	exon	72369	72801	0.998	+	.	Parent=gene116
###
1877523	gth	gene	72275	72752	0.872	+	.	ID=gene117;Target=19855736 1 420 -
1877523	gth	exon	72275	72296	1	+	.	Parent=gene117
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene117
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene117
1877523	gth	exon	72369	72752	0.872	+	.	Parent=gene117
###
1877523	gth	gene	72277	72753	1	+	.	ID=gene118;Target=8695920 1 405 -
1877523	gth	exon	72277	72296	1	+	.	Parent=gene118
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene118
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene118
1877523	gth	exon	72369	72753	1	+	.	Parent=gene118
###
1877523	gth	gene	72359	72801	0.985	-	.	ID=gene119;Target=19841232 1 443 +
1877523	gth	exon	72359	72801	0.985	-	.	Parent=gene119
###
1877523	gth	gene	72367	72810	1	-	.	ID=gene120;Target=19826275 1 444 +
1877523	gth	exon	72367	72810	1	-	.	Parent=gene120
###
1877523	gth	gene	72371	72801	0.995	-	.	ID=gene121;Target=19834843 1 430 +
1877523	gth	exon	72371	72801	0.995	-	.	Parent=gene121
###
1877523	gth	gene	72372	72801	0.99	-	.	ID=gene122;Target=19828253 1 431 +
1877523	gth	exon	72372	72801	0.99	-	.	Parent=gene122
###
1877523	gth	gene	72372	72801	1	-	.	ID=gene123;Target=19825742 1 430 +
1877523	gth	exon	72372	72801	1	-	.	Parent=gene123
###
1877523	gth	gene	72374	72827	0.992	-	.	ID=gene124;Target=19828054 1 455 +
1877523	gth	exon	72374	72827	0.992	-	.	Parent=gene124
###
1877523	gth	gene	72383	72801	0.995	-	.	ID=gene125;Target=19844666 1 418 +
1877523	gth	exon	72383	72801	0.995	-	.	Parent=gene125
###
1877523	gth	gene	72384	72801	1	-	.	ID=gene126;Target=19829934 1 418 +
1877523	gth	exon	72384	72801	1	-	.	Parent=gene126
###
1877523	gth	gene	72386	72802	0.993	-	.	ID=gene127;Target=19842362 1 417 +
1877523	gth	exon	72386	72802	0.993	-	.	Parent=gene127
###
1877523	gth	gene	72386	72803	0.974	-	.	ID=gene128;Target=19837074 1 417 +
1877523	gth	exon	72386	72803	0.974	-	.	Parent=gene128
###
1877523	gth	gene	72390	72754	0.997	-	.	ID=gene129;Target=8728304 1 365 +
1877523	gth	exon	72390	72754	0.997	-	.	Parent=gene129
###
1877523	gth	gene	72390	72804	0.98	-	.	ID=gene130;Target=19827775 1 416 +
1877523	gth	exon	72390	72804	0.98	-	.	Parent=gene130
###
1877523	gth	gene	72399	72801	1	-	.	ID=gene131;Target=19855995 1 403 +
1877523	gth	exon	72399	72801	1	-	.	Parent=gene131
###
1877523	gth	gene	72400	72753	1	-	.	ID=gene132;Target=8694120 1 354 +
1877523	gth	exon	72400	72753	1	-	.	Parent=gene132
###
1877523	gth	gene	72404	72804	0.998	-	.	ID=gene133;Target=19831839 1 401 +
1877523	gth	exon	72404	72804	0.998	-	.	Parent=gene133
###
1877523	gth	gene	72422	72826	0.998	-	.	ID=gene134;Target=19833332 1 405 +
1877523	gth	exon	72422	72826	0.998	-	.	Parent=gene134
###
1877523	gth	gene	72424	72753	0.929	+	.	ID=gene135;Target=3449674 1 333 +
1877523	gth	exon	72424	72753	0.929	+	.	Parent=gene135
###
1877523	gth	gene	72437	72805	0.981	-	.	ID=gene136;Target=8732348 1 369 +
1877523	gth	exon	72437	72805	0.981	-	.	Parent=gene136
###
1877523	gth	gene	72522	72801	0.971	-	.	ID=gene137;Target=8695842 1 280 +
1877523	gth	exon	72522	72801	0.971	-	.	Parent=gene137
###
1877523	gth	gene	72653	74046	0.978	-	.	ID=gene138;Target=2597485 1 163 -
1877523	gth	exon	72653	72789	0.978	-	.	Parent=gene138
1877523	gth	three_prime_cis_splice_site	72789	72790	0	-	.	Parent=gene138
1877523	gth	five_prime_cis_splice_site	74020	74021	0.514	-	.	Parent=gene138
1877523	gth	exon	74021	74046	0.615	-	.	Parent=gene138
###
1877523	gth	gene	72653	74920	0.919	-	.	ID=gene139;Target=3450080 1 166 -
1877523	gth	exon	72653	72800	0.919	-	.	Parent=gene139
1877523	gth	three_prime_cis_splice_site	72800	72801	0	-	.	Parent=gene139
1877523	gth	five_prime_cis_splice_site	74900	74901	0.919	-	.	Parent=gene139
1877523	gth	exon	74901	74920	0.75	-	.	Parent=gene139
###
1877523	gth	gene	79098	79663	0.866	-	.	ID=gene140;Target=19857409 11 314 -
1877523	gth	exon	79098	79127	0.767	-	.	Parent=gene140
1877523	gth	three_prime_cis_splice_site	79127	79128	0	-	.	Parent=gene140
1877523	gth	five_prime_cis_splice_site	79240	79241	0	-	.	Parent=gene140
1877523	gth	exon	79241	79487	0.866	-	.	Parent=gene140
1877523	gth	three_prime_cis_splice_site	79487	79488	0.899	-	.	Parent=gene140
1877523	gth	five_prime_cis_splice_site	79635	79636	0.999	-	.	Parent=gene140
1877523	gth	exon	79636	79663	1	-	.	Parent=gene140
###
1877523	gth	gene	86444	89957	0.741	-	.	ID=gene141;Target=19873300 87 582 +
1877523	gth	exon	86444	86516	0.767	-	.	Parent=gene141
1877523	gth	three_prime_cis_splice_site	86516	86517	0.999	-	.	Parent=gene141
1877523	gth	five_prime_cis_splice_site	89439	89440	0.999	-	.	Parent=gene141
1877523	gth	exon	89440	89702	0.683	-	.	Parent=gene141
1877523	gth	three_prime_cis_splice_site	89702	89703	0.846	-	.	Parent=gene141
1877523	gth	five_prime_cis_splice_site	89793	89794	0.933	-	.	Parent=gene141
1877523	gth	exon	89794	89957	0.823	-	.	Parent=gene141
###
1877523	gth	gene	90829	91133	0.948	+	.	ID=gene142;Target=5845361 1 307 +
1877523	gth	exon	90829	91133	0.948	+	.	Parent=gene142
###
1877523	gth	gene	91050	91786	1	-	.	ID=gene143;Target=8735154 1 543 -
1877523	gth	exon	91050	91401	1	-	.	Parent=gene143
1877523	gth	three_prime_cis_splice_site	91401	91402	1	-	.	Parent=gene143
1877523	gth	five_prime_cis_splice_site	91523	91524	0.917	-	.	Parent=gene143
1877523	gth	exon	91524	91713	1	-	.	Parent=gene143
1877523	gth	three_prime_cis_splice_site	91713	91714	0.848	-	.	Parent=gene143
1877523	gth	five_prime_cis_splice_site	91785	91786	0.993	-	.	Parent=gene143
1877523	gth	exon	91786	91786	1	-	.	Parent=gene143
###
1877523	gth	gene	92903	93265	1	-	.	ID=gene144;Target=9786193 1 266 +
1877523	gth	exon	92903	93008	1	-	.	Parent=gene144
1877523	gth	three_prime_cis_splice_site	93008	93009	0.987	-	.	Parent=gene144
1877523	gth	five_prime_cis_splice_site	93105	93106	0.925	-	.	Parent=gene144
1877523	gth	exon	93106	93265	1	-	.	Parent=gene144
###
1877523	gth	gene	93551	94053	0.957	-	.	ID=gene145;Target=19806050 1 401 -
1877523	gth	exon	93551	93913	0.957	-	.	Parent=gene145
1877523	gth	three_prime_cis_splice_site	93913	93914	0.992	-	.	Parent=gene145
1877523	gth	five_prime_cis_splice_site	94016	94017	0.996	-	.	Parent=gene145
1877523	gth	exon	94017	94053	0.919	-	.	Parent=gene145
###
1877523	gth	gene	93552	93837	0.83	-	.	ID=gene146;Target=2047981 81 377 +
1877523	gth	exon	93552	93837	0.83	-	.	Parent=gene146
###
1877523	gth	gene	93633	94384	1	-	.	ID=gene147;Target=19857902 1 407 -
1877523	gth	exon	93633	93913	1	-	.	Parent=gene147
1877523	gth	three_prime_cis_splice_site	93913	93914	0.992	-	.	Parent=gene147
1877523	gth	five_prime_cis_splice_site	94016	94017	0.996	-	.	Parent=gene147
1877523	gth	exon	94017	94124	1	-	.	Parent=gene147
1877523	gth	three_prime_cis_splice_site	94124	94125	0.998	-	.	Parent=gene147
1877523	gth	five_prime_cis_splice_site	94366	94367	0.994	-	.	Parent=gene147
1877523	gth	exon	94367	94384	1	-	.	Parent=gene147
###
1877523	gth	gene	94706	95368	0.95	-	.	ID=gene148;Target=9782167 1 392 +
1877523	gth	exon	94706	94771	0.871	-	.	Parent=gene148
1877523	gth	three_prime_cis_splice_site	94771	94772	0.993	-	.	Parent=gene148
1877523	gth	five_prime_cis_splice_site	94876	94877	0.985	-	.	Parent=gene148
1877523	gth	exon	94877	94985	0.954	-	.	Parent=gene148
1877523	gth	three_prime_cis_splice_site	94985	94986	0.957	-	.	Parent=gene148
1877523	gth	five_prime_cis_splice_site	95070	95071	0.958	-	.	Parent=gene148
1877523	gth	exon	95071	95147	1	-	.	Parent=gene148
1877523	gth	three_prime_cis_splice_site	95147	95148	0.992	-	.	Parent=gene148
1877523	gth	five_prime_cis_splice_site	95233	95234	0.937	-	.	Parent=gene148
1877523	gth	exon	95234	95368	0.956	-	.	Parent=gene148
###
1877523	gth	gene	95317	96614	0.995	-	.	ID=gene149;Target=19866748 1 646 +
1877523	gth	exon	95317	95454	1	-	.	Parent=gene149
1877523	gth	three_prime_cis_splice_site	95454	95455	0.938	-	.	Parent=gene149
1877523	gth	five_prime_cis_splice_site	95841	95842	0.988	-	.	Parent=gene149
1877523	gth	exon	95842	95947	0.991	-	.	Parent=gene149
1877523	gth	three_prime_cis_splice_site	95947	95948	0.999	-	.	Parent=gene149
1877523	gth	five_prime_cis_splice_site	96035	96036	0.993	-	.	Parent=gene149
1877523	gth	exon	96036	96140	1	-	.	Parent=gene149
1877523	gth	three_prime_cis_splice_site	96140	96141	0.869	-	.	Parent=gene149
1877523	gth	five_prime_cis_splice_site	96231	96232	0.996	-	.	Parent=gene149
1877523	gth	exon	96232	96330	1	-	.	Parent=gene149
1877523	gth	three_prime_cis_splice_site	96330	96331	0.996	-	.	Parent=gene149
1877523	gth	five_prime_cis_splice_site	96417	96418	0.958	-	.	Parent=gene149
1877523	gth	exon	96418	96614	0.987	-	.	Parent=gene149
###
1877523	gth	gene	95905	96592	0.989	-	.	ID=gene150;Target=9778306 1 422 +
1877523	gth	exon	95905	95947	0.907	-	.	Parent=gene150
1877523	gth	three_prime_cis_splice_site	95947	95948	0.999	-	.	Parent=gene150
1877523	gth	five_prime_cis_splice_site	96035	96036	0.993	-	.	Parent=gene150
1877523	gth	exon	96036	96140	1	-	.	Parent=gene150
1877523	gth	three_prime_cis_splice_site	96140	96141	0.869	-	.	Parent=gene150
1877523	gth	five_prime_cis_splice_site	96231	96232	0.996	-	.	Parent=gene150
1877523	gth	exon	96232	96330	1	-	.	Parent=gene150
1877523	gth	three_prime_cis_splice_site	96330	96331	0.996	-	.	Parent=gene150
1877523	gth	five_prime_cis_splice_site	96417	96418	0.958	-	.	Parent=gene150
1877523	gth	exon	96418	96592	0.977	-	.	Parent=gene150
###
1877523	gth	gene	95929	96592	0.984	-	.	ID=gene151;Target=9778321 1 398 +
1877523	gth	exon	95929	95947	0.947	-	.	Parent=gene151
1877523	gth	three_prime_cis_splice_site	95947	95948	0.999	-	.	Parent=gene151
1877523	gth	five_prime_cis_splice_site	96035	96036	0.993	-	.	Parent=gene151
1877523	gth	exon	96036	96140	0.981	-	.	Parent=gene151
1877523	gth	three_prime_cis_splice_site	96140	96141	0.869	-	.	Parent=gene151
1877523	gth	five_prime_cis_splice_site	96231	96232	0.996	-	.	Parent=gene151
1877523	gth	exon	96232	96330	1	-	.	Parent=gene151
1877523	gth	three_prime_cis_splice_site	96330	96331	0.996	-	.	Parent=gene151
1877523	gth	five_prime_cis_splice_site	96417	96418	0.958	-	.	Parent=gene151
1877523	gth	exon	96418	96592	0.977	-	.	Parent=gene151
###
1877523	gth	gene	98857	99326	1	-	.	ID=gene152;Target=19836538 1 392 -
1877523	gth	exon	98857	99121	1	-	.	Parent=gene152
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene152
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene152
1877523	gth	exon	99200	99326	1	-	.	Parent=gene152
###
1877523	gth	gene	98861	99271	1	-	.	ID=gene153;Target=8737545 1 333 -
1877523	gth	exon	98861	99121	1	-	.	Parent=gene153
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene153
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene153
1877523	gth	exon	99200	99271	1	-	.	Parent=gene153
###
1877523	gth	gene	98861	99511	0.9	-	.	ID=gene154;Target=2446000 47 535 +
1877523	gth	exon	98861	99121	0.992	-	.	Parent=gene154
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene154
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene154
1877523	gth	exon	99200	99361	0.883	-	.	Parent=gene154
1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene154
1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene154
1877523	gth	exon	99443	99511	0.594	-	.	Parent=gene154
###
1877523	gth	gene	98878	99663	0.987	-	.	ID=gene155;Target=5846455 1 525 -
1877523	gth	exon	98878	99121	0.996	-	.	Parent=gene155
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene155
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene155
1877523	gth	exon	99200	99361	1	-	.	Parent=gene155
1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene155
1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene155
1877523	gth	exon	99443	99511	1	-	.	Parent=gene155
1877523	gth	three_prime_cis_splice_site	99511	99512	0.998	-	.	Parent=gene155
1877523	gth	five_prime_cis_splice_site	99612	99613	0.999	-	.	Parent=gene155
1877523	gth	exon	99613	99663	0.882	-	.	Parent=gene155
###
1877523	gth	gene	98909	99450	1	-	.	ID=gene156;Target=8734273 1 383 -
1877523	gth	exon	98909	99121	1	-	.	Parent=gene156
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene156
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene156
1877523	gth	exon	99200	99361	1	-	.	Parent=gene156
1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene156
1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene156
1877523	gth	exon	99443	99450	1	-	.	Parent=gene156
###
1877523	gth	gene	98987	99504	0.962	-	.	ID=gene157;Target=397246 1 362 +
1877523	gth	exon	98987	99121	0.9	-	.	Parent=gene157
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene157
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene157
1877523	gth	exon	99200	99361	1	-	.	Parent=gene157
1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene157
1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene157
1877523	gth	exon	99443	99504	1	-	.	Parent=gene157
###
1877523	gth	gene	99613	100804	0.998	-	.	ID=gene158;Target=19863867 1 661 +
1877523	gth	exon	99613	99877	1	-	.	Parent=gene158
1877523	gth	three_prime_cis_splice_site	99877	99878	0.981	-	.	Parent=gene158
1877523	gth	five_prime_cis_splice_site	100101	100102	0.978	-	.	Parent=gene158
1877523	gth	exon	100102	100226	1	-	.	Parent=gene158
1877523	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene158
1877523	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene158
1877523	gth	exon	100327	100434	1	-	.	Parent=gene158
1877523	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene158
1877523	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene158
1877523	gth	exon	100539	100646	1	-	.	Parent=gene158
1877523	gth	three_prime_cis_splice_site	100646	100647	0	-	.	Parent=gene158
1877523	gth	five_prime_cis_splice_site	100748	100749	0.995	-	.	Parent=gene158
1877523	gth	exon	100749	100804	0.982	-	.	Parent=gene158
###
1877523	gth	gene	99698	100804	0.997	-	.	ID=gene159;Target=19870774 1 577 +
1877523	gth	exon	99698	99877	0.994	-	.	Parent=gene159
1877523	gth	three_prime_cis_splice_site	99877	99878	0.981	-	.	Parent=gene159
1877523	gth	five_prime_cis_splice_site	100101	100102	0.978	-	.	Parent=gene159
1877523	gth	exon	100102	100226	1	-	.	Parent=gene159
1877523	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene159
1877523	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene159
1877523	gth	exon	100327	100434	1	-	.	Parent=gene159
1877523	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene159
1877523	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene159
1877523	gth	exon	100539	100646	1	-	.	Parent=gene159
1877523	gth	three_prime_cis_splice_site	100646	100647	0	-	.	Parent=gene159
1877523	gth	five_prime_cis_splice_site	100748	100749	0.995	-	.	Parent=gene159
1877523	gth	exon	100749	100804	0.982	-	.	Parent=gene159
###
1877523	gth	gene	99801	100766	0.933	-	.	ID=gene160;Target=958152 1 437 +
1877523	gth	exon	99801	99877	0.76	-	.	Parent=gene160
1877523	gth	three_prime_cis_splice_site	99877	99878	0.981	-	.	Parent=gene160
1877523	gth	five_prime_cis_splice_site	100101	100102	0.978	-	.	Parent=gene160
1877523	gth	exon	100102	100226	0.948	-	.	Parent=gene160
1877523	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene160
1877523	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene160
1877523	gth	exon	100327	100434	1	-	.	Parent=gene160
1877523	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene160
1877523	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene160
1877523	gth	exon	100539	100646	0.972	-	.	Parent=gene160
1877523	gth	three_prime_cis_splice_site	100646	100647	0	-	.	Parent=gene160
1877523	gth	five_prime_cis_splice_site	100748	100749	0.995	-	.	Parent=gene160
1877523	gth	exon	100749	100766	1	-	.	Parent=gene160
###
1877523	gth	gene	100105	100634	1	-	.	ID=gene161;Target=8732177 1 326 +
1877523	gth	exon	100105	100226	1	-	.	Parent=gene161
1877523	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene161
1877523	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene161
1877523	gth	exon	100327	100434	1	-	.	Parent=gene161
1877523	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene161
1877523	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene161
1877523	gth	exon	100539	100634	1	-	.	Parent=gene161
###
1877523	gth	gene	103616	104455	0.96	+	.	ID=gene162;Target=2580948 1 435 +
1877523	gth	exon	103616	103753	0.975	+	.	Parent=gene162
1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene162
1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene162
1877523	gth	exon	103982	104035	0.981	+	.	Parent=gene162
1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene162
1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene162
1877523	gth	exon	104118	104198	0.975	+	.	Parent=gene162
1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene162
1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene162
1877523	gth	exon	104295	104455	0.932	+	.	Parent=gene162
###
1877523	gth	gene	103616	104478	0.909	+	.	ID=gene163;Target=2759743 1 460 +
1877523	gth	exon	103616	103753	1	+	.	Parent=gene163
1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene163
1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene163
1877523	gth	exon	103982	104035	0.981	+	.	Parent=gene163
1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene163
1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene163
1877523	gth	exon	104118	104198	1	+	.	Parent=gene163
1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene163
1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene163
1877523	gth	exon	104295	104478	0.78	+	.	Parent=gene163
###
1877523	gth	gene	103616	104819	0.952	+	.	ID=gene164;Target=5840051 1 700 +
1877523	gth	exon	103616	103753	1	+	.	Parent=gene164
1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene164
1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene164
1877523	gth	exon	103982	104035	1	+	.	Parent=gene164
1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene164
1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene164
1877523	gth	exon	104118	104198	1	+	.	Parent=gene164
1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene164
1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene164
1877523	gth	exon	104295	104724	0.921	+	.	Parent=gene164
1877523	gth	five_prime_cis_splice_site	104725	104726	0.953	+	.	Parent=gene164
1877523	gth	three_prime_cis_splice_site	104801	104802	0.814	+	.	Parent=gene164
1877523	gth	exon	104803	104819	0.765	+	.	Parent=gene164
###
1877523	gth	gene	103706	104416	0.829	+	.	ID=gene165;Target=8686177 99 409 +
1877523	gth	exon	103706	103731	0.885	+	.	Parent=gene165
1877523	gth	five_prime_cis_splice_site	103732	103733	0	+	.	Parent=gene165
1877523	gth	three_prime_cis_splice_site	103797	103798	0	+	.	Parent=gene165
1877523	gth	exon	103799	103826	0.518	+	.	Parent=gene165
1877523	gth	five_prime_cis_splice_site	103827	103828	0.326	+	.	Parent=gene165
1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene165
1877523	gth	exon	103982	104035	0.778	+	.	Parent=gene165
1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene165
1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene165
1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene165
1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene165
1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene165
1877523	gth	exon	104295	104416	0.844	+	.	Parent=gene165
###
1877523	gth	gene	103713	104391	0.812	+	.	ID=gene166;Target=453733 78 357 +
1877523	gth	exon	103713	103731	1	+	.	Parent=gene166
1877523	gth	five_prime_cis_splice_site	103732	103733	0	+	.	Parent=gene166
1877523	gth	three_prime_cis_splice_site	103797	103798	0	+	.	Parent=gene166
1877523	gth	exon	103799	103826	0.518	+	.	Parent=gene166
1877523	gth	five_prime_cis_splice_site	103827	103828	0.326	+	.	Parent=gene166
1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene166
1877523	gth	exon	103982	104035	0.778	+	.	Parent=gene166
1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene166
1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene166
1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene166
1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene166
1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene166
1877523	gth	exon	104295	104391	0.809	+	.	Parent=gene166
###
1877523	gth	gene	103746	104415	0.824	+	.	ID=gene167;Target=8722221 103 366 +
1877523	gth	exon	103746	103753	0.875	+	.	Parent=gene167
1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene167
1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene167
1877523	gth	exon	103982	104035	0.778	+	.	Parent=gene167
1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene167
1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene167
1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene167
1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene167
1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene167
1877523	gth	exon	104295	104415	0.835	+	.	Parent=gene167
###
1877523	gth	gene	103746	104440	0.829	+	.	ID=gene168;Target=623629 87 375 +
1877523	gth	exon	103746	103753	0.875	+	.	Parent=gene168
1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene168
1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene168
1877523	gth	exon	103982	104035	0.778	+	.	Parent=gene168
1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene168
1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene168
1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene168
1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene168
1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene168
1877523	gth	exon	104295	104440	0.842	+	.	Parent=gene168
###
1877523	gth	gene	103982	104683	0.818	+	.	ID=gene169;Target=9778203 71 401 +
1877523	gth	exon	103982	104035	0.759	+	.	Parent=gene169
1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene169
1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene169
1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene169
1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene169
1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene169
1877523	gth	exon	104295	104455	0.826	+	.	Parent=gene169
1877523	gth	five_prime_cis_splice_site	104456	104457	0.522	+	.	Parent=gene169
1877523	gth	three_prime_cis_splice_site	104647	104648	0	+	.	Parent=gene169
1877523	gth	exon	104649	104683	0.971	+	.	Parent=gene169
###
1877523	gth	gene	103982	104881	0.909	+	.	ID=gene170;Target=8731408 68 518 +
1877523	gth	exon	103982	104035	0.944	+	.	Parent=gene170
1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene170
1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene170
1877523	gth	exon	104118	104198	0.951	+	.	Parent=gene170
1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene170
1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene170
1877523	gth	exon	104295	104455	0.888	+	.	Parent=gene170
1877523	gth	five_prime_cis_splice_site	104456	104457	0.522	+	.	Parent=gene170
1877523	gth	three_prime_cis_splice_site	104647	104648	0	+	.	Parent=gene170
1877523	gth	exon	104649	104724	0.934	+	.	Parent=gene170
1877523	gth	five_prime_cis_splice_site	104725	104726	0.953	+	.	Parent=gene170
1877523	gth	three_prime_cis_splice_site	104801	104802	0.814	+	.	Parent=gene170
1877523	gth	exon	104803	104881	0.861	+	.	Parent=gene170
###
1877523	gth	gene	104394	105201	0.83	+	.	ID=gene171;Target=937871 1 457 +
1877523	gth	exon	104394	104455	0.887	+	.	Parent=gene171
1877523	gth	five_prime_cis_splice_site	104456	104457	0.522	+	.	Parent=gene171
1877523	gth	three_prime_cis_splice_site	104647	104648	0	+	.	Parent=gene171
1877523	gth	exon	104649	104724	0.921	+	.	Parent=gene171
1877523	gth	five_prime_cis_splice_site	104725	104726	0.953	+	.	Parent=gene171
1877523	gth	three_prime_cis_splice_site	104801	104802	0.814	+	.	Parent=gene171
1877523	gth	exon	104803	104928	0.841	+	.	Parent=gene171
1877523	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene171
1877523	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene171
1877523	gth	exon	105010	105201	0.768	+	.	Parent=gene171
###
1877523	gth	gene	104803	105220	0.852	+	.	ID=gene172;Target=9781141 22 358 +
1877523	gth	exon	104803	104928	0.841	+	.	Parent=gene172
1877523	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene172
1877523	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene172
1877523	gth	exon	105010	105220	0.858	+	.	Parent=gene172
###
1877523	gth	gene	104912	105793	0.887	+	.	ID=gene173;Target=7611662 1 549 -
1877523	gth	exon	104912	104928	0.824	+	.	Parent=gene173
1877523	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene173
1877523	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene173
1877523	gth	exon	105010	105228	0.863	+	.	Parent=gene173
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene173
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene173
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene173
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene173
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene173
1877523	gth	exon	105500	105535	1	+	.	Parent=gene173
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene173
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene173
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene173
###
1877523	gth	gene	105009	105793	0.884	+	.	ID=gene174;Target=8734901 1 533 -
1877523	gth	exon	105009	105228	0.864	+	.	Parent=gene174
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene174
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene174
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene174
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene174
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene174
1877523	gth	exon	105500	105535	1	+	.	Parent=gene174
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene174
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene174
1877523	gth	exon	105630	105793	0.89	+	.	Parent=gene174
###
1877523	gth	gene	105069	105815	0.876	+	.	ID=gene175;Target=19801855 1 495 -
1877523	gth	exon	105069	105228	0.831	+	.	Parent=gene175
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene175
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene175
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene175
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene175
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene175
1877523	gth	exon	105500	105535	1	+	.	Parent=gene175
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene175
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene175
1877523	gth	exon	105630	105815	0.892	+	.	Parent=gene175
###
1877523	gth	gene	105090	105793	0.878	+	.	ID=gene176;Target=8695006 1 452 -
1877523	gth	exon	105090	105228	0.82	+	.	Parent=gene176
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene176
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene176
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene176
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene176
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene176
1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene176
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene176
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene176
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene176
###
1877523	gth	gene	105091	105793	0.857	+	.	ID=gene177;Target=8702125 1 452 -
1877523	gth	exon	105091	105228	0.786	+	.	Parent=gene177
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene177
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene177
1877523	gth	exon	105315	105428	0.886	+	.	Parent=gene177
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene177
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene177
1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene177
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene177
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene177
1877523	gth	exon	105630	105793	0.896	+	.	Parent=gene177
###
1877523	gth	gene	105140	105793	0.88	+	.	ID=gene178;Target=19825204 1 402 -
1877523	gth	exon	105140	105228	0.798	+	.	Parent=gene178
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene178
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene178
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene178
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene178
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene178
1877523	gth	exon	105500	105535	1	+	.	Parent=gene178
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene178
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene178
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene178
###
1877523	gth	gene	105170	105793	0.862	+	.	ID=gene179;Target=2748033 88 460 -
1877523	gth	exon	105170	105228	0.686	+	.	Parent=gene179
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene179
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene179
1877523	gth	exon	105315	105428	0.904	+	.	Parent=gene179
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene179
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene179
1877523	gth	exon	105500	105535	1	+	.	Parent=gene179
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene179
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene179
1877523	gth	exon	105630	105793	0.896	+	.	Parent=gene179
###
1877523	gth	gene	105175	105793	0.901	+	.	ID=gene180;Target=19835442 1 367 -
1877523	gth	exon	105175	105228	0.87	+	.	Parent=gene180
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene180
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene180
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene180
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene180
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene180
1877523	gth	exon	105500	105535	1	+	.	Parent=gene180
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene180
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene180
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene180
###
1877523	gth	gene	105189	105793	0.896	+	.	ID=gene181;Target=8734878 1 354 -
1877523	gth	exon	105189	105228	0.875	+	.	Parent=gene181
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene181
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene181
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene181
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene181
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene181
1877523	gth	exon	105500	105535	1	+	.	Parent=gene181
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene181
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene181
1877523	gth	exon	105630	105793	0.884	+	.	Parent=gene181
###
1877523	gth	gene	105190	105793	0.906	+	.	ID=gene182;Target=19823987 1 352 -
1877523	gth	exon	105190	105228	0.872	+	.	Parent=gene182
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene182
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene182
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene182
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene182
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene182
1877523	gth	exon	105500	105535	1	+	.	Parent=gene182
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene182
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene182
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene182
###
1877523	gth	gene	105199	105793	0.845	+	.	ID=gene183;Target=19841468 39 385 -
1877523	gth	exon	105199	105228	0.833	+	.	Parent=gene183
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene183
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene183
1877523	gth	exon	105315	105428	0.904	+	.	Parent=gene183
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene183
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene183
1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene183
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene183
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene183
1877523	gth	exon	105630	105793	0.805	+	.	Parent=gene183
###
1877523	gth	gene	105348	105815	0.895	+	.	ID=gene184;Target=2747682 1 302 +
1877523	gth	exon	105348	105428	0.914	+	.	Parent=gene184
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene184
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene184
1877523	gth	exon	105500	105535	1	+	.	Parent=gene184
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene184
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene184
1877523	gth	exon	105630	105815	0.887	+	.	Parent=gene184
###
1877523	gth	gene	105348	105815	0.899	+	.	ID=gene185;Target=2412846 1 302 +
1877523	gth	exon	105348	105428	0.914	+	.	Parent=gene185
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene185
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene185
1877523	gth	exon	105500	105535	1	+	.	Parent=gene185
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene185
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene185
1877523	gth	exon	105630	105815	0.892	+	.	Parent=gene185
###
1877523	gth	gene	105371	105813	0.897	+	.	ID=gene186;Target=17325 1 277 -
1877523	gth	exon	105371	105428	0.931	+	.	Parent=gene186
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene186
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene186
1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene186
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene186
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene186
1877523	gth	exon	105630	105813	0.886	+	.	Parent=gene186
###
1877523	gth	gene	105382	105851	0.986	+	.	ID=gene187;Target=3449578 65 370 +
1877523	gth	exon	105382	105428	0.979	+	.	Parent=gene187
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene187
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene187
1877523	gth	exon	105500	105535	0.903	+	.	Parent=gene187
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene187
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene187
1877523	gth	exon	105630	105851	0.986	+	.	Parent=gene187
###
1877523	gth	gene	105394	105860	0.827	+	.	ID=gene188;Target=19859011 1 296 -
1877523	gth	exon	105394	105428	0.971	+	.	Parent=gene188
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene188
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene188
1877523	gth	exon	105500	105535	1	+	.	Parent=gene188
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene188
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene188
1877523	gth	exon	105630	105860	0.827	+	.	Parent=gene188
###
1877523	gth	gene	105662	105806	0.855	-	.	ID=gene189;Target=8735385 30 173 +
1877523	gth	exon	105662	105806	0.855	-	.	Parent=gene189
###
1877523	gth	gene	106097	106973	0.998	+	.	ID=gene190;Target=19871766 1 425 +
1877523	gth	exon	106097	106290	0.995	+	.	Parent=gene190
1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene190
1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene190
1877523	gth	exon	106566	106619	1	+	.	Parent=gene190
1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene190
1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene190
1877523	gth	exon	106702	106782	1	+	.	Parent=gene190
1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene190
1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene190
1877523	gth	exon	106878	106973	1	+	.	Parent=gene190
###
1877523	gth	gene	106133	106934	0.966	+	.	ID=gene191;Target=17300 1 350 +
1877523	gth	exon	106133	106290	0.962	+	.	Parent=gene191
1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene191
1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene191
1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene191
1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene191
1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene191
1877523	gth	exon	106702	106782	1	+	.	Parent=gene191
1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene191
1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene191
1877523	gth	exon	106878	106934	0.912	+	.	Parent=gene191
###
1877523	gth	gene	106148	106751	0.966	+	.	ID=gene192;Target=7612621 1 248 +
1877523	gth	exon	106148	106290	0.948	+	.	Parent=gene192
1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene192
1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene192
1877523	gth	exon	106566	106619	1	+	.	Parent=gene192
1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene192
1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene192
1877523	gth	exon	106702	106751	0.98	+	.	Parent=gene192
###
1877523	gth	gene	106149	106973	0.924	+	.	ID=gene193;Target=935362 1 377 +
1877523	gth	exon	106149	106290	0.979	+	.	Parent=gene193
1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene193
1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene193
1877523	gth	exon	106566	106619	0.944	+	.	Parent=gene193
1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene193
1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene193
1877523	gth	exon	106702	106782	0.975	+	.	Parent=gene193
1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene193
1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene193
1877523	gth	exon	106878	106973	0.786	+	.	Parent=gene193
###
1877523	gth	gene	106156	106973	0.915	+	.	ID=gene194;Target=936803 1 374 +
1877523	gth	exon	106156	106290	0.97	+	.	Parent=gene194
1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene194
1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene194
1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene194
1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene194
1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene194
1877523	gth	exon	106702	106782	1	+	.	Parent=gene194
1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene194
1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene194
1877523	gth	exon	106878	106973	0.729	+	.	Parent=gene194
###
1877523	gth	gene	106156	106973	1	+	.	ID=gene195;Target=7612394 1 366 +
1877523	gth	exon	106156	106290	1	+	.	Parent=gene195
1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene195
1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene195
1877523	gth	exon	106566	106619	1	+	.	Parent=gene195
1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene195
1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene195
1877523	gth	exon	106702	106782	1	+	.	Parent=gene195
1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene195
1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene195
1877523	gth	exon	106878	106973	1	+	.	Parent=gene195
###
1877523	gth	gene	106161	106750	0.967	+	.	ID=gene196;Target=2733258 26 261 +
1877523	gth	exon	106161	106290	0.962	+	.	Parent=gene196
1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene196
1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene196
1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene196
1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene196
1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene196
1877523	gth	exon	106702	106750	0.724	+	.	Parent=gene196
###
1877523	gth	gene	106168	106917	0.981	+	.	ID=gene197;Target=8729681 1 298 +
1877523	gth	exon	106168	106290	0.976	+	.	Parent=gene197
1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene197
1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene197
1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene197
1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene197
1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene197
1877523	gth	exon	106702	106782	0.988	+	.	Parent=gene197
1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene197
1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene197
1877523	gth	exon	106878	106917	0.95	+	.	Parent=gene197
###
1877523	gth	gene	106224	106710	0.959	+	.	ID=gene198;Target=2759942 1 130 +
1877523	gth	exon	106224	106290	0.94	+	.	Parent=gene198
1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene198
1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene198
1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene198
1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene198
1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene198
1877523	gth	exon	106702	106710	1	+	.	Parent=gene198
###
1877523	gth	gene	106716	106973	0.847	+	.	ID=gene199;Target=9778889 1 162 +
1877523	gth	exon	106716	106782	0.806	+	.	Parent=gene199
1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene199
1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene199
1877523	gth	exon	106878	106973	0.875	+	.	Parent=gene199
###
genometools-1.5.1/testdata/U89959_sas.gff3md5000066400000000000000000004523041211610345200205440ustar00rootroot00000000000000##gff-version   3
##sequence-region   md5:063b1024d68e26716b7f38caf958316f:1877523 1 106973
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	1074	1540	1	+	.	ID=gene1;Target=md5:14c0ff5e76ef8ac009fdcc923f701356:8721428 1 303 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	1074	1171	1	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	1172	1173	0.866	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	1257	1258	0.994	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	1259	1354	1	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	1355	1356	0	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	1430	1431	0.745	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	1432	1540	1	+	.	Parent=gene1
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	2779	3355	0.84	+	.	ID=gene2;Target=md5:527995da853a37f9c47e616ce237d523:8732738 1 337 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	2779	2801	0.696	+	.	Parent=gene2
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	2802	2803	0.459	+	.	Parent=gene2
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	3041	3042	0	+	.	Parent=gene2
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	3043	3355	0.84	+	.	Parent=gene2
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	3025	3351	1	+	.	ID=gene3;Target=md5:f1a0d426e93585553b21aa1a47aa2970:19837778 1 327 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	3025	3351	1	+	.	Parent=gene3
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	3041	3651	0.996	-	.	ID=gene4;Target=md5:cabe5b677d534fb65e0d2245f61e2bd1:8732878 1 536 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	3041	3550	0.996	-	.	Parent=gene4
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	3550	3551	1	-	.	Parent=gene4
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	3625	3626	0.741	-	.	Parent=gene4
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	3626	3651	1	-	.	Parent=gene4
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	3077	3506	0.974	+	.	ID=gene5;Target=md5:a9dcd316817972a94c0af505715b10bc:19843099 1 426 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	3077	3506	0.974	+	.	Parent=gene5
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	4768	5357	0.987	-	.	ID=gene6;Target=md5:e40253c45f8d96170d6af32f8d8e3e05:19871046 1 591 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	4768	5357	0.987	-	.	Parent=gene6
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	9505	10058	1	+	.	ID=gene7;Target=md5:f28eda487869903339de7a431f00fccd:8682455 1 554 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	9505	10058	1	+	.	Parent=gene7
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	12024	12542	1	-	.	ID=gene8;Target=md5:300d9c80d9f566412745a6bda32e3e12:8688760 1 519 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	12024	12542	1	-	.	Parent=gene8
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	13014	13465	0.881	-	.	ID=gene9;Target=md5:c6826f50615c7fb2eb70e294bb7202cb:2748705 1 459 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	13014	13465	0.881	-	.	Parent=gene9
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	15955	16603	0.997	+	.	ID=gene10;Target=md5:bceada3d0ee38c76dafe93fd74e71dfe:19878194 1 649 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	15955	16603	0.997	+	.	Parent=gene10
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	17165	17684	0.985	+	.	ID=gene11;Target=md5:8bbc72e5847196327c25661544c6bdf9:19798999 1 396 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	17165	17247	0.97	+	.	Parent=gene11
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	17248	17249	1	+	.	Parent=gene11
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	17372	17373	0.994	+	.	Parent=gene11
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	17374	17684	0.989	+	.	Parent=gene11
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	25221	26100	1	+	.	ID=gene12;Target=md5:ff7357d7a1877d31d94543a13d64fa0e:8690053 1 521 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	25221	25310	1	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	25311	25312	0.993	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	25508	25509	0.439	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	25510	25626	1	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	25627	25628	0.998	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	25711	25712	0.996	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	25713	25841	1	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	25842	25843	0.63	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	25914	25915	0.926	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	25916	26100	1	+	.	Parent=gene12
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	27900	28989	1	+	.	ID=gene13;Target=md5:c69c15ebe466171a13ee5aa610e90e61:8726341 1 499 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	27900	28003	1	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	28004	28005	0.999	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	28267	28268	0.995	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	28269	28424	1	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	28425	28426	0.936	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	28505	28506	0	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	28507	28579	1	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	28580	28581	0.989	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	28684	28685	0.994	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	28686	28753	1	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	28754	28755	0.999	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	28890	28891	0.999	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	28892	28989	1	+	.	Parent=gene13
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	28990	29817	1	+	.	ID=gene14;Target=md5:0870e7d5d9d76766ebd3dce1758b733f:8726286 1 477 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	28990	29037	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	29038	29039	0.907	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	29132	29133	0	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	29134	29242	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	29243	29244	0.84	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	29329	29330	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	29331	29477	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	29478	29479	0.983	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	29569	29570	0.998	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	29571	29618	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	29619	29620	0	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	29691	29692	0.993	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	29693	29817	1	+	.	Parent=gene14
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	30278	31355	1	+	.	ID=gene15;Target=md5:97350772e29b7881b149afbedf09290d:8690080 1 524 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	30278	30391	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	30392	30393	0.985	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	30475	30476	0.918	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	30477	30562	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	30563	30564	0.938	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	30656	30657	0.973	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	30658	30763	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	30764	30765	0.996	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	30988	30989	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	30990	31085	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	31086	31087	0.644	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	31232	31233	0.987	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	31234	31355	1	+	.	Parent=gene15
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	31265	31820	1	+	.	ID=gene16;Target=md5:cc954bf1761c4c9f05f8822afb1079e3:8689616 1 333 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	31265	31386	1	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	31387	31388	0.996	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	31536	31537	0.99	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	31538	31720	1	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	31721	31722	0.994	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	31791	31792	0.995	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	31793	31820	1	+	.	Parent=gene16
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	31855	32362	1	+	.	ID=gene17;Target=md5:70facb44682374068ef43fd0a6e116b5:8689215 1 334 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	31855	32022	1	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	32023	32024	0	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	32116	32117	0.558	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	32118	32220	1	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	32221	32222	0.912	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	32298	32299	0.895	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	32300	32362	1	+	.	Parent=gene17
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	31907	32349	1	+	.	ID=gene18;Target=md5:c7084aa0f01934072f9e244363059ca0:9784594 1 269 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	31907	32022	1	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	32023	32024	0	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	32116	32117	0.558	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	32118	32220	1	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	32221	32222	0.912	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	32298	32299	0.895	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	32300	32349	1	+	.	Parent=gene18
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	32928	33488	0.967	+	.	ID=gene19;Target=md5:4e8ae3a74fefacbbb8650ba892c2b2da:19875482 1 227 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	32928	32955	1	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	32956	32957	0.985	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	33189	33190	0.999	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	33191	33317	0.98	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	33318	33319	0.956	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	33416	33417	0.983	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	33418	33488	0.944	+	.	Parent=gene19
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	33296	34560	1	+	.	ID=gene20;Target=md5:f53ad09e45a4038f2261b9ee90353658:9782568 1 427 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	33296	33317	0.636	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	33318	33319	0.956	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	33416	33417	0.983	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	33418	33518	1	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	33519	33520	0.993	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	33781	33782	0.99	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	33783	33917	1	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	33918	33919	0.705	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	33994	33995	0.988	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	33996	34076	1	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	34077	34078	0.961	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	34470	34471	0.999	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	34472	34560	1	+	.	Parent=gene20
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	35628	36362	0.921	+	.	ID=gene21;Target=md5:a7fa97bc84c3aebaea34e169b73094c9:2759121 1 451 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	35628	35712	0.959	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	35713	35714	0.988	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	35818	35819	0.971	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	35820	36011	0.979	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36012	36013	0.955	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36099	36100	0.992	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36101	36205	0.924	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36206	36207	0.99	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36295	36296	0.979	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36297	36362	0.697	+	.	Parent=gene21
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	35628	36392	0.984	+	.	ID=gene22;Target=md5:cdced248d13c7c0f89e7e889cc30164a:5841805 1 479 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	35628	35712	1	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	35713	35714	0.988	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	35818	35819	0.971	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	35820	36011	1	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36012	36013	0.955	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36099	36100	0.992	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36101	36205	1	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36206	36207	0.99	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36295	36296	0.979	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36297	36392	0.922	+	.	Parent=gene22
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	36370	37156	1	+	.	ID=gene23;Target=md5:0d914f8b8fdfef05d05e32a617ce8737:8683519 1 604 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36370	36431	1	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36432	36433	0.994	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36519	36520	1	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36521	36721	1	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36816	37156	1	+	.	Parent=gene23
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	36402	37106	1	+	.	ID=gene24;Target=md5:634e9a3d54562a834a900edb41abe7d4:8682814 1 522 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36402	36431	1	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36432	36433	0.994	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36519	36520	1	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36521	36721	1	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36816	37106	1	+	.	Parent=gene24
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	36531	37190	1	+	.	ID=gene25;Target=md5:e24a612b49c52c8aca23eb196c1ebe06:8690927 1 566 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36531	36721	1	+	.	Parent=gene25
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene25
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene25
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36816	37190	1	+	.	Parent=gene25
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	36546	37186	0.99	+	.	ID=gene26;Target=md5:835eb4298c428885b3d16d0e4514c30b:5845530 1 547 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36546	36721	0.969	+	.	Parent=gene26
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene26
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene26
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36816	37186	1	+	.	Parent=gene26
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	36594	37208	1	+	.	ID=gene27;Target=md5:b280ddc383280ca975eeaa3329e34c14:8717375 1 521 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36594	36721	1	+	.	Parent=gene27
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene27
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene27
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36816	37208	1	+	.	Parent=gene27
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	36812	37235	0.998	-	.	ID=gene28;Target=md5:26ebd521c00f7b4d595086f162ab00e1:8735393 1 424 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36812	37235	0.998	-	.	Parent=gene28
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	36816	37208	0.964	+	.	ID=gene29;Target=md5:3ff6374febf91a5f28c3f7bcc4ccd774:2048630 53 438 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36816	37208	0.964	+	.	Parent=gene29
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	36827	37206	0.997	-	.	ID=gene30;Target=md5:7f0facaa45cacec8ffaa0c98a51edf56:19741846 1 380 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36827	37206	0.997	-	.	Parent=gene30
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	36840	37234	1	-	.	ID=gene31;Target=md5:275dc2512038a6501b7d27e38165bec7:8738747 1 395 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	36840	37234	1	-	.	Parent=gene31
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	37071	37203	1	-	.	ID=gene32;Target=md5:af2486ba93823b9389100222c0ddffdb:8679389 1 133 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	37071	37203	1	-	.	Parent=gene32
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	37669	39259	1	-	.	ID=gene33;Target=md5:b1da76b1bfdf36225429a5be70ff88a2:8738841 1 588 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	37669	37891	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	37972	38060	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	38656	38794	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38794	38795	0.976	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	38926	38927	0.977	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	38927	38997	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39104	39148	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39239	39259	1	-	.	Parent=gene33
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	37691	38766	0.995	-	.	ID=gene34;Target=md5:354c93700a73d01ea73f641c62c593cd:19831991 1 401 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	37691	37891	0.99	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	37972	38060	1	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	38656	38766	1	-	.	Parent=gene34
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	37692	38756	1	-	.	ID=gene35;Target=md5:f42df1d200fb31e1bed322fab31540d6:19840745 1 390 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	37692	37891	1	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	37972	38060	1	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	38656	38756	1	-	.	Parent=gene35
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	37716	39118	0.967	-	.	ID=gene36;Target=md5:f55d7bcc44b78111563b02f8a19805ee:5843191 1 490 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	37716	37891	0.977	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	37972	38060	1	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	38656	38794	0.953	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38794	38795	0.976	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	38926	38927	0.977	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	38927	38997	0.93	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39104	39118	0.933	-	.	Parent=gene36
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	38927	40032	0.996	-	.	ID=gene37;Target=md5:a3f1555a0375aea877145c8c372ae4af:19869427 1 606 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	38927	38997	0.986	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39104	39148	1	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39239	39328	1	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	39328	39329	0.974	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39437	39438	0.999	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39438	39526	1	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	39526	39527	0.453	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39613	39614	0.986	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39614	39689	1	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	39689	39690	0.973	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39797	39798	0.999	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39798	40032	0.996	-	.	Parent=gene37
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	38938	40006	0.998	-	.	ID=gene38;Target=md5:a5f947d297585356da9380d22ac8c974:8722075 1 568 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	38938	38997	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39104	39148	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39239	39328	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	39328	39329	0.974	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39437	39438	0.999	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39438	39526	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	39526	39527	0.453	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39613	39614	0.986	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39614	39689	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	39689	39690	0.973	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	39797	39798	0.999	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	39798	40006	0.995	-	.	Parent=gene38
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	42783	43204	1	-	.	ID=gene39;Target=md5:bdc426cd84a477b9b48d7e7d1538fc85:19858773 1 422 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	42783	43204	1	-	.	Parent=gene39
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	44029	44540	0.972	+	.	ID=gene40;Target=md5:0f6d1e4ce29d042b5804f8ae8bd9c43a:402959 1 423 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	44029	44263	0.991	+	.	Parent=gene40
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	44264	44265	0.99	+	.	Parent=gene40
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	44352	44353	0.998	+	.	Parent=gene40
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	44354	44540	0.947	+	.	Parent=gene40
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	45542	45866	0.991	-	.	ID=gene41;Target=md5:7ba0b8c1bb50abf3c5a844abacf9fe67:8682693 1 322 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	45542	45866	0.991	-	.	Parent=gene41
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	45559	45941	0.924	-	.	ID=gene42;Target=md5:38229ac075d9c6d15fd1152c4eccc834:402964 1 388 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	45559	45941	0.924	-	.	Parent=gene42
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	45843	45920	0.949	+	.	ID=gene43;Target=md5:6d3b4b9db4531cda588528f2c69c0a57:8720010 1 78 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	45843	45920	0.949	+	.	Parent=gene43
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	49874	50547	1	-	.	ID=gene44;Target=md5:494051ed1147d22a2b2967b64c329678:19837290 1 412 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	49874	50284	1	-	.	Parent=gene44
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	50284	50285	0.587	-	.	Parent=gene44
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	50546	50547	0.677	-	.	Parent=gene44
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	50547	50547	1	-	.	Parent=gene44
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	50433	51134	0.978	-	.	ID=gene45;Target=md5:634ef96163dc4d4f8a585fe8059d867b:19807151 1 426 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	50433	50834	0.978	-	.	Parent=gene45
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene45
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene45
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51113	51134	1	-	.	Parent=gene45
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	50475	50702	1	+	.	ID=gene46;Target=md5:950b7715ab6cc030a8c810a0dba2dd33:8727457 1 228 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	50475	50702	1	+	.	Parent=gene46
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	50475	51193	1	-	.	ID=gene47;Target=md5:754b35896aef0625da39ee42e61db715:8731976 1 441 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	50475	50834	1	-	.	Parent=gene47
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene47
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene47
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51113	51193	1	-	.	Parent=gene47
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	50590	51354	1	-	.	ID=gene48;Target=md5:741ff4d6dd193d77cc75fb61f373ca5b:19805724 1 385 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	50590	50834	1	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51113	51216	1	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51319	51354	1	-	.	Parent=gene48
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	50758	52232	0.991	-	.	ID=gene49;Target=md5:597ada174987f3f2f0b2e4046f09247d:19866668 1 647 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	50758	50834	0.948	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51113	51216	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51319	51474	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51552	51623	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51711	51758	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51849	51896	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51983	52055	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	52163	52232	0.986	-	.	Parent=gene49
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	51139	51852	0.915	-	.	ID=gene50;Target=md5:8fdc30d821ff25b48b6182936cf72cd5:2747604 1 362 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51139	51216	0.718	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51319	51474	0.974	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51552	51623	1	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51711	51758	0.979	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51849	51852	1	-	.	Parent=gene50
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	51334	52222	0.905	-	.	ID=gene51;Target=md5:26e5980fbaaefb58d84de6755d521845:2596256 1 446 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51334	51474	0.766	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51552	51623	1	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51711	51758	1	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51849	51896	0.979	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51983	52055	1	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	52163	52222	1	-	.	Parent=gene51
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	51376	52048	0.939	-	.	ID=gene52;Target=md5:d342e4ee66b1c4db3e83e076c5dd7d44:2596953 1 336 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51376	51474	0.854	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51552	51623	1	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51711	51758	1	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51849	51896	0.979	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51983	52048	1	-	.	Parent=gene52
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	51376	52224	0.91	-	.	ID=gene53;Target=md5:7f11e59ff50ce68b25c6120418df3d51:5839790 1 404 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51376	51474	0.848	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51552	51623	0.931	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51711	51758	0.823	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51849	51896	0.958	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51983	52055	0.959	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	52163	52224	0.927	-	.	Parent=gene53
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	51446	52242	0.996	-	.	ID=gene54;Target=md5:b0183ab4aa646b9e8f95f61daf0e23a3:403229 1 350 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51446	51474	0.966	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51552	51623	1	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51711	51758	1	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51849	51896	1	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51983	52055	0.986	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	52163	52242	1	-	.	Parent=gene54
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	51599	52231	0.993	-	.	ID=gene55;Target=md5:8ed84d5653334535562a21058880db81:9785390 1 263 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51599	51623	1	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51711	51758	1	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51849	51896	1	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	51983	52055	1	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	52163	52231	0.986	-	.	Parent=gene55
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	53602	54271	0.994	-	.	ID=gene56;Target=md5:16258f1ad08d9c0c91c627eefad05949:8697180 1 427 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	53602	53914	0.992	-	.	Parent=gene56
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene56
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene56
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54159	54271	1	-	.	Parent=gene56
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	53602	54710	0.995	-	.	ID=gene57;Target=md5:2642a22855698a3125c99a9759f9147c:19803773 1 627 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	53602	53914	0.994	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54159	54335	1	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54574	54710	0.993	-	.	Parent=gene57
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	53624	54279	0.989	-	.	ID=gene58;Target=md5:752fa8c75ecef45cfa9cf0c5a59afe49:19840006 1 413 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	53624	53914	0.988	-	.	Parent=gene58
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene58
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene58
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54159	54279	0.992	-	.	Parent=gene58
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	53624	54283	0.992	-	.	ID=gene59;Target=md5:0743a82e324754dfc94ed4c0cd8a8816:19823046 1 417 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	53624	53914	0.988	-	.	Parent=gene59
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene59
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene59
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54159	54283	1	-	.	Parent=gene59
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	53631	54335	0.866	-	.	ID=gene60;Target=md5:198a4aa7626135303d0e996d4e2775ef:2393553 57 528 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	53631	53914	0.991	-	.	Parent=gene60
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene60
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene60
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54159	54335	0.664	-	.	Parent=gene60
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	53632	53909	0.991	+	.	ID=gene61;Target=md5:5a03dd7605925c94812a9550acc2d354:8697126 1 279 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	53632	53909	0.991	+	.	Parent=gene61
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	53645	54320	0.99	-	.	ID=gene62;Target=md5:f692730f2bd8700f690f8a231d2e446b:19843722 1 431 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	53645	53914	0.991	-	.	Parent=gene62
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene62
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene62
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54159	54320	0.988	-	.	Parent=gene62
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	53829	54829	0.991	-	.	ID=gene63;Target=md5:18fb5ebf5d11ec1db0d36de3ea2a049d:8696505 49 568 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	53829	53914	0.971	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54159	54335	1	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54574	54829	0.992	-	.	Parent=gene63
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	53850	54807	0.913	-	.	ID=gene64;Target=md5:ed9e14d2b83e7ea606c9d1d5fdbeb857:5839694 1 477 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	53850	53914	0.746	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54159	54335	0.887	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54574	54807	0.979	-	.	Parent=gene64
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	54167	54769	0.997	-	.	ID=gene65;Target=md5:7db3e698f27f19f0343e6b23af07a5b3:9778953 1 365 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54167	54335	0.994	-	.	Parent=gene65
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene65
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene65
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54574	54769	1	-	.	Parent=gene65
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	54178	54828	0.979	-	.	ID=gene66;Target=md5:6021387359d7e25495b6b804ebbbb0aa:19865963 1 414 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54178	54335	0.953	-	.	Parent=gene66
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene66
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene66
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54574	54828	0.996	-	.	Parent=gene66
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	54212	54697	0.952	-	.	ID=gene67;Target=md5:72f3e9cbd94835f59aa0a43b22a01b0f:9784661 1 248 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54212	54335	0.96	-	.	Parent=gene67
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene67
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene67
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54574	54697	0.944	-	.	Parent=gene67
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	54263	54808	0.93	-	.	ID=gene68;Target=md5:2fa0ef57b1f4391f7a2ae4283410311c:933584 1 311 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54263	54335	0.815	-	.	Parent=gene68
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene68
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene68
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54574	54808	0.966	-	.	Parent=gene68
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	54321	54829	0.992	-	.	ID=gene69;Target=md5:215d14a53287c2aca2d8bd12b09aca14:8696543 49 319 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54321	54335	1	-	.	Parent=gene69
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene69
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene69
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54574	54829	0.992	-	.	Parent=gene69
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	54991	56652	0.998	+	.	ID=gene70;Target=md5:dd287e28fe668e94028c1a241a6a1c7d:19874826 1 651 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	54991	55057	0.985	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	55058	55059	0.896	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	55143	55144	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	55145	55230	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	55231	55232	0.997	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	55298	55299	0	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	55300	55341	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	55342	55343	0.997	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	55451	55452	0.898	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	55453	55498	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	55499	55500	0.237	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	55616	55617	0.997	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	55618	55704	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	55705	55706	0.991	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	55816	55817	0.952	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	55818	55873	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	55874	55875	0.983	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	56034	56035	0.0357	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	56036	56153	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	56154	56155	0.99	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	56279	56280	0.703	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	56281	56339	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	56340	56341	0.464	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	56447	56448	0.287	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	56449	56520	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	56521	56522	0.187	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	56633	56634	0.791	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	56635	56652	1	+	.	Parent=gene70
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	58115	59001	0.984	+	.	ID=gene71;Target=md5:a12796a152e829b54f2f56b4910d701c:19741042 1 460 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	58115	58209	0.958	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	58210	58211	0.856	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	58459	58460	1	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	58461	58526	1	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	58527	58528	0.784	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	58622	58623	0.977	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	58624	58717	1	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	58718	58719	0	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	58794	58795	1	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	58796	59001	0.983	+	.	Parent=gene71
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	59010	59484	1	+	.	ID=gene72;Target=md5:cc404517a12f1a399ab48b948f4e71ff:8715845 1 475 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	59010	59484	1	+	.	Parent=gene72
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	59148	59880	0.991	+	.	ID=gene73;Target=md5:33eefc92073ab38229f0ce775746b219:19864079 1 653 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	59148	59526	0.989	+	.	Parent=gene73
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	59527	59528	0.993	+	.	Parent=gene73
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	59605	59606	0.997	+	.	Parent=gene73
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	59607	59880	0.993	+	.	Parent=gene73
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	59164	59418	0.996	+	.	ID=gene74;Target=md5:cdbabc0602366c37167aba18498d8232:9787190 1 255 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	59164	59418	0.996	+	.	Parent=gene74
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	59643	59976	0.991	+	.	ID=gene75;Target=md5:e72969c46cd2e7d078d339cda62260a8:397215 1 333 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	59643	59976	0.991	+	.	Parent=gene75
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	60190	60487	0.987	+	.	ID=gene76;Target=md5:322e03bbf0f0ddac43d4ca12dd0cc795:398270 1 298 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	60190	60487	0.987	+	.	Parent=gene76
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	60319	61000	0.997	-	.	ID=gene77;Target=md5:c94289917098254e5d5b7c3ed48e81b7:19801463 1 682 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	60319	61000	0.997	-	.	Parent=gene77
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	60410	60968	1	-	.	ID=gene78;Target=md5:48f4c66f41d3805c7213639bcb949d6a:8692149 1 559 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	60410	60968	1	-	.	Parent=gene78
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	60450	60902	0.998	-	.	ID=gene79;Target=md5:1b775af1ef6f8f8b80ba60a8245cba0b:19827386 1 453 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	60450	60902	0.998	-	.	Parent=gene79
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	60459	60958	0.996	-	.	ID=gene80;Target=md5:2acbf49eaca817b303d60c7c22dfdd15:7610825 1 500 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	60459	60958	0.996	-	.	Parent=gene80
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	60463	60958	0.996	-	.	ID=gene81;Target=md5:9b6924737e47f2eed133a565b35dd804:8736724 1 496 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	60463	60958	0.996	-	.	Parent=gene81
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	60508	60959	0.983	-	.	ID=gene82;Target=md5:653662b06e7e300256655269264f4004:19828552 1 452 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	60508	60959	0.983	-	.	Parent=gene82
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	60542	60950	1	-	.	ID=gene83;Target=md5:81a8f87434a337a21077462e2a1cb5c9:19838343 1 409 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	60542	60950	1	-	.	Parent=gene83
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	60558	60947	0.995	-	.	ID=gene84;Target=md5:1634572862a7fc3d7dcb1ca5950cf137:397216 1 390 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	60558	60947	0.995	-	.	Parent=gene84
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	61186	61922	0.957	+	.	ID=gene85;Target=md5:3ab44e284886cca199c6a4d221725734:2722481 1 371 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	61186	61281	0.99	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	61282	61283	0.316	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	61563	61564	0.959	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	61565	61641	0.948	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	61642	61643	0	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	61722	61723	0.994	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	61724	61922	0.945	+	.	Parent=gene85
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	61212	61974	1	+	.	ID=gene86;Target=md5:f63fe9c59e53d9587766136a15864412:19837990 1 398 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	61212	61281	1	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	61282	61283	0.316	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	61563	61564	0.959	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	61565	61641	1	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	61642	61643	0	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	61722	61723	0.994	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	61724	61974	1	+	.	Parent=gene86
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	62196	62646	0.921	+	.	ID=gene87;Target=md5:77ba8b822b44308184b4dcab6ecfa75e:2747645 1 448 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	62196	62646	0.921	+	.	Parent=gene87
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	63106	63942	1	+	.	ID=gene88;Target=md5:c4e23aeca494361878d3407ae5c05e3d:8701755 1 598 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	63106	63178	1	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	63179	63180	0	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	63269	63270	0.999	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	63271	63391	1	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	63392	63393	0.823	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	63466	63467	0	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	63468	63683	1	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	63684	63685	0.999	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	63753	63754	0.992	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	63755	63942	1	+	.	Parent=gene88
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	63306	63942	1	+	.	ID=gene89;Target=md5:bbbbef70abd153db9376c364e9fafbae:8735505 1 490 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	63306	63391	1	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	63392	63393	0.823	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	63466	63467	0	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	63468	63683	1	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	63684	63685	0.999	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	63753	63754	0.992	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	63755	63942	1	+	.	Parent=gene89
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	63910	64320	0.979	+	.	ID=gene90;Target=md5:67e8b62becffff524bac4f51bfa344e1:19798134 1 412 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	63910	64320	0.979	+	.	Parent=gene90
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	63935	64280	0.986	+	.	ID=gene91;Target=md5:3b10d6f56bfea7b6b57a41146f6c140b:5846657 1 345 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	63935	64280	0.986	+	.	Parent=gene91
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	64196	65033	0.998	-	.	ID=gene92;Target=md5:e5089d2bdb42934617cd38749662eb21:19877649 1 632 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	64196	64605	1	-	.	Parent=gene92
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	64605	64606	0.942	-	.	Parent=gene92
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	64811	64812	0.991	-	.	Parent=gene92
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	64812	65033	0.995	-	.	Parent=gene92
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	65467	66157	0.992	+	.	ID=gene93;Target=md5:f19b5223816de3060184fb9250936fce:19875812 1 621 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	65467	66058	0.992	+	.	Parent=gene93
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	66059	66060	1	+	.	Parent=gene93
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	66128	66129	0.994	+	.	Parent=gene93
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	66130	66157	0.964	+	.	Parent=gene93
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	67358	68298	0.982	+	.	ID=gene94;Target=md5:893d07af699d973ed4e8e3423fc87165:396603 1 749 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	67358	67550	1	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	67551	67552	0.896	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	67634	67635	0.998	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	67636	67908	0.969	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	67909	67910	1	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	68009	68010	0.999	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	68011	68298	0.983	+	.	Parent=gene94
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	67871	68396	0.99	+	.	ID=gene95;Target=md5:3b9295d3ee44af4cf4f79b2e27003f1b:19742246 1 423 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	67871	67908	0.947	+	.	Parent=gene95
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	67909	67910	1	+	.	Parent=gene95
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	68009	68010	0.999	+	.	Parent=gene95
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	68011	68396	0.99	+	.	Parent=gene95
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	69163	69893	0.98	+	.	ID=gene96;Target=md5:79435902b3753af094ba24f8a4847978:19872996 1 536 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69163	69265	0.971	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69375	69598	1	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69685	69893	0.964	+	.	Parent=gene96
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	69171	69968	0.997	+	.	ID=gene97;Target=md5:811cb37790973c1b417241d62fe2a569:19869130 1 603 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69171	69265	0.989	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69375	69598	1	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69685	69968	0.996	+	.	Parent=gene97
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	69173	69853	0.992	+	.	ID=gene98;Target=md5:bce4ec40fb993e1733ea6d2d16398ed0:19870921 1 486 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69173	69265	0.989	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69375	69598	1	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69685	69853	0.982	+	.	Parent=gene98
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	69196	70072	0.932	+	.	ID=gene99;Target=md5:49b16de93b5b34374e7e2a7e71253124:905849 1 455 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69196	69265	0.986	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69375	69598	0.991	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69685	69831	0.816	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69832	69833	0.48	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	70061	70062	0.999	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	70063	70072	0.4	+	.	Parent=gene99
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	69219	69775	1	+	.	ID=gene100;Target=md5:979a4ec86ab17d2a4625c90ed575c145:7612059 1 362 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69219	69265	1	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69375	69598	1	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	69685	69775	1	+	.	Parent=gene100
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	71414	71679	0.958	+	.	ID=gene101;Target=md5:e311a17e67c458d42ed86de05242f87b:17520 1 168 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	71414	71479	1	+	.	Parent=gene101
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	71480	71481	0.948	+	.	Parent=gene101
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	71577	71578	0.982	+	.	Parent=gene101
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	71579	71679	0.931	+	.	Parent=gene101
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	71458	72009	0.99	+	.	ID=gene102;Target=md5:1f44f865b53e6414d5296a088f0a75e7:8734707 1 319 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	71458	71479	1	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	71480	71481	0.948	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	71577	71578	0.982	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	71579	71779	0.985	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	71780	71781	0.998	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	71912	71913	0.977	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	71914	72009	1	+	.	Parent=gene102
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72121	72340	0.966	+	.	ID=gene103;Target=md5:7d5ceada204939fc948a837d482fe57c:2597031 1 221 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72121	72340	0.966	+	.	Parent=gene103
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72121	72603	0.931	+	.	ID=gene104;Target=md5:a8b76267e5f1749ca29c5465c631ab8e:958004 1 484 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72121	72603	0.931	+	.	Parent=gene104
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72137	72552	0.917	+	.	ID=gene105;Target=md5:7882e88f260382672a97918b652cad4a:1159193 1 351 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72137	72296	1	+	.	Parent=gene105
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene105
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene105
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72552	0.845	+	.	Parent=gene105
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72185	72753	1	+	.	ID=gene106;Target=md5:fa15dcef7c84118ca9ee3f95600132c8:8737761 1 497 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72185	72296	1	+	.	Parent=gene106
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene106
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene106
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72753	1	+	.	Parent=gene106
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72204	72660	0.856	+	.	ID=gene107;Target=md5:03636fa4a9e17baae04ad57d13cdc386:2749490 79 466 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72204	72296	0.634	+	.	Parent=gene107
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene107
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene107
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72660	0.926	+	.	Parent=gene107
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72214	72751	0.987	+	.	ID=gene108;Target=md5:9a5ec5d4597ac1be9d10ba63ecc457c1:7610337 1 466 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72214	72296	1	+	.	Parent=gene108
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene108
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene108
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72751	0.984	+	.	Parent=gene108
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72231	72731	0.998	+	.	ID=gene109;Target=md5:df066a65ac8236486c7d59f90157d43e:19829297 1 429 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72231	72296	1	+	.	Parent=gene109
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene109
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene109
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72731	0.997	+	.	Parent=gene109
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72246	72753	0.995	+	.	ID=gene110;Target=md5:ace313cc0542136c91ac52da3c676d77:19829716 1 434 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72246	72296	0.98	+	.	Parent=gene110
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene110
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene110
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72753	0.997	+	.	Parent=gene110
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72252	72753	0.988	+	.	ID=gene111;Target=md5:2d0e152a577c91a47f0b5781e67cd3b0:19831127 1 431 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72252	72296	1	+	.	Parent=gene111
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene111
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene111
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72753	0.988	+	.	Parent=gene111
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72252	72803	1	+	.	ID=gene112;Target=md5:6db92a6a61672ceedb192c31b975e370:8731753 1 480 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72252	72296	1	+	.	Parent=gene112
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene112
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene112
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72803	1	+	.	Parent=gene112
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72262	72754	1	+	.	ID=gene113;Target=md5:14f58b2b12e291455a69d48e56728992:19839622 1 421 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72262	72296	1	+	.	Parent=gene113
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene113
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene113
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72754	1	+	.	Parent=gene113
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72264	72572	0.966	+	.	ID=gene114;Target=md5:1c07f0f3b1115fb653b7f47df5b1344b:2762921 1 237 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72264	72296	0.939	+	.	Parent=gene114
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene114
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene114
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72572	0.966	+	.	Parent=gene114
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72264	72670	0.93	+	.	ID=gene115;Target=md5:061cac88caefa5d8bba4a1ff47031dc3:2762922 1 337 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72264	72296	0.97	+	.	Parent=gene115
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene115
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene115
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72670	0.93	+	.	Parent=gene115
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72270	72801	0.998	+	.	ID=gene116;Target=md5:9b19d8ea196896df9be4cf56b285abf2:19825274 1 460 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72270	72296	0.963	+	.	Parent=gene116
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene116
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene116
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72801	0.998	+	.	Parent=gene116
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72275	72752	0.872	+	.	ID=gene117;Target=md5:a179a430866ce2f2826fec132cd9e71f:19855736 1 420 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72275	72296	1	+	.	Parent=gene117
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene117
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene117
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72752	0.872	+	.	Parent=gene117
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72277	72753	1	+	.	ID=gene118;Target=md5:b2925aa2103833c4c0e3e2ba4e27e66f:8695920 1 405 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72277	72296	1	+	.	Parent=gene118
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene118
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene118
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72369	72753	1	+	.	Parent=gene118
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72359	72801	0.985	-	.	ID=gene119;Target=md5:80d8c2289eb0b45dd9ab395572f44eae:19841232 1 443 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72359	72801	0.985	-	.	Parent=gene119
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72367	72810	1	-	.	ID=gene120;Target=md5:3c0dc775fc37af77e71cd10a45d4723c:19826275 1 444 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72367	72810	1	-	.	Parent=gene120
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72371	72801	0.995	-	.	ID=gene121;Target=md5:f2f65df067412c3be8da37366e71763f:19834843 1 430 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72371	72801	0.995	-	.	Parent=gene121
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72372	72801	0.99	-	.	ID=gene122;Target=md5:faf314d3fa8ba5d3d99734b83ebb7f7b:19828253 1 431 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72372	72801	0.99	-	.	Parent=gene122
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72372	72801	1	-	.	ID=gene123;Target=md5:897eae7810009eb141a5f887289d95c8:19825742 1 430 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72372	72801	1	-	.	Parent=gene123
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72374	72827	0.992	-	.	ID=gene124;Target=md5:e252994eb503f22fdc871a97738a525a:19828054 1 455 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72374	72827	0.992	-	.	Parent=gene124
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72383	72801	0.995	-	.	ID=gene125;Target=md5:11f83a01fda0f6e2061e6e17dc9cc0fe:19844666 1 418 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72383	72801	0.995	-	.	Parent=gene125
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72384	72801	1	-	.	ID=gene126;Target=md5:8e8cf2914e87c5de17ca1cea5185961d:19829934 1 418 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72384	72801	1	-	.	Parent=gene126
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72386	72802	0.993	-	.	ID=gene127;Target=md5:c39b7a42d0e463287ec636842fe38b67:19842362 1 417 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72386	72802	0.993	-	.	Parent=gene127
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72386	72803	0.974	-	.	ID=gene128;Target=md5:dc0b347c18391d65d897b1c1f14bc31f:19837074 1 417 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72386	72803	0.974	-	.	Parent=gene128
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72390	72754	0.997	-	.	ID=gene129;Target=md5:5a9fcf1a7370455e62e2701803939c8e:8728304 1 365 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72390	72754	0.997	-	.	Parent=gene129
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72390	72804	0.98	-	.	ID=gene130;Target=md5:3f342edcab14d21711f3d75e3ff81743:19827775 1 416 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72390	72804	0.98	-	.	Parent=gene130
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72399	72801	1	-	.	ID=gene131;Target=md5:a3891b57fd37552bdad1be4e20266a5a:19855995 1 403 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72399	72801	1	-	.	Parent=gene131
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72400	72753	1	-	.	ID=gene132;Target=md5:cc7281740fd5e50cb1f19a22a728e790:8694120 1 354 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72400	72753	1	-	.	Parent=gene132
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72404	72804	0.998	-	.	ID=gene133;Target=md5:b9d8ea84787a6573a7bd2acdb795af44:19831839 1 401 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72404	72804	0.998	-	.	Parent=gene133
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72422	72826	0.998	-	.	ID=gene134;Target=md5:d056310e74cdfca4f2f5de040aabc6c6:19833332 1 405 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72422	72826	0.998	-	.	Parent=gene134
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72424	72753	0.929	+	.	ID=gene135;Target=md5:b7056f0f128b406b094ebf5cb33fb74f:3449674 1 333 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72424	72753	0.929	+	.	Parent=gene135
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72437	72805	0.981	-	.	ID=gene136;Target=md5:fd4ec29ab7c96a341ad546c954b7f557:8732348 1 369 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72437	72805	0.981	-	.	Parent=gene136
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72522	72801	0.971	-	.	ID=gene137;Target=md5:fd65d023d2d6b71c478da3cfa418cbbc:8695842 1 280 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72522	72801	0.971	-	.	Parent=gene137
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72653	74046	0.978	-	.	ID=gene138;Target=md5:2c08f2fc011c03e5aa709690db242c3b:2597485 1 163 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72653	72789	0.978	-	.	Parent=gene138
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72789	72790	0	-	.	Parent=gene138
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	74020	74021	0.514	-	.	Parent=gene138
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	74021	74046	0.615	-	.	Parent=gene138
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	72653	74920	0.919	-	.	ID=gene139;Target=md5:44f49124e83c2c61713d3c50b3a9a47c:3450080 1 166 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	72653	72800	0.919	-	.	Parent=gene139
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	72800	72801	0	-	.	Parent=gene139
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	74900	74901	0.919	-	.	Parent=gene139
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	74901	74920	0.75	-	.	Parent=gene139
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	79098	79663	0.866	-	.	ID=gene140;Target=md5:e7ffec1ba9f35a3e29c9946f86b8fe72:19857409 11 314 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	79098	79127	0.767	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	79127	79128	0	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	79240	79241	0	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	79241	79487	0.866	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	79487	79488	0.899	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	79635	79636	0.999	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	79636	79663	1	-	.	Parent=gene140
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	86444	89957	0.741	-	.	ID=gene141;Target=md5:2276b4a96eb715159638ed0f90239b89:19873300 87 582 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	86444	86516	0.767	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	86516	86517	0.999	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	89439	89440	0.999	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	89440	89702	0.683	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	89702	89703	0.846	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	89793	89794	0.933	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	89794	89957	0.823	-	.	Parent=gene141
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	90829	91133	0.948	+	.	ID=gene142;Target=md5:88e24a075574a85734a081b57a7ec852:5845361 1 307 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	90829	91133	0.948	+	.	Parent=gene142
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	91050	91786	1	-	.	ID=gene143;Target=md5:b18a91dba09f9ffefbe7b4a6aed19945:8735154 1 543 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	91050	91401	1	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	91401	91402	1	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	91523	91524	0.917	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	91524	91713	1	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	91713	91714	0.848	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	91785	91786	0.993	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	91786	91786	1	-	.	Parent=gene143
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	92903	93265	1	-	.	ID=gene144;Target=md5:ddbfcce4683cac59087c5f26e674349b:9786193 1 266 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	92903	93008	1	-	.	Parent=gene144
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	93008	93009	0.987	-	.	Parent=gene144
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	93105	93106	0.925	-	.	Parent=gene144
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	93106	93265	1	-	.	Parent=gene144
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	93551	94053	0.957	-	.	ID=gene145;Target=md5:d9d61048b8d25d868bda7f00a0831100:19806050 1 401 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	93551	93913	0.957	-	.	Parent=gene145
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	93913	93914	0.992	-	.	Parent=gene145
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	94016	94017	0.996	-	.	Parent=gene145
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	94017	94053	0.919	-	.	Parent=gene145
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	93552	93837	0.83	-	.	ID=gene146;Target=md5:a0d33d57c705a829d80c318c595fcccb:2047981 81 377 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	93552	93837	0.83	-	.	Parent=gene146
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	93633	94384	1	-	.	ID=gene147;Target=md5:41d17c6950c12d0d8ec2b305108f08ac:19857902 1 407 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	93633	93913	1	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	93913	93914	0.992	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	94016	94017	0.996	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	94017	94124	1	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	94124	94125	0.998	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	94366	94367	0.994	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	94367	94384	1	-	.	Parent=gene147
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	94706	95368	0.95	-	.	ID=gene148;Target=md5:da4c1ce6a2ee20bb9c4c5d9462be98de:9782167 1 392 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	94706	94771	0.871	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	94771	94772	0.993	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	94876	94877	0.985	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	94877	94985	0.954	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	94985	94986	0.957	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	95070	95071	0.958	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	95071	95147	1	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	95147	95148	0.992	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	95233	95234	0.937	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	95234	95368	0.956	-	.	Parent=gene148
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	95317	96614	0.995	-	.	ID=gene149;Target=md5:c9a4247a29baa59833607fc71f58bb40:19866748 1 646 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	95317	95454	1	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	95454	95455	0.938	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	95841	95842	0.988	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	95842	95947	0.991	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	95947	95948	0.999	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	96035	96036	0.993	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	96036	96140	1	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	96140	96141	0.869	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	96231	96232	0.996	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	96232	96330	1	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	96330	96331	0.996	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	96417	96418	0.958	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	96418	96614	0.987	-	.	Parent=gene149
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	95905	96592	0.989	-	.	ID=gene150;Target=md5:e6343ecf374a95dd0356831650af82f1:9778306 1 422 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	95905	95947	0.907	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	95947	95948	0.999	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	96035	96036	0.993	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	96036	96140	1	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	96140	96141	0.869	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	96231	96232	0.996	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	96232	96330	1	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	96330	96331	0.996	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	96417	96418	0.958	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	96418	96592	0.977	-	.	Parent=gene150
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	95929	96592	0.984	-	.	ID=gene151;Target=md5:29b2d16dd6ee3e8669ae77b4e053ee20:9778321 1 398 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	95929	95947	0.947	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	95947	95948	0.999	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	96035	96036	0.993	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	96036	96140	0.981	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	96140	96141	0.869	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	96231	96232	0.996	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	96232	96330	1	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	96330	96331	0.996	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	96417	96418	0.958	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	96418	96592	0.977	-	.	Parent=gene151
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	98857	99326	1	-	.	ID=gene152;Target=md5:4a2861ff4a54b0b8a099c7ca178c113f:19836538 1 392 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	98857	99121	1	-	.	Parent=gene152
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene152
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene152
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99200	99326	1	-	.	Parent=gene152
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	98861	99271	1	-	.	ID=gene153;Target=md5:432d83294aa0f2f3fc1b7673977ea4d1:8737545 1 333 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	98861	99121	1	-	.	Parent=gene153
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene153
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene153
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99200	99271	1	-	.	Parent=gene153
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	98861	99511	0.9	-	.	ID=gene154;Target=md5:50590ee6555b56ad95151d25d300c6fe:2446000 47 535 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	98861	99121	0.992	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99200	99361	0.883	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99443	99511	0.594	-	.	Parent=gene154
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	98878	99663	0.987	-	.	ID=gene155;Target=md5:08f77d13c4ad88c1c44c0314426f2218:5846455 1 525 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	98878	99121	0.996	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99200	99361	1	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99443	99511	1	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99511	99512	0.998	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99612	99613	0.999	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99613	99663	0.882	-	.	Parent=gene155
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	98909	99450	1	-	.	ID=gene156;Target=md5:d75212b190b11adfcbc1b62e6d392ed1:8734273 1 383 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	98909	99121	1	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99200	99361	1	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99443	99450	1	-	.	Parent=gene156
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	98987	99504	0.962	-	.	ID=gene157;Target=md5:dd3ace06137c29bf383632984aadf8af:397246 1 362 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	98987	99121	0.9	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99200	99361	1	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99443	99504	1	-	.	Parent=gene157
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	99613	100804	0.998	-	.	ID=gene158;Target=md5:eaca300e106a2e1c1897455c6a2cb618:19863867 1 661 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99613	99877	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99877	99878	0.981	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100101	100102	0.978	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100102	100226	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100327	100434	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100539	100646	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100646	100647	0	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100748	100749	0.995	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100749	100804	0.982	-	.	Parent=gene158
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	99698	100804	0.997	-	.	ID=gene159;Target=md5:1fd1b5316d6ec8962be7986ceebf3ce6:19870774 1 577 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99698	99877	0.994	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99877	99878	0.981	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100101	100102	0.978	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100102	100226	1	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100327	100434	1	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100539	100646	1	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100646	100647	0	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100748	100749	0.995	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100749	100804	0.982	-	.	Parent=gene159
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	99801	100766	0.933	-	.	ID=gene160;Target=md5:8bfbb0491705b51d42ef6d8ba0c3e2ef:958152 1 437 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	99801	99877	0.76	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	99877	99878	0.981	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100101	100102	0.978	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100102	100226	0.948	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100327	100434	1	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100539	100646	0.972	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100646	100647	0	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100748	100749	0.995	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100749	100766	1	-	.	Parent=gene160
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	100105	100634	1	-	.	ID=gene161;Target=md5:8e46b5509ea749211c8c5cacdc1e2500:8732177 1 326 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100105	100226	1	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100327	100434	1	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	100539	100634	1	-	.	Parent=gene161
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	103616	104455	0.96	+	.	ID=gene162;Target=md5:0c4c41ad6668fd55d5f1140088f1064d:2580948 1 435 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103616	103753	0.975	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103982	104035	0.981	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104118	104198	0.975	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104295	104455	0.932	+	.	Parent=gene162
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	103616	104478	0.909	+	.	ID=gene163;Target=md5:d4793f2935cfa07221be201386cb079b:2759743 1 460 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103616	103753	1	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103982	104035	0.981	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104118	104198	1	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104295	104478	0.78	+	.	Parent=gene163
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	103616	104819	0.952	+	.	ID=gene164;Target=md5:e47b883ccda180d280195029954ea7f5:5840051 1 700 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103616	103753	1	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103982	104035	1	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104118	104198	1	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104295	104724	0.921	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104725	104726	0.953	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104801	104802	0.814	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104803	104819	0.765	+	.	Parent=gene164
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	103706	104416	0.829	+	.	ID=gene165;Target=md5:41ccefe046c76c005c6f83a09aac40de:8686177 99 409 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103706	103731	0.885	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	103732	103733	0	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	103797	103798	0	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103799	103826	0.518	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	103827	103828	0.326	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103982	104035	0.778	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104295	104416	0.844	+	.	Parent=gene165
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	103713	104391	0.812	+	.	ID=gene166;Target=md5:556ae7f08b7cc887b54786f0bc100dd4:453733 78 357 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103713	103731	1	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	103732	103733	0	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	103797	103798	0	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103799	103826	0.518	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	103827	103828	0.326	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103982	104035	0.778	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104295	104391	0.809	+	.	Parent=gene166
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	103746	104415	0.824	+	.	ID=gene167;Target=md5:b9155494bf5b0de513f322e685542888:8722221 103 366 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103746	103753	0.875	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103982	104035	0.778	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104295	104415	0.835	+	.	Parent=gene167
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	103746	104440	0.829	+	.	ID=gene168;Target=md5:0e851efbbe2bfb244a388865f785495d:623629 87 375 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103746	103753	0.875	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103982	104035	0.778	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104295	104440	0.842	+	.	Parent=gene168
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	103982	104683	0.818	+	.	ID=gene169;Target=md5:f1cb6a33be382d29ff291be589f1ed70:9778203 71 401 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103982	104035	0.759	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104118	104198	0.84	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104295	104455	0.826	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104456	104457	0.522	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104647	104648	0	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104649	104683	0.971	+	.	Parent=gene169
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	103982	104881	0.909	+	.	ID=gene170;Target=md5:b289385ff9ca374ceb056d5950d090b5:8731408 68 518 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	103982	104035	0.944	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104118	104198	0.951	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104295	104455	0.888	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104456	104457	0.522	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104647	104648	0	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104649	104724	0.934	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104725	104726	0.953	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104801	104802	0.814	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104803	104881	0.861	+	.	Parent=gene170
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	104394	105201	0.83	+	.	ID=gene171;Target=md5:ddab1d6f7c76a6508e85423cd56d46e5:937871 1 457 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104394	104455	0.887	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104456	104457	0.522	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104647	104648	0	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104649	104724	0.921	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104725	104726	0.953	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	104801	104802	0.814	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104803	104928	0.841	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105010	105201	0.768	+	.	Parent=gene171
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	104803	105220	0.852	+	.	ID=gene172;Target=md5:257d2dc2f7c0bb730fe685a8052aaa63:9781141 22 358 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104803	104928	0.841	+	.	Parent=gene172
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene172
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene172
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105010	105220	0.858	+	.	Parent=gene172
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	104912	105793	0.887	+	.	ID=gene173;Target=md5:649b4501a3ba1d922dce7b623c7f6de9:7611662 1 549 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	104912	104928	0.824	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105010	105228	0.863	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene173
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105009	105793	0.884	+	.	ID=gene174;Target=md5:c6730817f9a41f80296421e6b7da6f25:8734901 1 533 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105009	105228	0.864	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.89	+	.	Parent=gene174
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105069	105815	0.876	+	.	ID=gene175;Target=md5:c24d4bd4c7cae864049bd096522750b1:19801855 1 495 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105069	105228	0.831	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105815	0.892	+	.	Parent=gene175
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105090	105793	0.878	+	.	ID=gene176;Target=md5:52b0aff6e54274ccb35b371b7630b68a:8695006 1 452 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105090	105228	0.82	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene176
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105091	105793	0.857	+	.	ID=gene177;Target=md5:085f029e3f483828cb30f70b141fa58a:8702125 1 452 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105091	105228	0.786	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.886	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.896	+	.	Parent=gene177
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105140	105793	0.88	+	.	ID=gene178;Target=md5:174d324a9dca8baddcdcd0dbef55f969:19825204 1 402 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105140	105228	0.798	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene178
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105170	105793	0.862	+	.	ID=gene179;Target=md5:0920b24475a189fbfc148593eec03cb6:2748033 88 460 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105170	105228	0.686	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.904	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.896	+	.	Parent=gene179
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105175	105793	0.901	+	.	ID=gene180;Target=md5:15ed737c8deffb63f79d93a8fecb5a93:19835442 1 367 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105175	105228	0.87	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene180
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105189	105793	0.896	+	.	ID=gene181;Target=md5:f8e9d021f04423c2ad6499f4ce6eca57:8734878 1 354 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105189	105228	0.875	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.884	+	.	Parent=gene181
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105190	105793	0.906	+	.	ID=gene182;Target=md5:a45d1a65f8024adcc2ce8bdcdfb36569:19823987 1 352 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105190	105228	0.872	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene182
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105199	105793	0.845	+	.	ID=gene183;Target=md5:07c4180bd9082b53416a778fee66e3f3:19841468 39 385 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105199	105228	0.833	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105315	105428	0.904	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105793	0.805	+	.	Parent=gene183
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105348	105815	0.895	+	.	ID=gene184;Target=md5:15adef11b8ee98d85e7a5e3106495193:2747682 1 302 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105348	105428	0.914	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105815	0.887	+	.	Parent=gene184
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105348	105815	0.899	+	.	ID=gene185;Target=md5:f74aca5cee266c7bc442898be20363ae:2412846 1 302 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105348	105428	0.914	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105815	0.892	+	.	Parent=gene185
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105371	105813	0.897	+	.	ID=gene186;Target=md5:5db2b668ce1df476a932c078b6e77122:17325 1 277 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105371	105428	0.931	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105813	0.886	+	.	Parent=gene186
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105382	105851	0.986	+	.	ID=gene187;Target=md5:e6338114b6c0dcc78811d3be5b36ff63:3449578 65 370 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105382	105428	0.979	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	0.903	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105851	0.986	+	.	Parent=gene187
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105394	105860	0.827	+	.	ID=gene188;Target=md5:940e92280507db531e4654cc1f1054ef:19859011 1 296 -
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105394	105428	0.971	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105500	105535	1	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105630	105860	0.827	+	.	Parent=gene188
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	105662	105806	0.855	-	.	ID=gene189;Target=md5:816e83d74c3a633c3ccc005f1c14d55a:8735385 30 173 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	105662	105806	0.855	-	.	Parent=gene189
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106097	106973	0.998	+	.	ID=gene190;Target=md5:1adc4b78b212af1a83a6460bd27222f0:19871766 1 425 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106097	106290	0.995	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106566	106619	1	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106702	106782	1	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106878	106973	1	+	.	Parent=gene190
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106133	106934	0.966	+	.	ID=gene191;Target=md5:21c1b9817f74d01695e650726543cfbc:17300 1 350 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106133	106290	0.962	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106702	106782	1	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106878	106934	0.912	+	.	Parent=gene191
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106148	106751	0.966	+	.	ID=gene192;Target=md5:c446b7e0b708aafe5473ef397e104ae3:7612621 1 248 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106148	106290	0.948	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106566	106619	1	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106702	106751	0.98	+	.	Parent=gene192
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106149	106973	0.924	+	.	ID=gene193;Target=md5:5b0a1904c2c8e69fe643091fee181037:935362 1 377 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106149	106290	0.979	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106566	106619	0.944	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106702	106782	0.975	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106878	106973	0.786	+	.	Parent=gene193
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106156	106973	0.915	+	.	ID=gene194;Target=md5:11a2689b92ee76c83cd57591ae940971:936803 1 374 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106156	106290	0.97	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106702	106782	1	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106878	106973	0.729	+	.	Parent=gene194
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106156	106973	1	+	.	ID=gene195;Target=md5:d1a97200c69d88855784612802e7c024:7612394 1 366 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106156	106290	1	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106566	106619	1	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106702	106782	1	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106878	106973	1	+	.	Parent=gene195
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106161	106750	0.967	+	.	ID=gene196;Target=md5:5ae608a9518c5417787d0da5f4dc93b7:2733258 26 261 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106161	106290	0.962	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106702	106750	0.724	+	.	Parent=gene196
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106168	106917	0.981	+	.	ID=gene197;Target=md5:7be43cab2c3d57b779ea0f8ceeacfc0c:8729681 1 298 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106168	106290	0.976	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106702	106782	0.988	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106878	106917	0.95	+	.	Parent=gene197
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106224	106710	0.959	+	.	ID=gene198;Target=md5:802e6347770300a7bbc0064a90f1f061:2759942 1 130 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106224	106290	0.94	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106566	106619	0.981	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106702	106710	1	+	.	Parent=gene198
###
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	106716	106973	0.847	+	.	ID=gene199;Target=md5:e5c6d7f52bae4b6b57c6320ef95f9b66:9778889 1 162 +
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106716	106782	0.806	+	.	Parent=gene199
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene199
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene199
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	exon	106878	106973	0.875	+	.	Parent=gene199
###
genometools-1.5.1/testdata/U89959_sas.gff3md5old000066400000000000000000004212551211610345200212440ustar00rootroot00000000000000##gff-version   3
##sequence-region   md5:063b1024d68e26716b7f38caf958316f 1 106973
md5:063b1024d68e26716b7f38caf958316f	gth	gene	1074	1540	1	+	.	ID=gene1;Target=md5:14c0ff5e76ef8ac009fdcc923f701356 1 303 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	1074	1171	1	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	1172	1173	0.866	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	1257	1258	0.994	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f	gth	exon	1259	1354	1	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	1355	1356	0	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	1430	1431	0.745	+	.	Parent=gene1
md5:063b1024d68e26716b7f38caf958316f	gth	exon	1432	1540	1	+	.	Parent=gene1
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	2779	3355	0.84	+	.	ID=gene2;Target=md5:527995da853a37f9c47e616ce237d523 1 337 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	2779	2801	0.696	+	.	Parent=gene2
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	2802	2803	0.459	+	.	Parent=gene2
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	3041	3042	0	+	.	Parent=gene2
md5:063b1024d68e26716b7f38caf958316f	gth	exon	3043	3355	0.84	+	.	Parent=gene2
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	3025	3351	1	+	.	ID=gene3;Target=md5:f1a0d426e93585553b21aa1a47aa2970 1 327 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	3025	3351	1	+	.	Parent=gene3
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	3041	3651	0.996	-	.	ID=gene4;Target=md5:cabe5b677d534fb65e0d2245f61e2bd1 1 536 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	3041	3550	0.996	-	.	Parent=gene4
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	3550	3551	1	-	.	Parent=gene4
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	3625	3626	0.741	-	.	Parent=gene4
md5:063b1024d68e26716b7f38caf958316f	gth	exon	3626	3651	1	-	.	Parent=gene4
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	3077	3506	0.974	+	.	ID=gene5;Target=md5:a9dcd316817972a94c0af505715b10bc 1 426 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	3077	3506	0.974	+	.	Parent=gene5
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	4768	5357	0.987	-	.	ID=gene6;Target=md5:e40253c45f8d96170d6af32f8d8e3e05 1 591 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	4768	5357	0.987	-	.	Parent=gene6
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	9505	10058	1	+	.	ID=gene7;Target=md5:f28eda487869903339de7a431f00fccd 1 554 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	9505	10058	1	+	.	Parent=gene7
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	12024	12542	1	-	.	ID=gene8;Target=md5:300d9c80d9f566412745a6bda32e3e12 1 519 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	12024	12542	1	-	.	Parent=gene8
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	13014	13465	0.881	-	.	ID=gene9;Target=md5:c6826f50615c7fb2eb70e294bb7202cb 1 459 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	13014	13465	0.881	-	.	Parent=gene9
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	15955	16603	0.997	+	.	ID=gene10;Target=md5:bceada3d0ee38c76dafe93fd74e71dfe 1 649 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	15955	16603	0.997	+	.	Parent=gene10
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	17165	17684	0.985	+	.	ID=gene11;Target=md5:8bbc72e5847196327c25661544c6bdf9 1 396 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	17165	17247	0.97	+	.	Parent=gene11
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	17248	17249	1	+	.	Parent=gene11
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	17372	17373	0.994	+	.	Parent=gene11
md5:063b1024d68e26716b7f38caf958316f	gth	exon	17374	17684	0.989	+	.	Parent=gene11
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	25221	26100	1	+	.	ID=gene12;Target=md5:ff7357d7a1877d31d94543a13d64fa0e 1 521 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	25221	25310	1	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	25311	25312	0.993	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	25508	25509	0.439	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f	gth	exon	25510	25626	1	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	25627	25628	0.998	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	25711	25712	0.996	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f	gth	exon	25713	25841	1	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	25842	25843	0.63	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	25914	25915	0.926	+	.	Parent=gene12
md5:063b1024d68e26716b7f38caf958316f	gth	exon	25916	26100	1	+	.	Parent=gene12
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	27900	28989	1	+	.	ID=gene13;Target=md5:c69c15ebe466171a13ee5aa610e90e61 1 499 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	27900	28003	1	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	28004	28005	0.999	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	28267	28268	0.995	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	exon	28269	28424	1	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	28425	28426	0.936	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	28505	28506	0	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	exon	28507	28579	1	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	28580	28581	0.989	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	28684	28685	0.994	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	exon	28686	28753	1	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	28754	28755	0.999	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	28890	28891	0.999	+	.	Parent=gene13
md5:063b1024d68e26716b7f38caf958316f	gth	exon	28892	28989	1	+	.	Parent=gene13
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	28990	29817	1	+	.	ID=gene14;Target=md5:0870e7d5d9d76766ebd3dce1758b733f 1 477 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	28990	29037	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	29038	29039	0.907	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	29132	29133	0	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	exon	29134	29242	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	29243	29244	0.84	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	29329	29330	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	exon	29331	29477	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	29478	29479	0.983	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	29569	29570	0.998	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	exon	29571	29618	1	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	29619	29620	0	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	29691	29692	0.993	+	.	Parent=gene14
md5:063b1024d68e26716b7f38caf958316f	gth	exon	29693	29817	1	+	.	Parent=gene14
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	30278	31355	1	+	.	ID=gene15;Target=md5:97350772e29b7881b149afbedf09290d 1 524 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	30278	30391	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	30392	30393	0.985	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	30475	30476	0.918	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	exon	30477	30562	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	30563	30564	0.938	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	30656	30657	0.973	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	exon	30658	30763	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	30764	30765	0.996	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	30988	30989	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	exon	30990	31085	1	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	31086	31087	0.644	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	31232	31233	0.987	+	.	Parent=gene15
md5:063b1024d68e26716b7f38caf958316f	gth	exon	31234	31355	1	+	.	Parent=gene15
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	31265	31820	1	+	.	ID=gene16;Target=md5:cc954bf1761c4c9f05f8822afb1079e3 1 333 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	31265	31386	1	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	31387	31388	0.996	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	31536	31537	0.99	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f	gth	exon	31538	31720	1	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	31721	31722	0.994	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	31791	31792	0.995	+	.	Parent=gene16
md5:063b1024d68e26716b7f38caf958316f	gth	exon	31793	31820	1	+	.	Parent=gene16
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	31855	32362	1	+	.	ID=gene17;Target=md5:70facb44682374068ef43fd0a6e116b5 1 334 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	31855	32022	1	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	32023	32024	0	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	32116	32117	0.558	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f	gth	exon	32118	32220	1	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	32221	32222	0.912	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	32298	32299	0.895	+	.	Parent=gene17
md5:063b1024d68e26716b7f38caf958316f	gth	exon	32300	32362	1	+	.	Parent=gene17
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	31907	32349	1	+	.	ID=gene18;Target=md5:c7084aa0f01934072f9e244363059ca0 1 269 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	31907	32022	1	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	32023	32024	0	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	32116	32117	0.558	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f	gth	exon	32118	32220	1	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	32221	32222	0.912	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	32298	32299	0.895	+	.	Parent=gene18
md5:063b1024d68e26716b7f38caf958316f	gth	exon	32300	32349	1	+	.	Parent=gene18
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	32928	33488	0.967	+	.	ID=gene19;Target=md5:4e8ae3a74fefacbbb8650ba892c2b2da 1 227 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	32928	32955	1	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	32956	32957	0.985	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	33189	33190	0.999	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f	gth	exon	33191	33317	0.98	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	33318	33319	0.956	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	33416	33417	0.983	+	.	Parent=gene19
md5:063b1024d68e26716b7f38caf958316f	gth	exon	33418	33488	0.944	+	.	Parent=gene19
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	33296	34560	1	+	.	ID=gene20;Target=md5:f53ad09e45a4038f2261b9ee90353658 1 427 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	33296	33317	0.636	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	33318	33319	0.956	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	33416	33417	0.983	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	exon	33418	33518	1	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	33519	33520	0.993	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	33781	33782	0.99	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	exon	33783	33917	1	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	33918	33919	0.705	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	33994	33995	0.988	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	exon	33996	34076	1	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	34077	34078	0.961	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	34470	34471	0.999	+	.	Parent=gene20
md5:063b1024d68e26716b7f38caf958316f	gth	exon	34472	34560	1	+	.	Parent=gene20
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	35628	36362	0.921	+	.	ID=gene21;Target=md5:a7fa97bc84c3aebaea34e169b73094c9 1 451 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	35628	35712	0.959	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	35713	35714	0.988	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	35818	35819	0.971	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f	gth	exon	35820	36011	0.979	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36012	36013	0.955	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36099	36100	0.992	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36101	36205	0.924	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36206	36207	0.99	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36295	36296	0.979	+	.	Parent=gene21
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36297	36362	0.697	+	.	Parent=gene21
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	35628	36392	0.984	+	.	ID=gene22;Target=md5:cdced248d13c7c0f89e7e889cc30164a 1 479 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	35628	35712	1	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	35713	35714	0.988	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	35818	35819	0.971	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f	gth	exon	35820	36011	1	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36012	36013	0.955	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36099	36100	0.992	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36101	36205	1	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36206	36207	0.99	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36295	36296	0.979	+	.	Parent=gene22
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36297	36392	0.922	+	.	Parent=gene22
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	36370	37156	1	+	.	ID=gene23;Target=md5:0d914f8b8fdfef05d05e32a617ce8737 1 604 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36370	36431	1	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36432	36433	0.994	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36519	36520	1	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36521	36721	1	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene23
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36816	37156	1	+	.	Parent=gene23
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	36402	37106	1	+	.	ID=gene24;Target=md5:634e9a3d54562a834a900edb41abe7d4 1 522 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36402	36431	1	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36432	36433	0.994	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36519	36520	1	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36521	36721	1	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene24
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36816	37106	1	+	.	Parent=gene24
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	36531	37190	1	+	.	ID=gene25;Target=md5:e24a612b49c52c8aca23eb196c1ebe06 1 566 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36531	36721	1	+	.	Parent=gene25
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene25
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene25
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36816	37190	1	+	.	Parent=gene25
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	36546	37186	0.99	+	.	ID=gene26;Target=md5:835eb4298c428885b3d16d0e4514c30b 1 547 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36546	36721	0.969	+	.	Parent=gene26
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene26
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene26
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36816	37186	1	+	.	Parent=gene26
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	36594	37208	1	+	.	ID=gene27;Target=md5:b280ddc383280ca975eeaa3329e34c14 1 521 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36594	36721	1	+	.	Parent=gene27
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene27
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene27
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36816	37208	1	+	.	Parent=gene27
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	36812	37235	0.998	-	.	ID=gene28;Target=md5:26ebd521c00f7b4d595086f162ab00e1 1 424 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36812	37235	0.998	-	.	Parent=gene28
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	36816	37208	0.964	+	.	ID=gene29;Target=md5:3ff6374febf91a5f28c3f7bcc4ccd774 53 438 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36816	37208	0.964	+	.	Parent=gene29
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	36827	37206	0.997	-	.	ID=gene30;Target=md5:7f0facaa45cacec8ffaa0c98a51edf56 1 380 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36827	37206	0.997	-	.	Parent=gene30
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	36840	37234	1	-	.	ID=gene31;Target=md5:275dc2512038a6501b7d27e38165bec7 1 395 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	36840	37234	1	-	.	Parent=gene31
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	37071	37203	1	-	.	ID=gene32;Target=md5:af2486ba93823b9389100222c0ddffdb 1 133 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	37071	37203	1	-	.	Parent=gene32
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	37669	39259	1	-	.	ID=gene33;Target=md5:b1da76b1bfdf36225429a5be70ff88a2 1 588 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	37669	37891	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	exon	37972	38060	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	exon	38656	38794	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38794	38795	0.976	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	38926	38927	0.977	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	exon	38927	38997	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39104	39148	1	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene33
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39239	39259	1	-	.	Parent=gene33
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	37691	38766	0.995	-	.	ID=gene34;Target=md5:354c93700a73d01ea73f641c62c593cd 1 401 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	37691	37891	0.99	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f	gth	exon	37972	38060	1	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene34
md5:063b1024d68e26716b7f38caf958316f	gth	exon	38656	38766	1	-	.	Parent=gene34
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	37692	38756	1	-	.	ID=gene35;Target=md5:f42df1d200fb31e1bed322fab31540d6 1 390 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	37692	37891	1	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f	gth	exon	37972	38060	1	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene35
md5:063b1024d68e26716b7f38caf958316f	gth	exon	38656	38756	1	-	.	Parent=gene35
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	37716	39118	0.967	-	.	ID=gene36;Target=md5:f55d7bcc44b78111563b02f8a19805ee 1 490 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	37716	37891	0.977	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	exon	37972	38060	1	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	exon	38656	38794	0.953	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38794	38795	0.976	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	38926	38927	0.977	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	exon	38927	38997	0.93	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene36
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39104	39118	0.933	-	.	Parent=gene36
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	38927	40032	0.996	-	.	ID=gene37;Target=md5:a3f1555a0375aea877145c8c372ae4af 1 606 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	38927	38997	0.986	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39104	39148	1	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39239	39328	1	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	39328	39329	0.974	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39437	39438	0.999	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39438	39526	1	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	39526	39527	0.453	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39613	39614	0.986	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39614	39689	1	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	39689	39690	0.973	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39797	39798	0.999	-	.	Parent=gene37
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39798	40032	0.996	-	.	Parent=gene37
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	38938	40006	0.998	-	.	ID=gene38;Target=md5:a5f947d297585356da9380d22ac8c974 1 568 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	38938	38997	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39104	39148	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39239	39328	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	39328	39329	0.974	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39437	39438	0.999	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39438	39526	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	39526	39527	0.453	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39613	39614	0.986	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39614	39689	1	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	39689	39690	0.973	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	39797	39798	0.999	-	.	Parent=gene38
md5:063b1024d68e26716b7f38caf958316f	gth	exon	39798	40006	0.995	-	.	Parent=gene38
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	42783	43204	1	-	.	ID=gene39;Target=md5:bdc426cd84a477b9b48d7e7d1538fc85 1 422 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	42783	43204	1	-	.	Parent=gene39
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	44029	44540	0.972	+	.	ID=gene40;Target=md5:0f6d1e4ce29d042b5804f8ae8bd9c43a 1 423 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	44029	44263	0.991	+	.	Parent=gene40
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	44264	44265	0.99	+	.	Parent=gene40
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	44352	44353	0.998	+	.	Parent=gene40
md5:063b1024d68e26716b7f38caf958316f	gth	exon	44354	44540	0.947	+	.	Parent=gene40
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	45542	45866	0.991	-	.	ID=gene41;Target=md5:7ba0b8c1bb50abf3c5a844abacf9fe67 1 322 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	45542	45866	0.991	-	.	Parent=gene41
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	45559	45941	0.924	-	.	ID=gene42;Target=md5:38229ac075d9c6d15fd1152c4eccc834 1 388 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	45559	45941	0.924	-	.	Parent=gene42
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	45843	45920	0.949	+	.	ID=gene43;Target=md5:6d3b4b9db4531cda588528f2c69c0a57 1 78 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	45843	45920	0.949	+	.	Parent=gene43
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	49874	50547	1	-	.	ID=gene44;Target=md5:494051ed1147d22a2b2967b64c329678 1 412 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	49874	50284	1	-	.	Parent=gene44
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	50284	50285	0.587	-	.	Parent=gene44
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	50546	50547	0.677	-	.	Parent=gene44
md5:063b1024d68e26716b7f38caf958316f	gth	exon	50547	50547	1	-	.	Parent=gene44
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	50433	51134	0.978	-	.	ID=gene45;Target=md5:634ef96163dc4d4f8a585fe8059d867b 1 426 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	50433	50834	0.978	-	.	Parent=gene45
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene45
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene45
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51113	51134	1	-	.	Parent=gene45
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	50475	50702	1	+	.	ID=gene46;Target=md5:950b7715ab6cc030a8c810a0dba2dd33 1 228 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	50475	50702	1	+	.	Parent=gene46
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	50475	51193	1	-	.	ID=gene47;Target=md5:754b35896aef0625da39ee42e61db715 1 441 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	50475	50834	1	-	.	Parent=gene47
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene47
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene47
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51113	51193	1	-	.	Parent=gene47
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	50590	51354	1	-	.	ID=gene48;Target=md5:741ff4d6dd193d77cc75fb61f373ca5b 1 385 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	50590	50834	1	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51113	51216	1	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene48
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51319	51354	1	-	.	Parent=gene48
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	50758	52232	0.991	-	.	ID=gene49;Target=md5:597ada174987f3f2f0b2e4046f09247d 1 647 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	50758	50834	0.948	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51113	51216	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51319	51474	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51552	51623	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51711	51758	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51849	51896	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51983	52055	1	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene49
md5:063b1024d68e26716b7f38caf958316f	gth	exon	52163	52232	0.986	-	.	Parent=gene49
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	51139	51852	0.915	-	.	ID=gene50;Target=md5:8fdc30d821ff25b48b6182936cf72cd5 1 362 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51139	51216	0.718	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51319	51474	0.974	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51552	51623	1	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51711	51758	0.979	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene50
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51849	51852	1	-	.	Parent=gene50
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	51334	52222	0.905	-	.	ID=gene51;Target=md5:26e5980fbaaefb58d84de6755d521845 1 446 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51334	51474	0.766	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51552	51623	1	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51711	51758	1	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51849	51896	0.979	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51983	52055	1	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene51
md5:063b1024d68e26716b7f38caf958316f	gth	exon	52163	52222	1	-	.	Parent=gene51
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	51376	52048	0.939	-	.	ID=gene52;Target=md5:d342e4ee66b1c4db3e83e076c5dd7d44 1 336 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51376	51474	0.854	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51552	51623	1	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51711	51758	1	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51849	51896	0.979	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene52
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51983	52048	1	-	.	Parent=gene52
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	51376	52224	0.91	-	.	ID=gene53;Target=md5:7f11e59ff50ce68b25c6120418df3d51 1 404 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51376	51474	0.848	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51552	51623	0.931	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51711	51758	0.823	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51849	51896	0.958	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51983	52055	0.959	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene53
md5:063b1024d68e26716b7f38caf958316f	gth	exon	52163	52224	0.927	-	.	Parent=gene53
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	51446	52242	0.996	-	.	ID=gene54;Target=md5:b0183ab4aa646b9e8f95f61daf0e23a3 1 350 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51446	51474	0.966	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51474	51475	0.889	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51551	51552	0.984	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51552	51623	1	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51711	51758	1	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51849	51896	1	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51983	52055	0.986	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene54
md5:063b1024d68e26716b7f38caf958316f	gth	exon	52163	52242	1	-	.	Parent=gene54
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	51599	52231	0.993	-	.	ID=gene55;Target=md5:8ed84d5653334535562a21058880db81 1 263 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51599	51623	1	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51623	51624	0.986	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51710	51711	0.977	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51711	51758	1	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51758	51759	0.962	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51848	51849	0.637	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51849	51896	1	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	51896	51897	0.99	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	51982	51983	0.978	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	exon	51983	52055	1	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	52055	52056	0.887	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	52162	52163	0.902	-	.	Parent=gene55
md5:063b1024d68e26716b7f38caf958316f	gth	exon	52163	52231	0.986	-	.	Parent=gene55
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	53602	54271	0.994	-	.	ID=gene56;Target=md5:16258f1ad08d9c0c91c627eefad05949 1 427 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	53602	53914	0.992	-	.	Parent=gene56
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene56
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene56
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54159	54271	1	-	.	Parent=gene56
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	53602	54710	0.995	-	.	ID=gene57;Target=md5:2642a22855698a3125c99a9759f9147c 1 627 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	53602	53914	0.994	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54159	54335	1	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene57
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54574	54710	0.993	-	.	Parent=gene57
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	53624	54279	0.989	-	.	ID=gene58;Target=md5:752fa8c75ecef45cfa9cf0c5a59afe49 1 413 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	53624	53914	0.988	-	.	Parent=gene58
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene58
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene58
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54159	54279	0.992	-	.	Parent=gene58
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	53624	54283	0.992	-	.	ID=gene59;Target=md5:0743a82e324754dfc94ed4c0cd8a8816 1 417 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	53624	53914	0.988	-	.	Parent=gene59
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene59
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene59
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54159	54283	1	-	.	Parent=gene59
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	53631	54335	0.866	-	.	ID=gene60;Target=md5:198a4aa7626135303d0e996d4e2775ef 57 528 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	53631	53914	0.991	-	.	Parent=gene60
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene60
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene60
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54159	54335	0.664	-	.	Parent=gene60
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	53632	53909	0.991	+	.	ID=gene61;Target=md5:5a03dd7605925c94812a9550acc2d354 1 279 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	53632	53909	0.991	+	.	Parent=gene61
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	53645	54320	0.99	-	.	ID=gene62;Target=md5:f692730f2bd8700f690f8a231d2e446b 1 431 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	53645	53914	0.991	-	.	Parent=gene62
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene62
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene62
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54159	54320	0.988	-	.	Parent=gene62
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	53829	54829	0.991	-	.	ID=gene63;Target=md5:18fb5ebf5d11ec1db0d36de3ea2a049d 49 568 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	53829	53914	0.971	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54159	54335	1	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene63
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54574	54829	0.992	-	.	Parent=gene63
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	53850	54807	0.913	-	.	ID=gene64;Target=md5:ed9e14d2b83e7ea606c9d1d5fdbeb857 1 477 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	53850	53914	0.746	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54159	54335	0.887	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene64
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54574	54807	0.979	-	.	Parent=gene64
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	54167	54769	0.997	-	.	ID=gene65;Target=md5:7db3e698f27f19f0343e6b23af07a5b3 1 365 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54167	54335	0.994	-	.	Parent=gene65
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene65
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene65
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54574	54769	1	-	.	Parent=gene65
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	54178	54828	0.979	-	.	ID=gene66;Target=md5:6021387359d7e25495b6b804ebbbb0aa 1 414 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54178	54335	0.953	-	.	Parent=gene66
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene66
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene66
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54574	54828	0.996	-	.	Parent=gene66
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	54212	54697	0.952	-	.	ID=gene67;Target=md5:72f3e9cbd94835f59aa0a43b22a01b0f 1 248 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54212	54335	0.96	-	.	Parent=gene67
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene67
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene67
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54574	54697	0.944	-	.	Parent=gene67
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	54263	54808	0.93	-	.	ID=gene68;Target=md5:2fa0ef57b1f4391f7a2ae4283410311c 1 311 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54263	54335	0.815	-	.	Parent=gene68
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene68
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene68
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54574	54808	0.966	-	.	Parent=gene68
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	54321	54829	0.992	-	.	ID=gene69;Target=md5:215d14a53287c2aca2d8bd12b09aca14 49 319 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54321	54335	1	-	.	Parent=gene69
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene69
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene69
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54574	54829	0.992	-	.	Parent=gene69
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	54991	56652	0.998	+	.	ID=gene70;Target=md5:dd287e28fe668e94028c1a241a6a1c7d 1 651 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	54991	55057	0.985	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	55058	55059	0.896	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	55143	55144	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	exon	55145	55230	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	55231	55232	0.997	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	55298	55299	0	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	exon	55300	55341	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	55342	55343	0.997	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	55451	55452	0.898	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	exon	55453	55498	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	55499	55500	0.237	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	55616	55617	0.997	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	exon	55618	55704	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	55705	55706	0.991	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	55816	55817	0.952	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	exon	55818	55873	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	55874	55875	0.983	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	56034	56035	0.0357	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	exon	56036	56153	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	56154	56155	0.99	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	56279	56280	0.703	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	exon	56281	56339	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	56340	56341	0.464	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	56447	56448	0.287	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	exon	56449	56520	1	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	56521	56522	0.187	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	56633	56634	0.791	+	.	Parent=gene70
md5:063b1024d68e26716b7f38caf958316f	gth	exon	56635	56652	1	+	.	Parent=gene70
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	58115	59001	0.984	+	.	ID=gene71;Target=md5:a12796a152e829b54f2f56b4910d701c 1 460 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	58115	58209	0.958	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	58210	58211	0.856	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	58459	58460	1	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f	gth	exon	58461	58526	1	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	58527	58528	0.784	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	58622	58623	0.977	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f	gth	exon	58624	58717	1	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	58718	58719	0	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	58794	58795	1	+	.	Parent=gene71
md5:063b1024d68e26716b7f38caf958316f	gth	exon	58796	59001	0.983	+	.	Parent=gene71
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	59010	59484	1	+	.	ID=gene72;Target=md5:cc404517a12f1a399ab48b948f4e71ff 1 475 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	59010	59484	1	+	.	Parent=gene72
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	59148	59880	0.991	+	.	ID=gene73;Target=md5:33eefc92073ab38229f0ce775746b219 1 653 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	59148	59526	0.989	+	.	Parent=gene73
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	59527	59528	0.993	+	.	Parent=gene73
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	59605	59606	0.997	+	.	Parent=gene73
md5:063b1024d68e26716b7f38caf958316f	gth	exon	59607	59880	0.993	+	.	Parent=gene73
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	59164	59418	0.996	+	.	ID=gene74;Target=md5:cdbabc0602366c37167aba18498d8232 1 255 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	59164	59418	0.996	+	.	Parent=gene74
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	59643	59976	0.991	+	.	ID=gene75;Target=md5:e72969c46cd2e7d078d339cda62260a8 1 333 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	59643	59976	0.991	+	.	Parent=gene75
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	60190	60487	0.987	+	.	ID=gene76;Target=md5:322e03bbf0f0ddac43d4ca12dd0cc795 1 298 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	60190	60487	0.987	+	.	Parent=gene76
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	60319	61000	0.997	-	.	ID=gene77;Target=md5:c94289917098254e5d5b7c3ed48e81b7 1 682 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	60319	61000	0.997	-	.	Parent=gene77
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	60410	60968	1	-	.	ID=gene78;Target=md5:48f4c66f41d3805c7213639bcb949d6a 1 559 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	60410	60968	1	-	.	Parent=gene78
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	60450	60902	0.998	-	.	ID=gene79;Target=md5:1b775af1ef6f8f8b80ba60a8245cba0b 1 453 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	60450	60902	0.998	-	.	Parent=gene79
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	60459	60958	0.996	-	.	ID=gene80;Target=md5:2acbf49eaca817b303d60c7c22dfdd15 1 500 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	60459	60958	0.996	-	.	Parent=gene80
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	60463	60958	0.996	-	.	ID=gene81;Target=md5:9b6924737e47f2eed133a565b35dd804 1 496 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	60463	60958	0.996	-	.	Parent=gene81
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	60508	60959	0.983	-	.	ID=gene82;Target=md5:653662b06e7e300256655269264f4004 1 452 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	60508	60959	0.983	-	.	Parent=gene82
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	60542	60950	1	-	.	ID=gene83;Target=md5:81a8f87434a337a21077462e2a1cb5c9 1 409 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	60542	60950	1	-	.	Parent=gene83
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	60558	60947	0.995	-	.	ID=gene84;Target=md5:1634572862a7fc3d7dcb1ca5950cf137 1 390 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	60558	60947	0.995	-	.	Parent=gene84
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	61186	61922	0.957	+	.	ID=gene85;Target=md5:3ab44e284886cca199c6a4d221725734 1 371 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	61186	61281	0.99	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	61282	61283	0.316	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	61563	61564	0.959	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f	gth	exon	61565	61641	0.948	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	61642	61643	0	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	61722	61723	0.994	+	.	Parent=gene85
md5:063b1024d68e26716b7f38caf958316f	gth	exon	61724	61922	0.945	+	.	Parent=gene85
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	61212	61974	1	+	.	ID=gene86;Target=md5:f63fe9c59e53d9587766136a15864412 1 398 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	61212	61281	1	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	61282	61283	0.316	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	61563	61564	0.959	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f	gth	exon	61565	61641	1	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	61642	61643	0	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	61722	61723	0.994	+	.	Parent=gene86
md5:063b1024d68e26716b7f38caf958316f	gth	exon	61724	61974	1	+	.	Parent=gene86
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	62196	62646	0.921	+	.	ID=gene87;Target=md5:77ba8b822b44308184b4dcab6ecfa75e 1 448 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	62196	62646	0.921	+	.	Parent=gene87
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	63106	63942	1	+	.	ID=gene88;Target=md5:c4e23aeca494361878d3407ae5c05e3d 1 598 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	63106	63178	1	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	63179	63180	0	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	63269	63270	0.999	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f	gth	exon	63271	63391	1	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	63392	63393	0.823	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	63466	63467	0	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f	gth	exon	63468	63683	1	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	63684	63685	0.999	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	63753	63754	0.992	+	.	Parent=gene88
md5:063b1024d68e26716b7f38caf958316f	gth	exon	63755	63942	1	+	.	Parent=gene88
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	63306	63942	1	+	.	ID=gene89;Target=md5:bbbbef70abd153db9376c364e9fafbae 1 490 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	63306	63391	1	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	63392	63393	0.823	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	63466	63467	0	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f	gth	exon	63468	63683	1	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	63684	63685	0.999	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	63753	63754	0.992	+	.	Parent=gene89
md5:063b1024d68e26716b7f38caf958316f	gth	exon	63755	63942	1	+	.	Parent=gene89
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	63910	64320	0.979	+	.	ID=gene90;Target=md5:67e8b62becffff524bac4f51bfa344e1 1 412 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	63910	64320	0.979	+	.	Parent=gene90
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	63935	64280	0.986	+	.	ID=gene91;Target=md5:3b10d6f56bfea7b6b57a41146f6c140b 1 345 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	63935	64280	0.986	+	.	Parent=gene91
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	64196	65033	0.998	-	.	ID=gene92;Target=md5:e5089d2bdb42934617cd38749662eb21 1 632 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	64196	64605	1	-	.	Parent=gene92
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	64605	64606	0.942	-	.	Parent=gene92
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	64811	64812	0.991	-	.	Parent=gene92
md5:063b1024d68e26716b7f38caf958316f	gth	exon	64812	65033	0.995	-	.	Parent=gene92
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	65467	66157	0.992	+	.	ID=gene93;Target=md5:f19b5223816de3060184fb9250936fce 1 621 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	65467	66058	0.992	+	.	Parent=gene93
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	66059	66060	1	+	.	Parent=gene93
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	66128	66129	0.994	+	.	Parent=gene93
md5:063b1024d68e26716b7f38caf958316f	gth	exon	66130	66157	0.964	+	.	Parent=gene93
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	67358	68298	0.982	+	.	ID=gene94;Target=md5:893d07af699d973ed4e8e3423fc87165 1 749 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	67358	67550	1	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	67551	67552	0.896	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	67634	67635	0.998	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f	gth	exon	67636	67908	0.969	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	67909	67910	1	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	68009	68010	0.999	+	.	Parent=gene94
md5:063b1024d68e26716b7f38caf958316f	gth	exon	68011	68298	0.983	+	.	Parent=gene94
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	67871	68396	0.99	+	.	ID=gene95;Target=md5:3b9295d3ee44af4cf4f79b2e27003f1b 1 423 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	67871	67908	0.947	+	.	Parent=gene95
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	67909	67910	1	+	.	Parent=gene95
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	68009	68010	0.999	+	.	Parent=gene95
md5:063b1024d68e26716b7f38caf958316f	gth	exon	68011	68396	0.99	+	.	Parent=gene95
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	69163	69893	0.98	+	.	ID=gene96;Target=md5:79435902b3753af094ba24f8a4847978 1 536 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69163	69265	0.971	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69375	69598	1	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene96
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69685	69893	0.964	+	.	Parent=gene96
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	69171	69968	0.997	+	.	ID=gene97;Target=md5:811cb37790973c1b417241d62fe2a569 1 603 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69171	69265	0.989	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69375	69598	1	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene97
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69685	69968	0.996	+	.	Parent=gene97
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	69173	69853	0.992	+	.	ID=gene98;Target=md5:bce4ec40fb993e1733ea6d2d16398ed0 1 486 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69173	69265	0.989	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69375	69598	1	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene98
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69685	69853	0.982	+	.	Parent=gene98
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	69196	70072	0.932	+	.	ID=gene99;Target=md5:49b16de93b5b34374e7e2a7e71253124 1 455 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69196	69265	0.986	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69375	69598	0.991	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69685	69831	0.816	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69832	69833	0.48	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	70061	70062	0.999	+	.	Parent=gene99
md5:063b1024d68e26716b7f38caf958316f	gth	exon	70063	70072	0.4	+	.	Parent=gene99
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	69219	69775	1	+	.	ID=gene100;Target=md5:979a4ec86ab17d2a4625c90ed575c145 1 362 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69219	69265	1	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69266	69267	0.981	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69373	69374	0	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69375	69598	1	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	69599	69600	0.996	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	69683	69684	0.993	+	.	Parent=gene100
md5:063b1024d68e26716b7f38caf958316f	gth	exon	69685	69775	1	+	.	Parent=gene100
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	71414	71679	0.958	+	.	ID=gene101;Target=md5:e311a17e67c458d42ed86de05242f87b 1 168 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	71414	71479	1	+	.	Parent=gene101
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	71480	71481	0.948	+	.	Parent=gene101
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	71577	71578	0.982	+	.	Parent=gene101
md5:063b1024d68e26716b7f38caf958316f	gth	exon	71579	71679	0.931	+	.	Parent=gene101
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	71458	72009	0.99	+	.	ID=gene102;Target=md5:1f44f865b53e6414d5296a088f0a75e7 1 319 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	71458	71479	1	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	71480	71481	0.948	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	71577	71578	0.982	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f	gth	exon	71579	71779	0.985	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	71780	71781	0.998	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	71912	71913	0.977	+	.	Parent=gene102
md5:063b1024d68e26716b7f38caf958316f	gth	exon	71914	72009	1	+	.	Parent=gene102
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72121	72340	0.966	+	.	ID=gene103;Target=md5:7d5ceada204939fc948a837d482fe57c 1 221 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72121	72340	0.966	+	.	Parent=gene103
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72121	72603	0.931	+	.	ID=gene104;Target=md5:a8b76267e5f1749ca29c5465c631ab8e 1 484 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72121	72603	0.931	+	.	Parent=gene104
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72137	72552	0.917	+	.	ID=gene105;Target=md5:7882e88f260382672a97918b652cad4a 1 351 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72137	72296	1	+	.	Parent=gene105
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene105
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene105
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72552	0.845	+	.	Parent=gene105
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72185	72753	1	+	.	ID=gene106;Target=md5:fa15dcef7c84118ca9ee3f95600132c8 1 497 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72185	72296	1	+	.	Parent=gene106
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene106
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene106
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72753	1	+	.	Parent=gene106
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72204	72660	0.856	+	.	ID=gene107;Target=md5:03636fa4a9e17baae04ad57d13cdc386 79 466 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72204	72296	0.634	+	.	Parent=gene107
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene107
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene107
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72660	0.926	+	.	Parent=gene107
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72214	72751	0.987	+	.	ID=gene108;Target=md5:9a5ec5d4597ac1be9d10ba63ecc457c1 1 466 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72214	72296	1	+	.	Parent=gene108
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene108
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene108
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72751	0.984	+	.	Parent=gene108
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72231	72731	0.998	+	.	ID=gene109;Target=md5:df066a65ac8236486c7d59f90157d43e 1 429 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72231	72296	1	+	.	Parent=gene109
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene109
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene109
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72731	0.997	+	.	Parent=gene109
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72246	72753	0.995	+	.	ID=gene110;Target=md5:ace313cc0542136c91ac52da3c676d77 1 434 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72246	72296	0.98	+	.	Parent=gene110
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene110
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene110
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72753	0.997	+	.	Parent=gene110
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72252	72753	0.988	+	.	ID=gene111;Target=md5:2d0e152a577c91a47f0b5781e67cd3b0 1 431 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72252	72296	1	+	.	Parent=gene111
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene111
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene111
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72753	0.988	+	.	Parent=gene111
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72252	72803	1	+	.	ID=gene112;Target=md5:6db92a6a61672ceedb192c31b975e370 1 480 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72252	72296	1	+	.	Parent=gene112
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene112
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene112
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72803	1	+	.	Parent=gene112
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72262	72754	1	+	.	ID=gene113;Target=md5:14f58b2b12e291455a69d48e56728992 1 421 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72262	72296	1	+	.	Parent=gene113
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene113
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene113
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72754	1	+	.	Parent=gene113
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72264	72572	0.966	+	.	ID=gene114;Target=md5:1c07f0f3b1115fb653b7f47df5b1344b 1 237 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72264	72296	0.939	+	.	Parent=gene114
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene114
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene114
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72572	0.966	+	.	Parent=gene114
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72264	72670	0.93	+	.	ID=gene115;Target=md5:061cac88caefa5d8bba4a1ff47031dc3 1 337 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72264	72296	0.97	+	.	Parent=gene115
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene115
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene115
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72670	0.93	+	.	Parent=gene115
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72270	72801	0.998	+	.	ID=gene116;Target=md5:9b19d8ea196896df9be4cf56b285abf2 1 460 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72270	72296	0.963	+	.	Parent=gene116
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene116
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene116
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72801	0.998	+	.	Parent=gene116
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72275	72752	0.872	+	.	ID=gene117;Target=md5:a179a430866ce2f2826fec132cd9e71f 1 420 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72275	72296	1	+	.	Parent=gene117
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene117
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene117
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72752	0.872	+	.	Parent=gene117
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72277	72753	1	+	.	ID=gene118;Target=md5:b2925aa2103833c4c0e3e2ba4e27e66f 1 405 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72277	72296	1	+	.	Parent=gene118
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene118
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene118
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72369	72753	1	+	.	Parent=gene118
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72359	72801	0.985	-	.	ID=gene119;Target=md5:80d8c2289eb0b45dd9ab395572f44eae 1 443 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72359	72801	0.985	-	.	Parent=gene119
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72367	72810	1	-	.	ID=gene120;Target=md5:3c0dc775fc37af77e71cd10a45d4723c 1 444 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72367	72810	1	-	.	Parent=gene120
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72371	72801	0.995	-	.	ID=gene121;Target=md5:f2f65df067412c3be8da37366e71763f 1 430 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72371	72801	0.995	-	.	Parent=gene121
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72372	72801	0.99	-	.	ID=gene122;Target=md5:faf314d3fa8ba5d3d99734b83ebb7f7b 1 431 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72372	72801	0.99	-	.	Parent=gene122
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72372	72801	1	-	.	ID=gene123;Target=md5:897eae7810009eb141a5f887289d95c8 1 430 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72372	72801	1	-	.	Parent=gene123
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72374	72827	0.992	-	.	ID=gene124;Target=md5:e252994eb503f22fdc871a97738a525a 1 455 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72374	72827	0.992	-	.	Parent=gene124
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72383	72801	0.995	-	.	ID=gene125;Target=md5:11f83a01fda0f6e2061e6e17dc9cc0fe 1 418 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72383	72801	0.995	-	.	Parent=gene125
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72384	72801	1	-	.	ID=gene126;Target=md5:8e8cf2914e87c5de17ca1cea5185961d 1 418 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72384	72801	1	-	.	Parent=gene126
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72386	72802	0.993	-	.	ID=gene127;Target=md5:c39b7a42d0e463287ec636842fe38b67 1 417 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72386	72802	0.993	-	.	Parent=gene127
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72386	72803	0.974	-	.	ID=gene128;Target=md5:dc0b347c18391d65d897b1c1f14bc31f 1 417 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72386	72803	0.974	-	.	Parent=gene128
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72390	72754	0.997	-	.	ID=gene129;Target=md5:5a9fcf1a7370455e62e2701803939c8e 1 365 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72390	72754	0.997	-	.	Parent=gene129
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72390	72804	0.98	-	.	ID=gene130;Target=md5:3f342edcab14d21711f3d75e3ff81743 1 416 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72390	72804	0.98	-	.	Parent=gene130
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72399	72801	1	-	.	ID=gene131;Target=md5:a3891b57fd37552bdad1be4e20266a5a 1 403 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72399	72801	1	-	.	Parent=gene131
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72400	72753	1	-	.	ID=gene132;Target=md5:cc7281740fd5e50cb1f19a22a728e790 1 354 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72400	72753	1	-	.	Parent=gene132
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72404	72804	0.998	-	.	ID=gene133;Target=md5:b9d8ea84787a6573a7bd2acdb795af44 1 401 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72404	72804	0.998	-	.	Parent=gene133
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72422	72826	0.998	-	.	ID=gene134;Target=md5:d056310e74cdfca4f2f5de040aabc6c6 1 405 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72422	72826	0.998	-	.	Parent=gene134
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72424	72753	0.929	+	.	ID=gene135;Target=md5:b7056f0f128b406b094ebf5cb33fb74f 1 333 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72424	72753	0.929	+	.	Parent=gene135
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72437	72805	0.981	-	.	ID=gene136;Target=md5:fd4ec29ab7c96a341ad546c954b7f557 1 369 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72437	72805	0.981	-	.	Parent=gene136
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72522	72801	0.971	-	.	ID=gene137;Target=md5:fd65d023d2d6b71c478da3cfa418cbbc 1 280 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72522	72801	0.971	-	.	Parent=gene137
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72653	74046	0.978	-	.	ID=gene138;Target=md5:2c08f2fc011c03e5aa709690db242c3b 1 163 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72653	72789	0.978	-	.	Parent=gene138
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72789	72790	0	-	.	Parent=gene138
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	74020	74021	0.514	-	.	Parent=gene138
md5:063b1024d68e26716b7f38caf958316f	gth	exon	74021	74046	0.615	-	.	Parent=gene138
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	72653	74920	0.919	-	.	ID=gene139;Target=md5:44f49124e83c2c61713d3c50b3a9a47c 1 166 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	72653	72800	0.919	-	.	Parent=gene139
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	72800	72801	0	-	.	Parent=gene139
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	74900	74901	0.919	-	.	Parent=gene139
md5:063b1024d68e26716b7f38caf958316f	gth	exon	74901	74920	0.75	-	.	Parent=gene139
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	79098	79663	0.866	-	.	ID=gene140;Target=md5:e7ffec1ba9f35a3e29c9946f86b8fe72 11 314 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	79098	79127	0.767	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	79127	79128	0	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	79240	79241	0	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f	gth	exon	79241	79487	0.866	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	79487	79488	0.899	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	79635	79636	0.999	-	.	Parent=gene140
md5:063b1024d68e26716b7f38caf958316f	gth	exon	79636	79663	1	-	.	Parent=gene140
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	86444	89957	0.741	-	.	ID=gene141;Target=md5:2276b4a96eb715159638ed0f90239b89 87 582 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	86444	86516	0.767	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	86516	86517	0.999	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	89439	89440	0.999	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f	gth	exon	89440	89702	0.683	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	89702	89703	0.846	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	89793	89794	0.933	-	.	Parent=gene141
md5:063b1024d68e26716b7f38caf958316f	gth	exon	89794	89957	0.823	-	.	Parent=gene141
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	90829	91133	0.948	+	.	ID=gene142;Target=md5:88e24a075574a85734a081b57a7ec852 1 307 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	90829	91133	0.948	+	.	Parent=gene142
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	91050	91786	1	-	.	ID=gene143;Target=md5:b18a91dba09f9ffefbe7b4a6aed19945 1 543 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	91050	91401	1	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	91401	91402	1	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	91523	91524	0.917	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f	gth	exon	91524	91713	1	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	91713	91714	0.848	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	91785	91786	0.993	-	.	Parent=gene143
md5:063b1024d68e26716b7f38caf958316f	gth	exon	91786	91786	1	-	.	Parent=gene143
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	92903	93265	1	-	.	ID=gene144;Target=md5:ddbfcce4683cac59087c5f26e674349b 1 266 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	92903	93008	1	-	.	Parent=gene144
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	93008	93009	0.987	-	.	Parent=gene144
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	93105	93106	0.925	-	.	Parent=gene144
md5:063b1024d68e26716b7f38caf958316f	gth	exon	93106	93265	1	-	.	Parent=gene144
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	93551	94053	0.957	-	.	ID=gene145;Target=md5:d9d61048b8d25d868bda7f00a0831100 1 401 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	93551	93913	0.957	-	.	Parent=gene145
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	93913	93914	0.992	-	.	Parent=gene145
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	94016	94017	0.996	-	.	Parent=gene145
md5:063b1024d68e26716b7f38caf958316f	gth	exon	94017	94053	0.919	-	.	Parent=gene145
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	93552	93837	0.83	-	.	ID=gene146;Target=md5:a0d33d57c705a829d80c318c595fcccb 81 377 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	93552	93837	0.83	-	.	Parent=gene146
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	93633	94384	1	-	.	ID=gene147;Target=md5:41d17c6950c12d0d8ec2b305108f08ac 1 407 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	93633	93913	1	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	93913	93914	0.992	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	94016	94017	0.996	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f	gth	exon	94017	94124	1	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	94124	94125	0.998	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	94366	94367	0.994	-	.	Parent=gene147
md5:063b1024d68e26716b7f38caf958316f	gth	exon	94367	94384	1	-	.	Parent=gene147
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	94706	95368	0.95	-	.	ID=gene148;Target=md5:da4c1ce6a2ee20bb9c4c5d9462be98de 1 392 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	94706	94771	0.871	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	94771	94772	0.993	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	94876	94877	0.985	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f	gth	exon	94877	94985	0.954	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	94985	94986	0.957	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	95070	95071	0.958	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f	gth	exon	95071	95147	1	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	95147	95148	0.992	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	95233	95234	0.937	-	.	Parent=gene148
md5:063b1024d68e26716b7f38caf958316f	gth	exon	95234	95368	0.956	-	.	Parent=gene148
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	95317	96614	0.995	-	.	ID=gene149;Target=md5:c9a4247a29baa59833607fc71f58bb40 1 646 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	95317	95454	1	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	95454	95455	0.938	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	95841	95842	0.988	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	exon	95842	95947	0.991	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	95947	95948	0.999	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	96035	96036	0.993	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	exon	96036	96140	1	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	96140	96141	0.869	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	96231	96232	0.996	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	exon	96232	96330	1	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	96330	96331	0.996	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	96417	96418	0.958	-	.	Parent=gene149
md5:063b1024d68e26716b7f38caf958316f	gth	exon	96418	96614	0.987	-	.	Parent=gene149
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	95905	96592	0.989	-	.	ID=gene150;Target=md5:e6343ecf374a95dd0356831650af82f1 1 422 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	95905	95947	0.907	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	95947	95948	0.999	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	96035	96036	0.993	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f	gth	exon	96036	96140	1	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	96140	96141	0.869	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	96231	96232	0.996	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f	gth	exon	96232	96330	1	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	96330	96331	0.996	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	96417	96418	0.958	-	.	Parent=gene150
md5:063b1024d68e26716b7f38caf958316f	gth	exon	96418	96592	0.977	-	.	Parent=gene150
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	95929	96592	0.984	-	.	ID=gene151;Target=md5:29b2d16dd6ee3e8669ae77b4e053ee20 1 398 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	95929	95947	0.947	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	95947	95948	0.999	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	96035	96036	0.993	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f	gth	exon	96036	96140	0.981	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	96140	96141	0.869	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	96231	96232	0.996	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f	gth	exon	96232	96330	1	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	96330	96331	0.996	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	96417	96418	0.958	-	.	Parent=gene151
md5:063b1024d68e26716b7f38caf958316f	gth	exon	96418	96592	0.977	-	.	Parent=gene151
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	98857	99326	1	-	.	ID=gene152;Target=md5:4a2861ff4a54b0b8a099c7ca178c113f 1 392 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	98857	99121	1	-	.	Parent=gene152
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene152
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene152
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99200	99326	1	-	.	Parent=gene152
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	98861	99271	1	-	.	ID=gene153;Target=md5:432d83294aa0f2f3fc1b7673977ea4d1 1 333 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	98861	99121	1	-	.	Parent=gene153
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene153
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene153
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99200	99271	1	-	.	Parent=gene153
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	98861	99511	0.9	-	.	ID=gene154;Target=md5:50590ee6555b56ad95151d25d300c6fe 47 535 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	98861	99121	0.992	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99200	99361	0.883	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene154
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99443	99511	0.594	-	.	Parent=gene154
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	98878	99663	0.987	-	.	ID=gene155;Target=md5:08f77d13c4ad88c1c44c0314426f2218 1 525 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	98878	99121	0.996	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99200	99361	1	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99443	99511	1	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99511	99512	0.998	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99612	99613	0.999	-	.	Parent=gene155
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99613	99663	0.882	-	.	Parent=gene155
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	98909	99450	1	-	.	ID=gene156;Target=md5:d75212b190b11adfcbc1b62e6d392ed1 1 383 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	98909	99121	1	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99200	99361	1	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene156
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99443	99450	1	-	.	Parent=gene156
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	98987	99504	0.962	-	.	ID=gene157;Target=md5:dd3ace06137c29bf383632984aadf8af 1 362 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	98987	99121	0.9	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99200	99361	1	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene157
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99443	99504	1	-	.	Parent=gene157
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	99613	100804	0.998	-	.	ID=gene158;Target=md5:eaca300e106a2e1c1897455c6a2cb618 1 661 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99613	99877	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99877	99878	0.981	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100101	100102	0.978	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100102	100226	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100327	100434	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100539	100646	1	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100646	100647	0	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100748	100749	0.995	-	.	Parent=gene158
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100749	100804	0.982	-	.	Parent=gene158
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	99698	100804	0.997	-	.	ID=gene159;Target=md5:1fd1b5316d6ec8962be7986ceebf3ce6 1 577 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99698	99877	0.994	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99877	99878	0.981	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100101	100102	0.978	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100102	100226	1	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100327	100434	1	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100539	100646	1	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100646	100647	0	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100748	100749	0.995	-	.	Parent=gene159
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100749	100804	0.982	-	.	Parent=gene159
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	99801	100766	0.933	-	.	ID=gene160;Target=md5:8bfbb0491705b51d42ef6d8ba0c3e2ef 1 437 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	99801	99877	0.76	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	99877	99878	0.981	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100101	100102	0.978	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100102	100226	0.948	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100327	100434	1	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100539	100646	0.972	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100646	100647	0	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100748	100749	0.995	-	.	Parent=gene160
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100749	100766	1	-	.	Parent=gene160
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	100105	100634	1	-	.	ID=gene161;Target=md5:8e46b5509ea749211c8c5cacdc1e2500 1 326 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100105	100226	1	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100226	100227	1	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100326	100327	0.999	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100327	100434	1	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	100434	100435	0.979	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	100538	100539	0.922	-	.	Parent=gene161
md5:063b1024d68e26716b7f38caf958316f	gth	exon	100539	100634	1	-	.	Parent=gene161
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	103616	104455	0.96	+	.	ID=gene162;Target=md5:0c4c41ad6668fd55d5f1140088f1064d 1 435 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103616	103753	0.975	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103982	104035	0.981	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104118	104198	0.975	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene162
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104295	104455	0.932	+	.	Parent=gene162
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	103616	104478	0.909	+	.	ID=gene163;Target=md5:d4793f2935cfa07221be201386cb079b 1 460 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103616	103753	1	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103982	104035	0.981	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104118	104198	1	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene163
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104295	104478	0.78	+	.	Parent=gene163
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	103616	104819	0.952	+	.	ID=gene164;Target=md5:e47b883ccda180d280195029954ea7f5 1 700 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103616	103753	1	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103982	104035	1	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104118	104198	1	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104295	104724	0.921	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104725	104726	0.953	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104801	104802	0.814	+	.	Parent=gene164
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104803	104819	0.765	+	.	Parent=gene164
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	103706	104416	0.829	+	.	ID=gene165;Target=md5:41ccefe046c76c005c6f83a09aac40de 99 409 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103706	103731	0.885	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	103732	103733	0	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	103797	103798	0	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103799	103826	0.518	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	103827	103828	0.326	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103982	104035	0.778	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104118	104198	0.84	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene165
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104295	104416	0.844	+	.	Parent=gene165
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	103713	104391	0.812	+	.	ID=gene166;Target=md5:556ae7f08b7cc887b54786f0bc100dd4 78 357 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103713	103731	1	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	103732	103733	0	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	103797	103798	0	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103799	103826	0.518	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	103827	103828	0.326	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103982	104035	0.778	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104118	104198	0.84	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene166
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104295	104391	0.809	+	.	Parent=gene166
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	103746	104415	0.824	+	.	ID=gene167;Target=md5:b9155494bf5b0de513f322e685542888 103 366 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103746	103753	0.875	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103982	104035	0.778	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104118	104198	0.84	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene167
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104295	104415	0.835	+	.	Parent=gene167
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	103746	104440	0.829	+	.	ID=gene168;Target=md5:0e851efbbe2bfb244a388865f785495d 87 375 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103746	103753	0.875	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	103754	103755	0.99	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	103980	103981	0.996	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103982	104035	0.778	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104118	104198	0.84	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene168
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104295	104440	0.842	+	.	Parent=gene168
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	103982	104683	0.818	+	.	ID=gene169;Target=md5:f1cb6a33be382d29ff291be589f1ed70 71 401 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103982	104035	0.759	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104118	104198	0.84	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104295	104455	0.826	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104456	104457	0.522	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104647	104648	0	+	.	Parent=gene169
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104649	104683	0.971	+	.	Parent=gene169
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	103982	104881	0.909	+	.	ID=gene170;Target=md5:b289385ff9ca374ceb056d5950d090b5 68 518 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	103982	104035	0.944	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104036	104037	0.997	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104116	104117	0.982	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104118	104198	0.951	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104199	104200	0.992	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104293	104294	1	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104295	104455	0.888	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104456	104457	0.522	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104647	104648	0	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104649	104724	0.934	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104725	104726	0.953	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104801	104802	0.814	+	.	Parent=gene170
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104803	104881	0.861	+	.	Parent=gene170
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	104394	105201	0.83	+	.	ID=gene171;Target=md5:ddab1d6f7c76a6508e85423cd56d46e5 1 457 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104394	104455	0.887	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104456	104457	0.522	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104647	104648	0	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104649	104724	0.921	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104725	104726	0.953	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	104801	104802	0.814	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104803	104928	0.841	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene171
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105010	105201	0.768	+	.	Parent=gene171
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	104803	105220	0.852	+	.	ID=gene172;Target=md5:257d2dc2f7c0bb730fe685a8052aaa63 22 358 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104803	104928	0.841	+	.	Parent=gene172
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene172
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene172
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105010	105220	0.858	+	.	Parent=gene172
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	104912	105793	0.887	+	.	ID=gene173;Target=md5:649b4501a3ba1d922dce7b623c7f6de9 1 549 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	104912	104928	0.824	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105010	105228	0.863	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.912	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene173
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.902	+	.	Parent=gene173
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105009	105793	0.884	+	.	ID=gene174;Target=md5:c6730817f9a41f80296421e6b7da6f25 1 533 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105009	105228	0.864	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.912	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene174
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.89	+	.	Parent=gene174
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105069	105815	0.876	+	.	ID=gene175;Target=md5:c24d4bd4c7cae864049bd096522750b1 1 495 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105069	105228	0.831	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.912	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene175
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105815	0.892	+	.	Parent=gene175
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105090	105793	0.878	+	.	ID=gene176;Target=md5:52b0aff6e54274ccb35b371b7630b68a 1 452 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105090	105228	0.82	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.912	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	0.972	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene176
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.902	+	.	Parent=gene176
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105091	105793	0.857	+	.	ID=gene177;Target=md5:085f029e3f483828cb30f70b141fa58a 1 452 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105091	105228	0.786	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.886	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	0.972	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene177
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.896	+	.	Parent=gene177
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105140	105793	0.88	+	.	ID=gene178;Target=md5:174d324a9dca8baddcdcd0dbef55f969 1 402 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105140	105228	0.798	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.912	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene178
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.902	+	.	Parent=gene178
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105170	105793	0.862	+	.	ID=gene179;Target=md5:0920b24475a189fbfc148593eec03cb6 88 460 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105170	105228	0.686	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.904	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene179
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.896	+	.	Parent=gene179
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105175	105793	0.901	+	.	ID=gene180;Target=md5:15ed737c8deffb63f79d93a8fecb5a93 1 367 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105175	105228	0.87	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.912	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene180
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.902	+	.	Parent=gene180
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105189	105793	0.896	+	.	ID=gene181;Target=md5:f8e9d021f04423c2ad6499f4ce6eca57 1 354 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105189	105228	0.875	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.912	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene181
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.884	+	.	Parent=gene181
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105190	105793	0.906	+	.	ID=gene182;Target=md5:a45d1a65f8024adcc2ce8bdcdfb36569 1 352 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105190	105228	0.872	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.912	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene182
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.902	+	.	Parent=gene182
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105199	105793	0.845	+	.	ID=gene183;Target=md5:07c4180bd9082b53416a778fee66e3f3 39 385 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105199	105228	0.833	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105315	105428	0.904	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	0.972	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene183
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105793	0.805	+	.	Parent=gene183
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105348	105815	0.895	+	.	ID=gene184;Target=md5:15adef11b8ee98d85e7a5e3106495193 1 302 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105348	105428	0.914	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene184
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105815	0.887	+	.	Parent=gene184
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105348	105815	0.899	+	.	ID=gene185;Target=md5:f74aca5cee266c7bc442898be20363ae 1 302 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105348	105428	0.914	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene185
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105815	0.892	+	.	Parent=gene185
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105371	105813	0.897	+	.	ID=gene186;Target=md5:5db2b668ce1df476a932c078b6e77122 1 277 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105371	105428	0.931	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	0.972	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene186
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105813	0.886	+	.	Parent=gene186
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105382	105851	0.986	+	.	ID=gene187;Target=md5:e6338114b6c0dcc78811d3be5b36ff63 65 370 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105382	105428	0.979	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	0.903	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene187
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105851	0.986	+	.	Parent=gene187
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105394	105860	0.827	+	.	ID=gene188;Target=md5:940e92280507db531e4654cc1f1054ef 1 296 -
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105394	105428	0.971	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105500	105535	1	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene188
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105630	105860	0.827	+	.	Parent=gene188
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	105662	105806	0.855	-	.	ID=gene189;Target=md5:816e83d74c3a633c3ccc005f1c14d55a 30 173 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	105662	105806	0.855	-	.	Parent=gene189
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106097	106973	0.998	+	.	ID=gene190;Target=md5:1adc4b78b212af1a83a6460bd27222f0 1 425 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106097	106290	0.995	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106566	106619	1	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106702	106782	1	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene190
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106878	106973	1	+	.	Parent=gene190
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106133	106934	0.966	+	.	ID=gene191;Target=md5:21c1b9817f74d01695e650726543cfbc 1 350 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106133	106290	0.962	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106566	106619	0.981	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106702	106782	1	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene191
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106878	106934	0.912	+	.	Parent=gene191
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106148	106751	0.966	+	.	ID=gene192;Target=md5:c446b7e0b708aafe5473ef397e104ae3 1 248 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106148	106290	0.948	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106566	106619	1	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene192
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106702	106751	0.98	+	.	Parent=gene192
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106149	106973	0.924	+	.	ID=gene193;Target=md5:5b0a1904c2c8e69fe643091fee181037 1 377 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106149	106290	0.979	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106566	106619	0.944	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106702	106782	0.975	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene193
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106878	106973	0.786	+	.	Parent=gene193
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106156	106973	0.915	+	.	ID=gene194;Target=md5:11a2689b92ee76c83cd57591ae940971 1 374 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106156	106290	0.97	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106566	106619	0.981	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106702	106782	1	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene194
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106878	106973	0.729	+	.	Parent=gene194
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106156	106973	1	+	.	ID=gene195;Target=md5:d1a97200c69d88855784612802e7c024 1 366 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106156	106290	1	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106566	106619	1	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106702	106782	1	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene195
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106878	106973	1	+	.	Parent=gene195
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106161	106750	0.967	+	.	ID=gene196;Target=md5:5ae608a9518c5417787d0da5f4dc93b7 26 261 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106161	106290	0.962	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106566	106619	0.981	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene196
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106702	106750	0.724	+	.	Parent=gene196
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106168	106917	0.981	+	.	ID=gene197;Target=md5:7be43cab2c3d57b779ea0f8ceeacfc0c 1 298 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106168	106290	0.976	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106566	106619	0.981	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106702	106782	0.988	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene197
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106878	106917	0.95	+	.	Parent=gene197
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106224	106710	0.959	+	.	ID=gene198;Target=md5:802e6347770300a7bbc0064a90f1f061 1 130 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106224	106290	0.94	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106291	106292	0.97	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106564	106565	0.986	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106566	106619	0.981	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106620	106621	0.998	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106700	106701	0.973	+	.	Parent=gene198
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106702	106710	1	+	.	Parent=gene198
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	106716	106973	0.847	+	.	ID=gene199;Target=md5:e5c6d7f52bae4b6b57c6320ef95f9b66 1 162 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106716	106782	0.806	+	.	Parent=gene199
md5:063b1024d68e26716b7f38caf958316f	gth	five_prime_cis_splice_site	106783	106784	0.997	+	.	Parent=gene199
md5:063b1024d68e26716b7f38caf958316f	gth	three_prime_cis_splice_site	106876	106877	1	+	.	Parent=gene199
md5:063b1024d68e26716b7f38caf958316f	gth	exon	106878	106973	0.875	+	.	Parent=gene199
###
genometools-1.5.1/testdata/U89959_sas.minus_targets000066400000000000000000000706221211610345200221740ustar00rootroot00000000000000##gff-version   3
##sequence-region   1877523 1 106973
1877523	gth	gene	3041	3651	0.996	-	.	ID=gene1;Target=8732878 1 536 -
1877523	gth	exon	3041	3550	0.996	-	.	Parent=gene1
1877523	gth	three_prime_cis_splice_site	3550	3551	1	-	.	Parent=gene1
1877523	gth	five_prime_cis_splice_site	3625	3626	0.741	-	.	Parent=gene1
1877523	gth	exon	3626	3651	1	-	.	Parent=gene1
###
1877523	gth	gene	17165	17684	0.985	+	.	ID=gene2;Target=19798999 1 396 -
1877523	gth	exon	17165	17247	0.97	+	.	Parent=gene2
1877523	gth	five_prime_cis_splice_site	17248	17249	1	+	.	Parent=gene2
1877523	gth	three_prime_cis_splice_site	17372	17373	0.994	+	.	Parent=gene2
1877523	gth	exon	17374	17684	0.989	+	.	Parent=gene2
###
1877523	gth	gene	36370	37156	1	+	.	ID=gene3;Target=8683519 1 604 -
1877523	gth	exon	36370	36431	1	+	.	Parent=gene3
1877523	gth	five_prime_cis_splice_site	36432	36433	0.994	+	.	Parent=gene3
1877523	gth	three_prime_cis_splice_site	36519	36520	1	+	.	Parent=gene3
1877523	gth	exon	36521	36721	1	+	.	Parent=gene3
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene3
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene3
1877523	gth	exon	36816	37156	1	+	.	Parent=gene3
###
1877523	gth	gene	36402	37106	1	+	.	ID=gene4;Target=8682814 1 522 -
1877523	gth	exon	36402	36431	1	+	.	Parent=gene4
1877523	gth	five_prime_cis_splice_site	36432	36433	0.994	+	.	Parent=gene4
1877523	gth	three_prime_cis_splice_site	36519	36520	1	+	.	Parent=gene4
1877523	gth	exon	36521	36721	1	+	.	Parent=gene4
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene4
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene4
1877523	gth	exon	36816	37106	1	+	.	Parent=gene4
###
1877523	gth	gene	36531	37190	1	+	.	ID=gene5;Target=8690927 1 566 -
1877523	gth	exon	36531	36721	1	+	.	Parent=gene5
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene5
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene5
1877523	gth	exon	36816	37190	1	+	.	Parent=gene5
###
1877523	gth	gene	36546	37186	0.99	+	.	ID=gene6;Target=5845530 1 547 -
1877523	gth	exon	36546	36721	0.969	+	.	Parent=gene6
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene6
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene6
1877523	gth	exon	36816	37186	1	+	.	Parent=gene6
###
1877523	gth	gene	36594	37208	1	+	.	ID=gene7;Target=8717375 1 521 -
1877523	gth	exon	36594	36721	1	+	.	Parent=gene7
1877523	gth	five_prime_cis_splice_site	36722	36723	0.91	+	.	Parent=gene7
1877523	gth	three_prime_cis_splice_site	36814	36815	0.968	+	.	Parent=gene7
1877523	gth	exon	36816	37208	1	+	.	Parent=gene7
###
1877523	gth	gene	37669	39259	1	-	.	ID=gene8;Target=8738841 1 588 -
1877523	gth	exon	37669	37891	1	-	.	Parent=gene8
1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene8
1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene8
1877523	gth	exon	37972	38060	1	-	.	Parent=gene8
1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene8
1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene8
1877523	gth	exon	38656	38794	1	-	.	Parent=gene8
1877523	gth	three_prime_cis_splice_site	38794	38795	0.976	-	.	Parent=gene8
1877523	gth	five_prime_cis_splice_site	38926	38927	0.977	-	.	Parent=gene8
1877523	gth	exon	38927	38997	1	-	.	Parent=gene8
1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene8
1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene8
1877523	gth	exon	39104	39148	1	-	.	Parent=gene8
1877523	gth	three_prime_cis_splice_site	39148	39149	0.991	-	.	Parent=gene8
1877523	gth	five_prime_cis_splice_site	39238	39239	0.998	-	.	Parent=gene8
1877523	gth	exon	39239	39259	1	-	.	Parent=gene8
###
1877523	gth	gene	37691	38766	0.995	-	.	ID=gene9;Target=19831991 1 401 -
1877523	gth	exon	37691	37891	0.99	-	.	Parent=gene9
1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene9
1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene9
1877523	gth	exon	37972	38060	1	-	.	Parent=gene9
1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene9
1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene9
1877523	gth	exon	38656	38766	1	-	.	Parent=gene9
###
1877523	gth	gene	37692	38756	1	-	.	ID=gene10;Target=19840745 1 390 -
1877523	gth	exon	37692	37891	1	-	.	Parent=gene10
1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene10
1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene10
1877523	gth	exon	37972	38060	1	-	.	Parent=gene10
1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene10
1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene10
1877523	gth	exon	38656	38756	1	-	.	Parent=gene10
###
1877523	gth	gene	37716	39118	0.967	-	.	ID=gene11;Target=5843191 1 490 -
1877523	gth	exon	37716	37891	0.977	-	.	Parent=gene11
1877523	gth	three_prime_cis_splice_site	37891	37892	0.935	-	.	Parent=gene11
1877523	gth	five_prime_cis_splice_site	37971	37972	0.873	-	.	Parent=gene11
1877523	gth	exon	37972	38060	1	-	.	Parent=gene11
1877523	gth	three_prime_cis_splice_site	38060	38061	0.978	-	.	Parent=gene11
1877523	gth	five_prime_cis_splice_site	38655	38656	0.856	-	.	Parent=gene11
1877523	gth	exon	38656	38794	0.953	-	.	Parent=gene11
1877523	gth	three_prime_cis_splice_site	38794	38795	0.976	-	.	Parent=gene11
1877523	gth	five_prime_cis_splice_site	38926	38927	0.977	-	.	Parent=gene11
1877523	gth	exon	38927	38997	0.93	-	.	Parent=gene11
1877523	gth	three_prime_cis_splice_site	38997	38998	0.768	-	.	Parent=gene11
1877523	gth	five_prime_cis_splice_site	39103	39104	0.491	-	.	Parent=gene11
1877523	gth	exon	39104	39118	0.933	-	.	Parent=gene11
###
1877523	gth	gene	45843	45920	0.949	+	.	ID=gene12;Target=8720010 1 78 -
1877523	gth	exon	45843	45920	0.949	+	.	Parent=gene12
###
1877523	gth	gene	50433	51134	0.978	-	.	ID=gene13;Target=19807151 1 426 -
1877523	gth	exon	50433	50834	0.978	-	.	Parent=gene13
1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene13
1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene13
1877523	gth	exon	51113	51134	1	-	.	Parent=gene13
###
1877523	gth	gene	50475	51193	1	-	.	ID=gene14;Target=8731976 1 441 -
1877523	gth	exon	50475	50834	1	-	.	Parent=gene14
1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene14
1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene14
1877523	gth	exon	51113	51193	1	-	.	Parent=gene14
###
1877523	gth	gene	50590	51354	1	-	.	ID=gene15;Target=19805724 1 385 -
1877523	gth	exon	50590	50834	1	-	.	Parent=gene15
1877523	gth	three_prime_cis_splice_site	50834	50835	0.998	-	.	Parent=gene15
1877523	gth	five_prime_cis_splice_site	51112	51113	0.998	-	.	Parent=gene15
1877523	gth	exon	51113	51216	1	-	.	Parent=gene15
1877523	gth	three_prime_cis_splice_site	51216	51217	0.988	-	.	Parent=gene15
1877523	gth	five_prime_cis_splice_site	51318	51319	1	-	.	Parent=gene15
1877523	gth	exon	51319	51354	1	-	.	Parent=gene15
###
1877523	gth	gene	53602	54271	0.994	-	.	ID=gene16;Target=8697180 1 427 -
1877523	gth	exon	53602	53914	0.992	-	.	Parent=gene16
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene16
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene16
1877523	gth	exon	54159	54271	1	-	.	Parent=gene16
###
1877523	gth	gene	53602	54710	0.995	-	.	ID=gene17;Target=19803773 1 627 -
1877523	gth	exon	53602	53914	0.994	-	.	Parent=gene17
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene17
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene17
1877523	gth	exon	54159	54335	1	-	.	Parent=gene17
1877523	gth	three_prime_cis_splice_site	54335	54336	0.998	-	.	Parent=gene17
1877523	gth	five_prime_cis_splice_site	54573	54574	0.951	-	.	Parent=gene17
1877523	gth	exon	54574	54710	0.993	-	.	Parent=gene17
###
1877523	gth	gene	53624	54279	0.989	-	.	ID=gene18;Target=19840006 1 413 -
1877523	gth	exon	53624	53914	0.988	-	.	Parent=gene18
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene18
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene18
1877523	gth	exon	54159	54279	0.992	-	.	Parent=gene18
###
1877523	gth	gene	53624	54283	0.992	-	.	ID=gene19;Target=19823046 1 417 -
1877523	gth	exon	53624	53914	0.988	-	.	Parent=gene19
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene19
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene19
1877523	gth	exon	54159	54283	1	-	.	Parent=gene19
###
1877523	gth	gene	53645	54320	0.99	-	.	ID=gene20;Target=19843722 1 431 -
1877523	gth	exon	53645	53914	0.991	-	.	Parent=gene20
1877523	gth	three_prime_cis_splice_site	53914	53915	0.991	-	.	Parent=gene20
1877523	gth	five_prime_cis_splice_site	54158	54159	0.994	-	.	Parent=gene20
1877523	gth	exon	54159	54320	0.988	-	.	Parent=gene20
###
1877523	gth	gene	58115	59001	0.984	+	.	ID=gene21;Target=19741042 1 460 -
1877523	gth	exon	58115	58209	0.958	+	.	Parent=gene21
1877523	gth	five_prime_cis_splice_site	58210	58211	0.856	+	.	Parent=gene21
1877523	gth	three_prime_cis_splice_site	58459	58460	1	+	.	Parent=gene21
1877523	gth	exon	58461	58526	1	+	.	Parent=gene21
1877523	gth	five_prime_cis_splice_site	58527	58528	0.784	+	.	Parent=gene21
1877523	gth	three_prime_cis_splice_site	58622	58623	0.977	+	.	Parent=gene21
1877523	gth	exon	58624	58717	1	+	.	Parent=gene21
1877523	gth	five_prime_cis_splice_site	58718	58719	0	+	.	Parent=gene21
1877523	gth	three_prime_cis_splice_site	58794	58795	1	+	.	Parent=gene21
1877523	gth	exon	58796	59001	0.983	+	.	Parent=gene21
###
1877523	gth	gene	61212	61974	1	+	.	ID=gene22;Target=19837990 1 398 -
1877523	gth	exon	61212	61281	1	+	.	Parent=gene22
1877523	gth	five_prime_cis_splice_site	61282	61283	0.316	+	.	Parent=gene22
1877523	gth	three_prime_cis_splice_site	61563	61564	0.959	+	.	Parent=gene22
1877523	gth	exon	61565	61641	1	+	.	Parent=gene22
1877523	gth	five_prime_cis_splice_site	61642	61643	0	+	.	Parent=gene22
1877523	gth	three_prime_cis_splice_site	61722	61723	0.994	+	.	Parent=gene22
1877523	gth	exon	61724	61974	1	+	.	Parent=gene22
###
1877523	gth	gene	63106	63942	1	+	.	ID=gene23;Target=8701755 1 598 -
1877523	gth	exon	63106	63178	1	+	.	Parent=gene23
1877523	gth	five_prime_cis_splice_site	63179	63180	0	+	.	Parent=gene23
1877523	gth	three_prime_cis_splice_site	63269	63270	0.999	+	.	Parent=gene23
1877523	gth	exon	63271	63391	1	+	.	Parent=gene23
1877523	gth	five_prime_cis_splice_site	63392	63393	0.823	+	.	Parent=gene23
1877523	gth	three_prime_cis_splice_site	63466	63467	0	+	.	Parent=gene23
1877523	gth	exon	63468	63683	1	+	.	Parent=gene23
1877523	gth	five_prime_cis_splice_site	63684	63685	0.999	+	.	Parent=gene23
1877523	gth	three_prime_cis_splice_site	63753	63754	0.992	+	.	Parent=gene23
1877523	gth	exon	63755	63942	1	+	.	Parent=gene23
###
1877523	gth	gene	63306	63942	1	+	.	ID=gene24;Target=8735505 1 490 -
1877523	gth	exon	63306	63391	1	+	.	Parent=gene24
1877523	gth	five_prime_cis_splice_site	63392	63393	0.823	+	.	Parent=gene24
1877523	gth	three_prime_cis_splice_site	63466	63467	0	+	.	Parent=gene24
1877523	gth	exon	63468	63683	1	+	.	Parent=gene24
1877523	gth	five_prime_cis_splice_site	63684	63685	0.999	+	.	Parent=gene24
1877523	gth	three_prime_cis_splice_site	63753	63754	0.992	+	.	Parent=gene24
1877523	gth	exon	63755	63942	1	+	.	Parent=gene24
###
1877523	gth	gene	67871	68396	0.99	+	.	ID=gene25;Target=19742246 1 423 -
1877523	gth	exon	67871	67908	0.947	+	.	Parent=gene25
1877523	gth	five_prime_cis_splice_site	67909	67910	1	+	.	Parent=gene25
1877523	gth	three_prime_cis_splice_site	68009	68010	0.999	+	.	Parent=gene25
1877523	gth	exon	68011	68396	0.99	+	.	Parent=gene25
###
1877523	gth	gene	72185	72753	1	+	.	ID=gene26;Target=8737761 1 497 -
1877523	gth	exon	72185	72296	1	+	.	Parent=gene26
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene26
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene26
1877523	gth	exon	72369	72753	1	+	.	Parent=gene26
###
1877523	gth	gene	72214	72751	0.987	+	.	ID=gene27;Target=7610337 1 466 -
1877523	gth	exon	72214	72296	1	+	.	Parent=gene27
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene27
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene27
1877523	gth	exon	72369	72751	0.984	+	.	Parent=gene27
###
1877523	gth	gene	72231	72731	0.998	+	.	ID=gene28;Target=19829297 1 429 -
1877523	gth	exon	72231	72296	1	+	.	Parent=gene28
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene28
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene28
1877523	gth	exon	72369	72731	0.997	+	.	Parent=gene28
###
1877523	gth	gene	72246	72753	0.995	+	.	ID=gene29;Target=19829716 1 434 -
1877523	gth	exon	72246	72296	0.98	+	.	Parent=gene29
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene29
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene29
1877523	gth	exon	72369	72753	0.997	+	.	Parent=gene29
###
1877523	gth	gene	72252	72753	0.988	+	.	ID=gene30;Target=19831127 1 431 -
1877523	gth	exon	72252	72296	1	+	.	Parent=gene30
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene30
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene30
1877523	gth	exon	72369	72753	0.988	+	.	Parent=gene30
###
1877523	gth	gene	72252	72803	1	+	.	ID=gene31;Target=8731753 1 480 -
1877523	gth	exon	72252	72296	1	+	.	Parent=gene31
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene31
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene31
1877523	gth	exon	72369	72803	1	+	.	Parent=gene31
###
1877523	gth	gene	72262	72754	1	+	.	ID=gene32;Target=19839622 1 421 -
1877523	gth	exon	72262	72296	1	+	.	Parent=gene32
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene32
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene32
1877523	gth	exon	72369	72754	1	+	.	Parent=gene32
###
1877523	gth	gene	72270	72801	0.998	+	.	ID=gene33;Target=19825274 1 460 -
1877523	gth	exon	72270	72296	0.963	+	.	Parent=gene33
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene33
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene33
1877523	gth	exon	72369	72801	0.998	+	.	Parent=gene33
###
1877523	gth	gene	72275	72752	0.872	+	.	ID=gene34;Target=19855736 1 420 -
1877523	gth	exon	72275	72296	1	+	.	Parent=gene34
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene34
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene34
1877523	gth	exon	72369	72752	0.872	+	.	Parent=gene34
###
1877523	gth	gene	72277	72753	1	+	.	ID=gene35;Target=8695920 1 405 -
1877523	gth	exon	72277	72296	1	+	.	Parent=gene35
1877523	gth	five_prime_cis_splice_site	72297	72298	0.995	+	.	Parent=gene35
1877523	gth	three_prime_cis_splice_site	72367	72368	0.696	+	.	Parent=gene35
1877523	gth	exon	72369	72753	1	+	.	Parent=gene35
###
1877523	gth	gene	72653	74046	0.978	-	.	ID=gene36;Target=2597485 1 163 -
1877523	gth	exon	72653	72789	0.978	-	.	Parent=gene36
1877523	gth	three_prime_cis_splice_site	72789	72790	0	-	.	Parent=gene36
1877523	gth	five_prime_cis_splice_site	74020	74021	0.514	-	.	Parent=gene36
1877523	gth	exon	74021	74046	0.615	-	.	Parent=gene36
###
1877523	gth	gene	72653	74920	0.919	-	.	ID=gene37;Target=3450080 1 166 -
1877523	gth	exon	72653	72800	0.919	-	.	Parent=gene37
1877523	gth	three_prime_cis_splice_site	72800	72801	0	-	.	Parent=gene37
1877523	gth	five_prime_cis_splice_site	74900	74901	0.919	-	.	Parent=gene37
1877523	gth	exon	74901	74920	0.75	-	.	Parent=gene37
###
1877523	gth	gene	79098	79663	0.866	-	.	ID=gene38;Target=19857409 11 314 -
1877523	gth	exon	79098	79127	0.767	-	.	Parent=gene38
1877523	gth	three_prime_cis_splice_site	79127	79128	0	-	.	Parent=gene38
1877523	gth	five_prime_cis_splice_site	79240	79241	0	-	.	Parent=gene38
1877523	gth	exon	79241	79487	0.866	-	.	Parent=gene38
1877523	gth	three_prime_cis_splice_site	79487	79488	0.899	-	.	Parent=gene38
1877523	gth	five_prime_cis_splice_site	79635	79636	0.999	-	.	Parent=gene38
1877523	gth	exon	79636	79663	1	-	.	Parent=gene38
###
1877523	gth	gene	91050	91786	1	-	.	ID=gene39;Target=8735154 1 543 -
1877523	gth	exon	91050	91401	1	-	.	Parent=gene39
1877523	gth	three_prime_cis_splice_site	91401	91402	1	-	.	Parent=gene39
1877523	gth	five_prime_cis_splice_site	91523	91524	0.917	-	.	Parent=gene39
1877523	gth	exon	91524	91713	1	-	.	Parent=gene39
1877523	gth	three_prime_cis_splice_site	91713	91714	0.848	-	.	Parent=gene39
1877523	gth	five_prime_cis_splice_site	91785	91786	0.993	-	.	Parent=gene39
1877523	gth	exon	91786	91786	1	-	.	Parent=gene39
###
1877523	gth	gene	93551	94053	0.957	-	.	ID=gene40;Target=19806050 1 401 -
1877523	gth	exon	93551	93913	0.957	-	.	Parent=gene40
1877523	gth	three_prime_cis_splice_site	93913	93914	0.992	-	.	Parent=gene40
1877523	gth	five_prime_cis_splice_site	94016	94017	0.996	-	.	Parent=gene40
1877523	gth	exon	94017	94053	0.919	-	.	Parent=gene40
###
1877523	gth	gene	93633	94384	1	-	.	ID=gene41;Target=19857902 1 407 -
1877523	gth	exon	93633	93913	1	-	.	Parent=gene41
1877523	gth	three_prime_cis_splice_site	93913	93914	0.992	-	.	Parent=gene41
1877523	gth	five_prime_cis_splice_site	94016	94017	0.996	-	.	Parent=gene41
1877523	gth	exon	94017	94124	1	-	.	Parent=gene41
1877523	gth	three_prime_cis_splice_site	94124	94125	0.998	-	.	Parent=gene41
1877523	gth	five_prime_cis_splice_site	94366	94367	0.994	-	.	Parent=gene41
1877523	gth	exon	94367	94384	1	-	.	Parent=gene41
###
1877523	gth	gene	98857	99326	1	-	.	ID=gene42;Target=19836538 1 392 -
1877523	gth	exon	98857	99121	1	-	.	Parent=gene42
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene42
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene42
1877523	gth	exon	99200	99326	1	-	.	Parent=gene42
###
1877523	gth	gene	98861	99271	1	-	.	ID=gene43;Target=8737545 1 333 -
1877523	gth	exon	98861	99121	1	-	.	Parent=gene43
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene43
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene43
1877523	gth	exon	99200	99271	1	-	.	Parent=gene43
###
1877523	gth	gene	98878	99663	0.987	-	.	ID=gene44;Target=5846455 1 525 -
1877523	gth	exon	98878	99121	0.996	-	.	Parent=gene44
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene44
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene44
1877523	gth	exon	99200	99361	1	-	.	Parent=gene44
1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene44
1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene44
1877523	gth	exon	99443	99511	1	-	.	Parent=gene44
1877523	gth	three_prime_cis_splice_site	99511	99512	0.998	-	.	Parent=gene44
1877523	gth	five_prime_cis_splice_site	99612	99613	0.999	-	.	Parent=gene44
1877523	gth	exon	99613	99663	0.882	-	.	Parent=gene44
###
1877523	gth	gene	98909	99450	1	-	.	ID=gene45;Target=8734273 1 383 -
1877523	gth	exon	98909	99121	1	-	.	Parent=gene45
1877523	gth	three_prime_cis_splice_site	99121	99122	0.995	-	.	Parent=gene45
1877523	gth	five_prime_cis_splice_site	99199	99200	1	-	.	Parent=gene45
1877523	gth	exon	99200	99361	1	-	.	Parent=gene45
1877523	gth	three_prime_cis_splice_site	99361	99362	0	-	.	Parent=gene45
1877523	gth	five_prime_cis_splice_site	99442	99443	0.798	-	.	Parent=gene45
1877523	gth	exon	99443	99450	1	-	.	Parent=gene45
###
1877523	gth	gene	104912	105793	0.887	+	.	ID=gene46;Target=7611662 1 549 -
1877523	gth	exon	104912	104928	0.824	+	.	Parent=gene46
1877523	gth	five_prime_cis_splice_site	104929	104930	0.881	+	.	Parent=gene46
1877523	gth	three_prime_cis_splice_site	105008	105009	0.99	+	.	Parent=gene46
1877523	gth	exon	105010	105228	0.863	+	.	Parent=gene46
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene46
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene46
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene46
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene46
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene46
1877523	gth	exon	105500	105535	1	+	.	Parent=gene46
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene46
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene46
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene46
###
1877523	gth	gene	105009	105793	0.884	+	.	ID=gene47;Target=8734901 1 533 -
1877523	gth	exon	105009	105228	0.864	+	.	Parent=gene47
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene47
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene47
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene47
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene47
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene47
1877523	gth	exon	105500	105535	1	+	.	Parent=gene47
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene47
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene47
1877523	gth	exon	105630	105793	0.89	+	.	Parent=gene47
###
1877523	gth	gene	105069	105815	0.876	+	.	ID=gene48;Target=19801855 1 495 -
1877523	gth	exon	105069	105228	0.831	+	.	Parent=gene48
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene48
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene48
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene48
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene48
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene48
1877523	gth	exon	105500	105535	1	+	.	Parent=gene48
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene48
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene48
1877523	gth	exon	105630	105815	0.892	+	.	Parent=gene48
###
1877523	gth	gene	105090	105793	0.878	+	.	ID=gene49;Target=8695006 1 452 -
1877523	gth	exon	105090	105228	0.82	+	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene49
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene49
1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene49
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene49
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene49
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene49
###
1877523	gth	gene	105091	105793	0.857	+	.	ID=gene50;Target=8702125 1 452 -
1877523	gth	exon	105091	105228	0.786	+	.	Parent=gene50
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene50
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene50
1877523	gth	exon	105315	105428	0.886	+	.	Parent=gene50
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene50
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene50
1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene50
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene50
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene50
1877523	gth	exon	105630	105793	0.896	+	.	Parent=gene50
###
1877523	gth	gene	105140	105793	0.88	+	.	ID=gene51;Target=19825204 1 402 -
1877523	gth	exon	105140	105228	0.798	+	.	Parent=gene51
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene51
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene51
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene51
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene51
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene51
1877523	gth	exon	105500	105535	1	+	.	Parent=gene51
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene51
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene51
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene51
###
1877523	gth	gene	105170	105793	0.862	+	.	ID=gene52;Target=2748033 88 460 -
1877523	gth	exon	105170	105228	0.686	+	.	Parent=gene52
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene52
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene52
1877523	gth	exon	105315	105428	0.904	+	.	Parent=gene52
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene52
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene52
1877523	gth	exon	105500	105535	1	+	.	Parent=gene52
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene52
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene52
1877523	gth	exon	105630	105793	0.896	+	.	Parent=gene52
###
1877523	gth	gene	105175	105793	0.901	+	.	ID=gene53;Target=19835442 1 367 -
1877523	gth	exon	105175	105228	0.87	+	.	Parent=gene53
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene53
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene53
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene53
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene53
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene53
1877523	gth	exon	105500	105535	1	+	.	Parent=gene53
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene53
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene53
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene53
###
1877523	gth	gene	105189	105793	0.896	+	.	ID=gene54;Target=8734878 1 354 -
1877523	gth	exon	105189	105228	0.875	+	.	Parent=gene54
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene54
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene54
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene54
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene54
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene54
1877523	gth	exon	105500	105535	1	+	.	Parent=gene54
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene54
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene54
1877523	gth	exon	105630	105793	0.884	+	.	Parent=gene54
###
1877523	gth	gene	105190	105793	0.906	+	.	ID=gene55;Target=19823987 1 352 -
1877523	gth	exon	105190	105228	0.872	+	.	Parent=gene55
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene55
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene55
1877523	gth	exon	105315	105428	0.912	+	.	Parent=gene55
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene55
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene55
1877523	gth	exon	105500	105535	1	+	.	Parent=gene55
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene55
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene55
1877523	gth	exon	105630	105793	0.902	+	.	Parent=gene55
###
1877523	gth	gene	105199	105793	0.845	+	.	ID=gene56;Target=19841468 39 385 -
1877523	gth	exon	105199	105228	0.833	+	.	Parent=gene56
1877523	gth	five_prime_cis_splice_site	105229	105230	0.996	+	.	Parent=gene56
1877523	gth	three_prime_cis_splice_site	105313	105314	0.995	+	.	Parent=gene56
1877523	gth	exon	105315	105428	0.904	+	.	Parent=gene56
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene56
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene56
1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene56
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene56
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene56
1877523	gth	exon	105630	105793	0.805	+	.	Parent=gene56
###
1877523	gth	gene	105371	105813	0.897	+	.	ID=gene57;Target=17325 1 277 -
1877523	gth	exon	105371	105428	0.931	+	.	Parent=gene57
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene57
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene57
1877523	gth	exon	105500	105535	0.972	+	.	Parent=gene57
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene57
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene57
1877523	gth	exon	105630	105813	0.886	+	.	Parent=gene57
###
1877523	gth	gene	105394	105860	0.827	+	.	ID=gene58;Target=19859011 1 296 -
1877523	gth	exon	105394	105428	0.971	+	.	Parent=gene58
1877523	gth	five_prime_cis_splice_site	105429	105430	0.955	+	.	Parent=gene58
1877523	gth	three_prime_cis_splice_site	105498	105499	0.994	+	.	Parent=gene58
1877523	gth	exon	105500	105535	1	+	.	Parent=gene58
1877523	gth	five_prime_cis_splice_site	105536	105537	0.957	+	.	Parent=gene58
1877523	gth	three_prime_cis_splice_site	105628	105629	0.503	+	.	Parent=gene58
1877523	gth	exon	105630	105860	0.827	+	.	Parent=gene58
###
genometools-1.5.1/testdata/Verysmall.embl000066400000000000000000000005311211610345200204730ustar00rootroot00000000000000ID   sequence0
XX
DE   
XX
SQ
     ac                                                                        2
//

ID   sequence1
XX
DE   
XX
SQ
     nn                                                                        2
//

ID   sequence2
XX
DE   
XX
SQ
     nt                                                                        2
//

genometools-1.5.1/testdata/Verysmall.fna000066400000000000000000000000171211610345200203170ustar00rootroot00000000000000>
ac
>
nn
>
nt
genometools-1.5.1/testdata/Verysmall.gbk000066400000000000000000000003001211610345200203110ustar00rootroot00000000000000LOCUS       sequence0
DEFINITION  
ORIGIN      
        1 ac
//
LOCUS       sequence1
DEFINITION  
ORIGIN      
        1 nn
//
LOCUS       sequence2
DEFINITION  
ORIGIN      
        1 nt
//
genometools-1.5.1/testdata/addintrons.gff3000066400000000000000000000014361211610345200205750ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
# comment
ctg123	.	gene	1000	9000	0.500000	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/addintrons.out000066400000000000000000000022011211610345200205460ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
# comment
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	intron	1501	2999	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	intron	3903	4999	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	intron	5501	6999	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	intron	1501	4999	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	intron	5501	6999	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	intron	1501	2999	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	intron	3903	4999	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	intron	5501	6999	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/additional_attribute.gff3000066400000000000000000000002031211610345200226120ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	.	+	.	ID=gene1;foo=bar
seq	.	exon	1	1000	.	+	.	Parent=gene1
###
genometools-1.5.1/testdata/at100K1000066400000000000000000002246461211610345200166370ustar00rootroot00000000000000>the first 100000K of at1MB
AGTGGCTACGGCGGCGGTGGCGGCGATGGAAGTAGACGGATGGTGGTAGGAATGAAAGGCTAGAAGCGGC
GGAGAAGTATGTGGATAAGAAATAACAAAAACTGAGGGGATCATGAAGTTCTTCGTTATATTATAGTTTT
CAATCTGAATTTCAATTCCGCCGCTCGCCTTTTTCCTCTCCGCCTTTTCCGTCTCTCCGATCTGCTCCCG
CCGCCGACCTTGTGATGATTATAGCTCTGAAGGTCCATACAAGGATATAAAAAAAAAAAAAAAAA
ATGRAYAMTCAAAAATGGAGTMTAGGTTTCATATCTCTCGCTTTTCTCTTCATCACTTCCTCTTCAGCTG
AGTTCATCATTCAACAGGTCACAAAGGGCARAGGAATAGAGTACAACAGTTCTTACAGTCTCGAGGAGAA
TCTTGGAGTGACRAGAGAGTTGAGAGAAGAGCGACCATCGAGTAAGATAGTGACAATAACAAGCTTCTCA
GTGATTAAAGGCAGAGGAGAACCCTATGAATCCTCTGTTTTTGAGGCTGCTGGTTACAAATGGAGATTGG
TTTTGTACGTGAATGGTAATAAAAACGACGGTGGAAATGATCATATTTCCCTTTACGCAAGGATCGAAGA
GACAAACTCTCTTCCATTAGGTTGGGAAGTGAATGTTGATCTCAAACTCTTTGTCCATAATGGGAAGCTA
CACAAATATTTGACTGTTACAGATGGCTTARTTGAAGCGATATAACAATGCSAAAAAAGAATGGGGTTTC
GGACAATTGATTCCTCNATCAACATTCTACAACGCGAACGAAGGTTACCTTTGACCAAGGACACTGGTTC
CTTTTGGGTGGCYGGAAAANCCTTTATTGTTTAAACCNGSTCCACCAACMAARAAAAWWAYTTTCTWTYM
MTYYTCCAACAYSYTYCCCWWCSAATGTTTTTTCCCTTNGGAAAAANACCTNCGTTTCCTCCTACCTTTG
GGAAAAANAAANTTCNTTTTTACTCCCGAATGAATTTTCCCCCTTTGNAAAAACCGAATNCCTGGTTGGA
CTTAGGAATTTTAACCCCCNAAAGGGGGAATGGAANGAAAGAAAAAACCCCTTTGCCCNTTCCCAATCCT
TCCCTANTTTGC
GTGARTGTTGATCTCAAACTCTTTGTCCATAATGGGAAGCTACACAAATATTTGACTGTTACAGATGGCT
TAGTGAAGCGATATAACAATGCGAAAAAAGAATGGGGTTTCGGACAATTGATTCCTCGATCAACATTCTA
CAACGCGAACGAAGGTTACCTTGACCAGGACACTGGTTCTTTTGGTGCTGAGATCTTTATTGTTAAACCG
GCTCAACAACAAGAGAAAGTTACATTCATATCAAACCCTCCAAACAATGTTTTCACTTGGAAGATACTTC
GTTTCTCTACCTTGGAAGATAAATTCTATTACTCCGATGATTTTCTCGTTGAAGACCGATACTGGAGACT
AGGATTTAACCCGAAAGGGGATGGAGGAGGAAGACCACATGCACTTCCAATCTTCCTATTTGCTCAAGGC
CATAAGGCAAATGCAGTTGCTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAAGAATCAACGAARTT
CTAACCATAGACAATATWTCTGCACTTGGTACCCATTGGAAACGTTATGGTKTGGGAKTAACATATCTAC
TGTTGCTGATTAACGAGCATCCAAAGGATTTTGGTGATGAGCCYTATCTTGAACTGAATGGTTAAGKCCT
ATACCACTCTCTCCCTWAATTCTCCTTCTTNTCWCNACATCNCYTTRATAAAAAATTTATTGATAATTTT
TTARAAACTTATTTTTKTA
GTGAAGCGATACAACGATGCAAAAAAAGAGTGGGGATTCACACAATTGATTTCTCTTCCAACATTCTACA
ACGCGAACGAAGGGTACYTTGTGCAGGACACAGCTTCTTTTGGTGCTGAGATCTTCATCGTTAACCCGAC
AGAAAAACAAGAGAAAGTCACATTCATATCAAACCCTCCGAACAATGTTTTCACTTGGAAGATACTTCGT
TTCTCTACCTTGGAAGATAAATTCTATTACTCTGATGATTTTCTCGTTGAAGACCGATACTGGAGATTAG
GATTTAACCCGAAAGGATCTGGTGGAGGGAGACCACATGCACTTCCAATCTTCCTATATGCTCAAGGCCA
TAAGGCAAACGCAGTTGTTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAAGAATCAACGAAGCTCC
AACCACAAACAATTATATTCTGCAGCTTGGTACCCCGATTCGAAGCGATTATGGTGTGGGAGTGAACAAT
ATCATATTGATGTCAGAAGCTAAAAGATGCATCMAAAGGGTATATGGTGAATGATGCCATTATCTTTTGA
AACTGAAATGGTTAAGGTCTCTGTGAACAACATARTCTCCSCTTAAATATATNTCACTACTTCTTTATCC
CCCGNAATAACCTTACAAAGAAAAATTGATGATTTAATTTGTTATACNACACTTTATTNATGCCTGTGAN
GTAACCTTGTTTCCGCTCCCCNAATTTCCTTTTTTTTCCTGTTTTT
TCAAAATATGGATAGTCACAAATGGAGTCTAGGTTTCACATTACTTGCTTTCCTCTTCATCACTTCCTCT
TCCGCTGAGCTCATCATTAAACAGGTCACACAGGGCAGAGGAATAGAGTACAACAACTCTTACAGTCTCA
CGTCGAATCTTGGAGTGACGACAAGAGAGTTGAGAGACGAGCGACCATCAAGTAAGATAGTGACAATCAC
AAGCTTCTCTGTGATTAAGGACAGAGGAGAACCCTATGAATCATCTATTTTTGAGGCTGCCGGTTACAAA
TGGAGATTAGTTTTGTACGTGAAGGGTAATCCGAAAGGCGGTATAAATAATCATATTTCACTTTACGCGA
GGATAGAAGAGACAGAAACTCTTCCAAGAGGGTGGGAAGTGAATGTTGATCTCAAACTCTTTGTCCACAA
TCGGAAKTTAAAGAAATATTTGTCTGTTACAGATGGAACAGTGAAGCGATACAACGATGCAAAAAAAGAG
TGGGGATTCNCACAATTGATTTCTCTTCCAACATTCTACAACGCGAACGAAGGGTTCCTTGTGCCAGGAC
ACARCTTCCTTTGGGTGCTGARAACTTCATCGTTAACCCGACCGAAAAACCAGAAAAAATCCCTTTCTTT
TCAAACCCCCCGAAACATGTTTTTCCCTTTGGAAAAAA
GGAAGTTAAAGAAATATTTGTCTGTTACAGATGGAACAGTGAAGCGATACAACGATGCAAAAAAAGAGTG
GGGATTCACACAATTGATTTCTCTTCCAACATTCTACAACGCGAACGAAGGGTACCTTGTGCAGGACACA
GCTTCTTTTGGTGCTGAGATCTTCATCGTTAACCCGACAGAAAAACAAGAGAAAGTCACATTCATATCAA
ACCCTCCAGACAATGTTTTCACTTGGAAGATACTTCGTTTCTCTACCTTGGAAGATAAATTCTATTACTC
CGATGATTTTCTCGTTGAAGACCGATACTGGAGACTAGGATTTAACCCGAAAGGGGATGGAGGAGGAAGA
CCACATGCACTTCCAATCTTCCTATTTGCTCAAGGCCATAAGGCAAACGCAGTTGCTACAAACACTTGGG
GAGCGGTTAATCTGCGGTTAAAGAATCAACGAAGTACTAACCATAGACAAATATATTCTGCAGCTTGGTA
CCCGATTGGAAGCGGTTATGGTGTGGGAGTGAACAATATCATACTGTTAGCTGATTTAAACGATGCATCA
AAAGGATATTTGGTGAATGATGCCATTATCTTTGAAGCTGAAATGGTTAAGGTCTCTATAACCAACATCG
TCTCCGCTTAAATATCTGCACTTCTTTGTCTACGATCAATCAACCTTATGAATAAAGAGATATTTGATGA
GTTTGTAATAAGAAAACGTTAATGTTTGTGAATTGTGAAGTTATTACTTCTGTTCTTCTGAGTTTTTTTA
TTTCAATGAAAATAAAACTCTTACCGGTTT
GTGAAGCGATMCMWCGATGMWMAAAAMKARTGKGGATTYRCAYRATWGATYTCTCTTCYWMYATTCTWSW
MCGCGAAYGAAGGGTACCTTGTGYASGACRMWSCTTCTTTYGGTGCTGAKATCTTCATGCGWTAMCCCGA
CAGAAAMACMMKAKAWAGTCWCATTCATATCMWACCCTCCRAACAATGTTTTCACTTGGAAGATACTTCG
TTTCTCTACCTTGGAAGATAAATTCTATTACTCTGATGATTTTCTCGTTGAAGACCGATACTGGAGATTA
GGATTTAACCCGAAAGGATCTGGTGGAGGGAGACCACATGCACTTCCAATCTTCCTATATGCTCAAGGCC
ATAAGGCAAACGCAGTTGTTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAAGAATCAACGAAGCTC
CAACCACAAACAATTATATTCTGCAGCTTGGTACCCGATTCGAAGCGATTATGGTGTGGGAGTGAACAAT
ATAATATTGATGTCAGAGCTAAAAGATGCATCCAAAAGGGTATATGGTGAATGATGCCATTATCTTTGAA
GCTGAAATGGTTAAGGTCTCTGTGACAAACATAGTCTCCGTTTAAATATCACTACTTCTTTTTCAACAAC
AACCTTACGAATAAAGTGGACTTTGATGAGTTTAATTTGTTATACGACAACGTTGTTGATGCTTGTGATG
TAATCGTTGTTTCTGCTCTCCGAGTTTTCGTTTTACTTTTTTTTTCATGTTTTGCTATCAATGAAATAAA
GGTATAAAACTCTCTTGGTTTTAAAGT
GGAAGTTAAAGAAATATTTGTCTGTTACAGATGGAACAGTGAAGCGATACAACGATGCAAAAAAAGAGTG
GGGATTCACACAATTGATTTCTCTTCCAACATTCTACAACGCGAACGAAGGGTACCTTGTGCAGGACACA
GCTTCTTTTGGTGCTGAGATCTTCATCGTTAACCCGACAGAAAAACAAGAGAAAGTCACATTCATATCAA
ACCMTSSWRMCMRKRTYYTCACTTGGAAGATACTTCGTTTCTCTACCTTGTCACCTAAATTCAATTCATC
GTACCCGGATCCTCGATTCTTTTGCTTTTTACCCTGGAAGAAATACTCATAAGCCACCTCTGTTATTTAC
CCCCAATCTTCACAAGAAAAA
CGTCTCCATACGTTGTTCCCGAAGACATGTCCTTGACAAAGGTATACAATCTTTTCCGGCAACTTGGGTT
GCGACATCTATTCGTTGTTCCCCGTCCTTCCCGTGTGATAGGCTTGATCACCAGAAAGGATTTACTGATT
GAGGAAAATGGGGAATCATCAGCAGTGGAACTCCAACAGTCAACTAGTAGGTCGGTACAGTGAGACAGCA
ACGCGGATGGACGCTGCACGACCGCTTCTAGACGATCTTTTAGGTTAATAAAACAGACCAAACATATACA
AGCAGTTGAAGCTGGTAGCTAAGATCTTTAGTCGGGCCAATTCTTCGTCCATACAAGGATACAAGCTTGT
TCCGCATGTTGCCACCCAAATCCGGTATGGAGGATATATGATCGTCTCTTGAGATGGGATTGTGTTGTTC
GCTAACCGATCTCATTCTCCGTTCACAGAGAGTAGAAAGATTATATATGTTTAAGGCTTTTGATTGTTGT
AATTGTGCAATCTTTGAWTATTTTCTTGGTCCCTGTAAAATAATCCACCTTTTGATATATTTACTTGATT
AACTT
TCTGNTCCGTCTNANACATCGNATCAGGTGGNGNGTACAATCATCTCNCCGTTCANTAGGTGTTTACGGA
TTTCNGCGGTCGTATANCTNGCNTGACTAAGGCTTTAACC
GGTRAGATCTACSTTGCTGGAGGTGGTGGTGGTTCGGAKGTTGCGGCGGCGGTGGAASTAGTATGATCCG
GAGTTGAATCGGTGGGAAGTTGTGACTCAATCGGCSAGGAASAGATACGGTTGCATCGGAGCAGCCGTTG
ACGGAGTTTTTTATGTGATCGGTGGATTGAAAATTGGGAATGAGACCTCACGCGCGGTGGCGGCGCGTGC
TTATGCGAGCTCTATGGATCTTTTCGATGTGGAGTCGCGTCAGTGGTTAAGGAGTCGTTCGGTTCCTGGC
GGTGGATGTGTAGTGGCGGCGTGTGCGGCGGTTGGATATGTGTATGTGCTAACCAGTCACGCGGTGGAGC
TTTCGTTTTTGGCGATTTGATGCGCGTCGTCGTGGTGGAAACACCGGGTTTGGAAAAATGGCAGAAGCTG
AAAAGTCCCCCGTTACCGGCACAAGGTGCSGGTTAAGATGGAACCGGTGAAGGTTTAACCTGCGTCGGAG
TGGAAGATAAAGTGGCGGTGGTTCAGGTGGTGGGATGCATTGACGATTTGCTTCGGCGGAGTGGGAGGGG
TGAGAGAGGGATTAGAGAAAGCCTTGTGTTGCTGTATGATACGACGGAGGGAGAGTGGAGGAGAGCGGCG
GATTTACCTGAGATGATTACACGCGCCGCCTGTGCGTGTGTGGAGTGGTAAGAGNGGAGACCACGGCGCA
GGATTATGGGTACGAGAAGTTGGAAGATGCTAVCGTACGCAGGATATATTAAAGTGGGCAAAAACAATAT
CATTATGATTGGTGCACATGTTTACTGTMTGAAAAGCAATAGCGT
CGGGGCTTCTRAAAGACNCAATCTNATGTACTCGTACATGCTANGTNCTATCTCTTCTATAATGTCTNAT
CCTTTCTGCCCTCCCACWCGTTNCCGTAGCCKCAAAWTCTCCTKTGAYATTTMCCTGMTCAGAYTGTCCT
GATGGATGSGGAYGTTCACMTAGATACCAAAGCACAAGAAATTCGAAGGTGCTGGAGAAAAGGCGACCAC
TTTCACTAAGAGCATTTGGCTCGAGGAAGCTGATGCGAGYGCCATATCCGTTGGTGAGGAAGTAACTTTG
ATGGATTGGGGAAATGCTATCGTAAAGGAAATCMCMAAKGACGAGGAGGGTCGTGTCACTGCCTTATCTG
GTGTCTTGAATCTCCAAGGTTCTGTWAAGACTACAAAGCTGAAGCTGACATGGCTTCCTGATACTAATGA
ATTGGTCCATCTCRCMTTAACAGAGTTTGATTATCTAATCCCCMANAAGAAACTGGAANATGATGATGAA
ATTTGCTGATTTTGCTGAATCCYMMCCCNAAAAANGAANACMTTTGGCMCTTKGGTNGATTCCCAATATT
GAGAGAATCTTGAAATTGTTGGAAAATNTTTATTCCCCCTTT
TCAGCTGTTTCGTTCAACGATCTAAACTATCTCAATGCTTCTTTGAATCTATTGTCGGTTTCCTTGTACT
CGTCAATTTCATGTTTTTTTTG
CCCTCCCNCTCCTNNTTTCTANTTNGNTTCNGNTTCTGTTATCGNGTTTTTCNCNNGGGTCTTTTNTCGN
NGCCCTGGACCGGAATTCNCGNGTCGACCAACTCNTCAGATGTGGTGCTNCNCTACAATGAANCAAANNG
ANTCACACTCTCGGACTNANNCTCTCCCCTCCGCTTCTGTAACCATANCNNCTCNACNTCTATGTCTCCN
ATCTAACCANCTCTNNGGGTTCGAGGAGANATAAGGAGAAAAGTANGGANGGACGANTATGCTTGCCCGT
TCTGTNCAGACTATTTTGATNTCNTCTCTCTNNGCNGTCACATTGATGAANATCNTCCTATGGATGCTTA
AANTGGGGTNTGTCCCGTCCTGTGCGGTGAAAGTGAGCTCNGGATATGATTGCNTCNTATANCCCCNCGN
CNCNGCCNATATGTTCAAGGTGACCCNGATCANGAAATCAA
GTTTATCACGCCTTGCATTGATCAGAASCCCTTGCTACGGCATTGAGCCAKGCTGCCGAAGCTGTTTCTT
CGGGAAATTCAGATGCAAGTGATGCCACTGCAAAAGCTGGAATCATTTTGTTGCCCAGCACACATCAACT
TGACGAAGAGGTTACTGMGGAACATAGTGAGGAGGAAATGACTGAAGAGGAACCAACTCTTCTCAAGTGG
CCAAATAAGCCCGGGATTCCAGATTCTGATTTGTTTGACCGTGATCAATCGTGGTTTGATGGACCTCCAG
AGGGCTTCAATCTCACATTATCAAATTTCGCTGTGATGTGGGATTCACTGTTTGGCTGGGTATCATCGTC
CTCTCTGGCATACATATATGGGAAGGAAGAATCTGCTCATGARGAGTTCTTATTGGTTAACGGGAAGGAG
TACCCCCGGAGGATTATCATGGTAGATGGGCTTTCCTCAGARATCAAGCANACAATTGCTGGGTTGCCTT
GCCAGAACTTTACCGAAAATCGTCACTCATCTCAGGGCTGCCAATANCGATATCCRATTTTAAAAA
ATAGGCGANATCCCCCCCAAANGATTNCCTGATGTGAGGAACATGGGGANATCATCNTGGAATCGAGCNC
NNGNAGTCNCCGGTNAAGTNGGTGGGTNNACANTCNCNCCCNNACNGACNCNGCATGACCNCTTCACTAC
NANCTGTTANGTTTNTGGGACTGNTCCTACGATATACCNTCTCTTGGTGGTGGNNCCNCGAAACTCNNCT
CAGGACTNGGCTCCTCGAAATTCNGATGAAGNNTGTCCCGCCTGTGACNACGNNNTTCNGGATTGGANCG
ATCTANGAGNNGACACTCTGAGAATGTGATCGGTGATTNNTCGGTNCNCTGNATCACATTNCTCNCCTTN
CCANTACCACTTTTNACANANTTCCCCTTCTTTTTCNCAACGNGCGATNCTNGNAGAANGNATGGNTAAC
TCGGNTNCCNGCTCTGNATCGNAGATANCGTNGTCCTCTCGGGGTTCCAGAGGNTC
GGTAATAAAAACGACGGTGGAAATGATCATATTTCCCTTTACGCAAGGATCGAAGAGACAAACTCTCTTC
CATTAGGTTGGGAAGTGAATGTTGATCTCAAACTCTTTGTCCATAATGGGAAGCTACACAAATATTTGAC
TGTTACAGATGGCTTAGTGAAGCGATATAACAATGCGAAAAAAGAATGGGGTTTCGGACAATTGATTCCT
CGATCAACATTCTACAACGCGAACGAAGGTTACCTTGACCAGGACACTGGTTCTTTTGGTGCTGAGATCT
TTATTGTTAAACCGGCTCAACAACAAGAGAAAGTTACATTCATATCAAACCCTCCAAACAATGTTTTCAC
TTGGAAGATACTTCGTTTCTCTACCTTGGAAGATAAATTCTATTACTCCGATGATWTTCTCGTTGAAGAC
CGATACTGGAGACTAGGATTTAACCCGAAAGGGGATGGAGGAGGAAGACCACATGCACTTCCAATCTTCC
TATTTGCTCAAGGCCATAAGGCAAATGCAGTTGCTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAA
GAATCAACGAAGTACTAACCATAGACAAATATATTCTGCAGCTTGGTACCCGATTGGAAACGGTTATGGT
GTGGGAGTGAACAATATCATACTGTTAGCTGATTTAAACGATGCATCCAAAGGATATTTGGTGAATGATG
CCATTATCTTTGAAGCTGAAATGGTTAAGGTCTCTATAACCAACATCGTCTCCGCTTAAATATCTGCMCT
TCTTTGTCTACRAYCAATCCACCTTATGAATAAAAAAATTTTAATTTGATGAATTTGTTATAANAAAACT
TTAATGTTTGTTAAATGTGAAATTT
GGGACGAACCGGTGTACCACGATTTGGTTCGTCACTGTCTGGCCTACCCAAAAGCGGATGGAATCTTGGT
GAATACATGGGAAGAGATGGAGCCCAAATCATTAAAGTCCCTTCAAGACCCGAAACTTTTGGGCCGGGTC
GCTCGTGTACCGGTTTATCCGGTTGGTCCGTTATGCAGACCGATACAATCATCCACGACCGATCACCCGG
TTTTTGATTGGTTAAACAAACAACCAAACGAGTCGGTTCTCTACATTTCCTTCGGGAGTGGTGGTTCTCT
AACGGCTCAACAGTTAACCGAATTGGCGTGGGGGCTCGAGGAGAGCCAGCAACGGTTTATATGGGTGGTT
CGACCGCCCGTTGACGGCTCGTCTTGCAGTGATTATTTCTCGGCTAAAGGCGGTGTAACCAAAGACAACA
CGCCAGAATATCTACCAAAAANGGTTCGTGACTCSTACTTTGCGATAAAAGTTTCATGATCCCATCATGG
GCACCGCAAGCTGAAATCCTAACCCATCCAGGCCGTTGGTGGGTTTTTAACACATTTGTTGGTTTGGAAC
TCCACTTTGGRAAACCTTCCTTTTGCCGGCGTTCCCAWTRANAACCTTKGCCCCCTTTTCCCCCAACC
CCTGTCCCATCGGGCCGTTRGTGGGTTTTTGACCCATTGCGGTTGGAGCTCGACGTTSGAAAGCGTCGTT
GGCGGCGTTCCGATSATCGCATGGCCACTTTTTGCCGAGCAGAATATGAATGCGGCGTTGCTCAGCGACG
AACTGGGAATCGCAGTCAGATTGGATGATCCAAAGGAGGATATTTCTAGGTGGAANATTGAGGCGTTGGT
GAGGAAGGTTATGACTGAGAAGGAAGGTGAAGCGATGAGAAGGAAAGTGAAGAAGTTGAGAGACTCGGCG
GAGATGTCACTGAGCATTGACGGTGGTGGTTTGGCGCACGAGTCGCTTTGCAGAGTCACCAAGGAGTGTC
AACGGTTTTTGGAACGTGTCGTGGACTTGTCACGTGGTGCTTAAAAATTGTTACCGTTTTCTAACTCTTT
TATTATTARTTGGTTGAATTATACGTGTCGTTCCTCTGTTAGTTGTTATAATATAATAAATCGATTTACT
CTTTGTT
CGTTTCTGCCACATTAAAACAGAAGAGTGCAACAATTGAAGGCATAGAAAAGTGGCCTTATGAAGCAGCT
GCCATTGCTTTCGAGGCTATTCCACGTACCCTGGCTCAAAACTGTGGGGTTAACGTGATCCGTACTATGA
CTGCATTGCAAGGGAAGCATGCAAATGGTGAAAACGCATGGACTGGTATTGACGGGAACACTGGTGCAAT
AGCTGATATGAAAGAGAGCAAGATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATA
GAAGCAGCGTGTATGCTTCTAAGGGATCGATGATATAGTGAGTGGAATCAAGAAGAAGCAAGCTCCTGGA
TCTGGACCTTCAAAGCCTACCATTGAGACAGAAGGAGATGCAGACAACGAACAAATTCTTCCCGACTAAG
CGAAGGGAGAAACACTTTGGTCTCAGCATAACTCAATCTCTGTTTTCACTTGTTTAATGGTTGCACTCTT
TTGGCTATTATCTTCCCTTGACATATCTTTTTAATTCTGCAGTTTTGACTTNGGTGAGATAAAATTTTCC
CAAGGTGGTTTTTTTTTGTTTGTTTTGGGAATATTAACTTTTTTGAATTTTCNTANTCCCTTTGTTGGTT
TTTAAAATTCCAATTGTTATTGTTCTTTTTG
CGCSCCTAAGAAGGAAAAGATGAGAAGAAGAAGAAGAAGAAAACTGAGGTCTGAAGAGACCTTTAATATT
TTTGCGTGGTCTAGTTTACTTTGTTATCAGAAACAAAGAAAATCTTTTGTGGCGTTAGGTGTTAAGTAAG
GTTTTTGTTTTGTTTGAAACTTAAAAAAAAGAACTACTCTTCGTTTTGTAAGGTTATAATATGTTTGGTT
TAGTCCTTATCCCAAAAACTTGCATTTTGCC
ATTTTCTTGTATGTTGGAATGGATGCCTTGGACATTGACAAGTGGAGATCCGTGAGTGACACACCGGGAA
CATCGATCGCAGTGAGCTCAATCCTAATGGGTCTGGTCATGGTTGGAAGAGCAGCGTTCGTCTTTCCGTT
ATCGTTTCTATCTAACTTAGCCAAGAAGAATCAAAGCGAGAAAATCAACTTTAACATGCAGGTTGTGATT
TGGTGGTCTGGTCTCATGAGAGGTGCTGTATCTATGGCTCTTGCATACAACAAGTTTACAAGGGCCGGGC
ACACAGATGTACGCGGGAATGCAATCATGATCACGAGTACGATAACTGTCTGTCTTTTTAGCACAGTGGT
GTTTGGTATGCTGACCAAACCACTCATAAGCTACCTATTACCGCACCAGAACGCCACCACGAGCATGTTA
TCTGATGACAACACCCCAAAATCCATACATATCCCTTTGTTGGACCAAGACCGTTCATTGAGCCTTCAGG
GAACCACAATGTGCCTCGGCCTGACAGTATACGTGGCTTCTTGACACGGSCCCCTCSAACCGTGCATTAC
TACTGGGAGACAATTTGATGACTCCTTCCTGCGACCCGTCTTTGGGAGGTCGTGGCTTTGTACCCTTTGT
TTCCARGGTTCTCCAACTGAR
GGTTTATTACCGATGCAATCCTATGTCTCACCACCGTATCGGGGATAAGTATAAGATATATCCAACATAT
GACTTTGCTTGCCCGTTTGTTGATTCCCTTGAAGGTATAACGCATGCTCTTCGGTCTAGTGAGTATCATG
ACCGAAATGCTCAGTACTTTAAAGTTCTGGAGGATATGGGACTGCGACAGGTTCAGCTTTACGAATTCAG
CCGGTTAAACCTAGTTTTTACACTTCTCAGTAAGCGCAAGCTTCTCTGGTTTGTCCAAACTGGATTGGTT
GACGGGTGGGATGATCCACGTTTCCCGACAGTCCAAGGAATTGTTCGTAAAGGTTTGAAAATCGAGGCTC
TGATTCAATTCATTCTCGAGCAGGGGGCTTCGAAGAATCTAAATTTGATGGAATGGGACAAACTTTGGTC
TATAAATAAGAGAATAATTGATCCTGTGTGCCCTARACACACTGCTGTGGTTGCAGAACGTCGTGTACTA
TTTACCTTAACGGATGGTCCTGATGAACCGTTTTGTTCGCATGATACCAAAGCACAAAAAATTCCAAAGG
TGCTGGAAAAAAAGGCGAACACTTTCCCTAAAAAACATTTGGCTCCAAGGAAACTGATGCCAATTGCCCA
TATCCGTTGGGTGAAGGAAATTTACTTTTGAAG
CTTGAATGCGGAAGCTAGGTGTATGACAAAGGCAAGAAAGCTCGGGGTTTGTACTCCAGTCCTATATGCT
GTGGATACTCTGCTTCACTCTTTAACACTTGAGTACATTGAGGGGGTCTCTGTTAAGGATATTTTCCTTG
AGTTTGGGACCAATGGGGTTGTTGAGGAACGTTTAGATGATGTTGCTGCTCAGATTGGGGCTGCAATTGC
TAAGCTCCATGATGGTGGCTTGGCTCATGGTGATTTGACCACATCAAATATGTTAGTCAGAAGTGGAACA
AATCAGCTGGTACTAATTGATTTTGGCTTGAGCGTCACATCGACCTTGCCTGAAGACAAAGCTGTTGATT
TATATGTACTTGAAAGAGCCTTACTCTCAATGCATTCGTCATGCGGGAATGTGATGGATCGTATACTGAC
GGCGTATARGAATCCTCAAAGCAATGGTCAGCCACGTTTAACAAAGCTCGCACAAGTGAAACACCGAAGG
GAAAAAAGCGGACTATGATTGGATGAAGGCGANGAACCCAAGTTCTCCCATTGGTACTGTCCTTAAAACT
TTGAACMCAAAACCCCCCAAAWCTGTCCYGTTATWATTAATCC
TGGATCATTCATAAGCTTCTACTCACTGGCGTTTATGGGATGGTGTTCTTGATGTACAACTCTAGGTGGA
GAGAAAAATTGCCTGCAAGGCCTGCATTCTACAACTACATAATCATCATGTTCGCCTTATACAGCCTTTA
CCTAGTTGCATCTGCGTTTACCGCAAACAACGCGCATTTTGGTTTCTGGTTATATGGGATCATGAGTGTT
TGCTACCACGCATTATACCTTCCTCTTCTTTACATAACGTTCCTCGCAGACTTTTTCCAGGAAGAAGATT
TGAACTTGGAGAATGTATACTACTCAGAGATGAAGGATGCTGGATTTTTCGACTCTGATTGGGAATAGGA
CTAGGGTAACAAACATCTTCCTCATTTTCTCAATCTGTAAATACACGTTGGGTAGGATCTCCTAGAAGTC
ATGGCTGCTTTTTCCGGCTTTGGCGGGTTACATTTTARGGTCTAATCTTTTGTATGTCTGTACTTTTTCC
TCATGTTTCTTTCTCTTTTATAAATCCAAAATGTCTTGTGAATCTCTTTGTTCCTTAAAKCCTGAATAAT
CT
CCAAAGGAAGAGGCCCAAACCGAGAAGATAGCTATTGAAACGGTTATGATTGATGAGTCAAACCTTGCGG
ATTATGTAGGAAAACCGGTATTCCATGCAGAGAAGCTCTATGAGCAGACACCGGTAGGTGTTGTGATGGG
TCTAGCTTGGACATCAATGGGTGGTTCAACATTGTACATAGAGACGACTGTTGTGGAGGAAGGGGAAGGT
AAAGGTGGCCTGAATATAACGGGTCAGCTCGGTGATGTGATGAAAGAAAGTGCACAAATTGCTCACACAG
TCGCCAGAAAGATCATGCTAGAGAAAGAACCAGAGAATCAGTTCTTTGCAAACTCCAAGCTTCATCTCCA
TGTTCCTGCAGGAGCCACTCCCAAGGATGGTCCAAGTGCAGGCTGCACCATGATCACATCTTTACTATCA
CTTGCCACGAAAAAACCCGTTAGGAAGGACCTTGCAATGACTGGAGAAGTCACACTAACCGGAAAAATTC
TTCCTATTGGTGGGGGTGAAAGAAAAAACTATACCGGCGAAGGCGGAATCCGATTAAAACCAATAATATT
TCCCNAAGCAANCCGAAAAACTTGATAACTGCNAAAAATGTNAAAAAAGGNTTATTTTCCTTCCTGGATG
ATATGGAAAAACTCCAACCTGCCTTTGGTT
CAGGTCCTGGTCCGGAATCCCGGGTCGACCCACGCGTCCGGAAGCGACAGTGGTAGATGGAAATGGAACA
GAGACTGGACATATCATTGTGACTACTATTGGTGGTAGAAATGGCCAACCAAAACAGACAATTAGCTACA
TGGCTGAGCGTGTTGTTGGTCACGGATCTTTTGGTGTTGTGTTCCAAGCGAAATGTCTTGAGACAGGAGA
AACTGTTGCGATAAAGAAAGTTTTACAAGATAGGAGGTACAAGAACCGTGAGCTTCAAACCATGAGGCTA
CTTGACCATCCTAATGTTGTGTCTCTGAAACATTGTTTCTTCTCAACCACTGAAAAAGATGAGCTTTACC
TCAATCTTGTTCTTGAGTACGTTCCACAAACTGTTCATCGTGTTATCAAACACTACAACAAACTGAATCA
GAGAATGCCTCTTATATACGTCAAACTTTACACTTATCAGATTTTTAGAGCCTTATCTTACATTCACCGA
TGCATTGGTGTGTGTCATCGTGACATAAAACCTCAAAACTTGTTGGTAAATCCGCACACTCATCAAGTAA
AGCTATGTGATTTTGGAAGTGCAAAAGTATTGGTAAAAGGAGAACCAAACATTTCCTACATCTGCTCGAG
GTATTACAGAGCACCTGAACTTATTTTTGGAGCAACCGAGTATACGACAGCCATTGATGTCTGGTCTGCA
GGATGTGTTCTAGCTGAACTATTGCTTGGACAGCCCTTGTTCCCTGGTGAGAGCGGTGTTGATCAACTTG
TAGAGATTATCAAGGTCTTGGGAACCCCTACCTAAAANAAGAAATCAAGTTGCATGAACCAAACTACACG
GAATTCAAATTCCCTCAGATTAAAGCTCATCCATGGCACAAGATTTTCCACAAACGCNTGCCTCCCAAAA
CCTGTTGAATTGGGTCTCAAGAANTTCTTCAATACTCCTCCTAATCTACNAAATTGCCGCTCCCCAACCA
TTAATTCCACCCATTCCTTGATGAATTAAGAAAANCAAA
CAGCGAACACGGAGTTCCGGCATCATTTAAGGTTCCAACTGGAGTTGTCATACCTTTTGGATCGATGGAA
TTAGCTTTAAAGCAAAATAATTCGGAAGAAAAGTTTGCGTCTTTGCTAGAAAAACTAGAAACCGCCAGAC
CTGAGGGTGGTGAGCTAGACGACATATGTGACCAGATCCATGAAGTGATGAAAACGTTGCAAGTGCCTAA
AGAAACAATCAACAGCATAAGCAAAGCGTTTCTCAAAGATGCTCGTCTCATTGTTCGTTCAAGTGCTAAC
GTCGAGGACTTAGCCGGAATGTCAGCTGCAGGACTCTATGAATCAATCCCTAACGTGAGTCCCTCGGATC
CTTTGGTGTTTTCAGATTCGGTTTGCCAAGTTTGGGCTTCTCTCTACACAAGAAGACTGTTCTAAGCCGT
AGAGCTGCTGGTGTCTCTCAAAGAGAARCTTCAATGGCTGTTCTCGTTCAAGAAATGCTTTCGCCGGACT
TATCATTCGTTCTGCACACAGTGAGTCCAGCTGATCCGGACAGTAACCTTTGTTGGAAGCCCGAAAATCG
CTCCTGGGTTTAAGGTGAAAACTTTAACCTTCCGGAACCAGAAGGAACCCCCC
ACCAAACCAAAGTATCTCTAAGGAATCGCTGTCCTTCGATGAGGACATACCTGCCGGTTCAATGGTTGAG
GACGAAGTGACGAGTGAACTCTCTGTGCGTTTCCCCCCAAGAGGATCTCCCTCACCATCTATTCCTCAAG
TTATCAGCATTGGACAGCTCATGGAATCTGCGCTTGAGGTCGCTGGTCAAGTGGTTGGGTCATCTGTCTC
TACTTCTCCGCTTCCTTATGACACAATGACTAACCGCTGTGAAACCTTTGGGACTGGTACTAGAGAGAAG
CTCTCAAGGTGGTTGGCCACTGAGAACCGTCAGATGAATGGGCTCTATGGAAATTCACTTGAGGAATCAT
CTGCACTTGAGAAGGTAGTATAAGATGGGAACATCTATGGGAGAGAATCTGGAATGTTGCAGGATTCATG
GTCCATGATGAGACTACCTCCAGCTAGTCCCTTTGACAATTTCCTCMAAGCASCAGGAGCTGGAAGATGA
TTCCACTAACTTGATCATATCAATCTCTGTTAAAAAGTGTGTAATCTTGTTGTTCTTATTGGGATTTGTT
AAAAAACTAACTTTTTCTAGGGGCAATCCCCAAGCTTCTCCTTATTATCTAAAATCATTAATTAATTTAT
GCCTGTTTCCTTTAGGAC
AGCAGGGGGCTTCGAAGAATCTAAATTTGATGGAATGGGACAAACTTTGGTCTATAAATAAGAGAATAAT
TGATCCTGTGTGCCCTAGACACACTGCTGTGGTTGCAGAACGTCGTGTACTATTTACCTTAACGGATGGT
CCTGATGAGCCGTTTGTTCGCATGATACCAAAGCACAAGAAATTCGAAGGTGCTGGAGAAAAGGCGACCA
CTTTCACTAAGAGCATTTGGCTCGAGGAAGCTGATGCGAGTGCCATATCCGTTGGTGAGGAAGTAACTTT
GATGGATTGGGGAAATGCTATCGTAAAGGAAATCACAAAGGACGAGGAGGGTCGTGTCACTGCCTTATCT
GGTGTCTTGAATCTCCAAGGTTCTGTAAAGACTACAAAGCTGAAGCTGACATGGCTTCCTGATACTAATG
AATTGGTCAATCTCACATTAACAGAGTTTGATTATCTAATCACCAAGAAAAAACTGGAAGATGATGATGA
AGTTGCTGATTTTGTGAATCCTAACCCCAAGAAGGAACATTGGCMCTTGGTGATTCCAATATGAAGAATC
TGAAATGTGGAAATKTGATTCCCCTTTGAAAAGGAAAAGGCTATTTCCSAATTTGATGTTGCCTTTTGTT
CAAATCCTCCCAARCCCMCTTTGTTCTTATTCCCCCCTTCCCCAAATGGAAAAAA
TCAGNGGACGATGTCAAAGATCAAAACATACCTATTGATGCAGTGCATACATCGATGATTNTCTCTTGTG
TGATCNAGTTTNAANNCCNNNATGNTANNCGGATNCTCTCTTTCATCAGANTCCGGTCCGTGTAAGTAGA
TGGGTCTAACCCGGANCTNTNTGGGTGGNCCAACCTTCTCCATAAAAACTGNTGTTGTGGAGGA
CTCTGTCTCTTTCTTCTTCTTCTTCTTCTTCTCATTAAAAGCTGAACACAAAGATCTATTCTTTCACTAA
CACATTACCAGTTTCTGCATTTGTATTATATCCTTTTCTAAAACTTTTAACCATTCTTTCTCCATTCCCA
GTTCTTAGAAAGAGTCAAGAGCAATGAGGAAGCTTTTCTTGTTAGGGTTTATAGTTGCAGGACTGGTTCT
TGGGAATGAGGCAAATGGGTATTTAGAGTTCAATGTCACCTAAATTCAATTCACCCATGGTACCCGGATC
CTC
GCCTCATGAAANAATCATGGACACTTGATTTACCTCATGGTGGACATCTTTCTCATGGTTANCANACTGA
CACNAAGAAAATATCNGCTGTATCCATCTTTTTTGAGACAATGCCATACAGATTGGATGANAACACTGGT
TACATTGATTATGACCAGCTAGAAAAGAGTGCCGTGCTTTTCAGACCGAAACTTATTGTTGCGGGTGCAA
GTGCTTATGCTCGTCTATATGACTATGCACGTATTCGTAAGGTCTGTAACAAGCAAAAGGCAGTTATGTT
GGCTGATATGGCTCATATTAGTGGGTTGGTTGCTGCTGGCGTTATTCCTTCTCCTTTTGAGTATGCAGAT
GTTGTTACGACTACAACTCACAAATCTCTTCGCGGTCCTAGAGGGGCTATGATATTCTTTAGGAAGGGGT
TAAAAGAGATTAACAAACAAGGGAAAGAAGTCATGTATGACTATGAAGACAGAATTAATCAAGCTGTTTT
TCCTGGACTGCAAGGTGGTCCACATAATCACCTATAACGGGTCTAACAGTTGCTCTGAAACCAGCAAGAA
CCCCTGAATTCAAGGCCTACCAGGAAACAATTTCTCCGTAATTGCCCCCAATTTGCCTGAAACTTTGCTT
GCGAAAGGATATGATTTAGTGTCTGGAGGCACTGATAATCATTTAGTTTTGGTGAATCTGAAAAACAAGG
GAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCC
TGGGTGATGTTTCTGCCATGGGTTCCCCGGTGGGCATCCATATGGGAAACAACCAGCCCTCACATCAAGA
AGATTCATTGAAGAAGATTTTGCAAAAGTTGGCGGAATATTTTGATTTAACCNTCCAAAATANCCTTAAA
GAACCAAACCANAATTCTCCAAGGAACCAAAATTTGAAAANANTTTTGTTTNCCAACCAATGCCNATCCA
ATTGANAAAATTACCNTTCCNAAAATTTNCAAACCTCCCTTGAAAATNGTTAAAAAAAA
CCATGGTACCCGGATCCTCGAATTCTTTTGCTTTTTACCCTGGAAGAAATACTCATAAGCCACCTCTGTT
ATTTACCCCCAATCTTCACAAGAAAAACTGAGRATAGGAACGTGTGGAACAGGAGGATGAGGATGANCAA
GGTGAAACACAGTGTGGAGCATGTGGTGAGAGCTATGCAGCTGATGAGTTCTGGATTTGCTGTGACCTCT
GTGAGATGTGGTTTCATGGAAAGTGTGTTAAGATAACACCAGCAAGAGCTGAGCACATCAAGCAATACAA
GTGCCCTTCTTGCAGCAACAAAAGGGCTCGTTCCTAAATTTGTTGANCGCTCGCTTCTGTGTATCTACCT
TTGCATATGATGATGAACANCTTAACTGTTTGGTTTAGATCAGATTTGTCNTATGGATTTGGTAATTTTA
GGAAGA
GTGGTGGAGGAAGCAGCTGGTCCCGAGGTGGTAGTAGTTCCAGAGGAAGTTCTGATGATTGGTTGATCGG
TGGCAGAAGTTCATCAAGCAGCAGAGCTCCTTCGCGGGAGAGAAGTTTTGGAGGTTCATGCTTCATTTGT
GGGAAATCTGGACACAGGGCAACAGATTGTCCTGATAAGAGAGGATTTTAGAGTTATCGTAGCAAATGGT
TTCTGCTCTTGGGAGAAAGATCCTTGTCCTTTTTGGTGTTCTTAATGCGAATCTTTTCGTGCTTGCTTCA
ACGGTTTGTTTCAGACGGTAGAGAAGCAATCAGGGAGGAGGATACATGCTTCGGACAAGGTAGAGCAGAA
ATAAATAAGAGAGAGGCAATAGCAAAAGTAAAGGAGAAGGTTTTCCTCAAATTGGCATTTTCAGAGTTTG
CGTGAGAAACAAGGGAAAGCTGATGGATCTTTTTATGTTAGGGTTATTATAATAGTCTTAATGATCAGTT
TCCATGTTTCTAAGGTTTTGTTTGATTTAAGTTGGTTATTAATTCAGTCTACTTACACTACTTTTATTTT
CATTTTTGTACSTTTTCAATTGTTATATGTTAATTCCGATCMCATTTTTTTGGACAGAATTACTATTTCT
TTATAATAAAATCTTATGCC
ATTTGTAATAATCTTCGTAGAAAAAATGGATTCTGATTCTTGGAGTGATCGTCTCGCATCGGCTTCAAGA
AGATATCAGCTCGATTTCTTGTCTCGATCTGACAATTTCTTGGGGTTTGAGGAGATAGAAGGAGAAGATG
ACTTCAGGGAGGAGTATGCTTGCCCGTTCTGTTCAGACTATTTTGATATCGTCTCTCTATGCTGTCACAT
TGATGAAGATCATCCTATGGATGCAAAAAATGGGGTATGTCCCGTTTGTGCGGTGAAAGTGAGCTCTGAT
ATGATTGCTCATATAACCCTACAACATGCAAATATGTTCAAGGTGACGCGGAAAAGGAAATCAAGAAGAT
GCGGGGCTCAATCCATGCTATCGATCTTGAAGAGAGAGTTTCCTGATGGAAATTTTCAGAGCCTATTTGA
AGGAACATCACGTGCTGTATCCTCTTCTTCTGCCAGTATAGCTGCTGATCCTTTACTGTCTTCATTCATT
TCACCAATGGCTGATGACTTTTTCATTTCTGAATCAAGTCTATGTTGCANAACACCAATTTCTGCCCCAG
AAAAACATTGGAATCCCAAATTTTGCCCTGAAAAGGGAAATGTTTGAAAAAAACCATTTCTCCTTTT
ATAAATATGGGTAATATATCTATCTTGCTTCTACTCTCTCTTTTCACTTTTTCTCTGTGTCTATTTGTCT
CTCCGTAAGAAACATTATGCCTTCATCTGATTCCACGATGATGAAGAAAGGAACAAAGCGCAAAATCGAA
ATAAAGAAACGAGAAACCAAAGAGCAACGAGCCGTGACTTGCTCTAAACGTCGTCAAACTGTTTTTTCCA
AAGCCGCCGATCTCTGTCTTAACTCCGGTGCCAACATCGCCGTCTTCGTAACCTCTCCCTCCGATAGTTC
CGATGTTGTCTATTCCTTCTCCGGTTACTCCTCTGCCTACGAAATCGCTGATTGTCACCTAAATTCAATT
CACCCATGGTACCCGGATCCTCGAA
AAGTGTCGAACAAATACTACTTAGGTCCAGCTCCATTGGAAGAAATGGCGAGGCAAATCGCTACGGCTTC
GGGACCTTGTGGGAACAACCGAGAGTATCTTTTCAAGCTAGAGAAAGCAATGTTCGACATTGAGCATGAG
GAAGAGTATGTGATTGAGTTAGCGAATGAGGTTAGGAAGCAACTCGATTTACCGGAGGAAGTGAAGGCAT
TGTTGAAGCCTATTGTTTCTCATGTATCCGTCAAGTCTCAAGCTCATGTTTCCACTCGTCAACGGGTCTT
TGCATCATGAAGACAGCAAAAGTTATGGAGCTAACTTAAAAAAGCATTGTGGTGACGAGGCTAATGTTAA
CTCTTTATCTTTCAGCTTAATATTTGATCACATCTTGACCTTGAGATGTTTTGTTTTGCTCTGCATTTAT
TGAGAATTCATAACATTGTATGATATGAGATGCAATTTATGAGAATAATAACCGATCTTTAGCTCTGCC
CGTTCTTTCTCTCGCAAACCCAAATTCTCTCAGCGCCGGTCAAATACTTGTCTCTCTCTCTCTCTCTCTT
TCACTCTTGTCTTGTCTCCTTCGAAGCTGTTTGTTCTGTAAGAAAGATGGAAGCAGGTGGCGCGTACAAT
CCACGCACTGTTGAAGAGGTGTTTAGGGATTTTAAGGGTCGTAGAGCTGGCATGATTAAGGCTTTAACCA
CTGATGTTCAGGAGTTTTTCCGACTTTGTGATCCCGAAAAGGAGAACCTTTGCCTTTACGGACATCCAAA
TGAGCACTGGGAAGTGAATTTGCCAGCTGAAGAGGTTCCTCCTGAGCTCCCAGAGCCTGTCTTGGGTATC
AATTTTGCCAGAGACGGGATGGCGGAAAAGGATTGGTTGTCCCTTGTTGCTGTCCACAGTGATGCTTGGC
TTCTTGCTGTTGCTTTCTTTTTTGGAGCCAGGTTTGGATTTGACAAAGCTGATAGGAAGAGGCTTTTCAA
TATGGTGAATGACCTCCCAACAATCTTTGAGGTTGTAGCTGGCACTGCTAAGAAACAAGGAAAAGATAAG
TCCTCTGTTTCCAACAACAGCAGCAACAGATCCAAATCAAGCTCCAAGCGAGGATCTGAATCCCGTGCCA
AGTTCTCAAAGCCGGAGCCGAAAGATGATGAGGAGGAGGAAGAGGAAGGTGTGGAAGAGGAGGATGAGGA
TGAGCAAGGTGAAACACAGTGTGGAGCATGTGGTGAGAGCTATGCAGCTGATGAGTTCTGGATTTGCTGT
GACCTCTGTGAGATGTGGTTTCATGGAAAGTGTGTTAAGATAACACCAGCAAGAGCTGAGCACATCAAGC
AATACAAGTGCCCTTCTTGCAGCAACAAAAGGGCTCGTTCCTAAATTTGTTGACCGCTCGCTTCTGTGTA
TCTACCTTTGCATATGATGATGAACAGCTTAACTGTTTGGTTTAGATCAGATTTGTCATATGGATTTGGT
AATTTAGGAAGACATTTTAGTTTTTTCCTTGTTACATTTTTGGGCGAATTGAAAGGGATAACTCCTTTGT
TTTAAGGGGGTTAATGGAACCTTTTGGCCCCCGTTTTTAAWAGTTTTGGTTT
GTGAATGTTGATCTCAAACTCTTTGTCCATAATGGGAAGCTACACAAATATTTGACTGTTACAGATGGAA
CAGTGAAGCGATACAACGATGCWAAAAAAGAGTGGGGATTCACACAATTGATTTCTCTTCCAACATTCTA
CAACGCGAACGAAGGGTACCTTGTGCAGGACACAGCTTCTTTTGGTGCTGAGATCTTCATCGTTAACCCG
ACAGAAAAACAAGAGAAAGTCACATTCATATCAAACCCTCCAAACAATGTTTTCACTTGGAAGATACTTC
GTTTCTCTACCTTGGAAGATAAATTCTATTACTCTGATGATTTTCTYGTTGGAGACCGATACTGGAGACT
AGGATTTAACCCGAAAGGATCTGGTGGAGGAAGACCACATGCACTTCCAATCTTCCTATATGCTCAAGGC
CATAAGGCAAACGCAGTTGTTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAAGAATCAACGAAGCT
CCAACCACAAACAATTATATTCTGCAGCTTGGTACCCGATTCGAAGCGATTATGGTGTGGGAGTGAACAA
TATAATATTGATGTCAGAGCTAAAAGATGCATCAAAAGGGTATATGGTGAATGATGCCATTATCTTTGAA
GCTGAAATGGTTAAGGTCTCTGTGACAAACATAGTCTCCGTTTAAATATCACTACTTCTTTTTCAACAAC
AACCTTACGAATAAAGTGGACTTTGATGAGTTTAATTTGTTATACGACAACGTTGTTGATGCTTGTGATG
TWATCGTTGTTTCTGCTCTCCGAGTTTTCGTTTTACTTTTTTTTTCATGTTTTGCTATCCAATGAAAATA
AAAGGTTTAAAACTCTCCTTTGGTTTTTAAAAGT
GGCTGAGGAGTACAAGAACAACGTTCCCGAGCACGAGACACCAACGGTCGCAACAGAGGAATCACCAGCG
ACGACAACAGAGGTTACGGATCGTGGATTGTTTGATTTCTTGGGGAAGAAGGAAGAGGAAGTGAAACCTC
AAGAGACAACGACGCTGAAGATTGAGGCGATGGTGAGGAAGGTTATGGCTGAGGACGAAGGTGAAGAGAT
GAGAAGGAAAGTGAAGAAGTTGAGAGACACGGCGGAGATGTCACTTAGTATTCACGGTGGTGGTTCGGCG
CATGAGTCGCTTTGCAGAGTCACGAAGGAGTGTCAACGGTTTTTGGAATGTGTCGGGGACTTGGGACGTG
GTGCTTAGTAATGGTTACTGTTTTCTAGCTCTTTAGTGGTTGAATTTACTTGTCGTTTCTTAATGTGTAT
TTTTCATTGTAATAGAATAATCGATGTTTTGTAATATATTAATGTATTTGATATTTCTCAACTAATTTCC
ATTGTAATATTG
GGCGAGGGAATGGAGAGTTGCTGTCGGAGCGTCATAGCTTCAAGGACGTTTCATCTGCGGTCAAGTGGCC
GTCTATTTCCCTCTCTTAGCTTAACTCATCTCAAGGGCAAGCTATCTCTCTCCATCAACTCGTTTTCCTC
CAAGATTCAGTCTCATGCTCTCCGAGGAGTTGGTATAGGCGAGTCAGATAAGAAAAATCCCCTGCCGCGA
GGGGCCGGAGAAGGAGTCAAGGAAGATGCGAGGAGTAAGCTGCTTCATGTAGTTTTGGTCTCTCCTCAGA
TTCCTGGGAATACAGGTTGCATTGCAAGAACATGTGCTGCCTCAGCTGTTGGTCTGCATTTAGTCGGGCC
ATTAGGTTTTCAAGTGGATGACGCCAGAGTTAAGCGAGCTGGTTTGGATTATTGGCCCTTTGTGGTTGTC
AAAGCGCATAGCTCATGGGCTGAATTTCAAGAATATTTCAGGCTTCAGGAAGGGANAAAAAACCAATGAT
ANCTTTTACCANNAAGAAGAAACAAGGATACTTTC
ATTTGTAATAATCTTCGTAGAAAAAATGGATTCTGATTCTTGGAGTGATCGTCTCGCATCGGCTTCAAGA
AGATATCAGCTCGATTTCTTGTCTCGATCTGACAATTTCTTGGGGTTTGAGGAGATAGAAGGAGAAGATG
ACTTCAGGGAGGAGTATGCTTGCCCGTTCTGTTCAGACTATTTTGATATCGTCTCTCTATGCTGTCACCT
AAATTCAATTCACCCATGGTACCCGGATCCTCGAATTCAGCTTGGACTTAACCAGGCTGAACTTGCTCAA
AAGGTGGGGACTACCCACCAAA
AAAACAACGCGCATTTTGGTTTCTGGTTATATGGGATCATGAGTGTTTGCTACCACGCATTATACCTTCC
TCTTCTTTACATAACGTTCCTCGCAGACTTTTTC
AGTTTTTGATCAACGAGTTTAACCGTTGTTCTTATGAGATTCCTCATAATTGGTTGTTACTCGACTCGCT
CCCACTCGCTAGAGAGAACATGAAGTCTGTAGAGCCAACGGTTAAGCTAAGTTCATCGTTGGAAGCGCTT
GCTGACTACTATAGTCTTACAAGGGAGGGTGATGCTCACAGGGCCTTGTCAGATGTGTTACTCTTATCTA
AGGTGTTCCAGAAACTCACCATTGATCTCAAGCTCTCACTCTCTGATCTCGTCCTTCGCTGTCACACTGC
ATCTGATATCAGTGCTGCCATGGCCAAGAACAAGAAGGCCTGAAACATTTTAGACATAGCTATAAGCTTA
TTTTGGGATATTCATCTCTCATTCTATTGTTAATGTACCTAACTCTGAAATTATGTAACCGATTATTTAA
TCTGATCTTAAAATCAAAAAAAAAAAAAA
AACTNNTCCCAAAGGTGGGGACTACNNAGCANCCCTANTGCTNGACANNTCNTGNATNCCTCTNCNGCTA
AGTTCGGGCTNCCTNACGTCCCAACGCGGCGCAAGAATTAATTANAGCACTTNTNNCAGTCTCCATNACA
ATCTNGGAGTGATGCCANACTTGACAGGTCANCGACCNCCGACTACGATNGTCACCATNCNCNGCCTCNC
AGNGATTACANGCTNAGGATAACCCGGTGNNACCNCNGTTTCGNAGCTGCTGNTCACTNGNNGAGATAGG
TNNTGTGGATNATTNGTA
GGACTCGAGCAGAGCCAGCAACGGTTCGTATGGGTGGTTCGACCACCGGTCGACGGTTCGTGTTGTAGCG
AGTATGTCTCGGCTAACGGTGGTGGAACCGAAGACAACACGCCAGAGTATCTACCGGAAGGGTTCGTGAG
TCGTACTAGTGATAGAGGTTTCGTGGTCCCCTCATGGGCCCCACAAGCTGAAATCCTGTCCCATCGGGCC
GTTGGTGGGTTTTTGACCCATTGCGGTTGGAGCTCGACGTTGGAAAGCGTCGTTGGCGGCGTTCCGATGA
TCGCATGGCCACTTTTTGCCGAGCAGAATATGAATGCGGCGTTGCTCAGCGACGAACTGGGAATCGCCGT
CNGATTGGATGATCCAAAGGAGGATATTTCTANGTGGAANATTGAAGCGTTGGTGAAGAANGTTATGACT
GAAAAGGAANGTGAANCGATGAAAANGAAAGTGAAAAAATTTGAAANACTCNGCGGANATGTCACTGAAC
CATTGACNGTGGGTGGTTTGGCGCCCCAAATCCCCTTTTGCCNNAATTCCCCCAAGGAATTTTCCACCGG
TTTTTTGGAAACNTTTTCCTTGGAACTTGTTCCCCTTTGTTGCCTTAAAAAAA
CACAAATGGAGTCTAGGTTTCACATTACTTGCTTTCCTCTTCATCACTTCCTCTTCCGCTGAGCTCATCA
TTAAACAGGTCACACAGGGCAGAGGAATAGAGTACAACAACTCTTACAGTCTCACGTCGAATCTTGGAGT
GACGACAAGAGAGTTGAGAGACGAGCGACCATCAAGTAAGATAGTGACAATCACAAGCTTCTCTGTGATT
AAGGACAGAGGAGAACCCTATGAATCATCTATTTTTGAGGCTGCCGGTTACAAATGGAGATTANTTTTGT
ACGTGAAGGGTAATCCGAAAGGCGGTATANATAATCATATTTCACTTTACGCGAGGATAGAAGAGACAGA
AACTCTTCCAAGAAGGTGGGAAGTGAATGTTGATCTCAAACTCTTTGTCCACAATCGGAAGTNAAAGAAT
ATTGTCTGTTACAGATGGACATGAANCGATCCACNATGCNAAAAAAGATGGGGATCCACATTGATTCTCT
CCACATCTCACCGAAGAAGGTACTTTCAGACCACTCTTTGGTGCTGANACTCTCNTTACCGACGAAACAG
AAATCCTTCTTCNACCNCCNAAANTTCCTGGAGACTCTTCCCNCTGGAGAATCATANCGAGATTCTNTGA
ACGAACGGAACAGATACCNAGGACGGTGAGAAACATNCTCACTCTTTTCCAGCTAGGAACCTTTTCANNT
TGGGACGTNCCCCGTNAGACCCAACCCCCCCCTTNTCC
ACCAGGGGGCATNCAAAAATCTAAATTAGATNTGAATGGGACAGTCTTTNGTCAATAATNAAGATAATCA
AGAGATCCTGTGTGCCCTAGTACACCCTGCTGTAGNTGCCTAACGTCCATGTACTATGTTACGTGTAACT
GATGGGTCTGATGAGCCGTTTGTNCGGTGGTATCCCAATTCTCAATNAAATACGAATGTGCTGGAGAA
GACGAAAGCAATCAGAAACTCAGGTGAATCAGAAGCATGATTCGAGTTACGAAACCAAAAGCGATCATCG
AATCACTGAGTTACCATCTTATCCAAAGATGCTCCGCAAGTGGAACTCCTAAAGGAAAAGCAAAGCTGAA
GACAGGTCAGCCATTGAAGCGTAACAAACTCTCCATCAAGAAAGGTGGTGGCGGCGGCGGAGCACCTGTT
GAAGGAGAGGAAGCAGTTAAAGGAAAAGGTAGAATTTCCGATGAGAAGCAGAAACTCTACGAGCAATGCT
TAAACGCTCCTTGTCCTGTTCGCTACTTGACCCCCCAAGAGATCGAGCGTGAGGCGCAACGTGAGAAGCT
AGGTTTGATTAGTAAAGAGAACAACGAGATATGGAGATCCAGAAGAAAGGAGGAGTATGCTTGCCCGTTC
TGTTCAGACTATTTTGATATCGTCTCTCTATGCTGTCCCTAAATTCCATTCACCCATGGTACCCGGACCT
CNAATTCACTTGGACTTAACCAGGCTGACTTGCTCCAAAGGTGGGGATCCCCAC
CAAATTCTCTCCGTGTTTCCTTCTGCTTCAGGTGATATTTTAACAAANTTCTTANTACAATGGGATCTGT
TGATGCTGCTAATGGAANTGGGAAAAAACCTACAGTTATATTTGTTCTTGGTGGTCCAGGAANTGGAAAA
GGTACCCAGTGTGCTTATATTGTTGAACATTATGGTTACACACATCTGANTGCTGGANATCTTCTTAAAG
CTGANATTAAATCAGAACTATGATCCAGAATATGATTAAAGAGGGGAAGATTGTACCTTCTGAGGTTACT
ATCAAGCTTCTACAGAAAGCTATTCAGGAAAACGGGAATGACAAGTTCCTCATTGATGGTTTCCCTCGTA
ATGAGGAAAACCGAGCAGCATTTGAAAAAGTTACTGAGATTGAACCAAAGTTTGTCTTATTCTTCGATTG
TCCTGAGGAAGANATGGAGAANCGCCTGTTGGGCCGAAACCAGGGGAGAAAAGATGACAATATTGAAACT
ATNANGAANCGCTTTAAGGTGTTTCTTGAATCTANCTTACCANTGATTCNTTACTACCAAACCTAAGGGG
AAANTTAGGAAGANTAATTGCTGCCAAACCCCTTTGAAACTTTCTTCCAAGAANGTNAAAGCANTTTTTC
CNCCCGAAACTNAAAAAGGTTA
TGGGGCNACCANCAANCTAANGAAGATCGAATTGGACACACTCNCGTCTATCACGCCAACANCNCTGCAT
CTCTGTCTGCCCNATACGACTGCACGTG
GGCTGAAGCAGCGAGAAGACAAGGTGGTGGGAGACCATTACCGCCACCTCCGAGAGGCGTTAACCAACAA
CCTCCTCGCCCTAAACCTGAACCTGTCGATCGTGAAAAGACATGTCCCCTTCTTCTTCGTGTTTTCACCA
AGAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCAAAGGATGAAGTTCAAAT
CTACACTTGGAAAGATGCCAGTCTTCGCGAGCTAACAGATTTGGTTAAAGAAGTTTCTGTANCAGCTAGG
AGAAGGAATGCTAGATTGTCTTTTGCGTTTGTTTATCCTAACAATAAAGGTGGCTATAATGTNANAAAAG
TTGGGGAGACGATGGCTTATCCNAACCGAAAACAACCANATGACANTAAAACNCTTTCCCAACTTCCGTT
TGAGATTGGAGATTATCTGGATGTGGCAATTTATTANGAGGTTTCTGTTTCTTGTTAAGTGGGATTTGGG
TGCGTGCACCATGGAAGAAGTACACATTCNTATGGTTGTATCATCTTAAACTTCGTTTANACATGTTTGT
NTTTTTT
GAGGAATTTTGCCAACATACAGTTACAACCATTTGGCATTACCATGGAGGATGCGTTGTGGGCAGAGTGG
TCGATGGGGATTATAAAGTTATTGGTATCGACCGGCTTAGAGTCATTGATATGTCGACCGTTGGTTATTG
TCCCGGGACAAATCCTCAAGCCACGGTTATGATGCTTGGCAGGTATATGGGTGTGAAGATCTTGAGAGAG
AGACTCACCAAGAAGTAGGGTTTTGAATCGGATCAGGGGTTTTGGGAAAACGTTATATTAAAAATGAAAT
GAATCAAGATATTACTAATCGATGTTATTAATAGCTGAATATGTATTGTTCTTGGTAATTTCTGTTTGGT
ACTTATTATTAGACCAAACTGAGATGTATACGGAAATATATGTATAGACTCATTCCCAATTTTCAAAAAA
AAAAAAA
TTTNGGNGGNCCTNGTAAGGAATTCNTGGGTCGACCCACTCNTCCGATTTGTAATAATCTTCGTAGAAAA
AATGGATTCTGATTCTTGGAGTGATCGTCTCGCATCNGCTTCAAAAATATATCAGCTCGATTTCTTGTCT
CGATCTGACAATTTCTTGGGGTTTGAGGAGATANAAGGAGAAGATGACTTCAGGGAGGANTATGCCATGG
TACCCGGATCCTC
GGACGAACCGGTGTACCACGATTTGGTTCGTCACTGTCTGGCCTACCCAAAAGCGGATGGAATCTTGGTG
AATACATGGGAAGAGAATAGTTCAGGGAGGAGTTAGACTANCCATGATACTAAACCGGGTTTTTAGTGAC
GATCATGCTATTGCTGGTGTTGCTGCCACTTGAACCAAACCCGACATACCGGGTCATCAAAGCATTTGAT
TAAGAGATTATTTGATACATTCACAAAATTAATTAAGGCTGATCAGACATTCTTTTCTTTTAGTAGCTTT
ATCTATGTGACAGCTAATGCCTGTGGACTGCTTTGTTTAGAAGTGTTTAGCATTAGATCATATGCTAATT
CAATGTTATTAAGTCATCGTATGATCGTTTTAG
GCAAGAGCTTTGATAAACTATCGTATCAAGGAAAACATTGGCACAGGAAGCTCCTCGAGTGCCCCAGTTC
CATTTGCAAAGAAGTTCTTTATGCAGAACCTTAGACCAACAAGTCCACAGCCTTCTCCTGCAACCACATC
GAGAATCTTACCCTTTATTTGCCCAAAACAACCTTCCAGAAGCAGCANATCATCCTTAGCAGCAACTTCC
GGTATTGACAGAATTATGGCAGCAGCCTTGGAAAGCCGCAGCTACCAGCGGCCTCAGCAGAGATTTGCAA
ATCCGCCTTATGTTCCTATGAGGCAATTTAGATCGCAATGCCATGGGATGGCTCCACCTGTCNCAATCAG
AACCGCTGTACCGGTCTTCTCTGCACCTCCAATGCCTCCTCCACCATGTACAAACAACACTCAGCTACCT
TCTTCTGTGTATGTCCCATCGCTGATGCGAACTGCACCACCTGTGANGATCGCGCCGCCTGTCACAATCA
GAACCGCGGTGCCCGTATTTGCTTCTGCGCCACCGGTTAGAATTANAACCGCTGTGAAGCCCACAGTTGA
AGGCAGGAGAAAACCCGCNTATCATCNNTCCCAGAAAAAGGAGAATTATNCCCNGTCTTGGCCTGATANT
CTTGAAAATT
AGCTCGTCAATCAATGGCGTCGTCTCTATCTCCACCGGAAGAAGCTTCGTATCACCACCGTCATACCAAA
AGGTACACCTCCTCCGCTTCCTCCGCTTCCTCCACCACCAACGGAACCGTCGAATCATCGGTTTCCGATT
TCGTCANACGTCCCAAAATCTCTCATCCGAATTACATATCAAGTTCCGAGATCGAATCAGAGTTTTCTCA
TCACGATCCAGATTTCGCAAGAATCNACAACGGTAGTTTTGGTTGTTGTCCGTCATCAATCCTAGCTTTA
CAACGAGATTGGCAGCTCCGGTTCCTTCGTCAACCGGATCGATTCTATTTCGACGAACTCNANCCANAAA
TCTCCGATTCTAGATCTGTAATCNAACGGTTAATAAACGCCGAGCATGGCGATGAAGTCTCGATCGTCGA
TAACGCAACAACCGCAGCTTGCAATCGTTCTTCACAAACCCCTTGGGCTTTTTCCTTGAAGGTCGGTTCG
ATAAAAGGCGNANGCGGTGGTTATGCTTCATTAAGCTTATGGGCTCTGTTGAAAAAAA
AAGAGTATTCTAAAAGCAACCTTTTCTTGGTGGGGAAGTCACCGGAAGGTTCTGTAGCGTCAGGGATAAA
CGTAAGAAGCGACACGCCTGAGCTTGGACCGATCGGGAATTTGTTAACGGAAAGCGAAAGTGTTTCGACG
GTGGCATCAGTGTTGGTGGTGCAACAGTATATAGCAAGCCGTCCGGTCGGAATTTCGAAGAACGTCACGA
CTGAAGAGTCTCAAGGAACAAAGTTGAAAGACTTTGTAGCAACAATGCAATCAAATGAGAAATTACAGTC
AGAGATGTCAAAGCTCCGTGAGATGGTAGAAGAATATGCTAAGCAATTCCCAACGATTGGGTTCGAGAAA
GAGACGATGAGATACCNNGAGTAGTTTTCATCGTGTGGATTGACACGTTTCCCCATCTCTGANATGCTTT
AGTGATCATGGACCANAGGCGCCACCGATGGTCTGAAGTATCGCTGAAACTAAAGTTGAACTAAAAAAAT
CGCACTCCAATGTTTGTCTCTTACCCTTTCCCTTTTGTCTCTCAAATTTTTATCTTTGGCTT
GTCGGCTCGTTCTGCGATCACNNAGCAAAAGCTGGCTCGATCCTTTGGGGAAAGTCTGATTGGTGCCTCN
CGTTCGGNGGTTTCGACTCNAGGACCGGCGATTCGGTNCTTCNCTGACGAGANNGGTCGTGTGCTCANCG
GANAGGAACNCGCGANACANAGCATGTCTATNCCANAAATGGAGAGGGANNGACTGGAGAACAAGAGGAA
ACTCGAGCCAGATANGCTANATGGTGAGAAAGGANGTGCCCACAANAANCCTGACACCAGCNAGCCATGA
GTTTATCACTCACAGTATACNTGAANCCTGTCNTAAGGCAAGCAGTAGTNAAAAACAATAATGCCTTTGA
CCTGGTTTCTCTCTTGGTATGAGAGATCTTGTACTTGTNCAGAGATCTTTGTCCNTCTGACGTGTGTGTT
NGTNTGTTCTAANAAATCAANTTTNCATAATCC
ATTTCGATTCTCTGTAATTAAAGACAAAATTGGAATAGAGGAGACATTGTCTCTTTGATTCTTGAGCTTA
TTTGGGGGAGAGAAAGAGAGAGCGAGAGGATCTGATGTGTATCTCAATCTCGCAAGTCTCTAGATTGAGA
ATCCATTCATTTGGAAGTTCTTGCTGTGAGCGTGTTCATGGATGGATCAAGAACAGCTCTAGCTTGAAGC
TGCTTGATGTTAGAGCTTCTTCTGTTGATGGTAAAGCAAGATGGATCAGACGTAACGTGAGTACAACTAC
ACAAGGTAGTAGAAGCAACACTAANANCAGTGTGTTGGGAGGAACAGTTCCTGTTACCAGGGATTATAGA
TNAAGAGAGTANAACCNAGGTACAGCCTTTTGGTAATCTTCAGCAACGGCTTGCGCNAGATAAAGATCTG
TCTAAGCTCCTCNCGGTTTATAGTCTCTGATCTTTGAAACAACTGGGTTTGCATCNGGAAAAATGAGCNG
ATAATTTGAAATTTGCCANCTCCGGAATNTAACTTNGGTGGGTNGGGGTTCNACCACCATTTTCAAAANC
TCNTTGTTCCACCCCCGGGGGTGTTTNGTTTCCCC
AGGNTCCTCTACGATCGACCTGACTANNCTACNNCTGCNTGCGACATCTTTTNNCTTCTCTAATGTNGCC
TACANNTNTNCCNGACNTGGTGGTCNGANCCTCAACTCCAANCNNGACANCTNNANGNTGAACTGGTNCC
ACGTGTGAGGACTATCCACCAATGGACCGATATCAAAGAAATGAAGGCGATACAAGTCCACCAATGGACC
GATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGAAATGAAGGCGATACAAG
TCGACCAATGGATCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGAAAT
GAAGGCCCNGATATCTGAAAAGCATAATAAATGAATCAATATCTAAAATCTGGTGTTTTTCTCTCTTTCT
TCTTCCCAACAATGATTGAAAAACTCTTTCTTGTTATGAATAAAGATGGATGCCCATTATAAGGGCCATC
NTCTAAGCCCATCATCTANATGTTTCTAGGGTTTTACCCTTTCCTTGTTCTCCTATATAAAGAACCTTTA
TCTCATGGATACCNCTCCTTCTCT
CAAAGCGTTCTAAAAGAATTTCAAAGAAGAAGTGAAAATGGAAACCACTGCTTATAACACAACATCACGA
ATTGGAAACTGGTCATCGGCTATTTCTCGACCTCTACAANCATGTGGATCTTTCAAGTGCCAATTACCAC
CACGAANAGGTGTTATTGTAGCTGANCTTCGAAACTCAAACTTCCGATGGAGGAAAGCAACGACAACAAG
CAGAGGAAATGTTGCAGCNGAGGCAGTTAAAATTCCTACGTCAGTACCAGTAAGAGTGGCGCGTGAGCTA
GCTCAAGCAGGATACCGCTATCTCGACGTGAGGACACCAGACGAATTCAGCATCGGACATCCGACTAGAG
CCATCAACGTACCTTACATGTNCAGAGTCGGATCANGAATGGTTAANAACCCGAGTTTTCTAAGACAGGT
CTCGTCCCACTTCAGGGAAACACGATGAAATCATAATCNGTTGTGAGANCNGTCCAATGTCTTTATGGNC
TCACTGATCTTCTCCCTGCTGGCTTCNCGGGGANCACNGACATTGCTGGANGATACTCCCTGGACAAAAA
TGACTGCC
AGACGACTTTCBACTGAATATCTAGCTAGCTCACACTCTAGCTGTAACTGTGTTTATTCTCACTAGCTAA
TAATTAGATATTATATATTGAGTTGGTTTAATTTTGCTAGTAAAGGATGGACTGATAGGGTTTGATCAAT
GGGACAAGAGAGCCACTAAGGTGAAGGGACATGACTTCATTGGTGGAGCCAACAAGCTTGCCTCCGACAA
AGACAGCTGGAACCGCCGTGGAACAGCCGAGCCGGAGAAGAGCCTTCTCGATCTCACGGCAGTCCGGGTC
GTTGTCGATCTCGTGGATGGTTGGTTGAACCCTAAGGTCACGGAACAGGATCTGAACGGCGTAMAGAAGA
ACAACATGAGCTCTTCGTGAAGATCACCACTCCTTTCTCTGAAGACATTCTCATCACTTTGTCCATGAYC
CTCAGAAGTCTGAAGATCTGATGATGGCGAGGGGTTWAAACTTTAGCGTTTTGA
CACGAAAGTCTTACGCGTCTCCTTGAAGATGCGAAATCTATTATTGAGAAATATTGGAAACTCAGATGGA
GCAGACACGTTTGCAGGAAGTACAGGTACATCAAAAAACTCGAATCGATAGAACTTGAATTAGTAAGGGT
AGCACGTGAGATACAAGTCCACCAATGGACCGATATCAAAGAAATGAAGGCGATACAAGTCCACCAATGG
ACCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGAAATGAAGGCGATAC
AAGTCGACCAATGGATCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGA
AATGAAGGCCAGATATCTGAAAAGCATAATAAATGAATCAATATCTAAAATCTGGTGTTTTTCTCTCTTT
CTTCTTCCCCACAATGATTGAAAAACTCTTCTTGTTATGAATAAAGATGGATGCCCATTTATAAGGGCCA
TCATCTAAGCCCATCATCTAGATTTTT
CACGAAAGTCTTACGCGTCTCCTTGAAGATGCGAAATCTATTATTGAGAAATATTGGAAACTCAGATGGA
GCAGACACGTTTGCAGGAAGTACAGGTACATCAAAAAACTCGAATCGATAGAACTTGAATTAGTAAGGGT
AGCACGTGAGATACAAGTCCACCAATGGACCGATATCAAAGAAATGAAGGCGATACAAGTCCACCAATGG
ACCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGAAATGAAGGCGATAC
AAGTCGACCAATGGATCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGA
AATGAAGGCCAGATATCTGAAAAGCATAATAAATGAATCAATATCTAAAATCTGGTGTTTTTCTCTCTTT
CTTCTTCCCCACAATGATTGAAAAACTCTTCTTGTTATGAATAAAGATGGATGCCCATTTATAAGGGCCA
TCATCTAAGCCCATCATCTAGATTTTTCTAGGGGTTTTACCCCTTCCCTTGTTCCCCCTATATTNAAAGA
AANCCCTTTTATCTCCCATTGGGAAATAAACCCC
GTTNACGANCANGGTAAATANATGATNNTNAANNTTNTCANCTNGATACACTCCGCNNATANTTCCCNGA
TNNTCCACTGCGGTGGTTCGGCNCCNNAGTCGCANNTGCNCATTCACCACCGATTNTCTACGGNCNCTGG
NNTCTGTCGNGGACNTGGGACGTGGTGCTTANTAATGGTTACTGTTTTCTAGCTCTTTAGTGGTTGAATT
TACTTGTCGTTTCTTAATGTGTATTTTTCATTGTAATAGAATAATCGATGTTTTGTAATATATTAATGTA
TTTGATATTTCTCAACTAATTTCCATTGTAATATTG
CCTACGGAGGTCTANNCCCCCTTCCGGTACANGNNCGNAATNNNCAGGNCGGTNCTNGCTTACGANAAAT
GTNAGCAAATGAGAAGGAAGTTGANGANGTTGACAAACGTGGCGGAAATATCACTGAAATTTACACAAGT
GGNGGTACGGCGCNNAAATCTCTCTGCATATTCACGNTGGAGTNTCNGCGGTT
TNAGTCGNCGGNNGCTCCATAGGATCCTNACTTACGTACNCNTGCANGCGACTTCGNNACTNNTCTATNC
TGTCANCTAAATNCAATTNNNGGGGCNNCATTANAATCCCNCTNCTNCCACTNCNNATCCGGAAACCATG
NCNACCAGGGANTANCGGATGTNGCTTCTCGGANTCCGCNGGCCCTNTATGAAAGTTCAANGTTTNTGGG
TTCCNGGGGGAATATGGTCCCAAGGCTNANNCTTAAGAGATTTGACTAAAGGGCGNCCGNTCTTTAGGAG
CCCNACTAACATCCGCTTGCNTNCNACTTCCTACCTCTTCTAAAGTGTCCCTGGATNCANTNCTCNCATG
GTNCCCAGANCCNCGNATNCNTCTTGGACTTCACCATGCTGAGNTTNCTCGGGGAGTGGGGACTACCGCC
AAAAACTTNNNNGAATTGACNAAAGGGCGGNCGCTCTANAAGACCANCTTACTTCCCTNCNTGCNACNTC
TNCTCTTCTATNNTGTCCCTNNATCCNTCCCCCNTGGTNCCNGATCCNCCAATCNCTTGGACTTNNCCNG
GCTGAACTTGCTCCNNNGGTGGGGAA
CCCGCCCTTTNAANCGAGTACAANACNGGGGGAAANGTTCCGAATAAAAAGTGGGG
GNANTCGATCATACCCAGNANAGGTGTCGTATGAGGTGGTGTCNANCAATCNGTCNCACGGNACNTTGTG
GTTGCGACTTCTTTTCGGTGTNCCNCGNCCTTCCCGTGTAATANGCTNNATNANCNCAAANGATTTGGTG
ATTGAGNAANATGGGGAATCANCGTCNCTGGATCTCCNCCAGTNNNCTACTAGGTCNGTACNNTNAGACA
CCGGCNCGGANGGANTCTGCNNNACCGCTTCNAGACAATCTTNTATGTNAATACNTCANACGAGGCATAT
ACAANGCAGTTGAAGCTGGTANCTAGCATCTTTAATCGGGCCAATTCTTCGTCCATACAAGGATACGNGC
TTGTCCCGCATNTTGCCNCCCNCATCCGGTNTGGAGGATATGTGATCGNCTCTTGAGATGGGATCGTGTT
GTTTCGCTAGCCGATCTCATTCTCCGTTCCCAGAAGAGTTAGAANAGATTATTTATGNTAANACGGCNTT
CAGAATTGTTTGTTAAATTTGTTGCCNAATCCTTTTGNATANTTNTTCCCTCGGGGTNCCCTCGTTT
ATGGTGGTGACGTCTTTCTCTTCAGCGCCGCCTATCTTCTTCTTACCTGGAGCTGATGCTCAGTTTTCTT
CTTCCAATGGAAGGTTTGCTATTCCTTCCTCTTCTCTCGTAAAGGGACTAAGAAGACACCAAGATGCAAA
GTTGGTGGGCAACAGAGCCAGAGTTGGAGTANTACGAGTCCTAGCGAACCCAAATGTATCTCCTCCTCCT
CCTCCAGGAAAAGCAAAGGTAAAAAAAGAGGTAATCATGGTAGACCCTCTTGAGGCTAAGCGGTTAGCTA
GTAAGCAAATGGAAGAGATTAAAGGCAGAGAAAAGCAACAGAGAAGGCGTGAAATAGAGGCTATTAACGA
AGCATGGGCAATCATANGACTCATGATAGGGCTGGTGATCGAAGCTCAAACGGGGAAGGGTATTCTGGCT
CATTGGCTGGTTATTGGTCTGCANTTGTCCATTTGTTCACTCCATCAACTTANAATGAATTAAGTTTCAT
TTGGTTTTCTCTACTCTCAACTGTGACCAAATCTAATGTTGTGTTCATGCCAGTTAANTTGTTAAACACA
TACCTTTGTTAATCCTCCCTTGTTTCAAAACTTCNAATCCTGCCNTTTGTTAAAAAACAAAATTTAAANA
TTTTACNCTTAAATAAAANCNACNTCCCTTTTGTTAC
AGNCNGGNGCCGCTCTACANGAACCAAACTNANNTTNACNTNCGNNCTAATCNCNCCTCTNCGNTNCTGT
AACATATNTTCNCTTACNCCNATGGTCCCACGGATCCTCTACTTCTGGGTCTGANGACACTGNNNGAAAA
TAATCACTATCACCGGATNAGTATATCTTAGCCCCTNCCGTCCCAACTAAAAACGGGAATCGTCTCTCTA
TGCTGTCACATTGATGAAGATCATCCTATGGATGCAAAAAATGGGGTATGTCCCGTTTGTGCGGTGAAAG
TGAGCTCTGATATGATTGCTCATATAACCCTACAACATGCAAATATGTTCAAGGTGACGCGGAAAAGGAA
ATCAAGAAGATGCGGGGCTCAATCCATGCTATCGATCTTGAAGAGAGAGTTTCCTGATGGAAATTTTCNG
AGCCTATTTGAAGGAACATCACGTGCTGTATCCTCTTCTTCTGCCAGTATACTGCTGATCCTTTACTGTC
TTCATTCATTTCCCCAATGGCTGATGACTTTTTCCTTTCTGAATCAATCTATGTGCA
CCATGGTACCCGGATCCTCCGAATTCTTTTGCTTTNTACCCTGGAAGAAATACTCATAAGCCACCTCTGT
NATTTACCCCCAATCTTCACAAGAAAAACTGGNGATTTNGATATCGTCTCTCTATGCTGTCACCTANATT
CAATTCACATTGATGAAGATCATCCTATGGATGCNAAAAATGGGGTATGTCCCGTNTGTGCGGTGAAAGT
GAGCTCTGATATGA
AAGATTGANGCNATGGTNACNAAAGTTAAGGCTGAGGACNAANGTGAATAGANGANAAGGAAANTNAANA
AATNNAAACACNCGGCNGACATGTCACTTAGTNTTCTCCGNGGTGGTTCNGCCCNTGAGTCGCNGGGCNC
ANTCGCCAAGGAGTGTCAACGGTGNCCTGGGAATGTGTCNGGGACGGGGGACNTGGGGNNTCCCTAATGG
TNACTG
TGGATCCAGGATGGGGTTTCTAANATCAGACTCCGACCAAATCCCAAACAGCTTGANNTAGTTCTCCAAA
CTCGCGAACTCGGATGAGCTTAACTCCTCCTTAACCCGATATTGCCANGGGATCCANTATCNGGTTTGGT
GACCGAACGCATGGGCATTGATATCCTTCTTTCTCCATCCACAGACTTTGACTTAAGTTTGTTTAACCCC
CATAC
CGGGTTGGTGGGGAACCCATGGGTTGATGACTGTGCGGCCGCACGGGTTTCATCTGACAACACTCGCCTA
TCTCCTTAACCCCATACTAGATCT
GGAAATTCGAAACTCGATTGGTTGGTTGACTTCTCTCTCTTCTCTCCCTAATATTTTTCAGAGAGAGAGG
TTCTTATATGTTATCTCCGTCCGGTTTGTTTTTACCGGAGTTTATACTCGGATGAAGTCCGGTTCTGCTG
TTAGTTAGCCGTCAACACGACTTCTCCGTTGTCGTGTTCTTGCCGTCAACACAGCTTTTTCGTTGCTGTG
TTCTTACCGTTAACATGGCTTTCTATTGCCATGTCCTTTTGCTCATACAAAAGCTTGATGTTGAAGACTA
TGGCTTCTAGGATTGTTGAATCGGGAGAGTTTCGTATGCGCCAAATCTATTCTCTTTTGCCATAATATAC
TTCATCCATTGAGATTTTGCTTTTGGATCTGATGGTTTTCTAACGATGTGTGGTTTTCACTTCCACACAA
AAACGTTGGATCCATCGGATTTACGACAGCTTATGTTACCTGCGTCTAAGGTTTGGTTAAAAACTCATTT
CCATCTTAAATTTCGATTCCCTTTTGCTGCTTATAAAAATATTCAGAGATTCACTTATATTATCAAGGGT
GGATTACTTCAATCTCTACATCTTATTTCATGATTACGATGGTTTTCTTATGAATCTATCAATCATTTGA
GATTAGTAGATTGATTTGTTCTGTAATCCATTATTATCATTATCAGTGAGAAAAAAAGAAGAATTCGTAA
TCGGTTGTAGTTCCGGCAACGTATTCTGATTCACTGGATTTGGAATCTCTGCATGCGGTGAAGGATGTGA
AATAAACACGTATCCTCAACTTATCCCCATCGATGAGACACGTTCTTGAGTTTATCCTTTCTTGGGCCTC
TTGTTTGGGCTTCGTTGAAAGTTGTCTTTGATGTTTATGTAATTGGGTGTGATGTTATGTATTATTATTT
CAATAAAACTGCAGTTTCAGAGG
CTTTTCTGTCTAGAGAGAGAAGCTTTTATCTTTCATCGCCGTTAACAGGGCTATTCCGTTGCCGTGTTCT
TGCCGTCAACATGATTTTTTCATTGCCGTAGACATGGCTTTCCGTTGCCGTGTTTTTATGTCGTCGCTTT
TGTTAGGTGTTGTTTGTTTGCTTCCAATAAAGGGGAATTGTCTTTCGTCTCTGTCTTTACAGAGTTTTAT
GAGAGATGACACACCTATCTTATATGTTTATAGTTTATACAAGTGTTTTTATGTTTGTTGGATTTGAAGC
GAAGCTTAACCATCTTATGGTGACTTAGATCTATTTAGAACCTTTAGTTGGTGGCTTTTCTCCGGATCGT
CATGTTGGGTATACGGATTACTGAAATTTCAAGGATAGTTTGCAAATAAAATTGAAGAAAAGAAAGAAAT
TTCCTTCGCGATTTTAAGATGCCTTTTAGCCGTGATTTCAATTGTTCGGAGTTTTGATTCGTTTTGCAAC
CAGCTTTGTCGGTGAAAATCAGAAGAATCAATAGTCGAATTTCAGTTATCGGCAATGATTTTCTTCACCA
GAATCAGCATCTTAGATGGCGGTGGTGATGTCGGAAAGCTTTTAGAATTTTCATCCAACACGTGTACCAC
TGTTGACACGTTTGTTTGGGAATGAAACTAATGATAAACTTTCTTCAAGTTGAAGCAATATATTGTGTGG
GCCTTTATGGGCTGTAATCTGTTTTGTAACCCATGTTGTTATGAATAAAATCCTAATCTTGCGAG
CCACGCGTCCGGTGTTGGCTGGCTCTTGCCCGGCAGCGTTGTTTCCATGAGCGTCGTTGGCCGGATTTGG
TTTGTATCCAACGTTGTTTTGTTTTTCTTTCAATAATCTCATAGATCTTATGTTGGTGATAATGGTTTAG
GTGATTTTTCGCTTAAAGATCTTTATTATCCAATTCGATCTTTTGAGTTTGAGATTTGCAGGAATCAATT
TAGAGATTTGCATCTTAAGTTGAAGAAAAGAAGAAGTTTTCGTTGCATATTAATATTGCCCTTAGCTGCT
AAGTTTTTATCTGGAAGTTCGATTGGTTTGTTTAAGGTGAAACCCAGAAGAATCAAACTTGCTTTCATTA
TCAATGTTGATTTTTCTCACCGGAATCAATCTCAGACGGCAAAGGAAGATGTCGGAAATGCTTTTAGATT
ACTCATCCAAACGTGTGCTGTGTTGTTTTCAGCTGTTGACACGTAAGATTGGTTGGAGCCACAATATCAG
TTCTTCATCTTTAAGCAATGTTCTTGGACTCATTTAGGACTTCAAATGTTCTTGTAATCTCAGTGTATGT
TGGGCTTTTGGTTTTTTAGCCCATGTATGGTTGGTTAACGTTAATAAGATTTTCCACTTATGAG
CCACGCGTCCGATAATGGTGTCAGAGTTCTCTCCCTTCTCTCTCTAGGATTTTGATTTATGTTCTTCTTT
GTCGTTGTCTTTCACCGCCGTTAACATGGCTATTCCGTTGCCGTGTTCTTGCCGTCAACATGGCTATTCC
GTTGTCGTGTTTTATGTCGTAGACATGGCTTTCCGTTGCCATGTTTTTATGTCGTTGCTTTTGTTAGGTG
TTGTTTGTCTGCTTCCAATAAAAGGGAATTGTCTATCGTCTCTGTCTTTACAGAGTTTCATGAGAGATGA
CACACCTATCTTATATGTTTCTAGTTTATACAAGTGTTTTTATGTTCGTTGGATTTGAAGCGAGGCTTTA
CCATCTATGGTGAATCAGATCTATTTAGAACCTTTAGTTGGTGGCTTTTCTCCTTATCGTCATGTTGGGT
ATATGGATTACAGAAATTTCAGGGATAGTTGCAAATAATGTTGAAGAAAAGAAGAAATTTCATTCACCAT
TTTAAGATGCCTTTTATCCGTGATTTCAAGTGTTTGATCAAGTTTTGATTCGTATTGCAACCAGCTTTAT
CGGTGAAAATCAGAAAAATCAATGGTCGAATTTCAGTTATCGTCAATGGCGGAGGTTGATGTTGGAAAGC
TTTTAGAATTTCATCCAACATGTGTACCAGTGTTGACACGTTTGTTTGGAGATGAAATCAATGAGAAACT
TTCTTCAGATTGAAGCAATATTTTGTGTGGGCCTTTATGAGCTGTAATCTGTTTTGTAACCCATCTTGTT
ATGAATAAAATCTTAATATTGAG
AGAGGGGAGGGAGAGAAATGGAAGGCAAAGAAGAAGATGTACGAGTGGGAGCTAACAAGTTCCCGGAGAG
GCAACCCATCGGTACATCGGCTCAGTCCACCGACAAGGACTACAAAGAGCCACCTCCTGCGCCACTGTTC
GAGCCCGGCGAGCTCAGCTCATGGTCTTTCTACAGAGCCGGAATAGCTGAGTTTATCGCTACTTTCTTGT
TTCTCTAACA
GAAACCCAAACCCTCATTCCAAAAAATGGGGTCTCGCTCTCAAAACCTCTCCTTTCTCGTCCTCCTCCTC
CTTGGCTTCGTTGCCGTCTCCTATGCTTGCGACTGTACCCCTCCTAAACCATCACCAGCACCTCACAAAC
CACCAAAACATCCAGTCAAACCGCCTAAACCTCCTGCCGTCAAACCACCTAAACCACCGGCAGTAAAACC
ACCTACTCCAAAACCTNCCACCGTGAAACCCCATCCTAAACCACCCACCAAACCTCACCCCCACCCAAAA
CCTCCCATCGTAAAGCCACCAACCAAGCCTTCTCCGTCCACCCCTAAACCTNCCACCAAACCTTCCCCGT
CCACACCTAAACCTTCCACGACCAAGCCT
TGACTACTGACATATAGAAAAAGAGAGAGGAGGATAATAATATGGCGAGCAAGAAAGCAGCTATGGCTAT
GATGGCGATGATCGTGATAATGGCTATGTTGGTCGANACATCAGTAGCGATAGATNTCTGCGGCATGAGC
CAGGATGAGTTGAATGAGTGCAAACCAGCGGTTAGCAAGGAGAATCCGACGAGCCCATCACAGCCTTGCT
GCACCGCTCTGCAACACGCTAATTTTGCATGTCTTTGTGGTTACAAGAACTCTCCATGGCTCGGTTCTTT
CGGTGTTGATCCTGAACTCGCTTCTGCTCTCCCC
TGACTAATGACTGGAGGGTTTCTGTCTATGCGGCAAGGGGCTGGTGCTGCTTCGAGATCAGCTATTTTTG
GAGGGGTTTTGCTTGCTTTGATTGAAGGAGCTGGGATCATGTTGAACAAGGTACTGGCTCAGCCTCGGAA
TATGGTGATGGAGGACCCTGGAATGCAAGGAATG
TGTAACTGACAGAGTGGGATAAGAGACAAATAAGGAGAATCAAACAAGCAATCCGATCGATCTACCAGAT
CGCCATGATTCTTACAAGATGCTTACCCTTGATATGGCTATCTCTACTTACTGTGTGTGCTGCTGGGAGG
ACATTGCACCCTCTCCCCTGTTAAAGGACCCAAAACTGTCAAGCTTCAACTTCCGACTTCACGTCCTTAT
AACATCGCACACAGAGGTTCCAATGGAGAGATCCCAGAAGAAACTACAGCTGCATACTTGAAAGCAATTG
AAGAAGGCACAGACTTCATAGAAACAGATATCTTATCATCCAAAGATGGTGTGCTCATATGTTTCTATGA
TTGTATTCTCGACGAAACA
TGACTAACTGACGGGGAATACGACTTCTGATTTGAACAGTTAAAAACGAAAAGTCTAATAAAAGCTATAC
TTAACGGATAGCTTTCGCGACATAGGAAAGGGACATGATGCGTCGTGTAAATATTCTTTGCTCATTTGCT
CTGCTTTTTGCCAGCCATACTAGCCTGGCGGTAACTTATCCATTACCCCCGCGCGGCCGCGCGGCCGCGC
GG
TGACTAACTGACGATGGTGGTGGTGGTATNACAGGTGATGATATTGTTAGGACAAGAGATTGGTAAAGTG
TCGTCGACTCTATACAAAGTTGGGGACATGGACGCTTGGGGCATCCCAATTGATGCTAAGGTCNACTCCA
AATGGCCCAAATCTCACTCTTTCAAAATCGGTGACTCCCTCTTGTTCTTGNACCCACCAAGCGAAGACTC
ACTGATTCAAGTGACGCCTTCCAATTTCAAGAGCTGCAACACC
GCAAGGACAAAAAANGGGGGAAGAAATTAAGGGAAAATTAAGGACAAAGAACGCNCCAACAGATTTGTTN
TTCNGGAGNGGAGGGGGTATTTGGAGAAAAGAAATTTTTCNTTCTTTATTNAAGGNAAATAATTTTTAAN
GNGCACGGTAAACGGCCTTCCTTCCAGTAAATGGAATNGGAATAAAAAAAAGTTGGTGTNTGGNTTTCAA
GTATAAATAGACCGCAANNATNAATCTNGGTTTCCTCGTCATGGTTCTCGTTCCCTTTCTTCCTGGTTTC
TTTTTNGGCACAANATTTCAAGNTATACCAAGCATACAATCAACTCCAAGTGAATTCGGAAAAATTAAGA
TANGGAGGGANTCTNGAAGTTGTCAACTTTGGTGATTGTGTGCATGTTAGTGACCGCTCCAANGGCGTCC
GAGGCAGCAATNTCGTGCGGCGCAGTCACCGGCAGCTTAGGTCAATGCTATAANNACTNGACCCGAGGCG
GTTTCATTCCTAGAGGGTGTTGNTCNGGCGTTCAGAGGNTCAACAGCTTGGNTNGNACCACCCGTGACCG
CCAACAAGCTTGTNGTTGTATCCAGGGTGCAGCGAGAGCCTTGGGTTCTCGACTNAACGCTGGTCGTGCT
GCTNGTCTCCCCTGGTGCTTGCCGTGTTAGGATNTCTNACCCCATCAGTGCCAGAACC
GGACTAACTGACGATGTTTGTTGCGGGGCATATCTACCGCTATAATGTTGATCAGTTNGGCTGGTCAGCT
AAGTCCAGTGAATTTCTGGAAAAAAGGCAGCTGAAGTGGGGCAGTATTTTATTCCATTACGGAATNGNAT
TTGTTTTCTTTGGTCATGTAGCAGGTATTTTGGTTCCAAAGGCATTNTATGAAATGATTGGTGTAACAGA
CCATATG
TGACTAACTGACCATCCNACCTCATTTACTGTTCTGTTTCACTTTCTCTCTCTCTGTANACTCTCTAAAT
GATGGCAAAAAACTGTAATTTAGTCAGTGTTCTATGTGTATTTTTGGTATTGACCCTCTTTAACAAACCC
ATCACCGTCGCCGGGCAGAATATTCCGGCGGTGGGCTTGTTCACCTTTGGTGACTCCAACTTNGACGCC
AGGAGGAGAGTAGTGAACGGAATTAACCAGACAATTCACTCACAACCTAGCTAGCTAGTGAACAGTATTT
TCTATATACCAAAAATGGCTTCAAGTTCCATAGCTCTTTTCTTGGCTCTCAATCTTCTCTTTTTCACAAC
AATCTCCGCCTGTGGTAGCTGTACTCCGTGCGGCGGAGGTTGCCCCTCTCCCAAGCCAAAGCCAACTCCT
TTGGAGTTGACGGAATGATTATAAACCTTGCCACACTTCTAGCTAACATCGTGACGAATCCGTTTAATAA
CGGATATTACCAAGGCCCACCAACTGCACCGCTTGAAGCTGTGTCTGCTTGTCCTGGTATATTCGGGTCA
GGTTCTTATC
AGATGGGAAGTGGCATGATAAGGACATTGGTTATTCTAGCAATAGCTTTATACATGATCGGTTCCGACAA
CGTCCACGTGGCAAAAGCCCAGGTCTGTGGAGCTAACTTGTCGGGACTGATGAACGAATGTCAACGCTAC
GT
AGAGAGATAGTAAGAGTAGGCGCCCTCAAGAAAACAGAGTAAAAATGGATCAAACTTTGTATCGCAAGTG
TCTGGTTACTTTATCGATGATGGCAATGATCGGCACATCAATGGCTACATATGCCGGGACCCCATGGCGT
ACAGCCTCAGCC
TCACAGGAGGAACGGGTAGCTTAGGTACAGTCACTGGTGGAACGGGTAGCTAGATAACAAAATAACGGAG
TTGAAAATGATGTTTAATAAAATATCCCTAATCACTGCTCTGTTGTTTTTTCTATTAGGAACGAATGTGT
TCGCCCATTCCCATTTAGAAGATTCATCTCCTAAAGATGGCGCAGTGCTAACTGAATCATTGAAAGAAAT
CAAACTAACATTTGAAACGAGCCTTGAACCAACTAGTACATTTACG
CTCGTTGAAGACCAACAATTTCAAATCTCACTTCCTTATCACAATGTCTTCCTCTATCTCTCCCCTCCTC
ACAACCGTCATCTTCGTGTCGAGCCTCCTCTTCCTTACTATCTCCAAAGCGGCGACAATTCCAAACATCC
AC
TTCTCTCCAACTCGCGGAGCTCTTCGTGAGCTCTATTGTGCATTTGCTTTATGGGTTTTATATATTTAGC
TCCGCCGTTGCCGGAGATATCTCTCAGACGTTGAATGATTACTTGTTTAAGTCCAATGTCGCTTTCGGAG
AAACCGGTCAAAATCAAACCAATGTTGAGGGTTTGCCACCTATTGTATTGGC
AGTGGTGGTTTCCGGCTTAAAGATGAAAGCTTTCTACGTATTCGTTGTTGCTCTTCTTCTCACCTTGAAT
TATAGGGGAGAAGCAAGTGGTTCTGTTTTCTTCATTGATGGATCCAACAATCAATATCTTCGTCCACGAT
CATCCAGTGAGGCACTTCCCATGTCGCCTGTTGAAATATCTGCAGCAGTGTCTGCCTTGTTGGGTTTTGC
ACCTTCAGCAACTTTGACAGCTGATGGCTCATCCAAGTTGAACAAGATTCTAAAACCTAATCCA
AAGTTACTGCCGCCACGGCTGCTGCTACAAAGGTTAACACCCATACAAGAGTCACGGGTCACATTTAAGC
TTCAACTATATATTTGCATGTTATTTGCCAAAAGGATTTGACAATAATGCAACAAGAGTTTCATTGAAAA
TTTCAAGAACCCTAGTTAATAACGATAATGGGTTCGAGAGTTTTGGCTTCCTTCTTTGTTTTCTTAATCT
TCACGGTCATCACATTGCCTCCCACGATCCAAGCTTGCACTCCTTGTACTCGTCCTCATCCTCCGGTTCC
GAAACCTCCACAACACGGCGGTGGTGGAGGTGGTGGTAGCAAGCCGCCCCCACATCACGGTGGAAAAGGT
GGTGGTAAACCCCCACCCCACGGTGGAAAAGGTGGAGGACCGCCGCATCATGGTGGAGGAGGAGGAGGAG
GAGGGGAATCACCGCCGGTTGTTAGACCTCCTCCCGTAGTGGTGAGGCCACCGCCAATCATAAGACCTCT
TCGGTCGTCTATCCACCACCAATTGTGAGGCCACCGCCAATCACAAGACCTTCCATCATAATCCCTCCAA
TTCAACCCG
AGCATAATTATCGATCATGTTTATCATCTATCTTTTTATCTTTCTCTCATCTGCCATTATAGATTCAGAT
GGGGTTGCAATGGCCCAAAAGATCGAGGCAATTGGTGGGAAGGGAGGGAAACGGTGGGATGACGGTGCGA
ACCATGAT
CACACAACACAGACCTAAAAAAATGTCTTCTCTGCGTTTGCGTTTATGCCTTCTTCTACTCTTACCTATC
ACAATTAGCTGCGTCACAGTCACTCTCACTGACCTCCCCGCGTTTCGTGAAGCTCCGGCGTTTCGAAACG
GCAGAGAATGCTCCAAAACGACATGGATACCTTCGGATCACGAACACAACCCATCAATCATCCACATCGC
TATGACT
AAACTAAAACAACTCTCTCATAATCTCTCTCCCTCACTCTAACACCAAAAGAAGAAGAAGCATTTTCCAA
AGAGAAAGAGAGAGAAATGGGTTCTAAGATTGTCCAAGTTTTCTTGATGTTGGCTCTATTCGCCACTTCA
GCACTCGCTCAAGCCCCTGCTCCTACTCCCACCGCCACTCCTCCTCCCGCAACTCCCCCTCCAGTCGCAA
CTCCTCCTCCAGTGGCTACCCCACCACCTGCTGCAACCCCTGCCCCAGCCACGCCACCACCTGCTGCAAC
CCCAGCTCCTGCCACTACTCCACCGTCAGTTGCTCCTTCTCCTGCTGATGTTCCCACCGCCTCTCCACCA
GCACCGGAAGGTCCT
CGGAAGGTCTTCGCAACTATCGAACGGACCTCTTATCAAACACCAAACCACACCAGAACAGAACTCAGCC
ATGGCTTCTTCTTCTTCTTCTCTTCTAATCCTAGCCGTTGCTTGTTTCGTCTCGCTAATCTCACCGGCGA
TTTCACAACAGGCTTGCAAATCACAGAACTTGAACTCCGCCGGTCCGTTG
GGAGATGTTTTGGAAGACGAAGAGAGATTCGATTTCTCTGGATTTTTCAAAAATGATTCTCCAATCGCAA
AAGCTATGGACGATGTTTCTAATTCTAGCGATTTGGTCCCCAATTTCATACTCGCTTCACTTTGATCTAC
ACTCAGGTCGCACAAAGTGTATCGCCGAAGAC
TCAAACCTCACTCACCATGAGACACCTTAGCTCACCTCCATGGCCTCTCCTCCTTCTCCTCCTCCTCTCT
TCTTTCACCTCCGGCGAATCCTCTCTGTCCGCAGAAAAAAACAAATTGCAA
CAGAGGGGTTCCACGCGATGACGACGTTTTCAACGAGCTTTCTTTTCCTTTTGTTGGTTTTCTGTTTGAT
CGATCCACTAGCTGCCGATGATCTCCAACATAAATCCGGTCGTGACGTCTGCTCCGGTGGG
CGGAAGGTCTTCGCAACTATCGAACGGACCTCTTATCAAACACCAAACCACACCAGAACAGAACTCAGCC
ATGGCTTCTTCTTCTCCTTCTCTTCTAATCCTAGCCGTTGCTTGTTTCGTCTCGCTAATCTCACCGGCGA
TTTCACAACAGGCTAGCAAATCACAGAACTTGAACTCCTCCGGTCCGTTC
TGGAGATTGGAGCGGAGATCTCTTGAATAACGGCGAAGCAACAACAAAAGGAGATTAAAAGAGGAGCTAC
GGGTAAGATGATATCCTTAAGAATGAAAGGGCTTGGTCATTGCCTAGTTTATGTCGTGGTCTTTAGTGTC
ATTGCGGCTATAGTGACAGCATACGACTCACCCTCTTCAACACCACAATACACTTCCCCTTATCCACCTA
AAAACTATTCTCCTTATCTCTCAGAATCACCCCTG
ATACAACAATGGCTTCGTCATCTACAAGTATCTCTCTCCTTCTCTTCGTCTCTTTCCTTCTTCTTCTCGT
TAACTCGCGTGCAGAGAATGCGTGG
GTATTCTTTGATGAATCGTGAAATGACGTCAAGCTTTCTTCTCCTGACGTTCGCCATATGTAAACTGATC
ATAGCCGTGGGTCTAAACGTGGGCCCCAGTGAGCTCCTCCGCATCGGAGCCATAGATGTCGACGGCCACT
TCACC
TGGAGGAGGAAGTACAATGAGAATATTAAGCTACGGAATCGTTATTCTCTCTTTACTCGTTTTCTCTTTC
ATTGAATTTAGCGTTCACGCTCGTCCCGTTGCTCTCGTCCTCTCAAATGACGATCTC
CTGGTTGATACTTGAACCTACCCTTTGGTCCCTTTACGGCAACATGGACTCCTCCAAACTCTCATCTCTC
TCTCTTTGCCTCTTCCTCATTTGCATTATCTATCTCCCCCAACATTCTCTCGCATGCGGCTCG
GAAATCTCCCAAGAACCCGAAAAAGCGCCATGTCGCTCACTATCCCGACGAATCTCGTTCTCAACCCGAG
ATCTAACAAATCTCTCACTCAATCCGTACCTAAATCCTCCGCAAGATTCGTCTGCTCCGATGACAAATCC
TCCTCCTCCGCACCTCAATCCATGAAAGCTTTCTCCGCCGCCGTCGCCCTCTCTTCCATCCTCCTCTCTG
CTCCTATGCCAGCTGTCGCTGATATCTCAGGTTTGACTCCTTGCAAGGACTCAAAACAGTTCGCT
TGATTCAAAAATAATTTGGTTAGAGAGTCTTAAACGAAACTAAGAGAGCACACAAGTTTCTCAACATGGC
CAGTCCTAATTGGCCATCTTTACTTATGGTGGTCTTAGCCTTGTATCCCATGGCTGCGTATACAAGTGCT
CAATACTCTCCAACACCAA
AGAGAGAAAAAGCAAAAGCAAAAATGGCTCGATCTTTCGCTATTGCTGTGATCTGTATCGTCCTCATCGC
CGGCGTTACTGGTCAAGCTCCGACTTCACCACCAACCGNTACACCAGCTCCACCAACTCCAACAGCTCCT
CCACCAGCAGCAACTCCTCCTCCTGTCTCAGCACCACCACCAGTCACAACATCTCCTCCTCCAGTCACCA
CTGCTCCTCCTCCAGCAAATCCACCACCACCAGTCTCTTCTCCTCCTCCTGCTTCTCCTCTG
GCAGCTTTTGCTTCTTCGATAGAAAATCTAATTATCATCAATCATGTCTAAGTTCACGGGATTCTCATCT
CTCGCTATCTCTTATTTTCTCTTGGTTTCAACGATTGTTGCAGCCACCGATGTTCACTACTGCGATAATA
ACGAAGAGTATGAAGTAAAAGTACAAGGAGTTGATATAACTCCTTATCCTATAGCTAGAGGCGAGCCAAC
TACTTTCAGAATTTCTGCTAACACAGACACTGAGATCTCGAGCGGCAAGTTGGTGATCGAAGTTTCCTAC
TTTGGATGGCATATTCATTCTGAGACACATGATCTTTGTGATGAGACAAGTTGTCCTGTGGCCATTGGAG
ATTTCTTGGTAGCGCACTTG
AAATTCTGTTTCAGTGTTCTTCAAATTCTCAATCTTTCTCTCAATTCATCTAAAGGGTTCCTCAAAGTTT
CAATCTTTCTCTCTGAATCTAAACCATGGCTCGTTGTAGCAACAATCTCGTAGGGATACTCAATTTCCTA
GTATCTCTTCTCTCGATCCCAATCTTAGCTGGTGGAATCTGGCTAAGC
CGACATCTTCTAAGAAAGAAACAAAGAAAGACTTCACATTTTACCATTATTTGCTCTGAGCTCAGTAGGA
GAGTTCAGAAACAATGGCAAAGATGCAATTATCAATCTTTATCGCTGTCGTTGCGCTTATCGTCTGCTCT
GCATCTGCTAAGACCGCAAGCCCTCCAGCTCCAGTGCTGCCACCGACACCAGCTCCAGCACCAGCCCCGG
AAAATGTGAATCTCACCGAGCTTTTAAGT
CTCGTTGAAGACCAACTTTCCCAAAATCATTTAGTAACATCAAAATTTACAAAAAACAAAAAAACATGCT
ATCTCTCAAACTCTTCCTCGTAACACTCTTCTTACCTCTTCAAACACTCTTCATTGCTTCTCAAACTCTT
CTTCCTTCTTCTTCAAACACTTCATCAACCATCTGCAAAACAACACCCGATCCAAAATTCTGCAAATCAG
TGTTCCCACAAACATCT
TTCTTCTCATTTTCCCTCTATATATTCATATACTCTTTCGTATAGTTGCACCATCCACTCTACTCAACAT
GGACTCCTCCAAACTCTCATCTCTCTCTCTTTGCCTCTTCCTCATTTGCATTATCTATCTCCCCCAACAT
TCTCTCGCATGCGGCTCTTGCAACCCACGGAAGGGCGGAAAGCACTCCCCTAAAGCCCCTAAGCTACCAG
TTCCTCCGGTGACCGTCCCTAAGCTACCAGTTCCTCCGGTGACCGTCCCTAAGCTACCAGTCCCTCCGGT
GACCGTCCCTAAGCTACCCGTTCCTCCTGTGACCATCCCTAAGCTACCCGTT
TTGTTAGAGAGGGCCATGTCTCCAAGAATTGTTAATGAAGCTCGTTCAGATCTCATTCTCTGTTTCTTCT
TCCTCTCTCTTCCTTCCTTCTCTTCCCTTCCATCCTTCCAAACCCTATTCCCCAATTCTCATTCCCTTCC
TTGTGCTTCTCCCGTCTCCTTCCAACCCGGCTCCGACTCCGAGTCACTGCTAGAATCCGAATTTGAATCT
CGATAATGCTTGTGCTTGTTAAAGTTCTGAGATTATCCAAGACCCCAGCATTTCGTGTACAAATTGCTTC
ACTAATTGGTTTGTTAATTCGGCATTCTACTTCAATCGAAGATGACTTGGCAAATTCTGGTATTTTAGAC
TCTCTT
CAATTTTTCCTAAAGAGTAAAGAAACTTCTCTCCTGTCTTTTCTCCTTCTCTATCTCTCTCCCTCAAAGC
TAATAAATACAACATTTGCATCTAACGTTTCTCTAGCACAAAAATATGCACTCGAGTTGTTTATTGTACC
TCACCGTCCTCGTCGTCTTCATTGTCTCTTTCGCCGGCGGCGAGAGATTCAAAGAAGCTCCAAAGTTCTT
CAACTCCCCGGAGTGTCTAACCATCGAGAACGATGAAGATTTCGCTTGTTCAGACAAAGCCATCCACGTG
GCAATGACCTTAGAC
ATTCAACAAAACATAGAAAAAAACAAAGCAAATTCTTTTTTTCTCCTTAGTTACTTCTTTTACAGATTAT
CTCAATCTTACAGAGCACCATGGATCGTTGTATCTATGGTTGCTCCGTCATTACTATCTTCTTCTCCTTC
TTCTTCCTCCTCAATGCATCCGCTTTAGAATCGGGTCACCACAACATAACTGGGTCGGGTCAAATAAACT
CAAACTCCGTCCTCGTAGCTCTCCTCGATT
CTCGTTGAAAAACAACAATGACGAAGCTCTTCTTCTTCTTCTTCTTCTCCTTCCTCTACACAATCACAAC
CCTAACATTTCCGCCATTAACAACCTCAGCAGCAACATCATGCCGAACATTATGCGGCAACATCCCAATA
AACTACCCGTTCGGCATCGACGGCGGTTGCGGATCTCCTCAATACAGAGGAATGTTCAATTGCTCCACCG
ATCTATATTTCACCACTCCTTCCGGCAGC
CAGATCTACCGGAAGATGAACGGAGAAGAGATGATAAAACTCTTCGAGACTGGAGCAGATGTTGTGGTAA
TTGGAAGTGGGATAGGAGGATTATGTTGTGGTGCTATGTTCTCTATGTTTGGATTCTTCGTTCAAGCCAT
CGTCACTGGTAAGGGACCGATAGAGAACCTTGCT
TAAGGCAATGCAAGCTTTGATCTTTCTTGGTTTCTTGGGCACTTCATGTCTCGCTCAAGCTCCTGCACCA
GCACCAACC
AAAACACAAATCTTGGTTCATTTTAAATCTCTCCAAGAAACAAAATGGCAGCTTCCATGAAATTTCTCTG
CATTCTTGGTCTGATCCTCCTCATCGGAACAGTCGTTGACGGTGCAGGGGAGTGTGGTAGATCTTCGCCA
GACAATGGGGCGATGAAGCTGGCTCAATGTGCTGGTGCAGCTCAGGACGCTAACTCCGCCGTGCCAGGAG
GTTGCTGTACTCAGATTAAGAGATTTTCTCAAAACCCTAAATGG
TAGAGATAGTTGATTAGGTAAGCTACAGTTATTTTTATACCAGATTCAGTCCCATACAAAGAGTATAGTA
GGTCACATTGGTGATTAGTCATAAGTAACAGAAAGAATTATTATATAATGACATCTTCGACATTCTCGTC
CATGATATTTCTCCTCGTCCTCCTGTTTTCCCTTCATATGGGTGAAGCTCTTGGTGCTCAAACTGAGATC
CGCAAAATCAAAGAGACAATTAGGATGAGGAGGAATTTGGAAGGCAATGACTACAGAAACTCTAAAATTT
GGACTGGACGGAGCTATTCA
CACCGTCGAAGCTTTCTCTTTCCGATCTTTCAATGGCGATTCTCAAATCTCACTTCTTCTTACTCTTCCC
TCTTCATCTTCTCCACTTTCACACTGTCTCCTTTGCTCAGACGCTTTTTGTGTTCGGAGATGGTCTTTAC
GACGCCGGCAACAAACAGTTTCTCTCTCAGAACCGAGTTGACGCAAGT
GAACAGAAAATGGAAATGATACTGATCTCGTCATCGACACTCAGGTTCCATCCATTGAGGACATCACAAA
GAATCGCCACCGGAACCAATAGAAGACGAACCACCACCGTGTGTGCAGACTACTACAGAGGAGGAAGAAC
GGTGGACGANAACATGGTGGTCCTTAGGAAACGAATCCATGAGATGAANATGGTTGAACGCAACTTTGAA
CCTCCTTCTCATTGGATGCAATGGGAGAAACGTTTCTACTGCAACTACGACGCTACTATATGTGATGCAC
TCACTCTTCTCCAAACTTTTCTCATGAACTCTCGTCCCA
GGAGTCGCCATTAACATATTTCATCAAGCTCAGTCCACTCTTCTCATGAAACTTCATCATCATCGACCTT
GACCCTGATAGGTTTCAGACGACACCCATTATTGTAAATCTGCTGCTGGAGTCTTTTTTGTCTGAATCTT
CTTCTTGTTGAGACACTGTTTCTTCTTGGTCTGTGATTTTTGTTTTGTTCTCATTAGGACGTTCTTTATT
CCGGTTCAGATTTACTGGATCGTCATTTTCTCTTTGAAATTGTATTTTTTTGTTCCTTTTCTGGTATGTT
GTGAAAGCTATGA
GGCCGGTAACAGCAACGGGAATTTTCATGGCGGCGAGGTCACCGGACGTTATATAATTTGTATCCCAAAT
CAAAATTCTGAGAAGGAAGAGAAAGCAATGGAGGACGAATTGGAAGGTCTACGAGCTCATTTTCCTGTTT
CGTTCGGTAAGACATCGAAGGTTTCGGCGTCAACTGAAGCCATTCACAGCGCAACTCGCCGCACCGATGT
AGCCAACGACGCCGGAGTTTCGTCGGATATCACCACGAAGAAACCTGATTCCGATAAATCTGGATTCCCG
TCTCTATCTTCCTCATCTCAAACCTGGCTCCGAAGTGTTCGCGGTCCGAATCGTAACCCTAACAGCTCCG
GTGATGTTACAATGGGTCCGCCACCGCCACCGTCATCTAAACGGACCC
AATATTTTCTTCCAGCTGTTTTGGGTGGTTTTTCTCTTTTTTATCTCTTTTCTTGAAAAAAAACTAGTAG
TCTTTTTTTTATTTCTTCTTGGGAGGATATTTTT
NACCCCCCCGAGGAACACGAGACCCAAGAAAAAGATTTCAAAATGCTCACGACACCTCCACGAACCTTTG
TCTCTGTCCCTTTCTTCTTCTTCTTCCTCCTCTTCCTTTCTCTACCTCTCTCATCTTTCTCTCAATCGAA
CTCTGTATACAACTCTTTCCTCAA
GAGCTCCAAAAAGTCGGTGGTGGTGGAAANATCCGGCGTCGTCGGATCCGAAAAAAAAAATGAAGGTTTC
AAGCGGTGTGGTCGCTTCTGTCATTGCCGTCTCCACCGCTGCTCTCTCTTCTTCCTCCATTCTTCCTCCA
GTCTCCCCAAAGGTTTGGGAATCGAGGAAAACGAATGGGTCGGACAATTTCGAGCCGAGGTTTGATGGGT
TAAGGTTCATAAA
GGCAGCCGAACCCTAGCTTTCATAAAATTTTCATTCATCATCGTTCTTGCTTCTTGCTAAAGGCCTTGCC
TTGTGCTTCCTCGTCCTATCTCTCTTACCTCCGTAATTTGTTCGTAAGAAAAGTATCGTGATGGGTACTG
AGAGAAAGAGGAAAATTAGTCTGTTCGATGTTATGGACGATCCGTCTGCTCCGGCGAAAAACGCCAAAAC
CAGTGGTCTTCCCGACGGCGGAATCAACAGTCTGATCAATAAATGGAACGGGAAGCCTTATTCACAGA
GACACCACCATTGAATTGAACTTCCCTCACACGCAAGTACCACACCTTCTCTCTCTCTCTCTCTATCATC
TCTTTTCTTTTTCTCTCATCGCCTTGAAGCTCTGAGAAGTAGAGAGAAGCTCCGATCTGATAGGAACTGT
GAGTTTCCTTGAGTCTCCGGAGAAAGAAGTCGCCGATTTGCTCCTGATAATCTTAGTCTCGAAATCAAAA
CGATGTTTTGCGATTGCTTCTACTGGAATAAAGGTTTCTCCGAGTTGGAATCGGAATCGTCCGAGTCAAA
GCCCTTCTCGCTTCCATCTCCTCTTCCTCAATGGCCACAAGGCAGAGGTTTTGCTACTGGAAGGATAAGT
CTTGGAGAAA
GAGCCTTAAAACCAGGCAGCCACTAAAAAAAGGAAAAATATTGAGGGAAAAAAATCACTTTGATAAATTC
GCCGCCAATCTAAACCCGTTAATTTTCTTATTCGGAAAAAAAAAATGATTGGAAGCAAAAGGAAGGCAAC
CCCGGCAATTAGGAC
GATCCTCAAGCGATAACACCACAAACAAAACAATAATCCAAAAAAAAAAAGAAAAAAGAAAAAAAGAGCA
AATCTCCATCATCATCATGGACTCGTCTCCAAACGACGGTGTACACCAACCGCTTCTCCATCCTCAACCA
TCTCCATCTCCGCCGGATTTAACCAACGGGGAACTAAAAACTGTCCTCTCCGAC
GGTCTCTCTGTCTCTTCAATTTCATTCGTTTTCTGAGATAAAAGTGAGAGAGAAATCTAAATTCGAGAGG
AGAAGTTTTAATTTTTCTGAGTTAGATTCAATGGAAGAGATCACGGAAGGAGTTAACAACATGAACTTGG
CTGTTGATACCCAGAAGAAGAATCGGATTCAAGTTTCCAACACTAAGAAACCATTGTTCTTCTACGTCAA
TCTCGCCAAGAGGTACATGCAGCAGTACACTGATGTCGAATTGTCTGCACTAGGAATGGCTATTGCCACT
GTTGTTACGGTCGCTGAGATATTGAAGAACAATGGCTTTGCTGTTGAAAAGAAGATCATGACATCGACTG
TGGATATCAAGGGATGATTCAAGGGGTCGTCCTGTGCAGAAAGCTAAGATTGAGATCACGCTTGCCAAGT
CTGA
GAAAGTAGACAATGAATGATTAGGGATAGCGAATGAAGAAGGTGGAAGATGATGTTAACTTCGGATTGGC
GCGAAATAAGATAAAAAAGCTTGTTCTTCAGAGAAGAAAGTGTTTATGATTGGACAAAGAAAGAAAGAAG
CAAAGCCTATCCACTTCTCATCTTCTCTATTACCAACAAACCTTCCCCTTCTCTGTCGGTTCCTCCTTTT
CTATTATTTTTAATTCCAGATAATAAAAAGAAAATCTTTTTTTGCTTAAAGAGCTCAAACCGAAACCCAT
TTCAAGATTTCATCCTCCGGAGTGTTTCAACGAAGCTTGGGTACATAAGTCTGATATGAGAGGTTTCGTC
ATAACTTGTCTTCTAAGGTAAGTTTCCTCACCTGTGGCGTAGATTGCATCATCAATCCATGGACGTTGAA
TGACTAAAATATTTATTTTTATTTTCCTTCAAAAAATCTCCATTCGGTATCAGCCATAGCCAAACCTCTC
TTCTCTCTTATTGTTGGGATCGACAAATTTTGCCTTGATTAGCTCGGAAACTTGTAAATCAGAGACCCTC
GTAGAAACTACCCAGAAACAGCATCTCCAAGGAACAAATTAATCATTATACTAATGCCTCTGATGCTCTT
CTTTTGATTTTGTGATCGACTTCTCTTTATTAAGTCTACACCTACCAGATGCAGATTATAGGTTCATTTT
TTTGTATTGAACTTTAAGCCGATATAGAGTTGTTGTCATAGATATATACAGCGAGTTATTGAAGCAATGG
ATGTTAATGAGGTTGAAGAAAATTTCTTTGCCCCTGGTGATGCCAAGCTACACGGAAAAATGTGCAATGC
CCTTTCAGTGATCTACTGCAAGATCATGTCTATTTTCCCGTCGCTTGAAGCTGCTA
GTCACTAACCTTCTTCCTTCACAGTGAATCAATGGCGTCTTCTTCTCTATCAACTCTTTGCAGCTCAACT
TCTTCTTCTCTACATCCCAACTCCAAACTCTCACATTCTCTTTCAGCTAAATTATCCTCCAAAGCAAATG
TTTCCGTCCAATTTCTGGGAAAGAAACAGTCTCCGCTTCTCTCCTCAACTCCGAGATTTCTCACTGTTAT
CGCCATGGCTCCACCTAAACCCGGAGGCAAAGCTAAAAAAGTTGTGGGAGTTATCAAACTTGCTTTAGA
GGGTAAAACTGTAAAGACAGAGAGAAGAGCACTCCCCAGTCTCAGTGGTGCGGTGAGGAGAGCTTCGTTG
TCTTCCCCATTGCAATTAGGGTTTTCAAAACGGGTAATCGAATTCGGTGGTGCTCGGCTTTGAAATTGAG
GATGAGATCCTTTCCACTTCCTTCTACCTGCTGACAATGGGCAACTGCGGTACTAGAGACGAGGCTGCCG
TCTTCACTCCTCAAGCTCAAGCCCAACAGCTCCAGAAGAAGCACTCCCGATCCGTCTCAGATCTGAGCGA
TCCATCCACTCCTCGCTTCCGAGACGACTCTCGCACTCCTATTTCGTATGCCCAAGTCATCCCCTTTACT
TTGTTTGAGCTTGAGACCATCACCAAGAGCTTCCGCCCAGATTATATACTCCGGAAAAAGTGGTTTCGGT
ACCGTCTACAAAGGGTTACATTGATGACAATCTCCGCGTTCGGCTCAAGTCTCTCCCTGTTGCCGTC
GATGTCTTTCACTCTCTCTCTCTCTCTATATCCAAAGAATTAAAAACCATAATAAAAAAAGAAGATAAAA
AGACGAATTCCAGAAAAAAAAGACGCAAAATCGTCGTCGTCGTCTTCGTCTTTGCATTTCGTCGGAATCT
TTTGATTCTTGAATCGGAATATCTCTGTTTTTGTTTTATCCGGACTCAAGATCAATTCGGATTCTTGGAA
TTTATTTGATTTTTTGTTGTTGTTGTTGAAAAAGTGGATTCTTTGGTTTCGATTTGTAATAATCTTCGTA
GAAAAAATGGATTCTGATTCTTGGAGTGATCGTCTCGCATCGGCTTCAAGAAGATATCAGCTCGATTTCT
TGTCTCGATCTGACAATTTCTTGGGGTTTGAGGAGATAGAA
GAAAAACAGAACACAAACAAAAACACATTGTAACATTAGTTTAAGCATTAAGCTTCTTTATGTCGAATAA
TAATAATTCTCCGACCACCGTGAATCAAGAAACGACGACGTCTCGTGAAGTCTCAATCACATTGCCTACT
GATCAATCTCCTCAAACCTCACCAGGATCATCTTCTTCTCCTTCACCGAGACCTTCCGGTGGATCACCGG
CGAGAAGAACGGCGACTGGATTATCCGGCAAGCACTCTATTTTCAGGGGGATTCGACTACGTAACGGAAA
ATGGGTATCGGAGATTAGAGAGCCACGTAAAACGACAAGAATTTGGCTCGGGACTTATCCGGTACCGGAG
ATGGCTGCCGCCGCTTACGACGTGGCTGCGTTAGCTTTAAAAGGACCGACGCCGTTTTGAATTTTCCTGG
TTTAGCTTTGACTTACGTGGCTCCGGTTTCAAACTCTGCTGCGGATATAAAAACGCTGCTATTA
GATCCATTGCTTAGGGAGAGAAGAGATAATGCTGAGAGCTTCGCTGCTCTGTTCTTCGACCTCAATCACT
TTCACACCAATTCAACTATTCAATCCCAATAGTTCCCATCGTTTCCCAAGATTCGAACTATCTCGTCCTG
TCTCGGCTTTGTCTCGTACCAAATGTCACTTGAGTCTCCTGAGAGCTCGTGGGAAATCCAGCTTCCTCAC
TCGCAGCACCGCTACTGATGAAGCTGTTGAAACTAGTAGTAACAGTGGATTGGATTTGGTTGAGGTTGGA
TTCTTGTCTGGTGTTCATGGCCTTCAAGGCGAGATTTGCATAAAACCAAACACTGATTTTCCTGATTTAC
GTTTCTCTAAGCCTGGTAGAAGATGGTTAAAACAACAATTGTTGGGACAAGATAAGATTGATGAGGTTGA
ATTAGTC
TGGAGCAAGAACAATAAGAAGAAGAGAAGATGGGATTTGAAGAACGGAGGGATTCTATTAAAGGAGCTAA
TCGCTTCCTTCGACGGCAAAACCAATCCGATTCGTTGCTTCTCCTCCGATCAGATCCTTAAAGCTACCGA
CAATTTCTCCGAAAGCCGAATTATCTCCAGCTGGGGATACTTCATATGGTACAAAGGCGTAATCGAA
GCTCTCTCCTCTCTCGCTCGCTGGCTTCGAGGAGAAAAAAGAAAAATTGGAGAAATAATTTAACTGGTTC
TCGGAAAATCTAGGGTTCTTTTTAGCCACGCCTTGCTGATCTCCTTCGTGAATTCGATTCCGATTCTCAC
CTGAAAAAAACTTCTTTAAATTGGGTTAAAGCTGCTGCTA
AGTGTCAAATTCTGAGATCTGTAAAAGATGAGCGACGGAAACGACGCTGCTAAACGCCGTACCGCGGCGG
TGACTGATTACCGGAAGAAGCTCCTTCATCACAAGGAGCTCGAATCCCGTGTCCGAACAGCTAGGGAGAA
TTTAAGAGCAGCTAA
GATCATCTGGTATCCACTATCCACAACTGGGGTCAGCTTCTGGTTCTCTCTCTCGGTAACTTTCTGAGCT
GAAGAACCCTAATTCTTATCTTCACCGGATTCCGGGTATAGGGCTTTGTAAAGTTGTTGAATTTACAAAG
AAAGATATGCTGGTTTGTCTGGGTTTTGTAGAA
TGAATCGTCGTTATCAAGGTGATTTCTTTCTCTGCCTCAAACATCGCTTACCCTCTTGATTGATTCCTCC
AATCTTCTTCGTGTGGTTTCACAGGTTTTACTTATGGTTAATGCAATCAAAGGAGTGTTCGTCTCTTGCG
ATATTCCGATGACACAATTCATAGTGAACATGAACAATTCGATGCCTCCGTCTCAGAAATTCATAATTCA
TGTACTTGATAGTACTCACTTGTTCGTGCAACCACATGTAGAGCAAATGATCCGCAGCGCCATTTCTGAT
TTTAGAGATCAAAACTCTTACGAGAAAGCCCACTTCTTAGATCACATCACATTCACACTTGCTTCTTTGT
TTTTCTTTCATTT
GATCTCCANAATCAAAGATAAACGGAGGAGAAGAGAGCTTCGTCGTCTTCTTCTTCTTCGCCTCCATGAA
TCTCCTCAAGACGATTCATTACCAGTCTACCATTACTCGATTTTACCGTTTTGCCCCTACACGCTCCTTT
GCTTCTTCTGTGTCACTCTCTCCACAGAGACACATAATCTCTCTCGTTTCTATCTCTAATCGTGGAAGGT
GCTTCGCATTCTCGAGCGTCTCTTGGTGCTTCGCTTTATAATAATCAT
GGTGTATATAATTGTTCATTTCCTTGAAAACGGTTACAGAATTAGGGTTTTGTTTCTTCTCTCTCGCCGA
TTGATCTTGAAATGTCTTCCCCAATTATAATTAGGGCACCGAAGAAGCAACCGCCGGAGCCGCCATGTCT
GATTTCGTTACTCCCCGAAGAAATCGTCGTCGATATCGTAGCCCGTGTCCCTAGATGCTATTACCCTACT
CTCTCCCAAGTTTCAAGGCGTTTCCGATCACTCGTCGCTTCTCCGGAGATTTACAAGAGACGATCCTTCT
TCGGGATGCACAGAAACAATGTCTCTACATCGCAATCTCCAAAGATCAAACCTCT
GANTCACTTAACCAAACATGTCTGAAAAGGGGTTGATAAAAAAAGAAGACCACATGTTTCAAGAGGAGAA
GAGAAAGACAAACTATGGAGCAATTGGCTTGGCTTGCTTCATTTCTTGTTTCTTTGCATTCCAATTCATG
AAAATCGTAACAACACAACCTTCNACAACAACAACATCATCCATTGCCGTTATCGATAGCCCAATGTCCT
CCCATAAGCTATCTGATAGGAGAGAAATATGGAGAGTTATCCCACCATCTACCTATTGTCTCAAAATCGA
ATCTTTCATAAAATTCGCCACTTCTCCAAACGCC
AACCATATAAAGCTTGTTCTTCTCCTTCCTTCTCCAATTTCGTAAGCTCAAAAATTTCGATTTCGATTTT
GATTATTGCCAAAGGTTTAAAGATGGATATTTTCGACAACTCTGATCTTGAATACCTTGTTGATGAATTT
CACGCT
GAACAGAAAATGGAAATGATACTGATCTCGTCATCGACACTCAGGTTCCATCCATTGAGGACATCACAAA
GAATCGCCACCGGAACCAATAGAAGACGAACCACCACCGTGTGTGCAGACTACTACAGAGGAGGAAGAAC
GGTGGACGANAACATGGTGGTCCTTAGGAAACGAATCCATGAGATGAAGATGGTTGAACGCAACTTTGAA
CCTCCTTCTCATTGGATGCAATGGGAGAAACGTTTCTACTGCAACTACGACGCTACTATATGTGATGCAC
TCACTCTTCTCCAAACTTTTCTCATGAACTCTCGTCCCAGCGTCGCGTTTGGAACGTGTCTTCTTCTCCT
CGTCAGCGTTCCCGTCTCCTCCGCCCGTTTTTGCTTTTCGCATCCTTGATCTACTCTTTGGCTTTTGGAC
GCCCGTTC
GACCTCCACTTTCCCTTTTGCCCCTCTTTTTTACAGATTTCACTCTCTGCTCTACTACTCTCTCCTCCTC
CTCCTCCTAAAGAAAGTTCTTAACTCTCCTGGGTTCTTCAGGTTTTTCCTTTTCTGGAATAAAAAGAAGA
AGAAATGGGTGTTCTTGATCATGTCTCTGAAATGTTTGACTGCTCTCATGGTCACAAGATTAAAAAGCGC
AAACAGTTGCAGGTACTTTCCCTCTTCCTTTTCTTATCTTAGCAGATTCAGCTGATAACTTAGATCTTGG
TTTGCAAAAAAACAAACATAATAATTCGTTGAAAAGTTATGATGAATGAGTCTAGTTAGAAACTAGCTTC
GATGGTTACTA
TGATCACATCCTCACACACAAAAATAAATCATCACAAGACCAGAGTTAAAAGAGAGACATGTCGACTTCA
TTCACAATGATCGGCGGTGAAGGTCCCAACAGTTACCGGGAACATTCGAAATACCAGGGAGCACTGGTTA
TAGCTGCAAAGGAAAAGATGAATGAAGCCATCTCCACGAAACTCGATATCGACTTTACTTCAAATCTTGT
TAACATAGCTGATTTTGGTTGTTCCTCTGGACCGAACACTTTCACCGCGGTACAAACCTTAATTGATGCT
GTGGAAAACAAGTATAAGAAAGAAACAGGGAGCACTGGTTATAGCTGCAAAGGAAAAGATGAATGAAGCC
ATCTCCACGAAACTCGATATCGACTTTACTTCAAATCTTGTTAACATAGCTGATTTTGGTTGTTCCTCTG
GACCGAACACTTTCACCGCGGTACAAACCTTAATTGATGCTGTGGAAAACAAGTATAAGAAAGAAA
TTTTTTGATGATGACAAGGTCTTAGCTTTGGTGGACATAACTCCCCAGGGTCCTGTTCACATCCTCCTTA
TTCAAAAAGTGAGGGATGGCCTAACTGGCCTCTCTAAGGCTGAGGAAAGGCACATCGACATCTTGGGCCA
CCTACTCTACACTGCCTAACTTTTCTCAAAACAAAAAGGCCTAGCA
GACCTCATCATTCTTCCTTCTGGTTAACTGAAAATGGAGTGTAGTTCAGTGAGTGTACTAGGAATATTAC
TGGTATTTCCTCTCCTTCATAACCTTGTCACCATCTCCGGGCAGAATCTTCCGGCGGTGGGTTTGTTCAC
TTTCGGAGATTCCAACTTCGACGCTGGAAATAAAAAGTTCCTCACAAGTGCTCCACTTCCTCAAAACTTT
TGGCCTTACGGTAAATCTCGAGATGACCCTAAGGGCAAGTTTTCTGATGGCAAAATTGTCCCGGACTTTA
TTGCTACTCGTTTTTATAGGTACTCTATACTAAATGGAAATTTTGATTGGTAATTAAAGATATATGAAAT
TGATGAGGGGTGAATAAATCACAGCAAAATTCATGGGGATACCACACGATTTACCGCCGGCGCTAAAACC
C
GGTCTTCTTCTTCTACATAAAATTGATTCGCCTCGAAATTTACACAGACTTGTCGCTCTCTCTTTCTCTC
TTATTTCACAGAGCCCCTAAACATTTCCAAAAATCTTGCAAAGGAAGAAAAACAATGGACAAATTTTGGA
CTTTCCTCACTGCTCTTCATTCAGGCGCTGGGCCTATCGTGATGTTACTTTATCCATTGTACGCATCGGT
GATAGCAATGGAGAGCACAACAAAAGTGGACGATGAACAGTGGCTTGCGTATTGGATAATATATTCCGTT
CCTCTCACTCACGGAACTGATTCTGCAATCCGCTTATTGAGTGGATTCCGATTTTGGTATACGGTGAAAC
TTGTTGTTCGTGGCTTGGCTAGTTCTTCCTCCAGTTTCAAGGGCGCAGCTTTTATCTACAACCGTGTTGT
TTAGAGAACAAGTTCAAGAAAACACGGGGGTCCTCCGGCTCCACCCACTCCAAAGCCCACCAAGCCCCAA
CATCCTCCACTCCATTTTT
GGCTACCAAACTTCGCTAAACTTTAGTGCTTTACTCCAAAACCCAGAGTCCATCACACAAGTCCAAGCCC
GAAAACAAGGGTTCTTGCTCCGACACGACAACAAATCCAGATTTTGAGCTTAGGGAAACTTGAGAAGGAG
AAAAAAATGTCGAACATAGACATAGAAGGGATCTTGAAGGAGCTACCTAATGATGGGAGGATCCCAAAGA
CGAAGATAGTTTGCACATTAGGACCAGCTTCTCGCACTGTTTCCATGATCGAAAAGCTTTTGAAAGCCGG
TATGAATGTGGCTCGCTTCAACTTCTCACATGGAAGCCATGAATACCATCAAGAGACACTCGACAACCTC
CGCTCTGCTATGCAA
GGTTTTTTCGTTTTTGTTAACTTCGCCGTGTAGTTGTGGTGGTGAGATTGTGAGAGATATGGAGGCGGAG
AAAATGGAATTGAAGCTCTACAACACGATGACGCAACAGAAAGAAGTTTTGATTCCAATCACTCCTGGCA
AAATCGGATTATACGTCTGTGGTATCACCGCTTACGATTTCAGCCATATCGGCCATGCTCGCGCCGCCGT
TTCCTTCGATGTTCTTTACAGATACTTGAAGCATTTGGATTATGATGTTACTTTTGTCCGCAATTTCACT
GATGTTGATGACAAGATTATTGATCGTGCTAATAAGAATGGAGAAGACCCGTTAGATTTGAGTAATCGGT
TTTGCGATGAATATTTGGTAGATATGGGTGCTCTGCAGTGCCTCCCTCCCACCCAACAGCCTCGTGTC
CTTCCATTACTTTCTTTGCTTAAAGTTAATAACATTGGTATTTTGTTTAATCTCATCAGCAAGACTTTTT
AGATCTTAGGACAGCAAAAGAATTTAACTTATTGTTATGCACTGGAAACGAAAGTTGAAAAAAAAAAATC
TTATTTCCAAATGAGATCACCCATGAACTTAAGTGCGGGAACCCCTCTTATCTCTGCGTCTAGCAATGGC
GATTGGATCAATTTTAACCCCGAAAGTTCTGTATCATTCTGAATAAGTCCAAGCACACGCGTTTGTTCCT
TTCGTCTTATTGAGCAAAATTTGCAATCGGATTCAGATTGAGGTAGAAGCTGATTAACAATAAGCCGGTG
GACTGGCACA
TCGAAAATGGCGCAGCGATCTAGGGTTATCACCATGTCTCCTCTCATTCTCGATCAAGAAGTTGATCTCG
ATCTCTGGGAAGTTGTTAATCCTTCTGATGGAGAGTTCTCCGACGATTCTTTCTCCGTCGATAGTCTTTC
CGACGATGACGTCATATCTCTTGACGACGCTTCCTTTGTCGCACCCTCTGTCATTTCTCCGCCGCATGAG
ATAATTCCTATTGCTGACGGTGGTGATCTCGCCGNGGATCTGGATGGTGATGATGATGTTGGNGATGATG
TCGNTCGCGATGAAGTTGATGAGAATGA
ATTTCTGATCATTTACACCCCTAAAAAGAGTAGAGCTTTCGTGAAGCCACCATGTGTGGAGGAGCTATAA
TCTCCGATTTCATACCTCCGGCGAGGTCCCTCCGCGTCACTAACGAGTTTATCTGGCCGGATCTGAAAAA
CAAAGTGAAAGCTTCAAAGAAGAGATCGAATAAGCGATCCGATTTCTTCGATCTTGACGATGATTTCGAA
GCTGATTTCCAAGGGTTTAAGGATGACTCGGCTTTTGACTGCGAAGACGATGATGATGTCTTCGTCAATG
TTAAGCCCTTTTCGGTCTTCACCGCAAACTACTAAGCCCGTAGGCTTCCCGCTTTCGTCTTCCACTGGTT
CAGCATATGCCAAGAAAACTGGTAGAGTCCGCTGAGCAAGCTGAGAAATCTTCTTAAGAGGGAGGAGGGA
GGAATCAATTCCGCGGGATTTAGGCAGCGTCCCTTGGGGGAAAATT
GGTGGTTGTGTGGTGGTAGTAACACTAAAGATAGAGCAGAAGAAAGAGTCAATTCCTAAAGGATCTTCTT
CACTTAGTCCTTCACTGAAGAAGACTACTACTAGTAAGACTGGTTCTTCCTCTTCATCAGTGAAGAAGAC
CACGAGAGGATGGATTGGTAGAGGAGGATCAGGATCAGGAGGGGAAGAGGATAAGATTGGGAATGTGGCG
TTTCCTGAACCTGATGATCCAGAGTGGT
AGATAAATAATCTTCACCTCTACCATCGAAGACAAGTGGGATAAAACTCTCGCCTAAAAACAAGCAATGC
CATAAGGCCCATAACCCTTATTTGGATTAATCTGTGAGGTGAAACAATAGCAGCAACTACATATGTATCA
TTTAGCTCTGTGAGAGCTCGCGGCTTCGTTTAGCTGCAGCAACAACTGCATTCATAAGTGTTGCCCGGAA
AGAGCCTTTCTCTAGTTCATGAACTCCGGCTATTGTAGTGCCGCCAGGTGAGGTAACATCATCTTTCAAC
ACACCTGGGATGCTTCCCAGTTTGGCTAACCATCGTTGCAGCTCCAAGGAACGGTCTGTGAAGCTAAACT
CAATGCAAGCTCTCGGGGGTAAACCAGCAGGTACTCCTCCATCGGCTTAAAGCTTCCAATTGGCTAAAAA
TTTGT
CGGACGAGGAGCATACTTTCCTTCTTATTTAGGTATGATGCTTGTTATAACGTGGGCGATCTGCACCTTC
ATCGAGCTTCTGTCAATGTGGAATTTGACGAGACGAGAAGTTCAGCTATGCAATATGTTATCCCCTGAGG
CTCCCCGTCTCTCTCTTGCAACTTACAACTGGGGACTTGTTTTTGTAGCAATGCTTGTAGACAACTTCCT
ATATCCGATATCAGCTTTCCGGTCTCATTTTTCTCAATCCATAAACTGGTCTGGAATCAGATACCACTTG
AAAGATGGAAAGATATTCACGATGGAGAGACGAAAGGATATGGGACCAACAAAGACTGATTTAGGAGGCA
AACATTTGTTTGGTAAGAAAGGAGCTCCCTCAGAAAGCTTCATTCCT
TCAACCGTCTTGTCAGGCTTCACAACAGCTGGGCTTATCCTACTCGCTAAGCAGCTTTCATCAGAAAAAG
AGTGAATTCATAATCCTTCAGGGGTGGTCTCTATTACTCTCATGTACAGTGCCAAATATTCAAATTTACA
ATAGCAAATTTTTCTACTTCCTCTGTCTATGCGTTAAACTATGGAATGTGTTGAGTGTATATTCTTATAG
AGAAAACGAAATATCTTTGTTATGAATAATTGAAGTTTGCCA
CCGGTCCTCAATATAAGAAAACTTGACAAAGAAGAAACACAATGTCTATTGCTCATAAAATTTGGAGAGA
CTCGAATACAAAGACGGGTAAAAAGTCTGGGAAAAATAAAATCTGAAAATTGTWTCACTGGTCACCAGGA
ATTGACTTGATAATGTCAGAATCACCAGGATCAACAATGCTCAGACAAGAAACACGGAAGTACTTTCCGC
AAGCTGTTCCCAAATCAACGTTATTTCCATTGTAATGGTGGACACCAACTTTAGCGAGCATTGCGTAGTA
CTCAATCTCTGATCTTCTCAACGGTGGGCAATTGGTGGAGATTAGAATCAGTTTCCCTTTGGAGCCACGG
AGGGATTTGAGAACAGACTTGTAACCAAGAGTGT
CGCTTAGCTACTGGCTTCACTTATCTCGGCCCCAAATTTATGAAAGAAAATGGCATAAAGCATGTGGTGT
TTTCAACTGCAGACGGAGCACTGGAGGNAGCTCCAGCGATGGGGATAGCTGANGCCATCTTGGATCTCGT
GAGTAGTGGTATAACACTCAAAGAGAACAACTCGAAAGAAATTGAAGGAGGTGTTGNGCTGGCAAAGCCA
GGCGGCA
GTAGTTTTGTTCACTTTCGGAGACTCTTACTACGACGCCGGAAACAAAGTGTCTCTCAGCCAAAGGAAAG
ATCTCCTACAAACCTATTGGCCCTACGGAAAATCCCGCGACTACCCCAACGGTAAGTTTTCCGAGGGACA
CATCGTCCCCGACTTCATCGTTGATTTCATCTCTATCCCGAATGGAGTACTCCCACCGGTGTTTATACCG
GGTGTTGATATTTCACGTGGAGTCAGCTCTGACGCCGTCGATGCTTCT
TGTTCGCGAACTCGTCAAATTACTTGGTTGAATCTGAAGGTGGTGGGGTACCTCTCCCATCAGGAGGCAT
TCTTACTCCTAAGGGTCTTCAAACTCTTGGTCTTTCTGGTTTAGGATCAAGTACTGGTTTTGAGCGYCTG
CATTATATGTTGGAGAGAGTATGGGATCCTATTTTAGTTACTGGMGCTCCAAAGTGTATTAGYCAGTCCT
TCTTAAACGCTTTTGAGAGTTGGCATTCTTTTGATACAAMTCCACTATATGCTCTTCTCCACGAGGCCAT
ATACTGTGGAGGGTGCTTCATCAGGATGGTCTGCTCATMGATTACGGGATAAATATGAGTACAAATTCGA
CGCAA
CAATCTTCAAAATCTCTTCCTTCCATGATTCCGTTATCGTAAAGATTTGTCCTTTATCCAAATTTTAGGA
TTTTGAATTCTTCTTCTTTCCGATTACCGGATTCCAATGGCGCCTTTTGTTGAAGTCTGTAGGTATAAGC
CATTACCGCTTTCATTGAGCTCTCTCTGTACATGCCCTTGCCGTTCCTCTCCAAGGAAATATCTAATNCT
TCCTCAATTCTCTGAAAAGTACCCGAAACCATTGTTGTCTCATTCTCGCTTTACTCCGATTTCTGTTAAC
CGGAGAGTTATCACGGCCGTT
AAAAAAATGGGATCTTCACCACCGAAGAAGACGACTCTGCAACGGTACTTGTCACAGCTTCAACAACATC
CTTTAAGAACAAAGGCAATAACTGCTGGAGTTTTGTCTGGTGTTAGCGATGTTGTATCACAGAAGCTCTC
TGGCATACAGAAGATTCANCTGAGAAGGGTTCTNCTCAAAGTGATATTGCTGGTGGGTTTCTTGGACCAG
CAGGGCATTTCTT
TAATCACGAAAGAGGGGCTCGTCCAAATCCTGTGAAGGAAAAAGAAAGAGCTTCAGAAAGGGAATGGTCT
GGTTCATCTGATAGAAGGAATCGTGAGGATAAAGATGCTGGTTATGAAAGGGACATACCGAGGGAGAAAG
ATGTTGGTCACGGTTATGATATGCCAGAGAGAAGGCATCGTGATGATAGAGACACCGGTCGTGAGCGTGA
GAGGGAACATCATCATAAGGATCGTGAACGTTCAGAGAACATGTTCGTGA
AAACTTACACTTCATTCAGTTGCAGCCAAGATTCATTACCTGAATTTGCTAATAATCCTATCACTCCATG
CGACCTCGATATCTTGATAGCAAAACTCGCCCCTGGTCAGGAAATCGAGCTCGAAGCTCATGCGGTTAAG
GGCATTGGTAAAACACATGCAAAGTGGTCTCCAGTAGGGACTGCTTGGTATAGAATGCATCCTGAGGTGG
TTCTACGTGGGGAAGTTGAGGATGAACTTGCTGAACGACTTGTAACGATGCCCACAGAATGTTT
CTCTGAGCCACAAGAAGTGTTTTTNGTNGAAGGATCTACTGAACTGGTTTGTAATATGGGGGAAGATACA
AAGGCAACCATTGAGCCAACCGCAAACAAGACTACTTCTCTTGAAAAGCCATCAGAGGCTATGGCTGGAA
AGGAGAATGCTGGGGGTAAGGAAACACAAGANCTGGCGAAAGATGAGGATATGGCTGAGCCAGACAATAT
GGAGATAGATGCTCAGATTAAGAAAGATGATGAAAAAGCTGAGACGAAGATAAGAGTCA
AAATAATTGAGTTTTTTTTTTAATTAGAACAATGGGGTTGAGTGGTGTTCTTCATGTGGAGGTTGAGGTT
AAGTCTCCGGCTGAAAAGTTCTGGGTAGCCTCGCGACGGCATCAATCTCTTCCCCAAAGCTTTCCCTAAC
GACATCAAAACCATCCAAGTTCTAGCCGGCGACGAACGCTCCTGGCTCCATTCGCCTCATTACTTAGGAG
AAGGTCTCCAC
GAGAATGCTTGCCTAGAAAGCTATCAAGCGCAACGAGCCTTGGAAGCATGGAGGAGAGCTATTTTCTGCA
AGCTTCTCTTGATTCTTCAGATAAATTTTCTGAGAGCACGTGCCTGAGGCAACTATGAGTCCGTACTACA
TGAAGAGCATCACACCGAGTGCTTATGAAGCCACACTTCGACAGAAAGAGGGTGAACTTGCGGCATACAT
GACCCGCTTGGCATCAATGGAGTCTATCCGAGATTCCCTGGCTGAAGAACTAGTCAAATGACAGCAGAGT
GTGAGAGCTACGGGGAGGCAGATAGGTCCGGCATAAGCAGAGCTGGAA
GAAAGCTGTTCGATCAACAATACTAGAAAACCTCCCAAATACTGCAAGGAAAGCTAACAACACAGGAAGC
TTCTCTTTTGCACCTATCGTACACAACAACATCAACAACAGAACACCAATAGAGATCAACTCTCCTATGA
GATTCCCTCTCTT
GCGGTGATAGCAGAAGTGGATCGTGTTTTGAGACCGGAAGGGAAACTGATAGTTCGAGACGATGCGGAAA
CAATACAGCAAGTGGAAGGCATGGTGAAAGCAATGAAATGGGAAGGTTCGAATGCTTATTCTAAGGAAAA
AGAA
AAGAGAATAAACAATGGTGGGTTCTCACAAAGCAAGCGGAGTGCTTCTTGTGCTACTAGTGGTTATGGCC
ACCACAATAGCAAACGGGACACCGGTTGTCGATAAAGCAAAAAATGCAGCTACAGCAGTTGAAGATACAG
CAAAAATGCAGCTACAGCAGTTGGCGGTGCAGCTGCATCAGTTGGTGCTAAAGTATCAGGTGCCAAACCA
GGCGCGCATCGATGTTAAGCATCAGGAGCCAAAGGAGACGGCAAACTGATGAATG
CTAGCCTCTCTATCTTTATCTCTCACAACAAAATCTTTGAAATGGCGATCTCTAAGGCTTCCATTGTTGT
TCTCATGATGGTGATTATCTCCGTCGTTGCATCGGCACAATCTGAGGCACCAGCACCAAGTCCTACTTCT
GGATCTAGTGCGATCTCAGCGTCTTTCGTGTCAGTGGAGTTGCAGCAGTCG
CCTATGACGGTACCGCCGCCAAGTATGGAACCGTTGATAGCGCCTCTCTCATTATCTTATCCGACTATTT
CATGGCCGTTAACATCGTCGTTAACAACACTGCGCCACGACCAGATGGTAAAACTAAGGGAGCACAAGCT
TTATCCATGAGAATCTCCGGAAATTTGCTGCTTTCATCAAACTGCAAATTCTACGGTTTCAAGACACAAT
CTGTGACGATACAGGAAACATTCTCAAGGATGTACGTCGAG
GCACGAGGACCCTTCTCTTCAATTCCCTCTAAAACCCTAACCCCACACCAAAAGTCTTCCTTTGAATCAA
CTCTCCACCATTCCCTAATCACCCACGACACTGATGAAGCATGGAAGGTCTTCCGATCCTTCGCTGAAGA
TTCTTCTCTCCCGGACAAGCGTCTCCTCAATTCTCTCATCACCCACTTGTGCCTCCTTCCACAACACAGA
TCAAAACACCTCCCTCAGGCACAGACTCAAGCGTGCTTTGTTCACGACGG
CTGTCTTGAGCTTAANATCTACGGTCAGTGGATGTCCGGTGGTCAACGACGGCTCTCCCGGGTCGCCAAC
CCGACCAACCATCTCTCGGTCGTTGGGAACTTTGTTGGGGCCTTGCTTGGTGCGTCCATGGGGCTTAGAG
AAGGCCCTATATTCTTCTATGCTGTTGGGATGGCTCATTACTTGGTTCTNTTCGTGACTCTCTACCAAAG
GCTACCGACCAACNANACTTTGCCTAAAGATCTTCATCCTGTCTTCTTCCTCTTCGTTGCGGCTCCAAGT
GTTGCTTCCATGGCTTGGGCTAAGGTCACTGGCTCCTTCCATTATGGCTCCAAAGTTTGTTACTTTATCG
CCATTTTCCTCTATTTCTCATTGGCTGTTCGGATCAATTTC
GGAACAGGAAACATAGGGAAGAGTGATGCCAATCTAATCGTGGCACTGATCTACATCTATGTAGCGGGTT
TCGCGTGGTCATGGGGACCGTTGGGATGGTTGGTTCCTANTGAGATATCTCCACTAGAGATCCGATCAGC
AGCTCAAGCCATAAACGTTTCGGTCAACATGTTCTTCACATTCCTTGTGGCTCAGCTCTTCCTCACTATG
CTTTGTCACATGAAATTCGGACTATTCTTCTTCTTCGCCTTCTTTGTTGTCATAATGACAATATTCATCT
ACTTGATGTTGCCTGAGACAAAGAATGTGCCAATCGAAGAGATGAACAGAGTGTGGAAGGCACATTGGTT
CTGGGGAAAGTTTATTCCTGATGAAAGCTGTCAATATGGGTGCTGCTGAAATGCAACAGAAGTCCGTATG
ATGATGATCAAG
ATTTCTGTCTCTGTGGAGACAGCTGAAGAAGCAGCAGCACTATCAATGGCGTCTCTGAGATTGTTCTCAA
CGAATCATCAATCTCTTCTCCTTCCATCATCTCTCTCACAAAAGCCTCTAATATCTTCACCAAGATTCGT
CAATAACCCTAGCAGACGGAGTCCAATACGATCCGTTCTTCAATTTAATCNCNAACCGGAACTCGCCGGA
GAAACGCCGCGTATCGTCGTTATCACCTCCGGAAAAGGCGGTGTTGGAAAGACGACAACCACCGCAAATG
TCGGTCTCTCTCTCGCTCGTTACGGTTTCTCAGTTGTCGCCATTGACGCCGACCTTGGTCTCCGTAACCT
CGATCTCCTCCTAGGGTTAGAGAATCGAGTCAATTACACTTGCGTCGAGGTTATAAACGGAGATTGTCGT
CTCGATCAAGCTCTGGTACGTGATAAGCGTTGGTCGA
GGAAAATAGGGAAAGCCATGCGCATAGAGGTTGATCGAAGTGGAATGATTCCAAGGTTGAGGTTCCATGA
TCGTGAATCGTATGCAAGCAATAAAACCAAGGAGTATGATGACATTGCCATCAAATTCTTATCCTATGTG
CTCCTCCTCCTTGTCATTGGCTTGTCCATATATTCTCTCGCTTATGAACGCCACAAGAGCTGGTATTCTT
GGATACTATCTTCACTAACAAGCTGTGTCTACATGTTCGGTTTCATCATGATGTGTCCTCAGCTATTCGT
CAACTACAAGCTAAAATCAGTGGCACATTTACCATGGAGACAGATGACTTACAAGTTCCTCAACACCATT
ATCGACGATCTCTTTGCCTTTGTCATCAAAATGCCGATTTTACATCGACTTTCTGTATTCAGAGATGATG
TGATATTCTTGATATACTTATAC
TGATTTCTCTACCACTCACTACACCGATTTTACCCAGCCGGTGTCTCCTCCACAAAACCCGCCGGCAAAA
CTCGACTCGCCGCCGCTTATTGATTCGATCATCATCGAGCTTACAAGACCAATTCACCGTGGAGACGACG
AAGCGAGTGGTTCTTGTGAGACATGGACAGAGCACGTGGAACGAAGAAGGGAGGATTCAAGGAAGCTCCG
ATTTCTCCGTTTTGACGAAGAAAGGCGAGTCTCAGGCTGAAATTTCTCGTCAGATGCTCATCGACGACTC
CTTCGATGTCTGCTTCACCAGTCCATTGAAGAGATCAAAGAAAACAGCTGAAATCATATGGGGAAGTAGA
GAAAGTGAGATGATTTTCGATTACGATCTCAGAGAAATCGATCTCTACTCTTTTCAANGTCTACTTAAGA
A
ATCCCATTGTGCAAGATCAATGGAGTGAACCAGAGTCAGAACACAAAGAAGCCATCTCAAAAGTACCTTG
AAATAGTCACAATCGATAACTTCGACTTCTGGTTCATGGGATTCGTGAGCTACCAGAAAGCTTTCAACTG
TCTCGAGAAAGCGCTAAACAATGATGAGCAATAAACCGCAGTGGTTTTCTCTGACGGAGCTAATTAGTGC
AGGTGGAACAAGAAATATTTCATTTCTACTTTCCCCTGTTTCAGTCAGAGAATGTTTGTACAAACTCACA
AATTCTTTTTTTTTGCTTTACCCACTTTGGTTTCCATTGTAGACACGAGAAAGAGATGAATATATTTAGT
TGATCTCATCTGTTAACCTT
genometools-1.5.1/testdata/at1MB000066400000000000000000036406071211610345200165240ustar00rootroot00000000000000>gi|5587835|gb|AF078689.1|AF078689 AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana cDNA clone IFA2, mRNA sequence
AGTGGCTACGGCGGCGGTGGCGGCGATGGAAGTAGACGGATGGTGGTAGGAATGAAAGGCTAGAAGCGGC
GGAGAAGTATGTGGATAAGAAATAACAAAAACTGAGGGGATCATGAAGTTCTTCGTTATATTATAGTTTT
CAATCTGAATTTCAATTCCGCCGCTCGCCTTTTTCCTCTCCGCCTTTTCCGTCTCTCCGATCTGCTCCCG
CCGCCGACCTTGTGATGATTATAGCTCTGAAGGTCCATACAAGGATATAAAAAAAAAAAAAAAAA
>gi|4714049|dbj|C99932.1|C99932 C99932 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 88, mRNA sequence
ATGRAYAMTCAAAAATGGAGTMTAGGTTTCATATCTCTCGCTTTTCTCTTCATCACTTCCTCTTCAGCTG
AGTTCATCATTCAACAGGTCACAAAGGGCARAGGAATAGAGTACAACAGTTCTTACAGTCTCGAGGAGAA
TCTTGGAGTGACRAGAGAGTTGAGAGAAGAGCGACCATCGAGTAAGATAGTGACAATAACAAGCTTCTCA
GTGATTAAAGGCAGAGGAGAACCCTATGAATCCTCTGTTTTTGAGGCTGCTGGTTACAAATGGAGATTGG
TTTTGTACGTGAATGGTAATAAAAACGACGGTGGAAATGATCATATTTCCCTTTACGCAAGGATCGAAGA
GACAAACTCTCTTCCATTAGGTTGGGAAGTGAATGTTGATCTCAAACTCTTTGTCCATAATGGGAAGCTA
CACAAATATTTGACTGTTACAGATGGCTTARTTGAAGCGATATAACAATGCSAAAAAAGAATGGGGTTTC
GGACAATTGATTCCTCNATCAACATTCTACAACGCGAACGAAGGTTACCTTTGACCAAGGACACTGGTTC
CTTTTGGGTGGCYGGAAAANCCTTTATTGTTTAAACCNGSTCCACCAACMAARAAAAWWAYTTTCTWTYM
MTYYTCCAACAYSYTYCCCWWCSAATGTTTTTTCCCTTNGGAAAAANACCTNCGTTTCCTCCTACCTTTG
GGAAAAANAAANTTCNTTTTTACTCCCGAATGAATTTTCCCCCTTTGNAAAAACCGAATNCCTGGTTGGA
CTTAGGAATTTTAACCCCCNAAAGGGGGAATGGAANGAAAGAAAAAACCCCTTTGCCCNTTCCCAATCCT
TCCCTANTTTGC
>gi|4714048|dbj|C99931.1|C99931 C99931 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 87-1, mRNA sequence
GTGARTGTTGATCTCAAACTCTTTGTCCATAATGGGAAGCTACACAAATATTTGACTGTTACAGATGGCT
TAGTGAAGCGATATAACAATGCGAAAAAAGAATGGGGTTTCGGACAATTGATTCCTCGATCAACATTCTA
CAACGCGAACGAAGGTTACCTTGACCAGGACACTGGTTCTTTTGGTGCTGAGATCTTTATTGTTAAACCG
GCTCAACAACAAGAGAAAGTTACATTCATATCAAACCCTCCAAACAATGTTTTCACTTGGAAGATACTTC
GTTTCTCTACCTTGGAAGATAAATTCTATTACTCCGATGATTTTCTCGTTGAAGACCGATACTGGAGACT
AGGATTTAACCCGAAAGGGGATGGAGGAGGAAGACCACATGCACTTCCAATCTTCCTATTTGCTCAAGGC
CATAAGGCAAATGCAGTTGCTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAAGAATCAACGAARTT
CTAACCATAGACAATATWTCTGCACTTGGTACCCATTGGAAACGTTATGGTKTGGGAKTAACATATCTAC
TGTTGCTGATTAACGAGCATCCAAAGGATTTTGGTGATGAGCCYTATCTTGAACTGAATGGTTAAGKCCT
ATACCACTCTCTCCCTWAATTCTCCTTCTTNTCWCNACATCNCYTTRATAAAAAATTTATTGATAATTTT
TTARAAACTTATTTTTKTA
>gi|4714047|dbj|C99930.1|C99930 C99930 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 86, mRNA sequence
GTGAAGCGATACAACGATGCAAAAAAAGAGTGGGGATTCACACAATTGATTTCTCTTCCAACATTCTACA
ACGCGAACGAAGGGTACYTTGTGCAGGACACAGCTTCTTTTGGTGCTGAGATCTTCATCGTTAACCCGAC
AGAAAAACAAGAGAAAGTCACATTCATATCAAACCCTCCGAACAATGTTTTCACTTGGAAGATACTTCGT
TTCTCTACCTTGGAAGATAAATTCTATTACTCTGATGATTTTCTCGTTGAAGACCGATACTGGAGATTAG
GATTTAACCCGAAAGGATCTGGTGGAGGGAGACCACATGCACTTCCAATCTTCCTATATGCTCAAGGCCA
TAAGGCAAACGCAGTTGTTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAAGAATCAACGAAGCTCC
AACCACAAACAATTATATTCTGCAGCTTGGTACCCCGATTCGAAGCGATTATGGTGTGGGAGTGAACAAT
ATCATATTGATGTCAGAAGCTAAAAGATGCATCMAAAGGGTATATGGTGAATGATGCCATTATCTTTTGA
AACTGAAATGGTTAAGGTCTCTGTGAACAACATARTCTCCSCTTAAATATATNTCACTACTTCTTTATCC
CCCGNAATAACCTTACAAAGAAAAATTGATGATTTAATTTGTTATACNACACTTTATTNATGCCTGTGAN
GTAACCTTGTTTCCGCTCCCCNAATTTCCTTTTTTTTCCTGTTTTT
>gi|4714046|dbj|C99929.1|C99929 C99929 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 85, mRNA sequence
TCAAAATATGGATAGTCACAAATGGAGTCTAGGTTTCACATTACTTGCTTTCCTCTTCATCACTTCCTCT
TCCGCTGAGCTCATCATTAAACAGGTCACACAGGGCAGAGGAATAGAGTACAACAACTCTTACAGTCTCA
CGTCGAATCTTGGAGTGACGACAAGAGAGTTGAGAGACGAGCGACCATCAAGTAAGATAGTGACAATCAC
AAGCTTCTCTGTGATTAAGGACAGAGGAGAACCCTATGAATCATCTATTTTTGAGGCTGCCGGTTACAAA
TGGAGATTAGTTTTGTACGTGAAGGGTAATCCGAAAGGCGGTATAAATAATCATATTTCACTTTACGCGA
GGATAGAAGAGACAGAAACTCTTCCAAGAGGGTGGGAAGTGAATGTTGATCTCAAACTCTTTGTCCACAA
TCGGAAKTTAAAGAAATATTTGTCTGTTACAGATGGAACAGTGAAGCGATACAACGATGCAAAAAAAGAG
TGGGGATTCNCACAATTGATTTCTCTTCCAACATTCTACAACGCGAACGAAGGGTTCCTTGTGCCAGGAC
ACARCTTCCTTTGGGTGCTGARAACTTCATCGTTAACCCGACCGAAAAACCAGAAAAAATCCCTTTCTTT
TCAAACCCCCCGAAACATGTTTTTCCCTTTGGAAAAAA
>gi|4714045|dbj|C99928.1|C99928 C99928 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 84, mRNA sequence
GGAAGTTAAAGAAATATTTGTCTGTTACAGATGGAACAGTGAAGCGATACAACGATGCAAAAAAAGAGTG
GGGATTCACACAATTGATTTCTCTTCCAACATTCTACAACGCGAACGAAGGGTACCTTGTGCAGGACACA
GCTTCTTTTGGTGCTGAGATCTTCATCGTTAACCCGACAGAAAAACAAGAGAAAGTCACATTCATATCAA
ACCCTCCAGACAATGTTTTCACTTGGAAGATACTTCGTTTCTCTACCTTGGAAGATAAATTCTATTACTC
CGATGATTTTCTCGTTGAAGACCGATACTGGAGACTAGGATTTAACCCGAAAGGGGATGGAGGAGGAAGA
CCACATGCACTTCCAATCTTCCTATTTGCTCAAGGCCATAAGGCAAACGCAGTTGCTACAAACACTTGGG
GAGCGGTTAATCTGCGGTTAAAGAATCAACGAAGTACTAACCATAGACAAATATATTCTGCAGCTTGGTA
CCCGATTGGAAGCGGTTATGGTGTGGGAGTGAACAATATCATACTGTTAGCTGATTTAAACGATGCATCA
AAAGGATATTTGGTGAATGATGCCATTATCTTTGAAGCTGAAATGGTTAAGGTCTCTATAACCAACATCG
TCTCCGCTTAAATATCTGCACTTCTTTGTCTACGATCAATCAACCTTATGAATAAAGAGATATTTGATGA
GTTTGTAATAAGAAAACGTTAATGTTTGTGAATTGTGAAGTTATTACTTCTGTTCTTCTGAGTTTTTTTA
TTTCAATGAAAATAAAACTCTTACCGGTTT
>gi|4714044|dbj|C99927.1|C99927 C99927 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 83, mRNA sequence
GTGAAGCGATMCMWCGATGMWMAAAAMKARTGKGGATTYRCAYRATWGATYTCTCTTCYWMYATTCTWSW
MCGCGAAYGAAGGGTACCTTGTGYASGACRMWSCTTCTTTYGGTGCTGAKATCTTCATGCGWTAMCCCGA
CAGAAAMACMMKAKAWAGTCWCATTCATATCMWACCCTCCRAACAATGTTTTCACTTGGAAGATACTTCG
TTTCTCTACCTTGGAAGATAAATTCTATTACTCTGATGATTTTCTCGTTGAAGACCGATACTGGAGATTA
GGATTTAACCCGAAAGGATCTGGTGGAGGGAGACCACATGCACTTCCAATCTTCCTATATGCTCAAGGCC
ATAAGGCAAACGCAGTTGTTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAAGAATCAACGAAGCTC
CAACCACAAACAATTATATTCTGCAGCTTGGTACCCGATTCGAAGCGATTATGGTGTGGGAGTGAACAAT
ATAATATTGATGTCAGAGCTAAAAGATGCATCCAAAAGGGTATATGGTGAATGATGCCATTATCTTTGAA
GCTGAAATGGTTAAGGTCTCTGTGACAAACATAGTCTCCGTTTAAATATCACTACTTCTTTTTCAACAAC
AACCTTACGAATAAAGTGGACTTTGATGAGTTTAATTTGTTATACGACAACGTTGTTGATGCTTGTGATG
TAATCGTTGTTTCTGCTCTCCGAGTTTTCGTTTTACTTTTTTTTTCATGTTTTGCTATCAATGAAATAAA
GGTATAAAACTCTCTTGGTTTTAAAGT
>gi|4714043|dbj|C99926.1|C99926 C99926 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 82, mRNA sequence
GGAAGTTAAAGAAATATTTGTCTGTTACAGATGGAACAGTGAAGCGATACAACGATGCAAAAAAAGAGTG
GGGATTCACACAATTGATTTCTCTTCCAACATTCTACAACGCGAACGAAGGGTACCTTGTGCAGGACACA
GCTTCTTTTGGTGCTGAGATCTTCATCGTTAACCCGACAGAAAAACAAGAGAAAGTCACATTCATATCAA
ACCMTSSWRMCMRKRTYYTCACTTGGAAGATACTTCGTTTCTCTACCTTGTCACCTAAATTCAATTCATC
GTACCCGGATCCTCGATTCTTTTGCTTTTTACCCTGGAAGAAATACTCATAAGCCACCTCTGTTATTTAC
CCCCAATCTTCACAAGAAAAA
>gi|4714042|dbj|C99925.1|C99925 C99925 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 81, mRNA sequence
CGTCTCCATACGTTGTTCCCGAAGACATGTCCTTGACAAAGGTATACAATCTTTTCCGGCAACTTGGGTT
GCGACATCTATTCGTTGTTCCCCGTCCTTCCCGTGTGATAGGCTTGATCACCAGAAAGGATTTACTGATT
GAGGAAAATGGGGAATCATCAGCAGTGGAACTCCAACAGTCAACTAGTAGGTCGGTACAGTGAGACAGCA
ACGCGGATGGACGCTGCACGACCGCTTCTAGACGATCTTTTAGGTTAATAAAACAGACCAAACATATACA
AGCAGTTGAAGCTGGTAGCTAAGATCTTTAGTCGGGCCAATTCTTCGTCCATACAAGGATACAAGCTTGT
TCCGCATGTTGCCACCCAAATCCGGTATGGAGGATATATGATCGTCTCTTGAGATGGGATTGTGTTGTTC
GCTAACCGATCTCATTCTCCGTTCACAGAGAGTAGAAAGATTATATATGTTTAAGGCTTTTGATTGTTGT
AATTGTGCAATCTTTGAWTATTTTCTTGGTCCCTGTAAAATAATCCACCTTTTGATATATTTACTTGATT
AACTT
>gi|4714041|dbj|C99923.1|C99923 C99923 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 79, mRNA sequence
TCTGNTCCGTCTNANACATCGNATCAGGTGGNGNGTACAATCATCTCNCCGTTCANTAGGTGTTTACGGA
TTTCNGCGGTCGTATANCTNGCNTGACTAAGGCTTTAACC
>gi|4714040|dbj|C99922.1|C99922 C99922 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 78, mRNA sequence
GGTRAGATCTACSTTGCTGGAGGTGGTGGTGGTTCGGAKGTTGCGGCGGCGGTGGAASTAGTATGATCCG
GAGTTGAATCGGTGGGAAGTTGTGACTCAATCGGCSAGGAASAGATACGGTTGCATCGGAGCAGCCGTTG
ACGGAGTTTTTTATGTGATCGGTGGATTGAAAATTGGGAATGAGACCTCACGCGCGGTGGCGGCGCGTGC
TTATGCGAGCTCTATGGATCTTTTCGATGTGGAGTCGCGTCAGTGGTTAAGGAGTCGTTCGGTTCCTGGC
GGTGGATGTGTAGTGGCGGCGTGTGCGGCGGTTGGATATGTGTATGTGCTAACCAGTCACGCGGTGGAGC
TTTCGTTTTTGGCGATTTGATGCGCGTCGTCGTGGTGGAAACACCGGGTTTGGAAAAATGGCAGAAGCTG
AAAAGTCCCCCGTTACCGGCACAAGGTGCSGGTTAAGATGGAACCGGTGAAGGTTTAACCTGCGTCGGAG
TGGAAGATAAAGTGGCGGTGGTTCAGGTGGTGGGATGCATTGACGATTTGCTTCGGCGGAGTGGGAGGGG
TGAGAGAGGGATTAGAGAAAGCCTTGTGTTGCTGTATGATACGACGGAGGGAGAGTGGAGGAGAGCGGCG
GATTTACCTGAGATGATTACACGCGCCGCCTGTGCGTGTGTGGAGTGGTAAGAGNGGAGACCACGGCGCA
GGATTATGGGTACGAGAAGTTGGAAGATGCTAVCGTACGCAGGATATATTAAAGTGGGCAAAAACAATAT
CATTATGATTGGTGCACATGTTTACTGTMTGAAAAGCAATAGCGT
>gi|4714039|dbj|C99921.1|C99921 C99921 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 77, mRNA sequence
CGGGGCTTCTRAAAGACNCAATCTNATGTACTCGTACATGCTANGTNCTATCTCTTCTATAATGTCTNAT
CCTTTCTGCCCTCCCACWCGTTNCCGTAGCCKCAAAWTCTCCTKTGAYATTTMCCTGMTCAGAYTGTCCT
GATGGATGSGGAYGTTCACMTAGATACCAAAGCACAAGAAATTCGAAGGTGCTGGAGAAAAGGCGACCAC
TTTCACTAAGAGCATTTGGCTCGAGGAAGCTGATGCGAGYGCCATATCCGTTGGTGAGGAAGTAACTTTG
ATGGATTGGGGAAATGCTATCGTAAAGGAAATCMCMAAKGACGAGGAGGGTCGTGTCACTGCCTTATCTG
GTGTCTTGAATCTCCAAGGTTCTGTWAAGACTACAAAGCTGAAGCTGACATGGCTTCCTGATACTAATGA
ATTGGTCCATCTCRCMTTAACAGAGTTTGATTATCTAATCCCCMANAAGAAACTGGAANATGATGATGAA
ATTTGCTGATTTTGCTGAATCCYMMCCCNAAAAANGAANACMTTTGGCMCTTKGGTNGATTCCCAATATT
GAGAGAATCTTGAAATTGTTGGAAAATNTTTATTCCCCCTTT
>gi|4714038|dbj|C99920.1|C99920 C99920 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 76, mRNA sequence
TCAGCTGTTTCGTTCAACGATCTAAACTATCTCAATGCTTCTTTGAATCTATTGTCGGTTTCCTTGTACT
CGTCAATTTCATGTTTTTTTTG
>gi|4714037|dbj|C99919.1|C99919 C99919 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 75, mRNA sequence
CCCTCCCNCTCCTNNTTTCTANTTNGNTTCNGNTTCTGTTATCGNGTTTTTCNCNNGGGTCTTTTNTCGN
NGCCCTGGACCGGAATTCNCGNGTCGACCAACTCNTCAGATGTGGTGCTNCNCTACAATGAANCAAANNG
ANTCACACTCTCGGACTNANNCTCTCCCCTCCGCTTCTGTAACCATANCNNCTCNACNTCTATGTCTCCN
ATCTAACCANCTCTNNGGGTTCGAGGAGANATAAGGAGAAAAGTANGGANGGACGANTATGCTTGCCCGT
TCTGTNCAGACTATTTTGATNTCNTCTCTCTNNGCNGTCACATTGATGAANATCNTCCTATGGATGCTTA
AANTGGGGTNTGTCCCGTCCTGTGCGGTGAAAGTGAGCTCNGGATATGATTGCNTCNTATANCCCCNCGN
CNCNGCCNATATGTTCAAGGTGACCCNGATCANGAAATCAA
>gi|4714036|dbj|C99918.1|C99918 C99918 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 74, mRNA sequence
GTTTATCACGCCTTGCATTGATCAGAASCCCTTGCTACGGCATTGAGCCAKGCTGCCGAAGCTGTTTCTT
CGGGAAATTCAGATGCAAGTGATGCCACTGCAAAAGCTGGAATCATTTTGTTGCCCAGCACACATCAACT
TGACGAAGAGGTTACTGMGGAACATAGTGAGGAGGAAATGACTGAAGAGGAACCAACTCTTCTCAAGTGG
CCAAATAAGCCCGGGATTCCAGATTCTGATTTGTTTGACCGTGATCAATCGTGGTTTGATGGACCTCCAG
AGGGCTTCAATCTCACATTATCAAATTTCGCTGTGATGTGGGATTCACTGTTTGGCTGGGTATCATCGTC
CTCTCTGGCATACATATATGGGAAGGAAGAATCTGCTCATGARGAGTTCTTATTGGTTAACGGGAAGGAG
TACCCCCGGAGGATTATCATGGTAGATGGGCTTTCCTCAGARATCAAGCANACAATTGCTGGGTTGCCTT
GCCAGAACTTTACCGAAAATCGTCACTCATCTCAGGGCTGCCAATANCGATATCCRATTTTAAAAA
>gi|4714035|dbj|C99917.1|C99917 C99917 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 73, mRNA sequence
ATAGGCGANATCCCCCCCAAANGATTNCCTGATGTGAGGAACATGGGGANATCATCNTGGAATCGAGCNC
NNGNAGTCNCCGGTNAAGTNGGTGGGTNNACANTCNCNCCCNNACNGACNCNGCATGACCNCTTCACTAC
NANCTGTTANGTTTNTGGGACTGNTCCTACGATATACCNTCTCTTGGTGGTGGNNCCNCGAAACTCNNCT
CAGGACTNGGCTCCTCGAAATTCNGATGAAGNNTGTCCCGCCTGTGACNACGNNNTTCNGGATTGGANCG
ATCTANGAGNNGACACTCTGAGAATGTGATCGGTGATTNNTCGGTNCNCTGNATCACATTNCTCNCCTTN
CCANTACCACTTTTNACANANTTCCCCTTCTTTTTCNCAACGNGCGATNCTNGNAGAANGNATGGNTAAC
TCGGNTNCCNGCTCTGNATCGNAGATANCGTNGTCCTCTCGGGGTTCCAGAGGNTC
>gi|4714034|dbj|C99916.1|C99916 C99916 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 72, mRNA sequence
GGTAATAAAAACGACGGTGGAAATGATCATATTTCCCTTTACGCAAGGATCGAAGAGACAAACTCTCTTC
CATTAGGTTGGGAAGTGAATGTTGATCTCAAACTCTTTGTCCATAATGGGAAGCTACACAAATATTTGAC
TGTTACAGATGGCTTAGTGAAGCGATATAACAATGCGAAAAAAGAATGGGGTTTCGGACAATTGATTCCT
CGATCAACATTCTACAACGCGAACGAAGGTTACCTTGACCAGGACACTGGTTCTTTTGGTGCTGAGATCT
TTATTGTTAAACCGGCTCAACAACAAGAGAAAGTTACATTCATATCAAACCCTCCAAACAATGTTTTCAC
TTGGAAGATACTTCGTTTCTCTACCTTGGAAGATAAATTCTATTACTCCGATGATWTTCTCGTTGAAGAC
CGATACTGGAGACTAGGATTTAACCCGAAAGGGGATGGAGGAGGAAGACCACATGCACTTCCAATCTTCC
TATTTGCTCAAGGCCATAAGGCAAATGCAGTTGCTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAA
GAATCAACGAAGTACTAACCATAGACAAATATATTCTGCAGCTTGGTACCCGATTGGAAACGGTTATGGT
GTGGGAGTGAACAATATCATACTGTTAGCTGATTTAAACGATGCATCCAAAGGATATTTGGTGAATGATG
CCATTATCTTTGAAGCTGAAATGGTTAAGGTCTCTATAACCAACATCGTCTCCGCTTAAATATCTGCMCT
TCTTTGTCTACRAYCAATCCACCTTATGAATAAAAAAATTTTAATTTGATGAATTTGTTATAANAAAACT
TTAATGTTTGTTAAATGTGAAATTT
>gi|4714033|dbj|C99914.1|C99914 C99914 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 70, mRNA sequence
GGGACGAACCGGTGTACCACGATTTGGTTCGTCACTGTCTGGCCTACCCAAAAGCGGATGGAATCTTGGT
GAATACATGGGAAGAGATGGAGCCCAAATCATTAAAGTCCCTTCAAGACCCGAAACTTTTGGGCCGGGTC
GCTCGTGTACCGGTTTATCCGGTTGGTCCGTTATGCAGACCGATACAATCATCCACGACCGATCACCCGG
TTTTTGATTGGTTAAACAAACAACCAAACGAGTCGGTTCTCTACATTTCCTTCGGGAGTGGTGGTTCTCT
AACGGCTCAACAGTTAACCGAATTGGCGTGGGGGCTCGAGGAGAGCCAGCAACGGTTTATATGGGTGGTT
CGACCGCCCGTTGACGGCTCGTCTTGCAGTGATTATTTCTCGGCTAAAGGCGGTGTAACCAAAGACAACA
CGCCAGAATATCTACCAAAAANGGTTCGTGACTCSTACTTTGCGATAAAAGTTTCATGATCCCATCATGG
GCACCGCAAGCTGAAATCCTAACCCATCCAGGCCGTTGGTGGGTTTTTAACACATTTGTTGGTTTGGAAC
TCCACTTTGGRAAACCTTCCTTTTGCCGGCGTTCCCAWTRANAACCTTKGCCCCCTTTTCCCCCAACC
>gi|4714032|dbj|C99913.1|C99913 C99913 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 69, mRNA sequence
CCTGTCCCATCGGGCCGTTRGTGGGTTTTTGACCCATTGCGGTTGGAGCTCGACGTTSGAAAGCGTCGTT
GGCGGCGTTCCGATSATCGCATGGCCACTTTTTGCCGAGCAGAATATGAATGCGGCGTTGCTCAGCGACG
AACTGGGAATCGCAGTCAGATTGGATGATCCAAAGGAGGATATTTCTAGGTGGAANATTGAGGCGTTGGT
GAGGAAGGTTATGACTGAGAAGGAAGGTGAAGCGATGAGAAGGAAAGTGAAGAAGTTGAGAGACTCGGCG
GAGATGTCACTGAGCATTGACGGTGGTGGTTTGGCGCACGAGTCGCTTTGCAGAGTCACCAAGGAGTGTC
AACGGTTTTTGGAACGTGTCGTGGACTTGTCACGTGGTGCTTAAAAATTGTTACCGTTTTCTAACTCTTT
TATTATTARTTGGTTGAATTATACGTGTCGTTCCTCTGTTAGTTGTTATAATATAATAAATCGATTTACT
CTTTGTT
>gi|4714031|dbj|C99911.1|C99911 C99911 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 67, mRNA sequence
CGTTTCTGCCACATTAAAACAGAAGAGTGCAACAATTGAAGGCATAGAAAAGTGGCCTTATGAAGCAGCT
GCCATTGCTTTCGAGGCTATTCCACGTACCCTGGCTCAAAACTGTGGGGTTAACGTGATCCGTACTATGA
CTGCATTGCAAGGGAAGCATGCAAATGGTGAAAACGCATGGACTGGTATTGACGGGAACACTGGTGCAAT
AGCTGATATGAAAGAGAGCAAGATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATA
GAAGCAGCGTGTATGCTTCTAAGGGATCGATGATATAGTGAGTGGAATCAAGAAGAAGCAAGCTCCTGGA
TCTGGACCTTCAAAGCCTACCATTGAGACAGAAGGAGATGCAGACAACGAACAAATTCTTCCCGACTAAG
CGAAGGGAGAAACACTTTGGTCTCAGCATAACTCAATCTCTGTTTTCACTTGTTTAATGGTTGCACTCTT
TTGGCTATTATCTTCCCTTGACATATCTTTTTAATTCTGCAGTTTTGACTTNGGTGAGATAAAATTTTCC
CAAGGTGGTTTTTTTTTGTTTGTTTTGGGAATATTAACTTTTTTGAATTTTCNTANTCCCTTTGTTGGTT
TTTAAAATTCCAATTGTTATTGTTCTTTTTG
>gi|4714030|dbj|C99910.1|C99910 C99910 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 66, mRNA sequence
CGCSCCTAAGAAGGAAAAGATGAGAAGAAGAAGAAGAAGAAAACTGAGGTCTGAAGAGACCTTTAATATT
TTTGCGTGGTCTAGTTTACTTTGTTATCAGAAACAAAGAAAATCTTTTGTGGCGTTAGGTGTTAAGTAAG
GTTTTTGTTTTGTTTGAAACTTAAAAAAAAGAACTACTCTTCGTTTTGTAAGGTTATAATATGTTTGGTT
TAGTCCTTATCCCAAAAACTTGCATTTTGCC
>gi|4714029|dbj|C99909.1|C99909 C99909 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 65, mRNA sequence
ATTTTCTTGTATGTTGGAATGGATGCCTTGGACATTGACAAGTGGAGATCCGTGAGTGACACACCGGGAA
CATCGATCGCAGTGAGCTCAATCCTAATGGGTCTGGTCATGGTTGGAAGAGCAGCGTTCGTCTTTCCGTT
ATCGTTTCTATCTAACTTAGCCAAGAAGAATCAAAGCGAGAAAATCAACTTTAACATGCAGGTTGTGATT
TGGTGGTCTGGTCTCATGAGAGGTGCTGTATCTATGGCTCTTGCATACAACAAGTTTACAAGGGCCGGGC
ACACAGATGTACGCGGGAATGCAATCATGATCACGAGTACGATAACTGTCTGTCTTTTTAGCACAGTGGT
GTTTGGTATGCTGACCAAACCACTCATAAGCTACCTATTACCGCACCAGAACGCCACCACGAGCATGTTA
TCTGATGACAACACCCCAAAATCCATACATATCCCTTTGTTGGACCAAGACCGTTCATTGAGCCTTCAGG
GAACCACAATGTGCCTCGGCCTGACAGTATACGTGGCTTCTTGACACGGSCCCCTCSAACCGTGCATTAC
TACTGGGAGACAATTTGATGACTCCTTCCTGCGACCCGTCTTTGGGAGGTCGTGGCTTTGTACCCTTTGT
TTCCARGGTTCTCCAACTGAR
>gi|4714028|dbj|C99908.1|C99908 C99908 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 64, mRNA sequence
GGTTTATTACCGATGCAATCCTATGTCTCACCACCGTATCGGGGATAAGTATAAGATATATCCAACATAT
GACTTTGCTTGCCCGTTTGTTGATTCCCTTGAAGGTATAACGCATGCTCTTCGGTCTAGTGAGTATCATG
ACCGAAATGCTCAGTACTTTAAAGTTCTGGAGGATATGGGACTGCGACAGGTTCAGCTTTACGAATTCAG
CCGGTTAAACCTAGTTTTTACACTTCTCAGTAAGCGCAAGCTTCTCTGGTTTGTCCAAACTGGATTGGTT
GACGGGTGGGATGATCCACGTTTCCCGACAGTCCAAGGAATTGTTCGTAAAGGTTTGAAAATCGAGGCTC
TGATTCAATTCATTCTCGAGCAGGGGGCTTCGAAGAATCTAAATTTGATGGAATGGGACAAACTTTGGTC
TATAAATAAGAGAATAATTGATCCTGTGTGCCCTARACACACTGCTGTGGTTGCAGAACGTCGTGTACTA
TTTACCTTAACGGATGGTCCTGATGAACCGTTTTGTTCGCATGATACCAAAGCACAAAAAATTCCAAAGG
TGCTGGAAAAAAAGGCGAACACTTTCCCTAAAAAACATTTGGCTCCAAGGAAACTGATGCCAATTGCCCA
TATCCGTTGGGTGAAGGAAATTTACTTTTGAAG
>gi|4714027|dbj|C99907.1|C99907 C99907 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 63, mRNA sequence
CTTGAATGCGGAAGCTAGGTGTATGACAAAGGCAAGAAAGCTCGGGGTTTGTACTCCAGTCCTATATGCT
GTGGATACTCTGCTTCACTCTTTAACACTTGAGTACATTGAGGGGGTCTCTGTTAAGGATATTTTCCTTG
AGTTTGGGACCAATGGGGTTGTTGAGGAACGTTTAGATGATGTTGCTGCTCAGATTGGGGCTGCAATTGC
TAAGCTCCATGATGGTGGCTTGGCTCATGGTGATTTGACCACATCAAATATGTTAGTCAGAAGTGGAACA
AATCAGCTGGTACTAATTGATTTTGGCTTGAGCGTCACATCGACCTTGCCTGAAGACAAAGCTGTTGATT
TATATGTACTTGAAAGAGCCTTACTCTCAATGCATTCGTCATGCGGGAATGTGATGGATCGTATACTGAC
GGCGTATARGAATCCTCAAAGCAATGGTCAGCCACGTTTAACAAAGCTCGCACAAGTGAAACACCGAAGG
GAAAAAAGCGGACTATGATTGGATGAAGGCGANGAACCCAAGTTCTCCCATTGGTACTGTCCTTAAAACT
TTGAACMCAAAACCCCCCAAAWCTGTCCYGTTATWATTAATCC
>gi|4714026|dbj|C99906.1|C99906 C99906 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 62, mRNA sequence
TGGATCATTCATAAGCTTCTACTCACTGGCGTTTATGGGATGGTGTTCTTGATGTACAACTCTAGGTGGA
GAGAAAAATTGCCTGCAAGGCCTGCATTCTACAACTACATAATCATCATGTTCGCCTTATACAGCCTTTA
CCTAGTTGCATCTGCGTTTACCGCAAACAACGCGCATTTTGGTTTCTGGTTATATGGGATCATGAGTGTT
TGCTACCACGCATTATACCTTCCTCTTCTTTACATAACGTTCCTCGCAGACTTTTTCCAGGAAGAAGATT
TGAACTTGGAGAATGTATACTACTCAGAGATGAAGGATGCTGGATTTTTCGACTCTGATTGGGAATAGGA
CTAGGGTAACAAACATCTTCCTCATTTTCTCAATCTGTAAATACACGTTGGGTAGGATCTCCTAGAAGTC
ATGGCTGCTTTTTCCGGCTTTGGCGGGTTACATTTTARGGTCTAATCTTTTGTATGTCTGTACTTTTTCC
TCATGTTTCTTTCTCTTTTATAAATCCAAAATGTCTTGTGAATCTCTTTGTTCCTTAAAKCCTGAATAAT
CT
>gi|4714025|dbj|C99905.1|C99905 C99905 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 61, mRNA sequence
CCAAAGGAAGAGGCCCAAACCGAGAAGATAGCTATTGAAACGGTTATGATTGATGAGTCAAACCTTGCGG
ATTATGTAGGAAAACCGGTATTCCATGCAGAGAAGCTCTATGAGCAGACACCGGTAGGTGTTGTGATGGG
TCTAGCTTGGACATCAATGGGTGGTTCAACATTGTACATAGAGACGACTGTTGTGGAGGAAGGGGAAGGT
AAAGGTGGCCTGAATATAACGGGTCAGCTCGGTGATGTGATGAAAGAAAGTGCACAAATTGCTCACACAG
TCGCCAGAAAGATCATGCTAGAGAAAGAACCAGAGAATCAGTTCTTTGCAAACTCCAAGCTTCATCTCCA
TGTTCCTGCAGGAGCCACTCCCAAGGATGGTCCAAGTGCAGGCTGCACCATGATCACATCTTTACTATCA
CTTGCCACGAAAAAACCCGTTAGGAAGGACCTTGCAATGACTGGAGAAGTCACACTAACCGGAAAAATTC
TTCCTATTGGTGGGGGTGAAAGAAAAAACTATACCGGCGAAGGCGGAATCCGATTAAAACCAATAATATT
TCCCNAAGCAANCCGAAAAACTTGATAACTGCNAAAAATGTNAAAAAAGGNTTATTTTCCTTCCTGGATG
ATATGGAAAAACTCCAACCTGCCTTTGGTT
>gi|4714024|dbj|C99904.1|C99904 C99904 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 60, mRNA sequence
CAGGTCCTGGTCCGGAATCCCGGGTCGACCCACGCGTCCGGAAGCGACAGTGGTAGATGGAAATGGAACA
GAGACTGGACATATCATTGTGACTACTATTGGTGGTAGAAATGGCCAACCAAAACAGACAATTAGCTACA
TGGCTGAGCGTGTTGTTGGTCACGGATCTTTTGGTGTTGTGTTCCAAGCGAAATGTCTTGAGACAGGAGA
AACTGTTGCGATAAAGAAAGTTTTACAAGATAGGAGGTACAAGAACCGTGAGCTTCAAACCATGAGGCTA
CTTGACCATCCTAATGTTGTGTCTCTGAAACATTGTTTCTTCTCAACCACTGAAAAAGATGAGCTTTACC
TCAATCTTGTTCTTGAGTACGTTCCACAAACTGTTCATCGTGTTATCAAACACTACAACAAACTGAATCA
GAGAATGCCTCTTATATACGTCAAACTTTACACTTATCAGATTTTTAGAGCCTTATCTTACATTCACCGA
TGCATTGGTGTGTGTCATCGTGACATAAAACCTCAAAACTTGTTGGTAAATCCGCACACTCATCAAGTAA
AGCTATGTGATTTTGGAAGTGCAAAAGTATTGGTAAAAGGAGAACCAAACATTTCCTACATCTGCTCGAG
GTATTACAGAGCACCTGAACTTATTTTTGGAGCAACCGAGTATACGACAGCCATTGATGTCTGGTCTGCA
GGATGTGTTCTAGCTGAACTATTGCTTGGACAGCCCTTGTTCCCTGGTGAGAGCGGTGTTGATCAACTTG
TAGAGATTATCAAGGTCTTGGGAACCCCTACCTAAAANAAGAAATCAAGTTGCATGAACCAAACTACACG
GAATTCAAATTCCCTCAGATTAAAGCTCATCCATGGCACAAGATTTTCCACAAACGCNTGCCTCCCAAAA
CCTGTTGAATTGGGTCTCAAGAANTTCTTCAATACTCCTCCTAATCTACNAAATTGCCGCTCCCCAACCA
TTAATTCCACCCATTCCTTGATGAATTAAGAAAANCAAA
>gi|4714023|dbj|C99903.1|C99903 C99903 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 59, mRNA sequence
CAGCGAACACGGAGTTCCGGCATCATTTAAGGTTCCAACTGGAGTTGTCATACCTTTTGGATCGATGGAA
TTAGCTTTAAAGCAAAATAATTCGGAAGAAAAGTTTGCGTCTTTGCTAGAAAAACTAGAAACCGCCAGAC
CTGAGGGTGGTGAGCTAGACGACATATGTGACCAGATCCATGAAGTGATGAAAACGTTGCAAGTGCCTAA
AGAAACAATCAACAGCATAAGCAAAGCGTTTCTCAAAGATGCTCGTCTCATTGTTCGTTCAAGTGCTAAC
GTCGAGGACTTAGCCGGAATGTCAGCTGCAGGACTCTATGAATCAATCCCTAACGTGAGTCCCTCGGATC
CTTTGGTGTTTTCAGATTCGGTTTGCCAAGTTTGGGCTTCTCTCTACACAAGAAGACTGTTCTAAGCCGT
AGAGCTGCTGGTGTCTCTCAAAGAGAARCTTCAATGGCTGTTCTCGTTCAAGAAATGCTTTCGCCGGACT
TATCATTCGTTCTGCACACAGTGAGTCCAGCTGATCCGGACAGTAACCTTTGTTGGAAGCCCGAAAATCG
CTCCTGGGTTTAAGGTGAAAACTTTAACCTTCCGGAACCAGAAGGAACCCCCC
>gi|4714022|dbj|C99902.1|C99902 C99902 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 58, mRNA sequence
ACCAAACCAAAGTATCTCTAAGGAATCGCTGTCCTTCGATGAGGACATACCTGCCGGTTCAATGGTTGAG
GACGAAGTGACGAGTGAACTCTCTGTGCGTTTCCCCCCAAGAGGATCTCCCTCACCATCTATTCCTCAAG
TTATCAGCATTGGACAGCTCATGGAATCTGCGCTTGAGGTCGCTGGTCAAGTGGTTGGGTCATCTGTCTC
TACTTCTCCGCTTCCTTATGACACAATGACTAACCGCTGTGAAACCTTTGGGACTGGTACTAGAGAGAAG
CTCTCAAGGTGGTTGGCCACTGAGAACCGTCAGATGAATGGGCTCTATGGAAATTCACTTGAGGAATCAT
CTGCACTTGAGAAGGTAGTATAAGATGGGAACATCTATGGGAGAGAATCTGGAATGTTGCAGGATTCATG
GTCCATGATGAGACTACCTCCAGCTAGTCCCTTTGACAATTTCCTCMAAGCASCAGGAGCTGGAAGATGA
TTCCACTAACTTGATCATATCAATCTCTGTTAAAAAGTGTGTAATCTTGTTGTTCTTATTGGGATTTGTT
AAAAAACTAACTTTTTCTAGGGGCAATCCCCAAGCTTCTCCTTATTATCTAAAATCATTAATTAATTTAT
GCCTGTTTCCTTTAGGAC
>gi|4714021|dbj|C99899.1|C99899 C99899 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 55-2, mRNA sequence
AGCAGGGGGCTTCGAAGAATCTAAATTTGATGGAATGGGACAAACTTTGGTCTATAAATAAGAGAATAAT
TGATCCTGTGTGCCCTAGACACACTGCTGTGGTTGCAGAACGTCGTGTACTATTTACCTTAACGGATGGT
CCTGATGAGCCGTTTGTTCGCATGATACCAAAGCACAAGAAATTCGAAGGTGCTGGAGAAAAGGCGACCA
CTTTCACTAAGAGCATTTGGCTCGAGGAAGCTGATGCGAGTGCCATATCCGTTGGTGAGGAAGTAACTTT
GATGGATTGGGGAAATGCTATCGTAAAGGAAATCACAAAGGACGAGGAGGGTCGTGTCACTGCCTTATCT
GGTGTCTTGAATCTCCAAGGTTCTGTAAAGACTACAAAGCTGAAGCTGACATGGCTTCCTGATACTAATG
AATTGGTCAATCTCACATTAACAGAGTTTGATTATCTAATCACCAAGAAAAAACTGGAAGATGATGATGA
AGTTGCTGATTTTGTGAATCCTAACCCCAAGAAGGAACATTGGCMCTTGGTGATTCCAATATGAAGAATC
TGAAATGTGGAAATKTGATTCCCCTTTGAAAAGGAAAAGGCTATTTCCSAATTTGATGTTGCCTTTTGTT
CAAATCCTCCCAARCCCMCTTTGTTCTTATTCCCCCCTTCCCCAAATGGAAAAAA
>gi|4714020|dbj|C99898.1|C99898 C99898 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 55-1, mRNA sequence
TCAGNGGACGATGTCAAAGATCAAAACATACCTATTGATGCAGTGCATACATCGATGATTNTCTCTTGTG
TGATCNAGTTTNAANNCCNNNATGNTANNCGGATNCTCTCTTTCATCAGANTCCGGTCCGTGTAAGTAGA
TGGGTCTAACCCGGANCTNTNTGGGTGGNCCAACCTTCTCCATAAAAACTGNTGTTGTGGAGGA
>gi|4714019|dbj|C99896.1|C99896 C99896 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 53, mRNA sequence
CTCTGTCTCTTTCTTCTTCTTCTTCTTCTTCTCATTAAAAGCTGAACACAAAGATCTATTCTTTCACTAA
CACATTACCAGTTTCTGCATTTGTATTATATCCTTTTCTAAAACTTTTAACCATTCTTTCTCCATTCCCA
GTTCTTAGAAAGAGTCAAGAGCAATGAGGAAGCTTTTCTTGTTAGGGTTTATAGTTGCAGGACTGGTTCT
TGGGAATGAGGCAAATGGGTATTTAGAGTTCAATGTCACCTAAATTCAATTCACCCATGGTACCCGGATC
CTC
>gi|4714018|dbj|C99895.1|C99895 C99895 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 52, mRNA sequence
GCCTCATGAAANAATCATGGACACTTGATTTACCTCATGGTGGACATCTTTCTCATGGTTANCANACTGA
CACNAAGAAAATATCNGCTGTATCCATCTTTTTTGAGACAATGCCATACAGATTGGATGANAACACTGGT
TACATTGATTATGACCAGCTAGAAAAGAGTGCCGTGCTTTTCAGACCGAAACTTATTGTTGCGGGTGCAA
GTGCTTATGCTCGTCTATATGACTATGCACGTATTCGTAAGGTCTGTAACAAGCAAAAGGCAGTTATGTT
GGCTGATATGGCTCATATTAGTGGGTTGGTTGCTGCTGGCGTTATTCCTTCTCCTTTTGAGTATGCAGAT
GTTGTTACGACTACAACTCACAAATCTCTTCGCGGTCCTAGAGGGGCTATGATATTCTTTAGGAAGGGGT
TAAAAGAGATTAACAAACAAGGGAAAGAAGTCATGTATGACTATGAAGACAGAATTAATCAAGCTGTTTT
TCCTGGACTGCAAGGTGGTCCACATAATCACCTATAACGGGTCTAACAGTTGCTCTGAAACCAGCAAGAA
CCCCTGAATTCAAGGCCTACCAGGAAACAATTTCTCCGTAATTGCCCCCAATTTGCCTGAAACTTTGCTT
GCGAAAGGATATGATTTAGTGTCTGGAGGCACTGATAATCATTTAGTTTTGGTGAATCTGAAAAACAAGG
GAATAGATGGATCAAGAGTGGAAAAAGTATTAGAATTAGTACATATTGCAGCAAACAAGAATACTGTTCC
TGGGTGATGTTTCTGCCATGGGTTCCCCGGTGGGCATCCATATGGGAAACAACCAGCCCTCACATCAAGA
AGATTCATTGAAGAAGATTTTGCAAAAGTTGGCGGAATATTTTGATTTAACCNTCCAAAATANCCTTAAA
GAACCAAACCANAATTCTCCAAGGAACCAAAATTTGAAAANANTTTTGTTTNCCAACCAATGCCNATCCA
ATTGANAAAATTACCNTTCCNAAAATTTNCAAACCTCCCTTGAAAATNGTTAAAAAAAA
>gi|4714017|dbj|C99894.1|C99894 C99894 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 51, mRNA sequence
CCATGGTACCCGGATCCTCGAATTCTTTTGCTTTTTACCCTGGAAGAAATACTCATAAGCCACCTCTGTT
ATTTACCCCCAATCTTCACAAGAAAAACTGAGRATAGGAACGTGTGGAACAGGAGGATGAGGATGANCAA
GGTGAAACACAGTGTGGAGCATGTGGTGAGAGCTATGCAGCTGATGAGTTCTGGATTTGCTGTGACCTCT
GTGAGATGTGGTTTCATGGAAAGTGTGTTAAGATAACACCAGCAAGAGCTGAGCACATCAAGCAATACAA
GTGCCCTTCTTGCAGCAACAAAAGGGCTCGTTCCTAAATTTGTTGANCGCTCGCTTCTGTGTATCTACCT
TTGCATATGATGATGAACANCTTAACTGTTTGGTTTAGATCAGATTTGTCNTATGGATTTGGTAATTTTA
GGAAGA
>gi|4714016|dbj|C99892.1|C99892 C99892 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 49, mRNA sequence
GTGGTGGAGGAAGCAGCTGGTCCCGAGGTGGTAGTAGTTCCAGAGGAAGTTCTGATGATTGGTTGATCGG
TGGCAGAAGTTCATCAAGCAGCAGAGCTCCTTCGCGGGAGAGAAGTTTTGGAGGTTCATGCTTCATTTGT
GGGAAATCTGGACACAGGGCAACAGATTGTCCTGATAAGAGAGGATTTTAGAGTTATCGTAGCAAATGGT
TTCTGCTCTTGGGAGAAAGATCCTTGTCCTTTTTGGTGTTCTTAATGCGAATCTTTTCGTGCTTGCTTCA
ACGGTTTGTTTCAGACGGTAGAGAAGCAATCAGGGAGGAGGATACATGCTTCGGACAAGGTAGAGCAGAA
ATAAATAAGAGAGAGGCAATAGCAAAAGTAAAGGAGAAGGTTTTCCTCAAATTGGCATTTTCAGAGTTTG
CGTGAGAAACAAGGGAAAGCTGATGGATCTTTTTATGTTAGGGTTATTATAATAGTCTTAATGATCAGTT
TCCATGTTTCTAAGGTTTTGTTTGATTTAAGTTGGTTATTAATTCAGTCTACTTACACTACTTTTATTTT
CATTTTTGTACSTTTTCAATTGTTATATGTTAATTCCGATCMCATTTTTTTGGACAGAATTACTATTTCT
TTATAATAAAATCTTATGCC
>gi|4714015|dbj|C99891.1|C99891 C99891 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 48, mRNA sequence
ATTTGTAATAATCTTCGTAGAAAAAATGGATTCTGATTCTTGGAGTGATCGTCTCGCATCGGCTTCAAGA
AGATATCAGCTCGATTTCTTGTCTCGATCTGACAATTTCTTGGGGTTTGAGGAGATAGAAGGAGAAGATG
ACTTCAGGGAGGAGTATGCTTGCCCGTTCTGTTCAGACTATTTTGATATCGTCTCTCTATGCTGTCACAT
TGATGAAGATCATCCTATGGATGCAAAAAATGGGGTATGTCCCGTTTGTGCGGTGAAAGTGAGCTCTGAT
ATGATTGCTCATATAACCCTACAACATGCAAATATGTTCAAGGTGACGCGGAAAAGGAAATCAAGAAGAT
GCGGGGCTCAATCCATGCTATCGATCTTGAAGAGAGAGTTTCCTGATGGAAATTTTCAGAGCCTATTTGA
AGGAACATCACGTGCTGTATCCTCTTCTTCTGCCAGTATAGCTGCTGATCCTTTACTGTCTTCATTCATT
TCACCAATGGCTGATGACTTTTTCATTTCTGAATCAAGTCTATGTTGCANAACACCAATTTCTGCCCCAG
AAAAACATTGGAATCCCAAATTTTGCCCTGAAAAGGGAAATGTTTGAAAAAAACCATTTCTCCTTTT
>gi|4714014|dbj|C99890.1|C99890 C99890 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 47, mRNA sequence
ATAAATATGGGTAATATATCTATCTTGCTTCTACTCTCTCTTTTCACTTTTTCTCTGTGTCTATTTGTCT
CTCCGTAAGAAACATTATGCCTTCATCTGATTCCACGATGATGAAGAAAGGAACAAAGCGCAAAATCGAA
ATAAAGAAACGAGAAACCAAAGAGCAACGAGCCGTGACTTGCTCTAAACGTCGTCAAACTGTTTTTTCCA
AAGCCGCCGATCTCTGTCTTAACTCCGGTGCCAACATCGCCGTCTTCGTAACCTCTCCCTCCGATAGTTC
CGATGTTGTCTATTCCTTCTCCGGTTACTCCTCTGCCTACGAAATCGCTGATTGTCACCTAAATTCAATT
CACCCATGGTACCCGGATCCTCGAA
>gi|4714013|dbj|C99889.1|C99889 C99889 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 46-1, mRNA sequence
AAGTGTCGAACAAATACTACTTAGGTCCAGCTCCATTGGAAGAAATGGCGAGGCAAATCGCTACGGCTTC
GGGACCTTGTGGGAACAACCGAGAGTATCTTTTCAAGCTAGAGAAAGCAATGTTCGACATTGAGCATGAG
GAAGAGTATGTGATTGAGTTAGCGAATGAGGTTAGGAAGCAACTCGATTTACCGGAGGAAGTGAAGGCAT
TGTTGAAGCCTATTGTTTCTCATGTATCCGTCAAGTCTCAAGCTCATGTTTCCACTCGTCAACGGGTCTT
TGCATCATGAAGACAGCAAAAGTTATGGAGCTAACTTAAAAAAGCATTGTGGTGACGAGGCTAATGTTAA
CTCTTTATCTTTCAGCTTAATATTTGATCACATCTTGACCTTGAGATGTTTTGTTTTGCTCTGCATTTAT
TGAGAATTCATAACATTGTATGATATGAGATGCAATTTATGAGAATAATAACCGATCTTTAGCTCTGCC
>gi|4714012|dbj|C99888.1|C99888 C99888 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 45, mRNA sequence
CGTTCTTTCTCTCGCAAACCCAAATTCTCTCAGCGCCGGTCAAATACTTGTCTCTCTCTCTCTCTCTCTT
TCACTCTTGTCTTGTCTCCTTCGAAGCTGTTTGTTCTGTAAGAAAGATGGAAGCAGGTGGCGCGTACAAT
CCACGCACTGTTGAAGAGGTGTTTAGGGATTTTAAGGGTCGTAGAGCTGGCATGATTAAGGCTTTAACCA
CTGATGTTCAGGAGTTTTTCCGACTTTGTGATCCCGAAAAGGAGAACCTTTGCCTTTACGGACATCCAAA
TGAGCACTGGGAAGTGAATTTGCCAGCTGAAGAGGTTCCTCCTGAGCTCCCAGAGCCTGTCTTGGGTATC
AATTTTGCCAGAGACGGGATGGCGGAAAAGGATTGGTTGTCCCTTGTTGCTGTCCACAGTGATGCTTGGC
TTCTTGCTGTTGCTTTCTTTTTTGGAGCCAGGTTTGGATTTGACAAAGCTGATAGGAAGAGGCTTTTCAA
TATGGTGAATGACCTCCCAACAATCTTTGAGGTTGTAGCTGGCACTGCTAAGAAACAAGGAAAAGATAAG
TCCTCTGTTTCCAACAACAGCAGCAACAGATCCAAATCAAGCTCCAAGCGAGGATCTGAATCCCGTGCCA
AGTTCTCAAAGCCGGAGCCGAAAGATGATGAGGAGGAGGAAGAGGAAGGTGTGGAAGAGGAGGATGAGGA
TGAGCAAGGTGAAACACAGTGTGGAGCATGTGGTGAGAGCTATGCAGCTGATGAGTTCTGGATTTGCTGT
GACCTCTGTGAGATGTGGTTTCATGGAAAGTGTGTTAAGATAACACCAGCAAGAGCTGAGCACATCAAGC
AATACAAGTGCCCTTCTTGCAGCAACAAAAGGGCTCGTTCCTAAATTTGTTGACCGCTCGCTTCTGTGTA
TCTACCTTTGCATATGATGATGAACAGCTTAACTGTTTGGTTTAGATCAGATTTGTCATATGGATTTGGT
AATTTAGGAAGACATTTTAGTTTTTTCCTTGTTACATTTTTGGGCGAATTGAAAGGGATAACTCCTTTGT
TTTAAGGGGGTTAATGGAACCTTTTGGCCCCCGTTTTTAAWAGTTTTGGTTT
>gi|4714011|dbj|C99887.1|C99887 C99887 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 44, mRNA sequence
GTGAATGTTGATCTCAAACTCTTTGTCCATAATGGGAAGCTACACAAATATTTGACTGTTACAGATGGAA
CAGTGAAGCGATACAACGATGCWAAAAAAGAGTGGGGATTCACACAATTGATTTCTCTTCCAACATTCTA
CAACGCGAACGAAGGGTACCTTGTGCAGGACACAGCTTCTTTTGGTGCTGAGATCTTCATCGTTAACCCG
ACAGAAAAACAAGAGAAAGTCACATTCATATCAAACCCTCCAAACAATGTTTTCACTTGGAAGATACTTC
GTTTCTCTACCTTGGAAGATAAATTCTATTACTCTGATGATTTTCTYGTTGGAGACCGATACTGGAGACT
AGGATTTAACCCGAAAGGATCTGGTGGAGGAAGACCACATGCACTTCCAATCTTCCTATATGCTCAAGGC
CATAAGGCAAACGCAGTTGTTACAAACACTTGGGGAGCGGTTAATCTGCGGTTAAAGAATCAACGAAGCT
CCAACCACAAACAATTATATTCTGCAGCTTGGTACCCGATTCGAAGCGATTATGGTGTGGGAGTGAACAA
TATAATATTGATGTCAGAGCTAAAAGATGCATCAAAAGGGTATATGGTGAATGATGCCATTATCTTTGAA
GCTGAAATGGTTAAGGTCTCTGTGACAAACATAGTCTCCGTTTAAATATCACTACTTCTTTTTCAACAAC
AACCTTACGAATAAAGTGGACTTTGATGAGTTTAATTTGTTATACGACAACGTTGTTGATGCTTGTGATG
TWATCGTTGTTTCTGCTCTCCGAGTTTTCGTTTTACTTTTTTTTTCATGTTTTGCTATCCAATGAAAATA
AAAGGTTTAAAACTCTCCTTTGGTTTTTAAAAGT
>gi|4714010|dbj|C99886.1|C99886 C99886 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 43-2, mRNA sequence
GGCTGAGGAGTACAAGAACAACGTTCCCGAGCACGAGACACCAACGGTCGCAACAGAGGAATCACCAGCG
ACGACAACAGAGGTTACGGATCGTGGATTGTTTGATTTCTTGGGGAAGAAGGAAGAGGAAGTGAAACCTC
AAGAGACAACGACGCTGAAGATTGAGGCGATGGTGAGGAAGGTTATGGCTGAGGACGAAGGTGAAGAGAT
GAGAAGGAAAGTGAAGAAGTTGAGAGACACGGCGGAGATGTCACTTAGTATTCACGGTGGTGGTTCGGCG
CATGAGTCGCTTTGCAGAGTCACGAAGGAGTGTCAACGGTTTTTGGAATGTGTCGGGGACTTGGGACGTG
GTGCTTAGTAATGGTTACTGTTTTCTAGCTCTTTAGTGGTTGAATTTACTTGTCGTTTCTTAATGTGTAT
TTTTCATTGTAATAGAATAATCGATGTTTTGTAATATATTAATGTATTTGATATTTCTCAACTAATTTCC
ATTGTAATATTG
>gi|4714009|dbj|C99885.1|C99885 C99885 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 43-1, mRNA sequence
GGCGAGGGAATGGAGAGTTGCTGTCGGAGCGTCATAGCTTCAAGGACGTTTCATCTGCGGTCAAGTGGCC
GTCTATTTCCCTCTCTTAGCTTAACTCATCTCAAGGGCAAGCTATCTCTCTCCATCAACTCGTTTTCCTC
CAAGATTCAGTCTCATGCTCTCCGAGGAGTTGGTATAGGCGAGTCAGATAAGAAAAATCCCCTGCCGCGA
GGGGCCGGAGAAGGAGTCAAGGAAGATGCGAGGAGTAAGCTGCTTCATGTAGTTTTGGTCTCTCCTCAGA
TTCCTGGGAATACAGGTTGCATTGCAAGAACATGTGCTGCCTCAGCTGTTGGTCTGCATTTAGTCGGGCC
ATTAGGTTTTCAAGTGGATGACGCCAGAGTTAAGCGAGCTGGTTTGGATTATTGGCCCTTTGTGGTTGTC
AAAGCGCATAGCTCATGGGCTGAATTTCAAGAATATTTCAGGCTTCAGGAAGGGANAAAAAACCAATGAT
ANCTTTTACCANNAAGAAGAAACAAGGATACTTTC
>gi|4714008|dbj|C99884.1|C99884 C99884 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 42, mRNA sequence
ATTTGTAATAATCTTCGTAGAAAAAATGGATTCTGATTCTTGGAGTGATCGTCTCGCATCGGCTTCAAGA
AGATATCAGCTCGATTTCTTGTCTCGATCTGACAATTTCTTGGGGTTTGAGGAGATAGAAGGAGAAGATG
ACTTCAGGGAGGAGTATGCTTGCCCGTTCTGTTCAGACTATTTTGATATCGTCTCTCTATGCTGTCACCT
AAATTCAATTCACCCATGGTACCCGGATCCTCGAATTCAGCTTGGACTTAACCAGGCTGAACTTGCTCAA
AAGGTGGGGACTACCCACCAAA
>gi|4714007|dbj|C99883.1|C99883 C99883 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 41, mRNA sequence
AAAACAACGCGCATTTTGGTTTCTGGTTATATGGGATCATGAGTGTTTGCTACCACGCATTATACCTTCC
TCTTCTTTACATAACGTTCCTCGCAGACTTTTTC
>gi|4714006|dbj|C99882.1|C99882 C99882 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 40, mRNA sequence
AGTTTTTGATCAACGAGTTTAACCGTTGTTCTTATGAGATTCCTCATAATTGGTTGTTACTCGACTCGCT
CCCACTCGCTAGAGAGAACATGAAGTCTGTAGAGCCAACGGTTAAGCTAAGTTCATCGTTGGAAGCGCTT
GCTGACTACTATAGTCTTACAAGGGAGGGTGATGCTCACAGGGCCTTGTCAGATGTGTTACTCTTATCTA
AGGTGTTCCAGAAACTCACCATTGATCTCAAGCTCTCACTCTCTGATCTCGTCCTTCGCTGTCACACTGC
ATCTGATATCAGTGCTGCCATGGCCAAGAACAAGAAGGCCTGAAACATTTTAGACATAGCTATAAGCTTA
TTTTGGGATATTCATCTCTCATTCTATTGTTAATGTACCTAACTCTGAAATTATGTAACCGATTATTTAA
TCTGATCTTAAAATCAAAAAAAAAAAAAA
>gi|4714005|dbj|C99881.1|C99881 C99881 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 39, mRNA sequence
AACTNNTCCCAAAGGTGGGGACTACNNAGCANCCCTANTGCTNGACANNTCNTGNATNCCTCTNCNGCTA
AGTTCGGGCTNCCTNACGTCCCAACGCGGCGCAAGAATTAATTANAGCACTTNTNNCAGTCTCCATNACA
ATCTNGGAGTGATGCCANACTTGACAGGTCANCGACCNCCGACTACGATNGTCACCATNCNCNGCCTCNC
AGNGATTACANGCTNAGGATAACCCGGTGNNACCNCNGTTTCGNAGCTGCTGNTCACTNGNNGAGATAGG
TNNTGTGGATNATTNGTA
>gi|4714004|dbj|C99880.1|C99880 C99880 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 38, mRNA sequence
GGACTCGAGCAGAGCCAGCAACGGTTCGTATGGGTGGTTCGACCACCGGTCGACGGTTCGTGTTGTAGCG
AGTATGTCTCGGCTAACGGTGGTGGAACCGAAGACAACACGCCAGAGTATCTACCGGAAGGGTTCGTGAG
TCGTACTAGTGATAGAGGTTTCGTGGTCCCCTCATGGGCCCCACAAGCTGAAATCCTGTCCCATCGGGCC
GTTGGTGGGTTTTTGACCCATTGCGGTTGGAGCTCGACGTTGGAAAGCGTCGTTGGCGGCGTTCCGATGA
TCGCATGGCCACTTTTTGCCGAGCAGAATATGAATGCGGCGTTGCTCAGCGACGAACTGGGAATCGCCGT
CNGATTGGATGATCCAAAGGAGGATATTTCTANGTGGAANATTGAAGCGTTGGTGAAGAANGTTATGACT
GAAAAGGAANGTGAANCGATGAAAANGAAAGTGAAAAAATTTGAAANACTCNGCGGANATGTCACTGAAC
CATTGACNGTGGGTGGTTTGGCGCCCCAAATCCCCTTTTGCCNNAATTCCCCCAAGGAATTTTCCACCGG
TTTTTTGGAAACNTTTTCCTTGGAACTTGTTCCCCTTTGTTGCCTTAAAAAAA
>gi|4714003|dbj|C99879.1|C99879 C99879 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 33, mRNA sequence
CACAAATGGAGTCTAGGTTTCACATTACTTGCTTTCCTCTTCATCACTTCCTCTTCCGCTGAGCTCATCA
TTAAACAGGTCACACAGGGCAGAGGAATAGAGTACAACAACTCTTACAGTCTCACGTCGAATCTTGGAGT
GACGACAAGAGAGTTGAGAGACGAGCGACCATCAAGTAAGATAGTGACAATCACAAGCTTCTCTGTGATT
AAGGACAGAGGAGAACCCTATGAATCATCTATTTTTGAGGCTGCCGGTTACAAATGGAGATTANTTTTGT
ACGTGAAGGGTAATCCGAAAGGCGGTATANATAATCATATTTCACTTTACGCGAGGATAGAAGAGACAGA
AACTCTTCCAAGAAGGTGGGAAGTGAATGTTGATCTCAAACTCTTTGTCCACAATCGGAAGTNAAAGAAT
ATTGTCTGTTACAGATGGACATGAANCGATCCACNATGCNAAAAAAGATGGGGATCCACATTGATTCTCT
CCACATCTCACCGAAGAAGGTACTTTCAGACCACTCTTTGGTGCTGANACTCTCNTTACCGACGAAACAG
AAATCCTTCTTCNACCNCCNAAANTTCCTGGAGACTCTTCCCNCTGGAGAATCATANCGAGATTCTNTGA
ACGAACGGAACAGATACCNAGGACGGTGAGAAACATNCTCACTCTTTTCCAGCTAGGAACCTTTTCANNT
TGGGACGTNCCCCGTNAGACCCAACCCCCCCCTTNTCC
>gi|4714002|dbj|C99878.1|C99878 C99878 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 31, mRNA sequence
ACCAGGGGGCATNCAAAAATCTAAATTAGATNTGAATGGGACAGTCTTTNGTCAATAATNAAGATAATCA
AGAGATCCTGTGTGCCCTAGTACACCCTGCTGTAGNTGCCTAACGTCCATGTACTATGTTACGTGTAACT
GATGGGTCTGATGAGCCGTTTGTNCGGTGGTATCCCAATTCTCAATNAAATACGAATGTGCTGGAGAA
>gi|4714001|dbj|C99877.1|C99877 C99877 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 30, mRNA sequence
GACGAAAGCAATCAGAAACTCAGGTGAATCAGAAGCATGATTCGAGTTACGAAACCAAAAGCGATCATCG
AATCACTGAGTTACCATCTTATCCAAAGATGCTCCGCAAGTGGAACTCCTAAAGGAAAAGCAAAGCTGAA
GACAGGTCAGCCATTGAAGCGTAACAAACTCTCCATCAAGAAAGGTGGTGGCGGCGGCGGAGCACCTGTT
GAAGGAGAGGAAGCAGTTAAAGGAAAAGGTAGAATTTCCGATGAGAAGCAGAAACTCTACGAGCAATGCT
TAAACGCTCCTTGTCCTGTTCGCTACTTGACCCCCCAAGAGATCGAGCGTGAGGCGCAACGTGAGAAGCT
AGGTTTGATTAGTAAAGAGAACAACGAGATATGGAGATCCAGAAGAAAGGAGGAGTATGCTTGCCCGTTC
TGTTCAGACTATTTTGATATCGTCTCTCTATGCTGTCCCTAAATTCCATTCACCCATGGTACCCGGACCT
CNAATTCACTTGGACTTAACCAGGCTGACTTGCTCCAAAGGTGGGGATCCCCAC
>gi|4714000|dbj|C99876.1|C99876 C99876 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 29, mRNA sequence
CAAATTCTCTCCGTGTTTCCTTCTGCTTCAGGTGATATTTTAACAAANTTCTTANTACAATGGGATCTGT
TGATGCTGCTAATGGAANTGGGAAAAAACCTACAGTTATATTTGTTCTTGGTGGTCCAGGAANTGGAAAA
GGTACCCAGTGTGCTTATATTGTTGAACATTATGGTTACACACATCTGANTGCTGGANATCTTCTTAAAG
CTGANATTAAATCAGAACTATGATCCAGAATATGATTAAAGAGGGGAAGATTGTACCTTCTGAGGTTACT
ATCAAGCTTCTACAGAAAGCTATTCAGGAAAACGGGAATGACAAGTTCCTCATTGATGGTTTCCCTCGTA
ATGAGGAAAACCGAGCAGCATTTGAAAAAGTTACTGAGATTGAACCAAAGTTTGTCTTATTCTTCGATTG
TCCTGAGGAAGANATGGAGAANCGCCTGTTGGGCCGAAACCAGGGGAGAAAAGATGACAATATTGAAACT
ATNANGAANCGCTTTAAGGTGTTTCTTGAATCTANCTTACCANTGATTCNTTACTACCAAACCTAAGGGG
AAANTTAGGAAGANTAATTGCTGCCAAACCCCTTTGAAACTTTCTTCCAAGAANGTNAAAGCANTTTTTC
CNCCCGAAACTNAAAAAGGTTA
>gi|4713999|dbj|C99875.1|C99875 C99875 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 26, mRNA sequence
TGGGGCNACCANCAANCTAANGAAGATCGAATTGGACACACTCNCGTCTATCACGCCAACANCNCTGCAT
CTCTGTCTGCCCNATACGACTGCACGTG
>gi|4713998|dbj|C99874.1|C99874 C99874 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 25, mRNA sequence
GGCTGAAGCAGCGAGAAGACAAGGTGGTGGGAGACCATTACCGCCACCTCCGAGAGGCGTTAACCAACAA
CCTCCTCGCCCTAAACCTGAACCTGTCGATCGTGAAAAGACATGTCCCCTTCTTCTTCGTGTTTTCACCA
AGAGTGGTGGTCATCATACTAGTGAAGATTATGCTGTGAGAGGCAAAGAACCAAAGGATGAAGTTCAAAT
CTACACTTGGAAAGATGCCAGTCTTCGCGAGCTAACAGATTTGGTTAAAGAAGTTTCTGTANCAGCTAGG
AGAAGGAATGCTAGATTGTCTTTTGCGTTTGTTTATCCTAACAATAAAGGTGGCTATAATGTNANAAAAG
TTGGGGAGACGATGGCTTATCCNAACCGAAAACAACCANATGACANTAAAACNCTTTCCCAACTTCCGTT
TGAGATTGGAGATTATCTGGATGTGGCAATTTATTANGAGGTTTCTGTTTCTTGTTAAGTGGGATTTGGG
TGCGTGCACCATGGAAGAAGTACACATTCNTATGGTTGTATCATCTTAAACTTCGTTTANACATGTTTGT
NTTTTTT
>gi|4713997|dbj|C99873.1|C99873 C99873 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 24, mRNA sequence
GAGGAATTTTGCCAACATACAGTTACAACCATTTGGCATTACCATGGAGGATGCGTTGTGGGCAGAGTGG
TCGATGGGGATTATAAAGTTATTGGTATCGACCGGCTTAGAGTCATTGATATGTCGACCGTTGGTTATTG
TCCCGGGACAAATCCTCAAGCCACGGTTATGATGCTTGGCAGGTATATGGGTGTGAAGATCTTGAGAGAG
AGACTCACCAAGAAGTAGGGTTTTGAATCGGATCAGGGGTTTTGGGAAAACGTTATATTAAAAATGAAAT
GAATCAAGATATTACTAATCGATGTTATTAATAGCTGAATATGTATTGTTCTTGGTAATTTCTGTTTGGT
ACTTATTATTAGACCAAACTGAGATGTATACGGAAATATATGTATAGACTCATTCCCAATTTTCAAAAAA
AAAAAAA
>gi|4713996|dbj|C99872.1|C99872 C99872 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 23, mRNA sequence
TTTNGGNGGNCCTNGTAAGGAATTCNTGGGTCGACCCACTCNTCCGATTTGTAATAATCTTCGTAGAAAA
AATGGATTCTGATTCTTGGAGTGATCGTCTCGCATCNGCTTCAAAAATATATCAGCTCGATTTCTTGTCT
CGATCTGACAATTTCTTGGGGTTTGAGGAGATANAAGGAGAAGATGACTTCAGGGAGGANTATGCCATGG
TACCCGGATCCTC
>gi|4713995|dbj|C99871.1|C99871 C99871 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 22, mRNA sequence
GGACGAACCGGTGTACCACGATTTGGTTCGTCACTGTCTGGCCTACCCAAAAGCGGATGGAATCTTGGTG
AATACATGGGAAGAGAATAGTTCAGGGAGGAGTTAGACTANCCATGATACTAAACCGGGTTTTTAGTGAC
GATCATGCTATTGCTGGTGTTGCTGCCACTTGAACCAAACCCGACATACCGGGTCATCAAAGCATTTGAT
TAAGAGATTATTTGATACATTCACAAAATTAATTAAGGCTGATCAGACATTCTTTTCTTTTAGTAGCTTT
ATCTATGTGACAGCTAATGCCTGTGGACTGCTTTGTTTAGAAGTGTTTAGCATTAGATCATATGCTAATT
CAATGTTATTAAGTCATCGTATGATCGTTTTAG
>gi|4713994|dbj|C99870.1|C99870 C99870 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 21, mRNA sequence
GCAAGAGCTTTGATAAACTATCGTATCAAGGAAAACATTGGCACAGGAAGCTCCTCGAGTGCCCCAGTTC
CATTTGCAAAGAAGTTCTTTATGCAGAACCTTAGACCAACAAGTCCACAGCCTTCTCCTGCAACCACATC
GAGAATCTTACCCTTTATTTGCCCAAAACAACCTTCCAGAAGCAGCANATCATCCTTAGCAGCAACTTCC
GGTATTGACAGAATTATGGCAGCAGCCTTGGAAAGCCGCAGCTACCAGCGGCCTCAGCAGAGATTTGCAA
ATCCGCCTTATGTTCCTATGAGGCAATTTAGATCGCAATGCCATGGGATGGCTCCACCTGTCNCAATCAG
AACCGCTGTACCGGTCTTCTCTGCACCTCCAATGCCTCCTCCACCATGTACAAACAACACTCAGCTACCT
TCTTCTGTGTATGTCCCATCGCTGATGCGAACTGCACCACCTGTGANGATCGCGCCGCCTGTCACAATCA
GAACCGCGGTGCCCGTATTTGCTTCTGCGCCACCGGTTAGAATTANAACCGCTGTGAAGCCCACAGTTGA
AGGCAGGAGAAAACCCGCNTATCATCNNTCCCAGAAAAAGGAGAATTATNCCCNGTCTTGGCCTGATANT
CTTGAAAATT
>gi|4713993|dbj|C99869.1|C99869 C99869 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 20, mRNA sequence
AGCTCGTCAATCAATGGCGTCGTCTCTATCTCCACCGGAAGAAGCTTCGTATCACCACCGTCATACCAAA
AGGTACACCTCCTCCGCTTCCTCCGCTTCCTCCACCACCAACGGAACCGTCGAATCATCGGTTTCCGATT
TCGTCANACGTCCCAAAATCTCTCATCCGAATTACATATCAAGTTCCGAGATCGAATCAGAGTTTTCTCA
TCACGATCCAGATTTCGCAAGAATCNACAACGGTAGTTTTGGTTGTTGTCCGTCATCAATCCTAGCTTTA
CAACGAGATTGGCAGCTCCGGTTCCTTCGTCAACCGGATCGATTCTATTTCGACGAACTCNANCCANAAA
TCTCCGATTCTAGATCTGTAATCNAACGGTTAATAAACGCCGAGCATGGCGATGAAGTCTCGATCGTCGA
TAACGCAACAACCGCAGCTTGCAATCGTTCTTCACAAACCCCTTGGGCTTTTTCCTTGAAGGTCGGTTCG
ATAAAAGGCGNANGCGGTGGTTATGCTTCATTAAGCTTATGGGCTCTGTTGAAAAAAA
>gi|4713992|dbj|C99868.1|C99868 C99868 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 19, mRNA sequence
AAGAGTATTCTAAAAGCAACCTTTTCTTGGTGGGGAAGTCACCGGAAGGTTCTGTAGCGTCAGGGATAAA
CGTAAGAAGCGACACGCCTGAGCTTGGACCGATCGGGAATTTGTTAACGGAAAGCGAAAGTGTTTCGACG
GTGGCATCAGTGTTGGTGGTGCAACAGTATATAGCAAGCCGTCCGGTCGGAATTTCGAAGAACGTCACGA
CTGAAGAGTCTCAAGGAACAAAGTTGAAAGACTTTGTAGCAACAATGCAATCAAATGAGAAATTACAGTC
AGAGATGTCAAAGCTCCGTGAGATGGTAGAAGAATATGCTAAGCAATTCCCAACGATTGGGTTCGAGAAA
GAGACGATGAGATACCNNGAGTAGTTTTCATCGTGTGGATTGACACGTTTCCCCATCTCTGANATGCTTT
AGTGATCATGGACCANAGGCGCCACCGATGGTCTGAAGTATCGCTGAAACTAAAGTTGAACTAAAAAAAT
CGCACTCCAATGTTTGTCTCTTACCCTTTCCCTTTTGTCTCTCAAATTTTTATCTTTGGCTT
>gi|4713991|dbj|C99867.1|C99867 C99867 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 18, mRNA sequence
GTCGGCTCGTTCTGCGATCACNNAGCAAAAGCTGGCTCGATCCTTTGGGGAAAGTCTGATTGGTGCCTCN
CGTTCGGNGGTTTCGACTCNAGGACCGGCGATTCGGTNCTTCNCTGACGAGANNGGTCGTGTGCTCANCG
GANAGGAACNCGCGANACANAGCATGTCTATNCCANAAATGGAGAGGGANNGACTGGAGAACAAGAGGAA
ACTCGAGCCAGATANGCTANATGGTGAGAAAGGANGTGCCCACAANAANCCTGACACCAGCNAGCCATGA
GTTTATCACTCACAGTATACNTGAANCCTGTCNTAAGGCAAGCAGTAGTNAAAAACAATAATGCCTTTGA
CCTGGTTTCTCTCTTGGTATGAGAGATCTTGTACTTGTNCAGAGATCTTTGTCCNTCTGACGTGTGTGTT
NGTNTGTTCTAANAAATCAANTTTNCATAATCC
>gi|4713990|dbj|C99866.1|C99866 C99866 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 17, mRNA sequence
ATTTCGATTCTCTGTAATTAAAGACAAAATTGGAATAGAGGAGACATTGTCTCTTTGATTCTTGAGCTTA
TTTGGGGGAGAGAAAGAGAGAGCGAGAGGATCTGATGTGTATCTCAATCTCGCAAGTCTCTAGATTGAGA
ATCCATTCATTTGGAAGTTCTTGCTGTGAGCGTGTTCATGGATGGATCAAGAACAGCTCTAGCTTGAAGC
TGCTTGATGTTAGAGCTTCTTCTGTTGATGGTAAAGCAAGATGGATCAGACGTAACGTGAGTACAACTAC
ACAAGGTAGTAGAAGCAACACTAANANCAGTGTGTTGGGAGGAACAGTTCCTGTTACCAGGGATTATAGA
TNAAGAGAGTANAACCNAGGTACAGCCTTTTGGTAATCTTCAGCAACGGCTTGCGCNAGATAAAGATCTG
TCTAAGCTCCTCNCGGTTTATAGTCTCTGATCTTTGAAACAACTGGGTTTGCATCNGGAAAAATGAGCNG
ATAATTTGAAATTTGCCANCTCCGGAATNTAACTTNGGTGGGTNGGGGTTCNACCACCATTTTCAAAANC
TCNTTGTTCCACCCCCGGGGGTGTTTNGTTTCCCC
>gi|4713989|dbj|C99864.1|C99864 C99864 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 15, mRNA sequence
AGGNTCCTCTACGATCGACCTGACTANNCTACNNCTGCNTGCGACATCTTTTNNCTTCTCTAATGTNGCC
TACANNTNTNCCNGACNTGGTGGTCNGANCCTCAACTCCAANCNNGACANCTNNANGNTGAACTGGTNCC
ACGTGTGAGGACTATCCACCAATGGACCGATATCAAAGAAATGAAGGCGATACAAGTCCACCAATGGACC
GATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGAAATGAAGGCGATACAAG
TCGACCAATGGATCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGAAAT
GAAGGCCCNGATATCTGAAAAGCATAATAAATGAATCAATATCTAAAATCTGGTGTTTTTCTCTCTTTCT
TCTTCCCAACAATGATTGAAAAACTCTTTCTTGTTATGAATAAAGATGGATGCCCATTATAAGGGCCATC
NTCTAAGCCCATCATCTANATGTTTCTAGGGTTTTACCCTTTCCTTGTTCTCCTATATAAAGAACCTTTA
TCTCATGGATACCNCTCCTTCTCT
>gi|4713988|dbj|C99863.1|C99863 C99863 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 14, mRNA sequence
CAAAGCGTTCTAAAAGAATTTCAAAGAAGAAGTGAAAATGGAAACCACTGCTTATAACACAACATCACGA
ATTGGAAACTGGTCATCGGCTATTTCTCGACCTCTACAANCATGTGGATCTTTCAAGTGCCAATTACCAC
CACGAANAGGTGTTATTGTAGCTGANCTTCGAAACTCAAACTTCCGATGGAGGAAAGCAACGACAACAAG
CAGAGGAAATGTTGCAGCNGAGGCAGTTAAAATTCCTACGTCAGTACCAGTAAGAGTGGCGCGTGAGCTA
GCTCAAGCAGGATACCGCTATCTCGACGTGAGGACACCAGACGAATTCAGCATCGGACATCCGACTAGAG
CCATCAACGTACCTTACATGTNCAGAGTCGGATCANGAATGGTTAANAACCCGAGTTTTCTAAGACAGGT
CTCGTCCCACTTCAGGGAAACACGATGAAATCATAATCNGTTGTGAGANCNGTCCAATGTCTTTATGGNC
TCACTGATCTTCTCCCTGCTGGCTTCNCGGGGANCACNGACATTGCTGGANGATACTCCCTGGACAAAAA
TGACTGCC
>gi|4713987|dbj|C99862.1|C99862 C99862 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 13, mRNA sequence
AGACGACTTTCBACTGAATATCTAGCTAGCTCACACTCTAGCTGTAACTGTGTTTATTCTCACTAGCTAA
TAATTAGATATTATATATTGAGTTGGTTTAATTTTGCTAGTAAAGGATGGACTGATAGGGTTTGATCAAT
GGGACAAGAGAGCCACTAAGGTGAAGGGACATGACTTCATTGGTGGAGCCAACAAGCTTGCCTCCGACAA
AGACAGCTGGAACCGCCGTGGAACAGCCGAGCCGGAGAAGAGCCTTCTCGATCTCACGGCAGTCCGGGTC
GTTGTCGATCTCGTGGATGGTTGGTTGAACCCTAAGGTCACGGAACAGGATCTGAACGGCGTAMAGAAGA
ACAACATGAGCTCTTCGTGAAGATCACCACTCCTTTCTCTGAAGACATTCTCATCACTTTGTCCATGAYC
CTCAGAAGTCTGAAGATCTGATGATGGCGAGGGGTTWAAACTTTAGCGTTTTGA
>gi|4713986|dbj|C99861.1|C99861 C99861 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 12, mRNA sequence
CACGAAAGTCTTACGCGTCTCCTTGAAGATGCGAAATCTATTATTGAGAAATATTGGAAACTCAGATGGA
GCAGACACGTTTGCAGGAAGTACAGGTACATCAAAAAACTCGAATCGATAGAACTTGAATTAGTAAGGGT
AGCACGTGAGATACAAGTCCACCAATGGACCGATATCAAAGAAATGAAGGCGATACAAGTCCACCAATGG
ACCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGAAATGAAGGCGATAC
AAGTCGACCAATGGATCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGA
AATGAAGGCCAGATATCTGAAAAGCATAATAAATGAATCAATATCTAAAATCTGGTGTTTTTCTCTCTTT
CTTCTTCCCCACAATGATTGAAAAACTCTTCTTGTTATGAATAAAGATGGATGCCCATTTATAAGGGCCA
TCATCTAAGCCCATCATCTAGATTTTT
>gi|4713985|dbj|C99860.1|C99860 C99860 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 11, mRNA sequence
CACGAAAGTCTTACGCGTCTCCTTGAAGATGCGAAATCTATTATTGAGAAATATTGGAAACTCAGATGGA
GCAGACACGTTTGCAGGAAGTACAGGTACATCAAAAAACTCGAATCGATAGAACTTGAATTAGTAAGGGT
AGCACGTGAGATACAAGTCCACCAATGGACCGATATCAAAGAAATGAAGGCGATACAAGTCCACCAATGG
ACCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGAAATGAAGGCGATAC
AAGTCGACCAATGGATCGATATCAAAGAAATGAAGGCGATACAAGTCGACCAATGGACCGATATCAAAGA
AATGAAGGCCAGATATCTGAAAAGCATAATAAATGAATCAATATCTAAAATCTGGTGTTTTTCTCTCTTT
CTTCTTCCCCACAATGATTGAAAAACTCTTCTTGTTATGAATAAAGATGGATGCCCATTTATAAGGGCCA
TCATCTAAGCCCATCATCTAGATTTTTCTAGGGGTTTTACCCCTTCCCTTGTTCCCCCTATATTNAAAGA
AANCCCTTTTATCTCCCATTGGGAAATAAACCCC
>gi|4713984|dbj|C99859.1|C99859 C99859 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 10, mRNA sequence
GTTNACGANCANGGTAAATANATGATNNTNAANNTTNTCANCTNGATACACTCCGCNNATANTTCCCNGA
TNNTCCACTGCGGTGGTTCGGCNCCNNAGTCGCANNTGCNCATTCACCACCGATTNTCTACGGNCNCTGG
NNTCTGTCGNGGACNTGGGACGTGGTGCTTANTAATGGTTACTGTTTTCTAGCTCTTTAGTGGTTGAATT
TACTTGTCGTTTCTTAATGTGTATTTTTCATTGTAATAGAATAATCGATGTTTTGTAATATATTAATGTA
TTTGATATTTCTCAACTAATTTCCATTGTAATATTG
>gi|4713983|dbj|C99858.1|C99858 C99858 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 9, mRNA sequence
CCTACGGAGGTCTANNCCCCCTTCCGGTACANGNNCGNAATNNNCAGGNCGGTNCTNGCTTACGANAAAT
GTNAGCAAATGAGAAGGAAGTTGANGANGTTGACAAACGTGGCGGAAATATCACTGAAATTTACACAAGT
GGNGGTACGGCGCNNAAATCTCTCTGCATATTCACGNTGGAGTNTCNGCGGTT
>gi|4713982|dbj|C99856.1|C99856 C99856 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 7, mRNA sequence
TNAGTCGNCGGNNGCTCCATAGGATCCTNACTTACGTACNCNTGCANGCGACTTCGNNACTNNTCTATNC
TGTCANCTAAATNCAATTNNNGGGGCNNCATTANAATCCCNCTNCTNCCACTNCNNATCCGGAAACCATG
NCNACCAGGGANTANCGGATGTNGCTTCTCGGANTCCGCNGGCCCTNTATGAAAGTTCAANGTTTNTGGG
TTCCNGGGGGAATATGGTCCCAAGGCTNANNCTTAAGAGATTTGACTAAAGGGCGNCCGNTCTTTAGGAG
CCCNACTAACATCCGCTTGCNTNCNACTTCCTACCTCTTCTAAAGTGTCCCTGGATNCANTNCTCNCATG
GTNCCCAGANCCNCGNATNCNTCTTGGACTTCACCATGCTGAGNTTNCTCGGGGAGTGGGGACTACCGCC
AAAAACTTNNNNGAATTGACNAAAGGGCGGNCGCTCTANAAGACCANCTTACTTCCCTNCNTGCNACNTC
TNCTCTTCTATNNTGTCCCTNNATCCNTCCCCCNTGGTNCCNGATCCNCCAATCNCTTGGACTTNNCCNG
GCTGAACTTGCTCCNNNGGTGGGGAA
>gi|4713981|dbj|C99855.1|C99855 C99855 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 6, mRNA sequence
CCCGCCCTTTNAANCGAGTACAANACNGGGGGAAANGTTCCGAATAAAAAGTGGGG
>gi|4713980|dbj|C99854.1|C99854 C99854 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 5, mRNA sequence
GNANTCGATCATACCCAGNANAGGTGTCGTATGAGGTGGTGTCNANCAATCNGTCNCACGGNACNTTGTG
GTTGCGACTTCTTTTCGGTGTNCCNCGNCCTTCCCGTGTAATANGCTNNATNANCNCAAANGATTTGGTG
ATTGAGNAANATGGGGAATCANCGTCNCTGGATCTCCNCCAGTNNNCTACTAGGTCNGTACNNTNAGACA
CCGGCNCGGANGGANTCTGCNNNACCGCTTCNAGACAATCTTNTATGTNAATACNTCANACGAGGCATAT
ACAANGCAGTTGAAGCTGGTANCTAGCATCTTTAATCGGGCCAATTCTTCGTCCATACAAGGATACGNGC
TTGTCCCGCATNTTGCCNCCCNCATCCGGTNTGGAGGATATGTGATCGNCTCTTGAGATGGGATCGTGTT
GTTTCGCTAGCCGATCTCATTCTCCGTTCCCAGAAGAGTTAGAANAGATTATTTATGNTAANACGGCNTT
CAGAATTGTTTGTTAAATTTGTTGCCNAATCCTTTTGNATANTTNTTCCCTCGGGGTNCCCTCGTTT
>gi|4713979|dbj|C99853.1|C99853 C99853 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 4, mRNA sequence
ATGGTGGTGACGTCTTTCTCTTCAGCGCCGCCTATCTTCTTCTTACCTGGAGCTGATGCTCAGTTTTCTT
CTTCCAATGGAAGGTTTGCTATTCCTTCCTCTTCTCTCGTAAAGGGACTAAGAAGACACCAAGATGCAAA
GTTGGTGGGCAACAGAGCCAGAGTTGGAGTANTACGAGTCCTAGCGAACCCAAATGTATCTCCTCCTCCT
CCTCCAGGAAAAGCAAAGGTAAAAAAAGAGGTAATCATGGTAGACCCTCTTGAGGCTAAGCGGTTAGCTA
GTAAGCAAATGGAAGAGATTAAAGGCAGAGAAAAGCAACAGAGAAGGCGTGAAATAGAGGCTATTAACGA
AGCATGGGCAATCATANGACTCATGATAGGGCTGGTGATCGAAGCTCAAACGGGGAAGGGTATTCTGGCT
CATTGGCTGGTTATTGGTCTGCANTTGTCCATTTGTTCACTCCATCAACTTANAATGAATTAAGTTTCAT
TTGGTTTTCTCTACTCTCAACTGTGACCAAATCTAATGTTGTGTTCATGCCAGTTAANTTGTTAAACACA
TACCTTTGTTAATCCTCCCTTGTTTCAAAACTTCNAATCCTGCCNTTTGTTAAAAAACAAAATTTAAANA
TTTTACNCTTAAATAAAANCNACNTCCCTTTTGTTAC
>gi|4713978|dbj|C99852.1|C99852 C99852 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 3, mRNA sequence
AGNCNGGNGCCGCTCTACANGAACCAAACTNANNTTNACNTNCGNNCTAATCNCNCCTCTNCGNTNCTGT
AACATATNTTCNCTTACNCCNATGGTCCCACGGATCCTCTACTTCTGGGTCTGANGACACTGNNNGAAAA
TAATCACTATCACCGGATNAGTATATCTTAGCCCCTNCCGTCCCAACTAAAAACGGGAATCGTCTCTCTA
TGCTGTCACATTGATGAAGATCATCCTATGGATGCAAAAAATGGGGTATGTCCCGTTTGTGCGGTGAAAG
TGAGCTCTGATATGATTGCTCATATAACCCTACAACATGCAAATATGTTCAAGGTGACGCGGAAAAGGAA
ATCAAGAAGATGCGGGGCTCAATCCATGCTATCGATCTTGAAGAGAGAGTTTCCTGATGGAAATTTTCNG
AGCCTATTTGAAGGAACATCACGTGCTGTATCCTCTTCTTCTGCCAGTATACTGCTGATCCTTTACTGTC
TTCATTCATTTCCCCAATGGCTGATGACTTTTTCCTTTCTGAATCAATCTATGTGCA
>gi|4713977|dbj|C99851.1|C99851 C99851 Arabidopsis thaliana library (Motohashi R) Arabidopsis thaliana cDNA clone 2, mRNA sequence
CCATGGTACCCGGATCCTCCGAATTCTTTTGCTTTNTACCCTGGAAGAAATACTCATAAGCCACCTCTGT
NATTTACCCCCAATCTTCACAAGAAAAACTGGNGATTTNGATATCGTCTCTCTATGCTGTCACCTANATT
CAATTCACATTGATGAAGATCATCCTATGGATGCNAAAAATGGGGTATGTCCCGTNTGTGCGGTGAAAGT
GAGCTCTGATATGA
>gi|4699972|dbj|AB018246.1|AB018246 AB018246 Arabidopsis thaliana library (Shinozaki K) Arabidopsis thaliana cDNA clone CIC3B1-1, mRNA sequence
AAGATTGANGCNATGGTNACNAAAGTTAAGGCTGAGGACNAANGTGAATAGANGANAAGGAAANTNAANA
AATNNAAACACNCGGCNGACATGTCACTTAGTNTTCTCCGNGGTGGTTCNGCCCNTGAGTCGCNGGGCNC
ANTCGCCAAGGAGTGTCAACGGTGNCCTGGGAATGTGTCNGGGACGGGGGACNTGGGGNNTCCCTAATGG
TNACTG
>gi|4239698|emb|AJ132770.1|AJ132770 AJ132770 Arabidopsis thaliana library (Josefsson LG) Arabidopsis thaliana cDNA, mRNA sequence
TGGATCCAGGATGGGGTTTCTAANATCAGACTCCGACCAAATCCCAAACAGCTTGANNTAGTTCTCCAAA
CTCGCGAACTCGGATGAGCTTAACTCCTCCTTAACCCGATATTGCCANGGGATCCANTATCNGGTTTGGT
GACCGAACGCATGGGCATTGATATCCTTCTTTCTCCATCCACAGACTTTGACTTAAGTTTGTTTAACCCC
CATAC
>gi|4239697|emb|AJ132768.1|AJ132768 AJ132768 Arabidopsis thaliana library (Josefsson LG) Arabidopsis thaliana cDNA, mRNA sequence
CGGGTTGGTGGGGAACCCATGGGTTGATGACTGTGCGGCCGCACGGGTTTCATCTGACAACACTCGCCTA
TCTCCTTAACCCCATACTAGATCT
>gi|4239694|emb|AJ132747.1|AJ132747 AJ132747 Arabidopsis thaliana library (Josefsson LG) Arabidopsis thaliana cDNA clone LJ119, mRNA sequence
GGAAATTCGAAACTCGATTGGTTGGTTGACTTCTCTCTCTTCTCTCCCTAATATTTTTCAGAGAGAGAGG
TTCTTATATGTTATCTCCGTCCGGTTTGTTTTTACCGGAGTTTATACTCGGATGAAGTCCGGTTCTGCTG
TTAGTTAGCCGTCAACACGACTTCTCCGTTGTCGTGTTCTTGCCGTCAACACAGCTTTTTCGTTGCTGTG
TTCTTACCGTTAACATGGCTTTCTATTGCCATGTCCTTTTGCTCATACAAAAGCTTGATGTTGAAGACTA
TGGCTTCTAGGATTGTTGAATCGGGAGAGTTTCGTATGCGCCAAATCTATTCTCTTTTGCCATAATATAC
TTCATCCATTGAGATTTTGCTTTTGGATCTGATGGTTTTCTAACGATGTGTGGTTTTCACTTCCACACAA
AAACGTTGGATCCATCGGATTTACGACAGCTTATGTTACCTGCGTCTAAGGTTTGGTTAAAAACTCATTT
CCATCTTAAATTTCGATTCCCTTTTGCTGCTTATAAAAATATTCAGAGATTCACTTATATTATCAAGGGT
GGATTACTTCAATCTCTACATCTTATTTCATGATTACGATGGTTTTCTTATGAATCTATCAATCATTTGA
GATTAGTAGATTGATTTGTTCTGTAATCCATTATTATCATTATCAGTGAGAAAAAAAGAAGAATTCGTAA
TCGGTTGTAGTTCCGGCAACGTATTCTGATTCACTGGATTTGGAATCTCTGCATGCGGTGAAGGATGTGA
AATAAACACGTATCCTCAACTTATCCCCATCGATGAGACACGTTCTTGAGTTTATCCTTTCTTGGGCCTC
TTGTTTGGGCTTCGTTGAAAGTTGTCTTTGATGTTTATGTAATTGGGTGTGATGTTATGTATTATTATTT
CAATAAAACTGCAGTTTCAGAGG
>gi|4239693|emb|AJ132746.1|AJ132746 AJ132746 Arabidopsis thaliana library (Josefsson LG) Arabidopsis thaliana cDNA clone LJ177, mRNA sequence
CTTTTCTGTCTAGAGAGAGAAGCTTTTATCTTTCATCGCCGTTAACAGGGCTATTCCGTTGCCGTGTTCT
TGCCGTCAACATGATTTTTTCATTGCCGTAGACATGGCTTTCCGTTGCCGTGTTTTTATGTCGTCGCTTT
TGTTAGGTGTTGTTTGTTTGCTTCCAATAAAGGGGAATTGTCTTTCGTCTCTGTCTTTACAGAGTTTTAT
GAGAGATGACACACCTATCTTATATGTTTATAGTTTATACAAGTGTTTTTATGTTTGTTGGATTTGAAGC
GAAGCTTAACCATCTTATGGTGACTTAGATCTATTTAGAACCTTTAGTTGGTGGCTTTTCTCCGGATCGT
CATGTTGGGTATACGGATTACTGAAATTTCAAGGATAGTTTGCAAATAAAATTGAAGAAAAGAAAGAAAT
TTCCTTCGCGATTTTAAGATGCCTTTTAGCCGTGATTTCAATTGTTCGGAGTTTTGATTCGTTTTGCAAC
CAGCTTTGTCGGTGAAAATCAGAAGAATCAATAGTCGAATTTCAGTTATCGGCAATGATTTTCTTCACCA
GAATCAGCATCTTAGATGGCGGTGGTGATGTCGGAAAGCTTTTAGAATTTTCATCCAACACGTGTACCAC
TGTTGACACGTTTGTTTGGGAATGAAACTAATGATAAACTTTCTTCAAGTTGAAGCAATATATTGTGTGG
GCCTTTATGGGCTGTAATCTGTTTTGTAACCCATGTTGTTATGAATAAAATCCTAATCTTGCGAG
>gi|4239690|emb|AJ132744.1|AJ132744 AJ132744 Arabidopsis thaliana library (Josefsson LG) Arabidopsis thaliana cDNA clone EM179, mRNA sequence
CCACGCGTCCGGTGTTGGCTGGCTCTTGCCCGGCAGCGTTGTTTCCATGAGCGTCGTTGGCCGGATTTGG
TTTGTATCCAACGTTGTTTTGTTTTTCTTTCAATAATCTCATAGATCTTATGTTGGTGATAATGGTTTAG
GTGATTTTTCGCTTAAAGATCTTTATTATCCAATTCGATCTTTTGAGTTTGAGATTTGCAGGAATCAATT
TAGAGATTTGCATCTTAAGTTGAAGAAAAGAAGAAGTTTTCGTTGCATATTAATATTGCCCTTAGCTGCT
AAGTTTTTATCTGGAAGTTCGATTGGTTTGTTTAAGGTGAAACCCAGAAGAATCAAACTTGCTTTCATTA
TCAATGTTGATTTTTCTCACCGGAATCAATCTCAGACGGCAAAGGAAGATGTCGGAAATGCTTTTAGATT
ACTCATCCAAACGTGTGCTGTGTTGTTTTCAGCTGTTGACACGTAAGATTGGTTGGAGCCACAATATCAG
TTCTTCATCTTTAAGCAATGTTCTTGGACTCATTTAGGACTTCAAATGTTCTTGTAATCTCAGTGTATGT
TGGGCTTTTGGTTTTTTAGCCCATGTATGGTTGGTTAACGTTAATAAGATTTTCCACTTATGAG
>gi|4239689|emb|AJ132743.1|AJ132743 AJ132743 Arabidopsis thaliana library (Josefsson LG) Arabidopsis thaliana cDNA clone EMR03, mRNA sequence
CCACGCGTCCGATAATGGTGTCAGAGTTCTCTCCCTTCTCTCTCTAGGATTTTGATTTATGTTCTTCTTT
GTCGTTGTCTTTCACCGCCGTTAACATGGCTATTCCGTTGCCGTGTTCTTGCCGTCAACATGGCTATTCC
GTTGTCGTGTTTTATGTCGTAGACATGGCTTTCCGTTGCCATGTTTTTATGTCGTTGCTTTTGTTAGGTG
TTGTTTGTCTGCTTCCAATAAAAGGGAATTGTCTATCGTCTCTGTCTTTACAGAGTTTCATGAGAGATGA
CACACCTATCTTATATGTTTCTAGTTTATACAAGTGTTTTTATGTTCGTTGGATTTGAAGCGAGGCTTTA
CCATCTATGGTGAATCAGATCTATTTAGAACCTTTAGTTGGTGGCTTTTCTCCTTATCGTCATGTTGGGT
ATATGGATTACAGAAATTTCAGGGATAGTTGCAAATAATGTTGAAGAAAAGAAGAAATTTCATTCACCAT
TTTAAGATGCCTTTTATCCGTGATTTCAAGTGTTTGATCAAGTTTTGATTCGTATTGCAACCAGCTTTAT
CGGTGAAAATCAGAAAAATCAATGGTCGAATTTCAGTTATCGTCAATGGCGGAGGTTGATGTTGGAAAGC
TTTTAGAATTTCATCCAACATGTGTACCAGTGTTGACACGTTTGTTTGGAGATGAAATCAATGAGAAACT
TTCTTCAGATTGAAGCAATATTTTGTGTGGGCCTTTATGAGCTGTAATCTGTTTTGTAACCCATCTTGTT
ATGAATAAAATCTTAATATTGAG
>gi|17479|emb|Z18386.1|Z18386 ATTS0760 Grenoble-B Arabidopsis thaliana cDNA clone GBGa314 5' similar to hypothetical protein 1 - garden pea, mRNA sequence
AGAGGGGAGGGAGAGAAATGGAAGGCAAAGAAGAAGATGTACGAGTGGGAGCTAACAAGTTCCCGGAGAG
GCAACCCATCGGTACATCGGCTCAGTCCACCGACAAGGACTACAAAGAGCCACCTCCTGCGCCACTGTTC
GAGCCCGGCGAGCTCAGCTCATGGTCTTTCTACAGAGCCGGAATAGCTGAGTTTATCGCTACTTTCTTGT
TTCTCTAACA
>gi|4210261|gb|AI253275.1|AI253275 EST161 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
GAAACCCAAACCCTCATTCCAAAAAATGGGGTCTCGCTCTCAAAACCTCTCCTTTCTCGTCCTCCTCCTC
CTTGGCTTCGTTGCCGTCTCCTATGCTTGCGACTGTACCCCTCCTAAACCATCACCAGCACCTCACAAAC
CACCAAAACATCCAGTCAAACCGCCTAAACCTCCTGCCGTCAAACCACCTAAACCACCGGCAGTAAAACC
ACCTACTCCAAAACCTNCCACCGTGAAACCCCATCCTAAACCACCCACCAAACCTCACCCCCACCCAAAA
CCTCCCATCGTAAAGCCACCAACCAAGCCTTCTCCGTCCACCCCTAAACCTNCCACCAAACCTTCCCCGT
CCACACCTAAACCTTCCACGACCAAGCCT
>gi|4210260|gb|AI253274.1|AI253274 EST145 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TGACTACTGACATATAGAAAAAGAGAGAGGAGGATAATAATATGGCGAGCAAGAAAGCAGCTATGGCTAT
GATGGCGATGATCGTGATAATGGCTATGTTGGTCGANACATCAGTAGCGATAGATNTCTGCGGCATGAGC
CAGGATGAGTTGAATGAGTGCAAACCAGCGGTTAGCAAGGAGAATCCGACGAGCCCATCACAGCCTTGCT
GCACCGCTCTGCAACACGCTAATTTTGCATGTCTTTGTGGTTACAAGAACTCTCCATGGCTCGGTTCTTT
CGGTGTTGATCCTGAACTCGCTTCTGCTCTCCCC
>gi|4210259|gb|AI253273.1|AI253273 EST91 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TGACTAATGACTGGAGGGTTTCTGTCTATGCGGCAAGGGGCTGGTGCTGCTTCGAGATCAGCTATTTTTG
GAGGGGTTTTGCTTGCTTTGATTGAAGGAGCTGGGATCATGTTGAACAAGGTACTGGCTCAGCCTCGGAA
TATGGTGATGGAGGACCCTGGAATGCAAGGAATG
>gi|4210258|gb|AI253272.1|AI253272 EST59 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TGTAACTGACAGAGTGGGATAAGAGACAAATAAGGAGAATCAAACAAGCAATCCGATCGATCTACCAGAT
CGCCATGATTCTTACAAGATGCTTACCCTTGATATGGCTATCTCTACTTACTGTGTGTGCTGCTGGGAGG
ACATTGCACCCTCTCCCCTGTTAAAGGACCCAAAACTGTCAAGCTTCAACTTCCGACTTCACGTCCTTAT
AACATCGCACACAGAGGTTCCAATGGAGAGATCCCAGAAGAAACTACAGCTGCATACTTGAAAGCAATTG
AAGAAGGCACAGACTTCATAGAAACAGATATCTTATCATCCAAAGATGGTGTGCTCATATGTTTCTATGA
TTGTATTCTCGACGAAACA
>gi|4210257|gb|AI253271.1|AI253271 EST52 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TGACTAACTGACGGGGAATACGACTTCTGATTTGAACAGTTAAAAACGAAAAGTCTAATAAAAGCTATAC
TTAACGGATAGCTTTCGCGACATAGGAAAGGGACATGATGCGTCGTGTAAATATTCTTTGCTCATTTGCT
CTGCTTTTTGCCAGCCATACTAGCCTGGCGGTAACTTATCCATTACCCCCGCGCGGCCGCGCGGCCGCGC
GG
>gi|4210256|gb|AI253270.1|AI253270 EST47 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TGACTAACTGACGATGGTGGTGGTGGTATNACAGGTGATGATATTGTTAGGACAAGAGATTGGTAAAGTG
TCGTCGACTCTATACAAAGTTGGGGACATGGACGCTTGGGGCATCCCAATTGATGCTAAGGTCNACTCCA
AATGGCCCAAATCTCACTCTTTCAAAATCGGTGACTCCCTCTTGTTCTTGNACCCACCAAGCGAAGACTC
ACTGATTCAAGTGACGCCTTCCAATTTCAAGAGCTGCAACACC
>gi|4210255|gb|AI253269.1|AI253269 EST19 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
GCAAGGACAAAAAANGGGGGAAGAAATTAAGGGAAAATTAAGGACAAAGAACGCNCCAACAGATTTGTTN
TTCNGGAGNGGAGGGGGTATTTGGAGAAAAGAAATTTTTCNTTCTTTATTNAAGGNAAATAATTTTTAAN
GNGCACGGTAAACGGCCTTCCTTCCAGTAAATGGAATNGGAATAAAAAAAAGTTGGTGTNTGGNTTTCAA
GTATAAATAGACCGCAANNATNAATCTNGGTTTCCTCGTCATGGTTCTCGTTCCCTTTCTTCCTGGTTTC
TTTTTNGGCACAANATTTCAAGNTATACCAAGCATACAATCAACTCCAAGTGAATTCGGAAAAATTAAGA
TANGGAGGGANTCTNGAAGTTGTCAACTTTGGTGATTGTGTGCATGTTAGTGACCGCTCCAANGGCGTCC
GAGGCAGCAATNTCGTGCGGCGCAGTCACCGGCAGCTTAGGTCAATGCTATAANNACTNGACCCGAGGCG
GTTTCATTCCTAGAGGGTGTTGNTCNGGCGTTCAGAGGNTCAACAGCTTGGNTNGNACCACCCGTGACCG
CCAACAAGCTTGTNGTTGTATCCAGGGTGCAGCGAGAGCCTTGGGTTCTCGACTNAACGCTGGTCGTGCT
GCTNGTCTCCCCTGGTGCTTGCCGTGTTAGGATNTCTNACCCCATCAGTGCCAGAACC
>gi|4210254|gb|AI253268.1|AI253268 EST11 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
GGACTAACTGACGATGTTTGTTGCGGGGCATATCTACCGCTATAATGTTGATCAGTTNGGCTGGTCAGCT
AAGTCCAGTGAATTTCTGGAAAAAAGGCAGCTGAAGTGGGGCAGTATTTTATTCCATTACGGAATNGNAT
TTGTTTTCTTTGGTCATGTAGCAGGTATTTTGGTTCCAAAGGCATTNTATGAAATGATTGGTGTAACAGA
CCATATG
>gi|4210253|gb|AI253267.1|AI253267 EST54 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TGACTAACTGACCATCCNACCTCATTTACTGTTCTGTTTCACTTTCTCTCTCTCTGTANACTCTCTAAAT
GATGGCAAAAAACTGTAATTTAGTCAGTGTTCTATGTGTATTTTTGGTATTGACCCTCTTTAACAAACCC
ATCACCGTCGCCGGGCAGAATATTCCGGCGGTGGGCTTGTTCACCTTTGGTGACTCCAACTTNGACGCC
>gi|4210252|gb|AI239412.1|AI239412 EST162 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AGGAGGAGAGTAGTGAACGGAATTAACCAGACAATTCACTCACAACCTAGCTAGCTAGTGAACAGTATTT
TCTATATACCAAAAATGGCTTCAAGTTCCATAGCTCTTTTCTTGGCTCTCAATCTTCTCTTTTTCACAAC
AATCTCCGCCTGTGGTAGCTGTACTCCGTGCGGCGGAGGTTGCCCCTCTCCCAAGCCAAAGCCAACTCCT
>gi|4210251|gb|AI239411.1|AI239411 EST160 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TTGGAGTTGACGGAATGATTATAAACCTTGCCACACTTCTAGCTAACATCGTGACGAATCCGTTTAATAA
CGGATATTACCAAGGCCCACCAACTGCACCGCTTGAAGCTGTGTCTGCTTGTCCTGGTATATTCGGGTCA
GGTTCTTATC
>gi|4210250|gb|AI239410.1|AI239410 EST157 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AGATGGGAAGTGGCATGATAAGGACATTGGTTATTCTAGCAATAGCTTTATACATGATCGGTTCCGACAA
CGTCCACGTGGCAAAAGCCCAGGTCTGTGGAGCTAACTTGTCGGGACTGATGAACGAATGTCAACGCTAC
GT
>gi|4210249|gb|AI239409.1|AI239409 EST156 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AGAGAGATAGTAAGAGTAGGCGCCCTCAAGAAAACAGAGTAAAAATGGATCAAACTTTGTATCGCAAGTG
TCTGGTTACTTTATCGATGATGGCAATGATCGGCACATCAATGGCTACATATGCCGGGACCCCATGGCGT
ACAGCCTCAGCC
>gi|4210248|gb|AI239408.1|AI239408 EST154 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TCACAGGAGGAACGGGTAGCTTAGGTACAGTCACTGGTGGAACGGGTAGCTAGATAACAAAATAACGGAG
TTGAAAATGATGTTTAATAAAATATCCCTAATCACTGCTCTGTTGTTTTTTCTATTAGGAACGAATGTGT
TCGCCCATTCCCATTTAGAAGATTCATCTCCTAAAGATGGCGCAGTGCTAACTGAATCATTGAAAGAAAT
CAAACTAACATTTGAAACGAGCCTTGAACCAACTAGTACATTTACG
>gi|4210247|gb|AI239407.1|AI239407 EST153 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CTCGTTGAAGACCAACAATTTCAAATCTCACTTCCTTATCACAATGTCTTCCTCTATCTCTCCCCTCCTC
ACAACCGTCATCTTCGTGTCGAGCCTCCTCTTCCTTACTATCTCCAAAGCGGCGACAATTCCAAACATCC
AC
>gi|4210246|gb|AI239406.1|AI239406 EST147 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TTCTCTCCAACTCGCGGAGCTCTTCGTGAGCTCTATTGTGCATTTGCTTTATGGGTTTTATATATTTAGC
TCCGCCGTTGCCGGAGATATCTCTCAGACGTTGAATGATTACTTGTTTAAGTCCAATGTCGCTTTCGGAG
AAACCGGTCAAAATCAAACCAATGTTGAGGGTTTGCCACCTATTGTATTGGC
>gi|4210245|gb|AI239405.1|AI239405 EST137 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AGTGGTGGTTTCCGGCTTAAAGATGAAAGCTTTCTACGTATTCGTTGTTGCTCTTCTTCTCACCTTGAAT
TATAGGGGAGAAGCAAGTGGTTCTGTTTTCTTCATTGATGGATCCAACAATCAATATCTTCGTCCACGAT
CATCCAGTGAGGCACTTCCCATGTCGCCTGTTGAAATATCTGCAGCAGTGTCTGCCTTGTTGGGTTTTGC
ACCTTCAGCAACTTTGACAGCTGATGGCTCATCCAAGTTGAACAAGATTCTAAAACCTAATCCA
>gi|4210244|gb|AI239404.1|AI239404 EST130 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AAGTTACTGCCGCCACGGCTGCTGCTACAAAGGTTAACACCCATACAAGAGTCACGGGTCACATTTAAGC
TTCAACTATATATTTGCATGTTATTTGCCAAAAGGATTTGACAATAATGCAACAAGAGTTTCATTGAAAA
TTTCAAGAACCCTAGTTAATAACGATAATGGGTTCGAGAGTTTTGGCTTCCTTCTTTGTTTTCTTAATCT
TCACGGTCATCACATTGCCTCCCACGATCCAAGCTTGCACTCCTTGTACTCGTCCTCATCCTCCGGTTCC
GAAACCTCCACAACACGGCGGTGGTGGAGGTGGTGGTAGCAAGCCGCCCCCACATCACGGTGGAAAAGGT
GGTGGTAAACCCCCACCCCACGGTGGAAAAGGTGGAGGACCGCCGCATCATGGTGGAGGAGGAGGAGGAG
GAGGGGAATCACCGCCGGTTGTTAGACCTCCTCCCGTAGTGGTGAGGCCACCGCCAATCATAAGACCTCT
TCGGTCGTCTATCCACCACCAATTGTGAGGCCACCGCCAATCACAAGACCTTCCATCATAATCCCTCCAA
TTCAACCCG
>gi|4210243|gb|AI239403.1|AI239403 EST128 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AGCATAATTATCGATCATGTTTATCATCTATCTTTTTATCTTTCTCTCATCTGCCATTATAGATTCAGAT
GGGGTTGCAATGGCCCAAAAGATCGAGGCAATTGGTGGGAAGGGAGGGAAACGGTGGGATGACGGTGCGA
ACCATGAT
>gi|4210242|gb|AI239402.1|AI239402 EST148 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CACACAACACAGACCTAAAAAAATGTCTTCTCTGCGTTTGCGTTTATGCCTTCTTCTACTCTTACCTATC
ACAATTAGCTGCGTCACAGTCACTCTCACTGACCTCCCCGCGTTTCGTGAAGCTCCGGCGTTTCGAAACG
GCAGAGAATGCTCCAAAACGACATGGATACCTTCGGATCACGAACACAACCCATCAATCATCCACATCGC
TATGACT
>gi|4210241|gb|AI239401.1|AI239401 EST119 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AAACTAAAACAACTCTCTCATAATCTCTCTCCCTCACTCTAACACCAAAAGAAGAAGAAGCATTTTCCAA
AGAGAAAGAGAGAGAAATGGGTTCTAAGATTGTCCAAGTTTTCTTGATGTTGGCTCTATTCGCCACTTCA
GCACTCGCTCAAGCCCCTGCTCCTACTCCCACCGCCACTCCTCCTCCCGCAACTCCCCCTCCAGTCGCAA
CTCCTCCTCCAGTGGCTACCCCACCACCTGCTGCAACCCCTGCCCCAGCCACGCCACCACCTGCTGCAAC
CCCAGCTCCTGCCACTACTCCACCGTCAGTTGCTCCTTCTCCTGCTGATGTTCCCACCGCCTCTCCACCA
GCACCGGAAGGTCCT
>gi|4210240|gb|AI239400.1|AI239400 EST106 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CGGAAGGTCTTCGCAACTATCGAACGGACCTCTTATCAAACACCAAACCACACCAGAACAGAACTCAGCC
ATGGCTTCTTCTTCTTCTTCTCTTCTAATCCTAGCCGTTGCTTGTTTCGTCTCGCTAATCTCACCGGCGA
TTTCACAACAGGCTTGCAAATCACAGAACTTGAACTCCGCCGGTCCGTTG
>gi|4210239|gb|AI239399.1|AI239399 EST102 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
GGAGATGTTTTGGAAGACGAAGAGAGATTCGATTTCTCTGGATTTTTCAAAAATGATTCTCCAATCGCAA
AAGCTATGGACGATGTTTCTAATTCTAGCGATTTGGTCCCCAATTTCATACTCGCTTCACTTTGATCTAC
ACTCAGGTCGCACAAAGTGTATCGCCGAAGAC
>gi|4210238|gb|AI239398.1|AI239398 EST101 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TCAAACCTCACTCACCATGAGACACCTTAGCTCACCTCCATGGCCTCTCCTCCTTCTCCTCCTCCTCTCT
TCTTTCACCTCCGGCGAATCCTCTCTGTCCGCAGAAAAAAACAAATTGCAA
>gi|4210237|gb|AI239397.1|AI239397 EST100 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CAGAGGGGTTCCACGCGATGACGACGTTTTCAACGAGCTTTCTTTTCCTTTTGTTGGTTTTCTGTTTGAT
CGATCCACTAGCTGCCGATGATCTCCAACATAAATCCGGTCGTGACGTCTGCTCCGGTGGG
>gi|4210236|gb|AI239396.1|AI239396 EST099 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CGGAAGGTCTTCGCAACTATCGAACGGACCTCTTATCAAACACCAAACCACACCAGAACAGAACTCAGCC
ATGGCTTCTTCTTCTCCTTCTCTTCTAATCCTAGCCGTTGCTTGTTTCGTCTCGCTAATCTCACCGGCGA
TTTCACAACAGGCTAGCAAATCACAGAACTTGAACTCCTCCGGTCCGTTC
>gi|4210235|gb|AI239395.1|AI239395 EST098 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TGGAGATTGGAGCGGAGATCTCTTGAATAACGGCGAAGCAACAACAAAAGGAGATTAAAAGAGGAGCTAC
GGGTAAGATGATATCCTTAAGAATGAAAGGGCTTGGTCATTGCCTAGTTTATGTCGTGGTCTTTAGTGTC
ATTGCGGCTATAGTGACAGCATACGACTCACCCTCTTCAACACCACAATACACTTCCCCTTATCCACCTA
AAAACTATTCTCCTTATCTCTCAGAATCACCCCTG
>gi|4210234|gb|AI239394.1|AI239394 EST093 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
ATACAACAATGGCTTCGTCATCTACAAGTATCTCTCTCCTTCTCTTCGTCTCTTTCCTTCTTCTTCTCGT
TAACTCGCGTGCAGAGAATGCGTGG
>gi|4210233|gb|AI239393.1|AI239393 EST089 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
GTATTCTTTGATGAATCGTGAAATGACGTCAAGCTTTCTTCTCCTGACGTTCGCCATATGTAAACTGATC
ATAGCCGTGGGTCTAAACGTGGGCCCCAGTGAGCTCCTCCGCATCGGAGCCATAGATGTCGACGGCCACT
TCACC
>gi|4210232|gb|AI239392.1|AI239392 EST088 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TGGAGGAGGAAGTACAATGAGAATATTAAGCTACGGAATCGTTATTCTCTCTTTACTCGTTTTCTCTTTC
ATTGAATTTAGCGTTCACGCTCGTCCCGTTGCTCTCGTCCTCTCAAATGACGATCTC
>gi|4210231|gb|AI239391.1|AI239391 EST118 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CTGGTTGATACTTGAACCTACCCTTTGGTCCCTTTACGGCAACATGGACTCCTCCAAACTCTCATCTCTC
TCTCTTTGCCTCTTCCTCATTTGCATTATCTATCTCCCCCAACATTCTCTCGCATGCGGCTCG
>gi|4210230|gb|AI239390.1|AI239390 EST083 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
GAAATCTCCCAAGAACCCGAAAAAGCGCCATGTCGCTCACTATCCCGACGAATCTCGTTCTCAACCCGAG
ATCTAACAAATCTCTCACTCAATCCGTACCTAAATCCTCCGCAAGATTCGTCTGCTCCGATGACAAATCC
TCCTCCTCCGCACCTCAATCCATGAAAGCTTTCTCCGCCGCCGTCGCCCTCTCTTCCATCCTCCTCTCTG
CTCCTATGCCAGCTGTCGCTGATATCTCAGGTTTGACTCCTTGCAAGGACTCAAAACAGTTCGCT
>gi|4210229|gb|AI239389.1|AI239389 EST080 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TGATTCAAAAATAATTTGGTTAGAGAGTCTTAAACGAAACTAAGAGAGCACACAAGTTTCTCAACATGGC
CAGTCCTAATTGGCCATCTTTACTTATGGTGGTCTTAGCCTTGTATCCCATGGCTGCGTATACAAGTGCT
CAATACTCTCCAACACCAA
>gi|4210228|gb|AI239388.1|AI239388 EST067 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AGAGAGAAAAAGCAAAAGCAAAAATGGCTCGATCTTTCGCTATTGCTGTGATCTGTATCGTCCTCATCGC
CGGCGTTACTGGTCAAGCTCCGACTTCACCACCAACCGNTACACCAGCTCCACCAACTCCAACAGCTCCT
CCACCAGCAGCAACTCCTCCTCCTGTCTCAGCACCACCACCAGTCACAACATCTCCTCCTCCAGTCACCA
CTGCTCCTCCTCCAGCAAATCCACCACCACCAGTCTCTTCTCCTCCTCCTGCTTCTCCTCTG
>gi|4210227|gb|AI239387.1|AI239387 EST065 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
GCAGCTTTTGCTTCTTCGATAGAAAATCTAATTATCATCAATCATGTCTAAGTTCACGGGATTCTCATCT
CTCGCTATCTCTTATTTTCTCTTGGTTTCAACGATTGTTGCAGCCACCGATGTTCACTACTGCGATAATA
ACGAAGAGTATGAAGTAAAAGTACAAGGAGTTGATATAACTCCTTATCCTATAGCTAGAGGCGAGCCAAC
TACTTTCAGAATTTCTGCTAACACAGACACTGAGATCTCGAGCGGCAAGTTGGTGATCGAAGTTTCCTAC
TTTGGATGGCATATTCATTCTGAGACACATGATCTTTGTGATGAGACAAGTTGTCCTGTGGCCATTGGAG
ATTTCTTGGTAGCGCACTTG
>gi|4210226|gb|AI239386.1|AI239386 EST064 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AAATTCTGTTTCAGTGTTCTTCAAATTCTCAATCTTTCTCTCAATTCATCTAAAGGGTTCCTCAAAGTTT
CAATCTTTCTCTCTGAATCTAAACCATGGCTCGTTGTAGCAACAATCTCGTAGGGATACTCAATTTCCTA
GTATCTCTTCTCTCGATCCCAATCTTAGCTGGTGGAATCTGGCTAAGC
>gi|4210225|gb|AI239385.1|AI239385 EST060 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CGACATCTTCTAAGAAAGAAACAAAGAAAGACTTCACATTTTACCATTATTTGCTCTGAGCTCAGTAGGA
GAGTTCAGAAACAATGGCAAAGATGCAATTATCAATCTTTATCGCTGTCGTTGCGCTTATCGTCTGCTCT
GCATCTGCTAAGACCGCAAGCCCTCCAGCTCCAGTGCTGCCACCGACACCAGCTCCAGCACCAGCCCCGG
AAAATGTGAATCTCACCGAGCTTTTAAGT
>gi|4210224|gb|AI239384.1|AI239384 EST123 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CTCGTTGAAGACCAACTTTCCCAAAATCATTTAGTAACATCAAAATTTACAAAAAACAAAAAAACATGCT
ATCTCTCAAACTCTTCCTCGTAACACTCTTCTTACCTCTTCAAACACTCTTCATTGCTTCTCAAACTCTT
CTTCCTTCTTCTTCAAACACTTCATCAACCATCTGCAAAACAACACCCGATCCAAAATTCTGCAAATCAG
TGTTCCCACAAACATCT
>gi|4210223|gb|AI239383.1|AI239383 EST053 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TTCTTCTCATTTTCCCTCTATATATTCATATACTCTTTCGTATAGTTGCACCATCCACTCTACTCAACAT
GGACTCCTCCAAACTCTCATCTCTCTCTCTTTGCCTCTTCCTCATTTGCATTATCTATCTCCCCCAACAT
TCTCTCGCATGCGGCTCTTGCAACCCACGGAAGGGCGGAAAGCACTCCCCTAAAGCCCCTAAGCTACCAG
TTCCTCCGGTGACCGTCCCTAAGCTACCAGTTCCTCCGGTGACCGTCCCTAAGCTACCAGTCCCTCCGGT
GACCGTCCCTAAGCTACCCGTTCCTCCTGTGACCATCCCTAAGCTACCCGTT
>gi|4210222|gb|AI239382.1|AI239382 EST049 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TTGTTAGAGAGGGCCATGTCTCCAAGAATTGTTAATGAAGCTCGTTCAGATCTCATTCTCTGTTTCTTCT
TCCTCTCTCTTCCTTCCTTCTCTTCCCTTCCATCCTTCCAAACCCTATTCCCCAATTCTCATTCCCTTCC
TTGTGCTTCTCCCGTCTCCTTCCAACCCGGCTCCGACTCCGAGTCACTGCTAGAATCCGAATTTGAATCT
>gi|4210221|gb|AI239381.1|AI239381 EST046 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CGATAATGCTTGTGCTTGTTAAAGTTCTGAGATTATCCAAGACCCCAGCATTTCGTGTACAAATTGCTTC
ACTAATTGGTTTGTTAATTCGGCATTCTACTTCAATCGAAGATGACTTGGCAAATTCTGGTATTTTAGAC
TCTCTT
>gi|4210220|gb|AI239380.1|AI239380 EST152 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CAATTTTTCCTAAAGAGTAAAGAAACTTCTCTCCTGTCTTTTCTCCTTCTCTATCTCTCTCCCTCAAAGC
TAATAAATACAACATTTGCATCTAACGTTTCTCTAGCACAAAAATATGCACTCGAGTTGTTTATTGTACC
TCACCGTCCTCGTCGTCTTCATTGTCTCTTTCGCCGGCGGCGAGAGATTCAAAGAAGCTCCAAAGTTCTT
CAACTCCCCGGAGTGTCTAACCATCGAGAACGATGAAGATTTCGCTTGTTCAGACAAAGCCATCCACGTG
GCAATGACCTTAGAC
>gi|4210219|gb|AI239379.1|AI239379 EST036 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
ATTCAACAAAACATAGAAAAAAACAAAGCAAATTCTTTTTTTCTCCTTAGTTACTTCTTTTACAGATTAT
CTCAATCTTACAGAGCACCATGGATCGTTGTATCTATGGTTGCTCCGTCATTACTATCTTCTTCTCCTTC
TTCTTCCTCCTCAATGCATCCGCTTTAGAATCGGGTCACCACAACATAACTGGGTCGGGTCAAATAAACT
CAAACTCCGTCCTCGTAGCTCTCCTCGATT
>gi|4210218|gb|AI239378.1|AI239378 EST025 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CTCGTTGAAAAACAACAATGACGAAGCTCTTCTTCTTCTTCTTCTTCTCCTTCCTCTACACAATCACAAC
CCTAACATTTCCGCCATTAACAACCTCAGCAGCAACATCATGCCGAACATTATGCGGCAACATCCCAATA
AACTACCCGTTCGGCATCGACGGCGGTTGCGGATCTCCTCAATACAGAGGAATGTTCAATTGCTCCACCG
ATCTATATTTCACCACTCCTTCCGGCAGC
>gi|4210217|gb|AI239377.1|AI239377 EST014 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CAGATCTACCGGAAGATGAACGGAGAAGAGATGATAAAACTCTTCGAGACTGGAGCAGATGTTGTGGTAA
TTGGAAGTGGGATAGGAGGATTATGTTGTGGTGCTATGTTCTCTATGTTTGGATTCTTCGTTCAAGCCAT
CGTCACTGGTAAGGGACCGATAGAGAACCTTGCT
>gi|4210216|gb|AI239376.1|AI239376 EST078 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TAAGGCAATGCAAGCTTTGATCTTTCTTGGTTTCTTGGGCACTTCATGTCTCGCTCAAGCTCCTGCACCA
GCACCAACC
>gi|4210215|gb|AI239375.1|AI239375 EST037 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
AAAACACAAATCTTGGTTCATTTTAAATCTCTCCAAGAAACAAAATGGCAGCTTCCATGAAATTTCTCTG
CATTCTTGGTCTGATCCTCCTCATCGGAACAGTCGTTGACGGTGCAGGGGAGTGTGGTAGATCTTCGCCA
GACAATGGGGCGATGAAGCTGGCTCAATGTGCTGGTGCAGCTCAGGACGCTAACTCCGCCGTGCCAGGAG
GTTGCTGTACTCAGATTAAGAGATTTTCTCAAAACCCTAAATGG
>gi|4210214|gb|AI239374.1|AI239374 EST006 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
TAGAGATAGTTGATTAGGTAAGCTACAGTTATTTTTATACCAGATTCAGTCCCATACAAAGAGTATAGTA
GGTCACATTGGTGATTAGTCATAAGTAACAGAAAGAATTATTATATAATGACATCTTCGACATTCTCGTC
CATGATATTTCTCCTCGTCCTCCTGTTTTCCCTTCATATGGGTGAAGCTCTTGGTGCTCAAACTGAGATC
CGCAAAATCAAAGAGACAATTAGGATGAGGAGGAATTTGGAAGGCAATGACTACAGAAACTCTAAAATTT
GGACTGGACGGAGCTATTCA
>gi|4210213|gb|AI239373.1|AI239373 EST143 Arabidopsis pSMASH Library Arabidopsis thaliana cDNA 5', mRNA sequence
CACCGTCGAAGCTTTCTCTTTCCGATCTTTCAATGGCGATTCTCAAATCTCACTTCTTCTTACTCTTCCC
TCTTCATCTTCTCCACTTTCACACTGTCTCCTTTGCTCAGACGCTTTTTGTGTTCGGAGATGGTCTTTAC
GACGCCGGCAACAAACAGTTTCTCTCTCAGAACCGAGTTGACGCAAGT
>gi|3868979|dbj|AB015130.1|AB015130 AB015130 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-111, mRNA sequence
GAACAGAAAATGGAAATGATACTGATCTCGTCATCGACACTCAGGTTCCATCCATTGAGGACATCACAAA
GAATCGCCACCGGAACCAATAGAAGACGAACCACCACCGTGTGTGCAGACTACTACAGAGGAGGAAGAAC
GGTGGACGANAACATGGTGGTCCTTAGGAAACGAATCCATGAGATGAANATGGTTGAACGCAACTTTGAA
CCTCCTTCTCATTGGATGCAATGGGAGAAACGTTTCTACTGCAACTACGACGCTACTATATGTGATGCAC
TCACTCTTCTCCAAACTTTTCTCATGAACTCTCGTCCCA
>gi|3868978|dbj|AB015129.1|AB015129 AB015129 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-110, mRNA sequence
GGAGTCGCCATTAACATATTTCATCAAGCTCAGTCCACTCTTCTCATGAAACTTCATCATCATCGACCTT
GACCCTGATAGGTTTCAGACGACACCCATTATTGTAAATCTGCTGCTGGAGTCTTTTTTGTCTGAATCTT
CTTCTTGTTGAGACACTGTTTCTTCTTGGTCTGTGATTTTTGTTTTGTTCTCATTAGGACGTTCTTTATT
CCGGTTCAGATTTACTGGATCGTCATTTTCTCTTTGAAATTGTATTTTTTTGTTCCTTTTCTGGTATGTT
GTGAAAGCTATGA
>gi|3868977|dbj|AB015128.1|AB015128 AB015128 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-109, mRNA sequence
GGCCGGTAACAGCAACGGGAATTTTCATGGCGGCGAGGTCACCGGACGTTATATAATTTGTATCCCAAAT
CAAAATTCTGAGAAGGAAGAGAAAGCAATGGAGGACGAATTGGAAGGTCTACGAGCTCATTTTCCTGTTT
CGTTCGGTAAGACATCGAAGGTTTCGGCGTCAACTGAAGCCATTCACAGCGCAACTCGCCGCACCGATGT
AGCCAACGACGCCGGAGTTTCGTCGGATATCACCACGAAGAAACCTGATTCCGATAAATCTGGATTCCCG
TCTCTATCTTCCTCATCTCAAACCTGGCTCCGAAGTGTTCGCGGTCCGAATCGTAACCCTAACAGCTCCG
GTGATGTTACAATGGGTCCGCCACCGCCACCGTCATCTAAACGGACCC
>gi|3868976|dbj|AB015127.1|AB015127 AB015127 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-108, mRNA sequence
AATATTTTCTTCCAGCTGTTTTGGGTGGTTTTTCTCTTTTTTATCTCTTTTCTTGAAAAAAAACTAGTAG
TCTTTTTTTTATTTCTTCTTGGGAGGATATTTTT
>gi|3868975|dbj|AB015126.1|AB015126 AB015126 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-107, mRNA sequence
NACCCCCCCGAGGAACACGAGACCCAAGAAAAAGATTTCAAAATGCTCACGACACCTCCACGAACCTTTG
TCTCTGTCCCTTTCTTCTTCTTCTTCCTCCTCTTCCTTTCTCTACCTCTCTCATCTTTCTCTCAATCGAA
CTCTGTATACAACTCTTTCCTCAA
>gi|3868974|dbj|AB015125.1|AB015125 AB015125 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-106, mRNA sequence
GAGCTCCAAAAAGTCGGTGGTGGTGGAAANATCCGGCGTCGTCGGATCCGAAAAAAAAAATGAAGGTTTC
AAGCGGTGTGGTCGCTTCTGTCATTGCCGTCTCCACCGCTGCTCTCTCTTCTTCCTCCATTCTTCCTCCA
GTCTCCCCAAAGGTTTGGGAATCGAGGAAAACGAATGGGTCGGACAATTTCGAGCCGAGGTTTGATGGGT
TAAGGTTCATAAA
>gi|3868973|dbj|AB015124.1|AB015124 AB015124 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-105, mRNA sequence
GGCAGCCGAACCCTAGCTTTCATAAAATTTTCATTCATCATCGTTCTTGCTTCTTGCTAAAGGCCTTGCC
TTGTGCTTCCTCGTCCTATCTCTCTTACCTCCGTAATTTGTTCGTAAGAAAAGTATCGTGATGGGTACTG
AGAGAAAGAGGAAAATTAGTCTGTTCGATGTTATGGACGATCCGTCTGCTCCGGCGAAAAACGCCAAAAC
CAGTGGTCTTCCCGACGGCGGAATCAACAGTCTGATCAATAAATGGAACGGGAAGCCTTATTCACAGA
>gi|3868972|dbj|AB015123.1|AB015123 AB015123 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-104, mRNA sequence
GACACCACCATTGAATTGAACTTCCCTCACACGCAAGTACCACACCTTCTCTCTCTCTCTCTCTATCATC
TCTTTTCTTTTTCTCTCATCGCCTTGAAGCTCTGAGAAGTAGAGAGAAGCTCCGATCTGATAGGAACTGT
GAGTTTCCTTGAGTCTCCGGAGAAAGAAGTCGCCGATTTGCTCCTGATAATCTTAGTCTCGAAATCAAAA
CGATGTTTTGCGATTGCTTCTACTGGAATAAAGGTTTCTCCGAGTTGGAATCGGAATCGTCCGAGTCAAA
GCCCTTCTCGCTTCCATCTCCTCTTCCTCAATGGCCACAAGGCAGAGGTTTTGCTACTGGAAGGATAAGT
CTTGGAGAAA
>gi|3868971|dbj|AB015122.1|AB015122 AB015122 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-102, mRNA sequence
GAGCCTTAAAACCAGGCAGCCACTAAAAAAAGGAAAAATATTGAGGGAAAAAAATCACTTTGATAAATTC
GCCGCCAATCTAAACCCGTTAATTTTCTTATTCGGAAAAAAAAAATGATTGGAAGCAAAAGGAAGGCAAC
CCCGGCAATTAGGAC
>gi|3868970|dbj|AB015121.1|AB015121 AB015121 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-100, mRNA sequence
GATCCTCAAGCGATAACACCACAAACAAAACAATAATCCAAAAAAAAAAAGAAAAAAGAAAAAAAGAGCA
AATCTCCATCATCATCATGGACTCGTCTCCAAACGACGGTGTACACCAACCGCTTCTCCATCCTCAACCA
TCTCCATCTCCGCCGGATTTAACCAACGGGGAACTAAAAACTGTCCTCTCCGAC
>gi|3868969|dbj|AB015120.1|AB015120 AB015120 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-98, mRNA sequence
GGTCTCTCTGTCTCTTCAATTTCATTCGTTTTCTGAGATAAAAGTGAGAGAGAAATCTAAATTCGAGAGG
AGAAGTTTTAATTTTTCTGAGTTAGATTCAATGGAAGAGATCACGGAAGGAGTTAACAACATGAACTTGG
CTGTTGATACCCAGAAGAAGAATCGGATTCAAGTTTCCAACACTAAGAAACCATTGTTCTTCTACGTCAA
TCTCGCCAAGAGGTACATGCAGCAGTACACTGATGTCGAATTGTCTGCACTAGGAATGGCTATTGCCACT
GTTGTTACGGTCGCTGAGATATTGAAGAACAATGGCTTTGCTGTTGAAAAGAAGATCATGACATCGACTG
TGGATATCAAGGGATGATTCAAGGGGTCGTCCTGTGCAGAAAGCTAAGATTGAGATCACGCTTGCCAAGT
CTGA
>gi|3868968|dbj|AB015119.1|AB015119 AB015119 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-97, mRNA sequence
GAAAGTAGACAATGAATGATTAGGGATAGCGAATGAAGAAGGTGGAAGATGATGTTAACTTCGGATTGGC
GCGAAATAAGATAAAAAAGCTTGTTCTTCAGAGAAGAAAGTGTTTATGATTGGACAAAGAAAGAAAGAAG
CAAAGCCTATCCACTTCTCATCTTCTCTATTACCAACAAACCTTCCCCTTCTCTGTCGGTTCCTCCTTTT
CTATTATTTTTAATTCCAGATAATAAAAAGAAAATCTTTTTTTGCTTAAAGAGCTCAAACCGAAACCCAT
TTCAAGATTTCATCCTCCGGAGTGTTTCAACGAAGCTTGGGTACATAAGTCTGATATGAGAGGTTTCGTC
ATAACTTGTCTTCTAAGGTAAGTTTCCTCACCTGTGGCGTAGATTGCATCATCAATCCATGGACGTTGAA
>gi|3868967|dbj|AB015118.1|AB015118 AB015118 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-93, mRNA sequence
TGACTAAAATATTTATTTTTATTTTCCTTCAAAAAATCTCCATTCGGTATCAGCCATAGCCAAACCTCTC
TTCTCTCTTATTGTTGGGATCGACAAATTTTGCCTTGATTAGCTCGGAAACTTGTAAATCAGAGACCCTC
GTAGAAACTACCCAGAAACAGCATCTCCAAGGAACAAATTAATCATTATACTAATGCCTCTGATGCTCTT
CTTTTGATTTTGTGATCGACTTCTCTTTATTAAGTCTACACCTACCAGATGCAGATTATAGGTTCATTTT
TTTGTATTGAACTTTAAGCCGATATAGAGTTGTTGTCATAGATATATACAGCGAGTTATTGAAGCAATGG
ATGTTAATGAGGTTGAAGAAAATTTCTTTGCCCCTGGTGATGCCAAGCTACACGGAAAAATGTGCAATGC
CCTTTCAGTGATCTACTGCAAGATCATGTCTATTTTCCCGTCGCTTGAAGCTGCTA
>gi|3868966|dbj|AB015117.1|AB015117 AB015117 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-92, mRNA sequence
GTCACTAACCTTCTTCCTTCACAGTGAATCAATGGCGTCTTCTTCTCTATCAACTCTTTGCAGCTCAACT
TCTTCTTCTCTACATCCCAACTCCAAACTCTCACATTCTCTTTCAGCTAAATTATCCTCCAAAGCAAATG
TTTCCGTCCAATTTCTGGGAAAGAAACAGTCTCCGCTTCTCTCCTCAACTCCGAGATTTCTCACTGTTAT
CGCCATGGCTCCACCTAAACCCGGAGGCAAAGCTAAAAAAGTTGTGGGAGTTATCAAACTTGCTTTAGA
>gi|3868965|dbj|AB015116.1|AB015116 AB015116 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-90, mRNA sequence
GGGTAAAACTGTAAAGACAGAGAGAAGAGCACTCCCCAGTCTCAGTGGTGCGGTGAGGAGAGCTTCGTTG
TCTTCCCCATTGCAATTAGGGTTTTCAAAACGGGTAATCGAATTCGGTGGTGCTCGGCTTTGAAATTGAG
GATGAGATCCTTTCCACTTCCTTCTACCTGCTGACAATGGGCAACTGCGGTACTAGAGACGAGGCTGCCG
TCTTCACTCCTCAAGCTCAAGCCCAACAGCTCCAGAAGAAGCACTCCCGATCCGTCTCAGATCTGAGCGA
TCCATCCACTCCTCGCTTCCGAGACGACTCTCGCACTCCTATTTCGTATGCCCAAGTCATCCCCTTTACT
TTGTTTGAGCTTGAGACCATCACCAAGAGCTTCCGCCCAGATTATATACTCCGGAAAAAGTGGTTTCGGT
ACCGTCTACAAAGGGTTACATTGATGACAATCTCCGCGTTCGGCTCAAGTCTCTCCCTGTTGCCGTC
>gi|3868964|dbj|AB015115.1|AB015115 AB015115 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-88, mRNA sequence
GATGTCTTTCACTCTCTCTCTCTCTCTATATCCAAAGAATTAAAAACCATAATAAAAAAAGAAGATAAAA
AGACGAATTCCAGAAAAAAAAGACGCAAAATCGTCGTCGTCGTCTTCGTCTTTGCATTTCGTCGGAATCT
TTTGATTCTTGAATCGGAATATCTCTGTTTTTGTTTTATCCGGACTCAAGATCAATTCGGATTCTTGGAA
TTTATTTGATTTTTTGTTGTTGTTGTTGAAAAAGTGGATTCTTTGGTTTCGATTTGTAATAATCTTCGTA
GAAAAAATGGATTCTGATTCTTGGAGTGATCGTCTCGCATCGGCTTCAAGAAGATATCAGCTCGATTTCT
TGTCTCGATCTGACAATTTCTTGGGGTTTGAGGAGATAGAA
>gi|3868963|dbj|AB015114.1|AB015114 AB015114 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-86, mRNA sequence
GAAAAACAGAACACAAACAAAAACACATTGTAACATTAGTTTAAGCATTAAGCTTCTTTATGTCGAATAA
TAATAATTCTCCGACCACCGTGAATCAAGAAACGACGACGTCTCGTGAAGTCTCAATCACATTGCCTACT
GATCAATCTCCTCAAACCTCACCAGGATCATCTTCTTCTCCTTCACCGAGACCTTCCGGTGGATCACCGG
CGAGAAGAACGGCGACTGGATTATCCGGCAAGCACTCTATTTTCAGGGGGATTCGACTACGTAACGGAAA
ATGGGTATCGGAGATTAGAGAGCCACGTAAAACGACAAGAATTTGGCTCGGGACTTATCCGGTACCGGAG
ATGGCTGCCGCCGCTTACGACGTGGCTGCGTTAGCTTTAAAAGGACCGACGCCGTTTTGAATTTTCCTGG
TTTAGCTTTGACTTACGTGGCTCCGGTTTCAAACTCTGCTGCGGATATAAAAACGCTGCTATTA
>gi|3868962|dbj|AB015113.1|AB015113 AB015113 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-84, mRNA sequence
GATCCATTGCTTAGGGAGAGAAGAGATAATGCTGAGAGCTTCGCTGCTCTGTTCTTCGACCTCAATCACT
TTCACACCAATTCAACTATTCAATCCCAATAGTTCCCATCGTTTCCCAAGATTCGAACTATCTCGTCCTG
TCTCGGCTTTGTCTCGTACCAAATGTCACTTGAGTCTCCTGAGAGCTCGTGGGAAATCCAGCTTCCTCAC
TCGCAGCACCGCTACTGATGAAGCTGTTGAAACTAGTAGTAACAGTGGATTGGATTTGGTTGAGGTTGGA
TTCTTGTCTGGTGTTCATGGCCTTCAAGGCGAGATTTGCATAAAACCAAACACTGATTTTCCTGATTTAC
GTTTCTCTAAGCCTGGTAGAAGATGGTTAAAACAACAATTGTTGGGACAAGATAAGATTGATGAGGTTGA
ATTAGTC
>gi|3868961|dbj|AB015112.1|AB015112 AB015112 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-83, mRNA sequence
TGGAGCAAGAACAATAAGAAGAAGAGAAGATGGGATTTGAAGAACGGAGGGATTCTATTAAAGGAGCTAA
TCGCTTCCTTCGACGGCAAAACCAATCCGATTCGTTGCTTCTCCTCCGATCAGATCCTTAAAGCTACCGA
CAATTTCTCCGAAAGCCGAATTATCTCCAGCTGGGGATACTTCATATGGTACAAAGGCGTAATCGAA
>gi|3868960|dbj|AB015111.1|AB015111 AB015111 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-82, mRNA sequence
GCTCTCTCCTCTCTCGCTCGCTGGCTTCGAGGAGAAAAAAGAAAAATTGGAGAAATAATTTAACTGGTTC
TCGGAAAATCTAGGGTTCTTTTTAGCCACGCCTTGCTGATCTCCTTCGTGAATTCGATTCCGATTCTCAC
CTGAAAAAAACTTCTTTAAATTGGGTTAAAGCTGCTGCTA
>gi|3868959|dbj|AB015110.1|AB015110 AB015110 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-81, mRNA sequence
AGTGTCAAATTCTGAGATCTGTAAAAGATGAGCGACGGAAACGACGCTGCTAAACGCCGTACCGCGGCGG
TGACTGATTACCGGAAGAAGCTCCTTCATCACAAGGAGCTCGAATCCCGTGTCCGAACAGCTAGGGAGAA
TTTAAGAGCAGCTAA
>gi|3868958|dbj|AB015109.1|AB015109 AB015109 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-80, mRNA sequence
GATCATCTGGTATCCACTATCCACAACTGGGGTCAGCTTCTGGTTCTCTCTCTCGGTAACTTTCTGAGCT
GAAGAACCCTAATTCTTATCTTCACCGGATTCCGGGTATAGGGCTTTGTAAAGTTGTTGAATTTACAAAG
AAAGATATGCTGGTTTGTCTGGGTTTTGTAGAA
>gi|3868957|dbj|AB015108.1|AB015108 AB015108 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-78, mRNA sequence
TGAATCGTCGTTATCAAGGTGATTTCTTTCTCTGCCTCAAACATCGCTTACCCTCTTGATTGATTCCTCC
AATCTTCTTCGTGTGGTTTCACAGGTTTTACTTATGGTTAATGCAATCAAAGGAGTGTTCGTCTCTTGCG
ATATTCCGATGACACAATTCATAGTGAACATGAACAATTCGATGCCTCCGTCTCAGAAATTCATAATTCA
TGTACTTGATAGTACTCACTTGTTCGTGCAACCACATGTAGAGCAAATGATCCGCAGCGCCATTTCTGAT
TTTAGAGATCAAAACTCTTACGAGAAAGCCCACTTCTTAGATCACATCACATTCACACTTGCTTCTTTGT
TTTTCTTTCATTT
>gi|3868956|dbj|AB015107.1|AB015107 AB015107 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-77, mRNA sequence
GATCTCCANAATCAAAGATAAACGGAGGAGAAGAGAGCTTCGTCGTCTTCTTCTTCTTCGCCTCCATGAA
TCTCCTCAAGACGATTCATTACCAGTCTACCATTACTCGATTTTACCGTTTTGCCCCTACACGCTCCTTT
GCTTCTTCTGTGTCACTCTCTCCACAGAGACACATAATCTCTCTCGTTTCTATCTCTAATCGTGGAAGGT
GCTTCGCATTCTCGAGCGTCTCTTGGTGCTTCGCTTTATAATAATCAT
>gi|3868955|dbj|AB015106.1|AB015106 AB015106 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-76, mRNA sequence
GGTGTATATAATTGTTCATTTCCTTGAAAACGGTTACAGAATTAGGGTTTTGTTTCTTCTCTCTCGCCGA
TTGATCTTGAAATGTCTTCCCCAATTATAATTAGGGCACCGAAGAAGCAACCGCCGGAGCCGCCATGTCT
GATTTCGTTACTCCCCGAAGAAATCGTCGTCGATATCGTAGCCCGTGTCCCTAGATGCTATTACCCTACT
CTCTCCCAAGTTTCAAGGCGTTTCCGATCACTCGTCGCTTCTCCGGAGATTTACAAGAGACGATCCTTCT
TCGGGATGCACAGAAACAATGTCTCTACATCGCAATCTCCAAAGATCAAACCTCT
>gi|3868954|dbj|AB015105.1|AB015105 AB015105 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-70, mRNA sequence
GANTCACTTAACCAAACATGTCTGAAAAGGGGTTGATAAAAAAAGAAGACCACATGTTTCAAGAGGAGAA
GAGAAAGACAAACTATGGAGCAATTGGCTTGGCTTGCTTCATTTCTTGTTTCTTTGCATTCCAATTCATG
AAAATCGTAACAACACAACCTTCNACAACAACAACATCATCCATTGCCGTTATCGATAGCCCAATGTCCT
CCCATAAGCTATCTGATAGGAGAGAAATATGGAGAGTTATCCCACCATCTACCTATTGTCTCAAAATCGA
ATCTTTCATAAAATTCGCCACTTCTCCAAACGCC
>gi|3868953|dbj|AB015104.1|AB015104 AB015104 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-65, mRNA sequence
AACCATATAAAGCTTGTTCTTCTCCTTCCTTCTCCAATTTCGTAAGCTCAAAAATTTCGATTTCGATTTT
GATTATTGCCAAAGGTTTAAAGATGGATATTTTCGACAACTCTGATCTTGAATACCTTGTTGATGAATTT
CACGCT
>gi|3868952|dbj|AB015103.1|AB015103 AB015103 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-62, mRNA sequence
GAACAGAAAATGGAAATGATACTGATCTCGTCATCGACACTCAGGTTCCATCCATTGAGGACATCACAAA
GAATCGCCACCGGAACCAATAGAAGACGAACCACCACCGTGTGTGCAGACTACTACAGAGGAGGAAGAAC
GGTGGACGANAACATGGTGGTCCTTAGGAAACGAATCCATGAGATGAAGATGGTTGAACGCAACTTTGAA
CCTCCTTCTCATTGGATGCAATGGGAGAAACGTTTCTACTGCAACTACGACGCTACTATATGTGATGCAC
TCACTCTTCTCCAAACTTTTCTCATGAACTCTCGTCCCAGCGTCGCGTTTGGAACGTGTCTTCTTCTCCT
CGTCAGCGTTCCCGTCTCCTCCGCCCGTTTTTGCTTTTCGCATCCTTGATCTACTCTTTGGCTTTTGGAC
GCCCGTTC
>gi|3868951|dbj|AB015102.1|AB015102 AB015102 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-59, mRNA sequence
GACCTCCACTTTCCCTTTTGCCCCTCTTTTTTACAGATTTCACTCTCTGCTCTACTACTCTCTCCTCCTC
CTCCTCCTAAAGAAAGTTCTTAACTCTCCTGGGTTCTTCAGGTTTTTCCTTTTCTGGAATAAAAAGAAGA
AGAAATGGGTGTTCTTGATCATGTCTCTGAAATGTTTGACTGCTCTCATGGTCACAAGATTAAAAAGCGC
AAACAGTTGCAGGTACTTTCCCTCTTCCTTTTCTTATCTTAGCAGATTCAGCTGATAACTTAGATCTTGG
TTTGCAAAAAAACAAACATAATAATTCGTTGAAAAGTTATGATGAATGAGTCTAGTTAGAAACTAGCTTC
GATGGTTACTA
>gi|3868950|dbj|AB015101.1|AB015101 AB015101 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-56, mRNA sequence
TGATCACATCCTCACACACAAAAATAAATCATCACAAGACCAGAGTTAAAAGAGAGACATGTCGACTTCA
TTCACAATGATCGGCGGTGAAGGTCCCAACAGTTACCGGGAACATTCGAAATACCAGGGAGCACTGGTTA
TAGCTGCAAAGGAAAAGATGAATGAAGCCATCTCCACGAAACTCGATATCGACTTTACTTCAAATCTTGT
TAACATAGCTGATTTTGGTTGTTCCTCTGGACCGAACACTTTCACCGCGGTACAAACCTTAATTGATGCT
GTGGAAAACAAGTATAAGAAAGAAACAGGGAGCACTGGTTATAGCTGCAAAGGAAAAGATGAATGAAGCC
ATCTCCACGAAACTCGATATCGACTTTACTTCAAATCTTGTTAACATAGCTGATTTTGGTTGTTCCTCTG
GACCGAACACTTTCACCGCGGTACAAACCTTAATTGATGCTGTGGAAAACAAGTATAAGAAAGAAA
>gi|3868949|dbj|AB015100.1|AB015100 AB015100 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-55, mRNA sequence
TTTTTTGATGATGACAAGGTCTTAGCTTTGGTGGACATAACTCCCCAGGGTCCTGTTCACATCCTCCTTA
TTCAAAAAGTGAGGGATGGCCTAACTGGCCTCTCTAAGGCTGAGGAAAGGCACATCGACATCTTGGGCCA
CCTACTCTACACTGCCTAACTTTTCTCAAAACAAAAAGGCCTAGCA
>gi|3868948|dbj|AB015099.1|AB015099 AB015099 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-51, mRNA sequence
GACCTCATCATTCTTCCTTCTGGTTAACTGAAAATGGAGTGTAGTTCAGTGAGTGTACTAGGAATATTAC
TGGTATTTCCTCTCCTTCATAACCTTGTCACCATCTCCGGGCAGAATCTTCCGGCGGTGGGTTTGTTCAC
TTTCGGAGATTCCAACTTCGACGCTGGAAATAAAAAGTTCCTCACAAGTGCTCCACTTCCTCAAAACTTT
TGGCCTTACGGTAAATCTCGAGATGACCCTAAGGGCAAGTTTTCTGATGGCAAAATTGTCCCGGACTTTA
TTGCTACTCGTTTTTATAGGTACTCTATACTAAATGGAAATTTTGATTGGTAATTAAAGATATATGAAAT
TGATGAGGGGTGAATAAATCACAGCAAAATTCATGGGGATACCACACGATTTACCGCCGGCGCTAAAACC
C
>gi|3868947|dbj|AB015098.1|AB015098 AB015098 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-49, mRNA sequence
GGTCTTCTTCTTCTACATAAAATTGATTCGCCTCGAAATTTACACAGACTTGTCGCTCTCTCTTTCTCTC
TTATTTCACAGAGCCCCTAAACATTTCCAAAAATCTTGCAAAGGAAGAAAAACAATGGACAAATTTTGGA
CTTTCCTCACTGCTCTTCATTCAGGCGCTGGGCCTATCGTGATGTTACTTTATCCATTGTACGCATCGGT
GATAGCAATGGAGAGCACAACAAAAGTGGACGATGAACAGTGGCTTGCGTATTGGATAATATATTCCGTT
CCTCTCACTCACGGAACTGATTCTGCAATCCGCTTATTGAGTGGATTCCGATTTTGGTATACGGTGAAAC
TTGTTGTTCGTGGCTTGGCTAGTTCTTCCTCCAGTTTCAAGGGCGCAGCTTTTATCTACAACCGTGTTGT
TTAGAGAACAAGTTCAAGAAAACACGGGGGTCCTCCGGCTCCACCCACTCCAAAGCCCACCAAGCCCCAA
CATCCTCCACTCCATTTTT
>gi|3868946|dbj|AB015097.1|AB015097 AB015097 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-33, mRNA sequence
GGCTACCAAACTTCGCTAAACTTTAGTGCTTTACTCCAAAACCCAGAGTCCATCACACAAGTCCAAGCCC
GAAAACAAGGGTTCTTGCTCCGACACGACAACAAATCCAGATTTTGAGCTTAGGGAAACTTGAGAAGGAG
AAAAAAATGTCGAACATAGACATAGAAGGGATCTTGAAGGAGCTACCTAATGATGGGAGGATCCCAAAGA
CGAAGATAGTTTGCACATTAGGACCAGCTTCTCGCACTGTTTCCATGATCGAAAAGCTTTTGAAAGCCGG
TATGAATGTGGCTCGCTTCAACTTCTCACATGGAAGCCATGAATACCATCAAGAGACACTCGACAACCTC
CGCTCTGCTATGCAA
>gi|3868945|dbj|AB015096.1|AB015096 AB015096 RIKEN-PMB-FL1 Arabidopsis thaliana cDNA clone FL-32, mRNA sequence
GGTTTTTTCGTTTTTGTTAACTTCGCCGTGTAGTTGTGGTGGTGAGATTGTGAGAGATATGGAGGCGGAG
AAAATGGAATTGAAGCTCTACAACACGATGACGCAACAGAAAGAAGTTTTGATTCCAATCACTCCTGGCA
AAATCGGATTATACGTCTGTGGTATCACCGCTTACGATTTCAGCCATATCGGCCATGCTCGCGCCGCCGT
TTCCTTCGATGTTCTTTACAGATACTTGAAGCATTTGGATTATGATGTTACTTTTGTCCGCAATTTCACT
GATGTTGATGACAAGATTATTGATCGTGCTAATAAGAATGGAGAAGACCCGTTAGATTTGAGTAATCGGT
TTTGCGATGAATATTTGGTAGATATGGGTGCTCTGCAGTGCCTCCCTCCCACCCAACAGCCTCGTGTC
>gi|3805663|gb|AI223460.1|AI223460 sp22.1 Arabidopsis thaliana cell suspension Arabidopsis thaliana cDNA similar to ATPase, mRNA sequence
CTTCCATTACTTTCTTTGCTTAAAGTTAATAACATTGGTATTTTGTTTAATCTCATCAGCAAGACTTTTT
AGATCTTAGGACAGCAAAAGAATTTAACTTATTGTTATGCACTGGAAACGAAAGTTGAAAAAAAAAAATC
TTATTTCCAAATGAGATCACCCATGAACTTAAGTGCGGGAACCCCTCTTATCTCTGCGTCTAGCAATGGC
GATTGGATCAATTTTAACCCCGAAAGTTCTGTATCATTCTGAATAAGTCCAAGCACACGCGTTTGTTCCT
TTCGTCTTATTGAGCAAAATTTGCAATCGGATTCAGATTGAGGTAGAAGCTGATTAACAATAAGCCGGTG
GACTGGCACA
>gi|511963|emb|Z33723|Z33723 ATTS2814 Strasbourg-A Arabidopsis thaliana cDNA clone FAFK75 5', mRNA sequence
TCGAAAATGGCGCAGCGATCTAGGGTTATCACCATGTCTCCTCTCATTCTCGATCAAGAAGTTGATCTCG
ATCTCTGGGAAGTTGTTAATCCTTCTGATGGAGAGTTCTCCGACGATTCTTTCTCCGTCGATAGTCTTTC
CGACGATGACGTCATATCTCTTGACGACGCTTCCTTTGTCGCACCCTCTGTCATTTCTCCGCCGCATGAG
ATAATTCCTATTGCTGACGGTGGTGATCTCGCCGNGGATCTGGATGGTGATGATGATGTTGGNGATGATG
TCGNTCGCGATGAAGTTGATGAGAATGA
>gi|511962|emb|Z31677|Z31677 ATTS2690 Strasbourg-A Arabidopsis thaliana cDNA clone FAFJ30, mRNA sequence
ATTTCTGATCATTTACACCCCTAAAAAGAGTAGAGCTTTCGTGAAGCCACCATGTGTGGAGGAGCTATAA
TCTCCGATTTCATACCTCCGGCGAGGTCCCTCCGCGTCACTAACGAGTTTATCTGGCCGGATCTGAAAAA
CAAAGTGAAAGCTTCAAAGAAGAGATCGAATAAGCGATCCGATTTCTTCGATCTTGACGATGATTTCGAA
GCTGATTTCCAAGGGTTTAAGGATGACTCGGCTTTTGACTGCGAAGACGATGATGATGTCTTCGTCAATG
TTAAGCCCTTTTCGGTCTTCACCGCAAACTACTAAGCCCGTAGGCTTCCCGCTTTCGTCTTCCACTGGTT
CAGCATATGCCAAGAAAACTGGTAGAGTCCGCTGAGCAAGCTGAGAAATCTTCTTAAGAGGGAGGAGGGA
GGAATCAATTCCGCGGGATTTAGGCAGCGTCCCTTGGGGGAAAATT
>gi|511961|emb|Z31676|Z31676 ATTS2689 Strasbourg-A Arabidopsis thaliana cDNA clone FAFJ28, mRNA sequence
GGTGGTTGTGTGGTGGTAGTAACACTAAAGATAGAGCAGAAGAAAGAGTCAATTCCTAAAGGATCTTCTT
CACTTAGTCCTTCACTGAAGAAGACTACTACTAGTAAGACTGGTTCTTCCTCTTCATCAGTGAAGAAGAC
CACGAGAGGATGGATTGGTAGAGGAGGATCAGGATCAGGAGGGGAAGAGGATAAGATTGGGAATGTGGCG
TTTCCTGAACCTGATGATCCAGAGTGGT
>gi|511960|emb|Z31674|Z31674 ATTS2687 Strasbourg-A Arabidopsis thaliana cDNA clone FAFJ25 3', mRNA sequence
AGATAAATAATCTTCACCTCTACCATCGAAGACAAGTGGGATAAAACTCTCGCCTAAAAACAAGCAATGC
CATAAGGCCCATAACCCTTATTTGGATTAATCTGTGAGGTGAAACAATAGCAGCAACTACATATGTATCA
TTTAGCTCTGTGAGAGCTCGCGGCTTCGTTTAGCTGCAGCAACAACTGCATTCATAAGTGTTGCCCGGAA
AGAGCCTTTCTCTAGTTCATGAACTCCGGCTATTGTAGTGCCGCCAGGTGAGGTAACATCATCTTTCAAC
ACACCTGGGATGCTTCCCAGTTTGGCTAACCATCGTTGCAGCTCCAAGGAACGGTCTGTGAAGCTAAACT
CAATGCAAGCTCTCGGGGGTAAACCAGCAGGTACTCCTCCATCGGCTTAAAGCTTCCAATTGGCTAAAAA
TTTGT
>gi|511959|emb|Z31673|Z31673 ATTS2686 Strasbourg-A Arabidopsis thaliana cDNA clone FAFJ22, mRNA sequence
CGGACGAGGAGCATACTTTCCTTCTTATTTAGGTATGATGCTTGTTATAACGTGGGCGATCTGCACCTTC
ATCGAGCTTCTGTCAATGTGGAATTTGACGAGACGAGAAGTTCAGCTATGCAATATGTTATCCCCTGAGG
CTCCCCGTCTCTCTCTTGCAACTTACAACTGGGGACTTGTTTTTGTAGCAATGCTTGTAGACAACTTCCT
ATATCCGATATCAGCTTTCCGGTCTCATTTTTCTCAATCCATAAACTGGTCTGGAATCAGATACCACTTG
AAAGATGGAAAGATATTCACGATGGAGAGACGAAAGGATATGGGACCAACAAAGACTGATTTAGGAGGCA
AACATTTGTTTGGTAAGAAAGGAGCTCCCTCAGAAAGCTTCATTCCT
>gi|511958|emb|Z31672|Z31672 ATTS2685 Strasbourg-A Arabidopsis thaliana cDNA clone FAFJ20, mRNA sequence
TCAACCGTCTTGTCAGGCTTCACAACAGCTGGGCTTATCCTACTCGCTAAGCAGCTTTCATCAGAAAAAG
AGTGAATTCATAATCCTTCAGGGGTGGTCTCTATTACTCTCATGTACAGTGCCAAATATTCAAATTTACA
ATAGCAAATTTTTCTACTTCCTCTGTCTATGCGTTAAACTATGGAATGTGTTGAGTGTATATTCTTATAG
AGAAAACGAAATATCTTTGTTATGAATAATTGAAGTTTGCCA
>gi|511957|emb|Z31671|Z31671 ATTS2684 Strasbourg-A Arabidopsis thaliana cDNA clone FAFJ19, mRNA sequence
CCGGTCCTCAATATAAGAAAACTTGACAAAGAAGAAACACAATGTCTATTGCTCATAAAATTTGGAGAGA
CTCGAATACAAAGACGGGTAAAAAGTCTGGGAAAAATAAAATCTGAAAATTGTWTCACTGGTCACCAGGA
ATTGACTTGATAATGTCAGAATCACCAGGATCAACAATGCTCAGACAAGAAACACGGAAGTACTTTCCGC
AAGCTGTTCCCAAATCAACGTTATTTCCATTGTAATGGTGGACACCAACTTTAGCGAGCATTGCGTAGTA
CTCAATCTCTGATCTTCTCAACGGTGGGCAATTGGTGGAGATTAGAATCAGTTTCCCTTTGGAGCCACGG
AGGGATTTGAGAACAGACTTGTAACCAAGAGTGT
>gi|511956|emb|Z31670|Z31670 ATTS2683 Strasbourg-A Arabidopsis thaliana cDNA clone FAFJ09, mRNA sequence
CGCTTAGCTACTGGCTTCACTTATCTCGGCCCCAAATTTATGAAAGAAAATGGCATAAAGCATGTGGTGT
TTTCAACTGCAGACGGAGCACTGGAGGNAGCTCCAGCGATGGGGATAGCTGANGCCATCTTGGATCTCGT
GAGTAGTGGTATAACACTCAAAGAGAACAACTCGAAAGAAATTGAAGGAGGTGTTGNGCTGGCAAAGCCA
GGCGGCA
>gi|511955|emb|Z31669|Z31669 ATTS2682 Strasbourg-A Arabidopsis thaliana cDNA clone FAFJ08 5', mRNA sequence
GTAGTTTTGTTCACTTTCGGAGACTCTTACTACGACGCCGGAAACAAAGTGTCTCTCAGCCAAAGGAAAG
ATCTCCTACAAACCTATTGGCCCTACGGAAAATCCCGCGACTACCCCAACGGTAAGTTTTCCGAGGGACA
CATCGTCCCCGACTTCATCGTTGATTTCATCTCTATCCCGAATGGAGTACTCCCACCGGTGTTTATACCG
GGTGTTGATATTTCACGTGGAGTCAGCTCTGACGCCGTCGATGCTTCT
>gi|511954|emb|Z31668|Z31668 ATTS2681 Strasbourg-A Arabidopsis thaliana cDNA clone FAFJ03, mRNA sequence
TGTTCGCGAACTCGTCAAATTACTTGGTTGAATCTGAAGGTGGTGGGGTACCTCTCCCATCAGGAGGCAT
TCTTACTCCTAAGGGTCTTCAAACTCTTGGTCTTTCTGGTTTAGGATCAAGTACTGGTTTTGAGCGYCTG
CATTATATGTTGGAGAGAGTATGGGATCCTATTTTAGTTACTGGMGCTCCAAAGTGTATTAGYCAGTCCT
TCTTAAACGCTTTTGAGAGTTGGCATTCTTTTGATACAAMTCCACTATATGCTCTTCTCCACGAGGCCAT
ATACTGTGGAGGGTGCTTCATCAGGATGGTCTGCTCATMGATTACGGGATAAATATGAGTACAAATTCGA
CGCAA
>gi|17654|emb|Z18525|Z18525 ATTS0901 AC16H Arabidopsis thaliana cDNA clone TAY097 5', mRNA sequence
CAATCTTCAAAATCTCTTCCTTCCATGATTCCGTTATCGTAAAGATTTGTCCTTTATCCAAATTTTAGGA
TTTTGAATTCTTCTTCTTTCCGATTACCGGATTCCAATGGCGCCTTTTGTTGAAGTCTGTAGGTATAAGC
CATTACCGCTTTCATTGAGCTCTCTCTGTACATGCCCTTGCCGTTCCTCTCCAAGGAAATATCTAATNCT
TCCTCAATTCTCTGAAAAGTACCCGAAACCATTGTTGTCTCATTCTCGCTTTACTCCGATTTCTGTTAAC
CGGAGAGTTATCACGGCCGTT
>gi|17643|emb|Z18516|Z18516 ATTS0892 AC16H Arabidopsis thaliana cDNA clone TAY089 5', mRNA sequence
AAAAAAATGGGATCTTCACCACCGAAGAAGACGACTCTGCAACGGTACTTGTCACAGCTTCAACAACATC
CTTTAAGAACAAAGGCAATAACTGCTGGAGTTTTGTCTGGTGTTAGCGATGTTGTATCACAGAAGCTCTC
TGGCATACAGAAGATTCANCTGAGAAGGGTTCTNCTCAAAGTGATATTGCTGGTGGGTTTCTTGGACCAG
CAGGGCATTTCTT
>gi|17629|emb|Z18506|Z18506 ATTS0882 AC16H Arabidopsis thaliana cDNA clone TAY148 5', mRNA sequence
TAATCACGAAAGAGGGGCTCGTCCAAATCCTGTGAAGGAAAAAGAAAGAGCTTCAGAAAGGGAATGGTCT
GGTTCATCTGATAGAAGGAATCGTGAGGATAAAGATGCTGGTTATGAAAGGGACATACCGAGGGAGAAAG
ATGTTGGTCACGGTTATGATATGCCAGAGAGAAGGCATCGTGATGATAGAGACACCGGTCGTGAGCGTGA
GAGGGAACATCATCATAAGGATCGTGAACGTTCAGAGAACATGTTCGTGA
>gi|17604|emb|Z18486|Z18486 ATTS0862 AC16H Arabidopsis thaliana cDNA clone TAY143 5' similar to DNA-DIRECTED RNA POLYMERASES I AND III 40 KD POLYPEPTIDE, mRNA, mRNA sequence
AAACTTACACTTCATTCAGTTGCAGCCAAGATTCATTACCTGAATTTGCTAATAATCCTATCACTCCATG
CGACCTCGATATCTTGATAGCAAAACTCGCCCCTGGTCAGGAAATCGAGCTCGAAGCTCATGCGGTTAAG
GGCATTGGTAAAACACATGCAAAGTGGTCTCCAGTAGGGACTGCTTGGTATAGAATGCATCCTGAGGTGG
TTCTACGTGGGGAAGTTGAGGATGAACTTGCTGAACGACTTGTAACGATGCCCACAGAATGTTT
>gi|17589|emb|Z18476|Z18476 ATTS0852 AC16H Arabidopsis thaliana cDNA clone TAY055 5', mRNA sequence
CTCTGAGCCACAAGAAGTGTTTTTNGTNGAAGGATCTACTGAACTGGTTTGTAATATGGGGGAAGATACA
AAGGCAACCATTGAGCCAACCGCAAACAAGACTACTTCTCTTGAAAAGCCATCAGAGGCTATGGCTGGAA
AGGAGAATGCTGGGGGTAAGGAAACACAAGANCTGGCGAAAGATGAGGATATGGCTGAGCCAGACAATAT
GGAGATAGATGCTCAGATTAAGAAAGATGATGAAAAAGCTGAGACGAAGATAAGAGTCA
>gi|17563|emb|Z18457|Z18457 ATTS0832 Grenoble-B Arabidopsis thaliana cDNA clone GBGy8 5', mRNA sequence
AAATAATTGAGTTTTTTTTTTAATTAGAACAATGGGGTTGAGTGGTGTTCTTCATGTGGAGGTTGAGGTT
AAGTCTCCGGCTGAAAAGTTCTGGGTAGCCTCGCGACGGCATCAATCTCTTCCCCAAAGCTTTCCCTAAC
GACATCAAAACCATCCAAGTTCTAGCCGGCGACGAACGCTCCTGGCTCCATTCGCCTCATTACTTAGGAG
AAGGTCTCCAC
>gi|17552|emb|Z18447|Z18447 ATTS0822 Grenoble-B Arabidopsis thaliana cDNA clone GBGy16 5', mRNA sequence
GAGAATGCTTGCCTAGAAAGCTATCAAGCGCAACGAGCCTTGGAAGCATGGAGGAGAGCTATTTTCTGCA
AGCTTCTCTTGATTCTTCAGATAAATTTTCTGAGAGCACGTGCCTGAGGCAACTATGAGTCCGTACTACA
TGAAGAGCATCACACCGAGTGCTTATGAAGCCACACTTCGACAGAAAGAGGGTGAACTTGCGGCATACAT
GACCCGCTTGGCATCAATGGAGTCTATCCGAGATTCCCTGGCTGAAGAACTAGTCAAATGACAGCAGAGT
GTGAGAGCTACGGGGAGGCAGATAGGTCCGGCATAAGCAGAGCTGGAA
>gi|17541|emb|Z18437|Z18437 ATTS0812 Grenoble-B Arabidopsis thaliana cDNA clone GBGa496 5', mRNA sequence
GAAAGCTGTTCGATCAACAATACTAGAAAACCTCCCAAATACTGCAAGGAAAGCTAACAACACAGGAAGC
TTCTCTTTTGCACCTATCGTACACAACAACATCAACAACAGAACACCAATAGAGATCAACTCTCCTATGA
GATTCCCTCTCTT
>gi|17530|emb|Z18427|Z18427 ATTS0802 Grenoble-B Arabidopsis thaliana cDNA clone GBGa486 5', mRNA sequence
GCGGTGATAGCAGAAGTGGATCGTGTTTTGAGACCGGAAGGGAAACTGATAGTTCGAGACGATGCGGAAA
CAATACAGCAAGTGGAAGGCATGGTGAAAGCAATGAAATGGGAAGGTTCGAATGCTTATTCTAAGGAAAA
AGAA
>gi|17507|emb|Z18407|Z18407 ATTS0782 Grenoble-B Arabidopsis thaliana cDNA clone GBGa425 5', mRNA sequence
AAGAGAATAAACAATGGTGGGTTCTCACAAAGCAAGCGGAGTGCTTCTTGTGCTACTAGTGGTTATGGCC
ACCACAATAGCAAACGGGACACCGGTTGTCGATAAAGCAAAAAATGCAGCTACAGCAGTTGAAGATACAG
CAAAAATGCAGCTACAGCAGTTGGCGGTGCAGCTGCATCAGTTGGTGCTAAAGTATCAGGTGCCAAACCA
GGCGCGCATCGATGTTAAGCATCAGGAGCCAAAGGAGACGGCAAACTGATGAATG
>gi|17496|emb|Z18397|Z18397 ATTS0772 Grenoble-B Arabidopsis thaliana cDNA clone GBGa383 5', mRNA sequence
CTAGCCTCTCTATCTTTATCTCTCACAACAAAATCTTTGAAATGGCGATCTCTAAGGCTTCCATTGTTGT
TCTCATGATGGTGATTATCTCCGTCGTTGCATCGGCACAATCTGAGGCACCAGCACCAAGTCCTACTTCT
GGATCTAGTGCGATCTCAGCGTCTTTCGTGTCAGTGGAGTTGCAGCAGTCG
>gi|17452|emb|Z18367|Z18367 ATTS0741 Grenoble-B Arabidopsis thaliana cDNA clone GBGa263 5', mRNA sequence
CCTATGACGGTACCGCCGCCAAGTATGGAACCGTTGATAGCGCCTCTCTCATTATCTTATCCGACTATTT
CATGGCCGTTAACATCGTCGTTAACAACACTGCGCCACGACCAGATGGTAAAACTAAGGGAGCACAAGCT
TTATCCATGAGAATCTCCGGAAATTTGCTGCTTTCATCAAACTGCAAATTCTACGGTTTCAAGACACAAT
CTGTGACGATACAGGAAACATTCTCAAGGATGTACGTCGAG
>gi|17377|emb|Z18789|Z18789 ATTS0681 Ors-A Arabidopsis thaliana cDNA clone OAOM5 5', mRNA sequence
GCACGAGGACCCTTCTCTTCAATTCCCTCTAAAACCCTAACCCCACACCAAAAGTCTTCCTTTGAATCAA
CTCTCCACCATTCCCTAATCACCCACGACACTGATGAAGCATGGAAGGTCTTCCGATCCTTCGCTGAAGA
TTCTTCTCTCCCGGACAAGCGTCTCCTCAATTCTCTCATCACCCACTTGTGCCTCCTTCCACAACACAGA
TCAAAACACCTCCCTCAGGCACAGACTCAAGCGTGCTTTGTTCACGACGG
>gi|3719207|dbj|C99850.1|C99850 C99850 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTGTCTTGAGCTTAANATCTACGGTCAGTGGATGTCCGGTGGTCAACGACGGCTCTCCCGGGTCGCCAAC
CCGACCAACCATCTCTCGGTCGTTGGGAACTTTGTTGGGGCCTTGCTTGGTGCGTCCATGGGGCTTAGAG
AAGGCCCTATATTCTTCTATGCTGTTGGGATGGCTCATTACTTGGTTCTNTTCGTGACTCTCTACCAAAG
GCTACCGACCAACNANACTTTGCCTAAAGATCTTCATCCTGTCTTCTTCCTCTTCGTTGCGGCTCCAAGT
GTTGCTTCCATGGCTTGGGCTAAGGTCACTGGCTCCTTCCATTATGGCTCCAAAGTTTGTTACTTTATCG
CCATTTTCCTCTATTTCTCATTGGCTGTTCGGATCAATTTC
>gi|3719206|dbj|C99849.1|C99849 C99849 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GGAACAGGAAACATAGGGAAGAGTGATGCCAATCTAATCGTGGCACTGATCTACATCTATGTAGCGGGTT
TCGCGTGGTCATGGGGACCGTTGGGATGGTTGGTTCCTANTGAGATATCTCCACTAGAGATCCGATCAGC
AGCTCAAGCCATAAACGTTTCGGTCAACATGTTCTTCACATTCCTTGTGGCTCAGCTCTTCCTCACTATG
CTTTGTCACATGAAATTCGGACTATTCTTCTTCTTCGCCTTCTTTGTTGTCATAATGACAATATTCATCT
ACTTGATGTTGCCTGAGACAAAGAATGTGCCAATCGAAGAGATGAACAGAGTGTGGAAGGCACATTGGTT
CTGGGGAAAGTTTATTCCTGATGAAAGCTGTCAATATGGGTGCTGCTGAAATGCAACAGAAGTCCGTATG
ATGATGATCAAG
>gi|3719205|dbj|C99848.1|C99848 C99848 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ATTTCTGTCTCTGTGGAGACAGCTGAAGAAGCAGCAGCACTATCAATGGCGTCTCTGAGATTGTTCTCAA
CGAATCATCAATCTCTTCTCCTTCCATCATCTCTCTCACAAAAGCCTCTAATATCTTCACCAAGATTCGT
CAATAACCCTAGCAGACGGAGTCCAATACGATCCGTTCTTCAATTTAATCNCNAACCGGAACTCGCCGGA
GAAACGCCGCGTATCGTCGTTATCACCTCCGGAAAAGGCGGTGTTGGAAAGACGACAACCACCGCAAATG
TCGGTCTCTCTCTCGCTCGTTACGGTTTCTCAGTTGTCGCCATTGACGCCGACCTTGGTCTCCGTAACCT
CGATCTCCTCCTAGGGTTAGAGAATCGAGTCAATTACACTTGCGTCGAGGTTATAAACGGAGATTGTCGT
CTCGATCAAGCTCTGGTACGTGATAAGCGTTGGTCGA
>gi|3719204|dbj|C99847.1|C99847 C99847 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GGAAAATAGGGAAAGCCATGCGCATAGAGGTTGATCGAAGTGGAATGATTCCAAGGTTGAGGTTCCATGA
TCGTGAATCGTATGCAAGCAATAAAACCAAGGAGTATGATGACATTGCCATCAAATTCTTATCCTATGTG
CTCCTCCTCCTTGTCATTGGCTTGTCCATATATTCTCTCGCTTATGAACGCCACAAGAGCTGGTATTCTT
GGATACTATCTTCACTAACAAGCTGTGTCTACATGTTCGGTTTCATCATGATGTGTCCTCAGCTATTCGT
CAACTACAAGCTAAAATCAGTGGCACATTTACCATGGAGACAGATGACTTACAAGTTCCTCAACACCATT
ATCGACGATCTCTTTGCCTTTGTCATCAAAATGCCGATTTTACATCGACTTTCTGTATTCAGAGATGATG
TGATATTCTTGATATACTTATAC
>gi|3719203|dbj|C99846.1|C99846 C99846 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TGATTTCTCTACCACTCACTACACCGATTTTACCCAGCCGGTGTCTCCTCCACAAAACCCGCCGGCAAAA
CTCGACTCGCCGCCGCTTATTGATTCGATCATCATCGAGCTTACAAGACCAATTCACCGTGGAGACGACG
AAGCGAGTGGTTCTTGTGAGACATGGACAGAGCACGTGGAACGAAGAAGGGAGGATTCAAGGAAGCTCCG
ATTTCTCCGTTTTGACGAAGAAAGGCGAGTCTCAGGCTGAAATTTCTCGTCAGATGCTCATCGACGACTC
CTTCGATGTCTGCTTCACCAGTCCATTGAAGAGATCAAAGAAAACAGCTGAAATCATATGGGGAAGTAGA
GAAAGTGAGATGATTTTCGATTACGATCTCAGAGAAATCGATCTCTACTCTTTTCAANGTCTACTTAAGA
A
>gi|3719202|dbj|C99845.1|C99845 C99845 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ATCCCATTGTGCAAGATCAATGGAGTGAACCAGAGTCAGAACACAAAGAAGCCATCTCAAAAGTACCTTG
AAATAGTCACAATCGATAACTTCGACTTCTGGTTCATGGGATTCGTGAGCTACCAGAAAGCTTTCAACTG
TCTCGAGAAAGCGCTAAACAATGATGAGCAATAAACCGCAGTGGTTTTCTCTGACGGAGCTAATTAGTGC
AGGTGGAACAAGAAATATTTCATTTCTACTTTCCCCTGTTTCAGTCAGAGAATGTTTGTACAAACTCACA
AATTCTTTTTTTTTGCTTTACCCACTTTGGTTTCCATTGTAGACACGAGAAAGAGATGAATATATTTAGT
TGATCTCATCTGTTAACCTT
>gi|3719201|dbj|C99844.1|C99844 C99844 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CACTGTCACAGCGAGAGACTCATACAACTTCCTTGTCAACTGGTTCAAGAGATTTCCCCAGTACAAGTCA
CACGACTTCTACATTGCCGGAGAAAGCTACGCCGGCCATTACGTCCCACAACTTTCGGAGCTCATCTACA
AAGAAAACAAGATTGCGTCGAAGAAAGATTTCATTAATCTCAAGGGTTTAATGATAGGAAACGCGTTATT
GGATGACGAAACGGATCAAAAGGGGATGATAGAATATGCATGGGATCACGCGGTGATATCAGATGCATTG
TACGAGAAAGTTAATAAAAACTGCGATTTCAAACAAAAACTTGTGACCAAGGAATGCAACGACGCTTTAG
ATGAGTATTTTGATGTATACAAGATCCTTGACATGTACAGTCTGTACGCTCCAAAGTGTGTCCCACCTCC
ACGAACTCCTCTATTTCTCATTCCAGTCGCCGGAAACCGCC
>gi|3719200|dbj|C99843.1|C99843 C99843 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CCTTTTTATATGTCTTTCAATTTATGCAGTTCCCAAACGTGATTGGGTTTGTTCTAGGTGCACTTCAAAT
GATACTCTATGTGGTTTACAAATACTGCAAAACGCCGTCGGATTTGGTTGAGAAAGAACTTGAGGCTGCG
AAATTGCCAGAAGTGAGCATCGATATGGTGAAGTTAGGTACACTCACATCTCCTGAACCAGTAGCGATCA
CCGTCGTCCGATCGGTGAACACATGTAACTGTAACGATCGAAATGCTGAGATTGAAAATGGTCAGGGAGT
TAGAAACAGTGCTGCAACTACTTGAGTTTGCCCAAGAAACCCTAATAAGAAACCTATTTGTTGACTATTT
TGACTTTGTACCCTTCTTGATATACCTATCAATCACCATTGTCCACGTGTACTAGTTTCGTTGTAGTAAT
TTTCAAAGTTTATCGAAGTATGCGTATTCNAAGGATTAATTAAATCGGGAATTACATT
>gi|3719199|dbj|C99842.1|C99842 C99842 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AAAGTTTCTGTTTCCTTTACTCACACCATTAAAGCCATGGAGCCTTTCTTCTCTGTTTTATTGTCTGCTA
TGTTTCTCGGGGAGAAACCTACTCCATGGGTACTCGGTGCCATTGTACCAATTGTTGGTGGAGTTGCACT
TGCTTCAATTTCGGAGGTCTCATTCAACTGGGCTGGATTTTCGAGTGCAATGGCATCAAACTTGACTAAC
CAATCCCGTAATGTGCCGAGTAAGAAAGTCATGGTTAAGAAAGATGATTCTCTTGACAACATCACTCTCT
TCTCAATTATAACATTGATGTCTCTCGTTCTGATGGCTCCTGTGACTTTCTTTACGGAAGGCATCAAGTT
CACTCCTTCATACATTCAATCAGCTGGTGTGAATGTTAAACAAATATATACAAAGTCTCTTATCGCTGCA
CTCTGCTTCCACGCATACCAACANGTGTCGTACATGAATATTG
>gi|3719198|dbj|C99841.1|C99841 C99841 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ANAAGCTTTGAAGAACCATGGCGATGTCTCATGTCCAGCCTGTGCTTTTCTTCCTCGCATCACTCTTCTT
CTTACTGGCTTTGTGCAGCGCCAACGATTTTGAATATTGCACCAAAAATGGACATGATTATGGTGTCGTC
TCTTGGATCGAGGTCTTTCGGGTTGGGCCTCAGGAAAACCCAACCCTCACTATAAATGTATTTGGTACTG
CGACGAAAGAAATATCCGCGGGAACCCTTGTATATGTAGCCTATAGATCTGGGGATTTTACAGGCCTTTT
AAAAACTTACGACCTATGTGATGTGAGTTTGGCATGTAACATTGATTCTGAGATTGAAGCTGGCGACGTG
TTTGACTTCAGTCTTAAAGACTTCTTTATGTTGGTTTTGATGAGGGAATCAAGTATTCCGTATCTTTGCG
TCNAAAAACCGCAGAGGAAGAGGACCCNTAATAAAAATGTGT
>gi|3719197|dbj|C99840.1|C99840 C99840 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AAAGAATAGAGGAAGAGAAGAAAGAAGGATCAGTTAATCGAGATGCTGTTCTGGCTAGAGTTGAGACAGA
GAAGAGGATGTCACTTATCAAAGCTTGGGAAGAGGCTGAGAAATGCAAAGTGGAGAACAAAGCTGAGAAG
AAGCTTTCTTCAATTGGATCATGGGAGAACAACAAGAAAGCAGCTGTGGAAGCTGAGCTCAAGAAAATGG
AGGAGCATTTGGAGAAGAAAAAAGCAGAGTATGTGGAGCAGATGAAGAACAAAATAGCTCAAATTCACNA
GGAAGCAGAAGAGAAGAGAGCGATGATTGAAGCTAAGCGTGGAGAAGAAATTCTCAAAGCAGAGGAATTA
GCAGCCAAGTAACGTGCCACTGGAACCGCTCCCAAAAAGCTTTTCGGATGCATGTGATCTCTAATCATCT
CGATGGGGANACANATGAAATATGGTATTGATGT
>gi|3719196|dbj|C99839.1|C99839 C99839 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GAGTAGCCAAATCGCTTTGTCACCGGCCATCGCCGCCGCCATTCGCCGTCCGTCCTCTCACGACTGTCTA
TCCGCTTCCGCCACTACTGTTACCGCCACCCCCATGGCTCTCAAATCTTGCATCGTCGCGCCTCTCTCGC
TATTCACCTCTCAATCTCAAATCAAACACTCAAGCTCAAGAAAAACTTCTCGAACCACGATTCGATGCGA
TGTAGCGATAAAATCCGCAGATTCGATAAACGCAGACGCCAATCCTTCGTCCTCACCGTCATCAGAGGAA
GAAATCGAAGCGGAAGCGAAGGCGAAGATAGGATCTAGGGTTAGAGTAACTGCACCGTTGAAGGTTTATC
ATGTAAATCGAGTTCCAGAGGTTGATTTANAANGTATGGAAGGTNAACTCAAAGATTACGTTTGCTGTTT
GGAA
>gi|3719195|dbj|C99838.1|C99838 C99838 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GCAACGANAGCAANAAATGGGTAGTTTCAATCTCTGACTCTCCAAAACCACCGTCTGAGAGAATCACCTT
CACGTTCCCGGTCATCAACTCATCTGCACATGTAGCTCTAGTTGTTTGCGGTTCTGGGAAAGCTGAAGCT
GTGGAGGCAGCTTTAAAGAAGACTGGGAATGTACCACCTGCTGGTTCTGTTTCTGCTGAAGACAANTTGG
TTTGGTTCCTGGACAAACCAGCATCTTCCAAGCTCTAAAAACAGGTGCTATGCTTCCCATTCCNGTGAAC
TTACCAGTGTGACTAGTCCGGTTTTAGTTTTTGGATTTTGACTCNTTGGTTCTCTCCC
>gi|3719194|dbj|C99837.1|C99837 C99837 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CAATATTCTTATATTTGGGCGTGATTTAAAGCAGGAGATGAGCGTGGGGCCGAGTGCATATCCTCTGCTC
AAGGATTGGATCCGAAGTTCGGATGGAAAGCTGAGTTTCTTGGGGTACGCTAAGTTCTTGCATGGTGTGA
CCGTACGAAGCTCAAGCTCGAGACCTAGGTGACACACCATGATGTAAAAAGTCTTCTAACATGTGAATTG
AGTTTCAAGAAACATCCTAAACAATGTCGTCGTCAGAGACCTTGGATTCNAAGATTAAAAAAAAAAACTT
GAAATGGAATTGAANTCNGGTAGGTNTTTCCTTTGTAAATNATNCTTTGANCATTTTGTTTTCGAAACAA
>gi|3719193|dbj|C99836.1|C99836 C99836 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AGAAGACATCTAAAGCCATCAAAAATATATCCATAGAAGCTTCATCGAAATGGCGAATCAAGCAGCTGCT
GCAGCATTCTTCCTTTTCGCTTTAGCCGTCTTCTCCAACTTGGAGCTCTCAGCTTCTTCACTTGTCAGTG
GCAAGATCTCTTGCCTTGACTGCCACCGCGATTTCGACTTCTCAGGCATTAAGGTCCTCCTTAAATGCGA
CGGAAAGAAGAAACAAATAACCGCGATGGCAGCTGCAGACGGATCTTTCCGGTCAGTGCTTCCAACGGCT
GACAAAAAAGGCTCCATAAATTGTCTTGCAAAGCTCTTGGGAGGCCCTGAGCAACTCTATGCTCACAAAC
ACAACTTGGTCTCTGAATTGGTCAAGTCTAAACACGATTCCNAAGTTTTAACTACCTCAAACCCACTTGC
CTTCTCTCTCTCCTTGC
>gi|3719192|dbj|C99835.1|C99835 C99835 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGCGATAGCTGAGGCTACAGAGCATTTGAAGCAACACTGCTTGAACAACATCTGTCCACACGTGTATGCT
CCTCAAATAGAGGAAACGGTCGATGTGACTTCTGATTTATGTGCTTACAAGGTCCAACTTTCTGAAAAGC
TGATGAGCAATGTGATCTTCAAGAAGCTGGGAGATTCAGAAGTAGCTTGGGTGGATTCCGAAGTAGGGAA
GACAGAGAGGGACATGAGGTCTCTACTACCGATGCCAGGTGCTGCTTCGCCACACAAACCTGTTCTAGTA
GGTGATCTGAAAATCGCAGACTTCAAGCAGTTTCTGTCGAGCAAGGGTGTTCAGGTAGAATTTGCAGGTG
GAGGAGCTTTACGTTGTGGTGAATATGTCACTCTACCAAANGTTGGACCGACGGGTCA
>gi|3719191|dbj|C99834.1|C99834 C99834 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGAGTCTTCGACGAGTCTCCGGCTGCNAGTTTCTCTTGCTCCGGCAAACAGACCTGTCATTGCTTCTCTC
TCCGGCTAACTACACAGAAGCATGGTGTTTGGACAAGTAGTAATAGGTCCTCCAGGATCGGGAAAGACCA
CTTATTGTAATGGAATGTCTCAGTTCCTCTCTCTAATGGGCAGGAAGGTTGCTATTGTTAATCTGGATCC
TGCAAATGATGCATTACCTTATGAGTGTGGTGTGAATATAGAAGAATTGATCAAGTTAGAAGATGTTATG
TCGGAACACTCGCTTGGTCCTAATGGAGGTCTTGTATATTGTATGGAGTACTTGGAGAAAAACATTGACT
GGCTGGAATCTAAACTAAAGCCTCTTCTGAAGGATCATTACATTCTCTTTGAT
>gi|3719190|dbj|C99833.1|C99833 C99833 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GAAGAACAGTGAACCGGTTATATGAGAATAAGGCACAGATGAATTCTATATCAATGCATCTTGGAGAGAG
TGTTGCGATTGCTCGAACAGTTGGGCATTTGTCGAAGAGCGCAGAGGTTATGAAGCTTGTTAATAATCTC
ATGAAGGCTCCACAGATGGCTGCAACAATGCAAGAATTTAGCAAAGAGATGACTAAGGCCGGAGTTATTG
AAGAGTTTGTGAATGAGGCCATTGACAATGCTCTANATTCAGAGGATATGGAAGAAGAGATTGATGAAGA
GGTTGATAAAGTATTGACAGCAATTGCTGGAGAAACCGCTGCAGAGCTCCCAGTANCTGTTANGAAGGAG
AGGATAAAGGTACCTGCACAGAAGGCGAACACTTCACGTGAGGAAGA
>gi|3719189|dbj|C99832.1|C99832 C99832 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGACATCGATCCAGGAGATGTTTAGGCGTGTGAGCGAACAGTTCACAGCGATGTTCAGAAGAAAAGCTTT
CTTGCATTGGTACACAGGTGAAGGAATGGACGAGATGGAGTTCACAGAGGCAGAGAGCAACATGAATGAT
TTGGTATCAGAGTATCAACAGTACCAAGACGCAACGGCTGATGAGGAAGAAGGGTATGAGTATGAAGAAG
ACGAAGTGGAAGTGCAGGAGGAGCAATAACAACAGCTTCTCTGTTTTTCTTGATTCCTTTTTTTTNCTCG
TTTGTGTGAGTTTAGTGTCTTGTTATTCATTTNCTCTTCTGGTTTTCTTGTGTTGACATTTGGCTATGTG
TGATGGTGCGTTTATGTCTAAGGCTTAGGAAAATATATGTTTAT
>gi|3719188|dbj|C99831.1|C99831 C99831 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CAGACGAAATGGCTCAGAAAGTGGTGCTGAAGGTTTTAACCATGACTGATGATAAGACCAAGCAGAAAGC
CATAGAAGCTGCAGCTGATATCTTCGGTGATTATTTCTTCCTACTACTTCTTCTTTTCTTTAACTACTTT
TTGATTGAATTTCAATTCTTGTTTCTGTTTATTATTGTACTTTTTAGATTTTTAGGATTTGAAAAAACAA
AAAGAAAGGATTAATCAAGTTTGCTGCTGGTGTTTTCACTCACTAAATTACCATTTTTAGCTNAAGTTAT
ACGAAACAATCGGTATGAAATCTAGCTCGATTGTAGTATAATTGCGTCAGAATCTTGAGAGCTTGGATTA
TTTGACCTTTTTGACACATAGTCCACGAAATGATATTCTGAACATTTTGAAAGCCCGTATTTTATGGGCC
GGA
>gi|3719187|dbj|C99830.1|C99830 C99830 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CAATCTTCGAAAAGAGGCTGAAGAAGAGAGCCAGCGGATTTCAAAGTTGCAGTATGAATTGGAAGTTGAA
CGAAAAGCCTTGTCCATGGCCAGATCGTGGGCCGAGGAGGAAGCAAAGAAAGCTAGAGAACAAGGGAGGG
CCTTAGAAGAAGCTAGAAAGCGATGGGAAACAAATGGACTGAGAGTTGTTATTGACAAAGACCTTCAAGA
GACGAGCAGCAGAGAGACAGAACAAAGCATAGTACTAAACGAGATGGAGAGATCCTCAGTTGAAGAAACT
GAGAGGAGAGCCAAAACCCTGATGGATAAGCTGAAGGAGATGGCTGGAACCGTGAGTGGAAAGTCCCGGG
AAGTGATCTTCCCTGTGATGGA
>gi|3719186|dbj|C99829.1|C99829 C99829 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CAAAGGAGTGACATACAAAAATAAAGCAGGCGAAGAAACAACAGCCTTGGCACCTCTCACTGTAGTATGC
GACGGTTGCTACTCAAACCTTCGTCGGTCTCTAAACGATAACAATGCTGAGGTTCTGTCTTACCAAGTTG
CTTACATCTCGAANAATTGTCGGCTTGATGATCCCAAAAACCTTCATTTGATAATGTCCAAACCCTCCTA
CATCATGTTGTACCAATTAAGCAGCACTGATGTTCGTTGTGGTTTTGAACTTTTCTCCGCCAATTTTCCT
TCCATTGCAAAAGGTGAAATGGCTACTTTTGCGAAGAACACTCTAGCTCCTCAGGTACCTCCAAAACTTC
GCAAAATATTCTTGAAAGGTCTAGATNAAGGAGCACACATNAAAGCGGTGCCAGCAAAGCGCATGACAGC
TTCTTTAACCAAGA
>gi|3719185|dbj|C99828.1|C99828 C99828 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGGATGGGGTCACCTCCACGAAACCACGATGAAAACTATGACTTGGTAAGCCACAGATCAAATAGAGACC
CAAGCCCCACTGAAAGTCAGAAAGGAGGAAGATTCCAGTCACTCGTCATAAATAGGGAGAGGAGAGGAAG
ATTTTCAAACTTCGAGGGTCCTGTTTCAAATTTTTCAAGTGGAAATATGCCTGCTCCAAACATCCGCCCT
TCAAATATGTTCAAGCAGAGAGGGAACCATATGCCAGTTGAACAAGGGATCGATTCTCCTTCTGAAGAAA
ATATTGTTGAAGACATAATGGGAAAGCACAATCAATTTGTCAGCTCTATGCAGTCTCGTTTGGCTAAGTT
ACAGGTAGTTCGTANATATTGGGAAAGGAATGATGTTAAAAATTCGATAGGCTCGATAGA
>gi|3719184|dbj|C99827.1|C99827 C99827 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTCGCATTTTCTTCATCCTTTTTGCCTCAGAGCTCCGTGGAGAGCAGCAATCAGTAGCCATGGCTGAGCA
GACTGAGAAAGCTTTTCTTAAGCAACCCAAGGTCTTCCTTAGCTCGAAGATATCTGGGAAAGGAAAGAGA
CCTGGTAAAGGTGGAAACCGTTTCTGGAAGAACATTGGTTTGGGTTTCAAGACTCCTCGTGAAGCCATTG
ATGGAGCTTACATTGACAGTAAATGTCCATTCACTGGAACCGTTTCTATCAGAGGACGTATCTTAGCTGG
TACTTGCCACAGTGCCAAGATGCAGAGAACCATCATTGTTCGTAGGAATTACCTTCACTTTGTGAAGAAG
TATCAACGATATGAGAAGANACATTCCAACATCCCTGCCCATGTCTCACCGTGTTTCCGTGTCAAGGAAN
GTGACCATGTCNTCATTGG
>gi|3719183|dbj|C99826.1|C99826 C99826 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AGCCATTGGGGGCAAAAGGAGCAGCAGCAGATGTTGAGCAAGGGACAGTTCAGGTGAGCGATAAGGTGAA
GAAAATGGCTGAGGAGTGTAGAGATGGAGTTGGGAAGATCTCTCAGAGGTTCAAGACCTAAAGTAACAGT
CTTTTAACTTTTTTGTATCTTGTTTCTACATGATAAAAATAAAAGAGAATAATGGGATGGCCATTACATT
TACAGTATTGGTCAGTGATGTTCAGAATTCATAATTGTATCATTTTGTAATCTTTGTTATGTGGTTTACT
AATACTTACACTTT
>gi|3719182|dbj|C99825.1|C99825 C99825 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AGATTAACGGCGGTTTTATCCCGCCGGCGATAATAAACTCAATCGAAGCACCGGAAACATCCGCCGCAGC
CGGAGTTTCAGTCGGATCGAAACGATTGAGAAGACCTAGCGTTAGGTTAGGAGACATCGGCGGTGACCAG
TACCACCAACACGTGGTTGCGGCGTACGATTCTCCGCAAGTCCGACGGCCGAAATGGAGACCTANTGGTG
GTGGTGGTGGTGGTGGTGGTAACAGGAAGGAGCCGAATAATCANAGTGGGAAGACGACGTCTTCTTCGAG
GACTCGAACTATGACGAATTTGAGCTCCGGTGGGTATGAGAATACTGGAACCCTAGATGAAGACCGGTTT
CNATTGGGAGTTGGCGGG
>gi|3719181|dbj|C99824.1|C99824 C99824 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TGATACAATTCCTCCTCGAGCACAGGTACAATCTCCGCTTGAAGTGATGAACATCCGCCCTAGTAGGGAT
GTTGCAGTTTTGGATTTCTCCTACAAGTTTGGTACAAACGTGGTCAGTGCCAAATTACGCATCCCGGCAA
CCTTGAATAAGTTTCTTCAACCTCTACAATTGACATCTGAAGAGTTCTTCNCTCAATGGAGAGCAATCTC
AGGGCCACCCTTGAAACTTCAGGAAGTGGTAAGAGGTGTAAGACCTCTAGCTCTTCCGGAAATGGCAAAT
CTGTTCAACAGTTTTCATGTGACGATATGCCCTGGGCTTGATCCAAACCCTAATAATCTAGTGGCAAGCA
CAACCTTCTACTCTGAAACTACAGGANCCATGCTCTGTTTGGCAAGAATTGAAACAGACCAGCGGACAGA
ACCCACTAC
>gi|3719180|dbj|C99823.1|C99823 C99823 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TCCTTCACCTGTTCTTCTCCATCTTCGATTTTACCTATTATTGATACGAGAAGTGGGAATTTGCGATGCA
CATTTCAGTCTCAGGTTTCTTGTGGGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAAC
ATTGACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCNTTTGTGGAAGAGCAAGTGAGG
AAGATAAGAGAAGTTGGGAAAGTAATGACAATGGACATAGAGCAGCTTCTTTTGAGGGAAGACAATCGGT
TTGAATTTGTCAATAGCGTAGCAGCTGAAGCAACAGAGTACGTGGACAAGAACAGAGACGAATATGGAGG
TTCCAAAAAAGCTATCTTTCATGTTCTAAGCAACCGTGTGAACGATCTCGGCTTTGACCGCCCTGAGGCT
TATGT
>gi|3719179|dbj|C99822.1|C99822 C99822 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AGATTCATCGTTAAGGGAACGGTTGAAGAGAGAATGGAGGCGGTTCAGGCGAGGAAGCAGAGAATGATCT
CTGGGGCTTTAACCGATCAAGAAGTACGAAGTGCACGTATAGAGGAACTCAAGATGTTATTTACCTGAAA
CTATAGAAACTGTTCTCAAGCCTGAAGTCGATCATACAATTCTACATATNTGGGAAACTTGTCACACTAT
ATGCAAGGAGAATCAGAGATTATAACGCATCTAAAAACGGGTTTTGTTCTTTTCAAGAGATATGATGGAC
AATTGTCACAGTTTTGGGGAATGTGCAGTGAGAGTTCCCAAGTGTACCATAAGCCTATCTGGGTTTTGTT
GTTTTGTAATGGAAATCAGATTGTTTTTTGTACTTTTTCATTTATAATGAACTGTAACTTTATACTATTA
TATAGTTACTCAATATGACAAATTTGCAC
>gi|3719178|dbj|C99821.1|C99821 C99821 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TCTCCCCAGCAGAGAGAGGGGAAGTCTCTAAACCCTTGCTTGTCATCAAATCGATTCCTCGAGTGAGGAA
ACATTTCTCTTTTCGTGGATCTTACGAGACCGAGAAGAGAGTAAGATATGTCCGGCGCATCGTCTGAGGA
TAGCAGTATTTTCGCTCGCTGTGAAGACGTAGACTGTAACAAGAAAATACCTGTAGAGCTTGTAAGGATG
CACATTTGTTATGCTATGTTCCATAGGACTCTGGCTCGAGGTTTTGGGACACAAACTCAGGCTAAGAAGA
AACCTACAAACAAGAAGAAGTCAACAACATCTCTTACCGATTTTGCTGTCTTCATGAATCATTTCCGTAA
ATCTTTTAGAACAGATTATAATGGTGCATTGGTGAAAGAAGGTTCAAAGATCGGTTGGGAAATGTGGAAT
CTATGACTGAGGATGAG
>gi|3719177|dbj|C99820.1|C99820 C99820 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTTTTTCCGGGCTGAGCTGCAGAAGATGGGATTTGAGGTACTTGGAGACAATGATTCCCCAGTCATGCCT
ATAATGCTTTACAACCCAGCAAAAATCCCAGCTTTCTCAAGAGAATGTCTGCGACAAAAAGTGGCAGTGG
TGGTCGTGGGTTTCCCAGCTACACCTCTACTGCTGGCTAGGGCACGTATTTGCATCTCCGCATCTCATTC
AAGAGAAGATCTTATAAGAGCCCTCAAGGTTATAAGCAAAGTAGGTGACCTTAGCGGAATCAAATATTTC
CCGGCAGAGCCGAAGAAAATAGAACAGTCGAAAAACGACATCAAGCTGGATTGAAGAATTAACCAATGAA
ATAGAGATGCATCCCGGAAAACGCAAGCAAATGCTGTGTTATGTGTTAACTTCTCCATATCTCTCTGATG
TGACACAAATCTGATTTCTCAGGGGTC
>gi|3719176|dbj|C99819.1|C99819 C99819 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GAGTCTTAAAGATGATCAGTCGGCGAGTTTTGTGATAAGCAATTTGGGTTCATCCGCAAAAGCAGATATC
AAGGTTAGTTTTAATGTGAACGATATTTGGGATCTACCTGTCACGTTCGAGAGAAGCAATGTTGGTAAAT
TACTCACCGGGCTCTCAAGCATAAGGGACCTAACTATAAGTGGAACAACTTTGATGATCATTTGTCACTA
CTTGAAGCACGAACCGATGCCTCAGTTTTGTAACATGGTGCGGTTAAATGCGAGATTCTATGATTGTGAT
TTGGAAATGTTGCCATGCGTTCTTGAGAGCTGTCCAAATCTCAAATCCCTTGTCTTGGGTCTACTATCTT
CCGCTGAGACGGAACAACAATCAAGAATCTCGTCTGTGCCTCCGTGTTTCCTATCATCGCTAGAATTTGT
AGANAATAAGAACCAGACTCTGTAGAAAGCGTTATGTGATGA
>gi|3719175|dbj|C99818.1|C99818 C99818 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GATTGCGTTACGGGGAACTGTCCCAAGTGATGTGAGTGATTGGATACATAACAGCCGTATTGTACTCGAG
AAACTCCATGGCGGGGGTAAGCATATGCATGTCATTAGAAAAATCTATTCTTTGGTGGCCAAACACGGAA
ACACAGCTGTCTGGATCGCTGGACACTCTTTAGGAGCTGGCCTGGCACTACTCGCGGGAAAGGACATGGC
CATGTCTGGACTCCCTGTTGAGGCTTACATCTTCAACCCACCTATCTCCTTGATTCCTCTAGAGCAGTGC
GGTTACAATCACGAACTTAATTTTGTGTNTCGACTCACCANGGATCTCTTCAAAGCTGGCATAGCCAAAA
GTCGTANACCTTGATGAAGGTCAAGAAGGTCCACGATATAAGAACTTAGCTTCTTGGANACTCATTTGTT
TGTGAACCAATCTGATGTTATATGCTCAAAATATATT
>gi|3719174|dbj|C99817.1|C99817 C99817 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AGAGNTTAGCGGTTCTGTGAAATTGCCTCACGTTCCTAGGCCAAAGATGAAGNTTTGCATGCTTGGTGAT
GCCCAGCACGTCGAAGNGGCTGAGAAGNTTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGA
ACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTTTCCTTGCTTCTGAATCTGTCAT
TAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGGAAAATTCCCAACTCTTGTTAGCCAC
CAAGAGTCTTTGGAATCCAAAGTGAATGAGACAAAGGCAACAGTGAAGTTCCAGCTCAAGAAGGTTCTAT
GTATGGGAATTGCTGTCGGTAATCTTTCCATGGGAGGAAAAACAGATCTTTCAAAATGTTCAGATGAATG
TTTACTTCCTCGTTTCTCTCTTGAAGA
>gi|3719173|dbj|C99816.1|C99816 C99816 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGAGCAATTTCACTCTTCCGAGAACAACCCTAGATTCCGATGATGAGGGGTCTCGTTTCCGGCGCCAAGA
TGCTATCATCAACCCCATCGTCGATGGCGACAAGCATCGCCACTGGTAGAAGAAGCTACAGTCTGATTCC
GATGGTTATTGAGCACTCATCGCGAGGAGAGAGAGCTTACGACATCTTCTCTCGTTTGCTTAAGGAGCGT
ATTATCTGCATCAACGGTCCCATTAATGACGACACATCTCACGTCGTCGTCGCTCAGCTTCTTTACCTCG
AGTCTGAGAATCCTTCGAAGCCGATCCATATGTATCTCAATTCCCCTGGCGGCCATGTCACCGCCGGTCT
TGCAATTTATGATACTATGCAGTACATTCGTTCTCCTATTAGCACAATTTGTTTGGGTCANGNTGCATCA
ATGGCTTCTCTTCTGTTGGCAGCGGGTGCCAA
>gi|3719172|dbj|C99815.1|C99815 C99815 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ACTGTCCTACGATGTGGTCACACTATGCATCTAGAATGCACGAAAGATATGGGGCTACATAACCGATACA
CATGCCCTGTATGCTCCAAATCCATATGTGACATGTCTAATCTGTGGAAGAAACTTGATGAAGAGGTTGC
TGCATACCCAATGCCAAAGATGTATGAAAACAAGATGGTATGGATTCTCTGCAATGACTGCGGCTCAAAC
ACGAACGTTCGGTTTCATTTGATCGCGCATAAATGCAGTAGCTGTGGTTCCTACAATACAAGACAGACAC
AGAGAGGCTCTGATAGTCACTCTTGCTCCTCTGGAATGCCTCAGGTTGTTGGTTCAACCGGTTAATTTTT
AACCAGANCTGGTTTTGGTGTCTGAATTTCCCATGAAGANATTATTTGTACTTTCTATAAGTTTGGTATC
AGTCAATGCCTTTGGTTGTTAACAATTATATCATCACAGAATCCAAAGCTGCNTTGACCC
>gi|3719171|dbj|C99814.1|C99814 C99814 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GCTAGAGGCATTGTAACCGCAGTTTGTTATCAACCTGATGGGCAGGCAGTGATTATCGGAACTTTGACAA
GCGATTGTCGCTTCTACAATGTATCAGGCCACTGCCTTCAACTTGATGGTCATATATGTCTGCACAACAA
AAAGAAGTCGTCGAATAAACGAATAATCGGCTTTCAGTTTCTTCTGCAGTTTGATTCTACTGACCCAAGC
AGAGTCATGGTGGCATCAGCAGATTCACAAGTGAGGATCATTAGTGGTCGCAACGTTGTCCACAAATACA
AAGGATCTCGAAATGCTGGAAACCAGATATCGGCATCTTTTACAGCAGACGGGAAGCATATAGTCTCTGC
GTGTTGACGNATTCATCGGTCTACGTCTGGAAACTGCGTTGGGACACGACCCTGAAACAGTTCGTCTCCT
GGTTTTTTCTCTCACACCCAAACGACTTAAAATCCGATCATTCG
>gi|3719170|dbj|C99813.1|C99813 C99813 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AGCAAAAATAACTCACTCCCTAGAAAAGTTTGAAAATGGCGAAGGCAGATAAGAAACCAGCGGAGAAGAA
ACCGGCAGAGAAAACTCCGGCAGCCGAACCAGCAGCAGCGGCAGAGAAGAAACCAAAAGCCGGAAAGAAA
CTCCCCAAGGAACCAGCCGTCGCCGGAGACAAGAAGAAGAAGAGATCAAAGAAGAACGTTGAGACATACA
AGATCTACATCTTCAAGGTGTTGAAGCAAGTTCATCCAGACATCGGAATCTCAAGCAAAGCCATGGGAAT
CATGAACAGTTTCATCAACGATATCTTTGAGAAGCTTGCTGGTGAGTCTTCGAAGCTTGCAAGGTACAAC
AAGAAGCCGACGATTACTTCCAGGGAGATTCAGACTGCGGTTAGACTTGTTGTTGCCCGGTGAGTTGGCG
AAACATGCTGTGTCTTGAAGGGACTAAGGCGGTTAC
>gi|3719169|dbj|C99812.1|C99812 C99812 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GAAACCAAGAACGAGGGGGTTGTTGTAGAAGAAAGCCGGACACTTTGAGTCTCCCGGTAAACAGTCATGA
TTTAGCCTTCACGAAGCTGAAGGAAATGAACAGCTGGGCGGATGATAACTTAATAAGGGATGTATTGTTA
TCCACAGAGGATGATTTTGAAATGGCCTTAGCTTTTTTGAAAGGAATGGTTTCTTCTGGTAAGGAGGATG
AGGAGCCAACTTCAAAGATTGAGGGGTATTCATCCGATAACAGAAGATCGGAATATAGAACATTTGAGAA
AACAGTTACAAGTTCGGTGAAGATGGCTGCAAGTTCCACATTTGAGGATGCTGGCAAGTATGATCTGGAA
AATAGTGATGGAAGCTCGTTTCTGGTCAATGCATCTTGACAATGAAAAGTTCCCTGATGATATTTCTGAA
CTAGATAGTATCATTCAGCGGCTTCAGTCCATTCCGA
>gi|3719168|dbj|C99811.1|C99811 C99811 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CACGGAGATAACTACAGTGACCTAAGCCGCAAAATCAAGCTAGCTATGCGACTAGTTGAGCTTTACCAGC
CTTACTTACTCTTCAAGGGCATATTTGATGATTTAAATACCGAAAGACTGCGAATGAAAAGAAAGGAGAA
TATCAAAGAGTTAGATGGATCGTTCGAGTTCGATCCCAAGTCCATTGATTGGGACAATTATATCACAAAC
ACCCACATTCCTGGCCTCATCACCCATGTGCTTAAACAATAAATTATGCTGGTAATATGTTTGGAACTAT
TGTGAATCTCGTGTGTAATATTATTAAAGAATACGATTATATCATTCTAATCTTGTAATTTACAGTTTGT
GTTGGCGTGTAATATCAAAATAAATAAAAAAAAACTTATTCCACAATGGATAAGACTTTGAATCATGC
>gi|3719167|dbj|C99810.1|C99810 C99810 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CACGAGGCAACGTGAGGATCGGGGTTGGAAACACGGTTGGTGAGCGTGTCTCCAATGTCTTTGTTGATGT
CAAGAAGTTCCAAGAAAGATACGCTAAAGCTATGAGCAGAACCACAAAAGAGACCTCCCAGAGAGAAGTA
CAAATAAGTGCAGTAGAGGCGATAAGGTCTATATCCAATTGGCTATACTGGAGATCATCACCGTACACAA
AACCACTGAGTCCAGATTCAAACATGAGTCTAACTTTTATCAAAAGAAAGAAAGCGGTTGATCCAGATAT
CAGAAAGCTTCAAGATGTTGTGGCAGCGATGAAACAAGCAGAACAAAGCGGAAAACCCNAAGAGAAAGGA
TCAGCTTACTTGCTTGGGAGAAGATTATTGGAGTCCATCAAACGCAGCTCTTCCCTCATCTGGAAACAAC
AACGGTTCC
>gi|3719166|dbj|C99809.1|C99809 C99809 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTAAAAAAAAACCTAACAACCTCTCTTCTCTCTTCCTCGTTCAACGACAATGGAGTTCTGGGGAGTTGCG
GTGACACCAAAAAACGCTACTAAGGTGACTCCTGAANAANACAGCCTTGTCCACATTTCTCAGGCTTCAC
TTGACTGCACAGTGAAATCTGGANAATCTGTGGTTTTGAGTGTGACTGTTGGTGGGGCTAAACTTGTTAT
TGGAACACTTTCACAANACAAGTTCCCTCANATTAGCTTTGATTTGGTTTTTGATAAAAAATTTGAGCTT
TCACACAGCGGTACCAAAGCAAATGTTCATTTCATTGGGTACNAATCCCCCAACATCGANCAGGATGACT
TCCCTANTTCGGATGAAGAGGATNTTCCTGAA
>gi|3719165|dbj|C99808.1|C99808 C99808 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTGATGAATCACTTGGAGATTGGGCAAACTTGGAAACGATGCGGTATTGCCATCCGATGTATTTTGCCAG
GAGGATGGCCGAGGTTGCTTCAACTGACCCTGTAAATTGGATGGATCAGCCGTCCGCTGGCCTTGCTATC
CAAGGGCTCTTGAGTCGTGTCGTANTGGAANATCACTCGGATATCCAAAAACATATCTCTGGTTGTATAT
CTACAGGCACTGACAAAAACAAGGATGGAGAAAACTCANAAAGANAAATTTGAAGGCNTTANTGANAATG
AATCTGANATATTGCAGGTTGAAAATTCCAANAAATGCTATATCCGTACTACNAGCTGGANATAATA
>gi|3719164|dbj|C99807.1|C99807 C99807 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTCCCGGTGCAGCACTTACTCCACCGCANAAGTTAGAGATTGCCAGGCAGCTANCTAAACTCCGAGTAGA
CATCATGGAAGTTGGTTTTCTGGTGTCGTCTGAGGAAAAATTCNAANCTATTAAAACCATCGCCAAGACC
GTGGGGAACGAGGTGGATGAGGAAACCGGTTNCGTTCCTGTGATATGCGGCATTGCACGATGCTTTTTTT
ANANACATCNAGGCNNCTTGGGAGGCACTNAANTATGCNAANAGGCCNAAGGGTTATTGCT
>gi|3719163|dbj|C99806.1|C99806 C99806 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GTGGAGCCAAACATGGTCTTTACTCCACTTGTTCCCTCACAGCCTCATTACAATGTGAATCTGCTGAGCA
TCTCAGTAAATGGCCAAGCTTTACCTATCAATCCATCGGTCTTCTCTACATCAAACGGCCAGGGAACAAT
CATTGACACTGGTACAACATTGGCATACCTTTCTGAAGCAGCCTATGTTCCTTTCGTTGAAGCTATTACA
AATGCTGTTTCGCAGTCTGTCAGACCCGTTGTTTCGAAAGGGAACCAATGTTACGTAATAACCACAAGTG
TCGGANACATATTTCCTCCAGTTAGCTTGAACTTTGCTGGTGGGAACATCTATGTTTCTTGAATCCNCCA
GGGATTACCTCCATACAGCANAAACAATGTC
>gi|3719162|dbj|C99805.1|C99805 C99805 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GCTAATANAAGCACGAACGGCGTCGGGTTAGTCCGACGGAGGAACATGTCCTCGTCTCTTCTTCTCTCCG
GTTCTACTGTATCTTCTTCGTTTATCGCTCCATCTAAGCCTTCTCTCGTACGAAATTCCAGTAAGACATC
ACTGTTACCATTTCGTAATGTTTCGAGAAGCTTCAAAACCGTTAAGTGCACCGTTGATTCTTCATNTGGA
GGCAATGTTCCCACGTTCCCTCGGACNAAAGTTTGGGACCCGT
>gi|3719161|dbj|C99804.1|C99804 C99804 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AATGGCCAAACACCGGAGCTCAACCTTGCCGGCCACTGCAACCCTGCGGCGAACACTTGCACCCATTTTG
GCTCTCAGGTCAAAGATTGTCAGTCTCGTGGCATCAAGGTTATGTTGCCTCTCGGCGGCGGGATTGGAAA
CTACTCGATTGGGTCGAGGGAGGACGCAAAAGTTATCGCTGATTATCTGTGGAACAACTTCTTGGGAGGA
AAATCATCATCACGACCCTTAGGTGATGCTGTTCTANATGGTATCGATTTCAATATCGAGCTTGGCTCTC
CTCAACACTGGGATGATCTCGCCAGGACTCTCTCAAAGTTTANCCNCNGAAGGAAGAAAAATNTNTCTNA
>gi|3719160|dbj|C99803.1|C99803 C99803 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTTCGTTTCATTCATAATCGTCTTATAACCACAGATTCTAAAACATGGGAGAAGAAGTAAAACCAGAGGC
AAAGGAGGCAGCCTCTGCTCCACAGGCCGTCCCCGCTGAGGAGGAGGAGAAGAAGAAAGATGTNGCGGAG
GAGAAGAAAGTGGCGGCTGAGGAGGAGAAACCAAAGGAGGAAGAGGAGCCGCAACCACCACCACCGCCTC
CACCCTTCATACTCTACGTCGACTTGCATTGTGTTGGATGCGCTAANAANATTGAAAGATCTATTCTAAA
AATTAGAGGTGTGGAANAAGTGGTTGATGGATATNAATGANAACCNNNTTGACNAT
>gi|3719159|dbj|C99802.1|C99802 C99802 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TCGATGGCGGTTCGTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCAT
TTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTTCGGCTTCAACGGAACCGCCGGAATAT
GGAGAATAGCGGCGATAAATGAAGCTGGTGGGTGGAAAGATCGGACCACCGTGGAAGATATGGATCTCGC
CGTCCGAGCAAGTCTTCGCGGCTGGAAATTTCTCTACCTCGGTGACCTTCAGGTGAAAAGTGAGCTTCCA
AGTACTTTTAGAGCCTTCCGTTTTCAGCAACATANATGGTCTTGTGGACCTGGC
>gi|3719158|dbj|C99801.1|C99801 C99801 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TATCCACAAGTACGTCCATGAGTGGCCTTCAAACCCTCCTTCTTTCAAGGAAATAGTAAGTAAATACAGT
AGAGAAGTAAGAGAAGTGGGATTTAAAATAGAGGAATTAATATCAGAGAGCTTAGGTTTAGAAAAAGATT
ACATGAAGAAAGTGCTTGGTGAACAAGGTCAACACATGGCAGTAAACTATTATCCTCCATGTCCTGAACC
TGAGCTCACTTACGGTTTACCTGCTCATACCGACCCAAACGCCCTAACCATTCTTCTTCAANACACTACT
GTTTGCGGTCTCCAAATCTTGATCGACGGTCCAGTTGGTTCCGCCGTTAATCCGCATCCTGATGCTTTTG
TC
>gi|3719157|dbj|C99800.1|C99800 C99800 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GATGCCTCAAGAAGGCTGCGTCTTCAGGTTAACCTTAACAGCCACAAGTCAGAAACTGACAGTACACAAC
TTCAATTTATCAAGAAAGAGGTTAAGGACACAACAACGGAAACTATGACGAAAGGATGTGGAAATTTCAC
AAGATCAAAGAGCAGGACTAGTTTCATATTCAAGAAAATTGCAGCCATGGGATGTTCATACAGAGGGCTT
TTCAGAGTCGGTGTGGTANCGGTTGTGTGTGTGATGTCGGTCTGCANTCTAATCNCATAAATCCGCTGAA
TGTGATGTTTGTTCCGATCAATTCATATANTAAG
>gi|3719156|dbj|C99799.1|C99799 C99799 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AGAGAAAGAAAGAAAACAGAGCAATTACTTGAAGAATCCATAGGAAGCTGAAGATGAGAAGAATTCCTCG
TATCAAATTTCCTCAGAGACATTCTATCTCATCTGGTTCTGGACCGGCGCCGGGATCTGTTTCCGGCGTT
AAGAAAAATGTGACGGCGAGTTCTGATGTTCCGGCAGCTCCGAAGAACACTGCTGATGGAGGGAAAGCAT
CTCTCCAGCCGAAACGTNCACCTGTCTCCGACAAAGAAATCGAATCTATTATGTTGGGTGGTTGCATATG
ACATTTGGGGAGTTACGAANATTTGATCGAACNCNTTGGTGTTCTTGTCTNGTTCGGCTGGTGANGTTTA
T
>gi|3719155|dbj|C99798.1|C99798 C99798 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTCTCTGAACCATAGAACTCCAAGCTTGTACTGTACTCTACTAATACGTCGTCGTTTATATCTTACTCTT
TTGTTTCCTCTTACCAGAAAAAATAAATAAACAGCAATATTTTCAATTTTCGACTCAAATCATGCAAACC
ATTTCGCCTGCGTTCTCGTGCGATCTCAAATCCGTAATTCAACCAAATCTAACGGCTAAAAACGCGCGTT
ACTCGCACGTAAATGGAAAGCGCGTGTCTATTCGTTGCAGTTACAGGTCTGAGTCGTTTAGCTTCCCTAA
CGGTGTTGGNCAAGCCGAGCCGATTGGNAAAGCTCATGCGCCATCTTAGCCAGTAAAGTANTTTCGGNTG
AAAATTCAAGCTCCGTCGCCGTCGTTAA
>gi|3719154|dbj|C99797.1|C99797 C99797 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TGGATCTGCTTTCTCGTCGGCGGCTAATCAAATTCTTCCAGAGGGTTTTGACAGAAATTTCTCGAGATGG
GTCAAGCTCAAAGTGACGAGAACTCAATTCCGACGACGACGACAACGAACACTCCTCCTCCTTCTGCGAA
CTCACCTCGGGATTCTGAAGATACTTCGTCGCCATCGATGGATTCTCTTCTTGCAGAAGCTGCAGCATAT
GGTGAAGATGATAATGAGAATGAGTCTCTTGAAGCCAAAGCACAGAGAGCTCTCGATTGTCCTTGTATAN
CANATTTGCGTAATGGCTCTTGCGGGTCTCANTTTCTCCG
>gi|3719153|dbj|C99796.1|C99796 C99796 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GTTTGTTGCAGAGCAATTGTGGTGTAAGTGTATTGGACTTCATACCAAGAGCTGACGGTGGATCTCCTCA
CGTATGTCTTAATCGACTAAATCAGACACCTAATTCGCCTCTAGCTGGTGGAAGTTCTGGTGGCCGGAAA
GCTAGTAAGCAGATTATACTTGTCTGCCATGGTCAGGGGAATAATGAGGATTCTGCTGTTATTAACCAAG
CAGCTAATAATGATCAGGCAATGAACATGCTTGGTGTGATACATTCACAGAAAACCGCANAGCTTCTACT
TGATCTAAGGGGTTATTCAATANTTTGCA
>gi|3719152|dbj|C99795.1|C99795 C99795 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AACAAGTCAAAGCCAAGCTGGGATGACATTTGTGCGTTTAAAGTATTTCCTTTCAAATGCCAAACATTTC
TACAGTTATTTGAACTTGACGATGAGTACATTCAACAAGAGATAAGAAAGCCTCCCAAGCAGACTACTTG
TAATTATAAAACAGGATGGTTCTCTGAAGCGCTGCTTGACAATTTGAAACTCCGTGTANCTGTNATGTTT
GTATCTGTGTNNCCNGAGCCAGGTNTCGAANA
>gi|3719151|dbj|C99794.1|C99794 C99794 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AAAGAACCAAAGCTCTTGGAGGAGGTGATCTTCTCTTCTCAGATCATCTTCTACTCTTGAGTATACCCTT
CCTTTGAAGATAATTCCTAGTTTGGGACTTATCCTTACTTCTCCGGGATTTCACTTTAATCCACCGAAGA
GTTTTGACATCTGAATTGTATTGTTTTGGGTGTGATCCCGATAGAATTCGAGGGTAGGAATCGGAAAGTA
GGGTGATTTGGTTTANAANAAGAAAGAAATGGAGGGTTTTGTCGATCACTACATTGTTCTAGGTTTAGCT
TCTGGAGAGGAANCTCTGAANCTTACCGANAANGAAATTGC
>gi|3719150|dbj|C99793.1|C99793 C99793 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CATGGTCAGACACTTAAGTACAACATGAAAGTTAGAGCTGGAAAAGGATTCACTCTTGAAGAGCTTAAGG
TTGCTGGTATCCCAAAGAAGTTGGCTCCAACAATCGGAATTTCTGTTGATCACCGACGCAAGAACCGTTC
TTTGGAGGGTCTTCAGTCCAATGTCCAAAGGTTAAAGACTTACAAGGCTAAGTTGGTGGTGTTCCCTCGC
CGTTCCCGTCAAGTCAAGGCTGGTGATTCTACTCCAGAGGAGCTTGCCAATGCTACTCAAGTTCAAGGTG
ATTACATGCCAATTGCCAGTGTCAAGGCAGCTATGGAGCTANTTAAGCTGACTGCANATTTTGAANGCGT
TCA
>gi|3719149|dbj|C99792.1|C99792 C99792 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGAAGCTATTCCTTGTGATCAATTCGACGTTGCGTTTCAGGCGGTGGAGCTTTGGATCGCCGATCGTGCT
GTTCTCCCAGTTGAGAACTCTCTCGGTGGTTCGATTCATANAAATTACGATCTTCTCCTCCGTCACCGTC
TCCACATCGTCGGAGAAGTTCANATCCCGGTTCACCACTGTCTCTTANCTCTTCCCGGAGTTCGTATGGA
TTGCATCNCGCGAGTGATNTCGCNTCCTCNANCTCTGGNTCANANGGAANGATCGCTC
>gi|3719148|dbj|C99791.1|C99791 C99791 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ACTTGATCTCACGACTCCATCTTCTAAAATTCAGAATCTTTCTTTGAAACTTTTTTCGTGTGAAGAAAAT
GGCACCAAAGGCAGAGAAGAAGCCGGCAGAGAAGAAACCAGTGGAAGAGAAATCAAAAGCCGAGAAAGCT
CCGGCGGAGAAGAAACCAAAAGCCGGCAAGAAACTCCCGAAGGAAGCCGGTGCCGGCGGCGATAANAATA
AGAAGATGAAGAAGAAGAATGTTGAGACGTACAANATCTACATCTTCANGGTTCTGAAACAAGTTCATCC
AGATATTGGTATTTCAAGCAAAGCTATGGGGGATTATGAACAGTTTTCATCAACGACATCTTCCGNANAA
ATTGGCATCGGGAATCTTCCGAA
>gi|3719147|dbj|C99790.1|C99790 C99790 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AAGCAAATTAAGATCATAAAANGGTTTAGAGCTTTTCTAACAAACGTCAAAGCAAATCATCATCGGAGCA
ATCTTCAAATCATCATGATAACAGTAGCCATCGCAGCCGAGTTGCTTGAANAATATACGGNGGCGCTCAC
ACGCATCACCGCCANNCTCCTCCCTCCANNANCTANNAGTCNNCGTCGAAGTGTCCGANCTCCTA
>gi|3719146|dbj|C99789.1|C99789 C99789 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AAGGCGGCCAGCGATTTTATCCAACAAGACCTCAAGATGGACTATGTGTATGACTACATGTACCATCTTT
TAACCGAATACTCGAAACTCCTCCAGTTTAAACCCGAGATTCCGCGGAATGCCGTGGAGATTTGCTCGGA
AACAATGGCATGTCTGAGGAGTGGGAATGAGCGGAAGTTCATGACAGAATCACTCGTGAAGCAACCTGCG
GATTCTGGTCCGTGTGCCATGCCTCCTCCTTATGATACGGCTACGTATTACGAGGTTGTGAAGANGA
>gi|3719145|dbj|C99788.1|C99788 C99788 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GGCTAAAGTAATAAAATTAATGGCAACTTCAGGGTTTAAGCATTTGGTGGTTGTGAAGTTTAAGGAAGAT
ACAAAGGTTGATGAGATCTTGAAGGGCTTGGAGAATCTTGTTTCTCAGATTGATACTGTCAAATCCTTTG
AATGGGGAGAANATAAAGAGAGTCACGATATGCTTAGACAAGGATTCACTCATGCATTTTCGATGACCTT
TGAGAACAAAGATGGTTACGTCGCCTTCACAAGCCATCCTCTTCATGTTGAATTCTCANCCGCTTTCACC
GCCGTCATCGACAANATCGTTCTCCTCGATTTCCCCGTCGCCGCTGTCAAATCTTCCGTTGTTGCAACAC
CATGAATCTTGTTGATGGTTACATATCNTCTATGACNCATATCNAACTTGT
>gi|3719144|dbj|C99787.1|C99787 C99787 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GGGATTTAGGGCTTGCGTCGTGCTTGANGCTGAATCTATGTCATCCGAGTTATACGTAATTGATATCAAG
GTATGTTGTCNCTTGAGTGGTAAACNCANCAACCTCTTTGATTCCGCTGACTGTCGGGATNCCTNCTNNA
CNCCTCANATGGATNNTCNTTTGGTTATATTNGACCGTNGTCTCCCCCCAAACCAA
>gi|3719143|dbj|C99786.1|C99786 C99786 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGTTCTCACAAGATCAAGAATATCANGAAACAAGATCACTTCTCAATCCTCGAAGATGACATTGAGCAGA
GTTCATCAACAAGTTATTGCATTTCCTGCTGTCAATACTGCTCCGGTGGGTTACTTGCCTGATCCAGCTT
CCATCAACAAGCTTCAAATCCCAACTTCTTCAAAGGTTTCGATGCTTCAAAAGAAGAAAACCGATTTNTT
CTCTNNCGGAGCAAGAGATCGGGACAAGTTAGGACCCAAGCTAACCGAAACAGTAAAGNAGAAAGCTATC
CTTTGGGAGCTNAGATCCTTCCAATGGGGAGG
>gi|3719142|dbj|C99785.1|C99785 C99785 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GTTGATCTCTTCAGTTTAGGGTGTGTNCTGTTTAACTGTATGACTGGAGGTAAACATCCTTACGGAGACA
ATTATGAGAGGGACGTTNACGTTTTGAATGATCNNNAGGATCTTTTCTTGATCGANANTCTNCCANAANC
TGTNCATCTNCTCNNTGGTCTCCTAAACCCGGATCCNNNTTNGAGACCGANANC
>gi|3719141|dbj|C99784.1|C99784 C99784 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGAAGAAACTAGAAAACGAGATCGACGTTATGTCATCGTTACCTTATCACCCACACGTGTTAAGCTTTCT
CGGCCATGCCGAGAAAAAACTCATGGTCGTTGAGTACATGCCAAACGAATCGTTATACCAATTATTACAC
GTGTCNACTGATCCTCTTCCCACGTGGCTTAAACGCATCGAAATCGCTCTTCANATCGCGAGTGCGGTTN
TNTTCCTCCATGAACACGGTATCACCCACCGCGATA
>gi|3719140|dbj|C99783.1|C99783 C99783 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GGAAGAAATACGAGAGAAAGATCTCACCGACTCTAAACCATCTCCACCGCAACCACCACCGAAACGTGGT
CTCATCAGCCGCAAAAGACAGCTTGTGTTTCTCTCTTTCATGATTTTATTAGCCGCAAAAGGACTCGTTG
GGATCGGAGAAATAGCGTTTGTAATCTTGTGTTATATCTACTTGTATGAGTTTCTCTCAAGATTTGCCTT
CCCTCGCAAGCAAACAGAACAGAAGAAGAGACTCTCNNACCCTAAAAACAAACTCTTTCAAGCTTACTTC
CTCGCCACTGCAATTATAGGCCTACTCTTCCCTCTTTGTTACATCGGAGATGGAATATNCCGTGGAGACA
TTCCGGGGCTGGAGCCGCCGCN
>gi|3719139|dbj|C99782.1|C99782 C99782 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ATATAAAABCCCACTTAAGTTACATTTGATCTCACTACAAATACCACTGCTCTTCCACATTACATTCTAT
TTTATCGACCTTTTTGAGTACACTAWAACAATTGGCCAACCTGACTATGTWACAAAGAAGAATGATATGA
CGAGTCTTAAGGGGATATGATACAACAACAATGAAGTAACACAAAAGTATTTGCTAAGTTTGAGATCAAA
CAAATTTTCAGCTGTGTCGGAATTTAGGCCGCACTGTGATAACTCCTGGCCTTGTCTCGTCAAACCTATA
CCTGTTATCTTCAAAGAATGTCTTCACGGCTAGAGGAAGTGAAGCCTGTCCGCGACTGTGTTTACCAATA
CCTGTTATAACCTGCAATGAGTTTCTCAGTTCTCTAGAAGAAGTTCTTTGACAGTGCATGCCTTCCTCAT
CTAATCTACCAAAAGGCTCTTGTGATGCAGATCGCAGAGCTVDTTTCTTTGACCTACCTCTATTTGGTGA
TACTGAACGGTTCACAGTAAAGTGACCTTCAATCATTTGCAAACGTTCTTGAAGGCTTGAACAGCTYATG
TGGCATGGAGACCAT
>gi|3719138|dbj|C99781.1|C99781 C99781 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TGTTCAAAACTAGATACATCAAATATCTTTAATGTCTATCATCTATACATGCAATACACTTGTCTAGAAT
CAAGCAATGTGCTCTTCCTTCTCTCTGTACACGCAGATCACTTTTGAAGTTTGTGCTTCACCCTAGCTTT
TCGAATAGAGTTGCCACGAGATCTTCCCGAGCTTTCTCTAAGGCACTTGGGAGATTTTCAGGCTTTCTGC
GCCTGCCTGAGCAAAATTGGGCTTTCCACCACCTCCTCCGCCACACAGCTTAGCTATGGGGCCAATGAAT
TTCCCTGCTTGAACACCTAGGGAGACTACTCCAGGACTAAATGCAGCAACTAAACTAACCTTGTCTTTTT
CTGGAGATGAKCCTAGTACCACAGSGACTGGATCTTCCAATGTGCTTATCAAATGSTCAGCTGCACTCTT
TAATGAG
>gi|3719137|dbj|C99780.1|C99780 C99780 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AAATGAGACAANTACAAATCAGTTCAATCATCTTTGTTATCACCGGAGAAGTAAATCTCACAAGACCTAG
GAAGAAACACAGGCAACAAGAGACCAAACAGATTATAAAACCACATCACCGTGTTAACCGATGCAATCAC
TCTTCCTCCGTACAATCTCAACGGACCACCAGGACGTTGAGTGTCGGAGAATTCTGCTTTAACCCAATCC
AAAAGAGCGAAAATCCTACGAGCGTTGTAGAAAACCGGTCCAAGAATACCTATTGGCATCGAATACTTGT
CAGAGAAACCAWTAGGTTCTGTGAAAGCTTGACCTGRGAGGAGAAATAGATGTGGTGCGGSGG
>gi|3719136|dbj|C99779.1|C99779 C99779 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TATGYCCATGATRGTTATTATCAAGACATATGATCATGATTCCTACBATTATCATACGTCTAGAACAAAA
TGTTGGTAGGAATGTAGAATCGAACATCAATGCTGTTACATTGACTTGTATATATATGCCTACTAGACAA
ACACAAAGGCCAAAGATATATGTATCTTAGTTGTTTAGAAAATTCTCGAGGCAATGTTCTTGGTCCAGAT
TCCTACTCCAAAACTTCTTGTAATACTCTGCATAAGTGAAATCTTTGTAGACTGGTTTCGTTTCATCGTC
CTCAGCTTCCCACAAGGGCTTGGCGGGCTCATGACAGCACAGTCAGCTGGGCACARAAACGATGCGACCG
AWAKTC
>gi|3719135|dbj|C99778.1|C99778 C99778 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ACCAAGAATGAAGTACACGTATACAGATAAAAATAAAGAAGAAAAAAACAGAGACAACTTTTCCGGAGAT
TTTACTTTAGAAAGCAAAGAAAACTAAATCAAACCAAGCCTTCAAAAATTAGGTAGCTCTTATAAACCGG
ATCATAAAACCAAACATCAAAACATATGTATGCTCTTTCAAAACATGGTACCAACTCACGAGTCTTTTCA
TCAGGGCCGATTCTCACCATCACTCAATGGTCTAGACACCATCAGTTTGGGGTTCAACTTCTGATCTTTT
GGGTGGTGGTGGAGGTGGTGATCTGTCGTAATGCTCAGCAACAAGTGAACCATGAGAAGAAGGAAGAAAA
ACCTGASGAGACTCCAYCGATGGAAAAWAAGAGGATGGTA
>gi|3719134|dbj|C99777.1|C99777 C99777 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ACATTATCCGARGATAACAAAATTAAATGCTACTTACTACAAACGATAAATATATCATTCTGTTTAGCGA
TTGTTCTTCTGCTTGGATTTAGATGGTTGTTTTCTTTTTGTAACCAACCCAACCTTTTAACCCGACCCGA
TTCGATATTTGACCCGCAATTCATAAACTCTCACCANNBGCGGCAAGTTTGACCCGGCCACGTCAGCGTT
TCTCTCAACCGTTTTTTCCGCCGTTTCAGTTTAACAACCCGACGCAAAACGCTCATCCATAACGGCAAAC
TCTTCAACGGTTCCGCCAAACACGCCACTATCTCCGCCGTGATCTCCCCGAAACACGGTCGTGATTTCCM
CSGTCAGATGAAACGCWT
>gi|3719133|dbj|C99776.1|C99776 C99776 YAC clone CIC8B11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GAATTATATAAAGATCATAAAATCTGTGGGTAGAGAAAATATCAAAAGGGAAAAGTAGGAAGTTTCTTAT
TGCCTAGAAAATGATGAATGAGCTGAAGAGCTTCTCTAGGTTTAAATGTCGGAACCTGGTGTCCCGCTCC
TCTTACCGTCACAAACATTAAACCGTCATACTCCACCGTCCACCCTCCGACCTGTAGTTTGGTGTACCAA
GGTGTCCAGTCTTGGACTATCTTAAGACCTAGCTTCTTTAGTGAGTATCTGGTTGCGGTCACGGGGATTC
GCCCGTCTGTATCCCCACTGAAAACCCATACGCGTAATCCCGCTGAAACAAGTGTTCTTAAGGTTGGAAG
CATAGAAGCGGGAGCCAAGACCAGAATGAGACAGTGTCACTGCAATGAGTCCAAGGGTAAGAGATGTTGG
TGACATTAGCGTGAAGTGCCTCCTGAACATCTTTTCTGTTCAWATATTTTTCTGCGGACSSGTGGGTCGA
CCCGGGAATTCCGACCGGTACCTGCAGGCGTACCAACTTTCCCTCCATGGTACCCGGATCCTCGAATTCT
TTTGCTTTTTACCCTGGAAAAATAYTCATAAGCCACCTCTGTTATTTACCCCCAATCT
>gi|3719132|dbj|C99775.1|C99775 C99775 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GAAGAGGAAGAGAGAGGACAAGAGAATCATAAGAAGAAGACATAGTCATGGGAGAGGTGAAAGTAGACGA
CGATGCGATTCTTAAATCCTTCCTCGCCGAGGTCGGAGAANTTGAGAGAGATAACGAAGTCGGCAGGATT
CTCTCATGCTTCAAGCTGAATCCGTTTGAGCATCTTAACCTCTCTTTCGATTCTTCCACGGATGATGTTA
AAAGGCAGTACAGAAAGATTTCTTTGATGGTTCATCCTGATAAATGCAAACATCCACAAGCACAGGAGGC
TTTCGGAGCATTGGCAAAAGCGCAACAACTGCTGCTAAACGACCNAGAAAGAGATTATATTCTTACCCAA
GTCCATGCTGCAAAAGAAGAGCTTAAGATGAAGAGAAAGAGACAGTT
>gi|3719131|dbj|C99774.1|C99774 C99774 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GAGTCTTAAAGATGATCAGTCGGCGAGTTTTGTGATAAGCAATTTGGGTTCATCCGCAAAAGCAGATATC
AAGGTTAGTTTTAACGTGAACGATATTTGGGATCTACCTGTCACGTTCGAGAGAAGCAATGTTGGTAAAT
TACTCACCGGGCTCTCAAGCATAAGGGACCTAACTATAAGTGGAACAACTTTGATGATCATTTGTCACTA
CTTGAAGCACGAACCGATGCCTCAGTTTTGTAACATGGTGCGGTTAAATGCGAGATTCTATGATTGTGAT
TTGGAAATGTTGCCATGCGTTCTTGAGAGCTGTCCAAATCTCAAATCCCTTGTCTTGGGTCTACTATCTT
CCGCTGAGACGGAACAACAATCAAGAGTCTCGTCTGTGCCTCCGTGT
>gi|3719130|dbj|C99773.1|C99773 C99773 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GTTTCTTGTTGTTAAAAATATCGTACAAAAATGGCCGATGAGGTCACAATCGGGTTTCGCTTCTATCCCA
CGGAAGAAGAACTGGTTTCGTTCTACCTACGAAACCAGCTCGAAGGAAGGAGTGATGACTCAATGCATCG
TGTCATTCCCGTACTTGACGTCTTTGAGGTCGAGCCTAGTCATCTTCCAAATGTTGCTGGAGTGAGATGT
CGAGGAGACGCTGAGCAATGGCTCTTCTTCGTGCCACGACAAGAACGCGAAGCAAGAGGAGGCAGACCGA
GTANAACTACTGGTTCAGGATACTGGAAAGCAACTGGATCACCTGTCCAGTCTTTTCC
>gi|3719129|dbj|C99772.1|C99772 C99772 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GACGAGCAAGACATGGGGTAAGAAGGGAAGGCCACAGAAGCAGGTCGTCAAGTCAAGGACATCAACAGTT
CATGGTGTTCTCTTCGCAACCTAATGCTTCTTCTCCTCCACCTCATCCTCCCATGCCTTCTTCTCCATCT
CAGAGAGATGAGAGTGACACAGTGTCAAACCTTCCTCACAATGCTTTANGGGANGGTTCTCATCAGTCAA
ACACGCAGCCACCAACTTCTTCTCATCCCCGCCAGGTTTCTCCCTCAGCATCTGATTCAAACAGCAGGCC
TCTTAATCAATCTTCCCCAAGTGAACAAGATANAGCTGGACCATCAGAACTCCNGCCATTTTCGGAATCA
CTTAANTCTCGATTAAACGCTGTCTCCACNAGATACNAAGAATC
>gi|3719128|dbj|C99771.1|C99771 C99771 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGTATAGCCGGTTTATGAAGAACAAGCTGGAGGCATATGTGGATTTCCCGCTAGATAATCTTGATCTATC
AAGCTACATCTCCTACAAGAATGGTCAGACAACATATCGTTACATGCTCTATGCGATTAGCAATCACTAT
GGGAGCATGGGAGGTGGTCATTACACTGCATATGTTCACCATGGAGGTGATCGATGGTATGACTTTGATG
ATAGCCATGTCCACCAAATCAGCCAAGAAAAGATCAAGACCTCGGCTGCTTACGTTCTGTTCTATAAACG
CCTTGTAGACTAAAGAAACTGAAGCGGAAAAGACAAGAAAGAGGTATTTGCATTTTTGCCGGGTTTGGCT
TATTTAAAAACATCATTGGCTTGATTCTAATTCACTACAAGATCAAGATGAAAGCAGCTCTGCGTTGAGG
CTAATTTACAGA
>gi|3719127|dbj|C99770.1|C99770 C99770 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CACGGAGATAACTACAGTGACCTAAGCCGCAAAATCAAGCTAGCTATGCGACTAGTTGAGCTTTACCAGC
CTTACTTACTCTTCAAGGGCATATTTGATGATTTAAATACCGAAAGACTGCGAATGAAAAGAAAGGAGAA
TATCAAAGAGTTAGATGGATCGTTCGAGTTCGATCCCAAGTCCATTGATTGGGACAATTATATCACAAAC
ACCCACATTCCTGGCCTCATCACCCATGTGCTTAAACAATAAATTATGCTGGTAATATGTTTGGAACTAT
TGTGAATCTCGTGTGTAATATTATTAAAGAATACGATTATATCATTCTAATCTTGTAATTTACAGTTTGT
GTTGGCGTGTAATATCAAAATAAATAAAAAAAAACTTATTCCCCAATGGATAAGACTTTTGAATCNTGC
>gi|3719126|dbj|C99769.1|C99769 C99769 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ANAGATTAGCGGTTCTGTGAAATTGCCTCACGTTCCTAGGCCAAAGATGAAGATTTGCATGCTTGGTGAT
GCCCAGCACGTCGAAGAGGCTGAGAAGATTGGATTGGAATCTATGGATGTTGAAGCTCTTAAGAAGTTGA
ACAAGAACAAGAAACTTGTTAAGAAGCTTGCTAAGAAATTCCATGCTTTCCTTGCTTCTGAATCTGTCAT
TAAGCAGATTCCTCGTCTTCTTGGTCCTGGTCTCAACAAGGCAGGAAAATTCCCAACTCTTGTTAGCCAC
CAAGAGTCTTTGGAATCCAAAGTGAATGAGACAAAGGCAACAGTGAAGTTCCANCTCAAGAAGGTTCTAT
GTATGGGAGTTGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGA
>gi|3719125|dbj|C99768.1|C99768 C99768 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GTTTGTTGCAGAGCAATTGTGGTGTAAGTGTATTGGACTTCATACCAAGAGCTGACGGTGGATCTCCTCA
CGTATGTCTTAATCGACTAAATCANACACCTAATTCGCCTCTAGCTGGTGGAAGTNCTGGTGGCCGGAAA
GCTANTAAGCAGATTATACTTGTCTGCCATGGTCAGGGGAATAATGAGGATTCTGCTGTTATTAACCAAG
CAGCTAATAATGATCAGGCAATGAACATGCTTGGTGTGATACATTCACAGAAAACCGCAGAGCTTCTACT
TGATCTAAGGGTTAGTTCAATAGTTTGCAGCCCTAAAACAGCCTCCATTGAGTCTTCTGGAGTAATATCC
CGGGTGCAAGAAGCTGCGGGTTGTTTAGGTGTNGATAATG
>gi|3719124|dbj|C99767.1|C99767 C99767 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AGCCATCAAAAATATATCCATAGAAGCTTCATCGAAATGGCGAATCAAGCAGCTGCTGCAGCATTCTTCC
TTTTCGCTTTAGCCGTCTTCTCCAACTTGGAGCTCTCAGCTTCTTCACTTGTCAGTGGCAAGATCTCTTG
CCTTGACTGCCACCGCGATTTCGACTTCTCAGGCATTAAGGTCCTCCTTAAATGCGACGG
>gi|3719123|dbj|C99766.1|C99766 C99766 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TCGATGGCGGTTCGTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCAT
TTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTTCGGCTTCAACGGAACCGCCGGAATAT
GGAGAATAGCGGCGATAAATGAAGCTGGTGGGTGGAAAGATCGGACCACCGTGGGAAGATAT
>gi|3719122|dbj|C99765.1|C99765 C99765 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CACGACTACTTTCTTGCAACGCATCATCATCTTCTTCTCCTCCCGATAGCAGCTCCAGTGAATACCTCAA
AGACTCCGGCCTCTGGGAAACACCGGTTGGGGACATGAGCGTGGTTTTGTCGCTGCAAATTCANACAAAA
TGTTCTGATTTGTTTGCTGAAACTCCTGCTGTGTCTTGAGTCTCTCTTCTTCTGTATCNTTTNTCTCGAG
TTCTTANGCNCNNCAGGGCTTCTTT
>gi|3719121|dbj|C99764.1|C99764 C99764 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GNGATTTAGGGCTTGCGTCGTGCTTGATGCTGAATCTATGTCATCCGAGTTATACGTAATTGATATCAAG
GTATGTTGTCGCTTGAGTGGTAAACGCAGCAACCTCTTTGATTCCGCTGACTGTCGGGATGCCTTCTTTA
CACCTCAGATGGATAGTCATTTGGTTATATTTGATTGTTGTTTCCCTCTAAACCAAGATNACNTTCGTCT
AGCTGAACTGAACAATGATNAGGTGGTCACANAAGTTTCAGTTCACTANTATTTCTCGCTGCAAATAACA
GGAGTCGGTATACGCTTCCTCAGGGACTGT
>gi|3719120|dbj|C99763.1|C99763 C99763 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TGATACAATTCCTCCTCGAGCACAGGTACAATCTCCGCTTGAAGTGATGAACATCCGCCCTAGTAGGGAT
GTTGCAGTTTTGGATTTCTCCTACAAGTTTGGTACAAACGTGGTCAGTGCCAAATTACGCATCCCGGNAA
CCTTGAATAAGTTTCTTCAACCTCTACAATTGACATCTGAAGAGTTCTTCCCTC
>gi|3719119|dbj|C99762.1|C99762 C99762 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTGATGTTTTGTCTCTCTGATTGAAAAAGGTAAAGATCGGGTTTTGCAAGATGGGAAACAAAGCTACAAC
GGTAAAAGAAGAACGGGAAGANATCCNTTTGAAGATTGTNCCTCCATTGGACAAANTTTTTCTGCGTNGG
CTCNCAANANATCTCCANANANTTCNTGGATTCNA
>gi|3719118|dbj|C99761.1|C99761 C99761 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GGGAAAACGGAGGATTCCAAAGTATCTAGCAGTAATTCAGCTGCTCATGATTCTTCAGATGATGATTGGG
AAGCTCTTGCAGATGTTGAACCGANTAAGTTACTCCCCGTAGAANAGTTGCCTGAAATATCANAGCTTTC
GGCTGAANAACCTNNNNTTCAAGGACCTNNNANACGTGGANGGGGA
>gi|3719117|dbj|C99760.1|C99760 C99760 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CACAAAAGCCCATTTCTATAACTGTTCATAGGTTTGCCCATAAACCAATTGGTGTACCAAAGAGAAACTC
TCGATGGCCTATGGCTGATGAATTCGACACCAAATCCGATCTGTCGACTCCGGTGGTTCACTCTCTGCCG
CCGAGGCCAAGGGTGGCTCANCTTGCTCGATCAANAAANCCNCCGTCCANGGTGGANT
>gi|3719116|dbj|C99759.1|C99759 C99759 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TAAAACGANCGTCANANGANGCTGGTNGTCCTCCTGGCGNCGTAACTAATGTTGTATGAGATGATTGCCT
CCTCTCAAGAAAATCNTCCAAGAAGCCATCAACAACTTTCCAATAATCTTCNTCGTCAAAANTGCATGCA
CCNANGATNTNTGTTNGCTTCCTANTCGGCAGGGANGNCCNTGNCTAGACTANTTNNTCGGNGC
>gi|3719115|dbj|C99758.1|C99758 C99758 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GGAGGCAACCACTTCTTGAGCTTGATGCAGCTCCTAGCTTGTCTCAGAAACATCAGCAAATTGCAAAGAG
GGAAGAANCTGTCAAGGAGAATATCATCTTGTCACAAGAGAGACATATCCAGAGGCTAAACGACCTTGTN
CGAAGTCTTCAAATGCAGTTACNGCGATGC
>gi|3719114|dbj|C99757.1|C99757 C99757 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TATGCTTGATATGGAGTGCTTCTCATACTTGAACCGTGCTCTTGAGAGCTCATTATCTCCGATNGTGATA
TTTGCAACAAATAAAGGTGTTTGCAACGTAAGAGGGACTGATATGCCCANCCCCCATGGAGTCCCTATTG
ATCTATTANATCGATTGGTTATCATCCGGACTCAAATCTATGATCCCTCTGAAATGATCCNTATTATNNC
CNTTCGTGCGCAANTNGAANAAT
>gi|3719113|dbj|C99756.1|C99756 C99756 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TGAATTGGCAAAGTCTATAAAAAGACCCAAAAATAATACAATGAAAAGGAGAAAAGACAGAAGCAAATAT
TGGAGATCACTAAGATGCGCATGTTGATCACTGCTGGGCACATTGCACACGCTGAGCACCGCCTGGGTGA
TCTTCCTCATCGTCATCATAAGCCTCTCTTTGAGCTTGCGCCTTCCTTTTCATCTCATCCTCAATGTTCA
CATCATGCAGAGTCGTCTCTTCGCAGTCGTCTATTTCCATATCGCTTATAGCTGCCTTGGTTGGCTTTGG
CAAAACTGCTTCAATGGCCTTTGTCTGATCCGGGCTCAGCGATTCSGGGAATTCACCCGTGAAGTGAATG
TATAGCTYMCCCTTCATGAACCGCCTTTKGGTATATTGSCATC
>gi|3719112|dbj|C99755.1|C99755 C99755 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GTTACATAACCAAACAACTCAAACTTCGTTTAAATTAAGAAACAAGTTCGATATGAGTCATATGACGATA
TGTAACCATCACAAGATTCATGGTGTTGCAACAACGGAAGATTTGACAGCGGCGACGGGGAAATCGAGGA
GAACGATCTTGTCGATGACGGCGGTGAAAGCGGCTGAGAATTCAACATGAAGAGGATGGCTTGTGAAGGC
GACGTAACCATCTTTGTTCTCAAAGGTCATCGAAAATGCATGAGTGAAACCTTGTCTAAGCATATVGTGA
CTCTCTTTATCTTCTCCCATTCAAAGGATTTGACAGTATCAATCTGAGAAACAAGATTCTCCAAGCCCTT
HAAGATCTTATCAAYCCT
>gi|3719111|dbj|C99754.1|C99754 C99754 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TTATCGATTTCAATTACAACACAAGTCTTGAAGTTTACTACAGATAAACTTCATCAAATTACAGAGAAAG
TTTGGGTCTAACAAATGATCATTTGTTAGACGGATTCATCTTCCATTACCTTTGACGTCTTGAAGCTGAC
CGCTTTTCTCGGATGCTCCCTTATGTTCAAGCTAAACACTTCAGGCCTCGAGTAATGTCCGACCACATCA
AAATCAAACTTGGCTCGTGCTATGTCCCCAAGATCTAGATCAGCTGTGATAAGAGCTTCTCCTCTATAGT
TTGGTCCAGCTAAAACAATTCCCAAAGGTGAAATGATAGAGCTTCCACCAGCGCAGACAACAGAGTCCGG
GTGTTAGGCTCTCTTCTGAACCGGAAAACATGTATYCCGGSGGAGAAGGATAGTCTTTCCGACGAMAAAA
CTGGTTAGCTGA
>gi|3719110|dbj|C99753.1|C99753 C99753 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CAGCATGAAGAGTGCATAAAGGAAGGTTCTGAGGTTTTGGGATATGATGCAAGGAATGTCAAAGCCCTAT
ACAGAAGGGGTCAAGCTTACAGAGATTTGGGCTTGTTTGAAGATGCCGTCTCTGATCTAAGCAAGGCCCA
TGAAGTTTCCCCAGAAGATGAGACAATTGCCGATGTGTTAAGAGATGTTAAGGAAAGATTGGCTGTCGAG
GGACCTGGCAAGGCATCAAGAGGTGTGGTGATTGAAGACATAACTGAAGAAAATAATGTTACTTCCGGAG
AGAATAAAAAACCGTCNAAAGAGGCTAATGGTCATGCTCAGGGCGTNAAGACTGATGTTGATGGATTGCA
AGCTCTCANAGATAATCCAGAAGCAATCAGAACTTTCCAGAATTTCATTTCAAAAACTGATCCCGATACA
CTTGCTGCTCTAAGCGGANGCNAAGCTGGANACATTTCNCCGGACATTTCNAAACTGCGTCCAGTTTGAT
AGGC
>gi|3719109|dbj|C99752.1|C99752 C99752 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TTCTAAAGAAAATTTATACAAAACTCAGAAATCCAAAGATGCAGAGTAATGAAATTACTCGAAAGGTAGA
TTTTACATTTGAAGCGCAGAAAAGAGTAGATATTTTAGACAGGTTCAGGTCATAGAAGCTGAGCTCGGTC
TGTGGTCTTTGTGGCTGCTCAACCTTCTCCTTCTCATCCACTTTGTCTCACTAGAAGCTGGAGAAACGGC
TCCATCAGCTGACGGGAGTTCGCAAGGAAGTGCCATAGCCGAGCTGGTGAAGGCGTTGAGAACAAGGAAC
GCCAAAATGGGAGACAAATCTAATCCTCCAAGAGGCGGTATGAATCCCGGAAAATGTTCAAGTATGGATC
ACATAAAGTGCTGAGGGGGTTAACAATGGCAGGAGGAGCACTCGGGAACCAGGTGAGTWCTAAACGAMCG
ACAAGGATGGTGTTAATATATKTTG
>gi|3719108|dbj|C99751.1|C99751 C99751 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ACATTAGATACCAACATAAAGCAAAATCAACACACACTGAAACAATGAAATCAACACAAAAACAAACACA
AACACAAACAACATGATTACATCTGCACACAAGATGTAACCTCAAAACACAATAGGAATCAAACTTATAC
AAGTTTAGGATTTAGGCCTCTTGCCTTCCTTGTCTTCCCCACAAACAGATCCTTAGACTTGATCAAACCA
GGGAGGCAACCAACAACTGTCACAAACGGAAACTGAGCCACCGAGTCCTTCTTCCTAAAGATACAATGGC
CAACTCTGGACCGGGCTTGTAAGTBGACATCTTCTTCTTTTTCCCACCTGACANTCATTACCTTT
>gi|3719107|dbj|C99750.1|C99750 C99750 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GCYTCCCTGTSTCTGATGTATTTGGAAAGACGAATGAAGTTGGTGATGTACAAAGGGAAGAAACACAGAC
ACAAGAAGAGAGAGTCTGAGATTATCCTCGAGAAGACCAATATCTATCAATGTCAACAACAGCAAAAACA
AATGAAGGCAGAGATCAGCCTTTCTTGACCGGCCTTTGGASTAATGATTTGTTCGGATCCTCTGTCTTCA
ATTTTGGAGGTCGCGTCTCTCCTTTTTTGGCCTTCTTTCCTGCTTTCTGAAAGTCTCTCCAGCTTGATAC
CCTTTTTTCTCTTGTTCCTTCCCACTGTTCTTCATGCTCACGCTTTTTTCTTCCATATCTCCTTTTGTTC
TGCTTCATCCTTCTTCAGTCTCCCCTCTTCTTCTGATATTCTCMATTGCCATTTTTCTTCTACGCCAMTC
TTGGTCTGTTAATATCTCTCGGACCTTTAACTTGAGCTCCTTCTGAAACTCCTCAGATTG
>gi|3719106|dbj|C99749.1|C99749 C99749 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GGATCATGTGCGGATGAGGAATGTGGAAACGTGATATTCCAACTAGGAGTGTTGATGTTGGAGCTGATCA
CAGGACAATCATCAGACAGACAAGGCAATGACTTGATCGAATGGGTACAAGACTCGTGTATTGCAAACTC
AATTGATAAGATGATTGATCCAGATTTAGGTAACAACTATAGCTCTAGAGAACTCCAGAAAGTCTTAGCC
GTGGCTCGACTCTGCATAAAAACGAGGTATGAGCCTCCTTCATTCTCAATTACACATGTATACCGGTATC
TACAGAAGAAGATCGATGTTGCAACTTGAATACTAGTTTTTTTTTTGTGAATTGAATTTAGGTGACATNT
GGTTTANCNCCCTTATTTAGTCTTTNGCCTATTTTTACNCCNTNCTAAATNTAATANCNNCTTATAGTGT
ATANCATTGTACTTGTCTTGAAATAACTTTTGANATTTGTACTGATGGCAATTGATTTCTTTCTTACCTT
ATTTGAA
>gi|3719096|dbj|C99748.1|C99748 C99748 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CGAAGCTATTCCTTGTGATCAATTCGACGTTGCGTTTCAGGCGGTGGAGCTTTGGATCGCCGATCGTGCT
GTTCTCCCAGTTGANAACTCTCTCGGTGGTTCGATTCATANAAATTACGATCTTCTCCTCCGTCACCGTC
TCCACATCGTCGGAGAAGTTCAGATCCCGGTTCACCACTGTCTCTTAGCTCTTCCCGGAGTTCGTACGGA
TTGCATCNCGCGAGTGATTTCGCATCCTCAAGCTCTGGCTCAGACGGAAGGATCCGCTCACNAACTCACN
CCNAAAAGCAGCCGATTGAAAGCGTTTCACGACACAGCCCG
>gi|3719095|dbj|C99747.1|C99747 C99747 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTTAGACTTTTTCTTCTTGCTTTTGTGATCCTCATTGTTGACTTCTTCTTCTTCTGACTTATTTCTCTTA
GAGCTCTTCTTGCGTTTTCGATCTTCTTTAGATTGTTCCTCTTCTGYTGATTTATTGTGATAGGCATCAA
AGGTTTCATCATCGGCATCAAGCVATTAATGCTTTGCATTCCTTGAGCTTTTTTTCTAAGGGTTGAGCGT
TGAATACATTCACTGAAGGGAGAAGCAACGTTCTCACCTTCTTAGCTGACTTATCGTTATMAGAAATCGG
GTTTCCYCGAATATTCAGATTTCGCAAGCAARATAGTGTMCCCAAAMCCTCTAAACCAGAGAGTTGCGWA
AWCAMATTGTTCCCCA
>gi|3719094|dbj|C99746.1|C99746 C99746 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CTCTCTGAACCATAGAACTCCAAGCTTGTACTGTACTCTACTAATACGTCGTCGTTTATATCTTACTCTT
TTGTTTCCTCTTACCAGAAAAAATAAATAAACAGCAATATTTTCAATTTTCGACTCAAATCATGCAAACC
ATTTCGCCTGCGTTCTCGTGCGATCTCAAATCCGTAATTCAACCAAATCTAACGGCTAAAAACGCGNGTT
ACTCGCACGTAAATGGAAAGCGCGTGTCTATTCGTTGCAGTTACAGGTCTGAGTCGTTTAGCTTCCCTAA
CGGTGTTGGCCAAGCCGAGCCGATTGGCAAAGCTCATGCGCCATCTTAGCCAGTAAAGTAGTTTCGGCTG
ANAATTCAAGCTCCGTCGCCCGTCGTTAACGGACACAGTAACGGNTCCGTTGATTTAAGCCTTGGTTCCG
G
>gi|3719093|dbj|C99745.1|C99745 C99745 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
TTAAATCATAGTTGAAACAATACTCAGCCTAGAAGGAGACAATCATTCCTATTCACTACAAATCTTTCTT
TATATACAAAACTAGTTAGAAAACAAAATCATAAGAATACTTGTGGGTGTGGGTGTTTGTGTCAAGAGTC
AAGACCAATTTCGCTCCTGTCAAATGTGGTTTGTTTTCTCCTTATCCAAACATAAACGAGAGATCATCCA
TAGGAACCTCATCAAGACCTGCTGTATCAATATCCTGAAGACCCTCGAACCAGTTTCCAAGATCTGCCTG
TTCATCTATTTCGTCTAGATCACGGAACGCTAATTTCGAGAAATCTATGGGAGCTTCGTCGTCGACTGCA
CCATCTCCAGAGGTAACYCCYCGGTTTGAGGCCCCYCTGCTTGCKG
>gi|3719092|dbj|C99744.1|C99744 C99744 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
ATAATAGTATAAAGTTACAGTTCATTATAAATGAAAAAGTACAAAAAACAATCTGATTTCCATTACAAAA
CAACAAAGCCCAGATAGGCTTATGGTACACTTGGGAACTCTCACTGCACATTCCCCAAAACCGTGACAAT
TGTCCATCATATCTCTTGAAAAGAACAAAACCCGTTTTTTAGATGCGTTATAATCTCTGATTCTCCTTGC
ATATAGTGTGACAAGTTTCCCATATATGTAGAATTGTATGATCGACTTCAGGCTTGAGAACAGTTTCTAT
AGTTTCAGGTAAATAACATCTKTGAGTTYCCTCTATACGTGCACTTCGTACTTCBTGGATCGGKTAAAGC
CCCAA
>gi|3719091|dbj|C99743.1|C99743 C99743 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GTGGCTTTVANATTCGAACATTTTAGAGGCTGCGGTGGTGGGGGTGGTTGAGGCGGTGGGATTYTTGTGG
YTTGTCTAATGGAAGCACGATGTTTGTTTTTAAAGCGGTGACGATTTCGCGACGAGCTTTAAGCCATGTT
TAG
>gi|3719090|dbj|C99742.1|C99742 C99742 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AATAACATTCTCTTTTCTCTCTGAAACAACACAACTACTAACTCGGGACATAAGKCTYCCCCAGCCCAGC
CCACTGATGAAGAAAGACATTGTCTGAAGAAACAGGTAGATGAAGTAATTGTTCTTCCCGTGCACAAAGT
CATAGCATCCGCACACGAACAAGAAAGCCGCAAATCCAAGCTCCAATGTATTCAATCGATCAGGCAATTT
GAAGATTCTTGGGAACCTTTTGATCCCTTTAGTGTTTCCTTTAGCGCTCTGACCGCTTCCAAGCTTAGCA
GTCACTACCCACTCGTTAGCCCTTCCTGCCTCAAACAGACCAATGAGAGTGGCCTTTGTCCGGTGCAGCG
ACATCACATTCTCGAATAGAMCTCCAATAGAMCAGCAGATGAATTSACCTTGGA
>gi|3719089|dbj|C99741.1|C99741 C99741 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
AAAAGTTTTGAAACTCTTCTATACACATACATTCTCCGGATGTGGTTGTTACTAACTTCAAAATATAAAA
ATTTAACAAAACAATTGTTATCATCATTTCCTACGAGTCATTAAACCCAATCCCACTCGCCGTCGCCGGA
AAACACCTCGGAAAATCAGCCACCGAAAACGATCTCCAGGCACAAAAACCCAACGACGACTGAGACGAAT
AAATTACCAAAAGACCCTTGACTCCTAGGATACAACGGAGGAAGCTTCTTCATCTGATGTTGATGATGAT
GTAGCTGCCTCGGAGGAGATCCAGAAGTCGTCGGWYTTGATCCCGGCGACGAGTCACCTCCGGAAGAAGA
TCCTTCTCCGGTCATCACACCAGCGGCAACAGCTWATWGCTAGYGTCAAAGCGTTTCTGCTAAGCGGACG
>gi|3719088|dbj|C99740.1|C99740 C99740 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
GTTCAYTTTTKACCAMHACWAGTGTTCATCATTAGTCGAACGGTTAAATGGCAGGCATTCTGAGTTCAAG
CAAAACTAGAATCCGCTCTTAAACCCCAGAAACATCATAAATTCATCTGCBAATYYAGAAAAAAAAAACC
TTCGTTGTACAGACATGGAGATTCCAATAGAGACTTCTTGGAAAAAATTTGCCTGGAAACCGATGCGATT
GGCTTCTTATCTCTTTCTCTTGGCACCAGAGCCTCTYCCTGTAGCTTTCTTCTCAGCAGGCGTACCACCT
TTCCCTCCATGGTACCCGGATCCYCGAATTCTTTTGCTTTTTACCCTGGGAAGAAATAYTCA
>gi|3719087|dbj|C99739.1|C99739 C99739 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CAACAAGGTGTTGATTCATCGAGGACGTATTACCGTGGCCAAATAGATCCAAAATCAGGAATGGAGAAGC
AAGGCAGTGATCCAAGAGCTCAACCACAACACCAAGAAAATCCAAAAACCGGTTATGATAATAACCGTGG
GGTGCANACATTTGAAGGTCTTGAACAGAAGTTCATGGATGATATAACAAGACTAGCANAAGATCAAATC
GAAGCANAGGATGCAGAGATCGCCNGACATCGAGAGAAAATAAACACTATAAACGCTAGATACGAAGAAC
AGTTAGCTACACTTAGNAGCACGGCACACAGGTTAGANAGAANANATCNTGAGGAAAGAATCNCTANCTA
GGCAGCAACAATTCCAGCAGCAAACCATGGGGATGATGGACCCATNCCNTCC
>gi|3719086|dbj|C99738.1|C99738 C99738 YAC clone CIC7E11 region-specific cDNA Arabidopsis thaliana cDNA, mRNA sequence
CAGCAAAATTBYAGGGCAAGCTAGAGTAAAATGACCCTTTTTAAATGATATCTTCAACTATTCTTYTCTT
TCTGCACAACATCCGATTCTCTTAGGCTTCTGTTTCTCCAGCTTTGGACAAAATGTGATTCCGCAAATAA
GTGGTACAGCAAAGAAGAGTATATAATTCAAGACCGTAAACTCCATCCACGTGCAGCCAATTCACGCCGT
ATTCTCGTAGCTGCCTCTGCTGTGTCATTCAATGGCGGATAACTCCAACTTTCCGACATATYTTCGAAAC
CTGTAAATGAGCGGACAACTCCTCGCTCCCTMAAAGACTTTTGGAMTTCTGCA
>gi|3638925|gb|AI138148.1|AI138148 EST 2 Arabidopsis thaliana cell suspension Arabidopsis thaliana cDNA clone sp12 similar to hypothetical protein, mRNA sequence
CAAAGGANCCCATCTTATCATATGTACTGATAAAAGCTTCACAATAATGTCGCGGCTAANAATGAAATAT
TCAAATATTTCAAAGAGACAGCANAAATAAAACTAAATCCATTGCCCTAAAACCCCAAACTTCAAACCCT
GCAAATTTTGATTGCACCTCCTATTTACACAACAAACCACTCATCACTGCTGTATCCAGCATCTTNGGCT
TTAGACTCATCATCACCGACTGCATCTTTTGAGAGTTCCATCATTTGAATANCTCCTGGTTTCTCTGTTT
TAACATNGGGCATAATAGCTTCAGCTTTGTCTACAACTACATATTCGTCATCTGAATGACCTTTATCACC
TTCACCACTCTCATCATCANAATCGTTGTANAAATCAAACGTATCAACGGGGGGAATTTNCCTACNAGGT
CGGATCAGATATGGTAAAGGGAACTCCGTTGCANCCTCCCCTCTTCCGAGAATGCANAACANAAACAGCA
TGAACTGGGTGCCAATGTTGCCATGTCCTGATTCAAAAATGGTACCTTATCGAAAATTCANANAAAATCG
TTTATCATATCTTGANAAATTTGATCGTCNACAAATTATCAAAACTCAGTAAGAAAAAAACAAGACATCN
GCGGTGGCNAAAACTAAAAATTC
>gi|3638924|gb|AI138147.1|AI138147 EST 1 Arabidopsis thaliana cell suspension Arabidopsis thaliana cDNA clone sp2 similar to cytochrome P450, mRNA sequence
TTTTTTTTTTTTTTTTTTTATTGTAAGTAAAACTTTGTTATATTAAATGTTATCAAAAATGTAACTTGAC
ACATCTTTTATACAAAGCATCAAAACTCCAGACACAGATAAAGAAAAGTAAACTTTAAACAAGAAAACTC
AATTCAACATCCTTCTTACTTAAGCTGTGTAGAGTTTTGGATCGGACAACCTTGGAACAGGAATAGCCAC
AAGTGGAGACTTCAACTTAAGAACAAGACCAAACTTCTCTTCAACCTCAAACTTCTGTCCTTGAGGAGCT
TTCCAATCAAAAGAGTGAAGAAGTGAAGCAATGTTGAACAGAACAAGTCTCTCAGCCATGTTTATCGCCG
CACAAATCCTCCTTCCTGACCCAAAAGGCAAATACTTAAAATCACCTCCATTGAAATCAAGCGAATTCTC
CAAAAACCTCTCAGGTTTGAACTCGTTTGGTTCATCCCAATTCTTAGGATCTCTATGAATCGCCCAAACG
TTGATGAAAATCTTGGAGTCTTTAGGCACAGTGTATCCCGCAACCACCGAGGTTTCGCTGTTTCTGTGAG
GAACAAGAAGAGGAAGCGTTGGGTGAAGCCTAAGAGTCTCTTTCATAACCGCTTGTAGGTAAGGAAGCTT
AGGTAAATGTGATTCCTCAACGATGTTGTCTTTGCCAACAACTTGGTCAAGTTCTAGTCGGATCTTGTTT
AAACTTCCGGTCTGCTCCCAATCTC
>gi|3450634|gb|AI100673.1|AI100673 35048 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99P9XP 3', mRNA sequence
TTGCCGTTTACCCNCCCATGCCTGGNCTTACCNTCCAATAATGNTTGNTGNCCCATATATCCATNTNCCA
CCAAGNTAAGAAGAAAGCCCAACTAGTGAATAATTGATTGATGGAGATAATATGTGGTTAGAGAAATTCC
TAGAGGAAAGCCAAGAGGTAGATATTTTGGTTCCTGAAGCGACGACAACAGAAAAGGGGGACACCTTGGC
TTTTGACGTTGATCAACTTTGGAGTCTTTTCGATGGAGAGACTGTGAAATTTGATTAGTGTTTCGAACAT
TTGTTTGCGTTTGTGTATAGGTTTGCTTTCACCTTTTAATTTGTGTGTTTTGATAAATAAGCTAATAGTT
TTTAGCATTTTAATGAAATATTTCAAGTTTCCGTGTTAC
>gi|3450633|gb|AI100672.1|AI100672 35047 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99P4XP 3', mRNA sequence
GGACCNCGATCCAGGTGANTCCAGCCCGCCGCANTCATCTAGTCAGTGAAGCTGGGAAGTCACTGAACAG
CCCAGAGTCTAAGAAAGTGCTGAGCAATCTCATTTACAACTATAAGCCTACTTACTGTGGATNCGCAGGG
ATTGGTTACGACGAGGTTTACATCTTCACACAACAACGANCCCTTCTCTAATAACTATANCCTCTCCTGT
GTANCCTCTCGTGTGTATAGTGAAATATGTNCCTTCGACTCTGTTATTATCTGTGAACTTGTTGTAACTT
TGAACGTCAGCCTATGGCTTGTGTTTGACATTAAACTAGATAATGTACGCTTTTCTATCTTT
>gi|3450632|gb|AI100671.1|AI100671 35046 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99P23XP 3', mRNA sequence
GCTTCCAGGCTTTNTCAAATCGACTTTTNCANTNGGANCCCTTGAAGACCNCTGTGAAGAGGGGGACCCC
NATAACTACAACGAAAATACCATTCAGACCAGCCCGTTGANCCTATCCTTCATATCTGCTTCTACGGCAT
GGCTTTCTCTTACCTTGTCGCTCTCCCTAATGAGCGTCGCCATCTTGAGCATCAGCAGCATGCTAAGGAG
CACGGTGGTCATTGATCTCGTGGGAATCGTTTCGATCTCGAGATGATTTTAGGGGGGTTGCTGTGAAATC
TTTCTCTGCTTGATGGTGACGACGACTCAAGAATTGTGTCTTATTGTTTCGTTTTCTTGAATTTTCCTGG
ATAATGTTGACCTAAAGGAAAACCTTTCTTTCGAATTAC
>gi|3450631|gb|AI100670.1|AI100670 35045 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99P18XP 3', mRNA sequence
AAGACCGGATTTGTTGGGGTTGNTGGAGNATNTTGCCNCGGCGGATGGCCNAGTNTAATACCATGTGGGG
GCCCAGTATATAGTGTTTTAAGTCCCCAGGGGGAAAGTAGAAGAAATAGTACTNTAGTTGTCTTGTCTGA
TTTTTTTGAGTGGAACTCGTTTTGAAAAGTCGTTGGTGATGACGTGGCAGCTGATCAACGTTTTTATTCA
GAAAGAAACACGGCAACGCGAAAGCGGTGATTTCACACCCACCGCACTGTTTTTGTATTCTTCTAGTTTC
CGTTGTAAATAGTTCAGTTTAAATGTTATTTTATCTGTATATGCTATTGTCAAACAAAATGTATTTGTTT
CTGTTTACGTGTTGTTGGAATGCGATTTTCCTTGATGAGT
>gi|3450630|gb|AI100669.1|AI100669 35044 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99N17XP 3', mRNA sequence
GGNAGATTTTAAAATNTTAGTGGAAAAAATGGTGGGACCATTNCCGACCGCCGAATCCTTGGATACCAAG
AAACCTGTTCCCCGTGTGGACCACAGAGGTCGATCTCGTGAATCTGAAGCCGTTCATCACCGCTCTTACT
GAAGCTGGCCGGCTCAACTACGTGACCGCACCGTCCGCTGCTTGAATGTTGCCAGGAGTTAAAATTGTCG
GTGGATCAGGTAGTTATTTTTCTTTCCGGTCAGTAAGAGGTTGGGGATTATGTGTCGGGTCGACAACCAC
ACATACTGTCTCTGGTTCCAATGCTTTGGACGTTGACATGTGATTTGCTTTACTTTTTTGTCTATAATGT
GTGTTATCCTCAATTTTAGCGTCTATCTTCG
>gi|3450629|gb|AI100668.1|AI100668 35043 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99M17XP 3', mRNA sequence
GAGATTTGAAGGAATNGGGAGTGGATTTTNCCCAAGAACCCCAACGNTGGNAAGGATGGAGGATATCNCC
CTTCATTAAGGATCCCTGATGGCTACTGGATCGAGATCTTTGATCTCAAGACTATCGGAACTACTACCGT
AAACGCAGCTTGATCTCAAGACTATCGGAACTACTACCGTAAACGCAGCTTGATCTCAAGACTATCGGGA
CTACTACCGGAAACGCAGCTTGAGGAAGTAGCGATTGCGCTATTTGTGTTCTTTTGCTCATTCCACCCGA
GTGTGTGCATACAGTTAAAGAATTTTCATGTTTCATCGAATAATCGGAACAAGATGGTCGTTGTTTATCA
ATGTGGTCTGTTTCTTGAC
>gi|3450628|gb|AI100667.1|AI100667 35042 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99M14XP 3', mRNA sequence
CCTTTTTNAGCTACCGATNTGTTTGCCTTAACCCTTCANCCAGCTTGAAGGCCCCGAACATGTCCCCANG
TTGTTATGGAATTAAACGAGTGTTTGACCATCTGAAAATTCCAAGGGGAGGAGCCGATTCGAGACATGGA
CTCAGAAGGTTCTATAGAAGTAAGCTTGACCTTTGGTACCGAAGTGACCCCATTGGCTCGGTAGTTTACA
TGAAGAATTCAGCTTCTTTTTGAATTTTTGAATGGTTTCTTCTAAACACCATGTGAGAATAAGTCATCCA
CATATAACCATACAATGTTTTTCTAAGTTTTCTTACTCTCAAAATTTTGTGTTCAGCTTGAGGTTAATCG
AGGTATCCTAGTGGTTAATCGAAGTATACTTCTTC
>gi|3450627|gb|AI100666.1|AI100666 35041 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99M10XP 3', mRNA sequence
CTTTTTACCAGNAGNCCCCCGTTTGANAAATCTTCATCAAGCTGGNATCTGCCCAGGGAAAACCGCAAAG
ATGCTACTGGAGAAGGCCCAAAAAGTCGTTGGAGCATTAATGAGTTCTTGAAGCCGGCTGATGGAAAGAG
GTACAACGGGAGAGGTGGAGGCTCCCGCGGAAGAGGAGGTCGCGGTGGTCNTGNTGAAGGAGGAAACCAA
AGGTATGCAAAAGAAGCTGCAGCTCCGGCGATTGGAGACACAGCTCAGTTCCCTTCGTTGGGCTAGTAAA
GACCCCTGGTCCTTCAGCCTCGCTATCTCTGTCTTTCGTTTCTCTTTGGTTGAATTTTGTTAGTTTTATA
ATTTTTTGTTACACTTTCTGAAGGTCTTTTCTGCGAAACTATTACGTTTTTTAAGTTATGAAAAAAATTA
TTAAG
>gi|3450626|gb|AI100665.1|AI100665 35040 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99I5XP 3', mRNA sequence
TCCTCACANNGAAACGNCAGCCACATCAATGCATCAANACACATAAANGNGAGATTTACTACAAANGAAA
GNGNAACNAAGAACGATATGGCANGACTCAATCAACAAGATCGGAGACGCACTCCACATTGGAGGAGGCA
AACAAGGAAGGTGAGCACAAGAAGGAAGAGGAACACAAAGAAACACGTTGACGAGCACAAGAGTGGTGAG
CACAAAGAAGGTATTGTTGACAAGATCAAAGACAAGATCCACGGTGGTGAAGGTAAAAGCCACGACGGAG
AAGGCAAAAGCCACGACGGTGAGAAG
>gi|3450625|gb|AI100664.1|AI100664 35039 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99F4XP 3', mRNA sequence
CCATGCGGAAACCCCAATTTGNGCGTTCACTGCACGGTATGTCTTGGGGNCCCCCCNAATAGGGTAAGTC
CATCGAGACACCAGTAAGGCCGCATTTNCCCCCGCGCTGAGTTCCAAGTGAAACTCTAGCCCGGAGATCT
TAAAATTATATAGCAAACGAGAGAGAGAGAGAGAAAGCAGAAGAAGAAGTCTAAAGAAGAAGGTACTTGA
GGCGTTTTGTGTTTATATATAAAACTCTTTCTAGATTTATTTTAAGTTAAATNTTCGCGGTCGCAGAGCC
TGCCCGGTATCTTTGAACAACTCAACAACTTTGGTCTAAACCTTTCTCCTTTCTTTAGTCTCCAAACACA
CAAAAATTTGATTATTTTTGTTGTTGTTGAAATACCCTTTGGATATTTTTATGACTTATTTAAGACATTT
GGAGAAATTTTAT
>gi|3450624|gb|AI100663.1|AI100663 35038 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99F3XP 3', mRNA sequence
TCAGGAAGTTCCANAAGACCCTGACTTCTACCCGTAGCTTCCTTCCAGCGCTGGTCGTGAGATAGCCTCG
GATTCCAAGCCGGATCTGAGGTTCCAGAGCCANTGCTGTGCTGCTTACCAAGAGGCTGCTGAGGCTTACC
TTGTTGGTTTGTTTGAAGACCACTAACCNTTGCGCCCATTCACGCTAAGAGGGTCCACCATCATGCCCTA
AGGATATCCCAGCTCGCGAGGAGAATCAGAGGAGAAAGAGCTTGAAGACTGTTGTTATGGTTTATATCTT
TTGATTTAGTTCGTCAATGGAACTCTATTTCTGGATTTTGATTTGCGTTTTAGTAGTAATGGGTTCTTGT
AAGTGTTGAGCTTTGGCTCGTTTTAATTTTCAGTTGTTAGGTACTTTGGTTTAGTTAGCCTTGAAGTGTT
CGATGAAATACCCCAACGAAACTCTCTCCTGTTTAATAGAACTTATTTTCCTT
>gi|3450623|gb|AI100662.1|AI100662 35037 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99E21XP 3', mRNA sequence
TTCAGCCGGAGGATCCTCTGGATGGNCCCCTCTNGCTCTGCCACTTTTTGGNAGACCATGGNTTCNCCGG
CTGATAATGAGTGNTAGATAATGTTAATGGAGANGCTGTCCATAGGAAAGTNCCCCGCTCTTACAAGCCC
GGGAGGAAGAGTTTGTGTATGAGAGTTGTTCCCAGTTTTCCCAACAACTGCTGGATCCCATTGATGGCTC
TTTCACCTTTGTACCTGGAAGTTTGAGAGATCCAAAAGGGAGTCAATTCGAAGTCAAAGTCGTAGAGTTT
CCTCTGGAGTTACCGGACTACATCTTCTGAACTCTTTCTGGCACAAGGTTCGTTACTCTTTCAAGATAAT
TTGTTGTATCGTTTGCTTTGTCCGTACAGCATGCAATGTCCTAATAAAATAAAGGTGTTGGATCAACTGG
TTTACAAGTTCATGAGAACAGATTATTCTT
>gi|3450622|gb|AI100661.1|AI100661 35036 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99D14XP 3', mRNA sequence
GCGATCCATGGCNCCGGGNTACCCCATTGGCTGAGGCTTGATGAGTTCCGAAGACCAGNTGAAGGAAATT
GGAGAGCCATCTGCAACCCCAATCCATTGCCCAAGATGTACCCAAGGAGCTGGTGGTGAAAGCCGNTGGT
CCCAGGTGCCTCTGGTATGGACGATGATGCTCCCCCCTGCTTCAGGCGGTGCTGGACCTAAGATCGAGGA
GGTCGACTAATTTGTTGGACATTGACCTCTCTCTTTCTCCTATCTCTATCTCTTTTACTTGCTTTTTTTT
GATCTGTTAAGACTTTTTATGTTGGGCTTTTTTAAAGAAGCCCATTTTGTGGTGTTTTTTGGTTAGTACT
ATTTTGAACAATGGTTGG
>gi|3450621|gb|AI100660.1|AI100660 35035 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99C8XP 3', mRNA sequence
GGTANGCTCCCNCACATGTCCCCNCCTGCCTTTCATTGCNCCCTCTTGCTGNCTTAGCCAAGAGCNCCTC
GACGTAGTCTCTTCCAAGGTCGATGTTGACCGAATTGAACACTNTTGCTGAGGGAGTTTAAAGTTCCAGG
CAATGCCCAACGTTTATCTTCATGAAAGAAGGAGAGATCAAGGAGACTGTGGTTGGTGCTGCTAAAGAAG
AAATCATTGCCAATCTCGAGAAGCACAAGACAGTTGTTGCTGCTGCTTGATTTGCTTTTCTCTCTTACCT
ATTTTGCTAAAATATGTTTGGTGTTTTAATAAATCCTTTGTTCGCCCGAGTCTTTTCACCTTAAATGTGC
TCTTATGTGTGGTGGTGAATAAATGTTGTTGCAAACTTGATTACTCGCAGCTATGCTAATTGTTCGTTCA
TGGTTATGTTT
>gi|3450620|gb|AI100659.1|AI100659 35034 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99B20XP 3', mRNA sequence
CTGGATATTCTGGGGTGGGGCCCATTCATTGGGGGCNGCGATAGCTGCATTTNTCCCCCAATTTGTCCTA
AGGGCTTCAGGTTCCAAGTCACTTGGATCCTTCAGAAGTNCAGCCAACGTTTGNGTTTTTGCCNCNCAAA
AAAAAACCTNTCATAATNACCACNATTNCAAAATGGTTGTGTTATTATGTATGTACAAAAATTGGCAACT
TTGCTTGTAAAACTATGCNCTATATTTCTTCTTGTTTTTCTGTTTTCATTGTGGTGTAATACTTTGATAT
GTGCCAATGCCAATGTTTGTGTACTCGGGAAAACAATTAATGAAAACCAAATTGTTTTGCCTT
>gi|3450619|gb|AI100658.1|AI100658 35033 Lambda-PRL2 Arabidopsis thaliana cDNA clone 99B10XP 3', mRNA sequence
CCTTTTCNATTAAATCTGACCCTNTTGACGTNTCCCGTTTACCNACCCACNNTTGGNATGGTTAACTCCG
TGGGAAGTCACNACAGCCGNAGTTCCATGCAAAGTGCTCGTACCAAAGCTTTGATGTTGAGCAATGGCTT
GCGTCCGATACATCGCCGTATGAGCTCANTGCTGTTCGGAATAACTGNCCAGTTTCGCTTAGGGAAAGTG
TCGGTCGGGNCGGGCCTGAGATCCGGAAGACTCTCTCTTGGATCGTGTGAGAGTAGTGAATGAAATGTCA
AATGTGTATGTGTGTGTGTAACTTGGAGAGTTGTTCTTTGTTGTCTTGTGAACGTGTGATGGCNATAATG
AAAATGATTCGNTCGAATAAAAGTTCCGTTCTTTGTT
>gi|3450618|gb|AI100657.1|AI100657 35032 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98O4XP 3', mRNA sequence
ACGCCCCTTAGNCCCAAAGGGGGNTNATTTTCCAAAGGAAGCATTAATTATGCNTTATGGTAATNANCTA
AATATGTGTATATGTNGTCGAGTATGTNTTTTCCTCGAATATATATGCATATTANCCCAATAATTGTTGT
TGATCATGGTTTTTTCTCCCTTATTTTTCTCCTCTATATGTTTTACCACTTAATNCCTTGTTGGTTTGTG
GGTAAAAAGAAAGATAATTATAAAAAGAAAATAAAGAATCAAGAGTAGGAGAGGGAAGAAAGTTGAGGAG
TGAAAATTAGAAGTATAATTTATTGTTTTTAATGAGGTTTTTTACCTTGTTGGAGTAAGAAATATTTAAT
GATGAATGTTGTGTGTTGTAC
>gi|3450617|gb|AI100656.1|AI100656 35031 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98N1XP 3', mRNA sequence
TCCTGNTTTTTNCNNCTNGGTCCCTNAGAGGTTCTCCATTCCGCTGTTATGANGATNCCTTACTTCTTCA
AGNGGATCTACCCAACCCCTTGGAAACTTTTCCAAGGCTACATTCGATTGCTACAGAAGNCCATATGGGT
TCCTTACACCAGAGTTCTGGAAAGAGACTAGATTCTCCCAGATCGCCGTACCAAGAGCACACTGATTTCC
TGTCGACTAAGGCTGTTTCTGCAACCAAGGTTATCACTGAGGGTGAAGACCAAGCTTAAGACCTTCATGA
GATGAGTTTGGTTTATAGGTTTTGGTTATCGCAAATATTTATCTTTCCGGTCTTGTTTCTTGGTTGTCTT
TTATCAGTTTTTGATATTGGAGTTTCAGTTACAAGGATAATCATAATTTAGTTATGTTTGGCTTTTGTT
>gi|3450616|gb|AI100655.1|AI100655 35030 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98N18XP 3', mRNA sequence
CGGNCTACCCCNCGCGTCCGATTTATGCNAGAAGGGNATTNCCNCCNGGAATGTCCCCTCATCTTCCTCC
AATGGNTCCTCCCCGCCAGTTCGANCGTATTTATATACTTTTGGGTCCCCTGAGCCAAAGGCCCGATCCA
CTTGAGGAAATACAGGCACTGCTCAACAACTCTGTGCAATAATATCCATTTTTCTTTTTCTTTTTGGGTA
AATGNTCATATATATAAGTCGATTGTTGTTATTTGGTGTGAGTTTGAATGTGATCCGTGTGCGTATCAAA
TTTTGGATGGGAAATTTGAAACAGTAAAAATTTGTATATTCCTCGTTTGGGAAAAATGTATGTTTTGGTT
AGTTATATGCAAAAATGTTGTTGAAGAAGTTTATACATAAAAAGTTAAATACAAAAAGATGGTAAGAAAA
C
>gi|3450615|gb|AI100654.1|AI100654 35029 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98L24XP 3', mRNA sequence
TTGCCCCCNCATTCCCCGGTAAGCTTTGGGGGGNGGTNNCATTGGGAANATNTTGGAGAANCGCCCCCNA
CGTTCAAGAAANCATTAAAGAAGTNTTTGGACTTTGCTAAGTCGAATGACTTGAGTCATCTTTTGGTTTA
GTTTTTGTTATTATATAAGCNCAATAATAATAGGAGGGCACTTCCCCTGTTCTGAGAGTTTGTGAACATA
TTACTCAGTGGTTTAAATCACACATATGTATTTGTTTCCCCAATCGTAGGAACTCAATGGTTTCAAATCT
CATTATATAAACATAAAAATGAATAAAGGCATATTAAATTTGTCT
>gi|3450614|gb|AI100653.1|AI100653 35028 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98K18XP 3', mRNA sequence
CTTCCCCGTTTGAATTCCTCTGTGAGCCAAATCNCCAAAATGGGNCCACTCAAATGTTCTGNAACTCTCA
TCCGAAGGAAGTACGNTCCTGGATCTCGTTTATGCCGTGTGTGCGGGAACTCACACGGGCTTATCAGGAA
GTATGGTTTGAATTGCTGCAGACAGTGTTTCCGCAGTAACGCCAAGGAGATCGGATTCATTAAGTACCGT
TAAAGAGGCCTTTGACTGATGCTTATAATACACAAACATGTTGGTGTTGATGAATTGGCCTTGAATCTTT
TAAGTTGTTGTTGCATTCTTCTTTAAAGTTTATCTCTTATTTGGAACAATGATCTTTTGGTTTTGATTAA
TATTTTGCTTGTTAATATAGACCATTTTGGCAT
>gi|3450613|gb|AI100652.1|AI100652 35027 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98K16XP 3', mRNA sequence
TGATATGTGAGTTATAAATTTATAACTGTTTTGTTTGGTTNTAACTGGTTCTCCAAGTTTGTTAGCATGT
GCATGCTNCTNTATATTNCATTTTAATTNGTGAGGCTTTTNATGGGACAAGATAGTAGTGTTNCAAAAGG
TGGCACATTACTTAAAAATGTTGTNAATTTTTTTGTTTGTNTGTAGCTTTGTAAGTGTGGTGCATGGTGA
TCGATGTAAGAATTGTGTTTCTTTTGGCTTTAAANTATTTTCCATTTACTCC
>gi|3450612|gb|AI100651.1|AI100651 35026 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98K15XP 3', mRNA sequence
AAAAATTCCTCTACTTCATCCAGGCCNTAGTTCTCCNGTTTCTATCAAANCCCACCGCTCCCTCCGTCTC
CACCGAGAATAACGACGNTTACGAAGAATCCGTGTTATGGTTGTTATGTTCNCCGTAATTCCAGAAATAT
CTACCTTGTTCACAACGGCAATCACTGGCAATAACGTGAAGAATCTTCGAATATACGATT
>gi|3450611|gb|AI100650.1|AI100650 35025 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98J7XP 3', mRNA sequence
AGCTCANTAGNTCCCCATATCNTGCCAGCCNCTGGNCGGCCTCGGGNCACAGNATTANCGGAATGGGGAT
NGACTTGTTTCGGNAAGAAGTGGATTGTTTCTTCAAGATTCTGTTATCGGGGAGAGACACATTACTAGAG
NACCTAAGGTCGATGGGTGCATCAACCCTACAGGCAACATCGCCAAAAAAGGCTGCCGGAAAAAATTACA
GAGGATTCTGATAAACTATAAATGTTTGTACAGATGGTTTTACTTCAAGTGTTCCATCTTCTTGGTATTG
AATGTATTATTAGGTTTTTGTGCAATCTTAGTCGTTTGTATGAGATGCTTTGAAAGTAGTAGTTGTATAA
GTAAAGGTTTTACC
>gi|3450610|gb|AI100649.1|AI100649 35024 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98J3XP 3', mRNA sequence
GGGCTTTCAACGNGACCGTNGCCCAACGTCGGCCCGNCCAAACTCTTCCATTCCAAATCAAAGGTNGTCG
CANGTCCCGGNATCTAAAGCTTCGCATCAAGGTCNCCCCTTAGTGTCCTGTATTTTAAGACANTGAACGA
GAAGCAATCTTTTAGTGTCACTGTTACAGGCAGCGACGTTGACTCGGAAGTCCCTTCGTCTGCAAATCTA
ATTTGGTCTGACGGTACCCATAACGTGAGAAGTCCCATTGTTGTTTACATAATGGTTGTTGATGAGGCAT
GAGCAATTCATCATCGTCGTCAGTCATCACAAATAAATCTTTATTGTCGTTGTAACGTTTCTTCATTTTG
TGTTTACGTTATTTGATTGCTCTATGATGTTTCAGCTTCTTTTACTAT
>gi|3450609|gb|AI100648.1|AI100648 35023 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98J11XP 3', mRNA sequence
AAGTTTGGTTTGGCCAGACAAGATGAGCCACATCTNTACCGGAGGCGGTGCTAGTTTGGAGCTTCTTGAG
GGTAAGCCACTTCCAGGAGTCCTCGCTCTCGACGAAGCTTGAAAANCCTCACGTTGGATTTCATCGCTAT
TTTGTGTTGTTATATGTATAACAAGTCGTCTGGTTATCTTGTGACCAGACGAGCAAGCCATTATTTATCA
GCTTGAGATTTTCGTCTACGGCTCTCTTTTTATGAGTTTTTTAGTTTGGAGCCTTTTTTTAATAATAAGA
GATGAAACTCTGATTGACGAC
>gi|3450608|gb|AI100647.1|AI100647 35022 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98I13XP 3', mRNA sequence
CCCCTGGTTGGGCTGTAAAATGGCNNCTGGNATTGATGGCCCCCGGNCGACATCTCNACTNCCTACTCCA
ATAGNTTTAAATCCCGGCGGATGTGGCTGCTACCATGGACAGCTTCCGGAAACGCTCTCAGAAGCTGTTG
AAGCTCTGGACAAAGACAAAGTTCTCCCACGATTTGCTCGGACAAAAGCTTTTAGTTGCCATAAAAGGAG
TCCGTAAGGCTGAGGTCGAGTATTATTCGAAGAATCCGGATGCATATAAGCAACTCATTCACCGATACTA
ATCCTTTGAGCATCTCTATGATGATTGTTGGATCATTTGGTTTTATTGTGGACTTTGTGTCACATGAAGG
GTCGTATTTGCAAAATACTTGACATAAAGATGTGGTTCAGAAAATTAATAAACTAAATTTCAT
>gi|3450607|gb|AI100646.1|AI100646 35021 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98F3XP 3', mRNA sequence
TTGACCNGGGGAATCGGAGGNGGGGAAGGTTCNCCNTNAAAGAGNCTTTTAAAGGGNCCCNTCCTTACCA
TGGCTCATCCTCTTAANTTAACNCCTGTCACTCGACAACCACCCTTGACTTGGGATATGACACTGAATTT
GCAGACAATAAAAATAGATTTCNCTCTATTTTTTGTTTATGGGTTTCCCGGTATTAGTCTGGTTTGGCAT
TTGTAGAGGAGGATGTTGGGGCAATGATGTTGATCTTGTTTCTCGAACAGACCCTCTGTCGTTTTTACAT
TTAAATGGTTAAATTATTTTGTAATTCAGACTTGAGT
>gi|3450606|gb|AI100645.1|AI100645 35020 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98F23XP 3', mRNA sequence
TAGGCCTTGCCAATTTNGCCATCGGATCCGGTTCCGNGATTAGATAGCCCCCCCTAGAGGACTCCATGCC
GTTGACCCGGAAAGCTATCGTTCCANACCGGGTNGGGCCAGAANCTGAGTTTTGTTGTTAGGGTTAAGAC
CCACAGAGGTGAAGTTGTCCACCAGGAGCCGACAAATGTGGAGACTGGTCATATGGTTTGGTCAGATGGG
AAACGGAATGTGACAAGTCCCTTGGTGGTCACTCTTCAACAACCTCTTTGAAGGGTTTTAGAATCTGGTG
ACCGGGAAAATTCTGGTCTCTGTTTGTTGTACTAGTGAAAAAGAAAGATCATAAGTTGTTGTTGTCGTCG
TCTATGATCTTTGTTGGTGTAATATAAATATGTATCTTTGTTTTGTTGTTAAGAAAGATAGAGCGTCTAA
AG
>gi|3450605|gb|AI100644.1|AI100644 35019 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98F21XP 3', mRNA sequence
CCTATNCCCCACTGNTCNTTCCACTTGCTCCTCGAAGAACAGCTGTTTCGTCGTGCTCTTCNCCCTTTGG
GACTGATTCATCATTTATTTTATGTTATGAGCAATTGTATTCNCATTGTTGTATTTGCATTATTGTATAC
TTTCTGCTGATNTCAAGAAAAAATCGTTGGTTTATGTGAGGAATTTATTTATTTCGTTTAATTTGTACAA
TTGGTAAAATNTTNCAATGAGCAGGTTTGGATTCCGGACC
>gi|3450604|gb|AI100643.1|AI100643 35018 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98E6XP 3', mRNA sequence
TCCAGCCCTAATGCCACTGACACAATCCCCTTGGTGAGAGAATACGCTGATGGCACTCAAAAATTCTTCA
ATGCTTTTGTGGAAGCAATGAATAGAATGGGAAACATTACACCTCTCACTGGAACTCAAGGACAAATCAG
ACAGAATTGTAGGGTGGTTAACTCCAACTCGCTGCTACATGATGTGGTCGAAATCGTTGACTTTGTCAGC
TCTATGTAACATAACGTTGTCTCGATATATGTGGCAACCAAAAATATGTTTTATGAAATAAAGTGTTCTC
AAAATGTTTATGAAGAACATTTCGTCTT
>gi|3450603|gb|AI100642.1|AI100642 35017 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98C2XP 3', mRNA sequence
CGGTCGACCCCACGCGTCCGCGTCTTCTTCAACTCCCAGAGAGAGACCGTAGCAAAACAGGGCTTACCGG
AGCAGAACGGAAAACCCCATTTCGAAGCTGGAGATGATCGTGCTAAGGAGTACGTCAGTCTCTTGAAATC
GAACGATCCAATTGGATTCAACATTGTTGATGTTCTTGCTTGGGGTTCTATTGGACACATCGTTGCTTAC
TACATCTTGGCTACTTCCAGCAATGGATACGACCCAAGCTTCTTTGGATGATTCGTTTCAATGTCAATCT
CTCGTATATGTATATGTATATGTTTGACTTGTGTTGCAAGCTATCTAATCTGTTCTCTATCTCTGTTTCT
TCTTCTGTTGTTGTTGTTGTTGTCTAAGACTTGTCCCTCTTTTTGCAAATGTTTTATTTCTCCATTTACA
AAGATTGGTTTGCAGAGTTTT
>gi|3450602|gb|AI100641.1|AI100641 35016 Lambda-PRL2 Arabidopsis thaliana cDNA clone 98B15XP 3', mRNA sequence
CATGGTTGATGNCATATCCNCTGATGTTGCTCACCCAGATCAGGCAAGAATCTTGCCCNTGAATGCCTCA
TTTTCCCTCAAAACTGNTGGACACTTTGTTATCTCAATCAAGGCCAACTGTATCGACTCTACAGTTGCAG
CAGAAGCAGTCTTCCAGAGCGAGGTGAAGAAGCTGCAACAAGAGCAGTTTAAGCCAGCAGAACAGGTGAC
TCTCGAGCCGTTTGAGCGTGACCATGCCTGTGTTGTTGGTGGTTACCGCATGCCGAAGAAACAAAAGACC
CCAGCCTCATAGAGGAACTGTGGACAGTAGTGCCTGTGTATTAAGACTTATTTACTGGGTTTTGTTTTTA
TCTCCTTGCTTGTTGTATTAAGCTAGAGATGGATAATGCTTTTATGTCTCATTTGGAAAATTTTATCCTC
GTTTTAGAACTAATATATATTGATGCAACATTTTCGTCC
>gi|3450601|gb|AI100640.1|AI100640 35015 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97P6XP 3', mRNA sequence
GGAAAAAGTCCCTTGGCCCCCGGCTTNATCCTGCCTGGGGGGACCATTTTGGGGTATGGCCATCCGCAAA
AAGNATCCAATTGGAGGTGCAGAAAGGCTATCTTCCATANTTCGGGGGACAATTGTCCTTCCCCCCAACA
GGTGCCGCTCATGGTCTTCTGTGTACGGAAGGGGAAAAAGGATGGATGATGGGNTNCCTCTATGTCACTT
ACAGCGGAGAAACACATTTGGATTTGGATCTCCATAATAGAGACCTCTTGCTGGATATTTCATTTTACTC
CTCTCTATTTTCACCAAATATTTCATCTTCTTATTAATTACTAAGCAAGCAAGCCACCTATGTACTTATT
CTCTAAGGACCTTTGGTCGGGCGTTAATATGTACAGAAAACATAAAATAATGTATATAATCTTCTTTC
>gi|3450600|gb|AI100639.1|AI100639 35014 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97P23XP 3', mRNA sequence
CCTTGTGATGGAGCCATTNGTGGTTGATGTCCCGGAGGGAACCNCANAGGATGAGACTTGTTACTTTGTT
GAAGCTTTAATCAAATGCAATCTTAAATCTTTAGCTGATATCTCTGAACNTCTTGCGGTTCAAGNCACGA
CAGAATCGAGAGTCTAAAGATCAAAGGAGTAAGAAACTATTGAATCAGAGAGATTTTGGTTGCCATGGAT
GAAGCTCTCAAAGGGAAAAAGAGAGAGTGGGTGAGTTTCTTTGAGGATGGACAAGGCAAAAAAAGTATCA
TCATTTATCCAGTTACATAATAAGTTTCTCATTTGCTATTTTTGGGGTCATTTCACTTTCAAACCCTCTT
TTTAATTTCATGTGTCTAATTTAATGAATGTGTTTTTGGTTT
>gi|3450599|gb|AI100638.1|AI100638 35013 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97P17XP 3', mRNA sequence
TGCTGCTGNTTATGGAAGGAAAGAGTGTGTAACCCNCCNCCTAGAGAATANTGCTGCAGTACCTCAGCAA
AACTTGGACANTAAAAANCCCATTGATGTGGCCAGGCTAAACAATCAGCTAGATGTGGTGAAACTACTTG
AGAAGGACGCTTTCCTCTGNGCTGCTTTGACTCTTGANGGATATGTTTCTTCTCTGTCATGTAATAGTGT
CNCAGAGTCTGATTGCANCCTTGTCTTCTGNGGGGGTTTTCATCATTAAATCTGGAAAAAAGATGGAGAA
AATGGATGTTTATTATGGTTTTGTAATGAATTATTTTCTTCTTGAATTGGTTTTTTCTTTTGGCTCTT
>gi|3450598|gb|AI100637.1|AI100637 35012 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97P15XP 3', mRNA sequence
CGTTCCTTTTGGNGGAATCTGAAGGNGGTNTCAAGNCCAAATTTGTGTGGAAGTGACTACCANCTCAACT
TNCCTCGCTGTTCATAAACTTTGGAGGGNCCACTNGTAAGATCTGTTTCGACTTNCGGAATGTCTTTTCT
GTTGGTTACTAATAGCTGAAATCATGGTGGTATGTGTTGTTTATTATATTCTGTTTCGACTTTCGAAAAT
GTGAATGGATTCTTTCATGTAACACAAGACCAG
>gi|3450597|gb|AI100636.1|AI100636 35011 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97P11XP 3', mRNA sequence
TATTGCTNCATGTGTGCTTGCTCTGCTGCNACCAGTAAACGTAGTTGATGGCTTGAAAACCGCAGANGCC
AACTGAAAAATGCCCCGCTTTGCCCGTGAGGATGGGGGTTTATAAAGGTGCTGTTCACTTGGATGAGCTC
AATATTTTACTTAAGCGAAGCTGCAGAGACTATTGGGAAGAAAGGCGTAAAACAGAGAGAGCAGAAAGGT
TACAACAAGCAAAGGAATATTGGGATTACCAATGCCGAAGCTTCACTGGAATATGATATAGTTTGATTTG
TGGCTTCTTAAGTGAGATTCTTGATTTTGATAATAAGATAGTAAAAATAATCTTAATTTTGATTTGCTTT
CCTCTGTGAGTGTGTTTCCTTGCACAGAGAGTGACGATTTCTTTGTGAAAAAACTGAAAACTCTTAAGCA
TTAAATATGGTTTATAAGTTTGCAT
>gi|3450596|gb|AI100635.1|AI100635 35010 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97O24XP 3', mRNA sequence
TGTATCTTCCTCCNCCAGCTTCATGCATTCAACGTCNCGAANCGAAGANGAAGAAGCTGGTGAAACCCAA
GAACAAGGGGAAGNGGANCCCAAAGAAGCTGAATCAGAGACAAACTCTAGCAGCTCCACCAACAGGAGAG
GTCGAGGGAGATGGAGAGGCAGAGGCAGAAGCAGAGGCCGGGGNCCTACTGTCAATGAAAGGAAGCCGAA
TTCGCAAGATCCAAGAAAACCGACGAGACAATGGGTGCAGAGAGCCAGAGAAGGAGACAAATAATTTATG
CTAATCTTGTGTGATACATCAAACTCAAACTCAAACACAAGATATATATATATTGTGAGCATATTACCAA
CGAAAATACATTTCTGTGAGC
>gi|3450595|gb|AI100634.1|AI100634 35009 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97O20XP 3', mRNA sequence
ATTCCCGCTGATGGCTATGTGGCATTTGCTGATGATGTTGCCTTNCTAAAAGGTGCTTGTGGCAAAGCCT
CTTGCGTCTTTCCCCTCAAGGCTGTTTATTCCTCGNCCGCCATTNAGGTGGNCTTTAGGAGCTTCGAGAC
CCNTAAGAACCAAGATCCACTGCAGTTCCCTGCTAATGGGGGAGAAATTTGGGGAGCTNCCTTCAAGGTG
GAAGGAGCAACAGTTCTTGCAGATTGAAAATGAAAGAGAAACACAAAAGAAGTTTCATGTCTCTTAAAGC
TCTCGAACTGTAACAGCACAAACAAAAAAAAATATGTAGGAAAAACAAAAAGCTGTTCTATGAGTACTTG
AAGCTATCAATGGTTGGTGATAATGTGTGTAGTGTTGTATCTCTCTTATGTCTTATGCTTCTTTGTACAG
CACGTGTGTGTCTTCTGGTGTTAT
>gi|3450594|gb|AI100633.1|AI100633 35008 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97O14XP 3', mRNA sequence
TTTTCCCTCGTACGGGNCCATTGGTTCCATGGCACCCNTTTGCGGTCCCTTNCCTCTACTACAATTCCCA
TCTGNTANTCTCGAAAACNCCATTTGATAGACGTGCCAGAGATCTTCANCTTGCTTGATTGGGAAAAGAA
GAAACGACTCTTTCAAGCTCGCTTACATTATCCTCACTCTCTTTCTCACCATTTTCTGGTTAATCTATTC
AACACTTGATGATTACGAGGACTGAATCACGCTTGAAGATACACCCCTGTGACAGGCGACAACAAACGGT
TTGGTCAAACCCCTCTCTTAGTACTTGACACCGCGCTTGATACAATGGCATGAGAAGGAAGGCTTTTAGG
TTATGTAAGTTAATTAATGTGGCATTAGAGAGCTGTGTAAACCAGATTTTATAGTCATTAGAATTTCATT
GTGGATCTTTGTGGTGAAGCCAAGCAGTGAATTGTTAACCATGATTGGAACCCTCTAACT
>gi|3450593|gb|AI100632.1|AI100632 35007 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97O10XP 3', mRNA sequence
GAGGNCAAAACTGATGCCGCTGAANCCAGCGGTTTTNCGTTNCACCGCGAGTCCCCTCTTTATNCCGTTG
CANCNCCTTACTNGACTTAGGCATTNATATATATTAATGCTTTGGTATGTTATGTTGTGGATCTTTCTCT
TCATGGATTCTGGTTTTATATATGTGTTTTTCTTCTCTAAGTTGTTTTCGTTAATTGTTATGTGATTTTA
GTTATTTTAGTCAAATCATCTTTGCTCT
>gi|3450592|gb|AI100631.1|AI100631 35006 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97N9XP 3', mRNA sequence
GGCTAGTNCCAGGCTTACTTAAACGTTGGGGAAGTTNCTTCTCCTATTGCTAAGGCCNTTAGGCAAAGAC
TTGCAGTNCCGATGCACGAGCTGAGCCCGCAACCAATCAAATTCAACCAATCCGACCAAGGTGCGGGAAC
ATCTCAAGCTACTCAGAAATCAGCATGTTGCGGCACATAAAAATTGGGTCCACGACGCCTGTCAAAGGAG
AGAATCTGGCTAGTGAAAGAGAAATGGTATTTGGAAAGAAAAAATGAAAAAGGAAATCAATCTTCTTTTG
CTTTTCTTCTATATGAGATGGTGTTTCTACGTATTCTTTTAAGATTCTCTCTTTCCCTAATGGTATAGTG
TGACTGTGAAGGACACAATTCGTATTCCATATTTCTGGAATGGATTCTCTGACATCAGATTATGACTTAT
GATAATATCAGTTTATCTC
>gi|3450591|gb|AI100630.1|AI100630 35005 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97N7XP 3', mRNA sequence
GGCTGCTNGGCCCTGGTNCCAGTTTTTCNCGGGATTCCAGCCCCAGCCGGGGTNNCCAGGAACCACCGCG
GGGGCCNCAACCANTGGGTTTCCCCCTGATCATAACANCTGGGCGGGGATATTATCTTTNCCATTTAGNG
GATCATCATCAGATTTTAGCTTCAAGGNCCGGTTTTGTGGTTTATACATAAGTTATAGTGACTTGATTTT
TTTGTTTTGTTACAAAGTTACCATCTTTGGATTAGAATTGGGAAATTGAATCTGTTTGTATATTGTATTA
TTTGGAACATTGTGGATGCCCATGGATATGTTTCTGTTCAATTATTTTGGTTTTGGGTAATGAAATTTGA
AACCAACGAAAAACC
>gi|3450590|gb|AI100629.1|AI100629 35004 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97I5XP 3', mRNA sequence
TTGATNCTAAAGTTACCCTTTGNTNGNGGAGCCNGGAAGATCCAAGGGGNTTTGGATTTGNCCAACTCCA
ATGGATGAGGCCCTTGCAACNTGCTGCCATATCAGAGATGGCCGGAAAGGAACTGAATGGTCGTCACATC
CGAGTGAATCCTGCTAATGATAGACCAAGTGCTCCACGGGCTTATGGAGGCGGTGGTGGATACAGCGGAG
GAGGTGGTGGTGGCTATGGAGGAGGAGGTGGCAGCTACGGTGGTGGTGATGGTGGTGGTTACTAAACAGA
GGATGTGGTTGTGAAGAAGAGTTAATGGTTCTGTTTAGTTGGTTTCTTCTATTGAATCTTATGTTAGTAC
AAAACCTGAATGGGATTTGCTGAAAACTCATTACTCTTTTTTTTTTGGTTACCAATCAATTTGGTTGAAA
TATTTTATTGCC
>gi|3450589|gb|AI100628.1|AI100628 35003 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97F17XP 3', mRNA sequence
GTCTTTACCTTGGTCCCAGCTNCTTGGCTTTAATGCCCAACAGGNTGNATAANTGATANCCCGAGATTGG
AGTCCNCTNAGGGAAAGGACTTGAAANCCATTGGCCGATGGGGTTCAACTGTATCGGATGCCCACACAAT
TCTGGAACTGTGCTCGTGCCTGTCCAAAGGGATTGACCCCAGGGAAACAGATCACACACATCAAGCAGCT
TCAGAAATCTGGTTGAACAACAAATGAATCAGGCAGTACCTAATGGATTTTTGATTCTAATAATCTGCAA
GAAACTCCAATTTTGGATTCATTCTTGTATTGCTGTCACAACTATCAGAATTAGATTATTTTGTGGTATA
TCTTGATGAATTTTTTTTGCCTACAACAAGCAATAAAACTCTGCTTTTTTTATC
>gi|3450588|gb|AI100627.1|AI100627 35002 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97F13XP 3', mRNA sequence
CAAGAAGGTTTATTTCCCNCCGTAACAGCTTCCTTTCAAACAAGNAAGGATTTGGGAGATTCCTGTCTCC
ATCCCCATTCCTCCTCTTCCTCGGGCTACCGGTACTGTCTCNAATCCCTGGAATAAAAAAACAAAAAGAA
CAGCGTCGTATATGAATCTGTGTCTTGTCTTATTTATCATGTCCCGGAGAGAGTTCAGACGACAGAACTA
GGGGCAATACAAAGGGATGGTGAGTCTCTCTGCTCCTGTCGCTGTCTCTTTCCGAGACTATTTTTGGCTT
GCTTGCTCTTTTTTTTTTTTTGTTTTAATAATTTGGTTCAGTGGAGACTACTAATAAGTTTTGTTGCTTG
AAGCCAGTTTTTGGGTAAAACATCATGGTTTTGTGTTTGGTAATGAATTATTATGTTTGCGTTAACATAA
ACATC
>gi|3450587|gb|AI100626.1|AI100626 35001 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97E4XP 3', mRNA sequence
CCATGGAACGTCCTCTACGGAGGGTCCNCCATGTGGGTCAAGGTTCCCATTGATCCCAATGNCCNACATA
NTCTCACACTACTTATACTTCCTTGGCCTCATGGGTNTTGGAAGAGAAGACNCGGGGCCAAACGATGNGC
TCANTGCGCAGAACAGAAACCTTTCAACCCTTCAACTGTACCTTCCTCTTCCTCTTCGTAAGTCTTATGA
TATATCNCCGTTGCTCTCAAGTCTCTCTTGCTTAATGTTACGTAATAAGTGAAATTGCTTGTGGTAAAAA
AGAAGAAGTGTGTTTTTGTCCCTCTAGNACTTNTAATGCAAACAACATTACATTTTATATTTTTCTGTAT
GTAAAACCATATTTAATTATTGTATTGG
>gi|3450586|gb|AI100625.1|AI100625 35000 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97D21XP 3', mRNA sequence
TGATTTCCAAGGGATCCACCCTTTNGTTGANGGAAAGAAGATTTCCTTGTGCCGCTTATCATGGNCCCTT
AAGCTGTTACTTTAATTGGAGCTTCGATGCTTTCAATTCGGTGCAAAACATAAGAGTCTTCGTTCGATTC
CTTATCGGCGAGGATTTCTTACCGGAATCGGCGCTCAACGGTGGAGGTTGTTGCCGGAAAAACTTGTGAT
TACTCATCAGGCGTGGGACGTGGTTTAACCGGTTGTCGACACGTTTCCATGGATGGAGTTTAGATTGAAA
TTCTTCTACAGAAGTCGGTTATCTATTTGGTCTTTGTTGGCTATTTCTGTAAACCTGCTGTTTGGGCTTT
TGTTAAAGCCTATGTATGATATTGTGA
>gi|3450585|gb|AI100624.1|AI100624 34999 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97D19XP 3', mRNA sequence
CGGGACNTCGGAATCCNGGTTTTTGAAGGCCGAGGAGGAAACCGTTTGCCCGAGCTTTTTGAAGGNAAGC
TGGCCGTTCCCGGNACNTACAAGGCCCAANTCGCTCCCAGATCTTGATTGANCCAATGGCAAGNCNTCCG
AGGAAAGAGTCTTCTGCTAAGAAATGGCCCAGCCTCGGTTTCAAGTCTGAGGAAAAAATTATCATATAAA
ATAAATCATCCACATATATATTCAATATTTTATTTTATTGTTATTGTTATATTTTTTATCTGATCTATTT
TCTGTATCATAATCTGAGGTTGATGAATTAATTTCATGTATAGTGTTTTTATTTGAGTTTGGTGAAATAC
TGCCAAGATGGTGAGCTGTTTGTTTGAGTTTGAAATTTCTTTAATTCAATCACTTTTTTCTTCTTCTGAT
>gi|3450584|gb|AI100623.1|AI100623 34998 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97C9XP 3', mRNA sequence
TTTCCGGACTCGGGCCATCAAGATTGCNCGTGCCTTCNCCTTCATCGTGACCACCTTAAAGGTTTTCNCG
GTNCNTTAGACNCGGCTGAGAAANNCNCCGGAACCGGCGGAAAGAAGCGAGGACAAGCTCAGCTACGTGT
TTACAATCTGGGAAACACGTCCCCCGNTTCCGGTTGGGAGATTGGTCTCGATCTTGGAAGGATTGTTAGG
GACAAAAGCTAAGAAGCATCTTATCAAAATGCCAAGAAACGGTGACGTGCCTTACACGCATGCTAATGTG
AGTTTAGCGTATAAAGATTTCGGGTACAAACCGACGACGGATCTCGCGGCGGGGCTGAGGAAGTTCGTCA
AGTGGTACGTTGGTTATTATGGGATTCAGCCGAGGGTAAAAAAGGAAACTTCTCACGCCGAAGATTCCGC
TTAATAATTTTCTCTCTACCACCATCTCTCTCATCATCACATGCTTGTTTATTTTTCTTAC
>gi|3450583|gb|AI100622.1|AI100622 34997 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97C6XP 3', mRNA sequence
CAAGTTTGGCCACNTCGTTCCNTAGGGAAGGTGCCGTCAANTCGCGTGGTTCNCCCAATCCCGATCTTAG
CCCCTATGGGAAGGATCCCCGAGCCCCGAGCCCATCCATTGGACCGTTTTATTAGGATTCCGCCGACCAT
CCCTTGAGGTTCGGACCCGAGTTCGGGAAGTCGATGGTCAAAATGAGTCTCATAGAAGTTAAGACTGGAT
CAGATGGGGAGATTCGTCGGGTTTGTTCCGCCATCAACTAAGATTTAAAAAAACACAAATGTGAGCTTTG
TTTTTCATTTATGAATTCGTTAATTAATAATCACTTGTTTTAAATAAAAGCTTGCTACAGCATTTTGTGG
TCGATGGTTACGTTTTGATTNCCAAGTGTAAGATTGTACTTGTAAACAAAAAATGTATTATATAAAAGTG
TTATTTGTTT
>gi|3450582|gb|AI100621.1|AI100621 34996 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97C5XP 3', mRNA sequence
AGAAGGAGGGGCTAACCCGTGGAGTTCCGGTCCTCGCAAGCTGCGGAGGAGAAGAANCCANCCTTAGAAG
AGGAGAAGAAGACGGCGCCNNTGGAAGAGAAGAAGCCAGCTGTGGAAGAGGAGAAGAAGCCTGCCGTGGA
AGAGAAGAAACCTGTGGAGGAGGAGAAAAAAGAAGTTGTTGCCGCTGTTCCGGTGGCTGAAACTCCTTCG
ACTAAGGCTCCCGAAACTCCGGTGGTTGAAACTCCGGCCAAGGCTCCGGAAACTCCGGCGCTGCGCCACA
AAAGGCTTGAATTTTCTTCATGGTACATTTTTCTAAAAAAATATTGATTGTCTTTGTGTGGATAATTTAT
TTTCTTTGTTTATTTGTCTTATTATCCATGTGAATTTCCTCTATAAATTAATTTGCTTGCTTGAATTATA
TATTCTTATGATC
>gi|3450581|gb|AI100620.1|AI100620 34995 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97C1XP 3', mRNA sequence
TAGACGGAGTNTNAGCCCANTACAAAGCAGATTTGAGGNCNATGGCTTACAAGTCTTGGGTNCAGAGTTT
GGGGANTGANGGGTGCACAATGGAACAGCTTCTCTGGTTGTCCAGTNCCCAAGAGAACCTTCAAGTCCCT
AACTCCATCTACTATGTCGCCTGATTAAATCTTATTTACTAACAAAACAATAAGATCAGAGTTTCATTCT
GATNCTTGAGTCTTTTTTTTCTCTCTCCCTCTTTTCATTTCTGGTTTATATAACCAATTCAAATGCTTAT
GATCCATGCATGAACCATGATCATCTTTGTGTTTTTTTTTCCTTCTGTATTACCATTTTGGGCCTTTGTG
AAATTGATTTTGGGCTTTTGTT
>gi|3450580|gb|AI100619.1|AI100619 34994 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97C19XP 3', mRNA sequence
GACGATTCCGTTNCGNTTCGNGGAAAGCTTTTTGCAGAGTCANGGGCCAAGGTTCAAAGGCCGGTTTGCG
AAAAGAACNGANACAGAANACGACGACATTTCCCTTAGTCATGTTTATGCTTCAGCAGCACNCGCACAGT
ACGGTNTCGTACCAACGTTCTGATTCGAATCTACGGTGGATAAACAATCAACCTGAAGACTTCATNNCCT
CCACCGTTGATTTACAGTCGCGCTGTATAATAAGTATAGTGAGTCTTACCGTAGACAAACATCTTATCCT
CTTTACCGTTTTAATTACTTTTTTTTTACCGCGNTCTCACTGCCACTGTAACTCTTTTTTTTTCNCTTCC
CTATATATGTATGCTTATTTTTATTTAGAAAATGTTATGAAATC
>gi|3450579|gb|AI100618.1|AI100618 34993 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97C10XP 3', mRNA sequence
CCTTTAGCCAATACTATGTGCCCTTTGCCAAAGAAGNACGTNGAGCCCGCAGGAAGNTTCTTTAACCCAG
GTTTCANTGCTCAGTCCACCNTGNTTGTGATNCCNCCCNTAGAACAAACCATGGGTCGTAAGTGAAGCTT
ACATTGAGTCGAGTGGTCTAAACAGCACTTGTAATATTGAGTCGAGTGAAGCTTACACNCGTTGTGAAAA
CAAGTGTTTCTGTGGAACTCGAATCATGATCCTTGTTTTTTGCTTACTTTTTGAATAAGCCCTCTCTGGA
TGTAATTTGTCGCGTGTCTTTCTTTTTTTTTATCGAAAAACAAACATATGTATATCTTTATTGTACGNAT
TTGTTTTGAC
>gi|3450578|gb|AI100617.1|AI100617 34992 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97B9XP 3', mRNA sequence
CCTNCCTGTGNAATGATCCCCCCNGTNCAATCTTGNGGACCCNGGGAAGGTTTTCCNCCACCCTTATCCC
AACCATTAATCTACCAAAGGAATCCGCATTCAAGNCTTTGTAGTGTCTGATTTCTCCGACAAATACTCAA
AGTTCTTGGAGTTTGTGCTTCCCCACATTAGAGAAGGGAAGATAACNTACGTGGAAGATGTAGCTGATGG
GCTTGAGAAAGCTCCCGAAGCTCTTGTGGGACTCTTCCATGGTAAGAATGTTGGGAAACAAGTTGTTGTT
GTTGCTCGTGAGTGAAACTATGTTTGATACTTGTACTTTATCCAATTAGAGTTTGTGTGGGTGGTTTTTG
TTTTATGGATAAAGAGAATGTTTGTTATGGTTTCGAATCAAATAGATACAAAATTCGGTT
>gi|3450577|gb|AI100616.1|AI100616 34991 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97B20XP 3', mRNA sequence
CCAATTTTCNTCTTANAACGGATTNCGCATTCCAGGGCTTTGGTAGTGCCCTGATTTTCTCCGACAAATC
CCCAAAGTTCTTGGAGTTGGTGCTNCCGCGCATTAAAGAAGGGAAGATNCCGTATGTGGAAGATGTAGCT
GATGGGCTCGAGAAAGCTCCTGAAGCTCTTGTGGGGCTTTTCCATGGTAAGANCGTTGGGAAACAAGTTG
TTGTTATTGCTCGTGAGTGAAGAATACTTATTTGGGAGTAATGTCTTATTGCGCGTGAGTGAAGAATACT
TATTTGGGAGAAATGTTATATTTATCCAACAAGAGTTGGTATGTCTGTTGAACCCAACCGTGAGTTTTTG
GTTTATGAATAATAATAATTATAGT
>gi|3450576|gb|AI100615.1|AI100615 34990 Lambda-PRL2 Arabidopsis thaliana cDNA clone 97A11XP 3', mRNA sequence
GTTTCCCTCTATGNCCAACATTCCGGTTATTTCCCACTTCTCGCCATGTATGTCCTGTCTGTAATTCCAT
GGATGATTGATGTGCATTGNTGGCTAAGGAAGAGGTTAGACAGCNAAGACAAGGAATAGAAGAGACTGGG
AGTTTGTTGGTCTGTATGTGTTTGTCAGATTGAAAGAAAGAAAAGAAGAAAAGGGTNGTGAAAGAGTAAT
AATGGGGAAAAAAACAAATGGTGATGTGAAGAAGCTTTGTTATTTGCAGAGCAATCAATCAAACAATCAA
AGGAGGAGGAAAATAGATGTGTTTGGGTTCATCAGGGAAATGTGTTTGCAGGATGTTGAAGTTAACAACA
AGCAAAAGCTTTTCCTGATCTTTTTTTTTTAATATTCTTATTACTATTATTATTGTTATTTGTAATTGGA
TGATCTCTTGAGGATATCAAATTTGGATTCGGCTGTTT
>gi|3450575|gb|AI100614.1|AI100614 34989 Lambda-PRL2 Arabidopsis thaliana cDNA clone 96P12XP 3', mRNA sequence
GCATCNCATTGGTCTATTTTTTCAGGCTGCTATATCCCGTGGTACTGGCCCATCCTCATGCTGGGAACTT
GTGGTTTCTTGCATTAAGGCGGTACTCTATTCTATCGTAAGGCTCATCTTTTCACGGCGAGAAAAGCCAA
GGCAGAGCTGAATAGCTTTTACTTTTGATGAANTTACAGCAGGAATCCAATCCTTGTGTATATAATGTGG
TTTTGGTCAAAGAGGCAAACCAGTGAACCTTACCTTCACCTGTATTACTACCTACAGAGAAGATAAACTC
CGTTTTGTGAAAGATCCCATGGAAAAGCTTTTGACTTGTTTTGTTGTCATTGGTAAAATTGTTATTTT
>gi|3450574|gb|AI100613.1|AI100613 34988 Lambda-PRL2 Arabidopsis thaliana cDNA clone 96L18XP 3', mRNA sequence
GGCCATGGCTGCTGCGGCTGCTTTCTTNGCNTCAGNTGATTCTTCTTACATCACTGGAGAAACTTTGGTT
GTCGCTGGNGGAATGCCTTCAAGACTCTAAACAATTTCACATCAATAATAGCGTAAAGAATGCAATCAGG
GTATCAAGTAAGTAGAGATGTTTTTTTTAGNGTTTTCAACTAAACAAGACTTTAAGAAACGAAAGATGTT
CCAATAATATCACGAGGCCATTGGATACTTGTTGGTCTTGTAAAAGATAATTTCTTCATC
>gi|3450573|gb|AI100612.1|AI100612 34987 Lambda-PRL2 Arabidopsis thaliana cDNA clone 96K23XP 3', mRNA sequence
CCCTAAAGGGCCGTTCCAATATTTTTTCNGATCCGGGNACCTTACCAGGTCCCNCCNTTCCCTTGGTATT
AAGGACNCCATTTGGTNTTACANCTTNCACCANAAATCGAATCATAATCATGGCTTCAGATATCAATTAA
CTATTTCCATATTGATGCATCCGAGATGACAATGTAATGTGATCGAAGGTGTATGTGAGAAAGAAACTCT
CATTTACNGTTTCCTATAATTTTATTTAAATATTGAATTAAATATAAATAAGAAATTTTCCCCTTTTTTG
ACAGATACATAAGGGCNTGTACATATAGATATCAAAGAAAATAGAAAAAAATATTAAAAGTTCCCTTTTT
GCTTCAACCCGTCAACTAAAAAAAGGGTATAAAAGGAAAATAACAATAGTTGATA
>gi|3450572|gb|AI100611.1|AI100611 34986 Lambda-PRL2 Arabidopsis thaliana cDNA clone 96K12XP 3', mRNA sequence
CCAACAGGTTTTGTTTTCGTGCNACCGGAGTNTGACCCCCCAAGNATTCCCTGAATCAGGTTTCTCTATG
GGATGCCATTATTCCTGCCCAGGGAACATGCCAAATNCCGGATTCAAGTCTCAAACAAGTCCCGTTTCAT
CGATCAGGGACAGAATCTTCGGGGCAAAGACTTCAACTTGACATTACACTGGCATGTCATGCCCAAGACC
GGGAAGATGTTTGCTGACAAGATAGTCTTGCCTGGTTACAGTTTACCAGATGCATACAGATGATGAAGAT
TGAATAAAACATCAAACCTAGTCCAAGACTTTTTGTATTTCAGTTTTCTGAAAAGTTTTAGACTTTCTTT
TATTCCAAAGAAAACTAATTCAAAAGTACTATTGTTCTCTTAGAATCAAACAAAACTATTCTTTTTAGTG
ATCTTAATTAGTTGTTAATG
>gi|3450571|gb|AI100610.1|AI100610 34985 Lambda-PRL2 Arabidopsis thaliana cDNA clone 96H23XP 3', mRNA sequence
GGATCCCTGTTGAACAGCTCTGGATNCCCCGTNCCTTGCNAATTTGCACGGCCCNGATGATGNGCCAATC
TGTCAAAAGCCCATCCTCTTTTGAGTTCGGACAACAGCCTCTGGATGGAGGAACAGATAAAAGAGATGAT
CTACCAAGAAGCCATAGCACTCAATCCAACATACGGTTAGAAGTGCAGCAGCCCCGTGAATGCCTGGTAT
TACCCAATAACCATCCGAATGGCTACTTAGTATCTTTGCCTGTTCTTTTATTCATGTACTTCTTCCACAT
ATGTAATCTTGTAACTTTTATTTGTTTGTTCATGTTATTTACTGCTAGTGATTAAGTGTAGCTCCAATGT
AAAGTACTCCAGTTATTAAAGAATA
>gi|3450570|gb|AI100609.1|AI100609 34984 Lambda-PRL2 Arabidopsis thaliana cDNA clone 95H10XP 3', mRNA sequence
CAGGAGCTTAGGTNCCCCGAAACATTTTTCCAGTCACTCGACCTGGNCATGGACTCTCCTCAGAATCTTC
CCCCGTGAGTTACTTCACCGTATACCCGCGAAAACCCTTGATCAGTTTTACAGTCGCGATACCACCAACT
GAAGAACATAGTTTCTACTGCCTTGGTGTGATGATATGTCCAAATGCATCTTTATTTTTTACTTCTGCGG
TTGGATCACACCTCTGAGTCGTCCGTCCCAATAAATGGTGTTTGTTCCCAATCGCTAGACCCTTTATTAT
TGTCTTCGAAACTGAGCAAGCCAGGTTGATTATTCTTTTTGTAAGAGAAATTGAAATTCTTGTATAATTT
ATGAGATTTTGCNTCTTTTTTTTGGGGTACC
>gi|3450569|gb|AI100608.1|AI100608 34983 Lambda-PRL2 Arabidopsis thaliana cDNA clone 95D10XP 3', mRNA sequence
CCAAGCCTCTTAAAAGGAACCGNTTGTTTTCCCTGGGGCCTTAAGNCCGCGNCNTTNCGATTTNCTGNAC
AAAAATCTGGGATCTTGCAAGCTAAGTGGATGCCCGATCCAAGNGTATGTAGCCCACCCTGGAACCAAGG
AGGACGAGATGTTCCAAGTCATGGCTAACATTGCCCAAAAGAAGTGTGAGGAAGAATACTTGGGATTCGC
CATTGTGCCCAACTACCACATCATCTGGTAAAGAGAGCTTTATCTACTGCAATGCGGATCATGCCAAGCG
CCTTAAAGTATCGCGTGACCAAGCCTCTGCTTCTCTCTGAAAACATTCTCATCTGATTCTGTTTGATCTC
GGCATGTGTGTGTCCAGTGTGTACAAAACAGGAAACTTTCTTCTATATTATTCCGATTCTACAAAATTGC
GTCTAAATATTTAAGTTTATACCATCTCTATGAGCCACTGTAAAACTTGCCATCGACTTCTAGTCTATTT
CCAGTGATGGTTTGATTCTCCC
>gi|3450568|gb|AI100607.1|AI100607 34982 Lambda-PRL2 Arabidopsis thaliana cDNA clone 95C1XP 3', mRNA sequence
CGGCTTATCGNCCGCCTTTGGGCTTCCNNCAGGTGCTTAACCNNCTCGGGATTTCTTGCNNCTGTTGAAG
ACTGTACTCGGTATGATCGGNCCTGTGGATGCTGACGGCGATGGGAATGTTAATTTCGAAGAGTTTCAGA
AGATGATGACGTCGTCTTCTCTCCTCAACAGCAATGGATCCGCCGCTCCTCCTTCGACCTAGGGAGTTTT
CCAGATTTCAGATCTGGATTTCGGGAATNAGAATAACTATGGAAATTAGGTACTCTTTTCTTCTTAAATG
TGATCAATCATCATCNGTCTAACTTCAATCGGATCTCTTTTCATTCATACATNGTTGAGATTTAGATCTG
>gi|3450567|gb|AI100606.1|AI100606 34981 Lambda-PRL2 Arabidopsis thaliana cDNA clone 95A1XP 3', mRNA sequence
TTTCTTNCACCCTCTTGGGTTTGGGAAAGGTTGAGAAGTCACTGAAGGAGTTTGAAACTCAAGGAGGTCA
AGAACGGTAGACTGGCTATGCTCGCCATCCTCGGTTACTTTATCCAAGGACTAGTGACCGGTGTGGGACC
TTACCAGAACCTGCTTGATCACTTGGCTGATCCCGTCAACAACAACGTCTTGACCAGCCTCAAGTTCCAC
TGAGGTGATCATCATCTCATGTGTTTTTATGTCTCTTGTATCGTACAATATTTCCATCTTTCGCTACCAT
TGGCTTCTTCGTATTGTAACACCCTGTGTAAACATATTCGTGTTTTGTAAGAAATGACAATGTCAATGGC
CAAACGAAAAAACTTTTAGGNTT
>gi|3450566|gb|AI100605.1|AI100605 34980 Lambda-PRL2 Arabidopsis thaliana cDNA clone 94N15XP 3', mRNA sequence
GAGNGGGGCATTCCCACCAGTGAAGTNGCCCCAGGTTCTAGACTCGGCAGTGGCGAGTTTACCGCCTTGC
TGCTCGCAGAACCTTCCGATCTATACAGAGATTCAGAAGTGCATGGGAATCATANGAAACCAGATTCTNG
CCCTCGTACCCTCCTAAAGTANNAATCCTAAAACCATAACTTAACCTTTGTGTCTCTTCATAATGCTTGT
TTCTCTTTGTAAAATCAATATCTCCTTATNCNAAATCCTTTTATATACCCCATTTATTTGGAGTGACTCA
CAACAGTTTCTCGATTTCACATTTATTTATATGTAACACATCATTTGTT
>gi|3450565|gb|AI100604.1|AI100604 34979 Lambda-PRL2 Arabidopsis thaliana cDNA clone 94M15XP 3', mRNA sequence
ANATCCCAATTACCCTTTTTCATCACCCNGTGCCTCCAAGGTCTTCTCAATCTCGATCTCTTCNTCTNTC
ACCAGCTTCCCTTCCACGATATCAACGAAGCCATGCAGCTGCTTCACCAAGGCAAAGCTCTTCGTTGCCT
TCTCCACCTCTAAACTGAACAAACATCTTTTACATTTTCCAAATCCGTTTGANTGATTGTTCTNCTGCTT
TTAGNGTTTCCTTATTGGGTCTGGTCCNCCCCCNTACTAANATAANAGTTGGAAATGTTTTCTCC
>gi|3450564|gb|AI100603.1|AI100603 34978 Lambda-PRL2 Arabidopsis thaliana cDNA clone 94I6XP 3', mRNA sequence
ATTCCAGGNGAGGAGNTAGTGGCCGGTGNGAATACCCCCATGAAGGTTTTTAGGACTGGNAAGNTCCCCG
TGATGGAGCCAGCTCCAAGGTGTATGAGATCCGATTTCCAATTTTATTCCCCAGTCTGGAAGAAGATTGC
GTCTGCAAAATCACTATGATATGGGAGAAGCGCAACGATGATTCCCCCGAACCAAGCAGCTACATGCAAC
TCCTCAAGAGCATGGTTATTGATATGGAGGATCACGTCCTTAAAGCTTAATCAACATCACCATCATCCCT
ATATGTTTATTAAGTTGTTTTCAATTATATCTAATAAAGTGTGTTTCCTTTCGGAATACTATATTTTCAA
TTATATAGAATAAAGTGTGTTTCCTTTCGGAATACTATATACGTACCATGTGGTTTCTTAAATCAATATA
TAAGAAAATGGGTTTTGTGG
>gi|3450563|gb|AI100602.1|AI100602 34977 Lambda-PRL2 Arabidopsis thaliana cDNA clone 93C1XP 3', mRNA sequence
TAAGCCCTGGCGCCGGATGGAANCCGTGACTTGNGAGATAAATTATNTGACCCACTAGGTTTACTCGGCC
CATTGTCCCCATTCATGTCCGGNTTTTCCGCTCGGCGGCCAACTATCCGCAGTACCACCATATCGTCCCA
GAAGGTGCCCTTTCTGTTATCCTCCTCCTCCCCCAAAGGCTTTCCCAAAAAACTCACCAAGTCACTGATG
TCACTATAGCTACGAAATTGCGTCAATAAATGTATGCACGTTAATTTGTTTCATTTGTGATGTGTGGGGC
TCTTTATCTATTATATGCATGTCACGTGTTTGTCATATTTGCAATGTATCATGTATGTGGCTCTTTATCT
ATTATATGCATGTGTTTGTCAATTGTCATATTTGCGATGTATCATGTATGATGTATGTGGGCTCTTTATT
TATTATATGCATGTGTTTTTC
>gi|3450562|gb|AI100601.1|AI100601 34976 Lambda-PRL2 Arabidopsis thaliana cDNA clone 93C17XP 3', mRNA sequence
CGTCTTCAGGTCATTNGCCCCATCCCATCACCGGACCGGTATCAACCCGGCTCGTGCTTTGGAGCTGCCG
TTATTTCCAACAACGAAAAGGCCTGGGGACGACCAATGGATTTTTTGGGTTGGACCGATGATCGGAGCAG
CAGCAGCAGCGTTTTACCATCAGTTTATTTTAAGAGCGGCTGCGATTAAAGCTCTTGGCTCATTTGGCTC
CTTTGGCTCCTTTAGGAGCTTTGCTTAATATACATTTATTTTAAATTAAACCACAAGTTATAAATCTTTG
ATCAAAATTAAAAGGATGATTACAAATGAATTAAGTGGAAGTTACATGTGATCTTCTTTATATGTTTCTG
TTTTTTTGTTCTCTCTTTCATTTCATGGAATTTCCCATTCGTGTAATTGTAAATGTGGTTTTAATTAATG
TTGCTTTAAGAT
>gi|3450561|gb|AI100600.1|AI100600 34975 Lambda-PRL2 Arabidopsis thaliana cDNA clone 93B9XP 3', mRNA sequence
CCCCCGTGTTAGGCAACTNGGCCATGTTGATAGATTCCAAGGNCGGNCANGGAATTGAAGCNNTCNTCAC
ACTGCCTGAAGAGAACATGTCGTCCTTCGAGCAGNACCCAGAGTTGCTCGCCTTTGCTACCATGAACCCT
AGTGTCTTGGTTTAAATCCTGTACTGAAATTTGTTGTTTCCTCAATAAAGATTTGGATACACCGAATCTA
TATATATCTTCAAGATGTAATGCAAGAAATGTAAACTACTGGAATATCATTTATGTTTTAACT
>gi|3450560|gb|AI100599.1|AI100599 34974 Lambda-PRL2 Arabidopsis thaliana cDNA clone 93B10XP 3', mRNA sequence
GAGAAGGAAGCCTTCTTCAGCTTNTCTCTGACANAGCCACTATTNGACGACCCTGTTTTCCGNCCNTTGG
TCGAGAAATACGCNGCNGNTGAAGATNCCTTTTTCGCTGATTACGCTGAGGCCCACATGAAGCTTTCTGA
GCTTGGGTTTGCTGATGCTTAAGCTGTGACGTATGCTCTGTGTGTGTGTGTGTGTCTCCCCGAGAGTCAT
GGCTGTTTTTGGTTGGGGGCTGGAGGGGTCGCATTGCATTTGAACTTTGTCATATGATTGCTTAATGTAC
TCTCGGATTTACGTATCTGTTTTTTTCGGTGGGTTGCGATTTGAACACATCCGTTGCGCTTTTGCTGCTT
AGACACATTAATAAAATTAATTTCTCTCG
>gi|3450559|gb|AI100598.1|AI100598 34973 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92O13XP 3', mRNA sequence
ACAAGGGGATCCTTGTGTTGAATCGAGTTAGAGCNCGGATTTGTGTCCCTGAGCACGGAAACACTCCCGG
ATACTACGATGGACGGTACTGGACAATGTGGAAGCTTCCATTGTTCGGATGCACCGACTCCGCTCAAGTN
TTGAAGGAAGTTGAAGAATGCAAGAAGGAGTACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACA
CCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATTTCTTTT
CTAAAACATTCTTATGAATTATCTCTGCTCATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGA
GACAATTTCTATCGGATTGTCAAATGTCTGATTTATGAATATGTAATTTATAT
>gi|3450558|gb|AI100597.1|AI100597 34972 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92N7XP 3', mRNA sequence
TGGGAANCTTGTTCCNCTGCAGGTACCGTCCGGAATCCCCGGNTCGCCCCACGCGTCCGGAGAACGCTCC
GTTTATGATCGGAGGATGTTGCGNCGGAGCCGTCCTTTGACCGTCGGAACCTCCGGNTTGGGAAGCTACG
TCGGACGGAACTGGGAAACCGATCAGTGTTGGTAGTGAGTTAACTCGGTGACCGAGTTAGTAGAACGAGT
TAATTAGTGTAAATACGAAGCCATAAAATCCTTGTAATTTAATCATAGTAAGCTAACATGGACGGGAACT
AGTGTGCTAACATACGCCATGTGCTTACCGTACGCTCCCTCCCCCACGAGCGATCGGTGCCGTTTGTATC
CGTGTTTACGTAGGATC
>gi|3450557|gb|AI100596.1|AI100596 34971 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92N23XP 3', mRNA sequence
GGCAANCCGTGGCGNCCTTTACNCCTGNGGAATTTGAAAGAAAGACAGGCTANGGGATTGCAAGCCCCAG
AAATTCAGAACATTCTCACAGNTCCTGTAATGAGACAGGTACTGTCTGATCTCCNGGAGAATCCAGCAGC
AGCACAAAAGCACATGCAGANCCCAATGATCATGAACAAAATCCAAAAGCTTATCAGCTCAGGAATCGTC
CAGATGAAATAAACGAAGCCAAGACATTGATTTCGATTTTGCTGAGTCATTACTCTTTTATAACTCCAAA
CACTAAGATCGAATTCTTCTCATTTTTCAGACTTTTCTGATATATCAATTTTTCTTTC
>gi|3450556|gb|AI100595.1|AI100595 34970 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92N19XP 3', mRNA sequence
CCTATGNGCNGTGTTTTAATCGTAAGAGGTGCATATAAGTTGGATTTAGTTACATTCAGGAGCCCTTNTA
CCAATTCCGTTCTTCTTCTTCAATATGCTGTCCCNCCANCCATGAATCTAGGTACAATTACTCAGTTATT
TGGAACTGGGGAGANTGAATGCTCAGTGATTATGCTCTGGACTTACTCTTTGGCTTCGATTGCACTCACT
GTTTGGCCAACATTCTTCATGTGGCTTGTAGCTTAGAATAGACCCCCATACTCATCATGTTACATGTATT
GTTTTGTTCCATTGATTCAAGAATTGTTCTTGGACTTCCAGATGATTGGATCAAGTATAATAGAGAACAT
ATACTTAT
>gi|3450555|gb|AI100594.1|AI100594 34969 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92M9XP 3', mRNA sequence
ACTGTAGTTTAGTCAGTAGGTGCTAGTGTGCTCCATTGAAGGTAGTAGCCTCAAGTGTTGGTGCCCAAGA
GGTCAAAACTTTGTGTGTTAGCTTCCAAGGAATGTTGTGAAGCTAAGAACTACGAAGGGTGTGTGAGATG
TTTGCAGCAAGTGGATATTGAGTACAAGGCGTTAAAGACAAAGCTTCAAGATATGTTCAATCTTGAGAAA
CAGATCATTCAAGCTGGTGGTATAGTTCCTCAAGTGGATATTAACTAAAGAGACTAGTCCATAAGAAGAA
AAAAGATGATGACTTTCTTTCTTTAGTTTCTCTTCTAAATTATTTTGGATTTGGTGTTTGCTCAAAAACT
CAATAAAATATGTGCAAAAAGAAACAAAAACAAGTGATGGTTGTTTATAAATCAGTAGTATGTATTGTTT
GATCTC
>gi|3450554|gb|AI100593.1|AI100593 34968 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92M3XP 3', mRNA sequence
TTTGGTTGGGAAAGACTTGGGCCNCGAATTNCCAGAATGNGCCNCGATATGGTGAAGTTAGGTCCACTCA
CACTCCTGAACCAGTAGCGATCACCGTCGTCCGATCGGTGACCACTGTAACTGTAACGATCGAAATGCTG
AGATTGAAAATGGTCAGGGAGTTAGAAACAGTGCTGCAGCTACTTGAGTTTGCCCAAGAAACCCTAATAA
GAAACCTATTTGTTGACTATTTTGACTTTGTACCCTTCTTGATATACCTATCAATCACCATTGTCCACGT
GTACTAGTTTCGTTGTAGTGATTTTCAAAGTTTATCGAAGTATGCATATTCAAGGATTAATTAAATCAGG
ACTTACATTTTCCTGAGTTAATTTTTTCTCTTTTTCTTTTACTTATGGGACAATGTAATGAAACTATATG
TTGCATATAAATATTTTCCAAGTTG
>gi|3450553|gb|AI100592.1|AI100592 34967 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92L4XP 3', mRNA sequence
GCCGTCCAAGGCTTGTCCCAGCNTCATGCAATGCCCNNTTCACCCCAGGNTCTTGANTNCCTAAGCCCAC
TTTGNAAAGTTTGCTCTGGATCCCCATGTCACTCCTTGGCTCTGCTGTGTCGTACCCTACCCTTGCTGCT
CACCGCATATGTTCATCAATCGTACAAGAATGCCTTGGCTATTGCTGTTGCCCACTGAGTACACCTTCCC
TCAAGCAGAGAAGGTCAAGGAATACTTGAAGGATCCAAGCAAGTTTGCTGTTGCTTCAGTAGCTGCGGTG
TCTGCTGATGCAGGTGGTGGTGCCCCAGCTGCTGCTAAGGTAGAGGAGAAGGAAGAGTCCGACGAAGAAG
ACTATGGAGGTGATTTCGGTTTGTTCGATGAAGAGTAGATTTTGTCGGTTAAGATCTTACCTTTTTGTCG
TGGATTATAAGTGTTGCTTTGTTTTTAGTATGTTGGACCTCAATTTTCTTGGTTTTAGCCAATCCAGTTT
TATGTT
>gi|3450552|gb|AI100591.1|AI100591 34966 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92K12XP 3', mRNA sequence
AATTGCTCCNTCCAAAACTTGTNCAGGTCCAGCAATTTTACCAGCCTTTTNGNGANAAGTTAGCCATTTG
AAAATGNNCGGNCTTTTGTTCCCCTTTTGGATGGCCCNATATCTTTGTTAGGATGGAAGTAGAGATAGAC
ATATTTTNGCTCTTTTATCATCCTGACTATTTAACTGGTTTCACCTGAACTCAATGTACAATCTTATTTT
TTTACATCCTTTTTTCAGTGAGAAAATAATGTTTCATACTTGACCCTTTTGTAATCATCATGGTGGAAAA
CTAAAGACTAATCAGTAATCACTGTCCGGTTCTATCGATGTTCATGGATTGTGTCCTAGTTATTTAAGAA
CATGGAAATTGCG
>gi|3450551|gb|AI100590.1|AI100590 34965 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92J23XP 3', mRNA sequence
CTATGCGGCGAGANCANAGAGTAGCCCAGATGCTGAGAAGTATTACTCAGAAACTGTCCTCGAGTTTGAA
CAATGTCCTNGCCCAAGCNCGGTTAANGAAGAAAGACTTGCGTTGTAATCTGTTGATGTCGATGTTATTA
TAATTACTGCTATCCAAGTACNTTGTCTTTCTCCTTCTCNTCNTGTCTGATCAAATCGGTTATCTCTAAT
TTCAGTTTCAAGTTTTANCCAATATATTGGCTGGCTCTTTAGCAAAACATTATATATTCGTCCTCGAGCT
NACCACTTTGT
>gi|3450550|gb|AI100589.1|AI100589 34964 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92J13XP 3', mRNA sequence
CTGGGCTNTCCCTGAAGCAANAGGTAAACCATGGTACGGTTTGCTGATGCTGCTGAGNAAATACCCGGAG
CATTTCGTCATCAACACGAGATCAAAGGGAAGAGTTACCCTTGAATTCGTTTCCCTCGTTACCCTACTCT
CATGAGAACTTTACCTTAGTGACTCGGATTAAGATTTAAGAAGCTTTTCTCTCTTTTCTTTGTTTCATAT
GTNAAATATTTTGGCATTGATTAGTAACACGCTGTGTCGTTTTTCTGCACC
>gi|3450549|gb|AI100588.1|AI100588 34963 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92I8XP 3', mRNA sequence
TTGGCCCTANTTACCGTTTTTGNTGGTCCNCCACCCAAGGCTCNTTGTTGTNCACTTCTCAAGGNCTTGC
TAATNCTGGAAGCTGCGGTTTGGTCTCTGCACCGCTCTTTAAGCCAATGTCTTGGGNATTAATCTCAATG
TTCCTATTGATCTAACCTTGCTGTTGAACTATTGTGGCAAGAAAGTTCCTCATGGTTTCCAATGTTCTTG
AAGATTTGAGACTTTAAAAGAGAAAAATCTCTTTGGTTTGCTATGTTTTTATATGTTTGTTTCTACTGTT
ATCTATTGTTTTTGTGAGAAAAAGCTTTGTTCTGTCACTGTTGAGTTTGATGTAATGCTTGAGCTTGTTC
ATGATAGAACCTTTGTTCTCTCAATATTGAGTTTGATGTAATGCTTGAGCTTGTTAATGGATTTT
>gi|3450548|gb|AI100587.1|AI100587 34962 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92I20XP 3', mRNA sequence
ATTCCANGCCAAGCCCAAGGCAAAGNAGGATCCCNCCGNATCAGCAGNGATTGATCTCNCCGGAAAGCCG
CTCCGAAGATGGCGTACTNTGGCTGACTCCACATCCAGAAAGAATCTNCACTTCATCTTGTGTTGAGGCT
TAGAGGAGGTATTATTGNGCCTNCCTNGATGATGCTTGCCCGTAAGTACAATCAGGATAAGATGATATNC
CGCAAGTGCTATGCTCGTCTTCACCCAAGAGCTGTCAACTGCAGGAAGAAGAAGTGTGGTCACAGCAACC
AGTTGAGGCCTAAGAAGAAGATCAAGTAGAGAGACTCTTATCAAGAATCCCATCTCTTGCTTGCTTCTTT
TTGTTGTCTTCCCTTTGATAGGGTTTGTTTTTCTTGTTTCAGTGACTTTCTATGTTAAACGATAATGTCA
GTAAAAGGATTTGGTTTTCTATT
>gi|3450547|gb|AI100586.1|AI100586 34961 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92I17XP 3', mRNA sequence
CGAATCNCCCCTTCCAAACGGATGGGGGGGNGGTATAACGAACGCNTATNCATTTNAAGACNCTTTTGGT
NANNGATTAGATGTATGNAGGACCCGCGAAAGGCTTCATCAGTGATNAGAATTTGGGGANAGTTCTCTTA
CAAGATTGTAANGAAGTTGATAGNAAAGTTGANATGGATGNTGATNGTTCCGTTAATTTTGATGAGTTTA
AGAAGATGATGAGTAATGGTGGTGGTGCTTGAGGATTTGAAAGATTTCGCCGGAGATTAGATTAGTCGAC
GGTGATGATTCGTATTAGCAGATTAATTTTAGTGACGGCGATTAAAANCCCTAGAAGTATGTGGTGATTG
ATGAATATTGATTTTAACTATATAAGGTTGTTTCTATATCTTCTGCTCTTTTTATAATTAATATGCTTTG
TTGAGTGTTATTAGTCTTTAATATTCTGAATTAATTACTGATTTAACAGCT
>gi|3450546|gb|AI100585.1|AI100585 34960 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92H7XP 3', mRNA sequence
TCGGAAGGTAAANTCNNCGCGAAAGNTCCTCTCCCATCCGGATCNCGNCTAGTGAAGAAGATGNGTCNCN
GGGGACTGAAAGGTGATGATCCGACGGATTNTTCCATGGCTTTTCCCCTATCTGCTGNNTTCAATTAGTA
TCAGAACCAATCTACAGAAATTTCTAGGGTTTTCTCCGCCNCGAGGAGCTGCTGGTGCTGGTGGTTTGTT
CCCCATGCCTGATCCTAAGACCAACTGATCACTCCTTTGAGGTTTTTTTTTTTTGTTTTTGTTGAGATTT
TTGGAACAATTTTCATATAAACACACAGTTACAAGTTTTTGCAATCATCTGATGATTTTGGT
>gi|3450545|gb|AI100584.1|AI100584 34959 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92H21XP 3', mRNA sequence
TGNGCNTGCNATACAGTCCAGNTTTTTNTGTNCATTTGGGCCAACCNCCGGAATTGGCNTNCATGGGAAG
NCCCTCAGGCTGCAGGTTGTTTTANCTCAGATTGAANGGNCTACCANGANGGGGCCAAGGAATTCAAGTG
GACTGAGGAAGAGGAAGAAGCGTTCAAGAAGAAAACGGTGGATGCGTATGAGAGAGAGGCAAATCCTTAC
TACTCGACGGCGAGACTTTGGGATGATGGAGTGATTGATCCTTGTGATACCAGAAAGGTTTTGGGACTTT
GTCTCTCTGCTGCTTTAAACCGTCCTTTAGAAGATACTCGATTTGGTGTCTTTAGAATGTAAACAACTTT
TAACCAATAAACATTTTCAAATAAATGTATAAACTTTTGT
>gi|3450544|gb|AI100583.1|AI100583 34958 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92H17XP 3', mRNA sequence
TGCCAGACATTNTCGCGCANCAACTCATGNCCATTCGTAACCTGCCATTCCTGGTTNTGGATNACCCNTT
GGGCTACATNTTGCNTTATNCCCATCGGCCATGNTCATGNCGTCTTGAGGACGTTAACTCTCTTGTTGGN
AAATCAGCTAGNCCAGAGTATCTGCAGAAACTAACTTACCTGTGTTGGAACCACCATAAAGCCATTAGGC
ACATTGACACAGTGAGGGCATACACATTTGGCTCTCATTATTTTGTGGAGGTTGATATTGTTCTCCCAGC
TGACATGCCTCTGCAAGTGGCTCACGACATTGGAGAATCGCTGCAAGAGAAGCTCGAGCTACTAGAGGAG
ATCGAACGGGCTTTTGTGCATCTTGATTATGAGTACACTCACAAACCTGAGCACGCTAGATCCCACTGTT
AGCTGTTTATCCTTTTTAAAGATCTCTACGTTTCTATATCTTTACAAATTAATCTTCACTGTATTGTTGT
TTAGTAGACAATTGTGAGATAAAGGAATACCTTTGTAACT
>gi|3450543|gb|AI100582.1|AI100582 34957 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92E2XP 3', mRNA sequence
GTTCCCCGTGGGCTTTGATNCATGGTGAATCCATGNGGTGNGTATGCCGTAAAAAAACNGTACCCGNGCA
CTTGCTCTCGTCAATGGAGTAAATAGACAGCTTACAACGCGACTNTTGGTGTCTTGGAAGTTCCAATAGT
GGAAAGACTGGACCCAAGTAAGAGAAACCAAGAGTTAAAGAGTAGGTAGGAGGAAGATGTTGAGATGATG
CAAGTTTAGGTGTGGAGTTAGTTTTGAGATAGCTATAGGTGGATTCTCAAATAGCTGACACTTAGTCTCT
CTACTTCCATAATGTACGTCTCTTCTATACCAAAAATTCTCACCCCCAAAGTTTCTTTCCAACGCTTTTC
CTCACCTCATCATTTTTTCTTACGTTTCGAGTACCACCTATTTCAACAACATTAAATATTTTCTATAATT
TGACTATCAATTTTTAAT
>gi|3450542|gb|AI100581.1|AI100581 34956 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92D4XP 3', mRNA sequence
ANCACTGGATNTGCAACCCAGTTCACAAGCACCGTGAGTCAGAGGATTACCTCAGAGGGAAAGAAGAACA
GAGGTCNCCGGGGAAAGGGTCACAACAACCACAAGAACCGNCCATCTCNCAGGGCTACATGGNAGAAAAA
CAACTCTCNCAGCCTTCGNCGTTACCGTTGATTGCCTTTTGCTTNTATTATTACTGTNATCATCTTCTAG
GTTCCATGTTGTTGCACTTNTATCTCTCTCAGGATGACTTGTTTTTGCAAATTTTGGAGACTATACAATT
ATGCTTTGAACCT
>gi|3450541|gb|AI100580.1|AI100580 34955 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92D2XP 3', mRNA sequence
CGATTGTTACNCGGTTGTGATTCCTTCTTCACCGGAANCGGTGCTCGGACGACAAAGGAAGAAGTCGGTT
CACTTTTAGGCTTCTCGTCTCACACGTATAGGTCTTTCTCCTATTGACGACACGTGATCTGAGATAGAGA
CAAATTCCAGTTTCNTCTTCTGTAGGAAANCTCTTTGGGCCTTGTTGGGTCTAAATAATTTCTGTAATCT
TGCATTTTGAAAAGGCTTNTCTTAGGCCTTGTNTGAGTTGGATATGTTTAATACAAAATTTCTCTTGTG
>gi|3450540|gb|AI100579.1|AI100579 34954 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92D21XP 3', mRNA sequence
CCCCGGAACCCGCTNTGCCCATGATTNCNCCAAGCTCTAATCCGACTCACTATNGGNAAAGCTGTACCGC
CTGCAGTCCCGTCCCGGAATCCCCGGTCGACCCCACGCGTCCCGAGCGAGGAAAACACGTGGAAAGAGCT
TTGGATGATTCCAACGATGTTGATTGTGACGTACGAAGGAGAGCACCGTCATCACCAGTCCACGATGCAG
GAGCATGTAACTCCTAGCGTGAGTGGTTTGGTGTTTGGTTCGGCTTGAAGAATTAATTAGTTTGGTAGTT
TTGTAATATTTTGAGAAATTGAGGGGTTGGTTTTGTAATTTTTTTTCTATAACAAAATTAGTTTTAGATT
TTTCTTTAGTAGTCTTTTGAATGGATTTTAATCTTACCACCGAGAAAGAAAAAATTCTTACTACATTTTC
>gi|3450539|gb|AI100578.1|AI100578 34953 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92D20XP 3', mRNA sequence
CTGCCAATCCGGGAAGCGAAGCGCATCNCCTCGACCATTCTTNGGGGAGCNCGGTCCCATGATATGAAGA
GGCTCTCGTCGCTATTGACCGAAGATCCCAGCAATCATGGAGAGACGCAGTGCCATCTCAAAGCGGCTAG
AATTGTATCGAGCAGCCCAATCCGAGATCGATGCTGTTGCTTGGTCCCAAGTGATACCGGCATGTCATGT
CCACTGTTTTGCTCGGTTCTGGTCGGTGTGGCTCAGACTCGGAGCAGAGATTTAGGGTCTGTAATTTGTA
TAAGATGATCTTCCCGATACCATGCAGTATCGTTTTATATAACATCCACATTGTTTGTCCTACCTCTATG
TTTTTTGTCCATCACCCGATATG
>gi|3450538|gb|AI100577.1|AI100577 34952 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92D17XP 3', mRNA sequence
AGCCGTTNGGATTGGGCCGNTACCATTCCCCGGACCGTTTGCCCTGTTCCCCNAGTTTATCGGCCCCCCT
TGGGNAAGCTGTTNCCNCCTGCNGTCCCCGTCCGGATCCCCCGGTCGGCCCCACGGTCCGTCTNCCACTT
CAAGCCCCNCCGTNCCATGNGNAGAANCCCAACTCCAGGATTCCATCCGGTTCCCACCCACCATCCGAGA
TGTTGGGGGGAAGAGCCAAGGAGATCCAGATCACTCCCTGAGCCATCACCGCATGAAACAATAATAAGTA
TCTGCTTTTGTATTCTCGATTTTTGTTTCCAAGTGGTTTAATCATCAGTCAAAAGTATAATTTTAATTTG
CATATAAAATTTGGAAAAAANAAATATATATATTATATGGCGATGCTTGTTAATTATGATAATGTTCTGA
TGCTGGTTCAATCTCTATTCTTCTTTATATAGAGATTAAAATGTTTTGCATTATGTACAAGAAAATATAA
GATACTAATATCAATGTCGTCTGACTATTGAAGCTGTTGATG
>gi|3450537|gb|AI100576.1|AI100576 34951 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92D13XP 3', mRNA sequence
TGATGNGGAAGGNNCTNTGCCCCAAGAATATGTGCCCAATGNCCTGGNTGAGGATGNGGAGAAGAAGAAG
NCCGTCACCAAGATCACCCACCAGAAGCGTCGTGACGAAGCGATGAGTAACTAAACCCTCTCTGTGCTTA
GAGAGTGTAATGAGAATGTGTGTTTGCTTAGCCTCAAAAACTACTAAATAAAGAGCTAAGTCACATACCT
TTCTACATAATATCTTCCGACGTTGGTGTTGTGTTTGTTTGAATCTCTGTATTATTACTACAGAGTCTTC
GTACTGGTTCATAATAAGACCTTTAAGTGGTATTGGGTCACCATGTAACTGTTGCTACTCTGTTTCGTTT
TCTATCTATCGTTTTGTGTTATG
>gi|3450536|gb|AI100575.1|AI100575 34950 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92D11XP 3', mRNA sequence
AAGCNGGGGAGTTGTNNTTGTCCCTTGTCGTGGTTTAGTGATTGACCCGACCGGTTCAGATTTAATTNNC
CCTTAATTNNATAGTTAAACCGTTNATGGTTTNGTACAAACTCTTTAAAATTCCAGTTTCCACGCATATA
AATAAATAAATAACCCTTCCTGTAATCCTGTTCTAGCTCTTTGAAACTCTTTGTTATGTTTGAATGTTCA
AATCGGTCTGGTTATT
>gi|3450535|gb|AI100574.1|AI100574 34949 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C7XP 3', mRNA sequence
TGGGTNNGTGCCGTTGTTCTCTTAGNTTTGAACCGGTGGGGGGCAAATTCCAGNGTTGGGTTCTCTGNCG
GAGTCGGANCANTAAAGGTCTCGTCNTCGAGATGGTGANGATTTGGGGTCGTCTAAACGTNTACGCCAAA
GCCGTNGACCCAAGAACGNTAGTTTGGAACANTCGACAAATCNCATAGGTTNCACGTTGGAGCTAACATC
TNGGCGGTGGAGTTTCAGCGGAGTTNCATGAACCCAGCCGTTGNTTTCGGACCAGCCGTCGTAAGCTGGA
CGTGGACCAACACTGGGTTTACTGGGNTGGTCCTCTTATTGGTGGTGGANTCGCCGGAATTACTACGACT
TTGTNTTCATCGATGAAAATGCCCACGAGCAATTGCCTACCACCGATTACTGAAGACGTCAAATTCAACG
TTGTTAATCTGATGAATTTTTCGTGATTTGCTTTTTTAATTTGCATCGTAATGGGTTTNTGGNCGTTGGA
TCATTTTTAGATGAATCTTTGTCTANTGATTGATCATTTATGTGTNTTTGGGTTTGTTGTTGGAGTTGTA
ATATCTCTGGAAGGCTTTTGTGCAATTGTATTGTACGGTTTAATAACTATAATTGAGAAAACCAGGGAAT
GTGAATTATG
>gi|3450534|gb|AI100573.1|AI100573 34948 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C6XP 3', mRNA sequence
CANTTNTGGAGGCTTCTTTGAACTCAAGATNTCGAAAGAGCGAGCAAAAGCTGNAGTTGAGNATTGATTT
GCANACAGNTGGTTTGAAACGNTAATCGGGTGTTTACATGGANTTNCTTCAATGGAGNAAGNTNACAAAA
CCAAGAATGNTTTACATGTAGGAGAAGAATCAGATAGAGAGAAAGGAATGAATTTGCACATTCATANTCC
TGATGGTTTACCAAAACTGAACAANANTTGGAGGAAGAAGAGAAATCGAAAATGCCGGATTCAGCTTTCA
CTAGATTGCTTAGAAGTAAAGGAACTANCCCTGCTTGGTTNTCTCACGCTCCTGACCACGAAACCGACTG
AAAGCGGATTACGGATTACGGTACCTTTAGAAAGTTGTTATCTTATCACAGTTATANGTAAATATAGTTC
TTGGTTTTGCTTTAGTTCATGTAGTCTATCTTTTGTTAAGATGTGATCATANTGCCATAGAAATGTGGTT
GTTANTACTTGATGTTCGCCCAATGTTGAATTTGTTTAATGCTGTGTGCCTATTATAGTACTACGCATT
>gi|3450533|gb|AI100572.1|AI100572 34947 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C3XP 3', mRNA sequence
CNCCTCCTTCAAAATNGTCGNNAGTGNCNTCAAGAAGANCAAGACCGACAAGCCTTCGGAATTAACGGCA
GCATGGACTTGAGGGACGGCGTNGACCNCCGGCAGAAAGGGCAAGGGATACGGTGTTTACAAGTACGTCG
ACAAGTATGGAGCTAACGNCGATGGATACAGTCCTATTTACAACGAGAACGANTGGTCANCGAGTGGTGA
CGTGTACAAGGGAGGAGTCACTGGATTGGCAATTTGGGCGGTAACTCTCGCCGGAATTCTTGCCGGAGGT
GCTCTTCTTGTGTACAACACAAGTGCTTTGGCTCAGTAAATCTTAAAGTTGTTAGCGCATGTGTAANCAT
GTTTCTATAAATGTTTNTGTGTTGTTCTATNTCTCTCTAATGTTGTAAAACTCAGACATACTTTGAATTT
ATAAGACTTCTAGTGTTTGTAT
>gi|3450532|gb|AI100571.1|AI100571 34946 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C2XP 3', mRNA sequence
TCTGGTCCTNACGANACGAGTTCTTNTGGAGNCTAAGTAACGTTGAGACCTGGNTTAGTGCTTCCTTNNC
GGATGAGACAACGTGTCTGGATGGTTTCGATGGAAAGGTTATGGACGGTNTGGTCAAATCNGCGATTAGA
AGAAGAGTGGTTCATGTGGCTCGAGTTACTNGTAATGCATTGGCTCTTGTAAACCGGTTCGCGGCTNGGC
NTAAGTCATAGAATATTCGGCTAATAAATTAAAATTCGGTCCTTAATAAGGTTTTGTCATGTATTTTCTT
TTTTGTCCTAGTGGGTGATTTGTTTCTTTATGATACTTTGTATTTATGTGTAGGCTTGGGATGTTTATGC
TTTTGTCATGGTTTCGACTAGAGATAACGATGATTTTAACGGGTTTATGGAGAANAAAANT
>gi|3450531|gb|AI100570.1|AI100570 34945 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C24XP 3', mRNA sequence
CCCGCANNCGTTTTCANGATATNCNGTTTATCGCCTCCTCGCGTNTCAGTCTCNANGGCAAATGAAGATC
GTAACATANCCCATTNNCCACACGAAGAANTCCAAATANCATAGAAGAAGCATAAAAAGAGTGCATCAGA
TCTTGATGATCTTGACACGACCAATCCTTGACAATGATTAAGAGATTGGTCCTAAGATTATTCTTGCTTA
ATTACAAAGGTGTTGTGAGTTTGATAATGATTGGATGGTGATAGATGTCTTGATTGGAGATAAATATATA
TGTTCAAGTTTGTAATTGTAGTTCGAATCTAAAATTGGTTAAAGTTTATTAACAAGAAGAACCTTNTGGC
TGG
>gi|3450530|gb|AI100569.1|AI100569 34944 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C23XP 3', mRNA sequence
CTGGANCCTGGGTACAAGTTCCGGCCATCGTTCCGGNCCAAGATCTATNCCNATGCTANCCCGNCTGGAC
CATCGAGCTGATTCCCATCAAGAAGAGTCCCCGAAGTGAATCCACAAGGAGGGATAAGAGAGATGGAGCC
ATCCCGGCTCATATATTGGCTTACTACTCTCTGGCTGGCCCAGAGAACAGATTGTCCCAACAACTGTTAG
AGTCCTGAAGGAGCCAATATGATATGACCCAAAAAACAGGTTTGTATATAAAGATTTTTAGTCTCGAGTT
TTGGGGTTTCCACAAACTGTGTACTATACTACTTTGGTTCTTTTTTTGTTTCATGTTGTGTCGTCGATGT
TTTTGGGAGATTACATAGAGTCAGTCTTGTTTGTTGTATGGTCATTACTTCTTTATTTTTCCTCAGGGGT
CTGTTTACTTTAATTTCTTTAATAAAACCCCGAAGATTTTGAG
>gi|3450529|gb|AI100568.1|AI100568 34943 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C21XP 3', mRNA sequence
CGANNACCCCNCTTTTTNCGGGTTGAATAACCCCGTGTNCNTTTGGNGAGNGNTNTANGGGGTTTNCANT
GAAGTTTTGGNAGATGGCATCATGTCCGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAAGGAGTGG
ATGGTAACAATCGCGTGGTTGTGACGCTTGATGGAAAGTATCTTTCGCATTCCGAACAGAGGACGGAGAA
TATGGTCTCAAGGCTAAATCTCAAGGGAGGTACAAGCGAATGATAAGAAAGCCTTTACGTATCCATGAAG
GCCTTATTGTAAGTGGTAACGTTGTAATACCTATGTGTTTGTTTATCTGTAATATATGCAACTTCAGCAT
CTAGATTAAAAGCTGTTTCAGGTTGAATAACAGTGAATAAACAAAACTTATAAAACCTTTCTATG
>gi|3450528|gb|AI100567.1|AI100567 34942 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C1XP 3', mRNA sequence
CCCCNTTNATAATCTTGGCCCTTNATGGAATATGGGATGTGATCTCTANCCCNNGAGCNTNTAGGAGGAT
TGTCCTCCTCAACGCTNGANCCGCCCTAAAGCCGCCTATGCCGATTAGTTGGAGCAAGCCGTTTCGGCCT
GGGAGAAAAAGGAGGACGAGGATACCCCCTGGGATGATAATNTCAGTCGTCTGCCTATTNCCTCCATTCT
TCTTCATCGTCANCTCTATCACAACATCATCATGCCATGACGATTTTAAAGTAAAACTTTGTGTTGTAAA
TAGATCAGCGATGATGTTACATTTGTAACATTCCTTTTGAAATCCGAAATGCNTTTTTTTGGTCGAAGCC
>gi|3450527|gb|AI100566.1|AI100566 34941 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C16XP 3', mRNA sequence
GGTTTTNNNCCCCGAAATTGNCCCTNNNAANCCATTCNTGNATTCCGGNTNAAGNTTATCCCCGGTTTGN
TTACCAANCAGGATCGGNTCCAAANCCACAGTTACACTGGGNCCCCTGCCACTNTTGAGTACATCACTCG
CTACCATGCTGCCCTTCAACCAGAGTATACCCNAAATGTGGTGTCCAGACCCCTCGTCTTTCTACTCTTA
TCGTTGGCTTTGACCCCTTACTCTCGCCTCCCTTCCCCTATATCAGACTGATCCTTCTGGGACTTTCTCT
GCTTGGAAAGCTAATGCTACCGGCAGAAACTCCAACTCTATTAGGGAATTCCTCGAGAAGAACTACAAAG
AATCCTCTGGCCAAGAAACTATTAAACTCGCTATCCGTGCTCTGCTTGAGGTAGTTGAGAGTGGCGGAAA
GAACATTGAGGTTGTCGTAATGACACGGGAGGAAACTGGTGCGCCAGCTAGAAGAAGCTGAAATTGATTC
AATCGTGGCCAAGATCGAAGCTG
>gi|3450526|gb|AI100565.1|AI100565 34940 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C11XP 3', mRNA sequence
CTAGTGGTTTTANCATCCGAAAGNCCAGGGNCCCAATNCATCGAAAGTGCCACCACATTTACCACGGACA
AGNCACTGCCAAGGTCGCAAGGCAAGAGTTNCTTCTACAAGTGCTTCTGCCGCTGAAGCGATGCTGCAGC
TGCCAGTGACTCGCAAAGTGCTGCTGCACGTGCAAAGGGTAAGGTANTTCCGCATCAAGGGTGAAGGGTT
CCTCTGAGAAGAAGAAGAAGGACCGCAAAGGAAAAAAGGATTGAGCGTGAGGTGATCTCATATTCTCATG
CATGCGTATTCCTCAAACCTATATATTAATGATATCTTAAAAACTACAAACTCACAATCTCTTTCTTGTT
CATAAATAAAACCAGAGATT
>gi|3450525|gb|AI100564.1|AI100564 34939 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92C10XP 3', mRNA sequence
CCGGCCCCNNNGTGGCNNAATGGGTCNGTGTNCTCGGCCAGCAGACGCTNTGGCTCAGGCGCTAAAGCCA
TNCCTCTTAGCGAAACTCGAGTTCTTTCCAGGACGATCGTTGACTGGTTTAGNCGATTTGAGAATTGAGC
TGTCTCATGTATTGTTGAAAACAATGTTAAGATATCTNCCGACGAACAAGACTAGCGTTGATCAGCTTCA
AGACCNAAAAAACAACTGGTAAAAATATGTCTACATGTATATACATGGTCGACGCCTTACAAAGATTTCC
ATTGTTAATCACCTTTAATGCAGAATAACGAATATTGGTCTTGTTGAAGATTGGTTT
>gi|3450524|gb|AI100563.1|AI100563 34938 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92B3XP 3', mRNA sequence
ATACGATGTGCCAGCAGTCATTGCGTTGCCCCATCCCTGGTGGGNGCGCCNAGTATTTAGAATGGTTGAA
AAACAGTACCAAGGNACTGAGATCTCGACACCTCGTAGCTGCCCATCGTCAATGGCTTTCTAGTATTAGT
TNCTTTTACATTTCAGTAACCTCTGTATTAAAGATAANACGTGTGAAGTGTAATACTGGACCAGTTCGTC
AAATGAAATAAACAATGACATTGTTCCATAT
>gi|3450523|gb|AI100562.1|AI100562 34937 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92B20XP 3', mRNA sequence
GGAACCCAATTGCTTCTCATGGGTTGGTTGAANAGCAACGATGGGTCGATTTTCTTNACCCCGGATTNTC
AATCGTTGAATTGGNCAACGCCATGTTCGAAGNCCGCCGAGAATTCGCGAACTATACCGNCGATCAGGAT
ACCCCGNTGGGAGATTCTTCGATCCGTTGGGTCTCGCCGGGAAAAACCGCGACGGTGTTTATGAGCCGGA
CTTTGAGAAGCTGGAGANGCTGAAATTGGCAGAGATTAAGCACTCGAGGCTCGCAATGGTTGCCATGTTG
ATCTTTTACTTTGAGGCCGGGCAGGGGAAAACGCCTCTCGGTGCTCTTGGTTTGTGAGAAAACGGCATGA
TGTTTTTGATTCTGTAGATACAATTTCTCTTCCAAAAACCTAATGTTT
>gi|3450522|gb|AI100561.1|AI100561 34936 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92B1XP 3', mRNA sequence
TGAAAGATGAAGAGTNCAAAGGAGAGATTTGGGTGGNTCTCTACNTTCAAGCTTTCGGAAAACAGAACCA
GGGGTATGGNCGAGGAGTCATATGGGGGCTGGAAAAACTCTGAAGNANCATANTAAGAGAAGAAACAATT
GTGCGTGTAACTGTTTGATTTGAGTCTTGGGAACAAAATGTTGAGTTTTNATTTGAAAGNGTATTTTTTG
TTAAGATTGTTTTTAATGATTTCATAAAATCGTGAGATTTTTGATTNTTCTTTTNTAGAACTTGTTTTGG
T
>gi|3450521|gb|AI100560.1|AI100560 34935 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92B11XP 3', mRNA sequence
CATGGCCTCCGACTAATGGGTNTCCCAANCCTTAGNCCCAGANNTGGACGNNGGATATNNCAAGTTTTAG
CACACATTTGGTTGGANTCTGAGACTTATGCTGGCTCTACATTAGTAGACATCGCATCTTCTTCATCATC
TGCTGTGGTGTCAGCATCGTCCAAGAAAGGTGAGAGGTCTGATTTTGAGAAGAAACTGGTGAGTTTTTCA
AGCATCAAATCGAGTCGGATTCTTCATCGGCATATGGGGATGGGTTCAGGCAAGGTAACCAAGCAGTTCT
TAAGCATGGTCTGAGGCGAATCCTCGACCATATTCGCTTGACCGGTACATTTCCTTAAATGGAATTTAAA
CTATAAAAAGAGAGAAAACAAGCTTTGTTATAGTTTTTTAGAGTATAGACTTGAGAAGAAAAGAAAAAGA
AAAATGTATAGGTTACAACAATACACACATTTAAGTGTCATAAAGTTTCCACTTTTTAAGTAAAAAATCA
AGAGTCAAGAAACAAGACC
>gi|3450520|gb|AI100559.1|AI100559 34934 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A6XP 3', mRNA sequence
AAGCGAGTCNGGTNCAGCNGGATCAGGCATGGGTTGAATGGGAGGCATGGNCTNCTAGATCCNCTAAATT
CTGTCTTTTGTTTTCNCCAATCACCATCTTAACTTGAGAAGAGAGATACGATTCTTTTAGGAGTTTTAGT
CTTCGTCTTTGCCTTATTGTTGCTCAATAACCTCAAAAGTTTTACAATAANCAGAGCACACTTGGCAATG
TTNNGAGACACACTATTAGCATCAACAAATTTTCCTAAGGC
>gi|3450519|gb|AI100558.1|AI100558 34933 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A5XP 3', mRNA sequence
GCGTNCCCACACNCAGTTTTGGAAAGATTTGGAAAAGTTTGAAAGACCCNCCNANGCTGTGAAAGTTATT
AAGGAAAGGAGTTTNTTTGCAGCTGGTGCTGCATTCACACTCTTCACCGCCATTGTCTCTCAGTTCNACT
ACGTTTGCTACTCTCGTGCTAGAGATGCGTACCAGAATCCCTCCTACTAAAAATGTCAACTTCCACAGCA
AGCAAACGTTTAAGCATCAAGAGTTGGAATTTGTCTTTTTGTGTTTGTTTAGTATTGTCCAGTGTTTAGT
TATCCTATCAGGATGTTTAGGTTTTATGTTGTCTCTTAAGCAAACACTGATATGTTATATTCTAAGATTC
GTATATTGTTATGTTCTCTGTTGTAATGTGTGAATGAATATTAAAGAATAG
>gi|3450518|gb|AI100557.1|AI100557 34932 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A24XP 3', mRNA sequence
CCTCNTAGGCCCTTGCTAAGGNCCCTGAGCACAGGNGCTCTTTCTCAAAGTCANAGAGATCAAGAACGGG
AGATTAGCCATGTTTGCGATGCTCGGTTTCTTTATCCAAGCGTATGTTACCGGAGAAGGTCCTGTTGAGA
ACCTTGCAAAGCATNTCAGTGATCCTTTTGGAAACAACTTGCTTACCGTCATCGCTGGAACTGCCGAGAG
AGCTCCCACTCTCTAAGCCATTTCTACTTTTTTTAAGAGCTTCCAAAATGTACACTTTGTTCGATTGGAA
CTCCTTTTGACAATGTTAAAAAAACTTCCATCTG
>gi|3450517|gb|AI100556.1|AI100556 34931 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A23XP 3', mRNA sequence
TCGCTAGTTTCNCTCTTGGATGGGTTTTNCCATGNTGCGGNTCTTGCACCTCCCCNATNACCACTTCCCC
CAGAAGAATGNTGATGNCGTCTGGTGAAGCTNTCAAGTCCAAGAGTTCTTTGGACGCCTTCAAGCAGATC
CTCAAGAATGAAGGAGCCAAGTCACTCTTCAAGGGAGCTGGTGCCAACATTCTGCGTGCTGTTGCAGGTG
CTGGTGTGCTTTCTGGTTACGACAAATTGCAGCTGATTGTCTTCGGTAAGAAGTACGGATCAGGAGGTGC
CTAAGCATTGCTTCTTCCTCCTTTTTTCGATTTTAATTGCGGTTTTAAGGCCCGCAATAAACTGAGATGT
TGATGAAATTTTTTTTGCTTAAGACTTAGGGAGGCATGTGCCCTAAACCAAATTTTATATCGTTCTGACG
CCAACTATTTTTACTTATGGAATAATTCATGTTTGAGAGAGTTTGTTAGACTCTTCGATTTTAAAGAATT
TTGGATTTATGAGTTAAATTCTTCTTTTTT
>gi|3450516|gb|AI100555.1|AI100555 34930 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A21XP 3', mRNA sequence
TATGTCATCAGCAATGGAGCATTTGNCCTGACATTTTGAAAGAACAATGGAGTCCNNCACTCACCATATC
GAAGGTTTTGCTTTCGATATGTTCATTGTTAACGGNCCCAAACCCAGATGATCCATTGGTTCCAGAGATT
GCTCACATNTACAAAACCGNTAGAGCAAAGTATGAGTCTACTGCGAGAAGCTGGACTCAGAAATATGCAA
TGGGATGAAAGTTTGTGTCCTTTGATCCCTCNCAGACTCGGTTTTAATAGAGAGAGAGAGAGAAAGAGAG
AGGACTTCTTCACATAGGGATCTTCCATGAAATAAGTTAGATTCCTATGTTTTATCATCTCTTTGTTTGA
AACCTCTTTAATCTCAAACAAAAACATTACTTCACCTCTTTATTATCC
>gi|3450515|gb|AI100554.1|AI100554 34929 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A19XP 3', mRNA sequence
CAAAGACATATTNGGGNGCAGCTGAATCAAAGGGGGCNGAAGAAGAAGAAGAGCCTTTTTGAGGCCATTN
ATGAATTGGAATGAAGGATNTCAAAAGAATCTAACACAAAGGCCACGTCCTTCCTTCAATCCTTTCCTTC
TTGTAACTAAATAATTTTCATCCTTTCTCTCTCNCTGTCTCTGGCTCTTTTTTAGCTCAAAGTATCNTCC
ATTTATGTCAAAGTGTTGTAAATTCCTCAAGACTATATATGAGATGTTTTGTTTC
>gi|3450514|gb|AI100553.1|AI100553 34928 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A18XP 3', mRNA sequence
AGTCGGCCATCGGACCGGGGNGGACTTAATTTGCCCAATCCATTCCACGGACGATTCCGTTCTTAGCNCG
ATCTGACGGAGTCTCAGGCTNCTCGTTTTCCCAGCAGCTACGTATCTCAATGGGAAGAGAGTTCCCCTTC
TCTCCACTTACTCGTCCGTCAATGTGGCTTGCCGTCGTTTTGCGCGATTACGGTTACTCGATCGTGGGAT
GTGCCACGCGTTCCTACACCAAAAGATTACCGGATGGGAGTGATAATGCGCACCACCTATAACGACGCAN
TTTTGCAGCGGAGTCAGGGTAAAACTGTCATTATTATAAGATAGTCGGTGTTGAGCATTTTACTGGGCCT
TATGTTAATGATGGACAAGGCCCAACTTCTGTGAACGATTGCAAGGCCAAGTGCGATCGTGATTGCAAGT
GTTTGGGTTACTTCTACAAAGAGAAAGACAAGAAATGTTTGCTTGCTCCTCTGCTTGGTACACTTATCAA
AGATGCCAACACTTCTTCTGTTGCTTACATCAAATATTAGTGTTTTTTTGGGAAAGTTATTTACCGAATT
CTTTTTGAATTCTTAGAGATTTAATGAATAATCGGTGTGCTTGTAATGATCCACCGTTGAATATATTGTA
TTACCTT
>gi|3450513|gb|AI100552.1|AI100552 34927 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A16XP 3', mRNA sequence
GGATTTGTGCCACTAGCTCTTCCCAGAGTTCAGAAGCGATCAATCCCTGAATGGAGCAGATTTGGATGGA
AGACAATAAGAGCCCCAGAGGCTGAGGCTAGCCACCNAGAGGCCATTTTGAGCGNTCACACCTCTTTCAT
ATTCTCAAAAAATGCAAATTCTGGAGGGTTCCTTTGAAGCATATAGGGTTAGTGGAAAATGGCGGTTTCA
GACAGTAACTAAAACTCACTGCTGGTGCACGCTAGGCTTTATCCGCCTTTGATGCATGAAGGTCGTTAAG
GAATGGTCTTTTTTTGAGAAAGATAACAATTAGATTAAAGCAGAGAACCCATGTTTCTTGTCTGTTCGAA
TCCTGCGAGATTGGTTGTAGTTGAAGTTGCATTTTCTTCTTGTCTTTTTTGTTGGTATTTTGACACAATT
TGGCTTTTTGGCATATGAGAGTGACTGTAGCAGTCTGTTTTATTTGATGTTCTTGATCTTCTTATGTTCT
GAAAACCAGTTTTCCTAAAACTTAACAAATTTCGATATGGAACAAGAAATTTTCTGG
>gi|3450512|gb|AI100551.1|AI100551 34926 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A15XP 3', mRNA sequence
CACTTTCCCGTTGGCGCCGATGGATTTTCATGGGGTTCATGATGACCTCTAAGTGCNCCAGTTGATGGCC
NACTCAATGGCCTTTGCGCCCTCTAGAAGAACTCCTGGAAGGGCTCATTGCGATTGCGAGGGTTACAAAA
GGGAAGCAGCGGCTTCAAATCGNCCCTTACACCCTACCGTGATTAAAATCAAAGGCTCAGTGATCGCGAG
GTTGGTGACCCAAACGGGCATATATGATACGACTTTCTCATCATTTAAATAATCCCCACAAAAAAACTGT
TTATAATCTTCTCACTTTCAGTAGAGACTAGTTGCAAAAAGTGTGAACGTTTTAAAGAAGCACCATGTTA
ATGCATCATCTGTCATCACTGTTCTTGTTTACAAGAAGTTAAGAGATCAGAGATTGCTTCTGAAGAACTG
AAAATGTTGGGCTTCTCTTATATTGGCCCGGCAATATTCTTATTCATTTGTCTGAAACTTTTAGGTCT
>gi|3450511|gb|AI100550.1|AI100550 34925 Lambda-PRL2 Arabidopsis thaliana cDNA clone 92A13XP 3', mRNA sequence
GGGATNACCACTTGGATATNTTGGGTTAGGACCATTCATTGGAGNNTGCGATAGCTGCATTCTACCACCA
ATTCGTTCTGAGAGCTTCAGGTTCTAAGTCTCTCGGATCATTCAGAAGTGCTGCCAACGTCTAAACACAC
CAAACCAGATTTCTCAAGAATAAATGAAGTTGTAATCTCTCTGTACAAAATCTAAATCAGTCACTTTGCA
GTTTTCATTTCCCTTTCTTATATTTGTGTTGTCCACTTGCTCTTTTGTGAATTTTCTTCGGTGTAATTGT
TTTTTCTTTCGCTTTTAATCGAGTGATTGGAATTATAATCAATG
>gi|3450510|gb|AI100549.1|AI100549 34924 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91P23XP 3', mRNA sequence
GGGATTAGGTATTGGCCATATTTTCCTATAATCCCATTATCCNGNTTGGNATTTACCCCAGGAGCTCCCA
TAGGTAACCCCAATTACTAACCATTTGGGTATTATAGGTGCTTCTCTCTATATGGCTTCTCTTCTAACCA
GATCCCAAACCCCTGACGACCCCTCTGGTGCCCAGGATNGCTCACATATACAAAACTGACAAGACCAAAT
ATGGAAGCCATGGCTCGAAGCTGGACCCAGAAGTATGCCTTGTTTTAAAGCTCACAATTCCTCTTTTTTT
CCTTTTTATTTTGGTTTGGTCTTATTTGTAATAAAAAAAGAAGAAGAAGAAATTGTTATAATTTTAATAC
AAACATATATAATATATAAAGTAGAGTTTTCAAAGTTGTTAACTCATATGATTGATGAGATATCGACATG
TATTAAATCTAATTTTGTTAATATATAAAAAATCTTCTAACCTATCGGGAAAAT
>gi|3450509|gb|AI100548.1|AI100548 34923 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91P22XP 3', mRNA sequence
CTTGGCGTTGCCCNCCTCGTGGCCCTCTCTGGATCTTGGGGAGATGTGTTCCTTGGNAAATCCCNCNCCG
TATTNGACTTTGGTAACGAACAGGTCGGGTTTGCAGAGGCAGCCTAAACACGATCGGGTTGGTGTCNCGT
ATGGTTTTAGTATGNACAATCTGCGTCTCAAGTGTTGTTTGTATGTTTTCTGGAGTTGAGGACTTTGAGT
CGTAGTAGAAATGGTGGCGCAGTTCCTTTTAAGTTGTTTCCTAACGAAAAAAGGCCTTTGTAGTTTTGAA
GGCATTGGCTTTGTAAATNCCTTCTAAGTAAGTTCGATGGTGAAAAAACTGAAAACTTTAATAAAGCCTG
CCTCTTTTGTTT
>gi|3450508|gb|AI100547.1|AI100547 34922 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91O4XP 3', mRNA sequence
AGTGTGTGCAAGAGTGGTTGCGGATGAAGAGNTGGNGCCCANTCTGCAATGCCACAGCCGAAACCTCCTC
TANATACCCGTCTTCNNCTTCTTCCTCGTTCGTTGTATTAGTTCTTTCATCTAAAGCCTGTGAACAACAA
TGGAACCTGCGTAAAAAAGGCCTCACNATTTCCTTTGTGTACATACCAATTCACACCGGCTCTGTCTNTC
TCTCCCTTTTGTCTNATGACAANGCTATCCTGTGTTTCTCT
>gi|3450507|gb|AI100546.1|AI100546 34921 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91O23XP 3', mRNA sequence
CCTAAGGGTAANTTGNTACCCTGGTGGAATCTTAACCCCGCTTAACTTGGCTNCCTACGCAAGAGGCCAA
GGAGAAAGAGCTAGCAAACGGGAGGTTGGCCGATGTTGGCATTCTTAGGGTTTTGTGGTTCAACACAATG
TGACTGGAAAAGGACCATTTGAGAATCTGTTGCAGCACTTGTCTGACCCATGGCACAACACTATTGTCCA
AACCTTCAACTAAAGAGTGAAGACAGACTTATGATCTCATACCTATCTATCTTCCATCACTTTCATGTCT
GTCTGTGAGTGTGTTTCATCTTAGAGTTCTTGGTTTTTGAGCTTGAATTATTGTTGAACCGTTGTAGCTC
CATGAACAAATTTGGAATCTTCAATGTACAGAGGAACTAAGTTAATCAACATTGTTGTACTCTTTAATAT
CT
>gi|3450506|gb|AI100545.1|AI100545 34920 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91O11XP 3', mRNA sequence
TGNTAACTANCAGAGATTAATCTTCTGCCTGCTCGAGAAGGCAATGCTCGACATTTGGGCNTGAGGAGGA
CTATGTTATAGAGCTGGCAAACGAGGTGAGGAAGGTTCTGGCCGAGTCCTCGACTAAGAAGGTGACACCG
GTGAAGGAATCAAGAGCAAGCCGTGTAGCTAACAAGTCGAAGAACAATGTCCCCACGGCTCATCAGATAC
TACCTCATCATCCAGAAGCTGTTGCCACTACAATATAACTCTTGTAGTTTTCTTCTTAATTGGCTTTAGA
GATGAGTGAAATCAGGTCTTTTTTTTAATAATAATAACAAAGTAAGTTTGTTTTCTGAGT
>gi|3450505|gb|AI100544.1|AI100544 34919 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91L8XP 3', mRNA sequence
GTCCGTTTAACCATGGCTTTGTCCANCCNGGGGAATGGAGTGGTTGAANCCGNGTCACTTCCCCTNTGTT
TCCCAACTGGNGGAAGGGGNATTCNCCAATGGAGGATCTACTGATTCCAGCTTAAAAAAGAAATGATGTC
CATCGCAGACCCGCAAGTTAGCTCAACCCTTGGAAGGTAATGAGGAAGGCAGGACAGACCCAAAGGGACT
AGTGGTGAAATGTTGCGTGATGTGAAAAGAGGTAATGAGGAATTTATAAGAATTTAAGAGACAAAACAAT
GTATATAAACAGCATTTGAAGGGCTTTGAGATTGGCCTAAGAACCCTTTCTTCTATAGGCCTTCTTAATC
CTACCATTTGATTATGTATTATGTAATATTTGAGAATATATTCACCAAAAACAGGTGCCCTTAATAAACC
TCCACTCTTCTTC
>gi|3450504|gb|AI100543.1|AI100543 34918 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91K5XP 3', mRNA sequence
GGTTGAGAGGTTTGCCCCGATGGTTGGNGAATCCAGGNACATGGTGCAAAGCCTGATGGGTACTGGCCCT
AGGTATTAGCCCGAAAGACGCAGCTAGTGGTTGATGCTGTTAAAGAGTCTGTTGATAAAAACTATCAACA
GATTAGTCTCTCTGGTCGTTGAAGGAAAGGACTCAGACTATAAATGTTGTCGTGTGTTCTCTCCTCTCTC
GCTCTCTATGTTCAAACTTCGATCAACCGTTTAAGTGTTTGTTACCACTTACCAATATGTTCTGTCTTCT
GCTGTGTCCNCCTGTATGTATGTTAATTGTTTTAGACTCCAATTACTAGCCTTCAATTACTAAGTAAGTC
AATACTAAAAGTTACAGTTTAT
>gi|3450503|gb|AI100542.1|AI100542 34917 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91K10XP 3', mRNA sequence
GCCGCCTAATAACNCCTGAAGTGCTTTTACCGGGAGTTCCACCTCGGATTTTGTAGTGATGAACTAATGC
TGATGCTCTCAAAGGCCAAAGGTCTCGTCCATGGAGAGCCACATTCTTGATGATTCGGTATCGGTAGAGC
ATGCGAGAGATTATGGACATATCCATATATCTGAGATAGTAAATCATGCTGAAAAGTTTGAAAACAAAGC
AATCCTGCTAATCCACTTTTCGGCTCGGTATACAGTGAAGGAAATCGAAGATGCGGTTTCTGCATTGCCT
CCACCTTTAGAGGGACGTGTGTTTGCACTAACACAAGGATTCTAAACATTATAACACTCTTATAGGTTTT
ACATACTTTTGTTTTTGTATTCCACATGTAAACATTGTATTCTGTTGTTAATTTTAAGATTT
>gi|3450502|gb|AI100541.1|AI100541 34916 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91J9XP 3', mRNA sequence
AAATGGATNGGCNTTNTANCTTCCNTCGGNTACAAAGGTGTGGACTATNCCGNAAACCGGNTGNCGAGTN
GCCCAAGACTGGACCGTAAAGATTCNGTGATTGAACGNTTTGAACCAGTTTCACTCATGGCCGTTAGAGT
GGCCGAAATCTGCTTTTCCGGCGACGGAATATCACACTTTTTAATATATGTTTGGAGATTTAGACTTAAA
TAGTTGTAAGAGCTAACAGTTTGAAAGTCACTTTGCATTGTTGTTTATCTTCATATAAATGAGTTTAGAT
TTTGATAATTTCAGAATTCGTGGAATCATAATTAACAATTTTGATAGGGAAAAATAATTTGTTTTTTT
>gi|3450501|gb|AI100540.1|AI100540 34915 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91J7XP 3', mRNA sequence
GATTATAGGNACGCANTTCACGNTGCTGCAGAATGCTGACATATCTCTTGCACAAGCAATTGTGGTCANT
GCAGGAGTCANTTGTTCAGANCACANNTCTCACAGTCTGCTATGACGAGAGAGGTGCTAAAGTATGAGCT
ACCTAAGTATGTTCTAAGCGAGCCTACCAACTTGGAGGAAGAAAATTGATTTAAGATCAAGAATATTCGA
AAAGACAAGANAAGAANAGAACCAAATGTAAATCTTGTGTGTAAGTAGTTACATTAGGATTCTCTNCTTT
TGTCTATTTAAACACTTATTAAAAAGATTGANTCCC
>gi|3450500|gb|AI100539.1|AI100539 34914 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91J4XP 3', mRNA sequence
CTTCACTTGGTTCTTNGCCTTCGGGGTGNAGCTTCAAAGCTTTTTGTNATCNGATGANAAGTGGNTTGGT
TCGTGTCTCATGCANTTGGGAGGTGATCTATTTCACCTGGTGTAGTTTGTGTTNCCGTCAGTTGGAAAAA
CTTATCCCTATCGATTTCGTTTTCATTTTCTGCTTNTCTTTTATGTACCTTCGTTTGGGCTTGTAACGGG
CCTTTGTATTTCAACTCTCAATAATA
>gi|3450499|gb|AI100538.1|AI100538 34913 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91J3XP 3', mRNA sequence
ATTCCNTCGTCCANGTNATGGGGAATAGGCATGNATGAAAGTGGCTTCTTTATCCTGAATTCNTTCACCA
TGGATTGAAGAAGAAGGTCGAATCGAGGTNTAAACTTGTCAAAAAGAACAACATTGACTGCAGCCTTAGA
GAAATGCTGGACTGTAACACAAAGAAATTCCATGAGAAGTTTGGCTTTTCGGAGGTAACTGCAAGCTCCT
AGCTTTTATATCTCTCTCTAGTTTTTTCCTTCATCAGGCTCTCTCTGTAAGCTGTTTTCAGCTTGTGCAC
CAATTTCTAGCACGAGCTTTACCTTGAGTGATTNTGATATCAATAGAGTGTTTTCTTCCAG
>gi|3450498|gb|AI100537.1|AI100537 34912 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91J2XP 3', mRNA sequence
CGTGNCAACTTCATTCNACGGGATCAAAGNATCAAACNAACGCTGNGGTTGATTTCTCCGGCCNCATGGT
NCCGGACCCATTAGGATGATTGAGCCCTGCGATTCATGCCCATGGCTGGATAAGTTCCAATGATGTTGAT
TTCGTCAAATTAGATGTTGATGNACTTCCTGATGTGGCTAAAGAGTTTAATGTGACGGCAATGCCTACCT
TTGTGCTGGTGAAAAGGGGTAAAGAAATTGAAAGAATCATTGGTGCCAAAAAGGACGAACTTGAGAAGAA
AGTTAGCAAACTCAGAGCATAATGAGCATTGTTAACGCCTTAACCAATAGTCTTGTGTAAACTCAATAAT
AAATGGTATGTTTATGGGGAATGTGATGTTCTATACTCTCTGCTAATGTAAGACCTTCTGTGTGATGCCA
TGATTGATTGAAATGGTTTGTTG
>gi|3450497|gb|AI100536.1|AI100536 34911 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91J23XP 3', mRNA sequence
CGGNAACGGTATGGCCCCNCCAAATCCGATGCCATTTCCCGCATATCCANAAAACACGGTGAACCCGCTG
CATCCTAGGGCCATTTGNGGAATAATATCTTCTTTTCCGGTTCCCCATCTTTCTTCTTCTTTGTTTTGGG
GTTCCAGTCTCCGGCCCTTTGTAATTTGTGGAGAGGCCGAGTTTATTTCATTCTTTGCATCCCTGTGTAG
TTATGGAAACTCACAGGGGTTATTTGTTTGCCATTTTGGTTTTGTCATAGAATGGCTTTAGGTGTGTTTG
ATGCTGTCCTGCCCAGAGAGGGGAGGAGAGTATTGTTTTAGCAATTACTTATTTGTTGGTTTGGGCGAGT
TCTTATACTCGTTTTGGGAAATTGTAATGAATGAACTAGAATTTGTTTTCACTATTTATATAGGCTGCAC
ATCTTATATT
>gi|3450496|gb|AI100535.1|AI100535 34910 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91J21XP 3', mRNA sequence
CATCAATGCTGACTTCCCCGTGGCTTGGTCTACTGGNCCAATCAAANCCCGGTGCTCCNTNGCAAATNCC
GAGCGTCTTGCCAANTCAAACCAGCTTTNGCGGTATTGAGGAGGAGTTGGNANTCAGAGGCAATTTACGC
TGGAGTCAACTTCCGCAAACCTGTAGANCCNTACTAAATGGAGCTTTTAGAAGCAAAGTGGTCTTCTTTG
TGACGAGGAGAAGATGACCTGAGTTTGATCATTTGCTTTAATTAAATAAAACGTTCTGTTTTTGTTTCTT
CTTTGTTTGGTTTCTTACGTCTTTTGTTGAACCCTTTTTGGGAAAAGTTACTCATTTTTGTAAGGGAAAC
ATGAGAATGCTCTGCCTTTGTCGAGGACGGTAGCCCCTTATTTCAATCTAATTTCGGCTTTACTCTTT
>gi|3450495|gb|AI100534.1|AI100534 34909 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91J18XP 3', mRNA sequence
AAACCATTGNGGAAGGNTTTTTGACCCGTGGTGAGGAAAAATTGAGCCTTTTTGGTGNACCAAAAACCCG
AAAATCTTCGCTCACAGGCACAAGGATTTCAGAACAACAGGAACGCAGATGAGAAGAAAGATGTGGCTTC
AGAACATGAAGATAAAACTCATAGTGCTCGCCATCATTATCGCACTGATTCTCATCATCGTGCTCTCAGT
TTGCCATGGGTTTAAGTGTTAAGCCCAGAAAATTCAAAACTTCTGAGATCTTTCTCACTCGGTACATCGT
AGTGCCTTCTCTTTTATTGTTCGATCTTCAATCTAATGTTTCTGCTTGAATTGGTTTTGTATAGATAGAC
ATATATGTATGCTACTCATTTGCTATATTGCTTGCATCTGATGACATTGATCCC
>gi|3450494|gb|AI100533.1|AI100533 34908 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91I9XP 3', mRNA sequence
CTGAAACGAATTTGCANTANCGAANAAGGAGAAGTTAGAAGAAGAGTACAATCGGAGAATGGGGAAGTTG
AGTTTGGAGGATGCACAGGAGAGAAGGAGGAGGAGNTACGAGGAGTTAGANGCAATNCAGAGAGGGCAGA
GAGAGTTTTNTNAAATGAAGATGAGAATGGAGGAAGAGANGAGAGGGCTTCTCACCAAAATGGAAATGAC
GAAGCAGANTCTGGCCTTGTAATATTTGTAGTAGTAAATCACATGTAATGTACACAGAAACCTCCTCCTN
GTATGTAACCTAAAGATCAATGTAAGGTCTTTTCTTTTAGAG
>gi|3450493|gb|AI100532.1|AI100532 34907 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91I8XP 3', mRNA sequence
GGCCNCGNAANTTATCTACGGTAAAGGANCCCAGCAAGTAAAACCTGCCAGTTCNTGAAGGGTGTACTGA
TCCTGTGGCTGAAAACTNTGATCCAACGGCTAGAAGTGACGATGGANCCTGTGTCTACAACTTTTGAGCT
ATATTATCCTGCTTATTAANTTGCTGTTNTACTCCTATTGTCTCTTNTGGTTTATTTTTCTCCTTTGTGT
AATTGTGGATTGGATCTTGTCCTCTTTTGTTCCCTTTTTTTTTTTATGATNTACAACACATTGGT
>gi|3450492|gb|AI100531.1|AI100531 34906 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91I22XP 3', mRNA sequence
AGCCTGGGNAGAGGAGAAGAGGTCCCNCAGTCNCGTTGTTAGCCCAAGAAGGAGTGAGTATGACGGACCA
AGGCTGGAGTTTGGTTCCCATCCACTTGGAGCCAATCCCGCAGCACGAAGTGAGAAGTCCCCGTGCCATT
CTCTTGGAACCGGTTTTGATAAAAAAACTAACATCCCTAGTGATGATGTTTTCTATTTAAGTTATCTTGA
TTGGGTTTAGGCTAAACCAAAGCCCATCATGAGCCATAAGTAGTGGGAAGTGTTCTTGTGTGGTTTGGTT
TGAGTCATTGAGTGTGTAGGTGAAAGCATCCCAAAAAAAGTTAGGGATGATAAAAGAAAATGTTGTCAGG
AAAAGAACGTTGATGT
>gi|3450491|gb|AI100530.1|AI100530 34905 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91I21XP 3', mRNA sequence
TCCAAACCACGNCAACTCCNGCAGNGACCCCNCGGNGTCNGGATAATGGGAATGCTTTCTAGCCCCAGAA
GCCCCCACGGCGATATGGAATATGACCCACCATTCCATATACTTTGCTGCTTTTATAGTTTGGAATTTNC
CAGCGAAGAGTTATATGTATCTTCATTTCTTTGNTTCCACCTGCTTGCTTCATTTTTTATTGTTAATATA
TAATAGTCTTTTTTGTCATTTTTTCTTTTAAGGATTTTTCGAAGAGTGTCCTTTGTTGGTCTCTGCGTAG
TGTTTCTTTTTATTTGTGTCTTTGTTTGTTAACTTGAATAATGAATTATTATTTGTCCCTGTGAAAAC
>gi|3450490|gb|AI100529.1|AI100529 34904 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91I19XP 3', mRNA sequence
CCTCAAAATCTCCCNTTCAAGNCGCTGCATNTGNCAAAACTCAGGGGAAATGGCCCTCTTNGATCCCCTC
CAGGTCTCAAGCTCCTCTTCATATCAGGACCCAAGATGCGTGGCTTGGCNGAAGAAGAAAGAGAACCCAC
CAGATGGTTTCATGTGTCCCTCTGGTTGGAAGGTGTTGGTTGATTACTACGACAGTCTCAGTGCAGAGTC
TGGTAATGGAAGGGTTTCAGAGGCTGTTGCTTCTGCTTAAATGCAAAAGGTTCCTTGCCCCACAAGTTTC
ACATTTTCTGGTTGTTAAGTAACTATGCTCTGTAAGAAACAGCTTCCAATAAAACCAATGTAACAACTGT
GTGTTCTTTGCGTCTCTGTTGTCAAACTTGTCATCGGGTCGCATCTATTTGTACCATATTTGCTTATTGT
GTT
>gi|3450489|gb|AI100528.1|AI100528 34903 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91I18XP 3', mRNA sequence
GACTTGGTGGCCCCCTACAATGNCNAGGACTTCTTTCAAACCCCGTGNTCGCGCACAAGGCTTCTATTCT
ATGACATGGAAGATGGACTTCAAATCCGTGGTTTCCCTACACGTGGTGTTTAACTCAACGGAACACAAAG
GGACATGAACATAATGGGTGCTGATTTGATGATGGAGCCCAACAAGAGATCTATCGGTCGTTGGTGGGAC
AGGTGACTTCTTCATGGCTCGTGGGATCGCTACCTTCGTGACTGATTTATTTCAAGGGGCTAAGTATTTC
CGAGTTAAGATGGATATTAAGCTCTATGAATGTTACTAAGTAGCTAAGAATGTGTGTTTTGTTTGAAAAT
TTTATGTTGACACAGAGAAATGTGTTTACAATAATTAAGTTTTTTTTTTGCCTTTTCTTTTGCTGTTGTC
TTTTTGTTTATCTATAATTATTATGTGATTTATTTC
>gi|3450488|gb|AI100527.1|AI100527 34902 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91I15XP 3', mRNA sequence
AGGAAGTTGACTACCTTCTCCGCAANCAAGTGGANTCCNNNGTGTNNGAATTCGAGTTAGAGCACGGATT
TTGTGTACCCGTGAGCCACGGAAACACTCCCGGATACTACGATGGACGGTACTGGACAATGTGGAAGCTT
CCATTGTTCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTACCCGG
GCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAA
GCCCCCAAGCTTCACCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTCATTTCAT
TTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGATTGTCAAATGTCTGATTTATG
AATATGTAATTTAT
>gi|3450487|gb|AI100526.1|AI100526 34901 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91I10XP 3', mRNA sequence
CCAAAGNAAGGANCCTAGGACCNATCGCNTCCAATCGCCATCGGCTNNATAGTTTGGTGCCAACAATCCT
CGCTTNCTGGGTCCATTCAGTGNTGGCTCCATGAATCCAGCAAGGTCGTTCGGACCAGCTGTTGNCAGTG
GTGACTTGTCCCAAATCTGGATCTATTGGGTGGGACCACTTGTGGGTGGTGCACTCGCGGGACTTATCTA
CGGTGATGTGTTCATCGGTTCTTATGAAGCGGTAGAAACACGTGAGATCCGAGTGTAATTGACTGGGTTT
TGTGATTGCTTGATGGTTGGTTGATGTTTTGTTTGCGTGTGTATGTTTGGTGTCCACTTTCTTGCAAGAT
TGTATGTAGAGAAAAGAAAAAAAGTTATGTCCTGTTAATAAGAAAATGTATATACATTTCACTTC
>gi|3450486|gb|AI100525.1|AI100525 34900 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91H4XP 3', mRNA sequence
GTGGATGATGGAAACAGCCAGAGTGGTTTCCAGAGGAAAAAGCTAAAGCTTGGTGTGCTTCAAAGGGGAA
CATTCCTTACTTTGAGACCTCTGCCCAAGGTAGGTACTAATGTGGAGGAAGCTCTCCAATGCATTGCCAA
GGACGCATTGAAGAGCGGAGAAGAAGAAGAACTATACTTGCCAGACACAATCGATGTAGGGACGAGCAAT
CAACAGAGGTCTACAGGGTGTGAATGCTAAGGAGTATCACCAGAAGGAAACGAGGCCTCTCCTCCCATTA
TCTCTTTTCGCAAGTTATGTCTACATTATTACTATGTTGTAAATTTTTTCTTTTGTGTGGAAAAGGGATG
AGAACAAAAAAAGAAGGAACCCT
>gi|3450485|gb|AI100524.1|AI100524 34899 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91G9XP 3', mRNA sequence
GATCCGAATTGCTAAGGAAGTGACTTCCTTTACCGCAACAAGTGGATCCCTTGTGTTGAATTCGAGTTGG
AGCCCCGGATTTGTGTACCGTGAGCACGGTAACTCACCCGGATACTATGATGGACGGTACTGGACAATGT
GGAAGCTTCCCTTGGTTCGTTGCACCGACTCCGCTCAAGTGTTGAAGGAAGTGGAAGAGTGCAAGAAGGA
GTACCCCAATGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAGTGCATCAGTTTCATT
GCCTACAAGCCACCAAGCTTCACCGGTTAATTTCCCTTTGCTTTTGTGTAAACCTCAAAACTTTATCCCC
CATCTTTGATTTTATCCCTTGTTTTTCTGCTTTTTTCTTCTTTCTTGGGTTTTAATTTCCGGACTTAACG
TTTGTTTTCCGGTTTGCGAGACATATTCTATCGGATTCTCAACTGTCTGATGAAATAAATATGTAATGTT
CTATAAGTCTTTCAATTTGATATGCATATCAAC
>gi|3450484|gb|AI100523.1|AI100523 34898 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91G4XP 3', mRNA sequence
ATTCTTGCTCCCTCAGCACATTCCAGCCAGATGTGGACCTCCAAGGCCGAGTATGATGAGGCAGGNCCAG
GAATCGGTTCACCAGAAAATGTTTCTAAGCTCTCAAGATCAAAGGCTTAAAAAGCTGGGGTTTTATGAAT
GGGATCAAAGTTTCTTTTTTTCTTTTATATTTGCTTCTCCATTTGTTTGTTTCATTTCCCTTTTTGTTTT
CGTTTCTATGATGCACTTGTGTGTGACAAACTCTCTGGGTTTTTACTTACGTCTGCGTTTCAAAAAAAAA
AACCGCTTTCGTTTTGCGTTTTAGTCCCATTGTTTTGTAGCTCTGAGTGATCGAATTGATGCCTCTTTAT
TCCTTTTGTTCCCTATAATTTCTTTCAAAACTCAGAAGAAAAACCTTGAAACTCTTTGCAATGTTAATAA
GTATTGTATAAGATTTTTATT
>gi|3450483|gb|AI100522.1|AI100522 34897 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91G2XP 3', mRNA sequence
CCGGCTCATATATTGGCTTACTACTCTCTGGCTGGCCAGAGAACAGATTGTCCAACAACTGTTAGAGTCC
TGAAGGAGCCAATATGATATGACCCAAAAAACAGGTTTGTATATAAAGATTTTTAGTCTCGAGTTTTGGG
GTTTCCACAAACTGTGTACTATACTACTTTGGTTCTTTTTTTGTTTCATGTTGTGTCGTCGATGTTTTTG
GGAGATTACATAGAGTCAGTCTTGTTTGTTGTATGGTCATTACTTCTTTATTTTTCCTCAGGGGTCTGTT
TACTTTAATTTCTTTAATAAAACCCCGAAGATTTTGAGAG
>gi|3450482|gb|AI100521.1|AI100521 34896 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91G18XP 3', mRNA sequence
CAACTGCTCTCTTCCAATATCTCAGGAGGAGCCGAGTTCCCAGCCGCATCCAATAGTTTTAAAGCATCTT
CAAACAACCACCCTCCCTTTTTCAGAAGATATANCGGTTACGGACCCATGATTTTCTCCAGAAGATGGCT
TCTTCAACAACAGTGATATCTATGGTGGCTTGTAATATCCAAACAACAGATGCATTGGTACTTTGACTAA
CACAGTGAAAGAGAGTGTAGGCTTATTGTTCTCATTTAGGTTGGTTTGGTCTTTCATCTTTGTATAGAAA
CCTCAGTGATATGAGAGACCAAAGGAGTTTGTGATTTGCTGTAACCTACGGTCTACCGACCCATAGACAC
TAGATTTTTGTTTTTGTTTTTTGTTTCTCTGCCCTTTTAGTGATAGTGGGGTGAAATCTTAGATTATGAT
TTCTGCTAACACACTATGAAGTAATCATATTCTTTGTTTTTGCTTTTACTTTGATAACGATCTGTTAATA
G
>gi|3450481|gb|AI100520.1|AI100520 34895 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91G15XP 3', mRNA sequence
TAGTTGAAGCTGAGGATNCAAGGAGCTTTGTAGTGGGTTGTCCCGAGCCCCATCCTGTTACTTTGGAAAT
CCGGGGAATCNGAAAACATGCTGGATGCCATTATGTATCCGAGGTGAAAGGTGTAGAACAAGAGTTTGAT
GGGGAAGATGAAGAGGGAACGTTGTCTGGAGAGATGAGAGTAGAGTAGGAGACCTCCTCTTTGCTCTTTA
GTGTACAGAAAAATAAATCCCACTTTTTTCTTCAATCCTTGGTGTTGTTTCTGGGCTTTTGAATCACACT
CAAGGATCTGTTTACTGAGAGATCTGAGTTGTTGTTTTTTTGTAGCTTTTGTTGACTTACACTTGTTTTG
ATTATTTGAGGTTAAGCAACGAAAGATGTACCAGAATATTTGAAATTTCCGAGTATTATAACACGATTTA
CAAG
>gi|3450480|gb|AI100519.1|AI100519 34894 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91G12XP 3', mRNA sequence
AGCTCGAGATGAACTCCACAGNTCCTGAATGAGGACGAGCTGCGTGATGCTGTGTTGCTTTGTGTTGCCA
ACAAGCCAAGATCTTCCCAAATGCTATGAACGCTGCTGAAATCACAGATAAGCTTGGCCCTTCACTCCCT
CCGTCAGCGTCATTGGTATATCCAGAGCACATGTGCCACTTCAGGTGAAGGGCTTTATGAAGGTCTGGAC
TGGCTCTCCAACAACATCGCTGGCAAGGCATGATGAGGGAGAAATTGCGTTGCATCGAGATGATTCTGTC
TGCTGTGTTGGGATCTCTCTCTGTCTTGATGCAAGAGAGATTATAAATATTATCTGAACCTTTTTGCTTT
TTTGGGTATGTGAATGTTTCTTATTGTGCAAGTAGATGGTCTTGTACCTAAAAATTTACTAGAAGAACCC
TTTTAAATAGCTTTCGTGTATTGTGCCTGGATTAATATGATTGATTGTTTTGCTTTCT
>gi|3450479|gb|AI100518.1|AI100518 34893 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91F24XP 3', mRNA sequence
TGCCAGGAGGGGATCCACGCTTCCATTAGGAATTCCATTAGCTTTGACNCCCAAGCTCCACGAAGAGATC
AAGCTGTCTTCAAGAAGGNTATGAGGGAGCTCCCAAGTTTTTGCTCCCCAGGCTCAGTGACTTCCAATTC
TTTGTTGGGGAGGGTATGCATGATGACAGCACTTTGGTCTTTGCTTACTACAAGGAGGGTTCAACTAACC
CAACATTTTTGTACTTCGCTCATGGTTTGAAGGAGGTCAAGTGCTGAGAGAGAAGCTCTCGTTGGGTTAC
TGTGGTCGGTCGCAGCGACTCTCTAAGTTTATGTTTCTTTATATTGTCCTGTGTTTCGTCGTCGTCCCCT
ATTAAAATTACCTGCCAGTTTACTTTTCTCTCTTCTTGTTTTCTGTGTTGGAAGATTCTCAAGTTATTTA
TTCCGCAAAAAACGGTTTATCATTTACAATTAGTTGAATTTTGGTCGTTACTTTTTGTGTT
>gi|3450478|gb|AI100517.1|AI100517 34892 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91F19XP 3', mRNA sequence
GGGGAAGTTACTGCCGCCACGGCTGCTGCTACAAAGGTTACCATGGCTGCTCAAGGTGTTGTTCATATGC
CGGAGAAGCGGTTCAGACTCAGTCTGGTCACTAAATCTACATAATATATCAACCACCATGAGTGTACGAT
TTCATTTATATATACACTTACGTGTGTATGTGATATGACAATACACTTACGTTTGTAATGAAGTGCCTTA
AGTTTAAGAGGAGAAACTATCGGAATAAAGTTTCATAATGTAATGCCTTTGTGTTTATTTAAGTTGTTAT
TTGCGATGTTTGCATAATAAAGTTGTTTCTAGTTGAAGTT
>gi|3450477|gb|AI100516.1|AI100516 34891 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91F18XP 3', mRNA sequence
GTCTCNCTTCTGAGCTTAANCTCGCTGGCTCTTCCCTNCGTTNTTTGCGACGTTTCCTCTCTCCCCTGGT
TTTTCTACTGCGAAATCGGAAAGGTTCGGGAGTGACTTTTCNTTCTCGGAACTAAGGATGCTGAAGCCGC
CGTTGCGAAAGCTGTTGACGCCGGAGCTGTGAAAGTGGAGGTTACGGAGGCAGAAGTTGAACTGGGATTC
AAAGGAAAAGTTACGGATCCTTTTGGTGTCACTTGGATCTTCGCGGAGAAGAAGACCGTGATCACCGACG
AGAACAAAGAGGTTTAGAATCTGTCGTCGGATCTAATTCTTCGTCGGTTTCTGAACAAAAAAAACTATCT
ATTATCCTAGGTTTATGCTTTTATTTTGTCTTTTGTGGAATCCGGTAATCAGTAAACCGGATCGAGTAGG
CTAATGACTTTCGGATTCT
>gi|3450476|gb|AI100515.1|AI100515 34890 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91F15XP 3', mRNA sequence
TTAGATGNCCGATTCATCAAGCCCGNTAGCGTCAACCATGACCCATCTTCCCAAACNACAAACTGACGGG
CACAGACTTTGGTTACCCAGGTGGGTTATGGTTCGACCCGTTGGGTTGGGGATCCGGTAGCCCGGCTAAA
CTCAAGGAGTTGAGGNCCAAGGAGATCAAGAACGGAAGGTTGGCTATGTTGGCAGTGATGGGTGCTTGGT
TCCAACACATCTACACGGGCACTGGTCCTATTGATAACCTTTTTGCACATCTTGCTGATCCTGGTCACGC
CACAATCTTCGCTGCTTTCACACCCAAGTGAGACAACGAAAAAGGGTTATGGGGAGGTGAATGCGTTTGT
GTGTGATCATGTTTGTACAAATATCATTTTGAACTTAAAATTATTATGTACTTTATATAAATTGTGGTCG
AATGCAAATTAAGGTTCCCCGT
>gi|3450475|gb|AI100514.1|AI100514 34889 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91F14XP 3', mRNA sequence
ACGCGCCAATGCTTTTGANCTCATGTATGACCANGTCAAAGCTCTTAAGAATGGTATANCCGTCGAGAAA
CCGATTTATAACCATGTCCACTGGACTTCTTGACCCTCCGGAGCTTATTCAGCCCTCCTAAGATTCTTGT
CATCGAAGGTCTTCACCCAATGTTTGATGAGCGAGTAAGAGACTTACTAGACTTCAGTATCTACTTGGAC
ATTAGCAACGAAGTCAAATTCGCTTGGAAAATTCAGAGGGACATGGCTGAAAGAGGTCACAGTTTGGAGA
GCATCAAAGCGAGTATCGAAGCCCGAAAGCCCGACTTCGATGCATTCATCGACCCGCAAAAGCAGTACGC
GGATGCGGTCATAGAAGTGCTTCCTACGACTCTGATCCCAGATGACAACGAAGGGAAAGTGTTGAGAGTG
AGATTGATAATGAAGGAAGGTGTTAAGTACTTCAGCCCGGTTTACCTGTTCGATGAAGGTTCAACCATCT
CGTGGATTCCTT
>gi|3450474|gb|AI100513.1|AI100513 34888 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91F13XP 3', mRNA sequence
CACGGAGNATTTGATTCTCTTCCCGAACAGGCCTTTTACTTAGTGGGTAACATCGATGAAGCTACTGCGA
AGGCTACGAACTTAGAAATGGAGAGTAAATTGAAGAAATGACCTTAAATCTTTGTNTACTGACTCCGAAT
CGAATTGTTTGGGATTCAGAAGTAAAAGAAATCATTTTATCTACTAATAGTGGACAAATTGGTGTATTAG
CAAACCACGCGCCGATTGCCACAGCTGTTGATATAGGTATTTTGAAAATACGCCTTGCTAACCAATGGTT
AACGATGGCTCTG
>gi|3450473|gb|AI100512.1|AI100512 34887 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91F11XP 3', mRNA sequence
CCGCGGACCACAGAGGNCTTACTTGNCCACTGAATCCAGTCTTTNCACCGTGGATCCCCTCGTCGTGACA
CGGCGAAAATCGAGNTGCCTTTNCACACACAGACGCGTTGCTTTGGGTAGAGTACGAGAAAACGCGGAGG
CCNTGTAGCGTTTGCGAGAGCCAACCGGTGACGGAGTTTTCAATGCGATCATATGGGATGTTGTGGTTGA
TCCCATCGTTTCAAAGCTGTGGACTTGGGAAGGCGGTGATGGAGCGGTTGATTGAGGATTTACAGGTGAA
AGGGATTTGTAACATTGCTCTGTATTCAGAGCCTCGAGTTCTCGGGTTTTATCGCCCGCTTGGGTTCGTC
TCTGACCCGGATGGGATCAAAGGAATGGTTTTTATACGCAAACAGAGAAACAAGAAATAAAAAGTTTGAA
ACTTTATAAATTTTAATTTCGTAAATGCACAGATTACAATGTCTCTTTAACTACACTTTCTTGTACAAGC
TAAGAGAGTAATGAGAAGCACTTCTTCGTCT
>gi|3450472|gb|AI100511.1|AI100511 34886 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91F10XP 3', mRNA sequence
TCCATTGCCCCCAACCACAGTTGTGACTGCGAAGGCCTCTTCTTGCTTGGGGATGTGTGGAACCTATTCA
GGCTNTTCCCGCCAAGACTCCAGGAGGAATTTCATCTCAAGAATGCGCCTTGTGGATCCATTGCATGGNT
CCACTGTTGCTTGCACTGGTGTGCTTTGTGCCAGGAACACAGGGAGATGAAGAATCATCTTTCTGATACA
GAAGCCTCATCATCAACTACTATGGATCCTCCCCCAGTTCAAGAGATGAACACTGAGGAGAGAAGAGACG
CTTCATCTTCTTCGTCCTCATCCCCATCATCTGCCAAAAGCCAACACAATGATCTCGAGATGGTCCCTCT
ATAGGAAACGTTCCTTATTAATCTCTGCTGCTTATGCTTTAAGCTGTTTTTTCTGTGCAGAGAAGTTTTC
GTACCAGATGACTCTATTGTCCTTAGGTTTTAAATATGCAAAAGTTTGTTCTAAGAACAAGTTCAATAGT
ACTCTTAAGTTTTACAGAACTT
>gi|3450471|gb|AI100510.1|AI100510 34885 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91D6XP 3', mRNA sequence
CATCTCTTCCGTCGACTTGCATTGTGTTGGATNCCTTAAGAAGATTGAAAGATCTATTCTAAAAATTAGA
GGTGTGGAAGAAGTGGTGATGGATTATGAATGAGAACCAAGTGACGATAAAGGGAGTGTTGGATCCGCAA
GCAGTGTGCAACAAAATCAAGAAGAAGACTAAAAGAATGGCCAAAGTCCTCTCGCCGCTTCCGGCAGCTG
AGGGAGAGCCTCTGCCACCAATCATAACCTCTCAGGTCTCCGGCGGCCTCACCACCGTCGAGCTCAGCGT
TAACATGCACTGCCAAGCTTGTGCTGACCAGCTCAAGAAGAAGATTCTCAAAATGAGAGGGGTCCAAACA
ACTGTGACAGAGCACACCACGGGAAAAGTAATAGTGACTGGGACAATGGACGCTGAGAAGCTTGTGGATT
ACGTCTACCGTCGGACCAAAAAGCAAGCCCGAATCGTACCCCAACCTGACCCGGAACCTG
>gi|3450470|gb|AI100509.1|AI100509 34884 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91D3XP 3', mRNA sequence
GCAAACCAGCCATGCTTTCTAACCGGATCAAGGAGAGGGAAAAAATTCTTAGGGCTCAACCAGGAGCAGT
GGGATCAGCATAACCAAGGCCACAATATGCCTCCCCCTCTGCCACCGCAGCAGCACCAAATCCAGCATCC
TTACATGCTCTCTCATCAGCCATCTCCTTTTCTCAACATGGGTGGTCTGTATCAAGAAGATGATCCAATG
GCAATGAGGAGGAATGATCTCGAACTGACTCTTGAACCCGTTTACAACTGCAACCTTGGCTNTTCGCCGC
ATGAAGCATTTCCATATATATATTTGTAATCGTCAACAATAAAAACAGTTTGCCACATACATATAAATAG
TGGCTAGGCTCTTTTCATCCAATTAATATATTTTGGCAAATGTTCGATGTTCTTATATCATCATATATAA
ATTAGCAGGCTCCTTTCTTC
>gi|3450469|gb|AI100508.1|AI100508 34883 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91D2XP 3', mRNA sequence
CCCGCGATGACATCAGAGGATTGGTGGAGAAGGCCTTTGAGCAGATAGGAGGAATTCCTGACCGTGCAGT
GACACTGACGTTGGACATCCAAAAGACATACCGGTAAGTTGNTGAAGGACTTCAACAAGGGTTTGGTGAA
CAACAAAGATCTCGATCAGCTCAAGGCTGATGTCGAGAAGTTCTCGGCGTCTTATGAGATGCCTGGATTC
CTCATGTCTGAGATGAAGTACAAGGATTAGAGATCTTTCTCTATATGCAAGAGTAATCTTCTATTATTAT
CTACCATATATATAAAATATGCTTTTGTAGGATCGCCTTAAAGGCGAAGAGATGAAGATGCAAACAGTAA
AAAAAAAGGGTTTTCTTTTCAGCTATTTCTTCTTGAATGTTTTTTTTCTTTTTCTTTTGGTTTCTTATTG
AAATTGTTGTATTTTTGTTGGCTTTTTTCTAATAATATCAGCGAGTTTTTCTTTC
>gi|3450468|gb|AI100507.1|AI100507 34882 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91D1XP 3', mRNA sequence
TCCCCTCCTGNCAAAGTTATTGATTGTCCGGTTGGAAACTTGAAGAAGNTTGACTTTGCCAGCTCGAGTT
GNCTAAATTTGTGGGGTTAACTGGATTTCCAGGATATTGTCGAGGACTGCTTTGCTTTGCTCGCGTATGA
AAGCCTGAGGAATCATCGGTCTGGTATTTCCTAGAAGACTCACAGAGGGAATTAGTGGCTGATGCGGTGA
ATGCAGCAATACTATCAACAAATCCAAATAAGAAAGATGTGCAGAGAAGCTGTCACTTGCAATCCCATCT
AGAGAAACTGCTAAGACAGTTAACCGTGTGCTGTTTAGAAAGGCGGTCACTGAATGGAGACCAAGGTGAA
ACATTCCGGCTTCGACATGTTCTTAACAACAACAGATAAAGAAGATGAAAATGGCTTAGCCGCGCATATA
TTTTGAAAACTCTGTTTTTCTATGGTCGTTATCATCATAAGTGGCTTTTGTTCATTACTTGTGTGATATT
ATGTTGAACTTTCCATTATGTAAAGGAGAAAGTTAGAAAAATGGGTTCGACGTT
>gi|3450467|gb|AI100506.1|AI100506 34881 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91D13XP 3', mRNA sequence
AGCCCAGCGATTCCGTCGTCTTGCTCGTAGAGGAGGTNTGAAGAGAATCCAGTGGATTGATCTATGAAGA
AACGAGAGGTGTGTTGAAGATTTTTCTGGAGAATGTGATTAGAGATGCTGTTACTTACACTGAGCATGCG
AGGAGGAAGACGGTGACTGCTATGGATGTTGTTTATGCCTTGAAGAGACAAGGAAGAACTCTATATGGAT
TTGGTGGTTGATCAATTTGAGATCTGGGTTTTCTGGTGAATGATGATAATTTAAGTCTTGCGATCAAGAA
ATTCCAGAAATTGGGTTGAATTTTAGGGTTTCGTTTTGTGTTGTAATTAGGGCAGCATTGTAATGGATTA
ATGATAAGTACCATTTGCTCT
>gi|3450466|gb|AI100505.1|AI100505 34880 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91D12XP 3', mRNA sequence
CTTTCGTNAANCTTTTGACCGGGAAGACCCATCACCCCTTGAAAGTGGAAAGCTCCGACTCCATTGACAA
CGTCAAGGCCAAGATCCAGGACAAGGAAGGTATTCCTCCGGNCCAGCAGCGTCTCATCTTCNCTGGAAAG
CAGCTTGAGGATGGACGTACTTTGGCCGACTACAACATCCAGAAGGAGTCTACTCTTCACTTGGTCCTGC
GTCTTCGTGGTGGTTTCTAAATCTCGTCTCTGTTATGCTTAAGAAGTTCAATGTTTCGTTTCATGTAAAA
CTTTGGTGGTTTGTGTTTTGGGGCCTTGTATAATCCCTGATGAATAAGTGTTCTACTATGTTTCCGTTCC
TGTTATCTCTTTCTTTCTAATGACAAGTCGAACTTCTTCTT
>gi|3450465|gb|AI100504.1|AI100504 34879 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91D11XP 3', mRNA sequence
TGAAGGTTGCCCCCAATCGGAAGAGAAGTTGNGCNCTTTCTTCCTCCCTGCCNTTAGTGCCGTTGAATTG
GCTAAGGAAGTTGCTTCCTTCTCCGCAACAAGTGGATCCCTTGTGTTGAATTCGAGTTGGAGCACCGGAT
TNGTGTACCGTGAGCACGGAACCACTCCCGGATACTATGATGGACGGTACTGGACAATGTGGAAGCTTCC
ATTGGTTCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTACCCTGG
CGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAG
CCCCCAAGCTTCACCGAAGCTTAATCCCCTTTCTGGAATATTCAGCGTTGATTATTCTGGAACCCATTTC
TATGTGGTCAATGCAAATTTAAGAAATTATTTGCCGACTTAAAAGTTGAGGAACTATTGTTTGAAAGTGA
AAATGTTATTCCTATCAGTTTCTCTATAATTATAGTTATCATTTCATTTC
>gi|3450464|gb|AI100503.1|AI100503 34878 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91D10XP 3', mRNA sequence
TCAACTCAATGTTCGNTAATGGAGCCCCTTNTCCTTCAGGTCCCGGNTAAGAGTCTAGCGGAAAAAGCAG
GATTANCATCCGANNTCCCGGGGTTTTGCTGGTAAATATAGTGCTTGGAGATATCATTGTTGCAGTTGAT
GACAAACCTGTGAAGAACAAAGCCGAGTTGATGAAGATATTGGATGAGTACAGTGTAGGTGATAAGGTGA
CACTTAAGATTAAGAGAGGAAATGAAGATTTGGAGTTAAAGATCTCATTGGAAGAGAAAAGTTCATGAAA
ATATTATTGACAACATTTCATCTCTTCCTTTTGAATCTCTCTGTTTTTTCCCCCTTTGAGAATAGCAAAA
TTACAATCNTTGTCTAAATTCTCTGAATATATATATGTCTATGGGAATTTTTTTTATTAAT
>gi|3450463|gb|AI100502.1|AI100502 34877 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91C9XP 3', mRNA sequence
GTTTTTGCCNAAAGCCAACCAAGGCCAGCTNTNAAGNCGATNTGGGAAATNGACCNCTGCGAAGAGCCGA
CTCTGGCATGATGTGACCATTGAGGATGAGATGAAAAGGAAGGCGCAAGCTCAAAGAGAGGCTTATGATG
ACGATGAGGAAGATCACCCAGGCGGTGCTCAGCGTGTGCAATGTGCCCAGCAGTGATCAACATGCGCATC
TTAGTGATCTCCAATATTTGCTTCTGTCTTTTCTCCTTTTCATTGTATTATTTTTGGGTCTTTTTATAGA
CTTTGCCAATTCAGTGGGAAGAACCTCGTCCTAATTCAAATCCTTGTTACACCATTTTTTTTGGTTTGAG
AAATAAACTTGTAGTTCTTGAG
>gi|3450462|gb|AI100501.1|AI100501 34876 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91C23XP 3', mRNA sequence
GTATTTTCCAACCGGCTTTAGAGCCTTGGGCTCAAGTTGGGCAACTCGACATCGTGNACCNACGTAGGTT
TGAGTTATTTTGTAACNACCAAATGNNGAAANTGGNAAGCCCNCAAAAAATGAAGNATGAGNGCATCTGA
AAACAGNGGACTACTCTGAATAAATAGAGGGGTTGCTGCTGATATTTATTTTTACTCTGCGGCGGAATTA
GAAAATTTGAAAAACATCATGTATTGATAAGTTGTAAATATCAGAAAAAGGTGGGGGTGCAAAAATTTGT
ACTTTTTAGCTTTTGAAAGAGGCAAGTTTTTCGAATGTTTGTTTGATTTGTAAACAATTTCAGAATTATA
TAAACTTGGTTCC
>gi|3450461|gb|AI100500.1|AI100500 34875 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91C20XP 3', mRNA sequence
AAGACCCCNCNAAGATTTCATCCCCCNGTGGGTTTCCATGTCCTTNCCATCAACAGTCTCCAGTGCCAAT
TGCAGTGTTTCTGTTCACAATNCCATTACCGTACCTTGGGGTTGCATCATCACTACCNAAAGGGTTCATG
GGAGGGACAATCATACTTGTATTGGGAATGAGTCTTTATAGTTGGACACCNCNCGGAGCTAACTCTTCTC
ATACTGATTCAGTCATTCCTTCACCTCCTCCNACATAGAGAGGGCTTNACTAAGGGGTTTTGCTTTTATN
TAAAGATTTGAGAGATTTNTNCAAATTCGGTTTGTGTTTNAATAAACTTATATTTGATCATATGATGTTA
ATGGAAAAGTTGAC
>gi|3450460|gb|AI100499.1|AI100499 34874 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91C19XP 3', mRNA sequence
CATTTAGCCNCAGTGCCTTNGCCGAATGTTCCTTTGGCCGATGAGCNCAGGTTCTTCTGTTTCTGGCAAT
GCCNCCTACGTTTCCGGGTCCTCGGGNTCANTCATTCCTGGACCCGTGTCCCCGAGCTGAAGAGAGATGC
TGATGCTTACGGTAGAGCTGCAGTCTAGTGAAACAGACTGCAAAAGAAAAAAGAAAAAAAAAGCAAGAAA
CATATCTTGGGATTCTTTGATAGGATTCAATTCATCAATCATTTCATATTTTGTGGAGTTAGAGAAGGTC
AGATTCTTTCCTCAAGTAAACCACATTGTCTTTAGATCATACATGTTCCTTTCGGTTATTCTGGTTTCCT
ATTTTTATGTTGTTTGCATATTCTGAGATAAGAAATCTGTACAGGTTCATTTCTTCATTCATGTGTAAAC
AAAGAAATTTTGTTTCAGCAGTTTTCCACAAGCCATTAATAATAAAAAGGAGAGATAGTTTC
>gi|3450459|gb|AI100498.1|AI100498 34873 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91C11XP 3', mRNA sequence
CCGGCCACTGGGTTCCTCAACCNTTCTGCGCCACCTGGCCGTTTACGATCTGGAGCTCCTTATTACGCTC
ATGGATATCAAACTGTTCCCAGTCCCATGGTGGTGTTGCTGAAGGAAGACCTGTCAGACAACGTCGCCTT
CCTTGCTGTGGAATTGGTCTTGGATGGTTCCTGTTCATTGTTGGATTTTTCCTTGGAGCAATCCCTTGGT
ATGTCGGATTGTTCATCATGATGTTTGGAAGGAGAATCGATTACAGGGAGAAACCAGGATACATTGCCTG
CACTATCGCTGCTATTCTAGCAACAATCGCTGTGATTCTGGGTGTATCTAAAGGAGCAGACGACTGGTGA
TGGATCAATCATCTTGTGGGGTTACTCTAAAAATGTTTGTATAGGTTTCTTTATCGTGTGTTGTATTATC
TACTTCCTTTTTTACTTACTCTATGAAGAAACAAG
>gi|3450458|gb|AI100497.1|AI100497 34872 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91B7XP 3', mRNA sequence
CCATTNGTGCGGATTGCACCCGACTCCCGCTCAAGTGTTGGAAGGAAGNTTGAAGAATGCCNAGAAAGGN
GTACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATT
GCCTNCAAGCCCCCAAGCTTCACCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCT
CATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGATTGTCAAATGTCT
GATTTNTGAATATGTAATTTATAT
>gi|3450457|gb|AI100496.1|AI100496 34871 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91B24XP 3', mRNA sequence
CCCCCGTTGGAGGAGTCNTCCNTTCTGGGGGAGCTGNTCCGNTTNANGCGGNCTCCGTCGGTGATTGCTC
AGGTTCCNATGCCTTCNCCCTTTCGAGAGGTCTTTTTACTGCTGTGAGCCCTATCTGCAGCCCGGCTGGA
GACGGAATGGAGTTGGTTTAGATTCCATGTTGATCTCCGCAAATCCTGAGACTGAGAGGCCTCTTTATCT
TACGTAGAATAACNTCCCTTTTCTCTTTCTTTTGGACAACTATGGATATGAGACATTGTGCTATTCTCTC
GCAGGGAGGTCTAGGCATATCCTCCCTGCCTTAAAGAGAGCTTTTATCTTAGTAATGTTGAACTTTATGT
AGTACTTATGTAGGAGAGACTTTATAATTCTAATGCTTTATTCTGGATCTT
>gi|3450456|gb|AI100495.1|AI100495 34870 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91B10XP 3', mRNA sequence
GTGTTGAATTTCGAGTTTAGAGGCCCGGNTTTTTGTGTACCNTGAGCNNCGGAAACCACTCCCGGATACT
ACGATGGACGGTACTGGACAATGTGGAAAGCTTCCATTGTTCGGATGCACCGACTCCGCTCAAGTGTTGA
AGGAAGTTGAAGAATGCAAGAAGGAGTACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCG
TCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATTTCTTTTCTAA
AACATTCTTATGAATTATCTCTGCGTCATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGAC
AATTTCTATCGGATTGTCAAATGTCTGATT
>gi|3450455|gb|AI100494.1|AI100494 34869 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91A18XP 3', mRNA sequence
CCGGATGAACCCCCTGGTAAAGCTNCCTTTTTGGAGTAGTGCCAATGTGCATTGGGACGGGGATGGGTGC
AGCACTGTGTTTGAGAGAGGAGATGGAGTTGATGGACGTCGCAACGCAAGGAAAGTTGAAGCGCAAGGTC
TTTTGTCCAAGGACGCTCGCTAGAGAGGACCATGCACCAAAACCGTTTTTCACCTCACCTCTCTCTTTTC
TGGTCTTCTTGTCACTTTCTTCAGATATTATTATAGTTTCGAATAAAGCACACAACCAATGTTTGCCTGA
GTCTTGTGTTGTTCTTGACCAGGTCATGTGTTTAGTATTTTTTTTAAGTGAAGGGGGATAATCTTTAAAT
CTTTTATATGTAAGAATATTGTTCTTCTCGAATTTCATCAGTTGTTGCTTCTAGAAATTTTAGATTTTTT
GGGTGGCAGCC
>gi|3450454|gb|AI100493.1|AI100493 34868 Lambda-PRL2 Arabidopsis thaliana cDNA clone 91A13XP 3', mRNA sequence
TGAGATGAAGTNCATTTTGCCTAGAGGTGGACAGGATCTTGCGGCCGAGTGGATATGTTATAATCCGAGA
ATCGAGTTATTTCATGGACGCAATCCACAACGTTAGCGAAAGGGATAAGGTGGAGTTGCCGGAGAGAGGA
GACTGAGTATGCAGTCAAAAGTGAGAAGATTCTGGTTTGCCAGAAAAAGCTATGGTTTTCGTCAAACCAA
ACCTCTTGATGAGACCACCTGTATCATAGTGTTTATCATCTCCTGTGATGCACACTACAGAGAGAAGGAT
CTAGTCCTTTGAGTCCAAGATATAGCTCTATAAACAATCTCCTTTTTTTGTTCTCTTTAATTTCTTGGGT
ATTTCACGGTATAGATTGATATTATATATTTTTTAATTATATTTTTAATATATAGATATATTAGTATGTG
GTTTAAACACT
>gi|3450453|gb|AI100492.1|AI100492 34867 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90P19XP 3', mRNA sequence
TTCGTCCTGGTCCGTTCCGGTAACATTGGCCNGCAGGNAATCATTTGGTCACCCGGNTATCATATGGTTC
AACCGGTTCAAATNCGGGTCAGTTCTTCACAATACCNTCATGTNCCAATGGGATACCACCAACNTCAGAC
TCATCAGATGGCTGGTCCGGGTCAAGTTATATGGTGGAACGGTTAGGCCGGTTATGATGGCCAGTTGATG
GAATGAACCGGACGGGTTATTATGGAATGAAAACACCCGGTCCGGTTCAAATGTATCAGCATCACACTGG
TATGGTTGTTCCTGGTGTAGAAGAACAACAACAATACAGAACCGAAACGGATTCGGATACGGGTCGGGCT
TCTTAGCTGTTTGAAGAAGAAATATGAAAAATTATCACATCCGGGGTTTTCGTCTTTTCATTGGAGTCGT
TCTTATTCGTTACTGTGTGAACTGTGTATTATTTTTTGTTTTACTTTTGTAAAATTTATTTTTGTGTGTA
ATAATTTTGTATTACAAAAT
>gi|3450452|gb|AI100491.1|AI100491 34866 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90O6XP 3', mRNA sequence
TGGACTATTNGCCNTCACTGANTTCCGCCGGNCGGTGAAGGAATAAGAGTGCTNCCCTCTTTTGTGGGTC
ATTCTTTCCCACNTGGGAGTGTATTGGACAAATGGCTAGGTTTCTAGGTCTTCTTGTCCTTCTTGTCGCA
GGATTCTTACGCCGGTGAGATGTGACCGGTGTGGTCATGCTTCTACGGCGGAGATGAAAGATCAAGCTCA
TCGTCATCAACATCACCAACACTCTTCTACTACCATTCCTACGTTTCTTCCTTAATTAACACTAATTTTT
GTTTTATTATGGCAATAATTAATTGCATAAAAGTTATGTAAAGTGAGTTTAATTAGGATTAGAGAGATCT
TTTAAAGTTTTTCTCTCTTTTCTCCTTGTTGTAATCCAGTGTATTTAATCAAATCTCAGATGGAGTTC
>gi|3450451|gb|AI100490.1|AI100490 34865 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90O24XP 3', mRNA sequence
CGGATCTATGGGGGTTAGATGAATGGGGTACTATGTAGGTTTTACAAGGAAGNGAGGAGCAAGTAAGCTT
CTGAATGAGCAAGAGGGTTTCATGGACGAAGTACTAATGGAGGATGAGACCAAAGTTGTTNTTAACGAAG
CAGAGAGAAGAAATGATGAAGAGATAATGATGATGACGTCGATGAAACTTCCAAGGACGTGTTCGCTGGC
TCATTTGTTGGAAATGGATTACATGGGACCCGTCTCTCACATTGATAATTTTAGTCAGTTCGATCATCTT
CATCAACCTGATTCGGAGTCTAGTTGGTTCGGGGATCTACAGTTTAACCNAGNCGNGATCTTAAACCNTC
ATCNTCAAGCTATGTTTAAGTTTTAGTGATGGGGTCNGT
>gi|3450450|gb|AI100489.1|AI100489 34864 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90N7XP 3', mRNA sequence
GGAAAACCCCGTGGAGCTTGGAGCTTAGGTGAGGATCAATTCCAGCTGGAAGGAGCTTTTGAAGTGATCG
ATGGTCCCTAGTTGTAAATAAAGCTGTGTGGGATTTTGCCTGTTGGGGGATGGTACAAGTCACACCTCAA
GCTCTATGCATTGGTATCTCATGAGCCTCTCTTCCATAGAGAGTTTCTCTTTTAATTTTGTCGAAATAAA
AAAGGTGTGATGAAGTAAATAGAGGTATAATAATATCTATCTATTAAGTCTTGTTTTGTTCTTTCATTTT
TGTATTTCTTTTCTATTTAAAAGACAGTTTATTAGTCTTCTGAGCTCTCTTTTTGATCTTTGTTATAGCG
TATCATCACCCTCGAAAGTGTAATGTTTTGTACCCCCAAACTTGTTTAGCATTATAATAAAGTCTCTTTG
GAACT
>gi|3450449|gb|AI100488.1|AI100488 34863 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90M3XP 3', mRNA sequence
CCTATGGGNCAATGTCGAANGAAAGCATAGATCTTNGAANGGGTTTNCGTTAGATTTTATGTTGTTGTGA
TATCAAAAGATTATNGGATTTGAAGGTTTTAGGTTNCCTGAAAGGTTTCTAGGTTTGCTATATATNCCTT
TTGTACAGAGTATCTTGAACTGGTCAATTCGGTTACTTTGCCCCCATGTGAGATGCTTATACATAGAAAA
GGAAATAGAT
>gi|3450448|gb|AI100487.1|AI100487 34862 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90M17XP 3', mRNA sequence
TACCATGTCATCCTGGGCCTTNCGATAACTGGGTTCAATGCCTTGNCAGACGAGCTGGTGCAGAGACCAT
CCCNGGATAAGGGAGTACTTTTGTAGAGCCCNTAACAAAGTCTACTACAAACCTGCAAAGCTTGAGGTTG
TAGAATGCGGAAGAAGAAGACTGCACTTAACTAGAGGTAAGTAGACAAGGAATTATATAGAGAGAAAGAG
AGAGAGAGATCAAGAGCCGCCATTAGAGGTCTTTATCGTCCTGTACTGGGTTGTCTTAGTTATTTGCTGT
GCTTTTTGGTTCGTTTTGGTCATTTTGTATTGTATTAATTAATCTCCTCTGATCACAATCGGTCTTGAAT
GAAATCGCTACCCTTTGTATCCAAAAATACCATTGTGGTATAACTTCCACTATTCAATTCAAAATCCACT
CTCCAACT
>gi|3450447|gb|AI100486.1|AI100486 34861 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90M15XP 3', mRNA sequence
CCGCTTAACTTTGCTCCNTACGCAAGAGNCCAAGGAGAAAGAGCTAGCAAACGGGAGGTTGGCCGATGTT
GGCATTCTTAGGGTTTGTGGTTCAACACAATGTGACTGGAAAAGGACCATTTGAGAATCTGTTGCAGCAC
TTGTCTGACCCATGGCACAACACTATTGTCCAAACCTTCAACTAAAGAGTGAAGACAGACTTATGATCTC
ATACCTATCTATCTTCCATCACTTTCATGTCTGTCTGTGAGTGTGTTTCATCTTAGAGTTCTTGGTTTTT
GAGCTTGAATTATTGTTGAACCGTTGTAGCTCCATGAACAAATTTGGAATCTTCAATGTACAGAGGAACT
AAGTTAATCAACATTGTTGTACTCTT
>gi|3450446|gb|AI100485.1|AI100485 34860 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90L23XP 3', mRNA sequence
TACCCCCCACTAAGGAACCTNTTTGACGGGCGTCCACATNTCAGTGCTTGGGTTGCTGACATCACTTCTA
GGCCTTCTGCTAAGAAGGTTCTTTAAGTGNCNCNCAAACTGTTAATCAGNAGATTGAATAAAGTGGCGAT
GNCCTCATTGCCCTAATTCTCATAAACAATAAAAGTGGCGATGACCTAATTGCCAAATTCTCATACACTC
TGNGATTTTTTTGTGT
>gi|3450445|gb|AI100484.1|AI100484 34859 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90L20XP 3', mRNA sequence
TTTCAGCCCTTGNGGGCTTTTTGCAACCATCNGCATTGCCGGGGTTCCAAATGGGGCCAATTGGNGGAGG
CACTTCACAGGCTTGTCCCCACACTGCCAACTGGTCCTTGGGGGCTCGCTTANCCGTGGATTCAGTGCAT
AGAANCCCTAANCCGTCTTCGCATTTGTTTATNCCNCCAATCCCCAAATATTCCTATTTCGATTTGTTAT
GATTAAATCAGTATTCTCTCTGTATATCTCAGTATCATTTCCGTCGTCAGTGTGTAATTTCAAATTATGT
ATTTGCCATGTACAGAAGCTTNTAGAACTAAAGTTGAATGTATANAAGGTTTGTATATTATGATGTAAAC
TTGGGAGTTGTCAATCTCATGGATGGTTTACTTTTTGT
>gi|3450444|gb|AI100483.1|AI100483 34858 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90L19XP 3', mRNA sequence
CTTTGATCTTGAACCGNCAAANCATTTGCTGCATGCATATGGNTAATTTGGAAGAAGCTGAGACTCTACT
ACTTGAAGGCACTCAACCAGGGATGCTAAAGGACCCCAGAAACTCTTGCAAACCTCGTTGTATGCAGTCT
TCACGTCGGGAAATCATCTTCTCGCTACCTAAACCAGCTGAAACTTTCACATCCAGAACACGTCCTTGTG
AAGCGAGCAGCATCAGCTGAAGATAACTTCGAGAGAGCACTTCAATCTTTCGCCTGAAGTACCTCAAAGT
CCATGGAATCAATTTGCCTTATGATCTACCAGAAGAACATCATATTATTACCGACCCTATCTTGAAATTA
TCATAGATAAACAGTTTTTTCCATTGGATATGTTGCATTTTACTTTGATTTCTCACTGAAGCTTTTGTTT
TCATTGAGTTTCGAATCCAAC
>gi|3450443|gb|AI100482.1|AI100482 34857 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90K7XP 3', mRNA sequence
ACCGTCAAGTCCGCGTGGTTCTCCAATCCGATCTAGTCNTATGGAAGGATCCCGNGCCCCGAGCCCTTCA
TTGAACGTTTATTAGGATTACGCCCGACCATCCCTTGAGGTTCGGAACCGAGTTCGGGAAGTCGATGGTC
AAAATGAGTCTCATAGAAGTTAAGACTGGATCAGATGGGGAGATTCGTCGGGTTTGTTCCGCCATCAACT
AAGATTTAAAAAAACACAAATGTGAGCTTTGTTTTTCATTTATGAATTCGTTAATTAATAATCACTTGTT
TTAAATAAAAGCTTGCTACAGCATTTTGTGGTCGATGGTTACGTTTTGATTTTCAAGTGTAAGATTGTAC
TTGTAAACAAAAAATGTATTATATAAAAGTGTTATTTGTTTCTTC
>gi|3450442|gb|AI100481.1|AI100481 34856 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90J7XP 3', mRNA sequence
TAAAGTTTNTTGGATTCTNCAGCCATNGTTTGTGTGGAACAATCCCCAACAAACGGACCTTTGCTCCACA
TTCCTTTACAGACTTTGAGAACAACCCCGAGGTTGGGAGGGACCCGGAATTACTCGGTCTTGCAAGCTAC
GACACTAACTGCACCTGAAAAAATTGGCAAAACCTGAAAATGAAGAATTGGGGGGTGACCTTGTAAGAAC
ACTTCACCACTTTATCAAATATCACATCTACTATGTAATAAGTATATATATGTAGTCCAAAAAAAAAATG
AAGAATCGAATCAGTAATATCATCTGGTCTCAATTGAGAACTTTGAGGTCTGTGTATGTAAAATTTCTAA
ATGCGACTTTCGCGTACTGTAATGTTCGGTTGTGGGATTCTGAGAAGTAACATTTGTATTGGTATGGTAT
CAAGTTGTTCTGCCTTGTCTGC
>gi|3450441|gb|AI100480.1|AI100480 34855 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90J19XP 3', mRNA sequence
TGTTAACCAGCTGGGGTTCCCATTTGCNCTGATCTGGTGGAAGGTCTGATGAGGTTGATGGAGGGAGAAC
ATGTCGGTCCATTTAACCTTGGTACCCCCGTGAATTCACCATGCTCGAGCTCGCTAAGGTGGTTCAAGAG
ACAATTGGACCCGAACGCAAAGATAGAGTTCAGACCAAACACAGAGGACGACCCACACAAGAGGAAACCA
GACATCACAAAGGCCAAAGAGCTTCTTGGTTGGGAACCAAAGGTGGCTCTACGCCAAGGACTCCCACTTA
TGGTCAAAGATTTCCGTCAACGTGTCTTTGGCGACCAAAAGCAGGATTCTTCCACCACTTCATCATCAAC
AGAGTAACTGTCGCTGGAGATTCTCGTTTCTCTTCGTTTTCATTTTTAATTTTGATATTTCTATTCCTGT
CAATGTAGTGATATTGAAACCTCACCGATTTTAAAGTTTT
>gi|3450440|gb|AI100479.1|AI100479 34854 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90I22XP 3', mRNA sequence
GAAGAAGCCGAGGACAAGCTCANCTACGTGTTTCCAATCTTNGGAAACACGTCCCCGNTNCCGGTTGGGA
GATTGGTCTCGATCTTGGAAGGATTGTTAGGGACAAAAGCTAAGAAGCATCTTATCAAAATGCCAAGAAA
CGGTGACGTGCCTTACACGCATGCTAATGTGAGTTTAGCGTATAAAGATTTCGGGTACAAACCGACGACG
GATCTCGCGGCGGGGCTGAGGAAGTTCGTCAAGTGGTACGTTGGTTATTATGGGATTCAGCCGAGGGTAA
AAAAGGAAACTTCTCACGCCGAAGATTCCGCTTAATAATTTTCTCTCTACCACCATCTCTCTCATCATCA
CATGCTTGTTTATTTTTCTTAC
>gi|3450439|gb|AI100478.1|AI100478 34853 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90G12XP 3', mRNA sequence
TTACCCCTCGCCCAGTTCAANTCCCCAGACTGGTTTCTTNACCAGCCAAAAGGATTACCAAGGATGGGAA
ATACTCCCCAAGTTGTTTTCCCAATGCTCTTGACATGAAGTTGAGAGATGATCTTGAGCGTCTCAAGAAG
NTCAGAAACCATCGTGGTCTGAGGCACTACTGGGGTCTCCGTGTACGTGGACAGCACACCAAAACCACCG
GACGCCGTGGAAAGACTGTTGGTGTTTCCAAGAAGCGTTAAAAAGAGTTTGAGCTTGGTTCAATGGCTTT
GTTTTGTTTTTTGTATTGTTGTNTTTTGCAGAAGAGATAGTTTAAGAGATGTTGTTTCATCAAAAGACGG
TCTTAGCTTTTACAATATATAATTGAATCC
>gi|3450438|gb|AI100477.1|AI100477 34852 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90G10XP 3', mRNA sequence
AGTTGGGANAAGAAGTTCNCCCNGCCATACCCCGNGGTTGGACNGCCTATACTGCTGCCACTGTCGATGG
AAAGAATGGCCCCCCTCATGCATGGGCGGAAAGCTTCCGACCAACGAGCGAACTGATGATCTCTACTTCT
ATGCGGTCAATTCAGCTTAATGCGTGTCAAGATTTGTGTTGTGTGTGTGGCNCGTTAATATTTATTACTA
TCCAATAAGGAGCCCTAATGGTTTGCTGTATTATTACAAATTATCTGTGTGTGGGACTCGTCGAGCTTTT
TTACTCTAATGAGGCCTACTCATGGTTGTGTGAGTGGTTCCTCAAGTATCATTGTCCAATAAGGAGCCAA
TTTATTTATGGCTGGCTGTTTTATTACAAATTATGTGTATGTGTTAATAATTAAAGATTGAATTATCTAC
>gi|3450437|gb|AI100476.1|AI100476 34851 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90F8XP 3', mRNA sequence
AAGGAGATTGGATGCNACCAGGGACCATCATGNCCCCGGTCCCTGTGTGAGATTTGCCNCCAACAGTGAG
TCTTATGCTTCCAGGGTCTGAAGATGGTACCAATCAGAATTTGGCAAACTGGACCGGTGAATCCCTGAAG
AGATCCAGCGAGTCAAAGCCGAAGCAGAGTGTGGATGAGGTTGCTCGTAAGATTGAAGGCTTTCACATTA
ACAAGGAAGGAAAAACCGCAGAGAAACCATCTGATGCTTAAACCAAGAAAAGAACCAAGAAAAATGGCTG
CTTCTCTTTGTCTTCTTACTGTGTTTTTACTTCCAGACTGAATATACGGAAATTCAAAACAAGTGTTTGA
AAAACAGTCGTTGTCAATCTTCATTCGAGTCAAGTTTATGGATGTGGCTGAAAATTTACG
>gi|3450436|gb|AI100475.1|AI100475 34850 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90F16XP 3', mRNA sequence
ACAAATCTTCCCGGAAAGTCCCNGTTTNGTTAAGCTGGGTGAAATCTNCCTTGAGCCAGCCNGCAACAAC
AATTTGGAGGGATTATGGTAACAACAATCGTCGAATCCGATTCTCGTGGACGAGCTTCTGGATTCGAGTC
TTAGGGAGCAGTGATGCCAAGTGACGGAACTGGCCACTGAGTTGTACACAGCAAGATCCGGCAATGAGAC
CAACGATGAGAGATGCGGTGAAACTGTTGGAAGATGTGAAACATCTGGCAAGAAGCTGCTCCTCTGATTC
AGTTCGGTAATCTCGTTACTTTGTGCAGAGCAGGAGGAGGAAACTAAAGGACTGTTATCAGTGGTAACGT
AACTGGGCTTACTGGTAATATAACTGGGCCAATAATGTAAAATATGGCTTATTGAAGGCCCAAATATGAC
GGCCCTTTAATTGTAACCGTGTTTGTTTGTGAAATAAAATCTCGTTTATC
>gi|3450435|gb|AI100474.1|AI100474 34849 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90E8XP 3', mRNA sequence
GAAAAGCCTAGGTTCCCCCAGAATGCTTAGATCTATGCCNTAATAGCCCATCTAAAGACGGCCCAAGATC
CATCATCCATGGATTGTGTTTCCTAATGGTTTTGTCCTAGGTCTGATAGCTGTTTCGCTAGTTTGACTTG
AAAAAAGCTCATCGTTGAAAAAATTGTTTTAAACCGTCGGTTTAGGGACCCACTTGGATCAAATCCGGTT
TTCTGATTTGAAATTTTCGTCGGTAAATCAAAAATTGGTTTCTGTATGTGTTTTTGCCGGATTTGTTGTT
GTACTTTTGGAAAATTTTGGGCTAAAAGAATAATTTGGTGCTCTGTTTCTGTCTTTTATTCTTTCTCCAA
TTGCTAGCTAATATTCGGAATTCTGTTGCTGTGAGCTTAGTTAAACAAGAACAAAATGAAATGAAAATAT
GTTTATACT
>gi|3450434|gb|AI100473.1|AI100473 34848 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90E3XP 3', mRNA sequence
TGAAGCTGCTCCAGTTCCTTGTAAACCGTGTCCTGCCCTTTTTAAGACTCAAGAAGGNTGATGGTGGAGA
TGATAGGCCCCAGCAGCAGCAATTCATCTCAGGGAAATGAAAAACAAGATTAGATGCGAACAGTAGATCA
GGTACTGATCTCGACGTGGTGATAGGCGAAGCAAGAAAGGATACAAACTAAGGATATCAAAGTAAAATAT
ACTATAGCCATGCTGGTGGAATAGGAAAACAAAGTTCTTGAAGCTTAACAGAACTAAGAAATCTCTCTGA
GTTTTGAGTAATCTCCTGCATTTTCCGGTTTTTGCATTGTAATGTGTAACAGTGTATTTTACAATTATAC
GTTTAAATGAATTTGGGAATCACAAGT
>gi|3450433|gb|AI100472.1|AI100472 34847 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90E2XP 3', mRNA sequence
TGGACGGGTACTGGNCAAATGNTGGAANCTTCCATTTGNTCGGATGAACCGACNCCGCTCAAGTGTTGAA
AGGAAGTTGAAGAATGCAAGAAGGNGTACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCG
TCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACTGATGCTTAAATCCTTTTCTGG
AATATTCAATGTTGACTATCCGGAACCCAATTTTGTATGGTCAATGTAAATTTAAGTAATTATTTTGCCA
AAGTGAAAAAACTGAAGGTTTGTTTTTCTATCGTTTCCTCTATAAAAATCTCTATTCATATC
>gi|3450432|gb|AI100471.1|AI100471 34846 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90E16XP 3', mRNA sequence
GAAAGATNCCGTGGAGATACCCATCNTCAGGNGCNCGAGGAAATGNTTCCAAGGAGGATAGATTTGGAAC
CAGGAGATCTTGAGGGATACCGAGTACAACCTGGAGCCAGTCTGTTGATGCTCTTTGTGGGAGTTAGCCG
AGTGGGATCCCAATCCTAGAGGAGCTTCCAGGAGATGGGCTTCTGTGATGATGTGACGAACAAGAGACTG
CTGAAGAAGAACAATGGAAGCATCAAAGGCGTGGTAATGGATCTCCTCACAGGGGAGAAGGAGGCTTGAT
GAGCTCTTTGGTTTCTGGCAACTCTTCTCTATCTCTCTTATCTATCAGGAATAATTATGTTTTATAAATA
AAACCTGATCTCTTAGTTTGGTTTCGTGCTGCGTCACATGGTCTGTTCCTTTGCTTTGTGTTGGGATGAT
GTTACTATGTTAACTCTATCTAAGACATGGATGGTTTCTTTCTT
>gi|3450431|gb|AI100470.1|AI100470 34845 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90D8XP 3', mRNA sequence
CTCCCCCTTCATATGACCACCTGGCAGCAGCCAGCAGTTAGCAGTAGTGGTAGTAGCCTGATGAAAGGGT
GTTTGCTATTCTTGTTTTGATTCATTTGTAGAAGATGTAGTTAAGATGATTCTAGACACAAGACAACCCC
ATTGGTTGAGTCTAGGGCTCCACTAAACCCACTTGCTTCAATTGTCTAGATTTGTTAGAAAATTCAATTT
CTTTTGTTAAGATCCTCAATCATTACTTTTAGCATTGTACATGATGATACAAGTGCGATTAATTTTCATT
AAAAAAGAAGTTTAACTTTT
>gi|3450430|gb|AI100469.1|AI100469 34844 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90D5XP 3', mRNA sequence
TAATGTGTNCCCNAAGCTCTTTGGGGGAAGCGTNGAAGGACCCATTGAACGACTCGGTGGTTCCCTGGAT
GGGTACCAAGAATTACCCTCGACCTGTGCTTAAGCCAGCAACTTCGTACCGCTAGGCTCTGAAGAGTTTT
CTTTGCTTGATACTCGATATGGTTAATCACATTTGACTTGCTTCGTCCTTCTTCTTCGTCTTCTTCGTCA
TCTCGCTTTGAATAATTTCGCAGTTTAAAAACTGGCGATGCCCTTATTTATATGTAGCAATGTAATAGTT
AATGTACGATCGTCATATGGCGGAATTTTAGTACTATTTTTCGTTTTCAATGCAACATTAATACAATTGA
TCGTTTCTACTCTGAGAAGGATATGTGGGATATTTGTAATCTTCGTATATATTGACATTTTCTCTATTGA
TTTCGTT
>gi|3450429|gb|AI100468.1|AI100468 34843 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90C21XP 3', mRNA sequence
GAAGTGTTGCCTTTCTGCAAGNGAAAGGGCCTTACCGCCGCCGTTNGAACCNGTGAAGANCGATGAGCTT
TACCATTGCCGTTTGAGAGGCTTCGCAAGAACCGATGTTCGTTACAGATTTGTGGTTGATGTTGCAGGAA
GTAATCTGGTGGAGGAGGCTGCAACAACTACAAACTAAAGAGGGCAGGGCACATTGATACATGAACGAAA
AATTGTAACGGGCTTGTTTGTCCAACGAATGTTTTGTTGTTGTCTTTTTCAAATGGTTCAAACACGAATG
CTTTGGCTTTATTTTTTTCTAATCAATGTGGATTTTCTGTTTACGTGTGTTTGTCACAAGAAAATCATTA
TGATAAGAATTTTCTTC
>gi|3450428|gb|AI100467.1|AI100467 34842 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90B7XP 3', mRNA sequence
TGANGGATGGAGTACCCTATCCCGAAGAATTCGCGTTTGTGCGNCCGGGCAAAGNGNACGACNTACTAGG
CCTTTGTAAGGNAGATATACGAGCTTACGTGAAATTCGTCATATCCATACACGTTTGAGTATNTCTTGGG
AAGACTTGCAAGGTTACAAACAATGAGAGAGGATATATGTAGTAACAATCTAGTTTGACGTGATCTCAGC
TCGAGGTCTAAATTTTTATGTAATTCGAATTTGAAGTTCCAGTTTTTCTTTATATGCTTTTGTCATTCAT
GTTCTTTTAATTTTCTTTCCTTTTTCT
>gi|3450427|gb|AI100466.1|AI100466 34841 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89P9XP 3', mRNA sequence
GCAAGCNGCGGCAAGNCATCNTTGTATTGTTGAAGGTTGTTCTTTCGTTATGGNTCTTTATTTGTTNCAT
TTCTAAATCTCTGAACTCATTTTATTTTTTATTGAGCTTTTTTTGTGAAGCAAAANTCTTCTTTTTAGTT
TGGTTTTTGTCCTTTTTGATTTCGCTCGGTCTATCTGTAGATACAACTTTTGCATCTTGATGTTNTGGTA
ATGTAAAGTTTTTCAGTT
>gi|3450426|gb|AI100465.1|AI100465 34840 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89O24XP 3', mRNA sequence
TGAGCATGGNCGAATCCNGAAATGCAGGAGTGATTCATTACCAATGGAACCATGAACCCGTGGCTAGCCA
TTGCCGATGAACCAATACAAGTCTCTCTGGACTAAATATGTTGATAACGAAATGGAGTTTGTGCAGATGT
GCAATTTTGGTCTCTAAAGAGAGAACGATGAAAACAAACAAACCGGAAAGAGGAAAAAATAGGGAGAAGA
GGTAACCTCGGATCGATGTGTTTCTGTCTTTCTCGGCATTCTTTAACTGATGATACGTTTATCTTTATAT
AGGGTTAC
>gi|3450425|gb|AI100464.1|AI100464 34839 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89N8XP 3', mRNA sequence
GTTATGAAAGNGGTAACCGTCGTAGTGTGATCTCCCGNGTAAAAAAACCCCCTTACAAGGGCGAGAATCT
CAGAGCAGGATGTGGTGAAAACAAAGCAGGTTGGAGATGAGGACCCTAGCAAGGGCAAGCACTGCATATC
TTTCTTTACTCCCTTCAGAAAGCCCCGTTACTAGTTCTTCTGATCATCAACAGTTACNCGATTCAAGGCA
TTATTTTCTGGCCTGCCTTGTACAGTTTCTTTTTTGCTTGACCTAGTTTTTGACCTTAGAGACTGTTTTT
CTCCTTTTAGTTACTCTTTGATTCCTTTCCACTTAGAAATTNGAAACGCTCTATTACGTTTTCCTCTTTT
TTTTACCTTCATAAGAAAGGAAGTTTAATAGAGTTGCATATTCATTAGATTNTGCNCGAACCATTTAATT
>gi|3450424|gb|AI100463.1|AI100463 34838 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89N21XP 3', mRNA sequence
TTTATGGGGAAGCAGAAGCTGAAGGAGGTNCATTGTCCCATCCCACACGNTTAAAGAAGAGATTGTGGTT
GAGAAGCTGAAGAGTTTTTATCCCACCATTACAACTCCCCAAAGAAATACATTGATGCGGAAGATAGAGT
GAAGGTGAGTTCAGAGAAATTGCAGAAGTTGGGTTGGACTTACCGGCCGTTGGAGGAAACACTTGTGGAT
TCTGTTGAGAGCTACCGGAAAGCTAAGCTTGTGGACTGAAAACTTGGAAAGAAGAGCAAAATAGTGTTTT
AGCTTCATATGTTATAGTTATAGTGTTCCATTCTGCACACACACACACACTCTCTCATCGTTTACTCAAT
AATAAGAGTTGTGCATTCACCATGGATTTCTGAGTTTTTGTTATTTTCTTTTTAGATATCATTACTTTTA
TTACCAATCTACAATTTTCTTTCCATAAT
>gi|3450423|gb|AI100462.1|AI100462 34837 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89L22XP 3', mRNA sequence
CTCTGTCAAGAGAAGTNCTTAGNGGGGCTTCCTTCTTGCACCGTCTTTGTTNTCAAGGGTCGGACAATCT
CAACTCCTGCAACTAATGGACCAATTCTTGAAGGGATTCCGCGGAAAAGTGTGATGGAGATCGCAAGTGA
TCCAAGGTTATCAGGTAGTAGAGAAGGCAGTTCATGTGGATGAAGTAATGGATGCAGATGAAGTTTTTTG
CACCGGAACTGCTGTAGTAGTTGCTCCCGTGGGCACTATCACATATCAGGAAAAAAGAGTAGAGTATAAA
ACCGGGGATGAATCTGTCTGCCAGAACTGCGTTCAGTCCTCGTAGGTATCCAGACAGGATTGATTGAAGA
TAACAAGGGATGGGTCACAGATATCAACTGAAGAATAACAATCTTCAATATTTTGCCACAAAGGAGATTA
CTCTGCATTTTAAGCTGTGTATACACGACAATGAAGAACACTATAAACATATATATGAGATAGAAACAG
>gi|3450422|gb|AI100461.1|AI100461 34836 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89K24XP 3', mRNA sequence
CACCCGGTTAATGTGCCTGGATGAATGGAAGGNTGAAGAGGAGTTCCTCCATTGGCCAAGGANTTAGAGG
TGGGAGANTGGGAAGAGGAAGAGGTTCCAGGCCNTTCTGGAAGACGCTTTCCAGTCCAACAAAACCAACA
AGGTGGTCGAGGTGGTCGAGGCGGGGTCCGTGGTAGAGGCAGAGGTGCTGGTGGAGGCAGAGGGAATAAA
AGTGGTGGCCGAGGTGGAAAGAAGCCGGTGGAGAAGTCTGCTGCGGATCTCGACAAAGATCTCGAAAGCT
ATCATGCTGAAGCTATGAACATCTCTTAAAGCAAGACTTCGCATCTTGTCATGTACTTTTGTGTTCTTTA
TTCGTAGTCTCTGACTAAATATGTGCCAAAGTCTGGTTTGGTTTAATTACGTTTAGGATGGCTCTACTCT
GCTTTCGTTTTCCTCTTTTCTTGTTTCACACTTTCACAGTCACTTTTGGTTATTGAAGTTAAAAGAGATT
TAGCTGT
>gi|3450421|gb|AI100460.1|AI100460 34835 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89K19XP 3', mRNA sequence
CCGTTAGTNGCACTCCTCCAAGTTCCAGAAGGNNCCCAAGCTTTGGCCGGAGGAGTTACAGCCCTCGTGC
AANATCTCCCCCTCCTCCAAGGCGCCGCAGTCCTTCTCCTCCTCCTGCCCGTGGCCGCAGCTNCAGTNGA
TCNCCACCTCCATACAGAGCNCNTGAGGAAGTGCCATATGCTAATGGAAATGGACTGAAAGAAAGNCNCA
GAAGCAGGAGCTGAGTGAGTGATTTTGCAAGAAAACGAGTGTGTGGGAGGATACTTTGGAAGAGAAGAAG
AGAGGGACTAAGGGAAGTTACTATCATCTATGAATTTCAGTAAGAGAACATGTTTTAGGTCTGCTGGGTT
GGATAAAGCTTGCTACTTTTGCTTTTGGATATGAAACGTACGTAGTTGTGTATCTACCAATAGGTAAAAG
AACACTTGATTCGT
>gi|3450420|gb|AI100459.1|AI100459 34834 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89J22XP 3', mRNA sequence
ACTGGGATGGGATATGGATGCTGTCCAATGGTCTGGGAAAACCNGCCAGCAGAATTCCGATGCTNTATTC
CGCCAAGTGAAACCATGGGGCACCCCTTCTGAACCCGCTTGTNTAGCCACCGGGAACNTGGGAGATGGAA
CTTGATGTATAAAAGTTACAGATGCAATGCCTATGNAGGATGCAAAGCTGATGAAAGTGTTTCCTGAGGT
AGTGAGATCTCTGTATGAACTGGATGTGCTTGCGGAAGACACCATTCTGCACTGGTATCGCAAAGGGACC
AACCCTAAGGGCAGGCAAACGTTTGTGAAGGGATTGGAACCGTTTGTGAATTGGCTCGAAGAGGCCGAAG
AAGAGGAGTGAGTGAGACGCTCTGCTTCTTGTTTTCTCTTTTTACTCTCTTCTAATAAAAGAAAGACAAT
ATTTTACTTCTCTTAACGCAAAATTCAGATGCTCTACATTGTTGGTGACTTGGTGTGATCTCTTTTTTGA
ATGAATAAGTACTTCTTTAGTTG
>gi|3450419|gb|AI100458.1|AI100458 34833 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89I22XP 3', mRNA sequence
ACGNTTTTCCACGGTNTCGNTTGTTGGTGGAACGTTCGCAGGNNGAGAACCGTTTTAAGCTTTCTTTTAT
GTCAGAAGGTAAAGGAGCGTTCAANACAGGGCATTTTAGGTNTGTTGCTGATTCGNATCGAACGAGGCTA
ACGTTTTATAGTGCNTNTTATCATACAAAGCTTCATGACTTCGGCCATCTTTNTGGGCCTGGTCTTGATA
GCGTTGTTGTTACCCTGGCCCNTTAACAATTTGTGGCTTTTAATTCTTATTAGACTGAATATTCGAAACA
CTATACTCTATTCGTAACGAATTTGTGGTTGCACT
>gi|3450418|gb|AI100457.1|AI100457 34832 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89I19XP 3', mRNA sequence
GGGATTTTTTCCCTATTAAAAGCNCCCTGNTNGCGCCCGCGGTGAACTTGNNGATTACCTATGTGGACGA
GGAACTACGGTTATCNAAGCGNTGACAAAGGGAACTTGTTTATATTGAAGATGTTTGATCCCNCTTATCG
AATCCCTCTTTGATCTACCAAACAAATGGTACCGAGCCATCCATCATACATACTTGCTACAACTTGCTAT
GTCTCTCTTCATCATGTATGTAATCTAACATAAGAAAAATTAATAAGNGGGAAAAAATGAGACGAGCTTC
TGTCATTGTTTCAACTTGTTCAAATCAAAGATTCTGAATCTTGATTTGGTTGAGCNGTTNGTTCCAATCC
TAAACTATGTGATGCTCAAGCNGTACAACAAGAAGACCTTGAAGCTCCTCAAAAATGCTTNGATNATTTT
CTCTCT
>gi|3450417|gb|AI100456.1|AI100456 34831 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89H14XP 3', mRNA sequence
CATTGCCCATGGGGNNCCCTCTACAAAGCCAGGGGGACTAAGTTTNCCCAAGGATGGTATGAGTCCCCAC
TCGAGGACNATTATAGCGAAGGAGATGTATGGTGTGTTTGAGCTACTCAGAACTCGGGATTTCGTTCTCG
AAGTCACCGCCTTTCGTGTCAATGAGTATGTGTGCCCAAAAAAGATTTCCCTTTCATCAGCGATCTTGCA
GGTAGCTTTCCAAAGTTAAAATTTTATGTAGGGGTCTCTTAACCATTCTCTCTCTTGCATTGGTTGTCTC
TGTTCTAGTAGTGTTTTGAGTGAAATTTCAGGTTCCTATGTTTGGATGTGGATAAGTATTTGACGATTAT
AATAACCTCTGAGTGGGAAACTCTTTGTTTGAGTGGTAGCTAGGTTCAAAAGTAGAGTTGTATATACTTT
TATCTTCATCAGGATAATTATGTTTATTTGAATTGTTGATTATTATGGGTTTGTGTGGGTGAATCCAT
>gi|3450416|gb|AI100455.1|AI100455 34830 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89H13XP 3', mRNA sequence
ATCCTCCGCCGCATATGATGCCCCCNCCTTCTTCCTCGGAGTTCNAAGTGCCTTTTNCCGGTGAACCNCA
TGTCGTCCACCAAAACGCCGTTGGGTACTTTCATGGNTGGAAGGGGACTTTACGGAGNTGGCATGGAGTC
TATGGCCGGAGAAGTAAAGACTCATGGTGGTTCTTTGCCGGAGATGAGGAGGTTCNCCGGAGATAGTGAT
CGGAGTAGCGGAATTAAGTTAGAGAATGGTATTGGGCTGGACCTCCATTTAAGCCTTGGGCCATGAATGA
TTATAATTTTGGCCCAGTAAAGATCTGTAAAATACTACTAGGATTTCATTTTTATAGAGTATGTTTTTTT
CCTTAATTTCGGTTGAAATTGGTGAATATTTTTATCTCTTACTTACCAAATCTCATATTTCTATGTATGC
GTTTGCTTTCACTTTTTTTTTTTATATAATTCTTCTTGT
>gi|3450415|gb|AI100454.1|AI100454 34829 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89F7XP 3', mRNA sequence
CAGGTTGCAAACNTCTCCTNTCCCGTTTTTTGTCCCCCACTCGATTAGGGGNTTCCCGNTAGGTGNCNTC
NAGGAACNTCCATGGTTCCTAAAGAACCTGCCAAGGGAACTTACAGAAATAGCTCAAGCTGCATACTTCA
GGAAAGAGAACCCGACATTCTCACTCCAAAGCGTCGAAGAGATAATGAAGATTGTGGAAGAGGCAAAAAC
TCCAGCTCGTGTTTCTCGGTCGATTGGAGCATTTGGGTGGGGAGGAGGAGAAGATGCCGAGGGCAAGGAG
GAAGATGCAGAGGAAGAAGTTGAGGAAGTAGAAGAAGAAGAAGACGAAGAAGATGAGTATGATAAGACGG
TGAAGCAA
>gi|3450414|gb|AI100453.1|AI100453 34828 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89E5XP 3', mRNA sequence
AGCCGGTTTTTGAGGGNCCNAATGATTGTGGAACCNTTCGCTGGACNAGGCCAAGGTCATGGTGGACTAC
GNTTCTAAAGGAAAAGGCGGGTTTAGACGTGGGAGGCTTGTGTTCAAGGCAGTNTCGGCCAGGACACGTG
TCACTTTCTTGNGCACGTTTTACCACATGAAAAGCGATCACTCTGGCTCGCTATGTGGTCCGGTGATCGA
TGACGTTAGGCTGGTAGCGGTTGGGAAACTCCGAGGATGAAAGTTGGGGTCGTTGACTCATTCGGTTGAA
TATACTACATTAATGGATAATTGTAATTCATGTTACATAATAAAAATGTAATTTACGAACTAGTCCCACA
AAATTTATTAACTAGTTAATCACCGTTTCAACATATATTATATATAACGGAGTTTCATTTTTT
>gi|3450413|gb|AI100452.1|AI100452 34827 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89E10XP 3', mRNA sequence
TCTTTNGAACCCGAAGATTCTTAGCTTTTGGAAAAGTCCAGCTTTGTTTCCGGGGCCGACGCGATNCCAA
TCCAAAGTTTCTGCGGGAAAAATCGGAAATTTCTCTCTTGGTTCGAATTCAAAAGTTNGTGAGACTTGTG
GAGCCAAAGGAGCAATTGAATGTCCCGGTTGCAAGGGAACAGGTAAAAATAAGAAGAACGGAAATATGTT
TGAGAGGTGGAAATGTTTTGATTGTCAAGGATTTGGTATGAAGAGTTGTCCTAAATGTGGCAAGGGAGGC
TTGACGCCTGAACAGAGAGGGGAACGATAGACTTATACTATTTGTTTTTCCTACATAAGTTAATTTTGTG
ATACAAACATGTCTCTATTCCTATAACATTTCAGTCGTATAATTTGCATGTAAAAATAAAAATCATTAAT
>gi|3450412|gb|AI100451.1|AI100451 34826 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89B5XP 3', mRNA sequence
GAGTTTTGGGCCTACCGTTTACTTTAACCATCCNCTGTTTGGTGGGCTTCTTNGGGNGGCTGAAGAAGAA
TTTGGGTTTTCNCNAGAAGGTGGAATCNCTNTCCCTTGNCCTTACTCAGATTTCAAACGGGTCCAAACCC
GAATTGAATCCGGGTCGGGTTTCTGTAAATTTCCCTGGAGCCNGCCGGTGGCAATAACGNCGGTGGAAGA
AGATGATGATGATGAAAAAGTTCTTTAACTCTTTTTTACTATTTTCTNCCTTTTCNCTTTTGTTACTATT
TTTNCCCTTTTGTTAGATATGTACATATTCTGTATGTGAAAAGTGAGGTTTGAATTTAGGCGATAATGTN
AATAA
>gi|3450411|gb|AI100450.1|AI100450 34825 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89B3XP 3', mRNA sequence
CCTTCTCAGNCCGGTGGGGCCAGAAATCCCCTCCNCCATCCGNTGCCGGTGGTCAAGGNTNATTACTANC
CTCCGCCGTATTCCAGGAAACTATCCTTACGCCGCCCTCCGCCGAATCCCGANCGTCCCTTATTTCCCGT
TTTACTATCATACTCCACCACCAGGTTCTGGCTCAGATCGGTTTATGAGTTCTTACTCTATTATTTTTGC
TCTTTTTGCTGTCTTTCTCTGTTTAGTGTGACGGAAAATAGTCGGAAATTCGCCGGGAAAATGACGAAGA
AAAAGTCGAAATAATGTGGCAGATCCGTAGATCTATAAATCTTTAGATTTCTTTGATCATGGAAACTAAA
TGATGTTGGATCTTTTACTTTCTTCGATCTGTTTTAACTTTTTCTTTTGTTGTTGACAATTTGTATTTAA
TTGTTCTTGATTATTAATATATTAATTACTCGT
>gi|3450410|gb|AI100449.1|AI100449 34824 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89B11XP 3', mRNA sequence
CCGGTTTTTTGCCAAACCCCGTTCCCTAGACAACNTGAGAGATGTTCTGNCCTGATCTTCTCGAGCCCCG
GNTACTGTACGAGGCCATGTAAAGGCGATGGATGCCCCATGCCCCAGAGGAGTAATTCCGCTCCCGCCTT
CTTCTCCCGTAAAACATCGGAAGCTGATGTTCTCTGGTTTAATTGTGTACATATCAGAGATTGTCGGAGC
GTTTTGGATGATATCTTAAAACAGAAAGGGAATAACAAAATAGAAACTCTAAACCGGTATGTGTCCGTGG
CGATTTCGGTTATAGAGGAACAAGATGGTGGTGGTATAATCATACCATTTCAGATTACATGTTTGACTAA
TGTTGTATCCTTATATATGTAGTTACATTCTTATAAGAATTTGGATCGAGTTATGGATGCTTGTT
>gi|3450409|gb|AI100448.1|AI100448 34823 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89B10XP 3', mRNA sequence
AAGGCTACCGAATNCCCAGAAAATGGCCCATTGGGGAGAGCCCGAGGACTTGCTTTACCCCGNTGGCAGC
TTCGACCCATTGGGTTTGGCTCCCGCCCCAGAGGCATTCGCTGAGTTGAAGGTGAAGGAGCTCAAGAACG
GAAGATTGGCTATGTTCTCTATGTTTGGATTCTTCGTTCAAGCCATCGTCACTGGTAAGGGACCGATAGA
GANCCTTGCTGACCATTTGGCCGATCCAGTTAACAACAACGCATGGGCCTTCGCCACCAACTTTGTTCCC
GGAAAGTGAGCCAAGTTTTATCTGTATTTTGCTTCAGTCTTTGCTTCGTGAGTGTGAGAGGAGAAAGAGA
GCTTGTTTAGATGTAAAATTTGCAAGACTTTGTATTTTTTTTCATTAATCAAATAACTCGTTTTTCTCTC
>gi|3450408|gb|AI100447.1|AI100447 34822 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88P8XP 3', mRNA sequence
GATCCTGGACCAATTTGCTNGCCAACGNCAGNGAGGANCAAAGNGATTTGGGCCTTGTGATGAAGCAATA
TGTGCAGCCATAAGGAAAAATCCCATGAGCCATAGGAGGAGGCGGGGCATTTTTCTTGGGNTTCAGCCCA
ATCGCCAGTTGAATTCATAAACGCCCTGATCGAATCTCAGAGCAAGGATCTAAAGGTCGTTGCGGGAGAA
GCCAGTCGAAATGCTGAGAGAGAACGTCGATCAGACTTCTTCAACCAACCTTGGGTCGAAGATGCAGTTA
TACGTTACTTGAACCGGAGGCCAGCAGCTGGGAACGATGGGCCAGGGAGTTGGTGAGTTTCTTGACGATA
CAAGTCTCTTCATCTGTTTGAGCATTTTTAGTAGAAGATATTGTTGAGATTAGTCTGGTTTAAAAGTGAA
CTAGTGTATCTGTAATCTTGTGTATGTTGAAACATTACTACTTTATATAATTAGCTTTGTTTTGT
>gi|3450407|gb|AI100446.1|AI100446 34821 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88P16XP 3', mRNA sequence
AAGCTTTAGTTTATTGGNCCCAAGCAAAGCCNGAAGGGGCTAACATGTAATGTTNCCTTCTGTGCCAGGG
NTCCAATAGCAAGTGGATTGTCCATAGACTNCGGAAAGTTTGTAGTCCATGCACTTGATGAGAAAGCCCA
GAGGTTATTTCAATTTGGAAAGCCTTTGGTCTGCTGAATCCTCTGGTACTGATACTTCAGATCAGGATCT
CCAAAACGTTTTTGTAAAGGTCCGACCAAAGAACAATTCGAAAAGGAAACCGGCTAAAGTGAGTTCTTGA
TCCTGTCCGATGGATACAATTTCTCATAAACTTCTCGAGTCTAGACGAGTTAAGAATAGGAGGATTTTAA
AGCCTATTAAGTATTTATCTCCTTAATATTTTTTTTTGGTAAGTTTTATCTCCTTAATATTTGTAGTCAT
CTATCTATTTTTTCCTTAATATCTTTGCTT
>gi|3450406|gb|AI100445.1|AI100445 34820 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88O4XP 3', mRNA sequence
CGTATGAGGGTCTTAAGAANCNCGAGGTCGAACCCATCAAGGATTNCGTCGAGGAGATGAACCGATACCG
TTGNCCGTTTGACCAAATCTGTTCAAGAACTGAAGTTGTGTGGGAGTGCCCAAAGATCCAAGACCAGTTT
GCGTACCACATGAGTAATGCTCAGACTTGGACTAGTGCGGCTTTGACTGACGAGAACACTTGCTCCGATG
GGTTCTCGGGTCGGGTTATGGATGGGAGGATCAAGAACTCGGTTCGGGCTAGAATCATGAACGTGGGACA
TGAAACCAGCAACGCTTTGTCCTTGATTAATGCCTTTGCTAAAACTTACTAATTTAAAACTATATTTTGT
CCTGTAAAATATATATATAGATAAATGTAATGTCTTGCTAAGAGTTTGATGTGATATATTTTTTTCGATT
TTGGTAGTTTCTTTTTGTTTTGTAACGTGGTTTATAATAGTATAATGTGTATTTTGAGCT
>gi|3450405|gb|AI100444.1|AI100444 34819 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88N23XP 3', mRNA sequence
GAAAAGTTNCGTCTGGAACAGCGNCCANCNTCAGGCGNGGAAGATGCAGGNGAGAGGATNGANGCCGAGG
TGGNTCATGAAGGAGAAAGGAAGCGAGTCTTACCGNTACAAAGGNGGTTACTGGGAAGCCCGAGAGGATG
GATCATGGGTAGACTGTCCAGACATCTTCGGCCACATCGATTCCGATCAACAAATGATAGAGTAAAACGA
AATTACCATTCACATCGATTCTTGAATCACGAAGTATTAAATTCCTCCTATCTTCCTTTCTAATTACGTT
TTCGTTT
>gi|3450404|gb|AI100443.1|AI100443 34818 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88N18XP 3', mRNA sequence
AAGAGGGTATATGGATGGAAAAAGCCAAATCCATTTTCTGTGTATCTATCCAGTAGAAGGGTTTNTCAAC
AATGCACCAATGACAAAAACTTACGCCCAAGTTCAAGCTGCGGGTATTGGATCAAGTTAGCTGGAATCAT
GTTGAGGAATCAGGTTTGAGCTGGTTTGATGCAGAACTTCGGACCAAAGTGGCTTTGCGGATTTCATGCC
TCTGGGGAAACTAAATGAACCTTATTTGGTAAAGGATAAGCTTTATGTGGGAGTTGAGTTTGAAGTCGTT
TCTACCACTTATTACTGTTAGCTTCTAGGCTGTAATAAGTCTTATTGTGAGCTAAAAATAACAAGAAATG
TTATAATGTATTGAATAAAATGTTGGAGAATGTACCTACTGAGACTTGGAGGTGGAACTACATTGACCTA
GTCTTAGCCAAAGTC
>gi|3450403|gb|AI100442.1|AI100442 34817 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88M6XP 3', mRNA sequence
GANTTCACCCCCCTTGNCCTTACCAGCTTGNTNCCAAGGGTTCTCTCTTGGCTCCGANCCCANGCAATTC
TCTGTAGCCTGTGCACTCGAGCGTTGGANCGAACTCATACAAGCCCAGAGATTACTGTAGACTTGGAAGA
CTATGGGTGCAGAGAGAGGACATTTGAGTCTCTAGGAGAAGAGAGTGGAACAGTGATGTATCAGACGTTT
GAGAAGCTTGGTAAGTACTGTGGATCGCCTAGATCTACCTTGAAGTGTGAATGGAGCAGCAACAATAGCT
GCAGCAGCGAGGACGAGAAGGACGAGGGAATCTAGCAGAATTTTTCTTCCTAATAACTATTTTCGAGCTT
TCTGTTTTTGTTCTTTCTTTTTAAAAAACTTATTAAGTTCTTATGAATAATGACTTGTGAAGTTTGAGTT
CGTCTCCTTCACAAGCAAGTTGTATTGGTGTTTTCTACTTTATGAATATGGGTTTTATAT
>gi|3450402|gb|AI100441.1|AI100441 34816 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88M20XP 3', mRNA sequence
TGGCCCCTTCTCATCCGGATAAGGCTTGGTCTGCCCCTGAATTTCCCNAGTGTCCTACTATGAGATTCTC
CAATTCTTCAGACCAAAGCTTGTAACATGGCCCAAACAGGCTTTTGAGGAGGCCCATAGCTGAGCTTGAC
ACTCTGGGAGAGGAATCCTACAAAGACAGCACTCTCATAATGCAGTTGCTGAGGGACAATTTAACCCTTT
GGACCTCCGATATGCAGGAGCAGATGGACGAGGCCTGAGGATCTAGATGAAGGGGGGGAGGGTTGTTACG
CGATGTTTCTGCCACCAAATCGATCTCAAAATCCCCATAACCTTTGCTCAAAAACTGTGAAAAAAGATTG
AAGTGTTTATGATGATTATGATTGTGCACAGCTTGATGATTTATCTACTCTACTAAACCTCTGTGCTCTT
AATATTTATTGTCTCGACTCTGCTCAAGCCTTAAAAACATCTTTCTCCTT
>gi|3450401|gb|AI100440.1|AI100440 34815 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88M1XP 3', mRNA sequence
CANGGCTGAAAACCCGATAGCGGCTTTCAANTGCAATGGTGCCCTNCTAGGNTCTTNTCCCGATAAAGGG
GGANTCCATCCAAAGACACCGGTTCGTTCCCCGTGCTATCCCGCGACATCCAAATGCATTAACCGTAGCT
ACAAGNNTTATATATATTTCTGCTCCTCACAGACATGTAAAGAATGTTTGTCTGAAACTTCTGGTTCTTC
TGTTTTCCCGTATGTAATGCTAGAAGCTTGATGATGCTTCTGTTGCCTTTTGCTTTTGGGTAAATCTCTT
AGGGAGAGTTTTTTCGATTTGGGTTCCTACGTTTAGTAGTTTACACAGAGCAGAAGAGTAAAACACTGAG
AGAGGCTTTTGAAGATTGTCTCTGTTTTTTAGTTATTTATACTCTTACCCCTGAAGTTATTAGAAACTTG
CTTTGGTGCTT
>gi|3450400|gb|AI100439.1|AI100439 34814 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88M13XP 3', mRNA sequence
CCGTTCGTTCCCCAATGCCTTACCNGNGGNGGATTGGATTACTTACTGCTGCAAACCTATTCCTACTCCC
ATTTTTGGAAAGTAAATGAATATGTTTTTGTTTTTCATCTTCTCCTAAGAGAGAGAGAGAGGGAAGAGGA
AGGAGGAAGATGAAGATCAGTTACCGTCGCCGGTCACCGTTTAACTGTTTTATTCAGGTTAGTGTTTGTA
TATAAAGATGCAGTATTTAAAAGAAGTGTCGAATCTATGTATTCGTTTGGTGTTTTTCTGGGTCGGGCGG
ATCTTTATTACTGTTTCATATATAACTAAGAGGGAAGATTAGAAGAAGAAGAAGCTGTAAAATTTTCTTG
GGAAGAAAACTCTGGTTTCTATCTTCTCGTTGTAATATAGATAATCAACTTGGATTTATCTTCTTTCAGA
TT
>gi|3450399|gb|AI100438.1|AI100438 34813 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L7XP 3', mRNA sequence
CTGTTATGGTGNTACCCCTCCACTCCTGGTTATGGAGGTTATCCCTCCTGCACCTGGTCCATGGTGGTTA
CCCTCCTGCTGCTATCCTGCTCATCACTCAGGACACGCAGGAGGAATTGGGGNTATGATTGCAGGTGCTG
CAGCTGCCTATGGAGCTCACCACGTAGCTCATAGCTCTCACGGNCCTTACGGACATGCTGCATATGGTCA
CGGTTTTGGCCATGGTCATGGCTATGGCTATGGTCATGGTCATGGTAAGTTCAAGCATGGGAAGCACGGG
AAGTTCAAGCATGGGAAGCATGGAATGTTTGGAGGAGGCAAGTTCAAGAAGTGGAAGTGATCTAGTTAAT
ACCTTTTGTGAATCTGTCTGGACTGACCAATGTTTCAAATAAGCCCTAAACATTATATAAGTTGACTTTC
GTCGGTT
>gi|3450398|gb|AI100437.1|AI100437 34812 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L4XP 3', mRNA sequence
TTCCCTAGNGCCGTAGATTTCCNGCGGTAATCTAGCGTTCCAGANTGAATGGTCCNGTGGAGGATTCATG
GGAAGAATCTGATGGTGGATGTTGGTGGGTGGAGTCCGATGCTCGGGGATTTTTGACNGCGGGTCAAGTC
GAGTCAACCCGATTGTAATGGGTGGGCTACAATTNGAAGGCTTTATATTGGACTTTGATTTGGGTAACTC
AATGATGGGCTTTGGACAAAGAACACGCTCTGAANTCACTTCGTTGTAATACAGAAACCTTTGTAATTGT
AACCTTCTAATTATCTGGTAGATATCCTCAATTTTGATCTCTTTTGNGTGTACTCTTTTCTTACAATNCC
TGC
>gi|3450397|gb|AI100436.1|AI100436 34811 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L24XP 3', mRNA sequence
TCAAAATTGCCCCCATGCGTCAAGAGGTTCAAGCCGACAACCCTCGGAATTACGGCGCCTGGACTTGAGG
GACCGCGTCGGACCCTCCGGCAGAAAGGGCAAGGGATNCGGTGTTTACAAGTACGTCGACAAGTATGGAG
CTAACGTCGATGGATACAGTCCTATTTACAACGAGAACGAGTGGTCAGCGAGTGGTGACGTGTACAAGGG
AGGAGTCACCGGATTGGCAATTTGGGCGGTAACTCTCGCCGGAATTCTTGCCGGAGGTGCTCTTCTTGTG
TACAACACAAGTGCTTTGGCTCAGTAAATCTTAAAGTTGTTAGCGCATGTGTAATCATGTTTCTATAAAT
GTTTCTGTGTTGTTCTCTTTCTCTCTAATGTTGTAAAACTCAGACATACTTTGAATTTATAAGACTTCTA
GTGTTTGTAT
>gi|3450396|gb|AI100435.1|AI100435 34810 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L23XP 3', mRNA sequence
TGCCTTGTGCGTTGAATGGCTAGGGAGTTGCTCCTTCNCCGCACAGTGGTTCCTTGTGTTGATTCGAGTT
GGACCNCGGATTTGTGTCCCGTGGGCACGGAACCACTCCCCGGTACTATGATGGNCGGTACTGGACAATG
TGGAAGCTTCCATTGTTCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGG
AGTACCCTGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCAT
TGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATCCCCTTTCTGGAATATTCAGCGTTGATTATTCTGG
AACCCATTTCTATGTGGTCAATGCAAATTTAAGAAATTATTTGCCGACTTAAAAGTTGAGGAACTATTGT
TTGAAAGTGAAAATGTTATTCCTATCAGTTTCTCTATAATTATAGTTATCATTTCATTTC
>gi|3450395|gb|AI100434.1|AI100434 34809 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L22XP 3', mRNA sequence
CGGTGNCACTTCGACCCCATGGNTTTGGCTACCGACCCAGAGGCATTCGCTGAGTTGAAGGTGAAGGGAG
CTCAAGAACGGAAGATTGGCTATGTTCTCTATGTTTTGGATTCTTCGTTCAAGCCATCGTCACTGGTAAG
GGACCGATAGAGAACCTTGCTGACCATTTGGCCGATCCAGTTAACAACAACGCATGGGCCTTCGCCACCA
ACTTTGTTCCCGGAAAGTGAGCCAAGTTTTATCTGTATTTTGCTTCAGTCTTTGCTTCGTGAGTGTGAGA
GGAGAAAGAGAGCTTGTTTAGATGTAAAATTTGCAAGACTTTGTATTTTTTTCATTAATCAAATAACTCG
TTTTTCTCTC
>gi|3450394|gb|AI100433.1|AI100433 34808 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L20XP 3', mRNA sequence
CTGGGNCGGTTCACATTCAAGCGGNTCCGGTGTAGCAACTTGGCTGCGTGAATCAGCCACACTGAAACTC
TTAATCCTCCATGACCACATAACAACCGCCACAGCTNCTACTACAACAATGAAATCAACAGACCAACAAC
AACGGAAACAGACGTCGTTTGCTTTACAGCCTCTTCTTTTGTAGCTTAGTGTATGATGTAAAAGTAAAAC
AATTTGTGTTGATCATTAAAGTGTATAGGACCAATGGTCCTAACAATGTTTGGCTCTGTGCTAATATTTG
TAACAAAGCAACTCGATTGATTATGTGAAAATCGTTTTGTCTT
>gi|3450393|gb|AI100432.1|AI100432 34807 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L19XP 3', mRNA sequence
CTGGAGGTCCCTTTGNCCCTTACTGGCTCCATTTCCNGTGGGTTTGTCTCCTCGGNAAACGCTGTCNTAC
GTGCAGACACTCAACCCAGGACAGGTCATGNTTTTCCCCACAGGGGCTTGCTTCATTTCCCAGATCAACG
CGGGGAAAATCCTCTGCTTCCAGCCGTTGTCACTTTCAACAGCGCTAATCCGGGTCTGCAGATTCTCGAC
TTCGCACTCTTTGCTAACAGTCTTCCCACTGAACTCGTCGTGGGTACTACTTTCCTTGACGCCACTACAG
TCAAGAAGCTAAAGGGTGTTCTTGGAGGAACTGGCTAAAAAAAGACTTAGGACTACTCCTTGACTAAAAC
ACCAAAACCTGTTTCTTCATCTTTTTTTCTCTTTAATTGATTCTTGTCTTCTCTGTTTTGTGTGCCTTGT
AATTCTTCAAAACCTGTCAAAATTGTTAC
>gi|3450392|gb|AI100431.1|AI100431 34806 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L18XP 3', mRNA sequence
CGTGTTTNTGTGAGCTGGCGAGATGGCAATGTGNACNCNGGGTTGTTAAGCAAAGCACGTGTTTNGAGCT
GGCGAGCTGGCAATGCAAATGGACGTTAACGGCGATCGTTATTAACGTGGTTAACGTTTACTTTCTTTNC
CTTTTTGTATAAGAGCAACATGTTATGCTCATGCTTTCATTATCGAATAATCTGGTTGTCATCTCTCTCT
AGAGACTTCTAGATTTCCCTCATCGTTTTACCGGAGCTCTCGTCGAGTCTCTTGTAGGTGAGAAGTTGAT
ATCGCGTCTCTTAACGAACGTTGTATCAAGTGTGTTAATCGGAGTACTTTGTTTTCATCTCTCTGTTCTA
TTGATTTCAAACTCTGTTTATTCATTTCTGGTTTACG
>gi|3450391|gb|AI100430.1|AI100430 34805 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L16XP 3', mRNA sequence
TAAATCNGGAACCATTTGTTTCAAGGAAATTTCCTTATGTGNGCATAGTTTTCTAAACAAACCCCCCAAA
AACNCCAAAACACAAACACACACACACACACATCTGACACCACAAACTGAAATATCAAGGTCTCATCGAT
CTTCGATTTTTCAGTGAATACAATTCTTTTTCACATTCTTTCCCTTTTGTTCTTTTCTTTCTCACTGTCT
CTTGTTTGTTTCTTCTTGTTCATTGTTTTCTTCTTCCAACCCCCACATGAACAAAAAACTCTAGCTAAAA
GGTCTTTTAGATTATTTTGGAGTTGTAATTTCATCAGCAAGTCTCACACTTTTTTTTTTTCTCTTAAAAC
ATTTGTTGATTGGTT
>gi|3450390|gb|AI100429.1|AI100429 34804 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L11XP 3', mRNA sequence
CCACGTGTNCCTCGCTAAACTTTGANCGGCGNTGGNCCCAATATCTACGNCCNCCTATGNTGGACGCTCT
ACATTTGCGCTCACGGAATCGGGGAACTATCGCGTTTGGTGCAGGCGATCAGGGTCCAGCTTGGAACAGA
GCTTGGTAAGNCCAAAAAGAAAGGTGTGTCCCGGAAAAAGTGGATATCGATCTCAGCTAGCTTGCTGACT
TATGTGGTTTGGTTGGCAAGAACTACGTTTGACATCAAGGAAACAAAAACGCACGAAATTTGCGTTTGCT
TTTTATGTTCATAAGACTTGGAAGCTTGTACAAAAAGGGGAATAACATAAACTTGTCTTTAACATTTCAT
TGTATAGGGTTTTAGATTATTCTAATTGTTCATTGGTTAAGTTTTAGGTTATGTTGTTAATAATTATCAA
ATAATTTCATTAAATC
>gi|3450389|gb|AI100428.1|AI100428 34803 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88L10XP 3', mRNA sequence
CTTTTGGGCCCCTAATCCTTTGCGGAGCCCTTCAGGCCCTCGNGAAAGGGTTCTCCCCNAAGNCCCTTTG
GANCATCNCTTAAGAATTGTGTAAAGAAGGTGTTTACTGGGGAGCTGCTGGTGGAGTGTACCATTGGAAC
AGAATACGGAATCGAACGTATCCCGTGGCCAGCAGAGATTGGAAAAACGCAATGTTAGCAGGCGCGGCGA
CAGGAGCAGTGCTCTCAGCGGTTGGTAAGAAAGGCAAAGACACTATTGTGATCGATGCCATTCTTGGTGG
CGCGCTTGCAACCGCTTCTCAGTTCGTTAACAATCATTATTTCTACTGATTCTCCATCTTCCTTTAGGGA
CCAATTTGGTTCATATGGTGTGGATTCCTTTGTTTACTCTTTAAATAATAATAAAAAACAATGTAGTGTT
TTTGAAATGAATACATTCGAGTATTGTTGACGTT
>gi|3450388|gb|AI100427.1|AI100427 34802 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88K20XP 3', mRNA sequence
TTAAAGGGATTTCNCCGGTTGAAAANCNNTTGAAAGAAGCTNTTTGATGAGTATGTGGATGCACGTGGGA
TGAGATTACTCGGGCTTNCGGTGCAGACTTATTTGNCCGGACGTTCGCTACAAACGTCATCAAAGGTTCT
GAGGCTAATGTTTATAGCTTTGTTGTTACTTTTGTTTGGTCGTGATCAAATTCGTCATACTAGGTACGAC
TGTGGCCGTCTCTAGAGATTTGATGGACATTTTGTATTTTTTAGTGTGAGGTTGTGTGCTTTAAACTTTT
TTTGTGTGTTTCTTTTTCTTATAACATCCTCCTTTCTCAATATAACAAGAGTTTAC
>gi|3450387|gb|AI100426.1|AI100426 34801 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88J13XP 3', mRNA sequence
ATGTTAAACTGNTAGGCTTCCAGNGTAACNCCACCGATAAACCGATGCACAGGACGATCCNNCTGACTCA
TGTTCTTGATGACTGCAGGGCCATTTTGAACATCTAGTANCCGGAAAGATAATGACTTTTTAATCGTCTC
GAGTTGGGAATAAAGTTAAGACAGTTCTCCCTCCATTAGCGTTTGCAGATTCCAAATCCTCAACGTAATT
ACTAACTGGACTATGCAATGATGGTGTAGACATTCTCTGAATTGGTTGCTGCTGCGTTTGCCTCACCGCC
AAGAACGAAGGATCAAACTTCCCATTAGTCGTCGGTGATCCAAATCCATTACTAGTCGGTGATCCAAACT
GTCCATTACTCGTCGGTGAACTGAATCCACCATTAGTCGGTGAACCAAAATGCGCAGCTGCGATTTGACG
GTGGAACTGAGGCGGTTGTAAATGAGGATTAANTGCTGCA
>gi|3450386|gb|AI100425.1|AI100425 34800 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88I23XP 3', mRNA sequence
CAAGTTCTTATTGCATTANACGAATGTTTGGTATCTGAAAATTCNNGGGGAGGANCGAGTAGGGACATGG
ACTCAAAGAGTTCCCTAGAGGTAAGCTTGACATTTGATACTGATGTGAGCCCAACGGCTAGGTAGATTAC
ATGAAATATTATCATGCGGTATCACATAAATTTGTTTATATGTTTCTATTTACAGAACTATCCTCAAATT
TTTATCTCTCTTCTAGGCCACCTTTGTTAATGAACTCTGAACTTTTTGTCATTGATACATGTGAATAAAA
GTTCAAAGTCTATTATT
>gi|3450385|gb|AI100424.1|AI100424 34799 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88I13XP 3', mRNA sequence
CTTGGACCCNTAACATTGTGCTCAGGCAGACCNCATTTTNAACCACCCCGGAGTTGCAAATTGTGATAGA
GATGAAGGGCCCAGTGTCTCTCACATTTNCCCTGNGGGTACATGAATCCCTTCACAAGGGCAACTCCATT
GTCAGNCACAGTGACAATCAGCTTATCGTCGGAGTTGCCAGTGGTTGTGGAGTATAAGGTTGCTGAGATG
GGTTACATTCGTTACTACTTGGCTCCTAAGATTGAAGAAGAAGAAGACACTAATCCCTAAGACCCCTTTT
ATATCCACAATTTCTCTTCATTCTAAAATGTTGAAGATTTATTGACAATGTTGGTGTTTTTTTTTGGTGA
GATTCCTTTGTATCC
>gi|3450384|gb|AI100423.1|AI100423 34798 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88H7XP 3', mRNA sequence
TCTCGACGTGGGNCCCCNGCGATTCAGCATCGGACATCCGACTAGNGCCATCAACGTNCCTTACATGTAC
AGAGTCGGATCAGGAATGGTTAAGANCCCGAGTTTTCTAAGACAGGTCTCGTCCCCACTTCAGGAAACAC
GATGAAATCATAATCGGTTGTGAGAGCGGTCAAATGTCATTTATGGCCTCAACTGATCTTCTCACTGCTG
GCTTCACGGCGATCACAGACATTGCTGGAGGATACGTCGCTTGGACAGAGAATGAGCTGCCGGTAGAAGA
GTGAAAACAA
>gi|3450383|gb|AI100422.1|AI100422 34797 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88H5XP 3', mRNA sequence
TGCTACGGAACATTTTAAGCCCANCCTTTTANCCGTTGCTGCCCACCACTATTACGGCCCATCACAAGAA
AATNCATGCAAGTGGAANCGGTGATAGTAGCAGCTGGTATGACACGTTGGTNGCAGTAGCGGTGGTAATG
CCGATAGCGTGAGCGGCAATGGAAGCATTGGTGGTGTCAGAAGCAGTCATCAACGGGGACTTTCTATTTT
TGTATCATGTCTATTTGACATAGTAGATAGGTCGAGGATTGAAGTCTGGTTAGATGTTTTATATTTTTAA
ACACTTGCAAATTTTTGTAGATTTGTTGGATTAACATTTTATTATTGATTCTTGAGAGAATTTGATAAGT
T
>gi|3450382|gb|AI100421.1|AI100421 34796 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88F5XP 3', mRNA sequence
GACATGCCTTAATCAAAGTTGNNNTGCCGGGGGCCNTTTTGACCGGTNCTTGCACAAATGCACCCACACC
GCATCGCAGCCACACCCGCATATTCCCACCATCACATGTATGGTGGGAGGACGAGTTATGGTTGGGGCAG
CAAGTCCAATGGTGCCTTTCTACACTGTCTATCCTTATCATCAATCTCAAGCCATCGGGTTTCCACAACC
TTCATTTTCGAAACCTCTTTCTTTTTCCACTCCTCCTATATCAGGCACAGTTGGAGGAGAGAGCATACAG
AAGAAGGCCATACATTGATAGGCTAGAAGCTGTTAATCAAACGATTGACTCAGCCCAAAATTATTCATTT
TATCCATCTCACTAAGCTTTATTTTTT
>gi|3450381|gb|AI100420.1|AI100420 34795 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88F24XP 3', mRNA sequence
GTAANCCAAGGTGGCCTTTGGCCATTTCGNCTGNGGCCTTAAGTGGATTAGTTGGNCCNTAAGGCCAAGT
TATAGAGATGTGTTTACGGGTAAAGATGAANGCTTTAGGTTTTGATGTAATCTTCTTCGGTTTTTCAATT
CTCTGTATTTCTCTATCTTTTTAGTTTATCAAGTTTAAGTTTTATTTGGGGTTTCTTCTTCGTTTGGGTA
TCTTTCTGTTTTTCCTTAAGGTTCTTCGTTTGTTTCCGTGTCGTCTNGGTTAAGTCAAAGTAAAGAGATG
TAATTACTGGTTAGATGAATCTTAAGGTTTCCATGTAACCGTTTGTACTACAATTCTCTGTACTTCTCTA
TCTTTAATATTATCGAATTTAAGTTT
>gi|3450380|gb|AI100419.1|AI100419 34794 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88E7XP 3', mRNA sequence
GCCCTGGTGCTCCCCCTTGCCATGCCAGGAAGTCCCACGTNTAGCTGGTGGNCAGCAAGGGTNTGTGGAA
TTCGGGAGAAGAAGGCGGATAACATTTGGTTGGCAGCAGAAGGAGTCTACCTTCCCCTTAATGAGAGCAG
CAAGTAAGGTTAAGAGTGAAAAAACTTCTCTGGAGGACTTTGAATCTTATCTCTTACTCTCTAAACTCAC
AATCAAGAAAATAGAGATATATATTTCTTAATTTTCGATTGGTAATACTTTTAGTGGCACGAATATATCT
TGTTTTGGTAGATATTCTGCATTTATCTCTTTTTTAGGTCACCCTTAAGAGACACTATCTTATTATCCTG
ATAGTAAATCCAACAATCCTCTAAAAATATCGTCTTGTCTTTCT
>gi|3450379|gb|AI100418.1|AI100418 34793 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88E3XP 3', mRNA sequence
CTAGGTTTNTTAAGNGGTTGGTTGGGGTTNTTACGGNGCCCACNTCTCACCCTCNGAGACCGCTGGCATC
TGGAACTCTTANTGGTCTCAGGCTGATTCGATCCTTGGGACAGAAACTTGCANGCCNTCTGAACGTGNGG
CCAAGCATCTAGAGNCCAATCTCCATATAAGCTCANTCTATGTGAGGTACAATCAATCTCATCGATCTAT
CATCGCTTGGTCGTTAAATCCGTCAAAAAGATAATCACATGTGTTGTTGTTTCTTGTCTATATAATAATA
ATGCTTGTAATCCCAAAAACTCATGTTTCCTTCNTTTCTACTCTCACTGTCTTTGTAATCTCTTTTTACA
ATAAATCAATGTTTCTTGAAGC
>gi|3450378|gb|AI100417.1|AI100417 34792 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88E2XP 3', mRNA sequence
ACGGGCCTTAAGNCGGGTACCCTCACGTGNGGTGGCCCCTTTCCCGTCCTCGCCCCACTCCAGGTCCCTT
CCCCGCCGGTGATGGCTCTCATGAGNCATCAGGTTTGGGACTATNCTGCGTGGGAACCGGAAGTNTTCAA
GGAAAGGAAAGGGGTTGGNCGATGAGAATATGGTGATACGTTCAGAGGACTAGAAGGTCACGTCATGGAG
CAGCTTAAAGTGTATGATCTCATATATCAGTTCAGCCAAAAGTCTCCCGATGATATCGTATGCAAGATCA
CAATGATTTGGGAGAAGCGAACCGATGATTCGCCTGAGCCTAGCAACTACATGAAGTTCCTCAAAAGCGT
TGTTGCTGACATGGACGAGCATGTTCTCAAAGCCTAAATCCCTTTCGAACCATCGTCATCACCTATCATC
ATCATCATCATCATCATCATACATCTCCCTTTGTGTGTGTACTTGTATGGGTGTTTGAATCTTTCATTTG
CGTAGTACAAAATCATTTTTAAATAAATTATGGTTTGAGT
>gi|3450377|gb|AI100416.1|AI100416 34791 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88E1XP 3', mRNA sequence
GATCTGAATTAAAAGNTTTAGNTTGTGGTGGTCTTTAACNAACTTAATTGAGAGATAACGATTCAAAGAG
AAAGATTCAAAAACAGNGTTTTTTGTTCTGTTTCTTGAAACAGAGTAAATATNGCTCTGAAACTGCTCGG
GTTCTTGGGGAGAGATGTTTCATACANTCATACTTTGTGAATGTTTACCTCATCGGTAAAAAGAGAGATG
CTTAAAATGGTCTTAAGCATAAAAGTGTGAGAAAGATCTAAATCTAAACTTTAGCTGTAACTCTGTCTCC
ATTAAAGAGAAAGGTTTTGTGGTATTAGAAAGATCTAATCTGAAGATTATCTTTGTGTTTTTCACTTTTT
>gi|3450376|gb|AI100415.1|AI100415 34790 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88E11XP 3', mRNA sequence
GGGATGGCACCTGCTCAACCTGTCCNNTAGGACCCAAAGGAAAGNGCAATTGCTACCACTTGGNTTCGNT
ACCATTTGGNAGGGGAAATNCNTCCACTTAATGTATTGAGCCAGGGAACCAAGTCAGGTTTGATTGAGGA
AAAACCGNGCATACCTCCGATCAATGAGCAGTGTGGCTCAAATACTGCACCANCCTAAGCAAAACCGAAA
GAAGAAGAGAAGTGTGATGCCCATTCCACTTTGGTGTTTTAATGAGCATTTCGGTGTTTGTCATGAAACC
AAGTTTTGAAATGGCACTTGTCTACCTAAGTGTAACAGATTCTTAATTTCAACAATTTTGTTAGATAATT
TGTATTCATTCTCACTTAGTGCTTCCGTTGTTCTATCGTTATAAACGTTTTAAGATATACGCATGTAACT
GAAAGAAGAAAAGCCATTATTGATCC
>gi|3450375|gb|AI100414.1|AI100414 34789 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88D9XP 3', mRNA sequence
GTTGATCTTCTTCCAGATCCNTTTGATTTTGNTNGATATGGAGGTTTCTTTGNCCACTNATGCTGCTGAG
TTTTGATCAAGGATTCGATGGGAAGAATGTATTACCAAGCACCTTCCGAATTTGGCTTTTGGAAAGAATG
GGTGAGATGGTTAAGAAATCAAGTGGAAACAGGAGCCCGAGATCGATTGTGGAACCAGCTAAGTATGCGG
AAAAGCCAGCGAAATGGGGAAACCAGAGGGTTGCTGCTGCTCCGAGAAACATCCACCAGCCTCGCTGAAG
AGATATGTTGTTAACTAGTCAGAGAAGTCAGAGCAGTTCGGTCTGTGTATCTTTAGCCACCACTGTACCT
TTGTAATTTTTAGTATTTGCTTCCACAACAAAAATCTGTAACTTTGTATCTTTATGATGTTCATTCTCAA
ACTTGCTATCACAAAAATGTAAAAACAT
>gi|3450374|gb|AI100413.1|AI100413 34788 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88D7XP 3', mRNA sequence
CAAGNTTGNGAAGATGCTCCCTGGCCCNGNTAACTTCTCCCGGAATNTGGCCCGACATGGGAGCTGATGG
GGTCACTNTCAAACGCTAAAGTGAAAGTCCCGGTNAAGTCCATAATCCGGCGCCCAAGATCTGACATATC
ACATTCCCGGTAGCAAGAAGTACATCCACGATGGCCGGTTTAAGAGCCATGTCCCGTTGTTGGACGAAGT
TGTGGTAATTAAAGGCGTCGGTCATTTTATCCACGAGGAAAGGCCTGACGAGATAAGTAAACACATTCAC
GACTATTTTCTTACTTTTTAGAGCTAAATTGTATTTAGAAATCACAAACAAAAAGGAATAAAGAGTTATA
TACATCTTCCTTATCATGTGAAAGGGCAGAGCAAATAAAACGCTTTATTTGTCACAAACGAAAACGATTA
AAGCGTTATATTTCTTCCTTCT
>gi|3450373|gb|AI100412.1|AI100412 34787 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88C3XP 3', mRNA sequence
CAAATTCGCTGNTTCTTGCAACGCAGTTTCNCTGGCCTTTGAGNCCGTCGACTCGCGCTNTAACCNCCGC
AGTGTTCGTTAATCAGTCTACATNATCTTCAGAGCATATGGGAGTTTTGTCGACTGATCAGGAGCTTGTT
AAGGACCCCAAGGACTNTCCGCTTGTAAAGACTTTCGCAGAGCAATCACCTCAGATATTCAGACAGCAGT
TTGCTGTGTCGATGGCTAAGCTGGTCAACGTTGGTGTTCTCACTGGTGAAGATCGCGTCGGAGAGATCAG
GAAGGTTTGCAGCAAATCTAACTCCAGAGCTTACTAAATTATAATCATCATCCCTCATGAGAAGGATCTT
TTGTTTCTTGAAATAATTTCTTGTTTGGTTTTTGAGCTCTTTTCTATTGCAATTTTGTAATTTGTTGTAT
GAACAAGAACAAAAACTGTGAATTATTTTCGTTGCAACTTCG
>gi|3450372|gb|AI100411.1|AI100411 34786 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88A5XP 3', mRNA sequence
CGGGCNTTGGGGCCGACTCCATNCAAGCCCGGGGTTTCCTTTGGACTTGGAAGACTTTTGGGTTCCAGAG
AGAGGCCATTTGAGTCTCTAGGNGGAAGAGAGTGGACCANTGATNTATCCAGACGTTTGAGAAGCTTGGT
AAGTACTGTGGATCGCCTAGATCTACCTTGAAGTGTGAATGGAGCAGCAACAATAGCTGCAGCAGCGAGG
ACGAGAAGGACGAGGGAATCTAGCAGAATTTTTCTTCCTAATAACTATTTTCGAGCTTTCTGTTTTTGTT
CTTTCTTTTTAAAAAACTTATTAAGTTCTTATGAATAATGACTTGTGAAGTTTGAGTTCGTCTCCTTCAC
AAGCAAGTTGTATTGGTGTTTTCTACTTTATGAATATGGGTTTTATATACCT
>gi|3450371|gb|AI100410.1|AI100410 34785 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88A20XP 3', mRNA sequence
TCCCCTGTANCCGTTCCAANATGTTTATGGNGCCTCGACCAACAAATTGGGGGAATCCTCAGATTTTCCT
TCCTCATTNCNTGTTTTTGCCAAATCTCTTGATTGATGATTTTGGCCATGCAGATGGAATTGAATCTCTG
TTTGTGTAGCCTCCCTTCTCTGTTTAGCAGTTTCCGGTGAGAAAAAAACAAAAATCGATGGTTGCCCTTT
TTCGACGTTGATTGTGTTCACCGGATCGGAGTCTTTGACGGCAAAGGATGACAGGAACGTTTCATCGCTT
CTCTTGCAACACGTGTCTTGTTATACGATCGTGTTTTGTTAAAGAGATATCCTTCCTTTAAAGAAATGTA
ACTAAGTGGACCTTTGTTGGGCTGTATTCTGTGGATCATTAATAAACATAATCTTTCCAGTG
>gi|3450370|gb|AI100409.1|AI100409 34784 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88A17XP 3', mRNA sequence
GGGCCCCGATTTCAAAAGGTAGCGNGTTCCCTTAGCCGGTTANAAGNTCCNNCCCGAGTNTTNGTTGACC
CNCGATAGTCTTTAAGGTCCCAGGTGATGTTTGGTTTGGCTCCGGCGTTGTTCTCAAGGGCAAAGTGNCA
GTAAAGGCAAACNCCGGGACTAAACTTGAAATCCCTGACAATGCCGTGCTCGAGAATAAGGACATCAACG
GTCCAGNGGATCTGTGAAAAAACTTAAAAGACTTACTTTGATGCGTCTTCTTCTGTTTTTCACTTCTCTT
GTAAATGAGAGCACTTTTGATATGAAACCTCTTTCATGTGAAAAGACACAAGAATNACGAGAGTTGAATA
TGTTTTTGGCAGTTTAATTTAATCCCTCC
>gi|3450369|gb|AI100408.1|AI100408 34783 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88A15XP 3', mRNA sequence
TCATCCGCGTGGTNCCCGGATATTGCTAAGGTGAGAAGCCAAGATNATCTNCGCAAGCTCTAAGGACAGG
TTCAAGNGGGAACTNGATGGGATTCAAGTAGAGCTACAGGCAACTGATCCAACAGAGATGGATCNTCGAT
NTTTTCAGAAGCCGTGCCAACTAAAGAGTAAAAACCAAAGTTTATTATCATCATCCCCTTGAAAGATCTA
TTCTCTTATTCTGTTATTTTTGAGTGATGGTACTGGTACTTGATTATGTTTTTACATTGTGTTGTGAAGT
TATGAACCTATAAACAACTTCATTCTATCGGTGTTTCGGTCTTGTGTTCGATGTTGTCTTTGGTTTTAAA
ATGGTGTGTAAGGACCCCAAATCGTCTATTGAAGATGAACCCTTTTAGGT
>gi|3450368|gb|AI100407.1|AI100407 34782 Lambda-PRL2 Arabidopsis thaliana cDNA clone 88A13XP 3', mRNA sequence
ATCTGTTTAGGTAACNCCNATGNTTAATAAATCCATTTCAAAAAAAAAAAANGGGGGTCGCCGCTCGCGN
TCTTAGAACTAGTCTACAAGGNGGANACATGACATGTCCTTCCNTCCGGCGCTGACAAGCTTCCTCCAAG
ATGCAACTGTTGTCTTGCTCCCAAAAATTGTCCTCTCCATCTCGCTGATTCTACTACTNTCCATTGTAGC
AAATGATATATATCTAGTAAGAANTACCTGATGGTNTCCCTCCTTCGAANCCCATCCATTCCTCCCACTC
NTCGATTTCCCCCATTTCTGTAATCNCCATTTCTTCTTCTTCTTTCTTAAACTTTTGCATCAAACACTGA
AAATGTGATTAATATAAGGAAAATGGTTTCAATT
>gi|3450367|gb|AI100406.1|AI100406 34781 Lambda-PRL2 Arabidopsis thaliana cDNA clone 87H8XP 3', mRNA sequence
CTGGAATGATCCCNNTGAGAGGAGTGGTTGGTGCGACCCCNTAGNTTTGTGCCAGAGGACGCANCTGATT
NCCCAGAACTATCAAGTCATATGAAACACNCCTTTGGGGGCATCGGTTGTTTTNAATTTCTTCTATACTA
TCTGGTGTTGGATTTCGCTCTTTTTTTTGGATGCCAAAAGTACAATCTTAATTTTCTCGGATTTTGCTAG
GATATTTCTTTCTCAACTTAATTCTAAGACATTATACATATTCATATCTTCTTTTTTTACCAACTTCTTT
TTCAATGTTTTAAGGATACAAGTACGATTTACAATCGTTTTTTTACTTCT
>gi|3450366|gb|AI100405.1|AI100405 34780 Lambda-PRL2 Arabidopsis thaliana cDNA clone 87H6XP 3', mRNA sequence
GAGAACCNGTCCAGGGAAGGAGGCCAAAAAGAGTCCTCCAGCTGGNCACCAGAAGNCTGGAAAGAAANCA
ACTTGCGGAAGTCAAGCCAGTGAGAGCCCNCCGGAATGTAAGCAGCCAGTGAAGAAGTGAAGAATCTTGG
CTTAGTTATGATGAAGAAGAAGAGTGAAGAGTGTCTTTGAGCCGAGGTTGTGTTTCTTTAATTTGCAGAG
TCATGGTCCGGTTTATTATATATCAGTTTTGGGTGATTGGTTTGCTATTTAAAAAAAAAAAATGGGTTCT
TTGGTTTGGTTTGTGTCTCTTGATTTTTCCTTTTGTAATGATCTTATGAATTTGTTTCGAGTTAATGTCG
TTCTCTGGTCAGATTTCGAATTCAATTCTATTTATCCTCCCTCGTTAATGAGAGAATTTGTGAGACAATC
>gi|3450365|gb|AI100404.1|AI100404 34779 Lambda-PRL2 Arabidopsis thaliana cDNA clone 87G1XP 3', mRNA sequence
TTGATTTGATTAAGCCGGGATTGATGGAATATGAAGNTGGTTGCCTGGAGTTTCCCCCCCGTATAAAGGA
NCGNTTGATGTGCCTTGAAACCGGTGAAGCGGAAGGGATAATGTCTTNGTATAAAGGTTTTATCCCGACG
GTTTCGAGACAAGCCACCGTTCACGGTGGTTTTGTTTGTTACGCTTGAACAAGTTAAGAAGTTGTTCAAG
GACTATGACTTTTGAAAAAAACAAGAGTTGAATTATGTTGAAGAAGATGAATGATGGTGGCGACAATAAG
CTTCTCTTTTTTTCTGGTTATAATTTTCTTTTGATTATTTGAGTAGTTTTAAATTGTTTCCCATTTGTTG
GAATAGATCTATGATATGATAATTCTTCTCATGGAGAAGAAAGAAAGAAAGAAACAGTTCATTTGATTC
>gi|3450364|gb|AI100403.1|AI100403 34778 Lambda-PRL2 Arabidopsis thaliana cDNA clone 87F9XP 3', mRNA sequence
CATTTCCCANGTTNCCCGGGNAAAACCAGTNTGCCNATCAACTTGACAACCGGCTTCNAAAGGGNACTGG
ATCCAGTTAAGGCGTTAAGGCAAAAGGGGCCAAAGTGGTGGTATCCCATCATGTACGTTCTTTTGGTCGG
ACTCATCGGTCTAATTTTGGGATACATTATGAAGAGGACATAAACCACCCACCTTGAAATTAATCCCTCA
CCCGCCACGAAGGAAAAAAAAAAGACTTTTAACTCTTTTCAGTCGGACATTTTTTTCTCTTCTGTATTTG
TCAATTTCGCCTTAAAAAGGTGTCCTAGAAGATTTGTGTTTCGTAACTCAGTTTGCTATGTTTTTTTCAA
CTTTTGTAATCCAAATGACTTTGCGTTGGTTCTTTCTCCACT
>gi|3450363|gb|AI100402.1|AI100402 34777 Lambda-PRL2 Arabidopsis thaliana cDNA clone 87F10XP 3', mRNA sequence
GGACNCAATGGGAGAAGTGGGNTTCCGGACCTGGAGGTTAAGCNCATGCCCTGGCNATTACCATTGCCCT
GGTTCTCATCATCATCCTCTCAATTTGTGGGGGATTCAACTGCGGTAAATAAGTCTGGAACATTTCTTCC
CGGCGTTATCGACTGCGCTCTGTGCTTCCCAAGATCTCTGAGAATATCTTCATTCAGTTCGTTGTGCTAC
CTTTTTTTTGTTTTTGTTTTTGTGATTTCTATATTCTCATACTATATGTTTCTTCTTAGATTGTACTTCT
TGAAATTTGTTTTGTATAGGCTATATATATTATACATATATGTATGCATGTTCGACAATCTGCAATGTTG
CTATTGCTGGTACTGACACTAATTCTTGCAAACCAATATTTGGACGATACTTGTACTTGGCAATTTACT
>gi|3450362|gb|AI100401.1|AI100401 34776 Lambda-PRL2 Arabidopsis thaliana cDNA clone 87E9XP 3', mRNA sequence
CCTTTCCAATTACGGAGCTCTTGGAGGGAACCCTNTACTGNAAGCCCCCATTTCGCTCAGCTCTTCCAGG
GAGAAGGGANNTTACAACCACTTAATCAAATCCGCTTCCATCAAACGCTCTGCAGCCGCAGCAGTCGCCG
CCGGTGTACCAGCAGCCTCCGTTCCTGAATCTTAAAATCCAATAATTTCTCCTCTCTAGTCTAAAATTTG
AAGTTAATGCCAAACTGATTCAGTTTGATTTCTCTTTGTGAGAGCGTGTGTGTAATCTATGCTTTGATGT
TCTTATTTCCATTGATGTCTCCTAAAATTCTATGTTTGTGTGGTGATTTGGTTATCTATAAAAAGTCTGA
AACTTTCCTT
>gi|3450361|gb|AI100400.1|AI100400 34775 Lambda-PRL2 Arabidopsis thaliana cDNA clone 87E12XP 3', mRNA sequence
TACTTAACAAACCTNTTTGNGGGTTTCCGGATTNGTAAAAACNCCCGGATTTCGATACATTTGGGGNTCC
TTTTGNGTGTGGAATGTTGTATGNTAGGGTTTTGCGACCCGTGGAGCATCGANCCGAGTAGGACGTGATA
CGGAGAAAGAGGGGAAAGGATACTTTGGAGGACAGGAGGCCAGCTTCGAACATGGANCCTTACATTGTTA
CTTCCATGATTGCAGAGACCACCATCCTCTGGAATCCTTGATGATCATCAGATCAAGAAAAAATCTTGAA
TGTCACTCAAATTTGTGTTTCTTGCAAGATTCAAAGTTTGTGTTCTCTATCAAGCAATGTCTTAGGATAA
GTCAAAGATTTGCTCTGCTTATTCTGCTTTTTATTTACTTCACATCCTATTGAAAACATTTCTGTGTATT
ATTTATGAATAAACATTATCTT
>gi|3450360|gb|AI100399.1|AI100399 34774 Lambda-PRL2 Arabidopsis thaliana cDNA clone 86F12XP 3', mRNA sequence
ACTTCGGTGGCCGTNCTGGNCAATTTGGAAGCTCCCATTGTCCGGATGCNCCGGCTCCGCTCAAGTGTTG
AAGGNAAGTTGAAGATGCNAGGAAGGNGTCCCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACC
CGTTAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGTTCACCGAAGCTTAATTTCTTTTCTA
AAACATTCTTATGAATTATCTCTGCTCATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGAC
AATTTCTATCGGATTGTCAAATGTCTGATTTATGAATATGTAATTTATATATCCGTGCGTCTTGATTTTT
TCCGATGGTTAACTAGTTTGAAAATTTCCGATGAGATAAGACAACATAC
>gi|3450359|gb|AI100398.1|AI100398 34773 Lambda-PRL2 Arabidopsis thaliana cDNA clone 86D9XP 3', mRNA sequence
GGCACGGTTCCTTNTCCTACGCACGTCTTGCAGGACACTTGTCTGAAACATGGNCGGNCAGCCCCGNGAC
CGTTGACCGCAGCTCAGACCACTCTCTTGGCCCGTGCCAAGGCCAATTCGTTGGCTCAGCTCGGAAAATA
CACCGGTGAGGGTGAGTCCGAAGAGGCTAAGGAGGGCATGTTCGTCAAAGGGTACACCTATTGAAGAGAT
GATGCTGTGAAAAAAGAGATGAAGCAGATGTTTTAATCACATTTGTTTTTGAGTTTGCTTGTTATTAATC
ATGTCAAATCATTATTTTCTCTGCTTACTTTGCGTTAGCTACTCCTTCTAATAAGTTCTATTATATTGAA
GTTATCTATCTCTCTTGATCTATTTAAACTTGAAACTACAACTATTCCAT
>gi|3450358|gb|AI100397.1|AI100397 34772 Lambda-PRL2 Arabidopsis thaliana cDNA clone 86A6XP 3', mRNA sequence
TTCGATTGAAACATTCCGGGGNAAAGGACATGACGGAAGGGGATCNNGGAAATTTGTTGAGATTGCTCTT
AACTGTGTGAGTTCAAGACCTAAAGAGAGATGGTCAATGTTTCAGGCATACCAGTCACTGAAAGCTATTG
CTGAGAAACAAGGCTATTCGTTCTCCGAACAAGACGACGACTTCCCTTTGATTTTCGACACGCAAGAGAA
CGAGAAAGTGTGAAAATGAACCTTTTATGATACGAGGAGGAAGTAAGAGTATAATTATTTGTTGTCTATA
TCATCTTGTACTACTTGTAGAGACACTATATGTTATTGTAAAAACAGAAATGTATATGTTATTTGTTTTC
TCTTG
>gi|3450357|gb|AI100396.1|AI100396 34771 Lambda-PRL2 Arabidopsis thaliana cDNA clone 86A4XP 3', mRNA sequence
TTTGCCCATTATTCCCCCAAGCTNTTAATCCGACTCACTATNGGNAAACTTGTACNCCCTGCAGTTCCCG
GTCCGGAATCCCCCGNTTCGACCCNACGCGTCCGCTTGCTATCCACCGNTGGCTCCCGGCTTNTTTGAAG
GAAGCTTATGGACAGGTCAAGCTTCGTCAGCTTGTGTATCCTACGAAGCTGTTTTACACTTTCTACTTGA
AAGGTGTTGCTGCTGATTTACCTGTGGAGCTTACCGGAAAACATGTTGAGCCGTCGAAGGAAGTGAAACC
GGCGGCTGAAGCTCAGGCGACTCAGCCCGGCGCTACGATCGCTAACTTTACTAATTGAAATCTAAATCTT
TGTGGGTGTCTTTGTCATGGATCTTATTGGGCTGTTGTTCATTGTGTTTACATTTTAATAATGGGCCTAA
ATAATGAGCCTTTGTATTGGGCCGTTCTCGT
>gi|3450356|gb|AI100395.1|AI100395 34770 Lambda-PRL2 Arabidopsis thaliana cDNA clone 85D1XP 3', mRNA sequence
TGAAGAGTTGTGGAGGCCAAGNTCAATCTCCAGGAGTGTTGCCGTTTGAAAAGGCTTTCCTNCACCGACA
GGAAAACATGTCAGATTTGCCCGGTGATGAATGAGTTCAGTTTGAATCTTTCTTCTTGGAGTTGTGACAA
AAAGCCTCATATGTCTCGACTTTTTTTTTTTTTTTTTCTTGTTGTTGCTTGAAGATTCACAAATCTGATT
CTTGTTATTACCTTGTTGTTATTTTTCAATAACTAAAAGTGTAATCGGAATATGACTCTTTTCATTTTTA
TCTTCTCTTGCTTGTTGTGAAAAAAGGCTTTCAATTGTAGTCTATCCTAAACACTTAAAAATAAAAACCG
GACTTAACCGAT
>gi|3450355|gb|AI100394.1|AI100394 34769 Lambda-PRL2 Arabidopsis thaliana cDNA clone 85B2XP 3', mRNA sequence
GTCCCCGCGTGGNAGACTCCTTTTCAANTGTCCACGTTNNCCCCTGGGTGGCCCCCNTCTTAACCCGNCC
AGNCCNTCAATGCTTCACAAGTGCCCTGCTCGATCCCTGCCCCAAAGCGTCCAGTACGTGCGTAACGACC
GTGGCACCCCCCATGTGCTAGACAACAATTACTACCGTAACATCCTAGACAACAAGGGTTTGCTCCTTGT
GGACCATCAGCTCGCACACGACAAACGAACCAGACCAATCGTTAAGAAGATGGCTAAGGACCAGGCCTAC
TTCTTCAAGGAGTTCACTAGGGCAATCCAGATCTTATCCGAGAACAACCCCTTGACTGGCTCTAAGGGTG
AGATCAGGAAGCAATGTAATCTCGCAAACAAGAACCATTGAAGTTGGAAAAAGTGAGAAAGACAGGGGCT
CTGGTGTGTTGAGTTCTCTGCTTGGTACGAACCAAGATGAATAAAAAAATCTTTTAAGTT
>gi|3450354|gb|AI100393.1|AI100393 34768 Lambda-PRL2 Arabidopsis thaliana cDNA clone 85A8XP 3', mRNA sequence
AATTTCCCCCTCCCGNTTAAAAAATGGCCCTTNGGAGACTCCGNAGAAGNTGACCNCTAATGGNNCAGAA
CCCCGCAAGATNTTTCAAGNNGGAAACTGGTGNCAAGGTTCTCTTTATTACTAANGACCCACTTCCCTTT
AGTCTCCTTTGTAAATCTCTCCAGGAACACCTGGAAGCTCAAGCCAAGTACTAATATCTACTTAACCAAG
ACTTTNTATAAATAAGTTTATGCAGAAAAAAAAAGTTATTAGGAGATTTCTAGGTTAAGTAATAATATCG
AAGAATTCTCCTAGTAGTAGTGTCTCAAATAGATTTCTCTAGTACTTGTTATAATCAACTGTATCAATAT
TTACTCTGTTTTTCTCTGTCTCGTGCCAACAAAGTGATGAAATCATTAGCCTTTTTTACC
>gi|3450353|gb|AI100392.1|AI100392 34767 Lambda-PRL2 Arabidopsis thaliana cDNA clone 85A11XP 3', mRNA sequence
CAAATTTTGCCCACCCATGGAGTTTTNGCATCTTGAAACTATTGATTTTGGACTAAACTTNAGGTTAATG
TTTGTCTTTCCAATTTTCCGGTAGAGTTGTCTTCTTCCTCNGCGGATTTTATAATTTCCCTTCAATAAAT
TCTCCATTTCTGCTCTTGAGGAACCAACCATTGGGAACTCTGTAATAAAAAGAACAAGCTGTTGTGCTGC
TATGTTGGTTATGATTCGTTTTCCTTTTTCCTTATTGTTTGCTAGAAAAAAGAAAGAAAATAATAAATCG
TTGTGAGTTGCGTTATTTGGGCAACTACTACTACTATTCAT
>gi|3450352|gb|AI100391.1|AI100391 34766 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134M21XP 3', mRNA sequence
CGTATTTGCTAACANGCAGGATCCNCCCAAATGCTATGAATGCAGCTGAGATCACGGATAAGCTTGGTCT
CCACTCTTCTCCGTCAGCGTCACTGNTACATCCCAGAGCACATGTGCCACTTCAGGCGAGGGGCTTTACG
AAGGTCTTGACTGGTTGTCCAACAACATTGCCGGCAAGGCGTAGAGGGAAAGTTCGTGGTGGAGTTGATT
TGCTGAGCAAATCTGGATGCAGGGGCAAACATTATCTGAATTTTTTTTTTGGTTTCCGTTTTCGTTATTG
TTCTGCTTTTTTTTTTGGGATATGTCGATGGATTTTGTGATTGTACGTAGAACTTAGAAAAAAACTACCT
TTTATATAGTTTTGGTAAAACTGTAATCGAAGATTTCACCTACTGCTTT
>gi|3450351|gb|AI100390.1|AI100390 34765 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124B1XP 3', mRNA sequence
AAGCTTAGGAGACATTCGCTGATNACCCCNTNAACGGGGATTGTNTAGCNGCTTTGGGNCGNGGTGGAGG
AGCTGANTGCGNCGGCGAGTCATGCTAGGGACAAGAAGAAAGCTGTTGGCTCCGATCCTTTGGAAGAGTA
TTGCAATGATAATCCTGAGACTGATGAGTGTCGTACTTATGATAATTAAAAAATATGTTTTTGATGTTCG
AATTATGAAACTTTAGGTATGGATCAATGTTTGTTCTTCTTGTCCCTTGTTGTTATGTTTGTGTTTTTGG
TTTGGTTGATGATTGTAATGTGATAAATGAATATGAATAGTACAATACACAACATATGTTTCATAATGTG
TTTGGTTCGATTAC
>gi|3450350|gb|AI100389.1|AI100389 34764 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122H4XP 3', mRNA sequence
CCGGATCGGCGAAAGAAGTGNGGNCAANCTCAGCTACGTGTTACAATCTAGGAAACACGTCTCCTGTTCC
GGTTGGGAGATTGGTTTCGATCTTGGAAGGATTGTTAGGGACAAAAGCTAAGAAGCATCTTATCAAAATG
CCAAGAAACGGTGACGTGCCTTACACGCATGCTAATGTGAGTTTAGCGTATAAAGATTTCGGGTACAAAC
CGACGACGGATCTCGCGGCGGGGCTGAGGAAGTTCGTCAAGTGGTACGTTGGTTATTATGGGATTCAGCC
GAGGGTAAAAAAGGAAACTTCTCACGCCGAAGATTCCGCTTAATAATTTTCTCTCTACCACCATCTCTCT
CATCATCACATGCTTGTTTATTTTTCTTAC
>gi|3450349|gb|AI100388.1|AI100388 34763 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121M20XP 3', mRNA sequence
TGAGAATGTCAATGNANGCAAAGGCTTATTTGCACCTCTANTTGTTGTCACACGCAACCTAGTAGGCAAG
AAGAGGTTTAATCAGCTCAGAGGAAAAGCCATTGCCTTACACTCTCAGGTGATCACTGAGTTTTGCAAAT
CGATTGGAGCAGATGCAAAACAGAGACAAGGGCTTATCAGGCTTGCTAAGAAGAATGGAGAGAGGCTTGG
TTTCCTTGCTTAGGTCTTAAAAAGAACAAATCTTTCTCTCTGCTTGTGTCTGATATATACACTCACAACT
CCTCTTGTTGTTCTTGTCTAGATGTATTTTGTCNAAACCTATAATCTTGATTTTTGTTAC
>gi|3450348|gb|AI100387.1|AI100387 34762 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120M20XP 3', mRNA sequence
CTTCCGGTGAGCCNGCCTCTGAGGNAGGCTTTGACAACAATCNAGTGNCACCANCAAACATTCTGGAGTC
ATCATCTCAGGAAGTTGGTGGGAAACCCTACTATTACTTGTCTGTGTTGACAAGAACGGCTGATGGAGCC
GAAGGTGGGAAGCATCAGCTGATCACAGCAACCGTGAATGGAGGGAAGCTTTACATCTGCAAAGCACAAG
CTGGAGACAAGAGGTGGTTCAAGGGAGCCAGGAAATTTGTCGAGAGCGCAGCCACTTCTTTCAGTGTTGC
TTGAGTGAAAGCAACACAACGTAACAATGCTCTGCTTGCTTTCTTCATTTGTCTCTTGTAAAAAATGGAA
AATGAAACTGAGCTTTTGAG
>gi|3450347|gb|AI100386.1|AI100386 34761 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116D9XP 3', mRNA sequence
CCGTTGGGNAATGGCCGGAGAACTTGTCCCGNCNCCNGATTAGGTCAGAGGATTGTNACATTGGNNGCTT
GGATCGTTGATTCAATGCTTTGAATGGGAGAATGTGAAAGGGGAAGAGATGGATATGTCTGAGAGTACTG
GGTTGGGTATGCGTAAGATGGATCCTTTACGGGCCATGTGTAGGCCTAGGCCCATTATATCTAAGCTTTT
ACTCTAATAAGATGAGTAGAGGTT
>gi|3450346|gb|AI100385.1|AI100385 34760 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116D8XP 3', mRNA sequence
CCATCGACAGTGCTGANCCAANATCAANTCTCAGCTNGGAAGNTCAGTTCAGCTCACCAAAAAGTGNCAC
CCAATGGTTCNCGAAAGATGGAGTTCTTGTTGAGGGTTTATTCTGGAAAGACGTAGAAGCACTAATCAAG
AACTATGCAGAAGAAGAACCAAAGAAGAAGAAATGATCATCTTCCAGAGAAATATATGCTTTTGAAACTC
CATATGTTGGCGTTTTAGAATACTAAATCGATGGTGACTTTGTTTAGAGATGAAACTAATATTTGGATTT
TTCCTTATAGCCAACTTTTTGAATTAATCCGAGATTTTATGATCACTA
>gi|3450345|gb|AI100384.1|AI100384 34759 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116D4XP 3', mRNA sequence
GCCCATTGTGCCAAACNCTTTGGGTGGAGGCNGNANGGAGCAAAAGAAACCGCTGAGCTTTGGGNGAGNA
TCCCGAAGGAGACTTCTTCNCCTGAGCCCAAAGTTGTTAAAAGATTTCGATAAAGTTTGAGCTGATACTA
CANGCTTTGGAATATNANCANGAGCAAGGGAAAGATCTAGAAGAGTTTTTCCAATCAACAGCAGGTAAGT
NCCAGACTGATATAGNCAAGGCTTGGGCGTCAGAGATTGTTTCAAGAAGACGAAAGCAACATTAGTTCTC
ACTTGACTCTTTCTTTTTGTTTCTTAACGTCTAGCTCAGTGGAGTTCAAATACTCGTNCGTTTCAAATTT
AATCATCTAAGTTTTTTTTAAT
>gi|3450344|gb|AI100383.1|AI100383 34758 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116D3XP 3', mRNA sequence
AAGNGCCCTGNGGAAGGACACAGCTTTTCCATNTCCAAGATGGTCTTCTGATCACATNGCACTTTTGGCT
GAATTTCGCTGCATGCCCCAGGGCCAGACGGAACANTATTTTATAGAGATACTGCAGCTGTAATAACCCG
ATACCAAAGACTGGTTCCAATGGATATGGTTAAGCTACATGAAGTAGATAGCATGGCCATGTCCCTGGGG
TTTCTCCCGCTGGGTTTTTCGCTTGCGTTCTACTCTGTATCACAGTTTTATTTACTGCTTGGTTCGCTTG
GCTTTTCTTTCTATAGTTATTTCCTCTTTGCCAGAAAGTTTTGTCTTCACTGGCTTGTGATTGTAACAAT
GTAAACAATTAGATTCTTCAAGAAAATAGTGACTTCACCTTTTCCATATT
>gi|3450343|gb|AI100382.1|AI100382 34757 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116D22XP 3', mRNA sequence
CTTGTTGGCCTAANCCCGNTCNGTNGGAGCTAACGACCCGTNTTCAAGAGCTCCGGTTGATGGAAACTAT
AGAACAACCGCACAGGATCATAACAATTATCGCGGTGGTGGCTCGGGTCTTGATTCAAACGGGTTTGGTA
ATAGAAGAGATCATTTGTTTGGTAACAACAAAGTTTTGGATAACGAAAGTTAGAATCTTTGGATTACTTG
CAAATTCTGGCACGTTAATCACCACTTACTTCAAAAATTGTAATCTTTGTAACTTTATATAAACGCTAAA
GGGTTTTATT
>gi|3450342|gb|AI100381.1|AI100381 34756 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116D18XP 3', mRNA sequence
TCAAGGGAGGACCACAATCCCAAANCAAGNGCAGGCTTTTTACAANCGCATTCATTCAAAACTCGCTGGN
GGACAGATTTTAGCCATGTGCGTATGCGTTTNCCCTTTTGTTAAATANAAAANCTATTTGTTTNGTTTGT
TNGACTTGATAGCTTTTTGTGGGATTGAGGATTGAGAGAGATAGAGAGATTTTACAAACTTTCTCTCTTT
CTCTCTTTCTCTCTTTCTCATGGATAATTCGTGTCTCTTTGATTT
>gi|3450341|gb|AI100380.1|AI100380 34755 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116C9XP 3', mRNA sequence
CTGACCCAGGAACCGATCAAATTCATGCCNTGGGNAGAGAGATTGNTTCCCACNTTTCCCTGTCCCATCG
AATCATCGCACGATCCCTNGCTTGTGGCATAGACACNNCTGAGAGAAGTTGTGTCAGAACTCTACAGTCN
CCTGGGAGAATTCTATCAGGCTTNATGATCAATGTATAAAAGAAAACTGGGGACTTGTTTGATCGATCAA
AACTTGTTTATGATGTAACTATAACTGGTTTCCNATGTACATTGTGAGCTTTCCAAGAACAATTGTTNTA
ATTAATTAAACACAAGTTATCGAC
>gi|3450340|gb|AI100379.1|AI100379 34754 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116C6XP 3', mRNA sequence
CCGGATTGCCCNTTACGAGANCAGCTTGAATGTATTTGAGGGCTGAGACANGGACAGAAGCTGCGTTTGT
TAGGCTGGTTAGGACTTCTGATCCGACAGCAATTGTGGTAATGTTGGTCGCAGGGTAATATGCAGCTACA
TTTCTAGTCACCCAATTGGCTGCGGTTGCATTTGATTGGCTGATACCGAGAAGCTGGTCGTTAGGTACTG
AGATTATAACTTGAACCCCGGTGTGAGCAAACGCGAGAAGCATTGAGCGGTCTGCGTCATAGAGGCGGAC
GCGGTTGATGTTCTGTGATTTGAGGAGTGCTACTACTTGTGTTGGACTTGGCATGTTTGTCACTTCAGTA
CCAATATTCACACCGATC
>gi|3450339|gb|AI100378.1|AI100378 34753 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116C24XP 3', mRNA sequence
TGGGTTTTGACCAAAACNTTTGATTACCTTCCGAGNAAGNTCNATGTCATGNCAGGGGCAAAACAGACCN
TTNAAGTTGATGTTGATGCTTGCAAGCATCTTGNTGTAGTGGATGAGTATGGAAAGAGGAGANTCCCAAT
GGGTGAGCATAAGCTGCACATTGGTGACCTTAAACATNCTATTTTGGTCCAACCGCAACTTTGACGGACG
CATAAAAAAACCAACAAATAAGGAAAGCATTTTAACAAAGTGGAGTGTTTCCTCTTATTTATATAA
>gi|3450338|gb|AI100377.1|AI100377 34752 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116C23XP 3', mRNA sequence
ACCTTTTGTGGNTGCNACCTNCAAGNTTGNCCGCTGNGGACTAAGAGAGNGGGTACCCAAATGCCNTAGA
GTCGATAGCTCCCCAAATTGGGGCCGNTCAATCTAAACCGGAANTCATACACAAATTCACAAGCTCAGCA
TCTTCTCCCTCTTGTCTTGTCCCCTCTCTTTCGTTACATGTTTGAGTTACATTGAGAAAATAATTTCAAA
CCACAATGTTCTAAACGCGTTTATGTACATGTTTGAGGTGGGATTTGGAAAGGATGTCGAGTTTTGTGAA
ACTTTGGAATTACGAGACTACTAGACTTTTGTTTCTCTGTTTACGTTTCTTAAATCAATAAATAAATAAG
TTTTTATTTCATC
>gi|3450337|gb|AI100376.1|AI100376 34751 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116C19XP 3', mRNA sequence
AAGGTTGAAGGCCACNACCCCTTTAGTCTCCATTGTTGACATCCGTGCTGCAAGAAAAAGATCAAAGNTG
CTTTCCAAGAGATGTATGCCATTCAGACNAAGAAAGCAACACCCTCATTAGGCCCGATGGAACANAGAAG
GCGTATGTGAGGTTGACTCCTGATTATGATGCTTTGGATGTGGCTAACAAAATCGGGATCATCTAATCTG
ATCATTGTCGCTCTGTGATTTTACTTTTTCTGGTTTTTCTCTTCCATAGTCTCAGTTTTGCTAGAGAAGT
TAAGATATTACTATCACCATCTCTTTGTTATGCTTTTATCTTTGGATTCAAAAAGATTATATGTTTGGTA
TTTGTTGATGCGTCATAGTTTCTATTCAGATCGTGTTCCAATTCTT
>gi|3450336|gb|AI100375.1|AI100375 34750 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116C15XP 3', mRNA sequence
TTCATCTCGGGCAAACCGACCCNCGGCAGGATTTTCCCCCGCGGTCTGGATNTTGAGACCCCCTNGTNCA
AGNGGGANCTGGATAGAATGGTTGTGAGCTATGAGAAGCTGCTGGCTATAGGAGAAACAGATGATGCTTC
CTTCATCAAGACCCTCAAGAGGATTCCTTTGGTTACTTCTTTAGCCTCTGAGATCTTGGCTGCTTATCTC
ATGCCTCCTGTTGAGTCTGGCTCTGTTGATTTCGCCGAGTTTGAGCCTAATCTTGTCTATTAGTAGCTGC
AATGTCAAGTCTTGAGTTTACGGCTGGTTCTTGATTTCTTGTAATTGAATGATCGAAACTGAGAAACATC
GTCTTTTTTTTTTTGCAATAAACTTTTACTGCATATATTTGATC
>gi|3450335|gb|AI100374.1|AI100374 34749 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116B2XP 3', mRNA sequence
TAACCGNTCAAGCCNACTCNCCATTGTCCNGAAGCAGACGGGATTACACGGCTGTCGATTCTCCGATTCG
TCGCCCTCGTCGAGCCAATCTGGTCAAGTGCCTTACCACGGATGATCAGCTTAAAGCCATCTTTAGAATG
TTTGACCGCGATGGAAACGGTTACATAACGGCGGCGGAGTTAGCCCATTCGATGGCGAAGCTAGGTCACG
CGTTGACGGCGGAGGAGTTAACGGGAATGATCAAAGAAGCTGATCGAGACGGCGATGGTTGTATTGATTT
CCAAGAGTTTGTTCAAGCGATTACTTCAGCTGCGTTTGATAATGCTTGGGGTTGAAGAAAGAAAGGTATA
TATATACATAGTTTGAAATACTTGTGTTTTGTTTTTTTGGCTTCATCCTCAAATCAAAGACATTTGGAAG
TATATGTGTGTAGGTGCGATTCCATGGAAAATGTGTGTTATTTATTGTTT
>gi|3450334|gb|AI100373.1|AI100373 34748 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116B24XP 3', mRNA sequence
TCGAGTTAGCGCCCGGATTTTTNTACCGTGAGCNCGGAACACTCCCGGATACTCCGATGGACGGTNNTGG
NCAATGTGGAAGCTTCCATTNGTTCGGATGCACCGACNCCCGCTNAAGTGTTGAAGGAAGTTGAAGAATG
CAAGAAGGAGTACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCANC
AGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATNTCTTTTCTAAAACATTCTTATGAATT
ATCTCTGCTCATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGATTGT
CAAATGTCTGATTTATGAATATGTAATTTATAT
>gi|3450333|gb|AI100372.1|AI100372 34747 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116B15XP 3', mRNA sequence
CATTCAAGGCTNGCCCGGCNCCANTTTGGAAGNCAAAAACAGCAAAAAGGATAAGCGTTTGGTATTGGCC
AATGGAAGATCTTTCAAAAGCTTTGCGTGAGTATGGTNTGAACGTGAAGCATCCAGAATATTTTGCTGAT
AGCCCTTCGACTGGAATGGACCCTGCAACAAGGGACGAATAGAAACCAGGAATTCCTCAAAATCTTTGCC
TAGTAAGGACGGTCATGTGTCTCAGATCCCTGATTCTCTGTTGTGTTTCAGTTAAAAACAAAACTCACTT
GTCTTGCTAGTCCTCAATTACTACATTACATGTATATTCGTTTGTTGTTTGTTCTCTGGTGATTTTTGGG
GTTCTACATCACTTATCCACCATT
>gi|3450332|gb|AI100371.1|AI100371 34746 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116A6XP 3', mRNA sequence
CCAGCACTGGTTTGGTGGTATCTCCAAGTTGCCCNGTTCTCTGATCAGTACACTCTCACCTCGACAGTGC
TGATCCAAATTCATCTCAGCTGGGAAGTCAGTTCAGCTCACCAAAAGTGTCACCCAATGGTTCACGAAAG
ATGGAGTTCTTGTTGAGGGTTTATTCTGGAAAGACGTAGAAGCACTAATCAAGAACTATGCAGAAGAAGA
NCCAAAGAAGAAGAAATGATCATCTTCCAGAGAAATATATGCTTTTGAAACTCCATATGTTGGCGTTTTA
GAATACTAAATCGATGGTGACTTTGTTTAGAGATGAAACTAATATTTGGATTTTTCCTTATAGCCAACTT
TTTGAATTAATCCGAGATTTTATGATCACTATTTAGAAAAGAATAAAAAGCTTTACCT
>gi|3450331|gb|AI100370.1|AI100370 34745 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116A3XP 3', mRNA sequence
CCCTCAAGCCGCGNGAAGCTCCTGCAAGAAAGNCCGTGTTGATGTCCGATGTNCAGTGNTGCTGCAAAGG
CTCATGNTGNCTAAGTCGTCCCTGATTCTCTTGCTCTATCTGCANTCACACACCTACAATGTGCATCCAC
ACGATAGGTATCACTCTCCTAAGGAAGTTTCTCGACTCCTTTCCCNTCGTCAGCGCCCGTTCATGAGCTA
TTTGTGGATACACACTCTTCTCTGTACATACAGATCTCGTTCTTTCCTTTATCCAGAAGCTATANGATGA
CTACATGTATACGTAAAACAAGTCTTGGTGGTGGAAACACAATACCTCGCGATGAAAGTGCCATCGATTC
TGTATTTGTAACTTACTGTTTGAGAATGTTGTCTATGGATAAAAAGACTTCCATAGATGAGGGTTTGATA
CAGAGAACCATCATTTCTTTGTATCCTCCAACCGTCAAACACAGTTGGTGTTTTAACTCTTAAGCCCAAA
AGATCTTTTATTTGTGCCATAAGATAGAGATGTTGAAACACTATTTACAT
>gi|3450330|gb|AI100369.1|AI100369 34744 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115M6XP 3', mRNA sequence
GGATTAGGGCCTTTTGNCCCCCCNAAGNACCGGTTTAAACCCNTTTCCGGGNTGGNCATCTNCAGNTNAC
GTGTTTGGTGCACCCCTTAAAGGTTNGCCGCTGAGGACTAAGANGNGNGGGTTCCCAAAATGCCCTAGAG
TCGATAGCTCCCAAAATTGGGGCCGGTCATATCTAAACCGNAANTCATACACAAATCACAAGCTCAGCAT
CTTCTCCCTCTTGTCTTGTCCCCTCTCTTTCGTTACATGTTTGAGTTACATTGAGAAAATAATTTCAAAC
CACAATGTTCTAAACGCGTTTATGTACATGTTTGAGGTGGGATTTGGAAAGGATGTCGAGTTTTGTGAAA
CTTTGGAATTACGAGACTACTAGACTTTTGTTTCTCTGTTTACGTTTCTTAAATCAATAAATAAATAAGT
TTTT
>gi|3450329|gb|AI100368.1|AI100368 34743 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115M21XP 3', mRNA sequence
CCGATTCCNCTAAATTTTTTGAAGGAATTTTGAANATTGCCAANAGGGNNTTCCCCGNGCGCCTTCATNG
GATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTNCATTGCCTACAAGCCCCCAAGCTTC
CCCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTCATTTCATTTCCTATTGTCTG
TGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGATTGTCAAATNTCTGATTTATGAATATGTAATTTA
TATATCCGTGCGTCT
>gi|3450328|gb|AI100367.1|AI100367 34742 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115L23XP 3', mRNA sequence
GCCCCTTGGGCCCCTGGNGGGGTTCTNAGGACCNTTTCNAGTAGCCATCGTNCCGCTNTGNCCCCAGAAA
GGNGCTCCNCCCTGCNAGATCTCCNGGGCTGCTTCCAAAGGTGNCCCCCAGGTGGCTGAAAGAGCCAGAG
GAGGCAAGAGGTTGCCCATTATAGAGAAATGGATCCAGTGAGTATTACAGAGATTTAAGAGAAGAGCAAT
AGAGGAGCCAAACAAAAGTTTATTGCACTAAAAATCAACAAATAAAGAAACTAGGTGTTTTTGATTCGGT
TCGTGTAACAAAGTAAAAGCTTCACCAGGAATTTGTATTCCCTCAAACAAAATAATCTGATGTTTGTTTC
TCTATGGAGTGAATTCTGTAACTAATATCTGATTATATCGTGGCATTCATGAAAATGTTATGGAACAAAA
C
>gi|3450327|gb|AI100366.1|AI100366 34741 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115L16XP 3', mRNA sequence
TCCGGNTGGCCTGNTTAATCGGNTTCCCCGNACCAACAAACCTCACAACAAGGCTTGCCNGGGAAATTCA
TGCGTTGGGNGGCTCAATTGGAAGCTTCCAAAATCCGAAGTCATCAAATATTGCATAGGTCCACTTGTGT
CGGATTTCAGCAGTGGGACTCGCCGTCCTCGTATCATGATTTAAAGTACGATCCCAACACTCAACACTGC
TCTCTGCTTACAGGCTTAAAAGCCAAATTGATAACTTGTCATTTTTATTTGAATCCCATCAATATGCCAT
ATTATTTTTTTCTGGCGATCAGAGAATATTATTGTTTCTGTGATCTATTTTGCCATCATCCTTTCTAGGT
GTCAGGGTTTGAAAATTTGCACCGAGAATTATGTTA
>gi|3450326|gb|AI100365.1|AI100365 34740 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115L14XP 3', mRNA sequence
TCCAGTTCAANTTTGATAGAACAGGCAAAGTGAGTTCTCTTCCTGGATNCNAGACATTCCCANATCTCGN
TGNCAANATCTTAGGANCGTTCCTTGTNGTAGAAGAAAACCTCACCATATGAAACTNACCTTGTAGGCTT
GTAGTGATCAACATTTGTTCTTTATTNCCTTCACTTCAAGAAATCTATCTGAGTGTGATCTGATTGAAAG
TGTGCCTTTAGGGTCTAGTTTTTCAAATTTATGAGCTGTAAATCTATTTATTNCAATATTTCAATTGATC
TATCAAAGTGTGTGTTGTGGATTTTTACT
>gi|3450325|gb|AI100364.1|AI100364 34739 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115K17XP 3', mRNA sequence
ACCNAGNCTTTAGCCAAAGTAAAGGNACAGTTTAACTNGGAACCNAAAANTTTTCTCTGAGGGAGGGACT
GCCTCGCATGGTTAGTGACTTCCGTAACCGAATCTTAAACGAAGNCGAAGGTAAAGGTCTCTAAGTCAGT
CACACAGAGATATAGAGTATAATCCTTCTTCTGCTTTGATTTGATATATGTATAGTCTCTTTTTCAAGAG
CTCTGCTAAGTCTTTTTGTTCTCTCTGTTTTTTCTTTTTGGTTCTATCTCCAAGACACAGATTACTACTT
ATATTAGCTAATGTTTTTGACTTGGGATTTTGTCATTGGGCCATTCACCACTAGGCTCAATATTAGTGGA
AAGGTATTGATAT
>gi|3450324|gb|AI100363.1|AI100363 34738 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115J17XP 3', mRNA sequence
ACCCCANGTCCNAAATGCTGCCGTTACTTGTGNGGAATAGTGGNCCCAANTGCNAGGCAACCGGAGGCNT
NGATTTGGATGTAGCAATGTTCAATCAAATAGACACCGATGGTTTTGGCTATCAACAAGGCCATCTCATT
GTTGACTACCAATTTGTCGACTNTGGCAATGAGCTCATTGGGCANCCTGATTCCAGAAACATGCTTGTTT
CGGCCATTGATCGCGTTTGATATTATGTAATGATTTTGAGGTCAATATCGATCGGTCTACATAAAAATAA
TAAAGACCGCTATATATGTATTGTCGAGGGATATATGTTTCGTATCAATAAGGAAATTTTAAATATTATT
ATCATTCGAT
>gi|3450323|gb|AI100362.1|AI100362 34737 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115J14XP 3', mRNA sequence
TCCTTCCATNTCACTAAANTTGGGTTCTTGTAAAAAGTTAGCAGAAGCNGTAGTGGAAGTGAAGNTTGGA
ATTGTTAGNAGAGACGAANGGAAGCTCTTCTTCTTCTTTTTAACATGGTTTTAAAAAGTTNTCTTCTTTT
TTAGGATTTTGTACAAAAGAATAGCAATAAGTATAAGTACTAGGAAAACAAAAGAAACTCTCTTTTTAAA
CTTATGGAAAAAGTTGTACATAAAGAAATTCCTAAACTGGTTTTAATATTATTGTATATTTGGGTACCC
>gi|3450322|gb|AI100361.1|AI100361 34736 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115I6XP 3', mRNA sequence
TAAGGTGGAGANAGTCCGAGGNCCAATGTTGTTTNTCAAGTNTGAACGNNGANCAGATGAGGCGANAAGT
CAGNACCATCTGGAACACGGCGAGATGGAAANCCGTCAGGTGACACGCCTCTTTTGTCATCGCACCTGAA
ACGAGAAGGATCCTTTAGCTGCTTCAAACATCTTCAAGTCNCGNTTANGCTATNGCAACGTGCTAAAACT
CATCAGTAATTATTTCAGCTTAAGTTGGTTGGTTTCGGATTTCTGCTTGTCGCTTCAATAATTGACCCAT
CTTTTGGGATTTCACGTAACGTACTACACTTTGCTTTTTAGTTTTCTGCGAAACTAATGTATTTTGTAGC
CTCTCAATCCTGGCTCTCTGTCCCATACTTCAGTTTTTTACACAACGCACTGCTTATAAAAGNCNCAGTT
AAAGGTGTCTAAAGGAGAATGGTGTGTCTTTGACTGAGGCAACAAATAAAACAGTGAAAAGTTAAGGTTT
T
>gi|3450321|gb|AI100360.1|AI100360 34735 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115I17XP 3', mRNA sequence
CATTCCAGGNTTGAGTCACATCGTCCCNCGNCTTGTCCTNCAACTACNCTTGAGGGGTGATNCCGTCTCG
GNGACCGNGTTTTTNCCCTTTATCGAGGNANTCCCNTANCCTGGGATTTTCCCNCTCAGGACGTTTCAAC
TGCTCCTACCTGATGTGAACGAGTGGTCANGCCTCTCATGAAACAATGNCATGATGCTCGTTATCTATCT
ATCATCCCTCATCCGGAGTGTAATNCGCTCCACACTGATCAACAACAAGTTACTGAACAGGAACTGAAAA
AGCAGAGGACTCAAAGCCGTGGCCTACCTGCCACCAGCTAGATCAGGTTTTCTCGTGACTTACTGTAGTC
ATCATTGCCCGCGATGAAGGCAGCTATTGTGTGTTCTCTTCCCCAAAACAAAGGTCAAGTCAGGGTGGGG
GAACGAACGAGTTTAGTTTGATATCGACATTGTTGATTTCTCTCAGTTGTTCTGATTCAGAATGTATCAA
AGAGTCTTTTTTCATTTTATCTTTCAAGTTCGTTAGGCTTAGGCCTCTTTTTGAGGGGGTTTTAAGATAC
AAAAGTTCACGTCAATGTGTCGAAATCTCTTCAGAGATGGTCTTAACCTATTGAAATTAAGATATTTTTT
TTCACATT
>gi|3450320|gb|AI100359.1|AI100359 34734 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115H1XP 3', mRNA sequence
TGCCGCAATCCCAAAGCGTNCCATGCTTGCGCCTTCCTGATTNCNCNGTAGCTCCACGCTCGCANTGAAT
GAAGAGCGTGATGCCGAGNGGTCCATCTNTNCCCGGCACANCACGTCCGAGTNCTGATCCCGGCTCACAG
GTCCCACCGAGGGCATGAGAACATCATCGTTATGAAGATCGGTATGAGCTGTACGGCTCAGTTCCCGATA
GTCGTCCTCGATGGCTGAAGTCACCAGACTCATTGAGGAGGTTTCTCATTCATCTGGCTCCCCAAACCTG
TATCCGACGATTTTTTGGGGGTCTAAATGATTGATTTGAATATTGTTTGGGGTCAAGTTGCAATTCTTGA
ATAGTGTCGACCCCACTTCCCGCCTTTTTTCTACTTCTTCTTCTTTGTTCTTGTTCTAGTTTGTTCGTTA
ATTCTTGAGCCTCAAATTGAGATGAGACCTATCAGTTTCTTTTTTTCTTTCTTTCTACTTTTCTTTATTT
CCAAAGTTTTAAAAATGTCTATAAAACTATTGCTTTTGCTAATTTTTGTATAAATATATAGTTGATTGCG
TGTGAATAAATTGGTTTTTGTTTTCTTC
>gi|3450319|gb|AI100358.1|AI100358 34733 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115H13XP 3', mRNA sequence
AGATCAGCATTTTCCGACGCAANTCGTGTTCTTCCGTCGCCCGTNATCGNCCCGCGGTTTCTGAACANNC
GTGACGTAGTTTCATCCGGCTATCGAATGGCTCGATATATACAGTGGTGTTCTGATGGTCAGAGTTTGCT
CAGTTGGTTCCCANCATTCCTGGGATCGTCAGCCTTGTCAGCCATTAGAGATCTGTGTGATCCTTATCTT
AATCTCTTCAGGAACATTATCCCTCCAGTCTTTGATACGCTTGACGTTAGCCCTTTGCTTGCTTTCGCCG
TTTTGGGAACTCTAGGTTCGATTCTCAACAACAGCAGAGGATAGTCAATAGCCACTACTTACTCTGCTTT
GAGTGATGATGCAAAGGTTATGGATCGTATTCCGTTTATCTTTGGCGTTTATATTGTCTATAGTTATAGC
ATTTGGAAGTATTTATAAGGTAATGATGTATTAGACTCTAAAGTTTCAGTCTTTACTTCTGTTATGTGTT
ATTTATGTAAATGCACGAATATGGTTTCAAT
>gi|3450318|gb|AI100357.1|AI100357 34732 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115H10XP 3', mRNA sequence
TACCCAGCTTNTTCGNTCACTATGGGANAGCTTGTACNCTGCAGTACGTTCCGNATTCCNGTTCGACCCC
GCGTCCGATTCTGATNNTACNANAANCTTTTTTCAGACACNATTCNAAAATCTTGCCTTGAGTAGATCAA
GTTCTTTACATTATCGTTAGAAGATGAGCCANTACGATCACANCCAGTCTGCAGGAGCTANCCCACCGCC
ACCGATGTCTACCGTACATCACCACCACCGCCGATTGGTTACCCGACTAACCANCCGAGTCATGGTTCGG
TAGCTCAGGGTAAAGTGGAAACCAAGTCTAAGGGTGACGGATTCTTCAAAGGCTGTCTTGCGGCCATGTG
TTGCTGTTGTGCCCTGGACATTTGCTTCTAAGCCATTTGGGAATTGGGATGGNCTATTTATGACGAGTTT
ATGTGAATGTGATGTGAATTATTATTATTATTCTCTCCGTCCNTATTGTATAAATTCTCTATTTTTTGTT
TATTATTNTCTTGTAATACTTTGTGAGACGAAC
>gi|3450317|gb|AI100356.1|AI100356 34731 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115E14XP 3', mRNA sequence
CGGACGCACACGTGATCGCTNTCATCGATGATGGAAAAGTGGCTGAACANGGATCGCATTCGCATCTTCT
CAAGAACCTCCTGATGGAATCTACGCGCGATGATACAGTTGCAAAGATTTACGCATACACAGTGATTGGT
ATGACGTCAGGTTCAAGTTCTAGGGTTAAGGAAGATGATGCTTAGTACTTACTACTTTGGTCATATAGAA
GAAAAAAGAAGGAGAGTAAAAAACAACAAACACCAGAAGATGTTTCTGATAAAAAACTCTACGAACTCAT
CATTTTCTCTTTTTTTCTTTCTGTTTTGATTTTGGGGTTACTTATTTTTGGAATACGTTTCAGATTTGAT
GGTATAGTATTATTATTGTGTATTATCATAATTAATCTAATTTTTCACC
>gi|3450316|gb|AI100355.1|AI100355 34730 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115E13XP 3', mRNA sequence
TGACNCCCTGGATAACCGTGAAGTGGACCCCGACNGTAGCNAGACCCCCTGTGGNCCNTGGTCCCTCACA
TTTGTTCNCCCTNTGGTCCCTTCCCCNTGTGGAAGTGGTGTATCTGTTGTGGGATTTGCTGAAGGAAGAA
CTTTACTCGCTGAGCGGTTCGATTATTCACTCCTTGCTTCAGTCCTACAGATACTGGTTGTGTGCTGCTA
CTGAGATAGCATTAGGATTTGGGATCTTGAGAGCAAGTCTGTTGTTGAGGACTTGAAGGTTGATCTCAAG
TCTGAGGCAGAGAAGAATGAAGGTGGTGTTGGAACTGGTAACCAGAAGAAGGTTATCTACTGCACAAGCT
TGAACTGGAGTGCAGATGGAAGCACATTGTTCAGTGGTTACACTGATGGAGTTGTCAGGGTCTGGGGTAT
TGGTCGTTACTAGAGACACAACAAGATGAAGAAGAAGTCACGAAATCTCCGGAAAAAAGTTTAGCTGCTT
TTAATTTTTNCCAGATGCGTCAGTATTGTATTAGTCTCTCGCAAACCTCTATTTTGGCAATTTTTGTTTA
ATTTCCAGAAGAGAAAAAAACAATCCATTGATTATCATATCACTATATATCAAAAGGTCACGATTTTGAT
TAC
>gi|3450315|gb|AI100354.1|AI100354 34729 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115B13XP 3', mRNA sequence
TTTTTGGATTTGCGTCCNTCCCCGGNCCGCTTCCCTTTTCCCACCTATCGCCCTTGGAACTGTCCCCTCG
GTCCGCCGATCCCGNCGCCCCCTCCGTTCAAGCTCAATTTGCCTCTTAGATCGTAAATGCCAGCCAGCCA
NCGCAGAATCCCCTGGNGAAGCCCCGAGAAGCCACTGGCGACGAANCGCAGGAATCCGCTCCACCCCGAG
NNTGAAGANNCCACCAGTTCCGTCCGGAACAGTAGCGTGCGTGAAATCAGAAGTATCAAAAAGCACAGAG
CTTTGACCCGTAGCTTCCTTCCGAGATTGGTTCGTGAGATAGCTCAAGATTTCAGACGGATCTGAGGTTT
CAGAGTAGTGCAGTCGCAGCTCTTCAGGAAGCAGCTGAAGCTTATTTGGTTGGTTTGTTTGAAGATACTA
ATCTCTGTGCTATTCATGCTAAGAGGGTTACGATTATGCCGAAGGATATTCAACTTGCGAGGAGGATTAG
AGGTGAGAGGGCTTAAGATTTGAAGAAGATGAAGAAAAACAATGGTGTAGAATAGATTTGCTTGTTTGCT
TTCATCAGATTTGTAGATTCATGTTTTAGATCTGGTTTTGAGTTTCTTAGTCTTTTGTTCTGAAGTGTCT
TCCAGATGTTCGATGAAATGCCCAAATGAAAATTTTAATCTACTTTTGCTACTTTCTAAG
>gi|3450314|gb|AI100353.1|AI100353 34728 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115A22XP 3', mRNA sequence
TTTGCNACAGGCCNTCCGTTGTGGTCGGCCCTTGGTCGNCGAGGTTGGNCCCTCCTNGCAGTTTTACATG
CCNTTCCGNCCCTGACTATGAATGTTTCNCCAGGGCCCCGGTCNTNTTTTTCGCACTCTGCTCAGAGGTT
NTGGCTTTGGGGGAACCCGNGCCACTTGTGGACCAGACCTGGCCTCCAGCTGTGGACTAAGNCCTCTGAG
GAGTCCTACTGAACAGAGCTAGGCNCGTGACTTTACATTACGACCTCACGTTGCCAGCCTACACTTGAAG
AGGATCCGTGATGCAAACTACATGTGACTCGCGACCACACTTTCTAAGAGATCATGCATCAAGCAATCAG
CACAGAGCTCGTCAGCTTAACCCCACGAGTGAATACGCGCCTGGACTTGAGGACACACTTATCTTAACCA
TGAAGGGTATTGCTGCAGGATTGCAAAACACCGGTTAAGTGAGTCAGTGAAAGAAAACAAAACTTCGAAT
CTCTCTTTTTTATCTACCCTTTTTAATAATCTCTTTTTTTCTAGAATCCAAAATAATTACGGTTGGATTA
CAGTTTACTTTATGTATCCACCGTTGAAATCTTAATCTTCCATTGTATCAAACGTCACTGACTCTGTTTC
TGGAAGTGTAAACAAGAACAGAGACAGTGAATCTTAATGTTATCTTCTTTGTCTT
>gi|3450313|gb|AI100352.1|AI100352 34727 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115A20XP 3', mRNA sequence
GCCCGGTTTCCNAAATCATGGACATCGTCCGGTTCNNGGTTTCCCCGTNTTCCCANCGTCCGCTGAGCTC
CACGTCCGTTTGGCNCCCTCCGATGGGTTGCGTGTTATGGTCCTTGGCCCACTTTCCGATCACGNACCGN
ATCACCCCGNCTAGGAGTTNCGGAGCTGCCGTATCTTAACAGAGCAGCCCTGGGATGNCCANGGATATTC
TGGGTGGGNCCTTCATTGGAGCTGCGATAGCTGCATTTTATCACCATTTGTCCTAAGGGCTTCAGGTTCC
AGTCACTTGGATCCTTCAGAAGTGCAGCCAACGTTTGAGTTTTTGCCACACAAAAAAAAACCTATCATAA
TAACAACAATTACAAAATGGTTGTGTTATTATGTATGTACAAAAATTGGCAACTTTGCTTGTAAAACTAT
GCACTATATTTCTTCTTGTTTTTCTGTTTTCATTGTGGTGTAATACTTTGATATGTGCCAATGCCAATGT
TTGTGTACTCGGGAAAACAATTAATGAAAACCAAATTGTTTTGTCCTTCTCCTCCCTCTTTTTATTTTAT
ACAGATGATATTACCAGCTAAAAGCATATCTACATAGACTAC
>gi|3450312|gb|AI100351.1|AI100351 34726 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115A12XP 3', mRNA sequence
CAGTTTGGGGGGNCCAGTCNTGGAGTGATCTGACCTTGGGANGACTGNNCCTCGACCCTGCTGGACTGAG
TTCCATTGTCNGCCAGGGACTTTCCATGAGNGTCGCCGTTCTGTTGCTGTCCTANCTGGTTTGGAACTGG
NTGGGCTAANGCCGCGTTCGNCATCCCCTGTTAGGTTGACTGGTTGTAAATCCCCCACACTCNGGACTGC
AGGGATGTGACNCCTATCAGGTTGATTGAGAAGAGAATCCAGATTTGATGAGAGAGAGAGGCAAGCCCGA
AAGAGAAGAAGCTTTCAAGAGTGCACGCCATCAAAACGACTTCGGGTAGGCAGCAATGAGAGCCCTTCAT
CTCTTCTGAAGAAACGAAAGCAGCTGTCATGGATGATTATGGAAAGCGTAGGAAATAAGAAGGCTTGTGT
TGAATCCATCACTAAGTAATCAGAAAGATTTATGATCACTTCTAGGTTTGATTCCGAATCGGAGAATTAG
TTAGAAAAAGCTCCTTAGAGAGAAGGATCTAATATTTTGTACCCGCAAGCATCACTGCATTGTCTCCGAC
TTCTCTTATTTCTTCAACGTGTATTTTACTCTATTTTGTTTGTAGAAATATTCACCAC
>gi|3450311|gb|AI100350.1|AI100350 34725 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114L2XP 3', mRNA sequence
CAAAAAAGANGATATCCTCAAATTCTNTCTCCTNTTGGTNCTCTTCCTTCATAAACTTCAAGAGGCTATG
AATCAGGTGGATGAAGAATCCGAAGCCCTGCAAGAAAAGTTCCTAGAGAAGGAGATTGATACAGCAGCAT
TTGTGCAGAAATACAAGAAGCTTCGTACTACCTATCATCGACGAGCATTGATCCATCTTGCCNCTAAAAC
GTCAAACATTTGANATTAAAAAGCTTTACACATTGAATTCGAGACTTTGGTTGTGTATTATGACTCTTAC
CCATTGTTGTAAAANAAATGCTTTGCTGTTT
>gi|3450310|gb|AI100349.1|AI100349 34724 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114L1XP 3', mRNA sequence
TTTGCCCCACCTCCTTAGNTAGCCAATTNGGCCTCCNGAATCAGGANTAATAGTGCCAGGCCTTGGTTAA
GGAAGCCNATAGCTGNTNACNGTCAGGCAGCTGCTGCATTGAAAGCCCATTGGCTGGGAATCATGTCTNC
CCAACAACAGAAAGATGTTCCTTGTCCAAAGGGACTTCTATGACGAGAAAGACCTCAAGGATGATAAGAA
AGCAAAAGAGTCAACTGAAACAGACGCCGAAAACGGAACTGATGCTGAAGAAGATGAGGACGCGGTGTCG
GAAGATGGAGTGGAAAGTGACTCTGACGCAGATGAGGACGCAGTGTCAGAAAATGATGAAGAAGACGAGT
CAGATTCTGCTGAGTAATTTGGTTACACATGCAAAATTTTGTTTTTTGTTACTTGTAAACTTTTTTTTGT
CTTAATTAACTCAAAAGTGAGACTCTTATC
>gi|3450309|gb|AI100348.1|AI100348 34723 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114K7XP 3', mRNA sequence
CCCTTCCCGAACATGGGNTTCCTTNGGTTGGATTCGNNTTAGGGCCCGGATTTTTTTNCCTNGNGCACGG
AACCANTCCCGGATACTACGATGGNCGGTACTGGNCCATTTTGGAANGTTCCATTGTTCGGATGCACNGA
NTCCGCTCAANTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTACCCGGGCGCCTTCATTAGGATCATC
GGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAG
CTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTCATTTCATTTCCTATTGTCTGTGTTCTT
TTTCTCTTTATGAGACAATTTCTATCGGATTGTCAAATGTCTGATTTATGAATATGTAATTTATATATCC
GTGCGTCTTGATTT
>gi|3450308|gb|AI100347.1|AI100347 34722 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114K3XP 3', mRNA sequence
TTTTGTGAACCCATTCCGGNTAAACCCTNNTAGNTGAGGGAGCTTTTAACCTCNNCAAGGATCNANTGAG
CTATCAGCNCANTTGATTTACGTNTNCGCCACTCCACAGAAGCTAGAAGCTTTACTCTTATCCTGTCACA
CCACAGGATTGTTCCCAACTTCTTCAATAGTGAAAACCAAAAAGGTTTGATCAATCTAAAAAAATCATCT
TAAAAGAGCTTTTGCCCCCCATCATTGGTTTAGGTATAGAATATCCGCAGTTATGTTCCTGGCCCAGCCG
GATTTTGTACTGTGTCTGTCTGTATTTGATGATATATATCTGCAGTTGAACATTTTCAGAGAAACC
>gi|3450307|gb|AI100346.1|AI100346 34721 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114J24XP 3', mRNA sequence
AGGGGTCCCCAGTNTCTTTGAAAGGGAACTTCCAGCTGANGTTATGAGTNCAANGCTTTGATCAGCATCC
CCNTCAAGAATCGATGCGCGCGTCAGGAGACCGNGGACTTAAGAAGAAGAACGCCAGTGGACAAGCTAGT
TAANCCACCGCAACATCTCTCCAGGTGTCTCTTCTTCTTCTTCTTCTTCTTTGCCTCTTAGCTGTAATCT
TCTTAATAGTATGAGCTATGGATGTAGCTTCTTCAGACGGATCAGAAACCTTATGAATCTCTGTTGTAAA
ATTAGGATAAAACGGAACGGAGCCAACCAACTAGGTCTTTTTATTTTATCCTTTTTTACTTTGGATGTTT
CTGCATCTTTTGGGAACATTTTCAGGCTGATCCATTGTCGTATATTATCATCTATCTATCTAGTCTTTTC
AGAC
>gi|3450306|gb|AI100345.1|AI100345 34720 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114J22XP 3', mRNA sequence
CCTTCGATGTNAGAAAGCCTNTGAAGCTGCTCAAGTTTCCTGTAAACAGTGTCCTGACCTTTTTAAGACT
CCAAGAAGGNTGATGGTGGAGATGATAGGCCCCAGCNGCAGCAATTCCATCNTCAGGGAAATGAAAAACA
AGATTAGATGCGAACAGTAGATCAGGTACTGATCTCGACGTGGTGATAGGCGAAGCAAGAAAGGATACAA
ACTAAGGATATCAAAGTAAAATATACTATAGCCATGCTGGTGGAATAGGAAAACAAAGTTCTTGAAGCTT
AACAGAACTAAGAAATCTCTCTGAGTTTTGAGTAATCTCCTGCATTTTCCGGTTTTTGCATTGTAATGTG
TAACAGTGTATTTTACAATTATACGTTTAAATGAATTTGGGAATCACAAGTAGG
>gi|3450305|gb|AI100344.1|AI100344 34719 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114J21XP 3', mRNA sequence
CATTGCANTCTCAGCTATTGGTCCCATCCAGNTTTGCCCAGCCTNCAACAAATTCCAGACGCAGAACCCT
ACTGGACCCGGTACTAAGGCTCTGAAATAAAGGTCACTGAATCGCAAGGTTCGCCCCACGGGGAGATTCC
GTAGGCGGAGAGAGCAGAACGAGGTGATGATGGATTCATTATTTTTGAGTTTTTCTTACTGTATCTTCAT
AATTTACCATCATCGCTGGTAAAATAAGTGTACCATTTACTCTTTGTCCTCTACTGGAAAAATGCTAGAG
ATCCTCTGTGTGTGTTTTTTTTGTTCTCTTCATAATTTTCCCATACACATACTAATAAGTTCTTTGATGT
TTGGTTGAAAACTTGAATTGGATACATTTC
>gi|3450304|gb|AI100343.1|AI100343 34718 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114J1XP 3', mRNA sequence
TTCCCACCCAGTTCCAAGTGGGAANNAGAGATTGAGCATGCAACGAGTTTGTGAAGAAGAAGTTTGAGGA
GTTATATTACCAGAACNACGGCGCCGGATAGAGTGGACAGGGTATTCAAAATCTACAGGACGACGGCTTT
GGACCAGAAGCTTGTAAAGAAAACGTTCAAGCTCGTAGATGAGACACTAAGAAGGAGAAATTTACTGGAG
GCTGGCCTTTTATGACCTTATTATTACATATCTCTAGTAAATTACCTCTCCTTATTATTATAAGAAAAAC
TCGAAAACTGAATGACCGTGTAATTTATCTTTCGGGACAAAAGACTTAGCGATTCAAAATCTAATGTGTC
TCGATGGCTACGACTAGTTTCTATTTTATCATTGTTTTTGTTAAC
>gi|3450303|gb|AI100342.1|AI100342 34717 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114J17XP 3', mRNA sequence
CCAGTNCAGCTTTTACTNCAACCGCATTNACGACTGCTANTACTTCTGTTGNAGCCTGCAGAGCTTAACA
AGCAGATTCCTGCTGGTATCAAAACTCCTGTTAACAACTATGCCAGAGCTGAAGGACAGAACNCCGGCAA
CTTCCTCACTGACCGTCCTTCGACCAAAGTTCACGCAGCTCCGGGAGGAGGATCATCCTTGGATTATCTC
TTCACTGGTGGCAAGTAAAATAATTGCAAAGACCTTTATCTATCCATTGTCTTTGCTGCGTTATCTCACT
ATGAAACTGTTTGATGTGAGCCTTTAAATGATAAGAAGTCGGTTTCTTGTCTCAACTCTTATCTGTAATA
TTTTGCTGAAAAAATGTTTGAATC
>gi|3450302|gb|AI100341.1|AI100341 34716 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114J15XP 3', mRNA sequence
TGCAGTACCGGTCCGGATTCCCCGGNTCGACCCCNCGCGTCCNGAGGNTAATTCCGAGGCATCTTCTTCT
CGCGATAAGGAACGATGAAGAATTGGGGANACTTCTGAGTGGTGTCACAATCGCTCACGGTGGTGTTTTG
CCTAACATCAACTCTGTTCTATTGCCTAAGAAGTCTGCCACTAAACCAGCTGAAGAAAAGGCTACCAAAT
CACCAGTCAAGTCTCCAAAGAAAGCTTAATCTGCTAGAGTTTTCGTTGCTAGTTTGTGTTTGAGCTCTGG
TGAATGTAGAAATTTGAAGCTTTTGGATCTTAGTTTCTATGTATTTGGTGATTTAGAATGTTGTTCAAAA
TCCTTTTCCTAATC
>gi|3450301|gb|AI100340.1|AI100340 34715 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114I5XP 3', mRNA sequence
AGTCTTGTGGGAGATCTTAACCGGCGNGGNACCCATATGNTTAATATGCACCNCCGGTGCTTATNATGTA
GTGGGATANGTTGAACAACACACTGAGGCCGNCCATACCGAGCTACTNTGACTCGGACTGGCGAATATTA
ATGGAGGAGTGTTGGGCGCCTAACCCAACAGCAAGGCCATCCTTCACGGAGATAGCTGGTCGGTTACGTG
TTATGTCAACTGCAGCTACTTCGAACCAATCCAAACCACCAGCTCACAAGGCTTCAAAGTGAAACAGATT
CGATATTTTATAGGTTTCTCTTTACTCTTTCCAAGTGTTTTGGGGTCAGGAGGGAGATATTTGTTGACCC
TTTTNTCCTTTCCCCCTTTTTTTNCCAAAACAAAAC
>gi|3450300|gb|AI100339.1|AI100339 34714 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114I3XP 3', mRNA sequence
AATTTTGTCCCCTAAAGTAAACTTTGCCGNGNAACCAGTCNCTCTGCAAAGCTTAAACCGTCAGGTGTTN
CCGTATTCCCACTTCTTACCNCGTGCTGATGGCCAAGTCGAATCCTCTCATGCTCTCTTGCCAAGTTCCC
AGAAACTGAGAGAGGCGATAGAGAGACNCAATGTAGGAAGTATCAGTAACATCTCTTCTTCAGCTTCTGA
GAAAGTTGAAGATTCAAGTGAATAATCAATGCCTGGTTCAGATTGATCNCAGATTATTTTGTTAAATCGC
TTCCCTGTATATATGTTGACTGCATTTTCCATGTGGTGCATCATAATTTTTGTACATAAATAAATGAGTC
TGACTTCGAGTT
>gi|3450299|gb|AI100338.1|AI100338 34713 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114I2XP 3', mRNA sequence
CAGAACTTTGTGGNCCAGTTGAGAGGTTACCANGCCCCATGAAGTTCCCTTTGCACAAGACCGAAGCAAG
CTCTTGCGCTCTTCAAGGCTTTTATATCTGGAACTCCATTGTCCACACATGAGAACAGCATCAGCCGCGA
CATGTCTGAACTCGTTAGTGACTCATAATGAGTTCTGATTTGATGTAATGTGTGATTTGGATTCTCAATC
AAAAACTTTCCACATAGGCCGTTGAAATAAGAAGAGGGAAAGAGAATAAATCAGTGTTTTAAGTGATACG
TTCAATGCTTCTTCTTCTTCTGGTTGTTTGTTTGTTTGGATAAACATTTGCTGCTTGGAATCTAATAAAA
GAAGTTTCTACC
>gi|3450298|gb|AI100337.1|AI100337 34712 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114I14XP 3', mRNA sequence
TGGACGGTTACTGGACNATGTGGAAGCTTCTCATTGTTCGGAGCACCGACTCCGCTAAGTGTTGAAGGAA
GTTGAAGAATGCAAGAAGGAGTACCCGGGCNCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAG
TCCAATGCATCAGTNTCATTGCCTACAAGCCCCNAAGCTTCACCGAAGCTTAATTTCTTTTCTAAAACAT
TCTTATGAATTATCTCTGCTCATTTCATTTCCTATTGTCTGTGTTCTTTNTCTCTTTATGAGACAATTTC
TATCGGATTGTCNAATGTNTGATTTATGAATATGTAATTTATAT
>gi|3450297|gb|AI100336.1|AI100336 34711 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114I13XP 3', mRNA sequence
TTTTTCGATGCACCGANTCCGCTNAAGTNNTGANGGAAGTTGACGNATGCAAGAAGGNGTACCCGGGCGC
CTTCATTAGGATCATCGGATTCGACNACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCC
CCAAGCTTCACCGAAGCTTAANTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTCATTTCATTTCC
TATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGNTT
>gi|3450296|gb|AI100335.1|AI100335 34710 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114H5XP 3', mRNA sequence
TTGCCNGGNGGNTNTNCATNCCTTTCTTCCAGNGGCGCANGGCTCACCGAAGAAGTTGTGNCNGTTCAAC
AATGCTACCATGGANCTTGTCCCANGTTGGTGAAGGAGAAGCTAAGCCCCCATTGATCCTTACTTTGACA
AGCTTGCAGATGCTATGGTCACTTGGATTGAAGCTTGGGATGAGCTTAACCCACCCACTAAAGCTTGAGC
AGCAAAAAAACCACCACCGCAGTTTTGGTTATTAGCTCAACATATCATCTATCTTCTCCGTTTTGTTTTT
GTTTTGTCTTTTCTCAAATTTTCCGGCGATTCTTCAGTTCGTTTTTAAGTTGCCGGAGTTTATTTAAATA
GTGAATGGTGTAGTTCTATTT
>gi|3450295|gb|AI100334.1|AI100334 34709 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114G21XP 3', mRNA sequence
CACCCANCAGCTTCAGGNTTTTGNACAACCCTTCCAGCGTATGGGTATGGTCAAGCCGCCCACAGGGATA
TGGGTCTTATGGAGGATACACACAACCTGCTGCTGGTGGAGGTTACTCTTCAGACGGGTCTGCTGGAGCC
ACTGCTGGTGGTGGTGGTGGTACACCAGCTTCACAGAGTGCTGCTCCACCTGCTGGACCGCCCAAAGCAT
CCCCGAAAAGTTGATATGTGTATGGATAAATTTCTACTGTTATACAAAACATGCTTCCATGCTCTTATCT
TTTTCTTGAGGATTTATCAATGTTTGTGTTTCACATTT
>gi|3450294|gb|AI100333.1|AI100333 34708 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114F8XP 3', mRNA sequence
TTAGGGACCAGGCCAAAANTTGAGAGTTGTTCCCTTTGNTATTTTGGGNACCTTTTCGACGGGCAATCCA
GNTTGCATCCAGGAAAGTTGTTTTNCCCATCTGATGTATCAGGCTAGAGTTAGTACGAAGCTGGATCGAC
TTTTTGGTTGGGGAAAGATCGTCGGAGGAAAAGGNAAATCGATTGGAATTGATACGTTTGGAGCAAGTGC
ACCAGCAGGAAAGCTTTATAAAGAGTTTGGTATCACCATTGAAGCTATGGTTGAAGCAGCCAAGTCACTT
ATTTAAAAAAGTATCTTACAGGTACTACCGAGGTTTGCATTTGAAGTAAGAGACATTCCATAAGCATTAT
CTTCTTTGTCCAAATAAAAATATACTCCTTCCAATCTTTTTATAAATGATGTTTTAAGCTTTCATTTTGG
TTTTTAAATAAATGATGTTTTAAATTTTC
>gi|3450293|gb|AI100332.1|AI100332 34707 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114E7XP 3', mRNA sequence
CTGGTTTTCTATGNAGGTNANCCCGNAGGATNGAACCCGATCNATTTCNTGGAAATCCTGAAACGGGAAC
TGGATGCANTGGAGAAGGAGAAGGCAGAATTCCATCAGTGACTTCTCGAAAGAGGATTACGAGGATATTA
TAGGCGGGTGGAAGTCAAAGCTACTTAGGAGCTCAAGTGGTGAGCAGAAGTGGGGTTTGTTCATCGCCAA
GAGAAACTGATTATGGCATTTACTATAAGTTGGAAATAAATTTGGGTATGTATGTAGATCATCAAAACCC
AGTACCCTGCTATTATCTCTACAAGCTATATATATGTGGCTGTGAGGTTCCTTTAATGTCTCCATTTTAC
AGCATATCCAGTTTGGTATTTAATATATGTGATATTTTG
>gi|3450292|gb|AI100331.1|AI100331 34706 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114D24XP 3', mRNA sequence
AAACCNTCTCNACTTNTACGGGCATGAACCTTTGGCATATTTCNCCGATATCTCTNGGTGCACGACGNTT
AGCCTTGACCAGCGATGANGGCTCTCCTAGTTTNAGTTCCAGAAGGCAGCAACTCCAAAAGCTGATTTGA
AGACTAAGCTGAGGATGTTCCCTTTCTACTGATTCACAACTCTTGTACCAAGAAAAAGTGTCAAAAATAT
GGCCTCTTGAATAATGGTTGAGACAATACCAACCACTTGTGATTAGTTTGTGTGTTTTTTCTGGTATGAT
CAGT
>gi|3450291|gb|AI100330.1|AI100330 34705 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114C6XP 3', mRNA sequence
AAGTGGTTGCCTATAAAGGCCAACNTGNGGCCAAAAAGNGTTTAAGCCAAAGGGCAGNAGANAGGNTTCA
TTTCCCCACAGACATNTTGCCCAAATGTGNCCACTTCTTTTACCCTGCACCACCGATNCCAGGAATGGGA
GGTGGTGGTGGGTATGGTCNTCCACCACAAATGGGCCGGTATGCCAGGAATGCCTCCCATGCCACCATAT
GGAATGCCACCGATGGGCGGCTACTAAAGCAGACCAGCTTATGCTTTAATATCCGCATTTGGAAAAGTAT
CAGTAGCGCATAGAGTCGGCCCAATTTGCTAGGGCGGTGTTCATCTGCTAGCTAGCTTATATGTCTGACC
AGAATTTGTCTGGGAATAATGTGGATAATAACCTCCTTTCGTTGTAATATTCTGTTGGGTTTAGGTGAGT
AATTTTTTTTTAACTTTTTGTCAAAAGCCATTTTTGAGTATAT
>gi|3450290|gb|AI100329.1|AI100329 34704 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114C19XP 3', mRNA sequence
CATGCNGTATGTGCTGATTNTCCCCGAGTNCCGTCAACTACAGGGGACATCAAANAGCTTCCCCCCNTCA
CCGTCTAGCTGAAATCCGTCGCTTCTTTGGGGGACTNCAAGAAGAACGAGAACAAGAAAGTCGACGTTGA
AGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCATGGATCTTTACGCAGCTTACATC
AAAGCTGGCCTGCAACGCTAATGAAGAAACCAGTCCTTTTCCGTTCCTCCCGGTTTGCTTAGACATCACT
GAAGCCGCCTTCTATACTACATGCATGTTAGATAAAATTTCAATTGGTGCATTTAATTTCGTAATGCTCA
TCAGAAAACATTGTTGAACTTAAAGCTTTCTGATGATGATGAAAAATTTCCAGTACAATCAT
>gi|3450289|gb|AI100328.1|AI100328 34703 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114C16XP 3', mRNA sequence
TCCCCCCTCAGGNCCCGTCCGGATCCCCGGTCGGCCCACGCGTCCGNGAAGGCCATGTTGAACGAAATGG
TGTCGAANTGACAAGTGTGTGCTGGGACAAATGCATCACAAGCGCACCGGGAAGTAAGTTCAGCTCAAGC
GAGAGTTCTTGCCTCACTCATTGCGCTCAACGCTACATGGATATGAGTATGATCATCATGAAACGCTTTA
ATTCGCAGTAAGATTGATTGGAGATATCATACTTGTTGGGATTTTAATTTATCCTTTTTTTGTTTCTCTT
GGCAAGTGTTGAAATCCCTTTTATTACTCTAGTGATCTTGCAAGAGTATTCTCGGATAAGTGTTTTAGGT
GTTTCTTTATGGTTATGTGATTGAGATTGTTATTGATGGCTAGTAATATATTAAGAGACAAGTGTTGAAT
AATGTGGTTTTAAT
>gi|3450288|gb|AI100327.1|AI100327 34702 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114B3XP 3', mRNA sequence
GGGAAAGGCCTGGNGAAGAAGAGGNACCTCGAGCCAGNTAAGCTAGGNTGGTGAGNAANGNANGTGCCCA
ACCAAGAACCTGNGACCAAGCAAGCCATGAGTTTATCACTCACNGTATACAGAATCCGGTCATAAGGCAA
GCAGTAGTGAAAAACAATAATGCCTTTGACCTATGTTCTCTCTTGGTATGAGAGATCTTGTACTTGTACA
GAGATCTTTAACCTTCTGATGTGTGTGTTTGTATGTTCTAAGAAATCAAGTTTAAAATAATCGAAAAAAA
CAACCATATGCGTTGATTCAAAATACCAAAATGGTTACCAAACATATTTGTGTTTACAAAAAGCTTCCCT
ATACATT
>gi|3450287|gb|AI100326.1|AI100326 34701 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114B11XP 3', mRNA sequence
AATTTGGTANCCCTGGTGGAAACNTNAACCCGNTAACTTGCCCCNACCCCAGAGGCCNAAGGNGAAAGNN
CCTAGCAAACGGGGAGGTTGNCGATGTTAGGCATTCTTAGGGGTTTGTGGTTNAACACAATGTGNCTGGA
AAAGGACCATTTGAGAATCTGTTGCAGCACTTNTCTGACCCATGGCACAACACTATTGTCCAAACCTTCA
ACTAAAGAGTGAAGACAGACTTATGATCTCATACCTATCTATCTTCCATCACTTTCATGTCTGTCTGTGA
GTGTGTTTCATCTTAGAGTTCTTGGTTTTTGAGCTTGAATTATTGTTGAACCGTTGTAGCTCCATGAACA
AATTTGGAATCTTCAATGTACAGAGGAACTAAGTTAATCAACATTGTTGTACTCTTTAAT
>gi|3450286|gb|AI100325.1|AI100325 34700 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114A9XP 3', mRNA sequence
TTACGGGCGATTTTCGGCCGCAATTCCGGTAACGTNGNGNCAATNCTCAGGNGGTTACTTCCTCCATCCC
AGTCTTCAATCACNTCTCTTCNTCGCCACTGCGGCCGATTCCTATTTTCCGNCGGGTTGTACCGGGAAGC
TGANGTACATAAGCAGAGTTGATTATCTGTGGGAACATGTGAGGAGGAATGAGATAGAGATGCCGGAGTT
TGTATACGATCACGATGATGATCTGGAGTATCGTCCGATGATGGATTACGGTCAAGAAAGCGATCACGCG
AGGGTTTTCGCCGGAGCCGCCGTGGATTCATCAGTCTCAAGTTTCTCCATGAGGTGTATCTCATAGCGTA
AAAGGCTAAAACTCCACCCACTAGATATCGGATCGTATCTTATAAACCATATAATATACGAATACGATTA
ATAATATATC
>gi|3450285|gb|AI100324.1|AI100324 34699 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114A17XP 3', mRNA sequence
CCCAATGGCCCAANCCCCTTCGTTNATCTNACAAAGGNTCCCCCCNAGGTNGTGCCCAAGCTCCTTGGAA
GCCCAAGTCCTTNCCCCCACAAGGCCGCATTTGTGGGANCCAGAAAGAGTTCCGTGACCCTTGACGCTGA
CCAATGGCGTCGTCTCNAATGGGTTCGTATGAAGTGGACCCTCCTACAACTACTGTACCGACCGGACTAG
GTTCCCGGTTATGCCCAGCTGAATGTAAAAGGGACAGAGACGCATAAGTTACTACTCTTGAGGGTTTTAA
TGAATTTATGCTATCATTATTATTTGAATTATGCTTGTTCAAGAGATTGATATATGTATTGTTTGTTGGC
CCATGATGTTTATGCTATATTTGGGCCTAAAATTACATGTTATAATTCATATATGTATTGATTAGCTATG
TATTTTCATATGTTATGATCTACTTACAAGTTTTATTCTTTAACGTGGT
>gi|3450284|gb|AI100323.1|AI100323 34698 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114A13XP 3', mRNA sequence
CAAGATGNTTTCGAGCTTAGTTATNTGAATCTGTTCTCGTCTGGTTTATGATCTAANTGGAATCTTTTGT
GACTGTGTTACTTGCATTTANTTTTATGTCGTCTTTGNTTGGTCCACTGTATNGCTTGGGACTGAATTCT
TTTGGGATTTATTATCTTTCGNGAGAGGATNCTATTGAGAGCTTGAGATGGAGATNGCAGGATATTTTGA
TTGCAGATACTTTTGTGGNTTCATTTCTCATTCCATTTGAT
>gi|3450283|gb|AI100322.1|AI100322 34697 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113P20XP 3', mRNA sequence
ACCCGNGCCCTCTCTCCTCAANTGCTTCGAGTTCCTTNTTGTCGAAATCCCGGNGCCCATGGCTTCTCAT
NTGGCCCCATCATGAGTGCCNTGGNCACTGCTGATGTGCTGAGTCTCNCCAAGTGAGTGGAGGNCCGCTT
CGAGNTCCACGATCGACGTGGCCCAAGAGTTTTATGGAGAAGNTTTGATGACGCGACAGAGATCCCGACT
GACCTCTCACCCGTCAACTGGATGGACCCGAAGACGTCGCTTGGGACTTGCTTGAATCTACCTTAACATA
CCAGCACACGACTTATGCGGAGCCATTAAGAAGGCCACTTCAAAACCANTCGCATCTTAGAGGTCGTCTC
TCTTTACAAACACCTCAAATCATGTGGTGGCTACGATTCCATTCTTTCTTTTTAAAAAAAAAATTCTCCC
AACAGAAACCTTCTCTTCCCTTATTTTAGGCCATTCTAAACAAATATATCATGGTGGTTGATTCTAGTTT
ACGTTTTCCTTGTTATATAGTATTACTATTAATGTTTTTGAAATTCCTTTGTTTTGAAGCTTTATATCTT
GTATTTGTCCGAAACTAAAAAGGGAATGGTTTGTGCAAACT
>gi|3450282|gb|AI100321.1|AI100321 34696 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113P12XP 3', mRNA sequence
CGCCCCCGTGCTCGTAAGTGCNCTCCNACTTCTCTCCCTCNNCCCTCACTTGCGTTCTCCTCTCCTCCTC
ACGCCACCACATCGCNCCGCCGTCTCAGCTGTNCACCGCTCTATGGTAAGACCCGTGGTACCNGCTCACT
GATCGCAACGTCCTACCGCCTTTTCCAGGCTCGTCTCTGTTCTCATCTTTCCCANCACTCGAATTTCCTC
GAGAGCCCTAACTCTACGTCCGTGAGAAAGAAGCGTCTATGATCTTGAAACTAGCTGGTGGGCTCTGTGT
TGTAATCTTTTGCCCTGAGTGGATCGTTCTTGTTCTCGCCTTTTTCTTGAAGTACTACGCTTATGTCGAT
GGTGATAACAATGGAGTTGCTATGAAAAGGACTGGTAAGGTTCAGAGTGAAGAGACTCTCAAAAATTCCC
CATGGGCGTTCCAAGTTTGAAGAAAAATTCACTTCTTGTAATGATTTTGTTTAAGAGAAGAGAGGTTGTA
TCAAATGTTAGTTTGATCTGTGTTTNCAGGGTTTGGTTTATATGTATTGAAGAATTGAATTGGTTGATTA
CTTTGTTGATG
>gi|3450281|gb|AI100320.1|AI100320 34695 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113P10XP 3', mRNA sequence
CCTTCGTCATCCCCGCTAANCTCCNTTTTCCCGTNCCCCAGCCACACGNATTCTCCATCACAGCACGAGG
AGGTNGCTGCTGAGGTTGCCCCATCGGAAGAGAANTTGAACTCTTCTTCCTCCTNNCTTAGTGACGTGAT
TGGCTAAGGAAGTGACTCCTTCTCCGCACAGTGGATTCCTGTGTTGATTCGAGTTGGAGCACGGATTTGT
GTACCGTGAGCACGGAACACTCCCGGATACTATGATGGACGGTACTGGACAATGTGGAGCTTCCATTGTT
CGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTACCTGGCGCCTTCA
TTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAG
CTTCACCGAAGCTTAATCCCCTTTCTGGAATATTCAGCGTTGATTATTCTGGAACCCATTTCTATGTGGT
CAATGCAAATTTAAGAAATTATTTGCCGACTTAAAAGTTGAGGAACTATTGTTTGAAAGTGAAAATGTTA
TTCCTATCAGTTTCTCTATAATTATAGTTATCATTTCATTTC
>gi|3450280|gb|AI100319.1|AI100319 34694 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113O13XP 3', mRNA sequence
TTCTGTGGGGAGCAAGTGCAAGGGANNNTGAGCGTGATCCNAGAAANCTNATCCGTTCAGGNTTTAGAGG
TGATCTGATGAAGAGTACAGAGCTTCGTATCNCATCCANTGACTCCTAAGCATGGAGGTTCAGGGAGTNT
GGTGCATGGCACTCGAGTATGAGAAAATAACGAGGAGGTGGCTCATCCTGAGACTCTCCTCCAGTTTNCC
GTCGAAGTCTCCAAAGAAATCGACGAACATCTCTTGGCCGAGGAATAGAGGAGAATATTCCTCGTGTGAC
TATCTATTATCCTGTCCGTACATGTATGTGTGATTGAAGCATGCCGATTTTTATCACTCTTTGAATGTGG
AAAAATAAAGAGTTGTGTTGGATATATGAGAGTCATGTTGTATGTTTTTAAAGTGCTATACTCTAAATCT
GTATACGTATAATGTGTTTTGTTTGTTTAATAAAGTGTAAAATGTTTTTTTAATAAAATCTTAAGCCTCG
TCTTTTCTTT
>gi|3450279|gb|AI100318.1|AI100318 34693 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113N4XP 3', mRNA sequence
TTCCTTGGAATTTTCCCACAGATTGGAAGTGGTACCNTAGGATCCAACTNTGTACTGGNCCATNTTCCCC
TCCCGTGGAGTTNTNTGCNCTTTNTGCCCGATTGAGATCTGNGAAGAAAGGTCACTCTACTCAGAATCTC
AACGNGGGTGATGAATCCTGACTCTCTAACCCATTATGCACGCCAGGGAGTGTCCTTCATGTTGACAACT
GCTCAACCACAGCAAGATTGGGTTCGAGGAATGGGCGCCCGGTTTGACTACATCCTGACCCAACAAGCTC
TTGTGGCTGTGGACAGTGGTGCAGCAATCAACAGAGACCTAATCAGTAACTTCTTCTCTGATCCAGTCCA
TGGTGCCATTGAGGTCTGCGCACAGCTCAGGCCTACCGTTGATATCTCTGTGCCTGCTGATGCAGACTTT
GTTCGACCTGAGTTGCGTCAATCTAGCAACTGAGTGAAGGGTTGAAAGTTTGTCAGTCTCTTATTTGTAA
TCGGAGTATTAAGTCGAGAGTTTGTGATGTTTTCTTAGGCGTGACTGTTTGTTTTGTTTGAAGGATTATG
TCTCTTTGCTTTGGTCTTAAAATCTACTTAAATCAATAAAATAGTTTAACG
>gi|3450278|gb|AI100317.1|AI100317 34692 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113N15XP 3', mRNA sequence
CGTTGGCTCGCGATCCGNTTTTCGTCACCTCCTCCTTGATGACAGGTATCGACTGCAACGTGCTAAGTCC
ACGTAGTACNTCGCTAAACCAGTGAACGANCGGATGGTCCNATAAGTCTAACGAACTCCTATACTGGAAC
GCTCATACATTTGCGCTCACGGATCGGGGAAGCTATTCGCGTTTGGTGCAGGCGATCAGGGTCAGCTTGG
AACAGAGCTTGGTAAGAACCAAAAAGAAAGGTGTGTACCGGAAAAAGTGGATATCGATCTCAGCTAGCTA
GCTGACTTATGTGGTTTGGTTGGTAAGAAACTACGTTTGACATCAAGGAAACAAAAACGCAAGAAAATTT
GCGTTTGCTTTTTATGTTCATAAGACTTGGAAGCTTGTACAAAAAGGGGAATAACATAAACTTGTCTTTA
ACATTTCATTGTATAGGGTTTTTAGATTATTCTAATTGTTCATTGGTTAAGTTTTAGGTTATGTTGTTAA
TAATTATCAAATAATTTCATTAAATCAAATTATTGTCAG
>gi|3450277|gb|AI100316.1|AI100316 34691 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113M8XP 3', mRNA sequence
GGGCTAAGTGTCACCGGTTNCATGGCCCAGTGGTCGTTGTCCGGTTNGCAGTCCCCAAAGTACCTCCAGN
GNTNTTGGATCANGGGCCCCAAGCTGGTTCTTCTGGAGNCTTCCCCAACTCAGTCTCAACCCCTGACAAT
ATCCAAAGGATTGGCTCTACTGGAAACTTTGGGGTCGCTTCAGTGGTGAACAAGTTCATCGTACNTACGA
ACCCATCAGCAGTCAAAGTTAACTCTAATGGTGAAGTTCTTCAAACCATTCCTCTCAAAGATAAATTTGG
AGACACTTTGCTCAGCGAAGTCAACGAATTCGAGGGCAATTTATATATAGGAACTCTCACCGGACCATTT
GCTGGAATTCTTAAGCTCGAAAAGGGTTCTTGTCCTNCCACTTAGATCTCTTATTTGAATGCAGCCGATG
TGTTACAATCATATATATATATTTGAGCTTTTTATT
>gi|3450276|gb|AI100315.1|AI100315 34690 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113M5XP 3', mRNA sequence
ATTCATCTTGNACTGGCCATCAANCCTTTCACCCTGAGAGCNCGTTGCATTTCCTTGAAGCTGTTGATNN
CCGNGACACTTACAAGTTCTCTACATTCACCCGCCCATTACATTGTNTCGCAGAACGATATGGTTGGTTT
GTGGGAGGAAAAGATCGGTNAGACTCTCGAAAAGACTTATGTTTCAGAGGAAGAACTCCTCAAAACCATC
CAAGAGAGTAAGCCTCCAATGGATTTTTTGGTGGGTCTGATCCATACAANCCTTTGTGAAGAGTGACTTT
ACCTCCTTCACTATAGATCCTTCTTTTGGAGTTGAGGCTTCCGAGCTTTACCCTGAAGTCAAGTACACTA
GTGTTGATGAGTTTCTTAACCGGTTTATCTGAAAAAAATTCGTCCATTATTTTGTGTGTGTAGCTACTGT
TAATTCGAGTTTCGATATGGACGCAAATCTTATTTC
>gi|3450275|gb|AI100314.1|AI100314 34689 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113L3XP 3', mRNA sequence
AAGGGAACGTNTCAACGGAAAGGNNACTTTGTTTGGCCCCTGGGGNTAATTACGAATTCTGCAACGGTNC
ACCGTCAGATTCGGACTTAGTTACGTTGATTTCAATAATGTCACTGCTGATAGAGACCTCAAAGCTTCTG
GCTTATGGTACCAGTCGTTCTTGAGAGATCCACCAAGAACCAAGATATCCTCCGCTCAAGTCTGCCCTTT
AAGAACGGGGATAGGAAGAGCCTCACATGAAAGACCAAAACCACTTTATGCCCATCGAGATCATCT
>gi|3450274|gb|AI100313.1|AI100313 34688 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113K15XP 3', mRNA sequence
AACTTTNGGCCCNCGAATTTCCCAGAAATTGGCCTCGATATTGGGGAAGTTTGGNNCACTCANATCTCCT
GAACCAGTTGCGATCNCCGTCGTCCGATCGGTGAACCCATGTAACTGTTACGATCGAAATNCTGAGATTG
AAAATGGTCAGGGAGTTAGAAACAGTGCTGCAGCTACTTGAGTTTGCCCAAGAAACCCTAATAAGAAACC
TATTTGTTGACTATTTTGACTTTGTACCCTTCTTGATATACCTATCAATCACCATTGTCCACGTGTACTA
GTTTCGTTGTAGTGATTTTCAAAGTTTATCGAAGTATGCATATTCAAGGATTAATT
>gi|3450273|gb|AI100312.1|AI100312 34687 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113J6XP 3', mRNA sequence
TGAAACTTTATTCCNAGGGCTTGGGGGNACCCATCGCAGNAACCTGGCTGGTATGGGNANCATCCCTCTG
TGTTTCAAGGCTGGGGGAGGACGCNGAACCCCTTGGACTCCACTGGTCATGAACGCTACACAGTCCACCT
CCTACAAAAGTTAGTGACATTAGACCCGGTCAAGACGTCACTGTAACCACTGACAGTGGCAAATCCTTTG
TCTGCACCCTGCGTTTTGATACAGAGGTGGAATTGGCATACTATGATCACGGCGGTATTCTACCATACGT
CATCCGGAGTTTGAGCGCCAAGTGATCTCAAAGTGTTTTTCGCCTTTTGTTTTCTTCTTATGTTAAGATC
CCAATAAAGCAAGTTTTGTGAGCATCTTTTTTCTTTCAGGTTACACTAAACCTTTGTTGGCAAGAGTTGC
TATAAGAAAATGCAAAAATACACACTTCATTTTATAAACAGTTTAACGT
>gi|3450272|gb|AI100311.1|AI100311 34686 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113J4XP 3', mRNA sequence
AACCGNCATTAAACNCNTCTTTGAGCCGTGTGTNCCGAGGTTCCCGTCTGAGGCTACTGGGCGATATCAT
CATCCAACTCGCATCGGCTCGTGGAGTTTGTCCATGGCTGAAAGCGCGATAGCGGCTCTCAACTGCAGTG
GTGNCCTTCTTGGTTCTTTACCGATAAGGGTGAGTCCATCAAAGACACCGGTTCGTTCCCGTGCTATCCC
GCGACATCAAATGCATTAACCGTAGCTACAAGTTTTATATATTTCTGCTCCTCACAGACATGTAAAGAAT
GTTTGTCTGAAACTTCTGGTTCTTCTGTTTTCCCGTATGTAATGCTAGAAGCTTGATGATGCTTCTGTTG
CCTTTTGCTTTTGGGTAAATCTCTTAGGGAGAGTTTTTTC
>gi|3450271|gb|AI100310.1|AI100310 34685 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113J22XP 3', mRNA sequence
CCCGGTTTTNTGACGTTTACCCNGGGAACCNTTTTTNATGGGCAAGAACAGTCCGTTTAGCGTGAAGGCT
TTAAAGCGTNCACCCGCAATACCGTTCTNGGCAAAGNGCAGAAAGCNCATTGCGTAAGAAGNGGAAGNCA
AAAACATTGNGAATTCATCAAAAGCATTTTATGTTGTTGTTGTTCAGATTTAAAAATTGCTGATTCTGCT
GCTGAGGTTTTCTGTACATATAAAACCTCTCCCTAAGTTTCATTCAGTTTCATCATTGTTAAAGTAACTA
ACTCAGAACAAATGGGTTTGGTTATTAATCTCTTTCAACT
>gi|3450270|gb|AI100309.1|AI100309 34684 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113J10XP 3', mRNA sequence
CTANTATGGAAAACGCTATNGTTNTCCNCCACATTGCTTCTGCTTCCAAGTGGACTCGTNAAGGAATGGT
CCNTTGCAGCTCTCAACGTCCTCGGAAGAGTCAAAGGTACCCGATTTGGCATGACCCGAACCGAGTCGAT
CCATTCTTGAACGAAAACGCTTCACCGCCCAATGCCAGTCCAAGCATCGTCAACTCAAAGGCCTTAGGAT
TGCCTGTTTCGAAGCTATGAGTTAAGTATGAAGAAGGGGAGATTTGGAAGAATCCTTTTAGTGAATATAT
GATGGTGTCAAGTTGTGTTTATGTATTGTATATGAAACAACCATGTTGGATCATATAAATCACTCCTTTA
AAGTGTTACATTGTTGATGAGTCTATTAGACGATTACCCACTCTCTTTATTTCATAAATTTGCTAAGAAT
AC
>gi|3450269|gb|AI100308.1|AI100308 34683 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113I2XP 3', mRNA sequence
AAATTTTTTAANAAGGCAAGTTTGTTNCNCCCATGGNATGGGGAATTGGCTACTTGCCCCCAAAGGCCCC
CTTAAGGAGNAGAGATGTGCAAGTAGTTATGGGACAAAGNTGGCTGTGAAGGTTGCTGGTGGTGAGATCG
TGGAATCTGAACGNTGCGTGACCGACGACAAGCTGGTCACAGCCGCATCAACTTCCGATCTNCCCCCCTT
TTTGTATGCATTGTCGACTGCACTTGGTCTCTCTGTTGTATTCTAATGTCAAGTGGTGCTTTAACGTCTA
ATGCCT
>gi|3450268|gb|AI100307.1|AI100307 34682 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113I20XP 3', mRNA sequence
GACCGTTTTTCACCNCCNAAGCAGGCTTTGATGATNCATCGCTGGGTAGATCCATGGGTGGGGAATCATA
CAGGGCCAGTACCNCTGATTATGCAGCTTCTTAGAGACANTCTCACTCTCTGGACTTCAGATATGACTGA
CGAAGCAGGAGATGAGATTAAGGAGGCATCAAAGCCCGATGGTGCCGAGTAAACCCGAAGAAGAGGAAGA
GTCATTTTATAATGGTAGAAAACTTTCATGTGATAATCTGAGTGAGGGATAGCTCAGGATTCTTATAAGA
GACACAGTTTTATTGTTGTTTGTTTGTTTTGAAACTACTTGCGATTTATCATTCCTCCTTTAGCTTCCTC
AATATTTCCTATTCTCCTTTCTAATGAAATCAAAACTTGGTTATTTCTG
>gi|3450267|gb|AI100306.1|AI100306 34681 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113H5XP 3', mRNA sequence
GGTCATTGGTACCAAATTNGTGCTGGAGACTNANGGTAATGTTNNCAGTGGGTTCCATGGAAGAGATGGT
GGTTCTTCTGATGCTATTGGAGTATATTTCTCTCCAATGATATCTTCCTAAGCTACAGAAGTTTGTTCAT
GCATGGCTTCACGTATCTTTTACTACTTTAAAATACTTATCGATTCCGATGTTGTCAACTATGAACATCT
ATGTAACGAAATAAAAGTTTATCCAAAACTAATTTCAATATGTCATTTAAAATATTTTCGATCTATATTT
TATAATAAAACTTCAATTTTAC
>gi|3450266|gb|AI100305.1|AI100305 34680 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113H20XP 3', mRNA sequence
TGAGAATTCCCACTNAGGNTTCCTTAAGATCACTTCCAGAAANGCNCNCTNTGGTNAAGGTACCAATACT
TGGGGACAGGTTGAGCTCAGGGTTCACAANCGTGTCATCGATCTCTTCAGCTNCCCCTGACGTTGTTAAG
CAAATCACGTCTATCACCATTGAGCCCGGTGTTGAGGTCGAGGTCACTATTGCTGACTCTTAGACACTTG
TTCCAAAACCGCTTCAAAAGAATGTATTTTATCGTTTCTGGTCCTCCATTTTTGTTTNCAACCTTGTTTC
TTGGGTTTTNATAGTTCTGAGGTNGTTTTTGTCTATCGAATTTTTTTCATCTATAAGAGACCTTAATNAA
CC
>gi|3450265|gb|AI100304.1|AI100304 34679 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113H1XP 3', mRNA sequence
CCGGNACTTNTCAACCCCTNNCTTGAACCTNCTTCTGAATATTTNATTCTCCAGAGGAAGTCATGGACNC
TTAAGCTCTTAGCTGGTTGTGCACTCAACAAGTATATATCTTCTTGACGACTTCTTGCTCGCAACAACTC
TCTACCAGCTATCAAATGCATCGTACGGTTGTTGTCTGAGGAGAACATAACTGAGTCGTCGTCACAAACA
AGAGGAACATATGCAGTTTCGGTCAGAACCAGTCGTGTGAATGGTAGATATATGTATGTGTGTGTAGAAA
ATGGTTACCAATTGTATCTTCTTTTTGATAATTATTTTTTCATGCCTTTTGTAATATGTAAGTTTCTTTA
CCTCGTTCTCTGATTGGTTATTTTCTCGTTATCTGTTTAACC
>gi|3450264|gb|AI100303.1|AI100303 34678 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113G6XP 3', mRNA sequence
ATGGGCACTCATGNCTATGGCTTCTTCAAAAGGGCTTTGCTNGGGAGTGTGAGCGAGTATTGCGCCAAAC
GAGTCAAGTGTCCTGTGGTTATCNTCAAGAANCAAGCTCAAGATAATTAAGCTCATATGATTGCATTGTG
TATATGTTNCGAAAGAACTGGTGTAACNCTTGAGTCAATCTTCGTATGCGATAATAAAATACATNACGNT
TTAA
>gi|3450263|gb|AI100302.1|AI100302 34677 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113G2XP 3', mRNA sequence
GGATTNGNTCCCCANGCCAAGGNGATACCNAAAGATTGTTGAAGGGAGAGCTTCGACTTCCAGACCAGGA
ATGATTGNCAATTTAACCTTGACCTAAAAGAGAGGAGGAACCGGAAGNTTCTTGAAAACTGCGGCTTACG
GACACTTTGGAAGAGACGACCCTGACTTCACCTGGGAAGTCGTCAAGCCACTCAAGTGGGACAAACCTCA
AGCTTAAATTTTACCTACTCTGTTTCTGTCTTCATTCCACAAACCAATTATCTGCTCACTTTTTTATTTC
TCTGTTTTTGTGGTTTATTGTGTTTATGTATCATTGTACTTGAGCTATTTCAATTGGGTGTTTGTTTTTA
TGGCGACTTTTACACGGCTTGGAGT
>gi|3450262|gb|AI100301.1|AI100301 34676 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113G21XP 3', mRNA sequence
AAGGNAGAGTTTCCGGGAGTCCTNCCCNGANCACTNCAAGNCAAGGCCCAACNCNNNCAAACTAGCCAGC
CAATGAGGAATGAGTCATCCATTATGGTTTTGGTTACGCTAAAATAAAAAGAAGACCTTTGGCTTTTGTT
CTTCAATCCTTATGCATGCTTTCTAAAGTGGTTATGATGGATTTTGCTTGATGTTCCACATTATGGGTTA
TTCTATTTTCTTTGTTCTTGTAAGATGATGCTTCAGAAGAGTTTGTTACTTTTTACCGTATTTGTNATTT
ACATTTTCACTGAAAACAATTGGCGAGTAAAAAAGTGTCCTTGTCTT
>gi|3450261|gb|AI100300.1|AI100300 34675 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113G12XP 3', mRNA sequence
ACCGTANCATCCCTTTCCGATGAANTGGACNNAANATTCCCAGGATTTNNGAGCCCCAANANCTATTGCT
NAAGGANCCTAATTGGGACTCTTANGGGAGATTCTTGGAACGTGTGTCTCTGTGGGATGCACTGTTGATG
GGAAAGACCCTAAGGATCTTCAGCAGGAGATTCAAGAAGNTGAGATTGAGATTCCTGAGAATTAAGGAAC
AATGGAGTTTTTTTNTCTTCTTATGGGAATTTGAAATGCTTCTGTTGTTATCTTTCTCGTTTTACCATAT
TTTGTTTTTGTTTGGGAACTTAGCTGCTATGATGTTTCACTTAGAATGACTCTCAAGTTTTGGATTCTTA
TTATTCTCTGTTTCAAAACCCCAATGGTTCTCTATC
>gi|3450260|gb|AI100299.1|AI100299 34674 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113G11XP 3', mRNA sequence
ACCCGGNGCTNACNTTTCACCGGACGTGANCNCCTTTGGNGNGCAACCAACGTGGTTCACGCATCACCCA
GATTCGGATGTTCGTGATGNCCCTGAAGAAATTAGAGCTTCTCAAGGACTGAAACCTAAAATAAAACGAT
CACATCTCCAGTCATCAATGGGTTGGTACCAAATGCGAACTATCTTTTTCATATTGACCACATGGTTTGG
TTTGTTTTATTACTTCGTCGTACATAAGCTGCCGGAAATACCTAACTCTTCATATGGTTGTCTCTTTGAC
ACCTACCGGATTTTACTTCATTTATGCAAAGTATTGTAATAATAAAAAGAAAAAGAGGAT
>gi|3450259|gb|AI100298.1|AI100298 34673 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113C1XP 3', mRNA sequence
ATNCTNTTGGAGATTTTCCNGGGGGANTTTTANTGATGTCTGCCAGAAGCTTGANATAATNGAAAGGNTG
TGATGCTATTGGGNTTAGCTGCAGCTCCGGNGCAATGGAGAAATCGAAGATGAGAGCTTAAAAGATGGAA
CATGACAAAGCTTTCTAATTATACAAAAATATGTGCGATCTCTTTTGGTGGTGTTTTTAAATTTCAAAAC
ATCAATATCTCTAGTTTCTGAGATTTTTAAAAGAAGTAAGTAAGACCACGAATGTAAGGAAATGAAGAAG
AATTAAAAATGATCTATTTTTGTTGTTTGTTTGTTGCTTTAGTCAGTAAACTGGTCGTTGTTTTATGTTT
TGTGTTTGATTTGGATGTGTGGTTGACTTCT
>gi|3450258|gb|AI100297.1|AI100297 34672 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113A23XP 3', mRNA sequence
TTTGCCCCCCTGGGGACCGCCCCTGCTTGACTAAGNGTTTGGGNAAGGNCAGCTGNNTAACGGNCAAGCN
TGGGNGATACTGGATGGCATTGCCCAAGGGGACTGCGGAAGTTGTAACTCCGCTGGAACATACCAGGCAG
AACAAATGCCCAGTCTGGTTGTGGCGAGCCGACACAAAGATGGTATCATGTTCCGCGTTCGTGGTTGAAG
CCAAAAGGGAACTTGTTAGTACTTTTTGAAGAACTTGGTGGAGATATATCCAAAGTCTCTGTTGTGAAGA
GATCAGTAAACTAACTT
>gi|3450257|gb|AI100296.1|AI100296 34671 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113A22XP 3', mRNA sequence
AATTTNAAAGNTTCAGCCGGNACAATTGNNGGCATTAACANCATGNCCTAGTGGGTGGTTCGTGAGTTCC
GCTTTCAACTTTATGTTTGAATGGAGCGCACAAGGAACATTTTACATATTTGCGGCTGTCGGAGGAATGT
CATTCATTTTTATTTGGATGCTCGTACCGGAAACCAAAGGACAATCATTGGAAGAATTAACAANTTCGCT
TACGGGGACATCCTAAATGCACATTTATATTGTAATATACTATTAATTTTGTTTGGTAAAAAGATAAAAT
TTATTTTCTGTTGTCAGTCGCATTGCAAATAATAAATGTATTTTGTAACATTATTTGCATATTGATATTA
ATAATATTTTACATTTTTTTCCTTCGC
>gi|3450256|gb|AI100295.1|AI100295 34670 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113020XP 3', mRNA sequence
CGGTCTTGGCTNCCGTCCTTGCCAAGGTCTCCACTTGATCTCCTGGTCCGCAAGGAAGCGCACNCNCGCC
AACGGGAGCGCAAAGCCGAACTGCAGATCCACGTNCAGAATNTCNTTCCCCCATTCCACTGGTGGACANT
CTATGCTGCTCCACATGNCCTGCAGGTCCAACCATCCCANTACACGCACCACCACAANTACCGCGGGACC
CAGCCACAACTTCTATGGGAAGCCGCGTGGTCCACCTGGTCCAAACCGCTACCCTCCTAGCGGAAACCAG
AGCGGGGGTTATAATCAAAGCCGAGGAGGTTACAGCAGTGGATCATATCCTCCACAAGGACGTGGAGCTC
CTTATGTGGCTGGTCCTAGAGGGCCTAGTGGTGGCCCGTACGGGGTTGGACCTCCTAACTACACACAAGG
TGGTCAGTATGGTGGCTCTGGTAGCTCGGGAAGAGGGCAGAATCAGAGAAACCAGCAATACGGATGGCAA
CAGTAAAGAGCTCTAATGATTTGTTGATCTGATATCTTACTCTTACATTTAATGTGATACTAGTAATAAG
CTAATAATAGATTAATATGAGAAACTGAATCTCTTTCTTTTCCC
>gi|3450255|gb|AI100294.1|AI100294 34669 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113017XP 3', mRNA sequence
TACAAACCNCCGGTTNTGATCCCCAAGAAGCCTGCCCCCGCCGNTACCGGTATACAAACCACCGGTAGTG
GTGATTCCAAGANGCCATGTCCGCCANTTCCACAGCTTCCACCACTTCCAAAGTTTCCACCTCTTCCTCN
TAAATACATTCACCACCCCAAGTTCGGGAAATGNCCTCCGTTGCNTCCACACCNTTGAGAAACATTAAAT
ACGTATATATATAGATATACGTATACTCATGTATAATCAACGTGTTACCTTTTTTTAAATATTTTATCTT
TGCATATGTTTTATATTTTGTTTCATTTGTTGGCTTTGAGTTGTCTATGTGTAGACTGTTTGTTTATATT
CCCGTCAATCTTCCAACAATAATATGGTAATGATACGTTTCTCTT
>gi|3450254|gb|AI100293.1|AI100293 34668 Lambda-PRL2 Arabidopsis thaliana cDNA clone 113014XP 3', mRNA sequence
CTTTTGCANCCGNCGGAACGGAGGAACAAAAGCAGAGAGCTAATCAATCATGGGAAAGGTTCACGGATCT
TTGGCTCGTGCCGGTAAGGTTAGAGGACAAACTCCAAAGGTTGCGAAGCAAGATAAGAAAAAGAAGCCCA
GAGGTCGTGCTCACAAGCGTCTGCAGCACAACCGTCGTTTTGTCACCGCAGTTGTTGGTTTCGGAAAGAA
GAGAGGACCCAACTCTTCTGAGAAATAGAAGAAGTTAGAGAGAAAGATGTTGTCGTGAAACTTCTCAAGG
TCATTTGTAACTTTTTGTTTTCTTTGGCACCGAACTATTATGTTTTGATTCTATGCCTATGAAATACTGT
TTTTTCACTTATGATTTTGGTCAATTAAACATAAGATATGATTTTTGCC
>gi|3450253|gb|AI100292.1|AI100292 34667 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111O9XP 3', mRNA sequence
GCTTGGGCAGGGNCTGNTNCCCAAATCGGGCAATTGGAGGACCGAAGCTNCGNGAATTTCCCAAAGATGT
TGTGGATATGCTTCTGAAAAATGTGCCCACAGTGAACAACTGAGTATAATATCTCAAGGAAAACCATCAA
CTGTAAAATGGTGTGATATTTTCAGTGGATACGTTCATTCCTTTCTTTATATTGTTTTGTGGAATCCAGA
CTCGTCTGTTGCTATTGATTTTGAAATTGTGTCTTGAAGCATTGTATTCATTTCTACAGAAAGTCGCTTA
GGACTTTTGTGTGTTGTAATAAAATTGAGAACAAAGGAGCCCATTGGATTTTGTTTCATCAAGAAGATTG
AAAATATTCGAACAAGAACCGTCGGTTGTTTTGC
>gi|3450252|gb|AI100291.1|AI100291 34666 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111O21XP 3', mRNA sequence
CCCCANCCCCATTGNCCAGACTCCCTTTTGCTAGAAGGCTTCNCTTCACCGNTTCTTGGAGAAGAGAAAG
GNCAGAGTTNCGTCAAAGGCNCCATACCAATTATGCGATCCAGCCAAAGCGTCTTCAAACCCTCAANCCA
CAGGCAACATGTCGTGGCTCGGTTTAGCAGCTGAAATATGAATGCTAACCNCCCTCAAGCCGTACCAAGA
AATTCTTTTGACGACGTTGCTTCAAGACAAGATATAAAAGCNCCTATCTTCATGCTTTTTGATTTAAGAT
ACAAACTACTCAATGATTAGGAAACTTCATATATTTGTATGTATTGATTAGTGATCAATTATTGTTAGT
>gi|3450251|gb|AI100290.1|AI100290 34665 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111N9XP 3', mRNA sequence
CGAAATNCCGCGGCCTAAANCAGNCCACCTGGTAACGTCACAGCTGGTGCTTTAACTCTCTCGCCATCCT
CGGTATCCCCCAAGCCATTACGTTTAGCATTTCCTTTTNGCACTAGCTTCCATATTTCAACCAATTTCCG
GTGCCGGCCAAGGACTTTCCCTNGGTGTTCTGAATCTAGCCATTGTCGTCCCTCAGATGGTAATATCTGT
GGGAGGTGGACCATTCGACGAACTATTCGGTGGTGGAAACATTCCAGCATTTGTGTTAGGAGCGATTGCG
GCAGCGGTAAGTGGTGTATTGGCGTTGACGGTGTTGCCTTCACCGCCTCCGGATGCTCCTGCCTTCAAAG
CTACTATGGGATTTCATTGAATTTTAGCAGTGGTTGTTTGGCTCTCTTTCTCTCATAAAACAGTAGTGTT
GTGCAAATCCTACAT
>gi|3450250|gb|AI100289.1|AI100289 34664 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111M8XP 3', mRNA sequence
AGCTTTNTTTCGCCGGCCTNCTTTCCCGGANANTGAAAAATGGGATGATTTTCTTCCTTTTCCGNTAACT
TTATATTCTTCACATAACCTGCCTTTTGGCNATTCACTCTCAGATATGTTTTTGTGAGTCGTTAGAATTT
GAATCATGAAGAATTCAAAGGAGAAGAGGCAACAAGAAAAAATGAGTGTTCGTTGAGTTATGGCCCCCCT
TTCGACTTTTTGTTTGGTTGTATNCCTCTCTATAGGCTATATGGCTTCTGATTATTTTGCGTGGGCGGCA
AAGAAAATAAGATCGAACATTGTAGTTTTTTCTTTGGTTTAAATTAGTCTTTTTCCATT
>gi|3450249|gb|AI100288.1|AI100288 34663 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111M18XP 3', mRNA sequence
CGGTATTCTNCGGACCATCGTTCCGNCNGCGGGGAAAAGAGAGAGAGGGATNTGAAACAGGCCCCNTCGT
CGTGCGTGNTGGAGGCTTTTNCGCCNTAGNGTTNTGAGGAAGACCTNTGGAGGAGGAATAGAGGAAGATC
ATTCGGCGCGTACACGGAAAACGAAGCGCGTGGATATGTGAAACGCAATGATAGGCCTCAGCATCTTAGC
TTCTTGGATCATATCCGTATTTTCGTATCTTCTCCATGTGATTGATTTTTATTTCTTTCGTGGTCTCTCC
CGCTCGTCGCTTTTCTATGTTTGTTTGTTTTTTTCTCGGGACAAAAGAAAC
>gi|3450248|gb|AI100287.1|AI100287 34662 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111K6XP 3', mRNA sequence
GGATTTTGGAAGCCAGTTNTTTGGAACAAGCACCCCNGNGCATNTCNCTCATCGCGNTGNTGCTTAGCNC
CTCAGTTCCTTCATTGCTGACCGGCTCGAAACAGCAGTGAAGAANGTCATCGCTGAAGGAAAGTCCCGGA
CGAAAGATCTTGGTGGAACAAGCACGACTCAAGAGGTCGTTGATGCGGTCATTGCAAAACTAGACTGACT
TTGACAAATTACGTGTTCCCGCTCTGCATAAATCATCAAATTCCTGATACAGATTTTGTGTTGCCAAAAT
ATGGGGTATGATCCAAGCACAACGGTTATCTGGTTTTGTACCTCGAGTTTTATTATATTCTTTAGCCGTG
GAATATTTCGATAAGAAAAAAAAACATGTTCCAAATAATTCATGTTGCTACGTTTGTTGGCGCCTTTTGT
CATGTCAAAGTTTCTTAAACACTTGTTCGTGGAATATGCAAACTTTTATGGATTCGTAATTTC
>gi|3450247|gb|AI100286.1|AI100286 34661 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111K12XP 3', mRNA sequence
TGTTCGACACGTTTTACGATTTCTCGCTCCTCCACTGTGAAAGTACCGACGGTTGCGTTCCATTTCACGG
GAGGGAAGTCGCTGATTGCCGCGAAGAATTATCTGATCCCTGTGGATGATAGTGGAACGTTTCTGTCGCT
TTTGCTCCACGTCGTCGTCGTTGTCGATCATCGGGAATGTGCAGCAGCAAGGGACACGTATCACTTACGA
TCTATCCAAAAATGTTATCGGATTGTCAGGGAATAAATGCTAAACATGTCAAAGTAGAAAAATTAATAGT
TTTACGGGTAATCAGTAAAACTTTTTATGGTACTAGCTAGCTACGGTAACAAGATGAAAACAAAATCCTT
AAGTGTGAATTTTTGTACCTTTTTTTTAATTAATCATAAGTTATTGTCGTCTTTTATCGAAT
>gi|3450246|gb|AI100285.1|AI100285 34660 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111J7XP 3', mRNA sequence
ANCCNGTGCNAANCCACGCNGTCCAGNGGTCACCTTGGAAGTCCAGCCTGAAGAAGNCGGTGGNTCTCTC
CCCGNAGGTCCAAGNGTTCTTGGNCCGNTTCGCAAAACGCAAACCGCAACGTTGAGTAAGAGACAGAGAC
TTGGCACTTCATGCCAGTTTTGAGAGNCGTATAGTAAAAAGTAAAACTCGAGAAGTTAAAAGAGACAGTA
TGGAGTAAAAAACTGAAGACTTCTTCTTCAGTTCTATGGTAGTAAAAAACTAGTAGTTACTTTTGGAAGG
TTTGGCTTATGACAAGCGACGAGGTGAAGAAAAGGGGTTTTGTTTGTTTGTTTTTTTAACTGTTTTGTAA
ATATTTCTTTTACTACTCTTTGTGATCTTCTTTGTTTGTTTGTTTGGTTTTTTTTTTGCCCCTTTTATCA
CCTTCTCTTGTTTTTTTCTTTGGTATGTCCTTGTGGCTTGGCCTTGTCCCATAAATAATATTAGTCTTCT
TTCACT
>gi|3450245|gb|AI100284.1|AI100284 34659 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111J24XP 3', mRNA sequence
CAAAGCNCAGCTAAGAGGCCGCTAAGAAATCTNGGNNAAGTGTNCCATNAGCTTGTTAATTNCCAGCATC
TGATCCCTACTCGTACACACTCGACGTGGATCTCAAGGAANTGGCGACTCTTGATGCTCTTCAGAGTAAG
GATAAGAAGGTTGCTGCTCTTAAGGAAGCTAAGGCTAAGCTTGAGGAGAGGTTCAAGACTGGTAAGAACA
GATGGTTCTTTNCCAAGCTCAGGTTCTGAAGAAATTTTCTATTTCGTGNGGAATTCATTTTGAGCTTTTT
GTTATCGTGTTTTTTAGTTTCTAGGGTTCATTTCCCATGGTGAAAAATGTGGATCCTGTTTTGGATTGTG
GAAGATGTTTTGTTGAAGTTTGGATTATGGATTTGATCTTTTATTTTGATTCTCTAATGCATTCTTATTT
ACTC
>gi|3450244|gb|AI100283.1|AI100283 34658 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111F24XP 3', mRNA sequence
CACTCATGGTTTCTAGGACAGCACGTAACATTGCCCGGTTGACCATCGTGCTTCCGNTCCCCAACTTGAA
GNCGTTAGGACTGATCTCCAAAGNGGTTNTGGAAAGCTGACCCNCCAGNGNTAGCNCTTACTGACAACTC
CATTGTGGATCAGGCTCTCGGAAAGCATGGGATCATCTGCGTTGAGGATCTCATCCACGAGATCATGACT
GTTGGACCTCACTTCAAGGAAGCCAACAACTTCCTGTGGCCATTCCAATTGAAGGCACCACTCGGTGGCC
TTAAGAAGAAGAGAAACCACTACGTCGAAGGTGGTGATGCTGGAAACAGGGAGAATTTCATCAACGAGCT
TGTCAGGAGAATGAATTGATGAAAGCTTCCTTCTTTATCTTTGCAAATTTCAAAGATTTTGGGACCGAGT
TTTTTTTTTTTTGTTCAAGTTATCAGAGACTTGTGATCTTTTATCCGAGATAGGCTTTTTATGACTAATC
ATGTTATTTTCC
>gi|3450243|gb|AI100282.1|AI100282 34657 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111E24XP 3', mRNA sequence
GGAGCCGCAGAGTCTGAGAGTNGTGGCACNACAAGNGCTTTCACATTGGTGGAGATTTTAGNTGGGAAAA
TCNAGNAAATNGCAGAAATTTGGGTACATGTAAATGGAAGTATGGCTAAGATTGTGGNGGNAAATACTTT
GTTTGAAGATGTAACCTGATTTGAAATTTAAACAATTAATTCGGGACAAGACTGTAATAACTAATTATAC
ATTTGTCTTGGCGAACAAGTCCCTTTTAG
>gi|3450242|gb|AI100281.1|AI100281 34656 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111E18XP 3', mRNA sequence
TCACCCCATGGTGANCTGAGNGCCCTANCCTATNGCCCTGCCTTANGGCCTATTCCACAGGCCTCTTCTT
GTTCGAGAAATGGCTCTTTGATGNGCAAAGCCNCGATATGATCCATCAATAACATGTCACTAGNGGGTCA
GGAAGTGTTGTTCTAGAAAGCATTAAAGTTTGNCGATTTGCTTGAGGANCCACGAGGCTTAGTTATAAAC
AATTTGTATAATTAAGTACTCTTTAGTTTTGTTTTCAANCCTTATTATGATCATATTGCAGTAATTAGGG
ATTTTAGTCTTTAGTAGTAACTCTTAAGTTTTAACACATTTTTCTCTATCTTTTTAGTAGTAACTCTTTA
TTTTTTCCTTAAATCTTTGTCGACGTGGAGATGATATCTTCTATGTAGTAGAAACTCAAAAGTGTACATC
ATCTTTATTAATGTAACGTCTTTTT
>gi|3450241|gb|AI100280.1|AI100280 34655 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111E17XP 3', mRNA sequence
TTGGGGAACCCTTNACNCCCGNGACCCGGCTGACTCAATGAGCTTGGCTCACTGNCATTNACCCAAACTC
TAAAATGGTAATTTCTGGTGCCTATGCTGTATCAACCCTTAAAGATGCTGCAGTTGGGGACAGATTCCAA
TTCGAGAGGCTNGGTTATTACGCGGTGGACAAGGACTCTGAGCCNGGAAAGCTTGTGTTCAACCGGACGG
TCACACTCAGAGACAGCTACGGGAAAGGTGGAAAGTAAAACACTCCACCCATATTAACATTTTGTTGGTC
AAAATTCCCCCGAAAGGGTTTTATAACAACAGTAAATGAAATCGTTTGGTTTGATACGCACATTGTACAA
CAGTTGGTTTTTTATTTCTTGAATC
>gi|3450240|gb|AI100279.1|AI100279 34654 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111E10XP 3', mRNA sequence
CGGCTNTGAAGGGCTCCNNCGAGATAAGCTTGCCTAACTTTAAGGCTCGAACCGGTGTCACGTGCGTATC
ANGTGGTACCTGTTAAGAAGAGAAGGATCNGCGTGTTTGGCACGTGTCAGAAGGAGAGCACGTGTAAGAC
TGAGCTTATGCTCTAAGCTCCGTTTTAGCTATNCTCAGAAGTTTTGCCCCCATCAGCTCTATTCGGCTCG
GCTCTGATGATCTTCAAGTCGAGCCGGTAACTTTTTTTTAATATATAGTTCTCTATTTCCCCCTTTAATG
TTCACTTTCCATTTGTGACAAAAGAATAGAGTATATGTACAAAATTATTTACAGAGATTNNTTCAAGAAT
TGGCTGAGATATTATCTATTTTTTAACGAATAAAAGCAAAAAATTTAT
>gi|3450239|gb|AI100278.1|AI100278 34653 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111D11XP 3', mRNA sequence
CCCCAACTTGTGTAGCCCATCTCCNCAGTGGGCANTTCAGNGGCCAGACTNTAAAGGAAGGAACATCTCC
TGCTGCAAAGNGGGTGTNCAATAAACGGAGGCCAAGTTATTGGATACTTACATCAGTTGGGAACAGAACT
TCCAGTGACGTCAGATGTAGCTGGAGAAGTCCTTAAGCTTCTTTCAGATGACGGAGACTCCGTAGGTTAT
GGAGATCCTCTGGTTGCAGTCTTGCCATCTTTCCACGACATCAACATCCAGTGATGATGGTTTCTTCAGC
CCAATTCCATAGCAAATGAATAGTCTTTCATCCGGAGACTGTACTATTCATCTTCTCCTGTGTTTGTTCA
ATGAAGATTTGTAATCTGTTTAGTTGCAAAGAGTCTACTTTGATCTTGCTCTCATCATTTGTCACGTAAT
GTGGATTTTCTGCACCAGAGAAAAAAAACAATTGTGGAATTTTTATAG
>gi|3450238|gb|AI100277.1|AI100277 34652 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111C4XP 3', mRNA sequence
TGCTGGGNCCTTGGACCNCCAGNGGTCGTTCGTTTCCATGGGANTATCNCCGNTGGCTCTTACAGCGTTC
CATCAGGACTTCCTCCTCCNNCCCTGTAACTNGNCGCAATGGANACTGGAGTATTGTCCAAGGCCTTCCG
ATTGATGAAGTATCAAGGAAGAAGNTGGATTTGACTGCAGANGAGCTCAAGGAAGAGAAGGACTTGGCGT
ACTCATGCCTCTCTTAAACCCTTCTGGAGCAAAATTTTCATCTATAAGGTGTGAGATCATTTAAAGCCTT
TCAGGGCTTTGTCCGAATAAGAAGTGTGTTTGAAAGATCTCCAAACACTGTTTTATAACCTCTTTGGTCT
CTTTGATGAGTATTGTCCCTGGTCTGTTTCTAAACCAGGATATCGTTTTTTTCAATGTGTCTGATTTGGT
TTACCCATGAAAAGAAG
>gi|3450237|gb|AI100276.1|AI100276 34651 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111B9XP 3', mRNA sequence
CTGAGCNCTAAGGGTTTGCTGGGAAGGNAGGCTCTTTTCCTCGNGCCCTCTGCTTTAACGCACCATGTCG
GAAACTCCTTCAACACTCTAATGACTCANTATNCAATCCCGTGAACAAGAAGAATCTTGCATCTGAAGGC
GACTCAAATAACCCCGGTTCATTGGCTGGTAAGAAGATTCTCATCCCAGGTTCTGGACAGGAGATTCCCG
CTAAGACCAGCACTTGTTGTACTTCTTCTTGATCTGTCTCCTACTCAAGCAAGATTCATTTTTTTTCCTC
CTGAAATTTGTGATAGAGAATGCTACTTTCATTGTATATTCTTTTTCGAATCTGGCTTGTTTGCTAGTTC
ATTAAACATTGGTGTGCAATTGGACACCGATAGAAAGTATTGGAACAAATAGCTTTTGAATGAAATATGA
AACAAACAGTCTTTGAGAGTT
>gi|3450236|gb|AI100275.1|AI100275 34650 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111B21XP 3', mRNA sequence
ACNTCCAGTGGNGCTCCAGATGGTTACNGGGGGACCTGCCCAATATGGAGACTGAGGNTGGCAAAGCGAA
CCTTCATCCATGNTACCACGGGTNTTGNGAGCCCGTTAGATATGGNGAGATATTGGCTGAAGAAGAGGAA
GACAGATCTGCAGGACGCGGGAATGACAATCACAACAGGCTTTCAATTTGGGAACAATCCCGCTGCTCCC
GTTGGTGGATTCAAATTTGCCTGAAAAAGGTATACAGTAGTACAAATTGAAATCCTTTGGTTTGGGAAAC
ATGAGATTCAGCTTTTGCAACTGTTATTGACAATTGCCAGGTTCAAGTTCGACTTTTTGAGTTCTGGTGC
AAAAAGGCTTATTTTTCTGTTTTTTTTTTCTTTTTGTTGTTGATGTTGTCCTTATTTGTCTGAATCATTC
TCTGATTCTGTATCTTAAACTCTGCTATGAATTATGTGTAGTGTGGTTTCTGGTTTAGGATATGGTACAC
TTTGTATTTGTCACTTT
>gi|3450235|gb|AI100274.1|AI100274 34649 Lambda-PRL2 Arabidopsis thaliana cDNA clone 111A12XP 3', mRNA sequence
GAATTATNCGGGCCNTTTGNTTTTTTGGTGCCGAGAGAGTGNATTTNCGTCGGATCANTCGCTCNAGTCG
AAAAGGNTCTTGGGCCTTNATCTATGCGGGGNCCAGGGATATTAGCTGGAAGTGCCCCATCTTCAGAGTG
GAATGAGCTTGATCTTAAGATATCTCAGTTCACCAAGTCAATTGAATATGAAGCAACAACATCTCTACAG
GCGATTAATTGAAGAAAGAGTAACATTTGTATTTGATTGTTTTGTTTGTATGGGGGATAAGGGGTTCTCA
CAATAAGAAAGCAATGTTGTCTCTCTTGTAAATTAAAAAAGAAATGCTTTAATTTGTTAATGGGCCGAGC
CTTTTCGGGTTGTAACTAGGGCAGGCCTATCATGAATGTTCATAGGCCTAGCTGTTATGATTGTTAATGA
GC
>gi|3450234|gb|AI100273.1|AI100273 34648 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110P7XP 3', mRNA sequence
TTGGGAACCTCCCTTTTGGAGNTTATGNACNTNCCCCTTCACAACCACTGATTGCCCAGTTCCTCTTACT
GNCCCAACTCTATGTTGGTAGGCTGTTGTTGCCCATGCAGCCCCTGATGACCCTCGGAAAGGGAGGCCAT
GAACTCAGCCTGGCTACTGGAAACGCAGGCGGCCGTGTTGCTTGCGGCATCATTGGTCTCCAGGGCTAAA
GCTGCTNCGTTTCCAAAGAAGAGATTGATGTAATAAGGAGGTCCAACCTTAGACCTGGGTTTGGTAGTTG
TGTGTATCTTCTGGTGTGTGGCTAAAAACCTTTGAGCTTAGTGTGGCTCAAAGCATCTTTAATTCAGACA
GAAAACAGAGAAAATTCCGTACTTTTATTATTTCATGAATAAAAAAGAGTTGGTTTACAGTT
>gi|3450233|gb|AI100272.1|AI100272 34647 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110P5XP 3', mRNA sequence
AAAAAGTGGTTGATTNTTAAAGACTGGGTTTGNGATTCCTATGGCNCNTTCCTGGTTGTCCCACCCTTTG
NTGCCNTACCAGAACCCNTGTTAGGCCAGAGAATGAGAGACTTCACTCTATGCTCTGATCCAAAAAAACC
AACAGATATGGTCTGAGAAACTTAATCAGACAGCTGAAGAACCGTGGCAACCAGCAGCCATGTTAGAAGA
ACAAGGACTGAAGCATGGATTCAATTCAACACTCATCTTTTGAAAAGTACATATGATAAACATATTGAAT
GCTTGTCTGACACAATGATGTGGTTAGTGCATAAAATATAAATATAAAGGAAAGAGCTGCAGCATC
>gi|3450232|gb|AI100271.1|AI100271 34646 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110P4XP 3', mRNA sequence
CCATTGAAGTTTGGGTTANCCCTTGTTCCCCCTTTTCCGGGTGGTNATCNCGACCTTTGNANNCATTTTC
TTGCCNGGNGCCNAAAGGGATCCCGATAGGGGAGTGGGTCAAGTGTGGAGTCACACTGGTATTGGTCAAG
GTTTGTGGAGGATGGTGAGTATGGGAATGCGCTTGAGATGGGCAAGAACAGTAACCAAGCTGGAACGAAG
CATGTTTGATTTATCATTGTTTTTAATGAGAGTTTTAAGAAAGAAAGNAAAAAGATTTGTAATTTCTAAT
GTCGTAAAGGAAAAAGTGTATTAGCCTAGATATTTATTGGTGTTTATATAATTCAATACCACATGAAGAA
ATTATGCATATGATTCTTCGTT
>gi|3450231|gb|AI100270.1|AI100270 34645 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110P18XP 3', mRNA sequence
TCATTAAGGAAAGGTTTTAGGAANANNCTTGTTGTTGGCCGCTCNAAGAAGAGTGGGCATAAATAAAGNT
GCCCNTTCTGTGTGTGTGTGTGAAAATTGCTGTGTTTTTTAAGCTTTTGTGTGTCTCTAGGGAAGGTNGA
GATATGGGAAAATGGATGTAAAAAAGAATGTAAATAGAGAGCCCCCAAAGGCAAAGTGAGAGCATCATCA
TTAAGATAAAGCCAAATCGGCTTTTCTTTTGTAATTCAGCTCCTTTCCACGGGAGAGAGAGGGAATGGCA
AAAGTGTTGTTCCCTCTCTTTTGTTTCGAAAAAAGTGTGAATGAAAAGATCTTTGTT
>gi|3450230|gb|AI100269.1|AI100269 34644 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110O22XP 3', mRNA sequence
TGGCCCCCATTNCCTGATTTTGTGATCATCCCATCCCCCGAAAGAAGATNGATNTATCCATTGCNCCCTG
CTCAGGTTGTTACTCAAGCTGCTTTTGTACCCGGAAGCTCCATTACCCACCACAGATTATCCCAGCAATG
CCCAGTTGCTTAGAGAGCCTTTTCGTTTTCTGGTTTAAAACCCNATGGGGATGGTTCTTTTTTTGGGACA
GTACTCGNTNTCTCATGTTATTCTAAGTTAATACTTAAAGTTCTGGNGGTTGAATTACATCAAGGATATG
NATGTNTGTTTTTCGTTATCTTTTGTTTAAATTTTATTTATCTNTTANCGATTTGTCTTTTTTTAATTNG
NAAATTTGT
>gi|3450229|gb|AI100268.1|AI100268 34643 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110O13XP 3', mRNA sequence
AAAAGCCNCTAACCCCTCCCGTACTGGGGCCGNGCGTTTCCCNACTTTGTCCCTACCNTGANCCTNGCCT
TGCTTGNCCCAATTCACAATGTCACCATACTCCAAGGACTTGAATGATCTAAGTCCACTGGAATTGGTAT
TGGTTCTGATGATAATTGGATTGTTGTTGTCCTCACTACTAGCACACCGGAGGGTAGCTATTCTCCGGCC
TCTAACTCAGGANTTTCGCGTTCGGAGTTAATGGCCTTGTTTCTTCAAGTTTGATGTTTCTTCTCTTTTG
TTTCTTCATGTTTTGAGTCCCTTTTATGGTGTTTATCTAAACTACCTCCCTGTCTTTGTTTCTTATTATG
TTGTTATTATGGTGATTTGTATGAATTCGTAAGGCATTAAAGAGAATAACAATATTATCATTAAGTTTCT
GCT
>gi|3450228|gb|AI100267.1|AI100267 34642 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110N9XP 3', mRNA sequence
TTGTAGGNCCCGGTNGTGACANTTCGAAAGAGGCCCGGCNCCCTNTTGATGATGATTNCGAGCCAAACCG
CACTNCCCNTAGAGGAAGTGAGTCTCCTTAACTTTGATGGCTCATGGCCACGGCTTGCAGGCATTGTAGC
ATGTATACTATTGGATCGACTGTTCCTTTCTCTTTTAAGTGTGTTTGCTTTAGAACCTTTTAAGTTTCAT
GTTACCAAGAGTTTTTTCATTTGAGACATAATGTTGTTGCGTTTCTTTTGGACAAGTTTTCGAAGATTGT
TATAAGGATTTATAAAAGTTTC
>gi|3450227|gb|AI100266.1|AI100266 34641 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110N24XP 3', mRNA sequence
GCAATTCGNGGACGGAATTCGGGGGGAAGCNCCCGGCCCGGGACCCTTCGATGCGAACNCCGNTGCAACC
ACGAACGGATCTCAGTTCTCCATCTGCACCGTGAAGACCGATTGGCTTGATGGGAAGCACGTGGTNTTTG
GGCCAGGTCGTGGAAGGCTTAGACGTGGTAAAGGCCATCGAGAAGGTTGGATCATCATCTGGAAAGCCGA
CGAAGCCTGTGGTTGTTGCCGATTGTGGTCAGCTCTCTTAGGATCTTCCTATCATCATCCTTAATTTAGC
ATCATCGTCGTCATTGTGGTGTCTCTTTATGCTTTTGCTTTTGTTATGGAGTCGTTTTAAAATTTGTAGT
CATAAGTTTGGTGTGTGTTCTCATGGGAACATATATAAACTTGCCCCTTTAATATTAACTACCAG
>gi|3450226|gb|AI100265.1|AI100265 34640 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110M3XP 3', mRNA sequence
CCCTCCCCNAAAGGGGCTCCCTNTTTTAATTCGGTTGGCCCCGGTTTTTTCCCGGGGCCCGGAACCCNCC
CCGGTTCTNTGNTGGCCGGTACTGGACCAATGTGGAAGCTCCATGTTCGGATGCACCGACTCCGCTCAAG
TGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTCCCCTGGCGCCTTCATTAGGATCATCGGATTCGACAA
CACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATCCCCT
TTCTGGAATATTCAGCGTTGATTATTCTGGAACCCATTTCTATGTGGTCAATGCAAATTTAAGAAATTAT
TTGCCGACTTAAAAGTTGAGGAACTATTGTTTGAAAGTGAAAATGTTATTCCTATCAGTTTCTCTATAAT
TATAGTTATCATTTCATTTC
>gi|3450225|gb|AI100264.1|AI100264 34639 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110L11XP 3', mRNA sequence
CAATTTTTCCTTCCCTNTGACCCGTTGGCCCATTGACCNGGAAGTCCNTNCCCAACCAAGTCANGAGTTC
CCCGATGGCTGAGGAATTGCTGGCCCAAGACCGTGAGTGCTGATGTCGCTGCTACAACCCCGCATCATTT
ATGGGGGGATCCGTCAATGGTGGTAACTGCAAGGAGCTAGGTGGACAGGCCGATGTTGATGGTTTCTTGG
TCGGTGGTGCTTCTCTAAAGCCTGAGTTTATCGACATCATTAAGGCCGCAGAGGTGAAGAAAAGTGCCTA
ATGAGCTCATTAAGCAATTTAAAAGTCCTTTGCTTTTCCAGTCGCAACTCTGAAAAAATGAATAAGTTGG
TATTATGATATGATACATTTTGCTTCAGTTGTATTTGGCAAAAGTTTCTCTCTTACTATATTGTTTTGAG
AACGCAACAATC
>gi|3450224|gb|AI100263.1|AI100263 34638 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110L10XP 3', mRNA sequence
ACCGNATGGCCCTGGACNCCGNGGNACGTCGTTCCCTGGGGTTACCCCGTGCTNTACGCGTCCATCAGGC
TTATCNACCCCTCCCCTNTACTTGTCGCATGGAGACTGGAGTATTGTCCCAAGGCCTCCCGATTGATGAA
GTATCCAAGGAAGAAGATGGATTTGACTGCAGAGGAGCTCAAGGAAGAGAAGGACTTGGCGTACTCATGC
CTCTCTTAAACCCTTCTGGAGCAAAATTTTCATCTATAAGGTGTGAGATCAGTTAAAGCCTTTCAGGGCT
TTGTCCGAATAAGAAGTGTGTTTGAAAGATCTCCAAACACTGTTTTATAACCTCTTTGGTCTCTTTGATG
AGTATTGTCCCTGGTCTGTTTCTAAACCAGGATATCGTTTTTTTCAATGTGTCTGATTTGGTTTACCCAT
GAAAAGAAGAAAATTGGC
>gi|3450223|gb|AI100262.1|AI100262 34637 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110K9XP 3', mRNA sequence
CAAAAAAGATCCGNTGGTGGTTGGCCAGAGGAANNCGGTTNGGTGGTGNTGGAGGAAATCGGTTTGGCCG
NTGNTGGTGGCAGAGGGAAGAGGAGGCAGTGGTGGTAGAGGCCAGAGATATTGAAAACTGGAACCCAACT
TCTCCTTTCTATATAAAAAGAAACTAAACTCCGTCTTATAATTTCATTACTATCTTCTTACGCTGATGTT
TTCTACACTATAATAGGTGGCTTTTCTGTGTTTTCCTTTTTCTTTCCTTGAACAAACTTATGGAGGCTCT
CTTGTACCCTCTTATCAATTTTGTGTAATGTTGGATGATAATGATGATTAAATTATTATTCGTC
>gi|3450222|gb|AI100261.1|AI100261 34636 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110K22XP 3', mRNA sequence
TTNTTCTCTGCCCGATTGCTTCAGGGGGGGACNCTGCTCCAGTCCNCTTTTAAGTGGATCCGTTCTTGGT
ACAACCCTGTTGAAGTGCTTCCCCAGATCGACANTACTATGTCCAAATTGCTTCAACNGNGGAACTCTGC
TTCAAGTTCNCTTGTAAGTTGAATCATTCTTAGCAAGGNCCTANCCAGCGGTAAATATCCTTTCTTGCAT
TTATCACACTCGATTGATATCTCTTGTATCGCAATAACGGGTTGTTT
>gi|3450221|gb|AI100260.1|AI100260 34635 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110J2XP 3', mRNA sequence
TTCTGTTCATCCCCGCTTCGGCAAATCGCTGAAGGGNCTTTACGGNCCCTTGGGGCAGGCAGTCACTTTT
NTCAGNGGTTTTTCCCCATGCTTGCTGACCTCGTCACCGGCGGANTCAACAAGTGCAACAAATGAGTCGG
TTCTTAAAGTGGCTCTAGCCCATGGGAAGCAAGCCGGAGTGATCAAGTCACATGACAGAGTTGTGGTCTG
TCAGAAAGTGGGAGATGCGTCCGTGGTCAAAATCATCGAGCTAGAGGATTAGAAGAAGCAGAGTGAGTCG
TTGTCTCGGTCTTTTTTGTTCTGTTACTAATCAATTTTATTTCCTTCACTAAAACTCTTGGTGCCGTCCA
AGAAAAATCCTTGCAATCATTGTTTCTCGCCGGCTATATGCTAGATACCGGAGTGAAAATATATCTCCTG
GGCTTTTGTTTTCGTATTTAGGAGATTGATGTTTCCAAGTTATGATATAAACCACTTTCCACTT
>gi|3450220|gb|AI100259.1|AI100259 34634 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110I18XP 3', mRNA sequence
TCCGCCGAAATCAAGAGCCATCAAGGNGAATCTGAAGGCCAAATGAAGGGAATTTGGGATCACTGAGGAT
GATGTTGTGTCTACCGACTTTGTTGGTGACAACAGGTCAAGCATTTTCGATGCCAAGGCTGGGATTGCAT
TGAGCGACAAGTTTGTGAAGTTGGTGTCATGGTACGACAACGAATGGGGTTACAGTTCTCGTGTCGTTGA
CCTTATCGTTCACATGTCAAAGGCCTAAGCTTACACCGGCGAGAGTTTGTGTGTGGTTGAGTTCGTACTG
TTCTGAATAAAAAAAAGGAGAAAAGAAAACTCGAGTTGTTATGTTTTTTCACTGATTCCATGCGCAGTCA
TGAGAGTTTGTAGCTTTTGTCTTTTTGCTTTCTCTTAATGTTTCCCTGCTTTATTTACTGAAACCATTGG
TTTGGTTTTTTATGTTAATTAAGTTTTTAGTTC
>gi|3450219|gb|AI100258.1|AI100258 34633 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110H22XP 3', mRNA sequence
GACCCAGCGTCACCCGAAGGACTCCAGACTATTTCCTGTGATCACTGGACACAGACTCATCTCAATCAGC
AGCTGCAGGCACCCNCAAGTGAAAAGTCNCAGTTGGCTAACTCAAGATTCTGGTCCTATGCATTGTGTTC
AGGTTGCTCTGTTTAAAATTCAACTTAGTGCCCNCCNCCGGAATATAGTGTGTATTNTAGGCGAAGAAGG
CTTCTTATCTTCCTCTNTAACCAAGAAAAGAAAAAAGATNCCCATTNTGAACATTGTTTTGTTGATGTTA
TTAGCTTCTTCTTCTTCTCCCTTNTGCATCAGAATGTGGTTTCATGTGNG
>gi|3450218|gb|AI100257.1|AI100257 34632 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110H21XP 3', mRNA sequence
CCAAAAAGTTNCTTGAAGCNCCCAACAGNGGNGATCTATGGTGTTCCTCAAGGNTTCTTCCATTTCAGCT
AAACTCTGGGAAAGCCCTGCCTTGGCCTTTGTCGCATTCGGAAGCTCCTCCCCAGGGCTCCAAATTCTAC
CATTTGCTCTGTTTNCAAACGATTTGCCTTCAGAACTTGTTGAAGCCACAACGTTCCTTAGCGATGCAGA
AGTTAAGAAGCTTAAGGGTGTGCTTGGGGGAACTAATTAAGCTTCTCTTAGTTTCATTGTTCATTTTTTT
AAAAATGTGGTTGTGCGTTTTGTTATTTCGAGTTCCTTTAGCATTTTGAGTTTGTTTCTTCTAATGATTT
GGTTTTTCTTTATGAGTTGTTATTGTTCTCAATGTTTCATTTTATAGTCTCTTTGGCTTCAAATTGTAAT
AACTAATAAGCATTATATTGCAGATTTCT
>gi|3450217|gb|AI100256.1|AI100256 34631 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110H13XP 3', mRNA sequence
CCCACATGCCCCTAGCCAGTCCAAAAGGNTTTAGCTGAGTTCCAACAGNACTTGCNTCTGCCACANCAGN
TCTTGAGAAAGCAGAGGCACAGATTGGTGTTGAAGTTCACAGTGCCATCAACGCAGCTCTCTCGGGCTAA
AAGAAGGTTTCTTNCTTTATTTCNTCGAAGAAACAANNAAAAAACTAAATCATTTGGCTTTTCAAGTGAT
TAGTGAAGTCCCTTTTTACTACTGCAAAGGATGGAATATTGANTCTTCTTGTTTAATCGTGTTGGACTTT
TGTTTGAATAAATGATTTTGTTTAACGGGCACAAAAACCCACAAAAGTTTCTTGTGTTCATATCTCTGCA
CCTTTGTTTTTGTGTATGACTTTGTTGTGTTGAGAAACTAAGTTGGAATTTCTTA
>gi|3450216|gb|AI100255.1|AI100255 34630 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110H10XP 3', mRNA sequence
GGTTGCAAAACCAACTTGGCAGGCACTTGGCCATACCCAACTCCTTCATTTTCTGCTTTTTGACACTTGG
CAATGCAAAGTCTGTGCAACAATATGACNNTATTTGGGCGCAGTTGGGTGATCTAGCACTCATCCTCAAA
TCCTTACATGTGGCCTTGCCCTTACTACTTTTTTCATTACTATGCATGCCCGTGGCATTCCTTTTTGGCG
TGATCACTGCAATTGCCCATGTGAAATGGCTTTTAGTCACCATTAGCATTATATCTGGTGGATTCTTCCT
TTTCGCAATCTTTATCCTTGGCCCTCACGTCATGCTACAGCGCTCACACCTTCCGCCCAGTTCTGGTATA
TTTCTCAAGACTTTTATGCTGACTATAGACATATCTGAGTTGTTTGTGATTTTGATCAAAGCTTGTTTTG
GTTGTGTGGCGTGTTCCGAATAAATCATCAAAAGTTTATAGATCAAAGGATATTTTTCTTCTC
>gi|3450215|gb|AI100254.1|AI100254 34629 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110G24XP 3', mRNA sequence
TCCGGTGCCCCCGTCGTCATTGATTCCGGAAATTCTGCTTGNGGAACTCGATTGACTGCTCAGTNCGCAC
GGTGTGNGGTGCAAAATGTCCCTGCCTGGGTTCCCGCGNGACACCACACTGAGCTTTTGTCTTGGNCTTG
CACCCGCGATGAAGAATCAGTACGAGGCTTCAGGGGAGAGTAACAACGCTGAGAACGATGCTTGCAAGTG
TGGATCTGACTGCAAGTGTGANCCTTGCACCTGCAAGTGAAGAAGCCTTTTTAAATAAGCAGAGATAATC
GAGTCTCTTTAATTAATTAAGTTATTCAATAAGTAAACCATATATAGGATGGTGTTTTTAGGTTTGGTTT
ATGTGTAATAATGGCTTCAGCTTATCTTTTAGCCGATCATTGTCTTTTGTGTTTGTTTTGATCATATCTT
TTAGATGTCTAGCAACTCTGCCATGTGATGAGTTTGTACTTCCAGTGGAATGATAATAATATTATAGTTT
TAAATCTC
>gi|3450214|gb|AI100253.1|AI100253 34628 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110F23XP 3', mRNA sequence
TCCACCGNAGATTGGTCCATGTTATTGGTATAGTGGTTAGTTGGTTAGTTGGTTATACCGGTTATTTTGA
TCGGGATTAGTTCAGCGAGTTCTTTCCNGCCGAATTGACTTGGTGGATAGGGCTTCATCGTGATTTATTT
TATCAGTGGAATCGGNCAAATCGNAGNAAAAACNTCAAATTTAGTTAAACTNCCCCGGCAAACTTTTGCT
TCACTTAAGATAATTTTTATATGTAGTTGTGAGAATATTTGGGTTTGCTATTTTTCGTTTTGTGAAAATA
TNCAAAGTGATGTTGTATAATAATTGTTATTTGGAAAGGTATTGTTCAAAT
>gi|3450213|gb|AI100252.1|AI100252 34627 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110F21XP 3', mRNA sequence
CATTGTGACTGGTGAGGGGTTATCCNCCCNACCAAGATGGCTTTTNCCGGGGTTCTGTACTCACCGTGGT
TGTGGGAGGACTGACTTCAGGGAAGGANGCTCAGATCAACTCTNCGAGTCTGTACATTCACAGATATTTA
CATTGCCAAAGGACACATTGATCTATCCTGCTCACGACTACAAAGGTTTCGAGGTAAGTACAGTTGGAGA
AGAGATGCAACACAACCCGCGTCTAACTAAAGATAAAGAAACATTCAAAACCATTATGTCAAATCTGAAT
CTGTCGTATCCGAAGATGATTGATGTTGCAGTACCAGCAAATATGGTCTGTGGGTTACAAGATGTGCCTT
CTCAAGCCAACTAAAAAAAACTCTTACATATAATGTTTGTCTTTTTATCGATGTCA
>gi|3450212|gb|AI100251.1|AI100251 34626 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110F12XP 3', mRNA sequence
GGAGAAGGAATTTTGCTATCATGNGCAGCAGCACAACTCACCATTCCCAAACACAAGTAGTGATCAACAT
CCAAGTCAACAGCAAGAGATTCTTCAATGGTTTGGGAGCAGTAACTTTCAGACAGAAGCAATCAACGATA
TGTTCATAAACAACAACAACAACAACAACATAGTGAATCTTGAGACCATCGAGAACACAAAAGTCTATGG
AGACGCCTCAGTAGCCGGAGCCGCTGTCCGAGCAGCTTTGGCCGGAGGGACAACGAGTACATCGGCGGAT
CAAAGTACAATAAGTTGGGAGGATATAACTTCTCTAGTTAATTCCGAAGATGCAAGTTACTTCAATGCGC
CAAATCATGTGTAACATTTTGTTTAAAACTTTATTTGTACTTACATACATAAAGAGGGGTTTTCTATTTT
GT
>gi|3450211|gb|AI100250.1|AI100250 34625 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110E2XP 3', mRNA sequence
GTTCCCCTGTTGCCTTCCACCNTGGCCATTTTCAACTTCCAGCTTCGAGTTTGTCNCCGCATACCAGTGG
TGGACACCATGACCTCCNAGGCAAGCTGAGGGNTCCCTNCCATCTCTTCTTCCNCGGGCACAANGCTTCA
GGCCGATTACTGTAGATACAGACCGCACTGTGGTTGCATTTTACAAGTTCTTAAGGAAACACGCAACGAT
CCCATTCAAACTGGAGAAACCTGCATCAACCGAATCACCTAAAACTGCAGAGTCCACNCCAAAAGTAGAA
ACTACCGAGACCAAAGAATCACCCGATAGCACGACAAAGAGTAGCCAAAGTGACTCGAAGGACGAATTGT
GATCAGAAAAGGGTATAATATATATTACATGTCTCCTTAAGTTGTTATATGTATGATCAGAATTGTCACA
TCATGAGTTTGGACTAGATAAAGATGGGAATTAAAGTAATTTTAGTTTTGAG
>gi|3450210|gb|AI100249.1|AI100249 34624 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110E22XP 3', mRNA sequence
TCCCAGGTATGAAACCCANAAGGTGGTTCCGCTGGCATTCTAAGACAAAGCNCTAGATGGCACGGCCCTG
CAGTGCTGGTGTCTGACTTCCATGGCGAGTTACTGTTGCTCGGTCAAGGACTTTCAGCTGGTTGCGACCG
TTGACCAAAGTCACCGAGCGGTAAAGGCGATGAAGAAACAGTTCTTCTNCAGTTTGGTAAAGTGGGAGAT
GACACTTTCACTATGGATTATAGACAGCCTCTCTCTGCATTTCAGGCTTTTGCTATCTGTCTCACAAGTT
TCGGCACTAAACTTGCCTGCGAGTGAAACCCAACAAAAGGCAACAGAAAAGAAAAAGTGAACTGGCTTTG
CAAAAATGTAATGTTTTGATGTAATCATGTGTAAGTGTAAACACAAAGGTATGTGGAAAGGAGAAGCACA
TAAGTATTATTATGTAAGAAACATTATTTAAAACCCATAATCATAATGTATCTCTTAAGT
>gi|3450209|gb|AI100248.1|AI100248 34623 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110D1XP 3', mRNA sequence
CAAACCGTNAAGNGCTCCGTNTGGNGTGGCATTTACACTGGTGGCATTNGCAGATTCTTTTGCTAATTCG
TTTGGGACCAGCAGTTNTGAAGATCAACGCAATAAATNGCGCCGACTGAAGCGGGCTTGCCTCATCTTAG
TGTCGACGAAACCGTGAAGAACCCTAAATCTGAGAGCGCACAGGGAGACGCCGCAGGTGCAATGGGGAGA
GGACGCGGTGGAGGTCGTGGCCGTGGAATGCGAAGGCGATAAGCTCCGTCTCTAATGCCAAACTTGTGGG
ATTCTTCTTCTTCTTCTCTAATTTCGATTTTGTTGAATTTTTGTTTTGAAGTTAAAAAACCTATTATTGG
GTTTGTGTTTGTTCAATTAGAATACTGGTTGGGTATGTATGTCTATACAATCTGTGAAACATAAGTTTTA
GTGTTGTTTTGGTT
>gi|3450208|gb|AI100247.1|AI100247 34622 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110D18XP 3', mRNA sequence
CGTCGGTCGNGTGGTTANCGGGTTAGTTGATTCCGGTTGAATTGGGNGTTTATGAATTTAAGGGAAGCNC
GCGACGATTCGAAGTGTGACCNNGCAAGATGCCAGGNGCTATGAGAAATACTGTATCGGTGACGTGACCA
GTCAACGGTTCCGGTGACGCAACAGTATATTCCGCCGTGGGAGAAGGAATCTACGGCGGCGGAAACAACT
AAAGAAGAATCTGGAAAGAAGCTGCTTATCTACTTAATTCCTCTCTTGATACTCGGCGTTGNTTTCGCTC
TCAGATTCTACAACAACAAGTAGACCAAATTATGATGAACAGATTGATAAGAGTTTCTTACTGTTCTTGG
TTTTCGTTTGTTGGTAATAACGGGCTTCTTATGTGAAGATTTGGGCCATTTGGCCCATCGCTCAGAATTG
GACTATAATGTCTTATTTATTTTATGTTAATGGGCCGTATCAGTAGGCCCTTTGTTGATATATGCCAATC
CCAATT
>gi|3450207|gb|AI100246.1|AI100246 34621 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110D11XP 3', mRNA sequence
GTGATCCGTTGGAAGGAGNGGAGGAGGAAAAGAGCCAAAAGGTTGGTTATATGGATACTGATGGTATTAG
TTGCAGCCAAGCAGCCAGGGTTTTGTGATGTGAAGATCTCAAGCATTAGTAGAACAGGCAGCTTCTCTAC
TCTGCCTGCACCACCTTCTTCTTCTTCAAAGTCTCACTTTTGGACGAATGTGTATGCAGGACTAAAGCAA
GTGGTTCCATGGAAGAGCAAGAAGACTACAGTTTGAGATTCTGCCATATCAAAGATTCGAAAGATAAAAC
ACCAAGTAACAAGAAAGCTTCTATGGTTTCTACAAGTATTTTTAAGCTTTTGTTTATGATTTTTTTCAAT
ATTTCCAAGAAAATGACACGACTAGTAAAACCATTGTGAAACCCAGTTTTTTTTCACGCTTGTTGTTGTG
TTTGAATGTTTTTGAGACTTTTGTAAAGAGAAACAGAGAATCTTACGATGT
>gi|3450206|gb|AI100245.1|AI100245 34620 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110C2XP 3', mRNA sequence
CCCTGAGAATTTCCCCGCNTCNGGGAAGGGCTTAGACTTCTGACCTTCCCGGAAGGATNCTANGTTTCCC
CCGTCGCAACCTATCNAGGCCGGTTACTNTGGCTGGTCCACCTANTGCTCAGGGGCTAGAAGATCAGCAA
AAGGAAGTGAACCANTACAAGTCAGAGAGAGAAAATGGCTAATGAGTCTTGGTTACAGAGTCTGGGGNAT
GATGGGTGACCAATGGAGTAGCTTTGCAGGCTGTCCTCTTCCCAGGAGAACCTTCAAGCTCCCTAACTCC
ATCTACTATGTCGCCTGATCAAAACCAAACACAAAACTTTGATTTAGCTTCAAACAAAAAGAAGAATCCA
CGAATAAGAGAGAGCTGTTTTGAATCTGTTTCTTGTTTATTTTCCCCTTTTTCGTGTCATATTATATTGA
GAGACTTATGCATCCAAAAGAACAAACAAATGGTTATATGTAACAGAGAGAAATCAAATCAAAATCACAC
ATTATC
>gi|3450205|gb|AI100244.1|AI100244 34619 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110C18XP 3', mRNA sequence
TGGCGNGGCCACTGCTTTNGGCCTTCATGAANCCTGAGTGCAAGNGGCAATGNGCACACACCGTCCAAAC
CGTGGTTGAGAACTTTTACATGACAAACTCGATCACAAGAGCATTCAAAGATCATGGCGCAGTGCAGTGC
CGTGCTCTTGAAAAAGTGAGAGCTTTAACTTGGGTTTTCACATTTTCTCTCTTTTCGCAAAAATAAAGAT
ACTGATTCTTCGTTTGCTGTCCTCTTTATAGACCTTTTGTTTAAGCCTGAGTATCACTGTATCTCGGGTT
TAGCTTGCGGTGAAATCTATAAGCAATTTGCAATAAGCACATTGTTAGATTCAAAACTTTGCAGTGTTAA
TTGGATGCTTTGTGGCATCTTGTATTGTTCTTATTAGGACTCCCTTTTACATTTGCATATATGAATTTGG
AGGCATGGCGAT
>gi|3450204|gb|AI100243.1|AI100243 34618 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110C16XP 3', mRNA sequence
ACGAGGCTGGGNTTCTGCTNCCCCAATGTAAATCATTNTCCCCCTGGTAGAGTTTTCTTCCAGGCCGATT
GGTTTCCAGNCCAGTTAAGNAAACGGAGGTAGATTCGATACTGAACGGTGCGTAGAGAAGCTAACGGAAG
AGACCCGGAGACTCCAGAAGAGGCTATGGAGCTTCGAACTCTCAAGCTGTCTCCACAATTCTACGGTCAG
ATGACTCCACCAACTACACTCATCATGTGTCCTTCGTGCGAGCGTGTGGGTGGCCCATCATCATCGAACC
ATCACCACAATCACAGGCCCGTTTCTATCAATCCGTGGGTTGCTTGTGCTGGTCAGGTGGCTCATGGGCT
GAATTTTGAAGCCTTGCGTCCACGATCGTGATTTTTTATTTTAGTGGTGGGAAAAGGGTGTTTTGGTATT
TTTCGTTATCGTTATATAGTCTATCTGTGTGGGGTCATTGTAATTTTGGATGATTGGCCTTCTCATGAAC
TAGTCCTATGTATGATGCAACCTTAAAAAGATTTAAATTAGCNAAAATTAGTTAC
>gi|3450203|gb|AI100242.1|AI100242 34617 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110C10XP 3', mRNA sequence
CACACGGGAATTNCCTCATGAGGTGCCCCAATGGAAGAAGATTTGGCTTTTCTTNCCNCCTGCCTTAGTG
CGTCGAATGGCTAAGGAAGTTGACTNCTTCTCCGCAACAAGTGGATCCNTTGTGTTGAATTCGAGTTAGA
GCACGGATTTGTGTACCGTGAGCACGGAAACACTCCCGGATACTACGATGGACGGTACTGGACAATGTGG
AAGCTTCCATTGTTCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGT
ACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGC
CTACAAGCCCCCAAGCTTCACCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTCA
TTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGATTGTCAAATGTCTGA
TTTATGAATATGTAATTTAT
>gi|3450202|gb|AI100241.1|AI100241 34616 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110B6XP 3', mRNA sequence
GTTAAANCTNCTGGGACCANTTTTCAGCCATTTGNTTGACCCCNGCCAACCNTTTTTCCNAAGAGAAGCT
AATTNGCCAAGGCCCTTGATNTNTCCGGGCTAGGCTGAAGGNGTTCAGTATTGGCTGGTGAACTTTCCAC
TTTGACCGATCTTCACCACATTCCCGTGATTCAATACCTGCTCGGAACTCCCACCAAGAAGCTCTTCACG
GAGCGTCCACGTGTCAACGAGTGGGTGGCTGAGATCACCAAGAGGCCAGCTTCAGAGAAGGTTCTGTGAG
AAATTTCTAAAAGGACAAAAGTGGTTTTGCTTCAGTCACAGTAATAATGCTACAAGTAAATAAGCGTCTG
CCTCATTGCCCAGTTTCTCAGTACTTTCTTTCTGTTGTATCCTCTGTTTTTGTTTCAGCTTATGTGAGTG
TGTGTACGTTCTTGAGAGTATCTTAGGCAAAAACTATTTATCT
>gi|3450201|gb|AI100240.1|AI100240 34615 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110B23XP 3', mRNA sequence
CTTGTGCCCCACTTGACTTTGTNNCCCCTGGTAAAGGCTTCGTATCCCCAAGCTTCAAGGGCCCGTTGCC
TTTCCATNTGACGCTGTGGCACAACCGGAGCTGGAGATTCTTTGTCGGTGCTCTCTAAACCAGATTGTCG
ATGATCGATCCGTTCTCGAGGACGAAGAGAGATTGANGAAAGTGCTGAGATTCGCAAATGCTTGTGGAGC
AATCACAACGACCAAAAAAGGAGCCATTCCAGCTCTTCCCTCAGATGCTGAAGTTCGGAGCTTTCTCGAA
AAGAAATAGAAACAAAACAACTCAAGCTTCTATTACGTAATCTGTTTCCGCGATTATCTTCTCTTTTTGT
ATTCTTGTTTTCGGATGGTTGAATCGAGAAGAGAAACAAATTCGGCATTCCGCTCTGTTTTTGTTTCTCT
TCTTCAAATGTAATGATTTAGAAAAGACGTATGTTGCAATTTAAGGCTTCACTTGCTAATAAAATGATAA
GGTTTTTCC
>gi|3450200|gb|AI100239.1|AI100239 34614 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110B22XP 3', mRNA sequence
TCTTTTANCCCAGTTGCCGATGACCGATCCGTTCTCGAGACGACGNGNGATTGCCGGAAAAGTCCTGAGA
TTCGCAAATGCTTGTGGAGCAATCACAACGACCAAAAAAGGAGCCATTCCAGCTCTTCCCTCAGATGCTG
AAGTTCGGAGCTTTCTCGAAAAGAAATCGAAACAAAACAACTCAAGCTTCTATNACGTAANCNGTTNCCG
CGATNATCNTCNCTTTTTGNATTCTTGTTTTCGGATGGTTGAATCGAGAAGAGAAACAAATTCGGCATTC
CGCTCTGTTTTTGTTTCTCTTCTTCAAATGTAATGATTTAGAAAAGACGTATGTTGCAATTTAAGGCTTC
ACTTGCTAATAAAATGATAAGGTTTTTCC
>gi|3450199|gb|AI100238.1|AI100238 34613 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110B20XP 3', mRNA sequence
TCTTCCCGCCCCTGAAGGTTANCCCGNTCANTCGTGGCCTTGGGTCCNGGACGNCCCTTGAATCCCGGNT
GNTTCCGATTTACTNTGGCNCCGATATCCGTGAATTTGGCAAACGGACCCGCATTTCCGGCCATCGTTTA
CACAGCTGATGCAAAGTTTGAAGCGGCTTCAGGGTCTAAACATAAGCACCAGAGCGAATACGAGTGAAAG
TTTGATGTAAGATACGTTAGACAGAAGATGTTGCCTTACCTGGTCTGGTTCAAAGAGCCAACGGGTGGGG
ATTGCCATTCTTCTTTGCTTTTTTTTGTTCTTTTTGTTATTACGGTCAGACGAGAGGAGACAAACAAAAA
AAGATTGATGGGTTGGGGAAAAGCTTGTGGAGTTCAATCGAAGTGGGAGCTCAACAAGAAAAGAAAAAGC
CCTATTCTTAACCCTTTGTAACTATTATTATTATCATCATTGTTGTTGCTACTTGTAACGATAAAATTAG
GTGAATGAAC
>gi|3450198|gb|AI100237.1|AI100237 34612 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110B16XP 3', mRNA sequence
AGTCCGTCCCAACCGTCATGCCAGGGGCCATAANTCCAACATACCGCGCGAACTTGGTCCGACGTCCGTG
ACATCNCCGTCTTTCTGGANCACTGGANCTAANCATATTGCTGAGTTTACGCAAGATCTTTTCCCGTAAC
TCGTTGCTACAGGAGAGGTGTTCCGCTCGAGTCAGAGGTTAGAGTCTGTGAGGAGTGTAAGACAGGAGAT
ACGNTGACGATCGAGCTGAGTGATAGTGGTGGTTTATTGACTAATCACACGACCGGTAAAAACTATAAGC
TGAAGTCGATCGGTGATGCTGGACCGGTTATTGATGCTGGTGGTATTTTTGCTTATGCGAGGATGATGGG
AATGATTCCATCATTAGCTTAATCCTCTTCCATAACCATGATGGTGTTCTTGTATGCATAACTATTTGAT
GAATATTTGTGTTTTAGAGTTTTCTATTTTCTTAACTTTTTTATGTTTGTTTGATTTGGTATTGTTGTTG
TTACCTAAAGAATAAGAAATCAAAAGCAAAATAGACCGACATGTTCCAAGAT
>gi|3450197|gb|AI100236.1|AI100236 34611 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110A17XP 3', mRNA sequence
GCAAGNGGCCAAGGNGAAGAGCTTGNCAACGGGNAGGTTGCCATTTGGNATCCTAGGGTTTGTGGTTCAA
CNCAATGTGACTGGAAAAGGCCCATTGGAGAATCTGTTGCAGCCACTTGTCTGACCCCATGGCACAACAC
TTATTGTCCAAACCTTCAACTAAAGAGTGAAGACAGACTTATGATCTCATACCTATCTATCTTCCATCAC
TTTCATGTCTGTCTGTGAGTGTGTTTCATCTTAGAGTTCTTGGTTTTTGAGCTTGAATTATTGTTGAACC
GTTGTAGCTCCATGAACAAATTTGGAATCTTCAATGTACAGAGGAACTAAGTT
>gi|3450196|gb|AI100235.1|AI100235 34610 Lambda-PRL2 Arabidopsis thaliana cDNA clone 110A12XP 3', mRNA sequence
GGGTTTTCAAAGACNCNTCGATTGGTGAGAGGTGCNGCTGGTATNCNCCTGATATTGTAGGGGGTCACCC
AATACTAGAATNCAGGGCTTGAACACTTCTTCCCATCAGTCAGACCATGTCCTCGCCTTTGACCAGCCAT
CTACATCACTGCTTGGGGCCGAAGAACAGTTGGATAAGGTTTCAGGAGATAATCTTTGAGTTGTTGAGTG
TACCACATGTAGTGTTGTTTATCCTAATCCTTATTAGTTAGGAGTTTCCTCTAATAATGTGATCACAAGT
CGTTAATTCTCTAGGCACTATCACGAGCATGAAGAATGAATATGTCTGTGTTGTGCTGTAATTTGGTAGA
CACAAAACAAAATTACTCTTATTCCC
>gi|3450195|gb|AI100234.1|AI100234 34609 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109P5XP 3', mRNA sequence
CTGGGTCTTGCCCGCCGCTTTGGAGATGGTTNCAGNGAATTGNTTCCCGTCGAGAAGTGGATATGATGAG
TCCACCGGAAAGTCAAAGTTTCCCCGGTGAGGTTGTAACCGAGAAAGAAATGGTGTTTGAAGAGTATATG
ACCGTATCTGAGGTCATCTTCCGGCGTATCCAGACGGCTAAGGAGAAAGGTTTAGAGCTTTTGACGGCTG
AGATGGAAGGAGAGTTTGCTGGTTCGTGGAAAGAAGATGGGAAAGAGAAGAAAGTTGTTAGGTATCCGAT
TTATCTGTTGATCGGAAGAGTTGCAGAAGAACGTGTATAAATTGATATCTCTCAGTTAGGCATTTCGTCG
AACACCTTGTACTTACACACAAGAAGACATTAGTTTTGATTGGTTCAATGTAAAAATAAAACTTTGTCGT
TCCAGCATTCCTGGGGATCTCTAATCTTTCCTTTTTTACCCC
>gi|3450194|gb|AI100233.1|AI100233 34608 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109O2XP 3', mRNA sequence
AAACCCCTTCAACAGNCAAGGAGGGTCTGTTCAAACCATTTTCAAGGTCCCGGTNTCCTCCGGTGTATCC
CAGTTTAGGGTGAATATGAAAAGCTAGGCTACACTACCATTATCTCTTTCGAAGCAGATTCCCGGTGCGG
CCTTACAGACACAATGAGTATGAGAGATTTATCCCCACTGCGTATCCTTATTATGGAGCCTGCTTTACGA
CGATGGCTGGTTTCTTCGTCTTCAGCTTCGTCTACCTCTACCATAAGTAGAATCCCTTAAATGGTGGCCA
AGTCCCATAAAGTAAGCCAAACCTCCATATTTAGATGAGAAAAAACAACTTTCGAACTAGAGACCAATAT
TTTTGGGCAGCAAGGTTTTCATATGTTTCTAGTTTTAGCCAAACAGTTGCAACCTTCTTTTTGTTTCCCA
GATATTTCTATGTTAACGTAACTTTACACCC
>gi|3450193|gb|AI100232.1|AI100232 34607 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109O17XP 3', mRNA sequence
CCCNCGGACTTCNTAAAGCCGGGNGAGAAAAGGGTCCCNGTCCCGTTNTNGCCAGGAAGGNTTGGTTTNC
CCGACCAGGCTGAGTTNGGTTCCCATCACTGGGGCCATCCCGCAGCNCGAAGTGAGAAGTCCCCGTGCAT
CCTCTTGGAACCCCGNTTTGATAAAAAAATCTTACCATCCCCTAGTGATGATGTTTTCTATTTAAGTTAT
CTTGATTGGGTTTAGGCTAAACCAAAGCCCATCATGAGCCATAAGTAGTGGGAAGTGTTCTTGTGTGGTT
TGGTTTGAGTCATTGAGTGTGTAGGTGAAAGCATCCCAAAAAAAGTTAGGGATGATAAAAGAAAATGTTG
TCAGGAAAAGAACGTTGATGTCGTCATATGTAGTGCTTCAAGTTTCTTCATTTTAACCATCATACTGATG
TAATAGTATCTTTCAAATAAGCAACAAAAGTAATGTG
>gi|3450192|gb|AI100231.1|AI100231 34606 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109N9XP 3', mRNA sequence
ACCCCGCGTTCCTNNCCATTAACTGGGANCTCTNTAGNGTGGATCCNCCAAAGGAGGCTATTTCTCGTCG
AAGATGNGGCGATGGTGANGAAGGTTATGGNCTGAGGACGAAGGTGAAGAGATGAGAAGGAAAGTGAAGA
AGTTGAGAGNCACGGCGGAGATGTCACTTAGTATTCACGGTGGTGGTTCGGCGCATGAGTCGCTTTGCAG
AGTCACGAAGGAGTGTCAACGGTTTTTGGAATGTGTCGGGGACTTGGGACGTGGTGCTTAGTAATGGTTA
CTGTTTTCTAGCTCTTTAGTGGTTGAATTTACTTGTCGTTTCTTAATGTGTATTTTTCATTGTAATAGAA
TAATCGATGTTTTGTAAT
>gi|3450191|gb|AI100230.1|AI100230 34605 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109N11XP 3', mRNA sequence
CCTTGGCANATACNCTCCCGTTTNACCNCCCNAGGGCNTCTCTGATTCCAGGCNCTCACTTTCCTGGNAG
GTTNAATTGNGCCCAAGAAAGGACGTTGTGACTGTATTTAGGCCCCCAAACTATTGCTACCCGTTGTGGC
AACATGGCTGCGATTCTAGAGATCGGTGAGAACATGGACCAGAATTCCCTTCAGTTTGATCCCAGCTCCA
CGTCAAGTCGAACCCGAAACCACTCGCAAGACTCCAGATTATTTTTTGTAAGTACCAAAAGAACTAAAGC
TGCAATTCCACACACTAGCTCTTCGTCTCTTTTGCTTCTATTCTTAACCACTTTTTGTAATTTCATATNC
CTTACGTCTATTTCTGTTTGTTAAACTCTCCATTGTCTTTTAAAATCCGTAAACTTTTGTGTGCAAAGAT
TCTGGTACAAGTAACTGAAACCGCTATCACC
>gi|3450190|gb|AI100229.1|AI100229 34604 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109M7XP 3', mRNA sequence
CCCCGTCGNTACGTTTTGGGGGGTTCATTAGTCCCCCGNANCCCTGNTCCACTACGGTTCNAATCGGCCG
NCGTGAGAGATCCCNAAGCGATCCCGTGGTGAAAGCNGCGGAGCTTCAGAAGATATGATCAGAGCCGTTC
GATGCGTTGACTTTTCCCTCTCGTAAGTCTTCATTTCTACGCGTATGTGTGTCCTCCGTCCCCCGAGAAA
TACGGATGGTGTCGATTTGATTGATCTCAGCCGTTGGATCAAAAATGGTTTATTATTGTAAAAGATTGAT
TATGTATTTATCAAAGGGACACGTGTCACGTGGTTTTAGGATGGAGCCNTTTCGCTTTTTCTCCTTCATT
TTATTTTCTTTTTCCTTTCAGAAAGAAATAAGATTATTCGCGTTGGCTTTTTCTTTTTAT
>gi|3450189|gb|AI100228.1|AI100228 34603 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109M2XP 3', mRNA sequence
GGGGAAGNGNNCTAGATTGCTTGCCAAGAGGAGGAAATTGCTAAGGCTTAATTCCTGATNCTGCTGATTC
CCCAGANGCTTCTCNCCTCGAGGTTGAAGGACCAGCGTGACAGGAGGAGTGAGAGTTTGGCAAAGAAGAG
GTCGAGACTCTCTTCTGCTGCTGCCAAGCCCTCTGTCACAGCTTAAAAAAGCTTGAGAATCAAATCAAAG
ATGTCNCCTTTCTAGTTTTGTTCTCTTTTCTTCTCCGGCTATTAAAAAGTTAGTTCGAGTTCATATTCAG
CTGTTTTTGTTCCAAGACATGGGTACACAATCGCTTTGGGCTTGTTTCATGATTTATGCTTTTAGTTGAA
GACCATTTTAAACTC
>gi|3450188|gb|AI100227.1|AI100227 34602 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109M16XP 3', mRNA sequence
CCACTACTNGAACCCCNTTNCTGNTCCGGTATCGNCTCTCCCCGGGACACCCAGTTGGACCCTCCCCAGT
ACAGCTCAACACTCATCCGGTTCAGATTCCCTAGAGGACTGGGAGAAGTTTCTTGATGATGAAACAAGTG
ATTCTTGCTGGAAAAGTTTCTTAGACTTAACGTCACCCACATCGTCACCTGTCCCATGGTAGAACTGGAT
TTTGTTCGGGTCGTATACTCATAGTTTTAAAGACAATACATACACAAAGATATTCGATTAATACTCTTAA
TTTTGTTTGTTATTAAATATTGATTTAAAGTTTGTATATTTTCTTGTAAAGGAATTCTTATTTGTAATTT
GTTCTTATTTGGTTTGGTTGTTGTGTAAAGAAACACATTGTAATCACC
>gi|3450187|gb|AI100226.1|AI100226 34601 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109L6XP 3', mRNA sequence
TTCAAGAAGACTTCAAGNCACTGAANTTNAGGTGGGAAGTTNTGAAGNGCTNNTGACCCNTCTCTTCCGT
CCCCTGAGAACAGGGGAGATCGACGAGCACTTNACGGCCATTAGTGAACGTGACTGATCACTTTCACTGG
AACATTCAGTCGGGACTTTGCATCTCTTTCTTTTGCTTTAAATCTATCTAAGATGATTCACGTTTCAGAG
AAACGTGTTTCCATTAGTCATGAGTCGTGTAGTTTTCATTTGAATCATCTGCTTCCTCCTAATAGGAGTT
ACATGTAAGGGTGTCAAATTAAGGTCGAATGAGATGGTTTAAGGTTTTGAATTTTAAAAGGCAAAACAAA
GAAAGTTATTTAC
>gi|3450186|gb|AI100225.1|AI100225 34600 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109L23XP 3', mRNA sequence
CGAAGTTTTNCCCCTCCTGGNGCCATGNCCTCTGCAGCTTCGNCNTTCCCAAAGNTCGNGCCTGCGTNTA
AGTCCACTGCAAGCCGATCCTGCTCGATCTCAGCTGTTGACCCTAAACTCTATTCCNAAGAGGTTCAGAG
ACTTCATCANTAGGATCTTCCATTGAAGAGGGCTAAAGACANGAAGGCTAAAGTTTTTAACTAACATTCT
CGGCTCTACGGAAATGTGAAGAAACTGCGCGGGAAGAGTAAAAAGGTAAATCTCAAGGATAGAAGAAAAG
CGATTTCGGAATTTTATGTTTATATATTTTGAGATGACCAATCAAGTTTTTGGGTTGGGGAGGGGCTTTA
TTTATTTTTGTGGTGAGCCGTTTATATATATAATATTTATATATGTGAATATAGATTGAAGGTTTTTAGT
>gi|3450185|gb|AI100224.1|AI100224 34599 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109K4XP 3', mRNA sequence
TCTGAGCCANTCCCCCCGATCNTGTTGATCCATTGGAAGGNGATTAAGCCCTNTGGATCTNGCCGCCAAG
TCTAACTTGGGGAATCCTTCAAAAGATTGGGAGGGAAGATGCTGCCAACAGAGTCCATGCAAATGAACAT
CGACACTGGTGTATATGACCCTGTTGCTGAAAATATTACCAATGATGAACAGCTAAAGAGGTATGCAAAA
ATTCTCTCGGACGAAAGGAAATTAAGGAGACTAAGAAGCGACACAATGATTAAAGATTCATCAAATGAAT
CACAAGAGATAAAATAAAAGGAAATCATTCGTGCTTTTGTGTGAAATTGTTTGTTGCATATGTTTTACGT
GGTGACGTCCATTACTTTATATGCTGTGAGATGAAATTTTTTAAATAAAATTGGTTATCT
>gi|3450184|gb|AI100223.1|AI100223 34598 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109K21XP 3', mRNA sequence
TTTTTNCCTAANCACCTTTAAATTTGGGGNGTTCCCTACCNGGNGNGATATANCTGTTGGTTCTGAGTTG
GGACAACAAGTTGGACCTGGAAAGAGGNTTTTGTTCTCTGATGTGAGCGCTTATGAGGTCGATTTGGGAA
CCGATGCTAGGCATTGCTTCTGTAAAGAGAGTGACTTGTTGGCCCTCGTTGAGTGAAGTCTTGTCCAAGA
GGGAGAGATTTGAAGATTTTACAAGTTTTCTGTAATTTTCAGACAGCAATTGTTGTTTCTAGTTAATCCT
TCAATTTAATATCAATTGAGATCACTTTCAGAGATAGTCATATTC
>gi|3450183|gb|AI100222.1|AI100222 34597 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109K19XP 3', mRNA sequence
TGTGCCNTGAACCAGTTGATGNGGGGGAAGGATTTNGCTGTCCAATCCTTGTGGAATGTGATGNGCTCCN
TCATCATCCATTTACTTCAAAGCCCTGTTGTTCTTTTGACCCATNCCAGAGGAAAGAACAAGAAAGAAGC
CCTTGAGATTTGTTTTGAGATGAAGCTGCACATCTTGTCTTTTTGGATATGATATTTGTAAATGCAATAA
GTATATATAGTTCGGTTGGAAGATGTTTTTCATCGAGTCAGTTGTGATTTTAGCCGTTTGGTGTTTTTAA
GCAACGGATAAATTAGATTAATGTACGGTGATGAACCATGCATGTTTATAT
>gi|3450182|gb|AI100221.1|AI100221 34596 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109J4XP 3', mRNA sequence
TGGAACCCCGGTCAAGGNTCTCCCANGTGGGTCTCCCGGCTTNGTCCTACCGTNTGANGCCAAGGAAGGA
GATTGGNTGCTTGTTGGCGATGTCCCGTGGGGGATGTTTATTGGTTCAGTGAGAAGGCTCCGGATAATGA
AAACATCGGAGGCTACTGGTAAAGCTCAGATGATATTATGAAGCAAATAATAATCTACGAAGAACCCTTT
ATGTTTGAAGCAGTAATAAGACAGATCACAGATCAAAGAGAAGACAAAAACATTGTAAGAAGCTTCTTCT
TCTTCTCTCCCCTTTACAGTTTCTTTTTTGGCTCTGCCATTTTTCTTTTAGTTAGTTATATGTTCTCTTT
GTAAATCACACTTTAAAAATCTATAAGAAAACCCTTTCTTGCAC
>gi|3450181|gb|AI100220.1|AI100220 34595 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109J15XP 3', mRNA sequence
GGANCGNCCNCGGGNGTTTTCGGGCAATCTGCCCATGGTACATCCTGTTCTATGAGAGCCCTTGGCCCGA
CCAAGTGAAAGCTGAGAAAGCNGAAAGAAGGACTTTCCTCGTTTTTTTTCNCTTAACTATTATTAGTAAT
GGTATATGTTTGTCTTAAAAGTCAAACTCAATTGACAGTAACTTTTTTTTTTTTTTGGTTTTTGTTCTTT
CTCTGTGTCTCTCTCCCNAAGATATTTGGTGAGTTTTAAAATTGGAAGTTTTAACTGGAATTTGTATACT
TTGAAAAAGGCCATNTACAGTTTATGGC
>gi|3450180|gb|AI100219.1|AI100219 34594 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109I5XP 3', mRNA sequence
ATCCCCCAGNTTCNGATNTTTCGTGATGNCCTTGAAGAAATTTNGAGCTTCTCAAGGACTGAAACCTAAA
ATAAAACGATCNCATCTCCAGTCATCAATGGGTTGGTACCANATGCGAACTATCTTTTNCATATTGACCA
CATGGTTTGGTTTGTTTTATTACTTCGTCGTACATAAGCTGCCGGAAATACCTAACTCTTCATATGGTTG
TCTCTTTGACNCCTNCCGGATTTTACTTCATTTATGCAAAGTATTGTAATAATAAAAAGAAAA
>gi|3450179|gb|AI100218.1|AI100218 34593 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109H23XP 3', mRNA sequence
CACCGTAGACCANCTGGNTCGGCCCTCACACCTGAGGCCNTCCNGATCCCACGAGTCTTACGCTCAGGCA
TGNGCAACCCTTGGCCCTATGAGTATGGTGAAATCATCCATGATTGNGGAGCTCTGAAGAGATCCAGTTC
ATGTAAATAAGCTGCATGTTTGTGAGTTCCCGCATCGTTCGTTTATCAACCTCCAAAACTTTCTAATGTC
TGTTACTTGCATCTTCTTCTGCTGTCTCTGTCTGTCTCTCTCAGGAGTTCCTGTTTGCATTGCGAGAAGC
CATGAGCCTCTATCTTGAGGGTAGTTGTGATGAAGTTAAGTAGAGGCTTATTTTTAGGGGTTGTGGTAGT
TTTTGTTTTAGTGAATCTTTTGAATTCGTTTGTGTTTTGTTTTTGTTACTTTATGCCCCAAAACTCCTTT
AACATTTGTCATAATGTGTTTGAACCTCTCATCTGTTTAATCAAATAAATCTTCTTTGTATGCT
>gi|3450178|gb|AI100217.1|AI100217 34592 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109H1XP 3', mRNA sequence
ATGATGGACGATACTGGACCAATGTGGAAGCTTCCATTGTTCGGATGCACCGACTCCGCTCAAGTGTTGA
AGGAAGTTGAAGAATGCAAGAAGGAGTACCCTGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCG
TCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATCCCCTTTCTGG
AATATTCAGCGTTGATTATTCTGGAACCCATTTCTATGTGGTCAATGCAAATTTAAGAAATTATTTGCCG
ACTTAACAGTTGAGGAACTATTGTTTGAAAGTGAAAATGTTATTCCTATCAGTTTCTCTAT
>gi|3450177|gb|AI100216.1|AI100216 34591 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109H17XP 3', mRNA sequence
TTCCGGGGACATCGNAGTGGAGCANCTCANCTGGACGCATGACCAGGCACCAACCCTGGCACGTGTCCTT
CTCCTACGCACGTGCGTTGCAGAACACTTNTCTGAAACATGGGNCTGCAGACCCGAGNACNTGAACGCAG
CTCAGACCACTCTCTTGGCCCNTGCCAAGGCCAATTCGTTGGCTCAGCTCGGAAAATACACCGGTGAGGG
TGAGTCCGAAGAGGCTAAGGAGGGCATGTTCGTCAAAGGGTACACCTATTGAAGAGATGATGCTGTGAAA
AAAGAGATGAAGCAGATGTTTTAATCACATTTGTTTTTGAGTTTGCTTGTTATTAATCATGTCAAATCAT
TATTTTCTCTGCTTACTTTGCGTTAGCTACTCCTTCTAATAAGTTCTATTATATTGAAGTTATCT
>gi|3450176|gb|AI100215.1|AI100215 34590 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109F3XP 3', mRNA sequence
CTTCTAAGGGGGAAGGTTTCCTGATTCCGGCCCGGGAGATTTNCCCGNGCTTTTTCGGGNATNCAAACGC
CGGCGATCGTNAGCAAGTATGCGGNGGATCCAGTGGCTTTCTTCGAGCAATTCTCGAAAGTCGATGGTAA
AGATGGGGAACATTTTGAACTCTGAAAGCTTGNCTGATGGAGAAGTTNGAAGAAATTGCAGATTTGTGAA
TACATGATTCATCAACAACGAAACTAAAAAATGGAGAAAATAATCTATTTCTGATCTTTATTTATATAAG
AAAGAAAAAATTTAATTTGATGTTATTCTTTCCCTTATTTATTTCTACATTTTTAAAACTATAGGGTTCT
TGAATGTTTAAANCCTTATTCTAATGATTTTCAATTGATCTG
>gi|3450175|gb|AI100214.1|AI100214 34589 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109F21XP 3', mRNA sequence
GATTGGCCCCCNTTTGTGATGCCTCCAGATAAGTCCNGNCCGGAAATGGNAAGAGGAAGNTCANCCNNAC
AGGAGGGGNTGGGCCAAANCCCAGTTCNTCNTTGGGGAATTTGCTGGAGAAGTTACTGCCTTGAGAGAAA
AGGTAACTATGTGTGGATAAAACGTACTGTAAAATGTGTATTATGTATGATCTAGAGGGCCTTAGTGTGA
TGTATGACTTGGTCAGGGATTTTGGTGGTTTGCCCGAAGTCAAACCGAACCAAAACTGGTTTTCGGTTAC
TTTAGACTTTAGTCATAGTAAAATGAACATGTCTATAAATGAATAATATGCAACTCTTCCAATTGGTAGG
CTTGCTTTTGTCTATGTAATATCAATCCTTCTTGTTATGTATTTATCTTTGGCCAAATGTGATATTTTCT
GTAGTTTT
>gi|3450174|gb|AI100213.1|AI100213 34588 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109F15XP 3', mRNA sequence
ATTTGTTTTTGAAGGGTTGGTTGGNGTCCCNGGTGCACCTGNCACGGTNCCCCCATTTTGNTTAGGGTGT
TAAGATCCCTTNCGNCTTGGANCAATCCCTCGCCAGGTGATGGGAAGAGGCATGGATGAAGTGCTCTTAT
CCCTGAATTCTTTCNCCCATGGATTGAAGAAGAAGGTCGAATCGAGGTTTAAACTTGTCAAAAAGAACAA
CATTGACTGCAGCCTTAGAGAAATGCTGGACTGTAACACAAAGAAATTCCATGAGAAGTTTGGCTTTTCG
GAGGTAACTGCAAGCTCCTAGCTTTTATATCTCTCTCTAGTTTTTTCCTTCATCAGGCTCTCTCTGTAAG
CTGTTTTCAGCTTGTGCACCAATTTCTAGCACGAGCTTTACCTTGAGTGATTGTGATATCAATAGAGTGT
TTTCTTCCAGATATCATCGATTATTCACTATGCATTCGTTTATCATGGATTCTACACTTCCTTTTGAAAA
TTACCT
>gi|3450173|gb|AI100212.1|AI100212 34587 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109E3XP 3', mRNA sequence
CGCCCNTCACTTGGTTTCCTCCGCGTGGAGGTATNCAGATCTCGTCAAGACTTGGACCGGGAAAGCCATC
ACCCCTTGAAAGTGGAAAGTCCGACACCATTGACAACGTCAAGGCCAAGATCCCAGGACAAGGAAGGTAT
TCCTCCGGACCAGCAGCNTCTCATCTTCGCTGGAAAGCAGCTTGAGGATGGACGTACTTTGGCCGACTAC
AACATCCAGAAGGAGTCTACTCTTCACTTGGTCCTGCGTCTTCGTGGTGGTTTCTAAATCTCGTCTCTGT
TATGCTTAAGAAGTTCAATGTTTCGTTTCATGTAAAACTTTGGTGGTTTGTGTTTTGGGGCCTTGTATAA
TCCCTGATGAATAAGTGTTCTACTATGTTTCCGTTCCTGTTATCTCTTTCTTTCTAATGACAAGTCGAAC
TTCTTCTT
>gi|3450172|gb|AI100211.1|AI100211 34586 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109E16XP 3', mRNA sequence
GAAGGCAGTGGAATCGCTGTTAAAGACCGGTCANTTTGGTCTTGACTTNCGACTATCTCAATCTTCATAG
AGTTTTTTTNCATAATTTATAGAGAAACATCAAACCCCTTTTGGTTGGGANTATCATGTGTTTGTTCCAC
TTGTGTGTTGAAGTCATTTTCCTTCTTCTGTCTTATTGAGGCAGGGACTAATGTTTGTTTTATCTTTCAG
TTGTNTCGTTTAAATTCCACATTTGTNCAATGAACTGGTTGGTGTTTCTTTANGATATAATCATTTTGCC
>gi|3450171|gb|AI100210.1|AI100210 34585 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109E12XP 3', mRNA sequence
GTGTCCCCCAANCCTCGGCGTTCCCCNTATCCAATCCGGCCGCNCACACAGTNCCTTATGGATTGGTAAC
ATCCCATNATGCCCCCTGGNGCACTGCCGCCACCGCCGCTGGAACGTTGCCGCCGCATTGATGAATAATA
CACCCAACCAAATGCAGCTCAGCAACAAGCGCAACAAGGTCAGAGTTTTCATCCCACCGGGTATGATGTA
TTTTGGACCTCCACACCATTCTTAAGGTTAGTAAAAACAAACCAAAAAATCCAATTAGTTCTAGTATTAG
ATAGTTTCTGACCCACTTTATTTTATTTCATGTAACGCATATTGTAGAAAGTAGAAACGAGATCTTTTGT
CTTACAAATCTTGTACCTTGAGCTGTTTAGTCAATTTTTCTTCTTTGTAACATAGTTAGACTTCTATTGT
GTATCTGCGTTACATTTATATCTAGTATGCGTTTGTTTCAT
>gi|3450170|gb|AI100209.1|AI100209 34584 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109D17XP 3', mRNA sequence
CCCGGGTTCNATATGGCTCAACTTTTGGAANCCGGAACCNTGGGGCTGCNTTTAGTTCTTCAGATGTATT
GGGCTCCCCAACCCAGNCCCACTTAAACCAGTTGTTCGACAAAGTTAAAGACTACTTTGGGGATGCAAAA
GAGTCATTCGGGNAAGCTATCATCGCTGAACCCGGGGAGTGACGAAAAAACTGAAGAAACCTCGGATGAG
AAAGCCAAGGCCTGAGGCTGAACAATTGACACTTGGTTGGTTGATTTTGATGTCTCAACCGTCTCGGTAT
GGGCTGCAGAAGGTCACTGGATATGACGAGACTACCGCTATTTTGTGCACATTTTCTCTATACATCTCTC
ACAGAAACAGCTTCTGTTAAATCTCTTGTAACATATAACTTATTGTGTATTGTAGATTTGTTGAAAGAAA
GAGCCATTGGTTAC
>gi|3450169|gb|AI100208.1|AI100208 34583 Lambda-PRL2 Arabidopsis thaliana cDNA clone 109C5XP 3', mRNA sequence
GGGGGNAGCCTTCCTTTTCCGGACCNCAAGCTTTCGAAGAAGCGTNACTGTCCGGCATGCNCCNTGGNTC
NCAAGNTGGTCAAGGNGAAGTTGAGCCCCTAGNCCCCGTACTTGGCCAAGCTTGCAGGTTCCCATGGTTA
CATGGATTGAAGCTTGGGATGAGCTTAACCCACCAGCAGCCAGTGGCAAAGCTTGAGAGCAGTATGAGCC
AAAAAGAAAAAGCCACCAAAGTTTTGGTTATTTTTAGCTCAAATTATCGTTACTTTTAAATTTCTGATTT
TACGAACCTTTCTTGCTTTTTTTACACATTTGAGTAGTTTTCATCATCAGTACTTTCTCATTGTCCGGTT
ATGGTTTTTGCATTTGGTTTAAATATCACCGGTTTATTTATAAACAGTGGTGGATTAGTAGTACTATTTT
CTGAGTTTTTTTCTTTGTTTCATTAATAAAAAGGCCTTTTC
>gi|3450168|gb|AI100207.1|AI100207 34582 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108O9XP 3', mRNA sequence
TTCTTTCTCTGAGTAGAAGCTCACACATTTTCATGCTGCAAGGCCCGNAAAAATGGCAAGACTAAGCANG
CTAGGAAGAGGCAGAGAAAGAGATTGCCGATTACAAAGCTCAAACAGAGCAAGACTTCCAGAGGAAACTT
GAGGAGACAAGCGGAGACTCTGGTGCGAATGTGAAGAGGCTGGAGCAAGAGACTGATACCAAAATCGAGC
AGTTGAAGAACGAAGCATCGAGGATTTCCAAAGATGTTGTCGAAATGCTTCTGAAACATGTGACCACAGT
GAAGAACTGAGAGATATTTTTATAAGAAAGTAAAAAAAAAGTTTATGAAAAAAGTGGGAGTCATTTTTGA
GTGATCTGCTCTCTTTCTCTTTTGTGGGTATTTCTGGATTTGAGAGACTCATCTTATATTATTGTTGCTA
CTT
>gi|3450167|gb|AI100206.1|AI100206 34581 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108O19XP 3', mRNA sequence
TCCGTGCTCTTGATGGAGCCGNAGATTTCTACGNGTNCTCGTTTGTGGAGTCGACTCTGACTGATCCTCC
TTTCTTNGCATCNCGNGTTAAGATAGGGAAGAACGNTCTTGAAGCTGTGATTGAGTCNGNCCTTCAGGGA
TTGACTGAGTATGAGCAGAAAGCNCTAGAAGCTCTTAAGGTAGAATTGAAAGCTAGCATTGACAAGGGTG
TCGCATTTGCAAACAAACCANTGCTGCAGCAGCTAACTAGATCGCAAGCTGATAACATTTTTCTTCTGAT
CATTTCGAGTTTTGTTTTATTTTTCATATTTGTTGCATCGGCGAGACATTTTCGTGTTGTAGAATAAAGA
ATGTATTTGCTTCAGTTTG
>gi|3450166|gb|AI100205.1|AI100205 34580 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108N3XP 3', mRNA sequence
CCGGGTNCNGCTGGACGCCCTCTGGCCCTGTGNTGNGCTGTCCTCGCCTCTATGATAGNTTGGGNCCTTT
CACGACCCCCCTTTGGACAACTGCTCATACCANCGNGTNTGNTGCTCCATACACTTGGCCACACTNTTGT
TGATGTGTTGAACATGTATAAATTGATCACCGGAAAGGAACTGGATCTAAGTGTGGATCTTAACGCAGCT
AGTGCTGCAGAGGAGGAATGATGGAAAATATTGCAAGCTCTGTCTCTCTCTGTTAGTCACCAAATGATGT
AACCGGTTCTCTTTCTCCCTCTTCTTAAAAGTTGTCTCACCAAATGTTCTGTTAAAATACTAAATCAAAC
CGATCTCATCATGCGTACCTATTCCCGGTTATCGCAGTCTGTTTTTTTCTTCTCAAAAAACTAAAATGTT
GGATTTCGTGGTTTT
>gi|3450165|gb|AI100204.1|AI100204 34579 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108N1XP 3', mRNA sequence
CCTGCCNGAGGAAGAGTTTTCCCCGCANGAGTAGAGATCGTGACAGCACNATGACCACCGAGANCATGAC
AGAAACTATAATCAGTCACGTGGCTATGACTCAAGAAGCCGGCGCANTTCACGGTCCCGNTCTAGGGAAA
GACCGAGGGATCATGATCGCCGCAGACGCCATGACCGCTACTAAANCCCTGCCAAAGATGGTTGCACCTG
GTTTAAGAGGTTCTTACAGATGCGTTTAGGATCTATTTGGAGTTACAAACACTTTCTTTTTTCTTTGCTC
AAGTGTTTTAAGGATTTTTGAGATTGTAACTTACTTTAAGTTTGTAAGAGGAGCTTCTTCAGAT
>gi|3450164|gb|AI100203.1|AI100203 34578 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108N12XP 3', mRNA sequence
CCGTTGANTTCCCCCNTGGAATTCCGTTCGATTAACCCGGTGGTTNTGGTTAANGCTCCTCCGGAGGGAG
AGTNTCCGGAGAGGTGGAGAAGAGTTTTCCAGGAAGCTAAGGAGACATGCGCTGATGATCCGGTGAGCGG
GGAGTGTGTACCCGGCTTGGGACGAGGTGGAGGAGCTGAGTNCGGCGGCGAGTCATGCTAGGGACAAGAA
GAAAGCTGGTGGCTCCGATCCTTTGGAAGAGTATTGCAATGATAATCCTGAGACTGATGAGTGTCGTACT
TATGATAATTAAAAAATATGTTTTTGATGTTCGAATTATGAAACTTTAGGTATGGATCAATGTTTGTTCT
TCTTGTCCCTTGTTGTTATGTTTGTGTTTTTGGTTTGGTTGATGATTGTAATGTGATAAATGAATATGAA
TAGTACAATACAC
>gi|3450163|gb|AI100202.1|AI100202 34577 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108M8XP 3', mRNA sequence
CTGCANTGGAGNAAGTTCGGAAGTANCCAGGAGTCATNAGTCACAATCTCCACTGGTGGTGGAGCCAGCT
TGGAGCTGTTGGAAGGAAAAGTACTTCCCGGTGTGATCGCCCTTGATGAAGCAATCCCAGTCACTGTTTA
GAAACTCTNACCATCTATAAGGCAAACGTTGTATACTTAAAAGAGTTTCTTTCGCTTTAAATCTACCTAT
GCAAAACTTTACTATGTATCAGAGTCTCATTCCCCNGAAANGAAAACTCACATATTAAAATT
>gi|3450162|gb|AI100201.1|AI100201 34576 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108M6XP 3', mRNA sequence
CGATCAGTCTAGCAGGTTGTGATGAATTTGNGGGNTAAGTTGAAGGNGCTCGAGAGTTTTTTGCACCCCG
NTCATAGCAAAGATGTCCCAAGGCGGTGAAGCTGNTGGTCCCAGCTGCAGGAGGAATGGACGAGGATGTN
CCCCCTTCTGCCGGAGGTGCAGNCCCCAAGATTGAGGAAGTCGACTAATAACTTTCTCTCTTACTCTCAG
TCTTTGTGTTTGTATTTCAACATTTNCCTGTTTTGNCCCCTAGTTTTTGTTTTTTTTTTCTTTCTTGTAT
TGACTCTATTTTGGGGGCTCGNTTCTTTCGATGAGCTCCTTATTTTTTTTAATCTATANCAGGAATGTTT
TGATT
>gi|3450161|gb|AI100200.1|AI100200 34575 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108M20XP 3', mRNA sequence
GAACNCCTTAGNCNTGGGTAAATTGATTNAGGGGGAGAGGANTGAAGAATGACCAGGAGTGAAAAGGCAA
GCGAGNTTCGAAGTTGCAGCANCAGCTCGATGATGATGATCACTTAACGCCAGCAGAAAGGCGATACATA
GAGCAGAAACAAAGATTGGATGTGCAGAAGCTAGCTAAGGAAGCGAACAAGTCTCACCGTAACAGGATTG
AGGATTTCAATCAGTATCTGGCTAACATGAGTGAGCACTACGATATCCCTAAAGTCGGACCTGGTTAATA
TAATTCTTTCTTGTCTTTGTTTTACTCTGCTTATCTATTTTGCATCGTTAAACGACTACTTTGGATGTCT
GTTATGTTTAGTCCCTTTAACTTTTGAATGATGTGATCGCAAATCTGTAATGTCAAAAACACATTTTCTT
GG
>gi|3450160|gb|AI100199.1|AI100199 34574 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108M12XP 3', mRNA sequence
CAAAGNGGCTGNCGAAATTCCCCCNGCCACCCAATTNNCTNCANTGGTGCTGATCCCCTTGATTCCGTGG
AGGTTAGTTATGGGATTAGAGGAAGAGTTTGGGGATTGAAATGGCGGAGGAGAAAGCACAGTCTATCGCC
CACAGTTGAGCAAGCAGCTGCACTCATTGAGGAGCTCTTGTTGGAAAAGGCCAAGTAGAAAATCCTTTAC
TACATTAGCAAAAACGAAAAAAACCAAAACCCAAACCACTATCTTCTTATTGTTTGGTTAGCTAGAGAGC
AATTGTGTCCGTTGAGATTTTATGCTATTTTCGGATAATTATTACAAGGCTTGTATTTTAATATTTACTT
TCGTCTGAAACATTTTACTTTCACCTTTAAAATATTAGTACTTTCTGGT
>gi|3450159|gb|AI100198.1|AI100198 34573 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108L21XP 3', mRNA sequence
TGTGTTCNAGAAGANTCTTCCAGAGAGCCTTCAATGGNTGACATTCTTGTGATGATGANCAGTTCACTGT
TACTTTACCGATTCCAAAGCGATCTGGGTTTCTTCTTCGANCCATGAAAGACTCTAGAGATCCNCGCTCA
GGAGGTTCTGCTTCTGATCACTCTGCAACAAGCAAGTCTTTGCCTTTGTCTGTTGACGATTCTTCCATCA
CTATAGTTTATCCTCGTTGACTTCAACAATTAGTTCCAGTAATGTTATGTTGTAACTTGTAACTATGTGA
AACAAAGCAAAAACTTATTT
>gi|3450158|gb|AI100197.1|AI100197 34572 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108K7XP 3', mRNA sequence
GCTTCCGCCTCCCCAAGGGNCANGACCCGTCTTCCGGCTNGCCCCATTTTGGCATGGCCCGCGCTTGGAC
CCCNGGCNAACTGGTTAGNNCGAGAAATTATGGATTTCGTGAAGAGCTCGAGTCGTCATGTGTAACACTG
TTGAGACAGGGAAATGACCCAAGGATCTTGCCCTTTTAATCCATGGTCCCAAGGTGAGTAGGGATTTGTT
TTTGNACACGGAAGAGTTCATTGATGCAGTAGCCTCCAAGCTCAAAACACAGTTCAAAGAGCTTCCTCTT
GTCTGACCATTCCTGGGAATTGGGAACAATACAAAAATAATGCTCGCAATAATTCATAACCCAACACAAA
ACAAAAATAATATTGGCGGGTTTATATGAATATTTTGGTTGGAAATAAACGTTTTTGCTTAATTTTTCCA
ATTTATTTTAAAAATTTGAGTGAC
>gi|3450157|gb|AI100196.1|AI100196 34571 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108K18XP 3', mRNA sequence
CCGTNCTTAAAGGCCNTCGTTGAAATCGAACCCGCGGCTNGTCTCGGCACTACCCTCAAGCTCAAAGCTC
TTGNCCNTCATCTTTTATGTCCCTGTTGCTCTTCAGCTTCNCCTTACCTGTGGCAAAAATCCACTCCGGG
CTACACTTGTTCCATATGATAAACTCACTCCACTTATAAAGGATGCTTTGGAGAAAAAAGTGAGAAGAGA
ATGGCAGAGCTCCAATCTTNCCTGTCTTGGTTTACCAAATACATCATATCAAATCCTATCCCTTTGATTC
TTTCCTCTATCGTTCCCTTATGCTTGTATCATTAATTAATGTGTGCTTTTTAGATTAATGATTCTTCTCT
TGTATTAAAGTATGATTTGAAATCCT
>gi|3450156|gb|AI100195.1|AI100195 34570 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108K14XP 3', mRNA sequence
CCTTAAGGGGCTGCCGAATTNCGCTTCCCNCCAAATTCTCCCCTTGNGCTGATCCCCTTGATCCGTGGAG
TTGTGATGGGACCTAGGGGAAGAGTCCGGGATNGAAATGNCGGAGGAGAAAGCCNCAGTCAATCGCCCAC
AGTTGAGCCAAGCANTGCGCTCATTGAGGAGCTCTTGTTTGAAAAGGCCAAGTAGAATATCTTTATTACA
TTAGCAAAAACGAAAAAAATCAAAACCCAAACCACTATCTTATTGTTTCGTTAGCTAGAGAGCAATTGTG
TCTGTTGAAAGATTTTATGTTATTTTGGGGAAATTATTACAAGGCTTGTATCTGACTTTTATCTTTCTTC
TAAAACATTTTACTTTCAGCCTTCATCAAACTCTCTTACGAAACTTATGTAGTCTCATTTCCTAAATAAA
GATGTTTTTCCCT
>gi|3450155|gb|AI100194.1|AI100194 34569 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108K12XP 3', mRNA sequence
TCCTCCCNCCGTCTTGGCTGCAGCCAGTGACCTGAATCTGGATGGAGGNAATTCCCCGGAGATGATCCAG
AAGTGAGCATGTTGCTGAGCAGCTGTCAAGACCATTCCAGCCAGAGGTCTAACTCCTTGTTCCCTTATGA
ACTTCTGGAGGTTGTGCATGCTAAAGCTGAGGTAACCGGCGAGGCTGCAAAATACAACATGCTACTGAAG
TTGAAGAGGGGAGAAAAAGAGGAAAAGTTCAAGGTGGAAGTTCACAAGAACCATGAAGGTGCTCTTCATC
TCAACCACGCGGAGCAACACCATGACTAGTCCCTCTCCTTTGTTTATGTACTTTTGAGTGTTTACTTACT
CTGTAAGATATTTTAACTTCTGATGTAAAACTCTAAAACCTTAAATAACAAATCAGGAGAATAAATTAAG
TTTCAT
>gi|3450154|gb|AI100193.1|AI100193 34568 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108K11XP 3', mRNA sequence
CCCTGGGTCCATCACTCCCTGTCAGAGGTTTCCCGNTAAGCCCCCGTTCTTCNAGTTCCGNTTTNGANCC
CGTAATTTTCGGGCGGCAATCCAATCCTTAAGCCGCTCCAAACTTGAATATGGCCCTTCCGGTTGCGGAG
CCCAATCTGTTTCTGCTTGAGAAGAATGAAGANCCAACAAAAGAAATTATCCCAACTTCTTGGATCTTAT
TGGCAAAACTACAAATCAAGGTACATGATATTCACTTTCCTATGTGTTATTGGCGTAATCCCAACTCCTA
TAAAACTTATAAGCGCAAAAATAGTATATAACATGTCCAATTCACCCCGGAATGTTAATCTCAAGGAATT
GTATTGGCTACTAAATTGTTTTCCATTTTCCTTGTTATTAGCTTCAAAAATAGATTGTGAAACGAAGATT
TAACATT
>gi|3450153|gb|AI100192.1|AI100192 34567 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108K10XP 3', mRNA sequence
AAATCTTCTCCGGCGGTGCAACCCGGTCCCCNGCAATNCGGGCTCCCTCTTCNCCAAGNTTGTTGCCATG
GGNGGCAGATCCAATGNGCTGGNGCAAAGCATCAATGATCTAAGGGCCGAGATGGGAGTAGAAGGCCACT
CCTCCTCCAGCCTCCAAATCAGGCGNTGANCCCCAAAACACCGGCTAGTTCCTCTTAAAAAGGAATGTGG
TGTTCATTGACATGTCCGAAGGAAAAAGAAAAACTATGAAATATGTTAAGAGCAGTATTACTTTTAAAAT
TCCTGTTTTAAGAAACGAGTTTGTTGTTTATTAAAGTTCATCAAATAGATTGATGATGTGGTGCATTACA
TTATTCTCCACCTATGAATTGCATTTCTATTTTGGTCTTGAGAGAACTAAGAAGTCTTCTTATGCTCCTA
T
>gi|3450152|gb|AI100191.1|AI100191 34566 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108J24XP 3', mRNA sequence
CCATTTGGTNATCCGGGAAGGTAGTGNCAGTATTGNATNTGNTGTACCAAAGTCGAAGCTGAAGGAATCC
AGAGTGGAACTCCTAAGAGTAAAGTGTTGATTGTAGNCANTGGTGAGCTTCCCCTGTAACTCAACAACTC
TAGTTNTCTCCATCTGATCATCCATTGATGTGAGCTCTAGTGTGCTTGATGACTTTTGTGTTAAAACGAG
TGTCTTGGTTACTTTATGAAAGATTCTACCGGCTTTATTTCTTTCGTCTGCTTTCTAGCTCGAGCTATGT
CTGACTTTATACACAAATGTCTTTCAGTAGCAAAAATTCTGCACTTATGCCGTTTTGCATTGTCAACATT
TGTAGAATTTATAGAAGTTACACGATAATATAT
>gi|3450151|gb|AI100190.1|AI100190 34565 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108J1XP 3', mRNA sequence
GCAACATACTTTCTTCTCNTCTGTTTCCCAAGAAACTTGGGAAGTTAAATCCGTTTAAAAATGGGTCTAA
GGATACTCGCACATAGNTGAAGATCTTGGAGGTGTTGACATTACTAAGCCAAGGAGNCGAAGATTCNCAA
TCTCTTAAAAGAAACCGTTTGATCTAAGTGCTTTTGNGTGTTGTGTATAACTCTTTTAGACTAGTGTGCT
TATTGTTCCCTTCTTGATGCGTGATTTTTTTTTTTGGGTGTGTGTGTTTATTGTTTAATGNGCTTGGTTA
ATAAAATGAAAATCGAANCCAGATTGATTTNCT
>gi|3450150|gb|AI100189.1|AI100189 34564 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108I1XP 3', mRNA sequence
CCCTTTTTNGGCAGAATTCCATTGGGAACCCATCCGGGTCGGGGAANCCGGAATTCTNTTTGGCGNTCAC
GATCNATATNCCCAGTATTTCGAGACCTTTNGAGAAGGAAAAAGCCAGTGAACTCGGCTTCTTCGGGTTC
TAAGTTAGCTTAAAGAAGGTGTAAACTTTGCCTGAGGCAAAAAAGCAGAGCAGAAGAGGCTTTAGCTTCT
GTGCCCACCTCAAACACAGACAATTTGTGGTGGCACTTGGGTTAGACTACTTTTTTTTGTTGTTGTTGAA
ACGAAATTTTCTCTTTAGTCATTTATGTTTTTTTGTTACTTTTTACAAGTTAAAAAACTTATGTGATAGA
CGCT
>gi|3450149|gb|AI100188.1|AI100188 34563 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108I19XP 3', mRNA sequence
GGGGTTCCATGCTCGTACCCTCNGAAGAGTGCAGCATCAGCGGTCTAAATGCATGGTGNCCATCTAAACT
GACAAAGAGGATACCATAGCTGAGGAAGAAGATAATGAAACAGTTGCAGAGCTTACTGATAAAGTTGCTT
CTCTTCACAATTCTTAAAAATGATTTAGTTATTTTTTTTCTTTTCTTTTCTTTTTTCACGAAAGTTTTCT
GGTGAAAAGAAATTGGTTTCTCCATTCATCCACATCTATCTTCGTGGTTGGGTTTGATTTGTTGTATTTA
ATAGTTTTGGGGGTTTGATGAAACTTTAAATAAAAACATCGATCTCCATGTAATTTTTTTGTTTCTCTCT
TTTCTTTAAACACTCATATTTTGAAATTATTTATATACT
>gi|3450148|gb|AI100187.1|AI100187 34562 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108I11XP 3', mRNA sequence
CGGTTCTCGGCCTTGTTCCCCCNTAGACCTGGATTGCTCTACTNTGNACCAACCACGGGNAGNTCCACAG
AATTTGGCATGGCCCCGTCACAGCGCCAAGCAGATCTCCCCACATCCCTTCACCACTGGAGGAAGAGCTC
GAAACAAATCCCATTATGCGTGTTGATAAGCCCAGAGATACAGGAGAAACTCGGTTGCAAGTCGCCAATT
GATACAATGAGGGAAGTTCGGAACAAGAAGGATCAGTGGAGGGGATGATGATAAATGGAGAGCTTCTTGC
CTATGTTTTGTGTACTTGTGTTGAATGATCCTGTAAAAGGTGTATGAACCAGTAATGTTGATATTCTGTG
TGAAACTGTGAACCGGTTTGGTAAACCGAAATCAGACCGACCTGTAAGCCGTACTCCCTTTTTGAATTTT
CAGTTTACTATGGATAAT
>gi|3450147|gb|AI100186.1|AI100186 34561 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108I10XP 3', mRNA sequence
TTNCCCACATTCCTCTGATGCGNGCTTGAACCNTTGGGCCATTCGCAGATCATCTTTGGCAAGTAATATC
CGGGATACCCCGCAGGAGAGTATGTTGAACAAGGACTCTCGGTCATCAATCTCAAAGGAAATAAGGGATC
TTCATAGTTTCAGTGTTCAGCCGTGAACCAGTTGCATTCATGGGTCGACAAATATTTCCTACTTCCTGCT
GATTCTGAAGTTTTGAAATCTTTGCTTTTGTTAAAGCAACAGATGTTGATGAACTCAGAATTTGGTTGAA
TTTAGGACTTGTATTTGTTTCATTTGAACCGGTGTAAACTTTTTTATTGGTCAACTACAAAGAAGAATAA
AAAGCAATAGTTATGCCGTTCCCTTGT
>gi|3450146|gb|AI100185.1|AI100185 34560 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108H7XP 3', mRNA sequence
TAGGGAAAAGCTGGTACCCCTTCCAGGTNCCCGGTCCCGGATTTCCCGGTTCGACCCCACGCGTCCNGAG
AGGTTCTACCCAAAACACTCGGAAACTTTGTTAAGGCGACATTCGATTGCTTACAGAAGACATATGGGTT
CCTTACACCAGAGTTCTGGAAAGAGACTAGATTCTTCCAGATCGCCCTACCAAGAGCACACTGATTTCCT
GTCGACTAAGGCTCTTCAGGCCGCCAAAGTTGTCACCGAGGGTGAAGAACAAGCTTAAGACCTTCATGAG
ATGAGCTTGGTTTTATAGGTTCTGGTTGTGGCAAATATCTTTATCTTTTCTGGTCATGTTTCTTGGTTGT
CTTATCAGTTTTTGATATTGGAGATTTAATTACAAGGATAATCATATTTAGTTATGTTTGGGTT
>gi|3450145|gb|AI100184.1|AI100184 34559 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108G21XP 3', mRNA sequence
TTCCTGACCCNAGGTTGGTTNTACNGCTTCNATCTGGGGCCTGTCCAGGACCTCTGTGTTAGAAATGGTT
GCCGCTTTGAAAAAGCTTCCCGGCAAGAAAATCCCGATTAAGCTCTGTCCCGAGAAGGTCAGGAGATGCC
AACAGCCAGTTTATGCTTCAACAGAGAAGGCTGAGAAAGAACTTGGCTGGAAGGCAAAATATGGAGTGGA
TGAGATGTGCAGAGATCAGTGGAAATGGGCAAACAATAATCCATGGGGTTACCAGAATAAGCTTTGAATT
TACTTCTTTTGTTTGGAGTTACCATTTCTAATTACTCAAATCTAAAAGAAAGAAATATACATACATATGA
TGATATAGTTGTGCTTTATATTCCACATGTATCGAACTGATCTCTTACTTCGATGAATAAAATGGAAAGT
TGATTT
>gi|3450144|gb|AI100183.1|AI100183 34558 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108F4XP 3', mRNA sequence
GTTCCGGAGCGACAATCCTGAATGGGCCGATTGGNTGGNAGGCNAATAGGTCTCAGAGCTGAGCTAGGCC
ACCAAGGNGCCAATTGGGGCGGTCACACTCTTTCCATATCTCCAAAAAATGCAAATTCTGGNANGGTCTT
TGAACCATATANGGTTNGTGGAAAATGGCGGTTTCCAGACAGTAACTAAAACTCACTGCTGGTGCCACGC
TAGGCTTTATCCGCCTTTGATGCATGAAGGTCGTTAACGAATGGTCTTTTTTTGANAAAGATNACAATTA
GATTAANNCANAGAACCCATGTTTCTTGTCTGTTCGAATCCTGCGAGATTGGTTGTAGTTGAAGTTNCAT
TTTCTTCTTGTCTTTTTTGTTGGTATTTTGACACAATTTGGCTTTTTGGCATATGAGAGTGACTGTNCCA
GTCTGTTTT
>gi|3450143|gb|AI100182.1|AI100182 34557 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108F10XP 3', mRNA sequence
ATTTCCGGNAATTCCGGATTTTATGCGGGGTCAGACGGGTTTACCNCCNCTTGATNATTAAACGGAGACC
AGCGCCATGGGGAAGANTCCATTACTCCAGGGATTCTTTTCCCTCTACATTGGCTGGATGGATTGGGTGG
GTTGGAAGAAGCTACTTAATAGCTATTAGTGGTGAGAAGAAACCCGCGATGAAAGAGATCATCATCGATG
TTCCTTTGGCTAGTCGGATCATCTTCCGTGGTTTCATTTGGCCCGTTGCTGCCTACAGAGAGTTTCTCAA
TGGTGATCTCATTGCTAAGGATGTTTAAAAAGGGAACTTGTTTTCTGCTTTTGTGTTACTCTCTCTAATC
TCTTTGTTTTCCATTGTACTTATTGAAAAACAATGCATTGTCGAAAACCTTATAAAATTTGGATTGCGCA
>gi|3450142|gb|AI100181.1|AI100181 34556 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108D19XP 3', mRNA sequence
GCTTTTTAACCGGNGTTTTTGATGGAACTTCGGGACCAACCCTANCCCTTGTTTNTTNTGGNCGGGTATG
GAACCCGAGAATGGTCGTGACTACTGGATGTGAAAAAACTCGAGGGGNCGACACATGGGGGGAAGCTGGC
TACCATGAAGATGGCTCGCAACATTGCCCAATCCCAAGAGGCCCTATGTGGCATCGCAATGCGAGCTTCA
TACCCTCTCAAGAACTCGTTTTCTACGGATAAAGTTTCGGTTGCCTAATAATATGAACTAAATGTATGCC
ATGGAACGGATCGGTTAAGCCATTATCGTTATTCGACTTTGAAGGAAACTAAAAAGTAATGTGGTCGATT
GGTTTGGTTTTGTTATATATTATGCATTTGTATGGGGGTCAGTCAATGTTTGAACTTTGTATAATATTTC
TTTGGGTCTAGTGATAAATATTTTCCCTTTTGCG
>gi|3450141|gb|AI100180.1|AI100180 34555 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108C7XP 3', mRNA sequence
ATCCCTTGTTTGGAATTCGTNTTGGANCACGGNTTGTGTTCCGTGAGCACGGNAACCCTCCCGNNTACTA
TGATGGACGGTANTGGACAATGTGGAAGCTTCCNTTGTTCGGATGCACCGACTCCGCTCAAGTGTTGAAG
GAAGTTGAAGAATGCAAGAAGGAGTACCCTGGCGCCTTCATTAGGATCATCGGATTTCGACAACACCCGT
CAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATCCCCTTTCTGGA
ATATTCAGCGTTGATTATTCTGGAACCCATTTCTATGTGGTCAATNCAAATTTAAGAAATTATTTGCCGA
CTTAAAAGTTGAGGAACTATTGTTTGAAAGTGAAAATGTTATTCCTATCAGTTTCTCTATAATTATAGTT
ACCATTTCATTTC
>gi|3450140|gb|AI100179.1|AI100179 34554 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108C4XP 3', mRNA sequence
CCTTACCACGGNTTAGGANGTTCCCCNAGNGTGCTTAGCCGACNTTTNAGGACCTCCTTGAAAGANCCNG
CANCCTTTTNAAGTTGCTAAGCCAAAGNGGGAAGCTGTGTTCAAGAGNTAAGACTTGGGATGAGTTTATC
CAAGCTCTTAACGAAAGAAACTCATTTTGGCTCCCTGGTGTGATGAAGAGGAAGTGGAAAGAGATGTTAA
GGCACGTACGAAAGGTGAAACAGGAGCAGCTAAAACCCTTTGTTCTCCATTTGATCAGCCTGAACTCCCT
GAAGGCACTCTCTGCTTTGCTTCAGGAAAACCTGCAAAGAAATGGACCTATTGGGGCAGGAGTTACTAAG
TGTTCATCATGTTTTGATTCAATTCATGAAAATTTACTTTTGGCTTGTAAAGACTCTCTCAAGTGCATTG
TGCTTTGATCTGATATTTTGACCAAAAGCTATTTGAGTTATTTTGACTGTGATTGCACTAAGAATTATAA
AGAGTTGTTTGATTC
>gi|3450139|gb|AI100178.1|AI100178 34553 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108C1XP 3', mRNA sequence
CACAGGTTCCCCCGAACCATCCGTATGGTGTCNTCCNCCTGGAGGCCCCATTTTCCAAGGCTNCCTNAGG
NGAATTGCCGNGATTATGAGGTTAGGNCCCCAATGCTNCTTCTGTTCCATTCCNGACTCACTTTGGAGGT
GGTAAATCTTCTGGATATGGTTTGATCTATGATACTGTCGAGAACGCTAAGAAGTTTGAGCCCTAAGTAC
AGACTTATCAGGAATGGGACTTGACCACCAAGATTGAGAAATCCAAGGAAACAGATCCAAGGAGAGGAAG
AACAGGGCGAAGAAGATCCCGTGGTGTTAAGAAGACCAAGGCTGGTGATGCCAAGAAGAAGTAAGACGTT
TGAAGAGGACAGAAGCAGCAATATGGTTTTTGTTCTGCATCACTCCTTTGAAGCCATGTTTGCTATTAGA
CATCTTCTAATTATTTCTCGATTTTGTGCTTCTTTTTGTCACACTTGCTCTATTTTGGTTTGGATCTTGT
TTTAGAGAAACATGTGGTTAAGATTTTGTTTGAATACATTGATTTTAAACTT
>gi|3450138|gb|AI100177.1|AI100177 34552 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108C10XP 3', mRNA sequence
CCTCGTTTTGGTAGGCTTGGAAGCACATGGCACACCGTACTGGGCCCTCACGCTCTCATGGGTGCCAGTT
GTCTCTGCATTGCCCCGAAAGCGTTTTTGGAATCCATTTAACATCAAGAGATGCCTCCAGATCCGGAAGA
AGGGTCTCCAAAAAGACTCCATGAAGAAAGAATGAATCTTCCAGGTTTAAGTTACTACCAAGAATTTCCT
TCTTCTGAAGTTGTTGGTTTCTTGAAAAGCTTCTGTTCTGAATCTTTTGTAAGACTTGTACTCTTTAGTT
TTCTAAGTTTTTTATATTTTAAGATTAAAAACCCTAACGTACACGAATAATTTACTTCCTCTGTTTCTAT
TTATTAATTTAAGCAGTGTTGTATTGAATGTGTTTTTGCT
>gi|3450137|gb|AI100176.1|AI100176 34551 Lambda-PRL2 Arabidopsis thaliana cDNA clone 108A22XP 3', mRNA sequence
CTACCCCACNGTGTGGCCCCNCATCATCTGTGCCGGATCNCCCGNNCNNGCTTCGGGGNCTTNCATGGCC
TATGACCCTNTAGGCCCAGCTATGGATGGTATTTGCCGGCTTATATGGAAAGGAAGTTGAAGGAAATTAC
CCCCTCTCTCAGAAATATTAGCTATGACCATTGCTGACCCTTTACAATTTTATTGATGGTCTTGCTGACT
TGAGCGCTTTGGTCTATGACCCACTCGATAAGTGCATATCTGCCATATGACAGGCAATGGATTAAGCAGA
AGGCATTTCACCATCTGAAGAGAATTGCCAATGGAGGCAGATGAAGAAGAAGCATCATATGAAATTGTCT
TACCTGAAGAAACATATGTTGAGAGAGGCCATTTAAAGCATCATCACTCGTTATTATATATATTTGCCAA
TGTAACATTAATTAATATGCATAGAAAGAGTTGTGGTTCTCTTGGATGTGTTAGCCACTAAAAGTATCTT
TGCTATCC
>gi|3450136|gb|AI100175.1|AI100175 34550 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107O1XP 3', mRNA sequence
TTTTTTCGGGCTTGAGAGTTTAAANAACCTGGGATCCGGGACTCCCCTTTTGGNGNCNCTGCATACTGGA
GCACGCTNCCAAGCTAGAGCCCCAGCGATCCCTTTGGATGTCATCTTGCTTTGGTAAGTTTTGGTGCTTG
CAAGCTTCTAAGTCCAGAAAATGCCCAAGGCTCAATGTCGAAGTCATTGATGAACATCCTCCAGAGTCAA
GACCTGAGAGCTCTCCAGTTGAGAGGATATACATATACAGAACAGTCGCAGGACCGAGAATGGATACGCC
TGAATTTGTGTGGACGATACACAAGAATCCTGAGAATGGAGTTTCACATCTAGCCATAAAGTAAACTTGC
TGCTTCAGTCATATTTTCCTTTCCATCTTCAGTTTTTGCAGACATTGTTGTGGGAGAGATTCACCTTCCA
TTTNTTCCCTTTCATATTGTTTTTACTNANATATTAGAATATCAGTGATAGAAGC
>gi|3450135|gb|AI100174.1|AI100174 34549 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107N1XP 3', mRNA sequence
CCGAATTTGGGCTTGGAAATCCAGGGGTCCCTTCTTTCCGCGGTTCNAACCGTGGGTCCCCGGGGAAGAA
NCGACCTGGGGNGGGAGGTTTAAAATGTTAGTGAAAAAATGGTGGGACCATTACGACGACGAATCNTGGA
TACCAAGAAACCTGTTACCGTTGTGGACACAGAGTCGATCTCGTGAATCTGAAGCCGTTCATCACCGCTC
TTACTGAAGCTGGCCGGCTCAACTACGTGACCGCACCGTCCGCTGCTTGAATGTTGCCAGGAGTTAAAAT
TGTCGGTGGATCAGGTAGTTATTTTTCTTTCCGGTCAGTAAGAGGTTGGGGATTATGTGTCGGGTCGACA
ACCACACATACTGTCTCTGGTTCCAATGCTTTGGACGTTGACATGTGATTTGCTTTACTTTTTTGTCTAT
AATGTGTGTTATCCTCAATTTTAGCGTCTATCTTCGAATATCAAACTTGAGTGACAAAATAAATATTCCA
AAT
>gi|3450134|gb|AI100173.1|AI100173 34548 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107N19XP 3', mRNA sequence
CCCTTGCAATCTTGCAACCCCCGTCNTTCAAGNCCCNACTGGTTCTTGACNGGCANNAGTTTCCAAAGTT
GGNCAGTTATTCTCAAGTTNTCCTCCAATNCTCTGGACATGAAGCTGAGAGATGATCTTGGAACGTCTCA
AGAAGATCAGAAACCACCGTGGTTTGGAGGCATTACTGGGGTCTCCGTGTCAGAGGACAACACACCAAGA
CTACTGGTCGCAGAGGAAAGACTGTTGGTGTCTCAAAGAAGCGTTAAGAAAGATCCAATGTTGCTACTTA
CTTCTGTATTGGATACTTCATAAGGACCTGTTTTTATTTCGTACTAGGACCTTTTTGTGTGACGCTTTTC
GAGCTTTTTGTGATCACATTCCTCTGTTTTTCATTCTTGATCCCTCCAGTTTCCCTGAATAGTCTTATTT
ATTTTAATTTCCAGCTT
>gi|3450133|gb|AI100172.1|AI100172 34547 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107M22XP 3', mRNA sequence
CCGGGATAACGCGTTGGAGGAGGAGGGAGTAGTAATCAGATGTTTCCCGCTACCAGGATATGTTCATNTA
CATNCAGAAGCCCTTACTAGAAGGGAATTCCTTTCCTGCCGCCGAAACGCAACGCAAAACGACCCTCGTT
TTTGCGTTTATGGCAACACGAGACCGTTTTATATGGTCAATGAGTGTGCCGATTCGGCCATTAGATTTCT
GTTCAGTCTTCGTTTATTCTATAGNCCGTCCGATTTCAGATCATCCCTAATCGGACGGTGGTCGTTGGAT
GTATCAGTAGTGTATTACTGTGTTAGGTAGAAGAAAATCCACTTGTTCTTAAATTGGCATAAAAGTCAGA
AGCTAATATTTATATGTGCCGCAATCAATTTAATATTTTCTGTCT
>gi|3450132|gb|AI100171.1|AI100171 34546 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107M17XP 3', mRNA sequence
ACCCACCATGAGCTTTCTCAGCCTTGGGACCCGGTGATTGTCCNCGAGAGCGGTTTAGAGAGNCCATTGG
NCCATGCCCTTCGTGCATCTACAAGGATCCCACTAGATGGTTGCCCAGCTTCTGTGGAAGCCCAAGTACT
GTGCCCACACAAGGCCGCATGCCCTGGGATCAGAAAGAGTTCCGTGACCTTGACGCTGAACAATGGCGTC
GTCTCAAATGGGTTCGTATGAAGTGGACCATCTACAACTACTGTACCGACCGGACTAGGTTCCCGGTTAT
GCCAGCTGAATGTAAAAGGGACAGAGACGCATAAGTTACTACCCTTGAGGGTTTTAATGAATTTATGCTA
TCATTATTATTTGAATTATGCTTGTTCAAGAGATTGATATATGTATTGTTTGTTGGCCCATGATGTTTAT
GCTATATTTGGGCCTAAAATTACATGTTATAATTCATATATGTATTGATT
>gi|3450131|gb|AI100170.1|AI100170 34545 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107L1XP 3', mRNA sequence
CTCATCTTCAGGTGCTAAGCCAGTTCNCCCGATATCGGAAATCTCCAGCAAAGCGATGGGGATCTGAACA
GTTTCCATAACGATATCTTCGAGAAGCTTGCTCAAGAGGCGTCGANGCTTGCGAGGTACAATAAGAAACC
TACGATCACTTCTCGGGAGATTCAGACTGCTGTGAGATTGGTGCTTCCTGGAGAGTTGGCGAAGCATGCC
GTTTCTGAGGGGACTAAAGCCGTCACGAAATTCACCAGCTCTTGAATAATTGAGTTAGGGTTCTTATCAT
ATGGATGTTGCTCTGCTTTAGGGTTAATGGAATTTGGAAGATCTGAGTTAGGGTTTTAGAATGTCCTTTA
AGTATCTCTGTTTCGTTTGGAATTTCTACGTTTTGTAAGTACTGCTGCTATTGATAATGTTTGGAGTCTA
TATTTGCTCTTTGTGTCCC
>gi|3450130|gb|AI100169.1|AI100169 34544 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107K20XP 3', mRNA sequence
CCGTTTTGACTGAGTGGGNCGAGTTTAAGTCGTANGTTNCCCAGAGGTTTTCGACAACTGCCAGAAACCG
GCTTTATCCTCGACGGAAGAAACCATTATGAATGTTAACAAGTTAAGAGAGATTGGTNTCATTGTTTACT
CCATTGGTAAGCCACTTGACCCATGGCTCAAGGACATGCCTGCCTTTGTCTAATCACAAGGCAAAACCTG
GTTGATTCTTGTNTCTTACTTTCATTGTTTGTGCTTTTTTGCTTTCGCTTTCATATAAATTTTAGTCTCA
AGATTCGATTTGTGAAGTCTTGAAGAGTTGTTTCTTACATTTTACAATGTGTTTCTTATGCTA
>gi|3450129|gb|AI100168.1|AI100168 34543 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107J2XP 3', mRNA sequence
CCCAGCTCAACCCNTTATATCCCNAAATTTCCCACAAATCAAATNTCCNTNANTTTCCNAATTTCTATCC
CCNAACAACTTCCCATTCAATTTTCCCACCAGCATTTCCAACAATCCCATTCTTCNCTCCACCACCTTCC
AAATGAGAAGCTAATTAAGCTCTATAGCTAGCTACTGCCACACAACACATGACCACGATACCATCTATCT
ATTGTTTGCATATTATGTGTTGTAAACTTGTAATGTTTTTTATTCTTTTTTTTNTCTAAGTTTGTTATTC
TTTTACTGTCGTTTGATGTTATCCTTGTTGTTGATGTTGTTTTCTTTTAATCAGTTGTTTTTGTAATATA
TACAGCTTATTCTT
>gi|3450128|gb|AI100167.1|AI100167 34542 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107J19XP 3', mRNA sequence
AGCAATCTTGGGCTGATAACCCCTNCTCTGTGCCNTGCANTGACAATCGNTTCAGAACCCTAGGGACCCT
CTCAGGACTGTACCAGTGAAACCCTTGCCCCACGGATATCCTCAGTTATTGACCGCGACTGGTTCTGCTT
CTAAGCCAATGGGNTCCATTGAGGAGTATGATACGCCAGTGAGATTACTGGAGGGATAAGTCTTCCTCTT
TTTCTAAGCTTGTGGCTGAGTACACCTCAAGATCTAGTTCCAGTTTCGATTGAAGCAAAGACTCTGCTAT
TTTCCTGCTGATGATGACGATGAAGAAAAACTTAGGATGTCTGAATCTGGTTTAGCCACAACACTAGCTG
GATTATGATTCACACAAGAAGAAACACTATCTTTTGTTAAAAGCTTTTGTTCTTAGTTTATAGCTTCTAC
TACTGTTGAACCCCTAAAAACGATTATTCTACATCGCTAGTTTCAAATCAATGCAATAAAAGATTGTTC
>gi|3450127|gb|AI100166.1|AI100166 34541 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107I4XP 3', mRNA sequence
AATACTCCAACGTCTTTTTAGCGTCAAAAAGGAGGTGGGATGATNATGTTAGTATTCAAAANCCAGNCAC
GTGGTGAAATGAANGCTCCTAAGCNCTNCATCAATGATACAATCAGGAATGACTTCCACAGNAANTTCCT
GCNTAGATACATGAAGTGATTGTTTGTCAAGAGTGTTATTGCTACTTCTTTGTATGATGATTNTGACTAA
AAGCTTTTATTCTGTCTGGAATTACGATGTCTNTGTACTCAAACAACAAATGTTTTTAAGCTTTATATCA
AAAACTTNTGCATTTGATTTT
>gi|3450126|gb|AI100165.1|AI100165 34540 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107G13XP 3', mRNA sequence
AACTTGTCCCCCNTCNGGTCCCGTCCGGATTCCCGGTNGCCCCNAGGGTCCATCGNTGGGCCATGGACCC
CCGGNAACCNGTCCCGGTGCTTTGACCATTACCNTGGCCATTNGTATTCCAGGTTTGGNCCAATGATGGA
GTTATTGGGAGTGCTGAACCTTAGAGTGGTCGTGAATACAAGCCAAAGGGAGATTCTCAATACCATTCTT
CTTCTTCCCATCACATGAAGCCAATATTGAGCCATTGGAGGAGCTTATAAGTGAGGAAAACCCGCCTTGT
TATAAAAAGTACAATTGGGGAAAGTTCTTTGTTTCAAGAAACAGAAGTGATTTCAAGAAACTCGAGGTTG
AGAATATCCAGATTGATCACTTCAAGGCTTAGTTAATCACATTATAATTAAACCTTATGTTGATTTCTAT
TGGTTCTTTTTATATAAGTTAGCCAAGTTCATATTTCCCC
>gi|3450125|gb|AI100164.1|AI100164 34539 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107F20XP 3', mRNA sequence
TTCCTGGGGNAATTTTGGGNTTNCCTCCGGTTCGGCCAGGTCCTCCGCGGGAATTTGGGGAAGGCCAAGT
TTTTTTGGAAACCAAGGCAACCCCGGTGGCATNGCTTCTCTNATCGCGTGGTGCTTTAGACCCNTTCAGT
TTCCTTCATTTGCTGACCCGGCTCGAAACAGCAGTGAAGAAAGTCATCGCTGAAGGAAAGTGCCGGACGA
AAGATCTTGGTGGAACAAGCNCGACTCAAGAGGTCGTTGATGCGGTCATTGCAAAACTNGACTGACTTTG
ACAAATTACGTGTTCCCGCTCTGCATAAATCATCAAATTCCTGATACAGATTTTGTGTTGCCAAAATATG
GGGTNTGATCCAAGCNCAACGGTTATCTGGTTTTGTNCCTCGAGTTTTATTATATTCTTTANCCGTGGAA
TATTTCGNTAAGAAAAAAAAACATGTTCCAAATAATTCATGTTGCTACGTTTGTTGGCGCCT
>gi|3450124|gb|AI100163.1|AI100163 34538 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107E23XP 3', mRNA sequence
GGAGATGTCTAGCCATGGCCCTTANCGGATAAATCTCAACCNTTTCCAGAGGCGTGTTCCNCTGTTCAGT
ACAATACAGACAGTTTAATAGAGAGGTTCAAGGAACGACCCTCGAAGCATATGGTTCTTCAGCTAAGTCG
AGGCTTCCGTTNCCCCCAACATCAGGCCAGTGGAATGGCATGGAGCCAAACACACTCTTACGTGTTTTGT
GTTACCGTAACGACGAATCTGCCACGAGGTTTCTCAAGAAGACATATAATCTACCTAAGAAGCTTTAGTA
AACTTACGGCTACTACTGCAACGTATAATAACCTCACAAGATGAAGAGTGTGTGTTCCACTTGCAGGAGG
GAGCCTCCGAGATTTGTATAGTGAGTTTCATTTTTTTTGTTTTATGGTTTTTTTTCTAATACATTCCTAT
ACGTACTATATAATTCATTTATATC
>gi|3450123|gb|AI100162.1|AI100162 34537 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107A8XP 3', mRNA sequence
TAGGTTCCNCCACCTNATCGAACCGGCGAAATCCNGGAGGTGGAAAGCCAGAAGAAGGAAGAATTGGAGC
AAGGAAAGCAAAGGAGAAGGTGAACAACATGGTGCTGTTTGATCAAGCTACTTATGACAAGCTTCTCACT
GAAGCTCCCAAGTTCAAGCTCATTCACCCCTTCCATTCTCTCTGACCGTATGAGGATCAATGGGTCGCTA
GCAAGGAGAGCGATTAGGGAGCTAATGGCCAAAGGTGTGATCAGGATGGTCGCTGCTCACTCGAGCCAGC
AGATCTACACTCGTGCCACCAACACCTAAGATGTTTGGTTTCTTTATCCACCTAAGATGTTTGGCTTCTT
TTTCTTATCTCTTGTTGTTTGATTCTTCAGGAACTTGTTAGAATCTTTTGTTTCGTATTCCGTTTTTTTG
AGATATATGGTTATTTAAAACGCATC
>gi|3450122|gb|AI100161.1|AI100161 34536 Lambda-PRL2 Arabidopsis thaliana cDNA clone 107A4XP 3', mRNA sequence
CTTAATGAAACCGNCCCACCNGCATCAAGCTTTAAGGTGGTTACCTACGCATNCTACCAGGTTCCGNTGG
TATTAGTATGTTTNATGNAGCCACCNGAGAAGTGGTATTTTTCTCCNCCTTATTTTACCACGGTGGAAGT
TGTACAAAGGGACGCAGCACGCCGTTCAACAATTTGCAGAGTTGTGATTTATATGTAAATAAGCTTGGGA
AGGGTTTGTTATTGCNCCCCAAGAAAGAAGATGAAGAAGAAGAAGAAGCACATTGAGACTGGAGAATCTA
AGTCCATGTGTAGATTCTTTTGGTAGGAGCAAAACTGGGATTAGTTTATTCTCTGAGTTTTGCTTTGAAC
GTGTTTGTTGTTGCTGTTGTTGTAGTCGATACTATTAGATGAGACATTCTCTGCAATTATCTCATTGCTA
AATTTATGTAATGGTTTTTCTTTCTTTCTATGGAATGAAGCATATCAGTCTTGAAGT
>gi|3450121|gb|AI100160.1|AI100160 34535 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106H21XP 3', mRNA sequence
GGGCATTAGGGCTTTACATGGCGGNATCTTNGACCAAATTCCGAATCCTCTACTGTCATGTGATTGAANC
GAGATGAANNCAATGGGAGAAGTACATGCTTGTCCTCACACACTAATGCCGATGAGGAAACCCTTTAAGG
GGACTTTTATCTCCGCAGGAGGTTTCACGAGGGAAGATGGGAATGAGGCTGTGTCAAAGGGAAGAACTGA
TTTGGTGGCTTATGGTCGATGGTTTCTAGCCAACCCGGACCTGCCAAAGAGGTTCCAAGTGGATGCACCG
CTGAATAAGTACGATAGACCAACGTTTTACACTTCTGATCCAGTCAGTCGTTACACCGATTACCCTTTCC
TCGAATCAACAGCTTAAAATTGTTTCAATAATGTAATGTAGTGTGTTTCCCTTATATAAGATGTAATAAG
TTTCTGGC
>gi|3450120|gb|AI100159.1|AI100159 34534 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106H18XP 3', mRNA sequence
GTTACCCCGTTCGCAACCGTTANCCAAGCGGTNCCGGACATCNCCCAACCNCATGGTNCACGTGGNGCTA
CACCNCCTGGTGGACTTCAGCGNGCTCCAGAACCCCACCGTTGCTTTCGGCCCNCCGTCGTAAGCTGGAC
GTGGCCCACCCACTGGGTTTACTGGGCTGGNCCTCTTATTGGTGGTGGACTCGCCGGAATTATCTACGAC
TTTGTCTTCATCGATGAAAATGCCCACGAGCAATTGCCTACCACCGATTACTGAAGACGTCAAATTCAAC
GTTGTTAATCTGATGAATTTTTCGTGATTTGCTTTTTTAATTTGCATCGTAATGGGTTTCTGGCCGTTGG
ATCATTTTTAGATGAATCTTTGTCTATTGATTGATCATTTATGTGTCTTTGGGTTTGTTGTTGGAGTTGT
AATATCTCTGGAAGGCTTTTGTGCAATTGTATTGTACGGTTTAATAACTATAATTGAGAAAACCAGGGAA
TGTGAATTATGAAAATGATTTTTTTTGTT
>gi|3450119|gb|AI100158.1|AI100158 34533 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106H10XP 3', mRNA sequence
TCTTTGGTTCTTCAACTCTTTCCACATCCCTGCAATGNGACCGCTCAGNCTCAGGGCCACCACCNGAGAA
GAGTCTGATGNGGATGNGGTTAAGANATGGTTCACGCCCCTTAGAANGCGAACNCGGGTTAGAAGAAGNC
GATAATCAACAACNATACANAGAAGGAGANTCATCATCATCATCACTCTTGAAGAACTNCGAGCTCATGA
TACATTGATAAAAGATATTTATTTTGGATATCAATATGACAATATGTATGATGGAAAGGTAGAGAGATAG
TAGAGAAAATGTATTNCCTATAGTTTTTTAATTGGCATTATTTTTAGTAGCCTGTAGATAAAACAGAGCT
GGTCAAAAGATGCACACTATACTAAAAGTCTAAAACTATATATCTGGAAGATTCTTTCTTTAGTCTTAGA
GAATCTTGAAG
>gi|3450118|gb|AI100157.1|AI100157 34532 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106G7XP 3', mRNA sequence
CTCCGGGATGGCCATTAAGTTCCCCTTTGCCCATTTGCCGGTGCAACCGTTTGCCGCTTGCTGATTCNCC
GTCGATGATGCTCCAGNGCATGGAGAGGGCTTTTAATTTTGCAGTAATCCAAGTGCTGAAGCTGTATGGG
TTTAGCCACAGGGGACTGTTGAGTCCCCAAGATTAAAAGGATCAGAAATGAGACAGTCTCTCCTCTGGAG
TCAGTAGACAAGTTTGATATTCGAAGAATGCACATGGAAACCAAACCATAGAGCTAGGAAAATCAATGAG
TGAACGGAATCACAGTTTGGCAAGATTACANGAAACATATAGATGATATACAAATACTCTCACAAACACA
ATGCAATTTGTTTACCCTGCACTTGTTCCTTGTGCTTCATTGTTTGGTCTCATGAAGATAAGTTTTAACT
GTCAAATTCTTATTCCATAGATGTTTCTTGTCATTGTTGGTCAATATATGGAGAAATTTGATACTGC
>gi|3450117|gb|AI100156.1|AI100156 34531 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106G4XP 3', mRNA sequence
TCCCCTGGTGGNGCAAACTGGGTGGAGCTNTNGACNCAGGACCAGGAAACCGTCATCTCNGACACAGCTC
CAGTGACAAATGGGCCATGNGTGTTGTTTGAAGCCNCCATTGATGTTCACAGACTACAGAGGTCATCGCC
AAAGCGGTTGATTCGGCGGCGAATGTTCAACCGGAAAATGTGGAGTCGGTGTGGAACCTAAGAGGAGTTC
TTCAAACTTCGTGGCACCGTGTCCTTCTCCGGCTTGGCCACTCTAACTTGTAGACCAAGTTACCACTATG
CGTCTGGTCTCTCTTTATCTTTTCTTTAAGAACTAAAACATCCTTGAATATGCTTGTCCTTGTGGATCTG
TGAGAGCAAAATACTGTTTATAGTTAAATAAAATGGGAAAACCCATCTGTTGTCATGTGGTGGATTATAA
ATTATTTATTTATATGATAGAACTGTTATTCACTATTATATATTAATGAAATCATATGGTTGAGC
>gi|3450116|gb|AI100155.1|AI100155 34530 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106F9XP 3', mRNA sequence
CCCAACCCCGGTTGGTGCCCACACGGGACCTTGGGATGTCCAGGNCTACATCACCCCTGAATTCAAATGG
GCAAACTTCACATTGGAGGAGCAAGCTAAAGTCATTGTGGCTCCAAGAAGCAACAACGAGATGGATGCTT
CCAAGCTCAAGAAAGAGTTCCCTGAGCTACTCTCTATCAAGGAGTCTCTGATTAAGTATGCATACGGGCC
AAACAAGAAAACCTGAAGAGAATGATTGTGATTCGTCATTAGATAATCACCTTTAATATCAGTTTCGTGT
ATTTTGTTTTGTTATTGTTTAATTACCCCTTCTTTCATTAGATTTGCTTAAGGGGTGTATTTGTAGTTCG
AATATTATATGTAATAAGAGCTTGTTCTCATTTGTGTCATAAGTTGCTCTACTCTTATTATATTAGAATC
>gi|3450115|gb|AI100154.1|AI100154 34529 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106F1XP 3', mRNA sequence
GAAAGCCTTGATGAGCTATAGTGATGAGAGGAGTGATAAGGTTATTGGNGCTCCATGTGCGGTCCTGATG
CAGCTGAGATCATGCAGGGGATTGCAATTGCGCTCAAGTGTGGAGCAACCAAAGCACAATTTGATAGCAC
GGTTGGGATACATCCATCTTCTGCAGAGGAATTTGTGACAATGCGCAGTGTGACCAGACGCATTGCCCAC
AAACCCAAACCTAAGACAAATCTATGAACCGCAAAATATAAAGAGCTATATAGCATGAAAACTCGGTACA
CTTAGTTTGATCAAAGAGTCAGACAACGATGAGTTTAATCATACTCGTGTCCCAATAAAGGATTTGTAAT
TTTTGTTTGTTTGTATGATGCTTCTCTTCTTACTTACTTGAGAAAACATCAAGGTTTCTTCTCTTATTGC
TTAGTGGAACTTTATTACAAAGAATTATTCTATG
>gi|3450114|gb|AI100153.1|AI100153 34528 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106F16XP 3', mRNA sequence
CGGCGGTGCAGCCTNAAGCCCCGGGANTTTGACCNAGCCCTTTTTTAAGCAATCCNGCCTTCCNTAGGGT
GAAGTGGCTCCCTGGNGGAATCTTTACCCCGCTTAACTTTGCCTCNTACGCAAGAGCCCAAGGAGAAANA
GCTAGCCAAACGGGAGGTTGGCCGATGTTGGCATTCCTTAGGGTTTGTGGTTCAACACAATGTGACTGGA
AAAGGACCATTTGAGAATCTGTTGCAGCACTTGTCTGACCCATGGCACAACACTATTGTCCAAACCTTCA
ACTAAAGAGTGAAGACAGACTTATGATCTCATACCTATCTATCTTCCATCACTTTCATGTCTGTCTGTGA
GTGTGTTTCATCTTAGAGTTCTTGGTTTTTGAGCTTGAATTATTGTTGAACCGTTGTAGCTCCATGAACA
AATTTGGAATCTTCAATGTACAGAGGAACTAAGTTAATCAACATTGTTGTACTCTTTAATATCTATTATT
CATGTGGCAACAGTTATAT
>gi|3450113|gb|AI100152.1|AI100152 34527 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106E17XP 3', mRNA sequence
CTCTTTCTTCCNCCCTGCCCTTAGTGNCGTTGAATTGGCTAGGGAAGTTGCTTCCCTTCTCCGGCAACAA
GTGGATCCTTGTGTTGAATTCGAGTTGGAGCNCGGATTTGTGTNCCGTGAGCACGGAAACACTCCCGGAT
ACTATGATGGACGATACTGGACAATGTGGAAGCTTCCATTGTTCGGATGCACCGACTCCGCTCAAGTGTT
GAAGGAAGTTGAAGAATGCAAGAAGGAGTACCCTGGCGCCTTCATTAGGATCATCGGATTCGACAACACC
CGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATCCCCTTTCT
GGAATATTCAGCGTTGATTATTCTGGAACCCATTTCTATGTGGTCAATGCAAATTTAAGAAATTATTTGC
CGACTTAACAGTTGAGGAACTATTGTTTGAAAGTGAAAATGTTATTCCTATCAGTTTCTCT
>gi|3450112|gb|AI100151.1|AI100151 34526 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106D14XP 3', mRNA sequence
AGGGTNAACTTGTCCNTTAAANGAAGGTTCTCGTNCGATGATTGANCTTGATGACNAATTNCTTNCTNAG
CACATGGCTAAGCTTNGAATGGATAATGAAGAAATGAGTGTTGATGAGGGAAGCGAAGATGAAGAAGACA
CTGGAATGGGAGAAGTCGATATCGATGGAGGTANCGGGATAATTGAATGAACAAAAGCAAAAGCATTGTA
ACTGCTGTTTCTGCTTTAGATCCTACAATTTTGTTTCCCTTTGAGCAAAAACAGTATTTTTTGTTTGACC
CCAAACATGGTTAGTAGTACAAGCATCTCTTATTC
>gi|3450111|gb|AI100150.1|AI100150 34525 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106D13XP 3', mRNA sequence
CCCCGGTTGGGNCCCCCGTGGTNGCGATTTAGGAAAGGAGGANTGGCGATTTCGTTTTAGCGGATGATAN
GGANGTTTTCACCGTGGNACGGGAAAGGAGANGCGATAATGNTTGTGNTCGATAGGGAAAAGAANACGGT
GGAAGCTGATAATGGATACTACTATCTTGTTTGTGGCTGATGGTGGGATGAAGTTNGATAGAGGATTGGT
GTTGAAGGAGAAAGGAGTGAATGAGAGCTTAGGAATGGTTGTTTTGGTCGTTAGGCCGCCGAGAGATGAT
GATGATGAGTGGCAGATAAATGATGAAGATTGGGATTAGAATTCAATTAGAAGAATAGTTAAACAAATAC
TTATATGCTTTTGGTTTTGGCAAATATGTAATTTTTTGTTTGATTGCTTTTTATCTCATAAATGTTTCTT
TC
>gi|3450110|gb|AI100149.1|AI100149 34524 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106C5XP 3', mRNA sequence
GTGGGGAAGGTTAATTATTGNTTCCCGTGGTTNTTCAGNCGTTGGNTTGNAGANCGAAGCCATAAAGTTG
AATGTACCCCTTTGGATTTNGTGGGTTGCGNCAGCNGCNGAGATTGGCGANCGACGGTGAAANCGNTGGC
GGTGGAGATTGATGATAATCATGGTGAGCGGTAACGGCTCTAACGCTTTTTTTCAAGGAAATGACTGAAA
TGCCAACAGTTTCTTTGACTGTTGAGTTTTTTTTTTTTTGGGTTATTTAATTATGTTTTAAAAAATTTAA
TGTTAATTTCTTCTCTTAATTAATTAGTTTTGGCTAATGGCGTTTCTGAATCTTCTGATACTAAACTGGC
ATGTTATTTTAAATAATATAGTTTTTTGCCGTT
>gi|3450109|gb|AI100148.1|AI100148 34523 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106C1XP 3', mRNA sequence
GCACCNGCAGAACTCGAAGATATTGTCCCTTCTTCCCACAATTGTGGATGTCCTCATNTCAACCGTACTG
ATTATCAGCTGATTGACATTTCTGAAGATGGATATGTCAGTTTGTTGACTGATAACGGTAGTACCAAGGA
TGACCTTAAGCTCCCTAATGATGACACTCTGCTCCAACAGATCAAGAGTGGGTTTGATGATGGAAAAGAT
CTAGTGGTGAGTGTGATGTCAGCTATGGGAGAGGAACAGATCAATGCTCTTAAGGACATCGGTCCCAAGT
GAGACTAACAAAGCCTCCCCTTTGTTATGAGATTCTTCTTCTTCTTCTGTAGGCTTCCATTACTCATCGG
AGATTATCTTGTTTTTGGGTGACTCCTATTTTGGATATTTAAACTTTTGTTAATAATGCCATCTTCTTTA
ACC
>gi|3450108|gb|AI100147.1|AI100147 34522 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106B4XP 3', mRNA sequence
TCTTTCCCCCGTTTAAAGGTTTTTGGCCGGGGTCCCNCCTCCTTNTTGNCCAAGGTCAAGNGAATGGTCC
ATCCCTGATGCTCTCAAGGTGTTGAGGCTTCANGCTGGTCACAAGTACTGCTTGTTGGGACGTTTGTCTT
CTGAAGTTGGCTGGAACCATTACGATACCATCAAGGAGCTTGAGGTGAAGAGAAAGGAGAGGTCACAAGC
TTTGTATGAGCGTAAGAAGCAACTCACCAAGCTCAGGGCAAAGGCCGANAAGGTTGCAGAGGAGAAACTT
NGATCCCAGCTCGATGTTCTTGCATCGATCAAGTACTGAAGAAAATCAGCATCTATCTTTTGGTTTAACT
CTTGTTTTGGTTTTTATCTATTCAGATTTTGTTTTCTTCCTTGTATCACTGTTGAAGTTTATCACCTCAT
TTCAGTTTTATTTATC
>gi|3450107|gb|AI100146.1|AI100146 34521 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106A14XP 3', mRNA sequence
GGGCAAGGNAGGGGCCCANTTCNCCCCCTGAAGNCTTACCAGTGCCCCCCNATGCTCTGGTTTTCCCGAT
GGAGCTCCATTGGCCATTACCCTCGCCCAGCTGTGCATTTGGGGCCGCTTGCTTGTTACTGGAGGCCACA
GCAGAAGACCCGCAAGCCGAGGAGAAGGTGAAACTAAACTACAAGAAGGTCTTGATGTTTTCATAACTTA
CAGACAACAAACACAAAGGCTCTTGTTTGGAGTTGATATACCAAAGTCGCTTCCTGCAGGTCCTTTCCTT
GTAACTTTTGTCTCTGATTTTGAAAGATAGTCCAGATTCTTGTCTTGAATTTTGGGATACAAACACAGAG
AGACACTTGTGAATGTTGGGATCTTTATAGGAATCTTTATAGTGGTTTATAAATTTGTATTGGATCATAT
GGTTAGAGTTGTTGTGTAAGAATTCAAGATGAGTCTTCTTTGTCT
>gi|3450106|gb|AI100145.1|AI100145 34520 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106A13XP 3', mRNA sequence
CCGGGCTTTCCTTGNCGATNTTCTCCGTTCAGCANTCNCCAAACTGGACTGTTGAAGGGCNCTCACTTGG
AATNGTNACCACANGGAGCTGAGATTGACTGAAGGTCCATTGGAGAGGAGTACCAGCGCAGGAACAGCAT
TCCTTTGGAGAAAGCTATTACCAAAGACACTCGTGGAGATTACGAGAAGATGCTCGTCGCACTTCTCGGT
GAAGATGATGCTTAATCAATCAATCCTCCACAGAGAAACATAAGCTGCTCTACAGCTTCTGTTATCTCTT
ATCTCCCTCTCTCTCTCTTTGATGAGTTTCAAATCGTTTGATTTTGTTTCTACAAAAACCTTGTTTGTTT
CTGTTGTGTGTTTTGAGTTCCTAAATAATGCAAAAGAGAGAGACAGAGAGAACCAGTGTGGTCTCTTAAG
TTATATATATATGAAGAGCATTGGCCT
>gi|3450105|gb|AI100144.1|AI100144 34519 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105P15XP 3', mRNA sequence
AATCTGTTGTAATGTCNNGAGGATTTNCAGATCATTAAAGCCAAGGCTGTGCCNAANTCGTTTGCCTCCT
TTCCCTAATGGATGNATGTTTCATANTGAGACAGGNCTTAAGAGCTTTGACCATCCGACTAATATGATGA
AGGCAATGCCGAGGATTGATAGTGAAGGTGTTCTTTGTGGAGCTAGTTTCAAAGTTGATGCTTGTTCTAA
GATCAATAGTATCCCTAGAAGAGGAAGTGAAGCTAACTGGGCGCTGGCTAATTCTCGTTGATTTTGCTTC
TAGTTTCGTTAACTCTTGCTTCTTTGTTGCGTTTTCTTTTTATGTACTCTTGTTTATGTAAATATAGCCT
TATGAAGACGATAAAGAAATAAAATTGATTTGCTTCTTCGTG
>gi|3450104|gb|AI100143.1|AI100143 34518 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105P10XP 3', mRNA sequence
CGTTCCTNTTTCNCCGGTAGTACGAAGTGGNCGNTAGACCNAGCCCGGAGAATCTTCTCGTAAGTCATGG
GAAGTACTATCCGCTGACTCTGACTTCACCTACAGAAGATCCTTGAAGAGTTGCCATCATCCCACAAGAG
ACCCGCAACAAGATTGCTGGATTCTCCACCCATTGATGAACGTATCCAGAAGGGACCAGTCCGTGGAATC
TCACTCAAGCTTCAAGAAGAAGAGCGTGAACGCCGTATGGACTTTGTTCCCGATGAGTCTGCTATCAAGA
CTGATGAGATCAAGGTCGACAAAGAGACTCTTGAGATGCTTGCTTCTCTAGGAATGTCTGACACTCTCGG
CATCTCTGCAGTCGACCCACAACAAGCTATGGCACCAATCCCTGCTTTCGGCGGCGGCAGGGCACCCAGA
AGATACTAAGATGGACGATTGGCTCTCTTTTTTCACAGTTAGGGACAAGAAAGACTTGTGTGGTTGTTTA
TTGTTTCTTTTGATTATGTCTTAAACTCAATGTGAGTATCTTTCGTATTAAGGTTTTTGNATTNNGTGG
>gi|3450103|gb|AI100142.1|AI100142 34517 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105O6XP 3', mRNA sequence
AAACACCACATCACNANAGGGCAAANCCTAGATGATGTTGTTGTTGTTGATCNTGAGGCNNGTGATGTTA
GCTCCTCCAATTCAGAAACCTNGAAGATCAATACCCTTGGCGAAGAAGCAGCAGCTTCATGGGACTATCA
ACTATTGGATCATTCGNTAGGATAACCGCCCGTGGCTCGGGAAGGATCGCANCCGAAAACGAGCTGATGG
ACAAACCAATATTGTGAGGGATCGATTCCGTTTTAAGGGACATTTTGGGGCATGGGGGAGCAATTAAAAA
GATGAGGGGTGAAAATTGTGAGAATGTATAAAATATAGATGAATTTATGTTAGATCTTTTGTTGAAGGGA
GGAAGATTGAAATAAGGAAAAAGATGTGGGGAGGTGTGTAATGNCAAGGATTTGTTGTTTCTTTGATTAA
GTTTGGCCCAAAATTGTTTGTTGTTACTTGATATGAAAGGGAAACCCATAATCTTTTTGTCTC
>gi|3450102|gb|AI100141.1|AI100141 34516 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105O21XP 3', mRNA sequence
TCATGTTTNCGTGGCCCCCCGTCAGGAGCNCAATTCCGNTTTGNCCAGAGTCTCATCTGAAAGATCGGTG
ATGGNTCCCCCTTAGGCCNTTGNTTNTCAATCCCCAGACCTGCCCCCATGCTCTGTCAGGGATGATTAAC
TCTAAGCTCCGCTGGGTCATCCAACACATNGCTCAAACATAGCCAGAAGGTCTTCTTGGTATCAACTTTT
ACGCCACGATTTTGTATCTCTGGAGATTCAGGAGGTGGAGGAGCAATCACCGGAAGGGATTACCTCGCAT
TACTCCAGAAACACAAGCCAACTTTCCGTTGGGATAAAGAGAGCGGCGAACATCTTTTCATGTATAGAGA
TGATAAGAACATCAAGCATGCTGTTTTCTATCCTACATTGATGTCAATCCTTCTACGGCTTGAGAATGCT
CGTCTCTGGGGAATCGGCATTTCAATCTGGGAAATCGGACAAGGTTTAGATTATTTCTTTGATCTATTGT
AAGTTCCATACATTGCATCATGTTATGTTTTCTTAATGTTATACTTGATCCTC
>gi|3450101|gb|AI100140.1|AI100140 34515 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105O10XP 3', mRNA sequence
CATATCCTTGTCAACCCGTAAAGACTACTATGGTCGCGGTCCGNTCCAATCACTGGAACTACAACTATGG
TGCAGCCGNAANGTTCCCTGGACTTCCTCTCTTGAAGGACCCANATATGGTGGCTCGTAGCCCAACTGTG
GCTTTCCAGTGTGCCATGTGGTTTTGGAACAAGAATGTGCGTCCGGTTTTGAGCCAAGGGTTTGGTGCAA
CCACGAGGAGGATCAACGGTGGTGAATGTAATGGTGGGCNTCCAGCTGCAGTGCAGAGCAGGGTTAACCA
TTACTTGGACTTCTGCAAGAAGCTTGGGGTCACTCCTGGAACCAATCTCTCATGTTGAAGACACTACTAG
TTTATGAGGGTTTTTCATTAATGTCGTCTGGTTAAGAATTTCGTATCGAATAATAAAGTGAAGTCGAAAA
TACTAGAACTTATAAAATTTGTAAGAGATTAGAAGTTATATTGTGTGGTTGATGTCTCTTAAGGT
>gi|3450100|gb|AI100139.1|AI100139 34514 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105N3XP 3', mRNA sequence
CCGAGTTTTTTCCCGACCATAAGAGCTTATGTCNCTTTGGGCNCCCAACGAATTTGCCCACCATCCNAGT
GGTTCTACTCACGCGGTGGAATCGTTCTCGAGACNTCGTGGTGCCGTCCGATGATCGCGTGCCCNTTTTG
CGGAGCAATGATGAACGCGACACTCCTCAACGAAGAGCTTGGCGTTGCCTCCGCTCTAAGAAACTACCGT
CGGAGGGANTGATTACGAGGGCGGAGATCGAGGCGTTGGTGAGAAAGATCATGGTGGAGGAGGAAGGTGC
TGAGATGAGAAAGAAGATAAAGAGCTGAAAGAGACCGCTGCCGAATCGCTGAGTTGCGACGGTGGAGTGG
CGCATGAATCGTTGTCAAGAATCGCCGACGAGAGCGAGCATCTTTTGGAGCGTGTCAGGTGCATGGCACG
TGGTGCCTAGGAACGCTTACCGTTTATAGTATGTTACTTATAAACTGCGTGTCGTTTTACCCTTTTGGGT
ATCTTGTATTATATAGTTTCCGAGTCTTGGTTGCCACATGGTATCACGTGGTTTTGTTTTGGTCAATGCT
AGTCCCTATCAGTAATGTATTTTACAATGTAAAATAAATAATTAGTGTTTTAATTTGT
>gi|3450099|gb|AI100138.1|AI100138 34513 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105N21XP 3', mRNA sequence
TGACACTTGCACACATGGAGGCTTTTTANCCGGATTCTGCANCGNGTTNGTCANCATGTCCGACCTCANT
ACGNTTGGGAAGCTTCCCGCACCANCACTCGCGAACCAAACGAAAGTATAGCATATACCAGTACGTGCTA
TTCGTAGTTGNCAGTGGTTCTACTTGTGGTTGGGTTAACTGTTGCATTAGTGATGCTTTTCAAAGGAGAG
AATGGGAACAAACATTGCAAATGGTGTCATTACCTTAGCTGTTTCCCAACTTCTAAATGGACCTGCTAAT
CATCATCATCATCATCATAATCATATAGTAAAAGCTTTTATATGTGTTCATGTTAACATTTAATCTCTTT
GATCTCTCTAGCCTTTGATTACTTATATATGTGTACATTACAAAATTCGTCTTGTGTAAAAGGGGATAGA
AATAAAAGAGTGTATAATTTGGTTTATAGTACACACTTTATATAATCCATCTTAGGTCTTGT
>gi|3450098|gb|AI100137.1|AI100137 34512 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105M24XP 3', mRNA sequence
GGTTGGAATAGAAGTGTGANACNTTTGAGTTGTGCCTATTTGCTAGTTTTTCTTAGGTCNTGGTTACGGA
AATTAAGCNGGTCNACNGGTGTTCTGTGCNTGGATGCNAATATTGCATGCAAAATGGATCCCATAAACAT
GTGTCGTTCCTAGGTTACCTAATTCATATGACCCTTCAAGCCGCTACTTCAGAATTTCTTTGTCATGTAA
GACATCATTAGAACTATAGATGTACTTGTTGGTTTCCATATCTCTGGTCTCTATGGCAGTTGAAGGAAAG
AGAGCCTCAGATTCTAAATTCTCTGTTCGTGGGACTGCGTTTTTGCTGGCTTCTGATGCTACACAGTTTC
TTTGTTTCTGTAATAGATTTTAGATAAACTTTTGTTGATACTTGCTTTCTGTTAATTTTGAATGAAGCGC
CAGAAAACT
>gi|3450097|gb|AI100136.1|AI100136 34511 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105M17XP 3', mRNA sequence
CCTTTCCCAGNGGGAAANGGCTCTTGTTGGCTTGGNCCCCGTACCCNCATTGGCCTTCCAGTTTGTCATT
AGAGTCTCTTNAGGCCCATCNCCCCAGAANTGTTATGGCCGAGACCATCTCTCCGCGTCCCTNAAGCCGT
CGATCATCTCTTCTCCTAGAATCGACCGCTTAGAAGCCTCTTTATAGCGACTCGGGCTGTTGCCGANTCG
CGAGGCTAGTGGAATACGGAGAATGCACAGCGCATACCCTTGCTAACATCAGCGCGTGCGTTGCTTGGCC
CAGTCGGGAACGNTGGAAGCGGCTGAGTACATAAAGGTCGTGGAGGCAGAGCTGGTGGAAGTTCAATGGA
GAGGACAACAACTAATGGAGTATCAAAGTCAGCACCAGCAGCAACATAATCAACGGCGGAGAGGAAGCGA
GAGAGAGACCACGACGACGATGACGTTGATGGATGAAAACGGTGAGCCGTTGACTCCAGCATCAGCGTGG
AGAGCGGCTGAGAAACTGGCTAAGTTAGCTATGATGAAGAAGAGCGACTTGCACGGCTTCGAAAACGCTA
GGTTTTAAATGTTATTTTTTTTGTTTCGTCCAGAAATATGAATAATTTTTAATTCTGAC
>gi|3450096|gb|AI100135.1|AI100135 34510 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105M13XP 3', mRNA sequence
CTTGCCCTNTTTCCGCCAGCTCTATNCGACTNCTTAGGGAAGCTGGTCCGCTTCAGTCCCGTCCGGNTTC
CCGNTCGCCCACGCGTCCGAGNAGTCGTGTCTCTCCTTGCATGATACTTACGAGTGCTGAAGGGAGCCNC
CTTTGCGNNCCTGAGCCCTNTGNGCAGCCAACTGTATCTGATGGACNAGNCCTCATTCCGTTCCAAGGAT
NCACACCGATCTAAGAGAGTTATTGTGAATGCTGGGACGCAGNCATGAACCAGAGNCCGTCGTTTCTGGA
CATTCTCAAGAGACTTGAAAAGATCAAGGAAACTCTACCATCAGATCACCATTGGGGCTTATTCACTTCA
TAATACACAAAATCCATTATTTAAGCACAAAAACAACCAGAAACAAGAAAGTATCATTCTCTGTTTGCCT
TATTAATCTCTGTTTCATTTCTTTTGTAAAGATTGTTTCTTTTTCATCTTTTCATTTGCTTTAAAAGAGT
GTGAGATAGAAAGCTTTTATTGTTGTTACATGGATTGGATTGAGTTTGCAGGTTAATGAGAAGTTCATAT
CATATCAG
>gi|3450095|gb|AI100134.1|AI100134 34509 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105K5XP 3', mRNA sequence
GCTGGTGTCGCATCCGTGGAATGTTTAACGAAGGTCCATGGNTCCACTGAGGACGGCCCATGCGTCTTCT
TGNTANGTTGGGNGCGATATCTCAAAGGCGTTAAAATGAGGAGCTCTCGTTGCTTGCCACAAGTCGGTTT
ATATCGTGTACACATGCTAGGGGATGTTAGCTCTTCCTTGTTGGCAAGACGAGTATGATGAACTTGCTTT
GGCAGAAACCTCTATATCATAACAGCNGCTGTGAAAGCGTATGTGGAAAGCCGCCTACAGAGCGAGTGTT
TTTGGATAAATATGGAAGGATTTGCTTGTGCCTTGATGAAATCGTTTGGAACGGACTTCTGGAGAACACC
GACAAAGACAGGATCAAGCGACTCATCAGATTGAAACCTCCTTCTGAAGTTTGATATGCTCCAACCAACC
ACACATTCTTCTTCTACTCATTTTAAGAGCTTNCTCATTCTCCACCGATTGTTGTTTGTTGAATCACTTC
TCTATATCACATATTCACTATCAACTACTGCTGTTGTTCGATCAGTCCATNTTGTAGTGNTGTTTTTTAA
ATCTCCAGTTTTTAGTGTTACATANCAAAGAACNAATTNCTATCC
>gi|3450094|gb|AI100133.1|AI100133 34508 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105K20XP 3', mRNA sequence
TACCCCATCATCNCAGCAGTTTACCAGANATCNGGCGNAGCNCCAGGTGCAGGAGGAGAACCACCGACAG
AGGAGGAAGATGAGTCTCACGNTGAGCTCTAGATGTCCTTCGGTTATTGTTAATTTATTAAACCNTAGAG
ACAAGTTTTGAGGATGAAACTCCGTTTTTGTTTTTTGTATTTGGTTTCCTTTTTCTTANGGATTTTTAGG
AAAGGGGAGAGATTAAGTAGCGTCCCTTCTTTAGTCTCCCTGGACNTTCTCTTTATGTTCATCTGATAAC
TTTACTTCTTCATAACAAATACCTTTTTTTCTATTCAAC
>gi|3450093|gb|AI100132.1|AI100132 34507 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105K1XP 3', mRNA sequence
TTTGNTTCACCCGGTTAGCCACCTGTCGCTCCNTCACCGNTTGATGTCTCCGTGCTTCCCGTCNCCGCAN
CCCNCAGNCATCACTTCCTCGCAGCACGGGGAAGAGTNGCTNCATGAAGGTGTNGCCACCATTGGAAGAG
AAGTNTGAGACTCTATCTTACCTCCCTGACTTAGTGACGTCGATTGGCNAGGAAGTTGACTACCTTCACC
GCANCAGTGGATTCCCTGTGTTGAATTCGAGTTAGAGCACGGATTTGTGTACCGTGAGCACGGAAACACT
CCCGGATACTACGATGGACGGTACTGGACAATGTGGAAGCTTCCATTGTTCGGATGCACCGACTCCGCTC
AAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGANTACCCGGGCGCNTTCATTAGGATCATCGGATTCGA
CAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATTT
CTTTTCTAAAACATTCTTATGAATTATCTCTGCTCATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTT
TATGAGACAATTTCTATCGGATTGTCAAATGTCTGATTTATGAATATGTAATTTATAT
>gi|3450092|gb|AI100131.1|AI100131 34506 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105J21XP 3', mRNA sequence
CAGNCCAAATCCTCCATCGNCACGNAGTCCTCNCCACGTCAATCTCTCTACGTCNCCGNTTCCGTACCCG
TNTTCTCCCGTTTCTCTCTATTGAGATCGTTGGGGAGTAGAGATGGCGACGTTGGAGCTNTACAGGAGNT
CGACGACGGGATGTGTCTGACGGAGACTTGGNCGAGTGGTTCAGAGCGGTACGCTGANCCTGAGCTAGCT
ATCCAGTCCTGTTCAATTTGACANGTCCTGACTGAAGCTCTGGAGAGCCAANTGAAGACCAAGGTGTCCA
TCAAGGGACACCTGCACACTTACAGGTTCTGTGACAATGTCTGGACCTTCATATTACAGGACGCAATGTT
CAAGAGTGACGATCGTCAAGAGAATGTGAGCCGGGTGAAGATAGTGGCATGTGATTCCAAGCTGCTCACA
CAGTGAGATGCAAATTGTCTGCAGGGAATTTACTTTCCTTTGTACTAGATTTTGAGTTTTTTCACTTTGT
AAACTCAGCACTTGCTATATATGTTGAGCACTTGCTATATGTTGAGCTCCATCTGCAGCCATCAATTTAG
CCTATATGTAAATTCTCGGCCCAAGGACATAAGGATACATTCTGTTGCTATGAGAAAGTTCTTGAGCTT
>gi|3450091|gb|AI100130.1|AI100130 34505 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105J16XP 3', mRNA sequence
GGTTNCCTTTCTCCGCCGTTTTNTTGATTTGGCGGTACCATTCCCCGGNACACTTNCCCTGNTCCCCNAG
TNTATCGCTCCCTTGGGGAAGCTGGTCCCCCTCAGTCCCGTCCGGATTCCNGGTNGCCCCACGCGTCCGG
AACCCTNTCTGNTCAGCGATCTTGGTNCNGGAATCGTCNCCGTGCTGCTTCTCCGTTCTCCGCCATTTCA
AGTCCCAAAATTAGGNTAATGGAGGAGGATTAGGGATGGTGATAGAGTGTTCGTCGAGGCCACAGAAGAA
TCGACGGCTCATCACAGGAAGACGAGCCGAAGAAGACTCAGCCTGGGACATTAAGAGAAGCCTACTGTTT
ACGCTCCTCTTCCTCCTCTTCCGGCGGAATGGAGTCCGTTCACTCTCGCTTCTGACGACGGTGGTGCTGC
CACTGCTGCGGGAGATTTGGTTTCAGGCGCTGCCTAGTTGGTATGAGTTATCTGCTGATTTGGTTGTAAT
CTAGTTTGAGAACTTTTGTTGTTGTTTACTGTGTTTTCAGTTTTCTGATGTTTGTTGTTGGGTTTGTTTG
TGTTTGATTGGTGAATGAATGGACCAAATTTGCGATTTATAAAGCTTCAACCTTTCTCCT
>gi|3450090|gb|AI100129.1|AI100129 34504 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105I6XP 3', mRNA sequence
AATTCGAGTTGGAGCACGGATTTGTGTCAACGTGAGCACGGANCACTCCCGGATACTATGNTGGNCGATA
CTGGACANTGTGGAGCTNCNATTNCCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATG
CNAGAAGGNGTNCCCTGGCGCCTTCATTNGGATCATCGGATTCGNCNACNCCCGTCAAGTCCAATGCATC
AGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTATCCCCTTTCNGGAATATTCAGCGTTGATT
ATTCTGGAACCCATTTCTATGTGGTCAATGCAAATTTAAGAAATTATTTGCCGACTTAACAGTTGAGGAA
CTATTGTTTGAAAGTGAAAATGTTATTCCTATCAGTTTCTCTATAATTATAGTTATCATTTCATTTC
>gi|3450089|gb|AI100128.1|AI100128 34503 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105I4XP 3', mRNA sequence
TCAAGAAATANCGATTAAGATCCCGTTTCCCGGGGCCNTCATGAGGNTAACTCTCATCCANTCACCGTGG
ANTNCCCGACTCGTTGAGCCCANATCAGNCCATGCACTGGAAGCTGTTCTACCTANCCCGTCNCCGCTCA
NTTGAGTGACATGGAGATAGTGAATGCGAGGAGACCACNNACACGATGTCAACATTGAGGATGAGATGAG
GAGGAAGGCACAGCTCAAAGAGAGGCTTATGATGATGACGATGAAGATGATGACCATCCGGGTGGTGCTC
AAAGGGTGCAATGTGCCCAGCAGTAAGTAACTCCTTAGAGAGACTTTGACCCACATGGGTTTGGGCTCCA
ACCAATTTGTCTCTTGCTTTTTCATTCTAAGTGTATTGGAGTCTTTATGGGAGTTTGGTACGGTTTAAGA
ATTTGCCCACTTCGGTGGAACATCGAAACTTGTTTTCTCTTTTTCCTCTGACTTTAAAAATTAAGGCCTT
ATTACAATTTTGTGTTTTTTCTTTATGATTAAATTTGTAGTAATTTAATGTCTAAGAACATATATACTGT
GTGTTTTCTAT
>gi|3450088|gb|AI100127.1|AI100127 34502 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105G11XP 3', mRNA sequence
GCGGAAATTAAGTTGTTTAACNNCAGAAGNTAAGGGCGGAAAGAAGCCCAAAAGAAAGTATTGGGGTCGT
TTTGATAAANATTATTTTGTAGGGGTGGTTTAAATGTGTGAAGTGGATAAACCATNNGGGTAACTGNTAA
CCGCGTNTNTACCAAACCCTNTCACTCCCCACTTGTCTTTGTACATTTTGGTTTAATGGAAAAAAAGGAT
AGGGCTATTTTCAAGAAATGACAAAACGATCCTTTTCTTTTGGTT
>gi|3450087|gb|AI100126.1|AI100126 34501 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105E8XP 3', mRNA sequence
CACAACTTCGAGCCTCAGATATNCAAATTGGAGAGAGGAGCTCGTNACAAGCTCATTAATGACTNCAACA
CAATGAGCATTTGGGACTTTAATGACAAGTATGGTGATGTATGGGATTTCACCATTGAGAAAGATGATNT
CGCCACACGATAAGATATGGATTATGATCTCGTTATAATCATGACTTTTGATGTAAACTGTTTTATAAAA
TTGATGAATGAACGGGGTACAATGTGTATAATATGGATTGTTCATTCTCTTATTTTTCTTTAGTACCAT
>gi|3450086|gb|AI100125.1|AI100125 34500 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105E4XP 3', mRNA sequence
CAGGCTTCATTCCTGNTTGATGGGGGATATGTTCGTTGATTGNGNCCGAGNTATTTGATATGCCGTTTCN
CTTGCCGGATGNCTGATTTGACCNCGAAGAAGATCNAGATCATCCNCTTCGAGNAATACCTTATGATTAT
GNCCTCCGAGNCNTCTGCCNCGTATCGTAGTGTCTGAAGAAGGAGCTGAAGATTTCCTTATTTGAAGCNG
TGAAATTAGCTGATGTGAAGAGATTAGAGATTCTTTAATGAAGCTGAGGAAGAGCTNTTAGAATATTATG
CCACAGAGAGAGCNTGAAGCTATGATATCTACTCGCANCTAAAACGCGCAAAGATCTGAGTTTATCAGAT
TCCACGTACGATATGTTCTTTAAAAGCTCAAAGATTCACACNCATGCATGTCCTGATTCTTTCGGCTTAC
AATTTTTGAGACATTACGGCTTCTTTTGCTGATAGAACCAAGACTGATCAAGAGTGACAAAGATGGGTTT
TTATAAGATAGAAATGTAAATTGTAGACTTGGATTTATTAGAGAGGAGAAGAGATACATTTTTTTTTTCT
TTACATGAGAGATATGTAAAATGGTGGTGTGTTATTTTGGAAGTTAACATATGAATTTCTTTT
>gi|3450085|gb|AI100124.1|AI100124 34499 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105E19XP 3', mRNA sequence
TTAATCTGCGTTCTCNTTCGTGACCTNCGCCCTTATGCTCCCAAATCGAGCGAGTCTCCAAACTAGCTGG
GGTGAAGACGCGTCAAGAANCTTCCCCTAGNACCATNNTCGCCCCTGCAAATGTCGNTNTGAAGCAAGTN
CTGAACAATATGGCTATTTGGCCAATCTGGTGNAATTAAACCCGGCAAACCAAATACGCCCTGTTCATGT
GATGGATGTCGCCCCAGGNTCTGGCGAACCTTATGTCGAACCCTCAGATCTCGGGAACTCTCTCGCTACC
TGGACCTTCGACCTTGACCTATGAATATCTTCTGGACCTCGTATCATCAATCGCTATCACGGAACCTTCT
AAGGCCCCTGTCTTGCCGAAGGCAGTTGCGACTGCGCTTGCCAAGGTCGCTCAGAACGTCTGGTGGCCAG
CCCTCAGTCCTGATGAGGTCGAACGCCGGTACATCGACGATGCTGATGTCGAGGGCGATTGGGCTGCAGT
TGGTGTCGAGCCAACGGAGATCGAGAGCCACGCAGTCAAGTACCTAAGGCGTTATCGATCTGCGGAGAAT
TCGTCCGCCCAGCGGTATTCCCCGCCAGACCCTCGTTGGCTTCCGAATAGAGCAGTAGATCGTAGACGCC
TGAATATAATTGTCTTTGAGGTTTCGCGAG
>gi|3450084|gb|AI100123.1|AI100123 34498 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105C1XP 3', mRNA sequence
TGCCAATCCTACCCTGAGGTTTNTTCCCAACCCGTGAGGNTNTTANCCAAGCCCAGATCGCCCGTATATG
GCTTANCCCGNCTTTGACCCACCTANCCCACGGTGGGTTTCTTGATGGGCTCTTCAAGGGTCAAATGGCC
AAAGGNTCAGAGTGGGCTAGGCACGTTTCTAGGGCANCACAAGAGCCAAGAGGCTAAAAAGAGTCAGGAC
ATGGGAAGCTCTTGGGGCAACATGACCAGAAGAAAACTCATGAGACAAACAGTGGTCTTAATGGCCTTGG
AATGTTCATTAACAATGGTGAGAAGAAACATAGGAGGAAAAGTGAGCACAAGAAGAAGAACAAGGATGGG
CATGGCAGTGGTAATGAGAGTGGAAGCAGCAGCGGTAGCGACAGCGACTGAATATCATATGCTTGCTCTG
AAGAAAGTAACGCTTCTAAGAGTGACTAAATTAAGTACTTGGATGTAATACTTAAAATAAAATCACTTAG
GTGGTTGTCTTTGTGTGTCCTATATAACCTCGCTACTACATGAATCTACTTTTAT
>gi|3450083|gb|AI100122.1|AI100122 34497 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105C14XP 3', mRNA sequence
GAAGAAGAAGAAGAAGAAGGAGAAAAGATGATTTACCGAAAGTGGAGTTTGCTGTCCGGCCCACCGGTTA
TCCTCGGCGGAGCGGTAATTGCTGCCGTCGCCGTCGGATTCGTCTTGCAAAACGTAACGAAAGGGGAGCA
GAAGAAGAATGTCTCAACAAACAAGTGAGAAGACAAATGGAGAGATGCTACAAAATGTGGTGATCATGTG
ATTTGATACAATTTAGTTCTTGCAGTGTATAAGCTCAATAATGCTTTTGTAAGCTTTTGAATACACAGAT
CTTTGTGGTGTTTTTAGATTCTTGTTACTAATAATGATATTTCATTTTCC
>gi|3450082|gb|AI100121.1|AI100121 34496 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105C11XP 3', mRNA sequence
TTCCCCAGCTCTATTCGCCCACTTTGGGGAACTGGTCCGCCTCAGTCCCGTCCGNATCCCGNTCGNCCAC
GCGTCCGAATNCACAGTTCCGCTTANGCCCTCANATTGAAGGGAGANAGAGATGGGTTTGTTGCCATGGT
GAAGAACTAGGTTTCATCTCTTTCTTCTAGTTTCAGCTTCAGCGTTTGCTCTCTGTTCTGCAGGCCGATC
ATCCATTTTATCTATAGCCAAGAAGTGATCATCCCGAGGTAGTAGAAAGAGATACATGAGCATGAGAGAA
TTCTGAGAATGAATTCAAGAGACTATGGCCACTCCAGTCCTAAACCAAAGCTCGTGAGACCTCCTTTCAA
GCTTATTCCCAACTGATCATGCATATCACCGATCGACTATATATAGATGCCAGACTTTCTGAGATGTATA
ATATATGTAAACCTAAATACTAACACTGCAATAAGTTTGAATGATAATCATATATATAAGTTTCAAGATA
TGTTTTCTAGTAAATTAATGATTAGATAGTGCTCTTTGCTATCATGCAGAATGTAAATTTGGTGAATAGT
CATCATTAGATGAATATTACAATT
>gi|3450081|gb|AI100120.1|AI100120 34495 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105B3XP 3', mRNA sequence
AAAAACCCTTTTTTCTAGGANCCACTCATATTCCTCCCGTGCTTTGNGTGATTCNCTGCCCGTTTACGTC
TATNCCNCTCGCTCAGCATTCCCGTGGGCTCTNCCTCCACCTCCTGGCTCACCGCCTCATGGCCTCGTCG
ACGCCTACCCCTATTCAGGCCTCCTGGCTCGCCGCTCTCATGGCCTCGCCGACCTCCTACCTCCTATTCA
GAACTTCCTGGCTCACCCGCTCATCATGNCCTCGGTGTAGACTGGTCATTATCGGGCTTCTACCCNAGGA
TATGGATTATCTTTAGGTTCTGAGTCAGCAAGGATTGGAAAAGTGAGGACCAGAACTCTACGGTATCTCG
ATCCTTGTCCTATTCTGAAAGGTAACTAGCTGAAAAGTGATATGGAGAGTTTGTGCCATTGCCAAGAGGT
ATTTATAGGAGAGGAAACAAGAGCGGGAAAGAGGGTTATCGACTCAAACTTCTGTCGGAACTTGATCATA
TTACTATAGGATTTCTATTTTGTCGCTTGAGGATATATATTATATATCCATCTTCTTGTTTTATGTTAAT
TTCTTTATCCATCAGTTTCTGTTTTCGTTATTTATCCACTTTTCACTGTTGTTAACTATAATAAATCGGA
AAGTTGATC
>gi|3450080|gb|AI100119.1|AI100119 34494 Lambda-PRL2 Arabidopsis thaliana cDNA clone 105B20XP 3', mRNA sequence
GTGCTTNTTTTCCTTATGATCCAGCTCTTCCACGCNCNCATGAACTATGAAACATATATAANGCGCNCNC
ATTTTATGTTTCCNCGCNCACATATATTTATGCATATCAAGCTTTTGGTGATTATGGTATTGATAGAGTC
AAATTAAGCTCGGTGACTATGGTATTAATAAGAGTACTATTTCCTTATCTCTTTGTGAACTAAGANNCAT
ATATATATATATATATATATAAAGCAAACATGTTCCAGAAT
>gi|3450079|gb|AI100118.1|AI100118 34493 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104P22XP 3', mRNA sequence
TCACGNGATCGAAACGGTTTGATCAGGAGAACTGGGATGTTCTCCNTNCCAACAAGTGTTATCANTTGGA
TTTCACGGAAAGANCAACGNGTTCACTCTAATTCGANTGGTTCCAANNCAGTGGGAGTAGTATNGCTGNT
GCATGCTCTNCTAAAGCTTCAGAGAGAGATCTGAAAGGTGCTTTGGANTGGGCTTGTGGTCCTGGAAATG
TTGATTGCACANCTATTCAGCCAGCCAGCCTTGTTTTCAACCAGATACTTTGGTTTCTCATGCTTCTTTC
GTGTTCAATAGCTATTTCCAACAGAACAGAGCNACAGACGTTGCTTGCAGCTTTGGAGGAGCTGGTGTTA
AAGTCNACAAGGACCCTAGTTATGACAAATGCATATACATTACTGCAGGAGGGAACAAAACCAAGGCGAC
GAATGCAACTGCATTGACCTCCTCTGCTTCAACTCCACGTGGAAACGAACTACTCCAATGGATTTTGAAA
CTCTGTCTCATGATCTCGTTGTTCTTCAGTTTGCAAACTATGAATTCACAGGCACTGTAACCGAAATCTG
AAAGAAATGTAGCAATAGCAAGAAAAAGCAAAATTTGTTCCTG
>gi|3450078|gb|AI100117.1|AI100117 34492 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104P21XP 3', mRNA sequence
CCAAGGCNGCCAAAACGGCCAAGGTTACATCTCCGGCTAAGAAAGCTNTTNCTNCCNCGAAGAAAGTTGC
TNCGGTGGCCACAAAGAAGAAGACNCCGGTTAAGAAGGTTNTGAAGCCAAAGACGGTTAAGTNTCCNGCA
AAGAGGGCTTCTTCTAGGGTTAAGAAGTGAAGTTAGGGTTTGTAGGTAGAAGAATGGTTAACGATAGTTT
AGACTTGTATAATTCAATCATCTTTATGCGACTTTGTTTGCTTTTCTT
>gi|3450077|gb|AI100116.1|AI100116 34491 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104O22XP 3', mRNA sequence
GGATTTTTACCCCCGNTTACTTGCTCCTACGCAGGAGCCCAGGAGAAGNGCTACAANCGGGAGTTGNCGA
TNTTGGCATTCNGAGGGTTTGTGGTTCAACACATGTGACTGGAAAGGACCTTTGAGAATCTGTTGCAGCA
CTTGTCTGACCCTGGCACAACACTATTGTCNAANCNTTCAACTAAAGAGTGAAGACAGACTTATGATCTC
ATACCTATCTATCTTCCATCACTTTCATGTCTGTCTGTGAGTGTGTTTCATCTTAGAGTTCTTGGTTTTT
GAGCTTGAATTATTGTTGAACCGTTGTAGCTCCATGAACAAATTTGGAATCTTCAATGTACAGAGGAACT
AAGTTAATCAACATTGTTGTACT
>gi|3450076|gb|AI100115.1|AI100115 34490 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104O12XP 3', mRNA sequence
TCACACGACATTGAGCTGGTCCTCTCACTNCNCCATCCACACCACCGAGCGAATGANGCTATTTGTTGAT
GCGTCAGAAGGATTTATTTACCTTGTGAGCTCATTGGATTGACTGTTCACGATCATCTGTAAGCGGAAAG
GTTCAGTCGCTCTGAAGGATATCAAGAGGCGACAGACAAGCCGGTGGCAGTCGGTTTTGGAATATCAAAG
CCGGAGCATGTGAAACAGATAGCTGGATGGGGAGCTGATGGAGTGATCGTAGGCAGTGCATGGTAAAGCT
ATTGGGTGATGCAAAGTCGCCAACTGAAGGACTTAAGGAGCTTGAGAAACTAACCAAGTCTCTTAAATCT
GCTCTTCTTTGAAACACAAACATTTGCAGACAACATCTTTAGATTGTGTTTTTGATTATTATCGGTGTGT
GACAATGATGTNTCAATCTTTTGATACATTTCAAGTATGATTAATAAGTTACTGTGACTCAAGCCACACA
ACC
>gi|3450075|gb|AI100114.1|AI100114 34489 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104N23XP 3', mRNA sequence
CAGGTGTTTGAGNTATCGACTCGAGANTNGGANGCNTGGTCNCCCCAAGTGTCATTTGTTGCCATGATTC
TTTACTTCTAAGAGCTTGAAGATATCGTTCCTTCTTCCCACATTGTGATGTTCCACATGTGAATCGTGTT
GATTATCAGTTGATTGATATCTCTGAAGATGGCTTTGTTAGTCTTCTTACTGATAATGGTAGCACTAAGG
ATGATCTGAAGCTGCCAACAGATGAAGCTTTACTCACACAGCTCAAGAATGGATTTGAGGAGGGTAAGGA
TATTGTTGTGTCTGTCATGTCTGCAATGGGAGAGGAGCAGATGTGTGCNCNCAAGGAAGTTGGNCCCAAN
TNATAATAATAAGTAAGCATTCTCTCTTTTACAGAGGCTATGTATTATCAAGTTTGACAGAGTCAAATGT
TATAAGAACAAAGTTTGGNCCT
>gi|3450074|gb|AI100113.1|AI100113 34488 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104N20XP 3', mRNA sequence
CCTCTCCTCAGCCACTNTGAACCGAGTCTGCNGCTATATTAACNTAACAATGGTGCAAGACTTTCCCNAC
TGAGTTTCGGATGGGTTATGTAAAAGACGTAGCCATGCGCACATCCAAGCATTGAGGTCCCTCAGCTAAT
GGGCGTTATTGTTTGGTCGAGCGTGTCGTTCACCACTCCGAGATTGTTAACATTCTACGTGAGCTTTNCC
CAATCTCCCACTACCTGAAAGGTGTGTGGACGAGAATCCCTACGTGCCNACGTATCAAGTGTCCAAGGAT
AAAACGNGGAGCCTTGGCATAGACTACATACCCTTGAAGGTTAGCATCAAGGNGACCNTCGANTCCTTGA
AGGNNAAAGGTTTCGCNCAGTTCTGAGAAAGCATTTGAGCCAATGGATTTAATCCAGATTAGATAAAGTA
TTTGGAAGACTATTTCAGAAATAATATTTGGANCATGTCAATGTTCTCAAGGAGATATTAGTATGTTCTT
GTGTACTTTATTGTTGTTCCATCAAATGAGTTANTTTTCCTTTT
>gi|3450073|gb|AI100112.1|AI100112 34487 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104M7XP 3', mRNA sequence
CCTTGGACATTCCCCGTCGTTTCTTGTGACAACTCCCATCCGACGTCAAGAATGCTAGGATCTGNGATCC
GTTCCCCATCAACCACCATGAGCTACTCAGCCTTGGAACNCGATGATTGGCCCCGAGAGGCGTTTAGAGA
GNCCATGGNCCATGCNCCTTTCGTTGCATCTACAANGATNCCACATAGATGNTNCCCAGCTCTGTGGAAG
CCCAGTACTGTCCCACACAAGCCCGCATGTGGTGGAATCAGAAGANTNCCGTGACCCTTGACGCTGACCA
TGGCGTCGTCTCAATGGGTCCGTATGAAGTGGNCCATNTACAACTACTNTACCGACCGGACTAGGTTCCC
GNTTATGCCAGCTGAATNTAAAAGGGACAGAGACGCNTAAGTTACTACCNTTGAGGGTTTTAATGAATTT
ATGCTATCATTATTATTTGAATTATGCTTGTTCAAGAGATTGATATATGTATTGTTTGTTGGCCCATGAT
GTTTATGCTATATTTGGGCCTAAAATTACATGTTATAATTCATATATGTATTGATTAGCTATGTATTTTC
ATATGTTATGATCT
>gi|3450072|gb|AI100111.1|AI100111 34486 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104M18XP 3', mRNA sequence
ACCACACCACCGGTCCAATCCCAATTCGCCAACTCCCAATCCCAATCCCTATTCNTCNCCGATCCCGTGC
AAGCCTTCATTTCCTCCGCCCCGCAATCCTNGCTTTAATCGCCCNTTCGCTCCTCCTCGATGCCGAGCGA
TGGAGAAGCACAGCTCTCGATTCAATCTCACGCTCCCATCTCGTTGTTGAGTTTCTCTTCTTGATGTTCG
CTCTCGACAAGGTCTATTACTCTCCGCTTGGTAACTTCATGGATCAAGAGACGCTTCCTCAAAGAGAAGC
TCGCGAGTGTTAAGGACACTTCGACTGAAGTAAGGAGCTCGATGAGCAAGCCGCCGCCGTGATGAGAGCA
GCTAGGGCTGAGATCGCCGCCGCGCTTAACAAGATGAAGAAGGAGACTCAGGTTGAAGTCGAGGAGAAGC
TAGCGGAGGGAAGGAAGAAGGTGGAGGAAGAGCTAAAAGAAGCTTTGGCGAGCTTGGAGAGTCAGAAAGA
AGAAACCATTAAAGCTTTGGATTCTCAGATTGCTGCTCTTAGTGAAGACATTGTCAAGAAGGTTCTTCCT
TCTTAAATTATATTTTTGTTAACTGTGTAATTCTCTGTCTCTCTATCTCAAAACTTATTTACAAGAAATT
ACTGTAAATC
>gi|3450071|gb|AI100110.1|AI100110 34485 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104L23XP 3', mRNA sequence
CAATNNGGGTCCATGGCTTCCAAGCTGGATCAACCGGNGCTATTCNCATTNTGGTCCCGACCTTCCGTTG
GCCCTCCGACAGGAAGAGGATCTTATGATNCCGATCACGGGAGAAAGTGCTTGCATGNCACCGGACTTGA
ACGCCTCAACATCTCCCCTCAAGGTCGCTGCATTGACAAACTCAGGGGAAATGGCCCTCTTTGATCCCTC
CAGGTCTCAAGACTTCCTCTTCATATCAGGAACCAAGATGCGTGGCTTGGCGAAGAAGAAAGAGAACCCA
CCAGATGGTTTCATGTGTCCCTCTGGTTGGAAGGTGTTGGTTGATTACTACGACAGTCTCAGTGCAGAGT
CTGGTAATGGAAGGGTTTCAGAGGCTGTTGCTTCTGCTTAAATGCAAAAGGTTCCTTGCCCCACAAGTTT
CACATTTTCTGGTTGTTAAGTAACTATGCTCTGTAAGAAACAGCTTCCAATAAAACCAATGTAACAACTG
TGTGTTCTTTGCGTCTCTGTTGTCAAACTTGTCATCGGGTCGCATCTATTTGTACCATATTTGCTTATTG
TGTTAAAAATGTAACAATATTTGTGTATAAACTATTTCTCGTGG
>gi|3450070|gb|AI100109.1|AI100109 34484 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104L1XP 3', mRNA sequence
CCTTCCAGTNGCTCAGACTCCNCCGTCTCGAGATCTTCNGGATAGTAGGTTGGTCAGANNCCTGTTCTGA
ACTCTGCCACNATAGGTTCAAGGCTATTTCTCACTGGGGCATCCNTACAGTTTCCAGGGTCCGATCTCTT
TTCTGTTACGTCGCTGGTCTAAGCTGGTCTATCACGAGATTATTCGCTACTCATCTCGGCTTTAAGGAGC
TCTAGGCTTTGCACCTTCATGGCACTTGTGGCTCAGATACAGCAGCTTTTTATTGCTATACCTACCGGTA
TCACCAGCGAAGTTGGTCTTATCTACCTTGCCTTACCACACATCAAGACATCGGAGATGTACAGCGTTAG
GATGCCTAACATATTGAACTTCTCATTTGACTTCTTCTATGCAACGATACTCGTCCTTGCAATCTATGTC
CCAGGTAGCCCACACATGTACAGGTACATGCTTGGTCAGCGAAAGAGAGCTCTCTCCAAATCCAAGAGGG
AATAAAAGAAAAGATTTAGAAAGAGACGAAAAAGCTCATCAACTGTTTTCTCCTCTTGTCTTGTTCGTTC
ATGTACTACTAGTCTACTACTACAACTTGTCTT
>gi|3450069|gb|AI100108.1|AI100108 34483 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104L12XP 3', mRNA sequence
TGCCAGATCCCTTCCCAGTGACCANTCCNTGCTATAGTGATGGATGAGAGTCTTGAGTCAGGGAAGATAT
CACCACCGCACCGCTTCAGATGGTTTATTATTTACTGAACAGACCGNCCAAATGGTCAGGCTTGTCTTGA
TACGAAAGAGTTCAATATTTTGAGCAAAATGATGCAAGCCGTTGATGAAGAGCGATATGATGAAGCCGCT
GAGTGGAGAGACAAGCTTGGTCAGTTTCGGGCCAAACGTAACTTGAGGAAATACACATGAGAGAGCTCGA
TCAACAATTATTGGCTGTGTACATAAACTAAGAAGAAAGTCATTGGTCGGAATCAAAGTGGAGGAAGAAG
CCTGAAGTGTCGTCTCTGTATGATGGAGATCGAAGAATGCTTCTGCACTTTACCCATTTCCCTAAAAAAT
AAACAAAAAAAAATGTATAATGTATGTATGTAGCGTGATGTGTACATATTACTTATTAATCTATGCAAAT
TAAGCTC
>gi|3450068|gb|AI100107.1|AI100107 34482 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104K2XP 3', mRNA sequence
ACGAAGAAGAAAATGNTGAAGNTGATGTGGGTTNCCGTTTTAGCTCTGGCGNCGGCGATCTCCTTTGACG
GTCCCCGGTGNCAGAAGGGNTGACGTGCTCGCCCTATGCAGCCGCCATCGGAGGCGTNTTGCACAAAGCT
GAGAGAGCANCAGCCATGCCTTTGTGGGTACATGAGGAACCCTACCCTCCGCCAATACGTTAGCTCCCCT
AACGCAAGGAAAGTCTCCAACAGTTGCAAGATTCCTTCCCCAAGCTGTTAAGGAAATGTTAATCATGATT
AATTAGTGACAAGTTTCGCTGATTATAGTGGTTAATGCTGGTCTTATCTTCGTCACTACTATTTAGAATA
ATAAATGAAGTGATGATGATTGATGATTGATGATTGATGATTATCATCATCATGCTTGAATGTTATGTTT
TCTATCTTATAAAATATGAAATATACTTTAG
>gi|3450067|gb|AI100106.1|AI100106 34481 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104K18XP 3', mRNA sequence
ATGNTTTGCATCCTGAANATCTTCTNAAGGNNCANCGNTCCATATTNTGGACNCTCAAATCCATCGTTCC
NTCAAGGGAGCTGTTTGNGAACCCCTTNTTCAATCGTGGCNAGAGCTCTTCGTCCTGGTGGANTTNTGTN
CANTCAGCTGAAAGCTTGTGGCTTCACNGGACATCATCGAAGACATTGTTTCCAACNCCGTGAGATCTTC
AAGGGTTCTGTGAACTATGCTGGACCANCGTTCCAACATACCCCANTGGGGTCATTGGATTTATGCTTTG
TTCAACTGAAGGACCTGATGTTGACTTCAAACACCCACTGANCCCAATTGACGAGAGCTCCAGCAAATCA
AATGGACCTTTGAAGTTTTACAATGCCGAGATTCATTCAGCTGCATTCTGCTTGCCTTCTTTCGCCAAGA
AGGTCATTGAGTCAAAAGCCAATTGAAAAGGGAAAGAAAACTAATCTGGAGGATCGTTGAATTTATCAAA
AAATAAAAGCTTTTTACAGTTTTTAGAATGTTCTGTTGTTTCACTCATGTTTCTGTAACACAATGCAAGA
GCNACTATGTCTTCTTTTAGCA
>gi|3450066|gb|AI100105.1|AI100105 34480 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104K13XP 3', mRNA sequence
CATAGGAACTTACCAGATCGTGGGTTTGGATTGTNTCATGAGTTCTTTGGNCGANCTGAGNCACTGTGGA
GAAGTTCANCCGTTATGATCNTAACGGNCGTCTACTAACNTAAACAAGNCANCTCCAGNGGATCACGTCC
AGAACGTNCGCCTCGGGTATATGANCCGCATTCAGAGTATATGTAGGGAATCTACCATGGGATGTGGACA
ATGGCCGTCTAGAACAGCTTTTCAGTGAGCATGGTAAAGTTGTGGAAGCTAGGGTGGTTTACGACCGTGA
GACAGGTCGTTCACGTGGATTCGGGTTTGTCACAATGTCTGACGTGGATGAACTCAACGAAGCCATCTCT
GCCCTCGATGGACAGAACTTGGAGGGTAGAGCAATCAGAGTGAATGTAGCGGAAGAGCGTCCTCCAAGGC
GTGGATATTAAAGCTGAGATCTAGCTGTGCCCTCTCTCTCTCCCTATCTTGCATTTTGTTTAGACGAGAT
TCTTACACTCTTCAACGATTGTTTTTGGCTGAACTCTGAATGTGAAAGTTAAGCTGCTTCTAAAGTAATT
TGTATC
>gi|3450065|gb|AI100104.1|AI100104 34479 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104K11XP 3', mRNA sequence
ACTTCCCGGCTCCTTCACTCTTCACCTTCCCAATTGCCAAGGTTTCCCCGCGGTTGGGAATGTTCCCCCG
GTAGGGGTGGCCCACCCTGTCGTGTTGGGATTTAANCAGGAAGTGAAGTAAGAAAAGAAAANAACTGATA
AAATAGAGAGACCCTTAATAACCAAAAAGATGCAGAGGTGTAAAANATAAAAAGCAGGAAATTTGATGTA
AGAGATAGGAGAAGAGAAAGAAGGAAGATTGTTGTACCATTTCTCTAGTTTTAATGTGTTATGTGATGAT
GGACCACACAAGATGATGTAATATGATNTGATATGATATATATAATATAGGACAAGAAGTGTAATCTCTC
TAAAGNTATACAAAAGNAAAGAGAGATTATCATTTGAGTTTG
>gi|3450064|gb|AI100103.1|AI100103 34478 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104I4XP 3', mRNA sequence
CCCTCGGTCTCAAAGGACCAGGTCCCATGTTGGGNTNCACGAAGGCCGACCGAGTTATTCGTAGGAAGAT
TGGCNCCAGTTGGGNAATAGCATTTTCCACTGATAGGAGAGATTATTACCGGGAAAGGAGCATTAGCTCA
ACTCAACATTGAGACCGGTATACCAATTCAAGATATCGAACCACTTGTCCTCTTAAACGTTGCTTTCTTC
TTCTTCGCTGCCATTAATCCTGGTAATGGAAAATTCATCACCGATGATGGTGAAGAAAGCTAAATTATCA
TGTACTTAAATTTAGTAGAGAGTGTGTGACCTTCTCTTCATGTTGAGACAAAAGGAAATGGACAGCTTAA
ATTGTTGTAATACTTATATCCTTTTGTTTTTAACTTGGAATTTTCTGATT
>gi|3450063|gb|AI100102.1|AI100102 34477 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104H9XP 3', mRNA sequence
GTTCGAGTTCGAAACCTNGTTTCCCATCNCCCCCGGTCTTGAANCCTCTGTTGTGGCCCAGCCCAACGAN
CGGTGGCAAGGATCTCCGTGTGCGTTTGTGACCACTTAAGNGCGATTCCGAGAAGCATGACCCAGAATAA
GTTGGCTCAGGATATAATGAAATTCTGCCGGGAGAAGCTTCCGGCATATTGGGTCCCAAAGTCAGTGGTG
TTTGGGCCGTTACCAAAGACAGCAACTGGAAAAATTCAGAAGCATATTCTGAGGACCAAGGCCAAAGAGA
TGGGACCAGTACCAAGAAGCAGGTTATANGAAGTGATAAAGCTTTAAGAACAACATTTTGAAAATAATGT
GTTGTATGTTTTTGCGGAACTTTGCCTTGTGTGTAAACTTTCAAATGATAACAGAAAATATTCTCTTTAT
TTTC
>gi|3450062|gb|AI100101.1|AI100101 34476 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104H3XP 3', mRNA sequence
GCCCCGTTCCCATGGGTTGGGAATNCCCCCAAAGGTTNGTTTGGTTCCCTTNNGATCCAAACCNCTCGGC
CCTACCNGTATATATGCGATCCGATTCCTGGGGTGGNTTAANCTTTAACCNCACCATATTAATTACTAAT
TTTTGNTTGGTTGGATTAATTTGTGGTNTGGTAAAGTTGCGANAGAACTCCACCAAGGAGTGCGACAACT
GTAGCTGTGGATCAAACTGCAGCTGTGGGTCAAACTGTAACTGTTGATGAAATTATTATGGTCTAAAATC
ATATATATGGCAGAAAAATTGGGGAAAATATGTGTTTTATGCTAAGAGATGTGTGTGTGTTGTTGGAATA
AAGACGTGACCGTTGTGTTGCGTATCAACTCTCTTAAGCTTTGACTTTTCCCAGCTTTGTATTTTCCTAT
GTATGGTAATGGTGTGATTGTGTAATGTTTTCATATGTAACGTAAAAAAAATATTTATGTGACATTGACT
TTTGTGACT
>gi|3450061|gb|AI100100.1|AI100100 34475 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104H10XP 3', mRNA sequence
TTGGTNCAAGTCCATGGGGGGATTTCTGGNAATGATAGCGGNCCCACGCTACTACTTCTGGNCATTTGGT
GTACCCCCGGATGACGGATCGACGTCCCTTGAAAACTCCATCTTTTCCTCAAGGCCCCTATTTGCTGATG
AGCCCAGTCGTGATTGCAAGGCCCAGAAGATGTGAGATTTGCTCATGCGCCTTTTGATGAAATCCACCAA
GACTGAATCTTGATCCTCCACAAAACACCAGCCACAACGCACAGTTCAAGTGTACTCAGATAATGTTATT
GACTCTTGACCTTTATAGTTGTGGATAATGTGGAAGTGAGATAGTGTTGGCTCTGATTTTTTTCCCTAGT
TTTCTGTCTGCTTTTCTTGTCCGATACAAATGTGTTTCCTCCTTGTGCATATGAACTCAAATTGTGTACA
AAGTCTTCAAAAGTGCTAGTTTATAGTTTCGTC
>gi|3450060|gb|AI100099.1|AI100099 34474 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104G4XP 3', mRNA sequence
GAATTTTAGAATGGATAATTCGNGAAGGTNAAAGTTGAACCTTATNTTTGGGTTAATAAGATATCCTAGA
ATTTATGGAGAATGGGATTTCCGAGGAATGGAGANTGGTTCCACGCGGAGAATTCCGTGGAGACTTTTAG
AAAAATGTTGGAATGGAACAAGAATCCAAATGGGAAGAGCATGGAGGAGGCTGTAGGATCATTATTATCG
TCAGGGGATTAATTCTTGATGAGCTTGGCTAATCTTAGCAGAAGAGAGTAAGTGAGTAAGTAAAGAGTGG
GTTTTGAATAATGTGTTGTTGGAACTTGAAACAGAGTCTTCTATGTGATTTTGTTTGTGTTGTTATGGAT
ATCTTGTTGGCACTTTTTCTGATTTCAGTTGGAAACAGGTGCGTTTGCGGGCAATAGTTGCTTCGGANTG
GTTGTAGTAACAATTTATCATAAAGCCTACTAATATTATAG
>gi|3450059|gb|AI100098.1|AI100098 34473 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104G22XP 3', mRNA sequence
CGAGACCCGTCTTNGGNGGGCTTCCAGTCCATTTCCAAAGGTTAAAGACTTTACNAGGCTAAGTTGGTGG
TGTTCCCCTCGCCGTCCCGTCAAGTCCAAGGCTGGTGATTCTACTCCAGAGGAGCTTGCCCAATGCTACT
CAAGTTCNAAGGTGATTACATGCCCAATTGCCCAGTNTCAAGGCAGCTATGGAGCTAGTTAAGCTGACTG
CAGATTTGAAGGCGTTCAAGGCTTACGATAAGATTCGTTTGGAGCGCACAAACGCACGTCATGCTGGTGC
CAGAGCCAAGAGGGCTGCCGAGGCTGAGAAAGAAGAGAAGAAGTAAAATTCGTTGCTTTATAGAGCTTAA
TCATTCTTGAATTCTTGTTCTTCTGGTTTTTGATTTTGTGCACGACTCTGTTTTCTTTTTGGTGCGGTTT
ATCAATACATAGATCTCAAAGGTTTCTGGT
>gi|3450058|gb|AI100097.1|AI100097 34472 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104F23XP 3', mRNA sequence
GAATTGCCCAGGTCATCATGATCCAGTCTGGTCAAAGCTCAAGCGATGGGCGGCATGGGATCCGGATATG
ATGCTGGTGGCTACGGTGGTGAGCACCACGAGAAGAAGGGGATGATGGACAAGATCAAGGAAAAGCTTCC
CGGTGGTGGCCGTTAAGCTTCGAACAATCGTGTATACATATTAAATAAAAATAATGAGGGTTTGTAACGC
AGTCGCATTCGGTCGTTGTATTGTGCTTTTTATGTATGTACGTCCTGCGATGTGTGTTGTTTACTTACAT
GAGTGTGTAATGAGCATCTGGCTCTTTTTATGTTCTGAGATGTTTGTGTTATGTAATTTCACATCTATAT
AAATCTACTTTCTTCTGCTT
>gi|3450057|gb|AI100096.1|AI100096 34471 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104F19XP 3', mRNA sequence
TATCCNAAAGAAGGACCCTTGGGNCCCATCGNTCCAATCGCCATCGGCTTCATANTTGGTGCCCAACATC
CTCGGCTGCTGGNCCCATCCAGTGGTGGCTCCATGAATCCAGCAAGTCGTTCGGACCACTGTTGTCAGTG
GTGACTTGTCCCCAAATCTGGATCTATTGGGTGGGACCACTTGTGGGTGGTGCACTCGCGGGACTTATCT
ACGGTGATGTGTTCATCGGTTCTTATGAAGCGGTAGAAACACGTGAGATCCGAGTGTAATTGACTGGGTT
TTGTGATTGCTTGATGGTTGGTTGATGTTTTGTTTGCGTGTGTATGTTTGGTGTCCACTTTCTTGCAAGA
TTGTATGTAGAGAAAAGAAAAAAAGTTATGTCCTGTTAATAAGAAAATGTATATACATTTCACTTCATCT
C
>gi|3450056|gb|AI100095.1|AI100095 34470 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104E3XP 3', mRNA sequence
CAAAGAACCCGTTTGGATTTCTAANCAAAACNCTTGGACCGCTANCTATGNNTTTNCCGGCTNGTTTGAT
CNCCCGAGAANNATCTTCCTTCCCGGAGGTGACTNCTTCGCCGGNATCAAGTCCCGACGACTTCTGGATC
TCCTCCGAGGCAGCTACATCATCATCAACATCCAGATGAAGAAGCTTCCTCCGTTGTATCCTAGGAGTCA
AGGGTCTTTTGGTAATTTTGCTTCGTCTCAGTCGTCGTTGGGTTTTTGTGCCTGGAGATCGTTTTCGGTG
GCTGATTTTCCGAGGTGTTTTCCGGCGACGGCGAGTGGGATTGGGTTTAATGACTCGTAGGAAATGATGA
TAACAATTGTTTTGTTAAATTTTTATATTTTGAAGTTAGTAACAACCACATCCGGAGAATGTATGTGTAT
AGAAGAGTTTCAAAACTTTTGAATGGATCATCCACATCTTTTTTTTCC
>gi|3450055|gb|AI100094.1|AI100094 34469 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104E20XP 3', mRNA sequence
TACGGNAGNCCCTAAACCGGGACAGTCATGGTTNCCCNACAGGNTTGCTTCATTNCCAGATCAACGCGGG
AAAATCCTCTGCTTCCAGCCCGTGTCACTTTCAACAGCGCTAATCCGGGTCTGCAGATTCTCGACTCGCA
CTCTTTGCTAACAGTCTTCCCACTGAACTCGTCGTGGGTACTACTTTCCTTGACGCCACTACAGTCAAGA
AGCTAAAGGGTGTTCTTGGAGGAACTGGCTAAAAAAAGACTTAGGACTACTCCTTGACTAAAACACCAAA
ACCTGTTTCTTCATCTTTTTTTCTCTTTAATTGATTCTTGTCTTCTCTGTTTTGTGTGCCTTGTAATTCT
TCAAAACCTGTCAAAATTGTTACATTGTATGTGAGTTTTTTCAATTAAGATCCTGAGTTGGTCACACCGT
T
>gi|3450054|gb|AI100093.1|AI100093 34468 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104E1XP 3', mRNA sequence
TAGACAATGCGGGGNGAATGAAAATCATGGTGCCCTGANCTTCCGCCCCCTTACTTTGTTTTNTNNATAT
TGTTTTNGTGNACTTTATCAGAGTGGATAAAGTGNCGGGGAATGTTTTTCTTTTGTACAAAAAACTGTCT
TCCCNCCTAAGCAANGTGTGTTAGTTTCTGTTTTGGGCTGTGTTTTGCAAGTTTTTGTATTTCAGAGTTG
TAGTGTAGTTGCAAGTGGCGGTTGGATCTTTCACTATCTTGTTGGANTTTGATGATGGTTGATGCTTTTG
CTTTAATGTTAAATAAATAAGCATACTTTTGCTAGGTACCATTGCATC
>gi|3450053|gb|AI100092.1|AI100092 34467 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104E16XP 3', mRNA sequence
AATCCCCATTCNTGGCCCCATTGCCNGGNCCAAGGCCTTTGNCCCCGCCAGNGGGAATTGTCAAGATTTT
GGCTGTTAAGGGGCCGNCCAGATCTTGGGAGTTCACATTATGTCACCAACGCAGGAGAATTGATCCCATG
AGGCGGTTCTAGCTATCAACTATGATGCATCAAGTGAAGACATTGCTCGAGTCTGTCACGCTCATCCCAC
CATGAGTGAGGCTATCAAGGAAGCTGCCATGGCTACCTATGACAAGCCCATTCACATGTAGAAGCCCTCA
GGAGATGTGGATTGAGAGGGAGAAGGAAGTAAAGCCGCCTACGACAAGCCAAATCAAGATGACTTTGGTT
TAAACTTTTGATTTTTAATTTCTGGTGGATATGAGATGAGCTGAAAGAAAATACTTTAACGGTTTTACCA
CT
>gi|3450052|gb|AI100091.1|AI100091 34466 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104E13XP 3', mRNA sequence
GCTTCTTCCAAGTTAGGNGGGGNCCCAGAGGAAANTNAAAAAACGNNAGGTTCCCAAGGCCAAACCGGNT
ATGCCCCAGGCTTATGNCCCAANTCCCATACCGGNGTCCCTGCGCCTTCGTTCCAGCCGGCGGGCAGAAC
AATGCCNCCAACANCATCTCTTCATTCAGANTCTCCCCACACGAGACAACAAGCATGATGCTACAGCTTC
TCTTCGAACAGTCCCCTGGATTCAAAGAGATAAGAATGATCGACGCAAAACCAGGAATCGCGTTTGTAGA
GTACGAAGATGATGTTCAAGCTTCCATAGCTATGCAACCTCTTCAAGGTTTCAAAATCACTCCCCAGAAT
CCAATGGTCATCTCTTTCGCCAAGAAATGATAAGAGTCTTGTTTTTGTTTGTTTGTTGTCCTTTAAGACG
ATAGTACTGGACCAACCAAACCTGGTGTGTATAACCAACCAACGGTTCTATTGGTTAACGGATTAATCCG
GTTTTGGTTT
>gi|3450051|gb|AI100090.1|AI100090 34465 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104D23XP 3', mRNA sequence
CAAGNAAGTGATCGCCACATTTGAGAAAGTNGCCNGAGGAAGAGGAANGAGANGGCGAGGCTGGTGAGGN
TGAGGCCGAAGCTGCCGGGGCTGCACCAGCAGAACAAGGTGGTGGTGGTGCAGGTGACCAAGACGTGGCT
CCAATGGAAATGTAAGGCTTGTGTGTGTAACGCTGGATGGAACTATTTTATTTCGATGTTAGTTGGATTT
TTACTTTGCAAAATGGCTGCGGGTTTAGATTATATGCTTGAGAAGTTGAAACCATTTCGTCATTTTAACT
CAATAGCTGCCATCAAGACTTTCTCGT
>gi|3450050|gb|AI100089.1|AI100089 34464 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104D22XP 3', mRNA sequence
CCTTCTTCATTGCCATGGTCNCCGNCACTTCCAAAGTGAGAGGCCAGATGATTTTACGCGAGCTCTAANG
ATAGGTTCANGAGGGAACCTAGATGGGAATTTCAAGTGGAACTTCAAGCTACTGATNCCAACAGAAATGG
GTCTTGATGTTTTCCAAAAGCCGCACCAACTAAGTAAAACAAAACCCTGTAAGGGCATTTGAATAAGTTT
GGTTTCTGGAGTGAATATGTTTCCTCTGACTGTTATGAAAACTTTTTAACACCTTCAACTTCATTCTACT
TGGTATTATTGTATGTCTTTGATGTGTTATGTGTGCCTTGTGATGGTTTTCAATTAGTTTTACATGTACA
ATACTTGAAATCAGATTGTTGCTAGGCTTCAAGCCTTGTCTCAGTTATCTATCTGATAATTTATTCGTAT
ATGTTTGGAGTCCT
>gi|3450049|gb|AI100088.1|AI100088 34463 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104D20XP 3', mRNA sequence
ACCGTTTCTACGTGCANCCATCAACCCAGGACAGNTCATNGTTTTCCCCCAAGGCTTGCTTCATTTCCCA
NATCAACGCGGGAAAATCCTCTGCTTCCANCCTTGTCCACTTTCAACANCGCTAATCCCGGGTCTGCAGA
TTCTCGACTTCGCACTCTTTGCTAACAGTCTTCCCACTGAACTCGTCGTGGGTACTACTTTCCTTGACGC
CACTACAGTCAAGAAGCTAAAGGGTGTTCTTGGAGGAACTGGCTAAAAAAAGACTTAGGACTACTCCTTG
ACTAAAACACCAAAACCTGTTTCTTCATCTTTTTTTCTCTTTAATTGATTCTTGTCTTCTCTGTTTTGTG
TGCCTTGTAATTCTTCAAAACCTGTCAAAATTGTTACATTGTATGTGAGTTTTTTCAATTAAGATCCTGA
GTTGGTCACACCGTT
>gi|3450048|gb|AI100765.1|AI100765 34462 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104D14XP 3', mRNA sequence
CGTTANACGACCTTACTTTTTCCTGAACNNCCCCCNTNAAATTCCCTNCGTCGCNTTNCCCCCCGTNTGG
NAAACCCAATTTCCCGGNTTCGNGCTGGTAAATCCCGTACCCCGGTTTGGTTTCTGGCCGATTTGGAAAG
AGTTTGGTAAAGTAAAGTAACCAGCCCACGTCAGGAGAATAACTAAATAAAGGCTGCTTACGTGTCTGTG
TGTGGTTGGTTTGTTTGTTGTATGGGTTAAAAAGGATTTTGTTGCTGTTTTAAACGCGGTGTGGGCTTCT
GAGGCTACGGTCGCGTTTGGNTGTCGCTAGTTTTTTTTTTTTTTTAAGTTGTTTGTCTGAAAATTCGTGT
GGGTTTGTGTTTTTTAGTGGGAGCAAGTATGGGGAAACCCAAATCGACTTGTTGTCCCGTTGCGTTTGAT
GTAACGTTTGCTTATGTTATAATTGAAATAAAAAAGTGCTTTTGGGATCT
>gi|3450047|gb|AI100764.1|AI100764 34461 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104C2XP 3', mRNA sequence
CAATCCAAGGCTGAGAAGCTTAGGGAGAANCTCTGTCTGATCAGTTTGAGGCTAAGAGGNCGAAGNACCA
AGGCTTAGCCCGAGAAAGGAAGCATGCTAGGAGAGAGGACGTTTAGCTTAAGGGTCCCGGTGGAGATGTT
GCGCCTGTAGCTGCTCCAGCACCTGCTGCTACACCTGCTCCAACTGCAGCTGTACCGAAGAAGAAGTCTA
AGAAGTGAAGAGGATATATAGTGTGAAGCTATATCGATCATCAGTTCACGGATTAGACTCTGAAGAAGGT
TTTGAATGTTTTATCGAATGCGTTTGTGGAATAACTTTTATTTTCGCAAAGAACATAACTTATGTCAGTT
AATCTTTATGCTTTCAGATTTTTAGCTTACAGTGTTTCAACAGACCTACTTTGCAAGTTGTTCTTTTTTT
GGTTG
>gi|3450046|gb|AI100763.1|AI100763 34460 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104C12XP 3', mRNA sequence
CGGTCCGGGCCTTCGTGGGNTTNCCCCNCCCTCTCAAATTCCTTACCCGNCGGATAATTTCCCCTCAGAT
CATNTTGACGGAAACTCCCATTTAGGCCACGGGGAGAAGCTTCTGGAGAAACAGAGATTGTTCCCAGAGC
ATCCCAAAGGCACACTTACTTGAAAGGACCAATGGACAAGATCACTTCTGTTGCTATTCCTATTGCCTTG
GCTGCAAGTTCTCTCTACATGATTGGAACAGGAATCTACAACATGTCGAATGGAATCGGCAAAAAGGAAT
AAGCAGCTTCTTGATTTTTCCTTCTTTTTTATATGCTTTTGGTTTCTCAATGTATCAGTCACTGCCCATA
TGCAGTAGCAGACTAAGGTTGCACTGGTCTTTTTCTTGAAGCTGTTTATTCCGTCTTGCCAAATAATTGC
TTAGTTGCAGACAATGTCGAAAGCTAAAGATGTTTGATGTTATAAAGTTCCAATATTTTGGGGAT
>gi|3450045|gb|AI100762.1|AI100762 34459 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104A7XP 3', mRNA sequence
GCACTAGCCNGCGAGCTTGCCCCCTCACAGAAGGAAGCTGCAGGCATCTCTCCTGGGTCTTGTACGAATG
TCGGTGGGNTATGTGGGTACATTGGAGCAGAAGTGGACACAATTCGAGAAAGCATTCCTCAGAATGTAAA
ATGTCTTCTTCTATATATGATGGTTTTCTTTCCCCCAAATACCAACAATTCATCATCTGCGTTATATGTA
TGATGTGGCCAATGTTCAGTCTCTTATTTGTTATATCACAATGTTCTAGTCTTCGGGAGTCTTTTCTTGC
ATATGTAACTAAAAAATATTTGTGTTTTTGGTTAGAAAGTGAAATTTACCTATAAAAAAAACANCAAGGG
TATCCG
>gi|3450044|gb|AI100761.1|AI100761 34458 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104A18XP 3', mRNA sequence
TTTACCCAAAGAAAGGTTCCACCGGGNCCNATTGCTCCAATGCTATCGGTTNCATCGTTGGTGCCCAACA
TCCTCGCAGCGGGTCCCTTTAGCGGTGGGTTCCATGAACCCGGCCAGGTCATTTGGACCAGCTGTTGTCA
GTGGTGACTTCTCTCAGATATGGATCTACTGGGTGGGTCCACTAGTCGGTGGTGCACTTGCCGGACTCAT
CTACGGAGACGTCTTCATCGGATCCTACGCTCCAGCTCCCACCACAGAAAGCTACCCTTGATCAATCCTA
TAGCGTTTTAATTTGCTTGGCTTGCTTTTTGTTGTGTGAAAATGTTTGGTCCTCGTTTCTTCCAAAAATG
AATGATTGAATGTGGAGAAAAAGATCAAAGTTGTACTTTGTGTTGGTTATAAATAAGAATTGTATATTTT
CAAATTTT
>gi|3450043|gb|AI100760.1|AI100760 34457 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103P8XP 3', mRNA sequence
CGATATGAACGTGGAATTCNCCCCACTCCAGAAATAAAGNGGAAGCTGCAATTACTNGAGACCGGGACAC
CGAGCTGAGGAAGATCCCAGTGAGCTAAGAAGAAGGCTTAGTCGTGTTGGTGCTACAGAGAAGAGATTTT
GTGTGTGCATGTGTGTTTGTGGATGCGAGTACTCATTCAGGTAATCTTATGCTATGGATTGCTAATATAT
GAAGGTGCTTACAGTTTTGATTCTGGTTTGTTTCTATACAACAAGACAATAGGGTTTTGGTGGGTAAATA
TGCGATTCTACTGTCGTAAACGACGATTGTTATACGTTTTGGGGGTTTGAATTCTAATTATCTTTTACCA
TTACAGATTGTCTCTGTTTCTGTTAAATGTATTCACTCTTGGATG
>gi|3450042|gb|AI100759.1|AI100759 34456 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103P12XP 3', mRNA sequence
CCCCTGGGNTATACTTGTTAGGCTTGACCTCTTGCCGGGGTTGACCTGGAATCCATCTTCTCCATTGCCA
ACTACCCTTGGGGTATACTCCCTTATGGACCATGCCTTGGCCGAAGGATACTCCTCCTATATTCAAATGT
AAAGCTCGACTAAGAAATGAAACAGGCTTCAAAAACGGCAAAAGGACACTGATTTTCTCTACAGGTCGTT
CGTTTACATATTTTTGTGTGTATCAAGCCGTGTTTCTCAACTGGCCGCCTTTGAAACCGGTGTCATTTGA
ATGTTTAAAGAGAAGGATGAAACTTTTGGTGGTCAGAGCAGTTGATGTGTTATGTGTATATTGCCATATT
GGTTGCATTCTCTACTTATAATTATTTTCTTTCTTACATACATTTTGAGTCTCAGTCCTAATAATAAAAG
ACCACTTTGGAC
>gi|3450041|gb|AI100758.1|AI100758 34455 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103O2XP 3', mRNA sequence
GCCTGGTCAATATATCAAGATTAGAAGCACCTNTCCACAGCTCAATGNNATGTTGNATTCAAAANGAAAN
AGNCTTANTAAGCCGGGTGGNTCACAAGGTACTTGAAGANGGACAGNAGGTAAGATATCTGATCAATACA
GGGGAACTCATCGACACCATTGAGAAGTGGAAGCTACTTAAGGAGGCTAAGGATAAGGAAACCACCCAAG
TTNCAGTTACCTCCGCATCTTAGCGTCTCATTTCTTTCTTCTTCAGTGCACTTTTGATATAATAGACCTA
TGCATTGGATGGATGTATTGAAACCCTTTTAAGGTNAATTATAATATTTCTGCTCCC
>gi|3450040|gb|AI100757.1|AI100757 34454 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103N6XP 3', mRNA sequence
AGGCTNGTAGTCAGACCGCCGGAGATNCACTTCCGGCACCGCNTCGTCGGATAGTCTTCCNACCACCGCT
GCTGCTGCNCCCGGCGAAAGTTCCGNCCGCTAAGGCTAAACCTCCTCCAATTGGCCCAAAGAGAGGATCC
AAGGTCAAGATTCTANGGAAAGAATCATACTGGTACAAGAACGTTGGATCAGTTGTGGCCGTTGATCAGG
ACCCGAAGACCCGATATCCGGTTGTGGTCCGGTTCGCCAAGGTGAATTACGCGAATATATCGACCAACAA
CTACGCATTGGACGAGGTGGAAGAAGTAAAATGAGAGACATGGTTTATCTCTAAACCGGTTCGTCTGTTT
GTAATCTTAAACAAAACCGTATGTACCAAAAAGTTAACCAACAATTCATCTTTTATCTTTTACAATCTCA
AGATCGATTTCC
>gi|3450039|gb|AI100756.1|AI100756 34453 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103N4XP 3', mRNA sequence
AGGGNACCAGTCAATGTATCTACNGGGTNCCGTTGAGCACGTCTCAGTACTTCATTGAGACAAGACCGTC
CTCTTGCCGGTTTACGTGGTGGACATGGTATTGTTGCCGGAAGAGATGTTTGGAGAACGTAAGATCTCAC
CGATGGCGCCTCCACCAAAATCAAAATCTCCTGATGTCTCAGATGATTCAGAGTCCTCTAAGAAAGCGGC
TGCTCCGTCAGAGTCAGAGAAGTCTGGCTCCGGTGAGATGAATACTGGATTAGGGCTTGGTCTTGGACTT
GTTGTGTTGTGTTTGAAATTCCTCCTTTGAGTTTGTTTATATATATTGATTTAATTGTGCGGGTTGTAAT
AAGAAATTTCTATATGTTTATTATGATGCATGATTTGAAAACTGAAATAAGAGATTATTATTTCGTGTGC
AT
>gi|3450038|gb|AI100755.1|AI100755 34452 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103N12XP 3', mRNA sequence
AGAGCAAAAGACNGCCGGTTTCTCANCGCATTCATGTCGCNCCGATACNCTTTTGGGNCAGATNCNTGGA
CCGGATACTGAACTTANCANTAGTTTTGTTAGAATGGGAGTATGATTAGGCCATTCATTACAGTTTATGA
TTAGAGGCATGCGTATCCCTTGAGCTTTGGAGTAAGAAAATGGGGAAATGGTATAGATGTGAATGAAGTA
TAATTTTTCCTTTGGTATCATATCACCATCATTTGTCCGTCCATTCTAGCCCAATCTCTGGCAGGCGTTT
AATGTTCGAACCTTAAGTTTGCATTTTTGGTTGCTGGTTTTTAAAAATGTGTTAGTTAAGACTT
>gi|3450037|gb|AI100754.1|AI100754 34451 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103M24XP 3', mRNA sequence
GCTTCCTTCNNCGGCAACAAGTGGATCCTTGTGTTGGAATCGGATTTAGAGCNCCGGATTTGTGTACCGT
GAGCACGGAAACACTCCCGGATACTACGATGGACGGTACTGGACAATGTGGAAGCTTCCATTGTTCGGAT
GCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTACCCGGGCGCCTTCATTAG
GATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTC
ACCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTCATTTCATTTCCTATTGTCTG
TGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGATTGTCAAATGTCTGATTTATGAATATGTAATTTA
TAT
>gi|3450036|gb|AI100753.1|AI100753 34450 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103L23XP 3', mRNA sequence
GGAATTTCCAGTGTGGCGNCCCCACAGCTTGGCATTCCCAACGGCGATCTTAGTCGGCAATCCCCNCCGC
CAATTGGATGCCAGGATGGAAGCAAAGAATCCCCCTATGGAACTGATTAGTGAGGTTCCACCTATCAAAG
TTGATGGAAGGATTGTTGCTTGTGAAGGAGACNCCAATCCGGCCCTAGGTCATCCAATCGAGTTCATATG
CCTCGACCTAAATGAGCCTGCGATCTGCAAGTACTGCGGCCTTCGTTATGTTCAAGATCATCNCCATTGA
GGCAAATTCTGAAAGTGAATTGCTGGTCTCTCTCCCCTTTTTATTGCATTTTTAAGTTTGTGTATTGTTT
TTTTCTGGTGTGCCTACTACATCTTCAGCTATATTATCTAATAAAGGATTCGATCAAAGTCGGGTAAGTT
TGATT
>gi|3450035|gb|AI100752.1|AI100752 34449 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103L16XP 3', mRNA sequence
TTTTCCAAGGAAAAATTTCTGAAAAATTCNGGGACCACNAGAATGCCTTCCAAGCCCGTCAGGCCGCTGG
CCAAGCTGAGGAGAAGAGCAATGTTCTGCTGGACAAGGCCAAGGATGCTGCTGCTGCAGCTGGAGNTTCC
GCNCAACAGGCGGGAAAGAGTATATCGGATGCGGCAGTGGGAGGTGTTAACTCGTGAAGGACAAGACCGG
CCTGAACAAGTAGCGATCCGAGTCAACTTTGGGAGTTATAATTTCCCTTTTCTAATTAATTGTTGGGATT
TTCAAATAAAATTTGGGAGTCATAATTGATTCTCGTACTCATCGTACTTGTTGTTGTTTTTAGTGTTGTA
ATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGAACTTTAAGTTTAATCAACAAAATCTAG
TTTAAGTTC
>gi|3450034|gb|AI100751.1|AI100751 34448 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103L14XP 3', mRNA sequence
CCGGGAAGCTCAAGCCGCCAACGGATCCNAGGAAACGGATTGTGATAGACTTCACTGCAACATGGTGCCC
CACCTTGCCGTTTCATGCCACCCGTCTTTGCTGACTTAGCCCAAGAAGCACCTTGACGTAGTCTTCTTCA
AGGTCGATGTTGACGAATTGAACACTGTTGCTGAGGAGTTTAAAGTTCAGGCAATGCCAACGTTTATCTT
CATGAAAGAAGGAGAGATCAAGGAGACTGTGGTTGGTGCTGCGAAAGAAGAAATCATTGCCAATCTCGAG
AAGCACAAGACAGTTGTTGCTGCTGCTTGATTTGCTTTTCTCTCTTACCTATTTTGCTAAAATATGTTTG
GTGTTTTAATAAATCCTTTGTTCGCCCGAGTCTTTTCACCTTAAATGTGCTCTTATGTGTGGTGGTGAAT
AAATGTTGTTGCAAACTTGATTACTC
>gi|3450033|gb|AI100750.1|AI100750 34447 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103K9XP 3', mRNA sequence
TCCACACCGGTCCCATGGGCTTTCTCTCCAATCTATCCTGGAAANTCCGNTNCCATCGTGGTTGAGTCCC
TCANAGCTTCCGATGTTGAGGTACATGTCCAATATGTTCCAGGTAATTTTGGTGAAAAATGCAGGAACCA
TTCTGGGGGAAACGAGAATACTCACTGGAGAATTGAAGGTTTAATGTTAAGTTCATTGTCGGACCTAGAC
ATGGACTGGGAAGTGCTGCAACAGTCAATGCCGTACCTCAGGACCGTGACCGCAAACTGGTGTCCAGAGC
TAGAGTCTTTCGCGATTGAAGATGTTGGCTTTAGAGGCGGAGTGTGGATGAAAACACCATTGCACAGAAC
CTGATGAAACGTTTTAAGCAACTAGATCAATGTTTATTAAACAGTGACAATAAGTTGGTGTATTACATAT
ACCTTGATACAATGTAATGTTGCTTTGACCGTTTGGATTTC
>gi|3450032|gb|AI100749.1|AI100749 34446 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103J24XP 3', mRNA sequence
TTTGGGCCGNATCCGGAACCTGGAAAACCCNGGAGGGTTTTACCCCCGGANGGTTTATTGATTCCCCTGG
GATTACAAAGGACCATAGCTTTGAGTTGTTNCCATTTGGTTCTGGTCCGGAGAATTTGTCCCAGGAATAG
CTATGGCGATCGCAACCATTGAATTGGGGCTCTTGAATTTGCTCTACTTCTTTGATTGGAATATGCCTGA
GGAGAAGAAAGATATGGACATGGAAGAAGCTGGTGATCTCACTGTTGATAAGAAAGTTCCTCTTGAGCTT
CTGCCAGTTATTCGCATCAGTTTGTAGATGAGCTTGGAGAAAAACATATGGTATGCTTATCGTATAAACC
AGAACGCTTTTTCTTTCTATTTTGTTTTTTGAATCTAATGTTAAATTATATTCAAAATAAAAATAATCGT
TGTTAC
>gi|3450031|gb|AI100748.1|AI100748 34445 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103J22XP 3', mRNA sequence
TGATCCAAGGAGTTGTGGAGCCACGAGGTTGGTAAGANCGGAGTATCCAGACAAGTGATGAAAGGATTGT
ACTATGGAACGAGAGAGAGTGTAGGATTGGCTGCAGAGATGGTGAAGAGGAATTTGGTTGGAAGAAGTGA
GCTTAGATTCTTTGATGGGTATTGTGGTTGGGAAAAAGAGCAGTTAAAAGCAGAGATCTTGGGAGGGTAT
TGGACTGTTGCTGCTTGTAGCTCCACTGTTGTTGAGCTTGGTTCAGCTGTCCAAAGTCATGGTCTTTGGG
ATGAGGTTCTTGGGCTTATTGGGCCTCAAACGGGCTCTGTTATCTAAACCTTGTTTTTGTACTGCATTTC
ACTAATGGTTTATGGTATGACTATGTGTATGGTTTATCAATGTACTGTATGTATTAAACATCCATCACTA
ATTTATATTTGTTTGTTTCTCGTTT
>gi|3450030|gb|AI100747.1|AI100747 34444 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103G2XP 3', mRNA sequence
CAACCGATCCAACCGAGATGGANCTTGATGTTTTCAAAANCCGAGCCAATTGATGAAAGAAATCCCCTGA
AAATTTCGGTTGAATCAAACTTTTTCGTACTATTACNCAGTGATGCTTTTNCCTAAAGTTTGCTGTGACG
GTACCAACCTGAACAGCTNCATTTTANCAGTTTGGNCTTTGNCTTTGTCTTTGGTCTCCTTTTTGGGTCC
T
>gi|3450029|gb|AI100746.1|AI100746 34443 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103G20XP 3', mRNA sequence
TTCCGGGGCAAAACCCGGGTCGATTTCCCCNGGGNTTCACATACATCGNCGATTNTAGTGAAGGATNTTT
AGGATCTCTGGATTCATCGGGTAAAAGTNCCGGNNCGGNTGGTAAAAAACGTGGAGCAGCACGTACCGGA
TATTTAACCTGGGAAACACATCTCCGGTTACAGTACCGATTCTGGTGGATATATTGGAGAAGCATTTAAA
GGTGAAAGCGAAGAGGAACTTCGTGGAGATGCCAGGAAACGGCGACGTACCGTTCACACATGCCAATATT
AGCTCAGCCCGAAATGAATTCGGGTATAAACCGACAACCGATTTGGAAACCGGGTTGAAGAAGTTCGTTA
GATGGTATCTTTCTTATTACGGATACAATACTAAAG
>gi|3450028|gb|AI100745.1|AI100745 34442 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103G1XP 3', mRNA sequence
GGNTAATNATGTTATCAAGAAANGTATNCCTCCTGAAGNTGAGCATCTTAANTACATTAGAGCTCGTATG
GAGNAACTCAATATCAAATCTGCTTGATAAGGTTTTANAAAAATTCTAATGCTCACAGTATGTGTCTTTT
GTTCTTGTGTCAGTTGCTATGTTCTGTCACTTAATGTTTGCTATATTGAAACACGAAAATTTGAAGT
>gi|3450027|gb|AI100744.1|AI100744 34441 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103G18XP 3', mRNA sequence
CTGCCTTAGTGCCGTTGATTGGCTAAGGAGNTTGCTTCCTTCCCGCAACAAGTGGATTCCTTGTGTTGAA
TTCGAGTTGGAGCACGGATTTNTGTACCGTGGGCACGGAACCCTCCCGGATACTATGATGGACGGTACTG
GACAATGTGGAAGCTTCCCATTGTTCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATG
CAAGAAGGAGTACCCTGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATC
AGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATCCCCTTTCTGGAATATTCAGCGTTGAT
TATTCTGGAACCCATTTCTATGTGGTCAATGCAAATTTAAGAAATTATTTGCCGACTTAAAAGTTGAGGA
ACTATTGTTTGAAAGTGAAAATGTTATTCCTATCAGTTTCTCTATAATTATAGTTATCATTTC
>gi|3450026|gb|AI100743.1|AI100743 34440 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103G15XP 3', mRNA sequence
AAAGCCGAGACCNGCCCCGCGNGCCCCGATCCCCGACCCGACCGGGCGGTTACAATTCTCCTTGCTGNGA
ACCTTNCAGGCTCNNTCCTTTNCCCCAACAGGAGACGAGAGTTTACGAAACTTATCGGAGAATCGTGGAG
CATCTCTCTACCGAAGAACGAATGGTTTATCAAGACATTGGATTGAAGGATAAGGAAAGGTATCAGAGGG
AGTTGAATGAGTACAGAGAAACGTTGAGACTTAGGGATGGTGACATGACAAACGGCAAGGCTTTTTAGGT
GATTTAGTTAAAACGGCAAGTCGTTTTGTTGTAGGTCGTTTCTCTCTTTTAAGATTGGACGCCTCGCCGT
TTCTTTTATTTTCTAGCTTATTGTAGTTGTCCATGCTTGCTTAACTAGGCTCAGTGAGAGGCTAGACTTG
CCAAACTTGAAGAGTCTTTATTTATTTAAGAATTTTAGATGTTCTAATGTATTAATCCTTTTTCGT
>gi|3450025|gb|AI100742.1|AI100742 34439 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103F6XP 3', mRNA sequence
GCCACTTTTTTCATCACTCNCCATACAAGCAACAAGNCTTTGATTCTGATTTGGCTTACCTCNGTTGGTT
TGTGTTATTAGAATACCTGGAATTACCGGTGGCTTTGGTTCTTCTCGCCGTGGTGGCACCAAATTTGATT
GCTGGCACATTCAGAGACAGTTGGATTGGTTTAGCTATATGTTTAGGTATTGGATGTTACTTGCTTCAAG
AACACATTAGAGCTTCAGGTGGATTCAGAAATGCATTTACTAAAGCCAATGGTATCTCCAACACCGTCGG
GATCATCTGTCTCGTCGTCTTCCCCGTCTGGGCTCTTATCTTTTAAGTTAACTCTTCAGTTTCTTTTTCC
ATTTGTCTTTTTTTTTCATGTAAGAGTGATTGCTTTGTACGATCTGTCTCTCCTCGTAACTCTATCAATG
AATGTGATTTGAAT
>gi|3450024|gb|AI100741.1|AI100741 34438 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103F4XP 3', mRNA sequence
GGTTCCATTCNGTGGGTTCNGGTTTTGGACCCGATCAGAGNTTCGAGGGGGCTNTCTAGNAGGATCCATT
GAGATCNCAATGTGATGTTGAAGTTGACCCCTTATGCTAAGCCCGCGAAGGGGGATGTCACTGTTAGCTG
AAGCNCAGGGAGTTAAGGCTAAGAAGGAGAAGCTCGCCAAGAAGAGGAAAACCGTTACCAAGGAGGAGGC
GTTGGCAATCAAAGCAGCAGGCAAGTCGTGGTACAAGACTATGATCTCCGACAGTGATTACNCCGAGTTT
GATAACTTCNCCAAATGGCTCGGTGCTAGCCAGTAATAATCTCGTCTGCTTTGGAACACTTTCCATATTT
TAGTCAAAAGATTTTGGTTTTTTTAATCTGTTTTGTCTTTGGGTGTCTGGATATCAAGTTGAATTATGAA
CAAGTTTCACTTTTTTACATCTCCATTTCTT
>gi|3450023|gb|AI100740.1|AI100740 34437 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103E3XP 3', mRNA sequence
CACTTTTCATCCGTGCCNCTAGTGTGAANGNTGGTGGAAAGCTGTGATGATTGGACTCTCACAAGCTGGT
TCCCGTTGGAGAAATTGACATNANTCCGACTTGTTCGTGGAAAGATNAAAGTTATAGGNTCTTATGGAGG
AAGAGCAAGACAGGATCTTCCTAAAGTAGTGAAATTGGCAGAGTCAGGGATTTTCAATCTCACAAACGCA
GTCTCAAGTAAATACAAGTTTGAAGATGCAGGAAAAGCATTTCAAGATCTCAACGAAGGCAAAATCGTGA
GCCGAGGTGTTGTTGAGATACTATAACCAATATAGCCTTTTGATTCTGGTTTGTGAATGACTGCTTCACA
CCTGTTTCACTGAGGTCTATTTTTAGTTGCTACAATCTTCAGACAAGGTCATTGTTAATCTGATATTTGT
GTTTGTTTAGACAGTGAAAAGG
>gi|3450022|gb|AI100739.1|AI100739 34436 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103C8XP 3', mRNA sequence
CGGGATTANCCTTTTAGNCCCTNCACANAATGCCGTNCGAAATGATCCCAAGGATCAACTGGGATCTGCA
ACCCCTTGCACAAGCACAGAGACTCAGAGGTCTCACCTCCGAAGGAAAGAAGAATCGTGGTCTTCGTGGA
AAGGNTCACAACAACCACAAGAACAGACCTTCCCGCAGGGCAACCTGGAAGAAGAACAACAGTATCTCTC
TCCGTCGTTACCGGTGATCAGTTTTATGTTTTGTTTTTTCTCGAACTGGTATATCTTCAGTGTGGATTGT
GTTTCGGAATTCTGGAATTACATTGGGATGGAAGACTTTCACATTCAAGAGTTTGTTTCAAGTTTTGAGT
TCTTTGATTCTGACCATAAAGCAATGTTTCTTAGTTATTACTTATTTTTGATGATTAATTTTTCCCTACT
T
>gi|3450021|gb|AI100738.1|AI100738 34435 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103C6XP 3', mRNA sequence
CAATCACCAGGCNTATCGCGGGCCCTTACTCCTGGGGATTGAAGGGGGNCAGGCAAGGGATTGCAGCCCC
AGAAATCCAGACCATCCTCACAGATCCTGTAATGAGACAGGTACTGTCTGATCTTCAAGAGAATCCAAGC
GCAGCACAGAAGCACATGCAAAATCCAATGGTTATGAACAAGATTCAAAAGCTTATTAGCGCTGGGATCG
TCCAGATGAAATAAACTCAGAAGAGTTGAAACATCGAATATCCGTTTTGGCAGATTCATTTTTTCTCTTA
TATCTTTGCAATCTGCAACAATTCTAGATTTGTGACCGGCTGATTTCCCATGTTTACTGACGTTGTGTTC
CGAACAAATTGCAATCATATTTTCTTCTGATATAACATTTACTGCGATCCTTAAAGTTATGTTGCTTTAC
ATC
>gi|3450020|gb|AI100737.1|AI100737 34434 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103C24XP 3', mRNA sequence
GCAATNTTCCTANCGTGGCGATAAGGNGGTCTGNAACCTGGTTGTTGACCGGTTCGGCTCCGGTCCGGCG
ACCCAAGTGTAGGGTATAATTGGGATATGNGCAATTCTCGATGGTTAAAACTGGAAACACATGATAAATA
TGAAGGCCACGTTCAAGCTGGTTGCTTCTTGGAGATATAAAAAAACTTTAGAAAAGGTTCCGAATCTTTT
GTATGTCGTCCTTGCGAAATGACGGTAAATTTGGTCGGTTGATTTTTTCAAGTGTGACTGTATAAATATT
ATATTGTTATAGATAAATTTGTTAGCTTGATTGTAAAAAAATTATTGTCGAGTGATTTTATAGTTTTTAA
ACTTATTTTTGAAGTTGTTGTGTGATGTTACTAAAGTTAGCGTTAGATTTTATACTTAAAAAATTTAATG
TTAGTCCT
>gi|3450019|gb|AI100736.1|AI100736 34433 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103C16XP 3', mRNA sequence
TNCAGCGAAAGCAAGCGCGNGTNCAACAGGNGAGTGCGTGATGTTGTTGAGCAAAGCTGGACTGCTGACT
AGTAGTAGTTTGTTGTAAGCGTTGTAGCTCTCTCTACTTTCTCTCAATCNCGATTCNGCAACNGCTTTCT
TCTCTTTTCATTCATGTNTTGTGTTTCCAAAACTNTTTAAGTGATTCCATGCTTTGATGTAACCCAACAT
CCTTAAAAAAACAACTTTGTACC
>gi|3450018|gb|AI100735.1|AI100735 34432 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103B2XP 3', mRNA sequence
TTCNCATAACAATCAACCAAACCANTTGNCCACCATGGTTAGGAATTTCAGGTGAGAGGTATTCATCACC
TCTTTANCTCTCTTTTTTACTCTTCTTNCCTCTGTTTCTTCAAGACTAAAAACTCTCTTTTATGTAATTT
GTTGTCATANCTTGTAAGCTGTGTGTTTCTGATTCTATGTAAGAAAACTAAAACCTTTCATTTTCCATCC
TCGGTGGTTGGAGAATGAAACTGTGATTGCAATATTTTACTTTNATCTGAT
>gi|3450017|gb|AI100734.1|AI100734 34431 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103B24XP 3', mRNA sequence
AGAACGTTTTCCGCGGCNCCAAATCTTTTCCCNGATTCGGTTGGGGTAAGGNNGANGGATGGTGGGAAGT
GGNNCCCCNCGGGNGGGAAGTCCACNNCAACTGCAAGCATGCGTAGGAGGAAAGCCGGCCNGCGGTGCTT
GTTGGAGGAGGTGCCTCTGGTGGTGCAGCCGGATCCATGCTTCAGTTCTACACCGATGACGCACCTGGTC
TCAAGATCTCCCCCAATGTTGTTCTTATCATGAGCATCGGTTTCATTGCTTTCGTCGCTGTGCTTCATGT
TATGGGCAAGCTCTACTTTGTCAAATGATGACAAAGATAATAGTTGAAGACAATGCCACCCTAAGTGACT
GCTAGTGATCCAAATATTATACAGTGGTTTCAAGTTAATGTTTTAATTTTGTGGTTTATTACCAGAGTAT
AAACGATCTTTCACAATTCCAGTTTCTTTACATTCAAATTTTCAATATTCTTCACAC
>gi|3450016|gb|AI100733.1|AI100733 34430 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103A17XP 3', mRNA sequence
TGNCAAGAACANTCTTACCACCAAACTGCGGCAATAATNTCCTGCAATTTATGANGAGCNCAAAGNCGAA
GACGGGTTTCTNTNCATGAGTTACAGTGGTGAGAACACGTTCGGGATCTTCTTCTAATGCGCTTGGAATA
TGTGGATGCATCAGATTATCAATGTACAGTCTGTCTATTTCTCTGCTTGTCTCTAGTTTTCATGACATTG
GACGAAGCTTTTGAAACTTGCATGCTATGTTATTAACATGATAAGGTCTTCCGTTCATGGTGTTAATTTG
GCTTTATGCTACACTTAATTTCAAACTTAGTCGCTATANATAGTTGAGTTC
>gi|3450015|gb|AI100732.1|AI100732 34429 Lambda-PRL2 Arabidopsis thaliana cDNA clone 103A14XP 3', mRNA sequence
GGCTTGATTGTTGGATATGGGNACTGCGGTTCCACTGGTCCAAATGTCTGTGTAAGATTGAAGCTTCAGG
TGGTGAGCTCACTGAGACGTTGCAGAAGACTTTCCCACCTGATTGGAGCTCGCATCATCATCACCATGGC
TTCTTAGATCAAGTTTCTGATGTTGACTCCGATGAAGATGATGTTGATGGTGAAGATGGTGAGGACGATG
AAGATGTTAACTCTGTTTCGGATTTATTATCNCCTTACAAGTAAGAAAAAACTGATATTGTAACAACTTA
AGGAAAGAGCAATATCAGCATATTTTTGTAATTTTGTTTTCTTGTGTTTTACGTTTTTGCAAAATAAACC
TTATTGAACG
>gi|3450014|gb|AI100731.1|AI100731 34428 Lambda-PRL2 Arabidopsis thaliana cDNA clone 102B8XP 3', mRNA sequence
TGTTAAACCGGCTTCNCCCCGCCATCCTCCTCAGGATTGCAAATTTTGCNCNTTTAAGGAGGAAAGGCCC
CAAATGCCGGGCTCTTGATATAANCCGGGAGGATTCAGNAACTCTCTGCTTTGACACTGATGGGAGCTCC
GCTGGTTGATATGGAGATCAGAGGTGTCCCCTGCTCTGCGCTTCTTGGGCGATATCATTTGGAAATAAGA
TCATTACATATTATCNCCACAAGGATGAAGAACAAGCAGGTTCACTTGTATGAGATAGTGTTGGTTAATA
CATTACATAGTTTTTGGTATAGATGTTGATGTTTGTCTTTGATGGGTTTGGTCTTTGGCTAAAAATGAAT
ATCGACGAGTTTTTCAAACTGTTAACAGATTCAGTATTTGCTACATTTTGGTGGGTGT
>gi|3450013|gb|AI100730.1|AI100730 34427 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147K6TM 3', mRNA sequence
GATTTGGAGTCNTATAACGTCAGGGAATCAAACTGTCCANTCCATGGTGTGTGCTGAAGGAGACCTNTCA
GACAAGTCNCTTTCCTTGCTGGGGAATTGTTCTTGGATGGTTCCTGTTCATTGTTGGATTTTTCCTTGGA
GCAATCCCTTGGTATGTCGGATTGTTCATCATGATGTTTGGAAGGAGAATCGATTACAGGGAGAAACCAG
GATACATTGCCTGCACTATCGCTGCTATTCTAGCAACAATCGCTGTGATTCTGGGTGTATCTAAAGGAGC
AGACGACTGGTGATGGATCAATCATCTTGTGGGGTTACTCTAAAAATGTTTGTATAGGTTTCTTTATCGT
GTGTTGTATTATCTACTTCCTTTTTTACTTACTCTATGAAGAAACAAGAAAAAAAAAAGTGTAAACTTCA
CAAGAATTATTTGAGTTTTGTTATCTAAATAAGAAGAAGTC
>gi|3450012|gb|AI100729.1|AI100729 34426 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147K5TM 3', mRNA sequence
GACCAGGGNGTTTTCTAGAANATCAGAATATAGTTCGCANNTAGAGTGGGAGATTACNAATNGCAGTGAG
ACTTGGCACTCACTTAATCCGGCCTTCAGTTNTTCTTCGCNGATCAACCAAGAAGACGGTGACATTTTTC
ATCCCCCCAAAAATCAGCAGATGGTAGCATGGGGACTACGGGTAACTCGTCTTCCTTTCCTTAAGGATAG
ACATGTCAGATTTCAGCATATGGACTACAGTACATACTACATAAGTTGGGGACACTCTTGAACATTGTAC
ATTTTACTGTAAGTCTTGGTAAATAAACTGTTTATATCGTTGATCATTTCTCATTTGCAATTNATGTGTT
ACCAATGCAATGCTCTTTCTTATTNACCCGAGGGGGTAACTCTGTAACATTGAGGGTGAGAGTGTGCAAT
CTGTAGATATTTCCTTACCTCTTAATAAATAGAAATTTCTC
>gi|3450011|gb|AI100728.1|AI100728 34425 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147J24TM 3', mRNA sequence
GCCAGTCATGGGGGGAAGGCCGGNTTGAATTTGGGNTTGACCATGTATTGNCACCATATCCTTTTTTAAC
GGGGAGCTGGGGATTGTTGNTCAGATAAATTCACAGTTTGCNGATGCCAAATGGATCAGATAGGATCACT
TCACATACATTCAGGGANTTCTTAAAAAGACCATCGAAGACCCTGAGATCAAAGGGTGGTTAGCTTTGGG
CATCAAGAAGAAGAAAGGTGGTGGAAAGAAGAAGAAAGCCCAAAAGGCGGGAGAGAAAGGAGAGGCTTCA
ACAGAGGCTGAGCCAATGGACGCAAGTAGTAATGCTCAAGAATGAGTAGGAAGATTTGTCTTTGTTTCTT
TTAAAGAATTTTTGAAACTTGAGGTACCTCTTTCGTTGTATGTTTGGGTTTCAAGAGAGT
>gi|3450010|gb|AI100727.1|AI100727 34424 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147H10TM 3', mRNA sequence
GGGACCGGACCCCCTTNTCAGTATATTCCTAGGGATCCACGGGGGNGGTTGNTTTTTTAAGGNGGAGGAA
CAAACAGGGGNAAGGTACAGGAGGTNGAATNGTGTAAGTCGATGGTTCAATACCCAGGAAGCACGGGGAT
CAATACCGTAGACTCCTAACGGTTGTTGAGGGCTTCCGTGAAAATGAGGCTTCATCAAGTGCATCTATAA
ACAATAAAGAAGAAGAAGCAGTCAACTGTGAAGAAGACGATTTTATTGACATTGAGTCTCTTTTGAACGA
TGACACATTGATGATGTCTATTTCTCCTTGATTTTACTTTCTGACTCGTATTCATTTTTCCTTCTTTTAC
TTTCTAACTTTATTTCTTCTCTGTAAATACCATAGTTGATATTTACCGCTTAATTTATTACTTGGATTGA
AAT
>gi|3450009|gb|AI100726.1|AI100726 34423 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147G6TM 3', mRNA sequence
AGGGNAAAATTGAGAAGATNCCGAGGAGAGGAGTGAAGTTGAGGANTTTTAGGAACCCNAAAATTTTTTT
NTTTGCTAAACTTCAAANGAATCAAAACCAGCAACAGTCCAAGGTGTTCATCAAAGTCCCCTTGTTCAAT
CGAGCGAAGTCTTTCAACAAGGTTTTGCGAGTCTTTTATCGACTGGAGATAAACCATGAAACACTGGAAC
ATCGTCGCACATATATATAGATTATACAAAGCAAAAGAATTCTCAAGGTGTTGTCTCATTTTTTCCTACC
TAAATACCTCACTTCTTTAAATGACAGTTGAGTTCTTCTTTGTTGTAAGCTATAGAATAATTTGTTCCTT
CAATCATTCATAATTTGATCTTATTCCATTTT
>gi|3450008|gb|AI100725.1|AI100725 34422 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147F18TM 3', mRNA sequence
GTAAANACCNGGAGGGGGGGAGCATTGAACGGNTNGAAGGGGAGGGGTTGATCGTGCGGATGTTCTGGGA
AGTGTTTTTGGCGTGTAAACAAGAATGAAGAAATTGCAGCTAATTACCTTCTAAGATCAACATGCATGGA
GTTTGGAGGATCAATAAACAGAGCAAATCCATTCCTCCCTCTAAACTCAGACCATCTTTCGGTTTCTTTT
TCTTCTTCTTTTNAAAANGATAATTTTTTCTCCAATGCCATTTGACAGTTTCATGTTTATGTTCATGGGA
GTTGATGTGTTTATGTTACTATTAAAACTATCATAGTTTATCTGGTTTGAAGATGCTCCTCTTTTATCAT
ANTATTAGCCTTTGAATC
>gi|3450007|gb|AI100724.1|AI100724 34421 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147E14TM 3', mRNA sequence
TTAAAGGNCCANTCAGGGTTGTATAGAAATCCAGGGGGTGGTAGGGAGCATTTCAGCATTCAGGAAAGGA
TGTTTGGGCAAAATGTTATGGGGGGAGATATTTTTTCGGGAGGAGAGTTNTTAAAGAAACAGGCGGCAGG
TAAGAAGAGAATGAAAGCCATAGGTAGAGTTGATGTCCCTCAAGAAGCTTTCATGGCCGTTTTCAAACTT
GAACGAGAAGTATTGTGACATNTTGNGGGTTTTTCCACTGAGTCACTCAAGATTCACTACATCATATTTT
ATTTTATCATTTTGTAATATTNTGCAAACTAATTTCACATAATGCAATTATTTTTCGCATTTC
>gi|3450006|gb|AI100723.1|AI100723 34420 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146P14TM 3', mRNA sequence
TCAGGCGGTTCATTGGTTTTCAGGGGAATTTCAGGGATGGATCCNTCAGAGATNCCGTATAGCACAAANT
CATTNACNTCNTCATACTCCAAAGANCCATTTCAAATTGGTCAGCCCCTTTGGNTCCCATTGGAGCACCT
GANTCAACCACAAGGAGAAGAAACGATATTAACAAAGAGAGAAGAATGGCTTCTAAGGTCAAAGGCAAAA
GAATCGTTGTTTGAGATAATAATTATTATTCATCTCCAAATTTCAAAAGTTTCCTTTTTGATAGATTGAG
>gi|3450005|gb|AI100722.1|AI100722 34419 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146K17TM 3', mRNA sequence
AAATTTTTGTNGATTCCCAACCGGAAATGNTTNATCTGGAANGTAAANTTCAGGATGGCCCGANGAAGAT
TNGTTTCAGATTTTAAGATTGNTGGGAAATCACTACCACAAAACGGTAAAGGNGGTGTAATAGAATTAGT
CACTCCTGAGGAGGAGAGATGGGACATCAACGCAAACATTGCCTTTGACATGGACATGTTAATGTTCACA
CAATGTTCCGGAGGAAAAGAGAGATCAAGAGCTGAGTTTGAAGCTTTGGCTGCAGCTTCTGGCTTCTCCC
ATTGCCAGTTTGTTTGCCAAGCTTATCACTGCTGGATTATTGAGTTCTGTAAATAATATGTCTAAAATTA
TAATTAAAACTAAATCCTCATAATTGTTAATTTCATCTGTATTTCAGTTTTTTGTTTGAAATGGTCATGC
CTCTCTTTGTCTTTCGAGCAATATGAAATAAAAATCTTTTCTATTTTTG
>gi|3450004|gb|AI100721.1|AI100721 34418 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146H12TM 3', mRNA sequence
GGAAAAATTCCCGGGAAAATTNAGNTGGGGAGNAAANCTGGACAAGGNGGAAGTTTNCCATTTGTTCGGA
ATGCCACCGATTCGCGGTTCAAGTTGTTGAAGGAAGGTGAAAGAATGCAAGAAGGGAGNACCCTGGCGCC
TTCATTAGGATCATTGGGATTNGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCC
CCAAGGTTCACCGAAGCTTAATCCCCTTTTTGGAATATTCAGCGTTGATTATTNTGGAACCCATTTTTAT
GTGGTCAANGCAAATTTAAGAAATTATTTGCCGANTTAACAGTTGAGGAACTATTGTTTGAAAGTGAAAA
TGTTATTCCTATCAGTTTCTCTATAATTATAGTTATCATTTCATTTCATTTTTG
>gi|3450003|gb|AI100720.1|AI100720 34417 CD4-16 Arabidopsis thaliana cDNA clone H7B3RP 3', mRNA sequence
GGAACCAATTTCCNTCTGTTGTTTTNCCCCTAGCTACCCCNTNTCTTGGTCATCGGTGGCTATCAGGCTA
TAGACTGTGGAACACAATGGAGAACAAATGTATGACNTTAGCAGGCCACGAGTGTGTGATCTCTGCCTTG
GCTCAGTCGCCTTCGACGGGANTGGTTGCGTCTGCAAGTCATGACAAATCCGTAAAGATTTGGAAGTAGA
AATATTTCTATGTTCGTCTGAAAAGAAAAGGAAAAAAGAAGAAATAGCAGAGAGCTCAGGACTTTTTTTG
GGTCTAATTTTTTTTTTTTTTTTAATGTTACATTAATAAGTTGGTTTTTTTTTTAAATTGGGTTTGTTTA
TGTCAAAAGCAAAGAGACTTGTGATATTTC
>gi|3450002|gb|AI100719.1|AI100719 34416 CD4-15 Arabidopsis thaliana cDNA clone G2A1RP 3', mRNA sequence
TATTGGAATNATACAACGGTCCACNTTTTAAGGGACTTCCTCAATGTACTTCTGTTGTTGGGACCCCAAC
GGAAGATTGGTGGCGTCTGTTAGTGAAGACGCTGTAAAATTATGGTCACTGGAGTTCCAGGAGATTGCAT
CCCACGAGCTTAGCAACAGTGGAAACAAGTTCCACTCTGTTGTTTTTCACCCTAGCTATCCCGATCTCTT
GGTCATCGGTGGCTATCAGGCTATAGAGCTGTGGAACACAATGGAGAACAAATGTATGACGGTAGCAGGC
CACGAGTGTGTGATCTCTGCCTTGGCTCAGTCGCCTTCGACGGGAGTGGTTGCGTCTGCAAGTCATGACA
AATCCGTAAAGATTTGGAAGTAGAAGCGGC
>gi|3450001|gb|AI100718.1|AI100718 34415 CD4-13 Arabidopsis thaliana cDNA clone E4D12RP 3', mRNA sequence
CCCAACTTNAAGACCTTTAAGGACTGNTNTTCAAAAGGGTTNTGGAAANTGNAACCACCGNGGATAGCCC
TTACTGACAANTCCCATTNTGGGATCAGGCTCTCGGGAAAGCATGGGNATCCATCTGCGTTGAGGATCTC
ATCCACGAGATCATGACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTCCTGTGGCCATTCCAATTGA
AGGCACCACTCGGTGGCCTTAAGAAGAAGAGAAACCATACGTCGAAGGTGGTGATGCTGGAAACAGGGAG
AATTTCATCAACGAGCTTGTCAGGAGAATGAATTGATGAAAGCTTCCTTCTTTATCTTTGCAAATTTCAA
AGATTTTGGGACCGAGTTTTTTTTTTTTTGTTCAAGTTATCAGAGACTTGTGATCTTTTATCCGAGATAG
GCTTTTTGCGGCC
>gi|3450000|gb|AI100717.1|AI100717 34414 CD4-13 Arabidopsis thaliana cDNA clone E1D6RP 3', mRNA sequence
TTCACACCCTTTAATAACGGTGGCAAAGTTTGCATTNTNCCCCCNTGNCNNTAATTCCCCTTNGGGCCAN
AAGAACNTTAGATAACCCTTTGGGTATACATACCCAACAGGACCTCCCCCATCCAACATTGGGGGAATCC
AGATCTCTCCGGCGTTGACTNGATGGTTGGCTATTGATGGTCAAGAAGCCTTTGGAGTTGACTTTTATCA
GTTGCTCGTTTATTATCCTTGTCTCTGGCTGGAGTCCATCTAATTCAGACCAGGGACTGCTTTTAAGGTT
TCCAAGGCAGAGCTCCTTGAATTTCTCCTGAATATCTTCAACACTTTTCAGTGGGACAACCCATTCTTGT
TGAAGCTTCTTGTCACGTGCTCGCGGACGTGAGAACTGATGATCCGAGAGTGCGCGGCC
>gi|3449999|gb|AI100716.1|AI100716 34413 CD4-13 Arabidopsis thaliana cDNA clone E1B6RP 3', mRNA sequence
CCTTGCTTNAATCCTTTGGGCNCCAANCCCTTTCGGAAGTTANAGACNNTTNTTGTAGGNAGTCCCACAA
ACTTGTCGTTAACGGATACATGAGAGTTATGATTTCGCCGTCAGTTTTTAAAGAGTTCATACATAGATTT
AGCCCATGCAGGTCTCATCTCCGGTTCAATGGCACAGAAGAACACATAATCGAAGATGAGGTCGAATAAT
TCAGTAGGACGCCACGTGAAAACATCTTCCTTCACGAACGAAAAGTACTCTGCCTTTGGTGAGGAGCCGT
AAGTCTCATTAGCTTTCGCGAGTGCGCTTTCGGAAATATCCAATCCAACAACGAAGCGTTCAGGACTTGC
CATCGCAACGACGTCGTGTCCTCCACCACAGCCGGGGACCAGAGCACGGCC
>gi|3449998|gb|AI100715.1|AI100715 34412 CD4-13 Arabidopsis thaliana cDNA clone E12A9RP 3', mRNA sequence
AAATGNTGGNGCCATTCTACGTGGGAGAGATTGATCCACNACATACCAAGNAAGTCAAATACACCCTCCT
AAACAGCCTCACTTACATCCAAGACAAGACCTCTGAATTCATAATCAAGCTCCTTCCAGTTCCTCGTACC
CCTTGCCATTCTTGGTTTAGCAGTCGGAATCCGTATCTACACCAAATCNGGGTAGGCTTCTTTTTTTTCT
GAGCATTACTTCCTTATATCTTATATATAGAGAGAAAGATTCAAGTCTTTTGAAAAGACAAATCTGAAAG
TCTCTCCCTTTGTTATTGTCTCTTCCCATATTTTGCTGTTTGAATGTATTTTGGATAATTTCTTATCTAT
TGTGGTGTAAGCGGCCG
>gi|3449997|gb|AI100714.1|AI100714 34411 CD4-13 Arabidopsis thaliana cDNA clone E10E12RP 3', mRNA sequence
TCCAATCNTGGCCCCCNAGGGAACNTCTTTTNTGAACCCTCNATGGNAAACCCCCCGTTCCCCCAAAGGG
ACTTTGGGACTTAATCTCCCGGATTTCAACNTCAGNTTCTTTGGGAAATGGNATCTCTCCACATTTCTCC
AGCGGCAATGTCAGTCTTCCCAATACTGGCACATCCCACAATCAGATCAACCTTGATTCTGTAAGGTATG
ATCATCCCGGGGTTGATATCGTTGTAAGTGCTCTTGATGTCATCATAGATCAACGTCAATGGTATCTTCA
CAGTTTCTTCTCCATGAGCCTTGAGTGTTCCAGCATCCGGGATCAAACCAGAAACCAGTTTCCTCCCATC
GCTCTCGACCAGGTAGTTGACATCGATGAGAGGGATAGGAACTGGATTCGGGTTCTTGACAAGCACATCC
ACAACAATATGCGGCC
>gi|3449996|gb|AI100713.1|AI100713 34410 Lambda-PRL2 Arabidopsis thaliana cDNA clone 48C3XP 3', mRNA sequence
AANCCCGGNAACCAAATGATACGGTTGTTTGACCCGGNGAAGTGTCTTACTCCGCCGCNGGTGGGTCCAC
TTGTAAGATTCNAAGAGCCATAGTTGTTTATCTGGCATCTCAGGTCAATAATTTTATCATTTCAAGAAAA
TTCTCAAATTCAGANAAAAAAAAAAAAAAATTTTTTAGGAAATTTGCATTTTTATTTCGTGTTGTGTTTG
ATTTTATGTACAACGAATCATGTAGATATCGTTATTTTGTGATCTTTTGATGTATACGTAAAGTTTGTAG
TTGGGGTTTGTTGTTAAAATGTATATTTGTAAGGTCATAAACGAGAAAATGAAAACTTGTATGGACCAAA
CTAGAAATAATGTTAATAACTCTCC
>gi|3449995|gb|AI100712.1|AI100712 34409 Lambda-PRL2 Arabidopsis thaliana cDNA clone 246E4XP 3', mRNA sequence
GCTTNCCTTTTNCCNTTNTTGGANTTAAGCCAGGCTCGTANCCNTTATGGCGGGTTTTGGGNGCATCACC
TTACCGCCNTTTTCGGTTGAAACAAATGGATTCATGCTTTGGGCCTCACTGGTTTTCTAATTTCTACGNA
TAGTTGAAAATAAGCNAATAAATACTACGATTTAAATTAACGGATATTGGGATTTGGGTTTGAGATGACG
AAGTGAGGTTTTTTTTTTTTTTTTGTATAATTTCTTCTTATGATGCTTCTATATTATGTCAGTCTCTTCT
CCTCCATTTCTCTTATTGTGCGTTGANGTATTCTCACATATATATATTATGATAATTTAATGTNATATTT
ATNACTTACATTTATATTGT
>gi|3449994|gb|AI100711.1|AI100711 34408 Lambda-PRL2 Arabidopsis thaliana cDNA clone 231F12XP 3', mRNA sequence
CCGNTTTCCCTTTNACTCCCAGGTCNCNATTTTGNGCTCNCCGNTCCTTGGGGGACTGATTGNCCGTTNG
TGAAAGAGAGCCNAAGTGGTAGCTTTCATAAAAGGATCAAGGAGTGCTCCTCAAATGTGGATTCTCACAG
AGAGTTGTTGGGATTCTTGAAAGCCAAGGAGTTGATTATGAAACTGTTGATGTTCTTGACGATGAGTATA
ATCATGGGCTAAGGGAGACGCTTAAGAACTACAGCAATTGGCCAACGTTTCCACAGATATTTGTGAAAGG
AGAACTTGTAGGAGGATGTGATATTTTGACCTCAATGTATGAAAATGGTGAACTTGCCAATATCTTGAAC
TAGTTTCATCCGATTTTCTTCTCTATTTCTAGTTGTAACTCCAAACATTCATTATAGAGAAAACATGCTT
GGATTCTCTTC
>gi|3449993|gb|AI100710.1|AI100710 34407 Lambda-PRL2 Arabidopsis thaliana cDNA clone 214H4XP 3', mRNA sequence
CTGCCCANTGGTNATCNACCTGGATCTNTGATCCCAGATGGGGAATNTAGGTGAAGTGATCAATCATTCC
TTAGGACTGNCCCGAAAGAGNNCCTACAATGCAAGAAGTCACAGGATGGTTACGGGAGATCACGGGATTG
TCACCGAACGATGCTACACCGAAATTGTCACCTCTTTGGTGGGCAGAGTTGGAGGTTTTGTCCACGGCGT
AAGAGAGACCCCTTCACTAATAAAACTGTATATATTTTGAAGATGTGAGTTTTGTAAGTGTCTGTTTTAT
TTATCTCTCGTAATATTGGTAAAGCAAAATTGAAGTTCTCTTCAAGTTTAGTAAATTTACAAACATGTAT
ATGATAAATTAGTGTGCATATCGGAAAAAAGTTCTTGTGAAAATTATATCCGTTTTCTTCT
>gi|3449992|gb|AI100709.1|AI100709 34406 Lambda-PRL2 Arabidopsis thaliana cDNA clone 204J16XP 3', mRNA sequence
TTTTGTCTAAGGTACAAAACGTGGTNGAAAAGCCACATTAATGTCCNTTTTGCCATTNTTGGAAGCCAGC
AGGTTTGTGTNATATGGCCATCATATCACAAGTTCAACAAGTGAATCTGTTCGCNTTTCATGACNGTAAG
CTTCTTATGGNGACATGTCAAGAAGCCAAAAATCTGCGCAAGATTGTCACTCTCTTCTNCCTCGATTGAT
TCACATTCACTCTTTATTTTCTTCTCGTTNCAAAACAGNGAAGATAATCCTCCTTGTAAATTATGAATCT
TGATTAAACAAACACACACAACCNCAATTATATTCTTTTGTCTAAATTTTGATACACATC
>gi|3449991|gb|AI100708.1|AI100708 34405 Lambda-PRL2 Arabidopsis thaliana cDNA clone 176M9XP 3', mRNA sequence
CTTTCGGTNCTTNAACNTGGCNATNNCGNGTTTCACTTCCCGAAAGATCCNCCCCNTTGATTGGTTTNCA
ACTAAGGGCTTGGGAGTTCCCNGTGTTCAGTNCGCTGCTGGAGGANTGGCGACNCCGGCGGATGCCGGCG
TTGATGATGCAGTTGGGATGTGATGGAGTGTTTGTTGGGTCGGGTGTTTTCAAGAGTGGAGATCCGGTGA
AGAGGGCTAAGGCTATTGTTCAGGCGGTTACGAATTATAGAGACGCGGCNGTGTTGGCGGAGGTGAGCTG
TGGTTTAGGTGAAGCCATGGTTGGTCTTAATTTGGATGATAAGGTTGAGAGGTTCGCTAGTCGTTCTGAG
TAACCAATCAAATTTCAGATGTTTTTATCCATAACGTTTGTCACTTTAATATGTATCCACAAACCAATAT
TCTCGATTTATTCAAGATTTTATAG
>gi|3449990|gb|AI100707.1|AI100707 34404 Lambda-PRL2 Arabidopsis thaliana cDNA clone 172L4XP 3', mRNA sequence
CGGGGCCTTTCAACGAGCCAGNGTTGGACAACTGCNTNATATCAACGGGCTATNATGTTACAACACNCTT
TGNAGACAACTNTTGCGGATGTNTTGAACATGTATACTCTAATCACCGGAAAGCAACTGGACCTAAGTNT
TGACCTGAGTGCCGNAAGTNCTGCAGAGGAATGAAGAATCACCAGATCGCGCTCTCTCTCTCTCTCTCTA
GTTGATTTTCTAAAAGCTTGTTTTGCTCATTTCTCTGTTTCCGACTCTTGCTTTCGTGTTCTTTTTTGGT
TTGAACTTTGAATACAAAATCAGAATGATCCTTCATGTTTNGCAACTAACAACCATGTGTCTCCGTTTGA
TGTTGGATTCCTCGGTTAAAGACTTATAAATGCTCTTT
>gi|3449989|gb|AI100706.1|AI100706 34403 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162J6XP 3', mRNA sequence
TTCCAAGGAGGAGGAGGACGATCCCAAGGAGGCCGTGGGCGACAAGGAGGAGGGGGAAGTNGGGGAAGTT
ACTGCCGCCACGGCTGCTGCTACNGAGGTTACAACGGCTGCTCANGATGCTGCTCGTATGCCGGAGAAGC
TGTTCAGACTCAGCCCGGTCACTAACACNATATATTANCCAATCACCNCCATGCATGTATTGCATTATGT
ATGTATGCATTTTAAGTAAACCATGGTGCGTTTGTAATGAACTGCCTCAAGTTTTTGAGGCNCTATAGAT
TAAGAAGAGAACTATGGGAATAAAGTTTGATTATGTAATGTTTTATGTGGTTTGAGTTGTAATACTTGCT
GTTTGCATAATAAAATCGTTTGTAGTTTATGTT
>gi|3449988|gb|AI100705.1|AI100705 34402 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162J1XP 3', mRNA sequence
CAGGAGGTTGTTGCCAGGTGCAACGGAGTNTCATGTGCCCAGGACCAGCTGCAGAGCCAGTCAAGAAAGA
GGATGCATGAAGCTAAACTGGTTGAAATCNATGGGGAAAGAAGAGGTTCTCTTGGGAGCNGCAGTAGTNT
CANTGTCGCAACCGTTGCCGTGNTTACAGCATTTACAGAAGGTCAGGTTAAGAACCTGAACCACCCTCCT
CTTTTTACACTTTTAAGNAGAAACTTNATTTTTGGTAGCCNTATNATAGAAGTAAAGGAAGAAAAGAANA
CATGGAGAGGTNATAATCTTTTGGAACTATATAACCATCATTTGGTTTCGGTATGGGCAATGCAGGAATG
GGATGTAATCTTGCTTTTGACTCGGTTTAGTTTGGTTTATCTTATTATGTTGTCATTGGAAT
>gi|3449987|gb|AI100704.1|AI100704 34401 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162J11XP 3', mRNA sequence
AAANAGAGAGCTGCTGCGTTCCAGCGGGCTTTGTGTAGAGCAAAGAGTTTTGCCACGGAATGTNTTTGTT
GTCAAAGTNGTCGTATATCTGGTTATGGGAAAGTGACAGATTTAGNNNAATTAAGTTGAATCCCTTNTTA
GTCATATGCATTAAGTTAAGTAAACTTAATAAGTTGTGTGGCTTAGAAATAATATTGTTTTGTCTATTTT
TGGAGTGGGTTGCTCTTGGNGTGTAGAAAAATGTCACTCTTCATTGGATTAAGTGATATACATTTTTTTG
TTC
>gi|3449986|gb|AI100703.1|AI100703 34400 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162I9XP 3', mRNA sequence
GCCCCAGGGGTTTTGGAAGCCCCCCCGTNCNNGGCTATGTANACATCGTTGCCCCTTTCACTGNCTTTGT
AGCTGTGTTTGTNCGGTTCCNNATCATAATGTTGAAGAACTCAGCAGATAAAGAAGAGAAGAAGAAGAAA
AGGAGAAACTGAGGGGATGTAAAGTAAATTTAACTTTATGGTTGTTATCCGTGTGTGGCCACTTTGAAGA
TATTACTTGTTAGCACTCTCTATTNGTGACCAGACATGTTTCCACTNAAAAGGATCTGCTTGTTTCACTT
CTGCACAAGTACCATCTTCAGATTGTAAATGACTCGNGTGTTGTTCTTCTTTTCATAAACTTTTGTTCTT
TAAGAGTTTGGTTCTACTGATTGCATCTTA
>gi|3449985|gb|AI100702.1|AI100702 34399 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162I8XP 3', mRNA sequence
GTCCCCAAGGNCATGCNTTGCNCCGATTGCATNGGCCCGGTTGATGTGTNCAAAGCCGTGAAGTTATTAG
NTAGTCACCCAAGAGCTAGGAGGAAAGATCACTAGAGAAGCCGGCCCTCTTCCTGGACTCGGCACCAAGA
TTGTCTCATTCCTTGATCCAGATGGCTGGAAAACGGTTTTGGTGGACAACAAAGATTTTCTCAAGGAACT
GGAATGAGAAGAGCGATGAATGAAGGTCGAGATCACAAAACCATAATAATAAAAATGTGATCATAAAATA
AAAGGAAGACTTAGAGTTTGATCTNAAATAAGAAGATGTGGTTTAGTTTGTGTCGTGCTATGTGTGTGTG
CTCGTTTCTTTTGTCTTTGAGCTTAAAAGTTAAAACTCTAGTCTATATGGACCTGAATNAAAATATTTCC
ACC
>gi|3449984|gb|AI100701.1|AI100701 34398 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162I10XP 3', mRNA sequence
GCTAACGAGACNAAATCGTATACNGTGACGTTTACTGTAGACTCGTCGAAGCCGTCTGGCTCTAACAGCT
TTGGGAGTATTGAATGGTCGGATGGGAAACACGTGGTGGGAAGTCCCGTGGCGATTAGCTGGACATAGTC
GTCAATTATGAGAAATGAAAGGGGTNTTATGGAAAAGCAAAGGTGTTTACAGATTTATTGTAATGCCGTT
NTTAGATACGAAGAAACCTCTGTTTAGCAAAAACGACATGCAGTCTGTTAAGACTTGCCTAGTTTGTTTT
TGGGATGTCTTGCTGTTTTTAATTTTAAACNNAAATATATTCTCCGGCTACAACAGTAGCTGGGTCTCTC
TAGGTGTTTTATC
>gi|3449983|gb|AI100700.1|AI100700 34397 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162G2XP 3', mRNA sequence
TGGCGCCCCTTGGTTGGCCGTACATTTNCAATNCCCGATCACAAATGTGATCCATCCCGNGTATGAAGAG
GTGGTTCCTAAAGAGGGAATGCCACTCCAGAAAGCTCAGACANAGAAAGGGCACTTAAGGATCAAGTTCN
ATATCAAGTTTCCAGCGAGATTAACTGCGGAACAGAAAGCTGGGTTTAAGAAGCTTATTGNGTGATGATT
AAAGCATCTCTGTCTTGTGATGTGTGGAGATTGGGATNAATTTGGTCATATNCCNTTTATAGGGAATTAT
CTCCCTCTTCATTAAATTTCGTGTTGTTAAACAAGTCTTCTTTTTAAAGAATAGTTTTTTCAAG
>gi|3449982|gb|AI100699.1|AI100699 34396 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162G21XP 3', mRNA sequence
AAGGAGTTCCNGCACCNACATCATCTGTCCTAATGCAGGTTACCACAAGCTCATTTGAGGCCTTTGGAGG
CAAAGGTTATATTGTGGAAACACCCGATGAGCTTAAATCCCCTCTCGCTGAGTCGTTCGCCGCAAGAAAA
CCCGCGGTGGTAAATGTTATTATTGANCCTTTTGCTNGTGCTGAGAGTGGGAGATTACAGCACAAGAACT
NAAAAGCTTTGTGGAGAGTCCCTTTAAATAATGTTGAAGTTGTTTGTTGTGAACAAAAAGGATATACGTT
TTAGTTTTCTGTTTTTCACTATTGTAAACCGGATCATAAACCGGTCCATTTTAAACCATAATTGAATAAA
AACACGTTTCCGGTTC
>gi|3449981|gb|AI100698.1|AI100698 34395 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162G1XP 3', mRNA sequence
AAGGCCAAAAGGGCTCACACTGGNCAAGTGGTAATCATTGTCCACACGCTCTCNAAATAGTCGAGGTCAC
GAGGTTAAAACGCCATTGTTGTTGGACTGTTCTAAAGTCAGCTAGCTCACCGGACAGGTTGCTTGTTGAA
TGAAGGGAAAGTCTCGAGTTGGTGTCTGATGGGTTNTTAGAGGCTCGTTGTGCACAAGTGTTGACNTCTT
TCCTNTATTATTTTGTATTGTTTTGGACAATTTATTTCAGCATTTTTACACAGAAGATTAGACATTACTA
GAGAAATTCTAGCAAAAGCTTGGTTGTATTTTAGTGTATTTNTCTNTTTTACGTGGATATNTATTGCGAT
ATCTTTAATNTCATTCGAACTCTTTCTTTTGC
>gi|3449980|gb|AI100697.1|AI100697 34394 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162E9XP 3', mRNA sequence
GGCCCCTTTNCNCTGGNTTTAANGACCGNCCACNCGNTTTTNTCCCACTGGACCCGCATTGATGATGGGA
AGAAAGTGGCAACGGATGAATTTGTATTCCACAACCAGTACTGGGGAAAGNACATTCGACGGAGAAAGCT
TNAGAAGCNTTATATCAGGAGTGTTGTTGGTGGCTGGATCGCCACTTAATTCACTAAGTCTGCCTCATGC
TTTGTATCAAAGTGTGTGAGGATATTCTTTTAACTCGGAACTTATTACTTAATTTGATGTTAAATCTCTT
TCCCGCTTAAGTTTTCAGCAATCTGGAATATGAAGGGAATTATGTATTCTTATCAGTCTTTTGATGAAGT
GAGGTCTACTTCTGGGATT
>gi|3449979|gb|AI100696.1|AI100696 34393 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162D11XP 3', mRNA sequence
GCATTAGCTTTTCTCANCCGGTCTCGGGCATCGTCGGGAATCNCCGGGAAGNTCACCATGGTTGCCGATN
ATCTCAACAAGGCCGTCTTTACAATTTCTACTGGCTTGTGGCCGTACTTGTTGCCTTGAACTTCCTCATT
TTCCTAGTTTTCTCCAAGTGGTACGTTTACAAGGNAAAAAGACTAGCTGAGGTGGGGATTGAGTTGGATG
ATGAGCCGAGTATNCCAATGGGTCATTGATCATGAATTCATGATCATGATCATGATGATGAACATTATGC
ATGTCTATGTTGATATGTTTGAATTTGATTTTGAGTTTTGTTTGTATATTTTATGATGCTTTTCTTAATT
ACCTCTTGTTTCCGAGTCGACAAATAATGGACCGACCGATAAGGGATAAAAGTTAAAGTTTTCCCATCAG
GTTCTGTATAAAAGCAGAAATTGTAAC
>gi|3449978|gb|AI100695.1|AI100695 34392 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162A23XP 3', mRNA sequence
CATTGCAGCTCTTCCAACACACGAGCGATTGCGCCTCCTGTTCTTCCTCAATCGACAAAACCNATATCTT
CCCATGTATTGCCTCCAGAANGCAAGCAAGAACTTTTTGTTGCTNAAAAAACTGAGGCATAGATTGATGA
TCATNACAAAGAAAGNNAAAGCAAAAGATTGATGATCAATTTGATCATTGGTCACAAAAGCAAAACACAC
ATTTGTCTTCTTCATTTGATTTGTTGTTGNTCTTATACTGTTACATTTTTCCATTTGTGTTTGNGTGTTG
GAAATGCGAGGATTATGTATNATATACTCTATATTCTTGATCCAGGAAAAGTTACCTGGATAATATGTTT
TC
>gi|3449977|gb|AI100694.1|AI100694 34391 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161P4XP 3', mRNA sequence
CTCAGGNTCCCTCTGGGGCAAAATTGGCATTGGCGCCGAGNCGGTTGTGTTGCAGGGCACCCCAACTACT
ACTAACGNGCCTCTCAGATTAACAGTTGGGCAGTGTGGTAAGATAATTTTGGGTTCCACGATTAGTTCTC
AATGAACACTTATGGTGAATACTGGATCTCTCTAAGCATGTTGTTTCAGCTCTATCCTGTACTTGTACAT
AGGTAAGATCCAGAACCTTGACTGTTGTCTGACCTAGAATGCTAATATGCCCAAAATTGAATTTGTCACT
CTTTTGTTTGTTCCATGTTCCACTTTCTTTTTTTGTACATCTGAGATTTCACGAACTCAACATTTCCTGT
TGAGAAACGAGTGTAATGTGTACAACAACAAATCTTTACCAGTGAAACCTATCCATCTGTGTGTTAAGTA
AG
>gi|3449976|gb|AI100693.1|AI100693 34390 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161O4XP 3', mRNA sequence
TCCCGGGNCTCCGTTCAAGCTTNNCAAAAACCGGAACCGGATTGGATTAATGTGCCCGATGACATTCCGA
CCAAGGGACTTTGGTTCTGCGCTTTNGGATATGATTCGTGGTAAAGGAACNGGGTACACAATCNAAGGTA
ATATTNATGTTGATACNCCATTTGGAGCTATGAAGCTTCCTATTATCAAGGAAGGTGGAGAGACCCGTCT
GAAGAAGGAAGATGATGATGACGACGATGAGGAATAAGGAAACAAAGTGCTGCAGAGACAGAAT
>gi|3449975|gb|AI100692.1|AI100692 34389 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161M1XP 3', mRNA sequence
GGAAGTTTGGTTGGAGATTTTCACAGGACTNTGTTGTACCGTGGGATTTACGGGTACCCTCGTGACGCAA
AGCGCCNAAATGGAACGCTTAGGCTTTTGTATGCGTGTGCACCAATGAGTTTCATTGTTGAACAAGCTGG
AGGGAAAGGTTCTGATGGACATTCGAGAGTACTAGATATCCAACCGACTGAGATACATCAGAGGGTTCCT
CTATACATTGGAAGCACAGAGGAAGTAGAGAAGTTGGAGAAGTACTTGGCTTGACTCATGTACCAAACAT
AAGGCATTTAATTTCTATTGTAAGCCAGTTTCTGACTACATGGTATATGCAAATAGATGCATAATGGTGA
AAGTCCTATTTTGTTGTC
>gi|3449974|gb|AI100691.1|AI100691 34388 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161M14XP 3', mRNA sequence
CAAGCCAGAGATCACTGTAGACTTGGAAGCCTATGGGTGCAGAGAGAGGACATCTGAGTCTCTNGGAGAA
GAGAGTGGAACAGTGATGTNTCAGACGTCTGAGAAGCTTGGTAAGTACTGTGGATCGCCTAGATCTACCT
TGAAGTGTGAATGGAGCAGCAACAATAGCTGCAGCAGCGAGGACGAGAAGGACGAGGGAATCTAGCAGAA
TTTCTCTTCCTAATAACTATTNTCGAGCTTTCTGTTTTTGTTCTNTCTTTTTCAAAAACTTATTAAGCTC
TTATGAATAATGACTTGTGAAGTTTGAGTTCGTCTCCTTCACAAGCAAGTTGTATTNGTGTTTTCTACTT
TATGAATATGGGTTTTAT
>gi|3449973|gb|AI100690.1|AI100690 34387 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161L4XP 3', mRNA sequence
ACCTTCGGAAAGTGGAGGAGGGTCCACAGGNTCTTATNCGGTGCACTGCCTGCAGAGAATCACCACCACA
ATCACCAGTCTCAGCTTTACTATGAACAATGGATGCAGAAACTCATCAGACCATAAGGGNAAAGGCAAGN
ACTGATGATCTCAATTATTGCATCTTTGGTNTTGTTCAAATCCTCATNTTGTATGTTTATCTTTGGTTTA
TCTCAACACAAATGTTAATCTCTTTTGTTGTCTGATGTGTGTTAGGGTTTTGTTCTACATATGTATTGAG
GGTCTTTGGAAATCTTTTTGCATTGTGCTTGTAATGTTGTATTTTGTGATAATAGCATTTTGTTTGTGAG
TTTATAATTCAATTTTTGAATGTTATTTTTGCC
>gi|3449972|gb|AI100689.1|AI100689 34386 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161F8XP 3', mRNA sequence
CAATTGGGCNGTCGCAGAAGCTTTGGACTCTGCCCCTATGGCTCTNGCAGAGNACAGTGGATTACAGCCC
ANTGAGCCACTTTCTGCGGTTAAATCTCAGCAAATTAAGGAGNATATTCCCTTCTATGGAATAGATTGCA
ATGACGTGGGCACAAACGATATGAGGGAGCAGAACGTGTNTGAAACATTGATCGGGAAACAGCAGCAGAT
TTTGCTAGTACGCAAGTCGTTAAGATGATTCTAAAGATCGACGATGTCATCTCCAATTCTGAATACTGAT
GTGTTGCTACCATTGTACTACCCTTTGGCTTCTTGGGTGTTTTTTGTTTGCTTTCTATTAGCTTTTGATA
CTCTTCGACATCGTTTNCCTTAACTTGTTCCCTTCGTTTTGCAACCTTTTCTATAAGAACATCGTCAGGT
CT
>gi|3449971|gb|AI100688.1|AI100688 34385 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161F5XP 3', mRNA sequence
AGANGAGTGTGGACACTTTACAAGATCTCCATCTTTCAAGGTTCTGAANCAAGTTCATCCAGATATTGGT
ATCTCAAGCAAGGCTATGGGTATTATGAACAGTTTCATCAACGACATCTTCGAGAAATTGGCATCGGAAT
CTTCAAAGCTCGCTAGGTATAACAAGAAGCCGACGATTACTTCTCGGGAGATTCAGACTGCTGTTAGACT
CGTTCTTCCTGGTGAGCTCGCTAAACACGCTGTTTCTGAAGGAACCAAGGCTGTTACCAAATTCACAAGC
TCTTGAATTAGTNAATTAGGGTTTGTATACTCTGAATTTGATTCTGATGTTGTCATAACTTGTGTTAGGA
TTTCTCTTTCGTTTTATTAAGCTTTAATTATC
>gi|3449970|gb|AI100687.1|AI100687 34384 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161E21XP 3', mRNA sequence
GCTTGCACGAAGANCCATACCACTANAGGNACTGANCTTGATGTTNGACGCGGAGAAGATCCATNGGNTA
TATGTTNTGGATGATTTTGGTNNCCTTGAAGGACTCATCACTCTTAGAGACNTCATTGCNAGACTTGTCC
ATGAGCCATCCGGCTATTTTGGAGATTTCTTTGATGGTGTTATGCCTCTTCCCGAAAACTACCGAGTCTG
AGAGAAAAATGGTATCTTTCTTCTGTAAATTGTCTTTTGTTTGGTGATAATGCTTCTGTCTGTTTGTGCT
TAAGTTCTCGAAATTGTGTTATTAACGTTTAACAGAAATAAGAAAAGAAGAAAGAGCCTGTCTTTGAGTG
AATATGTCTGAAATACAATAACCCTTAAGATT
>gi|3449969|gb|AI099657.1|AI099657 34383 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161E14XP 3', mRNA sequence
ACCGGCGAACCGTTATCTCCNCNGGCAGTAGATNTCCTCTTGAGAGAGTNCCCTAAAGGTATNAAAGGGA
TGAGCACGNGTCTATTGTTGAGCACATTNGCATTNGGCTTTTTCTTCAGCTCGGTTCTCGTCACAATCGT
CGAGAAATTCACCGGGAAAGCTCATCCATGGATTGCCGATGATCTCAACAAGGGCCGTCTTTACAATTTC
TACTCGGCTTGTGGCCGTACTTGTTGCCTTGAACTTCCTCATTTTCCTAGTTNTCTCCAAGTGGTACGTT
TACAAGGCAAAAAGACTAGCTGAGGTGGGGATTGAGTTGGATGATGAGCCGAGTATNCCAATGGGTCATT
GATCATGAATTCATGATCATGATCATGATGATGAACATTATGCATGTCTATGTTGATATGTTTGAATTTG
ATTTTGAGTTTTGTTTGT
>gi|3449968|gb|AI099656.1|AI099656 34382 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161D15XP 3', mRNA sequence
GCCCNNCCTTTTGTTTTGGCCTCNNGCATTCAAAACTNTTCACCCGGAAAANTGGNTGGGAGCTTNCGCC
GGCCAGGAAGGAATTTNTGGGGCCACCCACAACAAGTCCAACTTCATCACCACCACCACCCGTTTTAGTT
TCCACTTTTCACTGCCTCGTCCGTCGTCACTCTTTTTTTTGTTTTTCTTTTTGGTTCTTGGGGTTGGGTT
TTGGGTAACGTCACGTGATGATGACGTGTCGCGATCCTAGCGGCGTTAATCACGTGACCGACGACGACGG
GAGCCTAAAATTTTTAGTGAACGTTGGAAAATCAAACCTCATTTAATTGTTAATTATTNANNAAAATTAT
ATCTTTGGGCT
>gi|3449967|gb|AI099655.1|AI099655 34381 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161A8XP 3', mRNA sequence
CCCNGTTAAAGTCCCGGGGCCCCTTGGNNCCCCCGCTNCTGGCCGACCGACGCNCNTCAATTNCTAGCCA
GCTGTGNCTCTTACTTCCCAAGCATCGTNCCCATCCAAGNCAACAGCAACGCCAGTGATCATGACAATGA
CCGGAGCTGTTNCGCCGACGTCTTTGTGCCCACCACTTCACCGTCGCACGATCANCACGGTGAATCATTG
GCTTTCTGGGGATGGCCTTAGAAAACCACTCTGATAATAAATGTGTGTTTATTTAAGTTCAAGAGTCATC
TTCTTGTTGTTTCCATGTTGACGATAATTGTTGACTCGTGGAATAATTCCGCTGTTCAACGGTATTTTTA
TCAGTTGCATT
>gi|3449966|gb|AI099654.1|AI099654 34380 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161A5XP 3', mRNA sequence
CCTTGANGCCCCCAATGTGGAGACNGCATTTCANNCCGTGTTAGCAGAGATTTACCACATCATCAGCAAA
AACAGCTTTGGCTGCTCNAGAAGCAGCGGTTGCTAATTCTGCCATTCCGGGGCAAGGAACNACGATTAAC
GTTGAAGACACATCTGGAGCTGGCAAAAGAGGTTGCTGCTCTACTTAATTGAAAGTTTAAACTTTCGTTT
TCTATTGCTTATTCACTGTCTTTTTTTCTCTTCAAGTTTTGGGTGATGAAATGTAACAACGATGCAAGAC
CATGTAGAATATATATCTCTTCATTTACTCTTGTCGTACC
>gi|3449965|gb|AI099653.1|AI099653 34379 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160P18XP 3', mRNA sequence
CACCGGTNGGGAGTTGCCCCCAAAGGGAACTGTTGATGTNCATCGCNNTGTTGTNTAAGCCNGCTGATTA
TNTGACCCNGAGGNGGTGAAACCGGANTATTCNCTCCGATGCATATGATTCTCTGCAGAAAACCGGAGTC
ACCGGAGGAGAGTTCTTGAGAAAGGTAGAAAGGAAACATCNCCGGAAAAAGTATGGAGAATTTTCTCAAT
TTGTTTTTATTTTTAAGTTAAATCAACTTGGTTATTGTACTATTTTTGTGTTTTAATTTGGTTTGTGTTT
CAAGAATTATTAGTTTTTTTTTGTTTTGTTGCATATGAGAATCTTACTCTTGATTTCTCCGCCGTAGTGC
CGGCGAGACATAGGGGATTATTAGTATTTTTAAGTGTGTTTAAGATTGATTAACAAGTTAGT
>gi|3449964|gb|AI099652.1|AI099652 34378 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160P16XP 3', mRNA sequence
CCCCAAACCGTTNCCCCNAAGACGGTNGCCCGGAAAANCGCCCCAACCCCNAAGGTTCCACGTGGGGCTA
CACCCNCCCTGGTGGACTTNCAGCGGAGCTTCCATGACCCCAGCCGTTGCTTTCGGACCAGCCGTCGTAA
GCTGGACGTGGACCAACCACTGGGTTTACTGGGCTGGTCCTCTTATTNGTGGTGGACTCGCCGGAATTAT
CTACGACTTTGTCTTCATCGATGAAAATGCCCACGAGCAATTGCCTACCACCGATTACTGAAGACGTCAA
ATTCAACGTTGTTAATCTGATGAATTTTTCGTGATTTGCTTTTTTAATTTGCATCGTAATGGGTTTCTGG
CCGTTGGATCATTTTTAGATGAATCTTTGTCTATTGATTGATCATTTATGTGTCTTTGGGTTTGTTGTTG
GAGTTGTAATATCTCTGGAAGGCTTTTGTGCAATTGTATTGTACGGTTTAAT
>gi|3449963|gb|AI099651.1|AI099651 34377 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160O21XP 3', mRNA sequence
TGCCAAGGCCTNNGCATTCTCAGCTATTGGCCCAATCCCAAGATTTGCCCAGACTACAACAAATTCAGAC
CGCAGAACCCTACTGGACCCGGTACTAAGGCTCTGAAATAAAGGTCACTGAATCGCAAGGTTCGCCCACG
GGGAGATTCCGTAGGCGGAGAGNTCAGAACGAGGTGATGATGGATTCATTATTTTTGAGTTTCTCTTACT
GTATCTTCATNATTTACCATCATCGCTGGTAAAATAAGTGTACCATTTACTCTTTGTCCTCTACTGGANA
AATGCTAGAGATCCTCTGTGTGTGTTTTTTTTGTTCTCTTCATAATTTTCCCATACACATACTAATAAGT
TCTTTGATGTTTGGTTGAAAACTTGAATTGGATACATTTCATTTCTTCTTGTGAAACTCT
>gi|3449962|gb|AI099650.1|AI099650 34376 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160O13XP 3', mRNA sequence
CCTAGAAAANGGGGNCCACNCCTCCGGTGGAATATTACCNCCANCCCTCTGGCCCCCACCCGGNGCCTTN
CCCAGATNTGGTCCCGGGGTNGAGTTNTGNATANGTTTGGTTTTGACGCTACTTGGGTATATCCCTGGGA
TCATATACGCCATTTATGTCCTCACCAAATGATTTNCCATCTATCATCATCTCCTTGAACAGCTGTTCCG
TCGTGTTCTCCTATCTTTGTGACTGATTCAGCGTTTCTTTTTCTTTCATCAGAGTTTTTATGTTTCAAGT
AATTTAATTAATCATCACTGTTGTGTTTGCATTGTTATATAAATGTTGTGTTGATATAAAAGAAGAGAGC
GTTGGTTTGTACTTTGTGTGAACATTTTTTAAAAATATAGTTGGTTTATTACAATAAATTGGAAATTGTG
TTGCCTTGGTGGATCACAGGACCACCATTAACCATTAT
>gi|3449961|gb|AI099649.1|AI099649 34375 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160N20XP 3', mRNA sequence
TCCAANTCANAACCNGCAGGGAGGAGGGATGAGAAGAGGAAGAGGCGGGTTTCGTGCTNGAGGGCGTGGT
AATGGTGGCCCGTGGTCGTGGTGGTGGAAGAGGCAATGGAAAGAAGCCAGTGGAGAAGTCAGCTGCTGAT
CTTGACAAAGATCTTGAGAGCTATCACGCTGATGCCATGAACACCTCTTAAATCGTGTTGTGTTGTTCTT
ACTAAACTAGTTTCAGATGAAATCATGCTTCTCTTTTTTTCATGCTCTTCGTTGGTTTTGTTGGATGTTG
ATTGTAAAGTAAATGGAAGCCTTTTAGAATTT
>gi|3449960|gb|AI099648.1|AI099648 34374 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160M19XP 3', mRNA sequence
CAAATCTGGCTGTTATTGGGTTTNTCGGGGGAAAGGTCANTGTGGAGGAGAAGNCTGCCTGGGTTAATAA
TGNTTCNCCAANGGGATTTACAGCTCTCGAGAAACTGTTGGTGAATTGCGCTGGGACACATGCGACTCGT
GATGAAATTTACCTGGCTGATCTCTTTCTGGCACCACAGATCCACGGAGCAATCAACAGATTCCAGATTA
ACATGGAACCGTACCCAACTCTTGCAAAATGTTACGAATCATACAACGAACTGCCTGCGTTTCAAAATGC
ACTACCGGAAAAGCAGCCAGATGCTCCTTCTTCCACCATCTGATTCTGTGAACCCATAAGCTACTCTCAC
TTTAATAAAACCTCAGACAACAACAACAACAACAATGATCATNATAATACCTTGTACTCATACATGTATC
ATATAAACCAGTTACGTATATTATACC
>gi|3449959|gb|AI099647.1|AI099647 34373 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160J23XP 3', mRNA sequence
ACCCCAATAATNGTGTTNAAAACCCGTTGACTAAGNGGANTACATTTGTACNCCAGGTATTCATCATAGC
GTGTGTCAAAAGAGGATGTGCTGATAAACTGGCAGATATTCTCAACTGATCTCATAGATAAAGAATTTGT
TGANGCTTCCGTTGGGCTCCACCCTTTCCGGGACCTGAAGGTAGGCCTTGAGGGAATGGNCCGTGTGGAN
ACAGACTTTGTGTATCTATTTTGAAGGAACAGAATCAGAACATGGTTGATGTGTTGTTAGGGTTGCTTGT
GTATAAGAGCACATGTGAGTGTGTATTTGTATGTGTGTGTGATTTACGAGTGTATATTCCAATTCAT
>gi|3449958|gb|AI099646.1|AI099646 34372 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160I7XP 3', mRNA sequence
CCTTGNGCTCTCTGTCCCTGAGACNTTGGATCTGCTAGATCTTTGCGAACAAGCTGGTTCTGCATAAGCC
GAAACGATCAACTTNGCAATGCCACGTTGCAAAGAGGGGGATCGTNTTGTATGAANTCTNTCNATATATG
TAAGACCTACCGTAAGAGCGTAAGCTTTTGGGATTTAGTTAAGAGTCGGATTCAAATGTATGTTTACTAA
GAAGGGATGAGAGTATGTGTGGTCTTAAGGCAAGCAAAAGAGCGAAGAGGCTCTGCCGNATAAGCGACTA
CTCTTGTTCTGTGTCGTGTCTGATGTGTGAGTGTGTGTCTGTGTTTGTGAGAGATTCGATACTCTTTGAA
ACAAAGATTTATGTAGAAGAATATAGAGAAAGAAAGACTACTATAAACAGAGCCAAAAAATGATGTGAGC
T
>gi|3449957|gb|AI099645.1|AI099645 34371 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160I23XP 3', mRNA sequence
CTTTGCAGNAAACAACAGACCTTAACCCCCGGGGGTTTTGACTGGTTGNNCCNATAACNNTGNGTAACAT
TNGNNCCAATTGGTGGTNAATTCGGNTCCCCNTCTTTTAAACNNACCCGGGAAGTTGCAAATCATCGCTT
CTTGGAAGAATCGAGAAAGTTCCAAATTCTCAAAAGAAGGAACTGTCTATCCTGCATCGATAATGATGGT
TAACATTGCTGCGGATCATAGAGTTCTAGATGGGGCAACGGTAGCTCGGTTTTGCTGCCAGTGGAAAGAG
TATGTCGAGAAACCGGAGCTGCTGATGCTTCAAATGAGATAAGAAGGAAAGGTTCATGTTTATTTGTGAA
TCATTATGTATGAAACCTTCATGTTCGAATAAGATCAAGAACTGAGCTAGCAGTTGTAAACTAAACAAGA
AAGTAAAAGTCATATCTAAT
>gi|3449956|gb|AI099644.1|AI099644 34370 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160G9XP 3', mRNA sequence
AGGGCTAAGGCTGCAGGNNAAGGTACCCCAATTGGAAGCTAACAGGAAAGCTATGTCGATTCAGTGCAAG
GTTTGTATGCACACATTCATCTGCACGACATCGGAAGTGAAATGCAGGGAGCACGCGGAGGCGANGCATC
CGAAAGCCGATGTTGTCGCTTGTTTCCCTCACCTCAAGAAGTGATGAAAGCTATTATCTCAACTATAAAG
GATTCCAATGTATNACGTATGGATCCTCATCTTTCCTATGTTTGTATCAAAGTCTCGACAAATTTTATGG
TTTCTATTTCTCTCTACTTGTTTCAACAATAAGTCTCTTGCTATGATTATATAATGAAGCTTTGTGTGGA
ACCTTTTTTTTT
>gi|3449955|gb|AI099643.1|AI099643 34369 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160G18XP 3', mRNA sequence
TTCCCNCTCCGGCCATCAGCATCGTCNGGATGNGATTTGCCGACCCCAGAGCATNCNGGTAGGANTCAAC
AGTGTTGGTGATCTGGCACTCCAGGGAGGAGATNTCAGTCGTTGCTAAGCTGGCGTGCCCCGCGTGCCAC
TGCTCTCTTCGNCTTGTTCTGTCTGATAGCTGCAGTGNCCNNATATATAACTCCCTTCCAGGTTGTGGCT
TTTGCCATTGGCTTGTATGTGCTTAGACACCCGAGGCTCAGGTACAAGCTCCCATCAGTTCCACTTAACT
TCTTCAGGAGGCTTCCAGCAAGAACTGATTGCATGCTCTGAGTNACTTAAGATTTCTCCATTTCAAGAAA
GACTCCTCTGTTCTAGTTTGTTATCGTTTTGAAGTCCTTACCTCTTCTTTGTGATGTTGGATGATCATGT
TTTTTTCTGTTTGACATNATTTATGTTTATGTCCTTTTGAAAACTTTCTTTGGAAAGTGGTAACTAGTAA
GATAAGTTTGTGTT
>gi|3449954|gb|AI099642.1|AI099642 34368 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160F7XP 3', mRNA sequence
CCAAGTTNTGCCCATTACAGGCGAGTGGACAACGTNTATGGAGCCCGTAATCTGGTGTGCACTCTCCAAC
CGGCGAACGAAGAACAGGCTGCAGCTGCAGTGTCTGCTTAAATGAAGCCACTATGAAGCGATTCGCACTC
GCACCAAAACCCACAATGGGGCGATTCGGACTCATACCGGATCCAGAAACGTATCTTTACTGGCTTTTAC
TTCTCTTCCCAGCCTCATCATCACTTTCACTTTCACTTCCTGTACAATGTACATACGTAGTCCTAAGTTC
TTCCCTCATTTATTTAATGAAATACATTTCTTTATGTTCCACTNTCTTATACGTATAACATTCCATTTGG
ATGATGTGATCACCATCGTGGTTATATTTATGCCATATGATCTCTTTG
>gi|3449953|gb|AI099641.1|AI099641 34367 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160F5XP 3', mRNA sequence
TCCGNGAAGTAAGCGGGGAGATCGGTTCGACGNGATCNCNCCGNGNCGGATTTGAGAGCCCCCCTGGTCT
CGCCGTTGTCGGACTTGACGTTCGCTGACCCGGAGGACCCCCGCAGTGGACGAGACGTTCTCGTTGGAGA
AGTATCCGTCGTACGAGATCGATTGGGATTCGATTCTAGCTTAGGGGCAAAATAGGAAATTCAGCCGCTT
GCAATGGAGTTTTTGTGAAATTGCATGACTGGCCCAAGAGTAATTAATTAAATATGGATTAGTGTTAAAT
TTCGTATGTTAATATTTGTATTATGGTTTGTATTAGTCTCTCTGTGTCGGTCCAGCTTGCGGTTTTTTGT
CAGGCTCGACCATGCCACAGTTTTCATTTTATGTAATCTTTTTTTCTTTTGTCTTATGTAATTTGTAGCT
TCAGTTTCTTCATCTATAATGCAATTTTATTATGATTATGT
>gi|3449952|gb|AI099640.1|AI099640 34366 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160E8XP 3', mRNA sequence
CTTTGGNACNGAAGTCNATGCNCACAGGGCTTGTTGATTCTGTGATGGGTCCCCGGACCATTCGGCATGC
NGCNTGTTGAGGCTGCTTCTGCATCTGCAGGCCCCTGCTGGAAGCTGCCATGCTNTCTAGCACCTGTGAC
ATTCATGCTAAGGCTTTCACAAGATTGCATCGGCAGCTATGGAAGCGAGATTCGCAAATGTCAGTTCTAC
ATGGACATGTTGTCCGAGTGCAGGAAGAACTCTGGTTCCGTGATTGGTGCCTAGAGTTTCCATTTCTCCT
ATTTGTTTTATCTTAAAGAATTATCCAGCTGTGATGATGCTGAGAATTTGGATATGATGATAT
>gi|3449951|gb|AI099639.1|AI099639 34365 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160E15XP 3', mRNA sequence
TGCGTCGAATTGGCNANGGAGTTACTACCTTCTCCGNAAACAGGGGGNCCCCTGGTGTNGACTTCGAGTT
TGGAGCACGGGATCTTGTGTACCGTGAGCACGGAACACTCCCGGATACTACGATGGACGGTACTGGACAA
TGTGGAAGCTTCCATTGTTCGGATGCACCGACTCTGCTCAAGTATTGAAGGAAGTTGAAGAATGCAAGAA
GGAGTACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAGTGCATCAGTTTC
ATTGCCTACAAGCCCCCAAGCTTCACTGATGCTTAAATCCTTTTCTGGAATATTCAATGTTGACTATCCG
GAACCCAATTTTGTATGGTCAATGTNNATTTAAGTAATTATTTTGCCAAAGTGAAAAAACTGAAGGTTTG
TTTTTC
>gi|3449950|gb|AI099638.1|AI099638 34364 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160D7XP 3', mRNA sequence
ATTGATNCCTTGTTANCCANTGGTCCACCGTGAAGATGCTACCAGGATTGGGATCTGCCTAGTNTGGTTA
GGANGCCAGGCTGTTGNTATCTCTCCTCCTANGACGTGTGAACCAAGCGATCATTCTTGCTTACAACTGG
TGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTTGCTGATGAACNCCATCAATG
CTGCAAAGGGATCTTCCAACAGCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAA
TCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGAGTTTTTGTGTTGTTTCCATTAGCT
TTGGATATGTTTCAGATGANCTCTCTATCTTTAATGAAATTTTGACGCTTATAATC
>gi|3449949|gb|AI099637.1|AI099637 34363 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160C2XP 3', mRNA sequence
TGGGNTAANCCAGTCAACGGTCTNAGCCCCCAAATGATCTCGCTCTGGNACGGGGCGTTGGATCGTCGAA
GGCTGTGATTCTTTNAGGGCTTGNCCTCGGTCCAGACGATCTATTGAAGAAGGTGGAAGAGTTNGAAGGC
CACTTCACTGGCTGCAGACACACTTACACAGCTATGGTCTTGTCAAATACTGATGGTGCAGCAGAGGATT
ACGTGGATGAAAAGGACCGGTCCGAAGAGTATTATAGTGACATAGACGATGACTTTGATGACGAGTGTTC
CGATGATGAGTCGCTAGANCCGGTTGGTCCAGTGGGATCTTTACCCGTTGACAAGATAGTTAGGAAGTTG
AGGGAAAGACTNAAATAGAGCAAAAGTGTTACTGTATTCTCATCATTGTTTTGTGTAAATGTTGTANACA
TACATACTNAAAACCCAAGTGCCATAACGAAGTACTTCTAGAG
>gi|3449948|gb|AI099636.1|AI099636 34362 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160C23XP 3', mRNA sequence
GGATTAGAGNNCTTTCTCNATATGCAAGAGTAATCNTCTATTATCTNCCNCATATATNAAATANGCTTTT
GTAGGATCGCCTTAAAGGCGAAGAGATGAAGATGCAAACAGTNAAAAAGGGTTTTCTTTTCAGCTATTTC
TTCTTGAATGTTTTTTTTTCTTTTTATTTTGGTTTCTTATTGAAATTGTTGTATTTTTGTTGGCTTTTTT
TCTAATAATATCAGCGAGTTTTTTCTTTCC
>gi|3449947|gb|AI099635.1|AI099635 34361 Lambda-PRL2 Arabidopsis thaliana cDNA clone 160C13XP 3', mRNA sequence
CTAGNTTCTTCCCCCCGGGGTTTCAGAACCGGTNCNCCGCNTGACATCGAGAGGATTNGTGGAGAAGGAC
TTTGAGAGATAGGAGAGTTCCNTGCACCGTGCCGTGACAATCCACGTTGGACATCCAGGAGCAGTACGGT
AAGGTGATGAAGGACTTCAACANGGGTTTNGTGAACAACAAGGAGATCGATGAGATAAAGGCTGACGTTG
AGGAGTTCACGTACGATTTTGATATGCCTGGATTTTTCATCTCTGAGTCAAGGAACGATTAGAGATCTCT
CACTCTCTACCCAATAGTAATCTTCTGTTATTTGTGTTTTTGTATGTTAAGCAAGCAAACAATNAAAAAC
TNATAAGCTTCAGTTATTTTTTCTTCTTGACTATTTTATTTCGTTGGATTTCTTAATAGTAACAGCAAAT
TTACTATATTTAACGAATAAATACAG
>gi|3449946|gb|AI099634.1|AI099634 34360 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159P22XP 3', mRNA sequence
CCCTTGTTTCGTCCCGTNTCGATTTNCACNCCGTCTCGTGGATCCGCNGGANAATNTTACNCCGATTCTC
GTACGAATTCTCGNTTTCGGTNTGGGACNCACAATGCATATGGTTNCGGAAGGGAACGTGCACTCGAAGC
TATGTGAGTACCAAGNTCTTACTTCTTCTTCGATGGACGTCACACACCAGAGAAGGCTCAGGAGGAAATG
GCTCATCTTCTATATGGAGCCGACCCTGACGTGGTCCAGCCAATGACGGTCCGTGAGCTAATCGTCTACC
CAACTGGAGAAACTATGCGTGAGTATTGGGAACCCAACAACTTGGCTATCCGTCGTCGGCCGTCTCGTGA
CTTTTACTTGGGCCTCGCCGCCTATTATTAGTTGGATGGCTTTGAGCTGAATATTTCGATATATATGAGA
GCTATTGTCTTATAATGTATAATCGATATCGTAACGTGGAATTATGCCTATATGACGTCAAATTATGCCT
TTGACGTTGTCGAATAAACTGCTTTTGAAT
>gi|3449945|gb|AI099633.1|AI099633 34359 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159P13XP 3', mRNA sequence
ACTTTGCNGANTACACCTCCCAGAAGGAGTCCNCGNTTCATTGGTCTTNCCTTCNNCANGGAGGTATGCA
NATCNTCGTAAAGACTTTNACCGGAAAGACCNATCACTCTTGAAAGTGAGAGCTCCGACACCATTGATAA
CGTGAAGGCTAAGATCCAGGACAAGGAAGGCATTCCTCCGGACCAGCAGCGTCTCATCTTCGCTGGAAAG
CAGCTTGAGGATGGACGTACTTTGGCCGACTACAACATCCAGAAGGAGTCTACTCTTCACTTGGTCCTCC
GTCTCCGTGGTGGTTTCTAAACCTTGTCTCTCTNTCTTATGGTTACTGAACCAAGTTCATGTATCGTTTC
ATCTAGTACTTTGGTGGTTTATGTTTTGGGGCCATGTACAGCCTNTGATAAATAATTGATCGACTATGTT
TCNGTTT
>gi|3449944|gb|AI099632.1|AI099632 34358 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159O18XP 3', mRNA sequence
GGGCCTTTGGCCAAGAGAAATCNAAGGTTTTGCAACAGTGGNGCNGGCNTTTTANCATTTTCNTCATCAT
GGCCANAGGCGATTGGANGCNGATAGGTTTTTTCAACGNGTGATTTCANTGAAAACGATTTACACNAAGA
AGGGGCTTGAATGGGTGAATACTACAGAGAGTCTCAAGGATGTGATTGATCGTCATTATCCTGATATGAC
AGACAAATGGATGAACTCTGAAAGTGCATTTTCAGTATGGGATTCACCTCCACTTACCAAAAATCCAATC
CCTCTCTATCTCCGAATTCCCTCTTAATTTGATCATTTTAATGTGATCTATGGCACTTCGAATGATTTTT
TTTCTTCCTTTTTTGGCATTTGTTGGCTGTGAGCTGTGTTTCGACATTGTAATGTACTATACAGATAAAT
NAATGGGTGATATACATGTGATTC
>gi|3449943|gb|AI099631.1|AI099631 34357 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159M9XP 3', mRNA sequence
CACTTCCCANNCCTTAAGNCCCCACTCACCACTGGAACNGCGATTGAAGAGNTTGAGGACAACAACACTC
TTGTTNCCATTGGTGGCCATTCGTGCTGACCAAGAAGANGATTAAGGATGCTGTTAAGAAGATGTATGAC
ATCCAGACCAAGAAAGTGAACACACTCATCAGGCCTGATGGAACCAAGAAGGCTTACGTGAGGCTTACAC
CAGACTATGATGCTTTGGATGTTGCTAACAAGATCGGCATCATCTAAGTCTATCTATCTCTGCAGTTATA
AAGACTATTGTGGTTTTGTCTCTTGTAGTCTCAGTTTTGCTTTTAAGATATTTATTATTACTATCATCTG
GTAATTGTAGTATTTTGGAGCAAAAACGTTTTACAATACATTCATGTTGCNGTTTATTGTTGAATTCAAG
TTCTATGTTTTTGACTTAAAAAAG
>gi|3449942|gb|AI099630.1|AI099630 34356 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159I8XP 3', mRNA sequence
GGGGGAAAGTTCCNCCTTGCTTTNAGTTGCGTTAAAAGGGGATCGTAAACAGCGGGNGTCCAGNATTTTG
GACATTTTCCCGGCGANTCAAGGTCCCNCCTCGATCTCAGNGTGTTACAGCTNTGGGAAGNTGATGTGGA
GCTGCTTTTGCCTTNGGTACGATCCGAATTCACAAGCCGGGGAAGAGAGAGAAGTCAAGATTCAGATTTG
CAGAAAACGTCATCCATTTGATTCCTCTCATTCTTCTTCTCTGTGTTGCAATCCTCTGGCTCTCCTCTTA
TTCAGCAGCGTTAAGGAGTTGAGTTCAAGAAGCAACATGTTGTCTTGTCTCCATGGAAACTCATCATATT
CAGTTTTGGGAAAGGAAACAATTATTTTACCGCCGGTGATTATGTGCCGCAAACCATACGTAACTCTTGT
AATTTTTGGTTCTGTAGACACATAAAAGGATCTCTCGTTTTCATGAAATGTATGTTTAATAGTTCACTAT
>gi|3449941|gb|AI099629.1|AI099629 34355 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159I6XP 3', mRNA sequence
TCAAATCACCGGCTCCAAANGCCTATCGACAAACGCCNTNTNTCNCTCCCAGGAAATCCGTGAAACCGGA
GAATACATAGCCGAACTCAAGCTTTCACCCCGATGTCACTGCTCGAGTTAAGATCAATGTTTCCGCTAAC
TAAACCTTCAACGATTCAAGNCTCCTACTGCATCCCAAGGAACGTATAGAGAGTGGACAAAGAGAGTAGC
CTCTTGTGGTGAGGATTGAAGGTTGTGAAGTTTTTCCTTTAGATTGTTTGATGCATTTGTATTTTTGCTA
TTTTTGGAATCTGGAAACGCTAAAAGTATNATATTCTCTTGCAAGTTATGATATTTACTTGAAGTT
>gi|3449940|gb|AI099628.1|AI099628 34354 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159G22XP 3', mRNA sequence
GCCCCGCGGGNGCNTAAGCCTGTGGTGCCGGAATCTTCCGTTAGGATCCTTTTCCAGGAACTGTGTAGCT
NCAGNTGAGTTTNCCCCGTTGGAATCGGAGGTTAGGATTTGCGACGAGTGCAAAACAGGGGATGTGGTGA
CAATCGAACACAAGGAAGNCGGTAGTAGTTTGCTGNTCAATCATACGACGAGGAAAGAATACAAACTGAA
ACCGCTCGGTGATGCCGGTCCGGTGATCGACGCCGGTGGAATCTTCGCTTATGCAAGAAAAGCCGGCATG
ATTCCTTCTGCTTGAATGTAATCGGATCCATAATTTATCGGTTCTGAGTTTAATCCGGTTTGGTTTATTT
GGTTCGAGAACCGGTACTAACGAAATAAATTATTACCAAACC
>gi|3449939|gb|AI099627.1|AI099627 34353 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159E18XP 3', mRNA sequence
GGCTGAATNNNCCGGACTTNAAAGGATTTGACTCCAATGGNGGNCTTCCCACACTCGGTATTGTGAAGGN
TGACTACTTGATGATTAAGGGGTGCNGTGTTGGTCCCAAGAAGAGAGTTGTAACTCTCAGACAGTCACTT
CTCANTCAGACTTCCCGTCTTGCCTTGGAGGAGATCAAACTCAAGTTTATTGACACCGCCTCCATTTTTG
GACATGGTCGCTTCCAGACCTCCCTTGAGAAGATGAGGTTTTACAACCGTGTCACGAAGTAAGAGTTGTT
TTATCACAATTCTTCTTAGAAAGTTTCATGTTTGGTTATCTGTTGCTACTTATCTCAGAGATGTTATCCT
TTAAACAATGTTATGGAGTTTTCTTTTGCTTTTAGTTTGTTACTTTTTTGGAAGTTNAAACGATTTGCTT
CTC
>gi|3449938|gb|AI099626.1|AI099626 34352 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159D2XP 3', mRNA sequence
TATGGGACCAGGANTAAAGCAGCANGCAGTGTTTNCTCCCACNGGACCCTGTTGCGGTTTACCCAAGTNA
ACCGCGNTCNTCTACCCGAAGGCAATCCNTGGGTACTGATGTCCCCTCCAATGCCTGCTCCCAGCTCCTG
CTCCTANTCGTTAGTGCTCCTTCGGATTCTCCTTCAGTTGCTGATTCTGAAGGAGCTTCTTCACCAAAGT
CCTCACACAAGAACTCCGGACAAAAGCTGCTACTTGCACCAATCTCCATGGTTATTTCCGGTTTGGTGGC
ATTGTTCTTGTGATCAGATGGTTTTGCAGATTGAGTTATGTTTTTAAGTTACAATGTGAAAGATTGTATT
ACATCATTTGAATTGTCTTTTTGATTTTTGAAACCCATTTTTTATTATACATTTTTATCATTATTATTGT
TTGTCATTACGATTGTTGTGAATTGAAATTGTTCCTCC
>gi|3449937|gb|AI099625.1|AI099625 34351 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159D24XP 3', mRNA sequence
CCCTGGAATTNACCCNGCNCATTTGGAACCGTTNTTNACCCGCTGACCGTCTTCGGTCCNTNTACCCCCG
GACAGGACGAGGCTGACCGTCGGGACCCTNTTAGCCCGAACAACAGGTGTTTCAGCTGTAACAAGAAGGT
TGGTGTAATGGGGTTTAAGTGCAAATGCGGTAGCACGTTTTGCGGGAGTCATAGGTACCCGGAGAAGCAT
GAGTGTAGCTTCGATTTCAAAGAAGTTGGACGTGANGCAATCGCAAAGGCGAATCCTTTGGTTAAGGCTG
ATAAAGTTCAGAGGATTTGAAGAANACAAACTTTGTTATTNTTAAGTATTTCTTTGTCTTCTGCATTTGA
TCAGTTTCTGCCTGGGATGTTCGATGTTTGGTTTCCATGAATCAAAATGAAAATTGCTGCT
>gi|3449936|gb|AI099624.1|AI099624 34350 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159D22XP 3', mRNA sequence
GGCCCCGCTTNGGCNNTGGACCTTTTGTGAGCCCCGNGTTTGTTACCCCTCGGAGCCTTNACATTTGGTA
TGTGCCCAAGAAGATGGATATCTTCAGAAAACCAGACGATGTGTTAACAGCTGCTGAGAAGTNCATTGCA
GAGAATGGACCTGATGCTTTTGAGAAGNTCTTAAGCCGGGCTGATAAATCNCANAGATATCATAAGCATG
AATATGAAAGCTATGAAACGATGTATGGTGAGGGTTATCAGTACTAAGAGAAATTTGAAAAAGCTNTTAA
TTTTAGAATGTGTGAAGCAACTTCATGTCTTTGTTGTTTGTTTATGCTTCCTTTTTGTGGATCTCTCTCG
TGTAAAAAAGTTGCTAATTAAAATAAAGATGCTTTCTGCTCC
>gi|3449935|gb|AI099623.1|AI099623 34349 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159D20XP 3', mRNA sequence
AGTCATGGGCCGCAGATGNNCCATNCGTTTCNTAGCAGGGAAGNGCCNCCATAAGGATGTGAAAGGCCGC
ACAAGCTGGCNTTTTAGACTCTACCTATGGGAAACCNGGATATTTATGTGTTACCTGCCTGTGNCTCTTG
CGGAGGTTCTGGTATATCATCCCTTCTTCTCATTGCAAAGAACCAATCTGAAAATCTCCTGAATGTCGTA
GTTGCTACATTAACACAGATTTCACCACTCTCTTTTCTCCTGGCTTTGACATTGTTCGGTTGGTCGATGA
AGCAGACCATTAATGTCATTCAGATGAAAACTGCTGCAGACGTTTGTGTACTGTATGATATAGAGAAGCA
GCAGAAGCCTTGATCATCTTCCTTTGTCTCAACCTGAAACTCTTTTTTTTCTTTCATTGTTTGTTCTCTT
TTCACTGTGGATGTAGATAATTGTTTTTAATGAAATGAAGAAATATTGATTTGCCTTTTGAC
>gi|3449934|gb|AI099622.1|AI099622 34348 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159D1XP 3', mRNA sequence
CCCAAGTGGNTCCCAAGGGGNAGGNGCCACAGGGGTTTACCGTCCCTGGTTTGGNANNTNACCCATCCAT
TGTTCATGCAGCTCCTGAAAGANCCAGAANCGAGTATGGATTCGATCAAAAGGNCACCATCACAATTCCT
TGTCACGTGGAGGAGTTTCGTTACGTTCAAGCTTTGATAGATGGAGAGAGATCAGTTNACAATGGTNACA
ACCATCATCATAGACATGGTGGCCGTGACCAGTATCATCATCTTGTTGGATGCTTCAGAGCTTGATGAAT
AATGATGAAATGAAATGATGGGTGGTGATTGTATGTGTTCAAATTTTAATGTTTTTTCTGGTTTAATCTT
GTGGAGTTGTGGAGCCAAAACTGGCCTAACCCACAAAAGAAGTGAATCTTCTAAATTCTATCGATTTGTA
GTATCTTTTTCTGTAATTTTAATGGAATTTTAAGATTT
>gi|3449933|gb|AI099621.1|AI099621 34347 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159D16XP 3', mRNA sequence
CTANAAGGTTTCCCGGGACCTACNCCAAAGCTGCGAGTTAAGCTACATCGGTGCCTCCTAGTCGCACCGT
TGGCGCTCNTGTTCCACTAGTGACGTAAGATTTTCCGGCGGTAGATCTAGCGTTGCAGAGTGAGATGGTG
CGGTGGAGGATTCATGGGAAGAATCTGATGGTGGATGTTGGTGGTGGAGTCCGATGCTCGGGGATTGTTG
ACGGCGGGTCAAGTCGAGTCAACCCGATTGTAATGGGTGGGCTACAATTAGAAGGCTTTATATTGGACTT
TGATTTGGGTAACTCAATGATGGGCTTTGGACAAAGAACACGCTCTGATTCACACTTCGTTGTAATACAG
AAACCTTTGTAATTGTAACCTTCTAATTATCTGGTAGATATCCTC
>gi|3449932|gb|AI099620.1|AI099620 34346 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159C4XP 3', mRNA sequence
AGCTNACGATTNTGGAATTGGCGGTTNTTACCACTTTTCCCTTATTTTCTCAGGGAAAGTATTGGGGATT
GCTTGGTTTGCAAGTTAGGGTTTACTTTAAAGATTAGGGCTATATTGTTTTTTTTGTCTTTTCTGGTGTG
TTGTGTCTTGTTTGGTATGTAGTCTTGTAGAGAGGCTGAAGCGGCTGCAGAAAGAAAGGGTTGGGATAAA
GATTCATGTAGCCCGCAGCTCTCTTTTACGTTATGATTGTANTNAAGTATATATATATCATGAAGAAATT
AAACATGGTTTCTTCGATTTATATAAAT
>gi|3449931|gb|AI099619.1|AI099619 34345 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159B14XP 3', mRNA sequence
CCTACNCATGGNCCCACAAACCGCANCCCGTNNNTCAAAGGTATTNGACAGGCTGNCAGAATTNTTTTGA
TAGATCCTCCAAAGTTTTTGGACTACATACNTCCACACAGTNAGAGACAGGGAAGATAACATATGTTGAG
GATATAGCCCAAGGACTTGAGAATGGACCTTCTGCTTTGATCGGANTCTTCCACGGTAAGAACGTCGGGA
AACAACTTGTCGCAAGTTGCTCGCGAGTGAGATTAAAATTAACAAATGTTTTATTACCGTTTGGTTTTAG
TTGTTGCTGGAAATAAGATCGGTTTGTACAAGCTGTGACAATGTTTTGTTTGTTGGTCAGAAATAAATGG
ACTTTGTTTGTCTGT
>gi|3449930|gb|AI099618.1|AI099618 34344 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159B11XP 3', mRNA sequence
TAAGCCTGGAGATTTTTCCCTGCATCCAACGGATGCTCGGCTACTTNTCGCAAGGCTGGCGTGCCTGCCT
TTGGGTTCTCTNCCCATATCAAAACACCCCGAGTCTGCTTCATGACCACAATGAGTATTTGGGTAAAGCT
GAGTACTTGAAAGGCATTGAGGTGTATGTTTCAATCATCAAAGCTTATGCATCATATGAAAGCAAAAGTG
GTTCACGAGATGAGTTATGAGGGTCTCAACACAGCCCATTCAAGTCTTCCTTTCGCAAATTTGTACAATC
AATAAGATCTGAATCCATCCTGTGTTTGTTGTGGTAAATCAGAGACATCTTGTTCTTGTTGTGAGACAGT
TGGCATTGGCAAATTGTATTATTCATTCCTGCTTTTTC
>gi|3449929|gb|AI099617.1|AI099617 34343 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158P6XP 3', mRNA sequence
CCCTTTTCCCGGCGAAGGTNCGGGATCAGTTTTTAGCCTTATACTGGATCAGTTGCGCTTTCAAAGCATC
TCGTAGGAACCCACCCAATACTTCCGCATAGCTGTCAGTTTTGGGNGTGTTAAGTCACTGATAAGCATGC
CATGCTTCATGTCACATGCANGCATACCTGCAGAAGTTCGTGAGGCCAGAGGTTTGACGGAAGATCTTGT
CCGTATATCTGCAGGAATTGAAGATGTTGATGATTTGATATCTGATCTTGACATTGCCTTCAAAACCTTC
CCTCTCTAGTTTTGGTTTGTTCTTGTCTCAGCTTTTGTAGTTTCATAGGTTCTTGAAATAAGGATCTATG
TAACAAACCATAAAACATAATTTGGTGTTTGAAAACACATCAAGCAATAAATTCATTATTGTT
>gi|3449928|gb|AI099616.1|AI099616 34342 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158N17XP 3', mRNA sequence
AAACCTCCCACTTTTACNTGGCNAATCGGATNTTACCCATTNTTAAAAGTTATGGGTGGGGCCATGAACA
TGTCTCAAATTAAGTGTACCTTTCAAGATTTGTAGTGTTCAACACAAGTCACAATNACTTAAAGCNCAAA
TGTCATTTTCTTGACACAGATACATCATAATCTNACGTACAAAAATGAAACACAGACATGGCAAGAGCAT
TAGCAGCTCCAGATACAGAGCATCCGAATGGAACAGAAGGTCACGATAGCAAAGGAATGAGTGTTATGCA
ACAACATGTTGCTTTCTTCGACCAAAACGACGATGGAATCGTCTATCCTTGGGAGACTTATAAGGGTAAT
TATTACTTGTTATAGTCTCTTCAAAGACTTCAATCTTCAG
>gi|3449927|gb|AI099615.1|AI099615 34341 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158M17XP 3', mRNA sequence
CCGTGCCTGNTTCCCCATGGGAAACAAGTTCCCCTAGANCCACGGTTGCGTCTCAGCCCCAACGGGGCCN
AAGGATAGGNAAATGGCCNAGGTGAAANCCGCCCNGATGCGACCAGAACTGAAGAGGCCCNAAAAGCTTA
GGANGNCTTTCGGGTGTTTCCGCTAAATTTGATTATTGGGNATGTTTTTTTCAAGACCAACAATCCTTAA
CTCTAGTTTCAAACGACCAAAGTGACAGAAGTGCAGAGGAAGAACGAAGAGTGGAGGATAGTCTCTCTTG
TATAGGATCGTTTTTTCTTCTTTCTTTATAAAAAAAATTGTTTGATTTTTGTGACTAAAGGATTATTTGA
TTTGGTTTGGTGTTGGTTTTTTCGGACAAAACCTCCTCAACTTAATATGAAGCTTGTCGTGAACAATGGA
TTATGACTTCACTTTTAAAAGTCGTGTAATAATTAATATCTTTGGTTATTGTTACTTTTCTACC
>gi|3449926|gb|AI099614.1|AI099614 34340 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158L10XP 3', mRNA sequence
TTGGGCTCCCNAAAGGNCATCCGGTAGTTGTTGGAGGGACTTCAACAAGGGTTTGGGTGACCACAAAGGA
TCCTCGATCAGCTCAAGGCTGNATGTCGAGAAGTTCTCGGCGTCTTATGAGATGCCTGGATTCCTCATGT
CTGAGATGAAGTACAAGGATTAGAGCATCTTTCTCTATATGCAAGAGTAATCCTCTATTATTATCTCCCC
CATATATCAAATATGCTTTTGTAGGATCGCCTTAAAGGCGAAGAGATGAAGATGCAAACAGTAAAACAAA
AGGGTTTTCTTTTCAGCTATTTCTTCTTGAATGTTTTTTTTCTTTTTCTTTTGGTTTCTTATTGAAATTG
TTGTATTTTTGTTGGCTTTTTTCTAATAATATCAGCGAGTTTTTC
>gi|3449925|gb|AI099613.1|AI099613 34339 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158K21XP 3', mRNA sequence
ATTACGCNCTGNTCGAAGCNGCGGCTATGCTGGAGCATATCATGAGGGNCGTGCGCTGGACTNGCTCCGG
GGAACCACCATGATCATGGAANTCAAAGGGAACATGAAGAAGCATGAATCTAAGGACCNTNAATTAGCTC
ATAATTTAAGAGTCTNTAATNTGTGTCGTTGTTTGGCCCTTATATAATGTTCCTCAATTATGAAAGCTTG
TGTTTCTGAGAGACCAAAGAGCTTTTAGTTTGGTCTCTGTAGCGTGTGAAGTNACTTGTATTTGTAGTAA
TCCGGATGGGTTGGTATATTTTGCAAGTGTGTCTAGGTTGGACCATAATTTCAATATCTCTTATGATTTT
GTTTCATATGTTTGTAAAACAGCTTATCTTTTGAGATATATAATCATGGTTTTGGTTCA
>gi|3449924|gb|AI099612.1|AI099612 34338 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158K20XP 3', mRNA sequence
CACAAACCCTCAGGGCCAGAGGGGGNTNGGAAGAAGTGAGGNCCTCCAAACCNTATGGCAACATCTCGTT
NGATGATGTGATTGAGATNGCTNAGATAATGCGTCCCTAGANTCTATCGCTAAGGAATTGAGTGGAACNG
TGAAGGAGATTCTTAGGACACTTGTGTCTCTTTTGGTTGCACTGTTGATGGTAAAGACCCTAAGGNTCTT
CAGGAAAATTNACCGTGCGTGACATTGATATTCCTNACGNGTGATAAAGGTTTTTACTTTTGAGTTCTCT
ATCGTTTTATNTTTTGTATTTGATTTTGAGGATTTNGTATTAGTAATACTATATTTCGGAAGTTGAGAAT
TGTTGGCTTTTGCCCATTTGAATCCTTTCTTGGGATTAATCAAAATGTTCAATTTTCTAC
>gi|3449923|gb|AI099611.1|AI099611 34337 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158K15XP 3', mRNA sequence
AGTACTTGACAAAAGAAGTNCTTGAAGAAAGCACAACCTTGAGGGATTGGCTTTAGAGTGATTGCGGCGA
ACAAGGACCCGTAACCTCTATGAGTTGAGGTACTTCAACATTGCCGAGAACGAAGCTGAGGAAGAAGATT
AAAACCGGTTTTGGTCTNGTGCTATATCCTCTGTTCCTCTATTTCTGTTGGTTTGGTTTTGATTCTTCAG
TTTTGTGTTAGATATTATTATGTAGTTTGATTGAAGTAATAGCTCTTTGCTTTTGTTCGTTGCCGTACGT
TGAGATTTTCTATGGAGTCTATTTCTTCCAAACAGTAATGATGTGAAATTGGACTAATATGATTTAGGGT
TTGATTAAGTT
>gi|3449922|gb|AI099610.1|AI099610 34336 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158J6XP 3', mRNA sequence
CCCCTTNTCCCACNGCCTCGGGACTNCCTTGCTCGNCTTCTCTTCTGGNGCANGCTATTGGGGCCATTNT
CTCCNGNGTTTGGAANATCGAATGGAACTGATGGAGGGCCCTGTCTTTTGACATGCGATGCCAATGGGTC
TGAGAACGTCCGCTTGAAGCTATCTTTATACATCTCAACATTGTCTTACATGCGTATCAGCGGCCTTGAC
ACTCTTAAACCAACAAAGTGGGCAAGTGACTAGGAGACAGGCCAGCCTTTGAGCTTTAGCTCTTGCACAT
ATATGCAGCTTTGTGCTGGCCTGAAAATTCATGGGCGAGGTAAAGTGTAACATAAGAAATCACTTCTACT
AAAATTATTTTTCGTTGCATTATCGTGTGATGGATCTGCAAAGCAATAAAGCTAAGTGTAATTGTATTCA
GGAATATACTCGTTTGGTCATTAAGTATAGTTTGTCCTAC
>gi|3449921|gb|AI099609.1|AI099609 34335 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158J1XP 3', mRNA sequence
AANTTGACCCCCNCCCTGGGCGCCAAATGGGAAGTTCCCTGGACGGGCCAAGACCGNTTAGTTTGNGGNC
NACATTTCCCCCTGATTTGGAACCCCCCTTGCTGGCCCAATCTCGTGATGAGTNGCNNTCAGNCCTGAGT
TTTGAAGGATGGGTGTCAGCTACTTGAGAAATGTATGCGTGTGCTTCTTTACCCGTGACAGATCTGCTAT
TAACAAGCTTCAGATAGCGAAGATCACGGAAGAGGGCGTGACGGTCTCACAGCCATACTCATTGAAGACA
TACTGGGAATTCTCGTCATTCCACAACCCAACTGCTGGTGCTGCAGGCTCCTGGTAAGAAGCCAAGCAAC
CACATCGGCTGGCGATCTTTTAAGGAAGCTTTTATTTTATTTTATGTGATGTTGTTAAACACTTTGTACT
GTAGTTGTTTTACTATTAAACTTGGTGGTTTCTTTCTGACAGTCCAGAGTTTAGATCAATGAGGATTTAT
AAAAAGTTCTGGATATCTTTGGGTAGTAATCCATACCTTTGTTCATTGTTAATCGTTCTCC
>gi|3449920|gb|AI099608.1|AI099608 34334 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158I5XP 3', mRNA sequence
ACCCTCANGGCCCCTAAGGGCTTGGNACATTCCACTGNACNGNTCTAACTGCTATGGATGCTCAAACCGG
AAGCAATGGATCGATTCGGGGTCATCCACTTCTACTATGGAGGCCCTGGNCAAAACCAGAAGTGTCCATA
AGCTAGGCTCCCAAGTNGTAGTGGCTCGTCTCTCGAGTTATCTTGTCTTGTGAATTCACCTTGTCTCTTT
CTACACACACTCACTCAAATCCGCCNTCTTGGGTAGTTCTTAGGGATGGTCAAAGTTATGTAATGGTNAA
AGTTTGGTGTCTTTTTCTCCATGTAAGTAGGTGGGGAAGAAGTGGAAAGGTGTGGCTTAAGTTTCTTTGA
AAACTCAGAAACTTTGGCCCTTNGTGTAATTTTACTTTGTCTCCTTTGTATTGTGATTTGTTTAAACAAG
TGAATGAATCTCTC
>gi|3449919|gb|AI099607.1|AI099607 34333 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158H11XP 3', mRNA sequence
GTGATGTAGGGACCAACGTTTGGAGCTATGATGATATCGGGGACAAAAGGCGGGACAACTTGCTCTTAAG
GCTTTGGGGCTACCGAATGCTATTGATGGAACTCTCGTCGGAAACCTAAGCCCGGAGCTGGTCTTAGCCG
CAGCAGATTCAGCTGAAACCGTAGATGCTTAAAATCAAAAGGTTTTAACTTTTAAGAAAATGTCCCTGTN
TCTTCGGATGTTGAAGGAGTGCAATAAAAGGAGTTTAGGTGTTTTATATGTCTTGAACTTTTCTNGTGTC
TTTGTTTCT
>gi|3449918|gb|AI099606.1|AI099606 34332 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158H10XP 3', mRNA sequence
TANATTGTTTTTGTGTACTTTATCCGAGTGGATAAAGTNNCGGGGAATGTTTTTCTTTTGTACAAAAAAC
TGTCTTCCCNCCTAAGCAATGNGTGTTAGTTTCTGTTTTGGGCTGTGTTTTGCAAGTTTTTGTATTTCAG
AGTTGTGTAGTGTAGTTGCAAGTGGCGGTTGGATCTTTCNCTATCTTGTTGGATTTTGATGATGGTTGAT
GCTTTTGCTTTAATGTTNAATAAATAAGCATACTTTTGCT
>gi|3449917|gb|AI099605.1|AI099605 34331 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158G3XP 3', mRNA sequence
GCNCAATGAAGGCCTTTCCCGTTTCACATTTGCAANCCAGGCGGGACTTNACATGCTGGAGGACNACATT
AGNTNCTCCTTCAGNCATCCTCTTTAGAGGAAGATATTTGATGACAATGGAAGAAAGACTCTTTGCTCTG
AGTTCCCACAGCTCATGCAACAGGGNTTCGCGTGCCTTCAAGGCGGGATATGTCTCTCAAGCATGGGGAG
ACCAGTNTCGTATGAGAGNGCAGTTGCTTGGAAAGTACTAAATGAAGAAGNAAATGCTCATTGCATCTGC
TTTGTGTTCATCAATTGGTCCTTTGTGTGAGATTTATTGTATTTTGTATTNTCAGACTAAGCTTTTGCCT
TTTGGCTGTATTGTAAAACGGTCATGTTGTTGTTGTTGTTGTTCTTGATGTTGCTGTGAACACGTAAAAC
AGTGTTTTGTTTCAAAACTCAAGAAATGCTTGCTT
>gi|3449916|gb|AI099604.1|AI099604 34330 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158G23XP 3', mRNA sequence
TAATCTTNACCAAGGGCAAGCCNTTGGATGACCCCCTGGATATTCTGGGGGTGGGGCCCATTCCATTGGG
AGGCCTCGATAGCTGCATTTTATCACCAATTCGTTCTAAGGGCCTCAGCTCCAAGTCCCTCGGTTCATTC
AGAGGTGCAGCCAACGTTTAAACTTAGCCACGAAAGGANAAAAGTGTGCCTACAATTATGTNGAAACATA
TCCTCTTTTCCACTCGTNTCTTAGCTTCTTCCTATTTTCTATTTCTAACTGTGTGATTCCATATTAAATC
GNGTGAAATGTTTTTCAATTCATCTTTGCAACGTATGTAAGTTTGGTGTATTGAGAANGAAAATCGNGAA
AGACAACTTTTTCTTCGCT
>gi|3449915|gb|AI099603.1|AI099603 34329 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158G14XP 3', mRNA sequence
CCTTTGGGCGTGTTAACCAACCNTTGTGATTGGGACCTCCNCAAAGGTTGCCATTTCTGGNGTCCACCAC
TGNGNAATTCGNTGGCCAAGTTTTTTTGGAAAGGTTGCTGAGAAGAAGAAGAAGNAAACAGAAGGCGAAT
TCTTCGAAGCTGAGAAAGAGGAGAAGAAGGAGATCCCACAGGAGAAGAAGGAAGACCAGAAAACCGTTGA
TGCTGCTCTGATCAAATCCATTGAAGCTGTCCCAGAGCTCAAGGTTTACCTTGGAGCCAGGTTCTCATTG
AGTCAAGGAATGAAACCACATGAGCTTGTTTTCTAGATTTCGTAATTGTTTCTCGAATTTTAAGAATATC
TGTTTCCCCGAGTTTTTTCATCTTTAATCGTCCTTGGATCTTAAAGACTATTTTCTCTGNTTTTATATAT
CAAATTTTCGAGC
>gi|3449914|gb|AI099602.1|AI099602 34328 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158G13XP 3', mRNA sequence
TGGTGCCTCCATCGNTCNCCAAACCGGTTCCATGNTCCCCAAAGAAACTGGGGACNCTACTCGACGNATG
AGCCCACAAACGCGTTCCAACTCAAGAATTGCTTTCTGCCCTCNACATGCATAACGAAGCTGTCAGAGCC
ATTGAGGTTTCCTCCTAACACTCACAAGGAGAANGAAAGCGATGAGAAGAGGAGAGAGAGGAAGCNACAG
GAAGAAGNGCTTGCTAAGCATATGGCTGAGGAAGACGATGATGATTNTTAGACAAAGGTCATCTATNTCT
NATAAGAGTTGACTCTCCATCTGTCTCACTTNTTTTATGTTCACAAGTTTACTTGGTACTCTTCTCATCG
TCTCTAAGTGTTTCTTTATTGAGGATTTTTATCCTCAGGAACCTTTTTATTACTCTGGTTTCACTTTAGG
AAAAGATATTTATCTTGTTGGTTTC
>gi|3449913|gb|AI099601.1|AI099601 34327 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158F8XP 3', mRNA sequence
CGTGGGCAATTTCACAGGAGGGTGCAATGTANTCGTTNCCCTCAAATCCGGTTACCCAACGGGNGCTCTC
CAAGCTGCAACCACNAGCNTGGGANAAGTNCCAAGACGTTTTCTTACTGTCTCAAAGCTCTTAGANAGCC
ACAGGAATCTCNCACAGTACCTGGCTCTGGATTTGGACAGAAAGNAGGTGTGTNCCATCTGAGGACNACA
ATCCTGCCAGCAGAAGATGAGATGCCGGAGATCATGGATAGCTTCAAGAAGTTCAACGACGAGTTCATGA
CTCAGTATGATAATNACTTTGGTTATTCGAAAATGTGATTACTTCTTCTTCTGAACGACTATTGTGTTCT
GCTACACTCTTTAAAGCTAAATCTCTGTAGTACACTCTTTCTCTTTGCCCTATTCTATAAACC
>gi|3449912|gb|AI099600.1|AI099600 34326 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158F20XP 3', mRNA sequence
GCCCCAACNNAGTGGTGATTCCTNTTGGGGAACAAGTTCCGATCTTCGTCNACTTGGTGGCANTCCAAAN
CAGNAGAGGCTAAACCCTTTGCTGAGANAGAATCCCCCTCTATTTCATGGAGACTTCAACCTCTAGNCCG
CAACCCCATGTTGAAAACCGCATTCCACGGAAGTGCTCACTCAATCCCACAAGATNGTGAGCAAAAGAAG
TGTTGATGGAGGAGGAGAGTCGGCTGATTTACCGGGAAAAGGAGAGACGATAAACGTTAAAGAAGACGGA
TCGGTTCTTAAGAGAATGGGTTGCTGCTCTAACTAGAGTGGGGGGATTGTAGATTTGGCTTGATTTGGTT
AGGGTGAGACNACAAATGATAATCTCTTTGGGTCTTGCAATCAAAAAAGAAATNAGAAACGATTACTTTT
AAGNTCATGTGTATGCTTTGGTAACTTTGGCCTGTAAGGTCCTTTAAAATTTAAGTACATGATTGGT
>gi|3449911|gb|AI099599.1|AI099599 34325 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158F13XP 3', mRNA sequence
TTCCAGTTTAGGCCCCCTGGCATGTACNTCACTGGAAACCGGGNGAGGCTGAATTTGGTNCCCGATAATT
CTTCCTTNAAGACGGTGACCAGGNTCGATTTACACGCTCGACATCTCGAAATGGGTTCCAAGACGCTNCC
TCTGTNGGAGCCCAATGTGAAGGGNTCTTTCGCATGGTCGTTGCTAGACNATCTCGAATGGGCAATGGGA
TACNCGGTCCGGTTTGGATTGGTTTATGTGGATCTCAAAGACGGATGTNAGAGATATCCCAAGNAATCNG
CTGAATGGTTCAGAACAGTTATTGANTGAAAAGAAAAACGATTGATGATGATGAGATATGTATATTTCAT
TATATTAGTTTCTCTGTTACTCTTGAGAGATTTATATATTTTTCCCCCCCTTTGGAAATAAAGAGAAATG
GTTTTAGCT
>gi|3449910|gb|AI099598.1|AI099598 34324 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158D6XP 3', mRNA sequence
ACCTGGACNTCAAGNATTTTGATTAGCCCGCGCGACAAAGTCGGTGTCGGAGGAGNAGGAAGGACGATAC
AGGCCAGGTCTACTATCTGTACGAGATAGATGGGGTTGGAAAGCACAGCCTGATCACAGTCACTTGCTCC
AAGAACAAGCTCTACGCCCATTTCGTAAACGCCCCTGCGCCCGAGTGGAACCGCGACCACGATACATTAA
CCCACCTTCGCGACTCCTTCAAGACTGTCTCTTCTTCTTGAAATTTCAATGTTTGCTTGTCGAAATGTAT
TTAATTTGGTGAGAACGAGAATGGGATACATAAACTGGAGTTTGTTTTGTGATCCTTTAATTATCATCAA
TTNTTATATAGGT
>gi|3449909|gb|AI099597.1|AI099597 34323 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158D16XP 3', mRNA sequence
CAAATTCGGNCNGGGGCCCTTAAGTTTTCAAGCTCTCTGGGTGCCCCCAACCCAGNTGATCCGTTTCTNG
AGGAACATTGCTAAGCACTGGNAGGGGTAATGAGGGCAGAAGCTGTGGATACAGCTAAGGAATGGACCCG
TCTTTATGCAAGCGGCGCATGATAAATTGGAGGGTGAAAACTGNAAAGATCTCTTTCATCCAAATNACAT
TACATTTGCTGAAATCTATCTCAACATCAAAGTTATAAGAAAGCTTTTATTTTGCTGGTTATTTCCCCCC
GCCACTGCTCTGTAATCTCTCTGAATCACACTGTATCATTACTCCTAGGATCAATACTCGTTCTTATATT
TGAAGTTCGTCAAAGTCTTTTGAGTCAAAAATATCTATGTTTCTCT
>gi|3449908|gb|AI099596.1|AI099596 34322 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158D13XP 3', mRNA sequence
AAATCCCTTTNAGGGTTNGGCCCCCTAATTTTAACATCCCTCGNGGGCAGNCATAGCCCGGAAGCCATGG
ACCAAAGTTCATCNAATTCTGAAANCCAGCCACTTNGCAGTTCCTGAGGCTGTTGATTTTGTGGACAAGT
TGCTGAGATATGATCACCAAGAAAGGCCAACAGCTAAAGAAGCAATGGCGCATCCATATNTCTATCCGAT
TAGAAATGCAGAGAGCAGCCGTACGCCGCGCAGCCAGTGATCTCGAAAACATTTGCTTGTTCAATCTTCT
GATTTNTCATNTCTTTACGGATTCAAATTTGTTATAAATCGATCTGTCATTGTTTCATTCTCTCAAGTGT
GCGTGTGTTACTGTT
>gi|3449907|gb|AI099595.1|AI099595 34321 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158D12XP 3', mRNA sequence
GTGGCCAATTANGGAGGAAAGGGATGGNAGNTCCCATTGAAAAATCCCAGGGAAGTNCCGATCAGGTANA
TCCGTTAAGCCTTTGTGAGTGTGAGAAGACCCAAAATAGGAATCGTCGTTGTGTAAATGGCCAAATGNGT
GTTAGTAAGTGACTTGTTGTGTCTTTGTTGCTTTTGTTTTCAGGAAAACCCCTTGTGATCAAAATTTGAG
GGGTTTTTGTTTTAGCTTGAGTTTCTGAATGTATATCAATTCAGCTACCCGTTTATNTNATAAATAATCT
CCAATTTTAAATGTTACTCTCTTTTCTTTTTGTGTGTTTTCTTCTTACTAGTGACCAATGTAACTTGACA
GTGTCTTCTTGTACTAGCGTACTAGCGTTTGCTTGTCCC
>gi|3449906|gb|AI099594.1|AI099594 34320 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158C8XP 3', mRNA sequence
AATTTCCCGGNCCANGCCCGNGGCCGTTTNNTGTTNCTNCGTGCCGNTCCCCACATCCAACTCCTCTATT
CAGATCTGGAATTTCATCGTTGATGGGNACACAATGGAGCAGCTCAAAGGGGAAGATAGACGTAGATGAA
AGAGAACCAAGTCGGTGTCTTTCTTAGCTCTTGAAGGAGATGTGTTAAAGCNATATAAGAGCTATAAGAT
AACACTTGACGTTGTTCCTAAGGATCATAAAGTTTGTATTGCAAAGTGGACATGGGAATACGAGAAGTTA
AATGACGACGTTCCTCCCCCTACCAGATCACTGCGTTCGTTGAAGATTACACACGCGACCTCGAGACTAG
ATTGTTGTCTGAATCATGAATATATCATCAATGTCTCCGAGTTCCTTGTCAAATAAATCAGATCTTGCTA
TGAAAATAATATTTTTAT
>gi|3449905|gb|AI099593.1|AI099593 34319 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158B8XP 3', mRNA sequence
CTGTAGGNCTTGGAAGNCTATGGGTTGCAGGAGAGGNGGCCATTGGAGTCTCTGGGAGAAGAGAGTCGGA
ACCAGTGATGTATCAGACGTCTGAGAAGCTTGGTAAGTACTGTGGATCGCCTAGATCTACCTTGAAGTGT
GAATGGAGCAGCAACAATAGCTGCAGCAGCGAGGACGAGAAGGACGAGGGAATCTAGCAGAATTTCTCTT
CCTAATAACTATTTTCGAGCTTTCTGTTTTTGTTCTCTCTTTTTCAAAAACTTATTAAGCTCTTATGAAT
AATGACTTGTGAAGTTTGAGTTCGTCTCCTTCACAAGCAAGTTGTATTGGTGTTTTCTACTTTATGAATA
TGGGTTTTATATACCTAAAGACTTGTTATGTTATTATTCT
>gi|3449904|gb|AI099592.1|AI099592 34318 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158A5XP 3', mRNA sequence
ACCTTNTTTCCAATTTNNAAAGCNGCGGGGGACNCCCTTTACCCCAGGTTCCAGGNTCCAGGTTCCCATT
TTTGATTGGTTCCACCACCTCAGGTGTCTGCTTTTAGCCCGGGAGCGTCCAAGGGCGNCGGGGACAACAC
CAACACAGGCACCTGCACCGGATACTCCCGCGGATGGACCAACGGGACCCACAACTAAATCAGGAATTCG
ACCCGTAGATCAGCCCATGCAACCCACCGGCCTCGCTCAATCTTCTACTTCTCCATTTCTCCCGTTGCTT
TTCATATCTCTTATCCTGTTGAACTTATAAGCCCAATCGACGTGTAAAGTCTTTAACCTGTTATGCATGT
GTTGTCAGATATTTTCATT
>gi|3449903|gb|AI099591.1|AI099591 34317 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158A15XP 3', mRNA sequence
TGGCCANACTTCTTTGCAGTTCCCCNTTGGCATTTTTGNAGATGGAAGCCCGGGGCTAGCTTGAAAGGCT
CTTGCAGTGGCTGAGAAGANGACTGTTGGGAGNTCGTTGGCCAGAGTACTACGACACCCGNTCTGGCAAA
TTCATTGGAAAGCAGTCTCGCCTCTACCAGACATGGACAGTCGCTGGATTCTTGACTTCTAAACTCCTCC
TNGCAAATCCAGAGATGGCATCACTGTTATTCTGGGAAGAAGATTACGAACTTCTCGATATTTGTGCATG
TGGTCTTAGAAAATCTGACCGGAAGAAATGCTCCCGAGTCGCTGCCAAGACTCAGATTCTTGTTCGATGA
ATGCAANACAGTCTCTTTTGCTACTCTGAACATTCGAACACAATAAGCTTTTTAGGCT
>gi|3449902|gb|AI099590.1|AI099590 34316 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157P9XP 3', mRNA sequence
CCCACAGGCCCCAAAGGGGGGTTTCAGGGCGGCCCCAAAGGGNGGGAGAAGGATCCCCATCGACTTTTGT
TCTTGGGNTTTATGACAAAAACAAGGNTCAGTTCTATGAGGACTAATCCCACTTCTAAAGAAGGTGGATG
AGAAAGAAGGCACCACCACCGGAGGCCGAGGAACCGTTCGCGGTGGTAAAAACTCAGCTCCGACGCCTGT
GCCGAAGAAGAGCGAGGGTGGATTTGGTGGCTTAGGAAGCCTCTTCAAGAAATAGAAGNCNNAAATGTAT
AGTNATTTGCATTATTCATGCCTCTGTTTTCATTCTCTATAATTCTTCGGATTTCACTNATATATAAGCT
ACTCTTTCTTAATCTTATTTGAC
>gi|3449901|gb|AI099589.1|AI099589 34315 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157P7XP 3', mRNA sequence
GAANCCGGGTTTCCCNGGCAGGTAAGGTTCCCGGAACAAAGTTGGGGGTATCNCAGTCCGATGTGGCGCG
CCCCTTAGTATTTGCTGCCATTGGAGCCGGGATATGCTCTTGCCTTATCCGTCCCCTCCACGGGCCAATG
GATCGGTTGCGCGCTGGGAGACTTGGCTGGTCCGATGGTTGTTTCGGTTTGCCTGCAGAAGACTCTTCAA
GCTGATTATTAAGTTCTTGTGTGGAAATTGAATTCTTCTACTTGAATCTTGATGATCCAAATGAAATCAT
AGAGCTTGTTTTTTGTTTCTGAAATTTCTTATTGTCTTCACTGAACCTTAAACACAATGATCAATAGATT
TCTCAAAATGTACCTACTTTTGACAACAGCACAATAAGTCAGGTATTTATTTTCCTC
>gi|3449900|gb|AI099588.1|AI099588 34314 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157P5XP 3', mRNA sequence
GCAAGGAACGAGAGGCCTTGGGAGCTCTACCACTATACCAGCGCACACTCCCATANGCATNCCTTTCCCC
TTNTCTTGTGGTCAACGCTGCTTCTCTGCATAAATCTGCAACATTGATATTTTNGTGCTCACTTTCTGNA
CAGAGCTATTTACTATTTGNAAAAGCATAAATCTGTGATAGTTTTCCTAAGTGGATATGTTGCTAGTTAC
ATTTTTATCGCTTTTGCTGGCTTGAATAAAATCGACGACGCAACTCAAGTCTGTCTCGATGATTT
>gi|3449899|gb|AI099587.1|AI099587 34313 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157P3XP 3', mRNA sequence
CCATGGGGNGAAAATCCGGAGGGACCTTCCAGGGCCTTTTTTAAATCCTACGTTGAAGTGGATGGCCAAT
ATGTGGAGGNGGGATGCGTGGGCCAAACCATGTAAGATATGCAAAAAGGACCCCAAAGGGTGAGGCAAGA
CAAGTGGACAAGTTAGGGAGATATGCTCATGTCTCTTGTCTTCAAAATCCTCCCTCTGGAAATTTCTTCA
CCAGGCTCTTCTCTAGATGATGATGATCAATTTCCCAAATCATATGAATGTGTTTGCTTGTAACTAAATT
ACTCTTGAAATTTTGTGTGTATTTTTATAGAAATCGAAATTCGTTCTACATACCAANACAAACATCACGG
TTATTTGGGATCTTGTTAAACAAGAGACAGAAGTGGATGTATACATTTTTGGTTTAAATGTTTTCAAGTT
TTTAT
>gi|3449898|gb|AI099586.1|AI099586 34312 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157P24XP 3', mRNA sequence
GGAGGNCNTTCCAAGGAGCCGGTGGGCCGACAAGGAGGACGGGGGACAGTCGGGGAAGTNACTGCCGCCA
CGGCTGCTGCTACAGAGGTTACAACGGCTGCTCAAGATGCTGCTCGTATGCCGGAGAAGCTGTTCAGACT
CAGCCCGGTCACTAACACNATATCTTAACCAATCACCACCATGCATGTATNGCATTATGTATGTATGATN
TTAAGTAAACCATGGTGCGTTTGTAATGAACTGCCTCAAGTTTNTGAGGCACTATAGATTAAGNAGAGAA
CTATGGGAATAAAGTTTGATTATGTAATGTTTTATGTGGTTTGAGTTGTAATACTTGCTGTTTGCATAAT
AAAATCGTTTGTAGTT
>gi|3449897|gb|AI099585.1|AI099585 34311 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157O14XP 3', mRNA sequence
CCGGGGGGATTCCAACGCTNCGGGCTTTGCACAGCCNTCTTCNGGATGTGCCCCNAAATTCAAGAGTTCT
TTTGGTGATGGTNAATTNGCAAGTGGCAACCGAGCTCAANGCTTATGGCAGGAGGAGACTCAGATGGGNT
CAGAAATACTTNATGNTCNATNATTATTGCTCTGATCTCAAAAGGTTCCCTCGTGGATTCCCTCCAGAAT
GCAAGAAGTCCAGAGTCTGATGAACACATATTACCTCATATTTCTCTGCTTGTTTGATGCAATTCTTAAA
TTCCTCTGTTATTCCATTGTACATTGTCAAGNTCAATAAAGCATTCCTGGTTTC
>gi|3449896|gb|AI099584.1|AI099584 34310 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157M6XP 3', mRNA sequence
CCCAGGACCATTTTTTGAANCCCGNTACAAGGGATTCATCGTTACACAGGATGATAATGGAGNGGTTATA
TGTGAAGGATACGATGAAGGTCCTCGTTGTCCCACACANGTCCCAATGGTAGCTTCTTACTCAAGAGAGG
TGGGAGATTCTTGATCTTCTGCAAAGAAGTTATCCAGGAGCTGAGCGATTCAAACAAGGATGGTCAAAGA
CCGATAATTGCTTCAGAACAAGAGTTCATGATGATCAAATGGAGCAGCTTTGACTTCCTCTAAATCCCCT
TTCTTTTTTCTTCATCGAAACATCAAAATCTGGTTCTCTCTTCAAAAAGGCCTCTTGAATAAGAATGTAC
AGAAAAAAGGCTATGAAAGAAGCAGCGATTTGCTTCTTTCTTGTTTCTCTTTTGTAAGAAA
>gi|3449895|gb|AI099583.1|AI099583 34309 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157M14XP 3', mRNA sequence
TCCCAAGGACCCCGGNCNTAGNAAGTNNTTGAGCCTCTTCTCTACCTTTTCANGAAGCANATGACTGGNA
AACTGTTTTGCTTCACAGACGGGGATCCATTTGTCCAGCACAAGGAGCNAAATTAGTAGCCGGGAGAGAT
ACTAAGAGTGGTTAAAAGAAGCGGAATGGCATCCATCACTTCACTGGAAAATCAATGCCAACAGAATTCG
CAGATGACTCTCCTTATGATCTTGTTTCAGCAGATGGCAAACAGACAGTAAATTCTTCAGAATGGACTTA
TTTCTGGGAAGAACAATGGGACTAAACATTTCAACACACACAACAACAACAACAAGACCCTATCTTCACA
TAATTCACTGTCTTAATGTGATAAAGCTTTGCATTAGATTGTTTACATTACAAGTGTCTCTGCTATAATC
TGATTCAGTTTCGCTCG
>gi|3449894|gb|AI099582.1|AI099582 34308 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157L22XP 3', mRNA sequence
GGTTTTTGGTNCCCAGGCTGCCNCTNNCGCCACCCNGATCNCNTATGGNAAGNGTGCCCCGGAGGGGGGG
TTNGCCCNAGGGAGTGNCCTATGTNATGNTGGGTGNTTTACCACCACCACCATTNAAACNGAGTNTTTTG
GGTTCGAGGAAGAGACTGACCCATGAGCTGGATGAACATTGTGGGAGAAAGCTGATGATAGTTGCTTGGA
CATCTTCTGAGAATTGGGGAGGTCTCAATTCTGATTCTCTCTTAGACCAATCTAGCAGCAATTACCCTAA
CTGGTGGGAGTTTTGGTCATAAAAGCATATAAGAAAAAAACAGAACATAAGCGAAGAGAAAGAGTGTGAA
TAGTTTGTAAATTATGTGTTAAGAAAAATAAATTTAGTTTAGTTTAAATCTTGTTTCGATCTATGTATCT
ACTATGTTCAATACTCTTTGTAGCTAATTAGTAGCTTATAATGAGACTAGAAAAGTTTTGAAGTCACCAA
GGTT
>gi|3449893|gb|AI099581.1|AI099581 34307 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157L21XP 3', mRNA sequence
CCTNTTNCAAAGTCTGGAANGCCGAAGCCGTTGAGATTTGGTCAAGAAGCTGGGCTAACTTTGTCCCCCA
GAAGATGCCCCTTCTAGAAAGTTGCTCGAGGAGGTGAAGAACAGCTACTATTTGGTAAGCTTNGTGGACA
ACAATTACATCAATGGTGATATCTTCTCTGTCTTTGCTTGATCTCCGAGAAAACCACCGGCGAAGAGGAA
ACATTCGATTTCGAGATTTGTTTTGTNCCTTTTAAAGTTATTTTTGATTCGTAATANCCTTACTTTGATG
AATCAACAAAAACATCAGTTTGATTGCAATGAAAAAAATCGCCTTAGCGGTTTGTTCTTTCAAAC
>gi|3449892|gb|AI099580.1|AI099580 34306 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157K5XP 3', mRNA sequence
ATNAAAGGAATTNAGGCCNGCAAACGGCCAGCNCNGTAGCNGTGNAATGTGAAGCNACNGCAAGCGNAAA
GACTCTGNTAAACTTAGGAACAGTTNAAAAGTGAATGACGNTCACCAGAAGTCCCAGATGTTGTCGTTGT
GTCTCCATTCGCCATGACATTCACAAGAATCAAACTCAATATCTTCAAAGTAGGCTCCTCTATACTATTC
TGTACCATTGTCTTGTAAATTGAGGATATGCAGATTCCATACATTTTGCAATGAAACACTGTGATAAGAA
ATATGTTGTTACATATGTGTTTTTGACTTATAATAAAGCATTTCATTTGTCT
>gi|3449891|gb|AI099579.1|AI099579 34305 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157J7XP 3', mRNA sequence
GAGGGNTTGCCCTTAAGGNTCTTGGTTCATGGGGCCAAAGCGGTGAAAGCAAACNGGGGGCAATTGNTCC
GGTAGATGGAGGGNCCAAGCCGGACNAGANNCAAAGCCGGAGTNAACCAAGAAACCAGCCTCGTGGTGAA
GAGATGAAAGNTCTGTTCAAGAGTGATATGGGCGAGAAGANACAGGGCAGAGCGGTGCCGCGGCTGCAGC
AAAACCTCGGACGAAGTCGAAGAACTCATTCAAGAGCAAAGCCAGATATAAGCGTAGGTNAAAGGNAAAA
GCATTTTTGAGAAGATATCGAAGGACAAACCCACGAGAAGAAGGACATTTCATTGAGAAGGGTTTAAACA
ANNTAAATTATTGTTGTAATATCATAATTTAGAACAAAACTGGTTAAGATGTTCGAAATTTTGTTTTCTT
TGTCCTATGGTTTTTATAATCTTTCAT
>gi|3449890|gb|AI099578.1|AI099578 34304 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157J6XP 3', mRNA sequence
CCTTGCCNTTNNTGCCGTCGAATTGCTAAGGAAGTTGCTACCTTCTCCGCAACAATGGATCCCTTGTGTT
GAANTCGAGTTGGAGCNCGGATTTGTGTACCGTGAGCACGGAANCACTCCCGGGATACTACGATGGACGG
TACTGGACAATGTGGAAGCTTCCATTGTTCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAG
AATGCAAGAAGGAGTACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATG
CATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACTGATGCTTAAATCCTTTTCTGGAATATTCAATGT
TGACTATCCGGAACCCAATTTTGTATGGTCAATGTAAATTTAAGTAATTATTTTGCCAAAGTGAAAAAAC
TGAAGGTTTGTTTTTCTATCGTTTCCTCTATAAAAATCTCTATTCATATC
>gi|3449889|gb|AI099577.1|AI099577 34303 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157J17XP 3', mRNA sequence
TTACCCCGTTTTNTCACCGGTTCTAGAAATCTTTTGAACACNCTGANNTCCTTCNCGGATACTGCCCGTG
ATNCGNACGAGGATGATTNNGACTTAAAATCGCCGCGGACNTACGACGAAGGAGAAGGATTNANCGGATN
CTCGAAACGGATGTTGGAACGGAGAGTGGGATGGTAAATCTGGAGTTTGTCCGAGGGTATTTTGGAGATT
TTGGAGTTTTGGTGTTCGGGAAAGTAAGAGAGCTATGACGGCGATACCTGTGCCGCCGTCAATCGCTCTG
CACCAGCTGTACTCGGTTCCTCCGACGGGTCGGGTCATGGATTTGGGTACCCGATTTGGCTCACTCATTA
TCCTTGAGAAAGAAGAGAGATTGTTTTCACTTTTTTGGGATTTTAAGATTTTACTTGTATCATATATTGT
CAGGTGGGTAAATATGGGGAAGATACAGTGACGTACCTTTTACTCGGTTAAGTGTAATTTTTCCGGTTTA
TCAACCAAATAGAAATGATTTTGC
>gi|3449888|gb|AI099576.1|AI099576 34302 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157H6XP 3', mRNA sequence
ACCCTACCTCAGCCAAAGTTTAGGGNCANCCCCCCCGTGTTTTTCTCGGGGTATGGGGATGAGATGTTAC
CGGATGGTCAGNNNCGATTGTTGGTCCACTAATGACCGCACGTGGNGTGTTNGCAGTTGTACCACGGTGA
CTCAAGGAGTCAGCCACCGTTAGGGATGGTCCGATGGAGTGTGACATGCCGGGTGATGNAAATATNGTGA
CCTGATCTTCCGCCACCTTACTTTGTNNCNNTTATATTGTTTTTGTGTACTTTATCNGAGTGGATAAAGT
GACGGGGAATGTTTTTCTTTTGTACAAAAAACTGTCTTCCCACCTAAGCAATGNGTGTTAGTTTCTGTTT
TGGGCTGTGTTTTGCAAGTTTTTGTATTTCAGAGTTGTGTAGTGTAGTTGCAAGTGGCGGTTGGATCTTT
CACTATCTTGTTGGATTTTGATGATGGTTGATGCTTTTGCTTTAATGTTAAATAAATAAGCATACTTTTG
CT
>gi|3449887|gb|AI099575.1|AI099575 34301 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157H19XP 3', mRNA sequence
TGCCANCAATNTNCCGNTATTGACAACGCGACCAGCCGGCTCGAGGATTTATTNCTCTTGGTGAGTATTT
CCAACGGCTTAGAGCCTTGAGCTCAAGTTGGGCAACTCGACATCGTGAACCAACGTAGGTTTGAGTTATT
TTGTAACAACCAAATGAAGAAAATGGAAAGACCTCAAAAAATGAAGAATGAGTGCATCTGAAAACAGAGG
ACTACTCTGAATAAATAGAGGGGTTGCTGCTGATATTTATTTTTACTCTGCGGCGGAATTAGAAAATTTG
AAAAACATCATGTATTGATAAGTTGTAAATATCAGAAAAAGGTGGGGGTGCAAAAATTTGTACTTTTTAG
CTTTTGAAAGAGGCAAGTTTTTCGAATGTTTGTTTGATTTGTAAACAATTTCAGAATTATATAAACTTGG
TTCC
>gi|3449886|gb|AI099574.1|AI099574 34300 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157G9XP 3', mRNA sequence
ACAGGACCACACTGTTCCCCCAGACTGATGCATCACTCAATCCCCCNCAAAGNGAAACCTACCCGTTCTC
CATCTGGCTCTCGGACCACCAGCACAACTCCTGCTCATGTGAATGATGATCTGATTTTTAACCATACGGT
ATTGAAGATGTCAATAGCAATATCACATCTTCAAGCGGTCAAGAATCAGGAGCTTCAGCTTCAGCTGCAT
GGCCTGATCATCTATTGGATGATTCTATATTTTCCGACATTCCTTAGCCTTCTTTTGTCTTTACTTTCAG
GTATGTACTTTGGAGGAACTCAAATCAAATTTACTCTTGGAATTGTGCTTGTTGGAGATTTTTATTTGCC
TATCTATATATATATAAATACTGTAGAGACATCATATATTTGTAACTCATGTTGTAGAATGTACAGTACA
GAGATTTCATACTCATATGCATATGTTGTTGTCAATGTTCTTTAGC
>gi|3449885|gb|AI099573.1|AI099573 34299 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157G24XP 3', mRNA sequence
AGGANTTCCAGGNTTGGGAGAGGGTAGTCCCGAAGGAATCTTGNGCTAGGCGTATCCTTGAGNGCTCGTT
CTGAAACCCAGGCTCTCGTTACTGTTTGCAAAGGGTAATGGCAATAATACTACCATGATGTCGAAGCAGG
AGTCTGCTGTGCTCTTGTTGGAATCCCTGCTGTTGGGTTCCCCTGCTTTGGCTTCTGGGAGTAAACNTCA
TTTGCCTATTCCCTTATATGTCCCACACAAAGTGTTGCCTCCTACGTCCAGAACCAGAAAAGCTGGTTCT
AAACGGGCTCGGGAGTAGTAGCAAACCGTCTTATACCGGCGTTAGTCGGAGATGTAAGGGTTCGAGGCCT
AGGATGAAATACCAAATCTTAACCCTTGCGGCGTGACAACGCCTTTTTTAACTGCTTCTTTTGCGCATTT
TGAGTTGTAGATGAGTGTCTTTTAGTTTTCTCTCTCTTGTTTTGTATTTCGCTGTTGAAAGTTTTCTGTC
TAATATCGATAAGTTAACAGTG
>gi|3449884|gb|AI099572.1|AI099572 34298 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157G22XP 3', mRNA sequence
CGTAAGGCCGNTCTGACCAAGGTTGGAGCCACCCATTAGGAGCTATTAATGGAATGGAATGTAACCCGTG
GTAATTCCGGTGCAGTCAACGCAAGGATTGGATACTATAGAGACTATTGTGGACAGCTTCNGTGTGGACC
CCTGGTCCTAACCTTAGTTGCTAAAAAACCTTTGAACCCAAACACGGACATATGTGACGTGGCATGTAAT
AAGTGAGATATACTAAAATTTCACACGTATGTACTTTATGTCGGGTCTCGGTGTTCCCTGCGTCACAAGC
AAAAAATTGTTGTAATAAACTTGTGAAAGTGATTTTCTTCTCTTATGTGACTTCTTATGAAAGAGAATTT
TAAGATTGATAGATGTTTGAGTTTGACACTTGCAGTATCTGATTTTGGGATACTCGCATAAATTGATATT
ATAAT
>gi|3449883|gb|AI099571.1|AI099571 34297 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157G19XP 3', mRNA sequence
AAGCCCGACAAGCCCNTCGGAATTACGGCAGCCATGATCTTGAGGGACNGCGTTCNGAACCTCCGGCAGA
AAGGGCAAGGNTACCGGTGTTTTACAAGTACCNTCCGACAAGTATGGGANCTTAACGTCGATGGATACCA
GGTCCTATTTACAACGAGAACGAGTGGTCAGCGAGTGGTNACGTGTACAAGGGAGGAGTCACCGGATTGG
CAATTTGGGCGGTAACTCTCGCCGGAATTCTTGCCGGAGGTGCTCTTCTTGTGTACAACACAAGTGCTTT
GGCTCAGTAAATCTTAAAGTTGTTAGCGCATGTGTAATCATGTTTCTATAAATGTTTCTGTGTTGTTCTC
TTTCTCTCTAATGTTGTAAAACTCAGACATACTTTGAATTTATAAGACTTCTAGTGTTTGTAT
>gi|3449882|gb|AI099570.1|AI099570 34296 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157G15XP 3', mRNA sequence
GGGGCCCAAACTCCGGTTTTGGTACGNACCACGTGCTCGGAGTGGNNCCCGATGCTTAGGNTGCGGTTAC
NAAGGGCATCGAACCTTGTGNGTACCAACGNCTTCCTATNCTCGACGGACGTCACAANCCGAGAAGGCGC
AAGAAATGTTTGCCCATCTTCTTTTTGGGAGCCGATACAATGTTGTCCAACCNNTGAACGTCCGTGAGCT
TACTGTTTACCCAGTCGATGAACCCATGCGTGAATTTTGGGTGCCTCCAACGCCAGCTACTGTCCACGCC
AGCGACTCTAGCTCGTCCACTAGCCGCGGTTACGAGTATTACTGAGTCTTTTTAAAACTCAATCTTTAGG
GTCAATCAGGTTTTCTACAATGGTCATGAGTTNATTTATAACCGAATCAAAATCGGAATCTTGATGTTTT
TGATTTGCAATGTTTTCCTGTTTCTCTAGTGAGTTTTTCTCTATAATAAAAGATTGATCTTATCAACTC
>gi|3449881|gb|AI099569.1|AI099569 34295 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157G14XP 3', mRNA sequence
CTTTNAATCCCGGAGAACCCTATGGATTCTTGACCGCAACCGCAGGATNTCTNCAGGNCATTCCCTTTNC
GNTTAGGTACNCGATCGTATCTTCTAGCCAGTTAAGAGCAAGANCACAGCTACTGGAGAGAAGCTTCATC
GCTTCTCCAAGACGTTTNACATCCGAAACATAACCAAGGACTCCATCAGAGGACACGAGAGATCTCTCAA
GCTCTTGAACCGTAGCAAAGACTCTCAGGACAGCGGATATTGGAGCAATNGTGTGACGGATATGATCAGA
GAAAGGAGAAGCCTTCCATCTCTCAACTTTAAGATCAGCTTCTAAAGACGACNACTTATGGTTGATCTCT
TCAATCTTGGATCCAGTCTTGTTAAGAACCAATGAAAAGGTTTCAGATTTCTCCATCTCACTCTTCAATA
AACTTCTCATTGCTTT
>gi|3449880|gb|AI099568.1|AI099568 34294 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157F22XP 3', mRNA sequence
GCCCATTGGTAACCNGCCATTTTTGGTGCTTCNACTTNGCACCTGNTTCCCNGCCCTCTCTAATCTTCAT
CCCCCAGGACCTCGGGNAATGCCCCGCATGGTACCANCCGTCTTAGTGATTCGATCTCGCACACCGCGTT
TTTGACATTAATACTATGTGAATCTGAAAGAGCTAAAGGNCTTATCCAGCGGATCAAGAGTTGTTTTCCA
GCCCTAATGCCACTGACACAATCCCCCTTGGTGAGAGAATACGCTGATGGCACTCAAAAATTCTTCAATG
CTTTTGTGGAAGCAATGAATAGAATGGGAAACATTACACCTCTCACTGGAACTCAAGGACAAATCAGACA
GAATTGTAGGGTGGTTAACTCCAACTCGCTGCTACATGATGTGGTCGAAATCGTTGACTTTGTCAGCTCT
ATGTAACATAACGTTGTCTCGATATATGTGGCAACCAAAAATATGTTTTATGAAATAAAGTGTTCTCAAA
ATGTTTATGAAGAACATTTCGTCTT
>gi|3449879|gb|AI099567.1|AI099567 34293 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157B8XP 3', mRNA sequence
GATTGGGTTTTANCAAGGGGGTTGGCCTAAATCTTTGCNCCATTCCTACAGGGTGTATGTCCCATAGTGA
AGGGGGTTNATGAGCTTTGNGCATCCAATGAACAAGCTCAAGGCGATGCCGAGGTAGACAGTGAAGGAGT
TCTATGCNGTGCCAACTTCAAGGTGGATGTGNACAATCGTGTTAACAGTATCCCTCGTCGAGGAAGTGAA
GCCAATTGGTCTCTCTGAATACTNTTAATAACACTNTCAATTTGGTTTCTNTTTCGCACTTGTGCTTCTT
CTCCGCTTTCATCTTAGTTATGGACTGTTCCTAAGCTTGCCATGAATAAAACTGTGAATNATAAAGCTTT
TAATGTTCTGTTTCTTACTTTAAGTCAGACAATAAACTTTTAACACTTGTGATC
>gi|3449878|gb|AI099566.1|AI099566 34292 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157B12XP 3', mRNA sequence
GANCGAGTGCCTTATGATATCCAACGGCCNCGGAATGTTGCTAGGGATCCGCACAAAGTCTTGNAGGCTA
AAAAATGCTAACAGGCCTAAAACTATATATAACTACATGGCCANCCNATAACTATNTNCAAATGTATNTG
ANTAACTCAAAACTATATTATGACAACAACAAAAANAAACGTATAAACAATAAAATGNCACTNAAAAAGG
CTATACACTNAATTCCGAATTGAGTTTTTCTGCAATTCTTTAGCTATCTTGTTAACTATGAATGTTTTTG
GAATGTGAACGATTTATGATCCATAGAACTATGTAAAGAGCATTAAATT
>gi|3449877|gb|AI099565.1|AI099565 34291 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157A23XP 3', mRNA sequence
ACAAGGNCGGACTTGAAGAGGTTGTGAGGAAGCTATACGAGACATTGGAGANAAAGNAGAAAGTCTCTTA
CAGAGTCTGAAGCTANGTATNAGNTCNGGATAACGANACAAGAAGATCACAAGGAAGGAGGTNACAAGAA
GGAAGGTAATGCTCAAGGTGTTCTTGTTGGAGCTGCCAGTTCAAGCCAGTAAAACTCTATATTTGGCAGT
TTGTTTTACTGTTGTATCTCTTTTTTGGNTCTTATGGTTAAAAGCCGTAAACTTTGCTGGANAAAATCAA
CATGTTTTGAATGTC
>gi|3449876|gb|AI099564.1|AI099564 34290 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157A22XP 3', mRNA sequence
TCCCATCAANTTGGATATGCCTTTGCATCAAGATNGAAATCACTTCACGGTAGGTAAGNGCATACTTCAA
CCTGTNCCTGATGATAAGGACGAGGGGAAGGCACTCCCTTNACTTATGTGGTCCAGAAGACGGCTTTGGN
GCAAATGCACCACCAAGTTTNTCAAGCATCCAATGCTTAGGCGCATTAAGCCTCNTCAGATGCTTCTTCA
AACCCCTCGCCATGTTTTGAGTTTNGCAAGCGTAGCTCCGANCCGAACTACCTGTTGTTNTCTTAGAAAC
AGCTCCGAACCACTGACTAGTTCT
>gi|3449875|gb|AI099563.1|AI099563 34289 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156G19XP 3', mRNA sequence
GACGTTNTGGGAGGATNCCAAGGTTTGANCCTACCCCTAATTCCCATCTTNNCCGNGATGTAGGGGGTCC
GCCTCAGNTGGGGGCAAGNTATGATATGNGTGTGGAGAGGTGTGTAAACTTGGATGGTCTGACAGAGCCA
CAGATTCTAAAGGCCCTTGAAAACCTTGTGAAATCCGGAGCTACAAAGGCCTAAGTTTGTTTGTTTGTTT
GTTTTTCTCTATATGATCCCGAATAAGATTAAACCGCAANACAATCATTTGACATTTCCTGTCATTCTAC
TACTTTGTAACTCCGTGGTGTCATATCGCCTTGCATTTGAGTTGGTTTTTTTGTGTAATCCTTGAACTTG
GAATTAAACCATTCCGTATAATTGAAATCACAGAAAGGAGAAAAATAAACCATCTCTGTTT
>gi|3449874|gb|AI099562.1|AI099562 34288 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156F22XP 3', mRNA sequence
CGGCTCNGAATTCTTGGCNTAACAGAAAGTTNCCTTNCCGGNTTCAAGTTCCCGTGTGGAAGCACTTCTG
TGGAACTNCATAGATATCCAGAGAGTCCACGAGTGCCAATTCGATTTCAAAGGAGTTGCGAGAGAAGCTA
TTGCTAAAGCTAATCCTGTNGTGAAGGCTGATAAGGTTGATAGGATATGAATTCGTGAAGAAACTGTTGT
GTTCTCTTTTGTTNTTTTATTTTCAAGTCTCGTGATGTTNGTGGTTTGGCTCTCTGTTTTCTGCTCTTAT
TATGGTTTTATTTGCTTTTAGGGTNTCTTAGGAAAGGCCTTAGATTCTGCTATTATGTGGTTTCATGTTT
TGCAACATTGGATTTGTTGTTCTGTAATAAAGTGTTGGTTATATT
>gi|3449873|gb|AI099561.1|AI099561 34287 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156C5XP 3', mRNA sequence
TTANGACCANGGNATCCNAANGCATNCTTTGCCAAGGTNCCCCAATACCAGGAGGGTAAGGCAGTCTTGC
TGCTCAAAGGAAAGCGTCGTTATGACCGTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTCTTCCA
CAAAAAGGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCNGTGTCAAAGCTGCAAGCACTTTTCGCAG
CGTCCTATCAAGAGGTGCAAGCATTTCGAGATCNGTGGTGACAAGAAGGGAAAGGGAACATCTCTGTTTT
AAGTTGGTTTCATCTTATTTTCTGCGATTTTTGTACTTGCTGGATTTGGAATCCATTTGTTTTAGCTCTC
TCGTACAAGATTGTCTCATCTTTGCTTGTTAACTCTATATTTTGAATCATCAAGATATGGTTTTGCTGTT
>gi|3449872|gb|AI099560.1|AI099560 34286 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156C18XP 3', mRNA sequence
CCCACGCGTCCGGCGAAGAAGGGNAGGAGTNGGAGGAAAGACGACAGAGGAGCTCCAGTGGTTGTGGAGG
AAGAGNAGAACCAGAGGCAGAGGAGGAGAAACCCGCCGTGGAAGCCTCCGTGACAGCTCCAGTGGAGAAG
GCTGATGAGTAAATGTGAAGNAAAAAACTGTCTTTTGAAAGACAAAAGAAGAAGAAAATGTTAGCAAGTA
ATTTATTTGCTACTTTAAGTACTTTGTGTCTTGTTATGTTTTTGAGTCTATGA
>gi|3449871|gb|AI099559.1|AI099559 34285 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156C11XP 3', mRNA sequence
AAATCTGTAAGNACNAGACCCAGATGCTCCGGTCCCAGATTTACTCCGATGATNCTAAGAGGATGAACGA
AGTTGTGACTCATGCAACAAAGCTCAATGACGCAATCTCTGGTATGAAAGGTGTNCCTGTCGTAAGAGCT
CAAATATCTTTTGGGGGTCACTACGATGGACTTTGAATCTCAGCCATCATAATAGTTCATAATGTACATA
CATGAATGTAGTATAAGGTTTTGTAAATCTCTATTATTTTGTTCAAATATTGATTAATTATGTGGTGTTA
ATAGATCTTTGTGAAATNTCATGTNNTNNNTTATTATTATTATTGTCAGTAAGAAGTTAAG
>gi|3449870|gb|AI099558.1|AI099558 34284 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156B23XP 3', mRNA sequence
TCGGGCCCACGTNTCACCCACGAGGATCCCGCGGCATCTGGATCNCTTACTGGTCTCAGGCTGATCGATC
CTTGGGACAGAAACTTGCAAGCCGTCTGAACGTGAGGCCAAGCATCTAGAGGCCAATCTCCATATAAGCT
CAGTCTATGTGAGGTACAATCAATCTCATCGNTCTATCATCGCTTGGTCGTTAAATCCGTCAAAAAGATA
ATCACATGTGTTGTTGTTTCTTGTCTATATNATAATAATGCTTGTAATCCCAAAAACTCATGTTTCCTTC
CTTTCTACTCTCACTGTCTTTGTAATCTCTTTTTACAATAAATCAATGTTTCTTGAAGC
>gi|3449869|gb|AI099557.1|AI099557 34283 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156B20XP 3', mRNA sequence
CCCTTGGNGATCCCATGTGATGTGAAGNTGGACCCCTATGCTAGGCCCNCGAAGGGATGTCCCCTGTTAG
CTGAAGCNCCAGAGAGTTAAGGCTAAGAAGGAGANGCTCGCCAAGAAGAGGAAANCCGTTACCAAGGAGG
AGGCGTTGGCAATCAAAGCNGCAGGCAAGTCGTGGTACAAGACTATGATCTCCGACAGTGATTACACCGA
GTTTGATAACTTCACCAAATGGCTCGGTGCTAGCCAGTNATAATCTCGTCTGCTTTGGAACACTTTCCAT
ATTTTAGTCNAAAGATTTTGGTTTTTTTAATCTGTTTTGTCTTTGGGTGTCTGGATATCAAGTTGAATTA
TGAACAAGTTTCACTTTTTTACATCTCC
>gi|3449868|gb|AI099556.1|AI099556 34282 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156A23XP 3', mRNA sequence
AGCCTCNGANAATAATGCATTAAGGCAACNGTTTCCTCTAGCAGTTTNCGTGGTGGACAGTGTGTTGTTG
CCGGAGGAGTTATTCGGNACAAAGACCACTCCCACCGGAGCTCCTGCCCCGAAATCCTCAACTTCATCGT
CTGATGCCGATTCTCCAGCTGCTGATGATGAGCACAAATCTGCCGGATCAAGCGTGAAGAGGACAAGTCT
AGGGATTGTTGTTAGCTTTGCATTGTTTTGTTGCTCGGTTATATATATTGCTTGAACCTTTAACTAAAAG
CGAGGGAAACGTTCCCGAAAAACAAACATTTATTTGCATG
>gi|3449867|gb|AI099555.1|AI099555 34281 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156A22XP 3', mRNA sequence
GGGCTCCCAAGCCCACCGNTGTTCATCGACGGACGGCANTAACGGCACTAAGNCTGNGCACACTCCTCGC
GGAAGAGCCCCATCCGAAAGAAGAAGGAGCGTCGCTGCTTGTTGATGTAAGAGCCCTGTGATTGGTCACT
CTAACATCGACTCGAGATCTGCACTATTACTATTTTATTTGTCGTTTTTAACTTTATTTAATCAAAAAAC
CCTNTCAACCAATAAGCCACGATAAGAGTCGTGCAGTCAAATTTATTTTGGTAGCCCTTGGATCTGCTAT
CAAGATTTTCTTGTATTATCGACTTGTAATTAATAGGACTGTAGCGATATCGTGCTTCTTTATTTATTTC
AAT
>gi|3449866|gb|AI099554.1|AI099554 34280 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156A17XP 3', mRNA sequence
GCTTNGTNCCAAACCAGTGGCTCAAAGTAGCCACAATAGTGCGATTAGAGATTTGAAAGACGCTCTCGAT
TTGTATGATCTGGATCGTCACGGAAGGNTCTCGGCTAATGAGNACACTCGGTTATGNAGAATCTTNGTGA
GAAGTGTTCGATTCAAGATTGTCAAAGGATGATTAGTAAAGTTGANTCTGATGGTGATGGTTGTGTTGAT
TTTGAAGAGTTTAAGAAGATGATGATGATAAATGGTAGTGCTTGATAGAATCGATTTAGAATTTGGAAAA
GTGATATCCTTTTTTTTGTTTGTAAATATTTTGTTTTATGATTTCGTTAATCTAATC
>gi|3449865|gb|AI099553.1|AI099553 34279 Lambda-PRL2 Arabidopsis thaliana cDNA clone 156A11XP 3', mRNA sequence
AGACTGGTTTTGGATTTCTCCGCNCTANTGGGGTTTTTAGGNTCTGGCAAAGCCGAAGTACCCCAAAATC
CAGGCTCTGCAGAAGGCGCCGCCATTATTGTGTAGATAAAGNAAGATGATAGGCTTATCTTTTCCTTCCT
TTTTTTTTTTNTCTTCTTCTTCTTCGTNTCTTAGATTCCCTCTATGTAAAAGATCGATCATTTCATTTGG
TCGGTCAAAACTATGGAAACTCAAGTTCGATCCGTCTCAGAAAACTAGAATATGGACGGCACTTTGAATA
TGTTTAACAATGAGTTACATATATAGTTTAGCTTCATTATATAAGCTCTCTTATTACATC
>gi|3449864|gb|AI099552.1|AI099552 34278 Lambda-PRL2 Arabidopsis thaliana cDNA clone 155M12XP 3', mRNA sequence
CGAAGCTTGNGAAGAAGANAAGGCAAGNGGANTCNAAAGGATCCNCCTGCTGAATCCGACGCTGAGGAAG
ANGCAGAAGATGNTGACAATGAAGGAGATGACTCAGACAATGAATCAAAGTCTGAGGAAACCAAGGAGGC
CGAGGAANCCAAGGAAGCCGAGGAAACCGATGCCGCCCATGACGAGCTCTAAGCAAAGAAGGTGGAGGAT
TAAAAAGTTTTCAGAGTCTTAATTGTTCTNTTAAACTTNTCTTTTAAAAGGAANTCTTTAGCTCTAGTTT
GGTTGGAATGTAGAACNTNTTAGCTATTATTATGGTGAAATGGTTGTGGTAACTTTGTTTTAGACTTTGA
GAAAATCCTGACTTTCTCCT
>gi|3449863|gb|AI099551.1|AI099551 34277 Lambda-PRL2 Arabidopsis thaliana cDNA clone 155I2XP 3', mRNA sequence
CCGGAACCNCNCCCGGTCCTTTGGTGGCCNNACTGGGCCCATTTGGAAGGTTCCCATNGTTCGGATGCCC
CCGGCTCCGCTCAAGTGTTGAGGGNAAGTTGAAGATGCAAGAAGGAGTACCCTGGCGCCTTCATTNGGAT
CATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGTTCACCG
AAGCTTAATCCCCTTTCTGGAATATTCAGCGTTGATTATTCTGGAACCCATTTCTATGTGGTCAATGCAA
ATTTAAGAAATTATTTGCCGACTTNACAGTTGAGGAACTATTGTTTGAAAGTGAAAATGTTATTCCTATC
AGTTTCTCTATAATTATAGTTATCATTTCATTTC
>gi|3449862|gb|AI099550.1|AI099550 34276 Lambda-PRL2 Arabidopsis thaliana cDNA clone 155C4XP 3', mRNA sequence
AATTTTGGGCCGGGTTNAACCTGGGGGGGNAAACCGGGNCTCGATCCGGNTTTGANGCCGGGAGAACGTT
TGCCGNGCTTTTGAGGAACTGGCGGTCGCGGACTACAAAGCCAAGTCGCTCCAGAATCTGATTGATCCAA
ATGCAAGACCTCCGAAGAAAGAGTCTTCTGCTAAGAAATGGCCCAGCCTCGGTTTCAAGTTCTGAGGNCN
NNATTATCATATNAAATAAATCATCCACANATATATTCAATATTTTATTTTATTGTTATTGTTATATTTT
TTATCTGATCTATTTTCTGTATCATAATCTGAGGTTGATGAATTAATTTCATG
>gi|3449861|gb|AI099549.1|AI099549 34275 Lambda-PRL2 Arabidopsis thaliana cDNA clone 155C22XP 3', mRNA sequence
GTAATGGTANNCATTGGGGTGGTNCCGGTTTACACTAACCAACCCATTATGGCTNATGATNTCAATATGT
ATTGATTAACCCAGTTAATCCACATAATTAGATGCCCCTTTTTTGTCTTTTTATCTTAAAATTTAGCCCA
TTTTGGTGTTTTTGGGTTGGTGTGATGATGTAATTATAGTACATGCATCTTTGATTGGTTGGAAGGATAA
ATATACCCNTCATATATATATTGGGGCATATATATATGAGTTGTACTTTGTCATGTATTGGTGTGTGTTT
TGTNATAATTATATGATNATATATGTTTATGTT
>gi|3449860|gb|AI099548.1|AI099548 34274 Lambda-PRL2 Arabidopsis thaliana cDNA clone 155C21XP 3', mRNA sequence
GGGGGCNCAGGGCTTGGTANCTGCCAGNCCNCNTAATNCACACACCAGTTNTTGCAGAAGCTTGAGCTTT
CTGCTTTTTGCGTAACCTGCTCTACAAAGCCGGTTTGGATTTGTTCGGTTCAATTAGGTGCCACTGTGCT
AGGTGTTTTGAAATATTTGGCTTGAATCTCGAGCCTTTACTCTATTTTTGTTCTGTTCCAGTATCAGCAA
CCATGATTTGGTCCAAAAGACTGAAAAACTGTGCGACTTACATCTATGAATAAGGGGCTAAGCTAGTTGT
ACTTTACCAAAAAT
>gi|3449859|gb|AI099547.1|AI099547 34273 Lambda-PRL2 Arabidopsis thaliana cDNA clone 155A6XP 3', mRNA sequence
TTTTGGTTTTTCANCNTCCCCTAANGAGAGAGAGAGAGGGAAGAGGAAGGAGGAAGATGAAGNTCAGTTA
CCGTCGCCGGTCACCGTTTAACTGTCTTATTCAGGTTAGTGTTCGTATATACAGATGCAGTATTTCAAAG
NAGAGTCGAATCTATGTATTCGTTTGGTGTTTTTCTGGGTCGGGCGGATCTTTAGTACTGTCTCATATAT
AACTAAGAGGGAAGATTAGAAGATGAAGAAGCTGTAAAATTNTCTTGGGAAGAAAACTCTGGTTTCTATC
TTCTCGTTGTNATATAGATAATCAACTTGGATTTATTTCTTTCAGATTCACCATTGT
>gi|3449858|gb|AI099546.1|AI099546 34272 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154P7XP 3', mRNA sequence
CTTCCCAGGGCCGGGTTCCCCCAATCTTCCCAAAACCGGATGCNTTTGGCGGNCCCNGGGAAGCANCCGA
TTGGNGTCCCTGTNCCCAAAAGGACCTCGTTGAGACCATCGCTGCCAATGGGAGACCAAGGATTCACAGA
CTTTGTGGCTCCATCTTCTTGAGATAAACCCAAAGAAGCGTCCTTCTGCAGCAGAGGCTCTGAAGCACCC
TTGGCTTTCATATCCATACGAACCAATCTCTGCTTANACAATTGGTGTCTGATTAGTGGAAATGTGAAAT
TTGAGATGAAAAGAANAAANACATTTGTGAAATTTGATTAGAGTGTAACAATGTGTTGTTAAACTTGTGA
TTATTATTCTCTTAGAACTGATTTAAGTNGTAAAACTTTTTGTATCATCTACTGATCCTTAGTNGTTAGT
CCTTTGATT
>gi|3449857|gb|AI099545.1|AI099545 34271 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154O12XP 3', mRNA sequence
CTTGNTTCGGCCCCCAGCCATCCCNGTAGCTNGCCCCCCGGCNTTGGGCCGACCCATNCAACCCGNGATT
NCTGTAGNCTGGAAGCCTATGGGTGCAGAGAGAGGNCATTTGAGTCTCTAGGAGAAGAGAGTGGAACAGT
GATGTNTCAGACGTTTGAGAAGCTTGGTAAGTACTGTGGATCGCCTAGATCTACCTTGAAGTGTGAATGG
AGCAGCAACAATAGCTGCAGCAGCGAGGACGAGAAGGACGAGGGAATCTAGCAGAATTTTTCTTCCTAAT
AACTATTTTCGAGCTTTCTGTTTTTGTTCTTTCTTTTTAAAAAACTTATTAAGTTCTTATGAATAATGAC
TTGTGAAGTTTGAGTTCGTCTCCTTCACAAGCAAGTTGTATTGGTGTTTTCTACTTTATGAATATGGGTT
TTATAT
>gi|3449856|gb|AI099544.1|AI099544 34270 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154N18XP 3', mRNA sequence
TCTGNTCCTTACTGGTCTCAGGTCTGAAATCTTGATCNCTGGTTACTGTCATTGTCTCGTTCTTCAAGTC
TCAGCCGTTGAAAAGTTGTCAAGTNTTAAACATTTTTGACTGATTGGTNNNAAATGTGTGAAACAGGCTG
ATAAGTCTTTGGGACAGAAGCTGGCAAGCCGTCTGAACGTGAGNCCAAGCATCTAAAACGAGTGAAAGAA
TTCTTGATTGGCCTTTCTGTGGTTGTTAATTAGCAGAGAAAAGNAAATGGGAAGAGATCAAAGTTGCGAT
AATACAATCTTCATCATGTGGATCTTCTGTGCTATGTTATAATAGTATCTGTTTAAAGACC
>gi|3449855|gb|AI099543.1|AI099543 34269 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154K13XP 3', mRNA sequence
TTGACTCAGAATTGGNGNNTGGGAAAACCATTGGGTTCCCCTTTNGGAANGCGGNTTTGGTTGAGGATCN
GAACCAGGTTGGGGACCAAAGGAAGTCCGTACGAGTTCAAGCCAGCGACATCATCGAGCATCAACGAAAA
CTTGTCTGCTTTGAACATCCTTTATCAATCTTCTATCGATAAACCAATCCAAGGGTCCCTCATCTTGCAA
GACTAGCCAATTTGCACCCCCTTTTCTATTGTCTGATCTTCTCTGTATCACACTTAGCCTCTTTATTCAT
CTCATCTCAGCCACTTTCAATATAGTTTTGGTAC
>gi|3449854|gb|AI099542.1|AI099542 34268 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154J19XP 3', mRNA sequence
GCTTAAGNCTTTNACCCAAACCAGNTNTCCNTGCCNATGCATTATGTTGGCTCACATCCCCGGGGCAAAG
ACGACCGAGAAAGAGTTTGAGGCATTCGCCAAGCATCAGGCTTCAAGGGCATCAAAGTTGCTGCGACGCT
TTTGGTGTTAACCTTATTGAGTTACTCAAGAAGCTCTAAAAACAAACAATGTTCCTATGAAGATGATTTA
TATGTAAACATTATCTCATATCTCCTTCCACGGTTCCAAAACTATGCTGTTTAATAATGGTTTTTACAAG
AATTTGATTATGAGTTTGTATTTTTGTTTGTTTGGAACAAAATTATGTGATTATAGGGAAAAATAAAATG
AGCTATTATTGAAG
>gi|3449853|gb|AI099541.1|AI099541 34267 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154I9XP 3', mRNA sequence
GAAACCGAAGGAATTTCCGTGTGNANTGGTTAGNTCNCAAGNCTTTAACCCTTGGGNTAAGGAAACCGTT
GAGNCCCCAGTGAGAAAGCTGGNCAGGCTTCTTATTAGCCATGAAGCTCCTGTTACANGAGGCTTTGGGG
CCGAGATCGCTGCAACTATAGTTGAGCGTTGCTTCTTGAGGTTAGAAGCACCTGTAAGCAGAGTTTGTGG
CCTGGACACTCCTTTCCCTCTAGTGTTCGAACCTTTCTACATGCCAACCAAGAACAAGATATTGGATGCA
ATCAGATCCACTGTGAATTACTAGCCCATCTTAGCATTGTACACATGATTCTCTGTCTCCTATCTTCGAA
ATAATTATTGATGCTGGTGGTTCAGACATGTAATGGATACTGTAATCACCACTTTTGTTATTTAATCTAT
GATCTTGAAACTCTCC
>gi|3449852|gb|AI099540.1|AI099540 34266 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154I7XP 3', mRNA sequence
ATTCGGGGCCGGAGTCCTGGGGATANAAGATCGGCCCTTGGGGAACGAACTTGTNNCTTGCTGAGGNTGN
NTTGAGACCCCCCCGTCCTGATGCTGAAGAGCGGATTTGTCTCGAAGCAGCGACGCTGGTGGTCGTAAGG
CCGACTNGTGTGGCTTCCGATGATAACGATGTTGAGCTGGTGACGGAGCGTTCGCCGGAGATGGCGACGA
TTGTATGTACGGAGAAGCTGTTACGGCGTTGCTTAAGCGTAGGAGAAATGTGTTAGAGATGAATTCTTTC
TAAGGCCTAGTGGGCTTTTTTTGGGCTTCCGTTTGTTTGGCCCTTTTTAATGTATATACATACGCATCGT
ACAAAGCCAACTGTACTATTGGCGTACGACTTTTGGGTCAAATGACATCAAATCCGAATTATTCCTCTAA
TATCATATGATTACCACATT
>gi|3449851|gb|AI099539.1|AI099539 34265 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154I3XP 3', mRNA sequence
CAGCTGTNCGAAACNCCCNGAGAAAATGGTTCCCCAAGAAAACGATTTGGNATCCGTTTTNCCCCGGTCA
GCTTNCGAGGAGCCCGAGCTGTTCCACAGAGCNTGCGGGNCTTGCTGCTACAGGTGCCAACTGTGTGCCC
CCCGGNTACGTACGGAAACTACGACAAGTGCCCAAGTCTACGCTAGCCTCACCACCCACGGTGGACGCCG
CAAGTGCCCCATAAGAAGAAACAAAGCTCTTAATTGCTGCGGATAATGGGACGATGTCGTTTTGTTAGTA
TTTACTTTGGCGTATATATGTGGATCGAATAATAAACGAGAACGTACGTTGTCGTTGTGAGTGTGAGTAC
TGTATTATTAATGGTTCTATTTGTTGTAACTTGCAAGTTTTCTTGTTTTGAATTTGTTTTTTTCATATTT
GTATATCGATTCGTGCATTATTGTATTATTTCAATTTGTAATAAGATTTTGTTACCTTTGAGTGGTTGTT
TATCAT
>gi|3449850|gb|AI099538.1|AI099538 34264 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154I1XP 3', mRNA sequence
AGGAGAGCAAANGNATATCCCNGACTCGGATGGCGCANTACGCAGCTGAGTTATGGGAGTTGNTGAAGAA
AGACAACACTTTTGTTNACATGTNTGGACTCAAGGGAATGGAGAAAGGAATTGATGACATTATGGTCTCA
TTGGCTGCAAATGACGGTATTGACTGGTTTGATTNCAAGAAGCAGTTGNAGAAGGCAGAGCAATGGAACG
TTGAAGTCTNCTGATCAAAAAGCCTTTGACATTTCTGTAGCAAAGTATAGCTGAACAAAACTGTAATTTT
CGCTTCTGAATTTCTGTATTTTGAAGATAAGTTTTTTAG
>gi|3449849|gb|AI099537.1|AI099537 34263 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154I13XP 3', mRNA sequence
TCTGCGGACGGGCCGNTCCCCCGGGNTTTCCGTGCTNGCTTTTCGCACAAGTTTGCGTCCGATTCACTGT
TTATGGCCCNANCAANGGCTTCTCTCTGGAGAACCCCCTTCANAATACAGAGTCATCGNCTTGAAAGAAT
CCNCAGNGGGATACTTCNAGAAAGGCCTCGATGGAACATCGTATCTGTCGCATTACAAGATATGAAAGNA
AAANACAATTGAAAGAGTAAATCATCTCAAGTTTATTGTAAGATATTGGTTCGTTTCATGCATCTATTGG
GTTCAGGTACTNGTCCAATTGTCAGATCTTGACAAATAAGTAAACCATTTCCTTTGTACCAAAAACAAAA
ACAACAAAGAAAGGTGTGTGTGTGTGTGTGTGTATAATTTTAGTGAATGCTTTAAATTGGGAATAAAGGT
TCAAACTTG
>gi|3449848|gb|AI099536.1|AI099536 34262 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154H21XP 3', mRNA sequence
CAAGGGNCCTGCCACTTATGGACTTNAGCAATTCATGCCACTTCAATGGAAACTCCGAGCCGAGGAAGAG
CCGGTTTTATGGGCGCCCTCGTGTGTGGTTTGGCCGTGNTAATTCCGAGTGGCAGGGAGCTAGAGGACGT
GGTGGTCGTGGCCAGTNGTGGAAGAGGACGTGATGAAAACGTATCTGCAGAGGATCTTGATGCTGAATTG
GACAAGTACCACAAAGAGGCAATGGAAACAAGTTAGAAAGGGGAGATTAAACCTATTGCATGTCTACATG
TATTCCTTCCTTTAGTGCCGATATGCTTTTGTATTAGTATGATCTTTAGATTGAATGTCAATGGGTCTGA
CATTTTCGAGCTTTAGCTTTTGTTTTTTCTTCTCTTGGTGAGCTTCTTAGCTTTTTGCAGTTGAGTTCAG
AGAAACAAGCATTGTGTGTACCGTGGAACTCAAAACTCTTCTAAAATATCAATTCAAAAC
>gi|3449847|gb|AI099535.1|AI099535 34261 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154H13XP 3', mRNA sequence
TTCCCCCAGCCTTTNTCGGCCNCCCTTTTGGGNAANCTGGTCCCCCTGNAGNTCCCGTCCGGAATTCCCC
GGNTNGCCCCCACGGNCCCCTTGGNCGNGCTTGGTTTACGGGGAAAGTCNCTTGGGCACCCTCTCGNCCA
AATTCTACGGGGAAGTCACTCAACAAATGCTCAAACATGCTGATTTCCCGGGTAGCAACAACGGTACTGG
TCTTTTCCAAACCATTGTTGGATTGAAGNTCAGAGATCTCTATGAGCAGCTCATTGCCAACAAAGCCACT
GCTCGTGCAGAAGCTAAAGCCTAANACAAACGAAGCGAAGCCAAATAGAACGCGTCGATAAATACATCCG
CAGTTTCTTCTTTTTCTTATTTCTTTCTTTCTTTATGCGTTGTTTACCGCGGATTTTCATGGCGAAAAGG
ACGGTCTTGCTTGTTTGT
>gi|3449846|gb|AI099534.1|AI099534 34260 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154G4XP 3', mRNA sequence
GCCGAAGGAAANAAGAGCNANCCAAATNGGGAAGGGAAGGAAGGGAGGATGGTGATAAAGGAAATCGANT
ATGCATAGGATNACGAAGATNACAATGGAGTTCTTGGTGGTGGGTGCTGACGCCGTCACAATCTTCTTAA
GGCAATCTTCTCCACCTCCTCCGGCTCTACTCCGCCATGGTCTCTACTCATACTCTGCCTCCCCTAATCC
TCCTTCTTCCCATTACATCATCGGCTTTCTTCCCTAAGTTTGTAATCGTTTCGTTTTAATGCTTTGTACA
TACTATACATATGTATATTCTTGCCTTTTTNTTTTATAATGAATGTCCTTGTATATTAATTTCTTAATTT
TCGAATAAATCACCTCTCACCTTACTTTCTCTATATGTATGTTTATTTTTATAAACAAGAACTAGTTTTT
AGCC
>gi|3449845|gb|AI099533.1|AI099533 34259 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154G22XP 3', mRNA sequence
CCTTTCAACNCCCCAGTTCGGTTGGAACCAATTTGTTCCAGCCCTNTGGAGGGCCTGGNCCTGGGCCNTC
ATCAATCCCCCCNTTTCATCATCATCATCNCNTCCTTGGTAGAGNAGAGGTTCCGGAACTGAACTGTTGA
AGAAACAGGATTTATGGCGAGGATAACAGCNGTGTTAAGAAGGAGACCAAGACCACCACCTTATAGCTCA
GGACGACCTGGTCAAAACAATTGATTCTGATTAACACTCCTGAAGACAAGCTTGTGTCTCTCCGTGTGGA
TCTTCTTGTTGTTTAAAATTCACTTATGATCTTTATTTTTTTTTACCATCTTTTTGGTTATGTGAGCGGT
TTGCTTTTTTTTTTCTTAATTTATCTGAAATAAGACAAAATTGGTAAGACTCTTTTGTAAAATAGTTTTC
ATGTTTACCTTCTTAAAATACGTGAGACTTTTTTT
>gi|3449844|gb|AI099532.1|AI099532 34258 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154E24XP 3', mRNA sequence
AANTCAAATGTTTCCGTNAGCTCGAGAACAATNGCCTGTGATTANCCCTGATGGAGAACTTCTCCNAAGA
GGCNCCCTGGTGTTANGCCGAGAAAAGCAGAAGACAAGAAGTGATGCTGCACCAAGCACGATCAATATCT
CTTGGTGTAATCTCATTGATTTGACAAATCTAGCTTTTCGGAATGTAAGATCGTTTGCTGTGTGCAACTC
GATATGTGTCTCAAGCTTNGGGTTTCGACTGATAGATTTGTATTGTTTTCTTGTTTATGTGAACCNCAAT
GGATGAACTTTTGGTCAGGAACCGGGACTATGACACTGTTATGGAAGCTATTGAAGCTCTGGGAATNAAA
ACCAATTTTTATAGGC
>gi|3449843|gb|AI099531.1|AI099531 34257 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154E1XP 3', mRNA sequence
CCGGTTTTCTGCAAAGGACCCACCNTCCTTGAACTTCAGCGTCCATCACAATGTCCCCATCATCATCAAA
CCTGTACAAGCCAGTGGCGATCCTAACATTGTAGAAGTTGATAGCATTTTTGCAAGTGGAGGGAGCACTT
GTGTTTCTCCACGTATTGCTGTCTTGATTAAAGCGGTTGTCAACTCTGTAAAGTCCCTCTACTTCAATAG
GTATGGTAAATGAGTTTGATTCTGGGAATAGGTTGTGGTTGTTATAAAGAATGCTCCACTCAGCAGCGTT
GAGCCAGCGCTGTGTTGATGTTTGAAGCACAGCTGCTACATCTGTCAAAAATAGCAACCAAACATATG
>gi|3449842|gb|AI099530.1|AI099530 34256 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154C7XP 3', mRNA sequence
ATGNTGGGTANCCGACTTGCTCNCTGTTGCTGGNGANAAAGGGAGGAAACCGNTCCGATCAGGGGNTGGT
AGACCAGNTAAGGCTCTTCGGATTTTTTCACGTCCGGTGCAAATTTACCGTTTGTGAATCTTGATGANAT
AGATATGTATGAACTTGAGATCAACGGAGGGAAGCCGGATTTCGTAAACTACACGATTCATGGGGTCGGA
GACAAAGGTGTTGTTTTGGTTTTTCCCAAGCAAAACTTTGCAAGGATTGTAAGTGTAGTGATGCCTGAAG
AAGNCCTTGCAAAACTCAAGGAGGAGGTGACTNATATGATTATATAACTTTGTATCTTCTTCTTGTTGTT
ATACATAAATGCTGTTTTTTACTCTTTGTAATTTCATTATCGAATTGTTGGGAAGCCTATCAATAAATTG
TTTGAACTGTTT
>gi|3449841|gb|AI099529.1|AI099529 34255 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154B9XP 3', mRNA sequence
CCGGGGATTAAAGCTCTGGGGNTTCNACTGCCTNGACATTTGGATGCCGTAGCNAGNGAAGATGATGCAC
TGAGGAGTCTNTTTAGAACTTTTATNTCAGACAGAGAGTCTCAAAGCTTNATAAATGTACATCTGGTNTT
TGTNATATATAAGAGTTAATCATTGGTNTTTTACTTTTTTTTTGGTCCAGAGAGACATTTGATCTGATCT
GATATTCCCATGTCTTCAAGACACTAGACGATGAGATTACATAAGCAATCTGTGTTTATAAGCATTTTAA
TTAATTAAGGAGATAATTAGAACATACTGTAATAATTATCTCATGCATGTCTGCAAAACTCTTTTTGAAA
AAAGAAGATGAAATTTTTATT
>gi|3449840|gb|AI099528.1|AI099528 34254 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154B21XP 3', mRNA sequence
GGATCTTTTNTCCAATCTTCTCANGGTGGCCTTCCCCGNTTATTCCNTNAAGGNGTTCACCCTCAATTGN
TGGNGNCCCAGNCCGNGACAACTTCAAATTCCGAATCTCACTCTGAGGACGAGGAAGTGTNAAAATGACA
CTGCTTGTTTGGGCTCTTCAGGATCTCTTGTCAAGACCAAGAGCTGCCGAATTCGGACAACCAAGAGCAA
GTGAAAAGACGTGAAATAGAACGACCATATTTCTATACCTGATACCAAAATGTGGAATATCGAATAAGAC
TAGTGTTGTAGGCTTGTGTAGCATGTCCCGCTGTTTCTCTTTTAAACAGTTGTTGTATATGTATATCTCT
GTTTCCTTGCTCTTTCACTTATTTAACAAAGAGTTCATGTT
>gi|3449839|gb|AI099527.1|AI099527 34253 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154B20XP 3', mRNA sequence
CCCAAATGGCTAAGGAAGTTGCTCCCTTCCCNGAAAAGGGGNCCCCCTGTGTTGAATTCGNGTTAGGGCC
CGGGATTTGGTGTNCCCNGNGCCCCGGAANCACTNCCCGGATACTACGATGGCCGGTACTGGACAATGTG
GANGCTTCCATTGTCCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAG
TACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTG
CCTACAAGCCCCCAAGCTTCACCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTC
ATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGATTGTCAAATGTCTG
ATTTATGAATATNTTATTTATAT
>gi|3449838|gb|AI099526.1|AI099526 34252 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154A1XP 3', mRNA sequence
TCATCCGGNAGCNTACNTTGTTATTCCGCATTCGGAAAANCCCCCNTGGTTTAAGGNCAACTGGTTAAAG
CCAGGGCTGCAGTAATTGATGTTGGAACTAATGCAGTCAGCGACCCGAGCAAGAAATCAGGATACCGGTT
GGTTGGAGATGTTGATTTCGCAGAAGCTTCAAAAGTTGCAGGTTTCATAACTCCGGTCCCTGGTGGTGTA
GGCCCAATGACAGTGGCAATGCTTCTCAGGAACACCGTAGACGGTGCCAAGCGTGTCTTTGGCGAGTAAA
ACAATCTACTGTATGTAATAAAGAAACCAAGAGTTTCTCCATTCTGTAATTGTGTACTTGGCTTGACGAT
ATTTTTCCACTCAAATAAATTGAAATTGGCGTT
>gi|3449837|gb|AI099525.1|AI099525 34251 Lambda-PRL2 Arabidopsis thaliana cDNA clone 154A12XP 3', mRNA sequence
TCCAGGGGCCCCAGGCGNACCNATTNCCCAACANTTCCCNATCCAGGTTGAAGGGTTGGACACTCNAGGG
GGGGGTNCAATTGGNACAAGGTAAGCGTTGGGCTTACACCTACAGGGCAAAGNCAAANGAGGANCGGTTC
TTCACTACCGTNGCATTTGGGGCAAAGTCACTAGGCCTCATGGTAACAGCGGTGTTGTCCGTTCTAAGTT
CACNTCAAACCTACCACCCAAGTCAATGGGAGCTAGAGTCAGAGTCTTCATGTACCCTAGCNACATATGA
GGAGGATAGATTTCAAGAAGTATCGGAAGGAATCGCCATTATCATTTCTCAGGAGCTGTAGTTTATCTAT
TCACTTTTGTTCTAAACTCTCTGTTGGTTTTGATTTTATCTTTAGACGAAGTAAAACATTTTTCTTCTTG
AGATAATATTAATGGNACTTC
>gi|3449836|gb|AI099524.1|AI099524 34250 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153K3XP 3', mRNA sequence
GATGATTTGGCAAACGGATGNGGTTGAAGANTCTGTNATTGGTACCCCTTCTAAGCTGATTTTGCAGTTT
TCGGTGAGCAAANACGAAAATCGACGATCACAAACCAAAATTCTGACGTCGATGGAGGTCACCGGAATCG
AAGACGTTGACGGCAAAGGATGATGGGGAAAGTTACGCAGCTCTCATGCAACACGTGTCTTTGTTATCTA
TTTGCTGGATATTGTGTTTGCTTGAGTATATCCTTCTTTTTCTTAGAATTGTAATCGTATGGGCTTTATG
GGCCTTTTTGGGATTGTAAACCTTGAATATTNATAAAGGTCACTTATGAG
>gi|3449835|gb|AI099523.1|AI099523 34249 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153I21XP 3', mRNA sequence
TCCACTACCCCAATGCCGAAGGTTTGNCGTGTTACCGCCANCTCGATGACTTGTCGCTTGAATNCCGACG
CGAAAGAGAAGTTTGACTGTATGCTAGTCATGCCATGGACAATGGTTGGATCCTTCCCGAGTTTGGGATT
TCTGCAACTCAGTGATTAGTGGTTCTCTTATCAGTTTCTTGTGTTTGTGCTTACGATACTTTCCTCACTA
TCTACATATATGTATGGATTCAGTTAGTAGATAAACATGAGATGTTTATATGTTCATGTGTTTCTGTCTG
GTTGTTGTGTTTTGTCTTTGTACTGATATCTTTTAGTGTGTTCTAATTTCTGATGGATTTTTGTTACATT
GAAAATAAGTTATTAGCATGGTTAATTTGTGTTAACTT
>gi|3449834|gb|AI099522.1|AI099522 34248 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153I12XP 3', mRNA sequence
GCTTGCTTTTGCCGGAAGANGGCCGANATTTGCCGTTGCCCGTCTTGGGGGTGCTATCCAATTTTGTCAA
ACATGTTAAAAAGACGTGTTTGATATACATTTTAGATCTCTTCTTCTGGTTATGTGTGTCCACGTTTTGG
GTTTGTATCTTTAATTTTCTTTAATTTTATGAATGAATCCGAATTTGACTTGAGGTCTTGTTTACTTTCA
TGACTATTGATTGATTCAGGGTATGTTNCCCATCTTTTGTATATGTGTGTTTTATCTTTTGTATAAAAGC
CATTCATTCTTTCCAACTNGGGGAACNCNAAAAAAGAAAGCANCCCAATTTTGTTCTCTTTCT
>gi|3449833|gb|AI099521.1|AI099521 34247 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153H3XP 3', mRNA sequence
CCCCAANTTGTGCGTTNTCAGGCCCCCAAGTGGCTTCTTNCGCTTATCAATGACCCGTTGAGGNGGGGGA
GAAAGTGGCACCTCCTTGGCCAANTGGCTGCGGAATGCCACAGCCACAGGCGATTCAAGTCACACATGAG
GAACGTGAAGCCCATTGAACGGCTTGAAGCGATGGGATTTGAGAGAGCATTCNCGTTTGGAAGTGTTCTT
TGCGTGCAACAAGAATGAAGAGTTGGCTGCAAACTATCTTCTAGATCACATGCATGAATTCGAGGAATAA
GCTTCTTCAGATTACTTTACCTACTCTCTATCTTTCGCATTGGTCCATATGTTTTAGCTATATATGTGTG
GGATGCCAAATCCATGACCTCGTCACTTTGTCCATGTTCATGGCTCAGTTCTCAGTTTAAAATGAAGTTT
GTC
>gi|3449832|gb|AI099520.1|AI099520 34246 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153G20XP 3', mRNA sequence
CCTGAGGCATANTCTGACCAGTATCGNAGAGACAGCTGGCGCCTAATGAGCTCGATGAGTGGCNCAAGGA
GGTGGATGTTGGACCCGATGGAAAGATCCGGTATGAAGATCTCATCGCAAGGATGGTTGCTAAGTGAGNT
CTAATCTNTTATGTTTTGAAAGTTGACACNTTTAAGAAGAGATTCTTTGTGTNTTTTTCACTTGTTTGTT
TGATCTCGAGCGAATCCTAGCTNGGGTTTGTTTTATCATTGTGGAATTTGCTTACTAACTTTGTCTTCTT
CATGTTTGTTTTCATTTTTAATGGAAATGTTGTCTGTGTGATTCCTCT
>gi|3449831|gb|AI099519.1|AI099519 34245 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153G18XP 3', mRNA sequence
TGGAGCANCCCAGGCATGGGGANACCGGCAACCACCTGGACCACGAATGCCTGATGGGAGCCAGAGGATT
CTCAATGGGACGGGCGAAAGCCGGTTATGGNTCAGGCAGAGTGANCCAGAGCTGTTTTGCAAAGGAGGTG
ATGTGGAATTGTGAATGGTCNCAAAGGGAGCTAAATAGAGAGAGAGCAAGAGAGANAGAGAGAGATTTAT
CCTTCCCATGGGGATTGGCTAGTTTTGCAGACTTTATATTTGTCTTACTTACTTCGAAATACTTTTCAAT
TACGCTTCTCTTACAAGGAAACAACANNAAAACTACATTTTCCTC
>gi|3449830|gb|AI099518.1|AI099518 34244 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153G15XP 3', mRNA sequence
CCGATCTTCTGGATCNCGGAGGGGACTACTCGTCTAATGGNTCATCATAAGGGGAAGTTATAGCTTCTGT
TGCAAGAAACGGCTCCCACGCGAATTCTTGAGCAGACAATGCGAAAGCCATGTCTACTTCATGTTTCACG
GGTTCTTGTTTGGTTGGGAGAGAAAAGACTCGCTTTCTCTTGTTTATNATTTGCCTCTCCATGTNAAATT
CGTTTGCTTCGTCGGAACTCTNACAGGGAGANACTTATATAGAGCAAANACTCACGAGAGAGAGAAAGAG
AAAGAGATGGTTTGGTAATGTATGTGAAAGGAGTAATGCNATATATATTAACTCATGTGATATTTGACAC
GATCGATCACACTTTATGAAGTTATTTCTTTTG
>gi|3449829|gb|AI099517.1|AI099517 34243 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153F18XP 3', mRNA sequence
CTTTCCCGGAANTTTTCCGCTTGCCCAAATGNTGGCAATTNCCTAACCGGGGTGGGGGGAAGCCCCCTTC
AAGTCCCCTGGNATTAAAGGGGAAGAGGAGGGGGGNGAACCAGAGGGNCGTGAGTTTTGTGGNCAAATNC
GGTTCAGTGTTCCTCAGTCATATGGACATGGCCAAACTCACTTGCTATGTATATNTTTTGTGTAGAACNA
AANACAGAAGATAATTTCTTCTTTTTGTCATTCCACATCTTTATGGGGCTGTATGCATAAGTTTGTATAG
TTTATAAACGCGTTACTGTATNACAAACACAAGAACTCCGGCTCGTTGCAATT
>gi|3449828|gb|AI099516.1|AI099516 34242 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153E8XP 3', mRNA sequence
TGGTTTGNGNACCCCCTTTNGCAAGTTTGGCCCAATCNTAAGCCCGGGGNGTGTTACATGGACGTAAGAC
CGGGAGAAACAGAGTCTTTGCCTCTCTTTCTTTTACAAGCGGTGAAGAACGTGATGCGGCTTTATCATTC
AATGGAACACAATATGAAGGTCGCAGAATCATCGTCAGAGAAGGTATCGAGAAGAGTGAGTCGTAAACCA
ACTGTTCTGCTTTTGCTGCAAAGACATCTCTTGGACACAAACAATGTGTAATGAATGTCTTCTGATTTCT
TCGACAAGTAACCTTTACATATTATATCCTTCTCGATTTTGTTTATCACCCATTATATCTACCTGTATAA
TTCTCTTTTCGATC
>gi|3449827|gb|AI099515.1|AI099515 34241 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153E1XP 3', mRNA sequence
ACCCCTTTTGGGGGTTTCAAGGGGCGACCCCAAGGGCCTTGGCTTGTAGAAAAGTCCTGAACANGGNGAT
CAAAGTGGNTGAATCCATAACACACAACTTGACCTTGGGAGAAATCAATAAGGCTNTCGATCTATTGCAC
GAAGGTACTTGCCTTCGTTGTGTCCTCGATACCNGCAAATGACTATATGGGTCCTCTCTGCTTTAATCTA
TGTGTTCTTGTGACTTTCGTCTTTTATCGGTATTGACATTTCCTAAGNGCAACAGACTACTCTACTCGTG
TGTGTCTCGTTTCTATCTTATGCTTCAATAAAATATCAATTAAGACCG
>gi|3449826|gb|AI100087.1|AI100087 34240 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153D23XP 3', mRNA sequence
CCCAANGGCCGAGGANNATGCCNAANGAAGGTCGAGTATGCNATCAAAAGCAACNGAAGTCACAAGTGAA
GGGNAATATCCCCAAGAGTGCTGCACCCAAGGCTGCTAAGATGGGTGGTGGTGGAGGCAGACGTTGAATG
GAGCTATAGAGTAGCCCACTCTTCTCTCTTCACTTATCTTTCTTTCTTGTTTTGACATTGTTTTGTTTTG
TCAGCCATTTTTTAGTTTTGCACCAGNTNTAATATATTCAGTTTATG
>gi|3449825|gb|AI100086.1|AI100086 34239 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153D10XP 3', mRNA sequence
GCGGGATTCCTTTGANGAATTGGTGGGTNATCAGGACCGTTTCCCCAANTCTGTAATCCCGGGGCCATGG
NTATTGGCGGAGGAGGAGGAAGCTAAGGNTTAGGTAGTAGGATGNGAAGGAGGTTGCTGCTGGATTCACC
CTCAACAGGAGGTTACCGCTGATGGTTTTTAAGACGCNNTTTATCTATTGGTCTTATAAGAGAGACACAG
AGTCAGGGTATGTTTCAGCCCCCAAATTCTGTACATTTGTACTTTTGTGCACATTAAAGTGACAGTCTAA
AGCTAAGATTGGCTTAGTGACTTTCAAAACTGT
>gi|3449824|gb|AI100085.1|AI100085 34238 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153C9XP 3', mRNA sequence
AGNCCCTCAGGGAAAAAGGTTNCTTCCCNGCCTGTTGATTNGTTAGGCCANCGTNAGNCCCATGGGCNCC
CNAAAAGGCCCGGTGTTTTCATGGTACCTTGGAAGATAATGCTGGAGTGATTGTGAACCCTAAGGGAGAA
ATGAAAGGTTCTGCAATTACTGGACCTATTGGGAAAGAGTGTGCGGATCTCTGGCCAAGGATTGCTAGTG
CTNTAACGCCATTGTCTGAAGATCATTTATCACTTTTGCTGGTTATGTATCTGTCTTCAACGAAACGCGA
AATAGTTGGTGTTTTGAGTGTTTTAAGTAGAGACGACAATCTTTTGTGAGCTTCAGACATATTTCCAGTT
TCTAAGAGATTTTGCTTAGATT
>gi|3449823|gb|AI100084.1|AI100084 34237 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153C19XP 3', mRNA sequence
TATTCNTTCCNTTAAAGCCNAGNTTATTGGGANGGAAAAAGGGTGNCCTCCCAAACCAATTGTCGGCCAT
TGCCCAAAGGTCCGCACCCAGGCTTATCCACCCTCNTACACTCCCTCAGGAGGTTGAAGCCGTCCATCCA
GTCGTCTATGAAGAAATAAACCGCCATTCTCTTCCTGTTATCTTACCTTGTCTGTTCGGTAATTTATCAG
GCTTCTGTCTGCTTCCGGTTCTCTAAACCGNAAATTAGTTTCGTTTAATCAGATAATGGATTTTATCGAG
TTGAGTTTTATTGAGCTTTCTATCTACATTTTTTTGTCGTTTTCAACAAGAAGTTAANACTCATAAATAT
CTGTCCAAAAGACAAAATCAGAACTTG
>gi|3449822|gb|AI100083.1|AI100083 34236 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153A24XP 3', mRNA sequence
GAAGCACTCAGCTCAAGAAAGCTGATGAATGCTTACTGTGACCGGCAATCTGTGGACATGAACTCCATTG
CTNTCTNGTTTGATGGGCGTCGTCCTTCGTGCTGAGCAAACTCCCGATGAGCTTGACATGGAGGATGGTG
ATGAGATCGATGCGATGCTCCATCAGACTNGTGGCAGCNGTGGTGGTGCTACGGCCTGACACTTCGTCCA
GGTTTAGGGCTTGTGTGTGATATGAATGGTTAAGGAGTAATCGGCATTAGGATTTGCAGACTTGTTTTTT
TATCGTGACCATTCTCTTTAGAAACTAAGTTATTATGGTCACGAAGGTTAAAGAACCCTTTGGTTGATTT
TTTGTCTTGTTCGTTTNGTATCGGATCCTATGATACTACTATTTCGGCTTAAAGGTGTTATTAACCCAAT
T
>gi|3449821|gb|AI100082.1|AI100082 34235 Lambda-PRL2 Arabidopsis thaliana cDNA clone 153A14XP 3', mRNA sequence
CCCNATNTTTCCATACCACAAATGGGTGGCTTANTCCATATNCCCGCCCGGAGCTTNCGACAAGAGAGCC
CCGCCGGGTTTTNTGAGGAAGTCGGNGCAGGCTNAGGCGCAGCCGGGAAGTACTGACGATAAGCTCATGT
CCCTCTTTAGCGACGAGAACCCTAACGCCTGCACCGTTATGTGAATAAGTATAGATNGCATGAGCCGATG
TTATAATTTGTAATGTATAACGTTTTATGAAGTTAAAGTACTGGAACCTTTTTTGTTACTGTATTATGTG
AGAAGCAACGCAANATATAGT
>gi|3449820|gb|AI100081.1|AI100081 34234 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152P8XP 3', mRNA sequence
TTCCGCCTATGGCGAANNCTTGTGACAACCGNGNCAGTTGGNGAAGAAGGGGTTCCCNATGGACTGTTTA
GNGATGAAGAACTAACTACGTCCTCGCCAAAGCTGTGCTANCTATGCGGNTCAAGGGATTGGGTTTGTGT
CAAATGGCTATGGACTAGGAGATAGTAACTGGTCGCCATTCACGAGGAGGGGTGCTTGGGATAACAACAT
GGGAATATCAGCTGATTTGATTGCTGCTCAGGCTGTCTCGGCGCTACAGATATCTGAAAATGCTGATGGG
AACGCCTTTGTGTTCAATGGGATGTTCCGGGGATGACAGATGCCACGACTCGTCCTCATTCGGTTTTTAA
AATAAACATTTGCCTTCTGCTTGCTTTGGTGTCAATGCTCTGTTTTTTTCTCTTGACGTTAGACCTTATA
CTCTGTTTTCGTTCGCTGTAATATNAAAGACGCATTTTGAGTTGT
>gi|3449819|gb|AI100080.1|AI100080 34233 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152K2XP 3', mRNA sequence
CTTCCCGCAACAGGGGTCCCTGGGTTGAATTNGNGTTGGGNCCCGGNTTTGTTTCCCGTGGNCCCGGAAC
CCNCCCGGNTNCTATGNTGGCCGGTNCTGGCCAATGTGGAAGCTCCATTGTTCGGATGCACCGACTCCGC
TCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTNCCCTGGCGCCTTCATTAGGATCATCGGATTC
GACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGTTCACCGAAGCTTAATC
CCCTTTCTGGAATATTCAGCGTTGATTATTCTGGAACCCNTTTCTATGTGGTCAATGCAAATTTAAGAAA
TTATTTGCCGACTTNAAAGTTGAGGAACTATTGTTTGAAAGTGAAAATGTTATTCCTATCAGTTTCTCTN
TAATTATAGTTATCATTTCATTTC
>gi|3449818|gb|AI100079.1|AI100079 34232 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152G2XP 3', mRNA sequence
CACATTNGAACCCCCTTTNNACACTGCGNTGGACCGAAGTGAGCCACAGTTTTTTAGCAGGACAGCNCCA
TAACTGTTGGAACACAGCACTTGGCTTGNCCCCCTTGCCCTCTGTGAAGGCTCGTGTCAATAGTGCGGGT
ATTGCAAGTGCTCTCATTCAACACGAGTGGAAACCCAAGTCATTCTTCACAATCTCTGGAGAAGTCGACA
CAAAGTCAATTGACAAGAGTGCTAAAGTTGGATTGGNTCTCGCACTCAAGCCTTGAAACTGAGATGGAAG
AAGAAGTTGCAATAGTTTTTTTAAACTAGTTTCTTTCTACGTACTCTGTTTTTTCTCTGCTTGGTTCATG
GTTTGAGTGGGCAACTACTGATCTTTCCCATTTTCCTGCCGGATTTGTAGAAGAATNAAAAGGTTGAAAA
TGATCATCTTGAGATGGT
>gi|3449817|gb|AI100078.1|AI100078 34231 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152G10XP 3', mRNA sequence
CAGGCCCNNTTTTGGANCNATGGGCCCATGGAAANCTGGGGAAACCAAGGAAAAGGNTGTGTATAAGNCG
ATCCNGGGTATTTGGAATGNGGAACCCCACACCAATGCCCACATCATCATCCAACATGTCTGTACCTATA
CAGACATTGGATCCCCCTACCCGGAGAAAATGTGTTATTTGGTCACATCCCCATCATCGCATATTCAAAC
CTTTCTACTCTTTGTTTGGGGCTTCTAATCAATTCATATTTGATCTCTTTTGTGGTTCTCTTAGTTTCTT
ATTTGTATAATCCCAAAACTGGTTACAACAGAAAGTTGTTTAGCGAGCAATCTAGGGTTTGAATGAATAG
TTGGGGAAGATTTATTTATATATACCGTTTTTGATATATATATTCTTCATTATTAAGGTGTGATATCTAA
CACAGTGGTATTACATATCTTTGGAAAAAAATCATTTGATAAG
>gi|3449816|gb|AI100077.1|AI100077 34230 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152A2XP 3', mRNA sequence
CATGAAATGCTTATGCGAAAGCGGCTCCCCGTACCCCTCAGTCCCCATTTGTGGAGTTTCCCAAGTGGAT
GCATATGGATACATGGCTGTCTGGTGGTGAAGTTTACTGGAAAACAAACTNGCAATTTCTCGAAAAGTAT
GCGCCTGAGAAAAGGAAAGAAGATACAGGAAGGTAACGATCAACGATGCTGTGTTTAGAGGAAGATTCGA
CTCACTTATTTCCTATTGCAACCTGAAACGACGGTATTGTTTGTTATAAGCATGTGTATACGTATGTTGC
ATTTGGGAGTGACAGATACAACTTGTTCAGAGAGTGAGATATTGGACAGGAACTTTTGTAAGCAGAACCA
GCTAGTGGAGATGGCAAGTGTAAGCTAATCAGATGCATTTGCTTCGTCTC
>gi|3449815|gb|AI100076.1|AI100076 34229 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151O2XP 3', mRNA sequence
TCTTGGTAATAAGGTNATATTGATGGGGGAATTGCCGAGTGGTATCTGANAGAAGGCTAGNGAATCGTGT
GCTGAAAAGGGANNCATNGTCTATTTCGAGACATCGGCTAAAGAAGATTNCAATGTCGATGACTCCTTCT
TGTGCATCACAAAACTTGCCCTTGCAAATGAACGCGACCNAGATATATATTTCCAGCCAGATACTGGTTC
GGTGCCTGAGCAAAGAGGAGGTTGTGCTTGCTGAATGCTGAAGAAACATNTCTTACTCTCTTGANTTATG
CATTACTTGTTGTGTGTGTCTATAATCTTAATGCTGAGAAGGACCAATAANACTTGTATTGTTCCCTAAG
TAAGGTTTTGTTNCCTTTCTGGTTCTTCATCTTTGACATTTGGTGGTTCACGATTTGTATGTNACAACAG
TTCAAGTGT
>gi|3449814|gb|AI100075.1|AI100075 34228 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151N20XP 3', mRNA sequence
GTTCCCTAAGCTTCGNCGGCCAGGACCAGGGCCCCAGTTGGGGGGCCTNAAGGAGGAGGCAGGACGCCAG
TTGAGGACGTCAAGGATGGAGCCCTGAAAGGAGAAGTGTGGTTTGTGTCCCCTTAGCTGCTAGCTNAGTT
TGGTAGTTTTGAGGCACATACACAGAAGAAGACAGAGCTCTGAGTAGACAGAGAGAAGACAAAGAGAGAG
ACGACAGACAGACAGAGAATCTCTTTATCTATTCATTAGGCTCTTATATGTGCACTCTTCAGAACAATAA
TGGCTGCCTCCTTTTCTTTTTTTTGGTTGATGTTACCTTTTTTTGTTTGAATTCAGTTCTCCTTTAATAT
AGTTTTTGAGGC
>gi|3449813|gb|AI100074.1|AI100074 34227 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151L4XP 3', mRNA sequence
TCAAGGGGAGCTGGGTGCCCAACCATTCTGCGGTGCCTGTTTGCCAGGTGCCGGGTGTGCCTTTCCCGGT
TACCGACAACATTTGCAGCTGATTGTCTTCGGGTAAGAAGTACGGATCAGGAGGTGCCTAAGCATTGCTT
CTTCCTCCTTTTTTCGATNTNAATTGCGGTTTTAAGGCCCGCAATAAACTGAGATGTTGATGAAATNTCT
TTTGCTTAAGACTTAGGGAGGCATGTGCCCTAAACCNAATTTTATATCGTTCTGACGCCAACTTTTTTCA
CTTATGGAATAATTCNTGTTTGAGAGAGTTTGTTAGACTCTTCGATTTTAAAGAATTTTGGATTTATGAA
ATAAATTCTTCTTTTTTATC
>gi|3449812|gb|AI100073.1|AI100073 34226 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151L19XP 3', mRNA sequence
TTTTTNACCGGTTCCCCCTTAGGCCCNAANAATTNGCCAAGNTTCCCTTTCCCTCANGATCNTTCNGCCC
AACTTTGGCCCCNGNCNAACCNTGGCCAACCCTGGAGGAAGCTAGCAGGACNGTTCCAGGAACAGGCTTC
TNGTGANGNTAATGCCGCCTCAGCACCCATACAAGAAGAGGATGATGACGATGTCCCAGAGCTTGTTGGA
GAGACATTCGAAACTGCTGCTGAAGAGAAAGCACCAGCTGCTGCTGCTTCTTCTTAGAGAGAAAAGAGCG
AGACCACATCCAAAAAAAAACCGCACTTTGATTTTTACATATCTTTATAATATGTTTGTTCGCTCGATCC
TTTTTGTAGTTTCCGACCAGAATCTTGTTTTCCATCTAATGACTTAAGGTTTTTATCCAATT
>gi|3449811|gb|AI100072.1|AI100072 34225 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151K18XP 3', mRNA sequence
AACTGGAGAACATCNGCAACCCAATCATTCGCCNNGATGTCCCAAGGAGCTGGTGCGTGAACGCCGGTGG
NCCAGGTGCCTCTGGTATGGCCGATGATGCTCCCCCTGCTTCAGGCGGTGCTGGACCTAAGATCGAGGAG
GTCGACTAATTTGTTGGACATTGNCCTCTCTCTTTCNCCTATCTCTATCTCTTTTACTTGCTTTTTTTTG
ANCTGTTAAGACTTTTTATGTTGGGCTTTTTTAAAGAAGCCCATTTTGTGGTGTTTTTTGGTTAGTACTA
TTTTGAACAATGGTTGGTTCTATACCAGTTTAGCTACGATGACGGATAAAATTAAAAGTTTGCC
>gi|3449810|gb|AI100071.1|AI100071 34224 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151J22XP 3', mRNA sequence
CCTCCAAGGATTCCCTCGGTGAACCNTCCGCNCGTGTTTCAGCACGAAGAACGTTGGCGTCACGCGCCTA
GGATACGCCGTACCGGAGATTCACCTCGTGCTTCATAGCAAAGACGTCCGTTTGGAGAATCTTTGGAGCT
AACTCGATGGTGAGTGTCAGTGATGACGTCATCTGTTTGGGTTTCGTTGACGGAGGAGTCAACCCAGGAG
CCTCTGTGGTGATCGGAGGGTTCCAGTTGGAGGATAATTTGATCGAATTTGATTTGGCGAGTAACAAATT
TGGGTTTAGTTCCACGTTATTGGGCCGTCAAACTAACTGCGCCAACTTTAATTTCACTTCCACTGCTTGA
TTNAATTTAGTTGATGCACTTTCTCCAAAATAAATGTGTTTCAGTAACACTANATAAATGTATTGTATTA
TGTTTAATTTGATCAGG
>gi|3449809|gb|AI100070.1|AI100070 34223 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151J12XP 3', mRNA sequence
AAAATGGGGGGAACCCAAAGGGGCCCTTGTGAACCCCCCGTATTGNCTGGCTAGTTNCCAAAGGATGGGG
NTTAGGCCCCTNGGGAAAATCGAAGGGCCCCATCCAANGGTTNCCGCCAATCTCGGTCCATCCTCACCGA
CCCTATGGAAAGCTTTTCCCACTGGGGGAAAAGATGTGAGCCATNGGGAATCTGCATCAAGGTTACACAC
ACATCTTGGAATCCACATTTGAGAGTAAAGAAGCTGTTGCAGAGTACATTGCTCATCCTGCTCACGTTGA
ATTCGCCACCATCTTCCTTGGCAGCTTGGATAAAGTTTTGGTTATTGACTACAAGCCTACCTCTGTCTCT
CTCTAATTATCTTGTAGCAGCATTTTCATCATTGATCTTTTTCTCGGGTATGCATCTTGTATGTTGAATA
AAGTATATTCCTTTTGAGTTTT
>gi|3449808|gb|AI100069.1|AI100069 34222 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151I21XP 3', mRNA sequence
CCTGNGCCAGCCGCTNGNAATACCGGTTGGNTGGTTGNTGGTGGGTCCTACTNCTGGACTCTCCTGCAGG
AATCCCCCAAAACTCTTCCGGNNCCAGGTAATGGATTCGAAAACCGTACCAGTAGGAGAAGGAGACGGAC
CCCCATCGTCTGATGGAAGCTCTATCAAGTTCTCATTTCCTCTTATTGCCTTCTTCTCCGCGGTTTCCTA
CATGGCAATCTTCTGAGTTACTATTTTCCCATACGCTTTTGTGCCACTCAGATTGCATTCTTTATTTGTC
CCTATTTATTCACATTTCGTTGTGATTTTGTGTGATGTATTTTATGCTCTGTAAATCCCTACTCTCCGGG
TGATATTGCTTTGTTGTACCAACGGAGAGCATTTTGGATCTCTTTACCTTTTATAATAAACATTACTTTC
CAG
>gi|3449807|gb|AI100068.1|AI100068 34221 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151H24XP 3', mRNA sequence
CTGGGAAAATTGNGGGGTTANTNACAAAACAAGGCCTACTGTAGCCATGACCAGATTTCAAGACTGACTC
TTGTAAGCAATCATTCANTTCTTGGGANTCAATCGTTTTTTTTTGGCCTCAGAAGCTTCATTCTTGACCA
GAGGGATTATTCTCTGACTTTCCTTGTCCAAACTCCGGTTTCTTCTTCTTCTTCNTCAGGCGTCTCACAC
TGATCAGGGTTCCATGAATTTTGTTCTTCTCTTGGTAGTTANAAAGGCAGGGAAGGAGATTTAGAGTAAT
TTAAACAATATGTGATTGTTGTATATGCCTTTGTATTTGTTTGTATACTCATAAATGTTTTTCTGTTTTG
TACTCGGCATTCTTGTAAATTAAAGACATTATCCACATT
>gi|3449806|gb|AI100067.1|AI100067 34220 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151H19XP 3', mRNA sequence
AAGNAAGNCCCCAGCTTCCCAGCTAAGGCCTGAGATCCAAACCAATGCTCGGTTAAGCCCATGGCTGGAT
CCCTTGGGTTTTCCGGTTTCAGGCGGCNTGCAACCGGTAAAGGACCGCTCAACAACTGGGCGACTCACCT
TAGTGACCCACTTCACACCACCATTATCGATACCTTCTCTTCCTCCTGATGTGGTGGCTTTTAGCTTCTA
CTGGTGTCATGTAATGATGTGGTGGCTTTTAGCTTCTACTGGTGTCATGTAATGATGTAACGTCGTTATT
TTAAAGNAAATTTGGCACCTTTTGTATAAACGG
>gi|3449805|gb|AI100066.1|AI100066 34219 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151H18XP 3', mRNA sequence
GTTTGCCCNCGNATGNTATGAGTTCACACTCGGGACCCACTATAGGCGAAGGAGATGAATGTGTGNNTGA
GCTACNCAGAACTCCGGGATCNCGCTCTCGAAGTCACCGCCTTTCGTGTCAATGAGTATGTGTGACCAAA
AAAGATTTCCCTATCATCAGCGNTCTTGCAGGTAGCTTTCCAAAGTCNNACTCNTATGTAGGGGTCTCTT
AACCATTCTCTCTCTCGCATTGGTTGTCTCTGTTCTAGTAGTGTTTTGAGTGAAATCTCAGGTTCCTATG
TTTGGATGTGGATAAGTATTTGACGATTATAATAACCTCTGAGTGGGAAACTCTTTGTTTGAGTGGTAGC
TAGGTTCAAAAGTAGAGTTGTATATACTTTTATCTTCATCAGGATAATTATGTTTATTTG
>gi|3449804|gb|AI100065.1|AI100065 34218 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151H12XP 3', mRNA sequence
TTANGATATGNCCTCTCCCTCTCTCTCNCTCTCGTTACCTGCAGAGTNATATATNTCATATGATAGCGNG
TGCTATCATCGGATTACAAGTCCAAACACCAACACAACGTCATGTTAAGTTTTGGTTGAGAGATTATTCA
TCAAATCTCTATGTACNCTNATAGAATTGGTTCNAATTATATGGCCCNGAATAGTAAAGCGGTGCGATGA
TAAGAATTGTTTTTTGGGCAAATATAATCATGAAATAGTAAAGGGAAAACCAAAATTCC
>gi|3449803|gb|AI100064.1|AI100064 34217 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151G21XP 3', mRNA sequence
TTTACCCAAACATGGGTTCTCTACNTAGGCCTCGATCCTCTGTTTCTACCAAACNATTCTTCCAGTNCTG
AAGATGTTGCTTGCCAATGAAGAAACCCCNATTTAAGAGGAATCTTCACAATTCCAGGTTCATCAGAGAG
TGAACTANCAGCGAGTTCTTGGCAAGGTCACAATTCTTATGGTTCCACTGGTCCAGTGAATCTTGATTGC
GTTTGGAAATTCTGAATTTGGAAAATCGAAAATTTGGATGTTAACTAGGGGGTATATAGGGTTTTTAAAA
ACAGTGTATATATGCGTTATGTGTTAGCTTTAGATTCTAGGATATACAAAGATGACACTAATAGATTCTT
ATAACATTTTGTAAAAAAAAAATCATTGTAGTGAATACTCTCTTGCCATTTGAAATCCATTGTGTTTGCA
T
>gi|3449802|gb|AI100063.1|AI100063 34216 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151G18XP 3', mRNA sequence
TGGTTTCCTGCGGGCCAGGCCATTGGATAATGCCTATGATTGCCCGGGNTGAAAAGGTGACAAGATCATT
GCAGTGTGTGTTGATGATCCTGGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTC
TCTGAAATCCGTCGTTTCTTCGAAGACTACAAGAAAAACGAGAACAAGGAAGTTGCNGTGAATGATTTTC
TGCCATCTGAGTCTGCGGTTGAAGCTATCCAGTACTCAATGGACCTCTATGCTGAATACATTCTCCACAC
CCTGAGGCGTTGAAGCTTCTCCTCAGAAGATTTCTGCAGCATCTATGTTTCTGTTACTTTTCATTGATAA
TAAGAAGCATATGATCCTAATTGATATTACTTTTATCTCTGCATTTTTCTTCCTTATCATTTGGTCCTTC
TGTAATTTCGTTTTAAAGACCCTTTCTTGGNNTTG
>gi|3449801|gb|AI100062.1|AI100062 34215 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151G15XP 3', mRNA sequence
CCTTAAACCCNATANTCCCGGTNGCCCATCCTACCCNGTTNCTAAANGGGGAGGAACATTGGCCCATGAG
AATTTTGGGTGGNACCATTCCGATAGTTAGAAGCCATTCGGGACAAGGTGGAAGNACCATGTATNAACAT
CAAGAGTCTATCCCAACAACTGCAATCTATGGAGCAGCCAAGCTCTTCTTGTTCAATAATGCTCTTGATG
CGACGGTTACGGCGTCGTTTACAGTTTGGCAAATGAACAGTGCTTTTATTCATCCTTACTCTGACGAAGC
TGTCCGTGCTCTCTCCCGTACCTGATTATTTTTACTTCCTTCTCATTTTTTATACATAGATTTATCTGTA
ATAATTAATGTTTTTTTCCGATTTATTTGATATTTGATTTAGAAAAAAAAGGCACTGAAACATCATTATC
AC
>gi|3449800|gb|AI100061.1|AI100061 34214 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151B24XP 3', mRNA sequence
CTTTGGNTCCNTAAACCGGGCTNCAAACANGCCCNTTTCCNGAAGCTGAAGCAGTGGCCTGGGTNAAACC
TGTTTCCGCATCTTGCCACAGGGGGGGTATNTACACTGGGAGACAAGCTTGGGATTATGCNNCTTAAGGC
CGACGGTATCAAGACCGAACTCATGGACCTGAGGAAAGACTAAGCNCCTTTAGTGCATTTAGCCAACCTT
ATCGGTTTGTTATTTCACTTCAACATCGAGCTTCCTGAGTTGTAGAACTCGTATGAAATGCTACTGGGTT
TGATNTTTTACAGTNAAAATCATGACTCGTGTTTGAAGTTTCTCCAAAACTGTTNCCTTATGTATNAGAA
TCACTCGAATCCTTGTCTTAAATCAATGTTTCTCTCACT
>gi|3449799|gb|AI100060.1|AI100060 34213 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151B13XP 3', mRNA sequence
TGGGANTCAATCGTTTTTTNTTGGCCTCAGAAGCTTCATNCNTGACCAGAGGGATTATTCTCTGACCCNC
CTTGTCCAAACTCCGGTCTCTTCTTCTTCTTCNTCAGGCGTCTCACACTGATCAGGGCTTCCATGAATTT
TGTTCCTTCTCTTGGTAGTTACAAAGGCAGGGAAGGAGATTTAGAGTAATTTACACAATATGTGATTGTT
GTATATGCCTTTGTATTTGTTTGTATACTCATAAATGTTTTTCTGTTTTGTACTCGGCATTCTTGTAAAT
TAAAGACATTATCCACATT
>gi|3449798|gb|AI100059.1|AI100059 34212 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151A8XP 3', mRNA sequence
CCCACAGGAANCCCGCAACGCCATCTCTTAACCCCACTTGTAAAGNCGCTCTTAACTTAAGGTATGTGCT
AACCGTGTTGGATGTGGTTAAGGTTTCTCTACCACCAACGTCCAACTGTTGCGCTCTTATCAAAGGTCTA
GTTGATCTTGAAGCCGCGGTCTGTCTTTGCACTGCCCTAAAGGCTAATGTTCTTGGTATCAACCTTAATG
TTCCCATTTCTTTGAACGTTGTCCTAAACCATTGTGGTAAGAAGGTTCCATCTGGTTTCAAATGTGCCTA
GAGATTACACATTTTAAATTGAGGTTCTATATACCATATTTCATTCTTGTTTTTCAAATTCCGCGTTTGA
TGATATCTTTATCTATTGTTGTAATTTGTTATATGTTTCATATATCAATGAAATAAAGTGTTTCCTTTTT
CG
>gi|3449797|gb|AI100058.1|AI100058 34211 Lambda-PRL2 Arabidopsis thaliana cDNA clone 151A15XP 3', mRNA sequence
GAANCGAANCCCTTGGGCCCTTCTTACANCNACNACCTTAACCCTTGGGCCGTGGAGTNCTCCAATCCGG
ATCAAGNCCTTTGNACCCGATCCAGCCACTAGCCCCATAGTGCAACCAATTGATGGCTCCTAGGAAGCCA
CCTTCAACGTTGAGTTTGCGAGGTCAATGGTCAGAATGAGTAATATCGGTGTGGTTACCGGAGCTAATGG
GGAAATCCGTAGGGTTTGCTCTGCGGTTAATTAATTAACCGATTAGAATCTGTCGTGATAAACTTTCATG
ACGCAAAGTACTTGTTTCGAGTGTGGTTTTAATCTGAACAATAAATAAACCAATAGAAAACGACATACAA
AGNAAAAACCCAAAAGTGGGTTGATGAAAATTGTATCTATAAGGTGTTGGTATTCGATTTCTTTTGGTTT
TAGTTAAAAAAAACTGTAATGTCTTCANAAAAATATTATAATGAGTTTGGTCCTAGTTTGGATTCTT
>gi|3449796|gb|AI100057.1|AI100057 34210 Lambda-PRL2 Arabidopsis thaliana cDNA clone 150P23XP 3', mRNA sequence
CAAAAGGGNTCCCTGGTTGAATTCGGTTNGNGCCCCGGATTTGTGTNCCCGTGNGCCCCGGAACCACCCC
CNGGTACTTCCGATGGACCGGTACTGGCCAATGTGGAAGNTTCCCATTGTTCGGATGCACCGACTCCGCT
CAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTACCCGGGCGCCTTCATTAGGATCATCGGATTCG
ACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATN
TCTTTTCTAAAACANTCTTATGAATTATCTCTGCTCATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCT
TTATGAGACAATTTCTATCGGATTGTCAAATGTCTGATTTATGAATATGTNATTTATATATCCGTGCGTC
TTGATTT
>gi|3449795|gb|AI100056.1|AI100056 34209 Lambda-PRL2 Arabidopsis thaliana cDNA clone 150P19XP 3', mRNA sequence
CCCCTTTGGGGAAAGCTGGTACCNCCTGCAGGTCCCCGGTCCGGGATTCCCCGGTCGNCCCCACGCGTCC
GGTCCGAAAGACGCCTTCAATCATAAATGTCTTTGACATCCAATTATACCACTGAAATTCTTTTTCATTT
TTGAATGGCAGTTCCACAAAAACGTACTTCTATCTCGCAAAAGCGTATTCGTNAACACATTTGGAAAAGG
AAGGGATATTGGACATCGTTGAAAGCTTTNTCATTAGGGAAATCACTTTCTACAGGTAATTCAAAAAGTT
TTTTTGTACAGCNANATAAATCNAAAACACTATNATAATTAGAATTAGCCTAACTTAAAAACCAATTTGT
TTAAATACATCTAAAAAAAATAGGAAGC
>gi|3449794|gb|AI100055.1|AI100055 34208 Lambda-PRL2 Arabidopsis thaliana cDNA clone 150P17XP 3', mRNA sequence
GTGGCCTTCCCCCNTTNNATTTAAAANTTGNTACCAGGAACCTTTTCCNCCNTGGAATTAATTGCTTGAA
NAGGGAATTTTGGGAAATTCNNCCATTGCCCCCTAGAAGATCCCGACCTGATNATCCGAGTCCGACGACT
GCGACGTTGAATTTTCGAAAATCGGAGTTCGAGCGTAGGATTGTGCTGGTTTGACTAGCGACGGGAGGAG
CTGAATGACGGAAACGCCGAGTTGTTTCGCGGCGGATTCTGCTTCTTTGGATTGGATTACGAAGCTTGGC
TTATCCATTGCGGGTTGATCCGGTTTGGGTCGCGTAAATGGGTCGGGTTATTTTTAGATGGGAGAGATCC
GGGAAATGAGGAATTATGAAATGGAAGCTCGAGAAACAAACTATTTATAGATACAACAACGTAGGAAACT
ACATTACGC
>gi|3449793|gb|AI100054.1|AI100054 34207 Lambda-PRL2 Arabidopsis thaliana cDNA clone 150N18XP 3', mRNA sequence
GCTGNGGTTNGACTTGGAAGGCCCNTGGGGGNGGGGTTTCCCNGCCCCAGNACCGGCATCCCTTNGGNGG
AAAGCCTNTTCCCNAAAGCCCTCGTGGAGATTCCGAGAAGATGCTCGTCGCACTTCTCNGGTGAAGATGA
TGCTTAATCAATCAATCCTCCACAGAGAAACATAAGCTGCTCTACAGCTTCTGTTATCTCTTATCTCCCT
CTCTCTCTCTTTGATGAGTTTCAAATCGTTTGATTTTGTTTCTACAAAAACCTTGTTTGTTTCTGTTGTG
TGTTTTGAGTTCCTAAATAATGCAAAAGAGAGAGACAGAGAGAACCNGTGTGGTNTCTTAAGTT
>gi|3449792|gb|AI100053.1|AI100053 34206 Lambda-PRL2 Arabidopsis thaliana cDNA clone 150M14XP 3', mRNA sequence
AAGTTNTTTGNNAATTCNGTGCCCCATTCACNAAGGNGGGGATTCCCCCCAAGTCTTGACCTGGGAGGAG
CTCTTTGCTTACTTATGTCAGCGCTACCTCTACCGGCGAAGTTCTTCCCATCAAGAGAGGTCCTCAGGAG
CCGCCTAAGCTCGGNCCTCGCGGCAAGCTCTGATCTATATTCATGTTNCCTTTCTCTTCTTCCTTCTAAA
ACTCATCAACATTTCTCAATACTGCAAACCCTTTTAAGTNNTNTTATGTATATTATGTTTATCTGTTACA
TTTGAGANGTTTTTTCTTCCCCT
>gi|3449791|gb|AI100052.1|AI100052 34205 Lambda-PRL2 Arabidopsis thaliana cDNA clone 150L23XP 3', mRNA sequence
CCCTTTCTGGAGGTCCCNGGNCNNCGGGTTTCCCCNACATTGGGGTCCCGGTTNCCCCCAATGGCCTTTG
ANCCCGGGTANCCCAGGCCCCNTAANTCCNGTTTTAACCAGTATGTGCTCGTGAATCCGGGAAACAAGTA
TGGTCTCATGGATGGCTGGATGGCTCTGCACTGTACATAAAACAGAGTCCTCACTTTCATTTCTCTCCAA
GATAAACTTTAAGGTGTTGTGGTTTAATCACTCGTTTATCTAAAGTTTACGCTGATGAATAGTAATTTGT
GACAAAACTCTGAAAACGGGTATTTGATCAAAACTGATTCGGTGTGGTTCAAAAAACAGAATGTGATTTA
GTGTGTTTAATACACTCTTGCTTTGGAG
>gi|3449790|gb|AI100051.1|AI100051 34204 Lambda-PRL2 Arabidopsis thaliana cDNA clone 150C17XP 3', mRNA sequence
ACCCCCAAACTTGTTCCGAGAAGGCTGAGGAGTGGCCCCAGNCTTTCAGNCNGGGGATTGCCGCAAGCAG
AANCCATGCTCGTGCAGACATCGTCGCTTCCACCCTGAGAGTGGACTGACGCTGAGTTCTGACGGGATAC
TAGGACCACTCGGATCTGAGTTACCAGATGATGGCGTAGATCTAACGGTCGACGACATTCCTTCTGCAGT
TGATATTTAGATTCTAAAGCTTTAGTGTATTTTTTCATACACAAAAACACCTCCTTGAGCTTAATTGAAT
ATGTAGTTTACTTCCTACAAGACATTTTATCATGTGTACTTTGTCTTTTGTAATCGATATGTTCTGTTAC
AATGTCAAGAAACCAAAGAAAGGCTTTGCCCAAG
>gi|3449789|gb|AI100050.1|AI100050 34203 Lambda-PRL2 Arabidopsis thaliana cDNA clone 150B17XP 3', mRNA sequence
TTTCCNCTAGACCCGGAGGCCGGTTTACCTGATGACCCCCCGGGATACCCGATTCTNTCAGGCCAAGTGA
GGCCGGGAAAGGTCCGTGANCCACGATTGGACAACCCAACCCTTTAAGAAGAAGAAGGTGCTCTACAGGT
CCCAAACCCCANGCATAAGATTATGTGTCCCGATCTTTGAATGAATGNAGAAACAAGAAAGATGGTTGGG
AATNNTAANTCATTTAATTTAGTACGNTTATTCATTTGTGTATTTTTGAAACCTNAAAGAAGGTTTGTGT
TTTATGGATGGTTTTGATTTGTTTTGGTGATGGGATTTTTTTTTGTTGATGANTCTNATATATACAAAAT
ATTTGTGTGCCAATGTGATTACCATTCAATTTTTTTGCTATGTGTGTAAATTTGNACTTATATTAGTCTT
TTTCT
>gi|3449788|gb|AI100049.1|AI100049 34202 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149P21XP 3', mRNA sequence
CCTGCCNTTAGTGNCGCCGAATGGCTAGGAAGTTGCTTCCTTCTCCGCAACAAGTGGATCCTTGTGTTTG
AATTCGAGTTAGAGCCACGGATTTGTGTACCGTGAGCACGGAAACACTCCCGGATACTACGATGGACGGT
ACTGGACAATGTGGAAGCTTCCATTGTTCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGA
ATGCAAGAAGGAGTACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGC
ATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGA
ATTATCTCTGCTCATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGAT
TGTCAAATGTCTGATTTATGAATATGTAATTTATAT
>gi|3449787|gb|AI100048.1|AI100048 34201 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149P15XP 3', mRNA sequence
ACCCCGGGGAAACCCTCCAATGGCTATCCGATTCCCGTTTTGGCCGCCCGGGGAAACCCTGCAAATNCNA
ACGAAGAGCCTCCATTTCCCAGTTAATGGGAACATAGTCTCTGTTTTGTGTTGCCCATTTACTTTGCCCC
TCCAGTTTTACAAGATTCGAGCCATTCATTATCAGCCCTTTCTCTTTTTGTTCTGATTTTTGGTACAAAA
ACTTTTATTTGAACATGAAATTGAATTGTATAGTTGTGACCTTTGTAG
>gi|3449786|gb|AI100047.1|AI100047 34200 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149N17XP 3', mRNA sequence
TTAGGGGCCCTTGGTAATTTGGGTCCTCCACCATCCAATACCNCCATNAGTGGGAGGTCTTNCATTNNCA
TTGGGATTTGTCTGGGAGTACAGAGATTTACTATTGGCTTCTTCTTTCTTCTCTTTTGGGATGAAATCTC
TTGTATGCATTGCTCACATTATATGGTTTGGGTCTGTGGCTTTAGTACTTTTGGTCCTTGGACAACTTCT
CTGCTTCTGATCCAGTATGTTGCGCT
>gi|3449785|gb|AI100046.1|AI100046 34199 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149M3XP 3', mRNA sequence
TTGGGGCCCGTNCCNTGNCCAAANGGGTTTGACCCCNGGAAACCGGNCCATCACATCANGCAACTCCAGC
GTGGAAACAGCTAAGTTTGTGTGCGGGATCCCGTTGGGAAACTCATCAGTCTTAACGTTTGAAGCTNATA
ATCTTCACAAAACCTCTTCGGATTTTCAANTCANTCTTGTATTGTTGTTGCCAAATATTAGCGCCTTAAA
AAAACTCGTTTGCAAGTCTTCCCAAGTAGATGAGCTTTGTGGTTGTATCTTGCTGAAAATCTCCTCTTTA
AGAATAAAACTCGAGTAAACTTAAACCT
>gi|3449784|gb|AI100045.1|AI100045 34198 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149M15XP 3', mRNA sequence
AGAGGCTACTACTCCCCCCAGTNGTGAGCCGACAAACTCTCGGACAAGAGTCACATTGAGCACAGAGTCG
TGGTAGATGGAAATGGTCATCACAAGCAGAGCTCCAGGGACTGCAATGGAGTTTTCACTTGCCATTGTCG
AAAAGTTTCACGGGCGAGAGAAAGCTCTTCAGCTCGGAAAGGCAACACTTGTGTGATCTCAAACAATGAA
AGTATGAGAGTGGCTTGAATAAAAAGAAGGCTTTGCCTNTTAGTTATCTCTCTCCATTAGTAATNACTTA
CTTTATGATATATGACATATGAGCTTGGCTTAGTGATTNGTGTGTAACTTTATGCCTTTATAAATGAATA
AACGAGATTTTTCT
>gi|3449783|gb|AI100044.1|AI100044 34197 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149L5XP 3', mRNA sequence
AACATCCCNTCATGTNNACCCCCCTCAGGTAGGGTGAGGANCAAGAGTTCTTGGAGCAAGTATCTTCTCT
TCTAACCCCANTGATGATATCCTTGTGGTTGTCAGAGTGGAGCCAGATCCTTAAAAGCCACAACTGAACT
TGTTGCTGCAGGTTACAAGAAAGTGAGAAACGTGGGAGGTGGCTACTTGGCTTGGGTGGATCACAGCTTT
CCCATCAACACGGAGGAGGAGGAGCCATCTGCTAATTAATAATCTTAAGATTCTCTTCTTTTCTTAATCA
AATAATATAACTGCCTGTGTGATGTAGTAATCATTTTCAATTTAAAATTCCAGTTTCTTGTAATCAAAAC
TTTCGTGTACCAAATTCAATAAAAGCTGTGTTTCTCT
>gi|3449782|gb|AI100043.1|AI100043 34196 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149L3XP 3', mRNA sequence
CCAATGGTAGNGATCCCNTTCGNTACCCTTCTCTACAAATTNGACTGGAGTCTACCNTAAGGGTTTAACC
CGGAGGATATAAAGTGGACGTCATGACTGGACTCGCTATGCACAAGAAAGAACACCTCGTTCTTGCACCA
ACGAAACACATCTGATGCTATATATATCATTAGGACGTTTCTGCTGGTAGATATGGCGTGACCAATGGTT
ATTTTTCATTGCAATATCCCTTTTTGTTTTAATGAGTACTATGTTCTCATTTTAACGAATAAAAATGTAT
CAGTGCTCTTGTTTTTGGACTAGAAAAGAAAGTAGTCCGATGTTTAAT
>gi|3449781|gb|AI100042.1|AI100042 34195 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149L16XP 3', mRNA sequence
AGGAAGTCTCCTTGTACCCAGGCTTGNNCAAACCCATTGGCCCNAACTTNTGTACGTNGTGANNAANNGA
ATCAAAGCTTGGAGCTGCAAAAGCCATCTTTGGCCTTTGTCAAGACACATTACCACCAACTGCGGCATTG
ATGTCTGCAATCCTACGAAGAACACAAAGNCGAAGACGGGTNTCTCTACATGACATACAGTGGAGAGAAC
ACATTTGGTGGCATCTTTCTACTGCTAATTACCTCAGCTTCTACGTCTGATCCTCTTGATGATTGTACAT
TCTCGTCGACCTTAATAATGTCATTTTACTNTCTTGGTTTAACCTTTTGAGCTCTCTTACTATCTCTTGC
ATTTGAAGATGGTATTTGAAACAAGATTCTAATTTGACTCTCT
>gi|3449780|gb|AI100041.1|AI100041 34194 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149K24XP 3', mRNA sequence
TTCCCCTTCCCCNCATCCCATCCCCAATCTGGGGAAGGAGCCCCNCCCCCAGGACTGNACCNATGTGGGC
CCCCATCAAGTCAGCTATAGNGCTGTGATCGAGTCCCCTCTCGGTATNACTCTCACCGTGACCCCACCAC
ACTCGTGTTTAAGTCTGCAGCTAAGAGAGTACTCACTTTCTCGGTTAAGGCTAAAACAAGTCACAAAGTC
AACACTGGCTACTTCTTTGGAAGCTTNACATGGAGTGATGGTGTTCATGATGTNATAATCCCTGTCTCTG
TTAAGACAACGATTTCGATGTAATAAAAAGAGCCATATGATGCTCATTGTGTTTGTTCTTATGTAATTTG
TTGCAAATCTAAGTCTAAAATGTCAAATCAAGATTCAAGATCATCATAATAAAAGATCAAATCAC
>gi|3449779|gb|AI100040.1|AI100040 34193 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149J19XP 3', mRNA sequence
GGGGAGGTTCCTCCATAGNCCTCCGTGCCCCNTCGNTCTCTTTGGGCCAGCTCGTCCACAGACCCACTTT
AAAGGAGGNACTTATTAAAACTTTAAAAACAAGAAACAGCGGAATCAAAAGTCTTGAAGAAGCATACTCA
TCACAAAGCTTGGAAGGATGTTTTAAAAAAGATCTTTGTTAATTAAGTNGNGTGAGATTCTCTTGATTAG
AACTTTATGGTTTTTGCTTTATGANGTATCTCTCCAGAGAAGATTGTAAATTTGGGTTGAAACTTTGTNA
TATATTTAGATACAACAAATAAGTTTG
>gi|3449778|gb|AI100039.1|AI100039 34192 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149I19XP 3', mRNA sequence
CTTCAAAAAACGGCCCGGGCAACCCNNGNGCAAAGGAGCCCCAGCCCCAGTTGGNTTTTGCCNNAAAATA
TCCATATCTCCCTGATTACCCGCATGCCCGTTGTACTATTTTAGAGCTCTTTGTTATTTTGGTCTCACAT
AAAATACATCATAGTTGGAAGTCTTTTATTTGCATTGGGATTTGTCTGGAGTACAGAGATTTACTATTTG
CTTCTTCTTTCTTTTTTTTTTGGGATGAAATCTCTTGTATGATTGATCAATTATATGGTTTGGGTCTGTG
GCTTTAGTACTTTTGGTCCTTGGACAACTTCTCTGCTTCTGATCCAGTATGTTGCGCTACTGCGTTTAAT
TTAAAAAAATCTCTTCCAAT
>gi|3449777|gb|AI100038.1|AI100038 34191 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149H23XP 3', mRNA sequence
GTTTCCCNTGGTGGATTNTGCCCGGGAAGTNTCCNGGGGTTNGTATATGGAATCNGCCGGCGTATAATCC
TAGTATGGGACCCATACAGCCGCGTTGGTNGATTATGTGGCTAATNGTGGTGGAGGAGGATACGAGAGGA
TCGTCGGAGCGGTTCTGGTGGAGAAAGNAGATGCNGTGGTGAGGCAAGAGCACACGGCGAGGTTGTTATT
AGAGACTATATCGCCGAAATGCGAATTCAAAGTGTTTCATTGCTATGAAGCTTAGAGAATCATTTAATTA
TCCGNAAAATAAAGGAATTTTTTAAAAAAAGGAATAAAAAGAAAATGAGACTTTTTAATTCTTAAAAGTG
TTGAAATTGACGAC
>gi|3449776|gb|AI100037.1|AI100037 34190 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149H11XP 3', mRNA sequence
TTTNCGCCCANTTGGNCCCTTAACGTCGAAAGCCAGAGANCGNAGNCGCNCGTTAGTATGATTCACCACG
GACGTTATCTTGAAAGGCCCAAGCATCAGCTTCTTGGAAAAGAAGCTTCCAGCAAAATGGCTCGTCGTGA
TCCTGACCCAATCTATGACCGTGAATGGGAAGACGACAAGAGGAGAGCAGAAAGGAAGCGGAGAGATCGG
AAGTAGAGAGTGATGATTTGCAGATCCTTTGGTTTGTTCAACGAAGAGAGAGACAAATACTGGTATTGAA
CACTGCTTATGTTGTACACGTACTATTCAATGACCGTGCGGGTCTACTTTGTCATTTGCTCCGCCGAGTT
TGATAAATGACTTGCCAGACTTCAGAT
>gi|3449775|gb|AI100036.1|AI100036 34189 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149G7XP 3', mRNA sequence
TTTTNCCGTTTTCCNGGGCCCCCATTGAGGGTTTTAATGGGCCCAAGNACNCCTGTCCCAAACGGAATCC
CAACGGGCCANCCCTTGTGGCTGTCCCNAACCGTTATCCATTTGAAGNTGATTGAAGAGCCTGTTGAACA
AAGCGCAGTGGAAAGTGCAGTCTGAAAGACGGGCTCATGCATATAACCGATAAGGACATTCTCTTCAACA
AAGCNACAGGCGAGTTCGACTTCTGATCTTGACACTAGTAATGCTTCTAGGAAAGTCAGAGTCCNTCAAA
TGTCGGATGTCTTTCTTTGTACCTTATGATTTAGACCGACCTCCGAGTGAGAGACATGATNATTTATGGG
AATATGTACTCTGGTTGGCTTGTTGTACAAAAAGNACAGATTTTTCCGGCCGAAGAAGGCTTATCAACTT
TGACTTGTTTC
>gi|3449774|gb|AI100035.1|AI100035 34188 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149G15XP 3', mRNA sequence
GGCCTCGGCCTCNNGCCCGGGNATGTTGCCAATTACCCNTGNCCNTAAAGNGNGGNGGAACCGGAAGGTT
CTNGAAACTGCGGGCTTACGNCCACTTGGGAAGAGACGACCCCTGACTTCACCTGGGAAGTCGTCAAGCC
ACTCAAGTGGGACAACCTCAAGCTTAAATTTTACCTACTCTGTTTCTGTCTTCATTCCACAAACCAATTA
TCTGCTCACTTTTTTATTTCTCTGTTTTTGTGGTTTATTGTGTTTATGTATCATTGTACTTGAGCTATTT
CAATTGGGTGTTTGTTTTTATGGCGACTTTTACACGGCTTGGAGTAAGTTTCATGTTGTTCTTATATAAT
TATAACCATGNNAANTTAATAT
>gi|3449773|gb|AI100034.1|AI100034 34187 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149G13XP 3', mRNA sequence
AATTCCCNCAACCGCANGGNCAAGGACGTTCGCCGGGATACTCANGGATTGTCATCTTCTGGAAGCTGTT
AGACTTAGTTTTTGGTCAGCTTCTCTCAATCCCCTTTTACATTCTCTTGTGGATTCTCTTGGAATAAGCC
ATATAGAGATGACTGTAATCATATACTTGTTCTGGCTTTTTTTTNCCTTTTTTTTTTCTTCTTCTGGTTA
CTGTGTTAAGATCACATCTCTTTCTNTCTATCATTGTGGACAAAAGAGAGATTTATAACATCAGATGTAT
TTCAGAATAAAATTTGTCTTTC
>gi|3449772|gb|AI100033.1|AI100033 34186 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149E17XP 3', mRNA sequence
ANCCGATCGTNAAGATGGGNAATANCTCCTCCCGTGAACAGGCCGCCCAAGGGAGNNCTCCAGGCCGCNA
TCCTGGTCCGGGGGGTTACCCTGGCTTATTAATACAATCCATCTTTATAATTATGTGCAATATAATGCTT
TCGTTTCTCATTGAGTTTTCAATTTCTTTTGGCTTTGTTTGCATGAGTGTGTATCATATGTTTATTACTC
AAATCTGATTTTGTTTCGG
>gi|3449771|gb|AI100032.1|AI100032 34185 Lambda-PRL2 Arabidopsis thaliana cDNA clone 149E11XP 3', mRNA sequence
TTCGCAAACCGCCTNTTCCCCGCGGCGATTNNCCGATTCATTNATGCAGCTNGCACGACAGGTTTCCCGA
CTGGAAAGCGCGGCAGTGAGCGCNACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTT
ACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCCGGATNACNATTTCACACAGGANACAG
CTATGACCATGATTACG
>gi|3449770|gb|AI100031.1|AI100031 34184 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148N24XP 3', mRNA sequence
CCCATACGACGGCNCGTGGGATAGTACNGTGAAGACGGTTAAAAACGNAGGAGCCATGGCTCTTTATAAA
GGCTTTGTNCCTACAGTTTGTAGGCAAGGTCCTTTCACTGTTGTTCTCTNCGTTACGTTGGAGCAAGTTA
GGAAGCTGCTTCGAGATTTTTGATACCANTCTTNTATTGATGATGATGATGGCGACTGNTTATATTGATT
TATTCATTTTTGAAATAGTGAACACAAGAAGGAANTAGGAAGAGGGGGATTCAATATATTNTTTGTTCAA
GCATTGTTGTTAAATACAANTCAATTTTAGTTTCTAT
>gi|3449769|gb|AI100030.1|AI100030 34183 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148M5XP 3', mRNA sequence
CGAGAANTCCCAGCGAGAGGATGGTNNCGACCATCCCTGGGGTTCTGACANCCGTTTATTGGGCGGAGAG
CCGTTTTNGCCTTACAAAGGCCAAGCCCGTAGNTGCTGATACCAAAGGGAAGAATCGAAAGCTTGATTGA
TGTATTGATTCAGATTACCGACTCTTCTGTTTTCTTGAAATTGATGAAACACTTCGATAAATNTCTTTAC
TTTGTGGAATTTTTTTTGGACTTCTGTTATTTTACCAGGACCGTTATTTATCATCTGATTTCTGCTAGTA
TTTGTTCCTTTTGTTTGGCGAATCATTGTTAACTTTACTTCAATGATNACAAAATTTTTGTATT
>gi|3449768|gb|AI100029.1|AI100029 34182 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148K17XP 3', mRNA sequence
ACCNTTTCAAGATTCGTGCTATACCCCNTCTTCTAGATGAGCCGCCAAGTCAAATCCTAAATCCNCCACA
ACCCTCGCCCGTATGGCCTTATCCAACCATGTGGANCTNATATCGGGAGTCAAGTTACGGCAGTAGGAGA
GAATTCTTGCAGACAAATTCCGAGGCCTCCTAAAACCAAAAAGAGGAAAATTCCAAAGCCTCTTAAAACC
AAANAGAAGAAAATCTCAAAGCCTCATGCAGCAGTTCCGTGATCTCCAAACAAGANNGTGTGGGAAAGGC
TTTCACAGATAAAACTACCACTTAGAATCCTTTTTTGGAATACACTTATCCTTTGAAAACTCATCAAGTA
TTTTATTGGATTGTACAATAAATCCTCGTTCTTC
>gi|3449767|gb|AI100028.1|AI100028 34181 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148K16XP 3', mRNA sequence
CCTTGGGGGAGTGNATCCCCGNTTTAAGCTAACCCGGNGNCCCAACTCCTTGTTCCGTTGGGGATGGGTG
ACCCCTGTNAAAGGCCNGTCTTGGAAGATCATCCAAGCTCACCTTCCCTCACTTGATTCTTCCCCTTCTT
GCACCATCCCACTTGATTTGATCGATATCGATTTCTCGGGACTANCCGTGGGATTGAGGNTCAAATATCT
TATATATATTTCTAGTTGTGAATTGTTTTCCAATAAATCCTTTACAATGGTAAAGGAAAGTTTGTTTCTT
CGATGATCTTTACGATTTCGTGCTCAATGTAGTGTTATTTCTCTAATAAATTACGGTGATATTAGCTGAA
TTCTAGACTCTGGACTCGAGATTTCGACTTATATTTGGTTTTGAAGTTATAGTTGTAATAAAACTACGAG
ATTTGATTGAAACCTAAGAGCCTTGAGTTG
>gi|3449766|gb|AI100027.1|AI100027 34180 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148I16XP 3', mRNA sequence
CCTTACGCGATTGCCCGTGACNAAAAANTTATGGGACAAACCCTGATGAGTTTACCCCTGATAGGTNCCT
TGAACAGCTCAATAGATTACAGAGGACTGAACTTTGAGCTATNACCGTTTGGNTCTNGTAGGAGGGATAT
GTCCAAGGGATTGNCAATGGGGACTCGCCATTGTTGAATTGGGACTATTGAATTTGCTTTACTTCTTCGA
CTGGGGGCTACCAGACGAAGGAAGAAGCCAAGGAGATCATCACCGGGAATGAAGTTGCTCTTGACCTTGT
TCAAGTTTNTCTCCACTGAATATGTGTTTTGGTTATGGAATGTTTGTACTACACTAAGCTTGATTCTCAN
TTNATNACATCTTACAAGTA
>gi|3449765|gb|AI100026.1|AI100026 34179 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148I10XP 3', mRNA sequence
ACCTTTNGAAANNCTNGGGAGGAANTTCCCCCAAGGAAGAACATGCTTGTGGNTGAATGCCACCAGCAAT
TGACANTTAAATATGGACCNTCCTGGGAAACANTATAATAGCTGGCCACTTTCTCTCCCTTTGAATTTTG
TCATTTGCTTTTTACATATTGTTGTTTGCTTCGAAATAAAGCTTTTCGAGACATCAAATTTCAATGAGAT
TGTTTTTGTTTAGATTTG
>gi|3449764|gb|AI100025.1|AI100025 34178 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148H3XP 3', mRNA sequence
TCAAACAAGCCTNCTTTANGTACAAGTGANTGGTGATACNCAAATGCACACCTTAGCTNCAGCTTCCACT
AAGCAGAAACCCAATCTCTGAAGAGTTCGACTACACCTCTGGACCAACCATTGAGGTAGCGAAGAAAGTT
GGGGAAGTGATAGCAAAATCTTGCTTGGAGAAAGGTATCACAAAGGTAGCCTTTGACCGTGGTGNTTACC
CTTACCATGGACGTATTGAGGCTCTTGCTGCTGCAGCACGTGAACACGGTCTTCAGTTTTAACCGTCGTT
TTCTTTCCTTGTTTCTTTCCGATGAACAGCAGTGTATGAATGTAGAGAACCCATTTTCCCCAATTGAAAT
GTTGAGATTTTTCT
>gi|3449763|gb|AI100024.1|AI100024 34177 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148G18XP 3', mRNA sequence
GTATCCCCCTNGAAAATTTTGTNGGAGCNAATGANCTAATGGAACCATNAGGTATAGGCNCAAAGGACTT
TGTGACANCCAGGGGGGNTATTATAGANCTTTTGGCACCCGGGAACTTTTTATCTGAAAGAGGTTGATNC
CTTGTACCGGAGATTCTTTGGCAAGAAAGGTGAAGATGGATCTGTAGCCAATGGACACTGATTCTTGAAA
GGGANCAANTCATAAAAAGTCCCCTGAAAATGTTATGTTTTACTTGCACCATTTTAATCGTTTTATAAGT
TTGTTGTTACTTTGATTTAGGGACAAAGAAGGAATGTATTCTCTGTTTTTATTT
>gi|3449762|gb|AI100023.1|AI100023 34176 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148E21XP 3', mRNA sequence
CTNTCCAGGGCCTTANGAAGGNGTTTAGCCTNNAGCCANGGTCNCTNAAANGCCCTTTAAGNNAGGATTC
CTNCTGCAATGGCACCCGTCGTNCCAGGACCTCTGANTTTAGGCCAGGTTANTCCAGCTTCAAGGTGATC
AGAGGAAGANCGTATCTACGTTCCTTGTTCAGGCTGGGCTTGTGAAGAAGGATAACATNAAAACCCATGG
TTTTTGAGCAATTCTAGAGATACTCCTTGTTCAGCTTGTATTTACGGGATCAGCCAGTCCCAAAAGGAAT
TTATAAACCATTACTTAAATGTATTAATGCTTTTATTATGTATTGTGTCAAAAAAATAATCTAATAGTTT
GCTTATGAGCGTATATATAAATGTATCAACTTTTGGTATGCATTTGTACTTGTAGTGTGAGTTTATCAAT
AAAATTTGCTTTGTG
>gi|3449761|gb|AI100022.1|AI100022 34175 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148E10XP 3', mRNA sequence
CCAAGTTGATGGNTTAACTCCTGGGCAACGTCGTGAAGAGATGCAAAAGCATTGCAAGNGAAGACTGCAA
AGAAAGCTGCTCAAGCCGCTGCTGCAGCTAGTTCCGGAGGAGGAGGAGGCAAAGGNAACNATAAGTGNGC
NNAAATGNTCTATGCTTCGATGTTTGTAACTGTGCTTTTGAATATGAAAGTTTGGTGTTTGTGTTGAGAA
TGTTTTGGCTTCGTTTGGTTTGAGTTTGTNTCAANACTTAGACTTGGTGATGTACTTTGATTAAACCAAT
GATTACTCTTNCNATATCTATGATTACAAGTACATTTGTCC
>gi|3449760|gb|AI100021.1|AI100021 34174 Lambda-PRL2 Arabidopsis thaliana cDNA clone 148D11XP 3', mRNA sequence
TTTTTAGGCCGGTGNCCCNAANCCCCCCNGTGGGAGGGGGCCAANCNCCGCCCNTNGTTTNAAAATNCAT
CCTTTTTCCGGTAACCACATTTAACCTCTTTTTATAAACCCGCGGGTTGTCCGGTGTGTGTTCTTGTGGT
TNCCCATACACTTCAGCTCAAAGTGTGATTTGTATTTTGCGGTTTCGTGGTTGTTATTTTTATTGAGTTG
GTTTTTAAGCCGTTAGGGCTTTCTAATGTAAGTTCGAGCTTAAACTGTTGGGAGATTATAAGCATTACTA
CGGGAC
>gi|3449759|gb|AI100020.1|AI100020 34173 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147K18XP 3', mRNA sequence
TAACCTGAGAAAAAANNTNCCCATTGGNGGNNCCAAAATCCGTCTTCNGTTGAAAGCNAGNTCAGATGCA
AATTTGCCGGAGTTTCATCAGATGGAAGATGCCGGTGATAAAGTGGTGATGAAGTGGAANCCCATGATGC
TTGATGTTGCAAGCCCTGTGTCTTCCGGAGCAGCTACTGTTGTCTGCTAAAAGGATTTTGTAATTCTCTT
CGAGGNNNNATATATATAATTGTTTNTCTTGTATTTTTTTCGGCTGATTGTATTTAAAAAGTTTCTTAAT
GTTTGAGAAAAACAAGAATAAAGCCATTTTTTAAACTGTTAATTGTATTTTAATGTAAAAGACTTGTTTG
ATTGAATAAAAGGAAAGAGAAGTTGG
>gi|3449758|gb|AI100019.1|AI100019 34172 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147K13XP 3', mRNA sequence
ACTANCGAANNACCANCCCCATAATGGCTCAAAGGNNTCGCAAGTNGAAAGTTCCTGGGAGAGTTAAANG
CCACAAGCAGAAGCCCAAGAAGAAGCGTGAGCCCAAGNAAAAAACAGGNGTACACGCCAGAACAAGCAAG
GAGCCAAAGCCCTGTCCCTAGGCAGAGCAGGAGCCCGACCCCAGTCCCTCGTGGAGCNCNAAATGGAGAC
CGTTCTCCAAGCCAGTGATTTAACNCCATGTATCTCTCTACTCTTCAGTTTTTCAGTCTTGTTCTGTTTG
ATCAGATATTTTGTTTGCCTCAGATTGATATTTCCCTACTTAGACAGATNTTTGTAGTGCTATTGGTATT
TTGCTTTATGTTTGATCC
>gi|3449757|gb|AI100018.1|AI100018 34171 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147H3XP 3', mRNA sequence
CCAAGGGTACCCTGAGNTCGAAGTGGATGTCACTGGTGTGTNCTACTTTGTCAAGCCTGACGCATANCTA
GTCTGCATGGCCTTAGCAAGTCTGTCATATGAAAATGAAGTCGGGATCATCGGAAATTATCAGCAGAAAA
ACCAGAGAGTNATATATGATACCACACAAGAGAGGCTAGGAATTGTCGGAGAAAACTGCAGAGTCTGATG
CCTACNCCATNACTTNATATCCATTTGTGTGCTCCCTTCATATCATGAAAGCCAATCATCTNTTTTGGCA
AAGCCAATTTGANTTCTCCC
>gi|3449756|gb|AI100017.1|AI100017 34170 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147F15XP 3', mRNA sequence
CGTGGAAAGGATACCTTNGGTTGGGTCNCTTGGGGGTTAANTACGNATTCTGGCAACGNTACCACNGTCA
GGATTCNGACTTNAGTTACGTTGGTTCTCAATAATGTCACTGCTGATAGAGACCTCAAAGCTTCTGGCTT
ATGGTNCCAGTCGTTCTTGAGAGATACCACCAAGAACCAAGATATCCTCCGCTCAAGTCTGCCCTTTAAG
AACGGGGATAGGAAGAGCCTCACATGAAAGACCAAAACCACTTTATGCCCATCGAGATCATCT
>gi|3449755|gb|AI100016.1|AI100016 34169 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147E1XP 3', mRNA sequence
AGGCACAGGAAAGGANCATGTAGCCCAGATGATNCGAAGACGCTGANCCATNTGNAAGGCGAGGCTCNTT
AGGACGCCAAATGCCTTAAGTGAAAAGGCTCTNAGATCTCCGTAGAGGTTNACTCTGTTACNCGTGTTNT
GATACCATCNAGAGAGTCCTTACCACCTTNTGAATCGNACTCGGGTTTAAGAACTAGTTGCTTCTCAATG
TTATTTTGACAGAATATTGTTCTNAAATACATTACAACTTCTAGTTATTGTNTTAATTTTGTTTTTTATT
ATCCAAACTCGTGTGTGTGACATTCTCTGTTTAAATTAGTTGCTTGGAAGATGCAAAGAATCTCGTTTAA
TGGGGCATACTGAATTTCATTTTAAAGTTGT
>gi|3449754|gb|AI100015.1|AI100015 34168 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147D12XP 3', mRNA sequence
CCNATTGGGGTCCACTTTGGATTAATCGGAGAAGAAGNTCAGGAATTCCATACNCAGCTTGTCAATGGAT
NNCAGTCTCTCACCGCAGAACTCTCCCATTACATCCCTGCTATCTTATCCGAACTTTAGTGTATCTTTGT
CAGTTTTTGTTACGAGTTTTGTGCTTTTTTCTTCCACCATTTGGCTTGGCTATATGTTTATCATTTCTGT
AATTCTTAGTTTAATGACAACAAGTGAGNNNNNANTTATAAATGACAATTGGTTGACTTCTAATTCAGAA
GCTTATGTTAT
>gi|3449753|gb|AI100014.1|AI100014 34167 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147C20XP 3', mRNA sequence
CCTGCAAGAAGTTAGACTNGATATGGAAAAGNCAATGTTAATGGAGGANCNATNGCTATTGCCNACCCCC
TGNGTCTTANAGNAGCTCGATGTGTTGCGACATTTTGCACGAGATGAAGCGGAGAGGAAAAAGATTGCCC
GCTTTGGAGTAATCTCAATGTGCATAGGCACTGGAATGGGAGCTGCAGCTGTTTTTGAGAGGGGAGACTC
TGTTGATAACTTGTCCAACGCTCGTGTGGCTAACGGGGATAGTCATTAGAACATCGAAGAGAGCTTGAAT
AAGTAGAAGTAATGATGCATTGAGTCTNATAAATATGATGCTTTAGCTCTTTCACATTGCTGAACAATGA
AAACTTTTGTCATTCTGAGTTTAAAATCAACTACTTTTCTCTG
>gi|3449752|gb|AI100013.1|AI100013 34166 Lambda-PRL2 Arabidopsis thaliana cDNA clone 147C18XP 3', mRNA sequence
CGGAAAAGATTTANGATNTCAGAGAAGAAATCAGCAGTTTCTTCAGGCAAGCTGATCGAGAACTGATGCT
GGAGATGTNTCAAGAGGTTTNGTCTGTGTGGAAACCGGTCTNATATACACTTACACACATACTTTGAACA
TTTCAGCTTGATGGTGTTTTGTTTATAGTCTTCTTGTTCTCTTCTGTGTGTGTAACTAACAACAACTCTG
GATTTTGTTGTATCACTCTGTCTAATGTATAGTATTGAGTGG
>gi|3449751|gb|AI100012.1|AI100012 34165 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146O7XP 3', mRNA sequence
AACCAGGATAAGACCTNTCCCCNAGAAGCGGGACTNCTGAGGAAGAAGAACTNNGCNGCATTAACAGNCT
GAGATGGCCCNCTAAGGTTANTCACCTCTCCGAGCAGAGACATGTATGCATTGATAGACACGAACAGACG
ATGTATATAAGGATCTGAATCAGATTAATTCGGAGCGAAAAACTTTTATAATCCCCGTCGTTAATGTTAT
CTGCAATTTGAGTGTTCTTCACATAATTTATCTTTTGTAATTTTTGTATCTTTTTATGACNCTTTTTCCT
TTGGTTAATAATCACTTTACTCCTATGTTC
>gi|3449750|gb|AI100011.1|AI100011 34164 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146N6XP 3', mRNA sequence
CCGGTTACTACGATTGGACGGTNCTGGACAATGTGGAAGNTTCCCATTGTTCGGATGCACCGANTCCGNT
CAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTACCCGGGCGCCTTCATTAGGATCATCGGATTCG
ACAACACCCGTCAAGTCCAATGCATCAGTTTCCCCNCNTACAAGCCCCCAAGCTTCANTGATGCTTAAAT
CCTTTTNTGGAATATTCAATGTTGACTATCCGGAACCCNCATTTGTATGGTCAATGTAAATTTAAGTAAT
TACTTTGCCCAAAGTGAAAAAACTGAAGGTTTGTTTTTNTATCGTTTCCTC
>gi|3449749|gb|AI100010.1|AI100010 34163 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146N22XP 3', mRNA sequence
ACCGAACACCATTGANAACGTGAAGGCTTAANNCCAAGGACACAAGGAAAGGCATTCCTCCGGNACCAGC
AGCGTATCATCTNCGCTGGNAAAGCNAGCTTGAGGATGGACGTACTATGGCCGACTACAAACATCCAGAA
GGAGTCTACTCTTCACTTGGTCCNCCGTCTCCGTGGTGGTTTCTAAACCTTGTCTCTCTCTCTTATGGTT
ACTGAACCAAGTTCATGTATCGTTTCATNTAGTACTTTGGTGGTTTATGTTTTGGGGCCNTGTNCAGCCT
CTG
>gi|3449748|gb|AI100009.1|AI100009 34162 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146N14XP 3', mRNA sequence
TGATGCTAATNATCCTGGTAAAGNAATGTGTTATATGTTTGGTCTGAACCACGAGACACCACTGTTCTTC
CATGTCGACATATGTGTATGTGTAGCNGGATGTGCTAAGGTATTGAGGTTTCAGACAAATCGATGCCCCA
TTTGCAGGCAACCTGTTGAAAGGCTTTTGGAGATAAAAGTTCACGGNNACANCGGAAGCGGGAATAACAC
CGGACAGGGAGAAACAGTTGAACAAGACCCCCCTAAACACGGCCGAGTATGGACCNAAATGCCATCGAAA
TATTAGTAGTATATGCATGTTCGATCCTTGTATGTTAACAACAAAATGTGTGATTGTCAATTCATAATAT
AGAGATTACG
>gi|3449747|gb|AI100008.1|AI100008 34161 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146M2XP 3', mRNA sequence
CGGGATGGCGGAAGCGACGAANGCAAAGGAGTGGTTTTTCGGAAAAAGGCGGATTGATCTTTGCNATATT
AAATGCTCGTTTTAGCAATGGTCCTTCACCGTCTCGGCTATATTGGAAACTAGAGGAAACAACGGTATCT
TAAGGCTTAATCCTTCGTGAAGATAAAACCAGTCTTCGGTGGGTTCGTTTAGTTTGTAAAACTGTANCCT
CGTTTTATCTTCTTTTTCTTTCCTCCNACTCTCAGCTTTTTGTTAGTCCCCTTGTGTCTAACCTTCTTTA
CACTTTCTTCTGTNGTGAATTTTAAATTAGAG
>gi|3449746|gb|AI100007.1|AI100007 34160 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146M15XP 3', mRNA sequence
TTTTNGCCCANGGGCCCCNAAGGGTGTTTTTTGGNAGGNTTNCCCCAANTCNGTTNAACCCCTTGCCATT
TCCAAAGGATTTGGCNCCTCCGGGAACCTTTTGGGTCCGCTTCAGTGGTGAACCAAGATCATCGTACCTA
CGACCCCATCAGCNGTCAAAGTTAACTCTAATGGTGAAGTTCTTCAAACAATTCCTCTCAAAGATAAATT
TGGAGACACTCTGCTCAGCGAAGTCAACGAATTCGAGGGCAATTTATATATAGGNACTCTCACCGGNCCA
TTTGCTGGAATTCTTAAGCTCGAAAAGGGTTCTTGTCCTGCCNCTTAGATCTCTTATTTGAATGCATCCG
ATGTGTTACAATAATATATATATATGAGCTTTTTATTTATTTCTG
>gi|3449745|gb|AI100006.1|AI100006 34159 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146L14XP 3', mRNA sequence
GTCNTCTTGGCCNTAATGCCTCCGAAACCAGGGGACTNCTACTGGGCTCGTGGTTNTCACAAGAGCNTTG
ACTCAACAGCTCAACAAAGGATGAGATGGNTGCAGAGGAACTACATGATCTATAATTATTGTACGGATGC
GAAGAGGTTCCCTCAAGGTCTTCCTAAAGCGTGCTTAGCTGCATAGAGAGAGTAAAGAGTTGAGAGAGGA
ACAAGATTTTATTTTTCTTTGTGGTTATAAAATTCTCCCTCATTTTATTGTAGATCACGTGAATTTTATC
CATTTCNTTTGTAGTATAC
>gi|3449744|gb|AI100005.1|AI100005 34158 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146K2XP 3', mRNA sequence
GGACAGTCCCAACTTTCACGGCGGAGTTACATTCGAATTCTCNCCGGAAGATTGTAGAGATGAGGAAGCC
GTATCAGTCCGGTGACGGTGACGGTGATCGGAAAGATTGTGGATAAAAAGTGATTAGGATTAATTTTTAT
TTTTTCGGNGAAACTTTTTTTTTTTTTTTTCGTTTAATTTCTCTTTATTTGTTTTTAAAGTCTGTTTTAG
GGTTTTGCAGTTGGAATTTAGGTTTTTAATTT
>gi|3449743|gb|AI100004.1|AI100004 34157 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146K20XP 3', mRNA sequence
CCCGGGNCCCGGGAACCCNCCCGGATANTNCGGATGGCCGGTACTGGCCAATTTGGNAAGCTTCCNATTG
TTCGGGATGCCACCGACTCCGCTCAAGTGTTGGAAGGAAGTTGGAAGAATGCAAGAAGGAGTACCCGGCG
CCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCC
CCCAAGCTTCACCGAAGCCCTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTCATTTCATTT
CCTATTGTCTGTGTTCTTTTTCTCTTCCCTGAGACAATTTCTATCGGATTGTCAAATGTCCGATTCCTGA
ATATGTAATTTATATATCCGTGCGTCTTGATTTTTTCCGATGGTTAACTAGTTTG
>gi|3449742|gb|AI100003.1|AI100003 34156 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146K10XP 3', mRNA sequence
CCGGGAAATTGAACCCCCNAACCCCTGGGTTGNTTCGGCCTTGCCGAATGCATCTATGTGGTTTCTTCCC
AAGAAGCTTNCCCTGTGATGCAATCGTGGAAGGACCAAACTTTGAGTTTGCAACCGAGACACATGAGGAA
ACTTCTGTATGACAAAGAGAAGCTTCTTGAGAATGGAGATAGGTGGGAGACAGAGATTGCAGAGAATCTG
AGGTCGGAGAGCCTCTACCGCTGAATATTGATCCGAAAATGCCTTTTGCCTAATTCTTAAGGAAACGTTT
TCGTTTGCTTCTGTTACAAATAAAGATGCTTCAGCCTTTGCACTGTTACCCCTATCTGTATTTCTTGAGT
TCATACCGATGGCAAAACCAAATTTGGCTTTGTTTCCGGTTTGAGCTGGACCGTGCGGTAAATGGATTAT
GATATG
>gi|3449741|gb|AI100002.1|AI100002 34155 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146J24XP 3', mRNA sequence
ATCTGGGACAANTGTTGGAANGTTNCCATTTTTCGGGATTGCACNGACTCCGCTCAAGTGTTTGAAGGAA
GTTGAAGAAATGCAAGAAGGNGTACCCGGGCGCCTTCATTAGGATCATCGGATCCGACANCACCCGTCAA
GTCCAATGCATCAGCNTCATTGCCTACAAGCCCCCACAGCTTCACCGAAGCTTAATTTCTTTTCTAAAAC
ATTCTTATGAATTATCTCTGCATGATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTACGCAGACAA
TTTCTATCGGATTGTCAAATGTCTGATTTATGAATATGTNATTTATAT
>gi|3449740|gb|AI100001.1|AI100001 34154 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146I19XP 3', mRNA sequence
TTTNGAATNCCAAANGCTGGGATTNCATTGNGCGACAAGTTTGTGAAANTTGGTGTCATGGTACGACAAC
GAATGGGGGTTACAGTTCTCGTGTCGTTGACCTTATCGTTCACATGTCAAAGGCCTAAGCTTACACCGGC
GAGAGTTTGTGTGTGGCCNGAGTTCGTACTGTTCTGAATANAAAAAAGGAGAAAAGAAAACTCGAGTTGT
TATGTTTTTTCACTGATTCCATGCCCCGTCATGAGAGTTTGTAGCTTTTGTCTTTTTGCTTTCCCTTAAT
GTTTCCCTGCTTTATTTACTGAAACCATTGGTTTGGTTTTTTATGTT
>gi|3449739|gb|AI100000.1|AI100000 34153 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146I15XP 3', mRNA sequence
TTGTTNCCCNCCCAGTATTCCATTGAACCCTCGNCCGAANGNCATGAGGCTACTCTTCGCTCTGGCGATG
AAAACGCGGTTTCCATGCCTGTAGCCGCGGCTGCAAACCGAGGCTTTTANGAAGGCGAGAAGCTTGGGAC
TAGGAGATCTCGACTTCTCTGCTGTGATTGAAGCTGTGAAATTCTCCCGCGAATAGCAAACTGTTTCAAA
ACATCCACTCATTTGGATAGGCTGAGTTACTGAAATCATTGTTATCTTCCCAAATAGAGATTTACTCATT
TGGCCAAACACACATTTTAATCCTTCACCAAATAAAAAGTCTTAACCAC
>gi|3449738|gb|AI099999.1|AI099999 34152 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146H10XP 3', mRNA sequence
TTCCAAANAATNCTGGCTAATNGCTTTTGCCCNCTNGANTACCACCTTCCCNTCAAAANCAGGAGAAAGN
TCAAANGAATACTTGAAACGATCNAAANAAAGTTGCTGTTGCTTCAAGTAGCTGCGGTGTCTGCTGAATG
CAGGTGGTGGTGCCCCCAGCTGCTGCTAAAGGTAGAGGAGAAGGAAGANTCCGACGAAGAAGACTATGGA
GGTGAATTTCGGTTTGTTCGATGAAGAGTAGATTTTGTCGGTTAAGATCTTACCTTTTTGTCGTGGATTA
TAAGTGTTGCTTTGTTTTTAGTATGTTGGACCTCAATTTTCTTGGTTTTAGCCAATCCAGTTTTATGTTA
CTACTGTCTTTTATTTTTTGG
>gi|3449737|gb|AI099998.1|AI099998 34151 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146G18XP 3', mRNA sequence
TTNGGGGGNGGAAATTGCCTTNGAATCTTTGGATCNCCCCAAACCATTTGCCCTTCAGTTCGGGTNCCCG
GTNCCCCCGTGGCCAAAATGCAAGGCTCTGTTCATNTCTTGAAACACTACNNATNTCAAGAACACAGTGT
CAAGAGTTTGATTCTTCTTTGGCNAAATCTCACAACTCTTGATTACAAGAAATGGAGAGAAGTGTGTTTG
AATGCTATCTATACCGTATGTTTTGAATTTCNATTCATCAAATAAAATATCTTGTTATAACCTTTTGTNT
CAGAACATGGTCCTCAAAGTTTTAAAACTAAAGGTTAAAAATATCCTCTTC
>gi|3449736|gb|AI099997.1|AI099997 34150 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146D2XP 3', mRNA sequence
GCCCCTCTGGGNAGCCCCATGGNTTTTCGGGGTTGGCCCCATNCATTGGNNCANTCTAGCAGCACTATAT
CNCCAGATTGTCATCAGAGCGATTCCTTTCAAGAGCAAGAGTTAGAGACACACAGAAAGATTCCACGGTC
CAGAATTTGTTCTTTAGTAGTTTCTTTGCTTATCTATCTAATGTAGCTTGTGTTTTGCAATGTAATGAGC
CTTTCAAGAATATGTATTTGGGATTTCTAATCAGCTTTTGTCTATGTAAAAACTATGTGTTTCTTTTTTC
TTCCTATACTCGTCTCAGATGCTTTATGGC
>gi|3449735|gb|AI099996.1|AI099996 34149 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146C9XP 3', mRNA sequence
TTGGGCCCNGTGANGGGAGATTCTTGGNACCGTGTATCNCTGTGGGGATGCACTNTAGATGGGAAAGNCC
CNAAGGATCTTCNNCAGGAGATTCAAGAAGGTGAGATTGAGATTCCTGAGAATTAAGGAACAATGGAGTT
TTTTTTCTTCTTATGGGAATTTGAAATGCTTCTGTTGTTATCTTTCTCGTTTTACCATATTTTGTTTTTG
TTTGGGAACTTAGCTGCTATGATGTTTCACTTAGAATGACTCTCAAGTTTTGGATTCTTATTATTCTCTG
TTTCAAAACCCCAATGGTTCTCTATCATCACTGTTTAATT
>gi|3449734|gb|AI099995.1|AI099995 34148 Lambda-PRL2 Arabidopsis thaliana cDNA clone 146B15XP 3', mRNA sequence
CCCCCGGGGCCCNCCGGGGGGNGGGTCCCCCGGAAANGGCCCCCTTTAGNCCCCCCCAACAGGTCCNGCG
GAACAGTAAGTCCNCTAACGCAGCGGTTGGCGNGAGCCACACCGTCGTTGTTCCACCCGCATTGGTCACG
ATCGCCGCCATAGCCGTCTCCGTGTCTCTCTGCTCTTAAAACCTTTCGTAATTACGCAGGCTGCCACTCC
CTTTGTTTATTTTTAATTTAATTATCTTTTCAATTTTTATTTTTGTGGTTATGTGTTGTTGAGTTTGAAA
ACATGGGATTAGTGAGTGAGGTTTTATTTAAATCGTTTGTTAATCACATTTTCATTATTGCTTTCAGTGT
TGATCTGATAGTATCTTGTTGAG
>gi|3449733|gb|AI099994.1|AI099994 34147 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145P10XP 3', mRNA sequence
AAGCATATTGNCTATATGGCGTGTCCAGTTGTGCTAATGGGGTTCCATTGAAGGNTNCAGAATCGGAGTG
GTCCTCTTGGGGAAGGGCTTGACCCGCTTTACCCGGGCGGGGCCTCGACCCGTTGAACTTAGCGGAGGAT
CCAGAAGCGTTTTCAGAGTTGAAAGTGAAGGAGCTTAAAAACGGTCGTCTTGCTATGTTCTCAATGTTTG
GATTCTTTGTCCAAGCCATAGTTACCGGTAAAGGTCCGATCGAAAATCTGTTCGATCACATTGCAGACCC
TGTGGCTAACAATGCTTGGTTACGCCACCAACTTCGTCCCCGGAAAATAGAGTTTGATCGGATAATTTAT
GTAAATTATATCTTTTAAACATTTATCAATGCATTAAAGTTATCCCTATATTTGATAC
>gi|3449732|gb|AI099993.1|AI099993 34146 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145O5XP 3', mRNA sequence
CAAGGAGNAGAAGGNTGCCAGGGAAGTCCCNGNGAGGATCNCCCAGCGGATGCCTCGTTGGCTTNGCCGT
AATGTTGGTCCTGTGTGTGATGCCGGTGTCGTTTNGCCGTCATGAGTGTAATGCTCGCATGGTTTTATTT
GTGATGAAAAGCTTTTTTTTTTTTGTGCTGATAAATTGTTATTTTTTATTACTCATGATTTTCTGCCATG
TGGGTGATTTTGGGGATATATTTGTGTCTTGGTTTTCATACGATTTTGTGTTAATCAATCCATTTGTTTT
TTATATTTTCGTTTATTTTTATTAATACAAATCATATTTTCCGTTTTCGTGCGAGTGAGAATTGTGTTTT
TGTTAATATCTCGTTTATCTTTGCTT
>gi|3449731|gb|AI099992.1|AI099992 34145 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145O4XP 3', mRNA sequence
AGTTGGGGTATCCAAANACCTGGGCTNGGGACCCAGCTTGCCATNTATGGGGAAAACCAGCTTGNACCCA
GGCGATTTTCTAGGACCACTGGTGGGTAGCAGCTCTAGCATTCGGGGAAGGATGCCACAACATCACCATG
CTTTGGAGTCNCAGCTCGACACGGCTTAGAATGGGTGGCAACTTGATATGACTTGGGTACGTCGTTAAGT
TCCTTCAAGCCATCGGTTTAGCAACTGATGTCAAGCTCCCATCGGAAGCTCAGAAACAAAGAATGGCATT
CACCAGCGACTGATCTTAAAAAACTACATGGTTATGCCTAAAGTCAAAACTGTCGGTTCGATTGAAGCTA
TGAAGGTTTTAAAAAAGGATTTTGTTCTGCTTTTTTGTGTTTACTTAAAGGTATATATCTGTGCAAGAGA
TTGTATGTGACAAACTGATTATGAATAATATCTATAATTACATTCAAT
>gi|3449730|gb|AI099991.1|AI099991 34144 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145O16XP 3', mRNA sequence
CCTGGGGGGCCATCCCGGGGCCCCCCNTGCGCNCGTTTTTTGGTCCCGTGAAGCTGGGNAGGCCCTGGAC
CAGGCCCGGGTCTCAGAAAGTGCTGGGCATCTCATATTCAACTATAAGCCCTACTTACTGTGGATACGCC
GGGAGGGGTTACGACGAGGTTTACATTTTTACNCNACCAAGATCCCCGTTTCTAAGAACTTTACTCGTCG
TCTTGTGTGTTTGTTTGTAACTCTTATTTACATTTAGGGAGCCGGATTGTCTTGCATGATTTCCCTTGTT
GATTTTATCTCTTTGGAATTACATTTCNAAAGATACAAACTGTGTTTGATTCGTCTTTCTTGCAAATAAC
ATTTNACTTTTGAG
>gi|3449729|gb|AI099990.1|AI099990 34143 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145N10XP 3', mRNA sequence
GTTTCGNTACAGCCATNGCCCCCAAAANCGGGNGTCTTGGAACAATNGCNCCCNATCGCAACCGGTTCCA
TTGTTGGNGCCNAACATCTTAGCTGGGAGGAGCTTTCTCTGGGAGCCTCCCATGAATCCCCGCCGTGGCT
TTCGGACCAGCGGTGGTGAGCTGGACATGGCCCAACCACTGGGTCTACTGGGCCGGACCTCTCGTCGGCG
GTGGAATCGCTGGACTCATCTACGAAGTTTTCTTCATCAACACCACACACGAGCAGCTCCCAACCACAGA
CTACTGAATTAATCTCTCTTTTTCTCTCTTGTGTAATTTTATTCGACTTTGAATTTGAATTTTAATGTCT
TTTTAATTTCCGTTTGTGTAATTTCGAATCATCAAGGGGTTTATGATCGTTCGATCTTTTAGATGAATCC
TTGTCCGTTGGTTTCAAGAGTGGCCATTGCAATTTCGACTATATAATGTGAATTATGTATCAATCTCATC
TTAAGTTTTC
>gi|3449728|gb|AI099989.1|AI099989 34142 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145F8XP 3', mRNA sequence
GTTCTTAGNCCAAGNGGTATTGGNGGTGTCTGAACCNACCCCNTTNTTCTCAAAGTTAGCANCCGGTTTG
TATCACNCCATTGTGGNCCCTCAACGTGGTCGCATTTTTGGGTTTGGCGATAACGAAAGAGCTCAGCTTG
GTCACGACTCACTCCGTGGCTGCTTAGAACCTACCGAAATCTTTCTCCATTCTGGCCGTTCTCGTAGCCG
GCTTTGTTGATCCAAGGTATAGATAAACAACCATGTTTGTATGAACCGGATTGAGATTCGATTTACCGGT
TAGTGTATCTTGTATTGATTTGTATCTGTTTGATTTCTTCAAGTTGTGAGNGTNA
>gi|3449727|gb|AI099988.1|AI099988 34141 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145E22XP 3', mRNA sequence
CGTTCTTGTGCACNTCCAACCGGCCTTCAGATCCTAGGTNTGGGNCCGTCCCNTTCACCACCNATGNGCT
TTNCTCACCCTTNGGACNCGGTTGTTGGCCCNCGGGGGCGGTTTAGGGAGCCCAATGGNCCAATGCCCTT
TCGGTGCATCTTNCAAGGGNTCCCNCATAGATGGTTNCCANGCTTCTGTGGAANCCAAGTACTGTGCCCA
CACAAGNCCGCATGTGGTGGNATCAGAAAGAGTTCCGTGCCCTTGACGCTGAACAATGGCGTCGTCTCAA
ATGGGTTCGTATGAAGTGGNCCATCTACAACTACTGTACCGACCGGACTAGGTTCCCGGTTATGCCAGCT
GAATGTAAAAGGGACAGAGACGCATAAGTTACTACTCTTGNGGGTTTTAATGAATTTATGCTATCATTAT
TATTTGAATTATGCTTGTTCAAGAGATTGATATATGTATTGTTTGTTGGCCCATGATGTTTATGCTATAT
TTGGGCCTAAAATTACATGTTATAATTCATATATGTATTGATTAGCTATGTATTTTCATATGTTATGATC
TACTTACAAGTTTTATTCTTT
>gi|3449726|gb|AI099987.1|AI099987 34140 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145C2XP 3', mRNA sequence
TCTCCCNCCTTTTGGCTTTCCCGTTCNCTCTNCACAGGGATGCCCCGATGTCTCCNNTTCGGNGTCCNCC
TCTGATAGTGAATNCGTCCTCGTCTTGACCACTTACTTGCAGCACACTCACCCTCGTTNCNTCACTNCGA
TTCATCCAGAGTGGGACTGGCTCAGGGGAGTTTGGCTACCGTAGCCAGAGACTACGGAATCTTGAACAAG
GTGTTCCACAACATTACAGACACACACGTGGCTCATCACCTGTTCTCGACAATGCCGCATTATAACGCAA
TGGAAGCTACAAAGGCGATAAAGCCAATTCTGGGAGACTATTACCAGTTCGATGGAACACCGTGGTATGT
AGCGATGTATAGGGAGGCAAAGGAGTGTATCTATGTAGAACCGGACAGGGAAGGTGACAAGAAAGGTGTG
TACTGGTACAACAATAAGTTATGAGGATGATGGTGAAGAAATTGTCGACCTTTCTCTTGTCTGTTTGTCT
TTTGTTAAAGAAGCTATGCTTCGTTTTAATAATCTTATTGTCCATTTTGTTGTGTTATGACATTTTGGCT
GCTCATTATGTTATGTGGGAAGTTAGTGTTC
>gi|3449725|gb|AI099986.1|AI099986 34139 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145C1XP 3', mRNA sequence
CCAAATATTGGGTTTGNGCCTGGAGGCCNTAATATGCTTNGGNTCCAAACCTATTAGGAAACCGTCNCCC
CCCTTGGGAATTGAAGCTGGCACAGCCTCGAACTCAAAGAAGAAGGTTGCAAGATCGTCGGGTTTCATGG
AAAAGTAAGTGCGGTGCTTCATCAGTTTGGAGTCCATGTCCTTCCTGTCACCAACTGATCCTCNCATATA
TATATATATATATATATATATATATATATATGTCTCTTCTATACCNCCAAGTTTGTCNCGTGTGATATCT
TCATTAAGTTTTAAGTTTTCTAATTTTTCTTGTTCTGTTTATCTATGTTTTAAGTGTCTTTAAGTATGGT
GTTTTGTGAAGTTGTTATGCCTGTAATATTATATGTGATTGGCTTTAATAAAAGTGGGTGATTATTATAC
>gi|3449724|gb|AI099985.1|AI099985 34138 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145A20XP 3', mRNA sequence
CCTTGGGNCCNGCAATAATCCGGTNGAACAACCGGGGCCCNCANCNGTGGCCTTNGGCCTTTGGGATCCC
GGTCCCGCTGCCGNGACTTGCCNGACCAACCCCGGTTTCCTCCTAGNGCTTAGGGNAACCTTCAAACCTC
AATACTGTCTTCTGCACTGGCCNCNTCAAGGTCGACTTNGGCAAACCGATGTGGTGAACCCNGATCTATG
GAAGCTTCGTNCCGGTCTTAAAAGGNGGGGAAATTGNCATGGGGAATCTTGGTTGATCATTCGATAGTAG
AAGGATTCGCACAAGGTGGAAGATCATGTATTACCTCAAGAGTATATCCCACAAAAGCTATCTATGGAGC
TACAAAGCTCTTCTTGTTCAATAACGCCATTGATGCGACCGTTACGGCGTCGTTTACAGTCTGGCAAATG
AACAATGCTTTTATTCATCCTTACTCTTCAGACGATCTCGGTGTTCCTTCCAGCACCTGATGAGTATTCT
CATCCTTCTTGTTAGTCTTTTGATTGTTGTTAAATAATGGGTTTGATTTTATCTGTGTTTGATTCATCAT
GTGAGTGAAGAGAAGAAAATAACATTTATTTTCTCCTTTTTTGAAAGAGTAAATTATTTTCTTCGT
>gi|3449723|gb|AI099984.1|AI099984 34137 Lambda-PRL2 Arabidopsis thaliana cDNA clone 145A11XP 3', mRNA sequence
GACTTNTTTGACCCTGACCCNTTCGACTTCCNAAGAGCTTAAGTGAGGCCCTGGGCCAAAAGCNCCCTTN
GTGGNGAGGTGCAGGCCGGTTCTCAACATGCCNTGAGTTAAGGCCTCTACGGTTATCCCTTNGGGGATGG
ATCCTGGGTTTAANCNTTTCCCAGCTGNCGTTGTTAANGCATTGNCCCACACTGGAGGTTGTGAATAAGA
CCCTTGAAGCGTATTACGACGCATGGGACAAGTACATCGATGCTTGGGTCGTCATCAAAATCCAGGACCC
AAGTTATGTATACCGGTGGCGTCTTCAGGCGGAAATCGCCATGAGGCAGGATGGCCAAGCTGGGATGTCG
GATGAGGAGGTGAATGACTTTGTGTCGCGGTATTTGCCGGCGTATAAGGCCTATCTTCCAACTCTTTACG
CGGAAGGGCCAAGCGGCTCAGACCCAGACCGTGTCCTTGCGATAGATATCGATGAAGAAAGGAACCCGAT
ACTCGCAAACTAATGCGATGCTGTCTCCATTGCCTTTATAGTATATCATCATTGTATGTAAAGGAGAGTA
ACATTACGTTCTTCTTCCTTCTATTTGACATTCTTTTTCCTACACTATACTTTCACATATATACATATTC
TTTTCTTG
>gi|3449722|gb|AI099983.1|AI099983 34136 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144O23XP 3', mRNA sequence
CNAAAATTGTTCTNAACCTCCAACAATGGGCNCCAATTTCCGGNAGAAATCACCCNCCCTTGGNGCTCCC
AANGAGGATCCCNTATCTGACTCAAGACCTGTTTCAGTCTNTCAGAGTCATGCAANGGAGAACTCACGTC
TGGCCTTTAACAGATCACAGGCGAGACGAAGAGAGAGCAAGACAGTGAGGTGGGTTACATTTGTTCACCA
TTTCTTCTGGTGTNAAAATCTGTGTTAGNATTTATAGGAATCGCTTTAATGGTTTTGGCAATTTGTTATA
GCATTTTGTTGACATTTTCTTCTGTGATTTGTAAATCTTAAATCTTTCTTCTCTTTGGGCAGTATAACAT
AATCTGATTCGAAT
>gi|3449721|gb|AI099982.1|AI099982 34135 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144N22XP 3', mRNA sequence
CTATCGCCCTTTGGGAACTGTCCCTCAGTCCGCCGGATCCNGGTNCCCANGTCGCCAACCCCTGGCGACA
TCCCGTTCCTGGTGATGCCGNCCCTTAAGGTTCAATTCNTNGTCCGANCATTCNCNGTCCTAAGCCNTNC
CCCNTCAACTCGTCCCCGGGAAAGAANCCCCGTCGCACAAGTTGTCCGCCATTACCCCTGGAAAACCCTA
CGTCTTATCCTTCTCTGTCGGAGATGCTAGCAACCTGCGCCGGATCAATGATCGTCGAACTTTCGCCGGA
AAAGACACGATCAAGGTCCCGTATGAATCGAAAGGGAAAGGAGGATTCAAGCGATCGTCATTGAGATTCG
TCGCTGTCTCGAGTCGGACTAGAGTTATGTTCTACAGTACGTTTTACGCGATGAGAAACGACGATTTCTC
GAGCTTATGTGGACCGGTGATCGACGACGTTAAGCTTCTCAGTGCTCGGAGGCCGTGAGCTTGCGGCGAC
GAGTTGATTCACGGGACAATGAATGATGACAGTCACTGTGGGTTTCTCGCGTCTAGTGAGAAATTGGGCT
TTTAGGCCCAGTGGCCCACTGTTTTTGTTGTTGTTTTAAAGCTTAATGTTATTTGACAAAG
>gi|3449720|gb|AI099981.1|AI099981 34134 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144N17XP 3', mRNA sequence
CTTGGTAAGNTCCGCCAACCGGCNCCAANAATCCGGTTTACCGGTAAGCTCCGCGTNCCGGGTTACTTCC
CGATAAACCGGATTTTGGTGGGGTTTAGGTTCTTTCCCNCATGTTCCAAGACCAATCCGGTTGCCTTCTT
CTTCANGAGGATTCTGCTTTCACCAAACTCACTTTTCCCTTTATAAGGGAGTAATATCTTCACCGTCCCT
TGGAAGGGCCCTCCAAGATAGGTATTAGGTGAAGCTTTCCTTTGAAGACTAGATTGAGAGATCTCTGAAT
TTATTTCAAGGTGGTGGCATGGAATCTTCAGCTGATGGAATCCGGCGAATTATGTGGAAGAAGCTCTTGG
TGTTGATTTGATTAAGCCCGACCGACGGAGCAGAGGTGGATCGTGGATCAGCCGGCAACGTCAGTTTCAA
CATCTCTTCATCTCACGTTGGACACGTGTTGGCAACGTGGCACTTTTTTTGTCTTAGCCTTATCTTTAGA
ATTGGGTGGGTTAAGCTGGGCTTTAAATTTTAATCAAAGTTGTAAATGGTGAGGGATTGGGCTTTTCATC
AGCATCTGTAACACCCTTTATTGGGTTTTAATATCCAATATGAAATTTGGCCGAC
>gi|3449719|gb|AI099980.1|AI099980 34133 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144M9XP 3', mRNA sequence
CCCGTCCCCGANCCAATGAGGGATCCAATGGGGCCTNTGGATGGACCAATGGATCCGTTACNNGGGCCCC
ACCACTTCTCCCNCTGCTTGGTTTGCTTAAAATTAGGGGAAAACTTGGTTATGGTTGGTGCACCAGCAGA
CCCGCTCGAGCTTCCTGTTTTTCCTCTCATCTTTGGGCGGAAGATGGTGGTGGGTAGTATGGTAGGAGGT
ATAAAGGAGACGCAAGAGATGGTGGATTTGGCTGGAAAACACAACATCACGGCGGATATTGAGCTCATCT
CTGCGGATTATGTCAACACCGCCATGGAACGGCTTGCAAAGGCTGACGTTAAGTACCGATTTGTGATTGA
TGTTGCCAACACGATGAAGCCAACTCCTTAACTAGAAAGCTTAAGAATTGAATATCCCCAAAGCTTTTTT
CATGTTTTTGCTTGTTTGTTTGATGTTGTTTGCTGGCGACTTTGTGTGTAGTATTACCACACTGCATGTA
CTTTATCAGTTGAATAAACTTGAATATTGTATTTAATAAGCTATCTACATTAGATT
>gi|3449718|gb|AI099979.1|AI099979 34132 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144J4XP 3', mRNA sequence
GAGCTCGCTTTGCCCTCGCTGTTATGCCCCCGAGGATGAGGTATGCTACCCGGCTGACAAATCGCCACTT
TGGTGAAACTGCTGGTGTTACCATTGAGTCATACTGGCCCAATGCTATTCGCCCAAGATGGCTGAGAAAC
GTAATGTCACTGATCTCATCATGAACGTTGGTGCTGGTGGTGGAGGTGGTGCGCCTGTTGCAGCTGCTGC
TCCTGCTGCTGGCGGTGGTGCTGCCGCTGCTGCTCCTGCTGCCGAGGAGAAGAAGAAGGACGAACCAGCA
GAAGAGAGTGATGGAGATTTGGGTTTTGGCTTGTTCGATTAAGTGCATTTTACTTGTTTTTTCTTCTTCG
ATTTGAGACTATTTTTTTTTCGTATCGAGCTATTACTTGTTTTGGTCTGGCTGAAGAACTATAATTAGTT
GTTTTCTGAACCATATGTTGTATGACACAAGTTTTCAAGCAAACCCATCGGCTCCTTCTTTCCTTAG
>gi|3449717|gb|AI099978.1|AI099978 34131 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144I9XP 3', mRNA sequence
GCCCCCAAGGTTTGGACCCCCAGTGTAACCCCTTTTTTTCTAGGGCGGGTNCNCTGGGGGTCTCCGGTTC
NGGCGTATGAAAAGATCCGTGTTATGCCCCCTNTTAGAGNTGAAAGGCATTNCACTTCTTGAGAGTGGTT
TGAAAGTGAGGGATTNCGACTNTTGAGGAGGAACTTCAGTGACACTGGCTGCTTTGGATCCGNTATCCCA
GGAGCACATTGATCTTGGAATCAAGTACGANCCTTCTACCGGTATCTNCGGTATGGATTTCTACGTTGTT
CTTGAACGTCCAGGATACCGTNTGGCCCGTCGCCGTAGATGCAAGACTCGCGTAGGTATCCAACATAGAN
TTACCAAGGATGATGCCATGAAGTGGTTCCAAGTTAAGTATGAAGGAGTTATCCTCAACAAGTCTCAGAA
CATCACTGGTTGAAGAGTTTTTTTTCATTTTGTTTTGTTTCAAGTTCTTATATTTAAGATTCTGGATAGT
AAGGATTTCGTGTTGTGGTAACCTTTTTGACTTAAGTTGGTTAAGAATCTT
>gi|3449716|gb|AI099977.1|AI099977 34130 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144I14XP 3', mRNA sequence
AAACCNTTTTGCCTGGNCGGGAAACCACCCATACANCNTCCCTNGGNTTGGNACCCGGGNCTAATAATNT
CAGGGGCCNACCNNTGNCCATGGTTGACATGCTTCTGGGCAAGCATCCAGAAGCTTTGGGCTTGAGGAAC
CTGATGGNGGAACCCCTNTGGAGAAGGGGGATGGATATCCCTCCCNTTCAGGGATTATCCAGGAAAATCT
CCAGCTCGTAATGGCACTAAAGGTGGCTGCCAAGGCCTACGGAACTGGGGACTGGCCCACGAGGTGCCTC
AGCCCAAGGACTGGAGCAGTGTGCTGAGAGCAGCATGTACAGCCCNTCGTATCGAAGTACCGCTGAGGAT
AAGCTTAATCTAATTTGTTATGTCTCATACGACTCTTATGGCCATTTCTCTCCTCTCCTATTCGTTCACC
TTCCACTTCCCGTGAGATTTTTGTTTGTTTGTTTGTCAGCATCTTTAAAATCTTGTGTTGTAATCACTGT
TTCCCTTGTTGTTTCTTTTTAAGTCCGTAATAATCCTCCTATGGAAATTGTTTCTCTGGGCC
>gi|3449715|gb|AI099976.1|AI099976 34129 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144H20XP 3', mRNA sequence
AAGGTNGGCTAGCCTTGATNGGGTNTNGGGATTGGCCCCCGAGGGGGTTTTAAGGGNGTTNGGGGTTCCA
GNGNTTCCCCAGTCCCCATGGCCTGCCCCGNTGGTTGTTGTTAGATTCCTGATGATAAGGNTGGGGAAGA
TGGGAAATCCCGGCGACCATGGTGGGGAGAATCTGATGGACCAGTGATAACTTCCATACCAGTGCCCTGA
GGTGGCTGAAGAAGAGGGAGATAAGGATGAGTACCATGATGCTTCGGATAAGCCAGTAGCCAGCAAGGCT
TTCATGTTGCCAGAAGGAGACCTCCCTAAGGAGACTTAGAAAGAAAAGAAAGCGTTCCTTTGCCCTTGGT
TTGTGTTCTTGAGTGTGCTTAATTGTGTTGTTTTTGGGGTTTGGGGTATTCTAGATCTCTTTTGTAAGTA
TTCTCTTGTTTCTTGGTTTTGTTTTAAACTCTATGGAATTTGGGATGAGTGGATTCGATGTCTTTTGTTT
GTCTTTGAAAAAGCAGTGAAAAGAATTTCAGTGGTCTTGTATATCTCTGCAGTTGAATAGTTGGTACAAA
ATAACATCTTTGACGGTTCCAAATAATATATCTTGTCAGTAATGACCATTAAAT
>gi|3449714|gb|AI099975.1|AI099975 34128 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144H18XP 3', mRNA sequence
CAAAGTCCTTCCAGGTNTTTGGAAGGCTGGANTCNTTNTGAGCCNGGGAAGGAGATGGGATTNCCNAGNG
NGGGGGAGGTTGAGTTTAGCATTAAGGAATTGTTGGAAGGAGAGGGANCAAGGGNTGGAGGAAGACGTGA
AGAAATGGAGAGACTTGGCTGTCAAGTCCACTCAATGAAGGAGGTTCTACGGATACTAACATTGATACAT
TTGTATCAAGGGTTCAGAGCAAATAGGTNACTCACATACAGTAGCAAAGGTCCTTCTATAATATCTTGTT
TTGTACGTCTTTCATTCAGCATAATCTTTTGTTGACTTTTCTTATGTTGTATGTTCAAATCCCCATATTG
CTTCTTGTTGTATGTTCAAATCCCCATATTGCTTCTTGTTGACAATAATAATAATAAAAACAATGCAACT
TTACCACC
>gi|3449713|gb|AI099974.1|AI099974 34127 Lambda-PRL2 Arabidopsis thaliana cDNA clone 144D5XP 3', mRNA sequence
CCAAGGGTGGAAGGATTAAGTTCCNGAAGGGTTTTTTACCGNTGNTGAAACCCGGGACCCNGTTTGGGGG
AAAAGCTTCGNGGCCATTACCCGGGAGGACCGGTTTNACAGTATCCAGCCNCAACTGGATGCCAGGATGC
GTCGTTGCCAGGTCAATGGTGATCCAAGATGAGAGAGGCTTAATCTGTGTCCACTCNCCAGTCTGGAAGA
TTGAATCAAAGGGATGCAAATCTTTCTTAATTTCTTAATTTTTATCTTCTTGGGTTGCTTTTTTTTTATG
NCACCACGATTAAAGCTTTTTAGGCATATAAAGTTGTAAGAGTTGTGTGTTTGATATCCTGGCTAATGAG
CGAGCTGAGTATGGGGATCAAGAGAGAAAAACCGTGTTGGCCTTTGGCTGTGTGTAGATATTTTGTATAA
TCTTGTGTTGATAAAAGATAATATCATC
>gi|3449712|gb|AI099973.1|AI099973 34126 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143P20XP 3', mRNA sequence
TAATGGTGACCCGTGGNCGATCCNTAGNGACCNAGATCTTTGGACCNGACCCGGAGNGGTTTACCCCTGA
GAGTTCACCGGTGGAGAAGGNGAAAAAGATGNTGTCCGTATGCTGATAGCGTTTGGAAGCGGACGGAGAA
TATGTCCCGGTGTTGGACTAGCGCACAAGATTGTGACATTAGCGTTAGGATCGTTAATTCAATGCTTTGA
TTGGAAAAAGGTGAACGAAAAAGAGATTGATATGAGTGAGGGTCCGGGGATGGCTATGCGTATGATGGTG
CCGTTACGAGCCTTGTGTAAGACTCGACCCATAATGAATAAGCTCCCGGCCTACACGAAAGTTTAGTTAT
GTTTTTGTATTTTTCAATGGAAAAATTGTTACATTATGTTGTGTAACCAAGACTACGAGTGTAATGCGCG
AATATATTGAAATAAAATGCTATATTTAGC
>gi|3449711|gb|AI099972.1|AI099972 34125 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143N21XP 3', mRNA sequence
ACGTTACGCCCCGGGCTTACCAACCGNGNTTTTGCCCCCCGNAACGTTCTCCCCGGTGGATTGGTCCGAT
CTGGAAAGCTTCCCGGAAAGGATTGGGGAAACCAATATGNTGCAAAGCTTCTCGCCAACATGGACGTAAG
TCCAGCCATTGNGTACCGTAATCTACTTTATGGTCGGCAACATATCCTTAATGGGCCAGGCTTTAGGTCT
ATTTGAAAAATATAGCCCCATCAACTTTATTTGATTTCTTTTACATGTATGTAGAAATGGAGATTCCACA
CCAAGCAGGGATAGGACATTTCTATCACATTTTCTATGAAGGATGTCTCACTGATCACGAAGTCGGAGAA
GACGAAGAAGCTTCTAGTCTTTATCCTGACGTCAAGTACAAACGCATGGATGATTACTTAAGAATGTTCC
TCTGATTTGACCAAGTCTTATCTATACTAAATACACATATCAAAAGTTTGATGTTTTATATTCATTCATG
TTCTGCTATATATGCAAATTTAAAAATATATTCTTCATGC
>gi|3449710|gb|AI099971.1|AI099971 34124 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143N14XP 3', mRNA sequence
TTCCCTGGCCATCGGGGTTCTCTCCCTNTTAAAACNGTTCCTTTCCGGAGTTTCCCCACGGNGGAAGAAG
TTGGATTTCCAATCATCCAAGTGTCTTGGTACGGGAGGGGAAAAGCTTTGTCGATGTATCTTGGCCTTAA
TGTGAATGAGATATTCAGCCCATATGAGAAGATTTATGTTCGAGCCAAGCTTCGAGCTCTTAACCAACTC
AATCTCAGTAACATCGAAAGGGAACTCGATATTTGGTACAATGGTCCGGGATATGGAGAATATAGCTGGG
GTTTCCCTGAGTTTATCTATTTCCCTTATCTCACAGATTCATCAAAGGGTTTCGTTAAGAACGATGTGTT
GATGGTTCAAGTTGAAATGGAGGCCATTTCTTCAACCAAGTACTTCCCGAGTTAGATTTTCTCTAAGCAA
AGAACTTGTACCTACCTCCATGTGTTTGATTTGTTATCAAATACTAATAAGAATTTGATTATGCATTTC
>gi|3449709|gb|AI099970.1|AI099970 34123 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143L23XP 3', mRNA sequence
TGGAAGNTGCCCCCCAATTGGAAAGAAGAANTTTGGGCCTTTTCTTCCNCCCTGGCCTTTAGTNCCNTCG
GAATTGGCTAAGGAAGTTGACTCCNTTCTCNGCAACAAATGGNTCCCTTGTGTTGAATTCGAGTTAGGGC
NCGGATTTGTGTCCCGTGAGCCCGGAAACACTCCCGGATACTACGATGGACCGGTACTGGACAATTGTGG
AAGCTTCCCATTGTTCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAG
TACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTG
CCTACAAGCCCCCAAGCTTCACCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTC
ATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGATTGTCAAATGTCTG
ATTTATGAATATGTAATTTATAT
>gi|3449708|gb|AI099969.1|AI099969 34122 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143K8XP 3', mRNA sequence
GTCACTAGCAAACCTATTGACATATCCCATTTGTGAGAGAAGGACTTGTGAAGGGAACACTTGCTTTGAA
GGGAGGCTACTTATGCTTCGTCAAGGGTGCTTTTGAGCTTTGGGGACTTGAATTTGGCCTCTCCGAAACT
AGCTCTGTATGAACCAATCCATCATCATCATCATCATCATGACCATCCATCATCATCATCATTATTATCA
TCGTATATAATATATATCTACCCCATATGTAATTTGTAATGTGCCTTTGACTGTGATGAGTTATCTCTCC
CTCTCTACCAACTTTCTTCATATATATAAAACAAAAAGGAAAAGC
>gi|3449707|gb|AI099968.1|AI099968 34121 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143K7XP 3', mRNA sequence
GGGCCAANGTCACGNAACACGGCTTTCAACAGNTTGGGGNCTTGGGGNCTNCTTTTGAGGGNATCCATTG
CTTNGGAACNCTTAACCCTTCTTCTGGTTTCAAACCCTCAAAATCCTCTGTAACCCTCTGTTGAAGCTTT
TGAAGCTGCAATTCGCATTGCAGACATTGTTGTTCCACGCAAAACGGTTATTCTTCGATGACAGTATTCG
TAACATCGCTAGTGCTAAAGCAACAGGGCTAAAAACCGTGTTTGTGGGGGAATCAGTGCTAGTTCCAGGT
GCTGACTATGCACTAAGCAGCATTCATAACATAAAGGAAGCAATACCTGATTTATGGGAAGACAACAAAG
ATGAGAAGCTCGAGCCAATTGTTCAGCAAGCCGCGGTTGCAACCATGGTCAATGCTTAGAGAGACATTCT
AATAAGAATCCCACATCGATTAAAAGAACTTATAACTCATGTATCCGAAATATATAATAAATAAAAGACC
NGAATTTG
>gi|3449706|gb|AI099967.1|AI099967 34120 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143H16XP 3', mRNA sequence
CCGTTNTTTTTNAAGNCCGGGGACCATCCAGCCTTNGAACCNTTGCTGNGCCTTGGAAGGTTCGAGGGTT
TTCCNCAAACCGNTCTTCTGNGCCCGNGTTCATCAGACCCTNGATTATATGTTCTCGTTCGTTAAAATGG
TCGAAGATGATTTGGTTGGGGAAGTCATAGCAGAGGAGAATAATGCGAGTTCTAAGAAACGGAAGAGAGA
AAATCATTCTAAAGGGACCAGAGATAGACGCAGGTGTAAACCATTGTCCAGACGAAAACAGAGAAGCAAT
GTCAAACGAAGAAGATAATATCAAGGAAAATCAAGAACTCAAAGCAAAATGATAAGATGATAATTGGTCC
GGATTCTTGAAAATTGCTTTCACTGTGACTCTAGTTTGTGTTTGGTCATCGTTGATGCCCTTAATGAACC
TTGGATAGTATTTTGCCAATTTAAAGGTT
>gi|3449705|gb|AI099966.1|AI099966 34119 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143G1XP 3', mRNA sequence
CCCGATCAANAAATGCTTTNCCGGAGTCTNTANTGGGTGCTCNTCTCTTCACTGNTGGACTCANTCTCNC
NGAGAAATGACTGCGGGTTTGCANAANCCAGCAGCAGTACAGAGACATCTACAGAGATCTCTGGTGAGGA
ACATGAAGATGACTGGCANTTACTTTGAACACTTCTCCTAGCCATTCTTTTCATTGTGTGACTTTGTTCA
ATTATCAAAATNCCATTCTTTTTACATCGATACTAAGATTTGATGTTGTATAAATAAAGAAAACCCCAGA
TTAAAGTATCACCCACTCTCACTTGATTTATGTATTAAGTATTAACT
>gi|3449704|gb|AI099965.1|AI099965 34118 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143E5XP 3', mRNA sequence
GAACGGTTGTGNTANCGTTGAANGAGGTTCCCCCACTGGGTCTTGCCAGAAATTTGCNNCGTTTTAGAAG
GGGGCTTTCGNACTGGNTGCCNCCGTCGAGAGGATTGCAGGAGCTGATGTCCCAATGCCGTATGCAGCTA
ACCTAGAGAGGATTGGCTCTTCCTCAGATAGAGGACATCGTTCGTGCATCAAAGAGAGCTTGTTACAGAT
CGAAATAAAATCGTCAACATCAACACATTTCTTCTTTGATCTTTAAAGGGAAAGGAAAATAAGAAAAAAG
GAGAAAAATGATCTCTCTGTCTCTCACTTTTGCTATAAGAAACCACCATTCCTCGTGATTTATTTCATCT
TTTGCTATTATTCTTTACTGCAGCGGTTTTCGTTTTTCTTTTTGTCCCTTCCCAAATTGATAATTCTAAT
CTTTGGGGTTAATTGATAAAAATTGATCG
>gi|3449703|gb|AI099964.1|AI099964 34117 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143B19XP 3', mRNA sequence
CCAACTGGGNGGATTATGGGCCCGTTNACAATACTCGGGNGGGGGATCNCGCATTTCNGGGGAGAGCCCC
TTTTACCTANCCCGACTTNGCCCTTAACCTAACCNCCGATNGCTCCCGCGATCNCCCATGGTTGGTACGT
TAATTACGTTGAGATCACGACGGCTGGTGTTCACGCACAGTGCTCGACGCAGGATTTTGAGATTGAGCAA
TGGCTCGCTACTGATACTTCTCCTTATGAGCTCACCGCCGTACGGAACAATTGTCCGGTCAAGCTTAGGG
ATAGTGTTAGTCGGGTCGGGTCTGAGATTCGGAAAAAGCTTTCTTGGGTCGTTTAAGTGATGTGTTGTGA
TTCGTGAGACTTGTCTGTATTTGTATTCTCGTTGTTCTTGTGAGTGTAATGTGGCGTTAATGAAATATGA
TTCAATAAAATAAAACCTTTTTNGTT
>gi|3449702|gb|AI099963.1|AI099963 34116 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142M7XP 3', mRNA sequence
CTGGTTCCATCGGAACCATTTGGCAAGGGTCTAGAATCTGNAAGNGCTTNTTNTCCAGCCCGGGTTCCAA
GTTGGNGTTNGATCTTNCCCGGGNAATCGAGTGGTCTGAAACTGGNTTACTCTGCACCAAATGCTATGCC
AGAATCAAGGCCTGCGATGNAACAAGTGGTGCAATACCTTAACCAAGACTTACCCTTACCGATTTTCTCG
CCGTCTACTCCAGGTATCGGGGCTTTTATGCCCAGTTTCTATGGAAGCATTATCTGCCATTGGGGTCTCC
AGTGTAAGGAACTCATCAGTTTCTATGTTTGTTACTCACACAATCTTGGACGGGCATGGAAGATAAGATC
TAAGAAATTCTATACTCTATACTCTTTTACTCTCTGCATCTAAATCTGTTTAGCTACGTAAATGTTTTAA
CTTAATGTATTGACTATGTTGTTGGTTGATGTTGTACTCAAACTTCTTTAGGTATCAATTGACAAATAAA
ACAGTTCTTCT
>gi|3449701|gb|AI099962.1|AI099962 34115 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142L7XP 3', mRNA sequence
TTCCCATGGCTTNCAATTTCCCANGGTTCCATTAAGGCTTCANAANGGNGTGGCCCNCCGGAAAGGCTTG
CCCCGTTTATCCCCGAGTGCTTCGACCCCATGAACTTGCTGAGGATCCCAGAGCTTCTCTGAGCTGAAGT
GAAGAGCTCAAGAACGGTCGTCTTGCCCATGTTCTCTATGTTTGGATTCTTTGTCCAAGCCATTGTTACT
GGTAAAGGTCCCATTGAGAACTTATTTGATCATTTGGCTGATCCTGTGGCTAACAACGCCTGGTCTTACG
CTACTAACTTTGTCCCCGGAAAGTAATTATCTTATGTATTTGCTTCATAATCTCTCTGCTTTGTAAACTC
GTGATTGTGTAATATTGACGTTTGATGTGAATTTGGCACTTAATGATGTTTCTTGGGACTT
>gi|3449700|gb|AI099961.1|AI099961 34114 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142L21XP 3', mRNA sequence
CCCTGGCCCCTTTTNGGGAAAGGTTCCAGNAGNCTTNTCCCAACGNCCCAGNTTACTGCATGGGCCGTTT
TTCCCCGGTGGTGGGATGGNTTTAACTACAAGTATGTGCCACTGCACTTCCGGGTCATCTTGCACAGCCT
GGTCGCATTCTTTTGGGGAATTTTCCTAACCCTGCGAGCGAGGTCAATGACACTAGCTTTGGCAAAGGCT
AAGTGATTAGGAAACACATGGATCGTGACAGAGAACTCAAGCCTTGGGACTCATTATGATCACTTAGTAC
TCTGTAAGTTAAAGCAAATCAAACAGCTCTGAAACCAAATAAAAATCTGTATTAAGATGATACCATTCTA
GGATAGCAATATGTTTTAAGTTATTACAAACACATTCAC
>gi|3449699|gb|AI099960.1|AI099960 34113 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142K12XP 3', mRNA sequence
TCCCCNCGCCGTGGGGAATCNTAGGATGACTNCCATGGTCCNTGGTGGTTGAACNTTTGCANCCAGGGTC
CACNCAAAGTTCCACCACACTTCCGTTGGTGGAGGTCATGTCAAGACCGCGAGTTTCAAGTTCAAGCGGT
TGAGGCAAGAACTAGAATTACTTTCTTCAGTGGTTTTTACCATACCAAGAAGACTGATACTGTATCTTTA
TGTGGTCCTGTCATTGACGAGATTGTGGTTTCTCATGTCGCTTAGATTAAGTTTTCTCTTTATGACAACT
GCACTTGTGTTCTTAGACTGGTCATGGACTTGGTGCCTTGCTTTGTATGTCTTGGCTCCTTTTGGAATTG
AGTTATTGTCATCAAGTTAAAATGAATGATATATTATTGT
>gi|3449698|gb|AI099959.1|AI099959 34112 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142I5XP 3', mRNA sequence
TCGGGTCCTGGCTGGAGAAAGGAANGNCCTTTTGATGCCCGGTTTGCAACTCAAGTACTTTGAGCTTGGA
AGGTGGTTGGTCCTGGGTGGGTCCTCCGGATGGTCACGGTGACGAAGACGATGAGCACCACCACTGATTC
CGGCCTCTCCNTTGCCGCAAATTTTTCTTTTTATATTTGCACATTTGCATATCTTTAAAAATTTTATGAA
TGGNATAAAACAAAATATCTACCGTTTTGGTGAAACACAGTTGAAAATGTTTTTTGATCTTTTTTGAACA
AGACTCGGCATCNGAGTTTCCCAAGTGCCAAAACTCTTATGACCGTTGTTCCTATTTTTGTAACACTCTT
GAATCAGAATCAGAATCATTCTTGCCTTTTGNTNNTT
>gi|3449697|gb|AI099958.1|AI099958 34111 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142H19XP 3', mRNA sequence
CTTACTTTNTTAACCCAAGCGGTCAGGTCCGATCCCCTTTTGGGNTAAAGCNCTTCCCNNGNGGGGGNTA
ATTCCCTTTCGCCCCTGGTCCAAGGTTTTTAGGGGTTNCCAATTTGGTGGCCCCCCAGTATGGNCCCTTC
CAATTAACCAATTATCTTTCCCCAAGTTGCTGGGAATTATAGCAACTAGTTAAAATGGTTAATTGATGTT
TGTCCTTTTTTACCCGTGAGCAAAAACAAAATTTCATTGTTAGGATAAGTTTTCCGGCGATGATCAATTG
ACCGGAGTTGAGCTCTTTGTGCGATGGAGGTTGGTGGGATAACACGTGTCCTCATACGTATCGTTAGACA
CGTCCTTTGAAGCATATCTTCTTCTTTGGTTTTTTGCTTGGGCTTCTTTGTAAGCTTTTGTTGTAATTGG
ACTGGCTTGTTGGGCTTGTAAAAGTTTATCAATAATAAAACAGTTGAGAC
>gi|3449696|gb|AI099957.1|AI099957 34110 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142G24XP 3', mRNA sequence
CCCCCCCCTNGGCACCGGGTTNACCCCCGTGTGCNTTTTCGCCGNAATGCTTNTGTGCCCCAAGGGCTCT
GATCGTCATCGGTCGTTGATTTCGAAGGTGGGATGGAGGAAGAGATCTCNGCTGTTAGATCTAGATCTTN
ATTGCCTCCTCCATCGGAACAGGCCTGAGCTTTTAACGGTGTCGTTTCAATTCGAAGCGCATGCGTTTCT
TCTTCTTTTTGAGCTGTGAAAATTCGTTTTCTCATAGTTTTTCCTCTCTCTCTCTCTCAGTCTAAATTTA
TTACCAGTTTTTAGAAAGAAAAAACAGATTAAATCTGAGAGAGAAAAATATAATTTTAGCTGACATGGAT
CGTTATGTACATATTATTACATAACCGGAGATCTGAACTG
>gi|3449695|gb|AI099956.1|AI099956 34109 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142G17XP 3', mRNA sequence
GATCANGAATTTNCNGANTNCTTAGNTNTCCTTTTACTAAGGANGAAGAAGAGGANCGATCGGTGGATTG
GGATTATCGATCTTTGTTCTCTACGTAATCTGAGCAGTTTGGAGATCAATAAGACCGGAAAATTGAATTC
TGGTAGAGAAAACAAAATGTTTTTCCGTAAAGGAGAAGTTGGTGATTGGAAGAACTATTTGACTCCTGAA
ATGGAGAACAAAATCGACATGATCATTCAAGAGAAACTTCAAAACTCTGGTTTGAAATTCTGAGTTTGTG
CATTGTAATAATAAGACTACCTCTTATGCTGTTGTTCTATCCCTTTTGATGTACAATGATTACCCATAAT
GGTCTTTGTTTTCGTTCCCC
>gi|3449694|gb|AI099955.1|AI099955 34108 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142G13XP 3', mRNA sequence
CTTGNCGGAANGCACTTTTCCCGTTTTTCCGCNCCCACTATNCCGGGATTTGANCAACCTGGCGCAATGT
GGGCCTTGATGNGAGCTTAATGTGCTCATCCCAGTTCTAAAGCCCGCCGGAAAAGAANTCGCCTTTTCTG
TGACCCCCGTTATCCCAGTGACCACCATGCTTCAAATTAACAATTCTACAAAAGTTGTATACTGGCAAGA
GGATCTAGAGACGGAAACTGCTCAATTGGGACCTTAATGGTACTGATAATAGAGCATTAGACATGTAGCT
GTTGACAGTGATGGCATCGAGCAGAAGGAACAAGTCAAGTCTGTACTGTGATTTTAGCATCTCTCACATC
TATGTTTGTCTAAAATGTGTGTGTGTTTTTAGTCTTCTCTCTGAATAATATTAGATTCTCATTTGTACTC
TCTATTTATTTAGGAGAACCCAAATTCAAAACTTTTTTTAGTCTC
>gi|3449693|gb|AI099954.1|AI099954 34107 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142D9XP 3', mRNA sequence
TCGNCTGTTCGGTACNATCGGGTNTCAACCATGNCTTGTNTCAACCATGTTACCGNCNTGGTGGATTCNA
AGAAGTTTGGGGTTCTTGCAAAACTGGCAAAGACAGTNNCACAATGGAGGACNATACTGACTCAATTGAA
GAAGGAGATGGCTGCATCGCATAACCGGAAGCTTGTTCAACCTCCCGAAGGAACTTTCTTCTAATACTCT
CAAAGCCTACCTTTGAGGGGCTTCTCCATTGTTGGTCTTCACNCTTTTCTTTCGTACCTTAAAGTAAAAA
CAATGGTGTCTGTCGATGAATGATGATGTTCGATTGATCATCTGGAGTCCCAATCCTTGTGTGCAAATAT
ATCTAGACAACCCTGTCCCACGACTTCATCTTCTCAGTTTAGATATAATATGGGAAACAACCTTNTAGAA
TC
>gi|3449692|gb|AI099953.1|AI099953 34106 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142D4XP 3', mRNA sequence
AGCGTTTGACGGCCCAGCCATCNATTGCGCGGTTCGACCGTTCGATCATGTCGCAACGNGAATTCTGCCT
TCCCGATTNGGTCCCGNAGTCNCACCNCCNCGGTTCTNTGAATCCCCCGAGATTTTAGAGGTTGNCGGTT
ATGGTGTTTTATTGATAGCGAGAGACCAGAGTCAGCCTCATTGGGAAGTTGAAGACGATTCGATGAAATG
GAAGGTAATTATGGATACGATTCGGCTTCCGGTGACGACGATGACTTCGGTTTTTGCTGGAAGTTTGAGT
GGCCAAGCGGTGGCAATGATTGGCGGTGGTGGTGAAGAAAGTGGAACGATGATGGTGAAGACNNCGGCGG
AGAAGAATGGCGGGAAGTGGAGCCACGTCAACACTCCCTCTGGTTTTTCGAGTCTTCCTTTCTCGTGTTC
CCCAATCTACGTTTGAAGAATCTCTGTTGTAGAACACNTTGACTTAAGTCAACGTTAATAGTTAATACTT
AATACATAAATCAAGTGAG
>gi|3449691|gb|AI099952.1|AI099952 34105 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142D24XP 3', mRNA sequence
AGGAATGTGTGCTTGGNGGATCTCCCCCNCGATTGGACCANTCTACNCGGGGATNNTGGCCAGGNGGGGG
NNGAAGAAGGGATTACCCCAAAGTCCAGGNGAATTGCCAGTCATCATGATCAGTCTGGTCAAGCTCAAGC
GATGGGCGGCATGGGNATCCGGATATGATGCTGGTGGCTACGGTGGTGAGCNCCNCGAGAAGAAGGGGAT
GATGGACAAGATCAAGGAAAAGCTTCCCGGTGGTGGCCGTTAAGCTTCGAACAATCGTGTATACATATTA
AATAAAAATAATGAGGGTTTGTAACGCAGTCGCATTCGGTCGTTGTATTGTGCTTTTTATGTATGTACGT
CCTGCGATGTGTGTTGTTTACTTACATGAGTGTGTAATGAGCATCTGGCTCTTTTTATGTTCTGAGATGT
TTGTGTTATGTAATTTCACATCTNTATAAATCTACTTTCTTCTG
>gi|3449690|gb|AI099951.1|AI099951 34104 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142D15XP 3', mRNA sequence
ACATGAGGGCANCCGCANCCTCCGGTTCAGCTTCGNTTGACCTGGGACCTTNTGGGGCTCTGTGCTTTTG
GGNTCGGCTAACGTGGTTCGCACTCTCCCCCGCGCATTGCCGAGGGGTACGAAGGACGCGGTTAGTGNTC
CGGTTAGGGAAGCTACCAGNGCTTGTNCCTACCATGGCCAAGCAAACCAACACTGCAGACATGTTAGAAG
AAGCAGTAGAATACGTGAAAGTTCTTCAAAGGCAGATCCAGGAGTTAACAGAAGAACAGAAGAGGTGCAC
ATGCATACCTAAGGAAGAACAATAAGGTTTGCTCCTGATTTGTTTTATATTTGCTTAACGGCAATGATCT
GATCGAAAAATTCGAAAGATGATCTTAGCTTGAATTTAGATGGATGTCATGTTGAAAAGTATATTATNCG
ATAAATGGATGTAGGTCTAATATAAAATTTTTGTACAATAATGAAGAAAGTTAAAAAGAATTAATGAAAA
CATATATTCTTTATGATATT
>gi|3449689|gb|AI099950.1|AI099950 34103 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140P1XP 3', mRNA sequence
TGGCCCCGTTCNNTGGGNCTTCTTCCCNCCNCGTTCTTTGCCTNCTGTCTTCACATCCCCAAGTCCNGGN
CCGTCATCCGAAGTGCTTCCNCAGTCCCTCGGNCCAGTCTTGCCAAGGTCGCAAGGCAAGAGTTTCTTCT
GCAAGTGCTTCTGCCGCTCCAGGTGAGGCTGCAGCTGCCAGTGACTCGCAAAGCTGCTGCTGCACGTGCA
AAGGGTAAGGTACTTCCGCATCAAGGGTGAAGGGTTCCTCTGAGAAGAAGAAGGGCAAAGGAAAGAAGGG
CAAAGGAAAAAAGGATTGAGCGTGAGGTCATCTCATATTCTCATGCATGCGTATTCCTCAAACCTATATA
TTAATAATATCCTAAAAACTACAAACTCACAATCTCTTTCTTGTTCATAAATAAAACCAGAGATT
>gi|3449688|gb|AI099949.1|AI099949 34102 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140P11XP 3', mRNA sequence
GGGGAAAAACGCCCNTTCAGTTGATGTTGATTCTTNCAAGCNTCTGGTTTAGTGGATGATTTGGAAAGGG
GAGACCCCCAATGGGTGAGCATAAGCTGCACATTGGTNCCCTTAAACATACTATTTTGGTCCAACCGCAA
CTTTGNCGGACGCATATAAAAGCCNACAAATNNGGAAAGCATTTTAACAAAGTGGAGTGTTNCCTCTTAT
TTATATAATATAGAGAGATAGGTTTATTTTCTTATGAAATTATTACTCAAGAAAGTATGAATTTGTAAAG
AAGCNCCAAAGGGTTGCTTCTTGGTTGTGTCTTTTTTCCTTTAATTTTTTTTTGGACCAAAGGTATTGTA
ACTTGTGGCTCCCAACATAAGAAATACAAGGAGCCCTTGT
>gi|3449687|gb|AI099948.1|AI099948 34101 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140O22XP 3', mRNA sequence
TGCGACCCCACGCGGAGGGTCCGAAGTNACCTTGGGTTAATTGGGCGTTTGGTTGTGCCCACCCTATNCA
AGTGGACCGNTGNCCGTNTCAACCTGTCCAATCCGGGTCCGTGGATTGTCNCNGTTGGGTTGTGNTAAGG
TTTTGGTAATGGTGGCTGAGAAAGATGCGTTGGTGAGGCCAGGNTTGGGGTTACGCGGCTAAGCTTGAGA
AGTCTGGTTGGAAAGGAGAGGTTGAAGTGGTGGAGAGTGAAGGAGAAGATCATGTTTTTCATTTGTTGAA
NCCTGAATGTGATAATGCTATTGAAGTCATGCATAAATTCTCAGGGTTTATTAAGGGAGGGAACTAGCTT
TGTGCTCTCTAGAGATATTGGAATAATTTGGTACTNCATATTTTAGTTGCGTCTCTCAGTTTCTGTAATG
TTTCAGTGATTGGCTTTTCGCCCAAAGCAACACAATAAAAATTGAAGATGAAAATATTTTAGT
>gi|3449686|gb|AI099947.1|AI099947 34100 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140O19XP 3', mRNA sequence
AGGTTCATTCCCCGGACCGTTNCCTTGTTCNCCAGTTTATCGCCCCTTTGGGNAACTGTCCCCTNCNGTC
CCGGTCCGNATTCCCGGTGGCCCCNNGGTCCGATGGCTTCTCTCAATGCTGNGATTGCATGCCGGTTTTT
GGGAAAACTGACTCTGGTATCGATTGGNTTATGGAATNGCCGACGTGAGTACTCCACCACCAGGAATGGG
CGAAATAGCACCAACAGCTGTTGACTCAACCCCGAGATGATCGAATACCAAGCACACTTCTCAACTTCTG
ATCCCAAATGTGTTACCTCACAACACTCCCTAAAATCATATACAAGGAGGGAGCAACTACAGAACGTGTA
TGAACCAATGGCAGGTGCGTTCCATACAATGTACCATTAGATTATGATTCATTTATCGCCTAGAGTGATG
TTGTAGAGGAGCACCGAGAAACTAATGTAAGTTTAACAGAGAATGTACTTCATCGGCTGCATTGGTACAC
TATTTGATTATAATATTTTTGACC
>gi|3449685|gb|AI099946.1|AI099946 34099 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140O12XP 3', mRNA sequence
AACCCCTATTCAGGCAACGAAACTCTACNGCTAGTCCCCCTAGGTTAGGTTGGGTAGGGNNATGGGAAAG
CCTTTACNAGTTCCGAACTTCCCTNAACTCGGGNTTTTAATCCGCTTAATCGTCAGGTCCCTGGGTAATC
ATAGTGGCTTTGTCCATTCGTCTGTGTCTTAAGTGGATTAGTTGGTCGTAAGACAAGTTATAGAGATGTG
TTTACGGGTAAAGATGAAGCTTAGGTTTTGATGTAATCTTCTTCGGTTTTTCAATTCTCTGTATTTCTCT
ATCTTTTTAGTTTATCAAGTTTAAGTTTTATTTGGGGTTTCTTCTTCGTTTGGGTATCTTTCTGTTTTTC
CTTAAGGTTCTTCGTTTGTTTCCGTGTCGTCTAGGTTAAGTCAAAGTAAAGAGATGTAATTACTGGTTAG
ATGAATCTTAAGGTTTCCATGTAACCGTTTGTACTACAATTCTCTGTACTTCTCTATCTTTAATATTATC
GAATTTAAGTTTTATC
>gi|3449684|gb|AI099945.1|AI099945 34098 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140N8XP 3', mRNA sequence
CCCCATATGAATGGCACCACATCCATTNCTTTGGNNCTTGGCTTCNANCTGTCTAATNCTACNCCCAGGN
CACCAGAGGNCNATGCTGGTNAGTGCTGTACCCGTTGNTGGAGCAGGTTGAGGCAGAGTCTGCAGCCAAA
GTGACTGGGATGCTTTTGGAGATGGACCAGACTGAAGTGCTCCATCTGTTGGAGTCACCCAGAAGCTCTC
AAGGCCAAAGTTGCAGAGGCTATGGATGTTCTCAGGAGTGTCGCTGCTGGTGGTGCAACCGAGCAGCTCG
CTTCCTTGAACCTCTCTTAAATTGCTTTTTATCATTTGATCTTTGGCTTTTGTCTCTCCCATACAATTGG
AGTTGTTTCTTTGCTATTCGTTTTCTCCCTGGGAATTTGGATTCCTCCACATAACTGCGTTTGTGTTATT
TTAAACCTTCGTTTTTAAACCACAAAGGAAAAACCTATCTGCTTTGTTCTTTTGATT
>gi|3449683|gb|AI099944.1|AI099944 34097 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140N23XP 3', mRNA sequence
GCACGAATTNCGGCATCTCAACCCGGGATTTTACTACCCTGNCATCCCNCAAGTCGAAATGGATCCCGGT
AGCCGAACCCCCTCGATCTAGCTACTACCGTCTGCCCTAAACGTCGTGGACTTTTGAGTCTGACGCTGCA
TGACTATGAATCCTGCGGCATTGGCTCAGGTCAAACCNTCGCCGGAGGATCGGAGCAAGAGTTCTTTGCT
GAGTTCTCCAACTCCATGGAGAAAATGGGAAGGATTGGGGTCAAAACAGGGTCGGATGGGGAGATTCGAA
GAACATGTGCATTTGTTAACTAAAAGTGTTTCTTACTTTTTCTTTCGCAACTTTTTTGTTTTGTTTTAAA
TATCTTTTATATTGGTTTTTATGTTCCTTTTGTCAACTTTTTTGGGTGTTTGGAAGAATTTCGAGATATG
TATTATTGTATGTGGTGAATATGTGATTTTCAAATAAATTTCACGTCTGTGAAAATCGTTGAACT
>gi|3449682|gb|AI099943.1|AI099943 34096 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140N18XP 3', mRNA sequence
CTGGGAGTTCGCCAGTGGTCCTTGGTNTTTGGGNTCCCNCCGGGNTAAAAGGGNNCCTCTNCCNCCGAGN
TCCCGCTAATAATTTCCCTCTTCCCNCCTCTCTCTCATCATCACATGCNTGTTTATTTTTCTTACCAAAA
AAANAAATCATTTACAGGGACAGATTTCTGTATTTNTCTTTATTTAAAAATTGCTCCCCAAAAAAAAAAA
ATCATAAATGTTTTTGTGGTGGTCCTTTTTTTAGGGGGATCAAAGTGTGGGAATTAAATTGTTACAGCTG
TATGTTATAATAGAAAGATATATAGAAATGAGGAGAGGAAAAAAAAGAAGAAAGGGGTAGAAGAATTGAA
AATATATGTGGGATTGTTATGTAATAAATGAAATAGGTTATGATCTTGCTGGAAAGTGTTTAGAGCAGAT
CTTAGCCGTTGGATTTTTATAATCAAGGAATGAAACCTGTGATCCATTATTAT
>gi|3449681|gb|AI099942.1|AI099942 34095 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140L20XP 3', mRNA sequence
TTGTTTGAAAGTNCCNTCCCCAGNANCCNTTCCATCCACCCTTTTGGTNTNCCCAANTNGCTTTNACGGG
TTGCTGCCCTTCAATCAGGAAGGCTCCCCNCNCGAGAAGAGTTAGAGGAGAGGCTACGAGCTCGATACTA
ATGACGGCCGGGTGTAGCCTTCTTCCAGGGATGAACGAGCGGTTGGAATGTGGGATTAGGATGATAAGAC
CTTGCGGATCACCCATTAACGTGGTTAGAGCTATGGATCCAGTGCTGGATGCATGGCGAGGAGCATCTGC
ATTTGCTGCTAATTTGAACTTCTTGGGGAATGCCTTTACTAAGATGGATTACGACGAGAAAGGTGAAGAT
TGGCTTAGAAATTATCAAATTCGATACAACTATTTGTGATTCCTCCAGTTGCTATTAATTGTGGAGTTTC
TTATTTGATTAGCTTTAGCTGTCTCTAGATCAATGAACGATGCTTTAGGACAAAAATACCAAAATTTATT
TGGAC
>gi|3449680|gb|AI099941.1|AI099941 34094 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140H7XP 3', mRNA sequence
CCTTTCCCCACCTTATCGCCCCTTGGGAACTGTCCCCNTCGNTCCGNCCGGATCCCGGCACCCNCCTCCG
NCAACAGTGGCTCCCAGACCGTGTGCCCAGTGNCAGTTTTATGAGAGTGTGTTCTGAACGAACAGTGGAN
GCCATTAAGGAAATCTCAGAATATGTTCTCCAACTTAGGAGACTTGGCCAAAGGACATGGAACATGGCAT
TTCGATCAGGAGCTTCTTGGTGCTGCTGCTTAATCTGAGTTTTAGCTGTAATCTCGCAGTTTGGTTAACT
TTTGAGTTATTTTGAGTATGAGATGTAACTTTTAAGGTAGATTTGATCAATATCGATTCTGTTGTGAGAG
AAAACAAGCTATTACGCTCCTTGGGGTTAACTTTCTTTGTGTTTTCAGTATTATGGTTTTGTCCCTTCGT
AATATCACTTTCCTTTAGAACATTTCAAATCAGCAGTTGTTTTGAGGTGTAATGTAATGGTCACTGATAT
TTTCT
>gi|3449679|gb|AI099940.1|AI099940 34093 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140H23XP 3', mRNA sequence
TTCCCCCCCGTTGGGATGGACCTCTGGACCCCGGCACTTTACCCATCGGGAGNTGATGTGATNCGGGAGC
NTTCCGGTACATGGCNCAGNGNGGACCCCTTTTCNCAGGTACNCTGCCGTTGGCCAAGGAATCACAGCCT
TGCACCAAGCAGCATGAAGATTAAGGTCGTGCACCACCTGAAAGGAAGTACAGTGTCTGGATCGGTGGTT
CCCATTCTTGCTTCCCCTCAGCACATTCCAGCAGATGTGGATCTCCAAGGCCGAGTATGATGAGGCAGGT
CCAGGAATCGTTCACAGAAAATGTTTCTAAGCTCTCAAGATCAAAGGCTTAAAAAGCTGGGGTTTTATGA
ATGGGATCAAAGTTTCTTTTTTTCTTTTATATTTGCTTCTCCATTTGTTTGTTTCATTTCCCTTTTTGTT
TTCGTTTCTATGATGCACTTGTGTGTGACAAACTCTCTGGGTTTTTA
>gi|3449678|gb|AI099939.1|AI099939 34092 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140G21XP 3', mRNA sequence
GANTTGCTAAAGCCCGGGNGCTTTTTNCATGNCCNAACNCGCCCATTTNCTGAGGTGTTCCCCCGTTTGA
TCNCAAGTTGATCTTATGTNCCCCCAAACGTGCTTCGTTCACTGGTATGTGGGTGAGGGTATGGAAGAAG
GAGAATTCTCAGAGGCACGTGAGGATCTTGCCAGCATTGGAGAAGGATTATGAAGAGGTCGGTGCTGAAG
GTGGTGACGATGAAGATGATGAAGGAGAGGAATACTAAGAAGAATGTTTCTAAAAACTTTGGATTTGTGT
GGGTTTCTCTATAATCTCGTCTTGTGAGAATGGGCTCAAAACTCTTGGGAGTCTTTAATCGTGTGTGTTT
TAAAACCTACTTCTCTATCTTTTCGTAGCCATGTTATCTCTCTATTATCTATTTCCTTTGTGTGTTAAAT
C
>gi|3449677|gb|AI099938.1|AI099938 34091 Lambda-PRL2 Arabidopsis thaliana cDNA clone 139J2XP 3', mRNA sequence
CGTTAACCCATCCCTNCCTTTCTCGTGGCCCCAGGCGAAAACATGNCCCCCNGGNNTNGCCTGATAACAT
CCCTTATAGTTCNCNGATATNGTAGTNCGCACTGATTATGCAGTCCCTAAGATGCATTCTCGGNGCAGCC
AGCCGTTTAGTGGGNTTATTTTTTTCGGGTCCCCCTGAGCAAAATCGGTTCTTGGCCTCTGGGTTTACCT
AGAGCAAAACCAGTTCCGATGGTTACTTGAGTTTTGCTCAGTTCTTATGGGATTGGAGTGGAAGGTCGTG
CGCTCGGCAGCATGGAAGCTTTCTCCTTTCAATCAGCTTCAGTAGAGTTTTGGTTTCTTTGTTTGTTTTT
TATTTGCTTTAAGAATTTAATGTAAATAAAAATCCAATGAGGATTATCATACAATGTCATGAAGGATCTA
TGAATTAGTATCTAATGTTAGTATATATTATGGTTTTTCCTAAGTTGGTACTTTCTCTGTTTGAAGTTTG
ATTATCATACATGTATTTGTTA
>gi|3449676|gb|AI099937.1|AI099937 34090 Lambda-PRL2 Arabidopsis thaliana cDNA clone 139A18XP 3', mRNA sequence
TTATTTTGGGGCNAATCNGGGAATTTGGNCCCNGGTCCGAGNCTCTTTTGGGGACCCNNNGTATGGNCCC
CNGGCTTGGTTCNTCTTCCCAGATCTGAGAGAGNCCNTNANCNCCGAGAGGAGTGCCTCAAGTAAAGCCN
TCTCGTCAAAAGGAAGGTTTATGGTTTNGTAAGATTTCCCGGTTTAATTACTTAATTAGTCGGTTAAGTG
GTTAAGTAAGTCGATGTCTAATACTTAAAATCGAAAACGACGTATCTATTATTGCAAATTCGGATTAGAT
GTGAATGTGATCGATTAAATCGATTTCGTGTTAGATCAGTTTTTTTTTTTTTGGGAGGGGTTTAGAGGTT
TTTTAAAAGTTGGTATATGGGATCTGGAGGACTTTGTAAATGTATAAATTTCGTTTTAATTAAATCTGTA
ATCTTTTGTTGTTATTTCAAATGTTTAATGTTATAATT
>gi|3449675|gb|AI099936.1|AI099936 34089 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138K1XP 3', mRNA sequence
CCCCCATTAAGGTTAAACTGACACTTNANCGAAGGGGANATATGNTNACCCAACTCCNNTACNAAGGNTG
GAAAGAGTGGCAGATATATGCACTNCTNTTTGCTTGTCANTGGCATCAGTGATAGCTTGCATACGTATTC
TTCGAGAACTCAGATTCGTTTTGGAAGTTACCAATGGGAAAAGATCAAAAAAGACCAAAGATTAGTCTAT
TTGGAGGTTCCTCCTCCACGCCTTCTGAGGATCATAGTAGGTGGAACTTGGACCTATAGAAAGATTATGT
AACTTTCCTCTGCTTTTTCTTCTTTCTTCCTTATCTTGTTGCAGCGTTTTTTTTTGTTTTTTTCCTTTCT
TCTGATTTTGCTCTGACAAATACCTGTTGATTAATTGATTTATTTACAGACAATTACTGTTGCT
>gi|3449674|gb|AI099935.1|AI099935 34088 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138J5XP 3', mRNA sequence
CCTTAGANGGTGGGAAATTGCATGAGTTTGGCACATCCCTTNTTCTNNCGGATTTNGGATCNNAGTATGG
GAAGCCCTGTCTCAGCCTNNGCTTCCAGCNTCTCCTCCTTCCACATCNTTAAAACTCCAACCTTGGAAGA
TTTTAGGAGAATGAGAGCGACACGCTCTGTGCTTCTTTTCCTTATGATCCAGCTCTTCCACGCACAAATG
AACTATGAAACATATATAAAGCGCACACATATATTTATGCATATCAAGCTTTTGGTGATTATGGTATTGA
TAGAGTCAAATTAAGCTCGGTGACTATGGTATTAATAAGAGTACTATTTCCTT
>gi|3449673|gb|AI099934.1|AI099934 34087 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138J22XP 3', mRNA sequence
TCCCCNANTGANNTTGAAGATTNNCTTTCCCANGGTTTTCAGAGGGGGGCTNAAACCAGNGATTTCTCCC
CTTTCACTCGCNNTCAACGCGCATAGATCTGAGCTCNCCNTGCAAATTCCGTGACTGGATCTTAGAAAAG
CCTTTCATATACAGAAGCTTCAAGACTCAATGCACTTGAGCCTACACTGATGATTCTCGCCAGCTTAATG
ACCTATACAATTTTCCAACCCCTATGGCCTTTTTCGCTGATTGAATTCAGTGGGTTTATTCATATAGTAG
TAATGTAAATGGTATAGAGATGAGCAAAAGCTATATTATATATTATATTCATTAGAGGGG
>gi|3449672|gb|AI099933.1|AI099933 34086 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138D19XP 3', mRNA sequence
CCGTAACTGGGNTCTTTNCCAAACCGGGTTTCCNNTGAAGGGAAAAANGTGAAATGCACTTATGTGGTTN
GCATAGCCAGGAAACTTGGTGCTCCATTTCTTACTCCCTGAAGATATAATCGAGGTGAATCCAGAAGATG
ATGCTGACATTGACGGCGAGTATAATGTATTGGACTCTAAAGCAACCTCTTCATCTGAATAAGCCTATCG
GATCTCCTGATAGCCACAATGGAAGTTTACTCGATGATTCTACGTCAGATTCCTCTATAGAATAAAATTG
TTTTACTGTGAAATTATATATTCTTAAGAACTTTATATGAATGATGTTATTAATTATTTTGCTCCTTTGT
ATTTTTTGGGTGTAAAAACTATATTAAAATTGAAATGTCATCAACGAAT
>gi|3449671|gb|AI099932.1|AI099932 34085 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138A20XP 3', mRNA sequence
AACGTACATCCCGGACAGTTTGCCTGTTCCCCAGNTATCGCTCCTTNGGAAGCTGTCCCCTCAGTCCCGT
CCGGATCCCCGGTCGACCCACGCGCCCGAAGAGAGGAACTNCAATGTTAATCATCAAAGNGAGTAAGANA
ATNGCAGTTCTAACTGTGGATGTGGCTCNTCCTGCAAATGTGGTGACTCTTGCAGTTGCGAGAAGAACTA
CAACAAGGAGTGCGACAACTGTAGCTGTGGATCAAACTGCAGCTGTGGGTCAAACTGTAACTGTTGATGA
AATTATTATGGTCTAAAATCATATATATGGCAGAAAAATTGGGGAAAATATGTGTTTTATGCTAAGAGAT
GTGTGTGTGTTGTTGGAATAAAGACGTGACCGTTGTGTTGCGTATCAACTCTCTTAAGCTTTGACTTTTC
CCAGCTTTGTATTTTCCTATGTATGGTAATNGTGTGATTGTGTAATGTTTTCATATGTAACGTAAAAAAA
ATATTTATGTGAC
>gi|3449670|gb|AI099931.1|AI099931 34084 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137O14XP 3', mRNA sequence
GTTCTCCAATTGCCCGACCCAAGCAGATACGTANCTGAACTCTAGNTNCTAGAAGGCCGATGCGAAGGAG
ATGATTTTGTGAGGCCGGTGGAGAAAAATGCACGTTGATCCTTCTCGTTGTGGGTAGTCGTGGCCTTGGC
AAGATCNAAAGAGNCGTTTCTTGGGAGCGTTAGCGATTACTGCGCTCATCACGCCAACTGCCCCATCCTT
ATTGTCAAGCCNCCTAAGGAGATGACTAAGTAATATGGAGCTGTTTACATGNTTGGGTTATTAGTACGAA
TTTTATAATGAGTGTGCCATAATTTACCT
>gi|3449669|gb|AI099930.1|AI099930 34083 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137N1XP 3', mRNA sequence
ATTNCCCNTAAGNTTAAAGCTCTGGCCCTCAATCTTTTATGGCCCCTNTTGCTCTTCAGCTTCNCCTNNC
CTGTGGCAAAAATCCCACCTCCGGGCTACACTTGTTCCATATGATAAACTCACTCCACTTATAAAGGATG
CTTTGGAGAAAAAAGTGAGAAGAGAATGGCAGAGCTCCAATCTTTCCTGTCTTGGTTTACCAAATATATC
ATATCAAATCCTATCCCTTTGATTCTTTCCTCTATCGTTCCCTTATGCTTGTATCATTAATTAATGTGTG
CTTTTTAGATTAATGATTCTTCTCTTGTATTAAAGTATGATTTGAAATCCT
>gi|3449668|gb|AI099929.1|AI099929 34082 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137N11XP 3', mRNA sequence
ATTCTNATCNGTGATNCAGTTCNTCTACTNCANCTTCTTCTTCTTCTTCTGTGTAAGTTGTTCAGTATAC
CANACTGATAATGAATAATATGCTTCTTACTTTNCAAGATCTCAGANCCCATGAAGCAGATGTGATGATT
CAGTTGTAAAAGGAAGCATACCTTTATAAACGTGTGAATGTATTATGTATGACAGTATATTTGTAATTCT
GAAGGACATGATAATAAACCTAGACTGAAAC
>gi|3449667|gb|AI099928.1|AI099928 34081 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137L9XP 3', mRNA sequence
GGTCTGAGATNTGGCNGGATCTGCTTTTTCCCGAAAGGAAAGNTCTGGGNTCGGTATGTTCTNAGACAAC
AGTTTGCGACCNGATTTACTAGCTACGGTCAAAATCCTGATGTTGTGATCTTGTCCGCAAAGGAATCTTG
TTAGCATCGAATATGGAAAGTGAGATTCGTGTTTTCCGGTGTACTGCCTTCATCAGATTNTACTGCGCTT
GTTTTTTCCGTTTTAGGCCNCTTCGTTTTTGTATATGTGTAATCTCTTACGGCCCATCAGCCAAAGCCTA
ATTCGGGANGTAATNATATATATATATT
>gi|3449666|gb|AI099927.1|AI099927 34080 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137L6XP 3', mRNA sequence
CATCGTTTTTNCCCCCGATACCGNNAGGTTGGGATGGAAAAGCTAACCATGGCTGCCCATCACATTCTTG
GGGATGATNGATTGGAGATGTTGCAACCGAATNGCGTGACCCTTGGAGCTAAACTCATCGGAGGATGTTG
CCAGGACTACACCTTCCACCATTAACGCTATCTCCCAGAGATTTGAAACGAAGATGATTTTTCTTCAGGG
AGAAAAGACTGAAGATTCTTTTTCAACTTTTTAACTAGCTTGACCATTGTTAGGGCTATCTATCTGTTTT
CTGTTGTTTTCTTGTTGTTCACGTTTTCTTTGTGGTTTGATGATATGTATTCGTAAACTAGGCCTTGGGC
GTTTTCAATGTAATGGCCCATAAAATATTTTCTTTATCAAAATTACCCGATTTGAATCTTT
>gi|3449665|gb|AI099926.1|AI099926 34079 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137L4XP 3', mRNA sequence
TGCCCACCAAGNGGAAGGTTATTTACCNGCACAAGCNTTAACTGGANNCGCTGATGGAAGCCACCCTCTN
NAGTGTTCCNCCGATGGAGTCATTAGAGTTTGGGGTATTNGNTCGTTACTAGTAATCTCATCACTTGTGC
TGTCGTTGCTCTCTGCTATCTGCTTGTTGGTTTTANCTATCACTTATGTTTTTATCGACAACTCATGAAG
TNCCTTGAGGTTTTTGGAAGGATGTTTGTTTTCTTGTCAATCTAGGTTTTTGCTTCTTTATCTTATCGTT
CGAGATCTTGGTTTTTAGAGTTACTTCTCCCATTTTGTGGCAAATGATTCCCATT
>gi|3449664|gb|AI099925.1|AI099925 34078 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137J6XP 3', mRNA sequence
GTCCCCCNTNGTTTTTNCCTCATTGNATTTNCGCCACCAATGGCACGCCGGATCAGAGCCATTGACGCCT
CCGCCANTCCATTGCCCGCCTCGCTGTCTCCAAACGCGGCATCTAAGGGAGTCATGAGCTATGGAATAAT
TGGAGTCACGATGATATTGATGTACGCTGTTATGACCTAAATAACAGGGTGGAAACAGAGCATTGTTTTG
CTCCATGTCTTTTTTGGTCGGCGGCCTTTGGAAATACTACANCNCTACGTGCTCTTTTGTGTGTAACGGA
ATTTTTTTGCCATTGACAATTTTTCCTTCTTCCTTCTTTTTTTAATTACTTGTAGGGGTTGATAAACGTT
ATAGCCATCT
>gi|3449663|gb|AI099924.1|AI099924 34077 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137J4XP 3', mRNA sequence
TCCTTGCCTNATAAACACATTTGAGGCNCCTNCGANAAGCTTGAGCTTTTTAAGCCATTTTTGCAGTGAC
GGTAGTTGTGGCTGTTGTGGTTTTAATAGCCGCCGTGATATACCGGAGACAGAAACGGGAAGATGGTTAC
CAATCACTTAGTACTTAAAAAAGAGCAAAAACCATGTCGACTCTATATATGTCTTCAAAGTGAATTCTGT
TTGTATACATAGAATAAAAGATTATTTTGTTGTCATCTTCCTCTGATGTGATATCTCTGTAATAGTTACG
TGTAAGAAGCACTTTTCTTTNTC
>gi|3449662|gb|AI099923.1|AI099923 34076 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137J19XP 3', mRNA sequence
TTAATTGCCCTTGGCNCACCGAATGGAACNNCCGTGAACTTGGANAGGATAAATTTATGCTNATTCCACT
AGGTTTTACNCGGCCCATTGTCCCCATTCATGTTCCGGGTTTTCCGCCTCGGCGGCCAACTATTCCGCAG
TTACCACCATATCGTCCCAGAAGGTGCCCTTTCTGTTATCCTCCTCCTCCCCCAAAGGCTTTCCCAAAAA
ACTCACCAAGTCACTGATGTCACTATAGCTACGAAATTGCGTCAATAAATGTATGCACGTTAATTTGTTT
CATTTGTGATGTGTGGGGCTCTTTATCTATTATATGCATGTCACGTGTTTGTCAT
>gi|3449661|gb|AI099922.1|AI099922 34075 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137H18XP 3', mRNA sequence
CGCATTTCTCCAAATCCTAGGCCCCTTNTGCAAGAAAGCTAATCAGTGTTCAGANNGCTGGATCAANTCC
CTTATGTTGTCGAGCTTNATGNAAGAGANGGATGNTTGGCGCATCANAGACTGCACTTGGGAGAGATTTG
TTGGAAGGCGAACAGTACCGCAAGTCTTCATTAACGGAAAACATCTCGGAGGATCAGATGATACCGTAGA
TGCGTATGAGAGCGGTGAACTCGCCAAGCTTCTTGGTGTTTCCGGGAACAAAGAAGCTGAACTCTAGGTT
ATATATAGTTGGAAGAATTGATAACACTCTCTGTGATGCTTAGGTGTAAGCAATTCAATTTCCATTTGTA
TTGTGTTCTGCAGCTTGATCATGACCTTGTGACAGCTTGATCTTGCCTTTTAAACGTATCTTATCAAAGA
CCACATTCTGAGTT
>gi|3449660|gb|AI099921.1|AI099921 34074 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137H16XP 3', mRNA sequence
CTCCGGGTTCACTGGTCCATATGTNNACTCACNCCACTTATAAAAGGATGCTTTNGNGNAAAAAGTNAGA
NGNGAATGGCAGNGCTCCATCTTNCCTGTCTTGGGTTTACCAAATATATCNTATCAAATCCTATCCCTTT
GATTCTTTCCTCAATCGTCCCTTATGCTTGTATCATTAATTAATGTGTGCTTTTTAGATTAATGATTCTT
CTCTTGTATTAAAGTATGATTTGAAATCCTTTTTTTTTCTCTATCTCTTTTTATTGAATGGAATTGACTG
CGTTCATGATACTGTCAAAAAGAGAGAAAAAGAGTACAATTTTATATATTTTTCGTATTAGTTGAACGAC
AAAATAAATTACATTTTAAAATGTAAAATATAAAATACAATGCCATTGAAAATATTTACAGGGGTGTNTT
GGAAG
>gi|3449659|gb|AI099920.1|AI099920 34073 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137B8XP 3', mRNA sequence
TTGACTGGTTTNTGAATCCCGCTCGAGTTCAGGACNTGCAAGAAGTTNCGACACTNTGATTCGACTGATC
GATGANGAGATCCANGTGAGTTTGATGACAGAGAGAGGCAAGCCCGCAAAGAGAAGAAGCTCGCGAAGAG
TGCAACACCNTCTAAGCGACCTTTAGGNAGACAAGCAAGTGAGAGTCCTTCATCGACGAANAAGCGGAAG
CNCCTGTCGATGAGATGAGATTATGTGTTTACGGATCTGTCGAGTCTTTGTTGTTACATATAGTTAAGCT
AATGTTAAANACATAGCAAATGGATTTCATTCTGCTTTCATGAATGTTTGTCCTGGTTTGACTTGGATTT
AATGAAATGACTTAATTAT
>gi|3449658|gb|AI099919.1|AI099919 34072 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137A5XP 3', mRNA sequence
TAATTTGGAAACTTTTTGCNTTTGGTGAGAACCTCACCGTGACTGCNAANCCCTGACTTGGACCTACTCT
GGATATGTTGATGCTGCAGAGGAAGGTCATGAACACTTAAGCTCNTAGCTGTTTGTGCACTCAACAAGTT
ATATATCTTCTTGACGACTTCTTGCTCGCAACAACTCTCTACCNGCTATCAAATGCATCGTACGGTTGTT
GTCTGAGGAGAACATAACTGAGTCGTCGTCACAAACAAGAGGAACATATGCNGTTTCGGTCAGAACCAGT
CGTGTGAATGGTAGATATATGTATGTGTGTGTAGAAAATGGTTACCAATTGTATCTTCTTTTTGATAATT
ATTTTTTCATGCCTTTTGTAATATGTAAGTTTCTTT
>gi|3449657|gb|AI099918.1|AI099918 34071 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137A20XP 3', mRNA sequence
GTCTTCAATTCGNTCCAACCNGCCCCGNTAGCCGCAGCTTTGTNCACTTTTCGATCAAACGTNCCCTGTG
CCCGCTTCCATGGCATCCAGGAAAATGCATTCGNATGGGGATCATCTGAATTCCCACACTCTGNGGNCGC
ATTCAGTGACTCAACATGCTGCAAATTATCTAGTCAGTGAAGCCAGAAAGTCAATGAACAGACCATCTTC
TGAGAAAGTGCTGAGCAATCTCATCTACAACTACAAGCCTACGTACTCCGGATACAAAGGGAGCGGTGAC
GACGAGGTTTATATTTTCACGTAACAAAGATCCCTTCTCTGTGTGTTTTCGCCAAAACATAGCAATTTAT
ATTAGTTACTAAGAGCAATACAGTGTTTCTCCTTATCCACCATTGATTGTAAGTTGTAACCAAGGTGTTG
AACTATAATTTAAAAAAACACAGTATAGATC
>gi|3449656|gb|AI099917.1|AI099917 34070 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137A14XP 3', mRNA sequence
CAAAGTTTTTCCNCTCCGTTTTGGAAACNATCTTATNCCTGGGGAGANNTACCCNGACATCTGGGCCNAT
GGNNCCAGATTTTCACAGNTGNCCCTNTGGGCTGATACAGAGACGCTGGAATGGAGGAANTGGGAGATGG
GTTTGGATCGNTGGAGCATCCCGGTCCTAGAGGATGGTGCGCGTTTGCAGCTGGATCACGAGATGGTAAG
CAAGGTCTGTTGGTTTATGGCGGGAACTCGCCGAGCAATGATAGGCTTGATGATATCTTCTTCTTCACTC
CCAACACTCTACTCAAGTGATTGGTAACTAAGTATGGTTTGGTTTTCTTGCCGGTGAGAGGGGCTGTGTG
AATGTTCCTTTTTTTTTAGTTTCCTTTTGGATTGGATGAACTATGAAGATGTGTGATGTGTTTCATTTTC
CTCTGTTATTTGTAATTAAATAATCGAAATTTTTCATTAAAGAAGATAACGAATAACATCAGCTT
>gi|3449655|gb|AI099916.1|AI099916 34069 Lambda-PRL2 Arabidopsis thaliana cDNA clone 136O1XP 3', mRNA sequence
TGTTTNCCCCTGGNACCCCTGGGGTNTTNTCCCTTGNTCAAGAAGCTTTTCCTTTCCNGCAAGCATCTTN
GGGGGACCGGGAAGGTTAGGGTTCCCAAATTCAGGCTGATTCTTGTTAGAGAGCCGGATCCCATCGTCTT
GCTCCGTTACTCCAAGAAGACCAAGAAGCTCCCACCCGTCTGGAAGTACGAGTCTACAACTGCAAGCACT
CTTGTGGCTTGAGAAGAATAGAGTTGATCATGTCCTTCAAGAAGGACCATTTCATTGTCTGCATTGCAAC
TCAAAGCTCTTCTTCTTTTGAACCTATGTATCTGTTTTCGCTNGTTTTGATGGGTTACAACTTGCTATGA
GATTTTGATTTTAGGGAACGAATTTGTTTATGCGAATCTTTCCATTATCGTTACAGCTTATCTTTCAATT
AACGTTAATTATCGTTCTCAGAG
>gi|3449654|gb|AI099915.1|AI099915 34068 Lambda-PRL2 Arabidopsis thaliana cDNA clone 136D14XP 3', mRNA sequence
CTTTCCGNCTTCCTTGGNCCNTTTGGGCCCCCCNAGNCTAGCTTTCGTTANGGNGGGGGCTTNNGCTNTG
ATTGACGTGATGAAAAGTTCTNGCNNGACACATGGCTAAGCTNCTCTTGACAATGAANAAATGAGCCGGC
GATGAAGATAGCGNAGACGAAGAAGAGGACACTGGTATGGGCGAAGTGGATCTCGATGCAGTTGCCGGAA
TCATCGAGTAAGATTGCCGGATTTTTCTTTCTATTAAATCTACCCAATCTCAACAGTCCCAGTATTTTGG
TTTAAGCTTTGACAAGGCAGTAGAAAAACCTCCGAGAGGATTTATGTGCTTTTTGATGACTCTGAGGCAT
TTTGTTTTACCCATAGGGGGTGGTTACATATCAATCATACATTCATGGTTTTATAAAAGATTTGATTCTT
TGC
>gi|3449653|gb|AI099914.1|AI099914 34067 Lambda-PRL2 Arabidopsis thaliana cDNA clone 136D11XP 3', mRNA sequence
CCCNGGTTCCCCGGTGTGAAACNCGCCNAATGCTACCGATTCCCNGTNGGGTTGAGTTCAAACANACCNA
ATCGCGCAATTCAACACTTTTCGCGGGGACGAACCCTTCAGTCTTTGAGNGGGTTTTCCCACTTGAAGTC
ATACCCAATGGGTTCCAANTCTCCCCCGANGAAGCAAGGAGGGTCAAGTTCAACACGCTCGAGACCACTT
TGACTCACAGCAGTGGCCCAGCTAGCTACGGAAGGCCAAGGGTGGCTGCAGCTTAAGAGCTTAAAACTGC
AGCTTAACAATGAACCTCGAGTACTGTAAAAGGAAGTTAAACAGTACGTAGTAATAATAATAATGTACGA
AAATGTGACTAGTTTTGTTGAGGTTTACCTGTAAAATGCAACTCCTTTTCTGAATAAAATCTTTTCAATT
TTCGATCAAGTC
>gi|3449652|gb|AI099913.1|AI099913 34066 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135P9XP 3', mRNA sequence
AGGAAATCCCTGGGGATGAGGATTCATGATGGAGGTTGCCTGTANTTATCCAGGGAAGATCTCTGTCCAA
CCCNTNTCACCTACTTCCAACAATGATGCTGATGAAGAGGATTTTGATGGAGATGATGATGGTGACGAAG
AGGGAGAAGAAGACGATGACGATGAAGAGGAGGAAGATGGTGAGGAATGATGGGAGCCCAAAGATAACAC
ATTGCTGGCTTGCTTCTATAACAGATGTGTAAAGTTTGTGTTATGAGGTTCTCAATTTTAGCAATGATGA
GACTAAGCTTTCTCTTTTGGAATATTTAGTTTATTTACTATCAATAGCTACATTCTGTTTGTACGAACCA
TTTCATCATCCATGTCCTAAATCTTGCC
>gi|3449651|gb|AI099912.1|AI099912 34065 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135P7XP 3', mRNA sequence
CCAGNCCGTGCCGGGGTCANTGCCGGGTTGATACTGNGGATGGTTATGAAGAGGAGGGAGGNCGATGACC
TAAGAAGNCTGAATGTTGGTAGCATTTAGTATAGATGGCTGCAAAAATCTCTCTGTTTTTATTCTTTACT
TGAAATGTTAAACGGGGCTGATTAAAATGGGTCTTTCTTTTTATCTTTTTATATTTCCACAATCTCTCAC
TAAAGCCCTCTGAATGGAGAAAGTGAATTGTAGAATGTTTAGATGGTGAAAGAGAGACTTGCAGCTCTGT
ACTCTTTGCTTTATAAAACGATTTAGTTTTCTTTTCTCAGTTTATTATATTGTTGAATTGATGATGATGT
TAGCTAAATTTCTTTATACTTTGT
>gi|3449650|gb|AI099911.1|AI099911 34064 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135P21XP 3', mRNA sequence
TCCAGANGGNTTACCCGGGCGCCTTCCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCA
TCNGTTTCATTGCCTACAAGCCCCCAAGTTCACCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGAAT
TATCTCTGCTCATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGATTG
TCAAATGTCTGATTTATGNATATGTNATTTAT
>gi|3449649|gb|AI099910.1|AI099910 34063 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135P18XP 3', mRNA sequence
GCGTTCACNAGGAGAAGANCNTNTTGGANTATTGAAGTCACATTTAAGAGCNTTTGTGCTCGNCNGAGGA
GTCGGATTCCGTGCCCGGTTCATGAATTCGNGTCGATCGAATGGACAGACGGTGAACACGTTGTTAAGAG
TCCGGTGGCCGTCCAATGGGGTCAGGGATCAGTTCAGTCCTTCTGATTGATCATTGAAATTGGGCTCTGG
TTGTATGTTTTCATT
>gi|3449648|gb|AI099909.1|AI099909 34062 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135N9XP 3', mRNA sequence
GAAAGNGCTTAAGGTAACCCTTGACGTCTGNTGATGAGCCTCNTGGCTCTGTTGACNTTCAGGTGCTCCG
ATGTATCCTCCACTATTGATTCTTCCCTCACAATGGTTATGGGAGATGATATGGTTAAAGTGATTGCTTG
GTATGACAATGAATGGGGTTACTCACAGAGAGTCGTTGATTTGGCTGACATTGTTGCCAATAACTGGAAG
TGAAGACTCAACAACCTCTTGATGTCTGCTCCATTATTTTTTACTGTTACATGATTCGGAATGTATAATT
GTAGTTCCTGAGTTTATTATGTATTTGTGCTCTATAATTTATAGTAATAAACTTGATTCAAAC
>gi|3449647|gb|AI099908.1|AI099908 34061 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135N12XP 3', mRNA sequence
ATCAAAAAGTTNTGNCCCTAAACTCNTAAAAAGCACATTCTNTCTNCCTCGTTCTCTAGGAATCCATCAA
TTTCGAGATTTTTCTTATTATGNCATTTTGCTGCATTGAGATTTCTTTGGGTAGATCAANTAAACAGAGA
GAAACTTAATTTATGTTTCCAATGAGAAAGATTAGGGCAGAGGGCACGAAACGTCTATTTCTTTTTGATG
CTTCCTACTTTGTGAAACTTTCAAAAAGCCACTNCCAATTCTTTCTCACCTTCNTGGTTTGTCAAGTATT
TGTTTTTATTTCTTTAANCC
>gi|3449646|gb|AI099907.1|AI099907 34060 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135L1XP 3', mRNA sequence
GCCGAAAANTGGCCNAAGCTGATGCTGGCCTGTGGCTCCTNGAGAGCCAANCCAAATGCCTCCATGACGA
TCAGCTCAGTCCGTGATAGTTGAGGATGTACAATTCATGGTGGAGAGGTGTTTTGTGGACTGTGTTGATA
GCTTCACACGCAATCTCTGCAGAAACAAGAGGAGACTTGTGTGATGCGTTGCGCTGAGAAGTTCCTTAAG
CATACGATGCGTGTTGGTATGCGGTTTGCTGAGCTCAATCAGAACGCACCAACCCAAGACTGATATAGTC
TGCTTTTTTCTGTTTGGTATTTCGTACGGTTTACGAGTCCGAAACCAGAATAAACCGGTTGTTTAGTTGT
TCAGGTTACTACTCCGATACTGTTTTTTGAACTTCTTGTACTGTGAAATTATTTTGACTATATCCAGTTC
TGATATTGATATTGATTTGTATTTCAATGGAGTCTAGAGAAAATCATATCATATCAAT
>gi|3449645|gb|AI099906.1|AI099906 34059 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135K20XP 3', mRNA sequence
ACAACCATTACCGGGNCCACTNGCGGGTNNATCAACTTNAAGCAATGGCATCNATNNCCATGCCGCTCCT
TCTTCCCGGCCTCGCCAAGGTCCNTNAGCCACCGNCGNCGAAGGCTTCCGTAGTCAGGCCTCCACGAGCG
ACAACACACCCAGCTTAGAAGTCAAGGAACAGAGCAGCACCACAATGAGGAGGGACCTCATGTTCACGGT
GCAGCTGCAGCGGTTTGTTCTTTGGCTAAGGTAGCCATGGCTGAAGAAGAAGAGCCCAAGCGAGGGACAG
AGGCGGCCAAGAAGAAATACGCACAAGTTTGTGTCACNAATNTACGGCCAAGATCTGCCGCTACTGATTC
AACAACCTACCTTCTGCATGTCTATCTCTCTCTTTCAATTTCGGTAAATTTTCTCAATTAAGTTTGGTCT
GTAATCGTATATTTGATCATCAATTTACCAAAAGCCCTTTTATC
>gi|3449644|gb|AI099905.1|AI099905 34058 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135K13XP 3', mRNA sequence
CACGCAAACTCTTGGATTTCACTGAGANACTGAAGCCNCTTGTGTTGGGACAGTGGCGTCNGGGAAAATG
CCCAAAGATCTTGCACTCATCATTCACGGCTCAAAGCTTTCGAGGGACACGTNCCTGAACACAGAGGNGT
TCATCGATGCNGTCGCTGCTGAGCTCAAAGAAAGACTCAATGCTTAAGAAACTGANGAAATTGGGTAAAA
TTCGAACGTCTCAGTTCCTAAGTGTCTTATCTGGTTGGTGGGGTTGGTTGGGATCGGGNGGNATAAACTT
TTGTGGAGAGGNGTGTTGAGAACGATTTGTTTCCTCTCTTATAATATTTCCAAAATATTGCGACATTTTT
CCATTTTTATTCNGATCTCGAATTTTATGTTTGATTGATTGGTT
>gi|3449643|gb|AI099904.1|AI099904 34057 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135K12XP 3', mRNA sequence
TTTGNCCCTTCCGNGTTTGCCCCGCAGGTGGAGATNAGTTCCGAGNTTTTNACGTGTTGAAACCGGACCG
NTTGGNGAAAGCTTCGNNCNGTACTCGGGGGACGGTTTAACAGTATCAGTCTCAAACTGATGCAAGATGC
CGTCGTTGCAGGTCAATGGTGATACAAGATGAGAGAGGCTTAATCTGTGTCACTCACCAGTCTGGAAGAT
TGAATCAAAGGGATGCAAATCTTTCTTAATTTCTTAATTTTTATCTTCTTGGGTTGCTTTTTTTTTATGA
CACCACGATTAAAGCTTTTTAGGCATATAAAGTTGTAAGAGTTGTGTGTTTGATATCCTGGCTAATGAGC
GAGCTGAGTATGGGGATCAAGAGAGAAAAACCGTGTTGGCCTTTGGCTGTGTGTAGATATTTTGTATAAT
CTTGTGTTGATAAAAGATAATATCATCAATTTTTCTTGTGATC
>gi|3449642|gb|AI099903.1|AI099903 34056 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135J9XP 3', mRNA sequence
TTCCCCCTGCCTTAGGCGTGATGNCTAGNAGTGCTNCTTCCCGCANAGTGNTCCTTNTGTTGAATCGAGT
GGNGCNCGGATTTTTTTCCGTGNGCACGNAACACTCCCGGTNCTATGATGGCCGGTACTGGAAATGTGGA
AGCTTCCATTGTTCGGATGCACCGATCCGNTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGGAGTAC
CCTGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCT
ACAAGCCCCCAAGCTTCACCGAAGCTTAATCCCCTTTCTGGAATATTCAGCGTTGATTATTCTGGAACCC
ATTTCTATGTGGTCAATGCAAATTTAAGAAATTATTTGCCGACTTAAAAGTTGAGGAACTATTGTTTGAA
AGTGAAAATGTTATTCCTATCAGTTTCTCTATAATTATAGTTATCATTTCATTTC
>gi|3449641|gb|AI099902.1|AI099902 34055 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135J16XP 3', mRNA sequence
CTGGGGCCATCTCCCNTTCCGCTTTTGTTGNCCCATGGATGTTTGCAAACTGTCCAAAGCTGAGAAAGCT
TCCATTAAATGCTACAAGTGTCCCATTNGTTGACGAATTTCAAATATGTATGTATCCTCCAGGACAGGGA
NATGAGCTTGAATGGGAGGACGANGATACCAAAAATCGATTCTTGCCTTTAATCAAACCGTACTNGTACG
TCGTCGACTAAAGATCCATTACTCAGGAATGGGATTCCTCAATGTCAAAAATCAGNATTCACGCTTCTTC
TTCTTCTATTGCTTTATCTATCTTCTTGTNGTGACGGTGTGTTGTTCATTTGGATTGTATAAACTGATTT
GCATTCTGATATCTTTGANGTGTGTTGTGCTGTTC
>gi|3449640|gb|AI099901.1|AI099901 34054 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135I12XP 3', mRNA sequence
GTCCANATTGATTCAGGNATTGGCCCTGGAATCNNCCCATCAATTGGGACTTAACCCATTGTTGATGNAA
ATTATTCCAAGTGGCAGGTGAAGAGGCTATTGAAACAGNCCAAGCTTCTTGCCCCTCAAAGAAGGATTAC
TGGTGGGAATATCCTCTGGGAAGCCCAGCAGCGGCTGCGTTAAAGGTTGCAAAGCGGCCAGAAAACGCGG
GGAAACTCATTGTGGTGGTTTTTCCTAGTGGAGGAGAACGTTATTTATCGACTAAACTGTTCGATTCGAT
TAGATATGAAGCAGAGAATTTGCCTATTGAATGAATGTTGGACGTGTGCCGGTTTCGTGTGTAATAAGAG
ACGTTCGTTCCAAGAGTCCAAGATTTCAATTTGCTTATTACTGGTCAATGTGAAATGTATAAAAAGTTGC
ATATTCGATTATGAATAATTTTAGTTGACTACTTCC
>gi|3449639|gb|AI099900.1|AI099900 34053 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135H4XP 3', mRNA sequence
TTCCATGCATTTCNTGCGTTTTAGGTAATTTTTCAAGGACAAGCGTTCTTGTGGNGGTTTCCCNCAGTCN
AAGGCTTAAAGGCTGGGANAAGCTCTTTCTAATCANTTTGAGGCTNANNGGGCGAAGGACCAAGGCTTAG
CCGAGAAAGNAGCATGCTAGGAGAGAGGAGCGTTTAGCTAAGGTTCCCGNTGGAGATGTTGCGCCTGTAG
CTGCTCCAGCACCTGCTGCTACACCTGCTCCAACTGCAGCTGTACCGAAGAAGAAGTCTAAGAAGTGAAG
AGGATATATAGTGTGAAGCTATATCGATCATCAGTTCACGGATTAGACTCTGAAGAAGGTTTTGAATGTT
TTATCGAATGCGTTTGTGGAATAACTTTTATTTTCGCAAAGAACATAACTTATGTCAGTTAATCTTTATG
CTTTCAGATTTTTAGCTTACAGTGTTTCAACAGACCTACTTTGCAAGTTGTTCTTTTTTTGGTTT
>gi|3449638|gb|AI099899.1|AI099899 34052 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135H24XP 3', mRNA sequence
CCAACCANNGGTTTACCNGGCCTGGTCCTCTTANTGGTTGGTGGCCTCGNCCGGAATATCTACGACTTTG
TCTTCATCGATGAAAATTGCCCACGNGCAATTGCCTACCACCGATTACTGAAGACGTCAAATTCAACGTT
GTTAATCTGATGAATTTTNCGTGATTTGCTTTTTTAATTTGCATCGTAATGGGTTTCTGGCCGTTGGATC
ATTTTTAGATGAATCTTTGTCTATTGATTGATCATTTATGTGTCTTTGGGTTTGTTGTTGGAGTTGTAAT
ATCTCTGGAAGGCTTTTGTGCAATTGTATTGTACGGTTTAATAACTATAATTGAGAAAACCNGGGAATGT
GAATTATGAAAAT
>gi|3449637|gb|AI099898.1|AI099898 34051 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135H16XP 3', mRNA sequence
GNTTTTCCCCGGNGTTAAAACCCTCAACGGGNTTGGCNAAGNCGNCCCCNAGCCGTCAGCAAGCTGCCAA
TTGCCATTCAAGGTCCCGCTAGACCCTTAGGCTNTGGTCTCAACGCTGGCCCGTGCAGCTGGAATTCCTA
AGGCNATGTGGAGTCAATATTCCTTACAAAATCAGCACCAGCACCAACTGCAAAACCGTGAGGTGATGAG
CTAGCAACGGTGAGATGATGCTACTACCGGAAGTTTCGAATCCTTATTATATAATGGATGAGATTAATAT
TAAATAAGATGTTCGAATGTTTGTTTTTAGAGTTTTTAATTTCTTGTCTTTTTCTATTGTGGTGTTCTTG
TTATATGGGTTTGTCTGTACTATGTTCGCAGGCAACAACGTTATATGAAATTTCAGNGTACTTGANGTTT
>gi|3449636|gb|AI099897.1|AI099897 34050 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135G2XP 3', mRNA sequence
TTGGAATCCTCTTCAACCATCCAATCCGAGATTGCGAAACTGCGCCATGAAGTCGAGGAATTCGCTAAGC
AGTTCCCAACAATTGGGTTTGAGAAAGAAACCATGAAGTACAAGAACTAAACTGTTTCACCCCACAAGTG
TTNTNTGTTATGCTNTGAATTCCCATGGAATGTATAGATGATACATGTAAAACTCTATTTTCACGCTATC
CGAAAAATAATGATCTGTTAAATTTTCTCTCT
>gi|3449635|gb|AI099896.1|AI099896 34049 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135G20XP 3', mRNA sequence
TCAATTTCCCCCATGGGGCTTTTGAGGCTTCAGNTCCCCCGNANATTTCCATGGGNGAAACCNAGGACTT
GCTTNCCCCAGTGGGAGCTTCGACCCCATGGGCCCTCGCTACTNNCCCCCGAGGCTTTCGCCGGANTTGA
AGGTGAAGGAGCTCAAGAACGGAAGGTTGGCTATGTTCTCTATGTTTGGGATTCTTCGTTCAGGCCATTN
TCACCGGAAAGGGACCGTTGGAGAACCTCGCGGACCACTTGGCTGATCCAGTCAACAACAATGCATGGGC
CTTCGCTACCAACTTCGTCCCCGGAAAGTGAGTTTAATTTGTGATCGAGTTGTGTGTATCCGGTTTGTTG
CATCTTGGAAATGTGATGCAGATTTCATATCTTGTAAATTACTTTGTATGTGTGTGAAATATTTAAGAAG
CTTTATGAT
>gi|3449634|gb|AI099895.1|AI099895 34048 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135F6XP 3', mRNA sequence
CCCCTTGGAGGCCAAGAGGNAGGGCCTGNGNCCAACCNGCTTAGAAGGGCCTAGGAGGAGAACCTGGGGT
TGACCAGCTNTAGAAGAGCCTAAGAAGGAAGAGACTGGTGGCGAACCCGCTNTAGAAGAGGCCAAAGAAG
GAAGAGACCGAGGCCAAAATCTAAAGAGTCCAAAAGGCATTTTTGTGGATTGTGATAGTTTGGGTTCTTG
AAGTTTAGCTTCTGAGAATTTGTGTTGTTTAATTTGGATAAGTTAAGTTGTGTGGGGGAACTCTAGAGAA
AATTTTGGTAGGGTCTTTTTTTTTATAATATCTCTCTGTCTCTTTTTTTTACCACATACTCTGTTGCAAT
TTTTAGGGTTTTGGGGTGTCTTTTATTTTTTACGAGTTGTACAATTTCATTATTGGTTTAAATCTGTCTT
TGAATT
>gi|3449633|gb|AI099894.1|AI099894 34047 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135F5XP 3', mRNA sequence
CCNTGGTTCAATGGGGNATTTCTTTCCGNGNAACCCCCGGTTTTCCCATTCGTCCCTCGAGANCCTCATG
GNGTTGGGGCCCAGTTTCCAGCTCTAGTGTCTGATCTCACGATNCAGATCTTCAGCAAACCACGCCACGA
GCTCANGCAGAAACTCGAGAGCTTGCAGAGCTTAATGGCTAAATTACGACCCCAAATCTAAAATTTATAC
TCCCAATAAGAAGTGAAGCAGGGCAGCTAATTCTTTGATGTAAATAGCATATATAGAGAAATGTGAGAAG
CGGCGGGGAATTTTTTTGTATCCTTTATATATAATGTGGAAACGAATTTTTGTGTATGTCTCATGAGTTA
TGAGCAATGCTTGTACTTGCTATCACCCAAAAAGGAACTGTCTTTTTGGATTCATAAGTTTCGAGAAATT
TTTGC
>gi|3449632|gb|AI099893.1|AI099893 34046 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135D2XP 3', mRNA sequence
CCCCTGNGGGGAACCNCAATCCGGGNTNACGTCGGGGGGATTNTTACTNCAATTGTCGACGTGCCGNTCA
GGCCAATCCTTTACTCTCGTGGCTGCAGCGCCATCACTCGTTGCCGGCGCTCAGAATCTATCCACTGTCA
GTCTCACTGTAATCTTTTTTCTTTTCTTTTTCTGATATATAATTTTTCAGAAATTTCTCTTTTCTTTTGT
TACCGGTTTATATTTCTAAGTTCATTGCGGATTATTAGAGTTTCATACACATGTAAATGTTTCTGGGAAT
TTATCTCTGTTATTGATGTAAGTTTGTTTACATAAACCAGAAAAAAAACTATGGAATAAATACATTATAA
TTAATAGTATCATCACTCATAAACG
>gi|3449631|gb|AI099892.1|AI099892 34045 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135B18XP 3', mRNA sequence
CCCCANTATTCAAGNTTTCCTTTTTAAAAATTGAAATNAANGGAGGGNCAAAGCAANGGNGAGAAGAAGT
GAACCNAAATAAGGATCGTGGCGTGGAATCAGAAACAAAACATCTCTAACAACGATCCACATCACTTCCT
CTTCTTCAATGTCGCTCNTCTTCCACTTGTGCATCATTATCTTTGCGTCTTCGTCAAGTCAAATTGTTTC
CAAGACCCTTTTAGATCGTATCATACTCCTCTTTGTTCCCTTTTGTTGTTAAGTGAAAAAATGGGTTTTG
GTAATTTAATTGTTGTGCATACATTTTCTATTTTGTTATTCTTCCGTTAATGTAATGAAAGAGTTGTTNG
CATNTAAAACAAAGTTCAGTTT
>gi|3449630|gb|AI099891.1|AI099891 34044 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135B11XP 3', mRNA sequence
GCCTCGCCGGATTCGGGAGCTTTCAATNTTNGAAACANCGTCGTANCACTTTCATTGCGTTGTGGGATGT
TGTTGCAGCTCATTTTCTCCTCGTTTGAAATGATTATTGAATTGGTCAGCCTCGATCGTTTTCTTGTAAT
TTACTTTCATATTTTTTTTCCCTCAAATTATTAGTGGTCATCATTTTATAATATTTGAGTTTGTGTTTGA
TGTACGATTCAGACATTTGTTTGCATTATGTGCTTAATAAGTTTATCGTTGACTCTACTTGAAGAGAGAC
TTTGTATGTGATGTAAATNTCTTCT
>gi|3449629|gb|AI099890.1|AI099890 34043 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135A3XP 3', mRNA sequence
CCTGGATNTNCTGAGNCGGCTAAAAGGTTGGGTTTGAGNTAGTTGAAGGAGAAGNATCTGGCGANTCCCA
CCGNTGACCCGTGTGNACTAGGCTTAAGATGGNTAGGCTTGCTTATNGGAGGAATCCACATTGTGGTTCC
AGATTTTGTCCAGCGGTTGGAGTTGCTCCTAAAGGAACTGTTGATGTTCATGAGATGTTGTTTAAGACTG
CTGATTATTTGACCAGAGGAGGTGAAACCGGAATATTCTCTCCGATGCATATGATTCTCTGCAGAAAACC
GGAGTCACCGGAGGAGAGTTCTTGAGAAAGGTAGAAAGGAAACATCACCGGAAAAAGTATGGAGAATTTT
CTCAATTTGTTTTTATTTTTAAGTTAAATCAACTTGGTTATTGTACTATTTTTGTGTTTTAATTTGGTTT
GTGTTTC
>gi|3449628|gb|AI099889.1|AI099889 34042 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134M20XP 3', mRNA sequence
GCCCAATGNATCTTCTGAACCCGCNGNCTTCCGTGGCAATTGTTTTCAAGCACGTTCATGAGGGCGTATT
CTCGAGTATATGGGCCAATCAANGATCTCCTGTCTGCAGAAAACCCTGCTAAGTATAGAGACTGCACCCT
CACCGAATTTTCAACCATCTTCAGCTCAAAAACGCTCGATGCTCCTAAGTTACACCATTTCAAAATCTAA
GACATTTGGGTTTAGNCCTTTTTTGTCTNCTAATCTATCAAACTCTCTCGGTACACNATGAAAACTGGTN
CTTCAT
>gi|3449627|gb|AI099888.1|AI099888 34041 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134M11XP 3', mRNA sequence
CAAGGCCCANGTTAGATTGCNGGNTACCCACCAGGTGCAACGGGGTTAAGAACTCATTGAATCATGCTTG
GTGTTCATTACTTTATCGGTATGCTCTTCACCTTCCTTGTCCCAGAGCCAAAGGGCAATAGTTCCACTCG
AAGAACATTTCTGGTGAAGCTGAAGTTAGCCATGACGAGAAATAATTATGTATTTNTATTTTNTTATTTG
GAGTGCGATATTTGGTTTTGTTNTCATTTTATTGGCTCGTTGACCTTAAGTTATGATGTTATAAGNATAT
TGATGATANCANTTAAATCTGGTTGAATATTNCG
>gi|3449626|gb|AI099887.1|AI099887 34040 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134K3XP 3', mRNA sequence
AAACGACCAAGCGAAAAGCGGTATGTTNGCNTTTCGAATGTTGTTGTCTTTACTTNGATCTGCTTGTCCT
NGTAAANGCAGATTAGNGATCTCTTGAGTTACAGCTTACAGGGATTGAAATTTGGNCTCATTTCACCCTG
GTTATTGACAAGAACAGTGAGGTCTTGTCTTGTCCACTTTTTACCCGGGCTTGGTTTATTTATCGCCTGG
AACTGTAAACTATTCTGAAATGTTGAACTACTTTTTAGTGACTTCTCCGGTNGATTTTTACATCTCGTGT
>gi|3449625|gb|AI099886.1|AI099886 34039 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134J7XP 3', mRNA sequence
CCCCTTTTGGGAANCTTTTTCCCCCTTNNGTTCCCGTTCCGNATTTCCCGGTTNGCCCCCCGGGTTCNGA
CNTAAGCTTNCCTTNGGNACCTTTCCCTGGAGGTTTGGAAGGCGAATCGCTNGCACTNGCATGCGGACCA
CCGCCCTATGATTCAGTTTCGTTGCAGCCAAATCTAGAGAAGATGGGTTACAACGTGAAGGAGGATCTCT
TAATCTTCTAGATTTGCTCAAGTTCTGTGCTATTGGAAATTCGAAAGTTGATAACAAGTATCGCTTATGT
GTGTATATACATGGTTATTTGGGCACTTTTGTTATAGTTGTTGTTTATCAGAGCTCCAAATTGTATATTG
TATAAAATTGTGTTTAATT
>gi|3449624|gb|AI099885.1|AI099885 34038 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134J3XP 3', mRNA sequence
AAATTTGGGNTGTGGANTGTTGAANGGNAAGATAGACTTGGGAGGAGATNGTTAGGGNATCAATTNCCAG
GGAAGAAGCTTGAGGAAGTTGGTGTGTGGTGGTTGCTGATGTTATACTTGGAGTTGAAGGAATGATTGAT
AGTATGAACAAGAGTAAGGAATATGGCTTCCTTGGTTTCAGGAACTCCAACAACTCTTTTATCTCTTGGA
TTGACAAGTACAAGGCGTTCAAGATCGTACCTTGATTCCAAAACATACTTGGATGTTTGTTTACTCTGGT
TTCATGTTTATGTTTCTCCCAAAATCTCAGTTCTTTGTTGTCTAAATGAAATAAAAGCGGTACCATCTTT
TTCTGTTCTTTTTTTTAATTCCATCTTTAGTCTTGTAAACTCTACTCTTTTGGGAATNGTTTTCAATTTT
T
>gi|3449623|gb|AI099884.1|AI099884 34037 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134I16XP 3', mRNA sequence
TAGCTTGAGAAGGNGGGCATCANNGATNAGNGNTACAAGGGCCTATGNTACTGTTAAAAATGCNCCACAA
AGACTTNCTTCAAGCANCAAATCGCTTCANGACTTGAAGACGNTTTCATGTAAAAGCTCTGAAGAAATGA
GAAACAAAACAAACCAAGTCGGTAACATTCTGCCAGAGATGATCTGGTACCGTCCTTCAAAGAAGGCTTA
TGATGTTCTACTCGCCTTAACTATGATGTTGATGGTTGTCCGGTTCTATGTTTTCTTTAAAAAAATCTTG
AATACCTAAAACCCTAATCTGGTTCTTGGACTCCTTGGTCCATTGAAATGTTTCAAAAGGATTGAATCTG
ATCTGTGGGAAAAAGGAGAGCATTATA
>gi|3449622|gb|AI099883.1|AI099883 34036 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134I12XP 3', mRNA sequence
GGCACANTTCCCTATAGGNGGTTTTTGNGTATCGTGNCAATGGTTCCNCTCTTGGGAGAAGACCTTGNCC
TTTTGGTGTCCTTAATGCGAATCTTTCGTGCTTGCTTCAACGGTTTGTTTCAGACGNTAGAGAAGCAATC
AGGGAGGAGGATACATGCTTCGGACAAGGTAGAGCAGAAATAAATAAGAGAGAGGCAATAGCAAAAGTAA
AGGAGAAGGTTTTCCTCAAATTGGCATTTTCAGNGTTTGCGTGAGAAACAAGGGAAAGCTGATGGATCTT
TTTATGTTAGGGTTATTATAATAGTCTTAATGATCAGTTTCCATGTTTCTAAGGTTTTGTTTGATTTAAG
TGGTTATTAGTCAGTCTACTTACACTACTTTTATTTTCATTTTTGTACGTTTTCTATTGTTATATGTGAA
TTCGGATCACATGTGTTTGGAC
>gi|3449621|gb|AI099882.1|AI099882 34035 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134G13XP 3', mRNA sequence
TGAAAGGGAGGCAANTGATTTTTCCACTAGCAAACCTNTTGNCNTATCCATTTNTGAGAGAAGGACTTNT
GAAGGGAACACTTGCTTTGAAGGGAGGCTACTTATGCTTCGTCAAGGGTGCTTTTGAGCTTTGGGGACTT
GAATTTGGCCTCTCCGAAACTAGCTCTGTATGAACCAATCCATCATCATCATCATCATCATGACCATCCA
TCATCATCATCATTATTATCATCGTATATNATATATATCTACCCCATATGTAATTTGTAATGTGCCTTTG
ACTGTGATGAGTTATCTCTCCCTCTCTACCAACTTTCTTCATATATATAAAACAAAAAGGAAAAGCNGAT
GATATNGATCTTTCGT
>gi|3449620|gb|AI099881.1|AI099881 34034 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134D5XP 3', mRNA sequence
CACTTTTAGTTCCTCGAATNGGTTCCAGNACANTTCCAGGGCTTTATTCTTGGGAGNAAGATAAGTTGAA
CGATGGANCTAAAGACTTACCATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTCACTCTT
GCGATCTCCGGATGGGAGCTTTCACACTCGGTGTTAATCGTGTGGCTCAAGCTACCATTCTCAGAGGCTG
GGGAGCTTAAAGATTATCTAATCTCTTATGCAATCTCTTTAGCAGCTCCTGAATAAGAATTGAGCCAAAC
TTTAATCTACTTTTTGTTTTATCCTCCTACTTTGGCTTAGAGGTCATCCTGAGTTAACAGATATGTGTTT
ACAAGTACTAGAAGACGCTTCTGTATGTAATAAAACCTTGGACTCTAATAGTTNATGAGCTTTTTT
>gi|3449619|gb|AI099880.1|AI099880 34033 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134D1XP 3', mRNA sequence
CAACCTTTAAGGTGAAGGGATANTAGTAGTGACCTCATGGGAGGTGTGATCCGATCTCTCTACGNAAGAG
CTTCNTCCAAGTGCAAGAAAAGTTGNAAAGATACTCAATACATCGGTCAATGTGTTCCGTTTATTCGACG
GAGACAAATGGACCATCCAAGTTTGGGGTGATGTGAGTCATCTGGAGGAAACCGGCTTCTTACAATCAGG
TTTTGGTGGTGATAGAACCTCTGGTTAGAGAGATTCTATACTCTTAGTCTTCTTCCCCTTGGAAGAGCAT
TTATGTAATTTAAGTTTCACTCCATAACTTTTCAATTTTTAACATTTGACCCCATTACTTTGATAAAGTG
ATTTGGGAGGATTGATAAAGTAAATTGCTATAAATTTCTAC
>gi|3449618|gb|AI099879.1|AI099879 34032 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134C20XP 3', mRNA sequence
GNGAGTTTCTGAATNGGTTNNGANCTTTACATCTNTGGCCNCTTATGTTNCGAANTCTCCAAGAGNGCTT
ATGTCNACTTCCATGGATCTTGATTGGGGAATGTATCTTGGAAAGGAAGAGACAAAGTACGAGGAAGGGA
AGAGTTGGGGAGTGAAGTATTTCAAGAACAATTTCGAGAGATTGGTGAGAGTGAAAACAAGCGTTGATCC
AACAGATTTCTTCTGTGATGAACAGAGCATTCCGCTACTGAAATCCGTTGACGACATCTAAGAATATCCT
TTGAAGTTTCATGTACGAGTCCTTTTCACTGTGAAATCATCTGTTTTTGTTTGAATAGTTATGCTTCAAC
TGTGTAACTTTTTTCTGTTGTTGTGACATATTTGCGTACGTTGAATAAAGATTTCATGGTTTTTATGTTT
>gi|3449617|gb|AI099878.1|AI099878 34031 Lambda-PRL2 Arabidopsis thaliana cDNA clone 133P20XP 3', mRNA sequence
CATGGNCCGTNTATGGATGATAGTTTCCCAGTCCGGTGATGTGGAGACACGTATCCAAGNCCTTGGGTGT
GCTCCTGACTTANCCGTCAAGCAATACATTGAGGCCCATTNTGGTTTCCAATCTGACTTTATGGGACCAG
TGGCGGCTGTACTCATCGCTTTCACCGTCTTCTTCGCCTTCATCTTCGCCTTCTGCATCAGAACTCTCAA
CTTCCAGACCAGATAAAACCATCTCTCAAACAACAAAGTCTCTTTCTTTTTTTGTATCCTCTGTGTTGTT
TATATGCACTATAAGCTTTGTATGTTCTAAATATGTATTGTAGTGTCATAACGAAATTTTTTTGAATATT
TTTATTTATTGTCTTATAGATGATGACGAATCGGAATCATGTAATATAATTCCACTT
>gi|3449616|gb|AI099877.1|AI099877 34030 Lambda-PRL2 Arabidopsis thaliana cDNA clone 133O17XP 3', mRNA sequence
ACCAATCTGGTCGGTGCTTNCCAAGTCTNTTTGCCAACCCNTCTTTNCCTTCGTCGAGAAGGAAGCTTCT
AGGTGGTTTCCAGAGAGCGAATTCGTCACAAAAGAGATCAAGATCCAACTCTTCCCGGGGAAGCCCTTTA
ACTTTGAATCTCTTCAGGCTNGTATGGAGGACGTTCTTCGTGATGACAACAACGTTGATCTCAATGTTAA
TGCCTTTCTTTAACGATGTAGTCGGTNTCTTGGGGGCNATTGGTTTTTGGCNTTTNNCGGTTTATTTCCN
NGTGGAAATGTANATTGCCACCACGATAGAATGTTCCGAGACTGGCGCGCACAAAGTGGGTTTGTCTACA
AGTCTTGAGTGTGANATGTCTTTTTGTGTC
>gi|3449615|gb|AI099876.1|AI099876 34029 Lambda-PRL2 Arabidopsis thaliana cDNA clone 133K4XP 3', mRNA sequence
TCCCCGNTTTGCCCTTTTCCTTCGGNTCCCTNNCTTGGGGGGTTCAAGGGATTNCNTTCAAGGGGGGTTC
CGGAAGCTTACCCCCGNGGGTNGCTTTGACTNGCCAACTCTATTGTAGNGCAGGCTCTTGGAANGCATGG
TATCATTGCACTGAGGATTTGATCCACGNGATTCTAACAGTAGGACCTCATTTCAAGGAAGCCAACAACT
TCCTTTGGCCATTCCAGCTTAAGGCACCACTAGGTGGCCTCAAGAAGAAGAGAANATCCTACGTGGAAGG
TGGTGATGCCGGAAACCGTGAGAACTTCATCAATGAGCTTATCAGGAGGATGAATTAGAATGTTATCGTT
TTCAATGTCAAACTTCTCTGCGTTTTCATTATGTGCCTCCTCCTGGATTTTGATCTTCTTTCTCAAGTTA
AAAGACATTTTGAATCTTCTCTTTTGTTCTCTTTGGATCTTAATTTGTGCTTTGATTACTGCAAGTGATT
CTAC
>gi|3449614|gb|AI099875.1|AI099875 34028 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132M15XP 3', mRNA sequence
TCAGCATGTCCTTCCCTTGTTTGGCTGGCNCAGGAGAGGGNTCTCTCCNCCAGAGGCCGAGGGAAGTGAA
GAGGCACTTTGCAGCCCTGAGGAGTCCAGAAGNGCACCCNCNCCTGAGAAAGATTGCAAGCCGTCAAGAG
GTCGCAGTCTTGATTCACACATTGAGGACCAATTTGCAAGTGGACGTTTGTTGGCTTGTACCCCTTCAAG
GCCTGGCCAGTGCGGGCGTGCTGATGGATACATCTTGGAAGGTAAAGAGTTGGAGTTCTACATGAAGAAG
ATCCAGAAGAAGAAGGGCAAGGGTGCTGCTTAGAGTCTCTTCTTATCTGCCTTGAGCTTTTGTCTTACAA
CATGTTTTGAGTTTTCAGTTTCAATTGTCTGAGAAACTATGTTTTTGGATTAGCTTGTGGTATTTCTTTG
AAACTCCCATTATGGTACAATGTTTTTGTCTTGGATTTTCTTTATAATTTTAATCGATAATTTC
>gi|3449613|gb|AI099874.1|AI099874 34027 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132H23XP 3', mRNA sequence
TTTGAGNTAACTACCCTGTTGTTCCAGNTGCTAGACCNCGCCNTNAGTTAGGCCANCNTCNACACAACCC
CTCAACGGTTAACTTCAATCATCAACAGCNCTNTTGCACGTTTAAGGCTTAAAGANGAGCAAATCACTTG
ACAGAGAAGAAGAATACGACGGCGCTTGAGCTTTTGTGAGTTTAATGAATCTTCTTTTTGGTTAATGAAC
CTGTTTTTGTTGCCTCAAAACACCACAGGTTTCTCTGGACAGAATCTCTGATATTACAGTTTCAAAAGGT
ATGTTCTTTTATTTCATGTTGGAATCTTCTGTGTAATCTTAAGAAGCTTTAGGAGGTAATGTAAAAAACC
AGATTCAAAGTTATGCCCTTATGTGAATTCTTTTGTACATGGGATAAACAAAATTTACAGGTATCCTTTT
TGTTCTTGTTGT
>gi|3449612|gb|AI099873.1|AI099873 34026 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132C22XP 3', mRNA sequence
TGGCTAGGAATTGACTCCTTCCCGAACANTGGNTCCTTTTTTGAATTCGNTTTGGNGCNCGGNTTTTTNN
CCCGTGNGCNCGNAACACTCCNGGTACTNTGATGGNCGGTACTGGACATTNTGGAAGCTTCCATTGTTCG
GATGCACCGACTCCGCTCAAGTGTTGAAGGAANTTGAAGAATGCAAGAAGGANTACCCTGGCGCCTTCAT
TAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGC
TTCACCGAAGCTTAATCCCCTTTCTGGAATATTCAGCGTTGATTATTCTGGAACCCATTTCTATGTGGTC
AATGCAAATTTAAGAAATTATTTGCCGACTTAAAAGTTGAGGAACTATTGTTTGAAAGTGAAAATGTTAT
TCCTATCAGTTTCTCT
>gi|3449611|gb|AI099872.1|AI099872 34025 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132C16XP 3', mRNA sequence
TCCCTTGTNTTGAATTGGAGTTNGNGCCCGGTTTTTTGTTNCCNTGAGCACGGAAACACTCCCGGNTATA
CGATNGACGGTACTGGACNATTNTGGNAGCTTCCCNTTGTTCGGATGCACCGACTCCGCTCAAGTGTTGA
ANGAAGTTGAAGAATGCAAGAAGGAGTACCCGGGCGCCTTCATTNGGATCATCGGATTCGACAACACCCG
TCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAAGCTTCACTGATGCTTAAATCCTTTTCTGG
AATATTCAATGTTGACTATCCGGAACCCAATTTTGTATGGTCAATGTAAATTTAAGTAATTATTTTGCCA
AAGTGAAAAAACTGANGGTTTGTTTTTCTATCGTTTCCTC
>gi|3449610|gb|AI099871.1|AI099871 34024 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132C14XP 3', mRNA sequence
CCCGGGCCCCCGCAGGCCCTTTGTTCGCAGCCTTCNTTTGGGGGNNGCAAGCAAGNTTATTCCCCGGAAA
TNTGGNACTCAGACGATTCAACGAAATCTCATTTCTTGCAAACTCAATGCACCTTCTCTAACATACATCG
ATCAATGTCCAACTCTATTATCTTACTCTCGATGTATGGAGCAACAACAACCATTAGTAGGCATGTTGCA
GCCAACAGAAGAGGAAAATCACTTTTTCGAAAAACCATGGACCGAATATGATCAATACAATTACTCCTCT
TTTGGTTAACTAACATATCGTCAACGCTTTGTATTTCTACTTATTCGATCTACCAATTTTTTCTCTCCCA
ATACAACTTCAGTCTGATTATTGCCTTCTTAGATATGTCTTCGAATGTTATGACTATACATGGGTGTATA
TAAAATTTGTGATCAAAGTCTTGT
>gi|3449609|gb|AI099870.1|AI099870 34023 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132B9XP 3', mRNA sequence
TGAACCAATGGACTGGAGGACAATGCNACTTGGTTGTCGAAAGGCTCGGGGATTACCTTANCGAGTCTGA
ACTCTNAAACCAAGGTTTCATTTCAGGTTCTGCTTAACTAAAGAGTGTCAATGCACTTTTTATTGTGATT
GATTGTAATGCTTTCAAACACAAATCATTTGTTACTTTNGAACCAATTGTGATTGNTTGGTCTCCTTCGT
TACCGAGTTTGAGTTTGTGTGTTCTTGTAATGACATTTGATCATCTTTTTTCTCCATATGTATTGAGTTT
TGATTTTTGTTTCTT
>gi|3449608|gb|AI099869.1|AI099869 34022 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132A2XP 3', mRNA sequence
CTAGTTTGGGGGCAAAAGNTCTCCTTNNCTTTNNAGNTTGGGNTACCCAACCNGTTCATGGGCCTTATCC
GGCTCTGAGGCNCTTCNCCTTACAATCNTCTTCAGGGCAAGTTCTTTGGGGACATTCGCTGCCCCATTCA
CCAAAGAGAGGATTGCTCCTCAAGTCTTGATCCTTGGAGGAGGCTCTTTGCTTACTTATGTCAGCGCTAC
CTCTACCGGCGAAGTTCTTCCCATCAAGAGAGGTCCTCAGGAGCCGCCTAAGCTCGGTCCTCGCGGCAAG
CTCTGATCTATATTCATGTTACCTTTCTCTTCTTCCTTCTAAAACTCNTCAACATTTCTCAATACTGCAA
ACCCTTTTAAGTAATTTTATGTATATTATGTTTATCTGTTACATTTGAAACGTTTTTTCTTCCCCTAATT
TTACAAAAGAAATCTTTTTTT
>gi|3449607|gb|AI099868.1|AI099868 34021 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132A15XP 3', mRNA sequence
ATTTTCCANCCAAATTGGGAAGCGGNANCCNCAGGAACATGCTGTTCACCATTGACTTCTCCNGGGNCCG
AGCATTTAAACAATTGAACCCAAAATGGATGGTTGTAATAACGACCCCTTGTGAGAAGTAAGGAATGANG
CCCCGGCTCATCTAGTTTTGAAGTTATGGATCATCATGCCCAGTGTTTCATTGATGTATATTGCTTCATT
TTATTCTTCCGAGTCTCTTAATCTGATTTTTATCCAATACATTACTTGGCTTCTTTTTTTCTTTTTCGGA
AACCAATAGAGTTGGGTTCTTACTTTCTTAGGATCGATAGTCTTAGGAAGATGCTTTTGCATTGACCAAT
AATGTCAAAACCTTTGGAAT
>gi|3449606|gb|AI099867.1|AI099867 34020 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131N6XP 3', mRNA sequence
GAGCCACANGNTCGTNGTTGAAGGCAANCGTGGAGGACACANTTCAANGTTTTTCCTCCTCAAACTCGTT
CAGACAAAGCCAGCTGCTAGCAAANCCAACTCCCCCAAATCTGCGAAANCAAAAACTCTCCGAGTGTNGT
ATCGTGCTTATTTCTCTTCTCTTTNCAAGTTTGGTGAAAAACACAGTCTCCTCTTTGCTTCATTTCTTCT
TTCTTTCCCCCTTATGTAAATGAGTTTAGTCAGAAGTTTTTTTATATAGT
>gi|3449605|gb|AI099866.1|AI099866 34019 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131M22XP 3', mRNA sequence
TTGCANCTTCCCAAGCAGGCGTTTGATTGANTCCNCCGCTGAGTTGGTTCCATTGGGTGGGGGATTCATA
CCAGGGNCNNTCCACTGATTTATGGCAGCTTTCTTNGAGACANTCTCACTCTCTGGACTTCAGATATGAC
TGACGAAGCAGGAGATGAGATTAAGGAGGCATCAAAGCCCGATGNTGCCGNGTAANCCCGAAGAAGAGGA
AGAGTCATTTTATAATGGTAGAAAACTTTCATGTGATAATCTGAGTGAGGGATAGCTCAGGATTCTTATA
AGAGACACAGTTTTATTGTTGTTTGTTTGTTTTGAAACTACTTGCGATTTATCATTCCTCCTTTAGCTTC
CTCAATATTTCCTATTCTCCTTTCTAATGAAATCAAAACTTGGTTATTTCTGATATGGTAGTTGTCTTTA
TTTTCT
>gi|3449604|gb|AI099865.1|AI099865 34018 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131K21XP 3', mRNA sequence
CCGAAGCANTTTGNTGGAATGGGATCCTTNCTTTNTNTTCAGGCGGATAAGTNCTGAGACCNTTGGCCTA
CGNGTCAGGAGCTTTACNCCATGGGCTCCCAACAATGTTAGTGAGTCAAACCANGACAAGATGTAACAGT
CGTCACANACAATGGCAAATCTTTCACATGTACACTCCGATTTGACACAGAGGTGGANTTGGCTTATTTC
GATCACGGAGGGATTTTGCAATACGTTATCAGGAACTTGATCAAACAATAAATCTGGTAACACCAGAGAC
TTGAGTTATATATCCCAAGGTTTGTTGCAATAAAAATGTTTGCAGGGATGAGGACGAGAATGACTTTAAT
TTAAACTTTTGCTTTTGTTCTTCTTCGTCTCTTGCTTCGTGCTAGTCAATTGGAAACATTATCACTGTCG
AGTCATTTTTTTTCTTTC
>gi|3449603|gb|AI099864.1|AI099864 34017 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131J6XP 3', mRNA sequence
TCCGAGCATCACNCACTTGTGCTNGTGTTTGGTATGNTGAGGCAACNATTTAAGATACNCATGATATGAG
NCAGACCNTGAGAAGATTCNGANGCTTAAAGATGATGCTGCTCGGGGACTCATCAATCACATGTTGTTTG
TAGCAGCGAAGCTGACAGGAGGCAAGGTTAGCCAGAGATCCTGATGCAGTCTGGTTGCAGACTCTCCCAT
TGTTATTCTCTCTCTATCTCTCTAGTCAATGCTTGTAGGCTAACAATGCAACTAAGTTGGCTTGAATAAT
AGACTTGATCGAGAAGCCTCAGTGACTCAACATTGAGGATTTTCCTGTGCAATCAATCAAGTGGTTCTCT
>gi|3449602|gb|AI099863.1|AI099863 34016 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131G7XP 3', mRNA sequence
CCTCAAAGGGCTCCCNCCAAATTTGGTATNTCCTCNACAGAATTCAATTTCTTCCCCTAAACGCGACGAC
GACGACATTCTCACTGCTGCTGAAAAATACATGGAACAACACGGTACCGAAGCGTTTGAGCGAATGATCG
TTAAGAAGGATAGTTATGAAAGAGGTAGGNGTAGTAGAGGAATCAATAATCACATGATCTTTGATGATGA
CTATAGGTACTAATAAGTTCTTAAACCGGTTTAATTAGCTACTTTCAGTTTATAAGTTTGCTATGTGACA
ATATATTGTCTGTTTCTATGGTTGTTATAATTTGCGTGGATTATGTATAAGCCCTTATTTAGGNCTGCTT
ATTTTTGTGAAAAATCAAATAAACATTTTCTCTC
>gi|3449601|gb|AI099862.1|AI099862 34015 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131G1XP 3', mRNA sequence
CGCTTNCGATGGGCTGGAAGAGATGGGGAGNGGATCCAGGACGCACCTGCGGATCTGATGCTGAAGNCGA
CCCAGNGGTTGATGAAGGAGGAGATGATTCCGATTCTGAATCTAAGGCCGAGGAGCCCAAATCAGTNGAT
AGCGAGGAANCCTCTGAGAAAGACGCCNCCGCTCATGATGAGCTATAGGTGAAAGGTTGAAGATTTGAAG
NCCAAAGTTTTCAGTCTCTTTATTGTTTTATCGTTTTCTTTTGAAGTATTTTAGCATCTAGTTTGTCGGA
GATAGAAACAAGTTTTAGCAAAACTAAAAGGGGGATACAATGTCTGTCAGATGCTCATTTTAGACTTTAA
AAAACCATGAAGANGTTTTGC
>gi|3449600|gb|AI099861.1|AI099861 34014 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131F22XP 3', mRNA sequence
TGACTCAGGAAGGGGAAACCCCNGTGGAGCTNTGGGNGCTTAGNTGAGATCATTTTCATGCTGGAAGGAG
ACTTTGAAGTGATCGATGGTCCCTTAGTTGTAAATAAAAGCTGTGTTGGATTTTGCTGTTGGGGGATGGT
ACAAGTCACACCTCAAGCTCTATGCATTGGTATCTCATGAGCCTCTCTTCCATAGAGAGTTTCTCTTTTA
ATTTTGTCGAAATAAAAAAGGTGTGATGAAGTAAATAGAGGTATAATAATATCTATCTATTAAGTCTTGT
TTTGTTCTTTCATTTTTGTATTTCTTTTCTATTTAAAAGACAGTTTATTAGTCTTCTGAGCTCTCTTTTT
GATCTTTGTTATAGCGTATCATCACCCTCGAAAGTGTAATGTTTTGTACCCCCAAACTTGTTTAGCATTA
TAATAAAGTCTCTTTGGAACT
>gi|3449599|gb|AI099860.1|AI099860 34013 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131D4XP 3', mRNA sequence
CAATGAGCTTGGATTAGGGTATGGTAAGGAAGGNGGCTATGATAGTCTTNCCTGCTGGGACTATCATCGC
TTNACCCGTNGACTCTGACACNTATATCAAGGCAATGCGGCTTTTCNTGGGTGAACCGGTATGGNCACCA
TACAATCGCCCACACGACCATCTTCCTGCAAGGAAAGAATATGTCGATAACTTCATGGTCAATGCCTCTG
CTTAGAGAGCTTCCTCTCTCTATATCTGGCTTTCTGAAACCAGGATCTATAAACAAGGCCTACAATAAAG
AAAGCTTTCCTGTCAAGTATTGGATATTTATATATATTCCTGTGTAGAATGATGGCTTTTGGTATGCTTG
AGTTGTTGTAAACTTAGTTACACTCTCTGATATGTCTCTCTTTACCATCTTTGTCGTATCCCATATACGA
AAAGATTACATTGGGATTCAT
>gi|3449598|gb|AI099859.1|AI099859 34012 Lambda-PRL2 Arabidopsis thaliana cDNA clone 130N23XP 3', mRNA sequence
GCTTCCGGTGGNGCNTACGACGGNGCTTCCCGTGGNACATCCGGNGGGGAAGAAGGGGNTTTTGGAAAAG
NTCAAAGAGAAGCTTCCNGGTTATCATGCCAAGACCNCTGAAGAGGAAGTGAAGAAAGAAAAAGAGTCTG
ATGATTAAGCAAAATGGTTAAAGNATGAATAATGATGTGGGAGTGGGACATTCGCTGTGTTTTGTGATCA
TTATCTTTCTCTTTTAAGTTGTTATTGTGGCTTTCGTTGATTGCATTTGATCCTTTATTTTGTAATTTCA
TTCTATCTTTTATATAAAGTTTGCATATGGTTT
>gi|3449597|gb|AI099858.1|AI099858 34011 Lambda-PRL2 Arabidopsis thaliana cDNA clone 130I19XP 3', mRNA sequence
GTGGNGTTTGTTNAGACATGAAGGAAGGTGGTCATGGGGGGATCTCTCAAAGNAGACACNACTGGANGTG
ACCTTTATGNTGGATTTGTCAAAGGCAAGATCGCTGAGAATGTGGAGGAGGCTGCTTTAGTGTAATTTCC
CNCATAGGTACATACATATAGTGTGGTGTTTATTGTATTCCTGTCTGATAAATAACTAGAGNGATCAAAC
CAGTAAGAGTGTTAAAGCTATAGATTTGCACAATTCTGGGTCAGNGTCAGAGCAAAGAGAAGCAAAATCA
AGATGATGTACACTTAGATGTATCCTATGAGTTTTCCTTGTACATCATCTTCATACTCTTAATCTCAAAT
ACTATGCATTTTTCTCC
>gi|3449596|gb|AI099857.1|AI099857 34010 Lambda-PRL2 Arabidopsis thaliana cDNA clone 130E5XP 3', mRNA sequence
AGTTTTTTGNGGGCCCNTTNAGCTTCGGGNCCCAGGAAATGGCCNTTGGGNNGGCCNGGNCTTTTTTCCC
CGGTGGCAGTTCGCCCCATTGGTTTTGGCTCCCGNCCCAGGGCATTCGCTGAGTTGAAGGTGAAGGNGCT
CAAGAACGGAAGATTGGCTATGTTCTCTATGTTTGGATTCTTCGTTCAAGCCATCGTCACTGGTAAGGGA
CCGATAGAGANCCTTGCTGACCATTTGGCCGATCCAGTTNACAACAACGCATGGGCCTTCGCCNCCAACT
TTGTTCCCGGAAAGTGAGCCAAGTTTTATCTGTATTTTGCTTCAGTCTTTGCTTCGTGAGTGTGAGAGGA
GAAAGAGAGCTTGTTTAGATGTAAAATTTGCAAGACTTTGTATTTTTTTTCATTAATCAAATAACTCGTT
TTTCTCTC
>gi|3449595|gb|AI099856.1|AI099856 34009 Lambda-PRL2 Arabidopsis thaliana cDNA clone 130D20XP 3', mRNA sequence
TTTCANTTCCTTGATGCTGCTTTTCNCGNTGANGAGTTTGAGTTAGAATCAAAGGCATTGCGTGTTGGTA
AAGCTGTTGCNGTNCTGAGTGTGGAGCTGAGGAAGAAGACGACTGGTAAGATTATTGCNCAAGGTCGTCA
TACCAAGTACTTTGCTCCTCGTTCCATCCTTTGATCGTTCAACCAACCTTTCTTCTTTTTTACATTCAAT
AAACAACATCAAGGTGTTTTTAGTCTTTGTCCNATTTGCTTCTTATTATTATTGATNCTNATAAAACTAC
ATTACTATATGTTTTTCTNATNATACANACAACCTTACTTTTTCTCT
>gi|3449594|gb|AI099855.1|AI099855 34008 Lambda-PRL2 Arabidopsis thaliana cDNA clone 129O23XP 3', mRNA sequence
AAAGGCCAGATCTTTTTCATTCAACCCTTTTTTCAGNTCCGCTTCNGCCCCTNTTGTCTTGGGNAGCCGA
GTTCGNGGNTTGGGCTCTCAGATCCATCCGCAGCNGGCGNGCCATTCAAGGCACCAGATCTCAGCAATGT
GATCTCAAAGGGTGAGTCATCGAGCGCTGCCAGTGGTTCAGGATGATGAGGAGGTTGACGAGGAAGGTGT
TGAGCCCAAAGGACATTGAGTTGGTGATGACTCAAGCAGGAGTGTCTAGGCCAAATGCTGTGAAGGCTCT
CAAGGCTGCAGATGGAGATATTGTCTCTGCCATCATGGAGCTTACCACCTAAACCAAAGTCTTTTCTACT
TATATGTGGTTTAACCTGAGTTATGTGCCAGAGATTGTCCAAAGAATTCGGAAATTTTTGGTTTCAATGT
TTTTCATGAAGTGATTTTCGATGTTGTATCAGTATAAACCTCATAAGTTTTTGATTTTCAGTTTGATTTT
ATATTGAATATC
>gi|3449593|gb|AI099854.1|AI099854 34007 Lambda-PRL2 Arabidopsis thaliana cDNA clone 129O20XP 3', mRNA sequence
CTTATCCCAAGAGGTTCTCTCGACCNNGNTCCTNCGCCATGTCTATCGTNGTGCAACATCTCGCCGCCGG
TCCATCTCCGNTGATCCATGAACCCAGCACGTTCCCTTGGACCACTGTTGCTNCCGGAGACTTCTCTGGT
CACTGGGTCTACTGGGTTGGACCACTCATCGGTGGTGGACTTGCCGGACTTATCTACGGAAATGTCTTCA
TGGGTTCTTCCGAACATGTTCCTCTTGCTTCTGCTGATTTCTAAGGAAACAAGTGATGATTCTTGATTCA
TGTTTCTGTGTTTGGTTACTTTGCCTCGATCTTTCTTGTTTTGTTTGGAGTTTGGTCCGGTTTCGTTGTA
ATTTTTATCCAATTTGTATGAATATTATTTAATGGATGGCTGTTTTGGTTATAAATTAACTAATGGATGT
ATGAATATATAGTTTCACCT
>gi|3449592|gb|AI099853.1|AI099853 34006 Lambda-PRL2 Arabidopsis thaliana cDNA clone 129G19XP 3', mRNA sequence
AAAGNGCATTNGTGCAGCCAAGGCGGTTTGTNCATTGCTGAATTCGACACTTACTGCAACAGGGGGCCCC
TTTTGCTGCATTCTCGNGAACTNCCAGCGAGAGGNTGGTNTCGACATTCCTGAGGTTCTGCAGCCGTTTN
TGGGCGGAGAGACGTTTTTGCCTTTCAAGGCCAAGCCCGTACTTGCTGATNCCAAAGGGAAGAAATCGAA
AGCTTGATTGATGTATTGATTCAGATTAACGNCTCTTCTGTTTTCTTGAAATTGATGAAACACTTCGATA
AATTTCTTTACTTTGTGGAATTTTTTTGGACTTCTGTTATTTTACCAGGACCGTTATTTATCATCTGATT
TCTGCTNGTATTTGTTC
>gi|3449591|gb|AI099852.1|AI099852 34005 Lambda-PRL2 Arabidopsis thaliana cDNA clone 129E7XP 3', mRNA sequence
AAACATACTCTTGGGTTAGAGAGGGTTTGGCCGTTTCAGGTACCCCGGTTCCCCCGGTGACCTTNTTCNA
CCCCTCTTGGNTTTGGGAAAGATGAGAATCACTGAAGGAGTTGAAACTCAAGGAGGTCAAGAACGGTAGA
CTGGCTATGCTCGCCATCCTCGGTTACTTTATCCAAGGACTNGTGACCGGTGTGGGACCTTATCAGAACC
TGCTTGATCACTTGGCTGATCCCGTCAACAACAACGTCTTGACCAGCCTCAAGTTCCACTGAGGTGATCA
TCATCTCATGTGTTTTTATGTCTCTTGTATCGTACAATATTTCCATCTTTCGCTACCATTGGCTTCTTCG
TATTGTAACACCCTGTGTAAACATATTCGTGTTTTGTAAGAAATGACAATGTCAATGGCC
>gi|3449590|gb|AI099851.1|AI099851 34004 Lambda-PRL2 Arabidopsis thaliana cDNA clone 129B18XP 3', mRNA sequence
CCACATGGTTGTTTCCACCGCAAGGTTNTGTTTCACNGTTCATCACCAAATTNCCAGTGACCGGCTCCAG
TGGCATCCTGAGAAAATGCATCGAGTGGGGATCATCTAAAATTCCACACTCTGAGGACGCGATCCAGGTG
AGTCAGCACGCCGCAAATCATCTAGTCAGTGAAGCTTAGGAAGTCACTGAACAGACCAGAGTCTAAGAAA
GTGCTGAGCAATCTCATTTACAACTATAAGCCTACTTACTGTGGATACGCAGGGATTGGTTACGACGAGG
TTTACATCTTCACACAACAACGATCCCTTCTCTAATAACTATAACCTCTCCTGTGTATCCTCTCGTGTGT
ATAGTGAAATATGTACCTTCGACTCTGTTATTATCTGTGAACTTGTTGTAACTTTGAACGTCAGCCTATG
GCTTGTGTTTGACATTAAACTAGATAATGTACGCTTTTCTNTCTT
>gi|3449589|gb|AI099850.1|AI099850 34003 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128O23XP 3', mRNA sequence
TGGACGCTGNTGTGGTTAGNAGTCAGNCTGTTGATATCCTCCCTCTAAGACNTNTGACCCAGCGATCTTC
TTGCTTACAACTGGTNCACNTGAAGCTGCCTTTAGAAACATCAAGACANTCGCTGAGTGCCTTGCTGATG
AACTCATCAATGCTGCAAAGGGATCTTCCAACAGCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGT
TGCTAAGGCCAATCGTTAAGGGATCTCCCTTTCCTCTAAGTTTGCATTATATCAAAGNGTTTTTGTGTTG
TTTCCATTAGCTTTGGATATGTTTCAGATGATCTCTCTATCTTTAATGAAATTTTGACGCTTATAATCGA
CTTGGGATCTTGATCATCAAACGGTTTCATATTTAAAATTATTTCATCT
>gi|3449588|gb|AI099849.1|AI099849 34002 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128L9XP 3', mRNA sequence
AGGAATCATTAAGCTTTTNNCCCCCNAGCTCANCGAAGANNTCAAGCTNTCTTCAAGAAGGTATTGGAGG
GNGCACCCTAGTTTTTGTTCCNCAGGCTCAGTGACTTCCAATTCTTTGTTGGGGAGGGTATGCATGATGA
CAGCACNNTGGTCTTTGCTACTACAAGGANGGTTCANCTAACCCAACATTTTTGTACTCGCTCATGGTTT
GAAGGAGGTCAAGTGCTGAGAGAGAAGCTCTCGTTGGGTTACTGTGGTCGGTCGCAGCGACTCTCTAAGT
TTATGTTTCTTTATATTGTCCTGTGTTTCGTCGTCGTCCCCTATTAAAATTACCTNCCAGTTTACTTTTC
TCTCTTCTTGTTTTCTGTGTTGGAAGATTCTCAAGTTATTTATTCCGCAAAAAACGGTTTATCATTTACA
ATTAGTTGAATTTTGGTCGTTACTTTTTGTGT
>gi|3449587|gb|AI099848.1|AI099848 34001 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128L23XP 3', mRNA sequence
CCCCCATCGTGCTANTGGCAGNCACTTGGAAAAGCCTATTCTCGNGNGTATGCTGCTTCCCTGCGCCTTG
GGTCCGTCCTCCAAGTTCTGGCCCACCACAGGGCGTGTGGACAATGTATATGGAGACAGGAAACTGGTGT
GCACTCTCCTCCCNGNGGNAGAACAAGTCGCAGCTGCNGTGTCTGCTTGATTACTGCTCTGTCCCATTGT
GTTGTGTCCCTTTCTCTCACCACGCACTCTTCTCTTTCACATTCTGTCCATAGTGTTCTCATTATACGCT
TTCTGTCTCTTACTCTNTTATTTCATTCGAATACA
>gi|3449586|gb|AI099847.1|AI099847 34000 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128K22XP 3', mRNA sequence
CCCNCCTTTTGNTCACCAGGCGTTGCAGGTTTCCTCGTGGANGCTTGGCTACTCNATGTCGAGGATTGGA
GGAAATGGAAATGATNNTGGATGGNTTTATGAATNTGGTTTACTAAGTTGTGGTGAAGAATGCTTGTAAT
TATGCTATGACGACTACAGGNTTGATGAGCCACATCTCGTTGCTTCTCAATCACTATGTTTTCTTAATGT
TCACAACTTTGCTTGTGTCAAAATAAAGTCACATCATTACAAACATCTAAATCGCATCTTAGCATCACAT
GACATCACTTCTAAATCGTGTTGTCGACCATGAGTCATCGGGTGTGTTCGTCTTTTTTTCTTTCATTTGG
ATGCAATATCTTGCATGTTGTTTCTATTTGCTAAATCAGTAAGCGAGTTTGGTTGCAAAATAAGTTGTAT
AAATAACTTGAATTTTTGTGCAAAAAGATTGATCCGATGCTGNNTAC
>gi|3449585|gb|AI099846.1|AI099846 33999 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128I4XP 3', mRNA sequence
TCCGTGCACAAGGTTTTTGCGCCCTTAGCAAGGGAATAGCTCTTCTCAAGCTAACCCTAACGTCCATCTT
CCTCNTGTCGTCTACTCCTTCGCNTTTGGGATATCGAGTCCCATAGGTGTCGGGATTGGCATAGGAATCA
ATGCCACTAGCCCAAGGAGCTGGTGGTGACTGGACCTACGCGATCTCTATGGGCCTTGCGTGTGGGGTTT
TTGTGTACGTTGCGGTTAACCATCTCATCTCAAAAGGGTATAAGCCTCGTGAGGAATGTTACTTCGACAA
GCCAATCTACAAGTTTATTGCCGTCTTCCTCGGTGTTGCTTTGCTCTCTGTTGTAATGATTTGGGATTGA
TTTTTGGTGATATATACTTAGTTTCAATAATTAGTTTTTTTTTCCCAATCCCTTTGTTCATGTTCTTCGT
TTTTATTAATTTTGCAGAATTTCACAATTCAATGTAACNGTTGTCAAAAAAGAATGTAAANATTTATGT
>gi|3449584|gb|AI099845.1|AI099845 33998 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128E15XP 3', mRNA sequence
AAGACACCGACCACACTTGTCCAGGNCTTTCCCCGGTCACAGCTTTTATAGTCCCAGAAGAACCTNCCAA
GGGGGANCCTNCCAAAGGGGAACCTGCCAAGGGGAAGNGCAGCGAAGCCCCCGNGGCCAAGGNGGNTTTT
GCAATCAAGGAGGCTTTTCGCAGTCAAAGAGGCGGCCTAATCAGCTCNGCTTCAGCNGNTNAAAGAGACC
CGAATTTTTAAGTGTNCTTCAAGAATTTGAACAAATCATGGAGAGTTAGTGTTTCTCACTGCTCTAACTA
TCATGTATTATCTACCTACCACTTGTTGCTGCTTGTTTTACCTGTAATAAGATATCAATATCATCCTCTT
CCTNT
>gi|3449583|gb|AI099844.1|AI099844 33997 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128D24XP 3', mRNA sequence
TTGCNAATGATGTTGAACCAACAGCNGGCNACNACAACNATCAACNACAAGCTGCAGCTCATGGTGGCTA
TGGCGGTGGTCACGGTGGCGACATNTACCATCCGATGATGTACGCTCGGCCTTATCCTGCAGTTAATTAT
GCTCACCCTCCACCAATGCCGCCTCCTCACTCGGATTCTTATACTCATATGTTCAGCGATGAGAATCCAG
GTAGTTGTNGTATTATGTGATCATCTTTTGTAATGTTATTTAGAATATGGACATGTATGCTTGTCTTNGT
CTTATGTTTTTTTTTTTGGGG
>gi|3449582|gb|AI099843.1|AI099843 33996 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128B7XP 3', mRNA sequence
TGGAAGNGTTGGAGAGTTTAGTGAGGCTNAAGCCAGCNGAGCCAGAGATGTTCNAGTTAAAAGCNATCGA
GNCAAAAGTGGAAGCNAGAGAGATTGGAAAGGATTGTGAAAAGCGANAAAGGAGAAAACNGAAGAGGAAT
ACGCAAGTAACTATTTGAAACTGAGGCTGAGCGAGGCGGAGGCAGAGAAAGAGTATCTGTTTGAAAAGAT
AAAAGNGCAGGAAAGTGGTGGGAATGGTGGTGAAGCGTCACAAGCAGTGATGTACTCAAAGATCAGAGAA
ATGCTGCATGGATACAATGCATCGTCGCCAAGGGTAGATCCAAGATCAAACCAGCGAAATCCTTTCAGAT
CCAATCCTTAGATGTTTGTATTGTCTCTCTTTGTTTGTATT
>gi|3449581|gb|AI099842.1|AI099842 33995 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128A16XP 3', mRNA sequence
TCTGGCCCGGCCAATTCTCCCGTNATTCAACGGGGNCCAATGGGTTTTTGGGCCCATGGGTGGGNAGCAA
AATCCCGGNTCCCTACAAAGTTTGTGATAGGGGGGCTTGATCTGGTCTACTATATGCCTGGTGTGAAGGN
ATATATACATGGTCCCCNGTTTAAGGAAGATGTGCCTTTGCTTGAAGAGCCTGTGGTCATGGAAGGNGTG
GCTCACTTCATTAACCAAGAAAAGCCTCAGGGGATTCTCCAAATTATCCTTGATTTCATCTCCAAATTCT
AATGTTGCTTTCCCTTAAATTACTCTTTTAATCAAGTTCCATAATAAGTTGAATTATGAGGATATACATC
CTCATGTATGGTTGTATCATCCTATAACCTATATAATCTATGTATGGAT
>gi|3449580|gb|AI099841.1|AI099841 33994 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128A14XP 3', mRNA sequence
AATCCCGGTAAGTTCGATTGAAAAGAGTGNCNCTGGTCAGTCCCTCGNCAAGGCTGAGAAGTATCTCAAC
GACTACGNGTCGTCACACTCCACCGGTGCTGGTGGTCCTCCTCCTCCGACGNGTCAGGCTGAGCCAGCAA
GTCAGCCTGANCCGGCGGCTAAGAAAGACGATGAAGAGTCTGGTGGTGGGCTTGGGGGTTATGCCAAGAT
GGCTCANGGTTTCTTGAGGTGATTTGATCTTTAATTGTTGTTCATCATTTTCGTNATAATAAATTAAATA
ACTGGTATCGTTTGTGACTGGTTTATGTTGCTTCGTTTATGTTTATGGGGGGTGACGNGTGNGTGTGATA
ACTTCTGGTGATCATGAATCTAATCCATCTTTGTTGTGNTT
>gi|3449579|gb|AI099840.1|AI099840 33993 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127O21XP 3', mRNA sequence
TTTCCCGAAACAANTGGGATCCCTTGGTGTTNAATCGGAGTTTGGNGCACGGATTTGTGTNCCGTGAGCA
CGGNAACCACTCCNGGATACTACGATGGACGNTACTGGACAATGTGGAAGCTTCCATTGTNCGGATGCAC
CGACTCCGCTCAAGTNTTGAAGGAAGTTGANGAATGCAAGAAGGNGTACCCGGGCGCCTTCATTNGGATC
ATCGGATTCGACAACACCCGTCAAGTCCAATGCATCNGTTTCATTGCCTACAAGCCCCCAAGCTTCACCG
AAGCTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGCTCATTTCATTTCCTATTGTCTGTGTT
CTTTTTCTCTTTATGAGACAATTTCTATCGGNTTGTCAAATGTCTGATTTATGNATATGTGATTT
>gi|3449578|gb|AI099839.1|AI099839 33992 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127K5XP 3', mRNA sequence
TTTCCAANTCGGGGNGTTTTACAANTTCCATANCGGGTACTTAAGNTTTGGNGGTNCATGCCANTTAANC
TCATTGGCTGGGGAACTTCTGATGACGGCGAAGATTATTGGTTGCTTGCAAATCAAATGGANCCGAAGCT
GGGGTGATGATGGTTACTTCAAGATCAGGNGAGGAACGAACGAATGTGGCATTGAACAGAGTNTTGTAGC
TGGTTTACCTTCAGNGAAGAACGTATTTAAAGGTATTACCACTTCAGATGATCTTCTGGTTTCCTCAGTC
TAAACAAGACGATGTGTCCCTACTTCTGTAATATATCATTTGCAACTGTGTTGTAAGTTTAATATACCAT
TGAAAGAATCACCTTCAATC
>gi|3449577|gb|AI099838.1|AI099838 33991 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127K23XP 3', mRNA sequence
CCGCTGGTTGGGGCTTCCGGCGGNGTTNCATTGACCCCNAGCCGTTNCTTTTCGGACCCACCCTTCGTAA
GCTGGACGTGGNCCCANCCANTGGGTTTTACTGGNCCTGGGNCCCTCTTTATTGGNTGGGTGNACTCNNC
CGGATTTAATTCTACGACTTTGTCTTCNTCCGATGGAAAATGCCCCACGAGCAATTGCCTCCCACCGATT
TACTGAAGACGTCAAATTCAACGTTGTTAATCTGATGAATTTTTCGTGATTTGCTTTTTTAATTTGCATC
GTAATGGGTTTCTGGCCGTTGGATCATTTTTAGATGAATCTTTGTCTATTGATTGATCATTTATGTGTCT
TTGGGTTTGTTGTTGGAGTTGTAATATCTCTGGAAGGCTTTTGTGCAATTGTATTGTACGGTTTAATAAC
TATAATTGAGAAAACCAGGGTATGTGNNTT
>gi|3449576|gb|AI099837.1|AI099837 33990 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127G15XP 3', mRNA sequence
TTCCGAGAGNTTTGAAGAATTGGGGAGTNGAGTTTNCCAAGAANCCCAAACGATGGAAAAGNTTGAAGAN
TATAGCCTTCATTAAGGATCCTGATGGCTACTGGATCGAGATCTTTGATCTCAAGACTATCGGAACTACT
ACCGTAAACGCNGCTTGATCTCAAGACTATCGGAANTACTACCGTAAACGCAGCTTGATCTCAAGACTAT
CGGGACTNCTCCCGGAAACGCAGCTTGAGGAAGTAGCGATTGCGCTATTTGTGTTCTTTTGCTCATTCCA
CCCGAGTGTGTGCATACCCTTAAAGAATTTTCATGTTTCATCGAATAATCCCNACCCGATGGTCGTTGTT
TATCAATGTGGTCTGTTTCTTG
>gi|3449575|gb|AI099836.1|AI099836 33989 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127B23XP 3', mRNA sequence
GTGGAATTTANCCGNGGGAATCGCACTTTGGGAAGTTATAGATCTGNCGAATCGCATTTGAATTCGAGTC
GATCGNATCTATGCCTGAGACGTATTTGGAGAAACTANGNGGGATTAATTCTGATTGGCCGTTAACGNCG
ATNNTGTTGAACGCGGTGGGAGATATGGTTTATGTACATGGTGCGGCGGAGAACGGCGGAGAGATTGTTG
CGGCGGAGATTGAAGGAGGAAAGCTTTGTAAGTGGAGGACTTTGCCAAACGCAGNCGCTACTTGGAAAAA
AAGTCACGCGGCTGAGAGNGTAATCGTTGCGTGTTCAAACGTTGGTTTTAGCGATTTGAAACTTGCGTTT
AGGNATAATTTGAGTTTTCTCT
>gi|3449574|gb|AI099835.1|AI099835 33988 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127A13XP 3', mRNA sequence
CACGGNTTTGTGTACCNGTGAGCACGGAACCACTCCCCGGNTNCTTACGATGGCCGGTACTGGACAATGT
GGAAGCTTCCATTGTTTCGGATGCACCGACTCCGCTCAAGTGTTGAAGGAAGTTGAAGAATGCAAGAAGG
NGTACCCGGGCGCCTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAATGCATCAGTTTCAT
TGCCTACAAGCCCCCAAGCTTCACCGAAGCTTAATTTCTTTTCTAAAACATTCTTATGAATTATCTCTGC
TCATTTCATTTCCTATTGTCTGTGTTCTTTTTCTCTTTATGAGACAATTTCTATCGGACNGTCAAATGTC
TGATTTATGAATATGTNATTTATATATCCGTGCGTCTTNATTT
>gi|3449573|gb|AI099834.1|AI099834 33987 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126P22XP 3', mRNA sequence
ACCNAAGACGGATTCGTTGANTTCGATTGAATTCGNGAAANTTCTAGANCGACGCCGTTTTCTAGATCTG
NTAACGGAGGAGACAATGGATTGATGAAAGATGTGTTTAAGGTGATGGATAAAGACGGAGATGGGAGACT
GAGTTACGGNGATCTGAAGNGTTATATGGATTCGGCTGGTTTAGCTGTAACCGACGATGAAATCAAATCT
ATGATTCGATTAGCCGGTGGTGNTTTAAACGACGGAGTTTCGTTCGACGGTCTGCTTAAGATCTTTGGGT
GTTGAAAAAAAAGTTCGTTTTTTTTTGACACCGCACATTTTCCAACTTTATTTTGTTTCTCAGTTTTGTT
TGTTTGTTTGCAGAAGTGTATTTGTGTCCACCCCGATTTTGTTTTATGTTGTTATAAAAATGTGAGAAAA
CTAATGTTGGTACACT
>gi|3449572|gb|AI099833.1|AI099833 33986 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126K5XP 3', mRNA sequence
GAAGATCTGTTTGTTAGCGCAATGCCTTTGAATCACCCTTTCAGCCCAGAAAATAGCGTGCCANTCAAGC
CCTTACAAACTAGAAGCTGATGGACACAGCCCCTAGTTGACCTGATACCCTTCCTTGAATATGTTGCACG
TAACAGTCCAGCAGACATCAGACCGGTTCTGGCCTCTTTTGAGAGAAAAGATATTGCCAAAGAGTTCATT
GACAGGTCCATAGAGTATCAAAAGCGAAAGCAAGGACAACTGGGACAAGGTCGATTCTGGAGGCGTTAAA
GGATCTAAGATTTATGTATAGAGCGAGAGACAATTATATCATCATTGATGGTGCACACCATAAAATAGGA
ACATGAGCTACCGTTCTTCGCTATGGATTTATTAGGTAAAATCCGAATTAAAATACTGTCTTTGTCATC
>gi|3449571|gb|AI099832.1|AI099832 33985 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126J7XP 3', mRNA sequence
TGGATTCCCAGGATTCNAGGGTTTTTTTGGTCGCCCCTGTGCTTNCCACAGGTGNTCCCATAATGGCGGC
GATGGATCTTTTTGAAGGACGTGGTTTGGNNTGTTCANGCAAATCCAANTGATTTGTGCGGATTTGCTGC
ACCTCCTGCACTATCGAAGCTTAACGNGAAATTCCCCGGGCTTCATGTATATGCTGGAATTATTGATCCT
GAAGTCAATGAAAAGGGGTACATAATCCCTGGGCTTGGAGACGCTGGAGACCGCAGTTTCGGGACAGAAA
CACATTGGGTGAAGTGATACTTGTATGAGTTGTTAAACTTTAACAGTCACAATCGTTAGATTATATATTG
CGTCTCTTGTACTTTGTTTTTGATGTGTGATTTCAGGTTCTTGAGAGGGTTTCGATAAAGAGTCAAAAGT
TCACAAACAAGAAAAACTGAATTCCTCATTATTACAAAACAGAGAACAAACTTGTCATCC
>gi|3449570|gb|AI099831.1|AI099831 33984 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126J3XP 3', mRNA sequence
TTGTGAATNTGAAGGTGGTNGCTGGANTTTCNCCNCCNGTTTNAAGGNNCGGTTGGATTGTGCTTTGGAN
ACGNTGAAAAGCGGAAGGGATTATGGCTTTGGTATAAGGGTTTTATCCCGACGGTTTCGAGACCAAGCAC
CGTTCACGGTGGTTTTGGTTTGTTACGCTTGAACAAGTTAAGAAGTTGTTCAAGGACTATGACTTTTGAA
AAAAACAAGAGTTGAATTATGTTGAAGAAGATGAATGATGGTGGCGACAATAAGCTTCTCTTTTTTTCTG
GTTATAATTTTCTTTTGATTATTTGAGTAGTTTTAAATTGTCTCCCATTTGTTGGAATAGATCTATGATA
TGATAATTCTTCTCATGGAGAAGAAAGAAAGAAAGAAACAGTTCATTTCCCTCATTATTCAAGGCAGTGA
AATACTTAGATCCGTTCCTGTTAATTTTGAACTATGTAATATTCGTTTCTTTTTCTTGAAAGCTTTATTT
TTAGTC
>gi|3449569|gb|AI099830.1|AI099830 33983 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126J22XP 3', mRNA sequence
TCTGGNTCTAAAATNATTTNCACCAGAGGGGNCCCGGCNTTAGAAAGTNTGATNTGCCAAGGTCACGTGT
CAANGGAGAGGATCATGTTCAATTTTGGTTCTCATCTGTTGATTCATGATCGGTCAGATAAATGTTTGTT
GTGGTATTTATGTCTCTTGTCGGAAGCAATTCTGATGGGGTNCCAAGGCAACAGAGAAGAGAAGAAAGCT
TTAATTGAAATGTTCATATGCCTTACTAATCCCCAGAATTAAATGTGGTGGAGAAACCANATTCATTAAG
TATGACAAACAGAGACCACATTAAACAGTTACTTGACGTCT
>gi|3449568|gb|AI099829.1|AI099829 33982 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126J12XP 3', mRNA sequence
CTTTTACCCCATTATGAGGTGTGATGNCGCATNCAGNAGGCCTTNTCCGGTACCATGTNCCCAGTGGTGG
ACCACATGTCCCCTGGATCGCCCGACAGAATGAGCAAGAGATCACTGCTTTGGCTCCAAGCAGCATGAAA
GATCCAAAGTCGTTGCCCCTCCAGAGAGGAAATACTCTGTCTGGATTGGAGGGTCCATCTTGGCCTCCCT
CAGTACCTTCCAGCAGATGTGGATCGCAAAGGCAGAGTATGACGAGTCAGGTCCATCGATTGTTCACAGG
AAGTGCTTCTGAGTTCAAAGTTGATCATTTTTCAGAGAAGAAGCACCGCCAGGGTTTTTCCGACCATTTC
TCAAGCCGGGTTTTTAATCTTCCGTTATTCTGCTCTTTGTTTTTGTTCTCTTATGTTTTGAAATTCATGC
CAAATACATTTTCATGGATTTATGGTAATCTGTTTGTAGTATGGTTTAAAATCTAATGCAACTGTGTTTT
TGAGTGAATAAGT
>gi|3449567|gb|AI099828.1|AI099828 33981 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126I6XP 3', mRNA sequence
TNTTTAATGTCNGCNATTCCAGCTGGACCAGCTTGTGAGAAGCCNCATGAATTCCATTNGATCCCAGCCC
GAGCCATCTCTGGNGCAACGACAACGACAACAACNACACCATGATCTGAATCTGAATCATCATCCTCTCA
AAGAAGGACAACAATCCAAAACAAGGGCAGGCTTTTTACAACGCATTCACTCAAAACTCGCTGGTGGACA
GATTTTAGCCATGTGCGTATGCGTTTGCCCTTTTGTTAAATAAAAAAACTATTTGTTTTGTTTGTTTGAC
TTGATATCTTTTTTTGGGATTGAGGATTGAGAGAGATAGAGNGATTTTACAAACTTTCTCTCTTTCTCTC
TTTCTCTCTTTCTCATGGATAATTCGTGTCTCTTTGATTTGTCTAAGGTTTGTCTTTGTTTGTTAGGAAG
TGGTCTNTATGAACGAAAAATTTGTGT
>gi|3449566|gb|AI099827.1|AI099827 33980 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126I13XP 3', mRNA sequence
CGGAGTCTTGCCTTTCCNGCTCAATTCTGNCCATGNCCTTGNGGATTCCGGCTTNCCTTTTCTGCCACAA
GNCGATATGCGATGGAGATGGCCGTTGTCCTGGTTGCAGAAAGCCTTATGAAAGGAACACAATCAAGTTT
GAAGCTNGTGTTCAAGGTGGTGGTCTGACTATTCGGCTTGCTCGTTCGTCTAGCATGTTTTGCNGGTCAT
GAAGAAAGGATGTGTGGCTTTTCTCGGCCTGTGTCTGTTTGTTTTCTCTCTTCTTCATTGTTTTCCTCGC
ATGTTCTACGTTTTTCNCCTGTCTTTAAAACTCTTTAGATATGGGTATAGGGATTTGTCTTTTGGCAACT
GAGAACTATGTTCTATGTTCTTCTATGTCAATGACTCTTCTTCATCTGAAACATGTGGTGGTGGTGGTGG
TGGTTATGTAGAGTGGTGTGTGAGTNCATAAGGTGGTACNCGAATTTCAAATACATAAAAGTTGCTAT
>gi|3449565|gb|AI099826.1|AI099826 33979 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126H7XP 3', mRNA sequence
TTTTTCCCTAGGCTTGNGACCCCCAGGTTNGATTTTGGGGNGGCCCTTTAGGCCTTCCCCCCAGGAACTT
GGGGGGAGGCCCAAGGGAGGTTGGGNATTTTGCCAGNCNGNTTCCNNGGGTNCATNGCCGGGGTTGTTCN
TGGGGTGGTTTTTTNANGGGNGGGGGGCCGTGGCCTAAGGAAGCTGAATGTTGGTNGCCATTAGTATAGA
TGGCTGCAAAAAATCTCTCTGTTTTTANCTTTACTTGAAATGTTAACGGGGCTGATTAAAATGGGTCTTT
CTTTTTATCTTTTTATATTTCCACAATCTCTCACGAAAGCCCTCTGAATGGAGAAAGTGAATTGTAGAAT
GTTTAGATGGTGAAAGAGAGACTTGCAGCTCTGTACTCTTTGCTTTATAAAACGATTTAGTTTTCTTTTC
TCAGT
>gi|3449564|gb|AI099825.1|AI099825 33978 Lambda-PRL2 Arabidopsis thaliana cDNA clone 126F23XP 3', mRNA sequence
CGGCTCTAGAGNTGGAACCGGGGNGTTTCAAAACATTTGACTTGAGCTACTTCACGCTAGTGGCTAAGAG
AAGAGGCCTTTTCCCAGTCGGATGCTGCTCTACTCGACAACTCCCAAGACTAGGGCTTATGTCTTGCAAC
AGATAAGAACTCATGGGTCAATGTTCTTTAACGACTTTGGTGTCTCTATGGTGAAAATGGGTCGGACTGG
AGTTCTTACGGGTAAGGCCGGGGAGATCCGTAAGACGTGTCGGTCTGCTAATTAAGAGATATAGAAATGA
AAATATCTCAATATATGTGAGTTTGATTATTATTGTTTGCTTCTTTTATTTTGTTGTCATCCCTATATTA
AATGTGATTGTTTTCTTGGGTATTGTTTCTTGGGAATAAGCTGTATCTAAAATTTATAAAAGTCTTGAAA
GTTCAGAATGTTNTTNTT
>gi|3449563|gb|AI099824.1|AI099824 33977 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125O9XP 3', mRNA sequence
ACCTAAGGGNGCTTTCTTAGGCTGGAATCTTTTTCCCNGGATCCATCGGGGCCNGCCCAAAAAAATGGGN
GTGTCCCCGAGGTCTTATGGGCGCAAAGAAGNTCTTTCAAGGTCGATCAATGGCAGCTTCGACACCAAAA
GGGTTTCTTGCNGTGTACGTTGGAGAAAGCCAGATGAAAAGATACATAGTGCCAGTCTCATATTTGAACC
AGCCTTCATTTCAAGCTTTGTTGAGTAAATCTGAACAAGAGTTTGGGTTTGATCATCCAATGGGCGGCTT
GACCATCCCTTGCCCTGTAGATACATTTATCACCGTCACTTCTCAGCTTCATTAGATCCAATTCACAAGG
ATCACATATATGTAACAATTTTTGAGGTCATTAATTAGATGTAGAAGATATTTAGAACCCAGCTGTGTAA
TTACTTACA
>gi|3449562|gb|AI099823.1|AI099823 33976 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125O6XP 3', mRNA sequence
TTGTTCAGTCACATNTACGGAGCTTGTCCATTTNAATTCCCNGATTCAACATCTCAAGGTANCTTANNCC
CTCCACTTGNTGTACNCTCTTTATAACCTGGAACCATCATTGATTCCACAGAATTGGTTAATCATTAACT
CTTTTTTTACATTTCTTCAGGATGCTATTGAGAAGCTTCTGATCTAAGGCATTCTCTGAATTGATTGCTC
GGTATGATGGGTCTCCGCGAATGGGAAGGCTTTGACTGAAGTTTTGTTTAGGCAACTACCAAATCAAAAA
CCGTCCATTATTCTACTATCTTCTCTTCAAGTTTGTAACGTAATTCACTTTTCTGCAACTTGGTTTCTTA
AGAATTTGTGTTGGTTTCTGGTTTTGGTTTGTAGCGAATCATTGTGTTATTTATAAGAACTTGTTTTGAT
>gi|3449561|gb|AI099822.1|AI099822 33975 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125O16XP 3', mRNA sequence
GNTCACTTGGGATGGANTTCCGCCGTTGGAGANTTTTTNCCCNGNTTTTCCCGATGATCTGTTTGCCCAT
TTTTTTGCTGATCCAGTNGCCGANTCGAAAAGTNCTNTTGCGAGGATTGGGGGNATTGGGATGGAGATCG
GCGAGGAGGTGAAGAGGGAGAGAGTGGAGAAGGTGGTTAAAGAGCTCATGGACGGAGAGAAGGGAAAGAG
GTTAAGAGAGAAGGTGGTGGAGTGGCGGCGCTTGGCGGAAGAAGCTTCGGCGCCACCGTTGGGATCATCG
TACGTGAATTTTGAAACGGTGGTTAATAAAGTCCTTACATGTCACACGATTAGATCGACCTAATTGGGCT
TTCCGTATCCAAATAGGCCCATTAGAAAAGGCCTGTTTGTTTCCACTATCATTTGGGCTGGCTTTAATGA
CAATTTTAAAAGATGTACTTACAAGTTGCAATAATCTTTAGTGTTCTTCTC
>gi|3449560|gb|AI099821.1|AI099821 33974 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125N6XP 3', mRNA sequence
TGGATTTTAGGGGCCANCATTTCGGGNTTCTTNCCGTTTGGGTCTNGACGANAGGATATGTCCCGGGATA
TCGATGGGGATGGCTNCTGTAGAATTGGGACTCTTGAACTTACTTTACTTCTTCGACTGGAAGTTGCCTG
ATGGGATGACACATAAAGATATCGATACTGATGAAGTTGGCACTCTTACAATCGCCAAGAAAGTACCNCT
AAAACTTCTTCCNGTTCGATTTCAGTGGTCAAACCAAACTCCAAACTTTGAAGATGTTTTGAATAAAAAT
ACTATGCAAAGTATGTAACCCTAGCTTCTCTAATGTATGTGAAGTACGTTTTCCNGTAAAATACTNGTTA
AAACTTTCATATCTTT
>gi|3449559|gb|AI099820.1|AI099820 33973 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125M17XP 3', mRNA sequence
GGTTNTTNCCNACAGGNTGGTTAATGGGAGGAAANGGCCAANTTNTGGATGGAGACAATGGATTCGTTTA
CNCCCATAAGGATCTTCCTGTCTTACAAAGGACAGAGGCTGTTGAGAATGGAATTTAGTTCTCTCTTTCT
CTGCTGATGTCATATTATGTTTTACAATTATGATTGAAGTTTTNCCCCCTTTTACATNGGATATAGTGTT
CCTTGAGGTTTGTACCNTCATANGAAGATCTCATTACTTAAGTGGTCTTTGATAATAGTGAAATGTTTNG
CNGCTTCTCTTCATGTCAAAAAAGCTCCATACATGTCCACAACCTTTGATTTACCACAACTATTTGTATC
ATTTCTCCATGCNGAATAAGTTATATTTTTTCT
>gi|3449558|gb|AI099819.1|AI099819 33972 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125L6XP 3', mRNA sequence
CGGCCTTGCCCCCCCTTNTTNTTGGCAACANTTNTNCCTTACCNTCNTTGNCAACCAGGNTTNCCCCNTT
GTGNCCCATCAGCTCGCACACGNCATCGACCAGNCCATCGTTAAGAAGATGGCTAAGGCCCAGGCCTACT
TCTTCAAGGAGTTCACTAGGGCAATCCAGATCTTATCCGAGAACAACCCCTTGACTGGCTCTAAGGGTGA
GATCAGGAAGCAATGTAATCTCGCAAACAAGAACCATTGAAGTTGGAAAAAGTGAGAAAGACAGGGGCTC
TGGTGTGTTGAGTTCTCTGCTTGGTACGAACCAAGATGAATAAAAAAATCTTTTAAGTTAAATCAAAGAA
AGGGTGATGATGAATACATCATGGTAGTGACCACCTCCTTCTTTTGTGTGTTCAGCCTTAATGCTTTAAT
TATGATGTTAGTGGCTTTGAGTTNTTT
>gi|3449557|gb|AI099818.1|AI099818 33971 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125K7XP 3', mRNA sequence
CCCNTCGTNATNCTCTTCGGCGGACANTCTCTTAATTCGCGGAGCCATCGCCCTGCACTCGTCGGAACTG
CATTTCCGATCCTCTTCAAACGCAAAGACACGTGTCCGGAATGTGATGGAGCAGGATTTGTGAGGAAAGG
AGGAGTGACTCTGAGAGCCAACGCCGCACGGAAGGATCTTCCTCAGATCGTTTGTGCTAATTGCAATGGA
CTCGGAAAGCTTAACCAGATTGATAAATCATAAGTCTTCTTCATATATATGTAAAAAGCTCCATTTCTCA
TTCCTCTTCTTATCTACAATATACCTCTGTAAGAGTAGATAGCTTCGAATGATCAATGGTTGCTTGGAGA
TGGATGGATATATATATACAATTGCTTTTTT
>gi|3449556|gb|AI099817.1|AI099817 33970 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125K4XP 3', mRNA sequence
GATAGTATGCTCGCANGGACGAGGATTACGATTCAATGCTTGGGATTNCCCTTGAAACTCCACCGGAGTT
GATTCTTCCCGACNATGTCTTACCAGGTGGTAAACCCGTCGCCAAGGTTCCGTCTACTCAGTACTTCTAA
TTCCAATCTCAGGTTGTTTTTGTGTGTTGAAATCATTTCAAGACAGGATTGATTCTCTGGAAGGTCAAGA
GAGATATTATTTTGGTTTTAACTTTTCTTCCGAGCAAGCAGGAGATTTATCATCCTTGCTCAATAATGTA
TGGTTGCATTATGAAGTCATTTCTTC
>gi|3449555|gb|AI099816.1|AI099816 33969 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125K13XP 3', mRNA sequence
CGGTGCTNTTCTAAACCCAGNTTTTCGATTAATCNATCCCGTTCCTCGANGACGGAGGAGAGATTTGAGG
AAAGTGCTGAGATTCGCAAATGCTTGTGGNGCNATCACAACGNCCANAAAAGGAGCCATTCCAGCTCTTC
CCTCAGATGCTGAAGTTCGGNGCTTTCTCGAAAAGAAATAGAAACANAACAACTCAAGCTTCTATTACGT
AATCTGTTTCCGCGATTATCTTCTCTTTTTGTATTCTTGTTTTCGGATGGTTGAATCGAGAAGAGAAACA
AATTCGGNNTTCCGCTCTGTTTTTGTTTCTCTTCTTCAAATGTAATGATTTAGAAAAGACGTATGTTGCN
ATTTAAGGCTTNACTTGCTNATAAAATGATAAGGTTTTTCCAAGTTTAAC
>gi|3449554|gb|AI099815.1|AI099815 33968 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125G6XP 3', mRNA sequence
CCGTTAAACCANCGGGGNTACGAACCCNCTTTNTAANCGNCGCGTTAAACTCTTTGTTTTCAAAAGTGGT
GAAGTTAGANGCCCATTTTTTTGGAGTTTATCNCGGGCCTAAGTTTGGGCCTAACACGNTGNCCCGGTGG
GTCGTNGCTGAGTTTCACCAATATCGGAGCTNGCCTGAGCTGAAGGTTCGGAATTGCTTCATGGGTNGGG
AAAACGAAAAGAAGAAGGGGTGACTCAGATTTTNGCCTTTTTTAATCGTAAAAATTATTAGTATTATACT
TGTCAGTTTTTTTTTTTCCTTCTTTTTGTAAGTAATAATATATAGGGAAATGTAACTGAGGCCTGTGTTT
TTTCGTGTATATACCATGGTTTTCTCTCCAATACTATATTTTTGGTACATAATACTGGTGTTACAAAACC
TT
>gi|3449553|gb|AI099814.1|AI099814 33967 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125G4XP 3', mRNA sequence
CCTGGNGCCCTCTCTNTGGAGCTNTGGNGNNCATACCACAATGGGGGNGTTCTGGATTGCTGTGATGTTT
GTGAACCTTTGGTCCCATGGGAAAAATGCGTCAAGATAACTCCGGCTAAAGCAGGGAGCATCCNNGCAGT
ATAAATGCCCCGCNTGCTGTGCAAAGAAAGGAAGACAGTGATGCTGATCAATTGATGATGATGATGATGA
TGATCTCTCAGAGAGACTCTGGTTCTCATGTTTTAATCAATATGTTAATCAACTTTTTTTCTTTTCTTCT
CTTTTTTTCTTTAACCTTCTTAATTTTAAAGCTTTCAAAACTCTCTCTTTAGATCTCAAGAAAGGGATTT
CAAGAAGTTGAGGGAGAGAGTAGCAAACTGTTTGAATAATATTATTATTATTCATATT
>gi|3449552|gb|AI099813.1|AI099813 33966 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125G23XP 3', mRNA sequence
GGGTTCCTTCCCGGAAAGCNGCTTCTGCTCTGGTGCTTGCTCAGCNTTNTCTCCTTTNTCTGCCCCTAAN
TCTGGAATTGGAAGCAGTCACNGTTTTATACAAAAGCCGCANCAACCAANCGCAGCAGCANCCCTTCTCT
CGGTTGGTAGGATCGACAACAACAGGAAGACAGATTAATGGGTACTGAGTCATCGTTCGTTTGTTCTCTC
GAATTGGTTTTAGTCCCGATTAATTGGATCTTAATNACACATCTTATGTGGTTTGGGATCNTTATTGGAG
ATTTGAATGTGATATGTTCCCTTAAGAACGGGGTCGGGTTACATAAGCCAGATATGATTACACTGTGTTC
TTC
>gi|3449551|gb|AI099812.1|AI099812 33965 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125G20XP 3', mRNA sequence
AACCCAATTNCTTCCAGGTCCNTCGANTCGNCGAGGTGCTTNCAGATTTGAATATTTTCCANACCNTCTC
GNACTTCTACGTGCATGAACGTTGGGCATATTCACCGATATCTCTGGTGCACGACGCTTAGCCTTGACCN
GCGATGAGGCTCTCCTAGTTAAGTTCCAGAAGGCAGCAACTCCAAAAGCTGATTTGAAGACTAAGCTGAG
GATNTTCCCTTTCTACTGATTCACAACTCTTGTACCAAGAAAAAGTGTCAAAAATATGGCCTCTTGAATA
ATGGTTGAGACAATNCCAACCACTTGTGATTAGTTTGTGTGTTTTTTCTGGTATGATCAGTGTGTCACTG
TCATGTGTTTTTTGCTTTGTTTAAGGATTATGCTTGTGTNTNAATGANTTNTAT
>gi|3449550|gb|AI099811.1|AI099811 33964 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125F24XP 3', mRNA sequence
CCCGCATCGTCGGCCTAGGCGGCTTNAAACNGTTTAATCCNNTCCTTCCGNTGTTCAAATGGGGNATTCT
TCNGTTTANGATGAACACTNTTTTACATACATGATAAATATGTCTTTTTTNCTCCGGTTTCATATGTGAT
TTGTTTTGTTTTTCATCTCANCTGAGATGTGTATGATTTGTGATTTGATCTTGGCTATTTTATGAGGCTT
TGTCTAGAATATCTTTTGGTTGGACTCCCTTTTAAGTCAATCNAAAATAATAGGGGAGTTTCAACAATTA
CTATCATTGTAATACCTAAAGATTTGGATTTTCTTTACTATTACAATAAAAAGCTATC
>gi|3449549|gb|AI099810.1|AI099810 33963 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125E15XP 3', mRNA sequence
GGCAGNGAANTTGCCCGTGGTCACTTGACGTCCCNGCAACAATNGGAGAGAAAGATCATGACTGAATCTT
GCNAGCTAAGAAATTCTACAGNGCTGAAGAGCNTCATCAACAGTATCTGTCAAAAGGTGGGCNGTTTGGC
CAAGGGCAATCCACTGCCAAAGGCTGCAACGACCCAATCCGCTGTTACGGTTAATAAGCTGCTTTCCTCT
GTCCCTCTCCGAAAACAGAGGACTTAGCATCAAAGGACTTGTGTGTCAAATAGATTGTGTAAAACTTTGA
CTAAGTTGTTCACACNCTATGTAACTACTTCTTTGGAATTTCATTCGCAATGTTGTAATATTGATGTTAT
ACTCTATAAACATAAACCAAATAATCATTNCGATC
>gi|3449548|gb|AI099809.1|AI099809 33962 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125D21XP 3', mRNA sequence
ATTTGCCGGATGGGTGCCTTTTTTTNCGCCCCNGAAGAAAATCCNTGCCAAAATTNGGAGAATTTCCAAG
TCCCCATGTTTATGACTTGTGGCCCTCCAAGCCTTAAGAGTAAAGAAACCCCATTGTCTATCTATCTATC
GCCTATGGTAAACTAATGCGGGTTTTAGCGAGGAGTCTTNGTTTTTGTAAGGCTGGTTTGNCTTTTGAGA
TATTGGTGGTAGCTTTTAGGACCTTTCCATATCAGTTAGGGGTACATGGTTCTGGTTCATGATCCTGTTT
CATCAGACTCTTAGGTGCTGTTTTGTTCAACTGAGATGTTAATCAAATCGGACCAACTTTATGTGTTTTG
GTTTAAGGTTTC
>gi|3449547|gb|AI099808.1|AI099808 33961 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125D20XP 3', mRNA sequence
TTTAGNCGGTTTAGGNTGTTTCNCCGGTGTATTGGTAAACCCCGTGGTATTGCGTTTTAAGNTGGTCTAG
GCGNACCCGGAGTGGTTTAGNTGGAGTTGGTGGTCNCCGGTAAGGCTGNTGGTATNGNTGTTGGTGGTGG
TATCGGTGGTGGACACGGCGTGGTCGGTGGTGTGATCGATCCACATCCTTAATAGAGAGTATTTGTTGGT
TAGGGTTTTAATTAAGGAATAATTAATTAGTTTCGATGTTATTGTTGGTCTTTTAATTCTGTGATCATTA
GGGTGACTTTTGATCTATTTTCTAGTTTGGGCTTTTGTAACGTTTGCTTTGATTTCGGCCGTGGTGTTAT
GAAATGTGCGACTCTCTATG
>gi|3449546|gb|AI099807.1|AI099807 33960 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125D18XP 3', mRNA sequence
CCTTGNTCTTTCCCTGGCTCACNGCTACCAANGTTTCCGAGGTAANTACAGTTGGAGAAGGGATGCAACA
CAACCCGCGTCTAACTAAAGATAAAGAAACATTCAAAACCATTATGTCAAATCTGAATCTGTCGTATCCG
AAGATGATTGATGTTGCAGTACCAGCAAATATGGTCTGTGGGTTACAAGATGTGCCTTCTCAAGCCAACT
AAAAAAAACTCTTACATATAATGTTTGTCTTTTTATCGATGTCA
>gi|3449545|gb|AI099806.1|AI099806 33959 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125A9XP 3', mRNA sequence
GGNTNTTTCGTTGCNCCTCCNTGATTCCCCCAATGGGGAAAGTNCGTCCGTTACTTANAGAGCTTTGGTT
CTGGAGCTTTAACAAGGGCTCTTGCTGCTGACCCTCGGATCGAGATCTGTATGCTCCCTGTTGGTGATGG
AATCACTNTCTGCCGTCGGATCAGTTGATTTGACTCCTCCCTACTCTGAGTTTGTCCACAGTGGATTACT
TTCCATCTTCTTATACCTTTCAATCGCATTTTCACCAACCNCTAAAATGGACCTTTTTATGTATTTGTGT
TAAGTAATATCTCCATTGTCCTTGTTTTGCTTTCTTCTGAACAAAGAAATAATATGTNCCTTACTTTT
>gi|3449544|gb|AI099805.1|AI099805 33958 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125A6XP 3', mRNA sequence
GGATCCCCNCCATTTCCCGGGANCTTGTTTTCCNTTCCGGTCCGAAGGCCCGGTTTTTGGNTCCCCCTTA
GGNTTCCGAGAGGGCCTCCGCGCAAATGTTAAGANGCCCAGNCACGGACTTTGAGTTTTACAAGTGAAGA
GAAAGCAGAAGTGGAACCAGATTATGGCTGTTGTTAAAATTCCAGTGTGTTTTGAGAATTATTAAGGACA
TGGAATCAAATTTGCAGTTAAATTAAGAACTAAGTTGCATCTCCTAATTTCTGTAACTCGAGTTCACATT
TGTTTTTAGTCTATCAGCTTTTTACAGTTTAATGTATAAGAAAAACTGGGGATGGTGTCCTTAGAATTGC
CAGAGCATGGTNATAATT
>gi|3449543|gb|AI099804.1|AI099804 33957 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125A2XP 3', mRNA sequence
CTCTCCCTTATGNTCCCATGANGCTGNGAATCTTTTGTCTAAAAGGNAGNTGATGNCTATGATCGNTGAA
TGAAAAACCCTTTTTGGTTTGATTCGGATCGGNGTTTGACTAAAGTTGACCGTGAAAGACGAAACTTCGG
GGTTTTGTCCGACGAGAGATCCATCTCTAGTGATGTTCTTTTTGTTTTTGTATTTAGATTTGAAGTTTGA
TGTAAAGATACATGAGATTTTATGTATAATACGGACACATACACAA
>gi|3449542|gb|AI099803.1|AI099803 33956 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125A10XP 3', mRNA sequence
GGGCCAAGTTGAATTCCATGCCCAAAGNGTCCCCACATTTCATGACCTCTGATGGGGAGNATAANGCATG
GCAGGTCCTAGTTCCGAAGACNGTGCCTCACCTTTCCGATGCTATGCATGCTGCAGTGACCCGCCTCGGC
TAAACTAGCGNCCATACATTTTTTTGCTGTTTCTACAAATAAAATGGGACAAAAAAAAAGAACNCCGTTT
TTGTTNGCTTATATACTATGGTTTTTTTCTGATGGTACCATATGTTTCCTCATGTCTTTTGACTAAAGAT
GGTTGAACCAAAACCAAAGTGAGGATTGTGACATTGAGATCTACCGTTTCTAAGAAAATATTGGTTNCTT
T
>gi|3449541|gb|AI099802.1|AI099802 33955 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124P22XP 3', mRNA sequence
CCCCGCCCCGGGGNGGGGGGACCCNGTCTCCCCCGGAGGCCCCNGATTTTTTCCTTTGATTCATGGCCNA
CAGCTCATCTTCAATCAGCNNGCTGCAGCCCCCCACAAGTGAAAAGTCACAGTTGGCTAACTCCAAGATT
CTGGTCCTATGCATTGTGTTCAGGTTGCTCTGTTTAAAATTCAACTTAGTGCCCACCACCGGAATATAGT
GTGTATTATAGGCGAAGAAGGCTTCTTATCTTCCTCTATAACCAAGAAAAGAAAAAAGATACCCATTATG
AACATTGTTTTGTTGATGTTATTAGCTTCTTCTTCTTCTCCCTTCTGCATCAGAATGTGGTTTCATGTGA
GAAATCTTCTAATTTTATTTCACGTAATTCGTTCTTG
>gi|3449540|gb|AI099801.1|AI099801 33954 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124O5XP 3', mRNA sequence
GGAAATTTCCTGGGGAANTTTTNTCGCAACCAAGAACCTTGNAATCATGCCTGGACTCAACAAGTTCTTC
ACTGATCCTACATACTGAAACCATCTTTGCACACCGCTTTGTCGTATTGTTTCTGGAATTGAATCTCTTT
GTGATATAAACCCGCATTTGTCAATTTCACATTGTTGATGTATCCTCCNGCTGATGACACTTGTTAATGC
TGGGCTTATGTTGTCACTTTTAAGCTGAAAATTGTATGACTTGCTTATGGC
>gi|3449539|gb|AI099800.1|AI099800 33953 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124N3XP 3', mRNA sequence
ATTCNCCCNTTGGGNCGGNANAGCNAGATCAGTNTCAAGTTCNCCATCCAAGGCAAGTGTCTCCATCGAA
GTCGGATTCGACATCCTCGGATAATNGCCCNGGTGGGAAAAAGGGATTAGTAGCCTATGATTAATGAATA
ATGATTCCCCTTAAGTTAAGTGTTTGTTCTTTTTACTGAGAAGAGATGGTAAAGAGAGTAAGTAGTTTAC
TTCTGTAAAACATAAGCATTGTCTTTTGCGTATGTTTGTTTGATTATGCTCCAAGATTGTTNAAAATTTC
TGTT
>gi|3449538|gb|AI099799.1|AI099799 33952 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124N17XP 3', mRNA sequence
CCCTATGCAGCTGGCTTNCATGGTGCGGCGGCGATGNCGTTCATTTTCGCCCCCCNTCGGAGGCNGTNTG
CACCAAAGCTGAGGAGAGCAGCAGCCATCCCTTTGTGGGTACATGNGGAACCCTCCCNTCCGCCAATACG
TTAGCTCCCCTAACGCAAGGAAAGTCTCCAACAGTTGCAAGATTCCTTCCCCAAGCTGTTAAGGAAATGT
TAATCATGATTAATTAGTGACAAGTTTCGCTGATTATAGTGGTTAATGCTGGTCTTATCTTCGTCAGTAC
TACTTAAAATAATAAATGAGTGATGATGATTGATGATTATCATCATCATGCTTGAATGTTATGTTNTCTA
TCTTATAAAATATGAAATATACTTTNG
>gi|3449537|gb|AI099798.1|AI099798 33951 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124K13XP 3', mRNA sequence
TTTTCGTCCCAAGAGGTNCCCTTTCTGTTANCCCTCNTCCTCCCCNAAGGCTTNCCCAAAANACTCACCA
AGTCACTGATGTCACTNTNGCTACGAAATTGCGTCAATAAATGTATGCNCGTTAATTTGTTTCATTTGTG
ATGTGTGGGGCTCTTTATCTATTATATGCATGTCACGTGTTTGNCATATTTGCAATGTATCATGTATGTG
GCTCTTTATCTATTATATGCATGTGTTTGTCAATTGTCATATTTGCGATGTATCATGTATGATGTATGTG
GGCTCTTTATTTATTATA
>gi|3449536|gb|AI099797.1|AI099797 33950 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124J13XP 3', mRNA sequence
GTACTCNNTTTTTNTCAACNAGTTGTGTTGGTCCTGCCTGACATNGTTGCACCACCTTNGAGACCAGTTG
GCTTTAAGTAACAATCCCTTATTGGATGAAATTGTCAGAAACCACTACCCTTCTTTTGCTCAACTCCAAT
CACTTTGCCACCCAATTTTATCTCATTCATTTTGCAAAAAAGATCAAAGAGAGAGAGAGAGAGAGAGAGA
GAAAGAAAAAAAGGAAAAAACCTTCCTCCGTTACAACCTCACAATTGCAACAAAGTTTCATATAAAAGAG
GACAGAAATTTCGCAGGTTCCTCCGTTGTCT
>gi|3449535|gb|AI099796.1|AI099796 33949 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124F4XP 3', mRNA sequence
TTTAATNCCCCTTCTTCCCANTTTGGGCCCCNTCGACTTTGGTTGGAGCTGAGTTTGCCNCAACTTCACG
GCCCANGGGNACNCCATCNCTGTCGGANTTCAACACGCGCTTGCCCCATTGNCCNCNGTGAAGGCAAGAG
TGAACAATGCTGGTGTGGNTAACGCTCTGATCCAACATGAGTGGCGTCCAAAGTCGTTCTTCACCGTTTC
TGGAGAGGTTGATTCTAAGGCGATCGATAAGAGTGCCAAGGTTGGGATTGCTCTCGCTCTCAAGCCCTGA
GAAGATACCNCCAAATGGGCCCTGAAGTGGGTAGAATAGGTGTTATTTCTTTTTCGTCTTCAAATCTTTG
GACAAATCGCTGTCTGGTTTGCTAAACAATCTTTCATTTGTTTTTTTTGTTCGGTGTTGGGATTTGTAGA
AAATAAAAGAGAAAAATACTATTGAAAGGATCGTCTTGACGAT
>gi|3449534|gb|AI099795.1|AI099795 33948 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124E5XP 3', mRNA sequence
TGGGACTNNGGGGTGGGNCCACTTAGTCGTTGTTGCACTTGCCGGACTTCATTCTACGGAGCCGTTCTTC
ATTCCGGNTCCTTACGTCCAGCTCCCACCACAGAAAGCTCCCCTTGANCAACCTNTAGCGTTTTAATTTG
CTTGGCTTGCTTTTTGTTGTGTGAAAATGTTTGGTCCTCGTTTCTTCCAAAAATGAATGATTGAATGTGG
NGAAAAAGATCAAAGTTGTACTTTGTGTTGGTTATAAATAAGAATTGTATATTTTCAAATTTTATATCTC
TGCCTTGTACTTTCTTGCATGTGTTAATGGCTAAAAATAACCGGTTTTAACTGTCC
>gi|3449533|gb|AI099794.1|AI099794 33947 Lambda-PRL2 Arabidopsis thaliana cDNA clone 124A19XP 3', mRNA sequence
CNGTGANTACGAAGTGTATTGACGGCCCCAANACGGTTTTCCGTGANGAGGCCTGCGATGATCTTGGAGG
TAGAATTCTGTGANCCTGACTTTCAAAAAGATGCCAACTAGNAGAANCNAGATTTTATGTCATGTGAATA
TGTGTTTGTATTTCTACAAGTCTTTGTAACCACTCCTTAATTTATGATATCTAGCTTCACTACTTAATCN
AGATTGATGTTATGGTTT
>gi|3449532|gb|AI099793.1|AI099793 33946 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123K7XP 3', mRNA sequence
GAGCATTGGGCTGGAGGCTTTTGNTGTNCCAGAGCCGTGTGGAGTCCTCACTACNAGTTTGGTCCGACAG
AGNTCGNTCCCTTTGAGAACNAGGACATAGGTGTTNTGNTATACACTAGGGTTCNCATTCCGTACCGTGC
CAAGAAGATTTTCCAGTGATGCCAACAATAGCATCTAGCTTTGNACTTAAACCGNTCAATTTCTTCGAAT
CGAACCCGGTACTTGGGATTTCACCTTTCTTCGAGAAAGACTTNCCAGTCTGTTAAACCAGATGCTTCAT
CTTATTCGACACTGTGCATTTTCAAATGTCATGTGTAGACTTTTCTGATTATAAATGTTGTGCATATTCT
ATTGATATATGTATATCAGTATATGAAATCAACATGCTCTTGATATTC
>gi|3449531|gb|AI099792.1|AI099792 33945 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123K6XP 3', mRNA sequence
TNTAAAAGTNTTTATTTTGTACTTTTGGAGAATNAGAANCNGAGTTGTTCTTGAAAGTTTTGGATTTTTN
ANTTTTTGTTTTGGGCGAGAGTTTTAACATTTTCCTTCTGTGTTTTTGATTTTCTTAATACTTTGGGAAG
TTTTGTATCGTTACTCTCACCTTTTTTTACCTACACTGCTCATTTGATAGGGNATTGTTTGGCTT
>gi|3449530|gb|AI099791.1|AI099791 33944 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123J11XP 3', mRNA sequence
ACATCTTCCAGTCANTCGTCCTGGCATGGNCCTCTCCTCAGAATCTTCCCCCGTGNGTTTCCTTCACCGT
ATACCCGCGAAACCCCTTGATCAGTTTTACAGTCNCGATNCCACCAACTGAAGANCATAGTTTCTACTGC
CTTGGTGTGATGATATGTCCAAATGCATCTTTATTTTTTACTTCTGCGGTTGGATCACACCTCTGTGTCG
TCCNTCCCAATAAATGGTGTTTGTTCCCAATCGCTAGACCCTTTATTATTGTCTTCNAAACTGANCAAGC
CAGGTTGATTATTCTTTTTGTAAGAGAAATTGAAATTCTTGTATAATTTATGAGATTTTNCATCTTTTTT
TTGGGGTACC
>gi|3449529|gb|AI099790.1|AI099790 33943 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123I7XP 3', mRNA sequence
GGATCCTTTNCGGCCTTGGCTTTCGAGCTTCCCAGGGNTGAAAACTTTTTANCTCAGATCTCCGACGNTG
GCNGTCTTCATGGTTCCTCGGTANAACAGCGATCCTTGACACTTGCGTCGCTTGTGCCGCTTTTCAAGGG
CATAAGCGTTGAGTCCAAGTCCAAAGGTATCATGACGTCAGACGCTGAGCTTTGGAACGGACGTTTCGCG
ATGCTCGGTTTGGTCGCGTTGGCGTTCACTGAGTTCGTCAAAGGTGGGACACTCGTCTAAGGAAAAGAGA
GCACGTTATGGGGAGGATGTTTTAATACGATTTTGCCCATGTAATTTCTCTGTAAAGTAATCTGTGTTAG
GCCTACTGTGTGTTTTATACATGTGTACTAAGTGACATTTTGAAACTTCGGGTTAAAAACACTTTAAAAT
T
>gi|3449528|gb|AI099789.1|AI099789 33942 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123I24XP 3', mRNA sequence
CCCTTCACACCGTTGGGGTTAACCGNTGGGGTGGAGGACCCGCACCNGCGTGGNGAAATGGTCTACGNTG
GGCCTGACGTCATTTGCTAAACTGATGGAGGTGACGTTGGANCCGCGTTCAGCTTCTTCAATCAAAGGCT
CTTTGTATGATGCCCAATCTCATTGGCAATGGCAATTTACCATTCTCAACTCCGGATACATCTTCAGTGG
TCAAGCCTGAGAACAATCCTCCACAGTAGGATTTCTGCAATAAAGAGTTTGTACAGCTAATCCAACTGTC
CAACATGGGTTTTTCTTCTGCTCTAATGACTCTGGTTTCTTCTCTCCTCTCTCACCCACTTGAAAGGTAA
AAAAGTGAAAAAGGCTTTGTAGATGGAATCAATGTAGGATTTGCAGTAGAGGGAAAAAAAATGTCAAAAA
GCTCAATTGATCAAGTATT
>gi|3449527|gb|AI099788.1|AI099788 33941 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123I21XP 3', mRNA sequence
AGTTGTCTTNGATCAAGCGATTCCCACTANTGGGANCCGACAAAGTTNTTCCCTCAGTCAGCAGAGTTCT
TGTNCGTCNTGAAGATCTTCCTATTAAATCCTCAGGTNGAGTATTGTTGCCTAANGCAGCTGTGAAGTTT
GAGAGTACCTAACAGGAGAGATTATATCTGTTGGTTCTGAGGTTGGACAACAAGTTGGACCTGGAAAGAG
GGTTTTGTTCTCTGATGTGAGCGCTTATGAGGTCGATTTGGGAACCGATGCTAGGCATTGCTTCTGTAAA
GAGAGTGACTTGTTGGCCCTCGTTGAGTGAAGTCTTGTCCAAGAGGGAGAGATTTGAAGATTTTACAAGT
TTTCTGTAATTTTCAGACAGCAATTGTTGTTTCTAGTTAATCCTTCAATTTAATATCAATTGAGATCACT
TTCAG
>gi|3449526|gb|AI099787.1|AI099787 33940 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123I18XP 3', mRNA sequence
AAGGCNGCAGANATAGCACAGNTTGAANCAAGGAACCTGTGATACAACTTATGACGGTAGATTATTAAGA
ACCTGATACATTGTTCCCTTTGGTATATCATTTTGCCTATGCAGTTGTGTGACTCTTACCGTTAGTTAGA
TAGGCATGGTTTTCAGCACGATGGAGGANCATCTTTGGGTTTAAAGGTTTTTCACACCNCTGTTTTGCTA
AAATATTCAGTTTCCATTTTATTCAGAGTCAGATAAGCAAAGACGTAAGTGTAGTTAGTCGAGATTTCTT
ACAAGTTTGTGTTGTATGNTCGTTTTAAGAGCAGCTGCAGACCAAAGTTCTTGCTTTAAAATTTCATATT
CAGTG
>gi|3449525|gb|AI099786.1|AI099786 33939 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123H3XP 3', mRNA sequence
CCTTGCCNGTTAAGNNGTCCTTAAGCTNTTNAATTTGGGGNTATNNTTGCGGNGGCCCNTTGATTTTTGC
CAAGGCNTTTGAATGTTCATTGGGNGCTCACTCTACGTGCTGGATCCACACCGNGGNGGACCAAGNGGAG
GACCTTGCAGAAGAACGACATCGCCGCTGCCATTCCAGGACCGACGTGTTTGATTTCCTTGTGGACATAA
TCCCGAGGGACGAGCTGAAAGAAGAAGGTTTAGGCGTGACCAAAGGGACCATACCATCGGTGGTGGGTTC
CCCGCCATACTATTACTTGCAACAACAGGGGATGATGCAACACTGGCCCCAGGAGTAACACCCTGATGAG
TCTTAAAACTTTTCCCCTTTCGTTTGTTTGGTTGTATCGTAGTAAGGTAGCTCTGCTCTGCTGGGAACCA
TTTCTATTGTGTTCTGTAATGACATGTTAGTATATCCCCAGTCTATATCTATGGCAATGCAGTTTCTGTT
>gi|3449524|gb|AI099785.1|AI099785 33938 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123H22XP 3', mRNA sequence
ATGTCCCNTAAACCNCCCTTTGNTTTTGACGTCNANCANCCGGTTTGGGAACCGGATCCTTAGGGNNGGG
GNTNCCATGTGCGTGTGGAGCCATNTGCCANCAGTCAAGNTGTGCTGAGGCGTTTAAACTCAGAAAGAAA
CAGAACGATGTGNTTAAGGCTGATNCTAAAGCCCAGAGGTGAGACTATCAGCACCAAGAGACAGCCTAAA
GGTCCTAAACCGGGTTTCATGGTTGAAGGTATGACATTGGAGACTGTCACTCCCATTCCTTACGATGTTG
TCAACGATCTCAAGGGTGGTTATTGAGTTGTTTCCATTTTATTATCATTCTCTACTCAGAATTTTTGCAC
TTGCTTTTTTAATTATGTTTTTGTATCAAACAAGACTGATTTATATACGATATGAGTTCAGATTTTGTTA
GG
>gi|3449523|gb|AI099784.1|AI099784 33937 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123E10XP 3', mRNA sequence
GNTTTAAGCTGACTTTAACTCGGCCGTTTCNCANCCANGAACCTTGTTGATTGATTCGTAATCACAACTC
GAGCNGCTACAGGGGATCAAAATCTTGCAAAACCNNTGACTCGCAAAATCAGGGGNGTTTCTTCGTCCTC
CCTGATCTCAACATGGCGCCATCCGAGGAAGAGATATTGTNCGGAACTAGCTAAAAACTGGCCTATNTGA
AGATTTGCGATCGAATTATAGTGAAGGGAAGAAGGGAGCTAGAGATGTCAACTAAGAAAAGTGAATGTAA
TAAGTGGTGTAATGAAACTCTCCCGTCACATTCTGGTTTTCCGTTTCCTTCTTTTTTTGGGGTAAAATGC
TNAATTACTTCTTGATTTTTTCTTAGGAAGAGGGTGAAAATTAGGTTTTT
>gi|3449522|gb|AI099783.1|AI099783 33936 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123D4XP 3', mRNA sequence
CCGTTAAGAATNCCCGNAGNGGNCCTTTGATTCCCAAGGTTCAGAGAGTACTCAATGATGTNCATTCTTC
AAAACATGTTACGCTGGTTTTGCTGGTTCCATGGGACGTGCCGGTGAGCGTCACGATGTTTGGAGCTGGT
CGTTTGAAAACTAAGTAAACCGGTTCGGTTCGGTTCAGTTTGGCTNGGTATCGTNTGCTTTGTTNTTGTA
ATTGTTGTAGAGTGAATAATTAAGGTATGAATAAAATAAGCCGACCTGTGGCTTACTCTGCATTGTATTT
TCATATTTGTGTAATCAGTCTGAATAATTCAGAGGTTTTCAATAAAATAAACTTCCTTTCC
>gi|3449521|gb|AI099782.1|AI099782 33935 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123D3XP 3', mRNA sequence
TCCCCCATTCGGATCCTGGAACCTNGTTAAAATTGCCTTTTCCGATTNCCCTTGCCAAGGGGGGTTGGGG
AACTTAAGGCTTCNTGGACCTCTGGCCTGCANCCTNTTGNGGGGACCGNNACCAATTCCGCTCATNCANG
TTCACACACGTNTCTATGNCCAGGTGTNTACATAGGCAACGTGAAAGTGTTAGTGAGGGCCACAGTTTGG
GAATGGACAGCTCAAAGGACATTGCAATGAAGCTGACAGTTAGAGCTGAAGACGTTTCTGTCGCCGAGGC
CATTCACGAGATTGTTGCCAGCGGCTAAAACCTCTTGCGTTTCTTCAGTATCAGAGAATGTCATCTATTC
CTGCTGCTAAACCTCAAAAATACATCAACTATTATAAATAGCATAGTATTACTTTCTTTCTTTTTTCCTT
GCATTATTACTGTCAAATACACTATGGAGGTTTTCTTTTTATTTTATGACGGTGCTTTTTGATTTCTC
>gi|3449520|gb|AI099781.1|AI099781 33934 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123C9XP 3', mRNA sequence
GTTCAAGCTTTTGAGTGGCCCNCCTTCTCACTGGCTGGAAGGTGAGACCCCGTGCCAATNTGGTGCTCAC
AGGGGGTCTTGCTGACCCACTTGGTCTAACCGAAGCAGGACTTCCNCCNTGCTCTTTGGTGTTTCCAAGG
ANTCTTGGCATCTGCTCTCAGCTTATATGGGNCCGAGCTCTTGGACTTGCACTTGAGAGGCCCAAAGAGT
NTTACCATGGACTGGCTTGAAGCCCATTGTAAGAAAGCTTCATCTGCTTAAGTCACCACCGAGTCCTGAG
TTGTCGCACTCTCTCGTGTTTCAACAAAAGTCATTCTCTTCCACACTGGATAGCTTTTTTTGTTTTTACC
TTCTATTGACAGAAGAAACATTTGTTCATGTAGAAATTGTTCCTGAGAAACACATGCTTGGTGCAAATTT
GCATTTCCGGGAAACTCGTGATAATAAATAAACAGTTGTATTCAGTTTGCGT
>gi|3449519|gb|AI099780.1|AI099780 33933 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123C7XP 3', mRNA sequence
CGCATCTTTNCGTCNCTCCNCTTNGGGCTGTTTGAGGANCTTGGCCTCTTTTCCATCNCAGNGCCTGNTC
NCCAACTGCGGAACTCGGGTTGATGGAAAANGTTCTTTCGACAAGTCAGGAGCCGATTATCTTACGAGCA
ATTTGGTGCATTTCTTGGAAATGTGAAGGATCTTAACGCCCACAAGCAAACAAGAGAAGAAACACTTAGG
AAAGCTGAAGAGATATTTGGAGGCGATAACAGAGATCTCTACGTCATATTCGAGGGCTTGATCACACGCA
ACGCTCACTAAGAGTTTGGCTTCTTCAGTTACACAAAGAACTTATATACTCGGAAACTCAGGATTCATCA
GTCTGCAACATTCAATTTCTTTTGTTTCCTTGGCTGTCAAGTAAGACCAAGTAAAACTGACAATTTGATT
GTATCATTTGTGCTCTCTCGTGTATCTATCTATCTCTCTCTTCTTGAATAAATTACATTTCATCATC
>gi|3449518|gb|AI099779.1|AI099779 33932 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123C1XP 3', mRNA sequence
GACAACGGAGGGGGCCCGGCNCAAGGGNGCCNGGTTTNCCAGTCGGTTCTGNTTCCCCCATATGCTTTCC
GGTTTCTGGACCAGCGGTTACAAATTTNGATATGTCNAGTTGAAGGAAGGCTTCCGGGTTAGCCAAGGAG
GATCAATCTACCATGCGACCATTCCGTGATGGAGCCCAGTGGTGGAGTTGCTAGGNTGTACCACGTTGGT
CCCGAAGGATGGACGAAACTATCAGGAGATGATGTTGGGGAGCTACACTACCATTACTACCCCGTGGCAC
CANTACCGCAGAACAAGTCATGGAGGAAGCAACAGCCGAATAAAAATCCTGTTTAGTTTTCTAATCGTTC
ACTCCCTTTCTTGTTGTTGCATTTTGTGGTAGTATATACTGAGTTGTCTCTAGCTGAAGCTTTGGTATTC
TATTTTACTGATCTGAAATGTTGCTCGCGGATTATTCTCTATAAGATTCTCTTTTTCTGC
>gi|3449517|gb|AI099778.1|AI099778 33931 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123B4XP 3', mRNA sequence
ACGTCCACCTTCAAGTNTNTCCGTGGCTTGACAGCGTCTCCTNGCGTTGGNTAATGGTGGGATTTTGNAC
ATAAGGTCGGAGAATTGGGCAAGATCANTATTTGGNGCNNCAATTCTATCCTTCGAGTTTACNCTTTCCT
CTACTTCGTACCGAGATGAATATCCACCACCAAAGAACNCTCTTATGTGCGGACGAGCTAAAGGCCGCCA
CACTAGNCCATTCTAAAAGGGATATTGGACGCAACGGCTCAACTGTTTTTTTAATCTTTGTTTTTTTAGA
TTGAATGATTTGAAATGTTTAGTATTGTCACGAGAGGGTGGCAAAGAGATGTGAGCTTCGTGGATTTATT
CACTACGGCACAAAAATTAGGAACAAGAAAAATTTGGAGCTTGACTTGAGCTTTCAACTTAGTTTTTATG
ACG
>gi|3449516|gb|AI099777.1|AI099777 33930 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123B2XP 3', mRNA sequence
CATTCNACCTTGNGGACCCCNTCCAGGCCGGAAGATCGCATCTAAGNTTTGACCNCGCTTCCAGAGGAAG
ATTGNGATTCAATCGCCCAAGCTATTGAATGGTTAGATTGGGATCANCTGGCTGAGGCAGATGAGTTCGA
GGATAAGATGAAGGNGCTCGAGTCTCTTTGCAACCCTATTATTGCAAGAATGTACCAAGGAGCTGGGCCT
GATATGGGTGGTGCAGGAGGAATGGATGACGACACACCTGCTGGTGGTAGCGGCGGTGCTGGCCCAAAGA
TTGAAGAAGTTGATTAAGCCTTTTGGCTTTTGTTTACTCTGTTTGCTTGAGATTCTAGTTGGTTTCTTGT
TCTTAGTTTTATCTTTCTATGTCACTCTGAAACTGGTGTGTGATCATTTTGATGTTTTAAGAATTTAGCT
TTACCGTT
>gi|3449515|gb|AI099776.1|AI099776 33929 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123B13XP 3', mRNA sequence
AGNCAAACAAGAAGGGANTCANAAGATAAGAANGAGGTGGGAGTTACGGTTCCTCCACCGCCAGNGAAAC
CAGAGCCTGGCGATTGTTGCGGTAGCGGTTGCNTCCGATNCGTTTGGGATGTTTATTACGATGAGCTCGA
AGATTNCNACAAGCAGCTTTCTGGAGAAACTAAATCAATTTGACTGATTTTNCCTCGCATTGTTAATGGA
GAAATTAAACATTTGTCTTTGTCGATTTGATGATACAGTGCTTTTGTTGAACAACATTTTNGATCTCTC
>gi|3449514|gb|AI099775.1|AI099775 33928 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123A9XP 3', mRNA sequence
CTTGGTANTTCCNCTGGTTTCTCAGGNCNCGGTGCGCTACTCATGCCATCTTNCAACATTCTTCAGCANG
CTTGNGACNCCGANCTTGAAGGCACGTTTAACACATTTAGGGAGGAATTCCGAGCAGTATGGGCGTAACT
CCAGCGAGATTTAGAGTAATCTTGTACCACCATGATCGTGTTCTGCTGAGGACATAACGCTGTAAAGACC
AAACTTACTGCCTTTCTCCAAGATAAACCCGGTTTCGTTAACACTGTACTATGGATGTTCAATCTGGATT
TGTTGCTCAATGACTGGGATCATCTGTTTTTTCTTTGATTTGAGATTTGAGCTCTGAGCTCTTTTTGCTA
GCAAAATCCTCTCTTTTTTTTGCTAAAGACTTGTAAAGCTAGCTTTGTTGTTCTTCGTTCTAACACAAAC
CCTTTGTGTAAAGTCCTAGAATCGTTTAAT
>gi|3449513|gb|AI099774.1|AI099774 33927 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123A5XP 3', mRNA sequence
GGGGATTCCTGGGGAAAANCCTTTCCCGNGAANCCNGGCCTNCCCCGTTCCATGGNCCCGTNCCCCAAGT
TTGGCCCATTANGGGCGGGTGGNCCACGTTNTGGNGNCCCGTAATCTGGTGTGCACTCTCCAACCGGCGA
ACGAAGAACAGGCTGCAGCTGCAGTGTCTGCTTAAATGAAGCCACTATGAAGCGATTCGCACTCGCACCA
AAACCCACAATGGGGCGATTCGGACTCATACCGGATCCAGAAACGTATCTTTACTGGCTTTTACTTCTCT
TCCCAGCCTCATCATCACTTTCACTTTCACTTCCTGTACAATGTACATACGTAGTCCTAAGTTCTTCCCT
CATTTATTTAATAAAATACATTTCTTTATGTTCCACTTTCTTATACGTATAACATTCCATTTGGATG
>gi|3449512|gb|AI099773.1|AI099773 33926 Lambda-PRL2 Arabidopsis thaliana cDNA clone 123A3XP 3', mRNA sequence
GGCCNACAACTTGGAACNAGTNACCTTACTTGGGATCGCNTACGATTGNNNCTAAGGACGCTCACGNTAT
CTNCATCNTGACCGAGTGGGATGAGTTCAAGAGATCTTTGATTTCCAGAAGATCTTTGACAACATGCAGA
AACCAGCTTTCGTGTTCGATGGAAGAAACATTATGAATCTGCAAAAGCTAAGGGAGATTGGTTGCATTGT
TTACGCCATTGTGTAAGCCTCTCGACGACTGGCTCAAGGACATGCCTGCCGTTGCCTAATGATGTTCATT
GCTGACTCTTTCGTCCTCCATCATTTGTGCTTTTTTTCTTCTTGTGGTTTGTCTTTAAGACTTGTTATAT
TTCTTACAATATGTTTGTTATGTTC
>gi|3449511|gb|AI099772.1|AI099772 33925 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122P7XP 3', mRNA sequence
CTCCACTTTGGAAATTTCCCCCAAGGNCAAGNCCTTTAGGGGTCCATTTGNGGNACATNTGGNGCAGGCT
GCTATTAGGGATTTTCAGGNAAGCTAGCGTCTATGGGGGGATACACATGCCGAAGCTATATGCAAAGACG
CAATACTGTGTCTCCTGTGCTATCCACTCTCATGTCGTTAGAGTCCGTTCCCGCACCAACCGCAGGGTTC
GTACTCCTCCACCTCGTTTCGCCAGACGCAAGGAGGATACTCCCAAGCCTGGGCAACCAGGACAGGCACC
TCGTCCTGCTGGACCTGGAAGCTCAGCTGCAGCTGCACCGCGTGTCTGAAGCCTTCAAGCAGAGCTTTCT
GTCTTGTTTTCCTATGTTCTTGTTACGTCTTTAAGGATGTTTGTCTCTGTTTAACATAGTTTTGCCATGT
GGATCTTGAATTCTGTCAAACTATTTCAATAGTTGATTCAACTTGTTTTTTTTTTTGTTCCTCT
>gi|3449510|gb|AI099771.1|AI099771 33924 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122P5XP 3', mRNA sequence
GTGGNGAATCCCCCCGTTTCAGGCTTTTTCCCGGAGTTTTCTTNTGGGGNGGNCCNANTNCTCGACAAGC
TTTTTNTGGAAGAGAAGTCAGAAGGCTTGCTTNNCCTTNGAGCCAGCAGTCCCATTACGCGGTATTCTTT
GCGTATATGGGNTTAAGAGNNGCAGGAGATCAGGANCCTTATGTGGATATCTGAATGTGTTGCACAGAAC
CAGAAGTCCAGGATCCACGACAGTGTCGTCTACATGTTCTGATTCTGGTGGTGAGTCAAAAACACATAAA
CAAATGTGAAATCTTGAGTCTGGTTTTCTTCATCGCTCCTCATGTACAATCGTTGGTTTTTACATTCCCT
GTTTCTGTCGCTCTGTGTTTACCAGAGTGCGTGTATTGAGTATCTCCCAATAAGAATCTCTTTTATTTGT
TTGTTTGTTGTTGGCCATACACTCTTGTAAGATCAAATTTATTTATGATGCATACGAATTACTT
>gi|3449509|gb|AI099770.1|AI099770 33923 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122O3XP 3', mRNA sequence
AGGGCCCTCCTGGNGTTNTCCCAAGGGGNGATTTCTCTTCGNGNTTTGTTGACCGTGTTTCTTGCTCTGG
NCTNCGTCANGCAAGAATTTGCTGATGCGGCTAAGGCAACGATGGAGAATAGGGGNGCAGNCNGGANGCT
TTGGGAGACGATTTGCAAGAACTTCCTCAAAGGCNGAGTTCCAACTAACTNGTTTCACTCCCAAATTATC
TATTTGGCTCTTGTCATATTGAAACAATTTGTGGATTTATGATCTTGCTTTATTTTTATTCAATGTATAA
CGACATATTAATCTCGGCGTGACTTATTTGTGTTATACCAGTTGATAAATGAATAAGAAGAACCTAAGCT
ATTTAAAGCCAT
>gi|3449508|gb|AI099769.1|AI099769 33922 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122O2XP 3', mRNA sequence
AATNTTCCCCCGAAGGCGGTTTTGGACTNNTTNGGCACCCCAAACCTTGGTCCNTGCTCAGGCTNTTTNA
GCCGCCTTTGGCTTCCAAGTCATCCCTCATGGGNTTTGGGTTGAAGGTTTCCCGCATNAACGGTCTTGAT
GGGTTTTGGCGAAGGCAACGACTTGTNCCCCGGTGGGCAATACTTTGNCCCGTTGGGTCTCGCTGATGAT
CCAGTTACTTTTGCTGAGCTTAAGGTGAAAGAGATCAAGAACGGAAGATTGGCTATGTTCTCTATGTTTG
GCTTCTTTGTTCAAGCCATTGTTACTGGAAAAGGTCCTTTGGAGAATCTCCTTGACCATCTTGACAACCC
TGTTGCTAACAATGCGTGGNTTTCGCAACTAAGTTTGCNCCTGGAGCTTAAATTTTCAAGTCTTGATGTG
ATTCTTGTAATGATATGAACATAACCTTTCTTGTTC
>gi|3449507|gb|AI099768.1|AI099768 33921 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122N17XP 3', mRNA sequence
GGTGTCCGTTTCCGGATTAGTNTTTTGGGCCCCNCTTTTTNGGGGAAGCTTNTTGGTCCCGTTTTNATCC
CCAANCTNATCGTCNGNTTNCCGGATCCCAAACGNTTCGTCCTCAAGTTGTTGNTCCCTATTCAAAACGA
TTCCGTTGGGTATTCTTTTTCCCAATTTAGCCGTTAACCCGAAGACGGAAAATTCCTCCGATANCGGAGC
TTCGACTAGCGGCACGACGACGGACGAGGATCTCCGGCAGAATGGGGAGTGTTATTATAGTGATAATTCA
GGACATATAAAGCTGAATTTGGATTTAACTCTTGGGTTTGGATCCTGGTCGGGTCGGATAGTCGGAGTCG
GGTCATCGGCTGATTCTAAACCGTGGTGCGACCCGGTGATGGAGGCNCGTTTGTCACTGTTGTAATAATT
TGTCAAAAAAATCCCAAAAAATGGGTTTTGTTACTTCATTTTTTTTTTGCTTGAGTCCTTTTGGATAAAT
ATAGAAATTCTTTACTTC
>gi|3449506|gb|AI099767.1|AI099767 33920 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122M17XP 3', mRNA sequence
TTNGCATTTGCCNTTCAAGNTCCCCCTTNGGCCCTTAGGCTCTGGTCTCAACGCTGGCCCGTGCAGCTGG
NATTCCTAAGGCATGTGGNGTCAATTTTCCTTACAAAATCAGCACCAGCNCCAACTGCAAAACCGTGAGG
TGATGAGCTNGCANCGGTGAGATGATGCTACTACCGGAAGTTTCGAATCCTTATTATATAATGGATGNGA
TTAATATTAAATAAGATGTTCGAATGTTTGTTTTTAGNGTTTTTAATTTCTTGTCTTTTTCTATTGTGGT
GTTCTTGTTATATGGGTTTGTCTGTACTATGTTCGCAGGCAACAACGTTNTNTGAAATTTCAGAGTAAC
>gi|3449505|gb|AI099766.1|AI099766 33919 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122L18XP 3', mRNA sequence
TGGGCTTTTACTCCTCAAGGGTAATTTGGTTCCCNGGAGAAGNTGGGTNTTAATGATAGTTCGTTTGGGG
CTTCCATTTTTGGTTTCTCCTGNTGNATGGAATGNTTCAGCCTTGGTAACCANGTCAAGGGNCCCTATTG
AACCCTATTGANCCCTATTGATACANGACAAAGAAAGAGATTGTGAAGAGACTNGTGANCCANCCGAAAG
AAAAAATGTTTGATAGAGACTTGTTTGTCACAAGCAAAATCATCTCATGTCATTTCATGTAATGTAGCAA
AAGCTTCTTTATCATTTGTCAACTATTTGATCTTGGGTTCATGTTAGCNGTTTTGTCTACAAAAAGCTTA
ATTGATTGATTGATAAGCTTAATTATTAGCTTTCTGTGAAAAAAAGTTTAGCACTTTGTAATAAAAACAA
GATAACTTGG
>gi|3449504|gb|AI099765.1|AI099765 33918 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122K4XP 3', mRNA sequence
CCCCGGGAGGTCGTNATGCNCTTAACCAGCGTTTAAGCTTCCTTGCCNTCTCCTGAAGCACGANTACCTC
CCCAGGGATCTTCAGGCGGTGCAGACCCCATTCCNTGGCTATCTTCAGGACATNCTTGCTNTTTGTTGAG
AGGGAAAGCAAGGAACGAGAGGCCTTGGGAGCTCTACCACTATACCAGCGCACACTCCCATAAGCATTCC
TTTCCCCTTTTCTTGTGGTCAACGCTGCTTCTCTGCATAAATCTGCAACATTGATATTTTGGTGCTCACT
TTCTGAACAGAGCTATTTACTATTTGAAAAAGCATAAATCTGTGATAGTTTTCCTAAGTGGATATGTTGC
TAGTTACATTTTTATCGCTTTTGCTGGCTTGAATAAAATCGACGACGCAACTCAAGTCTGTCTCGATGAT
T
>gi|3449503|gb|AI099764.1|AI099764 33917 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122J15XP 3', mRNA sequence
TGGGCNCCCTGGGCCNTCAGATTGGGACTCCCATTNNTGGGAANCCGGNATTTCAAGGAGAGGNGGGNGT
NGCCGTTGAAACATGGCGNTAACNTTCGTTGGACTAGAAGGTCACGTGATNGAGCAGCTTAAAGTGTATN
ATCCCATTTTACAGTTCATTCAAAAGTCCCCGGATGATATCNTTTGCAAGATCACTATGACCTGGGAGAA
GCGAGCCGATGACTCGCCTGAACCCNGCAACTACATGAAGTTGGTCAAGAGTCTCGCTGCTGACATGGAC
GCCCACGTTCTCAAAGCCTAATCCTTCTCACCTAAACCCATCATCATCGTGTGTGTAACTTTGTATGATG
TTTTCAATATAATAAATGGGGTTTGCATGTATGGTTTCATCTACTGTAATATGCTTTGATGTTGTTTATA
ATAATTAATGATTTAAAGAGT
>gi|3449502|gb|AI099763.1|AI099763 33916 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122I4XP 3', mRNA sequence
GGTTTCTTCCCCCATTTTCCCAGCNTGGCAGTATTAGCATGATGCTCAACTGATCTACTCNGCCCCAAAG
CCCAGAGCTGAGCAATTCTNCCTCAGGCACCCAATCCTGCAGCTGGTTCCCAGTCAAGAGTTTANCCCTG
AAGCCGAACTAGCCGAGCTGGAATCTGAATTTGGTAAGGTGGCTCGTGATTACTCTGCAGATGAGGTTGA
TGGATGGGAATTCGATGAACTGGAGAAAGAACTGCAGTAGTATGATCCATCACACGCCTGCCTCACATAC
ACTGATATGTTTTTCATTTACTTTCTTTGTTTGACCATAACTCCGAAGTTCCTTTGTTAATCTGTTTGGT
AATTTATGGTAACTGCCTGTTGACTTTTGTATGTCTACTTTTTTTTTTTTTGCTCATAAGTGTTGTCTCT
TATTT
>gi|3449501|gb|AI099762.1|AI099762 33915 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122I3XP 3', mRNA sequence
CAGGGCAAAGTTGAGTTGNGGGGACTTCCAGGTNTAATTGGGTCGATGTCAGAGTTGGCGAGTTCGTNCC
TGAGAAATCCGCTGCCGGAGAGATCACTTTCTCAATGTATGAGCATGTGGCTGGTGTTTGGAAGAAAGGG
CTCTCCCTCAANGGTGTTGCAATTCGTCCCAAACNGTNATAATTGTTATGGCATNGAAAAACATAAATCT
CCATATGCACCAATGGNCCTTCTCAACATATATTTCACATCATGTCATGTGTGTATAATAAGGTTGTTCT
ATCGTATTTTTAGTTTTAATAATAACTTTAATGTTGGTGTTGAATAAACTCAAAACGAGTGTTTTGANGG
TTGTTATATTCGAATCAATTCATTTAC
>gi|3449500|gb|AI099761.1|AI099761 33914 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122H1XP 3', mRNA sequence
GCTTTTAAGGAGGNGNCTTCCCCCAGAGCCTTNTTCAGGTCCNTGTTGNTCCTCCTTGNAGTTATTTCNG
NAGAAGNGNCTGANACCCTGAAGTTCGTGATCCANCCAGNGAAGCTTGCTCTGCGTGAGATCAAGGAANG
AATCAAAAAGACCAAAGATGAAAAGAAGGCTAAGAAGGTGGAATTTGCTTCTAAGCAACAGAAGGTCAAG
GCTAATTTCCCCAAAGCTGCTGCTGCATCCAAGGGTCCTAAGGTGGGAGGTGGTGGTGGCAAACGCTGAA
GAGCTTAAAGCCATCTTTTCTCACTCTGCGTCTTTTCTGCTAGTAGCTACTTTTAGTAGTTGATGTTCAT
TTCTGAATATTTGCAAAACATAAACCTTGTTATTTTCGTTTTTGTCTCTCACTTTTGCTACTCTTATAAT
ATCAGACTTGAG
>gi|3449499|gb|AI099760.1|AI099760 33913 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122H18XP 3', mRNA sequence
TTGGCCGNGCCCTCNAAAAANGCTCTCTNATGGCTTGGGCCAGGTACGCCAGGNGTATTTNGCCNAAGCT
CAGGCCCACTTTCCTGACCAGGTGCAAAGGGTAACTCGGACGCTACCCTCGGGAAATACACCGGCGGGGC
TTCTGGTGACTCGGCCGCCTCTGAGAGCTTGTATGAGGAAGGATACAAGTATTAGGAGCGTTTAAATACG
GNTGTCGTCCTTTTATACGATTTGAATATATGTCAAATGTTTCNTAGGNNTTTAACTGTTTAAATTTTTA
TCGATTTGGTTTAGCGTCTGTNTAATGTTCTTAAACTGTGTTGTGTTTTTTGTGATGGTTTCTATAATAT
TTTCGCGCCNTG
>gi|3449498|gb|AI099759.1|AI099759 33912 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122H16XP 3', mRNA sequence
TTCCCTNNTTTTCANCAAGGGNAANCCATGGGTTGTCCACTGNATATTTNGGGTTTGGACCNTTCATTGG
AGCTTCGATNGCTGCATTCTACCACCAATTCGTTCTGAGAGCTTCAGGTTCTAAGTCTCTTGGATCATTC
AGAAGTGCTGCCAACGTCTAAACACATCAAACCAGATTTCTCAAGAATAAATGAAGTTGTGATCTCTCTG
TACAAATCTAAATCAGTCACTTGCAGTTTTCATTTCCCTTTCTTATATTTGTGTTTTCCACTTGCTCTTT
TGTGAATTTTCTTCGGTGTAATTGTTTTTTCTTTCGCTTTTAAACGAGTGATTGGAATTATAATCAATGA
AATCAAAGAGGTTCTT
>gi|3449497|gb|AI099758.1|AI099758 33911 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122G7XP 3', mRNA sequence
CGNTGTNAATCAAATGANGAATTTGGTGTCCGTAAATTGTATGNGTAAAGGNTTGAAATCATTTGAATTC
GTGGANGGTTGGATCTTTCATTTTACTTGTNGCCAAAAATGTCAAATAGGTTTTGCACAAATTTGTAAAT
TCTGCTTTACTNTTTTTCACACATTGTCTTGAAACTTGAGTGTATTTTTTTTTAAAAAATAATTCGTCTT
TAAGGA
>gi|3449496|gb|AI099757.1|AI099757 33910 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122G6XP 3', mRNA sequence
TGGTCCCNCNCNGGAAAACNNNGGNTTCACAGACAAGGCATCAGCTAAGAAACGGCTNTCGTATCCCAAC
TTCGCCTGCATTGCCTAANCCNCGGCGGTTCTCAGCTCCCCCTAAGGTGGAGANTGGCGGCGTTACCGTG
ACCAACGGNGCAGGCAGCTGAGGTATTTTATTTAATATAATTATTTTCCCACTTATGAATGTGTCCGAGA
TTGTTGTCTCTTATGTGTTCCCTTCATTTCGTAATTCATTTGTGCAGTGTAAGCGCCAGTCATTTATTTT
TTTACTATAATAAATTTTATAACCTTTT
>gi|3449495|gb|AI099756.1|AI099756 33909 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122G13XP 3', mRNA sequence
CCTAAGTTTTTTGGTGGGGAATNGATTCTGATTCTTCATCTTTTGCTGAAGCACTTGCCCTGTACGGTCT
CATTGTTGGTATCATCCTCTCTTCTCGAGCTGGTCAGTCTAGNGCCGAGTGAAATCCAGAGTATCTCTCT
CTCTTATCGGCTACAGTCCTTGTAATGTTTTGGTATATTTTACTCTGTTTTCTTTTGTGGTATGTTTTTG
AGTTTCTCATGAAAACAAGCAACATGGGTGAAATTTATTTGACTTTTGTTTCAAAACCCATTTCTTTTCT
TTTTCATTTGCACACTATATATGGATACATCAATAAGTAATAAAATATGACGATTCAATG
>gi|3449494|gb|AI099755.1|AI099755 33908 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122F9XP 3', mRNA sequence
TTTACTNAACCGGNNTAAGGTTGAAAGNTTCATCCGGNGGCTCCTTGTTAATAATGATTTTCTTATTCTT
TGGCGCTTCTCATAATCTCCCACGCTCAATCACTTCCAGGTACCCNTATGGCGGCCCTGGTCCGTNTCCG
CGTAGTTACCCTGTGTGTTACCCACCGTATTGCCGTCCATGAGAGTTTCAATTTGGTCACATGAATGAAT
TATAGTCAAATACCTATATCAAGGTGATGTATGTGTGTATATTATTATATGTTTTCATCATTTGATGGAG
AATAAAAAGCTTAGGAAATATATCCATGTTATTATATGTTTCAGTTTGTAATATGTATAATGATATTGCT
GGCTCTGTCCCTT
>gi|3449493|gb|AI099754.1|AI099754 33907 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122F21XP 3', mRNA sequence
ACCAGGTATAANGCAACATCCTTTCTTTGAAGGANTGAATTGGGCTCTGGTTCNATGTGCCNGTCCACCG
GNGNTTCCTAANCCGGTTGATCTTGAAGCTTTGAATCCTACTCCTNCTGTGCCAGCAGCCNCATCTTCGN
GTGTAAGATCTGATCAGNGTAATTATCTTGAGTTTGATTTCTTCTGAAGAAACTGTTTCCACAGTTGATG
ATTCTCATTATTGTTTCTTTGCAAATTCTGTTTNGTGTTTTCTACAAATGTGTTTCTTTTTTTTTCTTCT
TTTTAATTTTCACGTCTTGGAAAAAGTTATGAGATTTGTAATCNTTCTTC
>gi|3449492|gb|AI099753.1|AI099753 33906 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122F16XP 3', mRNA sequence
GCTTTTTTCGCTTCGGGAATCNGAANAATTTGGGGNTGACAAGTCAANCAGGTCGATCAGGACTTTGNGG
AANCGATTCTTGTTTCGGAAGGGAGAANTGAGTGATTGGGTTAACTATTTGTCACCTTCACANGTGGAAA
GATTGTCNGCCTTNGTGGATGACAAGTTAGGTGGATCTGGTCTCACTTTCAGGTTGAGCTAAATATAAGG
CCACGTGCCCCCATTTCTACTCTTGTTCTGAGGGCCTNCTATATACGTTAAGCTAAGTTAAGGCNGTTGT
ATTGTTGTTACAGATAGACATCGAAGCAACGTAACGTCCATAATTAAGTTAATTTGTCGTTTTTATTTTT
GTCAACACCGAAGTTTGTCGAATTTTTATTTTATTAAATATCGCTTGTTTTTGC
>gi|3449491|gb|AI099752.1|AI099752 33905 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122E9XP 3', mRNA sequence
CCCAGAACTCGGCCTTNTGGNCCNTTGNTNGGATTTAGCTGGAAATGGGNCCGGNTNGGNGGGAAACGAA
AAGCCAGCCCATTTGCTTGGAACGCATCCAGCCGTCTCGCTGAACAGCAGAAGGAAACGGCTGTNTCACA
ACCGGAAGAAGAAGCTGANCCAACACATCCNGAATCCACCACAGAAGCTGCAGATACTTAAAGATTGTCT
TTGTTTTGGATCCTCGGGTCATCTCTTTCACGTACGTATGTTTATTATTCTCACTTTTTGTTTGTGCTAC
TCATCCTCCCTCGAGGTAGGATTCACGGTAGACGCGGAAGAGGGAAATGGCCTCCTTCTCCGATCTACTT
TTAACTTTATGGTGATATCTTTGTGTGGACAGAGCAATCTGGTCCACAGGNGAGAAAAGCAAATATGCAT
ACATACACGTCAACTTGTATCATTGTAACACTATGTTTGTAATCATTTCCACG
>gi|3449490|gb|AI099751.1|AI099751 33904 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122E7XP 3', mRNA sequence
GACCCCNTGCAAGTTTGAATTTATGTTGGAAGNAGNTNGGCCCTNCAACNTGNAGTCCNGATGGGTCCCT
AACAGNAGCTCAGATGGGTTTGCTCAGTAACTCGATGCACGATACAACTACTTTGGGGGACGANTCCAGC
ATAATAGGGNACGAAGCAGCTNTTAAGTCGCCCAATGTTGTCAAGTTTGAAATTCAGTTGTATAAAACTC
GGGACGACAAGTATCTACTGGATTTGCAGAGNGTACAAGGTCCTCAGTTCTTGTTCTTGGATCTGTGTGC
TGCTTTTCTTGCTCAGCTCCGAGTCCTCTGAATACTAAACCGGACCTCTTCAAGAATAATCCCCACTTAT
TCCTTTTTTTTTTTTTTTCTTATTCGTCTAAGAAATTATTTAGAAAACGTAACCCTTTTTTTCTTCTTCT
CTTTCTTTCTATTTCTATATGCGTGCTCTACTCAAATACCTCTTTTAACTTAAATGTAAGACTGAGCAAG
AGTAAAAAAAAGACACTTTGTACAT
>gi|3449489|gb|AI099750.1|AI099750 33903 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122E22XP 3', mRNA sequence
TTTCGGGTCAAGAATNTTTCNGCNACTCGCTNAANGTTCCTTCCTTGTTTTTGTNGGGGAAGCCATTTNT
GGGGTACANTTTCAGCCATTTACCGNAGCTTACNGATTTTTGTGTTGAAGCAAATTAAAANTCCNGATNG
GAAGGGACCGGAGGAATTTGATCCGTTCGATNTATACGACGAGGGATTGAACGGAATGAATNATCCAGAT
TGCGACACGTGGGAAGAATGGATGGGATGGGAGGGAGCAGGAACCCGTGATTACTCCTCTCACGTTAATC
CTTACGCTTGATAAACGAATGATTTCACTAATTAATTTCGAAAGAAATCATCCAAATGTGTATAAATAAC
AATCAGAGAGAGACTAAAAGCACAACAATGTAAATAAGTGAAATTTGTCTCGGATAATGATTGCTTAAAT
GTGAATAAAGTAATCTCTCCTTTGTGT
>gi|3449488|gb|AI099749.1|AI099749 33902 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122D8XP 3', mRNA sequence
GTTGGGCCCTNCAACNTGAAGTCCAGNTGGGTCCTTAACAGCGGCGCAGATGGTATGCNCCGGTAACTCG
TTGCACGTTAACAACTACTTTGGAGACGAGTCCAGCNTTAATTGGAGAACGAAGCNGCTGTTAAGTCGCC
CAATGTTGTCAAGTTTGAAATTCAGTTGTATAAAACTCGGGACGACAAGTATCTACTGGATTTGCAGAGA
GTACAAGGTCCTCAGTTCTTGTTCTTGGATCTGTGTGCTGCTTTTCTTGCTCAGCTCCGAGTCCTCTGAA
TACTAAACCGGACCTCTTCAAGAATAATCCCCACTTATTCCTTTTTTTTTTTTTTTCTTATTCGTCTAAG
AAATTATTTAGAAAACGTAACCCTTTTTTTCTTCTTCTCTTTCTTT
>gi|3449487|gb|AI099748.1|AI099748 33901 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122D21XP 3', mRNA sequence
TTTCCATGGGGGANCAATNTCNCAAATGGAATCGTGANGNTCACGGGCCTAAGCACTTCGAGGGCTTCNT
TTGTGAAAGAGACGGGTCCGGNCTTTCAAGCTGGTTGATCAGATGGCTGAGCATTGTCCTCCAGGGGAAT
TCATGAGGGAGATACAATTGCCGAATCGGATTCCGGAAGAAGCAAATATTGANGCATACTTTGATGGGAC
TGGACCNGTTTTAGAGATTGTGGTTCCAAAATTGAGAGGAGGTGTGGAGGANGAACACGNGGTTAGAGTT
TGTCTACGGTCACACCACCTCGGATGAAAGATGCAACCATGTTTTAAAGTGTTTGTAGAAGCATTTTGTT
GTGTACAATGGGGANATAAGNNTAAGCAAAAGCNGAAAGTGCTGTTTTTTAAGT
>gi|3449486|gb|AI099747.1|AI099747 33900 Lambda-PRL2 Arabidopsis thaliana cDNA clone 122C14XP 3', mRNA sequence
TTCCTAAAGTCTTGGNGTTATATTAACTTGGCTGGGGGGAAACCCAGCAAATTGGTTTGGAGACGGGNGC
ACTAAGACGAGCGGTTTGANGTTCTTTTGNGGGGAATGGATGCACCATTCCACCTGTCAAAATGCAACAT
GGGACGGTTCACATCAAGCGGTTCGGTGGTAGCAACTTGGCTGCGTGAATCAGCCACACTGAAACTCTTA
ATCCTCCNTGACCACATNACAACCGCCACAGCTNCTNCTACAACAATGAAATCAACAGACCAACAACGGA
AACAGACGTCGTTTGCTTTACAGCCTCTTCTTTTGTAGCTTNGTGTATGATGTAAAAGTAAAACAATTTG
TGTTGATCATTAANGTGTATAGGNCCAATGGTCCTAACAATGTTTGGCTCTGTGCTNATATTTGTAACAA
AGCAACTCGATTGATTATGTGAAAATCGTTTTGTCT
>gi|3449485|gb|AI099746.1|AI099746 33899 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121P8XP 3', mRNA sequence
TCAAANATTCNTTNCCCCCCGTTTAAANCGGGGGTCCCCTTTTTTGNNAAGGTNGCCCTGGATGGGCCCC
AAGCCCAGCGCCGATTTACGGGGTCTTGGAAATCCAACCGCAGGAGGATTCTTGGGTGGTCTCATTAAAT
GGAACTTTGAGAAGTTCTTGATTGATAAAAAGGGAAAGGTCGTTGAGAGGTACCCTCCCACCACATCCCC
TTTCCAAATCGAGAAAGACATCCAGAAGTTGCTTGCCGCTTAAAAACTTTTGCTCATGAGTGAGCATATA
GAGACTGATGGTTAAAGTAACCGTAAATTGTGACATAAAGTTTCCGGTTATTGCTTGTATACCTTCTTAC
ATTCTAAGTTGTACTAATCGCTTAATAATTTGCGTATAATGGT
>gi|3449484|gb|AI099745.1|AI099745 33898 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121P6XP 3', mRNA sequence
GGGAAAAGTGGTTGGAGCCATTTTTAGACGGTGGNAGTCCTGAAGTGAACAAATGCNATTGCTAAACTTG
CACGAGCACATCCTTCTTGTTGAGNGCCTTGANGTGCTATCTAAGGAAGGCCTTTCCTTCGCCACAAATA
TATAAATTGCCTTTCTAGGTTGTGTGTTGGTGTGAGCTTTGAGTTCAGNGTGGCTTTTATGTCACTTTGC
TNTTATGATAGCNGNGTCGANATTTTTGTTATTTGTTTGACCNNCTTTCTTGTGATTGTTTGGTTCCAAA
ATAAAATTGAAAGCT
>gi|3449483|gb|AI099744.1|AI099744 33897 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121P16XP 3', mRNA sequence
AGGGGTCCCTNGTNAAAATNGGGTTTGGGCCCCGGATTNTTTTCCCNGGGGCCCCGGAANCCCTCCCGGG
TNCTCGGTGGNCCGGTACTGGNCCAATGTGNAAGCTCCCATTGTCCGGATGCCACCGACTCCGCTCAAGT
GTTGAAGGAAGTTGAAAGAATGCAAAGAAGGAGTACCCGGCGCCTTCATTAGGATCATCGGATTCGACAA
CACCCGTCAAGTCCAATGCATCAGTTTCATTGCCTACAAGCCCCCAACTTCACCG
>gi|3449482|gb|AI099743.1|AI099743 33896 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121O22XP 3', mRNA sequence
GCATNGGGCCACNTTCATAATGGNTTGACATTTTTTCNTNATCCNTCTNTACGCAAGNCNAATGAACGAA
ATTCAAATGCAANCTCAAAGGCCTCCAAGCTCGCGAGTGTTTACAAAGGAGAANCAGAGAAGATTCTCCA
NGTGAAGAGAGCCGAAGCAGAAGCGGAAGCCAAGTACTTAGGTGGTGTCGGTGTGGCTAGACAAAGACAA
GCAATCACAGACGGATTGAGGGAGAACATATTGAACTTTTCTGACAAAGTAGAAGGCACATCCGCCAAAG
AAGTGATGGACTTGATCATGATCACACAGTACTTTGACACTATTAGAGACCTTGGAAACTCGTCAAAGAA
CACAACGGTGTTTCTCCCACACGGTCCGGGACATGTGAGGGACATCAGCGACCAGATACGCAACGGTATG
ATGG
>gi|3449481|gb|AI099742.1|AI099742 33895 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121N4XP 3', mRNA sequence
TGTGGCTTTTTNCTGTCAATCAGCCATGTNTGCTTTGGACACTTTCAGTNCCCTTCTTTTGCTGACAGGC
TTGAAACCNCTGTGAAGCNTGTTATCNGCTGAAGGGAATTGTNGGACTGAAGATCTTGGTGGAAACNGTA
CCACTCAAGAGGTCGTTGACGCTNTCATTGCAAATTTGGATTGACTTGACAATTCCAACTTCGCTTGTGT
AAAGCATCNGTCACACGTCGGTATGATTCACGCTTACTGGAAAATACTTCTNGTTCCCACATTCTTTCGA
GATAACTCGAATTGGGATTTCAGATTTCGAGAAAAATAACATATGGTTTTTTGTTTTGTTTTTCTTCTTT
TTGTTCATGTNATATGCAAAGTGCAAAGTGAAAACTGCCTCAGAG
>gi|3449480|gb|AI099741.1|AI099741 33894 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121N24XP 3', mRNA sequence
ATCCCCCCTTGGTTTTGTCATTCCTTATNATCAATTTCGGGCCCTNCCTTTTCTTTATTGCTTGTTAGGA
GCTNTTTTAAGAAGAATTATGGAGGGCTCATGCCAANGAACCACTTTTCATTTCCAGGNNTCATGAGCGG
NGCNTACTTTGACTCAGCTGATTGGGCTCTTGGAAAGCAAGGTNTTGCGAAGCCAAAGGGACCCCTGGAA
GCCCTTCGTCCCAAGTTACAGCCAACGCAGCAGCAGACACGTTACAGGAAGTCTCCATGTGCTCCATCTG
AGGGTGGTGAAGATGGAGGAGCTGCTCAGGCCGAGGGAGGTTCAGGCAACTGAGGCGTAGAGAGACAGAG
AGATGTATGAAAACTCTTGTGTAAGAAGTCTGTTATAATCGGATATTTTCTGTCCATTTGAAACATCAGA
TATGGCTTTCATTAAAATCTTAACTTGATCGAGAAATTATAGTTTACCCTTTTGGTCCGG
>gi|3449479|gb|AI099740.1|AI099740 33893 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121N10XP 3', mRNA sequence
ATTGGCCNAGTTTTATTCTAAATCCCTTGGCTGGGNCTTGGGGCATGGCCCCGTTGGCCTGGGGCCCCNC
CTTCGNGNTCCTNCGGATAATGNAGTTCCGGGTGCNCCATTGCCCATATCGCTTTCTATGTGTTCAAGGA
GAAGCTGAAGTCGTCCAACCGTTCCAGCTNTTGNCCAGATGCTCACTACTNGCTCAATTGCTCTCCGCAG
TCCCTCAACGACTTGGTTTTTTCGTCCGGAGTAGTAAACATGAACAAGTAGGATACTAGGATTAGTGGAT
CGTCTATCTATCAATACGTCCGCTCTTTGTTCAGTAGATGATGCTTTCCATTACTAATGTAGCTCCTCGT
TGAAGACAAAAGTCGCGATATATGATTTAGTCTATTGAATTAAGCATCGATCGACAACAAACAAAGGTTT
AGTTGTTAATTAGCTCTTTCTTAGGTTTTATAGTCTGTTTATTTGTTAGCATTAATTATAGCGTTTTTAC
GATTAAAGTAAAGCAAATAAATGGTGTAACATATATTGTACATGAAAATGTGTAATGGTGGAGGGAGGGA
ATCAAAACCTCTGAACAATGCATGTG
>gi|3449478|gb|AI099739.1|AI099739 33892 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121L8XP 3', mRNA sequence
TGGCCTACTATATTANTTCTTGCCNTTTGAATTGGCCCCTTCAGNTATCNAACTNGCTTTTTGANNGGAC
CCTCCGNNGATTGGGCTATTTATTTCTCGGTANCGAGGANTTAAGCAAAAGCCTTTATTTTTCGTGGGAA
AGAGTGGAAGTTNAAGAAGAAGATATGCCTTATGGTTTTTGGTTCCAATATTTGTGGAACACNACAAAAG
TACTTAGGATTTAGTGAACAAGACTTGAATGGATTAAGGATCTTGTCTTCATTAGACGCCAAGAAGAAAA
AATCTCTCTTCCTTACCTTTATTTTTTCATTTTCTGTTTTTGTTAATTTATGTGTAGATTTTGGNTAAGC
AGATATGTAATATGCNCCTTTTTTTATTAATTGAAGTTTCTAGTTAAGTGGTTT
>gi|3449477|gb|AI099738.1|AI099738 33891 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121L2XP 3', mRNA sequence
CAATNCCTCGGCGTATNCCTTGGGATTTCCGGTTGATCTTNCTGTTTATGGGNTCGTTCANCNCAATCGT
CGGAGTTTGAAAAGGGTTNGCATGTGATCTGTGTAAAGCANCGAATATAACTACAAGAAGTTTGGTAAGA
CAGACAAGAAAAAATGTATAGATCTTTTACATGAATCTGAAATAGAAAGATGGNGAGNAAGTNNGGATTG
TTGTATGATCATTTAATGGTGTCAGGATGCAGAGTCTTAAACAATTAACACACCGATTTTCCTTTTTTAG
TCTTCCTAATTCAATTTTCCAGATTTTGTTTTTATTTTTCTTTAATTTTT
>gi|3449476|gb|AI099737.1|AI099737 33890 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121L24XP 3', mRNA sequence
GAAGGTTCCATCAACGTCCCGGGCCATTTTCGGTNGGCCCACCCTTTTTCCAAGGCTCCNCNCCNGNGCT
GAGGGAAGGANCCGNTACGCTCTNGGNGGATTGGCTGGACCATGGAGAGTAGCCTTNGGTACCCTCGGGG
ATGTTAGTATTGTTCCANTCGAAGCTTCCAAAGAAGCTCAAGAAAAGAAAGGCGATCACTAGAGAAGACG
GGTCAACAGAGTACGAAGAATACATCGATTATTTATACCCAGAAGAATCGCAAACAACGAATCTCAAGAT
TCTTGAAGCTGCATACAAATGGAAGAAGCAGAAGGTTGCTGCTTCTGAGGATGATTGAGATTAAGCTTTT
TTCTTAAGTTATATCAAAAGTCAAAACTGTGAAATGTGTTTTGTATTCTTCCT
>gi|3449475|gb|AI099736.1|AI099736 33889 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121L17XP 3', mRNA sequence
CCAGGGNATCCCCNGCCTGGCCCNTCNTTNACCNCCAACTCGGNTGGNACCCGGAAACNNCGCTTNTGGG
ACTTGCTCGGGGTCGGCCTTNACCTTCCNGGCACCGGNCATACGCTGAAGCTGTGAAGAAGGCAACATCC
AAACCAGTGGCTTCCTTAAACTCTCCAAGCCCCCAACGAAACTCGTTAAACACGGCGTCATTTTGGCATT
TTACTCTATTCGATTCTATTTTTTTCATCCCAGAGAAAACTTTTTTTCTTTTTTCTTTTTAAGAAAACGA
TATAATCACGGTGGTTCGTTCCAAGTATACCTTTTCGTTTGTAAGTTTTCTCTTTTTGTTTGGTTTGTTT
GGCCATGTATGTCGGAGCTGTCAGAAAGCAAGAGGTTAATCGTTTGTAGCGAATGATAAATGTTCGAGTT
TATATTTTAAAATGCTTCGTTT
>gi|3449474|gb|AI099735.1|AI099735 33888 Lambda-PRL2 Arabidopsis thaliana cDNA clone 121K3XP 3', mRNA sequence
TTTCCCAAGCCGCTTTTTCCGGTCACCCCTTGTTTGGGGNACNNTTCTGGGGNACCGGGGGNAGGCTTCT
TCCAGCCGTTGGCNCTTTTNCCCCTGGGGACCTTGGTGGGGGGGATCCCATAAATGGTTNTTTTNGGACC
NCTGGGGTGTTGGGGGTTCCTTTGGATCNCCATTGNGGCTGGCATTTGTGTTGGNCCAATTGGAATCCCA
AACCNGCTNTNGCTTCTCTAAGCCAAGATCTTGGGGGGATGTGAAGGAGCACCCCCATGGTTCGGAGTAG
AGGCTGCAAAAGCCCTTGGTTTCATTGCAGATGAGAAGAGCAGAGAAGTACTCCAAGAACTTTCAGGCGA
CCTCGATCCCATTATCGCTAAAGGTTGTGATTCTTCATTGAGTATCTTGGAATTTAAGAATTCAAAAAAA
TATGACCCTCTCATATAAAATGGTGTGTGTGGGTCTGTTGTGTAATGAAAACATCTACGTTTCATCTTCC
TTTTGTTAAACTTTGTTTTGTATTCAAATGATTTGCAGACGGTTTAAGCTCTGTTTTAAGCT
>gi|3449473|gb|AI099734.1|AI099734 33887 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120P15XP 3', mRNA sequence
AGCTNGAGAAAACNTTTNCTNCCAGAGATTCAACTNCNCAAGANGATNAAAGANACTCCNTATCCGGATA
ANATGGAGATGGTATTTCATATACTCTGTCTTTATCAAAAGGAGATCACACNTACTCGACATCGAGTCTT
GTGNTGGAGTGAATGGTACTGAGCTTTACCCTGATGTCAAATACATGACCGTGAGCGAGTTTCTTGATAC
TCTTCTCTAGAATTATAAACCAAACAGCAAAGGGATCACTCTCATTTTTCAGAGTTTACCTTTTACACTT
CCAAAATTTCTCTGTTTTTGAGGGCTGAATCAATCTATCTCATGTAGCACTATCTTTACCCTATTGATCT
GAGTTTCGNCCTT
>gi|3449472|gb|AI099733.1|AI099733 33886 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120P11XP 3', mRNA sequence
CCTTGGGTTCCCCNNATCAGTGGGNAGTCCGNCTTATTTNTCGGTTGGAACTTGGCTCCCCTTTGNAGAA
TGGACTTTAGGTGGNCTGCTTTCCNGCCTTGATGGGATTCCGAGAGGGGCCNCGNTAAGTTCAAGCCTGT
NATCAAGAAAGCAATGGTGGAACTTGAAGGTGCACCCATTTAAGGAAATTTCGCAATCTGCGTGAAGAAT
GGGCATTGAAGAACCGATACATCAGCCTAGGTCCGATCCAATTCACTGGACCTGGTTCAGACTCTCTCAG
CCACACTCTACTTCTTGAACTCGGGGCTCAATAGTCTCTCGACTAACCACCATTCCTTTGCTTTTCTGCC
TTCCTTGGAATTTCGCATTCAGTCTTGTTTTATCTTGAATATTACGTCTCCGTAACATTTCGATTAAGTT
GATTCCTCTCGTGTTTCTTCAACATATAAGATAATTATAATATTATTTCTCTCGTGTTTCTTC
>gi|3449471|gb|AI099732.1|AI099732 33885 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120O6XP 3', mRNA sequence
GGGCTCTTTTCCTGCATNGAACCCCGCATTGANGCNATCAAGGAGNCNANGGGGGGNCCCTCCCGAGNCN
CNTTCCTCACGCAGAGCCACCCTTACCGNNTGATNCATGGGACCAANCTATAAGTCNGCCTATGAGACGG
GAGAGAAGAAAGAAGAGGCTGGATGTTCTTGTACTCACTAAAACTCTCCAGCTTCTCCACAAAGCCCCAA
GTGATTTTCCTCTGCACTGTTGTGACTGTAAAACTTTTGACAAGTTTTGTGTTTGCTGAGTTAGTTACAC
GAAACCCAANTACTATATATGGTGCGAAATGTAGTTTTTGTAATAAGGTTCTACTTTTTTGTAATAATAT
GCATATCCCTTGATGAGAAAAATACTTTGTATAAGCCAAATAACAGAAAATATCAACAATTTGATTAAAC
ATTCATTTTCGGTTTGGTTTACG
>gi|3449470|gb|AI099731.1|AI099731 33884 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120O3XP 3', mRNA sequence
AGGACCCNGGTTTTTTGACCCAGNCCCCTTTTTTTAGGCAATTCCGNTTTCCCTTAGGGTGAAAGTTNGT
TCCCCTGGTGGAATCTTTACCCCCGGTTAACTTNGGCTCCTTCCGCAAGGAGGCCCAGGGAGGAAGGAGC
TAGCANCCGGGAGGTTGGCGATGTTGGNATTCTTAGGGTTTGTGGTTCAACACAATGTGACTGGAAAAGG
ACCATTTGAGAATCTGTTGCAGCACTTGTCTGACCCATGGCACAACACTATTGTCCAAACCTTCAACTAA
AGAGTGAAGACAGACTTATGATCTCATACCTATCTATCTTCCATCACTTTCATGTCTGTCTGTGAGTGTG
TTTCATCTTAGAGTTCTTGGTTTTTGAGCTTGAATTATTGTTGAACCGTTGTAGCTCCATGAACAAATTT
GGAATCTTCAATGTACAGAGGAACTAAGTTAATC
>gi|3449469|gb|AI099730.1|AI099730 33883 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120O2XP 3', mRNA sequence
TGCNCAATCTTNGAAGAGCTGGCTNTGCCACACCNGCNAGCCCTTGCTNTGGTGCTTGCCTTGGTGGCCC
CGCAGACACNTACGCTCGCTGGAATGACCCTCAAGTGTGTGTCCTCAACGACANACAGGAACTTCCCCCG
GTCGGATGNGACACAAAGAAGGGCAAATTTACTTAGCGTCTCCTTACACTGCTGCAGCCTCGGCTTTAAC
CGGCCGTGTCGCTGACCCAAGGGAGTTCTTGCAGTAGGCTAATGTAATGGCTTCGTGTGAAAAATCATAT
GCTATGCATCGACGAAATATTGCTAAATGATGGGGCATTGTGAACTATATGTATGTATTTTCCTTATTTC
GCTGTTGGACTTGATAGTTTCAAGCACTATGTCAAACTTTGATGTTTTGAGTTTGAAATAATAAAAGAGA
GAAAAAGAGTGAGTTAGAT
>gi|3449468|gb|AI099729.1|AI099729 33882 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120O24XP 3', mRNA sequence
CCCAGGAAGGGGTGCNACTTTTCAGGAGGCCACNTTAACAGNANTNTTNCCTCAGNTTCATGGANGCTTT
GCTTTGAAGATGTTGCTTTNCCCCGCTGAGATTTGNTGGTAAGCGTTANTCGCTACCGTCTTGATGGTTC
CAAGATTCATGAAAGGTCNTTTATGGATGCCAAGGTAATAAGNACAACACAGAGTACAAGCTCGAGACTA
TGGTCGGTGTGTACCGTAAACTTACTGGCAAAGATGTTGTTTTTGAGTACCCAGTCGAAGCTTGAAAGAA
GATGATGANGAACCATCAGGATAGTGAAAGAGAGCTTTTGTTTATGTTTTGTGGTATTTAGGATGAAGGA
AACTCTCTTGATTCAGTTCCTTGTTCACAATCTTTAATGTTCTATTTACAATGACTACTTTTTGTGTTTT
TCAATT
>gi|3449467|gb|AI099728.1|AI099728 33881 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120O1XP 3', mRNA sequence
GATCCCNCCCCNAAGGNGTGGTTTACTTTGNGCTTAACCCAANNCCNNGCACTTCCAAAGTCTTACTTCA
ATGACCNCGTTTGAATTCNNCCTCCCATCCTTTCCCAGCTCCAANTACAAATCCAACTATCCTCCGNCGT
TATATCCACCCGGTCCTGTCCAAGAATCTGAAAGGAGTTAGTGTTAAGGTTCTTTTCTTCTGGGTTAATA
TTGCTGAAGTGTCTCTTGACGGCGCCGATCTCGACTTCTCCGTCGGAATCGCGTCGGCGAGTTTTCCGGC
TGCTAATTTTGAAGAGAGTCCTCAGTGTGGTTGTGGGTTTGATTGTAATAATGGGCTTTTATTTTCTTCT
TGAATCTGTTGGGCCTTGTGTTGTACTGAATAAAAAATGCCCTTCTCTTATGATTGGCTTATGAGTATTG
ATTAGTTAATTAATAAATTGATT
>gi|3449466|gb|AI099727.1|AI099727 33880 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120O15XP 3', mRNA sequence
TTNCANGTNGATCGNTATNTGAATTTGTTAAACCAAATAATCANGAAAGNGAGAGGGTGATGAAAGTTTT
CTTTTATTTGTTTAGTTCAAATCTTCTTCAATTTGTGNTGATATTATTTGTATATATATTTCAACGATCC
AATATTGTTATGTTTTATAAGCATATTACAAGTATTGGAAACAAAATTGTATGCTTTTGAGCNCATTTTG
ATTGGAAATGATTTTGAGTTTGAAAGC
>gi|3449465|gb|AI099726.1|AI099726 33879 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120O12XP 3', mRNA sequence
CCGTCACCGGTGACTTACTGGGTGCCTTTACATCGATCCTGACTTGCCAGCACGTTTTCATTNGCCTGCC
TTCCAGGAGTTNTTCCTCTGGATATTGAGCAGGACGGCGCAAATGGAGGAAGAGACGTATAAGCAGCTGG
TGGAGAAGGCAGTGGAGGAAGGTTATGACATCAGCAAGCTTCACAAGACTCCTCAGAGTGACACACCNCC
TGAGTCCAACACTGCCCCTGAAGACTCCAAGGGCGTTTGGTGGTTCAAATCTCTCTTCGGCAAATNGATT
NCNCGGCACACAAAGACTTTGTTTCACCTCTTTGATCCTTTTGTCTGTGTAATATACTACCCCCTTTGTC
TACTCTAGTTATCTTCCATC
>gi|3449464|gb|AI099725.1|AI099725 33878 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120O10XP 3', mRNA sequence
GGGCCTGGTTTTTTCCCAGNTTNTTGATTNTGANCTTTTTGGNCGGAANTTNTTCCNGGTTTCAGTGGTG
GATCCCNTGACATGGCCAGGCAGCTTGCTCTTAAAGAAGGTCTTCTTGTGGGNATATCATCCCGGGTCCA
GCAGCTGCTGCAGCAATTAAAACTTGCACAGAGGCCCAGAAAACGCTGGGAAGCTATTTGTGGCGATATT
CCCGAGTTTCGGGGAGAGGTATCTATCAACGGTACTTTTCGATGCGACAAGGAAAGAAGCGGAAGCCATG
ACCTTCGAGGCTTGAACATTCTCCATTTCTTCTTAAGAGACGCCAAAATAAAAGAGATGTTCAGTTTCTC
CTATAGAGACTCTTCATCTTTAGTTACATTGCGTCTTTGCTTCCATCTGTATCTTCTCTTGTGTGCCAAT
AAAAGTCAAACTAGATTTTCTCTGTTTCTTTTGTGAACCACTTGCTTGTTAATGAAGTTTAAATTTGCT
>gi|3449463|gb|AI099724.1|AI099724 33877 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120N3XP 3', mRNA sequence
TAAGGCTCCCTTCATGGCTTCTTNCGGAACTTTAGGTTGGCNTCGNANCCCCANCTCCCATTGGNTCCAC
TCANGAAATGNATTCCAACCANGCCAGNCTTGGNCTCAAATGGGTNCAGANGGATTACTTGATCTACATT
TATTGTACTGACCCATAGGNGGGTTTCCACAGGGAGCTCCTAAGGAATGCACAACAAGCTCATAGAATCT
CAAATTATATTCTATTTATTTATCTACACTTCCTCTCTTTCTTTTATGTGAAAATTGTGAATGCTCTGTT
TATAGCTTGTCTATTATGTCCGAGAATTTCTTTTTCTGTTTTTGATTCTTTTCGTTGTATATCTTTGTCC
AATAAAGGAAATGATGTGTCTTTACTCTTATAGATATGTATAAAAAGATGTCCCTGTTTTATTTGTTAAA
AAAAATTGTTTATGATAATGATAGTTCTTTCTT
>gi|3449462|gb|AI099723.1|AI099723 33876 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120N23XP 3', mRNA sequence
TTTCGNTCCCTTCCNGGTTTNCCCGGTTCCCGGTTTGGGGTCTTNCCTTNGNGANGGTTTTAGGANGAAG
GGGCAGGTTTCAATTCNCAGNCCCAANGNACTNGTCCACCNCACCTCAAGACTTGCCCTCCTCAGCTTCT
CTTTGTTCCACCAANGACAAAAAGATCTGAAGGAACTTCACTGGCACAACCAGATTCCGGGGATGATCAT
CTCAACTGCTGGTGATGGTTTCAACATCTTAATGCCTTACAACATTCAGAACACGCTTCCGTCTGAGCTA
CCAGCCTGAAAGACAAGGTCTTACTCTGAAAACTCTTGAAGTATTACTCATAGTTTTGTGTTGTCCTCTC
TCTGTTCTCTTTCCTTGTATCATTGATGGCAAGTTGCAAGAATTATACACTCTTTCACAAGTTTCAAGTT
TTCATCATCAGTTTATTTACTG
>gi|3449461|gb|AI099722.1|AI099722 33875 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120N19XP 3', mRNA sequence
CTNATTCAATCCTCCAANTCGTTCGGGNGTTNCTCATCCCTTGNTCCGGGGANTTNGCCACTGNNGGGGG
ACTTTTCCATAATTCGACAAGGAAGGAGTGATCCCAACATTCCACCATTCNACAATCTTGGGTATTGGCC
GAAGCNTTGATGAGACAATGAGAACCCTCCAGGCATTACAGTACATCCAGGAAAACCCGGATGAAGTCTG
CCCAGCAGGATGGAAGCCGGGTGAGAAGTCAATGAAACCCGACCCAAAACTCAGCAAAGAGTACTTCTCA
GCTATTTAGAAACTCTACTATGATAGCAAAAAGGTACAATCTTTGTTATATGTGAGCAGAGTTTTTTTTC
TTGTACGCTAAAACAATCCTTTGTTTGATTCTCACTTTGTCCCCAAAATTATAATAAAAAACTTTTTCCG
TT
>gi|3449460|gb|AI099721.1|AI099721 33874 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120N14XP 3', mRNA sequence
AAGNTTTCNNCCNCCAATTTTCGGTCCGGTGTCTCCNCCCAACTTCCCCTCATCCTGTGTCCCTTCGTGC
GAGCNTGTAGCTGGTCCATCATCATCGAACCATCACCACAATTCACAGGCCGGTTTCGATTAACCCGTGG
ATTGCTTGTGCTGGTCAGGTGGCTCATGGGCTGAATTTTGAAGCCTTGCGTCCACGATCGTAATTTTTAG
TGGTGGGGGAAGGGTGTTTTGGGTTTTTTCATTATCGTTATATAGTCTATCTGTGTGGGGTCATTGTAAT
TTTGGATGATTGGCCTTCTCATGAACTAGTCATATGTATGATGCAACCTTAAAAATATTTCAAGTAGCAA
AACTTAATTACAAACTTGCTATATTAACCAAAAATTATG
>gi|3449459|gb|AI099720.1|AI099720 33873 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120M11XP 3', mRNA sequence
TGAAGTTTATGGAAGGTGTCNTCCCCATNTGCCAGGTCAAGNGGATGNCCACCCTGATGCTTTCCAAGGT
TTGGNGGCTTCAAGCTGGTCACAAATACTGTCTATTGGNCCGTCTTTCTTCTGAAGTTGGGTGGACCCAT
TACGNCACCATCCAAGGAGCTGGAGNCAAAGAGGAAGGAGAGAGCCCACNTGGTTTNCGAGCGAAAGAAG
CAACTTAACAAACTTAGAGTTAAGGCCGAGAAGGTCGCTGAAGAGAAGCTCGGAGCACAGCTCGATATTC
TTGCGCCAGTTAAGTACTGAGCTTGTCAGTAGTAGTTTTTTTTTTTTGGTAAGGAGCTTGTCAGTAGTAG
TTTGTCTTGGCATGTTTTGAGCCAACCCAATACTTTTTTACTTTTTATCTTTTACTTAGGTCTTGTATCG
AAATTTGTACTCCTAACATTTTNTANGCTGAGAGTTATATATT
>gi|3449458|gb|AI099719.1|AI099719 33872 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120M10XP 3', mRNA sequence
TCTCATCAACTTCCAGNTCCTGCCNCCCGCTGGATATCGTGGACTGCTTATCAAGGGNTGCAATCGCTCA
GGAACTTCCGAGAAGAANTGCAAGACGTTGGGTGTTTGGAATGGNCCTCTGATACTCGTAAATGCAGAGG
AATTCCTAGTGAAACGACGTCTGCACACTCTTGCGCGCATGCCCCCCTGAGAAATCGGTTCTAAGGCAGC
CGGAGTTGGCTGATTCTTGAATGTTCAAAACGTTGCTATANCNGGATTTTAATNCCTTATGGGTTATACA
ANTAGGAACACGAGCTGCTCCATGAGAATGGTTGCAGACTTTGTGTAGTGTCTATATGTATGGATTCAAA
CACATCCTCCAAAATGTCCCTTTGCCTTTGTGTAAATAATGATCGCTACAACAATTGTACCTCTACTATG
ATATCACTGTATTCTATTTGAGGTTTGTTACATTTTATATGAATGATATTAGTGT
>gi|3449457|gb|AI099718.1|AI099718 33871 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120L20XP 3', mRNA sequence
AACCTGGTCCCCCTCCAGGTCCCGGCCCGGATNCCCGGTCGNCCCCACGCGTCCGCGATNCANTAATTGT
TGATTNNCTCAGGGAGAGGGATTTNTTCCCAGAATNGGGCCCAGGAANTGGGGACCATCCGTGTGTGCTT
TTGGACAAAGATCTCCAGGGAGCTGCACCCACCATTGCACCCGCTCTTAAAGACAAAGGGCAANCCGTTG
ATTTAGTATTGGAGAGTAAACCGCTGAAATGGGTGTTCAAGAGAGCGGCTCGGGTAAACGCAAGAAGGCC
GGTTCTGGTTGGGAAGTTGGTTCGGTCAGTGTCAAGGTTTTGTCTTCAGGTGAGCAATTTCAAGTCAAAC
TTAATGACTTGGAGTAGTAGTATCTAAGGCTTGAACAAATTGTTCAATTGTCCTTTTTTTCAAAAGCAAT
TGATTTGAGATTGGATTTTTATTTTGTCCTCAAAGGTTTCATTAAGAATTTTATTGATGGATCTTCAATA
CTCGTTTATTCGTCT
>gi|3449456|gb|AI099717.1|AI099717 33870 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120K5XP 3', mRNA sequence
TTGANTTCCCGGTTGGNAATTCCCGTTNTTGCGATNGCNGAGCTNANGCTATGATAATGCAGAAGGATTG
GTTAAGATTCTGGCCGATAAGGANCTGATAAGATCTTGGGCNTTCACATTTTGGCGCCAAACGCTGGAGA
GCTGATTCATGAGGCTGTTCTTGCGATTAACTNCGATGCATCAAGTGAAGACATTGCTCGAGTCTGCCAT
GCTCATCCCACTATGAGCGAGGCTCTTAAGGAAGCTGCCATGGCCACCTATGACAAGCCTATTCACATCT
AAAAGGGAACAAGGAAGACCTTAAAGGAGTGAGCCACCTATGACAAGCCAAATCGATATCTTAACCTGGT
TGGATTTTGGTTCGGTTTTCTGTGGTTTAGCCTTCAATTTGTCCTTTATACTGTGTTTTTATTCGTTAAT
GTTCAGATACGTGTTAAGCCTGATCTTTAATAAAATATTCAACATTCACTC
>gi|3449455|gb|AI099716.1|AI099716 33869 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120K16XP 3', mRNA sequence
TCATTGGNCCCTTNAGGATCNTGNTTGCTNAAGTCCATTCCTNAAGCTATTTGGCAGGGAGATTGAGAAG
GCANCTCCAGGGCATCTACCCTCTTCAGAATGTTTTCATCCGTAAAGTCAAGATCCTCAAGGCCCCTAAA
TTCGACCTTGGCAAGCTCATGGATGTTCACGGAGATTACTCAGCAGAAGATGTTGGTGTTAAGGTAGACA
GGCCGGCTGATGAGATGGCTGTTGAGGAACCTACTGAAATCATCGGAGCTTAAGAAATCGAGAGATGTCT
TTTTCTTCTAAACTTTAGCTTTTTGATGCTCTGTCGTTTCACACACTCTTTTGTTCCCGGTTTAATTTTG
CTGTATTGATGACTTTTCTCAGTGTAAACTTGCGAGTTTTTGATAATTTATGGAACACCTTTTCTCT
>gi|3449454|gb|AI099715.1|AI099715 33868 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120J7XP 3', mRNA sequence
TCCGGGAATTCCCCGGNTCGACCCCACGGCGTCCCGTGACAAGGCAACAAACNGGGNCACACCCTTGGCT
ATTTCCATGATTGTTCTTGCGGGTATTGTCCCAATGCAATCGCNATTTACAGCGATGCTTATGCGCTATT
CAAGAAGAACGCTCCTCGTGAGTAAATCCCGGTATGAGAAAATGTGCNGTTTGGTGTTTAGCTTTTGCTT
TTTCTTCTNTGTGAAATCAAATAATGAAGAAGACAAGACTTCTCTTCTCTTATATGTTTGTACTTTTGTC
GTTGAGTGTTCTAAGCGGACTTTTGCTTCGGTGTTATATACCACCATGAGTGTTGTTTGTAAAAAAACTC
TGTATAAAAATTGTAATGCNGATACATATTTTGCCT
>gi|3449453|gb|AI099714.1|AI099714 33867 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120J20XP 3', mRNA sequence
CCCCCCCACTCAAGGTGCTTCNTTGGAAATTGGGTGAGGTTGGCCNCTCCGCGGGGNCCAANTTCNAGGG
GGGCCTTAAAGGNCTTGNGCTNCGNTGATCCATTGCAACAANTNTGAGAGGGAGCTGTGACCGTATCCGC
TTGGAACTTGCTTTCGTCCCCATTCGTGAGAGCTGAGGTGGTGAAGACCACACTTGCAATAAGAGGAGGT
CACTACAATTTCGTCAAAGGAACGTTTGATCTCTGGGAGCTCGATTTCAAGACCACTCCTGCTTTTGCCT
TCTCTTAAGAAAGAAAGCTACCGGNACATATAAAACTCTTTTGAGATAAAAAAAGACACTTTGACTCATC
TTTCTTCATTCTCTCATGTTGATGATTCCTCTCCAACTTCTTTGATTTCTTTTTGTTAATTCAAAACTTC
AACTTTGCTGCTTCTATTTCAAAAGCTCAAACAATAAAGCTGTAACCAACGTTTGAAACTTCTATATTTG
TCTAATTGATGTTTGAACG
>gi|3449452|gb|AI099713.1|AI099713 33866 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119I8XP 3', mRNA sequence
AGGTCTGGGGTTANNTCAGGGATCNCAAGCTGCCATCGTCGTCTTGCCGTAGAGGTGGTTCAAGCGTATC
AGTGGTCTCATCTTACGAAGGGNCCAGAGGTGTCCTCAAGATCTTCCCTCGAGAATGTCATCCGTGACGC
CGTTACTTACACTGAGCACGCTAGAAGGAAGACGGTGACCGCCATGGATGTTGTCACGCTTTGAAGAGGC
AAGGTCGTACTCTCTACGGTTTCGGAGGTTAATCCGATTTGGGGGATTAGGGTTTATGCAAGTTTGGGGA
TTTCTTCTTGTTTCTGAGATCTGTGTTAAATGGTTTGAATTAGTCTAAAGTAAATCTAGGNGTGTTAGCT
ACTGCTTTTGTTTTCTATTGTGATGTCGTTGTTAGCCAATGCGGTGTNGTTGAAAATCTTTGCAAACTTA
AAGCTAAGAAAATCTAATGAGGATGAACAATTTACTC
>gi|3449451|gb|AI099712.1|AI099712 33865 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119D8XP 3', mRNA sequence
GGTGCCCCCCTTTCCTTAAATGTTATAGGTTTTCCAGGNNTTTTANGGTTGGTGGGATTTGACGCGAGCT
TACCCATCTTTATGGTGCTTTGGACTATTTAGACCNTTTAGTGGTGGCTTTCCTCCGGATCNTCATGTTG
GGTATCCGGATTACTGAAATTTCAAGGATAGTTTGCAAATAAAATTGAAGAAAAGAAAGAAATTTCCTTC
GCGATTTTAAGATGCCTTTTAGCCGTGATTTCAATTGTTCGGAGTTTTGATTCGTTTTGCAACCAGCTTT
GTCGGTGAAAATCAGAAGAATCAATAGTCGAATTTCAGTTATCGGCAATGATTTTCTTCACCAGAATCAG
CATCTTAGATGGCGGTGGTGATGTCGGAAAGCTTTTAGAATTTTCATCCAACACGTGTACCACTGTTGAC
ACGTTTGTTTGGGAATGAAACTAATGATAAACTTTCTTCAAGTTGAAGCAATATATTGTGTGGGCCTTTA
TGGGCTGTAATCTGTTTTGTAACCCATGTTGTTATGAATAAAATCCTAATCTTGCGAG
>gi|3449450|gb|AI099711.1|AI099711 33864 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119D7XP 3', mRNA sequence
GCNTGTTAGNTATTCCCTGCCGNATTCAACCGGNCCTGGGGGAATTAAGGCTCAATGGTTTACCTNCCCG
AAGAAGGCAAAGTGTCCCTTCCTTACAGAACTCGTTGCAATACCAAGATGCTCTAGCACATGTGTNGTCC
TTGTTCTTTAATTACTTGAAAGGTATTGATGAACTTTTCGTTTAAGGTCAATCTTTTGGTCGTTAAATTA
GTTGATTTTCGGAGGCTTTGAGCCACATGTAAATTTTGCNGTTAAGTCCTTCTTATGCTGGTTGCTGTTC
ATGTNATAATCATCAATCACCAAGTTTGTTTCGAATTTGATGGATACTTCCACCAAGTCGCTGTCAAATA
TTTTGTATGCTCCCATGGATAATTATTTTGTATTTTTGTAACTGAATGGTGATTCCTTACATTTCAGGCT
TGTTAGCTTTGCNATTTTGTTATTTGTATTTTGGTTTGAGTTAG
>gi|3449449|gb|AI099710.1|AI099710 33863 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119D6XP 3', mRNA sequence
ATTGGTTCCCCGGAAAACNTTTCNCNTGGCTGGTTTCCCTTTGTACATTGGNCGGGTCAGNCGGATATAT
GGCCCNCTTTTGGGTTTAAGNCCGGGACNACGAAAGCCGGGGATTTGNGNCCTTTCTGATGGATGCCCCT
CCGGGCGGTAATGCTATTGGGGCCATGGATTACATTCTGATCAATAGGGACTAGTAGTATGGATTTACTT
TGTACTTCAGACTAGGTTTTGGTCTCTTCCGTTTTAGTAGTTGTTCTCGTGTCGCTTAGAGTCTGTGTAG
GTGGTCTAAGAGATGATAATATTCTCATTTGTGGNGTATTATCTATCTCATTGTGGTTTAAAAATGCAAT
GGTTCCTCGATCAGGTAGCGCTGGATCCGATAGTGTTTCAGTTTGATATTAGATCAAACCATTGCATTTT
GGTCCAATTTGATAGAGGAGAATGTTATTTACCTTCAATTGGATGTAATCATTTGGTAAATAAAAGTTGA
TGTTGAACC
>gi|3449448|gb|AI099709.1|AI099709 33862 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119D12XP 3', mRNA sequence
AATATCCNTTTCGANACTATTNGTGTAAGTTTNACGTTGAAGAAACNAAAAGAATCAAAGGTCNGATATA
TTCGGCGATGATTTCTTATCCACCGGAATCTGTNGCTCAATATGGCGGAGGTTNNTGTCGGAAAGCTTAA
GATTTATCCTCCAACACGTGTATTTGCAAATCCAGCTANCGNCACGTGTCTCTGGGTGGANTCACGAATA
TCCCATCTTCTTCTTTAGGCGGTGCCCTTGTTGGACTCGTTTTGGGCCTCAAGTAATACATATGTAANCC
TTTGTTTGTAAGAACTTCTGTTATTTTGGCTTNGTATAGTTTGGTTTATTTAATAAAGCAAATCACTTAT
GAG
>gi|3449447|gb|AI099708.1|AI099708 33861 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119D10XP 3', mRNA sequence
CGTTTCCCAATCCCGGTGGGGGGAAAGGCCGGGGTTCCCCCGTTGGACCCCGTTAGGGGGGAAAGNTGGT
CCCCCAAGTTCCGNGTNGCCCTCCCCNNGCAGNTCCCTTTTCCCGNTCNTAAGGCCGTGCAGGTCCNNCC
TGGATCGGAGNCTCCCAAGCTTGCCTNTGGAGGNCCCGGGGATCCTCCTGGGGCCTTAGCTGCCCCTGNT
GGATCCTCTTAGCCTTAGCCCTGGGATCCAGGAGGGAGCCNTTAAGGAGTGAAATGAAGATGGGTTTGGG
GATTGTATCGAATTTCGATTTGAAATTTGTGGTCTTTTTAATGGTGTTTTGATGTGAGAATATAAACTTG
CGTTGATGATGCTCTATGTCTTCGTATTTTTATGTTATGATCATATAAAAAAGTAACTGATATTTTCTTA
TTAAATGGTTTGTTTCTAACT
>gi|3449446|gb|AI099707.1|AI099707 33860 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119C8XP 3', mRNA sequence
GGCCCAGTGGCCATTGNGACAACAGCTTTNGGTGCNNCCTTTGCAAGCTGGATTTAGCTGTGGGATTCTG
GAAGGATGCNGACATATTCGNGTCGGGAGAGAAGGCGAAGAACTCCAAAGTTTTCAGACCCGTCTATGGA
AGAAGGANTCAGGAAGAAGAAAGTGGCGTCTTGGTGCAAAGCGGTGGAAAGAACATTTGATCTCGCTGAC
CTCTCTATCTAAAACTTGAAGAAGTTGATCTCAGAGATNTCCTCTTTATTTACCNCAGTTGGGCTCTGTC
TTCCAAGTCACATAATGTTTTAAGGTCTAATATATGTTTGATTAAACCGTCTTTGAATGATTTATACATC
AATGCTTAATTCTGTTGGAAGT
>gi|3449445|gb|AI099706.1|AI099706 33859 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119C5XP 3', mRNA sequence
AGGGGGAAAGTNTCAGNGTNTTTGGGGCTCAACTNTNTAACGGTGGTNAGACCNGTAGCCGANGGGTCAG
NCAGCGACCCACTTTAGAAGTGCTTCTTCACATNTTGTTAACAAACTACTTTTGCTTACCACTCGTAAAC
AGATTAACCGGTTTATCTNGTATGTACCGAATGAAAGGGAAGCGGAGCCNGAAATCTTGTACCACAAGAG
AAGAGCTATGCGGCTGTGCACTAGTGATTAACCGGTGCTTAACCGGTGCTTCACCTTTCAGTTCCTTCAC
GTCTCTGTGGATTTTTGTTGTTGAGTCTTTTTTTCAAATTCTTTTCCCAGCTTCAAATTACTAGAAACTT
ATGATGATATAATAGAAAGAGTTAACTATATTCCTGTATGGNAGTTATAATCTTGCAACTTGTAACACNG
AATCCT
>gi|3449444|gb|AI099705.1|AI099705 33858 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119C13XP 3', mRNA sequence
TTGCCGGTTTGGTTTGTNCCCAACGTTGTTTGGNTTTCCTTCNATAACCCCATGGNCCTTNTGGTTGGNN
TAATGGTTTAGGNGTTTTTTCGCATTAAAGACTTTTATTANCCAATTCGACCTTTNNAGTTTGGGGATTT
GCNGGGATTCAATTTTGGAGATTGCATCNTTAAGTTGAAGAAAGAAGAAGTTTTCGTTGCATATTAATAT
TGCCCTTAGCTGCTAAGTTTTTATCTGGAAGTTCGATTGGTTTGTTTAAGGTGAAACCCAGAAGAATCAA
ACTTGCTTTCATTATCAATGTTGATTTTTCTCACCGGAATCAATCTCAGACGGCAAAGGAAGATGTCGGA
AATGCTTTTAGATTACTCATCCAAACGTGTGCTGTGTTGTTTTCAGCTGTTGACACGTAAGATTGGTTGG
AGCCACAATATCAGTTCTTCATCTTTAAGCAATGTTCTTGGACTCATTTAGGACTTCAAATGTTCTTGTA
ATCTCAGTGTATGTTGGGCTTTTGGTTTTTTAGCCCATGTATGGTTGGTTAACGTTAATAAGATTTTCCA
CTTATGAG
>gi|3449443|gb|AI099704.1|AI099704 33857 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119C10XP 3', mRNA sequence
AGAGGCGGGCCCAAATTNGGTTCCGGAGGACATTGCCTTCTGGTGAGTCCAGGNGCTTGGTTATCCAGAT
CTGTGCAAAGNGNGATNTGANGTAAGAGAGAAGAAGACTTCAAAGAAGAGNCCAAGNGGATTGAAGGCAA
TGGGGNGCATGGAAAGCGATTCGGAGTGAAGANCCNTCGAAGAAAGAACTTAAATGNGATATTCAAGATT
TTGGCGAGGGGTAGGAAGGTGTATTTCACTTTTTCGTTGCATTTTGAGATGCCTCTCTTCATTACTACAG
GTTAACTNTGAGGCACTTGTATTTTTGACGGATCTTTTGCTTTCAAAGCTAACCTATCTTCTTA
>gi|3449442|gb|AI099703.1|AI099703 33856 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119B15XP 3', mRNA sequence
CTTCCGGTGATCTNGCAGCTTTGAGCTCCCTTAAAGGNTTTGAAAGGACTCGGAACTTNCGATTACNCGA
TGGAGANAGGGTTGGTACATGCNTTCCATNCAGGAGGAGTNGTTCATATGCTTGAGGGTTGGAAGCATCA
TGAGGTTGGAGCCATTGATGTTGACCGTNTCGATTTGGTGTGGGAAGCAGCCATGAAGTATGGTCTTAGT
GCTGTTTCTTCACTCACAAATTGAGTGAAGAGAGAGACACGTTTCATTGTTGTCTTTTGACTCTCCCAAG
ATTGGTCATTCTTTGTACAGGTGAAAGGAGATGCAAGCAGGAAAAAAAAGTAGAATTTCACCTTATGTAT
TGTTTTATCTTTTATTAATGATGTATTACTTTCTTTTTAGATTTCCTTAATATTAA
>gi|3449441|gb|AI099702.1|AI099702 33855 Lambda-PRL2 Arabidopsis thaliana cDNA clone 119A10XP 3', mRNA sequence
TGGCTCAATACCCNTACCCTTGNAACCNTTGGGNTAGACTTGGTNTCCACAAGAAGCTCTTGAGGNAGAG
CGTGGCGANCTGATCCGTCAAAAGACATCCTTGTGGTTGGAGAATCTGGGTTATTCACTCCCGAAGATAT
CGCCTTTGTTCAAGAAGCCGGTGTCAAAGCAGTTTTAGTCGGCGAATCTCTTATTAAACAAAGCGATCCC
GGGAAGGCAATCAGCACCCTATTTGGAAGAGATGTCTCAGAGTAAATTCCGAGTAGAAACTTTTTGTATA
GAGAAAATCTTCATTGAAGTCTCTTTTTTTCTTCTTAAGTGCCGCTCAAGTGCGCAGAGGCTTGTGCCTT
TACAGAAATGTCCAATTATTATTATTTTCTTGTCTTACATACACATTGTGTACTTAAATTTATCCATCAA
ATGTC
>gi|3449440|gb|AI099701.1|AI099701 33854 Lambda-PRL2 Arabidopsis thaliana cDNA clone 118A10XP 3', mRNA sequence
CCGCGGACCTTACTNAAGNTTTTTCCCNAAAATTTTTGGCTTCAGGGTCCNCAACCCTTTNNCTAGGGCT
CTGCATTCTCCATGGGTGATCCATTTAGTGGCTCTNTAATTGCATCCGGNTGNGCAACTGAAATGATAGC
TGCGGTGACTGGNGCATACATCACCCATTGGGTTAGAGGATGAGAGCTGAAGTTGAAAGATGGAATCTTG
AAAGAATCTCATGAAGTTCCAAGAAAACTTAGAAGTGCAACAGCCTGGCTCATTGGGGGAAAAGANCGAC
ATACTTGGGTCTTGTTGTTGTCTCCGAAAAGATTTTCCCCAGTTAGTTGGATTTTGTTTTGAACTGTTGG
ATTATTATTCGTTTTTCTAATTTCATGTAAAACTCATAAATTTCAACTGAAGTATAACTTAGATC
>gi|3449439|gb|AI099700.1|AI099700 33853 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116O6XP 3', mRNA sequence
CGTTTTCNGGACAATCCNCCANTCNCCTTGGTTCCACGTGGGGCTACATCCNCGCCGGTGGANTTTCAGN
GGGGCTTCCATGACCCCACCGTTNCTTTCGGACCNNCCGTCTTAANCTGGACGTGGCCCACCCACTGGGT
TTTACTGGGCTGGNCCTCTTATTGGTGGTGGACTCGCCGGAATTATCTACGACTTTGTCTTCATCGATGA
AAATGCCCACGAGCAATTGCCTACCACCGATTACTGAAGACGTCAAATTCAACGTTGTTAATCTGATGAA
TTTTTCGTGATTTGCTTTTTTAATTTGCATCGTAATGGGTTTCTGGCCGTTGGATCATTTTTAGATGAAT
CTTTGTCTATTGATTGATCATTTATGTGTCTTTGGGTTTGTTGTTGGAGTTGTAATATCTCTGGAAGGCT
TTTGTGCAATTGTATTGTACGGTTTAATAACTATAATTGAGAAAACCAGGGAATGTGAATTATGAAAATG
AATTTTTTTGTT
>gi|3449438|gb|AI099699.1|AI099699 33852 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116N2XP 3', mRNA sequence
GGTTTTGGTTNTTCGGGTTCTTTTGAACNANTTCCAGGTTTGNGGCNTGGCTTNGTGAGGATTTCNGATC
AGGTTTCTGAAGGCGANGTGGCGCNCGAAGACTGATTTNGATCNCAAAGGTAGNTAGAATGTAAAAGCAC
GTTGTTCTCTCTTTACATATTCGCAGATTCTTTTGTTCTCTGTCTCTGTGATTCTGATCGCTAATGGGTG
TTTAAGAGTGGAGGAGACTGAGTCATCAATCTCTAACATTGGACCAACTCATGGAACATAACTGATTCAG
GAGACATGAAACTGTAGTTGTATTGAATTGTAGTCTGAACAAATTCCAGATCTTCTTGTATTGTATTCAT
TTCTTGTTTTGGATCACTCACCATTCATGATATATATCAATGTTGATATAACTCATCAATC
>gi|3449437|gb|AI099698.1|AI099698 33851 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116M13XP 3', mRNA sequence
ACCCCTTTCNGGTTTAGGAGACGNTCNACGTCGGATGCGTTCGAGAAGGCAGCNGGNGNNTCAGNGACTG
GACCAAGGAGCTCTCCTCCTACTTACGGCATGTGATCTCTAACACNCAACACAAGTCTTGAAAAAGAGNA
GAGANGAAGAAAACAGNGTACCCACCCTTAAACGATGTCGTTTAGACTGCATGAAGTGGTGGTTTTTTTG
CTTTTGTAGGCCAAAGAGGTGTTCAGTGTTCTCTTATGTATGCGTGTATGAGTTTGTTNGTGTGTTTGTT
TTTTATATGTAATCTCGTTTTTTACGGTAATGCTTTTATGCGTTTTGTAAATTTTTGCTGCAATGAAAAT
AAAAACTTGTAG
>gi|3449436|gb|AI099697.1|AI099697 33850 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116L17XP 3', mRNA sequence
AGTGAATTGCCAGTTTACTTTTCCCGTCCCGTTAGATCCNGGGNTCTTGNGTCAGCGTTCCACGTTGCTG
GGATTTTCACTGNGCCCCTGGNAAATTTNTCGCCCTTAAAGGAAATTNTCAACAGTTTTCCNGGNTTTGT
TGGATGNCAAGTACGATGATCTTCCGAACAATCGTTTTACATGGTTGGAGGTATCGATGAGGTGGTTGCA
AAGGCAGAGAAGATCGCTAAAGAGTCAGCAGCTTAAGAGATTGATTCAGATCTTTCATGCTTAATACTTC
TCTTTTTTTTCCTGACAATAACGAAAAAAAAAAACCAATGCGTGCGACTCTCCGACCAAACGGAATCTGA
GTTCCGTAATTATAGTTTCTTTTGGTTCAAATTCCATGAGAGCTGGCAAGATGATACTGAACAGATCCAT
TCACTGTTAATCAAATTTTTGGTTGTTTTGCTTCCTTTGTTGAAATAAAGATGAAAAATCTTGCAGATTC
T
>gi|3449435|gb|AI099696.1|AI099696 33849 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116L16XP 3', mRNA sequence
ATCGTGTTGGGGNACTTTTTTACTNTGGAGGTCCAGGAAANACCNTGGATTGTCCNTTGANGANTCNAGA
AANCNNAAGCNGAAAAAGGTTATTGATTATTATTCNTTACNTGTAGTGCACATGAATTTTTGGGATTAAG
GGAGATTAGGAATTTACATTGCCGCTAGGTGTTTTGCAAATATCATGTAGATGAGTTTTTTTTCTTTACC
ATAACAATATCACCNCGAGCGAACAAAATCTTGTTTGTTTTTTTCTATTTTGTTAAAAATGATCAGTATA
AAGTGTGGTAGTGTTATACTTTTTTTTTCTTTTCGAATTTGTGATGGCGTTACGGGTTTTGTAATGTTTA
TATTGATTAGTGTTACCAATGTGAGATGGACAGTCGAGTGTTGCTATGTT
>gi|3449434|gb|AI099695.1|AI099695 33848 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116L15XP 3', mRNA sequence
CTTTTCGCTNCGCTTTGTNGCANTCCTAGAAACNTCCCAAGGTACACCTTTCCCACAAGNANGCTTAANT
TTTTAGCTTGGNTTGATTCAAATTGANGGGTTTGGNGTAAATGTTGCATCCGTGNNGACCAACATNATTT
TCATGGATATGGAGGATGGTTCAAGACTTNCGGCTGAGAAACTGCGGAANAATCTTAGAGGAGAATGGCA
TTCTCCTTATCCGGGGAAACTCATCCCGGATCAGAATAGTTATACACCACCAGATAACAACAAGTGATGT
GCATTACACATTGATCTTNTTTCAGCAAGCAATGCTAACGATGCAGGAACCAAGCCGAACCTAATTTGGC
GAAACCGAAATGCTTCTTCTTTTCTTTTCAACTTATTAAATATTGTTGTCTAAAGTACATTTTAATTAAA
ACTATAAGCATTTCAATGAAATTGTCACCCTCATTCCTGG
>gi|3449433|gb|AI099694.1|AI099694 33847 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116K19XP 3', mRNA sequence
CATCTCTGTTTCCNCAGTTAAGTCCTCNAGGGGNAGNATTTNACGTGAAAGGATNTTTTGCTTGGTCTCT
NGGGATAATTTCCGNATTCTNTACCGNTTTTCCCGTNCAGATTCGGNCTAAGTACGTGATTTCGCAAATA
TCACTGNTGATAGAGACCTCAAAGCATCTGGCAAATGGTTCCAGANGTTCATAAACGTTACCGACGAAGA
CTCTACGAACCAAGATCTACTCCGCTCAAGCGTCTCCTCCAAGAACCGTGATCGGAAGAGTCTTGCAGAT
GCATGAAATATCCAATCCACTATATGTCCACCAAGATCATCTTCATGTTTCCTCTTTCTACTTGCTCCAT
AGATAAGGAGCTTTTTCTACCATATGTATTAAAATAAAATCCTAATAAAAGATGATCAATAATAATAAAG
ACTTTGTTTACTAC
>gi|3449432|gb|AI099693.1|AI099693 33846 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116J11XP 3', mRNA sequence
GCCCTTTTCTTCAAATCGGNGGCGGNAACCTTTTTGTTTNCGGAGGNGCCGGGCCAAAGGAGNTTCCTAA
GGCTCGTCGNCCAGACCANGGNCCCCAGTTGGAGACCCNTAGGAAGGTGGNANGAGNCAACTGNGGGAAG
TCAAGGATGANCTCTGAAAAGAGAAGTGTGTTGTGTCTCTTTAGCTGCTAGCTTAGTTTGGGTAGTTTTG
AGGAAAATACCCAGAAGAAGNCAGAGCATTGAGTAGACTNAGAGACAGAGAGAGAGAGACGACAGACAGA
CAGAGAGAATCTCTTTATCTATTCATTAGGTTTTTATATGTGCACTCTTCAGAACAATAATGGCTGCCTC
CTTTTCTTTTTTTTGGTTGATGTTACCTTTTTTTGTTTGAATTCAGTTCTCCTTTAATATAGTTTTTGAG
GCATTTCTTGGGACGAGTTCTAACACTAAAAATATATTAATTCTGAAGC
>gi|3449431|gb|AI099692.1|AI099692 33845 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116H21XP 3', mRNA sequence
ACGTCCCCGGGNTTNCCCAACTAACCGCTGAGGCTTTGCTCTATTGGTCTACTCCATCTTCAGATGAAAT
TCTACAGGCGCAANGATTTCTTGCATTNGTGGAACAAGTGAGCTTCGAACCCGTCCTCCAATCGTGAAAG
GGACTTTTTTCANACAGTTTTACCAAANTTTGGGGATAATAAATCGTGGACGTTTCATTGCATATTTCTT
TGTGGTGGAGATGCCATGTAAAGGAGTNTNTTTCTAAGTTTGTTGTGGAAACTTNATAAACTTAAGATGT
TTNTTGTCTGAGTTCTTTTATGGGCTCTTTTATTATATATCTCTCTCTACCAGTTTTCAGCT
>gi|3449430|gb|AI099691.1|AI099691 33844 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116G10XP 3', mRNA sequence
TTAGGACCTGANCCGTTGGGGTTTTCCGNCGGTATCTGATGAAGNGTNCAAGNGCTTCTTGCTCACGATC
CCNGTGCCCCCGTAGCTTGGAGCCCTGGAAGTATTTGTGCACTGGCACCCTTGAGTATGNGGAAAATAAG
CGGAGGAGGTAGCTCATCCGGAAACTCTCCTCCAATTCTGTGTCGAGGTCTCGAAAGAGATCGACGAACA
TCTTTTGGCCGAGGAATAGAGGAGTACTACTACTCTTCGTGTTTGAATTTAAATGCAATAAATAAGGACT
AAGAGCCATGTCTTTGTGAGATATATGAATGTGAGTGTGCATCATGAATGTATGTATACTAAGATCGTTT
TACGTTGGCTACTGTAACTTTGAGAAGCAATGTGTAGTAGCTGTGATGAAGCTAGTATAAATATATAATA
AGTATGTTATATATGTTTGCTAATAATAAATGTTTGGACT
>gi|3449429|gb|AI099690.1|AI099690 33843 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116F7XP 3', mRNA sequence
AAATCNTCCGTGNTGACCCTCTNCATTCCTANGGCCATTTTGGGGTAAATTANCNTCTTTTCGNTTCCAT
TCTTTCTTCNTTCTTTGTTTTGGGGGTNCAGTCTCCGGCCTTTNTATTTGTGGAGAGNCCGANTTTATTT
CATTCTTTGCATCCCTGTGTAGTTATGGAAACTCACAGGGGTTATTTGTTTNCCATTTTGGTTTTGTCAT
AGAATGGCTTTAGGTGTGTTTGATGCTGTCCTGCCCAGAGAGGGGAGGAGAGTATTGTTTTAGTCAATTA
CTTATTTGTTGGTTTGGGCGAGTTCTTATACTCGTTTTGGGAAATTGTAATGAATGAACTAGAATTTGTT
TTCACTATTTATATAGGTTGCACNTCTTATATT
>gi|3449428|gb|AI099689.1|AI099689 33842 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116F22XP 3', mRNA sequence
TCCAACCAAGCGGTCTNATCAANCNCAATGTACGNTGNTGGATACNAATGGTTNCCCTCCACAGCCACAG
GNCGGCTATGGTTATGCAGCTCAACCACCAACTCAAGACCCTAATGCGTACTATGGTGGTTACACTGGCT
ATGGCAACTATCAGCAGCAACGTCNGTGAAACATCAACATCAGCTATTTCTACCNATGTCTTGGAACAAA
AGATGAGCGATTGTGTCTTATTAGGNCTTCTAGATTAAAAGTGCTCTCTTTTTGTTTGNGTTTTATTTTG
CAAATGAGTCGATCTTGAATTTGCTNTGAACAAAGTGTTTNCTGAATGTTGAAACTTTATTCTGTTGTTT
TTTAAAATAAATATTTATCC
>gi|3449427|gb|AI099688.1|AI099688 33841 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116F11XP 3', mRNA sequence
CAAGTTATCNGGCNAGGACAGCNCCATACTNTTTGGTACACANCACTCGCTTGNCCCCTTGNCCCTCTGT
GAAGGCNCGTGTCAANTAGTGCGGGTTNTTGCANGTGCTCTCATTCAACACGTGTGGAAACCCAAGTCAT
TCTTCACAATCTCTGGAGANGTCGACACAAAGTCAATTGACAAGAGTGCTAAAGTTGGATTGGNTCTCGC
ACTCAAGCCTTGAAACTGAGATGGAAGAAGAAGTTGCAATAGTTTTTTTAAACTNGTTTCTTTCTACGTA
CTCTGTTTTTTCTCTGCTTGGTTCATGGTTTGAGTGGGCAACTNCTGATCTTTCCCATTTTCCTGCCGGA
TTTGTAGAAGAATAAAAAGGTTGAAAATGATCATCTTGAGATGGTGATGAAACTCTT
>gi|3449426|gb|AI099687.1|AI099687 33840 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116E18XP 3', mRNA sequence
TTTCCCCNGGCNAGGNTTTTNCGGNGCTNCCGTNNTCTTCACCAGGGGCAGTCCATGGGNTGGCCCACTG
GATATTTTGGGTTGGACCATTCATTGGAGCTGCGATAGCTGCATTCTTCCACCAATTCGTTCTGAGAGCT
TCAGNTTCTAAGTCTCTTGGATCATTCAGAAGTGCTGCCAACGTCTAAACACATCAAACCAGATTTCTCA
AGAATAAATGAAGTTGTGATCTCTCTGTACAAATCTAAATCAGTCACTTGCAGTTTTCATTTCCCTTTCT
TATATTTGTGTTTTCCACTTGCTCTTTTGTGAATTTTCTTCGGTGTAATTGTTTTTTCTTTCGCTTTTAA
ACGAGTGATTGGAATTATAATCAATGAAATCAAAGAGGTTCTT
>gi|3449425|gb|AI099686.1|AI099686 33839 Lambda-PRL2 Arabidopsis thaliana cDNA clone 116E16XP 3', mRNA sequence
AACAAGGTGTGCGACAACTGTAGCTGTGGATCAACTGCNGCTGTGGGTCAAACTNTANCTGTTGATGANA
TTATTATGGTCTAAANTCATATATATGGCNGAAAAATTGGGGAAAATNTGTGTTTTANGCTAAGAGATGT
GTGTGTGTTGTTGGNATAAAGGCGTGACCGTTGTGTTGCGTATCAACTCTCTTAAGCTTTGACTTTTCCC
AGCTTTGTATTTTCCTATGTNTGGTNATGGTGTGATTGTGTNATGTTTTCATATGTAACGTAAAAAAAAT
ATTTATGTGAAATTGACTTTTGTGACT
>gi|3449424|gb|AI099685.1|AI099685 33838 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115P10XP 3', mRNA sequence
CATGGCTGAATTTGCCTCTAAATTCCGGCGNCAGCAAAACCNGCGGCNTTCATGNCCGGAGGTAGGAAAG
AACGGGAACAANCACGCGAGATTGGGACAAAATCTNTGACAGATTCGCCACTTACTGTGATCACGNCGCC
GGAGCATTAATCGCCGCATTCGCCGGNGTAATCCTTATGCTCATCATCTCCGCCGCGTCAATCTCTCGTC
TCGTCCAACCTAATAAATGCTGCTCCACCACCGCATCTCCCTCGGTCGTCCCCTGAAAACATACACACGT
GTCACGTTCCCCTGTTATTTTCCTTTTCTTTTCTTACTTCTTTGTTTCTTCTTGAGTGTGTGGTGTGTAT
CTCGAGTGAATGTGATTGATCAGATTGTGTAAGCATTTGGCTCGT
>gi|3449423|gb|AI099684.1|AI099684 33837 Lambda-PRL2 Arabidopsis thaliana cDNA clone 115N6XP 3', mRNA sequence
CCCCCATCGAANCGGTTTCATTGTTNGNGCCNCANTCTTAGTGGAGGAGCTTCCCTTGAGCCTCCATGAA
TCCCCGCCTTNGCTTTTCGGNCCANCGGTGTTGAGCTGNACATNGGACCAACCACTGGNTCTACTGGGCC
GGACCTCTCGTCGGCGGTGGAATCGCTGGACTCATCTACGAAGTTTTCTTCATCAACACCACACACGAGC
AGCTCCCAACCACAGACTACTGAATTAATCTCTCTTTTTCTCTCTTGTGTAATTTTATTCGACTTTGAAT
TTGAATTTTAATGTCTTTTTAATTTCCGTTTGTGTAATTTCGAATCATCAAGGGGTTTATGATCGTTCGA
TCTTTTAGATGAATCCTTGTCCGTTGGTTTCAAGAGTGGCCATTGCAATTTCGACTATATAATGTGAATT
ATGTATCAATCT
>gi|3449422|gb|AI099683.1|AI099683 33836 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114P4XP 3', mRNA sequence
GGCTGGTCCTNATTGGGATTNGNGCANCCTGTCTTTTNGGGTTTCCTCTGCTNCTGCTTACCGTATTTNT
CTTCTNCCCTCGGACACNCNATATCAAAATCTGTAAGNACANGACCAGATGCTTCGNTCCCNGATTTACT
CCGATGATAATAAGAGGATGAAAGAAGTTGTGAATCATGCAACAAAGCTCAATGAAGCAATCTTTGGTAT
GAAAGGTGTTCCTGTCGTAAGAGCTCAAATATCTTTTGGGGGTCACTACGATGGACTTTGAATCTCAGCC
ATCATAATAGTTCATAATGTACATACATGAATGTAGTATAAGGTTTTGTAAATTTCTATTATTTTGTTCA
AATATTGATTAATTATGTGGTGTTAATAGATCTTTGTGAAATTTCATGT
>gi|3449421|gb|AI099682.1|AI099682 33835 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114O20XP 3', mRNA sequence
ATTTGCAAACTCACTTCCAGGTGCTTTCNTTTAGGAAGGATTTGAAGCTNAGGNGCNATCGAGGAGATTT
TCCAAGAAGGTTCACGCAGNTTTCCGANCAGACCCACCCATTNAGANANCCGAGAAATCTNCTCCCAAGG
AACACAAGAGGTACAACTTGAAGAAACTGACTTACGAAGAGAGGAAGAACAAGTTGATCGAGAGAGTGAA
GGCATTAAACGGAGCAGGTGGTGATGATGATGATGAGGATGATGAAGAGTAAATCACCAATCAAGCCTTC
TTTGTCTCATGCCTCTAGTAGCTTTTTACTTATTTATTTTCAGACTAAAACACTCAGTTTTTGTTTTCAC
ATTTTAGTTGCGTTTGAAGATTTTGAATTCGAGGATATGTTTTGTTTGAAGAATTTATTATCATCTCTTA
TTACACC
>gi|3449420|gb|AI099681.1|AI099681 33834 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114O13XP 3', mRNA sequence
GCCGTTCTTCAGGTTGCTGNAACTNTTTAGCCGTGCATTCATCGNTGCGGNTTACNTTGTTCCCGGAANT
GCAAGACTATTGGAGCCTTGGAGCTGAGAGTTGTCGCAAAAGGAACTTTCCGGAAGATTCAAGAACATTT
TCTCGNGCTTGGTTCATCGGCTGGACAGTTTANGATGCCAAGATGTGTGAAGCCAAGTAATGCTAAGGTT
CTCCAAATTCTGTGTGAGAATGTGGTGAGTAGCTACTTCAGCACAGCGTTTTGACTCACTAAAATTGTGT
GAAATCAAAGAAAGTGGTTTTTAGTTGTTTATTNCCGTCGTTGTTGTCTTTATTTGTCAATATAGTTTTC
TTTACGTTATTTAATTGAGCATAAACTTTTTTTATCTTTATAGAATTTGTATCACAGTGGTTTT
>gi|3449419|gb|AI099680.1|AI099680 33833 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114N10XP 3', mRNA sequence
TTTAAGGACANTGGNGGGTTTGAGCCATNGCCCCCTGCTCNNTGCTTTTGGCCCTTGGTGGCCATGGTAA
ATTCCAAGCACGGAAAGCATGGAGGCAAATTCAAGCCACGGAAGCATGGAANGCACGGGAAACATGGCAT
GTTTGGAGGAGGAGGCAAATTCAAGAAGTGGAAGTAATCTCAAAAACCCCACCTTTGATCCTCTCCTCCN
GTATAGTCTCATTACCTGACCGATGTTTCTAATAATCCCCCTTCAAACATATTTCATTTTAACTATGTCG
GTTTAGNGNTTACTGGTTGAGGAAATAATTGGAGAGTGCTNGTATAAACCTTATGGTATCTGCAGCAGAG
GTTTCTTTAATCTCTCAATAGTAGATGCTTTGAAACTTTTCT
>gi|3449418|gb|AI099679.1|AI099679 33832 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114M6XP 3', mRNA sequence
ATTTAGAATCANAAGNCGAGGACGAGNNTCTNCTGGCTACNATTTGGAAGATACTTTGCTCNTGGACCAA
TTNAAAGAGACGATTACGCTCTTGAAACTCGCCATGGGAGTTGAATAGAAACCAAAAGAANCATGTAAAC
TGTAAAGTGGCAGACTTTCTGTATTAGAGGTGACTAGTGAGTTCAACTTTCTTAGTCCTGAATNTCGTGG
TGCATCCTCGTAAATCTCTTACTGAACTCAACGATATTCCGATTAAACTTCTCAACAATTCAACATTTCA
TGAAAAACTTTACAATCATTTAACAATAAACTCCAAATCCG
>gi|3449417|gb|AI099678.1|AI099678 33831 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114M2XP 3', mRNA sequence
GCTGGACCNTTTTCGAGGAATTCAGGGCCAGGAACNCCTTTTCCACNTCAAGNATTCCTTCCCTTTGTGN
ATCTTTCGGATCTCAGTCAGCTTAGGGCAGCACCNTCAGGACAGCATTCCCACANTNTGTGTTTGATCAT
TGGGAAATGATGTCTTCTGNCCCTCTTGAGCCAGGTACTCAGGCTTCAGTTTTGGTGGCTNATATCAGGA
AGAGGAAGGGATTGAAGGAAGCGATGACTCCACTATCTGAGTTCGAAGACAAGCTTTAAGCTTCACCAAG
ACTCGTACTAGCCTTTTTCCCAATGGTTGCTACTCTCTCTATCTTAATTTTGTCTTGTTTTATTAATACT
CTTATGGTATGACGGATTGTGAAGACTTTTCTCTCGCCATCCCCTGAATGTTTTTTACTTTTTTCCTAGT
TGAGAACTTTGTTATTGTGTTCGC
>gi|3449416|gb|AI099677.1|AI099677 33830 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114L24XP 3', mRNA sequence
GGTTTTCCNACCCAATTGCGGCCTTTTCACGGGGNCCCAGGTNCCGGTTCGGTNANGGCTTTTGGNCCAG
GTTATTGGTCCAGGGGAAGGGATTTGGTNNCGGTNTTGGGNCGGGNTGGCCTTAGTGTAGTNGTCCCAGG
CACAAGATCCNTCCGTTANTGGTTTCCAGCGCACANTTCCCGGTTTTGTGATTCCAGGTATCACAGTTCC
TGGCTACGGTACTGGATGCCAAACAGGTGGCTGCAATCCGAACCCACCACACTACTATATCCCACCAAGC
TGTCCCCATTGTCCACCTTTCACATCAGGACAAGACAAACACATGTCAGACAAAGGAGCCATGACCGAAG
CTCTTGCACCCACTTCACCGGAGATACATGTTTAAGCTTTAAGAGTCCATGAAACACCAGTCTAATAAAT
CACTCATAATGAAATCTATTTTGGTTTATAAAAGCTTCACAGAAAGTTGAATAATACAACTTTCTTGCTC
>gi|3449415|gb|AI099676.1|AI099676 33829 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114L15XP 3', mRNA sequence
TCCGGGNAGCGNCTCTNTTNTTTTTCCGGCGCCGGNGCTGNTCGGAAAAGAAGCAGAGAAGGAGANGAAA
GGAGACCTATCCGAGATTTGTGTTTGAAGATTACNTGAAACTCTACTCTGCTGTCAAGTTTCAGNCCAAG
GANCCAAGGTTTTGAAGCCATGAAAGCTATGGAGACAACTGTGNCCAACAATGTTGGACCATTGGCCCTG
CGTGAATGATATGTAACTGGTNGGTNGATATATATATATATATATATAGTCTTTATATAATGTCTTAGAA
ACTTGATTATTCACTATACGAATAATTTTGTTCATGTTGTTGTATGTTTAAGTGGTGAATGTGTTTTATA
TATGGGAATTAATGTTTTCTGTTCGTAGAGTTCAAT
>gi|3449414|gb|AI099675.1|AI099675 33828 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114L10XP 3', mRNA sequence
TCGAGTTTCAAAGCCACAGGCTTACACTTGAGGACCCNTGTCACTNTTGNAGTNCATNACTCGCTTCCAT
GGCTNGCTTTCAAACNNAAGTATCCCCAAAGTGGTGGTGTCAGACCTTCGNTCTTTCTACTCTTATCGTT
GGCTTTGACCCTTACTCTCGCCTCCCTTCCCTATATCAGACTGATCCTTCTGGGACTNTCTCTGCTTGGA
AAGCTAATGCTACCGGCAGAAACTCCAACTCTATTAGGGAATTCCTCGAGAAGAACTACAAAGAATCCTC
TGGCCAAGAAACTATTAAACTCGCTATCCGTGCTCTGCTTGAGGTAGTTGAGAGTGGCGGAAAGAACATT
GAGGTTGCCGTAATGACACGGGAGGAAACTGGTGCGCCAGCTAGAAGAAGCTGAAATTGATGCAATCGTG
GCCAAGATCGAAGCTG
>gi|3449413|gb|AI099674.1|AI099674 33827 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114K11XP 3', mRNA sequence
GTAATTTCCATNCCTGGCNCCAATGNTTGGCCCTTTNATCCCCCNGGGATNTCTTCCNGCAATGTCNAAA
ATGCTNCGTTAAGCCAAGACGGACTAGTGAACGAGCTTTGCTGTGATGAAGCTCTTTCTCAAGAATATGC
GGAGTTGCTAAGACNTGATATCGAAGGCCGGCTAAAAGATGATCAAGGTCTATAAGATATTTGGTTGAAT
TGGTTCTGTAAGTGTCATATCTTTGAAGTATCTTTGTTTATTTGCTGAGATCCCTCACTTATNTATTAAG
AATTAGGGTTTGGGATGGTCTNTACTCTGCTAAACATAAGCAAACGTAATTTATCTGGTCTCTAAAGGGC
CGATTCAATTTGATATTTCCNTCTTT
>gi|3449412|gb|AI099673.1|AI099673 33826 Lambda-PRL2 Arabidopsis thaliana cDNA clone 114G23XP 3', mRNA sequence
CCCCGGTTCAGGTTCCCCGGGTCNNTTTCCNCCGGGGGGGNAAAGGNTTTGGGGCCTTGNCCCCNTTTTG
GTGTCNGATTGGGTTTAATGTTAACCCGGGNGTAAAAAAAGGAATTACTACAAGTCAACAGGCTTTTGTC
TAGGTGTTGATTTCGGCGCCCAAGGACACGTGGCGTAAACTGAGCTTCCAGGAATCAATATTCACCGTCT
ATTATGATTAGATAGGTTAGATAGATTTGTGTAACGATGTACAAAGTCATCTACAATATTGAATCTGTTT
CCATTTATTTTACCATATTCTTTTTTTTTATAATTTTCGAAGTTCTACAAACTCTTTTATGTAAAACACA
ATCCAATGGTCATAATTGTGATAAAGACTTTGCAT
>gi|3449411|gb|AI099672.1|AI099672 33825 CD4-13 Arabidopsis thaliana cDNA clone H2G5RP, mRNA sequence
CCTTAGTCANCCAATTCCCCGGTCTCGATTNGAAAGANCTTCTGGCTTTGTCTAGCTTAATCTGGATCTC
AAGCTTAGCNGTGTCACTTCACCNAAACGTCTTTGTCAGTGATTGCCAGGAACCTTATTTTGTCCAAGGC
ATCAGAAGCATTGGAGATCAACTCTCTTAAGAAAATGTCCTTGTTACTGTATAGAGAGTTGATAATAATG
TCCATAAGCCGAGAAACCTCAGCTTGGAACTCAAACTTCTCCGCGTTACTGCGAAGCGTCTTCTTTGACA
TCGACTCAGACTCTCTATGAACTACATCGGAATCCGTCGATAAACCACCGTGACCACCAATTTTCTCCTC
AACTTTTGGTGGATCTGTAACATCATCGGAACTCTCTTCTGCATTCGCGTGTAACTTTCTTCCTTGATCT
GGAAGAAGAAACAGAAGCGAGAAAAGGAACAAAA
>gi|3449410|gb|AI099671.1|AI099671 33824 CD4-13 Arabidopsis thaliana cDNA clone E1H7RP, mRNA sequence
GAATTGTGACNGCATNTTACTTTGATCCTGAAACGTTTNCCTTTGAACCGCCAAGCNGCATTCCCGTTCA
ATTTNATTGGGCGCCCCATGAAGACCGACCCCCTTGCCGTTTTTGCTTTNGNTTCCCNCCTGAATCTTCT
GTTTCAACTGGTACAATGTTCTTCTGTCGGTGCCAATCTTGACAGCACGACTCCCGCAGATTCACCGGCT
TGAATCACAAATGCTTTACACTCGACTGAATAAGAACCTTTGAAAATACCCATCTTGACAGAATTTCATG
AACTGGTCAACCACATTGGGAGCAGTATCCTTGAAGAGTTCAATGGTCACTGAACCTTTGCCCGTATCTA
AGGTAGCAAACCGCGGAAGATCAACATTCTTCATTCCAGGGAAGGCTGCATCCTCAAGAACTGATCTACC
ATTGTGCGTTGGGATCTCAGATCTGTGAGTCCAACGTCTGTAAGCAGAGAAGAGAACAAAGACAAGCAAA
AGCACAGCCAAAGTGTAAATGACGATGTTGGTTATGCTTATCCGAGACGGTCCTTTCTTCTTCTTGCTTT
GCTGCAACAATGCT
>gi|3449409|gb|AI099670.1|AI099670 33823 CD4-13 Arabidopsis thaliana cDNA clone E10A8RP, mRNA sequence
TGTTGCACCNNCCCTTCCAATGCNCTTGCCATTCTCCAAACGGCANTCTTTACCACGGCTTTNCATCTCG
TGCACAATGTAGCACACAACGCGCTCCTGTAGCGCCCCAAAGGATGGCTTATGGCCATTGCACCTCCGTT
GACATTGATTTTCTCTGGGTCAAGTCCCAATTTGTTACGGCAATAAACAAACTGAGATGCAAATGCCTCA
TTGATCTCAAACAAGTCGATGTCATCAAGTTCTAAACCAGCCGCCTTAACTGCAGCAGGAATGGCAACTG
CTGGACCGATACCCATGATTGCAGGGTCAACACCAACTGCAGCAAATGTCCTGAATACACCAAGAACGGG
AAGTCCTTTTTGCATTGCAACACTTCTCTTCATTAGGAGAACCGCTCCTGCACCATCACTTACTTGGCTG
GAATTTCCAGCAGTAGTGGTGCCATCCTT
>gi|3449408|gb|AI099669.1|AI099669 33819 Lambda-PRL2 Arabidopsis thaliana cDNA clone 89K6SP 3', mRNA sequence
TTTGGGNCCATTNCTAGGACCCCCCCTTTACAAAGTCCACCAGAGTGGAAAGTNCCACAACCGNTTTACC
TATGGAATGAATGGATGGGATGGACCTACCAAGGTCCGGTGGAAACCGAGGAAATCCATGAAGGCCCCTT
GCGAAACCANTCGGGGTTCCACAGGGTGGTCATTTTTGTGTTCATAGCAACCCAATTGGTTTTCATTCTG
CAGTGCTTTATGCTTGCCGCAAGTTTATATCTCAAGACTCCTCTCATGATCAACAACTCCTAGATGGTCT
ACGATTGGTTTAGTCATAGTATCTTGTTCCTTTTACCTTCCAAATTTATTCTATATGTGTATACAAGTAT
ATATGAAAAAGAACATAAAAAAGAATTACTTTCTTTATTTGAATATTCGGTTGTGTATTGGAGTTTCAAG
TCCTCTTTCCATGTCTAAAAGTTCTATTTGTAACGTTCTTGATTTCACTCTAAAACCTCTTAAAGTGTTT
CAAATGTGATCTCATTATCGAC
>gi|3449407|gb|AI099668.1|AI099668 33818 Lambda-PRL2 Arabidopsis thaliana cDNA clone 201D17SP 3', mRNA sequence
GGTTGGGNTNAATTCCGGGGGNATCCTGGACTTTGTAAATCTTTCCCNGCCCTTGACCCCTTTTCCNCGG
TGGANCNGAAGTTTATTGACNAGATCATCATCCCCCATCTTCTTCTTCGCCAGAGAAGAAATCATCGGTT
CTTGATTCNCCTGTTAGTCCTATTGCTAGCTGGAAGATCTCTAGTCCTGGTGATAATCCTGATGATGTTA
AAGCNAGGTTGAAATTTTGGGCACAAGCTGTGGCATGTNCTGTGAGGTTATGTACTTGAAGATGAGATTT
GGATTTGATCAACCAAAAGCTGAGGAATCAATGGAGGNGGAAGAAGATGGTGAAACCAGACAATTTGCAG
GNGTGAAATCTCTTATGAGACTGACCTGCTTGAAAACAACCATTGTTGTAG
>gi|3449406|gb|AI099667.1|AI099667 33817 Lambda-PRL2 Arabidopsis thaliana cDNA clone 200C5SP 3', mRNA sequence
CACGCGTCCGGCACTTTCTATCTCCCCCATCTTTANCACCCNCGTTCTGGTTATCTTTGAAATACCTGAG
ATAGAAGCNCATGATAGCGAGTGTCTGAAAGAATATGGGGGTGATGTTGGGTTTGGCTTCTGTGCGCCTA
AGATATTTCCGACGATTTGTTATAGAAATTGCCAAAAGGACAAGGGGGCTAATGGTGGAAAATGCCTCTG
GGGAGAGGGCGGTAAAGTGAAATGCTTATGCGACTTCTGCNGCAATGAATCTTTTAATCAGTTTATAAGT
CTTACTTGAAACTTGCATGTGTCGTCGTTTGTGTAATAAGCAAGG
>gi|3449405|gb|AI099666.1|AI099666 33816 Lambda-PRL2 Arabidopsis thaliana cDNA clone 172F16SP 3', mRNA sequence
TATTCAGCCCAACTGGTGNCATGGTATATCCACNACACTTTTCNCCCCCCNAAGGAGNGCCATTCAAATG
TTCATCCGACCATCCNGCCCAGAAATGGGACCGNTACAATCAAGCCAGTTCCAAGGCCGCNATATCCGGT
CCAGAATACCTCGGGTCCAGGTATAATGGAATTGAAGGATGAAGTGGCTAAGAGGCTGAAAGTTGATGCA
GGAACGTTCGATATCAAGTATCTTGACGATGATAACGAATGGGTTTTAATAGCTTGTGATGCTGATCTTC
AAGAATGTCTCGAGATCCCTAGATCCTCCCGCACGAAAATCGTAAGGCTCTTAGTTCATGATGTAACGAC
AAATCTAGGGAGCTCCTGCGAGAGCACTGGAGAATTGTGACCTGATAATTCATTCGAACTCTTTTGTAAA
TATGTTTTTTGAATTTTATTATTGTTTAGGGTTTCTTTGGACAAATTAAAGTTGTAAAAGAAAACATTTG
TTTGTAACTTTTAACTGTAAAAGTGTAAGAGAGAGAGAGGTTAGAAGT
>gi|3449404|gb|AI099665.1|AI099665 33815 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170L8SP 3', mRNA sequence
CCTTTGANGAATCTTGTTGAGTTTTGGAAGAGTTGGACCNNCGGGTTNCGTTTGGATGAAGCAAGCACTC
CTTACGAGCATTTCTTCGAGCCCACCAACACTCGTGTCTCCTACGGTCTCGAAGTCACCGCCTATGTCGA
CAAGTGTTGTATGAAGAAGATGACAGGAGTGAAGAGTAAGCAGATGTTTTTGTGGGTACCGATCGTGGAG
ATGAGTATGGAGGAGCCAAAAAGCAAGAAGATTTACTTCAAGACTCCTATGGGAATCGGCAGGTCTTTCC
CCGTTACCGCATTCATGGACGAGGAAGAGAAACGCAACTTTTACTTGGAGAATCCCAAAAATTAAACCAA
CTAATAATTATTCTTATGATTATTACATTTTGTGGTGCTTTTTATTTTATTTCTTGTAAGGTTTCTTTAT
GCTATTAATTTCTATCAATAATACATTTCTGGG
>gi|3449403|gb|AI099664.1|AI099664 33814 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170L10SP 3', mRNA sequence
CGAGTTAAAGGAAGAGTTGGTGGAAATGCCTTTATGTAAACACATATTTCATCTCGATTGTATTCACCTT
TGGCTTTATTCTCACAACACTTGTCCTCTTTGTCGATCCTCTGTCTCCATCTCCTCCACCAAAACCTCTG
TTGATGACGACAACGACCATCCAGATTCTCCTCAAACGTCACCGGTTTGATTCAAACCCCCGAAGGAAAT
AAGCAAATACACAAGTTTTGTTAGTGAATAGATCGATACAAGATGTAAATCTTAATTTTGCTGATACAAG
ATATCAAAATGTAATCCATCACATTATATATATTGGTTACACAGATTCATTC
>gi|3449402|gb|AI099663.1|AI099663 33813 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161F15SP 3', mRNA sequence
AAAANTGNCCTCGGCCGCCGAACCGGTNCCNCGGCCGTTTGCANGCGCAGAANTCCCGCGAAGATGGAGT
TCACCANTNCGNCGCGATGCTTCCCGTTTCTGCCGGNNTTATTCCCAACCGNCAGTGTGTGGGNCTTGGA
TGTGGTTGTTTGGGNAGAAGATGAANCGGAAGAAANCAGAGTTTATGGTCCCGGCGGTGGCTTCAGGNCT
AATCTGTTGGCGAAGGNCTTTGGGACTTTTTCCTGCCGCCGGTGCTTGCCCCTCGCCGGAGTAAAACCTC
CGATATGTATGAAGTTCTTAGCTTCATAGGATCAGTCAAAGAGATAAGAAGACTTGTGAAGTTAAGAGTA
GTTAGAAGACGTCAATGATATTAAAATCATCCTATTCTTAGAATAACAGGTAGACTTCTGAACAAGAACA
TCTCTTTTTCTAGGAATTAAGACTAAAATCTACTTACATCCGGATGATTCATGCTCTGTTTTTTGGTTTG
GTATAATTTGTCAACACATCTAGATCTGTTCCATTTCCGGTTA
>gi|3449401|gb|AI099662.1|AI099662 33812 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157O21SP 3', mRNA sequence
CCCCCCGGTTNCCCCTNAATCGGNCAAGGTTCAGGCCCATTGACCCTTCAGGNTCTGCCCCCNAAGTGGG
TTGCCCNTCCAGGAATTCTGCCAAGATGGGTATTTCAAAGNTTCTTAATCAGCCGAGTTGTAAANCATTT
TGTGATTCAAACCCGGTGACTCTGCGGAGTCCGATGCTGTCAAAGATTGGGCACTCGACAGAAAGAACAT
TGATACCAGTTTGAAACATGAAGAATTCATGGTGGGAACTCCTAAAGCTAAAAACGAGCAAGGAGGATTC
GAGTTCTTCATTGTGTCTGCTCAGATCAAAGATCTGAACGAGAAATTGACTGTCTTTGGTCGAGTTTCTA
AAGGACAAGACGTTGTTCAGGAGATCGAAGAGGTTGAGACAGATGATCAGTATCAACCAAAGTCGCCAAT
AGAGATCATGTCCGTCACTTTGCTTCAAGACATGTAAAAGCTTTTTTACTTCTTGTCTCTCTCTCTTGTA
TGAAACTCAAGTGATTTTTCTTGTGAATTTGAAACCCTTTTTATC
>gi|3449400|gb|AI099661.1|AI099661 33811 Lambda-PRL2 Arabidopsis thaliana cDNA clone 142P17SP 3', mRNA sequence
TTTCCCCCGGGAATGGGCCCACCCCCATGGCCGGTGANCNCAGGGATCCCCCTCAACAATCCCGGGGCCA
TAANCGGAGGCATNCCAACCTCCAGTTAACTGGACCACNAATTTGGATTGTGCACCAACCATTCTTGGCA
AACCCCGGAAACTGCTGGAAGAGGAATGACTTTCTTGAATTTTGCCGGGAATTGCGGTTCTTGCTGTAAT
CTTTGTGATTGTGTTTGTCCCTGAGACTCAAGGGCTAACGTTTTCGGAAGTTGAACAGATTTGGAAAGAA
AGAGCTTATGGAAATATCAGTGGCTGGGGCAGTAGCAGTGATAGCAACAACATGGAAGGGTTACTCGAGC
AGGGATCTCAATCTTAAAGATCTTGGATGGCTCATGAGTCATGCATGACTTACACATTGTGAAATCACAT
AGTAGTAAACCGGGATTGGTTCCGGTTTAGCAATGTGAGATGTATGTGATGTTGGAATTGTAATGTTCTT
AGGAACTGTGATTGTAAATAAATACATTACAAATTTACATTAAGGGTCCACTTTGGTACCCAATC
>gi|3449399|gb|AI099660.1|AI099660 33810 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140G18SP 3', mRNA sequence
CTCCAGTATTAGGGTTNTTAANTTTGTTAGAGCCCGGACNCCNCCGGTTGGTTTCCAGGTTCCTGCTAAA
TTATGTGGCTATGGTCCCATCAGGNCAAATATCCGACCAGTTCTCTGGAGAAAGGTCTACCGTATCTATT
TCGCGTTGGCTCTGGCCAGGTGATCAAAGGACTTGATGAAGGAATCTTGAGTATGAAAGCTGGTGGCAAA
CGTAGACTCTACATCCCAGGGCCTTTGGCGTTTCCAAAGGGTCTAGTTTCAGCTCCAGGGAGGCCGAGAG
TTGCGCCAAACAGCCCGGTGATATTTGACGTGAGCTTAGAGTTCATACCAGGTCTCGATTCAGAGGAAGA
GTGAAACTCTGTTTTTTCAAGTGCAAATTGTAATCTTCCATACACAATTACAAGATTCTATGTATGATAT
TTATCTCATTGTACTCATTCATTGAAGAACATCACATTGATTAAAAACGTCAGTATTTTTCAATTCT
>gi|3449398|gb|AI099659.1|AI099659 33809 Lambda-PRL2 Arabidopsis thaliana cDNA clone 127A14SP 3', mRNA sequence
GGAAGCATTATGCACGTTCTCTGGGAAACTGACCGTTGGCTTCAAAAATACTGTGTTCCAAACNACATCA
GATGCAGATACAAGTCCCGACCAGTCCAAAGAAGGGTCAGATTCTGCAGACAAAGTATCCACAGGCACAG
GTGGTGGTAATCCGGAGTTTGGTGAGCATGAAGTTCACTCCAAGCTCAGGAGATCACTTCTCTGAGTTCC
CAAAAGTGGTTCACTAGCCACATGCAGCATGCGAGTGCACTTGCAGAAACAGAGAGCACAAAAAAAGGCA
GATGCAACACAAACTTATTTTTCATACAAAACATTGATTCATAATAATATGAAAAAAAGTTTTTGAATTA
CTTGAAATGCTGGAAACACTCTTTCAAGTGCAAAACTTCGATC
>gi|3449397|gb|AI099658.1|AI099658 33808 Lambda-PRL2 Arabidopsis thaliana cDNA clone 120D15SP 3', mRNA sequence
AAAGGCTACTCGGNGTGGCCGACCAACTACAGGACTTCCACTNCGGACGTTTGGTCAAAGTCTCGGTCTT
GCCTTCNCGCCACCCGAACTTGTGGNTACAACCCAACTGTAGCTTTCAGGACGGGTTTGTGGTTTTGGAT
GAATAGCGTAAGGCCGGTTCTGAACCAAGGGTTTGGAGCCACCATTAGAGCTATTAATGGAATGGAATGT
AACGGTGGTAATTCCGGTGCAGTCAACGCAAGGATTGGATACTATAGAGACTATTGTGGACAGCTTGGTG
TGGACCCTGGTCCTAACCTTAGTTGCTAAAAAACCTTTGAACCCAAACACGGACATATGTGACGTGGCAT
GTAATAAGTGAGATATACTAAAATTTCACACGTATGTACTTTATGTCGGGTCTCGGTGTTCCCTGCGTCA
CAAGCAAAAAATTGTTGTAATAAACTTGTGAAAGTGATTTTCTTTTCTTATGTG
>gi|3449396|gb|AI100686.1|AI100686 33807 Lambda-PRL2 Arabidopsis thaliana cDNA clone 104N12SP 3', mRNA sequence
GTTAACCCCCTTGCTTTTGTCTGGGGNCTTTATGGNCTTTNCGCTTGGGGNAGAAGGACTCGNCCTTGAG
CTGATGCTGGCGAGTTTCGCGGTGGTGAACTGCTTGCCGATCTATGAGGCTATGGTGTTGAGGATAGACG
ATGGAAAATTACCAAAAAGGGTTTGTTTCGTAGCTGGAATCCTCACATTTGTGCTGATTGTGTCAGGTTA
CGTCTTCCTCAAGTAACTGGACCCATTATGGTTGGTTCTGTCGTTTCAGTTAAACTAATATTACATCTGT
ATTGTGGTAATTAGGAGAGAATAATGTGATGAATCCATTTCTCACCTCATTTTAGAACATACATTTCGGT
ATATTGCGTCTGTATTGTAGTAATTAGGAGAGAATAATGTGTTGAATCCATTTCTCACCTCATTTTAGAA
C
>gi|3449395|gb|AI100685.1|AI100685 33806 Lambda-PRL2 Arabidopsis thaliana cDNA clone 90J7XP 3', mRNA sequence
GAACTTTGAGAACAACCCGAGGTTGGAGGGACCGGAATTACTCGGTCTTGCAAGCTACGACACTAACTGC
ACCTGAAAAAATTGGCAAAACCTGAAAATGAAGAATTGGGGGGTGACCTTGTAAGAACACTTCACCACTT
TATCAAATATCACATCTACTATGTAATAAGTATATATATGTAGTCCAAAAAAAAAATGAAGAATCGAATC
AGTAATATCATCTGGNCTCAATTGAGAACTTTGAGGTCTGTGTATGTAAAATTTCTAAATGCGACTTTCG
CGTACTGTAATGTTCGGTTGTGGGATNCTGAGAAGTAACATTTGTATTGGTATGGTATCAAGTTGTTCTG
CCTTGTCTGC
>gi|3449394|gb|AI100684.1|AI100684 33805 Lambda-PRL2 Arabidopsis thaliana cDNA clone 219L11XP 3', mRNA sequence
TTAGTGACAACCAAGTCTCTGCGGTGGCCCCTTGACGACGTCATGTTAATAAACAAGGATATGGTTTTCT
GGTTTTAACTGAACCGGGTTATGTCTTTTTGCTGTTGCTCTTGTTTCGTTGGATCAAACTGGTGATATTT
TGCTTTTCATTTCTTCGTCTTTCAGATTTTAGTTTCTAAAGCTGAGATATGTTACTGGCAACGGACAGGT
ACACCGATCCAATATGGTTTGCGGTCTATGTACAATGAATCCGGAAGTAAAATCAAAAGCAATGTTATAG
AATTTAATTTCAAGATCTAG
>gi|3449393|gb|AI100683.1|AI100683 33804 Lambda-PRL2 Arabidopsis thaliana cDNA clone 187H5XP 3', mRNA sequence
CCCATTTCTTTGGGAAAATTGAAGTCTNTGTCTTTTTACGGCTTAATGACAACCGATTGACGGGGCCAAT
CCNTAGAGCACTCACTGCAATCCCAAGCCTTAAAGTTGTTGATGTCTCAAGCAATGATTTGTGTGGAACA
ATCCCAACAAACGGACCTTTTGCTCACATTCCTTTACAGAACTTTGAGAACAACCCGAGGTTGGAGGGAC
CGGAATTACTCGGTCTTGCAAGCTACGACACTAACTGCACCTGAAAAAATTGGCAAAACCTGAAAATGAA
GAATTGGGGGGTGACCTTGTAAGAACACTTCACCACTTTATCAAATATCACATCTACTATGTAATAAGTA
TATATATGTAGTCC
>gi|3449392|gb|AI100682.1|AI100682 33803 Lambda-PRL2 Arabidopsis thaliana cDNA clone 185L1XP 3', mRNA sequence
AAATTGAGTNTNTGTCTTTTTACGGCTTAATGACAACCGATTGACGGGGCCAATCCNTAGAGCACTCACT
GCAATCCCAAGCCTTAAAGTTGTTGATGTCTCAAGCAATGATTTGTGTGGAACAATCCCAACAAACGGAC
CTTTTGCTCACATTCCTTTACAGAACTTTGAGAACAACCCGAGGTTGGAGGGACCGGAATTACTCGNTCT
TGCAAGCTACGACACTAACTGCACCTGAAAAAATTGGCAAAACCTGAAAATGAAGAATTGGGGGGTGANC
TTGTAAGAACACTTCACCACTTTATCAAATATCACATCTACTATGTAATAAGTATATATATGTAGTCC
>gi|3449391|gb|AI100681.1|AI100681 33802 Lambda-PRL2 Arabidopsis thaliana cDNA clone 180F2XP 3', mRNA sequence
AATAATATGTTCAAAGGCAAATTCACGAACTCTGTAAATAGATCGATCTCCTCTGGTCTCAGACTAAGAC
ACTGCTCTTAGATATATCGTCAAAAGCTATGCTCTTCTTCGGATTATTTGCTGAAGAAACTGTAAATAAA
GCTTCTTTCAAGCTATGGCCGGACGAAAGAGTCCTCCATGGCTCTTCTACGTGGTCAGCTTTCAGGATCT
GTTTGGTTTGTTTATCTACTGANAGTGAACCAACATAAACTGTCACTCTTGTAAATATATGTAAATTCGA
AATATCGACTGTAATATATAATTGAATATCTTGCACAATAGAAAATCTATGTGAAGGT
>gi|3449390|gb|AI100680.1|AI100680 33801 Lambda-PRL2 Arabidopsis thaliana cDNA clone 179J19XP 3', mRNA sequence
GGAGGGACCGGAATTACTCGGTCTTGCAAGCTACGACACTAACTGCACCTGAAACAACTGGCAAAACCTG
AAAATGAAGAATTGGGGGGTGACCTTGTAAGAACACTTCACCACTTTATCAAATATCACATCTATTATGT
AATAAGTATATATATGTAGTAAAAACAAAAAAAATGAAGAATCGAATCGGTAATANCATCTGGTCNCAAT
TGAGAACTTCGAGGNCTGTATGTAAAATTTCTAAATGCGATTTTCGCTTACTGTAATGTTCGGTTGTGGG
ATTCTGAGAAGTAACATTTGTATTGGTATGGTATCAAGTTGTTCTGCCTTGTCTGC
>gi|3449389|gb|AI100679.1|AI100679 33800 Lambda-PRL2 Arabidopsis thaliana cDNA clone 179J11XP 3', mRNA sequence
TTGTTCTTTTTACGGCTTAATGACAACCGATTGACGGGGCCAATTCCCTAGAGCACTCACTGCATTCCCA
AGCCTTAAAGTTGTTGATNTCTCAAGCAATGATTTGTGTGGAACANTCCCAACAAACGGACCTTTTGCTC
ACATTCCTTTACAGAACTTTGAGAACAACCCGAGGTTGGAGGGACCGGAATTACTCGGGCTTGCAAGCTA
CGACACTAACTGCACCTGAAAAAATTGGCAAAANCTGAAAATGAAGAATTGGGGGGTGACCTTGTAAGAA
CACTTCACCACTTTAGCAAATANCACATCTACTATGTAATAAGTATATATATGTAGNCC
>gi|3449388|gb|AI100678.1|AI100678 33799 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157B6XP 3', mRNA sequence
CCCGAGGTTGGAGGGACCGGAATTACTCGTTCTTGCAAGCTACGACACTAACTGCACCTGAAAAAATTGG
CAAAACCTGAAAATGAAGAATTGGGGGGTGACCTTGTAAGAACACTTCACCACTTTATCAAATATCACAT
CTACTATGTAATAAGTATATATATGTAGTCCAAAAAAAAAATGAAGAATCGAATCAGTAATANCANCTGG
TCTCAATTGAGAACTTTGAGGNCTGTGTATGTAAAATTTCTAAATGCG
>gi|3449387|gb|AI100677.1|AI100677 33798 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137D13XP 3', mRNA sequence
TGTTCAAAGGCAATTCACGAACTCGGTANAATAGATCGGATCTCCCTCTGGTCTCAGACTAAGACACGTG
CTCCTCAGATATATCGGTCAAAAGCTATGCTCTTNCTTCGGATTATTTGCTGGAGAAACGGTAAATAAAG
CTTCTTTCAAGCTATGGCCGGACGAAAGAGTCCTCCATGGCTCTTCTACGTGGTCAGCTTTCAGGATCTG
TTTGGTTTGTTTATCTACTGAAGTGAACCAACATAAACTGTCACTCTNGTAAATATATGTAAATTCGAAA
TATCGTCTGTAATATATAATTGAATGTCTTGCACTC
>gi|3449386|gb|AI100676.1|AI100676 33797 Lambda-PRL2 Arabidopsis thaliana cDNA clone 130I1XP 3', mRNA sequence
AATAATTGGACNGGAATCACAATGGCATCACAGGGGTATTCCGGNTGAGNGGAGCAAAGCTTATTTTCAG
TTANTGAATGTTAGCTANAACAGACTGNGTGGACGCATCCCCAAAGGAGAGTATATTCAAAGATTTGTTN
TTATTCCTTTTTCCACAACAAGTGTTTATGTGGTGCACCTCTTCCTAGTTGCAAGTGAAGATTCCAGCAA
AA
>gi|3449385|gb|AI100675.1|AI100675 33796 Lambda-PRL2 Arabidopsis thaliana cDNA clone 125L11XP 3', mRNA sequence
AGCTTCAGGGGACTGATCTGCCAAACTTGNTCAATTCCGTCCTGAATAAAATAATATGTTCAAAGGCAAA
TTCACGAACTCTGTAAATAGATCGATCTCCTCTGGTCTCAGACTAAGACACTGCTCTTAGATATATCGTC
AAAAGCTATGCTCTTCTTCGGATTATTTGCTGAAGAAACTGTAAATAAAGCTTCTTTCAAGCTATGGCCG
GACGAAAGAGTCCTCCATGGCTCTTCTACGTGGTCAGCTTTCAGGATCTGTTTGGTTTGTTTATCTACTG
AGAGTGAACCAACATAAACTGTCACTCNTTGTAAATATATGTAAATTCGAAATATCGACTGTAATATAT
>gi|3449384|gb|AI100674.1|AI100674 33795 Lambda-PRL2 Arabidopsis thaliana cDNA clone 106G3XP 3', mRNA sequence
AGAANGGANATTTTNGACCTGGGATCCTGCAGTTTTTGNTAAGACATCAGGAAGTTCAGGNGANTGATCT
GCCAAACTGGTCAACTTCCGTCCNNGAATAAAATAAAATGTTCAAAGGCAAATTCACGAACTCTGTAAAT
AGATCGATNTCTTCGGGTCTCAGACTAAGACACTGNTCTTAGATATATCGTCAAAAGCTATGCTCTTCTT
CGGATTATTTGCTGAAGAAACTGTAAATAAAGCTTCTTTCAAGCTATGGCCGGACGAAAGAGTCCTCCAT
GGCTCTTNTACGTGGTCAGCTTTCAGGATCTGTTTGGTTTGTTTATCTACTGAGATGAACCAACATAAAC
TGTCACTCTTGTAAATATATGTAAATTCGAAATATCGACTGTAATATATAATTGAATATCTTGCACAAT
>gi|937780|gb|R65302.1|R65302 13806 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169D23T7, mRNA sequence
CATCACTTGCGCACAAGAAACCATCGTGATCGGACTAGCTGCTGACTCTGGCTGCGGCAAAAGTACCTTT
ATGCGGAGGCTCACCAGCNTCTTTGGTGGCGCTGCTAAGCCNGCAAAAGGCGGGAACCCTGATTCCAACA
CACTCATCAGCGACACGACCACTGTGATCTGTCTTGATGATTACCATTNTTTGGNTAGGTACGGTAGGAA
AGAGCAGAAAGTCACCGCTTTGGACCCACGCGCCAATGACTTTNATCTCATGTATGAGCAAGTCAAAGAT
CTTANGAANTNGTATAAGCCGTTCGAGAAACCGNNTTNATAACCCANTGNCA
>gi|937162|gb|R30511.1|R30511 13116 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164J6T7, mRNA sequence
ATTAGCCGGAGATGGCCGCAACATCCGCNGCTGCTGCAGCTGCTTCTNCCATCATGGGTACTCGGGTGGC
TCCCGGTATCCATCCCGGTTCAGGTCGGTTCACAGCCGTGTTCGGTTTCGGAAAGAAGAAGGCAGCTCCC
AAAAAGAGTGCCAAAAAGACGGTGACTACGGACCGGCCTCTTTGGTACCCAGGCGCCATTTCTCCTGACT
GGCTTGATGGTTCCTTNGTTGGAGATTACGGTTTTAATCCCTTCGGNTTTAGGCAAACCGGNCGAGTATC
TTTCAATTCGATATCGTTTCAACTAGACCCAGNNTCTGGCTTAAAGAACTTGGCCGGTAGAACGTGAATC
CGGAACCNCGGTACGNAANGNTTCCCGACGGCAAANTCNAACGGNCGTTTTTAATCCCGTNCA
>gi|2764392|gb|R30196.1|R30196 12801 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152J9T7, mRNA sequence
TTTTCAGANCGGGCTTTCGGGCTTTNAAAAACTAATCTTTCCATGGNCTATNATGTTGGCCTTGCCAAGA
GTAGCAGCAGTAGTCAGGTTAGATACTAGAAGTTGTGGTTTTAATTTAGGGAAAGTAATTTATTATAACA
NGTAAACGCAAATNCAGATAAATAACAATGTTTTAATTTNTAAGGTTAG
>gi|2764391|gb|R30011.1|R30011 12616 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163J17T7, mRNA sequence
GATTGAGGCCTCGCAGAAGGCACTGTTTGGTGAGGGCAAAGGCCAACTCACTGGCCCAGCTCGGCAAATA
CTCAGCCGAGGGAGAGAACGAGGATGCCAAGAAAGGAATGTTTGTNAAGGGTTACACCTACTGATTTGTT
AATTTCAGAGATCGTAATAAGGATTAAGGACCATTGTTGTCTTTNGTTTTTTTTTCCC
>gi|2764390|gb|T75640.1|T75640 10418 Lambda-PRL2 Arabidopsis thaliana cDNA clone 140P19T7, mRNA sequence
TAAAACAAACACAGAGAAGCTTCTTCTTAAACGATGCCGTACTATACCAGAGATGACAACGACGTCGACG
ATTTCGATGAGTTTGATCCAACGCCGTACAGTGGTGGTTACGACATCACGGTGATCTACGGCCGTCCGAT
TCCACCTTCCGATGAGACT
>gi|2764389|gb|T46600.1|T46600 9863 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137B19T7, mRNA sequence
ACGGTGTATTTCCTTTAATGTTTCTNTGGGCTCTTTTNAACAAACTTAAACTCGCGTGTGGTAAATNTTT
AATGACTTGAGAAGCGATTNAGGTTTAGGGTTTGGACCGTTTGGTTTTNCGTTTCCNCGTAATTAATTCT
GGGGGCTTTAATTGTGGTTTGTGGGTCAAAACTNTCAACTATCACTACTTGTAA
>gi|2764388|gb|T46590.1|T46590 9853 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135M16T7, mRNA sequence
TTTCTCCCTCAAATCGTTTTCTCCAGTTTNNTTGGGATAAATCTNCCTCCTTTCTGCAGACGCCATGTCG
GACAAAGGTCGTCCCTTGCCAAAANTTGGTGAATGGGATGTGAATGANCCAGCATCAGCAGA
>gi|2764387|gb|T46527.1|T46527 9790 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135B14T7, mRNA sequence
CAATATGGAGGACATCGATGAGGGTTTTNANGGTTATGATGATGAGAGGTCTATNCTAATGTCCCAGAGG
AGTGTAGAGAAGCGTTTTGGTCAGTCGCCGGTATTTNTTNCGGCAACCTTCATGGAACAAAGGCGGCATT
CCACCAACAANCCAATCCCCG
>gi|2764386|gb|T46503.1|T46503 9766 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134J3T7, mRNA sequence
GGCGGCGGTTGATCCGTATNCNAAGAACGAGGCGTTTAACTGCAACAATNCTGATATCTTCAAGTGGAAG
CATCTNTGGAAGATTCTAGCTGAGCAGTTTGGGATTNAGGAGTATGGATTTNAGGAAGGGAAGAATTTNG
GGTTGGTGGAGATGATGAAAGGGAAAGAGAGAGTCT
>gi|2764385|gb|T46502.1|T46502 9765 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134J2T7, mRNA sequence
CTGTGATCCGTTTCANTGCTAATAATCCAGGTGCNTGGNTTTTCNATTGTNATATCGATGTTCACTTACC
ATTCGGACTAGGGATGATATTNTTGGTTAAGAACGGACCGACCAAGTNGACCACCTTGCCACCGACACCA
CCAGATCTTCCCAAATGTTAAGCAAGATAAAAAAAACATATTT
>gi|2764384|gb|T46476.1|T46476 9739 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131P7T7, mRNA sequence
CACAATCACTGATCTNAAGCTGTTTCCATTTGGTAATGCCGAACTCTCCGATAATCTNACTGTNACTTGC
NAGCATGGTGAAGAGGAATGCAAACTAAACGCCCTTGANGCTTGCNCATTAAGAACTTGGCCCGATCAGA
AATCACAATACTCGTTCATACGGTGCGTCGAAAGCNATACG
>gi|2764383|gb|R84081.1|R84081 16040 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143M11T7, mRNA sequence
CAAACAAGCAAAGAACCTTAACCAAAAAGAAAACNTCTACGGAGACATATGGAGAGGAAACATCACTTCG
TGTTAGTTCACAACGNTTATAATGGAGCCTGGTTCTGGTACAAGCTCAAGCCCCTCCTTNANTCANCCGG
CCACCGCNTTACTGCTGTNGAACTCGCCGCCTCCGGG
>gi|2764382|gb|T46413.1|T46413 9676 Lambda-PRL2 Arabidopsis thaliana cDNA clone 143G15T7, mRNA sequence
CAGTATGCATCGGTGGCTCCGACCACCGCAAGANCGTATGCNAAACCNTCGCCGACGACTCAACGATCCC
ACCTTATTACAACAACTCCGCCGTTAGTCCGAGTNATTTCCCACCGGAATCTNATTTNTGGTCAAACGAT
GCTCAGCTAGAGTGGCTCAGCGNCAACGGCTTCTTT
>gi|2764381|gb|T46371.1|T46371 9634 Lambda-PRL2 Arabidopsis thaliana cDNA clone 141P19T7, mRNA sequence
CCAAAAACAGAGGGAGNAAGAAGAAGAAAAGATGCCTTCAAGCACATTCTCCGGGACTGTTAGCACGNCG
AAGCTGNCGGTGGCAGTGGACATGGGAAACCCTTTTNTNAATCTCACCGTTGATGNCTTCCTCANGATCG
GAGCTGTTGGAGTCACTAAATCTCTTGCAGAAGACACTTACAAGG
>gi|2764380|gb|R84078.1|R84078 16037 Lambda-PRL2 Arabidopsis thaliana cDNA clone 139K15T7, mRNA sequence
GTAGCTAACGATGTGGTTGTTTTAANTGACGATAGCTTCGAAAAGGAAGTNGGTAAAGATAAAGGAGCTC
TCGTCGAGTTTAACGCTCCCNGGTGTGGTCACNGCAAGAAACTTGCNCCANAGTATGAAAAGCTAGGGGC
AAGCTTCAAGAAGGCTAAGT
>gi|2764379|gb|R84077.1|R84077 16036 Lambda-PRL2 Arabidopsis thaliana cDNA clone 139B16T7, mRNA sequence
CTCTTTCTTTTCCANATTTCAATTCCNGAGGCTCGAAAGAAAACCGTAAATTTTTTCTCCNTTCACTCAA
TCAACCAAAGATGCGTGAAATTTTNCANATCCAGGGTGGTCAATGCGGTAACCAGATCGGAGCCAAGT
>gi|2764378|gb|T46241.1|T46241 9504 Lambda-PRL2 Arabidopsis thaliana cDNA clone 139A22T7, mRNA sequence
AAGGTTCATGGAGAATGGTTTCTATACACAGGAAGGAGTAGAGGGAGACATTTCGNTAACGAGGATCAGG
AGTTTAAAGACTTGANTGAAGCTTTAANAGTTAGTTNCGAAATGGGGTATCCAGTTCGATTTGTNAGGTC
T
>gi|2764377|gb|T46228.1|T46228 9491 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138J7T7, mRNA sequence
CTCACCGGAAACTTCAGATCGAGCTACTGCAATTTGCGGATCGTNTTTTTTTTTTTCCNTCAATTCACGG
TGTATTTATCTNGGGAGAAGAAGAATGGATACTTTCACGGCGGAGGNTCTNTCGACGATCGGCGGAATAG
CGACAGTATCGCTCCTTCACTTCGGTTTATNCCGCNGGATTTGGCTACCTTTTT
>gi|2764376|gb|T46208.1|T46208 9471 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138F12T7, mRNA sequence
TTTGAAGACAGTAATGATGAAGAAGAGACAGCAAAATNAGGAGACAAGAAGGATGATGCCGTTAAGGAGG
AAGGTCCTGCNACANANAAGGCACCAGCNGCAGAAGAAACAACATCTTTTAAGGAAGACAAGTGAAGACA
CTNTTCTAGAGATGCTGAAAA
>gi|2764375|gb|T46202.1|T46202 9465 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138E20T7, mRNA sequence
CTGTNCTNCTCGTCGTCTCAGAAGTAGCCGCGGCATCTNCTGCCACAGTNAATTCAGAGAGTAAGGAAAC
TNTGAAACCTGATCAACGTGGCTACGGTGACAATNGAGGAAATTACAATAACGGAGGAGGTTACCANGGA
GGAGGGGGTAATTACCAAGGAGGAGGAGGTAATTACCAAG
>gi|2764374|gb|T46197.1|T46197 9460 Lambda-PRL2 Arabidopsis thaliana cDNA clone 138D15T7, mRNA sequence
AATTTTTTTTNATTTCAGCAAAAAAGCAAAGGACTATACAGGTGATGGACATTCATGACATNCCTAAACC
TAAGAAAGGTGGATTTTNCCCAAGAAAAGGCGGGAGTNCTCAAGGTGGTAGACACNGGTAAATTGAGAAA
GATGAGAGTTAAGTNAGGAAGAGAAAAAAAGACAGAGANCAAAGCTCTGTTTCT
>gi|2764373|gb|T46163.1|T46163 9426 Lambda-PRL2 Arabidopsis thaliana cDNA clone 137F22T7, mRNA sequence
AATGCAGAGAGATGGTCGGAGTATCGCCGGTGAAGACTAAGCTGTGTNATCGNTTTAACCGATCCGTCGG
CGGCAGGAATTGCCACCGGAAACACGTCGAGGACGGGTGATCCANTTTTNTAAACTNTCGTCTCTCGAAT
TCTTCGAAGATATCGAAAAACTGTAAATNTTTTTTT
>gi|2764372|gb|R84073.1|R84073 16032 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135O8T7, mRNA sequence
AAACCTTCACATAAAAAAAATACTTTTAANTCCGNGTTTNATTCATCGAATCTTTTNCCGATAACNATGG
CTGAGGAAATCAAGAATGTCCCTGANCAGGAGGTGCCAAAGGTAGCAACAGAGGAATCATCGGCAGAGGT
TACAGATCGTGGATTGTCCGATT
>gi|2764371|gb|T46124.1|T46124 9387 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135L18T7, mRNA sequence
CCAAGCTCACATCCGATGCAGCCTTGGACCCCGCTGGTCTTGTNGCTGTCGCTGTGGCTCACGTCTTTNC
CCTTTNNGTTGGTGTTTCCATAGCCGNCAACATCTCCGGCGGACACCTTAACCCCGCCGTNACACTTCGG
TCTCGCCGTCGGTGGCAACATCACAG
>gi|2764370|gb|T46122.1|T46122 9385 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135L12T7, mRNA sequence
ATCCTTATTGATATTCTTCCAACTGCNATTTCCCGATCCCAAATTTGGGTTGATTGAATTCTAAAGTTTC
TATTTNAAGGAAATTTTNATCCTTTTNAATGGCNGCTTACGCGAATAANCTCCGGTTGGCACGACTTGGA
GGAACAAGTTCAGGTGTAAACCTGT
>gi|2764369|gb|T46104.1|T46104 9367 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135J11T7, mRNA sequence
TGTTTTCGAAGAGCTTCTNGTTNTGACAAAGCAAGAAACAACCGNCAACAACATCAACAATCTGAGCTTT
AATGGCGGATTTANTCATCATCATCATCAATTCTTCCCAAATGGGTATAATATGGNTTACCTCTGTTTCA
ACA
>gi|2764368|gb|T46078.1|T46078 9341 Lambda-PRL2 Arabidopsis thaliana cDNA clone 135F22T7, mRNA sequence
GAGGAGTGCAGCCAAAGACAAAGAGCTCAAGAAAAACGAAAAANTGCTTCAACAGATCGAAGCTAAAGCA
ACTNGTAGCTATCAGAAAGATATTNCAACTNCTCAGCAAGTAGCTAAAGCAAACGGTGCACCANAGGATG
GTACATCCGNGANTCATCACGAAAGAGCGAAACGGTTGCTTCTTTT
>gi|2764367|gb|T45844.1|T45844 9107 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132P11T7, mRNA sequence
TTGGAAATACAGTTTAAGGTCTCGGTGTTGGGTCAAATGCGAAGGAATGCATCGNCCTCGCNGCTTGATT
GCATCGGGAAGCCTCGGTGGGATTGCNATAGTTNCGGGAGGAACTGATATNAATNGGAATATACTAGCAT
CAGCTGAGCTTTATNATTCTCCGTCAGGGAGATGGGAGATT
>gi|2764366|gb|T45683.1|T45683 8946 Lambda-PRL2 Arabidopsis thaliana cDNA clone 130M16T7, mRNA sequence
AAGCTCTTCTTCTCTATCTCTCTCTCTCCCTCTCAACCTCTCACCATGGTAGCTCAAGCTCCTCATGATG
ATCATCAGGATGATGAGAAATNAGCAGCAGCGAGACAAAAGGGGTCNGAGATTGGTTACCAATAACTTCA
TCAAGAAATGCAAAGTGGTGGTACTNTNNTTTTNACAATNTCACC
>gi|2764365|gb|T45557.1|T45557 8820 Lambda-PRL2 Arabidopsis thaliana cDNA clone 134C6T7, mRNA sequence
GAGAGTTTTGTGAACTCAAGAAAATAAAAAAAGTTATAGTTAATGGGATTCGGCTTAGAGAGTATCAAAT
CAATCTCCGGCGGATGGGGCGCGGCGGCGGTTCCTNTNACGNTTGTAAATNAGTTACCGCNGC
>gi|2764364|gb|T45484.1|T45484 8747 Lambda-PRL2 Arabidopsis thaliana cDNA clone 132J6T7, mRNA sequence
ATCGCCATTGTTGCTCGCNTAGCTCTCGAAACGCCACTAATTAGCAAAACAACATTTAAAGATATCTNGT
TTGGAGGACTTTGGACAATCGTNCCGCTACTGTNCATTTNCTCTCTCTTTGAAGTTTTT
>gi|2764363|gb|R84050.1|R84050 16009 Lambda-PRL2 Arabidopsis thaliana cDNA clone 131A20T7, mRNA sequence
TTTCATCCTCTGTCGACAGTACTAAACCTTCTCCTTCTAANTCTCCTGTNAATCTNTCCCTTAGTCTCAC
ATTTCCTNCTACTGCTCCACAAAGAGAAGCAAGACAAGATTGGCCACCGNTAAAGTNTAGATTAAGAGAT
ACACTAAAGGGTCGTNGTCTTCTTCGTCGTGGTGATGACAC
>gi|2764362|gb|T45435.1|T45435 8698 Lambda-PRL2 Arabidopsis thaliana cDNA clone 129N8T7, mRNA sequence
ATGTTCATCCCTGTGACAACCNTTCAACTTCGTNCCCATTGANGAGTTGGGTCTGTATGTTAATCAGAAG
GNACTTATTGATCTNATNGGAGTTGTTCAAAGTGTATCTCCTACCATGAGTATTAGAAAGGNGAACTGAC
AATGTGATGATTCCTAAGAGGGATATAAACTTTGGCTGATGAGTCAAAGG
>gi|2764361|gb|R84047.1|R84047 16006 Lambda-PRL2 Arabidopsis thaliana cDNA clone 129M11T7, mRNA sequence
ATCAACGGAGTTTGAGTTTCTTTTCCGATTCCGGCGATGGGGTCAGTCCCNGNTCCAGGCGAGTTAACTG
AGTTAGCTCANCCGAGTTTCGAGGAGTTTCAGAAACAGACGTCGTTGATGACTAGCTGTACTCTTNTATG
GGAAGATGTATNCCATACANTTNACTTACTCAGATGAGATTCTGATGAAGGAA
>gi|2764360|gb|R84043.1|R84043 16002 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128E24T7, mRNA sequence
AAGTAAGAACAACAACACTNAAGCAAAAAAGAAAAGCTCAAGCNGAGAGAGACAATGGCATCAACATTCA
CGAGCTCAAGCAGTGTTCTTACCCCAACAACATNCCTTGGCCAGACTAAAGCNTCAAGCTTTAACCCCCT
TCGTGATGTNGTCTCNC
>gi|2764359|gb|T45427.1|T45427 8690 Lambda-PRL2 Arabidopsis thaliana cDNA clone 128E23T7, mRNA sequence
ATGAAGNNCGGGAAGGGCAAAGTTTGGNTCGATCCCAACGAAAGCNCCGACATCNCCATGGCCAATTCCC
GCCAAAACATCAGGAAGCTTGTNAAGGATGGTTTCATCATCAGGAAGCCAACCAAGATTCATTCTCGTTC
CAGAGCTCGCAAAATGA
>gi|2764358|gb|R65566.1|R65566 14070 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173E2T7, mRNA sequence
TCAGTCAGTCTGGAAAGAATGGTATGCNTCGTGATTGGCTAGTTCGGGACTGTAATACTGGAGAAACCTT
AACACGAGCATCAAGTGTGTGGGTGATGATGAATAAACTGACAAGGAGATTGTCAAAGATTCCTGAAGAG
GTTCGAGGGGAAATAGAGCCTTATTTTGTGAATTCTGATCCTGTCCTTNCCGAGGACAGCAGAAAGTTAA
CAAAAATTNATGACAAGACTGCTGACTATGTTCGATCTGGTCTCACTCCTCGATGGAGTGACCCNAGATG
TTAACCCACGCANTGTGAATAATGGTAAAAGTACATTTGGGTNGANTCCCTNNGAGAGTTCCTCCNACTT
GGGGGATTAATTGGANGAGGCAAGAAANNTTTNAAAAAGCATTNANCTCCTTGGAGGA
>gi|2764357|gb|R65565.1|R65565 14069 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173D7T7, mRNA sequence
CTTTCGCTTTTCCCACAGGCGAGTNAGAAGTTTGCGGTTGCGATTGTNATCGCTGCAACGATGATGGCAT
TGGTGCCTTGGAACAATCTGATTTTGGTGGTGTTTCTTGAACTGTTCACAAGATACTCACCACCACGAAG
AGCAAGCACGGAACGGTTGATGCGGCGGCTTAAAGAGTGGTGGTTTAGCATTCCGGCTGCTCCGGTCCTT
CTTGAACAGAGCAAAGACGATAACAAGAAAACCAAGTAAAAACATCTGAAAAAAAACTACGTCGGGTTTT
CNGTCCCAGGAGAGTACGNAAAAAACAGGAGNACATAGCAAAGTGTAATAGTTACGTATGTTTGTATATT
TACATGTATTCATGTATGTTATTAGGAAATAGGTNAATTGTTCCGTGGGTNAAATCCCATTTTGGCTGNA
TTAAATGGTNTTGGNGGNAAAATNCCCNTTTT
>gi|2764356|gb|R65563.1|R65563 14067 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173D4T7, mRNA sequence
TCCATTGACATGGCAAGGCAGCTTGCTCTTAAAGAAGGTCTTCTTGTGGGAATATCATCCGGTGCAGCAG
CTGCTNAGCAATTAAACTTGCACAGAGGCCAGAAAACGCTGGGAAGCTATTTTTGGCGATATTCCCGAGT
TTCGGGGAGAGGTATCTATCAACGGTACTTTTCGATGCGACAAGGCAAGAAGCGGAAGCCATGACCTTCG
AGGCTTGAACATTCTCCATTTNTNCTTAAGAGACGCCANAATAAAAGAGNTNTTCAGTTTNTCCCNATAG
GGGGCTCTTCAATCTTTAGGTTACCATTNGCGTCCTTTGCNTCCAANCNGTATCTTCCCATTGTNTGNCC
ANTAAAAAGTCAAAACTAGGTTTCCT
>gi|2764355|gb|R65562.1|R65562 14066 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173D3T7, mRNA sequence
CACCTGGGTCAGTCAGTCTGGAAAGAATGGTATGCGTCGTGANTGGCTAGTTCGGGACTGTAATACTGGA
GAAACCTTAACACGAGCATCAAGTGTGTGGGTGATGATGAATAAACTGACAAGGAGATTGTCAAAGATTC
CTGAAGAGGTTCGAGGGGAAATAGAGCCTTATTTTGTGAATTCTGATCCTGTCCTTGCCGAGGACAGCAG
AAAGTTAACAAAANTTGATGACAAGACTGCTGACTATGTTCGATCTGGTCTCACTCCTCGATGGAGTGAC
CTAGATGTTAACCAGCATGTGANTAATGTAAAGTACATTGGGTGGGNTCCTGGGGAGTGCTCCACTTGGG
GAATAATTGGCGAGGCAAGNAGCTGAAAAAAGCAATGGCCCTTTGGGNGTATTCGGNAGGGGAANTTCGG
NANNNNNACNANTTTTTNCTTT
>gi|2764354|gb|R65553.1|R65553 14057 Lambda-PRL2 Arabidopsis thaliana cDNA clone 172A8T7, mRNA sequence
AGTCGTCCATCACAACACCACTACTCCATCAGTCAACGGACAATGTTTGACTACTTTGGACAAATCACTC
TCCAGCTAATAATTACAAATGCCATTACCCAATTAAAAGGGAACAATGGTGTGCCGTTGTGTTTTATGAC
TTTNGTGTCTGCTTTTTTNCTTAGTGTTTTCTCTTCTTTTTTTTTTCTAAAAAATTATTAATTACCTAAG
AAAGGTTTTTGAAGAAAGGAAAAAAAAATGGTGGATGAGACATCATTGTTCATGAGGATGATGATGATGA
TGATAGTGATGAAGAAGACTATGTGGGAGCTTTGGATTGAGACTTTTCTATATATAANATCTGGCTGATA
TATTAGTGCCATTTTTTCCTTACANTTCTTTGTGGGGNTTTNTTTNCCNCNTATCATCAATAGGANTGTT
ATAATTTNNCATT
>gi|2764353|gb|R65549.1|R65549 14053 Lambda-PRL2 Arabidopsis thaliana cDNA clone 172A15T7, mRNA sequence
ATGAGACACAATCACATGGCTTAATGTTGTGCACAGAGTATCTAGGGTTTNANAGTTACGACATGAGGAT
NTCCGATAACGAGGTGGAGAACAAGATGACTTGTCATNCGGAGGTGGAGACCGAAAGGNTTGAAGCAAAG
AGGAGGAAGACGAAGGAGAATNTGGTGGTGCAAGCNCAGAAAAAACAGTTTCCTCCGCCTCTNTCGTCAT
TAAACAGCCGTGGACAGCGATATTTTTATCTCCGTCCGGTGAGAAAAGACGGTAGATTNGNACTTACGCA
AGTTATGGTCGATCGNCCAGAGATTTTCCACGNTTCTAGAGTAGATNGACGGTTNAAAATTACATTTTTT
>gi|2764352|gb|R65539.1|R65539 14043 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171O16T7, mRNA sequence
TCGTCTCTTTNTCCGTCGCCACCGTTCCTAAAACGTCTCCCGTCTTCTTCTAATGGCGATCAATCGTAGC
TCCGATCATGAATCCGACGAAAACACCCGTNTTTACCATCCTTACCAGAACTACCAGGTCCCGATCAAAT
CTCAGTATCTATACAAGCTTCCGACTTCTCCGGAATTTNTATTCACGGAAGAGTCTCTCAAGCAGCGTCG
ATCATGGGGAGAAAATCTCACTTTCTACACAGGGACGGGTTATCTAGCCGGCTCTGTAGCCGGTGCTTCA
ACCTGGGATCTNCTCTGGTATCAAGAGTTTCGAAAATGGAGACACGGCGAGCTTGNAAATCAACAGGATT
TTAAATTCNTCTTGGTCAGGCATGNTNGTANCTTCGGGTATTAGGGGGTTGGNNTTTTTNGGGTNAACCT
NNGANGGGNTTTTAAAAAGGG
>gi|2764351|gb|R65530.1|R65530 14034 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171N11T7, mRNA sequence
TTTNTCCTTCTTCTTCTCCAATTTTCAAAATTCGAAAAGATGTTGAAGCTTTCGTGTAATGTGACTGATT
CTAAGTTACAGAGAAGCTTACTCTTCTNCTCCCATTCATATCGATCTGATCCGGTGAATTTNATCCGTCG
GAGAATTGTCTCTTGTNCTCAGACGAAGAAGACAGGTTTGGTTCCTTTGCGTGCTGTTGTATCTNCTGAT
CAAGGAAGTGTGGTTCAAGGTTTGGCTACTCTCGCGGATCAGCTCCGATTAGGTAGTTTGACTGAAGATG
GTTTATCTTATAAAGAGAAGTTTTGTTGTTAGATCTNACGGAGTGGGGTAGTAACAAAACCCNCTACTGT
TNNAANCATTGCTAAACTTTTTACAAGGAGGTGGGNTGTAATCATGGCACAAAGNTGTTTGGTTTTTCCG
ACCNNANGGGTTTTNAAANAACANCCTCCTTTGGGG
>gi|2764350|gb|R65518.1|R65518 14022 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171J23T7, mRNA sequence
CACAAAAGCTTCACCGGAGATCAGAGACGCGAAAATGGTGAACATTCCAAAGACAAAGAACACTTACTGT
AAGANCAAGGAATGCAAAAAGCATACTTTGCACAAGGTTACCCAATACAAGAAGGGTAAAGACAGTNTTG
CTGCTCAAGGAAAGCNTCGTTATGACCGTAAACAATCTGGTTATGGTGGTCAGACTAAGCCTGTNTTCCA
CAAAAAGGCTAAGACCACGAAGAAGATTGTTTTNAGGCTTCANTGTCAAAGCTGCAANCNCTTTTTNGCA
GCGTCCTATCAAGAGGTGCAAGCNTTTGGGGATCCGGTGGTGCCAAGNAGGGGNAAGGGGCCATCTNTGT
TTTAAGGTTGGTTTCANCTTNTTTCCTGCG
>gi|2764349|gb|R65517.1|R65517 14021 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171J22T7, mRNA sequence
ACCCAGAAGATTTCTTGGGTTCCAGATCCCAAAACCGGTTATTACAGACCCGAAACCGGTTCCAACGAGA
TTGACGCGGCTGAGCTACGAGCAGCTCTCTTGAACAACAAGCAGTGATTGATTATTATTACATGTAATTT
TGTCAAGGTCTTTAAGAGGAGATTAGTGGGTAATGATCTGGTGCAGTGAACCCTATTTTCATATGTTAAG
TGCGGTTCTGTAATGAATATAATAGAGAAGCGTTTGGTTTCCNCTAATTGTAACAAAAGGATCGTTGGAT
GTATGATAGAGNTTTTCTTATAAAACCATTTTCAGGAACT
>gi|2764348|gb|R65515.1|R65515 14019 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171J20T7, mRNA sequence
CCGCTTGGTAACTTCATGGNTCAAAGAGACGCTTCCATCAAAGAGAAGCTCGCNAGTTTTAAGGACACTT
CGACTGAAGTAAAGGAGCTCGATGAGCAAGCCGCCGCCGTGATGAGAGCAGCTAGGGCTGAGATCGCCGC
CGCGCTTAACAAGATGAAGAAGGAGACTCAGGTTGAAGTCGAGGAGAAGCTAGCGGAGGGAAGGAAGAAG
GTGGAGGAAGAGCTAAAAGAAGCTTTGGCGAGCTTNGAGAGTCAGAAAGAAGGAACCATTAAAGCTTTGG
ATTCTCAGATTGCTGCTCTTAGTGAAAGNCATTTTTCAAGAAGGTCTTTCCTNCTTAAATTAAATTTTTT
TTTACCNCGNGTAATTCCCTGNNTTCCCNTANCNCAAAACTTTTTTTCCAAGGAANTTCCTGNNAAAC
>gi|2764347|gb|R65511.1|R65511 14015 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171J14T7, mRNA sequence
GGAAAATTCCAAGCTTCGAGATTTTNTTATGGNTCGTGGTCAGATTGTTGATACCTTACAAGGAGAAATT
NCTGTNATCTGTCAAGATGTGAAGCTGTTGAAAGAAAAATTTGAAAACCGAGTGCCTTTAACCAAATCGA
TCTCCTCAAGCTTCACTAGTTCATGCGGATCATCTATGAAAAGCTTGGTGCTCGAGAACCCTTCTNAGCG
ATTGANTGGAGTGACTGAAACCTCAAACAACAACAAGTTCCCAGAAGCAGCAGCTTTCTTCATGAACAAA
GAGAAAGATGATTGTAGAGATCTNCTTGNAGATGGATGGGNCATCTTTGTCAAGGNGNCCGACAAGTTGT
TTGGTACTGNAGGATGAAGTANTTGTNCANATAGGGGACCTTAATNCTTAAAAATAAAATGGGTTGGTTT
CC
>gi|2764346|gb|R65504.1|R65504 14008 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171I21T7, mRNA sequence
AGATCTCGTTAATATCCATCCTACTGAGCTTAAATTCCCCTTTGAGTTGAAGAAACAAAGTTCGTGTTCG
ATGCAATTGACCAACAAGACAACTACTCAATGTGTCGCTTTTAAGGNTAAAACAACCNATCCTCGCAAAT
ACTGTGTNCGTCCTAACACTGGTGTTGTCTTGCCCGGTGATTCCTGCAAATGTTACAGTGACGGTTGCAA
GCCCAGGAAAGNGGGACCACTTGATTATGCAATGCAANGCCAAGTTCCTTGTTNANACTGTTGTGGNCCC
TTGNTGGTCCTACTTTCCAAGGAAGGTCCTCNGCTTGAAAATTNTTCAAAAAAGGGGGCNTNGTTAGNGG
TGATTT
>gi|2764345|gb|R65497.1|R65497 14001 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171I11T7, mRNA sequence
AACACAATTGAAGCTTTTATAATATTTNCTCAGAAACTTTCAAAGAGCTTAGAAAATGAGTACAGCTACT
TTCGTTGATATTATTATCGCCATCCTCTTGCCTCCACTCGGTGTCTTTCTCAGATTTGGTTGCGGGGTTG
AGTTTTGGATATGTTTGGTTTTGACGCTACTTGGGTATATTCCTGGGATCATATACGCCATTTATGTCCT
CACCAAATGATTTACCATCTATCATCATCTCCTTGAACAGCTGTTCCGTCGTGTTCTCCTATCTTTGTGA
CTGATTCAGCGTTTCTTTTTCTTTCATCAGAGTTTTTATGTTTCAAGTAATTTAATTAATCATCACTGTT
GTGTTTGCATTGTNATATAAATGNGGTGTTGTATAAAAGAAGAGAGCGTTGGTTTTT
>gi|2764344|gb|R65493.1|R65493 13997 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171H2T7, mRNA sequence
AGGAAGGTCTAATCACCAGGAAGAGGAGTAAAAATGGCGGTTCCGTTGCTTACGAAGAAGGTGGTGAAGA
AGAGGTCTGCCAAATTNATCAGACCCCAGAGTGATCGCAGAATCACCGTCAAGGAAAGCTGGAGGAGGCC
TAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGN
TCTAATAAGAAGACCCGNCACTACCTCCCAAATGGNTTCAAGAAGTTCATTGTTCACAACACCTNTNAGC
TCGTGCTACTCATGATGCACAACAGGACTTACTTGTGCAGAGATTGCTCACAATATCTCAACAANGNAGG
GAAAGGCCATAGTGGNGAGAGTTTCTNAGCTAGACGTTGTTNTTCCAACAAGTTNGTAGGTTTNNTCCNG
GATGCGGNTTAAACCCNTAAANGTTTTTTTT
>gi|2764343|gb|R65492.1|R65492 13996 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171H24T7, mRNA sequence
CTGTTAAGCCACTAAAACCCTAAAGGCGTCTCCTTTNNTNGCCACCACTCTCCACAATACCCATTTNTGC
AAAATGGCTTCTNCTCGTATTTNTNTCCGCCTTGTTCGCCGATTTGCCTCAGCCGCCGCTGACGGTACGA
CCACCGCTCCCTCTTCAGGCAAAATCTCTGTNTCCAAAGCTAAGTCCACTCTCCGGAAAGAACACGATCC
CGACAAAGCTCTTAAGATCTACGCCAATGTNTCCGATCACTCAGCCTCTCCTGTTTCATCTNGCTACGGC
CAAGAGCTCACTGTTCGTGGGCTCGCCAAGTGTCGNCGTTTCTAAGACATNGNAACCCTAATTTGANTTC
CACAAAAATGATCCCAAAATNAAAG
>gi|2764342|gb|R65491.1|R65491 13995 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171H23T7, mRNA sequence
GGGAATATNAAGATGACATCTTCTATGGTCTCTNCCATGGCTCTNTTTCTCCTTCTCCTNCTTGTGTTTC
CGCATATGGATAAAGCCCTTGGCGCACAANAGGAAGCCCAGAAACAAAGGATTCCNCGTTTNAAATGTTC
TCCACGAATCCCCTTTTGTACAAATCCAAACCTACCTTCTCCTCCGCCCCACAGGTCTTTNAAAGGCACA
CTCGAACCTGGTCATTGACTTCACTCTAGCTTCGAATGCGTGTNAACGTGTGCATGTTTCTAACATTGTG
CTTTGGTTTGTGGTTTCNATCCTTGTTTATCTTTGCATGTGTTTGTAATATTTAACAGTTTTNNTCGNAC
CGTCGGTTGANTAAA
>gi|2764341|gb|R65487.1|R65487 13991 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171H11T7, mRNA sequence
GGAAAAGATTATGTTCAGCGATTGGGAGAATGGGTACAACGCAATGACTCATACATATGAGAATCTGTTC
GAAGCTGGAGTGATTGANCCGGCTAAAGTGACAAGATGTGCGCTACAGAACGCTGCTTCCGTAGCAGGAA
TGGTACTGACCACTCAGGCCATTGTTGTTGACAAACCGAAACCCAAGGCTCCTGCTGCTGCTGCTCCTGA
GGGTCTCATGGTGTAATCAAAACACAACATCTTATCATCACAATGGCATCTTTGTCTTTTTGCACATTTG
TCATCCCCATTTATCTGCAATGTTTTTCTTTTTTGGGGGAATATGAGTAGTTTNTTAACAGTNTCGGGAA
ATAATTATCATCTTTTTTGTCC
>gi|2764340|gb|R65486.1|R65486 13990 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171G9T7, mRNA sequence
AAGTACGTTTCGGTTTTCAGGCCAATCTCTGAATCTGCGTGACAAAAGCAACAAATTACATATCTCTCTC
TCTGCGCGACTTCGAAGATCAACATCCATGGCGTCACAGGTAAGGTCAGTAAAAGTTGGCAATCTCTCTT
CAGGAGCAACTGAGCATGATATTAAAGAGTTTTTCTCTTTCTCTGGTGAAGTTGAAAGCATCGATATCCA
AAGTAACGAGCATAGTGCTTATGTCACATTTAAAGAAACTCAAGGAGCAGAGACTGCTGTGCTCTTATCT
GGAGCGAGTATTGCCGATCAATCAGTCATCATTGAGTTGGCTCCCAACTACAGTCCACCAGCAGCCCCTC
ATGCTGAAACACAGAGCAGCGGTGCAGAAATCTNTTGTCCNGAAGGAAGAAGATGTTNTNAGCAGCATTT
TTGNAAAAGGGNTNNTTNNTTNGGAAAATTNTTTNGNAAAGAAAAAGTTTTTNTGGGAANATGGTTTTCN
TAACCCCCCCCNNGNGC
>gi|2764339|gb|R65482.1|R65482 13986 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171G1T7, mRNA sequence
GCTAAGCAGCCTAACTCTGCTATCCGTAAGTNTGCTAGAGTTCAGCNTATCAAGAATGGAAAGAAGATTG
CTGCCTTTNTCCCCAATGATGGTTGTTTGANCTACATCGAGGAAAACGATGAGGTCTTGATTNCTGGATT
TGGTCGTAAGGGTCACGCTGTGGGAGATATTCCCGGAGTTAGGTTCAAGGTCGTGAAGGTTTCTGGTGTT
TCACTCTTGGCCCTCTTCAAGGAAAAGAAGGAGAAGCCAAGATCTTAAGCAACCCATACAAAAAGCTTCA
AGCTTTTGAAATGGTTTTTNATAGTTCAGTTTAAGTCTTGTNCTGTNCTACTTTATGTTTCAAGAACTTG
ATTTTGTGTACANTTTATGAGGTTTTGAATTAAGGCATTATCGGTTAAAATTATTGGGGTTAANC
>gi|2764338|gb|R65480.1|R65480 13984 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171G13T7, mRNA sequence
GTTATCACCCAANAGAGAAGAGCAAACACAATGGCTTTCGCTTTGAGGTTCTTCACATGCTTTGTTTTGA
CAGTNTTCATCGTTGCATCAGTGGATGCAGCAATAACATGTGGCACAGTGGCAAGTAGCTTGAGTCCATG
TCTAGGCTACCTATCGAAGGGTGGGGTGGTGCCACCTCCGNGCTGTGCAGGNGTCAAAAAGTTGANCGGT
ATGGNTCAAACCACANCCGACCGTCAACATGGATGNAGATGCTTACAGTCCGCTGCANAAGGGGTTANTN
CAAGTNTAGNCTCTGGGCTTCCTGGGAAGTGCGGTGTTAGCATCCCTTATCCCATGTTCACG
>gi|2764337|gb|R65471.1|R65471 13975 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171F15T7, mRNA sequence
AGTTAAAATGTCTTGCTGTGGAGGAAACTGCGGATGTGGATCTGGCTGCAAGTGCGGCAACGGTTGTGGA
GGGTAAGTCTCCAACGTCTCGTTTGTATTTATATTTTCCGGTGAAATCGTTGCATGCAAGTATGCAACAA
CTGTGAATCGATGATGATATCTTGTTTTGATGAATGGTTTCTTGGAGATTTTNCTTGTAAAAAAGATACA
ACTCTTTTGAATTTACACGATCTCTGTTTTCATAGGATACTGATGGGTTTTTNCTTTCGATTGTTGCAGT
TGCAAAATGTACCCNGACTTGGGATTCTCCGGCGNGACAACCACAACTGAGACTTTTNTCTTTGGCGTTG
CACCNGCGNTGAAGNATCAGTACGNGGCTTCAGGGGGGGGTAACAACGCTGAGANCGATGNTTCAAGNNT
GGNNCTTACTTCNAGTGTNTNCCTTCACCTCAAGTNAAGAGGCCTTTTAATAANAGGGTAATCGGCCCCT
TAATAATAAAGTTTG
>gi|2764336|gb|R65469.1|R65469 13973 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171F13T7, mRNA sequence
CTTCCTTTCATATTGTGAGGATGTCCAAAACCAATATGAAATTTTGCAATAGTTATTTNCTGGTCGATCC
GACCANAGCAAGTTTTCTNGATCTCCTNTTGCTTTTGTTTTCCTCCAACCTGACCAGTGCAAGATTCATC
GATTCTCCTCCGGATACGNTTAAAGGCTTCCGGAGAAGTTTCGCGAGTCGATGGATCCNNGCGTTGGCCA
TNTTCCTTCAAAAAGTATTAATNCTCTTAAGTAAACCTNTTGCATTCANTGGGCAAAAGCTCACATATT
>gi|2764335|gb|R65466.1|R65466 13970 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171E13T7, mRNA sequence
ACTTNCACCAAGCAGCATGAAGATTAAGGTCGTTGCACCACCTGAAAGGAAGTACAGTGTCTGGNTCGGT
GGTTCCATTCTNGCTTCCCTCAGCACATTCCAGCAGATGTGGATCTCCAAGGCCGAGTATNNTANAGGCA
GGTCCAGGAATCGTTCACAGAAAATGTTTCTAAGCTCTCAAGATCAAAGGCTTAAGANAGCTGGGGGTTC
TNATGAANGGGCTCAAAGTTTCT
>gi|2764334|gb|R65465.1|R65465 13969 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171D8T7, mRNA sequence
AGATGTTCGCCGTGAAGTCCAGATTATGCACCATCTCAGCGGTCACCGGAACATAGTGGACTTNAAGGGA
GCCTACGAGGACAGACACTCTGTGAATCTNATAATGGAGTTGTGTGAAGGAGGGGAATTGTTCGATAGGN
TCATTTCTAAAGGTCTTTACTCAGAGAGAGCTGCTGCGGATTTNTNTAGGCAGATGGTGATGGTTGTNCA
TAGTTGTNATTCTATNGGTGTAATNCACCGAGNCTTTGAAGCCCGAAAACTTTCTCTTTCTTAGTAAAGA
TGAGAACTNACCATTGNAAAGNTTTCAGACTTTTGGTCTCTCTTGT
>gi|2764333|gb|R65461.1|R65461 13965 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171D22T7, mRNA sequence
TTCCATTAACGTCTTCGTTAATGGCGACTCCTATTCAAGCCTCTTCTNCCTCCACCATTGGTGAGACCAG
NNANGGCTTGAAGGTCCAGTCTCATGTTTCAATTGGAGCAAACGATCTGCTGATTGTNGGACCGGGTGTT
CTTGGACGCTTAGTTGCAGAACAGTGGAGACAGGNACATCCAGAGTCTCAAATCTTTTGGGCAGACAGTA
ACAACAANTCATCATGGTGAGTTGGAGAATTTGGGTATCAAANCANCTNTTNAAGGAACCGCATATGGGG
GAAAG
>gi|2764332|gb|R65457.1|R65457 13961 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171D14T7, mRNA sequence
AAGAGCCAATTCAGCCTAACCCGGCCTCTTTAGCCTGCGAACTCCCGATTGCAAGAAGAGCTTCACTTCA
TCGGTTCCTTGAGAAGAGGAAGGATAGGNTCACATCAAAGGCACCATACCAAATAGACGGTTCAGCTGAA
GCGTCTTCCAAGCCTACTAACCCAGCTTGGCTCAGTTCACGGTAAACTTCGAGCCTGTCCGACCCNGAAG
GCACAACTTGAGAGACCTTCTTGTAAGATTCTNCTGATGCTCCATCGTTACAAATATCAAGCTGCTCCTC
TGTTCATTTTTTCTATAGNTTAATTTCANCCCTAGTAGTTTTGGTTTTGTTTAACTNCCCCCGGAAAACT
CCATTTATATTTGTATGGAAATCCAATATCAATAGGNGTTCNAATCGTTTTNCTTCTTGGGGNTTTAAAG
TTTNAGCCAGTNGNGGNTAAANCNCTTTTCCNTTNCCGG
>gi|2764331|gb|R65454.1|R65454 13958 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171C4T7, mRNA sequence
GACGAAAGCGGCAAGGAAATCAGCTCCAGCCACCGGAGGAGTGAAGAAGCCACACAGATTCCGTCCAGGA
ACAGTAGCGTTGCGTGAAATCAGAAAGTATCAAAAAAGCACAGAGCTTTTGATCCGTAAGCTTCCTTTCC
AGAGATTGGTTCGTGAGATAGCTCAAGATTTCAAGACGGATCTGAGGTTTCANAGTAGTGCAGTCGCAGC
TCTTCAGGAAGCAGCTGNAGCTTATTTGGTTGGTTTNTTTGAAGATACTAATCTCTGTGCTATTCATGCT
AANGAGGGNTACGNTTTATNCCNAAGNNTATTCAACTTTTGCGAGGAGGATTTAGAGGGTNAANAGGGCT
TTAA
>gi|2764330|gb|R65444.1|R65444 13948 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171B22T7, mRNA sequence
AGAGAGACCAAAAAGAGATCGGAAGAGATGGCTTCTACCTCCGCGATGTCATTGGTCACACCACTTAACC
AGACCCGTTCGTNTCCTTTCCTCAAGCCATTACCTCTGAAACCATCCAAGGCTTTGGTTGCAACTGGAGG
CAGAGCACAGAGGCTTCAAGTTAAGGCCCTCAAGATGGACAAGGCTTTGACCGGTATCTCCGCGGCTGCT
CTTACTGCTTCGATGGTGATTCCGGAGATAGCTGAAGCTGCTGGTTCTGGAATCTNTCCTTCCCTCAAGA
ATTTNTTGCTCAGCATTGCTTTCTGGTGGCCTCGTCCTCACTTGTCATCATTGGTGTCGTCGTCGGCGTC
TCCAACTTTTGACCCTGTCAAGAGAACCTAAGNCCTATATAATCTTTNTTTACATNAATAATGNAATNCN
GTCTNCCTCCTGGGAATTCGNTNAAATTTTGCAGNAATNNACTTTTTTGGGNAAAAGGC
>gi|2764329|gb|R65443.1|R65443 13947 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171A8T7, mRNA sequence
AGAGGGTCGCAGTCTTGATTCACACATTGAGGACCAATTTGCAAGTGGACGTTTGTTGGCTTGTATCTCT
TCAAGGCCTGGCCAGTGCGGGCGTGCTGATGGATACATCTTGGAAGGTAAAGAGTTGGAGTTCTACATGA
NGAAGATCCAGAAGAAGAAGGGCAAGGGTGCTGCTTAGAGTCTCTTCTTATCTGCCTTGAGCTTTTGTCT
TACAACATGTTTTGAGTTTTCAGTTTCAATTGTCTGAGAAACTATGTTTTTGGATTAGCTTGTGGTATTT
CTTTGAAACTCCCATTATGGTACAATGTTTTTATCTTGGATTTCCTTTATAATTTTAATCGNNTAATTTC
ACTCT
>gi|2764328|gb|R65442.1|R65442 13946 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171A2T7, mRNA sequence
ACGACGATGCTAGATCGGGCTCTTTCCTCTCGCCGTCCTCACTCCGACGCCGATCTCTCTGCTTCCGGCG
AATCCGGAACCGACGAATCTAAAACCAAACGCCCACACATCTACCTCCTTGCTTCCAATTTCCTTTCTCG
GATCGGTCATCAGTGGTGGCCTTGTCTCATTCTCGCTCTCCTCTTCCTCGTCCTTCTCTTCCTCATCTCC
GTTGCTTTCCATTCTCACAGCTTTGTTTGCATCTCCCGNTTCGATCCCGCTGCTCGGATCGGGTTTTTNG
GTCTTGATGGCCTCGAATCGGATTTTGGTGCCCCTAGGTGTTCCTTGGTGCAGATCGAAACAATGGAAAA
NAAGTTGAGTGGACATCCAAAGATTTTACTTCAAGGGGCTAGAAGGAGGTTTGTGCCGNTATATGAAACA
CGGCCGTTAAAGGACAAATATTTATGGAANTNGGTTTTTGATCAAAAGGCTTTGGGGTAATGGNNAATNG
NCCGTTTGGGTAAAANCCAGNTATTNNTGANTNTAANANGNGGNCNTTTAAANGGGCAAT
>gi|2764327|gb|R65439.1|R65439 13943 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171A11T7, mRNA sequence
CNTGGTCGTGGGGCCCACTAGGGTGGTTAGTACCGAGTGAAATCTTCCCGTTGGAGATAAGGTCGGCGGC
GCAGAGTATCACCGTGTCCGTGAACATNATCTTCACGTTCATTATCGCGCAAATCTTCTTGACGATGCTT
TGTCATTTGAAGTTTGGGTTATNCCTTGTTTTCGCCTTTTTCGTGGTGGTGATGTCGATCTTTGTATACA
TTTNCTTGCCGGAGACGAAAGGGATTCCGATAGAGGAGATGGGTCAAGTGTGGAGGTCACACTGGTATTG
GTCAAGGTTTNTGGAGGGATGGTGAGTAATNGGAATGCNCTTGAAATGGGGCAAGAACAGTAACCAAGCT
GGAACGGAAGCATGTTTGATTTAATCATTTGTTTTTAATTGAGAGTTTANNGGAAGANANGANNAAAAGA
TTTTNNNAATTTCCAAATGTNCGTAAAGGNAAAAAGTGTTCT
>gi|2764326|gb|R65434.1|R65434 13938 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170O9T7, mRNA sequence
ATCTNTNTCTNTTTGCCTCTNCCTCATTTGCATTATCTATCTCCCCCAACATTCTCTCGCATGCGGCTCT
TGCAACCCACGGAAGGGCGGAAAGCACTCCCCTAAAGCCCCTAAGCTACCAGTTCCTCCGGTGACCGTCC
CTAAGCTACCAGTTCCTCCGGTGACCGTCCCTAAGCTACCAGTCCCTCCGGTGACCGTCCCTAAGCTACC
CGTTCCTCCTGTGACCATCCCTAAGCTACCCGTTCCACCAGTGACTGTACCTAAGCTACCCGTTCCTCCT
GTGACCGTTCCCAAGCTACCCGTTCCTCCAGTGACCGTTCNCAAGNTANCCGTTCCTCNAGTGACAGTCC
TAAGGTACCNGTTTCCCGGTAACTGTACCTAAGGTANCNGTTCTTCAGTNACGGTCCTAAGTTACCNTTC
TNCGNTTTTAAGGGNTCCAATNCTTAGNGGTGGGTCAT
>gi|2764325|gb|R65415.1|R65415 13919 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170N18T7, mRNA sequence
CTCATCTTCAAGCCATCTCCGATCATCATCAGACAATGGCAGCAGCTATGGCAACAGCAACCAAGTGCAT
GTTTCTAAACCCATCTCCTCCTAAACTCCAAAACCAAACCAAATCCAAACCATTCATCTCCCTACCAACC
CCACCAAAACCAAACGTNTCTNTCGCCGTCACAAGCACCGCCCTAGCCGGAGCCGTCTTCTCTTCCCTCA
GCTACTCTGAGCCAGCTTTAGCCATCCAACAGATCGCTCAGCTCGCTGCAGCAAACGGCAGTAGGCGNCA
ACCGTGGNTTAGNTCTTCTNCTTNCCCATCGTNCCAGGCATTGCATGGGGGCTTTTACAACATTCTTCAG
GCAGTNTTTNNCAGGGTAAAAANTTNGTGGGGTNAAGGGATNGTTNTTTGGGTTGGGTTTNTGGGGGGTT
TTTAA
>gi|2764324|gb|R65400.1|R65400 13904 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170L24T7, mRNA sequence
AGTTAACCGCATTTTTGACAAGTATTGGGACTTTNACTCAAGTGAGTCACTCGAACATGACCTTCCTGGT
CACTTGCTCCGCTACCCGATCGGTGTAGCCAGCGAAGGCGACATCACTGAGCTTCCAGGATTTGAATTCT
TCCCGGACACAAAGGCCCGTATCCTCGGCACCAAATCAGACTACCTGCCTCCAATCCTTACAACCTAATC
TCACTAAGCATGTCAAGTAATGATCTCTCTCTCCCTCTCTGCTTTGCTGCTGTTGTAGCTTTGAATAAAA
CTTGAGTGTCTACCTTTAGAATTAAGGAGTCAAATGGTTGTTATGATGATGCACTTCTTTACCCCTTTGG
TTTTTATATTCGNACAATGACGTGGTNAGAGAATGTAGCTTTGTNATCTTGNTTTGTTGTTGTNATGGAC
CCTTTGGGCTTATGAATCTAANATCTGACCNTTTNTT
>gi|2764323|gb|R65397.1|R65397 13901 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170L1T7, mRNA sequence
GAAGAAGAAGAAACTACAATAGTTAATCAATCAAAGAGAAGTAAGAGAAATGGCAGATTCTAACTGTGGA
TGTGGCTCCTCCTGCAAATNTGGTGACTCTTGCAGTTGCGAGAAGAACTACAACAAGGAGTGCGACAACT
GTAGCTGTGGATCAAACTGCAGCTGTGGGTCAAACTGTAACTNTTGATGAAATTATTATGGTCTAAAATC
ATATATATGGCAGAAAAATTGGGGAAAATATGTGTTTTATGCTAAGAGATGTGTGTGTNTTGTTGGAATA
AAGGCGTGACCGTTGTGTTGCGTATCAACTCTCTTAAGCTTTGACTTTTCCCAGCTTTGTATTTTCCNAT
GTATGGTAATGGTGTGATTGTNTAATGGTTTTCATATGTAACCGTAAAAAAAATATTTTTTGTG
>gi|2764322|gb|R65395.1|R65395 13899 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170L17T7, mRNA sequence
CACAATCTCGGCGATTCTTTCTTCCGTNTCGAGTCGCTGAGATCCATCAGTAAAAGGTCTGCAAAATGGT
TGCTCAGGGATTCACTGTGGATCTTAAAAAGCCCCTTGTATTTNAGGTTGGTCATCTTGGAGAAGATTAT
GAGGAATGGGTTCACCAACCTATCGCGACCAAGGAAGGCCCTCGGTTTTTTNAGAGTGACTTTTGGGAGT
NCTTGACACTTACAGTTTGGTGGGCAGTTCCTGTCATTTGGTTGCCAGTTGTAGTCTGGTGCATATCAAG
GTCAGTAAGTATGGGATGTTCACTTNCAGAAATCGTCCCAATTNTTGTCATGGGNATATTCATCTGGNCA
TTTTTTGAANACGTTCTTCACCGGTTCGGTTTTCCNCATAAAAACGNGGGGTACTTGGGNANACTGCACA
CTNTCTTTTTNCGGGGCCANCNTAAGANCC
>gi|2764321|gb|R65393.1|R65393 13897 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170L13T7, mRNA sequence
TTGAATTAGCCATGGAGAAGAATACTTCTNAAACCATCTTCTCCAACTTTTTCTTTCTCCTTCTCCTTTN
TTCATGTGTCTCTGCTCAGCTCCGGACAGGTTTCTACCAGAACTNATGTCCGAACGTGGAAACCATTGTA
CGTAACGNTGTCCGTNAGAAATTCCAGCAGACTTTNGTNACCGCTCCGGCCACTCTTCGCCTCTNCTTCC
ACGATTGCTTCGTTCGTGGATGTNATGCGTCAATAATGATAGCATCACCATCGGAGAGAGACCATCCAGA
TGACATGTNATTGGCCGGAGACGGATTCGACACGGTGGTGAAGGCGAAGAAAGCCGTTGATAGCAATCCC
AATTGCNGAAACAAAGTTCNATGTGCTGANATTTGGGTCTCGCANTCGTNAAGTCGTCGTTTTGNCCGGG
GNCCAAGTTACCCGGTGGTGGTTTGGGNGGGGG
>gi|2764320|gb|R65392.1|R65392 13896 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170L10T7, mRNA sequence
CGAGTTAAAGGAAGAGTTGGTGGAAATGCCTTTATGTAAACACATATTTNATCTCGATTGTATTCACCTT
TGGCTTTATTCTCACAACACTTGTCCTCTTTGTCGATCCTCTGTCTCCATCTCCTCCACCAAAACCTCTG
TTGATGACGACAACGACCATCCAGATTCTCCTCAAACGTCACCGGTTTGATTCAAACCCCCGAAGGAAAT
AAGCAAATACACAAGTTTTGTTAGTGAATAGATCGATACAAGATGTAAATCTTAATTTTNCTGATACAAG
ATATCAAAATGTAATCCATCACATTATATATATNGGTTACACAGATTCATTC
>gi|2764319|gb|R65389.1|R65389 13893 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170K20T7, mRNA sequence
CAGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGAC
TCTAGTCCGACTTTGTGAAATNACTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGTGCAAGTNAAATACC
ACTACTTTTAACGTTATTTTACTTACTCCGTGAATCGGAGGCGGGGTACAACCCCTGTTTTTGGTCCCAA
GGCTCGCTTCGGCGGGTCGATCCGGGCGGAGGACATTNTCAGGTGGGGAGTTTGGCTGGGGCGGCACATC
TNTTAAAAGATAACGCAGGTGTCCTAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGACAAAA
>gi|2764318|gb|R65380.1|R65380 13884 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170F17T7, mRNA sequence
CTCTNCTTTNTTTTGTCAACAAAGAAACATTTCCATTGAGTCTCTCTCAATGTNCTNCTTCTNCTTCTTC
TAAGATTAATTCAAAGTGTTTAATACTTTTAAAATTTTAAGTTTCTTTTTGGTCAGTTTCAAATGGGTGA
CATCATCGGTCACAAGGATAGGCAAATATGGCCACCCTCTNATCATGTNCTTCAAGATCCATTGTTTGAN
CATTCCAACAAACATCAGTTGCAGAAATATGTCAAGNACCACCATCACCACGGCAACGGTGAATTTGGTC
GGCCCGGGGCACCTCCTCTTAGGCAAACATTTCCTTTGNNCTNTTATNCANGGCAAAAGCACCCAAGCAA
ATTGGGAAAGGG
>gi|2764317|gb|R65376.1|R65376 13880 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170A9T7, mRNA sequence
TACAACATGGAGTTGTGGCAAACATCCGGACATGCTGACAATTACAAGGATAATATGTTTACNTTTAATA
TTGAGAAGCAAGAGTTCGGGCTCAAACCTATGANTTGTCCTGGTCACTGCTTGATATTCCAGCATAGGGT
TCGCTCATATAGAGAGTTACCTATGANACTGGCCGACTTTGGAGTGTTACACCGCAATGAGGCAAGTGGA
GCACTTAGTGGATTGACTCGTGTCCGACGGTTCCAGCAGGNTGATGCACACATATTCTGTACAACGGGTC
AGGTTAAGGGAGAAGTGCAGGGTGTGTTGGAGTTCATTTGNCTACGGGTACAAAGTTTNCGGGGGTTTAC
CTNTTGNGNCTAAAACTTTTNAACGGGGGCCCACNGANGTANCCNNTNGGGGTTTTTGGAAACA
>gi|2764316|gb|R65374.1|R65374 13878 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170A3T7, mRNA sequence
TCCTTCCACTCCATCACACACTCCAACTCCACACACTCCATCACACACGCCAACTCCACACACCCCTCCT
TGTAACTNTGGAAGTCCACCTTCCCACCCTTCCACGGCTTCACACCCTTCCACTCCTTCGNACCCAACGG
CATCACACCCTCCTTCTGGTGGATATTACTCATCTCCTCCACCAAGAACTCCGGTTGTTGTGACTCCACC
ATCACCCATTGTTGATCCAGGGACACCCATCATTGGAGGAAGCCCACCAACTTCTATNATTGACCCAGGG
ACTTCTGGNACTNCTTTNATTCCTGGCTCCTNTCTNANCCANTTNANTGGNACATGNGATTTTCTGGGAG
AAAACCAACCTACATTGNATATGGGGGTTT
>gi|2764315|gb|R65372.1|R65372 13876 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170A21T7, mRNA sequence
TTTGTNTTCAGCAGTCAGTGCGCATCCGTAGAGAAAAGTGTGAGAATCTNCCACCATGGGTCGTATGCAC
AGTCGAGGAAAGGGTATTTNAGCCTCTGCNTTGCCTTACAAGAGATCGTNTCCAAGCTGGCTCAAGACCA
CCTCTNAGGATGTTGATGAATCAATCTGCAAATTTGCCAAAAAGGGATTGACCCCTTCCCAGATTGGTGT
NATTCTCCGTNACTCTCACGGTATCCCTCAGGTCAAGAGTGTTACTGGAAGCAAAGATCTTGAGGATACT
CAAAGCTCATGGCCTTTGCTCCNTNNAATCCCTGNAGGNTCTTGNACCCATCTATTTAAGAAGGGCTCTT
T
>gi|2764314|gb|R65367.1|R65367 13871 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170A14T7, mRNA sequence
GTTTTCCTTTTCCCCACCGGAAAATCTCCGACTAATCGGCGTGATGAACCCGAAACTGCAAACCGTTAAC
CGAATTCGGNTCTTAGAAAAACCGGTTCACCACTCTNTACTCTATCTCCNAGCTGTGTTTCTTTTTATTC
CGACTTAAAAAAAGCTTCAAATTTATCCGATTTCGAATCCATTAGAGAAAACACATTTTTTTNTCCNTAA
AAGGGNTTTTTTTTTGAGGTTGTGTGTTTATNTCNGGGTCTGTNGCAAAANGTCGGACGNGACCC
>gi|2764313|gb|R65363.1|R65363 13867 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169P3T7, mRNA sequence
TCANTTGGAATTTGGNTCGTGGGATTTTGGAAATGGCATCGAAACGGATTTTNAAGGAATTGAAGGATCT
GCAGAAGGNTCCNCCTACTTCATGTAGCGCAGGACCCGTTGCGGAAGACATGTTTCATTGGCAGGCCACT
ATAATGGGTCCATCGGATAGCCCTTATTCTGGAGGAGTTTTTCTTGTAACCATCCATTTCCCNCCAGATT
ACCCATTTAAGCCTCCTAAGGTGGCTTTTAGGACGAAGGTGTTCCATCCAAACATTAACAGCAATGGAAG
CATCTGCCTCGACATCTTTGAAGGAGCAGTGGAGTCCTGCTCTCACAATTTCCAAGGTGCTGCTATCGAT
CTGGTTCNTTTTTTAACGGNTCCAAACCCAGATGGATCCTTTGGNCCCTGNNNTNAGNNNAA
>gi|2764312|gb|R65358.1|R65358 13862 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169P13T7, mRNA sequence
GGATAATGACAAGTTTGGGTAACAAGAAGANGAGGGATGCAGTTCGTCAAGCATGGATGGGGACTGGTGC
ATCACTTAAAAAACTTGAAAGTGAAAAGGGTGTGATTGCAAGATTTGTTATTGGAAGAAGTGCAAATAAA
GGGGACAGCATGGNCAAGAGCATTGATACTGAAAATAGTCAAACCGATGACTTCATTATTCTCGATGATG
TAGTTGAGGCACCCNNGGAAGCTTCTAAGAAGGTAAAANTGTTCTTTGCCTATNCTGCAGATAGGTGGGA
TGCACAGTTTTATGCAAAAGCCATCGACCAATATCTACGTAAATATAAGATGCNCTGGGNACTACGNTTT
GCAGGCACATTCTGGAAAACCCCNCGGGGCTTACATCCGGTTGCATTGAAATCAAGGCGAAGGNCTTTNT
NAGGNNCCGNACCCACANATTGGGTATTGGNCCCAGAGTTGGTTGGAAATTNCGG
>gi|2764311|gb|R84204.1|R84204 16163 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169N24T7, mRNA sequence
GGACCTGGCCNGAACTNCCTGGGNCTGCCCACTGTGTCCNGGGAGTTTCACGGATTATCANGTTTCATGA
ATAAAAGGACAGCTTATCAAAACAAACCAGCAAAATATACTAATCAGATCTCTCTTGTTAAAGAAGCAAA
AAGGCGAATCTAGTTCTAAAGACTCAAAAGGAACTGCTGAAGATGGTCCTAAAAAGAGGGCTGCAAATAG
AGCTCTNGACGACAGAAGCTCAGCTAAAAGAGCTGCTAATGCATCTAGACAAGAAGGNTCAAGCAGTCGC
ACAGGCGAAAGNGACTTTCAGTCTTTGACCGTTGAGANGCTCCGCGCCATGCTCAAGGNGANGGGCCTTN
CAACAAAAGGNNG
>gi|2764310|gb|R65343.1|R65343 13847 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169L8T7, mRNA sequence
ATCCATTTCTNTTTCTTCTTGACTCTACCATCGTTTCTCTAATCTCCGCAACTATGGCTTCATTTACGAA
AACGGTTTTNATCCCTATTGCGCACGGTACGGAGCCTCTAGAAGCGGTGGCGATGATTACCGTGTTGCGT
CGAGGTGGTGCTGACGTGACGGTGGCGTCTGTTGAGACTCAGGTTGGCGTTGATGCTTGTAATGGCATCA
AGATGGTCGCTGATACTCTNCTCTCTGATATTACCGACTCTNTTTTCGACCTTATTNTGCTCCCCGGAGG
CTTTCCCGGTGGCGAGACTCTTAAAAACTGTAAATNCTTNAGGGGNACATGGTCAAGAAACAANACTCTT
TGATGGGNCCGACTTTAACGCANNCTAATAATNGTTGGTGGTTCNTGCCCTTTGGCTCTTTGGGTAANTT
TGGGGNGTTACTTTGNATGG
>gi|2764309|gb|R65337.1|R65337 13841 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169L19T7, mRNA sequence
CTCTCTCGATATCATCTAAATCTNTCTCTTGATCTCAATTTCGCAAAATGGCTGACAAGAAGATCAGAAT
CGGAATCAACGGTTTCGGAAGAATCGGTCGTTTGGTTGCNAGAGTTGTNCTTCAGAGGGATGATGTTNAG
CTCGTCGCTGTTAACGATCCTTTNATCACCACCGAGTACATGNCATACATGTTTAAGTATGANAGTGTTC
ACGGTCAGTGGAAGCACCATGNGCTTAAGGTNAAGGNTGACAAAAAT
>gi|2764308|gb|R65332.1|R65332 13836 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169K23T7, mRNA sequence
GAGAAAGAAAAGAAGAAGCAAAACANAGAGAAAATGGCAGGATTNTTTGATAAACAAGCCGATCTATACC
TTNACGCCAGACCTAATTACCCCTCTAANTGGTTCTCGAAGCTCGCTGATCTCACCGATCACCACGGTTT
AGCCTGGNATGCTGCCACCGGAAATGGCCAAGCAGCTCTNGCCGTTNCAGAGCATTACGAGAGTTTCGTA
GCAACGGNCGTNAGT
>gi|2764307|gb|R65331.1|R65331 13835 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169K18T7, mRNA sequence
CAGAGAGTTAAGCCTTGAAGACGAAGAGATAACGAATTGGTTGTTGATCACTCGCTTTATAAATCTNTNA
GTTTCTTGCTCACACCAACATCTCTCTAAGCTTCTCCTTCTACCAATCTAATTCCTCTCTTCAGCTTCTT
GTGTTGTNACGCATACTCGTCGCAGTCTTGAGATATGGCCGCCGCAGTTTCCACCGTCGGTGCCATCAAC
AGAGCTCCGTTGAGCTTGAACGGGGTCAGGATCAGGAGCTGTATCAGCCCCAGCTTCAACCTTNNTTNGG
AAAGAAAGTTGTAACTGTTTNCGGGATTCGCACAGAGGCACCAAGAAGGTGCAACGGGNTCATTCNAAGG
GTGTTGGGCTTTNTTAAAGNNGGGCAAANAAANCCCNTTGGGG
>gi|2764306|gb|R65329.1|R65329 13833 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169I3T7, mRNA sequence
TTCTCGGGCAACAACTTTACTTGTTCAAGCCCTAAAACCAGTCTTGTTAACCTCAACTATCCTTCCATCA
CAGTTCCAAACTTAACATCAAGCAAAGTCACCGTTTCAAGGACTGCCAAAAACGTTGGACGNCCTTCGAT
GTATACCGTCAAGGTGAATAACCCACAGGGTGTTTATGTCGCGGTGAAGCCAACGAGCTTGANTTTCACC
AAAGTTGGAGAGCAAAANACGTTTAAAGTGNTCCTTGTGAAAAGTAAGGGNAATNTGGNTAAGGGCTATG
TGTTTGGGAGNAATTGGTTTNGGTCAGNCAAGGAGCATCGTGTGAGAAGTCCCNTTNGTTGGTGNAGCTC
TTACTTTTNAATTTTG
>gi|2764305|gb|R65328.1|R65328 13832 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169I20T7, mRNA sequence
TTATCACTACTCTAAAAGANTCTNCATCATGGCCTCAGTAACCTCAGCCACCGTTGCAATCCCATCTTTN
ACCGGCCTTAAAGCCTCAACCATCAAATCATCCGCCACCGTCAGAATCCAAACTGCTGCTGTTGCATCAC
CGAAGCTTACAGTGAAGTCATCTCTAAAGAACTTCGGAGTCGCGGCCGTAGCGGCTGCAGCTTCAATTGC
TTTGGCCGGAAACGCCATGGCAATAGAAGTTCTNTTGGGAGGAGGGGNTNGGNCGTTAAGCTTTTTATTC
CCAACGNNGTNTCTATAGCTNAAAGGGAGGAGAAGATTGTNTTNAAGAATCAAA
>gi|2764304|gb|R65326.1|R65326 13830 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169I15T7, mRNA sequence
CAAAAAAAAAAAAAAAAGAGATGGTTCTNCTAGAGAAGCTTTGGGATGATGTTGTGGCTGGACCTNAGCC
TGACCGTGGCCTTGGCCGCCTCCGTAAGATCACCACCCAACCCATTAATATCCGAGATATAGGAGAAGGG
AGCAGCAGTAAGGTGGTGATGCATAGGTCGTTGACCATGCCGGCGGAGTNAGCCCTGGAACTCCAACGNC
TCCAACCACTNCGACGNCGNCACGTAAGGNTANCGTGTNGAGGAGCGTCTTTAAT
>gi|2764303|gb|R65323.1|R65323 13827 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169H8T7, mRNA sequence
ATGGCCCAAATCCATCCGTNTTCAAAGGCAAAANAGGATCCTGAAGCAGAGGTTGAAGGTCCCTCCAGCT
CTTAACCAATTCACCAAGACTCTTGACAAGAATCTTGCTACCAGCCTCTTCAAGGTCCTTNTGAAGTACA
GGCCAGAAGACAAAGCTGCCAAGAAGGAGCGTCTTGTAAAGAAGGCCCAAGCTGAAGCTGAGGGAAAGCC
TTCTAAGTCTAAGAAGCCCATTGTAGTCAAATACGGCCTCAACCATGTNTCCTNCCTCATTGNGCAGAAC
AAGGNCCAACTTGTTGTTATTGCTCATNATGTCGNNCCAATTNAAGTTGGTTNTCTTNGTTTNCCTTGCT
>gi|2764302|gb|R65321.1|R65321 13825 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169H21T7, mRNA sequence
TTTNTTTCCNTCAAACCATAACAATCTCAATCCCTTATTCCCAGGGCAACGAAAGATTCAAGTAAGTNGC
GGTGGTAAGAGTGAGGTGTTGANGAGTGATACAATGGAACCTCATGAAGCAGAAACGTTTGTAAACAAGA
GAACCCTTTATNCTCCCATTGAGCCATATAGCAGTGGAAATTTAAAGGTTTCANATGTTCACACTCTCTA
CTGGGAGCAATCAGGCAAACCCGATGGNCACCCGGTTGTTTTTNTTCACGGCGGGCCGGGAGGAGGGNCG
GCTCCTAGTAATAGGGAGTTNTTNCGTTCCGGAGNTTT
>gi|2764301|gb|R65316.1|R65316 13820 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169H14T7, mRNA sequence
AAACGAGCAAAAGAAGAAGAGAAACAACAAGAAGTAGTAATGGCTTCCTCTATGCTCTCCTCCGCCGCTG
TGGTTACATCCCCGGCTCAGGCCACCATGGTCGCTCCATTCACCGGCTTGAAGTCATCCGCTGCATTCCC
GGTCACCCGCAAGACCAACAAGGACATCACTTCCATCGCAAGCAACGGGGGAAGAGTTAGCTGCATGAAG
GTGTGGCCACCAATTGGAAAGAAGAAGTTTGAGACTCTATCTTACCTCCCTGACCTTAGTGACGTCGNAT
TGGCTAAGGAAGTTGACTACCTTNTTCGCAACAAGTGGNTTCCTTGTNTTGGAATTTCGAGTTAGAGCAC
GGGATTTNTTNTTCCCGTTGAGCNCGGGGAANANTCCCCGGTTNNTTAGGNTNNGNCGGGTTCTGGNNAA
TTTGG
>gi|2764300|gb|R65315.1|R65315 13819 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169H12T7, mRNA sequence
GGTACGACAACGAATGGGGTTACAGTTCCCGTGTGGTCGACTTGATCGTCCACATGTCAAAGGCCTAAGC
TAAGAAGCAGATCTCGAATGATAGGGAGTGGAAAGTCATCTGTNCATCCCCTTTTATGGTCTGAATTTNT
CGTTTTCGAATAAAATTNCTTTGAACTTGGAACTTTTTTTTTTTTNGGTTTTCTTAATTCTCATTCATGT
NAGGTGATGGGAGTTTTTAGACCGATGTTTTACTTGGAAGCCCTTTGTTTTTGGCTTTTNATAT
>gi|2764299|gb|R65313.1|R65313 13817 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169G18T7, mRNA sequence
CCAAGAGATGGCAAGAGTTGTTAAAATCGATTCTNCAGAGTCATGGAATTNNTATGTAAGTCAAGCCAAG
AATCAGAATTGTCCCATTGTGGCTCATTTCACTGCATTATGGTGTATTCCTTCTGTNTTTATNAACTCCT
TCTTCGAAGAGCTTGCNTTTAACTATAAGGATGCTCTGTTTCTAATAGTTGATGTTGATGAAGTTAAGGA
AGTGGCAAGTCAACTAGAGGTAAAGGCGATGCCAACTTTNTTGTNCTTGAAGGATGGTAATNCGATGGCA
AACTCGTGGGCGCAAANNCCTCNATGAGATTANTGAAACGGGGTCCGATTGGTTTTCGTTCAGNCCCTCA
>gi|2764298|gb|R65311.1|R65311 13815 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169G15T7, mRNA sequence
GTTTATGTTTGGNCTGACAGTGAGACTGCAACAAGAGAACCAGCACTTGCTAAAGACTATGANCTGCCGT
TNCGGGTGGGGAGGTTTTTCAGATGGGTCAAATGGGTGGGCATTTGATAAAACAACAACACAATGGCAAA
AAGTGGTAAATATGTCANATGAGAGATCCCTCTTTTCCTTTNCTTTTTCCCGTCGTCTCTGTTATTTTAA
ATNAGTAGTCTCTCAATTTTATAACACGGTGGAAGCTTTTTNTNNGGTCACAANTTT
>gi|2764297|gb|R65309.1|R65309 13813 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169E7T7, mRNA sequence
TTGAAACCAGCTGGTTTCACGGTGGAGAAGACGCCGGCTAGAGGATTACCGTCGCTCACAAGAGCTCGTC
CCTCCTTCAAAATTNTCGCCAGTGGGTCAAGAAGATCAAGACCGACAAGCCCTTCGGAATTAACGGCAGC
ATGGACTTGAGGGACGGCGTCGACGCCTCCGGCAGAAAGGGCAAGGGATACGGTGTTTACAAGTACGTCG
ACAAGTATGGAGCTAACGTCGATGGATACAGTCCTATTTACAACGAGAACGAGTGGTCAGCGAGTGGTGA
CGTGTACAAGGGNGGNGTCAACCGGNATTNGCAATTTTTGGCGGTANCTCNTTNCCGGAATTNTTTTTCC
CGGNGGGTGNNTCTTTTTTNTTGTNCCAACAACAAGNNGCTTTTTGCCTCAG
>gi|2764296|gb|R65307.1|R65307 13811 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169E5T7, mRNA sequence
TCTCGCTGCTTCTCGAATCTCCTGTATCATCTNCTTCTTCTTCAAGTGAAAAATGGCCGATGGTGAGGAT
ATTCAGCCACTTGTCTGTGACAATGGAACTNGAATGGTGAAGGCTGGTTTTNCTGGTNATGATGCCCCGA
GAGCAGTGTTCCCAAGTATTGTTGGTCGTCCTAGGCACACTGGTGTCATGGTTGGTATGGGTCAGAAAGA
TGCTTACGTTGGTGATGAAGCTCAGTCCAAGAGAGGTATCCTCACTCTGAAGTATCCAATCGAACATGGT
ATTGTAAGTAACTGGGNTGACATNGAAAAGATATGGCATCACACTTTCTACAAACGNGCTTTCGANTTGC
CCNTNAGGGAGCANCCAGGTTCTACTNNNAGAGGNTACCTTTTTAACCNTAAAAGCTTACCAGGG
>gi|2764295|gb|R65305.1|R65305 13809 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169E12T7, mRNA sequence
CTCTGAACCGGAGACGGCGTCACGGGACGAATCTAATCGCCGGGAAACCGTTTTTTTTTTCTCTCGGAAA
ATCGATTTGAATCTCCGGCGATCTGATCGGNATGAGTAACATCGATCTGATTGGNATGAGTAACCGCNAT
CTGATCGGNATGAGTAACAGCNAGCTTCTCACCGTCGAGCCTCTCGATCTTCAATTCCCTTTTNAATTGA
AGAAGCAGATCTNTTGCTCTCTCTATTTGACGGACAAGACCGACAATAATNTTGCCTTTAAGGTTAAGAC
GNCGAATCCGNAAAAGTATTGTNTTAGGCCTAATACTGGNGTTGTCCTCCCGAAGGTCTACTTGNCGAAG
TTCTTTTGTCCATGCAAGGCTCAAAAGGAGGCTCTTTNCGANATGCAGNT
>gi|2764294|gb|R65299.1|R65299 13803 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169C4T7, mRNA sequence
CTAAATACCAAGCTTTTNAATTGATCCATGCNAGATGGGCTATGTNAGGAGCAGCTGGTTTCATCATTCC
TGAAGCTTTAAACAAATATGGCGCTAACTGTGGCCCTGAAGCTGTCTGGTTTAAGACTGGTGCTTTNCTT
CTNGATGGAAACACATTGAACTACTTTGGCAAGAACATCCCTATNAACCTTGTNCTCGCCGTAGTTNCTG
AGGTTGTNCTCCTCGGTGGAGCCGNGTACTACAGAATCACCAACGGNTTGGATTTCGAGGACAAGCT
>gi|2764293|gb|R65296.1|R65296 13800 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169C15T7, mRNA sequence
CTCTCTATCTCTATCTTCTTCCATTGATCCTTTCCTCTCTCTGGCTTGTTTCAGAGCTCTTCGATCTTCT
NCTTGATCGANCTACGNGCCACTGTTTATACCATTCACGATCTAATCCGGTTTCAATTATNACTCACGAA
ATCGAAGGAAGATGAGATCGGTTCAAGCACCAGTTGTTTGTCCTGCAATTCGACCAAGACAAGTAGGTGC
ATGTNCTTCACTAGTCAACTACACTGGTCTGAAACCTAGAAGCCAATTTTGGGGTAATCGGACAAAAGGT
GTCAAGTCTCAGGGCACTNCCACAACAATCACTCTTAGATTGTGCACAAGAGTATCAANGTGTGTTTTCA
GCTCTCACTCTGNTGGTAATGGAAGCACTCCTGAAAATTTCAANNGAAATTNNTGGAGGNNTATNTTAAC
CNCTNAGTGTAGGTGGGAGNTCTTTGAAGG
>gi|2764292|gb|R65289.1|R65289 13793 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168N8T7, mRNA sequence
GGAAACCATGTNTGTTTCAGCAATCTTTGGTACCGGAATCGTCACCGTTNCTGCTTCTCCGGTTCTCCGC
CAATTTAAAGTTCCAAAATTGGGTAATGGAGGAGGATTAGGGATGGTGATAGAGTGTTCGTCGAGGCCAC
AGAAGAAATCGACGGCTCATCACAGGAAGACGAGGCCGAAGAAGACTCAGCCTTGGNACATTAAGAGAAA
GCCTACTGTTTACGCTCCTNTTCCTCCTCTTCCGGCGGAATGGAGTCCGTTCACTCTCGCTTCTAACGAC
GGTGGTGCTGCCACTGCTGCGGGNGATTTGGTTTCAAGGCGCTGCCTAGTTGGTATNANNTATCTCCTGA
TTTGGTTGTAATCTAGTTTTNAGAACTTTTTGTTNGTTGGTTANCTGTGGTTTTTAAAGTTTTTCNTANN
TGGTTTTGNTNGTTNGGGNTTNGTTTGGCGTTTAAATTGGGTGAAATAAATGGGCC
>gi|2764291|gb|R65288.1|R65288 13792 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168N4T7, mRNA sequence
CTAGAGTNCAGCAAAATCCTGGAAGCTATCAAGGCCAACTTCAATGACAAGTACGAGGAGTACAGGAAGA
AATGGGGAGGAGGCATAATGGGATCTAAGTNTCAGGCAAAGACCAAGGCAAAGGAAAGANTTATTGCAAA
GNAGGCTGCCCAAAGGATGANTTAAGAGGCTAGCTTCTTTTGTTTGTGGTTTGCTCGGATTCGTAAAACT
TAATAGAGCTTTTTTTTTAGCTGGTTCTTGAAGTACCTCTTTTTNAGTTGAACCCTTTTATNATGGATGT
TTTGCAATTCNTTTGGGACAGTTTCAATGTTATNTCAAGCCTGCCTGGGTC
>gi|2764290|gb|R65286.1|R65286 13790 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168N15T7, mRNA sequence
AAGNTGCGAGATTGTGGACCCGAGAGCGTACAAAAGCCCGAGAAAAGACAAAGATCGGATTCACAGCTAG
AGTCGATGCGAAAATNAGGCATCTAAGGTCGAAACTGAACAAGAAACAGTCAAATCTNTCACATTTTTNA
GCTCAAGACGCAATGTCACCGAGATCATTGTAGCCTTGTATAGGGTTTGTNGTTTTNNTACAGGTCCAAT
TCTNTGATGCATCANACTTTGGAGACAGGTCTTGAAGCTAATTTTNTTGAGAGTTTATAATAGAGTGAGA
TCATGTAAAGAGTAGCCTCTGATGTTTTTCCTACTTGTNGGGTTCGAATNTTCCTTTATCTTTGTACACA
TTATACTTANGGGTTTGGNGTATACCTTAGGNCAGAAT
>gi|2764289|gb|R65285.1|R65285 13789 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168M24T7, mRNA sequence
TGGACCCGTCCTTAAACCCGGACCACGTCCCNNANATGCNACACAAGTTTCCTGACTTGNTCCCTGACCC
AAAGGTGGTCCAGTACGTGCNTAACGACCGTGGCACCCCCATGGTGCTAGACAACAATTACTACCGTAAC
ATCCTAGNCAACAAGGGTTTGCTCCTTGTGGACCATCAGCTCGCACACGACAAACGAACCAGACCAATCG
TTAAGAAGATGGCTAAGGACCAGGCCTACTTTTTCAAGGAGTTCACTAGGGCAATCCAGATCTTATCCGA
GAACAACCCCTTGATTGGNTCTAAGGGTGAGATCAGGANGCAATGTAATCTGGCAAACANGNACCNATTG
NAGTTGGAAAAAGTGAGAAAGGCCAGGGGGTNTTGGTGTTTTTGAGTTCTNTTGCTTTGGTACGGNCCCA
AGNTGGNTTAAAAAATTTCTTTTTAGGTTTAAAAAAG
>gi|2764288|gb|R65284.1|R65284 13788 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168L9T7, mRNA sequence
ACGAAAAAAATGGCAACCATTTCGAATCTNGCTAATCTTCCCCGCGCCACCTGCGTCGACTCCAAATNTN
CTTCCTCTTCCTCCGTCTTACCTAGATCCTTCGTCAATTTCCGCGCTTTGAATGCAAAGCTTTCCTCTTC
TNAGCTTTCTCTTCGTTATAACCAACGATCAATACCTTCCCTCTCTGTNAGGTGTTCAGTGTCTGGTGGA
AATGGAACTGCTGGAAAGAGANCGACTCTTCATNATCTATATGAGAAGGAAGGTCAGAGTCCTTGGTATG
ATAATATTTGCNGTCCACGTCACAGATCTTNTNCCCGNTGATTNNCTCGTGGTGTTAGAGGNGTTACTAG
CAACCCTGCG
>gi|2764287|gb|R65283.1|R65283 13787 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168L4T7, mRNA sequence
ATTACTTCGTCTCTNCCCCTGTAATGGCGCTTCCACACGTAGTCTCTTCACCTTCTTCAACTTCATTATC
TCCTTCCTTCAAATCCAAACCACCGTTTNANTCCCTTAGATCTTNATNACCGACGGTTGATAATCGCCGG
CGTTGTAAACTCAACAGTTCCTTCCGATGTTCATCTTCTTNATTCTCCGAGAAGCATCACAACGCGAAAT
CTCCAAAATCCGATGATATCGTCGAGCTTCCTCTGTTTCCACTCCCACTCGTTCTCTTCCCCGGGAGCAA
TNCTTCCTCTTTAGATCTTCGGAATTNCGTTACCGTATCAATGATGCACACGGGTCTTCCAATNTGATTC
TACGGNTTNNGGGCGTAGGTTTANTCCGNTTCCGTNTTTGGGNTCCGCCGCAGAAGTAAGGGTTT
>gi|2764286|gb|R84201.1|R84201 16160 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168K20T7, mRNA sequence
CAATGGCTTCCCCTATCCCCTCTCCCNCTACTATGGTTNCCTCTCCGGCTCAGGCCACTATGGTCGCNCC
TTTNAACGGACTTAAGTCCTCCCCTGCCTTCCCAGCCACCNGCAAGGCTAACAACGACATTACTTCCATN
ACAAGCAACGGCGGAAGAGTTAACTGCATGCAGGTGTGGCCTCCGATTGGAAAGAAGAAGTTTGAGACTC
TNTCTTACCTTCCTGACCTTACCGATTCCNAATTGGCTAAGGAAGTTGANTACCTTATCNGCAACAAGTG
GATTCCTTGTGTTGAATTCGAGTTGGAGCACGGTTTTNTGTANCGTNNGCACGGTAACTTAACCCGGATA
CTTATGATTGG
>gi|2764285|gb|R65281.1|R65281 13785 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168I8T7, mRNA sequence
ACCACTGGTTACATTGATTACGATAAGCTTGAAGAGAAGGCGTTGGATTTNAGGCCTAAGTTGCTTATCT
NTGGTGGTAGTGCGTATCCTAGGGATTGGAATTACGCTAGATTTAGAGCTATTGCTGATAAGGTTGGAGC
TCTTTTCCTTTNTNACATGGCTCACATCAGTGGTCTCGTTGCTGCTCAGGAAGCTGCAAACCCATTTAAG
TACTGTAACGTTGTGACAACCACAACCCACAAGAGTTTNNGGGGTCCAAGGGCTGGTATNATTTTTTACA
GGAAGGGTCCAAAACCACCANAGAAAGGGTCAACCCNAGNGGTGCAGTCTATNATTTTAAAGGGNCAAAA
ATCAACCTTTTNCTNGNTATTCCCC
>gi|2764284|gb|R65277.1|R65277 13781 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168I15T7, mRNA sequence
GAACCGTCATATTCATTACCAAAAAACGTCGCATTACTCACCCTCCAGGAGTTGGAAAATGGGGAAGTTC
TTCTAAGGCTTGCTCACTTATTCGAGGTTGGGGAGGATAGTNAGTACTCAGTTATGGCAAAAGTAGAGCT
CAAGAAACTATTCCACAACAAAAAGATAAGGGAAGTAAAGGAGNCAAGTCTTTCCGGGAACCAAGAGAAG
GCGGAGATGGAGAAGAGACGGCTAATCTGGAAANTAGAAGGCTCGGCCGGCGGAGGAAGTGANGAGAGGN
GAGGCGGGTGGACGCAGAGAAAGCTAGTGGTTTGNNCTTNTTTNCGCTGGANAATTCGNACCCTTTNTTT
GNTCCAA
>gi|2764283|gb|R65275.1|R65275 13779 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168I10T7, mRNA sequence
CTCTCTCGAAGTTCCGTGCGACTNTNTGCTCGAGCAAGATCTCCTACCGATACAATGATTATNTCANAGG
CTAACCGCAAAGAAATCTGCAAGTACCTCTTCAAAGAAGGAGTTTNCTTTGCNAAGAAGGATTTNAATCT
TGCTAAGCATCCGTTGATCGATGTCCCGAACCTACAAGTNATTAANCTTATGCAGAGTTTCAAATCCAAG
GAGTATGTTAGGGAGACATTTGCCTGGATGCATTACTATTGGTTTTTAACCAATGAAGGGATCGANTTCT
TNAGAACTTATCTTAATCTNCCATCTTGATGTTGTTCCCTGCTACTTTTNAAGAAGTCAGCTAAGCCTGG
NGGGCCGTCCATTTGGTGGCCCACCTGGTGATCGCNAAA
>gi|2764282|gb|R65274.1|R65274 13778 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168H9T7, mRNA sequence
ACCACCAAAGGNGATGNCTTCCACCGCNTATTCCTAAGANGCNTTGTCCACCTAAACCGCCGAAGATAGA
GCACCCACCTCCGGTTCCGGTTTTAAAGCCCCCGCCAAAGATAGAGCACCCACCTCCGGTTCCGGTTTAN
AAGCCCCCGCCAAAGATAGAGCACCCACCTCCNGTTCCGGTACACAAGCCACCGAAGAAGNCATGTCCGC
>gi|2764281|gb|R65267.1|R65267 13771 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168G5T7, mRNA sequence
GTGGAGTCCAGCNTCANATGTGGGCAAGATATGATATGGGTGTGGAGAGGTGTGTAAACTTGGATGGTCT
GACAGAGCCACAGATTCTAAAGGCCCTTGAAAACCTTGTNAAATCCGGAGCTACAAAGGCCTAAGTTTGT
TTGTTTGTTTGTTTTTCTCTATATGANCCCGAATAAGATTAAACCGCAAAACAATCATTTGACATTTCCT
GTCATTCTACTACTTTGTAACTCCGTGGTGTCATATCGCCTTGCATTTNAGTTGGTTTTTTTGTGTAATC
CTTGNACCTTGGAATNAAACCATTCCCGTATAATTTGANTCACAGTAAGGAGAAAANTNAACCNNCTCTG
TTTTAAACCTTNNGA
>gi|2764280|gb|R65266.1|R65266 13770 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168F4T7, mRNA sequence
GAAATGGCTTGCACCGTAGATTTCCGGTGCNTTGACGAAGGATTCGGCGGCAAAACCTACAAACGCAAAC
NCNAATCTAAAGANCAAGTCGCCGCCGAAGCAATCGCCGATGAAGCTTCCATGGACATCGATGGTGCTCC
TCCTGCCGCGAAACGTAGCGCCGTCGCTTCCTCTGAAAATCCAGACAAACCTATTGCTCTAGCTGTCGAG
AGACCAACCTACGACGGTGTAATCGCCGGGAAAGTNTNCGGACGGAACTNGAAACAGCCGGCGAACTCAT
AGNTCTTCAGGGAGGTTTTTTNNNGAACAGNGAAACCCNGATCTT
>gi|2764279|gb|R65263.1|R65263 13767 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168F21T7, mRNA sequence
TCAATACTCAAATCTCAATCATCTCTNTTTCTNATCTNCTTCTCCGATATGAAGCTCGCCGCTAGCCTCA
ACCGCCTCAGCCCCAAACGTCTCTNCCGTACCAAATCAAAAGCTTCCGTCTCCAGATCTGAGCCTTCTTC
CTTCAGCTCCAATGCTTCTNCCTCTTCCTCTGATGGATCTTACGGTAACCTCAAACAAGGTCCAACCGCG
ACTCCGATCAGTGTTCTCCCTCAAAACTCCGGCGATTTTNACACTGAGCTTGTTCAAGCTNTTAANCTGA
TCGNATCGNNATGCCGACGNTGTTGTTTCCAGAGGG
>gi|2764278|gb|R65261.1|R65261 13765 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168F17T7, mRNA sequence
TCTAAAGTTTCAATTTTTTTNTCCTGTNCTTTTNATTTTTTTAAAGAATGGCTTCAATTTCTNCAACTTT
NCCTTCGCCATTGTAACTCACACAGAGAAAATCCAATCTCACATCGATTCAAAAACTCCCATTTNCTCTA
ACTCGAGGTACGAATGANCTTNCTCCATTATCTCTTACTCGAAACCCTAGCAGCATCAGTCTGATGGTGA
AAGCTAGTGGAGAAAGCTCAGATTCATCGACTGANCTCGACGTTGTTAGTACGATTNANAATGTTTGGGA
TAAGTCTTAAAGATAGGTTAGGTCTNATTGGTTTTGGGGTNTTTCCTGGTATTTGGTAGCNCTTTGGGGG
AATCA
>gi|2764277|gb|R65259.1|R65259 13763 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168E4T7, mRNA sequence
ATTGTCCAGCGATGGTACACCCTTTTNCTTAAGTNCGATCGATCTCGGGAACAGCACGACGGTCTCCCTA
ACTNCTTTCAGAAACCGTTCAACAACTGTNCCTGAGTTGGGCTCACTTGGTGCAATATACACTTTCAGTC
TCACATGGGCTGAGATCCAGACCTTGACTCCTGCTATTTNAAACCCCTACAGAGTAACCAGCCTGTTTAG
GAATCCAAAACAGAAAAATGCTGGGAAGCTTTTNTNACTTTCTGATTTCCTAAGCTTGGCAAAAAACTCC
ACCTCTCTCTCCGGTGTTTTNATCAGTGTAGAGNATTGCGGGAATACCTNNANAGAGGAGCAAGGGGTTN
GACGGTTTTTAAAAGNGGTTNTTGG
>gi|2764276|gb|R65257.1|R65257 13761 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168E2T7, mRNA sequence
CCTCACCGAACCCACTTTTCCTTCGACCTAGGATTCAAATTCTAAGTATGACCATGAACAAGTCGCCGTC
TTTAGTGGTGGTTGCGGCTACTACTGCGGCAGAGAAGCAGAAGAAGAGGTATCCTGGAGAATCAAAGGGT
TTTNTGGAGGAGATGAGGTTTGTGGCTATNAGACTTCATACTAAAGATCAAGCTAAGGAAGGTGAGAAAG
AGACTAAATCTATTGAGGAACGTCCTGTTGCTAAATGGGAACCTACTGTTGAAGGTTACTTGAGGTTTCT
TGTGGATAGTAAATTGGTTTATNATACNCCTTGACCTGNTTATTCAAGNCTCCAATTTCCCCAAATTTAT
TNCCGNGTTNAAGGAACACGGGGCNTNGNAAAANCNGNGGAATTTTCCCCCGGTTTTTGNGGGGTT
>gi|2764275|gb|R65253.1|R65253 13757 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168E12T7, mRNA sequence
AAGGTGGAATCGTTAGAGCAGAATAGCTCCGGTACTGATGGTGTTGTTCCGGTGGAGAATCGGACGGTTA
GAATCCCGACGGTGAACGANAATTGCTTTGAAATGGATTTTACCGGAGGNTCTAAAGGCTTTNCTTATGG
AGGTGGTTACAATTNCATCANTCACAGCGTGTCATCATCGTCGATGGAAGTGGGAGTGGTGCCACATGGT
GGTTCGGTGGCTGNTGTATCGTATCCTTANGGNGGTCCTGCAACCANTGGAGCTNATNCGGGGGACACAG
NGGGGTTGTTCCCCTGACTTCAAC
>gi|2764274|gb|R65246.1|R65246 13750 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168C2T7, mRNA sequence
GTCGGATCATGGAAGAAGGTGATTGTTTGGAGTCTATAGTAAGTTTNCTTNTTTCTGGTCTCACAGTGGA
AGCNCAAGAAAATCCAGCGGCTACATTGTNCAGTCTCTCTGCAGTACACGAGTATAAGAAACGGATAGCG
ATTGTGGATCANTGCGTTGAGGCATTAGCGTTGCTGCTTCAAAACGGGACGCCGAGAGGGAAGAAAGATG
CGGTTACTGCGTTGTATAACTTATCGACACATCCAGATAACTNCAGTAGGNTGATTGAAGGAGGAGGTGT
TGTCTAGTCTTTGTTTGGAGCTTTAAAGAANCGAAGGTGTAGCAGAGNACGCAAGCANGGNNCTTTTGGN
CNTTTGT
>gi|2764273|gb|R65242.1|R65242 13746 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168B4T7, mRNA sequence
AAAATNTCTCTCTGCCAATCTNATCTTCAACCTCTCTCTAACTCTNGTTTTCGATTCTACAATGGCTGAC
AAGAAGATTAGGATCGGAATCAACGGATTCGGAAGAATTGGTCGTTTGGTTGCTAGAGTTGTTCTCCAGA
GGGACGATGTTNAGCTCGTCGNTGTCAACGACCCCTTCATCACTACTGAGTACATGACCTACATGTTCAA
GTACGACAGTGTTCACGGTCAATGGAAACACAATGAACTNAAGATCAAGGNTGAGAAGACCCTTNTTNTT
CGGTGAGAAGCCAGTCACTNTTTTCGGCATCAGGANCCCTGNAGGNTATTCCCACTGGGCCGAGGCNTGG
>gi|2764272|gb|R65229.1|R65229 13733 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168A14T7, mRNA sequence
GATGGGTGCACAATGGAACAGCTTCTNTGGTTGTCCAGTTCCCAAGAGAACCTTCAAGCTCCCTAACTCC
ATCTACTATGTCGCCTGATTAAATCTTATTTACTAACAAAACAATAAGATCAGAGTTTCATTCTGATTCT
NGAGTCTTTTTTTNCTCTCTCCCTCTTTTNATTTCTGGTTTATATAACCAATTCAAATGCTTATNATCCA
TGCATGAACCATGATCATCTTNGTNTTGTTTTTTCCNTCTGTATTACCATTTTGGGCCTTTGTGAAATTN
GTTTTGGGCTTTGNTNATATAATCTCCTCTATANACTTTCTCT
>gi|2764271|gb|R65225.1|R65225 13729 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167P14T7, mRNA sequence
GTNTTTAGACACACACAAAAATGGCTAACCCCAACGAGTGGTNTCAGTTCTACAACAATANCCAAACCTT
CTTCACAACTTCTACCACCGCTTCAACCGCTGTTACAACCACCACTGCCGGTGATACCACCTCCATAGAC
TCTNGTNTGAGTCCAGAAACTGGCCGTGTAACCAAGCCAACACGTAGAAGGTCCAGAGTCTCACGTAGAG
CACCANCAACGCTTNTCAACACCGNCACTTCCAACTTNCGTGCCATGGTTCAGCAATACACTGGTGGGTN
CATNCGCTATGGNTTTTTGGGTCCCGG
>gi|2764270|gb|R65223.1|R65223 13727 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167G9T7, mRNA sequence
ATCAAATATGGCTGGGAGAGCTACGATCCCTGCTCGCAACTCTGCCCTCATCGCAATGATCGCCGATGAG
GACACTGTTGTTGGATTTTTNATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATNACCTCA
TCGTGGATTCTNAGACAACTGTNAGACAAATTGAGGATGCTTTCAAGGAATTCTCAGCAAGGGATGATAT
CGCTATCATTCTTTTAAGCCAATATATCGCCAATATGATCCGGTTCTTGGTGGATAGCTACAACAAGCCA
GTTCCTGCAATCTTGGAGATCCCTTNCAAGGACCATCCCTATGATCCTGCTCATNATTCAGGTTCTCTCT
CNGTGTCAAGTACCTCCTTTTCCTGCAGAATCTTGTGTCACAGCGGTTAAACCATAATGCATTTTTCAAG
CTCTCGGGNGGCCTATATCATTTGGTTTGATTTNGNNAATCNTNGGNCTNTNTCCTTTCGGNCNCCGGAA
AA
>gi|2764269|gb|R65218.1|R65218 13722 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167F7T7, mRNA sequence
GCAACCTTCGATTTTGGTTTATNCGCATCCATCGGAGAGAGAAAACAATCAATAAGCGACCATGTTGGTG
TACCAAGATCTTCTNACCGGTGATGAGCTTCTNTNTGACTCTTTCCCTTACAAGGAGATTGANAATGGAA
TCCTCTGGGAAGTAGAAGGAAAGTGGGTTACTGTGGGAGCTGTAGATGTTAACATTGGTGCCAATCCATC
TNCTGAAGAAGGTGGTGAGGATGAAGGTGTTGATGACTCTNCTCAAAAGGTTGTTGACATTGTCGACACC
TTTCAGACTTCAGGAGCANCCANCTTATGNCAANGAAGGGGTTCATCGCTTTANCATTTANGGAAATNCA
TTAAGGCTTT
>gi|2764268|gb|R65210.1|R65210 13714 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167E3T7, mRNA sequence
CTTTTAAATTTCAAACCTTCACATAAAAAAAATACTTTTNAATCCGTGTTTCATTCATCGAATCTTTTTC
CGATAACTATGGCTGAGGAAATCAAGAATGTNCCTGAACAGGAGGTGCCAAAGGTAGCAACAGAGGAATC
ATCGGCAGAGGTTACAGATCGTGGATTGTNCGATTTCTTGGGAAAGAAGAAAGACGAAACAAAACCAGAG
GAGACTCCGATCGCTTCANAGTTTGAGCAGAAGGTTCATATTTNANAGCCGGAGCCAGAGGTTAAACACG
NAAGTNTTCTTGAAAAGCNTCACCGAAGCGACAGTTCTTCTAGCTCCTCAAGTGAGGNTGGAAGGTTCAA
NNTGGTNTGAAGNGG
>gi|2764267|gb|R65207.1|R65207 13711 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167E16T7, mRNA sequence
TCCACAGTGTGGGGAGGTCTTCCCTAAGCTTGAATCATTGGAGCATCATCAAGCAGTTCGTCACGCTGTG
TCGGAGTTGGGGCCAGAGGATTCAGGGAGAAACATAGTGGACATCATCTTCAAATCTAGCTGGTTACGTA
AAGACAGTCCCATCTACAAGATCGAACGGATATTAAAAGTCCACAACACTCAACGAACGATCCAACGGTT
TGAAGATTGTCGCGACGCAGTAAGGTCCCATGCACATGCCTCTACCAGAAAAGAGGCTCGGTCCGNCGTC
GACGNAAACGGAGCTTCTCCGCTTCCACTGCACCACAGTTTTCTTNCTCCCCTCGGCTCAAGGNGGNTTC
NNNCTTNCAATTTNNTTCCGCAATCCCTGNNCTGTCCGNGTTTTNAACCNATTTATCCGG
>gi|2764266|gb|R65205.1|R65205 13709 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167D8T7, mRNA sequence
CACACATTGTTGATGAAACCCAAACAGAGGTGATCACACTTCAAATTAGGAACTCCGCTGATGGAGGAAT
ACTTAAAGATGATCAGAGACAAGTTATGGGTGTNACAGACTCTGGTGAAACTNGCGTGCTTGCGGTTTAT
ACTGGTAGTTNCTGGTCTTTCCTGGACTCGAAATGGTCACTTAAGCAAATAAACGCCTCCACTGCAGATA
ATCCGCTCTTTGAGATTTTGGGCCCTCGAGTGGTGAAAATTTNNTCGGGGAGAAAGCTGGATTATNNACC
AAAACACTTNGCAAACCTTAGAAGTGATCCTAGGAGTTCANTGACNCTTNGTGGNAATTTTTCCAAGGCA
ACATTCCANTATTGGNAAAACTTNT
>gi|2764265|gb|R65200.1|R65200 13704 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165E11T7, mRNA sequence
CATGCTCTCAAACCCGAATTAAATCGACACTTTTAAGTTTTNTTTTTAACAAGTAGAGTTTCCCAAAATA
TTGGATATATTNTTTTTNCAAATTTNGGAAAAGAAATGAGTTGCAATGGATGTAGAGTTCTNCGAAAAGG
TTGCAGTGAAACATGCATCCTTCGTCCTTGCCTTCAATGGNTCGAATCCNNCGAGTCACAAGGNCACGCC
ACCGTCTTCGTCGCTAAATTCTTTGGTCGTGCTGGTCTCATGTNTTTNATCTCCTTCCGTACCTGNCACT
CCAACGTCCTGCTTTGGTTTCAGTCGGT
>gi|2764264|gb|R65195.1|R65195 13699 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163M9T7, mRNA sequence
CTTCATCACAATTTTNCTACGGTCAGAGATTCAAAAGAGTTCTTTCTCTCTATCTTATTCTCCGATCATC
ATGATGCAGCAGCCACCACCCGGAGGTATCCTTCCACATCACGNTCCTCCTCCTTCTGCGCAACAACAGT
ACGGTTACCAACAACCTTACGGGATTNCTGGAGCTGCTCCACCACCACCACAGATGTGGAATCCTCAAGC
GGCGGCGTCGCANTCAGTTCAGCCTACGACCCGCTTGANGNGATCCGGACTCTTTNGATCGGGGACTTAC
AGTATTGGNTGGNTGAGNATTTCCTNTTACGGNTTTGNTTTTGCTCATA
>gi|2764263|gb|R65192.1|R65192 13696 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163M3T7, mRNA sequence
CCAGCCCAGGCACGAAACCTGTTACCAGGTCGCTTTGGCCATCAAAGATGAAGTGGAAGACCTCGAGAAA
GGCGGTATTGGAGTCATTCAGATCGATGAAGCCGCACTTAGAGAAGGATTGCCTCTTAGGAAAGCCGAAC
ACTCTTTNTACTTGGNCTGGGCTGTTCACTCTTTCAGAATCACCAACTGTGGCGTCCATGACAGNACTNA
GNTTNACACTCACATGTGTTACTNAAACTTCANCGNCATNATCCACT
>gi|2764262|gb|R65183.1|R65183 13687 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163K21T7, mRNA sequence
CTATGGCACTGGAATTGANTCCTTCTCAAAACTGGGAGATTCCATATATTTNCAAGAAGATGGTGCAACT
CCAGCTCTTTATGTCACCCAATATATATCAAGCTCACTTGATTGGAAATCTGCTGGTCTTTCAATATCTC
AGAAAGTTAATCCTGTTGTGTCGTGGGATCCGTACATGCGTGTNACATTCACTCTTNCTNCTNCCAAAGT
GGGAGTGGCGAAGGAGTCGACTNTGAATCTAAGAATTCCTGTTTGGACTAACTCTATAGGTGCCAAAGGT
ANTCTTTGAATGGGCGACCCNTAAACGGTACCAACTTCAGGGAAATTTCCTNTCNATCAAANAGAAATTG
GAAAATCTTGGTGGTCCAAAGTATCCATTGGGAGNGNTCCNNTTAGGTATCA
>gi|2764261|gb|R65175.1|R65175 13679 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163H18T7, mRNA sequence
AAGAAAGATCACCATTTTGGGGACTCGATTAGACAGTNTGCAATCCCTTCTTGTNAAGGTTCCTGGCAAG
CAGCATGTTTCGGAGAAAGAGATGAATCGTCGCAAGGATATGGTTGGNAATTTAANATCAAAAACAAATC
AGGTGGCCTCTGCTTTGAATATNTCAAACTTTGCAAACAGAGACAGCTTGTTTNGAACAGATTTAAAGCC
GGATGATGCGNTAAATAGAGTCTCTGGCATGGACAACCAAGNAATTGTNGTATTTNAACGGGCAAGTTAT
GAGNGA
>gi|2764260|gb|R65171.1|R65171 13675 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163H11T7, mRNA sequence
TCTGACTACCTTGGAAAGGGTGTATCTAAGGCTGTTGGCAATGTGAACAACATCATCGGGCCAGCACTTA
TTGGAAAGGACCCAACTCAGCAGACTGCTATTGACAACTTCATGGTCCATGAACTTNACGGAACCCAAAA
CGAGTGGGGGTGGTGCAAGCAAAAGCTTGGAGCCAATGCNATTTTTGCTGTGTCTCTNGCTGTCTGCAAA
GCTGGGGCTGTTGTNAGCGGCATTCCTCTATACAAGCACATTGGCAACCTTGCTGGTAACCCCAAGATTG
TNCTACCAGTTCCTGGCTTTCAACGTCATCAATGNGTGGANCCCNATGCNGGAAACAAGCTTGCTAATGC
AGGNNNTTTAATGATNCTNCCCTGNTTNGGAAGCTTGCTTCTTTTCAAGG
>gi|2764259|gb|R84197.1|R84197 16156 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163G23T7, mRNA sequence
GCTTCCCCTGTTTTTTCTTNCGGCCTCCATNGTTCTTTTNAACTCCTTAGCTGCNATATTAAAGTCTAGA
CACAATGAGAGGAAGGAGCTACACGCCATCACCACCAAGGGGTTATGGAAGGAGGGGCCGGAGCCCTAGC
CCTCGGGGCCGGTTTGGTGGGAGTCGTGACAGTAATCTCCCAACCAGTCTCTTGGTTCGCAACTNACGTN
ATGATTGCAGGTAAGAAGACCTCANGAGGCCATTTAAGNAGTTTGGTNCNTGTCAAGGNCATCTACCTTC
CTAGGGGNTTTACTATACTTGG
>gi|2764258|gb|R65166.1|R65166 13670 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159L5T7, mRNA sequence
AAACTATCTCCTATATACAAGGTTGTAAAAACTGTATATGCATCACCTAGTCGTGTTAATTTTCATCTGG
ACTCAAAGAAGGAAGTGGAAACAACACCTGCCTACCCAGAAATTTNTTTTGCCGTAGATGATTTTGACTC
AACCTTTGATGCTGTGGTTCTGACAGATAAAGATCATTGCTATTGCGTACTACTTAATTCTCACGATGGG
GCAGCCTTTCCAAGTGCAACTGTTAAAGATTCGAGTGATTCTAATACGAATGCTGACCCTAGAACTGTGA
AAGATTCTAAGGTTACTCTGTTTTCTGGGTTTGNNAGCTATCANNTGGTTCGAGAAGCCTATGACAGGGG
NGAGGAATCGGTTTTGGAAGGTCTCCTATCTCTCGGGTCANTATTANCAGGAAAAGCAAGNCAGGNCTTN
ATATCGNGAGGNCCAAGGNGGNCCGTTGNCGAAGTTTAAGTAANCTTGTNNCTTG
>gi|2764257|gb|R65162.1|R65162 13666 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173E16T7, mRNA sequence
CATCAAATCAAAAATCAAACACAGAGAAGAGAAAATGGCCGCAGAAGGAGAAGTTATCGCTTGCCACACC
GTTGAAGATTGGACCGAGAAGCTCAAAGCCGCCAACGAATCCAAGAAACTGATTGTGATAGACTTCACTG
CAACATGGTGCCCACCTTGCCGTTTCATTGCACCCGTCTTTGCTGACTTAGCCAAGAAGCACCTCGACGT
AGNTTTCTTCAAGGTCGATGTTGACGAATTGAACACTGTTGCTGAGGAGTTTAAAGTTCAGGCAATGCCA
ACCGTTTATCTTCATGAAAGAAGGAGAGATCAAGGAGACTGTGGTTGGTGCTGCTAAAGAAGGAATCATT
TGCCAAATCTCGGNGAAGCCCAAGNCCAGTTTGTTGCCTGCTGCTTTGATTTTGCTTTTTNTCCTCTTAN
CCTATTTTTGCTAAAAANATGGTTTGGGGGTTTAAATAAANCCCTTTGTTCGCCCGAGNTTTTCACCTAA
ATNGTCCTCTTATGGTGTTGGGGGGNANAATGTTGTGCAAACTTTGTTCCNGGAGTATNNAATTNTCGGC
NTGGTATTTT
>gi|2764256|gb|R65161.1|R65161 13665 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173E15T7, mRNA sequence
AATATTCATTAAGATGGCATCTTCTATAGTCTCTTCCATGTTTCTNTTTCTCCTTCTTCTTCTTGTATTT
CCACATATAGATAATGTCCTTGGCGCACGAATGGAACTCCGTGAACTTGGAGAGATAAATNATGCTGATC
CACTAGGTTTTACTCGGCCCATTGTCCCCATTCATGTTCCGGGTTTTCCGCCTCGGCGGCCAACTATTCC
GCAGTTACCACCATATCGTCCCAGAAGGTGCCCTTTCTGTNATCCTCCTCCTCCCCCAAAGGCTTTCCCA
AAAAACTCACCAAGTCACTGATGTCACTATAGCTACGGAATTGCGTCAATAAATGTATGCACGGTAATTT
GTTTCATTTTGTGATGTGTGGGGCTCTTTATCTATTATATGCATGTCACGGGGTTTGNAANATTTGCAAA
TGTATCATGGATGTGGNNCTTAACCANTAAAATGCATGNGTTTGNNAATTGCAAAATTTGCGGNGNTNAT
GAATGANGATTGGGGNCCTTTATTATNAATGNATGGGTTTTNT
>gi|2764255|gb|R65155.1|R65155 13659 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173C3T7, mRNA sequence
GCACTGAAAACACTTCAGCCCAAACCACCTCCCATGTNTTATCTCAGCCAGGTACGTACACAACTATGGT
TCAACAACAACAACAACCTCTGGCTCAACAACCTTTCTTACACCAAGGCGTTCAGTATATCCCTCACCCA
TCACAATACATACCAATTTACTCTCATCAGCAACAAAACTACCCTGTTTACGNGATGTCCGTCCCACAAT
CTCAGCAGTATATCCCAGCAGGAACTCCCCCGNTCTACCCGNACTCAAAACCCGGCACAAACTCGAGACC
TGATAGCTGCCCAGAACGGTTTACCGAGCTGCTCCCCCTNATGGTTATTCAGGNTTCAGNAACAGNNTCA
GTACCATGGGTTNNGGTTGNGNTTCNTNAACCATTAG
>gi|2764254|gb|R65153.1|R65153 13657 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173C23T7, mRNA sequence
AAAGGTTTGAGTGAAGATGTCTTCAGATCGGAAGGTTCTAAGTTTTGAAGAAGTTTCAAAGCACAACAAA
ACTAAGGATTGTNGGCTNATNATTTCCGGCAAGGTGTATGATGTGACNCCATTCATGGATGATCATCCTG
GAGGCGATGAAGTCTTGTNGTCCTCAACAGGGAAAGATGCTACAAATNATTTTAAAGACGTTGGTCACAG
CGACACTGCAAGGGACATGATGGACAAATATTTCATTGGTGAGATTGATTCGTCTAGTGTTCCAGCAACT
AGGGCATACGTTGCACCNCAGNAACCAGCCTTCAACCAAGGCAAGGCACCTGNTTCATTTTCAAGATTTT
TCCAGTCCCTTTGTTCCGATCTTTNTCCTTGGGATTGGGTTCTTTTCGGCCCGNNACTTTTTCNTGGANG
GNTTGNAGGAGGCNAAAG
>gi|2764253|gb|R65148.1|R65148 13652 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173C12T7, mRNA sequence
AAAAACTCCACCATCTGANTTCAAATGTCCCGCTTAATCGATGTAGAACGTTGAGAGTCTCTGGACGACT
CCAAAAGTTTCGTTTCTTCAAGAAATTTGTTAGTTTCATGATCTATTTGGTAATGGGAGGTTAATCTGCA
TATGTNCGACCTTTAGTTACATGTTTCATTTGATACAATAAAAGGCGTTGTAATTTGGGTTTGAGATCTC
AATTTCTTTGGGTTTNCTTGTTATGTTGTACTTTTAAGAAGAAGAAAAAAAAACTGTTAAACGG
>gi|2764252|gb|R65147.1|R65147 13651 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173C11T7, mRNA sequence
GATCAAGAGAAGANGAAGAGACGCGAAGATGAGTAATAAGATGCGTAANNAGCAGCAACTCGTACCTAAT
TGTCACAAGACGGACAAGGTTTCGGTTCTCGACAAGACCATAGAGTATATGAAAAACCTTCAACTTCAAC
TTCAGATGATGTCAACAGTGGGGGTGANTCCTTATTTTCTTCCGGCGACATTAGGATTTGGAATGCACAA
CCACATGCTGACGGCAATGGCTTCGGCTCACGGCCTAAATCCGGCGAATCACATGATGCCATCGNCGCTA
ATTCCGGGCGTTAAAAATGGCCATTACCACCGTTTACTAAATATTTCATTCCCNCATTCATCTAGTCAAN
CTCTATTTTCTTACAACATCATCAACCAGCTTTCTTCTCCTCAGNNGTTTTCACGGNTTTGGNTNCNTTA
TTTNCCAAAGGTTTCTTTGGTTTTTNTTNCCNNTGCG
>gi|2764251|gb|R65142.1|R65142 13646 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173B22T7, mRNA sequence
GGAGATGGTCTAGCCATGGACCTGATCGATAAATTCTCAACCACTGTCAGAGGCGTGCTTCCTCTGTTCA
GTACAGATACAGACAGTTTAATAGAGAGGTTCAAGGGAACGACCCTCGAAGCATATGGTTCTTCAGCTAA
GTCGAGGCTTCCGTTGCCTCCAACATCAGGCCAGTGGAATGGCATGGAGCCAAACACACTCTTACGTGTT
TTGTGTTACCGTAACGACGAATCTGCCACGAGGTTTCTCAAGAAGNCATATAATCTACCTAAGAAGCTTT
AGTAAACTTACGGGCTACTACTGCAACGTATAATAACCTCACAAGATGAAGAGTGTGTGTTCCACTTTGC
AGGAGGGNAGCCTCCGAGNATTTTGATTAGTGAGTTTCAANTTTTTTTTGGTTTTAATGGGTTTTTTTTC
TAAAAACAATNCCTATANGGNCTTTTAAAATCCNTTTTTTTC
>gi|2764250|gb|R84196.1|R84196 16155 Lambda-PRL2 Arabidopsis thaliana cDNA clone 173A24T7, mRNA sequence
GGTAAACGGATNTTTTTGGTNCNTCGNACCGTAAGCTTAGACGACATAAAGCTAATCAAGAATACCATGA
AGATGACTGTCAACGATGTAGTACTTGGAGTCAGTCAGGCTGGCCTCTCGCAATATTTGGACAGAAGATA
TGGAGAAAAGAAGAAGAAGGTAGGAGAAGATCAAGATTCTAAAAGGAAAGCCACTGATATNCCTAANCGN
ATAAGGCTACGATCAGCTCTACTTGTTAACTTAAGACCCAACACTGGAATCCAGGNTCTAGCTGATATNA
TGGCTAAAGGTTCTACGTGTNGATNGGGGAAATTTGGTTCGGCTNACAATTGTCTTTTCCCNTTTTCCTA
TTCGGGATTAACGGNGACGGTCCCNTTACAACAT
>gi|2764249|gb|R65132.1|R65132 13636 Lambda-PRL2 Arabidopsis thaliana cDNA clone 172A5T7, mRNA sequence
TCCTCACTCCTCAGCTCCTCAAATCAGAATGANTCAATCCGCGCAAAATTACTTTNCCGTGCAAAAACCT
TCAGAGACTTCATCAGGGCCGTACACAAGTCCGCCACCAATTGGTTATCCGACTAGAGATGCGGTGGTGG
GTGATCCTCCGGCAGCAGCAGTGGAGACAAACTCCAAGGGCGTCAACCTCGAAGGCATAATGAGTTGTAT
CTTCTGCTGCGGCCTATGCTCCAGCTTCTGTGAGTAAATCAGCATGATGAGACAGAAGTCGTTGCCCAAA
CCTGAAAAACAACACGTGGTTAGAAAAATCTTTATATATATATATATATNTATNTATTTTTTTNTTAGGG
NGGCGGTTTNNTNTGGGGTTTTCCCCNGNTTTTAAAAGGTTNTNTTNNTTCCCCNGTTTAAAAAGG
>gi|2764248|gb|R65130.1|R65130 13634 Lambda-PRL2 Arabidopsis thaliana cDNA clone 172A2T7, mRNA sequence
TTTCTTTTGATCCTCTCTAATTTCCTTGTTGATTCATCGACTAGATCTAATTCTNCTCACAAAAGACTGA
GTGTGTTCTTNCTTTCAAATCTTTCAAAAACNAGGGTTTTTACTGTCTTGAAATCATATTTATNCTTCTA
AATTTAGCAAAAAGAACACGATTTACTTTCCATTTCAGTCGTCTTGTCACNCTCTCTCTCTTCTTTAAAG
TCTCCCTTTTTAGCAAAAATNCTCTCTCTCACAAAATTTATTTCCNCTGGCTTCTTCTTCCNCCTCCTCC
ATCTCTNCTCTTTACTCTCTCTTTAATCATCNCTCATTCTTGAATCTTGATCCATCAAAATCAAATCCCG
GTTCTGGNAAGNNCCNTTTAAAAATCAAAACCTAAGGTCTCTCCTCTGGGCTTCTAGGGGTTTTTTTNGT
NCGGTGGTGATGGNGGGGGGAAAGNTTCAG
>gi|2764247|gb|R65127.1|R65127 13631 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171P5T7, mRNA sequence
CAGNAGAGAGAACGTAGCAAAACAGGGCTTACCGGAGCAGAACGGAAAAACCCATTTCGAAGCTGGAGAT
GATCGTNCTAAGGAGTACGTCAGTCTCTTGAAATCGAACGATCCAATTGGATTCAACATTGTTGATGTTC
TTGCTTGGGGTTCTATTGGACACATCGTTGCTTACTACATCTTGGCTACTTCCAGCAATGGATACGACCC
AAGCTTCTTTGGATGATTCGTTTCAATGTCAATCTCTCGTATATGTATATGTATATGTTTGACTTGTGTT
GCAAGCTATCTAATCTGTNCTCTATCTCTGTTTCTCCCTTCTNGTNGTTGGTTGTTGGTTGNCCTAAGGC
TTNGTCCCCCCTTTTTTGCAAAANGTTTTTNTTTCTNCCCTTTTCAAAAGNTTNGGTTTCCAGGGTTTTT
NAAG
>gi|2764246|gb|R65117.1|R65117 13621 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171N2T7, mRNA sequence
TNTCGATCCATTTCCAATTCCACTGTCGACTTCTTAGTCGAGCGTCTTTACAAATGTAACATCCTCTCCT
GATCAACAATTCCACTGTCGACCTCTCCACTTATAATGTAAGGNATTTAAGTCCGTCCAAGTTCGTTTAT
CAAGTGTCAACTCTTTTTNAGGCTCTGTNATCTACGCGTCCCTCTCGCTAGGCTCGGTACCCGGTTTTCC
TTCTTTTTTCCAAGCAGTTCGCTTCCGGTTTCTTTTTTTCCAGTCAATGGTTTTTTTGCGGGGTTTCCTT
TTNATCAAGGGAACTCTAACTTATCTCGAAATCGGNAGGTTGTGTGTTGCTTTGAGAATATATTTANCGG
GGNATACGGGGATTTTAAGGGGTTATCAACNCCCNGTTTTTTGCNGCTTTGGGGGTTTTAAGGGGCCCNN
TTTTTCTTTNAAANCCCCNGGGGGNTT
>gi|2764245|gb|R65115.1|R65115 13619 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171M9T7, mRNA sequence
GAAAAACATGGAGCAAACTTTTATTATGATCAAGCCTGACGGCGTCCAGAGAGGACTCATCGGTGAAGTC
ATCTNCAGATTTGAGAAGAAGGGTTTCACTTTGAAAGGTCTGAAGTTGATCAGTGTAGAGAGATCTTTTG
CTGAGAAGCACTACGNNGACTTATCTTCAAAGTCTTTCTTCAGTGGACTTNTTGACTACANTGTATCCGG
CCCTNTTGTTGCTATGATCTNGGAAGGNAAGAAATNTTGTCTTGACCNGAAGAAAAT
>gi|2764244|gb|R65114.1|R65114 13618 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171M2T7, mRNA sequence
AGACAAGAGTTTTCTCAGGTTTCTATCTCTNTNGTCAAACACAACGGAAGNCATTGAAACTGAGNGAAAT
GGCTCTTAAGNCATTGCAAGCTCTGATCTTTCTTGGTCTATTTGCCGCCTCATGTCTAGCTCAAGCTCCG
GCTCCGGCACCTATCACGTTTNTCCCTCCGGTAGNGTCTCCTTCTCCAGTTGTTACACCAACTGNAG
>gi|2764243|gb|R65111.1|R65111 13615 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171M19T7, mRNA sequence
ATGGAGCTCTTGAACACGAAAAAGTTTCAGTCTTTCAGGTATATAAGAGAGGAAGAGAATGACTTGTTGA
TCAAGAAACTAACCGAATCCGCTCTGAAAAAATCACCGGTGAATCTGAAGAAGACCCTTTTCACGCTAGT
CGCGAGTATCGTGTGTAGGCTCGCGTTCGGGGTGAATATCCACAAGTGCGAGTTCGTAGACGAGGACAAC
GTTGCTGATCTAGTTAACAAGTTTGAGATGCTAGTCGCTGGTGTTGCCTTCACTGATTTCTTCCCTGGAG
TGGGTTGGCTTTTAGNCCCGAATTCTNAAGGTCAGNANCANTGNCACTTATNCAANTGTTTTTNTTTAGG
AACCTTTNANNAATTTTTTTTCCCAAAAACGGGGCCCCGGTNGNCCAAATTTTANCCTNGGGGGCCAAAG
TTTTTNGGGAACCCCGA
>gi|2764242|gb|R65108.1|R65108 13612 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171M16T7, mRNA sequence
AGCAAAAGAAGAAGAGAAACAACAAGAAGTAGTAATGGCTTCCTCTATGCTCTCCTCCGCCGCTGTGGTT
ACATCCCCGGCTCAGGCCACCATGGTCGCTCCATTCACCGGCTTGAAGTCATCCGCTGCATTCCCGGTCA
CCCGCAAGACCAACAAGGNCATCACTTCCATNGCAAGCAACGGGGGAAGAGTTAGCTGCATGAAGGTGTG
GCCACCAATTGGAAAGAAGNAGTTTNAGNCTCTATCTTACCTTCCTGACCTTAGTNANGGCGGAATTGNT
NAAGGGAGTTGACTNACCTTTTTCCGNAAACAAGTGGGGTTTCCTTGTTTTTTGAATTCGNGTTAGGAGC
ACGGGTTTTTTTNTTNCCNTTAGGC
>gi|2764241|gb|R65106.1|R65106 13610 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171M10T7, mRNA sequence
GAAAAACATGGAGCAAACTTTTATTATGATCAAGCCTGACGGCGTCCAGAGAGGACTCATCGGTGAAGTC
ATCTGCAGATTTGAGAAGAAGGGTTTCACTTTGAAAGGTCTGAAGTTGATCAGTGTAGAGAGATCTTTTG
CTGAGAAGCACTACGAAGACTTATCTTCAAAGTCTTTCTTCAGTGGACTTGTTGACTACATTGTATCCGG
CCCTGTTGTTGCTATGATCTGGGAAGGAAAGAATGTTGTCTTGACCGGAAGGAAGGTCCATTGGGGGTTA
CCAACCCAGCAAGNTTCTTGAGGCCTGGGAACTATTCCGTGGGGNNNTTNNTATTTGACAATTGGGAAGG
GAATNTGNTNCCCCGGGTAGGNNNCTNNTTTTNG
>gi|2764240|gb|R65103.1|R65103 13607 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171L5T7, mRNA sequence
CAACGAAGTAAGAAAAATGGTGAAGGTGATGTGGGTTTCCNTTTTAGCTCTGGCGGCGGCGATTCTCCTT
TTNACGGTCCCGGTGGCAGAAGGGGTGACGTGCTCGCCTATGCAGCTGGCTTCATGTGCGGCGGCGATGA
CGTCATCTTCGCCGCCATCGGAGGCGTGTTGCACAAAGCTGAGAGAGCAGCAGCCATGCCTTTTTGGGTA
CATGAGGAACCCTACCCTCCGCCAATACGTTAGCTCCCCTAACGCAAGGAAAGTNTCCAACAGTTGCAAG
ATTCCTTCCCCAAGCTGTTAAGGAAATGTTAATCATGNTTAATTAGTGACAAGNTTTCCGCTGATTATAA
GTGGTTAATGCTGGGCCTTATNTTTGGNCAGTACTNNTTTAAAATAATTAAATGNGTTNNTGATGNTTGG
TGGTTNTCANCCACNANGCTTT
>gi|2764239|gb|R65101.1|R65101 13605 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171L15T7, mRNA sequence
CTCTTCTCCCTCCGCCTCAATCGCACGAAGACGATAATCGAATATGGCGGAACTAAAGCTATCAGAGAGT
CGGGACTTAACCAGAGTCGAGCGAATCGGCGCACACTCACACATCAGAGGACTAGGTCTCGACTCTGCCC
TCGAGCCGCGAGCTGTTTCCGAAGTATGGTCGGTCAAGTGAAGGCGCGTAAAGCCGCCGGTGTAATCCTT
CAGATGATTAGAGAAGGGAAAATCGCGGGTCGGGCTATTCTAATAGCGGGTCAACCCGGAACGGTATAGA
CAGCGATTNCAATGGGTATGGCGAAATCTCTTGGCTTGGAAACTCCTTTTTNCGATGNTTTNCAAGGAAG
TGGAAATTTTCTCAATTAGNGGTGTCAAAAGNCCAGNANGNTTTGNCTNAAGCTTTTNGTAAAAGCGATT
TGGTGNTNAGGNTCAAAGGAAGGGGCCAGTGGTTNTTTAAAGGNGAANTTTTTTNGGTTCAAATTTT
>gi|2764238|gb|R65099.1|R65099 13603 Lambda-PRL2 Arabidopsis thaliana cDNA clone 171L11T7, mRNA sequence
TCGGAAGGATGATAACGTCGTCCCTAACCTCATCTCTGCAAGCNCTCAAGCTTTCGTNTCCGTTCGCCCA
TGGCTCCACTCCTCTNTCATCTCTCTCTAAGCCCAATTCCTTCCCGAACCACAGAATGCCCGCTTTAGTT
CCGGTCATCAGAGCCATGAAAACGATGCAGGGGCGCGTGGTGTGCGCAACCAGTGACAAGACTGTGGCGG
TGGAGGTGGTGAGGCTGGCTCCCCACCCCAAGTACAAGAGGCGCGTTAGGATGAAGNAGNAGTACCAAGG
TNAAGNCCCCGATAATNAGTTCAAGGTTNGNGGACNTTGGNNAAAA
>gi|2764237|gb|R65091.1|R65091 13595 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170N7T7, mRNA sequence
GATAAGTGTTACAAGATCTTGGGGTATTTTAATTGTACGCGTAGACTCAGCGACTCTCTCCAGGAAGGTT
ACTACCAAGCTGCGATCTACGAGTGTGCATCGCAGGCGTTCAAATTTATTGATACCCCTAACCCTTTCAA
CCTGTGGCCCAACAAGGNTCCTTTGTCCGTGAACGGGAATCTTTATTGGCTTGCTCATAACCACCCTGAG
ACTCTTGAGTATTTCATCGAAACCTTTGATTTCTCCATGGAGATTTTCAAACCCTTTTGTCTACTGCCGT
GTCGGAAGGACTTTGGTAGCAATGAACTTGTCCTGGNGGTTTTTAAGGAAGATCGGTTTNCAATTNTTAA
AGCANTGNTTTGGAANAACGGNGGTTTTGAGATTTTGGGTAACAAAGGTTGAANGTTTCTNGNNAGGGGG
AANTTGGNTTTGGNAAAANGTTTTTTACATTTNCGNAACCCAA
>gi|2764236|gb|R65082.1|R65082 13586 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170J8T7, mRNA sequence
GATTATGCTGGCAGTGATCTGTATGACTACAAGGGTTTTGGTGTTGAAGATTCANATGCTGAGTCTCCTA
GAGATATCCATTGTNCAGTCGAGAGTACAGACTTTNCCGCTAGAGTGAAAAAACATATTGAAGAACCTAT
TAAAGATATAGAAGTTTCTAGCGTTTCACCTACTGAAAACTGTTATCAATCAGGGAGAGAGGCTATACCC
TCAGTTACTCCCAGTACTCCTCTCACGGCCCTTAGATACACAACATCAGCTGNGAAACCTGCAAGTAAAA
CTACTGGCTCATCAACAGTAAATTCGAAGCGTTCTTCGGNCNTGGGGNAGNNGGAACGGCAAGAAAACAC
CTGCTAAAGGTTCCATTTGATTNCCTCAGGNAATTNNCGGNGCTTNTTNT
>gi|2764235|gb|R65078.1|R65078 13582 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170J22T7, mRNA sequence
TCCGTNTCATTTCGAGTGGCAAAACTTGTTAGCGGAGGCTGCTAAACAAGGATATACAGACGAAGAAGAG
CTTCANTGGGATTNTTACAACATCTTGGNTCAACAGANTCAACTGGAATGGCTGGAAAGTTTTGAGCAGA
GGAAAGCCATTAAAGGAGCTAAAAGTAACAGAAGAGCGCCAAAATCTCCTGANCAAAGAAGGAGAATTGC
AGAAGCAATAGCTGCTAAATGGGCTGNTCCATCTTACCGTGAAAGANTTTNCTCCGGCTTGGCAAAATAT
CACGGTATACCTTTTGGTNTCGAGAAGGCGTCGTAGNAAGNCCAAGGGAGCGGTTNCAGAACCCTTGAAA
GAAGGCCTCCTCCAANGAAAAGTTCCANGGGGTTTCAGGG
>gi|2764234|gb|R65068.1|R65068 13572 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170I4T7, mRNA sequence
TNTTGCTACTAAACCTAAAGACTCTCGCGGAAGCAGCAGCGATGAGATGATGATGAATGANCTGGATGAG
ATAATATTTGGTGAGAATAGTTTGGGTCATTCTTCATCTGCCTCTGGAAATNATCAGAAGAAGCAGAAAT
CGTCTAAAAACAATGAGCTCATTCACTTGTNAGATGTGTTTTGTTTTNNTTAGTGGATTTGGATTGGTGT
TTAGTCTTTGGGAATATGCATCAACAGTTGTTATGTAAGTAAACTAAAATTAGCAGCCTTGTGGGATTGA
AATATATTTNGGGTGTAACCTGTATATTTCNCTGCTC
>gi|2764233|gb|R65067.1|R65067 13571 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170I2T7, mRNA sequence
GTCTAATGGGTCATGCTAAACGTCTGCTTCACGAGTTAAAGCTCCCGGATAATATTCCTCGGGAAACCGC
TATCACCATTCTGGCTAAAGCTGGGAGAACGGAAGAGGCGACATGGGTTTTNCGTCAAGCCTTTGAATCC
GGGGAGGTAAAAGACATATCAGTATTTGGCTGTATGATCAATCTTTACTCAAGAAACCAAAGATACGTAA
ATNTCATCGAAGTGTTTGAGAAAATNAGAACCGCTGGTTACTTTCCGGATTCGAATGTNATAGCTATGGT
GTTGAACGCGTACGGGAAACAAAGAGAGTTTGAAAAAGCAGACACGGTTTACAGAGAAATGCAAGAGGAA
GGATGTGTTTTCCCTGATGAAGTTCATTTCCAAATGCCTGAGGTTTATACCTCATCCNAGGAAAGATTTT
TAAGATNGTTGAGTCCGTTGTTTTCAGAGGTTAGGATCCTNANCCNAATGNCAATAGCAAGGGGTTCCAT
TTGGGTTNTGGCGGCTTTNTNTTGAGNGNCNGGTAACTNACCGNTCCTCAAGGGCNNTNATCGGGTNAGG
GCCCGGGGGTNTTAA
>gi|2764232|gb|R65061.1|R65061 13565 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170H7T7, mRNA sequence
TGAGAAATCGCATAAACATTCGATTAAAGCAACTNATAATCATCACAAGCTAATATTTNTCCCTTCCAAG
AAAGTNTCAGATGAGTCTNACTCACTAGAGAAGAGTGGTTTGACAGATGANCTTGAGGAACCTCAAAAAC
ACCTTGGATATTTNTTTGATGGAAGTCAGAATAGTAAGANGAGGATTAGAGATGATTCTCCTCCGGCTGT
TGAAAGTNTCATCAAAGCTGCACCTGTAGCAGGTAAACCTCTACGGGNTTAGAATGGTCTTCAAAAAACC
AAAGGAGGAAGTTCCTACTCTNCCTAGAGNGGCTGTTTGTTTGCCCCACTACAGTTGCAAAGTCGNTCAG
TTACCCAGGTTGTCATANCAGGTNCTTTCTNAAGGT
>gi|2764231|gb|R65056.1|R65056 13560 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170H21T7, mRNA sequence
CTTACCCCTCTTGGTGACGCTTGTNCACGACTTGATCTCACAGCAATACATGAAATTNTCGAAAAGGTTG
GATACAAAGATGACGAGGGTGTAGCAAATGAGCTCTCGTTCCAAGTGTGGACCGACCATATTCAGGAGAC
TCTAAACTCCAAGAAACAAGGAGATGCTGCGTTCAAAGGCAAAGACTTTGTCACTGCTGTTGAATGTTAC
ACGCAGTTCATCGAAGATGGCACAATGGTATCGCCAACAGTTTTTGCAAGGAGGTGTTTGTGTTATCTGA
TGAGCAATATNCCTCAAGAGGCTCTTGGTGATGCAATGCAGGCGCAAGTAGTGTNTCCTGAATGGNCCAA
CGGNTTTTTTTTCTTAAGGCNGTTGTTCTNTTCAGCCTTGGAATGGTAAAANNGCCTTTNAACCCTAAAA
NTGGACTTCCTTGNAGCNAGGACCTTNCNNCAGGANCT
>gi|2764230|gb|R65054.1|R65054 13558 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170H19T7, mRNA sequence
CGGTTACATGAGAGCGTCTGTTGATACAGAGGTGTTCTTGAGAGGGAAGAAGCAGATTGAAACATTCAAT
GATCTTACCAATGACTGTAGAGATGGAATCGGCACTTGCAGCGTANAGCAAGCTGATCGCNCTGGTAAGT
ATTTCAAAAGCTTGTTATCAGAGNCAGTTGTTTGTTTGTAGGTTGATAGAAAACTTGAACCGTCTTGTTC
CACTTGTTTCCACTTTGGTACCTATAGAATAGCTGTTTGTATGTTC
>gi|2764229|gb|R65052.1|R65052 13556 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170H16T7, mRNA sequence
TGAANCTCAAAAACTCATTCANTGAGAAAAATGGAGACCCTTCTTTCCCCTCGTNCGCTCTCTCCTCCTC
TCAATCCCAAACCTTTGTCCCTTCACCAGACCAAACCCACTTCACATTCATTGTNTCTNTCAAAACCCAC
CACCTTCTCCGGTCCTAAACACCTCTCCACCCGGTTCACTAAACCGGAATCAAGAAACTGGTTAATAGAT
GCAAAGCAAGGACTAGCTGCTTTAGCTTTATCTCTAACTCTNACTTTCTCACCTGTNGGCACNTGCTTTA
GCNTCTGAGTTCAATATCCTCAACGGTGGTCCACCTAAAGGANATTTTCGTNGTNGNTGNCGGTGGTGTT
CTTAGGTCGGGT
>gi|2764228|gb|R65051.1|R65051 13555 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170H15T7, mRNA sequence
CGAGTTGGAGCACGGATTTNTGTACCGTGAGCACGGTAACTNACCCGGATACTATNATGGACGGTACTGG
ACAATGTGGAAGCTTCCNTTGTNCGGTTGCACCGACTCCNCTCAAGTNTTGAAGGAAGTGGAAGAGTGCA
AGAAGGAGTACCCCAATGCNTTCATTAGGATCATCGGATTCGACAACACCCGTCAAGTCCAGTGCATCAN
TTTCATTGCCTACAAGCCACCAAGCTTCACCGGTTAATTTCCCTTTNCTTTTGT
>gi|2764227|gb|R65046.1|R65046 13550 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170G24T7, mRNA sequence
ATAGCGATAGGCTGNACATGGTTTCTCATTGATTTTTGTTTGACAATCCTTTCTTTNCTTTTTTTTTGTN
CTTTCGAAAAACGAAAATTTTCGTTGGTTCCCTCCGATTTGGCCTGCTGGTGAAGATATGGCCGGAGCTA
AAGATTCGGGTTGCGATGATGATCTCCGAATTGCTGGTGGATGTNACCCTGGAAAACGCGGGAACCCGGA
GGATTCCTCGTCTCCTGTCGAAGTCTCGTGCTCGATTTGCCTCGAATCGGTGCTCGATGATGGTACCAGA
TCCAAGGCTAAGCTCCAATGTGGTCANCAGTTCCATTTGGATTGCATTGGATCAGCATTTAANATGAAAG
GNGCCATGNAATCCCTAACTGTNGGAATNTCGAAAAGGGTNAGTGGTTTNTTNAAAGGGTNTTATTGGCC
CTTTCCAGAGTTTCCATGGGAGGTTGNTCCCNTAANANGCTTTNCGGTTAAGGTT
>gi|2764226|gb|R65045.1|R65045 13549 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170G23T7, mRNA sequence
TGTGCTTAAGGCTGATGCTAAAGCCAGAGGAGAGACTATCAGCACCAAGAGACAGCCTAAAGGTCCTAAA
CCGGGTTTCATGGTCGAAGGTATGACATTGGAGACTGTCACTCCCATTCCTTACGATGTTGTCAACGATC
TCAAGGGTGGTTATTGAGTTGTTTCCATTTTTTNATCATTCTCTACTCAGAATTTTTGCACTTNCTTTTT
TAATGATGTTTTTGTATCAAACAAGAGTGAATTCTATATGGTATGAGTTCATATTTTGTNAGGAAAGATG
GTTTATCCCNATC
>gi|2764225|gb|R65044.1|R65044 13548 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170G22T7, mRNA sequence
AAGGTGTTCCTAGCACAGCAATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCATAGCAACATTGTCAA
ATTGCAGGATGTGGTGCACAGCGAGAAACGTTTGTATCTGGTTTTTNAGTATCTTGACTTGGATCTCAAA
AAGCACATGGATTCTACTCCTGATTTCTCCAAGGNTCTACATATGANCAAAACATATCTTTACCAGATTC
TCCGTGGAATTGCGTATTGCCACTCTCATAGGGTTCTCCATCGTNATCTGAAGNCACAGAATTTTTTTGN
TTGATCCGCGGGACAAACTCACTGGAGNTTTNCTGATTTTGGGCCTTGGCNCAGGAATTTNGGANTCCCT
TTCAAGGGCCNTTTCCCNNTGGGGGTTTTAAACTCTTNGG
>gi|2764224|gb|R65034.1|R65034 13538 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170E23T7, mRNA sequence
GCAAACCCTAAAAAGAGAGAGAAACATAAAAATCTCCATTGAAACAGATTGGATTGAGCAAGAGAAAGAG
ATCATGTATTTNTAAAAAGAGAGAGAAATCCTCTNATCTCCTCTCTNATTCGNTCGANATCGCATCATTT
CCCTAATGATTTCAAAAACCTAAAACGATCTCTNCTTTTTTTNCGCTTCGNTCTCCATTGAAAAGGATGA
TTTCAAATCCAACTTTATTATCGTACACTTGCATTGCGAAAGGAACCGTAGTTCTCGCGGAGTTCGTTTC
AAGGCAAGAGCCAGGAATCGAAGCTATAGCTTTACGNTGCATCGNGGACCACGGCTCCTCATCATTCAAT
GNTTTCTCATACAGTTCACAAGGNGGCGGTTTNCATTCGGAATCGCGGTNGATTCCTTTGGTTAANTCCC
GGNTTCCTGTGGATNCCT
>gi|2764223|gb|R65028.1|R65028 13532 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170D8T7, mRNA sequence
AANTCGGTGAAAATNAACGTGTCGTGGCTAAAGACAGCGGTAACGGAACTGGCGGAGGCGGTGGAGTATT
TCGGGCAGTACGACACGNCGAAGGTGGAGAAAGAGGTGTGCNAGAAANATCTGACGGCGAAAAAGGGGGA
GATGGAGGAGATGACGGCGGACTGGTGAAGAGGGAGAAGGAAATCAAAGANTGCAGAGAGAAGGTNACGG
TGGTCGCAGGGAGGCTAGGGCAGCTGGAGATGAAAGGTTCGAAATTNAACAAGAATCTCGACCTCTTCCA
GTCCAAAGTCCACAAATTCCAAGGNGAAGCCGTCCTTCTCCACCTTTAGCTCCGTCTCCAATTTNTTCCG
TTTTGGTNCTCATTTATTTCANTTATTTTCCTTATTTGACCATGNAATGTTTATNAATTTAAANGGTTTT
GGGGCCATTAGTGTAATTTTTTTAAAANGTT
>gi|2764222|gb|R65015.1|R65015 13519 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170C12T7, mRNA sequence
TGATCATAATGGACGATAACTTCAAAACAATAGTAAATGTGGCTAGATGGGGACGTGCTGTATATATAAN
CATTCAGAAGTTTGTCCAGTTCCAGCTAACTGTNAATGTGGTTNCCCTGATCATCAACTTTNTNTCTNCT
TGCATCACAGGNTCTGCTCCACTCACTGCTGTGCAACNCCTTTGGGTCAACATGATCATGGACACACTTG
GTGCATTGGCTCTAGCAACAGAACCTCCCAATGANGGTTTAATGAAACGTGCACCAATAGCTAGAACCGC
CAGCTTTATCACCAAAACCATGTGGNGGAACATCGCTGGTCAAAGCGTTTTNCCAGTTTGNTTGTTTTAG
GGATTNTNCAATTTCGNAGGGAAATCA
>gi|2764221|gb|R65013.1|R65013 13517 Lambda-PRL2 Arabidopsis thaliana cDNA clone 170B22T7, mRNA sequence
TTCATCGATTTCNCTCTTCCAAATCTCCCAAAANATGTCGAACCCTAGAGTTTTCTTCGACATGAGTCTC
AGCGGTACTCCCATCGGACGGNTCGANATGGAGCTTTTNGCTGATACAACCCCAAACACGGCGGAGAATT
TCCGTGGCTCTCTGTACCGGGGGANAAAGGAATGGGAAAGCTAGGTAAGCCACTTCACTTCAAAGNTTCG
ATCTTCCACCGTGTNATTTCCNGGATTCAATGTGTCAAGGAGGTGATTTCACCGCCAAGAAACGGAACCC
GGTGGTGAATCGATCTNCGGGTGCTAAGNTNAAGGNCGGGGACTTTTT
>gi|2764220|gb|R65007.1|R65007 13511 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169N6T7, mRNA sequence
TGGGGCTTNTNCACAAGCAAAACATTTCCTTTGTNATACNCCTCCTCCTCGGTCTCCTTGCCGTCTCTNA
TGCTTGTAATTGTNGTGACCCTCCTAAACCATCACCACACCCTGTTAAACCGCCAAAACATCCCGCTAAA
CCACCTAAGCCCCCTACCGTTAAACCACCTACTCACANCCCAAAGCCTCCCACTGTGAAGGCTCCACCTT
CCATACATTCCATGCCCTNCTCCGGCCTATACTTCAAAACCTTCAACCGTGNAAGCCANCAACAACTTCN
TTACG
>gi|2764219|gb|R65006.1|R65006 13510 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169N5T7, mRNA sequence
TGCTCCAGGAGTAGCTGCTGCTGGACCTGAGACAGCCGGATTTCTAGCTCCAAATCCTTCTTCAGGGAAC
GATGGATCTNCTTTGATTCCGACCTCGTTCACAACTGTACTCAGTGCCGTACTGTTCGTTTTGTNCTTCT
CTAGTGCGTAAAAAAAAAACTGAATCTTTTTTCACCAGCTAGATTTGGCTGTATGAAATTGATTAATGGG
TTTNATTAGGGNTAATCTATGTATGTTTTGGAGTGTNCTGTTTTGAGGCCATATCGGGTTCCCTATTACT
AGGGGTTACCCTTTTAGGTTATGGTNATAACCTTGNNTCAANACAATTGGGCCTTTAATTCGNNNTAACG
GNTTATTCCCTC
>gi|2764218|gb|R65005.1|R65005 13509 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169N3T7, mRNA sequence
AGAAAACAAAACTCGCTTCCTGATAATCAAATCAAAAGCTTCTCTATCAAGCTTATCGAAAAGTCACATC
TTTTGGAAGAAACAATGGCTCGTACCAAGCAAACCGCTAGGAAATCCACCGGAGGTAAAGCTCCCAGGAA
GCAGCTTGCCACCAAGGCGGCGAGGAAATCAGCACCAACCACCGGAGGAGTCAAGAAGCCTCACCGTTAC
CGTCCAGGAACCGTCGCTCTTCGTGAGATTCGTAAGTACCAGAAGAGTACTGAATTGTTGATCCGCAAGN
TTCCCTTTCCAGCGGCTTCGTTCGGGGAATAGCTCAGGACTTNAAGACGGGTCTNAGGGTTTCANAGGTC
ACGGGGGTGTTAGGCTCTTNNAAGAAGGCGGGTTAGGGGATANCCTAGTTNGGCTTTTTGGNGGGTANTT
AATCTTTTTGNGGTTTTTANGCCAANNGGGTTACGGTNANTCCCTAAGGGCANTNNATTTGGTTTAAAGA
TT
>gi|2764217|gb|R65004.1|R65004 13508 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169N2T7, mRNA sequence
TCAAAGGAAGCGAAGCCTAGCGTCCTCTCTCTGTNTTCTCGTTTCTNCGCCGATTCGTAGTCTGTTGTGC
GCTTGCCTCTCCTCTTTTGGATTAGCATACCTCTCACTCGCATCANATGCACTTTTGGTTATCCTCATAC
CAAAATGCAGATTTTNAGTTGCTTTTNCTATCCAAATGGACTGCAAGAAGTTCATCCAGATGGTCGAGGA
GANGAAACGAAGAGTTCTTGAGNANGCAAGAAGCTCCTTTGAAATGGGGAGCAGAAGCTAGAGGNGGCNN
CG
>gi|2764216|gb|R65001.1|R65001 13505 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169N17T7, mRNA sequence
GACCAAAACGATGGAGAGCACGAAGATTGCTCCTTCATTCGATCGTGCCAGTAAGCTTAAAGCTTTCGAT
GAGACGAAGACTGGTGTGAAAGGACTCGTTGACTCTGGAATCTCAAAGATTCCACGCATTTNCCATCACT
CATCTGTCGAACTAGCAAACCCTAAACCACTTCCCTCGGACCTGCTACATCTCAAGACGATCCCAACGAT
CGATCTCGGAGGACGGGACTTCCAGGACGCGATTAAGCACAAGAACGCGATTNAAGGGATTAAAGAAGCA
GCTNCCAAGTGGGGTTTCTTCCAAGTNATCAANCCATGGNAGTTTTNGNTCGANCTTTTTGAGGAAGATG
NAAGNNTTGGAGTTNCCGGNNCTTTTAATTG
>gi|2764215|gb|R64998.1|R64998 13502 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169N12T7, mRNA sequence
CCTCCGTTATGTTCCACTTGAGTCACTCGACCNGTCACTAGCTCTCGGATTCTATTGCCAGCACAAAGAT
GATTTTAATGATTTCTGTATCCGAGCAACAAAGCTAGCCGGAGACTCTAATGGTGCTCCTCTCTTCACTG
TGACTCAATCTCACAGAAGAAATGACTGCGGGATTGCAGAAACCAGCAGCAGTACAGAGGCATCTNCAGA
GGATCTCTGGTGAGGGACCATGNAGNTGNCTTGGCAATTACTTTGNACCACTTTTTCCTTAGGCCATTCT
TTTTCAAATTGTGGTGANCTTTGTCCAATTTTTCAAAAATACCCTTNTTTTTTTANANNNGTNCCTAAGG
TTTGANGGTGGG
>gi|2764214|gb|R64997.1|R64997 13501 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169M9T7, mRNA sequence
GAAACAACAAGAAGTAGTAATGGCTTCCTCTATGCTCTCCTCCGCCGCTGTGGTTACATCCCCGGCTCAG
GCCACCATGGTCGNTCCATTCACCGGCTTGAAGTCATCCGCTGCATTCCCGGTCAACCGCAAGACCAACA
AGGACATCACTTTCATCGNAAGCAACGGGGGGAGAGTTAGCTGCATGAAGGTGTGGCCACCAATTNGNAA
GAAGNAGTTTAGNNNTCTATCTTACCTCCTGACCTTAGTACGGNGGATTTGGTTAGGAAGTTGCTNACCT
TTTCGGAACAAGTGGNTTCNTT
>gi|2764213|gb|R64993.1|R64993 13497 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169M13T7, mRNA sequence
AGTTTNCTGTGTTGAATTTTGGGGAATCGAAGAAATTGAATTTCAAAAATCAATGGCGGAAGAAATTGAA
AAATCTGTGCCGACAGAGGAATCTCTGATGGAGAAGATCTCCGAGANGATTCACCATCACGATTCGTCGT
CATCGTCTGAATCCGAGTACGGGNAAACCTGATTCTCCTTCGGGNTGTGAAAGGGGAGATCTATTCGAAT
GTTTTNGCAGAGAGNAAGCCTTTTCACAAGGGTCTCGGTGGTGGGAAAGCCTCCTNNATGTNGTCCTTTT
GGNAGGGGTAAAAAAACTNTCAAGNTGCTGTTCTTT
>gi|2764212|gb|R64978.1|R64978 13482 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169J17T7, mRNA sequence
GGAATCTTGCAATTTCATCAAGCCAAATAGTCAATGGCGCAAAGTTCAGGACCGCTTAGAAGTGGATGAA
AGATGTTCGCGTCTCGAGAAAATTGATCAGCTAGAAATCTTTCAGGAGTATCTGCGTGATCTGGAAAGAG
AAGAAGAGGAGAAAAAGAAGATACAGAAGGAGGAACTCAAAAAAGTAGAGCGAAANNCCGTGATGAGTTC
CATGGGCTGTTAGATGAACATATTNCAACAGGAGAGCTTACTGCCAAAACTATATGGCGTGATTATTTAA
TGAAGGTCAAGGGTTTACCAGTATATTCAGCAATTGCGTCAAACTCCTCTGGNGCTACTCCAAAAGGCCT
TATTTGAAGGTTNCTGTTNAGGNTTTTGAAAAAAAGGGGCCNCGGGCTNAAGTCTNAAGGTAAAGGNTTN
TNTTTGAAATTGGGGAAAGNAAATTTTTCCCNTTGGGCACCATTTATTGGGTCCAAGGGTNTTTTTCCCG
GGGTTTTTGGTTCCCCCTTTTTCCCTGNGGTAGGCTAAGTNGGCTTTTGNTGNTTCTTTNAGGCCANGGG
GGGGGGAAAGGCCNTAACNCCCGGGGCTTAATTTTGTTTTTTGC
>gi|2764211|gb|R64974.1|R64974 13478 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169I24T7, mRNA sequence
ATTCAAGGTCTAAGGTTTTGGAGGAACTGCAAACCTTGCTTCCTGCTTCTNTNATAATCCCAGAAAAGAG
GTTGGAGTGTTTAGTTGAGAATTCACTTCATATTCAGCGGGATTCTTGTGTTTNCCATAATACTTTGGAT
AGTNATTTGTCTTTGTATTCTNATCATCAATGCGGGAAGCACCAAATTCCTTCTCAGACTGCTCAGATCT
TGGAGTCACATACCGATGAAGTTTGGTTCTTGCAATTTTNACATAATGGCAAATATTTGGCTTCATCTTC
CAAGGATCAAACCGCAATTATATGGGAGATCAGCGCAGATGGGCACATTTCATTGAAGCATACACTTTGT
TGGNCACCACAAAACCCGTGGTTTGCNATCTTATGGGGTCCNGATGATCCGCAAGTTCTTNCATGTGGGG
CAGAAGGGGGTTTNAGCCGCTGGGNTTTTGTTNAGGGGCCTTTTTCNAATGNTNNAAAAGGGGGNTTNAG
CCCNTTTTTT
>gi|2764210|gb|R64967.1|R64967 13471 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169F10T7, mRNA sequence
AAACAACAATGCAACTNTCACTGGTTCAAGTCTCTTCAGTGTCCAACTTCAGATCCCAATCAAACCCATC
TTGTTTACTTCTTCAAAAGTCCATCTTTCCCGGGTCCAAGTTAACCCTCCATCGAATTTTTCGTTATCCG
AAGAAAATCTCAAATGGCTCTACTCGTGCTTCACTGCTTGAGACCCCTATCTTATGGGCTGGTCGGATTT
GTGTCTTCTACGCTCTCGTGAAAGCTGGCTTTGCTGGATCCAAGTCTAACCCTATCGTTTCTGGTTTGGA
AACTGGTGGTGTTGATGTTGAATATGATGATCATTTTAGAGATGCAAACAATCTCACAAGGGTTGTCAAA
TCCGGCGGGGAGAGTGCGGAACGGGCAAAAGCGTATGTTGCAACAANTGTGAGNGCCNCTTGTTTTNATG
AGTTNCCGNCCGGCAACAATTTGGTNGGTGGGGNTCAAAACCTTTTNCAGGCGGGGCCCGCTTTNNGGGG
AATGNTTTCCTTANNGNTTTANAANNTTGGGGGGGNTTTTNAGG
>gi|2764209|gb|R64965.1|R64965 13469 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169E22T7, mRNA sequence
AACCAAGGAACATGGCAGAGCTTGCAAGTNTCTATCTNAACTATGTTGAACTTCGGTATATTTGGAGTTC
CCATGGTTGGTTCAGACATTTGTGGATTCTACCCACAACCAACAGAAGAACTCTGCAACCGTTGGNTCGA
AGTAGGCGCGTTTAACCCGTTTTNAAGAGATCACGCCAATTACTACTCACCAAGACAAGAGCTTTACCAA
TGGGACACAGTTGCAGACTCAGCTCGTAACGCTCTTGGTATGAGATACAAGATCCTTCCTTTCCTCTACA
CTCTTAACTACGNAGCGCATATGACTGGTGCACCCATCGNTAGACCGGTCTTCTTTCTCATTCCCCTGAA
TACACCGGAATGTNACGGGAAACAGCAGGCCAGTTTTTTNCTTTGGAAGGAAGCTTAATGGTATTTCCCG
GTTTTNCGGGCAAGGGAAAACCGGAGTAGGAGGATTTTTTCCCCCNAGGGTTTTTGGACCACNTGTTCGN
AATGNNTNANGNANTNGTTNAAGAACGGGGAACGGGNA
>gi|2764208|gb|R64956.1|R64956 13460 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169D20T7, mRNA sequence
ATTTATGAGTCTGTAGATGAACCTGAGGAAGCATTGAAGCTACTTCAGAAGTCTATGAAATNCCTTGAGG
ATAAGCCAGGNCAGCAGAGCGCCATTNCAGGGTTAGAGGCACGGATGGGAGTTATGTATTACACAGTGGG
GAGGTACGAGGACGCAAGAAACGCGTTTAANAGCNCTGTGNCAAAGCTACGGGCAGCAGGTGAGAAATCT
NCCTTCTTCGGTGTTGTATTAAACCAGATGGGACTAGCCTGCNTTCAGCTTTTCAAGATTGATGAAGCGG
GTNAGCTGTTTGAAGAAGCAAGAGGTATTCTTGAACAAGAACGTGGACCGTGCGATCAGGGCACTCTCGG
GTGTTTATAGCAATCTNAGCTTGCTACCTATTGNCGNTATTGGGNAGGNTNAGAGGATCCGTTTTAAATT
ATTGAGCCAGGTTNTTGAACCTTNGANAGG
>gi|2764207|gb|R64951.1|R64951 13455 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169B4T7, mRNA sequence
AAACGACGTAGTTTCTGATACAGAGGAAAAAAAAGCAAATATCTAAAGTNATAGAGGAACTTAATGGCAT
GGCACTTTGGACGGTTGANATTTATCTATAAAGTTTTTAGATATTTCGATCTGAGAGTTGTGAAGCGAAC
GACGTCTTATGAGTCAATCTACTGGTCTTAATGTGACAGTGTATTATTAATGTACAAAATCCCGTCTTTT
TCAAGTTTTNNTTTCTAAATTAACAACTCTGTATTATCATTTTAGAAACTTTTATTTCTTGATTACT
>gi|2764206|gb|R64950.1|R64950 13454 Lambda-PRL2 Arabidopsis thaliana cDNA clone 169B3T7, mRNA sequence
GGACCATTCAAGATCAATGGTGTTCCTCTGAGACGTGTTAACCAGGCCTATGTCATTGGTNNTTCCACAA
AGGTTGACATTTCTGGAGTTACCCTCGACAAATTCGATGATAAGTACTTCGGCAAGGTTGCTGAGAAGAA
AAAGAAGAAGACTGAAGGAGAGTTCTTCGAGGCTGAGAAAGAGGAGAAGAAAGAGATTCCACAGGGAAAG
AAAGATGACCAGAAAGCCGTGGACGCAGCTTTGATCAAAGCTATTGAAGCAGTTCCAGAGTTGAAGACTT
ACCTCGGAGCAAGGTTTTCATTGAAACAAGGAATGNAGCCCCATGAGCTTGTTTTCTAGATTTCATTACT
TTTTTCCTGAGGTTTCTAGTGTATCTGCCTCCTGAAGGTTTTACACTCCACCTGGTTGGTTCTGTTCTTG
TCCACTGNCCAGGGCATAAAATNTTGGCTNTTNNAATCTGGTTNNTGNCTAANNTGGGAATTTTCCAACC
NGTTTTTAAGGGGNCTTTTCCAAGG
>gi|2764205|gb|R64942.1|R64942 13446 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168P6T7, mRNA sequence
CAAGANCTCAAACACTTCATAACTAAAACATCCTTTAAAGCCTTTTCAAAAACTCAATCATGTCAAGCAA
CTGCGGAAGCTGCGACTGTNCTGACAAGACCCAGTGCGTAAAGAAGGGAACCAGCTACACCTTCGACATC
GTCGAGACTCAGGAGAGCTACAAGGAGGCCATGATCATGGACGTTGGTGCCGAGGAGAACAACGCAAATT
GCAAGTGCAAGTGCGGCTCCTCTTGCAGCTGCGTCAACTGCACTTGCTGCCCCAACTAATGAAGCTTCTT
TAATCAAAATGTAATATGNATAAAAGTTGATGTGGGCTCATCTATTGAGCTCATGTCTCTCTTATTACCT
ACTCTCTAGTATTGGTGTGATGTAATGGGTTATTGNCCCTTNTTTTCCNTTNCCCTNTAAACNTAANGGA
AACTTTCAAGGTTATTTGNAAAGGGTNGGTTTCTTTTTT
>gi|2764204|gb|R64931.1|R64931 13435 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168O19T7, mRNA sequence
ACGAGAAACCTTACTACAGCTACGCATACAATAATTGCACAGGTGGAAAACAATGCTTGCATTACACGCA
AGGGTTGTGGAGAGATTCAGTGAAGATAGGGTGTGCTAGGGTTCAATGCACCAATACTTGGTGGTTCGTG
AGTTGTAACTATAACTCACCCGGTAATTGGGTCGGAGAGTACCCTTACTGATCCTGATCACTAATACTGT
ATTACCTAAGACAATAAATATGATTTATGAATAAAACTAATTTGAATTACTGCATATGGAATTATAAATC
TTTNGTTTTAATCTCAAGGATGTAATAATTTATGNCCCTTCACATT
>gi|2764203|gb|R64930.1|R64930 13434 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168O18T7, mRNA sequence
AGAAACTACAATAGTTAATCAATCAAAGAGAAGTAAGAGAAATGGCAGATTCTAACTGTGGATGTGGCTC
CTCCTGCAAATGTGGTGACTCTTGCAGTTGCGAGAAGAACTACAACAAGGAGTGCGACAACTGTAGCTGT
GGATCAAACTGCAGCTGTGGGTCAAACTGTAACTNTTGATGAAATTATTATGGTCTAAAATCATATATAT
GGCAGAAAAATTGGGGAAAATATGTGTTTTATGCTAAGAGATGTGTGTGTGTTGTTGGAATAAAGACGTG
ACCGTTGTGTTGCGTATCAACTCTCTTAAGCTTTGACTTTTCCCAGCTTTTGTATTTNCCCATGGTATGG
GTAATNGGTGTGATTTGTGTAANNGTTTTCANAATGGAACCGNAAAAAAAAATTTTTTNTTTNTGG
>gi|2764202|gb|R64929.1|R64929 13433 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168O10T7, mRNA sequence
AGCTTTTCAAAGTTAAAACCTTTTTTNCCCGAAGAAGAATCAATACGACTCAAATCAATCAATTGAATCT
ATGGCGATGGCTATGAGACTTCCAGCGATATCTAGAGCTGTGACGGAAGTAGCTTCAGCTCCGGTTGGTT
TGAGACGACTGTCCTGTTCAAATGCTTCAAGGTTCTCTTTTTTGTCTCCACAAGCTGAATCCCAAACACC
GGCTCGTCCTCAGGCTGAACCTAGCACCAATCTCTTCGTCTCCGGGCTTAGTAAGCGCACCACTTCTGAA
GGACTAAGGACTGCTTTTTTNCTCAGTTTTGGAGAAGGTTNCTGATGNTAAGGGTTTTCACAGGCANGNG
NTTTCAGGGTTNNTTCCAAAAGGGTTTTNGGGTTTTTTAANNGAANTTCCCCTTTTNGANNGGTTTT
>gi|2764201|gb|R64924.1|R64924 13428 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168M6T7, mRNA sequence
TTCCTTCACAATCTCAAAAGCCATTTTCAAAATTTAAAACTCAGAGAGAGAGAGATGTGTCCTTCTGGTA
GAATCGCNATTCCAATAACCACCACCGCGAATCCAAATTTCCNACCAGCTTTCGAAATCATCGACACAGA
TCACGACGGTAAAATCAGCAGCGACGATCTCCGTGCATTCTACGCCGGAATCCCTTCCGGTGAAAACAAC
GACGAGACGATGATCGGAACGATGATATCAGTAGCGGACGCGAACAAAGNCGGATTCGTTGAGTTCGATG
AATTCGTGAAAGTTCTAGAAACGGCGCCGTTTTCTAGATCTGGTACCGGNGGNGACGNTGGNTTNATTGN
AAGATGTNTTTTAAGGTGNTTGGTTAAAGCCGGGGGNTTGGGNGCTTNAGTTTCGGGGNTTCTTAAGGTT
TNTTTGGNTTCGCCTTGGTT
>gi|2764200|gb|R64923.1|R64923 13427 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168K8T7, mRNA sequence
ACGAGTATGTACCTATGGTGGACAAAGCCGTTGACGCCACCTGGAAGGTGAAACCCGCCATCCAGAGAGT
TGCCTCAAGAGGAGCTTTAATGTCTCCCACCGTTCCAAAAGATCATNAAGGCATCAAGGCTCGANTCCTA
GTAATGTTCATGGCATTNTTNATGGCGGTTTTAACATTCTTCCGCACTGTAACAAAGAAACTTCCAGCGA
CTACTACTTCTTCCCCAGCAGAAACCCAAGGAAACGCAATAGAACTTGGTTCTANCGGTGAAGGAGTTAA
AGAGGGAGTGTCGTCCTCCTTCTCCCTGTTACCAGACCTNACGGGAAACTGNTCTTCCTTAAAACTTTTG
TTCCGGTGGGANCNTNCCAAGNNCTTGGANGGGTAAAAATCCGGGNNCGNTCCC
>gi|2764199|gb|R64922.1|R64922 13426 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168K4T7, mRNA sequence
AATCCAACCAGACCACACAGACCTTNTCCTTCTCCACGGAACAAAGTNTTCGTNAAGAAGACGACGAGAG
ACACCACGTNACACCTCGATTACTCCAATCTGGTTAAGCTGGAGAAGGCGGGATCGCACTCGGTTTCGAN
TCCNGCTCCGGCTTCGGGTTCGGTTCCTATTAACCGGGTTCCCCTCGCTCAGGTCGTCGAGGATTGCTTC
AAACGCTGGTTCCAGGATACGCTCAAGGAAGCCAAATNTGGTNACGTTGGTATGCAGGTTTTTGGTTGGG
CAAGATGTATTTCCAGCGGCTTATGGNATCCNTTAAAGNTGAAAACAATNGGTCGGTTGNTTTG
>gi|2764198|gb|R64921.1|R64921 13425 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168K2T7, mRNA sequence
CTGAAAAATAATTTAGACAAAACAAAGATGGTAGAGAGAGAGGTGAAACTTTTGGGAACATGGTACAGTC
CGGTCGTNATAAGAGTAAAGNTCGCNCTTCGTCTCAAATCGGTTGATTATNATTACNTTGAAGAGAACTT
NTNCGGTTCTAAGAGTGAGCTTCTCCTCAAATCGAACCCGGTTTACAAGAAAGTCCCGGTNCTNATCCAC
AGTAATAAATCGGTTTGTAAGTCTCTAAACATCGTTGGATACATAGACGAGACGTGGAACTCATCTGGTT
CGTNCATTCTTCCTTCTCATCNTCATGNTCCGTCCCCTTGCNCGGTTTCTGGG
>gi|2764197|gb|R64919.1|R64919 13423 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168K12T7, mRNA sequence
TCTTTTTCNTNAGTCTTCAAAGAGTTTCTAAGTAACCCAAATNAATGGCAGGTATCAAAGTTTTNGGACA
CCCAGCTTCCATTGCNACCAGGAGAGTCCTCATCGCCCTCCACGAGAAAAACCTCGACTTTAAGCTCGTT
CATGTCGAACTCAAAGACGGTGAGCACAAGANGGAGCCTTTCCTCTCCNGCAACCCTTTTGGTCAGGTTC
CAGCCTTTNAAGATGGAGACCTCAAGCTCTTCGAATCAAGAGCGATTACTCAGTACATAGCTCACCGNTA
TGAAAACCAAGGAACCAACCTTNTNCAAACCGNCTCCAAGNACATAT
>gi|2764196|gb|R64916.1|R64916 13420 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168J6T7, mRNA sequence
AAGACATGGAGTCACTCGCCACAGTACAAGATCGGTTATTGCCAACAGTGTCCGGACAAGGTGACATGGC
CAGAGGCAAGCTTGGTCCTAAGCCGCCTTTNTACTTCAACGCCGGTATGTTCGTTTACGAGCCTAACCTC
TCCACTTATCATAACCTCTTGGAGACGGTCAAAATTNTGCCTCCCACTCTTTTTGCTGAACAGGATTTTT
TGAATATGTACTTCAAGGNCATATACAAGCCAATACCACCAGTGTATAACTTGGTCTTGGCAATGCTTTT
GGAGGCATCCAGGGGATNTAGGGCTTTGACCCAAGNCAAAGTTGTTCANNTACTGTCCTGCTTGGTGCTA
AAANCCTTTGGGGNTTTCANCTGGGGGGAGGGNGGGGGNACCTTGGGCCTGGGTGGNCCTTTTAGNGTTN
CTTNNTAAAGAATTTGGGGGGG
>gi|2764195|gb|R64911.1|R64911 13415 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168J1T7, mRNA sequence
GGGAGGAAAGGTGAGATACTGAGCAGTCCAGTCTCGGATTCTCTCTACAGAGGCTCACTAGATGTNCACT
CCATACCAGTAGCAACAAGATGGAGATCTTCAAGCGCAATTTTNCCATTTTTGGAAACTAGAATGGGGAA
TTTAGAGAAACTTGGGATCCAGTGGGGAGCCATGGGATCAGATGTGGTTAGGGCCTGGGGATTTGGGAGA
GAAGAATTGCAGGAAATGAGGGAGAATCTGTCAAAAATGGTATCTGANCTGAATCCTCAGTTTTNCGAAT
CTCCGGATTCAGATTAAGTTATGTCTTAAAACGNATATNGTTGTATCACCTTTAAAAGATTTTTCNTTGG
TTTGGGTTTNNAAACTTTAATGGGCAAANCCCCGTTGTTTGNTTTGACTTAACCCCCCTTGGNGAAAGGC
CGGCTTTAANAGNGGTTTNATATTTGGGGGCANTTGGGGGGNANGGATTTTNCAAACAAGGCCCAACC
>gi|2764194|gb|R64907.1|R64907 13411 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168I24T7, mRNA sequence
CTGAAATCGTTGAATCTNCGGATGCTTATCTNTTTGCAGGTCCGATTTTAAACGATTACAGTNCTGTTGG
GTATTCTCTGCTTCTAAAGAAGGAGAAGGCAATCATCGTTCAGCCTGATCGGGTTACTATCGGTAACGGA
CCTGCGTTTGGATGTNTTCTTATGAAGGATTTTNTAAGCNAGTTGGCTAAACGAATTAAGCACAACAACA
CTTCTNATGAGAATTATCACAGGATCTATGTCCCAGAAGGAAAGCCTTTATNAGNTAACCCGNATAANCC
TTTAAGGGGTTAATGTACTGTTCCAACACATTCAGAATATGCNCTCTTCTNAGTCTGCTTGT
>gi|2764193|gb|R64904.1|R64904 13408 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168I21T7, mRNA sequence
TGTTTGGAGAAGAAGAAGAACAGATCAAATACGAGGAGAGATCTCTAAAGAGATTTATCGTTTCAAATTT
NTNCACGTTGAGAAGTTTAATTTAGATTAAACAACAAAAAGATGGGTTACTGGAATTCCAAGGTTGTNCC
AAAATTCAAGAAGTTATTCGAGAAAAATAGTGCTAAGAAGGCTGCTGCTGCTGAAGCTACCAAGACCTTT
NATGAATCTAAGGAAACANTCAACAAGGAAATTGAGGAGAAAAAGACAGAACTCCAACCAAAGGTCGTGG
AAACCTATGANGCCACGTNTGCAGAAGTCAAGGCTTTGGTGAGAGNCCCTAAGGTGGCTGGTTTNANGAA
AACTCAGCGGCTNNTCCAGGAAGTACCTCGAGGGGCTNGTCAAATTTGNNTTCCCCGGNTCCAAAAGCGG
GT
>gi|2764192|gb|R64897.1|R64897 13401 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168G18T7, mRNA sequence
AAGCTTACTTCGGTGAGACTGCCTCTGAAGGGAGGCTTTNACAACAATGCAGTGGCAACAGCAAACATTC
TGGAGTCATCATCTCAGGAAGTTGGTGGGAAACCCTACTATTACTTGTNTGTTTTGACAAGAACGGCTGA
TGGAGACGAAGGTGGGAAGCATCANCTGATCACAGCAACCGTGAATGGNGGGAAGCTTTACATCTGCAAA
GCACAAGCTGGAGACAAGAGGTGGTTCAAGGGAGCCNNGNAATTTTTCGNGAGCNCACCCACTTNTTTCA
AGTGTTNCTT
>gi|2764191|gb|R64896.1|R64896 13400 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168G16T7, mRNA sequence
CNCTTTCCNAAACCATCAAAACTCGCCNACAAGGCCCTCTGTTTAANCCCGGAAACCTACACTAAGTAAT
TTNAGTTTGAGTAATGCAATTTGCTTGNCGTCTCCTCCTGANCCAGATGATGATGGTGGTGGGTCACTTT
CTCCGCCAATGGATACTTCAACGAGAGACGAATTAGCAGCGAGGTTTCTCTTCTCCGGTACAGTGAAACC
CAAACGAGACGATTTTGGAGTAGTTAAGGGANNAAAGGAGTATCTGATGGATGGTGGAGNAGNACGGTGG
TCGGAAAGAAGAGCTGGTGGTGAAGGTAGTNGTGACGANAAAGTAGAAGAAGTCGCCATTGTTGAGNAGG
>gi|2764190|gb|R64895.1|R64895 13399 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168G11T7, mRNA sequence
CCTAAGCCTATGTCGGAAAGCTCTGAACAGGTCAAACCAATCGATGAGAAAGACAAGCTTAGACCGATTA
AAACCGGTGGAGGAGCACCAGGAGGAATAGAGAGGAGTCGATCTAACGGTGGAGGAGCTCAACGACATCA
TAGAACAACCGGAAGAGTTTCTCCGGCAGTGGACCCGCCGTCTCCGAGAATTTCGTCATGCGGTTTTTGC
TCTGCGTTTGGAAAGAATNCGCCGGGGGAGAAAAGTTAATTCNGGGGAAAGGNCCCCCGAACGTAGNTCG
AGGTAGGCGTCAGGGTTAATAAATATTCNTGNGGGGNAAAAATAGTTTTCNCCTGNCTTTCAANNTTTTT
NCTTCTTCTTTTTTTGNATGNGNGGGGGTCTTTNGTTATAAAAAACTTTTAAATTTG
>gi|2764189|gb|R64894.1|R64894 13398 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168E24T7, mRNA sequence
TCAACATACTTCTTTGTAGTGCTACTTNCCATTATATCAAACACTCAGCAACCTGATGGCAACGAGACGG
ATATTGAAAGATTTGANGGAGTTGCAAAGAGACCCTCCTGTATCANGCAGTGCAGGTCCAACAGGAGANG
ATATGTNCCACTGGCAAGCTACTATAATGGGTCCGANTGNAAGTCCTTACTCCGGAGGTGTTTTCCTTGT
NAATATCCATTTCCCTCCTGATTATCCTTTTAAACCTCCCAAGGTTGTATTCAGAACCAAAGTGTTTCAC
CCAAACATCANCAGTAATGGGANCATATGTTTGGGCATTNTNAAAGGCCC
>gi|2764188|gb|R64890.1|R64890 13394 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168C24T7, mRNA sequence
AAGNTCAACGAGGTAGGAAACTNTTTTGGAAGTGTGAGGNGCTTATTGACAAGATTAAAGGTGGTTTGGC
TGAAGCAACTNCTGCCAAATTNATATTAATGTTTTNNCAAGAGATCGAATCANACTCTNCGAAGAGCTTT
GAAAATGGAGAAGGTGGACGTTTGATGGCACCTCAGGATGCATGCAACCGAATTNCTGAAGTTGTACAAG
AGACTTTNAGGAAAATGGAGATAGTGGCTGAGGAGAAGATGAGAATGTNCAAGAAGGCACGCATGGCTCT
TGAGACATGCGATAGAGAGCTCGAAGNCAAAGCCAAGGAAGTTTCAGAACCTGAAAGCAGAGAGGCAAGA
AGNAAGAAACTTCAGATAGATGAGCCTAGAGAGGATCGTGAAGGCTNAAGCAAGCCGGAGGCAGACATGT
TCCAGCTTTAAAGCAATTGAGGCAAAGCGGGAGGCTTNTTAGGTTCAGAGGGTTTTCCTTCCGNAATTGG
TAAGCTTNGGNGGATTCGGAGAACCTTNTTAACCANAGGCTTGTTAGCCC
>gi|2764187|gb|R64889.1|R64889 13393 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168C23T7, mRNA sequence
AGCAACCATGCGGGCAGAGGTGTCANATGTATCAAAGAGCGCGATCAGCAATTNATTTTNACTAGACGAC
GATTCGAGCATCCCATTCTNGCTTGANGATATCTCCAAATCGATGCAAAACGTAGAGGTTGCAGAGGTTG
ATCCTCCTCCGTTGATCCGCCAAAACTCCAACTTCATGTNCTTNTTGGAAAGGTCAGATTGAGGTAGTCA
AAGTNCCCTATACCCGATCGANCGCNAGGACATTTTNANATTAGGAGATCAGTATTGTCCTTTCAAAAAC
AAAGCCTGTACATTAGTACATATGCCTATCTTTNCCAGTGGCTTTNTGGTACTGTCCTACTATTAANAGG
GGTATATNGGGTAGGGAAAAATATATATATGTAGACTAAATATTTGTGGTGTCCATGCGGTTNGTAGGCC
ATTTGCTTAATGG
>gi|2764186|gb|R64887.1|R64887 13391 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168C19T7, mRNA sequence
ACAAGAACTCAAACACTTCATAACTAAAACATCCTTTAANGCCTTTNNAAAAACTCAATCATGTCAAGCA
ACTNCGGAAGCTGCGACTGTCCTGACAAGACCCAGTGCGTAAAGAAGGGAACCAGCTACACCTTCGACAT
CGTCGAGACTCAGGAGAGCTACAAGGAGGCCATGATCATGGACGTTGGTGCCGAGGAGAACAACGCAAAT
TGCAAGTNCAAGTNCGGCTCCTCTTGCAGCTGCGTCAACTGCACTTGCTGCCCCAACTAATGANGCTTCT
TTAATCAAAATGTAATATGAATAAAAGTTGATGTGGGCTCATCTATTGAGCTCATGTNTCTNTTATTACT
ACTCTCTAGTATGGTGTGATGTAATGGGTTATGACCCTTCTTTCCCTTCCCTATAAAACTNAAGGANCTT
GCAAGGTT
>gi|2764185|gb|R64886.1|R64886 13390 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168C16T7, mRNA sequence
AACAAGAGCCAAGCTAATGAGATAAGTGTATCGGTGAGGCTGAGAGTTATTCACTTACAAAAAAAAAAAA
AAAACTTGAGTGTAACCAAAAAAAAAAAGTTGATATACTTNCTGGTTTTCNCCTTAACTTTNATNCTTTA
CAAATCCATCCCCCTTAGATCTGTTTATTTCCCGCTACTTTGATTCATTTCTGTNAGTAATCTGTCTTTC
GTATAGANGAAAACTGATTTCTNGGTTTGTATTTCCTTAAAGNGNTCAATCTTTTT
>gi|2764184|gb|R64881.1|R64881 13385 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168A8T7, mRNA sequence
CTTNTTCCTTCTTCCTCACTGTAGCTCGTCGTCGCTACACCATCTAGAAGACCCTTAACCATGGCTGTCG
GGAAGAACAAGAGGATTTCAAAGGGTAGGAAAGGAGGAAAGAAGAAGGCTGTTGATCCCTTCTCCAAGAA
GGATTGGTATGACGTGAAGGCTCCTGGTTCTTTCACGAACAGGAATGTTGGGAAGACTCTTGTTTCCAGG
ACTCAGGGTACCAAGATTGCCTCTNAGGGACTGAAACACAGGGTGTTTNAGGTTTCTNTTGCTGATCTAC
AAAATNATGAGGATAATGCCTACAGGAAGATCCGTCTTAGAGCTGAAGATGTTCAGGGAAGGAATGTGTT
GACCCAGTTCTGGGGTATTGGATTTCAACAACCGNCAAGCTNAAGGTCATTTGGGTGAAGAAGTGGCAGA
CTTTTNATTTAAGNCCNATTTNNGATTTTGAAACCNCAGNCGGGTTNACCTTTANGGNTTNTNTTTAATC
GCTTTAAAAANGGGCG
>gi|2764183|gb|R64880.1|R64880 13384 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168A7T7, mRNA sequence
CAAGANCTCAAACACTTCATAACTAAAACATCCTTTAAAGCCTTTTCAAAAACTCAATCATGTCAAGCAA
CTGCGGAAGCTGCGACTGTNCTGACAAGACCCAGTGCGTAAAGAAGGGAACCAGCTACACCTTCGACATC
GTCGAGACTCAGGAGAGCTACAAGGAGGCCATGATCATGGACGTTGGTGCCGAGGAGAACAACGCAAATT
GCAAGTGCAAGTNCGGCTCCTCTTGCAGCTGCGTCAACTGCACTTGCTGCCCCAACTAATGAAGCTTCTT
TAATCAAAATGTAATATGAATAAAAGTTGATGTGGGCTCATCTATTGAGCTCATGTCTCTNTTATTTACT
ACTCTCCTAGTATGGGTGTGATGTAATGGGGTTATGACCCTTCTTTCCCTTCCCTATTAAACCTAANGGA
ACTTTCAAGGTTAATTNGAAAGATGGGTTCTTTTT
>gi|2764182|gb|R64876.1|R64876 13380 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168A24T7, mRNA sequence
CTCCATGATCTCTACCTTCACNCCATGTNTCAACTTCATCACCGGANGCAGCGGCGGTTCCGTNACNCCC
ACCGCNGGNNGCTGCNACTCCTTGAAGACGTTGACCAACACTGGCATGGGCTGTGCTTGCNTCATCCTCA
CNGCTAACGTCCCGCTGCCTACTGGCTTCATCAATCGGACTCTGGCGCTTGCTCTACCTCGAGCCTGCAA
AATGGGCGGTGTACCTATTCAATGTCAAGCTGCGGGGACTCCTCTACCAGCTCCAGGTCAGGTTCCATTT
TTAATTGCTCCACCACCGTCAGGTGTCTTGCTTTTAGCCCGGGAGCGTCCAAGGCGGCGGGGACAACACC
AACAACAGGGACCTGNACCGGGATNACTTCCCGCGGGNTGGGNCCAACGGGGCCCNACANCTTAAATAAG
GAATT
>gi|2764181|gb|R64875.1|R64875 13379 Lambda-PRL2 Arabidopsis thaliana cDNA clone 168A1T7, mRNA sequence
GGCGTNTTCTCTTCCTACATTTCCCCAAGCNTTACCTTGCTCGTAAACCAAAACTTCTTCCTCCTTGGCT
ACCTTCCGATCTCCTTTNTTAAGATTCAATGGTGCCACTTCCTTAATCCCCTCCTCTATCTCCATCACTT
CACGTGGCACATCCTCCCCGACCATCATCCCACGTGCTGCCGCCTCANAATCCGACTCTAACGAAGCCCT
AGCCAACACAACCTTCCACGGCCTCTGCTATGTNTTGAAAGACAACATAGACACCGACCAGATCATCCCA
GCAGGAGCGGNTTGCACCTTTCCCATCGAACCAGCAAGAGCGTGATGAGATCGCGGGTNAAGGTNTCTCT
GGGTCTACCAGACTTTCCACAAAAAACGGGTTCANTTGAGCCAGGGNGGGACAGGTNAAAAGTACTNAAT
TAATAATNGGNGGNGNAAAANTTTGGTTGGGGTNGGTAAGGTGAAATGTTCGGGTTTTTTTTGGGGAANT
TGGGNTAAAGGCATAGTTTNTTNGTTTTCGGAAGATTTTTTTTCGGAATTGGTTTTAAGG
>gi|2764180|gb|R64874.1|R64874 13378 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167P2T7, mRNA sequence
GTATCTGACAAACGGGAAAAGATTAGAAAAAATAATGGAGAAGCTAGGATTCTCAAGTNATTCTNCAACT
GAGATCGTGATTNANGAAACCAACCCTAAACCATCAGAATCATCCAACCTGCCAAACTTCATACTCAACG
AGCAAGTGGTGTCATTTTAGTTGTAGGAAAAGGTCTTTACTCGGNTCATGGAAAAGCTGNGGAATCAAAG
TTGTCTTAAATGGCCGGTGTAGCAAGCATAACAGTGCTCACTTAACGGGAGAAGACGTTTTTCCGTATAT
GTACATACGTATGTATGANTGTCCANCTCCTACTTGGGTATCAAATCAAAATGCCCATTTTGNTNTTCT
>gi|2764179|gb|R64872.1|R64872 13376 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167O23T7, mRNA sequence
TTGGTCAAAATGTTTCCAGTGGAACCCAGGAAAAGCTGTATCAGAACGTTAGAACTGGGATCAGTTCAGC
TAGTGATCTGTTGAACCCCAAGGATTCTNATTACACATTTNCTTCAGCTGGTCAGAATTCGATATCAAGA
ACTAGCCCCAATGGAAGCTCAGAAAACATCGAAATCTTGGATGACTTATCTCCACCACATTTGGAGAAAA
ATGGTCTAAATCTGACAAGCGTTGATTCCTTGGAAGGAAGACATGAAAATNAGGTCTCCCGCGAATTAGA
TTTAGGTCACTACATGCTCACATCTATTAAGGTCAACACAACACCGGGNATCTGGNCCTAGCATTCCTCA
GATTNTNCCATATGTTCACCGGGTGTNNTGGAAGCCCTTTTTTTTGGAAGGAANTCTTGGCTNCNGNAAT
TTNTTTNANGCNCTTTG
>gi|2764178|gb|R64869.1|R64869 13373 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167N9T7, mRNA sequence
TCGCGNCTTTTGCTTCCTCCCGCTTTTTCGCCAATGTTTTCTTTAGATCTAGCTAATATGGCGACGATTT
TNTNCTTTCTCGCTTCTAATCACCGTAGAGATCCNCCCGATCTGCAAATCCGATCCGNATTCTCAACGAA
TTTGTAGATCTGATCTGTGATTCCATCGTTGACGACGGATCTTCGCTTACATCGTTTGANCTGTCGCAGA
TCTGCCGTTTTCTATAGATCTAGATCTGGATCGTCCTTCGCGGCTTCTTCACATGCAAGATTCTGTGAAN
NGTTCAANTTGAGGCANCATTTCNGGNTTACTAGGAGACGGATCTNTTGCAGACGGATGTGTGTGTGTTG
GNTTGAAATTGAGATTNGGGTGTAGAAGA
>gi|2764177|gb|R64867.1|R64867 13371 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167N23T7, mRNA sequence
GGAGATCGGAGACTCATCGTTGCAACAACAACAAATTTCAGAAGATCCGAAGACGAAACGATGCCTATAA
GTNCGACAATGGTCGGAGCTTTGCTGGGTCTCGGTACCCAGATGTACTCCAACGCCCTCCGCAAGCNCCC
TTATATGCGTCATCCGTGGGAGCATGTGGTGGGTATGGGACTTGGTGCTGTGTTTGCNAACCAGCTCGTG
AAATGGGATGTGAAGCTTAAGGAAGATCTTNATGTGATGCTCGCTAAGGCTAGAGCTGCTAATNAGCGCC
GTTACTTTGATGAAGATCGGGATTAATTTTGCGTGATCTTTGAAGTCTTCAGNAAAGGAATATCTTCCCC
TGAACTCATCTCAAGTGCTTGTTTTTGCCTGACCTTTCCCNGTATAAGGGTTTCTCCNNCCTNCTTTTTN
NACTCAGCCCTNGGNGTNTTTTTCATCACTGNTTTCGNATNT
>gi|2764176|gb|R64865.1|R64865 13369 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167N20T7, mRNA sequence
GTAACAACTCACCTGCCGAATCAACTAGCCCCGAAAANNGGTTNTNCAAAAGCNGCGACCTATACCCGGC
CGTCGGGGCAAGAGCCAGGCCTCGATGAGTAGGAGGGCGCGGCGGTCGCTGCAAAACCTAGGGCGCGAGC
CGCNGCGGANGGCCGTCGGTNCAGATCTTGGTGGTAGTAGCAAATATTCAAATGAGAACTTTNAAGGCCG
AAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGTCGGGGGAAACC
CGTCTNATAGCGCTTAAGCNGANACTTCGAAAGGGGATCCCGGTTAAAAATTCCCGGAACCGGGACGTGG
NGGTTTAACGGCAACNTTAGGGAGTNCCGAAACGTCGGCCGGGNGCTCCGGGAAGAGT
>gi|2764175|gb|R84195.1|R84195 16154 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167N19T7, mRNA sequence
TCAACGAGGCCTAACCAAATTCCGAACNAAACACCGAGCCACACTCCAAACCCAGCGTCANTANATCCAA
GCNTCACGTNTCCTAGCTCGAGCCCGAACCACACCCAAGAAATCTCAATCTCAATCTNTNGCCAAAACGG
CGCTCACCGAAGCTGATAATGTGATCGCAATTTNTCCAGATGATGCCGCCGGTCACATCGTCCGTGCCCT
AGCTCTAGATCTGCTCGGTCACCATACTTNTGCTCTCAAATNGTTCGATATGGCGNTGACTTATCCGCGT
TT
>gi|2764174|gb|R64861.1|R64861 13365 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167N14T7, mRNA sequence
ACTGGTGGAACNNCTACTGGAGTAGGGAAGTNCCTCAAGGAGCAGAACAAAGACATCAAGGTTTGTTTGG
TGGAACCAGTAGAAAGTCCGGTACTTAGCGGAGGTCAACCAGGTCCACATTTAATTCAGGGAATTGGCTC
TGGTATCGTCCCATTCAATTTGGACTTAACCATTGTNGATGAAATNNTTCAAGTGGCAGGTGAAGAGGCT
ATTGAAACAGCCAAGCTTCTTGCCCTCAAAGAAGGATTACTGGTGGGAATATCCTCTGGGGCNGCAGCAG
CGGTGTTTTTAAAGGNTTGCAAAGNGGCCAGAAAACCGGGGGGAAACCNCATTTTGGGNGGTTTTNCCCT
NNTGGGGG
>gi|2764173|gb|R64858.1|R64858 13362 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167M9T7, mRNA sequence
ACCAAAAAAAAGAAAACACAAAAACAAAGATTATAATGGCTTCCTCAACCATGGCTTTNTCCTCCCCTGC
NTTCGCCGGAAAGGCTGTNAAGCTGCCGCATCAAATGTCCTCGGAAGCGGCCGTGTGACCATGAGGAAGA
CTGTCGCCAAGCCAAAGGGTCCATCAGGCAGCCCATGGTACGGNTCTNACCGAGTCAAGTACTTGGNTCC
ATTCTCCGGCGAGCCCCCGAGCTACCTTACCGGTGAGTTCCCCGGTGACTACGGATGGGCACCGCTGGTC
TATCCGCCGACCCAGAGACCTTCGCCAGGAACCGTNAGCTAGAAGTTATCCACAGCAGATGGGCCATTGT
TCGGAGGCCTTAGGGTTGCGTTTTTCCCTGANGTTATTTGGNTAGGAACGGGGTTNAAGNTTCGGAGAAG
GCGGTTTTGGTTAAAGGGCCGGTTTAAAAGNTTTTTAAGNGCCGGGGGGTTTNGNTTNTTTNGGAACCCG
NGTTT
>gi|2764172|gb|R64856.1|R64856 13360 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167M6T7, mRNA sequence
AGTAGGTGGAAGTNCAGACGCAGATAGTTGGTCGACTGTNCAAGAAAGAGCTTTGGTTCAAGCTTTAAAG
ACATTCCCGAAAGAGACAANCCAAAGATGGGAGAGAGTAGCTGCAGCTGTCCCTGGTAAAACGATGAACC
AATGCAAGAAGAAGTTTGCAGAGCTTAAGGAAATCATTAGAAACAAGAAAACCGGAGTATGAGGTAAAAT
CATTTCGGAGTCCCATGAGAATTTTGGGTTTTAATCCTCTTGGGGCACCGTTACTTTNCGAGAAGCAAGA
CCTAAAACTTTTTTATTATTTGTAATGATTCATTTCCCCTTTNATGTCCCCTATATATTGAGAGTCCTGG
GGNCCCCTNTTATTGGGGTATGNTTTTTTTTTACCATAANCTTTNTGGNACCGGNTTNNTTTGGGGNNTA
GGTTCAAAGTTNTGNAATTAAAGCGGGATCGCCC
>gi|2764171|gb|R64849.1|R64849 13353 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167L9T7, mRNA sequence
AGTATATTGATGAGACTTGGAGAGACAATCCGATTCTCCCTCAAGANCCGTATGAAAGAACTATGGCTCG
ATTCTGGTCTAAATNCGTCGATGAACAGATTTATGTAACGGCNATGAAAGTTGTGGGGAAGACCGGAAAA
GAGAGAGATGCTGTGGTTGAAGCGACGAGAGATTTNTTGATGTTTTTGGAGAAAGANCTTNTTGGGAAAN
ATTTNNTCGGTGGGAAAAGTTTAGGGTTTNTGGATATTNTGGCGACTTTGGTGGCGTTTTGGCTGATGAN
AACGGAGGAGATCGTCGGGGTAAAGGTGGTTCCGGTGGAGAAGTTCCCCGGAGGTACATAGATGGGTTAA
NAATTTTTTTGGGNATNATGTTATCAAGAAAATG
>gi|2764170|gb|R64848.1|R64848 13352 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167L8T7, mRNA sequence
AACCTTCGGTTGTTCCTGTCCCTGGAGGAACTATACATCCATTGACAAGGTATGTAATGAATTACCTCAA
CTTGATCTCTGACTATAGGGAAACGTTGATTGANCTCATCATGACGAAACCATGTCGGGGTTTGAAATGT
ACCAATGATCGAAACGNTCCGGATATGGATATCTCTNAGCTTGAAGGAATATCTCCGTTAGCTTTGCATA
TNATATGGACAATGGTGATGCTACAATTCAATCTAGAAGAGAAGTCTTTGCATTACAGGGACGNACCTTT
ATCTCACATCTNCGTCATGAACAATGTCCCATTACATAGGTTCAGAAGGTCAAAAGCTCTCCGGGNGCTA
ATGGGNGTTGNTNAGGGGCCAAGTNTTTAAGGAAGCTTACCGGGNTATTTTGGCCAAGGAGCTTCCANGT
TTCNNGNGGGCTNCATGGGCCAGGGGTNTTGA
>gi|2764169|gb|R64845.1|R64845 13349 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167L24T7, mRNA sequence
AGCTATCGAAAATTCTGAATCTGAAAGGTTTGAGTGAAGATGTCTTCAGATCGGAAGGTTCTAAGTTTNG
AAGAAGTTTCAAAGCACAACAAAACTAAGGATTGTNGGCTTATNATTTCCGGCAAGGTGTATGATGTGAC
TCCATTCATGGATGATCATCCTGGAGGCGATGAAGTCTTGTTGTCCTCAACAGGGAAAGATGCTACAAAT
NATTTTAAAGACGTTGGTCACAGCGACACTGCAAGGGACATGATGGACAAATATTTCATTGGTGAGATTG
ATTCGTCTAGTGTTCCAGCAACTAGGNCATACGNTGCACCACAGCAACCAGCCTACAACCAAGGCAAGGC
ACCAGAATTCATTATCAAGATTCTTCCAAGTTCCTTGTTCCGATCTTAATCTTGGGGGTTTGGCTCTTTG
TCGNCCGTAACTNTTNCCAAGGANGGCTTGANGAAGCCAAAGNTTTCTTTGATGCTTTNNAATTGATNTN
TTTNCCGGCCTTTGGNTAANTNTTTTTNGGAAAAAGG
>gi|2764168|gb|R64843.1|R64843 13347 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167L1T7, mRNA sequence
ACCAAACACATAAAAGAGAGATTTAATACAAAAGAAAGAGAAAAAAGAAAGATATGGCAGGNCTCATCAA
CAAGATCGGAGACGCACTCCACATTGGAGGAGGCAACAAGGAAGGTGAGCACAAGAAGGAAGAGGAACAC
AAGAAACACGTTGACGAGCACAAGANTGGTGAGCACAAAGAAGGTATTNTTGACAAGATCAAAGACAAGA
TCCACGGTGGTGAAGGTAAAAGCCACGNCGGNGAAGGCAAAAGCCACGNCGGTNAGANGAAAAAGANGNN
GG
>gi|2764167|gb|R64841.1|R64841 13345 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167L10T7, mRNA sequence
CAATCCTTTCCTTTCATTGTAGTTAAACAAAGATTACGATTATGGCCACATCAGCTATCCAACAATCCTC
CTTCGCCGGCCAAACGGCTCTCAAGCCCTCCAGCGACCTCATCCAAAAGGTGGGCGTCTTGGGCGGTGGC
CGTGTGACCATGCGTCGTACCGTCAAGTCTACTCCCCAAAGCATCTGGTATGGACCAGACCGTCCCAAGT
ACTTGGGACCATTCTCGGAGAACACACCGTCTTACTTAACTGGAGAATACCCCGGAGACTACGGCTGGGA
CANCGCTGGACTCTCGGCTGACCCGGAGACATTCGCTAAGAACCGTGAGCTTGAAGTAATCCACAGCAGA
TGGGCTATGTTGGGTGCTCTTGGGTTGCACATTCCCTGAAATTTTTTTCCAAGAACGGTGTTAAATTNGG
GGAAGCCGTNTGGTCAAGGAAGGNTTTAAGATTTTTTAGAAGNGGGTTTNTTNCCTTGGAACCNTACTTT
TTCCCGGGAANGNTTTTAGCATTTGGGNTTTNAAGTNNCNATGGGTNTTAAGGTAAAATTTGGGGNGCCC
TTGGGGGGGTTCCCGTTNTCCGGGNGGTNNCNTAANTTNTT
>gi|2764166|gb|R64838.1|R64838 13342 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167K5T7, mRNA sequence
CAATTCTATCCAAAATCAACCCAAAAAAAGAAAGAAATATGTGGGATGAAACTNTAGCCGGACCTAAACC
GGAGCATGGCCTTGGCCGCCTCCGCAATAAGATCACCACCCAACCCCTTGACATCAAAGGTGTAGGAGAA
GGGAGCAGTAGTAAAACTNTGGCGGCGGTGGCCGGGAGTCCTGGAACTCCGACGACGCCAGGTTCGGCGC
GTAAGGAAAACGTGTGGAGAAGTGTGTTTCATCCAGGAAGTAACATCGCCACTAGAGGAATNGGCACAAA
CCTNTTCGACAAGCCTTCTNACCCAAACTNTTCCACCGTCTACGGTTGGCTATACAGCGACGGCACTAGG
NGCAAAGCACCCTTTTNGCCCGNGAGGGGTAGAGTGACATNNGGATNNTTGTAAAATAAATTATTNTTNT
TTANGGCCCGTGTTTATNGTTCCTGTTTNGGCTAATTTTTGG
>gi|2764165|gb|R64834.1|R64834 13338 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167K18T7, mRNA sequence
CAAGGATAGGTCTGGCTTCGAAGGTGCATGGACATCAAACCCTCTAATCTNCGACAACTCTNACTTCAAG
GAACTCTTGAGCGGAGAGAAGGAAGGCCTTCTTCAGCTTGTNTCTGACAAAGCACTATTGGACGACCCTG
TTTTCCGTCCTTTGGTCGAGAAATACGCTGCTGATGAAGATGCCTTTTTCGCTGATTACGCTGAGGCCCA
CATGTAGCTTTCTNAGCTTGGGTTTGCTGATGCTTAAGCTGTGACGTATGCNCTGTGTGTGTGTGTGTGT
CTCCCCGAGAGTCATGGCTGTTTTTGGTTGGGGNCTGGAGGGGTCGCATTTGCATTTGAAACTTTTGTCA
TATGATTTGCTTAAATGGACCTCTCGGNATTTACGGAATNCTGGTTTTTTTCCGGTGGGGTTGTNATTTG
AANAANATCCCTTGGCNGTTTTTNCCTGNTTANGCACATTAANTAAAATTAAAATTTCCCTCGG
>gi|2764164|gb|R64829.1|R64829 13333 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167J23T7, mRNA sequence
CCGAGAGCCAACTAGCGAGTAGAATCAACTATCAAGCAATGGCATCGATGACCATGACCGCTACCTTNTT
CCCGGCCGTCGCCAAGGTTCCCTCAGCCACCGGCGGACGAAGGCTCTCCGTAGTCAGAGCCTCCACGAGC
GACAACACACCCAGCTTAGAAGTCAAGGAACAGAGCAGCACCACAATGAGGAGGGACCTCATGTTCACGG
CTGCAGCTGCANCGGTTTGTNCTTTGGCTAAGGTAGCCATGGCTGAAGAAGAAGAGCCCAAGCNAGGGAC
AGAGGCGGCCAAGAAGAAATACGCACAAGTTTGTTTCACAATGCCTACGGCCAAGATCTGCCGGTACTGA
TTCAACAACCCACCTTCTTGATGTTTATCTNNCTNTTTTAAATTTCGGTAAATTTTTNAAATTAAGTTTG
GGCTGNAATCGNATNTTTGTNATAATTTNCCAAAGGCCTTTTTTT
>gi|2764163|gb|R64815.1|R64815 13319 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167H6T7, mRNA sequence
ACTACTCTNACTGTAATCCCTTAGATCTNCTTTNCAAATTTNAATGGCGTCCGGTGATGTTNAGTATCGG
TGCTTCGTTGGAGGTCTAGCATGGGCCACTGATGACAGAGCTCTTNAGACTGCCTTCGCTCAATANGGCG
ACGTTATTGATTCCAAGATCATTAACGATCGTAAGACTGGAAGATCAAGGGGATTCGGATTCGTCACCTT
CAAGGATGAGAAAGCCATGAAGGATGCNATTNAGGGAATNAACGGACAAGATCTCGATGGCCNTAGCATC
ACTNTTAACGAGGCTCAGTCACGNGGAAGCGGTNGCGGCGGAGGCCACCNTGGAGGTGGTTGCGGTGGAT
ACCCAAACGGGCGGTNGGTGGAGGTTACTCCGGTGGAGGTGGTAACTACG
>gi|2764162|gb|R64814.1|R64814 13318 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167H4T7, mRNA sequence
GAAAATGGCTTCCAAGACTTTCCTTCTTTTGGGTCTCTTTGCATTTNTTTNCATCGTCTCAGAAATGGCT
GCNGCGGGCACGGTGAAGTCAGAGAGTGAGGAAACTNTGAAACCTGAACAACATGGTGGTGGATTCGGTG
ACAATGGAGGAGGAAGATACCAAGGAGGAGGCGGCCATGGTGGCCACGGAGGGGGAGGATACCAAGGAGG
AGGAGGACGATACCAAGGAGGCGGTGGGCGACAAGGAGGAGGGGGAAGTTACTNCCGCCACGGCTGCTGC
TACAAAGGTTACCATGGCTGCTCAAGGTGTTGTTCATATGCCGGAGAAGCGGTTCANACTCAGTCTNGTC
ACTAAATCTNCATAATTTTTCAANCCACCATGAGTGTACGGTTTCATTTNTATATACACTTACGGGTGTA
TGTANTATTGCCAATACACTTNCGGTTTAAATNAAGTNCCTTAAGTTTTAGGGGGNAACTTNCGGATTAA
GTTTNNANAATGAATCCCTTNT
>gi|2764161|gb|R64813.1|R64813 13317 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167H3T7, mRNA sequence
AAAAATGAGAAAGTTGTTGGCATCGCCGTTTAGTTCATTACTCGCCGTCGTTTTCANTTCCGTCATCTCC
GTCGTCAGATNCTGCTCTCCTAAAGATCAGACGGCTCTCAATGCTTTCAAGTCGTCACTGAGCGANCCAA
ANCTCGGTATCTTCAACACTTGGNCTGAAAACACTGATTGTNGCAAGGAATGGTACGGTATCAGCTGCGA
TCCTNATTCGGGTCGGGTCACNGATATTTCTNTCCGGGGAGAATCTNAAGANGNCATTTTCCAAAAGGCA
GGCCGGTCCGGTTATATGTCCGGTTCGATT
>gi|2764160|gb|R64807.1|R64807 13311 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167H13T7, mRNA sequence
CTGAGCTCAACGCCATTTTTAACGATTTCNAATCTCTGTNTTCTCTGAGTTGTTCCAAGTAATCGGAGGG
AACTCGTAAAGTGGAAGAATAGGAGAAAGAGAGAAGGAAGAAGATTTNTNAATAGCTCTTGATCTGGTGA
AGAATGGATGCAATTAGAAAACAAGCTAGCAGGTTGAGAGAACAAGTTGCGAGACAGCAGCAGGCTGTCT
TTAAGCAATTTGGAGGAGGGGGATATGGCTCTGGTTTAGCTGATGAAGCAGAACTCAATCAGCATCAGAA
GCTAGAAAAGCTTTACATATCCACTCGTGCTGCTAANATTTACCAAAGAGGTATTTNTNCGTGGTGTNGA
AGGTATATAGTTACAGGGGCAAAACAAGTTGAAATAGGTCCGGAATTNTCTTTGGGTTGCAGGGAATTTG
GTNCCGGGNTTCATGTCCGGNTNGTACCGNTTTACNCCGGGGTCACCTNACCNTTGGGGGCCCCCNCCCC
AATTGGGNGGACCCTGGAAATTTTTAAGGCCCTTGGCCCCAGGTTCTNNCCTTCGGGATGNTTGGG
>gi|2764159|gb|R64806.1|R64806 13310 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167H11T7, mRNA sequence
AGGTCAACAATAAGAAAGAGAGAACAGATAAAGAGATAACAAATGANATGGAGGCTGTTGCTGCTGCTTA
TNACGTCTTCAACAATGTCGCTAAGCCAAACCACAATTACATAGAAGAAGATGACTTATTGAGGTTCATG
ATAAAGGAAGAAGTAGACCTTGTACTCCCATTAATAGAAGATGCCGACACCGGAAAAATCACACGCAAGA
CTTTTACAGAATGGGTGGTTAATGTATACACAAGTCGGAAAACTNTAGGGCATTCACTGAACGGCACAAA
AACAGCGGTTAAGCAGTTGGGCAAACTTATAACTGGAATCTTGNCCCGTTATCACATTCATTTGTTTTGG
NTGGTCTTTCTGGGGTATNGNATCGGCCCAGCTTTTTNTTGGGCTTNTCCCNCACAATTTTTGGGGCCTT
NNNTTTNTTGNNCGGNAGGCCTTTT
>gi|2764158|gb|R64803.1|R64803 13307 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167F12T7, mRNA sequence
AAAGTCTGAAGACAAATTCTTCCATTAGAAGAAGAAGATGGCTCTTCTCTGCTTCAATTCTCTCCCTTCT
CTCTCTTCTCTTTCTNCTTCTNCTTCCTCGCGCCTTCTTCAATCTCCGTCTTTCGCTTCTCCAGTTTTNA
GCCTTAAACCCAACGCTGTCGAGTCCAAGAACAGAGTCTCTCTCAGTGCTTACAGCTTGAACTCTAGCCA
TGGAAGAATTGTGGTGAAGGCGGCTGCTTCTGGCGTGGACGGGGCTGAGCCTGAGAGCAATGAGGAACCA
AAGACTGTTGTTGCTGCTGTTCCAGTGGATAAACTACCGTTGGAATCGAAAGAAAGCTAATGAGNAANCT
GCTCCTTGGAATTNAGGCTTGAAGATGAAGCTGGCCAAAAAGATTAGGGCTCCGAAGGAAACGGCTTGGT
TCGAAANCGTAAAATTNGGGAAGAAGGGGCCGATGGCNACCTTCCAAGGANGANGAAAACAAGNATTTNT
NAGNNGCTNAACTTGNTTNNTG
>gi|2764157|gb|R64802.1|R64802 13306 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167F11T7, mRNA sequence
AGCCGTTTCTACATGTTTATGGAGCTTCGATCGATCAAATTTGAGGAATACTCAGATTTTNNTTTCCTCA
TTACCTGTTTTTNCCAAATCTCTTGATTGATGATTTTGGCATGCAGATGGAATTGAATTCTCTGTTTGTG
TAGCCTCCCTTCTCTGTTTAGCAGTTTCCGGTGAGAAAAAAACAAAAATCGATGGTTGCCCTTTTTCGAC
GTTGATTGTGTTCACCGGATCGGAGTCTTTGACGGCAAAGGATGACAGGAACGTTTCATCGCTTCTNTTG
CAACACGTGTCTTGTTATACGATCGTGTTTTGTTAAAGAGATATCCTTCCTTTAAAGAAATGTAACTAAA
GTGGACCTTTGTTGGGCTGTATTCTGTGGNTCAATTAATAAACATAATCTTTCCAGTGG
>gi|2764156|gb|R64801.1|R64801 13305 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167C9T7, mRNA sequence
ACTTTGGACTCTATGACTCTGTGAAGCCTGTNCTCCTCACTGGTGACTTACAGGACAGTTTCTNCGCTAG
TTTCGCTCTTGGATGGGTTATNACCAATGGTGCGGGTCTTGCATCCTACCCCATTGACACTGTCCGCAGA
AGAATGATGATGACGTCTGGTGAAGCTGTCAAGTACAAGAGTTCTTTGGACGCCTTCAAGCAGATCCTCA
AGAATGAAGGAGCCAAGTNACTCTTCAAGGGAGCTGGTGCCAACATTCTGCGTGCTGTTGCAGGTGCTGG
TGTGCTTTCCGGTTACGGCAAATTGCAGCTGATTGTCTTTCGGTAAGAAGTACGGGATCAGGAGGGTGCC
TAAAGCATTGCTTCTTCCCTCCTTTTTCCGNTTTAAATTNCGGTTTTTAAGGCCNGAAATAAACTNGNGA
TGTTNNTGNAANTTTTTTTNNCNTNAAAGCTTNGGGGG
>gi|2764155|gb|R64793.1|R64793 13297 Lambda-PRL2 Arabidopsis thaliana cDNA clone 167B18T7, mRNA sequence
CCACCACNACCNCCGGTTACCGCAAAAGCCCCAACCTCATCCCCTGGAACCCCATCAACCAATGCACAAG
CACCTAGTGGACAAACCCGAATNACTCTATCTNTTCTACTTTCTGTTTTNGCAATGGTTCTTGCCTCTNT
TCTACTTCTGTNATCAACCCTTGATCTCATCTCCTCTGTTGATAATGTCTTCCACCCTCGTAAGATTTCC
CTGTGTGTGACTCAGTC
>gi|2764154|gb|R64784.1|R64784 13288 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166P17T7, mRNA sequence
CAATCTAGAGAGACCAAAAAGAGATCGGAAGAGATGGCTTCTACCTCCGCAATGTCATTGGTCACACCAC
TTAACCAGACCCGTTCGTNTCCTTTCCTCAAGCCATTACCTCTGAAACCATCCAAGGCTTTGGTTGCAAC
TGGAGGCAGAGCACAGAGGCTTCAAGTTAAGGCCCTCAAGATGGACAAGGCTTTGACCGGTATCTCCGCG
GCTGCTCTTACTGCTTCGATGGTGATTCCGGAGATAGCTGAAGCTGCTGGTTCTGGAATCTNTCCTTCCC
TCAAGAATTTNTTGCTCAGCATTGCTTCTGGTGGCCTCGTCCTCACTGTNATCATTGGTGTCGTCGTCGG
NGTCTTCAACTTTNACCCCTGTCAAGAGNACCTAAGACCTATAATATCTTTTTTTACCATCATTATTGGA
AACCTGGNCCCCCTCCTGNGGAATTCGGTTCAAATGTTGNAGCAATTNACCTTTTGGGNAAAAGNAAATT
TTGTGGNTTCCCNAATTCGG
>gi|2764153|gb|R64782.1|R64782 13286 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166P15T7, mRNA sequence
CCTTAATTNTTTTTNCGTGTATAGGTACAAGTAATGCTATTACAGGTTCGGTGAGCTGACCACAGAATAC
GGCAAGCCACCCGGGTATGATAGAGCAAGAGGAGTGGAGATAGGGAACAAAGATATCAAACTTGAACACT
TAGAAGANGCTTNCACAACATCCAACTGGNTAGTNCGTATTTNCAGAGTTAAACCNCCTACAAATAGGTT
GTNATGCTTCANTGTTACCAAAATGGTTTTAGATAGTGGA
>gi|2764152|gb|R64771.1|R64771 13275 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165O10T7, mRNA sequence
GATGACGACAGCATCTACGGTATTTNTNCTACCGGCCAATGTCACCTCGGTCGCCGGCGCTTCGTCGTCC
AGGAGCTCCGTGTCTTTCTTGCCGATGAGAAACGCCGGTTCTAGGCTCGTAGTCAGGGCAGCCGAAGATC
CTGCTCCGGCTTCCTCTTCTTCAAAAGATTCTCCGGCAGCTGCCGCTGCTCCGGATGGAGCTACTGCCAC
CAAACCCAAGCCACCACCGATTGGTCCTAAGAGAGGGTCTAAGGTCAAGATTCTAAGGAGAGAATCCTAT
TGGTTCAAGAACGTTGGATCAGTTGTTGCCGTTGATCAGGACCCTAAGGCTTGGTACCCGGTTGTGGGTC
CGGTTCGCAAAAGTCAATTTCGGCAAACATATTGNCCAACAACTATGNATTTGGTGAGGTCGAGAAGTTT
CAGGTTTAATGGGGGATTNAAAAAACNTNGNGATTTTTTNCCGGTTTNTCCCGTTTNAAATTNNCCCAAN
CGGTTNTCCCGNAAAGTTTTCCATTTTTTNTCNT
>gi|2764151|gb|R64765.1|R64765 13269 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163O7T7, mRNA sequence
ATCCAAAATCAACCCAAAAAAAGAAAGAAATATGTGGGATGAAACTNTAGCCGGACCTAAACCGGAGCAT
GGCCTTGGCCGNCTCCGCAATAAGNTCACCACCCAACCCCTNGACATCAAAGGTGTAGGAGAAGGGAGCA
GTAGTAAAACTNTGGCGGCGGTGNCCNGGAGTCCTGGAACTCCGACGACGCCAGGTTCGGCGCGTAAGGA
AAACGTGTGGNGAAGTGTGTTTCATCCAGGAAGTAACATCGCCACTAGAGGAATNGGCACAAACCTTTTC
GACAAGCCTTTCTCACCCAAACTNTNCCACCGTCTACGATTTGGCTATACAGCGACGGCACTNGGAGCAA
AGCACCNNTTGAGCCGNGAAGGGTTAGAGTG
>gi|2764150|gb|R64758.1|R64758 13262 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163N14T7, mRNA sequence
AATACAGAAGGAGAAACCTTTGGAACTCCCTCCACAGCCTCCCAAAACCAGGGATTTTAGAGGCAGCACC
ATGGCTCCTTTTGGTGGGAACAACATTCTTGTCCTATACAGTTGTCCCGCAGAATCCTCTCCCAAATACT
TCGTTCAGGTTCTGCACAATGAGCATCCTATTGCAGTGCCAGGTTGTGATGGAAAAGATTTCTGTCCTCT
TGAAGATTTCAAGGCCAAAGTGGTAACTCCTCATCTAAAGCATGCTTTTGACAACCTTTGCAATGCTGAT
CTAAATGACCTGAAACAGAAGNCTGCATCAAGTAAGTTATCTATACTGTCAAGTTGGCTGTTTGGGTCAA
GCCACGGTACCCGAGCTCTAGTTACTTCACAGCTCTTCTTACATACTGGCTGNTTCAGGTTTGACCTGAA
TNNCACAGGGNATTGTTGGCCTGTTTTTTTTTTNNCCCCTGNCANATTTNNTTCTTGGTAGGTCAANCCG
GTAANTTGAANATTTTGGNTTNAGNNTTGGG
>gi|2764149|gb|R64754.1|R64754 13258 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163M21T7, mRNA sequence
AATTCAGATGTTATTGAGACTGTAGCAGAATCTAAACCGAAACGAGCCCCGAGAAAAGCTACACTTGCTA
CTGAAACAAAGGCGAAGAAGAAGAAACTTGCAGCGGGTTCTACAGTTAGAGTTTTATCAGGGACATTTGC
TGAATTTNTTGGGAACCTAAAGAAACTAAACCGCAAAACTGCAAAGGCAACGGTGGGATTTACTTTGTTT
GGGAAGGAGACACTAGTGGAAATTGACATCAATGAACTTGTTCCTGAGATTCAATCTTAAATAGTTTGTT
CACTAGAATGTGAATTTTTTGGTTTGAAATATAAATCCATGATCACTTCAC
>gi|2764148|gb|R64752.1|R64752 13256 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163M16T7, mRNA sequence
AATATTAAGATGACATCTACTATGGTTCTATTCCTCCTTCTTCTTCTTGTGTTTCCGCATATGGATAAAG
CCCTAGGCGCACACGAGGAATCCCAGAAACAAGGTGCAGAAAAGACTTACCATGATGCACGCTTTACTAT
TCCTATTAAGCCAAAATATATTCCTAAGGTTATACGCCCTACGCCAAAAGATCCGCCTATTCCGGAATGT
CTTCGAAAAGGCACATGTAGTCGTCTTCATTTATCTCCTCCTCCGCCCCAGAGGTCTTTCAAAGGCACAA
ACGNACCTGGTCATTGACCTCAATCTAGCTTCGAATGCGTGTGTGTGTGCATGTTTCTTACANNGTGGTT
TGGTTTGTGGCNTCTGTCTTTTGTTTACCCATGCATGTGTTTGTCAAATTTTATAGGTTTGTCGAACCGG
GCCGCTATAATNAAATAAAACTTGNATTTCCCTTTTGTGTT
>gi|2764147|gb|R64751.1|R64751 13255 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163M15T7, mRNA sequence
TTCTTTTCTCTTCTCCTTCCACTTCCACTTCTTCTATCTCTCACAATTCAGCAATGGCTTCTNCTATAGT
NACCTCTAGCTTGAAGCCTTTAGCCATGGCCGATTCTNCCTCTTCTACCATTTTNTCCCATCCTTCCATC
TCCTCTACCATCTNTTCCTCCAGAATTCGCAGCTCCAGTGTTTCCCTCCTTACCGGACGCATTAACCTGC
CCCTCTCTTTCTCTCGCGTCTCTCTATCTCTTAAAACCAAAACCCACCTTAAAAAATCCCCCTTTGTCTC
CTTCGTTGCCCAGACTTCGGATTGGGCTGAAGAAGGTGGAGAAGGGAAGCGTCGCTGTTGAGGAGNNCGA
GAACAAGTTTAGAGGTCACAAAGATGTGAGGCGAAGGNTGNTTNAGGAGCGAAGGAGATTCGNNGCNAAG
GAGNTTNTNAGCGAGGAGGTTTNGG
>gi|2764146|gb|R64748.1|R64748 13252 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163I14T7, mRNA sequence
AAAGCTCATGGGGTAGGAAGCTTATCGTGCAGAAACGTAGGGCTAACCTTAACGACTTTGATAGGTTCAA
GATCATGTTGGCCAAGATCAAGAAAGCTGGTGTTGTCAGGCAAGAGCTTGCAAAACTCAAGAAGGAGATC
ACTGCCTGATCAAATATTATCTACAATTCTGTTGTCTTTCTTTTTTGATTTTGGATTCGGAAATTAGTGT
TTTTGGNACTATCAATATCAGTATGTGCTCAATTATCAGACATTATTCAAGTTTGAAACCTTGTTTGCAA
AACTCAAAGGTTTTTTGNCCTTTT
>gi|2764145|gb|R84194.1|R84194 16153 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159M9T7, mRNA sequence
TTTNAAGCNATNGTTTCCAGGCTAAAGTTGATACNACCAAGAAGGCTGATCCTAAGGCCAAGGCCTTGAA
GGCGGCAAAGGCTGTNAAGTCTGGTCAAGCCTTCAAGAAGAAGGACAAAAAGATTAGGACCAAGGTCACC
TTCCACAGGCCAAAGACTCTTACCAAGCCTAGAACTGGTAAGTACCCAAAANTCAGCGCTACTCCAAGGA
ACAAGTTGGNTCACTACCAAATCCTTAAGTACCCACTCACCACTGAATCTNCGATGAAGAAGATTGNNGN
CAACAACACTCTTGTTTTTCATTGTTGNCATTCGTGCTGNCAAGGAAGGAGGTTAAGGGTNCTTGTTAAG
GAGGTTGT
>gi|2764144|gb|R64742.1|R64742 13246 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159M2T7, mRNA sequence
ACTGATTGCNGGTGAAAAAAGAGAAGAAAACGGTGCGATCAAGAGGATGATAGAACAAGATAAAGGCTCT
TCGGATTTTTTCACGTACGGTGCAAATTTAACGTTTGTNAATCTTGATGAAATAGATATGTATGANCTTG
AGATCAACGGAGGGAAGCCGGATTTCGTAAACTACACGATTCATGGGGTCGGAGCAAAGGTGTTGTTTTG
GTTTTNCCCAAGCAAAACTTTGCAAGGATTGTAAGTGTAGTGATGCCTGANGAAGACCTTGCAAAACTCA
AGGAGGAGGTGACTAATATGATTATATAACTTTGTATCTCCTTCTTGTTGTTATACATAAATGCTGTTTT
TTNACCTCTTTGTAATTTCATTATCGNAATTGTTGGGAAGCCTATCAATAAAATTGTTTGACCTGNTTAC
TT
>gi|2764143|gb|R64735.1|R64735 13239 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159L15T7, mRNA sequence
TCGCATCAATGGCAGAAGAAAAGAGCTTCAAGTATGTAATCGTCGGAGGTGGTGTCGCCGCCGGATACGC
GGNNNGANAGTTCTTCAACCAAGGTGTCAAGCCTGGTGAACTTGCTATCATTTCCAGGGAACAAGTTCCT
CCATATNAGCGTCCTGCACTTAGCAAGGGATATATCCACCTCGAAAATAAAGCTACACTTCCGAATTTNT
ATGTTGCTGCTGGAATTGGGGGAGAGAGACAGTTCCCTCAATGGTACAAAGAGAAAGGTATTGANCTGAT
TTTGGGCACAGAGATTGTCAAAGCAGATCTTGCTGCGAAGACACTTNTNAAGTGGGGNCTGGACAAGTNT
TCAAGTACCCAAAACTTTGCTAGCGGCAACTGGGTTCTCCTGTCATAAGGGTTGTCAAGATTTTGGGNGT
CCNAGGGTGCAAATTNCTNANGATTNTTTTNTTCCCTTAG
>gi|2764142|gb|R84193.1|R84193 16152 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159L11T7, mRNA sequence
GCAACCTTCGATTTTNGTTTATNCGCATCCATCGGAGAGAGAAAACAATCAATAAGCGACCATGTTGGTG
TACCAAGATCTTCTNACCGGTNATGAGCTTCTNTTTNANTCTTTCCCTTACAAGGAGATTGANAATGGAA
TCCTCTGGGAAGTAGAAGGAAAGTGGGTTACTGTGGGAGCTGTAGATGTNAACATTGGTGCCAATCCATC
TCCTGAAGAAGGTGGTGAGGATGAAGGTGTTGATGACTCTACTCAAAAGGTTGTTGACATTNTNGNCACC
TTCAAACTTCAGGAGCAACCAACTTATG
>gi|2764141|gb|R30619.1|R30619 13224 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166K22T7, mRNA sequence
CACAACTCCACGACGAGAGGAAAAAAAAAAACTCAGAGAGACAAATCTAAATGGCGATGATTACGCGCAA
CACCGNCACGCGCCTCCNTNTCCTCCTCCAATCTNAACGCGCCGTCGCCGCTGCCTCGGTCTCTNACCTC
CACACATCCCTTCCCGCTCTCTCTCCCTNCACATCACCGACTTCCTANACCAGACCTGGTCCTCCTTCGA
CCTNCCCTCCTCCTCCTGGTNTCTNTAAAGCGGCCGAATTTNTNATCTCCAAGGTCGATGATCTCATGAA
CTGGGCTCGTACCGGATCGATCTGGGCCTATNACCTTTTGGTCTT
>gi|2764140|gb|R30618.1|R30618 13223 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166K20T7, mRNA sequence
TCACTGTAATCCCTTAGATCTNCTTTTCAAATTTNAATGGCGTCCGGTGATGTTNAGTATCGGTGCTTCG
TTGGAGGTCTAGCATGGGCCACTGATGACAGAGCTCTTNAGACTGCCTTCGCTCAATACGGCGACGTTAT
TGATTCCAAGATCATTAACGATCGTAAGACTGGAAGATCAAGGGGATTCGGATTCGTNACCTTCAAGGAT
GAGAAAGCCATGAAGGATGCGATTAAGGGAATGAACGGACAAGATCTCGATGGCCGTAGCATCACTGTTA
ACGAGGCTCAGTCACGNGGAAGCGGTGGCGGCGGAGGCCACCGTGGAGGTNGTTNGCGGTGGATACCCAG
CGGCGGTGGTGGAGGTTACTCCGNTGGAGGTTGTAGCTTCGGAGGTTNCGCCGGTAAACCGNAGNTTNAN
GAGGTACAACGNCGCNGNGGTTATTTCTNAAAAGTTGTTGTG
>gi|2764139|gb|R30614.1|R30614 13219 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166K15T7, mRNA sequence
TTGTTGGTGTCTCTNAGGAAACNACCACTGGTGTTAAGAGGCTTTACCAGATGCAGCAAAATGGAACTNT
TTTGTNCCCTGCCATTAACGTTAACGACTCTNTCACCAAGAGCAAGTTCGACAACTTGTATGGTTGCCGT
CACTCACTCCCTGATGGTCTCATGAGGGCCACTGATGTNATGATCGCTGGAAAGGTTGCTGTTATCTGTG
GATATGGTGATGTTGGAAAGGGTTGTGCTGCTGCCATGAAGACTGCTGGTGCTAGAGTCATTGTAACTGA
NATTTGATCCCATCTGTGCCCTTCAAAGCTTTTNATGGGAAGGGACCTTCAGGTTCTTACCCCTTNAGGN
TGTTGTNCTCAANAANCTGGTATCTTTTTNTAAACACCANCGGT
>gi|2764138|gb|R30612.1|R30612 13217 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166J23T7, mRNA sequence
TNATCCTTCTTTGGTGGAGGCCCCTTTGGAGGTAATACCAGCCGGCAAAGGAGGCAGAGGCGTGGTGAGG
ATGTTGTTCATCCCTTGAAGGTATCTCTTGAGGATGTGTACCTTGGTACAATGAAGAAGCTTTCACTTTC
TAGGAATGCTCTCTGCTCTAAGTGTAACGGAAAGGGATCAAAATCTGGAGCCTCCTTGAAATGTGGAGGG
TGTCAGGGATCTGGTATGAAGGTGTCTATTAGGCAGCTTGGACCTGGAATNATCCAGCAGATGCAGCATG
CATGTAAATGAATGCAAAGGGACAGGTGAGNCCATCAATGATNCGGGACAGGTGTCCACAATGCAAAGGG
GGCAAGGTCNTTCCTNAGAAGAAGGGTNCTTTAAGTTNATNTGGGAAGGGNNTNCAANCACAGTNAGGAG
TTCNNCATTTAGGCCAANCG
>gi|2764137|gb|R30609.1|R30609 13214 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166H5T7, mRNA sequence
GTTTTTNTCGTAGCTTGAAATAAGATTCATCAGAAGAGTAAATAAACATCAAAATCCAACAAACCAAACT
AGAAAAATNTCGGTAGTTTTACTCTCTNCTACTTCTGCAACANTCACCAAATCCCAATCCAAAAAGATTC
CCTTTTNATCTCCCACCACAAAATTCCCATTAANGGTCTCAATTTNTCCATCAAGATCGAAACTTTTNAN
CAACCCTTTACGNGTGGCGGCGCCGCCGTCTATACCCACTTNGGATTCGGCGGAGGAGAAGCGGNTCGAA
GAAGAATNCGGGTGGTGATAAGGAAGAAGAAGGGGTCTGAGTTCAAGTGGG
>gi|2764136|gb|R30608.1|R30608 13213 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166H4T7, mRNA sequence
TTTGAGAAACAAAAACGATGGAGATGATGAAGATTGATCCTTTATTCGATCGTNCCAGTAAGCTTAAAGC
TTTCGATGAAACGAAAACGGGTGTNAAAGGACTCGTCGACTCCGGAGTTTCACAAGTTCCACGCATCTTT
NATCATCCAACTGTCAAATTATCAACCCCAAAACCACTTCCCTCGGACCTGCTACATCTCAAGACGATCC
CAACGATCGATCTCGGAGGACGGGACTTCCAGGNCGCGATTAAGCGCAATAACGCGATTNAAGNGATTAA
AGAAGCAGCAGCGANGTNGGGGGTTTTCTTCCAGGGTGNTCAANCATNGNGGTTTCGNTTTGAACTTNTT
>gi|2764135|gb|R30606.1|R30606 13211 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166H15T7, mRNA sequence
ACATGATTGCGGCTCGGAAAAGAGAGAGGGAGTACTTTNCCAATACTACTGAGTATAGGCACCTTGCTAA
TAAAATGGGTTCCGAGCATTTGGCAAAGATGCTCTCCAAGCATCTAGAACGTNTGATCAAGTCGAGAATT
CCTGGCATTCAGTCACTTATTAACAAAACAGTATTAGAGCTGGAAACTGAACTAAGTCGCCTTGGAAAGC
CTATTGCAGCTGATGCAGGGGGGAAGTTGTACTCAATAATGGNGATATGTNGGCTTTTTGATCAAATATT
CAAAGAGCATCTTGATGGAGTGCGNGCTGGTGGTGNAAAAGTGTCCANCGTGTTTTTTAACCNCCTTNCT
NNGGTCTTAAGGNGCTCCCNNTTTTTCAAGAAGNTTTGCGGT
>gi|2764134|gb|R30605.1|R30605 13210 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166H14T7, mRNA sequence
ACTCTNCGTTCGTTTCATCTCCCAATTNAGTTTAACGACACCAAATTCGTCTCACGGCCTTGTTTCCTGG
CGAGATCCTTCCCGGTGGTTCGTTGTTCAAGCACCAGAGACGTACCTAAGCTTGAACTCTTCAGCCGCGA
AAAATTCGACCGGATTCTTCAAGATCCGCCACTTATTGAAAAAGCCGAATCCGAACTCTCAGATTACTGT
TCGACGCTTGAAGGTGATGACTCTTACAGTTTCTGGAGAGCTTACTTTGNACTCAAAGATCTCGAAAGAN
AGNAGCCAANGGTTGAAGTTNAGAATTTNATTTTNCCAAAACAGGTGGTTTTAAAATCGTTAATCGGGGG
NGTTTNNAATGGGNGTTNCTTNAATTGGG
>gi|2764133|gb|R30601.1|R30601 13206 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166E1T7, mRNA sequence
TCATTGCTCTAATTGTATTGATGGTTCTAACTTTNAGTTTTGCTTAANCGTGTAAACNCTGTAGTTGAAG
TTTTAGTGGAACTTGGTTTAGTAGAATAGCTGGTTGTTGGGATCTGATGGCAGATTAGAGAAATNCTNAT
TGTAACTTTTTAGAAACTGCAAACTTCTTTNATTAGAACTTAGTTTGTAGGTATCATAGAAACTAGTTGG
AGCTGGAATGCTACAAGAGGTTATTCTATGGTTGNAACCTTACTTCCTTGTAACCAAAGGCAGGTTTAGT
CTTTAANGNGGTGTTCAGGTAATNAAGGTTTGNNCANCCTCCACA
>gi|2764132|gb|R30588.1|R30588 13193 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166D12T7, mRNA sequence
AACTAACAATGATAATAAGAAGCGCGTNTNCACTGGACCTTAACCTACGCNCCGCCCAGAAACCGTCTGT
NCCAAGGNTGGTAACCACGGCTCGAACCGTCTCTCCTGCTACTCCTCGTNTTGCTAAACCGATTACAAGA
GCTTCTTCAGATGGAAACCTCTACAAGATTCATTCGCCGGAGAGCATAACGAAAACCATCAGCGTATATC
ACGAAGAAACGGCGTCTTTAAGGGTTTTGGAAGGNTCTCGACTCCCCCAAGGAGGTTCCAACGGTGGATT
TGGTGGTAGAGNCGGAGATGGTTCCGGAGGTNGCGGTGGAGGNTGNAAGGTTGGNAGCNTNGATTGGTTA
TTT
>gi|2764131|gb|R30585.1|R30585 13190 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166C2T7, mRNA sequence
TCCAGCCACCGTAGGGNTAATTCCGTAAATTTNTAACANAAACTCCATTCCCGCGGCGTATGCAGAGGGC
AATCCCGTAAACTTAACCCATCTCCGGTGATGAATAATATCAATTCCTTCACGCCGGAGTGATTTTCCAC
AAAAAAATAAGATATGAAAGCAAATCGCGGCGGCGGAGAGCACGGCCAACACGAGGCTCTAAAGCTTTCC
AGTTTCTNCTTCATGCCGGAGCGGCCACGTGATTACCTCGTGCTTTTAACACGTTTNTCCGTCCTCACGT
GCCTCATCGTCTCCGTATCTNTTNGTTCTCCGGGNCACTTTTTTATCCCCTTCCGGTCGAGACTATTTCC
ACCACCTACGGGTCTCAAATTNAACCGCCGTNNCCNCAAAAAGGCCATTGNTTTTNCTTNCGTNCG
>gi|2764130|gb|R30581.1|R30581 13186 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166C18T7, mRNA sequence
ATTAGCTACATAAGTNCTATAATGACCCTTTACGAAGGAGATGTCATCTTGACAGGCACACCAGAAGGTN
TTGGACCTGTAAAGATAGGTCAGAAGATAACGGCCGGAATCACCGGTCTATCTGAAGTTCAATTCGATGT
GGAGAGGCGTGTAAAGCCCTTGANCTAATAAGTGGTTTTATTTATCTTTCATACAAAAATGTCAATTTTA
TAAAANCATCTCTAAAATTTNNATCACTTACTGTGTTTCCTAAGGAAGGGAGAAATAAAACTNGTTACTC
ATTTNATTTGTAATCTCTATAACCANTGGCTCTAAGNCCGGTTTAAATTGTTTAAAAAANNANAC
>gi|2764129|gb|R30570.1|R30570 13175 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166A6T7, mRNA sequence
CCACAAACCTATTGGCCCTACGGAAAATCCCGCGACTACCCCAACGGCAAGTTTTCCGACGGCCACATCG
TCCCCGACTTCATCGCTGATTTNATCTCTATTCCGAATGGAGTACTCCCACCGGTGCTTAAACCGGGCGT
TGATATTTNACGTGGAGTCAGCTTTNNCGTCGCCGATGCTTCTATTCTCGGAGCGCCGGTTGAATCTATG
ACACTAAATCAACAGGTGGTTAAATTCAAAAATATGAANTCGNATTGGAACGNCAGCTACATCGAGAAAT
CACTGTTTATNATATNCATTGGTACGGAAGATTATTTGANTTTTNACCCAGGGCCAACCNCAATTGCAGA
CGGTTCTTNCTNAAGAA
>gi|2764128|gb|R84192.1|R84192 16151 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165N5T7, mRNA sequence
AAAGAAAACTGGTGTACGCGGCCTAGTCGATCTNCTGCTTGGAAACGCAGGTCCTTTTNCTGCATGTGGA
GATTGGNTCTTGCCGGACCTCTCAATCCAGGGATCAATGAAGCTAAACGCTAGTNTGCAGACTTTTCCAA
ACACGTTCTACTTCAGCTATGCGACTAAGCGTACCACTAAACCTNTTGGAATNATGACTGTNCCTTCAGG
TGTNATGGGGATTNANCCTCTGCTTTTAANCCGCGTGTTGCAGATGAGTCAGTGGCAATTTCCTCGTG
>gi|2764127|gb|R30560.1|R30560 13165 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165N2T7, mRNA sequence
AAGTGTCGAACAAATACTACTTAGGTCCAGCTCCATTGGAAGAAATGGCGAGGCAAATCGCTACGGCTTC
GGGACCTTNTGGGAACAACCGAGAGTATCTTTNCAAGCTAGAGAAAGCAATGTTCGACATTNAGCATGAG
GAAGAGTATGTAATTGATTTAGCGNATNAGGTTAGGAAGCAACTCGATTTACCGGAGGAAGTGAAGGCAT
TGTTGAAGCCTATTGTTTCTNATGTATCCGTCAAGTCTCAAGCTCATGTTTCCACTCGTCAACGGGTCTT
TGCATCATGAAGNCAGCAAAAGTTATGGGGCTAACTTAAAAAAGCATTNTGGTTGNCGNGGGCTAATTNT
TAACCTCCTTTATTCTTTCCAGCNTTAATATTTTGGNTCANCATCTNGACCCNT
>gi|2764126|gb|R30557.1|R30557 13162 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165N1T7, mRNA sequence
TCCTAGATTCATATTCAAATCAAGAAATNACTCTNGCTAAGAACCAAAAATCATCATTGTNACGACTATA
CAAGAAAGTTTCCTCGAAGAGATCAGAATCGTCAAGAAACCTTGAAGACGAATCAAGAACGAGCAGTAAT
AGTAGCGGAAGAGGCTCGTTAAACGTTAACGAGCTAAGANCCGTTTTTAACTATATGGNTGCAAACTCAG
ACGGGAAAATNTCCGGTGAAGAGCTACAAAGCTGCGTTAGTCTCTTAGGCGGCGCGTTATNGTCACGTGN
GGTGGTGGNAAGTGGTGANGTCANTCAGNCGTTGNCCGGTGACGGGTTTTTT
>gi|2764125|gb|R30551.1|R30551 13156 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165L19T7, mRNA sequence
GTTGAAGCTTTTACAACTTCCTTGCTTTCAAATCCTCCAGTGNTAATAAAAAGTTTAATTCTTGGCAGAT
TCTTTTNTTTGCCACTACAAAAGCACAATTATTTNTCCGAATAATTTATTATGAAAANCAGGTTTGCAGA
GATGTGGAAAGAGCTGCAGATTAAGGTGGCTTAACTATCTAANGCCTGGGGTTAGANGGGGCAANTNCAC
TCCTCAAGA
>gi|2764124|gb|R30550.1|R30550 13155 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165L17T7, mRNA sequence
AAAAATGTNTTGCTGTGGAGGAAACTNCGGATGTGGATCTGGCTGCAAGTNCGGCAACGGTTGTGGAGGT
TGCAAAATGTACCCTGACTTGGGATTCTCCGGCGAGACAACCACAACTNAGACTTTTGTNTTGGGCGTTG
CACCGGCGATGAAGAATCAGTACGAGGCTTCAGGGGAGAGTAACAACGCTGAGAACGATGCTTGCAAGTT
TGGATCTGACTGCAAGTGTGATCCTTGCACCTGCAAGTNAAGAAGCCTTTTTAAATAAGCAGAGATAATN
CGAGTCTNTTTTAATTAATTTAAGTTATTCAANTAAGTAAACCCATATTTTAGGATTGGTTGTTTTTAAG
GGTTTGGGTTTNATGTGTAAATAANTGGCNTTCAANCTTTATCTTTTTAGNCNGTTCAATTGNCCTTTTG
GNTGTTTGTTTTTGA
>gi|2764123|gb|R30549.1|R30549 13154 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165K11T7, mRNA sequence
GAAAAAAGAAAGATATGGCAGGNCTCATCAACAAGATCGGAGACGCACTCCACATTGGAGGAGGCAACAA
GGAAGGTGAGCACAAGAAGGAAGAGGANCACAAGAAACACGTTGACGAGCACAAGANTGGTGAGCACAAA
GAAGGTATTNTTGACAAGNTCAAAGACAAGNTCCACGGTGGTGAAGGTAAAANCCACGTCGGAGAAGGCA
AAANCCACGNCGGTG
>gi|2764122|gb|R30547.1|R30547 13152 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165I6T7, mRNA sequence
GTTCGAGAGAAGAATAGTTTGATCATCTTGTGAGAAAAATAATGGCTGCTTCANTNATGCTATCTTCGGT
GACATTGAAACCAGCTGGTTTCACGGTGGAGAAGACGGCGGCTAGAGGATTACCGTCGCTCACAAGAGCT
CGTCCCTCCTTCAAAATTNTCGCCAGTGGCGTCAAGAAGATCAAGACCGACAAGCCCTTCGGAATTAACG
GCAGCATGGACTTGAGGGACGGCGTCGACGCTTCCGGCAGAAAGGGCAAGGGATACGGTGTTTACAAGTA
CGGTCGACAAGTATGGAGCTAACGTCGATGGATACAGTCCTATTTACAACGGNGAACGANGTGGTCAAGC
GAGTNGGTGACGTGTACANGGGTGGNGTCACCGGATTTGNCAATTTTGGGCGGTAACTNTCGCCGGAATT
TTTTTCCCGGNNGGTGCTTTTNNTTNTTNTTCAACANAAAGNCTTTTGGCTNACT
>gi|2764121|gb|R30544.1|R30544 13149 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165I15T7, mRNA sequence
ATGGGGTTCAAGTTGGTGAGAGGGGCTTACATGTNTAGCGAAGTAGCNTNTGGCGGATTCCCTGGNTTGC
AAGTCGCCAGTCCACGACACAATTNAGGATACTCACTCTTGTNACAATNATTGTATGACATTCCTGATGG
AGAAAGCATCAAACGGTTCTGGTTTCGGTGTCGTTCTCGCAACACATAACGCTGATTCGGGGAGACTTGC
GTCGAGGAAAGCNAGTNACCTCGGGATCGATAAACAGAACGGGAAGATAGAGTTTNCACAGCTATATGGT
ATGTNANATGCATTGTCCTTCGGGTTAAAGAGAGCAGGGTTCAATTGTTTAGCAAGTACAATNCNGGTTT
TGGACCCCGTCGNAACCCGCTATTACCCGTATCTTTTTTCCG
>gi|2764120|gb|R84191.1|R84191 16150 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165C6T7, mRNA sequence
CCAATCATCGGAGCAATCATAATCCTCTCCGTNTGCCCCGGAATCTNCATCTNTTTCCGTAAACGAACCA
AACAAATCGAGGAACATACAGATTCANAATCCGGAGGAGAAACATTATCANTCTNCAGCTTCGACGGCAA
AGTCCGATACCAAGAGATCATCAAAGCAACAGGAGANTTCGATTCAAAATACCTAATCGGAACCGGAGGA
CACGGCAAAGTNTACAANGCAAAGCTACCAANCGCAATCATGGCGGTGAAAAAGCTAAACGGAACACCAG
NCTCATCA
>gi|2764119|gb|R30519.1|R30519 13124 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165C16T7, mRNA sequence
ATCATCTNTGGNATGATACTGTCGCTGGTCCACGGCCAGAGAACGGCCTTGGCAAGCTTCGTAAACACCA
TACCTTCAGTTTCCNACCTAGCTCCGGCAATNATCAATCGGAAGCTGGAAGTGCGAGATCGTACGGTGAG
GATTCGCTACCGGAAGAAGCAGTGAAAGTNACACGTAGTATCATGATAATTAANCCACCGGGTTACCAAG
GCAGTTCAGCTCCAGCTTCGCCTGCNGGTTCAACTCCGCNGCTATCACCTTTTTTTCCGCNGATGTCTTC
CGTTCTTTGGGGGAAAGGAACCCTTTCGGTTTAGGGAGNNCGGGTCGACGTNGGNTT
>gi|2764118|gb|R30514.1|R30514 13119 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165A10T7, mRNA sequence
AATAAACAAGATAAATGGAGGGTCTAATTCCGTTAGTATACAAAGCCGTCATGCAAATCCGTTACGGTAA
CGAGTCGCAGCAACTTTNTNCTTCTTACTACGTTCGTNTTCCCGGTGATTCGGGTCGGTTTGTAAGATCC
GATTTAGATGTATCGGGTCCTGGNTCTAATTCCTCCAATAGGGCGTCGTCGTCGACAAGCACAACTACGT
TTGCTGTTTACGNGGGAGTCCAGTCACCTGTTTCTCGTCAGGTTGTCACGTGATTCACACGCGCTTTTTG
AAGGAACCTNAAGTTGCGTGTNAGGGAAAGGGTTCGTGACTTTTTGTTTTTTGTGCGTTTTTTTTTTTTG
TAAGTNNAGGCTTNGNNCCGGCTTTAATNAAACCNGCCTGNAAAAA
>gi|2764117|gb|R30513.1|R30513 13118 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164O14T7, mRNA sequence
CACCATTGCNACACGTNCTCCACGAACTTNCCGATGCCCAGTCGTCGGAGACATAGCTACACCGTCGGAT
CTCCTGCAACCACATCTTCCAATTACAGTAACACTACTTTAACCGATCGTNCCTTCCCGACAACCCCTGC
CCGTACATCCACCGNCACAACCACCTCCATCGCTCGTGGCATCTCCGGTATCTTCATCAACTGCTTCANT
CCTCCCGATTCCGTTTCCTCCAACTACATCGACANTTCAAAGTACTCTTCCGNNANTAAATATCCGTAGT
AGACGTAGGTTGAACAGGAAGTAGTNGGTNTACAG
>gi|2764116|gb|R84190.1|R84190 16149 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164H8T7, mRNA sequence
CTGCCAGTAGTCATATGCTTGTTTCAAAGATTAAGCGATGCATGTNTAAGTATGANCGAATTCAGACTGT
GAAACTNCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTAACTACTACTCGGATAACCGNAGT
AATTCTAGAGCTAATACGTGCAACAANCCCCGACTTNTGGANGGGACGCATTTATTNGATAAAAGGTCGN
CGCGGGCTCTGCCGT
>gi|2764115|gb|R30500.1|R30500 13105 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164G19T7, mRNA sequence
GTNGCCTGTAAAGTGCTGATCGTNCTGTGAGGACAATCCTTGATGCCATAGAACAGGTCGGAGGGATATA
CGTTGTGACTGCAGATCATGGAAATNCTGAGGACATGGTTAAAAGGGACAAATCCGGCAAGCCTGCTCTC
GATAAGGAAGGGAACCTTCANATTCTTACCTCTCACACCCTTAAACCAGTGCCAATTGCCATAGGAGGTC
CTGGCTTGTNAGCAGGAGTTAGGTTTAGACAGGATATCGNGACACCTGGGCTTGCAAATGTAGCTGCGAC
AGTNATGAACCTCCATGGATTTNTGGCCCCGAGTGACTATGAGACAAGTCTGATCGAAGTCGTCGNGAAG
TGATGGATTNCTTGTTGTTGTAGTTTCTTTTTTAAAAGTCCCACCTGAGCCTCTATAGNCTTCTGNNTTC
TNTTTTAAGNTTACTTNTTTTCACCNGNTCGTCTA
>gi|2764114|gb|R30499.1|R30499 13104 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164G18T7, mRNA sequence
GCAAGATATCTGGATACGCGGAAAATAGAGAGAAGAAATCAAAAAGCATATTTTNATTTTATCTTTGAAA
AGAAGATTATTGTTTTNAGTCTACAATGGTGACTCTAAAAATGGAGATTTGCATCGAGTTGTTGAAATTN
ACCGTAGATTTCNTCGCCGCCGTTGCAGAATCAATCGAAGTAGCTTTCCGCCATCGTCCTCCACCGGTGA
TTCAATATTCTNCAGTGATGTATGGTCGCCGGAGTAATTACACCGCCGTTCCCATTCCTCTCGTGGGGTT
TCTGTAGTTAATATATTCTCCTTTTGTGGTTCTNTTGTTTTTTGTTCATNCTTGTTCTATTATAAATNAC
CTCCTTGCCTCGGACANAAAGGTNTATTTCTNATTGNAAGANCAAGATGTGTTTTGTGTATAAACCCCCA
AAAATCNCGNNAAGTTTACGGTGACCCGTGGTATATAAAAGTTTTGNNGGTTCCCCGATTGT
>gi|2764113|gb|R30496.1|R30496 13101 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164F22T7, mRNA sequence
AGCACGGATTTGTGTACCGTGAGCACGGTAACTCACCCGGATACTATGATGGACGGTACTGGACAATGTG
GAAGCTTCCCTTGTNCGGTTGCACCGANTCCGCTCAAGTNTTGAAGGAAGTGGAAGAGTGCAAGAAGGAG
TACCCCAATGCCTTCATTAGGNTCATCGGATTCGACAACACCCGTCAAGTCCAGTGCATCANTTTCATTG
CCTACAAGCCACCAAGCTTCACCGGTTAATTTCCCTTTGCTTTTGTGTAAACCTCAAAACTTTATCCCCC
ATCTTTNATTTTATCCCTTGTTTTTCTGCTTTTTTCTTCTTTCTTGGGTTTTAAATTTCCGGACTTAACG
TTTGTTTTCCGGTTTGCGNAGGACAATATTCTATCGGNTTTCTCAACTGTCTGATGNAATAAATAATGGT
AANTGNTTCTAT
>gi|2764112|gb|R30495.1|R30495 13100 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164F21T7, mRNA sequence
GCATTTTGGAAACCCGAAGCTTAAGTNATGTCGCTGCGATGCCTTCCCCCTTGAACGGAGCTTTTAATCG
CCCGATTTCTATGCCGCCGCTGGTTTTACCTGAGTTCGATCAGAATCAACCGGGTTTNATCGNAGAAAAG
AGCTTCGGGTTCGGGCTTCCTAGTTTTNCTTTTAATGGATCCANGGAGCTAATGGCTGTGCCTAANAAGA
AGATTTCTAAACACAAGAGAGGGATAAGAAATGGTNCAAAGGCTCTTAAGNCTGTNCCNCTNATCATCCG
TTGCAGGAGTTNCGGGCGAGTCAAG
>gi|2764111|gb|R30492.1|R30492 13097 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164E21T7, mRNA sequence
GACGAGTTTGAACTTTAGGATTCAAGGTCACAACTTAGTTCTTGCGGAATCAGAAGGNTCATACACAGTT
CAACAAAACTATACAAGCTTGGATATTCATGTTGGACAGTCTTATTCTTTCTTGGTTACAATGGATCAAA
ACGCGAGCNCTGATTACTACATTNTNGCGAGTGCTCGGNTTGTTAACGNAACCATATGGAGANGAGTCAC
TNGAGTTGGANTCTT
>gi|2764110|gb|R30491.1|R30491 13096 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164E17T7, mRNA sequence
CACGGTACGGAGCCTCTAGAAGCGGTGGCGATGATTACCGTGTTGCGTCGAGGTGGTGCTGACGTGACGG
TGGCGTCTNTTGAGACTCAGGTTGGCGTTGATGCTTGTAATGGCATCAAGATGGTCGCTGATACTCTTCT
CTCTNATATTACCGACTCTNTTTTCGACCTNATTGTGCTCCCCGGAGGCTTCCCGGTGGCGAGACTCTTA
AAAACTNTAAATCTTTAGAGAACATGGTCAAGAAACAAGACTCTNATGGCCGNCTTAACGCAGCTATATN
TTGTGCTCCTNCCTTGGCTCTTGGTACTTGGGGTCTACTAGAAGGCAAGAAAGCAACGGGTTACCCCCTT
TTNATGGAGAAACTTTTNGGNTACTTTTTTGCAACNNGCCTGTTGGAGTCAANAGTGCAAATTTNNTGGA
AGGAATAGTGACCACTCGTGGGCCAGGGAGCCACCCATTTGNATTCTNCCATCACGG
>gi|2764109|gb|R30489.1|R30489 13094 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164C9T7, mRNA sequence
GTCGTCGTTNAGAAACCTTCAAAAATGGCTGGAAAACTCATGCACGCTCTTNAGTACAACTTTNACGGTG
GTGGCGCCGCCGGATTAGAGCATGTNCAAGTTCCGGTTCCAACACCAAAGAGTAATNAGGTTTGCNTGAA
ATNAGAAGCTACTAGTCTAAACCCTGTCGATTGGAAAATTCAGAAAGGAATGNTACGCCCTTTTNTACCC
CGCAAGTTCCCCTGCATTCCAGGTATTCTAATAGCTTTNAAGATTTTAGTTTCTGTATAGANGAAAAAGG
TT
>gi|2764108|gb|R30480.1|R30480 13085 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164B9T7, mRNA sequence
CACAGCAACAAACAGAGAAAATNTGTGGCGGTGCTATTATTTCCNATTATGCCCCTCTCGTCACCAAGGC
CAAGGGCCGTAAACTCACGGCTGAGGAACTCTGGTCAGAGCTCGATGCTTCCGCCGACGNCGACTTCTGG
GGTTTCTATTCCACCTCCAAACTCCATCCCACCAACCAAGTTAACGTGAAANAGGAGGCAGTNAAGAAGG
AGCAGGCANCANAGCCGGGGAAACGGNGGANGAGGNAGAATGTTTNTAGAGGGATACGTAAGCTT
>gi|2764107|gb|R84189.1|R84189 16148 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164A11T7, mRNA sequence
CCGGGCCNGAATTNCCAGGGNNGCCCACTGCGTCCGGCCCCTAGCCGTCGCTGACAGCCTCCAATATCGG
CCGATTCCATTCGCCGGAGTATGTTGACTTCCTCGCTTCCGTTTCGCCGGAATCTATGGGCGATCCTTCC
GCTGCACGAAACCTAAGGCGATTNAATNTCGGTAAGGATTGTCCTGTCTTCNACGGACTTTTTAATTTTN
NCCGTGCTTCCGCCGGAGGTTCTATTGGTGCTGCCGTCAAATTAAACAGACAGGACGCTGATATCGCTAT
CAATTGGGGCGGTGGGCTTCACCATGCTAAGAAAAGCGAGGCTTCTGGGTTTTGCTATNTAAACNACATC
GTGCTAGGNATTCTGGGAGTTTNCTCAANAATGTTTAAGAGGNGTTCTCTANAATAGATAATT
>gi|2764106|gb|R30470.1|R30470 13075 Lambda-PRL2 Arabidopsis thaliana cDNA clone 163E7T7, mRNA sequence
GTTTCACCGCCGTCTCTCTCTATATCAAAATGGGTCGCCGTAGCTCAGGAGGAAGATCTGCCCCTCGCCC
TCGTCCTGCTGCTGCACGCAGCCCAGCTCCTCAACCTGTACACCGTGCACCTCCTCCAGCTCCAGCTCAG
GCCAGCGGTGGTGGTGGTGGCATGTTCTCAGGCATTGGTTCAACCATTGCTCAGGGTATGGCTTTTGGTA
CTNGAAGTGCAGTTGCACACAGGGCTGTTGATTCTGTNATGGGTTCACGAACCATTNAGCATGAGGCTNT
TGAGGCTGCTTCTTCATCNGNAGNCCCTTCTGGAAGGGCCCATGNNTTTCNTAGNTCCCNGTTAACATNC
ATGNCTTAAGGCTTTTCCAAGGNTT
>gi|2764105|gb|R30450.1|R30450 13055 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162L15T7, mRNA sequence
GGAGAGGCGAATTCGAATCGAGAAGATGGTGTCTGGCTCAGGGATATGTTCAAAGCGTGTCGTTNTTGAC
GCACGTNACCATATGTTTGGTCGTNTTGCTTCGATCATAGCTAAAGANTTGCTCAATGGACAGAGTGTTG
TTGTTGTCCGATGTGAGGAGATTTNTTTGTNTGGTGGTTTGGTTCGTNAGAAGATGAAGTACATAAGGTT
TCTNAGGAAACGCATGAACACTAAACCTTCTNATGGNCCTATTCATTTCCGAGCTCCGTCNTAANATCTT
CTGGCGTACCGTTCGTGGGATGATTCCCACACAAGNCCCAAGCCG
>gi|2764104|gb|R30447.1|R30447 13052 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162K7T7, mRNA sequence
ACTTGTNAAGAATTCACCTTTTGAGAGGCCCAGTTTTGAAATATGGCTGGCCAAAACGCGCGTTTNAATG
TGGTTCCCACTGTNACTATGCTCGGGGTTATGAAAGCNCGTNTTGTTGGCGCTACAAGAGGTCATGCTCT
CCTCAAGAAAAAGAGTGATGCTTTAACTGTTCAGTTTAGGGCACTTCTCAAGAAAATCGTTACAGCTAAG
GAGTCTATGGGAGATATGATGAAGACATCGTCTTTTGCTCTTACCGAAGTAAAGTATGTTGCTGGTGACA
ATGTCAAACATGTTGTCCTCCGAGAACGTTAAAGAAGCTACTTTGAAGGTTCGTTCTCGGACAGNGAATA
TCGCTGGAGTNAAGCTGCCCTAAGGTTTGATCACTTCTCTTNAAGGGTGGNGACCNNGGATTGGNCTTNN
CCGGNTTAGCTAGGAGGNGGNCAACA
>gi|2764103|gb|R30442.1|R30442 13047 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162J24T7, mRNA sequence
CTGTGTCTATGCAGCGATATGTAAGCATGAAGGGTCTCCGTTGTTGTTTCCTGGGAGCAAGAAAGCTTGG
GAAGGGTTCATNACGGCTTCTNACGCGGATTTNATTGCAGAGCAGCAGATTTGGGCGGCGGTTGATCCGT
ATGCNAAGAACGAGGCGTTTAACTGCAACAATGCTGATATCTTCAAGTGGAAGCATCTNTGGAAGATTCT
AGCTGAGCAGTTTGGGATTNAGGAGTATGGATTTNAGGAAGGGAAGAATTTNGGGTTGGTGGAGATGATN
AAAGGGNAAGAGAGAGTTTNGGAGGAGATNGTTAAGGAGNATCAATTNCAAGAGAAGAAGCTTTAGGAAG
TTNGTGTGTGGGTGGTTTTCCTGNTGTTATACTTTGGAGTTTGAAGGGAAAT
>gi|2764102|gb|R30441.1|R30441 13046 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162I8T7, mRNA sequence
AGANTGGTTTAGCTTTTTTNTACCGTACATCTTCTTCCCAGAAACATGGCTGAGGCTTCTAATTTGTTGG
AATGGCCTAAGAAGGATAACCGTCGTTTTCTCCATGTTGTCTACCGCGTTGGTGATCTTNATCGCACCAT
TGAGTTTNACACTGAGGTCTTTGGTATGAAGCTGTTGAGGAAAAGAGATATCCCNGAGGAGAAGTATTCT
AATGNTTTTNTTGGTTTTGGACCNGAAACATCTAACTTTNTTGTGGAGCTCACATATAACTATGGTGTTA
GCTCATATNATTATTGGAACNGGCCTTTNGGGCATTTTTGCCCATTTNNAAACTCAAAGATGTTTCCAAA
CTTGGTTGNAGAACGTCCGTCCCAAGGGGGTGAAAA
>gi|2764101|gb|R30438.1|R30438 13043 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162H8T7, mRNA sequence
TCCTTTGGTGGCAAACACATCGACAGATAGAGAGAAACGATGGCGTCGAACTCGCTTATAANCTGTGGCA
TAGCCGCCGTGTACCCTTCGCTTCTTTCTTCTTCCAAGTCTAAATTCGTATCCNCCGGAGTTCCACTCCC
AAACGCCGGGAATGTTGGTCGTATCANAATGGCTGCTCACTGGATGCCTGGCGAGCCACGACCAGCTTAC
CTTGACGGTTCTNCTCCTGGTGACTTTGGGTTTAACCCACTTGGACTTNGAGAAGTTCCAGCGAACCTTG
AGAGATACAAAGAGTCAGAGCTCATCCACTGTAGATGGGCTATGCTCGCTGTTCCTGGGATTTTGGTACC
AGAAGCATTAGGATATGGAAACTGGGTTAAGGCTTCAGGAATNGGCAGCACTACCAGGGGGTCAAGCCAC
TTACTTGGGNAACCCNGTCCCCGTGGGGTACTTTTNTCCACAAATCTTTTGNCATTGAGGTTTTTTAGGC
CNTTTNAATTTTTTTGNGCANCCCNNNNNAAGTNTTGGNGAAAAA
>gi|2764100|gb|R30437.1|R30437 13042 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162H7T7, mRNA sequence
GATTTGTAAGAAAATGGCTTCCAAGACTTTCCTTCTTTTGGGTCTCTTTGCATTTNTTTNCATCGTCTCA
GAAATGGCTGCCGCGGGCACGGTGAAGTCAGAGAGTGAGGAAACTNTGAAACCTGAACAACATGGTGGTG
GATTCGGTGACAATGGAGGAGGAAGATACCAAGGAGGAGGCGGCCATGGTGGCCACGGAGGGGGAGGATA
CCAAGGAGGAGGAGGACGATACCAAGGAGGCGGTGGGCGACAAGGAGGAGGGGGAAGTTACTGCCGCCAC
GGCTGCTGCTACAAAGGTTACCATGGCTGCTCAAGGTGTTGTTCATATGCCGGAGAAGCGGTTCANACTC
AGTCTGGTCACTAAATCTACATAATATATCAACCACCATGAGTGTACGATTTCATTTATATATACACTTA
CGTGTGTATGTNATATGACAATACAACTTACGTTTGTAATGAAGTGCCTTAAAGTTTAAGAGGNNGAANC
TTATCGGGAATAAAGTTTCATAANTGTAANA
>gi|2764099|gb|R84188.1|R84188 16147 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162H5T7, mRNA sequence
CGCAAGATTCCTTTNAAATTCTAACTTGCAGCTATGGGTAAAGAGAAGTTTCACATTAACATTGTGGTCA
TTGGTCATGTTGATTCTGGAAAATCGACCACAACTGGTCACTTGANCTATAAGCTTGGNGGTATTGACAA
GCGTGTNATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCCTTCAAGTACGCATGGGTG
TTGGACAAACTTAAGGCCGAGCGTGACNCGGGTATTACCATCGNTATTNCTCTATGGAAGTNCGNGACCA
CCAAGTACTACTGCACAGTCATTTGATGCCCCNGGACATCGTGNTTNNTCAAGGA
>gi|2764098|gb|R30435.1|R30435 13040 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162H21T7, mRNA sequence
AAAAGATGGAGCAATCTGAAATTNTGATTGCATAATCCACTAGTAAACGTCACAAAGCAATTGGGCATGC
CCATGGACGTTNATGGAGCTCTAGGGCTTCTCCGTTTTGGGTATCTTGCTATTGGCTCTCATATTCCATT
GCCTTGCGGANGGCGTCGCTGCTTTTACCGTTTGGNACCGGCCATGAGATCTATATTCCCCTGTATTTTG
GNTTTAAGNTTTATCTAGTTAGGATTGTATTTAGCCAATNAGGACATCAGATTATAAAAGAACACCATCT
TTNGGGNCTGATTAACATTGNTGGNTACTTCTGC
>gi|2764097|gb|R84187.1|R84187 16146 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162H18T7, mRNA sequence
ATTCTTTGCATTANCTCTTCGATCTCTCCAACTCTCCAAAACCTNCCTCAGATGGGAACTACCAATGGAA
CAGACTATGGAGCATACACATACAAGGAGCTAGAAAGAGAGCAATATTGGCCATCTNAGAATCTCAAGAT
ATCAATAACAGGAGCTGGAGGTTTCATTGCATCTNACATTGCTCGTNGTTTGANGCACGANGGTCATTAC
GTGATTGCTTCTGACTGGAAAAAGAATGANCACATGACTGANGACATGTNCTGTNATGAGTTCCATCTTG
TTGATCTTAGGGTTATGGAGAATTGTCTCAAAGTTNCTGAAGGAGTTGATCATGTTTTNAACTTAGCNGC
TGATATGGGTGGTATGGGTTTNATCCAGNGTAATCACTCTGTGGATTATG
>gi|2764096|gb|R30429.1|R30429 13034 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162H10T7, mRNA sequence
GATAGAGAGAGAGGTTACATTGATCTCAGTAAACGTAGGGTTAGTGATGAGGACAAAGAGGCTTGTAAGG
NGAGGTATAATAAGAGCAAGCTTGTNCACTCTATCATGCGTCATGTTGCTGAGACTNTTGGTGTCGATTT
GGAGGAGCTATACGTAAACATCGGTTGGCCATTGTATAAGANGCATGGACATGCTTTTAAGGCTTTCAAA
ATTNTTGTCACTGATCCTNATTCANTTTTCGATGCTCTTACCCGAGAAGTTAAAGAAACTGGACCTGATG
GTGTGGAGGTGACCAAAGTTGTCCCGGCTGTGTCTGAAGANTTGAAAGATGCATTTTTGAAGGNCATTAG
GAGGCGANTGNCACCNCAGCCAATGGAAGATTCGTGCTGNTATTGAATTGAAGTGTTTTCAGTTTGATGG
NGTTCTCCACATCAAGGAAGCCATGGNNGAAGGCAGAGGCTGTAGGGTNCCTGATTGATTTTTCCNGTCA
ANAATCANNGCTCNGTTGCTTCCACCCACTTTTATGTGCTTACCAACTTACAACCCTTTT
>gi|2764095|gb|R84186.1|R84186 16145 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162F7T7, mRNA sequence
CTCTATCCCTCTNAAAAATNAAGCTCTCTGTNCNTTTAATCTCCGCTGCTCTTCTNTTGTNCATGGTATT
CATTGCCACAGGGATGGGTCCAGTNACCGTGGAGGCACGCACGTTTAAGTCAAAGAGCCATAGGTTCAAG
GGTCCATGTNTGAGCACACACAACTGTGCAAACGTGTGCCACAACGAAGGCTTCGGCGGAGGTAAATGCC
GTGGATTCCGTCGTCGTTGCTACTGCACAAGACACTGCTGATCCATCCATTCTAATGNCTCAAATNTTTC
GATCCATCGTCAGTGTGTTANTTCTTTTTNATCTAAATNTTCCGTAACGGGACCATAT
>gi|2764094|gb|R84185.1|R84185 16144 Lambda-PRL2 Arabidopsis thaliana cDNA clone 162E1T7, mRNA sequence
AAACATTGGTTCANATTCAATGAGCCATGGNTGTTTAGTCGTNCCGGTNACGACAACGGAAAGAAAGCTC
CGGNACGTTNTTCACCGTACATCCCCGGTTATGGACAGCATTNTAAAGATGGGCGGTCTGGATACGAAGC
TTATNAAGTNAGTCACAACTTACTCTTGTNGCATGCTTACGCCGTTAACGCATTCAGAAAATGCAAACAG
TGTGCTGGAGGTAAAATAGGAATTGCACACAGTCCAGCTTGGTTCGAACCACAAGACCTTNNGCATGTTG
GAGGTTCCATTGAACGGTNTGCTTGATTTAATCCTAGGTTGGGCATTTGGTTCCAA
>gi|2764093|gb|R30426.1|R30426 13031 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161P24T7, mRNA sequence
TTCTTTNGTTTCCTCCAAATTCAAACACCATACTTNATCTCCTCCTCCTTCNCCTCCTCCTCCTCCTCCT
ATGGCTGCGTGCATCGACACCTGCCGCACTGGTAAACCCCAGATTTCTCCTCGCGATTCTNCTAAACACC
ACGACGATGAATCTGGCTTTCGTTACATGAACTACTTCCGTNATCCTGATCGATCTTCCTTCAATGGAAC
CCAGACCAAAACCCTCCATACTCGTCCTTTGCTTGAAGATCTCGATCGCNANGCTGAAGTCGATGATGTT
TGGGCCAAAANNCGNGAAGAGNNAAATCTGATATCGCCAAAGAACCTATTGTTTNCGCTTATTATNAACG
>gi|2764092|gb|R30417.1|R30417 13022 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161M4T7, mRNA sequence
CTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGATAATTTGCAAGATGA
TATGATGGACTTAATGGATGAGAGTNCTGAAATTCAAGAGACACTTGGTAGGAGCTACAANNTTCCTNAT
GACATTGNCGAAGATGACCTCCTGGGCGAGCTTTATGCTCTTNAAGCTGNCATNGGGAACG
>gi|2764091|gb|R30416.1|R30416 13021 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161M21T7, mRNA sequence
GAAGGAGGTCAAGTGCTGAGAGAGAAGCTCTCGTTGGGTTACTGTGGTCGGTCGCAGCGACTCTCTAAGT
TTATNTTTCTTTATATTGTCCTNTGTTTCGTCGTCGTCCCCTATTAAAATTACCTNCCAGTTTACTTTTC
TCTCTTCTTGTTTTCTGTGTTGGAAGATTCTCAAGTTATTTATTCCGCAAAAAACGGTTTATCATTTACA
ATTAGTTGAATTTTGGTCGTT
>gi|2764090|gb|R30415.1|R30415 13020 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161M1T7, mRNA sequence
CGTCGTCTCACCTTCTTCTCTCAAGCTCACGTCACGTGGCTTCATCATCCCNGCCNNCAATNCTTTCACC
GAGATCTCTCTTCTCCAACAACGGGAAACGAGCACCAACTGGAGTNAGAAACCATCAGTATGCGAGTGGA
GTNAGGTGTATGGCCGTAGCGGCGGATGCTTCTAAGACGAAAACGGCGGCGAGGAAGAAGAGTGGATACG
AACTTCAAACGTTGACGGGCTGGTTGCTGAGACAAGAGATGAAAGGAGAGATAGATNNAGAGCTNGACGN
TAGTNAATGTCGNGTATATCATTTGGCTTNTAAGCAAGATCCGCTTTA
>gi|2764089|gb|R30413.1|R30413 13018 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161M14T7, mRNA sequence
AGTCCAGCTTCTTTGTCTACCCCTACAAAGTCATCATCAAGACTTGCGGTACCACTAAGCTCCTCCTCTC
TATCCCACCACTTCTAAAGCTGGCTGGTGAGCTCTCTCTNAGTGTCAAGTCTGTNAAGTACACTCGCGGC
TCCTTCCTCTGCCCCGGAGGCCAGCCTTTTCCTCACCGCAGCTTCTCTGAAGAAGTCTCTGTTCTTNATG
GGCACTTTACTCAGCTGGGCTTGAACAGCGTAGCNTACTTGAATGGGCAATGATGATGAGACTAAGAAAT
GGCATGTCTATGCTGNCCTCTGCCCCAGGGACTCCAGCAACTGCAAACAACCAAATGGNCTACANTCTTC
GAGAATTGTGCAATTAATTTGGTCCTGGCCAANAGGGGAAAGGNTTGNCTGTNTNNTTNAAAGGGTTTNA
AGGTTTNCAAAGGNCTTGGGGGCAAATNGCCTGATAAACTTT
>gi|2764088|gb|R30410.1|R30410 13015 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161L7T7, mRNA sequence
CCCAAAAAAAAAAAAAAAGAGATGGTTCTGCTAGAGAAGCTTTGGGATGATGTTGTGGCTGGACCTCAGC
CTGACCGTGGCCTTGGCCGCCTCCGTAAGATCACCACCCAACCCATTAATATCCGAGATATAGGAGAAGG
GAGCAGCAGTAAGGTGGTGATGCATAGGTCGTTGACCATGCCGGCGGAGTGAGCCCTGGAACTCCAACGA
CTCCAACCACTCCGACGACGCCACGTAAGGNTAACGTGTGGAGGAGCGTCTTTAATCCGGGAAGCAACCT
CGCCACTAGAGCCATCGGNTCCAACATCTTTGANTAAACCCACCNATCCAANTNTCTCCNTNCCGTCTNA
GGACTNNGTTNGTAACAGCCGGTGACTNNAAGGNAGTCAGGCAACCNTTTAGG
>gi|2764087|gb|R30402.1|R30402 13007 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161L14T7, mRNA sequence
TTATCAAAGGTGGTTTTTNTTGCCACTGCTAATAGGGTTCAACCTATTCCACCTCCTCTNCTAGACAGGA
TGGAGCTAATTNAGTTGCCTGGTTATACGCAAGAGGAAAAACTTAAGATAGCTATGCGCCATCTGATTCC
TCGAGTTCTAGATCAGCATGGGCTTAGTTCCGAGTTCCTCAAGATTCCAGAGGCTATGGTAAAGAATATA
ATTCAGAGGTATACAAGGGAAGCCGGTGTTCGTAGTCTAGAGAGGAACTTGGCTGCTTTAGCTCGTGCAG
CTGCTGTGAATGGTGGCAGAGCATGAACAAAGTCTTCCGTTGAGCAAAGATTGTGCCAGAAACTTACATC
TTCCNCTNTTAATGGTAGNAATGNCCCCAGGAGNCGAAGTTGGAAATTGGAAGGTTTTTCCCANTNGGGT
GAAAANTNATCCATANGGTTTTGGGGNACCNTTCCAGNAGNCCCCCAGCTTTTNGTGGTGGATGAGGCCN
CCNCTTTTAAAAAAA
>gi|2764086|gb|R30396.1|R30396 13001 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161K3T7, mRNA sequence
CATCGAAACCCTAACTGCTCTCGGTGCTGAAGTCAGATGGTGTTCCTGCAACANCTTTTCCACTCAAGAC
CACGCCGCCGCAGCCATCGCTCGTAACTCCGCCGCTNTTTTCGCCTGGAAAGGTGAGACTCTTCAGGAGT
ACTGGTGGTGTACCGAGCGTGCTCTAGATTGGGGTCCAGGTGGTGGTCCTGATCTGATTGTTGATGATGG
TGGTGACGCTACTCTTTTGATTCATGAGGGTGTTAAAGCTGAGGAGATCTTTNAGAAGACTGGTCAAGTT
CCTGATCCTACTNNCTAACTGATAACCCTNAGTTTCAGATCGTNTTGTCCTANNATCAAAGGGNAGGTCT
TCAAAGTTTGATCCCTAAAGAAGTNNCCACCAAGGNTGAAGNNNGAGACT
>gi|2764085|gb|R30386.1|R30386 12991 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161J5T7, mRNA sequence
GAGAGAAGAAAGATAGAGAAAAAAAATGGGAGGCAAAGGTGTGATGATGGTGGCGATACTTTTCCTTTGG
GCACTCTCTGCAACATCTGAAGCAGTAACAGAGACTGAGCCAGGTTTNATGATGAACTTCTACAAGGACA
CGTGTCCTCAGGCCGAAGACATCATCCGTGAACAAGTCAAACTCCTCTACAAACGCCACAAGAACACCGC
TTTCTCTTGGCTCCGTAACATCTTCCATGACTGCNCCGTTGAGTCATGTGATGCGTCGCTTTTNCTGGNT
TCGACAAGAAGAGAGCTAGNNGAGAAAGACACGACAGGAGCTTCGGANTTAGAAACTTTAGGTACANTCG
AGGTGNTCAANGAAGCTCTNNNNGAGGGGAGTNTCCTCCGTGNTGTCTCA
>gi|2764084|gb|R30381.1|R30381 12986 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161J17T7, mRNA sequence
AGATTTTGGACAGAGTAGGGAACATTTCAGGTTTAAAGACTCCAACAGTTCTTTACCTTGCAGTAGCAGA
TACTCTCTTAGAAGAAAAAGAAGAAGATTCATCGGTTTTAAGTGGTTGGAGAGACGGTTTAATACCATTT
NAGAAGAAGAAGCTTGGGGTTAAAGAGGAGATATATGGGAAGTATTCATATTTNATACAATCGGCTATAG
ATTACGCGGTGTGTTTAANAGCGCNTGTTTTTTTTGGTAATAGCTTTTCGACTTTNTCTAGTCTCATTGT
TCTTCGAGAGGGCACAGAAAGCGCGANGGTTAGGGGNTTATAAAGTCNTCCTAAANATGGTTGGNAACAA
CGNNNNGGTCCT
>gi|2764083|gb|R30379.1|R30379 12984 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161J14T7, mRNA sequence
CTTCTTTATCATCATCGTCATCTTCAACAAGATCAACGGTCTCANATCATCCCCAGCTTCAAAGAAAAAA
CTTAATGATCATCATGTTACATCCCAGAGTCACGGGCCAAAGTTTCCACACGGAAGCTTNGGATGGCCCG
TNATCGGNGAACCATCGAGTTCGNCTCTNCTGCTTACTCAGACCGTCCTGNGAGTTTCNTGGTCAAGCGT
CGTCTCATGTNTGGGTGAGTGTTTAAGTCGCATANTTTTGGACCGGCGGCG
>gi|2764082|gb|R30374.1|R30374 12979 Lambda-PRL2 Arabidopsis thaliana cDNA clone 161I2T7, mRNA sequence
AAGTTAGTCATAAAAAAAAAAAACACACAAAAAAGTTTCANTGGCCGCCTCAACAATGGCTCTNTCCTCC
CCTGCTTTCGCCGGAAAGGCTGTGAACCTTTCCCCTGCGGCATCAGAAGTCCTTGGAAGCGGCCGTGTGA
CAATNAGGAAGACTGTTGCCAAGCCAAAGGGTCCATCAGGCAGCCCATGGTACGGTTCCGACCGAGTCAA
GTACTTGGGTCCATTCTNTGGCGAGTNACCCAGCTACCTTACCGGAGAGTTCCCTGGAGACTACGGATGG
GTCACANNTGGTCTNTCCGCTGNCCCCGAGANATTNNTAAGGAACCNNGAGCTAGAAGTTATCCTCAGCA
GG
>gi|2764081|gb|R30358.1|R30358 12963 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159P19T7, mRNA sequence
AAGACCCTCACTGGTAAAACAATCACCCTTNAGGTTNANAGTTCAGACACCATTGACAATGTCAAAGCTA
AGATCCAAGATAAAGAGGGAATTCCTCCGGTTCAGCAGAGGCTTATNTTTGCNGGTAAGCAGCTCGAAGA
TGGACGCACCCTTGCAGATTACAACATCCAAAAGGAGTCGACACTTCATCTTGTGCTTCGTCTCCGTGGT
GGTATGCAGATCTTTNTNAAGACCCTTACCGGNAAGACCATTACTNTGGAGGTTGAAAGCTCAGGCACCA
TCCGGTTAATTTCAAGGCTNANGGTTCCNGGGNCAAGGGAAAGGGGTTCCCACC
>gi|2764080|gb|R30354.1|R30354 12959 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159P13T7, mRNA sequence
TTCCAATTTNTTCAAACNCTAAAATCAATCTNTCAAATCTNTCAACCGTGATCAAGATGCAGATCTTCGT
TAAGACTCTCACCGGAAAGACTATCACCCTCGAGGTGGAAAGCTCTGACACCATCGACAACGTTAAGGCC
AAGATCCAGGATAAGGAAGGTATTCCTCCGGNTCAGCAGAGGCTTATNTTCGCCGGAAAGCAGTTGGAGG
ATGGCCGCACGTTGGCGGATTACAATATCCAGAAGGAATCCACCCCTCCACTTGGTTCTCAGGCTTCCGT
GGTGGGTATGCAGATTTTCGGTTAAAAACCNTTAACGGGGNAANGNCGGNTTACCNTTTTANGGNTGGGG
>gi|2764079|gb|R30352.1|R30352 12957 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159O6T7, mRNA sequence
GAACAATGGCTTCCTCTATGCTCTCTTCCGCTACTATGGTTGCTTCTCCGGCTCAGGCCACTATGGTCGC
TCCTTTAAACGGACTTAAGTCCTCCGCTGCCTTCCNAGCCACCNGCAAGGNTAACAACGACATTACTTCC
ATCACAAGCAACGGCGGAAGANTTAACTGCATGCAGGTNTGGCCTCCGATTGGAAAGAAGAAGTTTNANA
CTCTTTCTNACCTNCCTNACCTTACCGNTTCCAAATTGGCTAAGGAAGTTGACTACCTTTATCCGCAAAC
ANGTGGATTCCTTCGTGTTT
>gi|2764078|gb|R84183.1|R84183 16142 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159O3T7, mRNA sequence
GGCCNGNATTNCCNGGGCGGCCCACTGNGTCCGGTCNTTACCNGTNTTTAGTTANGTCTTGGTTGTGGTC
CNTTGCTCTTGTTTTCATTTGCCTACGTCGTCGCAAAGGAAGACCAGAGAAAGATGCTTATGTCTTCACT
CAGGAGGAAGGCCCATCTTTNTTGTTGAACAAAGTTCTTGCAGCAACTGACAATCTAAATGAAAAGTACA
CCATTGGAAGAGGAGCTCATGGAATTGTGTACAGAGCTTCTTTAGGCTCCGGAAAGGTCTACGCTGTGAA
GAGACTTTGTATTCGCGTCCTCACATCCCGCGNCTTAACCAGAAGTATTGNATTGAGGGGGAGAATTTGN
TTAACAATCCGGGTAAAGGTCAAGGCACAGGGAATCTTGATTTAAGTTAAGAAAGGGGTTTTTTGGCCTG
AGGGAAAAGNNCGANGGGTTTTAAATTCCTGGTATANGGTAACAATNCCCCAAAAGGGAAGGCCTTTTAC
GGCCGGTTNTCC
>gi|2764077|gb|R84182.1|R84182 16141 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159O22T7, mRNA sequence
GCCCACCGCGTCCGGTGACTACATGTNGTGACAACNNNTGAGTTTTCAAGACTAGCAAGAACAAAACAGC
TGGACCGTTTGGGATTGTATCTGGCACAAAGTTTGAATTCAAGAAGGAAGGTTACAAGATCACTGGGTTC
CACGGACGAGCTGGTGAGTATGTTAATNCTATTGGAGCTTATTTAGCTCCATCAGGCACCACCCCTTTGA
CTCCCTGCAACACAATCCCAAAAGGCTAGAAAGGAGCTGGGTAGTGAAGGCAGGGAACTTTTNATGGGGA
TGAATTGGGTGCTTTTCCGANCGGNTTGTAAAGGGAAAAGNTGTCCTTGTAGGGNCAAAGGCCCCAAAGG
ATGGGTTATTTGGGANGCCGGGTCCTCCGTTTTNGNTNTAACGGGCAAAAGCCAAGNGTCCAAGGGTTTG
TTAGGAANGGNAAAATGGA
>gi|2764076|gb|R30339.1|R30339 12944 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159N5T7, mRNA sequence
GTGGAATCTTTAACCCGCTTAACTTTGCTCCTACGCAAGAGGCCAAGGAGAAAGAGCTAGCAAACGGGAG
GTTGGCGATGTTGGCATTCTTAGGGTTTGTGGTTCAACACAATGTGACTGGAAAAGGACCATTTGAGAAT
CTNTTGCAGCACTTGTNTGACCCATGGCACAACACTATTGTCCAAACCTTCAACTAAAGAGTGAAGACAG
ACTTATGATCTCATACCTATCTATCTTCCATCACTTTCATGTCTGTCTGTGAGTGTGTTTCATCTTAGAG
TTCTTGGTTTTTAAGCTTGAATTATTGTTGAACCGTTGTAGCTCCATGAACAAATTTGGAATCTTCCAAT
GTACAGAGGGNCTAAGTTNATCAACATTNGTTTGNACNCTTT
>gi|2764075|gb|R84181.1|R84181 16140 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159N20T7, mRNA sequence
AGATTNCCGGGGNCCCACTGAGNCGGCAGAGTAAAGNTTGAAACTTTGGACTAAAAGAATGGCGTCTTTG
GGTGTNTCGGAAATGCTTGGTACTCCCCTTAACTTCAGGGCAGTTTCAAGATCGTNTGCTCCGTTGGCAT
CAAGCCCATCCACGTTCAAGACTGTTGCTCTCTTCTCTAAGAAAAAGCCAGCTCCTTGCTAAGTCCAAGG
CCTGTCTCTNAGACTAGCGGATGAGCTCGCCAAGTGGTATTGGTCCTGACAGGAGGAATTTTTCTTTGCC
CTGAATGGGTCCTTTTTGGGATAAGATTCAGNAGNTCCCCAAGAGGTTACTTTAAAAACGGGTGNAAGTT
TTCCTGGGAGATTTATTGGGTTATGNACCCCATTTTGGGTCCTTGGGAAAGAAAGCCCTTNAGNAANCTT
TTTGCTAAAATNACCCAAAGGNTTTTTTGAANTTTGATTCCCATTGNTG
>gi|2764074|gb|R30337.1|R30337 12942 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159N12T7, mRNA sequence
TTTCTTCAATCGAAAGGTAAAGAGTTTGAAGAAGTAAGTCACAGAGAAAGAGAAGATNTCTGAGAAAAAG
GGAAGGAAAGAGGAAGTGATTACCAGAGAGTACACCATTAACCTCCACAGACGCCTTCACAAATNCACCT
TTAAGAAGAAGGCACCGAAAGCCATCAAGGAAATCAGGAAGTTCGCAGAGAAAGCTATGGGGACTAAGGA
CGTTAGGGTAGACGTGAAATTNANCAAGCAAATCTGGAGCAAGGGANTCANAGGTCCACCAAGGAGGNTC
ANGGTTCGTTTTGCACGTAAGAGAANCGNCGATNNAAGATGCCGAAGGAAGAGTTCTTCTCCCTTGTCAC
TTTTGCTGAAATCCCTGCAGAAGGNCTCAGTGGTCTTTTGCACAAAGGNTCNTCGTAGNGGGAGGGTTTA
NGGGG
>gi|2764073|gb|R30334.1|R30334 12939 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159M20T7, mRNA sequence
ATTAAGATGACATCTACTATGGTTCTATTCCTCCTTCTTCTTCTTGTGTTTCCGCATATGGATAAAGCCC
TAGGCGCACACGAGGAATCCCAGAAACAAGGTGCAGAAAAGACTTACCATGATGCACGCTTTACTATTCC
TATTAAGCCAAAATATATTCCTAAGGTTATACGCCCTACGCCAAAAGATCCGCCTATTCCGGAATGTCTT
CGAAAAGGCACATGTAGTCGTCTTCATTTATCTCCTCCTCCGNCCCAGAGGTCTTTCAAAGGCACAAACG
AACCTGGTCATTGACCTCAATCTAGCTTCGAATTGCGTGTGTGTGTGCATGTTTCTTACATTTGTGGTTT
GGTTTTGTGGCTTCTNTCNTTTGTTTACCNNATGCNNTGTGTTNGTCANAATTTTNANAAGTTTTTNTCG
AANGGGCCGCTNNTNATTAAATAAAAACCTTNGGATTTCCCTTTTNGGGTTATAAAACGGCCTTTTAAAT
T
>gi|2764072|gb|R30330.1|R30330 12935 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159K2T7, mRNA sequence
AGCATTGAGAAGCTCAGGGCAGTGGCTGCTGAAAAGTCCGTTCTGGAATCACATTTTGAAGAACTTGAAA
AAACTTTNTCAGAGGTCAAAGCTCAGTTGAAAGAAAATNTGGAAAATNCAGCTACTGCGTCTGTAAAANT
GGCGGAATTGACCTCAAAACTGCAGGAACACGNACATATTGCTGGTGAACGAGATGTGCTCAACGAGCAA
GTNCTTCANCTTCAGAAAGAGCTTCAAGCGGCTCAGAGTTCCATTNNTGANCAGAAACANGCACACTCCC
AGAAGCAATCAGAGCTGGAGTNTGCATTAAAGAAATCACANGATG
>gi|2764071|gb|R30329.1|R30329 12934 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159K19T7, mRNA sequence
AAGTTTCANATTAACATTGTGGTCATTGGTCATGTTGATTCTGGAAAATCGACCACAACTGGTCACTTGA
NCTATAAGCTTGGTGGTATTGACAAGCGTGTNATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAA
GAGGTCCTTCAAGTACGCATGGNTGTTGGACAAACTTAAGGCCGAGCGTNACNCGNGTATTACCATCGAT
ATTGCTCTATGGAAGTTCGGGACCACCAAGTACTACTTGCACAGTCATTGTTTNCCCCCAGGGGNATTCG
GNNTTTTA
>gi|2764070|gb|R30327.1|R30327 12932 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159K17T7, mRNA sequence
TTGTGACCAGAACAGGAAAAATGCTAAGGTTGTNACCATTGATTCATATGAAGATGTCCCTGAGAACAGC
GAGGCGTCTCTAAAGAAAGCTTTGGCTCACCAGCCTATTAGTGTCGCCATTGAAGCGGGTGGTCGCNCTT
TCCAGCTCTATTCTTCGGGTGTATTTAATGGACTTTNTGGGACGGAGTTAGACCACGGTGTTGTGGCTGT
GGGTTATGGAACCGAGAACGGAAAGGACTACTGGGATTGTAAGAAACTCATGGGGAAACAAANTGGGGGN
GAAAGNGGNTNCATAAAGGTTGGNCCCGTAANNATTTNANGGCCCCA
>gi|2764069|gb|R84180.1|R84180 16139 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159J9T7, mRNA sequence
TACGGTCGGATTCCGGGTCGACCACGNTCCCTTTAGACAGCTAAAATAAATACAAGAAACAGAGATGGGT
TTGGTTACAGAGGAGGTGAGAGCTAAGGCAGAGATGTACACCGGAGATGAGATATGTAGAGAGAAGACAA
AGTNTTTCCTCAAGGAAATATCTATNCCCAATGGTTTATTACCATTGANGGATATAGAAGAGGTTGGGTA
TGACAGAGAGTCAGGTGTTGTATGGCTGANGCAGAAGAAGAGCATCACTCACAAGTTCACAGAGATAGAT
AAGCTTGTTTCCTATGGAACCGAAGTCACAGCCATTNTTGAGACCGGGAAANTCAAGANGCTCACTGGAG
TCAAAGCCAAGGAACTTCTTATTTGGGTCACTATCAATGNGATCTATACCGAGGANCCCCCTACCAAGAT
CACGTTCAAGACACCGNCCACACTGTCCAGGACTTTCCCGGTCACAGCTTTTNTNGTCCCNGANGTACCT
GCCANGGAGGNACCTGCCAAGAGGGNCCTNCCNGGNGAAGAGCAGCG
>gi|2764068|gb|R30324.1|R30324 12929 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159J6T7, mRNA sequence
AAACACTTCATAACTAAACATCCTTTAAAGCCTTTTCAAAAACTCAATCATGTCAAGCAACTGCGGAAGT
TGCGACTGTNCTGACAAGACCCAGTGCGTAAAGAAGGGAACCAGCTACACCTTCGACATCGTCGAGACTC
AGGAGAGCTACAAGGAGGCCATGATCATGGACGTTGGTGCCGAGGAGAACAACGCAAATTGCAAGTGCAA
GTNCGGCTCCTCTTGCAGCTGCGTCAACTGCACTTGCTGCCCCAACTAATGAAGCTTCTTTAATCAAAAT
GTAATATGAATAAAAGTTGATGTGGGCTCATCTATTGAGCTCATGTCTCTCTTATTACTACTCTCTAGTA
TGGTGTGATGTAATGGGTTATGACCCTTCTTTCCCTTCCCTATAAAACTAAAGANACTTGCAAGGATAAT
TGAAAAGATGGTTTCTNTTTATTAAAAAAANNTNT
>gi|2764067|gb|R30318.1|R30318 12923 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159J15T7, mRNA sequence
CCTAGCGATGGAATTCAGTATGGGCCGTTCGCTCTTCCTCAGAATGGATTGCCTATTGCCTTGGAACGAA
AACCATAGATGAATTACGAGAATACCATTTACCTTTCTTAAATTAGAAAGTGAGGAATTTTTTTCCTTAT
TTAAGAGGAAAATCTAATTCTTTTTTATAATAGAAATGAAAAGAAAGTAGANGAAAAAAATCCCAAGTGG
GACCCCCCAAGTGTATATAAGTTTTAGTTTATAAAATGTAGAGAATTAAATTTNCGGAGAAAAAAGAGAA
TTAGTTATATAAATGTCCCANGTGTATGTAANCTTGGTTCATGCCTCTATATCCTTAATTTTGNAANTTT
NCTCCAAANTGTTAAANNCCCCTTTATTACGGNNGTAAATGANCTNNNTGGAATG
>gi|2764066|gb|R30317.1|R30317 12922 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159J14T7, mRNA sequence
CAGAGGTTTCTATGTGAAACTTGCTAAAATAGATACAACACACATCTCATATCGACAATAAAAATTTGTT
TTCAAAGATCAGTATTTTTTGAAGCTTGCCAAGTGAAGCATCTTTTGGGTAATTAGAACCAGAGAAGCTT
CAAAAAATGGCTTAGAGTGAAGCATCTTGTGGCATTTCGACGGCATCATCTTAGGACGACTTATCTTGTT
CGTTTTCTTTCTCGTCTCTGTTGTAATTTTNCTATAAGTTTCTCATATATAGTTTCATTTTGTCTTTTGT
TCGTCCGTATTTGGTAGTTTGTCCAAATACAGNACATATGAAATTTTACAAGAGTGGATATTTTCAATTT
C
>gi|2764065|gb|R30313.1|R30313 12918 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159I8T7, mRNA sequence
AAGGAGTTGGAGAAGAAGATGAAACTAGCTGGATACAAACCGGAACTAGAGTTTNCTTTACACAATGTAG
AGGAAGAGCAGAAGGAGAAGCTATTGTAATGGCACAGCGAGAAGTTAGCTGTTGCNTTTGGTTGCATAAA
ACTCCCTGAAGGTTCACCAATACAAGTTTTCAAGAATTTAANAATCTGTGGTGATTGTAATAAAGCAATC
AAATTTATTTNGGNGATAGAGAAACGNGAGATCATTGTAAGGGGCACCNCAAGGTTTCACCATTTCAAAG
ATGGGTCTTGCTCTTGTGGCGGTTACTTGGTGNAAAGAGNAGNGCTTTNNCTCTNTCATTTGGTCAAACC
CTGCCTGGTTTTTTTATNNCGTTATTGTTTGG
>gi|2764064|gb|R30312.1|R30312 12917 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159I6T7, mRNA sequence
GAAATCAGCTTTGGCTATGGCTTCTNCGACACNTTTGTCTCTCTCATGGAGNTCCTCTCCTTGTTGGTCA
CACAGCTTCAATGGCGGTGCAAATGAAACCCTAAAAGTATCTGAGCGAAGGTTCAATTTTNAAGTTGTTT
CCCAGAAGNAAGNTAAGAAACTTCGCAAGGTAATTTTGAAAGAGGATGTGACGGATTTGGGTAAGCAAGG
GCAATTACTTGATGTGAAAGCTGGATTTTNCAGAAACTTCCTCTTGCCTACTGGAAAGGCTCAGCTTATG
ACTCCACTTCTGCTCAAGGAATTGAAGATGGAAGNCGNACGGATTGAAGGCAGAGAAGNAAAGGGTGAAA
GAAGGCGCACAACAACTGGCGATGGNTTTCCAAANCNGTTGGGTGCTTTTCAAAGGTTTAACCNCAAAGG
CGGTAAAGGCAAACTGNTATTTGGTTCTNTAACAGCTCAAGGNCCTNGTNGGCAT
>gi|2764063|gb|R30309.1|R30309 12914 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159I22T7, mRNA sequence
TTCTCTCTTGCATATTCGCTGCAAGGATGGGAAATTCAAAACCACTCCCTACAATTNNTTGTATTATAGT
TTCAGTCTTGTATTTTNNATTCTATTGCATAACACCAACTTCTTCATCAGCCTCCATCCAAGATCAATTC
ATAAACTGTGTCAAAAGAAACACACATGTTTCTTTTCCACTCGAGAAAACGTTATTCACCCCTGCGAAAA
ACGTCTCTTTGTTCAACCAAGTCCTTGANTCGACGGCTCAAAATCTCCAGTTCTTGGCAAANTCCATGCC
TAAACCGGGATTCATATTCAGACCGATTCACCAGTCTCAAGTCCAAGCTTCCATCATTTGTTCAAAGAAA
CTCGGGNTTCATTTTNGTGTTTGANGTGGCGGTCACGATTTTCGAGGCCTTTGTNTTTATGTTTCACGGT
TTGAAAAAACCGTTTATATTACTCGGCCTGTCAAANTTGNANNCAAAATCANATGTTGGATATTGNATTC
CAAATAGGTNCTTGGGGTNAACCTGGTGGCTANCGTTTGGTGAGCTTTTACTTTCAAGAATTTGCANGNG
GANGTGCAAAGATTCCATGGGATTTCCCGGGGGGTTTNTTGCACAATGTNNTGGGCATTGGTGGG
>gi|2764062|gb|R30308.1|R30308 12913 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159I19T7, mRNA sequence
ACTCAGTGGAGAAGAAGAAGAAGATCCAAATCGATCCGTTGAAAAGGAATTTCGAATTTCCTGTGCGATG
TCGAGTGCGGTGGACGCTACGGGAAACCCGATCCCTACTTCGGCGGTTTTAACGGCGTCACGAAGATATA
GGTATGAGGTGTATGCCGGAGAATGTTGCGTTCCTCAAATGCAAGAAGAATGATCCAAACCCAGAGAAGT
GTCTCGACAAAGGTCGTGACGTCACTCGCTGCGTGCTTGGCTTGCTGAAGGATCTTCACCAGAAGTGCCA
AAAGGAGATGGATGATTATNTTGGGTGTATGTATTACTACACAAACGAGTTTGATCTGTGTAGGAAAGAG
CAAGAAGCCTTCGAGAAAGTGTGTCCCTTGAAATNAGAATCACAAGTTCTTGTCATGTTTTNAATTTGTA
TCTCATAATAAAGCAAAATGTTTCATTTTTGGAATGAGCTTTNACNTCTCTCCATCTCTTGTTTTGTTGT
CATCCCATTTTATTTCCTCTCAAATGCTTTCCGTAGTGAGTTCCAAAGNCAACCTAAATGGCTCANGTTT
ATTNTTCGATTGGTCACTAAATTAAGCACAAGGATGGNACCAATTGTTTTT
>gi|2764061|gb|R30297.1|R30297 12902 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159H19T7, mRNA sequence
GGGTCAGAGTCTAAGACAGAAAGTNTTGCTGAAGAGGAGCCGGATCTTCCTGGGAGGTCTTCTATACAGG
ATGATGAATCAAATGCAGAAGAAACTGATGATCAACATCTTGCATCTNACCATGCCACAGACATCACAAG
AGAAGACTCGAATGATAAAAGCAAAGAGGTTGTTGAAGAGGAGACAGTAGAGCCATGTTTCACCACAAGA
GAAGACTCGGTTGACAAAAGCAAAGAGGTTGAAGAGGAAACAGTAAAGCCATGTCTCATAGAAGACGCGC
TTACAAGCCAGANTNNCAAAACCTCATCTGGTGACCATCCTGTTGAAATAAACGGNCCAATCCAGTTGAN
AGCAAGAATTTGGGAATCTGAAAACATTGGNACTGGTATCAAANTTGCTTCAACTGAGGTAGNGTCACCA
GCCTTTGATGATCTTNACCGCANCAGNTTTAAAGGNACCCCGNGGTTGATCTTNCAAGGNCCATTTTCAG
CTGNNTGTTNTTTTNACGGGTGGGCCATTTCTTGAAT
>gi|2764060|gb|R30288.1|R30288 12893 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159G21T7, mRNA sequence
AGTNAAGCATTACCTGTATGGNTTACTGGACCAGGACGAGATGTGCCAAGCNCTTTNTATGGTTTANAGC
ACCATGGGCAACACGTGACTTATGCTCCANCACAAGCTGGTCACGTCGCATTCCCAGGTATGTACCATCC
GGGACAAGCAGTAACAGCAACAGGNGTCCATCATCCGCTTTTACAACAGTTTCAAGGTGTGGCTGGAGCT
GAAATGGTTGCACCTGCGCCTAACGTTTTCCAACAGCCTCAGCAANCACAGATGAATTGGCCAAGTAATT
ACTGAAACAGGNTGTATAAAGGNGGAAAANATTTTTANAGGTTTCANCCANGTTTCAAATTTCCTGGGGG
ATTCA
>gi|2764059|gb|R30286.1|R30286 12891 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159G17T7, mRNA sequence
AGCTTCCNCNTTATTCANAGTGTAGAGGAGGATCCAAAAGAAAAGAGGAAAAAATGGACTATATGTATGG
NCCAGGGAGACACCATCTTTTTGTACCAGGACCAGTGAACATACCGGAACCGGTAATCCGGGCNATGAAC
CGGAACAACGAGGATTACCGGTCACCAGCCATTCCGGCGCTTACGAAAACATTGTTGGAGGATGTTAAGA
AGATATTCAAGACCACATCAGGGACACCTTTNNTTTTTCCNACGACCGGGACTGGTGCTTGGANGANTGC
TTTGGCCAACACGTTATCTCCTNGGGANAGG
>gi|2764058|gb|R30276.1|R30276 12881 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159E4T7, mRNA sequence
GAACAATGGCTTCCTCTATGCTCTCTTCCGCTACTATGGTTGCNTCTCCGGCTCAGGCCACTATGGTCGC
TCCTTTCAACGGACTTAAGTCCTCCGCTGCCTTCCCAGCCACCCGCAAGGCTAACAACGACATTACTTCC
ATCACAAGCAACGGCGGAAGAGTTAACTGCATGCAGGTGTGGCCTCCGATTGGAAAGAAGAAGTTTGAGA
CTCTCTCTTACCTTCCTGACCTTACCGATTCCGAATTGGCTAAGGAAGTTGANTACCTTATCCGCAACAA
GTGGATTCCTTGTGTTGAATTCGAGTTGGAGCACGGATTTTGTGTACCCGTGAGCACGGTAACTCAACCC
GGATACTATTGATTGACCGGTACTTGGNNCAATGTGGGAAGGCTTCCCTTGTTNCGGGTTNGNACCGGNN
TCCCNTTNAANGTNTTTNAAGGGAAGTGGGAGGNGTNNAAGAGGGGGGTNCCCCAATTGCCTTNATTTAG
GGTTNATCGG
>gi|2764057|gb|R30273.1|R30273 12878 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159E22T7, mRNA sequence
AATAAACCCTCTTTTTTGTATTCTCTGATTACTTCGTCTCTNCCCCTGTAATGGCGCTTCCACACGTAGT
CTCTTCACCTTCTTCAACTTCATTATCTCCTTCCTTCAAATCCAAACCACCGTTTCACTCCCTTAGATCT
TTATCACCGACGGTTGATAATCGCCGGCGTTGTAAACTCAACAGTTCCTTCCGATGTTCATCTTCTTNAT
TCTCCGAGAAGCATCACAACGCGAAATCTCCAAAATCCGATGATATCGTCGAGCTTCCTCTGTTTCACTN
CCACTCGTTCTCTTTCCCCGGAGCAATCCTTCCTCTTTCAGATCTTCGAATTTCCGTTACCGTATCATGA
TGCACACGGTCCTCCAATCTGNATCTANGNTTTCGGNNGTAGTTTNCTCCGATTTCCGGNTTNTNGGGTT
CGCGGCAAGAAGGAAGGNTTTTGTAGGNGNAGNNGGTNAAAAAGGNGCGTTTTGT
>gi|2764056|gb|R30271.1|R30271 12876 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159E20T7, mRNA sequence
AAAGAAAGTAAGATAATAATCCAAAAAAAAAAACCATATTTTTCCCAACGTTTTTAGACGATCAAATGGC
TTACACTAACCAAATTNNANCGGTTGCAGCGGTTGTTTTTCTAGCGGTTGNNATTGCNCCGCTATTAGCT
GAGCCACAGTCAACGATGTTTCCAGAGATGACTCCTGAATGTNCCACGGTTATGCCTGNCCTGCTCGAAA
AGTGTTTTGCAACCGGTAGTGTGACGCCAACAGAAGATTGNNGCACCGATCTAAAATCCGCAACCTCANC
GCA
>gi|2764055|gb|R84179.1|R84179 16138 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159E1T7, mRNA sequence
GNTGAGGGNCCGGGNCNGAANTNCCGGGNAGCCCACTGTGCCGGAGTATTTCTCCGTTCGTNCTCTCCCT
CTCTCTCGCTTCACGTTGGATCGAAATCGGACAAAAGTAAACGACAATGGCGGAAGAATTGGAGAAATCT
ATGCACAAGGAAGAATCTCTGATGGAAAAGATCGCTGATAAGATCCACGATCACGACTCTNCGTCGTCGT
CTGATTCCGAGCACGAGAAACCAGAGTCTCCGTCAGCTTTGAAGGCCAAGATATATCGTTTGTTTGGTAG
AGAGAAGCCTGTTCATAAGGTTCTCGGTGGTGGCTTACCGGCTGATGTGGTTCTTTGTGGAGGGACAAAA
AACTTCTCAGCTTCTGTTCTTGGTGTAGCGANNTGCNATATGGGGNTCTGGTTTGAATTGGTTGAGGATC
AATTTTCTTTNAGNCTTGGTGTGGNANCATTTT
>gi|2764054|gb|R30268.1|R30268 12873 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159E17T7, mRNA sequence
CTCAAACACTTCATAACTAAACATCCTTTAAAGCCTTTTCAAAAACTCAATCATGTCAAGCAACTGCGGA
AGCTGCGACTGTCCTGACAAGACCCAGTGCGTAAAGAAGGGAACCAGCTACACCTTCGACATCGTCGAGA
CTCAGGAGAGCTACAAGGAGGCCATGATCATGGACGTTGGTGCCGAGGAGAACAACGCAAATTGCAAGTN
CAAGTNCGGCTCCTCTTGCAGCTGCGTNAACTGCACTTGCTGCCCCCAACTAATGANGCTTCTTTAATCA
AAATGTAATATGNNTAAAAGTTTNATGTNGGGGCTCATCCTATTTGAGNCTCATGGTTTCTCTTTATTAC
TACCNCTCTNGTAATGGGGGTGATGTAATGGGGTTNTTACCCCNTCTTCCCNTNCCCNTTAAAAACT
>gi|2764053|gb|R30267.1|R30267 12872 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159E14T7, mRNA sequence
ATTAACTAAAGAGCCTTTNACTTGCGCCACACTCTCACCGCAATGGCCGCCTCGACAATGGCTCTCTCCT
CTCCTGCTTTGACCGGAAAGGCCGTTAAGCTATCCCCGGCGGCCTCCGAAGTATTTGGAACCGGCCGAAT
CACCATGCGCAAAGCCTCCAAGCCCACCGGTCCATCCGGCAGCCCATGGTACGGNTCCGACCGAGTCAAG
TACTTGGGTCCATTCTCCGGTGAGCCTCCGAGCTACCTCACTGGAGAGTTCCCCGGTGATTACGGGGTGG
GACACTTNCGGTCTATCCGCCGATCCCGAGACCTTTGNNTTAGGGAACCGTGAGCTAGAAGTTATTNCAN
CAGNAGNATGGGGCATNNGTCCGGNGCCCNTAAGGGCTGCNNTTTTNCCTGAAGGCTA
>gi|2764052|gb|R30255.1|R30255 12860 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159B16T7, mRNA sequence
CTACAAGACTCAAATAGTTTCTATTTAATNACTAAAAAGAAAAATGGGTCGTGGTTACAATTTGCTATTC
GTNCTAGTAACGTTTTTAGTATTGGTTGCAGCTGTAACCGCACAAGGGAACCGTGGCTCAAACAGCGGTG
GTGGTCGAAGCAANTNGNTTGGGTTTTATGGGAATAGATNCCGAAACGTAGAGTCTATTGTAAGATCTGT
AGTTCAGTCTCATGTCCGGTCTATCCCGGCTAATNCACCTGGAATTTTGCGAATNATTTCCACGATTGCT
TTNTCCANGGCTGCNATGGCTCGGTTCTCCCTCGCTGGTAACACCTCANNGAGAACC
>gi|2764051|gb|R30253.1|R30253 12858 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159B13T7, mRNA sequence
AAAAAAAAAAAANTTNTTCTTCTACTAACTTACGCTTCANTGGCGACTCCAACTCCATCTCTATCTCCTC
CTCCATTGAATCTCTGGATAATCTTATCAGAATCAAAACGNATNATCAACGNACACTCACGTCACTTCCT
AGCTCTCTCCGTTCTCTTCCTCCTCCCTCTCTGCTTCTCCATCACAGTTTACCCTNCCGTCTTCCTTCTC
ATCACCGATCAATCATCCGCTTCTNACAACACCGTCTNTCTCCTCCGCGGCGGACTCCACAACAACAACN
GATGATGACATCGNTNCCAAAAACAAACGGTCTTACTTGGTAATCGGTTACATCGTTNTGAT
>gi|2764050|gb|R30250.1|R30250 12855 Lambda-PRL2 Arabidopsis thaliana cDNA clone 159A23T7, mRNA sequence
ACTTTTTTGTTNAGTCTACTGGTGTNTTCACTGACAAAGACAAGGCTGCTGCTCACTTNAAGGGTGGTGC
TAAAAAGGTTGTAATCTCTNCCCCAAGCAAAGATGCGCCCATGTNCGTNGTTGGTGTCAACGAGCACGAG
TACAAGTTTGACCTTGANATTGTTTCCAACGCTAGTTGCACCACTAACTGCCTTGCTCCTNTNGCNAAGG
TTATTAATGACAGGTTTGGCATTNTTGAGGGACTCATGACCACTGTCCACTCTATCACTGCTACTCAGAA
GGCAGTT
>gi|2764049|gb|R84178.1|R84178 16137 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158P2T7, mRNA sequence
TTCATCTTCATCTTCACGCAGCGACTTCTTTNATTCTTTCTTTTNATTCTCAGCTCCAATTTCAACCTGC
ATTTNTNTCTTCTNAATTTTGGGTTTNTTTTTTNNATATCTCATTTGATCAGATCGACGAAGAGAGGAAG
AAGGTTTGANCTGAGAGATCTTTGGAGGTAGAAAGAAGATCTCAAAAACGATGTCGTTTACAGGAACTCA
GCAGAAATNCAGGGCGTGCGAGAAGACAGTGTACCCTGTGGAGCTTCTCTCAGCTGATGGAATCTCTTAT
CACAANGGCTTGCTTCAAATGCTCTCACTGCAAAAGCAGACTTNAANCTTGNGCAATTTATTCATCAATT
GGAAAGGAGTGGGTGTAATTGTNGGG
>gi|2764048|gb|R30242.1|R30242 12847 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158O8T7, mRNA sequence
ACAGATAAATGTACCCATCGTNTTTAGAGGACCCAATGGTGCTGCTGCTGGTGTTGGAGCTCAACATTCT
CAGTGCTATGCAGCGTGGTATGCCTCATTNCCTGGTTTGAAAGTCCTTGCTCCGTATTCAGCTGAAGATG
CTCGTGGTCTTCTTAAAGCTGCCATTAGAGACCCTGACCCTGTTGTTTTCCTTGAAAACGAGTTACTATA
TGGNGAATCATTCCCTNTTTNANAAGAAGCCCTTGNTTCANGTTTCTNTNTTCCCATAGGCAAAGCCAAG
ATTGANCGAGAAGGAAAGNACGTAACG
>gi|2764047|gb|R30241.1|R30241 12846 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158O18T7, mRNA sequence
TNAGAAGAGAACGAAGGAAGAAGAAGAAGAGGAACGATGGGGTACGTNTTTAGAGTACGATTGGNTTCTT
TNTTCGCCGGAGCTGCGACTGCNTCTTTAATCGGACTCTCCGTTCTCTACAAGGATTACAAAGTCGCTCA
CGAATCGATTTCTCAGCAGGCGAAGTCTTTTCATGACTCTNTGGATAGAAGGNTCTCTACTCTTGAAAGC
TTGAGACAAAGTGAAGCTCCTCANCTTGCTGAGACAACTGAATAGTAATCTGTCTCGACATTGAACACTC
TGCTTGGCAATNATGTTTTNAGTTGAGATGCTCTTTTTCNGGTTTTATGAATAACTTGGAAGTNCTTGTA
TGACTCTNCTGTTATAAAACAATGAAGTTTAAGGT
>gi|2764046|gb|R30238.1|R30238 12843 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158N2T7, mRNA sequence
CAAATTTCCTAGAGAGAGAAGGGCTTAGTTTTNTTNCCGCCATCCGGTGAATCCGGCAAAGCCATCTGGT
TGTNAAACCAGCTTCAGTCCAACAGCCTCCGGCTATTATAGAGGAGGTTGGTTGGNTTTTAACTGGCGGT
GTTGGCTCCCTCAGCAACGTCGGCCAGTTTTNTNTCCGGCAACGATGGCTCCGTAGCACCGTTTGGCTGG
CTCCNCTTGTATGCGGCATGTTTTCGGCTTTCNATGCGATGGTGTCCGCTTTTNTNTNTGGTCATTCCAC
CGGTAAATCTTTCCGGTGGTTTTTGGCCAGTAATGTACCCGGTGTNAGATCCGGGTTTAANTTGTGNCCG
>gi|2764045|gb|R30237.1|R30237 12842 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158M22T7, mRNA sequence
GTGGCTCAAGCTTTACTTTTGGTTTATGAGAAAGCAGAAGCTGAAGGAAGGTACATCTNCATAGGCCACA
CGGTTAGGGAACAAGAAGTCGCTGAGAAGCTGAAAAGTCTTTATCTAAATNACAACTACCCAAAGAGATA
CATCGAAGCGGNTGGAAAANTGAAGGTNAGTTCAGAGAAGTTGCAGAAGTTGGGTTGGACTTACCGGCCG
TTGGNGGAAACACTTGTGGATTCTTTTNNGAGCTACCGCAAAAGCTAAGCTTGTGGNCTTGTAAACCTGG
GNACGGANTAGCATACTGNA
>gi|2764044|gb|R30232.1|R30232 12837 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158F1T7, mRNA sequence
GAGAAAAGGAGGTAAGAAAGGCCGAGGAGGAGGTGGTGGAAACAAAGGNGTACGTGGAGTTGATTTTGGT
CTTGGTATTGGATTTAGCTCGGAATCTAGTAGGACACCTTCTTCTAAAGCTGCACCAAGTAGAAGTGGGG
CAATCAATTCAGTGAGAACTGGAGTAATGGCCCAATTCAAGAATAGTTTTGTCGCTNCAACGCCATCAAA
TCCACAAAACCAAGCTTATCCAAACAAGAGACCATCCCTAATGGGCTTTGTCTCAGGTGGTACTATTTGG
TGGAGACATGNGGTAGAACTCCAGGAGTCAAGCTTCCCCCAGTANCACCTACTTCAAAAACGGCTCATCA
CANAAATTNCAGCCCGGATTNACTTAACAGNGTTNTTNAGNATCGGGCCTTTATGNNTGGAAGGTGAAAN
ATCTTGNGTTGGGGNTAATTTTNG
>gi|2764043|gb|R30229.1|R30229 12834 Lambda-PRL2 Arabidopsis thaliana cDNA clone 158E19T7, mRNA sequence
CGAGTGTNAGCATGCCTGTNGGGACCCGAAAGATGGTGAACTATGCCTGANCGGGGTAAAGCCAGAGGAA
ACTNTGGTGGAAGCCCGCAGCGATACTNACGTGCAAATCGTTCGTNTGACTTGGGTATAGGGGCGAAAGA
CTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGGACGCGAGT
TCTATCGGGTAAAGCCAATNATTAGAGGCATTGGGGGCGCAACGCCCTCGACCTATTCTNAAACTTTAAA
TAGGTAGGACGTGTCGGCTGCTTTGTTGAGCCGTNACACGGAATTCGGAGAGCTCCCAANGTGGGCCCAT
TTTTTTGGTNAAGCAAGNACTTGGCCGATTGCNGGNNTTGAACC
>gi|2764042|gb|R30222.1|R30222 12827 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157L21T7, mRNA sequence
TCAACTCCAACGGTTTCCTGACCATTAATAGCCAACCATCAGTCAATGCAGCCAAATCCGATTCTCCAGC
TATTGGATGGGGTGGTCCTGGTGGTTACGTCTACCAGAAAGCTTATCTGGAGTTCTTCTGTTCAAAGGAT
AAGTTAGACACACTTGTGGAGAAATCCAAAGCTTTTCCTTCTATNACCTACATGGCCGTGAACAAATCAN
AGAATTGGGTATCAAACACCGGTGAGTCCGATGTGAATGCAGTTACTTGGGGAGTGTTNCCAGCTAAGGA
GGTTATTCAACCGACGGATCGTGGNTCCAGCCAGTTTNAAAGTCTGGAAAGTCGNGGCGTTTGAAATTTN
GGTNAAGAAAGCTGGGNTAAANTNNTNCCCAGAAGGTTGACCCTTTTTNGAAAGTTGNNTGA
>gi|2764041|gb|R30220.1|R30220 12825 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157L16T7, mRNA sequence
ATTAGCTACATAAGTNCTATAATGACCCTTTACGAAGGAGATGTCATCTTGACAGGCACACCAGAAGGTG
TTGGACCTNTAAAGATAGGTCAGAAGATAACGGCCGGAATCACCGGTCTATCTGAAGTTCAATTCGATGT
GGAGAGGCGTGTAAAGCCCTTGAGCTAATAAGTGGTTTTNTTTATCTTNNATACANAAATGTCAATTTTA
TAAAAGCATCTCTAAAATTTTNATCACTTACTGTGTTTCCTAAGGAAGGGNGAAATAAAACTNGTTACTC
ATTTTATTTGTAATCTCTATAACANTGGCTCTAAGACCCNGTTTAAATTGTTTAAANAAANAT
>gi|2764040|gb|R30217.1|R30217 12822 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157L10T7, mRNA sequence
GCTACACAACAATGGCTGCTTACACGTGTACTTCCCGTCCGCCGATTTCNATCCGGTCAGAGATGAGAAT
CGCTTCCTCGCCGACGGGTTCCTTCTCTACTCGACAGATGTNCTCTGTGTTGCCGGAATCGAGCGGATTG
AGGACTCGCGTTTCTNTATCTTCACTCTCGAAGAATTCTAGGGTTTCCCGATTACGNCGAGGCGTTATCT
NTNAAGCTCAGGACACTGCTACAGGAATTNCAGTGGTCAACGNTTCAACATNGGGACTNTCTAGTTNTCA
AGGCTGATGAGCCTGTTTTTTTGTNNGACCTTTTTGGGCACCATGGTTTTGGACCC
>gi|2764039|gb|R30212.1|R30212 12817 Lambda-PRL2 Arabidopsis thaliana cDNA clone 157K18T7, mRNA sequence
TTGTTTGATAGTCCCAGTNATGATGCTAAGCTTAAAGCTACAGACTTTGGTTTGTNTGTNTTCTACAAGC
CAGGGCAGTATCTGTATGATGTAGTTGGAAGTCCGTATTATGTTGCACCTNAGGTTCTGAAGAAATGTTA
TGGNCCAGAGATAGACGTGTGGAGCGCCGGTGTTATCTTGTACATCTTACTAAGTGGGGTTCCTCCTTTT
TGGGCAGAAACCGAGTCAGGAATCTTTAGGCAGATATTGCAAGGGAAGATAGNTTTTAAATCTNATCCGT
GGCCTANTATCTCANAAGGTGCTAAAGATTTTGNTTTNCAAAATNCTCNGATAGG
>gi|2764038|gb|R30208.1|R30208 12813 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152P24T7, mRNA sequence
CTCTCTTCTTCTTCTTTNATGTTTCTNCTTTNAGTTTTTNTTTTTNCGATTTAATCTGATCATCAAAACC
CTGCTCTCTCAAGATCATGCTTACTAAAAGAACCCATCCCATGATCGGAAAGATATCGGAGCTCCTTGTC
GGTGTCAACCGATTCCACGGCGGCTCCTTTNTTCGACGTCTTGATGACGAGCCCTAAAAGCCCACTGGAT
TTCAAGATTCTCCCTCAGATATCTCAAAGAAACAGTTCAAAGAGGTTCTACGATGACAATNTTGGTGGCT
CCGTTGGTCTAGGGATTGTAGCCGCGCTCGNGGAACTCAAACACTCGTCGGAATCACGAGGCGGTTTNTA
GGATCCGGAACCCGAACCAACCCCGGGNCGGGTCTTNTTCCGGGTTCAANTTCATGNGCCNATNGTNGAA
AGCACGGNCCGGTGGA
>gi|2764037|gb|R30207.1|R30207 12812 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152P23T7, mRNA sequence
CTCTNTTCTTCTTCTTTNATGTTTCTCCTTTNAGTTTTTNTTTTTNCGATTTAATCTGATCATCAAAACC
CTGCTCTCTCAAGATCATGCTTACTAAAAGAACCCATCCCATGATCGGAAAGATATCGGAGCTCCTTGTC
GGTGTCAACCGATCCACGGCGGCTCCTTTNTTCGACGTCTTGATGACGAGCCCTAAAAGCCCACTGGATT
TCAAGATTCTCCCTCAGATATCTCAAAGAAACAGTTCAAAGAGGTTCTACGNTGNCAATNTTGGTGGCTC
CGTTGGTCTAGGGATTGTNGCCGCGCTCGAGAACTTCAAACACTCGTCGGANTCAAGNNGCGTTTTTNGG
TCGGAACCGG
>gi|2764036|gb|R30204.1|R30204 12809 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152N24T7, mRNA sequence
TTTAATGGAGTTTTAAATTTAAAAATATTTGGTAACCGAGTGGNTCATCATGTTATTGAGAAGCACATCT
NCTCCGATACTGAACTCGTGGCTTCCACAACACTGCTCGAGAGAATCGTCTCCGGAACCGGAGTCACAGC
TCTGGCGCCGGTCAACATCATTGTNTCTTTCNTNATCAAAGTCCATAGATGGACACANTGGGGAGCAGCT
GCACCAAGCTCTCTNTGACAACAGGGAGATTATTATNCTTAAATCAAAAAGCAACGGGCACAGCTACAAA
ACTCCANCATCCANGCAGGGCAACGNAGGTNNATCTTTTAGGATGTAACACGGGT
>gi|2764035|gb|R30202.1|R30202 12807 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152M9T7, mRNA sequence
CAACAGAATGGTTAACCACTTTNTCCAAGAGTTCAAGAGGAAGAGTAAGAAGGATATCACCGGTAACCCA
AGAGCTCTTAGGAGGTTGAGAACTTCCTGTNAGAGAGCGAAGAGGACTCTTTCTTCCACTGCTCAGACCA
CCATCGAGATTGANTCTCTATACGAGGGTATCGACTTCTACTCCACCATCACCCGTGCTAGATTTNAGGA
ACTCAACATGGATCTNTTCAGGAAGTGTATGGAGCCANTTGAGAAGTGTCTTCGTGATGCTAAGATGGNC
AAGAGCACTGTTCATNATGGTNGTCCTTGTTGGTGGTTCTANCCGGAATCCCTAAGGTTTCAGCAAANTT
GCTCCCAGGGNCTTNCTTTTAACCGGGCAAANAGNCTTTTCCAAAGTNTT
>gi|2764034|gb|R30201.1|R30201 12806 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152M3T7, mRNA sequence
CGAAAAGGAAGCAGTGAAAGGGAATGATGTTAATGTAAAGAGGATCAAAGAGTATATGGAGAAGNTTGAG
TTAGAGCTTTCTAACATATGCNTTGATATTATGTCTGCNTTNGATGAGCATCTCATTCCTTCGGCTTCCG
NGGGTGAATCTACTGTNTTCTTCANCAAGATGAAAGGTGACTATTACCGCCATCTTGCTGAGTTCAAATC
AGGGAACGTCGAGGAAAGAGGCTGCTGNTCAGNCTTTGAAAGCCTCTGAGATNGCTACTACTTGCTGCTG
TGGCTAAGNTCCCTCCANCA
>gi|2764033|gb|R84175.1|R84175 16134 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152M2T7, mRNA sequence
AGAGGTTCTTTGGACGATGAAACAACTAATCCGCCGTTNATCGCGTGTNGGGACTCAACACAGTATAGCC
TCCTCCGGTCTGAATCCCAGCNTGGCCGCACCAAGAAGGAGAAACACAAATNTTGGGTTCCCGAGGGGCA
CGTGCCTGTTTACGTAGGCCACGANATGGAGCGGTTCGTGGTGAATNCGGANTGCTCAACCACCCCGTTT
TNNTAGCGTTGCTGAAGCAGTCGGCTCAANAGTATGGATACGAGCAACAAG
>gi|2764032|gb|R30195.1|R30195 12800 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152J7T7, mRNA sequence
ACTGCTGCATTGCCCGTNTACGCTAAAGGATTTAGAAAGCTTTTAAAGTACATCAAGGACAAATACGCAA
ACCCGGAGATTATGATAATGGAAAATGGATATGGAGATAAACTTGGGACCACAGATTCGGTTGACGTTGG
TACTGCTGATCATAACAGGAAATATTATCTNCAGAGGCATCTTCTGNCTATGNNCGNGNCTATTTGCATC
GATAAGGTGAGAGTTACGGGATACTTTGTNTGGTCATTGTTGGATAACTTNGAATGGNANAGATGGTTAC
AAAA
>gi|2764031|gb|R30194.1|R30194 12799 Lambda-PRL2 Arabidopsis thaliana cDNA clone 152J23T7, mRNA sequence
GATTCTNTGAAGTGTATATNAAGAGTGTAGCAGAAGAAGCGTTTTTCCCGGCGGCGGAGAGTTCGCCGGA
GTCTGAGCCACGTNTCGCGTTCACGGTTGTNCCAGGGTTTAGAATTGGGAAGACTTCAATACAATNCGAG
GTCTATCTNTCGCTTTCATGATCGCNGTTTGANCTAAGATCCGAAAACGGACGGTGAAGATTCTTGGGCG
GTTTGGTAATTNCTGAAAATGGTGGGGTATGTTTAGAAAATTGAGAAAAATTGTGGGCCGTTGGATTTGA
AGTAGCCGACCTAGAGTTGTGTTTATNTTTTCTNTTTTTCCCCCTCTTTTTNAGTTTTGTCGGT
>gi|2764030|gb|R30173.1|R30173 12778 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166M23T7, mRNA sequence
AATACCNGAGAAAATGGCGAANTTNTNGGGAACAACCGGCGAATTTTNCCGGCGAAGAGATGAATGGAGG
AAGCATCCGATGCTTTCGAATCAAATNAGACACGCTCTTCCCGGACTTGGAATCGGCGTCGCCGCCTTCT
GCNTTTATNTCGTCGGTGAGCAGATCTACAACAAAGCTTTGGCTCCTTCCAAATNATCTCACCACCACCA
GGAACAGACTGCTCCGTCTCACTGAAGAGCATCTTTTTTCTTCGATGAGATGCTTGAAACAGTGGCACAA
GGCTGAACTCAGGGTCTCTTCTTGGTTACTAGTTTTCGTTGGATTGNNTTAATAATCATGTTTAAATCGG
NTACAAAGANTTTNATATCTATATTTGAACTGTAAAGCTTTNTTNGCTCAAAGGGTCTCTTTG
>gi|2764029|gb|R30169.1|R30169 12774 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166M14T7, mRNA sequence
GATGACAAAGGAAGGAATTAGTCCTAATNTTGTAACTTATAATTCCATAATCGNTGCCTTTGGNCGTNCT
GCAACTATGGACAGATCAGCCGATTATAGCAATGGTGGATCTTTGCCTTTNTCTTCTNCTGCTCTGAGTG
CATTGACTGAAACAGAGGGTAATCGGGTAATACAGTTATTTGGGCAGTTAACAACTNAGAGTAACAACCG
TACGACGNAAGATTGTNAGGAGGGTATGCAGGAGCTCTCCTGTATATTGGANGTTTTCCGCAAAATGCAT
CAGCTGGAAATTAAACCCAATGTTGTAACCTTTTCAGCGNTTCTNAATGCTTGCAGTCGGTGTAACTCAT
TTNAAGNTGCATCAAT
>gi|2764028|gb|R30164.1|R30164 12769 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166L20T7, mRNA sequence
AAGATACAGTCTACCAAACTCAAGGATAATNATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACC
GACATTNACATTCAGGCAAATNAAATGCTGCATCACAAGGCAAACCTAAACGGTTACCTCGCATACCACA
CTGGTCAAAGCCTGGNGAAGATAAACCAGGACACAGACCGTNATTTNTTCATGAGTGCCAAAGAAGCAAA
AGAGTATGGACTTNTCGACGGNGTTATCATGAACCCNCTTAAAGCTCTCCAGCCACTTNCAGCAGCTTAN
TCGCCTAAAGGTAGTGGTTCAGCTTTAGCNCTTGTCCTTTTTTGGGCCTTTGATGNACCTGNGATTTTCC
NTGAAAAATGGTTCTATTCTCCAAGGGGGAATCAGNTTTTTTTTTGGGTCAAACT
>gi|2764027|gb|R30160.1|R30160 12765 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166J8T7, mRNA sequence
TCCTCTTCAGCTCCAACAGGCTCAAAAAGTGATCCAACTGATCACAACTCCATAAATTCTGAAGATGATT
TACTCTTGTNTGCAATGACCAAAGATGGACAGACCATTCTTTTGGATGGCAATACTGGGAAAATACTTGC
CTCTTGCCTGAGACCTCTAAAGAACCCAACTGCGATTTGTATGCACATTATAGAGAACTGCTATGAAAAC
TATGAAACGCCCAGTGAAAAACCAGCTGAAAATCCATCTGGGAAGGATAAACATGAGAACAAATCTCATA
TAATCAAAGCTAGTGAGAGTCATTCACCAGACGGTGNACAGAATGCTGTCACAGGAACAAAACTTTTTTG
ATCCAGATATTTGCGGNTTCATTATTTCTCATGGTGTTCTGAGGGTGCACTGNGGTTGTNTACCTGTAAA
GGTTCTNTNTCNGGGAGGCTTTNAGGGCTTTTTGGGGGGNAATNTCCAAGGCGNNTTCTTGGTGGGGTCC
TTAAAAAGNTGGNGGGGNTTTGAGGCTCCTTTTTCCNNCAGGGGTTTTTAANAGGNTTCCGGNNTGC
>gi|2764026|gb|R30155.1|R30155 12760 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166I22T7, mRNA sequence
CTTTGAACAGNTCATAGCTTCCGANGAGGNTAACTCCTTGAAGGNTCCAGCAACTAAGTCTTATGCTCAA
GTGTTTNCNCCCCACCATGGATGGGCTATACGGAAAGCTGTTTCTNTTGGGATGTATGCNCTTCCCACAA
GGGCTCACCTACTTAATATGCTCAAAGAGGATGAGGCGGCGGCTAAGATACATATGCAAAGCTATGTCAA
TTCATCGGCACCATTAATCACGTATCTTGATAATCTATTCCTCTCCAAGCAACTCGGTATTGATTGGNGA
AGAGCCTGNAAAAAAGGCATAACTATTGTAACTCTTTAGGCAAATTAACCTNTGTTCCTCACANCCAAGC
TATGTAATTGTCATAACAACCAGCGGCGGNATTACATTGGGNTTAAATTNGGGGATGNCCCTAAA
>gi|2764025|gb|R30153.1|R30153 12758 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166I18T7, mRNA sequence
GAATGTCCTACGATAGGGACCGGAGTAGAGGAGAGCAGTTCTTGGTGAGGTGGGCAATCCCACAGCTTCA
TGATATCGATGCATTGGGCAAAATGGTTGATCCATCTNTTAATGGACAATACCCTGCAAAGTCATTGTCA
CACTTTGCTGATATAATATCCCGGTGTGTTCAGTCTGAACCAGAATTTAGACCACTGATGTCAGAAGTTG
TTCAAGATCTACTAGATATGATCAGAAGAGAGCGTCATGGTTCGGGTGATTCTACCGCGGACTAGTGAAT
TGTAAAGAAGCATTTTTTTATCGGTCCATCTCTGTGAATTCGTGGGAANCAAGGAGATGTCCAGTTCTCA
GAAACAACAACACCAACATNGGGGCCTAAACCCGGCCCCTT
>gi|2764024|gb|R30152.1|R30152 12757 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166I16T7, mRNA sequence
ATTGCTTCTTTCTATCTNTNCTCTCGCTACACAACAATGGCTGCTTACACGTGTACTTCCCGTCCGCCGA
TTTCNATCCGGTCAGAGATGAGAATCGCTTCCTCGCCGACGGGTTCCTTCTCTACTCGACAGATGTTCTC
TGTGTTGCCGGAATCGAGCGGATTGAGGACTCGCGTTTNTNTATCTTCACTCTCGAAGAATTCTAGGGTT
TCCCGATTACNACGAGGCGTTATCTGTNAAGCTCAGGACACTGCTACAGGAATTCCAGTGGTCAACGATT
CAACATGGGACTCTCTAGTTCTCAAGGCTGATGAGCCTGTNTTTGTNGNCTTTTGGGANCATGGTGTGGA
CCCTGCAAAATNATTGACCCCATTGTNAAAGGANTTGNGNAAAAGTAACGCGGGCCAGTTCAAAGT
>gi|2764023|gb|R30151.1|R30151 12756 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166I15T7, mRNA sequence
AGTTTNTTGAGAAGAAAAAAAGGGTCAAGAAAGATNCCTAAAGACAGGAATATCGGAATCGCCATGGATT
TCTCAGAGAGCAGCAAGAACGCTCTGAAATGGGCGATCGANAACTTAGCAGACAAAGGAGACACGATTTA
CATCATCCACACTCTACCACTCTNTGGCGATGAATCTCGTAACTCCCTCTGGTTCAAATCCGGTTCTCCT
CTCATACCGTTGGCAGAGTTTAGGGAACCGGAGATTATGGAGAAATACGGTGTCAAAACCGGCATCGCAT
GCTTTGATATGCTCGNCACTGGTTCGAGGCAGAAAGAGGTCCATTTGGTGCCCATTTTTACTTGGGGGGN
TCAAGAGGGNAGGCTTTTTTNANCCCTTTTNAAGGTTTTAAAACCCCGGGTTNTNTTTTNATGGGG
>gi|2764022|gb|R30149.1|R30149 12754 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166I12T7, mRNA sequence
TTACTCGTGCCAGCCACTCGCATTTNTCCAGATTTAATTATCCTTCCTNGAAACAAGAGCTTAGCTAAGA
TGACGAAGAACTACCCAACCGTGAGCGAAGATTACAAGAAGGCTGTTGAGAAGTGCAGGAGGAAGCTCAG
AGGTTTGATCGNTGAGAAGAACTGTGCACCCATCATGGTCCGACTNGNATGGNACTCTGCTGGAACTTTC
GNTTGTNAATCAAGGACTGGAGGTCCATTCGGAACAATGAGGTTTGACGCTGAGCAAGCTCATNGAGCCA
ACAGTGGTATCCACATTGCTCTTAGGTTGTTGGACCCCATCAGGGNGCAATTCCNTACCATNTCTTTTNG
NTGATTTTCCATCAAGNTTGCTGGTGGTTNTGGCCGTTGAAGTTACTGGGGGGCC
>gi|2764021|gb|R30148.1|R30148 12753 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166I11T7, mRNA sequence
GTATTATNACACGAAAAGCGGAAGGTTTGTGGGGAAACAATCAAGGCTTTACCAGACTTGGACCATAGCG
GGTTTNTTGGCAGCTAAGAAACTAATAGAGCAATCTNAGAAAGCATCACTCTTGTCCTGGGAAGAGGACT
ATCAGCTGCTCGANACTTGTGTCTGTGGCCTCAGTAAAAGCAGCGGAAGGAAGAACAAGTGTTCGCNTTT
CACACCTCCAAGATCTTAGTTTCCTGAAACTTAATAAACTCACGNACCAAAGTCCATATTTAATCATATT
TNGCTTCTNACGTTTAGCAAAACATCCTTGCTAATTAGGNCGGTGNATCAGTTTCAAACTTAACGGATTT
TTAATTTTGAAAAAAGGGNTNTANTNTTTANGTTT
>gi|2764020|gb|R30139.1|R30139 12744 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166G24T7, mRNA sequence
CTCTGCTTAGCTCTCAGCTAGCTGAAATCTCTCTCAATCCGTGTAGCTTAGCTTCCCTAATCCAACCATG
GCAAAGTTCGGTGAAGGTGACAAGAGATGGNTCGTAGAAGACAGACCTGACGGCACCAACGTCCATAACT
GGCACTGGTCCGAAACCAATTGCNTTGAATGGTCTCGCAACTTCTTCACCAAACAATTCTCCGGCGTTGA
TATCCTCTCCGGCGAAGGTAATCTTTTCATCAAGGTCAGTAAGATCGNGAAAGTCGAAGGCGAGGCTTAT
GTGAATGTAAGGANGGGGNAGATTATCCCTGGGTACGNGCTTAACGNCTCTTTATCTTGGGAAGGTGAGG
CTAAAGATTCCGNTGGGNAGACGNTTTTTNAAAGCTNNTTGGNTTNGTCGNTATGCTTTATATNTCCGGT
GGGGATTCCTG
>gi|2764019|gb|R84174.1|R84174 16133 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166G11T7, mRNA sequence
AAGAAGAGAAACAACAAGAAGTAGTAATGGNTTCCNCTATGCTCTCCTCCGCCGCTGTGGTTACATCCCC
GGNTCAGGCCACCATGGTCGCTCCATTCACCGNCTTGAAGTCATCCGCTGCATTCCCGGTCACCCGCAAG
ACCAACAAGGACATCANTTCCATCGCAAGCAANGGGGGAAGAGTTAGCTGCATGANGGTNTGGCCACCAA
TTGGAAAGAAGAAGTTTGAGACTCTATCTTACCTCCNTNACCTTAGTGACGTCGAATTGGCTAAGGGAAG
TTGCTACCTTTTCCGNAACANGTGGATTC
>gi|2764018|gb|R30125.1|R30125 12730 Lambda-PRL2 Arabidopsis thaliana cDNA clone 166A2T7, mRNA sequence
AGAGAACGATTTTAAGGTCGGTTCTTTGAATTAATTTCACCTTGTNATTGGTAATTCGTTACGATTGANA
GAGGGACCGTGAAAGCAACGGACGAGCATCAGTTGACGATGTAGAAGATGCAGAAAAAACTCATCGAGTT
TCTTCGTCGACAAACGGGAGCAGAGAACGGCTGACGACTCGCATTAATGGGCCTTGTCAATGGGCTTTAC
TGTGAGATTGAAGAAGATCCAAAACTCATCGAGTTTCTTCGTGTTCAAACGGGGCAGAGAACGGCTCAAG
GCTTAAGGTTAATTCTCAGCCCATTTTCTTGTTTACTTAAATTCNTATATTTNATAATTTNNAGTTAATG
GGGNTTTTTCCNACGGGTTTTTAAAGNTTTTTTGCAATTTTTATTCAAGGTTTTGTTTAAAGGGAATTTT
TAAAAATTTTCNGGNAAAAANTTTTNTTANATNTCNTAANANTT
>gi|2764017|gb|R30121.1|R30121 12726 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165J7T7, mRNA sequence
CAGTCACTTAAAACCCTAAATNATGACGNTCGCACCGGCATTGCAGACGACGTTCGTNTCATCAACCAAC
TTCCTGAAACATTCTTCTTCGTGGGGATCACCATCACCAAACAATGTNATTCTNCCCAAAAACAAGAGAT
CTTNTTCCTCCGTAGTTGTCGCCGCCGTCGGTGATGTCTCTNCTGACGGAACAATCTACTTAATCGGCGG
ANATTCGCCGTTGCACTCGTCGGAACTGCATTCCCGATCCTNTTCAAACGCAAAGACACGTGTCCGGAAT
GTNACGGAGCAGGATTTGTNAGGAAAGGAGGAGTGACTCTAAGAGCCAACGNCGNACGGAAGGNTCTTCC
TCAGATCGTTTGTGCTAACTTGCAATGGGNCTCGGAAAAGCTTTAACCAGGATTGNTTAAATCATAAGGN
TTTCTTCATATNTTATGTAAAAAGGTCCATTTTTTAATTCCCCTTTCTTCTNTACAATATT
>gi|2764016|gb|R30119.1|R30119 12724 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165J20T7, mRNA sequence
CCTCACATTCAACATTCTTTTTTNAACTTTAACCACCGCATGTGGCGGTGNNTGCAGTTCCACCCCTAAA
CCCAAACCTAAGCCCAAGTCCACCGGAAGCTGCCCCAAAGACACTCTCAAGCTCGGTGTTTGCGCCAATG
TTCTCAAGGNTCTTNTCAAAATTNAGTTGGGAACACCACCAATGAAGCCTTGTNGCTCGCTCCTCAATGG
TTTGGTTGATCTTAAGGCTGCNGCTTGTTTCTGCACCGCCCTAAAGGCTAAAGTTTTAGGCATTAATCTT
AATGTTCCTGTCTCTNTNAGCCTTCTTCTNAATGTTTGTGGGCAAGAAGGGTTCCTTCTGGTTTCGTATG
TGCTTGAAATATCTATCCACCCTTNGATTGGTAAAATGGTTTTTTTGGGTACAATNCTTNAGGTTTCCCA
ATTNNAGTTNGGGGTTTT
>gi|2764015|gb|R30114.1|R30114 12719 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165I21T7, mRNA sequence
AACTAACTAACGACGCCGGAGATGGCCGCCACTTCAACCGCCGCTGCTGCTTCTTCAATCATGGGTACCC
GGGTGGTTTCCGACATTAGCTCCAATTCAAGCCGGTTCACAGCCCGGTTCGGATTCGGAACCAAGAAAGC
ATCTCCCAAAAAGGCTAAGACGGTTATCTCAGACCGGCCTCTATGGTTCCCAGGCGCAAAATCACCCGAA
TATCTCGACGGTTCACTTGTCGGGGACTACGGGTTCGATCCTTTTGGTTTAGGCAAACCGGCGGAGTATC
TCCAATTCGATTTGGATTCCTTGGACCAGAACTTAGCCAAGAACTTATACGGGGGAAGTNATCGGGGCTT
GTACCNAGGGCGGGTGGACCCCCAAATNGANGGCCGTTTTAGCCATATTAGTGAAGTNTTTNGGGGTTAA
AAAGNTTTAAGGNGNTTTAGGCTTTTTCAGGGNNGGTGGGGAATTTTNNCCANTTTTTGGGGNTTTTNCC
CGGNNNTTGCTCNCCGGTTTTTTTT
>gi|2764014|gb|R30111.1|R30111 12716 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165G6T7, mRNA sequence
TNAGGGAGCTACCAAGTTTTTNCTCCCCAGGCTCAGTGACTTCCAATTCTTTGTTGGGGAGGGTATGCAT
GATGACAGCACTTTGGTCTTTNCTTACTACAAGGAGGGTTCAACTAACCCAACATTTTTNTACTTCGCTC
ATGGTTTGAAGGAGGTCAAGTNCTGAGAGAGAAGCTCTCGTTGGGTTACTGTGGTCGGTCGCAGCGACTC
TCTAAGTTTATGTTTCTTTATATTGTCCTGTGTTTCGTCGTCGTCCCCTATTAAAATTACCTGCCAGTTT
ACTTTTCTCTCTTCTTGTTTTCTGTGTTGGAAGATTCTCAAGTTATTTATTCCGCAAAAAACGGTTTATC
ATTTACAATTAGTTGAATTTTGGGCGTT
>gi|2764013|gb|R30104.1|R30104 12709 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165G12T7, mRNA sequence
GGAAGNGATGGCTTCNACCTCCGCGATGTCANTGGNCACACCACTTAACCAGACCCGTTCGTCTCCTTTC
CTTAAGCCATTACCTCTGAAACCATCCAAGGCTTTGGTTGCAACTGGAGGCAGAGCACAGAGGCTTCAAG
TTAAGGCCCTCAAGATGGACAAGGCTTTGACCGGTATCTNCGCGGCTGCTCTTACTGNTTCGATGGTGAT
TCCGGAGATAGCTGAAGCTGCTGGTTCTGGAATCTNTCCTTCCCTCAAGAATTTNTTGCTCAGCATTNCT
TCTGGTGGCCTCNNCCTCACTGTCATCATTGGTGTCGTCGTCGGCGTCTCCAACTTTGACCCTGTCAAGN
GAACCTAAGNCCTATATATCNTTTCTTACATCATTATTGTAATCTGGTCTCCTTCTGTGGATTCGTTCAA
TGGTGCAGAATGAACTTTTNGTNAAAGCAT
>gi|2764012|gb|R30100.1|R30100 12705 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165F21T7, mRNA sequence
CTGTTGTCTTATCANTTANCTCTCTAACGGCGNGGCAATGGGTTTTCCGGNGGGATATTCTGAGCTACTT
CTCCCAAAAATCTTTTTCTACTTGTNATCTTTCTTAGGTTTGATACGTAAACTCATCTCCACAATGTTCA
AGATCATTGGTCTACCAGATTTCTTAGAACCTGAACCGGTTTCAACCTCATGGNCCGACCCACCACCCAC
GTTGACCAAACCTGACTCAGCAGCAATACTAGCCGGAGAGATGTTACCGGTTGTTCGATTCTCGGNTATA
AACCGACCGGNATCCGAGTNTTACGCAGTGTGNCTCTAAGATTTCGAGANCGNCGACGNGATCCGACGGG
G
>gi|2764011|gb|R30093.1|R30093 12698 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165D9T7, mRNA sequence
ACATCACATCACATAGCAATCACTTCACATCACAAAACACCTCATAGCCGCAAAATTTAATGGCAGACGT
CAAGATTCANTCCGAATCCGAATCCTCGGATTCTNATCCAGTGGTCGACAATCAACCACCTCCTCCGNCT
CCGCNGCCGCAACAGCCGGCGAAAGANGAGGAGAATCAACCAAAAACATCTCCGACTNCGCCGGCACACT
GGATGCGGTATCCACCAACGGTGATAATCCCTCATCAGATGATGTACGNGCCGNCGNCGTTCCCACCTTN
TCATCAGTATCCGNATNACCACCACCTTNAGCATCAATCTCGTGGTAATA
>gi|2764010|gb|R30092.1|R30092 12697 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165D8T7, mRNA sequence
CCCTAATNTAACATCACATCACATAGCAATCACTTCACATCACAAAACACCTCATAGCCGCAAAATTTAA
TGGCAGACGTCAAGATTCANTCCGAATCCNAATCCTCGGATTCTAATCCAGTGGTCGACAATCAACCACC
TCCTCCGCCTCCNCNGCCGCAACAGCCGGCGAAAGANGAGGAGANTCAACCAAAAACATCTCCGANTCCG
CCGCCACACTGGATGCGGTATCCACCAACGGTGATAATCCCTCATCAGATGATGTACGCGCNGCCGANGT
TCCCACCTTATCATCAGTATCCGAATCACCACNACCTTCAGCATCAATNTGGTGGTAATAAGCATCAAAA
CGNTTTTAATGGTGNGATTAAACCATATGGGTTGGTGATTTGATTANTGGATGGTTGAGGNTTNTTTTAA
TTTTT
>gi|2764009|gb|R30091.1|R30091 12696 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165D6T7, mRNA sequence
TCCATCTCCGGCACCGGCGCCTGANCCAGTNACCGCACCGACACCATCTCCAGCGGATGCACCTTCACCC
ACCGCAGCTTCACCACCGGNACCTCCNACGGACGAGTCACCGGAAAGTGCTCCTTCANACTCGCCAACAG
GTTCAGCGAACAGTAAGTNAGCTAACGCAGCGGTTGGNGTGAGACACCGTCGTTNTTCACCGCATTGGTC
ACGATCGCGGNCATAGCCGTNTCCGTGTTTTTTTGCTCTTAAAACCTTTNGTAATTACGGAGGCTGCNAC
TCCCTTTGTTTATTTTNAATTTAAATTATCTTTTCAATTTTAATTTTTGTGGGTATGNGTTGTTGAGTTT
GAAAACAT
>gi|2764008|gb|R30090.1|R30090 12695 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165D5T7, mRNA sequence
TCCCTNCTGAGCTATTCGGAAAATCTAAATCTCCATCTCCGGCACCGGCGCCTGANCCAGTTACCGNACC
GACACCATCTCCAGCGGATGCACCTTCACCCACCGNAGCTTCACCACCGGNACCTCCGACGGACGAGTCA
CCGGAAAGTGCTCCTTCAGACTCGGCAACAGGTTCAGCGAACAGTAAGTCANCTAACGCAGCGGTTGGCG
TAAGACACCGTCGTTNTTCACCGCATTGGTCACGATCGCCGTCATAGCCGTCTCCGTGTCTCTNTGCTCT
TAAAACCTTTCGNAATTACGCAGGCTGCCANTCCCTTTGGTTTANTTTTNAATTNAAATAATCTNTTCAA
TTTTT
>gi|2764007|gb|R30086.1|R30086 12691 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165B3T7, mRNA sequence
CCCTCCATCTTGTGCTTCGTCTCCGTGGTGGTATGCAGATATTTNTAAAGACCCTTACCGGAAAAACCAT
TACTCTTNAGGTTNAGAGCTCAGACACAATTGATAATGTCAAGGCTAAGATTCAGGACAAGGAAGGGNTC
CCACCGGACCAACAGAGACTCATCTTCGCTGGGAAGCAGCTTNAGGATGGTCGGACTCTTGCAGATTACA
ACATCCAGAAGGNGTCGACTCTTCACTTGGTTCTNCGTCTTCGTGGTGGAAGCTTCTAAGCTTTTNTAAN
GTGATCACAAGTGGTTNTTCGAGTCTCATGCACTTGGGAGGTGAGATCTTANCTGGGTTTGGGTTCTCCT
TCGGTCTTCGGGGAAAACCTTTTCCTTATCGGTGNTTCTGAAGGTTCATNTCCNGNTTCCTTTAATTTCC
NATGAANCC
>gi|2764006|gb|R84173.1|R84173 16132 Lambda-PRL2 Arabidopsis thaliana cDNA clone 165A4T7, mRNA sequence
TCAGGGACCNGGCCTGAATTCCCNGGGCGGCCCACTGCAGTCCGGGCAAAACCTTTGAGTATGAAACAAA
TTTNCCNTGTATCTCTCTCTCTTGTAATCTCCGACGAAGAAACACAGTTTTATGGCAACCACCAGATCGA
AGAGCTTTCAGTTGATCACCAGCTTAAGGAAACACCTAGTTAACACACGCGCTTCCACACGCGCCACCGN
CTCTNCTCTCTTCCCTTCACGTCGGAGTGGACATTCCTCGGCGTATGACAAGAACGTGGAGGATGAATTG
CATGCAAGTGCAGTACCTGACGAAGTTATAAAAGCCAGATTCTGATAAATATTGGTCTCCTCACCCCAAA
AACAGGGAGTCTTTCGGGTCCCTCTACGGCTGNGGAACAGNGGCACCGGCCGAGGGTGCACANCAGGGCA
AAGGAGTNCTTGGAGGAGACCCGCCTTGGTTTNGCCAANAAANGTTTTGGGGGNTTTGGNCAAGNNTTAC
CATNNTT
>gi|2764005|gb|R30077.1|R30077 12682 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164P11T7, mRNA sequence
GAACACATTGCCTCCAACTNCTGCATTGATGTCTGCAATCTATGAAGAACACAAAGATGAGGATGGGTTC
CTCTACATGACTTACAGTGGAGAGAACACTTTTGGTTCTNTTACCGTTGCTTGAATAAAAATCGATCTTT
GGATGACTTTNATGTACATACATAAATCAGGAAGATAAAGATGTACATNGCTTCCTTCTTTCCTCTGGCT
TTNAACTTTNCTTTGGATGTTTGGATATCTTTCCCTTTGGGTTTATNAATCGTCAGAAACTTCTCCT
>gi|2764004|gb|R30068.1|R30068 12673 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164N3T7, mRNA sequence
AAGATGACTCACACCACTTACAAGGCCAAAGGAAATGGCTGGCTTCTNCTCGCTGGGCTGCAGCCGCTCA
GTTTGCTCTGGCTGCNAGTNTTACTTCGTCGCACAACGATCTTCAAAGCCTTGAAATTGAAGATGACAGC
AGCATTTTGAAGAGAACAAACGATGCAGTTGTGACTCTGCGCAGTGTTCTCGAGGGGAAACACGACAAAG
AGATTGCAGAGTCGCTTGAGGAACATAATATCTCTAGAGAGGGATGGTTGTCATCACTCTATAGAATGGT
AGAAGGGCTTGCAGTGATGAGCAGATTGGCAAGGAACCGAATGCAACAACCGGATTACAATTTCGAAGGG
AATACATTTGACTGGGGCAACGTCGNGATGTTGNTAAGTTCATGTTAAACTAGGGNTCATTTGTCTCTTC
CGTAAGAACATATATTTTTCTTACCCAAATTTTNAGTTTGGTTNCNTTTCATAACCTTATTTTTNCCNCA
AAAAANGGG
>gi|2764003|gb|R30056.1|R30056 12661 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164L4T7, mRNA sequence
GAGAAGAATAGTTTGATCATCTTGTGAGAAAAATAATGGCTGCTTCAGTNATGCTATCTTCGGTGACATT
GAAACCAGCTGGTTTCACGGTGGAGAAGACGGCGGCTAGAGGATTACCGTCGCTCACAAGAGCTCGTCCC
TCCTTCAAAATTNTCGCCAGTGGCGTCAAGAAGATCAAGACCGACAAGCCCTTCGGAATTANCGGCAGCA
TGGACTTGAGGGACGGCGTCGACGCCTCCGGCAGAAAGGGCAAGGGATACGGTGTTTACAAGTACGTCGG
CAAGTATGGAGCTAACCGTCGATGGGATACAGTCCTTATTTTCAAACGGGGACCGNGTTGTCAACCGATT
GGTTNNCGTTTTCCAAGGGNNGGNGTCACCCGGNTTGGCAATTTTTTGGNCGGGTAANCTTTTCGCCGGN
ATTTNTTTCCCCGNNGGTNCCNTTTTTTTT
>gi|2764002|gb|R84172.1|R84172 16131 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164K16T7, mRNA sequence
TTTGTNCTGCACTACTCAACCTCAATGGCCGCCTCAACAATGGCTCTNTCCTCCCCTGCNTTCGCCGGTA
AGGCCGTCAAGCTTTCCCCCGCGGCATCTNAAGTCCTTGGAAGCGGCCGTGTGACAATNAGGAAGACTGT
TGCCAAGCCAAAGGGCCCATCAGGCAGCCCATGGTACGGTTCTNACCGTNTNAAGTACTTGGNTCCATTC
TTTGGCGAATNACCGAGCTACCTTACCGGAGAGTTCCCCGGAGACTACGGATGGGACACCGCCGGANTTT
>gi|2764001|gb|R30046.1|R30046 12651 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164J13T7, mRNA sequence
GCTCCTAGTTTGGTNGGGAAGCTAGAGACAGAAGTGGAGATCAANGNTTCGGCTGGACAGTTTCATCACA
TGTTTGCCGGGAAGCCACACCATGGTCTCCAAAGCAAGTCCAGGCAACATTCAGAGCTGTGATCTGCACG
AAGGCGACTGGGGCACTGTCGGCTCTATCGTCTTCTGGAATNACGTTCACGATGGGGAGGCAAAGGTGGC
GANGGAGAGNATCGNGGCGGTGGNGCCCNAGAAGANCTTGNTCACGATTAGGGTTATAGAAGGTGATCTG
CTGAAAGAGTACAAGAGCTTTTTGATCACGATCCAGNGTGNCCCCTAA
>gi|2764000|gb|R30044.1|R30044 12649 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164I7T7, mRNA sequence
ACCCTAGCCGCTTTACTCTCTTGCAATATCTCTAANATTTGTTTGANAGTCTCTAACCATGGGTAAAGAG
AAGTTTCACATCAACATTGTGGTCATTGGCCACGTCGATTCTGGAAAGTNGACCACCACTGGACACTTGA
NCTACAAGTNGGGTGGTATTGACAAGCGTGTNATTGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAA
GAGGTCCTTCAAGTACGCATGGNTTTTGGACAAACTTAAGGCTGAGCGTGANNGNGNGTATCACCATTGA
NATTGCTCTCTGGAAGTTCG
>gi|2763999|gb|R30040.1|R30040 12645 Lambda-PRL2 Arabidopsis thaliana cDNA clone 164I21T7, mRNA sequence
TGCAAACCATAACCAAACCATCATCATCATCATCTNTTGGTGACAGAAGAAAAGAGTTGAGGAACAGAGA
AAATGGCAGCACAAGCACTTGTNTCTTCTTCACTTACCTCCTCTNTTCAGACAGCTAGACAGATATTTGG
CTCAAAACCAGTTGCGTCTGCNTCACAGAAGAAGAGTTCCTTTNTNGTTAAAGCTGCTGCAACTCCACCT
GTCAAGCAATGAGCCAACAGACCATTGTGGTTTGCTTCATCGCAGAGTCTCTCTTACTTGGATGGCAGCT
TACCTGGTGACTATGGATTCGACCCTCTTGGTCTTTCAGACCCAGAAGGTACTGGAGGATTCATTGNGCC
AAGATGGCTAGCATACGGGNGNTNATCAACGGACGGTTCGCCATGTTGGGTNCAACTGGGGTTTTTNTCC
TAAGTTTTNTGGAAAGGCTTGGNTTNTTTCCNNCAAGANNTTTTTTTCCTTGGGT
genometools-1.5.1/testdata/attribute_after_dot.gff3000066400000000000000000000001301211610345200224500ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
seq1	.	gene	1000	9000	.	+	.	.;ID=foo
genometools-1.5.1/testdata/attribute_w_multiple_equals.gff3000066400000000000000000000001301211610345200242340ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
seq1	.	gene	1000	9000	.	+	.	foo==bar
genometools-1.5.1/testdata/bar.fas000066400000000000000000000000171211610345200171120ustar00rootroot00000000000000>bar
gggg
tttt
genometools-1.5.1/testdata/bed_files/000077500000000000000000000000001211610345200175715ustar00rootroot00000000000000genometools-1.5.1/testdata/bed_files/ct_example1.bed000066400000000000000000000004251211610345200224500ustar00rootroot00000000000000browser position chr22:20100000-20100900
track name=coords description="Chromosome coordinates list" visibility=2
chr22   20100000 20100100
chr22   20100011 20100200       
chr22   20100215 20100400
chr22   20100350 20100500
chr22   20100700 20100800
chr22   20100700 20100900
genometools-1.5.1/testdata/bed_files/ct_example1.gff3000066400000000000000000000005221211610345200225410ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr22 20100001 20100900
chr22	.	BED_feature	20100001	20100100	.	.	.	.
chr22	.	BED_feature	20100012	20100200	.	.	.	.
chr22	.	BED_feature	20100216	20100400	.	.	.	.
chr22	.	BED_feature	20100351	20100500	.	.	.	.
chr22	.	BED_feature	20100701	20100800	.	.	.	.
chr22	.	BED_feature	20100701	20100900	.	.	.	.
genometools-1.5.1/testdata/bed_files/ct_example2.bed000066400000000000000000000006061211610345200224520ustar00rootroot00000000000000browser position chr22:20100000-20140000
track name=spacer description="Blue ticks every 10000 bases" color=0,0,255,
chr22   20100000 20100001
chr22   20110000 20110001
chr22   20120000 20120001
track name=even description="Red ticks every 100 bases, skip 100" color=255,0,0
chr22   20100000 20100100       first
chr22   20100200 20100300       second
chr22   20100400 20100500       third
genometools-1.5.1/testdata/bed_files/ct_example2.gff3000066400000000000000000000005561211610345200225510ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr22 20100001 20120001
chr22	.	BED_feature	20100001	20100001	.	.	.	.
chr22	.	BED_feature	20110001	20110001	.	.	.	.
chr22	.	BED_feature	20120001	20120001	.	.	.	.
chr22	.	BED_feature	20100001	20100100	.	.	.	Name=first
chr22	.	BED_feature	20100201	20100300	.	.	.	Name=second
chr22	.	BED_feature	20100401	20100500	.	.	.	Name=third
genometools-1.5.1/testdata/bed_files/ct_example3.bed000066400000000000000000000005351211610345200224540ustar00rootroot00000000000000##Example 3 from Custom Annotation Tracks User's Guide
browser position chr22:1000-10000
browser hide all
track name="BED track" description="BED format custom track example" visibility=2 color=0,128,0 useScore=1
chr22 1000 5000 itemA 960 + 1100 4700 0 2 1567,1488, 0,2512
chr22 2000 7000 itemB 200 - 2200 6950 0 4 433,100,550,1500 0,500,2000,3500

genometools-1.5.1/testdata/bed_files/ct_example3.gff3000066400000000000000000000013501211610345200225430ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr22 1001 7000
chr22	.	BED_feature	1001	5000	960	+	.	ID=BED_feature1;Name=itemA
chr22	.	BED_block	1001	2567	960	+	.	Parent=BED_feature1;Name=itemA
chr22	.	BED_thick_feature	1101	4700	960	+	.	Parent=BED_feature1;Name=itemA
chr22	.	BED_block	3513	5000	960	+	.	Parent=BED_feature1;Name=itemA
###
chr22	.	BED_feature	2001	7000	200	-	.	ID=BED_feature2;Name=itemB
chr22	.	BED_block	2001	2433	200	-	.	Parent=BED_feature2;Name=itemB
chr22	.	BED_thick_feature	2201	6950	200	-	.	Parent=BED_feature2;Name=itemB
chr22	.	BED_block	2501	2600	200	-	.	Parent=BED_feature2;Name=itemB
chr22	.	BED_block	4001	4550	200	-	.	Parent=BED_feature2;Name=itemB
chr22	.	BED_block	5501	7000	200	-	.	Parent=BED_feature2;Name=itemB
###
genometools-1.5.1/testdata/bed_files/ct_example3.gff3_as_gene000066400000000000000000000011321211610345200242220ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr22 1001 7000
chr22	.	gene	1001	5000	960	+	.	ID=gene1;Name=itemA
chr22	.	exon	1001	2567	960	+	.	Parent=gene1;Name=itemA
chr22	.	CDS	1101	4700	960	+	.	Parent=gene1;Name=itemA
chr22	.	exon	3513	5000	960	+	.	Parent=gene1;Name=itemA
###
chr22	.	gene	2001	7000	200	-	.	ID=gene2;Name=itemB
chr22	.	exon	2001	2433	200	-	.	Parent=gene2;Name=itemB
chr22	.	CDS	2201	6950	200	-	.	Parent=gene2;Name=itemB
chr22	.	exon	2501	2600	200	-	.	Parent=gene2;Name=itemB
chr22	.	exon	4001	4550	200	-	.	Parent=gene2;Name=itemB
chr22	.	exon	5501	7000	200	-	.	Parent=gene2;Name=itemB
###
genometools-1.5.1/testdata/bed_files/ct_example4.bed000066400000000000000000000007211211610345200224520ustar00rootroot00000000000000##Example 4 from Custom Annotation Tracks User's Guide
browser position chr22:10000000-10020000
browser hide all
track name=clones description="Clones" visibility=2 color=0,128,0 useScore=1 url="http://genome.ucsc.edu/goldenPath/help/clones.html#$$"
chr22 10000000 10004000 cloneA 960 
chr22 10002000 10006000 cloneB 200 
chr22 10005000 10009000 cloneC 700 
chr22 10006000 10010000 cloneD 600
chr22 10011000 10015000 cloneE 300
chr22 10013000 10017000 cloneF 100 

genometools-1.5.1/testdata/bed_files/ct_example4.gff3000066400000000000000000000006321211610345200225460ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr22 10000001 10017000
chr22	.	BED_feature	10000001	10004000	960	.	.	Name=cloneA
chr22	.	BED_feature	10002001	10006000	200	.	.	Name=cloneB
chr22	.	BED_feature	10005001	10009000	700	.	.	Name=cloneC
chr22	.	BED_feature	10006001	10010000	600	.	.	Name=cloneD
chr22	.	BED_feature	10011001	10015000	300	.	.	Name=cloneE
chr22	.	BED_feature	10013001	10017000	100	.	.	Name=cloneF
genometools-1.5.1/testdata/bed_files/ct_example5.bed000066400000000000000000000013721211610345200224560ustar00rootroot00000000000000##Example 5 from Custom Annotation Tracks User's Guide
browser position chr7:127471196-127495720
browser hide all
track name="ItemRGBDemo" description="Item RGB demonstration" visibility=2 itemRgb="On"
chr7	127471196	127472363	Pos1	0	+	127471196	127472363	255,0,0
chr7	127472363	127473530	Pos2	0	+	127472363	127473530	255,0,0
chr7	127473530	127474697	Pos3	0	+	127473530	127474697	255,0,0
chr7	127474697	127475864	Pos4	0	+	127474697	127475864	255,0,0
chr7	127475864	127477031	Neg1	0	-	127475864	127477031	0,0,255
chr7	127477031	127478198	Neg2	0	-	127477031	127478198	0,0,255
chr7	127478198	127479365	Neg3	0	-	127478198	127479365	0,0,255
chr7	127479365	127480532	Pos5	0	+	127479365	127480532	255,0,0
chr7	127480532	127481699	Neg4	0	-	127480532	127481699	0,0,255


genometools-1.5.1/testdata/bed_files/ct_example5.gff3000066400000000000000000000026731211610345200225560ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr7 127471197 127481699
chr7	.	BED_feature	127471197	127472363	0	+	.	ID=BED_feature1;Name=Pos1
chr7	.	BED_thick_feature	127471197	127472363	0	+	.	Parent=BED_feature1;Name=Pos1
###
chr7	.	BED_feature	127472364	127473530	0	+	.	ID=BED_feature2;Name=Pos2
chr7	.	BED_thick_feature	127472364	127473530	0	+	.	Parent=BED_feature2;Name=Pos2
###
chr7	.	BED_feature	127473531	127474697	0	+	.	ID=BED_feature3;Name=Pos3
chr7	.	BED_thick_feature	127473531	127474697	0	+	.	Parent=BED_feature3;Name=Pos3
###
chr7	.	BED_feature	127474698	127475864	0	+	.	ID=BED_feature4;Name=Pos4
chr7	.	BED_thick_feature	127474698	127475864	0	+	.	Parent=BED_feature4;Name=Pos4
###
chr7	.	BED_feature	127475865	127477031	0	-	.	ID=BED_feature5;Name=Neg1
chr7	.	BED_thick_feature	127475865	127477031	0	-	.	Parent=BED_feature5;Name=Neg1
###
chr7	.	BED_feature	127477032	127478198	0	-	.	ID=BED_feature6;Name=Neg2
chr7	.	BED_thick_feature	127477032	127478198	0	-	.	Parent=BED_feature6;Name=Neg2
###
chr7	.	BED_feature	127478199	127479365	0	-	.	ID=BED_feature7;Name=Neg3
chr7	.	BED_thick_feature	127478199	127479365	0	-	.	Parent=BED_feature7;Name=Neg3
###
chr7	.	BED_feature	127479366	127480532	0	+	.	ID=BED_feature8;Name=Pos5
chr7	.	BED_thick_feature	127479366	127480532	0	+	.	Parent=BED_feature8;Name=Pos5
###
chr7	.	BED_feature	127480533	127481699	0	-	.	ID=BED_feature9;Name=Neg4
chr7	.	BED_thick_feature	127480533	127481699	0	-	.	Parent=BED_feature9;Name=Neg4
###
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s1.bed000066400000000000000000000230231211610345200224550ustar00rootroot00000000000000chr2L	14877642	14877669	15849196
chr2L	14879739	14879766	15849196
chr3L	3176656	3176706	10747896
chr3L	5541223	5543305	8562421
chr3L	5547581	5547777	8562421
chr3L	5550841	5550879	8562421
chr3L	6331375	6331408	8562421
chr2R	7044681	7044710	8562421
chr3R	7799777	7799811	8562421
chr3R	13521086	13521115	8562421
chr2L	19117404	19117717	2501149
chrX	9535652	9536720	8562425
chr2R	5447330	5447363	10545248
chr3R	7788805	7788848	7781065
chr3R	2580135	2580165	11159914
chrX	4231703	4231997	11080162
chr3L	1023563	1023594	12954775
chr3L	9357454	9357482	12954775
chr3R	8293508	8293549	7926771
chr3R	8303204	8303245	7926771
chr3R	8328185	8328237	7926771
chr3R	8331468	8331520	7926771
chr3R	8334751	8334803	7926771
chr4	1051903	1051998	16120280
chrX	10590260	10590297	10591997
chr2R	3551264	3551290	16533912
chr3L	14040656	14042361	9374395
chr3L	14044691	14044903	9374395
chr3R	22616627	22616653	15870289
chr3R	2613155	2613243	8617243
chr2R	15777876	15777904	16343659
chr3R	9790285	9790878	16343659
chr2L	14615342	14615373	1408750
chr3R	2824539	2824663	7914367
chrX	5748196	5748221	12890574
chr3L	11486022	11486097	2122237
chr3L	17552997	17553023	11682477
chrX	13045606	13047848	12662925
chr3R	15714105	15714143	2010085
chr3R	12589534	12589604	11416132
chr2R	7045733	7045824	2573829
chr2L	4877288	4879197	1411512
chr2L	4880284	4883113	1411512
chr3L	15475851	15475894	1899227
chr3R	2612775	2613155	1995417
chr3L	9357452	9357480	1904544
chr2R	7041087	7041114	2905420
chr3L	9351335	9351361	2905425
chr3R	8328188	8328214	2905425
chr3R	8331471	8331497	2905425
chr3R	8334754	8334780	2905425
chr3R	7782213	7782243	2370864
chr3R	7784278	7784308	2370864
chr3R	8293464	8293494	2370864
chr3R	8303160	8303190	2370864
chr3R	8328251	8328281	2370864
chr3R	8331534	8331564	2370864
chr3R	8334817	8334847	2370864
chr3L	9347860	9347922	6814763
chr3L	9355760	9355802	6814763
chr3R	7782290	7782338	6814763
chr3R	7784183	7784231	6814763
chr3R	8328156	8328204	6814763
chr3R	8331439	8331487	6814763
chr3R	8334722	8334770	6814763
chr3R	19883054	19883110	6814763
chr2R	16452736	16452761	16014933
chr3R	2581218	2581250	8344257
chr2L	2454709	2454735	7791801
chr2R	15777700	15777757	7559650
chr3R	17497451	17497479	7559650
chr2L	2446030	2446449	7821226
chr3R	12559898	12560106	2574106
chr3R	20574923	20574958	11159907
chr3R	2912165	2912262	8065369
chr3R	2689745	2689778	8355700
chr3L	17584725	17584816	2016053
chr2L	10388461	10388487	11731451
chr2L	3824313	3824350	11076769
chr3R	8898123	8898148	1533042
chr2L	19116325	19116352	12175493
chr2L	14348680	14348706	12626700
chr2R	20730342	20730906	2065664
chr3L	3176650	3176712	3685975
chr3R	2685019	2685185	1976571
chr3R	2581486	2581511	1582412
chr3L	14937407	14937851	15485919
chr3R	4100059	4100091	15485919
chr3R	6577359	6577389	15485919
chr3L	20640784	20641183	12466192
chrX	443844	443870	11752402
chrX	445080	445110	11752402
chr3R	2507403	2507466	10679014
chr3R	12562889	12562957	10679014
chrX	9898768	9898798	7851798
chr3L	17552997	17553023	7862168
chr3R	14059341	14059381	15939231
chr2R	8412632	8412669	9230443
chr3R	18961513	18961629	16207753
chr2L	2446089	2446347	7906203
chr3L	9357454	9357483	8375576
chr2R	19817982	19818028	8375576
chrX	9132426	9132620	14597205
chrX	7376019	7376050	11352058
chrX	3105718	3105980	9774480
chr3L	9357454	9357484	1913820
chr3R	2563023	2563074	7635058
chr2L	2446166	2446486	10934014
chr3R	26677687	26677721	12128207
chrX	4909577	4909707	9634487
chr3R	17209433	17209690	9694800
chr2L	14614966	14615056	1547943
chr3L	11485521	11485556	1898764
chr2R	2940406	2940432	15901665
chr2R	2944270	2944299	15901665
chr3R	18960438	18960468	15901665
chr3R	18961821	18961852	15901665
chr3R	2824539	2824673	2904838
chr3R	12559906	12560119	2904838
chr2R	3942374	3943350	6817923
chr2R	3945903	3947866	6817923
chr2R	3949270	3950074	6817923
chr2R	7046049	7046075	1971945
chr3L	11807698	11807725	8918795
chr3R	2689748	2689780	7768186
chr3R	2689745	2689780	2124348
chr3R	17458314	17458968	9748283
chr3L	9351283	9351314	8455632
chr3L	9357454	9357483	10882130
chr2L	9967202	9967229	9278447
chr2R	7714243	7714703	8218421
chr3R	2758520	2758570	8598298
chr3L	18786531	18786557	14982956
chr3R	12598960	12599583	8601485
chr2R	5485759	5485844	1671662
chr3R	22997071	22997816	14701680
chr3R	2758515	2758816	3215512
chrX	9898840	9898884	8422987
chrX	2000427	2001550	1765265
chr2R	5489850	5489931	12397102
chr3L	9357455	9357483	9466931
chr3L	15480791	15480818	9466931
chr3R	5235930	5235974	2504583
chr2R	17195238	17195296	11033359
chr2R	19841336	19841919	1459454
chr3L	11486107	11486138	2583107
chr3R	7782276	7782309	2583107
chr3R	7784212	7784245	2583107
chr3R	8328185	8328218	2583107
chr3R	8331468	8331501	2583107
chr3R	8334751	8334784	2583107
chr3L	9351342	9351378	2781290
chr3R	2912205	2912766	7984422
chrX	9899225	9899268	7984422
chrX	9898762	9898794	7720712
chr2L	10342667	10342696	15121905
chr3R	2611059	2613658	7910795
chr2R	20569607	20569637	8096813
chrX	219432	219469	10409499
chrX	220504	220542	10409499
chr2R	8412606	8412658	11262410
chr3R	12030968	12031017	10788480
chr4	727877	727911	9847251
chr4	730286	731300	9847251
chrX	2196512	2196546	10764759
chr3L	1157297	1157327	2104801
chr3R	27551503	27551594	2104801
chr3R	27552852	27554201	2104801
chr3R	27555352	27557046	2104801
chr2L	13827769	13827804	10930405
chr3R	4100049	4100279	15525530
chr3L	15005105	15005263	15882587
chr3L	20631200	20631253	1480489
chrX	8485631	8485676	9449676
chr3R	2689674	2689888	1851122
chr3R	12599003	12599569	1687458
chrX	3096421	3096451	11719067
chrX	3098844	3098874	11719067
chr2L	21241156	21241203	8479913
chr2L	21245459	21245560	8479913
chr2R	20734182	20734285	1985916
chr3R	174416	174464	10660305
chr3L	14141448	14141475	10844029
chr2R	11403526	11403695	10844029
chr2L	19117830	19117873	1426635
chr3L	9357454	9357482	2113880
chrX	9897789	9897990	2113880
chr3R	2689740	2690563	2113881
chrX	9898768	9898842	9134712
chrX	16387906	16389683	8849894
chr2R	5443380	5443692	9882489
chr3R	12526744	12526993	8404855
chr3R	17497441	17497479	9380507
chrX	10924673	10925117	1907377
chr3R	2685237	2685270	1640455
chr3L	7788286	7790270	9409684
chr3L	7827232	7827421	9409684
chr3R	11136418	11136478	9409684
chr2R	5485653	5485695	8787744
chr2L	2481562	2481768	10862738
chr2L	14615053	14615087	8164672
chr3R	2689743	2689778	8164672
chr2R	5497333	5497360	12482712
chr2L	4878293	4879189	2120114
chr2L	4880429	4881558	2120114
chrX	1896247	1896914	2120114
chr3L	17584542	17584574	1708722
chr2R	7043760	7043790	1708722
chr3R	12560119	12560151	1708722
chr3R	2689745	2689778	1852610
chr3L	9357456	9357487	9790883
chr2R	1602040	1602070	9790883
chr3R	12527039	12527064	1902784
chr3R	21822556	21822585	10452845
chr3R	21825205	21825343	10452845
chr3R	21850363	21850817	10452845
chr3R	12636462	12637611	10644409
chr3L	15622619	15623045	8557043
chr2R	2174101	2174267	1731341
chr2R	2179143	2179187	1731341
chr2L	13905165	13905259	15728670
chr2R	1216942	1217624	11262224
chr2R	7043588	7044212	3356339
chr3L	20627340	20627436	7969130
chr3L	14936909	14937854	7958878
chrX	226779	226809	7958878
chr2R	8296264	8296293	7958878
chr3R	21825184	21825215	7958878
chr3R	21850443	21850473	7958878
chr3R	21862517	21862645	7958878
chr3R	21865793	21865829	7958878
chr3L	4003947	4004010	7489720
chr3L	21407875	21410397	7489720
chr2L	3826259	3826317	7489720
chr2R	18376804	18376867	7489720
chrX	18075282	18075311	16277982
chr3R	2689743	2689778	1448096
chr3L	14909845	14909875	10603347
chr3L	14934454	14934484	10603347
chr3L	14937822	14937853	10603347
chr3R	4104930	4104985	10603347
chr3L	9357453	9357484	9580693
chrX	1896677	1896720	9580693
chr3R	12484743	12484783	1356765
chr3R	26675303	26675349	8543159
chr3R	26677808	26677880	8543159
chr3L	8682158	8682185	15128656
chr2R	20311058	20311086	10704846
chrX	7376019	7376050	11303087
chr3L	8640828	8640854	9250684
chrX	3105826	3105963	8890156
chr3L	21371558	21371592	1508206
chrX	6938207	6938242	7567454
chr3R	17204063	17204146	9211899
chr2L	2445758	2445918	11691840
chr3L	9357455	9357482	8007953
chr3L	14063391	14063426	8007953
chr3R	21824889	21825328	7590239
chr3R	21850363	21850623	7590239
chr3R	21865317	21865781	7590239
chr3R	20574969	20575185	8264640
chr2L	1992149	1992181	11729153
chrX	20223943	20223971	11729153
chrX	20226417	20227441	11729153
chrX	20229402	20229432	11729153
chr2R	6422830	6422858	11729153
chr2R	6425800	6425832	11729153
chr2R	10539699	10539731	11729153
chr2R	15214162	15214190	11729153
chr2R	15215644	15215672	11729153
chr2R	15218019	15218639	11729153
chr2R	15221585	15221613	11729153
chr2R	15227233	15227262	11729153
chr2R	15298880	15298912	11729153
chr2R	15330412	15330442	11729153
chr2R	16018502	16018532	11729153
chr2R	16063151	16063976	11729153
chr2R	16066131	16066750	11729153
chr3R	1931723	1931751	11729153
chr3R	1937965	1937996	11729153
chr3R	1940939	1940967	11729153
chr3R	25497413	25497442	11729153
chr2L	14615481	14615511	11493537
chr3R	12695176	12695321	11493537
chr2L	14615464	14615527	3159479
chr3L	15496338	15497308	15901661
chr2R	5490970	5491016	1672661
chr3L	17584384	17585044	2501151
chr2R	5566446	5566485	14731391
chr3R	26036494	26036530	14731391
chr2L	7303537	7307465	9502727
chr2R	7044640	7044740	1671661
chr2R	7239905	7240304	15075295
chr2R	7242144	7242175	15075295
chr2R	7327510	7327540	15075295
chr3R	10423057	10423085	15075295
chr3L	8702349	8702385	1280827
chrU	4976166	4976193	1671176
chr3R	2583622	2583649	1671176
chrX	5745754	5745824	2123290
chr3R	23064968	23065056	8662923
chr2R	19812220	19812254	9676198
chr2L	9967219	9968564	12758126
chr3L	9351682	9351719	8474442
chr2R	14380567	14380599	7537872
chr2L	14615099	14615131	1732738
chr2R	5490984	5491028	8406007
chr2L	14616171	14616209	7783192
chr3L	11485535	11485560	1903838
chr3R	7188390	7189913	11051550
chr3R	26678045	26678342	8430097
chr3R	26679685	26680087	8430097
chr3R	21070785	21070810	14561403
chr3R	12599090	12599336	10433918
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s1.gff3000066400000000000000000000427641211610345200225650ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr2L 1992150 21245560
##sequence-region   chr3L 1023564 21410397
##sequence-region   chrX 219433 20229432
##sequence-region   chr4 727878 1051998
##sequence-region   chrU 4976167 4976193
##sequence-region   chr2R 1216943 20734285
##sequence-region   chr3R 174417 27557046
chr2L	.	BED_feature	14877643	14877669	.	.	.	Name=15849196
chr2L	.	BED_feature	14879740	14879766	.	.	.	Name=15849196
chr3L	.	BED_feature	3176657	3176706	.	.	.	Name=10747896
chr3L	.	BED_feature	5541224	5543305	.	.	.	Name=8562421
chr3L	.	BED_feature	5547582	5547777	.	.	.	Name=8562421
chr3L	.	BED_feature	5550842	5550879	.	.	.	Name=8562421
chr3L	.	BED_feature	6331376	6331408	.	.	.	Name=8562421
chr2R	.	BED_feature	7044682	7044710	.	.	.	Name=8562421
chr3R	.	BED_feature	7799778	7799811	.	.	.	Name=8562421
chr3R	.	BED_feature	13521087	13521115	.	.	.	Name=8562421
chr2L	.	BED_feature	19117405	19117717	.	.	.	Name=2501149
chrX	.	BED_feature	9535653	9536720	.	.	.	Name=8562425
chr2R	.	BED_feature	5447331	5447363	.	.	.	Name=10545248
chr3R	.	BED_feature	7788806	7788848	.	.	.	Name=7781065
chr3R	.	BED_feature	2580136	2580165	.	.	.	Name=11159914
chrX	.	BED_feature	4231704	4231997	.	.	.	Name=11080162
chr3L	.	BED_feature	1023564	1023594	.	.	.	Name=12954775
chr3L	.	BED_feature	9357455	9357482	.	.	.	Name=12954775
chr3R	.	BED_feature	8293509	8293549	.	.	.	Name=7926771
chr3R	.	BED_feature	8303205	8303245	.	.	.	Name=7926771
chr3R	.	BED_feature	8328186	8328237	.	.	.	Name=7926771
chr3R	.	BED_feature	8331469	8331520	.	.	.	Name=7926771
chr3R	.	BED_feature	8334752	8334803	.	.	.	Name=7926771
chr4	.	BED_feature	1051904	1051998	.	.	.	Name=16120280
chrX	.	BED_feature	10590261	10590297	.	.	.	Name=10591997
chr2R	.	BED_feature	3551265	3551290	.	.	.	Name=16533912
chr3L	.	BED_feature	14040657	14042361	.	.	.	Name=9374395
chr3L	.	BED_feature	14044692	14044903	.	.	.	Name=9374395
chr3R	.	BED_feature	22616628	22616653	.	.	.	Name=15870289
chr3R	.	BED_feature	2613156	2613243	.	.	.	Name=8617243
chr2R	.	BED_feature	15777877	15777904	.	.	.	Name=16343659
chr3R	.	BED_feature	9790286	9790878	.	.	.	Name=16343659
chr2L	.	BED_feature	14615343	14615373	.	.	.	Name=1408750
chr3R	.	BED_feature	2824540	2824663	.	.	.	Name=7914367
chrX	.	BED_feature	5748197	5748221	.	.	.	Name=12890574
chr3L	.	BED_feature	11486023	11486097	.	.	.	Name=2122237
chr3L	.	BED_feature	17552998	17553023	.	.	.	Name=11682477
chrX	.	BED_feature	13045607	13047848	.	.	.	Name=12662925
chr3R	.	BED_feature	15714106	15714143	.	.	.	Name=2010085
chr3R	.	BED_feature	12589535	12589604	.	.	.	Name=11416132
chr2R	.	BED_feature	7045734	7045824	.	.	.	Name=2573829
chr2L	.	BED_feature	4877289	4879197	.	.	.	Name=1411512
chr2L	.	BED_feature	4880285	4883113	.	.	.	Name=1411512
chr3L	.	BED_feature	15475852	15475894	.	.	.	Name=1899227
chr3R	.	BED_feature	2612776	2613155	.	.	.	Name=1995417
chr3L	.	BED_feature	9357453	9357480	.	.	.	Name=1904544
chr2R	.	BED_feature	7041088	7041114	.	.	.	Name=2905420
chr3L	.	BED_feature	9351336	9351361	.	.	.	Name=2905425
chr3R	.	BED_feature	8328189	8328214	.	.	.	Name=2905425
chr3R	.	BED_feature	8331472	8331497	.	.	.	Name=2905425
chr3R	.	BED_feature	8334755	8334780	.	.	.	Name=2905425
chr3R	.	BED_feature	7782214	7782243	.	.	.	Name=2370864
chr3R	.	BED_feature	7784279	7784308	.	.	.	Name=2370864
chr3R	.	BED_feature	8293465	8293494	.	.	.	Name=2370864
chr3R	.	BED_feature	8303161	8303190	.	.	.	Name=2370864
chr3R	.	BED_feature	8328252	8328281	.	.	.	Name=2370864
chr3R	.	BED_feature	8331535	8331564	.	.	.	Name=2370864
chr3R	.	BED_feature	8334818	8334847	.	.	.	Name=2370864
chr3L	.	BED_feature	9347861	9347922	.	.	.	Name=6814763
chr3L	.	BED_feature	9355761	9355802	.	.	.	Name=6814763
chr3R	.	BED_feature	7782291	7782338	.	.	.	Name=6814763
chr3R	.	BED_feature	7784184	7784231	.	.	.	Name=6814763
chr3R	.	BED_feature	8328157	8328204	.	.	.	Name=6814763
chr3R	.	BED_feature	8331440	8331487	.	.	.	Name=6814763
chr3R	.	BED_feature	8334723	8334770	.	.	.	Name=6814763
chr3R	.	BED_feature	19883055	19883110	.	.	.	Name=6814763
chr2R	.	BED_feature	16452737	16452761	.	.	.	Name=16014933
chr3R	.	BED_feature	2581219	2581250	.	.	.	Name=8344257
chr2L	.	BED_feature	2454710	2454735	.	.	.	Name=7791801
chr2R	.	BED_feature	15777701	15777757	.	.	.	Name=7559650
chr3R	.	BED_feature	17497452	17497479	.	.	.	Name=7559650
chr2L	.	BED_feature	2446031	2446449	.	.	.	Name=7821226
chr3R	.	BED_feature	12559899	12560106	.	.	.	Name=2574106
chr3R	.	BED_feature	20574924	20574958	.	.	.	Name=11159907
chr3R	.	BED_feature	2912166	2912262	.	.	.	Name=8065369
chr3R	.	BED_feature	2689746	2689778	.	.	.	Name=8355700
chr3L	.	BED_feature	17584726	17584816	.	.	.	Name=2016053
chr2L	.	BED_feature	10388462	10388487	.	.	.	Name=11731451
chr2L	.	BED_feature	3824314	3824350	.	.	.	Name=11076769
chr3R	.	BED_feature	8898124	8898148	.	.	.	Name=1533042
chr2L	.	BED_feature	19116326	19116352	.	.	.	Name=12175493
chr2L	.	BED_feature	14348681	14348706	.	.	.	Name=12626700
chr2R	.	BED_feature	20730343	20730906	.	.	.	Name=2065664
chr3L	.	BED_feature	3176651	3176712	.	.	.	Name=3685975
chr3R	.	BED_feature	2685020	2685185	.	.	.	Name=1976571
chr3R	.	BED_feature	2581487	2581511	.	.	.	Name=1582412
chr3L	.	BED_feature	14937408	14937851	.	.	.	Name=15485919
chr3R	.	BED_feature	4100060	4100091	.	.	.	Name=15485919
chr3R	.	BED_feature	6577360	6577389	.	.	.	Name=15485919
chr3L	.	BED_feature	20640785	20641183	.	.	.	Name=12466192
chrX	.	BED_feature	443845	443870	.	.	.	Name=11752402
chrX	.	BED_feature	445081	445110	.	.	.	Name=11752402
chr3R	.	BED_feature	2507404	2507466	.	.	.	Name=10679014
chr3R	.	BED_feature	12562890	12562957	.	.	.	Name=10679014
chrX	.	BED_feature	9898769	9898798	.	.	.	Name=7851798
chr3L	.	BED_feature	17552998	17553023	.	.	.	Name=7862168
chr3R	.	BED_feature	14059342	14059381	.	.	.	Name=15939231
chr2R	.	BED_feature	8412633	8412669	.	.	.	Name=9230443
chr3R	.	BED_feature	18961514	18961629	.	.	.	Name=16207753
chr2L	.	BED_feature	2446090	2446347	.	.	.	Name=7906203
chr3L	.	BED_feature	9357455	9357483	.	.	.	Name=8375576
chr2R	.	BED_feature	19817983	19818028	.	.	.	Name=8375576
chrX	.	BED_feature	9132427	9132620	.	.	.	Name=14597205
chrX	.	BED_feature	7376020	7376050	.	.	.	Name=11352058
chrX	.	BED_feature	3105719	3105980	.	.	.	Name=9774480
chr3L	.	BED_feature	9357455	9357484	.	.	.	Name=1913820
chr3R	.	BED_feature	2563024	2563074	.	.	.	Name=7635058
chr2L	.	BED_feature	2446167	2446486	.	.	.	Name=10934014
chr3R	.	BED_feature	26677688	26677721	.	.	.	Name=12128207
chrX	.	BED_feature	4909578	4909707	.	.	.	Name=9634487
chr3R	.	BED_feature	17209434	17209690	.	.	.	Name=9694800
chr2L	.	BED_feature	14614967	14615056	.	.	.	Name=1547943
chr3L	.	BED_feature	11485522	11485556	.	.	.	Name=1898764
chr2R	.	BED_feature	2940407	2940432	.	.	.	Name=15901665
chr2R	.	BED_feature	2944271	2944299	.	.	.	Name=15901665
chr3R	.	BED_feature	18960439	18960468	.	.	.	Name=15901665
chr3R	.	BED_feature	18961822	18961852	.	.	.	Name=15901665
chr3R	.	BED_feature	2824540	2824673	.	.	.	Name=2904838
chr3R	.	BED_feature	12559907	12560119	.	.	.	Name=2904838
chr2R	.	BED_feature	3942375	3943350	.	.	.	Name=6817923
chr2R	.	BED_feature	3945904	3947866	.	.	.	Name=6817923
chr2R	.	BED_feature	3949271	3950074	.	.	.	Name=6817923
chr2R	.	BED_feature	7046050	7046075	.	.	.	Name=1971945
chr3L	.	BED_feature	11807699	11807725	.	.	.	Name=8918795
chr3R	.	BED_feature	2689749	2689780	.	.	.	Name=7768186
chr3R	.	BED_feature	2689746	2689780	.	.	.	Name=2124348
chr3R	.	BED_feature	17458315	17458968	.	.	.	Name=9748283
chr3L	.	BED_feature	9351284	9351314	.	.	.	Name=8455632
chr3L	.	BED_feature	9357455	9357483	.	.	.	Name=10882130
chr2L	.	BED_feature	9967203	9967229	.	.	.	Name=9278447
chr2R	.	BED_feature	7714244	7714703	.	.	.	Name=8218421
chr3R	.	BED_feature	2758521	2758570	.	.	.	Name=8598298
chr3L	.	BED_feature	18786532	18786557	.	.	.	Name=14982956
chr3R	.	BED_feature	12598961	12599583	.	.	.	Name=8601485
chr2R	.	BED_feature	5485760	5485844	.	.	.	Name=1671662
chr3R	.	BED_feature	22997072	22997816	.	.	.	Name=14701680
chr3R	.	BED_feature	2758516	2758816	.	.	.	Name=3215512
chrX	.	BED_feature	9898841	9898884	.	.	.	Name=8422987
chrX	.	BED_feature	2000428	2001550	.	.	.	Name=1765265
chr2R	.	BED_feature	5489851	5489931	.	.	.	Name=12397102
chr3L	.	BED_feature	9357456	9357483	.	.	.	Name=9466931
chr3L	.	BED_feature	15480792	15480818	.	.	.	Name=9466931
chr3R	.	BED_feature	5235931	5235974	.	.	.	Name=2504583
chr2R	.	BED_feature	17195239	17195296	.	.	.	Name=11033359
chr2R	.	BED_feature	19841337	19841919	.	.	.	Name=1459454
chr3L	.	BED_feature	11486108	11486138	.	.	.	Name=2583107
chr3R	.	BED_feature	7782277	7782309	.	.	.	Name=2583107
chr3R	.	BED_feature	7784213	7784245	.	.	.	Name=2583107
chr3R	.	BED_feature	8328186	8328218	.	.	.	Name=2583107
chr3R	.	BED_feature	8331469	8331501	.	.	.	Name=2583107
chr3R	.	BED_feature	8334752	8334784	.	.	.	Name=2583107
chr3L	.	BED_feature	9351343	9351378	.	.	.	Name=2781290
chr3R	.	BED_feature	2912206	2912766	.	.	.	Name=7984422
chrX	.	BED_feature	9899226	9899268	.	.	.	Name=7984422
chrX	.	BED_feature	9898763	9898794	.	.	.	Name=7720712
chr2L	.	BED_feature	10342668	10342696	.	.	.	Name=15121905
chr3R	.	BED_feature	2611060	2613658	.	.	.	Name=7910795
chr2R	.	BED_feature	20569608	20569637	.	.	.	Name=8096813
chrX	.	BED_feature	219433	219469	.	.	.	Name=10409499
chrX	.	BED_feature	220505	220542	.	.	.	Name=10409499
chr2R	.	BED_feature	8412607	8412658	.	.	.	Name=11262410
chr3R	.	BED_feature	12030969	12031017	.	.	.	Name=10788480
chr4	.	BED_feature	727878	727911	.	.	.	Name=9847251
chr4	.	BED_feature	730287	731300	.	.	.	Name=9847251
chrX	.	BED_feature	2196513	2196546	.	.	.	Name=10764759
chr3L	.	BED_feature	1157298	1157327	.	.	.	Name=2104801
chr3R	.	BED_feature	27551504	27551594	.	.	.	Name=2104801
chr3R	.	BED_feature	27552853	27554201	.	.	.	Name=2104801
chr3R	.	BED_feature	27555353	27557046	.	.	.	Name=2104801
chr2L	.	BED_feature	13827770	13827804	.	.	.	Name=10930405
chr3R	.	BED_feature	4100050	4100279	.	.	.	Name=15525530
chr3L	.	BED_feature	15005106	15005263	.	.	.	Name=15882587
chr3L	.	BED_feature	20631201	20631253	.	.	.	Name=1480489
chrX	.	BED_feature	8485632	8485676	.	.	.	Name=9449676
chr3R	.	BED_feature	2689675	2689888	.	.	.	Name=1851122
chr3R	.	BED_feature	12599004	12599569	.	.	.	Name=1687458
chrX	.	BED_feature	3096422	3096451	.	.	.	Name=11719067
chrX	.	BED_feature	3098845	3098874	.	.	.	Name=11719067
chr2L	.	BED_feature	21241157	21241203	.	.	.	Name=8479913
chr2L	.	BED_feature	21245460	21245560	.	.	.	Name=8479913
chr2R	.	BED_feature	20734183	20734285	.	.	.	Name=1985916
chr3R	.	BED_feature	174417	174464	.	.	.	Name=10660305
chr3L	.	BED_feature	14141449	14141475	.	.	.	Name=10844029
chr2R	.	BED_feature	11403527	11403695	.	.	.	Name=10844029
chr2L	.	BED_feature	19117831	19117873	.	.	.	Name=1426635
chr3L	.	BED_feature	9357455	9357482	.	.	.	Name=2113880
chrX	.	BED_feature	9897790	9897990	.	.	.	Name=2113880
chr3R	.	BED_feature	2689741	2690563	.	.	.	Name=2113881
chrX	.	BED_feature	9898769	9898842	.	.	.	Name=9134712
chrX	.	BED_feature	16387907	16389683	.	.	.	Name=8849894
chr2R	.	BED_feature	5443381	5443692	.	.	.	Name=9882489
chr3R	.	BED_feature	12526745	12526993	.	.	.	Name=8404855
chr3R	.	BED_feature	17497442	17497479	.	.	.	Name=9380507
chrX	.	BED_feature	10924674	10925117	.	.	.	Name=1907377
chr3R	.	BED_feature	2685238	2685270	.	.	.	Name=1640455
chr3L	.	BED_feature	7788287	7790270	.	.	.	Name=9409684
chr3L	.	BED_feature	7827233	7827421	.	.	.	Name=9409684
chr3R	.	BED_feature	11136419	11136478	.	.	.	Name=9409684
chr2R	.	BED_feature	5485654	5485695	.	.	.	Name=8787744
chr2L	.	BED_feature	2481563	2481768	.	.	.	Name=10862738
chr2L	.	BED_feature	14615054	14615087	.	.	.	Name=8164672
chr3R	.	BED_feature	2689744	2689778	.	.	.	Name=8164672
chr2R	.	BED_feature	5497334	5497360	.	.	.	Name=12482712
chr2L	.	BED_feature	4878294	4879189	.	.	.	Name=2120114
chr2L	.	BED_feature	4880430	4881558	.	.	.	Name=2120114
chrX	.	BED_feature	1896248	1896914	.	.	.	Name=2120114
chr3L	.	BED_feature	17584543	17584574	.	.	.	Name=1708722
chr2R	.	BED_feature	7043761	7043790	.	.	.	Name=1708722
chr3R	.	BED_feature	12560120	12560151	.	.	.	Name=1708722
chr3R	.	BED_feature	2689746	2689778	.	.	.	Name=1852610
chr3L	.	BED_feature	9357457	9357487	.	.	.	Name=9790883
chr2R	.	BED_feature	1602041	1602070	.	.	.	Name=9790883
chr3R	.	BED_feature	12527040	12527064	.	.	.	Name=1902784
chr3R	.	BED_feature	21822557	21822585	.	.	.	Name=10452845
chr3R	.	BED_feature	21825206	21825343	.	.	.	Name=10452845
chr3R	.	BED_feature	21850364	21850817	.	.	.	Name=10452845
chr3R	.	BED_feature	12636463	12637611	.	.	.	Name=10644409
chr3L	.	BED_feature	15622620	15623045	.	.	.	Name=8557043
chr2R	.	BED_feature	2174102	2174267	.	.	.	Name=1731341
chr2R	.	BED_feature	2179144	2179187	.	.	.	Name=1731341
chr2L	.	BED_feature	13905166	13905259	.	.	.	Name=15728670
chr2R	.	BED_feature	1216943	1217624	.	.	.	Name=11262224
chr2R	.	BED_feature	7043589	7044212	.	.	.	Name=3356339
chr3L	.	BED_feature	20627341	20627436	.	.	.	Name=7969130
chr3L	.	BED_feature	14936910	14937854	.	.	.	Name=7958878
chrX	.	BED_feature	226780	226809	.	.	.	Name=7958878
chr2R	.	BED_feature	8296265	8296293	.	.	.	Name=7958878
chr3R	.	BED_feature	21825185	21825215	.	.	.	Name=7958878
chr3R	.	BED_feature	21850444	21850473	.	.	.	Name=7958878
chr3R	.	BED_feature	21862518	21862645	.	.	.	Name=7958878
chr3R	.	BED_feature	21865794	21865829	.	.	.	Name=7958878
chr3L	.	BED_feature	4003948	4004010	.	.	.	Name=7489720
chr3L	.	BED_feature	21407876	21410397	.	.	.	Name=7489720
chr2L	.	BED_feature	3826260	3826317	.	.	.	Name=7489720
chr2R	.	BED_feature	18376805	18376867	.	.	.	Name=7489720
chrX	.	BED_feature	18075283	18075311	.	.	.	Name=16277982
chr3R	.	BED_feature	2689744	2689778	.	.	.	Name=1448096
chr3L	.	BED_feature	14909846	14909875	.	.	.	Name=10603347
chr3L	.	BED_feature	14934455	14934484	.	.	.	Name=10603347
chr3L	.	BED_feature	14937823	14937853	.	.	.	Name=10603347
chr3R	.	BED_feature	4104931	4104985	.	.	.	Name=10603347
chr3L	.	BED_feature	9357454	9357484	.	.	.	Name=9580693
chrX	.	BED_feature	1896678	1896720	.	.	.	Name=9580693
chr3R	.	BED_feature	12484744	12484783	.	.	.	Name=1356765
chr3R	.	BED_feature	26675304	26675349	.	.	.	Name=8543159
chr3R	.	BED_feature	26677809	26677880	.	.	.	Name=8543159
chr3L	.	BED_feature	8682159	8682185	.	.	.	Name=15128656
chr2R	.	BED_feature	20311059	20311086	.	.	.	Name=10704846
chrX	.	BED_feature	7376020	7376050	.	.	.	Name=11303087
chr3L	.	BED_feature	8640829	8640854	.	.	.	Name=9250684
chrX	.	BED_feature	3105827	3105963	.	.	.	Name=8890156
chr3L	.	BED_feature	21371559	21371592	.	.	.	Name=1508206
chrX	.	BED_feature	6938208	6938242	.	.	.	Name=7567454
chr3R	.	BED_feature	17204064	17204146	.	.	.	Name=9211899
chr2L	.	BED_feature	2445759	2445918	.	.	.	Name=11691840
chr3L	.	BED_feature	9357456	9357482	.	.	.	Name=8007953
chr3L	.	BED_feature	14063392	14063426	.	.	.	Name=8007953
chr3R	.	BED_feature	21824890	21825328	.	.	.	Name=7590239
chr3R	.	BED_feature	21850364	21850623	.	.	.	Name=7590239
chr3R	.	BED_feature	21865318	21865781	.	.	.	Name=7590239
chr3R	.	BED_feature	20574970	20575185	.	.	.	Name=8264640
chr2L	.	BED_feature	1992150	1992181	.	.	.	Name=11729153
chrX	.	BED_feature	20223944	20223971	.	.	.	Name=11729153
chrX	.	BED_feature	20226418	20227441	.	.	.	Name=11729153
chrX	.	BED_feature	20229403	20229432	.	.	.	Name=11729153
chr2R	.	BED_feature	6422831	6422858	.	.	.	Name=11729153
chr2R	.	BED_feature	6425801	6425832	.	.	.	Name=11729153
chr2R	.	BED_feature	10539700	10539731	.	.	.	Name=11729153
chr2R	.	BED_feature	15214163	15214190	.	.	.	Name=11729153
chr2R	.	BED_feature	15215645	15215672	.	.	.	Name=11729153
chr2R	.	BED_feature	15218020	15218639	.	.	.	Name=11729153
chr2R	.	BED_feature	15221586	15221613	.	.	.	Name=11729153
chr2R	.	BED_feature	15227234	15227262	.	.	.	Name=11729153
chr2R	.	BED_feature	15298881	15298912	.	.	.	Name=11729153
chr2R	.	BED_feature	15330413	15330442	.	.	.	Name=11729153
chr2R	.	BED_feature	16018503	16018532	.	.	.	Name=11729153
chr2R	.	BED_feature	16063152	16063976	.	.	.	Name=11729153
chr2R	.	BED_feature	16066132	16066750	.	.	.	Name=11729153
chr3R	.	BED_feature	1931724	1931751	.	.	.	Name=11729153
chr3R	.	BED_feature	1937966	1937996	.	.	.	Name=11729153
chr3R	.	BED_feature	1940940	1940967	.	.	.	Name=11729153
chr3R	.	BED_feature	25497414	25497442	.	.	.	Name=11729153
chr2L	.	BED_feature	14615482	14615511	.	.	.	Name=11493537
chr3R	.	BED_feature	12695177	12695321	.	.	.	Name=11493537
chr2L	.	BED_feature	14615465	14615527	.	.	.	Name=3159479
chr3L	.	BED_feature	15496339	15497308	.	.	.	Name=15901661
chr2R	.	BED_feature	5490971	5491016	.	.	.	Name=1672661
chr3L	.	BED_feature	17584385	17585044	.	.	.	Name=2501151
chr2R	.	BED_feature	5566447	5566485	.	.	.	Name=14731391
chr3R	.	BED_feature	26036495	26036530	.	.	.	Name=14731391
chr2L	.	BED_feature	7303538	7307465	.	.	.	Name=9502727
chr2R	.	BED_feature	7044641	7044740	.	.	.	Name=1671661
chr2R	.	BED_feature	7239906	7240304	.	.	.	Name=15075295
chr2R	.	BED_feature	7242145	7242175	.	.	.	Name=15075295
chr2R	.	BED_feature	7327511	7327540	.	.	.	Name=15075295
chr3R	.	BED_feature	10423058	10423085	.	.	.	Name=15075295
chr3L	.	BED_feature	8702350	8702385	.	.	.	Name=1280827
chrU	.	BED_feature	4976167	4976193	.	.	.	Name=1671176
chr3R	.	BED_feature	2583623	2583649	.	.	.	Name=1671176
chrX	.	BED_feature	5745755	5745824	.	.	.	Name=2123290
chr3R	.	BED_feature	23064969	23065056	.	.	.	Name=8662923
chr2R	.	BED_feature	19812221	19812254	.	.	.	Name=9676198
chr2L	.	BED_feature	9967220	9968564	.	.	.	Name=12758126
chr3L	.	BED_feature	9351683	9351719	.	.	.	Name=8474442
chr2R	.	BED_feature	14380568	14380599	.	.	.	Name=7537872
chr2L	.	BED_feature	14615100	14615131	.	.	.	Name=1732738
chr2R	.	BED_feature	5490985	5491028	.	.	.	Name=8406007
chr2L	.	BED_feature	14616172	14616209	.	.	.	Name=7783192
chr3L	.	BED_feature	11485536	11485560	.	.	.	Name=1903838
chr3R	.	BED_feature	7188391	7189913	.	.	.	Name=11051550
chr3R	.	BED_feature	26678046	26678342	.	.	.	Name=8430097
chr3R	.	BED_feature	26679686	26680087	.	.	.	Name=8430097
chr3R	.	BED_feature	21070786	21070810	.	.	.	Name=14561403
chr3R	.	BED_feature	12599091	12599336	.	.	.	Name=10433918
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s2.bed000066400000000000000000002537241211610345200224730ustar00rootroot00000000000000chr4	74488436	74488469	2247076
chr20	22978319	22978355	11257274
chr1	227636539	227636698	2300053
chr5	142760500	142760529	11463861
chr5	142795076	142795171	11463861
chr11	303985	304024	2123539
chr1	27871383	27871421	2123539
chr5	132037517	132037549	9686601
chr4	123597348	123597378	9686601
chr9	129656861	129656893	9845534
chr18	72858092	72858121	7527040
chr1	165754421	165754452	9510181
chr6	36754360	36754400	10506225
chr9	21067980	21068019	2037595
chr17	35109678	35109708	9045619
chr11	605677	605718	10924517
chr11	32405320	32405350	10455131
chr5	131434149	131434658	8460159
chr4	123597348	123597379	8460159
chr14	105142540	105142615	7635985
chr14	105261326	105261401	7635985
chr18	72858012	72858327	1696259
chr11	5227818	5227864	2458563
chr11	5232742	5232788	2458563
chr11	605674	605722	11877397
chr16	10897092	10897125	15247294
chr16	10908371	10909110	15247294
chr16	10880160	10880210	9491997
chr10	75339285	75339336	8071349
chr7	525969	526156	8415628
chr19	59077686	59077730	2246272
chr17	61729560	61729604	2246272
chr16	23755126	23755170	2246272
chr4	123597347	123597383	7624346
chr14	24173351	24173382	7624346
chr20	60962038	60962071	12923186
chr9	21067972	21068006	2139895
chr17	59307403	59307440	16239259
chr17	59315149	59315190	16239259
chr17	59329948	59329989	16239259
chr2	162717072	162717294	15828872
chr8	11697516	11697549	9092581
chr4	68303660	68303689	12089350
chr2	175741023	175741060	2145272
chr9	127043486	127043516	9837962
chr6	43247768	43247886	2009862
chr6	43249560	43249830	2009862
chr6	43251430	43251559	2009862
chr6	43254024	43254103	2009862
chr22	37970974	37971015	8662878
chrX	37524155	37524199	11781315
chr7	99227486	99227522	12514743
chr3	121018720	121018751	12514743
chr1	198409938	198409967	12514743
chr9	136358295	136358325	12514743
chr12	119900951	119900981	12514743
chr20	42491696	42491726	12514743
chr15	49322676	49322730	8395654
chr11	303985	304024	2919169
chr10	62207740	62208380	8524257
chr3	25444698	25444725	9886825
chr13	93928760	93930546	7929451
chr3	197293412	197293473	2519614
chr4	84474935	84475267	11779847
chr2	21173783	21173833	10859308
chr1	148070786	148070817	2367528
chr1	148099376	148099407	2367528
chr21	26464851	26464881	8703038
chr7	5535519	5535577	9847397
chr6	46280790	46280829	9847397
chr6	89043284	89043326	9847397
chr5	77116585	77116627	9847397
chr5	79634272	79634314	9847397
chr5	97702459	97702501	9847397
chr3	177178903	177178935	9847397
chr1	222119015	222119057	9847397
chr9	102533463	102533496	9847397
chrX	46033350	46033389	9847397
chr22	39801028	39801062	9847397
chr15	42069511	42069553	9847397
chr18	58260340	58260379	9847397
chr11	5204934	5204965	8663270
chr6	31891181	31891213	1696723
chr6	31903377	31903409	1696723
chr5	149772537	149772621	1899864
chr6	87861686	87861724	2476438
chr6	32515518	32515547	8756625
chr11	2139272	2139305	8832573
chr13	27389425	27389468	11003654
chr14	67360017	67360070	9878257
chr7	24290260	24290290	8123590
chr4	123597156	123597186	1712901
chr12	23578124	23578724	1396566
chr12	23580652	23580871	1396566
chr12	23587410	23587586	1396566
chr12	23590518	23590629	1396566
chr12	23607457	23607599	1396566
chr12	23619860	23620044	1396566
chr12	23685011	23685100	1396566
chr11	15967126	15967239	1396566
chr11	117692801	117692831	1396566
chr1	202359461	202360518	1396566
chr8	88869623	88871029	1396566
chr14	105142609	105142639	9317131
chr17	45632664	45634784	3480516
chr12	66839311	66839342	10227974
chr21	44378027	44378057	12808467
chr12	6517179	6517207	12933903
chr16	10910501	10910529	12933903
chr16	10917736	10917765	12933903
chr3	46880058	46880137	1699944
chr14	105142553	105142609	8759736
chr14	105261339	105261401	8759736
chr11	5203641	5204288	7499351
chr9	106691206	106691258	11839742
chr9	138991424	138991702	15743775
chr7	91602080	91602142	12145339
chr17	70254458	70255238	12145337
chr17	70256545	70256588	12145337
chr7	100159373	100159407	8387214
chr12	108038831	108038863	11076940
chr12	108053504	108053612	11076940
chr11	116213731	116213811	8626539
chr22_random	13234	13314	8626539
chr7	27140154	27140183	8759021
chr16	55199807	55199838	8759021
chr17	53714113	53714143	9287329
chr11	118463821	118463852	8408012
chr5	131907150	131907240	15826950
chr5	132043302	132043331	15826950
chr6	32515525	32515555	7784170
chr17	31441612	31441885	8355682
chr17	31548285	31548549	8355682
chr17	31649859	31650123	8355682
chr17_random	1227833	1228097	8355682
chr19	34994861	34995325	8618861
chr2	169927260	169927288	10799495
chr11	5204936	5204966	9642249
chr11	5227736	5227791	9642249
chr11	5232660	5232715	9642249
chr11	5247819	5247853	9642249
chr16	142778	142810	9642249
chr16	152990	153022	9642249
chr5	142673758	142673832	3037703
chr4	149219374	149222100	3037703
chr4	149254704	149254867	3037703
chr4	149260758	149260877	3037703
chr4	149293069	149293211	3037703
chr4	149295150	149295504	3037703
chr4	149335346	149335465	3037703
chr4	149400578	149400721	3037703
chr4	149575705	149577463	3037703
chr4	149582760	149582973	3037703
chr13	19032152	19032208	11986328
chr13	20733666	20733722	11986328
chr11	63839958	63840014	11986328
chr6	160034412	160034809	11853549
chr6	153113526	153113563	2320002
chr14	74815206	74815246	2320002
chr17	7531563	7531591	10348347
chr4	74488729	74488763	2320004
chr1	167341717	167341979	8392703
chr6	87861633	87861665	1701437
chr14	74814959	74815008	3004967
chr7	5536804	5536857	7828546
chr3	188870906	188870942	8645191
chr1	202402286	202402322	8645191
chr19	2200167	2200195	9774680
chr12	51132125	51132488	2438131
chr12	51153784	51154148	2438131
chr12	51173235	51173600	2438131
chr12	51476140	51476239	2438131
chr17	36232359	36232424	2438131
chr11	5204984	5205048	11756191
chr11	5258555	5258590	11756191
chr12	54713253	54713285	10978333
chr12	111829114	111829157	2174873
chr11	303988	304018	2174873
chr15	42790853	42790900	2174873
chr11	100505079	100505108	15084343
chr6	31651125	31651176	12560487
chr11	5262446	5262488	3879975
chrX	55670007	55670049	1946405
chr14	99813795	99813826	1946405
chr7	22733173	22733209	8207232
chr4	74825043	74825086	8207232
chr17	35425015	35425052	8207232
chr1	159760611	159760647	3198647
chr1	159842260	159842296	3198647
chr19	7245409	7246142	1324934
chr6	36752201	36753120	12640112
chr1	27060396	27060437	12640112
chr16	68973088	68973120	9473501
chr16	68989907	68989937	9473501
chr14	22974963	22975026	1577822
chr9	21067982	21068040	1532252
chr5	132019685	132021821	8605348
chr5	132200100	132200211	8605348
chr11	5227730	5227785	7914370
chr11	5232654	5232709	7914370
chrX	37524148	37524181	7914370
chrX	24621889	24621954	15615704
chr11	5227721	5227997	2734104
chr11	5232645	5232925	2734104
chr10	72033576	72033645	10072525
chr16	55199885	55199917	2494701
chr15	72826154	72826254	8120057
chr17	38820333	38820372	2349089
chr3	73242764	73242823	2349089
chr17_random	492577	492638	2349089
chr17_random	494190	494241	2349089
chr17_random	510842	510904	2349089
chr17_random	512334	512396	2349089
chr17_random	514636	514697	2349089
chr17_random	519525	519586	2349089
chr17_random	525673	525734	2349089
chr17_random	527778	527840	2349089
chr17_random	556025	556087	2349089
chr17_random	2607832	2607893	2349089
chr17_random	2614873	2614935	2349089
chr15	65919437	65919514	2349089
chr1	67925700	67925730	11090615
chr3	185578715	185578748	11790771
chr20	54400822	54400851	11790771
chr11	100505079	100505190	10894148
chr16	10878404	10878701	11777970
chr6	121798621	121798697	12644583
chr5	108416077	108416125	12644583
chr1	205186357	205186544	14644095
chr11	116213544	116213694	1846669
chr22_random	13278	13501	1846669
chr6	87861641	87861711	2828923
chr6	87861738	87861778	12193378
chr7	45894486	45894517	7688722
chr19	54351000	54351029	15082771
chr17	71229145	71229180	9837976
chr1	185064111	185064783	7800505
chr1	185090038	185090099	7800505
chr12	46798802	46799458	7800504
chr4	74825037	74825086	10928981
chr17	31231572	31231601	10928981
chr2	85969656	85969692	14644416
chr1	89303545	89303575	1729591
chr7	150316900	150317059	11013235
chr3	170965506	170965616	12586348
chr19	46551328	46551628	2808430
chr12	51782657	51782690	15961790
chr19	16298811	16298842	11750135
chr10	5126489	5126539	15814298
chr16	31632044	31632077	15814297
chr16	31792540	31792792	15814297
chr1	89303574	89303611	1901265
chr1	89645724	89645761	1901265
chr15	88150900	88151079	1680856
chr5	131907211	131907240	11152655
chr10	17310281	17310756	8654956
chr16	54247448	54248013	11333263
chr14	72672977	72673010	10446206
chr12	50731408	50731459	10567637
chr9	134927113	134927158	11945176
chr9	134947671	134947716	11945176
chr7	106472226	106472261	9175634
chr19	54219614	54219649	9175634
chr19	54226281	54226316	9175634
chr19	54232640	54232675	9175634
chr19	54238668	54238703	9175634
chr19	54244382	54244417	9175634
chr19	54251019	54251054	9175634
chr8	128817316	128817344	2690070
chr7	21434866	21436872	1454515
chr7	21483234	21483345	1454515
chr7	21488165	21488261	1454515
chr7	21517247	21517549	1454515
chr13	88810290	88812937	1454515
chr2	174481585	174483182	1454515
chr2	174486194	174486242	1454515
chr2	174491580	174491751	1454515
chr2	174527987	174529207	1454515
chrX	55074223	55074271	9334239
chr21	26464985	26465014	1380960
chr12	66839979	66840016	8756632
chr11	116205060	116205698	9295296
chr22_random	21342	21981	9295296
chr5	131423935	131423974	8611694
chr16	55199808	55199838	9171103
chr10	112826538	112826790	9249478
chr11	116204976	116205835	2834395
chr22_random	21205	22065	2834395
chr10	17311047	17311087	2293664
chr11	525485	525798	3012774
chr2	136592478	136592507	10229837
chr3	120761101	120761701	8906820
chr5	159778570	159778599	15016801
chr5	159780261	159781293	15016801
chr11	124999009	124999038	15016801
chr11	125000252	125000620	15016801
chr6	29798934	29798987	8657576
chr6	29867704	29867764	8657576
chr6	29903336	29903396	8657576
chr6	29963226	29963279	8657576
chr6	30001930	30001990	8657576
chr6	30018025	30018078	8657576
chr6	30082069	30082121	8657576
chr6	30335106	30335147	8657576
chr4	74825005	74825052	8175759
chr6	32742393	32742649	8315353
chr11	118463734	118463763	2771941
chr7	45930677	45930706	14963110
chr14	94117290	94117597	9601089
chr11	61942943	61942994	9468485
chr17	35727181	35727965	15831516
chr17	35732149	35732743	15831516
chr6	30565086	30565123	8702722
chr10	91051673	91051709	8702722
chr4	74825041	74825071	8413306
chr1	27060400	27060434	9659898
chr17	59304831	59304865	16517055
chr17	59327728	59327762	16517055
chr17	59342412	59342446	16517055
chr17	59349992	59350026	16517055
chr14	74814954	74815007	1639071
chr3	70068143	70068181	10938265
chr3	134947297	134947876	2495523
chr14	93924791	93924822	2495523
chr6	32742365	32742936	1985121
chr6	32839240	32839653	1985121
chr8	42184273	42184463	9016559
chr17	35740995	35741053	7479078
chr9	136448822	136448877	7479078
chr15	94678306	94678373	7479078
chr20	61844190	61844300	14625278
chr8	28270141	28270216	14625278
chr8	28273131	28273207	14625278
chr8	28274487	28274561	14625278
chr1	167969983	167970010	7518452
chr3	123384312	123384360	12036954
chr3	123385623	123385674	12036954
chr14	74814933	74814994	3029776
chr7	45894486	45894515	9261184
chr17	77650007	77650042	9261184
chr3	188042774	188043233	15850785
chr11	116213541	116213703	11714848
chr22_random	13342	13504	11714848
chr6	31891189	31891235	2342471
chr6	31903385	31903431	2342471
chr22	17200931	17200972	16107498
chr22	19826896	19826937	16107498
chr22	19952172	19952213	16107498
chr2	11523692	11523952	16107498
chr18	27425727	27425757	2019605
chr2	21119525	21119763	2019605
chr12	6925719	6926152	11376946
chr1	157951087	157951128	8621622
chr10	5228099	5228140	11284743
chr19	6671574	6671793	2247055
chr6	43247372	43247404	2200737
chr6	32515517	32515570	11046010
chr6	33016713	33016744	11046010
chr5	32747446	32747507	7641319
chr2	70634548	70634607	9162057
chr9	21067984	21068015	9199299
chr17	31231512	31231552	10023774
chr12	67488870	67488913	9233781
chr6	36752111	36753033	9233781
chr3	130730025	130730054	9579468
chrX	153059391	153059427	9579468
chrX	153062720	153062935	9579468
chrX	153101128	153101363	9579468
chrX	153138246	153138481	9579468
chr7	47058918	47058999	1465383
chr11	94410404	94410505	1465383
chr11	94440041	94440142	1465383
chr17	72244733	72246053	1465383
chrX	34315777	34315833	1465383
chr13	109236951	109236995	15048126
chr7	27114667	27114704	8264592
chr7	27135537	27135602	8264592
chr7	27151889	27151957	8264592
chr7	27161206	27161280	8264592
chr12	52709803	52709877	8264592
chr17	44009203	44009259	8264592
chr17	44024648	44024710	8264592
chr17	44028861	44028923	8264592
chr17	44040296	44040358	8264592
chr2	176725730	176725759	8264592
chr22	37970974	37971013	9341193
chr2	219354985	219355021	11867220
chr4	123597348	123597378	2123468
chr4	123597328	123597356	2204815
chr16	31346875	31346956	7687470
chr16	31348751	31348842	7687470
chr15	32875077	32875112	2123467
chr16	4247192	4248251	2123466
chr16	4250104	4250595	2123466
chr16	4251849	4252702	2123466
chr16	4262659	4262695	2123466
chr6	32260151	32260185	10829018
chr11	5227715	5227760	1698280
chr11	5232639	5232684	1698280
chr14	22095167	22095265	7774816
chr6	31891187	31891281	3031671
chr6	31903380	31903455	3031671
chr12	12761487	12761533	10542271
chr12	47864841	47865066	3839072
chr12	47866619	47868999	3839072
chr12	47949737	47949778	3839072
chr7	55054352	55054388	2170982
chr6	32515499	32515573	10072067
chr9	135490836	135491305	7688735
chr16	66202233	66203527	8246978
chr16	66208146	66208278	8246978
chr16	66212098	66212957	8246978
chr16	66217957	66218120	8246978
chr16	66219770	66220929	8246978
chr16	66229228	66230572	8246978
chr6	22395672	22395702	8015553
chr6	22402675	22402707	8015553
chr6	22405213	22405243	8015553
chr6	22411661	22413974	8015553
chr1	120737547	120737587	9144409
chr1	147635797	147635837	9144409
chr1	148020753	148020792	9144409
chr12	111900547	111900584	9813254
chr6	12120599	12120645	2106471
chr6	12228134	12232523	2106471
chr6	12269716	12270134	2106471
chr6	12271631	12273113	2106471
chr5	131434406	131434658	7891702
chr11	102219596	102219626	7891702
chr20	3013399	3013428	12403649
chr4	74825044	74825072	12767906
chr11	47372996	47373029	15767686
chr16	54247462	54248144	9928902
chr12	9159965	9160004	7507205
chr1	147635801	147635841	7507205
chr5	131854189	131854859	7507207
chr4	185632677	185632974	7507207
chr4	123597348	123597378	11994417
chr15	32875132	32875161	3477800
chr17	38306145	38306188	10960473
chr4	123597348	123597378	8524297
chr11	59612763	59612817	12697656
chr16	28850731	28850764	12218128
chr4	74824867	74824907	15085176
chr15	89228610	89228713	8657143
chr12	54408961	54409501	1599482
chr14	21999474	21999519	1833636
chr1	89303574	89303603	1833631
chr1	89645732	89645761	1833631
chr12	79625994	79626043	1659574
chr12	79635308	79635379	1659574
chr11	17698325	17698396	1659574
chr1	201318969	201322888	1659574
chr18	24010985	24011015	15541732
chr4	122964728	122964757	7760822
chr8	16094714	16094745	7760824
chrX	66681555	66683257	2911578
chrX	66779829	66779939	2911578
chrX	66822574	66822693	2911578
chrX	66848027	66848257	2911578
chrX	66854043	66854192	2911578
chrX	66858399	66860554	2911578
chr11	13474102	13474459	1977134
chr6	27899739	27899784	3071490
chr6	27907381	27907426	3071490
chr11	102174146	102174184	8139041
chr2	70634954	70635030	10828826
chr4	103737713	103737856	1992489
chr4	103741086	103741160	1992489
chr4	103746686	103747905	1992489
chr1	205560906	205561732	7678027
chr3	166279011	166279225	9806892
chr6	31891181	31891213	1569208
chr6	31903377	31903409	1569208
chr3	129689434	129690224	8972903
chr3	166279008	166279036	9822664
chr10	91001599	91001893	9799798
chr14	92458567	92459224	7588318
chr5	131423976	131424006	1695008
chr9	97121060	97121106	9063748
chr11	303985	304024	1832217
chr12	3499781	3499812	2531661
chr6	31891187	31891393	1986252
chr6	31903382	31903440	1986252
chr14	105399325	105399391	1986254
chr6	160309964	160310147	12857727
chr6	170705395	170705476	2363050
chr6	170707889	170708097	2363050
chr6	170712800	170713246	2363050
chr6	170715557	170715645	2363050
chr6	170717928	170718022	2363050
chr6	170720622	170720792	2363050
chr6	170722419	170723871	2363050
chr14	54950868	54950903	2363050
chr11	117692798	117692830	1639073
chr14	22095208	22095240	1639073
chr3	134944265	134944298	1748690
chr3	134947816	134947847	1748690
chr6	138230057	138230159	1381359
chr16	55199881	55199909	1530876
chr6	32515533	32515560	8687468
chr19	46188737	46188767	15563456
chr2	234334489	234334518	15563456
chr1	938620	938651	9268360
chr6	36754380	36754494	9268365
chr19	38484210	38484346	2112087
chr8	48812542	48812632	2112087
chr20	48240716	48242593	2112087
chr14	22656647	22656739	2112087
chr6	31891220	31891289	2474756
chr5	172129548	172129577	12890671
chr2	234191158	234191187	12847094
chr7	142294892	142294922	16574738
chr7	127668430	127668469	12215445
chr11	67107744	67107808	8702826
chr12	19152172	19152260	1748287
chr19	19117378	19119601	1748287
chr19	19152494	19152545	1748287
chr19	19157848	19158743	1748287
chr1	177683536	177684321	1748287
chr15	97956156	97956201	1748287
chr15	97990722	97990841	1748287
chr15	98003399	98003474	1748287
chr15	98029245	98029277	1748287
chr15	98032120	98033187	1748287
chr15	98048063	98048103	1748287
chr15	98064479	98064564	1748287
chr15	98068360	98068487	1748287
chr15	98070117	98071466	1748287
chr17	37121939	37121975	8294480
chr6	137517883	137517936	11390454
chr6	27208581	27208614	1535687
chr5	131437265	131437302	2342464
chr4	123597277	123597307	2342464
chr19	46551797	46551827	8016096
chr8	110168010	110168039	10208868
chr9	127043479	127043510	11779464
chr21	42513537	42513600	16024918
chr21	42528059	42528089	16024918
chr17	35827710	35828062	9126321
chr2	232951133	232951342	8314767
chr2	232979242	232979753	8314767
chr3	10306896	10306926	15142980
chr2	21120509	21120712	3165376
chr11	5227731	5227785	3181130
chr11	5232655	5232709	3181130
chr19	11349767	11349839	11756159
chr8	57521686	57521720	1372443
chr12	119900660	119900690	7984419
chr11	116199349	116199608	7984419
chr22_random	27425	27684	7984419
chr11	14950713	14950744	7476962
chr7	93861869	93861906	10201951
chr2	127892441	127892602	10333497
chr11	116213687	116213765	1904868
chr14	93924787	93924824	1904868
chr2	21120484	21120527	1904868
chr1	159460922	159460951	1904868
chr22_random	13280	13358	1904868
chr1	59022296	59022365	3142689
chr15	94674718	94674917	8706939
chr16	103419	103842	1569944
chr11	116196773	116196809	15583007
chr11	116199349	116199612	15583007
chr11	116205089	116205118	15583007
chr22_random	21923	21952	15583007
chr22_random	27421	27684	15583007
chr22_random	30224	30260	15583007
chr19	11061024	11061096	11250935
chr11	71527654	71528440	8106441
chr11	71547899	71547972	8106441
chr11	71565458	71566624	8106441
chr11	71584046	71584794	8106441
chr11	71605408	71605616	8106441
chr11	71607253	71607388	8106441
chr11	71609561	71610614	8106441
chr11	5227730	5227858	2468996
chr11	5232654	5232782	2468996
chr15	32875149	32875208	2823106
chr21	45786704	45787763	15214842
chr21	26465018	26465049	9407128
chr12	119900660	119900689	8290348
chr11	116213739	116213767	8290348
chr22_random	13278	13306	8290348
chr6	43844938	43844970	15039136
chr20	10596531	10596582	11641404
chr7	5533904	5534772	11322928
chr5	79631252	79631282	11322928
chr3	12087833	12087862	11322928
chr2	130548917	130548947	11322928
chr2	130937489	130937519	11322928
chr2	131131259	131131289	11322928
chr2	131738065	131738095	11322928
chr1	103914789	103914818	11322928
chr22	14635979	14636009	11322928
chr15	42069176	42069206	11322928
chr14	18655264	18655294	11322928
chr14	19058341	19058371	11322928
chr17	77092311	77092340	11322928
chr4	123597348	123597379	9837957
chr1	202402193	202402324	15353176
chr6	336164	336208	14581002
chr8	128816874	128816903	11777933
chr16	67328518	67328548	10706097
chr14	19992504	19995822	8086453
chr9_random	773107	774288	8086450
chr9	39644307	39645487	8086450
chr9	41018837	41020018	8086450
chr9	41789333	41790512	8086450
chr9	43340024	43341196	8086450
chr9	44498990	44500171	8086450
chr9	46838063	46839243	8086450
chr9	65798699	65799873	8086450
chr10	104279414	104279451	8086450
chr16	70596553	70597948	8086450
chr14	62140706	62141943	8086450
chr18	41917563	41922205	8086450
chr18	41923389	41929342	8086450
chr18	41930481	41933932	8086450
chr18	41935209	41935246	8086450
chr2	37237692	37237722	14645369
chr6	6265903	6265990	10037697
chr6	32929565	32929600	9858567
chr2	21120492	21120712	1660892
chr6	32742503	32742590	1923758
chr6	32839378	32839415	1923758
chr16	164052	164084	12854969
chr2	97628464	97628508	8806766
chr10	71914084	71915951	1309593
chr4	91974734	91974917	1309593
chr4	189161381	189161743	1309593
chrX	21785144	21785514	1309593
chrX	55669735	55670397	1309593
chr2	139371720	139372908	1309593
chr14	99775245	99776011	1309593
chr14	99798412	99798553	1309593
chr14	99810785	99810849	1309593
chr14	99812579	99814652	1309593
chr15	32874976	32875527	3785189
chr13	79809668	79809698	14644509
chr13	79814606	79814638	14644509
chr12	51200532	51200570	10825196
chr17	16666647	16666682	10825196
chr17	16689983	16690041	10825196
chr17	18270767	18270815	10825196
chr17	18294131	18294166	10825196
chr17	20338176	20338211	10825196
chr17	20361513	20361571	10825196
chr17	25922983	25923034	10825196
chr17	36996728	36996763	10825196
chr17	37034416	37034478	10825196
chr6	87861543	87861856	2481230
chr6	31661881	31662346	10944527
chr7	55054196	55054236	2556218
chr5	149446367	149446397	7969146
chr2	216008981	216009553	2170405
chr11	2139070	2139247	16461554
chr5	1348020	1348063	9973199
chr11	5258401	5258444	1631062
chr11	5227736	5227790	11544252
chr11	5232660	5232714	11544252
chr11	5247815	5247860	11544252
chr11	63831221	63831266	9058380
chr7	99219888	99219918	9770465
chr2	161932567	161932611	7769002
chr2	161935935	161936003	7769002
chr6	32076547	32076639	10608879
chr6	32109285	32109377	10608879
chr13	40431030	40431107	8493578
chr1	170894474	170894506	9395475
chr1	157951016	157951098	2154372
chr1	1581883	1581918	15087126
chr1	1647169	1647204	15087126
chr12	66838834	66839000	8670419
chr12	66840016	66840059	8670419
chr3	87391880	87391910	9626142
chr1	28375800	28375832	9058812
chr15	49420184	49420218	7626451
chr1	151240672	151240820	9889002
chr9	116920285	116920338	15001984
chr12	32723333	32723427	14741701
chr10	91051672	91051706	2236065
chr15	72447071	72447105	7798178
chr6	39629677	39630762	7958925
chr16	65783670	65784573	7958925
chr16	65785801	65787410	7958925
chr16	65789001	65789748	7958925
chr1	117098408	117098438	7929376
chr4	152240170	152240251	12463423
chr17	39822367	39822995	7518432
chr14	93924791	93924822	8621550
chr4	185587188	185587218	1579446
chr5	131424077	131424114	8704203
chr14	105142429	105142467	9190940
chr14	105261215	105261253	9190940
chr21	29636784	29636815	11069897
chr14	74815006	74815034	12242287
chr16	55199697	55199932	3821726
chr11	101896526	101896687	8294454
chr11	67107755	67107796	8206948
chr10	91051670	91051711	2342456
chr9	21067979	21068020	2495183
chr19	54226281	54226326	9182571
chr19	54232630	54232675	9182571
chr19	54238601	54238713	9182571
chr19	54244372	54244417	9182571
chr19	54251013	54251054	9182571
chr17	7063968	7063998	10607478
chr16	55199808	55199838	1852613
chr1	100957806	100957835	7499419
chr5	147996921	147996991	15575821
chr22_random	21651	21681	9322942
chr5	149772577	149772830	8164652
chr3	25444696	25444725	7931079
chr7	30970033	30970097	10207037
chr2	88926786	88926816	1406692
chr5	158690173	158690202	9497375
chrY	1693987	1694161	7989373
chrX	1693987	1694161	7989373
chr19	11061106	11061136	10671569
chr6	22405250	22405369	12223489
chr7	93861869	93861906	8621730
chr16	31178718	31178865	8955212
chr11	5662867	5663929	16289103
chrX	37524142	37524171	1885602
chr7	5535922	5535983	3422098
chr20	1922571	1922602	9819380
chr1	938621	938650	2606351
chr7	526008	526156	8349616
chr12	47637373	47638624	8473323
chr9	136468132	136468176	8264664
chr16	66022178	66022739	11850421
chrX	37524201	37524230	12732216
chr13	93930267	93930296	9447965
chr11	116205088	116205118	9592157
chr22_random	21923	21953	9592157
chr12	79625628	79626072	1374396
chr12	79635307	79635380	1374396
chr11	17698325	17698389	1374396
chr1	201321305	201321383	1374396
chr16	55199876	55199917	9155027
chr8	59575397	59575425	10777541
chr5	131424079	131424114	9036972
chr1	154477843	154478070	8388544
chr11	46934508	46934538	16227573
chr2	183836533	183837362	16227573
chr1	26626420	26627246	16227573
chr14	74814933	74814987	14737107
chr2	216008770	216009355	3031656
chr2	174538113	174538172	16024108
chr3	134947100	134947167	12459033
chr2	113258581	113258611	15863387
chr22	37970937	37971189	7961814
chr13	47775839	47775880	8620463
chr14	95791802	95791830	9553142
chr16	10880177	10880281	10202014
chr3	24511146	24511495	1339272
chr19	11061066	11061095	10579331
chr17	24099529	24099558	12788948
chr17	4491641	4492686	10657944
chr19	4767630	4767659	14960149
chr19	4783037	4783067	14960149
chr5	32747446	32747507	9492076
chr7	5534640	5534680	8474178
chr5	77117021	77117061	8474178
chr5	79631781	79631821	8474178
chr5	131023109	131023150	8474178
chr3	12087295	12087335	8474178
chr2	130937393	130937427	8474178
chr2	131131351	131131385	8474178
chr2	131738157	131738191	8474178
chr2	132100740	132100774	8474178
chr1	222118578	222118618	8474178
chr1	236157318	236157357	8474178
chr9	6825009	6825049	8474178
chr9	102533894	102533933	8474178
chr17	77093011	77093051	8474178
chr16	48650094	48650134	8474178
chr15	32453565	32453605	8474178
chr14	18655356	18655390	8474178
chr14	19058245	19058279	8474178
chr22	14635883	14635917	8474178
chr22	39800635	39800675	8474178
chr18	58260785	58260822	8474178
chr7	25129922	25129978	7926749
chr7	120825888	120825961	7926749
chr7	128544905	128544975	7926749
chr6	34295353	34295435	7926749
chr6	96058920	96059004	7926749
chr3	10017416	10017489	7926749
chr3	10074731	10074826	7926749
chr3	11895377	11895465	7926749
chr2	100353199	100353281	7926749
chr1	149143140	149143224	7926749
chr1	155364921	155365003	7926749
chr1	200605365	200605448	7926749
chrY	15562898	15562993	7926749
chrY	26956593	26956687	7926749
chr9	95840277	95840372	7926749
chrX	68621997	68622075	7926749
chrX	144065978	144066017	7926749
chrX	152760052	152760117	7926749
chr13	23873007	23873066	7926749
chr13	40335814	40335898	7926749
chr13	98080024	98080108	7926749
chr11	31258880	31258964	7926749
chr11	57529575	57529654	7926749
chr11	73871069	73871138	7926749
chr11	82717815	82717863	7926749
chr11	108198369	108198442	7926749
chr17	72707002	72707073	7926749
chr16	25373238	25373333	7926749
chr15	39188497	39188575	7926749
chr15	58576780	58577112	7926749
chr15	58579382	58580562	7926749
chr15	58582248	58583160	7926749
chr15	58584998	58585071	7926749
chr15	58590741	58591041	7926749
chr15	58594185	58594250	7926749
chr15	58636353	58636420	7926749
chr15	58637713	58637804	7926749
chr15	58706735	58706954	7926749
chr15	59308661	59308794	7926749
chr14	76169951	76170035	7926749
chr8	33946698	33946793	7926749
chr8	51837693	51837766	7926749
chr8	120699677	120699737	7926749
chr6	26140295	26140436	2928309
chr1	148070693	148070855	2928309
chr1	148099338	148099500	2928309
chr7	87068234	87069157	7961962
chr1	200246118	200246146	11313868
chr18	59294965	59295073	10692390
chr4	100493209	100493240	1320193
chr2	85749240	85749301	10617585
chr14	34943731	34944082	8262046
chr7	81237247	81237276	11112425
chr7	81238277	81238327	11112425
chr1	120737495	120737587	8455606
chr1	147635797	147635889	8455606
chr1	148020753	148020845	8455606
chr1	148070694	148070809	2768251
chr1	148099384	148099499	2768251
chr5	131434534	131434563	8809409
chr5	131437305	131437364	8809409
chr4	74516856	74516887	2708361
chr3	134944274	134944309	2708361
chr3	134947799	134947874	2708361
chr7	526480	526592	8486717
chr7_random	465929	466022	8486717
chr16	54068947	54068984	8610173
chr16	55199807	55199838	8610173
chr21	39099688	39099758	1888697
chr11	2139239	2139277	10601637
chr6	26216376	26216406	11098153
chr9	124711245	124711796	7958847
chr9	124712940	124714041	7958847
chr7	27135536	27136313	1970866
chr12	52734902	52734991	1970866
chr2	176725583	176725760	1970866
chr9	21067997	21068034	9446577
chr6	31658166	31658338	8786306
chr9	21067966	21068080	2910848
chr6	87861653	87861691	2159633
chr3	49701034	49701169	8702759
chr1	16844625	16844760	8702759
chr13	19033370	19033411	9865725
chr13	20732460	20732501	9865725
chr11	63831213	63831254	9865725
chr15	49322619	49322769	9865725
chr19	50100725	50100755	2188976
chr6	153113527	153113559	2842787
chr2	10505705	10505928	2318872
chr7	525926	526035	1417865
chr9	21067995	21068053	7523851
chr1	167969926	167970000	7523851
chr18	59138134	59138163	16186795
chr16	29983392	29983480	7473711
chr11	119683434	119683465	12624109
chr6	32515374	32515574	2851727
chr7	100556302	100557246	2840665
chr7	100558391	100558421	2840665
chr12	51001397	51001563	9811563
chr21	42660051	42660105	12021387
chr12	52063339	52063372	14593115
chr15	49420187	49420228	9817601
chr6	27208583	27208609	11566492
chr2	175330620	175330648	8441631
chr5	137695272	137695489	7828585
chr4	122964347	122964726	7556094
chr1	1580338	1580368	15656972
chr6	35562268	35562336	1851669
chr11	12652638	12653679	1851669
chr11	12742300	12742560	1851669
chr11	12840371	12840433	1851669
chr11	12842959	12843020	1851669
chr11	12857828	12857965	1851669
chr11	12859126	12860081	1851669
chr11	12861120	12861248	1851669
chr11	12880061	12880237	1851669
chr11	12903033	12903175	1851669
chr11	12908294	12908451	1851669
chr11	12915230	12917454	1851669
chr11	125553434	125554765	1851669
chr3	46186795	46186935	1851669
chr19	54554959	54555027	1851669
chr7	526001	526156	1460057
chr16	84494119	84494201	1460054
chr16	84509528	84509897	1460054
chr3	134947845	134947926	2839477
chr1	938619	938651	9234684
chr12	14740883	14740927	10889158
chr3	166279011	166279044	10889158
chr4	187424396	187424441	11891231
chr2	60961765	60962017	8666258
chr9	106642487	106642515	10858438
chr3	25444696	25444725	1335571
chr17	4794239	4795878	1840492
chr11	63824693	63825022	14978033
chr11	63828767	63829062	14978033
chr11	5227699	5228090	1406669
chr11	5232623	5233475	1406669
chr11	5235227	5235270	1406669
chr11	5245402	5245626	1406669
chr11	5247999	5248054	1406669
chr19	18252365	18252412	1527086
chr20	35157762	35157853	7791762
chr17	29507625	29507986	12957380
chr2	8739640	8739671	7758976
chr14	22095216	22095259	2237431
chr19	12763115	12763277	1708123
chr6	19945684	19945712	9516472
chr19	803187	803276	8035830
chrX	16575045	16575095	15217781
chrX	16578082	16578129	15217781
chr1	159466177	159467889	8114692
chr1	159469220	159469752	8114692
chr1	159472260	159473015	8114692
chr1	159474453	159474579	8114692
chrX	72958724	72958835	8114692
chr2	228272379	228272410	15217784
chr2	228275241	228275271	15217784
chr2	228290979	228291062	15217784
chr12	110689068	110689098	8964492
chr19	11060987	11061023	10787437
chr4	123597348	123597378	1722332
chr8	128817180	128817228	2324096
chr12	67488825	67488868	15550242
chr5	176769145	176769177	9794469
chr14	93924789	93924821	9794469
chr8	11603760	11603808	9486185
chr11	118463734	118463763	1875946
chr16	103521	103848	1875946
chr4	149583222	149583259	8961265
chr4	149585298	149585633	8961265
chr5	131437322	131437356	2233734
chr11	56914779	56914817	9558404
chr11	102174165	102174196	9850057
chr11	102175684	102175713	9850057
chr7	87067977	87068281	9187262
chr6	32515556	32515587	9187262
chr11	69165014	69165043	10318916
chr6	43566882	43566936	1846623
chr5	8673994	8674036	1846623
chr4	5457316	5457345	1846623
chr4	65155400	65155486	1846623
chr2	82900464	82900506	1846623
chr2	117226296	117226351	1846623
chr2	143566474	143566505	1846623
chr1	77209592	77209678	1846623
chr9	34989140	34989208	1846623
chr8	68655747	68655789	1846623
chr13	95146565	95146598	1846623
chr11	63711382	63711424	1846623
chr17	19441579	19441621	1846623
chr17	21944695	21944853	1846623
chrM	16412	16571	1846623
chrX	125692535	125692596	1846623
chr6	31891213	31891248	11306579
chr1	228904777	228904839	7961807
chr3	25444666	25444701	10629053
chr5	176446487	176446622	11981041
chr19	9490688	9490716	11022000
chr18	58261021	58261049	11022000
chr17	31231518	31231548	11022000
chr2	130548582	130548610	11022000
chr2	130937154	130937182	11022000
chr2	131131596	131131624	11022000
chr2	131738402	131738430	11022000
chr9	6825254	6825282	11022000
chr6	32515533	32515560	10675042
chrX	146800817	146801184	9199556
chr10	69125925	69126061	15302915
chrX	30581119	30581150	14654354
chr17	73694758	73694962	2914910
chr7	5533904	5534773	11509602
chr5	79631252	79631282	11509602
chr5	158689999	158690346	11509602
chr3	12087833	12087862	11509602
chr2	130548917	130548948	11509602
chr2	130937489	130937520	11509602
chr2	131131258	131131289	11509602
chr2	131738064	131738095	11509602
chr1	103914789	103914818	11509602
chr22	14635979	14636010	11509602
chr15	42069176	42069206	11509602
chr14	18655263	18655294	11509602
chr14	19058341	19058372	11509602
chr17	77092311	77092340	11509602
chr2	182251813	182251845	9714454
chr2	182253400	182253508	9714454
chr2	182254799	182254844	9714454
chr10	6144529	6144558	8475098
chr1	167969764	167969794	7525580
chrX	153904168	153904229	8628260
chr20	29655768	29655813	11700304
chr8	42314353	42315833	3182828
chr14	21999513	21999544	11781241
chr4	155703461	155703528	8423785
chr12	21417530	21417563	15243700
chr15	72805892	72805921	9415707
chr11	102176066	102176109	9115242
chr11	116168396	116168615	12709436
chr22	38626944	38626986	12554803
chr16	55217063	55217144	6095291
chr16	55223951	55224021	6095291
chr16	55249263	55249346	6095291
chr16	55259528	55259603	6095291
chr16	55261095	55261155	6095291
chr6	74286519	74288051	7961976
chr7	55054352	55054388	12894229
chr1	75962523	75962557	1328196
chr6	31433071	31433109	7907595
chr1	120737548	120737587	7907595
chr1	147635797	147635836	7907595
chr1	148020753	148020792	7907595
chr16	54068947	54068984	9343394
chr7	44805908	44805937	12377782
chr2	101257187	101257216	12377782
chr5	68498805	68498835	1582409
chr10	62209932	62209968	1582409
chr10	62214466	62214599	1582409
chr4	100431464	100431497	1996113
chr4	100461879	100461911	1996113
chr4	100493190	100493270	1996113
chr4	123597348	123597378	8335913
chr3	42281230	42281419	2118525
chr16	103674	103708	8455611
chr11	47238665	47240146	7744246
chr11	47246036	47246944	7744246
chr22	34343285	34343320	3796609
chr6	32515518	32515580	3133120
chr11	116213691	116213767	14563824
chr22_random	13278	13315	14563824
chr6	31891219	31891251	1674922
chr7	100556510	100556547	9765209
chr16	31311937	31312078	10722744
chr7	5533904	5534772	14761964
chr5	77116937	77116964	14761964
chr5	79631252	79631282	14761964
chr3	12087833	12087862	14761964
chr2	130548917	130548947	14761964
chr2	130937489	130937519	14761964
chr2	131131259	131131289	14761964
chr2	131738065	131738095	14761964
chr1	103914789	103914818	14761964
chr1	227633868	227633895	14761964
chr22	14635979	14636009	14761964
chr15	42069176	42069206	14761964
chr14	18655264	18655294	14761964
chr14	19058341	19058371	14761964
chr17	77092311	77092340	14761964
chr1	163028394	163028465	1967982
chr1	163055999	163056043	1967982
chrX	33133101	33133241	9092671
chr2	40593126	40593192	10212268
chr12	49852960	49853556	8157699
chr11	303949	304011	2492664
chrX	33139544	33139614	2403634
chr16	142730	142764	2403638
chr16	152942	152976	2403638
chr6	12398458	12398494	9588211
chr20	31728190	31728226	10336493
chr16	31273841	31274009	8621914
chr11	116205239	116205369	8675624
chr22_random	21671	21801	8675624
chr17	35727890	35728028	7585542
chr10	95351086	95351181	8810324
chr4	123597348	123597378	1639393
chr1	89303430	89303699	1898761
chr1	89645644	89645905	1898761
chr17	68677654	68677683	11208729
chr2	204279613	204279643	11342633
chr16_random	105102	105168	1502157
chr16	29726478	29727567	1502157
chr16	29729109	29729985	1502157
chr11	69299287	69299589	7929190
chr17	29603541	29603572	15223809
chr13	19665939	19666133	16314317
chr4	100493208	100493237	11051106
chr2	113313587	113313618	8413264
chr10	71006857	71006921	11334435
chr6	116556247	116556279	12435601
chr3	4996984	4997026	12624110
chr10	135190225	135190285	15345327
chr16	55199882	55199916	2033057
chr2	21120497	21120527	2033057
chr4	123597157	123597188	1652063
chr2	208169881	208169935	7745688
chr5	131423937	131424152	2263617
chr16	55199881	55199917	2263617
chr18	59138005	59138038	15117818
chr5	131437192	131437225	12704365
chr6	106642850	106642882	1851123
chr6	106650195	106650227	1851123
chr6	106659392	106659933	1851123
chr11	117692798	117692830	1989880
chr6	32515579	32515609	7673122
chr5	149772458	149772599	7673122
chr2	88938933	88939059	3037335
chr5	137828911	137828949	10391889
chr16	68318402	68318430	9601066
chr1	59020592	59020670	8253081
chr14	79748341	79748375	12775767
chr5	137695539	137695570	9679054
chr2	204279613	204279644	10510368
chr17	73694638	73695190	2005912
chr14	93924749	93924779	3263567
chr6	49682517	49682891	9442063
chr6	49688066	49688117	9442063
chr6	49691308	49691352	9442063
chr6	49694923	49695034	9442063
chr6	49712336	49712389	9442063
chr11	116205741	116205769	1406652
chr22_random	21271	21299	1406652
chrX	37524021	37524232	9593745
chr16	142740	142804	9642099
chr16	152952	153016	9642099
chr4	123597344	123597378	8473495
chr19	46878377	46878479	8349632
chr19	46914542	46914874	8349632
chr19	46917381	46917730	8349632
chr19	47716252	47716299	8349632
chr19	47784239	47784322	8349632
chr19	47821063	47821727	8349632
chr19	47858834	47859130	8349632
chr19	47924303	47925076	8349632
chr19	47936758	47937193	8349632
chr19	47950191	47950286	8349632
chr19	47961986	47962109	8349632
chr19	47981597	47981632	8349632
chr19	48039543	48040312	8349632
chr19	48052014	48052449	8349632
chr19	48063958	48064054	8349632
chr19	48075974	48076408	8349632
chr19	48102096	48102875	8349632
chr19	48121643	48121722	8349632
chr19	48145389	48145424	8349632
chr19	48210295	48211069	8349632
chr19	48222748	48222790	8349632
chr19	48266879	48267653	8349632
chr19	48370394	48371168	8349632
chr19	48382768	48382812	8349632
chr19	48390210	48390293	8349632
chr19	48401910	48401953	8349632
chr19	48415874	48415909	8349632
chr19	48453381	48454155	8349632
chr19	48465820	48466255	8349632
chr19	48479322	48479357	8349632
chr16	31178767	31178799	8095266
chr6	22405282	22405362	1655738
chr1	154478086	154478119	8825560
chr2	85748893	85748944	12161428
chr17	59364777	59364942	10446901
chr7	22733233	22733278	2183031
chr7	99219886	99219923	11679585
chr10	96686554	96686755	11679585
chr19	50100781	50100815	12444925
chr16	31178795	31178913	8096519
chr17	33144671	33144750	1677179
chr17	33167871	33167927	1677179
chr2	216008981	216009553	2542772
chr11	113672318	113672349	15486044
chr11	113688417	113688446	15486044
chr12	102847759	102848419	2546060
chr6	27968973	27969051	8628255
chr9	21067966	21068081	2542571
chr9	21358161	21358203	2542571
chr9	21430309	21430351	2542571
chr11	5204937	5204966	7545172
chr11	5227752	5227795	7545172
chr11	5232676	5232719	7545172
chr11	5247819	5247851	7545172
chr5	131410358	131410597	9047239
chr4	123597352	123597382	9047239
chr11	102219597	102219627	9047239
chr11	116213590	116213627	9507986
chr22_random	13418	13455	9507986
chr7	93042000	93042093	14623107
chr18	647735	647764	9218479
chrX	43626664	43626710	15024015
chr14	66896764	66896814	9856992
chr16	55199806	55199838	2191300
chr6	32515619	32515659	2105459
chr10	90739578	90739628	10903433
chr13	112824973	112825091	11159521
chr2	1874828	1874920	1280325
chr2	1900021	1900095	1280325
chr20	62313000	62313928	1280325
chr20	62318981	62319078	1280325
chr20	62320626	62321779	1280325
chr20	62323687	62323844	1280325
chr20	62325099	62325129	1280325
chr20	62329211	62329770	1280325
chr20	62333960	62334153	1280325
chr20	62338349	62339187	1280325
chr20	62341571	62342693	1280325
chrX	102918139	102918171	1280325
chr7	100556298	100557042	11423472
chr19	50501540	50502693	2903158
chr19	50506846	50506880	2903158
chr19	50513023	50513074	2903158
chr19	50514798	50514829	2903158
chr3	70068150	70068220	10973953
chr4	123597347	123597378	15471864
chr4	74953666	74953833	1906501
chr5	132037380	132037436	11781715
chr6	31650766	31650831	12655064
chr11	116205745	116205774	2777781
chr22_random	21266	21295	2777781
chr11	100414363	100415056	2328727
chr11	100503355	100503385	2328727
chr11	100505017	100506465	2328727
chr1	6562697	6563256	7969177
chr1	6571859	6571923	7969177
chr6	32742468	32742520	9032250
chr3	111118149	111118177	9032250
chr12	103041232	103041262	9032250
chr5	1348120	1348359	11454703
chr7	55054190	55054386	2768275
chr14	21999514	21999544	12244173
chr3	188943535	188943563	12150891
chr1	23759174	23759207	12150891
chr22	39903140	39903181	11116148
chr6	32515533	32515581	3174636
chr15	37660490	37660521	8444876
chr6	138230011	138230054	8444879
chr12	97562600	97562637	11896574
chr18	53404788	53404938	7983009
chr20	31737790	31738092	7935380
chr8	38127715	38127745	10919277
chr1	153302601	153302796	12030849
chr1	100957801	100957850	8547644
chr11	73371684	73372465	16282353
chr2	48727285	48727318	10364255
chr1	181826007	181826435	11781392
chrX	37524194	37524224	11781392
chr7	41970209	41972742	2118997
chr7	41973749	41974031	2118997
chr7	41978488	41978750	2118997
chr7	41983714	41983767	2118997
chr7	42029591	42029669	2118997
chr7	42031395	42032539	2118997
chr7	42046165	42046363	2118997
chr7	42051506	42051655	2118997
chr7	42054619	42054811	2118997
chr7	42082874	42082981	2118997
chr7	42154352	42154578	2118997
chr7	42229265	42229411	2118997
chr2	121462417	121462473	2118997
chr17	35827693	35827738	12769819
chr6	36754354	36754385	10749849
chr1	67925039	67925068	10749849
chr9	109287447	109287894	10749849
chr7	55054190	55054238	10363966
chr17	35109317	35109363	10363966
chr7	56161235	56161290	9334314
chr7	64181915	64181969	9334314
chr7	64876045	64876085	9334314
chr7	72227389	72227445	9334314
chr7	73781058	73781114	9334314
chr7	74270860	74270916	9334314
chr9	96441673	96441802	11023824
chr7	75769816	75769845	9328340
chr7	5533905	5535784	1710027
chr6	46280797	46281747	1710027
chr6	89042334	89043319	1710027
chr5	15504633	15504896	1710027
chr5	56813210	56814242	1710027
chr5	61163672	61163723	1710027
chr5	77116592	77117549	1710027
chr5	79631302	79631916	1710027
chr5	79634186	79634306	1710027
chr5	97702839	97703393	1710027
chr5	131022673	131023539	1710027
chr3	12086940	12087806	1710027
chr3	140695810	140696440	1710027
chr3	177177975	177178622	1710027
chr3	182021876	182022052	1710027
chr2	73972985	73974525	1710027
chr2	73980342	73983204	1710027
chr2	73988647	73989876	1710027
chr2	73994054	73995649	1710027
chr2	73997098	73997500	1710027
chr2	73999983	74000318	1710027
chr2	108082159	108082238	1710027
chr2	130548301	130549385	1710027
chr2	130936859	130937957	1710027
chr2	131130821	131131919	1710027
chr2	131737627	131738725	1710027
chr2	132100210	132101308	1710027
chr2	177199789	177199841	1710027
chr1	27524649	27524875	1710027
chr1	78012196	78013141	1710027
chr1	92467197	92467382	1710027
chr1	103914534	103914769	1710027
chr1	201109169	201109326	1710027
chr1	222118103	222119050	1710027
chr1	227633869	227635476	1710027
chr1	236156880	236157339	1710027
chr8	86023505	86024318	1710027
chr9	6824581	6825542	1710027
chr9	102534069	102534395	1710027
chrX	46032439	46033041	1710027
chrX	53188773	53189695	1710027
chr11	1780695	1781770	1710027
chr10	70452642	70452798	1710027
chr10	90684958	90685088	1710027
chr10	90687798	90687977	1710027
chr10	90689248	90689321	1710027
chr10	90690997	90691107	1710027
chr10	90693546	90693643	1710027
chr10	90696998	90697120	1710027
chr10	90698554	90698637	1710027
chr22	14635352	14636447	1710027
chr22	39800160	39801062	1710027
chrY	18378289	18379273	1710027
chrY	18769283	18770112	1710027
chr15	32453090	32453139	1710027
chr15	32869904	32873056	1710027
chr15	32874182	32874289	1710027
chr15	42068572	42069644	1710027
chr15	81192162	81192213	1710027
chr14	18654826	18655924	1710027
chr14	19057711	19058809	1710027
chr20	1090118	1090302	1710027
chr17	17086627	17086908	1710027
chr17	77092309	77093757	1710027
chr19	9489954	9490962	1710027
chr18	58260968	58261292	1710027
chr16	48649560	48650501	1710027
chr5	132037504	132037538	10069428
chr3	25444697	25444726	11943482
chr1	167969830	167969975	7520526
chr10	82039129	82039179	10677369
chr9	115882964	115883372	9729465
chr7	120478078	120478120	14621294
chr4	63058672	63058703	14621294
chr1	181178238	181178280	14621294
chrX	153698948	153698990	14621294
chr11	3967348	3967409	14621294
chr10	19817916	19817977	14621294
chr15	60441900	60441972	14621294
chr15	91055927	91055966	14621294
chr21	39642814	39643262	14621294
chr19	58963706	58963769	14621294
chr17_random	492683	492712	14557070
chr17_random	510775	510804	14557070
chr17_random	512267	512296	14557070
chr17_random	514742	514771	14557070
chr17_random	519631	519660	14557070
chr17_random	525779	525808	14557070
chr17_random	527711	527740	14557070
chr17_random	555958	555987	14557070
chr17_random	2607938	2607967	14557070
chr17_random	2614806	2614835	14557070
chr3	52463073	52463149	8413270
chr3	197293434	197293473	8022786
chr15	32875224	32875253	2494661
chr5	137695575	137695757	7479023
chrX_random	1443980	1444483	2044957
chrX	77245979	77246482	2044957
chr9	37024032	37024157	11223243
chr22	37970956	37970998	8077216
chr1	100957746	100957777	8077216
chr1	151147272	151147456	8550612
chr9	21067993	21068067	1886766
chr17	7423604	7423652	12676954
chr8	42191532	42191569	15466927
chr7	99219886	99219919	11027665
chr6	41760501	41760686	2115126
chr6	41761804	41763745	2115126
chr6	41765437	41766953	2115126
chr6	41811108	41811166	2115126
chr8	43016279	43016347	2115126
chrX	48775934	48775998	2115126
chr7	94791817	94791848	15380450
chr1	2072221	2072263	15380450
chr20	5048591	5048691	8095093
chr1	52642682	52642720	8943353
chr17	40348345	40348385	8702952
chr12	52196032	52197187	1694576
chr12	52306354	52306405	1694576
chr3	188870903	188870945	1694576
chr15	89212751	89212779	8132667
chr17	59304761	59304919	2033067
chr17	59312948	59313105	2033067
chr17	59327658	59327816	2033067
chr17	59342351	59342496	2033067
chr17	59349923	59350080	2033067
chr5	158690274	158690305	14976188
chr3	134944350	134944495	2033069
chr14	105142612	105142669	10510379
chr14	105261402	105261448	10510379
chrX	47326790	47326827	9182725
chr7	5536804	5536862	1762920
chr12	14930137	14930305	11425864
chr7	100159369	100159403	12354771
chr12	26167260	26167289	12354771
chr12	26169228	26169296	12354771
chr3	4995940	4995970	12354771
chrX	114183474	114183507	12776189
chrX	114184850	114184881	12776189
chr14	21999514	21999541	9584181
chr17	59349863	59349894	1744088
chr3	150065600	150065788	1744088
chr20	44070865	44071007	10359016
chr2	136592198	136592248	9379028
chr1	75962523	75962563	9271417
chr1	227636496	227636588	11096067
chr1	227637692	227637737	11096067
chr1	27871383	27871419	2721502
chr7	142216838	142216875	8264651
chr2	169596124	169596152	11387316
chr15	54998207	54999478	1312219
chr15	55000514	55000591	1312219
chr15	55143237	55143314	1312219
chr15	55171278	55171377	1312219
chr15	55245896	55245956	1312219
chr15	55271647	55271783	1312219
chr15	55277261	55277318	1312219
chr15	55310641	55310747	1312219
chr15	55311783	55312347	1312219
chr15	55313530	55313597	1312219
chr15	55322961	55323029	1312219
chr15	55330835	55330913	1312219
chr15	55332750	55332960	1312219
chr15	55341582	55342764	1312219
chr15	55352531	55352752	1312219
chr15	55361932	55362088	1312219
chr15	55365643	55367499	1312219
chr2	234190701	234190736	15470081
chr2	234209532	234209564	15470081
chr2	234254947	234254978	15470081
chr14	74815179	74815209	2233715
chr12	21175333	21175378	11483603
chr4	68302882	68302915	12947046
chr21	26465259	26465326	10333529
chr20	5048559	5048599	7602584
chr14	74814803	74814834	7602584
chr14	21999512	21999541	12097391
chr6	135544066	135544095	8137237
chr10	62208101	62208133	8137237
chrX	24621808	24621838	8137237
chr6	32076590	32076624	11463853
chr6	32109328	32109362	11463853
chr10	104587240	104587383	11463853
chr20	42463214	42463243	11585914
chr1	184915314	184915343	16397300
chr19	46551973	46552018	10843986
chr2	219990407	219990569	8387519
chr16	55199808	55199838	11522791
chr1	202402286	202402322	8999953
chr6	31651199	31651239	10521481
chr16	28850646	28850827	1375324
chr10	90741040	90741071	12788915
chr7	150316900	150316930	11960979
chr12	116253636	116253666	11960979
chr12	116361828	116361874	11960979
chr2	21120510	21120539	1901405
chr14	93924753	93924784	1901405
chr1	181826102	181826309	15513967
chr12	56432452	56432646	10688915
chr14	24173315	24173382	9857074
chr14	74814928	74815058	2849107
chr4	89115806	89115868	11126367
chr18	27425729	27425759	1620125
chr4	74488729	74488763	1620125
chr2	21120534	21120578	1620125
chr14	93924794	93924826	1620125
chr14	22974918	22974961	15572681
chr8	19840943	19840973	11090277
chr3	12368079	12368108	12821652
chr20	5048005	5049059	10488129
chr11	118463734	118463763	11154691
chr9	2611470	2611503	10064725
chr5	137695538	137695570	10559267
chr18	59136962	59137006	14555646
chr18	59138749	59139484	14555646
chr11	5227744	5227796	2476717
chr11	5232668	5232720	2476717
chr22	49363947	49363991	15356291
chr1	938622	938650	1654549
chr13	112808078	112808169	7559437
chr10	17310932	17311087	8417364
chr16	66535559	66535604	1659419
chr10	91142233	91142265	2118988
chr5	137828633	137828671	11739517
chr13	40405403	40405560	1527846
chr13	40454189	40454420	1527846
chr13	40491362	40491450	1527846
chr11	5202450	5202702	2461328
chr7	27169861	27169947	1756725
chr7	27178092	27178255	1756725
chr12	52669278	52669447	1756725
chr12	52682481	52682589	1756725
chr17	44045704	44045739	1756725
chr17	44055372	44055482	1756725
chr2	176689951	176690552	1756725
chr2	176691928	176692204	1756725
chr2	176695793	176697101	1756725
chr6	43845943	43845971	9264407
chr6	32114046	32114081	9518489
chr19	10242587	10242615	9831247
chr5	176450432	176450550	12642581
chr3	171422833	171422862	14670960
chr3	171485039	171485068	14670960
chrX	100679721	100679750	14670960
chr14	69333738	69333838	14701722
chr3	70068212	70068254	10747853
chr1	120737516	120737559	7565811
chr1	147635825	147635868	7565811
chr1	148020781	148020824	7565811
chr4	123597020	123597445	8233832
chr3	172227349	172227379	10748140
chr6	32515531	32515581	1454841
chr2	218739947	218739983	9867862
chrX	47326839	47326869	10692475
chr1	32511795	32511852	7499213
chr2	191586627	191586668	11909852
chr1	938620	938652	11909852
chr1	89303581	89303612	11909852
chr1	89645723	89645754	11909852
chr5	131423976	131424007	8632000
chr10	75338939	75339417	8632000
chr5	137828633	137828733	11520792
chr16	1782372	1782405	10650966
chr1	167969446	167970262	1710341
chr4	110942709	110942781	10524238
chr13	99432313	99432355	10984499
chr8	134378617	134379221	15377670
chr9	135491563	135491594	9011768
chr3	46481718	46481815	8621448
chr19	62042298	62043207	12554678
chr1	26105555	26105584	16757134
chr3	87408888	87408918	15998782
chr1	156923152	156923183	12196550
chr8	128817171	128817203	8197157
chr21	42660090	42660131	10620335
chr6	31891179	31891216	1871106
chr6	31903375	31903412	1871106
chr6	122762493	122762674	1871106
chr6	122775213	122775591	1871106
chr6	122782009	122783068	1871106
chr6	122784993	122786530	1871106
chr6	122790746	122790800	1871106
chr6	122794273	122795165	1871106
chr12	53802720	53804233	1871106
chr8_random	420976	422326	1871105
chr8_random	423591	423718	1871105
chr8_random	426243	426932	1871105
chr8	145503398	145504062	1871105
chr8	145506612	145506739	1871105
chr8	145508004	145509161	1871105
chr12	6547783	6547818	1754393
chr21	42609197	42609229	15177881
chr1	938616	938650	1406637
chr7	5533732	5533779	3244353
chr6	89042156	89042202	3244353
chr5	77117712	77117757	3244353
chr5	79631093	79631150	3244353
chr5	97703551	97703597	3244353
chr5	131022451	131022499	3244353
chr2	130548117	130548164	3244353
chr2	130936689	130936736	3244353
chr2	131132041	131132087	3244353
chr2	131738847	131738893	3244353
chr1	78011985	78012023	3244353
chr1	222117893	222117941	3244353
chr9	6825700	6825746	3244353
chr9	102534580	102534628	3244353
chrX	44538307	44538347	3244353
chrX	46032208	46032255	3244353
chrX	65835140	65835184	3244353
chr11	1780532	1780576	3244353
chr10	70453756	70453804	3244353
chr22	14635193	14635229	3244353
chr22	39799946	39799993	3244353
chr15	42068392	42068434	3244353
chr14	18656046	18656083	3244353
chr14	19057542	19057588	3244353
chr18	58261458	58261504	3244353
chr5	68498527	68498563	7739559
chr7	55054198	55054226	8887630
chr1	205012403	205012628	12817009
chr7	87068167	87068256	8103518
chr10	6144516	6144552	2308942
chr7	99173459	99173491	11495920
chr7	99219806	99219883	11495920
chr7	99222453	99222483	11495920
chr15	98070443	98070503	8035795
chr12	6104108	6104139	9444957
chr5	131424170	131424199	8035792
chr9	21067979	21068020	3368441
chr5	138986884	138986916	15656981
chr1	201321364	201321394	15656981
chr15	40536722	40537317	15656981
chr15	40545542	40545576	15656981
chrX	100527954	100527995	15850836
chr5	131434502	131434658	11509589
chr5	142641652	142641682	11509589
chr5	145700401	145700431	12606546
chr4	123597351	123597383	12606546
chr3	12367795	12367826	12606546
chrX	15529449	15529479	12606546
chr10	62207825	62207857	8420994
chr19	10242568	10242753	10092659
chr2	191586341	191586980	14654702
chr12	46681676	46682070	10856292
chr12	46684713	46684793	10856292
chr1	27544418	27544468	12137562
chr14	21999696	21999744	9584163
chr7	99219889	99219918	10757780
chr3	25444696	25444725	10757780
chr12	28014088	28014273	8371355
chr8	57521833	57521869	1828294
chr1	153429258	153432230	8387509
chr5	68498442	68498645	9218875
chr9	21358097	21358144	3040267
chr9	21430366	21430415	3040267
chr15	49322791	49322820	11245431
chr15	72805891	72805921	11120824
chr7	131000945	131000998	12850290
chr6	89031759	89031806	12850290
chr5	115926399	115926450	12850290
chr5	149806571	149806623	12850290
chr1	19807439	19807491	12850290
chr1	176647561	176647613	12850290
chr12	28007748	28007797	12850290
chr12	28014012	28014467	12850290
chr12	28016885	28016923	12850290
chr16	8498389	8498441	12850290
chr21	26464985	26465014	8541835
chr8	19840940	19841043	7753827
chr15	72805891	72805921	8816435
chr6	31651199	31651239	8816436
chr14	74814942	74814984	3316979
chr6	36752198	36752228	11030628
chr17	7520248	7520295	11030628
chr1	205329077	205329135	8598458
chr1	205344111	205344140	8598458
chr1	198263574	198263662	9786908
chr1	198284012	198284064	9786908
chr1	198409939	198410009	9786908
chr1	115373914	115373970	1321428
chr15	49307325	49307355	12351690
chr15	49361684	49361725	12351690
chr7	5535724	5535755	11744689
chr3	166279011	166279163	1378530
chr6	27943285	27943766	2829131
chr8	57521875	57521906	2850173
chr4	89115386	89115910	14712233
chr4	89123042	89123072	14712233
chr19	46188949	46188987	15722458
chr11	68336565	68336619	16271724
chr17	59304762	59304920	2181288
chr17	59312949	59313106	2181288
chr17	59327659	59327817	2181288
chr17	59342351	59342501	2181288
chr17	59349924	59350081	2181288
chr6	37244360	37245942	2181282
chr22	44923859	44923889	11981036
chr8	42314401	42315724	7590351
chr2	127130178	127130354	2584223
chr9	124173035	124173077	16105649
chr9	124186297	124186375	16105649
chr14	66896772	66896803	2584221
chr18	59703906	59704256	8916932
chr9	21067972	21068007	8916932
chr11	5202538	5202590	2481268
chr5	132037351	132037431	10973979
chr5	72779557	72779586	8988052
chr1	154478560	154478610	9388207
chr11	32414090	32414122	9388203
chrX	48914869	48915309	7622043
chr7	100159376	100159408	14741200
chr21	46842969	46843794	2394738
chr21	46846618	46846730	2394738
chr3	134947845	134947876	2911463
chr14	93924791	93924822	2911463
chr7	5536823	5536862	2911466
chr11	6367884	6367915	11788605
chr11	118463695	118463975	2911469
chr3	131176177	131176299	7565802
chr4	100461656	100461748	2050667
chr4	100493039	100493072	2050667
chr1	154478093	154478121	8262978
chr11	119681053	119681704	2905684
chr1	165456768	165456819	2905684
chr1	165568326	165568397	2905684
chr1	165601325	165601430	2905684
chr1	165607864	165607897	2905684
chr1	165609967	165610158	2905684
chr1	165611886	165612018	2905684
chr1	165619716	165619812	2905684
chr1	165625445	165625623	2905684
chr1	165632144	165632288	2905684
chr1	165633851	165633994	2905684
chr1	165635044	165635228	2905684
chr1	165637310	165637418	2905684
chr1	165647816	165648975	2905684
chr1	165651358	165651948	2905684
chr5	135259348	135259383	8663174
chr5	131437273	131437315	8934574
chr4	123597230	123597266	8934574
chr9	21067985	21068019	8934574
chr22	34102752	34103229	8077238
chr14	74814955	74814988	11108721
chr8	128822293	128822324	7539921
chr21	31953787	31953876	3160582
chr7	5533942	5533974	16702209
chr7	5535396	5535430	16702209
chr6	89042357	89042389	16702209
chr5	77116718	77117549	16702209
chr5	131023425	131023456	16702209
chr3	177178012	177178044	16702209
chr2	73989307	73989339	16702209
chr2	130548326	130549162	16702209
chr2	130936898	130937734	16702209
chr2	131131044	131131880	16702209
chr2	131737850	131738686	16702209
chr2	132100433	132101269	16702209
chr1	27524804	27524836	16702209
chr9	6825508	6825538	16702209
chr11	1780732	1781649	16702209
chr10	70452767	70452798	16702209
chr22	14635388	14636224	16702209
chr15	32872904	32872933	16702209
chr14	18655049	18655885	16702209
chr14	19057750	19058586	16702209
chr17	77093599	77093634	16702209
chr18	58261272	58261304	16702209
chr16	54068946	54068977	2174109
chr7	5533942	5533974	10479057
chr7	5535396	5535428	10479057
chr6	89042357	89042389	10479057
chr5	77116718	77117549	10479057
chr5	131023425	131023456	10479057
chr3	177178012	177178044	10479057
chr2	73989307	73989339	10479057
chr2	130548326	130549162	10479057
chr2	130936898	130937734	10479057
chr2	131131044	131131880	10479057
chr2	131737850	131738686	10479057
chr2	132100433	132101269	10479057
chr1	27524804	27524836	10479057
chr9	6825508	6825538	10479057
chr11	1780732	1781649	10479057
chr10	70452767	70452798	10479057
chr22	14635388	14636224	10479057
chr15	32872904	32872933	10479057
chr14	18655049	18655885	10479057
chr14	19057750	19058586	10479057
chr17	77093599	77093634	10479057
chr18	58261272	58261304	10479057
chr2	1390688	1390921	2174102
chr1	154478087	154478117	1662118
chr14	22947447	22947476	1662118
chr12	111900463	111900728	10524248
chr11	13474242	13474272	15297458
chr10	45188602	45189766	2251250
chr1	17317540	17317569	15854045
chr1	17318598	17318670	15854045
chr5	132037381	132037410	9013959
chr4	123597348	123597378	9013959
chr12	46521660	46525058	2835767
chr12	46526384	46526861	2835767
chr12	46535679	46535854	2835767
chr12	46537178	46537738	2835767
chr12	46545096	46545230	2835767
chr12	46559016	46559168	2835767
chr12	46562742	46562827	2835767
chr12	46585004	46585036	2835767
chr17	77217046	77217081	2835767
chr19	11061106	11061137	12947119
chr4	15549013	15549042	9668098
chr14	22095158	22095319	1534408
chr14	74815206	74815235	1534408
chr1	2448789	2448825	14757642
chr1	119759167	119759197	10406460
chr7	93862154	93862182	8900150
chr17	16666721	16666790	1703506
chr17	18294023	18294092	1703506
chr17	20338188	20338319	1703506
chr17	36996740	36996916	1703506
chr4	55686548	55686584	12560084
chr13	47952181	47952213	1406625
chr3	134944268	134944298	1851757
chr3	134947817	134948026	1851757
chr6	32515575	32515609	8943243
chr6	33656081	33656117	11850816
chr12	52060302	52060349	11294852
chr1	151269442	151269610	8388378
chr7	55054352	55054388	10830317
chr17	23928234	23928263	8348972
chr18	59138134	59138165	12970736
chr13	102516651	102516690	12055195
chr13	102518743	102518897	12055195
chr11	5227700	5227739	9763579
chr11	5232624	5232663	9763579
chr16	162927	162961	9763579
chr16	166731	166765	9763579
chr10	59815101	59815201	8108407
chr5	139993036	139993066	7522257
chr7	116099208	116099369	8633043
chr14	74814951	74815012	3561415
chrX	139414744	139414777	15656994
chr9	89532337	89532368	11742542
chr1	120737494	120737582	8035786
chr1	147635802	147635890	8035786
chr1	148020758	148020846	8035786
chr14	21999474	21999519	1328863
chr3	126434265	126435864	8355710
chr3	126479255	126479345	8355710
chr3	126480655	126480781	8355710
chr3	126489636	126489762	8355710
chr3	126514836	126515191	8355710
chr3	126524841	126524980	8355710
chr3	126532690	126532773	8355710
chr3	126576656	126576781	8355710
chr1	198644522	198644626	8355710
chr7	5534001	5534623	8939459
chr6	46281346	46281734	8939459
chr6	89042422	89042712	8939459
chr5	15504843	15504873	8939459
chr5	61163678	61163733	8939459
chr5	77117196	77117492	8939459
chr5	79631358	79631581	8939459
chr5	97703198	97703252	8939459
chr3	12087411	12087591	8939459
chr3	140696029	140696413	8939459
chr3	177178242	177178299	8939459
chr3	182021771	182021993	8939459
chr2	73995378	73995432	8939459
chr2	73997331	73997392	8939459
chr2	113258477	113258678	8939459
chr2	130548383	130548798	8939459
chr2	130936955	130937370	8939459
chr2	131131408	131131823	8939459
chr2	131738214	131738629	8939459
chr2	132100798	132101212	8939459
chr2	177199802	177199832	8939459
chr1	27524781	27524811	8939459
chr1	78012359	78012539	8939459
chr1	103914371	103914667	8939459
chr1	222118159	222118387	8939459
chr1	227634431	227634490	8939459
chr1	236157433	236157485	8939459
chr8	86024150	86024198	8939459
chr9	6825149	6825481	8939459
chr9	102534312	102534359	8939459
chrX	46032662	46032719	8939459
chrX	53188784	53189155	8939459
chr11	1780967	1781216	8939459
chr10	90689314	90689371	8939459
chr22	14635561	14635859	8939459
chr22	39800216	39800503	8939459
chrY	18378426	18378484	8939459
chrY	18770072	18770130	8939459
chr15	32871653	32871766	8939459
chr15	42068656	42068877	8939459
chr15	81192521	81192565	8939459
chr14	18655413	18655712	8939459
chr14	19057923	19058221	8939459
chr17	17086477	17086530	8939459
chr17	77092373	77092935	8939459
chr19	9490688	9490921	8939459
chr18	58261015	58261239	8939459
chr7	100556366	100556452	10092624
chr4	55686311	55686706	15941713
chr22	37971039	37971068	2651898
chr7	99166659	99166694	16171783
chr7	99204178	99204208	16171783
chr7	99215592	99215627	16171783
chr5	174803080	174803675	1557411
chr11	5227727	5227786	9792700
chr11	5232651	5232710	9792700
chrX	37524126	37524187	9792700
chr6	32515517	32515571	1956787
chr6	32549430	32549476	1956787
chr6	32606136	32606182	1956787
chr6	32665653	32665699	1956787
chr6	32713039	32713089	1956787
chr6	32742503	32742540	1956787
chr6	32839378	32839415	1956787
chr6	33151595	33151641	1956787
chr6	33188069	33188115	1956787
chr4	74488494	74488536	2571419
chr14	93924751	93924784	2571419
chr7	5535762	5535811	8647842
chr5	77116469	77116518	8647842
chr2	130937934	130937983	8647842
chr2	131737601	131737650	8647842
chr1	222119124	222119173	8647842
chr9	6824457	6824505	8647842
chr14	20429813	20429854	8647842
chr14	20494019	20494067	8647842
chr9	21068006	21068050	10848607
chr17	7520607	7520634	10942770
chr1	67925041	67925068	10942770
chr17	73695040	73695086	9374541
chr11	2139936	2139969	7639703
chr1	184916221	184916248	12914528
chr4	175649783	175649813	12914529
chr4	175650944	175651026	12914529
chr4	175653284	175653325	12914529
chr4	175666422	175666513	12914529
chr4	175675714	175675787	12914529
chr4	175679674	175679704	12914529
chr4	175682129	175682169	12914529
chr1	167865992	167866032	7693674
chr8	57521753	57521785	2903436
chr3	188870904	188870949	2903436
chr14	74814951	74815007	2903436
chr22	38248080	38248109	10667576
chr6	31891276	31891343	3185540
chr14	23071809	23071877	1719379
chr16	71378561	71380251	1719379
chr16	71384654	71390115	1719379
chr16	71391426	71391530	1719379
chr16	71402974	71403440	1719379
chr16	71421178	71421262	1719379
chr16	71481130	71481364	1719379
chr16	71541868	71542365	1719379
chr16	71650002	71650035	1719379
chr8	77782582	77782774	1719379
chr8	77939156	77939199	1719379
chr15	32875131	32875172	3185542
chr6	31891249	31891297	7891680
chr6	160852090	160852152	8051057
chr6	161005297	161005359	8051057
chr6	161043164	161043237	8051057
chr6	161114847	161114920	8051057
chr2	87102506	87102536	8051057
chr2	87828662	87828698	8051057
chr2	106364916	106364971	8051057
chr19	48747326	48747708	16596326
chr3	49041757	49042120	9278455
chr8	128815945	128816007	2211718
chr10	75339385	75339416	9482739
chr10	75339385	75339418	10381567
chr2	113313571	113313625	7935442
chr6	31891219	31891298	2294402
chr6	31903415	31903493	2294402
chr11	117692798	117692833	9233811
chr1	148070779	148070820	8475055
chr1	148099373	148099414	8475055
chr2	10505825	10507350	1598217
chr6	31433068	31433100	11087747
chr1	55454213	55454275	2105456
chr15	41590465	41590493	12411430
chr5	131854277	131855640	7678055
chr11	303989	304023	7678055
chr1	27871381	27871462	7678055
chr17	77649441	77649508	10759542
chr11	100504116	100504150	1326555
chr17	35740996	35741025	1326555
chr3	25680704	25680732	12197834
chr3	197293365	197293455	2211668
chr1	16713403	16713597	2211668
chr1	16866066	16866259	2211668
chr1	16939368	16939545	2211668
chr1	17094832	17095009	2211668
chr1	142465000	142465030	2211668
chr1	144680988	144681018	2211668
chr1	145023125	145023155	2211668
chr1	145977989	145978019	2211668
chr1	146202147	146202177	2211668
chr1	146327614	146327644	2211668
chr1	147491060	147491090	2211668
chr10	75338916	75338950	9295342
chr2	1390804	1390838	1922026
chr17	29636805	29636846	11076795
chr17	39822516	39822558	9305885
chr19	47291338	47291924	1967834
chr11	119681053	119681704	1967834
chr1	165568332	165568397	1967834
chr1	165601332	165601380	1967834
chr1	165606040	165606075	1967834
chr1	165607798	165607887	1967834
chr1	165610012	165610157	1967834
chr1	165611902	165611983	1967834
chr1	165619741	165619800	1967834
chr1	165625445	165625623	1967834
chr1	165632144	165632288	1967834
chr1	165633851	165633994	1967834
chr1	165635118	165635173	1967834
chr1	165637310	165637397	1967834
chr1	165647830	165648975	1967834
chr1	165651372	165651799	1967834
chrX	146800430	146801657	9328468
chr5	137828677	137828706	10050673
chr11	5248169	5248250	8196619
chr7	97339597	97339755	8098842
chr8	47648439	47648477	8098842
chr11	116213772	116213811	2254327
chr22_random	13234	13273	2254327
chr2	136592146	136592180	9468539
chr8	31041348	31041376	9774636
chr6	36754236	36754267	10899165
chr10	80990399	80990429	8770068
chr10	81310344	81310374	8770068
chr7	100530837	100530867	14963043
chr7	100538831	100538860	14963043
chr7	100546037	100546066	14963043
chr7	100552573	100552602	14963043
chr1	228916450	228916637	9120024
chr14	69333741	69333779	11031103
chr12	102848231	102848267	7891720
chr9	127043547	127043582	7891720
chr19	10242283	10242711	11278281
chr7	27135513	27135556	1346761
chr7	27151871	27152020	1346761
chr7	27161182	27161337	1346761
chr12	52691282	52691317	1346761
chr12	52709750	52715423	1346761
chr17	44009179	44009226	1346761
chr17	44024627	44024671	1346761
chr17	44028843	44028890	1346761
chr17	44045683	44045736	1346761
chr2	176725736	176725784	1346761
chr13	27396544	27396591	1346761
chr11	5227819	5227865	8662744
chr11	5232743	5232789	8662744
chr2	85748902	85748942	8687389
chr11	69164859	69165095	11024050
chr15	42790870	42790904	11024050
chr1	151596550	151596591	12167632
chr12	111829065	111829297	2456211
chr11	32405320	32405350	9361007
chr4	123597348	123597378	8468470
chr9	124630642	124630672	10899582
chr17	6840198	6840229	9164849
chr11	67107743	67107826	9540834
chr12	111829115	111829152	2243138
chr11	303983	304028	2243138
chr15	42790852	42790899	2243138
chr1	27871371	27871421	2243138
chr14	66896772	66896808	8327497
chr8	128817143	128817192	2498322
chr4	74520898	74520930	12167706
chr1	151145504	151145545	11850802
chr3	197293419	197293452	12439744
chr5	1348961	1348990	10805720
chr6	32515575	32515609	9857002
chr12	66839927	66839961	9857002
chr15	32875086	32875160	1570331
chr19	46551777	46551809	1419910
chr14	74815178	74815210	1419910
chr2	37237626	37237664	9007065
chr17	59304592	59304709	2983311
chr17	59312779	59312896	2983311
chr17	59327489	59327606	2983311
chr17	59342175	59342291	2983311
chr17	59349754	59349997	2983311
chr20	33223226	33223554	12560236
chr11	2139185	2139263	8216223
chr6	32929568	32929603	8617938
chr1	227637706	227637741	7753622
chr6	32515533	32515582	1903200
chr6	32742549	32742590	1903200
chr21	43132720	43132757	9873055
chr21	45165275	45165326	9873055
chr9	112059027	112059075	11279008
chr5	142763772	142763812	1894621
chr3	25444698	25444727	12133007
chr17	7531624	7531657	11032029
chr19	10242220	10242349	7532665
chr11	101906778	101906820	10514384
chr2	15998066	15998098	9233765
chr1	100956789	100957652	11590177
chr19	45471155	45471341	11948187
chr19	45472647	45472677	11948187
chr3	30622936	30622975	9694866
chr19	48382519	48382548	9083102
chr11	118463733	118463762	9737995
chr1	202407711	202407751	9737995
chr6	32515525	32515556	10982343
chr15	88159423	88159454	9786929
chr11	63824992	63825022	16024613
chr11	63829031	63829062	16024613
chr21	42660037	42660066	16024613
chr10	75338939	75339417	9482740
chr11	5255941	5256828	6897566
chr20	42708280	42708453	1508212
chr2	21123156	21123191	1939218
chr20	47696917	47696945	15263012
chr6	12398430	12398463	8833653
chr7	5534741	5534772	15217903
chr22	14635979	14636009	15217903
chr2	130548917	130548947	15217903
chr2	130937489	130937519	15217903
chr2	131131259	131131289	15217903
chr2	131738065	131738095	15217903
chr15	42069176	42069206	15217903
chr14	18655264	18655294	15217903
chr14	19058341	19058371	15217903
chr11	18024442	18024482	9645961
chr14	74814929	74814993	7588632
chr16	31178723	31178757	9295357
chr1	151805759	151805864	9481475
chr12	4253265	4253295	11719506
chr11	123106706	123106844	12611910
chr2	217268556	217268956	11973331
chr17	59307441	59307479	14673137
chr17	59315189	59315228	14673137
chr17	59329988	59330029	14673137
chr17	59344718	59344758	14673137
chr17	59377579	59378017	14673137
chr17	45634045	45634202	7590335
chr14	22947834	22947866	8416951
chr17	40349935	40349985	1918004
chr4	74825037	74825076	2250017
chr12	52060149	52060190	12513689
chr11	46696387	46696487	1918008
chr14	93924741	93924782	1918008
chr12	51476289	51476355	7525574
chr6	32515512	32515556	2016543
chr8	56954440	56955182	1508184
chr6	27899785	27899820	8336726
chr6	27907345	27907380	8336726
chr9	21068000	21068044	1898993
chr14	22095175	22095205	8196665
chr7	5534741	5534772	16339564
chr22	14635979	14636009	16339564
chr2	130548917	130548947	16339564
chr2	130937489	130937519	16339564
chr2	131131259	131131289	16339564
chr2	131738065	131738095	16339564
chr15	42069176	42069206	16339564
chr14	18655264	18655294	16339564
chr14	19058341	19058371	16339564
chr5	132037275	132037307	1541828
chr17	37121994	37122111	2187875
chr17	45634909	45635219	8175678
chr1	938616	938651	7518927
chr1	89303581	89303611	7518927
chr1	89645724	89645754	7518927
chr1	120737546	120737587	7518927
chr1	147635797	147635838	7518927
chr1	148020753	148020792	7518927
chr14	74814955	74814988	8756667
chr1	119759218	119759250	9065466
chr4	89115427	89115840	15479859
chr12	6513463	6513878	2164673
chr4	72078086	72078236	14514691
chr11	5247784	5248022	2017165
chr17	38306149	38306188	14597389
chr17	59327755	59327785	8294429
chr2	210888128	210888286	3405213
chrX	47327469	47327515	11032844
chr12	46537651	46537683	15456860
chr12	46559131	46559163	15456860
chrX	47381397	47381456	8386592
chr6	18472236	18473222	8861962
chr5	98043411	98043638	8861962
chr2	118293735	118293797	8861962
chr2	118295287	118295330	8861962
chr2	118299492	118299589	8861962
chr2	118303368	118303415	8861962
chr11	129670570	129670813	8861962
chr10	92803202	92804189	8861962
chr15	57951590	57952578	8861962
chr14	68620263	68621288	8861962
chr17	4795691	4795723	7565752
chr11	2139122	2139152	12368292
chr5	131854463	131854496	9368052
chr17	7531791	7531822	9368052
chr1	94780074	94780113	9867853
chr10	6281227	6281257	15466858
chr10	6283878	6283906	15466858
chr12	20854814	20854844	12055601
chr1	3639475	3639508	12080043
chr11	5258553	5258587	7937919
chr15	32875013	32875470	2796988
chr11	5202389	5202423	1946439
chr22	37970960	37971036	8662647
chr4	74953829	74954108	7479086
chr4	75028915	75029081	7479086
chr4	75123136	75123400	7479086
chr4	75183645	75183902	7479086
chr1	205186279	205187034	9182878
chr2	8739418	8739559	14761970
chr15	48345223	48345254	10409643
chr19	46551981	46552060	11053476
chr15	48345249	48345309	16357063
chr12	48630222	48630839	9277587
chr4	123597345	123597384	7517940
chr14	22095239	22095269	7517940
chr5	142795001	142795489	15044598
chr10	8137502	8137861	1871134
chr10	8140273	8140733	1871134
chr10	8146027	8146107	1871134
chr10	8151498	8151561	1871134
chr10	8155748	8155994	1871134
chr3	129682555	129683405	1871134
chr14	21999512	21999547	1871134
chr14	22095233	22095269	1871134
chr7	107318886	107318916	1332063
chr7	73080030	73080095	10429948
chr6	152167451	152167479	15367686
chr13	71394396	71394424	4039788
chr17	31455514	31457004	1894635
chr17	31562759	31564270	1894635
chr17	31664325	31665836	1894635
chr17_random	1242288	1243799	1894635
chr11	56914779	56914815	10438731
chr2	182029787	182029822	8195215
chr10	6148030	6148063	10594041
chr6	32515522	32515566	1709740
chr6	33149491	33149520	1709740
chr1	27113297	27113401	14627819
chr19	47724401	47724778	8910434
chr5	137695409	137695439	9396797
chr4	74921135	74922824	7929219
chr4	75081443	75083546	7929219
chr14	74814952	74814992	1945851
chr3	46370268	46370476	9988701
chr3_random	648540	648748	9988701
chr19	44920681	44920916	8400237
chr6	31651256	31651286	8376940
chrX	114159733	114159767	12816724
chr8	128817589	128817629	2524830
chr5	43349214	43349642	9604010
chr8	11697452	11697753	9604010
chr10	90740302	90740383	10022897
chr5	137828633	137828672	10806199
chr14	101841353	101841385	15327990
chr10	44201420	44201453	15808852
chr11	14950630	14950660	8816445
chr9	21067978	21068014	2536920
chrX	37523961	37524023	9801155
chr16	4247188	4247551	7933101
chr19	34993942	34994211	11919196
chr2	119580525	119580552	8790425
chr15	71426296	71426323	8790425
chr4	68303208	68303255	12538612
chr4	68304321	68304355	12538612
chr5	131854471	131854502	8306959
chrX	47394499	47394719	9880555
chr2	104839654	104839708	1979677
chr1	38283895	38284447	1979677
chr19	11061106	11061136	12235180
chr2	201806431	201806506	12748179
chr2	234318980	234319013	12566446
chr2	234330338	234330368	12566446
chr19	46311999	46312030	15860659
chr6	31651199	31651239	8552071
chr4	68304321	68304356	10772899
chr16	31273884	31274003	8649405
chr14	79747955	79747985	10614643
chr5	131437179	131437349	2838738
chr11	5258553	5258587	9195958
chr5	131907199	131907240	9195954
chr4	123597347	123597383	9195954
chr5	112101285	112101326	16150893
chr2	127768229	127768259	1741247
chr10	17310524	17310564	2922288
chr19	3559877	3559949	8702673
chr19	2200271	2200331	10993829
chr11	5227694	5227882	7684493
chr11	5232618	5232806	7684493
chr11	102250957	102251015	11444842
chr10	31648169	31648227	8138542
chr10	31790066	31790113	8138542
chr10	31839605	31839721	8138542
chr10	31849359	31850420	8138542
chr10	31855839	31855881	8138542
chr1	116717289	116717322	8138542
chr21	43659942	43660006	8138542
chr6	37244967	37244997	10068671
chr10	6148027	6148065	10068671
chr10	6144519	6144547	2497520
chr7	100156090	100156279	2387842
chr7	142216838	142216875	1409722
chr18	58946946	58946974	12086670
chr17	7474036	7474067	9852068
chr20	31737398	31739058	7958836
chr8	59573682	59574907	10869351
chrX	37524131	37524171	10869351
chr6	32920138	32920168	9632673
chr9	21068004	21068033	12077266
chr6	32114038	32114072	2162843
chr17	29603571	29604369	8051410
chr17	29606270	29606521	8051410
chr12	6513783	6513814	11955624
chr1	167969972	167970010	10964678
chr11	67107756	67107830	8557630
chr7	45891666	45891703	8776721
chr6	87861614	87861646	12527202
chr5	153837897	153838113	12527202
chr12	52091275	52091305	15955096
chr3	132096089	132096297	15955096
chr3	132155382	132155411	15955096
chr12	66839960	66839994	8228802
chr14	22095220	22095259	2388624
chr6	22405282	22405315	2388622
chr6	22406504	22407281	2388622
chr10	90739750	90739790	10575005
chr6	12398422	12398453	2388628
chr6	43844936	43844975	11056166
chr6	153112337	153112383	11259431
chr14	21999392	21999642	2156339
chr4	55218755	55218801	9834219
chr11	117692798	117692831	9622621
chr4	111761803	111761837	9685346
chr11	5225333	5225684	2050690
chr6	87861521	87861558	12177069
chr14	21999514	21999544	10767553
chr9	132310019	132310204	2005889
chr1	202432234	202432264	16260418
chr19	46551726	46551753	8702877
chr6	32713075	32713109	8530481
chr6	32817060	32817097	8530481
chr11	118463820	118463849	9168923
chr3	99795249	99795281	9168923
chr5	131437289	131437343	7636192
chr4	123597347	123597383	7636192
chr19	523492	523522	11814679
chr3	30622822	30623077	11205746
chr5	132037328	132037541	11687571
chr22	37970954	37971002	9300179
chr7	142216684	142216868	2144610
chr14	22095176	22095210	2144610
chr7	44071654	44071920	1328854
chr16	30391085	30391720	8097887
chr19	10242732	10242764	7972116
chr7	5534742	5534772	11359804
chr22	14635979	14636009	11359804
chr2	130548917	130548947	11359804
chr2	130937489	130937519	11359804
chr2	131131259	131131289	11359804
chr2	131738065	131738095	11359804
chr15	42069176	42069206	11359804
chr14	18655264	18655294	11359804
chr14	19058341	19058371	11359804
chr7	107997468	107997500	15882996
chr5	139706797	139706829	9360990
chr7	5533903	5533935	14623878
chr5	79631251	79631283	14623878
chr3	12087832	12087862	14623878
chr1	103914788	103914818	14623878
chr8	23016740	23016771	14623878
chr8	23105152	23105183	14623878
chr17	77092311	77092341	14623878
chr5	132037328	132037543	9845517
chr11	5205125	5205155	2587218
chr19	803196	803226	9689920
chr22_random	21341	21371	1900840
chr11	116205669	116205699	1900840
chr4	74488729	74488764	1900840
chr2	21120496	21120528	1900840
chr14	93924784	93924824	1900840
chr20	44771564	44771612	16051383
chr7	87068171	87068216	11350951
chr15	72805408	72805921	8382688
chr10	6144637	6144674	9417809
chr6	31650994	31651095	9293772
chr3	129682402	129682467	1370462
chr3	129687328	129687456	1370462
chr10	5228099	5228140	12220531
chr17	10501487	10501527	11971910
chr17	31441742	31441775	8474441
chr17	31548412	31548445	8474441
chr17	31649986	31650019	8474441
chr17_random	1227960	1227993	8474441
chr17_random	510636	510705	3601664
chr17_random	512128	512197	3601664
chr17_random	514841	514910	3601664
chr17_random	519730	519799	3601664
chr17_random	525878	525947	3601664
chr17_random	555819	555888	3601664
chr17_random	2608037	2608106	3601664
chr11	2139131	2139351	2186040
chr6	31891225	31891261	2824993
chr6	31903421	31903455	2824993
chr19	49838998	49839103	9880562
chr2	219526621	219526659	6091127
chr2	219991953	219992007	6091127
chr2	219993215	219994527	6091127
chr2	219998626	219999624	6091127
chr9	101108425	101108465	6091127
chrX	45376724	45376793	6091127
chr12	47977236	47977628	6091127
chr12	50925645	50925684	6091127
chr12	51108311	51108364	6091127
chr12	51127833	51127915	6091127
chr12	51149725	51149807	6091127
chr12	51168383	51168465	6091127
chr12	51196693	51196745	6091127
chr12	51248224	51248258	6091127
chr12	51267686	51267745	6091127
chr12	51290670	51290703	6091127
chr12	51326795	51326855	6091127
chr12	51372473	51372523	6091127
chr12	51451054	51451107	6091127
chr12	51471261	51471324	6091127
chr12	51487699	51487760	6091127
chr12	51503068	51503134	6091127
chr12	51519819	51519866	6091127
chr12	51578728	51578767	6091127
chr10	8595899	8595938	6091127
chr10	17317279	17317392	6091127
chr17	40344128	40344242	6091127
chr15	75058645	75058683	6091127
chr20	43316656	43316700	10498899
chr1	938620	938650	12055236
chr13	29938058	29938152	11245470
chr19	3413759	3413788	11245470
chr15	49418595	49420743	8132535
chr9	106730620	106730953	15528481
chr15	32834226	32834262	14565956
chr17	59303127	59303178	8370519
chr17	59311325	59311376	8370519
chr17	59326028	59326078	8370519
chr17	59340720	59340767	8370519
chr17	59348313	59348364	8370519
chr14	21999513	21999541	10359663
chr3	197023272	197023300	11418607
chr11	2136189	2136325	9013771
chr4	74825037	74825076	8035808
chr3	124822085	124822163	9142867
chr2	233880782	233881067	8321239
chr19	15869835	15869863	10860554
chr7	45894487	45894516	12011061
chr19	46551008	46551037	12011061
chr1	216584694	216585098	12011061
chr1	216586732	216586761	12011061
chr22	40856850	40856894	8810289
chr22	40870522	40870566	8810289
chr22	40881064	40881104	8810289
chr1	3596999	3597060	11909952
chr1	938623	938655	3476954
chr2	86866999	86867277	8413295
chr11	69165071	69165101	8196642
chr3	25444697	25444726	1657595
chr1	98159129	98159155	11072080
chrX	48771250	48772496	2338243
chrX	48774414	48774496	2338243
chrX	48778663	48778710	2338243
chrX	48782531	48782585	2338243
chr11	118463734	118463763	2211589
chr2	127129933	127129963	2211589
chr7	5533904	5534773	14993214
chr5	79631252	79631282	14993214
chr5	131854471	131854502	14993214
chr3	12087833	12087862	14993214
chr2	130548917	130548948	14993214
chr2	130937489	130937520	14993214
chr2	131131258	131131289	14993214
chr2	131738064	131738095	14993214
chr2	201806407	201806452	14993214
chr1	103914789	103914818	14993214
chr22	14635979	14636010	14993214
chr15	42069176	42069206	14993214
chr14	18655263	18655294	14993214
chr14	19058341	19058372	14993214
chr17	77092311	77092340	14993214
chr8	128817488	128817516	7555706
chr11	100504990	100505108	14684847
chr19	50100731	50100772	11038359
chr11	73371478	73371508	10558866
chr4	39205934	39206031	16002992
chr9	130911609	130911651	10585862
chr9	130913432	130913464	10585862
chr22	21962546	21962884	8144670
chr21	42660037	42660066	14966289
chr12	52653727	52653757	9582375
chr4	123597151	123597181	9016343
chr11	71632648	71632702	11549713
chr9	127043487	127043556	1480470
chr10	6285226	6285271	10673355
chrX	47326669	47326715	11259407
chr8	128816012	128816041	8649373
chr8	128817628	128817676	8649373
chr20	42708337	42708374	9016677
chr7	5533942	5534628	15604281
chr6	89042357	89042389	15604281
chr5	77117519	77117549	15604281
chr3	177178012	177178044	15604281
chr2	130548326	130548356	15604281
chr2	130936898	130936928	15604281
chr2	131131850	131131880	15604281
chr2	131738656	131738686	15604281
chr2	132101239	132101269	15604281
chr1	27524804	27524836	15604281
chr9	6825508	6825538	15604281
chr11	1780732	1780764	15604281
chr22	14635388	14635418	15604281
chr14	18655855	18655885	15604281
chr14	19057750	19057780	15604281
chr18	58261272	58261304	15604281
chr14	105142547	105142618	8515067
chr14	105261333	105261401	8515067
chr14	21999511	21999542	2050118
chr6	32515517	32515589	9378978
chr7	139175314	139175364	11956185
chr7	55054191	55054238	3393529
chr5	137828926	137828975	8065330
chr7	100556400	100556570	12738229
chr8	128817555	128817620	2721961
chr12	90097176	90098190	8276854
chr7	55054206	55054237	12062800
chr8	28230632	28230749	12062800
chr19	2224334	2224407	9501877
chr1	68688176	68692149	9501877
chr9	21068005	21068035	15664995
chr4	123597329	123597379	7673240
chr1	154478086	154478119	10077002
chr1	148070712	148070740	3029724
chr1	148099453	148099481	3029724
chr3	166279008	166279036	11283019
chr12	54645489	54645518	12819038
chr7	5534469	5534499	10545204
chr17	37122023	37122063	2566164
chr4	123597212	123597383	1545787
chr14	22095239	22095319	1545787
chr2	127892037	127892602	7592627
chr1	120737547	120737589	8483949
chr1	147635795	147635837	8483949
chr1	148020751	148020792	8483949
chr6	31650908	31650946	10369255
chr11	5227822	5227863	2336386
chr11	5232746	5232787	2336386
chr4	109130501	109130558	9716664
chr4	109155033	109155063	9716664
chr4	109160211	109160247	9716664
chr4	109164121	109164158	9716664
chr4	109174854	109175558	9716664
chr10	17310515	17310544	7986748
chr17	59304826	59305028	3595566
chr17	59313055	59313213	3595566
chr17	59327723	59327925	3595566
chr17	59342380	59342606	3595566
chr17	59349960	59350263	3595566
chr16	67328704	67328733	16617148
chr7	87068135	87068286	8095499
chr11	2868568	2868621	12790805
chr17	8054645	8054674	15033491
chr19	7245592	7245654	8376587
chr16	31273920	31273960	9360988
chr7	26191772	26191800	10037736
chr17	42858367	42858395	10037736
chr4	159864008	159864049	11525247
chr11	117692801	117692831	8227043
chr5	137828633	137828733	16037570
chr14	105129372	105129408	10652350
chr14	105250343	105250379	10652350
chr2	151922249	151922282	8885246
chr13	27967303	27967353	8940064
chr14	94148352	94148401	9461605
chr1	206151284	206151338	10572091
chr17	59300847	59300883	8052268
chr17	59323741	59323775	8052268
chr17	59338489	59338525	8052268
chr2	10505924	10506001	9570735
chr2	127892443	127892602	9553065
chr19	46048242	46048291	15671201
chr5	132037322	132037358	12374808
chr11	5258547	5258578	2123346
chr14	36059170	36059310	10684967
chr13	31787485	31787523	10961992
chr11	116205662	116205692	8036173
chr22_random	21348	21378	8036173
chr6	26195613	26195650	15467009
chr1	205344108	205344140	10777590
chr1	170901753	170901782	10725705
chr6	336158	336488	16272311
chr17	7423622	7423653	16272311
chr19	59927683	59927724	16818466
chr19	59941630	59941780	16818466
chr19	59958151	59958244	16818466
chr19	59972979	59973072	16818466
chr19	59989483	59989576	16818466
chr19	60019574	60019743	16818466
chr19	60035838	60035989	16818466
chr19	60053550	60053700	16818466
chr19_random	150473	150514	16818466
chr19_random	164436	164586	16818466
chr19_random	181033	181126	16818466
chr19_random	212603	212772	16818466
chr19_random	229299	229392	16818466
chr19_random	240698	240791	16818466
chr19_random	257665	257758	16818466
chr19_random	273964	274114	16818466
chr19_random	290145	290295	16818466
chr2	42441468	42441499	9418891
chr8	110621515	110621547	9418891
chr6	160033827	160033861	8602839
chr5	132037484	132037518	1532661
chr21	42660090	42660131	10619353
chr7	143763141	143763174	11101876
chr16	10878363	10878396	11101876
chr6	87861615	87861644	7690722
chr11	5247661	5248033	7882983
chr21	45788563	45789001	15652157
chr10	90702792	90702824	9546431
chr2	1395338	1396616	2306241
chr6	32515523	32515555	15798210
chr12	28007916	28007970	11590145
chr12	28014206	28014257	11590145
chr11	127855335	127855387	11590145
chrX	134545609	134545664	11590145
chr21	39113467	39113522	11590145
chr19	50140986	50141031	9651383
chr19	11060975	11061028	8969230
chr11	61474296	61474475	14982938
chr13	27968203	27968239	9295307
chr7	100159368	100159403	9295307
chr6	43844939	43844973	9295307
chr11	14950483	14950770	1335241
chr19	5794123	5794155	16199102
chr1	151145503	151145560	9512462
chrX	133421460	133421557	8524221
chr12	55326299	55326340	9512469
chr7	148494900	148494944	11779858
chr7	148507369	148507398	11779858
chr6	152170740	152170769	11779858
chr4	123597348	123597380	7935406
chr22	20928907	20929221	11994467
chr5	131434252	131434284	10706706
chr4	123597155	123597265	10706706
chr2	69467758	69469928	15878746
chr15	72448909	72448940	8703023
chr4	155703459	155703510	8226773
chr11	14951375	14951415	1738589
chr1	53434579	53434614	12408750
chr16	29739213	29739242	16418217
chr8	37942249	37942857	11316759
chr6	87861601	87861689	7685765
chr4	123597348	123597379	9819402
chr6	31891134	31891163	8524643
chr11	5247819	5247851	8524643
chr7	5535953	5535982	3185543
chr1	227636540	227636569	3185543
chr14	74815995	74816043	11997340
chr11	5258375	5258749	1924329
chr14	74814950	74815009	1833404
chr16	55553246	55553307	8530390
chr14	22974975	22975043	1449500
chr1	148070779	148070957	9874597
chr1	148099236	148099414	9874597
chr16	55199808	55199836	2822255
chr16	29983412	29983440	14966291
chr20	30103721	30103934	9822652
chr12	19152055	19152167	1516833
chr19	19117402	19119608	1516833
chr19	19121034	19121241	1516833
chr19	19122486	19122569	1516833
chr19	19152494	19152573	1516833
chr19	19154381	19154494	1516833
chr19	19163889	19163921	1516833
chr1	154718852	154719060	1516833
chr1	177683436	177684327	1516833
chr15	97956184	97956240	1516833
chr15	97990703	97990903	1516833
chr15	98003432	98003480	1516833
chr15	98029054	98029292	1516833
chr15	98032161	98032342	1516833
chr15	98047985	98048131	1516833
chr15	98064459	98064576	1516833
chr15	98068360	98068488	1516833
chr15	98070117	98071422	1516833
chr17	59349958	59349992	11890700
chr19	56049581	56049616	8626436
chrX	138440552	138440581	8626436
chr5	131437265	131437302	3257571
chr1	151145508	151145546	15790882
chr11	116205752	116205859	11839757
chr22_random	21181	21288	11839757
chr7	55054182	55054234	2847030
chr2	210861534	210861562	2243772
chr7	66438244	66438537	11714687
chr5	88155358	88155501	11714687
chr5	88235485	88235778	11714687
chr11	5258533	5258592	2116990
chr11	61942927	61942978	1711673
chr2	85748894	85748950	8065304
chr16	55259658	55259699	1903400
chr4	122964230	122964882	8202514
chr1	59022164	59022500	8355696
chr11	5258550	5258586	8355692
chr16	162862	163413	8355692
chr16	166666	167217	8355692
chr9	21792570	21792811	15535799
chr1	227636732	227637755	1318069
chr4	123597348	123597378	9065434
chr10	104144209	104144265	9528780
chr3	195336539	195336569	9528780
chr11	2139215	2139245	1915886
chr11	118463735	118463763	8265578
chr7	22733214	22733253	10657660
chr17	29606345	29606384	10657660
chr2	21119497	21119597	1545795
chr21	45786201	45786247	11078737
chr1	233095014	233095257	1870965
chr6	32549434	32549462	1903538
chr6	32665657	32665685	1903538
chr6	32742509	32742537	1903538
chr11	116199349	116199380	2020548
chr2	21120500	21120538	2020548
chr22_random	27653	27684	2020548
chr4	123597348	123597378	10816557
chr10	6144341	6144375	8642278
chr17	59304619	59305041	3018491
chr17	59312806	59313226	3018491
chr17	59327516	59327938	3018491
chr17	59342201	59342563	3018491
chr17	59349781	59350202	3018491
chr8	128818307	128818364	10085075
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s2.gff3000066400000000000000000004641231211610345200225630ustar00rootroot00000000000000##gff-version   3
##sequence-region   chrX 1693988 153904229
##sequence-region   chr3_random 648541 648748
##sequence-region   chrY 1693988 26956687
##sequence-region   chr14 18654827 105399391
##sequence-region   chr15 32453091 98071466
##sequence-region   chr12 3499782 119900981
##sequence-region   chr13 19032153 112825091
##sequence-region   chr18 647736 72858327
##sequence-region   chr16_random 105103 105168
##sequence-region   chr19 523493 62043207
##sequence-region   chr16 103420 84509897
##sequence-region   chr17 4491642 77650042
##sequence-region   chr7_random 465930 466022
##sequence-region   chr10 5126490 135190285
##sequence-region   chr8_random 420977 426932
##sequence-region   chr11 303950 129670813
##sequence-region   chrX_random 1443981 1444483
##sequence-region   chrM 16413 16571
##sequence-region   chr7 525927 150317059
##sequence-region   chr8 11603761 145509161
##sequence-region   chr9 2611471 138991702
##sequence-region   chr17_random 492578 2614935
##sequence-region   chr3 4995941 197293473
##sequence-region   chr9_random 773108 774288
##sequence-region   chr4 5457317 189161743
##sequence-region   chr22_random 13235 30260
##sequence-region   chr5 1348021 176769177
##sequence-region   chr6 336159 170723871
##sequence-region   chr22 14635194 49363991
##sequence-region   chr21 26464852 46846730
##sequence-region   chr20 1090119 62342693
##sequence-region   chr1 938617 236157485
##sequence-region   chr2 1390689 234334518
##sequence-region   chr19_random 150474 290295
chr4	.	BED_feature	74488437	74488469	.	.	.	Name=2247076
chr20	.	BED_feature	22978320	22978355	.	.	.	Name=11257274
chr1	.	BED_feature	227636540	227636698	.	.	.	Name=2300053
chr5	.	BED_feature	142760501	142760529	.	.	.	Name=11463861
chr5	.	BED_feature	142795077	142795171	.	.	.	Name=11463861
chr11	.	BED_feature	303986	304024	.	.	.	Name=2123539
chr1	.	BED_feature	27871384	27871421	.	.	.	Name=2123539
chr5	.	BED_feature	132037518	132037549	.	.	.	Name=9686601
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=9686601
chr9	.	BED_feature	129656862	129656893	.	.	.	Name=9845534
chr18	.	BED_feature	72858093	72858121	.	.	.	Name=7527040
chr1	.	BED_feature	165754422	165754452	.	.	.	Name=9510181
chr6	.	BED_feature	36754361	36754400	.	.	.	Name=10506225
chr9	.	BED_feature	21067981	21068019	.	.	.	Name=2037595
chr17	.	BED_feature	35109679	35109708	.	.	.	Name=9045619
chr11	.	BED_feature	605678	605718	.	.	.	Name=10924517
chr11	.	BED_feature	32405321	32405350	.	.	.	Name=10455131
chr5	.	BED_feature	131434150	131434658	.	.	.	Name=8460159
chr4	.	BED_feature	123597349	123597379	.	.	.	Name=8460159
chr14	.	BED_feature	105142541	105142615	.	.	.	Name=7635985
chr14	.	BED_feature	105261327	105261401	.	.	.	Name=7635985
chr18	.	BED_feature	72858013	72858327	.	.	.	Name=1696259
chr11	.	BED_feature	5227819	5227864	.	.	.	Name=2458563
chr11	.	BED_feature	5232743	5232788	.	.	.	Name=2458563
chr11	.	BED_feature	605675	605722	.	.	.	Name=11877397
chr16	.	BED_feature	10897093	10897125	.	.	.	Name=15247294
chr16	.	BED_feature	10908372	10909110	.	.	.	Name=15247294
chr16	.	BED_feature	10880161	10880210	.	.	.	Name=9491997
chr10	.	BED_feature	75339286	75339336	.	.	.	Name=8071349
chr7	.	BED_feature	525970	526156	.	.	.	Name=8415628
chr19	.	BED_feature	59077687	59077730	.	.	.	Name=2246272
chr17	.	BED_feature	61729561	61729604	.	.	.	Name=2246272
chr16	.	BED_feature	23755127	23755170	.	.	.	Name=2246272
chr4	.	BED_feature	123597348	123597383	.	.	.	Name=7624346
chr14	.	BED_feature	24173352	24173382	.	.	.	Name=7624346
chr20	.	BED_feature	60962039	60962071	.	.	.	Name=12923186
chr9	.	BED_feature	21067973	21068006	.	.	.	Name=2139895
chr17	.	BED_feature	59307404	59307440	.	.	.	Name=16239259
chr17	.	BED_feature	59315150	59315190	.	.	.	Name=16239259
chr17	.	BED_feature	59329949	59329989	.	.	.	Name=16239259
chr2	.	BED_feature	162717073	162717294	.	.	.	Name=15828872
chr8	.	BED_feature	11697517	11697549	.	.	.	Name=9092581
chr4	.	BED_feature	68303661	68303689	.	.	.	Name=12089350
chr2	.	BED_feature	175741024	175741060	.	.	.	Name=2145272
chr9	.	BED_feature	127043487	127043516	.	.	.	Name=9837962
chr6	.	BED_feature	43247769	43247886	.	.	.	Name=2009862
chr6	.	BED_feature	43249561	43249830	.	.	.	Name=2009862
chr6	.	BED_feature	43251431	43251559	.	.	.	Name=2009862
chr6	.	BED_feature	43254025	43254103	.	.	.	Name=2009862
chr22	.	BED_feature	37970975	37971015	.	.	.	Name=8662878
chrX	.	BED_feature	37524156	37524199	.	.	.	Name=11781315
chr7	.	BED_feature	99227487	99227522	.	.	.	Name=12514743
chr3	.	BED_feature	121018721	121018751	.	.	.	Name=12514743
chr1	.	BED_feature	198409939	198409967	.	.	.	Name=12514743
chr9	.	BED_feature	136358296	136358325	.	.	.	Name=12514743
chr12	.	BED_feature	119900952	119900981	.	.	.	Name=12514743
chr20	.	BED_feature	42491697	42491726	.	.	.	Name=12514743
chr15	.	BED_feature	49322677	49322730	.	.	.	Name=8395654
chr11	.	BED_feature	303986	304024	.	.	.	Name=2919169
chr10	.	BED_feature	62207741	62208380	.	.	.	Name=8524257
chr3	.	BED_feature	25444699	25444725	.	.	.	Name=9886825
chr13	.	BED_feature	93928761	93930546	.	.	.	Name=7929451
chr3	.	BED_feature	197293413	197293473	.	.	.	Name=2519614
chr4	.	BED_feature	84474936	84475267	.	.	.	Name=11779847
chr2	.	BED_feature	21173784	21173833	.	.	.	Name=10859308
chr1	.	BED_feature	148070787	148070817	.	.	.	Name=2367528
chr1	.	BED_feature	148099377	148099407	.	.	.	Name=2367528
chr21	.	BED_feature	26464852	26464881	.	.	.	Name=8703038
chr7	.	BED_feature	5535520	5535577	.	.	.	Name=9847397
chr6	.	BED_feature	46280791	46280829	.	.	.	Name=9847397
chr6	.	BED_feature	89043285	89043326	.	.	.	Name=9847397
chr5	.	BED_feature	77116586	77116627	.	.	.	Name=9847397
chr5	.	BED_feature	79634273	79634314	.	.	.	Name=9847397
chr5	.	BED_feature	97702460	97702501	.	.	.	Name=9847397
chr3	.	BED_feature	177178904	177178935	.	.	.	Name=9847397
chr1	.	BED_feature	222119016	222119057	.	.	.	Name=9847397
chr9	.	BED_feature	102533464	102533496	.	.	.	Name=9847397
chrX	.	BED_feature	46033351	46033389	.	.	.	Name=9847397
chr22	.	BED_feature	39801029	39801062	.	.	.	Name=9847397
chr15	.	BED_feature	42069512	42069553	.	.	.	Name=9847397
chr18	.	BED_feature	58260341	58260379	.	.	.	Name=9847397
chr11	.	BED_feature	5204935	5204965	.	.	.	Name=8663270
chr6	.	BED_feature	31891182	31891213	.	.	.	Name=1696723
chr6	.	BED_feature	31903378	31903409	.	.	.	Name=1696723
chr5	.	BED_feature	149772538	149772621	.	.	.	Name=1899864
chr6	.	BED_feature	87861687	87861724	.	.	.	Name=2476438
chr6	.	BED_feature	32515519	32515547	.	.	.	Name=8756625
chr11	.	BED_feature	2139273	2139305	.	.	.	Name=8832573
chr13	.	BED_feature	27389426	27389468	.	.	.	Name=11003654
chr14	.	BED_feature	67360018	67360070	.	.	.	Name=9878257
chr7	.	BED_feature	24290261	24290290	.	.	.	Name=8123590
chr4	.	BED_feature	123597157	123597186	.	.	.	Name=1712901
chr12	.	BED_feature	23578125	23578724	.	.	.	Name=1396566
chr12	.	BED_feature	23580653	23580871	.	.	.	Name=1396566
chr12	.	BED_feature	23587411	23587586	.	.	.	Name=1396566
chr12	.	BED_feature	23590519	23590629	.	.	.	Name=1396566
chr12	.	BED_feature	23607458	23607599	.	.	.	Name=1396566
chr12	.	BED_feature	23619861	23620044	.	.	.	Name=1396566
chr12	.	BED_feature	23685012	23685100	.	.	.	Name=1396566
chr11	.	BED_feature	15967127	15967239	.	.	.	Name=1396566
chr11	.	BED_feature	117692802	117692831	.	.	.	Name=1396566
chr1	.	BED_feature	202359462	202360518	.	.	.	Name=1396566
chr8	.	BED_feature	88869624	88871029	.	.	.	Name=1396566
chr14	.	BED_feature	105142610	105142639	.	.	.	Name=9317131
chr17	.	BED_feature	45632665	45634784	.	.	.	Name=3480516
chr12	.	BED_feature	66839312	66839342	.	.	.	Name=10227974
chr21	.	BED_feature	44378028	44378057	.	.	.	Name=12808467
chr12	.	BED_feature	6517180	6517207	.	.	.	Name=12933903
chr16	.	BED_feature	10910502	10910529	.	.	.	Name=12933903
chr16	.	BED_feature	10917737	10917765	.	.	.	Name=12933903
chr3	.	BED_feature	46880059	46880137	.	.	.	Name=1699944
chr14	.	BED_feature	105142554	105142609	.	.	.	Name=8759736
chr14	.	BED_feature	105261340	105261401	.	.	.	Name=8759736
chr11	.	BED_feature	5203642	5204288	.	.	.	Name=7499351
chr9	.	BED_feature	106691207	106691258	.	.	.	Name=11839742
chr9	.	BED_feature	138991425	138991702	.	.	.	Name=15743775
chr7	.	BED_feature	91602081	91602142	.	.	.	Name=12145339
chr17	.	BED_feature	70254459	70255238	.	.	.	Name=12145337
chr17	.	BED_feature	70256546	70256588	.	.	.	Name=12145337
chr7	.	BED_feature	100159374	100159407	.	.	.	Name=8387214
chr12	.	BED_feature	108038832	108038863	.	.	.	Name=11076940
chr12	.	BED_feature	108053505	108053612	.	.	.	Name=11076940
chr11	.	BED_feature	116213732	116213811	.	.	.	Name=8626539
chr22_random	.	BED_feature	13235	13314	.	.	.	Name=8626539
chr7	.	BED_feature	27140155	27140183	.	.	.	Name=8759021
chr16	.	BED_feature	55199808	55199838	.	.	.	Name=8759021
chr17	.	BED_feature	53714114	53714143	.	.	.	Name=9287329
chr11	.	BED_feature	118463822	118463852	.	.	.	Name=8408012
chr5	.	BED_feature	131907151	131907240	.	.	.	Name=15826950
chr5	.	BED_feature	132043303	132043331	.	.	.	Name=15826950
chr6	.	BED_feature	32515526	32515555	.	.	.	Name=7784170
chr17	.	BED_feature	31441613	31441885	.	.	.	Name=8355682
chr17	.	BED_feature	31548286	31548549	.	.	.	Name=8355682
chr17	.	BED_feature	31649860	31650123	.	.	.	Name=8355682
chr17_random	.	BED_feature	1227834	1228097	.	.	.	Name=8355682
chr19	.	BED_feature	34994862	34995325	.	.	.	Name=8618861
chr2	.	BED_feature	169927261	169927288	.	.	.	Name=10799495
chr11	.	BED_feature	5204937	5204966	.	.	.	Name=9642249
chr11	.	BED_feature	5227737	5227791	.	.	.	Name=9642249
chr11	.	BED_feature	5232661	5232715	.	.	.	Name=9642249
chr11	.	BED_feature	5247820	5247853	.	.	.	Name=9642249
chr16	.	BED_feature	142779	142810	.	.	.	Name=9642249
chr16	.	BED_feature	152991	153022	.	.	.	Name=9642249
chr5	.	BED_feature	142673759	142673832	.	.	.	Name=3037703
chr4	.	BED_feature	149219375	149222100	.	.	.	Name=3037703
chr4	.	BED_feature	149254705	149254867	.	.	.	Name=3037703
chr4	.	BED_feature	149260759	149260877	.	.	.	Name=3037703
chr4	.	BED_feature	149293070	149293211	.	.	.	Name=3037703
chr4	.	BED_feature	149295151	149295504	.	.	.	Name=3037703
chr4	.	BED_feature	149335347	149335465	.	.	.	Name=3037703
chr4	.	BED_feature	149400579	149400721	.	.	.	Name=3037703
chr4	.	BED_feature	149575706	149577463	.	.	.	Name=3037703
chr4	.	BED_feature	149582761	149582973	.	.	.	Name=3037703
chr13	.	BED_feature	19032153	19032208	.	.	.	Name=11986328
chr13	.	BED_feature	20733667	20733722	.	.	.	Name=11986328
chr11	.	BED_feature	63839959	63840014	.	.	.	Name=11986328
chr6	.	BED_feature	160034413	160034809	.	.	.	Name=11853549
chr6	.	BED_feature	153113527	153113563	.	.	.	Name=2320002
chr14	.	BED_feature	74815207	74815246	.	.	.	Name=2320002
chr17	.	BED_feature	7531564	7531591	.	.	.	Name=10348347
chr4	.	BED_feature	74488730	74488763	.	.	.	Name=2320004
chr1	.	BED_feature	167341718	167341979	.	.	.	Name=8392703
chr6	.	BED_feature	87861634	87861665	.	.	.	Name=1701437
chr14	.	BED_feature	74814960	74815008	.	.	.	Name=3004967
chr7	.	BED_feature	5536805	5536857	.	.	.	Name=7828546
chr3	.	BED_feature	188870907	188870942	.	.	.	Name=8645191
chr1	.	BED_feature	202402287	202402322	.	.	.	Name=8645191
chr19	.	BED_feature	2200168	2200195	.	.	.	Name=9774680
chr12	.	BED_feature	51132126	51132488	.	.	.	Name=2438131
chr12	.	BED_feature	51153785	51154148	.	.	.	Name=2438131
chr12	.	BED_feature	51173236	51173600	.	.	.	Name=2438131
chr12	.	BED_feature	51476141	51476239	.	.	.	Name=2438131
chr17	.	BED_feature	36232360	36232424	.	.	.	Name=2438131
chr11	.	BED_feature	5204985	5205048	.	.	.	Name=11756191
chr11	.	BED_feature	5258556	5258590	.	.	.	Name=11756191
chr12	.	BED_feature	54713254	54713285	.	.	.	Name=10978333
chr12	.	BED_feature	111829115	111829157	.	.	.	Name=2174873
chr11	.	BED_feature	303989	304018	.	.	.	Name=2174873
chr15	.	BED_feature	42790854	42790900	.	.	.	Name=2174873
chr11	.	BED_feature	100505080	100505108	.	.	.	Name=15084343
chr6	.	BED_feature	31651126	31651176	.	.	.	Name=12560487
chr11	.	BED_feature	5262447	5262488	.	.	.	Name=3879975
chrX	.	BED_feature	55670008	55670049	.	.	.	Name=1946405
chr14	.	BED_feature	99813796	99813826	.	.	.	Name=1946405
chr7	.	BED_feature	22733174	22733209	.	.	.	Name=8207232
chr4	.	BED_feature	74825044	74825086	.	.	.	Name=8207232
chr17	.	BED_feature	35425016	35425052	.	.	.	Name=8207232
chr1	.	BED_feature	159760612	159760647	.	.	.	Name=3198647
chr1	.	BED_feature	159842261	159842296	.	.	.	Name=3198647
chr19	.	BED_feature	7245410	7246142	.	.	.	Name=1324934
chr6	.	BED_feature	36752202	36753120	.	.	.	Name=12640112
chr1	.	BED_feature	27060397	27060437	.	.	.	Name=12640112
chr16	.	BED_feature	68973089	68973120	.	.	.	Name=9473501
chr16	.	BED_feature	68989908	68989937	.	.	.	Name=9473501
chr14	.	BED_feature	22974964	22975026	.	.	.	Name=1577822
chr9	.	BED_feature	21067983	21068040	.	.	.	Name=1532252
chr5	.	BED_feature	132019686	132021821	.	.	.	Name=8605348
chr5	.	BED_feature	132200101	132200211	.	.	.	Name=8605348
chr11	.	BED_feature	5227731	5227785	.	.	.	Name=7914370
chr11	.	BED_feature	5232655	5232709	.	.	.	Name=7914370
chrX	.	BED_feature	37524149	37524181	.	.	.	Name=7914370
chrX	.	BED_feature	24621890	24621954	.	.	.	Name=15615704
chr11	.	BED_feature	5227722	5227997	.	.	.	Name=2734104
chr11	.	BED_feature	5232646	5232925	.	.	.	Name=2734104
chr10	.	BED_feature	72033577	72033645	.	.	.	Name=10072525
chr16	.	BED_feature	55199886	55199917	.	.	.	Name=2494701
chr15	.	BED_feature	72826155	72826254	.	.	.	Name=8120057
chr17	.	BED_feature	38820334	38820372	.	.	.	Name=2349089
chr3	.	BED_feature	73242765	73242823	.	.	.	Name=2349089
chr17_random	.	BED_feature	492578	492638	.	.	.	Name=2349089
chr17_random	.	BED_feature	494191	494241	.	.	.	Name=2349089
chr17_random	.	BED_feature	510843	510904	.	.	.	Name=2349089
chr17_random	.	BED_feature	512335	512396	.	.	.	Name=2349089
chr17_random	.	BED_feature	514637	514697	.	.	.	Name=2349089
chr17_random	.	BED_feature	519526	519586	.	.	.	Name=2349089
chr17_random	.	BED_feature	525674	525734	.	.	.	Name=2349089
chr17_random	.	BED_feature	527779	527840	.	.	.	Name=2349089
chr17_random	.	BED_feature	556026	556087	.	.	.	Name=2349089
chr17_random	.	BED_feature	2607833	2607893	.	.	.	Name=2349089
chr17_random	.	BED_feature	2614874	2614935	.	.	.	Name=2349089
chr15	.	BED_feature	65919438	65919514	.	.	.	Name=2349089
chr1	.	BED_feature	67925701	67925730	.	.	.	Name=11090615
chr3	.	BED_feature	185578716	185578748	.	.	.	Name=11790771
chr20	.	BED_feature	54400823	54400851	.	.	.	Name=11790771
chr11	.	BED_feature	100505080	100505190	.	.	.	Name=10894148
chr16	.	BED_feature	10878405	10878701	.	.	.	Name=11777970
chr6	.	BED_feature	121798622	121798697	.	.	.	Name=12644583
chr5	.	BED_feature	108416078	108416125	.	.	.	Name=12644583
chr1	.	BED_feature	205186358	205186544	.	.	.	Name=14644095
chr11	.	BED_feature	116213545	116213694	.	.	.	Name=1846669
chr22_random	.	BED_feature	13279	13501	.	.	.	Name=1846669
chr6	.	BED_feature	87861642	87861711	.	.	.	Name=2828923
chr6	.	BED_feature	87861739	87861778	.	.	.	Name=12193378
chr7	.	BED_feature	45894487	45894517	.	.	.	Name=7688722
chr19	.	BED_feature	54351001	54351029	.	.	.	Name=15082771
chr17	.	BED_feature	71229146	71229180	.	.	.	Name=9837976
chr1	.	BED_feature	185064112	185064783	.	.	.	Name=7800505
chr1	.	BED_feature	185090039	185090099	.	.	.	Name=7800505
chr12	.	BED_feature	46798803	46799458	.	.	.	Name=7800504
chr4	.	BED_feature	74825038	74825086	.	.	.	Name=10928981
chr17	.	BED_feature	31231573	31231601	.	.	.	Name=10928981
chr2	.	BED_feature	85969657	85969692	.	.	.	Name=14644416
chr1	.	BED_feature	89303546	89303575	.	.	.	Name=1729591
chr7	.	BED_feature	150316901	150317059	.	.	.	Name=11013235
chr3	.	BED_feature	170965507	170965616	.	.	.	Name=12586348
chr19	.	BED_feature	46551329	46551628	.	.	.	Name=2808430
chr12	.	BED_feature	51782658	51782690	.	.	.	Name=15961790
chr19	.	BED_feature	16298812	16298842	.	.	.	Name=11750135
chr10	.	BED_feature	5126490	5126539	.	.	.	Name=15814298
chr16	.	BED_feature	31632045	31632077	.	.	.	Name=15814297
chr16	.	BED_feature	31792541	31792792	.	.	.	Name=15814297
chr1	.	BED_feature	89303575	89303611	.	.	.	Name=1901265
chr1	.	BED_feature	89645725	89645761	.	.	.	Name=1901265
chr15	.	BED_feature	88150901	88151079	.	.	.	Name=1680856
chr5	.	BED_feature	131907212	131907240	.	.	.	Name=11152655
chr10	.	BED_feature	17310282	17310756	.	.	.	Name=8654956
chr16	.	BED_feature	54247449	54248013	.	.	.	Name=11333263
chr14	.	BED_feature	72672978	72673010	.	.	.	Name=10446206
chr12	.	BED_feature	50731409	50731459	.	.	.	Name=10567637
chr9	.	BED_feature	134927114	134927158	.	.	.	Name=11945176
chr9	.	BED_feature	134947672	134947716	.	.	.	Name=11945176
chr7	.	BED_feature	106472227	106472261	.	.	.	Name=9175634
chr19	.	BED_feature	54219615	54219649	.	.	.	Name=9175634
chr19	.	BED_feature	54226282	54226316	.	.	.	Name=9175634
chr19	.	BED_feature	54232641	54232675	.	.	.	Name=9175634
chr19	.	BED_feature	54238669	54238703	.	.	.	Name=9175634
chr19	.	BED_feature	54244383	54244417	.	.	.	Name=9175634
chr19	.	BED_feature	54251020	54251054	.	.	.	Name=9175634
chr8	.	BED_feature	128817317	128817344	.	.	.	Name=2690070
chr7	.	BED_feature	21434867	21436872	.	.	.	Name=1454515
chr7	.	BED_feature	21483235	21483345	.	.	.	Name=1454515
chr7	.	BED_feature	21488166	21488261	.	.	.	Name=1454515
chr7	.	BED_feature	21517248	21517549	.	.	.	Name=1454515
chr13	.	BED_feature	88810291	88812937	.	.	.	Name=1454515
chr2	.	BED_feature	174481586	174483182	.	.	.	Name=1454515
chr2	.	BED_feature	174486195	174486242	.	.	.	Name=1454515
chr2	.	BED_feature	174491581	174491751	.	.	.	Name=1454515
chr2	.	BED_feature	174527988	174529207	.	.	.	Name=1454515
chrX	.	BED_feature	55074224	55074271	.	.	.	Name=9334239
chr21	.	BED_feature	26464986	26465014	.	.	.	Name=1380960
chr12	.	BED_feature	66839980	66840016	.	.	.	Name=8756632
chr11	.	BED_feature	116205061	116205698	.	.	.	Name=9295296
chr22_random	.	BED_feature	21343	21981	.	.	.	Name=9295296
chr5	.	BED_feature	131423936	131423974	.	.	.	Name=8611694
chr16	.	BED_feature	55199809	55199838	.	.	.	Name=9171103
chr10	.	BED_feature	112826539	112826790	.	.	.	Name=9249478
chr11	.	BED_feature	116204977	116205835	.	.	.	Name=2834395
chr22_random	.	BED_feature	21206	22065	.	.	.	Name=2834395
chr10	.	BED_feature	17311048	17311087	.	.	.	Name=2293664
chr11	.	BED_feature	525486	525798	.	.	.	Name=3012774
chr2	.	BED_feature	136592479	136592507	.	.	.	Name=10229837
chr3	.	BED_feature	120761102	120761701	.	.	.	Name=8906820
chr5	.	BED_feature	159778571	159778599	.	.	.	Name=15016801
chr5	.	BED_feature	159780262	159781293	.	.	.	Name=15016801
chr11	.	BED_feature	124999010	124999038	.	.	.	Name=15016801
chr11	.	BED_feature	125000253	125000620	.	.	.	Name=15016801
chr6	.	BED_feature	29798935	29798987	.	.	.	Name=8657576
chr6	.	BED_feature	29867705	29867764	.	.	.	Name=8657576
chr6	.	BED_feature	29903337	29903396	.	.	.	Name=8657576
chr6	.	BED_feature	29963227	29963279	.	.	.	Name=8657576
chr6	.	BED_feature	30001931	30001990	.	.	.	Name=8657576
chr6	.	BED_feature	30018026	30018078	.	.	.	Name=8657576
chr6	.	BED_feature	30082070	30082121	.	.	.	Name=8657576
chr6	.	BED_feature	30335107	30335147	.	.	.	Name=8657576
chr4	.	BED_feature	74825006	74825052	.	.	.	Name=8175759
chr6	.	BED_feature	32742394	32742649	.	.	.	Name=8315353
chr11	.	BED_feature	118463735	118463763	.	.	.	Name=2771941
chr7	.	BED_feature	45930678	45930706	.	.	.	Name=14963110
chr14	.	BED_feature	94117291	94117597	.	.	.	Name=9601089
chr11	.	BED_feature	61942944	61942994	.	.	.	Name=9468485
chr17	.	BED_feature	35727182	35727965	.	.	.	Name=15831516
chr17	.	BED_feature	35732150	35732743	.	.	.	Name=15831516
chr6	.	BED_feature	30565087	30565123	.	.	.	Name=8702722
chr10	.	BED_feature	91051674	91051709	.	.	.	Name=8702722
chr4	.	BED_feature	74825042	74825071	.	.	.	Name=8413306
chr1	.	BED_feature	27060401	27060434	.	.	.	Name=9659898
chr17	.	BED_feature	59304832	59304865	.	.	.	Name=16517055
chr17	.	BED_feature	59327729	59327762	.	.	.	Name=16517055
chr17	.	BED_feature	59342413	59342446	.	.	.	Name=16517055
chr17	.	BED_feature	59349993	59350026	.	.	.	Name=16517055
chr14	.	BED_feature	74814955	74815007	.	.	.	Name=1639071
chr3	.	BED_feature	70068144	70068181	.	.	.	Name=10938265
chr3	.	BED_feature	134947298	134947876	.	.	.	Name=2495523
chr14	.	BED_feature	93924792	93924822	.	.	.	Name=2495523
chr6	.	BED_feature	32742366	32742936	.	.	.	Name=1985121
chr6	.	BED_feature	32839241	32839653	.	.	.	Name=1985121
chr8	.	BED_feature	42184274	42184463	.	.	.	Name=9016559
chr17	.	BED_feature	35740996	35741053	.	.	.	Name=7479078
chr9	.	BED_feature	136448823	136448877	.	.	.	Name=7479078
chr15	.	BED_feature	94678307	94678373	.	.	.	Name=7479078
chr20	.	BED_feature	61844191	61844300	.	.	.	Name=14625278
chr8	.	BED_feature	28270142	28270216	.	.	.	Name=14625278
chr8	.	BED_feature	28273132	28273207	.	.	.	Name=14625278
chr8	.	BED_feature	28274488	28274561	.	.	.	Name=14625278
chr1	.	BED_feature	167969984	167970010	.	.	.	Name=7518452
chr3	.	BED_feature	123384313	123384360	.	.	.	Name=12036954
chr3	.	BED_feature	123385624	123385674	.	.	.	Name=12036954
chr14	.	BED_feature	74814934	74814994	.	.	.	Name=3029776
chr7	.	BED_feature	45894487	45894515	.	.	.	Name=9261184
chr17	.	BED_feature	77650008	77650042	.	.	.	Name=9261184
chr3	.	BED_feature	188042775	188043233	.	.	.	Name=15850785
chr11	.	BED_feature	116213542	116213703	.	.	.	Name=11714848
chr22_random	.	BED_feature	13343	13504	.	.	.	Name=11714848
chr6	.	BED_feature	31891190	31891235	.	.	.	Name=2342471
chr6	.	BED_feature	31903386	31903431	.	.	.	Name=2342471
chr22	.	BED_feature	17200932	17200972	.	.	.	Name=16107498
chr22	.	BED_feature	19826897	19826937	.	.	.	Name=16107498
chr22	.	BED_feature	19952173	19952213	.	.	.	Name=16107498
chr2	.	BED_feature	11523693	11523952	.	.	.	Name=16107498
chr18	.	BED_feature	27425728	27425757	.	.	.	Name=2019605
chr2	.	BED_feature	21119526	21119763	.	.	.	Name=2019605
chr12	.	BED_feature	6925720	6926152	.	.	.	Name=11376946
chr1	.	BED_feature	157951088	157951128	.	.	.	Name=8621622
chr10	.	BED_feature	5228100	5228140	.	.	.	Name=11284743
chr19	.	BED_feature	6671575	6671793	.	.	.	Name=2247055
chr6	.	BED_feature	43247373	43247404	.	.	.	Name=2200737
chr6	.	BED_feature	32515518	32515570	.	.	.	Name=11046010
chr6	.	BED_feature	33016714	33016744	.	.	.	Name=11046010
chr5	.	BED_feature	32747447	32747507	.	.	.	Name=7641319
chr2	.	BED_feature	70634549	70634607	.	.	.	Name=9162057
chr9	.	BED_feature	21067985	21068015	.	.	.	Name=9199299
chr17	.	BED_feature	31231513	31231552	.	.	.	Name=10023774
chr12	.	BED_feature	67488871	67488913	.	.	.	Name=9233781
chr6	.	BED_feature	36752112	36753033	.	.	.	Name=9233781
chr3	.	BED_feature	130730026	130730054	.	.	.	Name=9579468
chrX	.	BED_feature	153059392	153059427	.	.	.	Name=9579468
chrX	.	BED_feature	153062721	153062935	.	.	.	Name=9579468
chrX	.	BED_feature	153101129	153101363	.	.	.	Name=9579468
chrX	.	BED_feature	153138247	153138481	.	.	.	Name=9579468
chr7	.	BED_feature	47058919	47058999	.	.	.	Name=1465383
chr11	.	BED_feature	94410405	94410505	.	.	.	Name=1465383
chr11	.	BED_feature	94440042	94440142	.	.	.	Name=1465383
chr17	.	BED_feature	72244734	72246053	.	.	.	Name=1465383
chrX	.	BED_feature	34315778	34315833	.	.	.	Name=1465383
chr13	.	BED_feature	109236952	109236995	.	.	.	Name=15048126
chr7	.	BED_feature	27114668	27114704	.	.	.	Name=8264592
chr7	.	BED_feature	27135538	27135602	.	.	.	Name=8264592
chr7	.	BED_feature	27151890	27151957	.	.	.	Name=8264592
chr7	.	BED_feature	27161207	27161280	.	.	.	Name=8264592
chr12	.	BED_feature	52709804	52709877	.	.	.	Name=8264592
chr17	.	BED_feature	44009204	44009259	.	.	.	Name=8264592
chr17	.	BED_feature	44024649	44024710	.	.	.	Name=8264592
chr17	.	BED_feature	44028862	44028923	.	.	.	Name=8264592
chr17	.	BED_feature	44040297	44040358	.	.	.	Name=8264592
chr2	.	BED_feature	176725731	176725759	.	.	.	Name=8264592
chr22	.	BED_feature	37970975	37971013	.	.	.	Name=9341193
chr2	.	BED_feature	219354986	219355021	.	.	.	Name=11867220
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=2123468
chr4	.	BED_feature	123597329	123597356	.	.	.	Name=2204815
chr16	.	BED_feature	31346876	31346956	.	.	.	Name=7687470
chr16	.	BED_feature	31348752	31348842	.	.	.	Name=7687470
chr15	.	BED_feature	32875078	32875112	.	.	.	Name=2123467
chr16	.	BED_feature	4247193	4248251	.	.	.	Name=2123466
chr16	.	BED_feature	4250105	4250595	.	.	.	Name=2123466
chr16	.	BED_feature	4251850	4252702	.	.	.	Name=2123466
chr16	.	BED_feature	4262660	4262695	.	.	.	Name=2123466
chr6	.	BED_feature	32260152	32260185	.	.	.	Name=10829018
chr11	.	BED_feature	5227716	5227760	.	.	.	Name=1698280
chr11	.	BED_feature	5232640	5232684	.	.	.	Name=1698280
chr14	.	BED_feature	22095168	22095265	.	.	.	Name=7774816
chr6	.	BED_feature	31891188	31891281	.	.	.	Name=3031671
chr6	.	BED_feature	31903381	31903455	.	.	.	Name=3031671
chr12	.	BED_feature	12761488	12761533	.	.	.	Name=10542271
chr12	.	BED_feature	47864842	47865066	.	.	.	Name=3839072
chr12	.	BED_feature	47866620	47868999	.	.	.	Name=3839072
chr12	.	BED_feature	47949738	47949778	.	.	.	Name=3839072
chr7	.	BED_feature	55054353	55054388	.	.	.	Name=2170982
chr6	.	BED_feature	32515500	32515573	.	.	.	Name=10072067
chr9	.	BED_feature	135490837	135491305	.	.	.	Name=7688735
chr16	.	BED_feature	66202234	66203527	.	.	.	Name=8246978
chr16	.	BED_feature	66208147	66208278	.	.	.	Name=8246978
chr16	.	BED_feature	66212099	66212957	.	.	.	Name=8246978
chr16	.	BED_feature	66217958	66218120	.	.	.	Name=8246978
chr16	.	BED_feature	66219771	66220929	.	.	.	Name=8246978
chr16	.	BED_feature	66229229	66230572	.	.	.	Name=8246978
chr6	.	BED_feature	22395673	22395702	.	.	.	Name=8015553
chr6	.	BED_feature	22402676	22402707	.	.	.	Name=8015553
chr6	.	BED_feature	22405214	22405243	.	.	.	Name=8015553
chr6	.	BED_feature	22411662	22413974	.	.	.	Name=8015553
chr1	.	BED_feature	120737548	120737587	.	.	.	Name=9144409
chr1	.	BED_feature	147635798	147635837	.	.	.	Name=9144409
chr1	.	BED_feature	148020754	148020792	.	.	.	Name=9144409
chr12	.	BED_feature	111900548	111900584	.	.	.	Name=9813254
chr6	.	BED_feature	12120600	12120645	.	.	.	Name=2106471
chr6	.	BED_feature	12228135	12232523	.	.	.	Name=2106471
chr6	.	BED_feature	12269717	12270134	.	.	.	Name=2106471
chr6	.	BED_feature	12271632	12273113	.	.	.	Name=2106471
chr5	.	BED_feature	131434407	131434658	.	.	.	Name=7891702
chr11	.	BED_feature	102219597	102219626	.	.	.	Name=7891702
chr20	.	BED_feature	3013400	3013428	.	.	.	Name=12403649
chr4	.	BED_feature	74825045	74825072	.	.	.	Name=12767906
chr11	.	BED_feature	47372997	47373029	.	.	.	Name=15767686
chr16	.	BED_feature	54247463	54248144	.	.	.	Name=9928902
chr12	.	BED_feature	9159966	9160004	.	.	.	Name=7507205
chr1	.	BED_feature	147635802	147635841	.	.	.	Name=7507205
chr5	.	BED_feature	131854190	131854859	.	.	.	Name=7507207
chr4	.	BED_feature	185632678	185632974	.	.	.	Name=7507207
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=11994417
chr15	.	BED_feature	32875133	32875161	.	.	.	Name=3477800
chr17	.	BED_feature	38306146	38306188	.	.	.	Name=10960473
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=8524297
chr11	.	BED_feature	59612764	59612817	.	.	.	Name=12697656
chr16	.	BED_feature	28850732	28850764	.	.	.	Name=12218128
chr4	.	BED_feature	74824868	74824907	.	.	.	Name=15085176
chr15	.	BED_feature	89228611	89228713	.	.	.	Name=8657143
chr12	.	BED_feature	54408962	54409501	.	.	.	Name=1599482
chr14	.	BED_feature	21999475	21999519	.	.	.	Name=1833636
chr1	.	BED_feature	89303575	89303603	.	.	.	Name=1833631
chr1	.	BED_feature	89645733	89645761	.	.	.	Name=1833631
chr12	.	BED_feature	79625995	79626043	.	.	.	Name=1659574
chr12	.	BED_feature	79635309	79635379	.	.	.	Name=1659574
chr11	.	BED_feature	17698326	17698396	.	.	.	Name=1659574
chr1	.	BED_feature	201318970	201322888	.	.	.	Name=1659574
chr18	.	BED_feature	24010986	24011015	.	.	.	Name=15541732
chr4	.	BED_feature	122964729	122964757	.	.	.	Name=7760822
chr8	.	BED_feature	16094715	16094745	.	.	.	Name=7760824
chrX	.	BED_feature	66681556	66683257	.	.	.	Name=2911578
chrX	.	BED_feature	66779830	66779939	.	.	.	Name=2911578
chrX	.	BED_feature	66822575	66822693	.	.	.	Name=2911578
chrX	.	BED_feature	66848028	66848257	.	.	.	Name=2911578
chrX	.	BED_feature	66854044	66854192	.	.	.	Name=2911578
chrX	.	BED_feature	66858400	66860554	.	.	.	Name=2911578
chr11	.	BED_feature	13474103	13474459	.	.	.	Name=1977134
chr6	.	BED_feature	27899740	27899784	.	.	.	Name=3071490
chr6	.	BED_feature	27907382	27907426	.	.	.	Name=3071490
chr11	.	BED_feature	102174147	102174184	.	.	.	Name=8139041
chr2	.	BED_feature	70634955	70635030	.	.	.	Name=10828826
chr4	.	BED_feature	103737714	103737856	.	.	.	Name=1992489
chr4	.	BED_feature	103741087	103741160	.	.	.	Name=1992489
chr4	.	BED_feature	103746687	103747905	.	.	.	Name=1992489
chr1	.	BED_feature	205560907	205561732	.	.	.	Name=7678027
chr3	.	BED_feature	166279012	166279225	.	.	.	Name=9806892
chr6	.	BED_feature	31891182	31891213	.	.	.	Name=1569208
chr6	.	BED_feature	31903378	31903409	.	.	.	Name=1569208
chr3	.	BED_feature	129689435	129690224	.	.	.	Name=8972903
chr3	.	BED_feature	166279009	166279036	.	.	.	Name=9822664
chr10	.	BED_feature	91001600	91001893	.	.	.	Name=9799798
chr14	.	BED_feature	92458568	92459224	.	.	.	Name=7588318
chr5	.	BED_feature	131423977	131424006	.	.	.	Name=1695008
chr9	.	BED_feature	97121061	97121106	.	.	.	Name=9063748
chr11	.	BED_feature	303986	304024	.	.	.	Name=1832217
chr12	.	BED_feature	3499782	3499812	.	.	.	Name=2531661
chr6	.	BED_feature	31891188	31891393	.	.	.	Name=1986252
chr6	.	BED_feature	31903383	31903440	.	.	.	Name=1986252
chr14	.	BED_feature	105399326	105399391	.	.	.	Name=1986254
chr6	.	BED_feature	160309965	160310147	.	.	.	Name=12857727
chr6	.	BED_feature	170705396	170705476	.	.	.	Name=2363050
chr6	.	BED_feature	170707890	170708097	.	.	.	Name=2363050
chr6	.	BED_feature	170712801	170713246	.	.	.	Name=2363050
chr6	.	BED_feature	170715558	170715645	.	.	.	Name=2363050
chr6	.	BED_feature	170717929	170718022	.	.	.	Name=2363050
chr6	.	BED_feature	170720623	170720792	.	.	.	Name=2363050
chr6	.	BED_feature	170722420	170723871	.	.	.	Name=2363050
chr14	.	BED_feature	54950869	54950903	.	.	.	Name=2363050
chr11	.	BED_feature	117692799	117692830	.	.	.	Name=1639073
chr14	.	BED_feature	22095209	22095240	.	.	.	Name=1639073
chr3	.	BED_feature	134944266	134944298	.	.	.	Name=1748690
chr3	.	BED_feature	134947817	134947847	.	.	.	Name=1748690
chr6	.	BED_feature	138230058	138230159	.	.	.	Name=1381359
chr16	.	BED_feature	55199882	55199909	.	.	.	Name=1530876
chr6	.	BED_feature	32515534	32515560	.	.	.	Name=8687468
chr19	.	BED_feature	46188738	46188767	.	.	.	Name=15563456
chr2	.	BED_feature	234334490	234334518	.	.	.	Name=15563456
chr1	.	BED_feature	938621	938651	.	.	.	Name=9268360
chr6	.	BED_feature	36754381	36754494	.	.	.	Name=9268365
chr19	.	BED_feature	38484211	38484346	.	.	.	Name=2112087
chr8	.	BED_feature	48812543	48812632	.	.	.	Name=2112087
chr20	.	BED_feature	48240717	48242593	.	.	.	Name=2112087
chr14	.	BED_feature	22656648	22656739	.	.	.	Name=2112087
chr6	.	BED_feature	31891221	31891289	.	.	.	Name=2474756
chr5	.	BED_feature	172129549	172129577	.	.	.	Name=12890671
chr2	.	BED_feature	234191159	234191187	.	.	.	Name=12847094
chr7	.	BED_feature	142294893	142294922	.	.	.	Name=16574738
chr7	.	BED_feature	127668431	127668469	.	.	.	Name=12215445
chr11	.	BED_feature	67107745	67107808	.	.	.	Name=8702826
chr12	.	BED_feature	19152173	19152260	.	.	.	Name=1748287
chr19	.	BED_feature	19117379	19119601	.	.	.	Name=1748287
chr19	.	BED_feature	19152495	19152545	.	.	.	Name=1748287
chr19	.	BED_feature	19157849	19158743	.	.	.	Name=1748287
chr1	.	BED_feature	177683537	177684321	.	.	.	Name=1748287
chr15	.	BED_feature	97956157	97956201	.	.	.	Name=1748287
chr15	.	BED_feature	97990723	97990841	.	.	.	Name=1748287
chr15	.	BED_feature	98003400	98003474	.	.	.	Name=1748287
chr15	.	BED_feature	98029246	98029277	.	.	.	Name=1748287
chr15	.	BED_feature	98032121	98033187	.	.	.	Name=1748287
chr15	.	BED_feature	98048064	98048103	.	.	.	Name=1748287
chr15	.	BED_feature	98064480	98064564	.	.	.	Name=1748287
chr15	.	BED_feature	98068361	98068487	.	.	.	Name=1748287
chr15	.	BED_feature	98070118	98071466	.	.	.	Name=1748287
chr17	.	BED_feature	37121940	37121975	.	.	.	Name=8294480
chr6	.	BED_feature	137517884	137517936	.	.	.	Name=11390454
chr6	.	BED_feature	27208582	27208614	.	.	.	Name=1535687
chr5	.	BED_feature	131437266	131437302	.	.	.	Name=2342464
chr4	.	BED_feature	123597278	123597307	.	.	.	Name=2342464
chr19	.	BED_feature	46551798	46551827	.	.	.	Name=8016096
chr8	.	BED_feature	110168011	110168039	.	.	.	Name=10208868
chr9	.	BED_feature	127043480	127043510	.	.	.	Name=11779464
chr21	.	BED_feature	42513538	42513600	.	.	.	Name=16024918
chr21	.	BED_feature	42528060	42528089	.	.	.	Name=16024918
chr17	.	BED_feature	35827711	35828062	.	.	.	Name=9126321
chr2	.	BED_feature	232951134	232951342	.	.	.	Name=8314767
chr2	.	BED_feature	232979243	232979753	.	.	.	Name=8314767
chr3	.	BED_feature	10306897	10306926	.	.	.	Name=15142980
chr2	.	BED_feature	21120510	21120712	.	.	.	Name=3165376
chr11	.	BED_feature	5227732	5227785	.	.	.	Name=3181130
chr11	.	BED_feature	5232656	5232709	.	.	.	Name=3181130
chr19	.	BED_feature	11349768	11349839	.	.	.	Name=11756159
chr8	.	BED_feature	57521687	57521720	.	.	.	Name=1372443
chr12	.	BED_feature	119900661	119900690	.	.	.	Name=7984419
chr11	.	BED_feature	116199350	116199608	.	.	.	Name=7984419
chr22_random	.	BED_feature	27426	27684	.	.	.	Name=7984419
chr11	.	BED_feature	14950714	14950744	.	.	.	Name=7476962
chr7	.	BED_feature	93861870	93861906	.	.	.	Name=10201951
chr2	.	BED_feature	127892442	127892602	.	.	.	Name=10333497
chr11	.	BED_feature	116213688	116213765	.	.	.	Name=1904868
chr14	.	BED_feature	93924788	93924824	.	.	.	Name=1904868
chr2	.	BED_feature	21120485	21120527	.	.	.	Name=1904868
chr1	.	BED_feature	159460923	159460951	.	.	.	Name=1904868
chr22_random	.	BED_feature	13281	13358	.	.	.	Name=1904868
chr1	.	BED_feature	59022297	59022365	.	.	.	Name=3142689
chr15	.	BED_feature	94674719	94674917	.	.	.	Name=8706939
chr16	.	BED_feature	103420	103842	.	.	.	Name=1569944
chr11	.	BED_feature	116196774	116196809	.	.	.	Name=15583007
chr11	.	BED_feature	116199350	116199612	.	.	.	Name=15583007
chr11	.	BED_feature	116205090	116205118	.	.	.	Name=15583007
chr22_random	.	BED_feature	21924	21952	.	.	.	Name=15583007
chr22_random	.	BED_feature	27422	27684	.	.	.	Name=15583007
chr22_random	.	BED_feature	30225	30260	.	.	.	Name=15583007
chr19	.	BED_feature	11061025	11061096	.	.	.	Name=11250935
chr11	.	BED_feature	71527655	71528440	.	.	.	Name=8106441
chr11	.	BED_feature	71547900	71547972	.	.	.	Name=8106441
chr11	.	BED_feature	71565459	71566624	.	.	.	Name=8106441
chr11	.	BED_feature	71584047	71584794	.	.	.	Name=8106441
chr11	.	BED_feature	71605409	71605616	.	.	.	Name=8106441
chr11	.	BED_feature	71607254	71607388	.	.	.	Name=8106441
chr11	.	BED_feature	71609562	71610614	.	.	.	Name=8106441
chr11	.	BED_feature	5227731	5227858	.	.	.	Name=2468996
chr11	.	BED_feature	5232655	5232782	.	.	.	Name=2468996
chr15	.	BED_feature	32875150	32875208	.	.	.	Name=2823106
chr21	.	BED_feature	45786705	45787763	.	.	.	Name=15214842
chr21	.	BED_feature	26465019	26465049	.	.	.	Name=9407128
chr12	.	BED_feature	119900661	119900689	.	.	.	Name=8290348
chr11	.	BED_feature	116213740	116213767	.	.	.	Name=8290348
chr22_random	.	BED_feature	13279	13306	.	.	.	Name=8290348
chr6	.	BED_feature	43844939	43844970	.	.	.	Name=15039136
chr20	.	BED_feature	10596532	10596582	.	.	.	Name=11641404
chr7	.	BED_feature	5533905	5534772	.	.	.	Name=11322928
chr5	.	BED_feature	79631253	79631282	.	.	.	Name=11322928
chr3	.	BED_feature	12087834	12087862	.	.	.	Name=11322928
chr2	.	BED_feature	130548918	130548947	.	.	.	Name=11322928
chr2	.	BED_feature	130937490	130937519	.	.	.	Name=11322928
chr2	.	BED_feature	131131260	131131289	.	.	.	Name=11322928
chr2	.	BED_feature	131738066	131738095	.	.	.	Name=11322928
chr1	.	BED_feature	103914790	103914818	.	.	.	Name=11322928
chr22	.	BED_feature	14635980	14636009	.	.	.	Name=11322928
chr15	.	BED_feature	42069177	42069206	.	.	.	Name=11322928
chr14	.	BED_feature	18655265	18655294	.	.	.	Name=11322928
chr14	.	BED_feature	19058342	19058371	.	.	.	Name=11322928
chr17	.	BED_feature	77092312	77092340	.	.	.	Name=11322928
chr4	.	BED_feature	123597349	123597379	.	.	.	Name=9837957
chr1	.	BED_feature	202402194	202402324	.	.	.	Name=15353176
chr6	.	BED_feature	336165	336208	.	.	.	Name=14581002
chr8	.	BED_feature	128816875	128816903	.	.	.	Name=11777933
chr16	.	BED_feature	67328519	67328548	.	.	.	Name=10706097
chr14	.	BED_feature	19992505	19995822	.	.	.	Name=8086453
chr9_random	.	BED_feature	773108	774288	.	.	.	Name=8086450
chr9	.	BED_feature	39644308	39645487	.	.	.	Name=8086450
chr9	.	BED_feature	41018838	41020018	.	.	.	Name=8086450
chr9	.	BED_feature	41789334	41790512	.	.	.	Name=8086450
chr9	.	BED_feature	43340025	43341196	.	.	.	Name=8086450
chr9	.	BED_feature	44498991	44500171	.	.	.	Name=8086450
chr9	.	BED_feature	46838064	46839243	.	.	.	Name=8086450
chr9	.	BED_feature	65798700	65799873	.	.	.	Name=8086450
chr10	.	BED_feature	104279415	104279451	.	.	.	Name=8086450
chr16	.	BED_feature	70596554	70597948	.	.	.	Name=8086450
chr14	.	BED_feature	62140707	62141943	.	.	.	Name=8086450
chr18	.	BED_feature	41917564	41922205	.	.	.	Name=8086450
chr18	.	BED_feature	41923390	41929342	.	.	.	Name=8086450
chr18	.	BED_feature	41930482	41933932	.	.	.	Name=8086450
chr18	.	BED_feature	41935210	41935246	.	.	.	Name=8086450
chr2	.	BED_feature	37237693	37237722	.	.	.	Name=14645369
chr6	.	BED_feature	6265904	6265990	.	.	.	Name=10037697
chr6	.	BED_feature	32929566	32929600	.	.	.	Name=9858567
chr2	.	BED_feature	21120493	21120712	.	.	.	Name=1660892
chr6	.	BED_feature	32742504	32742590	.	.	.	Name=1923758
chr6	.	BED_feature	32839379	32839415	.	.	.	Name=1923758
chr16	.	BED_feature	164053	164084	.	.	.	Name=12854969
chr2	.	BED_feature	97628465	97628508	.	.	.	Name=8806766
chr10	.	BED_feature	71914085	71915951	.	.	.	Name=1309593
chr4	.	BED_feature	91974735	91974917	.	.	.	Name=1309593
chr4	.	BED_feature	189161382	189161743	.	.	.	Name=1309593
chrX	.	BED_feature	21785145	21785514	.	.	.	Name=1309593
chrX	.	BED_feature	55669736	55670397	.	.	.	Name=1309593
chr2	.	BED_feature	139371721	139372908	.	.	.	Name=1309593
chr14	.	BED_feature	99775246	99776011	.	.	.	Name=1309593
chr14	.	BED_feature	99798413	99798553	.	.	.	Name=1309593
chr14	.	BED_feature	99810786	99810849	.	.	.	Name=1309593
chr14	.	BED_feature	99812580	99814652	.	.	.	Name=1309593
chr15	.	BED_feature	32874977	32875527	.	.	.	Name=3785189
chr13	.	BED_feature	79809669	79809698	.	.	.	Name=14644509
chr13	.	BED_feature	79814607	79814638	.	.	.	Name=14644509
chr12	.	BED_feature	51200533	51200570	.	.	.	Name=10825196
chr17	.	BED_feature	16666648	16666682	.	.	.	Name=10825196
chr17	.	BED_feature	16689984	16690041	.	.	.	Name=10825196
chr17	.	BED_feature	18270768	18270815	.	.	.	Name=10825196
chr17	.	BED_feature	18294132	18294166	.	.	.	Name=10825196
chr17	.	BED_feature	20338177	20338211	.	.	.	Name=10825196
chr17	.	BED_feature	20361514	20361571	.	.	.	Name=10825196
chr17	.	BED_feature	25922984	25923034	.	.	.	Name=10825196
chr17	.	BED_feature	36996729	36996763	.	.	.	Name=10825196
chr17	.	BED_feature	37034417	37034478	.	.	.	Name=10825196
chr6	.	BED_feature	87861544	87861856	.	.	.	Name=2481230
chr6	.	BED_feature	31661882	31662346	.	.	.	Name=10944527
chr7	.	BED_feature	55054197	55054236	.	.	.	Name=2556218
chr5	.	BED_feature	149446368	149446397	.	.	.	Name=7969146
chr2	.	BED_feature	216008982	216009553	.	.	.	Name=2170405
chr11	.	BED_feature	2139071	2139247	.	.	.	Name=16461554
chr5	.	BED_feature	1348021	1348063	.	.	.	Name=9973199
chr11	.	BED_feature	5258402	5258444	.	.	.	Name=1631062
chr11	.	BED_feature	5227737	5227790	.	.	.	Name=11544252
chr11	.	BED_feature	5232661	5232714	.	.	.	Name=11544252
chr11	.	BED_feature	5247816	5247860	.	.	.	Name=11544252
chr11	.	BED_feature	63831222	63831266	.	.	.	Name=9058380
chr7	.	BED_feature	99219889	99219918	.	.	.	Name=9770465
chr2	.	BED_feature	161932568	161932611	.	.	.	Name=7769002
chr2	.	BED_feature	161935936	161936003	.	.	.	Name=7769002
chr6	.	BED_feature	32076548	32076639	.	.	.	Name=10608879
chr6	.	BED_feature	32109286	32109377	.	.	.	Name=10608879
chr13	.	BED_feature	40431031	40431107	.	.	.	Name=8493578
chr1	.	BED_feature	170894475	170894506	.	.	.	Name=9395475
chr1	.	BED_feature	157951017	157951098	.	.	.	Name=2154372
chr1	.	BED_feature	1581884	1581918	.	.	.	Name=15087126
chr1	.	BED_feature	1647170	1647204	.	.	.	Name=15087126
chr12	.	BED_feature	66838835	66839000	.	.	.	Name=8670419
chr12	.	BED_feature	66840017	66840059	.	.	.	Name=8670419
chr3	.	BED_feature	87391881	87391910	.	.	.	Name=9626142
chr1	.	BED_feature	28375801	28375832	.	.	.	Name=9058812
chr15	.	BED_feature	49420185	49420218	.	.	.	Name=7626451
chr1	.	BED_feature	151240673	151240820	.	.	.	Name=9889002
chr9	.	BED_feature	116920286	116920338	.	.	.	Name=15001984
chr12	.	BED_feature	32723334	32723427	.	.	.	Name=14741701
chr10	.	BED_feature	91051673	91051706	.	.	.	Name=2236065
chr15	.	BED_feature	72447072	72447105	.	.	.	Name=7798178
chr6	.	BED_feature	39629678	39630762	.	.	.	Name=7958925
chr16	.	BED_feature	65783671	65784573	.	.	.	Name=7958925
chr16	.	BED_feature	65785802	65787410	.	.	.	Name=7958925
chr16	.	BED_feature	65789002	65789748	.	.	.	Name=7958925
chr1	.	BED_feature	117098409	117098438	.	.	.	Name=7929376
chr4	.	BED_feature	152240171	152240251	.	.	.	Name=12463423
chr17	.	BED_feature	39822368	39822995	.	.	.	Name=7518432
chr14	.	BED_feature	93924792	93924822	.	.	.	Name=8621550
chr4	.	BED_feature	185587189	185587218	.	.	.	Name=1579446
chr5	.	BED_feature	131424078	131424114	.	.	.	Name=8704203
chr14	.	BED_feature	105142430	105142467	.	.	.	Name=9190940
chr14	.	BED_feature	105261216	105261253	.	.	.	Name=9190940
chr21	.	BED_feature	29636785	29636815	.	.	.	Name=11069897
chr14	.	BED_feature	74815007	74815034	.	.	.	Name=12242287
chr16	.	BED_feature	55199698	55199932	.	.	.	Name=3821726
chr11	.	BED_feature	101896527	101896687	.	.	.	Name=8294454
chr11	.	BED_feature	67107756	67107796	.	.	.	Name=8206948
chr10	.	BED_feature	91051671	91051711	.	.	.	Name=2342456
chr9	.	BED_feature	21067980	21068020	.	.	.	Name=2495183
chr19	.	BED_feature	54226282	54226326	.	.	.	Name=9182571
chr19	.	BED_feature	54232631	54232675	.	.	.	Name=9182571
chr19	.	BED_feature	54238602	54238713	.	.	.	Name=9182571
chr19	.	BED_feature	54244373	54244417	.	.	.	Name=9182571
chr19	.	BED_feature	54251014	54251054	.	.	.	Name=9182571
chr17	.	BED_feature	7063969	7063998	.	.	.	Name=10607478
chr16	.	BED_feature	55199809	55199838	.	.	.	Name=1852613
chr1	.	BED_feature	100957807	100957835	.	.	.	Name=7499419
chr5	.	BED_feature	147996922	147996991	.	.	.	Name=15575821
chr22_random	.	BED_feature	21652	21681	.	.	.	Name=9322942
chr5	.	BED_feature	149772578	149772830	.	.	.	Name=8164652
chr3	.	BED_feature	25444697	25444725	.	.	.	Name=7931079
chr7	.	BED_feature	30970034	30970097	.	.	.	Name=10207037
chr2	.	BED_feature	88926787	88926816	.	.	.	Name=1406692
chr5	.	BED_feature	158690174	158690202	.	.	.	Name=9497375
chrY	.	BED_feature	1693988	1694161	.	.	.	Name=7989373
chrX	.	BED_feature	1693988	1694161	.	.	.	Name=7989373
chr19	.	BED_feature	11061107	11061136	.	.	.	Name=10671569
chr6	.	BED_feature	22405251	22405369	.	.	.	Name=12223489
chr7	.	BED_feature	93861870	93861906	.	.	.	Name=8621730
chr16	.	BED_feature	31178719	31178865	.	.	.	Name=8955212
chr11	.	BED_feature	5662868	5663929	.	.	.	Name=16289103
chrX	.	BED_feature	37524143	37524171	.	.	.	Name=1885602
chr7	.	BED_feature	5535923	5535983	.	.	.	Name=3422098
chr20	.	BED_feature	1922572	1922602	.	.	.	Name=9819380
chr1	.	BED_feature	938622	938650	.	.	.	Name=2606351
chr7	.	BED_feature	526009	526156	.	.	.	Name=8349616
chr12	.	BED_feature	47637374	47638624	.	.	.	Name=8473323
chr9	.	BED_feature	136468133	136468176	.	.	.	Name=8264664
chr16	.	BED_feature	66022179	66022739	.	.	.	Name=11850421
chrX	.	BED_feature	37524202	37524230	.	.	.	Name=12732216
chr13	.	BED_feature	93930268	93930296	.	.	.	Name=9447965
chr11	.	BED_feature	116205089	116205118	.	.	.	Name=9592157
chr22_random	.	BED_feature	21924	21953	.	.	.	Name=9592157
chr12	.	BED_feature	79625629	79626072	.	.	.	Name=1374396
chr12	.	BED_feature	79635308	79635380	.	.	.	Name=1374396
chr11	.	BED_feature	17698326	17698389	.	.	.	Name=1374396
chr1	.	BED_feature	201321306	201321383	.	.	.	Name=1374396
chr16	.	BED_feature	55199877	55199917	.	.	.	Name=9155027
chr8	.	BED_feature	59575398	59575425	.	.	.	Name=10777541
chr5	.	BED_feature	131424080	131424114	.	.	.	Name=9036972
chr1	.	BED_feature	154477844	154478070	.	.	.	Name=8388544
chr11	.	BED_feature	46934509	46934538	.	.	.	Name=16227573
chr2	.	BED_feature	183836534	183837362	.	.	.	Name=16227573
chr1	.	BED_feature	26626421	26627246	.	.	.	Name=16227573
chr14	.	BED_feature	74814934	74814987	.	.	.	Name=14737107
chr2	.	BED_feature	216008771	216009355	.	.	.	Name=3031656
chr2	.	BED_feature	174538114	174538172	.	.	.	Name=16024108
chr3	.	BED_feature	134947101	134947167	.	.	.	Name=12459033
chr2	.	BED_feature	113258582	113258611	.	.	.	Name=15863387
chr22	.	BED_feature	37970938	37971189	.	.	.	Name=7961814
chr13	.	BED_feature	47775840	47775880	.	.	.	Name=8620463
chr14	.	BED_feature	95791803	95791830	.	.	.	Name=9553142
chr16	.	BED_feature	10880178	10880281	.	.	.	Name=10202014
chr3	.	BED_feature	24511147	24511495	.	.	.	Name=1339272
chr19	.	BED_feature	11061067	11061095	.	.	.	Name=10579331
chr17	.	BED_feature	24099530	24099558	.	.	.	Name=12788948
chr17	.	BED_feature	4491642	4492686	.	.	.	Name=10657944
chr19	.	BED_feature	4767631	4767659	.	.	.	Name=14960149
chr19	.	BED_feature	4783038	4783067	.	.	.	Name=14960149
chr5	.	BED_feature	32747447	32747507	.	.	.	Name=9492076
chr7	.	BED_feature	5534641	5534680	.	.	.	Name=8474178
chr5	.	BED_feature	77117022	77117061	.	.	.	Name=8474178
chr5	.	BED_feature	79631782	79631821	.	.	.	Name=8474178
chr5	.	BED_feature	131023110	131023150	.	.	.	Name=8474178
chr3	.	BED_feature	12087296	12087335	.	.	.	Name=8474178
chr2	.	BED_feature	130937394	130937427	.	.	.	Name=8474178
chr2	.	BED_feature	131131352	131131385	.	.	.	Name=8474178
chr2	.	BED_feature	131738158	131738191	.	.	.	Name=8474178
chr2	.	BED_feature	132100741	132100774	.	.	.	Name=8474178
chr1	.	BED_feature	222118579	222118618	.	.	.	Name=8474178
chr1	.	BED_feature	236157319	236157357	.	.	.	Name=8474178
chr9	.	BED_feature	6825010	6825049	.	.	.	Name=8474178
chr9	.	BED_feature	102533895	102533933	.	.	.	Name=8474178
chr17	.	BED_feature	77093012	77093051	.	.	.	Name=8474178
chr16	.	BED_feature	48650095	48650134	.	.	.	Name=8474178
chr15	.	BED_feature	32453566	32453605	.	.	.	Name=8474178
chr14	.	BED_feature	18655357	18655390	.	.	.	Name=8474178
chr14	.	BED_feature	19058246	19058279	.	.	.	Name=8474178
chr22	.	BED_feature	14635884	14635917	.	.	.	Name=8474178
chr22	.	BED_feature	39800636	39800675	.	.	.	Name=8474178
chr18	.	BED_feature	58260786	58260822	.	.	.	Name=8474178
chr7	.	BED_feature	25129923	25129978	.	.	.	Name=7926749
chr7	.	BED_feature	120825889	120825961	.	.	.	Name=7926749
chr7	.	BED_feature	128544906	128544975	.	.	.	Name=7926749
chr6	.	BED_feature	34295354	34295435	.	.	.	Name=7926749
chr6	.	BED_feature	96058921	96059004	.	.	.	Name=7926749
chr3	.	BED_feature	10017417	10017489	.	.	.	Name=7926749
chr3	.	BED_feature	10074732	10074826	.	.	.	Name=7926749
chr3	.	BED_feature	11895378	11895465	.	.	.	Name=7926749
chr2	.	BED_feature	100353200	100353281	.	.	.	Name=7926749
chr1	.	BED_feature	149143141	149143224	.	.	.	Name=7926749
chr1	.	BED_feature	155364922	155365003	.	.	.	Name=7926749
chr1	.	BED_feature	200605366	200605448	.	.	.	Name=7926749
chrY	.	BED_feature	15562899	15562993	.	.	.	Name=7926749
chrY	.	BED_feature	26956594	26956687	.	.	.	Name=7926749
chr9	.	BED_feature	95840278	95840372	.	.	.	Name=7926749
chrX	.	BED_feature	68621998	68622075	.	.	.	Name=7926749
chrX	.	BED_feature	144065979	144066017	.	.	.	Name=7926749
chrX	.	BED_feature	152760053	152760117	.	.	.	Name=7926749
chr13	.	BED_feature	23873008	23873066	.	.	.	Name=7926749
chr13	.	BED_feature	40335815	40335898	.	.	.	Name=7926749
chr13	.	BED_feature	98080025	98080108	.	.	.	Name=7926749
chr11	.	BED_feature	31258881	31258964	.	.	.	Name=7926749
chr11	.	BED_feature	57529576	57529654	.	.	.	Name=7926749
chr11	.	BED_feature	73871070	73871138	.	.	.	Name=7926749
chr11	.	BED_feature	82717816	82717863	.	.	.	Name=7926749
chr11	.	BED_feature	108198370	108198442	.	.	.	Name=7926749
chr17	.	BED_feature	72707003	72707073	.	.	.	Name=7926749
chr16	.	BED_feature	25373239	25373333	.	.	.	Name=7926749
chr15	.	BED_feature	39188498	39188575	.	.	.	Name=7926749
chr15	.	BED_feature	58576781	58577112	.	.	.	Name=7926749
chr15	.	BED_feature	58579383	58580562	.	.	.	Name=7926749
chr15	.	BED_feature	58582249	58583160	.	.	.	Name=7926749
chr15	.	BED_feature	58584999	58585071	.	.	.	Name=7926749
chr15	.	BED_feature	58590742	58591041	.	.	.	Name=7926749
chr15	.	BED_feature	58594186	58594250	.	.	.	Name=7926749
chr15	.	BED_feature	58636354	58636420	.	.	.	Name=7926749
chr15	.	BED_feature	58637714	58637804	.	.	.	Name=7926749
chr15	.	BED_feature	58706736	58706954	.	.	.	Name=7926749
chr15	.	BED_feature	59308662	59308794	.	.	.	Name=7926749
chr14	.	BED_feature	76169952	76170035	.	.	.	Name=7926749
chr8	.	BED_feature	33946699	33946793	.	.	.	Name=7926749
chr8	.	BED_feature	51837694	51837766	.	.	.	Name=7926749
chr8	.	BED_feature	120699678	120699737	.	.	.	Name=7926749
chr6	.	BED_feature	26140296	26140436	.	.	.	Name=2928309
chr1	.	BED_feature	148070694	148070855	.	.	.	Name=2928309
chr1	.	BED_feature	148099339	148099500	.	.	.	Name=2928309
chr7	.	BED_feature	87068235	87069157	.	.	.	Name=7961962
chr1	.	BED_feature	200246119	200246146	.	.	.	Name=11313868
chr18	.	BED_feature	59294966	59295073	.	.	.	Name=10692390
chr4	.	BED_feature	100493210	100493240	.	.	.	Name=1320193
chr2	.	BED_feature	85749241	85749301	.	.	.	Name=10617585
chr14	.	BED_feature	34943732	34944082	.	.	.	Name=8262046
chr7	.	BED_feature	81237248	81237276	.	.	.	Name=11112425
chr7	.	BED_feature	81238278	81238327	.	.	.	Name=11112425
chr1	.	BED_feature	120737496	120737587	.	.	.	Name=8455606
chr1	.	BED_feature	147635798	147635889	.	.	.	Name=8455606
chr1	.	BED_feature	148020754	148020845	.	.	.	Name=8455606
chr1	.	BED_feature	148070695	148070809	.	.	.	Name=2768251
chr1	.	BED_feature	148099385	148099499	.	.	.	Name=2768251
chr5	.	BED_feature	131434535	131434563	.	.	.	Name=8809409
chr5	.	BED_feature	131437306	131437364	.	.	.	Name=8809409
chr4	.	BED_feature	74516857	74516887	.	.	.	Name=2708361
chr3	.	BED_feature	134944275	134944309	.	.	.	Name=2708361
chr3	.	BED_feature	134947800	134947874	.	.	.	Name=2708361
chr7	.	BED_feature	526481	526592	.	.	.	Name=8486717
chr7_random	.	BED_feature	465930	466022	.	.	.	Name=8486717
chr16	.	BED_feature	54068948	54068984	.	.	.	Name=8610173
chr16	.	BED_feature	55199808	55199838	.	.	.	Name=8610173
chr21	.	BED_feature	39099689	39099758	.	.	.	Name=1888697
chr11	.	BED_feature	2139240	2139277	.	.	.	Name=10601637
chr6	.	BED_feature	26216377	26216406	.	.	.	Name=11098153
chr9	.	BED_feature	124711246	124711796	.	.	.	Name=7958847
chr9	.	BED_feature	124712941	124714041	.	.	.	Name=7958847
chr7	.	BED_feature	27135537	27136313	.	.	.	Name=1970866
chr12	.	BED_feature	52734903	52734991	.	.	.	Name=1970866
chr2	.	BED_feature	176725584	176725760	.	.	.	Name=1970866
chr9	.	BED_feature	21067998	21068034	.	.	.	Name=9446577
chr6	.	BED_feature	31658167	31658338	.	.	.	Name=8786306
chr9	.	BED_feature	21067967	21068080	.	.	.	Name=2910848
chr6	.	BED_feature	87861654	87861691	.	.	.	Name=2159633
chr3	.	BED_feature	49701035	49701169	.	.	.	Name=8702759
chr1	.	BED_feature	16844626	16844760	.	.	.	Name=8702759
chr13	.	BED_feature	19033371	19033411	.	.	.	Name=9865725
chr13	.	BED_feature	20732461	20732501	.	.	.	Name=9865725
chr11	.	BED_feature	63831214	63831254	.	.	.	Name=9865725
chr15	.	BED_feature	49322620	49322769	.	.	.	Name=9865725
chr19	.	BED_feature	50100726	50100755	.	.	.	Name=2188976
chr6	.	BED_feature	153113528	153113559	.	.	.	Name=2842787
chr2	.	BED_feature	10505706	10505928	.	.	.	Name=2318872
chr7	.	BED_feature	525927	526035	.	.	.	Name=1417865
chr9	.	BED_feature	21067996	21068053	.	.	.	Name=7523851
chr1	.	BED_feature	167969927	167970000	.	.	.	Name=7523851
chr18	.	BED_feature	59138135	59138163	.	.	.	Name=16186795
chr16	.	BED_feature	29983393	29983480	.	.	.	Name=7473711
chr11	.	BED_feature	119683435	119683465	.	.	.	Name=12624109
chr6	.	BED_feature	32515375	32515574	.	.	.	Name=2851727
chr7	.	BED_feature	100556303	100557246	.	.	.	Name=2840665
chr7	.	BED_feature	100558392	100558421	.	.	.	Name=2840665
chr12	.	BED_feature	51001398	51001563	.	.	.	Name=9811563
chr21	.	BED_feature	42660052	42660105	.	.	.	Name=12021387
chr12	.	BED_feature	52063340	52063372	.	.	.	Name=14593115
chr15	.	BED_feature	49420188	49420228	.	.	.	Name=9817601
chr6	.	BED_feature	27208584	27208609	.	.	.	Name=11566492
chr2	.	BED_feature	175330621	175330648	.	.	.	Name=8441631
chr5	.	BED_feature	137695273	137695489	.	.	.	Name=7828585
chr4	.	BED_feature	122964348	122964726	.	.	.	Name=7556094
chr1	.	BED_feature	1580339	1580368	.	.	.	Name=15656972
chr6	.	BED_feature	35562269	35562336	.	.	.	Name=1851669
chr11	.	BED_feature	12652639	12653679	.	.	.	Name=1851669
chr11	.	BED_feature	12742301	12742560	.	.	.	Name=1851669
chr11	.	BED_feature	12840372	12840433	.	.	.	Name=1851669
chr11	.	BED_feature	12842960	12843020	.	.	.	Name=1851669
chr11	.	BED_feature	12857829	12857965	.	.	.	Name=1851669
chr11	.	BED_feature	12859127	12860081	.	.	.	Name=1851669
chr11	.	BED_feature	12861121	12861248	.	.	.	Name=1851669
chr11	.	BED_feature	12880062	12880237	.	.	.	Name=1851669
chr11	.	BED_feature	12903034	12903175	.	.	.	Name=1851669
chr11	.	BED_feature	12908295	12908451	.	.	.	Name=1851669
chr11	.	BED_feature	12915231	12917454	.	.	.	Name=1851669
chr11	.	BED_feature	125553435	125554765	.	.	.	Name=1851669
chr3	.	BED_feature	46186796	46186935	.	.	.	Name=1851669
chr19	.	BED_feature	54554960	54555027	.	.	.	Name=1851669
chr7	.	BED_feature	526002	526156	.	.	.	Name=1460057
chr16	.	BED_feature	84494120	84494201	.	.	.	Name=1460054
chr16	.	BED_feature	84509529	84509897	.	.	.	Name=1460054
chr3	.	BED_feature	134947846	134947926	.	.	.	Name=2839477
chr1	.	BED_feature	938620	938651	.	.	.	Name=9234684
chr12	.	BED_feature	14740884	14740927	.	.	.	Name=10889158
chr3	.	BED_feature	166279012	166279044	.	.	.	Name=10889158
chr4	.	BED_feature	187424397	187424441	.	.	.	Name=11891231
chr2	.	BED_feature	60961766	60962017	.	.	.	Name=8666258
chr9	.	BED_feature	106642488	106642515	.	.	.	Name=10858438
chr3	.	BED_feature	25444697	25444725	.	.	.	Name=1335571
chr17	.	BED_feature	4794240	4795878	.	.	.	Name=1840492
chr11	.	BED_feature	63824694	63825022	.	.	.	Name=14978033
chr11	.	BED_feature	63828768	63829062	.	.	.	Name=14978033
chr11	.	BED_feature	5227700	5228090	.	.	.	Name=1406669
chr11	.	BED_feature	5232624	5233475	.	.	.	Name=1406669
chr11	.	BED_feature	5235228	5235270	.	.	.	Name=1406669
chr11	.	BED_feature	5245403	5245626	.	.	.	Name=1406669
chr11	.	BED_feature	5248000	5248054	.	.	.	Name=1406669
chr19	.	BED_feature	18252366	18252412	.	.	.	Name=1527086
chr20	.	BED_feature	35157763	35157853	.	.	.	Name=7791762
chr17	.	BED_feature	29507626	29507986	.	.	.	Name=12957380
chr2	.	BED_feature	8739641	8739671	.	.	.	Name=7758976
chr14	.	BED_feature	22095217	22095259	.	.	.	Name=2237431
chr19	.	BED_feature	12763116	12763277	.	.	.	Name=1708123
chr6	.	BED_feature	19945685	19945712	.	.	.	Name=9516472
chr19	.	BED_feature	803188	803276	.	.	.	Name=8035830
chrX	.	BED_feature	16575046	16575095	.	.	.	Name=15217781
chrX	.	BED_feature	16578083	16578129	.	.	.	Name=15217781
chr1	.	BED_feature	159466178	159467889	.	.	.	Name=8114692
chr1	.	BED_feature	159469221	159469752	.	.	.	Name=8114692
chr1	.	BED_feature	159472261	159473015	.	.	.	Name=8114692
chr1	.	BED_feature	159474454	159474579	.	.	.	Name=8114692
chrX	.	BED_feature	72958725	72958835	.	.	.	Name=8114692
chr2	.	BED_feature	228272380	228272410	.	.	.	Name=15217784
chr2	.	BED_feature	228275242	228275271	.	.	.	Name=15217784
chr2	.	BED_feature	228290980	228291062	.	.	.	Name=15217784
chr12	.	BED_feature	110689069	110689098	.	.	.	Name=8964492
chr19	.	BED_feature	11060988	11061023	.	.	.	Name=10787437
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=1722332
chr8	.	BED_feature	128817181	128817228	.	.	.	Name=2324096
chr12	.	BED_feature	67488826	67488868	.	.	.	Name=15550242
chr5	.	BED_feature	176769146	176769177	.	.	.	Name=9794469
chr14	.	BED_feature	93924790	93924821	.	.	.	Name=9794469
chr8	.	BED_feature	11603761	11603808	.	.	.	Name=9486185
chr11	.	BED_feature	118463735	118463763	.	.	.	Name=1875946
chr16	.	BED_feature	103522	103848	.	.	.	Name=1875946
chr4	.	BED_feature	149583223	149583259	.	.	.	Name=8961265
chr4	.	BED_feature	149585299	149585633	.	.	.	Name=8961265
chr5	.	BED_feature	131437323	131437356	.	.	.	Name=2233734
chr11	.	BED_feature	56914780	56914817	.	.	.	Name=9558404
chr11	.	BED_feature	102174166	102174196	.	.	.	Name=9850057
chr11	.	BED_feature	102175685	102175713	.	.	.	Name=9850057
chr7	.	BED_feature	87067978	87068281	.	.	.	Name=9187262
chr6	.	BED_feature	32515557	32515587	.	.	.	Name=9187262
chr11	.	BED_feature	69165015	69165043	.	.	.	Name=10318916
chr6	.	BED_feature	43566883	43566936	.	.	.	Name=1846623
chr5	.	BED_feature	8673995	8674036	.	.	.	Name=1846623
chr4	.	BED_feature	5457317	5457345	.	.	.	Name=1846623
chr4	.	BED_feature	65155401	65155486	.	.	.	Name=1846623
chr2	.	BED_feature	82900465	82900506	.	.	.	Name=1846623
chr2	.	BED_feature	117226297	117226351	.	.	.	Name=1846623
chr2	.	BED_feature	143566475	143566505	.	.	.	Name=1846623
chr1	.	BED_feature	77209593	77209678	.	.	.	Name=1846623
chr9	.	BED_feature	34989141	34989208	.	.	.	Name=1846623
chr8	.	BED_feature	68655748	68655789	.	.	.	Name=1846623
chr13	.	BED_feature	95146566	95146598	.	.	.	Name=1846623
chr11	.	BED_feature	63711383	63711424	.	.	.	Name=1846623
chr17	.	BED_feature	19441580	19441621	.	.	.	Name=1846623
chr17	.	BED_feature	21944696	21944853	.	.	.	Name=1846623
chrM	.	BED_feature	16413	16571	.	.	.	Name=1846623
chrX	.	BED_feature	125692536	125692596	.	.	.	Name=1846623
chr6	.	BED_feature	31891214	31891248	.	.	.	Name=11306579
chr1	.	BED_feature	228904778	228904839	.	.	.	Name=7961807
chr3	.	BED_feature	25444667	25444701	.	.	.	Name=10629053
chr5	.	BED_feature	176446488	176446622	.	.	.	Name=11981041
chr19	.	BED_feature	9490689	9490716	.	.	.	Name=11022000
chr18	.	BED_feature	58261022	58261049	.	.	.	Name=11022000
chr17	.	BED_feature	31231519	31231548	.	.	.	Name=11022000
chr2	.	BED_feature	130548583	130548610	.	.	.	Name=11022000
chr2	.	BED_feature	130937155	130937182	.	.	.	Name=11022000
chr2	.	BED_feature	131131597	131131624	.	.	.	Name=11022000
chr2	.	BED_feature	131738403	131738430	.	.	.	Name=11022000
chr9	.	BED_feature	6825255	6825282	.	.	.	Name=11022000
chr6	.	BED_feature	32515534	32515560	.	.	.	Name=10675042
chrX	.	BED_feature	146800818	146801184	.	.	.	Name=9199556
chr10	.	BED_feature	69125926	69126061	.	.	.	Name=15302915
chrX	.	BED_feature	30581120	30581150	.	.	.	Name=14654354
chr17	.	BED_feature	73694759	73694962	.	.	.	Name=2914910
chr7	.	BED_feature	5533905	5534773	.	.	.	Name=11509602
chr5	.	BED_feature	79631253	79631282	.	.	.	Name=11509602
chr5	.	BED_feature	158690000	158690346	.	.	.	Name=11509602
chr3	.	BED_feature	12087834	12087862	.	.	.	Name=11509602
chr2	.	BED_feature	130548918	130548948	.	.	.	Name=11509602
chr2	.	BED_feature	130937490	130937520	.	.	.	Name=11509602
chr2	.	BED_feature	131131259	131131289	.	.	.	Name=11509602
chr2	.	BED_feature	131738065	131738095	.	.	.	Name=11509602
chr1	.	BED_feature	103914790	103914818	.	.	.	Name=11509602
chr22	.	BED_feature	14635980	14636010	.	.	.	Name=11509602
chr15	.	BED_feature	42069177	42069206	.	.	.	Name=11509602
chr14	.	BED_feature	18655264	18655294	.	.	.	Name=11509602
chr14	.	BED_feature	19058342	19058372	.	.	.	Name=11509602
chr17	.	BED_feature	77092312	77092340	.	.	.	Name=11509602
chr2	.	BED_feature	182251814	182251845	.	.	.	Name=9714454
chr2	.	BED_feature	182253401	182253508	.	.	.	Name=9714454
chr2	.	BED_feature	182254800	182254844	.	.	.	Name=9714454
chr10	.	BED_feature	6144530	6144558	.	.	.	Name=8475098
chr1	.	BED_feature	167969765	167969794	.	.	.	Name=7525580
chrX	.	BED_feature	153904169	153904229	.	.	.	Name=8628260
chr20	.	BED_feature	29655769	29655813	.	.	.	Name=11700304
chr8	.	BED_feature	42314354	42315833	.	.	.	Name=3182828
chr14	.	BED_feature	21999514	21999544	.	.	.	Name=11781241
chr4	.	BED_feature	155703462	155703528	.	.	.	Name=8423785
chr12	.	BED_feature	21417531	21417563	.	.	.	Name=15243700
chr15	.	BED_feature	72805893	72805921	.	.	.	Name=9415707
chr11	.	BED_feature	102176067	102176109	.	.	.	Name=9115242
chr11	.	BED_feature	116168397	116168615	.	.	.	Name=12709436
chr22	.	BED_feature	38626945	38626986	.	.	.	Name=12554803
chr16	.	BED_feature	55217064	55217144	.	.	.	Name=6095291
chr16	.	BED_feature	55223952	55224021	.	.	.	Name=6095291
chr16	.	BED_feature	55249264	55249346	.	.	.	Name=6095291
chr16	.	BED_feature	55259529	55259603	.	.	.	Name=6095291
chr16	.	BED_feature	55261096	55261155	.	.	.	Name=6095291
chr6	.	BED_feature	74286520	74288051	.	.	.	Name=7961976
chr7	.	BED_feature	55054353	55054388	.	.	.	Name=12894229
chr1	.	BED_feature	75962524	75962557	.	.	.	Name=1328196
chr6	.	BED_feature	31433072	31433109	.	.	.	Name=7907595
chr1	.	BED_feature	120737549	120737587	.	.	.	Name=7907595
chr1	.	BED_feature	147635798	147635836	.	.	.	Name=7907595
chr1	.	BED_feature	148020754	148020792	.	.	.	Name=7907595
chr16	.	BED_feature	54068948	54068984	.	.	.	Name=9343394
chr7	.	BED_feature	44805909	44805937	.	.	.	Name=12377782
chr2	.	BED_feature	101257188	101257216	.	.	.	Name=12377782
chr5	.	BED_feature	68498806	68498835	.	.	.	Name=1582409
chr10	.	BED_feature	62209933	62209968	.	.	.	Name=1582409
chr10	.	BED_feature	62214467	62214599	.	.	.	Name=1582409
chr4	.	BED_feature	100431465	100431497	.	.	.	Name=1996113
chr4	.	BED_feature	100461880	100461911	.	.	.	Name=1996113
chr4	.	BED_feature	100493191	100493270	.	.	.	Name=1996113
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=8335913
chr3	.	BED_feature	42281231	42281419	.	.	.	Name=2118525
chr16	.	BED_feature	103675	103708	.	.	.	Name=8455611
chr11	.	BED_feature	47238666	47240146	.	.	.	Name=7744246
chr11	.	BED_feature	47246037	47246944	.	.	.	Name=7744246
chr22	.	BED_feature	34343286	34343320	.	.	.	Name=3796609
chr6	.	BED_feature	32515519	32515580	.	.	.	Name=3133120
chr11	.	BED_feature	116213692	116213767	.	.	.	Name=14563824
chr22_random	.	BED_feature	13279	13315	.	.	.	Name=14563824
chr6	.	BED_feature	31891220	31891251	.	.	.	Name=1674922
chr7	.	BED_feature	100556511	100556547	.	.	.	Name=9765209
chr16	.	BED_feature	31311938	31312078	.	.	.	Name=10722744
chr7	.	BED_feature	5533905	5534772	.	.	.	Name=14761964
chr5	.	BED_feature	77116938	77116964	.	.	.	Name=14761964
chr5	.	BED_feature	79631253	79631282	.	.	.	Name=14761964
chr3	.	BED_feature	12087834	12087862	.	.	.	Name=14761964
chr2	.	BED_feature	130548918	130548947	.	.	.	Name=14761964
chr2	.	BED_feature	130937490	130937519	.	.	.	Name=14761964
chr2	.	BED_feature	131131260	131131289	.	.	.	Name=14761964
chr2	.	BED_feature	131738066	131738095	.	.	.	Name=14761964
chr1	.	BED_feature	103914790	103914818	.	.	.	Name=14761964
chr1	.	BED_feature	227633869	227633895	.	.	.	Name=14761964
chr22	.	BED_feature	14635980	14636009	.	.	.	Name=14761964
chr15	.	BED_feature	42069177	42069206	.	.	.	Name=14761964
chr14	.	BED_feature	18655265	18655294	.	.	.	Name=14761964
chr14	.	BED_feature	19058342	19058371	.	.	.	Name=14761964
chr17	.	BED_feature	77092312	77092340	.	.	.	Name=14761964
chr1	.	BED_feature	163028395	163028465	.	.	.	Name=1967982
chr1	.	BED_feature	163056000	163056043	.	.	.	Name=1967982
chrX	.	BED_feature	33133102	33133241	.	.	.	Name=9092671
chr2	.	BED_feature	40593127	40593192	.	.	.	Name=10212268
chr12	.	BED_feature	49852961	49853556	.	.	.	Name=8157699
chr11	.	BED_feature	303950	304011	.	.	.	Name=2492664
chrX	.	BED_feature	33139545	33139614	.	.	.	Name=2403634
chr16	.	BED_feature	142731	142764	.	.	.	Name=2403638
chr16	.	BED_feature	152943	152976	.	.	.	Name=2403638
chr6	.	BED_feature	12398459	12398494	.	.	.	Name=9588211
chr20	.	BED_feature	31728191	31728226	.	.	.	Name=10336493
chr16	.	BED_feature	31273842	31274009	.	.	.	Name=8621914
chr11	.	BED_feature	116205240	116205369	.	.	.	Name=8675624
chr22_random	.	BED_feature	21672	21801	.	.	.	Name=8675624
chr17	.	BED_feature	35727891	35728028	.	.	.	Name=7585542
chr10	.	BED_feature	95351087	95351181	.	.	.	Name=8810324
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=1639393
chr1	.	BED_feature	89303431	89303699	.	.	.	Name=1898761
chr1	.	BED_feature	89645645	89645905	.	.	.	Name=1898761
chr17	.	BED_feature	68677655	68677683	.	.	.	Name=11208729
chr2	.	BED_feature	204279614	204279643	.	.	.	Name=11342633
chr16_random	.	BED_feature	105103	105168	.	.	.	Name=1502157
chr16	.	BED_feature	29726479	29727567	.	.	.	Name=1502157
chr16	.	BED_feature	29729110	29729985	.	.	.	Name=1502157
chr11	.	BED_feature	69299288	69299589	.	.	.	Name=7929190
chr17	.	BED_feature	29603542	29603572	.	.	.	Name=15223809
chr13	.	BED_feature	19665940	19666133	.	.	.	Name=16314317
chr4	.	BED_feature	100493209	100493237	.	.	.	Name=11051106
chr2	.	BED_feature	113313588	113313618	.	.	.	Name=8413264
chr10	.	BED_feature	71006858	71006921	.	.	.	Name=11334435
chr6	.	BED_feature	116556248	116556279	.	.	.	Name=12435601
chr3	.	BED_feature	4996985	4997026	.	.	.	Name=12624110
chr10	.	BED_feature	135190226	135190285	.	.	.	Name=15345327
chr16	.	BED_feature	55199883	55199916	.	.	.	Name=2033057
chr2	.	BED_feature	21120498	21120527	.	.	.	Name=2033057
chr4	.	BED_feature	123597158	123597188	.	.	.	Name=1652063
chr2	.	BED_feature	208169882	208169935	.	.	.	Name=7745688
chr5	.	BED_feature	131423938	131424152	.	.	.	Name=2263617
chr16	.	BED_feature	55199882	55199917	.	.	.	Name=2263617
chr18	.	BED_feature	59138006	59138038	.	.	.	Name=15117818
chr5	.	BED_feature	131437193	131437225	.	.	.	Name=12704365
chr6	.	BED_feature	106642851	106642882	.	.	.	Name=1851123
chr6	.	BED_feature	106650196	106650227	.	.	.	Name=1851123
chr6	.	BED_feature	106659393	106659933	.	.	.	Name=1851123
chr11	.	BED_feature	117692799	117692830	.	.	.	Name=1989880
chr6	.	BED_feature	32515580	32515609	.	.	.	Name=7673122
chr5	.	BED_feature	149772459	149772599	.	.	.	Name=7673122
chr2	.	BED_feature	88938934	88939059	.	.	.	Name=3037335
chr5	.	BED_feature	137828912	137828949	.	.	.	Name=10391889
chr16	.	BED_feature	68318403	68318430	.	.	.	Name=9601066
chr1	.	BED_feature	59020593	59020670	.	.	.	Name=8253081
chr14	.	BED_feature	79748342	79748375	.	.	.	Name=12775767
chr5	.	BED_feature	137695540	137695570	.	.	.	Name=9679054
chr2	.	BED_feature	204279614	204279644	.	.	.	Name=10510368
chr17	.	BED_feature	73694639	73695190	.	.	.	Name=2005912
chr14	.	BED_feature	93924750	93924779	.	.	.	Name=3263567
chr6	.	BED_feature	49682518	49682891	.	.	.	Name=9442063
chr6	.	BED_feature	49688067	49688117	.	.	.	Name=9442063
chr6	.	BED_feature	49691309	49691352	.	.	.	Name=9442063
chr6	.	BED_feature	49694924	49695034	.	.	.	Name=9442063
chr6	.	BED_feature	49712337	49712389	.	.	.	Name=9442063
chr11	.	BED_feature	116205742	116205769	.	.	.	Name=1406652
chr22_random	.	BED_feature	21272	21299	.	.	.	Name=1406652
chrX	.	BED_feature	37524022	37524232	.	.	.	Name=9593745
chr16	.	BED_feature	142741	142804	.	.	.	Name=9642099
chr16	.	BED_feature	152953	153016	.	.	.	Name=9642099
chr4	.	BED_feature	123597345	123597378	.	.	.	Name=8473495
chr19	.	BED_feature	46878378	46878479	.	.	.	Name=8349632
chr19	.	BED_feature	46914543	46914874	.	.	.	Name=8349632
chr19	.	BED_feature	46917382	46917730	.	.	.	Name=8349632
chr19	.	BED_feature	47716253	47716299	.	.	.	Name=8349632
chr19	.	BED_feature	47784240	47784322	.	.	.	Name=8349632
chr19	.	BED_feature	47821064	47821727	.	.	.	Name=8349632
chr19	.	BED_feature	47858835	47859130	.	.	.	Name=8349632
chr19	.	BED_feature	47924304	47925076	.	.	.	Name=8349632
chr19	.	BED_feature	47936759	47937193	.	.	.	Name=8349632
chr19	.	BED_feature	47950192	47950286	.	.	.	Name=8349632
chr19	.	BED_feature	47961987	47962109	.	.	.	Name=8349632
chr19	.	BED_feature	47981598	47981632	.	.	.	Name=8349632
chr19	.	BED_feature	48039544	48040312	.	.	.	Name=8349632
chr19	.	BED_feature	48052015	48052449	.	.	.	Name=8349632
chr19	.	BED_feature	48063959	48064054	.	.	.	Name=8349632
chr19	.	BED_feature	48075975	48076408	.	.	.	Name=8349632
chr19	.	BED_feature	48102097	48102875	.	.	.	Name=8349632
chr19	.	BED_feature	48121644	48121722	.	.	.	Name=8349632
chr19	.	BED_feature	48145390	48145424	.	.	.	Name=8349632
chr19	.	BED_feature	48210296	48211069	.	.	.	Name=8349632
chr19	.	BED_feature	48222749	48222790	.	.	.	Name=8349632
chr19	.	BED_feature	48266880	48267653	.	.	.	Name=8349632
chr19	.	BED_feature	48370395	48371168	.	.	.	Name=8349632
chr19	.	BED_feature	48382769	48382812	.	.	.	Name=8349632
chr19	.	BED_feature	48390211	48390293	.	.	.	Name=8349632
chr19	.	BED_feature	48401911	48401953	.	.	.	Name=8349632
chr19	.	BED_feature	48415875	48415909	.	.	.	Name=8349632
chr19	.	BED_feature	48453382	48454155	.	.	.	Name=8349632
chr19	.	BED_feature	48465821	48466255	.	.	.	Name=8349632
chr19	.	BED_feature	48479323	48479357	.	.	.	Name=8349632
chr16	.	BED_feature	31178768	31178799	.	.	.	Name=8095266
chr6	.	BED_feature	22405283	22405362	.	.	.	Name=1655738
chr1	.	BED_feature	154478087	154478119	.	.	.	Name=8825560
chr2	.	BED_feature	85748894	85748944	.	.	.	Name=12161428
chr17	.	BED_feature	59364778	59364942	.	.	.	Name=10446901
chr7	.	BED_feature	22733234	22733278	.	.	.	Name=2183031
chr7	.	BED_feature	99219887	99219923	.	.	.	Name=11679585
chr10	.	BED_feature	96686555	96686755	.	.	.	Name=11679585
chr19	.	BED_feature	50100782	50100815	.	.	.	Name=12444925
chr16	.	BED_feature	31178796	31178913	.	.	.	Name=8096519
chr17	.	BED_feature	33144672	33144750	.	.	.	Name=1677179
chr17	.	BED_feature	33167872	33167927	.	.	.	Name=1677179
chr2	.	BED_feature	216008982	216009553	.	.	.	Name=2542772
chr11	.	BED_feature	113672319	113672349	.	.	.	Name=15486044
chr11	.	BED_feature	113688418	113688446	.	.	.	Name=15486044
chr12	.	BED_feature	102847760	102848419	.	.	.	Name=2546060
chr6	.	BED_feature	27968974	27969051	.	.	.	Name=8628255
chr9	.	BED_feature	21067967	21068081	.	.	.	Name=2542571
chr9	.	BED_feature	21358162	21358203	.	.	.	Name=2542571
chr9	.	BED_feature	21430310	21430351	.	.	.	Name=2542571
chr11	.	BED_feature	5204938	5204966	.	.	.	Name=7545172
chr11	.	BED_feature	5227753	5227795	.	.	.	Name=7545172
chr11	.	BED_feature	5232677	5232719	.	.	.	Name=7545172
chr11	.	BED_feature	5247820	5247851	.	.	.	Name=7545172
chr5	.	BED_feature	131410359	131410597	.	.	.	Name=9047239
chr4	.	BED_feature	123597353	123597382	.	.	.	Name=9047239
chr11	.	BED_feature	102219598	102219627	.	.	.	Name=9047239
chr11	.	BED_feature	116213591	116213627	.	.	.	Name=9507986
chr22_random	.	BED_feature	13419	13455	.	.	.	Name=9507986
chr7	.	BED_feature	93042001	93042093	.	.	.	Name=14623107
chr18	.	BED_feature	647736	647764	.	.	.	Name=9218479
chrX	.	BED_feature	43626665	43626710	.	.	.	Name=15024015
chr14	.	BED_feature	66896765	66896814	.	.	.	Name=9856992
chr16	.	BED_feature	55199807	55199838	.	.	.	Name=2191300
chr6	.	BED_feature	32515620	32515659	.	.	.	Name=2105459
chr10	.	BED_feature	90739579	90739628	.	.	.	Name=10903433
chr13	.	BED_feature	112824974	112825091	.	.	.	Name=11159521
chr2	.	BED_feature	1874829	1874920	.	.	.	Name=1280325
chr2	.	BED_feature	1900022	1900095	.	.	.	Name=1280325
chr20	.	BED_feature	62313001	62313928	.	.	.	Name=1280325
chr20	.	BED_feature	62318982	62319078	.	.	.	Name=1280325
chr20	.	BED_feature	62320627	62321779	.	.	.	Name=1280325
chr20	.	BED_feature	62323688	62323844	.	.	.	Name=1280325
chr20	.	BED_feature	62325100	62325129	.	.	.	Name=1280325
chr20	.	BED_feature	62329212	62329770	.	.	.	Name=1280325
chr20	.	BED_feature	62333961	62334153	.	.	.	Name=1280325
chr20	.	BED_feature	62338350	62339187	.	.	.	Name=1280325
chr20	.	BED_feature	62341572	62342693	.	.	.	Name=1280325
chrX	.	BED_feature	102918140	102918171	.	.	.	Name=1280325
chr7	.	BED_feature	100556299	100557042	.	.	.	Name=11423472
chr19	.	BED_feature	50501541	50502693	.	.	.	Name=2903158
chr19	.	BED_feature	50506847	50506880	.	.	.	Name=2903158
chr19	.	BED_feature	50513024	50513074	.	.	.	Name=2903158
chr19	.	BED_feature	50514799	50514829	.	.	.	Name=2903158
chr3	.	BED_feature	70068151	70068220	.	.	.	Name=10973953
chr4	.	BED_feature	123597348	123597378	.	.	.	Name=15471864
chr4	.	BED_feature	74953667	74953833	.	.	.	Name=1906501
chr5	.	BED_feature	132037381	132037436	.	.	.	Name=11781715
chr6	.	BED_feature	31650767	31650831	.	.	.	Name=12655064
chr11	.	BED_feature	116205746	116205774	.	.	.	Name=2777781
chr22_random	.	BED_feature	21267	21295	.	.	.	Name=2777781
chr11	.	BED_feature	100414364	100415056	.	.	.	Name=2328727
chr11	.	BED_feature	100503356	100503385	.	.	.	Name=2328727
chr11	.	BED_feature	100505018	100506465	.	.	.	Name=2328727
chr1	.	BED_feature	6562698	6563256	.	.	.	Name=7969177
chr1	.	BED_feature	6571860	6571923	.	.	.	Name=7969177
chr6	.	BED_feature	32742469	32742520	.	.	.	Name=9032250
chr3	.	BED_feature	111118150	111118177	.	.	.	Name=9032250
chr12	.	BED_feature	103041233	103041262	.	.	.	Name=9032250
chr5	.	BED_feature	1348121	1348359	.	.	.	Name=11454703
chr7	.	BED_feature	55054191	55054386	.	.	.	Name=2768275
chr14	.	BED_feature	21999515	21999544	.	.	.	Name=12244173
chr3	.	BED_feature	188943536	188943563	.	.	.	Name=12150891
chr1	.	BED_feature	23759175	23759207	.	.	.	Name=12150891
chr22	.	BED_feature	39903141	39903181	.	.	.	Name=11116148
chr6	.	BED_feature	32515534	32515581	.	.	.	Name=3174636
chr15	.	BED_feature	37660491	37660521	.	.	.	Name=8444876
chr6	.	BED_feature	138230012	138230054	.	.	.	Name=8444879
chr12	.	BED_feature	97562601	97562637	.	.	.	Name=11896574
chr18	.	BED_feature	53404789	53404938	.	.	.	Name=7983009
chr20	.	BED_feature	31737791	31738092	.	.	.	Name=7935380
chr8	.	BED_feature	38127716	38127745	.	.	.	Name=10919277
chr1	.	BED_feature	153302602	153302796	.	.	.	Name=12030849
chr1	.	BED_feature	100957802	100957850	.	.	.	Name=8547644
chr11	.	BED_feature	73371685	73372465	.	.	.	Name=16282353
chr2	.	BED_feature	48727286	48727318	.	.	.	Name=10364255
chr1	.	BED_feature	181826008	181826435	.	.	.	Name=11781392
chrX	.	BED_feature	37524195	37524224	.	.	.	Name=11781392
chr7	.	BED_feature	41970210	41972742	.	.	.	Name=2118997
chr7	.	BED_feature	41973750	41974031	.	.	.	Name=2118997
chr7	.	BED_feature	41978489	41978750	.	.	.	Name=2118997
chr7	.	BED_feature	41983715	41983767	.	.	.	Name=2118997
chr7	.	BED_feature	42029592	42029669	.	.	.	Name=2118997
chr7	.	BED_feature	42031396	42032539	.	.	.	Name=2118997
chr7	.	BED_feature	42046166	42046363	.	.	.	Name=2118997
chr7	.	BED_feature	42051507	42051655	.	.	.	Name=2118997
chr7	.	BED_feature	42054620	42054811	.	.	.	Name=2118997
chr7	.	BED_feature	42082875	42082981	.	.	.	Name=2118997
chr7	.	BED_feature	42154353	42154578	.	.	.	Name=2118997
chr7	.	BED_feature	42229266	42229411	.	.	.	Name=2118997
chr2	.	BED_feature	121462418	121462473	.	.	.	Name=2118997
chr17	.	BED_feature	35827694	35827738	.	.	.	Name=12769819
chr6	.	BED_feature	36754355	36754385	.	.	.	Name=10749849
chr1	.	BED_feature	67925040	67925068	.	.	.	Name=10749849
chr9	.	BED_feature	109287448	109287894	.	.	.	Name=10749849
chr7	.	BED_feature	55054191	55054238	.	.	.	Name=10363966
chr17	.	BED_feature	35109318	35109363	.	.	.	Name=10363966
chr7	.	BED_feature	56161236	56161290	.	.	.	Name=9334314
chr7	.	BED_feature	64181916	64181969	.	.	.	Name=9334314
chr7	.	BED_feature	64876046	64876085	.	.	.	Name=9334314
chr7	.	BED_feature	72227390	72227445	.	.	.	Name=9334314
chr7	.	BED_feature	73781059	73781114	.	.	.	Name=9334314
chr7	.	BED_feature	74270861	74270916	.	.	.	Name=9334314
chr9	.	BED_feature	96441674	96441802	.	.	.	Name=11023824
chr7	.	BED_feature	75769817	75769845	.	.	.	Name=9328340
chr7	.	BED_feature	5533906	5535784	.	.	.	Name=1710027
chr6	.	BED_feature	46280798	46281747	.	.	.	Name=1710027
chr6	.	BED_feature	89042335	89043319	.	.	.	Name=1710027
chr5	.	BED_feature	15504634	15504896	.	.	.	Name=1710027
chr5	.	BED_feature	56813211	56814242	.	.	.	Name=1710027
chr5	.	BED_feature	61163673	61163723	.	.	.	Name=1710027
chr5	.	BED_feature	77116593	77117549	.	.	.	Name=1710027
chr5	.	BED_feature	79631303	79631916	.	.	.	Name=1710027
chr5	.	BED_feature	79634187	79634306	.	.	.	Name=1710027
chr5	.	BED_feature	97702840	97703393	.	.	.	Name=1710027
chr5	.	BED_feature	131022674	131023539	.	.	.	Name=1710027
chr3	.	BED_feature	12086941	12087806	.	.	.	Name=1710027
chr3	.	BED_feature	140695811	140696440	.	.	.	Name=1710027
chr3	.	BED_feature	177177976	177178622	.	.	.	Name=1710027
chr3	.	BED_feature	182021877	182022052	.	.	.	Name=1710027
chr2	.	BED_feature	73972986	73974525	.	.	.	Name=1710027
chr2	.	BED_feature	73980343	73983204	.	.	.	Name=1710027
chr2	.	BED_feature	73988648	73989876	.	.	.	Name=1710027
chr2	.	BED_feature	73994055	73995649	.	.	.	Name=1710027
chr2	.	BED_feature	73997099	73997500	.	.	.	Name=1710027
chr2	.	BED_feature	73999984	74000318	.	.	.	Name=1710027
chr2	.	BED_feature	108082160	108082238	.	.	.	Name=1710027
chr2	.	BED_feature	130548302	130549385	.	.	.	Name=1710027
chr2	.	BED_feature	130936860	130937957	.	.	.	Name=1710027
chr2	.	BED_feature	131130822	131131919	.	.	.	Name=1710027
chr2	.	BED_feature	131737628	131738725	.	.	.	Name=1710027
chr2	.	BED_feature	132100211	132101308	.	.	.	Name=1710027
chr2	.	BED_feature	177199790	177199841	.	.	.	Name=1710027
chr1	.	BED_feature	27524650	27524875	.	.	.	Name=1710027
chr1	.	BED_feature	78012197	78013141	.	.	.	Name=1710027
chr1	.	BED_feature	92467198	92467382	.	.	.	Name=1710027
chr1	.	BED_feature	103914535	103914769	.	.	.	Name=1710027
chr1	.	BED_feature	201109170	201109326	.	.	.	Name=1710027
chr1	.	BED_feature	222118104	222119050	.	.	.	Name=1710027
chr1	.	BED_feature	227633870	227635476	.	.	.	Name=1710027
chr1	.	BED_feature	236156881	236157339	.	.	.	Name=1710027
chr8	.	BED_feature	86023506	86024318	.	.	.	Name=1710027
chr9	.	BED_feature	6824582	6825542	.	.	.	Name=1710027
chr9	.	BED_feature	102534070	102534395	.	.	.	Name=1710027
chrX	.	BED_feature	46032440	46033041	.	.	.	Name=1710027
chrX	.	BED_feature	53188774	53189695	.	.	.	Name=1710027
chr11	.	BED_feature	1780696	1781770	.	.	.	Name=1710027
chr10	.	BED_feature	70452643	70452798	.	.	.	Name=1710027
chr10	.	BED_feature	90684959	90685088	.	.	.	Name=1710027
chr10	.	BED_feature	90687799	90687977	.	.	.	Name=1710027
chr10	.	BED_feature	90689249	90689321	.	.	.	Name=1710027
chr10	.	BED_feature	90690998	90691107	.	.	.	Name=1710027
chr10	.	BED_feature	90693547	90693643	.	.	.	Name=1710027
chr10	.	BED_feature	90696999	90697120	.	.	.	Name=1710027
chr10	.	BED_feature	90698555	90698637	.	.	.	Name=1710027
chr22	.	BED_feature	14635353	14636447	.	.	.	Name=1710027
chr22	.	BED_feature	39800161	39801062	.	.	.	Name=1710027
chrY	.	BED_feature	18378290	18379273	.	.	.	Name=1710027
chrY	.	BED_feature	18769284	18770112	.	.	.	Name=1710027
chr15	.	BED_feature	32453091	32453139	.	.	.	Name=1710027
chr15	.	BED_feature	32869905	32873056	.	.	.	Name=1710027
chr15	.	BED_feature	32874183	32874289	.	.	.	Name=1710027
chr15	.	BED_feature	42068573	42069644	.	.	.	Name=1710027
chr15	.	BED_feature	81192163	81192213	.	.	.	Name=1710027
chr14	.	BED_feature	18654827	18655924	.	.	.	Name=1710027
chr14	.	BED_feature	19057712	19058809	.	.	.	Name=1710027
chr20	.	BED_feature	1090119	1090302	.	.	.	Name=1710027
chr17	.	BED_feature	17086628	17086908	.	.	.	Name=1710027
chr17	.	BED_feature	77092310	77093757	.	.	.	Name=1710027
chr19	.	BED_feature	9489955	9490962	.	.	.	Name=1710027
chr18	.	BED_feature	58260969	58261292	.	.	.	Name=1710027
chr16	.	BED_feature	48649561	48650501	.	.	.	Name=1710027
chr5	.	BED_feature	132037505	132037538	.	.	.	Name=10069428
chr3	.	BED_feature	25444698	25444726	.	.	.	Name=11943482
chr1	.	BED_feature	167969831	167969975	.	.	.	Name=7520526
chr10	.	BED_feature	82039130	82039179	.	.	.	Name=10677369
chr9	.	BED_feature	115882965	115883372	.	.	.	Name=9729465
chr7	.	BED_feature	120478079	120478120	.	.	.	Name=14621294
chr4	.	BED_feature	63058673	63058703	.	.	.	Name=14621294
chr1	.	BED_feature	181178239	181178280	.	.	.	Name=14621294
chrX	.	BED_feature	153698949	153698990	.	.	.	Name=14621294
chr11	.	BED_feature	3967349	3967409	.	.	.	Name=14621294
chr10	.	BED_feature	19817917	19817977	.	.	.	Name=14621294
chr15	.	BED_feature	60441901	60441972	.	.	.	Name=14621294
chr15	.	BED_feature	91055928	91055966	.	.	.	Name=14621294
chr21	.	BED_feature	39642815	39643262	.	.	.	Name=14621294
chr19	.	BED_feature	58963707	58963769	.	.	.	Name=14621294
chr17_random	.	BED_feature	492684	492712	.	.	.	Name=14557070
chr17_random	.	BED_feature	510776	510804	.	.	.	Name=14557070
chr17_random	.	BED_feature	512268	512296	.	.	.	Name=14557070
chr17_random	.	BED_feature	514743	514771	.	.	.	Name=14557070
chr17_random	.	BED_feature	519632	519660	.	.	.	Name=14557070
chr17_random	.	BED_feature	525780	525808	.	.	.	Name=14557070
chr17_random	.	BED_feature	527712	527740	.	.	.	Name=14557070
chr17_random	.	BED_feature	555959	555987	.	.	.	Name=14557070
chr17_random	.	BED_feature	2607939	2607967	.	.	.	Name=14557070
chr17_random	.	BED_feature	2614807	2614835	.	.	.	Name=14557070
chr3	.	BED_feature	52463074	52463149	.	.	.	Name=8413270
chr3	.	BED_feature	197293435	197293473	.	.	.	Name=8022786
chr15	.	BED_feature	32875225	32875253	.	.	.	Name=2494661
chr5	.	BED_feature	137695576	137695757	.	.	.	Name=7479023
chrX_random	.	BED_feature	1443981	1444483	.	.	.	Name=2044957
chrX	.	BED_feature	77245980	77246482	.	.	.	Name=2044957
chr9	.	BED_feature	37024033	37024157	.	.	.	Name=11223243
chr22	.	BED_feature	37970957	37970998	.	.	.	Name=8077216
chr1	.	BED_feature	100957747	100957777	.	.	.	Name=8077216
chr1	.	BED_feature	151147273	151147456	.	.	.	Name=8550612
chr9	.	BED_feature	21067994	21068067	.	.	.	Name=1886766
chr17	.	BED_feature	7423605	7423652	.	.	.	Name=12676954
chr8	.	BED_feature	42191533	42191569	.	.	.	Name=15466927
chr7	.	BED_feature	99219887	99219919	.	.	.	Name=11027665
chr6	.	BED_feature	41760502	41760686	.	.	.	Name=2115126
chr6	.	BED_feature	41761805	41763745	.	.	.	Name=2115126
chr6	.	BED_feature	41765438	41766953	.	.	.	Name=2115126
chr6	.	BED_feature	41811109	41811166	.	.	.	Name=2115126
chr8	.	BED_feature	43016280	43016347	.	.	.	Name=2115126
chrX	.	BED_feature	48775935	48775998	.	.	.	Name=2115126
chr7	.	BED_feature	94791818	94791848	.	.	.	Name=15380450
chr1	.	BED_feature	2072222	2072263	.	.	.	Name=15380450
chr20	.	BED_feature	5048592	5048691	.	.	.	Name=8095093
chr1	.	BED_feature	52642683	52642720	.	.	.	Name=8943353
chr17	.	BED_feature	40348346	40348385	.	.	.	Name=8702952
chr12	.	BED_feature	52196033	52197187	.	.	.	Name=1694576
chr12	.	BED_feature	52306355	52306405	.	.	.	Name=1694576
chr3	.	BED_feature	188870904	188870945	.	.	.	Name=1694576
chr15	.	BED_feature	89212752	89212779	.	.	.	Name=8132667
chr17	.	BED_feature	59304762	59304919	.	.	.	Name=2033067
chr17	.	BED_feature	59312949	59313105	.	.	.	Name=2033067
chr17	.	BED_feature	59327659	59327816	.	.	.	Name=2033067
chr17	.	BED_feature	59342352	59342496	.	.	.	Name=2033067
chr17	.	BED_feature	59349924	59350080	.	.	.	Name=2033067
chr5	.	BED_feature	158690275	158690305	.	.	.	Name=14976188
chr3	.	BED_feature	134944351	134944495	.	.	.	Name=2033069
chr14	.	BED_feature	105142613	105142669	.	.	.	Name=10510379
chr14	.	BED_feature	105261403	105261448	.	.	.	Name=10510379
chrX	.	BED_feature	47326791	47326827	.	.	.	Name=9182725
chr7	.	BED_feature	5536805	5536862	.	.	.	Name=1762920
chr12	.	BED_feature	14930138	14930305	.	.	.	Name=11425864
chr7	.	BED_feature	100159370	100159403	.	.	.	Name=12354771
chr12	.	BED_feature	26167261	26167289	.	.	.	Name=12354771
chr12	.	BED_feature	26169229	26169296	.	.	.	Name=12354771
chr3	.	BED_feature	4995941	4995970	.	.	.	Name=12354771
chrX	.	BED_feature	114183475	114183507	.	.	.	Name=12776189
chrX	.	BED_feature	114184851	114184881	.	.	.	Name=12776189
chr14	.	BED_feature	21999515	21999541	.	.	.	Name=9584181
chr17	.	BED_feature	59349864	59349894	.	.	.	Name=1744088
chr3	.	BED_feature	150065601	150065788	.	.	.	Name=1744088
chr20	.	BED_feature	44070866	44071007	.	.	.	Name=10359016
chr2	.	BED_feature	136592199	136592248	.	.	.	Name=9379028
chr1	.	BED_feature	75962524	75962563	.	.	.	Name=9271417
chr1	.	BED_feature	227636497	227636588	.	.	.	Name=11096067
chr1	.	BED_feature	227637693	227637737	.	.	.	Name=11096067
chr1	.	BED_feature	27871384	27871419	.	.	.	Name=2721502
chr7	.	BED_feature	142216839	142216875	.	.	.	Name=8264651
chr2	.	BED_feature	169596125	169596152	.	.	.	Name=11387316
chr15	.	BED_feature	54998208	54999478	.	.	.	Name=1312219
chr15	.	BED_feature	55000515	55000591	.	.	.	Name=1312219
chr15	.	BED_feature	55143238	55143314	.	.	.	Name=1312219
chr15	.	BED_feature	55171279	55171377	.	.	.	Name=1312219
chr15	.	BED_feature	55245897	55245956	.	.	.	Name=1312219
chr15	.	BED_feature	55271648	55271783	.	.	.	Name=1312219
chr15	.	BED_feature	55277262	55277318	.	.	.	Name=1312219
chr15	.	BED_feature	55310642	55310747	.	.	.	Name=1312219
chr15	.	BED_feature	55311784	55312347	.	.	.	Name=1312219
chr15	.	BED_feature	55313531	55313597	.	.	.	Name=1312219
chr15	.	BED_feature	55322962	55323029	.	.	.	Name=1312219
chr15	.	BED_feature	55330836	55330913	.	.	.	Name=1312219
chr15	.	BED_feature	55332751	55332960	.	.	.	Name=1312219
chr15	.	BED_feature	55341583	55342764	.	.	.	Name=1312219
chr15	.	BED_feature	55352532	55352752	.	.	.	Name=1312219
chr15	.	BED_feature	55361933	55362088	.	.	.	Name=1312219
chr15	.	BED_feature	55365644	55367499	.	.	.	Name=1312219
chr2	.	BED_feature	234190702	234190736	.	.	.	Name=15470081
chr2	.	BED_feature	234209533	234209564	.	.	.	Name=15470081
chr2	.	BED_feature	234254948	234254978	.	.	.	Name=15470081
chr14	.	BED_feature	74815180	74815209	.	.	.	Name=2233715
chr12	.	BED_feature	21175334	21175378	.	.	.	Name=11483603
chr4	.	BED_feature	68302883	68302915	.	.	.	Name=12947046
chr21	.	BED_feature	26465260	26465326	.	.	.	Name=10333529
chr20	.	BED_feature	5048560	5048599	.	.	.	Name=7602584
chr14	.	BED_feature	74814804	74814834	.	.	.	Name=7602584
chr14	.	BED_feature	21999513	21999541	.	.	.	Name=12097391
chr6	.	BED_feature	135544067	135544095	.	.	.	Name=8137237
chr10	.	BED_feature	62208102	62208133	.	.	.	Name=8137237
chrX	.	BED_feature	24621809	24621838	.	.	.	Name=8137237
chr6	.	BED_feature	32076591	32076624	.	.	.	Name=11463853
chr6	.	BED_feature	32109329	32109362	.	.	.	Name=11463853
chr10	.	BED_feature	104587241	104587383	.	.	.	Name=11463853
chr20	.	BED_feature	42463215	42463243	.	.	.	Name=11585914
chr1	.	BED_feature	184915315	184915343	.	.	.	Name=16397300
chr19	.	BED_feature	46551974	46552018	.	.	.	Name=10843986
chr2	.	BED_feature	219990408	219990569	.	.	.	Name=8387519
chr16	.	BED_feature	55199809	55199838	.	.	.	Name=11522791
chr1	.	BED_feature	202402287	202402322	.	.	.	Name=8999953
chr6	.	BED_feature	31651200	31651239	.	.	.	Name=10521481
chr16	.	BED_feature	28850647	28850827	.	.	.	Name=1375324
chr10	.	BED_feature	90741041	90741071	.	.	.	Name=12788915
chr7	.	BED_feature	150316901	150316930	.	.	.	Name=11960979
chr12	.	BED_feature	116253637	116253666	.	.	.	Name=11960979
chr12	.	BED_feature	116361829	116361874	.	.	.	Name=11960979
chr2	.	BED_feature	21120511	21120539	.	.	.	Name=1901405
chr14	.	BED_feature	93924754	93924784	.	.	.	Name=1901405
chr1	.	BED_feature	181826103	181826309	.	.	.	Name=15513967
chr12	.	BED_feature	56432453	56432646	.	.	.	Name=10688915
chr14	.	BED_feature	24173316	24173382	.	.	.	Name=9857074
chr14	.	BED_feature	74814929	74815058	.	.	.	Name=2849107
chr4	.	BED_feature	89115807	89115868	.	.	.	Name=11126367
chr18	.	BED_feature	27425730	27425759	.	.	.	Name=1620125
chr4	.	BED_feature	74488730	74488763	.	.	.	Name=1620125
chr2	.	BED_feature	21120535	21120578	.	.	.	Name=1620125
chr14	.	BED_feature	93924795	93924826	.	.	.	Name=1620125
chr14	.	BED_feature	22974919	22974961	.	.	.	Name=15572681
chr8	.	BED_feature	19840944	19840973	.	.	.	Name=11090277
chr3	.	BED_feature	12368080	12368108	.	.	.	Name=12821652
chr20	.	BED_feature	5048006	5049059	.	.	.	Name=10488129
chr11	.	BED_feature	118463735	118463763	.	.	.	Name=11154691
chr9	.	BED_feature	2611471	2611503	.	.	.	Name=10064725
chr5	.	BED_feature	137695539	137695570	.	.	.	Name=10559267
chr18	.	BED_feature	59136963	59137006	.	.	.	Name=14555646
chr18	.	BED_feature	59138750	59139484	.	.	.	Name=14555646
chr11	.	BED_feature	5227745	5227796	.	.	.	Name=2476717
chr11	.	BED_feature	5232669	5232720	.	.	.	Name=2476717
chr22	.	BED_feature	49363948	49363991	.	.	.	Name=15356291
chr1	.	BED_feature	938623	938650	.	.	.	Name=1654549
chr13	.	BED_feature	112808079	112808169	.	.	.	Name=7559437
chr10	.	BED_feature	17310933	17311087	.	.	.	Name=8417364
chr16	.	BED_feature	66535560	66535604	.	.	.	Name=1659419
chr10	.	BED_feature	91142234	91142265	.	.	.	Name=2118988
chr5	.	BED_feature	137828634	137828671	.	.	.	Name=11739517
chr13	.	BED_feature	40405404	40405560	.	.	.	Name=1527846
chr13	.	BED_feature	40454190	40454420	.	.	.	Name=1527846
chr13	.	BED_feature	40491363	40491450	.	.	.	Name=1527846
chr11	.	BED_feature	5202451	5202702	.	.	.	Name=2461328
chr7	.	BED_feature	27169862	27169947	.	.	.	Name=1756725
chr7	.	BED_feature	27178093	27178255	.	.	.	Name=1756725
chr12	.	BED_feature	52669279	52669447	.	.	.	Name=1756725
chr12	.	BED_feature	52682482	52682589	.	.	.	Name=1756725
chr17	.	BED_feature	44045705	44045739	.	.	.	Name=1756725
chr17	.	BED_feature	44055373	44055482	.	.	.	Name=1756725
chr2	.	BED_feature	176689952	176690552	.	.	.	Name=1756725
chr2	.	BED_feature	176691929	176692204	.	.	.	Name=1756725
chr2	.	BED_feature	176695794	176697101	.	.	.	Name=1756725
chr6	.	BED_feature	43845944	43845971	.	.	.	Name=9264407
chr6	.	BED_feature	32114047	32114081	.	.	.	Name=9518489
chr19	.	BED_feature	10242588	10242615	.	.	.	Name=9831247
chr5	.	BED_feature	176450433	176450550	.	.	.	Name=12642581
chr3	.	BED_feature	171422834	171422862	.	.	.	Name=14670960
chr3	.	BED_feature	171485040	171485068	.	.	.	Name=14670960
chrX	.	BED_feature	100679722	100679750	.	.	.	Name=14670960
chr14	.	BED_feature	69333739	69333838	.	.	.	Name=14701722
chr3	.	BED_feature	70068213	70068254	.	.	.	Name=10747853
chr1	.	BED_feature	120737517	120737559	.	.	.	Name=7565811
chr1	.	BED_feature	147635826	147635868	.	.	.	Name=7565811
chr1	.	BED_feature	148020782	148020824	.	.	.	Name=7565811
chr4	.	BED_feature	123597021	123597445	.	.	.	Name=8233832
chr3	.	BED_feature	172227350	172227379	.	.	.	Name=10748140
chr6	.	BED_feature	32515532	32515581	.	.	.	Name=1454841
chr2	.	BED_feature	218739948	218739983	.	.	.	Name=9867862
chrX	.	BED_feature	47326840	47326869	.	.	.	Name=10692475
chr1	.	BED_feature	32511796	32511852	.	.	.	Name=7499213
chr2	.	BED_feature	191586628	191586668	.	.	.	Name=11909852
chr1	.	BED_feature	938621	938652	.	.	.	Name=11909852
chr1	.	BED_feature	89303582	89303612	.	.	.	Name=11909852
chr1	.	BED_feature	89645724	89645754	.	.	.	Name=11909852
chr5	.	BED_feature	131423977	131424007	.	.	.	Name=8632000
chr10	.	BED_feature	75338940	75339417	.	.	.	Name=8632000
chr5	.	BED_feature	137828634	137828733	.	.	.	Name=11520792
chr16	.	BED_feature	1782373	1782405	.	.	.	Name=10650966
chr1	.	BED_feature	167969447	167970262	.	.	.	Name=1710341
chr4	.	BED_feature	110942710	110942781	.	.	.	Name=10524238
chr13	.	BED_feature	99432314	99432355	.	.	.	Name=10984499
chr8	.	BED_feature	134378618	134379221	.	.	.	Name=15377670
chr9	.	BED_feature	135491564	135491594	.	.	.	Name=9011768
chr3	.	BED_feature	46481719	46481815	.	.	.	Name=8621448
chr19	.	BED_feature	62042299	62043207	.	.	.	Name=12554678
chr1	.	BED_feature	26105556	26105584	.	.	.	Name=16757134
chr3	.	BED_feature	87408889	87408918	.	.	.	Name=15998782
chr1	.	BED_feature	156923153	156923183	.	.	.	Name=12196550
chr8	.	BED_feature	128817172	128817203	.	.	.	Name=8197157
chr21	.	BED_feature	42660091	42660131	.	.	.	Name=10620335
chr6	.	BED_feature	31891180	31891216	.	.	.	Name=1871106
chr6	.	BED_feature	31903376	31903412	.	.	.	Name=1871106
chr6	.	BED_feature	122762494	122762674	.	.	.	Name=1871106
chr6	.	BED_feature	122775214	122775591	.	.	.	Name=1871106
chr6	.	BED_feature	122782010	122783068	.	.	.	Name=1871106
chr6	.	BED_feature	122784994	122786530	.	.	.	Name=1871106
chr6	.	BED_feature	122790747	122790800	.	.	.	Name=1871106
chr6	.	BED_feature	122794274	122795165	.	.	.	Name=1871106
chr12	.	BED_feature	53802721	53804233	.	.	.	Name=1871106
chr8_random	.	BED_feature	420977	422326	.	.	.	Name=1871105
chr8_random	.	BED_feature	423592	423718	.	.	.	Name=1871105
chr8_random	.	BED_feature	426244	426932	.	.	.	Name=1871105
chr8	.	BED_feature	145503399	145504062	.	.	.	Name=1871105
chr8	.	BED_feature	145506613	145506739	.	.	.	Name=1871105
chr8	.	BED_feature	145508005	145509161	.	.	.	Name=1871105
chr12	.	BED_feature	6547784	6547818	.	.	.	Name=1754393
chr21	.	BED_feature	42609198	42609229	.	.	.	Name=15177881
chr1	.	BED_feature	938617	938650	.	.	.	Name=1406637
chr7	.	BED_feature	5533733	5533779	.	.	.	Name=3244353
chr6	.	BED_feature	89042157	89042202	.	.	.	Name=3244353
chr5	.	BED_feature	77117713	77117757	.	.	.	Name=3244353
chr5	.	BED_feature	79631094	79631150	.	.	.	Name=3244353
chr5	.	BED_feature	97703552	97703597	.	.	.	Name=3244353
chr5	.	BED_feature	131022452	131022499	.	.	.	Name=3244353
chr2	.	BED_feature	130548118	130548164	.	.	.	Name=3244353
chr2	.	BED_feature	130936690	130936736	.	.	.	Name=3244353
chr2	.	BED_feature	131132042	131132087	.	.	.	Name=3244353
chr2	.	BED_feature	131738848	131738893	.	.	.	Name=3244353
chr1	.	BED_feature	78011986	78012023	.	.	.	Name=3244353
chr1	.	BED_feature	222117894	222117941	.	.	.	Name=3244353
chr9	.	BED_feature	6825701	6825746	.	.	.	Name=3244353
chr9	.	BED_feature	102534581	102534628	.	.	.	Name=3244353
chrX	.	BED_feature	44538308	44538347	.	.	.	Name=3244353
chrX	.	BED_feature	46032209	46032255	.	.	.	Name=3244353
chrX	.	BED_feature	65835141	65835184	.	.	.	Name=3244353
chr11	.	BED_feature	1780533	1780576	.	.	.	Name=3244353
chr10	.	BED_feature	70453757	70453804	.	.	.	Name=3244353
chr22	.	BED_feature	14635194	14635229	.	.	.	Name=3244353
chr22	.	BED_feature	39799947	39799993	.	.	.	Name=3244353
chr15	.	BED_feature	42068393	42068434	.	.	.	Name=3244353
chr14	.	BED_feature	18656047	18656083	.	.	.	Name=3244353
chr14	.	BED_feature	19057543	19057588	.	.	.	Name=3244353
chr18	.	BED_feature	58261459	58261504	.	.	.	Name=3244353
chr5	.	BED_feature	68498528	68498563	.	.	.	Name=7739559
chr7	.	BED_feature	55054199	55054226	.	.	.	Name=8887630
chr1	.	BED_feature	205012404	205012628	.	.	.	Name=12817009
chr7	.	BED_feature	87068168	87068256	.	.	.	Name=8103518
chr10	.	BED_feature	6144517	6144552	.	.	.	Name=2308942
chr7	.	BED_feature	99173460	99173491	.	.	.	Name=11495920
chr7	.	BED_feature	99219807	99219883	.	.	.	Name=11495920
chr7	.	BED_feature	99222454	99222483	.	.	.	Name=11495920
chr15	.	BED_feature	98070444	98070503	.	.	.	Name=8035795
chr12	.	BED_feature	6104109	6104139	.	.	.	Name=9444957
chr5	.	BED_feature	131424171	131424199	.	.	.	Name=8035792
chr9	.	BED_feature	21067980	21068020	.	.	.	Name=3368441
chr5	.	BED_feature	138986885	138986916	.	.	.	Name=15656981
chr1	.	BED_feature	201321365	201321394	.	.	.	Name=15656981
chr15	.	BED_feature	40536723	40537317	.	.	.	Name=15656981
chr15	.	BED_feature	40545543	40545576	.	.	.	Name=15656981
chrX	.	BED_feature	100527955	100527995	.	.	.	Name=15850836
chr5	.	BED_feature	131434503	131434658	.	.	.	Name=11509589
chr5	.	BED_feature	142641653	142641682	.	.	.	Name=11509589
chr5	.	BED_feature	145700402	145700431	.	.	.	Name=12606546
chr4	.	BED_feature	123597352	123597383	.	.	.	Name=12606546
chr3	.	BED_feature	12367796	12367826	.	.	.	Name=12606546
chrX	.	BED_feature	15529450	15529479	.	.	.	Name=12606546
chr10	.	BED_feature	62207826	62207857	.	.	.	Name=8420994
chr19	.	BED_feature	10242569	10242753	.	.	.	Name=10092659
chr2	.	BED_feature	191586342	191586980	.	.	.	Name=14654702
chr12	.	BED_feature	46681677	46682070	.	.	.	Name=10856292
chr12	.	BED_feature	46684714	46684793	.	.	.	Name=10856292
chr1	.	BED_feature	27544419	27544468	.	.	.	Name=12137562
chr14	.	BED_feature	21999697	21999744	.	.	.	Name=9584163
chr7	.	BED_feature	99219890	99219918	.	.	.	Name=10757780
chr3	.	BED_feature	25444697	25444725	.	.	.	Name=10757780
chr12	.	BED_feature	28014089	28014273	.	.	.	Name=8371355
chr8	.	BED_feature	57521834	57521869	.	.	.	Name=1828294
chr1	.	BED_feature	153429259	153432230	.	.	.	Name=8387509
chr5	.	BED_feature	68498443	68498645	.	.	.	Name=9218875
chr9	.	BED_feature	21358098	21358144	.	.	.	Name=3040267
chr9	.	BED_feature	21430367	21430415	.	.	.	Name=3040267
chr15	.	BED_feature	49322792	49322820	.	.	.	Name=11245431
chr15	.	BED_feature	72805892	72805921	.	.	.	Name=11120824
chr7	.	BED_feature	131000946	131000998	.	.	.	Name=12850290
chr6	.	BED_feature	89031760	89031806	.	.	.	Name=12850290
chr5	.	BED_feature	115926400	115926450	.	.	.	Name=12850290
chr5	.	BED_feature	149806572	149806623	.	.	.	Name=12850290
chr1	.	BED_feature	19807440	19807491	.	.	.	Name=12850290
chr1	.	BED_feature	176647562	176647613	.	.	.	Name=12850290
chr12	.	BED_feature	28007749	28007797	.	.	.	Name=12850290
chr12	.	BED_feature	28014013	28014467	.	.	.	Name=12850290
chr12	.	BED_feature	28016886	28016923	.	.	.	Name=12850290
chr16	.	BED_feature	8498390	8498441	.	.	.	Name=12850290
chr21	.	BED_feature	26464986	26465014	.	.	.	Name=8541835
chr8	.	BED_feature	19840941	19841043	.	.	.	Name=7753827
chr15	.	BED_feature	72805892	72805921	.	.	.	Name=8816435
chr6	.	BED_feature	31651200	31651239	.	.	.	Name=8816436
chr14	.	BED_feature	74814943	74814984	.	.	.	Name=3316979
chr6	.	BED_feature	36752199	36752228	.	.	.	Name=11030628
chr17	.	BED_feature	7520249	7520295	.	.	.	Name=11030628
chr1	.	BED_feature	205329078	205329135	.	.	.	Name=8598458
chr1	.	BED_feature	205344112	205344140	.	.	.	Name=8598458
chr1	.	BED_feature	198263575	198263662	.	.	.	Name=9786908
chr1	.	BED_feature	198284013	198284064	.	.	.	Name=9786908
chr1	.	BED_feature	198409940	198410009	.	.	.	Name=9786908
chr1	.	BED_feature	115373915	115373970	.	.	.	Name=1321428
chr15	.	BED_feature	49307326	49307355	.	.	.	Name=12351690
chr15	.	BED_feature	49361685	49361725	.	.	.	Name=12351690
chr7	.	BED_feature	5535725	5535755	.	.	.	Name=11744689
chr3	.	BED_feature	166279012	166279163	.	.	.	Name=1378530
chr6	.	BED_feature	27943286	27943766	.	.	.	Name=2829131
chr8	.	BED_feature	57521876	57521906	.	.	.	Name=2850173
chr4	.	BED_feature	89115387	89115910	.	.	.	Name=14712233
chr4	.	BED_feature	89123043	89123072	.	.	.	Name=14712233
chr19	.	BED_feature	46188950	46188987	.	.	.	Name=15722458
chr11	.	BED_feature	68336566	68336619	.	.	.	Name=16271724
chr17	.	BED_feature	59304763	59304920	.	.	.	Name=2181288
chr17	.	BED_feature	59312950	59313106	.	.	.	Name=2181288
chr17	.	BED_feature	59327660	59327817	.	.	.	Name=2181288
chr17	.	BED_feature	59342352	59342501	.	.	.	Name=2181288
chr17	.	BED_feature	59349925	59350081	.	.	.	Name=2181288
chr6	.	BED_feature	37244361	37245942	.	.	.	Name=2181282
chr22	.	BED_feature	44923860	44923889	.	.	.	Name=11981036
chr8	.	BED_feature	42314402	42315724	.	.	.	Name=7590351
chr2	.	BED_feature	127130179	127130354	.	.	.	Name=2584223
chr9	.	BED_feature	124173036	124173077	.	.	.	Name=16105649
chr9	.	BED_feature	124186298	124186375	.	.	.	Name=16105649
chr14	.	BED_feature	66896773	66896803	.	.	.	Name=2584221
chr18	.	BED_feature	59703907	59704256	.	.	.	Name=8916932
chr9	.	BED_feature	21067973	21068007	.	.	.	Name=8916932
chr11	.	BED_feature	5202539	5202590	.	.	.	Name=2481268
chr5	.	BED_feature	132037352	132037431	.	.	.	Name=10973979
chr5	.	BED_feature	72779558	72779586	.	.	.	Name=8988052
chr1	.	BED_feature	154478561	154478610	.	.	.	Name=9388207
chr11	.	BED_feature	32414091	32414122	.	.	.	Name=9388203
chrX	.	BED_feature	48914870	48915309	.	.	.	Name=7622043
chr7	.	BED_feature	100159377	100159408	.	.	.	Name=14741200
chr21	.	BED_feature	46842970	46843794	.	.	.	Name=2394738
chr21	.	BED_feature	46846619	46846730	.	.	.	Name=2394738
chr3	.	BED_feature	134947846	134947876	.	.	.	Name=2911463
chr14	.	BED_feature	93924792	93924822	.	.	.	Name=2911463
chr7	.	BED_feature	5536824	5536862	.	.	.	Name=2911466
chr11	.	BED_feature	6367885	6367915	.	.	.	Name=11788605
chr11	.	BED_feature	118463696	118463975	.	.	.	Name=2911469
chr3	.	BED_feature	131176178	131176299	.	.	.	Name=7565802
chr4	.	BED_feature	100461657	100461748	.	.	.	Name=2050667
chr4	.	BED_feature	100493040	100493072	.	.	.	Name=2050667
chr1	.	BED_feature	154478094	154478121	.	.	.	Name=8262978
chr11	.	BED_feature	119681054	119681704	.	.	.	Name=2905684
chr1	.	BED_feature	165456769	165456819	.	.	.	Name=2905684
chr1	.	BED_feature	165568327	165568397	.	.	.	Name=2905684
chr1	.	BED_feature	165601326	165601430	.	.	.	Name=2905684
chr1	.	BED_feature	165607865	165607897	.	.	.	Name=2905684
chr1	.	BED_feature	165609968	165610158	.	.	.	Name=2905684
chr1	.	BED_feature	165611887	165612018	.	.	.	Name=2905684
chr1	.	BED_feature	165619717	165619812	.	.	.	Name=2905684
chr1	.	BED_feature	165625446	165625623	.	.	.	Name=2905684
chr1	.	BED_feature	165632145	165632288	.	.	.	Name=2905684
chr1	.	BED_feature	165633852	165633994	.	.	.	Name=2905684
chr1	.	BED_feature	165635045	165635228	.	.	.	Name=2905684
chr1	.	BED_feature	165637311	165637418	.	.	.	Name=2905684
chr1	.	BED_feature	165647817	165648975	.	.	.	Name=2905684
chr1	.	BED_feature	165651359	165651948	.	.	.	Name=2905684
chr5	.	BED_feature	135259349	135259383	.	.	.	Name=8663174
chr5	.	BED_feature	131437274	131437315	.	.	.	Name=8934574
chr4	.	BED_feature	123597231	123597266	.	.	.	Name=8934574
chr9	.	BED_feature	21067986	21068019	.	.	.	Name=8934574
chr22	.	BED_feature	34102753	34103229	.	.	.	Name=8077238
chr14	.	BED_feature	74814956	74814988	.	.	.	Name=11108721
chr8	.	BED_feature	128822294	128822324	.	.	.	Name=7539921
chr21	.	BED_feature	31953788	31953876	.	.	.	Name=3160582
chr7	.	BED_feature	5533943	5533974	.	.	.	Name=16702209
chr7	.	BED_feature	5535397	5535430	.	.	.	Name=16702209
chr6	.	BED_feature	89042358	89042389	.	.	.	Name=16702209
chr5	.	BED_feature	77116719	77117549	.	.	.	Name=16702209
chr5	.	BED_feature	131023426	131023456	.	.	.	Name=16702209
chr3	.	BED_feature	177178013	177178044	.	.	.	Name=16702209
chr2	.	BED_feature	73989308	73989339	.	.	.	Name=16702209
chr2	.	BED_feature	130548327	130549162	.	.	.	Name=16702209
chr2	.	BED_feature	130936899	130937734	.	.	.	Name=16702209
chr2	.	BED_feature	131131045	131131880	.	.	.	Name=16702209
chr2	.	BED_feature	131737851	131738686	.	.	.	Name=16702209
chr2	.	BED_feature	132100434	132101269	.	.	.	Name=16702209
chr1	.	BED_feature	27524805	27524836	.	.	.	Name=16702209
chr9	.	BED_feature	6825509	6825538	.	.	.	Name=16702209
chr11	.	BED_feature	1780733	1781649	.	.	.	Name=16702209
chr10	.	BED_feature	70452768	70452798	.	.	.	Name=16702209
chr22	.	BED_feature	14635389	14636224	.	.	.	Name=16702209
chr15	.	BED_feature	32872905	32872933	.	.	.	Name=16702209
chr14	.	BED_feature	18655050	18655885	.	.	.	Name=16702209
chr14	.	BED_feature	19057751	19058586	.	.	.	Name=16702209
chr17	.	BED_feature	77093600	77093634	.	.	.	Name=16702209
chr18	.	BED_feature	58261273	58261304	.	.	.	Name=16702209
chr16	.	BED_feature	54068947	54068977	.	.	.	Name=2174109
chr7	.	BED_feature	5533943	5533974	.	.	.	Name=10479057
chr7	.	BED_feature	5535397	5535428	.	.	.	Name=10479057
chr6	.	BED_feature	89042358	89042389	.	.	.	Name=10479057
chr5	.	BED_feature	77116719	77117549	.	.	.	Name=10479057
chr5	.	BED_feature	131023426	131023456	.	.	.	Name=10479057
chr3	.	BED_feature	177178013	177178044	.	.	.	Name=10479057
chr2	.	BED_feature	73989308	73989339	.	.	.	Name=10479057
chr2	.	BED_feature	130548327	130549162	.	.	.	Name=10479057
chr2	.	BED_feature	130936899	130937734	.	.	.	Name=10479057
chr2	.	BED_feature	131131045	131131880	.	.	.	Name=10479057
chr2	.	BED_feature	131737851	131738686	.	.	.	Name=10479057
chr2	.	BED_feature	132100434	132101269	.	.	.	Name=10479057
chr1	.	BED_feature	27524805	27524836	.	.	.	Name=10479057
chr9	.	BED_feature	6825509	6825538	.	.	.	Name=10479057
chr11	.	BED_feature	1780733	1781649	.	.	.	Name=10479057
chr10	.	BED_feature	70452768	70452798	.	.	.	Name=10479057
chr22	.	BED_feature	14635389	14636224	.	.	.	Name=10479057
chr15	.	BED_feature	32872905	32872933	.	.	.	Name=10479057
chr14	.	BED_feature	18655050	18655885	.	.	.	Name=10479057
chr14	.	BED_feature	19057751	19058586	.	.	.	Name=10479057
chr17	.	BED_feature	77093600	77093634	.	.	.	Name=10479057
chr18	.	BED_feature	58261273	58261304	.	.	.	Name=10479057
chr2	.	BED_feature	1390689	1390921	.	.	.	Name=2174102
chr1	.	BED_feature	154478088	154478117	.	.	.	Name=1662118
chr14	.	BED_feature	22947448	22947476	.	.	.	Name=1662118
chr12	.	BED_feature	111900464	111900728	.	.	.	Name=10524248
chr11	.	BED_feature	13474243	13474272	.	.	.	Name=15297458
chr10	.	BED_feature	45188603	45189766	.	.	.	Name=2251250
chr1	.	BED_feature	17317541	17317569	.	.	.	Name=15854045
chr1	.	BED_feature	17318599	17318670	.	.	.	Name=15854045
chr5	.	BED_feature	132037382	132037410	.	.	.	Name=9013959
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=9013959
chr12	.	BED_feature	46521661	46525058	.	.	.	Name=2835767
chr12	.	BED_feature	46526385	46526861	.	.	.	Name=2835767
chr12	.	BED_feature	46535680	46535854	.	.	.	Name=2835767
chr12	.	BED_feature	46537179	46537738	.	.	.	Name=2835767
chr12	.	BED_feature	46545097	46545230	.	.	.	Name=2835767
chr12	.	BED_feature	46559017	46559168	.	.	.	Name=2835767
chr12	.	BED_feature	46562743	46562827	.	.	.	Name=2835767
chr12	.	BED_feature	46585005	46585036	.	.	.	Name=2835767
chr17	.	BED_feature	77217047	77217081	.	.	.	Name=2835767
chr19	.	BED_feature	11061107	11061137	.	.	.	Name=12947119
chr4	.	BED_feature	15549014	15549042	.	.	.	Name=9668098
chr14	.	BED_feature	22095159	22095319	.	.	.	Name=1534408
chr14	.	BED_feature	74815207	74815235	.	.	.	Name=1534408
chr1	.	BED_feature	2448790	2448825	.	.	.	Name=14757642
chr1	.	BED_feature	119759168	119759197	.	.	.	Name=10406460
chr7	.	BED_feature	93862155	93862182	.	.	.	Name=8900150
chr17	.	BED_feature	16666722	16666790	.	.	.	Name=1703506
chr17	.	BED_feature	18294024	18294092	.	.	.	Name=1703506
chr17	.	BED_feature	20338189	20338319	.	.	.	Name=1703506
chr17	.	BED_feature	36996741	36996916	.	.	.	Name=1703506
chr4	.	BED_feature	55686549	55686584	.	.	.	Name=12560084
chr13	.	BED_feature	47952182	47952213	.	.	.	Name=1406625
chr3	.	BED_feature	134944269	134944298	.	.	.	Name=1851757
chr3	.	BED_feature	134947818	134948026	.	.	.	Name=1851757
chr6	.	BED_feature	32515576	32515609	.	.	.	Name=8943243
chr6	.	BED_feature	33656082	33656117	.	.	.	Name=11850816
chr12	.	BED_feature	52060303	52060349	.	.	.	Name=11294852
chr1	.	BED_feature	151269443	151269610	.	.	.	Name=8388378
chr7	.	BED_feature	55054353	55054388	.	.	.	Name=10830317
chr17	.	BED_feature	23928235	23928263	.	.	.	Name=8348972
chr18	.	BED_feature	59138135	59138165	.	.	.	Name=12970736
chr13	.	BED_feature	102516652	102516690	.	.	.	Name=12055195
chr13	.	BED_feature	102518744	102518897	.	.	.	Name=12055195
chr11	.	BED_feature	5227701	5227739	.	.	.	Name=9763579
chr11	.	BED_feature	5232625	5232663	.	.	.	Name=9763579
chr16	.	BED_feature	162928	162961	.	.	.	Name=9763579
chr16	.	BED_feature	166732	166765	.	.	.	Name=9763579
chr10	.	BED_feature	59815102	59815201	.	.	.	Name=8108407
chr5	.	BED_feature	139993037	139993066	.	.	.	Name=7522257
chr7	.	BED_feature	116099209	116099369	.	.	.	Name=8633043
chr14	.	BED_feature	74814952	74815012	.	.	.	Name=3561415
chrX	.	BED_feature	139414745	139414777	.	.	.	Name=15656994
chr9	.	BED_feature	89532338	89532368	.	.	.	Name=11742542
chr1	.	BED_feature	120737495	120737582	.	.	.	Name=8035786
chr1	.	BED_feature	147635803	147635890	.	.	.	Name=8035786
chr1	.	BED_feature	148020759	148020846	.	.	.	Name=8035786
chr14	.	BED_feature	21999475	21999519	.	.	.	Name=1328863
chr3	.	BED_feature	126434266	126435864	.	.	.	Name=8355710
chr3	.	BED_feature	126479256	126479345	.	.	.	Name=8355710
chr3	.	BED_feature	126480656	126480781	.	.	.	Name=8355710
chr3	.	BED_feature	126489637	126489762	.	.	.	Name=8355710
chr3	.	BED_feature	126514837	126515191	.	.	.	Name=8355710
chr3	.	BED_feature	126524842	126524980	.	.	.	Name=8355710
chr3	.	BED_feature	126532691	126532773	.	.	.	Name=8355710
chr3	.	BED_feature	126576657	126576781	.	.	.	Name=8355710
chr1	.	BED_feature	198644523	198644626	.	.	.	Name=8355710
chr7	.	BED_feature	5534002	5534623	.	.	.	Name=8939459
chr6	.	BED_feature	46281347	46281734	.	.	.	Name=8939459
chr6	.	BED_feature	89042423	89042712	.	.	.	Name=8939459
chr5	.	BED_feature	15504844	15504873	.	.	.	Name=8939459
chr5	.	BED_feature	61163679	61163733	.	.	.	Name=8939459
chr5	.	BED_feature	77117197	77117492	.	.	.	Name=8939459
chr5	.	BED_feature	79631359	79631581	.	.	.	Name=8939459
chr5	.	BED_feature	97703199	97703252	.	.	.	Name=8939459
chr3	.	BED_feature	12087412	12087591	.	.	.	Name=8939459
chr3	.	BED_feature	140696030	140696413	.	.	.	Name=8939459
chr3	.	BED_feature	177178243	177178299	.	.	.	Name=8939459
chr3	.	BED_feature	182021772	182021993	.	.	.	Name=8939459
chr2	.	BED_feature	73995379	73995432	.	.	.	Name=8939459
chr2	.	BED_feature	73997332	73997392	.	.	.	Name=8939459
chr2	.	BED_feature	113258478	113258678	.	.	.	Name=8939459
chr2	.	BED_feature	130548384	130548798	.	.	.	Name=8939459
chr2	.	BED_feature	130936956	130937370	.	.	.	Name=8939459
chr2	.	BED_feature	131131409	131131823	.	.	.	Name=8939459
chr2	.	BED_feature	131738215	131738629	.	.	.	Name=8939459
chr2	.	BED_feature	132100799	132101212	.	.	.	Name=8939459
chr2	.	BED_feature	177199803	177199832	.	.	.	Name=8939459
chr1	.	BED_feature	27524782	27524811	.	.	.	Name=8939459
chr1	.	BED_feature	78012360	78012539	.	.	.	Name=8939459
chr1	.	BED_feature	103914372	103914667	.	.	.	Name=8939459
chr1	.	BED_feature	222118160	222118387	.	.	.	Name=8939459
chr1	.	BED_feature	227634432	227634490	.	.	.	Name=8939459
chr1	.	BED_feature	236157434	236157485	.	.	.	Name=8939459
chr8	.	BED_feature	86024151	86024198	.	.	.	Name=8939459
chr9	.	BED_feature	6825150	6825481	.	.	.	Name=8939459
chr9	.	BED_feature	102534313	102534359	.	.	.	Name=8939459
chrX	.	BED_feature	46032663	46032719	.	.	.	Name=8939459
chrX	.	BED_feature	53188785	53189155	.	.	.	Name=8939459
chr11	.	BED_feature	1780968	1781216	.	.	.	Name=8939459
chr10	.	BED_feature	90689315	90689371	.	.	.	Name=8939459
chr22	.	BED_feature	14635562	14635859	.	.	.	Name=8939459
chr22	.	BED_feature	39800217	39800503	.	.	.	Name=8939459
chrY	.	BED_feature	18378427	18378484	.	.	.	Name=8939459
chrY	.	BED_feature	18770073	18770130	.	.	.	Name=8939459
chr15	.	BED_feature	32871654	32871766	.	.	.	Name=8939459
chr15	.	BED_feature	42068657	42068877	.	.	.	Name=8939459
chr15	.	BED_feature	81192522	81192565	.	.	.	Name=8939459
chr14	.	BED_feature	18655414	18655712	.	.	.	Name=8939459
chr14	.	BED_feature	19057924	19058221	.	.	.	Name=8939459
chr17	.	BED_feature	17086478	17086530	.	.	.	Name=8939459
chr17	.	BED_feature	77092374	77092935	.	.	.	Name=8939459
chr19	.	BED_feature	9490689	9490921	.	.	.	Name=8939459
chr18	.	BED_feature	58261016	58261239	.	.	.	Name=8939459
chr7	.	BED_feature	100556367	100556452	.	.	.	Name=10092624
chr4	.	BED_feature	55686312	55686706	.	.	.	Name=15941713
chr22	.	BED_feature	37971040	37971068	.	.	.	Name=2651898
chr7	.	BED_feature	99166660	99166694	.	.	.	Name=16171783
chr7	.	BED_feature	99204179	99204208	.	.	.	Name=16171783
chr7	.	BED_feature	99215593	99215627	.	.	.	Name=16171783
chr5	.	BED_feature	174803081	174803675	.	.	.	Name=1557411
chr11	.	BED_feature	5227728	5227786	.	.	.	Name=9792700
chr11	.	BED_feature	5232652	5232710	.	.	.	Name=9792700
chrX	.	BED_feature	37524127	37524187	.	.	.	Name=9792700
chr6	.	BED_feature	32515518	32515571	.	.	.	Name=1956787
chr6	.	BED_feature	32549431	32549476	.	.	.	Name=1956787
chr6	.	BED_feature	32606137	32606182	.	.	.	Name=1956787
chr6	.	BED_feature	32665654	32665699	.	.	.	Name=1956787
chr6	.	BED_feature	32713040	32713089	.	.	.	Name=1956787
chr6	.	BED_feature	32742504	32742540	.	.	.	Name=1956787
chr6	.	BED_feature	32839379	32839415	.	.	.	Name=1956787
chr6	.	BED_feature	33151596	33151641	.	.	.	Name=1956787
chr6	.	BED_feature	33188070	33188115	.	.	.	Name=1956787
chr4	.	BED_feature	74488495	74488536	.	.	.	Name=2571419
chr14	.	BED_feature	93924752	93924784	.	.	.	Name=2571419
chr7	.	BED_feature	5535763	5535811	.	.	.	Name=8647842
chr5	.	BED_feature	77116470	77116518	.	.	.	Name=8647842
chr2	.	BED_feature	130937935	130937983	.	.	.	Name=8647842
chr2	.	BED_feature	131737602	131737650	.	.	.	Name=8647842
chr1	.	BED_feature	222119125	222119173	.	.	.	Name=8647842
chr9	.	BED_feature	6824458	6824505	.	.	.	Name=8647842
chr14	.	BED_feature	20429814	20429854	.	.	.	Name=8647842
chr14	.	BED_feature	20494020	20494067	.	.	.	Name=8647842
chr9	.	BED_feature	21068007	21068050	.	.	.	Name=10848607
chr17	.	BED_feature	7520608	7520634	.	.	.	Name=10942770
chr1	.	BED_feature	67925042	67925068	.	.	.	Name=10942770
chr17	.	BED_feature	73695041	73695086	.	.	.	Name=9374541
chr11	.	BED_feature	2139937	2139969	.	.	.	Name=7639703
chr1	.	BED_feature	184916222	184916248	.	.	.	Name=12914528
chr4	.	BED_feature	175649784	175649813	.	.	.	Name=12914529
chr4	.	BED_feature	175650945	175651026	.	.	.	Name=12914529
chr4	.	BED_feature	175653285	175653325	.	.	.	Name=12914529
chr4	.	BED_feature	175666423	175666513	.	.	.	Name=12914529
chr4	.	BED_feature	175675715	175675787	.	.	.	Name=12914529
chr4	.	BED_feature	175679675	175679704	.	.	.	Name=12914529
chr4	.	BED_feature	175682130	175682169	.	.	.	Name=12914529
chr1	.	BED_feature	167865993	167866032	.	.	.	Name=7693674
chr8	.	BED_feature	57521754	57521785	.	.	.	Name=2903436
chr3	.	BED_feature	188870905	188870949	.	.	.	Name=2903436
chr14	.	BED_feature	74814952	74815007	.	.	.	Name=2903436
chr22	.	BED_feature	38248081	38248109	.	.	.	Name=10667576
chr6	.	BED_feature	31891277	31891343	.	.	.	Name=3185540
chr14	.	BED_feature	23071810	23071877	.	.	.	Name=1719379
chr16	.	BED_feature	71378562	71380251	.	.	.	Name=1719379
chr16	.	BED_feature	71384655	71390115	.	.	.	Name=1719379
chr16	.	BED_feature	71391427	71391530	.	.	.	Name=1719379
chr16	.	BED_feature	71402975	71403440	.	.	.	Name=1719379
chr16	.	BED_feature	71421179	71421262	.	.	.	Name=1719379
chr16	.	BED_feature	71481131	71481364	.	.	.	Name=1719379
chr16	.	BED_feature	71541869	71542365	.	.	.	Name=1719379
chr16	.	BED_feature	71650003	71650035	.	.	.	Name=1719379
chr8	.	BED_feature	77782583	77782774	.	.	.	Name=1719379
chr8	.	BED_feature	77939157	77939199	.	.	.	Name=1719379
chr15	.	BED_feature	32875132	32875172	.	.	.	Name=3185542
chr6	.	BED_feature	31891250	31891297	.	.	.	Name=7891680
chr6	.	BED_feature	160852091	160852152	.	.	.	Name=8051057
chr6	.	BED_feature	161005298	161005359	.	.	.	Name=8051057
chr6	.	BED_feature	161043165	161043237	.	.	.	Name=8051057
chr6	.	BED_feature	161114848	161114920	.	.	.	Name=8051057
chr2	.	BED_feature	87102507	87102536	.	.	.	Name=8051057
chr2	.	BED_feature	87828663	87828698	.	.	.	Name=8051057
chr2	.	BED_feature	106364917	106364971	.	.	.	Name=8051057
chr19	.	BED_feature	48747327	48747708	.	.	.	Name=16596326
chr3	.	BED_feature	49041758	49042120	.	.	.	Name=9278455
chr8	.	BED_feature	128815946	128816007	.	.	.	Name=2211718
chr10	.	BED_feature	75339386	75339416	.	.	.	Name=9482739
chr10	.	BED_feature	75339386	75339418	.	.	.	Name=10381567
chr2	.	BED_feature	113313572	113313625	.	.	.	Name=7935442
chr6	.	BED_feature	31891220	31891298	.	.	.	Name=2294402
chr6	.	BED_feature	31903416	31903493	.	.	.	Name=2294402
chr11	.	BED_feature	117692799	117692833	.	.	.	Name=9233811
chr1	.	BED_feature	148070780	148070820	.	.	.	Name=8475055
chr1	.	BED_feature	148099374	148099414	.	.	.	Name=8475055
chr2	.	BED_feature	10505826	10507350	.	.	.	Name=1598217
chr6	.	BED_feature	31433069	31433100	.	.	.	Name=11087747
chr1	.	BED_feature	55454214	55454275	.	.	.	Name=2105456
chr15	.	BED_feature	41590466	41590493	.	.	.	Name=12411430
chr5	.	BED_feature	131854278	131855640	.	.	.	Name=7678055
chr11	.	BED_feature	303990	304023	.	.	.	Name=7678055
chr1	.	BED_feature	27871382	27871462	.	.	.	Name=7678055
chr17	.	BED_feature	77649442	77649508	.	.	.	Name=10759542
chr11	.	BED_feature	100504117	100504150	.	.	.	Name=1326555
chr17	.	BED_feature	35740997	35741025	.	.	.	Name=1326555
chr3	.	BED_feature	25680705	25680732	.	.	.	Name=12197834
chr3	.	BED_feature	197293366	197293455	.	.	.	Name=2211668
chr1	.	BED_feature	16713404	16713597	.	.	.	Name=2211668
chr1	.	BED_feature	16866067	16866259	.	.	.	Name=2211668
chr1	.	BED_feature	16939369	16939545	.	.	.	Name=2211668
chr1	.	BED_feature	17094833	17095009	.	.	.	Name=2211668
chr1	.	BED_feature	142465001	142465030	.	.	.	Name=2211668
chr1	.	BED_feature	144680989	144681018	.	.	.	Name=2211668
chr1	.	BED_feature	145023126	145023155	.	.	.	Name=2211668
chr1	.	BED_feature	145977990	145978019	.	.	.	Name=2211668
chr1	.	BED_feature	146202148	146202177	.	.	.	Name=2211668
chr1	.	BED_feature	146327615	146327644	.	.	.	Name=2211668
chr1	.	BED_feature	147491061	147491090	.	.	.	Name=2211668
chr10	.	BED_feature	75338917	75338950	.	.	.	Name=9295342
chr2	.	BED_feature	1390805	1390838	.	.	.	Name=1922026
chr17	.	BED_feature	29636806	29636846	.	.	.	Name=11076795
chr17	.	BED_feature	39822517	39822558	.	.	.	Name=9305885
chr19	.	BED_feature	47291339	47291924	.	.	.	Name=1967834
chr11	.	BED_feature	119681054	119681704	.	.	.	Name=1967834
chr1	.	BED_feature	165568333	165568397	.	.	.	Name=1967834
chr1	.	BED_feature	165601333	165601380	.	.	.	Name=1967834
chr1	.	BED_feature	165606041	165606075	.	.	.	Name=1967834
chr1	.	BED_feature	165607799	165607887	.	.	.	Name=1967834
chr1	.	BED_feature	165610013	165610157	.	.	.	Name=1967834
chr1	.	BED_feature	165611903	165611983	.	.	.	Name=1967834
chr1	.	BED_feature	165619742	165619800	.	.	.	Name=1967834
chr1	.	BED_feature	165625446	165625623	.	.	.	Name=1967834
chr1	.	BED_feature	165632145	165632288	.	.	.	Name=1967834
chr1	.	BED_feature	165633852	165633994	.	.	.	Name=1967834
chr1	.	BED_feature	165635119	165635173	.	.	.	Name=1967834
chr1	.	BED_feature	165637311	165637397	.	.	.	Name=1967834
chr1	.	BED_feature	165647831	165648975	.	.	.	Name=1967834
chr1	.	BED_feature	165651373	165651799	.	.	.	Name=1967834
chrX	.	BED_feature	146800431	146801657	.	.	.	Name=9328468
chr5	.	BED_feature	137828678	137828706	.	.	.	Name=10050673
chr11	.	BED_feature	5248170	5248250	.	.	.	Name=8196619
chr7	.	BED_feature	97339598	97339755	.	.	.	Name=8098842
chr8	.	BED_feature	47648440	47648477	.	.	.	Name=8098842
chr11	.	BED_feature	116213773	116213811	.	.	.	Name=2254327
chr22_random	.	BED_feature	13235	13273	.	.	.	Name=2254327
chr2	.	BED_feature	136592147	136592180	.	.	.	Name=9468539
chr8	.	BED_feature	31041349	31041376	.	.	.	Name=9774636
chr6	.	BED_feature	36754237	36754267	.	.	.	Name=10899165
chr10	.	BED_feature	80990400	80990429	.	.	.	Name=8770068
chr10	.	BED_feature	81310345	81310374	.	.	.	Name=8770068
chr7	.	BED_feature	100530838	100530867	.	.	.	Name=14963043
chr7	.	BED_feature	100538832	100538860	.	.	.	Name=14963043
chr7	.	BED_feature	100546038	100546066	.	.	.	Name=14963043
chr7	.	BED_feature	100552574	100552602	.	.	.	Name=14963043
chr1	.	BED_feature	228916451	228916637	.	.	.	Name=9120024
chr14	.	BED_feature	69333742	69333779	.	.	.	Name=11031103
chr12	.	BED_feature	102848232	102848267	.	.	.	Name=7891720
chr9	.	BED_feature	127043548	127043582	.	.	.	Name=7891720
chr19	.	BED_feature	10242284	10242711	.	.	.	Name=11278281
chr7	.	BED_feature	27135514	27135556	.	.	.	Name=1346761
chr7	.	BED_feature	27151872	27152020	.	.	.	Name=1346761
chr7	.	BED_feature	27161183	27161337	.	.	.	Name=1346761
chr12	.	BED_feature	52691283	52691317	.	.	.	Name=1346761
chr12	.	BED_feature	52709751	52715423	.	.	.	Name=1346761
chr17	.	BED_feature	44009180	44009226	.	.	.	Name=1346761
chr17	.	BED_feature	44024628	44024671	.	.	.	Name=1346761
chr17	.	BED_feature	44028844	44028890	.	.	.	Name=1346761
chr17	.	BED_feature	44045684	44045736	.	.	.	Name=1346761
chr2	.	BED_feature	176725737	176725784	.	.	.	Name=1346761
chr13	.	BED_feature	27396545	27396591	.	.	.	Name=1346761
chr11	.	BED_feature	5227820	5227865	.	.	.	Name=8662744
chr11	.	BED_feature	5232744	5232789	.	.	.	Name=8662744
chr2	.	BED_feature	85748903	85748942	.	.	.	Name=8687389
chr11	.	BED_feature	69164860	69165095	.	.	.	Name=11024050
chr15	.	BED_feature	42790871	42790904	.	.	.	Name=11024050
chr1	.	BED_feature	151596551	151596591	.	.	.	Name=12167632
chr12	.	BED_feature	111829066	111829297	.	.	.	Name=2456211
chr11	.	BED_feature	32405321	32405350	.	.	.	Name=9361007
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=8468470
chr9	.	BED_feature	124630643	124630672	.	.	.	Name=10899582
chr17	.	BED_feature	6840199	6840229	.	.	.	Name=9164849
chr11	.	BED_feature	67107744	67107826	.	.	.	Name=9540834
chr12	.	BED_feature	111829116	111829152	.	.	.	Name=2243138
chr11	.	BED_feature	303984	304028	.	.	.	Name=2243138
chr15	.	BED_feature	42790853	42790899	.	.	.	Name=2243138
chr1	.	BED_feature	27871372	27871421	.	.	.	Name=2243138
chr14	.	BED_feature	66896773	66896808	.	.	.	Name=8327497
chr8	.	BED_feature	128817144	128817192	.	.	.	Name=2498322
chr4	.	BED_feature	74520899	74520930	.	.	.	Name=12167706
chr1	.	BED_feature	151145505	151145545	.	.	.	Name=11850802
chr3	.	BED_feature	197293420	197293452	.	.	.	Name=12439744
chr5	.	BED_feature	1348962	1348990	.	.	.	Name=10805720
chr6	.	BED_feature	32515576	32515609	.	.	.	Name=9857002
chr12	.	BED_feature	66839928	66839961	.	.	.	Name=9857002
chr15	.	BED_feature	32875087	32875160	.	.	.	Name=1570331
chr19	.	BED_feature	46551778	46551809	.	.	.	Name=1419910
chr14	.	BED_feature	74815179	74815210	.	.	.	Name=1419910
chr2	.	BED_feature	37237627	37237664	.	.	.	Name=9007065
chr17	.	BED_feature	59304593	59304709	.	.	.	Name=2983311
chr17	.	BED_feature	59312780	59312896	.	.	.	Name=2983311
chr17	.	BED_feature	59327490	59327606	.	.	.	Name=2983311
chr17	.	BED_feature	59342176	59342291	.	.	.	Name=2983311
chr17	.	BED_feature	59349755	59349997	.	.	.	Name=2983311
chr20	.	BED_feature	33223227	33223554	.	.	.	Name=12560236
chr11	.	BED_feature	2139186	2139263	.	.	.	Name=8216223
chr6	.	BED_feature	32929569	32929603	.	.	.	Name=8617938
chr1	.	BED_feature	227637707	227637741	.	.	.	Name=7753622
chr6	.	BED_feature	32515534	32515582	.	.	.	Name=1903200
chr6	.	BED_feature	32742550	32742590	.	.	.	Name=1903200
chr21	.	BED_feature	43132721	43132757	.	.	.	Name=9873055
chr21	.	BED_feature	45165276	45165326	.	.	.	Name=9873055
chr9	.	BED_feature	112059028	112059075	.	.	.	Name=11279008
chr5	.	BED_feature	142763773	142763812	.	.	.	Name=1894621
chr3	.	BED_feature	25444699	25444727	.	.	.	Name=12133007
chr17	.	BED_feature	7531625	7531657	.	.	.	Name=11032029
chr19	.	BED_feature	10242221	10242349	.	.	.	Name=7532665
chr11	.	BED_feature	101906779	101906820	.	.	.	Name=10514384
chr2	.	BED_feature	15998067	15998098	.	.	.	Name=9233765
chr1	.	BED_feature	100956790	100957652	.	.	.	Name=11590177
chr19	.	BED_feature	45471156	45471341	.	.	.	Name=11948187
chr19	.	BED_feature	45472648	45472677	.	.	.	Name=11948187
chr3	.	BED_feature	30622937	30622975	.	.	.	Name=9694866
chr19	.	BED_feature	48382520	48382548	.	.	.	Name=9083102
chr11	.	BED_feature	118463734	118463762	.	.	.	Name=9737995
chr1	.	BED_feature	202407712	202407751	.	.	.	Name=9737995
chr6	.	BED_feature	32515526	32515556	.	.	.	Name=10982343
chr15	.	BED_feature	88159424	88159454	.	.	.	Name=9786929
chr11	.	BED_feature	63824993	63825022	.	.	.	Name=16024613
chr11	.	BED_feature	63829032	63829062	.	.	.	Name=16024613
chr21	.	BED_feature	42660038	42660066	.	.	.	Name=16024613
chr10	.	BED_feature	75338940	75339417	.	.	.	Name=9482740
chr11	.	BED_feature	5255942	5256828	.	.	.	Name=6897566
chr20	.	BED_feature	42708281	42708453	.	.	.	Name=1508212
chr2	.	BED_feature	21123157	21123191	.	.	.	Name=1939218
chr20	.	BED_feature	47696918	47696945	.	.	.	Name=15263012
chr6	.	BED_feature	12398431	12398463	.	.	.	Name=8833653
chr7	.	BED_feature	5534742	5534772	.	.	.	Name=15217903
chr22	.	BED_feature	14635980	14636009	.	.	.	Name=15217903
chr2	.	BED_feature	130548918	130548947	.	.	.	Name=15217903
chr2	.	BED_feature	130937490	130937519	.	.	.	Name=15217903
chr2	.	BED_feature	131131260	131131289	.	.	.	Name=15217903
chr2	.	BED_feature	131738066	131738095	.	.	.	Name=15217903
chr15	.	BED_feature	42069177	42069206	.	.	.	Name=15217903
chr14	.	BED_feature	18655265	18655294	.	.	.	Name=15217903
chr14	.	BED_feature	19058342	19058371	.	.	.	Name=15217903
chr11	.	BED_feature	18024443	18024482	.	.	.	Name=9645961
chr14	.	BED_feature	74814930	74814993	.	.	.	Name=7588632
chr16	.	BED_feature	31178724	31178757	.	.	.	Name=9295357
chr1	.	BED_feature	151805760	151805864	.	.	.	Name=9481475
chr12	.	BED_feature	4253266	4253295	.	.	.	Name=11719506
chr11	.	BED_feature	123106707	123106844	.	.	.	Name=12611910
chr2	.	BED_feature	217268557	217268956	.	.	.	Name=11973331
chr17	.	BED_feature	59307442	59307479	.	.	.	Name=14673137
chr17	.	BED_feature	59315190	59315228	.	.	.	Name=14673137
chr17	.	BED_feature	59329989	59330029	.	.	.	Name=14673137
chr17	.	BED_feature	59344719	59344758	.	.	.	Name=14673137
chr17	.	BED_feature	59377580	59378017	.	.	.	Name=14673137
chr17	.	BED_feature	45634046	45634202	.	.	.	Name=7590335
chr14	.	BED_feature	22947835	22947866	.	.	.	Name=8416951
chr17	.	BED_feature	40349936	40349985	.	.	.	Name=1918004
chr4	.	BED_feature	74825038	74825076	.	.	.	Name=2250017
chr12	.	BED_feature	52060150	52060190	.	.	.	Name=12513689
chr11	.	BED_feature	46696388	46696487	.	.	.	Name=1918008
chr14	.	BED_feature	93924742	93924782	.	.	.	Name=1918008
chr12	.	BED_feature	51476290	51476355	.	.	.	Name=7525574
chr6	.	BED_feature	32515513	32515556	.	.	.	Name=2016543
chr8	.	BED_feature	56954441	56955182	.	.	.	Name=1508184
chr6	.	BED_feature	27899786	27899820	.	.	.	Name=8336726
chr6	.	BED_feature	27907346	27907380	.	.	.	Name=8336726
chr9	.	BED_feature	21068001	21068044	.	.	.	Name=1898993
chr14	.	BED_feature	22095176	22095205	.	.	.	Name=8196665
chr7	.	BED_feature	5534742	5534772	.	.	.	Name=16339564
chr22	.	BED_feature	14635980	14636009	.	.	.	Name=16339564
chr2	.	BED_feature	130548918	130548947	.	.	.	Name=16339564
chr2	.	BED_feature	130937490	130937519	.	.	.	Name=16339564
chr2	.	BED_feature	131131260	131131289	.	.	.	Name=16339564
chr2	.	BED_feature	131738066	131738095	.	.	.	Name=16339564
chr15	.	BED_feature	42069177	42069206	.	.	.	Name=16339564
chr14	.	BED_feature	18655265	18655294	.	.	.	Name=16339564
chr14	.	BED_feature	19058342	19058371	.	.	.	Name=16339564
chr5	.	BED_feature	132037276	132037307	.	.	.	Name=1541828
chr17	.	BED_feature	37121995	37122111	.	.	.	Name=2187875
chr17	.	BED_feature	45634910	45635219	.	.	.	Name=8175678
chr1	.	BED_feature	938617	938651	.	.	.	Name=7518927
chr1	.	BED_feature	89303582	89303611	.	.	.	Name=7518927
chr1	.	BED_feature	89645725	89645754	.	.	.	Name=7518927
chr1	.	BED_feature	120737547	120737587	.	.	.	Name=7518927
chr1	.	BED_feature	147635798	147635838	.	.	.	Name=7518927
chr1	.	BED_feature	148020754	148020792	.	.	.	Name=7518927
chr14	.	BED_feature	74814956	74814988	.	.	.	Name=8756667
chr1	.	BED_feature	119759219	119759250	.	.	.	Name=9065466
chr4	.	BED_feature	89115428	89115840	.	.	.	Name=15479859
chr12	.	BED_feature	6513464	6513878	.	.	.	Name=2164673
chr4	.	BED_feature	72078087	72078236	.	.	.	Name=14514691
chr11	.	BED_feature	5247785	5248022	.	.	.	Name=2017165
chr17	.	BED_feature	38306150	38306188	.	.	.	Name=14597389
chr17	.	BED_feature	59327756	59327785	.	.	.	Name=8294429
chr2	.	BED_feature	210888129	210888286	.	.	.	Name=3405213
chrX	.	BED_feature	47327470	47327515	.	.	.	Name=11032844
chr12	.	BED_feature	46537652	46537683	.	.	.	Name=15456860
chr12	.	BED_feature	46559132	46559163	.	.	.	Name=15456860
chrX	.	BED_feature	47381398	47381456	.	.	.	Name=8386592
chr6	.	BED_feature	18472237	18473222	.	.	.	Name=8861962
chr5	.	BED_feature	98043412	98043638	.	.	.	Name=8861962
chr2	.	BED_feature	118293736	118293797	.	.	.	Name=8861962
chr2	.	BED_feature	118295288	118295330	.	.	.	Name=8861962
chr2	.	BED_feature	118299493	118299589	.	.	.	Name=8861962
chr2	.	BED_feature	118303369	118303415	.	.	.	Name=8861962
chr11	.	BED_feature	129670571	129670813	.	.	.	Name=8861962
chr10	.	BED_feature	92803203	92804189	.	.	.	Name=8861962
chr15	.	BED_feature	57951591	57952578	.	.	.	Name=8861962
chr14	.	BED_feature	68620264	68621288	.	.	.	Name=8861962
chr17	.	BED_feature	4795692	4795723	.	.	.	Name=7565752
chr11	.	BED_feature	2139123	2139152	.	.	.	Name=12368292
chr5	.	BED_feature	131854464	131854496	.	.	.	Name=9368052
chr17	.	BED_feature	7531792	7531822	.	.	.	Name=9368052
chr1	.	BED_feature	94780075	94780113	.	.	.	Name=9867853
chr10	.	BED_feature	6281228	6281257	.	.	.	Name=15466858
chr10	.	BED_feature	6283879	6283906	.	.	.	Name=15466858
chr12	.	BED_feature	20854815	20854844	.	.	.	Name=12055601
chr1	.	BED_feature	3639476	3639508	.	.	.	Name=12080043
chr11	.	BED_feature	5258554	5258587	.	.	.	Name=7937919
chr15	.	BED_feature	32875014	32875470	.	.	.	Name=2796988
chr11	.	BED_feature	5202390	5202423	.	.	.	Name=1946439
chr22	.	BED_feature	37970961	37971036	.	.	.	Name=8662647
chr4	.	BED_feature	74953830	74954108	.	.	.	Name=7479086
chr4	.	BED_feature	75028916	75029081	.	.	.	Name=7479086
chr4	.	BED_feature	75123137	75123400	.	.	.	Name=7479086
chr4	.	BED_feature	75183646	75183902	.	.	.	Name=7479086
chr1	.	BED_feature	205186280	205187034	.	.	.	Name=9182878
chr2	.	BED_feature	8739419	8739559	.	.	.	Name=14761970
chr15	.	BED_feature	48345224	48345254	.	.	.	Name=10409643
chr19	.	BED_feature	46551982	46552060	.	.	.	Name=11053476
chr15	.	BED_feature	48345250	48345309	.	.	.	Name=16357063
chr12	.	BED_feature	48630223	48630839	.	.	.	Name=9277587
chr4	.	BED_feature	123597346	123597384	.	.	.	Name=7517940
chr14	.	BED_feature	22095240	22095269	.	.	.	Name=7517940
chr5	.	BED_feature	142795002	142795489	.	.	.	Name=15044598
chr10	.	BED_feature	8137503	8137861	.	.	.	Name=1871134
chr10	.	BED_feature	8140274	8140733	.	.	.	Name=1871134
chr10	.	BED_feature	8146028	8146107	.	.	.	Name=1871134
chr10	.	BED_feature	8151499	8151561	.	.	.	Name=1871134
chr10	.	BED_feature	8155749	8155994	.	.	.	Name=1871134
chr3	.	BED_feature	129682556	129683405	.	.	.	Name=1871134
chr14	.	BED_feature	21999513	21999547	.	.	.	Name=1871134
chr14	.	BED_feature	22095234	22095269	.	.	.	Name=1871134
chr7	.	BED_feature	107318887	107318916	.	.	.	Name=1332063
chr7	.	BED_feature	73080031	73080095	.	.	.	Name=10429948
chr6	.	BED_feature	152167452	152167479	.	.	.	Name=15367686
chr13	.	BED_feature	71394397	71394424	.	.	.	Name=4039788
chr17	.	BED_feature	31455515	31457004	.	.	.	Name=1894635
chr17	.	BED_feature	31562760	31564270	.	.	.	Name=1894635
chr17	.	BED_feature	31664326	31665836	.	.	.	Name=1894635
chr17_random	.	BED_feature	1242289	1243799	.	.	.	Name=1894635
chr11	.	BED_feature	56914780	56914815	.	.	.	Name=10438731
chr2	.	BED_feature	182029788	182029822	.	.	.	Name=8195215
chr10	.	BED_feature	6148031	6148063	.	.	.	Name=10594041
chr6	.	BED_feature	32515523	32515566	.	.	.	Name=1709740
chr6	.	BED_feature	33149492	33149520	.	.	.	Name=1709740
chr1	.	BED_feature	27113298	27113401	.	.	.	Name=14627819
chr19	.	BED_feature	47724402	47724778	.	.	.	Name=8910434
chr5	.	BED_feature	137695410	137695439	.	.	.	Name=9396797
chr4	.	BED_feature	74921136	74922824	.	.	.	Name=7929219
chr4	.	BED_feature	75081444	75083546	.	.	.	Name=7929219
chr14	.	BED_feature	74814953	74814992	.	.	.	Name=1945851
chr3	.	BED_feature	46370269	46370476	.	.	.	Name=9988701
chr3_random	.	BED_feature	648541	648748	.	.	.	Name=9988701
chr19	.	BED_feature	44920682	44920916	.	.	.	Name=8400237
chr6	.	BED_feature	31651257	31651286	.	.	.	Name=8376940
chrX	.	BED_feature	114159734	114159767	.	.	.	Name=12816724
chr8	.	BED_feature	128817590	128817629	.	.	.	Name=2524830
chr5	.	BED_feature	43349215	43349642	.	.	.	Name=9604010
chr8	.	BED_feature	11697453	11697753	.	.	.	Name=9604010
chr10	.	BED_feature	90740303	90740383	.	.	.	Name=10022897
chr5	.	BED_feature	137828634	137828672	.	.	.	Name=10806199
chr14	.	BED_feature	101841354	101841385	.	.	.	Name=15327990
chr10	.	BED_feature	44201421	44201453	.	.	.	Name=15808852
chr11	.	BED_feature	14950631	14950660	.	.	.	Name=8816445
chr9	.	BED_feature	21067979	21068014	.	.	.	Name=2536920
chrX	.	BED_feature	37523962	37524023	.	.	.	Name=9801155
chr16	.	BED_feature	4247189	4247551	.	.	.	Name=7933101
chr19	.	BED_feature	34993943	34994211	.	.	.	Name=11919196
chr2	.	BED_feature	119580526	119580552	.	.	.	Name=8790425
chr15	.	BED_feature	71426297	71426323	.	.	.	Name=8790425
chr4	.	BED_feature	68303209	68303255	.	.	.	Name=12538612
chr4	.	BED_feature	68304322	68304355	.	.	.	Name=12538612
chr5	.	BED_feature	131854472	131854502	.	.	.	Name=8306959
chrX	.	BED_feature	47394500	47394719	.	.	.	Name=9880555
chr2	.	BED_feature	104839655	104839708	.	.	.	Name=1979677
chr1	.	BED_feature	38283896	38284447	.	.	.	Name=1979677
chr19	.	BED_feature	11061107	11061136	.	.	.	Name=12235180
chr2	.	BED_feature	201806432	201806506	.	.	.	Name=12748179
chr2	.	BED_feature	234318981	234319013	.	.	.	Name=12566446
chr2	.	BED_feature	234330339	234330368	.	.	.	Name=12566446
chr19	.	BED_feature	46312000	46312030	.	.	.	Name=15860659
chr6	.	BED_feature	31651200	31651239	.	.	.	Name=8552071
chr4	.	BED_feature	68304322	68304356	.	.	.	Name=10772899
chr16	.	BED_feature	31273885	31274003	.	.	.	Name=8649405
chr14	.	BED_feature	79747956	79747985	.	.	.	Name=10614643
chr5	.	BED_feature	131437180	131437349	.	.	.	Name=2838738
chr11	.	BED_feature	5258554	5258587	.	.	.	Name=9195958
chr5	.	BED_feature	131907200	131907240	.	.	.	Name=9195954
chr4	.	BED_feature	123597348	123597383	.	.	.	Name=9195954
chr5	.	BED_feature	112101286	112101326	.	.	.	Name=16150893
chr2	.	BED_feature	127768230	127768259	.	.	.	Name=1741247
chr10	.	BED_feature	17310525	17310564	.	.	.	Name=2922288
chr19	.	BED_feature	3559878	3559949	.	.	.	Name=8702673
chr19	.	BED_feature	2200272	2200331	.	.	.	Name=10993829
chr11	.	BED_feature	5227695	5227882	.	.	.	Name=7684493
chr11	.	BED_feature	5232619	5232806	.	.	.	Name=7684493
chr11	.	BED_feature	102250958	102251015	.	.	.	Name=11444842
chr10	.	BED_feature	31648170	31648227	.	.	.	Name=8138542
chr10	.	BED_feature	31790067	31790113	.	.	.	Name=8138542
chr10	.	BED_feature	31839606	31839721	.	.	.	Name=8138542
chr10	.	BED_feature	31849360	31850420	.	.	.	Name=8138542
chr10	.	BED_feature	31855840	31855881	.	.	.	Name=8138542
chr1	.	BED_feature	116717290	116717322	.	.	.	Name=8138542
chr21	.	BED_feature	43659943	43660006	.	.	.	Name=8138542
chr6	.	BED_feature	37244968	37244997	.	.	.	Name=10068671
chr10	.	BED_feature	6148028	6148065	.	.	.	Name=10068671
chr10	.	BED_feature	6144520	6144547	.	.	.	Name=2497520
chr7	.	BED_feature	100156091	100156279	.	.	.	Name=2387842
chr7	.	BED_feature	142216839	142216875	.	.	.	Name=1409722
chr18	.	BED_feature	58946947	58946974	.	.	.	Name=12086670
chr17	.	BED_feature	7474037	7474067	.	.	.	Name=9852068
chr20	.	BED_feature	31737399	31739058	.	.	.	Name=7958836
chr8	.	BED_feature	59573683	59574907	.	.	.	Name=10869351
chrX	.	BED_feature	37524132	37524171	.	.	.	Name=10869351
chr6	.	BED_feature	32920139	32920168	.	.	.	Name=9632673
chr9	.	BED_feature	21068005	21068033	.	.	.	Name=12077266
chr6	.	BED_feature	32114039	32114072	.	.	.	Name=2162843
chr17	.	BED_feature	29603572	29604369	.	.	.	Name=8051410
chr17	.	BED_feature	29606271	29606521	.	.	.	Name=8051410
chr12	.	BED_feature	6513784	6513814	.	.	.	Name=11955624
chr1	.	BED_feature	167969973	167970010	.	.	.	Name=10964678
chr11	.	BED_feature	67107757	67107830	.	.	.	Name=8557630
chr7	.	BED_feature	45891667	45891703	.	.	.	Name=8776721
chr6	.	BED_feature	87861615	87861646	.	.	.	Name=12527202
chr5	.	BED_feature	153837898	153838113	.	.	.	Name=12527202
chr12	.	BED_feature	52091276	52091305	.	.	.	Name=15955096
chr3	.	BED_feature	132096090	132096297	.	.	.	Name=15955096
chr3	.	BED_feature	132155383	132155411	.	.	.	Name=15955096
chr12	.	BED_feature	66839961	66839994	.	.	.	Name=8228802
chr14	.	BED_feature	22095221	22095259	.	.	.	Name=2388624
chr6	.	BED_feature	22405283	22405315	.	.	.	Name=2388622
chr6	.	BED_feature	22406505	22407281	.	.	.	Name=2388622
chr10	.	BED_feature	90739751	90739790	.	.	.	Name=10575005
chr6	.	BED_feature	12398423	12398453	.	.	.	Name=2388628
chr6	.	BED_feature	43844937	43844975	.	.	.	Name=11056166
chr6	.	BED_feature	153112338	153112383	.	.	.	Name=11259431
chr14	.	BED_feature	21999393	21999642	.	.	.	Name=2156339
chr4	.	BED_feature	55218756	55218801	.	.	.	Name=9834219
chr11	.	BED_feature	117692799	117692831	.	.	.	Name=9622621
chr4	.	BED_feature	111761804	111761837	.	.	.	Name=9685346
chr11	.	BED_feature	5225334	5225684	.	.	.	Name=2050690
chr6	.	BED_feature	87861522	87861558	.	.	.	Name=12177069
chr14	.	BED_feature	21999515	21999544	.	.	.	Name=10767553
chr9	.	BED_feature	132310020	132310204	.	.	.	Name=2005889
chr1	.	BED_feature	202432235	202432264	.	.	.	Name=16260418
chr19	.	BED_feature	46551727	46551753	.	.	.	Name=8702877
chr6	.	BED_feature	32713076	32713109	.	.	.	Name=8530481
chr6	.	BED_feature	32817061	32817097	.	.	.	Name=8530481
chr11	.	BED_feature	118463821	118463849	.	.	.	Name=9168923
chr3	.	BED_feature	99795250	99795281	.	.	.	Name=9168923
chr5	.	BED_feature	131437290	131437343	.	.	.	Name=7636192
chr4	.	BED_feature	123597348	123597383	.	.	.	Name=7636192
chr19	.	BED_feature	523493	523522	.	.	.	Name=11814679
chr3	.	BED_feature	30622823	30623077	.	.	.	Name=11205746
chr5	.	BED_feature	132037329	132037541	.	.	.	Name=11687571
chr22	.	BED_feature	37970955	37971002	.	.	.	Name=9300179
chr7	.	BED_feature	142216685	142216868	.	.	.	Name=2144610
chr14	.	BED_feature	22095177	22095210	.	.	.	Name=2144610
chr7	.	BED_feature	44071655	44071920	.	.	.	Name=1328854
chr16	.	BED_feature	30391086	30391720	.	.	.	Name=8097887
chr19	.	BED_feature	10242733	10242764	.	.	.	Name=7972116
chr7	.	BED_feature	5534743	5534772	.	.	.	Name=11359804
chr22	.	BED_feature	14635980	14636009	.	.	.	Name=11359804
chr2	.	BED_feature	130548918	130548947	.	.	.	Name=11359804
chr2	.	BED_feature	130937490	130937519	.	.	.	Name=11359804
chr2	.	BED_feature	131131260	131131289	.	.	.	Name=11359804
chr2	.	BED_feature	131738066	131738095	.	.	.	Name=11359804
chr15	.	BED_feature	42069177	42069206	.	.	.	Name=11359804
chr14	.	BED_feature	18655265	18655294	.	.	.	Name=11359804
chr14	.	BED_feature	19058342	19058371	.	.	.	Name=11359804
chr7	.	BED_feature	107997469	107997500	.	.	.	Name=15882996
chr5	.	BED_feature	139706798	139706829	.	.	.	Name=9360990
chr7	.	BED_feature	5533904	5533935	.	.	.	Name=14623878
chr5	.	BED_feature	79631252	79631283	.	.	.	Name=14623878
chr3	.	BED_feature	12087833	12087862	.	.	.	Name=14623878
chr1	.	BED_feature	103914789	103914818	.	.	.	Name=14623878
chr8	.	BED_feature	23016741	23016771	.	.	.	Name=14623878
chr8	.	BED_feature	23105153	23105183	.	.	.	Name=14623878
chr17	.	BED_feature	77092312	77092341	.	.	.	Name=14623878
chr5	.	BED_feature	132037329	132037543	.	.	.	Name=9845517
chr11	.	BED_feature	5205126	5205155	.	.	.	Name=2587218
chr19	.	BED_feature	803197	803226	.	.	.	Name=9689920
chr22_random	.	BED_feature	21342	21371	.	.	.	Name=1900840
chr11	.	BED_feature	116205670	116205699	.	.	.	Name=1900840
chr4	.	BED_feature	74488730	74488764	.	.	.	Name=1900840
chr2	.	BED_feature	21120497	21120528	.	.	.	Name=1900840
chr14	.	BED_feature	93924785	93924824	.	.	.	Name=1900840
chr20	.	BED_feature	44771565	44771612	.	.	.	Name=16051383
chr7	.	BED_feature	87068172	87068216	.	.	.	Name=11350951
chr15	.	BED_feature	72805409	72805921	.	.	.	Name=8382688
chr10	.	BED_feature	6144638	6144674	.	.	.	Name=9417809
chr6	.	BED_feature	31650995	31651095	.	.	.	Name=9293772
chr3	.	BED_feature	129682403	129682467	.	.	.	Name=1370462
chr3	.	BED_feature	129687329	129687456	.	.	.	Name=1370462
chr10	.	BED_feature	5228100	5228140	.	.	.	Name=12220531
chr17	.	BED_feature	10501488	10501527	.	.	.	Name=11971910
chr17	.	BED_feature	31441743	31441775	.	.	.	Name=8474441
chr17	.	BED_feature	31548413	31548445	.	.	.	Name=8474441
chr17	.	BED_feature	31649987	31650019	.	.	.	Name=8474441
chr17_random	.	BED_feature	1227961	1227993	.	.	.	Name=8474441
chr17_random	.	BED_feature	510637	510705	.	.	.	Name=3601664
chr17_random	.	BED_feature	512129	512197	.	.	.	Name=3601664
chr17_random	.	BED_feature	514842	514910	.	.	.	Name=3601664
chr17_random	.	BED_feature	519731	519799	.	.	.	Name=3601664
chr17_random	.	BED_feature	525879	525947	.	.	.	Name=3601664
chr17_random	.	BED_feature	555820	555888	.	.	.	Name=3601664
chr17_random	.	BED_feature	2608038	2608106	.	.	.	Name=3601664
chr11	.	BED_feature	2139132	2139351	.	.	.	Name=2186040
chr6	.	BED_feature	31891226	31891261	.	.	.	Name=2824993
chr6	.	BED_feature	31903422	31903455	.	.	.	Name=2824993
chr19	.	BED_feature	49838999	49839103	.	.	.	Name=9880562
chr2	.	BED_feature	219526622	219526659	.	.	.	Name=6091127
chr2	.	BED_feature	219991954	219992007	.	.	.	Name=6091127
chr2	.	BED_feature	219993216	219994527	.	.	.	Name=6091127
chr2	.	BED_feature	219998627	219999624	.	.	.	Name=6091127
chr9	.	BED_feature	101108426	101108465	.	.	.	Name=6091127
chrX	.	BED_feature	45376725	45376793	.	.	.	Name=6091127
chr12	.	BED_feature	47977237	47977628	.	.	.	Name=6091127
chr12	.	BED_feature	50925646	50925684	.	.	.	Name=6091127
chr12	.	BED_feature	51108312	51108364	.	.	.	Name=6091127
chr12	.	BED_feature	51127834	51127915	.	.	.	Name=6091127
chr12	.	BED_feature	51149726	51149807	.	.	.	Name=6091127
chr12	.	BED_feature	51168384	51168465	.	.	.	Name=6091127
chr12	.	BED_feature	51196694	51196745	.	.	.	Name=6091127
chr12	.	BED_feature	51248225	51248258	.	.	.	Name=6091127
chr12	.	BED_feature	51267687	51267745	.	.	.	Name=6091127
chr12	.	BED_feature	51290671	51290703	.	.	.	Name=6091127
chr12	.	BED_feature	51326796	51326855	.	.	.	Name=6091127
chr12	.	BED_feature	51372474	51372523	.	.	.	Name=6091127
chr12	.	BED_feature	51451055	51451107	.	.	.	Name=6091127
chr12	.	BED_feature	51471262	51471324	.	.	.	Name=6091127
chr12	.	BED_feature	51487700	51487760	.	.	.	Name=6091127
chr12	.	BED_feature	51503069	51503134	.	.	.	Name=6091127
chr12	.	BED_feature	51519820	51519866	.	.	.	Name=6091127
chr12	.	BED_feature	51578729	51578767	.	.	.	Name=6091127
chr10	.	BED_feature	8595900	8595938	.	.	.	Name=6091127
chr10	.	BED_feature	17317280	17317392	.	.	.	Name=6091127
chr17	.	BED_feature	40344129	40344242	.	.	.	Name=6091127
chr15	.	BED_feature	75058646	75058683	.	.	.	Name=6091127
chr20	.	BED_feature	43316657	43316700	.	.	.	Name=10498899
chr1	.	BED_feature	938621	938650	.	.	.	Name=12055236
chr13	.	BED_feature	29938059	29938152	.	.	.	Name=11245470
chr19	.	BED_feature	3413760	3413788	.	.	.	Name=11245470
chr15	.	BED_feature	49418596	49420743	.	.	.	Name=8132535
chr9	.	BED_feature	106730621	106730953	.	.	.	Name=15528481
chr15	.	BED_feature	32834227	32834262	.	.	.	Name=14565956
chr17	.	BED_feature	59303128	59303178	.	.	.	Name=8370519
chr17	.	BED_feature	59311326	59311376	.	.	.	Name=8370519
chr17	.	BED_feature	59326029	59326078	.	.	.	Name=8370519
chr17	.	BED_feature	59340721	59340767	.	.	.	Name=8370519
chr17	.	BED_feature	59348314	59348364	.	.	.	Name=8370519
chr14	.	BED_feature	21999514	21999541	.	.	.	Name=10359663
chr3	.	BED_feature	197023273	197023300	.	.	.	Name=11418607
chr11	.	BED_feature	2136190	2136325	.	.	.	Name=9013771
chr4	.	BED_feature	74825038	74825076	.	.	.	Name=8035808
chr3	.	BED_feature	124822086	124822163	.	.	.	Name=9142867
chr2	.	BED_feature	233880783	233881067	.	.	.	Name=8321239
chr19	.	BED_feature	15869836	15869863	.	.	.	Name=10860554
chr7	.	BED_feature	45894488	45894516	.	.	.	Name=12011061
chr19	.	BED_feature	46551009	46551037	.	.	.	Name=12011061
chr1	.	BED_feature	216584695	216585098	.	.	.	Name=12011061
chr1	.	BED_feature	216586733	216586761	.	.	.	Name=12011061
chr22	.	BED_feature	40856851	40856894	.	.	.	Name=8810289
chr22	.	BED_feature	40870523	40870566	.	.	.	Name=8810289
chr22	.	BED_feature	40881065	40881104	.	.	.	Name=8810289
chr1	.	BED_feature	3597000	3597060	.	.	.	Name=11909952
chr1	.	BED_feature	938624	938655	.	.	.	Name=3476954
chr2	.	BED_feature	86867000	86867277	.	.	.	Name=8413295
chr11	.	BED_feature	69165072	69165101	.	.	.	Name=8196642
chr3	.	BED_feature	25444698	25444726	.	.	.	Name=1657595
chr1	.	BED_feature	98159130	98159155	.	.	.	Name=11072080
chrX	.	BED_feature	48771251	48772496	.	.	.	Name=2338243
chrX	.	BED_feature	48774415	48774496	.	.	.	Name=2338243
chrX	.	BED_feature	48778664	48778710	.	.	.	Name=2338243
chrX	.	BED_feature	48782532	48782585	.	.	.	Name=2338243
chr11	.	BED_feature	118463735	118463763	.	.	.	Name=2211589
chr2	.	BED_feature	127129934	127129963	.	.	.	Name=2211589
chr7	.	BED_feature	5533905	5534773	.	.	.	Name=14993214
chr5	.	BED_feature	79631253	79631282	.	.	.	Name=14993214
chr5	.	BED_feature	131854472	131854502	.	.	.	Name=14993214
chr3	.	BED_feature	12087834	12087862	.	.	.	Name=14993214
chr2	.	BED_feature	130548918	130548948	.	.	.	Name=14993214
chr2	.	BED_feature	130937490	130937520	.	.	.	Name=14993214
chr2	.	BED_feature	131131259	131131289	.	.	.	Name=14993214
chr2	.	BED_feature	131738065	131738095	.	.	.	Name=14993214
chr2	.	BED_feature	201806408	201806452	.	.	.	Name=14993214
chr1	.	BED_feature	103914790	103914818	.	.	.	Name=14993214
chr22	.	BED_feature	14635980	14636010	.	.	.	Name=14993214
chr15	.	BED_feature	42069177	42069206	.	.	.	Name=14993214
chr14	.	BED_feature	18655264	18655294	.	.	.	Name=14993214
chr14	.	BED_feature	19058342	19058372	.	.	.	Name=14993214
chr17	.	BED_feature	77092312	77092340	.	.	.	Name=14993214
chr8	.	BED_feature	128817489	128817516	.	.	.	Name=7555706
chr11	.	BED_feature	100504991	100505108	.	.	.	Name=14684847
chr19	.	BED_feature	50100732	50100772	.	.	.	Name=11038359
chr11	.	BED_feature	73371479	73371508	.	.	.	Name=10558866
chr4	.	BED_feature	39205935	39206031	.	.	.	Name=16002992
chr9	.	BED_feature	130911610	130911651	.	.	.	Name=10585862
chr9	.	BED_feature	130913433	130913464	.	.	.	Name=10585862
chr22	.	BED_feature	21962547	21962884	.	.	.	Name=8144670
chr21	.	BED_feature	42660038	42660066	.	.	.	Name=14966289
chr12	.	BED_feature	52653728	52653757	.	.	.	Name=9582375
chr4	.	BED_feature	123597152	123597181	.	.	.	Name=9016343
chr11	.	BED_feature	71632649	71632702	.	.	.	Name=11549713
chr9	.	BED_feature	127043488	127043556	.	.	.	Name=1480470
chr10	.	BED_feature	6285227	6285271	.	.	.	Name=10673355
chrX	.	BED_feature	47326670	47326715	.	.	.	Name=11259407
chr8	.	BED_feature	128816013	128816041	.	.	.	Name=8649373
chr8	.	BED_feature	128817629	128817676	.	.	.	Name=8649373
chr20	.	BED_feature	42708338	42708374	.	.	.	Name=9016677
chr7	.	BED_feature	5533943	5534628	.	.	.	Name=15604281
chr6	.	BED_feature	89042358	89042389	.	.	.	Name=15604281
chr5	.	BED_feature	77117520	77117549	.	.	.	Name=15604281
chr3	.	BED_feature	177178013	177178044	.	.	.	Name=15604281
chr2	.	BED_feature	130548327	130548356	.	.	.	Name=15604281
chr2	.	BED_feature	130936899	130936928	.	.	.	Name=15604281
chr2	.	BED_feature	131131851	131131880	.	.	.	Name=15604281
chr2	.	BED_feature	131738657	131738686	.	.	.	Name=15604281
chr2	.	BED_feature	132101240	132101269	.	.	.	Name=15604281
chr1	.	BED_feature	27524805	27524836	.	.	.	Name=15604281
chr9	.	BED_feature	6825509	6825538	.	.	.	Name=15604281
chr11	.	BED_feature	1780733	1780764	.	.	.	Name=15604281
chr22	.	BED_feature	14635389	14635418	.	.	.	Name=15604281
chr14	.	BED_feature	18655856	18655885	.	.	.	Name=15604281
chr14	.	BED_feature	19057751	19057780	.	.	.	Name=15604281
chr18	.	BED_feature	58261273	58261304	.	.	.	Name=15604281
chr14	.	BED_feature	105142548	105142618	.	.	.	Name=8515067
chr14	.	BED_feature	105261334	105261401	.	.	.	Name=8515067
chr14	.	BED_feature	21999512	21999542	.	.	.	Name=2050118
chr6	.	BED_feature	32515518	32515589	.	.	.	Name=9378978
chr7	.	BED_feature	139175315	139175364	.	.	.	Name=11956185
chr7	.	BED_feature	55054192	55054238	.	.	.	Name=3393529
chr5	.	BED_feature	137828927	137828975	.	.	.	Name=8065330
chr7	.	BED_feature	100556401	100556570	.	.	.	Name=12738229
chr8	.	BED_feature	128817556	128817620	.	.	.	Name=2721961
chr12	.	BED_feature	90097177	90098190	.	.	.	Name=8276854
chr7	.	BED_feature	55054207	55054237	.	.	.	Name=12062800
chr8	.	BED_feature	28230633	28230749	.	.	.	Name=12062800
chr19	.	BED_feature	2224335	2224407	.	.	.	Name=9501877
chr1	.	BED_feature	68688177	68692149	.	.	.	Name=9501877
chr9	.	BED_feature	21068006	21068035	.	.	.	Name=15664995
chr4	.	BED_feature	123597330	123597379	.	.	.	Name=7673240
chr1	.	BED_feature	154478087	154478119	.	.	.	Name=10077002
chr1	.	BED_feature	148070713	148070740	.	.	.	Name=3029724
chr1	.	BED_feature	148099454	148099481	.	.	.	Name=3029724
chr3	.	BED_feature	166279009	166279036	.	.	.	Name=11283019
chr12	.	BED_feature	54645490	54645518	.	.	.	Name=12819038
chr7	.	BED_feature	5534470	5534499	.	.	.	Name=10545204
chr17	.	BED_feature	37122024	37122063	.	.	.	Name=2566164
chr4	.	BED_feature	123597213	123597383	.	.	.	Name=1545787
chr14	.	BED_feature	22095240	22095319	.	.	.	Name=1545787
chr2	.	BED_feature	127892038	127892602	.	.	.	Name=7592627
chr1	.	BED_feature	120737548	120737589	.	.	.	Name=8483949
chr1	.	BED_feature	147635796	147635837	.	.	.	Name=8483949
chr1	.	BED_feature	148020752	148020792	.	.	.	Name=8483949
chr6	.	BED_feature	31650909	31650946	.	.	.	Name=10369255
chr11	.	BED_feature	5227823	5227863	.	.	.	Name=2336386
chr11	.	BED_feature	5232747	5232787	.	.	.	Name=2336386
chr4	.	BED_feature	109130502	109130558	.	.	.	Name=9716664
chr4	.	BED_feature	109155034	109155063	.	.	.	Name=9716664
chr4	.	BED_feature	109160212	109160247	.	.	.	Name=9716664
chr4	.	BED_feature	109164122	109164158	.	.	.	Name=9716664
chr4	.	BED_feature	109174855	109175558	.	.	.	Name=9716664
chr10	.	BED_feature	17310516	17310544	.	.	.	Name=7986748
chr17	.	BED_feature	59304827	59305028	.	.	.	Name=3595566
chr17	.	BED_feature	59313056	59313213	.	.	.	Name=3595566
chr17	.	BED_feature	59327724	59327925	.	.	.	Name=3595566
chr17	.	BED_feature	59342381	59342606	.	.	.	Name=3595566
chr17	.	BED_feature	59349961	59350263	.	.	.	Name=3595566
chr16	.	BED_feature	67328705	67328733	.	.	.	Name=16617148
chr7	.	BED_feature	87068136	87068286	.	.	.	Name=8095499
chr11	.	BED_feature	2868569	2868621	.	.	.	Name=12790805
chr17	.	BED_feature	8054646	8054674	.	.	.	Name=15033491
chr19	.	BED_feature	7245593	7245654	.	.	.	Name=8376587
chr16	.	BED_feature	31273921	31273960	.	.	.	Name=9360988
chr7	.	BED_feature	26191773	26191800	.	.	.	Name=10037736
chr17	.	BED_feature	42858368	42858395	.	.	.	Name=10037736
chr4	.	BED_feature	159864009	159864049	.	.	.	Name=11525247
chr11	.	BED_feature	117692802	117692831	.	.	.	Name=8227043
chr5	.	BED_feature	137828634	137828733	.	.	.	Name=16037570
chr14	.	BED_feature	105129373	105129408	.	.	.	Name=10652350
chr14	.	BED_feature	105250344	105250379	.	.	.	Name=10652350
chr2	.	BED_feature	151922250	151922282	.	.	.	Name=8885246
chr13	.	BED_feature	27967304	27967353	.	.	.	Name=8940064
chr14	.	BED_feature	94148353	94148401	.	.	.	Name=9461605
chr1	.	BED_feature	206151285	206151338	.	.	.	Name=10572091
chr17	.	BED_feature	59300848	59300883	.	.	.	Name=8052268
chr17	.	BED_feature	59323742	59323775	.	.	.	Name=8052268
chr17	.	BED_feature	59338490	59338525	.	.	.	Name=8052268
chr2	.	BED_feature	10505925	10506001	.	.	.	Name=9570735
chr2	.	BED_feature	127892444	127892602	.	.	.	Name=9553065
chr19	.	BED_feature	46048243	46048291	.	.	.	Name=15671201
chr5	.	BED_feature	132037323	132037358	.	.	.	Name=12374808
chr11	.	BED_feature	5258548	5258578	.	.	.	Name=2123346
chr14	.	BED_feature	36059171	36059310	.	.	.	Name=10684967
chr13	.	BED_feature	31787486	31787523	.	.	.	Name=10961992
chr11	.	BED_feature	116205663	116205692	.	.	.	Name=8036173
chr22_random	.	BED_feature	21349	21378	.	.	.	Name=8036173
chr6	.	BED_feature	26195614	26195650	.	.	.	Name=15467009
chr1	.	BED_feature	205344109	205344140	.	.	.	Name=10777590
chr1	.	BED_feature	170901754	170901782	.	.	.	Name=10725705
chr6	.	BED_feature	336159	336488	.	.	.	Name=16272311
chr17	.	BED_feature	7423623	7423653	.	.	.	Name=16272311
chr19	.	BED_feature	59927684	59927724	.	.	.	Name=16818466
chr19	.	BED_feature	59941631	59941780	.	.	.	Name=16818466
chr19	.	BED_feature	59958152	59958244	.	.	.	Name=16818466
chr19	.	BED_feature	59972980	59973072	.	.	.	Name=16818466
chr19	.	BED_feature	59989484	59989576	.	.	.	Name=16818466
chr19	.	BED_feature	60019575	60019743	.	.	.	Name=16818466
chr19	.	BED_feature	60035839	60035989	.	.	.	Name=16818466
chr19	.	BED_feature	60053551	60053700	.	.	.	Name=16818466
chr19_random	.	BED_feature	150474	150514	.	.	.	Name=16818466
chr19_random	.	BED_feature	164437	164586	.	.	.	Name=16818466
chr19_random	.	BED_feature	181034	181126	.	.	.	Name=16818466
chr19_random	.	BED_feature	212604	212772	.	.	.	Name=16818466
chr19_random	.	BED_feature	229300	229392	.	.	.	Name=16818466
chr19_random	.	BED_feature	240699	240791	.	.	.	Name=16818466
chr19_random	.	BED_feature	257666	257758	.	.	.	Name=16818466
chr19_random	.	BED_feature	273965	274114	.	.	.	Name=16818466
chr19_random	.	BED_feature	290146	290295	.	.	.	Name=16818466
chr2	.	BED_feature	42441469	42441499	.	.	.	Name=9418891
chr8	.	BED_feature	110621516	110621547	.	.	.	Name=9418891
chr6	.	BED_feature	160033828	160033861	.	.	.	Name=8602839
chr5	.	BED_feature	132037485	132037518	.	.	.	Name=1532661
chr21	.	BED_feature	42660091	42660131	.	.	.	Name=10619353
chr7	.	BED_feature	143763142	143763174	.	.	.	Name=11101876
chr16	.	BED_feature	10878364	10878396	.	.	.	Name=11101876
chr6	.	BED_feature	87861616	87861644	.	.	.	Name=7690722
chr11	.	BED_feature	5247662	5248033	.	.	.	Name=7882983
chr21	.	BED_feature	45788564	45789001	.	.	.	Name=15652157
chr10	.	BED_feature	90702793	90702824	.	.	.	Name=9546431
chr2	.	BED_feature	1395339	1396616	.	.	.	Name=2306241
chr6	.	BED_feature	32515524	32515555	.	.	.	Name=15798210
chr12	.	BED_feature	28007917	28007970	.	.	.	Name=11590145
chr12	.	BED_feature	28014207	28014257	.	.	.	Name=11590145
chr11	.	BED_feature	127855336	127855387	.	.	.	Name=11590145
chrX	.	BED_feature	134545610	134545664	.	.	.	Name=11590145
chr21	.	BED_feature	39113468	39113522	.	.	.	Name=11590145
chr19	.	BED_feature	50140987	50141031	.	.	.	Name=9651383
chr19	.	BED_feature	11060976	11061028	.	.	.	Name=8969230
chr11	.	BED_feature	61474297	61474475	.	.	.	Name=14982938
chr13	.	BED_feature	27968204	27968239	.	.	.	Name=9295307
chr7	.	BED_feature	100159369	100159403	.	.	.	Name=9295307
chr6	.	BED_feature	43844940	43844973	.	.	.	Name=9295307
chr11	.	BED_feature	14950484	14950770	.	.	.	Name=1335241
chr19	.	BED_feature	5794124	5794155	.	.	.	Name=16199102
chr1	.	BED_feature	151145504	151145560	.	.	.	Name=9512462
chrX	.	BED_feature	133421461	133421557	.	.	.	Name=8524221
chr12	.	BED_feature	55326300	55326340	.	.	.	Name=9512469
chr7	.	BED_feature	148494901	148494944	.	.	.	Name=11779858
chr7	.	BED_feature	148507370	148507398	.	.	.	Name=11779858
chr6	.	BED_feature	152170741	152170769	.	.	.	Name=11779858
chr4	.	BED_feature	123597349	123597380	.	.	.	Name=7935406
chr22	.	BED_feature	20928908	20929221	.	.	.	Name=11994467
chr5	.	BED_feature	131434253	131434284	.	.	.	Name=10706706
chr4	.	BED_feature	123597156	123597265	.	.	.	Name=10706706
chr2	.	BED_feature	69467759	69469928	.	.	.	Name=15878746
chr15	.	BED_feature	72448910	72448940	.	.	.	Name=8703023
chr4	.	BED_feature	155703460	155703510	.	.	.	Name=8226773
chr11	.	BED_feature	14951376	14951415	.	.	.	Name=1738589
chr1	.	BED_feature	53434580	53434614	.	.	.	Name=12408750
chr16	.	BED_feature	29739214	29739242	.	.	.	Name=16418217
chr8	.	BED_feature	37942250	37942857	.	.	.	Name=11316759
chr6	.	BED_feature	87861602	87861689	.	.	.	Name=7685765
chr4	.	BED_feature	123597349	123597379	.	.	.	Name=9819402
chr6	.	BED_feature	31891135	31891163	.	.	.	Name=8524643
chr11	.	BED_feature	5247820	5247851	.	.	.	Name=8524643
chr7	.	BED_feature	5535954	5535982	.	.	.	Name=3185543
chr1	.	BED_feature	227636541	227636569	.	.	.	Name=3185543
chr14	.	BED_feature	74815996	74816043	.	.	.	Name=11997340
chr11	.	BED_feature	5258376	5258749	.	.	.	Name=1924329
chr14	.	BED_feature	74814951	74815009	.	.	.	Name=1833404
chr16	.	BED_feature	55553247	55553307	.	.	.	Name=8530390
chr14	.	BED_feature	22974976	22975043	.	.	.	Name=1449500
chr1	.	BED_feature	148070780	148070957	.	.	.	Name=9874597
chr1	.	BED_feature	148099237	148099414	.	.	.	Name=9874597
chr16	.	BED_feature	55199809	55199836	.	.	.	Name=2822255
chr16	.	BED_feature	29983413	29983440	.	.	.	Name=14966291
chr20	.	BED_feature	30103722	30103934	.	.	.	Name=9822652
chr12	.	BED_feature	19152056	19152167	.	.	.	Name=1516833
chr19	.	BED_feature	19117403	19119608	.	.	.	Name=1516833
chr19	.	BED_feature	19121035	19121241	.	.	.	Name=1516833
chr19	.	BED_feature	19122487	19122569	.	.	.	Name=1516833
chr19	.	BED_feature	19152495	19152573	.	.	.	Name=1516833
chr19	.	BED_feature	19154382	19154494	.	.	.	Name=1516833
chr19	.	BED_feature	19163890	19163921	.	.	.	Name=1516833
chr1	.	BED_feature	154718853	154719060	.	.	.	Name=1516833
chr1	.	BED_feature	177683437	177684327	.	.	.	Name=1516833
chr15	.	BED_feature	97956185	97956240	.	.	.	Name=1516833
chr15	.	BED_feature	97990704	97990903	.	.	.	Name=1516833
chr15	.	BED_feature	98003433	98003480	.	.	.	Name=1516833
chr15	.	BED_feature	98029055	98029292	.	.	.	Name=1516833
chr15	.	BED_feature	98032162	98032342	.	.	.	Name=1516833
chr15	.	BED_feature	98047986	98048131	.	.	.	Name=1516833
chr15	.	BED_feature	98064460	98064576	.	.	.	Name=1516833
chr15	.	BED_feature	98068361	98068488	.	.	.	Name=1516833
chr15	.	BED_feature	98070118	98071422	.	.	.	Name=1516833
chr17	.	BED_feature	59349959	59349992	.	.	.	Name=11890700
chr19	.	BED_feature	56049582	56049616	.	.	.	Name=8626436
chrX	.	BED_feature	138440553	138440581	.	.	.	Name=8626436
chr5	.	BED_feature	131437266	131437302	.	.	.	Name=3257571
chr1	.	BED_feature	151145509	151145546	.	.	.	Name=15790882
chr11	.	BED_feature	116205753	116205859	.	.	.	Name=11839757
chr22_random	.	BED_feature	21182	21288	.	.	.	Name=11839757
chr7	.	BED_feature	55054183	55054234	.	.	.	Name=2847030
chr2	.	BED_feature	210861535	210861562	.	.	.	Name=2243772
chr7	.	BED_feature	66438245	66438537	.	.	.	Name=11714687
chr5	.	BED_feature	88155359	88155501	.	.	.	Name=11714687
chr5	.	BED_feature	88235486	88235778	.	.	.	Name=11714687
chr11	.	BED_feature	5258534	5258592	.	.	.	Name=2116990
chr11	.	BED_feature	61942928	61942978	.	.	.	Name=1711673
chr2	.	BED_feature	85748895	85748950	.	.	.	Name=8065304
chr16	.	BED_feature	55259659	55259699	.	.	.	Name=1903400
chr4	.	BED_feature	122964231	122964882	.	.	.	Name=8202514
chr1	.	BED_feature	59022165	59022500	.	.	.	Name=8355696
chr11	.	BED_feature	5258551	5258586	.	.	.	Name=8355692
chr16	.	BED_feature	162863	163413	.	.	.	Name=8355692
chr16	.	BED_feature	166667	167217	.	.	.	Name=8355692
chr9	.	BED_feature	21792571	21792811	.	.	.	Name=15535799
chr1	.	BED_feature	227636733	227637755	.	.	.	Name=1318069
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=9065434
chr10	.	BED_feature	104144210	104144265	.	.	.	Name=9528780
chr3	.	BED_feature	195336540	195336569	.	.	.	Name=9528780
chr11	.	BED_feature	2139216	2139245	.	.	.	Name=1915886
chr11	.	BED_feature	118463736	118463763	.	.	.	Name=8265578
chr7	.	BED_feature	22733215	22733253	.	.	.	Name=10657660
chr17	.	BED_feature	29606346	29606384	.	.	.	Name=10657660
chr2	.	BED_feature	21119498	21119597	.	.	.	Name=1545795
chr21	.	BED_feature	45786202	45786247	.	.	.	Name=11078737
chr1	.	BED_feature	233095015	233095257	.	.	.	Name=1870965
chr6	.	BED_feature	32549435	32549462	.	.	.	Name=1903538
chr6	.	BED_feature	32665658	32665685	.	.	.	Name=1903538
chr6	.	BED_feature	32742510	32742537	.	.	.	Name=1903538
chr11	.	BED_feature	116199350	116199380	.	.	.	Name=2020548
chr2	.	BED_feature	21120501	21120538	.	.	.	Name=2020548
chr22_random	.	BED_feature	27654	27684	.	.	.	Name=2020548
chr4	.	BED_feature	123597349	123597378	.	.	.	Name=10816557
chr10	.	BED_feature	6144342	6144375	.	.	.	Name=8642278
chr17	.	BED_feature	59304620	59305041	.	.	.	Name=3018491
chr17	.	BED_feature	59312807	59313226	.	.	.	Name=3018491
chr17	.	BED_feature	59327517	59327938	.	.	.	Name=3018491
chr17	.	BED_feature	59342202	59342563	.	.	.	Name=3018491
chr17	.	BED_feature	59349782	59350202	.	.	.	Name=3018491
chr8	.	BED_feature	128818308	128818364	.	.	.	Name=10085075
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s3.bed000066400000000000000000002110321211610345200224560ustar00rootroot00000000000000chr13	12855405	12855438	8065334
chr13	13072135	13072165	8065334
chr2	172240870	172240910	12801994
chr3	88033298	88034734	1327537
chr3	131173868	131173905	8892228
chr4	129060997	129061031	11278409
chr9	44737715	44737752	11278409
chr12	113725369	113725411	8144891
chr18	61336786	61336835	9325159
chr9	57494751	57494779	1986235
chr6	5447222	5447252	12820900
chr12	86362676	86362711	2498646
chr11	96087147	96087322	1360646
chr14	53921088	53921125	8449897
chr9	49551489	49551554	11696550
chr4	134425053	134425134	8341710
chr4	134427381	134427503	8341710
chr17	43959177	43959286	8341710
chr17	44070860	44071424	8341710
chr17	44073079	44073136	8341710
chr17	44102719	44102884	8341710
chr17	44121573	44121747	8341710
chr17	44180245	44180353	8341710
chr17	44187798	44187958	8341710
chr17	44198285	44198718	8341710
chr16	92584340	92584421	8341710
chr7	46713822	46713869	2708350
chr14	15368765	15368800	2164682
chr5	137356956	137356986	9427542
chr7	28088021	28088093	7559666
chr18	82688825	82688871	1690988
chr6	70655272	70655306	10623825
chr16	29984999	29985028	10623825
chr17	33644477	33644637	1652422
chr17	33646781	33647960	1652422
chr2	27563777	27563952	1652422
chr2	27570622	27570757	1652422
chr2	27574323	27574451	1652422
chr2	27576228	27576364	1652422
chr2	27578214	27578297	1652422
chr2	27581548	27581681	1652422
chr1	169461605	169461748	1652422
chr1	169463963	169464146	1652422
chr1	169467907	169468035	1652422
chr1	169469185	169469322	1652422
chr1	169471116	169471201	1652422
chr1	169475799	169475944	1652422
chr3	88464665	88464699	10514508
chr3	88470430	88470464	10514508
chr19	54097640	54099571	7487893
chr6	41474206	41474734	2349098
chr6	29009780	29010375	8633022
chr6	29018960	29018996	8633022
chr6	29021164	29021200	8633022
chr10	80208262	80208306	10446911
chr16	23806221	23806263	1834659
chr3	37317758	37317792	8417328
chr12	77084391	77084433	9058381
chr12	77086129	77086167	9058381
chr5	91525243	91525437	1990282
chr12	113875335	113875479	3125419
chr6	145348608	145348648	2365680
chr5	21110586	21110672	2365680
chr5	41630394	41630480	2365680
chr5	83411420	83411506	2365680
chr1	16088802	16088888	2365680
chr9	31532481	31532530	2365680
chr9	109815632	109815704	2365680
chrX	33099689	33099764	2365680
chrX	148997346	148997395	2365680
chr11	29452949	29452989	2365680
chr11	46571264	46571350	2365680
chr17	32591324	32591409	2365680
chr15	59040612	59040698	2365680
chr13	12855407	12855435	2744462
chr13	13072135	13072165	2744462
chr11	76965962	76966562	1986236
chr1	173252806	173252912	1986236
chr1	173254314	173254471	1986236
chr12	113680202	113680232	9755173
chr12	113701766	113701797	9755173
chr12	57453027	57453073	9211870
chr4	94544520	94544623	1851295
chr15	82280025	82280079	2387871
chr8	75247914	75247946	10433980
chr15	98883162	98883205	1639068
chr15	9476871	9477448	2038316
chr7	99225294	99226309	12235161
chr5	104676199	104676297	9649510
chr12	86362631	86362992	9584171
chr1	163623783	163623811	10684974
chr1	163625032	163625063	10684974
chr14	67037128	67037160	11733514
chr8	109492103	109492670	1763063
chr6	52096109	52096149	10068641
chr5	89609349	89609379	9529146
chr8	42873633	42873667	16500425
chr9	43794365	43794438	1672442
chr17	33610895	33610924	1727488
chr17	34870963	34870992	1727488
chr12	104139374	104139403	1701020
chr12	104174806	104174835	1701020
chr12	104358132	104358161	1701020
chr5	91535986	91536016	1701020
chr4	62830792	62830821	1701020
chr4	62848682	62848711	1701020
chr2	167381276	167381623	1701020
chr9	78015522	78015661	2166952
chr9	78041998	78042137	2166952
chr9	78068395	78068448	2166952
chr9	78074867	78074935	2166952
chr9	78133948	78134089	2166952
chr2	167380096	167380135	15299028
chr11	44243408	44243440	12876285
chr11	78736086	78736120	12876285
chr9	50306076	50306110	12876285
chr6	91649566	91649596	15142033
chr8	71809515	71809738	11796707
chr5	16065429	16065458	12163028
chr12	113875354	113875416	1899229
chr7	31525873	31525902	12520165
chr7	32254522	32254551	12520165
chr4	84395387	84395416	12520165
chr1	146946112	146946144	12520165
chr8	43108455	43108485	12520165
chr12	5616599	5616628	12520165
chr11	33176704	33176733	12520165
chr17	61467014	61467046	12520165
chr12	116052275	116052307	1970570
chr11	70478627	70478705	2734297
chr2	62284557	62284607	10938089
chr1	64467140	64467218	7628390
chr1	75242512	75243687	8382796
chrX	20027120	20027366	1849903
chr17	89109205	89109235	11145741
chr2	147728349	147728401	9118802
chr6	34342452	34342485	11145742
chr13	52980564	52982323	12023274
chr3	88458959	88459035	7891679
chr3	88464662	88464736	7891679
chr3	88470428	88470501	7891679
chr7	79608338	79608384	14726448
chr3	89465235	89467184	7937772
chr8	78299165	78299266	7937772
chr13	13756611	13757727	7937772
chr10	26982957	26983076	7937772
chrX	8811751	8812446	7937772
chr18	76271049	76271168	7937772
chr6	42910196	42910222	3119226
chr6	68185881	68185907	3119226
chr16	3493056	3493082	3119226
chr6	70655343	70655376	3145404
chr12	113875435	113875464	3145404
chr12	114508180	114508208	3145404
chr3	113284901	113284941	8874496
chr5	115209361	115211104	2263635
chr5	115221021	115221214	2263635
chr5	115231516	115231801	2263635
chr11	83672139	83672273	2263635
chr12	86362645	86362702	2928331
chr5	146313738	146313765	7651384
chr5	146383577	146383604	7651384
chr11	95403796	95403832	7565756
chr15	78753913	78753944	9931450
chr11	53564136	53564178	9498775
chr11	94767984	94768013	2779548
chr10	66907643	66907888	12538520
chr15	76304476	76304854	9829985
chrX	79208617	79208790	11259421
chr7	45334856	45334916	15466854
chr7	120806481	120806510	15466854
chr6	71571314	71571343	15466854
chr6	78426650	78426679	15466854
chr6	123184769	123184798	15466854
chr4	105292420	105292449	15466854
chr3	39409200	39409229	15466854
chr3	41582548	41582577	15466854
chr3	122249021	122249050	15466854
chr3	122624993	122625022	15466854
chr3	138542153	138542182	15466854
chr2	51693326	51693355	15466854
chr2	83191233	83191262	15466854
chr2	129441625	129441654	15466854
chr2	166191671	166191700	15466854
chr9	96705281	96705310	15466854
chr8	4465785	4465814	15466854
chr13	64639250	64639279	15466854
chr11	6319198	6319227	15466854
chr10	57470992	57471021	15466854
chr17	37555516	37555545	15466854
chr15	25785031	25785060	15466854
chr14	28044921	28044950	15466854
chr19	28099719	28099748	15466854
chr18	34171912	34171941	15466854
chr6	115407117	115407162	9099735
chr1	135178146	135178175	9201991
chr6	70655242	70655313	2501761
chr15	74816721	74816777	9746780
chr15	74827421	74827479	9746780
chr15	74878324	74878382	9746780
chr15	74893029	74893087	9746780
chr15	74942699	74942755	9746780
chr15	74965414	74965466	9746780
chr15	74980244	74980287	9746780
chr15	75013880	75013926	9746780
chr15	75093111	75093165	9746780
chr1	136106233	136106418	1324403
chr6	142920945	142921305	11098147
chr9	57494748	57494782	3413062
chr19	37762873	37762946	10976925
chr8	97068193	97068366	2993866
chr12	114344857	114344899	2710122
chr12	116052274	116052307	2710122
chr3	37317567	37317596	1620122
chr6	40976305	40976479	3259318
chr6	40977840	40977872	3259318
chr6	40988922	40989030	3259318
chr6	40991876	40991970	3259318
chr6	41043028	41043170	3259318
chr6	41045568	41045620	3259318
chr6	41048329	41048467	3259318
chr6	41059623	41059730	3259318
chr6	41081350	41081400	3259318
chr6	41092531	41092629	3259318
chr6	41107825	41107980	3259318
chr5	143168935	143169346	12855690
chr8	126778096	126778129	12855690
chr16	37802843	37802876	12855690
chr1	163625140	163625648	12855690
chrX	147774588	147774621	12855690
chrX	147831147	147831180	12855690
chr13_random	132570	132601	1527023
chr12	77628972	77629001	10037687
chr10	79980249	79980309	11390978
chr12	86362672	86362727	10462507
chr15	78753913	78753944	10760565
chr7	46729236	46729273	11673270
chr5	104675337	104675366	7799957
chr7	70234441	70234497	15541767
chr12	86362675	86362704	9032301
chr11	98775789	98776740	1658797
chr2	38536505	38536605	9013759
chr4	28981910	28981959	16314414
chr11	53462146	53462176	9233810
chr19	6989379	6989414	12960079
chr5	91565804	91565841	2601711
chr9	71648331	71648487	1321336
chr9	71654864	71655099	1321336
chr9	71657043	71657515	1321336
chr9	71666629	71666826	1321336
chr9	71668636	71668711	1321336
chr9	71674546	71674627	1321336
chr9	71681665	71682326	1321336
chr9	71683753	71683834	1321336
chr9	71721211	71721347	1321336
chr9	71742549	71742582	1321336
chr9	71798974	71799076	1321336
chr9	71814199	71814273	1321336
chr9	71908240	71910179	1321336
chr13	30756011	30756039	10770796
chr5	28489137	28489196	8625814
chr7	4732187	4732219	15117948
chr6	133727976	133728008	15117948
chr5	143170455	143170487	15117948
chr4	103061585	103061617	15117948
chr9	38824924	38824956	15117948
chr8	47728061	47728093	15117948
chr8	126779399	126779431	15117948
chr13	81528371	81528403	15117948
chr11	120163804	120163836	15117948
chr17	63032641	63032673	15117948
chr16	64861024	64861056	15117948
chrX	47464339	47464368	15117948
chr6	70068751	70068784	2120037
chr6	70144885	70144924	2120037
chr6	70190599	70190638	2120037
chr6	70300921	70300960	2120037
chr6	70336658	70336697	2120037
chr6	70365142	70365181	2120037
chr6	70387690	70387729	2120037
chr10	20847653	20847700	2678098
chr1	151861904	151862280	11668179
chr12	86362673	86362701	8230424
chr9	21881079	21881113	11481336
chr17	34810552	34810729	2181276
chr14	30037250	30037316	1569934
chr12	115568097	115568139	3099286
chr12	115606693	115606794	3099286
chr12	115656385	115656486	3099286
chr12	115807430	115807483	3099286
chr12	115820291	115820392	3099286
chr12	115909278	115909389	3099286
chr12	116071453	116071506	3099286
chr12	116206263	116206374	3099286
chrX	164531361	164531393	10859305
chr19	44346955	44346991	10580438
chrX	20027145	20027210	1420363
chr7	18568360	18568556	3336366
chr14	15368771	15368799	8900181
chr5	113309936	113310329	8543177
chr4	94543039	94543091	2504580
chr2	16328369	16328636	2504580
chr8	73628069	73629605	2504580
chr8	87867632	87867742	2504580
chr10	85729844	85730358	9182717
chr1	169461713	169461741	9006910
chr13	93455924	93455965	1545788
chr2	31581775	31581805	1349742
chr14	53185317	53185689	10790370
chr11	44461601	44461636	10942392
chr7	120806753	120806784	10766845
chr4	105292148	105292179	10766845
chr3	122248747	122248778	10766845
chr9	96705007	96705038	10766845
chr11	6315911	6315942	10766845
chr11	101183574	101183977	10766845
chr17	4837105	4837136	10766845
chr19	16231795	16231826	10766845
chr18	87608841	87608872	10766845
chr6	70655320	70655353	2556265
chr7	87369182	87369215	9819381
chr4	80305381	80305413	9819381
chr17	33610876	33610910	2457903
chr17	34870977	34871011	2457903
chr7	87369276	87369308	9700169
chr16	32350556	32350657	10216289
chr2	131944655	131944684	7910946
chr16	23805150	23805182	9731698
chr2	133245496	133245525	15342482
chr2	172586092	172586121	15342482
chr6	69157051	69157078	2481271
chr6	69213987	69214014	2481271
chr6	69347093	69347120	2481271
chr6	70655322	70655357	2481271
chr11	120639879	120639912	7772036
chr10	128336543	128336903	16129691
chr9	44093332	44093532	2037597
chr9	44095105	44095166	2037597
chr5	121148229	121148258	2026593
chr5	121168143	121168172	2026593
chr4	87994130	87994169	2026593
chr8	71809238	71809268	11562371
chr10	128343724	128345927	8253814
chr7	30299251	30299279	15632058
chr3	37317761	37317795	15632058
chr9	110863709	110864259	1480183
chr9	44732403	44732438	3142692
chrX	49232094	49232130	1551910
chr13	30758119	30758261	2111015
chr8	123625795	123625969	2111015
chr8	123629680	123629867	2111015
chr8	123631596	123631685	2111015
chr8	123633179	123633258	2111015
chr8	123634272	123634323	2111015
chr8	123639326	123642395	2111015
chr8	97068207	97068290	8824273
chr13	93455256	93455303	1569952
chr8	87791998	87792041	8195185
chr16	32350641	32350671	12642588
chr6	115387056	115387717	9367890
chr5	147578457	147578510	9315659
chr8	27273950	27273980	11773448
chr5	51844143	51844171	16513826
chr3	37317757	37317793	9310836
chr2	180429410	180429448	10514493
chr2	163238505	163238534	7523862
chr2	91037773	91037825	11971958
chr8	107512201	107512230	10516284
chr8	107513469	107513532	10516284
chr11	81849316	81849357	10542218
chr11	81851708	81851742	10542218
chr2	124845235	124845263	8621642
chr2	152426553	152426611	9368060
chr18	82688764	82688795	9671582
chr10	57472915	57473069	9671582
chr3	88060265	88060484	9671582
chr11	53462156	53462186	9889198
chr13	75555770	75555825	8999965
chr5	30404334	30404547	3782103
chr10	87396563	87396641	3782103
chr11	105791182	105791252	8901568
chr7	15939803	15939845	10777687
chr7	44396073	44396199	8474451
chr2	90897750	90897786	8474451
chr2	90915909	90916194	8474451
chr15	93508176	93508213	8474450
chr8	44805768	44806075	8474450
chr11	76966327	76966386	2249772
chrX	105323846	105323903	2249772
chr2	157839523	157839561	8832580
chr5	101905549	101905590	15056733
chr7	15939815	15939845	10777688
chr11	53478193	53478236	11893731
chr1	137071498	137071528	11893733
chr9	116023944	116024038	11893733
chr1	182533617	182533667	12095687
chr18	20808308	20808340	8325367
chr12	31850934	31851552	1339296
chr1	151861394	151862302	15213229
chr2	14147042	14147079	10085160
chr12	31850891	31850937	2171781
chr3	83928641	83928671	11254708
chr11	81997260	81997507	9163346
chr8	97068202	97068251	3103216
chr11	94209036	94209066	15824121
chr13	31633525	31633555	9676429
chr1	136106796	136106834	2068103
chr19	34317826	34317856	9334258
chr14	15368772	15368799	9685410
chr6	17413781	17413845	9920903
chr2	148099616	148099652	8284209
chr9	74676018	74676052	11279202
chr7	103701810	103701840	3476205
chr11	53563731	53564142	9694515
chr12	105964108	105964139	12791684
chr11	98840319	98840351	10567217
chr13	93455891	93455921	8063775
chr6	147221062	147221104	8063775
chr11	69611842	69612488	1317551
chr7	18568521	18568554	1532229
chr5	122361520	122361550	1532229
chr5	137711873	137711904	11050012
chrX	97579919	97579953	7862137
chr5	93422255	93422964	8454640
chr11	78736932	78736978	9169456
chr12	102955870	102955959	7615829
chr10	56065272	56065311	15354864
chr10	79067593	79067637	7724598
chr15	7757333	7757977	11146111
chr11	78736089	78736126	10356322
chr10	3557641	3557685	15322094
chr8	95715469	95715515	9830047
chr10	79818297	79818338	2181401
chr1	132851832	132851861	10861063
chr11	100755891	100755921	9497331
chr7	46729297	46729336	9153323
chr12	86362670	86362706	7623850
chr7	34827848	34827882	8346250
chr2	127027474	127027553	8649402
chr10	20848227	20848287	2403925
chr1	64985457	64985502	1996107
chr1	64997746	64997791	1996107
chr1	65860720	65860763	1996107
chr5	112496064	112496118	1996106
chr1	196639493	196639543	10989198
chr14	15368770	15368799	7969156
chr3	37317664	37317719	10586058
chr10	106898874	106898903	7739551
chr12	113875398	113875444	2196446
chr17	33589423	33589453	2196446
chr17	33610899	33610932	2196446
chr17	34870955	34870988	2196446
chr17	35001956	35001991	2196446
chr17	35032707	35032742	2196446
chr17	35806747	35806780	2196446
chr2	106860546	106860855	12730328
chr17	31406531	31406617	2247086
chr10	20847863	20847892	1727489
chr2	131642318	131642346	15358521
chr6	4455267	4455308	8348960
chr5	75433216	75433314	8552100
chr3	10196488	10196521	8552100
chr7	24606071	24606102	1915300
chr3	104943574	104943618	8065313
chr16	16777810	16777861	10779354
chr11	32183600	32183643	3464831
chr11	32196417	32196460	3464831
chr11	40592292	40595782	7957050
chr11	40597227	40598909	7957050
chr10	50327588	50328153	7957050
chr16	89519564	89519651	7957050
chr16	89521161	89521226	7957050
chr16	89522758	89522823	7957050
chr15	64004943	64005302	7957050
chr7	46729275	46729306	11447215
chr8	86177921	86178017	8264627
chr15	91019737	91019768	16249184
chr6	38306347	38306384	1946404
chrX	11614219	11614256	1946404
chrX	68056340	68056377	1946404
chrX	101481733	101481770	1946404
chrX	111098291	111098328	1946404
chr13	94549173	94549210	1946404
chr12	99448212	99448249	1946404
chr12	109263470	109263980	1946404
chr11	49522510	49522547	1946404
chr10	68720566	68720603	1946404
chr17	27257588	27257625	1946404
chr15	34387770	34387808	1946404
chr15	46499811	46499872	1946404
chr5	91535960	91535995	7911235
chr3	52357150	52357179	11919188
chr3	52433183	52433215	11919188
chr5	137346133	137349588	2406566
chr5	137351451	137352549	2406566
chr5	137353936	137354174	2406566
chr5	137355659	137357672	2406566
chr17	34808214	34808473	11856733
chr17	34809794	34809832	11856733
chrX	7128196	7128619	10331989
chr15	6333855	6334153	10944463
chr16	23806221	23806263	2137455
chr16	23806226	23806257	2850259
chr9	110863758	110863786	7623814
chr9	78015620	78015661	8849333
chr9	78042096	78042137	8849333
chr9	78074894	78074935	8849333
chr9	78133950	78133992	8849333
chr15	97736653	97736790	11432806
chr11	69482256	69482478	9479000
chr10	34079088	34079121	10965899
chr3	135522463	135522506	2203532
chr3	135526729	135529046	2203532
chr3	135531227	135532450	2203532
chr3	135538892	135538930	2203532
chr3	135541107	135541219	2203532
chr3	135542511	135542546	2203532
chr3	135545562	135545639	2203532
chr3	135551037	135551076	2203532
chr3	135552716	135552747	2203532
chr3	135556263	135556337	2203532
chr3	135564041	135564076	2203532
chr3	135592916	135592988	2203532
chr2	154261297	154261340	14576826
chr6	70655293	70655351	3200827
chr14	19622832	19622901	1762914
chr2	163447471	163447505	9765260
chr2	101425358	101425386	10082526
chr11	69396269	69396375	7899088
chr10	128360717	128360798	8360188
chr16	29985935	29987443	7906273
chrY_random	10870093	10870143	1722214
chrY_random	13323096	13323146	1722214
chrX	3009683	3009733	1722214
chrX	3017960	3018010	1722214
chrX	3115122	3115172	1722214
chrX	4465683	4465733	1722214
chrX	22744973	22745023	1722214
chrX	22753220	22753270	1722214
chrX	26169219	26169269	1722214
chrX	26574925	26574975	1722214
chrX	26583121	26583171	1722214
chrX	26931225	26931275	1722214
chrX	26939417	26939467	1722214
chrX	27409098	27409148	1722214
chrX	27732892	27732942	1722214
chrX	27741087	27741137	1722214
chrX	28081472	28081522	1722214
chrX	28089664	28089714	1722214
chrX	28668795	28668845	1722214
chrX	28676986	28677036	1722214
chrX	29009586	29009636	1722214
chrX	29485223	29485273	1722214
chrX	29493413	29493463	1722214
chrX	31327235	31327285	1722214
chrX	31335425	31335475	1722214
chrX	31661399	31661449	1722214
chrX	34425138	34425188	1722214
chrX	35208831	35208881	1722214
chrX	75140326	75140376	1722214
chrX	75148644	75148694	1722214
chrX	75320330	75320385	1722214
chrX	75328610	75328660	1722214
chrX	85264455	85264505	1722214
chrX	85272706	85272739	1722214
chrX	91766287	91766337	1722214
chrX	116197071	116197121	1722214
chrX	116205325	116205375	1722214
chrX	122485740	122485790	1722214
chrX	122494042	122494092	1722214
chrX	161150988	161151038	1722214
chrX	161159175	161159225	1722214
chr13	3172350	3172400	1722214
chr13	3180623	3180673	1722214
chr13	20657911	20657961	1722214
chr13	20666168	20666218	1722214
chr13	23132765	23132815	1722214
chr13	50724470	50724520	1722214
chr13	50732658	50732708	1722214
chr13	68290753	68290786	1722214
chr13	68917941	68917976	1722214
chr13	86661091	86661141	1722214
chr13	86669337	86669387	1722214
chr13	112849498	112849548	1722214
chr13	112857748	112857798	1722214
chr12	7169146	7169196	1722214
chr12	7177153	7177203	1722214
chr12	17896568	17896620	1722214
chr12	17900940	17900992	1722214
chr12	18036284	18036336	1722214
chr12	18040656	18040708	1722214
chr12	23055567	23055600	1722214
chr12	23063799	23063832	1722214
chr12	23088189	23088239	1722214
chr12	23092809	23092859	1722214
chr12	23601407	23601457	1722214
chr12	24421688	24421738	1722214
chr12	24429943	24429993	1722214
chr12	24439174	24439224	1722214
chr12	24670098	24670148	1722214
chr12	24674623	24674673	1722214
chr11	40977828	40977878	1722214
chr11	47262714	47262764	1722214
chr11	47270976	47271026	1722214
chr11	75173503	75173553	1722214
chr11	75181733	75181783	1722214
chr10	4258034	4258084	1722214
chr10	4266282	4266332	1722214
chr10	55324932	55324982	1722214
chr17	32790742	32790792	1722214
chr17	39075050	39075100	1722214
chr16	7785281	7785331	1722214
chr16	90966441	90966515	1722214
chr16	93711301	93711351	1722214
chr15	14818325	14818375	1722214
chr15	14823347	14823397	1722214
chr15	32814261	32814311	1722214
chr15	32822376	32822426	1722214
chr15	48999398	48999431	1722214
chr15	49007610	49007643	1722214
chr15	89789277	89789327	1722214
chr14	37020437	37020492	1722214
chr14	37028669	37028719	1722214
chr14	39035000	39035050	1722214
chr14	88457370	88457420	1722214
chr14	93991712	93991762	1722214
chr19	3247630	3247680	1722214
chr19	5315958	5316008	1722214
chr18	6346818	6346868	1722214
chr18	24695015	24695065	1722214
chr18	42609937	42609987	1722214
chr18	74384430	74384480	1722214
chr18	74392645	74392695	1722214
chr18	86326694	86326744	1722214
chr18	86334965	86335015	1722214
chr7	10085931	10085981	1722214
chr7	10354049	10354082	1722214
chr7	13631318	13631368	1722214
chr7	20202464	20202514	1722214
chr7	20210639	20210689	1722214
chr7	21397582	21397632	1722214
chr7	21405749	21405799	1722214
chr7	22620775	22620825	1722214
chr7	22628942	22628992	1722214
chr7	42162234	42162283	1722214
chr7	42172197	42172248	1722214
chr7	42288598	42288648	1722214
chr7	56555120	56555170	1722214
chr7	56788445	56788478	1722214
chr7	56796666	56796699	1722214
chr7	86481797	86481830	1722214
chr7	104697627	104697677	1722214
chr7	106162553	106162603	1722214
chr7	106170815	106170848	1722214
chr6	10346850	10346900	1722214
chr6	10870104	10870154	1722214
chr6	10878373	10878423	1722214
chr6	19594162	19594212	1722214
chr6	19602448	19602498	1722214
chr6	37677445	37677495	1722214
chr6	37714374	37714407	1722214
chr6	60354538	60354596	1722214
chr6	129770051	129770101	1722214
chr6	129778244	129778294	1722214
chr6	149181491	149181541	1722214
chr6	149315601	149315651	1722214
chr5	6489487	6489534	1722214
chr5	6497763	6497809	1722214
chr5	10627434	10627484	1722214
chr5	10635523	10635573	1722214
chr5	40980943	40980993	1722214
chr5	58606236	58606286	1722214
chr5	58614422	58614472	1722214
chr5	76673818	76673868	1722214
chr5	94676967	94677017	1722214
chr5	110132629	110132676	1722214
chr4	3016162	3016212	1722214
chr4	21052314	21052364	1722214
chr4	39044180	39044230	1722214
chr4	39052460	39052506	1722214
chr4	90366958	90367008	1722214
chr4	90374761	90374811	1722214
chr4	120664481	120664531	1722214
chr4	142945743	142945793	1722214
chr4	142954024	142954074	1722214
chr4	143285448	143285498	1722214
chr4	143293672	143293722	1722214
chr4	143351271	143351321	1722214
chr4	143359490	143359540	1722214
chr3	3241274	3241324	1722214
chr3	3249537	3249587	1722214
chr3	10857776	10857826	1722214
chr3	12567506	12567556	1722214
chr3	12571905	12571955	1722214
chr3	33945159	33945209	1722214
chr3	106717674	106717724	1722214
chr2	7527752	7527802	1722214
chr2	67930630	67930680	1722214
chr2	67938792	67938842	1722214
chr2	68347341	68347387	1722214
chr2	68356904	68356950	1722214
chr2	84699422	84699472	1722214
chr2	84707729	84707779	1722214
chr2	85819243	85819295	1722214
chr2	85823908	85823960	1722214
chr2	147154879	147154929	1722214
chr2	181848744	181848794	1722214
chr2	181857002	181857052	1722214
chr1	3166624	3166674	1722214
chr1	8835489	8835539	1722214
chr1	27450634	27450684	1722214
chr1	85016324	85016374	1722214
chr1	85024599	85024649	1722214
chr1	87299789	87299839	1722214
chr1	114428567	114428617	1722214
chr1	147958427	147958477	1722214
chr1	157306337	157306370	1722214
chr9	4855448	4855498	1722214
chr9	7407082	7407131	1722214
chr9	7415343	7415393	1722214
chr9	11773779	11773829	1722214
chr9	17995539	17995589	1722214
chr9	21977708	21977758	1722214
chr9	122696573	122696623	1722214
chr8	4959297	4959347	1722214
chr8	20164969	20165002	1722214
chr8	20173229	20173262	1722214
chr8	20181489	20181522	1722214
chr8	28769711	28769761	1722214
chr8	28777978	28778011	1722214
chr8	75759229	75759279	1722214
chr8	75767504	75767554	1722214
chr5_random	345218	345268	1722214
chr5_random	353511	353561	1722214
chr5_random	2061321	2061371	1722214
chr5_random	2907786	2907836	1722214
chr11	69396553	69396580	8441640
chr8	70421336	70421372	12904181
chr8	70422668	70422702	12904181
chr8	95715465	95715494	16079501
chr13	48677006	48678457	7669690
chr2	62284543	62284592	10567552
chr17	45496858	45496893	9113979
chr2	113744277	113744418	2552286
chr14	30040519	30040552	2753913
chr3	88464656	88464702	14634012
chr3	88470423	88470467	14634012
chr17	33589423	33589453	3501825
chr17	33610899	33610931	3501825
chr17	34870956	34870988	3501825
chr17	35001959	35001991	3501825
chr17	35032710	35032742	3501825
chr17	35806747	35806779	3501825
chr11	94936170	94936217	10473625
chr16	15800733	15800853	9528783
chr2	154260940	154261469	7958837
chr10	92678683	92679911	7958835
chr10	92684495	92684612	7958835
chr10	92694678	92695473	7958835
chr10	92714567	92714777	7958835
chr10	92740547	92740689	7958835
chr9	77845411	77845447	8962155
chr6	122708372	122708403	15054091
chr6	69157052	69157080	2107525
chr6	69213988	69214016	2107525
chr6	69347094	69347122	2107525
chr6	70655272	70655356	2107525
chr8	71809512	71809738	15755745
chr5	91525400	91525435	7523856
chr5	91565756	91565785	7523856
chr9	45687004	45687060	14654367
chr16	18940692	18940773	2116989
chr16	19092810	19093359	2116989
chr17	33589424	33589463	8413217
chr17	33610900	33610939	8413217
chr17	34870937	34870987	8413217
chr17	35001951	35001990	8413217
chr17	35032702	35032741	8413217
chr17	35806748	35806787	8413217
chr14	15368771	15368799	8413217
chr15	101094619	101094686	8413214
chr19	34321287	34321853	2398068
chr14	72059964	72059993	10330185
chr7	18566378	18566430	7969181
chr7	18569429	18569630	7969181
chr5	91547710	91547739	9614204
chr3	30143758	30143790	8557637
chr7	24801415	24801450	2011512
chr5	91525364	91525437	1875930
chr5	91536003	91536054	1875930
chr4	44737695	44738377	10662641
chr1	137869063	137869092	12407098
chr5	147585147	147585174	9252422
chr16	23806221	23806252	2147227
chr9	32483529	32483756	2163347
chr16	23806221	23806263	2898727
chr12	86362675	86362712	2147223
chr7	18568409	18568449	2163343
chr16	23806224	23806260	7926024
chr11	69403129	69403157	14707287
chr12	86362491	86362522	8506157
chr12	31850900	31850935	1850696
chr2	109475449	109475487	12114522
chr11	70435389	70435612	8464921
chr11	78736932	78736990	7508926
chr11	69561763	69562338	9151733
chr6	92210104	92210244	10537125
chr7	109852584	109852907	10657238
chr6	41045108	41045728	2557542
chr6	41050929	41051019	2557542
chr6	41059680	41059770	2557542
chr2	147056498	147057506	1889089
chr3	101733720	101733827	1324413
chrX	7128568	7128597	12045237
chr5	30343756	30343798	12177065
chr18	20808310	20808340	9668124
chr12	113712845	113713747	1401921
chr6	70655322	70655353	8268924
chr4	124154605	124154641	8948648
chr11	9017788	9017822	11559567
chr5	93403445	93403483	12403783
chr9	49551485	49551548	7910552
chr3	28888904	28889034	8544849
chr17	46016862	46016889	2108863
chr1	82171130	82171170	8544845
chr9	50505293	50505415	15522290
chr17	33589422	33589465	2540425
chr17	33610898	33610942	2540425
chr17	34870943	34870989	2540425
chr17	35001948	35001992	2540425
chr17	35032699	35032743	2540425
chr17	35047044	35047084	2540425
chr17	35077933	35077979	2540425
chr17	35806746	35806791	2540425
chr15	78322201	78322469	15752766
chr2	163441548	163441592	1881892
chr7	41898471	41899356	7862144
chr7	51614715	51615599	7862144
chr7	89482897	89482927	7862144
chr7	100635009	100635893	7862144
chr6	22654269	22654299	7862144
chr6	83840154	83841038	7862144
chr6	84777897	84778787	7862144
chr6	91394386	91394416	7862144
chr6	125127878	125127908	7862144
chr6	128167883	128168852	7862144
chr5	13048556	13049440	7862144
chr5	96102015	96102899	7862144
chr5	106103120	106104004	7862144
chr4	57465124	57466008	7862144
chr4	83576985	83577015	7862144
chr4	84395390	84395420	7862144
chr4	91343803	91344687	7862144
chr3	52700763	52701647	7862144
chr3	61549905	61549935	7862144
chr3	79003184	79004068	7862144
chr3	122222334	122223218	7862144
chr3	139586765	139587649	7862144
chr3	142899996	142900880	7862144
chr2	11327000	11327884	7862144
chr2	28755734	28756618	7862144
chr2	43340523	43341407	7862144
chr2	146446256	146446286	7862144
chr2	149434615	149435499	7862144
chr2	151065448	151065478	7862144
chr2	152427791	152428488	7862144
chr1	12551452	12551482	7862144
chr1	13771214	13771244	7862144
chr1	15254130	15254160	7862144
chr1	102112597	102112627	7862144
chr1	182163963	182163993	7862144
chr18	54109689	54110579	7862144
chr9	51324882	51324912	7862144
chr9	51376165	51376195	7862144
chr9	75479679	75479709	7862144
chr8	43107602	43107632	7862144
chr8	60442443	60443327	7862144
chr8	78301707	78302591	7862144
chr8	94578591	94578621	7862144
chr8	95605172	95606056	7862144
chr13	17606087	17606117	7862144
chr13	94394533	94394563	7862144
chr13	98558423	98558453	7862144
chr13	99502369	99503240	7862144
chr12	5616602	5616632	7862144
chr12	15753646	15753676	7862144
chr12	70840066	70840096	7862144
chr12	82292039	82292069	7862144
chr11	4464477	4464507	7862144
chr11	17873911	17873941	7862144
chr11	20235132	20236016	7862144
chr11	26686632	26687516	7862144
chr11	33176707	33176737	7862144
chr11	63128622	63128652	7862144
chr11	99495075	99495105	7862144
chr10	13580962	13580991	7862144
chr10	33498884	33498914	7862144
chr10	39701281	39701311	7862144
chr17	14510585	14510615	7862144
chr17	25054329	25054359	7862144
chr17	61466363	61466393	7862144
chr15	4833188	4833218	7862144
chr15	12519613	12520497	7862144
chr15	18109329	18109359	7862144
chr15	93024774	93025660	7862144
chr14	10074300	10075184	7862144
chr14	47331430	47331460	7862144
chr14	102256261	102257125	7862144
chr19	40266542	40266572	7862144
chrX	76446687	76447571	7862144
chrX	84824888	84824917	7862144
chrX	111575955	111575985	7862144
chrX	116277653	116277683	7862144
chrX	147286083	147286965	7862144
chr11	68915207	68915237	12483227
chr2	164639182	164639220	16166639
chr12	113875362	113875392	2068097
chr15	101094792	101094846	7969116
chr6	52133966	52134176	2565857
chr11	96119436	96119750	2565857
chr6	71192163	71192201	15890826
chr7	51614689	51614718	12972592
chr7	100635890	100635919	12972592
chr6	83841035	83841064	12972592
chr6	91394360	91394389	12972592
chr5	13049437	13049466	12972592
chr5	28869330	28869359	12972592
chr5	96101989	96102018	12972592
chr5	106104001	106104030	12972592
chr4	57466005	57466034	12972592
chr4	91344684	91344713	12972592
chr3	122223215	122223244	12972592
chr3	142899970	142899999	12972592
chr2	28756615	28756644	12972592
chr2	43341404	43341433	12972592
chr2	149434589	149434618	12972592
chr2	160946895	160946924	12972592
chr1	15255008	15255037	12972592
chr1	182164856	182164885	12972592
chr9	51324856	51324885	12972592
chr9	113379040	113379069	12972592
chr8	35791338	35791367	12972592
chr8	60442417	60442446	12972592
chr8	78302588	78302617	12972592
chr8	95606053	95606082	12972592
chr13	99503237	99503266	12972592
chr12	50717875	50717904	12972592
chr11	20236013	20236042	12972592
chr11	63129503	63129532	12972592
chr10	33498911	33498940	12972592
chr15	4832308	4832337	12972592
chr15	12519587	12519616	12972592
chr14	10075181	10075210	12972592
chr19	16344789	16344818	12972592
chrX	12483975	12484004	12972592
chrX	76447568	76447597	12972592
chr2	102702389	102702429	10657993
chr11	98584304	98584335	12150932
chr11	98589151	98589199	12150932
chr10	84581012	84581043	12150932
chr3	94476562	94476591	12150932
chr2	92213483	92213532	12150932
chr9	78015471	78015501	15155840
chr9	78041947	78041977	15155840
chr9	78068344	78068374	15155840
chr9	78134110	78134140	15155840
chr17	33589362	33589817	3510743
chr17	33610692	33611369	3510743
chr17	34870572	34871119	3510743
chr17	34906604	34906783	3510743
chr17	34987031	34987633	3510743
chr17	35001576	35002052	3510743
chr17	35032549	35032803	3510743
chr17	35046695	35047148	3510743
chr17	35790654	35790691	3510743
chr17	35806743	35806790	3510743
chr7	46244212	46244242	8127707
chr5	16065673	16065702	7935420
chr16	23806222	23806263	2564850
chr6	122821684	122821919	16854466
chr11	100724804	100724845	11438543
chr11	100727322	100727361	11438543
chr13	55339730	55339779	12444919
chr11	54093064	54093105	8289796
chrX	20027114	20027144	9478976
chr17	35113681	35114128	8289793
chr12	86362675	86362704	1922053
chr2	127817488	127817521	16162916
chr7	105441520	105441574	7800475
chr7	105448137	105448378	7800475
chr9	18051052	18051105	7800475
chr1	136106263	136106470	10548518
chrX	164531361	164531392	16595692
chr9	45687017	45687057	9545312
chr6	68946741	68946794	3537963
chr6	69041093	69041146	3537963
chr6	69115022	69115075	3537963
chr6	69157044	69157097	3537963
chr6	69173349	69173399	3537963
chr6	69198073	69198124	3537963
chr6	69213980	69214033	3537963
chr6	69235024	69235077	3537963
chr6	69308133	69308186	3537963
chr6	69330005	69330055	3537963
chr6	69347086	69347139	3537963
chr6	69368402	69368455	3537963
chr6	69537462	69537512	3537963
chr6	69561843	69561892	3537963
chr12	114380256	114380293	3537963
chr12	114442777	114442823	3537963
chr12	114508147	114508198	3537963
chr12	115130944	115130981	3537963
chr12	115156960	115156997	3537963
chr12	115194585	115194638	3537963
chr12	115299502	115299555	3537963
chr12	115362911	115362964	3537963
chr2	28437363	28437397	11696536
chr16	10699184	10700012	11696536
chr16	87618776	87618809	9565602
chr17	33611945	33611997	7984430
chr17	35000757	35000789	7984430
chr17	35045857	35045889	7984430
chr17	35076933	35076965	7984430
chr5	8897866	8900457	8877103
chr10	61524837	61524867	10825208
chr10	61527575	61527605	10825208
chr6	108626135	108626168	14581485
chr11	68914963	68914995	14581485
chr10	66933148	66933181	8483478
chr12	86362677	86362712	8483478
chr18	34987075	34987125	8483478
chr7	109913092	109913392	11500387
chr1	74833834	74833863	15538371
chr1	97497672	97498061	9516473
chr5	147580550	147580997	7907546
chr5	147584725	147585523	7907546
chr11	96121128	96121172	7907546
chr15	102838905	102838963	7907546
chr15	102863817	102863869	7907546
chr16	23806259	23806295	7907546
chr5	75856697	75856747	8695840
chr15	97830430	97830470	10825206
chr3	138464665	138464701	8756633
chrX	58046027	58046063	8756633
chr7	32068072	32068100	11340077
chr7	33021287	33021315	11340077
chr7	35943485	35943513	11340077
chr7	41898900	41898928	11340077
chr7	51615143	51615171	11340077
chr7	67656832	67656860	11340077
chr7	72863210	72863238	11340077
chr7	89483314	89483342	11340077
chr7	100635437	100635465	11340077
chr6	18095167	18095195	11340077
chr6	22653843	22653871	11340077
chr6	83840582	83840610	11340077
chr6	91394814	91394842	11340077
chr6	93103035	93103063	11340077
chr6	94786420	94786448	11340077
chr6	125128524	125128552	11340077
chr6	128168396	128168424	11340077
chr5	13048984	13049012	11340077
chr5	16020545	16020573	11340077
chr5	96102443	96102471	11340077
chr5	106103548	106103576	11340077
chr5	108386069	108386097	11340077
chr4	41357701	41357729	11340077
chr4	57465552	57465580	11340077
chr4	82665651	82665679	11340077
chr4	83576559	83576587	11340077
chr4	84394958	84394986	11340077
chr4	91344231	91344259	11340077
chr4	128371236	128371264	11340077
chr3	8599115	8599143	11340077
chr3	14488377	14488405	11340077
chr3	14950850	14950878	11340077
chr3	36055858	36055886	11340077
chr3	52701191	52701219	11340077
chr3	61550334	61550362	11340077
chr3	79003612	79003640	11340077
chr3	121172660	121172688	11340077
chr3	122222762	122222790	11340077
chr3	125034829	125034857	11340077
chr3	139587193	139587221	11340077
chr3	142900424	142900452	11340077
chr2	11327428	11327456	11340077
chr2	28756162	28756190	11340077
chr2	43340951	43340979	11340077
chr2	45631918	45631946	11340077
chr2	56895567	56895595	11340077
chr2	81923535	81923563	11340077
chr2	104338709	104338737	11340077
chr2	146446685	146446713	11340077
chr2	149435042	149435070	11340077
chr2	151065882	151065910	11340077
chr2	160946436	160946464	11340077
chr2	162674240	162674268	11340077
chr1	13771642	13771670	11340077
chr1	15254558	15254586	11340077
chr1	52448315	52448343	11340077
chr1	182164391	182164419	11340077
chr18	23360040	23360068	11340077
chr18	56098088	56098116	11340077
chr18	89668694	89668722	11340077
chr9	45587468	45587496	11340077
chr9	51755184	51755212	11340077
chr8	37841689	37841717	11340077
chr8	43108024	43108052	11340077
chr8	47754033	47754061	11340077
chr8	53777747	53777775	11340077
chr8	66670675	66670703	11340077
chr8	78302135	78302163	11340077
chr8	95605600	95605628	11340077
chr8	100455260	100455288	11340077
chr13	20712385	20712413	11340077
chr13	98558850	98558878	11340077
chr13	99502796	99502824	11340077
chr12	5616170	5616198	11340077
chr12	13778754	13778782	11340077
chr12	15754079	15754107	11340077
chr12	70839622	70839650	11340077
chr12	72765419	72765447	11340077
chr12	82291607	82291635	11340077
chr11	3852158	3852186	11340077
chr11	4464070	4464098	11340077
chr11	17874340	17874368	11340077
chr11	20235560	20235588	11340077
chr11	26687060	26687088	11340077
chr11	48578522	48578550	11340077
chr11	63129050	63129078	11340077
chr11	79188004	79188032	11340077
chr11	99494649	99494677	11340077
chr11	108975822	108975850	11340077
chr10	22481183	22481211	11340077
chr10	33498458	33498486	11340077
chr10	39701715	39701743	11340077
chr10	43510079	43510107	11340077
chr10	44694958	44694986	11340077
chr10	126716524	126716552	11340077
chr17	61466791	61466819	11340077
chr17	79163004	79163032	11340077
chr16	9958744	9958772	11340077
chr15	12520041	12520069	11340077
chr15	43047769	43047797	11340077
chr15	84694507	84694535	11340077
chr15	93025204	93025232	11340077
chr14	10074728	10074756	11340077
chr14	47331004	47331032	11340077
chr14	102256689	102256717	11340077
chr19	16345220	16345248	11340077
chr19	25863452	25863480	11340077
chr19	40266122	40266150	11340077
chr19	46728128	46728156	11340077
chrX	76447115	76447143	11340077
chrX	84825316	84825344	11340077
chrX	111576383	111576411	11340077
chrX	135023391	135023419	11340077
chrX	137121172	137121200	11340077
chrX	147286510	147286538	11340077
chrX	148744323	148744351	11340077
chr7	24606069	24606218	12446773
chr12	113713039	113713078	10748032
chr1	173050697	173050731	9295294
chr18	36852669	36852801	1383228
chr2	62284546	62284588	9372951
chr6	85417666	85417702	10561509
chr5	130102072	130102109	10561509
chr3	88383090	88383129	10561509
chr11	22890632	22890669	10561509
chr10	116467502	116467538	10561509
chr17	12759732	12759768	10561509
chr16	87384799	87384835	10561509
chr15	31546066	31546480	10561509
chr12	86368563	86368595	10037443
chr9	45686921	45687188	9121477
chr5	30343758	30343787	9535723
chr8	71809363	71809400	9535723
chr15	74683441	74683480	2783417
chr2	155442606	155442644	10777534
chr13	27064876	27064908	9717847
chr15	85410289	85410319	11914369
chr14	30038416	30038468	8114720
chr7	3538563	3538594	8798433
chr7	3859546	3859577	8798433
chr7	25430522	25430560	8798433
chr17	34870980	34871010	1986360
chr7	46583869	46583914	8007954
chr11	78736003	78736032	8649986
chr15	97830452	97830489	9614106
chr2	101425472	101425503	10845919
chr7	28059498	28059529	8961261
chr9	86493186	86493221	1314168
chr11	54093149	54093179	7623820
chr17	35114028	35114070	8152920
chr12	86362670	86362705	2062642
chr3	145584297	145585034	2062642
chr3	145586517	145589421	2062642
chr12	104139374	104139661	2836860
chr12	104174806	104175094	2836860
chr12	104229502	104229533	2836860
chr12	104358132	104358161	2836860
chr5	91535984	91536015	2836860
chr18	20806563	20806636	2836860
chr5	121148229	121148258	2542764
chr5	121168143	121168172	2542764
chr12	91806440	91806470	7997232
chrX	7133613	7133659	9089398
chr2	73619656	73619758	2529117
chr16	23806224	23806260	2529117
chr6	68684617	68684724	6425835
chr6	68698141	68698686	6425835
chr6	68736759	68737358	6425835
chr6	68840000	68840564	6425835
chr6	68890968	68891062	6425835
chr6	68920338	68921728	6425835
chr6	68946141	68946963	6425835
chr6	68972552	68973158	6425835
chr6	68989285	68990099	6425835
chr6	69040491	69041384	6425835
chr6	69085698	69087114	6425835
chr6	69114421	69115312	6425835
chr6	69127163	69128068	6425835
chr6	69156434	69157335	6425835
chr6	69172740	69173640	6425835
chr6	69197464	69198364	6425835
chr6	69213370	69214271	6425835
chr6	69234414	69235314	6425835
chr6	69272068	69272593	6425835
chr6	69307547	69308424	6425835
chr6	69329407	69330297	6425835
chr6	69346488	69347377	6425835
chr6	69367798	69368693	6425835
chr6	69392781	69393073	6425835
chr6	69429835	69430439	6425835
chr6	69473954	69475278	6425835
chr6	69505555	69506447	6425835
chr6	69516875	69517762	6425835
chr6	69536855	69537753	6425835
chr6	69561245	69562130	6425835
chr6	69578404	69578943	6425835
chr6	69610987	69612347	6425835
chr6	69630362	69630940	6425835
chr6	70652142	70652210	6425835
chr9	54560093	54560196	10714763
chr3	19885848	19887595	11278361
chr2	181294771	181294837	11890680
chr16	14204867	14204896	9529161
chr16	14206006	14206115	9529161
chr16	15801942	15802019	1714459
chr19	25572693	25572730	11870074
chr11	83478593	83478783	7835696
chr12	109901105	109901145	9822638
chr11	78736047	78736116	7520478
chr10	60693068	60693125	8871649
chr3	10166295	10166330	10629058
chr3	10190983	10191043	10629058
chr13	42174356	42175365	1694016
chr13	42178530	42178635	1694016
chr13	42192407	42192904	1694016
chr13	42194361	42195998	1694016
chr5	126371778	126372395	1694016
chr10	13829637	13829679	1694016
chr3	142601284	142602903	1694016
chrX	92424645	92425011	1694016
chr12	31850891	31850939	2556699
chr2	172795579	172795617	7532283
chr4	140282527	140282656	16321658
chr11	69764186	69765140	2404278
chr11	78736811	78736954	9164945
chr12	86362675	86362716	12137955
chr2	133243977	133244008	12511606
chr12	113787245	113787280	8089482
chr17	33897270	33897310	8089482
chr5	107965132	107965162	15131254
chr5	107966946	107966977	15131254
chr7	18568531	18568560	9614136
chr12	113875209	113875260	9614136
chr11	67052883	67053961	9614136
chr17	34470750	34470826	2174104
chr9	57494749	57494781	2174107
chr3	68778500	68778530	11602633
chr6	92210030	92210058	8910392
chr6	92212007	92212036	8910392
chr2	76161191	76162902	9166696
chr9	110863758	110863788	1584212
chr4	88312923	88312952	1614874
chr9	54562792	54562841	9092560
chr17	25093747	25093807	8839840
chr6	65067755	65067784	10998423
chr9	86492889	86493178	2332433
chr9	107764658	107765245	9467940
chr3	159534366	159534406	12759335
chr8	119981734	119981808	12759335
chr4	63533051	63537026	7534412
chr1	151860747	151860789	10859338
chr6	4455593	4455637	2072909
chr4	15808178	15808216	8464915
chr9	21713832	21713868	1650452
chrX	7116697	7116727	1650452
chr1	172895950	172895985	8070412
chr12	17570230	17570438	1650455
chr3	28888878	28888913	15886523
chr12	113875218	113875262	2357966
chr3	135628873	135628907	9190210
chr2	105465566	105465607	12962539
chr6	134199218	134199263	9009269
chr11	106130522	106130913	2508087
chr19	43579561	43579614	10527950
chr5	91535981	91536012	10527950
chr8	87866666	87866694	8537375
chr11	65087251	65087284	14645532
chr2	104927051	104927087	9336463
chr9	21881604	21881649	15563837
chr6	41043106	41043146	12082086
chr17	33955130	33955170	2564635
chr18	43863434	43863477	7935489
chr3	89222379	89222424	1315961
chr16	18515177	18515212	12533514
chr7	46243934	46243963	12135926
chr16	23806221	23806263	9832447
chr9	53991723	53991761	9832447
chr8	93960201	93960321	10760507
chr2	83525256	83525288	10899572
chr12	86362670	86362704	11279108
chr9	45687017	45687189	11279108
chr15	102815626	102815660	9860988
chr6	122673019	122673057	15743839
chr11	53460767	53460830	8052653
chr3	37317765	37317795	7815567
chr5	104410880	104410914	15292199
chr1	72808169	72808198	11978764
chr5	91525400	91525436	8455618
chr8	97068302	97068335	3371659
chr14	53032877	53033063	8417120
chr19	39339059	39339105	15155833
chr11	100150361	100150496	15292219
chr12	113875209	113875262	2143023
chr8	77980068	77980098	10821856
chr7	34758869	34759579	1709121
chr7	34765225	34765304	1709121
chr11	98517240	98517282	1709121
chr11	117785319	117785367	10821852
chr12	8797292	8797321	8647862
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chr2	26024982	26025025	7708713
chr17	56913368	56913420	1590761
chr18	5705041	5705226	7935395
chr18	5748702	5748854	7935395
chr18	5766261	5768013	7935395
chr18	5770384	5770456	7935395
chr18	5772921	5774892	7935395
chr18	82688764	82688797	1379237
chr12	113725300	113725411	1922063
chr17	33897271	33897383	1922063
chr6	70655311	70655364	1922063
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chr6	103929892	103930362	1967980
chr4	124160870	124160929	1967980
chr3	3814640	3815822	1967980
chr3	129425688	129426847	1967980
chr2	18070878	18070935	1967980
chr1	42642750	42642809	1967980
chr1	161130490	161130863	1967980
chr1	167734340	167734399	1967980
chr9	45912366	45912537	1967980
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chrX	138022310	138022583	1967980
chr13	78488859	78489006	1967980
chr17	35114103	35114536	1967980
chr17	35117153	35118822	1967980
chr14	15898868	15899489	1967980
chr5	93424229	93424259	9169460
chr5	143171910	143171940	1425594
chr1	72808042	72808222	7476973
chr11	98517240	98517364	1691438
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chr8	97068089	97068120	9854025
chr11	106118005	106118034	3561414
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chr19	10045617	10045708	8051121
chr16	42260014	42260042	8703010
chr12	3954578	3954608	7902581
chr3	37317568	37317597	7902581
chr16	23806224	23806252	1824920
chr8	87866699	87866741	8265655
chr8	87868841	87868887	8265655
chr2	11559184	11559294	10082534
chr10	20847628	20848108	8683983
chr3	80999455	80999483	11256962
chr4	62830852	62830882	8417341
chr4	4066006	4066034	1827203
chr9	57494749	57494781	2160969
chr7	144670749	144670781	10669750
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chr6	85477484	85477552	2496302
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chr10	66935018	66936588	2496302
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chr7	100366077	100366121	10333481
chr7	100367250	100367300	10333481
chr7	87369182	87369306	10707962
chr12	113875195	113875343	3019664
chr8	26983469	26984665	1312839
chr8	3694204	3694256	8977198
chr8	73627360	73627975	1714380
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chr10	82182229	82182364	1698608
chr10	82184841	82184895	1698608
chr10	82186500	82186594	1698608
chr10	82191631	82191714	1698608
chr10	82193799	82193936	1698608
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chr17	47856870	47859122	1698608
chr17	47866011	47866148	1698608
chr17	47875191	47875254	1698608
chr18	82688931	82688970	1698607
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chr11	96133654	96134849	7969151
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chr12	86362674	86362704	2493627
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chr5	89839308	89839533	15548386
chr8	97068207	97068238	10096565
chr8	83388451	83389772	8690723
chr8	89614668	89614698	14985507
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chrX	159418071	159418353	14985507
chr8	77985762	77985790	7929191
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chr8	107736165	107736201	16527247
chr14	53185362	53185593	2524381
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chr8	87792031	87792079	7682653
chr8	87795040	87795392	7682653
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chr12	14520677	14520705	15589317
chr10	94842340	94842368	15589317
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chr11	78315407	78315439	11997100
chr1	133107821	133107866	15939554
chr8	27273863	27273894	16109738
chr12	114935221	114935265	7499271
chr12	114981056	114981115	7499271
chr12	114986580	114986620	7499271
chr12	115031654	115031718	7499271
chr12	115094657	115094721	7499271
chr12	115113957	115114011	7499271
chr12	115124833	115124892	7499271
chr12	115156735	115156789	7499271
chr12	115184332	115184386	7499271
chr12	115411466	115411555	7499271
chr12	115439193	115439249	7499271
chr12	115567833	115567914	7499271
chr12	115579468	115579522	7499271
chr12	115593572	115593661	7499271
chr12	115606488	115606578	7499271
chr12	115641760	115641804	7499271
chr12	115656180	115656270	7499271
chr12	115783167	115783248	7499271
chr12	115792630	115792684	7499271
chr12	115807225	115807314	7499271
chr12	115820070	115820159	7499271
chr12	115834780	115834842	7499271
chr12	115894502	115894564	7499271
chr12	115909084	115909173	7499271
chr12	115943710	115943774	7499271
chr12	115955630	115955720	7499271
chr12	116041195	116041259	7499271
chr12	116052025	116052089	7499271
chr12	116071246	116071312	7499271
chr12	116139974	116140036	7499271
chr12	116190298	116190360	7499271
chr12	116206069	116206159	7499271
chr12	116238679	116238743	7499271
chr12	116250733	116250823	7499271
chr12	116295974	116296030	7499271
chr12	116309960	116310014	7499271
chr12	116336182	116336245	7499271
chr12	116360429	116360493	7499271
chr12	116368364	116368428	7499271
chr12	116400623	116400687	7499271
chr12	116448113	116448167	7499271
chr12	116457746	116457835	7499271
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chr1	77405308	77405349	9425139
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chr12	104139349	104139711	2835657
chr12	104174783	104175144	2835657
chr12	104229223	104229583	2835657
chr12	104264774	104265134	2835657
chr12	104306111	104306471	2835657
chr12	104358109	104358469	2835657
chr9	109977127	109977179	16288722
chr11	117784319	117784347	16055089
chr7	119936637	119936667	1944285
chr7	26015815	26015923	15115437
chr7	26543961	26544069	15115437
chr6	52134627	52134846	10075847
chr11	53462119	53462152	8674125
chr12	86362654	86362945	8547224
chr7	18568360	18568567	8474439
chr12	86362674	86362703	1508214
chr3	37317570	37317599	8920856
chr3	37317767	37317796	1740667
chr18	20808310	20808338	9278450
chr5	30404403	30404433	2041767
chr8	95715469	95715515	9278454
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chr13	15805218	15805248	9645703
chr13	15808167	15808197	9645703
chr3	88459030	88459063	12551949
chr3	88464736	88464769	12551949
chr3	88470501	88470534	12551949
chr17	16374737	16374767	10488087
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chr17	31406531	31406588	3170605
chr15	102814722	102814982	8575334
chr11	4139834	4140014	8605875
chr16	87588033	87588301	11530014
chr10	106896028	106896057	11782449
chr17	39672035	39672210	8441629
chr10	80208260	80208289	10913126
chr9	57813047	57813102	10913126
chr5	88773939	88774182	8065333
chr15	85562971	85563000	12554753
chr2	91732737	91734451	7982887
chr11	60026654	60026701	10918064
chr2	105483208	105483268	7529875
chr14	62371254	62371322	10553071
chr1	182533904	182533975	15982639
chr4	134425012	134425135	8164679
chr17	44180251	44180353	8164679
chr17	44198285	44198415	8164679
chr16	92492846	92494983	8164679
chr16	92502457	92502618	8164679
chr16	92533012	92533204	8164679
chr16	92557568	92557673	8164679
chr16	92577833	92577993	8164679
chr16	92584340	92586187	8164679
chr8	4349461	4349655	16517733
chr8	74508957	74508987	9353271
chr9	110861572	110864453	1939212
chr13	30756677	30756725	7541907
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chr11	32183543	32183592	9144493
chr11	32196360	32196409	9144493
chr17	34871047	34871100	9144493
chr8	3622333	3626083	2065970
chr6	70655323	70655353	1598211
chr17	34871062	34871092	1598211
chr17	26566988	26567223	7586217
chr18	34987527	34987557	8737376
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chr6	132083311	132083546	1747160
chr6	132176165	132176400	1747160
chr6	132280378	132280602	1747160
chr6	132329756	132329991	1747160
chr6	132407373	132407597	1747160
chr6	133257934	133257987	1747160
chr6	133494907	133494960	1747160
chr12	105964105	105964142	15805112
chr4	122502564	122502605	10655054
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chr18	60929071	60929106	2115119
chr8	24223212	24223318	2172788
chr11	94936097	94936174	14670999
chr4	144513603	144513631	9190933
chr13	93455946	93455976	9121444
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chr2	90900268	90900344	1985210
chr2	90914130	90916592	1985210
chr8	27273933	27273962	9832418
chr17	24360202	24360244	10891372
chr7	78926828	78926857	9368062
chr17	33896554	33896590	7722306
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chr16	15801215	15801865	1840554
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chr6	115387317	115387351	10862621
chr2	167380225	167380831	10862621
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chr7	51615247	51615275	12890683
chr7	89483418	89483446	12890683
chr7	100635333	100635361	12890683
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chr6	83840478	83840506	12890683
chr6	84778435	84778463	12890683
chr6	91394918	91394946	12890683
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chr6	128168292	128168320	12890683
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chr5	28869888	28869916	12890683
chr5	96102547	96102575	12890683
chr5	106103444	106103472	12890683
chr4	57465448	57465476	12890683
chr4	83576663	83576691	12890683
chr4	91344127	91344155	12890683
chr3	52701295	52701323	12890683
chr3	61550230	61550258	12890683
chr3	69654804	69654832	12890683
chr3	79003716	79003744	12890683
chr3	122222658	122222686	12890683
chr3	139587297	139587325	12890683
chr3	142900528	142900556	12890683
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chr2	128249130	128249158	12890683
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chr1	152899145	152899173	12890683
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chr8	37841585	37841613	12890683
chr8	60442975	60443003	12890683
chr8	78302031	78302059	12890683
chr8	95605496	95605524	12890683
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chr12	72765315	72765343	12890683
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chr11	20235456	20235484	12890683
chr11	26687164	26687192	12890683
chr11	99494753	99494781	12890683
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chr10	22481287	22481315	12890683
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chr10	39701819	39701847	12890683
chr10	118296364	118296392	12890683
chr10	121572953	121572981	12890683
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chr14	47331108	47331136	12890683
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chr12	113676860	113676889	14583460
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chr8	43745980	43746034	3198687
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chr16	38185264	38185310	9489701
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chr7	18461602	18465370	1741260
chr7	18466539	18469320	1741260
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chr8	97068173	97068435	6095286
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chr12	113093401	113093434	15105421
chr9	20703219	20703262	12799438
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chr11	81851530	81851898	8630731
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chr19	44460945	44460975	9689914
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chr5	91535955	91535987	2371282
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chr4	41236704	41236739	11679588
chr12	105964109	105964139	10748162
chr11	96181620	96181650	7600572
chr12	113676249	113676300	10931834
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chr5	142653989	142654515	8007964
chr5	142687614	142687800	8007964
chr5	142701158	142701318	8007964
chr5	142702712	142702861	8007964
chr5	142703909	142704069	8007964
chr5	142705987	142706514	8007964
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chr11	32183600	32183676	2233727
chr11	32196417	32196493	2233727
chr10	79293961	79293990	12949072
chr17	6012317	6012892	2554307
chr17	33643283	33644637	2554307
chr17	33646106	33648848	2554307
chr2	27563769	27563934	2554307
chr2	27578206	27578276	2554307
chr2	27581548	27581678	2554307
chr2	56926045	56926100	2554307
chr1	169463963	169464125	2554307
chr1	169475799	169475921	2554307
chr1	75243574	75244102	8120103
chr1	75245461	75246840	8120103
chr8	27273959	27274009	12239105
chr6	55381695	55381725	12031496
chr6	70655318	70655350	2542770
chr2	38532664	38532706	10684809
chr2	38536570	38536607	10684809
chr5	91525395	91525435	7520913
chr5	91559417	91559470	7520913
chr1	77985885	77986724	2022185
chr1	78004722	78005858	2022185
chr1	78015511	78015563	2022185
chr1	78075618	78075680	2022185
chr1	78079923	78080193	2022185
chr4	63231533	63231725	15702971
chr2	131944599	131944719	8557653
chr8	87866606	87866694	11904151
chr8	86177898	86177931	8668156
chr5	8803880	8803912	9019155
chr4	94544510	94544564	1542579
chr6	4455529	4455626	2043139
chr11	94752150	94752179	2043139
chr5	148037297	148037332	15192019
chr4	124304902	124304947	8467794
chr4	124306961	124307422	8467794
chr4	124322517	124323663	8467794
chr4	124326589	124327487	8467794
chr4	124333420	124333500	8467794
chr4	124340000	124341221	8467794
chr4	124344831	124344896	8467794
chr4	124346445	124347053	8467794
chr17	33610798	33610831	9344877
chr12	58461347	58461377	11297512
chr2	9775726	9776222	2017177
chr2	9795441	9795542	2017177
chr6	132083388	132083423	10506207
chr6	132329829	132329868	10506207
chr12	74028104	74028132	8628654
chr12	74032218	74032246	8628654
chr6	70655321	70655351	2536725
chr2	154261286	154261338	9218478
chr4	146844271	146844309	10903346
chr4	35082315	35082343	7513049
chr17	33896148	33896263	2105455
chr3	152169789	152170157	8125259
chr2	130801038	130801228	8125259
chr7	46713835	46713863	7998973
chr11	54093096	54093125	1944268
chr11	98517360	98517391	1944268
chr5	104539335	104539412	10788516
chr6	92210237	92210394	9421415
chr19	8779922	8780386	2761540
chr9	78015620	78015661	11708801
chr9	78042096	78042137	11708801
chr9	78074894	78074935	11708801
chr9	78133950	78133991	11708801
chr7	34827854	34827883	7862113
chr16	15800733	15800808	10867011
chr16	4039921	4039963	9492053
chr16	4043853	4043886	9492053
chr18	34987316	34987459	3141919
chr18	34989742	34990942	3141919
chrX	107018248	107018296	8876240
chr12	86362674	86362703	1658630
chr6	4455157	4455412	9143363
chr2	28444014	28444043	15718298
chr11	120640141	120640174	9164847
chr11	120640251	120640290	10207099
chr12	86362666	86362711	2504586
chr12	115955870	115955901	2826127
chr12	116250973	116251004	2826127
chr19	41082388	41082741	1922043
chr16	16777513	16777740	1922043
chr16	16782846	16782880	1922043
chr16	17893921	17893955	1922043
chr11	4848070	4848108	8621737
chrX	7124905	7125430	2044960
chr19	34358328	34358380	10660538
chr5	38112880	38113050	9278425
chr5	30404330	30404483	2779579
chr10	87396585	87396649	2779579
chr10	119879322	119879355	10558886
chr5	150790872	150790995	14680822
chr16	33415499	33415540	10359087
chr8	40781886	40781927	10359087
chr2	109476879	109476932	9873054
chr17	34870978	34871011	8468472
chr2	164134294	164134877	9276666
chr2	155208949	155209172	11435428
chr6	70655321	70655362	3141781
chr17	33955281	33955665	3141781
chr5	30343800	30343834	12027462
chr5	93403443	93403474	7561042
chr11	78736110	78736146	12225970
chr11	60593721	60593756	11327713
chr4	80305182	80305455	10480898
chr2	38536497	38536614	12390883
chr7	141130600	141130635	12482979
chr17	31406473	31406643	2584197
chrX	134431612	134431645	7988464
chr6	52086644	52086674	7623795
chr2	74526281	74526312	7623795
chr1	4481330	4481746	8636240
chr1	4483852	4483924	8636240
chr1	4486477	4486838	8636240
chr6	42910191	42910222	3131743
chr6	67825649	67825684	3131743
chr6	68185876	68185913	3131743
chr16	3493051	3493082	3131743
chr5	115232111	115232141	10760574
chrX	97579346	97579925	10760574
chr7	46535461	46535502	7552299
chr1	36636087	36636117	8383622
chr17	33913426	33913513	8290364
chr6	70144946	70144979	11254715
chr6	70190541	70190577	11254715
chr6	70300982	70301015	11254715
chr6	70336600	70336636	11254715
chr6	70365085	70365120	11254715
chr6	70387632	70387668	11254715
chrX	53558787	53558827	11254715
chr12	86362813	86362848	8552086
chr12	86362673	86362702	2110508
chr17	33610878	33610910	3322806
chr17	34870977	34871009	3322806
chr6	70448421	70448458	2109186
chr6	70484008	70484045	2109186
chr6	70502797	70502848	2109186
chr6	70537608	70537645	2109186
chr6	70573133	70573170	2109186
chr6	70593462	70593513	2109186
chr6	70601944	70601986	2109186
chr6	70617101	70617143	2109186
chr6	70628635	70628676	2109186
chr6	70633746	70633786	2109186
chr6	70648480	70648955	2109186
chr6	70656039	70656317	2109186
chr8	123621640	123622385	8321202
chr9	110614453	110614482	2211821
chr11	67124722	67124828	2211821
chr11	104403209	104403305	2211821
chr2	113744201	113744247	2211821
chr1	66878146	66878195	2211821
chr14	53898486	53898586	2211821
chr14	53926896	53926996	2211821
chr7	18568521	18568552	2601707
chr18	61170453	61170480	11282029
chr2	9775383	9776029	7629014
chr6	4455417	4455633	8702912
chr6	70655483	70655561	2511430
chr9	65221178	65221381	16357058
chr4	106933762	106933860	12042312
chr12	113875344	113875373	2111447
chr11	21457190	21457445	3172222
chr11	21471745	21472279	3172222
chr19	43577766	43577815	3172222
chr3	14863350	14863383	8463242
chr16	23806223	23806249	1977662
chr2	163441532	163441769	8265639
chr5	137314748	137314782	11755530
chr5	16065362	16065393	9315634
chr5	121148158	121148265	2457496
chr5	121168072	121168261	2457496
chr17	33610870	33610899	2457496
chr6	4455528	4455560	10477728
chr7	126592040	126592074	9395505
chr12	91806421	91806453	7989366
chr2	91426321	91426350	9565620
chr2	91429247	91429276	9565620
chr15	61814749	61814779	3313385
chr19	44805743	44805811	11807024
chr19	44809825	44809960	11807024
chr11	101367971	101367998	10660629
chr11	69396532	69396570	8051093
chr4	80305182	80305213	9710594
chr12	104874217	104874665	9417125
chr2	104927782	104928263	1671709
chr2	104933774	104934343	1671709
chr2	104943920	104945031	1671709
chr2	104964163	104964261	1671709
chr2	104967653	104967727	1671709
chr2	104973145	104974452	1671709
chr16	97567922	97567998	2974922
chr16	97690826	97690879	2974922
chr5	113875448	113875531	15792532
chr5	113904661	113904724	15792532
chr7	46239063	46239781	1328870
chr1	135178144	135178237	7962542
chr3	113284917	113284950	1699843
chr1	196792904	196792939	11023821
chr5	91560912	91561133	2452972
chr17	33589430	33589465	2014233
chr17	33610906	33610942	2014233
chr17	34870944	34870981	2014233
chr17	35806754	35806791	2014233
chr5	51786341	51786388	16825189
chr1	173050608	173050662	16825189
chr3	95744114	95744143	10454566
chr9	21709248	21709315	2162479
chr9	21713752	21714429	2162479
chr11	98228303	98228335	1672439
chr12	86362675	86362706	1645787
chr6	72234547	72235407	8928820
chr6	72239288	72239420	8928820
chr6	70655323	70655353	1630463
chr17	33610949	33610989	1630463
chr17	34987443	34987473	1630463
chr11	72777304	72777372	12119294
chr12	113875208	113875259	8663022
chr2	109493202	109493238	9581764
chr18	34986757	34986789	11566878
chr9	45687022	45687053	10642500
chr11	53462119	53462180	10438901
chr9	86493075	86493107	2738073
chr7	142489137	142489357	3006925
chr19	52317501	52317720	3006925
chr10	59672846	59673011	9582364
chr18	12647433	12647697	9651314
chr19	27859699	27859759	2253877
chr17	56462962	56463119	2253877
chr17	56465108	56466004	2253877
chr8	86964017	86964118	2253877
chr8	86969966	86970077	2253877
chr8	86977850	86977971	2253877
chr8	86980214	86981576	2253877
chr8	86982719	86982979	2253877
chr8	86984855	86986055	2253877
chr10	128334592	128334626	14525975
chr2	181600901	181600934	11353810
chr2	167380193	167381855	2253878
chr5	89602412	89602443	9748293
chr2	130274028	130274059	1339438
chr16	18940724	18940965	1729607
chr16	19092845	19093083	1729607
chr11	52097308	52097387	1827138
chr11	52099679	52101227	1827138
chr11	52102275	52102368	1827138
chr11	52103951	52105048	1827138
chr11	52125544	52125640	1827138
chr3	131183843	131183935	1827138
chr3	131189467	131189547	1827138
chr19	55972778	55972867	1827138
chr19	44460893	44460987	2606350
chr3	10191197	10191235	2606350
chr5	121148235	121148291	2243086
chr5	121168149	121168205	2243086
chr14	15368772	15368800	10692469
chr5	115216352	115216429	2044952
chr11	83666965	83667587	2044952
chr11	83672096	83672298	2044952
chr11	83677988	83678176	2044952
chr11	83680135	83680374	2044952
chr11	83698843	83699008	2044952
chr11	83705242	83705350	2044952
chr11	83709577	83709771	2044952
chr11	83712466	83712535	2044952
chr11	83721101	83721728	2044952
chr19	7263832	7264780	2044952
chr19	37499334	37499918	10101294
chr1	173254771	173254799	9374551
chr7	18566396	18566426	10359011
chrX	7124723	7125567	1656391
chr15	78855142	78855177	8559662
chrX	20027145	20027175	8559663
chr16	65428100	65428821	8504933
chr10	20847864	20847892	2236022
chr11	54093061	54093102	8246960
chr16	16777743	16777785	10435576
chr9	57494748	57494781	1852076
chr6	132534899	132534934	9015393
chr6	132561001	132561036	9015393
chr6	122821684	122821919	16116202
chr5	89530296	89530325	11451945
chr5	147574433	147574465	14701942
chr17	31406530	31406560	7823934
chr16	85692593	85692625	15256533
chr3	131099625	131100626	1827423
chr3	131212271	131212484	1827423
chr14	53185518	53185560	1827423
chr19	4593965	4593995	15917242
chrX	33695886	33696975	16414020
chrX	33737548	33738601	16414020
chrX	33785401	33786461	16414020
chrX	33819419	33820515	16414020
chrX	33862493	33863610	16414020
chrX	33913449	33914538	16414020
chrX	33957041	33958155	16414020
chr1	172992090	172992151	9360965
chr12	113875221	113875251	2555786
chr10	66933144	66933179	1969796
chr8	74497415	74497448	9933587
chr9	45686866	45686898	16224064
chr5	146184209	146184269	10860926
chr17	45495931	45495959	11040101
chr9	32503846	32503882	1409581
chr5	93424229	93424258	8757327
chr6	70144909	70144947	9858563
chr6	70190578	70190612	9858563
chr6	70300947	70300983	9858563
chr6	70336637	70336671	9858563
chr6	70365121	70365154	9858563
chr6	70387667	70387705	9858563
chr11	106130693	106130743	9858563
chr11	120640248	120640290	9786926
chr2	90897654	90897832	2180582
chr2	90900268	90900365	2180582
chr2	90914092	90916595	2180582
chr9	57494748	57494776	7892203
chr3	37317761	37317792	8406004
chr12	114344857	114344899	2507313
chr12	115568086	115568114	2507313
chr12	115783417	115783448	2507313
chr12	115909335	115909363	2507313
chr12	115955880	115955911	2507313
chr12	116206320	116206348	2507313
chr12	116250983	116251014	2507313
chrX	20027146	20027174	8557686
chr10	57174928	57175016	1717345
chr10	57184314	57184694	1717345
chr10	57185910	57186026	1717345
chr10	57189783	57189817	1717345
chr10	57191035	57191096	1717345
chr10	57192996	57194717	1717345
chr10	57200325	57200865	1717345
chr17	34567380	34567418	1717345
chr17	34580298	34580336	1717345
chr15	76304716	76304894	1717345
chr15	76323707	76323847	1717345
chr15	76325250	76325758	1717345
chr15	76327668	76328171	1717345
chr4	135145012	135145050	16181749
chr2	167380290	167380318	9374525
chr5	91533696	91533726	11825903
chr19	52317533	52317563	11825903
chr3	28888378	28888408	11825903
chr2	62284565	62284595	11825903
chr3	159533953	159534406	10896939
chr6	70654962	70654995	7816634
chr13	19227291	19227351	1309596
chr13	19280451	19280510	1309596
chr13	19307968	19308027	1309596
chr12	113875294	113875358	1309596
chr6	4455597	4455637	3733754
chr6	41451085	41451559	3641189
chr4	141097307	141098498	3641189
chr3	37317570	37317603	7565783
chr5	137517686	137518116	8429032
chr5	137519818	137519872	8429032
chr9	98232312	98234392	1648481
chr9	98255700	98255873	1648481
chr4	140565201	140565232	9733765
chr12	113875218	113875262	2573524
chr12	113875218	113875262	2573523
chr10	34079088	34079121	9369451
chr7	56431087	56431124	1697928
chr5	23371707	23371770	1697928
chr5	97089578	97089620	1697928
chr3	30711032	30711074	1697928
chr3	52891298	52891340	1697928
chr3	93460309	93460347	1697928
chr2	137786746	137786785	1697928
chr1	92688074	92688115	1697928
chr9	43210266	43210308	1697928
chr9	76557075	76557115	1697928
chr8	30070831	30070925	1697928
chr8	46973628	46973670	1697928
chr15	51612591	51612633	1697928
chr15	74806792	74806890	1697928
chr15	74808755	74808824	1697928
chr15	74809950	74812614	1697928
chr15	74816189	74816902	1697928
chr15	74822132	74828327	1697928
chr15	74872275	74872371	1697928
chr15	74874186	74874290	1697928
chr15	74875398	74879211	1697928
chr15	74892909	74893338	1697928
chr15	74896474	74897345	1697928
chr15	74898448	74898535	1697928
chr15	74899816	74899910	1697928
chr15	74902178	74902265	1697928
chr15	74920671	74920711	1697928
chr15	74935467	74935513	1697928
chr15	74937344	74937445	1697928
chr15	74938555	74938851	1697928
chr15	74940928	74940981	1697928
chr15	74942002	74942875	1697928
chr15	74958547	74958643	1697928
chr15	74960529	74960628	1697928
chr15	74961910	74962001	1697928
chr15	74964083	74965592	1697928
chr15	74979361	74981877	1697928
chr15	74982978	74983061	1697928
chr15	74984384	74984484	1697928
chr15	74986286	74986369	1697928
chr15	75013080	75013858	1697928
chr15	75023387	75023485	1697928
chr15	75024579	75024617	1697928
chr15	75044017	75044295	1697928
chr15	75045393	75045459	1697928
chr15	75064362	75064531	1697928
chr15	75065854	75066353	1697928
chr15	75067374	75068275	1697928
chr15	75072019	75072091	1697928
chr15	75073987	75074156	1697928
chr15	75075532	75075620	1697928
chr15	75092998	75093404	1697928
chr15	75094477	75094527	1697928
chr15	75096055	75096146	1697928
chr15	75097472	75097640	1697928
chr15	75099451	75099490	1697928
chr15	75122783	75122886	1697928
chr15	75124190	75124276	1697928
chr15	75131424	75133048	1697928
chr15	75141973	75142141	1697928
chr15	75155958	75156028	1697928
chr15	75177864	75177968	1697928
chr15	75180068	75181772	1697928
chr15	75201590	75201693	1697928
chr15	75204355	75204439	1697928
chr15	75256790	75256855	1697928
chr15	75258518	75258613	1697928
chr15	75261788	75262172	1697928
chr15	75268430	75269094	1697928
chr14	61763897	61763939	1697928
chr18	21560809	21560851	1697928
chr6	147221086	147221118	9280059
chrX	99686013	99686377	9426246
chr6	115407219	115407269	7838156
chr19	40243903	40245132	7838156
chr19	40247090	40247900	7838156
chr14	16999527	16999931	7838156
chr14	17000987	17001191	7838156
chr14	17004848	17005036	7838156
chr14	17007942	17008565	7838156
chr14	17009720	17009866	7838156
chr14	17013049	17013104	7838156
chr14	17014695	17014956	7838156
chr14	17031224	17032189	7838156
chr7	24606265	24606297	1545794
chr11	87609641	87609721	8384306
chr12	114345283	114345346	1922039
chr12	31850891	31850937	1661245
chr6	113401689	113401718	1339452
chr12	86362674	86362707	7698311
chr8	27273950	27273980	14673133
chr9	98298948	98300034	8288643
chr6	72234141	72236749	7900819
chr4	152974996	152975053	7900819
chr8	72525044	72525233	7900819
chr12	86362673	86362701	8346248
chr11	106130609	106130812	8555489
chr11	54091603	54091662	3876931
chr11	54093026	54093177	3876931
chr12	25295983	25296021	7559662
chr12	25297228	25297303	7559662
chr11	32183543	32183620	9032265
chr11	32196360	32196437	9032265
chr19	5637774	5641675	2001591
chr19	5645514	5645555	2001591
chr19	5646807	5648105	2001591
chr18	20808271	20808309	1870969
chr3	10196460	10196574	1545801
chr18	3281798	3281831	10799536
chr18	43863436	43863471	1508185
chr9	108198553	108199203	8413228
chr17	26571739	26572245	9778505
chr2	113751483	113752125	8164695
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s3.gff3000066400000000000000000003654651211610345200225750ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr7 3538564 144670781
##sequence-region   chrX 3009684 164531393
##sequence-region   chr8 3622334 126779431
##sequence-region   chr9 4855449 122696623
##sequence-region   chr3 3241275 159534406
##sequence-region   chr4 3016163 152975053
##sequence-region   chr5 6489488 150790995
##sequence-region   chr6 4455158 149315651
##sequence-region   chr14 10074301 102257125
##sequence-region   chr15 4832309 102863869
##sequence-region   chr12 3954579 116457835
##sequence-region   chr13 3172351 112857798
##sequence-region   chr18 3281799 89668722
##sequence-region   chr19 3247631 55972867
##sequence-region   chr16 3493052 97690879
##sequence-region   chr17 4837106 89109235
##sequence-region   chr10 3557642 128360798
##sequence-region   chr13_random 132571 132601
##sequence-region   chr5_random 345219 2907836
##sequence-region   chr11 3852159 121112225
##sequence-region   chrY_random 10870094 13323146
##sequence-region   chr1 3166625 196792939
##sequence-region   chr2 7527753 181857052
chr13	.	BED_feature	12855406	12855438	.	.	.	Name=8065334
chr13	.	BED_feature	13072136	13072165	.	.	.	Name=8065334
chr2	.	BED_feature	172240871	172240910	.	.	.	Name=12801994
chr3	.	BED_feature	88033299	88034734	.	.	.	Name=1327537
chr3	.	BED_feature	131173869	131173905	.	.	.	Name=8892228
chr4	.	BED_feature	129060998	129061031	.	.	.	Name=11278409
chr9	.	BED_feature	44737716	44737752	.	.	.	Name=11278409
chr12	.	BED_feature	113725370	113725411	.	.	.	Name=8144891
chr18	.	BED_feature	61336787	61336835	.	.	.	Name=9325159
chr9	.	BED_feature	57494752	57494779	.	.	.	Name=1986235
chr6	.	BED_feature	5447223	5447252	.	.	.	Name=12820900
chr12	.	BED_feature	86362677	86362711	.	.	.	Name=2498646
chr11	.	BED_feature	96087148	96087322	.	.	.	Name=1360646
chr14	.	BED_feature	53921089	53921125	.	.	.	Name=8449897
chr9	.	BED_feature	49551490	49551554	.	.	.	Name=11696550
chr4	.	BED_feature	134425054	134425134	.	.	.	Name=8341710
chr4	.	BED_feature	134427382	134427503	.	.	.	Name=8341710
chr17	.	BED_feature	43959178	43959286	.	.	.	Name=8341710
chr17	.	BED_feature	44070861	44071424	.	.	.	Name=8341710
chr17	.	BED_feature	44073080	44073136	.	.	.	Name=8341710
chr17	.	BED_feature	44102720	44102884	.	.	.	Name=8341710
chr17	.	BED_feature	44121574	44121747	.	.	.	Name=8341710
chr17	.	BED_feature	44180246	44180353	.	.	.	Name=8341710
chr17	.	BED_feature	44187799	44187958	.	.	.	Name=8341710
chr17	.	BED_feature	44198286	44198718	.	.	.	Name=8341710
chr16	.	BED_feature	92584341	92584421	.	.	.	Name=8341710
chr7	.	BED_feature	46713823	46713869	.	.	.	Name=2708350
chr14	.	BED_feature	15368766	15368800	.	.	.	Name=2164682
chr5	.	BED_feature	137356957	137356986	.	.	.	Name=9427542
chr7	.	BED_feature	28088022	28088093	.	.	.	Name=7559666
chr18	.	BED_feature	82688826	82688871	.	.	.	Name=1690988
chr6	.	BED_feature	70655273	70655306	.	.	.	Name=10623825
chr16	.	BED_feature	29985000	29985028	.	.	.	Name=10623825
chr17	.	BED_feature	33644478	33644637	.	.	.	Name=1652422
chr17	.	BED_feature	33646782	33647960	.	.	.	Name=1652422
chr2	.	BED_feature	27563778	27563952	.	.	.	Name=1652422
chr2	.	BED_feature	27570623	27570757	.	.	.	Name=1652422
chr2	.	BED_feature	27574324	27574451	.	.	.	Name=1652422
chr2	.	BED_feature	27576229	27576364	.	.	.	Name=1652422
chr2	.	BED_feature	27578215	27578297	.	.	.	Name=1652422
chr2	.	BED_feature	27581549	27581681	.	.	.	Name=1652422
chr1	.	BED_feature	169461606	169461748	.	.	.	Name=1652422
chr1	.	BED_feature	169463964	169464146	.	.	.	Name=1652422
chr1	.	BED_feature	169467908	169468035	.	.	.	Name=1652422
chr1	.	BED_feature	169469186	169469322	.	.	.	Name=1652422
chr1	.	BED_feature	169471117	169471201	.	.	.	Name=1652422
chr1	.	BED_feature	169475800	169475944	.	.	.	Name=1652422
chr3	.	BED_feature	88464666	88464699	.	.	.	Name=10514508
chr3	.	BED_feature	88470431	88470464	.	.	.	Name=10514508
chr19	.	BED_feature	54097641	54099571	.	.	.	Name=7487893
chr6	.	BED_feature	41474207	41474734	.	.	.	Name=2349098
chr6	.	BED_feature	29009781	29010375	.	.	.	Name=8633022
chr6	.	BED_feature	29018961	29018996	.	.	.	Name=8633022
chr6	.	BED_feature	29021165	29021200	.	.	.	Name=8633022
chr10	.	BED_feature	80208263	80208306	.	.	.	Name=10446911
chr16	.	BED_feature	23806222	23806263	.	.	.	Name=1834659
chr3	.	BED_feature	37317759	37317792	.	.	.	Name=8417328
chr12	.	BED_feature	77084392	77084433	.	.	.	Name=9058381
chr12	.	BED_feature	77086130	77086167	.	.	.	Name=9058381
chr5	.	BED_feature	91525244	91525437	.	.	.	Name=1990282
chr12	.	BED_feature	113875336	113875479	.	.	.	Name=3125419
chr6	.	BED_feature	145348609	145348648	.	.	.	Name=2365680
chr5	.	BED_feature	21110587	21110672	.	.	.	Name=2365680
chr5	.	BED_feature	41630395	41630480	.	.	.	Name=2365680
chr5	.	BED_feature	83411421	83411506	.	.	.	Name=2365680
chr1	.	BED_feature	16088803	16088888	.	.	.	Name=2365680
chr9	.	BED_feature	31532482	31532530	.	.	.	Name=2365680
chr9	.	BED_feature	109815633	109815704	.	.	.	Name=2365680
chrX	.	BED_feature	33099690	33099764	.	.	.	Name=2365680
chrX	.	BED_feature	148997347	148997395	.	.	.	Name=2365680
chr11	.	BED_feature	29452950	29452989	.	.	.	Name=2365680
chr11	.	BED_feature	46571265	46571350	.	.	.	Name=2365680
chr17	.	BED_feature	32591325	32591409	.	.	.	Name=2365680
chr15	.	BED_feature	59040613	59040698	.	.	.	Name=2365680
chr13	.	BED_feature	12855408	12855435	.	.	.	Name=2744462
chr13	.	BED_feature	13072136	13072165	.	.	.	Name=2744462
chr11	.	BED_feature	76965963	76966562	.	.	.	Name=1986236
chr1	.	BED_feature	173252807	173252912	.	.	.	Name=1986236
chr1	.	BED_feature	173254315	173254471	.	.	.	Name=1986236
chr12	.	BED_feature	113680203	113680232	.	.	.	Name=9755173
chr12	.	BED_feature	113701767	113701797	.	.	.	Name=9755173
chr12	.	BED_feature	57453028	57453073	.	.	.	Name=9211870
chr4	.	BED_feature	94544521	94544623	.	.	.	Name=1851295
chr15	.	BED_feature	82280026	82280079	.	.	.	Name=2387871
chr8	.	BED_feature	75247915	75247946	.	.	.	Name=10433980
chr15	.	BED_feature	98883163	98883205	.	.	.	Name=1639068
chr15	.	BED_feature	9476872	9477448	.	.	.	Name=2038316
chr7	.	BED_feature	99225295	99226309	.	.	.	Name=12235161
chr5	.	BED_feature	104676200	104676297	.	.	.	Name=9649510
chr12	.	BED_feature	86362632	86362992	.	.	.	Name=9584171
chr1	.	BED_feature	163623784	163623811	.	.	.	Name=10684974
chr1	.	BED_feature	163625033	163625063	.	.	.	Name=10684974
chr14	.	BED_feature	67037129	67037160	.	.	.	Name=11733514
chr8	.	BED_feature	109492104	109492670	.	.	.	Name=1763063
chr6	.	BED_feature	52096110	52096149	.	.	.	Name=10068641
chr5	.	BED_feature	89609350	89609379	.	.	.	Name=9529146
chr8	.	BED_feature	42873634	42873667	.	.	.	Name=16500425
chr9	.	BED_feature	43794366	43794438	.	.	.	Name=1672442
chr17	.	BED_feature	33610896	33610924	.	.	.	Name=1727488
chr17	.	BED_feature	34870964	34870992	.	.	.	Name=1727488
chr12	.	BED_feature	104139375	104139403	.	.	.	Name=1701020
chr12	.	BED_feature	104174807	104174835	.	.	.	Name=1701020
chr12	.	BED_feature	104358133	104358161	.	.	.	Name=1701020
chr5	.	BED_feature	91535987	91536016	.	.	.	Name=1701020
chr4	.	BED_feature	62830793	62830821	.	.	.	Name=1701020
chr4	.	BED_feature	62848683	62848711	.	.	.	Name=1701020
chr2	.	BED_feature	167381277	167381623	.	.	.	Name=1701020
chr9	.	BED_feature	78015523	78015661	.	.	.	Name=2166952
chr9	.	BED_feature	78041999	78042137	.	.	.	Name=2166952
chr9	.	BED_feature	78068396	78068448	.	.	.	Name=2166952
chr9	.	BED_feature	78074868	78074935	.	.	.	Name=2166952
chr9	.	BED_feature	78133949	78134089	.	.	.	Name=2166952
chr2	.	BED_feature	167380097	167380135	.	.	.	Name=15299028
chr11	.	BED_feature	44243409	44243440	.	.	.	Name=12876285
chr11	.	BED_feature	78736087	78736120	.	.	.	Name=12876285
chr9	.	BED_feature	50306077	50306110	.	.	.	Name=12876285
chr6	.	BED_feature	91649567	91649596	.	.	.	Name=15142033
chr8	.	BED_feature	71809516	71809738	.	.	.	Name=11796707
chr5	.	BED_feature	16065430	16065458	.	.	.	Name=12163028
chr12	.	BED_feature	113875355	113875416	.	.	.	Name=1899229
chr7	.	BED_feature	31525874	31525902	.	.	.	Name=12520165
chr7	.	BED_feature	32254523	32254551	.	.	.	Name=12520165
chr4	.	BED_feature	84395388	84395416	.	.	.	Name=12520165
chr1	.	BED_feature	146946113	146946144	.	.	.	Name=12520165
chr8	.	BED_feature	43108456	43108485	.	.	.	Name=12520165
chr12	.	BED_feature	5616600	5616628	.	.	.	Name=12520165
chr11	.	BED_feature	33176705	33176733	.	.	.	Name=12520165
chr17	.	BED_feature	61467015	61467046	.	.	.	Name=12520165
chr12	.	BED_feature	116052276	116052307	.	.	.	Name=1970570
chr11	.	BED_feature	70478628	70478705	.	.	.	Name=2734297
chr2	.	BED_feature	62284558	62284607	.	.	.	Name=10938089
chr1	.	BED_feature	64467141	64467218	.	.	.	Name=7628390
chr1	.	BED_feature	75242513	75243687	.	.	.	Name=8382796
chrX	.	BED_feature	20027121	20027366	.	.	.	Name=1849903
chr17	.	BED_feature	89109206	89109235	.	.	.	Name=11145741
chr2	.	BED_feature	147728350	147728401	.	.	.	Name=9118802
chr6	.	BED_feature	34342453	34342485	.	.	.	Name=11145742
chr13	.	BED_feature	52980565	52982323	.	.	.	Name=12023274
chr3	.	BED_feature	88458960	88459035	.	.	.	Name=7891679
chr3	.	BED_feature	88464663	88464736	.	.	.	Name=7891679
chr3	.	BED_feature	88470429	88470501	.	.	.	Name=7891679
chr7	.	BED_feature	79608339	79608384	.	.	.	Name=14726448
chr3	.	BED_feature	89465236	89467184	.	.	.	Name=7937772
chr8	.	BED_feature	78299166	78299266	.	.	.	Name=7937772
chr13	.	BED_feature	13756612	13757727	.	.	.	Name=7937772
chr10	.	BED_feature	26982958	26983076	.	.	.	Name=7937772
chrX	.	BED_feature	8811752	8812446	.	.	.	Name=7937772
chr18	.	BED_feature	76271050	76271168	.	.	.	Name=7937772
chr6	.	BED_feature	42910197	42910222	.	.	.	Name=3119226
chr6	.	BED_feature	68185882	68185907	.	.	.	Name=3119226
chr16	.	BED_feature	3493057	3493082	.	.	.	Name=3119226
chr6	.	BED_feature	70655344	70655376	.	.	.	Name=3145404
chr12	.	BED_feature	113875436	113875464	.	.	.	Name=3145404
chr12	.	BED_feature	114508181	114508208	.	.	.	Name=3145404
chr3	.	BED_feature	113284902	113284941	.	.	.	Name=8874496
chr5	.	BED_feature	115209362	115211104	.	.	.	Name=2263635
chr5	.	BED_feature	115221022	115221214	.	.	.	Name=2263635
chr5	.	BED_feature	115231517	115231801	.	.	.	Name=2263635
chr11	.	BED_feature	83672140	83672273	.	.	.	Name=2263635
chr12	.	BED_feature	86362646	86362702	.	.	.	Name=2928331
chr5	.	BED_feature	146313739	146313765	.	.	.	Name=7651384
chr5	.	BED_feature	146383578	146383604	.	.	.	Name=7651384
chr11	.	BED_feature	95403797	95403832	.	.	.	Name=7565756
chr15	.	BED_feature	78753914	78753944	.	.	.	Name=9931450
chr11	.	BED_feature	53564137	53564178	.	.	.	Name=9498775
chr11	.	BED_feature	94767985	94768013	.	.	.	Name=2779548
chr10	.	BED_feature	66907644	66907888	.	.	.	Name=12538520
chr15	.	BED_feature	76304477	76304854	.	.	.	Name=9829985
chrX	.	BED_feature	79208618	79208790	.	.	.	Name=11259421
chr7	.	BED_feature	45334857	45334916	.	.	.	Name=15466854
chr7	.	BED_feature	120806482	120806510	.	.	.	Name=15466854
chr6	.	BED_feature	71571315	71571343	.	.	.	Name=15466854
chr6	.	BED_feature	78426651	78426679	.	.	.	Name=15466854
chr6	.	BED_feature	123184770	123184798	.	.	.	Name=15466854
chr4	.	BED_feature	105292421	105292449	.	.	.	Name=15466854
chr3	.	BED_feature	39409201	39409229	.	.	.	Name=15466854
chr3	.	BED_feature	41582549	41582577	.	.	.	Name=15466854
chr3	.	BED_feature	122249022	122249050	.	.	.	Name=15466854
chr3	.	BED_feature	122624994	122625022	.	.	.	Name=15466854
chr3	.	BED_feature	138542154	138542182	.	.	.	Name=15466854
chr2	.	BED_feature	51693327	51693355	.	.	.	Name=15466854
chr2	.	BED_feature	83191234	83191262	.	.	.	Name=15466854
chr2	.	BED_feature	129441626	129441654	.	.	.	Name=15466854
chr2	.	BED_feature	166191672	166191700	.	.	.	Name=15466854
chr9	.	BED_feature	96705282	96705310	.	.	.	Name=15466854
chr8	.	BED_feature	4465786	4465814	.	.	.	Name=15466854
chr13	.	BED_feature	64639251	64639279	.	.	.	Name=15466854
chr11	.	BED_feature	6319199	6319227	.	.	.	Name=15466854
chr10	.	BED_feature	57470993	57471021	.	.	.	Name=15466854
chr17	.	BED_feature	37555517	37555545	.	.	.	Name=15466854
chr15	.	BED_feature	25785032	25785060	.	.	.	Name=15466854
chr14	.	BED_feature	28044922	28044950	.	.	.	Name=15466854
chr19	.	BED_feature	28099720	28099748	.	.	.	Name=15466854
chr18	.	BED_feature	34171913	34171941	.	.	.	Name=15466854
chr6	.	BED_feature	115407118	115407162	.	.	.	Name=9099735
chr1	.	BED_feature	135178147	135178175	.	.	.	Name=9201991
chr6	.	BED_feature	70655243	70655313	.	.	.	Name=2501761
chr15	.	BED_feature	74816722	74816777	.	.	.	Name=9746780
chr15	.	BED_feature	74827422	74827479	.	.	.	Name=9746780
chr15	.	BED_feature	74878325	74878382	.	.	.	Name=9746780
chr15	.	BED_feature	74893030	74893087	.	.	.	Name=9746780
chr15	.	BED_feature	74942700	74942755	.	.	.	Name=9746780
chr15	.	BED_feature	74965415	74965466	.	.	.	Name=9746780
chr15	.	BED_feature	74980245	74980287	.	.	.	Name=9746780
chr15	.	BED_feature	75013881	75013926	.	.	.	Name=9746780
chr15	.	BED_feature	75093112	75093165	.	.	.	Name=9746780
chr1	.	BED_feature	136106234	136106418	.	.	.	Name=1324403
chr6	.	BED_feature	142920946	142921305	.	.	.	Name=11098147
chr9	.	BED_feature	57494749	57494782	.	.	.	Name=3413062
chr19	.	BED_feature	37762874	37762946	.	.	.	Name=10976925
chr8	.	BED_feature	97068194	97068366	.	.	.	Name=2993866
chr12	.	BED_feature	114344858	114344899	.	.	.	Name=2710122
chr12	.	BED_feature	116052275	116052307	.	.	.	Name=2710122
chr3	.	BED_feature	37317568	37317596	.	.	.	Name=1620122
chr6	.	BED_feature	40976306	40976479	.	.	.	Name=3259318
chr6	.	BED_feature	40977841	40977872	.	.	.	Name=3259318
chr6	.	BED_feature	40988923	40989030	.	.	.	Name=3259318
chr6	.	BED_feature	40991877	40991970	.	.	.	Name=3259318
chr6	.	BED_feature	41043029	41043170	.	.	.	Name=3259318
chr6	.	BED_feature	41045569	41045620	.	.	.	Name=3259318
chr6	.	BED_feature	41048330	41048467	.	.	.	Name=3259318
chr6	.	BED_feature	41059624	41059730	.	.	.	Name=3259318
chr6	.	BED_feature	41081351	41081400	.	.	.	Name=3259318
chr6	.	BED_feature	41092532	41092629	.	.	.	Name=3259318
chr6	.	BED_feature	41107826	41107980	.	.	.	Name=3259318
chr5	.	BED_feature	143168936	143169346	.	.	.	Name=12855690
chr8	.	BED_feature	126778097	126778129	.	.	.	Name=12855690
chr16	.	BED_feature	37802844	37802876	.	.	.	Name=12855690
chr1	.	BED_feature	163625141	163625648	.	.	.	Name=12855690
chrX	.	BED_feature	147774589	147774621	.	.	.	Name=12855690
chrX	.	BED_feature	147831148	147831180	.	.	.	Name=12855690
chr13_random	.	BED_feature	132571	132601	.	.	.	Name=1527023
chr12	.	BED_feature	77628973	77629001	.	.	.	Name=10037687
chr10	.	BED_feature	79980250	79980309	.	.	.	Name=11390978
chr12	.	BED_feature	86362673	86362727	.	.	.	Name=10462507
chr15	.	BED_feature	78753914	78753944	.	.	.	Name=10760565
chr7	.	BED_feature	46729237	46729273	.	.	.	Name=11673270
chr5	.	BED_feature	104675338	104675366	.	.	.	Name=7799957
chr7	.	BED_feature	70234442	70234497	.	.	.	Name=15541767
chr12	.	BED_feature	86362676	86362704	.	.	.	Name=9032301
chr11	.	BED_feature	98775790	98776740	.	.	.	Name=1658797
chr2	.	BED_feature	38536506	38536605	.	.	.	Name=9013759
chr4	.	BED_feature	28981911	28981959	.	.	.	Name=16314414
chr11	.	BED_feature	53462147	53462176	.	.	.	Name=9233810
chr19	.	BED_feature	6989380	6989414	.	.	.	Name=12960079
chr5	.	BED_feature	91565805	91565841	.	.	.	Name=2601711
chr9	.	BED_feature	71648332	71648487	.	.	.	Name=1321336
chr9	.	BED_feature	71654865	71655099	.	.	.	Name=1321336
chr9	.	BED_feature	71657044	71657515	.	.	.	Name=1321336
chr9	.	BED_feature	71666630	71666826	.	.	.	Name=1321336
chr9	.	BED_feature	71668637	71668711	.	.	.	Name=1321336
chr9	.	BED_feature	71674547	71674627	.	.	.	Name=1321336
chr9	.	BED_feature	71681666	71682326	.	.	.	Name=1321336
chr9	.	BED_feature	71683754	71683834	.	.	.	Name=1321336
chr9	.	BED_feature	71721212	71721347	.	.	.	Name=1321336
chr9	.	BED_feature	71742550	71742582	.	.	.	Name=1321336
chr9	.	BED_feature	71798975	71799076	.	.	.	Name=1321336
chr9	.	BED_feature	71814200	71814273	.	.	.	Name=1321336
chr9	.	BED_feature	71908241	71910179	.	.	.	Name=1321336
chr13	.	BED_feature	30756012	30756039	.	.	.	Name=10770796
chr5	.	BED_feature	28489138	28489196	.	.	.	Name=8625814
chr7	.	BED_feature	4732188	4732219	.	.	.	Name=15117948
chr6	.	BED_feature	133727977	133728008	.	.	.	Name=15117948
chr5	.	BED_feature	143170456	143170487	.	.	.	Name=15117948
chr4	.	BED_feature	103061586	103061617	.	.	.	Name=15117948
chr9	.	BED_feature	38824925	38824956	.	.	.	Name=15117948
chr8	.	BED_feature	47728062	47728093	.	.	.	Name=15117948
chr8	.	BED_feature	126779400	126779431	.	.	.	Name=15117948
chr13	.	BED_feature	81528372	81528403	.	.	.	Name=15117948
chr11	.	BED_feature	120163805	120163836	.	.	.	Name=15117948
chr17	.	BED_feature	63032642	63032673	.	.	.	Name=15117948
chr16	.	BED_feature	64861025	64861056	.	.	.	Name=15117948
chrX	.	BED_feature	47464340	47464368	.	.	.	Name=15117948
chr6	.	BED_feature	70068752	70068784	.	.	.	Name=2120037
chr6	.	BED_feature	70144886	70144924	.	.	.	Name=2120037
chr6	.	BED_feature	70190600	70190638	.	.	.	Name=2120037
chr6	.	BED_feature	70300922	70300960	.	.	.	Name=2120037
chr6	.	BED_feature	70336659	70336697	.	.	.	Name=2120037
chr6	.	BED_feature	70365143	70365181	.	.	.	Name=2120037
chr6	.	BED_feature	70387691	70387729	.	.	.	Name=2120037
chr10	.	BED_feature	20847654	20847700	.	.	.	Name=2678098
chr1	.	BED_feature	151861905	151862280	.	.	.	Name=11668179
chr12	.	BED_feature	86362674	86362701	.	.	.	Name=8230424
chr9	.	BED_feature	21881080	21881113	.	.	.	Name=11481336
chr17	.	BED_feature	34810553	34810729	.	.	.	Name=2181276
chr14	.	BED_feature	30037251	30037316	.	.	.	Name=1569934
chr12	.	BED_feature	115568098	115568139	.	.	.	Name=3099286
chr12	.	BED_feature	115606694	115606794	.	.	.	Name=3099286
chr12	.	BED_feature	115656386	115656486	.	.	.	Name=3099286
chr12	.	BED_feature	115807431	115807483	.	.	.	Name=3099286
chr12	.	BED_feature	115820292	115820392	.	.	.	Name=3099286
chr12	.	BED_feature	115909279	115909389	.	.	.	Name=3099286
chr12	.	BED_feature	116071454	116071506	.	.	.	Name=3099286
chr12	.	BED_feature	116206264	116206374	.	.	.	Name=3099286
chrX	.	BED_feature	164531362	164531393	.	.	.	Name=10859305
chr19	.	BED_feature	44346956	44346991	.	.	.	Name=10580438
chrX	.	BED_feature	20027146	20027210	.	.	.	Name=1420363
chr7	.	BED_feature	18568361	18568556	.	.	.	Name=3336366
chr14	.	BED_feature	15368772	15368799	.	.	.	Name=8900181
chr5	.	BED_feature	113309937	113310329	.	.	.	Name=8543177
chr4	.	BED_feature	94543040	94543091	.	.	.	Name=2504580
chr2	.	BED_feature	16328370	16328636	.	.	.	Name=2504580
chr8	.	BED_feature	73628070	73629605	.	.	.	Name=2504580
chr8	.	BED_feature	87867633	87867742	.	.	.	Name=2504580
chr10	.	BED_feature	85729845	85730358	.	.	.	Name=9182717
chr1	.	BED_feature	169461714	169461741	.	.	.	Name=9006910
chr13	.	BED_feature	93455925	93455965	.	.	.	Name=1545788
chr2	.	BED_feature	31581776	31581805	.	.	.	Name=1349742
chr14	.	BED_feature	53185318	53185689	.	.	.	Name=10790370
chr11	.	BED_feature	44461602	44461636	.	.	.	Name=10942392
chr7	.	BED_feature	120806754	120806784	.	.	.	Name=10766845
chr4	.	BED_feature	105292149	105292179	.	.	.	Name=10766845
chr3	.	BED_feature	122248748	122248778	.	.	.	Name=10766845
chr9	.	BED_feature	96705008	96705038	.	.	.	Name=10766845
chr11	.	BED_feature	6315912	6315942	.	.	.	Name=10766845
chr11	.	BED_feature	101183575	101183977	.	.	.	Name=10766845
chr17	.	BED_feature	4837106	4837136	.	.	.	Name=10766845
chr19	.	BED_feature	16231796	16231826	.	.	.	Name=10766845
chr18	.	BED_feature	87608842	87608872	.	.	.	Name=10766845
chr6	.	BED_feature	70655321	70655353	.	.	.	Name=2556265
chr7	.	BED_feature	87369183	87369215	.	.	.	Name=9819381
chr4	.	BED_feature	80305382	80305413	.	.	.	Name=9819381
chr17	.	BED_feature	33610877	33610910	.	.	.	Name=2457903
chr17	.	BED_feature	34870978	34871011	.	.	.	Name=2457903
chr7	.	BED_feature	87369277	87369308	.	.	.	Name=9700169
chr16	.	BED_feature	32350557	32350657	.	.	.	Name=10216289
chr2	.	BED_feature	131944656	131944684	.	.	.	Name=7910946
chr16	.	BED_feature	23805151	23805182	.	.	.	Name=9731698
chr2	.	BED_feature	133245497	133245525	.	.	.	Name=15342482
chr2	.	BED_feature	172586093	172586121	.	.	.	Name=15342482
chr6	.	BED_feature	69157052	69157078	.	.	.	Name=2481271
chr6	.	BED_feature	69213988	69214014	.	.	.	Name=2481271
chr6	.	BED_feature	69347094	69347120	.	.	.	Name=2481271
chr6	.	BED_feature	70655323	70655357	.	.	.	Name=2481271
chr11	.	BED_feature	120639880	120639912	.	.	.	Name=7772036
chr10	.	BED_feature	128336544	128336903	.	.	.	Name=16129691
chr9	.	BED_feature	44093333	44093532	.	.	.	Name=2037597
chr9	.	BED_feature	44095106	44095166	.	.	.	Name=2037597
chr5	.	BED_feature	121148230	121148258	.	.	.	Name=2026593
chr5	.	BED_feature	121168144	121168172	.	.	.	Name=2026593
chr4	.	BED_feature	87994131	87994169	.	.	.	Name=2026593
chr8	.	BED_feature	71809239	71809268	.	.	.	Name=11562371
chr10	.	BED_feature	128343725	128345927	.	.	.	Name=8253814
chr7	.	BED_feature	30299252	30299279	.	.	.	Name=15632058
chr3	.	BED_feature	37317762	37317795	.	.	.	Name=15632058
chr9	.	BED_feature	110863710	110864259	.	.	.	Name=1480183
chr9	.	BED_feature	44732404	44732438	.	.	.	Name=3142692
chrX	.	BED_feature	49232095	49232130	.	.	.	Name=1551910
chr13	.	BED_feature	30758120	30758261	.	.	.	Name=2111015
chr8	.	BED_feature	123625796	123625969	.	.	.	Name=2111015
chr8	.	BED_feature	123629681	123629867	.	.	.	Name=2111015
chr8	.	BED_feature	123631597	123631685	.	.	.	Name=2111015
chr8	.	BED_feature	123633180	123633258	.	.	.	Name=2111015
chr8	.	BED_feature	123634273	123634323	.	.	.	Name=2111015
chr8	.	BED_feature	123639327	123642395	.	.	.	Name=2111015
chr8	.	BED_feature	97068208	97068290	.	.	.	Name=8824273
chr13	.	BED_feature	93455257	93455303	.	.	.	Name=1569952
chr8	.	BED_feature	87791999	87792041	.	.	.	Name=8195185
chr16	.	BED_feature	32350642	32350671	.	.	.	Name=12642588
chr6	.	BED_feature	115387057	115387717	.	.	.	Name=9367890
chr5	.	BED_feature	147578458	147578510	.	.	.	Name=9315659
chr8	.	BED_feature	27273951	27273980	.	.	.	Name=11773448
chr5	.	BED_feature	51844144	51844171	.	.	.	Name=16513826
chr3	.	BED_feature	37317758	37317793	.	.	.	Name=9310836
chr2	.	BED_feature	180429411	180429448	.	.	.	Name=10514493
chr2	.	BED_feature	163238506	163238534	.	.	.	Name=7523862
chr2	.	BED_feature	91037774	91037825	.	.	.	Name=11971958
chr8	.	BED_feature	107512202	107512230	.	.	.	Name=10516284
chr8	.	BED_feature	107513470	107513532	.	.	.	Name=10516284
chr11	.	BED_feature	81849317	81849357	.	.	.	Name=10542218
chr11	.	BED_feature	81851709	81851742	.	.	.	Name=10542218
chr2	.	BED_feature	124845236	124845263	.	.	.	Name=8621642
chr2	.	BED_feature	152426554	152426611	.	.	.	Name=9368060
chr18	.	BED_feature	82688765	82688795	.	.	.	Name=9671582
chr10	.	BED_feature	57472916	57473069	.	.	.	Name=9671582
chr3	.	BED_feature	88060266	88060484	.	.	.	Name=9671582
chr11	.	BED_feature	53462157	53462186	.	.	.	Name=9889198
chr13	.	BED_feature	75555771	75555825	.	.	.	Name=8999965
chr5	.	BED_feature	30404335	30404547	.	.	.	Name=3782103
chr10	.	BED_feature	87396564	87396641	.	.	.	Name=3782103
chr11	.	BED_feature	105791183	105791252	.	.	.	Name=8901568
chr7	.	BED_feature	15939804	15939845	.	.	.	Name=10777687
chr7	.	BED_feature	44396074	44396199	.	.	.	Name=8474451
chr2	.	BED_feature	90897751	90897786	.	.	.	Name=8474451
chr2	.	BED_feature	90915910	90916194	.	.	.	Name=8474451
chr15	.	BED_feature	93508177	93508213	.	.	.	Name=8474450
chr8	.	BED_feature	44805769	44806075	.	.	.	Name=8474450
chr11	.	BED_feature	76966328	76966386	.	.	.	Name=2249772
chrX	.	BED_feature	105323847	105323903	.	.	.	Name=2249772
chr2	.	BED_feature	157839524	157839561	.	.	.	Name=8832580
chr5	.	BED_feature	101905550	101905590	.	.	.	Name=15056733
chr7	.	BED_feature	15939816	15939845	.	.	.	Name=10777688
chr11	.	BED_feature	53478194	53478236	.	.	.	Name=11893731
chr1	.	BED_feature	137071499	137071528	.	.	.	Name=11893733
chr9	.	BED_feature	116023945	116024038	.	.	.	Name=11893733
chr1	.	BED_feature	182533618	182533667	.	.	.	Name=12095687
chr18	.	BED_feature	20808309	20808340	.	.	.	Name=8325367
chr12	.	BED_feature	31850935	31851552	.	.	.	Name=1339296
chr1	.	BED_feature	151861395	151862302	.	.	.	Name=15213229
chr2	.	BED_feature	14147043	14147079	.	.	.	Name=10085160
chr12	.	BED_feature	31850892	31850937	.	.	.	Name=2171781
chr3	.	BED_feature	83928642	83928671	.	.	.	Name=11254708
chr11	.	BED_feature	81997261	81997507	.	.	.	Name=9163346
chr8	.	BED_feature	97068203	97068251	.	.	.	Name=3103216
chr11	.	BED_feature	94209037	94209066	.	.	.	Name=15824121
chr13	.	BED_feature	31633526	31633555	.	.	.	Name=9676429
chr1	.	BED_feature	136106797	136106834	.	.	.	Name=2068103
chr19	.	BED_feature	34317827	34317856	.	.	.	Name=9334258
chr14	.	BED_feature	15368773	15368799	.	.	.	Name=9685410
chr6	.	BED_feature	17413782	17413845	.	.	.	Name=9920903
chr2	.	BED_feature	148099617	148099652	.	.	.	Name=8284209
chr9	.	BED_feature	74676019	74676052	.	.	.	Name=11279202
chr7	.	BED_feature	103701811	103701840	.	.	.	Name=3476205
chr11	.	BED_feature	53563732	53564142	.	.	.	Name=9694515
chr12	.	BED_feature	105964109	105964139	.	.	.	Name=12791684
chr11	.	BED_feature	98840320	98840351	.	.	.	Name=10567217
chr13	.	BED_feature	93455892	93455921	.	.	.	Name=8063775
chr6	.	BED_feature	147221063	147221104	.	.	.	Name=8063775
chr11	.	BED_feature	69611843	69612488	.	.	.	Name=1317551
chr7	.	BED_feature	18568522	18568554	.	.	.	Name=1532229
chr5	.	BED_feature	122361521	122361550	.	.	.	Name=1532229
chr5	.	BED_feature	137711874	137711904	.	.	.	Name=11050012
chrX	.	BED_feature	97579920	97579953	.	.	.	Name=7862137
chr5	.	BED_feature	93422256	93422964	.	.	.	Name=8454640
chr11	.	BED_feature	78736933	78736978	.	.	.	Name=9169456
chr12	.	BED_feature	102955871	102955959	.	.	.	Name=7615829
chr10	.	BED_feature	56065273	56065311	.	.	.	Name=15354864
chr10	.	BED_feature	79067594	79067637	.	.	.	Name=7724598
chr15	.	BED_feature	7757334	7757977	.	.	.	Name=11146111
chr11	.	BED_feature	78736090	78736126	.	.	.	Name=10356322
chr10	.	BED_feature	3557642	3557685	.	.	.	Name=15322094
chr8	.	BED_feature	95715470	95715515	.	.	.	Name=9830047
chr10	.	BED_feature	79818298	79818338	.	.	.	Name=2181401
chr1	.	BED_feature	132851833	132851861	.	.	.	Name=10861063
chr11	.	BED_feature	100755892	100755921	.	.	.	Name=9497331
chr7	.	BED_feature	46729298	46729336	.	.	.	Name=9153323
chr12	.	BED_feature	86362671	86362706	.	.	.	Name=7623850
chr7	.	BED_feature	34827849	34827882	.	.	.	Name=8346250
chr2	.	BED_feature	127027475	127027553	.	.	.	Name=8649402
chr10	.	BED_feature	20848228	20848287	.	.	.	Name=2403925
chr1	.	BED_feature	64985458	64985502	.	.	.	Name=1996107
chr1	.	BED_feature	64997747	64997791	.	.	.	Name=1996107
chr1	.	BED_feature	65860721	65860763	.	.	.	Name=1996107
chr5	.	BED_feature	112496065	112496118	.	.	.	Name=1996106
chr1	.	BED_feature	196639494	196639543	.	.	.	Name=10989198
chr14	.	BED_feature	15368771	15368799	.	.	.	Name=7969156
chr3	.	BED_feature	37317665	37317719	.	.	.	Name=10586058
chr10	.	BED_feature	106898875	106898903	.	.	.	Name=7739551
chr12	.	BED_feature	113875399	113875444	.	.	.	Name=2196446
chr17	.	BED_feature	33589424	33589453	.	.	.	Name=2196446
chr17	.	BED_feature	33610900	33610932	.	.	.	Name=2196446
chr17	.	BED_feature	34870956	34870988	.	.	.	Name=2196446
chr17	.	BED_feature	35001957	35001991	.	.	.	Name=2196446
chr17	.	BED_feature	35032708	35032742	.	.	.	Name=2196446
chr17	.	BED_feature	35806748	35806780	.	.	.	Name=2196446
chr2	.	BED_feature	106860547	106860855	.	.	.	Name=12730328
chr17	.	BED_feature	31406532	31406617	.	.	.	Name=2247086
chr10	.	BED_feature	20847864	20847892	.	.	.	Name=1727489
chr2	.	BED_feature	131642319	131642346	.	.	.	Name=15358521
chr6	.	BED_feature	4455268	4455308	.	.	.	Name=8348960
chr5	.	BED_feature	75433217	75433314	.	.	.	Name=8552100
chr3	.	BED_feature	10196489	10196521	.	.	.	Name=8552100
chr7	.	BED_feature	24606072	24606102	.	.	.	Name=1915300
chr3	.	BED_feature	104943575	104943618	.	.	.	Name=8065313
chr16	.	BED_feature	16777811	16777861	.	.	.	Name=10779354
chr11	.	BED_feature	32183601	32183643	.	.	.	Name=3464831
chr11	.	BED_feature	32196418	32196460	.	.	.	Name=3464831
chr11	.	BED_feature	40592293	40595782	.	.	.	Name=7957050
chr11	.	BED_feature	40597228	40598909	.	.	.	Name=7957050
chr10	.	BED_feature	50327589	50328153	.	.	.	Name=7957050
chr16	.	BED_feature	89519565	89519651	.	.	.	Name=7957050
chr16	.	BED_feature	89521162	89521226	.	.	.	Name=7957050
chr16	.	BED_feature	89522759	89522823	.	.	.	Name=7957050
chr15	.	BED_feature	64004944	64005302	.	.	.	Name=7957050
chr7	.	BED_feature	46729276	46729306	.	.	.	Name=11447215
chr8	.	BED_feature	86177922	86178017	.	.	.	Name=8264627
chr15	.	BED_feature	91019738	91019768	.	.	.	Name=16249184
chr6	.	BED_feature	38306348	38306384	.	.	.	Name=1946404
chrX	.	BED_feature	11614220	11614256	.	.	.	Name=1946404
chrX	.	BED_feature	68056341	68056377	.	.	.	Name=1946404
chrX	.	BED_feature	101481734	101481770	.	.	.	Name=1946404
chrX	.	BED_feature	111098292	111098328	.	.	.	Name=1946404
chr13	.	BED_feature	94549174	94549210	.	.	.	Name=1946404
chr12	.	BED_feature	99448213	99448249	.	.	.	Name=1946404
chr12	.	BED_feature	109263471	109263980	.	.	.	Name=1946404
chr11	.	BED_feature	49522511	49522547	.	.	.	Name=1946404
chr10	.	BED_feature	68720567	68720603	.	.	.	Name=1946404
chr17	.	BED_feature	27257589	27257625	.	.	.	Name=1946404
chr15	.	BED_feature	34387771	34387808	.	.	.	Name=1946404
chr15	.	BED_feature	46499812	46499872	.	.	.	Name=1946404
chr5	.	BED_feature	91535961	91535995	.	.	.	Name=7911235
chr3	.	BED_feature	52357151	52357179	.	.	.	Name=11919188
chr3	.	BED_feature	52433184	52433215	.	.	.	Name=11919188
chr5	.	BED_feature	137346134	137349588	.	.	.	Name=2406566
chr5	.	BED_feature	137351452	137352549	.	.	.	Name=2406566
chr5	.	BED_feature	137353937	137354174	.	.	.	Name=2406566
chr5	.	BED_feature	137355660	137357672	.	.	.	Name=2406566
chr17	.	BED_feature	34808215	34808473	.	.	.	Name=11856733
chr17	.	BED_feature	34809795	34809832	.	.	.	Name=11856733
chrX	.	BED_feature	7128197	7128619	.	.	.	Name=10331989
chr15	.	BED_feature	6333856	6334153	.	.	.	Name=10944463
chr16	.	BED_feature	23806222	23806263	.	.	.	Name=2137455
chr16	.	BED_feature	23806227	23806257	.	.	.	Name=2850259
chr9	.	BED_feature	110863759	110863786	.	.	.	Name=7623814
chr9	.	BED_feature	78015621	78015661	.	.	.	Name=8849333
chr9	.	BED_feature	78042097	78042137	.	.	.	Name=8849333
chr9	.	BED_feature	78074895	78074935	.	.	.	Name=8849333
chr9	.	BED_feature	78133951	78133992	.	.	.	Name=8849333
chr15	.	BED_feature	97736654	97736790	.	.	.	Name=11432806
chr11	.	BED_feature	69482257	69482478	.	.	.	Name=9479000
chr10	.	BED_feature	34079089	34079121	.	.	.	Name=10965899
chr3	.	BED_feature	135522464	135522506	.	.	.	Name=2203532
chr3	.	BED_feature	135526730	135529046	.	.	.	Name=2203532
chr3	.	BED_feature	135531228	135532450	.	.	.	Name=2203532
chr3	.	BED_feature	135538893	135538930	.	.	.	Name=2203532
chr3	.	BED_feature	135541108	135541219	.	.	.	Name=2203532
chr3	.	BED_feature	135542512	135542546	.	.	.	Name=2203532
chr3	.	BED_feature	135545563	135545639	.	.	.	Name=2203532
chr3	.	BED_feature	135551038	135551076	.	.	.	Name=2203532
chr3	.	BED_feature	135552717	135552747	.	.	.	Name=2203532
chr3	.	BED_feature	135556264	135556337	.	.	.	Name=2203532
chr3	.	BED_feature	135564042	135564076	.	.	.	Name=2203532
chr3	.	BED_feature	135592917	135592988	.	.	.	Name=2203532
chr2	.	BED_feature	154261298	154261340	.	.	.	Name=14576826
chr6	.	BED_feature	70655294	70655351	.	.	.	Name=3200827
chr14	.	BED_feature	19622833	19622901	.	.	.	Name=1762914
chr2	.	BED_feature	163447472	163447505	.	.	.	Name=9765260
chr2	.	BED_feature	101425359	101425386	.	.	.	Name=10082526
chr11	.	BED_feature	69396270	69396375	.	.	.	Name=7899088
chr10	.	BED_feature	128360718	128360798	.	.	.	Name=8360188
chr16	.	BED_feature	29985936	29987443	.	.	.	Name=7906273
chrY_random	.	BED_feature	10870094	10870143	.	.	.	Name=1722214
chrY_random	.	BED_feature	13323097	13323146	.	.	.	Name=1722214
chrX	.	BED_feature	3009684	3009733	.	.	.	Name=1722214
chrX	.	BED_feature	3017961	3018010	.	.	.	Name=1722214
chrX	.	BED_feature	3115123	3115172	.	.	.	Name=1722214
chrX	.	BED_feature	4465684	4465733	.	.	.	Name=1722214
chrX	.	BED_feature	22744974	22745023	.	.	.	Name=1722214
chrX	.	BED_feature	22753221	22753270	.	.	.	Name=1722214
chrX	.	BED_feature	26169220	26169269	.	.	.	Name=1722214
chrX	.	BED_feature	26574926	26574975	.	.	.	Name=1722214
chrX	.	BED_feature	26583122	26583171	.	.	.	Name=1722214
chrX	.	BED_feature	26931226	26931275	.	.	.	Name=1722214
chrX	.	BED_feature	26939418	26939467	.	.	.	Name=1722214
chrX	.	BED_feature	27409099	27409148	.	.	.	Name=1722214
chrX	.	BED_feature	27732893	27732942	.	.	.	Name=1722214
chrX	.	BED_feature	27741088	27741137	.	.	.	Name=1722214
chrX	.	BED_feature	28081473	28081522	.	.	.	Name=1722214
chrX	.	BED_feature	28089665	28089714	.	.	.	Name=1722214
chrX	.	BED_feature	28668796	28668845	.	.	.	Name=1722214
chrX	.	BED_feature	28676987	28677036	.	.	.	Name=1722214
chrX	.	BED_feature	29009587	29009636	.	.	.	Name=1722214
chrX	.	BED_feature	29485224	29485273	.	.	.	Name=1722214
chrX	.	BED_feature	29493414	29493463	.	.	.	Name=1722214
chrX	.	BED_feature	31327236	31327285	.	.	.	Name=1722214
chrX	.	BED_feature	31335426	31335475	.	.	.	Name=1722214
chrX	.	BED_feature	31661400	31661449	.	.	.	Name=1722214
chrX	.	BED_feature	34425139	34425188	.	.	.	Name=1722214
chrX	.	BED_feature	35208832	35208881	.	.	.	Name=1722214
chrX	.	BED_feature	75140327	75140376	.	.	.	Name=1722214
chrX	.	BED_feature	75148645	75148694	.	.	.	Name=1722214
chrX	.	BED_feature	75320331	75320385	.	.	.	Name=1722214
chrX	.	BED_feature	75328611	75328660	.	.	.	Name=1722214
chrX	.	BED_feature	85264456	85264505	.	.	.	Name=1722214
chrX	.	BED_feature	85272707	85272739	.	.	.	Name=1722214
chrX	.	BED_feature	91766288	91766337	.	.	.	Name=1722214
chrX	.	BED_feature	116197072	116197121	.	.	.	Name=1722214
chrX	.	BED_feature	116205326	116205375	.	.	.	Name=1722214
chrX	.	BED_feature	122485741	122485790	.	.	.	Name=1722214
chrX	.	BED_feature	122494043	122494092	.	.	.	Name=1722214
chrX	.	BED_feature	161150989	161151038	.	.	.	Name=1722214
chrX	.	BED_feature	161159176	161159225	.	.	.	Name=1722214
chr13	.	BED_feature	3172351	3172400	.	.	.	Name=1722214
chr13	.	BED_feature	3180624	3180673	.	.	.	Name=1722214
chr13	.	BED_feature	20657912	20657961	.	.	.	Name=1722214
chr13	.	BED_feature	20666169	20666218	.	.	.	Name=1722214
chr13	.	BED_feature	23132766	23132815	.	.	.	Name=1722214
chr13	.	BED_feature	50724471	50724520	.	.	.	Name=1722214
chr13	.	BED_feature	50732659	50732708	.	.	.	Name=1722214
chr13	.	BED_feature	68290754	68290786	.	.	.	Name=1722214
chr13	.	BED_feature	68917942	68917976	.	.	.	Name=1722214
chr13	.	BED_feature	86661092	86661141	.	.	.	Name=1722214
chr13	.	BED_feature	86669338	86669387	.	.	.	Name=1722214
chr13	.	BED_feature	112849499	112849548	.	.	.	Name=1722214
chr13	.	BED_feature	112857749	112857798	.	.	.	Name=1722214
chr12	.	BED_feature	7169147	7169196	.	.	.	Name=1722214
chr12	.	BED_feature	7177154	7177203	.	.	.	Name=1722214
chr12	.	BED_feature	17896569	17896620	.	.	.	Name=1722214
chr12	.	BED_feature	17900941	17900992	.	.	.	Name=1722214
chr12	.	BED_feature	18036285	18036336	.	.	.	Name=1722214
chr12	.	BED_feature	18040657	18040708	.	.	.	Name=1722214
chr12	.	BED_feature	23055568	23055600	.	.	.	Name=1722214
chr12	.	BED_feature	23063800	23063832	.	.	.	Name=1722214
chr12	.	BED_feature	23088190	23088239	.	.	.	Name=1722214
chr12	.	BED_feature	23092810	23092859	.	.	.	Name=1722214
chr12	.	BED_feature	23601408	23601457	.	.	.	Name=1722214
chr12	.	BED_feature	24421689	24421738	.	.	.	Name=1722214
chr12	.	BED_feature	24429944	24429993	.	.	.	Name=1722214
chr12	.	BED_feature	24439175	24439224	.	.	.	Name=1722214
chr12	.	BED_feature	24670099	24670148	.	.	.	Name=1722214
chr12	.	BED_feature	24674624	24674673	.	.	.	Name=1722214
chr11	.	BED_feature	40977829	40977878	.	.	.	Name=1722214
chr11	.	BED_feature	47262715	47262764	.	.	.	Name=1722214
chr11	.	BED_feature	47270977	47271026	.	.	.	Name=1722214
chr11	.	BED_feature	75173504	75173553	.	.	.	Name=1722214
chr11	.	BED_feature	75181734	75181783	.	.	.	Name=1722214
chr10	.	BED_feature	4258035	4258084	.	.	.	Name=1722214
chr10	.	BED_feature	4266283	4266332	.	.	.	Name=1722214
chr10	.	BED_feature	55324933	55324982	.	.	.	Name=1722214
chr17	.	BED_feature	32790743	32790792	.	.	.	Name=1722214
chr17	.	BED_feature	39075051	39075100	.	.	.	Name=1722214
chr16	.	BED_feature	7785282	7785331	.	.	.	Name=1722214
chr16	.	BED_feature	90966442	90966515	.	.	.	Name=1722214
chr16	.	BED_feature	93711302	93711351	.	.	.	Name=1722214
chr15	.	BED_feature	14818326	14818375	.	.	.	Name=1722214
chr15	.	BED_feature	14823348	14823397	.	.	.	Name=1722214
chr15	.	BED_feature	32814262	32814311	.	.	.	Name=1722214
chr15	.	BED_feature	32822377	32822426	.	.	.	Name=1722214
chr15	.	BED_feature	48999399	48999431	.	.	.	Name=1722214
chr15	.	BED_feature	49007611	49007643	.	.	.	Name=1722214
chr15	.	BED_feature	89789278	89789327	.	.	.	Name=1722214
chr14	.	BED_feature	37020438	37020492	.	.	.	Name=1722214
chr14	.	BED_feature	37028670	37028719	.	.	.	Name=1722214
chr14	.	BED_feature	39035001	39035050	.	.	.	Name=1722214
chr14	.	BED_feature	88457371	88457420	.	.	.	Name=1722214
chr14	.	BED_feature	93991713	93991762	.	.	.	Name=1722214
chr19	.	BED_feature	3247631	3247680	.	.	.	Name=1722214
chr19	.	BED_feature	5315959	5316008	.	.	.	Name=1722214
chr18	.	BED_feature	6346819	6346868	.	.	.	Name=1722214
chr18	.	BED_feature	24695016	24695065	.	.	.	Name=1722214
chr18	.	BED_feature	42609938	42609987	.	.	.	Name=1722214
chr18	.	BED_feature	74384431	74384480	.	.	.	Name=1722214
chr18	.	BED_feature	74392646	74392695	.	.	.	Name=1722214
chr18	.	BED_feature	86326695	86326744	.	.	.	Name=1722214
chr18	.	BED_feature	86334966	86335015	.	.	.	Name=1722214
chr7	.	BED_feature	10085932	10085981	.	.	.	Name=1722214
chr7	.	BED_feature	10354050	10354082	.	.	.	Name=1722214
chr7	.	BED_feature	13631319	13631368	.	.	.	Name=1722214
chr7	.	BED_feature	20202465	20202514	.	.	.	Name=1722214
chr7	.	BED_feature	20210640	20210689	.	.	.	Name=1722214
chr7	.	BED_feature	21397583	21397632	.	.	.	Name=1722214
chr7	.	BED_feature	21405750	21405799	.	.	.	Name=1722214
chr7	.	BED_feature	22620776	22620825	.	.	.	Name=1722214
chr7	.	BED_feature	22628943	22628992	.	.	.	Name=1722214
chr7	.	BED_feature	42162235	42162283	.	.	.	Name=1722214
chr7	.	BED_feature	42172198	42172248	.	.	.	Name=1722214
chr7	.	BED_feature	42288599	42288648	.	.	.	Name=1722214
chr7	.	BED_feature	56555121	56555170	.	.	.	Name=1722214
chr7	.	BED_feature	56788446	56788478	.	.	.	Name=1722214
chr7	.	BED_feature	56796667	56796699	.	.	.	Name=1722214
chr7	.	BED_feature	86481798	86481830	.	.	.	Name=1722214
chr7	.	BED_feature	104697628	104697677	.	.	.	Name=1722214
chr7	.	BED_feature	106162554	106162603	.	.	.	Name=1722214
chr7	.	BED_feature	106170816	106170848	.	.	.	Name=1722214
chr6	.	BED_feature	10346851	10346900	.	.	.	Name=1722214
chr6	.	BED_feature	10870105	10870154	.	.	.	Name=1722214
chr6	.	BED_feature	10878374	10878423	.	.	.	Name=1722214
chr6	.	BED_feature	19594163	19594212	.	.	.	Name=1722214
chr6	.	BED_feature	19602449	19602498	.	.	.	Name=1722214
chr6	.	BED_feature	37677446	37677495	.	.	.	Name=1722214
chr6	.	BED_feature	37714375	37714407	.	.	.	Name=1722214
chr6	.	BED_feature	60354539	60354596	.	.	.	Name=1722214
chr6	.	BED_feature	129770052	129770101	.	.	.	Name=1722214
chr6	.	BED_feature	129778245	129778294	.	.	.	Name=1722214
chr6	.	BED_feature	149181492	149181541	.	.	.	Name=1722214
chr6	.	BED_feature	149315602	149315651	.	.	.	Name=1722214
chr5	.	BED_feature	6489488	6489534	.	.	.	Name=1722214
chr5	.	BED_feature	6497764	6497809	.	.	.	Name=1722214
chr5	.	BED_feature	10627435	10627484	.	.	.	Name=1722214
chr5	.	BED_feature	10635524	10635573	.	.	.	Name=1722214
chr5	.	BED_feature	40980944	40980993	.	.	.	Name=1722214
chr5	.	BED_feature	58606237	58606286	.	.	.	Name=1722214
chr5	.	BED_feature	58614423	58614472	.	.	.	Name=1722214
chr5	.	BED_feature	76673819	76673868	.	.	.	Name=1722214
chr5	.	BED_feature	94676968	94677017	.	.	.	Name=1722214
chr5	.	BED_feature	110132630	110132676	.	.	.	Name=1722214
chr4	.	BED_feature	3016163	3016212	.	.	.	Name=1722214
chr4	.	BED_feature	21052315	21052364	.	.	.	Name=1722214
chr4	.	BED_feature	39044181	39044230	.	.	.	Name=1722214
chr4	.	BED_feature	39052461	39052506	.	.	.	Name=1722214
chr4	.	BED_feature	90366959	90367008	.	.	.	Name=1722214
chr4	.	BED_feature	90374762	90374811	.	.	.	Name=1722214
chr4	.	BED_feature	120664482	120664531	.	.	.	Name=1722214
chr4	.	BED_feature	142945744	142945793	.	.	.	Name=1722214
chr4	.	BED_feature	142954025	142954074	.	.	.	Name=1722214
chr4	.	BED_feature	143285449	143285498	.	.	.	Name=1722214
chr4	.	BED_feature	143293673	143293722	.	.	.	Name=1722214
chr4	.	BED_feature	143351272	143351321	.	.	.	Name=1722214
chr4	.	BED_feature	143359491	143359540	.	.	.	Name=1722214
chr3	.	BED_feature	3241275	3241324	.	.	.	Name=1722214
chr3	.	BED_feature	3249538	3249587	.	.	.	Name=1722214
chr3	.	BED_feature	10857777	10857826	.	.	.	Name=1722214
chr3	.	BED_feature	12567507	12567556	.	.	.	Name=1722214
chr3	.	BED_feature	12571906	12571955	.	.	.	Name=1722214
chr3	.	BED_feature	33945160	33945209	.	.	.	Name=1722214
chr3	.	BED_feature	106717675	106717724	.	.	.	Name=1722214
chr2	.	BED_feature	7527753	7527802	.	.	.	Name=1722214
chr2	.	BED_feature	67930631	67930680	.	.	.	Name=1722214
chr2	.	BED_feature	67938793	67938842	.	.	.	Name=1722214
chr2	.	BED_feature	68347342	68347387	.	.	.	Name=1722214
chr2	.	BED_feature	68356905	68356950	.	.	.	Name=1722214
chr2	.	BED_feature	84699423	84699472	.	.	.	Name=1722214
chr2	.	BED_feature	84707730	84707779	.	.	.	Name=1722214
chr2	.	BED_feature	85819244	85819295	.	.	.	Name=1722214
chr2	.	BED_feature	85823909	85823960	.	.	.	Name=1722214
chr2	.	BED_feature	147154880	147154929	.	.	.	Name=1722214
chr2	.	BED_feature	181848745	181848794	.	.	.	Name=1722214
chr2	.	BED_feature	181857003	181857052	.	.	.	Name=1722214
chr1	.	BED_feature	3166625	3166674	.	.	.	Name=1722214
chr1	.	BED_feature	8835490	8835539	.	.	.	Name=1722214
chr1	.	BED_feature	27450635	27450684	.	.	.	Name=1722214
chr1	.	BED_feature	85016325	85016374	.	.	.	Name=1722214
chr1	.	BED_feature	85024600	85024649	.	.	.	Name=1722214
chr1	.	BED_feature	87299790	87299839	.	.	.	Name=1722214
chr1	.	BED_feature	114428568	114428617	.	.	.	Name=1722214
chr1	.	BED_feature	147958428	147958477	.	.	.	Name=1722214
chr1	.	BED_feature	157306338	157306370	.	.	.	Name=1722214
chr9	.	BED_feature	4855449	4855498	.	.	.	Name=1722214
chr9	.	BED_feature	7407083	7407131	.	.	.	Name=1722214
chr9	.	BED_feature	7415344	7415393	.	.	.	Name=1722214
chr9	.	BED_feature	11773780	11773829	.	.	.	Name=1722214
chr9	.	BED_feature	17995540	17995589	.	.	.	Name=1722214
chr9	.	BED_feature	21977709	21977758	.	.	.	Name=1722214
chr9	.	BED_feature	122696574	122696623	.	.	.	Name=1722214
chr8	.	BED_feature	4959298	4959347	.	.	.	Name=1722214
chr8	.	BED_feature	20164970	20165002	.	.	.	Name=1722214
chr8	.	BED_feature	20173230	20173262	.	.	.	Name=1722214
chr8	.	BED_feature	20181490	20181522	.	.	.	Name=1722214
chr8	.	BED_feature	28769712	28769761	.	.	.	Name=1722214
chr8	.	BED_feature	28777979	28778011	.	.	.	Name=1722214
chr8	.	BED_feature	75759230	75759279	.	.	.	Name=1722214
chr8	.	BED_feature	75767505	75767554	.	.	.	Name=1722214
chr5_random	.	BED_feature	345219	345268	.	.	.	Name=1722214
chr5_random	.	BED_feature	353512	353561	.	.	.	Name=1722214
chr5_random	.	BED_feature	2061322	2061371	.	.	.	Name=1722214
chr5_random	.	BED_feature	2907787	2907836	.	.	.	Name=1722214
chr11	.	BED_feature	69396554	69396580	.	.	.	Name=8441640
chr8	.	BED_feature	70421337	70421372	.	.	.	Name=12904181
chr8	.	BED_feature	70422669	70422702	.	.	.	Name=12904181
chr8	.	BED_feature	95715466	95715494	.	.	.	Name=16079501
chr13	.	BED_feature	48677007	48678457	.	.	.	Name=7669690
chr2	.	BED_feature	62284544	62284592	.	.	.	Name=10567552
chr17	.	BED_feature	45496859	45496893	.	.	.	Name=9113979
chr2	.	BED_feature	113744278	113744418	.	.	.	Name=2552286
chr14	.	BED_feature	30040520	30040552	.	.	.	Name=2753913
chr3	.	BED_feature	88464657	88464702	.	.	.	Name=14634012
chr3	.	BED_feature	88470424	88470467	.	.	.	Name=14634012
chr17	.	BED_feature	33589424	33589453	.	.	.	Name=3501825
chr17	.	BED_feature	33610900	33610931	.	.	.	Name=3501825
chr17	.	BED_feature	34870957	34870988	.	.	.	Name=3501825
chr17	.	BED_feature	35001960	35001991	.	.	.	Name=3501825
chr17	.	BED_feature	35032711	35032742	.	.	.	Name=3501825
chr17	.	BED_feature	35806748	35806779	.	.	.	Name=3501825
chr11	.	BED_feature	94936171	94936217	.	.	.	Name=10473625
chr16	.	BED_feature	15800734	15800853	.	.	.	Name=9528783
chr2	.	BED_feature	154260941	154261469	.	.	.	Name=7958837
chr10	.	BED_feature	92678684	92679911	.	.	.	Name=7958835
chr10	.	BED_feature	92684496	92684612	.	.	.	Name=7958835
chr10	.	BED_feature	92694679	92695473	.	.	.	Name=7958835
chr10	.	BED_feature	92714568	92714777	.	.	.	Name=7958835
chr10	.	BED_feature	92740548	92740689	.	.	.	Name=7958835
chr9	.	BED_feature	77845412	77845447	.	.	.	Name=8962155
chr6	.	BED_feature	122708373	122708403	.	.	.	Name=15054091
chr6	.	BED_feature	69157053	69157080	.	.	.	Name=2107525
chr6	.	BED_feature	69213989	69214016	.	.	.	Name=2107525
chr6	.	BED_feature	69347095	69347122	.	.	.	Name=2107525
chr6	.	BED_feature	70655273	70655356	.	.	.	Name=2107525
chr8	.	BED_feature	71809513	71809738	.	.	.	Name=15755745
chr5	.	BED_feature	91525401	91525435	.	.	.	Name=7523856
chr5	.	BED_feature	91565757	91565785	.	.	.	Name=7523856
chr9	.	BED_feature	45687005	45687060	.	.	.	Name=14654367
chr16	.	BED_feature	18940693	18940773	.	.	.	Name=2116989
chr16	.	BED_feature	19092811	19093359	.	.	.	Name=2116989
chr17	.	BED_feature	33589425	33589463	.	.	.	Name=8413217
chr17	.	BED_feature	33610901	33610939	.	.	.	Name=8413217
chr17	.	BED_feature	34870938	34870987	.	.	.	Name=8413217
chr17	.	BED_feature	35001952	35001990	.	.	.	Name=8413217
chr17	.	BED_feature	35032703	35032741	.	.	.	Name=8413217
chr17	.	BED_feature	35806749	35806787	.	.	.	Name=8413217
chr14	.	BED_feature	15368772	15368799	.	.	.	Name=8413217
chr15	.	BED_feature	101094620	101094686	.	.	.	Name=8413214
chr19	.	BED_feature	34321288	34321853	.	.	.	Name=2398068
chr14	.	BED_feature	72059965	72059993	.	.	.	Name=10330185
chr7	.	BED_feature	18566379	18566430	.	.	.	Name=7969181
chr7	.	BED_feature	18569430	18569630	.	.	.	Name=7969181
chr5	.	BED_feature	91547711	91547739	.	.	.	Name=9614204
chr3	.	BED_feature	30143759	30143790	.	.	.	Name=8557637
chr7	.	BED_feature	24801416	24801450	.	.	.	Name=2011512
chr5	.	BED_feature	91525365	91525437	.	.	.	Name=1875930
chr5	.	BED_feature	91536004	91536054	.	.	.	Name=1875930
chr4	.	BED_feature	44737696	44738377	.	.	.	Name=10662641
chr1	.	BED_feature	137869064	137869092	.	.	.	Name=12407098
chr5	.	BED_feature	147585148	147585174	.	.	.	Name=9252422
chr16	.	BED_feature	23806222	23806252	.	.	.	Name=2147227
chr9	.	BED_feature	32483530	32483756	.	.	.	Name=2163347
chr16	.	BED_feature	23806222	23806263	.	.	.	Name=2898727
chr12	.	BED_feature	86362676	86362712	.	.	.	Name=2147223
chr7	.	BED_feature	18568410	18568449	.	.	.	Name=2163343
chr16	.	BED_feature	23806225	23806260	.	.	.	Name=7926024
chr11	.	BED_feature	69403130	69403157	.	.	.	Name=14707287
chr12	.	BED_feature	86362492	86362522	.	.	.	Name=8506157
chr12	.	BED_feature	31850901	31850935	.	.	.	Name=1850696
chr2	.	BED_feature	109475450	109475487	.	.	.	Name=12114522
chr11	.	BED_feature	70435390	70435612	.	.	.	Name=8464921
chr11	.	BED_feature	78736933	78736990	.	.	.	Name=7508926
chr11	.	BED_feature	69561764	69562338	.	.	.	Name=9151733
chr6	.	BED_feature	92210105	92210244	.	.	.	Name=10537125
chr7	.	BED_feature	109852585	109852907	.	.	.	Name=10657238
chr6	.	BED_feature	41045109	41045728	.	.	.	Name=2557542
chr6	.	BED_feature	41050930	41051019	.	.	.	Name=2557542
chr6	.	BED_feature	41059681	41059770	.	.	.	Name=2557542
chr2	.	BED_feature	147056499	147057506	.	.	.	Name=1889089
chr3	.	BED_feature	101733721	101733827	.	.	.	Name=1324413
chrX	.	BED_feature	7128569	7128597	.	.	.	Name=12045237
chr5	.	BED_feature	30343757	30343798	.	.	.	Name=12177065
chr18	.	BED_feature	20808311	20808340	.	.	.	Name=9668124
chr12	.	BED_feature	113712846	113713747	.	.	.	Name=1401921
chr6	.	BED_feature	70655323	70655353	.	.	.	Name=8268924
chr4	.	BED_feature	124154606	124154641	.	.	.	Name=8948648
chr11	.	BED_feature	9017789	9017822	.	.	.	Name=11559567
chr5	.	BED_feature	93403446	93403483	.	.	.	Name=12403783
chr9	.	BED_feature	49551486	49551548	.	.	.	Name=7910552
chr3	.	BED_feature	28888905	28889034	.	.	.	Name=8544849
chr17	.	BED_feature	46016863	46016889	.	.	.	Name=2108863
chr1	.	BED_feature	82171131	82171170	.	.	.	Name=8544845
chr9	.	BED_feature	50505294	50505415	.	.	.	Name=15522290
chr17	.	BED_feature	33589423	33589465	.	.	.	Name=2540425
chr17	.	BED_feature	33610899	33610942	.	.	.	Name=2540425
chr17	.	BED_feature	34870944	34870989	.	.	.	Name=2540425
chr17	.	BED_feature	35001949	35001992	.	.	.	Name=2540425
chr17	.	BED_feature	35032700	35032743	.	.	.	Name=2540425
chr17	.	BED_feature	35047045	35047084	.	.	.	Name=2540425
chr17	.	BED_feature	35077934	35077979	.	.	.	Name=2540425
chr17	.	BED_feature	35806747	35806791	.	.	.	Name=2540425
chr15	.	BED_feature	78322202	78322469	.	.	.	Name=15752766
chr2	.	BED_feature	163441549	163441592	.	.	.	Name=1881892
chr7	.	BED_feature	41898472	41899356	.	.	.	Name=7862144
chr7	.	BED_feature	51614716	51615599	.	.	.	Name=7862144
chr7	.	BED_feature	89482898	89482927	.	.	.	Name=7862144
chr7	.	BED_feature	100635010	100635893	.	.	.	Name=7862144
chr6	.	BED_feature	22654270	22654299	.	.	.	Name=7862144
chr6	.	BED_feature	83840155	83841038	.	.	.	Name=7862144
chr6	.	BED_feature	84777898	84778787	.	.	.	Name=7862144
chr6	.	BED_feature	91394387	91394416	.	.	.	Name=7862144
chr6	.	BED_feature	125127879	125127908	.	.	.	Name=7862144
chr6	.	BED_feature	128167884	128168852	.	.	.	Name=7862144
chr5	.	BED_feature	13048557	13049440	.	.	.	Name=7862144
chr5	.	BED_feature	96102016	96102899	.	.	.	Name=7862144
chr5	.	BED_feature	106103121	106104004	.	.	.	Name=7862144
chr4	.	BED_feature	57465125	57466008	.	.	.	Name=7862144
chr4	.	BED_feature	83576986	83577015	.	.	.	Name=7862144
chr4	.	BED_feature	84395391	84395420	.	.	.	Name=7862144
chr4	.	BED_feature	91343804	91344687	.	.	.	Name=7862144
chr3	.	BED_feature	52700764	52701647	.	.	.	Name=7862144
chr3	.	BED_feature	61549906	61549935	.	.	.	Name=7862144
chr3	.	BED_feature	79003185	79004068	.	.	.	Name=7862144
chr3	.	BED_feature	122222335	122223218	.	.	.	Name=7862144
chr3	.	BED_feature	139586766	139587649	.	.	.	Name=7862144
chr3	.	BED_feature	142899997	142900880	.	.	.	Name=7862144
chr2	.	BED_feature	11327001	11327884	.	.	.	Name=7862144
chr2	.	BED_feature	28755735	28756618	.	.	.	Name=7862144
chr2	.	BED_feature	43340524	43341407	.	.	.	Name=7862144
chr2	.	BED_feature	146446257	146446286	.	.	.	Name=7862144
chr2	.	BED_feature	149434616	149435499	.	.	.	Name=7862144
chr2	.	BED_feature	151065449	151065478	.	.	.	Name=7862144
chr2	.	BED_feature	152427792	152428488	.	.	.	Name=7862144
chr1	.	BED_feature	12551453	12551482	.	.	.	Name=7862144
chr1	.	BED_feature	13771215	13771244	.	.	.	Name=7862144
chr1	.	BED_feature	15254131	15254160	.	.	.	Name=7862144
chr1	.	BED_feature	102112598	102112627	.	.	.	Name=7862144
chr1	.	BED_feature	182163964	182163993	.	.	.	Name=7862144
chr18	.	BED_feature	54109690	54110579	.	.	.	Name=7862144
chr9	.	BED_feature	51324883	51324912	.	.	.	Name=7862144
chr9	.	BED_feature	51376166	51376195	.	.	.	Name=7862144
chr9	.	BED_feature	75479680	75479709	.	.	.	Name=7862144
chr8	.	BED_feature	43107603	43107632	.	.	.	Name=7862144
chr8	.	BED_feature	60442444	60443327	.	.	.	Name=7862144
chr8	.	BED_feature	78301708	78302591	.	.	.	Name=7862144
chr8	.	BED_feature	94578592	94578621	.	.	.	Name=7862144
chr8	.	BED_feature	95605173	95606056	.	.	.	Name=7862144
chr13	.	BED_feature	17606088	17606117	.	.	.	Name=7862144
chr13	.	BED_feature	94394534	94394563	.	.	.	Name=7862144
chr13	.	BED_feature	98558424	98558453	.	.	.	Name=7862144
chr13	.	BED_feature	99502370	99503240	.	.	.	Name=7862144
chr12	.	BED_feature	5616603	5616632	.	.	.	Name=7862144
chr12	.	BED_feature	15753647	15753676	.	.	.	Name=7862144
chr12	.	BED_feature	70840067	70840096	.	.	.	Name=7862144
chr12	.	BED_feature	82292040	82292069	.	.	.	Name=7862144
chr11	.	BED_feature	4464478	4464507	.	.	.	Name=7862144
chr11	.	BED_feature	17873912	17873941	.	.	.	Name=7862144
chr11	.	BED_feature	20235133	20236016	.	.	.	Name=7862144
chr11	.	BED_feature	26686633	26687516	.	.	.	Name=7862144
chr11	.	BED_feature	33176708	33176737	.	.	.	Name=7862144
chr11	.	BED_feature	63128623	63128652	.	.	.	Name=7862144
chr11	.	BED_feature	99495076	99495105	.	.	.	Name=7862144
chr10	.	BED_feature	13580963	13580991	.	.	.	Name=7862144
chr10	.	BED_feature	33498885	33498914	.	.	.	Name=7862144
chr10	.	BED_feature	39701282	39701311	.	.	.	Name=7862144
chr17	.	BED_feature	14510586	14510615	.	.	.	Name=7862144
chr17	.	BED_feature	25054330	25054359	.	.	.	Name=7862144
chr17	.	BED_feature	61466364	61466393	.	.	.	Name=7862144
chr15	.	BED_feature	4833189	4833218	.	.	.	Name=7862144
chr15	.	BED_feature	12519614	12520497	.	.	.	Name=7862144
chr15	.	BED_feature	18109330	18109359	.	.	.	Name=7862144
chr15	.	BED_feature	93024775	93025660	.	.	.	Name=7862144
chr14	.	BED_feature	10074301	10075184	.	.	.	Name=7862144
chr14	.	BED_feature	47331431	47331460	.	.	.	Name=7862144
chr14	.	BED_feature	102256262	102257125	.	.	.	Name=7862144
chr19	.	BED_feature	40266543	40266572	.	.	.	Name=7862144
chrX	.	BED_feature	76446688	76447571	.	.	.	Name=7862144
chrX	.	BED_feature	84824889	84824917	.	.	.	Name=7862144
chrX	.	BED_feature	111575956	111575985	.	.	.	Name=7862144
chrX	.	BED_feature	116277654	116277683	.	.	.	Name=7862144
chrX	.	BED_feature	147286084	147286965	.	.	.	Name=7862144
chr11	.	BED_feature	68915208	68915237	.	.	.	Name=12483227
chr2	.	BED_feature	164639183	164639220	.	.	.	Name=16166639
chr12	.	BED_feature	113875363	113875392	.	.	.	Name=2068097
chr15	.	BED_feature	101094793	101094846	.	.	.	Name=7969116
chr6	.	BED_feature	52133967	52134176	.	.	.	Name=2565857
chr11	.	BED_feature	96119437	96119750	.	.	.	Name=2565857
chr6	.	BED_feature	71192164	71192201	.	.	.	Name=15890826
chr7	.	BED_feature	51614690	51614718	.	.	.	Name=12972592
chr7	.	BED_feature	100635891	100635919	.	.	.	Name=12972592
chr6	.	BED_feature	83841036	83841064	.	.	.	Name=12972592
chr6	.	BED_feature	91394361	91394389	.	.	.	Name=12972592
chr5	.	BED_feature	13049438	13049466	.	.	.	Name=12972592
chr5	.	BED_feature	28869331	28869359	.	.	.	Name=12972592
chr5	.	BED_feature	96101990	96102018	.	.	.	Name=12972592
chr5	.	BED_feature	106104002	106104030	.	.	.	Name=12972592
chr4	.	BED_feature	57466006	57466034	.	.	.	Name=12972592
chr4	.	BED_feature	91344685	91344713	.	.	.	Name=12972592
chr3	.	BED_feature	122223216	122223244	.	.	.	Name=12972592
chr3	.	BED_feature	142899971	142899999	.	.	.	Name=12972592
chr2	.	BED_feature	28756616	28756644	.	.	.	Name=12972592
chr2	.	BED_feature	43341405	43341433	.	.	.	Name=12972592
chr2	.	BED_feature	149434590	149434618	.	.	.	Name=12972592
chr2	.	BED_feature	160946896	160946924	.	.	.	Name=12972592
chr1	.	BED_feature	15255009	15255037	.	.	.	Name=12972592
chr1	.	BED_feature	182164857	182164885	.	.	.	Name=12972592
chr9	.	BED_feature	51324857	51324885	.	.	.	Name=12972592
chr9	.	BED_feature	113379041	113379069	.	.	.	Name=12972592
chr8	.	BED_feature	35791339	35791367	.	.	.	Name=12972592
chr8	.	BED_feature	60442418	60442446	.	.	.	Name=12972592
chr8	.	BED_feature	78302589	78302617	.	.	.	Name=12972592
chr8	.	BED_feature	95606054	95606082	.	.	.	Name=12972592
chr13	.	BED_feature	99503238	99503266	.	.	.	Name=12972592
chr12	.	BED_feature	50717876	50717904	.	.	.	Name=12972592
chr11	.	BED_feature	20236014	20236042	.	.	.	Name=12972592
chr11	.	BED_feature	63129504	63129532	.	.	.	Name=12972592
chr10	.	BED_feature	33498912	33498940	.	.	.	Name=12972592
chr15	.	BED_feature	4832309	4832337	.	.	.	Name=12972592
chr15	.	BED_feature	12519588	12519616	.	.	.	Name=12972592
chr14	.	BED_feature	10075182	10075210	.	.	.	Name=12972592
chr19	.	BED_feature	16344790	16344818	.	.	.	Name=12972592
chrX	.	BED_feature	12483976	12484004	.	.	.	Name=12972592
chrX	.	BED_feature	76447569	76447597	.	.	.	Name=12972592
chr2	.	BED_feature	102702390	102702429	.	.	.	Name=10657993
chr11	.	BED_feature	98584305	98584335	.	.	.	Name=12150932
chr11	.	BED_feature	98589152	98589199	.	.	.	Name=12150932
chr10	.	BED_feature	84581013	84581043	.	.	.	Name=12150932
chr3	.	BED_feature	94476563	94476591	.	.	.	Name=12150932
chr2	.	BED_feature	92213484	92213532	.	.	.	Name=12150932
chr9	.	BED_feature	78015472	78015501	.	.	.	Name=15155840
chr9	.	BED_feature	78041948	78041977	.	.	.	Name=15155840
chr9	.	BED_feature	78068345	78068374	.	.	.	Name=15155840
chr9	.	BED_feature	78134111	78134140	.	.	.	Name=15155840
chr17	.	BED_feature	33589363	33589817	.	.	.	Name=3510743
chr17	.	BED_feature	33610693	33611369	.	.	.	Name=3510743
chr17	.	BED_feature	34870573	34871119	.	.	.	Name=3510743
chr17	.	BED_feature	34906605	34906783	.	.	.	Name=3510743
chr17	.	BED_feature	34987032	34987633	.	.	.	Name=3510743
chr17	.	BED_feature	35001577	35002052	.	.	.	Name=3510743
chr17	.	BED_feature	35032550	35032803	.	.	.	Name=3510743
chr17	.	BED_feature	35046696	35047148	.	.	.	Name=3510743
chr17	.	BED_feature	35790655	35790691	.	.	.	Name=3510743
chr17	.	BED_feature	35806744	35806790	.	.	.	Name=3510743
chr7	.	BED_feature	46244213	46244242	.	.	.	Name=8127707
chr5	.	BED_feature	16065674	16065702	.	.	.	Name=7935420
chr16	.	BED_feature	23806223	23806263	.	.	.	Name=2564850
chr6	.	BED_feature	122821685	122821919	.	.	.	Name=16854466
chr11	.	BED_feature	100724805	100724845	.	.	.	Name=11438543
chr11	.	BED_feature	100727323	100727361	.	.	.	Name=11438543
chr13	.	BED_feature	55339731	55339779	.	.	.	Name=12444919
chr11	.	BED_feature	54093065	54093105	.	.	.	Name=8289796
chrX	.	BED_feature	20027115	20027144	.	.	.	Name=9478976
chr17	.	BED_feature	35113682	35114128	.	.	.	Name=8289793
chr12	.	BED_feature	86362676	86362704	.	.	.	Name=1922053
chr2	.	BED_feature	127817489	127817521	.	.	.	Name=16162916
chr7	.	BED_feature	105441521	105441574	.	.	.	Name=7800475
chr7	.	BED_feature	105448138	105448378	.	.	.	Name=7800475
chr9	.	BED_feature	18051053	18051105	.	.	.	Name=7800475
chr1	.	BED_feature	136106264	136106470	.	.	.	Name=10548518
chrX	.	BED_feature	164531362	164531392	.	.	.	Name=16595692
chr9	.	BED_feature	45687018	45687057	.	.	.	Name=9545312
chr6	.	BED_feature	68946742	68946794	.	.	.	Name=3537963
chr6	.	BED_feature	69041094	69041146	.	.	.	Name=3537963
chr6	.	BED_feature	69115023	69115075	.	.	.	Name=3537963
chr6	.	BED_feature	69157045	69157097	.	.	.	Name=3537963
chr6	.	BED_feature	69173350	69173399	.	.	.	Name=3537963
chr6	.	BED_feature	69198074	69198124	.	.	.	Name=3537963
chr6	.	BED_feature	69213981	69214033	.	.	.	Name=3537963
chr6	.	BED_feature	69235025	69235077	.	.	.	Name=3537963
chr6	.	BED_feature	69308134	69308186	.	.	.	Name=3537963
chr6	.	BED_feature	69330006	69330055	.	.	.	Name=3537963
chr6	.	BED_feature	69347087	69347139	.	.	.	Name=3537963
chr6	.	BED_feature	69368403	69368455	.	.	.	Name=3537963
chr6	.	BED_feature	69537463	69537512	.	.	.	Name=3537963
chr6	.	BED_feature	69561844	69561892	.	.	.	Name=3537963
chr12	.	BED_feature	114380257	114380293	.	.	.	Name=3537963
chr12	.	BED_feature	114442778	114442823	.	.	.	Name=3537963
chr12	.	BED_feature	114508148	114508198	.	.	.	Name=3537963
chr12	.	BED_feature	115130945	115130981	.	.	.	Name=3537963
chr12	.	BED_feature	115156961	115156997	.	.	.	Name=3537963
chr12	.	BED_feature	115194586	115194638	.	.	.	Name=3537963
chr12	.	BED_feature	115299503	115299555	.	.	.	Name=3537963
chr12	.	BED_feature	115362912	115362964	.	.	.	Name=3537963
chr2	.	BED_feature	28437364	28437397	.	.	.	Name=11696536
chr16	.	BED_feature	10699185	10700012	.	.	.	Name=11696536
chr16	.	BED_feature	87618777	87618809	.	.	.	Name=9565602
chr17	.	BED_feature	33611946	33611997	.	.	.	Name=7984430
chr17	.	BED_feature	35000758	35000789	.	.	.	Name=7984430
chr17	.	BED_feature	35045858	35045889	.	.	.	Name=7984430
chr17	.	BED_feature	35076934	35076965	.	.	.	Name=7984430
chr5	.	BED_feature	8897867	8900457	.	.	.	Name=8877103
chr10	.	BED_feature	61524838	61524867	.	.	.	Name=10825208
chr10	.	BED_feature	61527576	61527605	.	.	.	Name=10825208
chr6	.	BED_feature	108626136	108626168	.	.	.	Name=14581485
chr11	.	BED_feature	68914964	68914995	.	.	.	Name=14581485
chr10	.	BED_feature	66933149	66933181	.	.	.	Name=8483478
chr12	.	BED_feature	86362678	86362712	.	.	.	Name=8483478
chr18	.	BED_feature	34987076	34987125	.	.	.	Name=8483478
chr7	.	BED_feature	109913093	109913392	.	.	.	Name=11500387
chr1	.	BED_feature	74833835	74833863	.	.	.	Name=15538371
chr1	.	BED_feature	97497673	97498061	.	.	.	Name=9516473
chr5	.	BED_feature	147580551	147580997	.	.	.	Name=7907546
chr5	.	BED_feature	147584726	147585523	.	.	.	Name=7907546
chr11	.	BED_feature	96121129	96121172	.	.	.	Name=7907546
chr15	.	BED_feature	102838906	102838963	.	.	.	Name=7907546
chr15	.	BED_feature	102863818	102863869	.	.	.	Name=7907546
chr16	.	BED_feature	23806260	23806295	.	.	.	Name=7907546
chr5	.	BED_feature	75856698	75856747	.	.	.	Name=8695840
chr15	.	BED_feature	97830431	97830470	.	.	.	Name=10825206
chr3	.	BED_feature	138464666	138464701	.	.	.	Name=8756633
chrX	.	BED_feature	58046028	58046063	.	.	.	Name=8756633
chr7	.	BED_feature	32068073	32068100	.	.	.	Name=11340077
chr7	.	BED_feature	33021288	33021315	.	.	.	Name=11340077
chr7	.	BED_feature	35943486	35943513	.	.	.	Name=11340077
chr7	.	BED_feature	41898901	41898928	.	.	.	Name=11340077
chr7	.	BED_feature	51615144	51615171	.	.	.	Name=11340077
chr7	.	BED_feature	67656833	67656860	.	.	.	Name=11340077
chr7	.	BED_feature	72863211	72863238	.	.	.	Name=11340077
chr7	.	BED_feature	89483315	89483342	.	.	.	Name=11340077
chr7	.	BED_feature	100635438	100635465	.	.	.	Name=11340077
chr6	.	BED_feature	18095168	18095195	.	.	.	Name=11340077
chr6	.	BED_feature	22653844	22653871	.	.	.	Name=11340077
chr6	.	BED_feature	83840583	83840610	.	.	.	Name=11340077
chr6	.	BED_feature	91394815	91394842	.	.	.	Name=11340077
chr6	.	BED_feature	93103036	93103063	.	.	.	Name=11340077
chr6	.	BED_feature	94786421	94786448	.	.	.	Name=11340077
chr6	.	BED_feature	125128525	125128552	.	.	.	Name=11340077
chr6	.	BED_feature	128168397	128168424	.	.	.	Name=11340077
chr5	.	BED_feature	13048985	13049012	.	.	.	Name=11340077
chr5	.	BED_feature	16020546	16020573	.	.	.	Name=11340077
chr5	.	BED_feature	96102444	96102471	.	.	.	Name=11340077
chr5	.	BED_feature	106103549	106103576	.	.	.	Name=11340077
chr5	.	BED_feature	108386070	108386097	.	.	.	Name=11340077
chr4	.	BED_feature	41357702	41357729	.	.	.	Name=11340077
chr4	.	BED_feature	57465553	57465580	.	.	.	Name=11340077
chr4	.	BED_feature	82665652	82665679	.	.	.	Name=11340077
chr4	.	BED_feature	83576560	83576587	.	.	.	Name=11340077
chr4	.	BED_feature	84394959	84394986	.	.	.	Name=11340077
chr4	.	BED_feature	91344232	91344259	.	.	.	Name=11340077
chr4	.	BED_feature	128371237	128371264	.	.	.	Name=11340077
chr3	.	BED_feature	8599116	8599143	.	.	.	Name=11340077
chr3	.	BED_feature	14488378	14488405	.	.	.	Name=11340077
chr3	.	BED_feature	14950851	14950878	.	.	.	Name=11340077
chr3	.	BED_feature	36055859	36055886	.	.	.	Name=11340077
chr3	.	BED_feature	52701192	52701219	.	.	.	Name=11340077
chr3	.	BED_feature	61550335	61550362	.	.	.	Name=11340077
chr3	.	BED_feature	79003613	79003640	.	.	.	Name=11340077
chr3	.	BED_feature	121172661	121172688	.	.	.	Name=11340077
chr3	.	BED_feature	122222763	122222790	.	.	.	Name=11340077
chr3	.	BED_feature	125034830	125034857	.	.	.	Name=11340077
chr3	.	BED_feature	139587194	139587221	.	.	.	Name=11340077
chr3	.	BED_feature	142900425	142900452	.	.	.	Name=11340077
chr2	.	BED_feature	11327429	11327456	.	.	.	Name=11340077
chr2	.	BED_feature	28756163	28756190	.	.	.	Name=11340077
chr2	.	BED_feature	43340952	43340979	.	.	.	Name=11340077
chr2	.	BED_feature	45631919	45631946	.	.	.	Name=11340077
chr2	.	BED_feature	56895568	56895595	.	.	.	Name=11340077
chr2	.	BED_feature	81923536	81923563	.	.	.	Name=11340077
chr2	.	BED_feature	104338710	104338737	.	.	.	Name=11340077
chr2	.	BED_feature	146446686	146446713	.	.	.	Name=11340077
chr2	.	BED_feature	149435043	149435070	.	.	.	Name=11340077
chr2	.	BED_feature	151065883	151065910	.	.	.	Name=11340077
chr2	.	BED_feature	160946437	160946464	.	.	.	Name=11340077
chr2	.	BED_feature	162674241	162674268	.	.	.	Name=11340077
chr1	.	BED_feature	13771643	13771670	.	.	.	Name=11340077
chr1	.	BED_feature	15254559	15254586	.	.	.	Name=11340077
chr1	.	BED_feature	52448316	52448343	.	.	.	Name=11340077
chr1	.	BED_feature	182164392	182164419	.	.	.	Name=11340077
chr18	.	BED_feature	23360041	23360068	.	.	.	Name=11340077
chr18	.	BED_feature	56098089	56098116	.	.	.	Name=11340077
chr18	.	BED_feature	89668695	89668722	.	.	.	Name=11340077
chr9	.	BED_feature	45587469	45587496	.	.	.	Name=11340077
chr9	.	BED_feature	51755185	51755212	.	.	.	Name=11340077
chr8	.	BED_feature	37841690	37841717	.	.	.	Name=11340077
chr8	.	BED_feature	43108025	43108052	.	.	.	Name=11340077
chr8	.	BED_feature	47754034	47754061	.	.	.	Name=11340077
chr8	.	BED_feature	53777748	53777775	.	.	.	Name=11340077
chr8	.	BED_feature	66670676	66670703	.	.	.	Name=11340077
chr8	.	BED_feature	78302136	78302163	.	.	.	Name=11340077
chr8	.	BED_feature	95605601	95605628	.	.	.	Name=11340077
chr8	.	BED_feature	100455261	100455288	.	.	.	Name=11340077
chr13	.	BED_feature	20712386	20712413	.	.	.	Name=11340077
chr13	.	BED_feature	98558851	98558878	.	.	.	Name=11340077
chr13	.	BED_feature	99502797	99502824	.	.	.	Name=11340077
chr12	.	BED_feature	5616171	5616198	.	.	.	Name=11340077
chr12	.	BED_feature	13778755	13778782	.	.	.	Name=11340077
chr12	.	BED_feature	15754080	15754107	.	.	.	Name=11340077
chr12	.	BED_feature	70839623	70839650	.	.	.	Name=11340077
chr12	.	BED_feature	72765420	72765447	.	.	.	Name=11340077
chr12	.	BED_feature	82291608	82291635	.	.	.	Name=11340077
chr11	.	BED_feature	3852159	3852186	.	.	.	Name=11340077
chr11	.	BED_feature	4464071	4464098	.	.	.	Name=11340077
chr11	.	BED_feature	17874341	17874368	.	.	.	Name=11340077
chr11	.	BED_feature	20235561	20235588	.	.	.	Name=11340077
chr11	.	BED_feature	26687061	26687088	.	.	.	Name=11340077
chr11	.	BED_feature	48578523	48578550	.	.	.	Name=11340077
chr11	.	BED_feature	63129051	63129078	.	.	.	Name=11340077
chr11	.	BED_feature	79188005	79188032	.	.	.	Name=11340077
chr11	.	BED_feature	99494650	99494677	.	.	.	Name=11340077
chr11	.	BED_feature	108975823	108975850	.	.	.	Name=11340077
chr10	.	BED_feature	22481184	22481211	.	.	.	Name=11340077
chr10	.	BED_feature	33498459	33498486	.	.	.	Name=11340077
chr10	.	BED_feature	39701716	39701743	.	.	.	Name=11340077
chr10	.	BED_feature	43510080	43510107	.	.	.	Name=11340077
chr10	.	BED_feature	44694959	44694986	.	.	.	Name=11340077
chr10	.	BED_feature	126716525	126716552	.	.	.	Name=11340077
chr17	.	BED_feature	61466792	61466819	.	.	.	Name=11340077
chr17	.	BED_feature	79163005	79163032	.	.	.	Name=11340077
chr16	.	BED_feature	9958745	9958772	.	.	.	Name=11340077
chr15	.	BED_feature	12520042	12520069	.	.	.	Name=11340077
chr15	.	BED_feature	43047770	43047797	.	.	.	Name=11340077
chr15	.	BED_feature	84694508	84694535	.	.	.	Name=11340077
chr15	.	BED_feature	93025205	93025232	.	.	.	Name=11340077
chr14	.	BED_feature	10074729	10074756	.	.	.	Name=11340077
chr14	.	BED_feature	47331005	47331032	.	.	.	Name=11340077
chr14	.	BED_feature	102256690	102256717	.	.	.	Name=11340077
chr19	.	BED_feature	16345221	16345248	.	.	.	Name=11340077
chr19	.	BED_feature	25863453	25863480	.	.	.	Name=11340077
chr19	.	BED_feature	40266123	40266150	.	.	.	Name=11340077
chr19	.	BED_feature	46728129	46728156	.	.	.	Name=11340077
chrX	.	BED_feature	76447116	76447143	.	.	.	Name=11340077
chrX	.	BED_feature	84825317	84825344	.	.	.	Name=11340077
chrX	.	BED_feature	111576384	111576411	.	.	.	Name=11340077
chrX	.	BED_feature	135023392	135023419	.	.	.	Name=11340077
chrX	.	BED_feature	137121173	137121200	.	.	.	Name=11340077
chrX	.	BED_feature	147286511	147286538	.	.	.	Name=11340077
chrX	.	BED_feature	148744324	148744351	.	.	.	Name=11340077
chr7	.	BED_feature	24606070	24606218	.	.	.	Name=12446773
chr12	.	BED_feature	113713040	113713078	.	.	.	Name=10748032
chr1	.	BED_feature	173050698	173050731	.	.	.	Name=9295294
chr18	.	BED_feature	36852670	36852801	.	.	.	Name=1383228
chr2	.	BED_feature	62284547	62284588	.	.	.	Name=9372951
chr6	.	BED_feature	85417667	85417702	.	.	.	Name=10561509
chr5	.	BED_feature	130102073	130102109	.	.	.	Name=10561509
chr3	.	BED_feature	88383091	88383129	.	.	.	Name=10561509
chr11	.	BED_feature	22890633	22890669	.	.	.	Name=10561509
chr10	.	BED_feature	116467503	116467538	.	.	.	Name=10561509
chr17	.	BED_feature	12759733	12759768	.	.	.	Name=10561509
chr16	.	BED_feature	87384800	87384835	.	.	.	Name=10561509
chr15	.	BED_feature	31546067	31546480	.	.	.	Name=10561509
chr12	.	BED_feature	86368564	86368595	.	.	.	Name=10037443
chr9	.	BED_feature	45686922	45687188	.	.	.	Name=9121477
chr5	.	BED_feature	30343759	30343787	.	.	.	Name=9535723
chr8	.	BED_feature	71809364	71809400	.	.	.	Name=9535723
chr15	.	BED_feature	74683442	74683480	.	.	.	Name=2783417
chr2	.	BED_feature	155442607	155442644	.	.	.	Name=10777534
chr13	.	BED_feature	27064877	27064908	.	.	.	Name=9717847
chr15	.	BED_feature	85410290	85410319	.	.	.	Name=11914369
chr14	.	BED_feature	30038417	30038468	.	.	.	Name=8114720
chr7	.	BED_feature	3538564	3538594	.	.	.	Name=8798433
chr7	.	BED_feature	3859547	3859577	.	.	.	Name=8798433
chr7	.	BED_feature	25430523	25430560	.	.	.	Name=8798433
chr17	.	BED_feature	34870981	34871010	.	.	.	Name=1986360
chr7	.	BED_feature	46583870	46583914	.	.	.	Name=8007954
chr11	.	BED_feature	78736004	78736032	.	.	.	Name=8649986
chr15	.	BED_feature	97830453	97830489	.	.	.	Name=9614106
chr2	.	BED_feature	101425473	101425503	.	.	.	Name=10845919
chr7	.	BED_feature	28059499	28059529	.	.	.	Name=8961261
chr9	.	BED_feature	86493187	86493221	.	.	.	Name=1314168
chr11	.	BED_feature	54093150	54093179	.	.	.	Name=7623820
chr17	.	BED_feature	35114029	35114070	.	.	.	Name=8152920
chr12	.	BED_feature	86362671	86362705	.	.	.	Name=2062642
chr3	.	BED_feature	145584298	145585034	.	.	.	Name=2062642
chr3	.	BED_feature	145586518	145589421	.	.	.	Name=2062642
chr12	.	BED_feature	104139375	104139661	.	.	.	Name=2836860
chr12	.	BED_feature	104174807	104175094	.	.	.	Name=2836860
chr12	.	BED_feature	104229503	104229533	.	.	.	Name=2836860
chr12	.	BED_feature	104358133	104358161	.	.	.	Name=2836860
chr5	.	BED_feature	91535985	91536015	.	.	.	Name=2836860
chr18	.	BED_feature	20806564	20806636	.	.	.	Name=2836860
chr5	.	BED_feature	121148230	121148258	.	.	.	Name=2542764
chr5	.	BED_feature	121168144	121168172	.	.	.	Name=2542764
chr12	.	BED_feature	91806441	91806470	.	.	.	Name=7997232
chrX	.	BED_feature	7133614	7133659	.	.	.	Name=9089398
chr2	.	BED_feature	73619657	73619758	.	.	.	Name=2529117
chr16	.	BED_feature	23806225	23806260	.	.	.	Name=2529117
chr6	.	BED_feature	68684618	68684724	.	.	.	Name=6425835
chr6	.	BED_feature	68698142	68698686	.	.	.	Name=6425835
chr6	.	BED_feature	68736760	68737358	.	.	.	Name=6425835
chr6	.	BED_feature	68840001	68840564	.	.	.	Name=6425835
chr6	.	BED_feature	68890969	68891062	.	.	.	Name=6425835
chr6	.	BED_feature	68920339	68921728	.	.	.	Name=6425835
chr6	.	BED_feature	68946142	68946963	.	.	.	Name=6425835
chr6	.	BED_feature	68972553	68973158	.	.	.	Name=6425835
chr6	.	BED_feature	68989286	68990099	.	.	.	Name=6425835
chr6	.	BED_feature	69040492	69041384	.	.	.	Name=6425835
chr6	.	BED_feature	69085699	69087114	.	.	.	Name=6425835
chr6	.	BED_feature	69114422	69115312	.	.	.	Name=6425835
chr6	.	BED_feature	69127164	69128068	.	.	.	Name=6425835
chr6	.	BED_feature	69156435	69157335	.	.	.	Name=6425835
chr6	.	BED_feature	69172741	69173640	.	.	.	Name=6425835
chr6	.	BED_feature	69197465	69198364	.	.	.	Name=6425835
chr6	.	BED_feature	69213371	69214271	.	.	.	Name=6425835
chr6	.	BED_feature	69234415	69235314	.	.	.	Name=6425835
chr6	.	BED_feature	69272069	69272593	.	.	.	Name=6425835
chr6	.	BED_feature	69307548	69308424	.	.	.	Name=6425835
chr6	.	BED_feature	69329408	69330297	.	.	.	Name=6425835
chr6	.	BED_feature	69346489	69347377	.	.	.	Name=6425835
chr6	.	BED_feature	69367799	69368693	.	.	.	Name=6425835
chr6	.	BED_feature	69392782	69393073	.	.	.	Name=6425835
chr6	.	BED_feature	69429836	69430439	.	.	.	Name=6425835
chr6	.	BED_feature	69473955	69475278	.	.	.	Name=6425835
chr6	.	BED_feature	69505556	69506447	.	.	.	Name=6425835
chr6	.	BED_feature	69516876	69517762	.	.	.	Name=6425835
chr6	.	BED_feature	69536856	69537753	.	.	.	Name=6425835
chr6	.	BED_feature	69561246	69562130	.	.	.	Name=6425835
chr6	.	BED_feature	69578405	69578943	.	.	.	Name=6425835
chr6	.	BED_feature	69610988	69612347	.	.	.	Name=6425835
chr6	.	BED_feature	69630363	69630940	.	.	.	Name=6425835
chr6	.	BED_feature	70652143	70652210	.	.	.	Name=6425835
chr9	.	BED_feature	54560094	54560196	.	.	.	Name=10714763
chr3	.	BED_feature	19885849	19887595	.	.	.	Name=11278361
chr2	.	BED_feature	181294772	181294837	.	.	.	Name=11890680
chr16	.	BED_feature	14204868	14204896	.	.	.	Name=9529161
chr16	.	BED_feature	14206007	14206115	.	.	.	Name=9529161
chr16	.	BED_feature	15801943	15802019	.	.	.	Name=1714459
chr19	.	BED_feature	25572694	25572730	.	.	.	Name=11870074
chr11	.	BED_feature	83478594	83478783	.	.	.	Name=7835696
chr12	.	BED_feature	109901106	109901145	.	.	.	Name=9822638
chr11	.	BED_feature	78736048	78736116	.	.	.	Name=7520478
chr10	.	BED_feature	60693069	60693125	.	.	.	Name=8871649
chr3	.	BED_feature	10166296	10166330	.	.	.	Name=10629058
chr3	.	BED_feature	10190984	10191043	.	.	.	Name=10629058
chr13	.	BED_feature	42174357	42175365	.	.	.	Name=1694016
chr13	.	BED_feature	42178531	42178635	.	.	.	Name=1694016
chr13	.	BED_feature	42192408	42192904	.	.	.	Name=1694016
chr13	.	BED_feature	42194362	42195998	.	.	.	Name=1694016
chr5	.	BED_feature	126371779	126372395	.	.	.	Name=1694016
chr10	.	BED_feature	13829638	13829679	.	.	.	Name=1694016
chr3	.	BED_feature	142601285	142602903	.	.	.	Name=1694016
chrX	.	BED_feature	92424646	92425011	.	.	.	Name=1694016
chr12	.	BED_feature	31850892	31850939	.	.	.	Name=2556699
chr2	.	BED_feature	172795580	172795617	.	.	.	Name=7532283
chr4	.	BED_feature	140282528	140282656	.	.	.	Name=16321658
chr11	.	BED_feature	69764187	69765140	.	.	.	Name=2404278
chr11	.	BED_feature	78736812	78736954	.	.	.	Name=9164945
chr12	.	BED_feature	86362676	86362716	.	.	.	Name=12137955
chr2	.	BED_feature	133243978	133244008	.	.	.	Name=12511606
chr12	.	BED_feature	113787246	113787280	.	.	.	Name=8089482
chr17	.	BED_feature	33897271	33897310	.	.	.	Name=8089482
chr5	.	BED_feature	107965133	107965162	.	.	.	Name=15131254
chr5	.	BED_feature	107966947	107966977	.	.	.	Name=15131254
chr7	.	BED_feature	18568532	18568560	.	.	.	Name=9614136
chr12	.	BED_feature	113875210	113875260	.	.	.	Name=9614136
chr11	.	BED_feature	67052884	67053961	.	.	.	Name=9614136
chr17	.	BED_feature	34470751	34470826	.	.	.	Name=2174104
chr9	.	BED_feature	57494750	57494781	.	.	.	Name=2174107
chr3	.	BED_feature	68778501	68778530	.	.	.	Name=11602633
chr6	.	BED_feature	92210031	92210058	.	.	.	Name=8910392
chr6	.	BED_feature	92212008	92212036	.	.	.	Name=8910392
chr2	.	BED_feature	76161192	76162902	.	.	.	Name=9166696
chr9	.	BED_feature	110863759	110863788	.	.	.	Name=1584212
chr4	.	BED_feature	88312924	88312952	.	.	.	Name=1614874
chr9	.	BED_feature	54562793	54562841	.	.	.	Name=9092560
chr17	.	BED_feature	25093748	25093807	.	.	.	Name=8839840
chr6	.	BED_feature	65067756	65067784	.	.	.	Name=10998423
chr9	.	BED_feature	86492890	86493178	.	.	.	Name=2332433
chr9	.	BED_feature	107764659	107765245	.	.	.	Name=9467940
chr3	.	BED_feature	159534367	159534406	.	.	.	Name=12759335
chr8	.	BED_feature	119981735	119981808	.	.	.	Name=12759335
chr4	.	BED_feature	63533052	63537026	.	.	.	Name=7534412
chr1	.	BED_feature	151860748	151860789	.	.	.	Name=10859338
chr6	.	BED_feature	4455594	4455637	.	.	.	Name=2072909
chr4	.	BED_feature	15808179	15808216	.	.	.	Name=8464915
chr9	.	BED_feature	21713833	21713868	.	.	.	Name=1650452
chrX	.	BED_feature	7116698	7116727	.	.	.	Name=1650452
chr1	.	BED_feature	172895951	172895985	.	.	.	Name=8070412
chr12	.	BED_feature	17570231	17570438	.	.	.	Name=1650455
chr3	.	BED_feature	28888879	28888913	.	.	.	Name=15886523
chr12	.	BED_feature	113875219	113875262	.	.	.	Name=2357966
chr3	.	BED_feature	135628874	135628907	.	.	.	Name=9190210
chr2	.	BED_feature	105465567	105465607	.	.	.	Name=12962539
chr6	.	BED_feature	134199219	134199263	.	.	.	Name=9009269
chr11	.	BED_feature	106130523	106130913	.	.	.	Name=2508087
chr19	.	BED_feature	43579562	43579614	.	.	.	Name=10527950
chr5	.	BED_feature	91535982	91536012	.	.	.	Name=10527950
chr8	.	BED_feature	87866667	87866694	.	.	.	Name=8537375
chr11	.	BED_feature	65087252	65087284	.	.	.	Name=14645532
chr2	.	BED_feature	104927052	104927087	.	.	.	Name=9336463
chr9	.	BED_feature	21881605	21881649	.	.	.	Name=15563837
chr6	.	BED_feature	41043107	41043146	.	.	.	Name=12082086
chr17	.	BED_feature	33955131	33955170	.	.	.	Name=2564635
chr18	.	BED_feature	43863435	43863477	.	.	.	Name=7935489
chr3	.	BED_feature	89222380	89222424	.	.	.	Name=1315961
chr16	.	BED_feature	18515178	18515212	.	.	.	Name=12533514
chr7	.	BED_feature	46243935	46243963	.	.	.	Name=12135926
chr16	.	BED_feature	23806222	23806263	.	.	.	Name=9832447
chr9	.	BED_feature	53991724	53991761	.	.	.	Name=9832447
chr8	.	BED_feature	93960202	93960321	.	.	.	Name=10760507
chr2	.	BED_feature	83525257	83525288	.	.	.	Name=10899572
chr12	.	BED_feature	86362671	86362704	.	.	.	Name=11279108
chr9	.	BED_feature	45687018	45687189	.	.	.	Name=11279108
chr15	.	BED_feature	102815627	102815660	.	.	.	Name=9860988
chr6	.	BED_feature	122673020	122673057	.	.	.	Name=15743839
chr11	.	BED_feature	53460768	53460830	.	.	.	Name=8052653
chr3	.	BED_feature	37317766	37317795	.	.	.	Name=7815567
chr5	.	BED_feature	104410881	104410914	.	.	.	Name=15292199
chr1	.	BED_feature	72808170	72808198	.	.	.	Name=11978764
chr5	.	BED_feature	91525401	91525436	.	.	.	Name=8455618
chr8	.	BED_feature	97068303	97068335	.	.	.	Name=3371659
chr14	.	BED_feature	53032878	53033063	.	.	.	Name=8417120
chr19	.	BED_feature	39339060	39339105	.	.	.	Name=15155833
chr11	.	BED_feature	100150362	100150496	.	.	.	Name=15292219
chr12	.	BED_feature	113875210	113875262	.	.	.	Name=2143023
chr8	.	BED_feature	77980069	77980098	.	.	.	Name=10821856
chr7	.	BED_feature	34758870	34759579	.	.	.	Name=1709121
chr7	.	BED_feature	34765226	34765304	.	.	.	Name=1709121
chr11	.	BED_feature	98517241	98517282	.	.	.	Name=1709121
chr11	.	BED_feature	117785320	117785367	.	.	.	Name=10821852
chr12	.	BED_feature	8797293	8797321	.	.	.	Name=8647862
chr2	.	BED_feature	26022961	26023284	.	.	.	Name=7708713
chr2	.	BED_feature	26024983	26025025	.	.	.	Name=7708713
chr17	.	BED_feature	56913369	56913420	.	.	.	Name=1590761
chr18	.	BED_feature	5705042	5705226	.	.	.	Name=7935395
chr18	.	BED_feature	5748703	5748854	.	.	.	Name=7935395
chr18	.	BED_feature	5766262	5768013	.	.	.	Name=7935395
chr18	.	BED_feature	5770385	5770456	.	.	.	Name=7935395
chr18	.	BED_feature	5772922	5774892	.	.	.	Name=7935395
chr18	.	BED_feature	82688765	82688797	.	.	.	Name=1379237
chr12	.	BED_feature	113725301	113725411	.	.	.	Name=1922063
chr17	.	BED_feature	33897272	33897383	.	.	.	Name=1922063
chr6	.	BED_feature	70655312	70655364	.	.	.	Name=1922063
chr10	.	BED_feature	75304094	75304140	.	.	.	Name=12083786
chr6	.	BED_feature	103929893	103930362	.	.	.	Name=1967980
chr4	.	BED_feature	124160871	124160929	.	.	.	Name=1967980
chr3	.	BED_feature	3814641	3815822	.	.	.	Name=1967980
chr3	.	BED_feature	129425689	129426847	.	.	.	Name=1967980
chr2	.	BED_feature	18070879	18070935	.	.	.	Name=1967980
chr1	.	BED_feature	42642751	42642809	.	.	.	Name=1967980
chr1	.	BED_feature	161130491	161130863	.	.	.	Name=1967980
chr1	.	BED_feature	167734341	167734399	.	.	.	Name=1967980
chr9	.	BED_feature	45912367	45912537	.	.	.	Name=1967980
chrX	.	BED_feature	49123968	49124378	.	.	.	Name=1967980
chrX	.	BED_feature	138022311	138022583	.	.	.	Name=1967980
chr13	.	BED_feature	78488860	78489006	.	.	.	Name=1967980
chr17	.	BED_feature	35114104	35114536	.	.	.	Name=1967980
chr17	.	BED_feature	35117154	35118822	.	.	.	Name=1967980
chr14	.	BED_feature	15898869	15899489	.	.	.	Name=1967980
chr5	.	BED_feature	93424230	93424259	.	.	.	Name=9169460
chr5	.	BED_feature	143171911	143171940	.	.	.	Name=1425594
chr1	.	BED_feature	72808043	72808222	.	.	.	Name=7476973
chr11	.	BED_feature	98517241	98517364	.	.	.	Name=1691438
chr17	.	BED_feature	33897321	33897361	.	.	.	Name=1691438
chr8	.	BED_feature	97068090	97068120	.	.	.	Name=9854025
chr11	.	BED_feature	106118006	106118034	.	.	.	Name=3561414
chr19	.	BED_feature	45794030	45794485	.	.	.	Name=10026229
chr19	.	BED_feature	10045618	10045708	.	.	.	Name=8051121
chr16	.	BED_feature	42260015	42260042	.	.	.	Name=8703010
chr12	.	BED_feature	3954579	3954608	.	.	.	Name=7902581
chr3	.	BED_feature	37317569	37317597	.	.	.	Name=7902581
chr16	.	BED_feature	23806225	23806252	.	.	.	Name=1824920
chr8	.	BED_feature	87866700	87866741	.	.	.	Name=8265655
chr8	.	BED_feature	87868842	87868887	.	.	.	Name=8265655
chr2	.	BED_feature	11559185	11559294	.	.	.	Name=10082534
chr10	.	BED_feature	20847629	20848108	.	.	.	Name=8683983
chr3	.	BED_feature	80999456	80999483	.	.	.	Name=11256962
chr4	.	BED_feature	62830853	62830882	.	.	.	Name=8417341
chr4	.	BED_feature	4066007	4066034	.	.	.	Name=1827203
chr9	.	BED_feature	57494750	57494781	.	.	.	Name=2160969
chr7	.	BED_feature	144670750	144670781	.	.	.	Name=10669750
chr2	.	BED_feature	129062604	129062632	.	.	.	Name=1630455
chr5	.	BED_feature	93424174	93424204	.	.	.	Name=7730628
chr18	.	BED_feature	34989185	34989285	.	.	.	Name=2496302
chr6	.	BED_feature	85477485	85477552	.	.	.	Name=2496302
chr10	.	BED_feature	66931539	66933967	.	.	.	Name=2496302
chr10	.	BED_feature	66935019	66936588	.	.	.	Name=2496302
chr14	.	BED_feature	68814683	68814794	.	.	.	Name=2496302
chr7	.	BED_feature	100366078	100366121	.	.	.	Name=10333481
chr7	.	BED_feature	100367251	100367300	.	.	.	Name=10333481
chr7	.	BED_feature	87369183	87369306	.	.	.	Name=10707962
chr12	.	BED_feature	113875196	113875343	.	.	.	Name=3019664
chr8	.	BED_feature	26983470	26984665	.	.	.	Name=1312839
chr8	.	BED_feature	3694205	3694256	.	.	.	Name=8977198
chr8	.	BED_feature	73627361	73627975	.	.	.	Name=1714380
chr10	.	BED_feature	82179843	82180616	.	.	.	Name=1698608
chr10	.	BED_feature	82182230	82182364	.	.	.	Name=1698608
chr10	.	BED_feature	82184842	82184895	.	.	.	Name=1698608
chr10	.	BED_feature	82186501	82186594	.	.	.	Name=1698608
chr10	.	BED_feature	82191632	82191714	.	.	.	Name=1698608
chr10	.	BED_feature	82193800	82193936	.	.	.	Name=1698608
chr17	.	BED_feature	47853529	47854911	.	.	.	Name=1698608
chr17	.	BED_feature	47856871	47859122	.	.	.	Name=1698608
chr17	.	BED_feature	47866012	47866148	.	.	.	Name=1698608
chr17	.	BED_feature	47875192	47875254	.	.	.	Name=1698608
chr18	.	BED_feature	82688932	82688970	.	.	.	Name=1698607
chr12	.	BED_feature	77323392	77323422	.	.	.	Name=14766014
chr15	.	BED_feature	88848027	88848126	.	.	.	Name=12754203
chr11	.	BED_feature	96133655	96134849	.	.	.	Name=7969151
chr2	.	BED_feature	26738276	26738484	.	.	.	Name=1996091
chr12	.	BED_feature	86362675	86362704	.	.	.	Name=2493627
chr6	.	BED_feature	4455388	4455417	.	.	.	Name=2019574
chr11	.	BED_feature	94751575	94752273	.	.	.	Name=2019574
chr5	.	BED_feature	89839309	89839533	.	.	.	Name=15548386
chr8	.	BED_feature	97068208	97068238	.	.	.	Name=10096565
chr8	.	BED_feature	83388452	83389772	.	.	.	Name=8690723
chr8	.	BED_feature	89614669	89614698	.	.	.	Name=14985507
chr15	.	BED_feature	38519949	38519977	.	.	.	Name=14985507
chrX	.	BED_feature	159414902	159414931	.	.	.	Name=14985507
chrX	.	BED_feature	159418072	159418353	.	.	.	Name=14985507
chr8	.	BED_feature	77985763	77985790	.	.	.	Name=7929191
chr1	.	BED_feature	66868621	66868649	.	.	.	Name=7721942
chr8	.	BED_feature	107736166	107736201	.	.	.	Name=16527247
chr14	.	BED_feature	53185363	53185593	.	.	.	Name=2524381
chr11	.	BED_feature	44456143	44456435	.	.	.	Name=12077253
chr16	.	BED_feature	16777811	16777842	.	.	.	Name=12077253
chr8	.	BED_feature	87792032	87792079	.	.	.	Name=7682653
chr8	.	BED_feature	87795041	87795392	.	.	.	Name=7682653
chr11	.	BED_feature	69406866	69406896	.	.	.	Name=11919084
chr12	.	BED_feature	14520678	14520705	.	.	.	Name=15589317
chr10	.	BED_feature	94842341	94842368	.	.	.	Name=15589317
chr15	.	BED_feature	74813844	74813871	.	.	.	Name=15589317
chr11	.	BED_feature	78315408	78315439	.	.	.	Name=11997100
chr1	.	BED_feature	133107822	133107866	.	.	.	Name=15939554
chr8	.	BED_feature	27273864	27273894	.	.	.	Name=16109738
chr12	.	BED_feature	114935222	114935265	.	.	.	Name=7499271
chr12	.	BED_feature	114981057	114981115	.	.	.	Name=7499271
chr12	.	BED_feature	114986581	114986620	.	.	.	Name=7499271
chr12	.	BED_feature	115031655	115031718	.	.	.	Name=7499271
chr12	.	BED_feature	115094658	115094721	.	.	.	Name=7499271
chr12	.	BED_feature	115113958	115114011	.	.	.	Name=7499271
chr12	.	BED_feature	115124834	115124892	.	.	.	Name=7499271
chr12	.	BED_feature	115156736	115156789	.	.	.	Name=7499271
chr12	.	BED_feature	115184333	115184386	.	.	.	Name=7499271
chr12	.	BED_feature	115411467	115411555	.	.	.	Name=7499271
chr12	.	BED_feature	115439194	115439249	.	.	.	Name=7499271
chr12	.	BED_feature	115567834	115567914	.	.	.	Name=7499271
chr12	.	BED_feature	115579469	115579522	.	.	.	Name=7499271
chr12	.	BED_feature	115593573	115593661	.	.	.	Name=7499271
chr12	.	BED_feature	115606489	115606578	.	.	.	Name=7499271
chr12	.	BED_feature	115641761	115641804	.	.	.	Name=7499271
chr12	.	BED_feature	115656181	115656270	.	.	.	Name=7499271
chr12	.	BED_feature	115783168	115783248	.	.	.	Name=7499271
chr12	.	BED_feature	115792631	115792684	.	.	.	Name=7499271
chr12	.	BED_feature	115807226	115807314	.	.	.	Name=7499271
chr12	.	BED_feature	115820071	115820159	.	.	.	Name=7499271
chr12	.	BED_feature	115834781	115834842	.	.	.	Name=7499271
chr12	.	BED_feature	115894503	115894564	.	.	.	Name=7499271
chr12	.	BED_feature	115909085	115909173	.	.	.	Name=7499271
chr12	.	BED_feature	115943711	115943774	.	.	.	Name=7499271
chr12	.	BED_feature	115955631	115955720	.	.	.	Name=7499271
chr12	.	BED_feature	116041196	116041259	.	.	.	Name=7499271
chr12	.	BED_feature	116052026	116052089	.	.	.	Name=7499271
chr12	.	BED_feature	116071247	116071312	.	.	.	Name=7499271
chr12	.	BED_feature	116139975	116140036	.	.	.	Name=7499271
chr12	.	BED_feature	116190299	116190360	.	.	.	Name=7499271
chr12	.	BED_feature	116206070	116206159	.	.	.	Name=7499271
chr12	.	BED_feature	116238680	116238743	.	.	.	Name=7499271
chr12	.	BED_feature	116250734	116250823	.	.	.	Name=7499271
chr12	.	BED_feature	116295975	116296030	.	.	.	Name=7499271
chr12	.	BED_feature	116309961	116310014	.	.	.	Name=7499271
chr12	.	BED_feature	116336183	116336245	.	.	.	Name=7499271
chr12	.	BED_feature	116360430	116360493	.	.	.	Name=7499271
chr12	.	BED_feature	116368365	116368428	.	.	.	Name=7499271
chr12	.	BED_feature	116400624	116400687	.	.	.	Name=7499271
chr12	.	BED_feature	116448114	116448167	.	.	.	Name=7499271
chr12	.	BED_feature	116457747	116457835	.	.	.	Name=7499271
chrX	.	BED_feature	6930810	6930883	.	.	.	Name=1732746
chr1	.	BED_feature	77405309	77405349	.	.	.	Name=9425139
chr2	.	BED_feature	104927481	104927514	.	.	.	Name=9572484
chr12	.	BED_feature	104139350	104139711	.	.	.	Name=2835657
chr12	.	BED_feature	104174784	104175144	.	.	.	Name=2835657
chr12	.	BED_feature	104229224	104229583	.	.	.	Name=2835657
chr12	.	BED_feature	104264775	104265134	.	.	.	Name=2835657
chr12	.	BED_feature	104306112	104306471	.	.	.	Name=2835657
chr12	.	BED_feature	104358110	104358469	.	.	.	Name=2835657
chr9	.	BED_feature	109977128	109977179	.	.	.	Name=16288722
chr11	.	BED_feature	117784320	117784347	.	.	.	Name=16055089
chr7	.	BED_feature	119936638	119936667	.	.	.	Name=1944285
chr7	.	BED_feature	26015816	26015923	.	.	.	Name=15115437
chr7	.	BED_feature	26543962	26544069	.	.	.	Name=15115437
chr6	.	BED_feature	52134628	52134846	.	.	.	Name=10075847
chr11	.	BED_feature	53462120	53462152	.	.	.	Name=8674125
chr12	.	BED_feature	86362655	86362945	.	.	.	Name=8547224
chr7	.	BED_feature	18568361	18568567	.	.	.	Name=8474439
chr12	.	BED_feature	86362675	86362703	.	.	.	Name=1508214
chr3	.	BED_feature	37317571	37317599	.	.	.	Name=8920856
chr3	.	BED_feature	37317768	37317796	.	.	.	Name=1740667
chr18	.	BED_feature	20808311	20808338	.	.	.	Name=9278450
chr5	.	BED_feature	30404404	30404433	.	.	.	Name=2041767
chr8	.	BED_feature	95715470	95715515	.	.	.	Name=9278454
chrX	.	BED_feature	145890538	145890592	.	.	.	Name=17038566
chr13	.	BED_feature	15805219	15805248	.	.	.	Name=9645703
chr13	.	BED_feature	15808168	15808197	.	.	.	Name=9645703
chr3	.	BED_feature	88459031	88459063	.	.	.	Name=12551949
chr3	.	BED_feature	88464737	88464769	.	.	.	Name=12551949
chr3	.	BED_feature	88470502	88470534	.	.	.	Name=12551949
chr17	.	BED_feature	16374738	16374767	.	.	.	Name=10488087
chr2	.	BED_feature	162764103	162764132	.	.	.	Name=10488087
chr17	.	BED_feature	31406532	31406588	.	.	.	Name=3170605
chr15	.	BED_feature	102814723	102814982	.	.	.	Name=8575334
chr11	.	BED_feature	4139835	4140014	.	.	.	Name=8605875
chr16	.	BED_feature	87588034	87588301	.	.	.	Name=11530014
chr10	.	BED_feature	106896029	106896057	.	.	.	Name=11782449
chr17	.	BED_feature	39672036	39672210	.	.	.	Name=8441629
chr10	.	BED_feature	80208261	80208289	.	.	.	Name=10913126
chr9	.	BED_feature	57813048	57813102	.	.	.	Name=10913126
chr5	.	BED_feature	88773940	88774182	.	.	.	Name=8065333
chr15	.	BED_feature	85562972	85563000	.	.	.	Name=12554753
chr2	.	BED_feature	91732738	91734451	.	.	.	Name=7982887
chr11	.	BED_feature	60026655	60026701	.	.	.	Name=10918064
chr2	.	BED_feature	105483209	105483268	.	.	.	Name=7529875
chr14	.	BED_feature	62371255	62371322	.	.	.	Name=10553071
chr1	.	BED_feature	182533905	182533975	.	.	.	Name=15982639
chr4	.	BED_feature	134425013	134425135	.	.	.	Name=8164679
chr17	.	BED_feature	44180252	44180353	.	.	.	Name=8164679
chr17	.	BED_feature	44198286	44198415	.	.	.	Name=8164679
chr16	.	BED_feature	92492847	92494983	.	.	.	Name=8164679
chr16	.	BED_feature	92502458	92502618	.	.	.	Name=8164679
chr16	.	BED_feature	92533013	92533204	.	.	.	Name=8164679
chr16	.	BED_feature	92557569	92557673	.	.	.	Name=8164679
chr16	.	BED_feature	92577834	92577993	.	.	.	Name=8164679
chr16	.	BED_feature	92584341	92586187	.	.	.	Name=8164679
chr8	.	BED_feature	4349462	4349655	.	.	.	Name=16517733
chr8	.	BED_feature	74508958	74508987	.	.	.	Name=9353271
chr9	.	BED_feature	110861573	110864453	.	.	.	Name=1939212
chr13	.	BED_feature	30756678	30756725	.	.	.	Name=7541907
chr16	.	BED_feature	23806222	23806253	.	.	.	Name=9671480
chr11	.	BED_feature	32183544	32183592	.	.	.	Name=9144493
chr11	.	BED_feature	32196361	32196409	.	.	.	Name=9144493
chr17	.	BED_feature	34871048	34871100	.	.	.	Name=9144493
chr8	.	BED_feature	3622334	3626083	.	.	.	Name=2065970
chr6	.	BED_feature	70655324	70655353	.	.	.	Name=1598211
chr17	.	BED_feature	34871063	34871092	.	.	.	Name=1598211
chr17	.	BED_feature	26566989	26567223	.	.	.	Name=7586217
chr18	.	BED_feature	34987528	34987557	.	.	.	Name=8737376
chr6	.	BED_feature	132024025	132024248	.	.	.	Name=1747160
chr6	.	BED_feature	132083312	132083546	.	.	.	Name=1747160
chr6	.	BED_feature	132176166	132176400	.	.	.	Name=1747160
chr6	.	BED_feature	132280379	132280602	.	.	.	Name=1747160
chr6	.	BED_feature	132329757	132329991	.	.	.	Name=1747160
chr6	.	BED_feature	132407374	132407597	.	.	.	Name=1747160
chr6	.	BED_feature	133257935	133257987	.	.	.	Name=1747160
chr6	.	BED_feature	133494908	133494960	.	.	.	Name=1747160
chr12	.	BED_feature	105964106	105964142	.	.	.	Name=15805112
chr4	.	BED_feature	122502565	122502605	.	.	.	Name=10655054
chr3	.	BED_feature	89222380	89222424	.	.	.	Name=9234678
chr18	.	BED_feature	60929072	60929106	.	.	.	Name=2115119
chr8	.	BED_feature	24223213	24223318	.	.	.	Name=2172788
chr11	.	BED_feature	94936098	94936174	.	.	.	Name=14670999
chr4	.	BED_feature	144513604	144513631	.	.	.	Name=9190933
chr13	.	BED_feature	93455947	93455976	.	.	.	Name=9121444
chr2	.	BED_feature	90897636	90897832	.	.	.	Name=1985210
chr2	.	BED_feature	90900269	90900344	.	.	.	Name=1985210
chr2	.	BED_feature	90914131	90916592	.	.	.	Name=1985210
chr8	.	BED_feature	27273934	27273962	.	.	.	Name=9832418
chr17	.	BED_feature	24360203	24360244	.	.	.	Name=10891372
chr7	.	BED_feature	78926829	78926857	.	.	.	Name=9368062
chr17	.	BED_feature	33896555	33896590	.	.	.	Name=7722306
chr6	.	BED_feature	145033119	145033148	.	.	.	Name=1340466
chr16	.	BED_feature	15801216	15801865	.	.	.	Name=1840554
chr2	.	BED_feature	167381024	167381533	.	.	.	Name=1840554
chr6	.	BED_feature	115387318	115387351	.	.	.	Name=10862621
chr2	.	BED_feature	167380226	167380831	.	.	.	Name=10862621
chr13	.	BED_feature	63575640	63575677	.	.	.	Name=15087129
chr7	.	BED_feature	41898797	41898824	.	.	.	Name=12890683
chr7	.	BED_feature	51615248	51615275	.	.	.	Name=12890683
chr7	.	BED_feature	89483419	89483446	.	.	.	Name=12890683
chr7	.	BED_feature	100635334	100635361	.	.	.	Name=12890683
chr6	.	BED_feature	22653948	22653975	.	.	.	Name=12890683
chr6	.	BED_feature	83840479	83840506	.	.	.	Name=12890683
chr6	.	BED_feature	84778436	84778463	.	.	.	Name=12890683
chr6	.	BED_feature	91394919	91394946	.	.	.	Name=12890683
chr6	.	BED_feature	125128287	125128314	.	.	.	Name=12890683
chr6	.	BED_feature	128168293	128168320	.	.	.	Name=12890683
chr5	.	BED_feature	13048881	13048908	.	.	.	Name=12890683
chr5	.	BED_feature	28869889	28869916	.	.	.	Name=12890683
chr5	.	BED_feature	96102548	96102575	.	.	.	Name=12890683
chr5	.	BED_feature	106103445	106103472	.	.	.	Name=12890683
chr4	.	BED_feature	57465449	57465476	.	.	.	Name=12890683
chr4	.	BED_feature	83576664	83576691	.	.	.	Name=12890683
chr4	.	BED_feature	91344128	91344155	.	.	.	Name=12890683
chr3	.	BED_feature	52701296	52701323	.	.	.	Name=12890683
chr3	.	BED_feature	61550231	61550258	.	.	.	Name=12890683
chr3	.	BED_feature	69654805	69654832	.	.	.	Name=12890683
chr3	.	BED_feature	79003717	79003744	.	.	.	Name=12890683
chr3	.	BED_feature	122222659	122222686	.	.	.	Name=12890683
chr3	.	BED_feature	139587298	139587325	.	.	.	Name=12890683
chr3	.	BED_feature	142900529	142900556	.	.	.	Name=12890683
chr2	.	BED_feature	28756059	28756086	.	.	.	Name=12890683
chr2	.	BED_feature	43340848	43340875	.	.	.	Name=12890683
chr2	.	BED_feature	104092945	104092972	.	.	.	Name=12890683
chr2	.	BED_feature	128249131	128249158	.	.	.	Name=12890683
chr2	.	BED_feature	149435148	149435175	.	.	.	Name=12890683
chr2	.	BED_feature	151066019	151066046	.	.	.	Name=12890683
chr1	.	BED_feature	13771539	13771566	.	.	.	Name=12890683
chr1	.	BED_feature	15254455	15254482	.	.	.	Name=12890683
chr1	.	BED_feature	152899146	152899173	.	.	.	Name=12890683
chr1	.	BED_feature	182164288	182164315	.	.	.	Name=12890683
chr18	.	BED_feature	54110228	54110255	.	.	.	Name=12890683
chr9	.	BED_feature	49938710	49938737	.	.	.	Name=12890683
chr9	.	BED_feature	75480004	75480031	.	.	.	Name=12890683
chr8	.	BED_feature	37841586	37841613	.	.	.	Name=12890683
chr8	.	BED_feature	60442976	60443003	.	.	.	Name=12890683
chr8	.	BED_feature	78302032	78302059	.	.	.	Name=12890683
chr8	.	BED_feature	95605497	95605524	.	.	.	Name=12890683
chr13	.	BED_feature	11994119	11994146	.	.	.	Name=12890683
chr13	.	BED_feature	17606626	17606653	.	.	.	Name=12890683
chr12	.	BED_feature	70839519	70839546	.	.	.	Name=12890683
chr12	.	BED_feature	72765316	72765343	.	.	.	Name=12890683
chr11	.	BED_feature	3852263	3852290	.	.	.	Name=12890683
chr11	.	BED_feature	17874237	17874264	.	.	.	Name=12890683
chr11	.	BED_feature	20235457	20235484	.	.	.	Name=12890683
chr11	.	BED_feature	26687165	26687192	.	.	.	Name=12890683
chr11	.	BED_feature	99494754	99494781	.	.	.	Name=12890683
chr10	.	BED_feature	13581286	13581313	.	.	.	Name=12890683
chr10	.	BED_feature	22481288	22481315	.	.	.	Name=12890683
chr10	.	BED_feature	33498352	33498379	.	.	.	Name=12890683
chr10	.	BED_feature	39701820	39701847	.	.	.	Name=12890683
chr10	.	BED_feature	118296365	118296392	.	.	.	Name=12890683
chr10	.	BED_feature	121572954	121572981	.	.	.	Name=12890683
chr17	.	BED_feature	61466688	61466715	.	.	.	Name=12890683
chr15	.	BED_feature	12520146	12520173	.	.	.	Name=12890683
chr15	.	BED_feature	93025309	93025336	.	.	.	Name=12890683
chr14	.	BED_feature	10074625	10074652	.	.	.	Name=12890683
chr14	.	BED_feature	47331109	47331136	.	.	.	Name=12890683
chr19	.	BED_feature	25863349	25863376	.	.	.	Name=12890683
chrX	.	BED_feature	12483421	12483448	.	.	.	Name=12890683
chrX	.	BED_feature	76447012	76447039	.	.	.	Name=12890683
chrX	.	BED_feature	137121069	137121096	.	.	.	Name=12890683
chrX	.	BED_feature	147286615	147286642	.	.	.	Name=12890683
chr7	.	BED_feature	18568428	18568476	.	.	.	Name=7673178
chr15	.	BED_feature	75583533	75583563	.	.	.	Name=16847327
chr12	.	BED_feature	113675504	113675532	.	.	.	Name=14583460
chr12	.	BED_feature	113676861	113676889	.	.	.	Name=14583460
chr19	.	BED_feature	5492747	5492800	.	.	.	Name=3198687
chr1	.	BED_feature	89020344	89021805	.	.	.	Name=3198687
chr8	.	BED_feature	43745981	43746034	.	.	.	Name=3198687
chr3	.	BED_feature	20300211	20301022	.	.	.	Name=8923460
chrX	.	BED_feature	118218832	118219048	.	.	.	Name=8923460
chr7	.	BED_feature	18568517	18568562	.	.	.	Name=8321243
chr16	.	BED_feature	38172278	38173137	.	.	.	Name=9489701
chr16	.	BED_feature	38185265	38185310	.	.	.	Name=9489701
chr17	.	BED_feature	34810548	34810577	.	.	.	Name=9281604
chr12	.	BED_feature	86362672	86362700	.	.	.	Name=3071491
chr7	.	BED_feature	18461603	18465370	.	.	.	Name=1741260
chr7	.	BED_feature	18466540	18469320	.	.	.	Name=1741260
chr16	.	BED_feature	32350557	32350657	.	.	.	Name=10744779
chr8	.	BED_feature	27273944	27273974	.	.	.	Name=12790807
chr18	.	BED_feature	34986768	34986829	.	.	.	Name=10829028
chr8	.	BED_feature	97068174	97068435	.	.	.	Name=6095286
chr12	.	BED_feature	86362673	86362702	.	.	.	Name=2557547
chr12	.	BED_feature	113093402	113093434	.	.	.	Name=15105421
chr9	.	BED_feature	20703220	20703262	.	.	.	Name=12799438
chr3	.	BED_feature	37317566	37317601	.	.	.	Name=12896977
chr17	.	BED_feature	31406584	31406614	.	.	.	Name=8876643
chr11	.	BED_feature	81849374	81849433	.	.	.	Name=8630731
chr11	.	BED_feature	81851531	81851898	.	.	.	Name=8630731
chr4	.	BED_feature	35082683	35082711	.	.	.	Name=1379672
chr18	.	BED_feature	43862651	43862930	.	.	.	Name=3399394
chr19	.	BED_feature	44460946	44460975	.	.	.	Name=9689914
chr11	.	BED_feature	94892869	94893018	.	.	.	Name=16475024
chr5	.	BED_feature	91525396	91525436	.	.	.	Name=2371282
chr5	.	BED_feature	91535956	91535987	.	.	.	Name=2371282
chr7	.	BED_feature	18568473	18568552	.	.	.	Name=2814500
chr3	.	BED_feature	159534199	159534229	.	.	.	Name=15900016
chr4	.	BED_feature	41236705	41236739	.	.	.	Name=11679588
chr12	.	BED_feature	105964110	105964139	.	.	.	Name=10748162
chr11	.	BED_feature	96181621	96181650	.	.	.	Name=7600572
chr12	.	BED_feature	113676250	113676300	.	.	.	Name=10931834
chr5	.	BED_feature	88774020	88774051	.	.	.	Name=12151092
chr17	.	BED_feature	33871428	33871472	.	.	.	Name=1986250
chr5	.	BED_feature	142653990	142654515	.	.	.	Name=8007964
chr5	.	BED_feature	142687615	142687800	.	.	.	Name=8007964
chr5	.	BED_feature	142701159	142701318	.	.	.	Name=8007964
chr5	.	BED_feature	142702713	142702861	.	.	.	Name=8007964
chr5	.	BED_feature	142703910	142704069	.	.	.	Name=8007964
chr5	.	BED_feature	142705988	142706514	.	.	.	Name=8007964
chr5	.	BED_feature	142707824	142709438	.	.	.	Name=8007964
chr11	.	BED_feature	121076365	121076591	.	.	.	Name=8007964
chr11	.	BED_feature	121112131	121112225	.	.	.	Name=8007964
chr11	.	BED_feature	32183601	32183676	.	.	.	Name=2233727
chr11	.	BED_feature	32196418	32196493	.	.	.	Name=2233727
chr10	.	BED_feature	79293962	79293990	.	.	.	Name=12949072
chr17	.	BED_feature	6012318	6012892	.	.	.	Name=2554307
chr17	.	BED_feature	33643284	33644637	.	.	.	Name=2554307
chr17	.	BED_feature	33646107	33648848	.	.	.	Name=2554307
chr2	.	BED_feature	27563770	27563934	.	.	.	Name=2554307
chr2	.	BED_feature	27578207	27578276	.	.	.	Name=2554307
chr2	.	BED_feature	27581549	27581678	.	.	.	Name=2554307
chr2	.	BED_feature	56926046	56926100	.	.	.	Name=2554307
chr1	.	BED_feature	169463964	169464125	.	.	.	Name=2554307
chr1	.	BED_feature	169475800	169475921	.	.	.	Name=2554307
chr1	.	BED_feature	75243575	75244102	.	.	.	Name=8120103
chr1	.	BED_feature	75245462	75246840	.	.	.	Name=8120103
chr8	.	BED_feature	27273960	27274009	.	.	.	Name=12239105
chr6	.	BED_feature	55381696	55381725	.	.	.	Name=12031496
chr6	.	BED_feature	70655319	70655350	.	.	.	Name=2542770
chr2	.	BED_feature	38532665	38532706	.	.	.	Name=10684809
chr2	.	BED_feature	38536571	38536607	.	.	.	Name=10684809
chr5	.	BED_feature	91525396	91525435	.	.	.	Name=7520913
chr5	.	BED_feature	91559418	91559470	.	.	.	Name=7520913
chr1	.	BED_feature	77985886	77986724	.	.	.	Name=2022185
chr1	.	BED_feature	78004723	78005858	.	.	.	Name=2022185
chr1	.	BED_feature	78015512	78015563	.	.	.	Name=2022185
chr1	.	BED_feature	78075619	78075680	.	.	.	Name=2022185
chr1	.	BED_feature	78079924	78080193	.	.	.	Name=2022185
chr4	.	BED_feature	63231534	63231725	.	.	.	Name=15702971
chr2	.	BED_feature	131944600	131944719	.	.	.	Name=8557653
chr8	.	BED_feature	87866607	87866694	.	.	.	Name=11904151
chr8	.	BED_feature	86177899	86177931	.	.	.	Name=8668156
chr5	.	BED_feature	8803881	8803912	.	.	.	Name=9019155
chr4	.	BED_feature	94544511	94544564	.	.	.	Name=1542579
chr6	.	BED_feature	4455530	4455626	.	.	.	Name=2043139
chr11	.	BED_feature	94752151	94752179	.	.	.	Name=2043139
chr5	.	BED_feature	148037298	148037332	.	.	.	Name=15192019
chr4	.	BED_feature	124304903	124304947	.	.	.	Name=8467794
chr4	.	BED_feature	124306962	124307422	.	.	.	Name=8467794
chr4	.	BED_feature	124322518	124323663	.	.	.	Name=8467794
chr4	.	BED_feature	124326590	124327487	.	.	.	Name=8467794
chr4	.	BED_feature	124333421	124333500	.	.	.	Name=8467794
chr4	.	BED_feature	124340001	124341221	.	.	.	Name=8467794
chr4	.	BED_feature	124344832	124344896	.	.	.	Name=8467794
chr4	.	BED_feature	124346446	124347053	.	.	.	Name=8467794
chr17	.	BED_feature	33610799	33610831	.	.	.	Name=9344877
chr12	.	BED_feature	58461348	58461377	.	.	.	Name=11297512
chr2	.	BED_feature	9775727	9776222	.	.	.	Name=2017177
chr2	.	BED_feature	9795442	9795542	.	.	.	Name=2017177
chr6	.	BED_feature	132083389	132083423	.	.	.	Name=10506207
chr6	.	BED_feature	132329830	132329868	.	.	.	Name=10506207
chr12	.	BED_feature	74028105	74028132	.	.	.	Name=8628654
chr12	.	BED_feature	74032219	74032246	.	.	.	Name=8628654
chr6	.	BED_feature	70655322	70655351	.	.	.	Name=2536725
chr2	.	BED_feature	154261287	154261338	.	.	.	Name=9218478
chr4	.	BED_feature	146844272	146844309	.	.	.	Name=10903346
chr4	.	BED_feature	35082316	35082343	.	.	.	Name=7513049
chr17	.	BED_feature	33896149	33896263	.	.	.	Name=2105455
chr3	.	BED_feature	152169790	152170157	.	.	.	Name=8125259
chr2	.	BED_feature	130801039	130801228	.	.	.	Name=8125259
chr7	.	BED_feature	46713836	46713863	.	.	.	Name=7998973
chr11	.	BED_feature	54093097	54093125	.	.	.	Name=1944268
chr11	.	BED_feature	98517361	98517391	.	.	.	Name=1944268
chr5	.	BED_feature	104539336	104539412	.	.	.	Name=10788516
chr6	.	BED_feature	92210238	92210394	.	.	.	Name=9421415
chr19	.	BED_feature	8779923	8780386	.	.	.	Name=2761540
chr9	.	BED_feature	78015621	78015661	.	.	.	Name=11708801
chr9	.	BED_feature	78042097	78042137	.	.	.	Name=11708801
chr9	.	BED_feature	78074895	78074935	.	.	.	Name=11708801
chr9	.	BED_feature	78133951	78133991	.	.	.	Name=11708801
chr7	.	BED_feature	34827855	34827883	.	.	.	Name=7862113
chr16	.	BED_feature	15800734	15800808	.	.	.	Name=10867011
chr16	.	BED_feature	4039922	4039963	.	.	.	Name=9492053
chr16	.	BED_feature	4043854	4043886	.	.	.	Name=9492053
chr18	.	BED_feature	34987317	34987459	.	.	.	Name=3141919
chr18	.	BED_feature	34989743	34990942	.	.	.	Name=3141919
chrX	.	BED_feature	107018249	107018296	.	.	.	Name=8876240
chr12	.	BED_feature	86362675	86362703	.	.	.	Name=1658630
chr6	.	BED_feature	4455158	4455412	.	.	.	Name=9143363
chr2	.	BED_feature	28444015	28444043	.	.	.	Name=15718298
chr11	.	BED_feature	120640142	120640174	.	.	.	Name=9164847
chr11	.	BED_feature	120640252	120640290	.	.	.	Name=10207099
chr12	.	BED_feature	86362667	86362711	.	.	.	Name=2504586
chr12	.	BED_feature	115955871	115955901	.	.	.	Name=2826127
chr12	.	BED_feature	116250974	116251004	.	.	.	Name=2826127
chr19	.	BED_feature	41082389	41082741	.	.	.	Name=1922043
chr16	.	BED_feature	16777514	16777740	.	.	.	Name=1922043
chr16	.	BED_feature	16782847	16782880	.	.	.	Name=1922043
chr16	.	BED_feature	17893922	17893955	.	.	.	Name=1922043
chr11	.	BED_feature	4848071	4848108	.	.	.	Name=8621737
chrX	.	BED_feature	7124906	7125430	.	.	.	Name=2044960
chr19	.	BED_feature	34358329	34358380	.	.	.	Name=10660538
chr5	.	BED_feature	38112881	38113050	.	.	.	Name=9278425
chr5	.	BED_feature	30404331	30404483	.	.	.	Name=2779579
chr10	.	BED_feature	87396586	87396649	.	.	.	Name=2779579
chr10	.	BED_feature	119879323	119879355	.	.	.	Name=10558886
chr5	.	BED_feature	150790873	150790995	.	.	.	Name=14680822
chr16	.	BED_feature	33415500	33415540	.	.	.	Name=10359087
chr8	.	BED_feature	40781887	40781927	.	.	.	Name=10359087
chr2	.	BED_feature	109476880	109476932	.	.	.	Name=9873054
chr17	.	BED_feature	34870979	34871011	.	.	.	Name=8468472
chr2	.	BED_feature	164134295	164134877	.	.	.	Name=9276666
chr2	.	BED_feature	155208950	155209172	.	.	.	Name=11435428
chr6	.	BED_feature	70655322	70655362	.	.	.	Name=3141781
chr17	.	BED_feature	33955282	33955665	.	.	.	Name=3141781
chr5	.	BED_feature	30343801	30343834	.	.	.	Name=12027462
chr5	.	BED_feature	93403444	93403474	.	.	.	Name=7561042
chr11	.	BED_feature	78736111	78736146	.	.	.	Name=12225970
chr11	.	BED_feature	60593722	60593756	.	.	.	Name=11327713
chr4	.	BED_feature	80305183	80305455	.	.	.	Name=10480898
chr2	.	BED_feature	38536498	38536614	.	.	.	Name=12390883
chr7	.	BED_feature	141130601	141130635	.	.	.	Name=12482979
chr17	.	BED_feature	31406474	31406643	.	.	.	Name=2584197
chrX	.	BED_feature	134431613	134431645	.	.	.	Name=7988464
chr6	.	BED_feature	52086645	52086674	.	.	.	Name=7623795
chr2	.	BED_feature	74526282	74526312	.	.	.	Name=7623795
chr1	.	BED_feature	4481331	4481746	.	.	.	Name=8636240
chr1	.	BED_feature	4483853	4483924	.	.	.	Name=8636240
chr1	.	BED_feature	4486478	4486838	.	.	.	Name=8636240
chr6	.	BED_feature	42910192	42910222	.	.	.	Name=3131743
chr6	.	BED_feature	67825650	67825684	.	.	.	Name=3131743
chr6	.	BED_feature	68185877	68185913	.	.	.	Name=3131743
chr16	.	BED_feature	3493052	3493082	.	.	.	Name=3131743
chr5	.	BED_feature	115232112	115232141	.	.	.	Name=10760574
chrX	.	BED_feature	97579347	97579925	.	.	.	Name=10760574
chr7	.	BED_feature	46535462	46535502	.	.	.	Name=7552299
chr1	.	BED_feature	36636088	36636117	.	.	.	Name=8383622
chr17	.	BED_feature	33913427	33913513	.	.	.	Name=8290364
chr6	.	BED_feature	70144947	70144979	.	.	.	Name=11254715
chr6	.	BED_feature	70190542	70190577	.	.	.	Name=11254715
chr6	.	BED_feature	70300983	70301015	.	.	.	Name=11254715
chr6	.	BED_feature	70336601	70336636	.	.	.	Name=11254715
chr6	.	BED_feature	70365086	70365120	.	.	.	Name=11254715
chr6	.	BED_feature	70387633	70387668	.	.	.	Name=11254715
chrX	.	BED_feature	53558788	53558827	.	.	.	Name=11254715
chr12	.	BED_feature	86362814	86362848	.	.	.	Name=8552086
chr12	.	BED_feature	86362674	86362702	.	.	.	Name=2110508
chr17	.	BED_feature	33610879	33610910	.	.	.	Name=3322806
chr17	.	BED_feature	34870978	34871009	.	.	.	Name=3322806
chr6	.	BED_feature	70448422	70448458	.	.	.	Name=2109186
chr6	.	BED_feature	70484009	70484045	.	.	.	Name=2109186
chr6	.	BED_feature	70502798	70502848	.	.	.	Name=2109186
chr6	.	BED_feature	70537609	70537645	.	.	.	Name=2109186
chr6	.	BED_feature	70573134	70573170	.	.	.	Name=2109186
chr6	.	BED_feature	70593463	70593513	.	.	.	Name=2109186
chr6	.	BED_feature	70601945	70601986	.	.	.	Name=2109186
chr6	.	BED_feature	70617102	70617143	.	.	.	Name=2109186
chr6	.	BED_feature	70628636	70628676	.	.	.	Name=2109186
chr6	.	BED_feature	70633747	70633786	.	.	.	Name=2109186
chr6	.	BED_feature	70648481	70648955	.	.	.	Name=2109186
chr6	.	BED_feature	70656040	70656317	.	.	.	Name=2109186
chr8	.	BED_feature	123621641	123622385	.	.	.	Name=8321202
chr9	.	BED_feature	110614454	110614482	.	.	.	Name=2211821
chr11	.	BED_feature	67124723	67124828	.	.	.	Name=2211821
chr11	.	BED_feature	104403210	104403305	.	.	.	Name=2211821
chr2	.	BED_feature	113744202	113744247	.	.	.	Name=2211821
chr1	.	BED_feature	66878147	66878195	.	.	.	Name=2211821
chr14	.	BED_feature	53898487	53898586	.	.	.	Name=2211821
chr14	.	BED_feature	53926897	53926996	.	.	.	Name=2211821
chr7	.	BED_feature	18568522	18568552	.	.	.	Name=2601707
chr18	.	BED_feature	61170454	61170480	.	.	.	Name=11282029
chr2	.	BED_feature	9775384	9776029	.	.	.	Name=7629014
chr6	.	BED_feature	4455418	4455633	.	.	.	Name=8702912
chr6	.	BED_feature	70655484	70655561	.	.	.	Name=2511430
chr9	.	BED_feature	65221179	65221381	.	.	.	Name=16357058
chr4	.	BED_feature	106933763	106933860	.	.	.	Name=12042312
chr12	.	BED_feature	113875345	113875373	.	.	.	Name=2111447
chr11	.	BED_feature	21457191	21457445	.	.	.	Name=3172222
chr11	.	BED_feature	21471746	21472279	.	.	.	Name=3172222
chr19	.	BED_feature	43577767	43577815	.	.	.	Name=3172222
chr3	.	BED_feature	14863351	14863383	.	.	.	Name=8463242
chr16	.	BED_feature	23806224	23806249	.	.	.	Name=1977662
chr2	.	BED_feature	163441533	163441769	.	.	.	Name=8265639
chr5	.	BED_feature	137314749	137314782	.	.	.	Name=11755530
chr5	.	BED_feature	16065363	16065393	.	.	.	Name=9315634
chr5	.	BED_feature	121148159	121148265	.	.	.	Name=2457496
chr5	.	BED_feature	121168073	121168261	.	.	.	Name=2457496
chr17	.	BED_feature	33610871	33610899	.	.	.	Name=2457496
chr6	.	BED_feature	4455529	4455560	.	.	.	Name=10477728
chr7	.	BED_feature	126592041	126592074	.	.	.	Name=9395505
chr12	.	BED_feature	91806422	91806453	.	.	.	Name=7989366
chr2	.	BED_feature	91426322	91426350	.	.	.	Name=9565620
chr2	.	BED_feature	91429248	91429276	.	.	.	Name=9565620
chr15	.	BED_feature	61814750	61814779	.	.	.	Name=3313385
chr19	.	BED_feature	44805744	44805811	.	.	.	Name=11807024
chr19	.	BED_feature	44809826	44809960	.	.	.	Name=11807024
chr11	.	BED_feature	101367972	101367998	.	.	.	Name=10660629
chr11	.	BED_feature	69396533	69396570	.	.	.	Name=8051093
chr4	.	BED_feature	80305183	80305213	.	.	.	Name=9710594
chr12	.	BED_feature	104874218	104874665	.	.	.	Name=9417125
chr2	.	BED_feature	104927783	104928263	.	.	.	Name=1671709
chr2	.	BED_feature	104933775	104934343	.	.	.	Name=1671709
chr2	.	BED_feature	104943921	104945031	.	.	.	Name=1671709
chr2	.	BED_feature	104964164	104964261	.	.	.	Name=1671709
chr2	.	BED_feature	104967654	104967727	.	.	.	Name=1671709
chr2	.	BED_feature	104973146	104974452	.	.	.	Name=1671709
chr16	.	BED_feature	97567923	97567998	.	.	.	Name=2974922
chr16	.	BED_feature	97690827	97690879	.	.	.	Name=2974922
chr5	.	BED_feature	113875449	113875531	.	.	.	Name=15792532
chr5	.	BED_feature	113904662	113904724	.	.	.	Name=15792532
chr7	.	BED_feature	46239064	46239781	.	.	.	Name=1328870
chr1	.	BED_feature	135178145	135178237	.	.	.	Name=7962542
chr3	.	BED_feature	113284918	113284950	.	.	.	Name=1699843
chr1	.	BED_feature	196792905	196792939	.	.	.	Name=11023821
chr5	.	BED_feature	91560913	91561133	.	.	.	Name=2452972
chr17	.	BED_feature	33589431	33589465	.	.	.	Name=2014233
chr17	.	BED_feature	33610907	33610942	.	.	.	Name=2014233
chr17	.	BED_feature	34870945	34870981	.	.	.	Name=2014233
chr17	.	BED_feature	35806755	35806791	.	.	.	Name=2014233
chr5	.	BED_feature	51786342	51786388	.	.	.	Name=16825189
chr1	.	BED_feature	173050609	173050662	.	.	.	Name=16825189
chr3	.	BED_feature	95744115	95744143	.	.	.	Name=10454566
chr9	.	BED_feature	21709249	21709315	.	.	.	Name=2162479
chr9	.	BED_feature	21713753	21714429	.	.	.	Name=2162479
chr11	.	BED_feature	98228304	98228335	.	.	.	Name=1672439
chr12	.	BED_feature	86362676	86362706	.	.	.	Name=1645787
chr6	.	BED_feature	72234548	72235407	.	.	.	Name=8928820
chr6	.	BED_feature	72239289	72239420	.	.	.	Name=8928820
chr6	.	BED_feature	70655324	70655353	.	.	.	Name=1630463
chr17	.	BED_feature	33610950	33610989	.	.	.	Name=1630463
chr17	.	BED_feature	34987444	34987473	.	.	.	Name=1630463
chr11	.	BED_feature	72777305	72777372	.	.	.	Name=12119294
chr12	.	BED_feature	113875209	113875259	.	.	.	Name=8663022
chr2	.	BED_feature	109493203	109493238	.	.	.	Name=9581764
chr18	.	BED_feature	34986758	34986789	.	.	.	Name=11566878
chr9	.	BED_feature	45687023	45687053	.	.	.	Name=10642500
chr11	.	BED_feature	53462120	53462180	.	.	.	Name=10438901
chr9	.	BED_feature	86493076	86493107	.	.	.	Name=2738073
chr7	.	BED_feature	142489138	142489357	.	.	.	Name=3006925
chr19	.	BED_feature	52317502	52317720	.	.	.	Name=3006925
chr10	.	BED_feature	59672847	59673011	.	.	.	Name=9582364
chr18	.	BED_feature	12647434	12647697	.	.	.	Name=9651314
chr19	.	BED_feature	27859700	27859759	.	.	.	Name=2253877
chr17	.	BED_feature	56462963	56463119	.	.	.	Name=2253877
chr17	.	BED_feature	56465109	56466004	.	.	.	Name=2253877
chr8	.	BED_feature	86964018	86964118	.	.	.	Name=2253877
chr8	.	BED_feature	86969967	86970077	.	.	.	Name=2253877
chr8	.	BED_feature	86977851	86977971	.	.	.	Name=2253877
chr8	.	BED_feature	86980215	86981576	.	.	.	Name=2253877
chr8	.	BED_feature	86982720	86982979	.	.	.	Name=2253877
chr8	.	BED_feature	86984856	86986055	.	.	.	Name=2253877
chr10	.	BED_feature	128334593	128334626	.	.	.	Name=14525975
chr2	.	BED_feature	181600902	181600934	.	.	.	Name=11353810
chr2	.	BED_feature	167380194	167381855	.	.	.	Name=2253878
chr5	.	BED_feature	89602413	89602443	.	.	.	Name=9748293
chr2	.	BED_feature	130274029	130274059	.	.	.	Name=1339438
chr16	.	BED_feature	18940725	18940965	.	.	.	Name=1729607
chr16	.	BED_feature	19092846	19093083	.	.	.	Name=1729607
chr11	.	BED_feature	52097309	52097387	.	.	.	Name=1827138
chr11	.	BED_feature	52099680	52101227	.	.	.	Name=1827138
chr11	.	BED_feature	52102276	52102368	.	.	.	Name=1827138
chr11	.	BED_feature	52103952	52105048	.	.	.	Name=1827138
chr11	.	BED_feature	52125545	52125640	.	.	.	Name=1827138
chr3	.	BED_feature	131183844	131183935	.	.	.	Name=1827138
chr3	.	BED_feature	131189468	131189547	.	.	.	Name=1827138
chr19	.	BED_feature	55972779	55972867	.	.	.	Name=1827138
chr19	.	BED_feature	44460894	44460987	.	.	.	Name=2606350
chr3	.	BED_feature	10191198	10191235	.	.	.	Name=2606350
chr5	.	BED_feature	121148236	121148291	.	.	.	Name=2243086
chr5	.	BED_feature	121168150	121168205	.	.	.	Name=2243086
chr14	.	BED_feature	15368773	15368800	.	.	.	Name=10692469
chr5	.	BED_feature	115216353	115216429	.	.	.	Name=2044952
chr11	.	BED_feature	83666966	83667587	.	.	.	Name=2044952
chr11	.	BED_feature	83672097	83672298	.	.	.	Name=2044952
chr11	.	BED_feature	83677989	83678176	.	.	.	Name=2044952
chr11	.	BED_feature	83680136	83680374	.	.	.	Name=2044952
chr11	.	BED_feature	83698844	83699008	.	.	.	Name=2044952
chr11	.	BED_feature	83705243	83705350	.	.	.	Name=2044952
chr11	.	BED_feature	83709578	83709771	.	.	.	Name=2044952
chr11	.	BED_feature	83712467	83712535	.	.	.	Name=2044952
chr11	.	BED_feature	83721102	83721728	.	.	.	Name=2044952
chr19	.	BED_feature	7263833	7264780	.	.	.	Name=2044952
chr19	.	BED_feature	37499335	37499918	.	.	.	Name=10101294
chr1	.	BED_feature	173254772	173254799	.	.	.	Name=9374551
chr7	.	BED_feature	18566397	18566426	.	.	.	Name=10359011
chrX	.	BED_feature	7124724	7125567	.	.	.	Name=1656391
chr15	.	BED_feature	78855143	78855177	.	.	.	Name=8559662
chrX	.	BED_feature	20027146	20027175	.	.	.	Name=8559663
chr16	.	BED_feature	65428101	65428821	.	.	.	Name=8504933
chr10	.	BED_feature	20847865	20847892	.	.	.	Name=2236022
chr11	.	BED_feature	54093062	54093102	.	.	.	Name=8246960
chr16	.	BED_feature	16777744	16777785	.	.	.	Name=10435576
chr9	.	BED_feature	57494749	57494781	.	.	.	Name=1852076
chr6	.	BED_feature	132534900	132534934	.	.	.	Name=9015393
chr6	.	BED_feature	132561002	132561036	.	.	.	Name=9015393
chr6	.	BED_feature	122821685	122821919	.	.	.	Name=16116202
chr5	.	BED_feature	89530297	89530325	.	.	.	Name=11451945
chr5	.	BED_feature	147574434	147574465	.	.	.	Name=14701942
chr17	.	BED_feature	31406531	31406560	.	.	.	Name=7823934
chr16	.	BED_feature	85692594	85692625	.	.	.	Name=15256533
chr3	.	BED_feature	131099626	131100626	.	.	.	Name=1827423
chr3	.	BED_feature	131212272	131212484	.	.	.	Name=1827423
chr14	.	BED_feature	53185519	53185560	.	.	.	Name=1827423
chr19	.	BED_feature	4593966	4593995	.	.	.	Name=15917242
chrX	.	BED_feature	33695887	33696975	.	.	.	Name=16414020
chrX	.	BED_feature	33737549	33738601	.	.	.	Name=16414020
chrX	.	BED_feature	33785402	33786461	.	.	.	Name=16414020
chrX	.	BED_feature	33819420	33820515	.	.	.	Name=16414020
chrX	.	BED_feature	33862494	33863610	.	.	.	Name=16414020
chrX	.	BED_feature	33913450	33914538	.	.	.	Name=16414020
chrX	.	BED_feature	33957042	33958155	.	.	.	Name=16414020
chr1	.	BED_feature	172992091	172992151	.	.	.	Name=9360965
chr12	.	BED_feature	113875222	113875251	.	.	.	Name=2555786
chr10	.	BED_feature	66933145	66933179	.	.	.	Name=1969796
chr8	.	BED_feature	74497416	74497448	.	.	.	Name=9933587
chr9	.	BED_feature	45686867	45686898	.	.	.	Name=16224064
chr5	.	BED_feature	146184210	146184269	.	.	.	Name=10860926
chr17	.	BED_feature	45495932	45495959	.	.	.	Name=11040101
chr9	.	BED_feature	32503847	32503882	.	.	.	Name=1409581
chr5	.	BED_feature	93424230	93424258	.	.	.	Name=8757327
chr6	.	BED_feature	70144910	70144947	.	.	.	Name=9858563
chr6	.	BED_feature	70190579	70190612	.	.	.	Name=9858563
chr6	.	BED_feature	70300948	70300983	.	.	.	Name=9858563
chr6	.	BED_feature	70336638	70336671	.	.	.	Name=9858563
chr6	.	BED_feature	70365122	70365154	.	.	.	Name=9858563
chr6	.	BED_feature	70387668	70387705	.	.	.	Name=9858563
chr11	.	BED_feature	106130694	106130743	.	.	.	Name=9858563
chr11	.	BED_feature	120640249	120640290	.	.	.	Name=9786926
chr2	.	BED_feature	90897655	90897832	.	.	.	Name=2180582
chr2	.	BED_feature	90900269	90900365	.	.	.	Name=2180582
chr2	.	BED_feature	90914093	90916595	.	.	.	Name=2180582
chr9	.	BED_feature	57494749	57494776	.	.	.	Name=7892203
chr3	.	BED_feature	37317762	37317792	.	.	.	Name=8406004
chr12	.	BED_feature	114344858	114344899	.	.	.	Name=2507313
chr12	.	BED_feature	115568087	115568114	.	.	.	Name=2507313
chr12	.	BED_feature	115783418	115783448	.	.	.	Name=2507313
chr12	.	BED_feature	115909336	115909363	.	.	.	Name=2507313
chr12	.	BED_feature	115955881	115955911	.	.	.	Name=2507313
chr12	.	BED_feature	116206321	116206348	.	.	.	Name=2507313
chr12	.	BED_feature	116250984	116251014	.	.	.	Name=2507313
chrX	.	BED_feature	20027147	20027174	.	.	.	Name=8557686
chr10	.	BED_feature	57174929	57175016	.	.	.	Name=1717345
chr10	.	BED_feature	57184315	57184694	.	.	.	Name=1717345
chr10	.	BED_feature	57185911	57186026	.	.	.	Name=1717345
chr10	.	BED_feature	57189784	57189817	.	.	.	Name=1717345
chr10	.	BED_feature	57191036	57191096	.	.	.	Name=1717345
chr10	.	BED_feature	57192997	57194717	.	.	.	Name=1717345
chr10	.	BED_feature	57200326	57200865	.	.	.	Name=1717345
chr17	.	BED_feature	34567381	34567418	.	.	.	Name=1717345
chr17	.	BED_feature	34580299	34580336	.	.	.	Name=1717345
chr15	.	BED_feature	76304717	76304894	.	.	.	Name=1717345
chr15	.	BED_feature	76323708	76323847	.	.	.	Name=1717345
chr15	.	BED_feature	76325251	76325758	.	.	.	Name=1717345
chr15	.	BED_feature	76327669	76328171	.	.	.	Name=1717345
chr4	.	BED_feature	135145013	135145050	.	.	.	Name=16181749
chr2	.	BED_feature	167380291	167380318	.	.	.	Name=9374525
chr5	.	BED_feature	91533697	91533726	.	.	.	Name=11825903
chr19	.	BED_feature	52317534	52317563	.	.	.	Name=11825903
chr3	.	BED_feature	28888379	28888408	.	.	.	Name=11825903
chr2	.	BED_feature	62284566	62284595	.	.	.	Name=11825903
chr3	.	BED_feature	159533954	159534406	.	.	.	Name=10896939
chr6	.	BED_feature	70654963	70654995	.	.	.	Name=7816634
chr13	.	BED_feature	19227292	19227351	.	.	.	Name=1309596
chr13	.	BED_feature	19280452	19280510	.	.	.	Name=1309596
chr13	.	BED_feature	19307969	19308027	.	.	.	Name=1309596
chr12	.	BED_feature	113875295	113875358	.	.	.	Name=1309596
chr6	.	BED_feature	4455598	4455637	.	.	.	Name=3733754
chr6	.	BED_feature	41451086	41451559	.	.	.	Name=3641189
chr4	.	BED_feature	141097308	141098498	.	.	.	Name=3641189
chr3	.	BED_feature	37317571	37317603	.	.	.	Name=7565783
chr5	.	BED_feature	137517687	137518116	.	.	.	Name=8429032
chr5	.	BED_feature	137519819	137519872	.	.	.	Name=8429032
chr9	.	BED_feature	98232313	98234392	.	.	.	Name=1648481
chr9	.	BED_feature	98255701	98255873	.	.	.	Name=1648481
chr4	.	BED_feature	140565202	140565232	.	.	.	Name=9733765
chr12	.	BED_feature	113875219	113875262	.	.	.	Name=2573524
chr12	.	BED_feature	113875219	113875262	.	.	.	Name=2573523
chr10	.	BED_feature	34079089	34079121	.	.	.	Name=9369451
chr7	.	BED_feature	56431088	56431124	.	.	.	Name=1697928
chr5	.	BED_feature	23371708	23371770	.	.	.	Name=1697928
chr5	.	BED_feature	97089579	97089620	.	.	.	Name=1697928
chr3	.	BED_feature	30711033	30711074	.	.	.	Name=1697928
chr3	.	BED_feature	52891299	52891340	.	.	.	Name=1697928
chr3	.	BED_feature	93460310	93460347	.	.	.	Name=1697928
chr2	.	BED_feature	137786747	137786785	.	.	.	Name=1697928
chr1	.	BED_feature	92688075	92688115	.	.	.	Name=1697928
chr9	.	BED_feature	43210267	43210308	.	.	.	Name=1697928
chr9	.	BED_feature	76557076	76557115	.	.	.	Name=1697928
chr8	.	BED_feature	30070832	30070925	.	.	.	Name=1697928
chr8	.	BED_feature	46973629	46973670	.	.	.	Name=1697928
chr15	.	BED_feature	51612592	51612633	.	.	.	Name=1697928
chr15	.	BED_feature	74806793	74806890	.	.	.	Name=1697928
chr15	.	BED_feature	74808756	74808824	.	.	.	Name=1697928
chr15	.	BED_feature	74809951	74812614	.	.	.	Name=1697928
chr15	.	BED_feature	74816190	74816902	.	.	.	Name=1697928
chr15	.	BED_feature	74822133	74828327	.	.	.	Name=1697928
chr15	.	BED_feature	74872276	74872371	.	.	.	Name=1697928
chr15	.	BED_feature	74874187	74874290	.	.	.	Name=1697928
chr15	.	BED_feature	74875399	74879211	.	.	.	Name=1697928
chr15	.	BED_feature	74892910	74893338	.	.	.	Name=1697928
chr15	.	BED_feature	74896475	74897345	.	.	.	Name=1697928
chr15	.	BED_feature	74898449	74898535	.	.	.	Name=1697928
chr15	.	BED_feature	74899817	74899910	.	.	.	Name=1697928
chr15	.	BED_feature	74902179	74902265	.	.	.	Name=1697928
chr15	.	BED_feature	74920672	74920711	.	.	.	Name=1697928
chr15	.	BED_feature	74935468	74935513	.	.	.	Name=1697928
chr15	.	BED_feature	74937345	74937445	.	.	.	Name=1697928
chr15	.	BED_feature	74938556	74938851	.	.	.	Name=1697928
chr15	.	BED_feature	74940929	74940981	.	.	.	Name=1697928
chr15	.	BED_feature	74942003	74942875	.	.	.	Name=1697928
chr15	.	BED_feature	74958548	74958643	.	.	.	Name=1697928
chr15	.	BED_feature	74960530	74960628	.	.	.	Name=1697928
chr15	.	BED_feature	74961911	74962001	.	.	.	Name=1697928
chr15	.	BED_feature	74964084	74965592	.	.	.	Name=1697928
chr15	.	BED_feature	74979362	74981877	.	.	.	Name=1697928
chr15	.	BED_feature	74982979	74983061	.	.	.	Name=1697928
chr15	.	BED_feature	74984385	74984484	.	.	.	Name=1697928
chr15	.	BED_feature	74986287	74986369	.	.	.	Name=1697928
chr15	.	BED_feature	75013081	75013858	.	.	.	Name=1697928
chr15	.	BED_feature	75023388	75023485	.	.	.	Name=1697928
chr15	.	BED_feature	75024580	75024617	.	.	.	Name=1697928
chr15	.	BED_feature	75044018	75044295	.	.	.	Name=1697928
chr15	.	BED_feature	75045394	75045459	.	.	.	Name=1697928
chr15	.	BED_feature	75064363	75064531	.	.	.	Name=1697928
chr15	.	BED_feature	75065855	75066353	.	.	.	Name=1697928
chr15	.	BED_feature	75067375	75068275	.	.	.	Name=1697928
chr15	.	BED_feature	75072020	75072091	.	.	.	Name=1697928
chr15	.	BED_feature	75073988	75074156	.	.	.	Name=1697928
chr15	.	BED_feature	75075533	75075620	.	.	.	Name=1697928
chr15	.	BED_feature	75092999	75093404	.	.	.	Name=1697928
chr15	.	BED_feature	75094478	75094527	.	.	.	Name=1697928
chr15	.	BED_feature	75096056	75096146	.	.	.	Name=1697928
chr15	.	BED_feature	75097473	75097640	.	.	.	Name=1697928
chr15	.	BED_feature	75099452	75099490	.	.	.	Name=1697928
chr15	.	BED_feature	75122784	75122886	.	.	.	Name=1697928
chr15	.	BED_feature	75124191	75124276	.	.	.	Name=1697928
chr15	.	BED_feature	75131425	75133048	.	.	.	Name=1697928
chr15	.	BED_feature	75141974	75142141	.	.	.	Name=1697928
chr15	.	BED_feature	75155959	75156028	.	.	.	Name=1697928
chr15	.	BED_feature	75177865	75177968	.	.	.	Name=1697928
chr15	.	BED_feature	75180069	75181772	.	.	.	Name=1697928
chr15	.	BED_feature	75201591	75201693	.	.	.	Name=1697928
chr15	.	BED_feature	75204356	75204439	.	.	.	Name=1697928
chr15	.	BED_feature	75256791	75256855	.	.	.	Name=1697928
chr15	.	BED_feature	75258519	75258613	.	.	.	Name=1697928
chr15	.	BED_feature	75261789	75262172	.	.	.	Name=1697928
chr15	.	BED_feature	75268431	75269094	.	.	.	Name=1697928
chr14	.	BED_feature	61763898	61763939	.	.	.	Name=1697928
chr18	.	BED_feature	21560810	21560851	.	.	.	Name=1697928
chr6	.	BED_feature	147221087	147221118	.	.	.	Name=9280059
chrX	.	BED_feature	99686014	99686377	.	.	.	Name=9426246
chr6	.	BED_feature	115407220	115407269	.	.	.	Name=7838156
chr19	.	BED_feature	40243904	40245132	.	.	.	Name=7838156
chr19	.	BED_feature	40247091	40247900	.	.	.	Name=7838156
chr14	.	BED_feature	16999528	16999931	.	.	.	Name=7838156
chr14	.	BED_feature	17000988	17001191	.	.	.	Name=7838156
chr14	.	BED_feature	17004849	17005036	.	.	.	Name=7838156
chr14	.	BED_feature	17007943	17008565	.	.	.	Name=7838156
chr14	.	BED_feature	17009721	17009866	.	.	.	Name=7838156
chr14	.	BED_feature	17013050	17013104	.	.	.	Name=7838156
chr14	.	BED_feature	17014696	17014956	.	.	.	Name=7838156
chr14	.	BED_feature	17031225	17032189	.	.	.	Name=7838156
chr7	.	BED_feature	24606266	24606297	.	.	.	Name=1545794
chr11	.	BED_feature	87609642	87609721	.	.	.	Name=8384306
chr12	.	BED_feature	114345284	114345346	.	.	.	Name=1922039
chr12	.	BED_feature	31850892	31850937	.	.	.	Name=1661245
chr6	.	BED_feature	113401690	113401718	.	.	.	Name=1339452
chr12	.	BED_feature	86362675	86362707	.	.	.	Name=7698311
chr8	.	BED_feature	27273951	27273980	.	.	.	Name=14673133
chr9	.	BED_feature	98298949	98300034	.	.	.	Name=8288643
chr6	.	BED_feature	72234142	72236749	.	.	.	Name=7900819
chr4	.	BED_feature	152974997	152975053	.	.	.	Name=7900819
chr8	.	BED_feature	72525045	72525233	.	.	.	Name=7900819
chr12	.	BED_feature	86362674	86362701	.	.	.	Name=8346248
chr11	.	BED_feature	106130610	106130812	.	.	.	Name=8555489
chr11	.	BED_feature	54091604	54091662	.	.	.	Name=3876931
chr11	.	BED_feature	54093027	54093177	.	.	.	Name=3876931
chr12	.	BED_feature	25295984	25296021	.	.	.	Name=7559662
chr12	.	BED_feature	25297229	25297303	.	.	.	Name=7559662
chr11	.	BED_feature	32183544	32183620	.	.	.	Name=9032265
chr11	.	BED_feature	32196361	32196437	.	.	.	Name=9032265
chr19	.	BED_feature	5637775	5641675	.	.	.	Name=2001591
chr19	.	BED_feature	5645515	5645555	.	.	.	Name=2001591
chr19	.	BED_feature	5646808	5648105	.	.	.	Name=2001591
chr18	.	BED_feature	20808272	20808309	.	.	.	Name=1870969
chr3	.	BED_feature	10196461	10196574	.	.	.	Name=1545801
chr18	.	BED_feature	3281799	3281831	.	.	.	Name=10799536
chr18	.	BED_feature	43863437	43863471	.	.	.	Name=1508185
chr9	.	BED_feature	108198554	108199203	.	.	.	Name=8413228
chr17	.	BED_feature	26571740	26572245	.	.	.	Name=9778505
chr2	.	BED_feature	113751484	113752125	.	.	.	Name=8164695
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s4.bed000066400000000000000000000016351211610345200224650ustar00rootroot00000000000000chrV	10924506	10924531	16159881
chrX	11351801	11351828	16159881
chrV	13813816	13814105	9425137
chrIV	10461777	10462129	1361171
chrIV	11059126	11059319	14660442
chrX	5100804	5100851	9927589
chrX	420877	421717	7671811
chrII	11928523	11928560	7671813
chrX	421407	421433	7671813
chrIII	7676726	7676849	11003845
chrII	9731983	9732106	11003845
chrV	11977977	11978018	9761670
chrX	12467618	12467665	9834189
chrV	20250986	20251013	8798416
chrX	12467632	12467664	11203704
chrV	20250981	20251012	1406665
chrV	20750852	20750890	9584117
chrX	7175608	7175678	15282167
chrV	10673746	10673772	14738885
chrX	14743479	14745201	12871707
chrV	10674211	10678331	7925019
chrX	12467547	12467661	7925019
chrX	12467617	12467660	12095247
chrV	6694719	6694758	10514435
chrV	20250979	20251008	10698188
chrI	8470263	8470841	10882527
chrV	20250982	20251016	11328853
chrX	5909768	5909804	1350087
chrV	4770527	4770557	15734735
chrIV	383476	383519	15734735
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s4.gff3000066400000000000000000000036311211610345200225560ustar00rootroot00000000000000##gff-version   3
##sequence-region   chrX 420878 14745201
##sequence-region   chrI 8470264 8470841
##sequence-region   chrV 4770528 20750890
##sequence-region   chrIV 383477 11059319
##sequence-region   chrIII 7676727 7676849
##sequence-region   chrII 9731984 11928560
chrV	.	BED_feature	10924507	10924531	.	.	.	Name=16159881
chrX	.	BED_feature	11351802	11351828	.	.	.	Name=16159881
chrV	.	BED_feature	13813817	13814105	.	.	.	Name=9425137
chrIV	.	BED_feature	10461778	10462129	.	.	.	Name=1361171
chrIV	.	BED_feature	11059127	11059319	.	.	.	Name=14660442
chrX	.	BED_feature	5100805	5100851	.	.	.	Name=9927589
chrX	.	BED_feature	420878	421717	.	.	.	Name=7671811
chrII	.	BED_feature	11928524	11928560	.	.	.	Name=7671813
chrX	.	BED_feature	421408	421433	.	.	.	Name=7671813
chrIII	.	BED_feature	7676727	7676849	.	.	.	Name=11003845
chrII	.	BED_feature	9731984	9732106	.	.	.	Name=11003845
chrV	.	BED_feature	11977978	11978018	.	.	.	Name=9761670
chrX	.	BED_feature	12467619	12467665	.	.	.	Name=9834189
chrV	.	BED_feature	20250987	20251013	.	.	.	Name=8798416
chrX	.	BED_feature	12467633	12467664	.	.	.	Name=11203704
chrV	.	BED_feature	20250982	20251012	.	.	.	Name=1406665
chrV	.	BED_feature	20750853	20750890	.	.	.	Name=9584117
chrX	.	BED_feature	7175609	7175678	.	.	.	Name=15282167
chrV	.	BED_feature	10673747	10673772	.	.	.	Name=14738885
chrX	.	BED_feature	14743480	14745201	.	.	.	Name=12871707
chrV	.	BED_feature	10674212	10678331	.	.	.	Name=7925019
chrX	.	BED_feature	12467548	12467661	.	.	.	Name=7925019
chrX	.	BED_feature	12467618	12467660	.	.	.	Name=12095247
chrV	.	BED_feature	6694720	6694758	.	.	.	Name=10514435
chrV	.	BED_feature	20250980	20251008	.	.	.	Name=10698188
chrI	.	BED_feature	8470264	8470841	.	.	.	Name=10882527
chrV	.	BED_feature	20250983	20251016	.	.	.	Name=11328853
chrX	.	BED_feature	5909769	5909804	.	.	.	Name=1350087
chrV	.	BED_feature	4770528	4770557	.	.	.	Name=15734735
chrIV	.	BED_feature	383477	383519	.	.	.	Name=15734735
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s5.bed000066400000000000000000001006231211610345200224630ustar00rootroot00000000000000chr17	48290000	48290096	2300056
chr1	154651620	154652041	1764039
chr19	51023882	51024004	1656236
chr1	96909742	96909912	8120060
chr14	21847875	21847906	1644820
chr12	42931185	42931218	1970973
chr12	42936616	42937377	1970973
chr12	42938680	42938932	1970973
chr12	42940081	42940247	1970973
chr12	42941798	42942075	1970973
chr12	42944041	42944415	1970973
chr10_random	695959	696024	1970973
chr19	49636890	49637016	14641110
chr18	27413271	27413302	14563555
chrX	85120367	85120397	14563555
chr3	44441218	44441254	11773447
chr8	4158720	4158774	15026307
chr2	180483396	180483436	8643513
chr4	42955731	42955763	9380697
chrUn_random	3207748	3207780	9380697
chr2	116034041	116034070	10969836
chr5	165074245	165074283	12023302
chr12	37288388	37288959	8110830
chr10	95694184	95694256	9614069
chr1	95892856	95892967	9614069
chr14	87395429	87395512	8188706
chr1	35713101	35713134	11517190
chr4	158186009	158186097	1672118
chr4	158187269	158188218	1672118
chr4	158283950	158284038	1672118
chr4	158285259	158285436	1672118
chr4	158286504	158286547	1672118
chr4	158371741	158371800	1672118
chr4	158372955	158373132	1672118
chr4	158381375	158381418	1672118
chr4	158628591	158629557	1672118
chr4	158630708	158630790	1672118
chr3	136739008	136739571	1672118
chr3	136743016	136743200	1672118
chr1	78368025	78368381	1672118
chrUn	17400462	17400493	15661834
chr7	104035596	104035776	2540196
chr11	79124930	79124959	2540196
chrX	85949213	85949621	2282981
chr1	81264615	81264651	15656786
chr1	81343180	81343216	15656786
chr6	128386905	128386950	2246271
chr6	128436431	128436476	2246271
chr15	33068745	33069093	8782063
chr10	95694184	95694327	2836398
chr14	21847815	21847937	2046676
chr5	19717055	19717123	8182075
chr9	65906943	65906974	2476660
chrX	24685182	24685227	2476660
chr2	212297453	212297490	7683412
chr5	139690797	139690826	11689000
chr7	20348252	20348302	10953033
chr5	139863924	139863974	10953033
chr10	40445098	40445148	10953033
chr1	175179962	175180012	10953033
chr19	41616222	41616268	2424007
chr3	13783500	13783534	3185564
chr1	87626143	87626171	2697636
chr10	87747756	87747878	1846602
chr10	87750094	87751145	1846602
chr7	140995634	140997920	1846602
chr15_random	316858	316978	1846602
chr15_random	319399	319577	1846602
chr15	10490902	10490978	1846602
chr1	154651795	154651898	10551830
chr7	10727329	10727442	8790352
chr18	60548760	60548879	8790352
chr18	60594285	60594347	8790352
chr8	79644353	79645644	8790352
chr8	79671772	79672729	8790352
chr17	15651980	15652011	10531380
chr13	41043407	41043439	7926010
chr11	79124923	79124960	1693237
chr3	164012297	164012333	1693237
chr6	23664539	23664573	2914621
chr6	64172472	64172537	2914621
chr6	127304430	127305147	2914621
chr5	25294694	25295538	2914621
chr5	130925073	130925668	2914621
chr5	167401635	167402455	2914621
chr5	167404507	167404608	2914621
chr4	154051425	154052369	2914621
chr4	160892813	160893011	2914621
chr4	160895520	160896074	2914621
chr3	55201686	55202606	2914621
chr3	103228388	103228499	2914621
chr3	136274407	136275173	2914621
chr3	144110234	144111155	2914621
chr2	174389981	174390441	2914621
chr2	178470348	178470412	2914621
chr2	186081639	186082574	2914621
chr1	106191088	106192032	2914621
chr1	171347087	171347715	2914621
chr1	222252059	222252969	2914621
chr14	18734493	18734615	2914621
chr9	52001271	52002013	2914621
chr9	66781668	66781736	2914621
chrX	41099239	41100182	2914621
chrX	86260051	86260662	2914621
chr11	22930565	22931429	2914621
chr10	44889478	44889836	2914621
chr10	53300168	53300233	2914621
chr10	57537626	57538981	2914621
chr10	57540453	57542319	2914621
chr17	34304641	34305374	2914621
chr16	24233574	24234505	2914621
chr16	36524019	36524476	2914621
chr15	22783095	22783169	2914621
chr8	35316221	35316575	2914621
chr8	113075747	113076196	2914621
chr18	83076444	83076889	2914621
chr20	13828233	13828266	12654506
chr12	42919433	42919463	10674400
chr8	79644223	79644252	10674400
chr10	95694184	95694216	10194769
chr2	22607196	22607228	8552092
chr6	98775386	98775815	11731618
chr1	35522839	35522868	11731618
chr10	57535198	57537754	2269373
chr12	22154906	22154939	9224811
chr5	165074363	165074416	12480945
chr6	26931684	26931784	8248179
chr2	104765996	104766025	8248179
chr3	164011948	164011980	14722127
chr12	35664735	35664778	10207035
chr1	97291099	97291128	11278660
chr2	180483362	180483392	11668178
chr10	57501537	57503604	8034713
chr18	58177377	58177406	9855630
chr18	58179240	58179269	9855630
chr8	115124281	115124352	11116210
chr20_random	40416	40502	3125612
chr20_random	59038	59086	3125612
chr20_random	89200	89262	3125612
chr20_random	130973	131037	3125612
chr20	2646401	2646490	3125612
chr20	3409894	3409958	3125612
chr20	3425424	3425469	3125612
chr20	3468402	3468465	3125612
chr20	3513816	3513902	3125612
chr20	3539747	3539811	3125612
chr20	3555754	3555801	3125612
chr20	4998442	4998530	3125612
chr20	5021610	5021673	3125612
chr20	5056562	5056626	3125612
chr6	104749304	104749414	8662994
chr4	78827912	78828679	2827005
chr2	94946369	94946454	2827005
chr1	34635073	34635160	2827005
chr1	73096720	73096825	2827005
chr8	20038113	20038177	2827005
chr8	83529634	83529729	2827005
chr16	13318993	13319098	2827005
chr14	65603825	65603874	2827005
chr19	26190596	26190713	2827005
chr18	63217240	63217296	2827005
chr20	3663805	3663835	9794408
chr3	44441216	44441254	10026208
chr14	21847849	21847898	8114709
chr18	75499627	75499678	10995747
chr15	45392496	45392525	9334243
chr7	9773672	9774076	3053160
chr5	101403546	101403934	3053160
chr5	118165240	118165774	3053160
chr5	118350318	118350388	3053160
chr5	118394687	118394763	3053160
chr5	118409475	118409593	3053160
chr5	118415944	118416076	3053160
chr5	118437031	118437153	3053160
chr5	118459474	118459582	3053160
chr5	118461707	118461873	3053160
chr5	118477298	118477390	3053160
chr5	118506520	118506720	3053160
chr19	25046470	25046886	3053160
chr1	96173572	96173902	2331750
chr1	96174920	96175332	2331750
chr1	96176572	96176787	2331750
chr1	96177989	96178484	2331750
chr7	40484147	40484205	7791794
chrX	89455372	89455402	8241260
chr3	118194032	118194154	1371278
chr14	18813520	18813556	12732210
chr19	39851519	39851548	1683601
chr19	39853854	39853884	1683601
chr6	140857803	140857843	2555700
chr9	95631140	95631173	2555700
chr1	238896304	238896339	2555700
chr6	128386905	128386950	7559615
chr6	128436431	128436476	7559615
chr14	21847857	21847907	7559615
chr2	191044260	191044300	1472472
chr3	17196019	17196062	16873660
chr2	15998843	15998884	16873660
chr10	95694276	95694305	2555064
chr13	47243579	47243618	8413246
chr12	35664756	35664796	8413246
chr10	53776749	53776789	8413246
chr1	185975627	185975692	8413246
chr14	19110724	19110779	9792724
chr7	104034950	104035847	3671079
chr5	165074084	165074416	10022871
chr8	4315515	4315591	2176152
chr10	64312804	64313175	9822647
chr6	128386904	128386951	7929335
chr6	128436430	128436477	7929335
chr14	21847786	21847818	8246951
chr3	164011396	164011436	11399762
chr1	154653109	154653138	9210417
chr2	116033483	116033516	9873817
chr2	219591237	219591361	1527171
chr4	119765287	119767565	2072895
chr15	50479669	50479749	2072895
chr20	21885315	21885395	2072895
chr7	120165048	120165105	1922023
chr7	120174377	120174551	1922023
chr7	120176595	120176761	1922023
chr10	78750075	78750175	1922023
chr1	202936739	202936792	1549125
chr1	258000873	258000924	1549125
chr14	86614962	86615007	1549125
chr3	92571982	92572093	12145338
chr1	95892888	95892918	12145338
chr1	154651765	154651796	9346922
chr11	81471200	81471233	8910619
chr14	86587826	86587854	9677331
chr20_random	40466	40500	2668878
chr20	4998446	4998480	2668878
chr20	5056566	5056600	2668878
chr15	47303022	47303121	8734471
chr6	77976383	77976930	2227418
chr6	78005397	78005442	2227418
chr18	12406442	12406471	2227418
chr10	95694332	95694366	11022037
chr2	182740364	182740398	11022037
chr2_random	3022960	3022990	10620495
chr11	79124932	79124960	10620495
chr5	66293895	66294054	9737987
chr2	181214699	181214790	9737987
chr14	97746094	97746125	10702298
chr19	26538094	26538123	11050084
chr8	109400317	109400350	12750453
chr1	212019618	212019648	12750453
chrX	63597603	63597754	12750453
chr19	51023955	51023991	7799916
chr20_random	40466	40501	3554244
chr20_random	89200	89236	3554244
chr3	108927748	108927779	3554244
chr20	2646427	2646483	3554244
chr20	3409894	3409932	3554244
chr20	3468402	3468439	3554244
chr20	3555764	3555801	3554244
chr20	4998442	4998478	3554244
chr20	5056562	5056598	3554244
chr14	18813519	18813556	12609849
chr1	155389162	155389765	8474458
chr1	185974615	185975610	1959592
chr1	154653097	154653127	8132677
chr3	3480431	3480463	9038213
chr8	126655173	126657278	8948424
chr4	152057521	152057550	11278588
chr1	78760688	78762243	2761536
chr16	89936885	89936920	16481392
chr15	45392169	45392292	11058537
chr6	76916982	76918759	1976511
chr6	76919760	76920131	1976511
chr6	77008394	77008444	1976511
chr10	16608130	16608178	1976511
chr3	135730135	135730333	1976511
chr3	135838136	135838303	1976511
chr15	49715149	49715266	1976511
chr1	247222016	247222126	1976511
chr19	39447682	39447713	9845337
chr19	39843037	39843093	8101632
chr1	202936620	202936833	7720874
chr1	258000893	258000923	7720874
chr6	27117535	27118509	7689152
chr18	63640869	63641571	7689152
chr2	142434224	142434369	7689152
chr1	95655412	95656362	7689152
chrX	157575696	157576066	7689152
chr3	88648904	88648943	1588955
chr7	137835952	137835980	1588954
chr1	247323760	247323799	8955092
chr6	138156550	138159155	7980439
chr17	5126485	5126515	7980439
chr2	180483680	180483736	9013768
chr12	32389730	32389761	10385395
chrX	52446766	52446801	10417310
chr6	140857780	140857813	9013645
chr14	3050866	3050961	10521429
chr10	95694276	95694305	3396073
chr2	174775177	174775205	9642117
chr15	33068940	33069010	8007990
chr6	78803193	78803228	10674398
chr19	54750738	54750768	8144615
chr12	20903148	20903271	8756618
chr7	139326342	139326400	7901208
chr6	140857814	140857843	15013809
chr3	161554290	161554330	8940000
chr14	19142236	19142407	3422457
chr10	87514443	87514574	8051130
chr6	54941257	54942924	1840505
chr6	99528685	99530007	1840505
chr6	99531310	99531403	1840505
chr6	99545286	99545324	1840505
chr6	99553814	99553889	1840505
chr5	145853250	145854686	1840505
chr3	28852192	28852596	1840505
chr3	28868191	28869835	1840505
chr2	137155206	137156708	1840505
chr17	43385498	43385784	1840505
chr17	43387083	43387346	1840505
chr19	39851654	39851706	2881624
chr3	44441283	44441329	12783165
chr1	37535825	37535854	11572871
chr11	79124880	79124916	10567553
chr3	44441290	44441323	10567553
chr3	164012141	164012176	8188712
chr10	95694183	95694256	9564856
chr8	91956205	91956239	9564856
chr2	181395721	181395758	12388348
chr2	27149658	27149820	6088070
chr3	18499638	18499678	12697699
chr3	44441185	44441224	10869353
chr12	9541108	9541163	9632670
chr12	9596065	9596154	9632670
chr12_random	286811	286853	9632670
chr10	95692836	95692883	2155782
chr2	172385320	172385350	9712644
chr14	19110784	19110913	2454390
chr14	19142283	19142414	2454390
chr1	97290828	97291185	1869549
chr10	109920807	109920836	11955627
chr1	154653085	154653116	11955627
chr17	48289920	48289961	2011515
chr9	86012058	86012095	1655408
chr14	21847809	21847906	9252424
chr2	95334253	95334289	9756936
chr16	89939107	89939142	11509565
chr1	78761020	78761064	2388627
chr5	80324941	80324968	1717823
chr1	154653097	154653129	7499393
chr10	82582871	82582904	12010125
chr10	82587870	82587900	12010125
chr20	11570120	11570153	12010125
chr6	128386882	128386944	1549467
chr6	128436437	128436537	1549467
chr1	161658867	161658950	7828582
chr1	161662318	161662382	7828582
chr1	202936489	202936523	2552288
chr20	32000189	32000224	10640442
chr12	8296009	8296065	1358758
chr1	258000873	258000924	1358758
chr4	120355608	120355637	9174059
chr20	4636223	4636265	10986117
chr2_random	3022509	3022541	9464279
chr20_random	40466	40502	2555174
chr20	2646427	2646490	2555174
chr20	3409894	3409932	2555174
chr20	3468402	3468439	2555174
chr20	3555764	3555801	2555174
chr20	4998442	4998480	2555174
chr20	5056562	5056600	2555174
chr7	114015509	114015668	8625802
chr6	139276088	139276214	8625802
chr2	120968977	120971415	8625802
chr2	121155102	121155493	8625802
chr2	137574738	137575993	8625802
chrX	146510408	146511733	8625802
chr17	91004377	91004637	8625802
chr16	82007129	82007983	8625802
chr16	82009207	82009325	8625802
chr15	77298062	77298283	8625802
chr15	77300424	77301661	8625802
chr15	77303608	77303680	8625802
chr15	103122683	103122943	8625802
chr8	104738234	104738483	8625802
chr1	240316238	240316283	12384280
chr7	140523538	140523575	1406681
chr6	31079809	31079847	1406681
chr6	80532951	80533645	1406681
chr6	83786387	83786555	1406681
chr6	135414911	135415048	1406681
chr5	36372663	36373037	1406681
chr5	123984234	123984853	1406681
chr5	145207153	145207290	1406681
chr3	36635545	36636263	1406681
chr3	83669417	83670112	1406681
chr3	84729561	84730254	1406681
chr2	18125793	18126300	1406681
chr2	73041141	73041836	1406681
chr2	78744789	78745497	1406681
chr2	170307486	170308190	1406681
chr2	174025967	174026672	1406681
chr2	223129727	223130032	1406681
chr1	106346776	106347489	1406681
chr1	123765542	123765900	1406681
chr15	62765793	62766509	1406681
chr9	11037643	11038897	1406681
chr9	25152172	25152851	1406681
chr9	42474740	42475492	1406681
chr9	50106926	50106979	1406681
chr9	57733720	57733811	1406681
chr9	93406236	93406297	1406681
chr8	39475606	39476005	1406681
chr8	88315847	88316563	1406681
chr13	2231202	2231322	1406681
chr13	22886638	22886775	1406681
chr16	64644794	64644858	1406681
chr6_random	21171	21797	1406681
chr14	70509836	70510407	1406681
chr14	87563708	87564093	1406681
chrUn	42219678	42219745	1406681
chrUn	73050412	73050514	1406681
chr19	34283394	34284137	1406681
chrX	81946175	81946308	1406681
chrX	106098538	106099101	1406681
chrX	106808582	106808720	1406681
chrX	106992316	106992748	1406681
chrX	120503399	120503828	1406681
chrX	131350579	131350664	1406681
chrX	141824751	141825452	1406681
chr4	158103485	158103531	2479916
chr19	26190655	26190706	2547796
chr4	78827972	78828212	2547796
chr16	13318993	13319040	2547796
chr1	73096776	73096825	2547796
chr18	83076551	83077187	2005901
chr6	14985891	14986418	2005901
chr6	23664340	23664625	2005901
chr6	64172067	64172842	2005901
chr6	127304347	127305042	2005901
chr5	25294682	25295361	2005901
chr5	81560511	81560554	2005901
chr5	130924972	130925713	2005901
chr5	167402249	167405212	2005901
chr4	89799037	89799689	2005901
chr4	154051342	154052264	2005901
chr3	55201791	55202713	2005901
chr3	66685186	66686036	2005901
chr3	71112136	71112785	2005901
chr3	85607215	85607750	2005901
chr3	103228337	103228777	2005901
chr3	136274324	136275069	2005901
chr3	144110490	144111247	2005901
chr2	165012789	165013084	2005901
chr2	174389981	174390338	2005901
chr2	178470052	178470703	2005901
chr2	186081556	186082318	2005901
chr1	106191005	106191855	2005901
chr1	171346715	171347440	2005901
chr1	222252312	222253089	2005901
chr9	52001361	52001893	2005901
chr9	66781379	66782133	2005901
chrX	41099156	41099927	2005901
chrX	86260154	86261037	2005901
chr13	71982146	71982779	2005901
chr11	22930446	22931154	2005901
chr10	44889482	44890201	2005901
chr10	53300162	53300307	2005901
chr10	88930810	88931356	2005901
chr17	34304729	34305481	2005901
chr16	24233491	24234263	2005901
chr16	36523621	36524467	2005901
chr15	8792275	8792305	2005901
chr15	12501945	12502378	2005901
chr15	22783119	22783160	2005901
chr15	27983963	27984038	2005901
chr14	18733881	18734697	2005901
chrUn	12670678	12670862	2005901
chr8	35315945	35316663	2005901
chr8	113075836	113076605	2005901
chr7	24531797	24531830	9395525
chr17	53131797	53131831	12813463
chr3_random	930755	930827	9454838
chr1	76254921	76255087	15337603
chr10	28527477	28527527	9478977
chr10	28533061	28533222	9478977
chr14	45723216	45723246	9478977
chr7	104035607	104035780	1406708
chr17	44709066	44709095	3244361
chr17	28309948	28309990	11278891
chr4	165389257	165389286	9242644
chr11	81471198	81471237	10660604
chr15	10518098	10518126	10660604
chr6	26931361	26932057	2586521
chr6	26933508	26933558	2586521
chr2	212297456	212297487	10377075
chr1	97290920	97290965	8065357
chr4	182898552	182898623	2181446
chr7	139891414	139891863	2479823
chr7	140011921	140012881	2479823
chr7	136708095	136708571	10652357
chr8	48907764	48907795	12848620
chr16	7975039	7975080	10973977
chr6	109559289	109559347	7791782
chr1	208090837	208091088	7791782
chr10	70256299	70256356	2106664
chr10	70257550	70258029	2106664
chr6	26931941	26931969	7609882
chr13	80234980	80235020	10988288
chr12	27707601	27707682	7896732
chr7	139452798	139452865	1717824
chr19	41616253	41616300	1717824
chr2	209447545	209447595	1717824
chr2	209478539	209478590	1717824
chr2	209482203	209482254	1717824
chr2	209518566	209518614	1717824
chrUn	57509249	57509414	8964505
chr5	157654588	157654799	12188923
chr17	44709020	44709206	3683387
chr5	66296324	66296355	12466545
chr6	55895759	55895951	8098844
chr6	55955923	55957044	8098844
chrX_random	1831766	1831958	8098844
chr8	5783961	5783999	9058379
chr10	53776841	53776882	2830491
chr4	126331068	126331108	8016112
chr10	53800558	53800643	2999140
chr19	25703364	25703401	12917378
chr2	36432960	36432992	12917378
chr11	81471195	81471231	9556573
chr13	48867699	48867826	12505064
chr2	180483706	180483735	2175918
chr6	13161173	13161439	11451360
chr1	205852195	205852261	12493735
chr6	26931644	26931680	12145309
chr3	136743228	136743302	1732730
chr6	48025823	48025859	1732732
chr4	158185718	158185812	1694011
chr4	158283657	158283750	1694011
chr4	158371448	158371541	1694011
chr4	158630996	158631088	1694011
chr1	62324044	62324077	10594026
chr8	38028961	38028994	10594026
chr11	81471202	81471237	10708554
chr2	95334253	95334290	8969196
chr16	7975040	7975081	8969196
chr2	94554720	94554750	10075714
chr16	17570715	17570762	8928809
chr5	19717000	19717032	9875228
chr12	35664744	35664778	8366095
chr15	33068993	33069065	8366095
chr19	39850451	39850479	1584217
chr2	95334253	95334288	10196233
chr20_random	40467	40502	11297551
chr20_random	89200	89235	11297551
chr20	3409894	3409931	11297551
chr20	3468402	3468438	11297551
chr20	3555765	3555801	11297551
chr20	4998442	4998479	11297551
chr20	5056562	5056599	11297551
chr7	137223755	137223785	1328867
chr8	82724142	82724194	16198230
chr15	33068730	33068775	8537395
chr4	104412023	104412065	9099714
chr3	118194034	118194191	8195142
chr5	17514004	17514366	9030569
chr7	2230888	2230993	1315319
chr7	2235952	2236200	1315319
chr7	2237964	2238851	1315319
chr7	2240117	2242058	1315319
chr7	2244989	2245138	1315319
chr7	2247707	2248383	1315319
chr7	2250256	2251833	1315319
chr7	2264295	2264914	1315319
chr7	2268746	2269326	1315319
chr18	30199963	30200062	3441006
chr2	133015599	133015640	3441006
chr1	185972978	185973069	3441006
chr1	185974484	185975490	3441006
chr14	87968313	87968342	9030565
chr15	60794026	60794055	10395650
chrX	26568278	26568315	10395650
chrX	26571541	26571580	10395650
chr1	205848279	205848607	10956641
chr4	116975598	116975634	8663388
chr14	35418312	35418365	7615828
chr15	83103031	83103065	12568725
chr17	6287887	6287919	14563703
chr13	96309606	96309637	11278663
chr2	174775177	174775259	3499668
chr11	67609816	67609854	10896677
chr10	664791	664820	10896677
chr10	666717	666745	10896677
chr6	103124700	103124740	7575462
chr8	4315525	4315554	1850695
chr1	206632400	206632440	7592662
chr14	19142319	19142351	2711183
chr1	203172021	203172059	16165221
chr5	24455787	24455867	3035717
chr4	173815402	173815466	3035717
chr4	173852416	173852480	3035717
chr17	48465672	48465812	3035717
chr17	48519754	48519834	3035717
chr17	48523723	48523879	3035717
chr17	48775744	48775897	3035717
chr17	50113535	50113801	3035717
chr17	50332549	50332689	3035717
chr17	50339160	50339316	3035717
chr17	50391419	50391575	3035717
chr17	50410854	50410994	3035717
chr2	191075806	191076046	3035717
chr8	58583592	58585211	8144606
chr13	48829905	48829943	8413291
chr1	155389340	155389374	9211912
chrX	85948905	85948939	12841583
chr10	95694105	95694356	2745428
chr1	258000869	258000907	16055439
chr5	17513955	17514362	8232318
chr7	20348754	20348787	10082537
chr5	139859997	139860030	10082537
chr4	119854762	119854795	10082537
chr3	143750248	143750278	10082537
chr1	175179476	175179509	10082537
chr9	110546714	110546747	10082537
chr10	40444612	40444645	10082537
chr10	44043303	44043336	10082537
chr19	21185692	21185724	10082537
chr1_random	3871142	3871176	10082537
chr13	46262765	46262805	15792957
chr10	95694267	95694326	2909514
chr7	20348057	20349168	2247479
chr7	70298135	70298199	2247479
chr6	70354275	70354542	2247479
chr6	133082150	133083081	2247479
chr5	6275484	6276397	2247479
chr5	139859183	139860110	2247479
chr5	139863888	139864450	2247479
chr4	119854134	119855181	2247479
chr4	169092273	169092364	2247479
chr3	51272284	51273397	2247479
chr3	143749836	143750919	2247479
chr2	14253133	14253530	2247479
chr1	80026396	80027532	2247479
chr1	102489385	102489756	2247479
chr1	102992034	102992318	2247479
chr1	106199076	106199114	2247479
chr1	106201863	106202525	2247479
chr1	175179033	175180207	2247479
chr9	110546071	110547179	2247479
chr8	77796417	77796507	2247479
chr8	83946535	83946581	2247479
chr11	4594930	4595910	2247479
chr10	40444168	40445298	2247479
chr10	44042140	44043989	2247479
chr10	56783679	56783745	2247479
chr17	55638302	55638455	2247479
chr17	59194874	59195997	2247479
chr14	17065458	17066754	2247479
chr14	111622953	111623002	2247479
chr19	8117802	8118410	2247479
chr19	21185045	21186127	2247479
chrX	47406746	47407102	2247479
chr1_random	3870550	3871524	2247479
chr16	19045992	19046073	9328356
chr1	201389130	201389160	1870124
chr14	19142260	19142290	3169549
chr1	154651720	154651751	2341405
chr15	33068829	33068859	1328857
chr8	91956210	91956240	1328857
chr7	139452730	139452944	3352608
chr4	103908885	103908942	1729611
chr2_random	3022490	3022519	7913466
chr1	163327123	163327175	8120047
chr13	19107283	19108726	7913462
chr12	21478628	21478724	7913462
chr12	21479815	21480655	7913462
chr12	21482682	21483542	7913462
chr12	21501021	21501328	7913462
chr12	21504988	21505178	7913462
chr12	21510879	21510992	7913462
chr12	21515571	21516930	7913462
chr12	35901883	35901946	7913462
chr12	35904907	35904996	7913462
chr18	66312589	66312649	7913462
chr18	66318408	66318542	7913462
chr18	66326667	66326715	7913462
chr18	66327811	66327891	7913462
chr18	66330330	66330411	7913462
chr18	66333039	66333223	7913462
chr18	66352909	66353047	7913462
chr18	66354979	66355144	7913462
chr18	66358386	66359978	7913462
chr7	10809378	10809585	7913462
chr1	203171679	203171722	7913462
chr1	23506891	23508078	8647846
chr10	90393457	90393489	12556524
chr1	9014798	9015335	2017183
chr1	9020504	9020678	2017183
chr1	9023159	9024837	2017183
chr1	9029875	9031714	2017183
chr6	138450709	138450752	2536161
chr8	61461104	61461178	2536161
chr11	81471198	81471236	8390676
chr2	181214725	181214790	2586516
chr6	26931934	26931971	2061309
chr10	95694277	95694306	2358443
chr5	143982939	143984529	1652060
chr1	95892870	95892955	16087728
chr10	95694276	95694305	8382533
chr3	164012082	164012111	8382533
chr15	33068822	33068861	9111345
chr1	200918368	200918409	2388615
chr7	80014128	80014162	15860457
chr4	159190579	159190614	15860457
chr1	205295185	205295222	15860457
chr19	37266476	37266518	9264553
chr8	83313648	83313688	9264553
chr8	83316459	83316499	9264553
chr3	13783502	13783539	7885844
chr2	191044262	191044302	7885844
chr3	75548101	75549203	7892230
chr1	95027230	95028125	7892230
chr1	95029404	95032465	7892230
chr15	47303027	47303121	8838143
chr3	164012305	164012334	9786935
chr1	154651966	154652069	2925653
chr9	65714903	65715023	1847512
chr10	95694198	95694316	8144557
chr6	42178107	42178450	1309950
chr3	158101547	158101667	1309950
chrX	52445629	52446887	1309950
chr3	44441287	44441317	1651499
chr1	205848582	205848676	12107181
chr1	205886158	205886188	12107181
chr13	87039697	87040484	12643284
chr3	154459842	154459899	2279702
chr3	154482821	154483158	2279702
chr1	203171509	203172300	2884660
chr2	180483712	180483741	8612541
chr2	180483405	180483435	8612540
chr2	182784706	182784953	8793102
chr2	182787266	182787383	8793102
chr2	182789355	182789416	8793102
chr1	97291100	97291130	10601277
chr7	120765072	120765114	8289814
chr7	120783233	120783275	8289814
chr7	104035612	104035727	2775280
chr10	89471416	89471519	10801800
chr1	81944731	81944764	9722582
chr1	155389339	155389372	9722582
chr3	44441053	44441355	3062372
chr4	21709925	21709984	8891341
chr4	21828017	21829568	8891341
chr20_random	40456	40502	2501084
chr20_random	89200	89236	2501084
chr20	3409894	3409932	2501084
chr20	3425428	3425469	2501084
chr20	3468402	3468439	2501084
chr20	3513856	3513896	2501084
chr20	3555754	3555801	2501084
chr20	4998442	4998490	2501084
chr20	5056562	5056610	2501084
chr2	180483680	180483774	2153298
chr12	9541107	9541165	10600171
chr12	9596068	9596154	10600171
chr12_random	286811	286853	10600171
chr4	152057520	152057550	8910484
chr5	165071744	165073864	2967498
chr5	165200540	165200948	2967498
chr4	184900212	184900300	8663213
chr10	83620724	83620765	8663211
chr17	44344417	44344480	10076996
chr3	6052522	6052554	8613746
chr1	159277324	159277731	8613746
chr6	26931686	26931782	1508198
chr6	26935226	26935264	1508198
chr10	95694184	95694257	8636081
chr1	95892856	95892900	8636081
chr5	165074076	165074115	8264645
chr18	12406442	12406471	2601716
chr2	174775175	174775207	2601716
chr6	109558820	109558850	10580097
chr5	80324938	80324968	10580097
chr3	3459945	3459989	9712664
chr3	92572010	92572045	8754772
chr3	75542194	75543137	7935418
chr3	75547824	75550800	7935418
chr1	95029922	95030802	7935418
chr2	51736527	51736910	2869036
chr2	51745856	51745910	2869036
chr6	21417632	21417664	9658104
chr19	39853069	39853122	2889531
chr9	70772381	70772413	12372417
chr14	21847825	21847883	8264581
chr1	83489340	83489368	11129950
chr1	212163558	212163699	8224520
chr1	212298955	212299096	8224520
chr17	44709066	44709212	3169002
chr1	81230296	81230356	2726759
chr1	81266715	81266995	2726759
chr1	81345295	81345575	2726759
chr1	81408545	81408605	2726759
chr1	81628278	81628339	2726759
chr1	81780214	81780279	2726759
chr1	81840001	81840083	2726759
chr1	81867028	81867110	2726759
chr5	165074127	165074170	2522932
chr2	174775175	174775205	2847919
chr10	56410821	56410853	9624121
chr4	21829155	21829196	9624121
chr9	20158681	20158710	9624121
chr6	13161119	13161490	9773974
chr3	137776221	137776254	8262963
chr3	137792319	137792352	8262963
chr3	137861856	137862694	8262963
chr3	138088127	138089463	8262963
chr3	138233789	138233822	8262963
chr3	138333350	138334178	8262963
chr3	138495772	138496574	8262963
chr12	42931109	42931193	1673926
chr12	42936667	42937243	1673926
chr10	72081210	72081418	1673926
chr10	72086082	72086284	1673926
chr10	72162125	72162289	1673926
chr10	72168712	72168798	1673926
chr10	72186369	72186997	1673926
chr10_random	695945	696073	1673926
chr7	10791310	10791383	2200736
chr7	10813078	10813165	2200736
chr19	41616265	41616293	2200736
chr1	20998723	20999025	2026618
chr1	90576756	90576785	8668155
chr2	181214665	181214792	16204235
chr3	161554279	161554804	8036172
chr4	158103526	158103571	9731707
chr2	59677643	59677674	9731707
chr2	59680754	59680784	9731707
chr14	21847876	21847906	1557422
chr7	10419996	10420281	1603088
chr17	44709071	44709101	2717408
chr3	44441290	44441325	9668074
chr5	66296280	66296332	1956774
chr2	181214742	181214791	1956774
chr9	71966731	71966762	7693708
chr7	11164584	11164626	15225122
chr6	26931485	26932030	2046665
chr11	81471198	81471236	8389766
chr7	24458489	24458520	16339156
chr2	36432960	36432991	10713139
chrX	24685277	24685478	2304462
chrX	24696391	24696625	2304462
chr18	25027872	25028105	1847666
chr9	63212560	63212590	1847666
chr9	63234519	63234645	1847666
chr4	115454231	115454259	1847666
chr3	13783502	13783539	11018030
chr2	191044179	191044302	11018030
chr5	165074298	165074326	15764815
chr17	28309967	28310005	15764815
chr7	24531800	24531832	8702983
chr11	79124934	79124965	8702983
chr14	19110765	19110885	2455718
chr6	26931932	26931970	2388831
chr12	42919573	42919608	1748280
chr2	212297455	212297499	7537851
chr6	76920418	76920446	8920965
chr1	211761740	211761769	8920965
chr3	44441287	44441328	2160464
chr13	85793036	85793185	15731358
chr13	40500600	40500630	2027757
chr1	78324518	78324548	2027757
chr5	19716825	19716853	8405996
chrX	85946855	85949621	8379933
chr3	76307197	76307240	8617799
chr3	44441330	44441385	15085339
chr10	95694183	95694216	2211620
chr8	83313854	83313884	8391636
chr18	25622616	25622645	7799965
chr8	61793835	61793978	8119192
chr3	164012014	164012064	9544984
chr3	151428679	151428718	8524227
chr1	128843971	128844010	8524227
chr2	212297456	212297489	7692229
chr12	9541091	9541139	7499421
chr12	9596052	9596131	7499421
chr12_random	286795	286844	7499421
chr14	92788597	92789167	8626808
chr14	87950091	87950131	9497382
chr10	65036946	65036974	9714306
chr6	21417532	21417638	7667089
chr17	44710578	44710640	3481434
chr10	95694279	95694309	8132622
chr2	181214117	181214342	8449904
chr3	76301109	76301137	8662964
chr3	164011949	164011986	1848696
chr2	174727220	174727250	1942067
chr12	42919433	42919644	8367288
chr1	211761740	211761797	8216221
chr8	5784010	5784039	7588292
chr14	87950091	87950127	10358076
chr6	26931644	26931676	11861523
chr1	228933318	228933690	14673170
chr2	212297456	212297490	10833420
chr2	181214753	181214782	8165139
chr19	37266477	37266518	9144242
chr8	83313648	83313688	9144242
chr8	83316459	83316499	9144242
chr1	80309880	80309922	9224955
chr10	95694110	95694156	9765286
chr4	158103539	158103572	11319221
chr1	95892547	95892583	11682622
chr5	17161945	17162352	2439693
chr17	48290091	48290226	1718964
chr1	95892880	95892915	15961509
chr14	87950096	87950131	10880363
chr1	95892543	95892900	10935547
chr10	72460509	72460539	7545164
chr2	180483338	180483780	2308930
chr19	37266472	37266506	12023900
chr5	16139724	16139762	3165490
chr11	50537235	50537273	3165490
chr15	1142333	1142393	3165490
chr6	78009635	78009664	11891324
chr11	80031565	80032076	8413271
chr11	80109178	80109689	8413271
chr11	80169745	80170257	8413271
chrX	24685339	24685443	8496174
chr12	19555414	19555468	8288642
chr14	18813329	18813382	8288642
chr5	78091353	78091417	2463987
chr5	78165899	78165963	2463987
chr5	78218630	78218694	2463987
chr5	78244114	78244178	2463987
chr5	78270734	78270798	2463987
chr5	78316189	78316251	2463987
chr5	78409805	78409869	2463987
chr5	78440085	78440143	2463987
chr5	78490562	78490627	2463987
chr5	78644225	78644288	2463987
chr5	78683814	78683877	2463987
chr5	78709791	78709856	2463987
chr5	78770225	78770289	2463987
chr5	78805327	78805391	2463987
chr5	78820149	78820213	2463987
chr5	78911594	78911634	2463987
chr5	78936470	78936534	2463987
chr5	78990257	78990320	2463987
chr5	79017594	79017659	2463987
chr5	79083558	79083622	2463987
chr5	79101331	79101395	2463987
chr19	13962433	13963095	12637567
chr5	66296210	66296240	11095981
chr19	37266470	37266506	8396148
chr8	83313655	83313690	8396148
chr8	83316466	83316501	8396148
chr7	141772421	141775242	1684715
chr7	141778585	141778731	1684715
chr10	85020102	85020245	1684715
chr10	85032736	85032897	1684715
chr10	85036913	85037064	1684715
chr4	80490430	80490494	1684715
chr4	80502677	80502724	1684715
chr4	80506432	80506593	1684715
chr4	80515871	80516035	1684715
chr9	87036984	87037018	8632018
chr2	181178017	181178044	7665553
chr1	74359077	74359121	15502011
chr1	74605347	74605424	15502011
chr1	75708122	75708199	15502011
chr2	180483273	180483302	8381969
chr3	6666297	6666564	8381967
chr3	6670336	6670447	8381967
chr3	6678139	6678293	8381967
chr3	6683840	6683951	8381967
chr3	6685833	6685928	8381967
chr3	6689100	6689303	8381967
chr2	181214666	181214850	8246989
chr20	4636130	4636184	3114745
chr2	181214567	181214598	2019572
chr1	97291101	97291130	10529375
chr7	24531804	24531838	12791769
chr14	19142221	19142286	2601696
chr18	27343019	27343172	7877619
chr15	33068742	33068778	11136726
chr1	170639998	170640038	11136726
chr1	170642590	170642636	11136726
chr2	180483318	180483749	7877617
chr7	104035678	104035708	1508216
chr10	83622835	83623072	2127540
chr5	165062214	165062246	8164667
chr13	88048989	88049077	8289804
chr2	197102305	197102390	8289804
chr3	164012333	164012366	2850495
chr5	128719270	128719301	12385751
chr5	128736712	128736741	12385751
chr1	231981144	231981173	12385751
chr4	152057615	152057756	1827795
chr1	95027477	95027555	7971966
chr9	70771185	70771269	1404598
chr7	141164179	141164224	1356762
chr7	141165431	141167383	1356762
chr7	141182388	141182557	1356762
chr7	141188408	141189249	1356762
chr3	55445237	55445302	1356762
chr1	226420947	226421923	1356762
chr1	226444826	226446364	1356762
chr10	90393479	90393509	12954759
chr3	6052519	6052553	14506227
chr13	87039904	87039934	1705013
chr5	143983099	143983218	1705013
chr17	40685479	40685549	9931418
chr10	39220654	39220779	2342469
chr10	39221785	39221872	2342469
chr10	39223214	39227535	2342469
chr12	35664737	35664965	7935447
chr12	35664750	35664780	7961957
chr15	33068724	33068767	7961957
chr10	95694177	95694216	1976240
chr11	81471198	81471236	10428876
chr4_random	1954228	1954274	12397359
chr2	181177986	181178044	8798690
chr3	164007860	164007902	2355922
chr8	83312931	83313881	2160079
chr8	83315616	83316501	2160079
chr4	158102467	158103731	2466233
chr1	203171632	203171747	10842166
chr14	86614942	86614971	1406648
chr11	79124923	79124960	2875459
chr3	164012297	164012333	2875459
chr2	174775175	174775205	1922032
chr20	6541436	6541465	10634806
chr6	21417657	21417732	9512555
chr5	17514716	17514750	2837758
chr11	79124930	79124959	2837758
chr14	86615061	86615092	12540614
chr10	95694276	95694307	1985929
chr3	44441219	44441254	8164696
genometools-1.5.1/testdata/bed_files/gb-2008-9-2-r31-s5.gff3000066400000000000000000001661401211610345200225640ustar00rootroot00000000000000##gff-version   3
##sequence-region   chrX 24685183 157576066
##sequence-region   chr3_random 930756 930827
##sequence-region   chr14 3050867 111623002
##sequence-region   chr15 1142334 103122943
##sequence-region   chr12 8296010 42944415
##sequence-region   chr13 2231203 96309637
##sequence-region   chr18 12406443 83077187
##sequence-region   chr19 8117803 54750768
##sequence-region   chr16 7975040 89939142
##sequence-region   chr4_random 1954229 1954274
##sequence-region   chr17 5126486 91004637
##sequence-region   chr1_random 3870551 3871524
##sequence-region   chr6_random 21172 21797
##sequence-region   chr10 664792 109920836
##sequence-region   chr11 4594931 81471237
##sequence-region   chrUn 12670679 73050514
##sequence-region   chrX_random 1831767 1831958
##sequence-region   chr7 2230889 141778731
##sequence-region   chr10_random 695946 696073
##sequence-region   chr8 4158721 126657278
##sequence-region   chr12_random 286796 286853
##sequence-region   chr9 11037644 110547179
##sequence-region   chr3 3459946 164012366
##sequence-region   chr4 21709926 184900300
##sequence-region   chr5 6275485 167405212
##sequence-region   chr6 13161120 140857843
##sequence-region   chr20 2646402 32000224
##sequence-region   chr15_random 316859 319577
##sequence-region   chr1 9014799 258000924
##sequence-region   chr20_random 40417 131037
##sequence-region   chr2 14253134 223130032
##sequence-region   chrUn_random 3207749 3207780
##sequence-region   chr2_random 3022491 3022990
chr17	.	BED_feature	48290001	48290096	.	.	.	Name=2300056
chr1	.	BED_feature	154651621	154652041	.	.	.	Name=1764039
chr19	.	BED_feature	51023883	51024004	.	.	.	Name=1656236
chr1	.	BED_feature	96909743	96909912	.	.	.	Name=8120060
chr14	.	BED_feature	21847876	21847906	.	.	.	Name=1644820
chr12	.	BED_feature	42931186	42931218	.	.	.	Name=1970973
chr12	.	BED_feature	42936617	42937377	.	.	.	Name=1970973
chr12	.	BED_feature	42938681	42938932	.	.	.	Name=1970973
chr12	.	BED_feature	42940082	42940247	.	.	.	Name=1970973
chr12	.	BED_feature	42941799	42942075	.	.	.	Name=1970973
chr12	.	BED_feature	42944042	42944415	.	.	.	Name=1970973
chr10_random	.	BED_feature	695960	696024	.	.	.	Name=1970973
chr19	.	BED_feature	49636891	49637016	.	.	.	Name=14641110
chr18	.	BED_feature	27413272	27413302	.	.	.	Name=14563555
chrX	.	BED_feature	85120368	85120397	.	.	.	Name=14563555
chr3	.	BED_feature	44441219	44441254	.	.	.	Name=11773447
chr8	.	BED_feature	4158721	4158774	.	.	.	Name=15026307
chr2	.	BED_feature	180483397	180483436	.	.	.	Name=8643513
chr4	.	BED_feature	42955732	42955763	.	.	.	Name=9380697
chrUn_random	.	BED_feature	3207749	3207780	.	.	.	Name=9380697
chr2	.	BED_feature	116034042	116034070	.	.	.	Name=10969836
chr5	.	BED_feature	165074246	165074283	.	.	.	Name=12023302
chr12	.	BED_feature	37288389	37288959	.	.	.	Name=8110830
chr10	.	BED_feature	95694185	95694256	.	.	.	Name=9614069
chr1	.	BED_feature	95892857	95892967	.	.	.	Name=9614069
chr14	.	BED_feature	87395430	87395512	.	.	.	Name=8188706
chr1	.	BED_feature	35713102	35713134	.	.	.	Name=11517190
chr4	.	BED_feature	158186010	158186097	.	.	.	Name=1672118
chr4	.	BED_feature	158187270	158188218	.	.	.	Name=1672118
chr4	.	BED_feature	158283951	158284038	.	.	.	Name=1672118
chr4	.	BED_feature	158285260	158285436	.	.	.	Name=1672118
chr4	.	BED_feature	158286505	158286547	.	.	.	Name=1672118
chr4	.	BED_feature	158371742	158371800	.	.	.	Name=1672118
chr4	.	BED_feature	158372956	158373132	.	.	.	Name=1672118
chr4	.	BED_feature	158381376	158381418	.	.	.	Name=1672118
chr4	.	BED_feature	158628592	158629557	.	.	.	Name=1672118
chr4	.	BED_feature	158630709	158630790	.	.	.	Name=1672118
chr3	.	BED_feature	136739009	136739571	.	.	.	Name=1672118
chr3	.	BED_feature	136743017	136743200	.	.	.	Name=1672118
chr1	.	BED_feature	78368026	78368381	.	.	.	Name=1672118
chrUn	.	BED_feature	17400463	17400493	.	.	.	Name=15661834
chr7	.	BED_feature	104035597	104035776	.	.	.	Name=2540196
chr11	.	BED_feature	79124931	79124959	.	.	.	Name=2540196
chrX	.	BED_feature	85949214	85949621	.	.	.	Name=2282981
chr1	.	BED_feature	81264616	81264651	.	.	.	Name=15656786
chr1	.	BED_feature	81343181	81343216	.	.	.	Name=15656786
chr6	.	BED_feature	128386906	128386950	.	.	.	Name=2246271
chr6	.	BED_feature	128436432	128436476	.	.	.	Name=2246271
chr15	.	BED_feature	33068746	33069093	.	.	.	Name=8782063
chr10	.	BED_feature	95694185	95694327	.	.	.	Name=2836398
chr14	.	BED_feature	21847816	21847937	.	.	.	Name=2046676
chr5	.	BED_feature	19717056	19717123	.	.	.	Name=8182075
chr9	.	BED_feature	65906944	65906974	.	.	.	Name=2476660
chrX	.	BED_feature	24685183	24685227	.	.	.	Name=2476660
chr2	.	BED_feature	212297454	212297490	.	.	.	Name=7683412
chr5	.	BED_feature	139690798	139690826	.	.	.	Name=11689000
chr7	.	BED_feature	20348253	20348302	.	.	.	Name=10953033
chr5	.	BED_feature	139863925	139863974	.	.	.	Name=10953033
chr10	.	BED_feature	40445099	40445148	.	.	.	Name=10953033
chr1	.	BED_feature	175179963	175180012	.	.	.	Name=10953033
chr19	.	BED_feature	41616223	41616268	.	.	.	Name=2424007
chr3	.	BED_feature	13783501	13783534	.	.	.	Name=3185564
chr1	.	BED_feature	87626144	87626171	.	.	.	Name=2697636
chr10	.	BED_feature	87747757	87747878	.	.	.	Name=1846602
chr10	.	BED_feature	87750095	87751145	.	.	.	Name=1846602
chr7	.	BED_feature	140995635	140997920	.	.	.	Name=1846602
chr15_random	.	BED_feature	316859	316978	.	.	.	Name=1846602
chr15_random	.	BED_feature	319400	319577	.	.	.	Name=1846602
chr15	.	BED_feature	10490903	10490978	.	.	.	Name=1846602
chr1	.	BED_feature	154651796	154651898	.	.	.	Name=10551830
chr7	.	BED_feature	10727330	10727442	.	.	.	Name=8790352
chr18	.	BED_feature	60548761	60548879	.	.	.	Name=8790352
chr18	.	BED_feature	60594286	60594347	.	.	.	Name=8790352
chr8	.	BED_feature	79644354	79645644	.	.	.	Name=8790352
chr8	.	BED_feature	79671773	79672729	.	.	.	Name=8790352
chr17	.	BED_feature	15651981	15652011	.	.	.	Name=10531380
chr13	.	BED_feature	41043408	41043439	.	.	.	Name=7926010
chr11	.	BED_feature	79124924	79124960	.	.	.	Name=1693237
chr3	.	BED_feature	164012298	164012333	.	.	.	Name=1693237
chr6	.	BED_feature	23664540	23664573	.	.	.	Name=2914621
chr6	.	BED_feature	64172473	64172537	.	.	.	Name=2914621
chr6	.	BED_feature	127304431	127305147	.	.	.	Name=2914621
chr5	.	BED_feature	25294695	25295538	.	.	.	Name=2914621
chr5	.	BED_feature	130925074	130925668	.	.	.	Name=2914621
chr5	.	BED_feature	167401636	167402455	.	.	.	Name=2914621
chr5	.	BED_feature	167404508	167404608	.	.	.	Name=2914621
chr4	.	BED_feature	154051426	154052369	.	.	.	Name=2914621
chr4	.	BED_feature	160892814	160893011	.	.	.	Name=2914621
chr4	.	BED_feature	160895521	160896074	.	.	.	Name=2914621
chr3	.	BED_feature	55201687	55202606	.	.	.	Name=2914621
chr3	.	BED_feature	103228389	103228499	.	.	.	Name=2914621
chr3	.	BED_feature	136274408	136275173	.	.	.	Name=2914621
chr3	.	BED_feature	144110235	144111155	.	.	.	Name=2914621
chr2	.	BED_feature	174389982	174390441	.	.	.	Name=2914621
chr2	.	BED_feature	178470349	178470412	.	.	.	Name=2914621
chr2	.	BED_feature	186081640	186082574	.	.	.	Name=2914621
chr1	.	BED_feature	106191089	106192032	.	.	.	Name=2914621
chr1	.	BED_feature	171347088	171347715	.	.	.	Name=2914621
chr1	.	BED_feature	222252060	222252969	.	.	.	Name=2914621
chr14	.	BED_feature	18734494	18734615	.	.	.	Name=2914621
chr9	.	BED_feature	52001272	52002013	.	.	.	Name=2914621
chr9	.	BED_feature	66781669	66781736	.	.	.	Name=2914621
chrX	.	BED_feature	41099240	41100182	.	.	.	Name=2914621
chrX	.	BED_feature	86260052	86260662	.	.	.	Name=2914621
chr11	.	BED_feature	22930566	22931429	.	.	.	Name=2914621
chr10	.	BED_feature	44889479	44889836	.	.	.	Name=2914621
chr10	.	BED_feature	53300169	53300233	.	.	.	Name=2914621
chr10	.	BED_feature	57537627	57538981	.	.	.	Name=2914621
chr10	.	BED_feature	57540454	57542319	.	.	.	Name=2914621
chr17	.	BED_feature	34304642	34305374	.	.	.	Name=2914621
chr16	.	BED_feature	24233575	24234505	.	.	.	Name=2914621
chr16	.	BED_feature	36524020	36524476	.	.	.	Name=2914621
chr15	.	BED_feature	22783096	22783169	.	.	.	Name=2914621
chr8	.	BED_feature	35316222	35316575	.	.	.	Name=2914621
chr8	.	BED_feature	113075748	113076196	.	.	.	Name=2914621
chr18	.	BED_feature	83076445	83076889	.	.	.	Name=2914621
chr20	.	BED_feature	13828234	13828266	.	.	.	Name=12654506
chr12	.	BED_feature	42919434	42919463	.	.	.	Name=10674400
chr8	.	BED_feature	79644224	79644252	.	.	.	Name=10674400
chr10	.	BED_feature	95694185	95694216	.	.	.	Name=10194769
chr2	.	BED_feature	22607197	22607228	.	.	.	Name=8552092
chr6	.	BED_feature	98775387	98775815	.	.	.	Name=11731618
chr1	.	BED_feature	35522840	35522868	.	.	.	Name=11731618
chr10	.	BED_feature	57535199	57537754	.	.	.	Name=2269373
chr12	.	BED_feature	22154907	22154939	.	.	.	Name=9224811
chr5	.	BED_feature	165074364	165074416	.	.	.	Name=12480945
chr6	.	BED_feature	26931685	26931784	.	.	.	Name=8248179
chr2	.	BED_feature	104765997	104766025	.	.	.	Name=8248179
chr3	.	BED_feature	164011949	164011980	.	.	.	Name=14722127
chr12	.	BED_feature	35664736	35664778	.	.	.	Name=10207035
chr1	.	BED_feature	97291100	97291128	.	.	.	Name=11278660
chr2	.	BED_feature	180483363	180483392	.	.	.	Name=11668178
chr10	.	BED_feature	57501538	57503604	.	.	.	Name=8034713
chr18	.	BED_feature	58177378	58177406	.	.	.	Name=9855630
chr18	.	BED_feature	58179241	58179269	.	.	.	Name=9855630
chr8	.	BED_feature	115124282	115124352	.	.	.	Name=11116210
chr20_random	.	BED_feature	40417	40502	.	.	.	Name=3125612
chr20_random	.	BED_feature	59039	59086	.	.	.	Name=3125612
chr20_random	.	BED_feature	89201	89262	.	.	.	Name=3125612
chr20_random	.	BED_feature	130974	131037	.	.	.	Name=3125612
chr20	.	BED_feature	2646402	2646490	.	.	.	Name=3125612
chr20	.	BED_feature	3409895	3409958	.	.	.	Name=3125612
chr20	.	BED_feature	3425425	3425469	.	.	.	Name=3125612
chr20	.	BED_feature	3468403	3468465	.	.	.	Name=3125612
chr20	.	BED_feature	3513817	3513902	.	.	.	Name=3125612
chr20	.	BED_feature	3539748	3539811	.	.	.	Name=3125612
chr20	.	BED_feature	3555755	3555801	.	.	.	Name=3125612
chr20	.	BED_feature	4998443	4998530	.	.	.	Name=3125612
chr20	.	BED_feature	5021611	5021673	.	.	.	Name=3125612
chr20	.	BED_feature	5056563	5056626	.	.	.	Name=3125612
chr6	.	BED_feature	104749305	104749414	.	.	.	Name=8662994
chr4	.	BED_feature	78827913	78828679	.	.	.	Name=2827005
chr2	.	BED_feature	94946370	94946454	.	.	.	Name=2827005
chr1	.	BED_feature	34635074	34635160	.	.	.	Name=2827005
chr1	.	BED_feature	73096721	73096825	.	.	.	Name=2827005
chr8	.	BED_feature	20038114	20038177	.	.	.	Name=2827005
chr8	.	BED_feature	83529635	83529729	.	.	.	Name=2827005
chr16	.	BED_feature	13318994	13319098	.	.	.	Name=2827005
chr14	.	BED_feature	65603826	65603874	.	.	.	Name=2827005
chr19	.	BED_feature	26190597	26190713	.	.	.	Name=2827005
chr18	.	BED_feature	63217241	63217296	.	.	.	Name=2827005
chr20	.	BED_feature	3663806	3663835	.	.	.	Name=9794408
chr3	.	BED_feature	44441217	44441254	.	.	.	Name=10026208
chr14	.	BED_feature	21847850	21847898	.	.	.	Name=8114709
chr18	.	BED_feature	75499628	75499678	.	.	.	Name=10995747
chr15	.	BED_feature	45392497	45392525	.	.	.	Name=9334243
chr7	.	BED_feature	9773673	9774076	.	.	.	Name=3053160
chr5	.	BED_feature	101403547	101403934	.	.	.	Name=3053160
chr5	.	BED_feature	118165241	118165774	.	.	.	Name=3053160
chr5	.	BED_feature	118350319	118350388	.	.	.	Name=3053160
chr5	.	BED_feature	118394688	118394763	.	.	.	Name=3053160
chr5	.	BED_feature	118409476	118409593	.	.	.	Name=3053160
chr5	.	BED_feature	118415945	118416076	.	.	.	Name=3053160
chr5	.	BED_feature	118437032	118437153	.	.	.	Name=3053160
chr5	.	BED_feature	118459475	118459582	.	.	.	Name=3053160
chr5	.	BED_feature	118461708	118461873	.	.	.	Name=3053160
chr5	.	BED_feature	118477299	118477390	.	.	.	Name=3053160
chr5	.	BED_feature	118506521	118506720	.	.	.	Name=3053160
chr19	.	BED_feature	25046471	25046886	.	.	.	Name=3053160
chr1	.	BED_feature	96173573	96173902	.	.	.	Name=2331750
chr1	.	BED_feature	96174921	96175332	.	.	.	Name=2331750
chr1	.	BED_feature	96176573	96176787	.	.	.	Name=2331750
chr1	.	BED_feature	96177990	96178484	.	.	.	Name=2331750
chr7	.	BED_feature	40484148	40484205	.	.	.	Name=7791794
chrX	.	BED_feature	89455373	89455402	.	.	.	Name=8241260
chr3	.	BED_feature	118194033	118194154	.	.	.	Name=1371278
chr14	.	BED_feature	18813521	18813556	.	.	.	Name=12732210
chr19	.	BED_feature	39851520	39851548	.	.	.	Name=1683601
chr19	.	BED_feature	39853855	39853884	.	.	.	Name=1683601
chr6	.	BED_feature	140857804	140857843	.	.	.	Name=2555700
chr9	.	BED_feature	95631141	95631173	.	.	.	Name=2555700
chr1	.	BED_feature	238896305	238896339	.	.	.	Name=2555700
chr6	.	BED_feature	128386906	128386950	.	.	.	Name=7559615
chr6	.	BED_feature	128436432	128436476	.	.	.	Name=7559615
chr14	.	BED_feature	21847858	21847907	.	.	.	Name=7559615
chr2	.	BED_feature	191044261	191044300	.	.	.	Name=1472472
chr3	.	BED_feature	17196020	17196062	.	.	.	Name=16873660
chr2	.	BED_feature	15998844	15998884	.	.	.	Name=16873660
chr10	.	BED_feature	95694277	95694305	.	.	.	Name=2555064
chr13	.	BED_feature	47243580	47243618	.	.	.	Name=8413246
chr12	.	BED_feature	35664757	35664796	.	.	.	Name=8413246
chr10	.	BED_feature	53776750	53776789	.	.	.	Name=8413246
chr1	.	BED_feature	185975628	185975692	.	.	.	Name=8413246
chr14	.	BED_feature	19110725	19110779	.	.	.	Name=9792724
chr7	.	BED_feature	104034951	104035847	.	.	.	Name=3671079
chr5	.	BED_feature	165074085	165074416	.	.	.	Name=10022871
chr8	.	BED_feature	4315516	4315591	.	.	.	Name=2176152
chr10	.	BED_feature	64312805	64313175	.	.	.	Name=9822647
chr6	.	BED_feature	128386905	128386951	.	.	.	Name=7929335
chr6	.	BED_feature	128436431	128436477	.	.	.	Name=7929335
chr14	.	BED_feature	21847787	21847818	.	.	.	Name=8246951
chr3	.	BED_feature	164011397	164011436	.	.	.	Name=11399762
chr1	.	BED_feature	154653110	154653138	.	.	.	Name=9210417
chr2	.	BED_feature	116033484	116033516	.	.	.	Name=9873817
chr2	.	BED_feature	219591238	219591361	.	.	.	Name=1527171
chr4	.	BED_feature	119765288	119767565	.	.	.	Name=2072895
chr15	.	BED_feature	50479670	50479749	.	.	.	Name=2072895
chr20	.	BED_feature	21885316	21885395	.	.	.	Name=2072895
chr7	.	BED_feature	120165049	120165105	.	.	.	Name=1922023
chr7	.	BED_feature	120174378	120174551	.	.	.	Name=1922023
chr7	.	BED_feature	120176596	120176761	.	.	.	Name=1922023
chr10	.	BED_feature	78750076	78750175	.	.	.	Name=1922023
chr1	.	BED_feature	202936740	202936792	.	.	.	Name=1549125
chr1	.	BED_feature	258000874	258000924	.	.	.	Name=1549125
chr14	.	BED_feature	86614963	86615007	.	.	.	Name=1549125
chr3	.	BED_feature	92571983	92572093	.	.	.	Name=12145338
chr1	.	BED_feature	95892889	95892918	.	.	.	Name=12145338
chr1	.	BED_feature	154651766	154651796	.	.	.	Name=9346922
chr11	.	BED_feature	81471201	81471233	.	.	.	Name=8910619
chr14	.	BED_feature	86587827	86587854	.	.	.	Name=9677331
chr20_random	.	BED_feature	40467	40500	.	.	.	Name=2668878
chr20	.	BED_feature	4998447	4998480	.	.	.	Name=2668878
chr20	.	BED_feature	5056567	5056600	.	.	.	Name=2668878
chr15	.	BED_feature	47303023	47303121	.	.	.	Name=8734471
chr6	.	BED_feature	77976384	77976930	.	.	.	Name=2227418
chr6	.	BED_feature	78005398	78005442	.	.	.	Name=2227418
chr18	.	BED_feature	12406443	12406471	.	.	.	Name=2227418
chr10	.	BED_feature	95694333	95694366	.	.	.	Name=11022037
chr2	.	BED_feature	182740365	182740398	.	.	.	Name=11022037
chr2_random	.	BED_feature	3022961	3022990	.	.	.	Name=10620495
chr11	.	BED_feature	79124933	79124960	.	.	.	Name=10620495
chr5	.	BED_feature	66293896	66294054	.	.	.	Name=9737987
chr2	.	BED_feature	181214700	181214790	.	.	.	Name=9737987
chr14	.	BED_feature	97746095	97746125	.	.	.	Name=10702298
chr19	.	BED_feature	26538095	26538123	.	.	.	Name=11050084
chr8	.	BED_feature	109400318	109400350	.	.	.	Name=12750453
chr1	.	BED_feature	212019619	212019648	.	.	.	Name=12750453
chrX	.	BED_feature	63597604	63597754	.	.	.	Name=12750453
chr19	.	BED_feature	51023956	51023991	.	.	.	Name=7799916
chr20_random	.	BED_feature	40467	40501	.	.	.	Name=3554244
chr20_random	.	BED_feature	89201	89236	.	.	.	Name=3554244
chr3	.	BED_feature	108927749	108927779	.	.	.	Name=3554244
chr20	.	BED_feature	2646428	2646483	.	.	.	Name=3554244
chr20	.	BED_feature	3409895	3409932	.	.	.	Name=3554244
chr20	.	BED_feature	3468403	3468439	.	.	.	Name=3554244
chr20	.	BED_feature	3555765	3555801	.	.	.	Name=3554244
chr20	.	BED_feature	4998443	4998478	.	.	.	Name=3554244
chr20	.	BED_feature	5056563	5056598	.	.	.	Name=3554244
chr14	.	BED_feature	18813520	18813556	.	.	.	Name=12609849
chr1	.	BED_feature	155389163	155389765	.	.	.	Name=8474458
chr1	.	BED_feature	185974616	185975610	.	.	.	Name=1959592
chr1	.	BED_feature	154653098	154653127	.	.	.	Name=8132677
chr3	.	BED_feature	3480432	3480463	.	.	.	Name=9038213
chr8	.	BED_feature	126655174	126657278	.	.	.	Name=8948424
chr4	.	BED_feature	152057522	152057550	.	.	.	Name=11278588
chr1	.	BED_feature	78760689	78762243	.	.	.	Name=2761536
chr16	.	BED_feature	89936886	89936920	.	.	.	Name=16481392
chr15	.	BED_feature	45392170	45392292	.	.	.	Name=11058537
chr6	.	BED_feature	76916983	76918759	.	.	.	Name=1976511
chr6	.	BED_feature	76919761	76920131	.	.	.	Name=1976511
chr6	.	BED_feature	77008395	77008444	.	.	.	Name=1976511
chr10	.	BED_feature	16608131	16608178	.	.	.	Name=1976511
chr3	.	BED_feature	135730136	135730333	.	.	.	Name=1976511
chr3	.	BED_feature	135838137	135838303	.	.	.	Name=1976511
chr15	.	BED_feature	49715150	49715266	.	.	.	Name=1976511
chr1	.	BED_feature	247222017	247222126	.	.	.	Name=1976511
chr19	.	BED_feature	39447683	39447713	.	.	.	Name=9845337
chr19	.	BED_feature	39843038	39843093	.	.	.	Name=8101632
chr1	.	BED_feature	202936621	202936833	.	.	.	Name=7720874
chr1	.	BED_feature	258000894	258000923	.	.	.	Name=7720874
chr6	.	BED_feature	27117536	27118509	.	.	.	Name=7689152
chr18	.	BED_feature	63640870	63641571	.	.	.	Name=7689152
chr2	.	BED_feature	142434225	142434369	.	.	.	Name=7689152
chr1	.	BED_feature	95655413	95656362	.	.	.	Name=7689152
chrX	.	BED_feature	157575697	157576066	.	.	.	Name=7689152
chr3	.	BED_feature	88648905	88648943	.	.	.	Name=1588955
chr7	.	BED_feature	137835953	137835980	.	.	.	Name=1588954
chr1	.	BED_feature	247323761	247323799	.	.	.	Name=8955092
chr6	.	BED_feature	138156551	138159155	.	.	.	Name=7980439
chr17	.	BED_feature	5126486	5126515	.	.	.	Name=7980439
chr2	.	BED_feature	180483681	180483736	.	.	.	Name=9013768
chr12	.	BED_feature	32389731	32389761	.	.	.	Name=10385395
chrX	.	BED_feature	52446767	52446801	.	.	.	Name=10417310
chr6	.	BED_feature	140857781	140857813	.	.	.	Name=9013645
chr14	.	BED_feature	3050867	3050961	.	.	.	Name=10521429
chr10	.	BED_feature	95694277	95694305	.	.	.	Name=3396073
chr2	.	BED_feature	174775178	174775205	.	.	.	Name=9642117
chr15	.	BED_feature	33068941	33069010	.	.	.	Name=8007990
chr6	.	BED_feature	78803194	78803228	.	.	.	Name=10674398
chr19	.	BED_feature	54750739	54750768	.	.	.	Name=8144615
chr12	.	BED_feature	20903149	20903271	.	.	.	Name=8756618
chr7	.	BED_feature	139326343	139326400	.	.	.	Name=7901208
chr6	.	BED_feature	140857815	140857843	.	.	.	Name=15013809
chr3	.	BED_feature	161554291	161554330	.	.	.	Name=8940000
chr14	.	BED_feature	19142237	19142407	.	.	.	Name=3422457
chr10	.	BED_feature	87514444	87514574	.	.	.	Name=8051130
chr6	.	BED_feature	54941258	54942924	.	.	.	Name=1840505
chr6	.	BED_feature	99528686	99530007	.	.	.	Name=1840505
chr6	.	BED_feature	99531311	99531403	.	.	.	Name=1840505
chr6	.	BED_feature	99545287	99545324	.	.	.	Name=1840505
chr6	.	BED_feature	99553815	99553889	.	.	.	Name=1840505
chr5	.	BED_feature	145853251	145854686	.	.	.	Name=1840505
chr3	.	BED_feature	28852193	28852596	.	.	.	Name=1840505
chr3	.	BED_feature	28868192	28869835	.	.	.	Name=1840505
chr2	.	BED_feature	137155207	137156708	.	.	.	Name=1840505
chr17	.	BED_feature	43385499	43385784	.	.	.	Name=1840505
chr17	.	BED_feature	43387084	43387346	.	.	.	Name=1840505
chr19	.	BED_feature	39851655	39851706	.	.	.	Name=2881624
chr3	.	BED_feature	44441284	44441329	.	.	.	Name=12783165
chr1	.	BED_feature	37535826	37535854	.	.	.	Name=11572871
chr11	.	BED_feature	79124881	79124916	.	.	.	Name=10567553
chr3	.	BED_feature	44441291	44441323	.	.	.	Name=10567553
chr3	.	BED_feature	164012142	164012176	.	.	.	Name=8188712
chr10	.	BED_feature	95694184	95694256	.	.	.	Name=9564856
chr8	.	BED_feature	91956206	91956239	.	.	.	Name=9564856
chr2	.	BED_feature	181395722	181395758	.	.	.	Name=12388348
chr2	.	BED_feature	27149659	27149820	.	.	.	Name=6088070
chr3	.	BED_feature	18499639	18499678	.	.	.	Name=12697699
chr3	.	BED_feature	44441186	44441224	.	.	.	Name=10869353
chr12	.	BED_feature	9541109	9541163	.	.	.	Name=9632670
chr12	.	BED_feature	9596066	9596154	.	.	.	Name=9632670
chr12_random	.	BED_feature	286812	286853	.	.	.	Name=9632670
chr10	.	BED_feature	95692837	95692883	.	.	.	Name=2155782
chr2	.	BED_feature	172385321	172385350	.	.	.	Name=9712644
chr14	.	BED_feature	19110785	19110913	.	.	.	Name=2454390
chr14	.	BED_feature	19142284	19142414	.	.	.	Name=2454390
chr1	.	BED_feature	97290829	97291185	.	.	.	Name=1869549
chr10	.	BED_feature	109920808	109920836	.	.	.	Name=11955627
chr1	.	BED_feature	154653086	154653116	.	.	.	Name=11955627
chr17	.	BED_feature	48289921	48289961	.	.	.	Name=2011515
chr9	.	BED_feature	86012059	86012095	.	.	.	Name=1655408
chr14	.	BED_feature	21847810	21847906	.	.	.	Name=9252424
chr2	.	BED_feature	95334254	95334289	.	.	.	Name=9756936
chr16	.	BED_feature	89939108	89939142	.	.	.	Name=11509565
chr1	.	BED_feature	78761021	78761064	.	.	.	Name=2388627
chr5	.	BED_feature	80324942	80324968	.	.	.	Name=1717823
chr1	.	BED_feature	154653098	154653129	.	.	.	Name=7499393
chr10	.	BED_feature	82582872	82582904	.	.	.	Name=12010125
chr10	.	BED_feature	82587871	82587900	.	.	.	Name=12010125
chr20	.	BED_feature	11570121	11570153	.	.	.	Name=12010125
chr6	.	BED_feature	128386883	128386944	.	.	.	Name=1549467
chr6	.	BED_feature	128436438	128436537	.	.	.	Name=1549467
chr1	.	BED_feature	161658868	161658950	.	.	.	Name=7828582
chr1	.	BED_feature	161662319	161662382	.	.	.	Name=7828582
chr1	.	BED_feature	202936490	202936523	.	.	.	Name=2552288
chr20	.	BED_feature	32000190	32000224	.	.	.	Name=10640442
chr12	.	BED_feature	8296010	8296065	.	.	.	Name=1358758
chr1	.	BED_feature	258000874	258000924	.	.	.	Name=1358758
chr4	.	BED_feature	120355609	120355637	.	.	.	Name=9174059
chr20	.	BED_feature	4636224	4636265	.	.	.	Name=10986117
chr2_random	.	BED_feature	3022510	3022541	.	.	.	Name=9464279
chr20_random	.	BED_feature	40467	40502	.	.	.	Name=2555174
chr20	.	BED_feature	2646428	2646490	.	.	.	Name=2555174
chr20	.	BED_feature	3409895	3409932	.	.	.	Name=2555174
chr20	.	BED_feature	3468403	3468439	.	.	.	Name=2555174
chr20	.	BED_feature	3555765	3555801	.	.	.	Name=2555174
chr20	.	BED_feature	4998443	4998480	.	.	.	Name=2555174
chr20	.	BED_feature	5056563	5056600	.	.	.	Name=2555174
chr7	.	BED_feature	114015510	114015668	.	.	.	Name=8625802
chr6	.	BED_feature	139276089	139276214	.	.	.	Name=8625802
chr2	.	BED_feature	120968978	120971415	.	.	.	Name=8625802
chr2	.	BED_feature	121155103	121155493	.	.	.	Name=8625802
chr2	.	BED_feature	137574739	137575993	.	.	.	Name=8625802
chrX	.	BED_feature	146510409	146511733	.	.	.	Name=8625802
chr17	.	BED_feature	91004378	91004637	.	.	.	Name=8625802
chr16	.	BED_feature	82007130	82007983	.	.	.	Name=8625802
chr16	.	BED_feature	82009208	82009325	.	.	.	Name=8625802
chr15	.	BED_feature	77298063	77298283	.	.	.	Name=8625802
chr15	.	BED_feature	77300425	77301661	.	.	.	Name=8625802
chr15	.	BED_feature	77303609	77303680	.	.	.	Name=8625802
chr15	.	BED_feature	103122684	103122943	.	.	.	Name=8625802
chr8	.	BED_feature	104738235	104738483	.	.	.	Name=8625802
chr1	.	BED_feature	240316239	240316283	.	.	.	Name=12384280
chr7	.	BED_feature	140523539	140523575	.	.	.	Name=1406681
chr6	.	BED_feature	31079810	31079847	.	.	.	Name=1406681
chr6	.	BED_feature	80532952	80533645	.	.	.	Name=1406681
chr6	.	BED_feature	83786388	83786555	.	.	.	Name=1406681
chr6	.	BED_feature	135414912	135415048	.	.	.	Name=1406681
chr5	.	BED_feature	36372664	36373037	.	.	.	Name=1406681
chr5	.	BED_feature	123984235	123984853	.	.	.	Name=1406681
chr5	.	BED_feature	145207154	145207290	.	.	.	Name=1406681
chr3	.	BED_feature	36635546	36636263	.	.	.	Name=1406681
chr3	.	BED_feature	83669418	83670112	.	.	.	Name=1406681
chr3	.	BED_feature	84729562	84730254	.	.	.	Name=1406681
chr2	.	BED_feature	18125794	18126300	.	.	.	Name=1406681
chr2	.	BED_feature	73041142	73041836	.	.	.	Name=1406681
chr2	.	BED_feature	78744790	78745497	.	.	.	Name=1406681
chr2	.	BED_feature	170307487	170308190	.	.	.	Name=1406681
chr2	.	BED_feature	174025968	174026672	.	.	.	Name=1406681
chr2	.	BED_feature	223129728	223130032	.	.	.	Name=1406681
chr1	.	BED_feature	106346777	106347489	.	.	.	Name=1406681
chr1	.	BED_feature	123765543	123765900	.	.	.	Name=1406681
chr15	.	BED_feature	62765794	62766509	.	.	.	Name=1406681
chr9	.	BED_feature	11037644	11038897	.	.	.	Name=1406681
chr9	.	BED_feature	25152173	25152851	.	.	.	Name=1406681
chr9	.	BED_feature	42474741	42475492	.	.	.	Name=1406681
chr9	.	BED_feature	50106927	50106979	.	.	.	Name=1406681
chr9	.	BED_feature	57733721	57733811	.	.	.	Name=1406681
chr9	.	BED_feature	93406237	93406297	.	.	.	Name=1406681
chr8	.	BED_feature	39475607	39476005	.	.	.	Name=1406681
chr8	.	BED_feature	88315848	88316563	.	.	.	Name=1406681
chr13	.	BED_feature	2231203	2231322	.	.	.	Name=1406681
chr13	.	BED_feature	22886639	22886775	.	.	.	Name=1406681
chr16	.	BED_feature	64644795	64644858	.	.	.	Name=1406681
chr6_random	.	BED_feature	21172	21797	.	.	.	Name=1406681
chr14	.	BED_feature	70509837	70510407	.	.	.	Name=1406681
chr14	.	BED_feature	87563709	87564093	.	.	.	Name=1406681
chrUn	.	BED_feature	42219679	42219745	.	.	.	Name=1406681
chrUn	.	BED_feature	73050413	73050514	.	.	.	Name=1406681
chr19	.	BED_feature	34283395	34284137	.	.	.	Name=1406681
chrX	.	BED_feature	81946176	81946308	.	.	.	Name=1406681
chrX	.	BED_feature	106098539	106099101	.	.	.	Name=1406681
chrX	.	BED_feature	106808583	106808720	.	.	.	Name=1406681
chrX	.	BED_feature	106992317	106992748	.	.	.	Name=1406681
chrX	.	BED_feature	120503400	120503828	.	.	.	Name=1406681
chrX	.	BED_feature	131350580	131350664	.	.	.	Name=1406681
chrX	.	BED_feature	141824752	141825452	.	.	.	Name=1406681
chr4	.	BED_feature	158103486	158103531	.	.	.	Name=2479916
chr19	.	BED_feature	26190656	26190706	.	.	.	Name=2547796
chr4	.	BED_feature	78827973	78828212	.	.	.	Name=2547796
chr16	.	BED_feature	13318994	13319040	.	.	.	Name=2547796
chr1	.	BED_feature	73096777	73096825	.	.	.	Name=2547796
chr18	.	BED_feature	83076552	83077187	.	.	.	Name=2005901
chr6	.	BED_feature	14985892	14986418	.	.	.	Name=2005901
chr6	.	BED_feature	23664341	23664625	.	.	.	Name=2005901
chr6	.	BED_feature	64172068	64172842	.	.	.	Name=2005901
chr6	.	BED_feature	127304348	127305042	.	.	.	Name=2005901
chr5	.	BED_feature	25294683	25295361	.	.	.	Name=2005901
chr5	.	BED_feature	81560512	81560554	.	.	.	Name=2005901
chr5	.	BED_feature	130924973	130925713	.	.	.	Name=2005901
chr5	.	BED_feature	167402250	167405212	.	.	.	Name=2005901
chr4	.	BED_feature	89799038	89799689	.	.	.	Name=2005901
chr4	.	BED_feature	154051343	154052264	.	.	.	Name=2005901
chr3	.	BED_feature	55201792	55202713	.	.	.	Name=2005901
chr3	.	BED_feature	66685187	66686036	.	.	.	Name=2005901
chr3	.	BED_feature	71112137	71112785	.	.	.	Name=2005901
chr3	.	BED_feature	85607216	85607750	.	.	.	Name=2005901
chr3	.	BED_feature	103228338	103228777	.	.	.	Name=2005901
chr3	.	BED_feature	136274325	136275069	.	.	.	Name=2005901
chr3	.	BED_feature	144110491	144111247	.	.	.	Name=2005901
chr2	.	BED_feature	165012790	165013084	.	.	.	Name=2005901
chr2	.	BED_feature	174389982	174390338	.	.	.	Name=2005901
chr2	.	BED_feature	178470053	178470703	.	.	.	Name=2005901
chr2	.	BED_feature	186081557	186082318	.	.	.	Name=2005901
chr1	.	BED_feature	106191006	106191855	.	.	.	Name=2005901
chr1	.	BED_feature	171346716	171347440	.	.	.	Name=2005901
chr1	.	BED_feature	222252313	222253089	.	.	.	Name=2005901
chr9	.	BED_feature	52001362	52001893	.	.	.	Name=2005901
chr9	.	BED_feature	66781380	66782133	.	.	.	Name=2005901
chrX	.	BED_feature	41099157	41099927	.	.	.	Name=2005901
chrX	.	BED_feature	86260155	86261037	.	.	.	Name=2005901
chr13	.	BED_feature	71982147	71982779	.	.	.	Name=2005901
chr11	.	BED_feature	22930447	22931154	.	.	.	Name=2005901
chr10	.	BED_feature	44889483	44890201	.	.	.	Name=2005901
chr10	.	BED_feature	53300163	53300307	.	.	.	Name=2005901
chr10	.	BED_feature	88930811	88931356	.	.	.	Name=2005901
chr17	.	BED_feature	34304730	34305481	.	.	.	Name=2005901
chr16	.	BED_feature	24233492	24234263	.	.	.	Name=2005901
chr16	.	BED_feature	36523622	36524467	.	.	.	Name=2005901
chr15	.	BED_feature	8792276	8792305	.	.	.	Name=2005901
chr15	.	BED_feature	12501946	12502378	.	.	.	Name=2005901
chr15	.	BED_feature	22783120	22783160	.	.	.	Name=2005901
chr15	.	BED_feature	27983964	27984038	.	.	.	Name=2005901
chr14	.	BED_feature	18733882	18734697	.	.	.	Name=2005901
chrUn	.	BED_feature	12670679	12670862	.	.	.	Name=2005901
chr8	.	BED_feature	35315946	35316663	.	.	.	Name=2005901
chr8	.	BED_feature	113075837	113076605	.	.	.	Name=2005901
chr7	.	BED_feature	24531798	24531830	.	.	.	Name=9395525
chr17	.	BED_feature	53131798	53131831	.	.	.	Name=12813463
chr3_random	.	BED_feature	930756	930827	.	.	.	Name=9454838
chr1	.	BED_feature	76254922	76255087	.	.	.	Name=15337603
chr10	.	BED_feature	28527478	28527527	.	.	.	Name=9478977
chr10	.	BED_feature	28533062	28533222	.	.	.	Name=9478977
chr14	.	BED_feature	45723217	45723246	.	.	.	Name=9478977
chr7	.	BED_feature	104035608	104035780	.	.	.	Name=1406708
chr17	.	BED_feature	44709067	44709095	.	.	.	Name=3244361
chr17	.	BED_feature	28309949	28309990	.	.	.	Name=11278891
chr4	.	BED_feature	165389258	165389286	.	.	.	Name=9242644
chr11	.	BED_feature	81471199	81471237	.	.	.	Name=10660604
chr15	.	BED_feature	10518099	10518126	.	.	.	Name=10660604
chr6	.	BED_feature	26931362	26932057	.	.	.	Name=2586521
chr6	.	BED_feature	26933509	26933558	.	.	.	Name=2586521
chr2	.	BED_feature	212297457	212297487	.	.	.	Name=10377075
chr1	.	BED_feature	97290921	97290965	.	.	.	Name=8065357
chr4	.	BED_feature	182898553	182898623	.	.	.	Name=2181446
chr7	.	BED_feature	139891415	139891863	.	.	.	Name=2479823
chr7	.	BED_feature	140011922	140012881	.	.	.	Name=2479823
chr7	.	BED_feature	136708096	136708571	.	.	.	Name=10652357
chr8	.	BED_feature	48907765	48907795	.	.	.	Name=12848620
chr16	.	BED_feature	7975040	7975080	.	.	.	Name=10973977
chr6	.	BED_feature	109559290	109559347	.	.	.	Name=7791782
chr1	.	BED_feature	208090838	208091088	.	.	.	Name=7791782
chr10	.	BED_feature	70256300	70256356	.	.	.	Name=2106664
chr10	.	BED_feature	70257551	70258029	.	.	.	Name=2106664
chr6	.	BED_feature	26931942	26931969	.	.	.	Name=7609882
chr13	.	BED_feature	80234981	80235020	.	.	.	Name=10988288
chr12	.	BED_feature	27707602	27707682	.	.	.	Name=7896732
chr7	.	BED_feature	139452799	139452865	.	.	.	Name=1717824
chr19	.	BED_feature	41616254	41616300	.	.	.	Name=1717824
chr2	.	BED_feature	209447546	209447595	.	.	.	Name=1717824
chr2	.	BED_feature	209478540	209478590	.	.	.	Name=1717824
chr2	.	BED_feature	209482204	209482254	.	.	.	Name=1717824
chr2	.	BED_feature	209518567	209518614	.	.	.	Name=1717824
chrUn	.	BED_feature	57509250	57509414	.	.	.	Name=8964505
chr5	.	BED_feature	157654589	157654799	.	.	.	Name=12188923
chr17	.	BED_feature	44709021	44709206	.	.	.	Name=3683387
chr5	.	BED_feature	66296325	66296355	.	.	.	Name=12466545
chr6	.	BED_feature	55895760	55895951	.	.	.	Name=8098844
chr6	.	BED_feature	55955924	55957044	.	.	.	Name=8098844
chrX_random	.	BED_feature	1831767	1831958	.	.	.	Name=8098844
chr8	.	BED_feature	5783962	5783999	.	.	.	Name=9058379
chr10	.	BED_feature	53776842	53776882	.	.	.	Name=2830491
chr4	.	BED_feature	126331069	126331108	.	.	.	Name=8016112
chr10	.	BED_feature	53800559	53800643	.	.	.	Name=2999140
chr19	.	BED_feature	25703365	25703401	.	.	.	Name=12917378
chr2	.	BED_feature	36432961	36432992	.	.	.	Name=12917378
chr11	.	BED_feature	81471196	81471231	.	.	.	Name=9556573
chr13	.	BED_feature	48867700	48867826	.	.	.	Name=12505064
chr2	.	BED_feature	180483707	180483735	.	.	.	Name=2175918
chr6	.	BED_feature	13161174	13161439	.	.	.	Name=11451360
chr1	.	BED_feature	205852196	205852261	.	.	.	Name=12493735
chr6	.	BED_feature	26931645	26931680	.	.	.	Name=12145309
chr3	.	BED_feature	136743229	136743302	.	.	.	Name=1732730
chr6	.	BED_feature	48025824	48025859	.	.	.	Name=1732732
chr4	.	BED_feature	158185719	158185812	.	.	.	Name=1694011
chr4	.	BED_feature	158283658	158283750	.	.	.	Name=1694011
chr4	.	BED_feature	158371449	158371541	.	.	.	Name=1694011
chr4	.	BED_feature	158630997	158631088	.	.	.	Name=1694011
chr1	.	BED_feature	62324045	62324077	.	.	.	Name=10594026
chr8	.	BED_feature	38028962	38028994	.	.	.	Name=10594026
chr11	.	BED_feature	81471203	81471237	.	.	.	Name=10708554
chr2	.	BED_feature	95334254	95334290	.	.	.	Name=8969196
chr16	.	BED_feature	7975041	7975081	.	.	.	Name=8969196
chr2	.	BED_feature	94554721	94554750	.	.	.	Name=10075714
chr16	.	BED_feature	17570716	17570762	.	.	.	Name=8928809
chr5	.	BED_feature	19717001	19717032	.	.	.	Name=9875228
chr12	.	BED_feature	35664745	35664778	.	.	.	Name=8366095
chr15	.	BED_feature	33068994	33069065	.	.	.	Name=8366095
chr19	.	BED_feature	39850452	39850479	.	.	.	Name=1584217
chr2	.	BED_feature	95334254	95334288	.	.	.	Name=10196233
chr20_random	.	BED_feature	40468	40502	.	.	.	Name=11297551
chr20_random	.	BED_feature	89201	89235	.	.	.	Name=11297551
chr20	.	BED_feature	3409895	3409931	.	.	.	Name=11297551
chr20	.	BED_feature	3468403	3468438	.	.	.	Name=11297551
chr20	.	BED_feature	3555766	3555801	.	.	.	Name=11297551
chr20	.	BED_feature	4998443	4998479	.	.	.	Name=11297551
chr20	.	BED_feature	5056563	5056599	.	.	.	Name=11297551
chr7	.	BED_feature	137223756	137223785	.	.	.	Name=1328867
chr8	.	BED_feature	82724143	82724194	.	.	.	Name=16198230
chr15	.	BED_feature	33068731	33068775	.	.	.	Name=8537395
chr4	.	BED_feature	104412024	104412065	.	.	.	Name=9099714
chr3	.	BED_feature	118194035	118194191	.	.	.	Name=8195142
chr5	.	BED_feature	17514005	17514366	.	.	.	Name=9030569
chr7	.	BED_feature	2230889	2230993	.	.	.	Name=1315319
chr7	.	BED_feature	2235953	2236200	.	.	.	Name=1315319
chr7	.	BED_feature	2237965	2238851	.	.	.	Name=1315319
chr7	.	BED_feature	2240118	2242058	.	.	.	Name=1315319
chr7	.	BED_feature	2244990	2245138	.	.	.	Name=1315319
chr7	.	BED_feature	2247708	2248383	.	.	.	Name=1315319
chr7	.	BED_feature	2250257	2251833	.	.	.	Name=1315319
chr7	.	BED_feature	2264296	2264914	.	.	.	Name=1315319
chr7	.	BED_feature	2268747	2269326	.	.	.	Name=1315319
chr18	.	BED_feature	30199964	30200062	.	.	.	Name=3441006
chr2	.	BED_feature	133015600	133015640	.	.	.	Name=3441006
chr1	.	BED_feature	185972979	185973069	.	.	.	Name=3441006
chr1	.	BED_feature	185974485	185975490	.	.	.	Name=3441006
chr14	.	BED_feature	87968314	87968342	.	.	.	Name=9030565
chr15	.	BED_feature	60794027	60794055	.	.	.	Name=10395650
chrX	.	BED_feature	26568279	26568315	.	.	.	Name=10395650
chrX	.	BED_feature	26571542	26571580	.	.	.	Name=10395650
chr1	.	BED_feature	205848280	205848607	.	.	.	Name=10956641
chr4	.	BED_feature	116975599	116975634	.	.	.	Name=8663388
chr14	.	BED_feature	35418313	35418365	.	.	.	Name=7615828
chr15	.	BED_feature	83103032	83103065	.	.	.	Name=12568725
chr17	.	BED_feature	6287888	6287919	.	.	.	Name=14563703
chr13	.	BED_feature	96309607	96309637	.	.	.	Name=11278663
chr2	.	BED_feature	174775178	174775259	.	.	.	Name=3499668
chr11	.	BED_feature	67609817	67609854	.	.	.	Name=10896677
chr10	.	BED_feature	664792	664820	.	.	.	Name=10896677
chr10	.	BED_feature	666718	666745	.	.	.	Name=10896677
chr6	.	BED_feature	103124701	103124740	.	.	.	Name=7575462
chr8	.	BED_feature	4315526	4315554	.	.	.	Name=1850695
chr1	.	BED_feature	206632401	206632440	.	.	.	Name=7592662
chr14	.	BED_feature	19142320	19142351	.	.	.	Name=2711183
chr1	.	BED_feature	203172022	203172059	.	.	.	Name=16165221
chr5	.	BED_feature	24455788	24455867	.	.	.	Name=3035717
chr4	.	BED_feature	173815403	173815466	.	.	.	Name=3035717
chr4	.	BED_feature	173852417	173852480	.	.	.	Name=3035717
chr17	.	BED_feature	48465673	48465812	.	.	.	Name=3035717
chr17	.	BED_feature	48519755	48519834	.	.	.	Name=3035717
chr17	.	BED_feature	48523724	48523879	.	.	.	Name=3035717
chr17	.	BED_feature	48775745	48775897	.	.	.	Name=3035717
chr17	.	BED_feature	50113536	50113801	.	.	.	Name=3035717
chr17	.	BED_feature	50332550	50332689	.	.	.	Name=3035717
chr17	.	BED_feature	50339161	50339316	.	.	.	Name=3035717
chr17	.	BED_feature	50391420	50391575	.	.	.	Name=3035717
chr17	.	BED_feature	50410855	50410994	.	.	.	Name=3035717
chr2	.	BED_feature	191075807	191076046	.	.	.	Name=3035717
chr8	.	BED_feature	58583593	58585211	.	.	.	Name=8144606
chr13	.	BED_feature	48829906	48829943	.	.	.	Name=8413291
chr1	.	BED_feature	155389341	155389374	.	.	.	Name=9211912
chrX	.	BED_feature	85948906	85948939	.	.	.	Name=12841583
chr10	.	BED_feature	95694106	95694356	.	.	.	Name=2745428
chr1	.	BED_feature	258000870	258000907	.	.	.	Name=16055439
chr5	.	BED_feature	17513956	17514362	.	.	.	Name=8232318
chr7	.	BED_feature	20348755	20348787	.	.	.	Name=10082537
chr5	.	BED_feature	139859998	139860030	.	.	.	Name=10082537
chr4	.	BED_feature	119854763	119854795	.	.	.	Name=10082537
chr3	.	BED_feature	143750249	143750278	.	.	.	Name=10082537
chr1	.	BED_feature	175179477	175179509	.	.	.	Name=10082537
chr9	.	BED_feature	110546715	110546747	.	.	.	Name=10082537
chr10	.	BED_feature	40444613	40444645	.	.	.	Name=10082537
chr10	.	BED_feature	44043304	44043336	.	.	.	Name=10082537
chr19	.	BED_feature	21185693	21185724	.	.	.	Name=10082537
chr1_random	.	BED_feature	3871143	3871176	.	.	.	Name=10082537
chr13	.	BED_feature	46262766	46262805	.	.	.	Name=15792957
chr10	.	BED_feature	95694268	95694326	.	.	.	Name=2909514
chr7	.	BED_feature	20348058	20349168	.	.	.	Name=2247479
chr7	.	BED_feature	70298136	70298199	.	.	.	Name=2247479
chr6	.	BED_feature	70354276	70354542	.	.	.	Name=2247479
chr6	.	BED_feature	133082151	133083081	.	.	.	Name=2247479
chr5	.	BED_feature	6275485	6276397	.	.	.	Name=2247479
chr5	.	BED_feature	139859184	139860110	.	.	.	Name=2247479
chr5	.	BED_feature	139863889	139864450	.	.	.	Name=2247479
chr4	.	BED_feature	119854135	119855181	.	.	.	Name=2247479
chr4	.	BED_feature	169092274	169092364	.	.	.	Name=2247479
chr3	.	BED_feature	51272285	51273397	.	.	.	Name=2247479
chr3	.	BED_feature	143749837	143750919	.	.	.	Name=2247479
chr2	.	BED_feature	14253134	14253530	.	.	.	Name=2247479
chr1	.	BED_feature	80026397	80027532	.	.	.	Name=2247479
chr1	.	BED_feature	102489386	102489756	.	.	.	Name=2247479
chr1	.	BED_feature	102992035	102992318	.	.	.	Name=2247479
chr1	.	BED_feature	106199077	106199114	.	.	.	Name=2247479
chr1	.	BED_feature	106201864	106202525	.	.	.	Name=2247479
chr1	.	BED_feature	175179034	175180207	.	.	.	Name=2247479
chr9	.	BED_feature	110546072	110547179	.	.	.	Name=2247479
chr8	.	BED_feature	77796418	77796507	.	.	.	Name=2247479
chr8	.	BED_feature	83946536	83946581	.	.	.	Name=2247479
chr11	.	BED_feature	4594931	4595910	.	.	.	Name=2247479
chr10	.	BED_feature	40444169	40445298	.	.	.	Name=2247479
chr10	.	BED_feature	44042141	44043989	.	.	.	Name=2247479
chr10	.	BED_feature	56783680	56783745	.	.	.	Name=2247479
chr17	.	BED_feature	55638303	55638455	.	.	.	Name=2247479
chr17	.	BED_feature	59194875	59195997	.	.	.	Name=2247479
chr14	.	BED_feature	17065459	17066754	.	.	.	Name=2247479
chr14	.	BED_feature	111622954	111623002	.	.	.	Name=2247479
chr19	.	BED_feature	8117803	8118410	.	.	.	Name=2247479
chr19	.	BED_feature	21185046	21186127	.	.	.	Name=2247479
chrX	.	BED_feature	47406747	47407102	.	.	.	Name=2247479
chr1_random	.	BED_feature	3870551	3871524	.	.	.	Name=2247479
chr16	.	BED_feature	19045993	19046073	.	.	.	Name=9328356
chr1	.	BED_feature	201389131	201389160	.	.	.	Name=1870124
chr14	.	BED_feature	19142261	19142290	.	.	.	Name=3169549
chr1	.	BED_feature	154651721	154651751	.	.	.	Name=2341405
chr15	.	BED_feature	33068830	33068859	.	.	.	Name=1328857
chr8	.	BED_feature	91956211	91956240	.	.	.	Name=1328857
chr7	.	BED_feature	139452731	139452944	.	.	.	Name=3352608
chr4	.	BED_feature	103908886	103908942	.	.	.	Name=1729611
chr2_random	.	BED_feature	3022491	3022519	.	.	.	Name=7913466
chr1	.	BED_feature	163327124	163327175	.	.	.	Name=8120047
chr13	.	BED_feature	19107284	19108726	.	.	.	Name=7913462
chr12	.	BED_feature	21478629	21478724	.	.	.	Name=7913462
chr12	.	BED_feature	21479816	21480655	.	.	.	Name=7913462
chr12	.	BED_feature	21482683	21483542	.	.	.	Name=7913462
chr12	.	BED_feature	21501022	21501328	.	.	.	Name=7913462
chr12	.	BED_feature	21504989	21505178	.	.	.	Name=7913462
chr12	.	BED_feature	21510880	21510992	.	.	.	Name=7913462
chr12	.	BED_feature	21515572	21516930	.	.	.	Name=7913462
chr12	.	BED_feature	35901884	35901946	.	.	.	Name=7913462
chr12	.	BED_feature	35904908	35904996	.	.	.	Name=7913462
chr18	.	BED_feature	66312590	66312649	.	.	.	Name=7913462
chr18	.	BED_feature	66318409	66318542	.	.	.	Name=7913462
chr18	.	BED_feature	66326668	66326715	.	.	.	Name=7913462
chr18	.	BED_feature	66327812	66327891	.	.	.	Name=7913462
chr18	.	BED_feature	66330331	66330411	.	.	.	Name=7913462
chr18	.	BED_feature	66333040	66333223	.	.	.	Name=7913462
chr18	.	BED_feature	66352910	66353047	.	.	.	Name=7913462
chr18	.	BED_feature	66354980	66355144	.	.	.	Name=7913462
chr18	.	BED_feature	66358387	66359978	.	.	.	Name=7913462
chr7	.	BED_feature	10809379	10809585	.	.	.	Name=7913462
chr1	.	BED_feature	203171680	203171722	.	.	.	Name=7913462
chr1	.	BED_feature	23506892	23508078	.	.	.	Name=8647846
chr10	.	BED_feature	90393458	90393489	.	.	.	Name=12556524
chr1	.	BED_feature	9014799	9015335	.	.	.	Name=2017183
chr1	.	BED_feature	9020505	9020678	.	.	.	Name=2017183
chr1	.	BED_feature	9023160	9024837	.	.	.	Name=2017183
chr1	.	BED_feature	9029876	9031714	.	.	.	Name=2017183
chr6	.	BED_feature	138450710	138450752	.	.	.	Name=2536161
chr8	.	BED_feature	61461105	61461178	.	.	.	Name=2536161
chr11	.	BED_feature	81471199	81471236	.	.	.	Name=8390676
chr2	.	BED_feature	181214726	181214790	.	.	.	Name=2586516
chr6	.	BED_feature	26931935	26931971	.	.	.	Name=2061309
chr10	.	BED_feature	95694278	95694306	.	.	.	Name=2358443
chr5	.	BED_feature	143982940	143984529	.	.	.	Name=1652060
chr1	.	BED_feature	95892871	95892955	.	.	.	Name=16087728
chr10	.	BED_feature	95694277	95694305	.	.	.	Name=8382533
chr3	.	BED_feature	164012083	164012111	.	.	.	Name=8382533
chr15	.	BED_feature	33068823	33068861	.	.	.	Name=9111345
chr1	.	BED_feature	200918369	200918409	.	.	.	Name=2388615
chr7	.	BED_feature	80014129	80014162	.	.	.	Name=15860457
chr4	.	BED_feature	159190580	159190614	.	.	.	Name=15860457
chr1	.	BED_feature	205295186	205295222	.	.	.	Name=15860457
chr19	.	BED_feature	37266477	37266518	.	.	.	Name=9264553
chr8	.	BED_feature	83313649	83313688	.	.	.	Name=9264553
chr8	.	BED_feature	83316460	83316499	.	.	.	Name=9264553
chr3	.	BED_feature	13783503	13783539	.	.	.	Name=7885844
chr2	.	BED_feature	191044263	191044302	.	.	.	Name=7885844
chr3	.	BED_feature	75548102	75549203	.	.	.	Name=7892230
chr1	.	BED_feature	95027231	95028125	.	.	.	Name=7892230
chr1	.	BED_feature	95029405	95032465	.	.	.	Name=7892230
chr15	.	BED_feature	47303028	47303121	.	.	.	Name=8838143
chr3	.	BED_feature	164012306	164012334	.	.	.	Name=9786935
chr1	.	BED_feature	154651967	154652069	.	.	.	Name=2925653
chr9	.	BED_feature	65714904	65715023	.	.	.	Name=1847512
chr10	.	BED_feature	95694199	95694316	.	.	.	Name=8144557
chr6	.	BED_feature	42178108	42178450	.	.	.	Name=1309950
chr3	.	BED_feature	158101548	158101667	.	.	.	Name=1309950
chrX	.	BED_feature	52445630	52446887	.	.	.	Name=1309950
chr3	.	BED_feature	44441288	44441317	.	.	.	Name=1651499
chr1	.	BED_feature	205848583	205848676	.	.	.	Name=12107181
chr1	.	BED_feature	205886159	205886188	.	.	.	Name=12107181
chr13	.	BED_feature	87039698	87040484	.	.	.	Name=12643284
chr3	.	BED_feature	154459843	154459899	.	.	.	Name=2279702
chr3	.	BED_feature	154482822	154483158	.	.	.	Name=2279702
chr1	.	BED_feature	203171510	203172300	.	.	.	Name=2884660
chr2	.	BED_feature	180483713	180483741	.	.	.	Name=8612541
chr2	.	BED_feature	180483406	180483435	.	.	.	Name=8612540
chr2	.	BED_feature	182784707	182784953	.	.	.	Name=8793102
chr2	.	BED_feature	182787267	182787383	.	.	.	Name=8793102
chr2	.	BED_feature	182789356	182789416	.	.	.	Name=8793102
chr1	.	BED_feature	97291101	97291130	.	.	.	Name=10601277
chr7	.	BED_feature	120765073	120765114	.	.	.	Name=8289814
chr7	.	BED_feature	120783234	120783275	.	.	.	Name=8289814
chr7	.	BED_feature	104035613	104035727	.	.	.	Name=2775280
chr10	.	BED_feature	89471417	89471519	.	.	.	Name=10801800
chr1	.	BED_feature	81944732	81944764	.	.	.	Name=9722582
chr1	.	BED_feature	155389340	155389372	.	.	.	Name=9722582
chr3	.	BED_feature	44441054	44441355	.	.	.	Name=3062372
chr4	.	BED_feature	21709926	21709984	.	.	.	Name=8891341
chr4	.	BED_feature	21828018	21829568	.	.	.	Name=8891341
chr20_random	.	BED_feature	40457	40502	.	.	.	Name=2501084
chr20_random	.	BED_feature	89201	89236	.	.	.	Name=2501084
chr20	.	BED_feature	3409895	3409932	.	.	.	Name=2501084
chr20	.	BED_feature	3425429	3425469	.	.	.	Name=2501084
chr20	.	BED_feature	3468403	3468439	.	.	.	Name=2501084
chr20	.	BED_feature	3513857	3513896	.	.	.	Name=2501084
chr20	.	BED_feature	3555755	3555801	.	.	.	Name=2501084
chr20	.	BED_feature	4998443	4998490	.	.	.	Name=2501084
chr20	.	BED_feature	5056563	5056610	.	.	.	Name=2501084
chr2	.	BED_feature	180483681	180483774	.	.	.	Name=2153298
chr12	.	BED_feature	9541108	9541165	.	.	.	Name=10600171
chr12	.	BED_feature	9596069	9596154	.	.	.	Name=10600171
chr12_random	.	BED_feature	286812	286853	.	.	.	Name=10600171
chr4	.	BED_feature	152057521	152057550	.	.	.	Name=8910484
chr5	.	BED_feature	165071745	165073864	.	.	.	Name=2967498
chr5	.	BED_feature	165200541	165200948	.	.	.	Name=2967498
chr4	.	BED_feature	184900213	184900300	.	.	.	Name=8663213
chr10	.	BED_feature	83620725	83620765	.	.	.	Name=8663211
chr17	.	BED_feature	44344418	44344480	.	.	.	Name=10076996
chr3	.	BED_feature	6052523	6052554	.	.	.	Name=8613746
chr1	.	BED_feature	159277325	159277731	.	.	.	Name=8613746
chr6	.	BED_feature	26931687	26931782	.	.	.	Name=1508198
chr6	.	BED_feature	26935227	26935264	.	.	.	Name=1508198
chr10	.	BED_feature	95694185	95694257	.	.	.	Name=8636081
chr1	.	BED_feature	95892857	95892900	.	.	.	Name=8636081
chr5	.	BED_feature	165074077	165074115	.	.	.	Name=8264645
chr18	.	BED_feature	12406443	12406471	.	.	.	Name=2601716
chr2	.	BED_feature	174775176	174775207	.	.	.	Name=2601716
chr6	.	BED_feature	109558821	109558850	.	.	.	Name=10580097
chr5	.	BED_feature	80324939	80324968	.	.	.	Name=10580097
chr3	.	BED_feature	3459946	3459989	.	.	.	Name=9712664
chr3	.	BED_feature	92572011	92572045	.	.	.	Name=8754772
chr3	.	BED_feature	75542195	75543137	.	.	.	Name=7935418
chr3	.	BED_feature	75547825	75550800	.	.	.	Name=7935418
chr1	.	BED_feature	95029923	95030802	.	.	.	Name=7935418
chr2	.	BED_feature	51736528	51736910	.	.	.	Name=2869036
chr2	.	BED_feature	51745857	51745910	.	.	.	Name=2869036
chr6	.	BED_feature	21417633	21417664	.	.	.	Name=9658104
chr19	.	BED_feature	39853070	39853122	.	.	.	Name=2889531
chr9	.	BED_feature	70772382	70772413	.	.	.	Name=12372417
chr14	.	BED_feature	21847826	21847883	.	.	.	Name=8264581
chr1	.	BED_feature	83489341	83489368	.	.	.	Name=11129950
chr1	.	BED_feature	212163559	212163699	.	.	.	Name=8224520
chr1	.	BED_feature	212298956	212299096	.	.	.	Name=8224520
chr17	.	BED_feature	44709067	44709212	.	.	.	Name=3169002
chr1	.	BED_feature	81230297	81230356	.	.	.	Name=2726759
chr1	.	BED_feature	81266716	81266995	.	.	.	Name=2726759
chr1	.	BED_feature	81345296	81345575	.	.	.	Name=2726759
chr1	.	BED_feature	81408546	81408605	.	.	.	Name=2726759
chr1	.	BED_feature	81628279	81628339	.	.	.	Name=2726759
chr1	.	BED_feature	81780215	81780279	.	.	.	Name=2726759
chr1	.	BED_feature	81840002	81840083	.	.	.	Name=2726759
chr1	.	BED_feature	81867029	81867110	.	.	.	Name=2726759
chr5	.	BED_feature	165074128	165074170	.	.	.	Name=2522932
chr2	.	BED_feature	174775176	174775205	.	.	.	Name=2847919
chr10	.	BED_feature	56410822	56410853	.	.	.	Name=9624121
chr4	.	BED_feature	21829156	21829196	.	.	.	Name=9624121
chr9	.	BED_feature	20158682	20158710	.	.	.	Name=9624121
chr6	.	BED_feature	13161120	13161490	.	.	.	Name=9773974
chr3	.	BED_feature	137776222	137776254	.	.	.	Name=8262963
chr3	.	BED_feature	137792320	137792352	.	.	.	Name=8262963
chr3	.	BED_feature	137861857	137862694	.	.	.	Name=8262963
chr3	.	BED_feature	138088128	138089463	.	.	.	Name=8262963
chr3	.	BED_feature	138233790	138233822	.	.	.	Name=8262963
chr3	.	BED_feature	138333351	138334178	.	.	.	Name=8262963
chr3	.	BED_feature	138495773	138496574	.	.	.	Name=8262963
chr12	.	BED_feature	42931110	42931193	.	.	.	Name=1673926
chr12	.	BED_feature	42936668	42937243	.	.	.	Name=1673926
chr10	.	BED_feature	72081211	72081418	.	.	.	Name=1673926
chr10	.	BED_feature	72086083	72086284	.	.	.	Name=1673926
chr10	.	BED_feature	72162126	72162289	.	.	.	Name=1673926
chr10	.	BED_feature	72168713	72168798	.	.	.	Name=1673926
chr10	.	BED_feature	72186370	72186997	.	.	.	Name=1673926
chr10_random	.	BED_feature	695946	696073	.	.	.	Name=1673926
chr7	.	BED_feature	10791311	10791383	.	.	.	Name=2200736
chr7	.	BED_feature	10813079	10813165	.	.	.	Name=2200736
chr19	.	BED_feature	41616266	41616293	.	.	.	Name=2200736
chr1	.	BED_feature	20998724	20999025	.	.	.	Name=2026618
chr1	.	BED_feature	90576757	90576785	.	.	.	Name=8668155
chr2	.	BED_feature	181214666	181214792	.	.	.	Name=16204235
chr3	.	BED_feature	161554280	161554804	.	.	.	Name=8036172
chr4	.	BED_feature	158103527	158103571	.	.	.	Name=9731707
chr2	.	BED_feature	59677644	59677674	.	.	.	Name=9731707
chr2	.	BED_feature	59680755	59680784	.	.	.	Name=9731707
chr14	.	BED_feature	21847877	21847906	.	.	.	Name=1557422
chr7	.	BED_feature	10419997	10420281	.	.	.	Name=1603088
chr17	.	BED_feature	44709072	44709101	.	.	.	Name=2717408
chr3	.	BED_feature	44441291	44441325	.	.	.	Name=9668074
chr5	.	BED_feature	66296281	66296332	.	.	.	Name=1956774
chr2	.	BED_feature	181214743	181214791	.	.	.	Name=1956774
chr9	.	BED_feature	71966732	71966762	.	.	.	Name=7693708
chr7	.	BED_feature	11164585	11164626	.	.	.	Name=15225122
chr6	.	BED_feature	26931486	26932030	.	.	.	Name=2046665
chr11	.	BED_feature	81471199	81471236	.	.	.	Name=8389766
chr7	.	BED_feature	24458490	24458520	.	.	.	Name=16339156
chr2	.	BED_feature	36432961	36432991	.	.	.	Name=10713139
chrX	.	BED_feature	24685278	24685478	.	.	.	Name=2304462
chrX	.	BED_feature	24696392	24696625	.	.	.	Name=2304462
chr18	.	BED_feature	25027873	25028105	.	.	.	Name=1847666
chr9	.	BED_feature	63212561	63212590	.	.	.	Name=1847666
chr9	.	BED_feature	63234520	63234645	.	.	.	Name=1847666
chr4	.	BED_feature	115454232	115454259	.	.	.	Name=1847666
chr3	.	BED_feature	13783503	13783539	.	.	.	Name=11018030
chr2	.	BED_feature	191044180	191044302	.	.	.	Name=11018030
chr5	.	BED_feature	165074299	165074326	.	.	.	Name=15764815
chr17	.	BED_feature	28309968	28310005	.	.	.	Name=15764815
chr7	.	BED_feature	24531801	24531832	.	.	.	Name=8702983
chr11	.	BED_feature	79124935	79124965	.	.	.	Name=8702983
chr14	.	BED_feature	19110766	19110885	.	.	.	Name=2455718
chr6	.	BED_feature	26931933	26931970	.	.	.	Name=2388831
chr12	.	BED_feature	42919574	42919608	.	.	.	Name=1748280
chr2	.	BED_feature	212297456	212297499	.	.	.	Name=7537851
chr6	.	BED_feature	76920419	76920446	.	.	.	Name=8920965
chr1	.	BED_feature	211761741	211761769	.	.	.	Name=8920965
chr3	.	BED_feature	44441288	44441328	.	.	.	Name=2160464
chr13	.	BED_feature	85793037	85793185	.	.	.	Name=15731358
chr13	.	BED_feature	40500601	40500630	.	.	.	Name=2027757
chr1	.	BED_feature	78324519	78324548	.	.	.	Name=2027757
chr5	.	BED_feature	19716826	19716853	.	.	.	Name=8405996
chrX	.	BED_feature	85946856	85949621	.	.	.	Name=8379933
chr3	.	BED_feature	76307198	76307240	.	.	.	Name=8617799
chr3	.	BED_feature	44441331	44441385	.	.	.	Name=15085339
chr10	.	BED_feature	95694184	95694216	.	.	.	Name=2211620
chr8	.	BED_feature	83313855	83313884	.	.	.	Name=8391636
chr18	.	BED_feature	25622617	25622645	.	.	.	Name=7799965
chr8	.	BED_feature	61793836	61793978	.	.	.	Name=8119192
chr3	.	BED_feature	164012015	164012064	.	.	.	Name=9544984
chr3	.	BED_feature	151428680	151428718	.	.	.	Name=8524227
chr1	.	BED_feature	128843972	128844010	.	.	.	Name=8524227
chr2	.	BED_feature	212297457	212297489	.	.	.	Name=7692229
chr12	.	BED_feature	9541092	9541139	.	.	.	Name=7499421
chr12	.	BED_feature	9596053	9596131	.	.	.	Name=7499421
chr12_random	.	BED_feature	286796	286844	.	.	.	Name=7499421
chr14	.	BED_feature	92788598	92789167	.	.	.	Name=8626808
chr14	.	BED_feature	87950092	87950131	.	.	.	Name=9497382
chr10	.	BED_feature	65036947	65036974	.	.	.	Name=9714306
chr6	.	BED_feature	21417533	21417638	.	.	.	Name=7667089
chr17	.	BED_feature	44710579	44710640	.	.	.	Name=3481434
chr10	.	BED_feature	95694280	95694309	.	.	.	Name=8132622
chr2	.	BED_feature	181214118	181214342	.	.	.	Name=8449904
chr3	.	BED_feature	76301110	76301137	.	.	.	Name=8662964
chr3	.	BED_feature	164011950	164011986	.	.	.	Name=1848696
chr2	.	BED_feature	174727221	174727250	.	.	.	Name=1942067
chr12	.	BED_feature	42919434	42919644	.	.	.	Name=8367288
chr1	.	BED_feature	211761741	211761797	.	.	.	Name=8216221
chr8	.	BED_feature	5784011	5784039	.	.	.	Name=7588292
chr14	.	BED_feature	87950092	87950127	.	.	.	Name=10358076
chr6	.	BED_feature	26931645	26931676	.	.	.	Name=11861523
chr1	.	BED_feature	228933319	228933690	.	.	.	Name=14673170
chr2	.	BED_feature	212297457	212297490	.	.	.	Name=10833420
chr2	.	BED_feature	181214754	181214782	.	.	.	Name=8165139
chr19	.	BED_feature	37266478	37266518	.	.	.	Name=9144242
chr8	.	BED_feature	83313649	83313688	.	.	.	Name=9144242
chr8	.	BED_feature	83316460	83316499	.	.	.	Name=9144242
chr1	.	BED_feature	80309881	80309922	.	.	.	Name=9224955
chr10	.	BED_feature	95694111	95694156	.	.	.	Name=9765286
chr4	.	BED_feature	158103540	158103572	.	.	.	Name=11319221
chr1	.	BED_feature	95892548	95892583	.	.	.	Name=11682622
chr5	.	BED_feature	17161946	17162352	.	.	.	Name=2439693
chr17	.	BED_feature	48290092	48290226	.	.	.	Name=1718964
chr1	.	BED_feature	95892881	95892915	.	.	.	Name=15961509
chr14	.	BED_feature	87950097	87950131	.	.	.	Name=10880363
chr1	.	BED_feature	95892544	95892900	.	.	.	Name=10935547
chr10	.	BED_feature	72460510	72460539	.	.	.	Name=7545164
chr2	.	BED_feature	180483339	180483780	.	.	.	Name=2308930
chr19	.	BED_feature	37266473	37266506	.	.	.	Name=12023900
chr5	.	BED_feature	16139725	16139762	.	.	.	Name=3165490
chr11	.	BED_feature	50537236	50537273	.	.	.	Name=3165490
chr15	.	BED_feature	1142334	1142393	.	.	.	Name=3165490
chr6	.	BED_feature	78009636	78009664	.	.	.	Name=11891324
chr11	.	BED_feature	80031566	80032076	.	.	.	Name=8413271
chr11	.	BED_feature	80109179	80109689	.	.	.	Name=8413271
chr11	.	BED_feature	80169746	80170257	.	.	.	Name=8413271
chrX	.	BED_feature	24685340	24685443	.	.	.	Name=8496174
chr12	.	BED_feature	19555415	19555468	.	.	.	Name=8288642
chr14	.	BED_feature	18813330	18813382	.	.	.	Name=8288642
chr5	.	BED_feature	78091354	78091417	.	.	.	Name=2463987
chr5	.	BED_feature	78165900	78165963	.	.	.	Name=2463987
chr5	.	BED_feature	78218631	78218694	.	.	.	Name=2463987
chr5	.	BED_feature	78244115	78244178	.	.	.	Name=2463987
chr5	.	BED_feature	78270735	78270798	.	.	.	Name=2463987
chr5	.	BED_feature	78316190	78316251	.	.	.	Name=2463987
chr5	.	BED_feature	78409806	78409869	.	.	.	Name=2463987
chr5	.	BED_feature	78440086	78440143	.	.	.	Name=2463987
chr5	.	BED_feature	78490563	78490627	.	.	.	Name=2463987
chr5	.	BED_feature	78644226	78644288	.	.	.	Name=2463987
chr5	.	BED_feature	78683815	78683877	.	.	.	Name=2463987
chr5	.	BED_feature	78709792	78709856	.	.	.	Name=2463987
chr5	.	BED_feature	78770226	78770289	.	.	.	Name=2463987
chr5	.	BED_feature	78805328	78805391	.	.	.	Name=2463987
chr5	.	BED_feature	78820150	78820213	.	.	.	Name=2463987
chr5	.	BED_feature	78911595	78911634	.	.	.	Name=2463987
chr5	.	BED_feature	78936471	78936534	.	.	.	Name=2463987
chr5	.	BED_feature	78990258	78990320	.	.	.	Name=2463987
chr5	.	BED_feature	79017595	79017659	.	.	.	Name=2463987
chr5	.	BED_feature	79083559	79083622	.	.	.	Name=2463987
chr5	.	BED_feature	79101332	79101395	.	.	.	Name=2463987
chr19	.	BED_feature	13962434	13963095	.	.	.	Name=12637567
chr5	.	BED_feature	66296211	66296240	.	.	.	Name=11095981
chr19	.	BED_feature	37266471	37266506	.	.	.	Name=8396148
chr8	.	BED_feature	83313656	83313690	.	.	.	Name=8396148
chr8	.	BED_feature	83316467	83316501	.	.	.	Name=8396148
chr7	.	BED_feature	141772422	141775242	.	.	.	Name=1684715
chr7	.	BED_feature	141778586	141778731	.	.	.	Name=1684715
chr10	.	BED_feature	85020103	85020245	.	.	.	Name=1684715
chr10	.	BED_feature	85032737	85032897	.	.	.	Name=1684715
chr10	.	BED_feature	85036914	85037064	.	.	.	Name=1684715
chr4	.	BED_feature	80490431	80490494	.	.	.	Name=1684715
chr4	.	BED_feature	80502678	80502724	.	.	.	Name=1684715
chr4	.	BED_feature	80506433	80506593	.	.	.	Name=1684715
chr4	.	BED_feature	80515872	80516035	.	.	.	Name=1684715
chr9	.	BED_feature	87036985	87037018	.	.	.	Name=8632018
chr2	.	BED_feature	181178018	181178044	.	.	.	Name=7665553
chr1	.	BED_feature	74359078	74359121	.	.	.	Name=15502011
chr1	.	BED_feature	74605348	74605424	.	.	.	Name=15502011
chr1	.	BED_feature	75708123	75708199	.	.	.	Name=15502011
chr2	.	BED_feature	180483274	180483302	.	.	.	Name=8381969
chr3	.	BED_feature	6666298	6666564	.	.	.	Name=8381967
chr3	.	BED_feature	6670337	6670447	.	.	.	Name=8381967
chr3	.	BED_feature	6678140	6678293	.	.	.	Name=8381967
chr3	.	BED_feature	6683841	6683951	.	.	.	Name=8381967
chr3	.	BED_feature	6685834	6685928	.	.	.	Name=8381967
chr3	.	BED_feature	6689101	6689303	.	.	.	Name=8381967
chr2	.	BED_feature	181214667	181214850	.	.	.	Name=8246989
chr20	.	BED_feature	4636131	4636184	.	.	.	Name=3114745
chr2	.	BED_feature	181214568	181214598	.	.	.	Name=2019572
chr1	.	BED_feature	97291102	97291130	.	.	.	Name=10529375
chr7	.	BED_feature	24531805	24531838	.	.	.	Name=12791769
chr14	.	BED_feature	19142222	19142286	.	.	.	Name=2601696
chr18	.	BED_feature	27343020	27343172	.	.	.	Name=7877619
chr15	.	BED_feature	33068743	33068778	.	.	.	Name=11136726
chr1	.	BED_feature	170639999	170640038	.	.	.	Name=11136726
chr1	.	BED_feature	170642591	170642636	.	.	.	Name=11136726
chr2	.	BED_feature	180483319	180483749	.	.	.	Name=7877617
chr7	.	BED_feature	104035679	104035708	.	.	.	Name=1508216
chr10	.	BED_feature	83622836	83623072	.	.	.	Name=2127540
chr5	.	BED_feature	165062215	165062246	.	.	.	Name=8164667
chr13	.	BED_feature	88048990	88049077	.	.	.	Name=8289804
chr2	.	BED_feature	197102306	197102390	.	.	.	Name=8289804
chr3	.	BED_feature	164012334	164012366	.	.	.	Name=2850495
chr5	.	BED_feature	128719271	128719301	.	.	.	Name=12385751
chr5	.	BED_feature	128736713	128736741	.	.	.	Name=12385751
chr1	.	BED_feature	231981145	231981173	.	.	.	Name=12385751
chr4	.	BED_feature	152057616	152057756	.	.	.	Name=1827795
chr1	.	BED_feature	95027478	95027555	.	.	.	Name=7971966
chr9	.	BED_feature	70771186	70771269	.	.	.	Name=1404598
chr7	.	BED_feature	141164180	141164224	.	.	.	Name=1356762
chr7	.	BED_feature	141165432	141167383	.	.	.	Name=1356762
chr7	.	BED_feature	141182389	141182557	.	.	.	Name=1356762
chr7	.	BED_feature	141188409	141189249	.	.	.	Name=1356762
chr3	.	BED_feature	55445238	55445302	.	.	.	Name=1356762
chr1	.	BED_feature	226420948	226421923	.	.	.	Name=1356762
chr1	.	BED_feature	226444827	226446364	.	.	.	Name=1356762
chr10	.	BED_feature	90393480	90393509	.	.	.	Name=12954759
chr3	.	BED_feature	6052520	6052553	.	.	.	Name=14506227
chr13	.	BED_feature	87039905	87039934	.	.	.	Name=1705013
chr5	.	BED_feature	143983100	143983218	.	.	.	Name=1705013
chr17	.	BED_feature	40685480	40685549	.	.	.	Name=9931418
chr10	.	BED_feature	39220655	39220779	.	.	.	Name=2342469
chr10	.	BED_feature	39221786	39221872	.	.	.	Name=2342469
chr10	.	BED_feature	39223215	39227535	.	.	.	Name=2342469
chr12	.	BED_feature	35664738	35664965	.	.	.	Name=7935447
chr12	.	BED_feature	35664751	35664780	.	.	.	Name=7961957
chr15	.	BED_feature	33068725	33068767	.	.	.	Name=7961957
chr10	.	BED_feature	95694178	95694216	.	.	.	Name=1976240
chr11	.	BED_feature	81471199	81471236	.	.	.	Name=10428876
chr4_random	.	BED_feature	1954229	1954274	.	.	.	Name=12397359
chr2	.	BED_feature	181177987	181178044	.	.	.	Name=8798690
chr3	.	BED_feature	164007861	164007902	.	.	.	Name=2355922
chr8	.	BED_feature	83312932	83313881	.	.	.	Name=2160079
chr8	.	BED_feature	83315617	83316501	.	.	.	Name=2160079
chr4	.	BED_feature	158102468	158103731	.	.	.	Name=2466233
chr1	.	BED_feature	203171633	203171747	.	.	.	Name=10842166
chr14	.	BED_feature	86614943	86614971	.	.	.	Name=1406648
chr11	.	BED_feature	79124924	79124960	.	.	.	Name=2875459
chr3	.	BED_feature	164012298	164012333	.	.	.	Name=2875459
chr2	.	BED_feature	174775176	174775205	.	.	.	Name=1922032
chr20	.	BED_feature	6541437	6541465	.	.	.	Name=10634806
chr6	.	BED_feature	21417658	21417732	.	.	.	Name=9512555
chr5	.	BED_feature	17514717	17514750	.	.	.	Name=2837758
chr11	.	BED_feature	79124931	79124959	.	.	.	Name=2837758
chr14	.	BED_feature	86615062	86615092	.	.	.	Name=12540614
chr10	.	BED_feature	95694277	95694307	.	.	.	Name=1985929
chr3	.	BED_feature	44441220	44441254	.	.	.	Name=8164696
genometools-1.5.1/testdata/bed_files/no_thick_region.bed000066400000000000000000000004401211610345200234040ustar00rootroot00000000000000chr1    11873   14409   uc001aaa.3  0   +   11873   11873   0   3   354,109,1189,   0,739,1347,
chr1    11873   14409   uc010nxq.1  0   +   12189   13639   0   3   354,127,1007,   0,721,1529,
chr1    11873   14409   uc010nxr.1  0   +   11873   11873   0   3   354,52,1189,    0,772,1347,
genometools-1.5.1/testdata/bed_files/no_thick_region.gff3000066400000000000000000000017401211610345200235030ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr1 11874 14409
chr1	.	BED_feature	11874	14409	0	+	.	ID=BED_feature1;Name=uc001aaa.3
chr1	.	BED_block	11874	12227	0	+	.	Parent=BED_feature1;Name=uc001aaa.3
chr1	.	BED_block	12613	12721	0	+	.	Parent=BED_feature1;Name=uc001aaa.3
chr1	.	BED_block	13221	14409	0	+	.	Parent=BED_feature1;Name=uc001aaa.3
###
chr1	.	BED_feature	11874	14409	0	+	.	ID=BED_feature2;Name=uc010nxq.1
chr1	.	BED_block	11874	12227	0	+	.	Parent=BED_feature2;Name=uc010nxq.1
chr1	.	BED_thick_feature	12190	13639	0	+	.	Parent=BED_feature2;Name=uc010nxq.1
chr1	.	BED_block	12595	12721	0	+	.	Parent=BED_feature2;Name=uc010nxq.1
chr1	.	BED_block	13403	14409	0	+	.	Parent=BED_feature2;Name=uc010nxq.1
###
chr1	.	BED_feature	11874	14409	0	+	.	ID=BED_feature3;Name=uc010nxr.1
chr1	.	BED_block	11874	12227	0	+	.	Parent=BED_feature3;Name=uc010nxr.1
chr1	.	BED_block	12646	12697	0	+	.	Parent=BED_feature3;Name=uc010nxr.1
chr1	.	BED_block	13221	14409	0	+	.	Parent=BED_feature3;Name=uc010nxr.1
###
genometools-1.5.1/testdata/bed_files/track_offset.bed000066400000000000000000000005511211610345200227200ustar00rootroot00000000000000##Example 3 from Custom Annotation Tracks User's Guide
browser position chr22:1000-10000
browser hide all
track name="BED track" description="BED format custom track example" visibility=2 color=0,128,0 offset=1000 useScore=1
chr22 1000 5000 itemA 960 + 1100 4700 0 2 1567,1488, 0,2512
chr22 2000 7000 itemB 200 - 2200 6950 0 4 433,100,550,1500 0,500,2000,3500

genometools-1.5.1/testdata/bed_files/track_offset.gff3000066400000000000000000000013501211610345200230110ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr22 2001 8000
chr22	.	BED_feature	2001	6000	960	+	.	ID=BED_feature1;Name=itemA
chr22	.	BED_block	2001	3567	960	+	.	Parent=BED_feature1;Name=itemA
chr22	.	BED_thick_feature	2101	5700	960	+	.	Parent=BED_feature1;Name=itemA
chr22	.	BED_block	4513	6000	960	+	.	Parent=BED_feature1;Name=itemA
###
chr22	.	BED_feature	3001	8000	200	-	.	ID=BED_feature2;Name=itemB
chr22	.	BED_block	3001	3433	200	-	.	Parent=BED_feature2;Name=itemB
chr22	.	BED_thick_feature	3201	7950	200	-	.	Parent=BED_feature2;Name=itemB
chr22	.	BED_block	3501	3600	200	-	.	Parent=BED_feature2;Name=itemB
chr22	.	BED_block	5001	5550	200	-	.	Parent=BED_feature2;Name=itemB
chr22	.	BED_block	6501	8000	200	-	.	Parent=BED_feature2;Name=itemB
###
genometools-1.5.1/testdata/bigfonts.style000066400000000000000000000043431211610345200205560ustar00rootroot00000000000000--[[
  This is the GenomeTools annotation viewer config file.
  All options must be set inside the 'style' table.
  All items in this table must be tables, called 'sections'.
  Typically there is one section per feature type.

  Color definitions
  -----------------
  Colors are given as RGB triplets
       {red=,green=,blue=(,alpha=)}
  where  is a decimal value between 0 and 1.
  The alpha value is optional, as a default 0.5 will be used.

  Global format settings
  ----------------------
  Global settings, such as margins, spacers, etc. are found at the end of this
  file, in the "format" section.
]]--


style =
{
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 20, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 19, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 8, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/blank_attributes.gff3000066400000000000000000000002621211610345200217610ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1;
ctg123	.	gene	1000	9000	.	+	.	ID=gene2; 
ctg123	.	gene	1000	9000	.	+	.	ID=gene3;  
genometools-1.5.1/testdata/blosum62.c000066400000000000000000000325501211610345200174770ustar00rootroot00000000000000#include 

int main(int argc, char *argv[])
{
  int score_matrix[CHAR_MAX][CHAR_MAX] = {{0}};
  score_matrix['L']['L'] = 4;
  score_matrix['L']['V'] = 1;
  score_matrix['L']['I'] = 2;
  score_matrix['L']['F'] = 0;
  score_matrix['L']['K'] = -2;
  score_matrix['L']['R'] = -2;
  score_matrix['L']['E'] = -3;
  score_matrix['L']['D'] = -4;
  score_matrix['L']['A'] = -1;
  score_matrix['L']['G'] = -4;
  score_matrix['L']['S'] = -2;
  score_matrix['L']['T'] = -1;
  score_matrix['L']['N'] = -3;
  score_matrix['L']['Q'] = -2;
  score_matrix['L']['Y'] = -1;
  score_matrix['L']['W'] = -2;
  score_matrix['L']['P'] = -3;
  score_matrix['L']['H'] = -3;
  score_matrix['L']['M'] = 2;
  score_matrix['L']['C'] = -1;
  score_matrix['L']['X'] = -1;
  score_matrix['V']['L'] = 1;
  score_matrix['V']['V'] = 4;
  score_matrix['V']['I'] = 3;
  score_matrix['V']['F'] = -1;
  score_matrix['V']['K'] = -2;
  score_matrix['V']['R'] = -3;
  score_matrix['V']['E'] = -2;
  score_matrix['V']['D'] = -3;
  score_matrix['V']['A'] = 0;
  score_matrix['V']['G'] = -3;
  score_matrix['V']['S'] = -2;
  score_matrix['V']['T'] = 0;
  score_matrix['V']['N'] = -3;
  score_matrix['V']['Q'] = -2;
  score_matrix['V']['Y'] = -1;
  score_matrix['V']['W'] = -3;
  score_matrix['V']['P'] = -2;
  score_matrix['V']['H'] = -3;
  score_matrix['V']['M'] = 1;
  score_matrix['V']['C'] = -1;
  score_matrix['V']['X'] = -1;
  score_matrix['I']['L'] = 2;
  score_matrix['I']['V'] = 3;
  score_matrix['I']['I'] = 4;
  score_matrix['I']['F'] = 0;
  score_matrix['I']['K'] = -3;
  score_matrix['I']['R'] = -3;
  score_matrix['I']['E'] = -3;
  score_matrix['I']['D'] = -3;
  score_matrix['I']['A'] = -1;
  score_matrix['I']['G'] = -4;
  score_matrix['I']['S'] = -2;
  score_matrix['I']['T'] = -1;
  score_matrix['I']['N'] = -3;
  score_matrix['I']['Q'] = -3;
  score_matrix['I']['Y'] = -1;
  score_matrix['I']['W'] = -3;
  score_matrix['I']['P'] = -3;
  score_matrix['I']['H'] = -3;
  score_matrix['I']['M'] = 1;
  score_matrix['I']['C'] = -1;
  score_matrix['I']['X'] = -1;
  score_matrix['F']['L'] = 0;
  score_matrix['F']['V'] = -1;
  score_matrix['F']['I'] = 0;
  score_matrix['F']['F'] = 6;
  score_matrix['F']['K'] = -3;
  score_matrix['F']['R'] = -3;
  score_matrix['F']['E'] = -3;
  score_matrix['F']['D'] = -3;
  score_matrix['F']['A'] = -2;
  score_matrix['F']['G'] = -3;
  score_matrix['F']['S'] = -2;
  score_matrix['F']['T'] = -2;
  score_matrix['F']['N'] = -3;
  score_matrix['F']['Q'] = -3;
  score_matrix['F']['Y'] = 3;
  score_matrix['F']['W'] = 1;
  score_matrix['F']['P'] = -4;
  score_matrix['F']['H'] = -1;
  score_matrix['F']['M'] = 0;
  score_matrix['F']['C'] = -2;
  score_matrix['F']['X'] = -1;
  score_matrix['K']['L'] = -2;
  score_matrix['K']['V'] = -2;
  score_matrix['K']['I'] = -3;
  score_matrix['K']['F'] = -3;
  score_matrix['K']['K'] = 5;
  score_matrix['K']['R'] = 2;
  score_matrix['K']['E'] = 1;
  score_matrix['K']['D'] = -1;
  score_matrix['K']['A'] = -1;
  score_matrix['K']['G'] = -2;
  score_matrix['K']['S'] = 0;
  score_matrix['K']['T'] = -1;
  score_matrix['K']['N'] = 0;
  score_matrix['K']['Q'] = 1;
  score_matrix['K']['Y'] = -2;
  score_matrix['K']['W'] = -3;
  score_matrix['K']['P'] = -1;
  score_matrix['K']['H'] = -1;
  score_matrix['K']['M'] = -1;
  score_matrix['K']['C'] = -3;
  score_matrix['K']['X'] = -1;
  score_matrix['R']['L'] = -2;
  score_matrix['R']['V'] = -3;
  score_matrix['R']['I'] = -3;
  score_matrix['R']['F'] = -3;
  score_matrix['R']['K'] = 2;
  score_matrix['R']['R'] = 5;
  score_matrix['R']['E'] = 0;
  score_matrix['R']['D'] = -2;
  score_matrix['R']['A'] = -1;
  score_matrix['R']['G'] = -2;
  score_matrix['R']['S'] = -1;
  score_matrix['R']['T'] = -1;
  score_matrix['R']['N'] = 0;
  score_matrix['R']['Q'] = 1;
  score_matrix['R']['Y'] = -2;
  score_matrix['R']['W'] = -3;
  score_matrix['R']['P'] = -2;
  score_matrix['R']['H'] = 0;
  score_matrix['R']['M'] = -1;
  score_matrix['R']['C'] = -3;
  score_matrix['R']['X'] = -1;
  score_matrix['E']['L'] = -3;
  score_matrix['E']['V'] = -2;
  score_matrix['E']['I'] = -3;
  score_matrix['E']['F'] = -3;
  score_matrix['E']['K'] = 1;
  score_matrix['E']['R'] = 0;
  score_matrix['E']['E'] = 5;
  score_matrix['E']['D'] = 2;
  score_matrix['E']['A'] = -1;
  score_matrix['E']['G'] = -2;
  score_matrix['E']['S'] = 0;
  score_matrix['E']['T'] = -1;
  score_matrix['E']['N'] = 0;
  score_matrix['E']['Q'] = 2;
  score_matrix['E']['Y'] = -2;
  score_matrix['E']['W'] = -3;
  score_matrix['E']['P'] = -1;
  score_matrix['E']['H'] = 0;
  score_matrix['E']['M'] = -2;
  score_matrix['E']['C'] = -4;
  score_matrix['E']['X'] = -1;
  score_matrix['D']['L'] = -4;
  score_matrix['D']['V'] = -3;
  score_matrix['D']['I'] = -3;
  score_matrix['D']['F'] = -3;
  score_matrix['D']['K'] = -1;
  score_matrix['D']['R'] = -2;
  score_matrix['D']['E'] = 2;
  score_matrix['D']['D'] = 6;
  score_matrix['D']['A'] = -2;
  score_matrix['D']['G'] = -1;
  score_matrix['D']['S'] = 0;
  score_matrix['D']['T'] = -1;
  score_matrix['D']['N'] = 1;
  score_matrix['D']['Q'] = 0;
  score_matrix['D']['Y'] = -3;
  score_matrix['D']['W'] = -4;
  score_matrix['D']['P'] = -1;
  score_matrix['D']['H'] = -1;
  score_matrix['D']['M'] = -3;
  score_matrix['D']['C'] = -3;
  score_matrix['D']['X'] = -1;
  score_matrix['A']['L'] = -1;
  score_matrix['A']['V'] = 0;
  score_matrix['A']['I'] = -1;
  score_matrix['A']['F'] = -2;
  score_matrix['A']['K'] = -1;
  score_matrix['A']['R'] = -1;
  score_matrix['A']['E'] = -1;
  score_matrix['A']['D'] = -2;
  score_matrix['A']['A'] = 4;
  score_matrix['A']['G'] = 0;
  score_matrix['A']['S'] = 1;
  score_matrix['A']['T'] = 0;
  score_matrix['A']['N'] = -2;
  score_matrix['A']['Q'] = -1;
  score_matrix['A']['Y'] = -2;
  score_matrix['A']['W'] = -3;
  score_matrix['A']['P'] = -1;
  score_matrix['A']['H'] = -2;
  score_matrix['A']['M'] = -1;
  score_matrix['A']['C'] = 0;
  score_matrix['A']['X'] = 0;
  score_matrix['G']['L'] = -4;
  score_matrix['G']['V'] = -3;
  score_matrix['G']['I'] = -4;
  score_matrix['G']['F'] = -3;
  score_matrix['G']['K'] = -2;
  score_matrix['G']['R'] = -2;
  score_matrix['G']['E'] = -2;
  score_matrix['G']['D'] = -1;
  score_matrix['G']['A'] = 0;
  score_matrix['G']['G'] = 6;
  score_matrix['G']['S'] = 0;
  score_matrix['G']['T'] = -2;
  score_matrix['G']['N'] = 0;
  score_matrix['G']['Q'] = -2;
  score_matrix['G']['Y'] = -3;
  score_matrix['G']['W'] = -2;
  score_matrix['G']['P'] = -2;
  score_matrix['G']['H'] = -2;
  score_matrix['G']['M'] = -3;
  score_matrix['G']['C'] = -3;
  score_matrix['G']['X'] = -1;
  score_matrix['S']['L'] = -2;
  score_matrix['S']['V'] = -2;
  score_matrix['S']['I'] = -2;
  score_matrix['S']['F'] = -2;
  score_matrix['S']['K'] = 0;
  score_matrix['S']['R'] = -1;
  score_matrix['S']['E'] = 0;
  score_matrix['S']['D'] = 0;
  score_matrix['S']['A'] = 1;
  score_matrix['S']['G'] = 0;
  score_matrix['S']['S'] = 4;
  score_matrix['S']['T'] = 1;
  score_matrix['S']['N'] = 1;
  score_matrix['S']['Q'] = 0;
  score_matrix['S']['Y'] = -2;
  score_matrix['S']['W'] = -3;
  score_matrix['S']['P'] = -1;
  score_matrix['S']['H'] = -1;
  score_matrix['S']['M'] = -1;
  score_matrix['S']['C'] = -1;
  score_matrix['S']['X'] = 0;
  score_matrix['T']['L'] = -1;
  score_matrix['T']['V'] = 0;
  score_matrix['T']['I'] = -1;
  score_matrix['T']['F'] = -2;
  score_matrix['T']['K'] = -1;
  score_matrix['T']['R'] = -1;
  score_matrix['T']['E'] = -1;
  score_matrix['T']['D'] = -1;
  score_matrix['T']['A'] = 0;
  score_matrix['T']['G'] = -2;
  score_matrix['T']['S'] = 1;
  score_matrix['T']['T'] = 5;
  score_matrix['T']['N'] = 0;
  score_matrix['T']['Q'] = -1;
  score_matrix['T']['Y'] = -2;
  score_matrix['T']['W'] = -2;
  score_matrix['T']['P'] = -1;
  score_matrix['T']['H'] = -2;
  score_matrix['T']['M'] = -1;
  score_matrix['T']['C'] = -1;
  score_matrix['T']['X'] = 0;
  score_matrix['N']['L'] = -3;
  score_matrix['N']['V'] = -3;
  score_matrix['N']['I'] = -3;
  score_matrix['N']['F'] = -3;
  score_matrix['N']['K'] = 0;
  score_matrix['N']['R'] = 0;
  score_matrix['N']['E'] = 0;
  score_matrix['N']['D'] = 1;
  score_matrix['N']['A'] = -2;
  score_matrix['N']['G'] = 0;
  score_matrix['N']['S'] = 1;
  score_matrix['N']['T'] = 0;
  score_matrix['N']['N'] = 6;
  score_matrix['N']['Q'] = 0;
  score_matrix['N']['Y'] = -2;
  score_matrix['N']['W'] = -4;
  score_matrix['N']['P'] = -2;
  score_matrix['N']['H'] = 1;
  score_matrix['N']['M'] = -2;
  score_matrix['N']['C'] = -3;
  score_matrix['N']['X'] = -1;
  score_matrix['Q']['L'] = -2;
  score_matrix['Q']['V'] = -2;
  score_matrix['Q']['I'] = -3;
  score_matrix['Q']['F'] = -3;
  score_matrix['Q']['K'] = 1;
  score_matrix['Q']['R'] = 1;
  score_matrix['Q']['E'] = 2;
  score_matrix['Q']['D'] = 0;
  score_matrix['Q']['A'] = -1;
  score_matrix['Q']['G'] = -2;
  score_matrix['Q']['S'] = 0;
  score_matrix['Q']['T'] = -1;
  score_matrix['Q']['N'] = 0;
  score_matrix['Q']['Q'] = 5;
  score_matrix['Q']['Y'] = -1;
  score_matrix['Q']['W'] = -2;
  score_matrix['Q']['P'] = -1;
  score_matrix['Q']['H'] = 0;
  score_matrix['Q']['M'] = 0;
  score_matrix['Q']['C'] = -3;
  score_matrix['Q']['X'] = -1;
  score_matrix['Y']['L'] = -1;
  score_matrix['Y']['V'] = -1;
  score_matrix['Y']['I'] = -1;
  score_matrix['Y']['F'] = 3;
  score_matrix['Y']['K'] = -2;
  score_matrix['Y']['R'] = -2;
  score_matrix['Y']['E'] = -2;
  score_matrix['Y']['D'] = -3;
  score_matrix['Y']['A'] = -2;
  score_matrix['Y']['G'] = -3;
  score_matrix['Y']['S'] = -2;
  score_matrix['Y']['T'] = -2;
  score_matrix['Y']['N'] = -2;
  score_matrix['Y']['Q'] = -1;
  score_matrix['Y']['Y'] = 7;
  score_matrix['Y']['W'] = 2;
  score_matrix['Y']['P'] = -3;
  score_matrix['Y']['H'] = 2;
  score_matrix['Y']['M'] = -1;
  score_matrix['Y']['C'] = -2;
  score_matrix['Y']['X'] = -1;
  score_matrix['W']['L'] = -2;
  score_matrix['W']['V'] = -3;
  score_matrix['W']['I'] = -3;
  score_matrix['W']['F'] = 1;
  score_matrix['W']['K'] = -3;
  score_matrix['W']['R'] = -3;
  score_matrix['W']['E'] = -3;
  score_matrix['W']['D'] = -4;
  score_matrix['W']['A'] = -3;
  score_matrix['W']['G'] = -2;
  score_matrix['W']['S'] = -3;
  score_matrix['W']['T'] = -2;
  score_matrix['W']['N'] = -4;
  score_matrix['W']['Q'] = -2;
  score_matrix['W']['Y'] = 2;
  score_matrix['W']['W'] = 11;
  score_matrix['W']['P'] = -4;
  score_matrix['W']['H'] = -2;
  score_matrix['W']['M'] = -1;
  score_matrix['W']['C'] = -2;
  score_matrix['W']['X'] = -2;
  score_matrix['P']['L'] = -3;
  score_matrix['P']['V'] = -2;
  score_matrix['P']['I'] = -3;
  score_matrix['P']['F'] = -4;
  score_matrix['P']['K'] = -1;
  score_matrix['P']['R'] = -2;
  score_matrix['P']['E'] = -1;
  score_matrix['P']['D'] = -1;
  score_matrix['P']['A'] = -1;
  score_matrix['P']['G'] = -2;
  score_matrix['P']['S'] = -1;
  score_matrix['P']['T'] = -1;
  score_matrix['P']['N'] = -2;
  score_matrix['P']['Q'] = -1;
  score_matrix['P']['Y'] = -3;
  score_matrix['P']['W'] = -4;
  score_matrix['P']['P'] = 7;
  score_matrix['P']['H'] = -2;
  score_matrix['P']['M'] = -2;
  score_matrix['P']['C'] = -3;
  score_matrix['P']['X'] = -2;
  score_matrix['H']['L'] = -3;
  score_matrix['H']['V'] = -3;
  score_matrix['H']['I'] = -3;
  score_matrix['H']['F'] = -1;
  score_matrix['H']['K'] = -1;
  score_matrix['H']['R'] = 0;
  score_matrix['H']['E'] = 0;
  score_matrix['H']['D'] = -1;
  score_matrix['H']['A'] = -2;
  score_matrix['H']['G'] = -2;
  score_matrix['H']['S'] = -1;
  score_matrix['H']['T'] = -2;
  score_matrix['H']['N'] = 1;
  score_matrix['H']['Q'] = 0;
  score_matrix['H']['Y'] = 2;
  score_matrix['H']['W'] = -2;
  score_matrix['H']['P'] = -2;
  score_matrix['H']['H'] = 8;
  score_matrix['H']['M'] = -2;
  score_matrix['H']['C'] = -3;
  score_matrix['H']['X'] = -1;
  score_matrix['M']['L'] = 2;
  score_matrix['M']['V'] = 1;
  score_matrix['M']['I'] = 1;
  score_matrix['M']['F'] = 0;
  score_matrix['M']['K'] = -1;
  score_matrix['M']['R'] = -1;
  score_matrix['M']['E'] = -2;
  score_matrix['M']['D'] = -3;
  score_matrix['M']['A'] = -1;
  score_matrix['M']['G'] = -3;
  score_matrix['M']['S'] = -1;
  score_matrix['M']['T'] = -1;
  score_matrix['M']['N'] = -2;
  score_matrix['M']['Q'] = 0;
  score_matrix['M']['Y'] = -1;
  score_matrix['M']['W'] = -1;
  score_matrix['M']['P'] = -2;
  score_matrix['M']['H'] = -2;
  score_matrix['M']['M'] = 5;
  score_matrix['M']['C'] = -1;
  score_matrix['M']['X'] = -1;
  score_matrix['C']['L'] = -1;
  score_matrix['C']['V'] = -1;
  score_matrix['C']['I'] = -1;
  score_matrix['C']['F'] = -2;
  score_matrix['C']['K'] = -3;
  score_matrix['C']['R'] = -3;
  score_matrix['C']['E'] = -4;
  score_matrix['C']['D'] = -3;
  score_matrix['C']['A'] = 0;
  score_matrix['C']['G'] = -3;
  score_matrix['C']['S'] = -1;
  score_matrix['C']['T'] = -1;
  score_matrix['C']['N'] = -3;
  score_matrix['C']['Q'] = -3;
  score_matrix['C']['Y'] = -2;
  score_matrix['C']['W'] = -2;
  score_matrix['C']['P'] = -3;
  score_matrix['C']['H'] = -3;
  score_matrix['C']['M'] = -1;
  score_matrix['C']['C'] = 9;
  score_matrix['C']['X'] = -2;
  score_matrix['X']['L'] = -1;
  score_matrix['X']['V'] = -1;
  score_matrix['X']['I'] = -1;
  score_matrix['X']['F'] = -1;
  score_matrix['X']['K'] = -1;
  score_matrix['X']['R'] = -1;
  score_matrix['X']['E'] = -1;
  score_matrix['X']['D'] = -1;
  score_matrix['X']['A'] = 0;
  score_matrix['X']['G'] = -1;
  score_matrix['X']['S'] = 0;
  score_matrix['X']['T'] = 0;
  score_matrix['X']['N'] = -1;
  score_matrix['X']['Q'] = -1;
  score_matrix['X']['Y'] = -1;
  score_matrix['X']['W'] = -2;
  score_matrix['X']['P'] = -2;
  score_matrix['X']['H'] = -1;
  score_matrix['X']['M'] = -1;
  score_matrix['X']['C'] = -2;
  score_matrix['X']['X'] = -1;
  return 0;
}
genometools-1.5.1/testdata/broken_hmmer.hmm000066400000000000000000001071651211610345200210420ustar00rootroot00000000000000HMMER2.0  [2.3.1]
NAME  RVP
ACC   PF00077.9
DESC  Retroviral aspartyl protease
LENG  111
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   hmmbuild -f -F HMM_fs.ann SEED.ann
COM   hmmcalibrate --seed 0 HMM_fs.ann
NSEQ  51
DATE  Sun Jun 19 21:22:26 2005
CKSUM 8953
GA    30.90 30.90
TC    30.90 30.90
NC    30.80 30.80
XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4
        233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10298 -11340   -894  -1115   -701  -1378  -7822  -7693
    15  -1344  -3399  -2246  -1189  -3934  -3326    399  -1314   1230  -2615   -318    979    718   2359   1307  -1220    845  -1030  -3371   -516    15
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -  -2052 -10298   -409   -894  -1115   -701  -1378  -7822  -7687
    16  -1064  -1060  -2605  -2018   1290   1413  -1327   1050  -1765   -922   -261    501    936  -1530  -1840  -1543    595   -488   2600  -1126    16
     -   -148   -501    234     42   -377    398    105   -627    209   -465   -721    274    393     46     95    361    118   -367   -295   -250
     -  -3424   -151  -9302    -24  -5897  -4950    -47  -7822  -7679
    17   -980  -2449   -783    986  -2767  -1938   2568  -2517   -196  -2464  -1541   1261    203   1330   -704   1146    386  -2070  -2634  -1951    18
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14  -8260  -9302   -894  -1115  -4950    -47  -7822  -7672
    18  -1437  -1925  -3535  -3416  -3097  -2390  -2946  -2573  -3088  -2770   2381  -2691   3308  -2954  -3088  -1718   2041  -2209  -3572  -3270    19
     -   -149   -503    230     43   -379    399    109   -625    212   -469   -723    273    396     52     98    359    117   -369   -297   -252
     -  -1302   -767  -9302  -1975   -423  -4950    -47  -7822  -7665
    19  -1259  -2312  -1318   -722  -2538  -2258   -838  -2179    858  -2253  -1440   1068  -2332    975    695  -1219  -1178   2213  -2513   1561    27
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14  -8260  -9302   -894  -1115    -29  -5627  -7822  -7658
    20   -847  -3432   -957    462   -960  -3340  -1981  -1448    436   -634  -2791   -491   2118   1051   -687   -383    749  -2144   2315    731    28
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10298 -11341   -894  -1115   -701  -1378  -7822  -7651
    21  -1088   1131  -4662  -4188   1612  -4069  -2874   1932    204    637  -1639  -3681  -4046  -3427   -761   -943    -34   1511  -2605   -216    29
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10298 -11341   -894  -1115   -701  -1378  -7822  -7644
    22  -2452  -3925   -942   1691  -4246  -3426  -2084  -3997   1649   -936  -3014   1287  -1040   1294    828   -630    677  -1079  -4108  -3426    30
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10298 -11341   -894  -1115   -701  -1378  -7822  -7637
    23   2034   2398  -5057  -4421   1810   1016  -3131  -2025  -4016   -924   1844  -3905  -4309  -3639  -3816  -3344  -2652    555   1332  -2653    31
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7629
    24  -2647  -2308  -4662  -4193  -2391  -4068  -2871    472  -3829   2987    518  -3682  -4043  -3429  -3629  -3243  -2572     26  -2596  -2516    32
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7622
    25  -5628  -5023  -8088  -7549   -856  -7921  -6741   1263  -7391   2619    169  -7635  -6994  -6230  -6935  -7315  -5497   1828  -5249  -5452    33
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7615
    26  -8180  -7105   4231  -7058  -8479  -6868  -7237  -9512  -8031  -8873  -8805  -7310  -7332  -7649  -7848  -8365  -8325  -9151  -7244  -8340    34
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7607
    27  -3487  -4085  -6477  -6831  -6723  -4352  -6027  -6620  -6658  -6860  -5914  -5147  -5159  -6133  -6310  -1193   4043  -5308  -6869  -6874    35
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7600
    28   -984  -4629   -642  -4548  -6971   3728  -5313  -6910  -5869  -7027  -6197  -4439  -5302  -5176  -6223  -4083  -4357  -5729  -6988  -6725    36
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7592
    29   3617  -3983  -6576  -6931  -6685  -4259  -6003  -6539  -6673  -6792  -5825  -5082  -5073  -6107  -6289   -405  -3859  -5208  -6873  -6875    37
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7585
    30   -393  -6315   3652    -42  -6580  -4422  -3782  -6502  -4022  -6372  -5690  -3028  -4955   -231  -4876   -986   1082  -5957  -6567  -5554    38
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7577
    31   -387  -3589   1933   -316   -745  -3531   2259   1195    684  -1254    -98     19  -3619  -1810   -354  -2453   -749    738  -3858  -3268    39
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7570
    32  -3238    922  -5844  -5748  -5592  -4175    579  -5266  -5519  -5557  -4748    831  -4898  -5194  -5465   1981   3125   -632  -5913  -5671    40
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7562
    33   -951    492  -5561  -4960  -3005  -4827  -3763   2456  -4588  -1116   1090  -4473  -4849  -4235  -4413  -3933  -1056   2756  -3607     -1    41
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7555
    34  -4818  -4371  -7292  -6760   -123  -6859  -5861   2732  -6519   2013    132  -6529  -6451  -5825  -6265  -6093      3    757  -5014  -4957    42
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7547
    35   -447  -3926  -2300    566  -4247  -3427  -2085  -3997   1138  -1776  -3015   1277   1513   1048    403    811   1097  -3548  -4109  -3426    43
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -     -9 -10299 -11341   -894  -1115   -701  -1378  -7822  -7539
    36   -626  -3923    105   1878  -4244     -1  -2085   -227    240  -1767  -3013   -244   -666   1431   -372    148   -130   -929    469     59    44
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -10 -10300 -11342   -894  -1115   -701  -1378  -7822  -7532
    37    342    449  -2745    461   -784  -3637   1575    860   -408  -2336   1053   1731    496  -2010    850   -871    -83   -848  -3657   -671    45
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -10 -10299 -11341   -894  -1115   -701  -1378  -7822  -7524
    38   -887  -3913   1994     29  -4228  -3429   2046   -325   -112   -168   -709    315   -335   1034  -1323    149  -1572  -1538   1726   -588    46
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -10 -10299 -11341   -894  -1115   -701  -1378  -7822  -7516
    39  -1445    226   -919  -1030   1427    700  -3113    334  -3975   1271   -166  -1412  -4295  -3606   -998  -3327  -2642   -412   4026   -118    47
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -10 -10299 -11341   -894  -1115   -701  -1378  -7822  -7508
    40  -2452    384    318   -750   -402   -946    472  -3992    465  -1507  -3012    229   2812   1267   -946     73  -2391  -1217  -4106  -3424    48
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -56 -10299  -4990   -894  -1115   -701  -1378  -7822  -7500
    41  -1143   1797  -1376   -217    135   1193  -2574   -308   -201    899    -15  -2836   -446  -2447   1085   -603   -108      6  -3299  -2869    49
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -10 -10253 -11296   -894  -1115  -1503   -628  -7822  -7492
    42  -1201  -3885    482   -362  -4206   -813    770    213    628   -651  -2974   1844    624  -1585    240   1186    -41  -3507  -4068  -3386    50
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -   -678 -10253  -1440   -894  -1115  -1503   -628  -7822  -7484
    43  -2035  -2138  -3250  -2671  -2124     20  -2208    558    778  -2002  -1329   1239  -1072  -2276  -2636  -2435   -401    118   4345   2029    51
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     -   -149   -500    232     43   -377    398    109   -627    211   -466   -721    278    393     45     95    359    117   -370   -295   -250
     -  -2201   -995  -1873    -51  -4860  -5018    -45  -7822  -7000
    94  -1034  -2366   1575    -86  -2658  -1728   -660  -2397   -425    257  -1589   2646  -1987   -262   -971    679  -1018  -2004  -2663  -1968   109
     -   -149   -500    232     43   -381    398    105   -624    214   -466   -721    277    393     47     95    359    117   -370   -295   -250
     -  -2718   -256  -8595    -42  -5122  -3960    -96  -7822  -6989
    95  -3496  -3478  -3449  -3298  -1444  -3728  -2105  -3771  -2213  -3376  -3150  -3114  -4001   2913  -2214  -3522  -3501  -3719   5513   -998   111
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -21  -7831  -8873   -894  -1115  -2196   -355  -7822  -6977
    96   1533  -1633  -2290  -1725  -1657  -2673  -1472  -1221  -1553    733   2484  -1782   1029    811  -1821    116     89  -1092  -2060  -1649   112
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -17  -8758  -9800   -894  -1115    -34  -5436  -7822  -6967
    97  -5096  -4536  -7708  -7309  -3871  -7586  -7043   3206  -7240   2066  -2605  -7269  -6974  -6548  -7087  -6996  -5041    -21  -5739  -5735   113
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -13 -10303 -11345   -894  -1115   -701  -1378  -7822  -6954
    98  -3960  -3686  -6317  -5705    -14  -5623  -4441   2510  -5340   2110  -2015  -5270  -5497  -4800  -5092  -1079  -3885   -611   3306  -3745   114
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -13 -10303 -11345   -894  -1115   -701  -1378  -7822  -6943
    99  -7966  -6939  -7945  -8331  -8524   3865  -7619  -9551  -8535  -8932  -8840  -8214  -7400  -8391  -7975  -8393  -8242  -9053  -7247  -8536   115
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14 -10304 -11346   -894  -1115   -701  -1378  -7822  -6932
   100  -3913    889  -6386  -5373  -4680  -2438  -4227    196  -3250  -1379  -3699  -4762  -5305  -4045   3985  -4266  -4055  -3520  -5078  -4834   116
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14 -10303 -11345   -894  -1115   -701  -1378  -7822  -6919
   101  -1086  -6563   3346   -716  -6717  -4458  -3836  -6664   -221  -6515  -5872   2434  -5008  -3510  -5038     19  -4667  -6122  -6713  -5652   117
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14 -10303 -11345   -894  -1115   -701  -1378  -7822  -6907
   102    246    640  -5170  -4539    842  -4383  -3262   2219  -4139   1682    163    957  -4425  -3762  -3942  -3471  -2759    416  -3119  -2779   118
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14 -10303 -11345   -894  -1115   -701  -1378  -7822  -6895
   103  -5754  -5164   -708  -7498  -3236  -7836  -6427    234  -7272   2938   2737  -7547  -6901  -6038  -6743  -7170  -5587  -3596   -317  -5208   119
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14 -10303 -11346   -894  -1115   -701  -1378  -7822  -6883
   104   1330   -301  -2336   -923  -4157  -3445  -2107  -1330    517  -3868  -2961  -2092  -3538   2299    920     -5   1872  -1396  -4065  -3400   120
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14 -10304 -11346   -894  -1115   -701  -1378  -7822  -6870
   105   -763  -3456    655   -237  -3983   -789     92  -3834   1973  -2289  -2816   -487   -750   2700    437     76  -2335  -3440  -3438  -3231   121
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14 -10304 -11346   -894  -1115   -701  -1378  -7822  -6858
   106    896   2070  -5057  -4421    859  -1031  -3129    893  -4015   2043   1719  -3905  -4308  -3638  -3815  -3344  -2652  -1949    931    -22   122
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14 -10304 -11346   -894  -1115   -701  -1378  -7822  -6845
   107  -2455  -3928  -1135   -465  -4249   2591    439  -4000   1136  -3944  -3017    281  -3522   1601   -868  -1088  -2395   -710  -4111    -14   123
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -14 -10304 -11346   -894  -1115   -701  -1378  -7822  -6833
   108   1936   2988  -4614   -916  -2395    281  -2858    761  -3788   -249    598  -3655  -4033  -3398  -3605   -204   -337    621  -2597  -2515   124
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -15 -10305 -11347   -894  -1115   -701  -1378  -7822  -6821
   109  -2471    123  -2402   -699  -3991   -188  -2145     90   1638  -2049  -2856  -2147   -641   1128    747    685   1074    669  -3977   -573   125
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -15 -10304 -11346   -894  -1115   -701  -1378  -7822  -6807
   110  -5507  -4974  -7880  -7278     72  -7521  -6198   2146  -7030   2611    897  -7218  -6755  -5932  -6567  -6803  -5364   -466  -4956     52   126
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249
     -    -15 -10304 -11346   -894  -1115   -701  -1378  -7822  -6794
   111  -2645   1149   -833  -3299   -187  -4026   1245    835  -3089  -2603    203   1841  -4090   -467   -631    681    947    906  -3168   1512   127
     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *
     -      *      *      *      *      *      *      *  -7822      0

genometools-1.5.1/testdata/cds_check_fail_1.gff3000066400000000000000000000004501211610345200215440ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	9	.	+	.	Parent=gene1
dna	.	CDS	1	9	.	+	0	Parent=gene1
dna	.	exon	11	19	.	+	.	Parent=gene1
dna		CDS	11	19	.	+	0	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	1	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_fail_2.gff3000066400000000000000000000004521211610345200215470ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	10	.	+	.	Parent=gene1
dna	.	CDS	1	10	.	+	0	Parent=gene1
dna	.	exon	11	20	.	+	.	Parent=gene1
dna		CDS	11	20	.	+	2	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	2	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_fail_3.gff3000066400000000000000000000004521211610345200215500ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	11	.	+	.	Parent=gene1
dna	.	CDS	1	11	.	+	0	Parent=gene1
dna	.	exon	11	21	.	+	.	Parent=gene1
dna		CDS	11	21	.	+	1	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	0	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_fail_4.gff3000066400000000000000000000004521211610345200215510ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	110	.	-	.	ID=gene1
dna	.	exon	1	10	.	-	.	Parent=gene1
dna	.	CDS	1	10	.	-	0	Parent=gene1
dna	.	exon	11	20	.	-	.	Parent=gene1
dna		CDS	11	20	.	-	2	Parent=gene1
dna	.	exon	101	110	.	-	.	Parent=gene1
dna	.	CDS	101	110	.	-	0	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_1.gff3000066400000000000000000000004501211610345200215660ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	9	.	+	.	Parent=gene1
dna	.	CDS	1	9	.	+	0	Parent=gene1
dna	.	exon	11	19	.	+	.	Parent=gene1
dna		CDS	11	19	.	+	0	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	0	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_10.gff3000066400000000000000000000004521211610345200216500ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	-	.	ID=gene1
dna	.	exon	1	10	.	-	.	Parent=gene1
dna	.	CDS	1	10	.	-	0	Parent=gene1
dna	.	exon	11	19	.	-	.	Parent=gene1
dna		CDS	11	19	.	-	0	Parent=gene1
dna	.	exon	101	109	.	-	.	Parent=gene1
dna	.	CDS	101	109	.	-	0	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_11.gff3000066400000000000000000000004521211610345200216510ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	110	.	-	.	ID=gene1
dna	.	exon	1	10	.	-	.	Parent=gene1
dna	.	CDS	1	10	.	-	2	Parent=gene1
dna	.	exon	11	19	.	-	.	Parent=gene1
dna		CDS	11	19	.	-	2	Parent=gene1
dna	.	exon	101	110	.	-	.	Parent=gene1
dna	.	CDS	101	110	.	-	0	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_12.gff3000066400000000000000000000004521211610345200216520ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	110	.	-	.	ID=gene1
dna	.	exon	1	10	.	-	.	Parent=gene1
dna	.	CDS	1	10	.	-	1	Parent=gene1
dna	.	exon	11	20	.	-	.	Parent=gene1
dna		CDS	11	20	.	-	2	Parent=gene1
dna	.	exon	101	110	.	-	.	Parent=gene1
dna	.	CDS	101	110	.	-	0	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_2.gff3000066400000000000000000000004501211610345200215670ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	9	.	+	.	Parent=gene1
dna	.	CDS	1	9	.	+	0	Parent=gene1
dna	.	exon	11	20	.	+	.	Parent=gene1
dna		CDS	11	20	.	+	0	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	2	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_3.gff3000066400000000000000000000004501211610345200215700ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	9	.	+	.	Parent=gene1
dna	.	CDS	1	9	.	+	0	Parent=gene1
dna	.	exon	11	21	.	+	.	Parent=gene1
dna		CDS	11	21	.	+	0	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	1	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_4.gff3000066400000000000000000000004521211610345200215730ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	10	.	+	.	Parent=gene1
dna	.	CDS	1	10	.	+	0	Parent=gene1
dna	.	exon	11	19	.	+	.	Parent=gene1
dna		CDS	11	19	.	+	2	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	2	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_5.gff3000066400000000000000000000004521211610345200215740ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	10	.	+	.	Parent=gene1
dna	.	CDS	1	10	.	+	0	Parent=gene1
dna	.	exon	11	20	.	+	.	Parent=gene1
dna		CDS	11	20	.	+	2	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	1	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_6.gff3000066400000000000000000000004521211610345200215750ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	10	.	+	.	Parent=gene1
dna	.	CDS	1	10	.	+	0	Parent=gene1
dna	.	exon	11	21	.	+	.	Parent=gene1
dna		CDS	11	21	.	+	2	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	0	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_7.gff3000066400000000000000000000004521211610345200215760ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	11	.	+	.	Parent=gene1
dna	.	CDS	1	11	.	+	0	Parent=gene1
dna	.	exon	11	19	.	+	.	Parent=gene1
dna		CDS	11	19	.	+	1	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	1	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_8.gff3000066400000000000000000000004521211610345200215770ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	11	.	+	.	Parent=gene1
dna	.	CDS	1	11	.	+	0	Parent=gene1
dna	.	exon	11	20	.	+	.	Parent=gene1
dna		CDS	11	20	.	+	1	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	0	Parent=gene1
###
genometools-1.5.1/testdata/cds_check_succ_9.gff3000066400000000000000000000004521211610345200216000ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 200
dna	.	gene	1	109	.	+	.	ID=gene1
dna	.	exon	1	11	.	+	.	Parent=gene1
dna	.	CDS	1	11	.	+	0	Parent=gene1
dna	.	exon	11	21	.	+	.	Parent=gene1
dna		CDS	11	21	.	+	1	Parent=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	.	CDS	101	109	.	+	2	Parent=gene1
###
genometools-1.5.1/testdata/cds_feature_with_multiple_parents.gff3000066400000000000000000000060241211610345200254140ustar00rootroot00000000000000##gff-version   3
##sequence-region   3L 8617473 8631957
3L	FlyBase	gene	8617473	8631773	.	+	.	ID=gene1;Name=Zasp66;fullname=Z band alternatively spliced PDZ-motif protein 66;Alias=FBgn0045924,anon-WO0153538.30,CG6416,Zasp66;Ontology_term=SO:0000010,SO:0000087,GO:0007498,GO:0030018,GO:0008157;Dbxref=FlyBase:FBan0006416,FlyBase_Annotation_IDs:CG6416,GB_protein:AAN11990,GB_protein:ACZ94656,GB_protein:ACZ94657,GB_protein:AAN11991,GB_protein:ACZ94655,GB_protein:ACZ94653,GB_protein:AAN11992,GB_protein:ACZ94654,GB_protein:AAF50384,GB_protein:AAO41263,GB_protein:AAO41264,GB_protein:AAF50386,GB_protein:AAO41265,GB:AA697154,GB:AI388325,GB:AW940728,GB:AW941338,GB:AX201646,GB:AY058415,GB_protein:AAL13644,GB:AY060961,GB_protein:AAL28509,UniProt/TrEMBL:Q7KUB5,UniProt/TrEMBL:Q86BH5,UniProt/TrEMBL:Q86BH6,UniProt/TrEMBL:Q8IQB4,UniProt/TrEMBL:Q95S47,UniProt/TrEMBL:Q95TZ7,UniProt/TrEMBL:Q9VSN0,UniProt/TrEMBL:Q9VSN2,INTERPRO:IPR001478,INTERPRO:IPR006643,EntrezGene:38988,UniProt/TrEMBL:E1JI73,UniProt/TrEMBL:E1JI76,UniProt/TrEMBL:E1JI74,UniProt/TrEMBL:E1JI77,UniProt/TrEMBL:Q058U1,InterologFinder:38988,BIOGRID:64396,FlyAtlas:CG6416-RG%3BCG6416-RG%3BCG6416-RE,GenomeRNAi:38988;gbunit=AE014296;derived_computed_cyto=66D9-66D9
3L	FlyBase	mRNA	8617473	8631773	.	+	.	ID=mRNA1;Parent=gene1;Name=Zasp66-RE;Alias=CG6416-RE;Dbxref=FlyBase_Annotation_IDs:CG6416-RE,REFSEQ:NM_168283;score_text=Moderately Supported;score=7
3L	FlyBase	CDS	8617583	8617783	.	+	0	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8620061	8620209	.	+	0	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8620527	8620830	.	+	1	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8628781	8628852	.	+	1	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8630539	8630698	.	+	1	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8631367	8631453	.	+	0	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	mRNA	8623308	8631773	.	+	.	ID=mRNA11;Parent=gene1;Name=Zasp66-RH;Alias=CG6416-RH;Dbxref=FlyBase_Annotation_IDs:CG6416-RH,REFSEQ:NM_176304;score_text=Strongly Supported;score=15
3L	FlyBase	CDS	8623655	8623735	.	+	0	Parent=mRNA11;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8627683	8627883	.	+	0	Parent=mRNA1,mRNA11;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8628102	8628181	.	+	0	Parent=mRNA1,mRNA11;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8631257	8631295	.	+	1	Parent=mRNA1,mRNA11;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8631367	8631373	.	+	1	Parent=mRNA11;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	mRNA	8623308	8631773	.	+	.	ID=mRNA12;Parent=gene1;Name=Zasp66-RI;Alias=CG6416-RI;Dbxref=FlyBase_Annotation_IDs:CG6416-RI,REFSEQ:NM_176303;score_text=Moderately Supported;score=7
3L	FlyBase	mRNA	8623370	8631773	.	+	.	ID=mRNA13;Parent=gene1;Name=Zasp66-RJ;Alias=CG6416-RG,CG6416-RJ;Dbxref=FlyBase_Annotation_IDs:CG6416-RJ,REFSEQ:NM_176306;score_text=Moderately Supported;score=7
3L	FlyBase	CDS	8623655	8623735	.	+	0	Parent=mRNA13;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8630539	8630698	.	+	1	Parent=mRNA13;Name=Zasp66-cds;parent_type=mRNA
###
genometools-1.5.1/testdata/cds_feature_with_multiple_parents_tidied.gff3000066400000000000000000000061161211610345200267400ustar00rootroot00000000000000##gff-version   3
##sequence-region   3L 8617473 8631957
3L	FlyBase	gene	8617473	8631773	.	+	.	ID=gene1;Name=Zasp66;fullname=Z band alternatively spliced PDZ-motif protein 66;Alias=FBgn0045924,anon-WO0153538.30,CG6416,Zasp66;Ontology_term=SO:0000010,SO:0000087,GO:0007498,GO:0030018,GO:0008157;Dbxref=FlyBase:FBan0006416,FlyBase_Annotation_IDs:CG6416,GB_protein:AAN11990,GB_protein:ACZ94656,GB_protein:ACZ94657,GB_protein:AAN11991,GB_protein:ACZ94655,GB_protein:ACZ94653,GB_protein:AAN11992,GB_protein:ACZ94654,GB_protein:AAF50384,GB_protein:AAO41263,GB_protein:AAO41264,GB_protein:AAF50386,GB_protein:AAO41265,GB:AA697154,GB:AI388325,GB:AW940728,GB:AW941338,GB:AX201646,GB:AY058415,GB_protein:AAL13644,GB:AY060961,GB_protein:AAL28509,UniProt/TrEMBL:Q7KUB5,UniProt/TrEMBL:Q86BH5,UniProt/TrEMBL:Q86BH6,UniProt/TrEMBL:Q8IQB4,UniProt/TrEMBL:Q95S47,UniProt/TrEMBL:Q95TZ7,UniProt/TrEMBL:Q9VSN0,UniProt/TrEMBL:Q9VSN2,INTERPRO:IPR001478,INTERPRO:IPR006643,EntrezGene:38988,UniProt/TrEMBL:E1JI73,UniProt/TrEMBL:E1JI76,UniProt/TrEMBL:E1JI74,UniProt/TrEMBL:E1JI77,UniProt/TrEMBL:Q058U1,InterologFinder:38988,BIOGRID:64396,FlyAtlas:CG6416-RG%3BCG6416-RG%3BCG6416-RE,GenomeRNAi:38988;gbunit=AE014296;derived_computed_cyto=66D9-66D9
3L	FlyBase	mRNA	8617473	8631773	.	+	.	ID=mRNA1;Parent=gene1;Name=Zasp66-RE;Alias=CG6416-RE;Dbxref=FlyBase_Annotation_IDs:CG6416-RE,REFSEQ:NM_168283;score_text=Moderately Supported;score=7
3L	FlyBase	CDS	8617583	8617783	.	+	0	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8620061	8620209	.	+	0	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8620527	8620830	.	+	1	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8628781	8628852	.	+	1	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8630539	8630698	.	+	1	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8631257	8631295	.	+	0	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8631367	8631453	.	+	0	Parent=mRNA1;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	mRNA	8623308	8631773	.	+	.	ID=mRNA2;Parent=gene1;Name=Zasp66-RH;Alias=CG6416-RH;Dbxref=FlyBase_Annotation_IDs:CG6416-RH,REFSEQ:NM_176304;score_text=Strongly Supported;score=15
3L	FlyBase	CDS	8623655	8623735	.	+	0	Parent=mRNA2;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8627683	8627883	.	+	0	Parent=mRNA1,mRNA2;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8628102	8628181	.	+	0	Parent=mRNA1,mRNA2;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8631257	8631295	.	+	1	Parent=mRNA2;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8631367	8631373	.	+	1	Parent=mRNA2;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	mRNA	8623308	8631773	.	+	.	Parent=gene1;Name=Zasp66-RI;Alias=CG6416-RI;Dbxref=FlyBase_Annotation_IDs:CG6416-RI,REFSEQ:NM_176303;score_text=Moderately Supported;score=7
3L	FlyBase	mRNA	8623370	8631773	.	+	.	ID=mRNA3;Parent=gene1;Name=Zasp66-RJ;Alias=CG6416-RG,CG6416-RJ;Dbxref=FlyBase_Annotation_IDs:CG6416-RJ,REFSEQ:NM_176306;score_text=Moderately Supported;score=7
3L	FlyBase	CDS	8623655	8623735	.	+	0	Parent=mRNA3;Name=Zasp66-cds;parent_type=mRNA
3L	FlyBase	CDS	8630539	8630698	.	+	0	Parent=mRNA3;Name=Zasp66-cds;parent_type=mRNA
###
genometools-1.5.1/testdata/cds_with_multiple_parents_1.gff3000066400000000000000000000011161211610345200241160ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1;Name=EDEN
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1;Name=EDEN.1
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA2;Parent=gene1;Name=EDEN.3
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	CDS	1201	1500	.	+	0	Parent=mRNA1
ctg123	.	CDS	3000	3902	.	+	0	Parent=mRNA1
ctg123	.	CDS	5000	5500	.	+	0	Parent=mRNA1,mRNA2
ctg123	.	CDS	3301	3902	.	+	0	Parent=mRNA2
genometools-1.5.1/testdata/cds_with_multiple_parents_1_tidied.gff3000066400000000000000000000011661211610345200254450ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1;Name=EDEN
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1;Name=EDEN.1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	CDS	1201	1500	.	+	0	Parent=mRNA1
ctg123	.	CDS	3000	3902	.	+	0	Parent=mRNA1
ctg123	.	CDS	5000	5500	.	+	0	Parent=mRNA1
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA2;Parent=gene1;Name=EDEN.3
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	CDS	3301	3902	.	+	0	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	CDS	5000	5500	.	+	1	Parent=mRNA2
###
genometools-1.5.1/testdata/cds_with_multiple_parents_2.gff3000066400000000000000000000015151211610345200241220ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1;Name=EDEN
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1;Name=EDEN.1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1;Name=EDEN.2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1;Name=EDEN.3
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1,mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	CDS	1201	1500	.	+	0	Parent=mRNA1,mRNA2
ctg123	.	CDS	3000	3902	.	+	0	Parent=mRNA1
ctg123	.	CDS	5000	5500	.	+	0	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	CDS	7000	7600	.	+	0	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	CDS	3301	3902	.	+	0	Parent=mRNA3
###
genometools-1.5.1/testdata/cds_with_multiple_parents_2_tidied.gff3000066400000000000000000000017351211610345200254500ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1;Name=EDEN
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1;Name=EDEN.1
ctg123	.	CDS	3000	3902	.	+	0	Parent=mRNA1
ctg123	.	CDS	5000	5500	.	+	0	Parent=mRNA1
ctg123	.	CDS	7000	7600	.	+	0	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1;Name=EDEN.2
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	CDS	1201	1500	.	+	0	Parent=mRNA1,mRNA2
ctg123	.	CDS	5000	5500	.	+	0	Parent=mRNA2
ctg123	.	CDS	7000	7600	.	+	0	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1;Name=EDEN.3
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1,mRNA3
ctg123	.	CDS	3301	3902	.	+	0	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	CDS	5000	5500	.	+	1	Parent=mRNA3
ctg123	.	CDS	7000	7600	.	+	1	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1,mRNA2,mRNA3
###
genometools-1.5.1/testdata/chaindata/000077500000000000000000000000001211610345200175715ustar00rootroot00000000000000genometools-1.5.1/testdata/chaindata/chain-global000066400000000000000000004446051211610345200220510ustar00rootroot00000000000000# chain 0: length 4258 score 2988370
5851 6237 5868 6254 774
7627 7937 7644 7954 622
8079 8457 8096 8474 758
8687 8994 8704 9011 616
8996 9375 9013 9392 760
9377 9666 9394 9683 580
10024 10406 10041 10423 766
10408 10715 10425 10732 616
11439 11663 11456 11680 450
11695 11898 11712 11915 408
12026 12235 12043 12252 420
12384 12712 12401 12729 658
13131 13339 13148 13356 418
13719 14230 13736 14247 1024
14232 14645 14249 14662 828
15174 15389 15191 15406 432
17569 17786 16237 16454 436
18477 18763 17145 17431 574
19377 19794 18045 18462 836
20813 21272 25219 25678 920
21304 21615 25716 26027 624
22048 22265 26460 26677 436
23335 23639 27747 28051 610
25045 25447 29457 29859 806
26789 27024 31164 31399 472
27712 28067 32087 32442 712
28223 28446 32598 32821 448
29506 29843 33881 34218 676
30706 30913 35081 35288 416
31887 32116 36262 36491 460
33552 33766 37927 38141 430
34112 34597 38486 38971 972
35170 35491 39577 39898 644
35499 35831 39906 40238 666
36263 36479 40670 40886 434
37032 37439 41439 41846 816
37534 37775 41941 42182 484
37777 38103 42184 42510 654
38777 39003 43184 43410 454
40129 40508 44536 44915 760
41188 41408 45595 45815 442
43562 43773 47976 48187 424
44455 44660 48869 49074 412
45555 45805 49969 50219 502
45950 46173 50365 50588 448
46253 46632 50668 51047 760
46901 47137 51316 51552 474
47515 47785 51930 52200 542
49571 49940 53986 54355 740
51097 51551 56073 56527 910
51621 51901 56597 56877 562
51924 52135 56900 57111 424
53284 53627 58260 58603 688
53902 54335 58878 59311 868
54337 54981 59313 59957 1290
54983 56483 59959 61459 3002
56485 56939 61461 61915 910
56941 57835 61917 62811 1790
57928 58141 62904 63117 428
59485 59772 64418 64705 576
59831 60053 64764 64986 446
60245 60545 65178 65478 602
60547 60890 65480 65823 688
60943 61457 65876 66390 1030
61459 61700 66392 66633 484
62923 63424 67856 68357 1004
64749 65026 69681 69958 556
65826 66030 70758 70962 410
66970 67169 71817 72016 400
67312 67544 72159 72391 466
67596 67832 72443 72679 474
68693 68945 73540 73792 506
70473 71000 75320 75847 1056
71214 71540 76061 76387 654
74737 75132 79557 79952 792
75226 75461 80046 80281 472
76775 76988 82604 82817 428
81083 81302 85691 85910 440
82978 83294 87586 87902 634
83392 83799 88000 88407 816
84493 84737 89099 89343 490
84949 85210 89555 89816 524
85881 86098 90487 90704 436
87279 87522 91885 92128 488
87794 88118 92400 92724 650
88120 88349 92726 92955 460
89754 90328 94360 94934 1150
90591 90949 95197 95555 718
91187 91785 95793 96391 1198
92474 92682 97080 97288 418
93089 93369 97695 97975 562
94167 94384 98773 98990 436
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95152 95370 99758 99976 438
95905 96359 100511 100965 910
97113 97513 101719 102119 802
98322 98775 102928 103381 908
98906 99228 103512 103834 646
99254 99649 103860 104255 792
99651 99869 104257 104475 438
100432 100691 105038 105297 520
101175 101494 105781 106100 640
101721 101923 106327 106529 406
102613 102831 107219 107437 438
102833 103359 107439 107965 1054
103604 103840 108210 108446 474
103842 104168 108448 108774 654
104548 104822 109154 109428 550
104857 105545 109463 110151 1378
106099 107460 110705 112066 2724
107686 107909 112292 112515 448
108007 108211 112613 112817 410
108293 108597 112899 113203 610
108848 109485 113454 114091 1276
109496 109707 114102 114313 424
109927 110184 114533 114790 516
110441 110658 115047 115264 436
110660 110901 115266 115507 484
110903 111227 115509 115833 650
111661 112144 116151 116634 968
112146 112457 116636 116947 624
112459 112834 116949 117324 752
112836 113047 117326 117537 424
113049 113268 117539 117758 440
113270 114090 117760 118580 1642
116535 116843 121025 121333 618
117226 117573 121716 122063 696
117842 118158 122332 122648 634
118514 119177 123004 123667 1328
119259 119491 123749 123981 466
119493 119812 123983 124302 640
120595 120848 125085 125338 508
121891 122239 126381 126729 698
122496 122797 126986 127287 604
122808 123161 127298 127651 708
123931 124169 128421 128659 478
124522 124796 129012 129286 550
125410 125818 129900 130308 818
127257 127734 131747 132224 956
127882 128266 132255 132639 770
128406 128650 132779 133023 490
128991 129196 133364 133569 412
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135663 136121 140036 140494 918
136240 136604 140613 140977 730
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141797 142087 146170 146460 582
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143270 143496 147643 147869 454
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144256 144630 148629 149003 750
145072 145290 149445 149663 438
146145 146732 150518 151105 1176
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159237 159483 163560 163806 494
160020 160261 164343 164584 484
160401 161512 164724 165835 2224
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164644 164931 168967 169254 576
166100 166500 170423 170823 802
166502 166932 170825 171255 862
168428 168768 172751 173091 682
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169759 169994 174082 174317 472
172286 172617 176609 176940 664
174673 175242 178873 179442 1140
175991 176292 180191 180492 604
176294 176862 180494 181062 1138
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177648 177933 181848 182133 572
178131 178465 182331 182665 670
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179070 179513 183270 183713 888
180127 180427 184327 184627 602
180820 181388 185020 185588 1138
181390 181646 185590 185846 514
181663 181940 185863 186140 556
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183133 183406 187333 187606 548
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183701 184121 187901 188321 842
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188339 188709 191826 192196 742
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193063 194127 196408 197472 2130
194165 194669 197510 198014 1010
195040 197671 198385 201016 5264
197790 198378 201135 201723 1178
198380 198621 201725 201966 484
199262 199926 202607 203271 1330
199928 200418 203273 203763 982
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200811 201187 204155 204531 754
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201640 202500 204984 205844 1722
202808 203026 206152 206370 438
203135 203440 206479 206784 612
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205269 205525 208613 208869 514
206068 206371 209412 209715 608
207123 207337 210467 210681 430
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213337 213554 216681 216898 436
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220515 220882 223846 224213 736
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221550 221915 224881 225246 732
222448 222986 225779 226317 1078
222988 223316 226319 226647 658
223538 223739 226870 227071 404
223915 224888 227247 228220 1948
224890 225585 228222 228917 1392
225900 226112 229232 229444 426
226604 226927 229936 230259 648
226936 227481 230267 230812 1092
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227969 228550 231300 231881 1164
228768 229025 232098 232355 516
229598 229840 232928 233170 486
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232837 233051 236388 236602 430
233158 233399 236709 236950 484
233401 233636 236952 237187 472
233638 233959 237189 237510 644
233961 234277 237512 237828 634
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237263 237536 240815 241088 548
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240031 240397 278100 278466 734
241492 241701 279561 279770 420
241703 242018 279772 280087 632
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245952 246203 283920 284171 504
250050 250279 287937 288166 460
251614 251828 289501 289715 430
252573 252783 290460 290670 422
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254361 254617 292249 292505 514
255687 256313 293575 294201 1254
256486 256872 294374 294760 774
257033 257260 294921 295148 456
258635 258918 296523 296806 568
259430 259675 297318 297563 492
260217 260431 298105 298319 430
260706 260991 298594 298879 572
297132 297463 330317 330648 664
299169 299479 332354 332664 622
300524 300783 333709 333968 520
301750 302005 334935 335190 512
305109 305541 338294 338726 866
306139 306369 339324 339554 462
306382 306626 339567 339811 490
306907 307106 340092 340291 400
308316 308640 341501 341825 650
309476 309792 342661 342977 634
313588 313860 353941 354213 546
316129 316360 358934 359165 464
318125 318630 361618 362123 1012
318632 318938 362125 362431 614
319028 319326 362521 362819 598
319744 320032 363237 363525 578
321266 321471 364759 364964 412
321473 321699 364966 365192 454
322401 323072 365894 366565 1344
323968 324172 367461 367665 410
328133 328560 376575 377002 856
328661 329008 377103 377450 696
329022 329383 377464 377825 724
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genometools-1.5.1/testdata/chaindata/chain-local-wf0.5000066400000000000000000000007251211610345200225270ustar00rootroot00000000000000# chain 0: length 12 score 12566
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genometools-1.5.1/testdata/chaindata/chain-local-wf1.8-maxgap20000066400000000000000000000005541211610345200241500ustar00rootroot00000000000000# chain 0: length 9 score 25016
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1091338 1091738 1418838 1419238 1443
1091740 1092322 1419240 1419822 2098
genometools-1.5.1/testdata/chaindata/chain-local20000066400000000000000000004701661211610345200220460ustar00rootroot00000000000000# chain 0: length 1 score 774
5851 6237 5868 6254 774
# chain 1: length 14 score 3784
7627 7937 7644 7954 622
8079 8457 8096 8474 758
8687 8994 8704 9011 616
8996 9375 9013 9392 760
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10024 10406 10041 10423 766
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12026 12235 12043 12252 420
12384 12712 12401 12729 658
13131 13339 13148 13356 418
13719 14230 13736 14247 1024
14232 14645 14249 14662 828
# chain 2: length 1 score 574
18477 18763 17145 17431 574
# chain 3: length 1 score 836
19377 19794 18045 18462 836
# chain 4: length 2 score 1474
20813 21272 25219 25678 920
21304 21615 25716 26027 624
# chain 5: length 1 score 610
23335 23639 27747 28051 610
# chain 6: length 1 score 806
25045 25447 29457 29859 806
# chain 7: length 1 score 472
26789 27024 31164 31399 472
# chain 8: length 2 score 848
27712 28067 32087 32442 712
28223 28446 32598 32821 448
# chain 9: length 1 score 676
29506 29843 33881 34218 676
# chain 10: length 1 score 416
30706 30913 35081 35288 416
# chain 11: length 1 score 460
31887 32116 36262 36491 460
# chain 12: length 1 score 430
33552 33766 37927 38141 430
# chain 13: length 1 score 972
34112 34597 38486 38971 972
# chain 14: length 2 score 1294
35170 35491 39577 39898 644
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# chain 15: length 3 score 1760
37032 37439 41439 41846 816
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37777 38103 42184 42510 654
# chain 16: length 1 score 760
40129 40508 44536 44915 760
# chain 17: length 1 score 442
41188 41408 45595 45815 442
# chain 18: length 1 score 424
43562 43773 47976 48187 424
# chain 19: length 1 score 412
44455 44660 48869 49074 412
# chain 20: length 3 score 1259
45555 45805 49969 50219 502
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46253 46632 50668 51047 760
# chain 21: length 1 score 740
49571 49940 53986 54355 740
# chain 22: length 3 score 1710
51097 51551 56073 56527 910
51621 51901 56597 56877 562
51924 52135 56900 57111 424
# chain 23: length 13 score 8789
53284 53627 58260 58603 688
53902 54335 58878 59311 868
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54983 56483 59959 61459 3002
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60245 60545 65178 65478 602
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61459 61700 66392 66633 484
# chain 24: length 2 score 1282
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71214 71540 76061 76387 654
# chain 25: length 2 score 1076
74737 75132 79557 79952 792
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# chain 26: length 1 score 428
76775 76988 82604 82817 428
# chain 27: length 1 score 440
81083 81302 85691 85910 440
# chain 28: length 2 score 1254
82978 83294 87586 87902 634
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# chain 29: length 2 score 590
84493 84737 89099 89343 490
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# chain 30: length 1 score 436
85881 86098 90487 90704 436
# chain 31: length 1 score 488
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# chain 32: length 2 score 1106
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88120 88349 92726 92955 460
# chain 33: length 3 score 2064
89754 90328 94360 94934 1150
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91187 91785 95793 96391 1198
# chain 34: length 2 score 596
94167 94384 98773 98990 436
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# chain 35: length 1 score 438
95152 95370 99758 99976 438
# chain 36: length 1 score 910
95905 96359 100511 100965 910
# chain 37: length 1 score 802
97113 97513 101719 102119 802
# chain 38: length 29 score 11974
98322 98775 102928 103381 908
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101175 101494 105781 106100 640
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112459 112834 116949 117324 752
112836 113047 117326 117537 424
113049 113268 117539 117758 440
113270 114090 117760 118580 1642
# chain 39: length 7 score 4472
133795 134045 138168 138418 502
134047 134547 138420 138920 1002
134594 134876 138967 139249 566
134968 135254 139341 139627 574
135256 135635 139629 140008 760
135663 136121 140036 140494 918
136240 136604 140613 140977 730
# chain 40: length 6 score 1780
141040 141304 145413 145677 530
141343 141710 145716 146083 736
141797 142087 146170 146460 582
142452 142814 146825 147187 726
143270 143496 147643 147869 454
143498 143822 147871 148195 650
# chain 41: length 1 score 1176
146145 146732 150518 151105 1176
# chain 42: length 6 score 2828
157544 157954 161867 162277 822
158023 158489 162346 162812 934
158578 158792 162901 163115 430
159237 159483 163560 163806 494
160020 160261 164343 164584 484
160401 161512 164724 165835 2224
# chain 43: length 1 score 576
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# chain 44: length 2 score 1660
166100 166500 170423 170823 802
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# chain 45: length 2 score 816
168428 168768 172751 173091 682
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# chain 46: length 1 score 664
172286 172617 176609 176940 664
# chain 47: length 1 score 1140
174673 175242 178873 179442 1140
# chain 48: length 15 score 5530
175991 176292 180191 180492 604
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176876 177372 181076 181572 994
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178131 178465 182331 182665 670
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179070 179513 183270 183713 888
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182343 182661 186543 186861 638
183133 183406 187333 187606 548
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183701 184121 187901 188321 842
# chain 49: length 21 score 20527
188339 188709 191826 192196 742
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201640 202500 204984 205844 1722
202808 203026 206152 206370 438
203135 203440 206479 206784 612
# chain 50: length 7 score 4701
4164382 4165237 227247 228102 1712
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# chain 51: length 7 score 4292
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4206762 4207279 228140 228657 1036
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4208850 4209342 230318 230810 986
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4209832 4210413 231300 231881 1164
# chain 52: length 7 score 5021
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4034682 4035035 228665 229018 708
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4037310 4037891 231300 231881 1164
# chain 53: length 10 score 4482
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3940467 3940984 228140 228657 1036
3941255 3941460 229020 229225 412
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3943441 3943705 231204 231468 530
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# chain 54: length 1 score 402
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# chain 55: length 1 score 488
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# chain 56: length 2 score 943
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# chain 57: length 2 score 997
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# chain 58: length 1 score 734
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# chain 59: length 2 score 1048
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# chain 60: length 2 score 716
245371 245714 283339 283682 688
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# chain 61: length 1 score 460
250050 250279 287937 288166 460
# chain 62: length 1 score 430
251614 251828 289501 289715 430
# chain 63: length 1 score 422
252573 252783 290460 290670 422
# chain 64: length 1 score 590
253387 253681 291275 291569 590
# chain 65: length 1 score 514
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# chain 66: length 3 score 1816
255687 256313 293575 294201 1254
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# chain 67: length 1 score 568
258635 258918 296523 296806 568
# chain 68: length 1 score 492
259430 259675 297318 297563 492
# chain 69: length 1 score 430
260217 260431 298105 298319 430
# chain 70: length 1 score 572
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# chain 71: length 1 score 664
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# chain 72: length 1 score 622
299169 299479 332354 332664 622
# chain 73: length 1 score 520
300524 300783 333709 333968 520
# chain 74: length 1 score 512
301750 302005 334935 335190 512
# chain 75: length 1 score 866
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# chain 76: length 2 score 926
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306382 306626 339567 339811 490
# chain 77: length 1 score 650
308316 308640 341501 341825 650
# chain 78: length 1 score 634
309476 309792 342661 342977 634
# chain 79: length 1 score 546
313588 313860 353941 354213 546
# chain 80: length 1 score 464
316129 316360 358934 359165 464
# chain 81: length 3 score 2040
318125 318630 361618 362123 1012
318632 318938 362125 362431 614
319028 319326 362521 362819 598
# chain 82: length 2 score 862
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# chain 83: length 1 score 1344
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# chain 84: length 1 score 410
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# chain 85: length 6 score 3328
328133 328560 376575 377002 856
328661 329008 377103 377450 696
329022 329383 377464 377825 724
329619 330088 378061 378530 940
330090 330409 378532 378851 640
330540 330759 378982 379201 440
# chain 86: length 1 score 658
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# chain 87: length 2 score 1090
334160 334386 386435 386661 454
334409 334749 386684 387024 682
# chain 88: length 1 score 586
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# chain 89: length 1 score 538
338028 338296 390303 390571 538
# chain 90: length 1 score 418
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# chain 91: length 1 score 486
341549 341791 393917 394159 486
# chain 92: length 3 score 1894
342414 343104 399888 400578 1382
343301 343735 400775 401209 870
343919 344120 401393 401594 404
# chain 93: length 1 score 984
351607 352098 408800 409291 984
# chain 94: length 1 score 558
352888 353166 410081 410359 558
# chain 95: length 1 score 532
354178 354443 411935 412200 532
# chain 96: length 2 score 1308
355443 355817 413200 413574 750
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# chain 97: length 1 score 568
358310 358593 415864 416147 568
# chain 98: length 1 score 466
361300 361532 418854 419086 466
# chain 99: length 2 score 1014
362254 362582 419808 420136 658
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# chain 100: length 1 score 406
367228 367430 426606 426808 406
# chain 101: length 1 score 410
368110 368314 427488 427692 410
# chain 102: length 1 score 792
368569 368964 427947 428342 792
# chain 103: length 3 score 1386
369620 370014 428998 429392 790
370352 370704 429730 430082 706
370840 371258 430218 430636 838
# chain 104: length 2 score 1016
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# chain 105: length 1 score 690
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# chain 106: length 3 score 902
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385631 385848 447411 447628 436
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# chain 107: length 1 score 418
388046 388254 449826 450034 418
# chain 108: length 19 score 3906
392824 393267 453381 453824 888
393274 393475 453831 454032 404
393537 394358 454094 454915 1644
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394843 395354 455400 455911 1024
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# chain 109: length 1 score 778
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# chain 110: length 3 score 2268
409019 409683 471883 472547 1330
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# chain 111: length 10 score 10990
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# chain 112: length 1 score 408
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# chain 113: length 1 score 424
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# chain 114: length 1 score 442
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# chain 115: length 19 score 8681
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# chain 281: length 3 score 1410
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# chain 282: length 1 score 488
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# chain 283: length 2 score 1000
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# chain 284: length 1 score 1208
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# chain 288: length 3 score 1630
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# chain 289: length 1 score 500
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# chain 291: length 2 score 1208
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# chain 298: length 1 score 806
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# chain 305: length 2 score 2032
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# chain 306: length 1 score 704
1083213 1083564 1410714 1411065 704
# chain 307: length 13 score 15980
1084147 1084615 1411647 1412115 938
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# chain 308: length 1 score 430
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# chain 309: length 1 score 440
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# chain 310: length 1 score 490
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# chain 311: length 1 score 716
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# chain 313: length 1 score 588
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# chain 314: length 1 score 586
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# chain 315: length 2 score 772
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# chain 316: length 10 score 2891
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# chain 317: length 1 score 580
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# chain 318: length 4 score 1586
1108271 1108657 1553275 1553661 774
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# chain 319: length 1 score 1050
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# chain 320: length 1 score 1052
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# chain 321: length 6 score 1380
1117589 1117965 1562593 1562969 754
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# chain 322: length 7 score 2838
1122359 1122620 1567366 1567627 524
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# chain 323: length 5 score 2118
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# chain 324: length 5 score 1648
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# chain 325: length 1 score 400
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# chain 326: length 33 score 11298
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# chain 327: length 2 score 1100
1181855 1182215 1625567 1625927 722
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# chain 328: length 2 score 858
2066961 2067174 1670009 1670222 428
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# chain 329: length 4 score 978
1465932 1466145 1670009 1670222 428
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# chain 330: length 4 score 976
2994382 2994594 1670010 1670222 426
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# chain 331: length 1 score 884
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# chain 332: length 1 score 1900
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# chain 334: length 2 score 1488
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# chain 335: length 6 score 1782
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# chain 336: length 1 score 1022
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# chain 337: length 1 score 540
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# chain 338: length 1 score 444
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# chain 339: length 3 score 2328
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# chain 340: length 2 score 1162
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# chain 343: length 1 score 1286
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# chain 345: length 2 score 1190
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# chain 346: length 4 score 1418
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# chain 347: length 1 score 622
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# chain 349: length 1 score 472
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# chain 350: length 1 score 712
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# chain 352: length 1 score 712
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# chain 358: length 22 score 9410
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# chain 359: length 1 score 838
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# chain 360: length 8 score 2405
1289330 1289537 1823087 1823294 416
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1292980 1293260 1826736 1827016 562
# chain 361: length 4 score 1824
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# chain 362: length 1 score 542
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# chain 363: length 1 score 410
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# chain 364: length 2 score 1396
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# chain 365: length 12 score 4281
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# chain 366: length 3 score 960
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# chain 367: length 2 score 662
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# chain 368: length 1 score 598
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# chain 370: length 2 score 1174
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# chain 371: length 1 score 1068
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# chain 373: length 2 score 1378
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# chain 374: length 1 score 554
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# chain 376: length 22 score 8609
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# chain 377: length 1 score 502
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# chain 378: length 1 score 660
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# chain 380: length 1 score 690
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# chain 381: length 2 score 800
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# chain 382: length 2 score 1168
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# chain 383: length 1 score 524
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# chain 384: length 1 score 466
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# chain 385: length 9 score 3438
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# chain 386: length 2 score 990
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# chain 387: length 1 score 478
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# chain 388: length 2 score 686
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# chain 389: length 1 score 400
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# chain 390: length 1 score 468
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# chain 391: length 6 score 1115
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# chain 392: length 9 score 4136
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# chain 393: length 1 score 430
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# chain 395: length 1 score 434
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# chain 398: length 1 score 458
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# chain 400: length 1 score 404
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# chain 401: length 5 score 1354
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# chain 402: length 1 score 474
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# chain 403: length 3 score 2496
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# chain 405: length 1 score 646
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# chain 406: length 1 score 778
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# chain 408: length 1 score 588
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# chain 409: length 1 score 494
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# chain 413: length 7 score 3822
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# chain 414: length 1 score 476
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# chain 416: length 9 score 3278
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# chain 417: length 1 score 484
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# chain 418: length 1 score 626
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# chain 419: length 1 score 436
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# chain 420: length 1 score 648
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# chain 599: length 1 score 430
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# chain 600: length 1 score 1294
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# chain 602: length 1 score 404
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# chain 604: length 1 score 706
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# chain 608: length 24 score 9962
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# chain 609: length 3 score 2982
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# chain 610: length 1 score 406
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# chain 643: length 3 score 1164
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# chain 644: length 1 score 494
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# chain 745: length 2 score 945
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2922916 2923166 3656996 3657246 502
2923198 2923523 3657278 3657603 652
2923525 2923743 3657605 3657823 438
2924110 2924627 3658190 3658707 1036
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2938372 2938889 3672452 3672969 1036
# chain 753: length 1 score 634
2952130 2952446 3686210 3686526 634
# chain 754: length 2 score 1240
2952793 2953194 3686873 3687274 804
2953196 2953415 3687276 3687495 440
# chain 755: length 3 score 1142
2954286 2954592 3688366 3688672 614
2954594 2954832 3688674 3688912 478
2955038 2955270 3689118 3689350 466
# chain 756: length 1 score 454
2956154 2956380 3690234 3690460 454
# chain 757: length 1 score 444
2956706 2956927 3690786 3691007 444
# chain 758: length 1 score 552
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# chain 759: length 1 score 442
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# chain 760: length 1 score 588
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# chain 761: length 1 score 592
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# chain 762: length 21 score 5108
2963712 2964359 3697792 3698439 1296
2964361 2964757 3698441 3698837 794
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2976543 2976934 3710625 3711016 784
# chain 763: length 1 score 596
2982386 2982683 3716468 3716765 596
# chain 764: length 3 score 1616
2983764 2984022 3717846 3718104 518
2984063 2984382 3718145 3718464 640
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# chain 765: length 1 score 452
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# chain 766: length 2 score 936
2987686 2987900 3721769 3721983 430
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# chain 767: length 1 score 584
2990962 2991253 3725284 3725575 584
# chain 768: length 2 score 1096
2993831 2994088 3728158 3728415 516
2994090 2994381 3728417 3728708 584
# chain 769: length 1 score 582
2995755 2996045 3745699 3745989 582
# chain 770: length 1 score 878
2996478 2996916 3746417 3746855 878
# chain 771: length 1 score 438
2998837 2999055 3748856 3749074 438
# chain 772: length 1 score 430
2999656 2999870 3749675 3749889 430
# chain 773: length 3 score 1484
3000361 3000871 3750380 3750890 1022
3001232 3001571 3751251 3751590 680
3001673 3002026 3751692 3752045 708
# chain 774: length 1 score 610
3005398 3005702 3755418 3755722 610
# chain 775: length 10 score 3552
3006022 3006285 3756042 3756305 528
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3006640 3006902 3756660 3756922 526
3007576 3007988 3757596 3758008 826
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3008562 3008883 3758582 3758903 644
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3010599 3011015 3760439 3760855 834
3011226 3011824 3761066 3761664 1198
# chain 776: length 1 score 514
3023592 3023848 3773433 3773689 514
# chain 777: length 12 score 3029
3024824 3025117 3774665 3774958 588
3025119 3025385 3774960 3775226 534
3025387 3025675 3775228 3775516 578
3025911 3026158 3775753 3776000 496
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3029244 3029744 3779086 3779586 1002
3029796 3030092 3779638 3779934 594
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3030870 3031319 3780712 3781161 900
# chain 778: length 1 score 424
3036792 3037003 3786633 3786844 424
# chain 779: length 1 score 902
3037599 3038049 3787440 3787890 902
# chain 780: length 5 score 1644
3040459 3040735 3790181 3790457 554
3040791 3041035 3790513 3790757 490
3041133 3041336 3790855 3791058 408
3041443 3041752 3791165 3791474 620
3042030 3042354 3791752 3792076 650
# chain 781: length 1 score 464
3045415 3045646 3794236 3794467 464
# chain 782: length 1 score 624
3047381 3047692 3796201 3796512 624
# chain 783: length 2 score 1228
3048253 3048570 3797073 3797390 636
3048572 3048869 3797392 3797689 596
# chain 784: length 1 score 418
3051344 3051552 3800165 3800373 418
# chain 785: length 5 score 2428
3052159 3052440 3800980 3801261 564
3052674 3053112 3801495 3801933 878
3053387 3053839 3802208 3802660 906
3053841 3054360 3802662 3803181 1040
3054575 3054820 3803396 3803641 492
# chain 786: length 13 score 5610
3055879 3056177 3805093 3805391 598
3056206 3056447 3805420 3805661 484
3056621 3056852 3805834 3806065 464
3056911 3057456 3806124 3806669 1092
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3058950 3059224 3808118 3808392 550
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3063007 3063221 3812175 3812389 430
3063280 3063649 3812448 3812817 740
3063651 3063920 3812819 3813088 540
# chain 787: length 7 score 2253
3073825 3074209 3826128 3826512 770
3074211 3074467 3826514 3826770 514
3074675 3075016 3826978 3827319 684
3075018 3075219 3827321 3827522 404
3075627 3075887 3827931 3828191 522
3076093 3076307 3828397 3828611 430
3076675 3077333 3828979 3829637 1318
# chain 788: length 3 score 1610
3079514 3079872 3831818 3832176 718
3079982 3080259 3832286 3832563 556
3080471 3080960 3832775 3833264 980
# chain 789: length 1 score 446
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# chain 790: length 6 score 2970
3083760 3084104 3836939 3837283 690
3084106 3084555 3837285 3837734 900
3084557 3084791 3837736 3837970 470
3084793 3084995 3837972 3838174 406
3084997 3085235 3838176 3838414 478
3085432 3085649 3838611 3838828 436
# chain 791: length 1 score 446
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# chain 792: length 4 score 1960
3089701 3089960 3842893 3843152 520
3090100 3090440 3843292 3843632 682
3090550 3090840 3843742 3844032 582
3090842 3091181 3844034 3844373 680
# chain 793: length 2 score 1362
3093004 3093438 3846207 3846641 870
3093603 3094013 3846806 3847216 822
# chain 794: length 1 score 474
3096735 3096971 3850026 3850262 474
# chain 795: length 6 score 3127
3098602 3099146 3851893 3852437 1090
3099400 3099657 3852691 3852948 516
3099873 3100304 3853165 3853596 864
3100306 3100536 3853598 3853828 462
3100613 3100873 3853905 3854165 522
3100875 3101262 3854167 3854554 776
# chain 796: length 1 score 538
3102828 3103096 3856120 3856388 538
# chain 797: length 5 score 1926
3104010 3104371 3857302 3857663 724
3104373 3104650 3857665 3857942 556
3105070 3105450 3858362 3858742 762
3105587 3105795 3858879 3859087 418
3105926 3106348 3859218 3859640 846
# chain 798: length 1 score 574
3107815 3108101 3861108 3861394 574
# chain 799: length 1 score 974
3136370 3136856 3888426 3888912 974
# chain 800: length 4 score 858
3138726 3138940 3890782 3890996 430
3139130 3139374 3891186 3891430 490
3139601 3139866 3891657 3891922 532
3139964 3140181 3892020 3892237 436
# chain 801: length 10 score 5188
3140690 3141215 3892746 3893271 1052
3141217 3141434 3893273 3893490 436
3141757 3141962 3893813 3894018 412
3141964 3142233 3894020 3894289 540
3142235 3142542 3894291 3894598 616
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3143751 3144101 3895807 3896157 702
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3144779 3145142 3896835 3897198 728
# chain 802: length 2 score 738
3149634 3149851 3901693 3901910 436
3149949 3150197 3902008 3902256 498
# chain 803: length 1 score 604
3150769 3151070 3902828 3903129 604
# chain 804: length 3 score 1205
3151429 3151741 3903488 3903800 626
3151748 3152031 3903807 3904090 568
3152247 3152475 3904307 3904535 458
# chain 805: length 1 score 758
3153099 3153477 3905159 3905537 758
# chain 806: length 1 score 418
3154115 3154323 3906175 3906383 418
# chain 807: length 1 score 1072
3154885 3155420 3906945 3907480 1072
# chain 808: length 1 score 494
3155961 3156207 3908018 3908264 494
# chain 809: length 3 score 1174
3158209 3158522 3910262 3910575 628
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3158947 3159233 3911000 3911286 574
# chain 810: length 2 score 1238
3159946 3160291 3911999 3912344 692
3160293 3160567 3912346 3912620 550
# chain 811: length 8 score 4242
3161369 3161848 3913422 3913901 960
3162085 3162284 3914138 3914337 400
3162322 3162671 3914375 3914724 700
3162673 3162950 3914726 3915003 556
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3163717 3164081 3915770 3916134 730
3164320 3164886 3916373 3916939 1134
3164994 3165304 3917047 3917357 622
# chain 812: length 1 score 474
3171648 3171884 3929445 3929681 474
# chain 813: length 5 score 2670
3173031 3173423 3930828 3931220 786
3173425 3173841 3931222 3931638 834
3173843 3174134 3931640 3931931 584
3174940 3175571 3932737 3933368 1264
3175780 3176399 3933577 3934196 1240
# chain 814: length 4 score 1880
3177742 3178153 3935539 3935950 824
3178395 3178722 3936192 3936519 656
3178763 3178995 3936560 3936792 466
3179171 3179596 3936968 3937393 852
# chain 815: length 1 score 1378
3182294 3182982 3940091 3940779 1378
# chain 816: length 1 score 426
3189914 3190126 3941146 3941358 426
# chain 817: length 1 score 670
3191023 3191357 3942255 3942589 670
# chain 818: length 3 score 1400
3193642 3194308 3945248 3945914 1334
3194640 3194932 3946246 3946538 586
3195231 3195601 3946837 3947207 742
# chain 819: length 1 score 662
3196380 3196710 3947986 3948316 662
# chain 820: length 6 score 2084
3197240 3197516 3948846 3949122 554
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3198565 3198932 3950171 3950538 736
3198983 3199325 3950589 3950931 686
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# chain 821: length 2 score 1134
3203844 3204146 3955452 3955754 606
3204148 3204413 3955756 3956021 532
# chain 822: length 2 score 804
3206894 3207129 3958503 3958738 472
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# chain 823: length 4 score 3332
3208065 3208985 3959674 3960594 1842
3209410 3209690 3961019 3961299 562
3209935 3210217 3961544 3961826 566
3210362 3211357 3961971 3962966 1992
# chain 824: length 3 score 1390
3216091 3216301 3967700 3967910 422
3216321 3216588 3967930 3968197 536
3216590 3216827 3968199 3968436 476
# chain 825: length 5 score 1708
3218904 3219257 3970513 3970866 708
3219430 3219860 3971039 3971469 862
3220178 3220382 3971787 3971991 410
3220699 3221095 3972308 3972704 794
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# chain 826: length 2 score 962
3223413 3223624 3975022 3975233 424
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# chain 827: length 2 score 678
3224945 3225207 3976554 3976816 526
3225341 3225550 3976950 3977159 420
# chain 828: length 2 score 636
3231339 3231637 3982948 3983246 598
3231818 3232017 3983427 3983626 400
# chain 829: length 1 score 424
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# chain 830: length 2 score 1454
3233117 3233332 3984726 3984941 432
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# chain 831: length 1 score 484
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# chain 832: length 1 score 840
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# chain 833: length 1 score 634
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# chain 834: length 1 score 1090
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# chain 835: length 8 score 3793
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3246641 3247195 3998253 3998807 1110
# chain 836: length 1 score 456
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# chain 837: length 1 score 442
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# chain 838: length 1 score 984
3256891 3257382 4008498 4008989 984
# chain 839: length 1 score 448
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# chain 840: length 2 score 846
3260420 3260640 4012028 4012248 442
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# chain 841: length 16 score 5824
3261585 3261826 4013193 4013434 484
3261954 3262468 4013562 4014076 1030
3262470 3263170 4014078 4014778 1402
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# chain 842: length 1 score 404
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# chain 843: length 2 score 588
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# chain 844: length 1 score 430
3281503 3281717 4035022 4035236 430
# chain 845: length 4 score 1214
3282107 3282345 4035626 4035864 478
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# chain 846: length 1 score 500
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# chain 847: length 4 score 1104
3287555 3287899 4041074 4041418 690
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# chain 848: length 6 score 3238
3289655 3289855 4044132 4044332 402
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3290115 3290582 4044592 4045059 936
3290755 3291112 4045232 4045589 716
3291114 3291324 4045591 4045801 422
3291448 3291914 4045925 4046391 934
# chain 849: length 1 score 534
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# chain 850: length 1 score 438
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# chain 851: length 1 score 808
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# chain 852: length 1 score 400
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# chain 853: length 2 score 1652
3298340 3298676 4052817 4053153 674
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# chain 854: length 2 score 986
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# chain 855: length 1 score 444
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# chain 856: length 1 score 1022
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# chain 857: length 2 score 3002
3305400 3306657 4059876 4061133 2516
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# chain 858: length 2 score 876
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# chain 859: length 7 score 4402
3313095 3314016 4067572 4068493 1844
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# chain 860: length 1 score 556
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# chain 861: length 39 score 11929
3321517 3321738 4075994 4076215 444
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# chain 862: length 1 score 608
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# chain 863: length 1 score 464
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# chain 864: length 1 score 442
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# chain 865: length 3 score 1174
3370660 3371060 4117893 4118293 802
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# chain 866: length 1 score 406
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# chain 867: length 9 score 6202
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# chain 868: length 98 score 36877
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# chain 869: length 1 score 414
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# chain 876: length 18 score 9395
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# chain 998: length 1 score 566
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4020843 4021207 4830731 4831095 730
4021209 4021554 4831097 4831442 692
4021683 4021942 4831570 4831829 520
# chain 1001: length 1 score 448
3939284 3939507 4842675 4842898 448
# chain 1002: length 8 score 4845
4164576 4164974 4843160 4843558 798
4164976 4165237 4843560 4843821 524
4165275 4165798 4843859 4844382 1048
4166150 4166354 4844740 4844944 410
4166769 4167388 4845361 4845980 1240
4167430 4167873 4846021 4846464 888
4168084 4168420 4846675 4847011 674
4168430 4169134 4847021 4847725 1410
# chain 1003: length 9 score 5707
224109 224507 4843160 4843558 798
224509 224888 4843560 4843939 760
224890 225585 4843941 4844636 1392
225900 226112 4844951 4845163 426
226308 226602 4845361 4845655 590
226604 226927 4845657 4845980 648
226987 227412 4846039 4846464 852
227623 227959 4846675 4847011 674
227969 228550 4847021 4847602 1164
# chain 1004: length 8 score 4048
4205569 4205867 4842666 4842964 598
4206063 4206461 4843160 4843558 798
4206463 4206724 4843560 4843821 524
4206762 4207279 4843859 4844376 1036
4208171 4208790 4845361 4845980 1240
4208832 4209275 4846021 4846464 888
4209486 4209822 4846675 4847011 674
4209832 4210413 4847021 4847602 1164
# chain 1005: length 7 score 3595
3939769 3940167 4843160 4843558 798
3940467 3940984 4843859 4844376 1036
3941255 3941460 4844739 4844944 412
3941876 3942495 4845361 4845980 1240
3942537 3942980 4846021 4846464 888
3943061 3943705 4846545 4847189 1290
3943851 3944118 4847335 4847602 536
# chain 1006: length 18 score 6818
4033458 4033856 4843160 4843558 798
4033858 4034119 4843560 4843821 524
4034157 4034674 4843859 4844376 1036
4034682 4035035 4844384 4844737 708
4035648 4036270 4845361 4845983 1246
4036272 4036751 4845985 4846464 960
4036971 4037300 4846682 4847011 660
4037310 4037891 4847021 4847602 1164
4038498 4039102 4848038 4848642 1210
4039724 4039958 4849264 4849498 470
4040674 4040905 4850213 4850444 464
4040907 4041365 4850446 4850904 918
4041665 4042311 4851205 4851851 1294
4042313 4042580 4851853 4852120 536
4042808 4043242 4852348 4852782 870
4043940 4044491 4853480 4854031 1104
4044493 4044810 4854033 4854350 636
4045175 4045638 4854715 4855178 928
# chain 1007: length 1 score 460
4055063 4055292 4864450 4864679 460
# chain 1008: length 6 score 4309
4055827 4056695 4865214 4866082 1738
4056823 4057370 4866210 4866757 1096
4057496 4057758 4866883 4867145 526
4057779 4058383 4867167 4867771 1210
4058682 4058912 4868070 4868300 462
4058914 4059128 4868302 4868516 430
# chain 1009: length 1 score 508
4065903 4066156 4875289 4875542 508
# chain 1010: length 1 score 788
4070076 4070469 4880235 4880628 788
# chain 1011: length 1 score 426
4071254 4071466 4881413 4881625 426
# chain 1012: length 1 score 448
4072146 4072369 4882305 4882528 448
# chain 1013: length 1 score 458
4073229 4073457 4883388 4883616 458
# chain 1014: length 4 score 3024
4073818 4074128 4883977 4884287 622
4074145 4074371 4884304 4884530 454
4074451 4074664 4884610 4884823 428
4074666 4075524 4884825 4885683 1718
# chain 1015: length 1 score 560
4076865 4077144 4889090 4889369 560
# chain 1016: length 4 score 1898
4078137 4078378 4890361 4890602 484
4078380 4078660 4890604 4890884 562
4078874 4079490 4891098 4891714 1234
4079740 4080014 4891964 4892238 550
# chain 1017: length 6 score 3650
4082241 4082495 4894465 4894719 510
4082650 4083118 4894874 4895342 938
4083120 4083610 4895344 4895834 982
4083612 4083818 4895836 4896042 414
4083823 4084085 4896047 4896309 526
4084114 4084446 4896338 4896670 666
# chain 1018: length 3 score 1068
4088405 4088620 4900628 4900843 432
4088622 4088887 4900845 4901110 532
4089204 4089568 4901415 4901779 730
# chain 1019: length 3 score 3300
4093600 4094019 4907147 4907566 840
4094283 4095506 4907830 4909053 2448
4095607 4095977 4909154 4909524 742
# chain 1020: length 1 score 528
4099287 4099550 4912834 4913097 528
# chain 1021: length 2 score 792
4099936 4100150 4913483 4913697 430
4100221 4100472 4913768 4914019 504
# chain 1022: length 6 score 2681
4101847 4102396 4915394 4915943 1100
4102832 4103518 4916379 4917065 1374
4103648 4103949 4917196 4917497 604
4104111 4104346 4917659 4917894 472
4104468 4104676 4918016 4918224 418
4104678 4104886 4918226 4918434 418
# chain 1023: length 1 score 680
4108950 4109289 4922497 4922836 680
# chain 1024: length 3 score 1112
4109737 4110009 4923284 4923556 546
4110197 4110431 4923744 4923978 470
4110433 4110670 4923980 4924217 476
# chain 1025: length 1 score 484
4112872 4113113 4926419 4926660 484
# chain 1026: length 3 score 1114
4113531 4113841 4927173 4927483 622
4114131 4114333 4927773 4927975 406
4114335 4114669 4927977 4928311 670
# chain 1027: length 1 score 652
4115275 4115600 4928917 4929242 652
# chain 1028: length 1 score 916
4116503 4116960 4931583 4932040 916
# chain 1029: length 8 score 4294
4117834 4118324 4932914 4933404 982
4118491 4118702 4933571 4933782 424
4118758 4119248 4933838 4934328 982
4119603 4120087 4934683 4935167 970
4120353 4120633 4935433 4935713 562
4120662 4121417 4935742 4936497 1512
4121652 4121888 4936732 4936968 474
4121923 4122259 4937003 4937339 674
# chain 1030: length 1 score 776
4124464 4124851 4939544 4939931 776
# chain 1031: length 1 score 564
3759943 3760224 4940178 4940459 564
# chain 1032: length 1 score 564
3616956 3617237 4940178 4940459 564
# chain 1033: length 1 score 452
3760536 3760761 4940772 4940997 452
# chain 1034: length 1 score 452
3617549 3617774 4940772 4940997 452
# chain 1035: length 1 score 632
3761284 3761599 4941521 4941836 632
# chain 1036: length 1 score 632
3618297 3618612 4941521 4941836 632
# chain 1037: length 4 score 1415
729265 729530 4940505 4940770 532
729532 729757 4940772 4940997 452
730140 730432 4941381 4941673 586
730483 730841 4941724 4942082 718
# chain 1038: length 1 score 520
3762518 3762777 4942755 4943014 520
# chain 1039: length 1 score 520
3619531 3619790 4942755 4943014 520
# chain 1040: length 1 score 654
4125654 4125980 4946126 4946452 654
# chain 1041: length 1 score 704
4127211 4127562 4947683 4948034 704
# chain 1042: length 2 score 884
4129938 4130145 4950410 4950617 416
4130200 4130488 4950672 4950960 578
# chain 1043: length 1 score 490
4131927 4132171 4952399 4952643 490
# chain 1044: length 1 score 410
4135402 4135606 4955874 4956078 410
# chain 1045: length 1 score 720
4136436 4136795 4956908 4957267 720
# chain 1046: length 3 score 1190
4137236 4137510 4957708 4957982 550
4137555 4137781 4958027 4958253 454
4137861 4138078 4958333 4958550 436
# chain 1047: length 1 score 418
4139421 4139629 4959893 4960101 418
# chain 1048: length 1 score 620
4139953 4140262 4960426 4960735 620
# chain 1049: length 1 score 404
4141642 4141843 4962115 4962316 404
# chain 1050: length 1 score 670
4142728 4143062 4963201 4963535 670
# chain 1051: length 2 score 584
4143891 4144140 4964364 4964613 500
4144322 4144545 4964795 4965018 448
# chain 1052: length 3 score 1316
4144994 4145292 4965467 4965765 598
4145384 4145652 4965857 4966125 538
4145692 4145913 4966165 4966386 444
# chain 1053: length 2 score 594
4146763 4147047 4967236 4967520 570
4147330 4147624 4967803 4968097 590
# chain 1054: length 1 score 828
4149229 4149642 4969703 4970116 828
# chain 1055: length 5 score 1458
4150207 4150508 4970681 4970982 604
4150552 4150888 4971026 4971362 674
4151440 4151657 4971668 4971885 436
4151809 4152222 4972037 4972450 828
4152388 4152636 4972616 4972864 498
# chain 1056: length 2 score 978
4153810 4154138 4974038 4974366 658
4154273 4154567 4974501 4974795 590
# chain 1057: length 1 score 1062
4155818 4156348 4976046 4976576 1062
# chain 1058: length 2 score 1116
4157626 4158023 4977854 4978251 796
4158157 4158450 4978385 4978678 588
# chain 1059: length 2 score 1228
4158561 4158838 4981417 4981694 556
4158861 4159219 4981717 4982075 718
# chain 1060: length 1 score 1086
4160709 4161251 4983565 4984107 1086
# chain 1061: length 8 score 4511
4032883 4033317 4986857 4987291 870
4033319 4033530 4987293 4987504 424
4033654 4034119 4987628 4988093 932
4034157 4034539 4988131 4988513 766
4035078 4035341 4988969 4989232 528
4035414 4035639 4989305 4989530 452
4035648 4036270 4989541 4990163 1246
4036272 4036664 4990165 4990557 786
# chain 1062: length 5 score 2293
3939965 3940331 4987628 4987994 734
3940467 3940849 4988131 4988513 766
3941256 3941568 4988920 4989232 626
3941876 3942495 4989541 4990160 1240
3942537 3942893 4990201 4990557 714
# chain 1063: length 8 score 4276
4205714 4205922 4987083 4987291 418
4205924 4206135 4987293 4987504 424
4206259 4206724 4987628 4988093 932
4206762 4207144 4988131 4988513 766
4207599 4207864 4988967 4989232 532
4207866 4208162 4989234 4989530 594
4208171 4208790 4989541 4990160 1240
4208832 4209188 4990201 4990557 714
# chain 1064: length 9 score 4171
223760 223968 4987083 4987291 418
223970 224181 4987293 4987504 424
224305 224888 4987628 4988211 1168
224890 225190 4988213 4988513 602
225736 226001 4988967 4989232 532
226022 226298 4989253 4989529 554
226308 226602 4989541 4989835 590
226604 226927 4989837 4990160 648
226987 227325 4990219 4990557 678
# chain 1065: length 37 score 15736
4162354 4162742 4985210 4985598 778
4162744 4163523 4985600 4986379 1560
4163525 4163789 4986381 4986645 530
4164001 4164435 4986857 4987291 870
4164437 4164648 4987293 4987504 424
4164772 4165237 4987628 4988093 932
4165275 4165657 4988131 4988513 766
4165950 4166462 4988720 4989232 1026
4166464 4166760 4989234 4989530 594
4166769 4167388 4989541 4990160 1240
4167430 4167786 4990201 4990557 714
4168430 4168872 4991201 4991643 886
4168874 4169134 4991645 4991905 522
4170257 4170470 4992862 4993075 428
4172858 4173811 4995446 4996399 1908
4173886 4174106 4996474 4996694 442
4174116 4175013 4996704 4997601 1796
4175015 4175909 4997603 4998497 1790
4175950 4176241 4998539 4998830 584
4176243 4176538 4998832 4999127 592
4176894 4177208 4999483 4999797 630
4177351 4178584 4999819 5001052 2468
4178586 4179345 5001054 5001813 1520
4179578 4179837 5002046 5002305 520
4180073 4180287 5002541 5002755 430
4180289 4180605 5002757 5003073 634
4181117 4181358 5003585 5003826 484
4181831 4182169 5004299 5004637 678
4182488 4182726 5004956 5005194 478
4182882 4183189 5005350 5005657 616
4183488 4183996 5005956 5006464 1018
4184046 4184630 5006514 5007098 1170
4184817 4185043 5007285 5007511 454
4185045 4185443 5007513 5007911 798
4185445 4185778 5007913 5008246 668
4186344 4186612 5008812 5009080 538
4186737 4187343 5009205 5009811 1214
# chain 1066: length 1 score 448
3939284 3939507 5027956 5028179 448
# chain 1067: length 2 score 742
223741 224022 5028073 5028354 564
224183 224432 5028515 5028764 500
# chain 1068: length 1 score 602
224890 225190 5029222 5029522 602
# chain 1069: length 1 score 1124
225736 226297 5029976 5030537 1124
# chain 1070: length 5 score 1311
3939843 3940092 5028515 5028764 500
3940331 3940849 5029004 5029522 1038
3941256 3941587 5029929 5030260 664
3941982 3942322 5030654 5030994 682
3942559 3943049 5031230 5031720 982
# chain 1071: length 8 score 3181
4164227 4164489 5028092 5028354 526
4164650 4164899 5028515 5028764 500
4165083 4165657 5028948 5029522 1150
4166150 4166481 5029929 5030260 664
4166483 4166758 5030262 5030537 552
4166875 4167215 5030654 5030994 682
4167452 4167940 5031230 5031718 978
4168430 4169134 5032208 5032912 1410
# chain 1072: length 2 score 1170
226991 227481 5031230 5031720 982
227969 228550 5032208 5032789 1164
# chain 1073: length 10 score 3698
4204214 4204438 5026590 5026814 450
4204652 4205249 5027028 5027625 1196
4205569 4205976 5027947 5028354 816
4206137 4206386 5028515 5028764 500
4206570 4207144 5028948 5029522 1150
4207599 4207883 5029976 5030260 570
4207885 4208160 5030262 5030537 552
4208277 4208617 5030654 5030994 682
4208854 4209342 5031230 5031718 978
4209832 4210413 5032208 5032789 1164
# chain 1074: length 8 score 2541
4033109 4033371 5028092 5028354 526
4033532 4033781 5028515 5028764 500
4033965 4034539 5028948 5029522 1150
4035078 4035360 5029978 5030260 566
4035414 4035637 5030314 5030537 448
4035754 4036094 5030654 5030994 682
4036330 4036820 5031230 5031720 982
4037310 4037891 5032208 5032789 1164
# chain 1075: length 1 score 536
3943851 3944118 5032522 5032789 536
# chain 1076: length 1 score 528
4217734 4217997 5039704 5039967 528
# chain 1077: length 1 score 410
4218639 4218843 5040609 5040813 410
# chain 1078: length 3 score 1359
4220056 4220269 5042026 5042239 428
4220349 4220555 5042320 5042526 414
4220557 4220897 5042528 5042868 682
# chain 1079: length 1 score 436
4222189 4222406 5044160 5044377 436
# chain 1080: length 1 score 442
4223590 4223810 5045561 5045781 442
# chain 1081: length 3 score 900
4224226 4224461 5046197 5046432 472
4224517 4224776 5046488 5046747 520
4225045 4225323 5047016 5047294 558
# chain 1082: length 5 score 2710
4229111 4229551 5057182 5057622 882
4229679 4229908 5057750 5057979 460
4229994 4230336 5058065 5058407 686
4230657 4231155 5058728 5059226 998
4231157 4231535 5059228 5059606 758
# chain 1083: length 1 score 634
4235356 4235672 5063441 5063757 634
# chain 1084: length 17 score 5538
4237564 4237988 5065649 5066073 850
4238057 4238268 5066142 5066353 424
4238406 4238620 5066491 5066705 430
4238622 4238986 5066707 5067071 730
4239483 4240332 5067568 5068417 1700
4240577 4240851 5068662 5068936 550
4241194 4241513 5069279 5069598 640
4241860 4242134 5069945 5070219 550
4242340 4242595 5070425 5070680 512
4242692 4242965 5070777 5071050 548
4243246 4243553 5071331 5071638 616
4243777 4244103 5071862 5072188 654
4244267 4244585 5072352 5072670 638
4244704 4245302 5072789 5073387 1198
4245304 4245658 5073389 5073743 710
4245858 4246069 5073943 5074154 424
4246359 4246764 5074444 5074849 812
# chain 1085: length 4 score 2058
4253485 4253771 5081478 5081764 574
4253773 4254142 5081766 5082135 740
4254248 4254495 5082241 5082488 496
4254560 4254856 5082553 5082849 594
# chain 1086: length 1 score 922
4256676 4257136 5084669 5085129 922
# chain 1087: length 1 score 430
4259211 4259425 5087175 5087389 430
# chain 1088: length 1 score 452
4262253 4262478 5090217 5090442 452
# chain 1089: length 2 score 1458
4263080 4263430 5091044 5091394 702
4263432 4263811 5091396 5091775 760
# chain 1090: length 1 score 430
4264612 4264826 5092576 5092790 430
# chain 1091: length 2 score 1144
4267726 4267949 5095682 5095905 448
4267951 4268300 5095907 5096256 700
# chain 1092: length 1 score 830
4271274 4271688 5099230 5099644 830
# chain 1093: length 1 score 484
4272543 4272784 5100500 5100741 484
# chain 1094: length 3 score 1546
4274885 4275144 5102841 5103100 520
4275257 4275698 5103213 5103654 884
4275783 4276051 5103739 5104007 538
# chain 1095: length 1 score 574
4280733 4281019 5108691 5108977 574
# chain 1096: length 4 score 1349
4282323 4282554 5110281 5110512 464
4282634 4282898 5110592 5110856 530
4282979 4283305 5110938 5111264 654
4283580 4283866 5111539 5111825 574
# chain 1097: length 7 score 2866
4284575 4284796 5112534 5112755 444
4284945 4285241 5112904 5113200 594
4285243 4285625 5113202 5113584 766
4285817 4286408 5113776 5114367 1184
4286746 4286983 5114705 5114942 476
4287171 4287708 5115130 5115667 1076
4287908 4288139 5115867 5116098 464
# chain 1098: length 1 score 944
4291742 4292213 5119701 5120172 944
# chain 1099: length 7 score 3416
4294024 4294328 5121519 5121823 610
4294488 4294792 5121983 5122287 610
4295091 4295297 5122586 5122792 414
4295299 4295540 5122794 5123035 484
4295545 4295804 5123040 5123299 520
4295971 4296203 5123466 5123698 466
4296217 4297019 5123712 5124514 1606
# chain 1100: length 1 score 422
4300511 4300721 5128006 5128216 422
# chain 1101: length 2 score 780
4301558 4301780 5129053 5129275 446
4301827 4302040 5129322 5129535 428
# chain 1102: length 1 score 762
4303916 4304296 5131411 5131791 762
# chain 1103: length 1 score 494
4312689 4312935 5142354 5142600 494
# chain 1104: length 1 score 436
4315512 4315729 5145178 5145395 436
# chain 1105: length 1 score 464
4318700 4318931 5148366 5148597 464
# chain 1106: length 2 score 1068
4323945 4324269 5153204 5153528 650
4324271 4324481 5153530 5153740 422
# chain 1107: length 1 score 1218
4325926 4326534 5155186 5155794 1218
# chain 1108: length 8 score 4490
4327881 4328194 5157141 5157454 628
4328196 4328668 5157456 5157928 946
4328796 4329079 5158056 5158339 568
4329081 4329292 5158341 5158552 424
4330003 4330414 5159263 5159674 824
4330464 4330844 5159724 5160104 762
4330881 4331442 5160141 5160702 1124
4331444 4331982 5160704 5161242 1078
# chain 1109: length 3 score 926
4336113 4336322 5165373 5165582 420
4336393 4336693 5165653 5165953 602
4336927 4337183 5166187 5166443 514
# chain 1110: length 1 score 490
4337794 4338038 5167054 5167298 490
# chain 1111: length 2 score 1266
4338994 4339308 5168254 5168568 630
4339353 4339715 5168613 5168975 726
# chain 1112: length 1 score 502
4340892 4341142 5170152 5170402 502
# chain 1113: length 1 score 752
4341624 4341999 5170884 5171259 752
# chain 1114: length 10 score 3484
4344740 4344957 5174001 5174218 436
4344959 4345211 5174220 5174472 506
4345213 4345571 5174474 5174832 718
4346026 4346523 5175287 5175784 996
4346631 4346834 5175892 5176095 408
4347166 4347790 5176427 5177051 1250
4347927 4348213 5177188 5177474 574
4348434 4348726 5177695 5177987 586
4348728 4348972 5177989 5178233 490
4349163 4349372 5178424 5178633 420
# chain 1115: length 24 score 12303
4353534 4354238 5182795 5183499 1410
4354273 4354526 5183534 5183787 508
4354528 4354910 5183789 5184171 766
4354912 4355495 5184173 5184756 1168
4355497 4355732 5184758 5184993 472
4355851 4356510 5185112 5185771 1320
4356602 4356917 5185863 5186178 632
4356919 4357185 5186180 5186446 534
4357376 4357687 5186637 5186948 624
4358283 4358518 5187545 5187780 472
4358531 4358953 5187793 5188215 846
4359009 4359406 5188271 5188668 796
4359408 4359650 5188670 5188912 486
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4361109 4361356 5190371 5190618 496
4361397 4361736 5190659 5190998 680
4361967 4362177 5191229 5191439 422
4362309 4362521 5191571 5191783 426
4362523 4362876 5191785 5192138 708
4363046 4363258 5192308 5192520 426
4363260 4363546 5192522 5192808 574
4363548 4364194 5192810 5193456 1294
4364202 4364791 5193464 5194053 1180
4364793 4364992 5194055 5194254 400
# chain 1116: length 1 score 986
4389846 4390338 5218382 5218874 986
# chain 1117: length 2 score 1458
4390965 4391449 5219501 5219985 970
4391451 4391696 5219987 5220232 492
# chain 1118: length 3 score 1588
4392660 4392949 5221196 5221485 580
4392951 4393314 5221487 5221850 728
4393390 4393607 5221926 5222143 436
# chain 1119: length 1 score 628
4394572 4394885 5223108 5223421 628
# chain 1120: length 2 score 1704
4396694 4397281 5225230 5225817 1176
4397605 4398192 5226141 5226728 1176
# chain 1121: length 8 score 5414
4398186 4398649 5226723 5227186 928
4398699 4399042 5227236 5227579 688
4399262 4399973 5227799 5228510 1424
4400047 4400534 5228584 5229071 976
4400536 4400837 5229073 5229374 604
4400839 4401199 5229376 5229736 722
4401291 4401502 5229828 5230039 424
4401693 4402147 5230230 5230684 910
# chain 1122: length 1 score 568
4409733 4410016 5238272 5238555 568
# chain 1123: length 2 score 2280
4410543 4411443 5239082 5239982 1802
4411568 4411931 5240107 5240470 728
# chain 1124: length 58 score 9155
4413245 4413458 5241784 5241997 428
4413460 4414119 5241999 5242658 1320
4414166 4414590 5242705 5243129 850
4415106 4415865 5243645 5244404 1520
4415867 4416119 5244406 5244658 506
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4418721 4419265 5247260 5247804 1090
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4422028 4422356 5250566 5250894 658
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4423235 4423484 5251773 5252022 500
4423486 4423779 5252024 5252317 588
4423832 4424168 5252370 5252706 674
4424170 4424765 5252708 5253303 1192
4425009 4425265 5253547 5253803 514
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4426044 4426243 5256330 5256529 400
4426245 4426957 5256531 5257243 1426
4427159 4427541 5257445 5257827 766
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4430365 4430680 5260651 5260966 632
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4432539 4432756 5262814 5263031 436
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4433601 4433926 5263876 5264201 652
4433963 4434274 5264238 5264549 624
4435031 4435251 5265306 5265526 442
4435253 4435481 5265528 5265756 458
4436111 4436332 5266387 5266608 444
4436615 4437230 5266891 5267506 1232
4437503 4437711 5267796 5268004 418
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4438730 4438975 5269023 5269268 492
4439166 4439479 5269459 5269772 628
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4440303 4440757 5270596 5271050 910
4441584 4441911 5271877 5272204 656
4443981 4444452 5274274 5274745 944
4444454 4444845 5274747 5275138 784
4444973 4445194 5275266 5275487 444
4445391 4445813 5275684 5276106 846
4445815 4446120 5276108 5276413 612
4446140 4446428 5276433 5276721 578
4446534 4447021 5276827 5277314 976
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4449229 4449635 5279524 5279930 814
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# chain 1125: length 1 score 668
4476003 4476336 5306344 5306677 668
# chain 1126: length 1 score 402
4478263 4478463 5308503 5308703 402
# chain 1127: length 1 score 868
4478850 4479283 5309086 5309519 868
# chain 1128: length 1 score 418
4480524 4480732 5310760 5310968 418
# chain 1129: length 12 score 6036
4481043 4481572 5311279 5311808 1060
4481615 4481848 5311851 5312084 468
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# chain 1130: length 2 score 806
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# chain 1131: length 1 score 402
4535262 4535462 5365009 5365209 402
# chain 1132: length 1 score 1174
4536431 4537017 5366178 5366764 1174
# chain 1133: length 2 score 732
4538109 4538335 5367856 5368082 454
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# chain 1134: length 1 score 508
4539505 4539758 5369252 5369505 508
# chain 1135: length 2 score 972
4540615 4540884 5370345 5370614 540
4540886 4541103 5370616 5370833 436
# chain 1136: length 1 score 588
4542032 4542325 5371762 5372055 588
# chain 1137: length 2 score 1328
4542802 4543107 5372531 5372836 612
4543111 4543472 5372840 5373201 724
# chain 1138: length 1 score 460
4544659 4544888 5374388 5374617 460
# chain 1139: length 2 score 904
4548476 4548708 5378136 5378368 466
4548909 4549328 5378569 5378988 840
# chain 1140: length 1 score 500
4550051 4550300 5379711 5379960 500
# chain 1141: length 2 score 658
4551504 4551751 5381165 5381412 496
4551873 4552075 5381534 5381736 406
# chain 1142: length 2 score 1130
4554158 4554568 5383819 5384229 822
4554676 4554937 5384337 5384598 524
# chain 1143: length 4 score 2106
4556607 4556926 5386268 5386587 640
4556976 4557328 5386637 5386989 706
4557330 4557696 5386991 5387357 734
4557847 4558062 5387508 5387723 432
# chain 1144: length 1 score 426
4561823 4562035 5399775 5399987 426
# chain 1145: length 1 score 594
4567898 4568194 5405866 5406162 594
# chain 1146: length 1 score 414
4586391 4586597 5418882 5419088 414
# chain 1147: length 3 score 1478
4589247 4589498 5422424 5422675 504
4589544 4589756 5422721 5422933 426
4589758 4590079 5422935 5423256 644
# chain 1148: length 4 score 2033
4591606 4591905 5424792 5425091 600
4592020 4592269 5425206 5425455 500
4592317 4592556 5425504 5425743 480
4592558 4592949 5425745 5426136 784
# chain 1149: length 1 score 1064
4594693 4595224 5427880 5428411 1064
# chain 1150: length 30 score 10456
4595901 4596268 5429088 5429455 736
4596459 4596916 5429646 5430103 916
4596918 4597156 5430105 5430343 478
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4600811 4601319 5434000 5434508 1018
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4601827 4602472 5435016 5435661 1292
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4606201 4607439 5439076 5440314 2478
4607576 4607775 5440451 5440650 400
4607972 4608300 5440847 5441175 658
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4608604 4609160 5441479 5442035 1114
4609548 4610186 5442423 5443061 1278
4610318 4610595 5443193 5443470 556
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4613016 4613327 5445687 5445998 624
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4614243 4614763 5446914 5447434 1042
4615143 4615543 5447814 5448214 802
4615599 4616269 5448270 5448940 1342
4616649 4616956 5449320 5449627 616
4617023 4617937 5449694 5450608 1830
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# chain 1151: length 2 score 1974
4637081 4637382 5468709 5469010 604
4637525 4638352 5469153 5469980 1656
genometools-1.5.1/testdata/chaindata/chain-local20-wf1.8000066400000000000000000003756361211610345200227150ustar00rootroot00000000000000# chain 0: length 1 score 1393
5851 6237 5868 6254 1393
# chain 1: length 14 score 10918
7627 7937 7644 7954 1119
8079 8457 8096 8474 1364
8687 8994 8704 9011 1108
8996 9375 9013 9392 1368
9377 9666 9394 9683 1044
10024 10406 10041 10423 1378
10408 10715 10425 10732 1108
11439 11663 11456 11680 810
11695 11898 11712 11915 734
12026 12235 12043 12252 756
12384 12712 12401 12729 1184
13131 13339 13148 13356 752
13719 14230 13736 14247 1843
14232 14645 14249 14662 1490
# chain 2: length 1 score 1450
25045 25447 29457 29859 1450
# chain 3: length 1 score 849
26789 27024 31164 31399 849
# chain 4: length 2 score 1775
27712 28067 32087 32442 1281
28223 28446 32598 32821 806
# chain 5: length 1 score 1216
29506 29843 33881 34218 1216
# chain 6: length 1 score 748
30706 30913 35081 35288 748
# chain 7: length 1 score 828
31887 32116 36262 36491 828
# chain 8: length 8 score 5127
33552 33766 37927 38141 774
34112 34597 38486 38971 1749
35170 35491 39577 39898 1159
35499 35831 39906 40238 1198
36263 36479 40670 40886 781
37032 37439 41439 41846 1468
37534 37775 41941 42182 871
37777 38103 42184 42510 1177
# chain 9: length 1 score 763
43562 43773 47976 48187 763
# chain 10: length 1 score 741
44455 44660 48869 49074 741
# chain 11: length 5 score 3160
45555 45805 49969 50219 903
45950 46173 50365 50588 806
46253 46632 50668 51047 1368
46901 47137 51316 51552 853
47515 47785 51930 52200 975
# chain 12: length 1 score 1332
49571 49940 53986 54355 1332
# chain 13: length 16 score 19954
51097 51551 56073 56527 1638
51621 51901 56597 56877 1011
51924 52135 56900 57111 763
53284 53627 58260 58603 1238
53902 54335 58878 59311 1562
54337 54981 59313 59957 2322
54983 56483 59959 61459 5403
56485 56939 61461 61915 1638
56941 57835 61917 62811 3222
57928 58141 62904 63117 770
59485 59772 64418 64705 1036
59831 60053 64764 64986 802
60245 60545 65178 65478 1083
60547 60890 65480 65823 1238
60943 61457 65876 66390 1854
61459 61700 66392 66633 871
# chain 14: length 4 score 2428
82978 83294 87586 87902 1141
83392 83799 88000 88407 1468
84493 84737 89099 89343 882
84949 85210 89555 89816 943
# chain 15: length 3 score 2328
87279 87522 91885 92128 878
87794 88118 92400 92724 1170
88120 88349 92726 92955 828
# chain 16: length 7 score 10388
4164382 4165237 227247 228102 3081
4165275 4165798 228140 228663 1886
4166150 4166354 229021 229225 738
4166865 4167388 229736 230259 1886
4167448 4167940 230318 230810 1774
4168084 4168332 230954 231202 896
4168430 4169134 231300 232004 2538
# chain 17: length 7 score 9922
4205569 4205867 226947 227245 1076
4205869 4206724 227247 228102 3081
4206762 4207279 228140 228657 1864
4208267 4208790 229736 230259 1886
4208850 4209342 230318 230810 1774
4209486 4209734 230954 231202 896
4209832 4210413 231300 231881 2095
# chain 18: length 7 score 10737
4033264 4034119 227247 228102 3081
4034157 4034674 228140 228657 1864
4034682 4035035 228665 229018 1274
4035744 4036270 229736 230262 1897
4036326 4036820 230318 230812 1782
4036971 4037212 230961 231202 871
4037310 4037891 231300 231881 2095
# chain 19: length 10 score 10545
3939284 3939507 226956 227179 806
3939656 3940331 227328 228003 2433
3940467 3940984 228140 228657 1864
3941255 3941460 229020 229225 741
3941972 3942495 229736 230259 1886
3942555 3943049 230318 230812 1782
3943061 3943439 230824 231202 1364
3943441 3943705 231204 231468 954
3943851 3944118 231614 231881 964
3944336 3944572 232098 232334 853
# chain 20: length 166 score 81460
89754 90328 94360 94934 2070
90591 90949 95197 95555 1292
91187 91785 95793 96391 2156
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93089 93369 97695 97975 1011
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101175 101494 105781 106100 1152
101721 101923 106327 106529 730
102613 102831 107219 107437 788
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103604 103840 108210 108446 853
103842 104168 108448 108774 1177
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106099 107460 110705 112066 4903
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110903 111227 115509 115833 1170
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119259 119491 123749 123981 838
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135256 135635 139629 140008 1368
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179070 179513 183270 183713 1598
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181390 181646 185590 185846 925
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183133 183406 187333 187606 986
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188339 188709 191826 192196 1335
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195040 197671 198385 201016 9475
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199262 199926 202607 203271 2394
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201640 202500 204984 205844 3099
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203135 203440 206479 206784 1101
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213337 213554 216681 216898 784
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215380 215675 218713 219008 1065
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218188 218576 221520 221908 1400
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220515 220882 223846 224213 1324
220884 221193 224215 224524 1116
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222448 222986 225779 226317 1940
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224890 225585 228222 228917 2505
225900 226112 229232 229444 766
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227969 228550 231300 231881 2095
228768 229025 232098 232355 928
229598 229840 232928 233170 874
229853 230143 233183 233473 1047
# chain 21: length 1 score 723
3622269 3622469 272913 273113 723
# chain 22: length 1 score 878
3622911 3623154 273555 273798 878
# chain 23: length 4 score 2458
1527877 1528098 275467 275688 799
1528181 1528512 275770 276101 1195
1529096 1529346 276684 276934 903
1529348 1529596 276935 277183 896
# chain 24: length 1 score 1195
297132 297463 330317 330648 1195
# chain 25: length 1 score 1119
299169 299479 332354 332664 1119
# chain 26: length 1 score 936
300524 300783 333709 333968 936
# chain 27: length 1 score 921
301750 302005 334935 335190 921
# chain 28: length 4 score 2207
305109 305541 338294 338726 1558
306139 306369 339324 339554 831
306382 306626 339567 339811 882
306907 307106 340092 340291 720
# chain 29: length 1 score 1170
308316 308640 341501 341825 1170
# chain 30: length 1 score 1141
309476 309792 342661 342977 1141
# chain 31: length 1 score 982
313588 313860 353941 354213 982
# chain 32: length 1 score 835
316129 316360 358934 359165 835
# chain 33: length 7 score 4123
318125 318630 361618 362123 1821
318632 318938 362125 362431 1105
319028 319326 362521 362819 1076
319744 320032 363237 363525 1040
321266 321471 364759 364964 741
321473 321699 364966 365192 817
322401 323072 365894 366565 2419
# chain 34: length 6 score 6763
328133 328560 376575 377002 1540
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329022 329383 377464 377825 1303
329619 330088 378061 378530 1692
330090 330409 378532 378851 1152
330540 330759 378982 379201 792
# chain 35: length 1 score 1184
332518 332846 384784 385112 1184
# chain 36: length 5 score 2850
334160 334386 386435 386661 817
334409 334749 386684 387024 1227
335190 335460 387465 387735 975
335793 336128 388068 388403 1209
336547 336839 388822 389114 1054
# chain 37: length 1 score 752
340819 341027 393187 393395 752
# chain 38: length 1 score 874
341549 341791 393917 394159 874
# chain 39: length 3 score 4018
342414 343104 399888 400578 2487
343301 343735 400775 401209 1566
343919 344120 401393 401594 727
# chain 40: length 1 score 1771
351607 352098 408800 409291 1771
# chain 41: length 1 score 957
354178 354443 411935 412200 957
# chain 42: length 2 score 2357
355443 355817 413200 413574 1350
355819 356099 413576 413856 1011
# chain 43: length 1 score 1022
358310 358593 415864 416147 1022
# chain 44: length 1 score 838
361300 361532 418854 419086 838
# chain 45: length 2 score 1914
362254 362582 419808 420136 1184
362638 362871 420192 420425 842
# chain 46: length 1 score 730
367228 367430 426606 426808 730
# chain 47: length 5 score 3593
368110 368314 427488 427692 738
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369620 370014 428998 429392 1422
370352 370704 429730 430082 1270
370840 371258 430218 430636 1508
# chain 48: length 2 score 2136
374964 375281 433940 434257 1144
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# chain 49: length 1 score 1242
378703 379047 437579 437923 1242
# chain 50: length 3 score 2201
385128 385475 446908 447255 1252
385631 385848 447411 447628 784
386054 386300 447834 448080 889
# chain 51: length 1 score 752
388046 388254 449826 450034 752
# chain 52: length 153 score 87550
392824 393267 453381 453824 1598
393274 393475 453831 454032 727
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# chain 53: length 2 score 1282
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# chain 54: length 2 score 2486
632574 632966 714602 714994 1414
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# chain 55: length 104 score 32611
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# chain 56: length 3 score 2390
3759827 3760224 807809 808206 1432
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# chain 57: length 3 score 2164
3616903 3617237 807872 808206 1206
3617546 3617774 808515 808743 824
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# chain 58: length 1 score 936
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# chain 59: length 2 score 1244
3762518 3762777 810500 810759 936
3762983 3763182 810965 811164 720
# chain 60: length 1 score 720
3762983 3763182 812836 813035 720
# chain 61: length 1 score 1198
3622137 3622469 816144 816476 1198
# chain 62: length 11 score 9994
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# chain 63: length 12 score 10001
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# chain 64: length 7 score 4336
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# chain 65: length 2 score 2150
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# chain 66: length 2 score 1148
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# chain 67: length 2 score 1426
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# chain 68: length 1 score 1026
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# chain 69: length 1 score 824
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# chain 70: length 1 score 817
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# chain 71: length 3 score 2031
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# chain 72: length 5 score 7605
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# chain 73: length 1 score 856
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# chain 74: length 1 score 1206
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# chain 75: length 1 score 738
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# chain 76: length 2 score 2571
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# chain 77: length 1 score 1526
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# chain 78: length 18 score 5729
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# chain 81: length 1 score 788
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# chain 82: length 1 score 968
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# chain 83: length 1 score 979
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# chain 84: length 1 score 1202
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# chain 85: length 1 score 813
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# chain 86: length 2 score 1913
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# chain 87: length 12 score 10252
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# chain 88: length 1 score 882
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# chain 90: length 1 score 828
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# chain 91: length 138 score 89859
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# chain 92: length 1 score 741
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# chain 93: length 1 score 781
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# chain 94: length 1 score 982
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# chain 95: length 1 score 763
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# chain 96: length 1 score 1602
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# chain 97: length 16 score 30875
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# chain 98: length 1 score 774
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# chain 99: length 1 score 792
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# chain 100: length 1 score 882
4505653 4505897 1465417 1465661 882
# chain 101: length 1 score 1288
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# chain 102: length 1 score 828
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# chain 103: length 1 score 1058
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# chain 104: length 3 score 1928
1098625 1098917 1543627 1543919 1054
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# chain 105: length 92 score 37342
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# chain 106: length 3 score 1630
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# chain 110: length 8 score 5216
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# chain 115: length 1 score 2314
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# chain 117: length 1 score 1281
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# chain 118: length 1 score 741
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# chain 119: length 1 score 784
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# chain 120: length 1 score 2725
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# chain 121: length 1 score 871
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# chain 122: length 1 score 774
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# chain 123: length 78 score 39659
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# chain 124: length 3 score 2275
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# chain 125: length 3 score 1710
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# chain 126: length 403 score 125842
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# chain 180: length 1 score 2869
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# chain 188: length 30 score 13231
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# chain 194: length 1 score 1126
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# chain 199: length 2 score 1996
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# chain 203: length 1 score 2700
1467373 1468122 3500250 3500999 2700
# chain 204: length 1 score 2520
269818 270517 3500250 3500949 2520
# chain 205: length 1 score 1378
2788875 2789257 3522735 3523117 1378
# chain 206: length 1 score 720
2792327 2792526 3526187 3526386 720
# chain 207: length 22 score 11001
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# chain 208: length 1 score 1738
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# chain 209: length 1 score 914
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# chain 210: length 1 score 835
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# chain 211: length 2 score 1698
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# chain 212: length 1 score 781
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# chain 213: length 1 score 939
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# chain 214: length 1 score 1076
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# chain 215: length 14 score 6566
2846859 2847158 3582222 3582521 1080
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# chain 216: length 14 score 12141
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# chain 217: length 2 score 1971
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# chain 218: length 1 score 831
2888055 2888285 3619852 3620082 831
# chain 219: length 2 score 1233
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# chain 220: length 1 score 756
2891093 2891302 3622890 3623099 756
# chain 221: length 1 score 774
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# chain 222: length 1 score 1173
2898460 2898785 3630257 3630582 1173
# chain 223: length 1 score 1022
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# chain 224: length 100 score 48279
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# chain 225: length 1 score 1753
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# chain 226: length 44 score 19157
3138726 3138940 3890782 3890996 774
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# chain 227: length 9 score 12478
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# chain 228: length 376 score 179068
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# chain 229: length 4 score 2761
3616903 3617237 4514597 4514931 1206
3617546 3617774 4515240 4515468 824
3617776 3618000 4515470 4515694 810
3618297 3618612 4515991 4516306 1137
# chain 230: length 3 score 3749
729222 729757 4514933 4515468 1929
730140 730432 4515851 4516143 1054
730483 730936 4516194 4516647 1634
# chain 231: length 1 score 849
3907598 3907833 4708063 4708298 849
# chain 232: length 1 score 928
3908983 3909240 4709448 4709705 928
# chain 233: length 1 score 943
3911180 3911441 4718382 4718643 943
# chain 234: length 1 score 781
224672 224888 4747537 4747753 781
# chain 235: length 8 score 12899
4164227 4165138 4746626 4747537 3283
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4166483 4166760 4748795 4749072 1000
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4168430 4169134 4750743 4751447 2538
# chain 236: length 8 score 12768
4205631 4206625 4746543 4747537 3582
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4207885 4208162 4748795 4749072 1000
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4209832 4210413 4750743 4751324 2095
# chain 237: length 8 score 12273
4033109 4034020 4746626 4747537 3283
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4037310 4037891 4750743 4751324 2095
# chain 238: length 9 score 12310
223741 224671 4746607 4747537 3351
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227969 228550 4750743 4751324 2095
228768 229004 4751541 4751777 853
# chain 239: length 8 score 10437
4164576 4164974 4843160 4843558 1436
4164976 4165237 4843560 4843821 943
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# chain 240: length 9 score 11547
224109 224507 4843160 4843558 1436
224509 224888 4843560 4843939 1368
224890 225585 4843941 4844636 2505
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# chain 241: length 8 score 9583
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# chain 242: length 8 score 8834
3939284 3939507 4842675 4842898 806
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# chain 243: length 3 score 1293
3759943 3760224 4940178 4940459 1015
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# chain 244: length 3 score 1293
3616956 3617237 4940178 4940459 1015
3617549 3617774 4940772 4940997 813
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# chain 245: length 4 score 3243
729265 729530 4940505 4940770 957
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# chain 246: length 1 score 936
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# chain 247: length 2 score 1244
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# chain 248: length 6 score 5922
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# chain 249: length 10 score 8965
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# chain 250: length 9 score 9614
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# chain 251: length 6 score 4536
3939284 3939507 5027956 5028179 806
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# chain 252: length 6 score 4282
223741 224022 5028073 5028354 1015
224183 224432 5028515 5028764 900
224890 225190 5029222 5029522 1083
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# chain 253: length 8 score 7352
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4033532 4033781 5028515 5028764 900
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4037310 4037891 5032208 5032789 2095
# chain 254: length 643 score 139694
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genometools-1.5.1/testdata/chaindata/chain-local2b-wf1.8-maxgap10000066400000000000000000000010371211610345200243700ustar00rootroot00000000000000# chain 0: length 7 score 21507
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genometools-1.5.1/testdata/chaindata/chain-local2p000066400000000000000000000070041211610345200221310ustar00rootroot00000000000000# chain 0: length 98 score 36877
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genometools-1.5.1/testdata/chaindata/chain-local2p-wf1.8000066400000000000000000000327341211610345200230020ustar00rootroot00000000000000# chain 0: length 376 score 179068
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3527798 3528156 4251980 4252338 1292
3529862 3530732 4254044 4254914 3135
3531598 3531959 4255780 4256141 1303
3533168 3533540 4257350 4257722 1342
3533605 3533840 4257787 4258022 849
3533944 3534609 4258126 4258791 2397
3534872 3535125 4259054 4259307 914
3535502 3535933 4259684 4260115 1555
3537716 3538058 4261881 4262223 1234
3538118 3538388 4262283 4262553 975
3538720 3538988 4262885 4263153 968
3539188 3539423 4263353 4263588 849
3542064 3542270 4266227 4266433 745
3543166 3543377 4267329 4267540 763
3544363 3544621 4268530 4268788 932
3545028 3545338 4269195 4269505 1119
3546156 3546421 4270257 4270522 957
3547430 3547650 4271531 4271751 795
3547653 3548003 4271754 4272104 1263
3548005 3548356 4272106 4272457 1267
3548687 3548920 4272788 4273021 842
3549389 3549652 4273490 4273753 950
3549996 3550236 4274097 4274337 867
3550457 3550734 4274558 4274835 1000
3550966 3551195 4275067 4275296 828
3551197 3551564 4275298 4275665 1324
3551566 3551783 4275667 4275884 784
3552517 3552752 4276618 4276853 849
3557336 3557543 4282277 4282484 748
3557579 3557826 4282520 4282767 892
3558241 3558696 4283182 4283637 1641
3558933 3559148 4283874 4284089 777
3559415 3559617 4284356 4284558 730
3559675 3559992 4284616 4284933 1144
3560557 3560792 4285498 4285733 849
3561803 3562239 4289596 4290032 1573
3562646 3563634 4290439 4291427 3560
3563858 3564327 4291651 4292120 1692
3564329 3564567 4292122 4292360 860
3564976 3565428 4292769 4293221 1630
3565472 3566159 4293265 4293952 2476
3566161 3566576 4293954 4294369 1497
3566584 3567271 4294377 4295064 2476
3567273 3567496 4295066 4295289 806
3567597 3567963 4295390 4295756 1321
3568254 3568461 4296047 4296254 748
3568479 3569058 4296272 4296851 2088
3569644 3569895 4297437 4297688 907
3570512 3570762 4298305 4298555 903
3570926 3571649 4298719 4299442 2606
3571651 3571952 4299444 4299745 1087
3572002 3572237 4299795 4300030 849
3572517 3572896 4300309 4300688 1368
genometools-1.5.1/testdata/chaindata/chain-local2p-wf1.8-maxgap10000066400000000000000000000010371211610345200244060ustar00rootroot00000000000000# chain 0: length 7 score 21507
1085337 1086089 1412837 1413589 2710
1086091 1086892 1413591 1414392 2887
1086894 1088334 1414394 1415834 5187
1088336 1088973 1415836 1416473 2296
1088975 1089198 1416475 1416698 806
1089200 1090692 1416700 1418192 5374
1090694 1091324 1418194 1418824 2271
# chain 1: length 6 score 21134
3442567 3445133 4189568 4192134 9241
3445135 3445932 4192136 4192933 2872
3445934 3446766 4192935 4193767 2998
3446768 3447008 4193769 4194009 867
3447010 3447961 4194011 4194962 3427
3447963 3448448 4194964 4195449 1749
genometools-1.5.1/testdata/chaindata/chain-local55p-silent000066400000000000000000000002041211610345200235100ustar00rootroot00000000000000# chain 0: length 21 score 20527
# chain 1: length 26 score 24372
# chain 2: length 98 score 36877
# chain 3: length 50 score 19920
genometools-1.5.1/testdata/chaindata/chain-silent-global000066400000000000000000000000451211610345200233270ustar00rootroot00000000000000# chain 0: length 4258 score 2988370
genometools-1.5.1/testdata/chaindata/matches-nd.chains000066400000000000000000000007301211610345200230030ustar00rootroot00000000000000# chain 0: length 2 score 2
0 32 530 551 1
33 75 654 695 1
# chain 1: length 2 score 2
0 32 618 639 1
33 75 654 695 1
# chain 2: length 2 score 2
0 32 530 551 1
33 75 679 695 1
# chain 3: length 2 score 2
0 32 618 639 1
33 75 679 695 1
# chain 4: length 2 score 2
0 32 530 551 1
33 75 723 750 1
# chain 5: length 2 score 2
0 32 618 639 1
33 75 723 750 1
# chain 6: length 2 score 2
0 32 530 551 1
33 75 727 758 1
# chain 7: length 2 score 2
0 32 618 639 1
33 75 727 758 1
genometools-1.5.1/testdata/chaindata/matches-nd.txt000066400000000000000000000002341211610345200223540ustar00rootroot0000000000000033 75 43 61 1
33 75 381 411 1
33 75 382 415 1
33 75 390 415 1
0 32 530 551 1
0 32 618 639 1
33 75 654 695 1
33 75 679 695 1
33 75 723 750 1
33 75 727 758 1
genometools-1.5.1/testdata/consensus_sa/000077500000000000000000000000001211610345200203605ustar00rootroot00000000000000genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input.in000066400000000000000000000012731211610345200252610ustar00rootroot00000000000000gi|19742504|gb|AU227857.1|AU227857,-,48228-48472,49045-49140,49222-49331
gi|8731880|gb|AV560454.1|AV560454,-,48231-48472,49045-49140,49222-49485
gi|21404343|gb|AY085633.1|,-,48232-48472,48847-48974,49045-49140,49222-49760,50200-50360
gi|22531065|gb|AY136371.1|,-,48271-48472,48913-48974,49045-49140,49222-49760,50200-50410
gi|23198031|gb|BT000224.1|,-,48417-48472,48913-48974,49045-49140,49222-49760,50200-50299
gi|5839305|gb|AI992400.1|AI992400,-,49340-49760,50200-50356
gi|19876023|gb|AU236854.1|AU236854,-,49441-49760,50200-50363
gi|1054435|gb|H77184.1|H77184,-,49474-49760,50200-50356
gi|26019954|gb|CA781911.1|CA781911,-,49526-49760,50200-50449
gi|19871952|gb|AV829892.1|AV829892,-,50275-50422
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input.out000066400000000000000000000001111211610345200254500ustar00rootroot00000000000000contains [0,1,5,6,7,8,9]
contains [3,4,5,6,7,8,9]
contains [2,5,6,7,8,9]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input10.in000066400000000000000000000257451211610345200254340ustar00rootroot00000000000000gi|8690382|gb|AV530099.1|AV530099,+,73361-73629,74908-75027,75121-75265
gi|19865640|gb|AV823580.1|AV823580,+,73485-73629,74908-75027,75121-75261
gi|19869340|gb|AV827280.1|AV827280,+,73485-73629,74908-75027,75121-75357,75442-75545
gi|19870458|gb|AV828398.1|AV828398,+,73485-73629,74908-75027,75121-75281
gi|19867428|gb|AV825368.1|AV825368,+,73485-73629,74908-75027,75121-75357,75442-75535
gi|19870789|gb|AV828729.1|AV828729,+,73485-73629,74908-75027,75121-75357,75442-75471
gi|19871830|gb|AV829770.1|AV829770,+,73485-73629,74908-75027,75121-75357,75442-75537
gi|19872557|gb|AV830497.1|AV830497,+,73488-73629,74908-75027,75121-75357,75442-75506
gi|19872786|gb|AV830726.1|AV830726,+,73489-73629,74908-75027,75121-75161
gi|166745|gb|M24107.1|ATHHATPA,+,73497-73629,74908-75027,75121-75357,75442-76203,76299-76421,76500-76604,76696-76840,76930-77094,77187-77425,77520-77552,77643-77724,77812-77972,78102-78275,78360-78542,78629-78810,78902-79266
gi|8689542|gb|AV529259.1|AV529259,+,73504-73629,74908-75027,75121-75357,75442-75460
gi|9788776|gb|BE530786.1|BE530786,+,73505-73629,74908-75025
gi|8689093|gb|AV528810.1|AV528810,+,73506-73629,74908-75027,75121-75357,75442-75468
gi|8690319|gb|AV530036.1|AV530036,+,73507-73629,74908-75027,75121-75357,75442-75460
gi|8688689|gb|AV528406.1|AV528406,+,73509-73629,74908-75027,75121-75357,75442-75469
gi|8332698|gb|BE037682.1|BE037682,+,73509-73629,74908-75027,75121-75357,75442-75672
gi|8689631|gb|AV529348.1|AV529348,+,73513-73629,74908-75027,75121-75357,75442-75523
gi|8688745|gb|AV528462.1|AV528462,+,73540-73629,74908-75027,75121-75357,75442-75544
gi|8689405|gb|AV529122.1|AV529122,+,73548-73629,74908-75027,75121-75357,75442-75527
gi|8687701|gb|AV528173.1|AV528173,+,73556-73629,74908-75027,75121-75357,75442-75566
gi|8690042|gb|AV529759.1|AV529759,+,73576-73629,74908-75027,75121-75357,75442-75511
gi|8718164|gb|AV546750.1|AV546750,+,73590-73629,74908-75027,75121-75369
gi|8689841|gb|AV529558.1|AV529558,+,74948-75027,75121-75357,75442-75636
gi|8726312|gb|AV554897.1|AV554897,+,74980-75027,75121-75357,75442-75619
gi|8689350|gb|AV529067.1|AV529067,+,75154-75357,75442-75550
gi|8688899|gb|AV528616.1|AV528616,+,75188-75357,75442-75542
gi|8690214|gb|AV529931.1|AV529931,+,75207-75357,75442-75625
gi|8689229|gb|AV528946.1|AV528946,+,75279-75357,75442-75876
gi|8689793|gb|AV529510.1|AV529510,+,75464-75994
gi|8689759|gb|AV529476.1|AV529476,+,75520-75831
gi|8688977|gb|AV528694.1|AV528694,+,75603-76133
gi|26019912|gb|CA781870.1|CA781870,+,75832-76203,76299-76421,76500-76604,76696-76804
gi|8687299|gb|AV527771.1|AV527771,+,76104-76203,76299-76421,76500-76604,76696-76840,76930-76968
gi|7612388|gb|AV441989.1|AV441989,+,76129-76203,76299-76421,76500-76604,76696-76723
gi|2759986|gb|R86801.1|R86801,+,76142-76203,76299-76350
gi|8721274|gb|AV549861.1|AV549861,+,76329-76421,76500-76604,76696-76816
gi|8684108|gb|AV524580.1|AV524580,+,76398-76421,76500-76604,76696-76840,76930-77094,77187-77271
gi|8722317|gb|AV550904.1|AV550904,+,76934-77094,77187-77425,77520-77552,77643-77693
gi|8721865|gb|AV550452.1|AV550452,+,77012-77094,77187-77425,77520-77532
gi|8686414|gb|AV526886.1|AV526886,+,77019-77094,77187-77425,77520-77552,77643-77724,77812-77898
gi|1217037|gb|N65411.1|N65411,+,77060-77094,77187-77425,77520-77552,77643-77678
gi|7610962|gb|AV440594.1|AV440594,+,77206-77425,77520-77552,77643-77724,77812-77916
gi|315407|gb|T04247.1|T04247,+,77226-77425,77520-77552,77643-77724,77812-77897
gi|8727635|gb|AV556220.1|AV556220,+,77524-77552,77643-77724,77812-77884
gi|935616|gb|T76642.1|T76642,+,77525-77552,77643-77724,77812-77972,78102-78206
gi|8722019|gb|AV550606.1|AV550606,+,77704-77724,77812-77972,78102-78275,78360-78489
gi|8721631|gb|AV550218.1|AV550218,+,77824-77972,78102-78275,78360-78540
gi|937030|gb|R30368.1|R30368,+,77846-77972,78102-78253
gi|935549|gb|T76572.1|T76572,+,78117-78275,78360-78436
gi|906807|gb|H37308.1|H37308,+,78142-78275,78360-78542,78629-78753
gi|2759636|gb|T44843.1|T44843,+,78368-78542,78629-78788
gi|957845|gb|R90305.1|R90305,+,78375-78542,78629-78759
gi|8717301|gb|AV545887.1|AV545887,+,78377-78542,78629-78810,78902-79178
gi|957844|gb|R90304.1|R90304,+,78394-78542,78629-78790
gi|8683156|gb|AV523628.1|AV523628,+,78394-78542,78629-78810,78902-79170
gi|8683282|gb|AV523754.1|AV523754,+,78409-78542,78629-78810,78902-79200
gi|2596846|gb|T22192.1|T22192,+,78414-78542,78629-78702
gi|8698528|gb|AV538245.1|AV538245,+,78434-78542,78629-78810,78902-79206
gi|8683763|gb|AV524235.1|AV524235,+,78438-78542,78629-78810,78902-79246
gi|8682933|gb|AV523405.1|AV523405,+,78450-78542,78629-78810,78902-79221
gi|8678752|gb|AV519225.1|AV519225,+,78461-78542,78629-78810,78902-79206
gi|8683333|gb|AV523805.1|AV523805,+,78462-78542,78629-78810,78902-79173
gi|8682631|gb|AV523104.1|AV523104,+,78475-78542,78629-78810,78902-79256
gi|8700351|gb|AV538595.1|AV538595,+,78476-78542,78629-78810,78902-79188
gi|8682397|gb|AV522870.1|AV522870,+,78506-78542,78629-78810,78902-79137
gi|2733910|gb|AA720300.1|AA720300,+,78507-78542,78629-78737
gi|8716477|gb|AV545063.1|AV545063,+,78511-78542,78629-78810,78902-79242
gi|8725117|gb|AV553704.1|AV553704,+,78511-78542,78629-78810,78902-79239
gi|8677570|gb|AV518043.1|AV518043,+,78525-78542,78629-78810,78902-79245
gi|8718102|gb|AV546688.1|AV546688,+,78525-78542,78629-78810,78902-79243
gi|8732297|gb|AV560871.1|AV560871,+,78525-78542,78629-78810,78902-79312
gi|8682974|gb|AV523446.1|AV523446,+,78525-78542,78629-78810,78902-79192
gi|8719568|gb|AV548155.1|AV548155,+,78628-78810,78902-79250
gi|8719555|gb|AV548142.1|AV548142,+,78628-78810,78902-79264
gi|8717378|gb|AV545964.1|AV545964,+,78629-78810,78902-79292
gi|5851401|gb|AW004372.1|AW004372,+,78630-78810,78902-79230
gi|8718761|gb|AV547347.1|AV547347,+,78642-78810,78902-79292
gi|8727397|gb|AV555982.1|AV555982,+,78643-78810,78902-79286
gi|19825183|gb|AV791200.1|AV791200,+,78645-78810,78902-79192
gi|19825611|gb|AV791628.1|AV791628,+,78652-78810,78902-79187
gi|930537|gb|R84103.1|R84103,+,78657-78810,78902-79065
gi|19825971|gb|AV791988.1|AV791988,+,78663-78810,78902-79177
gi|19843957|gb|AV809972.1|AV809972,+,78664-78810,78902-79178
gi|19803368|gb|AV784578.1|AV784578,+,78666-78810,78902-79263
gi|19826955|gb|AV792972.1|AV792972,+,78667-78810,78902-79192
gi|19839851|gb|AV805866.1|AV805866,+,78671-78810,78902-79159
gi|19844231|gb|AV810246.1|AV810246,+,78672-78810,78902-79187
gi|8682609|gb|AV523082.1|AV523082,+,78673-78810,78902-79211
gi|8693713|gb|AV533430.1|AV533430,+,78673-78810,78902-79154
gi|19836591|gb|AV802606.1|AV802606,+,78674-78810,78902-79159
gi|8698353|gb|AV538070.1|AV538070,+,78675-78810,78902-79348
gi|8704263|gb|AV542503.1|AV542503,+,78675-78810,78902-79289
gi|19844632|gb|AV810647.1|AV810647,+,78677-78810,78902-79187
gi|19837593|gb|AV803608.1|AV803608,+,78680-78810,78902-79178
gi|19826840|gb|AV792857.1|AV792857,+,78686-78810,78902-79219
gi|8703224|gb|AV541465.1|AV541465,+,78688-78810,78902-79305
gi|8719849|gb|AV548436.1|AV548436,+,78688-78810,78902-79281
gi|8718953|gb|AV547539.1|AV547539,+,78689-78810,78902-79222
gi|19860396|gb|AV818478.1|AV818478,+,78691-78810,78902-79179
gi|19861182|gb|AV819243.1|AV819243,+,78694-78810,78902-79219
gi|19841851|gb|AV807866.1|AV807866,+,78699-78810,78902-79219
gi|19839963|gb|AV805978.1|AV805978,+,78702-78810,78902-79188
gi|19826611|gb|AV792628.1|AV792628,+,78703-78810,78902-79219
gi|19843657|gb|AV809672.1|AV809672,+,78705-78810,78902-79219
gi|19830534|gb|AV796551.1|AV796551,+,78705-78810,78902-79219
gi|19861682|gb|AV819737.1|AV819737,+,78709-78810,78902-79219
gi|19861604|gb|AV819661.1|AV819661,+,78710-78810,78902-79219
gi|8683089|gb|AV523561.1|AV523561,+,78711-78810,78902-79256
gi|8698102|gb|AV537819.1|AV537819,+,78712-78810,78902-79193
gi|8719443|gb|AV548030.1|AV548030,+,78713-78810,78902-79312
gi|19858883|gb|AV817015.1|AV817015,+,78716-78810,78902-79219
gi|8739161|gb|AV567707.1|AV567707,+,78718-78810,78902-79202
gi|19846778|gb|AV812793.1|AV812793,+,78720-78810,78902-79219
gi|8700100|gb|AV538344.1|AV538344,+,78724-78810,78902-79292
gi|19841052|gb|AV807067.1|AV807067,+,78729-78810,78902-79226
gi|19844191|gb|AV810206.1|AV810206,+,78731-78810,78902-79243
gi|19835847|gb|AV801862.1|AV801862,+,78731-78810,78902-79219
gi|8719704|gb|AV548291.1|AV548291,+,78738-78810,78902-79292
gi|8718763|gb|AV547349.1|AV547349,+,78739-78810,78902-79275
gi|19830408|gb|AV796425.1|AV796425,+,78741-78810,78902-79263
gi|19862839|gb|AV820854.1|AV820854,+,78741-78810,78902-79219
gi|19831700|gb|AV797717.1|AV797717,+,78742-78810,78902-79264
gi|8683627|gb|AV524099.1|AV524099,+,78744-78810,78902-79276
gi|19825879|gb|AV791896.1|AV791896,+,78744-78810,78902-79266
gi|19829664|gb|AV795681.1|AV795681,+,78745-78810,78902-79262
gi|19842507|gb|AV808522.1|AV808522,+,78745-78810,78902-79260
gi|19836959|gb|AV802974.1|AV802974,+,78751-78810,78902-79243
gi|19832759|gb|AV798776.1|AV798776,+,78752-78810,78902-79267
gi|19845923|gb|AV811938.1|AV811938,+,78753-78810,78902-79243
gi|19844492|gb|AV810507.1|AV810507,+,78754-78810,78902-79250
gi|19861081|gb|AV819143.1|AV819143,+,78755-78810,78902-79267
gi|8719463|gb|AV548050.1|AV548050,+,78756-78810,78902-79296
gi|19860142|gb|AV818235.1|AV818235,+,78757-78810,78902-79262
gi|19860788|gb|AV818856.1|AV818856,+,78764-78810,78902-79267
gi|19836747|gb|AV802762.1|AV802762,+,78764-78810,78902-79294
gi|19857562|gb|AV815724.1|AV815724,+,78767-78810,78902-79264
gi|19856594|gb|AV814785.1|AV814785,+,78767-78810,78902-79264
gi|19847790|gb|AV813805.1|AV813805,+,78768-78810,78902-79264
gi|19840031|gb|AV806046.1|AV806046,+,78769-78810,78902-79296
gi|19800221|gb|AV781431.1|AV781431,+,78769-78810,78902-79219
gi|19826509|gb|AV792526.1|AV792526,+,78774-78810,78902-79289
gi|8683390|gb|AV523862.1|AV523862,+,78776-78810,78902-79240
gi|19862239|gb|AV820279.1|AV820279,+,78780-78810,78902-79267
gi|19838855|gb|AV804870.1|AV804870,+,78782-78810,78902-79296
gi|19858089|gb|AV816237.1|AV816237,+,78783-78810,78902-79289
gi|19827485|gb|AV793502.1|AV793502,+,78784-78810,78902-79296
gi|19838386|gb|AV804401.1|AV804401,+,78785-78810,78902-79292
gi|19856843|gb|AV815025.1|AV815025,+,78788-78810,78902-79288
gi|19834164|gb|AV800179.1|AV800179,+,78790-78810,78902-79292
gi|8693278|gb|AV532995.1|AV532995,+,78792-78810,78902-79222
gi|19833673|gb|AV799688.1|AV799688,+,78793-78810,78902-79292
gi|19856138|gb|AV814353.1|AV814353,+,78795-78810,78902-79292
gi|19834374|gb|AV800389.1|AV800389,+,78800-78810,78902-79293
gi|19857373|gb|AV815541.1|AV815541,+,78900-79293
gi|8718558|gb|AV547144.1|AV547144,+,78900-79220
gi|19836630|gb|AV802645.1|AV802645,+,78900-79296
gi|8717883|gb|AV546469.1|AV546469,+,78904-79292
gi|8683858|gb|AV524330.1|AV524330,+,78911-79257
gi|19825083|gb|AV791100.1|AV791100,+,78915-79347
gi|8718249|gb|AV546835.1|AV546835,+,78944-79292
gi|498468|gb|Z34112.1|Z34112,+,78946-79292
gi|19837870|gb|AV803885.1|AV803885,+,78947-79348
gi|8704456|gb|AV542696.1|AV542696,+,78964-79292
gi|8718245|gb|AV546831.1|AV546831,+,78965-79292
gi|8718893|gb|AV547479.1|AV547479,+,79021-79348
gi|8704620|gb|AV542860.1|AV542860,+,79039-79289
gi|8703313|gb|AV541554.1|AV541554,+,79040-79288
gi|8717589|gb|AV546175.1|AV546175,+,79052-79241
gi|8701476|gb|AV539719.1|AV539719,+,79082-79349
gi|8736645|gb|AV565207.1|AV565207,+,79084-79283
gi|8718230|gb|AV546816.1|AV546816,+,79085-79254
gi|8704463|gb|AV542703.1|AV542703,+,79124-79292
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input10.out000066400000000000000000000020331211610345200256160ustar00rootroot00000000000000contains [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171]
contains [72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171]
contains [153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171]
contains [0,5,6,8,11,21]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input10_minusFL.in000066400000000000000000000254041211610345200270610ustar00rootroot00000000000000gi|8690382|gb|AV530099.1|AV530099,+,73361-73629,74908-75027,75121-75265
gi|19865640|gb|AV823580.1|AV823580,+,73485-73629,74908-75027,75121-75261
gi|19869340|gb|AV827280.1|AV827280,+,73485-73629,74908-75027,75121-75357,75442-75545
gi|19870458|gb|AV828398.1|AV828398,+,73485-73629,74908-75027,75121-75281
gi|19867428|gb|AV825368.1|AV825368,+,73485-73629,74908-75027,75121-75357,75442-75535
gi|19870789|gb|AV828729.1|AV828729,+,73485-73629,74908-75027,75121-75357,75442-75471
gi|19871830|gb|AV829770.1|AV829770,+,73485-73629,74908-75027,75121-75357,75442-75537
gi|19872557|gb|AV830497.1|AV830497,+,73488-73629,74908-75027,75121-75357,75442-75506
gi|19872786|gb|AV830726.1|AV830726,+,73489-73629,74908-75027,75121-75161
gi|8689542|gb|AV529259.1|AV529259,+,73504-73629,74908-75027,75121-75357,75442-75460
gi|9788776|gb|BE530786.1|BE530786,+,73505-73629,74908-75025
gi|8689093|gb|AV528810.1|AV528810,+,73506-73629,74908-75027,75121-75357,75442-75468
gi|8690319|gb|AV530036.1|AV530036,+,73507-73629,74908-75027,75121-75357,75442-75460
gi|8688689|gb|AV528406.1|AV528406,+,73509-73629,74908-75027,75121-75357,75442-75469
gi|8332698|gb|BE037682.1|BE037682,+,73509-73629,74908-75027,75121-75357,75442-75672
gi|8689631|gb|AV529348.1|AV529348,+,73513-73629,74908-75027,75121-75357,75442-75523
gi|8688745|gb|AV528462.1|AV528462,+,73540-73629,74908-75027,75121-75357,75442-75544
gi|8689405|gb|AV529122.1|AV529122,+,73548-73629,74908-75027,75121-75357,75442-75527
gi|8687701|gb|AV528173.1|AV528173,+,73556-73629,74908-75027,75121-75357,75442-75566
gi|8690042|gb|AV529759.1|AV529759,+,73576-73629,74908-75027,75121-75357,75442-75511
gi|8718164|gb|AV546750.1|AV546750,+,73590-73629,74908-75027,75121-75369
gi|8689841|gb|AV529558.1|AV529558,+,74948-75027,75121-75357,75442-75636
gi|8726312|gb|AV554897.1|AV554897,+,74980-75027,75121-75357,75442-75619
gi|8689350|gb|AV529067.1|AV529067,+,75154-75357,75442-75550
gi|8688899|gb|AV528616.1|AV528616,+,75188-75357,75442-75542
gi|8690214|gb|AV529931.1|AV529931,+,75207-75357,75442-75625
gi|8689229|gb|AV528946.1|AV528946,+,75279-75357,75442-75876
gi|8689793|gb|AV529510.1|AV529510,+,75464-75994
gi|8689759|gb|AV529476.1|AV529476,+,75520-75831
gi|8688977|gb|AV528694.1|AV528694,+,75603-76133
gi|26019912|gb|CA781870.1|CA781870,+,75832-76203,76299-76421,76500-76604,76696-76804
gi|8687299|gb|AV527771.1|AV527771,+,76104-76203,76299-76421,76500-76604,76696-76840,76930-76968
gi|7612388|gb|AV441989.1|AV441989,+,76129-76203,76299-76421,76500-76604,76696-76723
gi|2759986|gb|R86801.1|R86801,+,76142-76203,76299-76350
gi|8721274|gb|AV549861.1|AV549861,+,76329-76421,76500-76604,76696-76816
gi|8684108|gb|AV524580.1|AV524580,+,76398-76421,76500-76604,76696-76840,76930-77094,77187-77271
gi|8722317|gb|AV550904.1|AV550904,+,76934-77094,77187-77425,77520-77552,77643-77693
gi|8721865|gb|AV550452.1|AV550452,+,77012-77094,77187-77425,77520-77532
gi|8686414|gb|AV526886.1|AV526886,+,77019-77094,77187-77425,77520-77552,77643-77724,77812-77898
gi|1217037|gb|N65411.1|N65411,+,77060-77094,77187-77425,77520-77552,77643-77678
gi|7610962|gb|AV440594.1|AV440594,+,77206-77425,77520-77552,77643-77724,77812-77916
gi|315407|gb|T04247.1|T04247,+,77226-77425,77520-77552,77643-77724,77812-77897
gi|8727635|gb|AV556220.1|AV556220,+,77524-77552,77643-77724,77812-77884
gi|935616|gb|T76642.1|T76642,+,77525-77552,77643-77724,77812-77972,78102-78206
gi|8722019|gb|AV550606.1|AV550606,+,77704-77724,77812-77972,78102-78275,78360-78489
gi|8721631|gb|AV550218.1|AV550218,+,77824-77972,78102-78275,78360-78540
gi|937030|gb|R30368.1|R30368,+,77846-77972,78102-78253
gi|935549|gb|T76572.1|T76572,+,78117-78275,78360-78436
gi|906807|gb|H37308.1|H37308,+,78142-78275,78360-78542,78629-78753
gi|2759636|gb|T44843.1|T44843,+,78368-78542,78629-78788
gi|957845|gb|R90305.1|R90305,+,78375-78542,78629-78759
gi|8717301|gb|AV545887.1|AV545887,+,78377-78542,78629-78810,78902-79178
gi|957844|gb|R90304.1|R90304,+,78394-78542,78629-78790
gi|8683156|gb|AV523628.1|AV523628,+,78394-78542,78629-78810,78902-79170
gi|8683282|gb|AV523754.1|AV523754,+,78409-78542,78629-78810,78902-79200
gi|2596846|gb|T22192.1|T22192,+,78414-78542,78629-78702
gi|8698528|gb|AV538245.1|AV538245,+,78434-78542,78629-78810,78902-79206
gi|8683763|gb|AV524235.1|AV524235,+,78438-78542,78629-78810,78902-79246
gi|8682933|gb|AV523405.1|AV523405,+,78450-78542,78629-78810,78902-79221
gi|8678752|gb|AV519225.1|AV519225,+,78461-78542,78629-78810,78902-79206
gi|8683333|gb|AV523805.1|AV523805,+,78462-78542,78629-78810,78902-79173
gi|8682631|gb|AV523104.1|AV523104,+,78475-78542,78629-78810,78902-79256
gi|8700351|gb|AV538595.1|AV538595,+,78476-78542,78629-78810,78902-79188
gi|8682397|gb|AV522870.1|AV522870,+,78506-78542,78629-78810,78902-79137
gi|2733910|gb|AA720300.1|AA720300,+,78507-78542,78629-78737
gi|8716477|gb|AV545063.1|AV545063,+,78511-78542,78629-78810,78902-79242
gi|8725117|gb|AV553704.1|AV553704,+,78511-78542,78629-78810,78902-79239
gi|8677570|gb|AV518043.1|AV518043,+,78525-78542,78629-78810,78902-79245
gi|8718102|gb|AV546688.1|AV546688,+,78525-78542,78629-78810,78902-79243
gi|8732297|gb|AV560871.1|AV560871,+,78525-78542,78629-78810,78902-79312
gi|8682974|gb|AV523446.1|AV523446,+,78525-78542,78629-78810,78902-79192
gi|8719568|gb|AV548155.1|AV548155,+,78628-78810,78902-79250
gi|8719555|gb|AV548142.1|AV548142,+,78628-78810,78902-79264
gi|8717378|gb|AV545964.1|AV545964,+,78629-78810,78902-79292
gi|5851401|gb|AW004372.1|AW004372,+,78630-78810,78902-79230
gi|8718761|gb|AV547347.1|AV547347,+,78642-78810,78902-79292
gi|8727397|gb|AV555982.1|AV555982,+,78643-78810,78902-79286
gi|19825183|gb|AV791200.1|AV791200,+,78645-78810,78902-79192
gi|19825611|gb|AV791628.1|AV791628,+,78652-78810,78902-79187
gi|930537|gb|R84103.1|R84103,+,78657-78810,78902-79065
gi|19825971|gb|AV791988.1|AV791988,+,78663-78810,78902-79177
gi|19843957|gb|AV809972.1|AV809972,+,78664-78810,78902-79178
gi|19803368|gb|AV784578.1|AV784578,+,78666-78810,78902-79263
gi|19826955|gb|AV792972.1|AV792972,+,78667-78810,78902-79192
gi|19839851|gb|AV805866.1|AV805866,+,78671-78810,78902-79159
gi|19844231|gb|AV810246.1|AV810246,+,78672-78810,78902-79187
gi|8682609|gb|AV523082.1|AV523082,+,78673-78810,78902-79211
gi|8693713|gb|AV533430.1|AV533430,+,78673-78810,78902-79154
gi|19836591|gb|AV802606.1|AV802606,+,78674-78810,78902-79159
gi|8698353|gb|AV538070.1|AV538070,+,78675-78810,78902-79348
gi|8704263|gb|AV542503.1|AV542503,+,78675-78810,78902-79289
gi|19844632|gb|AV810647.1|AV810647,+,78677-78810,78902-79187
gi|19837593|gb|AV803608.1|AV803608,+,78680-78810,78902-79178
gi|19826840|gb|AV792857.1|AV792857,+,78686-78810,78902-79219
gi|8703224|gb|AV541465.1|AV541465,+,78688-78810,78902-79305
gi|8719849|gb|AV548436.1|AV548436,+,78688-78810,78902-79281
gi|8718953|gb|AV547539.1|AV547539,+,78689-78810,78902-79222
gi|19860396|gb|AV818478.1|AV818478,+,78691-78810,78902-79179
gi|19861182|gb|AV819243.1|AV819243,+,78694-78810,78902-79219
gi|19841851|gb|AV807866.1|AV807866,+,78699-78810,78902-79219
gi|19839963|gb|AV805978.1|AV805978,+,78702-78810,78902-79188
gi|19826611|gb|AV792628.1|AV792628,+,78703-78810,78902-79219
gi|19843657|gb|AV809672.1|AV809672,+,78705-78810,78902-79219
gi|19830534|gb|AV796551.1|AV796551,+,78705-78810,78902-79219
gi|19861682|gb|AV819737.1|AV819737,+,78709-78810,78902-79219
gi|19861604|gb|AV819661.1|AV819661,+,78710-78810,78902-79219
gi|8683089|gb|AV523561.1|AV523561,+,78711-78810,78902-79256
gi|8698102|gb|AV537819.1|AV537819,+,78712-78810,78902-79193
gi|8719443|gb|AV548030.1|AV548030,+,78713-78810,78902-79312
gi|19858883|gb|AV817015.1|AV817015,+,78716-78810,78902-79219
gi|8739161|gb|AV567707.1|AV567707,+,78718-78810,78902-79202
gi|19846778|gb|AV812793.1|AV812793,+,78720-78810,78902-79219
gi|8700100|gb|AV538344.1|AV538344,+,78724-78810,78902-79292
gi|19841052|gb|AV807067.1|AV807067,+,78729-78810,78902-79226
gi|19844191|gb|AV810206.1|AV810206,+,78731-78810,78902-79243
gi|19835847|gb|AV801862.1|AV801862,+,78731-78810,78902-79219
gi|8719704|gb|AV548291.1|AV548291,+,78738-78810,78902-79292
gi|8718763|gb|AV547349.1|AV547349,+,78739-78810,78902-79275
gi|19830408|gb|AV796425.1|AV796425,+,78741-78810,78902-79263
gi|19862839|gb|AV820854.1|AV820854,+,78741-78810,78902-79219
gi|19831700|gb|AV797717.1|AV797717,+,78742-78810,78902-79264
gi|8683627|gb|AV524099.1|AV524099,+,78744-78810,78902-79276
gi|19825879|gb|AV791896.1|AV791896,+,78744-78810,78902-79266
gi|19829664|gb|AV795681.1|AV795681,+,78745-78810,78902-79262
gi|19842507|gb|AV808522.1|AV808522,+,78745-78810,78902-79260
gi|19836959|gb|AV802974.1|AV802974,+,78751-78810,78902-79243
gi|19832759|gb|AV798776.1|AV798776,+,78752-78810,78902-79267
gi|19845923|gb|AV811938.1|AV811938,+,78753-78810,78902-79243
gi|19844492|gb|AV810507.1|AV810507,+,78754-78810,78902-79250
gi|19861081|gb|AV819143.1|AV819143,+,78755-78810,78902-79267
gi|8719463|gb|AV548050.1|AV548050,+,78756-78810,78902-79296
gi|19860142|gb|AV818235.1|AV818235,+,78757-78810,78902-79262
gi|19860788|gb|AV818856.1|AV818856,+,78764-78810,78902-79267
gi|19836747|gb|AV802762.1|AV802762,+,78764-78810,78902-79294
gi|19857562|gb|AV815724.1|AV815724,+,78767-78810,78902-79264
gi|19856594|gb|AV814785.1|AV814785,+,78767-78810,78902-79264
gi|19847790|gb|AV813805.1|AV813805,+,78768-78810,78902-79264
gi|19840031|gb|AV806046.1|AV806046,+,78769-78810,78902-79296
gi|19800221|gb|AV781431.1|AV781431,+,78769-78810,78902-79219
gi|19826509|gb|AV792526.1|AV792526,+,78774-78810,78902-79289
gi|8683390|gb|AV523862.1|AV523862,+,78776-78810,78902-79240
gi|19862239|gb|AV820279.1|AV820279,+,78780-78810,78902-79267
gi|19838855|gb|AV804870.1|AV804870,+,78782-78810,78902-79296
gi|19858089|gb|AV816237.1|AV816237,+,78783-78810,78902-79289
gi|19827485|gb|AV793502.1|AV793502,+,78784-78810,78902-79296
gi|19838386|gb|AV804401.1|AV804401,+,78785-78810,78902-79292
gi|19856843|gb|AV815025.1|AV815025,+,78788-78810,78902-79288
gi|19834164|gb|AV800179.1|AV800179,+,78790-78810,78902-79292
gi|8693278|gb|AV532995.1|AV532995,+,78792-78810,78902-79222
gi|19833673|gb|AV799688.1|AV799688,+,78793-78810,78902-79292
gi|19856138|gb|AV814353.1|AV814353,+,78795-78810,78902-79292
gi|19834374|gb|AV800389.1|AV800389,+,78800-78810,78902-79293
gi|19857373|gb|AV815541.1|AV815541,+,78900-79293
gi|8718558|gb|AV547144.1|AV547144,+,78900-79220
gi|19836630|gb|AV802645.1|AV802645,+,78900-79296
gi|8717883|gb|AV546469.1|AV546469,+,78904-79292
gi|8683858|gb|AV524330.1|AV524330,+,78911-79257
gi|19825083|gb|AV791100.1|AV791100,+,78915-79347
gi|8718249|gb|AV546835.1|AV546835,+,78944-79292
gi|498468|gb|Z34112.1|Z34112,+,78946-79292
gi|19837870|gb|AV803885.1|AV803885,+,78947-79348
gi|8704456|gb|AV542696.1|AV542696,+,78964-79292
gi|8718245|gb|AV546831.1|AV546831,+,78965-79292
gi|8718893|gb|AV547479.1|AV547479,+,79021-79348
gi|8704620|gb|AV542860.1|AV542860,+,79039-79289
gi|8703313|gb|AV541554.1|AV541554,+,79040-79288
gi|8717589|gb|AV546175.1|AV546175,+,79052-79241
gi|8701476|gb|AV539719.1|AV539719,+,79082-79349
gi|8736645|gb|AV565207.1|AV565207,+,79084-79283
gi|8718230|gb|AV546816.1|AV546816,+,79085-79254
gi|8704463|gb|AV542703.1|AV542703,+,79124-79292
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input10_minusFL.out000066400000000000000000000020261211610345200272550ustar00rootroot00000000000000contains [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170]
contains [71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170]
contains [152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170]
contains [0,5,6,8,10,20]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input2.in000066400000000000000000000066121211610345200253450ustar00rootroot00000000000000gi|19866237|gb|AV824177.1|AV824177,+,41330-41802,41989-42098,42186-42243,42347-42367
gi|21404866|gb|AY086156.1|,+,41405-41802,41989-42098,42186-42243,42347-42610,42881-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44447
gi|17529179|gb|AY065375.1|,+,41438-41802,41989-42098,42186-42243,42347-42610,42881-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44447
gi|19866590|gb|AV824530.1|AV824530,+,41438-41802,41989-42098,42186-42243,42347-42469
gi|572516|emb|X81698.1|ATCPACS1,+,41519-41802,41989-42098,42186-42243,42347-42610,42881-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44447
gi|8684020|gb|AV524492.1|AV524492,+,41525-41802
gi|2597281|gb|T22739.1|T22739,+,41528-41732
gi|8724974|gb|AV553561.1|AV553561,+,41531-41802,41989-42098,42186-42243,42347-42435
gi|6983575|emb|X80377.2|ATOACLY2,+,41548-41802,41989-42098,42186-42243,42347-42610,42881-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44447
gi|20465692|gb|AY096681.1|,+,41560-41802,41989-42098,42186-42243,42347-42610,42881-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44309
gi|8685733|gb|AV526205.1|AV526205,+,41567-41802,41989-42098,42186-42243,42347-42442
gi|8685927|gb|AV526399.1|AV526399,+,41677-41802,41989-42098,42186-42243,42347-42610
gi|8716380|gb|AV544966.1|AV544966,+,42879-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44419
gi|8677483|gb|AV517956.1|AV517956,+,42885-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44326
gi|8679632|gb|AV520105.1|AV520105,+,42888-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44343
gi|8677468|gb|AV517941.1|AV517941,+,42978-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44218
gi|8702419|gb|AV540661.1|AV540661,+,42992-43018,43151-43202,43288-43367,43475-43534,43663-43743,44186-44447
gi|19803678|gb|AV784888.1|AV784888,+,43149-43202,43288-43367,43475-43534,43663-43743,44186-44447
gi|8678738|gb|AV519211.1|AV519211,+,43173-43202,43288-43367,43475-43534,43663-43743,44186-44437
gi|19804146|gb|AV785356.1|AV785356,+,43287-43367,43475-43534,43663-43743,44186-44452
gi|8677566|gb|AV518039.1|AV518039,+,43314-43367,43475-43534,43663-43743,44186-44418
gi|19805318|gb|AV786528.1|AV786528,+,43320-43367,43475-43534,43663-43743,44186-44447
gi|19827168|gb|AV793185.1|AV793185,+,43323-43367,43475-43534,43663-43743,44186-44447
gi|19825688|gb|AV791705.1|AV791705,+,43332-43367,43475-43534,43663-43743,44186-44447
gi|19842398|gb|AV808413.1|AV808413,+,43340-43367,43475-43534,43663-43743,44186-44447
gi|19826477|gb|AV792494.1|AV792494,+,43341-43367,43475-43534,43663-43743,44186-44447
gi|19824696|gb|AV790713.1|AV790713,+,43344-43367,43475-43534,43663-43743,44186-44447
gi|19844342|gb|AV810357.1|AV810357,+,43346-43367,43475-43534,43663-43743,44186-44447
gi|8680597|gb|AV521070.1|AV521070,+,43350-43367,43475-43534,43663-43743,44186-44411
gi|19847294|gb|AV813309.1|AV813309,+,43474-43534,43663-43743,44186-44447
gi|19838233|gb|AV804248.1|AV804248,+,43490-43534,43663-43743,44186-44471
gi|8704976|gb|AV543216.1|AV543216,+,43490-43534,43663-43743,44186-44411
gi|19856418|gb|AV814618.1|AV814618,+,43500-43534,43663-43743,44186-44447
gi|8679776|gb|AV520249.1|AV520249,+,43663-43743,44186-44389
gi|5845705|gb|AI998800.1|AI998800,+,43698-43743,44186-44423
gi|8678411|gb|AV518884.1|AV518884,+,43698-43743,44186-44447
gi|8679146|gb|AV519619.1|AV519619,+,44216-44447
gi|8679129|gb|AV519602.1|AV519602,+,44233-44441
gi|8719276|gb|AV547862.1|AV547862,+,44250-44447
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input2.out000066400000000000000000000005611211610345200255430ustar00rootroot00000000000000contains [0,1,2,3,4,5,6,7,8,9,10,11,13,14,15,16,18,20,21,22,23,24,25,26,27,28,30,31,32,33,34,35,36,37,38]
contains [12,13,14,15,16,18,20,21,22,23,24,25,26,27,28,30,31,32,33,34,35,36,37,38]
contains [17,18,20,21,22,23,24,25,26,27,28,30,31,32,33,34,35,36,37,38]
contains [19,20,21,22,23,24,25,26,27,28,30,31,32,33,34,35,36,37,38]
contains [29,30,31,32,33,34,35,36,37,38]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input3.in000066400000000000000000000056371211610345200253540ustar00rootroot00000000000000gi|19803967|gb|AV785177.1|AV785177,+,75231-75271,75949-76329
gi|17979510|gb|AY070752.1|,+,75231-75271,75949-76329
gi|19866103|gb|AV824043.1|AV824043,+,75231-75271,75949-76329
gi|1269508|gb|N97141.1|N97141,+,75948-76310
gi|1269507|gb|N97140.1|N97140,+,75948-76353
gi|8696433|gb|AV536150.1|AV536150,+,75948-76331
gi|8681418|gb|AV521891.1|AV521891,+,75948-76370
gi|19860798|gb|AV818866.1|AV818866,+,75948-76361
gi|19861087|gb|AV819149.1|AV819149,+,75948-76384
gi|19862295|gb|AV820333.1|AV820333,+,75956-76362
gi|19862579|gb|AV820602.1|AV820602,+,75965-76384
gi|20147288|gb|AY093734.1|,+,75970-76164
gi|19860019|gb|AV818115.1|AV818115,-,76268-76554,76631-76751
gi|8718730|gb|AV547316.1|AV547316,-,76275-76554,76631-76777
gi|19829930|gb|AV795947.1|AV795947,-,76277-76554,76631-76775
gi|8719356|gb|AV547943.1|AV547943,-,76328-76554,76631-76732
gi|899206|gb|F14396.1|F14396,-,76337-76554,76631-76747
gi|19830370|gb|AV796387.1|AV796387,-,76342-76554,76631-76846
gi|19804575|gb|AV785785.1|AV785785,-,76354-76554,76631-76832
gi|19844768|gb|AV810783.1|AV810783,-,76354-76554,76631-76852
gi|19838754|gb|AV804769.1|AV804769,-,76354-76554,76631-76847
gi|19828596|gb|AV794613.1|AV794613,-,76356-76554,76631-76876
gi|3449398|gb|AI099659.1|AI099659,-,76366-76554,76631-76833
gi|5843898|gb|AI996993.1|AI996993,-,76370-76554,76631-76923,77023-77163
gi|8683659|gb|AV524131.1|AV524131,-,76374-76554,76631-76923,77023-77160,77262-77288
gi|18086369|gb|AY064997.1|,-,76378-76554,76631-76923,77023-77160,77262-77411,77502-77562,77763-77828,77938-78396,78500-78799,78916-79044,79139-80120,80223-80641
gi|19830356|gb|AV796373.1|AV796373,-,76378-76554,76631-76881
gi|8683675|gb|AV524147.1|AV524147,+,76383-76489
gi|8682321|gb|AV522794.1|AV522794,-,76395-76554,76631-76923,77023-77032
gi|8719862|gb|AV548449.1|AV548449,-,76410-76554,76631-76811
gi|19860520|gb|AV818602.1|AV818602,-,76411-76554,76631-76898
gi|19824889|gb|AV790906.1|AV790906,-,76414-76554,76631-76908
gi|8683706|gb|AV524178.1|AV524178,-,76446-76554,76631-76923,77023-77160,77262-77361
gi|8682202|gb|AV522675.1|AV522675,-,76464-76554,76631-76923
gi|27363293|gb|BT002650.1|,-,76631-76923,77023-77160,77262-77411,77502-77562,77763-77828,77938-78396,78500-78799,78916-79044,79139-80120,80223-80529
gi|8722920|gb|AV551507.1|AV551507,-,77994-78396,78500-78629
gi|2759707|gb|T44919.1|T44919,-,78050-78396,78500-78525
gi|1054484|gb|H77233.1|H77233,-,78153-78396,78500-78621
gi|19840029|gb|AV806044.1|AV806044,-,78317-78396,78500-78799,78916-78945
gi|20466188|gb|AY099560.1|,-,78318-78396,78500-78799,78916-79044,79139-80120,80223-80607
gi|8688602|gb|AV528319.1|AV528319,-,79906-80120,80223-80575
gi|19868889|gb|AV826829.1|AV826829,-,79917-80120,80223-80641
gi|8690307|gb|AV530024.1|AV530024,-,79919-80120,80223-80517
gi|8687705|gb|AV528177.1|AV528177,-,79970-80120,80223-80574
gi|8690249|gb|AV529966.1|AV529966,-,80023-80120,80223-80459
gi|8690200|gb|AV529917.1|AV529917,-,80059-80120,80223-80507
gi|19871485|gb|AV829425.1|AV829425,+,80231-80607
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input3.out000066400000000000000000000003701211610345200255420ustar00rootroot00000000000000contains [12,13,14,15,16,17,18,19,20,21,22,24,25,26,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45]
contains [12,13,14,15,16,17,18,19,20,21,22,23,26,28,29,30,31,33]
contains [3,4,5,6,7,8,9,10,11,27]
contains [0,1,2,9,10,11,27]
contains [46]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input4.in000066400000000000000000000032701211610345200253440ustar00rootroot00000000000000gi|14326503|gb|AF385705.1|AF385705,+,138076-138318,138595-139073,139377-139429,139703-139834,139929-140090,140180-140715
gi|19864280|gb|AV822240.1|AV822240,+,138076-138318,138595-139021
gi|2598226|emb|AJ222585.1|ATAHP1,+,138122-139073,139377-139429,139703-139834,139929-140090,140180-140719
gi|19548036|gb|AY081729.1|,+,138605-139073,139377-139429,139703-139834,139929-140090,140180-140419
gi|19801732|gb|AV782942.1|AV782942,+,139933-140090,140180-140718
gi|8738838|gb|AV567384.1|AV567384,+,140011-140090,140180-140695
gi|8690601|gb|AV530318.1|AV530318,+,140247-140739
gi|19834658|gb|AV800673.1|AV800673,+,140310-140737
gi|8730014|gb|AV558588.1|AV558588,+,140358-140814
gi|19862206|gb|AV820247.1|AV820247,+,140686-141077
gi|19827286|gb|AV793303.1|AV793303,+,140693-141141
gi|498675|gb|Z34237.1|Z34237,+,140707-141086
gi|8716825|gb|AV545411.1|AV545411,+,140708-141188
gi|19825131|gb|AV791148.1|AV791148,+,140711-141162
gi|19844121|gb|AV810136.1|AV810136,+,140711-141126
gi|19803663|gb|AV784873.1|AV784873,-,140734-141250,141327-141437
gi|20260207|gb|AY093003.1|,-,140736-141250,141327-141523,141598-141866,141942-142284,142401-142628
gi|19846192|gb|AV812207.1|AV812207,+,140763-141160
gi|16226672|gb|AF428460.1|AF428460,-,140763-141250,141327-141523,141598-141866,141942-142284,142401-142645
gi|905764|gb|H36265.1|H36265,+,140959-141414
gi|5840280|gb|AI993375.1|AI993375,-,141230-141250,141327-141523,141598-141756
gi|934961|gb|T75909.1|T75909,-,141325-141523,141598-141756
gi|8725556|gb|AV554143.1|AV554143,-,141346-141523,141598-141807
gi|19872652|gb|AV830592.1|AV830592,-,141964-142284,142401-142646
gi|506556|gb|Z34647.1|Z34647,-,142035-142284,142401-142546
gi|931026|gb|T14033.1|T14033,-,142091-142284,142401-142578
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input4.out000066400000000000000000000002261211610345200255430ustar00rootroot00000000000000contains [0,1,3,4,5,6,7,8,9,10,11,12,13,14,18,19]
contains [2,3,4,5,6,7,8,9,10,11,12,13,14,18,19]
contains [15,16,17,20,22,23,24,25]
contains [21,22]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input5.in000066400000000000000000000142521211610345200253470ustar00rootroot00000000000000gi|9785240|gb|BE527262.1|BE527262,+,49350-49566,49979-50016
gi|19866728|gb|AV824668.1|AV824668,+,49351-49566,49979-50055,50164-50248,50331-50457,50547-50591
gi|15450668|gb|AY052702.1|,+,49351-49566,49979-50055,50164-50248,50331-50457,50547-50645,50719-50786,50867-50974,51064-51141,51259-51391,51486-51582,51750-51873,51966-52074,52362-52445,52537-52881
gi|2981615|dbj|AB008854.1|,+,49369-49566,49979-50055,50164-50248,50331-50457,50547-50645,50719-50786,50867-50974,51064-51141,51259-51391,51486-51582,51750-51873,51966-52074,52362-52445,52537-52914
gi|11993852|gb|AF327529.1|,+,49369-49566,49979-50055,50164-50248,50331-50457,50547-50645,50719-50786,50867-50974,51064-51141,51259-51391,51486-51582,51750-51873,51966-52074,52362-52445,52537-52885
gi|473334|gb|Z32626.1|Z32626,+,49399-49566,49979-50055,50164-50241
gi|21406281|gb|AY087543.1|,+,49401-49566,49979-50055,50164-50248,50331-50457,50547-50645,50719-50786,50867-50974,51064-51141,51259-51391,51486-51582,51750-51873,51966-52074,52362-52445,52537-52762
gi|19866690|gb|AV824630.1|AV824630,+,49412-49566,49979-50055,50164-50248,50331-50433
gi|19867178|gb|AV825118.1|AV825118,+,49413-49566,49979-50055,50164-50248,50331-50457,50547-50645,50719-50786,50867-50906
gi|19869071|gb|AV827011.1|AV827011,+,49413-49566,49979-50055,50164-50248,50331-50457,50547-50645,50719-50784
gi|16648798|gb|AY058176.1|,+,49413-49566,49979-50055,50164-50248,50331-50457,50547-50645,50719-50786,50867-50974,51064-51141,51259-51391,51486-51582,51750-51873,51966-52074,52362-52445,52537-52887
gi|1158981|gb|N37839.1|N37839,+,49430-49566,49979-50055,50164-50248,50331-50348
gi|17200|gb|Z18059.1|Z18059,+,49432-49566,49979-50055,50164-50239
gi|937814|gb|R65341.1|R65341,+,49432-49566,49979-50055,50164-50210
gi|9785234|gb|BE527256.1|BE527256,+,49433-49566,49979-50055,50164-50192
gi|9788396|gb|BE530406.1|BE530406,+,49433-49566,49979-50055,50164-50226
gi|8684021|gb|AV524493.1|AV524493,+,49435-49566,49979-50055,50164-50248,50331-50348
gi|9782970|gb|BE524992.1|BE524992,+,49436-49566,49979-50055,50164-50232
gi|9784292|gb|BE526314.1|BE526314,+,49438-49566,49979-50055,50164-50216
gi|315555|gb|T04395.1|T04395,+,49440-49566,49979-50055,50164-50248,50331-50401
gi|9780402|gb|BE522424.1|BE522424,+,49445-49566,49979-50055,50164-50248,50331-50391
gi|9781498|gb|BE523520.1|BE523520,+,49446-49566,49979-50055,50164-50248
gi|17380613|gb|AY063720.1|,+,49477-49566,49979-50055,50164-50248,50331-50457,50547-50645,50719-50786,50867-50974,51064-51141,51259-51391,51486-51582,51750-51873,51966-52074,52362-52445,52537-52646
gi|13194829|gb|AF349530.1|,+,49477-49566,49979-50055,50164-50248,50331-50457,50547-50645,50719-50786,50867-50974,51064-51141,51259-51391,51486-51582,51750-51873,51966-52074,52362-52445,52537-52695
gi|623731|gb|Z47692.1|Z47692,+,49483-49566,49979-50055,50164-50248,50331-50385
gi|515607|gb|Z35397.1|Z35397,+,49492-49566,49979-50055,50164-50248,50331-50382
gi|9785772|gb|BE527794.1|BE527794,+,50167-50248,50331-50457,50547-50585
gi|9780266|gb|BE522288.1|BE522288,+,50384-50457,50547-50645,50719-50786,50867-50976
gi|550171|gb|Z37598.1|Z37598,+,50728-50786,50867-50974,51064-51141,51259-51387
gi|9785291|gb|BE527313.1|BE527313,+,50770-50786,50867-50974,51064-51141,51259-51300
gi|9786325|gb|BE528347.1|BE528347,+,50774-50786,50867-50974,51064-51141,51259-51315
gi|8731702|gb|AV560276.1|AV560276,+,50866-50974,51064-51141,51259-51391,51486-51518
gi|8723740|gb|AV552327.1|AV552327,+,50953-50974,51064-51141,51259-51391,51486-51582,51750-51775
gi|9781811|gb|BE523833.1|BE523833,+,50959-50974,51064-51141,51259-51391,51486-51582,51750-51817
gi|3449409|gb|AI099670.1|AI099670,+,51370-51391,51486-51582,51750-51873,51966-52074,52362-52396
gi|8715297|gb|AV543883.1|AV543883,+,51550-51582,51750-51873,51966-52074,52362-52445,52537-52795
gi|516126|gb|Z35342.1|Z35342,+,51742-51873,51966-52074,52362-52396
gi|8694629|gb|AV534346.1|AV534346,+,51841-51873,51966-52074,52362-52445,52537-52887
gi|8730313|gb|AV558887.1|AV558887,+,51857-51873,51966-52074,52362-52445,52537-52885
gi|8677485|gb|AV517958.1|AV517958,+,51964-52074,52362-52445,52537-52949
gi|1327565|gb|W43093.1|W43093,+,51968-52074,52362-52445,52537-52651
gi|19843107|gb|AV809122.1|AV809122,+,51980-52074,52362-52445,52537-52795
gi|8727674|gb|AV556259.1|AV556259,+,51999-52074,52362-52445,52537-52887
gi|19827955|gb|AV793972.1|AV793972,+,52002-52074,52362-52445,52537-52835
gi|5845245|gb|AI998340.1|AI998340,+,52016-52074,52362-52445,52537-52871
gi|19846995|gb|AV813010.1|AV813010,+,52025-52074,52362-52445,52537-52835
gi|8738253|gb|AV566799.1|AV566799,+,52050-52074,52362-52445,52537-52880
gi|19861724|gb|AV819775.1|AV819775,+,52054-52074,52362-52445,52537-52864
gi|8727800|gb|AV556385.1|AV556385,+,52056-52074,52362-52445,52537-52887
gi|19827180|gb|AV793197.1|AV793197,+,52058-52074,52362-52445,52537-52884
gi|19806231|gb|AV787441.1|AV787441,+,52358-52445,52537-52871
gi|19827743|gb|AV793760.1|AV793760,+,52358-52445,52537-52885
gi|506499|gb|Z34664.1|Z34664,+,52358-52445,52537-52837
gi|19829466|gb|AV795483.1|AV795483,+,52359-52445,52537-52885
gi|19831010|gb|AV797027.1|AV797027,+,52359-52445,52537-52885
gi|8735476|gb|AV564050.1|AV564050,+,52363-52445,52537-52885
gi|19842891|gb|AV808906.1|AV808906,+,52380-52445,52537-52884
gi|8714952|gb|AV543538.1|AV543538,+,52381-52445,52537-52863
gi|19838813|gb|AV804828.1|AV804828,+,52381-52445,52537-52885
gi|19827894|gb|AV793911.1|AV793911,+,52386-52445,52537-52920
gi|19860622|gb|AV818702.1|AV818702,+,52387-52445,52537-52888
gi|19856550|gb|AV814742.1|AV814742,+,52388-52445,52537-52885
gi|19831995|gb|AV798012.1|AV798012,+,52390-52445,52537-52884
gi|19840944|gb|AV806959.1|AV806959,+,52390-52445,52537-52885
gi|19805980|gb|AV787190.1|AV787190,+,52390-52445,52537-52882
gi|2722183|gb|AA712266.1|AA712266,+,52398-52445,52537-52884
gi|3450455|gb|AI100494.1|AI100494,+,52398-52445,52537-52914
gi|2596196|gb|T12940.1|T12940,+,52400-52445,52537-52981
gi|19805843|gb|AV787053.1|AV787053,+,52402-52445,52537-52863
gi|473345|gb|Z32625.1|Z32625,+,52542-52887
gi|407360|gb|Z26868.1|Z26868,+,52545-52942
gi|8727822|gb|AV556407.1|AV556407,+,52570-52887
gi|19824094|gb|AV790111.1|AV790111,+,52574-52982
gi|8680902|gb|AV521375.1|AV521375,+,52601-52860
gi|2413380|gb|AA597957.1|AA597957,+,52660-52887
gi|9780267|gb|BE522289.1|BE522289,+,52688-52899
gi|9780403|gb|BE522425.1|BE522425,+,52705-52887
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input5.out000066400000000000000000000013201211610345200255400ustar00rootroot00000000000000contains [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,28,29,30,32,33,34,35,37,38,40,41,42,43,44,45,46,47,48,49,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76]
contains [31,32,33,34,35,37,38,40,41,42,43,44,45,46,47,48,49,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76]
contains [36,37,38,40,41,42,43,44,45,46,47,48,49,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76]
contains [39,40,41,42,43,44,45,46,47,48,49,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76]
contains [50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76]
contains [0,2,5,7,9,10,11,12,13,14,15,16,17,18,19,20,21,24,25,26,27]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input6.in000066400000000000000000000015471211610345200253530ustar00rootroot00000000000000gi|19799769|gb|AU231059.1|AU231059,-,74058-74299,74383-74532,74629-74658
gi|26452696|dbj|AK118842.1|,-,74058-74299,74383-74532,74629-74763,74849-74907,75088-75204,75425-75605,75750-75833,75955-76023,76121-76261,76702-76794,77012-77140,77454-77740,78192-78299
gi|22531021|gb|AY136349.1|,-,74060-74299,74383-74532,74629-74763,74849-74907,75088-75204,75425-75605,75750-75833,75955-76023,76121-76261,76702-76794,77012-77140,77454-77740,77849-77876,78192-78299
gi|23197969|gb|BT000193.1|,-,74073-74299,74383-74532,74629-74763,74849-74907,75088-75204,75425-75605,75750-75833,75955-76023,76121-76261,76702-76794,77012-77140,77454-77735
gi|5842992|gb|AI996087.1|AI996087,-,74084-74299,74383-74532,74629-74763,74849-74907,75088-75110
gi|19878892|gb|AU239723.1|AU239723,-,76718-76794,77012-77140,77454-77740,78192-78299
gi|19870561|gb|AV828501.1|AV828501,-,77851-77876,78192-78299
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input6.out000066400000000000000000000000521211610345200255420ustar00rootroot00000000000000contains [0,1,3,4,5]
contains [1,2,3,4,6]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input7.in000066400000000000000000000075101211610345200253500ustar00rootroot00000000000000gi|14517455|gb|AY039563.1|,+,47126-47616,48151-48776,48851-49644
gi|19863139|gb|AV821120.1|AV821120,+,47126-47616,48151-48368
gi|23397315|gb|BT000804.1|,+,47126-47616,48151-49850
gi|12597466|gb|AF337910.1|,+,47126-47616,48151-48776,48851-49644
gi|19870179|gb|AV828119.1|AV828119,+,47126-47616,48151-48240
gi|406835|gb|Z26809.1|Z26809,+,47128-47442
gi|9782758|gb|BE524780.1|BE524780,+,47154-47541
gi|8685434|gb|AV525906.1|AV525906,+,47168-47517
gi|7610529|gb|AV440173.1|AV440173,+,47171-47608
gi|315505|gb|T04345.1|T04345,+,47187-47587
gi|8731245|gb|AV559819.1|AV559819,+,47198-47616,48151-48296
gi|8687397|gb|AV527869.1|AV527869,+,47198-47616,48151-48266
gi|26983881|gb|BT002360.1|,+,47209-47616,48151-48776,48851-49500
gi|23506206|gb|AY149961.1|,+,47209-47616,48151-48776,48851-49469
gi|9785802|gb|BE527824.1|BE527824,+,47213-47451
gi|9787637|gb|BE529736.1|BE529736,+,47226-47482
gi|9785034|gb|BE527056.1|BE527056,+,47325-47566
gi|9782433|gb|BE524455.1|BE524455,+,47380-47616,48151-48241
gi|9779113|gb|BE521135.1|BE521135,+,47383-47616,48151-48241
gi|23303764|gb|BU636509.1|BU636509,+,48192-48874
gi|9787020|gb|BE529042.1|BE529042,+,48201-48446
gi|9783629|gb|BE525651.1|BE525651,+,48245-48502
gi|9780133|gb|BE522155.1|BE522155,+,48558-48776,48851-48951
gi|9785079|gb|BE527101.1|BE527101,+,48622-48776,48851-48931
gi|9784997|gb|BE527019.1|BE527019,+,48622-48776,48851-48940
gi|498656|gb|Z34218.1|Z34218,+,48649-48776,48851-49123
gi|9783800|gb|BE525822.1|BE525822,+,48653-48776,48851-48969
gi|9783275|gb|BE525297.1|BE525297,+,48666-48776,48851-49129
gi|8681760|gb|AV522233.1|AV522233,+,49045-49617
gi|19800167|gb|AV781377.1|AV781377,+,49056-49644
gi|8737386|gb|AV565936.1|AV565936,+,49104-49677
gi|8737462|gb|AV566012.1|AV566012,+,49174-49677
gi|8732199|gb|AV560773.1|AV560773,+,49226-49699
gi|8689943|gb|AV529660.1|AV529660,+,49232-49775
gi|8731481|gb|AV560055.1|AV560055,+,49232-49757
gi|19830277|gb|AV796294.1|AV796294,+,49243-49673
gi|19844479|gb|AV810494.1|AV810494,+,49261-49677
gi|19856883|gb|AV815065.1|AV815065,+,49266-49677
gi|19859820|gb|AV817921.1|AV817921,+,49269-49677
gi|19856857|gb|AV815039.1|AV815039,+,49271-49677
gi|19833909|gb|AV799924.1|AV799924,+,49277-49694
gi|8735506|gb|AV564080.1|AV564080,+,49283-49756
gi|8735017|gb|AV563591.1|AV563591,+,49285-49757
gi|8735173|gb|AV563747.1|AV563747,+,49300-49761
gi|19859557|gb|AV817662.1|AV817662,+,49302-49699
gi|19840727|gb|AV806742.1|AV806742,+,49309-49699
gi|19831382|gb|AV797399.1|AV797399,+,49310-49762
gi|8690769|gb|AV530486.1|AV530486,+,49315-49757
gi|19829779|gb|AV795796.1|AV795796,+,49326-49755
gi|19832380|gb|AV798397.1|AV798397,+,49328-49757
gi|19842869|gb|AV808884.1|AV808884,+,49330-49756
gi|19828773|gb|AV794790.1|AV794790,+,49334-49773
gi|19830179|gb|AV796196.1|AV796196,+,49335-49762
gi|2747529|gb|AA728572.1|AA728572,+,49339-49707
gi|19827328|gb|AV793345.1|AV793345,+,49340-49773
gi|19842834|gb|AV808849.1|AV808849,+,49342-49757
gi|8737819|gb|AV566368.1|AV566368,+,49345-49701
gi|8733531|gb|AV562105.1|AV562105,+,49346-49757
gi|19804819|gb|AV786029.1|AV786029,+,49348-49762
gi|19857015|gb|AV815196.1|AV815196,+,49348-49756
gi|19833437|gb|AV799452.1|AV799452,+,49354-49757
gi|19855948|gb|AV814168.1|AV814168,+,49356-49756
gi|19840135|gb|AV806150.1|AV806150,+,49359-49762
gi|1268616|gb|N96115.1|N96115,+,49384-49735
gi|19846793|gb|AV812808.1|AV812808,+,49388-49801
gi|2747436|gb|AA728479.1|AA728479,+,49396-49756
gi|9779114|gb|BE521136.1|BE521136,+,49396-49762
gi|19827363|gb|AV793380.1|AV793380,+,49398-49847
gi|8732995|gb|AV561569.1|AV561569,+,49402-49762
gi|8678897|gb|AV519370.1|AV519370,+,49418-49683
gi|8733039|gb|AV561613.1|AV561613,+,49425-49756
gi|406836|gb|Z26810.1|Z26810,+,49428-49694
gi|8678597|gb|AV519070.1|AV519070,+,49430-49753
gi|8731178|gb|AV559752.1|AV559752,+,49432-49686
gi|19834417|gb|AV800432.1|AV800432,+,49469-49852
gi|7610667|gb|AV440308.1|AV440308,+,49478-49703
gi|506541|gb|Z34631.1|Z34631,+,49531-49748
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input7.out000066400000000000000000000006571211610345200255560ustar00rootroot00000000000000contains [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76]
contains [0,3,4,5,6,7,8,9,10,11,14,15,16,17,18,19,20,21,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input8.in000066400000000000000000000105771211610345200253600ustar00rootroot00000000000000gi|19837565|gb|AV803580.1|AV803580,-,35507-35919
gi|19825492|gb|AV791509.1|AV791509,-,35531-35965
gi|8700559|gb|AV538803.1|AV538803,-,35538-35973
gi|19839682|gb|AV805697.1|AV805697,-,35542-35948
gi|15810398|gb|AY056238.1|,-,35542-36128,36203-36364,36541-36609,36700-36747,36840-36942,37041-37120,37200-37271,37358-37452,37545-37626,37699-38485
gi|19827946|gb|AV793963.1|AV793963,-,35542-35782
gi|19839681|gb|AV805696.1|AV805696,-,35542-35957
gi|19829874|gb|AV795891.1|AV795891,-,35542-35973
gi|8703969|gb|AV542209.1|AV542209,-,35542-35988
gi|8681919|gb|AV522392.1|AV522392,-,35542-36021
gi|19827536|gb|AV793553.1|AV793553,-,35555-35988
gi|8702123|gb|AV540365.1|AV540365,-,35555-35978
gi|8719907|gb|AV548494.1|AV548494,-,35555-35977
gi|19845606|gb|AV811621.1|AV811621,-,35556-35970
gi|19829898|gb|AV795915.1|AV795915,-,35557-35968
gi|8680505|gb|AV520978.1|AV520978,-,35576-35912
gi|8680273|gb|AV520746.1|AV520746,-,35578-35985
gi|8715596|gb|AV544182.1|AV544182,-,35579-36128,36203-36286
gi|8735002|gb|AV563576.1|AV563576,-,35591-36128,36203-36228
gi|3449831|gb|AI099519.1|AI099519,-,35591-35911
gi|14030638|gb|AF375410.1|,-,35591-36128,36203-36364,36541-36609,36700-36747,36840-36942,37041-37120,37200-37271,37358-37452,37545-37626,37699-38424
gi|19842855|gb|AV808870.1|AV808870,-,35592-36006
gi|8702166|gb|AV540408.1|AV540408,-,35593-36128,36203-36227
gi|15724223|gb|AF412052.1|AF412052,-,35611-36128,36203-36364,36541-36609,36700-36747,36840-36942,37041-37120,37200-37271,37358-37452,37545-37626,37699-37788
gi|8717470|gb|AV546056.1|AV546056,-,35614-35901
gi|19806340|gb|AV787550.1|AV787550,-,35617-36043
gi|8697406|gb|AV537123.1|AV537123,-,35626-35944
gi|398292|gb|Z26004.1|Z26004,-,35633-36014
gi|2413150|gb|AA597727.1|AA597727,-,35635-35946
gi|14194142|gb|AF367277.1|AF367277,-,35637-36128,36203-36364,36541-36609,36700-36747,36840-36942,37041-37120,37200-37271,37358-37452,37545-37626,37699-38485
gi|19831513|gb|AV797530.1|AV797530,-,35639-36071
gi|19843216|gb|AV809231.1|AV809231,-,35639-36070
gi|8716920|gb|AV545506.1|AV545506,-,35647-36078
gi|5841254|gb|AI994349.1|AI994349,-,35681-35949
gi|8725941|gb|AV554528.1|AV554528,-,35767-36128,36203-36364,36541-36578
gi|22136547|gb|AY129474.1|,-,35802-36128,36203-36364,36541-36609,36700-36747,36840-36942,37041-37120,37200-37271,37358-37452,37545-37626,37699-38298
gi|12744918|gb|AF332565.1|AF332565,-,35802-36128,36203-36364,36541-36609,36700-36747,36840-36942,37041-37120,37200-37271,37358-37452,37545-37626,37699-38298
gi|8686903|gb|AV527375.1|AV527375,-,35858-36128,36203-36364,36541-36609,36700-36710
gi|2757876|gb|T42611.1|T42611,-,35931-36128,36203-36309
gi|8723296|gb|AV551883.1|AV551883,-,35988-36128,36203-36364,36541-36609,36700-36747,36840-36919
gi|8724197|gb|AV552784.1|AV552784,-,36014-36128,36203-36364,36541-36609,36840-36942,37041-37120,37200-37243
gi|23303295|gb|BU636040.1|BU636040,-,36021-36128,36203-36364,36541-36609,36700-36747,36840-36942,37041-37086
gi|8696888|gb|AV536605.1|AV536605,-,36212-36364,36541-36609,36700-36747,36840-36942,37041-37084
gi|8724072|gb|AV552659.1|AV552659,-,36698-36747,36840-36942,37041-37120,37200-37271,37358-37420
gi|9781551|gb|BE523573.1|BE523573,-,36700-36747,36840-36942,37041-37120,37200-37271,37358-37451
gi|23303782|gb|BU636527.1|BU636527,-,36875-36942,37041-37120,37200-37271,37358-37452,37545-37626,37699-37828
gi|1159223|gb|N38081.1|N38081,-,36917-36942,37041-37120,37200-37271,37358-37452,37545-37626,37699-37767
gi|2733957|gb|AA720347.1|AA720347,-,36918-36942,37041-37120,37200-37271,37358-37452,37545-37627
gi|8687069|gb|AV527541.1|AV527541,-,37109-37120,37200-37271,37358-37452,37545-37626,37699-37745
gi|23303593|gb|BU636338.1|BU636338,-,37200-37271,37358-37452,37545-37626,37699-38118
gi|23302408|gb|BU635153.1|BU635153,-,37724-38368
gi|23303539|gb|BU636284.1|BU636284,-,37747-38427
gi|8686720|gb|AV527192.1|AV527192,-,37759-38289
gi|23303436|gb|BU636181.1|BU636181,-,37842-38462
gi|19868260|gb|AV826200.1|AV826200,-,37863-38485
gi|8684991|gb|AV525463.1|AV525463,-,37865-38392
gi|19869270|gb|AV827210.1|AV827210,-,37875-38485
gi|19873982|gb|AV831922.1|AV831922,-,37901-38485
gi|27490486|gb|CA963929.1|CA963929,-,37902-38447
gi|19869921|gb|AV827861.1|AV827861,-,37904-38485
gi|8725652|gb|AV554239.1|AV554239,-,37974-38444
gi|19863160|gb|AV821141.1|AV821141,-,38024-38424
gi|19871970|gb|AV829910.1|AV829910,-,38116-38485
gi|2748351|gb|N96745.1|N96745,-,38120-38449
gi|8722537|gb|AV551124.1|AV551124,-,38128-38472
gi|8684177|gb|AV524649.1|AV524649,-,38277-38412
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input8.out000066400000000000000000000010401211610345200255420ustar00rootroot00000000000000contains [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,41,42,44,45,46,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65]
contains [0,1,2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,24,25,26,27,28,30,31,32,33,34,38,40,45,46,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65]
contains [0,1,2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,24,25,26,27,28,30,31,32,33,34,37,38,39,41,42,44,47]
contains [43,44,45,46,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65]
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input9.in000066400000000000000000000036541211610345200253570ustar00rootroot00000000000000gi|21406321|gb|AY087583.1|,-,79309-79812,79899-79978,80154-80211,80295-80392,80496-80975
gi|19804477|gb|AV785687.1|AV785687,-,79321-79719
gi|19830949|gb|AV796966.1|AV796966,-,79325-79751
gi|19834432|gb|AV800447.1|AV800447,-,79328-79736
gi|19846701|gb|AV812716.1|AV812716,-,79328-79720
gi|8695548|gb|AV535265.1|AV535265,-,79336-79707
gi|27311546|gb|BT002379.1|,-,79342-79812,79899-79978,80154-80211,80295-80392,80496-80674,81024-81093
gi|19860983|gb|AV819047.1|AV819047,-,79342-79774
gi|19830437|gb|AV796454.1|AV796454,-,79342-79770
gi|19823793|gb|AV789810.1|AV789810,-,79347-79786
gi|15450712|gb|AY052724.1|,-,79361-79812,79899-79978,80154-80211,80295-80392,80496-80674,81024-81057
gi|19825939|gb|AV791956.1|AV791956,-,79361-79783
gi|19806020|gb|AV787230.1|AV787230,-,79361-79762
gi|17473919|gb|AY065196.1|,-,79377-79812,79899-79978,80154-80211,80295-80392,80496-80674,81024-81057
gi|19801335|gb|AV782545.1|AV782545,-,79377-79812,79899-79978,80154-80211,80295-80324
gi|19833085|gb|AV799102.1|AV799102,-,79380-79786
gi|3450001|gb|AI100718.1|AI100718,-,79383-79689
gi|20148290|gb|AY081474.1|,-,79441-79812,79899-79978,80154-80211,80295-80392,80496-80669
gi|17386141|gb|AF446884.1|AF446884,-,79494-79812,79899-79978,80154-80211,80295-80392,80496-80669
gi|1053888|gb|H76637.1|H76637,-,79512-79678
gi|19866739|gb|AV824679.1|AV824679,-,79609-79812,79899-79978,80154-80211,80295-80392,80496-80674,81024-81048
gi|19867171|gb|AV825111.1|AV825111,-,79646-79812,79899-79978,80154-80211,80295-80392,80496-80674,81024-81097
gi|2414013|gb|AA042210.1|AA042210,-,79743-79812,79899-79978,80154-80211,80295-80392,80496-80674,81024-81044
gi|5839903|gb|AI992918.1|AI992918,-,79769-79812,79899-79978,80154-80211,80295-80392,80496-80674,81024-81063
gi|2758082|gb|T42834.1|T42834,-,80154-80211,80295-80392,80496-80674,81024-81038
gi|9782374|gb|BE524396.1|BE524396,-,80166-80211,80295-80392,80496-80641,81024-81065
gi|19863986|gb|AV821955.1|AV821955,-,80343-80392,80496-80674,81024-81048
genometools-1.5.1/testdata/consensus_sa/pasa_cpp_sample_input9.out000066400000000000000000000002621211610345200255500ustar00rootroot00000000000000contains [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,26]
contains [0,1,2,3,4,5,7,8,9,11,12,14,15,16,17,18,19]
contains [1,2,3,4,5,7,8,9,11,12,14,15,16,19,25]
genometools-1.5.1/testdata/consensus_sa/pasa_example_in_fig1.in000066400000000000000000000012251211610345200247430ustar00rootroot00000000000000gi|7613116|gb|AV442701.1|AV442701,+,60898-61317
gi|15724317|gb|AF412099.1|AF412099,+,60935-61402,61481-61699,61778-61912,62002-62073,62155-62283,62375-62787
gi|19866821|gb|AV824761.1|AV824761,+,60935-61305
gi|18700241|gb|AY078030.1|,+,61019-61402,61481-61699,61778-61912,62002-62073,62155-62283,62375-62443
gi|20127067|gb|AF488597.1|,+,61070-61402,61481-61699,61778-61912,62002-62073,62149-62283,62375-62771
gi|7611199|gb|AV440826.1|AV440826,+,61882-61912,62002-62073,62149-62283,62375-62710
gi|8681782|gb|AV522255.1|AV522255,+,62147-62283,62375-62708
gi|19806362|gb|AV787572.1|AV787572,+,62260-62283,62375-62780
gi|8679410|gb|AV519883.1|AV519883,+,62412-62796
genometools-1.5.1/testdata/consensus_sa/pasa_example_in_fig1.out000066400000000000000000000000771211610345200251500ustar00rootroot00000000000000contains [0,1,2,3,7,8]
contains [0,2,4,5,7,8]
contains [6,7,8]
genometools-1.5.1/testdata/corrupt.fas000066400000000000000000000000151211610345200200420ustar00rootroot00000000000000%foo
gattaca
genometools-1.5.1/testdata/corrupt.gff3000066400000000000000000000002201211610345200201140ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
##sequence-region   seq2 1 10000
seq1	.	gene	1000	9000	.	X	.	.
seq2	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/corrupt_gff3_header.txt000066400000000000000000000137171211610345200223420ustar00rootroot00000000000000##gff-version gff3
chr1	gth	exon	148017797	148017914	1.000000	+	.	.
chr1	gth	exon	148017797	148017914	1.000000	+	.	.
chr1	gth	exon	148018100	148018252	1.000000	+	.	.
chr1	gth	exon	148018100	148018252	1.000000	+	.	.
chr1	gth	exon	148018880	148018947	1.000000	+	.	.
chr1	gth	exon	148018880	148018947	1.000000	+	.	.
chr1	gth	exon	148019746	148019916	1.000000	+	.	.
chr1	gth	exon	148019746	148019916	1.000000	+	.	.
chr1	gth	exon	148017797	148017914	1.000000	+	.	.
chr1	gth	exon	148017797	148017914	1.000000	+	.	.
chr1	gth	exon	148018100	148018252	1.000000	+	.	.
chr1	gth	exon	148018100	148018252	1.000000	+	.	.
chr1	gth	exon	148018880	148018947	1.000000	+	.	.
chr1	gth	exon	148018880	148018947	1.000000	+	.	.
chr1	gth	exon	148019746	148019916	1.000000	+	.	.
chr1	gth	exon	148019746	148019916	1.000000	+	.	.
chr1	gth	exon	148022107	148022312	1.000000	+	.	.
chr1	gth	exon	148022107	148022312	1.000000	+	.	.
chr1	gth	exon	148019171	148019333	1.000000	+	.	.
chr1	gth	exon	148019171	148019333	1.000000	+	.	.
chr1	gth	exon	148019746	148020045	1.000000	+	.	.
chr1	gth	exon	148019746	148020045	1.000000	+	.	.
chr1	gth	exon	148022107	148022312	1.000000	+	.	.
chr1	gth	exon	148022107	148022312	1.000000	+	.	.
chr1	gth	exon	148050381	148050418	1.000000	+	.	.
chr1	gth	exon	148050381	148050418	1.000000	+	.	.
chr1	gth	exon	148051092	148051158	1.000000	+	.	.
chr1	gth	exon	148051092	148051158	1.000000	+	.	.
chr1	gth	exon	148051553	148051747	1.000000	+	.	.
chr1	gth	exon	148051553	148051747	1.000000	+	.	.
chr1	gth	exon	148127509	148127634	1.000000	-	.	.
chr1	gth	exon	148127509	148127634	1.000000	-	.	.
chr1	gth	exon	148128623	148128727	1.000000	-	.	.
chr1	gth	exon	148128623	148128727	1.000000	-	.	.
chr1	gth	exon	148127509	148127634	1.000000	-	.	.
chr1	gth	exon	148127509	148127634	1.000000	-	.	.
chr1	gth	exon	148128623	148128727	1.000000	-	.	.
chr1	gth	exon	148128623	148128727	1.000000	-	.	.
chr1	gth	exon	148128891	148128991	1.000000	-	.	.
chr1	gth	exon	148128891	148128991	1.000000	-	.	.
chr1	gth	exon	148129230	148129431	1.000000	-	.	.
chr1	gth	exon	148129230	148129431	1.000000	-	.	.
chr1	gth	exon	148128891	148128991	1.000000	-	.	.
chr1	gth	exon	148128891	148128991	1.000000	-	.	.
chr1	gth	exon	148129230	148129431	1.000000	-	.	.
chr1	gth	exon	148129230	148129431	1.000000	-	.	.
chr1	gth	exon	148129746	148129827	1.000000	-	.	.
chr1	gth	exon	148129746	148129827	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148130277	148130396	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148129882	148130085	1.000000	-	.	.
chr1	gth	exon	148130277	148130396	1.000000	-	.	.
chr1	gth	exon	148130277	148130396	1.000000	-	.	.
chr1	gth	exon	148130277	148130396	1.000000	-	.	.
chr1	gth	exon	148130277	148130396	1.000000	-	.	.
chr1	gth	exon	148130655	148130737	1.000000	-	.	.
chr1	gth	exon	148130655	148130737	1.000000	-	.	.
chr1	gth	exon	148130277	148130396	1.000000	-	.	.
chr1	gth	exon	148130277	148130396	1.000000	-	.	.
chr1	gth	exon	148130655	148130737	1.000000	-	.	.
chr1	gth	exon	148130655	148130737	1.000000	-	.	.
chr1	gth	exon	148132700	148132713	0.571429	-	.	.
chr1	gth	exon	148132700	148132713	0.571429	-	.	.
chr1	gth	exon	148186313	148186904	1.000000	+	.	.
chr1	gth	exon	148186313	148186904	1.000000	+	.	.
chr1	gth	exon	148187091	148187179	1.000000	+	.	.
chr1	gth	exon	148187091	148187179	1.000000	+	.	.
chr1	gth	exon	148187366	148187486	1.000000	+	.	.
chr1	gth	exon	148187366	148187486	1.000000	+	.	.
chr1	gth	exon	148185991	148186904	1.000000	+	.	.
chr1	gth	exon	148185991	148186904	1.000000	+	.	.
chr1	gth	exon	148188273	148192013	1.000000	-	.	.
chr1	gth	exon	148188273	148192013	1.000000	-	.	.
chr1	gth	exon	148197174	148197320	1.000000	-	.	.
chr1	gth	exon	148197174	148197320	1.000000	-	.	.
chr1	gth	exon	148192156	148192180	1.000000	-	.	.
chr1	gth	exon	148192156	148192180	1.000000	-	.	.
chr1	gth	exon	148192460	148192572	1.000000	-	.	.
chr1	gth	exon	148192460	148192572	1.000000	-	.	.
chr1	gth	exon	148192784	148192840	1.000000	-	.	.
chr1	gth	exon	148192784	148192840	1.000000	-	.	.
chr1	gth	exon	148193649	148193789	1.000000	-	.	.
chr1	gth	exon	148193649	148193789	1.000000	-	.	.
chr1	gth	exon	148193958	148194130	1.000000	-	.	.
chr1	gth	exon	148193958	148194130	1.000000	-	.	.
chr1	gth	exon	148194243	148194377	1.000000	-	.	.
chr1	gth	exon	148194243	148194377	1.000000	-	.	.
chr1	gth	exon	148197845	148197945	1.000000	-	.	.
chr1	gth	exon	148197845	148197945	1.000000	-	.	.
chr1	gth	exon	148208946	148209100	1.000000	-	.	.
chr1	gth	exon	148208946	148209100	1.000000	-	.	.
chr1	gth	exon	148210504	148210610	1.000000	-	.	.
chr1	gth	exon	148210504	148210610	1.000000	-	.	.
chr1	gth	exon	148213372	148213590	1.000000	-	.	.
chr1	gth	exon	148213372	148213590	1.000000	-	.	.
chr1	gth	exon	148209498	148209835	1.000000	-	.	.
chr1	gth	exon	148209498	148209835	1.000000	-	.	.
chr1	gth	exon	148213672	148213962	1.000000	-	.	.
chr1	gth	exon	148213672	148213962	1.000000	-	.	.
chr1	gth	exon	148215152	148215260	1.000000	-	.	.
chr1	gth	exon	148215152	148215260	1.000000	-	.	.
chr1	gth	exon	148216215	148216390	1.000000	-	.	.
chr1	gth	exon	148216215	148216390	1.000000	-	.	.
chr1	gth	exon	148227630	148227754	1.000000	-	.	.
chr1	gth	exon	148227630	148227754	1.000000	-	.	.
chr1	gth	exon	148296936	148297064	1.000000	+	.	.
chr1	gth	exon	148296936	148297064	1.000000	+	.	.
chr1	gth	exon	148303080	148303202	0.975610	+	.	.
chr1	gth	exon	148303080	148303202	0.975610	+	.	.
chr1	gth	exon	148359819	148359886	1.000000	+	.	.
chr1	gth	exon	148359819	148359886	1.000000	+	.	.
chr1	gth	exon	148367650	148369125	1.000000	+	.	.
chr1	gth	exon	148367650	148369125	1.000000	+	.	.
chr1	gth	exon	148359819	148359947	1.000000	+	.	.
genometools-1.5.1/testdata/corrupt_large.gff3000066400000000000000000000024551211610345200213020ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.500	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	+	.	.
###
ctg123	.	gene	1000	9000	.	X	.	.
###
genometools-1.5.1/testdata/corrupt_target_attribute.gff3000066400000000000000000000001361211610345200235530ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr 1 10000
chr	.	gene	1000	9000	0.500	+	.	Target=est 1
genometools-1.5.1/testdata/corruptpatternfile.fna000066400000000000000000000000231211610345200222720ustar00rootroot00000000000000EDVSLMTSIDNMIEEIDF
genometools-1.5.1/testdata/csa_example_consensus_spliced_alignments.gff3000066400000000000000000000006711211610345200267350ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 290
seq	gt csa	gene	1	290	.	+	.	ID=gene1
seq	gt csa	mRNA	1	290	.	+	.	ID=mRNA1;Parent=gene1
seq	gt csa	exon	1	90	.	+	.	Parent=mRNA1
seq	gt csa	exon	110	190	.	+	.	Parent=mRNA1
seq	gt csa	exon	201	290	.	+	.	Parent=mRNA1
seq	gt csa	mRNA	1	290	.	+	.	ID=mRNA2;Parent=gene1
seq	gt csa	exon	1	90	.	+	.	Parent=mRNA2
seq	gt csa	exon	101	190	.	+	.	Parent=mRNA2
seq	gt csa	exon	201	290	.	+	.	Parent=mRNA2
###
genometools-1.5.1/testdata/csa_example_spliced_alignments.gff3000066400000000000000000000011351211610345200246310ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 290
seq	.	gene	1	209	.	+	.	ID=gene1
seq	.	exon	1	90	.	+	.	Parent=gene1
seq	.	exon	110	190	.	+	.	Parent=gene1
seq	.	exon	201	209	.	+	.	Parent=gene1
###
seq	.	gene	1	290	.	+	.	ID=gene2
seq	.	exon	1	90	.	+	.	Parent=gene2
seq	.	exon	101	190	.	+	.	Parent=gene2
seq	.	exon	201	290	.	+	.	Parent=gene2
###
seq	.	gene	10	290	.	+	.	ID=gene3
seq	.	exon	10	90	.	+	.	Parent=gene3
seq	.	exon	110	190	.	+	.	Parent=gene3
seq	.	exon	201	290	.	+	.	Parent=gene3
###
seq	.	gene	181	290	.	+	.	ID=gene4
seq	.	exon	181	190	.	+	.	Parent=gene4
seq	.	exon	201	290	.	+	.	Parent=gene4
###
genometools-1.5.1/testdata/csr_testcase.fastq000066400000000000000000000211211211610345200213740ustar00rootroot00000000000000@TEST.1 TESTXX_487 length=27
AAAAAAAAAAAAAAAAAAAAAAAAAAA
+
IIIIIIIIIIIITrifolium repens mRNA for non-cyanogenic beta-glucosidase
aaacaaaccaaatatggattttattgtagccatatttgctctgtttgttattagctcatt
cacaattacttccacaaatgcagttgaagcttctactcttcttgacataggtaacctgag
tcggagcagttttcctcgtggcttcatctttggtgctggatcttcagcataccaatttga
aggtgcagtaaacgaaggcggtagaggaccaagtatttgggataccttcacccataaata
tccagaaaaaataagggatggaagcaatgcagacatcacggttgaccaatatcaccgcta
caaggaagatgttgggattatgaaggatcaaaatatggattcgtatagattctcaatctc
ttggccaagaatactcccaaagggaaagttgagcggaggcataaatcacgaaggaatcaa
atattacaacaaccttatcaacgaactattggctaacggtatacaaccatttgtaactct
ttttcattgggatcttccccaagtcttagaagatgagtatggtggtttcttaaactccgg
tgtaataaatgattttcgagactatacggatctttgcttcaaggaatttggagatagagt
gaggtattggagtactctaaatgagccatgggtgtttagcaattctggatatgcactagg
aacaaatgcaccaggtcgatgttcggcctccaacgtggccaagcctggtgattctggaac
aggaccttatatagttacacacaatcaaattcttgctcatgcagaagctgtacatgtgta
taagactaaataccaggcatatcaaaagggaaagataggcataacgttggtatctaactg
gttaatgccacttgatgataatagcataccagatataaaggctgccgagagatcacttga
cttccaatttggattgtttatggaacaattaacaacaggagattattctaagagcatgcg
gcgtatagttaaaaaccgattacctaagttctcaaaattcgaatcaagcctagtgaatgg
ttcatttgattttattggtataaactattactcttctagttatattagcaatgccccttc
acatggcaatgccaaacccagttactcaacaaatcctatgaccaatatttcatttgaaaa
acatgggatacccttaggtccaagggctgcttcaatttggatatatgtttatccatatat
gtttatccaagaggacttcgagatcttttgttacatattaaaaataaatataacaatcct
gcaattttcaatcactgaaaatggtatgaatgaattcaacgatgcaacacttccagtaga
agaagctcttttgaatacttacagaattgattactattaccgtcacttatactacattcg
ttctgcaatcagggctggctcaaatgtgaagggtttttacgcatggtcatttttggactg
taatgaatggtttgcaggctttactgttcgttttggattaaactttgtagattagaaaga
tggattaaaaaggtaccctaagctttctgcccaatggtacaagaactttctcaaaagaaa
ctagctagtattattaaaagaactttgtagtagattacagtacatcgtttgaagttgagt
tggtgcacctaattaaataaaagaggttactcttaacatatttttaggccattcgttgtg
aagttgttaggctgttatttctattatactatgttgtagtaataagtgcattgttgtacc
agaagctatgatcataactataggttgatccttcatgtatcagtttgatgttgagaatac
tttgaattaaaagtctttttttatttttttaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
genometools-1.5.1/testdata/embl_test6.embl000066400000000000000000000010301211610345200205540ustar00rootroot00000000000000ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
XX
AC   X56734; S46826;
XX
DT   12-SEP-1991 (Rel. 29, Created)
DT   25-NOV-2005 (Rel. 85, Last updated, Version 11)
XX
DE   Trifolium repens mRNA for
DE   non-cyanogenic beta-glucosidase
XX
KW   beta-glucosidase.
//
ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
XX
AC   X56734; S46826;
XX
DT   12-SEP-1991 (Rel. 29, Created)
DT   25-NOV-2005 (Rel. 85, Last updated, Version 11)
XX
DE   Trifolium repens mRNA for
DE   non-cyanogenic beta-glucosidase
XX
KW   beta-glucosidase.
//
genometools-1.5.1/testdata/empty_attribute.gff3000066400000000000000000000001271211610345200216450ustar00rootroot00000000000000##gff-version   3
##sequence-region   seqid 1 10000
seqid	.	gene	1000	9000	0.500	+	.	=
genometools-1.5.1/testdata/empty_attribute_name.gff3000066400000000000000000000001341211610345200226430ustar00rootroot00000000000000##gff-version   3
##sequence-region   seqid 1 10000
seqid	.	gene	1000	9000	0.500	+	.	=other
genometools-1.5.1/testdata/empty_attribute_value.gff3000066400000000000000000000060041211610345200230410ustar00rootroot00000000000000##gff-version 3
167631690	yrGATE	gene	87461	94610	.	-	.	ID=gene1;Name=ZmPLCf;organism=Zea mays;submitted_by=xiazhang
167631690	yrGATE	exon	87461	87831	.	-	.	ID=exon1;Parent=gene1
167631690	yrGATE	exon	87957	88053	.	-	.	ID=exon2;Parent=gene1
167631690	yrGATE	exon	88140	88292	.	-	.	ID=exon3;Parent=gene1
167631690	yrGATE	exon	88768	88885	.	-	.	ID=exon4;Parent=gene1
167631690	yrGATE	exon	89020	89249	.	-	.	ID=exon5;Parent=gene1
167631690	yrGATE	exon	89344	89595	.	-	.	ID=exon6;Parent=gene1
167631690	yrGATE	exon	89669	89804	.	-	.	ID=exon7;Parent=gene1
167631690	yrGATE	exon	89950	90152	.	-	.	ID=exon8;Parent=gene1
167631690	yrGATE	exon	94360	94610	.	-	.	ID=exon9;Parent=gene1
167631690	yrGATE	CDS	87719	87831	.	-	0	ID=CDS1;Parent=gene1;Name=;
167631690	yrGATE	CDS	87957	88053	.	-	1	ID=CDS2;Parent=gene1;Name=;
167631690	yrGATE	CDS	88140	88292	.	-	0	ID=CDS3;Parent=gene1;Name=;
167631690	yrGATE	CDS	88768	88885	.	-	0	ID=CDS4;Parent=gene1;Name=;
167631690	yrGATE	CDS	89020	89249	.	-	2	ID=CDS5;Parent=gene1;Name=;
167631690	yrGATE	CDS	89344	89595	.	-	0	ID=CDS6;Parent=gene1;Name=;
167631690	yrGATE	CDS	89669	89804	.	-	0	ID=CDS7;Parent=gene1;Name=;
167631690	yrGATE	CDS	89950	90152	.	-	2	ID=CDS8;Parent=gene1;Name=;
167631690	yrGATE	CDS	94360	94554	.	-	0	ID=CDS9;Parent=gene1;Name=;
167631690	ZmGDB	GeneSeqer_EST_native	87461	87831	0.992	-	.	ID=evidence1;Evidence_for=exon1;
167631690	ZmGDB	GeneSeqer_EST_native	87461	87831	1	-	.	ID=evidence3;Evidence_for=exon1;
167631690	ZmGDB	GenomeThreader_Protein_homologous	87957	88053	0.773	-	.	ID=evidence4;Evidence_for=exon2;
167631690	ZmGDB	GeneSeqer_EST_native	88140	88292	1	-	.	ID=evidence5;Evidence_for=exon3;
167631690	ZmGDB	GeneSeqer_EST_native	88140	88292	1	-	.	ID=evidence6;Evidence_for=exon3;
167631690	ZmGDB	GeneSeqer_EST_native	88140	88292	0.993	-	.	ID=evidence7;Evidence_for=exon3;
167631690	ZmGDB	GenomeThreader_Protein_homologous	88768	88885	0.941	-	.	ID=evidence8;Evidence_for=exon4;
167631690	ZmGDB	GenomeThreader_Protein_homologous	89020	89249	0.679	-	.	ID=evidence9;Evidence_for=exon5;
167631690	ZmGDB	GenomeThreader_Protein_homologous	89344	89595	0.777	-	.	ID=evidence10;Evidence_for=exon6;
167631690	ZmGDB	GeneSeqer_EST_native	89344	89595	0.992	-	.	ID=evidence11;Evidence_for=exon6;
167631690	ZmGDB	GenomeThreader_Protein_homologous	89669	89804	0.895	-	.	ID=evidence12;Evidence_for=exon7;
167631690	ZmGDB	GeneSeqer_EST_native	89669	89804	1	-	.	ID=evidence13;Evidence_for=exon7;
167631690	ZmGDB	GeneSeqer_EST_native	89669	89804	1	-	.	ID=evidence14;Evidence_for=exon7;
167631690	ZmGDB	GeneSeqer_EST_native	89669	89804	1	-	.	ID=evidence15;Evidence_for=exon7;
167631690	ZmGDB	GeneSeqer_EST_native	89669	89804	1	-	.	ID=evidence16;Evidence_for=exon7;
167631690	ZmGDB	GeneSeqer_EST_native	89669	89804	1	-	.	ID=evidence17;Evidence_for=exon7;
167631690	ZmGDB	GenomeThreader_Protein_homologous	89950	90152	0.903	-	.	ID=evidence18;Evidence_for=exon8;
167631690	ZmGDB	GeneSeqer_EST_native	94360	94610	1	-	.	ID=evidence19;Evidence_for=exon9;
167631690	ZmGDB	GeneSeqer_EST_native	94360	94610	1	-	.	ID=evidence20;Evidence_for=exon9;

genometools-1.5.1/testdata/empty_file000066400000000000000000000000001211610345200177230ustar00rootroot00000000000000genometools-1.5.1/testdata/empty_id_attribute.gff3000066400000000000000000000001311211610345200223140ustar00rootroot00000000000000##gff-version   3
##sequence-region   seqid 1 10000
seqid	.	gene	1000	9000	0.500	+	.	ID=
genometools-1.5.1/testdata/empty_other_attribute.gff3000066400000000000000000000001341211610345200230440ustar00rootroot00000000000000##gff-version   3
##sequence-region   seqid 1 10000
seqid	.	gene	1000	9000	0.500	+	.	other=
genometools-1.5.1/testdata/empty_parent_attribute.gff3000066400000000000000000000001351211610345200232150ustar00rootroot00000000000000##gff-version   3
##sequence-region   seqid 1 10000
seqid	.	gene	1000	9000	0.500	+	.	Parent=
genometools-1.5.1/testdata/empty_seq.fas000066400000000000000000000000101211610345200203450ustar00rootroot00000000000000>empty

genometools-1.5.1/testdata/encode_known_genes_Mar07.gff3000066400000000000000000075161771211610345200232540ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr1 147971134 148468994
##sequence-region   chr10 55232537 55643814
##sequence-region   chr11 1710216 131036335
##sequence-region   chr12 38629559 39125713
##sequence-region   chr13 29419740 112832621
##sequence-region   chr14 98705377 98950024
##sequence-region   chr15 41520749 42003799
##sequence-region   chr16 4043 26056510
##sequence-region   chr18 23784928 59823258
##sequence-region   chr19 59061289 60023279
##sequence-region   chr2 118288456 234767778
##sequence-region   chr20 33305669 33793648
##sequence-region   chr21 32669578 39739894
##sequence-region   chr22 30131552 31778912
##sequence-region   chr5 55887725 142374155
##sequence-region   chr6 41411371 132691426
##sequence-region   chr7 26905852 126835803
##sequence-region   chr8 118886142 119279152
##sequence-region   chr9 128768701 129020095
##sequence-region   chrX 122525028 153939916
chr1	ENCODE	gene	147971134	147975692	.	-	.	ID=gene1;name2=VPS72;Name=RP11-68I18.8-005
chr1	ENCODE	exon	147971134	147971499	.	-	.	Parent=gene1
chr1	ENCODE	exon	147975554	147975692	.	-	.	Parent=gene1
###
chr1	ENCODE	gene	147971134	147975694	.	-	.	ID=gene2;Name=RP11-68I18.8-007;name2=VPS72
chr1	ENCODE	exon	147971134	147971169	.	-	.	Parent=gene2
chr1	ENCODE	exon	147971347	147971499	.	-	.	Parent=gene2
chr1	ENCODE	exon	147975673	147975694	.	-	.	Parent=gene2
###
chr1	ENCODE	gene	147971134	147975707	.	-	.	ID=gene3;Name=RP11-68I18.8-002;name2=VPS72
chr1	ENCODE	exon	147971134	147971169	.	-	.	Parent=gene3
chr1	ENCODE	exon	147971347	147971499	.	-	.	Parent=gene3
chr1	ENCODE	exon	147975554	147975707	.	-	.	Parent=gene3
###
chr1	ENCODE	gene	147971134	147975720	.	-	.	ID=gene4;Name=RP11-68I18.8-006;name2=VPS72
chr1	ENCODE	exon	147971134	147971169	.	-	.	Parent=gene4
chr1	ENCODE	exon	147971347	147971499	.	-	.	Parent=gene4
chr1	ENCODE	exon	147975554	147975720	.	-	.	Parent=gene4
###
chr1	ENCODE	gene	147971134	147975737	.	-	.	ID=gene5;Name=RP11-68I18.8-003;name2=VPS72
chr1	ENCODE	exon	147971134	147971169	.	-	.	Parent=gene5
chr1	ENCODE	exon	147971347	147971499	.	-	.	Parent=gene5
chr1	ENCODE	exon	147975554	147975737	.	-	.	Parent=gene5
###
chr1	ENCODE	gene	147971134	147975762	.	-	.	ID=gene6;name2=VPS72;Name=RP11-68I18.8-001
chr1	ENCODE	exon	147971134	147971169	.	-	.	Parent=gene6
chr1	ENCODE	exon	147971347	147971499	.	-	.	Parent=gene6
chr1	ENCODE	exon	147975554	147975762	.	-	.	Parent=gene6
###
chr1	ENCODE	gene	147971134	147980870	.	-	.	ID=gene7;Name=RP11-68I18.8-004;name2=VPS72
chr1	ENCODE	exon	147971134	147971169	.	-	.	Parent=gene7
chr1	ENCODE	exon	147971347	147971499	.	-	.	Parent=gene7
chr1	ENCODE	exon	147980828	147980870	.	-	.	Parent=gene7
###
chr1	ENCODE	gene	147983498	148017310	.	+	.	ID=gene8;Name=RP11-68I18.9-011;name2=PIP5K1A
chr1	ENCODE	exon	147983498	147983666	.	+	.	Parent=gene8
chr1	ENCODE	CDS	147983567	147983666	.	+	0	Parent=gene8
chr1	ENCODE	exon	148009797	148009828	.	+	.	Parent=gene8
chr1	ENCODE	CDS	148009797	148009828	.	+	2	Parent=gene8
chr1	ENCODE	exon	148012869	148012949	.	+	.	Parent=gene8
chr1	ENCODE	CDS	148012869	148012949	.	+	0	Parent=gene8
chr1	ENCODE	exon	148017220	148017310	.	+	.	Parent=gene8
chr1	ENCODE	CDS	148017220	148017310	.	+	0	Parent=gene8
###
chr1	ENCODE	gene	147984100	148035085	.	+	.	ID=gene9;Name=RP11-68I18.9-001;name2=PIP5K1A
chr1	ENCODE	exon	147984100	147984630	.	+	.	Parent=gene9
chr1	ENCODE	CDS	147984546	147984630	.	+	0	Parent=gene9
chr1	ENCODE	exon	148009797	148009828	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148009797	148009828	.	+	2	Parent=gene9
chr1	ENCODE	exon	148012869	148012949	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148012869	148012949	.	+	0	Parent=gene9
chr1	ENCODE	exon	148017220	148017350	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148017220	148017350	.	+	0	Parent=gene9
chr1	ENCODE	exon	148017797	148017914	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148017797	148017914	.	+	1	Parent=gene9
chr1	ENCODE	exon	148018100	148018252	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148018100	148018252	.	+	0	Parent=gene9
chr1	ENCODE	exon	148019746	148020045	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148019746	148020045	.	+	0	Parent=gene9
chr1	ENCODE	exon	148022107	148022312	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148022107	148022312	.	+	0	Parent=gene9
chr1	ENCODE	exon	148023731	148023814	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148023731	148023814	.	+	1	Parent=gene9
chr1	ENCODE	exon	148024679	148024727	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148024679	148024727	.	+	1	Parent=gene9
chr1	ENCODE	exon	148025504	148025588	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148025504	148025588	.	+	0	Parent=gene9
chr1	ENCODE	exon	148027672	148027818	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148027672	148027818	.	+	2	Parent=gene9
chr1	ENCODE	exon	148027987	148028116	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148027987	148028116	.	+	2	Parent=gene9
chr1	ENCODE	exon	148032469	148032514	.	+	.	Parent=gene9
chr1	ENCODE	CDS	148032469	148032514	.	+	1	Parent=gene9
chr1	ENCODE	CDS	148033412	148033414	.	+	0	Parent=gene9
chr1	ENCODE	exon	148033412	148035085	.	+	.	Parent=gene9
###
chr1	ENCODE	gene	147984101	148012946	.	+	.	ID=gene10;Name=RP11-68I18.9-015;name2=PIP5K1A
chr1	ENCODE	exon	147984101	147984630	.	+	.	Parent=gene10
chr1	ENCODE	CDS	147984546	147984630	.	+	0	Parent=gene10
chr1	ENCODE	exon	148009794	148009828	.	+	.	Parent=gene10
chr1	ENCODE	CDS	148009794	148009828	.	+	2	Parent=gene10
chr1	ENCODE	exon	148012869	148012946	.	+	.	Parent=gene10
chr1	ENCODE	CDS	148012869	148012946	.	+	0	Parent=gene10
###
chr1	ENCODE	gene	147984102	148035080	.	+	.	ID=gene11;Name=RP11-68I18.9-002;name2=PIP5K1A
chr1	ENCODE	exon	147984102	147984630	.	+	.	Parent=gene11
chr1	ENCODE	CDS	147984546	147984630	.	+	0	Parent=gene11
chr1	ENCODE	exon	148009797	148009828	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148009797	148009828	.	+	2	Parent=gene11
chr1	ENCODE	exon	148012869	148012949	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148012869	148012949	.	+	0	Parent=gene11
chr1	ENCODE	exon	148017220	148017350	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148017220	148017350	.	+	0	Parent=gene11
chr1	ENCODE	exon	148017797	148017914	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148017797	148017914	.	+	1	Parent=gene11
chr1	ENCODE	exon	148018100	148018252	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148018100	148018252	.	+	0	Parent=gene11
chr1	ENCODE	exon	148019746	148020045	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148019746	148020045	.	+	0	Parent=gene11
chr1	ENCODE	exon	148022107	148022312	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148022107	148022312	.	+	0	Parent=gene11
chr1	ENCODE	exon	148023731	148023814	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148023731	148023814	.	+	1	Parent=gene11
chr1	ENCODE	exon	148024679	148024727	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148024679	148024727	.	+	1	Parent=gene11
chr1	ENCODE	exon	148025504	148025588	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148025504	148025588	.	+	0	Parent=gene11
chr1	ENCODE	exon	148027987	148028116	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148027987	148028116	.	+	2	Parent=gene11
chr1	ENCODE	exon	148032469	148032514	.	+	.	Parent=gene11
chr1	ENCODE	CDS	148032469	148032514	.	+	1	Parent=gene11
chr1	ENCODE	CDS	148033412	148033414	.	+	0	Parent=gene11
chr1	ENCODE	exon	148033412	148035080	.	+	.	Parent=gene11
###
chr1	ENCODE	gene	147984103	148001549	.	+	.	ID=gene12;Name=RP11-68I18.9-014;name2=PIP5K1A
chr1	ENCODE	exon	147984103	147984630	.	+	.	Parent=gene12
chr1	ENCODE	CDS	147984546	147984630	.	+	0	Parent=gene12
chr1	ENCODE	exon	148001511	148001549	.	+	.	Parent=gene12
chr1	ENCODE	CDS	148001511	148001549	.	+	2	Parent=gene12
###
chr1	ENCODE	gene	147984124	148033437	.	+	.	ID=gene13;name2=PIP5K1A;Name=RP11-68I18.9-003
chr1	ENCODE	exon	147984124	147984630	.	+	.	Parent=gene13
chr1	ENCODE	CDS	147984546	147984630	.	+	0	Parent=gene13
chr1	ENCODE	exon	148009794	148009828	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148009794	148009828	.	+	2	Parent=gene13
chr1	ENCODE	exon	148009920	148009955	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148009920	148009955	.	+	0	Parent=gene13
chr1	ENCODE	exon	148012869	148012949	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148012869	148012949	.	+	0	Parent=gene13
chr1	ENCODE	exon	148017220	148017350	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148017220	148017350	.	+	0	Parent=gene13
chr1	ENCODE	exon	148017797	148017914	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148017797	148017914	.	+	1	Parent=gene13
chr1	ENCODE	exon	148018100	148018252	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148018100	148018252	.	+	0	Parent=gene13
chr1	ENCODE	exon	148019746	148020045	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148019746	148020045	.	+	0	Parent=gene13
chr1	ENCODE	exon	148022107	148022312	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148022107	148022312	.	+	0	Parent=gene13
chr1	ENCODE	exon	148023731	148023814	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148023731	148023814	.	+	1	Parent=gene13
chr1	ENCODE	exon	148024679	148024727	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148024679	148024727	.	+	1	Parent=gene13
chr1	ENCODE	exon	148025504	148025588	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148025504	148025588	.	+	0	Parent=gene13
chr1	ENCODE	exon	148027672	148027818	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148027672	148027818	.	+	2	Parent=gene13
chr1	ENCODE	exon	148027987	148028116	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148027987	148028116	.	+	2	Parent=gene13
chr1	ENCODE	exon	148032469	148032514	.	+	.	Parent=gene13
chr1	ENCODE	CDS	148032469	148032514	.	+	1	Parent=gene13
chr1	ENCODE	CDS	148033412	148033414	.	+	0	Parent=gene13
chr1	ENCODE	exon	148033412	148033437	.	+	.	Parent=gene13
###
chr1	ENCODE	gene	147999066	148017350	.	+	.	ID=gene14;Name=RP11-68I18.9-004;name2=PIP5K1A
chr1	ENCODE	exon	147999066	147999096	.	+	.	Parent=gene14
chr1	ENCODE	exon	148001511	148001549	.	+	.	Parent=gene14
chr1	ENCODE	exon	148009794	148009828	.	+	.	Parent=gene14
chr1	ENCODE	CDS	148009817	148009828	.	+	0	Parent=gene14
chr1	ENCODE	exon	148009920	148009955	.	+	.	Parent=gene14
chr1	ENCODE	CDS	148009920	148009955	.	+	0	Parent=gene14
chr1	ENCODE	exon	148012869	148012949	.	+	.	Parent=gene14
chr1	ENCODE	CDS	148012869	148012949	.	+	0	Parent=gene14
chr1	ENCODE	exon	148017220	148017350	.	+	.	Parent=gene14
chr1	ENCODE	CDS	148017220	148017350	.	+	0	Parent=gene14
###
chr1	ENCODE	gene	148009429	148017894	.	+	.	ID=gene15;Name=RP11-68I18.9-005;name2=PIP5K1A
chr1	ENCODE	exon	148009429	148009828	.	+	.	Parent=gene15
chr1	ENCODE	exon	148012869	148012949	.	+	.	Parent=gene15
chr1	ENCODE	exon	148017220	148017350	.	+	.	Parent=gene15
chr1	ENCODE	exon	148017797	148017894	.	+	.	Parent=gene15
###
chr1	ENCODE	gene	148009688	148017856	.	+	.	ID=gene16;Name=RP11-68I18.9-009;name2=PIP5K1A
chr1	ENCODE	exon	148009688	148009828	.	+	.	Parent=gene16
chr1	ENCODE	exon	148009920	148009955	.	+	.	Parent=gene16
chr1	ENCODE	exon	148012869	148012949	.	+	.	Parent=gene16
chr1	ENCODE	exon	148017220	148017350	.	+	.	Parent=gene16
chr1	ENCODE	exon	148017797	148017856	.	+	.	Parent=gene16
###
chr1	ENCODE	gene	148012816	148018190	.	+	.	ID=gene17;Name=RP11-68I18.9-006;name2=PIP5K1A
chr1	ENCODE	exon	148012816	148012949	.	+	.	Parent=gene17
chr1	ENCODE	exon	148017220	148017350	.	+	.	Parent=gene17
chr1	ENCODE	exon	148017797	148017914	.	+	.	Parent=gene17
chr1	ENCODE	exon	148018100	148018190	.	+	.	Parent=gene17
###
chr1	ENCODE	gene	148017801	148019916	.	+	.	ID=gene18;Name=RP11-68I18.9-012;name2=PIP5K1A
chr1	ENCODE	exon	148017801	148017914	.	+	.	Parent=gene18
chr1	ENCODE	exon	148018100	148018252	.	+	.	Parent=gene18
chr1	ENCODE	exon	148018880	148018947	.	+	.	Parent=gene18
chr1	ENCODE	exon	148019746	148019916	.	+	.	Parent=gene18
###
chr1	ENCODE	gene	148019171	148022296	.	+	.	ID=gene19;name2=PIP5K1A;Name=RP11-68I18.9-007
chr1	ENCODE	exon	148019171	148019333	.	+	.	Parent=gene19
chr1	ENCODE	exon	148019746	148020045	.	+	.	Parent=gene19
chr1	ENCODE	exon	148022107	148022296	.	+	.	Parent=gene19
###
chr1	ENCODE	gene	148022183	148024154	.	+	.	ID=gene20;Name=RP11-68I18.9-013;name2=PIP5K1A
chr1	ENCODE	exon	148022183	148022312	.	+	.	Parent=gene20
chr1	ENCODE	exon	148023731	148024154	.	+	.	Parent=gene20
###
chr1	ENCODE	gene	148022183	148025840	.	+	.	ID=gene21;Name=RP11-68I18.9-008;name2=PIP5K1A
chr1	ENCODE	exon	148022183	148022312	.	+	.	Parent=gene21
chr1	ENCODE	exon	148023731	148023814	.	+	.	Parent=gene21
chr1	ENCODE	exon	148024679	148024727	.	+	.	Parent=gene21
chr1	ENCODE	exon	148025504	148025840	.	+	.	Parent=gene21
###
chr1	ENCODE	gene	148027661	148034032	.	+	.	ID=gene22;Name=RP11-68I18.9-010;name2=PIP5K1A
chr1	ENCODE	exon	148027661	148027818	.	+	.	Parent=gene22
chr1	ENCODE	exon	148027987	148028116	.	+	.	Parent=gene22
chr1	ENCODE	exon	148032469	148032514	.	+	.	Parent=gene22
chr1	ENCODE	exon	148033412	148034032	.	+	.	Parent=gene22
###
chr1	ENCODE	gene	148040252	148053028	.	+	.	ID=gene23;Name=RP11-126K1.1-001;name2=PSMD4
chr1	ENCODE	exon	148040252	148040357	.	+	.	Parent=gene23
chr1	ENCODE	CDS	148040332	148040357	.	+	0	Parent=gene23
chr1	ENCODE	exon	148047710	148047850	.	+	.	Parent=gene23
chr1	ENCODE	CDS	148047710	148047850	.	+	1	Parent=gene23
chr1	ENCODE	exon	148049463	148049577	.	+	.	Parent=gene23
chr1	ENCODE	CDS	148049463	148049577	.	+	1	Parent=gene23
chr1	ENCODE	exon	148050381	148050467	.	+	.	Parent=gene23
chr1	ENCODE	CDS	148050381	148050467	.	+	0	Parent=gene23
chr1	ENCODE	exon	148050715	148050783	.	+	.	Parent=gene23
chr1	ENCODE	CDS	148050715	148050783	.	+	0	Parent=gene23
chr1	ENCODE	exon	148050943	148051158	.	+	.	Parent=gene23
chr1	ENCODE	CDS	148050943	148051158	.	+	0	Parent=gene23
chr1	ENCODE	exon	148051553	148051661	.	+	.	Parent=gene23
chr1	ENCODE	CDS	148051553	148051661	.	+	0	Parent=gene23
chr1	ENCODE	exon	148051857	148051988	.	+	.	Parent=gene23
chr1	ENCODE	CDS	148051857	148051988	.	+	2	Parent=gene23
chr1	ENCODE	exon	148052069	148052136	.	+	.	Parent=gene23
chr1	ENCODE	CDS	148052069	148052136	.	+	2	Parent=gene23
chr1	ENCODE	CDS	148052722	148052892	.	+	0	Parent=gene23
chr1	ENCODE	exon	148052722	148053028	.	+	.	Parent=gene23
###
chr1	ENCODE	gene	148040258	148053008	.	+	.	ID=gene24;Name=RP11-126K1.1-002;name2=PSMD4
chr1	ENCODE	exon	148040258	148040357	.	+	.	Parent=gene24
chr1	ENCODE	CDS	148040332	148040357	.	+	0	Parent=gene24
chr1	ENCODE	exon	148047710	148047850	.	+	.	Parent=gene24
chr1	ENCODE	CDS	148047710	148047850	.	+	1	Parent=gene24
chr1	ENCODE	exon	148049463	148049577	.	+	.	Parent=gene24
chr1	ENCODE	CDS	148049463	148049577	.	+	1	Parent=gene24
chr1	ENCODE	exon	148050381	148050467	.	+	.	Parent=gene24
chr1	ENCODE	CDS	148050381	148050467	.	+	0	Parent=gene24
chr1	ENCODE	exon	148050715	148050783	.	+	.	Parent=gene24
chr1	ENCODE	CDS	148050715	148050783	.	+	0	Parent=gene24
chr1	ENCODE	exon	148050943	148051158	.	+	.	Parent=gene24
chr1	ENCODE	CDS	148050943	148051158	.	+	0	Parent=gene24
chr1	ENCODE	exon	148051553	148051670	.	+	.	Parent=gene24
chr1	ENCODE	CDS	148051553	148051670	.	+	0	Parent=gene24
chr1	ENCODE	exon	148051857	148051988	.	+	.	Parent=gene24
chr1	ENCODE	CDS	148051857	148051988	.	+	2	Parent=gene24
chr1	ENCODE	exon	148052069	148052136	.	+	.	Parent=gene24
chr1	ENCODE	CDS	148052069	148052136	.	+	2	Parent=gene24
chr1	ENCODE	CDS	148052722	148052892	.	+	0	Parent=gene24
chr1	ENCODE	exon	148052722	148053008	.	+	.	Parent=gene24
###
chr1	ENCODE	gene	148040307	148048459	.	+	.	ID=gene25;Name=RP11-126K1.1-012;name2=PSMD4
chr1	ENCODE	exon	148040307	148040357	.	+	.	Parent=gene25
chr1	ENCODE	exon	148047710	148048459	.	+	.	Parent=gene25
###
chr1	ENCODE	gene	148040312	148051137	.	+	.	ID=gene26;Name=RP11-126K1.1-004;name2=PSMD4
chr1	ENCODE	exon	148040312	148040357	.	+	.	Parent=gene26
chr1	ENCODE	exon	148047710	148047850	.	+	.	Parent=gene26
chr1	ENCODE	exon	148049463	148049577	.	+	.	Parent=gene26
chr1	ENCODE	exon	148050381	148050783	.	+	.	Parent=gene26
chr1	ENCODE	exon	148050943	148051137	.	+	.	Parent=gene26
###
chr1	ENCODE	gene	148040318	148052781	.	+	.	ID=gene27;Name=RP11-126K1.1-006;name2=PSMD4
chr1	ENCODE	exon	148040318	148040357	.	+	.	Parent=gene27
chr1	ENCODE	exon	148047710	148047850	.	+	.	Parent=gene27
chr1	ENCODE	exon	148049463	148049577	.	+	.	Parent=gene27
chr1	ENCODE	exon	148050381	148050467	.	+	.	Parent=gene27
chr1	ENCODE	exon	148050715	148050783	.	+	.	Parent=gene27
chr1	ENCODE	exon	148050943	148051158	.	+	.	Parent=gene27
chr1	ENCODE	exon	148051553	148051988	.	+	.	Parent=gene27
chr1	ENCODE	exon	148052069	148052136	.	+	.	Parent=gene27
chr1	ENCODE	exon	148052722	148052781	.	+	.	Parent=gene27
###
chr1	ENCODE	gene	148044612	148051158	.	+	.	ID=gene28;Name=RP11-126K1.1-014;name2=PSMD4
chr1	ENCODE	exon	148044612	148044770	.	+	.	Parent=gene28
chr1	ENCODE	exon	148047710	148047850	.	+	.	Parent=gene28
chr1	ENCODE	CDS	148047729	148047850	.	+	0	Parent=gene28
chr1	ENCODE	exon	148049463	148049577	.	+	.	Parent=gene28
chr1	ENCODE	CDS	148049463	148049577	.	+	1	Parent=gene28
chr1	ENCODE	exon	148050381	148050467	.	+	.	Parent=gene28
chr1	ENCODE	CDS	148050381	148050467	.	+	0	Parent=gene28
chr1	ENCODE	exon	148050715	148050783	.	+	.	Parent=gene28
chr1	ENCODE	CDS	148050715	148050783	.	+	0	Parent=gene28
chr1	ENCODE	exon	148050943	148051158	.	+	.	Parent=gene28
chr1	ENCODE	CDS	148050943	148051158	.	+	0	Parent=gene28
###
chr1	ENCODE	gene	148048109	148050488	.	+	.	ID=gene29;name2=PSMD4;Name=RP11-126K1.1-011
chr1	ENCODE	exon	148048109	148048152	.	+	.	Parent=gene29
chr1	ENCODE	exon	148049323	148049577	.	+	.	Parent=gene29
chr1	ENCODE	exon	148050381	148050488	.	+	.	Parent=gene29
###
chr1	ENCODE	gene	148049463	148052921	.	+	.	ID=gene30;Name=RP11-126K1.1-005;name2=PSMD4
chr1	ENCODE	exon	148049463	148049577	.	+	.	Parent=gene30
chr1	ENCODE	exon	148050381	148050419	.	+	.	Parent=gene30
chr1	ENCODE	exon	148051093	148051158	.	+	.	Parent=gene30
chr1	ENCODE	exon	148051553	148051661	.	+	.	Parent=gene30
chr1	ENCODE	exon	148051857	148051988	.	+	.	Parent=gene30
chr1	ENCODE	exon	148052117	148052136	.	+	.	Parent=gene30
chr1	ENCODE	exon	148052722	148052921	.	+	.	Parent=gene30
###
chr1	ENCODE	gene	148050437	148053015	.	+	.	ID=gene31;Name=RP11-126K1.1-008;name2=PSMD4
chr1	ENCODE	exon	148050437	148050467	.	+	.	Parent=gene31
chr1	ENCODE	CDS	148050437	148050467	.	+	0	Parent=gene31
chr1	ENCODE	exon	148050715	148050783	.	+	.	Parent=gene31
chr1	ENCODE	CDS	148050715	148050783	.	+	2	Parent=gene31
chr1	ENCODE	exon	148051553	148051661	.	+	.	Parent=gene31
chr1	ENCODE	CDS	148051553	148051661	.	+	2	Parent=gene31
chr1	ENCODE	exon	148051857	148051988	.	+	.	Parent=gene31
chr1	ENCODE	CDS	148051857	148051988	.	+	1	Parent=gene31
chr1	ENCODE	exon	148052069	148052136	.	+	.	Parent=gene31
chr1	ENCODE	CDS	148052069	148052136	.	+	1	Parent=gene31
chr1	ENCODE	CDS	148052722	148052892	.	+	2	Parent=gene31
chr1	ENCODE	exon	148052722	148053015	.	+	.	Parent=gene31
###
chr1	ENCODE	gene	148050793	148051647	.	+	.	ID=gene32;Name=RP11-126K1.1-009;name2=PSMD4
chr1	ENCODE	exon	148050793	148051158	.	+	.	Parent=gene32
chr1	ENCODE	exon	148051553	148051647	.	+	.	Parent=gene32
###
chr1	ENCODE	gene	148051587	148053009	.	+	.	ID=gene33;Name=RP11-126K1.1-013;name2=PSMD4
chr1	ENCODE	exon	148051587	148051747	.	+	.	Parent=gene33
chr1	ENCODE	exon	148051857	148051988	.	+	.	Parent=gene33
chr1	ENCODE	exon	148052069	148052136	.	+	.	Parent=gene33
chr1	ENCODE	exon	148052722	148053009	.	+	.	Parent=gene33
###
chr1	ENCODE	gene	148051857	148052274	.	+	.	ID=gene34;Name=RP11-126K1.1-007;name2=PSMD4
chr1	ENCODE	exon	148051857	148051988	.	+	.	Parent=gene34
chr1	ENCODE	exon	148052069	148052274	.	+	.	Parent=gene34
###
chr1	ENCODE	gene	148052093	148053009	.	+	.	ID=gene35;Name=RP11-126K1.1-010;name2=PSMD4
chr1	ENCODE	exon	148052093	148052136	.	+	.	Parent=gene35
chr1	ENCODE	CDS	148052093	148052136	.	+	0	Parent=gene35
chr1	ENCODE	exon	148052489	148052527	.	+	.	Parent=gene35
chr1	ENCODE	CDS	148052489	148052527	.	+	1	Parent=gene35
chr1	ENCODE	CDS	148052722	148052892	.	+	1	Parent=gene35
chr1	ENCODE	exon	148052722	148053009	.	+	.	Parent=gene35
###
chr1	ENCODE	gene	148065573	148067429	.	-	.	ID=gene36;Name=RP11-126K1.2-002;name2=RP11-126K1.2
chr1	ENCODE	exon	148065573	148065807	.	-	.	Parent=gene36
chr1	ENCODE	exon	148067358	148067429	.	-	.	Parent=gene36
###
chr1	ENCODE	gene	148065573	148067478	.	-	.	ID=gene37;Name=RP11-126K1.2-001;name2=RP11-126K1.2
chr1	ENCODE	exon	148065573	148065807	.	-	.	Parent=gene37
chr1	ENCODE	CDS	148065745	148065807	.	-	0	Parent=gene37
chr1	ENCODE	CDS	148067092	148067208	.	-	0	Parent=gene37
chr1	ENCODE	exon	148067092	148067478	.	-	.	Parent=gene37
###
chr1	ENCODE	gene	148067167	148072254	.	+	.	ID=gene38;Name=RP11-126K1.3-004;name2=ZNF687
chr1	ENCODE	exon	148067167	148067628	.	+	.	Parent=gene38
chr1	ENCODE	CDS	148067619	148067628	.	+	0	Parent=gene38
chr1	ENCODE	exon	148071824	148072254	.	+	.	Parent=gene38
chr1	ENCODE	CDS	148071824	148072254	.	+	2	Parent=gene38
###
chr1	ENCODE	gene	148067816	148077454	.	+	.	ID=gene39;Name=RP11-126K1.3-001;name2=ZNF687
chr1	ENCODE	exon	148067816	148067944	.	+	.	Parent=gene39
chr1	ENCODE	exon	148071824	148073955	.	+	.	Parent=gene39
chr1	ENCODE	CDS	148071841	148073955	.	+	0	Parent=gene39
chr1	ENCODE	exon	148074077	148074255	.	+	.	Parent=gene39
chr1	ENCODE	CDS	148074077	148074255	.	+	0	Parent=gene39
chr1	ENCODE	exon	148074644	148074820	.	+	.	Parent=gene39
chr1	ENCODE	CDS	148074644	148074820	.	+	1	Parent=gene39
chr1	ENCODE	exon	148074927	148075089	.	+	.	Parent=gene39
chr1	ENCODE	CDS	148074927	148075089	.	+	1	Parent=gene39
chr1	ENCODE	exon	148075227	148075556	.	+	.	Parent=gene39
chr1	ENCODE	CDS	148075227	148075556	.	+	0	Parent=gene39
chr1	ENCODE	exon	148075671	148075783	.	+	.	Parent=gene39
chr1	ENCODE	CDS	148075671	148075783	.	+	0	Parent=gene39
chr1	ENCODE	exon	148075981	148076122	.	+	.	Parent=gene39
chr1	ENCODE	CDS	148075981	148076122	.	+	1	Parent=gene39
chr1	ENCODE	CDS	148076264	148076758	.	+	0	Parent=gene39
chr1	ENCODE	exon	148076264	148077454	.	+	.	Parent=gene39
###
chr1	ENCODE	gene	148067861	148077452	.	+	.	ID=gene40;Name=RP11-126K1.3-002;name2=ZNF687
chr1	ENCODE	exon	148067861	148067944	.	+	.	Parent=gene40
chr1	ENCODE	exon	148070755	148071623	.	+	.	Parent=gene40
chr1	ENCODE	exon	148071824	148073955	.	+	.	Parent=gene40
chr1	ENCODE	CDS	148071841	148073955	.	+	0	Parent=gene40
chr1	ENCODE	exon	148074077	148074255	.	+	.	Parent=gene40
chr1	ENCODE	CDS	148074077	148074255	.	+	0	Parent=gene40
chr1	ENCODE	exon	148074644	148074820	.	+	.	Parent=gene40
chr1	ENCODE	CDS	148074644	148074820	.	+	1	Parent=gene40
chr1	ENCODE	exon	148074927	148075089	.	+	.	Parent=gene40
chr1	ENCODE	CDS	148074927	148075089	.	+	1	Parent=gene40
chr1	ENCODE	exon	148075227	148075556	.	+	.	Parent=gene40
chr1	ENCODE	CDS	148075227	148075556	.	+	0	Parent=gene40
chr1	ENCODE	exon	148075671	148075783	.	+	.	Parent=gene40
chr1	ENCODE	CDS	148075671	148075783	.	+	0	Parent=gene40
chr1	ENCODE	exon	148075981	148076122	.	+	.	Parent=gene40
chr1	ENCODE	CDS	148075981	148076122	.	+	1	Parent=gene40
chr1	ENCODE	CDS	148076264	148076758	.	+	0	Parent=gene40
chr1	ENCODE	exon	148076264	148077452	.	+	.	Parent=gene40
###
chr1	ENCODE	gene	148073033	148077452	.	+	.	ID=gene41;Name=RP11-126K1.3-003;name2=ZNF687
chr1	ENCODE	exon	148073033	148073955	.	+	.	Parent=gene41
chr1	ENCODE	CDS	148073033	148073955	.	+	0	Parent=gene41
chr1	ENCODE	exon	148074077	148074255	.	+	.	Parent=gene41
chr1	ENCODE	CDS	148074077	148074255	.	+	1	Parent=gene41
chr1	ENCODE	exon	148074644	148074820	.	+	.	Parent=gene41
chr1	ENCODE	CDS	148074644	148074820	.	+	2	Parent=gene41
chr1	ENCODE	exon	148074927	148075089	.	+	.	Parent=gene41
chr1	ENCODE	CDS	148074927	148075089	.	+	2	Parent=gene41
chr1	ENCODE	exon	148075227	148075556	.	+	.	Parent=gene41
chr1	ENCODE	CDS	148075227	148075556	.	+	1	Parent=gene41
chr1	ENCODE	exon	148075671	148075783	.	+	.	Parent=gene41
chr1	ENCODE	CDS	148075671	148075783	.	+	1	Parent=gene41
chr1	ENCODE	exon	148075920	148076122	.	+	.	Parent=gene41
chr1	ENCODE	CDS	148075920	148076122	.	+	2	Parent=gene41
chr1	ENCODE	CDS	148076264	148076295	.	+	0	Parent=gene41
chr1	ENCODE	exon	148076264	148077452	.	+	.	Parent=gene41
###
chr1	ENCODE	gene	148073740	148075088	.	+	.	ID=gene42;Name=RP11-126K1.3-005;name2=ZNF687
chr1	ENCODE	exon	148073740	148073955	.	+	.	Parent=gene42
chr1	ENCODE	exon	148074077	148074255	.	+	.	Parent=gene42
chr1	ENCODE	exon	148074644	148075088	.	+	.	Parent=gene42
###
chr1	ENCODE	gene	148076000	148076886	.	+	.	ID=gene43;Name=RP11-126K1.3-006;name2=ZNF687
chr1	ENCODE	exon	148076000	148076122	.	+	.	Parent=gene43
chr1	ENCODE	CDS	148076000	148076122	.	+	0	Parent=gene43
chr1	ENCODE	CDS	148076244	148076420	.	+	0	Parent=gene43
chr1	ENCODE	exon	148076244	148076886	.	+	.	Parent=gene43
###
chr1	ENCODE	gene	148077486	148112985	.	-	.	ID=gene44;Name=RP11-126K1.4-003;name2=PIK4CB
chr1	ENCODE	exon	148077486	148078582	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148078401	148078582	.	-	2	Parent=gene44
chr1	ENCODE	exon	148079567	148079687	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148079567	148079687	.	-	0	Parent=gene44
chr1	ENCODE	exon	148079958	148080090	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148079958	148080090	.	-	1	Parent=gene44
chr1	ENCODE	exon	148084357	148084622	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148084357	148084622	.	-	0	Parent=gene44
chr1	ENCODE	exon	148087393	148087516	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148087393	148087516	.	-	1	Parent=gene44
chr1	ENCODE	exon	148087743	148087847	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148087743	148087847	.	-	1	Parent=gene44
chr1	ENCODE	exon	148089090	148089199	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148089090	148089199	.	-	0	Parent=gene44
chr1	ENCODE	exon	148091685	148091912	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148091685	148091912	.	-	0	Parent=gene44
chr1	ENCODE	exon	148093123	148093350	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148093123	148093350	.	-	0	Parent=gene44
chr1	ENCODE	exon	148095760	148095804	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148095760	148095804	.	-	0	Parent=gene44
chr1	ENCODE	exon	148101122	148102058	.	-	.	Parent=gene44
chr1	ENCODE	CDS	148101122	148102058	.	-	1	Parent=gene44
chr1	ENCODE	CDS	148111721	148111728	.	-	0	Parent=gene44
chr1	ENCODE	exon	148111721	148111922	.	-	.	Parent=gene44
chr1	ENCODE	exon	148112820	148112985	.	-	.	Parent=gene44
###
chr1	ENCODE	gene	148077680	148113264	.	-	.	ID=gene45;Name=RP11-126K1.4-001;name2=PIK4CB
chr1	ENCODE	exon	148077680	148078582	.	-	.	Parent=gene45
chr1	ENCODE	CDS	148078401	148078582	.	-	2	Parent=gene45
chr1	ENCODE	exon	148079567	148079687	.	-	.	Parent=gene45
chr1	ENCODE	CDS	148079567	148079687	.	-	0	Parent=gene45
chr1	ENCODE	exon	148079958	148080090	.	-	.	Parent=gene45
chr1	ENCODE	CDS	148079958	148080090	.	-	1	Parent=gene45
chr1	ENCODE	exon	148084357	148084622	.	-	.	Parent=gene45
chr1	ENCODE	CDS	148084357	148084622	.	-	0	Parent=gene45
chr1	ENCODE	exon	148087393	148087516	.	-	.	Parent=gene45
chr1	ENCODE	CDS	148087393	148087516	.	-	1	Parent=gene45
chr1	ENCODE	exon	148087743	148087847	.	-	.	Parent=gene45
chr1	ENCODE	CDS	148087743	148087847	.	-	1	Parent=gene45
chr1	ENCODE	exon	148089090	148089199	.	-	.	Parent=gene45
chr1	ENCODE	CDS	148089090	148089199	.	-	0	Parent=gene45
chr1	ENCODE	exon	148091685	148091912	.	-	.	Parent=gene45
chr1	ENCODE	CDS	148091685	148091912	.	-	0	Parent=gene45
chr1	ENCODE	exon	148093123	148093350	.	-	.	Parent=gene45
chr1	ENCODE	CDS	148093123	148093350	.	-	0	Parent=gene45
chr1	ENCODE	CDS	148101122	148102030	.	-	0	Parent=gene45
chr1	ENCODE	exon	148101122	148102058	.	-	.	Parent=gene45
chr1	ENCODE	exon	148112820	148113264	.	-	.	Parent=gene45
###
chr1	ENCODE	gene	148077681	148112960	.	-	.	ID=gene46;Name=RP11-126K1.4-002;name2=PIK4CB
chr1	ENCODE	exon	148077681	148078582	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148078401	148078582	.	-	2	Parent=gene46
chr1	ENCODE	exon	148079567	148079687	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148079567	148079687	.	-	0	Parent=gene46
chr1	ENCODE	exon	148079958	148080090	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148079958	148080090	.	-	1	Parent=gene46
chr1	ENCODE	exon	148084357	148084622	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148084357	148084622	.	-	0	Parent=gene46
chr1	ENCODE	exon	148087393	148087516	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148087393	148087516	.	-	1	Parent=gene46
chr1	ENCODE	exon	148087743	148087847	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148087743	148087847	.	-	1	Parent=gene46
chr1	ENCODE	exon	148089090	148089199	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148089090	148089199	.	-	0	Parent=gene46
chr1	ENCODE	exon	148091685	148091912	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148091685	148091912	.	-	0	Parent=gene46
chr1	ENCODE	exon	148093123	148093350	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148093123	148093350	.	-	0	Parent=gene46
chr1	ENCODE	exon	148095760	148095804	.	-	.	Parent=gene46
chr1	ENCODE	CDS	148095760	148095804	.	-	0	Parent=gene46
chr1	ENCODE	CDS	148101122	148102030	.	-	0	Parent=gene46
chr1	ENCODE	exon	148101122	148102058	.	-	.	Parent=gene46
chr1	ENCODE	exon	148112820	148112960	.	-	.	Parent=gene46
###
chr1	ENCODE	gene	148078028	148112968	.	-	.	ID=gene47;name2=PIK4CB;Name=RP11-126K1.4-004
chr1	ENCODE	exon	148078028	148078582	.	-	.	Parent=gene47
chr1	ENCODE	CDS	148078401	148078582	.	-	2	Parent=gene47
chr1	ENCODE	exon	148079567	148079687	.	-	.	Parent=gene47
chr1	ENCODE	CDS	148079567	148079687	.	-	0	Parent=gene47
chr1	ENCODE	exon	148079958	148080090	.	-	.	Parent=gene47
chr1	ENCODE	CDS	148079958	148080090	.	-	1	Parent=gene47
chr1	ENCODE	exon	148084357	148084622	.	-	.	Parent=gene47
chr1	ENCODE	CDS	148084357	148084622	.	-	0	Parent=gene47
chr1	ENCODE	exon	148087393	148087516	.	-	.	Parent=gene47
chr1	ENCODE	CDS	148087393	148087516	.	-	1	Parent=gene47
chr1	ENCODE	exon	148087743	148087847	.	-	.	Parent=gene47
chr1	ENCODE	CDS	148087743	148087847	.	-	1	Parent=gene47
chr1	ENCODE	exon	148089090	148089199	.	-	.	Parent=gene47
chr1	ENCODE	CDS	148089090	148089199	.	-	0	Parent=gene47
chr1	ENCODE	exon	148091685	148091912	.	-	.	Parent=gene47
chr1	ENCODE	CDS	148091685	148091912	.	-	0	Parent=gene47
chr1	ENCODE	exon	148093123	148093350	.	-	.	Parent=gene47
chr1	ENCODE	CDS	148093123	148093350	.	-	0	Parent=gene47
chr1	ENCODE	CDS	148101122	148102030	.	-	0	Parent=gene47
chr1	ENCODE	exon	148101122	148102058	.	-	.	Parent=gene47
chr1	ENCODE	exon	148110294	148110466	.	-	.	Parent=gene47
chr1	ENCODE	exon	148111721	148111922	.	-	.	Parent=gene47
chr1	ENCODE	exon	148112820	148112968	.	-	.	Parent=gene47
###
chr1	ENCODE	gene	148078151	148084541	.	-	.	ID=gene48;Name=RP11-126K1.4-005;name2=PIK4CB
chr1	ENCODE	exon	148078151	148078582	.	-	.	Parent=gene48
chr1	ENCODE	CDS	148078401	148078582	.	-	2	Parent=gene48
chr1	ENCODE	exon	148078949	148079011	.	-	.	Parent=gene48
chr1	ENCODE	CDS	148078949	148079011	.	-	2	Parent=gene48
chr1	ENCODE	exon	148079567	148079687	.	-	.	Parent=gene48
chr1	ENCODE	CDS	148079567	148079687	.	-	0	Parent=gene48
chr1	ENCODE	exon	148079958	148080090	.	-	.	Parent=gene48
chr1	ENCODE	CDS	148079958	148080090	.	-	1	Parent=gene48
chr1	ENCODE	exon	148084357	148084541	.	-	.	Parent=gene48
chr1	ENCODE	CDS	148084357	148084541	.	-	0	Parent=gene48
###
chr1	ENCODE	gene	148078172	148080022	.	-	.	ID=gene49;name2=PIK4CB;Name=RP11-126K1.4-006
chr1	ENCODE	exon	148078172	148078582	.	-	.	Parent=gene49
chr1	ENCODE	exon	148079598	148079687	.	-	.	Parent=gene49
chr1	ENCODE	exon	148079958	148080022	.	-	.	Parent=gene49
###
chr1	ENCODE	gene	148079414	148084583	.	-	.	ID=gene50;Name=RP11-126K1.4-011;name2=PIK4CB
chr1	ENCODE	exon	148079414	148079687	.	-	.	Parent=gene50
chr1	ENCODE	exon	148079958	148080090	.	-	.	Parent=gene50
chr1	ENCODE	exon	148084357	148084583	.	-	.	Parent=gene50
###
chr1	ENCODE	gene	148083974	148087415	.	-	.	ID=gene51;Name=RP11-126K1.4-010;name2=PIK4CB
chr1	ENCODE	exon	148083974	148084622	.	-	.	Parent=gene51
chr1	ENCODE	exon	148087393	148087415	.	-	.	Parent=gene51
###
chr1	ENCODE	gene	148087797	148112965	.	-	.	ID=gene52;Name=RP11-126K1.4-008;name2=PIK4CB
chr1	ENCODE	exon	148087797	148087847	.	-	.	Parent=gene52
chr1	ENCODE	CDS	148087797	148087847	.	-	1	Parent=gene52
chr1	ENCODE	exon	148089090	148089199	.	-	.	Parent=gene52
chr1	ENCODE	CDS	148089090	148089199	.	-	0	Parent=gene52
chr1	ENCODE	exon	148091685	148091912	.	-	.	Parent=gene52
chr1	ENCODE	CDS	148091685	148091912	.	-	0	Parent=gene52
chr1	ENCODE	exon	148093123	148093350	.	-	.	Parent=gene52
chr1	ENCODE	CDS	148093123	148093350	.	-	0	Parent=gene52
chr1	ENCODE	CDS	148111721	148111753	.	-	0	Parent=gene52
chr1	ENCODE	exon	148111721	148111922	.	-	.	Parent=gene52
chr1	ENCODE	exon	148112820	148112965	.	-	.	Parent=gene52
###
chr1	ENCODE	gene	148088903	148091982	.	-	.	ID=gene53;Name=RP11-126K1.4-007;name2=PIK4CB
chr1	ENCODE	exon	148088903	148089199	.	-	.	Parent=gene53
chr1	ENCODE	exon	148091685	148091982	.	-	.	Parent=gene53
###
chr1	ENCODE	gene	148091840	148112967	.	-	.	ID=gene54;Name=RP11-126K1.4-012;name2=PIK4CB
chr1	ENCODE	exon	148091840	148091912	.	-	.	Parent=gene54
chr1	ENCODE	exon	148093123	148093350	.	-	.	Parent=gene54
chr1	ENCODE	exon	148112820	148112967	.	-	.	Parent=gene54
###
chr1	ENCODE	gene	148101340	148112926	.	-	.	ID=gene55;Name=RP11-126K1.4-009;name2=PIK4CB
chr1	ENCODE	CDS	148101340	148102030	.	-	0	Parent=gene55
chr1	ENCODE	exon	148101340	148102058	.	-	.	Parent=gene55
chr1	ENCODE	exon	148110294	148110466	.	-	.	Parent=gene55
chr1	ENCODE	exon	148112820	148112926	.	-	.	Parent=gene55
###
chr1	ENCODE	gene	148126189	148132800	.	-	.	ID=gene56;Name=RP11-126K1.5-001;name2=RFX5
chr1	ENCODE	exon	148126189	148128727	.	-	.	Parent=gene56
chr1	ENCODE	CDS	148127735	148128727	.	-	0	Parent=gene56
chr1	ENCODE	exon	148128891	148128991	.	-	.	Parent=gene56
chr1	ENCODE	CDS	148128891	148128991	.	-	2	Parent=gene56
chr1	ENCODE	exon	148129230	148129431	.	-	.	Parent=gene56
chr1	ENCODE	CDS	148129230	148129431	.	-	0	Parent=gene56
chr1	ENCODE	exon	148129746	148129827	.	-	.	Parent=gene56
chr1	ENCODE	CDS	148129746	148129827	.	-	1	Parent=gene56
chr1	ENCODE	exon	148129966	148130085	.	-	.	Parent=gene56
chr1	ENCODE	CDS	148129966	148130085	.	-	1	Parent=gene56
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene56
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene56
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene56
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene56
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene56
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene56
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene56
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene56
chr1	ENCODE	exon	148132031	148132155	.	-	.	Parent=gene56
chr1	ENCODE	exon	148132760	148132800	.	-	.	Parent=gene56
###
chr1	ENCODE	gene	148127378	148132875	.	-	.	ID=gene57;name2=RFX5;Name=RP11-126K1.5-020
chr1	ENCODE	exon	148127378	148128727	.	-	.	Parent=gene57
chr1	ENCODE	CDS	148127735	148128727	.	-	0	Parent=gene57
chr1	ENCODE	exon	148128891	148128991	.	-	.	Parent=gene57
chr1	ENCODE	CDS	148128891	148128991	.	-	2	Parent=gene57
chr1	ENCODE	exon	148129230	148129431	.	-	.	Parent=gene57
chr1	ENCODE	CDS	148129230	148129431	.	-	0	Parent=gene57
chr1	ENCODE	exon	148129746	148129827	.	-	.	Parent=gene57
chr1	ENCODE	CDS	148129746	148129827	.	-	1	Parent=gene57
chr1	ENCODE	exon	148129966	148130085	.	-	.	Parent=gene57
chr1	ENCODE	CDS	148129966	148130085	.	-	1	Parent=gene57
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene57
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene57
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene57
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene57
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene57
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene57
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene57
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene57
chr1	ENCODE	exon	148132034	148132155	.	-	.	Parent=gene57
chr1	ENCODE	exon	148132760	148132875	.	-	.	Parent=gene57
###
chr1	ENCODE	gene	148127509	148130305	.	-	.	ID=gene58;Name=RP11-126K1.5-010;name2=RFX5
chr1	ENCODE	exon	148127509	148127634	.	-	.	Parent=gene58
chr1	ENCODE	CDS	148127566	148127634	.	-	0	Parent=gene58
chr1	ENCODE	exon	148128623	148128727	.	-	.	Parent=gene58
chr1	ENCODE	CDS	148128623	148128727	.	-	0	Parent=gene58
chr1	ENCODE	exon	148128891	148128991	.	-	.	Parent=gene58
chr1	ENCODE	CDS	148128891	148128991	.	-	2	Parent=gene58
chr1	ENCODE	exon	148129230	148129431	.	-	.	Parent=gene58
chr1	ENCODE	CDS	148129230	148129431	.	-	0	Parent=gene58
chr1	ENCODE	exon	148129746	148129827	.	-	.	Parent=gene58
chr1	ENCODE	CDS	148129746	148129827	.	-	1	Parent=gene58
chr1	ENCODE	exon	148129966	148130085	.	-	.	Parent=gene58
chr1	ENCODE	CDS	148129966	148130085	.	-	1	Parent=gene58
chr1	ENCODE	exon	148130277	148130305	.	-	.	Parent=gene58
chr1	ENCODE	CDS	148130277	148130305	.	-	0	Parent=gene58
###
chr1	ENCODE	gene	148127509	148132906	.	-	.	ID=gene59;Name=RP11-126K1.5-002;name2=RFX5
chr1	ENCODE	exon	148127509	148128727	.	-	.	Parent=gene59
chr1	ENCODE	CDS	148127735	148128727	.	-	0	Parent=gene59
chr1	ENCODE	exon	148128891	148128991	.	-	.	Parent=gene59
chr1	ENCODE	CDS	148128891	148128991	.	-	2	Parent=gene59
chr1	ENCODE	exon	148129230	148129431	.	-	.	Parent=gene59
chr1	ENCODE	CDS	148129230	148129431	.	-	0	Parent=gene59
chr1	ENCODE	exon	148129746	148129827	.	-	.	Parent=gene59
chr1	ENCODE	CDS	148129746	148129827	.	-	1	Parent=gene59
chr1	ENCODE	exon	148129966	148130085	.	-	.	Parent=gene59
chr1	ENCODE	CDS	148129966	148130085	.	-	1	Parent=gene59
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene59
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene59
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene59
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene59
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene59
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene59
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene59
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene59
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene59
chr1	ENCODE	exon	148132760	148132906	.	-	.	Parent=gene59
###
chr1	ENCODE	gene	148127796	148132371	.	-	.	ID=gene60;Name=RP11-126K1.5-008;name2=RFX5
chr1	ENCODE	exon	148127796	148128727	.	-	.	Parent=gene60
chr1	ENCODE	CDS	148127796	148128727	.	-	0	Parent=gene60
chr1	ENCODE	exon	148128891	148128991	.	-	.	Parent=gene60
chr1	ENCODE	CDS	148128891	148128991	.	-	2	Parent=gene60
chr1	ENCODE	exon	148129230	148129431	.	-	.	Parent=gene60
chr1	ENCODE	CDS	148129230	148129431	.	-	0	Parent=gene60
chr1	ENCODE	exon	148129746	148129827	.	-	.	Parent=gene60
chr1	ENCODE	CDS	148129746	148129827	.	-	1	Parent=gene60
chr1	ENCODE	exon	148129966	148130085	.	-	.	Parent=gene60
chr1	ENCODE	CDS	148129966	148130085	.	-	1	Parent=gene60
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene60
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene60
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene60
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene60
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene60
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene60
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene60
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene60
chr1	ENCODE	exon	148131971	148132155	.	-	.	Parent=gene60
chr1	ENCODE	exon	148132304	148132371	.	-	.	Parent=gene60
###
chr1	ENCODE	gene	148129246	148130216	.	-	.	ID=gene61;Name=RP11-126K1.5-007;name2=RFX5
chr1	ENCODE	exon	148129246	148129431	.	-	.	Parent=gene61
chr1	ENCODE	exon	148129746	148129827	.	-	.	Parent=gene61
chr1	ENCODE	exon	148129966	148130216	.	-	.	Parent=gene61
###
chr1	ENCODE	gene	148129298	148132570	.	-	.	ID=gene62;Name=RP11-126K1.5-004;name2=RFX5
chr1	ENCODE	exon	148129298	148129431	.	-	.	Parent=gene62
chr1	ENCODE	CDS	148129298	148129431	.	-	0	Parent=gene62
chr1	ENCODE	exon	148129746	148129827	.	-	.	Parent=gene62
chr1	ENCODE	CDS	148129746	148129827	.	-	1	Parent=gene62
chr1	ENCODE	exon	148129966	148130085	.	-	.	Parent=gene62
chr1	ENCODE	CDS	148129966	148130085	.	-	1	Parent=gene62
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene62
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene62
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene62
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene62
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene62
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene62
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene62
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene62
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene62
chr1	ENCODE	exon	148132489	148132570	.	-	.	Parent=gene62
###
chr1	ENCODE	gene	148129748	148132522	.	-	.	ID=gene63;Name=RP11-126K1.5-003;name2=RFX5
chr1	ENCODE	exon	148129748	148129827	.	-	.	Parent=gene63
chr1	ENCODE	CDS	148129748	148129827	.	-	1	Parent=gene63
chr1	ENCODE	exon	148129966	148130085	.	-	.	Parent=gene63
chr1	ENCODE	CDS	148129966	148130085	.	-	1	Parent=gene63
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene63
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene63
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene63
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene63
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene63
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene63
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene63
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene63
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene63
chr1	ENCODE	exon	148132304	148132522	.	-	.	Parent=gene63
###
chr1	ENCODE	gene	148129805	148132155	.	-	.	ID=gene64;Name=RP11-126K1.5-009;name2=RFX5
chr1	ENCODE	exon	148129805	148129827	.	-	.	Parent=gene64
chr1	ENCODE	CDS	148129805	148129827	.	-	1	Parent=gene64
chr1	ENCODE	exon	148129966	148130085	.	-	.	Parent=gene64
chr1	ENCODE	CDS	148129966	148130085	.	-	1	Parent=gene64
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene64
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene64
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene64
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene64
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene64
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene64
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene64
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene64
chr1	ENCODE	exon	148132128	148132155	.	-	.	Parent=gene64
###
chr1	ENCODE	gene	148129882	148130726	.	-	.	ID=gene65;Name=RP11-126K1.5-006;name2=RFX5
chr1	ENCODE	exon	148129882	148130085	.	-	.	Parent=gene65
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene65
chr1	ENCODE	exon	148130655	148130726	.	-	.	Parent=gene65
###
chr1	ENCODE	gene	148130064	148132755	.	-	.	ID=gene66;Name=RP11-126K1.5-017;name2=RFX5
chr1	ENCODE	exon	148130064	148130085	.	-	.	Parent=gene66
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene66
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene66
chr1	ENCODE	exon	148131477	148131506	.	-	.	Parent=gene66
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene66
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene66
chr1	ENCODE	exon	148132700	148132755	.	-	.	Parent=gene66
###
chr1	ENCODE	gene	148130070	148132777	.	-	.	ID=gene67;Name=RP11-126K1.5-012;name2=RFX5
chr1	ENCODE	exon	148130070	148130085	.	-	.	Parent=gene67
chr1	ENCODE	CDS	148130070	148130085	.	-	1	Parent=gene67
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene67
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene67
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene67
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene67
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene67
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene67
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene67
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene67
chr1	ENCODE	exon	148132031	148132155	.	-	.	Parent=gene67
chr1	ENCODE	exon	148132700	148132777	.	-	.	Parent=gene67
###
chr1	ENCODE	gene	148130109	148132367	.	-	.	ID=gene68;Name=RP11-126K1.5-018;name2=RFX5
chr1	ENCODE	exon	148130109	148130153	.	-	.	Parent=gene68
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene68
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene68
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene68
chr1	ENCODE	exon	148131764	148131882	.	-	.	Parent=gene68
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene68
chr1	ENCODE	exon	148132304	148132367	.	-	.	Parent=gene68
###
chr1	ENCODE	gene	148130126	148132790	.	-	.	ID=gene69;Name=RP11-126K1.5-019;name2=RFX5
chr1	ENCODE	exon	148130126	148130153	.	-	.	Parent=gene69
chr1	ENCODE	CDS	148130126	148130153	.	-	1	Parent=gene69
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene69
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene69
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene69
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene69
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene69
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene69
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene69
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene69
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene69
chr1	ENCODE	exon	148132304	148132315	.	-	.	Parent=gene69
chr1	ENCODE	exon	148132760	148132790	.	-	.	Parent=gene69
###
chr1	ENCODE	gene	148130277	148132777	.	-	.	ID=gene70;Name=RP11-126K1.5-005;name2=RFX5
chr1	ENCODE	exon	148130277	148130396	.	-	.	Parent=gene70
chr1	ENCODE	CDS	148130277	148130396	.	-	1	Parent=gene70
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene70
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene70
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene70
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene70
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene70
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene70
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene70
chr1	ENCODE	exon	148132700	148132777	.	-	.	Parent=gene70
###
chr1	ENCODE	gene	148130313	148132841	.	-	.	ID=gene71;Name=RP11-126K1.5-011;name2=RFX5
chr1	ENCODE	exon	148130313	148130396	.	-	.	Parent=gene71
chr1	ENCODE	CDS	148130313	148130396	.	-	1	Parent=gene71
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene71
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene71
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene71
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene71
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene71
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene71
chr1	ENCODE	exon	148131971	148132155	.	-	.	Parent=gene71
chr1	ENCODE	exon	148132760	148132841	.	-	.	Parent=gene71
###
chr1	ENCODE	gene	148130341	148132421	.	-	.	ID=gene72;Name=RP11-126K1.5-021;name2=RFX5
chr1	ENCODE	exon	148130341	148130396	.	-	.	Parent=gene72
chr1	ENCODE	CDS	148130341	148130396	.	-	1	Parent=gene72
chr1	ENCODE	exon	148130655	148130737	.	-	.	Parent=gene72
chr1	ENCODE	CDS	148130655	148130737	.	-	0	Parent=gene72
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene72
chr1	ENCODE	CDS	148131477	148131510	.	-	1	Parent=gene72
chr1	ENCODE	CDS	148131754	148131869	.	-	0	Parent=gene72
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene72
chr1	ENCODE	exon	148132031	148132155	.	-	.	Parent=gene72
chr1	ENCODE	exon	148132304	148132421	.	-	.	Parent=gene72
###
chr1	ENCODE	gene	148130511	148132843	.	-	.	ID=gene73;Name=RP11-126K1.5-016;name2=RFX5
chr1	ENCODE	exon	148130511	148130737	.	-	.	Parent=gene73
chr1	ENCODE	exon	148131477	148131506	.	-	.	Parent=gene73
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene73
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene73
chr1	ENCODE	exon	148132760	148132843	.	-	.	Parent=gene73
###
chr1	ENCODE	gene	148130538	148132405	.	-	.	ID=gene74;name2=RFX5;Name=RP11-126K1.5-015
chr1	ENCODE	exon	148130538	148130737	.	-	.	Parent=gene74
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene74
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene74
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene74
chr1	ENCODE	exon	148132304	148132405	.	-	.	Parent=gene74
###
chr1	ENCODE	gene	148130671	148132842	.	-	.	ID=gene75;Name=RP11-126K1.5-014;name2=RFX5
chr1	ENCODE	exon	148130671	148130737	.	-	.	Parent=gene75
chr1	ENCODE	exon	148130835	148130992	.	-	.	Parent=gene75
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene75
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene75
chr1	ENCODE	exon	148132031	148132155	.	-	.	Parent=gene75
chr1	ENCODE	exon	148132760	148132842	.	-	.	Parent=gene75
###
chr1	ENCODE	gene	148130691	148132384	.	-	.	ID=gene76;Name=RP11-126K1.5-013;name2=RFX5
chr1	ENCODE	exon	148130691	148130737	.	-	.	Parent=gene76
chr1	ENCODE	exon	148130835	148130992	.	-	.	Parent=gene76
chr1	ENCODE	exon	148131477	148131510	.	-	.	Parent=gene76
chr1	ENCODE	exon	148131754	148131882	.	-	.	Parent=gene76
chr1	ENCODE	exon	148132038	148132155	.	-	.	Parent=gene76
chr1	ENCODE	exon	148132304	148132384	.	-	.	Parent=gene76
###
chr1	ENCODE	gene	148149851	148158282	.	-	.	ID=gene77;Name=RP11-126K1.7-001;name2=SELENBP1
chr1	ENCODE	exon	148149851	148150254	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148150092	148150254	.	-	1	Parent=gene77
chr1	ENCODE	exon	148150475	148150593	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148150475	148150593	.	-	0	Parent=gene77
chr1	ENCODE	exon	148150738	148150830	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148150738	148150830	.	-	0	Parent=gene77
chr1	ENCODE	exon	148151112	148151233	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148151112	148151233	.	-	2	Parent=gene77
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148151317	148151395	.	-	0	Parent=gene77
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148151824	148152002	.	-	2	Parent=gene77
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148152271	148152453	.	-	2	Parent=gene77
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148153748	148153868	.	-	0	Parent=gene77
chr1	ENCODE	exon	148154553	148154738	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148154553	148154738	.	-	0	Parent=gene77
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148154991	148155103	.	-	2	Parent=gene77
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene77
chr1	ENCODE	CDS	148155262	148155318	.	-	2	Parent=gene77
chr1	ENCODE	CDS	148158187	148158190	.	-	0	Parent=gene77
chr1	ENCODE	exon	148158187	148158282	.	-	.	Parent=gene77
###
chr1	ENCODE	gene	148149853	148158243	.	-	.	ID=gene78;Name=RP11-126K1.7-011;name2=SELENBP1
chr1	ENCODE	exon	148149853	148150254	.	-	.	Parent=gene78
chr1	ENCODE	exon	148150475	148150593	.	-	.	Parent=gene78
chr1	ENCODE	exon	148150738	148150830	.	-	.	Parent=gene78
chr1	ENCODE	exon	148151112	148151233	.	-	.	Parent=gene78
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene78
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene78
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene78
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene78
chr1	ENCODE	exon	148154553	148155103	.	-	.	Parent=gene78
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene78
chr1	ENCODE	exon	148158187	148158243	.	-	.	Parent=gene78
###
chr1	ENCODE	gene	148149854	148158254	.	-	.	ID=gene79;Name=RP11-126K1.7-003;name2=SELENBP1
chr1	ENCODE	exon	148149854	148150254	.	-	.	Parent=gene79
chr1	ENCODE	exon	148150475	148150593	.	-	.	Parent=gene79
chr1	ENCODE	exon	148150738	148151233	.	-	.	Parent=gene79
chr1	ENCODE	exon	148151317	148152002	.	-	.	Parent=gene79
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene79
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene79
chr1	ENCODE	exon	148154553	148155318	.	-	.	Parent=gene79
chr1	ENCODE	exon	148158187	148158254	.	-	.	Parent=gene79
###
chr1	ENCODE	gene	148149857	148158256	.	-	.	ID=gene80;Name=RP11-126K1.7-017;name2=SELENBP1
chr1	ENCODE	exon	148149857	148150254	.	-	.	Parent=gene80
chr1	ENCODE	exon	148150475	148150593	.	-	.	Parent=gene80
chr1	ENCODE	exon	148150738	148150830	.	-	.	Parent=gene80
chr1	ENCODE	exon	148151112	148151233	.	-	.	Parent=gene80
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene80
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene80
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene80
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene80
chr1	ENCODE	exon	148154549	148154738	.	-	.	Parent=gene80
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene80
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene80
chr1	ENCODE	exon	148158187	148158256	.	-	.	Parent=gene80
###
chr1	ENCODE	gene	148149858	148158255	.	-	.	ID=gene81;Name=RP11-126K1.7-002;name2=SELENBP1
chr1	ENCODE	exon	148149858	148150254	.	-	.	Parent=gene81
chr1	ENCODE	exon	148150475	148150593	.	-	.	Parent=gene81
chr1	ENCODE	exon	148150738	148150830	.	-	.	Parent=gene81
chr1	ENCODE	exon	148151112	148151233	.	-	.	Parent=gene81
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene81
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene81
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene81
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene81
chr1	ENCODE	exon	148154553	148155318	.	-	.	Parent=gene81
chr1	ENCODE	exon	148158187	148158255	.	-	.	Parent=gene81
###
chr1	ENCODE	gene	148149861	148158240	.	-	.	ID=gene82;Name=RP11-126K1.7-016;name2=SELENBP1
chr1	ENCODE	exon	148149861	148150254	.	-	.	Parent=gene82
chr1	ENCODE	exon	148150475	148150593	.	-	.	Parent=gene82
chr1	ENCODE	exon	148150738	148150830	.	-	.	Parent=gene82
chr1	ENCODE	exon	148151112	148151233	.	-	.	Parent=gene82
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene82
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene82
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene82
chr1	ENCODE	exon	148154549	148154738	.	-	.	Parent=gene82
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene82
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene82
chr1	ENCODE	exon	148158187	148158240	.	-	.	Parent=gene82
###
chr1	ENCODE	gene	148149870	148158256	.	-	.	ID=gene83;Name=RP11-126K1.7-012;name2=SELENBP1
chr1	ENCODE	exon	148149870	148150254	.	-	.	Parent=gene83
chr1	ENCODE	exon	148150475	148150593	.	-	.	Parent=gene83
chr1	ENCODE	exon	148150738	148150787	.	-	.	Parent=gene83
chr1	ENCODE	exon	148151155	148151233	.	-	.	Parent=gene83
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene83
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene83
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene83
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene83
chr1	ENCODE	exon	148154549	148154738	.	-	.	Parent=gene83
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene83
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene83
chr1	ENCODE	exon	148158187	148158256	.	-	.	Parent=gene83
###
chr1	ENCODE	gene	148149888	148158241	.	-	.	ID=gene84;Name=RP11-126K1.7-015;name2=SELENBP1
chr1	ENCODE	exon	148149888	148150254	.	-	.	Parent=gene84
chr1	ENCODE	exon	148150475	148150593	.	-	.	Parent=gene84
chr1	ENCODE	exon	148150738	148150830	.	-	.	Parent=gene84
chr1	ENCODE	exon	148151112	148151233	.	-	.	Parent=gene84
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene84
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene84
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene84
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene84
chr1	ENCODE	exon	148154549	148154738	.	-	.	Parent=gene84
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene84
chr1	ENCODE	exon	148155262	148155527	.	-	.	Parent=gene84
chr1	ENCODE	exon	148158187	148158241	.	-	.	Parent=gene84
###
chr1	ENCODE	gene	148149894	148158243	.	-	.	ID=gene85;Name=RP11-126K1.7-014;name2=SELENBP1
chr1	ENCODE	exon	148149894	148150254	.	-	.	Parent=gene85
chr1	ENCODE	exon	148150475	148150593	.	-	.	Parent=gene85
chr1	ENCODE	exon	148150738	148150830	.	-	.	Parent=gene85
chr1	ENCODE	exon	148151112	148151233	.	-	.	Parent=gene85
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene85
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene85
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene85
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene85
chr1	ENCODE	exon	148154553	148155103	.	-	.	Parent=gene85
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene85
chr1	ENCODE	exon	148158187	148158243	.	-	.	Parent=gene85
###
chr1	ENCODE	gene	148151122	148155390	.	-	.	ID=gene86;Name=RP11-126K1.7-005;name2=SELENBP1
chr1	ENCODE	exon	148151122	148151233	.	-	.	Parent=gene86
chr1	ENCODE	CDS	148151122	148151233	.	-	0	Parent=gene86
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene86
chr1	ENCODE	CDS	148151317	148151395	.	-	1	Parent=gene86
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene86
chr1	ENCODE	CDS	148151824	148152002	.	-	0	Parent=gene86
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene86
chr1	ENCODE	CDS	148152271	148152453	.	-	0	Parent=gene86
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene86
chr1	ENCODE	CDS	148153748	148153868	.	-	1	Parent=gene86
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene86
chr1	ENCODE	CDS	148154991	148155103	.	-	0	Parent=gene86
chr1	ENCODE	exon	148155262	148155390	.	-	.	Parent=gene86
chr1	ENCODE	CDS	148155262	148155390	.	-	0	Parent=gene86
###
chr1	ENCODE	gene	148151221	148158232	.	-	.	ID=gene87;Name=RP11-126K1.7-019;name2=SELENBP1
chr1	ENCODE	exon	148151221	148151233	.	-	.	Parent=gene87
chr1	ENCODE	CDS	148151221	148151233	.	-	2	Parent=gene87
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene87
chr1	ENCODE	CDS	148151317	148151395	.	-	0	Parent=gene87
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene87
chr1	ENCODE	CDS	148151824	148152002	.	-	2	Parent=gene87
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene87
chr1	ENCODE	CDS	148152271	148152453	.	-	2	Parent=gene87
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene87
chr1	ENCODE	CDS	148153748	148153868	.	-	0	Parent=gene87
chr1	ENCODE	exon	148154553	148154738	.	-	.	Parent=gene87
chr1	ENCODE	CDS	148154553	148154738	.	-	0	Parent=gene87
chr1	ENCODE	exon	148154991	148155055	.	-	.	Parent=gene87
chr1	ENCODE	CDS	148154991	148155055	.	-	2	Parent=gene87
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene87
chr1	ENCODE	CDS	148155262	148155318	.	-	2	Parent=gene87
chr1	ENCODE	CDS	148158187	148158190	.	-	0	Parent=gene87
chr1	ENCODE	exon	148158187	148158232	.	-	.	Parent=gene87
###
chr1	ENCODE	gene	148151317	148158253	.	-	.	ID=gene88;Name=RP11-126K1.7-006;name2=SELENBP1
chr1	ENCODE	exon	148151317	148151395	.	-	.	Parent=gene88
chr1	ENCODE	CDS	148151317	148151395	.	-	0	Parent=gene88
chr1	ENCODE	exon	148151824	148152002	.	-	.	Parent=gene88
chr1	ENCODE	CDS	148151824	148152002	.	-	2	Parent=gene88
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene88
chr1	ENCODE	CDS	148152271	148152453	.	-	2	Parent=gene88
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene88
chr1	ENCODE	CDS	148153748	148153868	.	-	0	Parent=gene88
chr1	ENCODE	exon	148154553	148154738	.	-	.	Parent=gene88
chr1	ENCODE	CDS	148154553	148154738	.	-	0	Parent=gene88
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene88
chr1	ENCODE	CDS	148154991	148155103	.	-	2	Parent=gene88
chr1	ENCODE	CDS	148155262	148155448	.	-	0	Parent=gene88
chr1	ENCODE	exon	148155262	148155527	.	-	.	Parent=gene88
chr1	ENCODE	exon	148158187	148158253	.	-	.	Parent=gene88
###
chr1	ENCODE	gene	148151990	148158254	.	-	.	ID=gene89;name2=SELENBP1;Name=RP11-126K1.7-007
chr1	ENCODE	exon	148151990	148152002	.	-	.	Parent=gene89
chr1	ENCODE	exon	148152271	148152453	.	-	.	Parent=gene89
chr1	ENCODE	exon	148152565	148152724	.	-	.	Parent=gene89
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene89
chr1	ENCODE	exon	148154553	148154738	.	-	.	Parent=gene89
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene89
chr1	ENCODE	exon	148158187	148158254	.	-	.	Parent=gene89
###
chr1	ENCODE	gene	148152230	148153865	.	-	.	ID=gene90;Name=RP11-126K1.7-004;name2=SELENBP1
chr1	ENCODE	exon	148152230	148152453	.	-	.	Parent=gene90
chr1	ENCODE	exon	148153748	148153865	.	-	.	Parent=gene90
###
chr1	ENCODE	gene	148152437	148158254	.	-	.	ID=gene91;Name=RP11-126K1.7-008;name2=SELENBP1
chr1	ENCODE	exon	148152437	148152453	.	-	.	Parent=gene91
chr1	ENCODE	exon	148152565	148152724	.	-	.	Parent=gene91
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene91
chr1	ENCODE	exon	148154553	148154738	.	-	.	Parent=gene91
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene91
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene91
chr1	ENCODE	exon	148158187	148158254	.	-	.	Parent=gene91
###
chr1	ENCODE	gene	148152757	148158256	.	-	.	ID=gene92;Name=RP11-126K1.7-010;name2=SELENBP1
chr1	ENCODE	exon	148152757	148152890	.	-	.	Parent=gene92
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene92
chr1	ENCODE	exon	148154553	148155103	.	-	.	Parent=gene92
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene92
chr1	ENCODE	exon	148158187	148158256	.	-	.	Parent=gene92
###
chr1	ENCODE	gene	148152770	148158240	.	-	.	ID=gene93;Name=RP11-126K1.7-009;name2=SELENBP1
chr1	ENCODE	exon	148152770	148152890	.	-	.	Parent=gene93
chr1	ENCODE	CDS	148152770	148152890	.	-	2	Parent=gene93
chr1	ENCODE	exon	148153748	148153868	.	-	.	Parent=gene93
chr1	ENCODE	CDS	148153748	148153868	.	-	0	Parent=gene93
chr1	ENCODE	exon	148154553	148154738	.	-	.	Parent=gene93
chr1	ENCODE	CDS	148154553	148154738	.	-	0	Parent=gene93
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene93
chr1	ENCODE	CDS	148154991	148155103	.	-	2	Parent=gene93
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene93
chr1	ENCODE	CDS	148155262	148155318	.	-	2	Parent=gene93
chr1	ENCODE	CDS	148158187	148158190	.	-	0	Parent=gene93
chr1	ENCODE	exon	148158187	148158240	.	-	.	Parent=gene93
###
chr1	ENCODE	gene	148154617	148155835	.	-	.	ID=gene94;Name=RP11-126K1.7-018;name2=SELENBP1
chr1	ENCODE	exon	148154617	148154738	.	-	.	Parent=gene94
chr1	ENCODE	CDS	148154617	148154738	.	-	2	Parent=gene94
chr1	ENCODE	exon	148154991	148155103	.	-	.	Parent=gene94
chr1	ENCODE	CDS	148154991	148155103	.	-	1	Parent=gene94
chr1	ENCODE	exon	148155262	148155318	.	-	.	Parent=gene94
chr1	ENCODE	CDS	148155262	148155318	.	-	1	Parent=gene94
chr1	ENCODE	exon	148155750	148155835	.	-	.	Parent=gene94
chr1	ENCODE	CDS	148155750	148155835	.	-	0	Parent=gene94
###
chr1	ENCODE	gene	148185083	148187493	.	+	.	ID=gene95;name2=PSMB4;Name=RP11-806J18.1-001
chr1	ENCODE	exon	148185083	148185276	.	+	.	Parent=gene95
chr1	ENCODE	CDS	148185137	148185276	.	+	0	Parent=gene95
chr1	ENCODE	exon	148185530	148185736	.	+	.	Parent=gene95
chr1	ENCODE	CDS	148185530	148185736	.	+	1	Parent=gene95
chr1	ENCODE	exon	148185991	148186137	.	+	.	Parent=gene95
chr1	ENCODE	CDS	148185991	148186137	.	+	1	Parent=gene95
chr1	ENCODE	exon	148186313	148186394	.	+	.	Parent=gene95
chr1	ENCODE	CDS	148186313	148186394	.	+	1	Parent=gene95
chr1	ENCODE	exon	148186788	148186904	.	+	.	Parent=gene95
chr1	ENCODE	CDS	148186788	148186904	.	+	0	Parent=gene95
chr1	ENCODE	exon	148187091	148187179	.	+	.	Parent=gene95
chr1	ENCODE	CDS	148187091	148187179	.	+	0	Parent=gene95
chr1	ENCODE	CDS	148187366	148187378	.	+	1	Parent=gene95
chr1	ENCODE	exon	148187366	148187493	.	+	.	Parent=gene95
###
chr1	ENCODE	gene	148185109	148186601	.	+	.	ID=gene96;Name=RP11-806J18.1-002;name2=PSMB4
chr1	ENCODE	exon	148185109	148185276	.	+	.	Parent=gene96
chr1	ENCODE	exon	148185530	148185736	.	+	.	Parent=gene96
chr1	ENCODE	exon	148185991	148186601	.	+	.	Parent=gene96
###
chr1	ENCODE	gene	148185128	148186620	.	+	.	ID=gene97;Name=RP11-806J18.1-004;name2=PSMB4
chr1	ENCODE	exon	148185128	148185276	.	+	.	Parent=gene97
chr1	ENCODE	exon	148185530	148185736	.	+	.	Parent=gene97
chr1	ENCODE	exon	148185991	148186137	.	+	.	Parent=gene97
chr1	ENCODE	exon	148186313	148186620	.	+	.	Parent=gene97
###
chr1	ENCODE	gene	148185136	148187455	.	+	.	ID=gene98;Name=RP11-806J18.1-003;name2=PSMB4
chr1	ENCODE	exon	148185136	148185276	.	+	.	Parent=gene98
chr1	ENCODE	exon	148185530	148187455	.	+	.	Parent=gene98
###
chr1	ENCODE	gene	148185139	148187483	.	+	.	ID=gene99;Name=RP11-806J18.1-007;name2=PSMB4
chr1	ENCODE	exon	148185139	148185276	.	+	.	Parent=gene99
chr1	ENCODE	exon	148185530	148185734	.	+	.	Parent=gene99
chr1	ENCODE	exon	148185991	148186904	.	+	.	Parent=gene99
chr1	ENCODE	exon	148187091	148187483	.	+	.	Parent=gene99
###
chr1	ENCODE	gene	148185723	148187485	.	+	.	ID=gene100;Name=RP11-806J18.1-005;name2=PSMB4
chr1	ENCODE	exon	148185723	148185736	.	+	.	Parent=gene100
chr1	ENCODE	exon	148185991	148186137	.	+	.	Parent=gene100
chr1	ENCODE	exon	148186313	148186394	.	+	.	Parent=gene100
chr1	ENCODE	exon	148186788	148187179	.	+	.	Parent=gene100
chr1	ENCODE	exon	148187366	148187485	.	+	.	Parent=gene100
###
chr1	ENCODE	gene	148186450	148187486	.	+	.	ID=gene101;Name=RP11-806J18.1-006;name2=PSMB4
chr1	ENCODE	exon	148186450	148186904	.	+	.	Parent=gene101
chr1	ENCODE	exon	148187091	148187179	.	+	.	Parent=gene101
chr1	ENCODE	exon	148187366	148187486	.	+	.	Parent=gene101
###
chr1	ENCODE	gene	148188273	148227753	.	-	.	ID=gene102;Name=RP11-806J18.2-002;name2=POGZ
chr1	ENCODE	exon	148188273	148192013	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148190351	148192013	.	-	1	Parent=gene102
chr1	ENCODE	exon	148192156	148192180	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148192156	148192180	.	-	2	Parent=gene102
chr1	ENCODE	exon	148192460	148192572	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148192460	148192572	.	-	1	Parent=gene102
chr1	ENCODE	exon	148192784	148192840	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148192784	148192840	.	-	1	Parent=gene102
chr1	ENCODE	exon	148193649	148193789	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148193649	148193789	.	-	1	Parent=gene102
chr1	ENCODE	exon	148193958	148194130	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148193958	148194130	.	-	0	Parent=gene102
chr1	ENCODE	exon	148194243	148194377	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148194243	148194377	.	-	0	Parent=gene102
chr1	ENCODE	exon	148197174	148197320	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148197174	148197320	.	-	0	Parent=gene102
chr1	ENCODE	exon	148197845	148197945	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148197845	148197945	.	-	2	Parent=gene102
chr1	ENCODE	exon	148208946	148209100	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148208946	148209100	.	-	1	Parent=gene102
chr1	ENCODE	exon	148209498	148209835	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148209498	148209835	.	-	0	Parent=gene102
chr1	ENCODE	exon	148210504	148210610	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148210504	148210610	.	-	2	Parent=gene102
chr1	ENCODE	exon	148213372	148213590	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148213372	148213590	.	-	2	Parent=gene102
chr1	ENCODE	exon	148213672	148213962	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148213672	148213962	.	-	2	Parent=gene102
chr1	ENCODE	exon	148215152	148215260	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148215152	148215260	.	-	0	Parent=gene102
chr1	ENCODE	exon	148216215	148216390	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148216215	148216390	.	-	2	Parent=gene102
chr1	ENCODE	exon	148227630	148227753	.	-	.	Parent=gene102
chr1	ENCODE	CDS	148227630	148227753	.	-	0	Parent=gene102
###
chr1	ENCODE	gene	148188273	148244727	.	-	.	ID=gene103;Name=RP11-806J18.2-004;name2=POGZ
chr1	ENCODE	exon	148188273	148192013	.	-	.	Parent=gene103
chr1	ENCODE	exon	148192156	148192572	.	-	.	Parent=gene103
chr1	ENCODE	exon	148192784	148192840	.	-	.	Parent=gene103
chr1	ENCODE	exon	148193649	148193789	.	-	.	Parent=gene103
chr1	ENCODE	exon	148193958	148194130	.	-	.	Parent=gene103
chr1	ENCODE	exon	148194243	148194377	.	-	.	Parent=gene103
chr1	ENCODE	exon	148197174	148197320	.	-	.	Parent=gene103
chr1	ENCODE	exon	148197845	148197945	.	-	.	Parent=gene103
chr1	ENCODE	exon	148208946	148209100	.	-	.	Parent=gene103
chr1	ENCODE	exon	148209498	148209835	.	-	.	Parent=gene103
chr1	ENCODE	exon	148210504	148210610	.	-	.	Parent=gene103
chr1	ENCODE	exon	148213372	148213590	.	-	.	Parent=gene103
chr1	ENCODE	exon	148213672	148213962	.	-	.	Parent=gene103
chr1	ENCODE	exon	148215152	148215260	.	-	.	Parent=gene103
chr1	ENCODE	exon	148216215	148216390	.	-	.	Parent=gene103
chr1	ENCODE	exon	148227630	148227754	.	-	.	Parent=gene103
chr1	ENCODE	exon	148244701	148244727	.	-	.	Parent=gene103
###
chr1	ENCODE	gene	148188273	148245014	.	-	.	ID=gene104;Name=RP11-806J18.2-001;name2=POGZ
chr1	ENCODE	exon	148188273	148192013	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148190351	148192013	.	-	1	Parent=gene104
chr1	ENCODE	exon	148192156	148192180	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148192156	148192180	.	-	2	Parent=gene104
chr1	ENCODE	exon	148192460	148192572	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148192460	148192572	.	-	1	Parent=gene104
chr1	ENCODE	exon	148192784	148192840	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148192784	148192840	.	-	1	Parent=gene104
chr1	ENCODE	exon	148193649	148193789	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148193649	148193789	.	-	1	Parent=gene104
chr1	ENCODE	exon	148193958	148194130	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148193958	148194130	.	-	0	Parent=gene104
chr1	ENCODE	exon	148194243	148194377	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148194243	148194377	.	-	0	Parent=gene104
chr1	ENCODE	exon	148197174	148197320	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148197174	148197320	.	-	0	Parent=gene104
chr1	ENCODE	exon	148197845	148197945	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148197845	148197945	.	-	2	Parent=gene104
chr1	ENCODE	exon	148208946	148209100	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148208946	148209100	.	-	1	Parent=gene104
chr1	ENCODE	exon	148209498	148209835	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148209498	148209835	.	-	0	Parent=gene104
chr1	ENCODE	exon	148210504	148210610	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148210504	148210610	.	-	2	Parent=gene104
chr1	ENCODE	exon	148213372	148213590	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148213372	148213590	.	-	2	Parent=gene104
chr1	ENCODE	exon	148213672	148213962	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148213672	148213962	.	-	2	Parent=gene104
chr1	ENCODE	exon	148215152	148215260	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148215152	148215260	.	-	0	Parent=gene104
chr1	ENCODE	exon	148216215	148216390	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148216215	148216390	.	-	2	Parent=gene104
chr1	ENCODE	exon	148226477	148226635	.	-	.	Parent=gene104
chr1	ENCODE	CDS	148226477	148226635	.	-	2	Parent=gene104
chr1	ENCODE	CDS	148227630	148227753	.	-	0	Parent=gene104
chr1	ENCODE	exon	148227630	148227754	.	-	.	Parent=gene104
chr1	ENCODE	exon	148244701	148245014	.	-	.	Parent=gene104
###
chr1	ENCODE	gene	148188274	148244728	.	-	.	ID=gene105;Name=RP11-806J18.2-003;name2=POGZ
chr1	ENCODE	exon	148188274	148192013	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148190351	148192013	.	-	1	Parent=gene105
chr1	ENCODE	exon	148192156	148192180	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148192156	148192180	.	-	2	Parent=gene105
chr1	ENCODE	exon	148192460	148192572	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148192460	148192572	.	-	1	Parent=gene105
chr1	ENCODE	exon	148192784	148192840	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148192784	148192840	.	-	1	Parent=gene105
chr1	ENCODE	exon	148193649	148193789	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148193649	148193789	.	-	1	Parent=gene105
chr1	ENCODE	exon	148193958	148194130	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148193958	148194130	.	-	0	Parent=gene105
chr1	ENCODE	exon	148194243	148194377	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148194243	148194377	.	-	0	Parent=gene105
chr1	ENCODE	exon	148197174	148197320	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148197174	148197320	.	-	0	Parent=gene105
chr1	ENCODE	exon	148197845	148197945	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148197845	148197945	.	-	2	Parent=gene105
chr1	ENCODE	exon	148208946	148209100	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148208946	148209100	.	-	1	Parent=gene105
chr1	ENCODE	exon	148209498	148209835	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148209498	148209835	.	-	0	Parent=gene105
chr1	ENCODE	exon	148210504	148210610	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148210504	148210610	.	-	2	Parent=gene105
chr1	ENCODE	exon	148213372	148213590	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148213372	148213590	.	-	2	Parent=gene105
chr1	ENCODE	exon	148213672	148213962	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148213672	148213962	.	-	2	Parent=gene105
chr1	ENCODE	exon	148226477	148226635	.	-	.	Parent=gene105
chr1	ENCODE	CDS	148226477	148226635	.	-	2	Parent=gene105
chr1	ENCODE	CDS	148227630	148227753	.	-	0	Parent=gene105
chr1	ENCODE	exon	148227630	148227754	.	-	.	Parent=gene105
chr1	ENCODE	exon	148244701	148244728	.	-	.	Parent=gene105
###
chr1	ENCODE	gene	148190351	148244728	.	-	.	ID=gene106;Name=RP11-806J18.2-011;name2=POGZ
chr1	ENCODE	exon	148190351	148192013	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148190351	148192013	.	-	1	Parent=gene106
chr1	ENCODE	exon	148192156	148192180	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148192156	148192180	.	-	2	Parent=gene106
chr1	ENCODE	exon	148192460	148192572	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148192460	148192572	.	-	1	Parent=gene106
chr1	ENCODE	exon	148192784	148192840	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148192784	148192840	.	-	1	Parent=gene106
chr1	ENCODE	exon	148193649	148193789	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148193649	148193789	.	-	1	Parent=gene106
chr1	ENCODE	exon	148193958	148194130	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148193958	148194130	.	-	0	Parent=gene106
chr1	ENCODE	exon	148194243	148194377	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148194243	148194377	.	-	0	Parent=gene106
chr1	ENCODE	exon	148197174	148197347	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148197174	148197347	.	-	0	Parent=gene106
chr1	ENCODE	exon	148197845	148197945	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148197845	148197945	.	-	2	Parent=gene106
chr1	ENCODE	exon	148208946	148209100	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148208946	148209100	.	-	1	Parent=gene106
chr1	ENCODE	exon	148209498	148209835	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148209498	148209835	.	-	0	Parent=gene106
chr1	ENCODE	exon	148210504	148210610	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148210504	148210610	.	-	2	Parent=gene106
chr1	ENCODE	exon	148213372	148213590	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148213372	148213590	.	-	2	Parent=gene106
chr1	ENCODE	exon	148213672	148213962	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148213672	148213962	.	-	2	Parent=gene106
chr1	ENCODE	exon	148215152	148215260	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148215152	148215260	.	-	0	Parent=gene106
chr1	ENCODE	exon	148216215	148216390	.	-	.	Parent=gene106
chr1	ENCODE	CDS	148216215	148216390	.	-	2	Parent=gene106
chr1	ENCODE	CDS	148227630	148227753	.	-	0	Parent=gene106
chr1	ENCODE	exon	148227630	148227754	.	-	.	Parent=gene106
chr1	ENCODE	exon	148244701	148244728	.	-	.	Parent=gene106
###
chr1	ENCODE	gene	148192448	148193745	.	-	.	ID=gene107;Name=RP11-806J18.2-006;name2=POGZ
chr1	ENCODE	exon	148192448	148192840	.	-	.	Parent=gene107
chr1	ENCODE	exon	148193649	148193745	.	-	.	Parent=gene107
###
chr1	ENCODE	gene	148192787	148194102	.	-	.	ID=gene108;Name=RP11-806J18.2-015;name2=POGZ
chr1	ENCODE	exon	148192787	148192840	.	-	.	Parent=gene108
chr1	ENCODE	exon	148193649	148194102	.	-	.	Parent=gene108
###
chr1	ENCODE	gene	148209048	148210012	.	-	.	ID=gene109;Name=RP11-806J18.2-014;name2=POGZ
chr1	ENCODE	exon	148209048	148209100	.	-	.	Parent=gene109
chr1	ENCODE	exon	148209498	148210012	.	-	.	Parent=gene109
###
chr1	ENCODE	gene	148209071	148213529	.	-	.	ID=gene110;Name=RP11-806J18.2-007;name2=POGZ
chr1	ENCODE	exon	148209071	148209100	.	-	.	Parent=gene110
chr1	ENCODE	exon	148209498	148209835	.	-	.	Parent=gene110
chr1	ENCODE	exon	148213372	148213529	.	-	.	Parent=gene110
###
chr1	ENCODE	gene	148209559	148210843	.	-	.	ID=gene111;Name=RP11-806J18.2-008;name2=POGZ
chr1	ENCODE	exon	148209559	148209835	.	-	.	Parent=gene111
chr1	ENCODE	exon	148210504	148210843	.	-	.	Parent=gene111
###
chr1	ENCODE	gene	148211738	148244728	.	-	.	ID=gene112;Name=RP11-806J18.2-005;name2=POGZ
chr1	ENCODE	exon	148211738	148213590	.	-	.	Parent=gene112
chr1	ENCODE	exon	148213672	148213962	.	-	.	Parent=gene112
chr1	ENCODE	exon	148215152	148215260	.	-	.	Parent=gene112
chr1	ENCODE	exon	148216215	148216390	.	-	.	Parent=gene112
chr1	ENCODE	exon	148226477	148226635	.	-	.	Parent=gene112
chr1	ENCODE	exon	148227630	148227754	.	-	.	Parent=gene112
chr1	ENCODE	exon	148244701	148244728	.	-	.	Parent=gene112
###
chr1	ENCODE	gene	148214949	148244736	.	-	.	ID=gene113;Name=RP11-806J18.2-012;name2=POGZ
chr1	ENCODE	exon	148214949	148215260	.	-	.	Parent=gene113
chr1	ENCODE	exon	148216215	148216390	.	-	.	Parent=gene113
chr1	ENCODE	exon	148226477	148226635	.	-	.	Parent=gene113
chr1	ENCODE	exon	148227630	148227754	.	-	.	Parent=gene113
chr1	ENCODE	exon	148244701	148244736	.	-	.	Parent=gene113
###
chr1	ENCODE	gene	148216263	148240746	.	-	.	ID=gene114;Name=RP11-806J18.2-010;name2=POGZ
chr1	ENCODE	exon	148216263	148216390	.	-	.	Parent=gene114
chr1	ENCODE	CDS	148216263	148216390	.	-	2	Parent=gene114
chr1	ENCODE	CDS	148227630	148227753	.	-	0	Parent=gene114
chr1	ENCODE	exon	148227630	148227754	.	-	.	Parent=gene114
chr1	ENCODE	exon	148240511	148240746	.	-	.	Parent=gene114
###
chr1	ENCODE	gene	148226392	148244728	.	-	.	ID=gene115;Name=RP11-806J18.2-013;name2=POGZ
chr1	ENCODE	exon	148226392	148226635	.	-	.	Parent=gene115
chr1	ENCODE	exon	148227630	148227754	.	-	.	Parent=gene115
chr1	ENCODE	exon	148244701	148244728	.	-	.	Parent=gene115
###
chr1	ENCODE	gene	148227730	148228027	.	-	.	ID=gene116;Name=RP11-806J18.2-009;name2=POGZ
chr1	ENCODE	CDS	148227730	148227753	.	-	0	Parent=gene116
chr1	ENCODE	exon	148227730	148227754	.	-	.	Parent=gene116
chr1	ENCODE	exon	148227854	148228027	.	-	.	Parent=gene116
###
chr1	ENCODE	gene	148296059	148304578	.	+	.	ID=gene117;name2=CGN;Name=RP11-74C1.3-005
chr1	ENCODE	exon	148296059	148296098	.	+	.	Parent=gene117
chr1	ENCODE	exon	148304055	148304578	.	+	.	Parent=gene117
chr1	ENCODE	CDS	148304069	148304578	.	+	0	Parent=gene117
###
chr1	ENCODE	gene	148296485	148304578	.	+	.	ID=gene118;Name=RP11-74C1.3-006;name2=CGN
chr1	ENCODE	exon	148296485	148296549	.	+	.	Parent=gene118
chr1	ENCODE	exon	148304055	148304578	.	+	.	Parent=gene118
chr1	ENCODE	CDS	148304069	148304578	.	+	0	Parent=gene118
###
chr1	ENCODE	gene	148296936	148304941	.	+	.	ID=gene119;Name=RP11-74C1.3-007;name2=CGN
chr1	ENCODE	exon	148296936	148297068	.	+	.	Parent=gene119
chr1	ENCODE	exon	148303084	148303202	.	+	.	Parent=gene119
chr1	ENCODE	exon	148304055	148304941	.	+	.	Parent=gene119
chr1	ENCODE	CDS	148304069	148304941	.	+	0	Parent=gene119
###
chr1	ENCODE	gene	148296946	148324241	.	+	.	ID=gene120;Name=RP11-74C1.3-001;name2=CGN
chr1	ENCODE	exon	148296946	148297064	.	+	.	Parent=gene120
chr1	ENCODE	exon	148304055	148304941	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148304069	148304941	.	+	0	Parent=gene120
chr1	ENCODE	exon	148305715	148305815	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148305715	148305815	.	+	0	Parent=gene120
chr1	ENCODE	exon	148305963	148306032	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148305963	148306032	.	+	1	Parent=gene120
chr1	ENCODE	exon	148306145	148306240	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148306145	148306240	.	+	0	Parent=gene120
chr1	ENCODE	exon	148308983	148309110	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148308983	148309110	.	+	0	Parent=gene120
chr1	ENCODE	exon	148309775	148309907	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148309775	148309907	.	+	1	Parent=gene120
chr1	ENCODE	exon	148310223	148310435	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148310223	148310435	.	+	0	Parent=gene120
chr1	ENCODE	exon	148311191	148311339	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148311191	148311339	.	+	0	Parent=gene120
chr1	ENCODE	exon	148312524	148312656	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148312524	148312656	.	+	1	Parent=gene120
chr1	ENCODE	exon	148314899	148315108	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148314899	148315108	.	+	0	Parent=gene120
chr1	ENCODE	exon	148315458	148315664	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148315458	148315664	.	+	0	Parent=gene120
chr1	ENCODE	exon	148316038	148316295	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148316038	148316295	.	+	0	Parent=gene120
chr1	ENCODE	exon	148317951	148318121	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148317951	148318121	.	+	0	Parent=gene120
chr1	ENCODE	exon	148319524	148319685	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148319524	148319685	.	+	0	Parent=gene120
chr1	ENCODE	exon	148320591	148320680	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148320591	148320680	.	+	0	Parent=gene120
chr1	ENCODE	exon	148321149	148321232	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148321149	148321232	.	+	0	Parent=gene120
chr1	ENCODE	exon	148321329	148321447	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148321329	148321447	.	+	0	Parent=gene120
chr1	ENCODE	exon	148321786	148321894	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148321786	148321894	.	+	1	Parent=gene120
chr1	ENCODE	exon	148322279	148322442	.	+	.	Parent=gene120
chr1	ENCODE	CDS	148322279	148322442	.	+	0	Parent=gene120
chr1	ENCODE	CDS	148322754	148322895	.	+	1	Parent=gene120
chr1	ENCODE	exon	148322754	148324241	.	+	.	Parent=gene120
###
chr1	ENCODE	gene	148311143	148314941	.	+	.	ID=gene121;Name=RP11-74C1.3-003;name2=CGN
chr1	ENCODE	exon	148311143	148311339	.	+	.	Parent=gene121
chr1	ENCODE	exon	148312524	148312656	.	+	.	Parent=gene121
chr1	ENCODE	exon	148314899	148314941	.	+	.	Parent=gene121
###
chr1	ENCODE	gene	148319689	148324241	.	+	.	ID=gene122;name2=CGN;Name=RP11-74C1.3-002
chr1	ENCODE	exon	148319689	148320680	.	+	.	Parent=gene122
chr1	ENCODE	exon	148321149	148321232	.	+	.	Parent=gene122
chr1	ENCODE	exon	148321329	148321447	.	+	.	Parent=gene122
chr1	ENCODE	exon	148321786	148321894	.	+	.	Parent=gene122
chr1	ENCODE	exon	148322279	148322442	.	+	.	Parent=gene122
chr1	ENCODE	exon	148322754	148324241	.	+	.	Parent=gene122
###
chr1	ENCODE	gene	148321427	148323051	.	+	.	ID=gene123;Name=RP11-74C1.3-004;name2=CGN
chr1	ENCODE	exon	148321427	148321894	.	+	.	Parent=gene123
chr1	ENCODE	exon	148322279	148322442	.	+	.	Parent=gene123
chr1	ENCODE	exon	148322754	148323051	.	+	.	Parent=gene123
###
chr1	ENCODE	gene	148325854	148369132	.	+	.	ID=gene124;Name=RP11-74C1.1-010;name2=TUFT1
chr1	ENCODE	exon	148325854	148325975	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148325916	148325975	.	+	0	Parent=gene124
chr1	ENCODE	exon	148348134	148348235	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148348134	148348235	.	+	0	Parent=gene124
chr1	ENCODE	exon	148349453	148349539	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148349453	148349539	.	+	0	Parent=gene124
chr1	ENCODE	exon	148351712	148351777	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148351712	148351777	.	+	0	Parent=gene124
chr1	ENCODE	exon	148355206	148355319	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148355206	148355319	.	+	0	Parent=gene124
chr1	ENCODE	exon	148359819	148359947	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148359819	148359947	.	+	0	Parent=gene124
chr1	ENCODE	exon	148360460	148360554	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148360460	148360554	.	+	0	Parent=gene124
chr1	ENCODE	exon	148364270	148364375	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148364270	148364375	.	+	1	Parent=gene124
chr1	ENCODE	exon	148365198	148365281	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148365198	148365281	.	+	0	Parent=gene124
chr1	ENCODE	exon	148366491	148366591	.	+	.	Parent=gene124
chr1	ENCODE	CDS	148366491	148366591	.	+	0	Parent=gene124
chr1	ENCODE	CDS	148367193	148367256	.	+	1	Parent=gene124
chr1	ENCODE	exon	148367193	148369132	.	+	.	Parent=gene124
###
chr1	ENCODE	gene	148325854	148369132	.	+	.	ID=gene125;name2=TUFT1;Name=RP11-74C1.1-006
chr1	ENCODE	exon	148325854	148325975	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148325916	148325975	.	+	0	Parent=gene125
chr1	ENCODE	exon	148347640	148347714	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148347640	148347714	.	+	0	Parent=gene125
chr1	ENCODE	exon	148348134	148348235	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148348134	148348235	.	+	0	Parent=gene125
chr1	ENCODE	exon	148349453	148349539	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148349453	148349539	.	+	0	Parent=gene125
chr1	ENCODE	exon	148350074	148350163	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148350074	148350163	.	+	0	Parent=gene125
chr1	ENCODE	exon	148351712	148351777	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148351712	148351777	.	+	0	Parent=gene125
chr1	ENCODE	exon	148355206	148355319	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148355206	148355319	.	+	0	Parent=gene125
chr1	ENCODE	exon	148359819	148359947	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148359819	148359947	.	+	0	Parent=gene125
chr1	ENCODE	exon	148360460	148360554	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148360460	148360554	.	+	0	Parent=gene125
chr1	ENCODE	exon	148364270	148364375	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148364270	148364375	.	+	1	Parent=gene125
chr1	ENCODE	exon	148365198	148365281	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148365198	148365281	.	+	0	Parent=gene125
chr1	ENCODE	exon	148366491	148366591	.	+	.	Parent=gene125
chr1	ENCODE	CDS	148366491	148366591	.	+	0	Parent=gene125
chr1	ENCODE	CDS	148367193	148367256	.	+	1	Parent=gene125
chr1	ENCODE	exon	148367193	148369132	.	+	.	Parent=gene125
###
chr1	ENCODE	gene	148325857	148369132	.	+	.	ID=gene126;name2=TUFT1;Name=RP11-74C1.1-008
chr1	ENCODE	exon	148325857	148325975	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148325916	148325975	.	+	0	Parent=gene126
chr1	ENCODE	exon	148348134	148348235	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148348134	148348235	.	+	0	Parent=gene126
chr1	ENCODE	exon	148349453	148349539	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148349453	148349539	.	+	0	Parent=gene126
chr1	ENCODE	exon	148350074	148350163	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148350074	148350163	.	+	0	Parent=gene126
chr1	ENCODE	exon	148351712	148351777	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148351712	148351777	.	+	0	Parent=gene126
chr1	ENCODE	exon	148355206	148355319	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148355206	148355319	.	+	0	Parent=gene126
chr1	ENCODE	exon	148359819	148359947	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148359819	148359947	.	+	0	Parent=gene126
chr1	ENCODE	exon	148360460	148360554	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148360460	148360554	.	+	0	Parent=gene126
chr1	ENCODE	exon	148364270	148364375	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148364270	148364375	.	+	1	Parent=gene126
chr1	ENCODE	exon	148365198	148365281	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148365198	148365281	.	+	0	Parent=gene126
chr1	ENCODE	exon	148366491	148366591	.	+	.	Parent=gene126
chr1	ENCODE	CDS	148366491	148366591	.	+	0	Parent=gene126
chr1	ENCODE	CDS	148367193	148367256	.	+	1	Parent=gene126
chr1	ENCODE	exon	148367193	148369132	.	+	.	Parent=gene126
###
chr1	ENCODE	gene	148325872	148369125	.	+	.	ID=gene127;Name=RP11-74C1.1-007;name2=TUFT1
chr1	ENCODE	exon	148325872	148325975	.	+	.	Parent=gene127
chr1	ENCODE	exon	148348134	148348235	.	+	.	Parent=gene127
chr1	ENCODE	exon	148349453	148349539	.	+	.	Parent=gene127
chr1	ENCODE	exon	148350074	148350163	.	+	.	Parent=gene127
chr1	ENCODE	exon	148351712	148351777	.	+	.	Parent=gene127
chr1	ENCODE	exon	148355206	148355319	.	+	.	Parent=gene127
chr1	ENCODE	exon	148359819	148359887	.	+	.	Parent=gene127
chr1	ENCODE	exon	148367651	148369125	.	+	.	Parent=gene127
###
chr1	ENCODE	gene	148325883	148355375	.	+	.	ID=gene128;Name=RP11-74C1.1-012;name2=TUFT1
chr1	ENCODE	exon	148325883	148325975	.	+	.	Parent=gene128
chr1	ENCODE	exon	148347640	148347714	.	+	.	Parent=gene128
chr1	ENCODE	exon	148348134	148348235	.	+	.	Parent=gene128
chr1	ENCODE	exon	148349453	148349539	.	+	.	Parent=gene128
chr1	ENCODE	exon	148350074	148350163	.	+	.	Parent=gene128
chr1	ENCODE	exon	148351712	148351777	.	+	.	Parent=gene128
chr1	ENCODE	exon	148355206	148355375	.	+	.	Parent=gene128
###
chr1	ENCODE	gene	148348071	148350570	.	+	.	ID=gene129;Name=RP11-74C1.1-009;name2=TUFT1
chr1	ENCODE	exon	148348071	148348235	.	+	.	Parent=gene129
chr1	ENCODE	exon	148349453	148349539	.	+	.	Parent=gene129
chr1	ENCODE	exon	148350074	148350570	.	+	.	Parent=gene129
###
chr1	ENCODE	gene	148351471	148360476	.	+	.	ID=gene130;Name=RP11-74C1.1-011;name2=TUFT1
chr1	ENCODE	exon	148351471	148351777	.	+	.	Parent=gene130
chr1	ENCODE	exon	148355206	148355319	.	+	.	Parent=gene130
chr1	ENCODE	exon	148359819	148359947	.	+	.	Parent=gene130
chr1	ENCODE	exon	148360460	148360476	.	+	.	Parent=gene130
###
chr1	ENCODE	gene	148397614	148468994	.	+	.	ID=gene131;Name=RP11-98D18.12-002;name2=SNX27
chr1	ENCODE	exon	148397614	148397930	.	+	.	Parent=gene131
chr1	ENCODE	exon	148424437	148424668	.	+	.	Parent=gene131
chr1	ENCODE	exon	148443784	148443976	.	+	.	Parent=gene131
chr1	ENCODE	exon	148446347	148446411	.	+	.	Parent=gene131
chr1	ENCODE	exon	148447715	148447819	.	+	.	Parent=gene131
chr1	ENCODE	exon	148451482	148451560	.	+	.	Parent=gene131
chr1	ENCODE	exon	148454021	148454184	.	+	.	Parent=gene131
chr1	ENCODE	exon	148468905	148468994	.	+	.	Parent=gene131
###
chr1	ENCODE	gene	148397631	148468994	.	+	.	ID=gene132;Name=RP11-98D18.12-001;name2=SNX27
chr1	ENCODE	exon	148397631	148398061	.	+	.	Parent=gene132
chr1	ENCODE	exon	148424437	148424668	.	+	.	Parent=gene132
chr1	ENCODE	exon	148443784	148443976	.	+	.	Parent=gene132
chr1	ENCODE	exon	148446347	148446411	.	+	.	Parent=gene132
chr1	ENCODE	exon	148447715	148447819	.	+	.	Parent=gene132
chr1	ENCODE	exon	148451482	148451560	.	+	.	Parent=gene132
chr1	ENCODE	exon	148454021	148454184	.	+	.	Parent=gene132
chr1	ENCODE	exon	148468905	148468994	.	+	.	Parent=gene132
###
chr1	ENCODE	gene	148397631	148468994	.	+	.	ID=gene133;Name=RP11-98D18.12-003;name2=SNX27
chr1	ENCODE	exon	148397631	148398061	.	+	.	Parent=gene133
chr1	ENCODE	exon	148424437	148424668	.	+	.	Parent=gene133
chr1	ENCODE	exon	148443784	148443976	.	+	.	Parent=gene133
chr1	ENCODE	exon	148446347	148446411	.	+	.	Parent=gene133
chr1	ENCODE	exon	148447715	148447819	.	+	.	Parent=gene133
chr1	ENCODE	exon	148451482	148451560	.	+	.	Parent=gene133
chr1	ENCODE	exon	148454021	148454184	.	+	.	Parent=gene133
chr1	ENCODE	exon	148468905	148468994	.	+	.	Parent=gene133
###
chr1	ENCODE	gene	148424405	148468994	.	+	.	ID=gene134;Name=RP11-98D18.12-004;name2=SNX27
chr1	ENCODE	exon	148424405	148424668	.	+	.	Parent=gene134
chr1	ENCODE	exon	148443784	148443976	.	+	.	Parent=gene134
chr1	ENCODE	exon	148446347	148446411	.	+	.	Parent=gene134
chr1	ENCODE	exon	148447715	148447819	.	+	.	Parent=gene134
chr1	ENCODE	exon	148451482	148451560	.	+	.	Parent=gene134
chr1	ENCODE	exon	148454021	148454184	.	+	.	Parent=gene134
chr1	ENCODE	exon	148468905	148468994	.	+	.	Parent=gene134
###
chr1	ENCODE	gene	148447793	148454910	.	+	.	ID=gene135;Name=RP11-98D18.12-005;name2=SNX27
chr1	ENCODE	exon	148447793	148447819	.	+	.	Parent=gene135
chr1	ENCODE	CDS	148447793	148447819	.	+	0	Parent=gene135
chr1	ENCODE	exon	148451482	148451560	.	+	.	Parent=gene135
chr1	ENCODE	CDS	148451482	148451560	.	+	0	Parent=gene135
chr1	ENCODE	exon	148454021	148454184	.	+	.	Parent=gene135
chr1	ENCODE	CDS	148454021	148454184	.	+	2	Parent=gene135
chr1	ENCODE	CDS	148454690	148454800	.	+	0	Parent=gene135
chr1	ENCODE	exon	148454690	148454910	.	+	.	Parent=gene135
###
chr10	ENCODE	gene	55232537	55643814	.	-	.	ID=gene136;Name=RP11-449J3.2-008;name2=PCDH15
chr10	ENCODE	exon	55232537	55236896	.	-	.	Parent=gene136
chr10	ENCODE	exon	55240322	55240430	.	-	.	Parent=gene136
chr10	ENCODE	exon	55254902	55254907	.	-	.	Parent=gene136
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene136
chr10	ENCODE	exon	55258331	55258339	.	-	.	Parent=gene136
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene136
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene136
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene136
chr10	ENCODE	exon	55296408	55296623	.	-	.	Parent=gene136
chr10	ENCODE	exon	55333009	55333136	.	-	.	Parent=gene136
chr10	ENCODE	exon	55368581	55368721	.	-	.	Parent=gene136
chr10	ENCODE	exon	55370632	55370741	.	-	.	Parent=gene136
chr10	ENCODE	exon	55389498	55389610	.	-	.	Parent=gene136
chr10	ENCODE	exon	55391518	55391658	.	-	.	Parent=gene136
chr10	ENCODE	exon	55425415	55425531	.	-	.	Parent=gene136
chr10	ENCODE	exon	55449958	55450182	.	-	.	Parent=gene136
chr10	ENCODE	exon	55452658	55452963	.	-	.	Parent=gene136
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene136
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene136
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene136
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene136
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene136
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene136
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene136
chr10	ENCODE	exon	55619130	55619150	.	-	.	Parent=gene136
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene136
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene136
###
chr10	ENCODE	gene	55236091	55287029	.	-	.	ID=gene137;Name=RP11-449J3.2-009;name2=PCDH15
chr10	ENCODE	exon	55236091	55236896	.	-	.	Parent=gene137
chr10	ENCODE	exon	55240322	55240430	.	-	.	Parent=gene137
chr10	ENCODE	exon	55241315	55241385	.	-	.	Parent=gene137
chr10	ENCODE	exon	55246005	55246043	.	-	.	Parent=gene137
chr10	ENCODE	exon	55247761	55247779	.	-	.	Parent=gene137
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene137
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene137
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene137
###
chr10	ENCODE	gene	55236752	55248150	.	-	.	ID=gene138;Name=RP11-449J3.2-010;name2=PCDH15
chr10	ENCODE	exon	55236752	55236896	.	-	.	Parent=gene138
chr10	ENCODE	exon	55240322	55240430	.	-	.	Parent=gene138
chr10	ENCODE	exon	55241315	55241385	.	-	.	Parent=gene138
chr10	ENCODE	exon	55246005	55246043	.	-	.	Parent=gene138
chr10	ENCODE	exon	55247761	55248150	.	-	.	Parent=gene138
###
chr10	ENCODE	gene	55238217	55625655	.	-	.	ID=gene139;Name=RP11-449J3.2-018;name2=PCDH15
chr10	ENCODE	exon	55238217	55239312	.	-	.	Parent=gene139
chr10	ENCODE	exon	55240322	55240430	.	-	.	Parent=gene139
chr10	ENCODE	exon	55241315	55241385	.	-	.	Parent=gene139
chr10	ENCODE	exon	55254902	55254907	.	-	.	Parent=gene139
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene139
chr10	ENCODE	exon	55258331	55258339	.	-	.	Parent=gene139
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene139
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene139
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene139
chr10	ENCODE	exon	55296408	55296623	.	-	.	Parent=gene139
chr10	ENCODE	exon	55333009	55333136	.	-	.	Parent=gene139
chr10	ENCODE	exon	55368581	55368721	.	-	.	Parent=gene139
chr10	ENCODE	exon	55370632	55370741	.	-	.	Parent=gene139
chr10	ENCODE	exon	55389498	55389610	.	-	.	Parent=gene139
chr10	ENCODE	exon	55391518	55391658	.	-	.	Parent=gene139
chr10	ENCODE	exon	55425415	55425531	.	-	.	Parent=gene139
chr10	ENCODE	exon	55449958	55450182	.	-	.	Parent=gene139
chr10	ENCODE	exon	55452658	55452963	.	-	.	Parent=gene139
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene139
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene139
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene139
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene139
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene139
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene139
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene139
chr10	ENCODE	exon	55619130	55619150	.	-	.	Parent=gene139
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene139
###
chr10	ENCODE	gene	55238217	55643814	.	-	.	ID=gene140;Name=RP11-449J3.2-017;name2=PCDH15
chr10	ENCODE	exon	55238217	55239312	.	-	.	Parent=gene140
chr10	ENCODE	exon	55240322	55240430	.	-	.	Parent=gene140
chr10	ENCODE	exon	55241315	55241385	.	-	.	Parent=gene140
chr10	ENCODE	exon	55254902	55254907	.	-	.	Parent=gene140
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene140
chr10	ENCODE	exon	55258331	55258339	.	-	.	Parent=gene140
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene140
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene140
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene140
chr10	ENCODE	exon	55296408	55296623	.	-	.	Parent=gene140
chr10	ENCODE	exon	55333009	55333136	.	-	.	Parent=gene140
chr10	ENCODE	exon	55368581	55368721	.	-	.	Parent=gene140
chr10	ENCODE	exon	55370632	55370741	.	-	.	Parent=gene140
chr10	ENCODE	exon	55389498	55389610	.	-	.	Parent=gene140
chr10	ENCODE	exon	55391518	55391658	.	-	.	Parent=gene140
chr10	ENCODE	exon	55425415	55425531	.	-	.	Parent=gene140
chr10	ENCODE	exon	55449958	55450182	.	-	.	Parent=gene140
chr10	ENCODE	exon	55452658	55452963	.	-	.	Parent=gene140
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene140
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene140
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene140
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene140
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene140
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene140
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene140
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene140
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene140
###
chr10	ENCODE	gene	55238349	55270262	.	-	.	ID=gene141;Name=RP11-449J3.2-006;name2=PCDH15
chr10	ENCODE	exon	55238349	55239312	.	-	.	Parent=gene141
chr10	ENCODE	exon	55240322	55240430	.	-	.	Parent=gene141
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene141
chr10	ENCODE	exon	55258331	55258339	.	-	.	Parent=gene141
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene141
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene141
###
chr10	ENCODE	gene	55238349	55643814	.	-	.	ID=gene142;Name=RP11-449J3.2-015;name2=PCDH15
chr10	ENCODE	exon	55238349	55239312	.	-	.	Parent=gene142
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene142
###
chr10	ENCODE	gene	55238349	55643814	.	-	.	ID=gene143;Name=RP11-449J3.2-016;name2=PCDH15
chr10	ENCODE	exon	55238349	55239312	.	-	.	Parent=gene143
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene143
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene143
###
chr10	ENCODE	gene	55238349	55643814	.	-	.	ID=gene144;Name=RP11-449J3.2-007;name2=PCDH15
chr10	ENCODE	exon	55238349	55239312	.	-	.	Parent=gene144
chr10	ENCODE	exon	55240322	55240430	.	-	.	Parent=gene144
chr10	ENCODE	exon	55254902	55254907	.	-	.	Parent=gene144
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene144
chr10	ENCODE	exon	55258331	55258339	.	-	.	Parent=gene144
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene144
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene144
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene144
chr10	ENCODE	exon	55296408	55296623	.	-	.	Parent=gene144
chr10	ENCODE	exon	55333009	55333136	.	-	.	Parent=gene144
chr10	ENCODE	exon	55368581	55368721	.	-	.	Parent=gene144
chr10	ENCODE	exon	55370632	55370741	.	-	.	Parent=gene144
chr10	ENCODE	exon	55389498	55389610	.	-	.	Parent=gene144
chr10	ENCODE	exon	55391518	55391658	.	-	.	Parent=gene144
chr10	ENCODE	exon	55425415	55425531	.	-	.	Parent=gene144
chr10	ENCODE	exon	55449958	55450182	.	-	.	Parent=gene144
chr10	ENCODE	exon	55452658	55452963	.	-	.	Parent=gene144
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene144
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene144
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene144
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene144
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene144
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene144
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene144
chr10	ENCODE	exon	55619130	55619150	.	-	.	Parent=gene144
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene144
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene144
###
chr10	ENCODE	gene	55238349	55643814	.	-	.	ID=gene145;Name=RP11-449J3.2-014;name2=PCDH15
chr10	ENCODE	exon	55238349	55239312	.	-	.	Parent=gene145
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene145
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene145
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene145
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene145
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene145
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene145
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene145
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene145
###
chr10	ENCODE	gene	55250936	55643814	.	-	.	ID=gene146;Name=RP11-449J3.2-011;name2=PCDH15
chr10	ENCODE	exon	55250936	55253124	.	-	.	Parent=gene146
chr10	ENCODE	exon	55254902	55254907	.	-	.	Parent=gene146
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene146
chr10	ENCODE	exon	55258331	55258339	.	-	.	Parent=gene146
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene146
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene146
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene146
chr10	ENCODE	exon	55296408	55296623	.	-	.	Parent=gene146
chr10	ENCODE	exon	55333009	55333136	.	-	.	Parent=gene146
chr10	ENCODE	exon	55368581	55368721	.	-	.	Parent=gene146
chr10	ENCODE	exon	55370632	55370741	.	-	.	Parent=gene146
chr10	ENCODE	exon	55389498	55389610	.	-	.	Parent=gene146
chr10	ENCODE	exon	55391518	55391658	.	-	.	Parent=gene146
chr10	ENCODE	exon	55425415	55425531	.	-	.	Parent=gene146
chr10	ENCODE	exon	55449958	55450182	.	-	.	Parent=gene146
chr10	ENCODE	exon	55452658	55452963	.	-	.	Parent=gene146
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene146
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene146
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene146
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene146
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene146
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene146
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene146
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene146
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene146
###
chr10	ENCODE	gene	55250936	55643814	.	-	.	ID=gene147;Name=RP11-449J3.2-013;name2=PCDH15
chr10	ENCODE	exon	55250936	55253124	.	-	.	Parent=gene147
chr10	ENCODE	exon	55254902	55254907	.	-	.	Parent=gene147
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene147
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene147
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene147
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene147
chr10	ENCODE	exon	55296408	55296623	.	-	.	Parent=gene147
chr10	ENCODE	exon	55333009	55333136	.	-	.	Parent=gene147
chr10	ENCODE	exon	55368581	55368721	.	-	.	Parent=gene147
chr10	ENCODE	exon	55370632	55370741	.	-	.	Parent=gene147
chr10	ENCODE	exon	55389498	55389610	.	-	.	Parent=gene147
chr10	ENCODE	exon	55391518	55391658	.	-	.	Parent=gene147
chr10	ENCODE	exon	55425415	55425531	.	-	.	Parent=gene147
chr10	ENCODE	exon	55449958	55450182	.	-	.	Parent=gene147
chr10	ENCODE	exon	55452658	55452963	.	-	.	Parent=gene147
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene147
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene147
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene147
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene147
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene147
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene147
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene147
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene147
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene147
###
chr10	ENCODE	gene	55251042	55336983	.	-	.	ID=gene148;Name=RP11-449J3.2-003;name2=PCDH15
chr10	ENCODE	exon	55251042	55253124	.	-	.	Parent=gene148
chr10	ENCODE	CDS	55251624	55253124	.	-	1	Parent=gene148
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene148
chr10	ENCODE	CDS	55257159	55257314	.	-	1	Parent=gene148
chr10	ENCODE	exon	55258331	55258339	.	-	.	Parent=gene148
chr10	ENCODE	CDS	55258331	55258339	.	-	1	Parent=gene148
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene148
chr10	ENCODE	CDS	55261081	55261299	.	-	1	Parent=gene148
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene148
chr10	ENCODE	CDS	55270086	55270262	.	-	1	Parent=gene148
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene148
chr10	ENCODE	CDS	55286941	55287029	.	-	0	Parent=gene148
chr10	ENCODE	exon	55296408	55296623	.	-	.	Parent=gene148
chr10	ENCODE	CDS	55296408	55296623	.	-	0	Parent=gene148
chr10	ENCODE	exon	55333009	55333136	.	-	.	Parent=gene148
chr10	ENCODE	CDS	55333009	55333136	.	-	2	Parent=gene148
chr10	ENCODE	CDS	55334959	55334977	.	-	0	Parent=gene148
chr10	ENCODE	exon	55334959	55335008	.	-	.	Parent=gene148
chr10	ENCODE	exon	55336642	55336983	.	-	.	Parent=gene148
###
chr10	ENCODE	gene	55251042	55643814	.	-	.	ID=gene149;name2=PCDH15;Name=RP11-449J3.2-001
chr10	ENCODE	exon	55251042	55253124	.	-	.	Parent=gene149
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene149
chr10	ENCODE	exon	55258331	55258339	.	-	.	Parent=gene149
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene149
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene149
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene149
chr10	ENCODE	exon	55296408	55296623	.	-	.	Parent=gene149
chr10	ENCODE	exon	55333009	55333136	.	-	.	Parent=gene149
chr10	ENCODE	exon	55368581	55368721	.	-	.	Parent=gene149
chr10	ENCODE	exon	55370632	55370741	.	-	.	Parent=gene149
chr10	ENCODE	exon	55389498	55389610	.	-	.	Parent=gene149
chr10	ENCODE	exon	55391518	55391658	.	-	.	Parent=gene149
chr10	ENCODE	exon	55425415	55425531	.	-	.	Parent=gene149
chr10	ENCODE	exon	55449958	55450182	.	-	.	Parent=gene149
chr10	ENCODE	exon	55452658	55452963	.	-	.	Parent=gene149
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene149
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene149
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene149
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene149
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene149
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene149
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene149
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene149
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene149
###
chr10	ENCODE	gene	55251042	55643814	.	-	.	ID=gene150;Name=RP11-449J3.2-012;name2=PCDH15
chr10	ENCODE	exon	55251042	55253124	.	-	.	Parent=gene150
chr10	ENCODE	exon	55257159	55257314	.	-	.	Parent=gene150
chr10	ENCODE	exon	55261081	55261299	.	-	.	Parent=gene150
chr10	ENCODE	exon	55270086	55270262	.	-	.	Parent=gene150
chr10	ENCODE	exon	55286941	55287029	.	-	.	Parent=gene150
chr10	ENCODE	exon	55296408	55296623	.	-	.	Parent=gene150
chr10	ENCODE	exon	55333009	55333136	.	-	.	Parent=gene150
chr10	ENCODE	exon	55368581	55368721	.	-	.	Parent=gene150
chr10	ENCODE	exon	55370632	55370741	.	-	.	Parent=gene150
chr10	ENCODE	exon	55389498	55389610	.	-	.	Parent=gene150
chr10	ENCODE	exon	55391518	55391658	.	-	.	Parent=gene150
chr10	ENCODE	exon	55425415	55425531	.	-	.	Parent=gene150
chr10	ENCODE	exon	55449958	55450182	.	-	.	Parent=gene150
chr10	ENCODE	exon	55452658	55452963	.	-	.	Parent=gene150
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene150
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene150
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene150
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene150
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene150
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene150
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene150
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene150
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene150
###
chr10	ENCODE	gene	55424345	55643814	.	-	.	ID=gene151;Name=RP11-449J3.2-002;name2=PCDH15
chr10	ENCODE	exon	55424345	55425531	.	-	.	Parent=gene151
chr10	ENCODE	exon	55449958	55450182	.	-	.	Parent=gene151
chr10	ENCODE	exon	55452658	55452963	.	-	.	Parent=gene151
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene151
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene151
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene151
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene151
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene151
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene151
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene151
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene151
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene151
###
chr10	ENCODE	gene	55496523	55643814	.	-	.	ID=gene152;Name=RP11-449J3.2-019;name2=PCDH15
chr10	ENCODE	exon	55496523	55496651	.	-	.	Parent=gene152
chr10	ENCODE	exon	55509097	55509190	.	-	.	Parent=gene152
chr10	ENCODE	exon	55519750	55519829	.	-	.	Parent=gene152
chr10	ENCODE	exon	55562641	55562773	.	-	.	Parent=gene152
chr10	ENCODE	exon	55582866	55583059	.	-	.	Parent=gene152
chr10	ENCODE	exon	55613210	55613359	.	-	.	Parent=gene152
chr10	ENCODE	exon	55614900	55615034	.	-	.	Parent=gene152
chr10	ENCODE	exon	55625449	55625655	.	-	.	Parent=gene152
chr10	ENCODE	exon	55643702	55643814	.	-	.	Parent=gene152
###
chr11	ENCODE	gene	1710216	1728386	.	-	.	ID=gene153;Name=AC068580.3-004;name2=AC068580.3
chr11	ENCODE	exon	1710216	1713235	.	-	.	Parent=gene153
chr11	ENCODE	CDS	1713086	1713235	.	-	0	Parent=gene153
chr11	ENCODE	CDS	1725473	1725715	.	-	0	Parent=gene153
chr11	ENCODE	exon	1725473	1725925	.	-	.	Parent=gene153
chr11	ENCODE	exon	1726821	1726932	.	-	.	Parent=gene153
chr11	ENCODE	exon	1728165	1728386	.	-	.	Parent=gene153
###
chr11	ENCODE	gene	1710216	1728397	.	-	.	ID=gene154;Name=AC068580.3-001;name2=AC068580.3
chr11	ENCODE	exon	1710216	1713235	.	-	.	Parent=gene154
chr11	ENCODE	CDS	1713086	1713235	.	-	0	Parent=gene154
chr11	ENCODE	exon	1725473	1725925	.	-	.	Parent=gene154
chr11	ENCODE	CDS	1725473	1725925	.	-	0	Parent=gene154
chr11	ENCODE	CDS	1728165	1728248	.	-	0	Parent=gene154
chr11	ENCODE	exon	1728165	1728397	.	-	.	Parent=gene154
###
chr11	ENCODE	gene	1713019	1726908	.	-	.	ID=gene155;Name=AC068580.3-003;name2=AC068580.3
chr11	ENCODE	exon	1713019	1713235	.	-	.	Parent=gene155
chr11	ENCODE	exon	1725563	1726908	.	-	.	Parent=gene155
###
chr11	ENCODE	gene	1725473	1736857	.	-	.	ID=gene156;Name=AC068580.4-007;name2=CTSD
chr11	ENCODE	exon	1725473	1725925	.	-	.	Parent=gene156
chr11	ENCODE	CDS	1725473	1725925	.	-	1	Parent=gene156
chr11	ENCODE	exon	1731609	1731707	.	-	.	Parent=gene156
chr11	ENCODE	CDS	1731609	1731707	.	-	1	Parent=gene156
chr11	ENCODE	exon	1731800	1731944	.	-	.	Parent=gene156
chr11	ENCODE	CDS	1731800	1731944	.	-	2	Parent=gene156
chr11	ENCODE	exon	1732712	1732834	.	-	.	Parent=gene156
chr11	ENCODE	CDS	1732712	1732834	.	-	2	Parent=gene156
chr11	ENCODE	exon	1735130	1735362	.	-	.	Parent=gene156
chr11	ENCODE	CDS	1735130	1735362	.	-	1	Parent=gene156
chr11	ENCODE	exon	1736775	1736857	.	-	.	Parent=gene156
chr11	ENCODE	CDS	1736775	1736857	.	-	0	Parent=gene156
###
chr11	ENCODE	gene	1725736	1727003	.	-	.	ID=gene157;Name=AC068580.3-005;name2=AC068580.3
chr11	ENCODE	exon	1725736	1725925	.	-	.	Parent=gene157
chr11	ENCODE	exon	1726825	1727003	.	-	.	Parent=gene157
###
chr11	ENCODE	gene	1730558	1741798	.	-	.	ID=gene158;Name=AC068580.4-001;name2=CTSD
chr11	ENCODE	exon	1730558	1731476	.	-	.	Parent=gene158
chr11	ENCODE	CDS	1731309	1731476	.	-	0	Parent=gene158
chr11	ENCODE	exon	1731609	1731707	.	-	.	Parent=gene158
chr11	ENCODE	CDS	1731609	1731707	.	-	0	Parent=gene158
chr11	ENCODE	exon	1731800	1731944	.	-	.	Parent=gene158
chr11	ENCODE	CDS	1731800	1731944	.	-	1	Parent=gene158
chr11	ENCODE	exon	1732712	1732834	.	-	.	Parent=gene158
chr11	ENCODE	CDS	1732712	1732834	.	-	1	Parent=gene158
chr11	ENCODE	exon	1735130	1735362	.	-	.	Parent=gene158
chr11	ENCODE	CDS	1735130	1735362	.	-	0	Parent=gene158
chr11	ENCODE	exon	1736775	1736893	.	-	.	Parent=gene158
chr11	ENCODE	CDS	1736775	1736893	.	-	2	Parent=gene158
chr11	ENCODE	exon	1737322	1737445	.	-	.	Parent=gene158
chr11	ENCODE	CDS	1737322	1737445	.	-	0	Parent=gene158
chr11	ENCODE	exon	1739115	1739274	.	-	.	Parent=gene158
chr11	ENCODE	CDS	1739115	1739274	.	-	1	Parent=gene158
chr11	ENCODE	CDS	1741598	1741665	.	-	0	Parent=gene158
chr11	ENCODE	exon	1741598	1741798	.	-	.	Parent=gene158
###
chr11	ENCODE	gene	1730581	1741707	.	-	.	ID=gene159;Name=AC068580.4-006;name2=CTSD
chr11	ENCODE	exon	1730581	1731476	.	-	.	Parent=gene159
chr11	ENCODE	exon	1731609	1731707	.	-	.	Parent=gene159
chr11	ENCODE	exon	1731800	1731937	.	-	.	Parent=gene159
chr11	ENCODE	exon	1732708	1732834	.	-	.	Parent=gene159
chr11	ENCODE	exon	1735130	1735362	.	-	.	Parent=gene159
chr11	ENCODE	exon	1736775	1736893	.	-	.	Parent=gene159
chr11	ENCODE	exon	1737322	1737445	.	-	.	Parent=gene159
chr11	ENCODE	exon	1739115	1739274	.	-	.	Parent=gene159
chr11	ENCODE	exon	1741598	1741707	.	-	.	Parent=gene159
###
chr11	ENCODE	gene	1731189	1732752	.	-	.	ID=gene160;Name=AC068580.4-004;name2=CTSD
chr11	ENCODE	exon	1731189	1731476	.	-	.	Parent=gene160
chr11	ENCODE	exon	1731609	1731707	.	-	.	Parent=gene160
chr11	ENCODE	exon	1731800	1732061	.	-	.	Parent=gene160
chr11	ENCODE	exon	1732712	1732752	.	-	.	Parent=gene160
###
chr11	ENCODE	gene	1731611	1733154	.	-	.	ID=gene161;Name=AC068580.4-003;name2=CTSD
chr11	ENCODE	exon	1731611	1731944	.	-	.	Parent=gene161
chr11	ENCODE	exon	1732712	1733154	.	-	.	Parent=gene161
###
chr11	ENCODE	gene	1731830	1739346	.	-	.	ID=gene162;name2=CTSD;Name=AC068580.4-005
chr11	ENCODE	exon	1731830	1731944	.	-	.	Parent=gene162
chr11	ENCODE	CDS	1731830	1731944	.	-	1	Parent=gene162
chr11	ENCODE	exon	1732712	1732834	.	-	.	Parent=gene162
chr11	ENCODE	CDS	1732712	1732834	.	-	1	Parent=gene162
chr11	ENCODE	exon	1735130	1735362	.	-	.	Parent=gene162
chr11	ENCODE	CDS	1735130	1735362	.	-	0	Parent=gene162
chr11	ENCODE	exon	1736775	1736893	.	-	.	Parent=gene162
chr11	ENCODE	CDS	1736775	1736893	.	-	2	Parent=gene162
chr11	ENCODE	exon	1737322	1737445	.	-	.	Parent=gene162
chr11	ENCODE	CDS	1737322	1737445	.	-	0	Parent=gene162
chr11	ENCODE	CDS	1739115	1739297	.	-	0	Parent=gene162
chr11	ENCODE	exon	1739115	1739346	.	-	.	Parent=gene162
###
chr11	ENCODE	gene	1735130	1740209	.	-	.	ID=gene163;Name=AC068580.4-002;name2=CTSD
chr11	ENCODE	exon	1735130	1735362	.	-	.	Parent=gene163
chr11	ENCODE	CDS	1735130	1735362	.	-	0	Parent=gene163
chr11	ENCODE	exon	1736775	1736893	.	-	.	Parent=gene163
chr11	ENCODE	CDS	1736775	1736893	.	-	2	Parent=gene163
chr11	ENCODE	exon	1737322	1737445	.	-	.	Parent=gene163
chr11	ENCODE	CDS	1737322	1737445	.	-	0	Parent=gene163
chr11	ENCODE	CDS	1739115	1739237	.	-	0	Parent=gene163
chr11	ENCODE	exon	1739115	1739274	.	-	.	Parent=gene163
chr11	ENCODE	exon	1739939	1740209	.	-	.	Parent=gene163
###
chr11	ENCODE	gene	1806113	1813740	.	+	.	ID=gene164;Name=AC051649.1-011;name2=SYT8
chr11	ENCODE	exon	1806113	1806199	.	+	.	Parent=gene164
chr11	ENCODE	exon	1806348	1806519	.	+	.	Parent=gene164
chr11	ENCODE	exon	1812903	1813005	.	+	.	Parent=gene164
chr11	ENCODE	CDS	1812912	1813005	.	+	0	Parent=gene164
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene164
chr11	ENCODE	CDS	1813102	1813265	.	+	2	Parent=gene164
chr11	ENCODE	exon	1813692	1813740	.	+	.	Parent=gene164
chr11	ENCODE	CDS	1813692	1813740	.	+	0	Parent=gene164
###
chr11	ENCODE	gene	1806349	1813732	.	+	.	ID=gene165;Name=AC051649.1-010;name2=SYT8
chr11	ENCODE	exon	1806349	1806519	.	+	.	Parent=gene165
chr11	ENCODE	exon	1812900	1813005	.	+	.	Parent=gene165
chr11	ENCODE	CDS	1812912	1813005	.	+	0	Parent=gene165
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene165
chr11	ENCODE	CDS	1813102	1813265	.	+	2	Parent=gene165
chr11	ENCODE	exon	1813692	1813732	.	+	.	Parent=gene165
chr11	ENCODE	CDS	1813692	1813732	.	+	0	Parent=gene165
###
chr11	ENCODE	gene	1808893	1815327	.	+	.	ID=gene166;Name=AC051649.1-007;name2=SYT8
chr11	ENCODE	exon	1808893	1809702	.	+	.	Parent=gene166
chr11	ENCODE	exon	1812900	1813005	.	+	.	Parent=gene166
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene166
chr11	ENCODE	exon	1813692	1814667	.	+	.	Parent=gene166
chr11	ENCODE	exon	1814763	1814896	.	+	.	Parent=gene166
chr11	ENCODE	exon	1814998	1815327	.	+	.	Parent=gene166
###
chr11	ENCODE	gene	1810118	1815327	.	+	.	ID=gene167;Name=AC051649.1-001;name2=SYT8
chr11	ENCODE	exon	1810118	1810163	.	+	.	Parent=gene167
chr11	ENCODE	exon	1812900	1813005	.	+	.	Parent=gene167
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene167
chr11	ENCODE	exon	1813692	1814090	.	+	.	Parent=gene167
chr11	ENCODE	exon	1814231	1814398	.	+	.	Parent=gene167
chr11	ENCODE	exon	1814562	1814667	.	+	.	Parent=gene167
chr11	ENCODE	exon	1814763	1814896	.	+	.	Parent=gene167
chr11	ENCODE	exon	1814998	1815327	.	+	.	Parent=gene167
###
chr11	ENCODE	gene	1811598	1815327	.	+	.	ID=gene168;Name=AC051649.1-009;name2=SYT8
chr11	ENCODE	exon	1811598	1814667	.	+	.	Parent=gene168
chr11	ENCODE	exon	1814763	1814896	.	+	.	Parent=gene168
chr11	ENCODE	exon	1814998	1815327	.	+	.	Parent=gene168
###
chr11	ENCODE	gene	1812116	1815327	.	+	.	ID=gene169;Name=AC051649.1-006;name2=SYT8
chr11	ENCODE	exon	1812116	1812423	.	+	.	Parent=gene169
chr11	ENCODE	exon	1812900	1813005	.	+	.	Parent=gene169
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene169
chr11	ENCODE	exon	1813692	1814398	.	+	.	Parent=gene169
chr11	ENCODE	exon	1814562	1814667	.	+	.	Parent=gene169
chr11	ENCODE	exon	1814763	1815327	.	+	.	Parent=gene169
###
chr11	ENCODE	gene	1812250	1815327	.	+	.	ID=gene170;Name=AC051649.1-002;name2=SYT8
chr11	ENCODE	exon	1812250	1812407	.	+	.	Parent=gene170
chr11	ENCODE	CDS	1812378	1812407	.	+	0	Parent=gene170
chr11	ENCODE	exon	1812900	1813005	.	+	.	Parent=gene170
chr11	ENCODE	CDS	1812900	1813005	.	+	0	Parent=gene170
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene170
chr11	ENCODE	CDS	1813102	1813265	.	+	2	Parent=gene170
chr11	ENCODE	exon	1813692	1813790	.	+	.	Parent=gene170
chr11	ENCODE	CDS	1813692	1813790	.	+	0	Parent=gene170
chr11	ENCODE	exon	1813932	1814090	.	+	.	Parent=gene170
chr11	ENCODE	CDS	1813932	1814090	.	+	0	Parent=gene170
chr11	ENCODE	exon	1814231	1814398	.	+	.	Parent=gene170
chr11	ENCODE	CDS	1814231	1814398	.	+	0	Parent=gene170
chr11	ENCODE	exon	1814562	1814667	.	+	.	Parent=gene170
chr11	ENCODE	CDS	1814562	1814667	.	+	0	Parent=gene170
chr11	ENCODE	exon	1814763	1814896	.	+	.	Parent=gene170
chr11	ENCODE	CDS	1814763	1814896	.	+	2	Parent=gene170
chr11	ENCODE	CDS	1814998	1815237	.	+	0	Parent=gene170
chr11	ENCODE	exon	1814998	1815327	.	+	.	Parent=gene170
###
chr11	ENCODE	gene	1812282	1815327	.	+	.	ID=gene171;Name=AC051649.1-003;name2=SYT8
chr11	ENCODE	exon	1812282	1812407	.	+	.	Parent=gene171
chr11	ENCODE	exon	1812900	1813005	.	+	.	Parent=gene171
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene171
chr11	ENCODE	exon	1813692	1814398	.	+	.	Parent=gene171
chr11	ENCODE	exon	1814562	1814667	.	+	.	Parent=gene171
chr11	ENCODE	exon	1814763	1814896	.	+	.	Parent=gene171
chr11	ENCODE	exon	1814998	1815327	.	+	.	Parent=gene171
###
chr11	ENCODE	gene	1812378	1813910	.	+	.	ID=gene172;name2=SYT8;Name=AC051649.1-013
chr11	ENCODE	exon	1812378	1812407	.	+	.	Parent=gene172
chr11	ENCODE	CDS	1812378	1812407	.	+	0	Parent=gene172
chr11	ENCODE	exon	1812900	1813005	.	+	.	Parent=gene172
chr11	ENCODE	CDS	1812900	1813005	.	+	0	Parent=gene172
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene172
chr11	ENCODE	CDS	1813102	1813265	.	+	2	Parent=gene172
chr11	ENCODE	exon	1813692	1813910	.	+	.	Parent=gene172
chr11	ENCODE	CDS	1813692	1813910	.	+	0	Parent=gene172
###
chr11	ENCODE	gene	1812396	1815327	.	+	.	ID=gene173;name2=SYT8;Name=AC051649.1-008
chr11	ENCODE	exon	1812396	1812423	.	+	.	Parent=gene173
chr11	ENCODE	CDS	1812396	1812423	.	+	0	Parent=gene173
chr11	ENCODE	exon	1812903	1813005	.	+	.	Parent=gene173
chr11	ENCODE	CDS	1812903	1813005	.	+	2	Parent=gene173
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene173
chr11	ENCODE	CDS	1813102	1813265	.	+	1	Parent=gene173
chr11	ENCODE	exon	1813692	1813790	.	+	.	Parent=gene173
chr11	ENCODE	CDS	1813692	1813790	.	+	2	Parent=gene173
chr11	ENCODE	exon	1813932	1814090	.	+	.	Parent=gene173
chr11	ENCODE	CDS	1813932	1814090	.	+	2	Parent=gene173
chr11	ENCODE	exon	1814231	1814398	.	+	.	Parent=gene173
chr11	ENCODE	CDS	1814231	1814398	.	+	2	Parent=gene173
chr11	ENCODE	exon	1814562	1814667	.	+	.	Parent=gene173
chr11	ENCODE	CDS	1814562	1814667	.	+	2	Parent=gene173
chr11	ENCODE	exon	1814763	1814896	.	+	.	Parent=gene173
chr11	ENCODE	CDS	1814763	1814896	.	+	1	Parent=gene173
chr11	ENCODE	CDS	1814998	1815237	.	+	2	Parent=gene173
chr11	ENCODE	exon	1814998	1815327	.	+	.	Parent=gene173
###
chr11	ENCODE	gene	1812610	1815327	.	+	.	ID=gene174;Name=AC051649.1-004;name2=SYT8
chr11	ENCODE	exon	1812610	1813005	.	+	.	Parent=gene174
chr11	ENCODE	CDS	1812912	1813005	.	+	0	Parent=gene174
chr11	ENCODE	exon	1813102	1813265	.	+	.	Parent=gene174
chr11	ENCODE	CDS	1813102	1813265	.	+	2	Parent=gene174
chr11	ENCODE	exon	1813692	1813790	.	+	.	Parent=gene174
chr11	ENCODE	CDS	1813692	1813790	.	+	0	Parent=gene174
chr11	ENCODE	exon	1813932	1814090	.	+	.	Parent=gene174
chr11	ENCODE	CDS	1813932	1814090	.	+	0	Parent=gene174
chr11	ENCODE	exon	1814231	1814398	.	+	.	Parent=gene174
chr11	ENCODE	CDS	1814231	1814398	.	+	0	Parent=gene174
chr11	ENCODE	exon	1814562	1814667	.	+	.	Parent=gene174
chr11	ENCODE	CDS	1814562	1814667	.	+	0	Parent=gene174
chr11	ENCODE	exon	1814763	1814896	.	+	.	Parent=gene174
chr11	ENCODE	CDS	1814763	1814896	.	+	2	Parent=gene174
chr11	ENCODE	CDS	1814998	1815237	.	+	0	Parent=gene174
chr11	ENCODE	exon	1814998	1815327	.	+	.	Parent=gene174
###
chr11	ENCODE	gene	1812912	1813388	.	+	.	ID=gene175;Name=AC051649.1-005;name2=SYT8
chr11	ENCODE	exon	1812912	1813005	.	+	.	Parent=gene175
chr11	ENCODE	exon	1813102	1813388	.	+	.	Parent=gene175
###
chr11	ENCODE	gene	1813366	1814224	.	+	.	ID=gene176;Name=AC051649.1-012;name2=SYT8
chr11	ENCODE	exon	1813366	1813422	.	+	.	Parent=gene176
chr11	ENCODE	exon	1813692	1814224	.	+	.	Parent=gene176
###
chr11	ENCODE	gene	1813835	1814358	.	+	.	ID=gene177;Name=AC051649.1-014;name2=SYT8
chr11	ENCODE	exon	1813835	1814090	.	+	.	Parent=gene177
chr11	ENCODE	exon	1814231	1814358	.	+	.	Parent=gene177
###
chr11	ENCODE	gene	1816795	1819484	.	+	.	ID=gene178;name2=TNNI2;Name=AC051649.2-002
chr11	ENCODE	exon	1816795	1816839	.	+	.	Parent=gene178
chr11	ENCODE	exon	1817481	1817510	.	+	.	Parent=gene178
chr11	ENCODE	CDS	1817503	1817510	.	+	0	Parent=gene178
chr11	ENCODE	exon	1817655	1817661	.	+	.	Parent=gene178
chr11	ENCODE	CDS	1817655	1817661	.	+	1	Parent=gene178
chr11	ENCODE	exon	1818209	1818250	.	+	.	Parent=gene178
chr11	ENCODE	CDS	1818209	1818250	.	+	0	Parent=gene178
chr11	ENCODE	exon	1818334	1818462	.	+	.	Parent=gene178
chr11	ENCODE	CDS	1818334	1818462	.	+	0	Parent=gene178
chr11	ENCODE	exon	1818625	1818714	.	+	.	Parent=gene178
chr11	ENCODE	CDS	1818625	1818714	.	+	0	Parent=gene178
chr11	ENCODE	exon	1818837	1819013	.	+	.	Parent=gene178
chr11	ENCODE	CDS	1818837	1819013	.	+	0	Parent=gene178
chr11	ENCODE	CDS	1819262	1819357	.	+	0	Parent=gene178
chr11	ENCODE	exon	1819262	1819484	.	+	.	Parent=gene178
###
chr11	ENCODE	gene	1817287	1819484	.	+	.	ID=gene179;Name=AC051649.2-001;name2=TNNI2
chr11	ENCODE	exon	1817287	1817333	.	+	.	Parent=gene179
chr11	ENCODE	exon	1817481	1817510	.	+	.	Parent=gene179
chr11	ENCODE	CDS	1817503	1817510	.	+	0	Parent=gene179
chr11	ENCODE	exon	1817655	1817661	.	+	.	Parent=gene179
chr11	ENCODE	CDS	1817655	1817661	.	+	1	Parent=gene179
chr11	ENCODE	exon	1818209	1818250	.	+	.	Parent=gene179
chr11	ENCODE	CDS	1818209	1818250	.	+	0	Parent=gene179
chr11	ENCODE	exon	1818334	1818462	.	+	.	Parent=gene179
chr11	ENCODE	CDS	1818334	1818462	.	+	0	Parent=gene179
chr11	ENCODE	exon	1818625	1818714	.	+	.	Parent=gene179
chr11	ENCODE	CDS	1818625	1818714	.	+	0	Parent=gene179
chr11	ENCODE	exon	1818837	1819013	.	+	.	Parent=gene179
chr11	ENCODE	CDS	1818837	1819013	.	+	0	Parent=gene179
chr11	ENCODE	CDS	1819262	1819357	.	+	0	Parent=gene179
chr11	ENCODE	exon	1819262	1819484	.	+	.	Parent=gene179
###
chr11	ENCODE	gene	1818000	1819484	.	+	.	ID=gene180;Name=AC051649.2-003;name2=TNNI2
chr11	ENCODE	exon	1818000	1818044	.	+	.	Parent=gene180
chr11	ENCODE	CDS	1818030	1818044	.	+	0	Parent=gene180
chr11	ENCODE	exon	1818209	1818250	.	+	.	Parent=gene180
chr11	ENCODE	CDS	1818209	1818250	.	+	0	Parent=gene180
chr11	ENCODE	exon	1818334	1818462	.	+	.	Parent=gene180
chr11	ENCODE	CDS	1818334	1818462	.	+	0	Parent=gene180
chr11	ENCODE	exon	1818625	1818714	.	+	.	Parent=gene180
chr11	ENCODE	CDS	1818625	1818714	.	+	0	Parent=gene180
chr11	ENCODE	exon	1818837	1819013	.	+	.	Parent=gene180
chr11	ENCODE	CDS	1818837	1819013	.	+	0	Parent=gene180
chr11	ENCODE	CDS	1819262	1819357	.	+	0	Parent=gene180
chr11	ENCODE	exon	1819262	1819484	.	+	.	Parent=gene180
###
chr11	ENCODE	gene	1818024	1818541	.	+	.	ID=gene181;Name=AC051649.2-004;name2=TNNI2
chr11	ENCODE	exon	1818024	1818250	.	+	.	Parent=gene181
chr11	ENCODE	exon	1818334	1818541	.	+	.	Parent=gene181
###
chr11	ENCODE	gene	1830776	1870069	.	+	.	ID=gene182;Name=AC051649.3-004;name2=LSP1
chr11	ENCODE	exon	1830776	1831003	.	+	.	Parent=gene182
chr11	ENCODE	CDS	1830951	1831003	.	+	0	Parent=gene182
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene182
chr11	ENCODE	CDS	1857893	1858030	.	+	1	Parent=gene182
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene182
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene182
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene182
chr11	ENCODE	CDS	1861225	1861366	.	+	1	Parent=gene182
chr11	ENCODE	exon	1861738	1861830	.	+	.	Parent=gene182
chr11	ENCODE	CDS	1861738	1861830	.	+	0	Parent=gene182
chr11	ENCODE	exon	1862086	1862129	.	+	.	Parent=gene182
chr11	ENCODE	CDS	1862086	1862129	.	+	0	Parent=gene182
chr11	ENCODE	exon	1862306	1862387	.	+	.	Parent=gene182
chr11	ENCODE	CDS	1862306	1862387	.	+	1	Parent=gene182
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene182
chr11	ENCODE	CDS	1864538	1864672	.	+	0	Parent=gene182
chr11	ENCODE	exon	1865043	1865120	.	+	.	Parent=gene182
chr11	ENCODE	CDS	1865043	1865120	.	+	0	Parent=gene182
chr11	ENCODE	CDS	1865280	1865369	.	+	0	Parent=gene182
chr11	ENCODE	exon	1865280	1865382	.	+	.	Parent=gene182
chr11	ENCODE	exon	1869579	1870069	.	+	.	Parent=gene182
###
chr11	ENCODE	gene	1841052	1861234	.	+	.	ID=gene183;Name=AC051649.3-013;name2=LSP1
chr11	ENCODE	exon	1841052	1841420	.	+	.	Parent=gene183
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene183
chr11	ENCODE	CDS	1858026	1858030	.	+	0	Parent=gene183
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene183
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene183
chr11	ENCODE	exon	1861225	1861234	.	+	.	Parent=gene183
chr11	ENCODE	CDS	1861225	1861234	.	+	1	Parent=gene183
###
chr11	ENCODE	gene	1841978	1861803	.	+	.	ID=gene184;Name=AC051649.3-014;name2=LSP1
chr11	ENCODE	exon	1841978	1842040	.	+	.	Parent=gene184
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene184
chr11	ENCODE	CDS	1858026	1858030	.	+	0	Parent=gene184
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene184
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene184
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene184
chr11	ENCODE	CDS	1861225	1861366	.	+	1	Parent=gene184
chr11	ENCODE	exon	1861738	1861803	.	+	.	Parent=gene184
chr11	ENCODE	CDS	1861738	1861803	.	+	0	Parent=gene184
###
chr11	ENCODE	gene	1842971	1870069	.	+	.	ID=gene185;Name=AC051649.3-001;name2=LSP1
chr11	ENCODE	exon	1842971	1843068	.	+	.	Parent=gene185
chr11	ENCODE	exon	1844271	1844717	.	+	.	Parent=gene185
chr11	ENCODE	CDS	1844281	1844717	.	+	0	Parent=gene185
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene185
chr11	ENCODE	CDS	1857893	1858030	.	+	1	Parent=gene185
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene185
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene185
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene185
chr11	ENCODE	CDS	1861225	1861366	.	+	1	Parent=gene185
chr11	ENCODE	exon	1861738	1861830	.	+	.	Parent=gene185
chr11	ENCODE	CDS	1861738	1861830	.	+	0	Parent=gene185
chr11	ENCODE	exon	1862086	1862129	.	+	.	Parent=gene185
chr11	ENCODE	CDS	1862086	1862129	.	+	0	Parent=gene185
chr11	ENCODE	exon	1862306	1862387	.	+	.	Parent=gene185
chr11	ENCODE	CDS	1862306	1862387	.	+	1	Parent=gene185
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene185
chr11	ENCODE	CDS	1864538	1864672	.	+	0	Parent=gene185
chr11	ENCODE	exon	1865043	1865120	.	+	.	Parent=gene185
chr11	ENCODE	CDS	1865043	1865120	.	+	0	Parent=gene185
chr11	ENCODE	CDS	1865280	1865369	.	+	0	Parent=gene185
chr11	ENCODE	exon	1865280	1865382	.	+	.	Parent=gene185
chr11	ENCODE	exon	1869579	1870069	.	+	.	Parent=gene185
###
chr11	ENCODE	gene	1846479	1870069	.	+	.	ID=gene186;Name=AC051649.3-005;name2=LSP1
chr11	ENCODE	exon	1846479	1846792	.	+	.	Parent=gene186
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene186
chr11	ENCODE	CDS	1858026	1858030	.	+	0	Parent=gene186
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene186
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene186
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene186
chr11	ENCODE	CDS	1861225	1861366	.	+	1	Parent=gene186
chr11	ENCODE	exon	1861738	1861830	.	+	.	Parent=gene186
chr11	ENCODE	CDS	1861738	1861830	.	+	0	Parent=gene186
chr11	ENCODE	exon	1862086	1862129	.	+	.	Parent=gene186
chr11	ENCODE	CDS	1862086	1862129	.	+	0	Parent=gene186
chr11	ENCODE	exon	1862306	1862387	.	+	.	Parent=gene186
chr11	ENCODE	CDS	1862306	1862387	.	+	1	Parent=gene186
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene186
chr11	ENCODE	CDS	1864538	1864672	.	+	0	Parent=gene186
chr11	ENCODE	exon	1865043	1865120	.	+	.	Parent=gene186
chr11	ENCODE	CDS	1865043	1865120	.	+	0	Parent=gene186
chr11	ENCODE	CDS	1865280	1865369	.	+	0	Parent=gene186
chr11	ENCODE	exon	1865280	1865382	.	+	.	Parent=gene186
chr11	ENCODE	exon	1869579	1870069	.	+	.	Parent=gene186
###
chr11	ENCODE	gene	1846950	1861248	.	+	.	ID=gene187;name2=LSP1;Name=AC051649.3-006
chr11	ENCODE	exon	1846950	1847039	.	+	.	Parent=gene187
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene187
chr11	ENCODE	CDS	1858026	1858030	.	+	0	Parent=gene187
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene187
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene187
chr11	ENCODE	exon	1861225	1861248	.	+	.	Parent=gene187
chr11	ENCODE	CDS	1861225	1861248	.	+	1	Parent=gene187
###
chr11	ENCODE	gene	1847448	1864672	.	+	.	ID=gene188;Name=AC051649.3-007;name2=LSP1
chr11	ENCODE	exon	1847448	1847535	.	+	.	Parent=gene188
chr11	ENCODE	CDS	1847510	1847535	.	+	0	Parent=gene188
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene188
chr11	ENCODE	CDS	1857893	1858030	.	+	1	Parent=gene188
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene188
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene188
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene188
chr11	ENCODE	CDS	1861225	1861366	.	+	1	Parent=gene188
chr11	ENCODE	exon	1861738	1861830	.	+	.	Parent=gene188
chr11	ENCODE	CDS	1861738	1861830	.	+	0	Parent=gene188
chr11	ENCODE	exon	1862086	1862129	.	+	.	Parent=gene188
chr11	ENCODE	CDS	1862086	1862129	.	+	0	Parent=gene188
chr11	ENCODE	exon	1862306	1862387	.	+	.	Parent=gene188
chr11	ENCODE	CDS	1862306	1862387	.	+	1	Parent=gene188
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene188
chr11	ENCODE	CDS	1864538	1864672	.	+	0	Parent=gene188
###
chr11	ENCODE	gene	1847956	1861815	.	+	.	ID=gene189;Name=AC051649.3-015;name2=LSP1
chr11	ENCODE	exon	1847956	1848014	.	+	.	Parent=gene189
chr11	ENCODE	CDS	1848013	1848014	.	+	0	Parent=gene189
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene189
chr11	ENCODE	CDS	1857893	1858030	.	+	1	Parent=gene189
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene189
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene189
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene189
chr11	ENCODE	CDS	1861225	1861366	.	+	1	Parent=gene189
chr11	ENCODE	exon	1861738	1861815	.	+	.	Parent=gene189
chr11	ENCODE	CDS	1861738	1861815	.	+	0	Parent=gene189
###
chr11	ENCODE	gene	1848050	1870069	.	+	.	ID=gene190;Name=AC051649.3-002;name2=LSP1
chr11	ENCODE	exon	1848050	1849218	.	+	.	Parent=gene190
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene190
chr11	ENCODE	CDS	1858026	1858030	.	+	0	Parent=gene190
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene190
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene190
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene190
chr11	ENCODE	CDS	1861225	1861366	.	+	1	Parent=gene190
chr11	ENCODE	exon	1861738	1861830	.	+	.	Parent=gene190
chr11	ENCODE	CDS	1861738	1861830	.	+	0	Parent=gene190
chr11	ENCODE	exon	1862086	1862129	.	+	.	Parent=gene190
chr11	ENCODE	CDS	1862086	1862129	.	+	0	Parent=gene190
chr11	ENCODE	exon	1862306	1862387	.	+	.	Parent=gene190
chr11	ENCODE	CDS	1862306	1862387	.	+	1	Parent=gene190
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene190
chr11	ENCODE	CDS	1864538	1864672	.	+	0	Parent=gene190
chr11	ENCODE	exon	1865043	1865120	.	+	.	Parent=gene190
chr11	ENCODE	CDS	1865043	1865120	.	+	0	Parent=gene190
chr11	ENCODE	CDS	1865280	1865369	.	+	0	Parent=gene190
chr11	ENCODE	exon	1865280	1865382	.	+	.	Parent=gene190
chr11	ENCODE	exon	1869579	1870069	.	+	.	Parent=gene190
###
chr11	ENCODE	gene	1848692	1864672	.	+	.	ID=gene191;Name=AC051649.3-008;name2=LSP1
chr11	ENCODE	exon	1848692	1848779	.	+	.	Parent=gene191
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene191
chr11	ENCODE	CDS	1858026	1858030	.	+	0	Parent=gene191
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene191
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene191
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene191
chr11	ENCODE	CDS	1861225	1861366	.	+	1	Parent=gene191
chr11	ENCODE	exon	1861738	1861830	.	+	.	Parent=gene191
chr11	ENCODE	CDS	1861738	1861830	.	+	0	Parent=gene191
chr11	ENCODE	exon	1862086	1862129	.	+	.	Parent=gene191
chr11	ENCODE	CDS	1862086	1862129	.	+	0	Parent=gene191
chr11	ENCODE	exon	1862306	1862387	.	+	.	Parent=gene191
chr11	ENCODE	CDS	1862306	1862387	.	+	1	Parent=gene191
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene191
chr11	ENCODE	CDS	1864538	1864672	.	+	0	Parent=gene191
###
chr11	ENCODE	gene	1849158	1865382	.	+	.	ID=gene192;Name=AC051649.3-009;name2=LSP1
chr11	ENCODE	exon	1849158	1849218	.	+	.	Parent=gene192
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene192
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene192
chr11	ENCODE	exon	1861738	1861830	.	+	.	Parent=gene192
chr11	ENCODE	exon	1862086	1862129	.	+	.	Parent=gene192
chr11	ENCODE	exon	1862306	1862387	.	+	.	Parent=gene192
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene192
chr11	ENCODE	exon	1865043	1865120	.	+	.	Parent=gene192
chr11	ENCODE	exon	1865280	1865382	.	+	.	Parent=gene192
###
chr11	ENCODE	gene	1854283	1864672	.	+	.	ID=gene193;Name=AC051649.3-010;name2=LSP1
chr11	ENCODE	exon	1854283	1854451	.	+	.	Parent=gene193
chr11	ENCODE	exon	1857893	1858030	.	+	.	Parent=gene193
chr11	ENCODE	CDS	1858026	1858030	.	+	0	Parent=gene193
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene193
chr11	ENCODE	CDS	1859238	1859402	.	+	1	Parent=gene193
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene193
chr11	ENCODE	CDS	1861225	1861366	.	+	1	Parent=gene193
chr11	ENCODE	exon	1861738	1861830	.	+	.	Parent=gene193
chr11	ENCODE	CDS	1861738	1861830	.	+	0	Parent=gene193
chr11	ENCODE	exon	1862086	1862129	.	+	.	Parent=gene193
chr11	ENCODE	CDS	1862086	1862129	.	+	0	Parent=gene193
chr11	ENCODE	exon	1862306	1862387	.	+	.	Parent=gene193
chr11	ENCODE	CDS	1862306	1862387	.	+	1	Parent=gene193
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene193
chr11	ENCODE	CDS	1864538	1864672	.	+	0	Parent=gene193
###
chr11	ENCODE	gene	1858483	1870073	.	+	.	ID=gene194;Name=AC051649.3-003;name2=LSP1
chr11	ENCODE	exon	1858483	1859169	.	+	.	Parent=gene194
chr11	ENCODE	exon	1859238	1859402	.	+	.	Parent=gene194
chr11	ENCODE	exon	1861225	1861366	.	+	.	Parent=gene194
chr11	ENCODE	exon	1861738	1861830	.	+	.	Parent=gene194
chr11	ENCODE	exon	1862086	1862129	.	+	.	Parent=gene194
chr11	ENCODE	exon	1862306	1862387	.	+	.	Parent=gene194
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene194
chr11	ENCODE	exon	1865043	1865120	.	+	.	Parent=gene194
chr11	ENCODE	exon	1865280	1865382	.	+	.	Parent=gene194
chr11	ENCODE	exon	1869579	1870073	.	+	.	Parent=gene194
###
chr11	ENCODE	gene	1862194	1865308	.	+	.	ID=gene195;Name=AC051649.3-011;name2=LSP1
chr11	ENCODE	exon	1862194	1862387	.	+	.	Parent=gene195
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene195
chr11	ENCODE	exon	1865043	1865120	.	+	.	Parent=gene195
chr11	ENCODE	exon	1865280	1865308	.	+	.	Parent=gene195
###
chr11	ENCODE	gene	1864538	1865151	.	+	.	ID=gene196;Name=AC051649.3-012;name2=LSP1
chr11	ENCODE	exon	1864538	1864672	.	+	.	Parent=gene196
chr11	ENCODE	exon	1865043	1865151	.	+	.	Parent=gene196
###
chr11	ENCODE	gene	1866951	1868660	.	-	.	ID=gene197;Name=AC051649.15-001;name2=AC051649.15
chr11	ENCODE	CDS	1866951	1868369	.	-	0	Parent=gene197
chr11	ENCODE	exon	1866951	1868660	.	-	.	Parent=gene197
###
chr11	ENCODE	gene	1897368	1916512	.	+	.	ID=gene198;Name=AC051649.4-001;name2=TNNT3
chr11	ENCODE	exon	1897368	1897568	.	+	.	Parent=gene198
chr11	ENCODE	exon	1900663	1900697	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene198
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene198
chr11	ENCODE	exon	1901361	1901378	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1901361	1901378	.	+	2	Parent=gene198
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene198
chr11	ENCODE	exon	1904501	1904515	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1904501	1904515	.	+	2	Parent=gene198
chr11	ENCODE	exon	1906926	1906949	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1906926	1906949	.	+	2	Parent=gene198
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene198
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene198
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene198
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene198
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene198
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene198
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene198
chr11	ENCODE	exon	1914769	1914809	.	+	.	Parent=gene198
chr11	ENCODE	CDS	1914769	1914809	.	+	0	Parent=gene198
chr11	ENCODE	CDS	1916244	1916298	.	+	1	Parent=gene198
chr11	ENCODE	exon	1916244	1916512	.	+	.	Parent=gene198
###
chr11	ENCODE	gene	1897512	1912725	.	+	.	ID=gene199;Name=AC051649.4-007;name2=TNNT3
chr11	ENCODE	exon	1897512	1897568	.	+	.	Parent=gene199
chr11	ENCODE	exon	1900663	1900697	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene199
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene199
chr11	ENCODE	exon	1901361	1901378	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1901361	1901378	.	+	2	Parent=gene199
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene199
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene199
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene199
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene199
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene199
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene199
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene199
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene199
###
chr11	ENCODE	gene	1897512	1916507	.	+	.	ID=gene200;Name=AC051649.4-006;name2=TNNT3
chr11	ENCODE	exon	1897512	1897568	.	+	.	Parent=gene200
chr11	ENCODE	exon	1900663	1900697	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene200
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene200
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene200
chr11	ENCODE	exon	1904501	1904515	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1904501	1904515	.	+	2	Parent=gene200
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene200
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene200
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene200
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene200
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene200
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene200
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene200
chr11	ENCODE	exon	1914769	1914809	.	+	.	Parent=gene200
chr11	ENCODE	CDS	1914769	1914809	.	+	0	Parent=gene200
chr11	ENCODE	CDS	1916244	1916298	.	+	1	Parent=gene200
chr11	ENCODE	exon	1916244	1916507	.	+	.	Parent=gene200
###
chr11	ENCODE	gene	1897512	1916512	.	+	.	ID=gene201;Name=AC051649.4-002;name2=TNNT3
chr11	ENCODE	exon	1897512	1897568	.	+	.	Parent=gene201
chr11	ENCODE	exon	1900663	1900697	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene201
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene201
chr11	ENCODE	exon	1901361	1901378	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1901361	1901378	.	+	2	Parent=gene201
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene201
chr11	ENCODE	exon	1903062	1903082	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1903062	1903082	.	+	2	Parent=gene201
chr11	ENCODE	exon	1904276	1904287	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1904276	1904287	.	+	2	Parent=gene201
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene201
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene201
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene201
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene201
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene201
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene201
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene201
chr11	ENCODE	exon	1914769	1914809	.	+	.	Parent=gene201
chr11	ENCODE	CDS	1914769	1914809	.	+	0	Parent=gene201
chr11	ENCODE	CDS	1916244	1916298	.	+	1	Parent=gene201
chr11	ENCODE	exon	1916244	1916512	.	+	.	Parent=gene201
###
chr11	ENCODE	gene	1897512	1916512	.	+	.	ID=gene202;Name=AC051649.4-003;name2=TNNT3
chr11	ENCODE	exon	1897512	1897568	.	+	.	Parent=gene202
chr11	ENCODE	exon	1900663	1900697	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene202
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene202
chr11	ENCODE	exon	1901361	1901378	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1901361	1901378	.	+	2	Parent=gene202
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene202
chr11	ENCODE	exon	1904501	1904515	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1904501	1904515	.	+	2	Parent=gene202
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene202
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene202
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene202
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene202
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene202
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene202
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene202
chr11	ENCODE	exon	1914020	1914060	.	+	.	Parent=gene202
chr11	ENCODE	CDS	1914020	1914060	.	+	0	Parent=gene202
chr11	ENCODE	CDS	1916244	1916298	.	+	1	Parent=gene202
chr11	ENCODE	exon	1916244	1916512	.	+	.	Parent=gene202
###
chr11	ENCODE	gene	1897529	1916298	.	+	.	ID=gene203;Name=AC051649.4-012;name2=TNNT3
chr11	ENCODE	exon	1897529	1897568	.	+	.	Parent=gene203
chr11	ENCODE	exon	1900663	1900697	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene203
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene203
chr11	ENCODE	exon	1901361	1901378	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1901361	1901378	.	+	2	Parent=gene203
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene203
chr11	ENCODE	exon	1903062	1903082	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1903062	1903082	.	+	2	Parent=gene203
chr11	ENCODE	exon	1904276	1904287	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1904276	1904287	.	+	2	Parent=gene203
chr11	ENCODE	exon	1904501	1904515	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1904501	1904515	.	+	2	Parent=gene203
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene203
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene203
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene203
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene203
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene203
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene203
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene203
chr11	ENCODE	exon	1914769	1914809	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1914769	1914809	.	+	0	Parent=gene203
chr11	ENCODE	exon	1916244	1916298	.	+	.	Parent=gene203
chr11	ENCODE	CDS	1916244	1916298	.	+	1	Parent=gene203
###
chr11	ENCODE	gene	1897531	1916298	.	+	.	ID=gene204;name2=TNNT3;Name=AC051649.4-011
chr11	ENCODE	exon	1897531	1897568	.	+	.	Parent=gene204
chr11	ENCODE	exon	1900663	1900697	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene204
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene204
chr11	ENCODE	exon	1901361	1901378	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1901361	1901378	.	+	2	Parent=gene204
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene204
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene204
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene204
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene204
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene204
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene204
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene204
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene204
chr11	ENCODE	exon	1914769	1914809	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1914769	1914809	.	+	0	Parent=gene204
chr11	ENCODE	exon	1916244	1916298	.	+	.	Parent=gene204
chr11	ENCODE	CDS	1916244	1916298	.	+	1	Parent=gene204
###
chr11	ENCODE	gene	1899165	1916512	.	+	.	ID=gene205;Name=AC051649.4-004;name2=TNNT3
chr11	ENCODE	exon	1899165	1899425	.	+	.	Parent=gene205
chr11	ENCODE	exon	1900663	1900697	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene205
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene205
chr11	ENCODE	exon	1901361	1901378	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1901361	1901378	.	+	2	Parent=gene205
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene205
chr11	ENCODE	exon	1904501	1904515	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1904501	1904515	.	+	2	Parent=gene205
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene205
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene205
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene205
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene205
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene205
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene205
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene205
chr11	ENCODE	exon	1914769	1914809	.	+	.	Parent=gene205
chr11	ENCODE	CDS	1914769	1914809	.	+	0	Parent=gene205
chr11	ENCODE	CDS	1916244	1916298	.	+	1	Parent=gene205
chr11	ENCODE	exon	1916244	1916512	.	+	.	Parent=gene205
###
chr11	ENCODE	gene	1900673	1916298	.	+	.	ID=gene206;Name=AC051649.4-010;name2=TNNT3
chr11	ENCODE	exon	1900673	1900697	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene206
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene206
chr11	ENCODE	exon	1901361	1901378	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1901361	1901378	.	+	2	Parent=gene206
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene206
chr11	ENCODE	exon	1903062	1903082	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1903062	1903082	.	+	2	Parent=gene206
chr11	ENCODE	exon	1904276	1904287	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1904276	1904287	.	+	2	Parent=gene206
chr11	ENCODE	exon	1904501	1904515	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1904501	1904515	.	+	2	Parent=gene206
chr11	ENCODE	exon	1906926	1906949	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1906926	1906949	.	+	2	Parent=gene206
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene206
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene206
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene206
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene206
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene206
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene206
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene206
chr11	ENCODE	exon	1914769	1914809	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1914769	1914809	.	+	0	Parent=gene206
chr11	ENCODE	exon	1916244	1916298	.	+	.	Parent=gene206
chr11	ENCODE	CDS	1916244	1916298	.	+	1	Parent=gene206
###
chr11	ENCODE	gene	1900681	1916292	.	+	.	ID=gene207;Name=AC051649.4-015;name2=TNNT3
chr11	ENCODE	exon	1900681	1900697	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene207
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene207
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene207
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene207
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene207
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene207
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene207
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene207
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene207
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene207
chr11	ENCODE	exon	1914020	1914060	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1914020	1914060	.	+	0	Parent=gene207
chr11	ENCODE	exon	1916244	1916292	.	+	.	Parent=gene207
chr11	ENCODE	CDS	1916244	1916292	.	+	1	Parent=gene207
###
chr11	ENCODE	gene	1900681	1916292	.	+	.	ID=gene208;Name=AC051649.4-014;name2=TNNT3
chr11	ENCODE	exon	1900681	1900697	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1900681	1900697	.	+	0	Parent=gene208
chr11	ENCODE	exon	1900854	1900867	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1900854	1900867	.	+	1	Parent=gene208
chr11	ENCODE	exon	1902905	1902922	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1902905	1902922	.	+	2	Parent=gene208
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1907616	1907634	.	+	2	Parent=gene208
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1910275	1910320	.	+	1	Parent=gene208
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1911527	1911643	.	+	0	Parent=gene208
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1911737	1911814	.	+	0	Parent=gene208
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1912138	1912251	.	+	0	Parent=gene208
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1912352	1912461	.	+	0	Parent=gene208
chr11	ENCODE	exon	1912635	1912725	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1912635	1912725	.	+	1	Parent=gene208
chr11	ENCODE	exon	1914769	1914809	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1914769	1914809	.	+	0	Parent=gene208
chr11	ENCODE	exon	1916244	1916292	.	+	.	Parent=gene208
chr11	ENCODE	CDS	1916244	1916292	.	+	1	Parent=gene208
###
chr11	ENCODE	gene	1902724	1912461	.	+	.	ID=gene209;Name=AC051649.4-009;name2=TNNT3
chr11	ENCODE	exon	1902724	1902922	.	+	.	Parent=gene209
chr11	ENCODE	exon	1903062	1903082	.	+	.	Parent=gene209
chr11	ENCODE	exon	1904276	1904287	.	+	.	Parent=gene209
chr11	ENCODE	exon	1904501	1904515	.	+	.	Parent=gene209
chr11	ENCODE	exon	1906874	1906949	.	+	.	Parent=gene209
chr11	ENCODE	exon	1907616	1907634	.	+	.	Parent=gene209
chr11	ENCODE	exon	1910275	1910320	.	+	.	Parent=gene209
chr11	ENCODE	exon	1911527	1911643	.	+	.	Parent=gene209
chr11	ENCODE	exon	1911737	1911814	.	+	.	Parent=gene209
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene209
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene209
###
chr11	ENCODE	gene	1911679	1913387	.	+	.	ID=gene210;Name=AC051649.4-008;name2=TNNT3
chr11	ENCODE	exon	1911679	1911814	.	+	.	Parent=gene210
chr11	ENCODE	exon	1912138	1912251	.	+	.	Parent=gene210
chr11	ENCODE	exon	1912352	1912461	.	+	.	Parent=gene210
chr11	ENCODE	exon	1912635	1913387	.	+	.	Parent=gene210
###
chr11	ENCODE	gene	1916006	1916508	.	+	.	ID=gene211;name2=TNNT3;Name=AC051649.4-016
chr11	ENCODE	exon	1916006	1916074	.	+	.	Parent=gene211
chr11	ENCODE	exon	1916244	1916508	.	+	.	Parent=gene211
###
chr11	ENCODE	gene	1925084	1934415	.	+	.	ID=gene212;Name=AC051649.5-001;name2=MRPL23
chr11	ENCODE	exon	1925084	1925185	.	+	.	Parent=gene212
chr11	ENCODE	CDS	1925169	1925185	.	+	0	Parent=gene212
chr11	ENCODE	exon	1928705	1928827	.	+	.	Parent=gene212
chr11	ENCODE	CDS	1928705	1928827	.	+	1	Parent=gene212
chr11	ENCODE	exon	1929933	1930015	.	+	.	Parent=gene212
chr11	ENCODE	CDS	1929933	1930015	.	+	1	Parent=gene212
chr11	ENCODE	exon	1930588	1930661	.	+	.	Parent=gene212
chr11	ENCODE	CDS	1930588	1930661	.	+	2	Parent=gene212
chr11	ENCODE	CDS	1934062	1934226	.	+	0	Parent=gene212
chr11	ENCODE	exon	1934062	1934415	.	+	.	Parent=gene212
###
chr11	ENCODE	gene	1925084	1934415	.	+	.	ID=gene213;Name=AC051649.5-007;name2=MRPL23
chr11	ENCODE	exon	1925084	1925185	.	+	.	Parent=gene213
chr11	ENCODE	CDS	1925169	1925185	.	+	0	Parent=gene213
chr11	ENCODE	exon	1928705	1928827	.	+	.	Parent=gene213
chr11	ENCODE	CDS	1928705	1928827	.	+	1	Parent=gene213
chr11	ENCODE	exon	1929933	1930015	.	+	.	Parent=gene213
chr11	ENCODE	CDS	1929933	1930015	.	+	1	Parent=gene213
chr11	ENCODE	exon	1930588	1930661	.	+	.	Parent=gene213
chr11	ENCODE	CDS	1930588	1930661	.	+	2	Parent=gene213
chr11	ENCODE	CDS	1934062	1934226	.	+	0	Parent=gene213
chr11	ENCODE	exon	1934062	1934254	.	+	.	Parent=gene213
chr11	ENCODE	exon	1934348	1934415	.	+	.	Parent=gene213
###
chr11	ENCODE	gene	1925138	1962328	.	+	.	ID=gene214;name2=MRPL23;Name=AC051649.5-009
chr11	ENCODE	exon	1925138	1925185	.	+	.	Parent=gene214
chr11	ENCODE	CDS	1925169	1925185	.	+	0	Parent=gene214
chr11	ENCODE	exon	1928705	1928827	.	+	.	Parent=gene214
chr11	ENCODE	CDS	1928705	1928827	.	+	1	Parent=gene214
chr11	ENCODE	exon	1929933	1930015	.	+	.	Parent=gene214
chr11	ENCODE	CDS	1929933	1930015	.	+	1	Parent=gene214
chr11	ENCODE	exon	1930588	1930661	.	+	.	Parent=gene214
chr11	ENCODE	CDS	1930588	1930661	.	+	2	Parent=gene214
chr11	ENCODE	exon	1950365	1950564	.	+	.	Parent=gene214
chr11	ENCODE	CDS	1950365	1950564	.	+	0	Parent=gene214
chr11	ENCODE	CDS	1962244	1962322	.	+	1	Parent=gene214
chr11	ENCODE	exon	1962244	1962328	.	+	.	Parent=gene214
###
chr11	ENCODE	gene	1925147	1940644	.	+	.	ID=gene215;Name=AC051649.5-002;name2=MRPL23
chr11	ENCODE	exon	1925147	1925185	.	+	.	Parent=gene215
chr11	ENCODE	CDS	1925169	1925185	.	+	0	Parent=gene215
chr11	ENCODE	exon	1928705	1928827	.	+	.	Parent=gene215
chr11	ENCODE	CDS	1928705	1928827	.	+	1	Parent=gene215
chr11	ENCODE	exon	1929933	1930015	.	+	.	Parent=gene215
chr11	ENCODE	CDS	1929933	1930015	.	+	1	Parent=gene215
chr11	ENCODE	exon	1930588	1930661	.	+	.	Parent=gene215
chr11	ENCODE	CDS	1930588	1930661	.	+	2	Parent=gene215
chr11	ENCODE	CDS	1940045	1940239	.	+	0	Parent=gene215
chr11	ENCODE	exon	1940045	1940644	.	+	.	Parent=gene215
###
chr11	ENCODE	gene	1925150	1950599	.	+	.	ID=gene216;Name=AC051649.5-011;name2=MRPL23
chr11	ENCODE	exon	1925150	1925185	.	+	.	Parent=gene216
chr11	ENCODE	CDS	1925169	1925185	.	+	0	Parent=gene216
chr11	ENCODE	exon	1928705	1928827	.	+	.	Parent=gene216
chr11	ENCODE	CDS	1928705	1928827	.	+	1	Parent=gene216
chr11	ENCODE	exon	1929933	1930015	.	+	.	Parent=gene216
chr11	ENCODE	CDS	1929933	1930015	.	+	1	Parent=gene216
chr11	ENCODE	exon	1930588	1930661	.	+	.	Parent=gene216
chr11	ENCODE	CDS	1930588	1930661	.	+	2	Parent=gene216
chr11	ENCODE	CDS	1950365	1950568	.	+	0	Parent=gene216
chr11	ENCODE	exon	1950365	1950599	.	+	.	Parent=gene216
###
chr11	ENCODE	gene	1925156	1956250	.	+	.	ID=gene217;Name=AC051649.5-010;name2=MRPL23
chr11	ENCODE	exon	1925156	1925185	.	+	.	Parent=gene217
chr11	ENCODE	exon	1928705	1928771	.	+	.	Parent=gene217
chr11	ENCODE	exon	1951565	1956250	.	+	.	Parent=gene217
###
chr11	ENCODE	gene	1925360	1934415	.	+	.	ID=gene218;Name=AC051649.5-004;name2=MRPL23
chr11	ENCODE	exon	1925360	1925384	.	+	.	Parent=gene218
chr11	ENCODE	exon	1928705	1928827	.	+	.	Parent=gene218
chr11	ENCODE	exon	1929933	1930015	.	+	.	Parent=gene218
chr11	ENCODE	exon	1930588	1930661	.	+	.	Parent=gene218
chr11	ENCODE	exon	1934062	1934415	.	+	.	Parent=gene218
###
chr11	ENCODE	gene	1927346	1928827	.	+	.	ID=gene219;Name=AC051649.5-008;name2=MRPL23
chr11	ENCODE	exon	1927346	1927967	.	+	.	Parent=gene219
chr11	ENCODE	exon	1928705	1928827	.	+	.	Parent=gene219
###
chr11	ENCODE	gene	1928705	1934415	.	+	.	ID=gene220;Name=AC051649.5-003;name2=MRPL23
chr11	ENCODE	exon	1928705	1928827	.	+	.	Parent=gene220
chr11	ENCODE	exon	1929933	1930015	.	+	.	Parent=gene220
chr11	ENCODE	exon	1930588	1930661	.	+	.	Parent=gene220
chr11	ENCODE	exon	1933417	1933587	.	+	.	Parent=gene220
chr11	ENCODE	exon	1934062	1934415	.	+	.	Parent=gene220
###
chr11	ENCODE	gene	1928716	1931128	.	+	.	ID=gene221;Name=AC051649.5-006;name2=MRPL23
chr11	ENCODE	exon	1928716	1928827	.	+	.	Parent=gene221
chr11	ENCODE	exon	1929933	1930015	.	+	.	Parent=gene221
chr11	ENCODE	exon	1930588	1931128	.	+	.	Parent=gene221
###
chr11	ENCODE	gene	1933383	1934152	.	+	.	ID=gene222;Name=AC051649.5-005;name2=MRPL23
chr11	ENCODE	exon	1933383	1933523	.	+	.	Parent=gene222
chr11	ENCODE	exon	1934062	1934152	.	+	.	Parent=gene222
###
chr11	ENCODE	gene	2106918	2115096	.	-	.	ID=gene223;Name=AC132217.1-003;name2=IGF2
chr11	ENCODE	exon	2106918	2111029	.	-	.	Parent=gene223
chr11	ENCODE	CDS	2110793	2111029	.	-	0	Parent=gene223
chr11	ENCODE	exon	2111323	2111471	.	-	.	Parent=gene223
chr11	ENCODE	CDS	2111323	2111471	.	-	2	Parent=gene223
chr11	ENCODE	CDS	2113173	2113329	.	-	0	Parent=gene223
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene223
chr11	ENCODE	exon	2114994	2115096	.	-	.	Parent=gene223
###
chr11	ENCODE	gene	2106918	2116780	.	-	.	ID=gene224;Name=AC132217.1-002;name2=IGF2
chr11	ENCODE	exon	2106918	2111029	.	-	.	Parent=gene224
chr11	ENCODE	CDS	2110793	2111029	.	-	0	Parent=gene224
chr11	ENCODE	exon	2111323	2111480	.	-	.	Parent=gene224
chr11	ENCODE	CDS	2111323	2111480	.	-	2	Parent=gene224
chr11	ENCODE	CDS	2113173	2113329	.	-	0	Parent=gene224
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene224
chr11	ENCODE	exon	2116035	2116780	.	-	.	Parent=gene224
###
chr11	ENCODE	gene	2106918	2117195	.	-	.	ID=gene225;Name=AC132217.1-001;name2=IGF2
chr11	ENCODE	exon	2106918	2111029	.	-	.	Parent=gene225
chr11	ENCODE	CDS	2110793	2111029	.	-	0	Parent=gene225
chr11	ENCODE	exon	2111323	2111471	.	-	.	Parent=gene225
chr11	ENCODE	CDS	2111323	2111471	.	-	2	Parent=gene225
chr11	ENCODE	CDS	2113173	2113329	.	-	0	Parent=gene225
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene225
chr11	ENCODE	exon	2116035	2117195	.	-	.	Parent=gene225
###
chr11	ENCODE	gene	2110344	2138796	.	-	.	ID=gene226;Name=AC132217.1-008;name2=IGF2
chr11	ENCODE	exon	2110344	2111029	.	-	.	Parent=gene226
chr11	ENCODE	exon	2111323	2111471	.	-	.	Parent=gene226
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene226
chr11	ENCODE	exon	2125372	2125613	.	-	.	Parent=gene226
chr11	ENCODE	exon	2126932	2127151	.	-	.	Parent=gene226
chr11	ENCODE	exon	2138591	2138796	.	-	.	Parent=gene226
###
chr11	ENCODE	gene	2110446	2115093	.	-	.	ID=gene227;Name=AC132217.1-004;name2=IGF2
chr11	ENCODE	exon	2110446	2111029	.	-	.	Parent=gene227
chr11	ENCODE	CDS	2110793	2111029	.	-	0	Parent=gene227
chr11	ENCODE	exon	2111323	2111480	.	-	.	Parent=gene227
chr11	ENCODE	CDS	2111323	2111480	.	-	2	Parent=gene227
chr11	ENCODE	CDS	2113173	2113329	.	-	0	Parent=gene227
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene227
chr11	ENCODE	exon	2114994	2115093	.	-	.	Parent=gene227
###
chr11	ENCODE	gene	2110479	2118822	.	-	.	ID=gene228;name2=IGF2;Name=AC132217.1-009
chr11	ENCODE	exon	2110479	2111029	.	-	.	Parent=gene228
chr11	ENCODE	CDS	2110793	2111029	.	-	0	Parent=gene228
chr11	ENCODE	exon	2111323	2111471	.	-	.	Parent=gene228
chr11	ENCODE	CDS	2111323	2111471	.	-	2	Parent=gene228
chr11	ENCODE	CDS	2113173	2113329	.	-	0	Parent=gene228
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene228
chr11	ENCODE	exon	2118663	2118822	.	-	.	Parent=gene228
###
chr11	ENCODE	gene	2110522	2115111	.	-	.	ID=gene229;Name=AC132217.1-005;name2=IGF2
chr11	ENCODE	exon	2110522	2111029	.	-	.	Parent=gene229
chr11	ENCODE	CDS	2110793	2111029	.	-	0	Parent=gene229
chr11	ENCODE	exon	2111323	2111471	.	-	.	Parent=gene229
chr11	ENCODE	CDS	2111323	2111471	.	-	2	Parent=gene229
chr11	ENCODE	CDS	2113173	2113329	.	-	0	Parent=gene229
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene229
chr11	ENCODE	exon	2114998	2115111	.	-	.	Parent=gene229
###
chr11	ENCODE	gene	2110619	2115093	.	-	.	ID=gene230;Name=AC132217.1-006;name2=IGF2
chr11	ENCODE	exon	2110619	2111029	.	-	.	Parent=gene230
chr11	ENCODE	CDS	2110793	2111029	.	-	0	Parent=gene230
chr11	ENCODE	exon	2111323	2111480	.	-	.	Parent=gene230
chr11	ENCODE	CDS	2111323	2111480	.	-	2	Parent=gene230
chr11	ENCODE	CDS	2113173	2113329	.	-	0	Parent=gene230
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene230
chr11	ENCODE	exon	2114998	2115093	.	-	.	Parent=gene230
###
chr11	ENCODE	gene	2110872	2115461	.	-	.	ID=gene231;Name=AC132217.1-012;name2=IGF2
chr11	ENCODE	exon	2110872	2111029	.	-	.	Parent=gene231
chr11	ENCODE	exon	2111323	2111480	.	-	.	Parent=gene231
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene231
chr11	ENCODE	exon	2115359	2115461	.	-	.	Parent=gene231
###
chr11	ENCODE	gene	2111357	2119044	.	-	.	ID=gene232;Name=AC132217.1-007;name2=IGF2
chr11	ENCODE	exon	2111357	2111471	.	-	.	Parent=gene232
chr11	ENCODE	CDS	2111357	2111471	.	-	2	Parent=gene232
chr11	ENCODE	exon	2113173	2113335	.	-	.	Parent=gene232
chr11	ENCODE	CDS	2113173	2113335	.	-	0	Parent=gene232
chr11	ENCODE	CDS	2117941	2118102	.	-	0	Parent=gene232
chr11	ENCODE	exon	2117941	2118105	.	-	.	Parent=gene232
chr11	ENCODE	exon	2118663	2119044	.	-	.	Parent=gene232
###
chr11	ENCODE	gene	2118307	2126448	.	+	.	ID=gene233;Name=AC132217.6-002;name2=IGF2AS
chr11	ENCODE	exon	2118307	2118753	.	+	.	Parent=gene233
chr11	ENCODE	exon	2124162	2124333	.	+	.	Parent=gene233
chr11	ENCODE	exon	2125124	2126448	.	+	.	Parent=gene233
###
chr11	ENCODE	gene	2118323	2126470	.	+	.	ID=gene234;Name=AC132217.6-001;name2=IGF2AS
chr11	ENCODE	exon	2118323	2118753	.	+	.	Parent=gene234
chr11	ENCODE	exon	2124051	2124333	.	+	.	Parent=gene234
chr11	ENCODE	exon	2125124	2126470	.	+	.	Parent=gene234
###
chr11	ENCODE	gene	2118450	2125613	.	+	.	ID=gene235;Name=AC132217.6-003;name2=IGF2AS
chr11	ENCODE	exon	2118450	2118753	.	+	.	Parent=gene235
chr11	ENCODE	CDS	2118450	2118753	.	+	0	Parent=gene235
chr11	ENCODE	CDS	2124051	2124253	.	+	2	Parent=gene235
chr11	ENCODE	exon	2124051	2125613	.	+	.	Parent=gene235
###
chr11	ENCODE	gene	2124429	2136464	.	-	.	ID=gene236;Name=AC132217.1-010;name2=IGF2
chr11	ENCODE	exon	2124429	2124551	.	-	.	Parent=gene236
chr11	ENCODE	exon	2125372	2125613	.	-	.	Parent=gene236
chr11	ENCODE	exon	2126932	2127151	.	-	.	Parent=gene236
chr11	ENCODE	exon	2136073	2136464	.	-	.	Parent=gene236
###
chr11	ENCODE	gene	2126740	2136142	.	-	.	ID=gene237;name2=IGF2;Name=AC132217.1-011
chr11	ENCODE	exon	2126740	2127151	.	-	.	Parent=gene237
chr11	ENCODE	exon	2136073	2136142	.	-	.	Parent=gene237
###
chr11	ENCODE	gene	2137584	2138797	.	-	.	ID=gene238;Name=AC132217.5-006;name2=INS
chr11	ENCODE	exon	2137584	2137767	.	-	.	Parent=gene238
chr11	ENCODE	CDS	2137658	2137767	.	-	2	Parent=gene238
chr11	ENCODE	CDS	2138591	2138777	.	-	0	Parent=gene238
chr11	ENCODE	exon	2138591	2138797	.	-	.	Parent=gene238
###
chr11	ENCODE	gene	2137585	2139000	.	-	.	ID=gene239;Name=AC132217.5-004;name2=INS
chr11	ENCODE	exon	2137585	2137833	.	-	.	Parent=gene239
chr11	ENCODE	exon	2138591	2138794	.	-	.	Parent=gene239
chr11	ENCODE	exon	2138974	2139000	.	-	.	Parent=gene239
###
chr11	ENCODE	gene	2137585	2139010	.	-	.	ID=gene240;Name=AC132217.5-003;name2=INS
chr11	ENCODE	exon	2137585	2137803	.	-	.	Parent=gene240
chr11	ENCODE	CDS	2137658	2137803	.	-	2	Parent=gene240
chr11	ENCODE	CDS	2138591	2138777	.	-	0	Parent=gene240
chr11	ENCODE	exon	2138591	2139010	.	-	.	Parent=gene240
###
chr11	ENCODE	gene	2137585	2139027	.	-	.	ID=gene241;Name=AC132217.5-002;name2=INS
chr11	ENCODE	exon	2137585	2137803	.	-	.	Parent=gene241
chr11	ENCODE	CDS	2137658	2137803	.	-	2	Parent=gene241
chr11	ENCODE	CDS	2138591	2138777	.	-	0	Parent=gene241
chr11	ENCODE	exon	2138591	2138794	.	-	.	Parent=gene241
chr11	ENCODE	exon	2138948	2139027	.	-	.	Parent=gene241
###
chr11	ENCODE	gene	2137585	2139147	.	-	.	ID=gene242;Name=AC132217.5-001;name2=INS
chr11	ENCODE	exon	2137585	2137803	.	-	.	Parent=gene242
chr11	ENCODE	CDS	2137658	2137803	.	-	2	Parent=gene242
chr11	ENCODE	CDS	2138591	2138777	.	-	0	Parent=gene242
chr11	ENCODE	exon	2138591	2138794	.	-	.	Parent=gene242
chr11	ENCODE	exon	2138974	2139147	.	-	.	Parent=gene242
###
chr11	ENCODE	gene	2137589	2138964	.	-	.	ID=gene243;Name=AC132217.5-005;name2=INS
chr11	ENCODE	exon	2137589	2137678	.	-	.	Parent=gene243
chr11	ENCODE	CDS	2137589	2137678	.	-	2	Parent=gene243
chr11	ENCODE	CDS	2138591	2138777	.	-	0	Parent=gene243
chr11	ENCODE	exon	2138591	2138964	.	-	.	Parent=gene243
###
chr11	ENCODE	gene	2141735	2149611	.	-	.	ID=gene244;Name=AC132217.7-003;name2=TH
chr11	ENCODE	exon	2141735	2142198	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2142039	2142198	.	-	1	Parent=gene244
chr11	ENCODE	exon	2143038	2143171	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2143038	2143171	.	-	0	Parent=gene244
chr11	ENCODE	exon	2143474	2143569	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2143474	2143569	.	-	0	Parent=gene244
chr11	ENCODE	exon	2143808	2143864	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2143808	2143864	.	-	0	Parent=gene244
chr11	ENCODE	exon	2144286	2144355	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2144286	2144355	.	-	1	Parent=gene244
chr11	ENCODE	exon	2144439	2144574	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2144439	2144574	.	-	2	Parent=gene244
chr11	ENCODE	exon	2144693	2144838	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2144693	2144838	.	-	1	Parent=gene244
chr11	ENCODE	exon	2145241	2145291	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2145241	2145291	.	-	1	Parent=gene244
chr11	ENCODE	exon	2145672	2145739	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2145672	2145739	.	-	0	Parent=gene244
chr11	ENCODE	exon	2145897	2145985	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2145897	2145985	.	-	2	Parent=gene244
chr11	ENCODE	exon	2146297	2146471	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2146297	2146471	.	-	0	Parent=gene244
chr11	ENCODE	exon	2147456	2147677	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2147456	2147677	.	-	0	Parent=gene244
chr11	ENCODE	exon	2148496	2148576	.	-	.	Parent=gene244
chr11	ENCODE	CDS	2148496	2148576	.	-	0	Parent=gene244
chr11	ENCODE	CDS	2149503	2149592	.	-	0	Parent=gene244
chr11	ENCODE	exon	2149503	2149611	.	-	.	Parent=gene244
###
chr11	ENCODE	gene	2141735	2149611	.	-	.	ID=gene245;Name=AC132217.7-002;name2=TH
chr11	ENCODE	exon	2141735	2142198	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2142039	2142198	.	-	1	Parent=gene245
chr11	ENCODE	exon	2143038	2143171	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2143038	2143171	.	-	0	Parent=gene245
chr11	ENCODE	exon	2143474	2143569	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2143474	2143569	.	-	0	Parent=gene245
chr11	ENCODE	exon	2143808	2143864	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2143808	2143864	.	-	0	Parent=gene245
chr11	ENCODE	exon	2144286	2144355	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2144286	2144355	.	-	1	Parent=gene245
chr11	ENCODE	exon	2144439	2144574	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2144439	2144574	.	-	2	Parent=gene245
chr11	ENCODE	exon	2144693	2144838	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2144693	2144838	.	-	1	Parent=gene245
chr11	ENCODE	exon	2145241	2145291	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2145241	2145291	.	-	1	Parent=gene245
chr11	ENCODE	exon	2145672	2145739	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2145672	2145739	.	-	0	Parent=gene245
chr11	ENCODE	exon	2145897	2145985	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2145897	2145985	.	-	2	Parent=gene245
chr11	ENCODE	exon	2146297	2146471	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2146297	2146471	.	-	0	Parent=gene245
chr11	ENCODE	exon	2147456	2147677	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2147456	2147677	.	-	0	Parent=gene245
chr11	ENCODE	exon	2148496	2148576	.	-	.	Parent=gene245
chr11	ENCODE	CDS	2148496	2148576	.	-	0	Parent=gene245
chr11	ENCODE	CDS	2149491	2149592	.	-	0	Parent=gene245
chr11	ENCODE	exon	2149491	2149611	.	-	.	Parent=gene245
###
chr11	ENCODE	gene	2141735	2149683	.	-	.	ID=gene246;name2=TH;Name=AC132217.7-001
chr11	ENCODE	exon	2141735	2142198	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2142039	2142198	.	-	1	Parent=gene246
chr11	ENCODE	exon	2143038	2143171	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2143038	2143171	.	-	0	Parent=gene246
chr11	ENCODE	exon	2143474	2143569	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2143474	2143569	.	-	0	Parent=gene246
chr11	ENCODE	exon	2143808	2143864	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2143808	2143864	.	-	0	Parent=gene246
chr11	ENCODE	exon	2144286	2144355	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2144286	2144355	.	-	1	Parent=gene246
chr11	ENCODE	exon	2144439	2144574	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2144439	2144574	.	-	2	Parent=gene246
chr11	ENCODE	exon	2144693	2144838	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2144693	2144838	.	-	1	Parent=gene246
chr11	ENCODE	exon	2145241	2145291	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2145241	2145291	.	-	1	Parent=gene246
chr11	ENCODE	exon	2145672	2145739	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2145672	2145739	.	-	0	Parent=gene246
chr11	ENCODE	exon	2145897	2145985	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2145897	2145985	.	-	2	Parent=gene246
chr11	ENCODE	exon	2146297	2146471	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2146297	2146471	.	-	0	Parent=gene246
chr11	ENCODE	exon	2147456	2147677	.	-	.	Parent=gene246
chr11	ENCODE	CDS	2147456	2147677	.	-	0	Parent=gene246
chr11	ENCODE	CDS	2149503	2149592	.	-	0	Parent=gene246
chr11	ENCODE	exon	2149503	2149683	.	-	.	Parent=gene246
###
chr11	ENCODE	gene	2143100	2149611	.	-	.	ID=gene247;Name=AC132217.7-006;name2=TH
chr11	ENCODE	exon	2143100	2143171	.	-	.	Parent=gene247
chr11	ENCODE	exon	2143474	2143569	.	-	.	Parent=gene247
chr11	ENCODE	exon	2143808	2143864	.	-	.	Parent=gene247
chr11	ENCODE	exon	2144286	2144355	.	-	.	Parent=gene247
chr11	ENCODE	exon	2144439	2144574	.	-	.	Parent=gene247
chr11	ENCODE	exon	2144693	2144838	.	-	.	Parent=gene247
chr11	ENCODE	exon	2145241	2145291	.	-	.	Parent=gene247
chr11	ENCODE	exon	2145672	2145739	.	-	.	Parent=gene247
chr11	ENCODE	exon	2145897	2145985	.	-	.	Parent=gene247
chr11	ENCODE	exon	2146297	2146471	.	-	.	Parent=gene247
chr11	ENCODE	exon	2147456	2147501	.	-	.	Parent=gene247
chr11	ENCODE	exon	2149503	2149611	.	-	.	Parent=gene247
###
chr11	ENCODE	gene	2143478	2145082	.	-	.	ID=gene248;name2=TH;Name=AC132217.7-008
chr11	ENCODE	exon	2143478	2143569	.	-	.	Parent=gene248
chr11	ENCODE	exon	2143808	2143864	.	-	.	Parent=gene248
chr11	ENCODE	exon	2144286	2144355	.	-	.	Parent=gene248
chr11	ENCODE	exon	2144439	2144574	.	-	.	Parent=gene248
chr11	ENCODE	exon	2144693	2145082	.	-	.	Parent=gene248
###
chr11	ENCODE	gene	2143485	2145912	.	-	.	ID=gene249;Name=AC132217.7-004;name2=TH
chr11	ENCODE	exon	2143485	2143569	.	-	.	Parent=gene249
chr11	ENCODE	exon	2143808	2143864	.	-	.	Parent=gene249
chr11	ENCODE	exon	2144286	2144355	.	-	.	Parent=gene249
chr11	ENCODE	exon	2144439	2144574	.	-	.	Parent=gene249
chr11	ENCODE	exon	2145241	2145291	.	-	.	Parent=gene249
chr11	ENCODE	exon	2145672	2145739	.	-	.	Parent=gene249
chr11	ENCODE	exon	2145897	2145912	.	-	.	Parent=gene249
###
chr11	ENCODE	gene	2143485	2145912	.	-	.	ID=gene250;Name=AC132217.7-005;name2=TH
chr11	ENCODE	exon	2143485	2143569	.	-	.	Parent=gene250
chr11	ENCODE	CDS	2143485	2143569	.	-	2	Parent=gene250
chr11	ENCODE	exon	2143808	2143864	.	-	.	Parent=gene250
chr11	ENCODE	CDS	2143808	2143864	.	-	2	Parent=gene250
chr11	ENCODE	exon	2144286	2144355	.	-	.	Parent=gene250
chr11	ENCODE	CDS	2144286	2144355	.	-	0	Parent=gene250
chr11	ENCODE	exon	2145241	2145291	.	-	.	Parent=gene250
chr11	ENCODE	CDS	2145241	2145291	.	-	0	Parent=gene250
chr11	ENCODE	exon	2145672	2145739	.	-	.	Parent=gene250
chr11	ENCODE	CDS	2145672	2145739	.	-	2	Parent=gene250
chr11	ENCODE	exon	2145897	2145912	.	-	.	Parent=gene250
chr11	ENCODE	CDS	2145897	2145912	.	-	0	Parent=gene250
###
chr11	ENCODE	gene	2143659	2144580	.	-	.	ID=gene251;Name=AC132217.7-010;name2=TH
chr11	ENCODE	exon	2143659	2144355	.	-	.	Parent=gene251
chr11	ENCODE	exon	2144439	2144580	.	-	.	Parent=gene251
###
chr11	ENCODE	gene	2143813	2149611	.	-	.	ID=gene252;name2=TH;Name=AC132217.7-007
chr11	ENCODE	exon	2143813	2143864	.	-	.	Parent=gene252
chr11	ENCODE	exon	2144286	2144355	.	-	.	Parent=gene252
chr11	ENCODE	exon	2144439	2144574	.	-	.	Parent=gene252
chr11	ENCODE	exon	2144693	2144838	.	-	.	Parent=gene252
chr11	ENCODE	exon	2145241	2145322	.	-	.	Parent=gene252
chr11	ENCODE	exon	2145672	2145739	.	-	.	Parent=gene252
chr11	ENCODE	exon	2145897	2145985	.	-	.	Parent=gene252
chr11	ENCODE	exon	2146297	2146471	.	-	.	Parent=gene252
chr11	ENCODE	exon	2147456	2147501	.	-	.	Parent=gene252
chr11	ENCODE	exon	2149491	2149611	.	-	.	Parent=gene252
###
chr11	ENCODE	gene	2144700	2146532	.	-	.	ID=gene253;Name=AC132217.7-009;name2=TH
chr11	ENCODE	exon	2144700	2144838	.	-	.	Parent=gene253
chr11	ENCODE	exon	2145241	2145739	.	-	.	Parent=gene253
chr11	ENCODE	exon	2145897	2145985	.	-	.	Parent=gene253
chr11	ENCODE	exon	2146297	2146532	.	-	.	Parent=gene253
###
chr11	ENCODE	gene	2246301	2248758	.	-	.	ID=gene254;Name=AC129929.1-001;name2=ASCL2
chr11	ENCODE	exon	2246301	2246932	.	-	.	Parent=gene254
chr11	ENCODE	exon	2247539	2248758	.	-	.	Parent=gene254
chr11	ENCODE	CDS	2247557	2248138	.	-	0	Parent=gene254
###
chr11	ENCODE	gene	2248315	2249421	.	-	.	ID=gene255;Name=AC129929.2-001;name2=AC129929.2
chr11	ENCODE	exon	2248315	2249421	.	-	.	Parent=gene255
chr11	ENCODE	CDS	2248315	2249421	.	-	0	Parent=gene255
###
chr11	ENCODE	gene	2273451	2279866	.	-	.	ID=gene256;Name=AC129929.3-001;name2=C11orf21
chr11	ENCODE	exon	2273451	2275727	.	-	.	Parent=gene256
chr11	ENCODE	exon	2277234	2277513	.	-	.	Parent=gene256
chr11	ENCODE	CDS	2277262	2277513	.	-	0	Parent=gene256
chr11	ENCODE	exon	2278326	2278419	.	-	.	Parent=gene256
chr11	ENCODE	CDS	2278326	2278419	.	-	1	Parent=gene256
chr11	ENCODE	CDS	2279562	2279614	.	-	0	Parent=gene256
chr11	ENCODE	exon	2279562	2279866	.	-	.	Parent=gene256
###
chr11	ENCODE	gene	2275630	2280855	.	-	.	ID=gene257;Name=AC129929.3-005;name2=C11orf21
chr11	ENCODE	exon	2275630	2275727	.	-	.	Parent=gene257
chr11	ENCODE	exon	2277234	2277513	.	-	.	Parent=gene257
chr11	ENCODE	exon	2280688	2280855	.	-	.	Parent=gene257
###
chr11	ENCODE	gene	2277231	2279678	.	-	.	ID=gene258;Name=AC129929.3-002;name2=C11orf21
chr11	ENCODE	exon	2277231	2277513	.	-	.	Parent=gene258
chr11	ENCODE	exon	2278490	2279678	.	-	.	Parent=gene258
###
chr11	ENCODE	gene	2277301	2279719	.	-	.	ID=gene259;Name=AC129929.3-004;name2=C11orf21
chr11	ENCODE	exon	2277301	2277513	.	-	.	Parent=gene259
chr11	ENCODE	CDS	2277301	2277513	.	-	0	Parent=gene259
chr11	ENCODE	exon	2278326	2278419	.	-	.	Parent=gene259
chr11	ENCODE	CDS	2278326	2278419	.	-	1	Parent=gene259
chr11	ENCODE	exon	2278490	2278574	.	-	.	Parent=gene259
chr11	ENCODE	CDS	2278490	2278574	.	-	2	Parent=gene259
chr11	ENCODE	CDS	2279562	2279667	.	-	0	Parent=gene259
chr11	ENCODE	exon	2279562	2279719	.	-	.	Parent=gene259
###
chr11	ENCODE	gene	2277345	2280766	.	-	.	ID=gene260;Name=AC129929.3-003;name2=C11orf21
chr11	ENCODE	exon	2277345	2277513	.	-	.	Parent=gene260
chr11	ENCODE	exon	2278326	2278419	.	-	.	Parent=gene260
chr11	ENCODE	exon	2280688	2280766	.	-	.	Parent=gene260
###
chr11	ENCODE	gene	2279803	2287824	.	+	.	ID=gene261;name2=TSPAN32;Name=AC129929.4-007
chr11	ENCODE	exon	2279803	2280028	.	+	.	Parent=gene261
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene261
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene261
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene261
chr11	ENCODE	exon	2287127	2287316	.	+	.	Parent=gene261
chr11	ENCODE	exon	2287795	2287824	.	+	.	Parent=gene261
###
chr11	ENCODE	gene	2279815	2296006	.	+	.	ID=gene262;Name=AC129929.4-006;name2=TSPAN32
chr11	ENCODE	exon	2279815	2280021	.	+	.	Parent=gene262
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene262
chr11	ENCODE	exon	2281216	2281287	.	+	.	Parent=gene262
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene262
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene262
chr11	ENCODE	exon	2291460	2291514	.	+	.	Parent=gene262
chr11	ENCODE	exon	2292291	2294473	.	+	.	Parent=gene262
chr11	ENCODE	exon	2295150	2295331	.	+	.	Parent=gene262
chr11	ENCODE	exon	2295669	2296006	.	+	.	Parent=gene262
###
chr11	ENCODE	gene	2279819	2295939	.	+	.	ID=gene263;Name=AC129929.4-015;name2=TSPAN32
chr11	ENCODE	exon	2279819	2280021	.	+	.	Parent=gene263
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene263
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene263
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene263
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene263
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene263
chr11	ENCODE	exon	2294035	2294118	.	+	.	Parent=gene263
chr11	ENCODE	exon	2294438	2294473	.	+	.	Parent=gene263
chr11	ENCODE	exon	2295150	2295331	.	+	.	Parent=gene263
chr11	ENCODE	exon	2295669	2295939	.	+	.	Parent=gene263
###
chr11	ENCODE	gene	2279819	2295948	.	+	.	ID=gene264;Name=AC129929.4-002;name2=TSPAN32
chr11	ENCODE	exon	2279819	2280021	.	+	.	Parent=gene264
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene264
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene264
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene264
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene264
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene264
chr11	ENCODE	exon	2294035	2294118	.	+	.	Parent=gene264
chr11	ENCODE	exon	2294438	2294473	.	+	.	Parent=gene264
chr11	ENCODE	exon	2295150	2295331	.	+	.	Parent=gene264
chr11	ENCODE	exon	2295669	2295948	.	+	.	Parent=gene264
###
chr11	ENCODE	gene	2279819	2295948	.	+	.	ID=gene265;Name=AC129929.4-001;name2=TSPAN32
chr11	ENCODE	exon	2279819	2280021	.	+	.	Parent=gene265
chr11	ENCODE	CDS	2279956	2280021	.	+	0	Parent=gene265
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene265
chr11	ENCODE	CDS	2280650	2280764	.	+	0	Parent=gene265
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene265
chr11	ENCODE	CDS	2281913	2282010	.	+	2	Parent=gene265
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene265
chr11	ENCODE	CDS	2286542	2286616	.	+	0	Parent=gene265
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene265
chr11	ENCODE	CDS	2291460	2291561	.	+	0	Parent=gene265
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene265
chr11	ENCODE	CDS	2292291	2292377	.	+	0	Parent=gene265
chr11	ENCODE	exon	2294035	2294118	.	+	.	Parent=gene265
chr11	ENCODE	CDS	2294035	2294118	.	+	0	Parent=gene265
chr11	ENCODE	exon	2294382	2294473	.	+	.	Parent=gene265
chr11	ENCODE	CDS	2294382	2294473	.	+	0	Parent=gene265
chr11	ENCODE	exon	2295150	2295331	.	+	.	Parent=gene265
chr11	ENCODE	CDS	2295150	2295331	.	+	1	Parent=gene265
chr11	ENCODE	CDS	2295669	2295730	.	+	2	Parent=gene265
chr11	ENCODE	exon	2295669	2295948	.	+	.	Parent=gene265
###
chr11	ENCODE	gene	2279832	2295948	.	+	.	ID=gene266;Name=AC129929.4-008;name2=TSPAN32
chr11	ENCODE	exon	2279832	2280028	.	+	.	Parent=gene266
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene266
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene266
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene266
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene266
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene266
chr11	ENCODE	exon	2294035	2294473	.	+	.	Parent=gene266
chr11	ENCODE	exon	2295152	2295331	.	+	.	Parent=gene266
chr11	ENCODE	exon	2295669	2295948	.	+	.	Parent=gene266
###
chr11	ENCODE	gene	2279837	2292440	.	+	.	ID=gene267;Name=AC129929.4-011;name2=TSPAN32
chr11	ENCODE	exon	2279837	2280021	.	+	.	Parent=gene267
chr11	ENCODE	CDS	2279956	2280021	.	+	0	Parent=gene267
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene267
chr11	ENCODE	CDS	2280650	2280764	.	+	0	Parent=gene267
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene267
chr11	ENCODE	CDS	2281913	2282010	.	+	2	Parent=gene267
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene267
chr11	ENCODE	CDS	2286542	2286616	.	+	0	Parent=gene267
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene267
chr11	ENCODE	CDS	2291460	2291561	.	+	0	Parent=gene267
chr11	ENCODE	exon	2292291	2292440	.	+	.	Parent=gene267
chr11	ENCODE	CDS	2292291	2292440	.	+	0	Parent=gene267
###
chr11	ENCODE	gene	2279846	2293762	.	+	.	ID=gene268;Name=AC129929.4-012;name2=TSPAN32
chr11	ENCODE	exon	2279846	2280021	.	+	.	Parent=gene268
chr11	ENCODE	CDS	2279956	2280021	.	+	0	Parent=gene268
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene268
chr11	ENCODE	CDS	2280650	2280764	.	+	0	Parent=gene268
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene268
chr11	ENCODE	CDS	2281913	2282010	.	+	2	Parent=gene268
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene268
chr11	ENCODE	CDS	2286542	2286616	.	+	0	Parent=gene268
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene268
chr11	ENCODE	CDS	2291460	2291561	.	+	0	Parent=gene268
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene268
chr11	ENCODE	CDS	2292291	2292377	.	+	0	Parent=gene268
chr11	ENCODE	exon	2293675	2293762	.	+	.	Parent=gene268
chr11	ENCODE	CDS	2293675	2293762	.	+	0	Parent=gene268
###
chr11	ENCODE	gene	2279947	2294470	.	+	.	ID=gene269;Name=AC129929.4-009;name2=TSPAN32
chr11	ENCODE	exon	2279947	2280021	.	+	.	Parent=gene269
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene269
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene269
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene269
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene269
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene269
chr11	ENCODE	exon	2294035	2294470	.	+	.	Parent=gene269
###
chr11	ENCODE	gene	2279956	2295948	.	+	.	ID=gene270;Name=AC129929.4-005;name2=TSPAN32
chr11	ENCODE	exon	2279956	2280021	.	+	.	Parent=gene270
chr11	ENCODE	CDS	2279956	2280021	.	+	0	Parent=gene270
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene270
chr11	ENCODE	CDS	2280650	2280764	.	+	0	Parent=gene270
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene270
chr11	ENCODE	CDS	2281913	2282010	.	+	2	Parent=gene270
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene270
chr11	ENCODE	CDS	2286542	2286616	.	+	0	Parent=gene270
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene270
chr11	ENCODE	CDS	2291460	2291561	.	+	0	Parent=gene270
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene270
chr11	ENCODE	CDS	2292291	2292377	.	+	0	Parent=gene270
chr11	ENCODE	exon	2294035	2294118	.	+	.	Parent=gene270
chr11	ENCODE	CDS	2294035	2294118	.	+	0	Parent=gene270
chr11	ENCODE	exon	2294382	2294473	.	+	.	Parent=gene270
chr11	ENCODE	CDS	2294382	2294473	.	+	0	Parent=gene270
chr11	ENCODE	CDS	2295669	2295711	.	+	1	Parent=gene270
chr11	ENCODE	exon	2295669	2295948	.	+	.	Parent=gene270
###
chr11	ENCODE	gene	2279960	2292472	.	+	.	ID=gene271;Name=AC129929.4-010;name2=TSPAN32
chr11	ENCODE	exon	2279960	2280028	.	+	.	Parent=gene271
chr11	ENCODE	exon	2280650	2280764	.	+	.	Parent=gene271
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene271
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene271
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene271
chr11	ENCODE	exon	2292291	2292472	.	+	.	Parent=gene271
###
chr11	ENCODE	gene	2280514	2295948	.	+	.	ID=gene272;Name=AC129929.4-004;name2=TSPAN32
chr11	ENCODE	exon	2280514	2280764	.	+	.	Parent=gene272
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene272
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene272
chr11	ENCODE	exon	2291460	2291514	.	+	.	Parent=gene272
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene272
chr11	ENCODE	exon	2294035	2294118	.	+	.	Parent=gene272
chr11	ENCODE	exon	2294382	2294473	.	+	.	Parent=gene272
chr11	ENCODE	exon	2295152	2295331	.	+	.	Parent=gene272
chr11	ENCODE	exon	2295669	2295948	.	+	.	Parent=gene272
###
chr11	ENCODE	gene	2280529	2295948	.	+	.	ID=gene273;Name=AC129929.4-003;name2=TSPAN32
chr11	ENCODE	exon	2280529	2280764	.	+	.	Parent=gene273
chr11	ENCODE	CDS	2280617	2280764	.	+	0	Parent=gene273
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene273
chr11	ENCODE	CDS	2281913	2282010	.	+	2	Parent=gene273
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene273
chr11	ENCODE	CDS	2286542	2286616	.	+	0	Parent=gene273
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene273
chr11	ENCODE	CDS	2291460	2291561	.	+	0	Parent=gene273
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene273
chr11	ENCODE	CDS	2292291	2292377	.	+	0	Parent=gene273
chr11	ENCODE	exon	2294035	2294118	.	+	.	Parent=gene273
chr11	ENCODE	CDS	2294035	2294118	.	+	0	Parent=gene273
chr11	ENCODE	exon	2294382	2294473	.	+	.	Parent=gene273
chr11	ENCODE	CDS	2294382	2294473	.	+	0	Parent=gene273
chr11	ENCODE	exon	2295150	2295331	.	+	.	Parent=gene273
chr11	ENCODE	CDS	2295150	2295331	.	+	1	Parent=gene273
chr11	ENCODE	CDS	2295669	2295730	.	+	2	Parent=gene273
chr11	ENCODE	exon	2295669	2295948	.	+	.	Parent=gene273
###
chr11	ENCODE	gene	2280674	2295730	.	+	.	ID=gene274;Name=AC129929.4-014;name2=TSPAN32
chr11	ENCODE	exon	2280674	2280764	.	+	.	Parent=gene274
chr11	ENCODE	CDS	2280674	2280764	.	+	0	Parent=gene274
chr11	ENCODE	exon	2281913	2282010	.	+	.	Parent=gene274
chr11	ENCODE	CDS	2281913	2282010	.	+	2	Parent=gene274
chr11	ENCODE	exon	2291460	2291561	.	+	.	Parent=gene274
chr11	ENCODE	CDS	2291460	2291561	.	+	0	Parent=gene274
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene274
chr11	ENCODE	CDS	2292291	2292377	.	+	0	Parent=gene274
chr11	ENCODE	exon	2294035	2294118	.	+	.	Parent=gene274
chr11	ENCODE	CDS	2294035	2294118	.	+	0	Parent=gene274
chr11	ENCODE	exon	2294382	2294473	.	+	.	Parent=gene274
chr11	ENCODE	CDS	2294382	2294473	.	+	0	Parent=gene274
chr11	ENCODE	exon	2295150	2295331	.	+	.	Parent=gene274
chr11	ENCODE	CDS	2295150	2295331	.	+	1	Parent=gene274
chr11	ENCODE	exon	2295669	2295730	.	+	.	Parent=gene274
chr11	ENCODE	CDS	2295669	2295730	.	+	2	Parent=gene274
###
chr11	ENCODE	gene	2284751	2293993	.	+	.	ID=gene275;name2=TSPAN32;Name=AC129929.4-016
chr11	ENCODE	exon	2284751	2284796	.	+	.	Parent=gene275
chr11	ENCODE	exon	2286542	2286616	.	+	.	Parent=gene275
chr11	ENCODE	exon	2291460	2291514	.	+	.	Parent=gene275
chr11	ENCODE	exon	2292291	2292377	.	+	.	Parent=gene275
chr11	ENCODE	exon	2293675	2293993	.	+	.	Parent=gene275
###
chr11	ENCODE	gene	2294442	2295948	.	+	.	ID=gene276;Name=AC129929.4-013;name2=TSPAN32
chr11	ENCODE	exon	2294442	2294473	.	+	.	Parent=gene276
chr11	ENCODE	exon	2295233	2295331	.	+	.	Parent=gene276
chr11	ENCODE	exon	2295669	2295948	.	+	.	Parent=gene276
###
chr11	ENCODE	gene	4745076	4967636	.	+	.	ID=gene277;name2=MMP26;Name=AC018375.2-002
chr11	ENCODE	exon	4745076	4745147	.	+	.	Parent=gene277
chr11	ENCODE	exon	4966076	4966116	.	+	.	Parent=gene277
chr11	ENCODE	exon	4967454	4967636	.	+	.	Parent=gene277
###
chr11	ENCODE	gene	4745076	4970235	.	+	.	ID=gene278;Name=AC018375.2-001;name2=MMP26
chr11	ENCODE	exon	4745076	4745147	.	+	.	Parent=gene278
chr11	ENCODE	exon	4965874	4966116	.	+	.	Parent=gene278
chr11	ENCODE	CDS	4966018	4966116	.	+	0	Parent=gene278
chr11	ENCODE	exon	4967454	4967674	.	+	.	Parent=gene278
chr11	ENCODE	CDS	4967454	4967674	.	+	0	Parent=gene278
chr11	ENCODE	exon	4968404	4968552	.	+	.	Parent=gene278
chr11	ENCODE	CDS	4968404	4968552	.	+	1	Parent=gene278
chr11	ENCODE	exon	4969177	4969302	.	+	.	Parent=gene278
chr11	ENCODE	CDS	4969177	4969302	.	+	2	Parent=gene278
chr11	ENCODE	exon	4969770	4969931	.	+	.	Parent=gene278
chr11	ENCODE	CDS	4969770	4969931	.	+	2	Parent=gene278
chr11	ENCODE	CDS	4970020	4970048	.	+	2	Parent=gene278
chr11	ENCODE	exon	4970020	4970235	.	+	.	Parent=gene278
###
chr11	ENCODE	gene	4746785	4747744	.	-	.	ID=gene279;Name=AC103710.1-001;name2=OR51F1
chr11	ENCODE	exon	4746785	4747744	.	-	.	Parent=gene279
chr11	ENCODE	CDS	4746785	4747744	.	-	0	Parent=gene279
###
chr11	ENCODE	gene	4781239	4782186	.	-	.	ID=gene280;name2=OR52R1;Name=AC103710.3-001
chr11	ENCODE	exon	4781239	4782186	.	-	.	Parent=gene280
chr11	ENCODE	CDS	4781239	4782186	.	-	0	Parent=gene280
###
chr11	ENCODE	gene	4799192	4800220	.	+	.	ID=gene281;Name=AC103710.5-001;name2=OR51F2
chr11	ENCODE	exon	4799192	4800220	.	+	.	Parent=gene281
chr11	ENCODE	CDS	4799192	4800220	.	+	0	Parent=gene281
###
chr11	ENCODE	gene	4826043	4827014	.	-	.	ID=gene282;Name=AC103710.7-001;name2=OR51S1
chr11	ENCODE	exon	4826043	4827014	.	-	.	Parent=gene282
chr11	ENCODE	CDS	4826043	4827014	.	-	0	Parent=gene282
###
chr11	ENCODE	gene	4837462	4838370	.	-	.	ID=gene283;Name=AC011711.1-001;name2=OR51H1P
chr11	ENCODE	exon	4837462	4838370	.	-	.	Parent=gene283
chr11	ENCODE	CDS	4837462	4838370	.	-	0	Parent=gene283
###
chr11	ENCODE	gene	4859706	4860689	.	+	.	ID=gene284;Name=AC011711.3-001;name2=OR51T1
chr11	ENCODE	exon	4859706	4860689	.	+	.	Parent=gene284
chr11	ENCODE	CDS	4859706	4860689	.	+	0	Parent=gene284
###
chr11	ENCODE	gene	4885176	4886114	.	+	.	ID=gene285;Name=AC018375.4-001;name2=OR51A7
chr11	ENCODE	exon	4885176	4886114	.	+	.	Parent=gene285
chr11	ENCODE	CDS	4885176	4886114	.	+	0	Parent=gene285
###
chr11	ENCODE	gene	4892525	4893469	.	-	.	ID=gene286;Name=AC018375.5-001;name2=OR51G2
chr11	ENCODE	exon	4892525	4893469	.	-	.	Parent=gene286
chr11	ENCODE	CDS	4892525	4893469	.	-	0	Parent=gene286
###
chr11	ENCODE	gene	4901180	4902145	.	-	.	ID=gene287;Name=AC018375.6-001;name2=OR51G1
chr11	ENCODE	exon	4901180	4902145	.	-	.	Parent=gene287
chr11	ENCODE	CDS	4901180	4902145	.	-	0	Parent=gene287
###
chr11	ENCODE	gene	4923965	4924906	.	-	.	ID=gene288;Name=AC018375.8-001;name2=OR51A4
chr11	ENCODE	exon	4923965	4924906	.	-	.	Parent=gene288
chr11	ENCODE	CDS	4923965	4924906	.	-	0	Parent=gene288
###
chr11	ENCODE	gene	4932578	4933519	.	-	.	ID=gene289;Name=AC018375.9-001;name2=OR51A2
chr11	ENCODE	exon	4932578	4933519	.	-	.	Parent=gene289
chr11	ENCODE	CDS	4932578	4933519	.	-	0	Parent=gene289
###
chr11	ENCODE	gene	4976789	4977736	.	+	.	ID=gene290;name2=OR51L1;Name=AC018375.11-001
chr11	ENCODE	exon	4976789	4977736	.	+	.	Parent=gene290
chr11	ENCODE	CDS	4976789	4977736	.	+	0	Parent=gene290
###
chr11	ENCODE	gene	5024332	5025267	.	+	.	ID=gene291;Name=AC113331.3-001;name2=OR52J3
chr11	ENCODE	exon	5024332	5025267	.	+	.	Parent=gene291
chr11	ENCODE	CDS	5024332	5025267	.	+	0	Parent=gene291
###
chr11	ENCODE	gene	5036456	5037433	.	-	.	ID=gene292;name2=OR52E2;Name=AC113331.4-001
chr11	ENCODE	exon	5036456	5037433	.	-	.	Parent=gene292
chr11	ENCODE	CDS	5036456	5037433	.	-	0	Parent=gene292
###
chr11	ENCODE	gene	5109498	5110448	.	-	.	ID=gene293;Name=AC129505.2-001;name2=OR52A5
chr11	ENCODE	exon	5109498	5110448	.	-	.	Parent=gene293
chr11	ENCODE	CDS	5109498	5110448	.	-	0	Parent=gene293
###
chr11	ENCODE	gene	5128815	5164188	.	-	.	ID=gene294;Name=AC129505.3-001;name2=OR52A1
chr11	ENCODE	exon	5128815	5130496	.	-	.	Parent=gene294
chr11	ENCODE	CDS	5129237	5130175	.	-	0	Parent=gene294
chr11	ENCODE	exon	5164092	5164188	.	-	.	Parent=gene294
###
chr11	ENCODE	gene	5177541	5178506	.	-	.	ID=gene295;Name=AC104389.15-001;name2=OR51V1
chr11	ENCODE	exon	5177541	5178506	.	-	.	Parent=gene295
chr11	ENCODE	CDS	5177541	5178506	.	-	0	Parent=gene295
###
chr11	ENCODE	gene	5203270	5205003	.	-	.	ID=gene296;Name=AC104389.17-001;name2=HBB
chr11	ENCODE	exon	5203270	5203532	.	-	.	Parent=gene296
chr11	ENCODE	CDS	5203404	5203532	.	-	0	Parent=gene296
chr11	ENCODE	exon	5204383	5204605	.	-	.	Parent=gene296
chr11	ENCODE	CDS	5204383	5204605	.	-	1	Parent=gene296
chr11	ENCODE	CDS	5204736	5204827	.	-	0	Parent=gene296
chr11	ENCODE	exon	5204736	5205003	.	-	.	Parent=gene296
###
chr11	ENCODE	gene	5203461	5204629	.	-	.	ID=gene297;Name=AC104389.17-003;name2=HBB
chr11	ENCODE	exon	5203461	5203532	.	-	.	Parent=gene297
chr11	ENCODE	exon	5204383	5204629	.	-	.	Parent=gene297
###
chr11	ENCODE	gene	5204069	5204878	.	-	.	ID=gene298;name2=HBB;Name=AC104389.17-002
chr11	ENCODE	exon	5204069	5204605	.	-	.	Parent=gene298
chr11	ENCODE	exon	5204736	5204878	.	-	.	Parent=gene298
###
chr11	ENCODE	gene	5204426	5207201	.	-	.	ID=gene299;Name=AC104389.17-004;name2=HBB
chr11	ENCODE	exon	5204426	5204605	.	-	.	Parent=gene299
chr11	ENCODE	CDS	5204426	5204605	.	-	1	Parent=gene299
chr11	ENCODE	CDS	5204736	5204827	.	-	0	Parent=gene299
chr11	ENCODE	exon	5204736	5204845	.	-	.	Parent=gene299
chr11	ENCODE	exon	5205318	5205385	.	-	.	Parent=gene299
chr11	ENCODE	exon	5207058	5207201	.	-	.	Parent=gene299
###
chr11	ENCODE	gene	5210484	5212289	.	-	.	ID=gene300;Name=AC104389.18-003;name2=HBD
chr11	ENCODE	exon	5210484	5210604	.	-	.	Parent=gene300
chr11	ENCODE	CDS	5210494	5210604	.	-	0	Parent=gene300
chr11	ENCODE	exon	5211797	5212019	.	-	.	Parent=gene300
chr11	ENCODE	CDS	5211797	5212019	.	-	1	Parent=gene300
chr11	ENCODE	CDS	5212148	5212239	.	-	0	Parent=gene300
chr11	ENCODE	exon	5212148	5212289	.	-	.	Parent=gene300
###
chr11	ENCODE	gene	5210644	5212454	.	-	.	ID=gene301;Name=AC104389.18-001;name2=HBD
chr11	ENCODE	exon	5210644	5210898	.	-	.	Parent=gene301
chr11	ENCODE	CDS	5210770	5210898	.	-	0	Parent=gene301
chr11	ENCODE	exon	5211797	5212019	.	-	.	Parent=gene301
chr11	ENCODE	CDS	5211797	5212019	.	-	1	Parent=gene301
chr11	ENCODE	CDS	5212148	5212239	.	-	0	Parent=gene301
chr11	ENCODE	exon	5212148	5212454	.	-	.	Parent=gene301
###
chr11	ENCODE	gene	5210736	5212289	.	-	.	ID=gene302;Name=AC104389.18-002;name2=HBD
chr11	ENCODE	exon	5210736	5210898	.	-	.	Parent=gene302
chr11	ENCODE	CDS	5210736	5210898	.	-	1	Parent=gene302
chr11	ENCODE	CDS	5212148	5212239	.	-	0	Parent=gene302
chr11	ENCODE	exon	5212148	5212289	.	-	.	Parent=gene302
###
chr11	ENCODE	gene	5211799	5213176	.	-	.	ID=gene303;Name=AC104389.18-004;name2=HBD
chr11	ENCODE	exon	5211799	5212019	.	-	.	Parent=gene303
chr11	ENCODE	CDS	5211799	5212019	.	-	1	Parent=gene303
chr11	ENCODE	CDS	5212148	5212239	.	-	0	Parent=gene303
chr11	ENCODE	exon	5212148	5212336	.	-	.	Parent=gene303
chr11	ENCODE	exon	5213021	5213176	.	-	.	Parent=gene303
###
chr11	ENCODE	gene	5225889	5227698	.	-	.	ID=gene304;Name=AC104389.20-001;name2=HBG1
chr11	ENCODE	exon	5225889	5226293	.	-	.	Parent=gene304
chr11	ENCODE	CDS	5226165	5226293	.	-	0	Parent=gene304
chr11	ENCODE	exon	5227174	5227396	.	-	.	Parent=gene304
chr11	ENCODE	CDS	5227174	5227396	.	-	1	Parent=gene304
chr11	ENCODE	CDS	5227519	5227610	.	-	0	Parent=gene304
chr11	ENCODE	exon	5227519	5227698	.	-	.	Parent=gene304
###
chr11	ENCODE	gene	5230996	5483411	.	-	.	ID=gene305;Name=AC104389.21-004;name2=HBG2
chr11	ENCODE	exon	5230996	5231211	.	-	.	Parent=gene305
chr11	ENCODE	CDS	5231083	5231211	.	-	0	Parent=gene305
chr11	ENCODE	exon	5232098	5232320	.	-	.	Parent=gene305
chr11	ENCODE	CDS	5232098	5232320	.	-	1	Parent=gene305
chr11	ENCODE	CDS	5483157	5483218	.	-	0	Parent=gene305
chr11	ENCODE	exon	5483157	5483411	.	-	.	Parent=gene305
###
chr11	ENCODE	gene	5230996	5623595	.	-	.	ID=gene306;Name=AC104389.21-001;name2=HBG2
chr11	ENCODE	exon	5230996	5231211	.	-	.	Parent=gene306
chr11	ENCODE	CDS	5231083	5231211	.	-	0	Parent=gene306
chr11	ENCODE	exon	5232098	5232320	.	-	.	Parent=gene306
chr11	ENCODE	CDS	5232098	5232320	.	-	1	Parent=gene306
chr11	ENCODE	CDS	5232443	5232534	.	-	0	Parent=gene306
chr11	ENCODE	exon	5232443	5232971	.	-	.	Parent=gene306
chr11	ENCODE	exon	5323579	5323705	.	-	.	Parent=gene306
chr11	ENCODE	exon	5568631	5568829	.	-	.	Parent=gene306
chr11	ENCODE	exon	5573038	5573156	.	-	.	Parent=gene306
chr11	ENCODE	exon	5604407	5604660	.	-	.	Parent=gene306
chr11	ENCODE	exon	5623491	5623595	.	-	.	Parent=gene306
###
chr11	ENCODE	gene	5230999	5232575	.	-	.	ID=gene307;Name=AC104389.21-002;name2=HBG2
chr11	ENCODE	exon	5230999	5231211	.	-	.	Parent=gene307
chr11	ENCODE	exon	5232098	5232320	.	-	.	Parent=gene307
chr11	ENCODE	exon	5232443	5232496	.	-	.	Parent=gene307
chr11	ENCODE	exon	5232528	5232575	.	-	.	Parent=gene307
###
chr11	ENCODE	gene	5231195	5232547	.	-	.	ID=gene308;Name=AC104389.21-003;name2=HBG2
chr11	ENCODE	exon	5231195	5231211	.	-	.	Parent=gene308
chr11	ENCODE	exon	5232098	5232320	.	-	.	Parent=gene308
chr11	ENCODE	exon	5232481	5232547	.	-	.	Parent=gene308
###
chr11	ENCODE	gene	5246158	5483410	.	-	.	ID=gene309;Name=AC104389.22-001;name2=HBE1
chr11	ENCODE	exon	5246158	5246403	.	-	.	Parent=gene309
chr11	ENCODE	CDS	5246275	5246403	.	-	0	Parent=gene309
chr11	ENCODE	exon	5247260	5247482	.	-	.	Parent=gene309
chr11	ENCODE	CDS	5247260	5247482	.	-	1	Parent=gene309
chr11	ENCODE	CDS	5247605	5247696	.	-	0	Parent=gene309
chr11	ENCODE	exon	5247605	5247962	.	-	.	Parent=gene309
chr11	ENCODE	exon	5259715	5259757	.	-	.	Parent=gene309
chr11	ENCODE	exon	5483375	5483410	.	-	.	Parent=gene309
###
chr11	ENCODE	gene	5247312	5483423	.	-	.	ID=gene310;Name=AC104389.22-002;name2=HBE1
chr11	ENCODE	exon	5247312	5247482	.	-	.	Parent=gene310
chr11	ENCODE	CDS	5247312	5247482	.	-	1	Parent=gene310
chr11	ENCODE	CDS	5247605	5247696	.	-	0	Parent=gene310
chr11	ENCODE	exon	5247605	5247962	.	-	.	Parent=gene310
chr11	ENCODE	exon	5483375	5483423	.	-	.	Parent=gene310
###
chr11	ENCODE	gene	5278820	5279802	.	-	.	ID=gene311;Name=AC104389.23-001;name2=OR51B4
chr11	ENCODE	CDS	5278820	5279752	.	-	0	Parent=gene311
chr11	ENCODE	exon	5278820	5279802	.	-	.	Parent=gene311
###
chr11	ENCODE	gene	5301165	5302103	.	-	.	ID=gene312;Name=AC104389.26-001;name2=OR51B2
chr11	ENCODE	exon	5301165	5302103	.	-	.	Parent=gene312
chr11	ENCODE	CDS	5301165	5302103	.	-	0	Parent=gene312
###
chr11	ENCODE	gene	5320392	5321330	.	-	.	ID=gene313;Name=AC104389.29-001;name2=OR51B5
chr11	ENCODE	exon	5320392	5321330	.	-	.	Parent=gene313
chr11	ENCODE	CDS	5320392	5321330	.	-	0	Parent=gene313
###
chr11	ENCODE	gene	5329314	5330252	.	+	.	ID=gene314;Name=AC104389.30-001;name2=OR51B6
chr11	ENCODE	exon	5329314	5330252	.	+	.	Parent=gene314
chr11	ENCODE	CDS	5329314	5330252	.	+	0	Parent=gene314
###
chr11	ENCODE	gene	5367205	5368185	.	+	.	ID=gene315;Name=AC104389.33-001;name2=OR51M1
chr11	ENCODE	exon	5367205	5368185	.	+	.	Parent=gene315
chr11	ENCODE	CDS	5367205	5368185	.	+	0	Parent=gene315
###
chr11	ENCODE	gene	5380403	5381353	.	+	.	ID=gene316;Name=AC104389.34-001;name2=OR51J1
chr11	ENCODE	exon	5380403	5381353	.	+	.	Parent=gene316
chr11	ENCODE	CDS	5380403	5381353	.	+	0	Parent=gene316
###
chr11	ENCODE	gene	5400007	5400960	.	+	.	ID=gene317;Name=AC087380.6-001;name2=OR51Q1
chr11	ENCODE	exon	5400007	5400960	.	+	.	Parent=gene317
chr11	ENCODE	CDS	5400007	5400960	.	+	0	Parent=gene317
###
chr11	ENCODE	gene	5418376	5419320	.	-	.	ID=gene318;Name=AC087380.8-001;name2=OR51I1
chr11	ENCODE	exon	5418376	5419320	.	-	.	Parent=gene318
chr11	ENCODE	CDS	5418376	5419320	.	-	0	Parent=gene318
###
chr11	ENCODE	gene	5431295	5432233	.	+	.	ID=gene319;Name=AC087380.9-001;name2=OR51I2
chr11	ENCODE	exon	5431295	5432233	.	+	.	Parent=gene319
chr11	ENCODE	CDS	5431295	5432233	.	+	0	Parent=gene319
###
chr11	ENCODE	gene	5466513	5467469	.	+	.	ID=gene320;Name=AC087380.11-001;name2=OR52D1
chr11	ENCODE	exon	5466513	5467469	.	+	.	Parent=gene320
chr11	ENCODE	CDS	5466513	5467469	.	+	0	Parent=gene320
###
chr11	ENCODE	gene	5485106	5487791	.	-	.	ID=gene321;Name=AC087380.12-001;name2=UBQLN3
chr11	ENCODE	exon	5485106	5487400	.	-	.	Parent=gene321
chr11	ENCODE	CDS	5485397	5487364	.	-	0	Parent=gene321
chr11	ENCODE	exon	5487680	5487791	.	-	.	Parent=gene321
###
chr11	ENCODE	gene	5486702	5487764	.	-	.	ID=gene322;Name=AC087380.12-002;name2=UBQLN3
chr11	ENCODE	CDS	5486702	5487364	.	-	0	Parent=gene322
chr11	ENCODE	exon	5486702	5487433	.	-	.	Parent=gene322
chr11	ENCODE	exon	5487680	5487764	.	-	.	Parent=gene322
###
chr11	ENCODE	gene	5492199	5494511	.	-	.	ID=gene323;Name=AC087380.13-001;name2=AC087380.13
chr11	ENCODE	exon	5492199	5494511	.	-	.	Parent=gene323
chr11	ENCODE	CDS	5492820	5494247	.	-	0	Parent=gene323
###
chr11	ENCODE	gene	5522367	5523329	.	-	.	ID=gene324;name2=OR52H1;Name=AC087380.16-001
chr11	ENCODE	exon	5522367	5523329	.	-	.	Parent=gene324
chr11	ENCODE	CDS	5522367	5523329	.	-	0	Parent=gene324
###
chr11	ENCODE	gene	5558683	5559690	.	+	.	ID=gene325;Name=AC015691.8-001;name2=OR52B6
chr11	ENCODE	exon	5558683	5559690	.	+	.	Parent=gene325
chr11	ENCODE	CDS	5558683	5559690	.	+	0	Parent=gene325
###
chr11	ENCODE	gene	5573915	5590758	.	+	.	ID=gene326;Name=AC015691.9-001;name2=TRIM6
chr11	ENCODE	exon	5573915	5573987	.	+	.	Parent=gene326
chr11	ENCODE	exon	5581052	5581541	.	+	.	Parent=gene326
chr11	ENCODE	CDS	5581119	5581541	.	+	0	Parent=gene326
chr11	ENCODE	exon	5582340	5582435	.	+	.	Parent=gene326
chr11	ENCODE	CDS	5582340	5582435	.	+	0	Parent=gene326
chr11	ENCODE	exon	5583143	5583373	.	+	.	Parent=gene326
chr11	ENCODE	CDS	5583143	5583373	.	+	0	Parent=gene326
chr11	ENCODE	exon	5586178	5586200	.	+	.	Parent=gene326
chr11	ENCODE	CDS	5586178	5586200	.	+	0	Parent=gene326
chr11	ENCODE	exon	5587951	5588051	.	+	.	Parent=gene326
chr11	ENCODE	CDS	5587951	5588051	.	+	1	Parent=gene326
chr11	ENCODE	exon	5588341	5588367	.	+	.	Parent=gene326
chr11	ENCODE	CDS	5588341	5588367	.	+	2	Parent=gene326
chr11	ENCODE	CDS	5588583	5589148	.	+	2	Parent=gene326
chr11	ENCODE	exon	5588583	5590758	.	+	.	Parent=gene326
###
chr11	ENCODE	gene	5573916	5587996	.	+	.	ID=gene327;Name=AC015691.9-007;name2=TRIM6
chr11	ENCODE	exon	5573916	5573987	.	+	.	Parent=gene327
chr11	ENCODE	exon	5582340	5582435	.	+	.	Parent=gene327
chr11	ENCODE	exon	5583143	5583373	.	+	.	Parent=gene327
chr11	ENCODE	exon	5586178	5586200	.	+	.	Parent=gene327
chr11	ENCODE	exon	5587951	5587996	.	+	.	Parent=gene327
###
chr11	ENCODE	gene	5573935	5590229	.	+	.	ID=gene328;Name=AC015691.9-002;name2=TRIM6
chr11	ENCODE	exon	5573935	5573987	.	+	.	Parent=gene328
chr11	ENCODE	exon	5581052	5581367	.	+	.	Parent=gene328
chr11	ENCODE	CDS	5581119	5581367	.	+	0	Parent=gene328
chr11	ENCODE	exon	5581446	5581541	.	+	.	Parent=gene328
chr11	ENCODE	CDS	5581446	5581541	.	+	0	Parent=gene328
chr11	ENCODE	exon	5582340	5582435	.	+	.	Parent=gene328
chr11	ENCODE	CDS	5582340	5582435	.	+	0	Parent=gene328
chr11	ENCODE	exon	5583143	5583373	.	+	.	Parent=gene328
chr11	ENCODE	CDS	5583143	5583373	.	+	0	Parent=gene328
chr11	ENCODE	exon	5586178	5586200	.	+	.	Parent=gene328
chr11	ENCODE	CDS	5586178	5586200	.	+	0	Parent=gene328
chr11	ENCODE	exon	5587951	5588051	.	+	.	Parent=gene328
chr11	ENCODE	CDS	5587951	5588051	.	+	1	Parent=gene328
chr11	ENCODE	exon	5588341	5588367	.	+	.	Parent=gene328
chr11	ENCODE	CDS	5588341	5588367	.	+	2	Parent=gene328
chr11	ENCODE	CDS	5588583	5589148	.	+	2	Parent=gene328
chr11	ENCODE	exon	5588583	5590229	.	+	.	Parent=gene328
###
chr11	ENCODE	gene	5574462	5590758	.	+	.	ID=gene329;Name=AC015691.9-003;name2=TRIM6
chr11	ENCODE	exon	5574462	5574720	.	+	.	Parent=gene329
chr11	ENCODE	CDS	5574704	5574720	.	+	0	Parent=gene329
chr11	ENCODE	exon	5581052	5581541	.	+	.	Parent=gene329
chr11	ENCODE	CDS	5581052	5581541	.	+	1	Parent=gene329
chr11	ENCODE	exon	5582340	5582435	.	+	.	Parent=gene329
chr11	ENCODE	CDS	5582340	5582435	.	+	0	Parent=gene329
chr11	ENCODE	exon	5583143	5583373	.	+	.	Parent=gene329
chr11	ENCODE	CDS	5583143	5583373	.	+	0	Parent=gene329
chr11	ENCODE	exon	5586178	5586200	.	+	.	Parent=gene329
chr11	ENCODE	CDS	5586178	5586200	.	+	0	Parent=gene329
chr11	ENCODE	exon	5587951	5588051	.	+	.	Parent=gene329
chr11	ENCODE	CDS	5587951	5588051	.	+	1	Parent=gene329
chr11	ENCODE	exon	5588341	5588367	.	+	.	Parent=gene329
chr11	ENCODE	CDS	5588341	5588367	.	+	2	Parent=gene329
chr11	ENCODE	CDS	5588583	5589148	.	+	2	Parent=gene329
chr11	ENCODE	exon	5588583	5590758	.	+	.	Parent=gene329
###
chr11	ENCODE	gene	5574531	5622204	.	+	.	ID=gene330;Name=AC015691.11-001;name2=TRIM6-TRIM34
chr11	ENCODE	exon	5574531	5574720	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5574704	5574720	.	+	0	Parent=gene330
chr11	ENCODE	exon	5581052	5581541	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5581052	5581541	.	+	1	Parent=gene330
chr11	ENCODE	exon	5582340	5582435	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5582340	5582435	.	+	0	Parent=gene330
chr11	ENCODE	exon	5583143	5583373	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5583143	5583373	.	+	0	Parent=gene330
chr11	ENCODE	exon	5586178	5586200	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5586178	5586200	.	+	0	Parent=gene330
chr11	ENCODE	exon	5587951	5588051	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5587951	5588051	.	+	1	Parent=gene330
chr11	ENCODE	exon	5588341	5588367	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5588341	5588367	.	+	2	Parent=gene330
chr11	ENCODE	exon	5610061	5610560	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5610061	5610560	.	+	2	Parent=gene330
chr11	ENCODE	exon	5611610	5611705	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5611610	5611705	.	+	0	Parent=gene330
chr11	ENCODE	exon	5612437	5612667	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5612437	5612667	.	+	0	Parent=gene330
chr11	ENCODE	exon	5618973	5618995	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5618973	5618995	.	+	0	Parent=gene330
chr11	ENCODE	exon	5620212	5620312	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5620212	5620312	.	+	1	Parent=gene330
chr11	ENCODE	exon	5620623	5620649	.	+	.	Parent=gene330
chr11	ENCODE	CDS	5620623	5620649	.	+	2	Parent=gene330
chr11	ENCODE	CDS	5620950	5621515	.	+	2	Parent=gene330
chr11	ENCODE	exon	5620950	5622204	.	+	.	Parent=gene330
###
chr11	ENCODE	gene	5574552	5590758	.	+	.	ID=gene331;Name=AC015691.9-004;name2=TRIM6
chr11	ENCODE	exon	5574552	5574720	.	+	.	Parent=gene331
chr11	ENCODE	exon	5581414	5581541	.	+	.	Parent=gene331
chr11	ENCODE	exon	5582340	5582435	.	+	.	Parent=gene331
chr11	ENCODE	exon	5583143	5583373	.	+	.	Parent=gene331
chr11	ENCODE	exon	5586178	5586200	.	+	.	Parent=gene331
chr11	ENCODE	exon	5587951	5588051	.	+	.	Parent=gene331
chr11	ENCODE	exon	5588341	5588367	.	+	.	Parent=gene331
chr11	ENCODE	exon	5588583	5590758	.	+	.	Parent=gene331
###
chr11	ENCODE	gene	5582978	5589085	.	+	.	ID=gene332;Name=AC015691.9-005;name2=TRIM6
chr11	ENCODE	exon	5582978	5583373	.	+	.	Parent=gene332
chr11	ENCODE	exon	5586178	5586200	.	+	.	Parent=gene332
chr11	ENCODE	exon	5587951	5588051	.	+	.	Parent=gene332
chr11	ENCODE	exon	5588341	5588367	.	+	.	Parent=gene332
chr11	ENCODE	exon	5588583	5589085	.	+	.	Parent=gene332
###
chr11	ENCODE	gene	5583355	5590764	.	+	.	ID=gene333;name2=TRIM6;Name=AC015691.9-006
chr11	ENCODE	exon	5583355	5583373	.	+	.	Parent=gene333
chr11	ENCODE	exon	5586178	5586200	.	+	.	Parent=gene333
chr11	ENCODE	exon	5587951	5588051	.	+	.	Parent=gene333
chr11	ENCODE	exon	5588211	5588367	.	+	.	Parent=gene333
chr11	ENCODE	exon	5588583	5590764	.	+	.	Parent=gene333
###
chr11	ENCODE	gene	5597570	5622204	.	+	.	ID=gene334;Name=AC015691.10-003;name2=TRIM34
chr11	ENCODE	exon	5597570	5597829	.	+	.	Parent=gene334
chr11	ENCODE	exon	5610061	5610560	.	+	.	Parent=gene334
chr11	ENCODE	CDS	5610138	5610560	.	+	0	Parent=gene334
chr11	ENCODE	exon	5611610	5611705	.	+	.	Parent=gene334
chr11	ENCODE	CDS	5611610	5611705	.	+	0	Parent=gene334
chr11	ENCODE	exon	5612437	5612667	.	+	.	Parent=gene334
chr11	ENCODE	CDS	5612437	5612667	.	+	0	Parent=gene334
chr11	ENCODE	exon	5618973	5618995	.	+	.	Parent=gene334
chr11	ENCODE	CDS	5618973	5618995	.	+	0	Parent=gene334
chr11	ENCODE	exon	5620212	5620312	.	+	.	Parent=gene334
chr11	ENCODE	CDS	5620212	5620312	.	+	1	Parent=gene334
chr11	ENCODE	exon	5620623	5620649	.	+	.	Parent=gene334
chr11	ENCODE	CDS	5620623	5620649	.	+	2	Parent=gene334
chr11	ENCODE	CDS	5620950	5621515	.	+	2	Parent=gene334
chr11	ENCODE	exon	5620950	5622204	.	+	.	Parent=gene334
###
chr11	ENCODE	gene	5602789	5622204	.	+	.	ID=gene335;Name=AC015691.10-001;name2=TRIM34
chr11	ENCODE	exon	5602789	5602866	.	+	.	Parent=gene335
chr11	ENCODE	exon	5610061	5610560	.	+	.	Parent=gene335
chr11	ENCODE	CDS	5610138	5610560	.	+	0	Parent=gene335
chr11	ENCODE	exon	5611610	5611705	.	+	.	Parent=gene335
chr11	ENCODE	CDS	5611610	5611705	.	+	0	Parent=gene335
chr11	ENCODE	exon	5612437	5612667	.	+	.	Parent=gene335
chr11	ENCODE	CDS	5612437	5612667	.	+	0	Parent=gene335
chr11	ENCODE	exon	5618973	5618995	.	+	.	Parent=gene335
chr11	ENCODE	CDS	5618973	5618995	.	+	0	Parent=gene335
chr11	ENCODE	exon	5620212	5620312	.	+	.	Parent=gene335
chr11	ENCODE	CDS	5620212	5620312	.	+	1	Parent=gene335
chr11	ENCODE	exon	5620623	5620649	.	+	.	Parent=gene335
chr11	ENCODE	CDS	5620623	5620649	.	+	2	Parent=gene335
chr11	ENCODE	CDS	5620950	5621515	.	+	2	Parent=gene335
chr11	ENCODE	exon	5620950	5622204	.	+	.	Parent=gene335
###
chr11	ENCODE	gene	5602823	5622204	.	+	.	ID=gene336;Name=AC015691.10-002;name2=TRIM34
chr11	ENCODE	exon	5602823	5602866	.	+	.	Parent=gene336
chr11	ENCODE	exon	5610061	5610475	.	+	.	Parent=gene336
chr11	ENCODE	exon	5610543	5610560	.	+	.	Parent=gene336
chr11	ENCODE	exon	5611610	5611705	.	+	.	Parent=gene336
chr11	ENCODE	exon	5612437	5612667	.	+	.	Parent=gene336
chr11	ENCODE	exon	5618973	5618995	.	+	.	Parent=gene336
chr11	ENCODE	exon	5620212	5620312	.	+	.	Parent=gene336
chr11	ENCODE	exon	5620623	5620649	.	+	.	Parent=gene336
chr11	ENCODE	exon	5620950	5622204	.	+	.	Parent=gene336
###
chr11	ENCODE	gene	5610087	5619104	.	+	.	ID=gene337;Name=AC015691.10-004;name2=TRIM34
chr11	ENCODE	exon	5610087	5610560	.	+	.	Parent=gene337
chr11	ENCODE	exon	5611610	5611705	.	+	.	Parent=gene337
chr11	ENCODE	exon	5612437	5612667	.	+	.	Parent=gene337
chr11	ENCODE	exon	5618973	5619104	.	+	.	Parent=gene337
###
chr11	ENCODE	gene	5612644	5621615	.	+	.	ID=gene338;Name=AC015691.10-005;name2=TRIM34
chr11	ENCODE	exon	5612644	5612667	.	+	.	Parent=gene338
chr11	ENCODE	exon	5618973	5618995	.	+	.	Parent=gene338
chr11	ENCODE	exon	5620212	5620312	.	+	.	Parent=gene338
chr11	ENCODE	exon	5620623	5620659	.	+	.	Parent=gene338
chr11	ENCODE	exon	5620950	5621615	.	+	.	Parent=gene338
###
chr11	ENCODE	gene	5641363	5662869	.	-	.	ID=gene339;Name=AC015691.12-001;name2=TRIM5
chr11	ENCODE	exon	5641363	5643201	.	-	.	Parent=gene339
chr11	ENCODE	CDS	5642615	5643201	.	-	2	Parent=gene339
chr11	ENCODE	exon	5643462	5643488	.	-	.	Parent=gene339
chr11	ENCODE	CDS	5643462	5643488	.	-	2	Parent=gene339
chr11	ENCODE	exon	5643787	5643887	.	-	.	Parent=gene339
chr11	ENCODE	CDS	5643787	5643887	.	-	1	Parent=gene339
chr11	ENCODE	exon	5645495	5645517	.	-	.	Parent=gene339
chr11	ENCODE	CDS	5645495	5645517	.	-	0	Parent=gene339
chr11	ENCODE	exon	5656010	5656240	.	-	.	Parent=gene339
chr11	ENCODE	CDS	5656010	5656240	.	-	0	Parent=gene339
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene339
chr11	ENCODE	CDS	5656880	5656975	.	-	0	Parent=gene339
chr11	ENCODE	CDS	5657567	5657983	.	-	0	Parent=gene339
chr11	ENCODE	exon	5657567	5658044	.	-	.	Parent=gene339
chr11	ENCODE	exon	5662674	5662869	.	-	.	Parent=gene339
###
chr11	ENCODE	gene	5641369	5663200	.	-	.	ID=gene340;Name=AC015691.12-003;name2=TRIM5
chr11	ENCODE	exon	5641369	5641979	.	-	.	Parent=gene340
chr11	ENCODE	exon	5643462	5643488	.	-	.	Parent=gene340
chr11	ENCODE	exon	5643787	5643887	.	-	.	Parent=gene340
chr11	ENCODE	exon	5645495	5645517	.	-	.	Parent=gene340
chr11	ENCODE	exon	5656010	5656240	.	-	.	Parent=gene340
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene340
chr11	ENCODE	exon	5657567	5658044	.	-	.	Parent=gene340
chr11	ENCODE	exon	5662822	5663200	.	-	.	Parent=gene340
###
chr11	ENCODE	gene	5641370	5658038	.	-	.	ID=gene341;Name=AC015691.12-005;name2=TRIM5
chr11	ENCODE	exon	5641370	5643201	.	-	.	Parent=gene341
chr11	ENCODE	exon	5643462	5643488	.	-	.	Parent=gene341
chr11	ENCODE	exon	5643787	5643887	.	-	.	Parent=gene341
chr11	ENCODE	exon	5656010	5656240	.	-	.	Parent=gene341
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene341
chr11	ENCODE	exon	5657567	5658038	.	-	.	Parent=gene341
###
chr11	ENCODE	gene	5641410	5662862	.	-	.	ID=gene342;Name=AC015691.12-002;name2=TRIM5
chr11	ENCODE	exon	5641410	5643488	.	-	.	Parent=gene342
chr11	ENCODE	exon	5645495	5645517	.	-	.	Parent=gene342
chr11	ENCODE	exon	5656010	5657961	.	-	.	Parent=gene342
chr11	ENCODE	exon	5658020	5658044	.	-	.	Parent=gene342
chr11	ENCODE	exon	5662674	5662862	.	-	.	Parent=gene342
###
chr11	ENCODE	gene	5641423	5662848	.	-	.	ID=gene343;Name=AC015691.12-004;name2=TRIM5
chr11	ENCODE	exon	5641423	5643488	.	-	.	Parent=gene343
chr11	ENCODE	CDS	5643313	5643488	.	-	2	Parent=gene343
chr11	ENCODE	exon	5643787	5643887	.	-	.	Parent=gene343
chr11	ENCODE	CDS	5643787	5643887	.	-	1	Parent=gene343
chr11	ENCODE	exon	5645495	5645517	.	-	.	Parent=gene343
chr11	ENCODE	CDS	5645495	5645517	.	-	0	Parent=gene343
chr11	ENCODE	exon	5656010	5656240	.	-	.	Parent=gene343
chr11	ENCODE	CDS	5656010	5656240	.	-	0	Parent=gene343
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene343
chr11	ENCODE	CDS	5656880	5656975	.	-	0	Parent=gene343
chr11	ENCODE	CDS	5657567	5657983	.	-	0	Parent=gene343
chr11	ENCODE	exon	5657567	5658044	.	-	.	Parent=gene343
chr11	ENCODE	exon	5662674	5662848	.	-	.	Parent=gene343
###
chr11	ENCODE	gene	5641637	5657613	.	-	.	ID=gene344;Name=AC015691.12-009;name2=TRIM5
chr11	ENCODE	exon	5641637	5641979	.	-	.	Parent=gene344
chr11	ENCODE	CDS	5641841	5641979	.	-	2	Parent=gene344
chr11	ENCODE	exon	5643462	5643488	.	-	.	Parent=gene344
chr11	ENCODE	CDS	5643462	5643488	.	-	2	Parent=gene344
chr11	ENCODE	exon	5645495	5645517	.	-	.	Parent=gene344
chr11	ENCODE	CDS	5645495	5645517	.	-	1	Parent=gene344
chr11	ENCODE	exon	5656010	5656240	.	-	.	Parent=gene344
chr11	ENCODE	CDS	5656010	5656240	.	-	1	Parent=gene344
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene344
chr11	ENCODE	CDS	5656880	5656975	.	-	1	Parent=gene344
chr11	ENCODE	exon	5657567	5657613	.	-	.	Parent=gene344
chr11	ENCODE	CDS	5657567	5657613	.	-	0	Parent=gene344
###
chr11	ENCODE	gene	5641864	5657663	.	-	.	ID=gene345;Name=AC015691.12-008;name2=TRIM5
chr11	ENCODE	exon	5641864	5641979	.	-	.	Parent=gene345
chr11	ENCODE	exon	5642975	5643201	.	-	.	Parent=gene345
chr11	ENCODE	exon	5643462	5643488	.	-	.	Parent=gene345
chr11	ENCODE	exon	5643787	5643887	.	-	.	Parent=gene345
chr11	ENCODE	exon	5645495	5645517	.	-	.	Parent=gene345
chr11	ENCODE	exon	5656010	5656240	.	-	.	Parent=gene345
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene345
chr11	ENCODE	exon	5657567	5657663	.	-	.	Parent=gene345
###
chr11	ENCODE	gene	5642381	5657906	.	-	.	ID=gene346;Name=AC015691.12-006;name2=TRIM5
chr11	ENCODE	exon	5642381	5642559	.	-	.	Parent=gene346
chr11	ENCODE	exon	5656104	5656240	.	-	.	Parent=gene346
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene346
chr11	ENCODE	exon	5657567	5657906	.	-	.	Parent=gene346
###
chr11	ENCODE	gene	5643226	5656946	.	-	.	ID=gene347;Name=AC015691.12-011;name2=TRIM5
chr11	ENCODE	exon	5643226	5643488	.	-	.	Parent=gene347
chr11	ENCODE	exon	5643787	5643887	.	-	.	Parent=gene347
chr11	ENCODE	exon	5656010	5656240	.	-	.	Parent=gene347
chr11	ENCODE	exon	5656880	5656946	.	-	.	Parent=gene347
###
chr11	ENCODE	gene	5643686	5657639	.	-	.	ID=gene348;name2=TRIM5;Name=AC015691.12-010
chr11	ENCODE	exon	5643686	5643887	.	-	.	Parent=gene348
chr11	ENCODE	exon	5656010	5656240	.	-	.	Parent=gene348
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene348
chr11	ENCODE	exon	5657567	5657639	.	-	.	Parent=gene348
###
chr11	ENCODE	gene	5655752	5657737	.	-	.	ID=gene349;Name=AC015691.12-007;name2=TRIM5
chr11	ENCODE	exon	5655752	5656240	.	-	.	Parent=gene349
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene349
chr11	ENCODE	exon	5657567	5657737	.	-	.	Parent=gene349
###
chr11	ENCODE	gene	5656126	5658044	.	-	.	ID=gene350;name2=TRIM5;Name=AC015691.12-012
chr11	ENCODE	exon	5656126	5656240	.	-	.	Parent=gene350
chr11	ENCODE	exon	5656880	5656975	.	-	.	Parent=gene350
chr11	ENCODE	exon	5657567	5658044	.	-	.	Parent=gene350
###
chr11	ENCODE	gene	5657768	5662849	.	-	.	ID=gene351;Name=AC015691.12-013;name2=TRIM5
chr11	ENCODE	CDS	5657768	5657983	.	-	0	Parent=gene351
chr11	ENCODE	exon	5657768	5658044	.	-	.	Parent=gene351
chr11	ENCODE	exon	5661792	5661945	.	-	.	Parent=gene351
chr11	ENCODE	exon	5662674	5662849	.	-	.	Parent=gene351
###
chr11	ENCODE	gene	5667495	5688669	.	+	.	ID=gene352;Name=AC109341.3-001;name2=TRIM22
chr11	ENCODE	exon	5667495	5667705	.	+	.	Parent=gene352
chr11	ENCODE	exon	5673973	5674461	.	+	.	Parent=gene352
chr11	ENCODE	CDS	5674039	5674461	.	+	0	Parent=gene352
chr11	ENCODE	exon	5675054	5675149	.	+	.	Parent=gene352
chr11	ENCODE	CDS	5675054	5675149	.	+	0	Parent=gene352
chr11	ENCODE	exon	5676121	5676351	.	+	.	Parent=gene352
chr11	ENCODE	CDS	5676121	5676351	.	+	0	Parent=gene352
chr11	ENCODE	exon	5684400	5684422	.	+	.	Parent=gene352
chr11	ENCODE	CDS	5684400	5684422	.	+	0	Parent=gene352
chr11	ENCODE	exon	5685979	5686079	.	+	.	Parent=gene352
chr11	ENCODE	CDS	5685979	5686079	.	+	1	Parent=gene352
chr11	ENCODE	exon	5686383	5686409	.	+	.	Parent=gene352
chr11	ENCODE	CDS	5686383	5686409	.	+	2	Parent=gene352
chr11	ENCODE	CDS	5686859	5687454	.	+	2	Parent=gene352
chr11	ENCODE	exon	5686859	5688669	.	+	.	Parent=gene352
###
chr11	ENCODE	gene	5667503	5676212	.	+	.	ID=gene353;Name=AC109341.3-003;name2=TRIM22
chr11	ENCODE	exon	5667503	5667510	.	+	.	Parent=gene353
chr11	ENCODE	exon	5667579	5667705	.	+	.	Parent=gene353
chr11	ENCODE	exon	5673973	5674461	.	+	.	Parent=gene353
chr11	ENCODE	CDS	5674039	5674461	.	+	0	Parent=gene353
chr11	ENCODE	exon	5675054	5675149	.	+	.	Parent=gene353
chr11	ENCODE	CDS	5675054	5675149	.	+	0	Parent=gene353
chr11	ENCODE	exon	5676121	5676212	.	+	.	Parent=gene353
chr11	ENCODE	CDS	5676121	5676212	.	+	0	Parent=gene353
###
chr11	ENCODE	gene	5667627	5674819	.	+	.	ID=gene354;Name=AC109341.3-004;name2=TRIM22
chr11	ENCODE	exon	5667627	5667705	.	+	.	Parent=gene354
chr11	ENCODE	exon	5673973	5674819	.	+	.	Parent=gene354
###
chr11	ENCODE	gene	5667686	5686969	.	+	.	ID=gene355;Name=AC109341.3-006;name2=TRIM22
chr11	ENCODE	exon	5667686	5667705	.	+	.	Parent=gene355
chr11	ENCODE	exon	5673973	5674461	.	+	.	Parent=gene355
chr11	ENCODE	CDS	5674039	5674461	.	+	0	Parent=gene355
chr11	ENCODE	exon	5676121	5676351	.	+	.	Parent=gene355
chr11	ENCODE	CDS	5676121	5676351	.	+	0	Parent=gene355
chr11	ENCODE	exon	5684400	5684422	.	+	.	Parent=gene355
chr11	ENCODE	CDS	5684400	5684422	.	+	0	Parent=gene355
chr11	ENCODE	exon	5685979	5686079	.	+	.	Parent=gene355
chr11	ENCODE	CDS	5685979	5686079	.	+	1	Parent=gene355
chr11	ENCODE	exon	5686383	5686409	.	+	.	Parent=gene355
chr11	ENCODE	CDS	5686383	5686409	.	+	2	Parent=gene355
chr11	ENCODE	exon	5686859	5686969	.	+	.	Parent=gene355
chr11	ENCODE	CDS	5686859	5686969	.	+	2	Parent=gene355
###
chr11	ENCODE	gene	5668833	5676282	.	+	.	ID=gene356;Name=AC109341.3-005;name2=TRIM22
chr11	ENCODE	exon	5668833	5668982	.	+	.	Parent=gene356
chr11	ENCODE	exon	5673973	5674461	.	+	.	Parent=gene356
chr11	ENCODE	CDS	5674039	5674461	.	+	0	Parent=gene356
chr11	ENCODE	exon	5675054	5675149	.	+	.	Parent=gene356
chr11	ENCODE	CDS	5675054	5675149	.	+	0	Parent=gene356
chr11	ENCODE	exon	5676121	5676282	.	+	.	Parent=gene356
chr11	ENCODE	CDS	5676121	5676282	.	+	0	Parent=gene356
###
chr11	ENCODE	gene	5674298	5687253	.	+	.	ID=gene357;Name=AC109341.3-002;name2=TRIM22
chr11	ENCODE	exon	5674298	5674461	.	+	.	Parent=gene357
chr11	ENCODE	exon	5675054	5676351	.	+	.	Parent=gene357
chr11	ENCODE	exon	5684400	5684422	.	+	.	Parent=gene357
chr11	ENCODE	exon	5685979	5686079	.	+	.	Parent=gene357
chr11	ENCODE	exon	5686383	5686409	.	+	.	Parent=gene357
chr11	ENCODE	exon	5686859	5687253	.	+	.	Parent=gene357
###
chr11	ENCODE	gene	5674308	5686943	.	+	.	ID=gene358;Name=AC109341.3-007;name2=TRIM22
chr11	ENCODE	exon	5674308	5674461	.	+	.	Parent=gene358
chr11	ENCODE	exon	5675054	5675149	.	+	.	Parent=gene358
chr11	ENCODE	exon	5676121	5676223	.	+	.	Parent=gene358
chr11	ENCODE	exon	5676286	5676351	.	+	.	Parent=gene358
chr11	ENCODE	exon	5684400	5684422	.	+	.	Parent=gene358
chr11	ENCODE	exon	5685979	5686079	.	+	.	Parent=gene358
chr11	ENCODE	exon	5686383	5686409	.	+	.	Parent=gene358
chr11	ENCODE	exon	5686859	5686943	.	+	.	Parent=gene358
###
chr11	ENCODE	gene	5684356	5687123	.	+	.	ID=gene359;name2=TRIM22;Name=AC109341.3-009
chr11	ENCODE	exon	5684356	5684422	.	+	.	Parent=gene359
chr11	ENCODE	exon	5685979	5686079	.	+	.	Parent=gene359
chr11	ENCODE	exon	5686383	5686409	.	+	.	Parent=gene359
chr11	ENCODE	exon	5686859	5687123	.	+	.	Parent=gene359
###
chr11	ENCODE	gene	5684400	5692849	.	+	.	ID=gene360;Name=AC109341.3-008;name2=TRIM22
chr11	ENCODE	exon	5684400	5684422	.	+	.	Parent=gene360
chr11	ENCODE	exon	5685979	5686079	.	+	.	Parent=gene360
chr11	ENCODE	exon	5686383	5686409	.	+	.	Parent=gene360
chr11	ENCODE	exon	5692493	5692849	.	+	.	Parent=gene360
###
chr11	ENCODE	gene	5686014	5714895	.	+	.	ID=gene361;Name=AC131574.4-003;name2=OR56B1
chr11	ENCODE	exon	5686014	5686079	.	+	.	Parent=gene361
chr11	ENCODE	exon	5686383	5686409	.	+	.	Parent=gene361
chr11	ENCODE	exon	5711985	5712041	.	+	.	Parent=gene361
chr11	ENCODE	exon	5713802	5714895	.	+	.	Parent=gene361
###
chr11	ENCODE	gene	5686014	5714895	.	+	.	ID=gene362;Name=AC131574.4-002;name2=OR56B1
chr11	ENCODE	exon	5686014	5686079	.	+	.	Parent=gene362
chr11	ENCODE	exon	5686383	5686409	.	+	.	Parent=gene362
chr11	ENCODE	exon	5711988	5712041	.	+	.	Parent=gene362
chr11	ENCODE	exon	5713802	5714895	.	+	.	Parent=gene362
###
chr11	ENCODE	gene	5714323	5715297	.	+	.	ID=gene363;Name=AC131574.4-001;name2=OR56B1
chr11	ENCODE	exon	5714323	5715297	.	+	.	Parent=gene363
chr11	ENCODE	CDS	5714323	5715297	.	+	0	Parent=gene363
###
chr11	ENCODE	gene	5732547	5732587	.	+	.	ID=gene364;name2=OR52N4;Name=AC131574.5-001
chr11	ENCODE	exon	5732547	5732587	.	+	.	Parent=gene364
chr11	ENCODE	CDS	5732547	5732587	.	+	0	Parent=gene364
###
chr11	ENCODE	gene	63973122	63975702	.	+	.	ID=gene365;Name=AP003774.4-001;name2=AP003774.4
chr11	ENCODE	exon	63973122	63973700	.	+	.	Parent=gene365
chr11	ENCODE	CDS	63973593	63973700	.	+	0	Parent=gene365
chr11	ENCODE	CDS	63973945	63974220	.	+	0	Parent=gene365
chr11	ENCODE	exon	63973945	63975702	.	+	.	Parent=gene365
###
chr11	ENCODE	gene	64079674	64096923	.	+	.	ID=gene366;Name=AP001092.1-001;name2=SLC22A11
chr11	ENCODE	exon	64079674	64080440	.	+	.	Parent=gene366
chr11	ENCODE	CDS	64080048	64080440	.	+	0	Parent=gene366
chr11	ENCODE	exon	64083183	64083286	.	+	.	Parent=gene366
chr11	ENCODE	CDS	64083183	64083286	.	+	0	Parent=gene366
chr11	ENCODE	exon	64086052	64086206	.	+	.	Parent=gene366
chr11	ENCODE	CDS	64086052	64086206	.	+	1	Parent=gene366
chr11	ENCODE	exon	64086315	64086483	.	+	.	Parent=gene366
chr11	ENCODE	CDS	64086315	64086483	.	+	2	Parent=gene366
chr11	ENCODE	exon	64088356	64088476	.	+	.	Parent=gene366
chr11	ENCODE	CDS	64088356	64088476	.	+	1	Parent=gene366
chr11	ENCODE	exon	64089270	64089385	.	+	.	Parent=gene366
chr11	ENCODE	CDS	64089270	64089385	.	+	0	Parent=gene366
chr11	ENCODE	exon	64091647	64091861	.	+	.	Parent=gene366
chr11	ENCODE	CDS	64091647	64091861	.	+	1	Parent=gene366
chr11	ENCODE	exon	64092718	64092826	.	+	.	Parent=gene366
chr11	ENCODE	CDS	64092718	64092826	.	+	2	Parent=gene366
chr11	ENCODE	exon	64093700	64093906	.	+	.	Parent=gene366
chr11	ENCODE	CDS	64093700	64093906	.	+	1	Parent=gene366
chr11	ENCODE	CDS	64095027	64095090	.	+	1	Parent=gene366
chr11	ENCODE	exon	64095027	64096923	.	+	.	Parent=gene366
###
chr11	ENCODE	gene	64079738	64095575	.	+	.	ID=gene367;Name=AP001092.1-002;name2=SLC22A11
chr11	ENCODE	exon	64079738	64080440	.	+	.	Parent=gene367
chr11	ENCODE	CDS	64080048	64080440	.	+	0	Parent=gene367
chr11	ENCODE	exon	64083183	64083286	.	+	.	Parent=gene367
chr11	ENCODE	CDS	64083183	64083286	.	+	0	Parent=gene367
chr11	ENCODE	exon	64086052	64086206	.	+	.	Parent=gene367
chr11	ENCODE	CDS	64086052	64086206	.	+	1	Parent=gene367
chr11	ENCODE	exon	64086315	64086483	.	+	.	Parent=gene367
chr11	ENCODE	CDS	64086315	64086483	.	+	2	Parent=gene367
chr11	ENCODE	exon	64088356	64088476	.	+	.	Parent=gene367
chr11	ENCODE	CDS	64088356	64088476	.	+	1	Parent=gene367
chr11	ENCODE	exon	64089270	64089385	.	+	.	Parent=gene367
chr11	ENCODE	CDS	64089270	64089385	.	+	0	Parent=gene367
chr11	ENCODE	exon	64093700	64093906	.	+	.	Parent=gene367
chr11	ENCODE	CDS	64093700	64093906	.	+	1	Parent=gene367
chr11	ENCODE	CDS	64095027	64095090	.	+	1	Parent=gene367
chr11	ENCODE	exon	64095027	64095575	.	+	.	Parent=gene367
###
chr11	ENCODE	gene	64080004	64095575	.	+	.	ID=gene368;name2=SLC22A11;Name=AP001092.1-003
chr11	ENCODE	exon	64080004	64080440	.	+	.	Parent=gene368
chr11	ENCODE	CDS	64080048	64080440	.	+	0	Parent=gene368
chr11	ENCODE	exon	64083183	64083286	.	+	.	Parent=gene368
chr11	ENCODE	CDS	64083183	64083286	.	+	0	Parent=gene368
chr11	ENCODE	exon	64086052	64086206	.	+	.	Parent=gene368
chr11	ENCODE	CDS	64086052	64086206	.	+	1	Parent=gene368
chr11	ENCODE	exon	64086315	64086483	.	+	.	Parent=gene368
chr11	ENCODE	CDS	64086315	64086483	.	+	2	Parent=gene368
chr11	ENCODE	exon	64088356	64088476	.	+	.	Parent=gene368
chr11	ENCODE	CDS	64088356	64088476	.	+	1	Parent=gene368
chr11	ENCODE	exon	64089270	64089385	.	+	.	Parent=gene368
chr11	ENCODE	CDS	64089270	64089385	.	+	0	Parent=gene368
chr11	ENCODE	exon	64091647	64091861	.	+	.	Parent=gene368
chr11	ENCODE	CDS	64091647	64091861	.	+	1	Parent=gene368
chr11	ENCODE	exon	64092718	64092826	.	+	.	Parent=gene368
chr11	ENCODE	CDS	64092718	64092826	.	+	2	Parent=gene368
chr11	ENCODE	CDS	64095027	64095090	.	+	1	Parent=gene368
chr11	ENCODE	exon	64095027	64095575	.	+	.	Parent=gene368
###
chr11	ENCODE	gene	64080015	64089413	.	+	.	ID=gene369;Name=AP001092.1-006;name2=SLC22A11
chr11	ENCODE	exon	64080015	64080440	.	+	.	Parent=gene369
chr11	ENCODE	exon	64086052	64086206	.	+	.	Parent=gene369
chr11	ENCODE	exon	64086315	64086483	.	+	.	Parent=gene369
chr11	ENCODE	exon	64089270	64089413	.	+	.	Parent=gene369
###
chr11	ENCODE	gene	64080015	64090331	.	+	.	ID=gene370;name2=SLC22A11;Name=AP001092.1-004
chr11	ENCODE	exon	64080015	64080440	.	+	.	Parent=gene370
chr11	ENCODE	exon	64083183	64083286	.	+	.	Parent=gene370
chr11	ENCODE	exon	64086052	64086206	.	+	.	Parent=gene370
chr11	ENCODE	exon	64086315	64086483	.	+	.	Parent=gene370
chr11	ENCODE	exon	64089270	64090331	.	+	.	Parent=gene370
###
chr11	ENCODE	gene	64086130	64090747	.	+	.	ID=gene371;Name=AP001092.1-005;name2=SLC22A11
chr11	ENCODE	exon	64086130	64086206	.	+	.	Parent=gene371
chr11	ENCODE	exon	64086315	64086483	.	+	.	Parent=gene371
chr11	ENCODE	exon	64088356	64088476	.	+	.	Parent=gene371
chr11	ENCODE	exon	64089270	64090747	.	+	.	Parent=gene371
###
chr11	ENCODE	gene	64091647	64095575	.	+	.	ID=gene372;Name=AP001092.1-008;name2=SLC22A11
chr11	ENCODE	exon	64091647	64091861	.	+	.	Parent=gene372
chr11	ENCODE	exon	64093700	64093906	.	+	.	Parent=gene372
chr11	ENCODE	exon	64095027	64095575	.	+	.	Parent=gene372
###
chr11	ENCODE	gene	64091648	64095575	.	+	.	ID=gene373;Name=AP001092.1-007;name2=SLC22A11
chr11	ENCODE	exon	64091648	64091861	.	+	.	Parent=gene373
chr11	ENCODE	CDS	64091648	64091861	.	+	0	Parent=gene373
chr11	ENCODE	exon	64092718	64092826	.	+	.	Parent=gene373
chr11	ENCODE	CDS	64092718	64092826	.	+	2	Parent=gene373
chr11	ENCODE	exon	64093832	64093906	.	+	.	Parent=gene373
chr11	ENCODE	CDS	64093832	64093906	.	+	1	Parent=gene373
chr11	ENCODE	CDS	64095027	64095090	.	+	1	Parent=gene373
chr11	ENCODE	exon	64095027	64095575	.	+	.	Parent=gene373
###
chr11	ENCODE	gene	64114689	64126396	.	+	.	ID=gene374;Name=AP001092.2-002;name2=SLC22A12
chr11	ENCODE	exon	64114689	64114866	.	+	.	Parent=gene374
chr11	ENCODE	exon	64115319	64116006	.	+	.	Parent=gene374
chr11	ENCODE	CDS	64115605	64116006	.	+	0	Parent=gene374
chr11	ENCODE	exon	64116827	64116930	.	+	.	Parent=gene374
chr11	ENCODE	CDS	64116827	64116930	.	+	0	Parent=gene374
chr11	ENCODE	exon	64122564	64122687	.	+	.	Parent=gene374
chr11	ENCODE	CDS	64122564	64122687	.	+	1	Parent=gene374
chr11	ENCODE	exon	64122856	64122971	.	+	.	Parent=gene374
chr11	ENCODE	CDS	64122856	64122971	.	+	0	Parent=gene374
chr11	ENCODE	exon	64123724	64123938	.	+	.	Parent=gene374
chr11	ENCODE	CDS	64123724	64123938	.	+	1	Parent=gene374
chr11	ENCODE	exon	64124415	64124523	.	+	.	Parent=gene374
chr11	ENCODE	CDS	64124415	64124523	.	+	2	Parent=gene374
chr11	ENCODE	exon	64124783	64124986	.	+	.	Parent=gene374
chr11	ENCODE	CDS	64124783	64124986	.	+	1	Parent=gene374
chr11	ENCODE	CDS	64125536	64125599	.	+	1	Parent=gene374
chr11	ENCODE	exon	64125536	64126396	.	+	.	Parent=gene374
###
chr11	ENCODE	gene	64114858	64126396	.	+	.	ID=gene375;Name=AP001092.2-001;name2=SLC22A12
chr11	ENCODE	exon	64114858	64116006	.	+	.	Parent=gene375
chr11	ENCODE	CDS	64115605	64116006	.	+	0	Parent=gene375
chr11	ENCODE	exon	64116827	64116930	.	+	.	Parent=gene375
chr11	ENCODE	CDS	64116827	64116930	.	+	0	Parent=gene375
chr11	ENCODE	exon	64117453	64117607	.	+	.	Parent=gene375
chr11	ENCODE	CDS	64117453	64117607	.	+	1	Parent=gene375
chr11	ENCODE	exon	64117683	64117851	.	+	.	Parent=gene375
chr11	ENCODE	CDS	64117683	64117851	.	+	2	Parent=gene375
chr11	ENCODE	exon	64122564	64122687	.	+	.	Parent=gene375
chr11	ENCODE	CDS	64122564	64122687	.	+	1	Parent=gene375
chr11	ENCODE	exon	64122856	64122971	.	+	.	Parent=gene375
chr11	ENCODE	CDS	64122856	64122971	.	+	0	Parent=gene375
chr11	ENCODE	exon	64123724	64123938	.	+	.	Parent=gene375
chr11	ENCODE	CDS	64123724	64123938	.	+	1	Parent=gene375
chr11	ENCODE	exon	64124415	64124523	.	+	.	Parent=gene375
chr11	ENCODE	CDS	64124415	64124523	.	+	2	Parent=gene375
chr11	ENCODE	exon	64124783	64124986	.	+	.	Parent=gene375
chr11	ENCODE	CDS	64124783	64124986	.	+	1	Parent=gene375
chr11	ENCODE	CDS	64125536	64125599	.	+	1	Parent=gene375
chr11	ENCODE	exon	64125536	64126396	.	+	.	Parent=gene375
###
chr11	ENCODE	gene	64115268	64126392	.	+	.	ID=gene376;Name=AP001092.2-003;name2=SLC22A12
chr11	ENCODE	exon	64115268	64116006	.	+	.	Parent=gene376
chr11	ENCODE	exon	64116827	64116930	.	+	.	Parent=gene376
chr11	ENCODE	exon	64117453	64117851	.	+	.	Parent=gene376
chr11	ENCODE	exon	64122564	64122687	.	+	.	Parent=gene376
chr11	ENCODE	exon	64122856	64122871	.	+	.	Parent=gene376
chr11	ENCODE	exon	64126271	64126392	.	+	.	Parent=gene376
###
chr11	ENCODE	gene	64115276	64126396	.	+	.	ID=gene377;Name=AP001092.2-004;name2=SLC22A12
chr11	ENCODE	exon	64115276	64115595	.	+	.	Parent=gene377
chr11	ENCODE	exon	64115707	64116006	.	+	.	Parent=gene377
chr11	ENCODE	exon	64116827	64116930	.	+	.	Parent=gene377
chr11	ENCODE	exon	64117683	64117851	.	+	.	Parent=gene377
chr11	ENCODE	exon	64122564	64122687	.	+	.	Parent=gene377
chr11	ENCODE	exon	64122856	64122971	.	+	.	Parent=gene377
chr11	ENCODE	exon	64123724	64123938	.	+	.	Parent=gene377
chr11	ENCODE	exon	64124415	64124523	.	+	.	Parent=gene377
chr11	ENCODE	exon	64124783	64124986	.	+	.	Parent=gene377
chr11	ENCODE	exon	64125536	64126396	.	+	.	Parent=gene377
###
chr11	ENCODE	gene	64130222	64148044	.	-	.	ID=gene378;Name=AP001092.3-005;name2=NRXN2
chr11	ENCODE	exon	64130222	64132130	.	-	.	Parent=gene378
chr11	ENCODE	exon	64144342	64144420	.	-	.	Parent=gene378
chr11	ENCODE	exon	64146801	64148044	.	-	.	Parent=gene378
###
chr11	ENCODE	gene	64130222	64167363	.	-	.	ID=gene379;Name=AP001092.3-003;name2=NRXN2
chr11	ENCODE	exon	64130222	64132130	.	-	.	Parent=gene379
chr11	ENCODE	CDS	64131244	64132130	.	-	2	Parent=gene379
chr11	ENCODE	exon	64144342	64144420	.	-	.	Parent=gene379
chr11	ENCODE	CDS	64144342	64144420	.	-	0	Parent=gene379
chr11	ENCODE	exon	64146801	64147126	.	-	.	Parent=gene379
chr11	ENCODE	CDS	64146801	64147126	.	-	2	Parent=gene379
chr11	ENCODE	exon	64150511	64150600	.	-	.	Parent=gene379
chr11	ENCODE	CDS	64150511	64150600	.	-	2	Parent=gene379
chr11	ENCODE	exon	64154450	64154621	.	-	.	Parent=gene379
chr11	ENCODE	CDS	64154450	64154621	.	-	0	Parent=gene379
chr11	ENCODE	exon	64159319	64159500	.	-	.	Parent=gene379
chr11	ENCODE	CDS	64159319	64159500	.	-	2	Parent=gene379
chr11	ENCODE	CDS	64166587	64166851	.	-	0	Parent=gene379
chr11	ENCODE	exon	64166587	64167363	.	-	.	Parent=gene379
###
chr11	ENCODE	gene	64130222	64237959	.	-	.	ID=gene380;Name=AP001092.3-001;name2=NRXN2
chr11	ENCODE	exon	64130222	64132130	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64131244	64132130	.	-	2	Parent=gene380
chr11	ENCODE	exon	64144342	64144420	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64144342	64144420	.	-	0	Parent=gene380
chr11	ENCODE	exon	64146801	64147126	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64146801	64147126	.	-	2	Parent=gene380
chr11	ENCODE	exon	64150511	64150600	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64150511	64150600	.	-	2	Parent=gene380
chr11	ENCODE	exon	64154450	64154621	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64154450	64154621	.	-	0	Parent=gene380
chr11	ENCODE	exon	64159319	64159500	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64159319	64159500	.	-	2	Parent=gene380
chr11	ENCODE	exon	64172267	64172386	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64172267	64172386	.	-	2	Parent=gene380
chr11	ENCODE	exon	64172782	64172955	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64172782	64172955	.	-	2	Parent=gene380
chr11	ENCODE	exon	64174496	64174686	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64174496	64174686	.	-	1	Parent=gene380
chr11	ENCODE	exon	64175303	64175684	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64175303	64175684	.	-	2	Parent=gene380
chr11	ENCODE	exon	64176083	64176202	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64176083	64176202	.	-	2	Parent=gene380
chr11	ENCODE	exon	64177744	64177770	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64177744	64177770	.	-	2	Parent=gene380
chr11	ENCODE	exon	64184380	64184583	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64184380	64184583	.	-	2	Parent=gene380
chr11	ENCODE	exon	64184801	64185187	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64184801	64185187	.	-	2	Parent=gene380
chr11	ENCODE	exon	64191298	64191736	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64191298	64191736	.	-	0	Parent=gene380
chr11	ENCODE	exon	64192491	64192652	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64192491	64192652	.	-	0	Parent=gene380
chr11	ENCODE	exon	64201041	64201085	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64201041	64201085	.	-	0	Parent=gene380
chr11	ENCODE	exon	64209694	64209995	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64209694	64209995	.	-	2	Parent=gene380
chr11	ENCODE	exon	64214453	64214524	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64214453	64214524	.	-	2	Parent=gene380
chr11	ENCODE	exon	64216895	64216924	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64216895	64216924	.	-	2	Parent=gene380
chr11	ENCODE	exon	64221823	64221840	.	-	.	Parent=gene380
chr11	ENCODE	CDS	64221823	64221840	.	-	2	Parent=gene380
chr11	ENCODE	CDS	64237018	64237747	.	-	0	Parent=gene380
chr11	ENCODE	exon	64237018	64237959	.	-	.	Parent=gene380
###
chr11	ENCODE	gene	64130222	64247236	.	-	.	ID=gene381;Name=AP001092.3-002;name2=NRXN2
chr11	ENCODE	exon	64130222	64132130	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64131244	64132130	.	-	2	Parent=gene381
chr11	ENCODE	exon	64144342	64144420	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64144342	64144420	.	-	0	Parent=gene381
chr11	ENCODE	exon	64146801	64147126	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64146801	64147126	.	-	2	Parent=gene381
chr11	ENCODE	exon	64154450	64154621	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64154450	64154621	.	-	0	Parent=gene381
chr11	ENCODE	exon	64159319	64159500	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64159319	64159500	.	-	2	Parent=gene381
chr11	ENCODE	exon	64172267	64172386	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64172267	64172386	.	-	2	Parent=gene381
chr11	ENCODE	exon	64172782	64172955	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64172782	64172955	.	-	2	Parent=gene381
chr11	ENCODE	exon	64174496	64174686	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64174496	64174686	.	-	1	Parent=gene381
chr11	ENCODE	exon	64175303	64175684	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64175303	64175684	.	-	2	Parent=gene381
chr11	ENCODE	exon	64176083	64176202	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64176083	64176202	.	-	2	Parent=gene381
chr11	ENCODE	exon	64184380	64184583	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64184380	64184583	.	-	2	Parent=gene381
chr11	ENCODE	exon	64184801	64185187	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64184801	64185187	.	-	2	Parent=gene381
chr11	ENCODE	exon	64191298	64191736	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64191298	64191736	.	-	0	Parent=gene381
chr11	ENCODE	exon	64192491	64192652	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64192491	64192652	.	-	0	Parent=gene381
chr11	ENCODE	exon	64201062	64201085	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64201062	64201085	.	-	0	Parent=gene381
chr11	ENCODE	exon	64209694	64209995	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64209694	64209995	.	-	2	Parent=gene381
chr11	ENCODE	exon	64216895	64216924	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64216895	64216924	.	-	2	Parent=gene381
chr11	ENCODE	exon	64221823	64221840	.	-	.	Parent=gene381
chr11	ENCODE	CDS	64221823	64221840	.	-	2	Parent=gene381
chr11	ENCODE	CDS	64237018	64237747	.	-	0	Parent=gene381
chr11	ENCODE	exon	64237018	64237991	.	-	.	Parent=gene381
chr11	ENCODE	exon	64247019	64247236	.	-	.	Parent=gene381
###
chr11	ENCODE	gene	64131092	64146844	.	-	.	ID=gene382;Name=AP001092.3-004;name2=NRXN2
chr11	ENCODE	exon	64131092	64131548	.	-	.	Parent=gene382
chr11	ENCODE	exon	64144342	64144420	.	-	.	Parent=gene382
chr11	ENCODE	exon	64146801	64146844	.	-	.	Parent=gene382
###
chr11	ENCODE	gene	64146801	64166734	.	-	.	ID=gene383;Name=AP001092.3-006;name2=NRXN2
chr11	ENCODE	exon	64146801	64147126	.	-	.	Parent=gene383
chr11	ENCODE	CDS	64146801	64147126	.	-	2	Parent=gene383
chr11	ENCODE	exon	64154450	64154621	.	-	.	Parent=gene383
chr11	ENCODE	CDS	64154450	64154621	.	-	0	Parent=gene383
chr11	ENCODE	exon	64159319	64159500	.	-	.	Parent=gene383
chr11	ENCODE	CDS	64159319	64159500	.	-	2	Parent=gene383
chr11	ENCODE	exon	64166587	64166734	.	-	.	Parent=gene383
chr11	ENCODE	CDS	64166587	64166734	.	-	0	Parent=gene383
###
chr11	ENCODE	gene	64154453	64161493	.	-	.	ID=gene384;Name=AP001092.3-007;name2=NRXN2
chr11	ENCODE	exon	64154453	64154621	.	-	.	Parent=gene384
chr11	ENCODE	exon	64159319	64159500	.	-	.	Parent=gene384
chr11	ENCODE	exon	64161453	64161493	.	-	.	Parent=gene384
###
chr11	ENCODE	gene	64154534	64167534	.	-	.	ID=gene385;Name=AP001092.3-008;name2=NRXN2
chr11	ENCODE	exon	64154534	64154621	.	-	.	Parent=gene385
chr11	ENCODE	exon	64159319	64159500	.	-	.	Parent=gene385
chr11	ENCODE	exon	64166587	64166648	.	-	.	Parent=gene385
chr11	ENCODE	exon	64167305	64167534	.	-	.	Parent=gene385
###
chr11	ENCODE	gene	64175327	64180168	.	-	.	ID=gene386;Name=AP001092.3-009;name2=NRXN2
chr11	ENCODE	exon	64175327	64175684	.	-	.	Parent=gene386
chr11	ENCODE	exon	64176083	64176202	.	-	.	Parent=gene386
chr11	ENCODE	exon	64177744	64177770	.	-	.	Parent=gene386
chr11	ENCODE	exon	64180136	64180168	.	-	.	Parent=gene386
###
chr11	ENCODE	gene	64184518	64185426	.	-	.	ID=gene387;Name=AP001092.3-010;name2=NRXN2
chr11	ENCODE	exon	64184518	64184583	.	-	.	Parent=gene387
chr11	ENCODE	exon	64184801	64185187	.	-	.	Parent=gene387
chr11	ENCODE	exon	64185269	64185426	.	-	.	Parent=gene387
###
chr11	ENCODE	gene	64250959	64264931	.	-	.	ID=gene388;Name=AP001462.3-006;name2=RASGRP2
chr11	ENCODE	exon	64250959	64251179	.	-	.	Parent=gene388
chr11	ENCODE	exon	64251344	64251411	.	-	.	Parent=gene388
chr11	ENCODE	exon	64252911	64253090	.	-	.	Parent=gene388
chr11	ENCODE	exon	64253810	64253846	.	-	.	Parent=gene388
chr11	ENCODE	exon	64254101	64254242	.	-	.	Parent=gene388
chr11	ENCODE	exon	64259160	64259275	.	-	.	Parent=gene388
chr11	ENCODE	exon	64259590	64259712	.	-	.	Parent=gene388
chr11	ENCODE	exon	64259951	64260028	.	-	.	Parent=gene388
chr11	ENCODE	exon	64260801	64261082	.	-	.	Parent=gene388
chr11	ENCODE	exon	64263408	64263524	.	-	.	Parent=gene388
chr11	ENCODE	exon	64263684	64263857	.	-	.	Parent=gene388
chr11	ENCODE	exon	64264061	64264931	.	-	.	Parent=gene388
###
chr11	ENCODE	gene	64250959	64267837	.	-	.	ID=gene389;Name=AP001462.3-007;name2=RASGRP2
chr11	ENCODE	exon	64250959	64251179	.	-	.	Parent=gene389
chr11	ENCODE	exon	64251344	64251411	.	-	.	Parent=gene389
chr11	ENCODE	exon	64252911	64253090	.	-	.	Parent=gene389
chr11	ENCODE	exon	64253810	64253846	.	-	.	Parent=gene389
chr11	ENCODE	exon	64254101	64254242	.	-	.	Parent=gene389
chr11	ENCODE	exon	64259160	64259275	.	-	.	Parent=gene389
chr11	ENCODE	exon	64259590	64259712	.	-	.	Parent=gene389
chr11	ENCODE	exon	64259951	64260028	.	-	.	Parent=gene389
chr11	ENCODE	exon	64260801	64261082	.	-	.	Parent=gene389
chr11	ENCODE	exon	64263408	64263524	.	-	.	Parent=gene389
chr11	ENCODE	exon	64263684	64263857	.	-	.	Parent=gene389
chr11	ENCODE	exon	64264061	64264211	.	-	.	Parent=gene389
chr11	ENCODE	exon	64264996	64265127	.	-	.	Parent=gene389
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene389
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene389
chr11	ENCODE	exon	64266842	64267837	.	-	.	Parent=gene389
###
chr11	ENCODE	gene	64250959	64268170	.	-	.	ID=gene390;Name=AP001462.3-004;name2=RASGRP2
chr11	ENCODE	exon	64250959	64251179	.	-	.	Parent=gene390
chr11	ENCODE	exon	64251344	64251408	.	-	.	Parent=gene390
chr11	ENCODE	exon	64252911	64253090	.	-	.	Parent=gene390
chr11	ENCODE	exon	64253810	64253846	.	-	.	Parent=gene390
chr11	ENCODE	exon	64254101	64254242	.	-	.	Parent=gene390
chr11	ENCODE	exon	64259160	64259275	.	-	.	Parent=gene390
chr11	ENCODE	exon	64259590	64259712	.	-	.	Parent=gene390
chr11	ENCODE	exon	64259951	64260028	.	-	.	Parent=gene390
chr11	ENCODE	exon	64260801	64261082	.	-	.	Parent=gene390
chr11	ENCODE	exon	64263408	64263524	.	-	.	Parent=gene390
chr11	ENCODE	exon	64263684	64263857	.	-	.	Parent=gene390
chr11	ENCODE	exon	64264061	64264211	.	-	.	Parent=gene390
chr11	ENCODE	exon	64264996	64265127	.	-	.	Parent=gene390
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene390
chr11	ENCODE	exon	64266058	64266080	.	-	.	Parent=gene390
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene390
chr11	ENCODE	exon	64268051	64268170	.	-	.	Parent=gene390
###
chr11	ENCODE	gene	64250959	64268226	.	-	.	ID=gene391;Name=AP001462.3-001;name2=RASGRP2
chr11	ENCODE	exon	64250959	64251179	.	-	.	Parent=gene391
chr11	ENCODE	exon	64251344	64251408	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64251350	64251408	.	-	2	Parent=gene391
chr11	ENCODE	exon	64252911	64253090	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64252911	64253090	.	-	2	Parent=gene391
chr11	ENCODE	exon	64253810	64253846	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64253810	64253846	.	-	0	Parent=gene391
chr11	ENCODE	exon	64254101	64254242	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64254101	64254242	.	-	1	Parent=gene391
chr11	ENCODE	exon	64259160	64259275	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64259160	64259275	.	-	0	Parent=gene391
chr11	ENCODE	exon	64259590	64259712	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64259590	64259712	.	-	0	Parent=gene391
chr11	ENCODE	exon	64259951	64260028	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64259951	64260028	.	-	0	Parent=gene391
chr11	ENCODE	exon	64260801	64261082	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64260801	64261082	.	-	0	Parent=gene391
chr11	ENCODE	exon	64263408	64263524	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64263408	64263524	.	-	0	Parent=gene391
chr11	ENCODE	exon	64263684	64263857	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64263684	64263857	.	-	0	Parent=gene391
chr11	ENCODE	exon	64264061	64264211	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64264061	64264211	.	-	1	Parent=gene391
chr11	ENCODE	exon	64264996	64265127	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64264996	64265127	.	-	1	Parent=gene391
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64265487	64265549	.	-	1	Parent=gene391
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene391
chr11	ENCODE	CDS	64266058	64266160	.	-	2	Parent=gene391
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene391
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene391
chr11	ENCODE	exon	64268051	64268226	.	-	.	Parent=gene391
###
chr11	ENCODE	gene	64250959	64268882	.	-	.	ID=gene392;Name=AP001462.3-003;name2=RASGRP2
chr11	ENCODE	exon	64250959	64251179	.	-	.	Parent=gene392
chr11	ENCODE	exon	64251344	64251408	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64251350	64251408	.	-	2	Parent=gene392
chr11	ENCODE	exon	64252911	64253090	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64252911	64253090	.	-	2	Parent=gene392
chr11	ENCODE	exon	64253810	64253846	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64253810	64253846	.	-	0	Parent=gene392
chr11	ENCODE	exon	64254101	64254242	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64254101	64254242	.	-	1	Parent=gene392
chr11	ENCODE	exon	64259160	64259275	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64259160	64259275	.	-	0	Parent=gene392
chr11	ENCODE	exon	64259590	64259712	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64259590	64259712	.	-	0	Parent=gene392
chr11	ENCODE	exon	64259951	64260028	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64259951	64260028	.	-	0	Parent=gene392
chr11	ENCODE	exon	64260801	64261082	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64260801	64261082	.	-	0	Parent=gene392
chr11	ENCODE	exon	64263408	64263524	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64263408	64263524	.	-	0	Parent=gene392
chr11	ENCODE	exon	64263684	64263857	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64263684	64263857	.	-	0	Parent=gene392
chr11	ENCODE	exon	64264061	64264211	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64264061	64264211	.	-	1	Parent=gene392
chr11	ENCODE	exon	64264996	64265127	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64264996	64265127	.	-	1	Parent=gene392
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64265487	64265549	.	-	1	Parent=gene392
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene392
chr11	ENCODE	CDS	64266058	64266160	.	-	2	Parent=gene392
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene392
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene392
chr11	ENCODE	exon	64268790	64268882	.	-	.	Parent=gene392
###
chr11	ENCODE	gene	64250959	64269504	.	-	.	ID=gene393;Name=AP001462.3-021;name2=RASGRP2
chr11	ENCODE	exon	64250959	64251179	.	-	.	Parent=gene393
chr11	ENCODE	exon	64251344	64251408	.	-	.	Parent=gene393
chr11	ENCODE	exon	64252911	64253090	.	-	.	Parent=gene393
chr11	ENCODE	exon	64253810	64253846	.	-	.	Parent=gene393
chr11	ENCODE	exon	64254101	64254242	.	-	.	Parent=gene393
chr11	ENCODE	exon	64259160	64259275	.	-	.	Parent=gene393
chr11	ENCODE	exon	64259590	64259712	.	-	.	Parent=gene393
chr11	ENCODE	exon	64259951	64260028	.	-	.	Parent=gene393
chr11	ENCODE	exon	64260801	64261082	.	-	.	Parent=gene393
chr11	ENCODE	exon	64263408	64263524	.	-	.	Parent=gene393
chr11	ENCODE	exon	64263684	64263857	.	-	.	Parent=gene393
chr11	ENCODE	exon	64264061	64264211	.	-	.	Parent=gene393
chr11	ENCODE	exon	64264996	64265127	.	-	.	Parent=gene393
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene393
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene393
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene393
chr11	ENCODE	exon	64268051	64268156	.	-	.	Parent=gene393
chr11	ENCODE	exon	64269323	64269504	.	-	.	Parent=gene393
###
chr11	ENCODE	gene	64250959	64269504	.	-	.	ID=gene394;Name=AP001462.3-002;name2=RASGRP2
chr11	ENCODE	exon	64250959	64251179	.	-	.	Parent=gene394
chr11	ENCODE	exon	64251344	64251408	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64251350	64251408	.	-	2	Parent=gene394
chr11	ENCODE	exon	64252911	64253090	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64252911	64253090	.	-	2	Parent=gene394
chr11	ENCODE	exon	64253810	64253846	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64253810	64253846	.	-	0	Parent=gene394
chr11	ENCODE	exon	64254101	64254242	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64254101	64254242	.	-	1	Parent=gene394
chr11	ENCODE	exon	64259160	64259275	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64259160	64259275	.	-	0	Parent=gene394
chr11	ENCODE	exon	64259590	64259712	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64259590	64259712	.	-	0	Parent=gene394
chr11	ENCODE	exon	64259951	64260028	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64259951	64260028	.	-	0	Parent=gene394
chr11	ENCODE	exon	64260801	64261082	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64260801	64261082	.	-	0	Parent=gene394
chr11	ENCODE	exon	64263408	64263524	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64263408	64263524	.	-	0	Parent=gene394
chr11	ENCODE	exon	64263684	64263857	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64263684	64263857	.	-	0	Parent=gene394
chr11	ENCODE	exon	64264061	64264211	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64264061	64264211	.	-	1	Parent=gene394
chr11	ENCODE	exon	64264996	64265127	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64264996	64265127	.	-	1	Parent=gene394
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64265487	64265549	.	-	1	Parent=gene394
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene394
chr11	ENCODE	CDS	64266058	64266160	.	-	2	Parent=gene394
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene394
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene394
chr11	ENCODE	exon	64269323	64269504	.	-	.	Parent=gene394
###
chr11	ENCODE	gene	64250994	64259314	.	-	.	ID=gene395;name2=RASGRP2;Name=AP001462.3-020
chr11	ENCODE	exon	64250994	64251408	.	-	.	Parent=gene395
chr11	ENCODE	exon	64252911	64253090	.	-	.	Parent=gene395
chr11	ENCODE	exon	64253810	64253846	.	-	.	Parent=gene395
chr11	ENCODE	exon	64254101	64254242	.	-	.	Parent=gene395
chr11	ENCODE	exon	64259160	64259314	.	-	.	Parent=gene395
###
chr11	ENCODE	gene	64254229	64261082	.	-	.	ID=gene396;Name=AP001462.3-024;name2=RASGRP2
chr11	ENCODE	exon	64254229	64254242	.	-	.	Parent=gene396
chr11	ENCODE	exon	64259160	64259275	.	-	.	Parent=gene396
chr11	ENCODE	exon	64259590	64260028	.	-	.	Parent=gene396
chr11	ENCODE	exon	64260801	64261082	.	-	.	Parent=gene396
###
chr11	ENCODE	gene	64259160	64261302	.	-	.	ID=gene397;Name=AP001462.3-018;name2=RASGRP2
chr11	ENCODE	exon	64259160	64259275	.	-	.	Parent=gene397
chr11	ENCODE	exon	64259590	64259712	.	-	.	Parent=gene397
chr11	ENCODE	exon	64259951	64260028	.	-	.	Parent=gene397
chr11	ENCODE	exon	64260801	64261302	.	-	.	Parent=gene397
###
chr11	ENCODE	gene	64259422	64261292	.	-	.	ID=gene398;Name=AP001462.3-019;name2=RASGRP2
chr11	ENCODE	exon	64259422	64259712	.	-	.	Parent=gene398
chr11	ENCODE	exon	64259951	64260028	.	-	.	Parent=gene398
chr11	ENCODE	exon	64260801	64261292	.	-	.	Parent=gene398
###
chr11	ENCODE	gene	64263427	64266994	.	-	.	ID=gene399;Name=AP001462.3-017;name2=RASGRP2
chr11	ENCODE	exon	64263427	64263524	.	-	.	Parent=gene399
chr11	ENCODE	exon	64263684	64263857	.	-	.	Parent=gene399
chr11	ENCODE	exon	64264061	64264211	.	-	.	Parent=gene399
chr11	ENCODE	exon	64264416	64264497	.	-	.	Parent=gene399
chr11	ENCODE	exon	64264996	64265127	.	-	.	Parent=gene399
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene399
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene399
chr11	ENCODE	exon	64266842	64266994	.	-	.	Parent=gene399
###
chr11	ENCODE	gene	64263684	64268166	.	-	.	ID=gene400;name2=RASGRP2;Name=AP001462.3-016
chr11	ENCODE	exon	64263684	64263857	.	-	.	Parent=gene400
chr11	ENCODE	CDS	64263684	64263857	.	-	0	Parent=gene400
chr11	ENCODE	exon	64264061	64264211	.	-	.	Parent=gene400
chr11	ENCODE	CDS	64264061	64264211	.	-	1	Parent=gene400
chr11	ENCODE	exon	64264996	64265127	.	-	.	Parent=gene400
chr11	ENCODE	CDS	64264996	64265127	.	-	1	Parent=gene400
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene400
chr11	ENCODE	CDS	64265487	64265549	.	-	1	Parent=gene400
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene400
chr11	ENCODE	CDS	64266058	64266160	.	-	2	Parent=gene400
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene400
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene400
chr11	ENCODE	exon	64267865	64267916	.	-	.	Parent=gene400
chr11	ENCODE	exon	64268051	64268166	.	-	.	Parent=gene400
###
chr11	ENCODE	gene	64264914	64266985	.	-	.	ID=gene401;Name=AP001462.3-011;name2=RASGRP2
chr11	ENCODE	exon	64264914	64265127	.	-	.	Parent=gene401
chr11	ENCODE	CDS	64265095	64265127	.	-	0	Parent=gene401
chr11	ENCODE	exon	64265487	64265581	.	-	.	Parent=gene401
chr11	ENCODE	CDS	64265487	64265581	.	-	2	Parent=gene401
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene401
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene401
###
chr11	ENCODE	gene	64264914	64266985	.	-	.	ID=gene402;Name=AP001462.3-012;name2=RASGRP2
chr11	ENCODE	exon	64264914	64265127	.	-	.	Parent=gene402
chr11	ENCODE	CDS	64265095	64265127	.	-	0	Parent=gene402
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene402
chr11	ENCODE	CDS	64265487	64265549	.	-	0	Parent=gene402
chr11	ENCODE	exon	64266058	64266080	.	-	.	Parent=gene402
chr11	ENCODE	CDS	64266058	64266080	.	-	2	Parent=gene402
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene402
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene402
###
chr11	ENCODE	gene	64264914	64268193	.	-	.	ID=gene403;Name=AP001462.3-010;name2=RASGRP2
chr11	ENCODE	exon	64264914	64265127	.	-	.	Parent=gene403
chr11	ENCODE	CDS	64264920	64265127	.	-	1	Parent=gene403
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene403
chr11	ENCODE	CDS	64265487	64265549	.	-	1	Parent=gene403
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene403
chr11	ENCODE	CDS	64266058	64266160	.	-	2	Parent=gene403
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene403
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene403
chr11	ENCODE	exon	64268051	64268193	.	-	.	Parent=gene403
###
chr11	ENCODE	gene	64264914	64268907	.	-	.	ID=gene404;Name=AP001462.3-009;name2=RASGRP2
chr11	ENCODE	exon	64264914	64265127	.	-	.	Parent=gene404
chr11	ENCODE	CDS	64264920	64265127	.	-	1	Parent=gene404
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene404
chr11	ENCODE	CDS	64265487	64265549	.	-	1	Parent=gene404
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene404
chr11	ENCODE	CDS	64266058	64266160	.	-	2	Parent=gene404
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene404
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene404
chr11	ENCODE	exon	64268790	64268907	.	-	.	Parent=gene404
###
chr11	ENCODE	gene	64264914	64269381	.	-	.	ID=gene405;Name=AP001462.3-008;name2=RASGRP2
chr11	ENCODE	exon	64264914	64265127	.	-	.	Parent=gene405
chr11	ENCODE	CDS	64264920	64265127	.	-	1	Parent=gene405
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene405
chr11	ENCODE	CDS	64265487	64265549	.	-	1	Parent=gene405
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene405
chr11	ENCODE	CDS	64266058	64266160	.	-	2	Parent=gene405
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene405
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene405
chr11	ENCODE	exon	64269323	64269381	.	-	.	Parent=gene405
###
chr11	ENCODE	gene	64264916	64268637	.	-	.	ID=gene406;Name=AP001462.3-005;name2=RASGRP2
chr11	ENCODE	exon	64264916	64265127	.	-	.	Parent=gene406
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene406
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene406
chr11	ENCODE	exon	64266842	64268637	.	-	.	Parent=gene406
###
chr11	ENCODE	gene	64265074	64269045	.	-	.	ID=gene407;Name=AP001462.3-013;name2=RASGRP2
chr11	ENCODE	exon	64265074	64265127	.	-	.	Parent=gene407
chr11	ENCODE	CDS	64265074	64265127	.	-	1	Parent=gene407
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene407
chr11	ENCODE	CDS	64265487	64265549	.	-	1	Parent=gene407
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene407
chr11	ENCODE	CDS	64266058	64266160	.	-	2	Parent=gene407
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene407
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene407
chr11	ENCODE	exon	64268981	64269045	.	-	.	Parent=gene407
###
chr11	ENCODE	gene	64265116	64268915	.	-	.	ID=gene408;Name=AP001462.3-022;name2=RASGRP2
chr11	ENCODE	exon	64265116	64265127	.	-	.	Parent=gene408
chr11	ENCODE	CDS	64265116	64265127	.	-	1	Parent=gene408
chr11	ENCODE	exon	64265487	64265549	.	-	.	Parent=gene408
chr11	ENCODE	CDS	64265487	64265549	.	-	1	Parent=gene408
chr11	ENCODE	exon	64266058	64266160	.	-	.	Parent=gene408
chr11	ENCODE	CDS	64266058	64266160	.	-	2	Parent=gene408
chr11	ENCODE	CDS	64266842	64266914	.	-	0	Parent=gene408
chr11	ENCODE	exon	64266842	64266985	.	-	.	Parent=gene408
chr11	ENCODE	exon	64268381	64268530	.	-	.	Parent=gene408
chr11	ENCODE	exon	64268790	64268915	.	-	.	Parent=gene408
###
chr11	ENCODE	gene	64266559	64268908	.	-	.	ID=gene409;Name=AP001462.3-023;name2=RASGRP2
chr11	ENCODE	exon	64266559	64266985	.	-	.	Parent=gene409
chr11	ENCODE	exon	64268790	64268908	.	-	.	Parent=gene409
###
chr11	ENCODE	gene	64266874	64268365	.	-	.	ID=gene410;Name=AP001462.3-014;name2=RASGRP2
chr11	ENCODE	CDS	64266874	64266914	.	-	0	Parent=gene410
chr11	ENCODE	exon	64266874	64266985	.	-	.	Parent=gene410
chr11	ENCODE	exon	64268078	64268365	.	-	.	Parent=gene410
###
chr11	ENCODE	gene	64270437	64272936	.	-	.	ID=gene411;Name=AP001462.4-003;name2=PYGM
chr11	ENCODE	exon	64270437	64270856	.	-	.	Parent=gene411
chr11	ENCODE	exon	64270969	64271035	.	-	.	Parent=gene411
chr11	ENCODE	exon	64271272	64272936	.	-	.	Parent=gene411
###
chr11	ENCODE	gene	64270437	64284022	.	-	.	ID=gene412;Name=AP001462.4-002;name2=PYGM
chr11	ENCODE	exon	64270437	64270856	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64270707	64270856	.	-	0	Parent=gene412
chr11	ENCODE	exon	64270969	64271035	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64270969	64271035	.	-	1	Parent=gene412
chr11	ENCODE	exon	64271272	64271406	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64271272	64271406	.	-	1	Parent=gene412
chr11	ENCODE	exon	64274424	64274631	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64274424	64274631	.	-	2	Parent=gene412
chr11	ENCODE	exon	64275373	64275514	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64275373	64275514	.	-	0	Parent=gene412
chr11	ENCODE	exon	64275645	64275703	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64275645	64275703	.	-	2	Parent=gene412
chr11	ENCODE	exon	64275972	64276119	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64275972	64276119	.	-	0	Parent=gene412
chr11	ENCODE	exon	64276451	64276552	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64276451	64276552	.	-	0	Parent=gene412
chr11	ENCODE	exon	64277121	64277235	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64277121	64277235	.	-	1	Parent=gene412
chr11	ENCODE	exon	64277567	64277730	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64277567	64277730	.	-	0	Parent=gene412
chr11	ENCODE	exon	64277927	64278073	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64277927	64278073	.	-	0	Parent=gene412
chr11	ENCODE	exon	64278301	64278393	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64278301	64278393	.	-	0	Parent=gene412
chr11	ENCODE	exon	64278741	64278884	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64278741	64278884	.	-	0	Parent=gene412
chr11	ENCODE	exon	64279321	64279403	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64279321	64279403	.	-	2	Parent=gene412
chr11	ENCODE	exon	64279495	64279606	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64279495	64279606	.	-	0	Parent=gene412
chr11	ENCODE	exon	64281827	64281958	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64281827	64281958	.	-	0	Parent=gene412
chr11	ENCODE	exon	64282294	64282314	.	-	.	Parent=gene412
chr11	ENCODE	CDS	64282294	64282314	.	-	0	Parent=gene412
chr11	ENCODE	CDS	64283704	64283946	.	-	0	Parent=gene412
chr11	ENCODE	exon	64283704	64284022	.	-	.	Parent=gene412
###
chr11	ENCODE	gene	64270437	64284345	.	-	.	ID=gene413;Name=AP001462.4-001;name2=PYGM
chr11	ENCODE	exon	64270437	64270856	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64270707	64270856	.	-	0	Parent=gene413
chr11	ENCODE	exon	64270969	64271035	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64270969	64271035	.	-	1	Parent=gene413
chr11	ENCODE	exon	64271272	64271406	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64271272	64271406	.	-	1	Parent=gene413
chr11	ENCODE	exon	64274424	64274631	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64274424	64274631	.	-	2	Parent=gene413
chr11	ENCODE	exon	64275373	64275514	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64275373	64275514	.	-	0	Parent=gene413
chr11	ENCODE	exon	64275645	64275703	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64275645	64275703	.	-	2	Parent=gene413
chr11	ENCODE	exon	64275972	64276119	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64275972	64276119	.	-	0	Parent=gene413
chr11	ENCODE	exon	64276451	64276552	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64276451	64276552	.	-	0	Parent=gene413
chr11	ENCODE	exon	64277121	64277235	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64277121	64277235	.	-	1	Parent=gene413
chr11	ENCODE	exon	64277567	64277730	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64277567	64277730	.	-	0	Parent=gene413
chr11	ENCODE	exon	64277927	64278073	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64277927	64278073	.	-	0	Parent=gene413
chr11	ENCODE	exon	64278301	64278393	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64278301	64278393	.	-	0	Parent=gene413
chr11	ENCODE	exon	64278741	64278884	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64278741	64278884	.	-	0	Parent=gene413
chr11	ENCODE	exon	64279321	64279403	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64279321	64279403	.	-	2	Parent=gene413
chr11	ENCODE	exon	64279495	64279606	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64279495	64279606	.	-	0	Parent=gene413
chr11	ENCODE	exon	64281827	64281958	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64281827	64281958	.	-	0	Parent=gene413
chr11	ENCODE	exon	64282294	64282397	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64282294	64282397	.	-	2	Parent=gene413
chr11	ENCODE	exon	64282485	64282563	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64282485	64282563	.	-	0	Parent=gene413
chr11	ENCODE	exon	64282651	64282752	.	-	.	Parent=gene413
chr11	ENCODE	CDS	64282651	64282752	.	-	0	Parent=gene413
chr11	ENCODE	CDS	64283704	64283946	.	-	0	Parent=gene413
chr11	ENCODE	exon	64283704	64284345	.	-	.	Parent=gene413
###
chr11	ENCODE	gene	64275196	64276063	.	-	.	ID=gene414;Name=AP001462.4-004;name2=PYGM
chr11	ENCODE	exon	64275196	64275514	.	-	.	Parent=gene414
chr11	ENCODE	exon	64275645	64275703	.	-	.	Parent=gene414
chr11	ENCODE	exon	64275972	64276063	.	-	.	Parent=gene414
###
chr11	ENCODE	gene	64277719	64278469	.	-	.	ID=gene415;Name=AP001462.4-005;name2=PYGM
chr11	ENCODE	exon	64277719	64277730	.	-	.	Parent=gene415
chr11	ENCODE	exon	64277927	64278073	.	-	.	Parent=gene415
chr11	ENCODE	exon	64278301	64278469	.	-	.	Parent=gene415
###
chr11	ENCODE	gene	64288654	64302517	.	-	.	ID=gene416;Name=AP001462.5-006;name2=SF1
chr11	ENCODE	exon	64288654	64289566	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64289502	64289566	.	-	2	Parent=gene416
chr11	ENCODE	exon	64290948	64291127	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64290948	64291127	.	-	2	Parent=gene416
chr11	ENCODE	exon	64291240	64291299	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64291240	64291299	.	-	2	Parent=gene416
chr11	ENCODE	exon	64291619	64291892	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64291619	64291892	.	-	0	Parent=gene416
chr11	ENCODE	exon	64292154	64292334	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64292154	64292334	.	-	1	Parent=gene416
chr11	ENCODE	exon	64293070	64293177	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64293070	64293177	.	-	1	Parent=gene416
chr11	ENCODE	exon	64293271	64293386	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64293271	64293386	.	-	0	Parent=gene416
chr11	ENCODE	exon	64293474	64293657	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64293474	64293657	.	-	1	Parent=gene416
chr11	ENCODE	exon	64294012	64294101	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64294012	64294101	.	-	1	Parent=gene416
chr11	ENCODE	exon	64294304	64294456	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64294304	64294456	.	-	1	Parent=gene416
chr11	ENCODE	exon	64297478	64297553	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64297478	64297553	.	-	2	Parent=gene416
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene416
chr11	ENCODE	CDS	64300546	64300674	.	-	2	Parent=gene416
chr11	ENCODE	CDS	64302035	64302440	.	-	0	Parent=gene416
chr11	ENCODE	exon	64302035	64302517	.	-	.	Parent=gene416
###
chr11	ENCODE	gene	64288654	64302778	.	-	.	ID=gene417;Name=AP001462.5-005;name2=SF1
chr11	ENCODE	exon	64288654	64290203	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64289866	64290203	.	-	2	Parent=gene417
chr11	ENCODE	exon	64290948	64291127	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64290948	64291127	.	-	2	Parent=gene417
chr11	ENCODE	exon	64291240	64291299	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64291240	64291299	.	-	2	Parent=gene417
chr11	ENCODE	exon	64291619	64291892	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64291619	64291892	.	-	0	Parent=gene417
chr11	ENCODE	exon	64292154	64292334	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64292154	64292334	.	-	1	Parent=gene417
chr11	ENCODE	exon	64293070	64293177	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64293070	64293177	.	-	1	Parent=gene417
chr11	ENCODE	exon	64293271	64293386	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64293271	64293386	.	-	0	Parent=gene417
chr11	ENCODE	exon	64293474	64293657	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64293474	64293657	.	-	1	Parent=gene417
chr11	ENCODE	exon	64294012	64294101	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64294012	64294101	.	-	1	Parent=gene417
chr11	ENCODE	exon	64294304	64294456	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64294304	64294456	.	-	1	Parent=gene417
chr11	ENCODE	exon	64297478	64297553	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64297478	64297553	.	-	2	Parent=gene417
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene417
chr11	ENCODE	CDS	64300546	64300674	.	-	2	Parent=gene417
chr11	ENCODE	CDS	64302410	64302440	.	-	0	Parent=gene417
chr11	ENCODE	exon	64302410	64302778	.	-	.	Parent=gene417
###
chr11	ENCODE	gene	64288654	64302795	.	-	.	ID=gene418;Name=AP001462.5-002;name2=SF1
chr11	ENCODE	exon	64288654	64289566	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64289502	64289566	.	-	2	Parent=gene418
chr11	ENCODE	exon	64290948	64291127	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64290948	64291127	.	-	2	Parent=gene418
chr11	ENCODE	exon	64291240	64291299	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64291240	64291299	.	-	2	Parent=gene418
chr11	ENCODE	exon	64291619	64291892	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64291619	64291892	.	-	0	Parent=gene418
chr11	ENCODE	exon	64292154	64292334	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64292154	64292334	.	-	1	Parent=gene418
chr11	ENCODE	exon	64293070	64293177	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64293070	64293177	.	-	1	Parent=gene418
chr11	ENCODE	exon	64293271	64293386	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64293271	64293386	.	-	0	Parent=gene418
chr11	ENCODE	exon	64293474	64293657	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64293474	64293657	.	-	1	Parent=gene418
chr11	ENCODE	exon	64294012	64294101	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64294012	64294101	.	-	1	Parent=gene418
chr11	ENCODE	exon	64294304	64294456	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64294304	64294456	.	-	1	Parent=gene418
chr11	ENCODE	exon	64297478	64297553	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64297478	64297553	.	-	2	Parent=gene418
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene418
chr11	ENCODE	CDS	64300546	64300674	.	-	2	Parent=gene418
chr11	ENCODE	CDS	64302410	64302440	.	-	0	Parent=gene418
chr11	ENCODE	exon	64302410	64302795	.	-	.	Parent=gene418
###
chr11	ENCODE	gene	64288654	64302795	.	-	.	ID=gene419;Name=AP001462.5-003;name2=SF1
chr11	ENCODE	exon	64288654	64289566	.	-	.	Parent=gene419
chr11	ENCODE	exon	64290948	64291127	.	-	.	Parent=gene419
chr11	ENCODE	exon	64291240	64291299	.	-	.	Parent=gene419
chr11	ENCODE	exon	64291615	64291892	.	-	.	Parent=gene419
chr11	ENCODE	exon	64292154	64292334	.	-	.	Parent=gene419
chr11	ENCODE	exon	64293070	64293177	.	-	.	Parent=gene419
chr11	ENCODE	exon	64293271	64293386	.	-	.	Parent=gene419
chr11	ENCODE	exon	64293474	64293657	.	-	.	Parent=gene419
chr11	ENCODE	exon	64294012	64294101	.	-	.	Parent=gene419
chr11	ENCODE	exon	64294304	64294456	.	-	.	Parent=gene419
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene419
chr11	ENCODE	exon	64302410	64302795	.	-	.	Parent=gene419
###
chr11	ENCODE	gene	64288654	64302795	.	-	.	ID=gene420;name2=SF1;Name=AP001462.5-004
chr11	ENCODE	exon	64288654	64289566	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64289437	64289566	.	-	1	Parent=gene420
chr11	ENCODE	exon	64290948	64291127	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64290948	64291127	.	-	1	Parent=gene420
chr11	ENCODE	exon	64291240	64291299	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64291240	64291299	.	-	1	Parent=gene420
chr11	ENCODE	exon	64291615	64291892	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64291615	64291892	.	-	0	Parent=gene420
chr11	ENCODE	exon	64292154	64292334	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64292154	64292334	.	-	1	Parent=gene420
chr11	ENCODE	exon	64293070	64293177	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64293070	64293177	.	-	1	Parent=gene420
chr11	ENCODE	exon	64293271	64293386	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64293271	64293386	.	-	0	Parent=gene420
chr11	ENCODE	exon	64293474	64293657	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64293474	64293657	.	-	1	Parent=gene420
chr11	ENCODE	exon	64294012	64294101	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64294012	64294101	.	-	1	Parent=gene420
chr11	ENCODE	exon	64294304	64294456	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64294304	64294456	.	-	1	Parent=gene420
chr11	ENCODE	exon	64297478	64297553	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64297478	64297553	.	-	2	Parent=gene420
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene420
chr11	ENCODE	CDS	64300546	64300674	.	-	2	Parent=gene420
chr11	ENCODE	CDS	64302410	64302440	.	-	0	Parent=gene420
chr11	ENCODE	exon	64302410	64302795	.	-	.	Parent=gene420
###
chr11	ENCODE	gene	64288654	64302811	.	-	.	ID=gene421;Name=AP001462.5-008;name2=SF1
chr11	ENCODE	exon	64288654	64289645	.	-	.	Parent=gene421
chr11	ENCODE	exon	64290029	64290203	.	-	.	Parent=gene421
chr11	ENCODE	exon	64290948	64291127	.	-	.	Parent=gene421
chr11	ENCODE	exon	64291240	64291299	.	-	.	Parent=gene421
chr11	ENCODE	exon	64291619	64291892	.	-	.	Parent=gene421
chr11	ENCODE	exon	64292154	64292334	.	-	.	Parent=gene421
chr11	ENCODE	exon	64293070	64293177	.	-	.	Parent=gene421
chr11	ENCODE	exon	64293271	64293386	.	-	.	Parent=gene421
chr11	ENCODE	exon	64293474	64293657	.	-	.	Parent=gene421
chr11	ENCODE	exon	64294012	64294101	.	-	.	Parent=gene421
chr11	ENCODE	exon	64294304	64294456	.	-	.	Parent=gene421
chr11	ENCODE	exon	64297478	64297553	.	-	.	Parent=gene421
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene421
chr11	ENCODE	exon	64302410	64302811	.	-	.	Parent=gene421
###
chr11	ENCODE	gene	64288654	64302834	.	-	.	ID=gene422;Name=AP001462.5-001;name2=SF1
chr11	ENCODE	exon	64288654	64289566	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64289437	64289566	.	-	1	Parent=gene422
chr11	ENCODE	exon	64289999	64290203	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64289999	64290203	.	-	2	Parent=gene422
chr11	ENCODE	exon	64290948	64291127	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64290948	64291127	.	-	2	Parent=gene422
chr11	ENCODE	exon	64291240	64291299	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64291240	64291299	.	-	2	Parent=gene422
chr11	ENCODE	exon	64291619	64291892	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64291619	64291892	.	-	0	Parent=gene422
chr11	ENCODE	exon	64292154	64292334	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64292154	64292334	.	-	1	Parent=gene422
chr11	ENCODE	exon	64293070	64293177	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64293070	64293177	.	-	1	Parent=gene422
chr11	ENCODE	exon	64293271	64293386	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64293271	64293386	.	-	0	Parent=gene422
chr11	ENCODE	exon	64293474	64293657	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64293474	64293657	.	-	1	Parent=gene422
chr11	ENCODE	exon	64294012	64294101	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64294012	64294101	.	-	1	Parent=gene422
chr11	ENCODE	exon	64294304	64294456	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64294304	64294456	.	-	1	Parent=gene422
chr11	ENCODE	exon	64297478	64297553	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64297478	64297553	.	-	2	Parent=gene422
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene422
chr11	ENCODE	CDS	64300546	64300674	.	-	2	Parent=gene422
chr11	ENCODE	CDS	64302410	64302440	.	-	0	Parent=gene422
chr11	ENCODE	exon	64302410	64302834	.	-	.	Parent=gene422
###
chr11	ENCODE	gene	64289338	64291892	.	-	.	ID=gene423;Name=AP001462.5-014;name2=SF1
chr11	ENCODE	exon	64289338	64289566	.	-	.	Parent=gene423
chr11	ENCODE	CDS	64289502	64289566	.	-	2	Parent=gene423
chr11	ENCODE	exon	64290948	64291127	.	-	.	Parent=gene423
chr11	ENCODE	CDS	64290948	64291127	.	-	2	Parent=gene423
chr11	ENCODE	exon	64291240	64291323	.	-	.	Parent=gene423
chr11	ENCODE	CDS	64291240	64291323	.	-	2	Parent=gene423
chr11	ENCODE	exon	64291619	64291892	.	-	.	Parent=gene423
chr11	ENCODE	CDS	64291619	64291892	.	-	0	Parent=gene423
###
chr11	ENCODE	gene	64290462	64291694	.	-	.	ID=gene424;Name=AP001462.5-015;name2=SF1
chr11	ENCODE	exon	64290462	64291127	.	-	.	Parent=gene424
chr11	ENCODE	exon	64291240	64291299	.	-	.	Parent=gene424
chr11	ENCODE	exon	64291619	64291694	.	-	.	Parent=gene424
###
chr11	ENCODE	gene	64292219	64293717	.	-	.	ID=gene425;Name=AP001462.5-017;name2=SF1
chr11	ENCODE	exon	64292219	64292334	.	-	.	Parent=gene425
chr11	ENCODE	exon	64293070	64293177	.	-	.	Parent=gene425
chr11	ENCODE	exon	64293271	64293386	.	-	.	Parent=gene425
chr11	ENCODE	exon	64293474	64293717	.	-	.	Parent=gene425
###
chr11	ENCODE	gene	64293326	64294687	.	-	.	ID=gene426;Name=AP001462.5-009;name2=SF1
chr11	ENCODE	exon	64293326	64293386	.	-	.	Parent=gene426
chr11	ENCODE	exon	64293474	64293657	.	-	.	Parent=gene426
chr11	ENCODE	exon	64294012	64294101	.	-	.	Parent=gene426
chr11	ENCODE	exon	64294304	64294687	.	-	.	Parent=gene426
###
chr11	ENCODE	gene	64293590	64295655	.	-	.	ID=gene427;Name=AP001462.5-013;name2=SF1
chr11	ENCODE	exon	64293590	64293657	.	-	.	Parent=gene427
chr11	ENCODE	exon	64294012	64294101	.	-	.	Parent=gene427
chr11	ENCODE	exon	64294304	64294456	.	-	.	Parent=gene427
chr11	ENCODE	exon	64295512	64295655	.	-	.	Parent=gene427
###
chr11	ENCODE	gene	64294096	64301793	.	-	.	ID=gene428;Name=AP001462.5-016;name2=SF1
chr11	ENCODE	exon	64294096	64294101	.	-	.	Parent=gene428
chr11	ENCODE	exon	64294304	64294456	.	-	.	Parent=gene428
chr11	ENCODE	exon	64297478	64297553	.	-	.	Parent=gene428
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene428
chr11	ENCODE	exon	64301547	64301793	.	-	.	Parent=gene428
###
chr11	ENCODE	gene	64294345	64302555	.	-	.	ID=gene429;Name=AP001462.5-011;name2=SF1
chr11	ENCODE	exon	64294345	64294456	.	-	.	Parent=gene429
chr11	ENCODE	exon	64297478	64297553	.	-	.	Parent=gene429
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene429
chr11	ENCODE	exon	64302035	64302194	.	-	.	Parent=gene429
chr11	ENCODE	exon	64302410	64302555	.	-	.	Parent=gene429
###
chr11	ENCODE	gene	64297071	64302552	.	-	.	ID=gene430;Name=AP001462.5-012;name2=SF1
chr11	ENCODE	exon	64297071	64297553	.	-	.	Parent=gene430
chr11	ENCODE	exon	64300546	64300674	.	-	.	Parent=gene430
chr11	ENCODE	exon	64302410	64302552	.	-	.	Parent=gene430
###
chr11	ENCODE	gene	64300094	64302085	.	-	.	ID=gene431;Name=AP001462.5-010;name2=SF1
chr11	ENCODE	exon	64300094	64300674	.	-	.	Parent=gene431
chr11	ENCODE	exon	64302035	64302085	.	-	.	Parent=gene431
###
chr11	ENCODE	gene	64300094	64302811	.	-	.	ID=gene432;Name=AP001462.5-007;name2=SF1
chr11	ENCODE	exon	64300094	64300674	.	-	.	Parent=gene432
chr11	ENCODE	exon	64302410	64302811	.	-	.	Parent=gene432
###
chr11	ENCODE	gene	64313185	64320546	.	-	.	ID=gene433;Name=AP001462.2-005;name2=MAP4K2
chr11	ENCODE	exon	64313185	64313672	.	-	.	Parent=gene433
chr11	ENCODE	exon	64313778	64313833	.	-	.	Parent=gene433
chr11	ENCODE	exon	64313937	64314007	.	-	.	Parent=gene433
chr11	ENCODE	exon	64314236	64314322	.	-	.	Parent=gene433
chr11	ENCODE	exon	64314442	64314498	.	-	.	Parent=gene433
chr11	ENCODE	exon	64316006	64316134	.	-	.	Parent=gene433
chr11	ENCODE	exon	64316220	64316323	.	-	.	Parent=gene433
chr11	ENCODE	exon	64316412	64316470	.	-	.	Parent=gene433
chr11	ENCODE	exon	64320321	64320438	.	-	.	Parent=gene433
chr11	ENCODE	exon	64320541	64320546	.	-	.	Parent=gene433
###
chr11	ENCODE	gene	64313185	64321391	.	-	.	ID=gene434;Name=AP001462.2-004;name2=MAP4K2
chr11	ENCODE	exon	64313185	64313672	.	-	.	Parent=gene434
chr11	ENCODE	exon	64313778	64313833	.	-	.	Parent=gene434
chr11	ENCODE	exon	64313937	64314007	.	-	.	Parent=gene434
chr11	ENCODE	exon	64314236	64314322	.	-	.	Parent=gene434
chr11	ENCODE	exon	64314442	64314510	.	-	.	Parent=gene434
chr11	ENCODE	exon	64315957	64316470	.	-	.	Parent=gene434
chr11	ENCODE	exon	64320321	64320438	.	-	.	Parent=gene434
chr11	ENCODE	exon	64320541	64320601	.	-	.	Parent=gene434
chr11	ENCODE	exon	64320682	64320761	.	-	.	Parent=gene434
chr11	ENCODE	exon	64320857	64320941	.	-	.	Parent=gene434
chr11	ENCODE	exon	64321030	64321071	.	-	.	Parent=gene434
chr11	ENCODE	exon	64321152	64321216	.	-	.	Parent=gene434
chr11	ENCODE	exon	64321323	64321391	.	-	.	Parent=gene434
###
chr11	ENCODE	gene	64313185	64327289	.	-	.	ID=gene435;Name=AP001462.2-001;name2=MAP4K2
chr11	ENCODE	exon	64313185	64313672	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64313585	64313672	.	-	1	Parent=gene435
chr11	ENCODE	exon	64313778	64313833	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64313778	64313833	.	-	0	Parent=gene435
chr11	ENCODE	exon	64313937	64314007	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64313937	64314007	.	-	2	Parent=gene435
chr11	ENCODE	exon	64314236	64314322	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64314236	64314322	.	-	2	Parent=gene435
chr11	ENCODE	exon	64314442	64314510	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64314442	64314510	.	-	2	Parent=gene435
chr11	ENCODE	exon	64315957	64316134	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64315957	64316134	.	-	0	Parent=gene435
chr11	ENCODE	exon	64316220	64316323	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64316220	64316323	.	-	2	Parent=gene435
chr11	ENCODE	exon	64316412	64316470	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64316412	64316470	.	-	1	Parent=gene435
chr11	ENCODE	exon	64320321	64320438	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64320321	64320438	.	-	2	Parent=gene435
chr11	ENCODE	exon	64320541	64320601	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64320541	64320601	.	-	0	Parent=gene435
chr11	ENCODE	exon	64320682	64320761	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64320682	64320761	.	-	2	Parent=gene435
chr11	ENCODE	exon	64320857	64320941	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64320857	64320941	.	-	0	Parent=gene435
chr11	ENCODE	exon	64321030	64321071	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64321030	64321071	.	-	0	Parent=gene435
chr11	ENCODE	exon	64321152	64321240	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64321152	64321240	.	-	2	Parent=gene435
chr11	ENCODE	exon	64321323	64321428	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64321323	64321428	.	-	0	Parent=gene435
chr11	ENCODE	exon	64321549	64321582	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64321549	64321582	.	-	1	Parent=gene435
chr11	ENCODE	exon	64321674	64321712	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64321674	64321712	.	-	1	Parent=gene435
chr11	ENCODE	exon	64322842	64322885	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64322842	64322885	.	-	0	Parent=gene435
chr11	ENCODE	exon	64323469	64323527	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64323469	64323527	.	-	2	Parent=gene435
chr11	ENCODE	exon	64323653	64323731	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64323653	64323731	.	-	0	Parent=gene435
chr11	ENCODE	exon	64324157	64324264	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64324157	64324264	.	-	0	Parent=gene435
chr11	ENCODE	exon	64324359	64324440	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64324359	64324440	.	-	1	Parent=gene435
chr11	ENCODE	exon	64324812	64324874	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64324812	64324874	.	-	1	Parent=gene435
chr11	ENCODE	exon	64324948	64325079	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64324948	64325079	.	-	1	Parent=gene435
chr11	ENCODE	exon	64325159	64325231	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64325159	64325231	.	-	2	Parent=gene435
chr11	ENCODE	exon	64325627	64325669	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64325627	64325669	.	-	0	Parent=gene435
chr11	ENCODE	exon	64325758	64325805	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64325758	64325805	.	-	0	Parent=gene435
chr11	ENCODE	exon	64326114	64326169	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64326114	64326169	.	-	2	Parent=gene435
chr11	ENCODE	exon	64326467	64326531	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64326467	64326531	.	-	1	Parent=gene435
chr11	ENCODE	exon	64326611	64326701	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64326611	64326701	.	-	2	Parent=gene435
chr11	ENCODE	exon	64326933	64326990	.	-	.	Parent=gene435
chr11	ENCODE	CDS	64326933	64326990	.	-	0	Parent=gene435
chr11	ENCODE	CDS	64327102	64327197	.	-	0	Parent=gene435
chr11	ENCODE	exon	64327102	64327289	.	-	.	Parent=gene435
###
chr11	ENCODE	gene	64313185	64327289	.	-	.	ID=gene436;Name=AP001462.2-002;name2=MAP4K2
chr11	ENCODE	exon	64313185	64313672	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64313585	64313672	.	-	1	Parent=gene436
chr11	ENCODE	exon	64313778	64313833	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64313778	64313833	.	-	0	Parent=gene436
chr11	ENCODE	exon	64313937	64314007	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64313937	64314007	.	-	2	Parent=gene436
chr11	ENCODE	exon	64314236	64314322	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64314236	64314322	.	-	2	Parent=gene436
chr11	ENCODE	exon	64314442	64314510	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64314442	64314510	.	-	2	Parent=gene436
chr11	ENCODE	exon	64315957	64316134	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64315957	64316134	.	-	0	Parent=gene436
chr11	ENCODE	exon	64316220	64316323	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64316220	64316323	.	-	2	Parent=gene436
chr11	ENCODE	exon	64316412	64316470	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64316412	64316470	.	-	1	Parent=gene436
chr11	ENCODE	exon	64320321	64320438	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64320321	64320438	.	-	2	Parent=gene436
chr11	ENCODE	exon	64320541	64320601	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64320541	64320601	.	-	0	Parent=gene436
chr11	ENCODE	exon	64320682	64320761	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64320682	64320761	.	-	2	Parent=gene436
chr11	ENCODE	exon	64320857	64320941	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64320857	64320941	.	-	0	Parent=gene436
chr11	ENCODE	exon	64321030	64321071	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64321030	64321071	.	-	0	Parent=gene436
chr11	ENCODE	exon	64321152	64321216	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64321152	64321216	.	-	2	Parent=gene436
chr11	ENCODE	exon	64321323	64321428	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64321323	64321428	.	-	0	Parent=gene436
chr11	ENCODE	exon	64321549	64321582	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64321549	64321582	.	-	1	Parent=gene436
chr11	ENCODE	exon	64321674	64321712	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64321674	64321712	.	-	1	Parent=gene436
chr11	ENCODE	exon	64322842	64322885	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64322842	64322885	.	-	0	Parent=gene436
chr11	ENCODE	exon	64323469	64323527	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64323469	64323527	.	-	2	Parent=gene436
chr11	ENCODE	exon	64323653	64323731	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64323653	64323731	.	-	0	Parent=gene436
chr11	ENCODE	exon	64324157	64324264	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64324157	64324264	.	-	0	Parent=gene436
chr11	ENCODE	exon	64324359	64324440	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64324359	64324440	.	-	1	Parent=gene436
chr11	ENCODE	exon	64324812	64324874	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64324812	64324874	.	-	1	Parent=gene436
chr11	ENCODE	exon	64324948	64325079	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64324948	64325079	.	-	1	Parent=gene436
chr11	ENCODE	exon	64325159	64325231	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64325159	64325231	.	-	2	Parent=gene436
chr11	ENCODE	exon	64325627	64325669	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64325627	64325669	.	-	0	Parent=gene436
chr11	ENCODE	exon	64325758	64325805	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64325758	64325805	.	-	0	Parent=gene436
chr11	ENCODE	exon	64326114	64326169	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64326114	64326169	.	-	2	Parent=gene436
chr11	ENCODE	exon	64326467	64326531	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64326467	64326531	.	-	1	Parent=gene436
chr11	ENCODE	exon	64326611	64326701	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64326611	64326701	.	-	2	Parent=gene436
chr11	ENCODE	exon	64326933	64326990	.	-	.	Parent=gene436
chr11	ENCODE	CDS	64326933	64326990	.	-	0	Parent=gene436
chr11	ENCODE	CDS	64327102	64327197	.	-	0	Parent=gene436
chr11	ENCODE	exon	64327102	64327289	.	-	.	Parent=gene436
###
chr11	ENCODE	gene	64313218	64327289	.	-	.	ID=gene437;Name=AP001462.2-003;name2=MAP4K2
chr11	ENCODE	exon	64313218	64313312	.	-	.	Parent=gene437
chr11	ENCODE	exon	64321152	64321216	.	-	.	Parent=gene437
chr11	ENCODE	exon	64321323	64321428	.	-	.	Parent=gene437
chr11	ENCODE	exon	64321549	64321582	.	-	.	Parent=gene437
chr11	ENCODE	exon	64321674	64321712	.	-	.	Parent=gene437
chr11	ENCODE	exon	64322842	64322885	.	-	.	Parent=gene437
chr11	ENCODE	exon	64323469	64323527	.	-	.	Parent=gene437
chr11	ENCODE	exon	64323653	64323731	.	-	.	Parent=gene437
chr11	ENCODE	exon	64324157	64324264	.	-	.	Parent=gene437
chr11	ENCODE	exon	64324359	64324440	.	-	.	Parent=gene437
chr11	ENCODE	exon	64324812	64324874	.	-	.	Parent=gene437
chr11	ENCODE	exon	64324948	64325079	.	-	.	Parent=gene437
chr11	ENCODE	exon	64325159	64325231	.	-	.	Parent=gene437
chr11	ENCODE	exon	64325627	64325669	.	-	.	Parent=gene437
chr11	ENCODE	exon	64325758	64325805	.	-	.	Parent=gene437
chr11	ENCODE	exon	64326114	64326169	.	-	.	Parent=gene437
chr11	ENCODE	exon	64326467	64326531	.	-	.	Parent=gene437
chr11	ENCODE	exon	64326611	64326701	.	-	.	Parent=gene437
chr11	ENCODE	exon	64326933	64326990	.	-	.	Parent=gene437
chr11	ENCODE	exon	64327102	64327289	.	-	.	Parent=gene437
###
chr11	ENCODE	gene	64313937	64323707	.	-	.	ID=gene438;Name=AP001462.2-008;name2=MAP4K2
chr11	ENCODE	exon	64313937	64314007	.	-	.	Parent=gene438
chr11	ENCODE	exon	64314236	64314322	.	-	.	Parent=gene438
chr11	ENCODE	exon	64314442	64314510	.	-	.	Parent=gene438
chr11	ENCODE	exon	64315957	64316134	.	-	.	Parent=gene438
chr11	ENCODE	exon	64316220	64316470	.	-	.	Parent=gene438
chr11	ENCODE	exon	64320321	64320438	.	-	.	Parent=gene438
chr11	ENCODE	exon	64320541	64320601	.	-	.	Parent=gene438
chr11	ENCODE	exon	64320682	64320761	.	-	.	Parent=gene438
chr11	ENCODE	exon	64320857	64320941	.	-	.	Parent=gene438
chr11	ENCODE	exon	64321030	64321071	.	-	.	Parent=gene438
chr11	ENCODE	exon	64321152	64321240	.	-	.	Parent=gene438
chr11	ENCODE	exon	64321323	64321428	.	-	.	Parent=gene438
chr11	ENCODE	exon	64321549	64321582	.	-	.	Parent=gene438
chr11	ENCODE	exon	64321674	64321712	.	-	.	Parent=gene438
chr11	ENCODE	exon	64322842	64322885	.	-	.	Parent=gene438
chr11	ENCODE	exon	64323469	64323527	.	-	.	Parent=gene438
chr11	ENCODE	exon	64323653	64323707	.	-	.	Parent=gene438
###
chr11	ENCODE	gene	64321019	64323682	.	-	.	ID=gene439;Name=AP001462.2-009;name2=MAP4K2
chr11	ENCODE	exon	64321019	64321071	.	-	.	Parent=gene439
chr11	ENCODE	exon	64321152	64321240	.	-	.	Parent=gene439
chr11	ENCODE	exon	64321323	64321582	.	-	.	Parent=gene439
chr11	ENCODE	exon	64321674	64321712	.	-	.	Parent=gene439
chr11	ENCODE	exon	64322842	64322885	.	-	.	Parent=gene439
chr11	ENCODE	exon	64323469	64323527	.	-	.	Parent=gene439
chr11	ENCODE	exon	64323653	64323682	.	-	.	Parent=gene439
###
chr11	ENCODE	gene	64323469	64327223	.	-	.	ID=gene440;Name=AP001462.2-006;name2=MAP4K2
chr11	ENCODE	exon	64323469	64323527	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64323469	64323527	.	-	2	Parent=gene440
chr11	ENCODE	exon	64323653	64323731	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64323653	64323731	.	-	0	Parent=gene440
chr11	ENCODE	exon	64324157	64324264	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64324157	64324264	.	-	0	Parent=gene440
chr11	ENCODE	exon	64324359	64324440	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64324359	64324440	.	-	1	Parent=gene440
chr11	ENCODE	exon	64324812	64324874	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64324812	64324874	.	-	1	Parent=gene440
chr11	ENCODE	exon	64325159	64325231	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64325159	64325231	.	-	2	Parent=gene440
chr11	ENCODE	exon	64325627	64325669	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64325627	64325669	.	-	0	Parent=gene440
chr11	ENCODE	exon	64325758	64325805	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64325758	64325805	.	-	0	Parent=gene440
chr11	ENCODE	exon	64326114	64326169	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64326114	64326169	.	-	2	Parent=gene440
chr11	ENCODE	exon	64326467	64326531	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64326467	64326531	.	-	1	Parent=gene440
chr11	ENCODE	exon	64326611	64326701	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64326611	64326701	.	-	2	Parent=gene440
chr11	ENCODE	exon	64326933	64326990	.	-	.	Parent=gene440
chr11	ENCODE	CDS	64326933	64326990	.	-	0	Parent=gene440
chr11	ENCODE	CDS	64327102	64327197	.	-	0	Parent=gene440
chr11	ENCODE	exon	64327102	64327223	.	-	.	Parent=gene440
###
chr11	ENCODE	gene	64324230	64325861	.	-	.	ID=gene441;Name=AP001462.2-011;name2=MAP4K2
chr11	ENCODE	exon	64324230	64324264	.	-	.	Parent=gene441
chr11	ENCODE	exon	64324359	64324440	.	-	.	Parent=gene441
chr11	ENCODE	exon	64324812	64324874	.	-	.	Parent=gene441
chr11	ENCODE	exon	64324948	64325079	.	-	.	Parent=gene441
chr11	ENCODE	exon	64325159	64325231	.	-	.	Parent=gene441
chr11	ENCODE	exon	64325627	64325669	.	-	.	Parent=gene441
chr11	ENCODE	exon	64325758	64325861	.	-	.	Parent=gene441
###
chr11	ENCODE	gene	64324384	64327058	.	-	.	ID=gene442;Name=AP001462.2-007;name2=MAP4K2
chr11	ENCODE	exon	64324384	64324440	.	-	.	Parent=gene442
chr11	ENCODE	exon	64324812	64324874	.	-	.	Parent=gene442
chr11	ENCODE	exon	64325159	64325231	.	-	.	Parent=gene442
chr11	ENCODE	exon	64325758	64325805	.	-	.	Parent=gene442
chr11	ENCODE	exon	64326114	64326169	.	-	.	Parent=gene442
chr11	ENCODE	exon	64326467	64326531	.	-	.	Parent=gene442
chr11	ENCODE	exon	64326611	64326701	.	-	.	Parent=gene442
chr11	ENCODE	exon	64326933	64327058	.	-	.	Parent=gene442
###
chr11	ENCODE	gene	64324396	64327177	.	-	.	ID=gene443;Name=AP001462.2-010;name2=MAP4K2
chr11	ENCODE	exon	64324396	64324440	.	-	.	Parent=gene443
chr11	ENCODE	exon	64324812	64324874	.	-	.	Parent=gene443
chr11	ENCODE	exon	64324948	64325079	.	-	.	Parent=gene443
chr11	ENCODE	exon	64325159	64325231	.	-	.	Parent=gene443
chr11	ENCODE	exon	64325758	64325805	.	-	.	Parent=gene443
chr11	ENCODE	exon	64326114	64326169	.	-	.	Parent=gene443
chr11	ENCODE	exon	64326467	64326531	.	-	.	Parent=gene443
chr11	ENCODE	exon	64326611	64326701	.	-	.	Parent=gene443
chr11	ENCODE	exon	64326933	64327177	.	-	.	Parent=gene443
###
chr11	ENCODE	gene	64327564	64334533	.	-	.	ID=gene444;Name=AP001462.1-008;name2=MEN1
chr11	ENCODE	exon	64327564	64328864	.	-	.	Parent=gene444
chr11	ENCODE	CDS	64328382	64328864	.	-	0	Parent=gene444
chr11	ENCODE	exon	64329683	64329818	.	-	.	Parent=gene444
chr11	ENCODE	CDS	64329683	64329818	.	-	1	Parent=gene444
chr11	ENCODE	exon	64330280	64330416	.	-	.	Parent=gene444
chr11	ENCODE	CDS	64330280	64330416	.	-	0	Parent=gene444
chr11	ENCODE	exon	64331059	64331146	.	-	.	Parent=gene444
chr11	ENCODE	CDS	64331059	64331146	.	-	1	Parent=gene444
chr11	ENCODE	exon	64331227	64331267	.	-	.	Parent=gene444
chr11	ENCODE	CDS	64331227	64331267	.	-	0	Parent=gene444
chr11	ENCODE	exon	64331600	64331728	.	-	.	Parent=gene444
chr11	ENCODE	CDS	64331600	64331728	.	-	0	Parent=gene444
chr11	ENCODE	exon	64331939	64332147	.	-	.	Parent=gene444
chr11	ENCODE	CDS	64331939	64332147	.	-	2	Parent=gene444
chr11	ENCODE	CDS	64333713	64334157	.	-	0	Parent=gene444
chr11	ENCODE	exon	64333713	64334533	.	-	.	Parent=gene444
###
chr11	ENCODE	gene	64327564	64334606	.	-	.	ID=gene445;Name=AP001462.1-002;name2=MEN1
chr11	ENCODE	exon	64327564	64328864	.	-	.	Parent=gene445
chr11	ENCODE	CDS	64328382	64328864	.	-	0	Parent=gene445
chr11	ENCODE	exon	64329082	64329246	.	-	.	Parent=gene445
chr11	ENCODE	CDS	64329082	64329246	.	-	0	Parent=gene445
chr11	ENCODE	exon	64329683	64329818	.	-	.	Parent=gene445
chr11	ENCODE	CDS	64329683	64329818	.	-	1	Parent=gene445
chr11	ENCODE	exon	64330280	64330416	.	-	.	Parent=gene445
chr11	ENCODE	CDS	64330280	64330416	.	-	0	Parent=gene445
chr11	ENCODE	exon	64331059	64331146	.	-	.	Parent=gene445
chr11	ENCODE	CDS	64331059	64331146	.	-	1	Parent=gene445
chr11	ENCODE	exon	64331227	64331267	.	-	.	Parent=gene445
chr11	ENCODE	CDS	64331227	64331267	.	-	0	Parent=gene445
chr11	ENCODE	exon	64331600	64331728	.	-	.	Parent=gene445
chr11	ENCODE	CDS	64331600	64331728	.	-	0	Parent=gene445
chr11	ENCODE	exon	64332044	64332147	.	-	.	Parent=gene445
chr11	ENCODE	CDS	64332044	64332147	.	-	2	Parent=gene445
chr11	ENCODE	CDS	64333713	64334157	.	-	0	Parent=gene445
chr11	ENCODE	exon	64333713	64334180	.	-	.	Parent=gene445
chr11	ENCODE	exon	64334562	64334606	.	-	.	Parent=gene445
###
chr11	ENCODE	gene	64327564	64334656	.	-	.	ID=gene446;Name=AP001462.1-007;name2=MEN1
chr11	ENCODE	exon	64327564	64328864	.	-	.	Parent=gene446
chr11	ENCODE	CDS	64328382	64328864	.	-	0	Parent=gene446
chr11	ENCODE	exon	64329082	64329246	.	-	.	Parent=gene446
chr11	ENCODE	CDS	64329082	64329246	.	-	0	Parent=gene446
chr11	ENCODE	exon	64329683	64329818	.	-	.	Parent=gene446
chr11	ENCODE	CDS	64329683	64329818	.	-	1	Parent=gene446
chr11	ENCODE	exon	64330280	64330416	.	-	.	Parent=gene446
chr11	ENCODE	CDS	64330280	64330416	.	-	0	Parent=gene446
chr11	ENCODE	exon	64331059	64331146	.	-	.	Parent=gene446
chr11	ENCODE	CDS	64331059	64331146	.	-	1	Parent=gene446
chr11	ENCODE	exon	64331227	64331267	.	-	.	Parent=gene446
chr11	ENCODE	CDS	64331227	64331267	.	-	0	Parent=gene446
chr11	ENCODE	exon	64331600	64331728	.	-	.	Parent=gene446
chr11	ENCODE	CDS	64331600	64331728	.	-	0	Parent=gene446
chr11	ENCODE	exon	64331939	64332147	.	-	.	Parent=gene446
chr11	ENCODE	CDS	64331939	64332147	.	-	2	Parent=gene446
chr11	ENCODE	CDS	64333713	64334157	.	-	0	Parent=gene446
chr11	ENCODE	exon	64333713	64334656	.	-	.	Parent=gene446
###
chr11	ENCODE	gene	64327564	64334764	.	-	.	ID=gene447;Name=AP001462.1-001;name2=MEN1
chr11	ENCODE	exon	64327564	64328864	.	-	.	Parent=gene447
chr11	ENCODE	CDS	64328382	64328864	.	-	0	Parent=gene447
chr11	ENCODE	exon	64329082	64329246	.	-	.	Parent=gene447
chr11	ENCODE	CDS	64329082	64329246	.	-	0	Parent=gene447
chr11	ENCODE	exon	64329683	64329818	.	-	.	Parent=gene447
chr11	ENCODE	CDS	64329683	64329818	.	-	1	Parent=gene447
chr11	ENCODE	exon	64330280	64330416	.	-	.	Parent=gene447
chr11	ENCODE	CDS	64330280	64330416	.	-	0	Parent=gene447
chr11	ENCODE	exon	64331059	64331146	.	-	.	Parent=gene447
chr11	ENCODE	CDS	64331059	64331146	.	-	1	Parent=gene447
chr11	ENCODE	exon	64331227	64331267	.	-	.	Parent=gene447
chr11	ENCODE	CDS	64331227	64331267	.	-	0	Parent=gene447
chr11	ENCODE	exon	64331600	64331728	.	-	.	Parent=gene447
chr11	ENCODE	CDS	64331600	64331728	.	-	0	Parent=gene447
chr11	ENCODE	exon	64331939	64332147	.	-	.	Parent=gene447
chr11	ENCODE	CDS	64331939	64332147	.	-	2	Parent=gene447
chr11	ENCODE	CDS	64333713	64334157	.	-	0	Parent=gene447
chr11	ENCODE	exon	64333713	64334180	.	-	.	Parent=gene447
chr11	ENCODE	exon	64334678	64334764	.	-	.	Parent=gene447
###
chr11	ENCODE	gene	64327564	64334789	.	-	.	ID=gene448;Name=AP001462.1-003;name2=MEN1
chr11	ENCODE	exon	64327564	64328864	.	-	.	Parent=gene448
chr11	ENCODE	CDS	64328382	64328864	.	-	0	Parent=gene448
chr11	ENCODE	exon	64329082	64329246	.	-	.	Parent=gene448
chr11	ENCODE	CDS	64329082	64329246	.	-	0	Parent=gene448
chr11	ENCODE	exon	64329683	64329818	.	-	.	Parent=gene448
chr11	ENCODE	CDS	64329683	64329818	.	-	1	Parent=gene448
chr11	ENCODE	exon	64330280	64330416	.	-	.	Parent=gene448
chr11	ENCODE	CDS	64330280	64330416	.	-	0	Parent=gene448
chr11	ENCODE	exon	64331059	64331146	.	-	.	Parent=gene448
chr11	ENCODE	CDS	64331059	64331146	.	-	1	Parent=gene448
chr11	ENCODE	exon	64331227	64331267	.	-	.	Parent=gene448
chr11	ENCODE	CDS	64331227	64331267	.	-	0	Parent=gene448
chr11	ENCODE	exon	64331600	64331728	.	-	.	Parent=gene448
chr11	ENCODE	CDS	64331600	64331728	.	-	0	Parent=gene448
chr11	ENCODE	exon	64331939	64332147	.	-	.	Parent=gene448
chr11	ENCODE	CDS	64331939	64332147	.	-	2	Parent=gene448
chr11	ENCODE	CDS	64333713	64334157	.	-	0	Parent=gene448
chr11	ENCODE	exon	64333713	64334180	.	-	.	Parent=gene448
chr11	ENCODE	exon	64334316	64334789	.	-	.	Parent=gene448
###
chr11	ENCODE	gene	64328382	64334180	.	-	.	ID=gene449;name2=MEN1;Name=AP001462.1-011
chr11	ENCODE	exon	64328382	64328864	.	-	.	Parent=gene449
chr11	ENCODE	CDS	64328382	64328864	.	-	0	Parent=gene449
chr11	ENCODE	exon	64329082	64329246	.	-	.	Parent=gene449
chr11	ENCODE	CDS	64329082	64329246	.	-	0	Parent=gene449
chr11	ENCODE	exon	64329683	64329818	.	-	.	Parent=gene449
chr11	ENCODE	CDS	64329683	64329818	.	-	1	Parent=gene449
chr11	ENCODE	exon	64330280	64330416	.	-	.	Parent=gene449
chr11	ENCODE	CDS	64330280	64330416	.	-	0	Parent=gene449
chr11	ENCODE	exon	64331059	64331146	.	-	.	Parent=gene449
chr11	ENCODE	CDS	64331059	64331146	.	-	1	Parent=gene449
chr11	ENCODE	exon	64331227	64331267	.	-	.	Parent=gene449
chr11	ENCODE	CDS	64331227	64331267	.	-	0	Parent=gene449
chr11	ENCODE	exon	64331600	64331728	.	-	.	Parent=gene449
chr11	ENCODE	CDS	64331600	64331728	.	-	0	Parent=gene449
chr11	ENCODE	exon	64331939	64332147	.	-	.	Parent=gene449
chr11	ENCODE	CDS	64331939	64332147	.	-	2	Parent=gene449
chr11	ENCODE	CDS	64333698	64334157	.	-	0	Parent=gene449
chr11	ENCODE	exon	64333698	64334180	.	-	.	Parent=gene449
###
chr11	ENCODE	gene	64328423	64330416	.	-	.	ID=gene450;Name=AP001462.1-012;name2=MEN1
chr11	ENCODE	exon	64328423	64328864	.	-	.	Parent=gene450
chr11	ENCODE	exon	64329082	64329246	.	-	.	Parent=gene450
chr11	ENCODE	exon	64329683	64330416	.	-	.	Parent=gene450
###
chr11	ENCODE	gene	64329174	64330040	.	-	.	ID=gene451;Name=AP001462.1-013;name2=MEN1
chr11	ENCODE	exon	64329174	64329246	.	-	.	Parent=gene451
chr11	ENCODE	exon	64329683	64329818	.	-	.	Parent=gene451
chr11	ENCODE	exon	64329936	64330040	.	-	.	Parent=gene451
###
chr11	ENCODE	gene	64330290	64334606	.	-	.	ID=gene452;Name=AP001462.1-009;name2=MEN1
chr11	ENCODE	exon	64330290	64330416	.	-	.	Parent=gene452
chr11	ENCODE	CDS	64330290	64330416	.	-	0	Parent=gene452
chr11	ENCODE	exon	64331059	64331146	.	-	.	Parent=gene452
chr11	ENCODE	CDS	64331059	64331146	.	-	1	Parent=gene452
chr11	ENCODE	exon	64331227	64331267	.	-	.	Parent=gene452
chr11	ENCODE	CDS	64331227	64331267	.	-	0	Parent=gene452
chr11	ENCODE	exon	64331600	64331728	.	-	.	Parent=gene452
chr11	ENCODE	CDS	64331600	64331728	.	-	0	Parent=gene452
chr11	ENCODE	exon	64331939	64332147	.	-	.	Parent=gene452
chr11	ENCODE	CDS	64331939	64332147	.	-	2	Parent=gene452
chr11	ENCODE	CDS	64333713	64334157	.	-	0	Parent=gene452
chr11	ENCODE	exon	64333713	64334180	.	-	.	Parent=gene452
chr11	ENCODE	exon	64334562	64334606	.	-	.	Parent=gene452
###
chr11	ENCODE	gene	64331128	64334629	.	-	.	ID=gene453;Name=AP001462.1-004;name2=MEN1
chr11	ENCODE	exon	64331128	64331146	.	-	.	Parent=gene453
chr11	ENCODE	CDS	64331128	64331146	.	-	1	Parent=gene453
chr11	ENCODE	exon	64331227	64331267	.	-	.	Parent=gene453
chr11	ENCODE	CDS	64331227	64331267	.	-	0	Parent=gene453
chr11	ENCODE	exon	64331600	64331728	.	-	.	Parent=gene453
chr11	ENCODE	CDS	64331600	64331728	.	-	0	Parent=gene453
chr11	ENCODE	exon	64331939	64332147	.	-	.	Parent=gene453
chr11	ENCODE	CDS	64331939	64332147	.	-	2	Parent=gene453
chr11	ENCODE	CDS	64333713	64334157	.	-	0	Parent=gene453
chr11	ENCODE	exon	64333713	64334180	.	-	.	Parent=gene453
chr11	ENCODE	exon	64334574	64334629	.	-	.	Parent=gene453
###
chr11	ENCODE	gene	64331600	64334569	.	-	.	ID=gene454;Name=AP001462.1-010;name2=MEN1
chr11	ENCODE	exon	64331600	64331728	.	-	.	Parent=gene454
chr11	ENCODE	CDS	64331600	64331728	.	-	0	Parent=gene454
chr11	ENCODE	exon	64331939	64332147	.	-	.	Parent=gene454
chr11	ENCODE	CDS	64331939	64332147	.	-	2	Parent=gene454
chr11	ENCODE	CDS	64333713	64334157	.	-	0	Parent=gene454
chr11	ENCODE	exon	64333713	64334180	.	-	.	Parent=gene454
chr11	ENCODE	exon	64334506	64334569	.	-	.	Parent=gene454
###
chr11	ENCODE	gene	64333718	64335342	.	-	.	ID=gene455;Name=AP001462.1-005;name2=MEN1
chr11	ENCODE	CDS	64333718	64334157	.	-	0	Parent=gene455
chr11	ENCODE	exon	64333718	64334180	.	-	.	Parent=gene455
chr11	ENCODE	exon	64334862	64335342	.	-	.	Parent=gene455
###
chr11	ENCODE	gene	64333718	64335342	.	-	.	ID=gene456;Name=AP001462.1-006;name2=MEN1
chr11	ENCODE	CDS	64333718	64334157	.	-	0	Parent=gene456
chr11	ENCODE	exon	64333718	64334180	.	-	.	Parent=gene456
chr11	ENCODE	exon	64334862	64334953	.	-	.	Parent=gene456
chr11	ENCODE	exon	64335082	64335342	.	-	.	Parent=gene456
###
chr11	ENCODE	gene	64347435	64368617	.	-	.	ID=gene457;Name=AP001187.3-001;name2=CDC42BPG
chr11	ENCODE	exon	64347435	64348577	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64348521	64348577	.	-	0	Parent=gene457
chr11	ENCODE	exon	64350518	64350603	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64350518	64350603	.	-	2	Parent=gene457
chr11	ENCODE	exon	64350719	64350842	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64350719	64350842	.	-	0	Parent=gene457
chr11	ENCODE	exon	64351098	64351215	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64351098	64351215	.	-	1	Parent=gene457
chr11	ENCODE	exon	64351326	64351446	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64351326	64351446	.	-	2	Parent=gene457
chr11	ENCODE	exon	64351575	64351659	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64351575	64351659	.	-	0	Parent=gene457
chr11	ENCODE	exon	64351734	64351831	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64351734	64351831	.	-	2	Parent=gene457
chr11	ENCODE	exon	64353519	64354118	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64353519	64354118	.	-	2	Parent=gene457
chr11	ENCODE	exon	64354242	64354304	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64354242	64354304	.	-	2	Parent=gene457
chr11	ENCODE	exon	64355553	64355769	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64355553	64355769	.	-	0	Parent=gene457
chr11	ENCODE	exon	64356476	64356557	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64356476	64356557	.	-	1	Parent=gene457
chr11	ENCODE	exon	64356652	64356791	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64356652	64356791	.	-	0	Parent=gene457
chr11	ENCODE	exon	64356874	64357007	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64356874	64357007	.	-	2	Parent=gene457
chr11	ENCODE	exon	64357279	64357384	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64357279	64357384	.	-	0	Parent=gene457
chr11	ENCODE	exon	64357648	64357707	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64357648	64357707	.	-	0	Parent=gene457
chr11	ENCODE	exon	64357786	64357884	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64357786	64357884	.	-	0	Parent=gene457
chr11	ENCODE	exon	64357973	64358025	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64357973	64358025	.	-	2	Parent=gene457
chr11	ENCODE	exon	64358314	64358402	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64358314	64358402	.	-	1	Parent=gene457
chr11	ENCODE	exon	64358477	64358625	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64358477	64358625	.	-	0	Parent=gene457
chr11	ENCODE	exon	64358897	64359011	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64358897	64359011	.	-	1	Parent=gene457
chr11	ENCODE	exon	64359095	64359201	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64359095	64359201	.	-	0	Parent=gene457
chr11	ENCODE	exon	64359395	64359467	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64359395	64359467	.	-	1	Parent=gene457
chr11	ENCODE	exon	64359548	64359669	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64359548	64359669	.	-	0	Parent=gene457
chr11	ENCODE	exon	64359810	64359899	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64359810	64359899	.	-	0	Parent=gene457
chr11	ENCODE	exon	64360165	64360344	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64360165	64360344	.	-	0	Parent=gene457
chr11	ENCODE	exon	64360475	64360578	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64360475	64360578	.	-	2	Parent=gene457
chr11	ENCODE	exon	64360787	64360867	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64360787	64360867	.	-	2	Parent=gene457
chr11	ENCODE	exon	64360970	64361067	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64360970	64361067	.	-	1	Parent=gene457
chr11	ENCODE	exon	64362131	64362210	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64362131	64362210	.	-	0	Parent=gene457
chr11	ENCODE	exon	64362702	64362950	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64362702	64362950	.	-	0	Parent=gene457
chr11	ENCODE	exon	64363081	64363281	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64363081	64363281	.	-	0	Parent=gene457
chr11	ENCODE	exon	64363526	64363619	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64363526	64363619	.	-	1	Parent=gene457
chr11	ENCODE	exon	64364168	64364316	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64364168	64364316	.	-	0	Parent=gene457
chr11	ENCODE	exon	64364601	64364696	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64364601	64364696	.	-	0	Parent=gene457
chr11	ENCODE	exon	64365698	64365781	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64365698	64365781	.	-	0	Parent=gene457
chr11	ENCODE	exon	64365861	64365952	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64365861	64365952	.	-	2	Parent=gene457
chr11	ENCODE	exon	64368458	64368617	.	-	.	Parent=gene457
chr11	ENCODE	CDS	64368458	64368617	.	-	0	Parent=gene457
###
chr11	ENCODE	gene	64354440	64356530	.	-	.	ID=gene458;Name=AP001187.3-004;name2=CDC42BPG
chr11	ENCODE	exon	64354440	64354506	.	-	.	Parent=gene458
chr11	ENCODE	exon	64355553	64355769	.	-	.	Parent=gene458
chr11	ENCODE	exon	64356476	64356530	.	-	.	Parent=gene458
###
chr11	ENCODE	gene	64356968	64357833	.	-	.	ID=gene459;Name=AP001187.3-003;name2=CDC42BPG
chr11	ENCODE	exon	64356968	64357007	.	-	.	Parent=gene459
chr11	ENCODE	exon	64357239	64357384	.	-	.	Parent=gene459
chr11	ENCODE	exon	64357648	64357707	.	-	.	Parent=gene459
chr11	ENCODE	exon	64357786	64357833	.	-	.	Parent=gene459
###
chr11	ENCODE	gene	64357328	64357859	.	-	.	ID=gene460;name2=CDC42BPG;Name=AP001187.3-002
chr11	ENCODE	exon	64357328	64357707	.	-	.	Parent=gene460
chr11	ENCODE	exon	64357786	64357859	.	-	.	Parent=gene460
###
chr11	ENCODE	gene	64375690	64402767	.	-	.	ID=gene461;Name=AP001187.8-001;name2=EHD1
chr11	ENCODE	exon	64375690	64378905	.	-	.	Parent=gene461
chr11	ENCODE	CDS	64378381	64378905	.	-	0	Parent=gene461
chr11	ENCODE	exon	64379370	64379534	.	-	.	Parent=gene461
chr11	ENCODE	CDS	64379370	64379534	.	-	0	Parent=gene461
chr11	ENCODE	exon	64383972	64384384	.	-	.	Parent=gene461
chr11	ENCODE	CDS	64383972	64384384	.	-	2	Parent=gene461
chr11	ENCODE	exon	64398469	64398566	.	-	.	Parent=gene461
chr11	ENCODE	CDS	64398469	64398566	.	-	1	Parent=gene461
chr11	ENCODE	CDS	64402109	64402512	.	-	0	Parent=gene461
chr11	ENCODE	exon	64402109	64402767	.	-	.	Parent=gene461
###
chr11	ENCODE	gene	64376779	64380711	.	-	.	ID=gene462;Name=AP001187.8-005;name2=EHD1
chr11	ENCODE	exon	64376779	64378905	.	-	.	Parent=gene462
chr11	ENCODE	exon	64379370	64380711	.	-	.	Parent=gene462
###
chr11	ENCODE	gene	64376779	64399881	.	-	.	ID=gene463;Name=AP001187.8-003;name2=EHD1
chr11	ENCODE	exon	64376779	64376974	.	-	.	Parent=gene463
chr11	ENCODE	exon	64377636	64378905	.	-	.	Parent=gene463
chr11	ENCODE	exon	64379370	64379845	.	-	.	Parent=gene463
chr11	ENCODE	exon	64383972	64384384	.	-	.	Parent=gene463
chr11	ENCODE	exon	64398469	64399881	.	-	.	Parent=gene463
###
chr11	ENCODE	gene	64376779	64402563	.	-	.	ID=gene464;Name=AP001187.8-004;name2=EHD1
chr11	ENCODE	exon	64376779	64377133	.	-	.	Parent=gene464
chr11	ENCODE	exon	64378399	64378905	.	-	.	Parent=gene464
chr11	ENCODE	exon	64379370	64379534	.	-	.	Parent=gene464
chr11	ENCODE	exon	64383972	64384384	.	-	.	Parent=gene464
chr11	ENCODE	exon	64398469	64398566	.	-	.	Parent=gene464
chr11	ENCODE	exon	64402109	64402563	.	-	.	Parent=gene464
###
chr11	ENCODE	gene	64376779	64403725	.	-	.	ID=gene465;Name=AP001187.8-002;name2=EHD1
chr11	ENCODE	exon	64376779	64378905	.	-	.	Parent=gene465
chr11	ENCODE	CDS	64378381	64378905	.	-	0	Parent=gene465
chr11	ENCODE	exon	64379370	64379534	.	-	.	Parent=gene465
chr11	ENCODE	CDS	64379370	64379534	.	-	0	Parent=gene465
chr11	ENCODE	exon	64383972	64384384	.	-	.	Parent=gene465
chr11	ENCODE	CDS	64383972	64384384	.	-	2	Parent=gene465
chr11	ENCODE	exon	64398469	64398566	.	-	.	Parent=gene465
chr11	ENCODE	CDS	64398469	64398566	.	-	1	Parent=gene465
chr11	ENCODE	CDS	64402109	64402512	.	-	0	Parent=gene465
chr11	ENCODE	exon	64402109	64402535	.	-	.	Parent=gene465
chr11	ENCODE	exon	64402883	64403204	.	-	.	Parent=gene465
chr11	ENCODE	exon	64403660	64403725	.	-	.	Parent=gene465
###
chr11	ENCODE	gene	64378154	64402672	.	-	.	ID=gene466;Name=AP001187.8-006;name2=EHD1
chr11	ENCODE	exon	64378154	64378645	.	-	.	Parent=gene466
chr11	ENCODE	exon	64378712	64378905	.	-	.	Parent=gene466
chr11	ENCODE	exon	64379370	64379534	.	-	.	Parent=gene466
chr11	ENCODE	exon	64383972	64384055	.	-	.	Parent=gene466
chr11	ENCODE	exon	64402267	64402672	.	-	.	Parent=gene466
###
chr11	ENCODE	gene	64378340	64379143	.	-	.	ID=gene467;Name=AP001187.8-009;name2=EHD1
chr11	ENCODE	exon	64378340	64378905	.	-	.	Parent=gene467
chr11	ENCODE	exon	64379062	64379143	.	-	.	Parent=gene467
###
chr11	ENCODE	gene	64378660	64401965	.	-	.	ID=gene468;Name=AP001187.8-008;name2=EHD1
chr11	ENCODE	exon	64378660	64378905	.	-	.	Parent=gene468
chr11	ENCODE	CDS	64378660	64378905	.	-	0	Parent=gene468
chr11	ENCODE	exon	64379370	64379534	.	-	.	Parent=gene468
chr11	ENCODE	CDS	64379370	64379534	.	-	0	Parent=gene468
chr11	ENCODE	exon	64383972	64384384	.	-	.	Parent=gene468
chr11	ENCODE	CDS	64383972	64384384	.	-	2	Parent=gene468
chr11	ENCODE	CDS	64398469	64398562	.	-	0	Parent=gene468
chr11	ENCODE	exon	64398469	64398566	.	-	.	Parent=gene468
chr11	ENCODE	exon	64401873	64401965	.	-	.	Parent=gene468
###
chr11	ENCODE	gene	64379100	64384093	.	-	.	ID=gene469;Name=AP001187.8-011;name2=EHD1
chr11	ENCODE	exon	64379100	64379534	.	-	.	Parent=gene469
chr11	ENCODE	exon	64383972	64384093	.	-	.	Parent=gene469
###
chr11	ENCODE	gene	64379370	64403747	.	-	.	ID=gene470;name2=EHD1;Name=AP001187.8-007
chr11	ENCODE	exon	64379370	64379534	.	-	.	Parent=gene470
chr11	ENCODE	CDS	64379370	64379534	.	-	0	Parent=gene470
chr11	ENCODE	exon	64383972	64384384	.	-	.	Parent=gene470
chr11	ENCODE	CDS	64383972	64384384	.	-	2	Parent=gene470
chr11	ENCODE	exon	64398469	64398566	.	-	.	Parent=gene470
chr11	ENCODE	CDS	64398469	64398566	.	-	1	Parent=gene470
chr11	ENCODE	CDS	64402109	64402512	.	-	0	Parent=gene470
chr11	ENCODE	exon	64402109	64402535	.	-	.	Parent=gene470
chr11	ENCODE	exon	64403660	64403747	.	-	.	Parent=gene470
###
chr11	ENCODE	gene	64379767	64380427	.	-	.	ID=gene471;Name=AP001187.8-012;name2=EHD1
chr11	ENCODE	exon	64379767	64379910	.	-	.	Parent=gene471
chr11	ENCODE	exon	64380007	64380427	.	-	.	Parent=gene471
###
chr11	ENCODE	gene	64383674	64402589	.	-	.	ID=gene472;Name=AP001187.8-010;name2=EHD1
chr11	ENCODE	exon	64383674	64384384	.	-	.	Parent=gene472
chr11	ENCODE	exon	64398469	64398566	.	-	.	Parent=gene472
chr11	ENCODE	exon	64402109	64402589	.	-	.	Parent=gene472
###
chr11	ENCODE	gene	64383993	64399714	.	-	.	ID=gene473;Name=AP001187.8-013;name2=EHD1
chr11	ENCODE	exon	64383993	64384384	.	-	.	Parent=gene473
chr11	ENCODE	exon	64398469	64398566	.	-	.	Parent=gene473
chr11	ENCODE	exon	64399659	64399714	.	-	.	Parent=gene473
###
chr11	ENCODE	gene	64398526	64412344	.	-	.	ID=gene474;Name=AP001187.8-016;name2=EHD1
chr11	ENCODE	exon	64398526	64398566	.	-	.	Parent=gene474
chr11	ENCODE	CDS	64398526	64398566	.	-	1	Parent=gene474
chr11	ENCODE	CDS	64402109	64402512	.	-	0	Parent=gene474
chr11	ENCODE	exon	64402109	64402532	.	-	.	Parent=gene474
chr11	ENCODE	exon	64412276	64412344	.	-	.	Parent=gene474
###
chr11	ENCODE	gene	64398536	64403748	.	-	.	ID=gene475;Name=AP001187.8-015;name2=EHD1
chr11	ENCODE	exon	64398536	64398566	.	-	.	Parent=gene475
chr11	ENCODE	CDS	64398536	64398566	.	-	1	Parent=gene475
chr11	ENCODE	CDS	64402109	64402512	.	-	0	Parent=gene475
chr11	ENCODE	exon	64402109	64402535	.	-	.	Parent=gene475
chr11	ENCODE	exon	64403650	64403748	.	-	.	Parent=gene475
###
chr11	ENCODE	gene	64402687	64403729	.	-	.	ID=gene476;Name=AP001187.8-014;name2=EHD1
chr11	ENCODE	exon	64402687	64403204	.	-	.	Parent=gene476
chr11	ENCODE	exon	64403660	64403729	.	-	.	Parent=gene476
###
chr11	ENCODE	gene	64418594	64437443	.	-	.	ID=gene477;Name=AP001187.10-004;name2=AP001187.10
chr11	ENCODE	exon	64418594	64419257	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64419021	64419257	.	-	2	Parent=gene477
chr11	ENCODE	exon	64419338	64419490	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64419338	64419490	.	-	2	Parent=gene477
chr11	ENCODE	exon	64420510	64420664	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64420510	64420664	.	-	1	Parent=gene477
chr11	ENCODE	exon	64420796	64420917	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64420796	64420917	.	-	0	Parent=gene477
chr11	ENCODE	exon	64421460	64421542	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64421460	64421542	.	-	2	Parent=gene477
chr11	ENCODE	exon	64421719	64421791	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64421719	64421791	.	-	0	Parent=gene477
chr11	ENCODE	exon	64421887	64422022	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64421887	64422022	.	-	1	Parent=gene477
chr11	ENCODE	exon	64422134	64422218	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64422134	64422218	.	-	2	Parent=gene477
chr11	ENCODE	exon	64422309	64422410	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64422309	64422410	.	-	2	Parent=gene477
chr11	ENCODE	exon	64422684	64422890	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64422684	64422890	.	-	2	Parent=gene477
chr11	ENCODE	exon	64424542	64424677	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64424542	64424677	.	-	0	Parent=gene477
chr11	ENCODE	exon	64424932	64425140	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64424932	64425140	.	-	2	Parent=gene477
chr11	ENCODE	exon	64426010	64426224	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64426010	64426224	.	-	1	Parent=gene477
chr11	ENCODE	exon	64426308	64426434	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64426308	64426434	.	-	2	Parent=gene477
chr11	ENCODE	exon	64426558	64426728	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64426558	64426728	.	-	2	Parent=gene477
chr11	ENCODE	exon	64427336	64427412	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64427336	64427412	.	-	1	Parent=gene477
chr11	ENCODE	exon	64427638	64427708	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64427638	64427708	.	-	0	Parent=gene477
chr11	ENCODE	exon	64429611	64429703	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64429611	64429703	.	-	0	Parent=gene477
chr11	ENCODE	exon	64429790	64429896	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64429790	64429896	.	-	2	Parent=gene477
chr11	ENCODE	exon	64430161	64430241	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64430161	64430241	.	-	2	Parent=gene477
chr11	ENCODE	exon	64430382	64430581	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64430382	64430581	.	-	1	Parent=gene477
chr11	ENCODE	exon	64430713	64430863	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64430713	64430863	.	-	2	Parent=gene477
chr11	ENCODE	exon	64431303	64431487	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64431303	64431487	.	-	1	Parent=gene477
chr11	ENCODE	exon	64431573	64431712	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64431573	64431712	.	-	0	Parent=gene477
chr11	ENCODE	exon	64431796	64431938	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64431796	64431938	.	-	2	Parent=gene477
chr11	ENCODE	exon	64433039	64433198	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64433039	64433198	.	-	0	Parent=gene477
chr11	ENCODE	exon	64433319	64433415	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64433319	64433415	.	-	1	Parent=gene477
chr11	ENCODE	exon	64433729	64433972	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64433729	64433972	.	-	2	Parent=gene477
chr11	ENCODE	exon	64434088	64434243	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64434088	64434243	.	-	2	Parent=gene477
chr11	ENCODE	exon	64434664	64434756	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64434664	64434756	.	-	2	Parent=gene477
chr11	ENCODE	exon	64434855	64435002	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64434855	64435002	.	-	0	Parent=gene477
chr11	ENCODE	exon	64435086	64435323	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64435086	64435323	.	-	1	Parent=gene477
chr11	ENCODE	exon	64435890	64436030	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64435890	64436030	.	-	1	Parent=gene477
chr11	ENCODE	exon	64436133	64436297	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64436133	64436297	.	-	1	Parent=gene477
chr11	ENCODE	exon	64436375	64436471	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64436375	64436471	.	-	2	Parent=gene477
chr11	ENCODE	exon	64437086	64437184	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64437086	64437184	.	-	2	Parent=gene477
chr11	ENCODE	exon	64437314	64437443	.	-	.	Parent=gene477
chr11	ENCODE	CDS	64437314	64437443	.	-	0	Parent=gene477
###
chr11	ENCODE	gene	64418594	64438548	.	-	.	ID=gene478;Name=AP001187.10-002;name2=AP001187.10
chr11	ENCODE	exon	64418594	64419257	.	-	.	Parent=gene478
chr11	ENCODE	exon	64419338	64419490	.	-	.	Parent=gene478
chr11	ENCODE	exon	64420510	64420664	.	-	.	Parent=gene478
chr11	ENCODE	exon	64420796	64420917	.	-	.	Parent=gene478
chr11	ENCODE	exon	64421460	64421542	.	-	.	Parent=gene478
chr11	ENCODE	exon	64421719	64421791	.	-	.	Parent=gene478
chr11	ENCODE	exon	64421887	64422022	.	-	.	Parent=gene478
chr11	ENCODE	exon	64422134	64422218	.	-	.	Parent=gene478
chr11	ENCODE	exon	64422309	64422410	.	-	.	Parent=gene478
chr11	ENCODE	exon	64422684	64422890	.	-	.	Parent=gene478
chr11	ENCODE	exon	64424542	64424677	.	-	.	Parent=gene478
chr11	ENCODE	exon	64424932	64425140	.	-	.	Parent=gene478
chr11	ENCODE	exon	64426010	64426224	.	-	.	Parent=gene478
chr11	ENCODE	exon	64426308	64426434	.	-	.	Parent=gene478
chr11	ENCODE	exon	64426564	64426728	.	-	.	Parent=gene478
chr11	ENCODE	exon	64427336	64427412	.	-	.	Parent=gene478
chr11	ENCODE	exon	64427638	64427708	.	-	.	Parent=gene478
chr11	ENCODE	exon	64429611	64429703	.	-	.	Parent=gene478
chr11	ENCODE	exon	64429790	64429896	.	-	.	Parent=gene478
chr11	ENCODE	exon	64430161	64430241	.	-	.	Parent=gene478
chr11	ENCODE	exon	64430382	64430581	.	-	.	Parent=gene478
chr11	ENCODE	exon	64430713	64430863	.	-	.	Parent=gene478
chr11	ENCODE	exon	64431303	64431463	.	-	.	Parent=gene478
chr11	ENCODE	exon	64431573	64431712	.	-	.	Parent=gene478
chr11	ENCODE	exon	64431796	64431938	.	-	.	Parent=gene478
chr11	ENCODE	exon	64433039	64433198	.	-	.	Parent=gene478
chr11	ENCODE	exon	64433319	64433415	.	-	.	Parent=gene478
chr11	ENCODE	exon	64433729	64433972	.	-	.	Parent=gene478
chr11	ENCODE	exon	64434088	64434243	.	-	.	Parent=gene478
chr11	ENCODE	exon	64434664	64434756	.	-	.	Parent=gene478
chr11	ENCODE	exon	64434855	64435002	.	-	.	Parent=gene478
chr11	ENCODE	exon	64435086	64435323	.	-	.	Parent=gene478
chr11	ENCODE	exon	64435890	64436030	.	-	.	Parent=gene478
chr11	ENCODE	exon	64436133	64436297	.	-	.	Parent=gene478
chr11	ENCODE	exon	64436375	64436471	.	-	.	Parent=gene478
chr11	ENCODE	exon	64437086	64437184	.	-	.	Parent=gene478
chr11	ENCODE	exon	64437314	64437449	.	-	.	Parent=gene478
chr11	ENCODE	exon	64437869	64437971	.	-	.	Parent=gene478
chr11	ENCODE	exon	64438129	64438275	.	-	.	Parent=gene478
chr11	ENCODE	exon	64438386	64438548	.	-	.	Parent=gene478
###
chr11	ENCODE	gene	64418594	64438548	.	-	.	ID=gene479;Name=AP001187.10-001;name2=AP001187.10
chr11	ENCODE	exon	64418594	64419257	.	-	.	Parent=gene479
chr11	ENCODE	exon	64419338	64419490	.	-	.	Parent=gene479
chr11	ENCODE	exon	64420510	64420664	.	-	.	Parent=gene479
chr11	ENCODE	exon	64420796	64420917	.	-	.	Parent=gene479
chr11	ENCODE	exon	64421460	64421542	.	-	.	Parent=gene479
chr11	ENCODE	exon	64421719	64421791	.	-	.	Parent=gene479
chr11	ENCODE	exon	64421887	64422022	.	-	.	Parent=gene479
chr11	ENCODE	exon	64422134	64422218	.	-	.	Parent=gene479
chr11	ENCODE	exon	64422309	64422410	.	-	.	Parent=gene479
chr11	ENCODE	exon	64422684	64422890	.	-	.	Parent=gene479
chr11	ENCODE	exon	64424542	64424677	.	-	.	Parent=gene479
chr11	ENCODE	exon	64424932	64425140	.	-	.	Parent=gene479
chr11	ENCODE	exon	64426010	64426224	.	-	.	Parent=gene479
chr11	ENCODE	exon	64426308	64426434	.	-	.	Parent=gene479
chr11	ENCODE	exon	64426564	64426728	.	-	.	Parent=gene479
chr11	ENCODE	exon	64427336	64427412	.	-	.	Parent=gene479
chr11	ENCODE	exon	64427638	64427708	.	-	.	Parent=gene479
chr11	ENCODE	exon	64429611	64429703	.	-	.	Parent=gene479
chr11	ENCODE	exon	64429790	64429896	.	-	.	Parent=gene479
chr11	ENCODE	exon	64430161	64430241	.	-	.	Parent=gene479
chr11	ENCODE	exon	64430382	64430581	.	-	.	Parent=gene479
chr11	ENCODE	exon	64430713	64430863	.	-	.	Parent=gene479
chr11	ENCODE	exon	64431303	64431487	.	-	.	Parent=gene479
chr11	ENCODE	exon	64431573	64431712	.	-	.	Parent=gene479
chr11	ENCODE	exon	64431796	64431938	.	-	.	Parent=gene479
chr11	ENCODE	exon	64433039	64433198	.	-	.	Parent=gene479
chr11	ENCODE	exon	64433319	64433415	.	-	.	Parent=gene479
chr11	ENCODE	exon	64433729	64433972	.	-	.	Parent=gene479
chr11	ENCODE	exon	64434088	64434243	.	-	.	Parent=gene479
chr11	ENCODE	exon	64434664	64434756	.	-	.	Parent=gene479
chr11	ENCODE	exon	64434855	64435002	.	-	.	Parent=gene479
chr11	ENCODE	exon	64435086	64435323	.	-	.	Parent=gene479
chr11	ENCODE	exon	64435890	64436030	.	-	.	Parent=gene479
chr11	ENCODE	exon	64436133	64436297	.	-	.	Parent=gene479
chr11	ENCODE	exon	64436375	64436471	.	-	.	Parent=gene479
chr11	ENCODE	exon	64437086	64437184	.	-	.	Parent=gene479
chr11	ENCODE	exon	64437314	64437449	.	-	.	Parent=gene479
chr11	ENCODE	exon	64437869	64437971	.	-	.	Parent=gene479
chr11	ENCODE	exon	64438129	64438281	.	-	.	Parent=gene479
chr11	ENCODE	exon	64438386	64438548	.	-	.	Parent=gene479
###
chr11	ENCODE	gene	64421088	64421778	.	-	.	ID=gene480;Name=AP001187.10-005;name2=AP001187.10
chr11	ENCODE	exon	64421088	64421542	.	-	.	Parent=gene480
chr11	ENCODE	exon	64421719	64421778	.	-	.	Parent=gene480
###
chr11	ENCODE	gene	64436659	64438548	.	-	.	ID=gene481;Name=AP001187.10-003;name2=AP001187.10
chr11	ENCODE	exon	64436659	64437184	.	-	.	Parent=gene481
chr11	ENCODE	exon	64437314	64438548	.	-	.	Parent=gene481
###
chr11	ENCODE	gene	64438244	64438548	.	-	.	ID=gene482;Name=AP001187.10-006;name2=AP001187.10
chr11	ENCODE	exon	64438244	64438548	.	-	.	Parent=gene482
###
chr11	ENCODE	gene	116124096	116138762	.	-	.	ID=gene483;Name=AP006216.1-003;name2=BUD13
chr11	ENCODE	exon	116124096	116124501	.	-	.	Parent=gene483
chr11	ENCODE	CDS	116124408	116124501	.	-	2	Parent=gene483
chr11	ENCODE	exon	116133072	116133153	.	-	.	Parent=gene483
chr11	ENCODE	CDS	116133072	116133153	.	-	0	Parent=gene483
chr11	ENCODE	exon	116133692	116133866	.	-	.	Parent=gene483
chr11	ENCODE	CDS	116133692	116133866	.	-	1	Parent=gene483
chr11	ENCODE	exon	116138479	116138762	.	-	.	Parent=gene483
chr11	ENCODE	CDS	116138479	116138762	.	-	0	Parent=gene483
###
chr11	ENCODE	gene	116124096	116148913	.	-	.	ID=gene484;Name=AP006216.1-002;name2=BUD13
chr11	ENCODE	exon	116124096	116124501	.	-	.	Parent=gene484
chr11	ENCODE	CDS	116124408	116124501	.	-	1	Parent=gene484
chr11	ENCODE	exon	116133072	116133153	.	-	.	Parent=gene484
chr11	ENCODE	CDS	116133072	116133153	.	-	2	Parent=gene484
chr11	ENCODE	exon	116133692	116133876	.	-	.	Parent=gene484
chr11	ENCODE	CDS	116133692	116133876	.	-	1	Parent=gene484
chr11	ENCODE	exon	116134195	116134333	.	-	.	Parent=gene484
chr11	ENCODE	CDS	116134195	116134333	.	-	2	Parent=gene484
chr11	ENCODE	exon	116135000	116135105	.	-	.	Parent=gene484
chr11	ENCODE	CDS	116135000	116135105	.	-	0	Parent=gene484
chr11	ENCODE	exon	116136661	116136878	.	-	.	Parent=gene484
chr11	ENCODE	CDS	116136661	116136878	.	-	2	Parent=gene484
chr11	ENCODE	exon	116138881	116139192	.	-	.	Parent=gene484
chr11	ENCODE	CDS	116138881	116139192	.	-	2	Parent=gene484
chr11	ENCODE	exon	116141288	116141372	.	-	.	Parent=gene484
chr11	ENCODE	CDS	116141288	116141372	.	-	0	Parent=gene484
chr11	ENCODE	exon	116146055	116146148	.	-	.	Parent=gene484
chr11	ENCODE	CDS	116146055	116146148	.	-	1	Parent=gene484
chr11	ENCODE	CDS	116148748	116148890	.	-	0	Parent=gene484
chr11	ENCODE	exon	116148748	116148913	.	-	.	Parent=gene484
###
chr11	ENCODE	gene	116124096	116148914	.	-	.	ID=gene485;Name=AP006216.1-001;name2=BUD13
chr11	ENCODE	exon	116124096	116124501	.	-	.	Parent=gene485
chr11	ENCODE	CDS	116124408	116124501	.	-	1	Parent=gene485
chr11	ENCODE	exon	116133072	116133153	.	-	.	Parent=gene485
chr11	ENCODE	CDS	116133072	116133153	.	-	2	Parent=gene485
chr11	ENCODE	exon	116133692	116133876	.	-	.	Parent=gene485
chr11	ENCODE	CDS	116133692	116133876	.	-	1	Parent=gene485
chr11	ENCODE	exon	116134195	116134333	.	-	.	Parent=gene485
chr11	ENCODE	CDS	116134195	116134333	.	-	2	Parent=gene485
chr11	ENCODE	exon	116135000	116135105	.	-	.	Parent=gene485
chr11	ENCODE	CDS	116135000	116135105	.	-	0	Parent=gene485
chr11	ENCODE	exon	116136661	116136878	.	-	.	Parent=gene485
chr11	ENCODE	CDS	116136661	116136878	.	-	2	Parent=gene485
chr11	ENCODE	exon	116138479	116139192	.	-	.	Parent=gene485
chr11	ENCODE	CDS	116138479	116139192	.	-	2	Parent=gene485
chr11	ENCODE	exon	116141288	116141372	.	-	.	Parent=gene485
chr11	ENCODE	CDS	116141288	116141372	.	-	0	Parent=gene485
chr11	ENCODE	exon	116146055	116146148	.	-	.	Parent=gene485
chr11	ENCODE	CDS	116146055	116146148	.	-	1	Parent=gene485
chr11	ENCODE	CDS	116148748	116148890	.	-	0	Parent=gene485
chr11	ENCODE	exon	116148748	116148914	.	-	.	Parent=gene485
###
chr11	ENCODE	gene	116151036	116151802	.	-	.	ID=gene486;Name=AP006216.11-001;name2=AP006216.11
chr11	ENCODE	exon	116151036	116151259	.	-	.	Parent=gene486
chr11	ENCODE	CDS	116151121	116151259	.	-	1	Parent=gene486
chr11	ENCODE	CDS	116151429	116151700	.	-	0	Parent=gene486
chr11	ENCODE	exon	116151429	116151802	.	-	.	Parent=gene486
###
chr11	ENCODE	gene	116153646	116163905	.	-	.	ID=gene487;Name=AP006216.3-003;name2=ZNF259
chr11	ENCODE	exon	116153646	116154985	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116154851	116154985	.	-	2	Parent=gene487
chr11	ENCODE	exon	116155698	116155763	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116155698	116155763	.	-	2	Parent=gene487
chr11	ENCODE	exon	116158084	116158170	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116158084	116158170	.	-	2	Parent=gene487
chr11	ENCODE	exon	116158845	116158955	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116158845	116158955	.	-	2	Parent=gene487
chr11	ENCODE	exon	116159456	116159545	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116159456	116159545	.	-	2	Parent=gene487
chr11	ENCODE	exon	116160304	116160374	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116160304	116160374	.	-	1	Parent=gene487
chr11	ENCODE	exon	116160781	116160847	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116160781	116160847	.	-	2	Parent=gene487
chr11	ENCODE	exon	116161440	116161562	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116161440	116161562	.	-	2	Parent=gene487
chr11	ENCODE	exon	116161722	116161808	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116161722	116161808	.	-	2	Parent=gene487
chr11	ENCODE	exon	116162437	116162507	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116162437	116162507	.	-	1	Parent=gene487
chr11	ENCODE	exon	116162895	116162985	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116162895	116162985	.	-	2	Parent=gene487
chr11	ENCODE	exon	116163746	116163905	.	-	.	Parent=gene487
chr11	ENCODE	CDS	116163746	116163905	.	-	0	Parent=gene487
###
chr11	ENCODE	gene	116153646	116163915	.	-	.	ID=gene488;name2=ZNF259;Name=AP006216.3-002
chr11	ENCODE	exon	116153646	116154985	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116154851	116154985	.	-	1	Parent=gene488
chr11	ENCODE	exon	116155698	116155763	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116155698	116155763	.	-	1	Parent=gene488
chr11	ENCODE	exon	116158845	116158955	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116158845	116158955	.	-	1	Parent=gene488
chr11	ENCODE	exon	116159456	116159545	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116159456	116159545	.	-	1	Parent=gene488
chr11	ENCODE	exon	116160304	116160374	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116160304	116160374	.	-	0	Parent=gene488
chr11	ENCODE	exon	116160781	116160847	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116160781	116160847	.	-	1	Parent=gene488
chr11	ENCODE	exon	116161025	116161072	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116161025	116161072	.	-	1	Parent=gene488
chr11	ENCODE	exon	116161440	116161562	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116161440	116161562	.	-	1	Parent=gene488
chr11	ENCODE	exon	116161722	116161808	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116161722	116161808	.	-	1	Parent=gene488
chr11	ENCODE	exon	116162437	116162507	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116162437	116162507	.	-	0	Parent=gene488
chr11	ENCODE	exon	116162895	116162985	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116162895	116162985	.	-	1	Parent=gene488
chr11	ENCODE	exon	116163408	116163569	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116163408	116163569	.	-	1	Parent=gene488
chr11	ENCODE	exon	116163746	116163915	.	-	.	Parent=gene488
chr11	ENCODE	CDS	116163746	116163915	.	-	0	Parent=gene488
###
chr11	ENCODE	gene	116153646	116163976	.	-	.	ID=gene489;Name=AP006216.3-001;name2=ZNF259
chr11	ENCODE	exon	116153646	116154985	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116154851	116154985	.	-	0	Parent=gene489
chr11	ENCODE	exon	116155698	116155763	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116155698	116155763	.	-	0	Parent=gene489
chr11	ENCODE	exon	116158084	116158170	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116158084	116158170	.	-	0	Parent=gene489
chr11	ENCODE	exon	116158845	116158955	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116158845	116158955	.	-	0	Parent=gene489
chr11	ENCODE	exon	116159456	116159545	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116159456	116159545	.	-	0	Parent=gene489
chr11	ENCODE	exon	116160304	116160374	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116160304	116160374	.	-	2	Parent=gene489
chr11	ENCODE	exon	116160781	116160847	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116160781	116160847	.	-	0	Parent=gene489
chr11	ENCODE	exon	116161025	116161072	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116161025	116161072	.	-	0	Parent=gene489
chr11	ENCODE	exon	116161440	116161562	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116161440	116161562	.	-	0	Parent=gene489
chr11	ENCODE	exon	116161722	116161808	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116161722	116161808	.	-	0	Parent=gene489
chr11	ENCODE	exon	116162437	116162507	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116162437	116162507	.	-	2	Parent=gene489
chr11	ENCODE	exon	116162895	116162985	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116162895	116162985	.	-	0	Parent=gene489
chr11	ENCODE	exon	116163408	116163569	.	-	.	Parent=gene489
chr11	ENCODE	CDS	116163408	116163569	.	-	0	Parent=gene489
chr11	ENCODE	CDS	116163746	116163916	.	-	0	Parent=gene489
chr11	ENCODE	exon	116163746	116163976	.	-	.	Parent=gene489
###
chr11	ENCODE	gene	116158084	116161769	.	-	.	ID=gene490;Name=AP006216.3-005;name2=ZNF259
chr11	ENCODE	exon	116158084	116158170	.	-	.	Parent=gene490
chr11	ENCODE	exon	116158845	116158955	.	-	.	Parent=gene490
chr11	ENCODE	exon	116159456	116159545	.	-	.	Parent=gene490
chr11	ENCODE	exon	116160304	116160424	.	-	.	Parent=gene490
chr11	ENCODE	exon	116160785	116160847	.	-	.	Parent=gene490
chr11	ENCODE	exon	116161025	116161072	.	-	.	Parent=gene490
chr11	ENCODE	exon	116161440	116161562	.	-	.	Parent=gene490
chr11	ENCODE	exon	116161722	116161769	.	-	.	Parent=gene490
###
chr11	ENCODE	gene	116161504	116163824	.	-	.	ID=gene491;Name=AP006216.3-006;name2=ZNF259
chr11	ENCODE	exon	116161504	116161562	.	-	.	Parent=gene491
chr11	ENCODE	exon	116161722	116161808	.	-	.	Parent=gene491
chr11	ENCODE	exon	116162437	116162507	.	-	.	Parent=gene491
chr11	ENCODE	exon	116162895	116162985	.	-	.	Parent=gene491
chr11	ENCODE	exon	116163408	116163528	.	-	.	Parent=gene491
chr11	ENCODE	exon	116163746	116163824	.	-	.	Parent=gene491
###
chr11	ENCODE	gene	116161722	116163965	.	-	.	ID=gene492;Name=AP006216.3-004;name2=ZNF259
chr11	ENCODE	exon	116161722	116161808	.	-	.	Parent=gene492
chr11	ENCODE	exon	116162437	116162507	.	-	.	Parent=gene492
chr11	ENCODE	exon	116162895	116162985	.	-	.	Parent=gene492
chr11	ENCODE	exon	116163408	116163569	.	-	.	Parent=gene492
chr11	ENCODE	exon	116163774	116163965	.	-	.	Parent=gene492
###
chr11	ENCODE	gene	116162451	116163262	.	-	.	ID=gene493;Name=AP006216.3-008;name2=ZNF259
chr11	ENCODE	exon	116162451	116162507	.	-	.	Parent=gene493
chr11	ENCODE	exon	116162895	116163262	.	-	.	Parent=gene493
###
chr11	ENCODE	gene	116162938	116163913	.	-	.	ID=gene494;Name=AP006216.3-007;name2=ZNF259
chr11	ENCODE	exon	116162938	116162985	.	-	.	Parent=gene494
chr11	ENCODE	exon	116163408	116163913	.	-	.	Parent=gene494
###
chr11	ENCODE	gene	116165293	116167821	.	-	.	ID=gene495;Name=AP006216.4-001;name2=APOA5
chr11	ENCODE	exon	116165293	116166993	.	-	.	Parent=gene495
chr11	ENCODE	CDS	116166054	116166993	.	-	1	Parent=gene495
chr11	ENCODE	exon	116167512	116167623	.	-	.	Parent=gene495
chr11	ENCODE	CDS	116167512	116167623	.	-	2	Parent=gene495
chr11	ENCODE	CDS	116167738	116167786	.	-	0	Parent=gene495
chr11	ENCODE	exon	116167738	116167821	.	-	.	Parent=gene495
###
chr11	ENCODE	gene	116166669	116168337	.	-	.	ID=gene496;Name=AP006216.4-002;name2=APOA5
chr11	ENCODE	exon	116166669	116166993	.	-	.	Parent=gene496
chr11	ENCODE	CDS	116166669	116166993	.	-	1	Parent=gene496
chr11	ENCODE	exon	116167512	116167623	.	-	.	Parent=gene496
chr11	ENCODE	CDS	116167512	116167623	.	-	2	Parent=gene496
chr11	ENCODE	CDS	116167738	116167786	.	-	0	Parent=gene496
chr11	ENCODE	exon	116167738	116167794	.	-	.	Parent=gene496
chr11	ENCODE	exon	116168306	116168337	.	-	.	Parent=gene496
###
chr11	ENCODE	gene	116196629	116199232	.	-	.	ID=gene497;Name=AP006216.6-001;name2=APOA4
chr11	ENCODE	exon	116196629	116197807	.	-	.	Parent=gene497
chr11	ENCODE	CDS	116196793	116197807	.	-	1	Parent=gene497
chr11	ENCODE	exon	116198585	116198711	.	-	.	Parent=gene497
chr11	ENCODE	CDS	116198585	116198711	.	-	2	Parent=gene497
chr11	ENCODE	CDS	116199069	116199117	.	-	0	Parent=gene497
chr11	ENCODE	exon	116199069	116199232	.	-	.	Parent=gene497
###
chr11	ENCODE	gene	116205632	116206808	.	+	.	ID=gene498;name2=APOC3;Name=AP006216.7-002
chr11	ENCODE	exon	116205632	116205812	.	+	.	Parent=gene498
chr11	ENCODE	exon	116206496	116206563	.	+	.	Parent=gene498
chr11	ENCODE	CDS	116206509	116206563	.	+	0	Parent=gene498
chr11	ENCODE	exon	116206699	116206808	.	+	.	Parent=gene498
chr11	ENCODE	CDS	116206699	116206808	.	+	2	Parent=gene498
###
chr11	ENCODE	gene	116205818	116208998	.	+	.	ID=gene499;Name=AP006216.7-001;name2=APOC3
chr11	ENCODE	exon	116205818	116205866	.	+	.	Parent=gene499
chr11	ENCODE	exon	116206496	116206563	.	+	.	Parent=gene499
chr11	ENCODE	CDS	116206509	116206563	.	+	0	Parent=gene499
chr11	ENCODE	exon	116206699	116206822	.	+	.	Parent=gene499
chr11	ENCODE	CDS	116206699	116206822	.	+	2	Parent=gene499
chr11	ENCODE	CDS	116208690	116208810	.	+	1	Parent=gene499
chr11	ENCODE	exon	116208690	116208998	.	+	.	Parent=gene499
###
chr11	ENCODE	gene	116205841	116208998	.	+	.	ID=gene500;Name=AP006216.7-003;name2=APOC3
chr11	ENCODE	exon	116205841	116205866	.	+	.	Parent=gene500
chr11	ENCODE	exon	116206419	116206563	.	+	.	Parent=gene500
chr11	ENCODE	CDS	116206455	116206563	.	+	0	Parent=gene500
chr11	ENCODE	exon	116206699	116206822	.	+	.	Parent=gene500
chr11	ENCODE	CDS	116206699	116206822	.	+	2	Parent=gene500
chr11	ENCODE	CDS	116208690	116208810	.	+	1	Parent=gene500
chr11	ENCODE	exon	116208690	116208998	.	+	.	Parent=gene500
###
chr11	ENCODE	gene	116205848	116207026	.	+	.	ID=gene501;Name=AP006216.7-004;name2=APOC3
chr11	ENCODE	exon	116205848	116205866	.	+	.	Parent=gene501
chr11	ENCODE	exon	116206496	116206563	.	+	.	Parent=gene501
chr11	ENCODE	exon	116206699	116206822	.	+	.	Parent=gene501
chr11	ENCODE	exon	116206969	116207026	.	+	.	Parent=gene501
###
chr11	ENCODE	gene	116211677	116213512	.	-	.	ID=gene502;Name=AP006216.8-002;name2=APOA1
chr11	ENCODE	exon	116211677	116212337	.	-	.	Parent=gene502
chr11	ENCODE	CDS	116211734	116212337	.	-	1	Parent=gene502
chr11	ENCODE	exon	116212927	116213083	.	-	.	Parent=gene502
chr11	ENCODE	CDS	116212927	116213083	.	-	2	Parent=gene502
chr11	ENCODE	CDS	116213271	116213313	.	-	0	Parent=gene502
chr11	ENCODE	exon	116213271	116213333	.	-	.	Parent=gene502
chr11	ENCODE	exon	116213454	116213512	.	-	.	Parent=gene502
###
chr11	ENCODE	gene	116211677	116213535	.	-	.	ID=gene503;Name=AP006216.8-004;name2=APOA1
chr11	ENCODE	exon	116211677	116212337	.	-	.	Parent=gene503
chr11	ENCODE	CDS	116211734	116212337	.	-	1	Parent=gene503
chr11	ENCODE	exon	116212927	116213083	.	-	.	Parent=gene503
chr11	ENCODE	CDS	116212927	116213083	.	-	2	Parent=gene503
chr11	ENCODE	CDS	116213271	116213313	.	-	0	Parent=gene503
chr11	ENCODE	exon	116213271	116213333	.	-	.	Parent=gene503
chr11	ENCODE	exon	116213485	116213535	.	-	.	Parent=gene503
###
chr11	ENCODE	gene	116211677	116213536	.	-	.	ID=gene504;Name=AP006216.8-005;name2=APOA1
chr11	ENCODE	exon	116211677	116212337	.	-	.	Parent=gene504
chr11	ENCODE	CDS	116211734	116212337	.	-	1	Parent=gene504
chr11	ENCODE	CDS	116213271	116213404	.	-	0	Parent=gene504
chr11	ENCODE	exon	116213271	116213536	.	-	.	Parent=gene504
###
chr11	ENCODE	gene	116211677	116213540	.	-	.	ID=gene505;Name=AP006216.8-003;name2=APOA1
chr11	ENCODE	exon	116211677	116212337	.	-	.	Parent=gene505
chr11	ENCODE	CDS	116211734	116212337	.	-	1	Parent=gene505
chr11	ENCODE	exon	116212927	116213083	.	-	.	Parent=gene505
chr11	ENCODE	CDS	116212927	116213083	.	-	2	Parent=gene505
chr11	ENCODE	CDS	116213271	116213313	.	-	0	Parent=gene505
chr11	ENCODE	exon	116213271	116213540	.	-	.	Parent=gene505
###
chr11	ENCODE	gene	116211677	116213876	.	-	.	ID=gene506;Name=AP006216.8-001;name2=APOA1
chr11	ENCODE	exon	116211677	116212337	.	-	.	Parent=gene506
chr11	ENCODE	CDS	116211734	116212337	.	-	1	Parent=gene506
chr11	ENCODE	exon	116212927	116213083	.	-	.	Parent=gene506
chr11	ENCODE	CDS	116212927	116213083	.	-	2	Parent=gene506
chr11	ENCODE	CDS	116213271	116213313	.	-	0	Parent=gene506
chr11	ENCODE	exon	116213271	116213333	.	-	.	Parent=gene506
chr11	ENCODE	exon	116213531	116213876	.	-	.	Parent=gene506
###
chr11	ENCODE	gene	116219328	116246177	.	-	.	ID=gene507;Name=AP006216.9-004;name2=AP006216.9
chr11	ENCODE	exon	116219328	116221555	.	-	.	Parent=gene507
chr11	ENCODE	exon	116222309	116222479	.	-	.	Parent=gene507
chr11	ENCODE	exon	116223402	116223534	.	-	.	Parent=gene507
chr11	ENCODE	exon	116225046	116225209	.	-	.	Parent=gene507
chr11	ENCODE	exon	116233736	116234445	.	-	.	Parent=gene507
chr11	ENCODE	exon	116235191	116235530	.	-	.	Parent=gene507
chr11	ENCODE	exon	116237767	116237852	.	-	.	Parent=gene507
chr11	ENCODE	exon	116238128	116238253	.	-	.	Parent=gene507
chr11	ENCODE	exon	116239594	116239744	.	-	.	Parent=gene507
chr11	ENCODE	exon	116246067	116246177	.	-	.	Parent=gene507
###
chr11	ENCODE	gene	116219328	116332990	.	-	.	ID=gene508;Name=AP006216.9-002;name2=AP006216.9
chr11	ENCODE	exon	116219328	116221555	.	-	.	Parent=gene508
chr11	ENCODE	exon	116222309	116222479	.	-	.	Parent=gene508
chr11	ENCODE	exon	116223402	116223534	.	-	.	Parent=gene508
chr11	ENCODE	exon	116225046	116225209	.	-	.	Parent=gene508
chr11	ENCODE	exon	116233736	116234625	.	-	.	Parent=gene508
chr11	ENCODE	exon	116235191	116235530	.	-	.	Parent=gene508
chr11	ENCODE	exon	116237200	116237309	.	-	.	Parent=gene508
chr11	ENCODE	exon	116237767	116237852	.	-	.	Parent=gene508
chr11	ENCODE	exon	116238128	116238253	.	-	.	Parent=gene508
chr11	ENCODE	exon	116239594	116239744	.	-	.	Parent=gene508
chr11	ENCODE	exon	116243872	116244015	.	-	.	Parent=gene508
chr11	ENCODE	exon	116246257	116246327	.	-	.	Parent=gene508
chr11	ENCODE	exon	116249407	116249562	.	-	.	Parent=gene508
chr11	ENCODE	exon	116249829	116249982	.	-	.	Parent=gene508
chr11	ENCODE	exon	116251084	116251193	.	-	.	Parent=gene508
chr11	ENCODE	exon	116251300	116251377	.	-	.	Parent=gene508
chr11	ENCODE	exon	116251792	116251935	.	-	.	Parent=gene508
chr11	ENCODE	exon	116252179	116252289	.	-	.	Parent=gene508
chr11	ENCODE	exon	116252850	116252968	.	-	.	Parent=gene508
chr11	ENCODE	exon	116272179	116272302	.	-	.	Parent=gene508
chr11	ENCODE	exon	116273119	116273243	.	-	.	Parent=gene508
chr11	ENCODE	exon	116303145	116303306	.	-	.	Parent=gene508
chr11	ENCODE	exon	116329970	116330033	.	-	.	Parent=gene508
chr11	ENCODE	exon	116332874	116332990	.	-	.	Parent=gene508
###
chr11	ENCODE	gene	116219328	116332990	.	-	.	ID=gene509;Name=AP006216.9-001;name2=AP006216.9
chr11	ENCODE	exon	116219328	116221555	.	-	.	Parent=gene509
chr11	ENCODE	exon	116222309	116222479	.	-	.	Parent=gene509
chr11	ENCODE	exon	116223402	116223534	.	-	.	Parent=gene509
chr11	ENCODE	exon	116225046	116225209	.	-	.	Parent=gene509
chr11	ENCODE	exon	116233736	116234625	.	-	.	Parent=gene509
chr11	ENCODE	exon	116235191	116235530	.	-	.	Parent=gene509
chr11	ENCODE	exon	116237200	116237309	.	-	.	Parent=gene509
chr11	ENCODE	exon	116237767	116237852	.	-	.	Parent=gene509
chr11	ENCODE	exon	116238128	116238253	.	-	.	Parent=gene509
chr11	ENCODE	exon	116239594	116239744	.	-	.	Parent=gene509
chr11	ENCODE	exon	116246257	116246327	.	-	.	Parent=gene509
chr11	ENCODE	exon	116249407	116249562	.	-	.	Parent=gene509
chr11	ENCODE	exon	116249829	116249982	.	-	.	Parent=gene509
chr11	ENCODE	exon	116251084	116251193	.	-	.	Parent=gene509
chr11	ENCODE	exon	116251300	116251377	.	-	.	Parent=gene509
chr11	ENCODE	exon	116251792	116251935	.	-	.	Parent=gene509
chr11	ENCODE	exon	116252179	116252289	.	-	.	Parent=gene509
chr11	ENCODE	exon	116252850	116252968	.	-	.	Parent=gene509
chr11	ENCODE	exon	116272179	116272302	.	-	.	Parent=gene509
chr11	ENCODE	exon	116273119	116273243	.	-	.	Parent=gene509
chr11	ENCODE	exon	116303145	116303306	.	-	.	Parent=gene509
chr11	ENCODE	exon	116329970	116330033	.	-	.	Parent=gene509
chr11	ENCODE	exon	116332874	116332990	.	-	.	Parent=gene509
###
chr11	ENCODE	gene	116221110	116225064	.	-	.	ID=gene510;Name=AP006216.9-012;name2=AP006216.9
chr11	ENCODE	exon	116221110	116221176	.	-	.	Parent=gene510
chr11	ENCODE	exon	116222309	116222383	.	-	.	Parent=gene510
chr11	ENCODE	exon	116223402	116223534	.	-	.	Parent=gene510
chr11	ENCODE	exon	116225046	116225064	.	-	.	Parent=gene510
###
chr11	ENCODE	gene	116221338	116240994	.	-	.	ID=gene511;Name=AP006216.9-005;name2=AP006216.9
chr11	ENCODE	exon	116221338	116221555	.	-	.	Parent=gene511
chr11	ENCODE	exon	116222309	116222479	.	-	.	Parent=gene511
chr11	ENCODE	exon	116223402	116223534	.	-	.	Parent=gene511
chr11	ENCODE	exon	116225046	116225209	.	-	.	Parent=gene511
chr11	ENCODE	exon	116233736	116234445	.	-	.	Parent=gene511
chr11	ENCODE	exon	116235191	116235530	.	-	.	Parent=gene511
chr11	ENCODE	exon	116237200	116237309	.	-	.	Parent=gene511
chr11	ENCODE	exon	116237767	116237852	.	-	.	Parent=gene511
chr11	ENCODE	exon	116238128	116238253	.	-	.	Parent=gene511
chr11	ENCODE	exon	116239594	116240994	.	-	.	Parent=gene511
###
chr11	ENCODE	gene	116232840	116237310	.	-	.	ID=gene512;Name=AP006216.9-006;name2=AP006216.9
chr11	ENCODE	exon	116232840	116234625	.	-	.	Parent=gene512
chr11	ENCODE	exon	116235191	116235530	.	-	.	Parent=gene512
chr11	ENCODE	exon	116237200	116237310	.	-	.	Parent=gene512
###
chr11	ENCODE	gene	116237810	116272302	.	-	.	ID=gene513;Name=AP006216.9-009;name2=AP006216.9
chr11	ENCODE	exon	116237810	116237852	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116237810	116237852	.	-	0	Parent=gene513
chr11	ENCODE	exon	116238128	116238253	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116238128	116238253	.	-	0	Parent=gene513
chr11	ENCODE	exon	116239594	116239744	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116239594	116239744	.	-	1	Parent=gene513
chr11	ENCODE	exon	116246257	116246327	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116246257	116246327	.	-	0	Parent=gene513
chr11	ENCODE	exon	116249407	116249562	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116249407	116249562	.	-	0	Parent=gene513
chr11	ENCODE	exon	116249829	116249982	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116249829	116249982	.	-	1	Parent=gene513
chr11	ENCODE	exon	116251084	116251193	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116251084	116251193	.	-	0	Parent=gene513
chr11	ENCODE	exon	116251300	116251377	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116251300	116251377	.	-	0	Parent=gene513
chr11	ENCODE	exon	116252179	116252289	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116252179	116252289	.	-	0	Parent=gene513
chr11	ENCODE	exon	116252850	116252968	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116252850	116252968	.	-	2	Parent=gene513
chr11	ENCODE	exon	116272179	116272302	.	-	.	Parent=gene513
chr11	ENCODE	CDS	116272179	116272302	.	-	0	Parent=gene513
###
chr11	ENCODE	gene	116243614	116249598	.	-	.	ID=gene514;Name=AP006216.9-011;name2=AP006216.9
chr11	ENCODE	exon	116243614	116244015	.	-	.	Parent=gene514
chr11	ENCODE	exon	116246257	116246327	.	-	.	Parent=gene514
chr11	ENCODE	exon	116249407	116249598	.	-	.	Parent=gene514
###
chr11	ENCODE	gene	116245450	116332970	.	-	.	ID=gene515;Name=AP006216.9-003;name2=AP006216.9
chr11	ENCODE	exon	116245450	116246327	.	-	.	Parent=gene515
chr11	ENCODE	exon	116249407	116249562	.	-	.	Parent=gene515
chr11	ENCODE	exon	116249829	116249982	.	-	.	Parent=gene515
chr11	ENCODE	exon	116251084	116251193	.	-	.	Parent=gene515
chr11	ENCODE	exon	116251300	116251377	.	-	.	Parent=gene515
chr11	ENCODE	exon	116251792	116251935	.	-	.	Parent=gene515
chr11	ENCODE	exon	116252179	116252289	.	-	.	Parent=gene515
chr11	ENCODE	exon	116252850	116252968	.	-	.	Parent=gene515
chr11	ENCODE	exon	116272179	116272302	.	-	.	Parent=gene515
chr11	ENCODE	exon	116273119	116273243	.	-	.	Parent=gene515
chr11	ENCODE	exon	116303145	116303306	.	-	.	Parent=gene515
chr11	ENCODE	exon	116329970	116330033	.	-	.	Parent=gene515
chr11	ENCODE	exon	116332874	116332970	.	-	.	Parent=gene515
###
chr11	ENCODE	gene	116249966	116251439	.	-	.	ID=gene516;Name=AP006216.9-010;name2=AP006216.9
chr11	ENCODE	exon	116249966	116249982	.	-	.	Parent=gene516
chr11	ENCODE	exon	116251084	116251193	.	-	.	Parent=gene516
chr11	ENCODE	exon	116251300	116251439	.	-	.	Parent=gene516
###
chr11	ENCODE	gene	116269771	116332990	.	-	.	ID=gene517;Name=AP006216.9-008;name2=AP006216.9
chr11	ENCODE	exon	116269771	116269893	.	-	.	Parent=gene517
chr11	ENCODE	exon	116272179	116272302	.	-	.	Parent=gene517
chr11	ENCODE	exon	116273119	116273243	.	-	.	Parent=gene517
chr11	ENCODE	exon	116303145	116303306	.	-	.	Parent=gene517
chr11	ENCODE	exon	116329970	116330033	.	-	.	Parent=gene517
chr11	ENCODE	exon	116332874	116332990	.	-	.	Parent=gene517
###
chr11	ENCODE	gene	116280672	116332990	.	-	.	ID=gene518;Name=AP006216.9-007;name2=AP006216.9
chr11	ENCODE	exon	116280672	116280929	.	-	.	Parent=gene518
chr11	ENCODE	exon	116303145	116303306	.	-	.	Parent=gene518
chr11	ENCODE	exon	116329970	116330033	.	-	.	Parent=gene518
chr11	ENCODE	exon	116332874	116332990	.	-	.	Parent=gene518
###
chr11	ENCODE	gene	130745583	130745993	.	+	.	ID=gene519;name2=HNT;Name=AP004248.3-002
chr11	ENCODE	exon	130745583	130745993	.	+	.	Parent=gene519
###
chr11	ENCODE	gene	130745731	131036152	.	+	.	ID=gene520;Name=AP004248.3-020;name2=HNT
chr11	ENCODE	exon	130745731	130745993	.	+	.	Parent=gene520
chr11	ENCODE	exon	131036033	131036152	.	+	.	Parent=gene520
###
chr11	ENCODE	gene	130745734	131036335	.	+	.	ID=gene521;name2=HNT;Name=AP004248.3-005
chr11	ENCODE	exon	130745734	130745993	.	+	.	Parent=gene521
chr11	ENCODE	exon	131036033	131036335	.	+	.	Parent=gene521
###
chr11	ENCODE	gene	130830567	131036152	.	+	.	ID=gene522;Name=AP004248.3-013;name2=HNT
chr11	ENCODE	exon	130830567	130830571	.	+	.	Parent=gene522
chr11	ENCODE	exon	131036033	131036152	.	+	.	Parent=gene522
###
chr11	ENCODE	gene	130957115	131036152	.	+	.	ID=gene523;Name=AP004248.3-014;name2=HNT
chr11	ENCODE	exon	130957115	130957482	.	+	.	Parent=gene523
chr11	ENCODE	exon	131036033	131036152	.	+	.	Parent=gene523
chr11	ENCODE	CDS	131036098	131036152	.	+	0	Parent=gene523
###
chr12	ENCODE	gene	38629559	38786158	.	-	.	ID=gene524;Name=AC121336.1-002;name2=SLC2A13
chr12	ENCODE	exon	38629559	38631434	.	-	.	Parent=gene524
chr12	ENCODE	CDS	38631286	38631434	.	-	2	Parent=gene524
chr12	ENCODE	exon	38708370	38708578	.	-	.	Parent=gene524
chr12	ENCODE	CDS	38708370	38708578	.	-	1	Parent=gene524
chr12	ENCODE	exon	38728120	38728279	.	-	.	Parent=gene524
chr12	ENCODE	CDS	38728120	38728279	.	-	2	Parent=gene524
chr12	ENCODE	CDS	38785322	38785877	.	-	0	Parent=gene524
chr12	ENCODE	exon	38785322	38786158	.	-	.	Parent=gene524
###
chr12	ENCODE	gene	38631326	38785928	.	-	.	ID=gene525;Name=AC121336.1-001;name2=SLC2A13
chr12	ENCODE	exon	38631326	38631434	.	-	.	Parent=gene525
chr12	ENCODE	exon	38708370	38708578	.	-	.	Parent=gene525
chr12	ENCODE	exon	38728120	38728279	.	-	.	Parent=gene525
chr12	ENCODE	exon	38785322	38785928	.	-	.	Parent=gene525
###
chr12	ENCODE	gene	38876813	38964021	.	+	.	ID=gene526;Name=AC084290.1-001;name2=LRRK2
chr12	ENCODE	exon	38876813	38876842	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38876813	38876842	.	+	0	Parent=gene526
chr12	ENCODE	exon	38905624	38905709	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38905624	38905709	.	+	0	Parent=gene526
chr12	ENCODE	exon	38912343	38912452	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38912343	38912452	.	+	1	Parent=gene526
chr12	ENCODE	exon	38915695	38915783	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38915695	38915783	.	+	2	Parent=gene526
chr12	ENCODE	exon	38918038	38918172	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38918038	38918172	.	+	0	Parent=gene526
chr12	ENCODE	exon	38923619	38923750	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38923619	38923750	.	+	0	Parent=gene526
chr12	ENCODE	exon	38929895	38930014	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38929895	38930014	.	+	0	Parent=gene526
chr12	ENCODE	exon	38933034	38933085	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38933034	38933085	.	+	0	Parent=gene526
chr12	ENCODE	exon	38939549	38939673	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38939549	38939673	.	+	2	Parent=gene526
chr12	ENCODE	exon	38943858	38943970	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38943858	38943970	.	+	0	Parent=gene526
chr12	ENCODE	exon	38954652	38954796	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38954652	38954796	.	+	1	Parent=gene526
chr12	ENCODE	exon	38954923	38955062	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38954923	38955062	.	+	0	Parent=gene526
chr12	ENCODE	exon	38957957	38958085	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38957957	38958085	.	+	1	Parent=gene526
chr12	ENCODE	exon	38958160	38958330	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38958160	38958330	.	+	1	Parent=gene526
chr12	ENCODE	exon	38963944	38964021	.	+	.	Parent=gene526
chr12	ENCODE	CDS	38963944	38964021	.	+	1	Parent=gene526
###
chr12	ENCODE	gene	38905080	38985045	.	+	.	ID=gene527;Name=AC084290.1-002;name2=LRRK2
chr12	ENCODE	exon	38905080	38905351	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38905201	38905351	.	+	0	Parent=gene527
chr12	ENCODE	exon	38905624	38905709	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38905624	38905709	.	+	2	Parent=gene527
chr12	ENCODE	exon	38912343	38912452	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38912343	38912452	.	+	0	Parent=gene527
chr12	ENCODE	exon	38915695	38915783	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38915695	38915783	.	+	1	Parent=gene527
chr12	ENCODE	exon	38918038	38918172	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38918038	38918172	.	+	2	Parent=gene527
chr12	ENCODE	exon	38920552	38920686	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38920552	38920686	.	+	2	Parent=gene527
chr12	ENCODE	exon	38923619	38923750	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38923619	38923750	.	+	2	Parent=gene527
chr12	ENCODE	exon	38929895	38930014	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38929895	38930014	.	+	2	Parent=gene527
chr12	ENCODE	exon	38931301	38931443	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38931301	38931443	.	+	2	Parent=gene527
chr12	ENCODE	exon	38931534	38931613	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38931534	38931613	.	+	0	Parent=gene527
chr12	ENCODE	exon	38932979	38933085	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38932979	38933085	.	+	1	Parent=gene527
chr12	ENCODE	exon	38937317	38937446	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38937317	38937446	.	+	2	Parent=gene527
chr12	ENCODE	exon	38939549	38939673	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38939549	38939673	.	+	1	Parent=gene527
chr12	ENCODE	exon	38943858	38943970	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38943858	38943970	.	+	2	Parent=gene527
chr12	ENCODE	exon	38954652	38954796	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38954652	38954796	.	+	0	Parent=gene527
chr12	ENCODE	exon	38954923	38955062	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38954923	38955062	.	+	2	Parent=gene527
chr12	ENCODE	exon	38957957	38958085	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38957957	38958085	.	+	0	Parent=gene527
chr12	ENCODE	exon	38958160	38958330	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38958160	38958330	.	+	0	Parent=gene527
chr12	ENCODE	exon	38963944	38964202	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38963944	38964202	.	+	0	Parent=gene527
chr12	ENCODE	exon	38967420	38967608	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38967420	38967608	.	+	2	Parent=gene527
chr12	ENCODE	exon	38973614	38973732	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38973614	38973732	.	+	2	Parent=gene527
chr12	ENCODE	exon	38974914	38974983	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38974914	38974983	.	+	0	Parent=gene527
chr12	ENCODE	exon	38975496	38975713	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38975496	38975713	.	+	2	Parent=gene527
chr12	ENCODE	exon	38978312	38978562	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38978312	38978562	.	+	0	Parent=gene527
chr12	ENCODE	exon	38979178	38979326	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38979178	38979326	.	+	1	Parent=gene527
chr12	ENCODE	exon	38982858	38982951	.	+	.	Parent=gene527
chr12	ENCODE	CDS	38982858	38982951	.	+	2	Parent=gene527
chr12	ENCODE	CDS	38984017	38984242	.	+	1	Parent=gene527
chr12	ENCODE	exon	38984017	38985045	.	+	.	Parent=gene527
###
chr12	ENCODE	gene	38905143	39049350	.	+	.	ID=gene528;Name=AC084290.1-004;name2=LRRK2
chr12	ENCODE	exon	38905143	38905351	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38905201	38905351	.	+	0	Parent=gene528
chr12	ENCODE	exon	38905624	38905709	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38905624	38905709	.	+	2	Parent=gene528
chr12	ENCODE	exon	38912343	38912452	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38912343	38912452	.	+	0	Parent=gene528
chr12	ENCODE	exon	38915695	38915783	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38915695	38915783	.	+	1	Parent=gene528
chr12	ENCODE	exon	38918038	38918172	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38918038	38918172	.	+	2	Parent=gene528
chr12	ENCODE	exon	38920552	38920686	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38920552	38920686	.	+	2	Parent=gene528
chr12	ENCODE	exon	38923619	38923750	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38923619	38923750	.	+	2	Parent=gene528
chr12	ENCODE	exon	38929895	38930014	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38929895	38930014	.	+	2	Parent=gene528
chr12	ENCODE	exon	38931301	38931443	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38931301	38931443	.	+	2	Parent=gene528
chr12	ENCODE	exon	38931534	38931613	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38931534	38931613	.	+	0	Parent=gene528
chr12	ENCODE	exon	38932979	38933085	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38932979	38933085	.	+	1	Parent=gene528
chr12	ENCODE	exon	38937317	38937446	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38937317	38937446	.	+	2	Parent=gene528
chr12	ENCODE	exon	38939549	38939673	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38939549	38939673	.	+	1	Parent=gene528
chr12	ENCODE	exon	38943858	38943970	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38943858	38943970	.	+	2	Parent=gene528
chr12	ENCODE	exon	38954652	38954796	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38954652	38954796	.	+	0	Parent=gene528
chr12	ENCODE	exon	38954923	38955062	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38954923	38955062	.	+	2	Parent=gene528
chr12	ENCODE	exon	38957957	38958085	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38957957	38958085	.	+	0	Parent=gene528
chr12	ENCODE	exon	38958160	38958330	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38958160	38958330	.	+	0	Parent=gene528
chr12	ENCODE	exon	38963944	38964202	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38963944	38964202	.	+	0	Parent=gene528
chr12	ENCODE	exon	38967420	38967608	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38967420	38967608	.	+	2	Parent=gene528
chr12	ENCODE	exon	38973614	38973732	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38973614	38973732	.	+	2	Parent=gene528
chr12	ENCODE	exon	38974914	38974983	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38974914	38974983	.	+	0	Parent=gene528
chr12	ENCODE	exon	38975496	38975713	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38975496	38975713	.	+	2	Parent=gene528
chr12	ENCODE	exon	38978312	38978562	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38978312	38978562	.	+	0	Parent=gene528
chr12	ENCODE	exon	38979178	38979326	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38979178	38979326	.	+	1	Parent=gene528
chr12	ENCODE	exon	38982858	38982951	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38982858	38982951	.	+	2	Parent=gene528
chr12	ENCODE	exon	38984017	38984203	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38984017	38984203	.	+	1	Parent=gene528
chr12	ENCODE	exon	38985854	38986035	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38985854	38986035	.	+	0	Parent=gene528
chr12	ENCODE	exon	38988536	38988765	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38988536	38988765	.	+	1	Parent=gene528
chr12	ENCODE	exon	38989175	38989302	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38989175	38989302	.	+	2	Parent=gene528
chr12	ENCODE	exon	38990500	38990718	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38990500	38990718	.	+	0	Parent=gene528
chr12	ENCODE	exon	38994041	38994242	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38994041	38994242	.	+	0	Parent=gene528
chr12	ENCODE	exon	38995281	38995369	.	+	.	Parent=gene528
chr12	ENCODE	CDS	38995281	38995369	.	+	2	Parent=gene528
chr12	ENCODE	exon	39000057	39000244	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39000057	39000244	.	+	0	Parent=gene528
chr12	ENCODE	exon	39001103	39001257	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39001103	39001257	.	+	1	Parent=gene528
chr12	ENCODE	exon	39002104	39002250	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39002104	39002250	.	+	2	Parent=gene528
chr12	ENCODE	exon	39002388	39002579	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39002388	39002579	.	+	2	Parent=gene528
chr12	ENCODE	exon	39003229	39003375	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39003229	39003375	.	+	2	Parent=gene528
chr12	ENCODE	exon	39008429	39008529	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39008429	39008529	.	+	2	Parent=gene528
chr12	ENCODE	exon	39015036	39015226	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39015036	39015226	.	+	0	Parent=gene528
chr12	ENCODE	exon	39020363	39020523	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39020363	39020523	.	+	1	Parent=gene528
chr12	ENCODE	exon	39026822	39026992	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39026822	39026992	.	+	2	Parent=gene528
chr12	ENCODE	exon	39028478	39028578	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39028478	39028578	.	+	2	Parent=gene528
chr12	ENCODE	exon	39031608	39031802	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39031608	39031802	.	+	0	Parent=gene528
chr12	ENCODE	exon	39034368	39034561	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39034368	39034561	.	+	0	Parent=gene528
chr12	ENCODE	exon	39036184	39036256	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39036184	39036256	.	+	1	Parent=gene528
chr12	ENCODE	exon	39039329	39039513	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39039329	39039513	.	+	0	Parent=gene528
chr12	ENCODE	exon	39043471	39043623	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39043471	39043623	.	+	1	Parent=gene528
chr12	ENCODE	exon	39044911	39045119	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39044911	39045119	.	+	1	Parent=gene528
chr12	ENCODE	exon	39047075	39047146	.	+	.	Parent=gene528
chr12	ENCODE	CDS	39047075	39047146	.	+	2	Parent=gene528
chr12	ENCODE	CDS	39047713	39047834	.	+	2	Parent=gene528
chr12	ENCODE	exon	39047713	39049350	.	+	.	Parent=gene528
###
chr12	ENCODE	gene	38905664	38912852	.	+	.	ID=gene529;Name=AC084290.1-006;name2=LRRK2
chr12	ENCODE	exon	38905664	38905709	.	+	.	Parent=gene529
chr12	ENCODE	exon	38912343	38912852	.	+	.	Parent=gene529
###
chr12	ENCODE	gene	38975574	39049354	.	+	.	ID=gene530;Name=AC084290.1-005;name2=LRRK2
chr12	ENCODE	exon	38975574	38975713	.	+	.	Parent=gene530
chr12	ENCODE	exon	38978312	38978562	.	+	.	Parent=gene530
chr12	ENCODE	exon	38979178	38979326	.	+	.	Parent=gene530
chr12	ENCODE	exon	38980882	38981133	.	+	.	Parent=gene530
chr12	ENCODE	exon	38982858	38982951	.	+	.	Parent=gene530
chr12	ENCODE	exon	38984017	38984203	.	+	.	Parent=gene530
chr12	ENCODE	exon	38985854	38986035	.	+	.	Parent=gene530
chr12	ENCODE	exon	38988536	38988765	.	+	.	Parent=gene530
chr12	ENCODE	exon	38989175	38989302	.	+	.	Parent=gene530
chr12	ENCODE	exon	38990500	38990718	.	+	.	Parent=gene530
chr12	ENCODE	exon	38994041	38994242	.	+	.	Parent=gene530
chr12	ENCODE	exon	38995281	38995369	.	+	.	Parent=gene530
chr12	ENCODE	exon	39000057	39000244	.	+	.	Parent=gene530
chr12	ENCODE	exon	39001103	39001257	.	+	.	Parent=gene530
chr12	ENCODE	exon	39002104	39002250	.	+	.	Parent=gene530
chr12	ENCODE	exon	39002388	39002579	.	+	.	Parent=gene530
chr12	ENCODE	exon	39003229	39003375	.	+	.	Parent=gene530
chr12	ENCODE	exon	39008429	39008529	.	+	.	Parent=gene530
chr12	ENCODE	exon	39015036	39015226	.	+	.	Parent=gene530
chr12	ENCODE	exon	39020363	39020523	.	+	.	Parent=gene530
chr12	ENCODE	exon	39026822	39026992	.	+	.	Parent=gene530
chr12	ENCODE	exon	39028478	39028578	.	+	.	Parent=gene530
chr12	ENCODE	exon	39031608	39031802	.	+	.	Parent=gene530
chr12	ENCODE	exon	39034368	39034561	.	+	.	Parent=gene530
chr12	ENCODE	exon	39036184	39036256	.	+	.	Parent=gene530
chr12	ENCODE	exon	39039329	39039513	.	+	.	Parent=gene530
chr12	ENCODE	exon	39043471	39043623	.	+	.	Parent=gene530
chr12	ENCODE	exon	39044911	39045119	.	+	.	Parent=gene530
chr12	ENCODE	exon	39047075	39047146	.	+	.	Parent=gene530
chr12	ENCODE	exon	39047713	39049354	.	+	.	Parent=gene530
###
chr12	ENCODE	gene	38978535	39049354	.	+	.	ID=gene531;Name=AC084290.1-003;name2=LRRK2
chr12	ENCODE	exon	38978535	38978562	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38978535	38978562	.	+	0	Parent=gene531
chr12	ENCODE	exon	38979178	38979326	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38979178	38979326	.	+	2	Parent=gene531
chr12	ENCODE	exon	38982858	38982951	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38982858	38982951	.	+	0	Parent=gene531
chr12	ENCODE	exon	38984017	38984203	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38984017	38984203	.	+	2	Parent=gene531
chr12	ENCODE	exon	38985854	38986035	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38985854	38986035	.	+	1	Parent=gene531
chr12	ENCODE	exon	38988536	38988765	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38988536	38988765	.	+	2	Parent=gene531
chr12	ENCODE	exon	38989175	38989302	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38989175	38989302	.	+	0	Parent=gene531
chr12	ENCODE	exon	38990500	38990718	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38990500	38990718	.	+	1	Parent=gene531
chr12	ENCODE	exon	38994041	38994242	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38994041	38994242	.	+	1	Parent=gene531
chr12	ENCODE	exon	38995281	38995369	.	+	.	Parent=gene531
chr12	ENCODE	CDS	38995281	38995369	.	+	0	Parent=gene531
chr12	ENCODE	exon	39000057	39000244	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39000057	39000244	.	+	1	Parent=gene531
chr12	ENCODE	exon	39001103	39001257	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39001103	39001257	.	+	2	Parent=gene531
chr12	ENCODE	exon	39002104	39002250	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39002104	39002250	.	+	0	Parent=gene531
chr12	ENCODE	exon	39002388	39002579	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39002388	39002579	.	+	0	Parent=gene531
chr12	ENCODE	exon	39003229	39003375	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39003229	39003375	.	+	0	Parent=gene531
chr12	ENCODE	exon	39008429	39008529	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39008429	39008529	.	+	0	Parent=gene531
chr12	ENCODE	exon	39015036	39015226	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39015036	39015226	.	+	1	Parent=gene531
chr12	ENCODE	exon	39020363	39020523	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39020363	39020523	.	+	2	Parent=gene531
chr12	ENCODE	exon	39026822	39026992	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39026822	39026992	.	+	0	Parent=gene531
chr12	ENCODE	exon	39028478	39028578	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39028478	39028578	.	+	0	Parent=gene531
chr12	ENCODE	exon	39031608	39031802	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39031608	39031802	.	+	1	Parent=gene531
chr12	ENCODE	exon	39034368	39034561	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39034368	39034561	.	+	1	Parent=gene531
chr12	ENCODE	exon	39036184	39036256	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39036184	39036256	.	+	2	Parent=gene531
chr12	ENCODE	exon	39039329	39039513	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39039329	39039513	.	+	1	Parent=gene531
chr12	ENCODE	exon	39043471	39043623	.	+	.	Parent=gene531
chr12	ENCODE	CDS	39043471	39043623	.	+	2	Parent=gene531
chr12	ENCODE	CDS	39044911	39045202	.	+	2	Parent=gene531
chr12	ENCODE	exon	39044911	39049354	.	+	.	Parent=gene531
###
chr12	ENCODE	gene	38992783	39000131	.	+	.	ID=gene532;Name=AC084290.1-007;name2=LRRK2
chr12	ENCODE	exon	38992783	38992977	.	+	.	Parent=gene532
chr12	ENCODE	exon	38994041	38994242	.	+	.	Parent=gene532
chr12	ENCODE	exon	38995281	38995369	.	+	.	Parent=gene532
chr12	ENCODE	exon	39000057	39000131	.	+	.	Parent=gene532
###
chr12	ENCODE	gene	39073464	39125713	.	+	.	ID=gene533;name2=MUC19;Name=AC079630.3-001
chr12	ENCODE	exon	39073464	39073568	.	+	.	Parent=gene533
chr12	ENCODE	exon	39077948	39077980	.	+	.	Parent=gene533
chr12	ENCODE	exon	39091676	39091696	.	+	.	Parent=gene533
chr12	ENCODE	exon	39092102	39092251	.	+	.	Parent=gene533
chr12	ENCODE	exon	39098199	39098249	.	+	.	Parent=gene533
chr12	ENCODE	exon	39099243	39099302	.	+	.	Parent=gene533
chr12	ENCODE	exon	39100276	39100504	.	+	.	Parent=gene533
chr12	ENCODE	exon	39101275	39101392	.	+	.	Parent=gene533
chr12	ENCODE	exon	39101909	39101969	.	+	.	Parent=gene533
chr12	ENCODE	exon	39102173	39102270	.	+	.	Parent=gene533
chr12	ENCODE	exon	39106476	39106686	.	+	.	Parent=gene533
chr12	ENCODE	exon	39107443	39107565	.	+	.	Parent=gene533
chr12	ENCODE	exon	39108039	39108162	.	+	.	Parent=gene533
chr12	ENCODE	exon	39109611	39109746	.	+	.	Parent=gene533
chr12	ENCODE	exon	39111695	39111787	.	+	.	Parent=gene533
chr12	ENCODE	exon	39112447	39112531	.	+	.	Parent=gene533
chr12	ENCODE	exon	39112696	39112833	.	+	.	Parent=gene533
chr12	ENCODE	exon	39113833	39113982	.	+	.	Parent=gene533
chr12	ENCODE	exon	39116166	39116260	.	+	.	Parent=gene533
chr12	ENCODE	exon	39116686	39116812	.	+	.	Parent=gene533
chr12	ENCODE	exon	39118197	39118443	.	+	.	Parent=gene533
chr12	ENCODE	exon	39120643	39120695	.	+	.	Parent=gene533
chr12	ENCODE	exon	39120793	39120893	.	+	.	Parent=gene533
chr12	ENCODE	exon	39121130	39121281	.	+	.	Parent=gene533
chr12	ENCODE	exon	39121941	39122079	.	+	.	Parent=gene533
chr12	ENCODE	exon	39123145	39123249	.	+	.	Parent=gene533
chr12	ENCODE	exon	39123335	39123529	.	+	.	Parent=gene533
chr12	ENCODE	exon	39124146	39124385	.	+	.	Parent=gene533
chr12	ENCODE	exon	39124458	39124614	.	+	.	Parent=gene533
chr12	ENCODE	exon	39125588	39125713	.	+	.	Parent=gene533
###
chr12	ENCODE	gene	39098246	39106570	.	+	.	ID=gene534;Name=AC079630.3-002;name2=MUC19
chr12	ENCODE	exon	39098246	39098249	.	+	.	Parent=gene534
chr12	ENCODE	exon	39099243	39099302	.	+	.	Parent=gene534
chr12	ENCODE	exon	39100276	39100504	.	+	.	Parent=gene534
chr12	ENCODE	exon	39101282	39101392	.	+	.	Parent=gene534
chr12	ENCODE	exon	39101909	39101969	.	+	.	Parent=gene534
chr12	ENCODE	exon	39102173	39102270	.	+	.	Parent=gene534
chr12	ENCODE	exon	39106476	39106570	.	+	.	Parent=gene534
###
chr13	ENCODE	gene	29419740	29422625	.	+	.	ID=gene535;name2=RP11-90M5.1;Name=RP11-90M5.1-001
chr13	ENCODE	exon	29419740	29419908	.	+	.	Parent=gene535
chr13	ENCODE	exon	29422454	29422625	.	+	.	Parent=gene535
###
chr13	ENCODE	gene	29674767	29779621	.	-	.	ID=gene536;Name=RP11-374F3.1-001;name2=KATNAL1
chr13	ENCODE	exon	29674767	29680875	.	-	.	Parent=gene536
chr13	ENCODE	CDS	29680677	29680875	.	-	1	Parent=gene536
chr13	ENCODE	exon	29682453	29682579	.	-	.	Parent=gene536
chr13	ENCODE	CDS	29682453	29682579	.	-	2	Parent=gene536
chr13	ENCODE	exon	29699549	29699683	.	-	.	Parent=gene536
chr13	ENCODE	CDS	29699549	29699683	.	-	2	Parent=gene536
chr13	ENCODE	exon	29702605	29702731	.	-	.	Parent=gene536
chr13	ENCODE	CDS	29702605	29702731	.	-	0	Parent=gene536
chr13	ENCODE	exon	29703451	29703609	.	-	.	Parent=gene536
chr13	ENCODE	CDS	29703451	29703609	.	-	0	Parent=gene536
chr13	ENCODE	exon	29712597	29712702	.	-	.	Parent=gene536
chr13	ENCODE	CDS	29712597	29712702	.	-	1	Parent=gene536
chr13	ENCODE	exon	29713096	29713223	.	-	.	Parent=gene536
chr13	ENCODE	CDS	29713096	29713223	.	-	0	Parent=gene536
chr13	ENCODE	exon	29727584	29727752	.	-	.	Parent=gene536
chr13	ENCODE	CDS	29727584	29727752	.	-	1	Parent=gene536
chr13	ENCODE	exon	29752200	29752360	.	-	.	Parent=gene536
chr13	ENCODE	CDS	29752200	29752360	.	-	0	Parent=gene536
chr13	ENCODE	CDS	29755753	29755914	.	-	0	Parent=gene536
chr13	ENCODE	exon	29755753	29755928	.	-	.	Parent=gene536
chr13	ENCODE	exon	29779468	29779621	.	-	.	Parent=gene536
###
chr13	ENCODE	gene	29680617	29779163	.	-	.	ID=gene537;Name=RP11-374F3.1-002;name2=KATNAL1
chr13	ENCODE	exon	29680617	29680875	.	-	.	Parent=gene537
chr13	ENCODE	CDS	29680677	29680875	.	-	1	Parent=gene537
chr13	ENCODE	exon	29682453	29682579	.	-	.	Parent=gene537
chr13	ENCODE	CDS	29682453	29682579	.	-	2	Parent=gene537
chr13	ENCODE	exon	29699549	29699683	.	-	.	Parent=gene537
chr13	ENCODE	CDS	29699549	29699683	.	-	2	Parent=gene537
chr13	ENCODE	exon	29702605	29702731	.	-	.	Parent=gene537
chr13	ENCODE	CDS	29702605	29702731	.	-	0	Parent=gene537
chr13	ENCODE	exon	29703451	29703609	.	-	.	Parent=gene537
chr13	ENCODE	CDS	29703451	29703609	.	-	0	Parent=gene537
chr13	ENCODE	exon	29712597	29712702	.	-	.	Parent=gene537
chr13	ENCODE	CDS	29712597	29712702	.	-	1	Parent=gene537
chr13	ENCODE	exon	29713096	29713223	.	-	.	Parent=gene537
chr13	ENCODE	CDS	29713096	29713223	.	-	0	Parent=gene537
chr13	ENCODE	exon	29727584	29727752	.	-	.	Parent=gene537
chr13	ENCODE	CDS	29727584	29727752	.	-	1	Parent=gene537
chr13	ENCODE	exon	29752200	29752360	.	-	.	Parent=gene537
chr13	ENCODE	CDS	29752200	29752360	.	-	0	Parent=gene537
chr13	ENCODE	CDS	29755753	29755914	.	-	0	Parent=gene537
chr13	ENCODE	exon	29755753	29755928	.	-	.	Parent=gene537
chr13	ENCODE	exon	29779077	29779163	.	-	.	Parent=gene537
###
chr13	ENCODE	gene	29680862	29682801	.	-	.	ID=gene538;name2=KATNAL1;Name=RP11-374F3.1-005
chr13	ENCODE	exon	29680862	29680875	.	-	.	Parent=gene538
chr13	ENCODE	exon	29682453	29682801	.	-	.	Parent=gene538
###
chr13	ENCODE	gene	29727617	29778993	.	-	.	ID=gene539;Name=RP11-374F3.1-004;name2=KATNAL1
chr13	ENCODE	exon	29727617	29727752	.	-	.	Parent=gene539
chr13	ENCODE	CDS	29727617	29727752	.	-	1	Parent=gene539
chr13	ENCODE	exon	29752200	29752360	.	-	.	Parent=gene539
chr13	ENCODE	CDS	29752200	29752360	.	-	0	Parent=gene539
chr13	ENCODE	CDS	29755753	29755914	.	-	0	Parent=gene539
chr13	ENCODE	exon	29755753	29755928	.	-	.	Parent=gene539
chr13	ENCODE	exon	29778901	29778993	.	-	.	Parent=gene539
###
chr13	ENCODE	gene	29727625	29779181	.	-	.	ID=gene540;Name=RP11-374F3.1-003;name2=KATNAL1
chr13	ENCODE	exon	29727625	29727752	.	-	.	Parent=gene540
chr13	ENCODE	CDS	29727625	29727752	.	-	1	Parent=gene540
chr13	ENCODE	exon	29752200	29752360	.	-	.	Parent=gene540
chr13	ENCODE	CDS	29752200	29752360	.	-	0	Parent=gene540
chr13	ENCODE	CDS	29755753	29755914	.	-	0	Parent=gene540
chr13	ENCODE	exon	29755753	29755928	.	-	.	Parent=gene540
chr13	ENCODE	exon	29778850	29779181	.	-	.	Parent=gene540
###
chr13	ENCODE	gene	112349359	112386812	.	+	.	ID=gene541;Name=RP11-88E10.3-001;name2=RP11-88E10.3
chr13	ENCODE	exon	112349359	112349913	.	+	.	Parent=gene541
chr13	ENCODE	exon	112381492	112381953	.	+	.	Parent=gene541
chr13	ENCODE	CDS	112381695	112381953	.	+	0	Parent=gene541
chr13	ENCODE	CDS	112385589	112385695	.	+	2	Parent=gene541
chr13	ENCODE	exon	112385589	112386812	.	+	.	Parent=gene541
###
chr13	ENCODE	gene	112392644	112589483	.	+	.	ID=gene542;Name=RP11-120K24.1-001;name2=ATP11A
chr13	ENCODE	exon	112392644	112392770	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112392732	112392770	.	+	0	Parent=gene542
chr13	ENCODE	exon	112487450	112487572	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112487450	112487572	.	+	0	Parent=gene542
chr13	ENCODE	exon	112507272	112507361	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112507272	112507361	.	+	0	Parent=gene542
chr13	ENCODE	exon	112508528	112508608	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112508528	112508608	.	+	0	Parent=gene542
chr13	ENCODE	exon	112512934	112513041	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112512934	112513041	.	+	0	Parent=gene542
chr13	ENCODE	exon	112518398	112518526	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112518398	112518526	.	+	0	Parent=gene542
chr13	ENCODE	exon	112521619	112521722	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112521619	112521722	.	+	0	Parent=gene542
chr13	ENCODE	exon	112522215	112522265	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112522215	112522265	.	+	1	Parent=gene542
chr13	ENCODE	exon	112525660	112525724	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112525660	112525724	.	+	1	Parent=gene542
chr13	ENCODE	exon	112526659	112526740	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112526659	112526740	.	+	2	Parent=gene542
chr13	ENCODE	exon	112527745	112527895	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112527745	112527895	.	+	1	Parent=gene542
chr13	ENCODE	exon	112529009	112529206	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112529009	112529206	.	+	0	Parent=gene542
chr13	ENCODE	exon	112533690	112533863	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112533690	112533863	.	+	0	Parent=gene542
chr13	ENCODE	exon	112535175	112535338	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112535175	112535338	.	+	0	Parent=gene542
chr13	ENCODE	exon	112536904	112536975	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112536904	112536975	.	+	1	Parent=gene542
chr13	ENCODE	exon	112538493	112538566	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112538493	112538566	.	+	1	Parent=gene542
chr13	ENCODE	exon	112544591	112544694	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112544591	112544694	.	+	2	Parent=gene542
chr13	ENCODE	exon	112553352	112553533	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112553352	112553533	.	+	0	Parent=gene542
chr13	ENCODE	exon	112556594	112556845	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112556594	112556845	.	+	1	Parent=gene542
chr13	ENCODE	exon	112558226	112558400	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112558226	112558400	.	+	1	Parent=gene542
chr13	ENCODE	exon	112560133	112560235	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112560133	112560235	.	+	0	Parent=gene542
chr13	ENCODE	exon	112560460	112560605	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112560460	112560605	.	+	2	Parent=gene542
chr13	ENCODE	exon	112561708	112561767	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112561708	112561767	.	+	0	Parent=gene542
chr13	ENCODE	exon	112562602	112562729	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112562602	112562729	.	+	0	Parent=gene542
chr13	ENCODE	exon	112564755	112564890	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112564755	112564890	.	+	1	Parent=gene542
chr13	ENCODE	exon	112574050	112574115	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112574050	112574115	.	+	0	Parent=gene542
chr13	ENCODE	exon	112575888	112575991	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112575888	112575991	.	+	0	Parent=gene542
chr13	ENCODE	exon	112578091	112578256	.	+	.	Parent=gene542
chr13	ENCODE	CDS	112578091	112578256	.	+	1	Parent=gene542
chr13	ENCODE	CDS	112580532	112580609	.	+	0	Parent=gene542
chr13	ENCODE	exon	112580532	112580618	.	+	.	Parent=gene542
chr13	ENCODE	exon	112584191	112589483	.	+	.	Parent=gene542
###
chr13	ENCODE	gene	112405602	112513014	.	+	.	ID=gene543;Name=RP11-120K24.1-007;name2=ATP11A
chr13	ENCODE	exon	112405602	112405657	.	+	.	Parent=gene543
chr13	ENCODE	exon	112487450	112487572	.	+	.	Parent=gene543
chr13	ENCODE	exon	112507272	112507361	.	+	.	Parent=gene543
chr13	ENCODE	exon	112508528	112508608	.	+	.	Parent=gene543
chr13	ENCODE	exon	112512934	112513014	.	+	.	Parent=gene543
###
chr13	ENCODE	gene	112487460	112563113	.	+	.	ID=gene544;name2=ATP11A;Name=RP11-120K24.1-002
chr13	ENCODE	exon	112487460	112487572	.	+	.	Parent=gene544
chr13	ENCODE	exon	112507272	112507361	.	+	.	Parent=gene544
chr13	ENCODE	exon	112508528	112508608	.	+	.	Parent=gene544
chr13	ENCODE	exon	112512934	112513041	.	+	.	Parent=gene544
chr13	ENCODE	exon	112518398	112518526	.	+	.	Parent=gene544
chr13	ENCODE	exon	112521619	112521722	.	+	.	Parent=gene544
chr13	ENCODE	exon	112522215	112522265	.	+	.	Parent=gene544
chr13	ENCODE	exon	112525660	112525724	.	+	.	Parent=gene544
chr13	ENCODE	exon	112526659	112526740	.	+	.	Parent=gene544
chr13	ENCODE	exon	112527745	112527895	.	+	.	Parent=gene544
chr13	ENCODE	exon	112529009	112529206	.	+	.	Parent=gene544
chr13	ENCODE	exon	112533690	112533863	.	+	.	Parent=gene544
chr13	ENCODE	exon	112535175	112535338	.	+	.	Parent=gene544
chr13	ENCODE	exon	112536904	112536975	.	+	.	Parent=gene544
chr13	ENCODE	exon	112538493	112538566	.	+	.	Parent=gene544
chr13	ENCODE	exon	112544591	112544694	.	+	.	Parent=gene544
chr13	ENCODE	exon	112553352	112553533	.	+	.	Parent=gene544
chr13	ENCODE	exon	112556594	112556845	.	+	.	Parent=gene544
chr13	ENCODE	exon	112558226	112558400	.	+	.	Parent=gene544
chr13	ENCODE	exon	112560133	112561767	.	+	.	Parent=gene544
chr13	ENCODE	exon	112562602	112563113	.	+	.	Parent=gene544
###
chr13	ENCODE	gene	112487487	112563113	.	+	.	ID=gene545;Name=RP11-120K24.1-003;name2=ATP11A
chr13	ENCODE	exon	112487487	112487572	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112487487	112487572	.	+	0	Parent=gene545
chr13	ENCODE	exon	112507272	112507361	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112507272	112507361	.	+	1	Parent=gene545
chr13	ENCODE	exon	112508528	112508608	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112508528	112508608	.	+	1	Parent=gene545
chr13	ENCODE	exon	112512934	112513041	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112512934	112513041	.	+	1	Parent=gene545
chr13	ENCODE	exon	112518398	112518526	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112518398	112518526	.	+	1	Parent=gene545
chr13	ENCODE	exon	112521619	112521722	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112521619	112521722	.	+	1	Parent=gene545
chr13	ENCODE	exon	112522215	112522265	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112522215	112522265	.	+	2	Parent=gene545
chr13	ENCODE	exon	112525660	112525724	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112525660	112525724	.	+	2	Parent=gene545
chr13	ENCODE	exon	112526659	112526740	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112526659	112526740	.	+	0	Parent=gene545
chr13	ENCODE	exon	112527745	112527895	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112527745	112527895	.	+	2	Parent=gene545
chr13	ENCODE	exon	112529009	112529206	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112529009	112529206	.	+	1	Parent=gene545
chr13	ENCODE	exon	112533690	112533863	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112533690	112533863	.	+	1	Parent=gene545
chr13	ENCODE	exon	112535175	112535338	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112535175	112535338	.	+	1	Parent=gene545
chr13	ENCODE	exon	112536904	112536975	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112536904	112536975	.	+	2	Parent=gene545
chr13	ENCODE	exon	112538493	112538566	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112538493	112538566	.	+	2	Parent=gene545
chr13	ENCODE	exon	112544591	112544694	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112544591	112544694	.	+	0	Parent=gene545
chr13	ENCODE	exon	112553352	112553533	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112553352	112553533	.	+	1	Parent=gene545
chr13	ENCODE	exon	112556594	112556845	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112556594	112556845	.	+	2	Parent=gene545
chr13	ENCODE	exon	112558226	112558400	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112558226	112558400	.	+	2	Parent=gene545
chr13	ENCODE	exon	112560133	112560235	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112560133	112560235	.	+	1	Parent=gene545
chr13	ENCODE	exon	112560460	112560605	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112560460	112560605	.	+	0	Parent=gene545
chr13	ENCODE	exon	112561708	112561767	.	+	.	Parent=gene545
chr13	ENCODE	CDS	112561708	112561767	.	+	1	Parent=gene545
chr13	ENCODE	CDS	112562602	112562757	.	+	1	Parent=gene545
chr13	ENCODE	exon	112562602	112563113	.	+	.	Parent=gene545
###
chr13	ENCODE	gene	112553495	112554169	.	+	.	ID=gene546;Name=RP11-120K24.1-009;name2=ATP11A
chr13	ENCODE	exon	112553495	112553533	.	+	.	Parent=gene546
chr13	ENCODE	exon	112553856	112554169	.	+	.	Parent=gene546
###
chr13	ENCODE	gene	112574083	112586273	.	+	.	ID=gene547;Name=RP11-120K24.1-004;name2=ATP11A
chr13	ENCODE	exon	112574083	112574115	.	+	.	Parent=gene547
chr13	ENCODE	CDS	112574083	112574115	.	+	0	Parent=gene547
chr13	ENCODE	exon	112575888	112575991	.	+	.	Parent=gene547
chr13	ENCODE	CDS	112575888	112575991	.	+	0	Parent=gene547
chr13	ENCODE	exon	112578091	112578256	.	+	.	Parent=gene547
chr13	ENCODE	CDS	112578091	112578256	.	+	1	Parent=gene547
chr13	ENCODE	CDS	112584131	112584379	.	+	0	Parent=gene547
chr13	ENCODE	exon	112584131	112586273	.	+	.	Parent=gene547
###
chr13	ENCODE	gene	112575747	112578409	.	+	.	ID=gene548;Name=RP11-120K24.1-008;name2=ATP11A
chr13	ENCODE	exon	112575747	112575991	.	+	.	Parent=gene548
chr13	ENCODE	exon	112578091	112578409	.	+	.	Parent=gene548
###
chr13	ENCODE	gene	112575818	112580774	.	+	.	ID=gene549;Name=RP11-120K24.1-006;name2=ATP11A
chr13	ENCODE	exon	112575818	112575991	.	+	.	Parent=gene549
chr13	ENCODE	exon	112578091	112578256	.	+	.	Parent=gene549
chr13	ENCODE	exon	112580532	112580774	.	+	.	Parent=gene549
###
chr13	ENCODE	gene	112578124	112584503	.	+	.	ID=gene550;Name=RP11-120K24.1-010;name2=ATP11A
chr13	ENCODE	exon	112578124	112578256	.	+	.	Parent=gene550
chr13	ENCODE	CDS	112578124	112578256	.	+	0	Parent=gene550
chr13	ENCODE	CDS	112582861	112582953	.	+	2	Parent=gene550
chr13	ENCODE	exon	112582861	112582964	.	+	.	Parent=gene550
chr13	ENCODE	exon	112584191	112584503	.	+	.	Parent=gene550
###
chr13	ENCODE	gene	112582616	112584462	.	+	.	ID=gene551;Name=RP11-120K24.1-005;name2=ATP11A
chr13	ENCODE	exon	112582616	112582964	.	+	.	Parent=gene551
chr13	ENCODE	exon	112584191	112584462	.	+	.	Parent=gene551
###
chr13	ENCODE	gene	112604510	112612934	.	+	.	ID=gene552;Name=RP11-98F14.2-015;name2=MCF2L
chr13	ENCODE	exon	112604510	112604686	.	+	.	Parent=gene552
chr13	ENCODE	CDS	112604518	112604686	.	+	0	Parent=gene552
chr13	ENCODE	CDS	112611568	112611593	.	+	2	Parent=gene552
chr13	ENCODE	exon	112611568	112612934	.	+	.	Parent=gene552
###
chr13	ENCODE	gene	112604510	112660479	.	+	.	ID=gene553;Name=RP11-98F14.2-016;name2=MCF2L
chr13	ENCODE	exon	112604510	112604686	.	+	.	Parent=gene553
chr13	ENCODE	exon	112619429	112619839	.	+	.	Parent=gene553
chr13	ENCODE	exon	112658358	112660479	.	+	.	Parent=gene553
###
chr13	ENCODE	gene	112604510	112799176	.	+	.	ID=gene554;Name=RP11-98F14.2-001;name2=MCF2L
chr13	ENCODE	exon	112604510	112604686	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112604518	112604686	.	+	0	Parent=gene554
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112717078	112717161	.	+	2	Parent=gene554
chr13	ENCODE	exon	112726959	112727073	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112726959	112727073	.	+	2	Parent=gene554
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112747586	112747676	.	+	1	Parent=gene554
chr13	ENCODE	exon	112762908	112763027	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112762908	112763027	.	+	0	Parent=gene554
chr13	ENCODE	exon	112766619	112766735	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112766619	112766735	.	+	0	Parent=gene554
chr13	ENCODE	exon	112767251	112767400	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112767251	112767400	.	+	0	Parent=gene554
chr13	ENCODE	exon	112768361	112768485	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112768361	112768485	.	+	0	Parent=gene554
chr13	ENCODE	exon	112772374	112772488	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112772374	112772488	.	+	1	Parent=gene554
chr13	ENCODE	exon	112776759	112776878	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112776759	112776878	.	+	0	Parent=gene554
chr13	ENCODE	exon	112777313	112777504	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112777313	112777504	.	+	0	Parent=gene554
chr13	ENCODE	exon	112778281	112778472	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112778281	112778472	.	+	0	Parent=gene554
chr13	ENCODE	exon	112779367	112779526	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112779367	112779526	.	+	0	Parent=gene554
chr13	ENCODE	exon	112780678	112780751	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112780678	112780751	.	+	2	Parent=gene554
chr13	ENCODE	exon	112780981	112781054	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112780981	112781054	.	+	0	Parent=gene554
chr13	ENCODE	exon	112783528	112783594	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112783528	112783594	.	+	1	Parent=gene554
chr13	ENCODE	exon	112784742	112784857	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112784742	112784857	.	+	0	Parent=gene554
chr13	ENCODE	exon	112786313	112786382	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112786313	112786382	.	+	1	Parent=gene554
chr13	ENCODE	exon	112787207	112787299	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112787207	112787299	.	+	0	Parent=gene554
chr13	ENCODE	exon	112787401	112787493	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112787401	112787493	.	+	0	Parent=gene554
chr13	ENCODE	exon	112788439	112788564	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112788439	112788564	.	+	0	Parent=gene554
chr13	ENCODE	exon	112789550	112789771	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112789550	112789771	.	+	0	Parent=gene554
chr13	ENCODE	exon	112790022	112790114	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112790022	112790114	.	+	0	Parent=gene554
chr13	ENCODE	exon	112790642	112790720	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112790642	112790720	.	+	0	Parent=gene554
chr13	ENCODE	exon	112790877	112790943	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112790877	112790943	.	+	2	Parent=gene554
chr13	ENCODE	exon	112791925	112792043	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112791925	112792043	.	+	1	Parent=gene554
chr13	ENCODE	exon	112796829	112796950	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112796829	112796950	.	+	2	Parent=gene554
chr13	ENCODE	exon	112798686	112798798	.	+	.	Parent=gene554
chr13	ENCODE	CDS	112798686	112798798	.	+	0	Parent=gene554
chr13	ENCODE	CDS	112798865	112799000	.	+	1	Parent=gene554
chr13	ENCODE	exon	112798865	112799176	.	+	.	Parent=gene554
###
chr13	ENCODE	gene	112670815	112802054	.	+	.	ID=gene555;Name=RP11-98F14.2-002;name2=MCF2L
chr13	ENCODE	exon	112670815	112671029	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112670852	112671029	.	+	0	Parent=gene555
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112717078	112717161	.	+	2	Parent=gene555
chr13	ENCODE	exon	112726959	112727073	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112726959	112727073	.	+	2	Parent=gene555
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112747586	112747676	.	+	1	Parent=gene555
chr13	ENCODE	exon	112762908	112763027	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112762908	112763027	.	+	0	Parent=gene555
chr13	ENCODE	exon	112766619	112766735	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112766619	112766735	.	+	0	Parent=gene555
chr13	ENCODE	exon	112767251	112767400	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112767251	112767400	.	+	0	Parent=gene555
chr13	ENCODE	exon	112768361	112768485	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112768361	112768485	.	+	0	Parent=gene555
chr13	ENCODE	exon	112772374	112772488	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112772374	112772488	.	+	1	Parent=gene555
chr13	ENCODE	exon	112776759	112776878	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112776759	112776878	.	+	0	Parent=gene555
chr13	ENCODE	exon	112777313	112777504	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112777313	112777504	.	+	0	Parent=gene555
chr13	ENCODE	exon	112778281	112778472	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112778281	112778472	.	+	0	Parent=gene555
chr13	ENCODE	exon	112779367	112779526	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112779367	112779526	.	+	0	Parent=gene555
chr13	ENCODE	exon	112780678	112780751	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112780678	112780751	.	+	2	Parent=gene555
chr13	ENCODE	exon	112780981	112781054	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112780981	112781054	.	+	0	Parent=gene555
chr13	ENCODE	exon	112783528	112783594	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112783528	112783594	.	+	1	Parent=gene555
chr13	ENCODE	exon	112784742	112784857	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112784742	112784857	.	+	0	Parent=gene555
chr13	ENCODE	exon	112786313	112786382	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112786313	112786382	.	+	1	Parent=gene555
chr13	ENCODE	exon	112787207	112787299	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112787207	112787299	.	+	0	Parent=gene555
chr13	ENCODE	exon	112787401	112787493	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112787401	112787493	.	+	0	Parent=gene555
chr13	ENCODE	exon	112788439	112788564	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112788439	112788564	.	+	0	Parent=gene555
chr13	ENCODE	exon	112789550	112789771	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112789550	112789771	.	+	0	Parent=gene555
chr13	ENCODE	exon	112790022	112790114	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112790022	112790114	.	+	0	Parent=gene555
chr13	ENCODE	exon	112790642	112790720	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112790642	112790720	.	+	0	Parent=gene555
chr13	ENCODE	exon	112790877	112790943	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112790877	112790943	.	+	2	Parent=gene555
chr13	ENCODE	exon	112791925	112792043	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112791925	112792043	.	+	1	Parent=gene555
chr13	ENCODE	exon	112796829	112796950	.	+	.	Parent=gene555
chr13	ENCODE	CDS	112796829	112796950	.	+	2	Parent=gene555
chr13	ENCODE	CDS	112798686	112798802	.	+	0	Parent=gene555
chr13	ENCODE	exon	112798686	112802054	.	+	.	Parent=gene555
###
chr13	ENCODE	gene	112671648	112767383	.	+	.	ID=gene556;Name=RP11-98F14.2-005;name2=MCF2L
chr13	ENCODE	exon	112671648	112671773	.	+	.	Parent=gene556
chr13	ENCODE	CDS	112671695	112671773	.	+	0	Parent=gene556
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene556
chr13	ENCODE	CDS	112717078	112717161	.	+	2	Parent=gene556
chr13	ENCODE	exon	112726959	112727073	.	+	.	Parent=gene556
chr13	ENCODE	CDS	112726959	112727073	.	+	2	Parent=gene556
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene556
chr13	ENCODE	CDS	112747586	112747676	.	+	1	Parent=gene556
chr13	ENCODE	exon	112762908	112763027	.	+	.	Parent=gene556
chr13	ENCODE	CDS	112762908	112763027	.	+	0	Parent=gene556
chr13	ENCODE	exon	112766619	112766735	.	+	.	Parent=gene556
chr13	ENCODE	CDS	112766619	112766735	.	+	0	Parent=gene556
chr13	ENCODE	exon	112767251	112767383	.	+	.	Parent=gene556
chr13	ENCODE	CDS	112767251	112767383	.	+	0	Parent=gene556
###
chr13	ENCODE	gene	112681627	112798802	.	+	.	ID=gene557;Name=RP11-98F14.2-024;name2=MCF2L
chr13	ENCODE	exon	112681627	112682073	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112681983	112682073	.	+	0	Parent=gene557
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112717078	112717161	.	+	2	Parent=gene557
chr13	ENCODE	exon	112726959	112727073	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112726959	112727073	.	+	2	Parent=gene557
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112747586	112747676	.	+	1	Parent=gene557
chr13	ENCODE	exon	112762908	112763027	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112762908	112763027	.	+	0	Parent=gene557
chr13	ENCODE	exon	112766619	112766735	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112766619	112766735	.	+	0	Parent=gene557
chr13	ENCODE	exon	112767251	112767400	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112767251	112767400	.	+	0	Parent=gene557
chr13	ENCODE	exon	112768361	112768485	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112768361	112768485	.	+	0	Parent=gene557
chr13	ENCODE	exon	112772374	112772488	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112772374	112772488	.	+	1	Parent=gene557
chr13	ENCODE	exon	112776759	112776878	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112776759	112776878	.	+	0	Parent=gene557
chr13	ENCODE	exon	112777313	112777504	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112777313	112777504	.	+	0	Parent=gene557
chr13	ENCODE	exon	112778281	112778472	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112778281	112778472	.	+	0	Parent=gene557
chr13	ENCODE	exon	112779367	112779526	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112779367	112779526	.	+	0	Parent=gene557
chr13	ENCODE	exon	112780678	112780751	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112780678	112780751	.	+	2	Parent=gene557
chr13	ENCODE	exon	112780981	112781054	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112780981	112781054	.	+	0	Parent=gene557
chr13	ENCODE	exon	112783528	112783594	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112783528	112783594	.	+	1	Parent=gene557
chr13	ENCODE	exon	112784742	112784857	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112784742	112784857	.	+	0	Parent=gene557
chr13	ENCODE	exon	112786313	112786382	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112786313	112786382	.	+	1	Parent=gene557
chr13	ENCODE	exon	112787207	112787299	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112787207	112787299	.	+	0	Parent=gene557
chr13	ENCODE	exon	112787401	112787493	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112787401	112787493	.	+	0	Parent=gene557
chr13	ENCODE	exon	112788439	112788564	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112788439	112788564	.	+	0	Parent=gene557
chr13	ENCODE	exon	112789550	112789771	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112789550	112789771	.	+	0	Parent=gene557
chr13	ENCODE	exon	112790022	112790114	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112790022	112790114	.	+	0	Parent=gene557
chr13	ENCODE	exon	112790642	112790720	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112790642	112790720	.	+	0	Parent=gene557
chr13	ENCODE	exon	112790877	112790943	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112790877	112790943	.	+	2	Parent=gene557
chr13	ENCODE	exon	112791925	112792043	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112791925	112792043	.	+	1	Parent=gene557
chr13	ENCODE	exon	112796829	112796950	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112796829	112796950	.	+	2	Parent=gene557
chr13	ENCODE	exon	112798686	112798802	.	+	.	Parent=gene557
chr13	ENCODE	CDS	112798686	112798802	.	+	0	Parent=gene557
###
chr13	ENCODE	gene	112682023	112727047	.	+	.	ID=gene558;Name=RP11-98F14.2-017;name2=MCF2L
chr13	ENCODE	exon	112682023	112682073	.	+	.	Parent=gene558
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene558
chr13	ENCODE	exon	112726959	112727047	.	+	.	Parent=gene558
###
chr13	ENCODE	gene	112687433	112727069	.	+	.	ID=gene559;Name=RP11-98F14.2-025;name2=MCF2L
chr13	ENCODE	exon	112687433	112687794	.	+	.	Parent=gene559
chr13	ENCODE	CDS	112687698	112687794	.	+	0	Parent=gene559
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene559
chr13	ENCODE	CDS	112717078	112717161	.	+	2	Parent=gene559
chr13	ENCODE	exon	112726959	112727069	.	+	.	Parent=gene559
chr13	ENCODE	CDS	112726959	112727069	.	+	2	Parent=gene559
###
chr13	ENCODE	gene	112703585	112766626	.	+	.	ID=gene560;Name=RP11-98F14.2-030;name2=MCF2L
chr13	ENCODE	exon	112703585	112703740	.	+	.	Parent=gene560
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene560
chr13	ENCODE	exon	112726959	112727073	.	+	.	Parent=gene560
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene560
chr13	ENCODE	exon	112762908	112763027	.	+	.	Parent=gene560
chr13	ENCODE	exon	112766619	112766626	.	+	.	Parent=gene560
###
chr13	ENCODE	gene	112704069	112792498	.	+	.	ID=gene561;Name=RP11-98F14.2-003;name2=MCF2L
chr13	ENCODE	exon	112704069	112704298	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112704226	112704298	.	+	0	Parent=gene561
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112717078	112717161	.	+	2	Parent=gene561
chr13	ENCODE	exon	112726959	112727073	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112726959	112727073	.	+	2	Parent=gene561
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112747586	112747676	.	+	1	Parent=gene561
chr13	ENCODE	exon	112762908	112763027	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112762908	112763027	.	+	0	Parent=gene561
chr13	ENCODE	exon	112766619	112766735	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112766619	112766735	.	+	0	Parent=gene561
chr13	ENCODE	exon	112767251	112767400	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112767251	112767400	.	+	0	Parent=gene561
chr13	ENCODE	exon	112768361	112768485	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112768361	112768485	.	+	0	Parent=gene561
chr13	ENCODE	exon	112772374	112772488	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112772374	112772488	.	+	1	Parent=gene561
chr13	ENCODE	exon	112776759	112776878	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112776759	112776878	.	+	0	Parent=gene561
chr13	ENCODE	exon	112777313	112777504	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112777313	112777504	.	+	0	Parent=gene561
chr13	ENCODE	exon	112778281	112778472	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112778281	112778472	.	+	0	Parent=gene561
chr13	ENCODE	exon	112779367	112779526	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112779367	112779526	.	+	0	Parent=gene561
chr13	ENCODE	exon	112780678	112780751	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112780678	112780751	.	+	2	Parent=gene561
chr13	ENCODE	exon	112780981	112781054	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112780981	112781054	.	+	0	Parent=gene561
chr13	ENCODE	exon	112783528	112783594	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112783528	112783594	.	+	1	Parent=gene561
chr13	ENCODE	exon	112784742	112784857	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112784742	112784857	.	+	0	Parent=gene561
chr13	ENCODE	exon	112786313	112786382	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112786313	112786382	.	+	1	Parent=gene561
chr13	ENCODE	exon	112787207	112787299	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112787207	112787299	.	+	0	Parent=gene561
chr13	ENCODE	exon	112787401	112787493	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112787401	112787493	.	+	0	Parent=gene561
chr13	ENCODE	exon	112788439	112788564	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112788439	112788564	.	+	0	Parent=gene561
chr13	ENCODE	exon	112789550	112789771	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112789550	112789771	.	+	0	Parent=gene561
chr13	ENCODE	exon	112790022	112790114	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112790022	112790114	.	+	0	Parent=gene561
chr13	ENCODE	exon	112790642	112790720	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112790642	112790720	.	+	0	Parent=gene561
chr13	ENCODE	exon	112790877	112790943	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112790877	112790943	.	+	2	Parent=gene561
chr13	ENCODE	exon	112791925	112792043	.	+	.	Parent=gene561
chr13	ENCODE	CDS	112791925	112792043	.	+	1	Parent=gene561
chr13	ENCODE	CDS	112792190	112792197	.	+	2	Parent=gene561
chr13	ENCODE	exon	112792190	112792498	.	+	.	Parent=gene561
###
chr13	ENCODE	gene	112704100	112727223	.	+	.	ID=gene562;Name=RP11-98F14.2-031;name2=MCF2L
chr13	ENCODE	exon	112704100	112704298	.	+	.	Parent=gene562
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene562
chr13	ENCODE	exon	112726959	112727223	.	+	.	Parent=gene562
###
chr13	ENCODE	gene	112704208	112729383	.	+	.	ID=gene563;Name=RP11-98F14.2-018;name2=MCF2L
chr13	ENCODE	exon	112704208	112704298	.	+	.	Parent=gene563
chr13	ENCODE	CDS	112704226	112704298	.	+	0	Parent=gene563
chr13	ENCODE	exon	112717078	112717161	.	+	.	Parent=gene563
chr13	ENCODE	CDS	112717078	112717161	.	+	2	Parent=gene563
chr13	ENCODE	exon	112726959	112727073	.	+	.	Parent=gene563
chr13	ENCODE	CDS	112726959	112727073	.	+	2	Parent=gene563
chr13	ENCODE	CDS	112729184	112729322	.	+	1	Parent=gene563
chr13	ENCODE	exon	112729184	112729383	.	+	.	Parent=gene563
###
chr13	ENCODE	gene	112726979	112736452	.	+	.	ID=gene564;Name=RP11-98F14.2-019;name2=MCF2L
chr13	ENCODE	exon	112726979	112727073	.	+	.	Parent=gene564
chr13	ENCODE	exon	112736187	112736452	.	+	.	Parent=gene564
###
chr13	ENCODE	gene	112727013	112755068	.	+	.	ID=gene565;Name=RP11-98F14.2-008;name2=MCF2L
chr13	ENCODE	exon	112727013	112727073	.	+	.	Parent=gene565
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene565
chr13	ENCODE	exon	112754822	112755068	.	+	.	Parent=gene565
###
chr13	ENCODE	gene	112742663	112749656	.	+	.	ID=gene566;Name=RP11-98F14.2-032;name2=MCF2L
chr13	ENCODE	exon	112742663	112743323	.	+	.	Parent=gene566
chr13	ENCODE	exon	112744591	112749656	.	+	.	Parent=gene566
###
chr13	ENCODE	gene	112746777	112747637	.	+	.	ID=gene567;Name=RP11-98F14.2-022;name2=MCF2L
chr13	ENCODE	exon	112746777	112747340	.	+	.	Parent=gene567
chr13	ENCODE	exon	112747586	112747637	.	+	.	Parent=gene567
###
chr13	ENCODE	gene	112746970	112797484	.	+	.	ID=gene568;Name=RP11-98F14.2-004;name2=MCF2L
chr13	ENCODE	exon	112746970	112747203	.	+	.	Parent=gene568
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene568
chr13	ENCODE	exon	112762908	112763027	.	+	.	Parent=gene568
chr13	ENCODE	exon	112766619	112766735	.	+	.	Parent=gene568
chr13	ENCODE	exon	112767251	112767400	.	+	.	Parent=gene568
chr13	ENCODE	exon	112768361	112768485	.	+	.	Parent=gene568
chr13	ENCODE	exon	112772374	112772488	.	+	.	Parent=gene568
chr13	ENCODE	exon	112776759	112776878	.	+	.	Parent=gene568
chr13	ENCODE	exon	112777313	112777504	.	+	.	Parent=gene568
chr13	ENCODE	exon	112778281	112778472	.	+	.	Parent=gene568
chr13	ENCODE	exon	112779367	112779526	.	+	.	Parent=gene568
chr13	ENCODE	exon	112780678	112780751	.	+	.	Parent=gene568
chr13	ENCODE	exon	112780981	112781054	.	+	.	Parent=gene568
chr13	ENCODE	exon	112783528	112783594	.	+	.	Parent=gene568
chr13	ENCODE	exon	112784742	112784857	.	+	.	Parent=gene568
chr13	ENCODE	exon	112786313	112786382	.	+	.	Parent=gene568
chr13	ENCODE	exon	112787207	112787299	.	+	.	Parent=gene568
chr13	ENCODE	exon	112787401	112787493	.	+	.	Parent=gene568
chr13	ENCODE	exon	112788439	112788564	.	+	.	Parent=gene568
chr13	ENCODE	exon	112789550	112789712	.	+	.	Parent=gene568
chr13	ENCODE	exon	112796919	112796950	.	+	.	Parent=gene568
chr13	ENCODE	exon	112797284	112797484	.	+	.	Parent=gene568
###
chr13	ENCODE	gene	112746977	112749170	.	+	.	ID=gene569;Name=RP11-98F14.2-007;name2=MCF2L
chr13	ENCODE	exon	112746977	112747203	.	+	.	Parent=gene569
chr13	ENCODE	CDS	112747040	112747203	.	+	0	Parent=gene569
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene569
chr13	ENCODE	CDS	112747586	112747676	.	+	1	Parent=gene569
chr13	ENCODE	CDS	112748913	112748918	.	+	0	Parent=gene569
chr13	ENCODE	exon	112748913	112749170	.	+	.	Parent=gene569
###
chr13	ENCODE	gene	112747003	112757220	.	+	.	ID=gene570;Name=RP11-98F14.2-006;name2=MCF2L
chr13	ENCODE	exon	112747003	112747203	.	+	.	Parent=gene570
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene570
chr13	ENCODE	exon	112756617	112757220	.	+	.	Parent=gene570
###
chr13	ENCODE	gene	112747166	112767618	.	+	.	ID=gene571;Name=RP11-98F14.2-023;name2=MCF2L
chr13	ENCODE	exon	112747166	112747203	.	+	.	Parent=gene571
chr13	ENCODE	CDS	112747166	112747203	.	+	0	Parent=gene571
chr13	ENCODE	exon	112747586	112747676	.	+	.	Parent=gene571
chr13	ENCODE	CDS	112747586	112747676	.	+	1	Parent=gene571
chr13	ENCODE	exon	112762908	112763027	.	+	.	Parent=gene571
chr13	ENCODE	CDS	112762908	112763027	.	+	0	Parent=gene571
chr13	ENCODE	exon	112766619	112766735	.	+	.	Parent=gene571
chr13	ENCODE	CDS	112766619	112766735	.	+	0	Parent=gene571
chr13	ENCODE	CDS	112767251	112767526	.	+	0	Parent=gene571
chr13	ENCODE	exon	112767251	112767618	.	+	.	Parent=gene571
###
chr13	ENCODE	gene	112766627	112772709	.	+	.	ID=gene572;Name=RP11-98F14.2-009;name2=MCF2L
chr13	ENCODE	exon	112766627	112766735	.	+	.	Parent=gene572
chr13	ENCODE	exon	112767251	112767400	.	+	.	Parent=gene572
chr13	ENCODE	exon	112768361	112768485	.	+	.	Parent=gene572
chr13	ENCODE	exon	112772374	112772709	.	+	.	Parent=gene572
###
chr13	ENCODE	gene	112767005	112777341	.	+	.	ID=gene573;Name=RP11-98F14.2-026;name2=MCF2L
chr13	ENCODE	exon	112767005	112767069	.	+	.	Parent=gene573
chr13	ENCODE	exon	112767251	112767400	.	+	.	Parent=gene573
chr13	ENCODE	exon	112768361	112768485	.	+	.	Parent=gene573
chr13	ENCODE	exon	112772374	112772488	.	+	.	Parent=gene573
chr13	ENCODE	exon	112776759	112776878	.	+	.	Parent=gene573
chr13	ENCODE	exon	112777313	112777341	.	+	.	Parent=gene573
###
chr13	ENCODE	gene	112786882	112788480	.	+	.	ID=gene574;Name=RP11-98F14.2-027;name2=MCF2L
chr13	ENCODE	exon	112786882	112787299	.	+	.	Parent=gene574
chr13	ENCODE	exon	112787401	112787493	.	+	.	Parent=gene574
chr13	ENCODE	exon	112788439	112788480	.	+	.	Parent=gene574
###
chr13	ENCODE	gene	112788476	112798756	.	+	.	ID=gene575;Name=RP11-98F14.2-010;name2=MCF2L
chr13	ENCODE	exon	112788476	112788564	.	+	.	Parent=gene575
chr13	ENCODE	CDS	112788476	112788564	.	+	0	Parent=gene575
chr13	ENCODE	exon	112789550	112789771	.	+	.	Parent=gene575
chr13	ENCODE	CDS	112789550	112789771	.	+	1	Parent=gene575
chr13	ENCODE	exon	112790022	112790114	.	+	.	Parent=gene575
chr13	ENCODE	CDS	112790022	112790114	.	+	1	Parent=gene575
chr13	ENCODE	exon	112790642	112790720	.	+	.	Parent=gene575
chr13	ENCODE	CDS	112790642	112790720	.	+	1	Parent=gene575
chr13	ENCODE	exon	112790877	112790943	.	+	.	Parent=gene575
chr13	ENCODE	CDS	112790877	112790943	.	+	0	Parent=gene575
chr13	ENCODE	exon	112791925	112792043	.	+	.	Parent=gene575
chr13	ENCODE	CDS	112791925	112792043	.	+	2	Parent=gene575
chr13	ENCODE	exon	112793436	112793510	.	+	.	Parent=gene575
chr13	ENCODE	CDS	112793436	112793510	.	+	0	Parent=gene575
chr13	ENCODE	exon	112796829	112796950	.	+	.	Parent=gene575
chr13	ENCODE	CDS	112796829	112796950	.	+	0	Parent=gene575
chr13	ENCODE	exon	112798686	112798756	.	+	.	Parent=gene575
chr13	ENCODE	CDS	112798686	112798756	.	+	1	Parent=gene575
###
chr13	ENCODE	gene	112788503	112798714	.	+	.	ID=gene576;Name=RP11-98F14.2-011;name2=MCF2L
chr13	ENCODE	exon	112788503	112788564	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112788503	112788564	.	+	0	Parent=gene576
chr13	ENCODE	exon	112789550	112789771	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112789550	112789771	.	+	1	Parent=gene576
chr13	ENCODE	exon	112790022	112790114	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112790022	112790114	.	+	1	Parent=gene576
chr13	ENCODE	exon	112790642	112790720	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112790642	112790720	.	+	1	Parent=gene576
chr13	ENCODE	exon	112790877	112790943	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112790877	112790943	.	+	0	Parent=gene576
chr13	ENCODE	exon	112791925	112792043	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112791925	112792043	.	+	2	Parent=gene576
chr13	ENCODE	exon	112792383	112792466	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112792383	112792466	.	+	0	Parent=gene576
chr13	ENCODE	exon	112793436	112793510	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112793436	112793510	.	+	0	Parent=gene576
chr13	ENCODE	exon	112796829	112796950	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112796829	112796950	.	+	0	Parent=gene576
chr13	ENCODE	exon	112798686	112798714	.	+	.	Parent=gene576
chr13	ENCODE	CDS	112798686	112798714	.	+	1	Parent=gene576
###
chr13	ENCODE	gene	112789714	112799984	.	+	.	ID=gene577;Name=RP11-98F14.2-029;name2=MCF2L
chr13	ENCODE	exon	112789714	112789771	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112789714	112789771	.	+	0	Parent=gene577
chr13	ENCODE	exon	112790022	112790114	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112790022	112790114	.	+	2	Parent=gene577
chr13	ENCODE	exon	112790642	112790720	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112790642	112790720	.	+	2	Parent=gene577
chr13	ENCODE	exon	112790877	112790943	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112790877	112790943	.	+	1	Parent=gene577
chr13	ENCODE	exon	112791925	112792043	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112791925	112792043	.	+	0	Parent=gene577
chr13	ENCODE	exon	112792383	112792475	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112792383	112792475	.	+	1	Parent=gene577
chr13	ENCODE	exon	112793436	112793510	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112793436	112793510	.	+	1	Parent=gene577
chr13	ENCODE	exon	112796829	112796950	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112796829	112796950	.	+	1	Parent=gene577
chr13	ENCODE	exon	112798686	112798798	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112798686	112798798	.	+	2	Parent=gene577
chr13	ENCODE	exon	112798865	112798968	.	+	.	Parent=gene577
chr13	ENCODE	CDS	112798865	112798968	.	+	0	Parent=gene577
chr13	ENCODE	CDS	112799089	112799174	.	+	1	Parent=gene577
chr13	ENCODE	exon	112799089	112799984	.	+	.	Parent=gene577
###
chr13	ENCODE	gene	112790111	112796919	.	+	.	ID=gene578;Name=RP11-98F14.2-012;name2=MCF2L
chr13	ENCODE	exon	112790111	112790114	.	+	.	Parent=gene578
chr13	ENCODE	CDS	112790111	112790114	.	+	0	Parent=gene578
chr13	ENCODE	exon	112790642	112790720	.	+	.	Parent=gene578
chr13	ENCODE	CDS	112790642	112790720	.	+	2	Parent=gene578
chr13	ENCODE	exon	112790877	112790943	.	+	.	Parent=gene578
chr13	ENCODE	CDS	112790877	112790943	.	+	1	Parent=gene578
chr13	ENCODE	exon	112791925	112792043	.	+	.	Parent=gene578
chr13	ENCODE	CDS	112791925	112792043	.	+	0	Parent=gene578
chr13	ENCODE	exon	112792383	112792475	.	+	.	Parent=gene578
chr13	ENCODE	CDS	112792383	112792475	.	+	1	Parent=gene578
chr13	ENCODE	exon	112796829	112796919	.	+	.	Parent=gene578
chr13	ENCODE	CDS	112796829	112796919	.	+	1	Parent=gene578
###
chr13	ENCODE	gene	112790930	112798769	.	+	.	ID=gene579;Name=RP11-98F14.2-013;name2=MCF2L
chr13	ENCODE	exon	112790930	112790943	.	+	.	Parent=gene579
chr13	ENCODE	CDS	112790930	112790943	.	+	0	Parent=gene579
chr13	ENCODE	exon	112791925	112792043	.	+	.	Parent=gene579
chr13	ENCODE	CDS	112791925	112792043	.	+	1	Parent=gene579
chr13	ENCODE	exon	112792383	112792475	.	+	.	Parent=gene579
chr13	ENCODE	CDS	112792383	112792475	.	+	2	Parent=gene579
chr13	ENCODE	exon	112793436	112793510	.	+	.	Parent=gene579
chr13	ENCODE	CDS	112793436	112793510	.	+	2	Parent=gene579
chr13	ENCODE	exon	112796829	112796950	.	+	.	Parent=gene579
chr13	ENCODE	CDS	112796829	112796950	.	+	2	Parent=gene579
chr13	ENCODE	exon	112798686	112798769	.	+	.	Parent=gene579
chr13	ENCODE	CDS	112798686	112798769	.	+	0	Parent=gene579
###
chr13	ENCODE	gene	112792006	112797493	.	+	.	ID=gene580;Name=RP11-98F14.2-014;name2=MCF2L
chr13	ENCODE	exon	112792006	112792043	.	+	.	Parent=gene580
chr13	ENCODE	exon	112796829	112796950	.	+	.	Parent=gene580
chr13	ENCODE	exon	112797284	112797493	.	+	.	Parent=gene580
###
chr13	ENCODE	gene	112793284	112797174	.	+	.	ID=gene581;Name=RP11-98F14.2-028;name2=MCF2L
chr13	ENCODE	exon	112793284	112793510	.	+	.	Parent=gene581
chr13	ENCODE	exon	112796829	112797174	.	+	.	Parent=gene581
###
chr13	ENCODE	gene	112795916	112800863	.	+	.	ID=gene582;name2=MCF2L;Name=RP11-98F14.2-021
chr13	ENCODE	exon	112795916	112796950	.	+	.	Parent=gene582
chr13	ENCODE	exon	112798686	112798798	.	+	.	Parent=gene582
chr13	ENCODE	exon	112798865	112798968	.	+	.	Parent=gene582
chr13	ENCODE	exon	112799089	112800863	.	+	.	Parent=gene582
###
chr13	ENCODE	gene	112797537	112800861	.	+	.	ID=gene583;Name=RP11-98F14.2-020;name2=MCF2L
chr13	ENCODE	exon	112797537	112798968	.	+	.	Parent=gene583
chr13	ENCODE	exon	112799089	112800861	.	+	.	Parent=gene583
###
chr13	ENCODE	gene	112808106	112822346	.	+	.	ID=gene584;Name=RP11-98F14.7-002;name2=F7
chr13	ENCODE	exon	112808106	112808220	.	+	.	Parent=gene584
chr13	ENCODE	CDS	112808157	112808220	.	+	0	Parent=gene584
chr13	ENCODE	exon	112813005	112813165	.	+	.	Parent=gene584
chr13	ENCODE	CDS	112813005	112813165	.	+	2	Parent=gene584
chr13	ENCODE	exon	112816067	112816091	.	+	.	Parent=gene584
chr13	ENCODE	CDS	112816067	112816091	.	+	0	Parent=gene584
chr13	ENCODE	exon	112816162	112816275	.	+	.	Parent=gene584
chr13	ENCODE	CDS	112816162	112816275	.	+	2	Parent=gene584
chr13	ENCODE	exon	112817975	112818115	.	+	.	Parent=gene584
chr13	ENCODE	CDS	112817975	112818115	.	+	2	Parent=gene584
chr13	ENCODE	exon	112819081	112819190	.	+	.	Parent=gene584
chr13	ENCODE	CDS	112819081	112819190	.	+	2	Parent=gene584
chr13	ENCODE	exon	112819788	112819911	.	+	.	Parent=gene584
chr13	ENCODE	CDS	112819788	112819911	.	+	0	Parent=gene584
chr13	ENCODE	CDS	112820728	112821323	.	+	2	Parent=gene584
chr13	ENCODE	exon	112820728	112822346	.	+	.	Parent=gene584
###
chr13	ENCODE	gene	112808122	112822996	.	+	.	ID=gene585;Name=RP11-98F14.7-001;name2=F7
chr13	ENCODE	exon	112808122	112808220	.	+	.	Parent=gene585
chr13	ENCODE	CDS	112808157	112808220	.	+	0	Parent=gene585
chr13	ENCODE	exon	112809160	112809225	.	+	.	Parent=gene585
chr13	ENCODE	CDS	112809160	112809225	.	+	2	Parent=gene585
chr13	ENCODE	exon	112813005	112813165	.	+	.	Parent=gene585
chr13	ENCODE	CDS	112813005	112813165	.	+	2	Parent=gene585
chr13	ENCODE	exon	112816067	112816091	.	+	.	Parent=gene585
chr13	ENCODE	CDS	112816067	112816091	.	+	0	Parent=gene585
chr13	ENCODE	exon	112816162	112816275	.	+	.	Parent=gene585
chr13	ENCODE	CDS	112816162	112816275	.	+	2	Parent=gene585
chr13	ENCODE	exon	112817975	112818115	.	+	.	Parent=gene585
chr13	ENCODE	CDS	112817975	112818115	.	+	2	Parent=gene585
chr13	ENCODE	exon	112819081	112819190	.	+	.	Parent=gene585
chr13	ENCODE	CDS	112819081	112819190	.	+	2	Parent=gene585
chr13	ENCODE	exon	112819788	112819911	.	+	.	Parent=gene585
chr13	ENCODE	CDS	112819788	112819911	.	+	0	Parent=gene585
chr13	ENCODE	CDS	112820728	112821323	.	+	2	Parent=gene585
chr13	ENCODE	exon	112820728	112822996	.	+	.	Parent=gene585
###
chr13	ENCODE	gene	112808154	112819103	.	+	.	ID=gene586;Name=RP11-98F14.7-004;name2=F7
chr13	ENCODE	exon	112808154	112808220	.	+	.	Parent=gene586
chr13	ENCODE	exon	112813019	112813165	.	+	.	Parent=gene586
chr13	ENCODE	exon	112816090	112816275	.	+	.	Parent=gene586
chr13	ENCODE	exon	112817975	112818115	.	+	.	Parent=gene586
chr13	ENCODE	exon	112819081	112819103	.	+	.	Parent=gene586
###
chr13	ENCODE	gene	112812655	112819150	.	+	.	ID=gene587;Name=RP11-98F14.7-003;name2=F7
chr13	ENCODE	exon	112812655	112813165	.	+	.	Parent=gene587
chr13	ENCODE	exon	112816090	112816275	.	+	.	Parent=gene587
chr13	ENCODE	exon	112819081	112819150	.	+	.	Parent=gene587
###
chr13	ENCODE	gene	112812994	112817218	.	+	.	ID=gene588;name2=F7;Name=RP11-98F14.7-005
chr13	ENCODE	exon	112812994	112813165	.	+	.	Parent=gene588
chr13	ENCODE	exon	112816067	112816091	.	+	.	Parent=gene588
chr13	ENCODE	exon	112816162	112816275	.	+	.	Parent=gene588
chr13	ENCODE	exon	112816879	112817099	.	+	.	Parent=gene588
chr13	ENCODE	exon	112817193	112817218	.	+	.	Parent=gene588
###
chr13	ENCODE	gene	112825129	112831927	.	+	.	ID=gene589;Name=RP11-98F14.9-002;name2=F10
chr13	ENCODE	exon	112825129	112825240	.	+	.	Parent=gene589
chr13	ENCODE	exon	112831767	112831927	.	+	.	Parent=gene589
###
chr13	ENCODE	gene	112825133	112831927	.	+	.	ID=gene590;Name=RP11-98F14.9-001;name2=F10
chr13	ENCODE	exon	112825133	112825240	.	+	.	Parent=gene590
chr13	ENCODE	exon	112831767	112831927	.	+	.	Parent=gene590
###
chr13	ENCODE	gene	112825134	112831927	.	+	.	ID=gene591;Name=RP11-98F14.9-003;name2=F10
chr13	ENCODE	exon	112825134	112825240	.	+	.	Parent=gene591
chr13	ENCODE	exon	112831767	112831927	.	+	.	Parent=gene591
###
chr13	ENCODE	gene	112825151	112832621	.	+	.	ID=gene592;Name=RP11-98F14.9-005;name2=F10
chr13	ENCODE	exon	112825151	112825240	.	+	.	Parent=gene592
chr13	ENCODE	exon	112831767	112831927	.	+	.	Parent=gene592
chr13	ENCODE	exon	112832309	112832621	.	+	.	Parent=gene592
###
chr13	ENCODE	gene	112825153	112831927	.	+	.	ID=gene593;Name=RP11-98F14.9-006;name2=F10
chr13	ENCODE	exon	112825153	112825240	.	+	.	Parent=gene593
chr13	ENCODE	exon	112831767	112831927	.	+	.	Parent=gene593
###
chr14	ENCODE	gene	98705377	98807318	.	-	.	ID=gene594;Name=AL162151.2-001;name2=BCL11B
chr14	ENCODE	exon	98705377	98712285	.	-	.	Parent=gene594
chr14	ENCODE	CDS	98710241	98712285	.	-	2	Parent=gene594
chr14	ENCODE	exon	98767435	98767647	.	-	.	Parent=gene594
chr14	ENCODE	CDS	98767435	98767647	.	-	2	Parent=gene594
chr14	ENCODE	exon	98793561	98793929	.	-	.	Parent=gene594
chr14	ENCODE	CDS	98793561	98793929	.	-	2	Parent=gene594
chr14	ENCODE	CDS	98807251	98807308	.	-	0	Parent=gene594
chr14	ENCODE	exon	98807251	98807318	.	-	.	Parent=gene594
###
chr14	ENCODE	gene	98705377	98807575	.	-	.	ID=gene595;Name=AL162151.2-002;name2=BCL11B
chr14	ENCODE	exon	98705377	98712285	.	-	.	Parent=gene595
chr14	ENCODE	CDS	98710241	98712285	.	-	2	Parent=gene595
chr14	ENCODE	exon	98793561	98793929	.	-	.	Parent=gene595
chr14	ENCODE	CDS	98793561	98793929	.	-	2	Parent=gene595
chr14	ENCODE	CDS	98807251	98807308	.	-	0	Parent=gene595
chr14	ENCODE	exon	98807251	98807575	.	-	.	Parent=gene595
###
chr14	ENCODE	gene	98710051	98807614	.	-	.	ID=gene596;Name=AL162151.2-003;name2=BCL11B
chr14	ENCODE	exon	98710051	98712285	.	-	.	Parent=gene596
chr14	ENCODE	CDS	98710241	98712285	.	-	2	Parent=gene596
chr14	ENCODE	CDS	98807251	98807308	.	-	0	Parent=gene596
chr14	ENCODE	exon	98807251	98807614	.	-	.	Parent=gene596
###
chr14	ENCODE	gene	98933836	98950024	.	-	.	ID=gene597;Name=AL132819.1-001;name2=SETD3
chr14	ENCODE	exon	98933836	98935215	.	-	.	Parent=gene597
chr14	ENCODE	exon	98936189	98936349	.	-	.	Parent=gene597
chr14	ENCODE	exon	98940315	98940400	.	-	.	Parent=gene597
chr14	ENCODE	exon	98941295	98941461	.	-	.	Parent=gene597
chr14	ENCODE	exon	98942606	98942680	.	-	.	Parent=gene597
chr14	ENCODE	exon	98949041	98949155	.	-	.	Parent=gene597
chr14	ENCODE	exon	98949966	98950024	.	-	.	Parent=gene597
###
chr14	ENCODE	gene	98934559	98942680	.	-	.	ID=gene598;Name=AL132819.1-005;name2=SETD3
chr14	ENCODE	exon	98934559	98935215	.	-	.	Parent=gene598
chr14	ENCODE	exon	98936189	98936349	.	-	.	Parent=gene598
chr14	ENCODE	exon	98940315	98940400	.	-	.	Parent=gene598
chr14	ENCODE	exon	98941295	98941461	.	-	.	Parent=gene598
chr14	ENCODE	exon	98942606	98942680	.	-	.	Parent=gene598
###
chr14	ENCODE	gene	98934822	98949340	.	-	.	ID=gene599;Name=AL132819.1-006;name2=SETD3
chr14	ENCODE	exon	98934822	98935215	.	-	.	Parent=gene599
chr14	ENCODE	exon	98936189	98936349	.	-	.	Parent=gene599
chr14	ENCODE	exon	98949041	98949340	.	-	.	Parent=gene599
###
chr14	ENCODE	gene	98941405	98950024	.	-	.	ID=gene600;Name=AL132819.1-008;name2=SETD3
chr14	ENCODE	exon	98941405	98941461	.	-	.	Parent=gene600
chr14	ENCODE	exon	98942606	98942680	.	-	.	Parent=gene600
chr14	ENCODE	exon	98949041	98949155	.	-	.	Parent=gene600
chr14	ENCODE	exon	98949966	98950024	.	-	.	Parent=gene600
###
chr14	ENCODE	gene	98945894	98950024	.	-	.	ID=gene601;Name=AL132819.1-003;name2=SETD3
chr14	ENCODE	exon	98945894	98946305	.	-	.	Parent=gene601
chr14	ENCODE	exon	98949041	98949155	.	-	.	Parent=gene601
chr14	ENCODE	exon	98949966	98950024	.	-	.	Parent=gene601
###
chr14	ENCODE	gene	98947369	98950024	.	-	.	ID=gene602;Name=AL132819.1-002;name2=SETD3
chr14	ENCODE	exon	98947369	98949155	.	-	.	Parent=gene602
chr14	ENCODE	exon	98949966	98950024	.	-	.	Parent=gene602
###
chr14	ENCODE	gene	98947668	98950024	.	-	.	ID=gene603;Name=AL132819.1-004;name2=SETD3
chr14	ENCODE	exon	98947668	98949155	.	-	.	Parent=gene603
chr14	ENCODE	exon	98949966	98950024	.	-	.	Parent=gene603
###
chr15	ENCODE	gene	41520749	41535642	.	-	.	ID=gene604;Name=AC018924.1-007;name2=TP53BP1
chr15	ENCODE	exon	41520749	41521073	.	-	.	Parent=gene604
chr15	ENCODE	exon	41535382	41535642	.	-	.	Parent=gene604
###
chr15	ENCODE	gene	41521016	41535821	.	-	.	ID=gene605;Name=AC018924.1-011;name2=TP53BP1
chr15	ENCODE	exon	41521016	41521073	.	-	.	Parent=gene605
chr15	ENCODE	exon	41525877	41526080	.	-	.	Parent=gene605
chr15	ENCODE	exon	41526256	41526404	.	-	.	Parent=gene605
chr15	ENCODE	exon	41526856	41526975	.	-	.	Parent=gene605
chr15	ENCODE	exon	41535382	41535821	.	-	.	Parent=gene605
###
chr15	ENCODE	gene	41521016	41572576	.	-	.	ID=gene606;Name=AC018924.1-005;name2=TP53BP1
chr15	ENCODE	exon	41521016	41521073	.	-	.	Parent=gene606
chr15	ENCODE	exon	41525877	41526080	.	-	.	Parent=gene606
chr15	ENCODE	exon	41535382	41536708	.	-	.	Parent=gene606
chr15	ENCODE	exon	41549348	41549556	.	-	.	Parent=gene606
chr15	ENCODE	exon	41554163	41554257	.	-	.	Parent=gene606
chr15	ENCODE	exon	41555055	41555184	.	-	.	Parent=gene606
chr15	ENCODE	exon	41557083	41557249	.	-	.	Parent=gene606
chr15	ENCODE	exon	41558887	41559016	.	-	.	Parent=gene606
chr15	ENCODE	exon	41559349	41559507	.	-	.	Parent=gene606
chr15	ENCODE	exon	41560385	41560512	.	-	.	Parent=gene606
chr15	ENCODE	exon	41571159	41571243	.	-	.	Parent=gene606
chr15	ENCODE	exon	41571492	41571585	.	-	.	Parent=gene606
chr15	ENCODE	exon	41571774	41571958	.	-	.	Parent=gene606
chr15	ENCODE	exon	41572527	41572576	.	-	.	Parent=gene606
###
chr15	ENCODE	gene	41521016	41572595	.	-	.	ID=gene607;Name=AC018924.1-004;name2=TP53BP1
chr15	ENCODE	exon	41521016	41521073	.	-	.	Parent=gene607
chr15	ENCODE	exon	41525877	41526080	.	-	.	Parent=gene607
chr15	ENCODE	exon	41526856	41526975	.	-	.	Parent=gene607
chr15	ENCODE	exon	41535382	41536708	.	-	.	Parent=gene607
chr15	ENCODE	exon	41549348	41549556	.	-	.	Parent=gene607
chr15	ENCODE	exon	41554163	41554257	.	-	.	Parent=gene607
chr15	ENCODE	exon	41555055	41555184	.	-	.	Parent=gene607
chr15	ENCODE	exon	41557083	41557249	.	-	.	Parent=gene607
chr15	ENCODE	exon	41558887	41559016	.	-	.	Parent=gene607
chr15	ENCODE	exon	41559349	41559507	.	-	.	Parent=gene607
chr15	ENCODE	exon	41560385	41560512	.	-	.	Parent=gene607
chr15	ENCODE	exon	41571159	41571243	.	-	.	Parent=gene607
chr15	ENCODE	exon	41571492	41571585	.	-	.	Parent=gene607
chr15	ENCODE	exon	41571774	41571958	.	-	.	Parent=gene607
chr15	ENCODE	exon	41572527	41572595	.	-	.	Parent=gene607
###
chr15	ENCODE	gene	41521016	41572661	.	-	.	ID=gene608;Name=AC018924.1-001;name2=TP53BP1
chr15	ENCODE	exon	41521016	41521073	.	-	.	Parent=gene608
chr15	ENCODE	exon	41525877	41526080	.	-	.	Parent=gene608
chr15	ENCODE	exon	41526856	41526975	.	-	.	Parent=gene608
chr15	ENCODE	exon	41535382	41536708	.	-	.	Parent=gene608
chr15	ENCODE	exon	41549348	41549556	.	-	.	Parent=gene608
chr15	ENCODE	exon	41554163	41554257	.	-	.	Parent=gene608
chr15	ENCODE	exon	41555055	41555184	.	-	.	Parent=gene608
chr15	ENCODE	exon	41557083	41557249	.	-	.	Parent=gene608
chr15	ENCODE	exon	41558887	41559016	.	-	.	Parent=gene608
chr15	ENCODE	exon	41559349	41559507	.	-	.	Parent=gene608
chr15	ENCODE	exon	41560385	41560512	.	-	.	Parent=gene608
chr15	ENCODE	exon	41571159	41571243	.	-	.	Parent=gene608
chr15	ENCODE	exon	41571492	41571585	.	-	.	Parent=gene608
chr15	ENCODE	exon	41571774	41571958	.	-	.	Parent=gene608
chr15	ENCODE	exon	41572527	41572661	.	-	.	Parent=gene608
###
chr15	ENCODE	gene	41521016	41590104	.	-	.	ID=gene609;Name=AC018924.1-002;name2=TP53BP1
chr15	ENCODE	exon	41521016	41521073	.	-	.	Parent=gene609
chr15	ENCODE	exon	41525877	41526080	.	-	.	Parent=gene609
chr15	ENCODE	exon	41526856	41526975	.	-	.	Parent=gene609
chr15	ENCODE	exon	41535382	41536708	.	-	.	Parent=gene609
chr15	ENCODE	exon	41549348	41549556	.	-	.	Parent=gene609
chr15	ENCODE	exon	41554163	41554257	.	-	.	Parent=gene609
chr15	ENCODE	exon	41555055	41555184	.	-	.	Parent=gene609
chr15	ENCODE	exon	41557083	41557249	.	-	.	Parent=gene609
chr15	ENCODE	exon	41558887	41559016	.	-	.	Parent=gene609
chr15	ENCODE	exon	41559349	41559507	.	-	.	Parent=gene609
chr15	ENCODE	exon	41560385	41560512	.	-	.	Parent=gene609
chr15	ENCODE	exon	41571159	41571243	.	-	.	Parent=gene609
chr15	ENCODE	exon	41571492	41571585	.	-	.	Parent=gene609
chr15	ENCODE	exon	41571774	41571958	.	-	.	Parent=gene609
chr15	ENCODE	exon	41589860	41590104	.	-	.	Parent=gene609
###
chr15	ENCODE	gene	41526645	41535514	.	-	.	ID=gene610;Name=AC018924.1-006;name2=TP53BP1
chr15	ENCODE	exon	41526645	41526975	.	-	.	Parent=gene610
chr15	ENCODE	CDS	41526848	41526975	.	-	2	Parent=gene610
chr15	ENCODE	exon	41535382	41535514	.	-	.	Parent=gene610
chr15	ENCODE	CDS	41535382	41535514	.	-	0	Parent=gene610
###
chr15	ENCODE	gene	41576928	41590218	.	-	.	ID=gene611;name2=TP53BP1;Name=AC018924.1-012
chr15	ENCODE	exon	41576928	41577028	.	-	.	Parent=gene611
chr15	ENCODE	exon	41589860	41590218	.	-	.	Parent=gene611
###
chr15	ENCODE	gene	41590448	41611110	.	+	.	ID=gene612;Name=AC019011.1-002;name2=MAP1A
chr15	ENCODE	exon	41590448	41590716	.	+	.	Parent=gene612
chr15	ENCODE	CDS	41590479	41590716	.	+	0	Parent=gene612
chr15	ENCODE	exon	41591680	41591781	.	+	.	Parent=gene612
chr15	ENCODE	CDS	41591680	41591781	.	+	2	Parent=gene612
chr15	ENCODE	exon	41600131	41600213	.	+	.	Parent=gene612
chr15	ENCODE	CDS	41600131	41600213	.	+	2	Parent=gene612
chr15	ENCODE	exon	41600462	41600602	.	+	.	Parent=gene612
chr15	ENCODE	CDS	41600462	41600602	.	+	0	Parent=gene612
chr15	ENCODE	exon	41600814	41608998	.	+	.	Parent=gene612
chr15	ENCODE	CDS	41600814	41608998	.	+	0	Parent=gene612
chr15	ENCODE	exon	41609140	41609360	.	+	.	Parent=gene612
chr15	ENCODE	CDS	41609140	41609360	.	+	2	Parent=gene612
chr15	ENCODE	CDS	41609559	41609714	.	+	0	Parent=gene612
chr15	ENCODE	exon	41609559	41611110	.	+	.	Parent=gene612
###
chr15	ENCODE	gene	41597115	41611110	.	+	.	ID=gene613;name2=MAP1A;Name=AC019011.1-001
chr15	ENCODE	exon	41597115	41597190	.	+	.	Parent=gene613
chr15	ENCODE	exon	41600131	41600213	.	+	.	Parent=gene613
chr15	ENCODE	exon	41600462	41600602	.	+	.	Parent=gene613
chr15	ENCODE	exon	41600814	41608998	.	+	.	Parent=gene613
chr15	ENCODE	CDS	41600964	41608998	.	+	0	Parent=gene613
chr15	ENCODE	exon	41609140	41609360	.	+	.	Parent=gene613
chr15	ENCODE	CDS	41609140	41609360	.	+	2	Parent=gene613
chr15	ENCODE	CDS	41609559	41609714	.	+	0	Parent=gene613
chr15	ENCODE	exon	41609559	41611110	.	+	.	Parent=gene613
###
chr15	ENCODE	gene	41612952	41664354	.	-	.	ID=gene614;Name=AC019011.2-006;name2=AC019011.2
chr15	ENCODE	exon	41612952	41614966	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41614164	41614966	.	-	2	Parent=gene614
chr15	ENCODE	exon	41618960	41619073	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41618960	41619073	.	-	2	Parent=gene614
chr15	ENCODE	exon	41638285	41638422	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41638285	41638422	.	-	2	Parent=gene614
chr15	ENCODE	exon	41643593	41643655	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41643593	41643655	.	-	2	Parent=gene614
chr15	ENCODE	exon	41644357	41644482	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41644357	41644482	.	-	2	Parent=gene614
chr15	ENCODE	exon	41647953	41648043	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41647953	41648043	.	-	0	Parent=gene614
chr15	ENCODE	exon	41650902	41651066	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41650902	41651066	.	-	0	Parent=gene614
chr15	ENCODE	exon	41651214	41651330	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41651214	41651330	.	-	0	Parent=gene614
chr15	ENCODE	exon	41652259	41652366	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41652259	41652366	.	-	0	Parent=gene614
chr15	ENCODE	exon	41652524	41652638	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41652524	41652638	.	-	1	Parent=gene614
chr15	ENCODE	exon	41652847	41652974	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41652847	41652974	.	-	0	Parent=gene614
chr15	ENCODE	exon	41653299	41653522	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41653299	41653522	.	-	2	Parent=gene614
chr15	ENCODE	exon	41653712	41653853	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41653712	41653853	.	-	0	Parent=gene614
chr15	ENCODE	exon	41655861	41656043	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41655861	41656043	.	-	0	Parent=gene614
chr15	ENCODE	exon	41656317	41656438	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41656317	41656438	.	-	2	Parent=gene614
chr15	ENCODE	exon	41656598	41656729	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41656598	41656729	.	-	2	Parent=gene614
chr15	ENCODE	exon	41656943	41657025	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41656943	41657025	.	-	1	Parent=gene614
chr15	ENCODE	exon	41657112	41657221	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41657112	41657221	.	-	0	Parent=gene614
chr15	ENCODE	exon	41657366	41657441	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41657366	41657441	.	-	1	Parent=gene614
chr15	ENCODE	exon	41657560	41657646	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41657560	41657646	.	-	1	Parent=gene614
chr15	ENCODE	exon	41658509	41658610	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41658509	41658610	.	-	1	Parent=gene614
chr15	ENCODE	exon	41660492	41660613	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41660492	41660613	.	-	0	Parent=gene614
chr15	ENCODE	exon	41660717	41660878	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41660717	41660878	.	-	0	Parent=gene614
chr15	ENCODE	exon	41661343	41661444	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41661343	41661444	.	-	0	Parent=gene614
chr15	ENCODE	exon	41661585	41661739	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41661585	41661739	.	-	2	Parent=gene614
chr15	ENCODE	exon	41662054	41662139	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41662054	41662139	.	-	1	Parent=gene614
chr15	ENCODE	exon	41662352	41662442	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41662352	41662442	.	-	2	Parent=gene614
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene614
chr15	ENCODE	CDS	41662894	41663089	.	-	0	Parent=gene614
chr15	ENCODE	CDS	41663848	41663994	.	-	0	Parent=gene614
chr15	ENCODE	exon	41663848	41664022	.	-	.	Parent=gene614
chr15	ENCODE	exon	41664289	41664354	.	-	.	Parent=gene614
###
chr15	ENCODE	gene	41612952	41669665	.	-	.	ID=gene615;Name=AC019011.2-003;name2=AC019011.2
chr15	ENCODE	exon	41612952	41614966	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41614164	41614966	.	-	2	Parent=gene615
chr15	ENCODE	exon	41618960	41619073	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41618960	41619073	.	-	2	Parent=gene615
chr15	ENCODE	exon	41638285	41638422	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41638285	41638422	.	-	2	Parent=gene615
chr15	ENCODE	exon	41644357	41644482	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41644357	41644482	.	-	2	Parent=gene615
chr15	ENCODE	exon	41647953	41648043	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41647953	41648043	.	-	0	Parent=gene615
chr15	ENCODE	exon	41650902	41651066	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41650902	41651066	.	-	0	Parent=gene615
chr15	ENCODE	exon	41651214	41651330	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41651214	41651330	.	-	0	Parent=gene615
chr15	ENCODE	exon	41652259	41652366	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41652259	41652366	.	-	0	Parent=gene615
chr15	ENCODE	exon	41652524	41652638	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41652524	41652638	.	-	1	Parent=gene615
chr15	ENCODE	exon	41652847	41652974	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41652847	41652974	.	-	0	Parent=gene615
chr15	ENCODE	exon	41653299	41653522	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41653299	41653522	.	-	2	Parent=gene615
chr15	ENCODE	exon	41653712	41653853	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41653712	41653853	.	-	0	Parent=gene615
chr15	ENCODE	exon	41655861	41656043	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41655861	41656043	.	-	0	Parent=gene615
chr15	ENCODE	exon	41656317	41656438	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41656317	41656438	.	-	2	Parent=gene615
chr15	ENCODE	exon	41656598	41656729	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41656598	41656729	.	-	2	Parent=gene615
chr15	ENCODE	exon	41656943	41657025	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41656943	41657025	.	-	1	Parent=gene615
chr15	ENCODE	exon	41657112	41657221	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41657112	41657221	.	-	0	Parent=gene615
chr15	ENCODE	exon	41657366	41657441	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41657366	41657441	.	-	1	Parent=gene615
chr15	ENCODE	exon	41657560	41657646	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41657560	41657646	.	-	1	Parent=gene615
chr15	ENCODE	exon	41658509	41658610	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41658509	41658610	.	-	1	Parent=gene615
chr15	ENCODE	exon	41660492	41660613	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41660492	41660613	.	-	0	Parent=gene615
chr15	ENCODE	exon	41660717	41660878	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41660717	41660878	.	-	0	Parent=gene615
chr15	ENCODE	exon	41661343	41661444	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41661343	41661444	.	-	0	Parent=gene615
chr15	ENCODE	exon	41661585	41661739	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41661585	41661739	.	-	2	Parent=gene615
chr15	ENCODE	exon	41662054	41662139	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41662054	41662139	.	-	1	Parent=gene615
chr15	ENCODE	exon	41662352	41662442	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41662352	41662442	.	-	2	Parent=gene615
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene615
chr15	ENCODE	CDS	41662894	41663089	.	-	0	Parent=gene615
chr15	ENCODE	CDS	41663848	41663994	.	-	0	Parent=gene615
chr15	ENCODE	exon	41663848	41664022	.	-	.	Parent=gene615
chr15	ENCODE	exon	41664289	41664382	.	-	.	Parent=gene615
chr15	ENCODE	exon	41669662	41669665	.	-	.	Parent=gene615
###
chr15	ENCODE	gene	41612952	41669665	.	-	.	ID=gene616;Name=AC019011.2-004;name2=AC019011.2
chr15	ENCODE	exon	41612952	41614966	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41614164	41614966	.	-	2	Parent=gene616
chr15	ENCODE	exon	41615625	41615744	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41615625	41615744	.	-	2	Parent=gene616
chr15	ENCODE	exon	41618960	41619073	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41618960	41619073	.	-	2	Parent=gene616
chr15	ENCODE	exon	41638285	41638422	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41638285	41638422	.	-	2	Parent=gene616
chr15	ENCODE	exon	41647953	41648043	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41647953	41648043	.	-	0	Parent=gene616
chr15	ENCODE	exon	41650902	41651066	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41650902	41651066	.	-	0	Parent=gene616
chr15	ENCODE	exon	41651214	41651330	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41651214	41651330	.	-	0	Parent=gene616
chr15	ENCODE	exon	41652259	41652366	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41652259	41652366	.	-	0	Parent=gene616
chr15	ENCODE	exon	41652524	41652638	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41652524	41652638	.	-	1	Parent=gene616
chr15	ENCODE	exon	41652847	41652974	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41652847	41652974	.	-	0	Parent=gene616
chr15	ENCODE	exon	41653299	41653522	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41653299	41653522	.	-	2	Parent=gene616
chr15	ENCODE	exon	41653712	41653853	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41653712	41653853	.	-	0	Parent=gene616
chr15	ENCODE	exon	41655861	41656043	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41655861	41656043	.	-	0	Parent=gene616
chr15	ENCODE	exon	41656317	41656438	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41656317	41656438	.	-	2	Parent=gene616
chr15	ENCODE	exon	41656598	41656729	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41656598	41656729	.	-	2	Parent=gene616
chr15	ENCODE	exon	41656943	41657025	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41656943	41657025	.	-	1	Parent=gene616
chr15	ENCODE	exon	41657112	41657221	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41657112	41657221	.	-	0	Parent=gene616
chr15	ENCODE	exon	41657366	41657441	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41657366	41657441	.	-	1	Parent=gene616
chr15	ENCODE	exon	41657560	41657646	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41657560	41657646	.	-	1	Parent=gene616
chr15	ENCODE	exon	41658509	41658610	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41658509	41658610	.	-	1	Parent=gene616
chr15	ENCODE	exon	41660492	41660613	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41660492	41660613	.	-	0	Parent=gene616
chr15	ENCODE	exon	41660717	41660878	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41660717	41660878	.	-	0	Parent=gene616
chr15	ENCODE	exon	41661343	41661444	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41661343	41661444	.	-	0	Parent=gene616
chr15	ENCODE	exon	41661585	41661739	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41661585	41661739	.	-	2	Parent=gene616
chr15	ENCODE	exon	41662054	41662139	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41662054	41662139	.	-	1	Parent=gene616
chr15	ENCODE	exon	41662352	41662442	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41662352	41662442	.	-	2	Parent=gene616
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene616
chr15	ENCODE	CDS	41662894	41663089	.	-	0	Parent=gene616
chr15	ENCODE	CDS	41663848	41663994	.	-	0	Parent=gene616
chr15	ENCODE	exon	41663848	41664022	.	-	.	Parent=gene616
chr15	ENCODE	exon	41664289	41664382	.	-	.	Parent=gene616
chr15	ENCODE	exon	41669662	41669665	.	-	.	Parent=gene616
###
chr15	ENCODE	gene	41612952	41669691	.	-	.	ID=gene617;name2=AC019011.2;Name=AC019011.2-005
chr15	ENCODE	exon	41612952	41614966	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41614164	41614966	.	-	2	Parent=gene617
chr15	ENCODE	exon	41618960	41619073	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41618960	41619073	.	-	2	Parent=gene617
chr15	ENCODE	exon	41638285	41638422	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41638285	41638422	.	-	2	Parent=gene617
chr15	ENCODE	exon	41644357	41644482	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41644357	41644482	.	-	2	Parent=gene617
chr15	ENCODE	exon	41647953	41648043	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41647953	41648043	.	-	0	Parent=gene617
chr15	ENCODE	exon	41650902	41651066	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41650902	41651066	.	-	0	Parent=gene617
chr15	ENCODE	exon	41651214	41651330	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41651214	41651330	.	-	0	Parent=gene617
chr15	ENCODE	exon	41652259	41652366	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41652259	41652366	.	-	0	Parent=gene617
chr15	ENCODE	exon	41652524	41652638	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41652524	41652638	.	-	1	Parent=gene617
chr15	ENCODE	exon	41652847	41652974	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41652847	41652974	.	-	0	Parent=gene617
chr15	ENCODE	exon	41653299	41653522	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41653299	41653522	.	-	2	Parent=gene617
chr15	ENCODE	exon	41653712	41653853	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41653712	41653853	.	-	0	Parent=gene617
chr15	ENCODE	exon	41655861	41656043	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41655861	41656043	.	-	0	Parent=gene617
chr15	ENCODE	exon	41656317	41656438	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41656317	41656438	.	-	2	Parent=gene617
chr15	ENCODE	exon	41656598	41656729	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41656598	41656729	.	-	2	Parent=gene617
chr15	ENCODE	exon	41656943	41657025	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41656943	41657025	.	-	1	Parent=gene617
chr15	ENCODE	exon	41657112	41657221	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41657112	41657221	.	-	0	Parent=gene617
chr15	ENCODE	exon	41657366	41657441	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41657366	41657441	.	-	1	Parent=gene617
chr15	ENCODE	exon	41657560	41657646	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41657560	41657646	.	-	1	Parent=gene617
chr15	ENCODE	exon	41658509	41658610	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41658509	41658610	.	-	1	Parent=gene617
chr15	ENCODE	exon	41660492	41660613	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41660492	41660613	.	-	0	Parent=gene617
chr15	ENCODE	exon	41660717	41660878	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41660717	41660878	.	-	0	Parent=gene617
chr15	ENCODE	exon	41661343	41661444	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41661343	41661444	.	-	0	Parent=gene617
chr15	ENCODE	exon	41661585	41661739	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41661585	41661739	.	-	2	Parent=gene617
chr15	ENCODE	exon	41662054	41662139	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41662054	41662139	.	-	1	Parent=gene617
chr15	ENCODE	exon	41662352	41662442	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41662352	41662442	.	-	2	Parent=gene617
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene617
chr15	ENCODE	CDS	41662894	41663089	.	-	0	Parent=gene617
chr15	ENCODE	CDS	41663848	41663994	.	-	0	Parent=gene617
chr15	ENCODE	exon	41663848	41664111	.	-	.	Parent=gene617
chr15	ENCODE	exon	41669662	41669691	.	-	.	Parent=gene617
###
chr15	ENCODE	gene	41612952	41669697	.	-	.	ID=gene618;Name=AC019011.2-001;name2=AC019011.2
chr15	ENCODE	exon	41612952	41614966	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41614164	41614966	.	-	2	Parent=gene618
chr15	ENCODE	exon	41618960	41619073	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41618960	41619073	.	-	2	Parent=gene618
chr15	ENCODE	exon	41638285	41638422	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41638285	41638422	.	-	2	Parent=gene618
chr15	ENCODE	exon	41644357	41644482	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41644357	41644482	.	-	2	Parent=gene618
chr15	ENCODE	exon	41647953	41648043	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41647953	41648043	.	-	0	Parent=gene618
chr15	ENCODE	exon	41650902	41651066	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41650902	41651066	.	-	0	Parent=gene618
chr15	ENCODE	exon	41651214	41651330	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41651214	41651330	.	-	0	Parent=gene618
chr15	ENCODE	exon	41652259	41652366	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41652259	41652366	.	-	0	Parent=gene618
chr15	ENCODE	exon	41652524	41652638	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41652524	41652638	.	-	1	Parent=gene618
chr15	ENCODE	exon	41652847	41652974	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41652847	41652974	.	-	0	Parent=gene618
chr15	ENCODE	exon	41653299	41653522	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41653299	41653522	.	-	2	Parent=gene618
chr15	ENCODE	exon	41653712	41653850	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41653712	41653850	.	-	0	Parent=gene618
chr15	ENCODE	exon	41655861	41656043	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41655861	41656043	.	-	0	Parent=gene618
chr15	ENCODE	exon	41656317	41656438	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41656317	41656438	.	-	2	Parent=gene618
chr15	ENCODE	exon	41656598	41656729	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41656598	41656729	.	-	2	Parent=gene618
chr15	ENCODE	exon	41656943	41657025	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41656943	41657025	.	-	1	Parent=gene618
chr15	ENCODE	exon	41657112	41657221	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41657112	41657221	.	-	0	Parent=gene618
chr15	ENCODE	exon	41657366	41657441	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41657366	41657441	.	-	1	Parent=gene618
chr15	ENCODE	exon	41657560	41657646	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41657560	41657646	.	-	1	Parent=gene618
chr15	ENCODE	exon	41658509	41658610	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41658509	41658610	.	-	1	Parent=gene618
chr15	ENCODE	exon	41660492	41660613	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41660492	41660613	.	-	0	Parent=gene618
chr15	ENCODE	exon	41660717	41660878	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41660717	41660878	.	-	0	Parent=gene618
chr15	ENCODE	exon	41661343	41661444	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41661343	41661444	.	-	0	Parent=gene618
chr15	ENCODE	exon	41661585	41661739	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41661585	41661739	.	-	2	Parent=gene618
chr15	ENCODE	exon	41662054	41662139	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41662054	41662139	.	-	1	Parent=gene618
chr15	ENCODE	exon	41662352	41662442	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41662352	41662442	.	-	2	Parent=gene618
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene618
chr15	ENCODE	CDS	41662894	41663089	.	-	0	Parent=gene618
chr15	ENCODE	CDS	41663848	41663994	.	-	0	Parent=gene618
chr15	ENCODE	exon	41663848	41664022	.	-	.	Parent=gene618
chr15	ENCODE	exon	41664289	41664382	.	-	.	Parent=gene618
chr15	ENCODE	exon	41669662	41669697	.	-	.	Parent=gene618
###
chr15	ENCODE	gene	41612952	41728419	.	-	.	ID=gene619;Name=AC019011.2-002;name2=AC019011.2
chr15	ENCODE	exon	41612952	41614966	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41614164	41614966	.	-	2	Parent=gene619
chr15	ENCODE	exon	41618960	41619073	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41618960	41619073	.	-	2	Parent=gene619
chr15	ENCODE	exon	41638285	41638422	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41638285	41638422	.	-	2	Parent=gene619
chr15	ENCODE	exon	41643593	41643655	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41643593	41643655	.	-	2	Parent=gene619
chr15	ENCODE	exon	41644357	41644482	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41644357	41644482	.	-	2	Parent=gene619
chr15	ENCODE	exon	41647953	41648043	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41647953	41648043	.	-	0	Parent=gene619
chr15	ENCODE	exon	41650902	41651066	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41650902	41651066	.	-	0	Parent=gene619
chr15	ENCODE	exon	41651214	41651330	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41651214	41651330	.	-	0	Parent=gene619
chr15	ENCODE	exon	41652259	41652366	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41652259	41652366	.	-	0	Parent=gene619
chr15	ENCODE	exon	41652524	41652650	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41652524	41652650	.	-	1	Parent=gene619
chr15	ENCODE	exon	41652847	41652974	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41652847	41652974	.	-	0	Parent=gene619
chr15	ENCODE	exon	41653299	41653522	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41653299	41653522	.	-	2	Parent=gene619
chr15	ENCODE	exon	41653712	41653853	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41653712	41653853	.	-	0	Parent=gene619
chr15	ENCODE	exon	41655861	41656043	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41655861	41656043	.	-	0	Parent=gene619
chr15	ENCODE	exon	41656317	41656438	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41656317	41656438	.	-	2	Parent=gene619
chr15	ENCODE	exon	41656598	41656729	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41656598	41656729	.	-	2	Parent=gene619
chr15	ENCODE	exon	41656943	41657025	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41656943	41657025	.	-	1	Parent=gene619
chr15	ENCODE	exon	41657112	41657221	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41657112	41657221	.	-	0	Parent=gene619
chr15	ENCODE	exon	41657366	41657441	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41657366	41657441	.	-	1	Parent=gene619
chr15	ENCODE	exon	41657560	41657646	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41657560	41657646	.	-	1	Parent=gene619
chr15	ENCODE	exon	41658509	41658610	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41658509	41658610	.	-	1	Parent=gene619
chr15	ENCODE	exon	41660492	41660613	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41660492	41660613	.	-	0	Parent=gene619
chr15	ENCODE	exon	41660717	41660878	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41660717	41660878	.	-	0	Parent=gene619
chr15	ENCODE	exon	41661343	41661444	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41661343	41661444	.	-	0	Parent=gene619
chr15	ENCODE	exon	41661585	41661739	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41661585	41661739	.	-	2	Parent=gene619
chr15	ENCODE	exon	41662054	41662139	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41662054	41662139	.	-	1	Parent=gene619
chr15	ENCODE	exon	41662352	41662442	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41662352	41662442	.	-	2	Parent=gene619
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene619
chr15	ENCODE	CDS	41662894	41663089	.	-	0	Parent=gene619
chr15	ENCODE	CDS	41663848	41663994	.	-	0	Parent=gene619
chr15	ENCODE	exon	41663848	41664022	.	-	.	Parent=gene619
chr15	ENCODE	exon	41664289	41664382	.	-	.	Parent=gene619
chr15	ENCODE	exon	41728412	41728419	.	-	.	Parent=gene619
###
chr15	ENCODE	gene	41613304	41664336	.	-	.	ID=gene620;Name=AC019011.2-007;name2=AC019011.2
chr15	ENCODE	exon	41613304	41614742	.	-	.	Parent=gene620
chr15	ENCODE	exon	41638349	41638422	.	-	.	Parent=gene620
chr15	ENCODE	exon	41643593	41643655	.	-	.	Parent=gene620
chr15	ENCODE	exon	41644357	41644482	.	-	.	Parent=gene620
chr15	ENCODE	exon	41647953	41648043	.	-	.	Parent=gene620
chr15	ENCODE	exon	41650902	41650999	.	-	.	Parent=gene620
chr15	ENCODE	exon	41652354	41652366	.	-	.	Parent=gene620
chr15	ENCODE	exon	41652524	41652638	.	-	.	Parent=gene620
chr15	ENCODE	exon	41652871	41652974	.	-	.	Parent=gene620
chr15	ENCODE	exon	41653299	41653522	.	-	.	Parent=gene620
chr15	ENCODE	exon	41653712	41653853	.	-	.	Parent=gene620
chr15	ENCODE	exon	41655861	41656043	.	-	.	Parent=gene620
chr15	ENCODE	exon	41656317	41656438	.	-	.	Parent=gene620
chr15	ENCODE	exon	41656598	41656729	.	-	.	Parent=gene620
chr15	ENCODE	exon	41656943	41657025	.	-	.	Parent=gene620
chr15	ENCODE	exon	41657112	41657221	.	-	.	Parent=gene620
chr15	ENCODE	exon	41657366	41657441	.	-	.	Parent=gene620
chr15	ENCODE	exon	41657560	41657646	.	-	.	Parent=gene620
chr15	ENCODE	exon	41658509	41658610	.	-	.	Parent=gene620
chr15	ENCODE	exon	41660492	41660613	.	-	.	Parent=gene620
chr15	ENCODE	exon	41660717	41660878	.	-	.	Parent=gene620
chr15	ENCODE	exon	41661343	41661444	.	-	.	Parent=gene620
chr15	ENCODE	exon	41661585	41661739	.	-	.	Parent=gene620
chr15	ENCODE	exon	41662054	41662139	.	-	.	Parent=gene620
chr15	ENCODE	exon	41662352	41662442	.	-	.	Parent=gene620
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene620
chr15	ENCODE	exon	41663848	41664022	.	-	.	Parent=gene620
chr15	ENCODE	exon	41664289	41664336	.	-	.	Parent=gene620
###
chr15	ENCODE	gene	41627897	41648006	.	-	.	ID=gene621;Name=AC019011.2-014;name2=AC019011.2
chr15	ENCODE	exon	41627897	41628173	.	-	.	Parent=gene621
chr15	ENCODE	exon	41638285	41638422	.	-	.	Parent=gene621
chr15	ENCODE	exon	41644357	41644482	.	-	.	Parent=gene621
chr15	ENCODE	exon	41647953	41648006	.	-	.	Parent=gene621
###
chr15	ENCODE	gene	41638320	41650987	.	-	.	ID=gene622;Name=AC019011.2-016;name2=AC019011.2
chr15	ENCODE	exon	41638320	41638422	.	-	.	Parent=gene622
chr15	ENCODE	CDS	41638320	41638422	.	-	0	Parent=gene622
chr15	ENCODE	exon	41639903	41640085	.	-	.	Parent=gene622
chr15	ENCODE	CDS	41639903	41640085	.	-	0	Parent=gene622
chr15	ENCODE	exon	41644357	41644482	.	-	.	Parent=gene622
chr15	ENCODE	CDS	41644357	41644482	.	-	0	Parent=gene622
chr15	ENCODE	exon	41647953	41648043	.	-	.	Parent=gene622
chr15	ENCODE	CDS	41647953	41648043	.	-	1	Parent=gene622
chr15	ENCODE	exon	41650902	41650987	.	-	.	Parent=gene622
chr15	ENCODE	CDS	41650902	41650987	.	-	0	Parent=gene622
###
chr15	ENCODE	gene	41644357	41652925	.	-	.	ID=gene623;Name=AC019011.2-012;name2=AC019011.2
chr15	ENCODE	exon	41644357	41644482	.	-	.	Parent=gene623
chr15	ENCODE	CDS	41644357	41644482	.	-	0	Parent=gene623
chr15	ENCODE	exon	41647953	41648043	.	-	.	Parent=gene623
chr15	ENCODE	CDS	41647953	41648043	.	-	1	Parent=gene623
chr15	ENCODE	exon	41650902	41651066	.	-	.	Parent=gene623
chr15	ENCODE	CDS	41650902	41651066	.	-	1	Parent=gene623
chr15	ENCODE	exon	41651214	41651330	.	-	.	Parent=gene623
chr15	ENCODE	CDS	41651214	41651330	.	-	1	Parent=gene623
chr15	ENCODE	exon	41652259	41652366	.	-	.	Parent=gene623
chr15	ENCODE	CDS	41652259	41652366	.	-	1	Parent=gene623
chr15	ENCODE	exon	41652524	41652638	.	-	.	Parent=gene623
chr15	ENCODE	CDS	41652524	41652638	.	-	2	Parent=gene623
chr15	ENCODE	exon	41652871	41652925	.	-	.	Parent=gene623
chr15	ENCODE	CDS	41652871	41652925	.	-	0	Parent=gene623
###
chr15	ENCODE	gene	41650951	41652672	.	-	.	ID=gene624;Name=AC019011.2-013;name2=AC019011.2
chr15	ENCODE	exon	41650951	41651066	.	-	.	Parent=gene624
chr15	ENCODE	exon	41651214	41651330	.	-	.	Parent=gene624
chr15	ENCODE	exon	41652259	41652672	.	-	.	Parent=gene624
###
chr15	ENCODE	gene	41652603	41669680	.	-	.	ID=gene625;Name=AC019011.2-015;name2=AC019011.2
chr15	ENCODE	exon	41652603	41652974	.	-	.	Parent=gene625
chr15	ENCODE	exon	41653299	41653522	.	-	.	Parent=gene625
chr15	ENCODE	exon	41653712	41653853	.	-	.	Parent=gene625
chr15	ENCODE	exon	41655861	41656043	.	-	.	Parent=gene625
chr15	ENCODE	exon	41656317	41656438	.	-	.	Parent=gene625
chr15	ENCODE	exon	41656598	41656729	.	-	.	Parent=gene625
chr15	ENCODE	exon	41656943	41657025	.	-	.	Parent=gene625
chr15	ENCODE	exon	41657112	41657221	.	-	.	Parent=gene625
chr15	ENCODE	exon	41657366	41657441	.	-	.	Parent=gene625
chr15	ENCODE	exon	41657560	41657646	.	-	.	Parent=gene625
chr15	ENCODE	exon	41658509	41658610	.	-	.	Parent=gene625
chr15	ENCODE	exon	41660492	41660613	.	-	.	Parent=gene625
chr15	ENCODE	exon	41660717	41660878	.	-	.	Parent=gene625
chr15	ENCODE	exon	41661343	41661444	.	-	.	Parent=gene625
chr15	ENCODE	exon	41661585	41661739	.	-	.	Parent=gene625
chr15	ENCODE	exon	41662054	41662139	.	-	.	Parent=gene625
chr15	ENCODE	exon	41662352	41662442	.	-	.	Parent=gene625
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene625
chr15	ENCODE	exon	41663848	41664111	.	-	.	Parent=gene625
chr15	ENCODE	exon	41669662	41669680	.	-	.	Parent=gene625
###
chr15	ENCODE	gene	41653330	41654125	.	-	.	ID=gene626;Name=AC019011.2-011;name2=AC019011.2
chr15	ENCODE	exon	41653330	41653522	.	-	.	Parent=gene626
chr15	ENCODE	exon	41653712	41654125	.	-	.	Parent=gene626
###
chr15	ENCODE	gene	41655658	41656330	.	-	.	ID=gene627;Name=AC019011.2-021;name2=AC019011.2
chr15	ENCODE	exon	41655658	41656043	.	-	.	Parent=gene627
chr15	ENCODE	exon	41656317	41656330	.	-	.	Parent=gene627
###
chr15	ENCODE	gene	41655832	41656438	.	-	.	ID=gene628;Name=AC019011.2-010;name2=AC019011.2
chr15	ENCODE	exon	41655832	41656043	.	-	.	Parent=gene628
chr15	ENCODE	exon	41656317	41656438	.	-	.	Parent=gene628
###
chr15	ENCODE	gene	41658564	41661682	.	-	.	ID=gene629;name2=AC019011.2;Name=AC019011.2-020
chr15	ENCODE	exon	41658564	41658610	.	-	.	Parent=gene629
chr15	ENCODE	exon	41660492	41660613	.	-	.	Parent=gene629
chr15	ENCODE	exon	41660717	41660919	.	-	.	Parent=gene629
chr15	ENCODE	exon	41661343	41661444	.	-	.	Parent=gene629
chr15	ENCODE	exon	41661585	41661682	.	-	.	Parent=gene629
###
chr15	ENCODE	gene	41661178	41661707	.	-	.	ID=gene630;Name=AC019011.2-019;name2=AC019011.2
chr15	ENCODE	exon	41661178	41661444	.	-	.	Parent=gene630
chr15	ENCODE	exon	41661585	41661707	.	-	.	Parent=gene630
###
chr15	ENCODE	gene	41662240	41663942	.	-	.	ID=gene631;Name=AC019011.2-018;name2=AC019011.2
chr15	ENCODE	exon	41662240	41662442	.	-	.	Parent=gene631
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene631
chr15	ENCODE	exon	41663848	41663942	.	-	.	Parent=gene631
###
chr15	ENCODE	gene	41662386	41669645	.	-	.	ID=gene632;Name=AC019011.2-017;name2=AC019011.2
chr15	ENCODE	exon	41662386	41662442	.	-	.	Parent=gene632
chr15	ENCODE	CDS	41662386	41662442	.	-	2	Parent=gene632
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene632
chr15	ENCODE	CDS	41662894	41663089	.	-	0	Parent=gene632
chr15	ENCODE	CDS	41663848	41663994	.	-	0	Parent=gene632
chr15	ENCODE	exon	41663848	41664022	.	-	.	Parent=gene632
chr15	ENCODE	exon	41664289	41664382	.	-	.	Parent=gene632
chr15	ENCODE	exon	41669372	41669645	.	-	.	Parent=gene632
###
chr15	ENCODE	gene	41662894	41669674	.	-	.	ID=gene633;Name=AC019011.2-008;name2=AC019011.2
chr15	ENCODE	exon	41662894	41663089	.	-	.	Parent=gene633
chr15	ENCODE	CDS	41662894	41663089	.	-	0	Parent=gene633
chr15	ENCODE	CDS	41663848	41663994	.	-	0	Parent=gene633
chr15	ENCODE	exon	41663848	41664079	.	-	.	Parent=gene633
chr15	ENCODE	exon	41664289	41664382	.	-	.	Parent=gene633
chr15	ENCODE	exon	41669662	41669674	.	-	.	Parent=gene633
###
chr15	ENCODE	gene	41663022	41669686	.	-	.	ID=gene634;Name=AC019011.2-009;name2=AC019011.2
chr15	ENCODE	exon	41663022	41663089	.	-	.	Parent=gene634
chr15	ENCODE	CDS	41663022	41663089	.	-	0	Parent=gene634
chr15	ENCODE	CDS	41663848	41663994	.	-	0	Parent=gene634
chr15	ENCODE	exon	41663848	41664022	.	-	.	Parent=gene634
chr15	ENCODE	exon	41669662	41669686	.	-	.	Parent=gene634
###
chr15	ENCODE	gene	41672544	41675754	.	+	.	ID=gene635;Name=AC011330.1-003;name2=CKMT1B
chr15	ENCODE	exon	41672544	41672761	.	+	.	Parent=gene635
chr15	ENCODE	exon	41673535	41673857	.	+	.	Parent=gene635
chr15	ENCODE	CDS	41673709	41673857	.	+	0	Parent=gene635
chr15	ENCODE	exon	41674462	41674660	.	+	.	Parent=gene635
chr15	ENCODE	CDS	41674462	41674660	.	+	1	Parent=gene635
chr15	ENCODE	exon	41674864	41674959	.	+	.	Parent=gene635
chr15	ENCODE	CDS	41674864	41674959	.	+	0	Parent=gene635
chr15	ENCODE	exon	41675346	41675567	.	+	.	Parent=gene635
chr15	ENCODE	CDS	41675346	41675567	.	+	0	Parent=gene635
chr15	ENCODE	exon	41675697	41675754	.	+	.	Parent=gene635
chr15	ENCODE	CDS	41675697	41675754	.	+	0	Parent=gene635
###
chr15	ENCODE	gene	41672553	41674902	.	+	.	ID=gene636;Name=AC011330.1-004;name2=CKMT1B
chr15	ENCODE	exon	41672553	41672761	.	+	.	Parent=gene636
chr15	ENCODE	exon	41673673	41673857	.	+	.	Parent=gene636
chr15	ENCODE	CDS	41673709	41673857	.	+	0	Parent=gene636
chr15	ENCODE	exon	41674462	41674660	.	+	.	Parent=gene636
chr15	ENCODE	CDS	41674462	41674660	.	+	1	Parent=gene636
chr15	ENCODE	exon	41674864	41674902	.	+	.	Parent=gene636
chr15	ENCODE	CDS	41674864	41674902	.	+	0	Parent=gene636
###
chr15	ENCODE	gene	41672577	41673912	.	+	.	ID=gene637;Name=AC011330.1-005;name2=CKMT1B
chr15	ENCODE	exon	41672577	41672761	.	+	.	Parent=gene637
chr15	ENCODE	exon	41673535	41673912	.	+	.	Parent=gene637
###
chr15	ENCODE	gene	41672698	41674597	.	+	.	ID=gene638;Name=AC011330.1-007;name2=CKMT1B
chr15	ENCODE	exon	41672698	41672761	.	+	.	Parent=gene638
chr15	ENCODE	exon	41673535	41673857	.	+	.	Parent=gene638
chr15	ENCODE	exon	41674185	41674597	.	+	.	Parent=gene638
###
chr15	ENCODE	gene	41673509	41674434	.	+	.	ID=gene639;Name=AC011330.1-006;name2=CKMT1B
chr15	ENCODE	exon	41673509	41673857	.	+	.	Parent=gene639
chr15	ENCODE	exon	41674185	41674434	.	+	.	Parent=gene639
###
chr15	ENCODE	gene	41673517	41678896	.	+	.	ID=gene640;Name=AC011330.1-002;name2=CKMT1B
chr15	ENCODE	exon	41673517	41673857	.	+	.	Parent=gene640
chr15	ENCODE	exon	41674462	41674660	.	+	.	Parent=gene640
chr15	ENCODE	exon	41674864	41674959	.	+	.	Parent=gene640
chr15	ENCODE	exon	41675346	41675567	.	+	.	Parent=gene640
chr15	ENCODE	exon	41675697	41675782	.	+	.	Parent=gene640
chr15	ENCODE	exon	41675898	41676021	.	+	.	Parent=gene640
chr15	ENCODE	exon	41676866	41677817	.	+	.	Parent=gene640
chr15	ENCODE	exon	41678317	41678442	.	+	.	Parent=gene640
chr15	ENCODE	exon	41678647	41678896	.	+	.	Parent=gene640
###
chr15	ENCODE	gene	41673529	41678896	.	+	.	ID=gene641;Name=AC011330.1-001;name2=CKMT1B
chr15	ENCODE	exon	41673529	41673857	.	+	.	Parent=gene641
chr15	ENCODE	CDS	41673709	41673857	.	+	0	Parent=gene641
chr15	ENCODE	exon	41674462	41674660	.	+	.	Parent=gene641
chr15	ENCODE	CDS	41674462	41674660	.	+	1	Parent=gene641
chr15	ENCODE	exon	41674864	41674959	.	+	.	Parent=gene641
chr15	ENCODE	CDS	41674864	41674959	.	+	0	Parent=gene641
chr15	ENCODE	exon	41675346	41675567	.	+	.	Parent=gene641
chr15	ENCODE	CDS	41675346	41675567	.	+	0	Parent=gene641
chr15	ENCODE	exon	41675697	41675782	.	+	.	Parent=gene641
chr15	ENCODE	CDS	41675697	41675782	.	+	0	Parent=gene641
chr15	ENCODE	exon	41675898	41676021	.	+	.	Parent=gene641
chr15	ENCODE	CDS	41675898	41676021	.	+	1	Parent=gene641
chr15	ENCODE	exon	41677683	41677817	.	+	.	Parent=gene641
chr15	ENCODE	CDS	41677683	41677817	.	+	0	Parent=gene641
chr15	ENCODE	exon	41678317	41678442	.	+	.	Parent=gene641
chr15	ENCODE	CDS	41678317	41678442	.	+	0	Parent=gene641
chr15	ENCODE	CDS	41678647	41678763	.	+	0	Parent=gene641
chr15	ENCODE	exon	41678647	41678896	.	+	.	Parent=gene641
###
chr15	ENCODE	gene	41678888	41698290	.	-	.	ID=gene642;Name=AC011330.2-001;name2=STRC
chr15	ENCODE	exon	41678888	41679250	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41679162	41679250	.	-	2	Parent=gene642
chr15	ENCODE	exon	41679450	41679597	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41679450	41679597	.	-	0	Parent=gene642
chr15	ENCODE	exon	41679686	41679783	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41679686	41679783	.	-	2	Parent=gene642
chr15	ENCODE	exon	41680024	41680172	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41680024	41680172	.	-	1	Parent=gene642
chr15	ENCODE	exon	41680362	41680504	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41680362	41680504	.	-	0	Parent=gene642
chr15	ENCODE	exon	41680886	41681041	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41680886	41681041	.	-	0	Parent=gene642
chr15	ENCODE	exon	41682732	41682901	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41682732	41682901	.	-	2	Parent=gene642
chr15	ENCODE	exon	41683486	41683642	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41683486	41683642	.	-	0	Parent=gene642
chr15	ENCODE	exon	41683851	41683941	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41683851	41683941	.	-	1	Parent=gene642
chr15	ENCODE	exon	41684140	41684336	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41684140	41684336	.	-	0	Parent=gene642
chr15	ENCODE	exon	41684754	41684889	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41684754	41684889	.	-	1	Parent=gene642
chr15	ENCODE	exon	41687353	41687465	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41687353	41687465	.	-	0	Parent=gene642
chr15	ENCODE	exon	41687570	41687693	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41687570	41687693	.	-	1	Parent=gene642
chr15	ENCODE	exon	41688766	41688824	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41688766	41688824	.	-	0	Parent=gene642
chr15	ENCODE	exon	41689802	41689927	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41689802	41689927	.	-	0	Parent=gene642
chr15	ENCODE	exon	41690409	41690474	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41690409	41690474	.	-	0	Parent=gene642
chr15	ENCODE	exon	41690638	41690805	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41690638	41690805	.	-	0	Parent=gene642
chr15	ENCODE	exon	41690989	41691027	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41690989	41691027	.	-	0	Parent=gene642
chr15	ENCODE	exon	41691332	41691514	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41691332	41691514	.	-	0	Parent=gene642
chr15	ENCODE	exon	41691867	41691999	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41691867	41691999	.	-	1	Parent=gene642
chr15	ENCODE	exon	41692281	41692396	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41692281	41692396	.	-	0	Parent=gene642
chr15	ENCODE	exon	41692535	41692721	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41692535	41692721	.	-	1	Parent=gene642
chr15	ENCODE	exon	41693377	41693543	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41693377	41693543	.	-	0	Parent=gene642
chr15	ENCODE	exon	41693686	41693802	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41693686	41693802	.	-	0	Parent=gene642
chr15	ENCODE	exon	41693904	41693966	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41693904	41693966	.	-	0	Parent=gene642
chr15	ENCODE	exon	41694923	41696180	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41694923	41696180	.	-	1	Parent=gene642
chr15	ENCODE	exon	41696948	41696972	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41696948	41696972	.	-	2	Parent=gene642
chr15	ENCODE	exon	41697061	41697846	.	-	.	Parent=gene642
chr15	ENCODE	CDS	41697061	41697846	.	-	2	Parent=gene642
chr15	ENCODE	CDS	41698149	41698212	.	-	0	Parent=gene642
chr15	ENCODE	exon	41698149	41698290	.	-	.	Parent=gene642
###
chr15	ENCODE	gene	41679080	41692595	.	-	.	ID=gene643;Name=AC011330.2-002;name2=STRC
chr15	ENCODE	exon	41679080	41679250	.	-	.	Parent=gene643
chr15	ENCODE	exon	41679450	41679597	.	-	.	Parent=gene643
chr15	ENCODE	exon	41679686	41679783	.	-	.	Parent=gene643
chr15	ENCODE	exon	41680024	41680172	.	-	.	Parent=gene643
chr15	ENCODE	exon	41680362	41680504	.	-	.	Parent=gene643
chr15	ENCODE	exon	41680886	41681041	.	-	.	Parent=gene643
chr15	ENCODE	exon	41682732	41682901	.	-	.	Parent=gene643
chr15	ENCODE	exon	41683486	41683642	.	-	.	Parent=gene643
chr15	ENCODE	exon	41683851	41683941	.	-	.	Parent=gene643
chr15	ENCODE	exon	41684140	41684336	.	-	.	Parent=gene643
chr15	ENCODE	exon	41684467	41684637	.	-	.	Parent=gene643
chr15	ENCODE	exon	41684754	41684889	.	-	.	Parent=gene643
chr15	ENCODE	exon	41687353	41687465	.	-	.	Parent=gene643
chr15	ENCODE	exon	41687570	41687693	.	-	.	Parent=gene643
chr15	ENCODE	exon	41688766	41688824	.	-	.	Parent=gene643
chr15	ENCODE	exon	41689802	41690805	.	-	.	Parent=gene643
chr15	ENCODE	exon	41690989	41691027	.	-	.	Parent=gene643
chr15	ENCODE	exon	41691332	41691400	.	-	.	Parent=gene643
chr15	ENCODE	exon	41692289	41692396	.	-	.	Parent=gene643
chr15	ENCODE	exon	41692535	41692595	.	-	.	Parent=gene643
###
chr15	ENCODE	gene	41679092	41692677	.	-	.	ID=gene644;Name=AC011330.2-003;name2=STRC
chr15	ENCODE	exon	41679092	41679250	.	-	.	Parent=gene644
chr15	ENCODE	exon	41679450	41679597	.	-	.	Parent=gene644
chr15	ENCODE	exon	41679686	41679783	.	-	.	Parent=gene644
chr15	ENCODE	exon	41680024	41680172	.	-	.	Parent=gene644
chr15	ENCODE	exon	41680362	41680504	.	-	.	Parent=gene644
chr15	ENCODE	exon	41680886	41681041	.	-	.	Parent=gene644
chr15	ENCODE	exon	41687353	41687465	.	-	.	Parent=gene644
chr15	ENCODE	exon	41687570	41687693	.	-	.	Parent=gene644
chr15	ENCODE	exon	41688766	41688824	.	-	.	Parent=gene644
chr15	ENCODE	exon	41689802	41690805	.	-	.	Parent=gene644
chr15	ENCODE	exon	41690989	41691027	.	-	.	Parent=gene644
chr15	ENCODE	exon	41691332	41691514	.	-	.	Parent=gene644
chr15	ENCODE	exon	41692535	41692677	.	-	.	Parent=gene644
###
chr15	ENCODE	gene	41679092	41692704	.	-	.	ID=gene645;Name=AC011330.2-004;name2=STRC
chr15	ENCODE	exon	41679092	41679250	.	-	.	Parent=gene645
chr15	ENCODE	exon	41679450	41679597	.	-	.	Parent=gene645
chr15	ENCODE	exon	41679686	41679783	.	-	.	Parent=gene645
chr15	ENCODE	exon	41680024	41680172	.	-	.	Parent=gene645
chr15	ENCODE	exon	41680362	41680504	.	-	.	Parent=gene645
chr15	ENCODE	exon	41680886	41681041	.	-	.	Parent=gene645
chr15	ENCODE	exon	41682732	41682901	.	-	.	Parent=gene645
chr15	ENCODE	exon	41683486	41683642	.	-	.	Parent=gene645
chr15	ENCODE	exon	41683851	41683941	.	-	.	Parent=gene645
chr15	ENCODE	exon	41684140	41684336	.	-	.	Parent=gene645
chr15	ENCODE	exon	41687353	41687465	.	-	.	Parent=gene645
chr15	ENCODE	exon	41687570	41687693	.	-	.	Parent=gene645
chr15	ENCODE	exon	41688766	41690805	.	-	.	Parent=gene645
chr15	ENCODE	exon	41690989	41691027	.	-	.	Parent=gene645
chr15	ENCODE	exon	41691332	41691514	.	-	.	Parent=gene645
chr15	ENCODE	exon	41692281	41692396	.	-	.	Parent=gene645
chr15	ENCODE	exon	41692535	41692704	.	-	.	Parent=gene645
###
chr15	ENCODE	gene	41680053	41681165	.	-	.	ID=gene646;Name=AC011330.2-007;name2=STRC
chr15	ENCODE	exon	41680053	41680172	.	-	.	Parent=gene646
chr15	ENCODE	exon	41680362	41680504	.	-	.	Parent=gene646
chr15	ENCODE	exon	41680886	41681165	.	-	.	Parent=gene646
###
chr15	ENCODE	gene	41680489	41683072	.	-	.	ID=gene647;Name=AC011330.2-010;name2=STRC
chr15	ENCODE	exon	41680489	41680504	.	-	.	Parent=gene647
chr15	ENCODE	exon	41680886	41681041	.	-	.	Parent=gene647
chr15	ENCODE	exon	41682732	41683072	.	-	.	Parent=gene647
###
chr15	ENCODE	gene	41684194	41692725	.	-	.	ID=gene648;Name=AC011330.2-006;name2=STRC
chr15	ENCODE	exon	41684194	41684336	.	-	.	Parent=gene648
chr15	ENCODE	exon	41684754	41684889	.	-	.	Parent=gene648
chr15	ENCODE	exon	41687353	41687465	.	-	.	Parent=gene648
chr15	ENCODE	exon	41687570	41687693	.	-	.	Parent=gene648
chr15	ENCODE	exon	41688766	41688824	.	-	.	Parent=gene648
chr15	ENCODE	exon	41690989	41691027	.	-	.	Parent=gene648
chr15	ENCODE	exon	41691332	41691514	.	-	.	Parent=gene648
chr15	ENCODE	exon	41692281	41692396	.	-	.	Parent=gene648
chr15	ENCODE	exon	41692535	41692725	.	-	.	Parent=gene648
###
chr15	ENCODE	gene	41690684	41692515	.	-	.	ID=gene649;Name=AC011330.2-008;name2=STRC
chr15	ENCODE	exon	41690684	41690805	.	-	.	Parent=gene649
chr15	ENCODE	exon	41690989	41691027	.	-	.	Parent=gene649
chr15	ENCODE	exon	41691332	41691514	.	-	.	Parent=gene649
chr15	ENCODE	exon	41692289	41692515	.	-	.	Parent=gene649
###
chr15	ENCODE	gene	41690689	41692510	.	-	.	ID=gene650;Name=AC011330.2-009;name2=STRC
chr15	ENCODE	exon	41690689	41690805	.	-	.	Parent=gene650
chr15	ENCODE	exon	41690989	41691027	.	-	.	Parent=gene650
chr15	ENCODE	exon	41691332	41691514	.	-	.	Parent=gene650
chr15	ENCODE	exon	41692281	41692510	.	-	.	Parent=gene650
###
chr15	ENCODE	gene	41694617	41697730	.	-	.	ID=gene651;Name=AC011330.2-005;name2=STRC
chr15	ENCODE	exon	41694617	41696180	.	-	.	Parent=gene651
chr15	ENCODE	CDS	41694884	41696180	.	-	1	Parent=gene651
chr15	ENCODE	exon	41696948	41696972	.	-	.	Parent=gene651
chr15	ENCODE	CDS	41696948	41696972	.	-	2	Parent=gene651
chr15	ENCODE	exon	41697061	41697730	.	-	.	Parent=gene651
chr15	ENCODE	CDS	41697061	41697730	.	-	0	Parent=gene651
###
chr15	ENCODE	gene	41707993	41728334	.	-	.	ID=gene652;Name=AC011330.3-001;name2=CATSPER2
chr15	ENCODE	exon	41707993	41710222	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41710191	41710222	.	-	2	Parent=gene652
chr15	ENCODE	exon	41711689	41711853	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41711689	41711853	.	-	2	Parent=gene652
chr15	ENCODE	exon	41712207	41712418	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41712207	41712418	.	-	1	Parent=gene652
chr15	ENCODE	exon	41714850	41714906	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41714850	41714906	.	-	1	Parent=gene652
chr15	ENCODE	exon	41715217	41715316	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41715217	41715316	.	-	2	Parent=gene652
chr15	ENCODE	exon	41715531	41715709	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41715531	41715709	.	-	1	Parent=gene652
chr15	ENCODE	exon	41718394	41718518	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41718394	41718518	.	-	0	Parent=gene652
chr15	ENCODE	exon	41719133	41719288	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41719133	41719288	.	-	0	Parent=gene652
chr15	ENCODE	exon	41719814	41719986	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41719814	41719986	.	-	2	Parent=gene652
chr15	ENCODE	exon	41726540	41726608	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41726540	41726608	.	-	2	Parent=gene652
chr15	ENCODE	exon	41726784	41726957	.	-	.	Parent=gene652
chr15	ENCODE	CDS	41726784	41726957	.	-	2	Parent=gene652
chr15	ENCODE	CDS	41727407	41727551	.	-	0	Parent=gene652
chr15	ENCODE	exon	41727407	41727556	.	-	.	Parent=gene652
chr15	ENCODE	exon	41728119	41728199	.	-	.	Parent=gene652
chr15	ENCODE	exon	41728308	41728334	.	-	.	Parent=gene652
###
chr15	ENCODE	gene	41710052	41727551	.	-	.	ID=gene653;name2=CATSPER2;Name=AC011330.3-002
chr15	ENCODE	exon	41710052	41710222	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41710191	41710222	.	-	2	Parent=gene653
chr15	ENCODE	exon	41711689	41711853	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41711689	41711853	.	-	2	Parent=gene653
chr15	ENCODE	exon	41712207	41712424	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41712207	41712424	.	-	1	Parent=gene653
chr15	ENCODE	exon	41714850	41714906	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41714850	41714906	.	-	1	Parent=gene653
chr15	ENCODE	exon	41715217	41715316	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41715217	41715316	.	-	2	Parent=gene653
chr15	ENCODE	exon	41715531	41715709	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41715531	41715709	.	-	1	Parent=gene653
chr15	ENCODE	exon	41718394	41718518	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41718394	41718518	.	-	0	Parent=gene653
chr15	ENCODE	exon	41719133	41719288	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41719133	41719288	.	-	0	Parent=gene653
chr15	ENCODE	exon	41719814	41719986	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41719814	41719986	.	-	2	Parent=gene653
chr15	ENCODE	exon	41726540	41726608	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41726540	41726608	.	-	2	Parent=gene653
chr15	ENCODE	exon	41726784	41726957	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41726784	41726957	.	-	2	Parent=gene653
chr15	ENCODE	exon	41727407	41727551	.	-	.	Parent=gene653
chr15	ENCODE	CDS	41727407	41727551	.	-	0	Parent=gene653
###
chr15	ENCODE	gene	41710052	41728338	.	-	.	ID=gene654;Name=AC011330.3-004;name2=CATSPER2
chr15	ENCODE	exon	41710052	41710222	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41710191	41710222	.	-	2	Parent=gene654
chr15	ENCODE	exon	41711689	41711853	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41711689	41711853	.	-	2	Parent=gene654
chr15	ENCODE	exon	41712207	41712418	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41712207	41712418	.	-	1	Parent=gene654
chr15	ENCODE	exon	41714850	41714906	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41714850	41714906	.	-	1	Parent=gene654
chr15	ENCODE	exon	41715217	41715316	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41715217	41715316	.	-	2	Parent=gene654
chr15	ENCODE	exon	41715531	41715709	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41715531	41715709	.	-	1	Parent=gene654
chr15	ENCODE	exon	41718394	41718518	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41718394	41718518	.	-	0	Parent=gene654
chr15	ENCODE	exon	41719133	41719288	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41719133	41719288	.	-	0	Parent=gene654
chr15	ENCODE	exon	41719814	41719986	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41719814	41719986	.	-	2	Parent=gene654
chr15	ENCODE	exon	41726540	41726608	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41726540	41726608	.	-	2	Parent=gene654
chr15	ENCODE	exon	41726784	41726957	.	-	.	Parent=gene654
chr15	ENCODE	CDS	41726784	41726957	.	-	2	Parent=gene654
chr15	ENCODE	CDS	41727407	41727551	.	-	0	Parent=gene654
chr15	ENCODE	exon	41727407	41727556	.	-	.	Parent=gene654
chr15	ENCODE	exon	41728312	41728338	.	-	.	Parent=gene654
###
chr15	ENCODE	gene	41710052	41728367	.	-	.	ID=gene655;Name=AC011330.3-006;name2=CATSPER2
chr15	ENCODE	exon	41710052	41710222	.	-	.	Parent=gene655
chr15	ENCODE	exon	41711689	41715316	.	-	.	Parent=gene655
chr15	ENCODE	exon	41715531	41715709	.	-	.	Parent=gene655
chr15	ENCODE	exon	41718394	41718518	.	-	.	Parent=gene655
chr15	ENCODE	exon	41719133	41719288	.	-	.	Parent=gene655
chr15	ENCODE	exon	41719814	41719986	.	-	.	Parent=gene655
chr15	ENCODE	exon	41726540	41726608	.	-	.	Parent=gene655
chr15	ENCODE	exon	41726784	41726957	.	-	.	Parent=gene655
chr15	ENCODE	exon	41727407	41727553	.	-	.	Parent=gene655
chr15	ENCODE	exon	41728119	41728367	.	-	.	Parent=gene655
###
chr15	ENCODE	gene	41710061	41712227	.	-	.	ID=gene656;Name=AC011330.3-013;name2=CATSPER2
chr15	ENCODE	exon	41710061	41710222	.	-	.	Parent=gene656
chr15	ENCODE	exon	41710920	41711028	.	-	.	Parent=gene656
chr15	ENCODE	exon	41711689	41711853	.	-	.	Parent=gene656
chr15	ENCODE	exon	41712207	41712227	.	-	.	Parent=gene656
###
chr15	ENCODE	gene	41710098	41727551	.	-	.	ID=gene657;Name=AC011330.3-003;name2=CATSPER2
chr15	ENCODE	exon	41710098	41710222	.	-	.	Parent=gene657
chr15	ENCODE	exon	41711689	41711853	.	-	.	Parent=gene657
chr15	ENCODE	exon	41714850	41714906	.	-	.	Parent=gene657
chr15	ENCODE	exon	41715217	41715316	.	-	.	Parent=gene657
chr15	ENCODE	exon	41715531	41715709	.	-	.	Parent=gene657
chr15	ENCODE	exon	41718394	41718518	.	-	.	Parent=gene657
chr15	ENCODE	exon	41719133	41719288	.	-	.	Parent=gene657
chr15	ENCODE	exon	41719814	41719986	.	-	.	Parent=gene657
chr15	ENCODE	exon	41726540	41726608	.	-	.	Parent=gene657
chr15	ENCODE	exon	41726784	41726957	.	-	.	Parent=gene657
chr15	ENCODE	exon	41727407	41727551	.	-	.	Parent=gene657
###
chr15	ENCODE	gene	41711689	41714882	.	-	.	ID=gene658;Name=AC011330.3-008;name2=CATSPER2
chr15	ENCODE	exon	41711689	41711853	.	-	.	Parent=gene658
chr15	ENCODE	exon	41712207	41712424	.	-	.	Parent=gene658
chr15	ENCODE	exon	41714599	41714644	.	-	.	Parent=gene658
chr15	ENCODE	exon	41714850	41714882	.	-	.	Parent=gene658
###
chr15	ENCODE	gene	41711761	41712709	.	-	.	ID=gene659;Name=AC011330.3-007;name2=CATSPER2
chr15	ENCODE	exon	41711761	41711853	.	-	.	Parent=gene659
chr15	ENCODE	exon	41712207	41712709	.	-	.	Parent=gene659
###
chr15	ENCODE	gene	41718912	41728337	.	-	.	ID=gene660;Name=AC011330.3-005;name2=CATSPER2
chr15	ENCODE	exon	41718912	41719986	.	-	.	Parent=gene660
chr15	ENCODE	exon	41726540	41726608	.	-	.	Parent=gene660
chr15	ENCODE	exon	41726784	41726957	.	-	.	Parent=gene660
chr15	ENCODE	exon	41727407	41727553	.	-	.	Parent=gene660
chr15	ENCODE	exon	41728119	41728337	.	-	.	Parent=gene660
###
chr15	ENCODE	gene	41726839	41747192	.	-	.	ID=gene661;Name=AC011330.3-012;name2=CATSPER2
chr15	ENCODE	exon	41726839	41726957	.	-	.	Parent=gene661
chr15	ENCODE	exon	41743908	41744033	.	-	.	Parent=gene661
chr15	ENCODE	exon	41747148	41747192	.	-	.	Parent=gene661
###
chr15	ENCODE	gene	41726864	41728315	.	-	.	ID=gene662;Name=AC011330.3-009;name2=CATSPER2
chr15	ENCODE	exon	41726864	41726957	.	-	.	Parent=gene662
chr15	ENCODE	CDS	41726864	41726957	.	-	2	Parent=gene662
chr15	ENCODE	CDS	41727407	41727551	.	-	0	Parent=gene662
chr15	ENCODE	exon	41727407	41727556	.	-	.	Parent=gene662
chr15	ENCODE	exon	41728308	41728315	.	-	.	Parent=gene662
###
chr15	ENCODE	gene	41726910	41747608	.	-	.	ID=gene663;Name=AC011330.3-010;name2=CATSPER2
chr15	ENCODE	exon	41726910	41726957	.	-	.	Parent=gene663
chr15	ENCODE	exon	41727407	41727556	.	-	.	Parent=gene663
chr15	ENCODE	exon	41729217	41729369	.	-	.	Parent=gene663
chr15	ENCODE	exon	41743908	41744033	.	-	.	Parent=gene663
chr15	ENCODE	exon	41747518	41747608	.	-	.	Parent=gene663
###
chr15	ENCODE	gene	41727407	41729344	.	-	.	ID=gene664;Name=AC011330.3-011;name2=CATSPER2
chr15	ENCODE	exon	41727407	41727553	.	-	.	Parent=gene664
chr15	ENCODE	exon	41729217	41729344	.	-	.	Parent=gene664
###
chr15	ENCODE	gene	41772376	41778712	.	+	.	ID=gene665;Name=AC011330.7-001;name2=CKMT1A
chr15	ENCODE	exon	41772376	41772593	.	+	.	Parent=gene665
chr15	ENCODE	exon	41773367	41773689	.	+	.	Parent=gene665
chr15	ENCODE	CDS	41773541	41773689	.	+	0	Parent=gene665
chr15	ENCODE	exon	41774294	41774492	.	+	.	Parent=gene665
chr15	ENCODE	CDS	41774294	41774492	.	+	1	Parent=gene665
chr15	ENCODE	exon	41774696	41774791	.	+	.	Parent=gene665
chr15	ENCODE	CDS	41774696	41774791	.	+	0	Parent=gene665
chr15	ENCODE	exon	41775178	41775399	.	+	.	Parent=gene665
chr15	ENCODE	CDS	41775178	41775399	.	+	0	Parent=gene665
chr15	ENCODE	exon	41775529	41775614	.	+	.	Parent=gene665
chr15	ENCODE	CDS	41775529	41775614	.	+	0	Parent=gene665
chr15	ENCODE	exon	41775730	41775853	.	+	.	Parent=gene665
chr15	ENCODE	CDS	41775730	41775853	.	+	1	Parent=gene665
chr15	ENCODE	exon	41777504	41777638	.	+	.	Parent=gene665
chr15	ENCODE	CDS	41777504	41777638	.	+	0	Parent=gene665
chr15	ENCODE	exon	41778131	41778256	.	+	.	Parent=gene665
chr15	ENCODE	CDS	41778131	41778256	.	+	0	Parent=gene665
chr15	ENCODE	CDS	41778463	41778579	.	+	0	Parent=gene665
chr15	ENCODE	exon	41778463	41778712	.	+	.	Parent=gene665
###
chr15	ENCODE	gene	41772390	41774791	.	+	.	ID=gene666;Name=AC011330.7-004;name2=CKMT1A
chr15	ENCODE	exon	41772390	41772593	.	+	.	Parent=gene666
chr15	ENCODE	exon	41773430	41773689	.	+	.	Parent=gene666
chr15	ENCODE	CDS	41773541	41773689	.	+	0	Parent=gene666
chr15	ENCODE	exon	41774294	41774492	.	+	.	Parent=gene666
chr15	ENCODE	CDS	41774294	41774492	.	+	1	Parent=gene666
chr15	ENCODE	exon	41774696	41774791	.	+	.	Parent=gene666
chr15	ENCODE	CDS	41774696	41774791	.	+	0	Parent=gene666
###
chr15	ENCODE	gene	41772530	41774770	.	+	.	ID=gene667;Name=AC011330.7-005;name2=CKMT1A
chr15	ENCODE	exon	41772530	41772593	.	+	.	Parent=gene667
chr15	ENCODE	exon	41773367	41773689	.	+	.	Parent=gene667
chr15	ENCODE	exon	41774017	41774492	.	+	.	Parent=gene667
chr15	ENCODE	exon	41774696	41774770	.	+	.	Parent=gene667
###
chr15	ENCODE	gene	41773017	41778712	.	+	.	ID=gene668;name2=CKMT1A;Name=AC011330.7-002
chr15	ENCODE	exon	41773017	41773689	.	+	.	Parent=gene668
chr15	ENCODE	CDS	41773541	41773689	.	+	0	Parent=gene668
chr15	ENCODE	exon	41774294	41774492	.	+	.	Parent=gene668
chr15	ENCODE	CDS	41774294	41774492	.	+	1	Parent=gene668
chr15	ENCODE	exon	41774696	41774791	.	+	.	Parent=gene668
chr15	ENCODE	CDS	41774696	41774791	.	+	0	Parent=gene668
chr15	ENCODE	exon	41775178	41775399	.	+	.	Parent=gene668
chr15	ENCODE	CDS	41775178	41775399	.	+	0	Parent=gene668
chr15	ENCODE	exon	41775529	41775614	.	+	.	Parent=gene668
chr15	ENCODE	CDS	41775529	41775614	.	+	0	Parent=gene668
chr15	ENCODE	exon	41775730	41775853	.	+	.	Parent=gene668
chr15	ENCODE	CDS	41775730	41775853	.	+	1	Parent=gene668
chr15	ENCODE	exon	41777504	41777638	.	+	.	Parent=gene668
chr15	ENCODE	CDS	41777504	41777638	.	+	0	Parent=gene668
chr15	ENCODE	exon	41778131	41778256	.	+	.	Parent=gene668
chr15	ENCODE	CDS	41778131	41778256	.	+	0	Parent=gene668
chr15	ENCODE	CDS	41778463	41778579	.	+	0	Parent=gene668
chr15	ENCODE	exon	41778463	41778712	.	+	.	Parent=gene668
###
chr15	ENCODE	gene	41773361	41775305	.	+	.	ID=gene669;name2=CKMT1A;Name=AC011330.7-003
chr15	ENCODE	exon	41773361	41773689	.	+	.	Parent=gene669
chr15	ENCODE	CDS	41773541	41773689	.	+	0	Parent=gene669
chr15	ENCODE	exon	41774201	41774492	.	+	.	Parent=gene669
chr15	ENCODE	CDS	41774201	41774492	.	+	1	Parent=gene669
chr15	ENCODE	exon	41774696	41774791	.	+	.	Parent=gene669
chr15	ENCODE	CDS	41774696	41774791	.	+	0	Parent=gene669
chr15	ENCODE	exon	41775178	41775305	.	+	.	Parent=gene669
chr15	ENCODE	CDS	41775178	41775305	.	+	0	Parent=gene669
###
chr15	ENCODE	gene	41775287	41776461	.	+	.	ID=gene670;name2=CKMT1A;Name=AC011330.7-007
chr15	ENCODE	exon	41775287	41775399	.	+	.	Parent=gene670
chr15	ENCODE	exon	41775529	41775614	.	+	.	Parent=gene670
chr15	ENCODE	exon	41775730	41776461	.	+	.	Parent=gene670
###
chr15	ENCODE	gene	41825882	41852769	.	+	.	ID=gene671;Name=AC018512.1-001;name2=PDIA3
chr15	ENCODE	exon	41825882	41826196	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41826030	41826196	.	+	0	Parent=gene671
chr15	ENCODE	exon	41833314	41833392	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41833314	41833392	.	+	1	Parent=gene671
chr15	ENCODE	exon	41836139	41836256	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41836139	41836256	.	+	0	Parent=gene671
chr15	ENCODE	exon	41840914	41841021	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41840914	41841021	.	+	2	Parent=gene671
chr15	ENCODE	exon	41842567	41842696	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41842567	41842696	.	+	2	Parent=gene671
chr15	ENCODE	exon	41844940	41845056	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41844940	41845056	.	+	1	Parent=gene671
chr15	ENCODE	exon	41845377	41845502	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41845377	41845502	.	+	1	Parent=gene671
chr15	ENCODE	exon	41846218	41846400	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41846218	41846400	.	+	1	Parent=gene671
chr15	ENCODE	exon	41847979	41848087	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41847979	41848087	.	+	1	Parent=gene671
chr15	ENCODE	exon	41849008	41849136	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41849008	41849136	.	+	0	Parent=gene671
chr15	ENCODE	exon	41849740	41849819	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41849740	41849819	.	+	0	Parent=gene671
chr15	ENCODE	exon	41850013	41850070	.	+	.	Parent=gene671
chr15	ENCODE	CDS	41850013	41850070	.	+	1	Parent=gene671
chr15	ENCODE	CDS	41850595	41850708	.	+	0	Parent=gene671
chr15	ENCODE	exon	41850595	41852769	.	+	.	Parent=gene671
###
chr15	ENCODE	gene	41825900	41836215	.	+	.	ID=gene672;Name=AC018512.1-003;name2=PDIA3
chr15	ENCODE	exon	41825900	41826196	.	+	.	Parent=gene672
chr15	ENCODE	exon	41836139	41836215	.	+	.	Parent=gene672
###
chr15	ENCODE	gene	41825907	41851035	.	+	.	ID=gene673;Name=AC018512.1-005;name2=PDIA3
chr15	ENCODE	exon	41825907	41826106	.	+	.	Parent=gene673
chr15	ENCODE	exon	41826182	41826196	.	+	.	Parent=gene673
chr15	ENCODE	exon	41833314	41833392	.	+	.	Parent=gene673
chr15	ENCODE	exon	41836139	41836256	.	+	.	Parent=gene673
chr15	ENCODE	exon	41840914	41841021	.	+	.	Parent=gene673
chr15	ENCODE	exon	41842567	41842696	.	+	.	Parent=gene673
chr15	ENCODE	exon	41844940	41845056	.	+	.	Parent=gene673
chr15	ENCODE	exon	41845377	41845502	.	+	.	Parent=gene673
chr15	ENCODE	exon	41846218	41846400	.	+	.	Parent=gene673
chr15	ENCODE	exon	41847979	41848087	.	+	.	Parent=gene673
chr15	ENCODE	exon	41849008	41849136	.	+	.	Parent=gene673
chr15	ENCODE	exon	41849740	41849819	.	+	.	Parent=gene673
chr15	ENCODE	exon	41850013	41850070	.	+	.	Parent=gene673
chr15	ENCODE	exon	41850595	41851035	.	+	.	Parent=gene673
###
chr15	ENCODE	gene	41825943	41836256	.	+	.	ID=gene674;Name=AC018512.1-002;name2=PDIA3
chr15	ENCODE	exon	41825943	41826196	.	+	.	Parent=gene674
chr15	ENCODE	exon	41832292	41832436	.	+	.	Parent=gene674
chr15	ENCODE	exon	41833314	41833392	.	+	.	Parent=gene674
chr15	ENCODE	exon	41836139	41836256	.	+	.	Parent=gene674
###
chr15	ENCODE	gene	41825943	41851035	.	+	.	ID=gene675;Name=AC018512.1-004;name2=PDIA3
chr15	ENCODE	exon	41825943	41826196	.	+	.	Parent=gene675
chr15	ENCODE	exon	41831074	41831248	.	+	.	Parent=gene675
chr15	ENCODE	exon	41833314	41833392	.	+	.	Parent=gene675
chr15	ENCODE	exon	41836139	41836256	.	+	.	Parent=gene675
chr15	ENCODE	exon	41840914	41841021	.	+	.	Parent=gene675
chr15	ENCODE	exon	41842567	41842696	.	+	.	Parent=gene675
chr15	ENCODE	exon	41844940	41845056	.	+	.	Parent=gene675
chr15	ENCODE	exon	41845377	41845502	.	+	.	Parent=gene675
chr15	ENCODE	exon	41846218	41846400	.	+	.	Parent=gene675
chr15	ENCODE	exon	41847979	41848087	.	+	.	Parent=gene675
chr15	ENCODE	exon	41849008	41849136	.	+	.	Parent=gene675
chr15	ENCODE	exon	41849740	41849819	.	+	.	Parent=gene675
chr15	ENCODE	exon	41850013	41850070	.	+	.	Parent=gene675
chr15	ENCODE	exon	41850595	41851035	.	+	.	Parent=gene675
###
chr15	ENCODE	gene	41826102	41847985	.	+	.	ID=gene676;Name=AC018512.1-006;name2=PDIA3
chr15	ENCODE	exon	41826102	41826196	.	+	.	Parent=gene676
chr15	ENCODE	exon	41833314	41833392	.	+	.	Parent=gene676
chr15	ENCODE	exon	41836139	41836256	.	+	.	Parent=gene676
chr15	ENCODE	exon	41844940	41845056	.	+	.	Parent=gene676
chr15	ENCODE	exon	41845377	41845502	.	+	.	Parent=gene676
chr15	ENCODE	exon	41846218	41846400	.	+	.	Parent=gene676
chr15	ENCODE	exon	41847979	41847985	.	+	.	Parent=gene676
###
chr15	ENCODE	gene	41849773	41851035	.	+	.	ID=gene677;Name=AC018512.1-007;name2=PDIA3
chr15	ENCODE	exon	41849773	41850070	.	+	.	Parent=gene677
chr15	ENCODE	exon	41850595	41851035	.	+	.	Parent=gene677
###
chr15	ENCODE	gene	41852090	41857033	.	-	.	ID=gene678;name2=ELL3;Name=AC018512.4-001
chr15	ENCODE	exon	41852090	41852716	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41852606	41852716	.	-	0	Parent=gene678
chr15	ENCODE	exon	41852794	41852838	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41852794	41852838	.	-	0	Parent=gene678
chr15	ENCODE	exon	41853672	41853843	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41853672	41853843	.	-	1	Parent=gene678
chr15	ENCODE	exon	41853966	41854008	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41853966	41854008	.	-	2	Parent=gene678
chr15	ENCODE	exon	41854086	41854263	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41854086	41854263	.	-	0	Parent=gene678
chr15	ENCODE	exon	41854796	41854871	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41854796	41854871	.	-	1	Parent=gene678
chr15	ENCODE	exon	41855015	41855100	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41855015	41855100	.	-	0	Parent=gene678
chr15	ENCODE	exon	41855212	41855413	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41855212	41855413	.	-	1	Parent=gene678
chr15	ENCODE	exon	41855529	41855641	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41855529	41855641	.	-	0	Parent=gene678
chr15	ENCODE	exon	41855999	41856034	.	-	.	Parent=gene678
chr15	ENCODE	CDS	41855999	41856034	.	-	0	Parent=gene678
chr15	ENCODE	CDS	41856260	41856391	.	-	0	Parent=gene678
chr15	ENCODE	exon	41856260	41857033	.	-	.	Parent=gene678
###
chr15	ENCODE	gene	41852095	41855873	.	-	.	ID=gene679;Name=AC018512.4-003;name2=ELL3
chr15	ENCODE	exon	41852095	41852716	.	-	.	Parent=gene679
chr15	ENCODE	exon	41852794	41852838	.	-	.	Parent=gene679
chr15	ENCODE	exon	41853672	41853843	.	-	.	Parent=gene679
chr15	ENCODE	exon	41853966	41854008	.	-	.	Parent=gene679
chr15	ENCODE	exon	41854086	41854263	.	-	.	Parent=gene679
chr15	ENCODE	exon	41854796	41854871	.	-	.	Parent=gene679
chr15	ENCODE	exon	41855015	41855100	.	-	.	Parent=gene679
chr15	ENCODE	exon	41855212	41855413	.	-	.	Parent=gene679
chr15	ENCODE	exon	41855529	41855873	.	-	.	Parent=gene679
###
chr15	ENCODE	gene	41852095	41878623	.	-	.	ID=gene680;Name=AC018512.4-002;name2=ELL3
chr15	ENCODE	exon	41852095	41852713	.	-	.	Parent=gene680
chr15	ENCODE	exon	41852794	41852838	.	-	.	Parent=gene680
chr15	ENCODE	exon	41853672	41853843	.	-	.	Parent=gene680
chr15	ENCODE	exon	41853966	41854008	.	-	.	Parent=gene680
chr15	ENCODE	exon	41854086	41854263	.	-	.	Parent=gene680
chr15	ENCODE	exon	41854796	41854871	.	-	.	Parent=gene680
chr15	ENCODE	exon	41855015	41855100	.	-	.	Parent=gene680
chr15	ENCODE	exon	41855212	41855413	.	-	.	Parent=gene680
chr15	ENCODE	exon	41855529	41855641	.	-	.	Parent=gene680
chr15	ENCODE	exon	41855999	41856034	.	-	.	Parent=gene680
chr15	ENCODE	exon	41874878	41875031	.	-	.	Parent=gene680
chr15	ENCODE	exon	41875178	41875226	.	-	.	Parent=gene680
chr15	ENCODE	exon	41875645	41875717	.	-	.	Parent=gene680
chr15	ENCODE	exon	41876106	41876232	.	-	.	Parent=gene680
chr15	ENCODE	exon	41876335	41876430	.	-	.	Parent=gene680
chr15	ENCODE	exon	41877410	41877503	.	-	.	Parent=gene680
chr15	ENCODE	exon	41878449	41878623	.	-	.	Parent=gene680
###
chr15	ENCODE	gene	41852391	41854995	.	-	.	ID=gene681;Name=AC018512.4-005;name2=ELL3
chr15	ENCODE	exon	41852391	41852716	.	-	.	Parent=gene681
chr15	ENCODE	exon	41852794	41852838	.	-	.	Parent=gene681
chr15	ENCODE	exon	41853672	41853843	.	-	.	Parent=gene681
chr15	ENCODE	exon	41853966	41854008	.	-	.	Parent=gene681
chr15	ENCODE	exon	41854086	41854263	.	-	.	Parent=gene681
chr15	ENCODE	exon	41854796	41854995	.	-	.	Parent=gene681
###
chr15	ENCODE	gene	41854202	41855930	.	-	.	ID=gene682;Name=AC018512.4-007;name2=ELL3
chr15	ENCODE	exon	41854202	41854263	.	-	.	Parent=gene682
chr15	ENCODE	exon	41854796	41854871	.	-	.	Parent=gene682
chr15	ENCODE	exon	41855015	41855100	.	-	.	Parent=gene682
chr15	ENCODE	exon	41855212	41855413	.	-	.	Parent=gene682
chr15	ENCODE	exon	41855529	41855641	.	-	.	Parent=gene682
chr15	ENCODE	exon	41855888	41855930	.	-	.	Parent=gene682
###
chr15	ENCODE	gene	41854982	41856456	.	-	.	ID=gene683;Name=AC018512.4-006;name2=ELL3
chr15	ENCODE	exon	41854982	41855100	.	-	.	Parent=gene683
chr15	ENCODE	exon	41855212	41855413	.	-	.	Parent=gene683
chr15	ENCODE	exon	41855529	41855641	.	-	.	Parent=gene683
chr15	ENCODE	exon	41855999	41856034	.	-	.	Parent=gene683
chr15	ENCODE	exon	41856260	41856456	.	-	.	Parent=gene683
###
chr15	ENCODE	gene	41855028	41856062	.	-	.	ID=gene684;Name=AC018512.4-009;name2=ELL3
chr15	ENCODE	exon	41855028	41855100	.	-	.	Parent=gene684
chr15	ENCODE	exon	41855212	41855413	.	-	.	Parent=gene684
chr15	ENCODE	exon	41855529	41855641	.	-	.	Parent=gene684
chr15	ENCODE	exon	41855999	41856062	.	-	.	Parent=gene684
###
chr15	ENCODE	gene	41855055	41856805	.	-	.	ID=gene685;Name=AC018512.4-004;name2=ELL3
chr15	ENCODE	exon	41855055	41855100	.	-	.	Parent=gene685
chr15	ENCODE	CDS	41855055	41855100	.	-	0	Parent=gene685
chr15	ENCODE	exon	41855212	41855413	.	-	.	Parent=gene685
chr15	ENCODE	CDS	41855212	41855413	.	-	1	Parent=gene685
chr15	ENCODE	exon	41855529	41855641	.	-	.	Parent=gene685
chr15	ENCODE	CDS	41855529	41855641	.	-	0	Parent=gene685
chr15	ENCODE	exon	41855999	41856034	.	-	.	Parent=gene685
chr15	ENCODE	CDS	41855999	41856034	.	-	0	Parent=gene685
chr15	ENCODE	CDS	41856260	41856391	.	-	0	Parent=gene685
chr15	ENCODE	exon	41856260	41856454	.	-	.	Parent=gene685
chr15	ENCODE	exon	41856606	41856805	.	-	.	Parent=gene685
###
chr15	ENCODE	gene	41855660	41856458	.	-	.	ID=gene686;Name=AC018512.4-008;name2=ELL3
chr15	ENCODE	exon	41855660	41856034	.	-	.	Parent=gene686
chr15	ENCODE	exon	41856260	41856458	.	-	.	Parent=gene686
###
chr15	ENCODE	gene	41856577	41857606	.	+	.	ID=gene687;Name=AC018512.5-012;name2=SERF2
chr15	ENCODE	exon	41856577	41856992	.	+	.	Parent=gene687
chr15	ENCODE	exon	41857475	41857606	.	+	.	Parent=gene687
###
chr15	ENCODE	gene	41856590	41874085	.	+	.	ID=gene688;Name=AC018512.5-001;name2=SERF2
chr15	ENCODE	exon	41856590	41856992	.	+	.	Parent=gene688
chr15	ENCODE	exon	41864900	41865024	.	+	.	Parent=gene688
chr15	ENCODE	exon	41871466	41871873	.	+	.	Parent=gene688
chr15	ENCODE	CDS	41871867	41871873	.	+	0	Parent=gene688
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene688
chr15	ENCODE	CDS	41872465	41872573	.	+	2	Parent=gene688
chr15	ENCODE	CDS	41873200	41873263	.	+	1	Parent=gene688
chr15	ENCODE	exon	41873200	41874085	.	+	.	Parent=gene688
###
chr15	ENCODE	gene	41871332	41874085	.	+	.	ID=gene689;Name=AC018512.5-002;name2=SERF2
chr15	ENCODE	exon	41871332	41871873	.	+	.	Parent=gene689
chr15	ENCODE	CDS	41871867	41871873	.	+	0	Parent=gene689
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene689
chr15	ENCODE	CDS	41872465	41872573	.	+	2	Parent=gene689
chr15	ENCODE	CDS	41873200	41873263	.	+	1	Parent=gene689
chr15	ENCODE	exon	41873200	41874085	.	+	.	Parent=gene689
###
chr15	ENCODE	gene	41871820	41873440	.	+	.	ID=gene690;Name=AC018512.5-004;name2=SERF2
chr15	ENCODE	exon	41871820	41871873	.	+	.	Parent=gene690
chr15	ENCODE	exon	41872465	41873440	.	+	.	Parent=gene690
###
chr15	ENCODE	gene	41871820	41879340	.	+	.	ID=gene691;Name=AC018512.5-014;name2=SERF2
chr15	ENCODE	exon	41871820	41871873	.	+	.	Parent=gene691
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene691
chr15	ENCODE	exon	41878434	41878597	.	+	.	Parent=gene691
chr15	ENCODE	exon	41879109	41879340	.	+	.	Parent=gene691
###
chr15	ENCODE	gene	41871827	41875579	.	+	.	ID=gene692;Name=AC018512.5-003;name2=SERF2
chr15	ENCODE	exon	41871827	41871873	.	+	.	Parent=gene692
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene692
chr15	ENCODE	exon	41873200	41873426	.	+	.	Parent=gene692
chr15	ENCODE	exon	41873864	41875579	.	+	.	Parent=gene692
###
chr15	ENCODE	gene	41871837	41873536	.	+	.	ID=gene693;Name=AC018512.5-005;name2=SERF2
chr15	ENCODE	exon	41871837	41871873	.	+	.	Parent=gene693
chr15	ENCODE	CDS	41871867	41871873	.	+	0	Parent=gene693
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene693
chr15	ENCODE	CDS	41872465	41872573	.	+	2	Parent=gene693
chr15	ENCODE	CDS	41873177	41873462	.	+	1	Parent=gene693
chr15	ENCODE	exon	41873177	41873536	.	+	.	Parent=gene693
###
chr15	ENCODE	gene	41871837	41879769	.	+	.	ID=gene694;Name=AC018512.5-013;name2=SERF2
chr15	ENCODE	exon	41871837	41871873	.	+	.	Parent=gene694
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene694
chr15	ENCODE	exon	41879109	41879769	.	+	.	Parent=gene694
###
chr15	ENCODE	gene	41871844	41882079	.	+	.	ID=gene695;Name=AC018512.5-0010;name2=SERF2
chr15	ENCODE	exon	41871844	41871873	.	+	.	Parent=gene695
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene695
chr15	ENCODE	exon	41878359	41878597	.	+	.	Parent=gene695
chr15	ENCODE	exon	41878848	41880274	.	+	.	Parent=gene695
chr15	ENCODE	exon	41880622	41880677	.	+	.	Parent=gene695
chr15	ENCODE	exon	41881008	41881059	.	+	.	Parent=gene695
chr15	ENCODE	exon	41881201	41882079	.	+	.	Parent=gene695
###
chr15	ENCODE	gene	41871844	41882079	.	+	.	ID=gene696;Name=AC018512.5-011;name2=SERF2
chr15	ENCODE	exon	41871844	41871873	.	+	.	Parent=gene696
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene696
chr15	ENCODE	exon	41879985	41880274	.	+	.	Parent=gene696
chr15	ENCODE	exon	41880622	41880677	.	+	.	Parent=gene696
chr15	ENCODE	exon	41881008	41881059	.	+	.	Parent=gene696
chr15	ENCODE	exon	41881201	41882079	.	+	.	Parent=gene696
###
chr15	ENCODE	gene	41871858	41872912	.	+	.	ID=gene697;name2=SERF2;Name=AC018512.5-008
chr15	ENCODE	exon	41871858	41872101	.	+	.	Parent=gene697
chr15	ENCODE	exon	41872465	41872912	.	+	.	Parent=gene697
###
chr15	ENCODE	gene	41871858	41873465	.	+	.	ID=gene698;Name=AC018512.5-006;name2=SERF2
chr15	ENCODE	exon	41871858	41872068	.	+	.	Parent=gene698
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene698
chr15	ENCODE	exon	41873200	41873465	.	+	.	Parent=gene698
###
chr15	ENCODE	gene	41871858	41873536	.	+	.	ID=gene699;Name=AC018512.5-007;name2=SERF2
chr15	ENCODE	exon	41871858	41872101	.	+	.	Parent=gene699
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene699
chr15	ENCODE	exon	41873200	41873536	.	+	.	Parent=gene699
###
chr15	ENCODE	gene	41871867	41878497	.	+	.	ID=gene700;name2=SERF2;Name=AC018512.5-015
chr15	ENCODE	exon	41871867	41872101	.	+	.	Parent=gene700
chr15	ENCODE	exon	41872465	41872573	.	+	.	Parent=gene700
chr15	ENCODE	exon	41878359	41878497	.	+	.	Parent=gene700
###
chr15	ENCODE	gene	41872329	41873536	.	+	.	ID=gene701;Name=AC018512.5-009;name2=SERF2
chr15	ENCODE	exon	41872329	41872573	.	+	.	Parent=gene701
chr15	ENCODE	exon	41873200	41873536	.	+	.	Parent=gene701
###
chr15	ENCODE	gene	41873652	41878623	.	-	.	ID=gene702;Name=AC018512.6-002;name2=AC018512.6
chr15	ENCODE	exon	41873652	41874703	.	-	.	Parent=gene702
chr15	ENCODE	exon	41874878	41875031	.	-	.	Parent=gene702
chr15	ENCODE	exon	41875178	41875226	.	-	.	Parent=gene702
chr15	ENCODE	exon	41875645	41875717	.	-	.	Parent=gene702
chr15	ENCODE	exon	41876106	41876232	.	-	.	Parent=gene702
chr15	ENCODE	exon	41876335	41876430	.	-	.	Parent=gene702
chr15	ENCODE	exon	41876631	41876846	.	-	.	Parent=gene702
chr15	ENCODE	exon	41877410	41877503	.	-	.	Parent=gene702
chr15	ENCODE	exon	41877915	41877994	.	-	.	Parent=gene702
chr15	ENCODE	exon	41878449	41878623	.	-	.	Parent=gene702
###
chr15	ENCODE	gene	41873652	41879587	.	-	.	ID=gene703;Name=AC018512.6-003;name2=AC018512.6
chr15	ENCODE	exon	41873652	41874703	.	-	.	Parent=gene703
chr15	ENCODE	exon	41874878	41875031	.	-	.	Parent=gene703
chr15	ENCODE	exon	41875178	41875226	.	-	.	Parent=gene703
chr15	ENCODE	exon	41875645	41875717	.	-	.	Parent=gene703
chr15	ENCODE	exon	41876106	41876232	.	-	.	Parent=gene703
chr15	ENCODE	exon	41876335	41876430	.	-	.	Parent=gene703
chr15	ENCODE	exon	41877410	41877503	.	-	.	Parent=gene703
chr15	ENCODE	exon	41877915	41877994	.	-	.	Parent=gene703
chr15	ENCODE	exon	41878449	41878627	.	-	.	Parent=gene703
chr15	ENCODE	exon	41878800	41879017	.	-	.	Parent=gene703
chr15	ENCODE	exon	41879375	41879587	.	-	.	Parent=gene703
###
chr15	ENCODE	gene	41873652	41879622	.	-	.	ID=gene704;name2=AC018512.6;Name=AC018512.6-004
chr15	ENCODE	exon	41873652	41874703	.	-	.	Parent=gene704
chr15	ENCODE	CDS	41874543	41874703	.	-	2	Parent=gene704
chr15	ENCODE	exon	41874878	41875031	.	-	.	Parent=gene704
chr15	ENCODE	CDS	41874878	41875031	.	-	0	Parent=gene704
chr15	ENCODE	exon	41875178	41875226	.	-	.	Parent=gene704
chr15	ENCODE	CDS	41875178	41875226	.	-	1	Parent=gene704
chr15	ENCODE	exon	41875645	41875717	.	-	.	Parent=gene704
chr15	ENCODE	CDS	41875645	41875717	.	-	2	Parent=gene704
chr15	ENCODE	exon	41876635	41876846	.	-	.	Parent=gene704
chr15	ENCODE	CDS	41876635	41876846	.	-	1	Parent=gene704
chr15	ENCODE	exon	41877410	41877503	.	-	.	Parent=gene704
chr15	ENCODE	CDS	41877410	41877503	.	-	2	Parent=gene704
chr15	ENCODE	exon	41877915	41877994	.	-	.	Parent=gene704
chr15	ENCODE	CDS	41877915	41877994	.	-	1	Parent=gene704
chr15	ENCODE	exon	41878449	41878627	.	-	.	Parent=gene704
chr15	ENCODE	CDS	41878449	41878627	.	-	0	Parent=gene704
chr15	ENCODE	exon	41878800	41878976	.	-	.	Parent=gene704
chr15	ENCODE	CDS	41878800	41878976	.	-	0	Parent=gene704
chr15	ENCODE	CDS	41879375	41879476	.	-	0	Parent=gene704
chr15	ENCODE	exon	41879375	41879622	.	-	.	Parent=gene704
###
chr15	ENCODE	gene	41873652	41879711	.	-	.	ID=gene705;Name=AC018512.6-001;name2=AC018512.6
chr15	ENCODE	exon	41873652	41874703	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41874490	41874703	.	-	1	Parent=gene705
chr15	ENCODE	exon	41874878	41875031	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41874878	41875031	.	-	2	Parent=gene705
chr15	ENCODE	exon	41875178	41875226	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41875178	41875226	.	-	0	Parent=gene705
chr15	ENCODE	exon	41875645	41875717	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41875645	41875717	.	-	1	Parent=gene705
chr15	ENCODE	exon	41876106	41876232	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41876106	41876232	.	-	2	Parent=gene705
chr15	ENCODE	exon	41876335	41876430	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41876335	41876430	.	-	2	Parent=gene705
chr15	ENCODE	exon	41876635	41876846	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41876635	41876846	.	-	1	Parent=gene705
chr15	ENCODE	exon	41877410	41877503	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41877410	41877503	.	-	2	Parent=gene705
chr15	ENCODE	exon	41877915	41877994	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41877915	41877994	.	-	1	Parent=gene705
chr15	ENCODE	exon	41878449	41878627	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41878449	41878627	.	-	0	Parent=gene705
chr15	ENCODE	exon	41878800	41878976	.	-	.	Parent=gene705
chr15	ENCODE	CDS	41878800	41878976	.	-	0	Parent=gene705
chr15	ENCODE	CDS	41879375	41879476	.	-	0	Parent=gene705
chr15	ENCODE	exon	41879375	41879711	.	-	.	Parent=gene705
###
chr15	ENCODE	gene	41873720	41878617	.	-	.	ID=gene706;Name=AC018512.6-005;name2=AC018512.6
chr15	ENCODE	exon	41873720	41874703	.	-	.	Parent=gene706
chr15	ENCODE	exon	41874878	41875031	.	-	.	Parent=gene706
chr15	ENCODE	exon	41875178	41875226	.	-	.	Parent=gene706
chr15	ENCODE	exon	41875645	41875717	.	-	.	Parent=gene706
chr15	ENCODE	exon	41877410	41877503	.	-	.	Parent=gene706
chr15	ENCODE	exon	41878449	41878617	.	-	.	Parent=gene706
###
chr15	ENCODE	gene	41875632	41881572	.	+	.	ID=gene707;Name=AC018512.7-007;name2=HYPK
chr15	ENCODE	exon	41875632	41879638	.	+	.	Parent=gene707
chr15	ENCODE	exon	41879985	41880274	.	+	.	Parent=gene707
chr15	ENCODE	exon	41880622	41880677	.	+	.	Parent=gene707
chr15	ENCODE	exon	41881008	41881059	.	+	.	Parent=gene707
chr15	ENCODE	exon	41881201	41881572	.	+	.	Parent=gene707
###
chr15	ENCODE	gene	41876220	41878585	.	-	.	ID=gene708;Name=AC018512.6-006;name2=AC018512.6
chr15	ENCODE	exon	41876220	41876846	.	-	.	Parent=gene708
chr15	ENCODE	exon	41877410	41877503	.	-	.	Parent=gene708
chr15	ENCODE	exon	41878449	41878585	.	-	.	Parent=gene708
###
chr15	ENCODE	gene	41879801	41881080	.	+	.	ID=gene709;name2=HYPK;Name=AC018512.7-006
chr15	ENCODE	exon	41879801	41880274	.	+	.	Parent=gene709
chr15	ENCODE	exon	41880622	41881080	.	+	.	Parent=gene709
###
chr15	ENCODE	gene	41879913	41881781	.	+	.	ID=gene710;Name=AC018512.7-001;name2=HYPK
chr15	ENCODE	exon	41879913	41880274	.	+	.	Parent=gene710
chr15	ENCODE	CDS	41880089	41880274	.	+	0	Parent=gene710
chr15	ENCODE	exon	41880622	41880677	.	+	.	Parent=gene710
chr15	ENCODE	CDS	41880622	41880677	.	+	0	Parent=gene710
chr15	ENCODE	exon	41881008	41881059	.	+	.	Parent=gene710
chr15	ENCODE	CDS	41881008	41881059	.	+	1	Parent=gene710
chr15	ENCODE	CDS	41881201	41881296	.	+	0	Parent=gene710
chr15	ENCODE	exon	41881201	41881781	.	+	.	Parent=gene710
###
chr15	ENCODE	gene	41880089	41882533	.	+	.	ID=gene711;Name=AC018512.7-004;name2=HYPK
chr15	ENCODE	exon	41880089	41880274	.	+	.	Parent=gene711
chr15	ENCODE	exon	41881008	41882533	.	+	.	Parent=gene711
###
chr15	ENCODE	gene	41880117	41881418	.	+	.	ID=gene712;Name=AC018512.7-005;name2=HYPK
chr15	ENCODE	exon	41880117	41880274	.	+	.	Parent=gene712
chr15	ENCODE	CDS	41880117	41880274	.	+	0	Parent=gene712
chr15	ENCODE	exon	41881008	41881059	.	+	.	Parent=gene712
chr15	ENCODE	CDS	41881008	41881059	.	+	1	Parent=gene712
chr15	ENCODE	CDS	41881201	41881296	.	+	0	Parent=gene712
chr15	ENCODE	exon	41881201	41881418	.	+	.	Parent=gene712
###
chr15	ENCODE	gene	41883982	41904292	.	-	.	ID=gene713;Name=AC018512.8-001;name2=MFAP1
chr15	ENCODE	exon	41883982	41884766	.	-	.	Parent=gene713
chr15	ENCODE	CDS	41884584	41884766	.	-	0	Parent=gene713
chr15	ENCODE	exon	41884866	41884955	.	-	.	Parent=gene713
chr15	ENCODE	CDS	41884866	41884955	.	-	0	Parent=gene713
chr15	ENCODE	exon	41889245	41889404	.	-	.	Parent=gene713
chr15	ENCODE	CDS	41889245	41889404	.	-	1	Parent=gene713
chr15	ENCODE	exon	41892477	41892637	.	-	.	Parent=gene713
chr15	ENCODE	CDS	41892477	41892637	.	-	0	Parent=gene713
chr15	ENCODE	exon	41892739	41892847	.	-	.	Parent=gene713
chr15	ENCODE	CDS	41892739	41892847	.	-	1	Parent=gene713
chr15	ENCODE	exon	41893991	41894178	.	-	.	Parent=gene713
chr15	ENCODE	CDS	41893991	41894178	.	-	0	Parent=gene713
chr15	ENCODE	exon	41894435	41894564	.	-	.	Parent=gene713
chr15	ENCODE	CDS	41894435	41894564	.	-	1	Parent=gene713
chr15	ENCODE	exon	41896719	41896938	.	-	.	Parent=gene713
chr15	ENCODE	CDS	41896719	41896938	.	-	2	Parent=gene713
chr15	ENCODE	CDS	41903981	41904059	.	-	0	Parent=gene713
chr15	ENCODE	exon	41903981	41904292	.	-	.	Parent=gene713
###
chr15	ENCODE	gene	41884396	41889622	.	-	.	ID=gene714;Name=AC018512.8-002;name2=MFAP1
chr15	ENCODE	exon	41884396	41884766	.	-	.	Parent=gene714
chr15	ENCODE	exon	41884866	41884955	.	-	.	Parent=gene714
chr15	ENCODE	exon	41889245	41889622	.	-	.	Parent=gene714
###
chr15	ENCODE	gene	41906453	41947909	.	+	.	ID=gene715;Name=AC023356.1-001;name2=WDR76
chr15	ENCODE	exon	41906453	41906582	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41906523	41906582	.	+	0	Parent=gene715
chr15	ENCODE	exon	41907455	41907856	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41907455	41907856	.	+	0	Parent=gene715
chr15	ENCODE	exon	41914551	41914640	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41914551	41914640	.	+	0	Parent=gene715
chr15	ENCODE	exon	41915651	41915706	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41915651	41915706	.	+	0	Parent=gene715
chr15	ENCODE	exon	41919095	41919218	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41919095	41919218	.	+	1	Parent=gene715
chr15	ENCODE	exon	41921905	41922006	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41921905	41922006	.	+	0	Parent=gene715
chr15	ENCODE	exon	41922118	41922161	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41922118	41922161	.	+	0	Parent=gene715
chr15	ENCODE	exon	41923391	41923544	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41923391	41923544	.	+	1	Parent=gene715
chr15	ENCODE	exon	41930577	41930735	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41930577	41930735	.	+	0	Parent=gene715
chr15	ENCODE	exon	41936436	41936653	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41936436	41936653	.	+	0	Parent=gene715
chr15	ENCODE	exon	41938161	41938313	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41938161	41938313	.	+	1	Parent=gene715
chr15	ENCODE	exon	41940823	41940876	.	+	.	Parent=gene715
chr15	ENCODE	CDS	41940823	41940876	.	+	1	Parent=gene715
chr15	ENCODE	CDS	41945618	41945882	.	+	1	Parent=gene715
chr15	ENCODE	exon	41945618	41947909	.	+	.	Parent=gene715
###
chr15	ENCODE	gene	41906470	41946508	.	+	.	ID=gene716;Name=AC023356.1-002;name2=WDR76
chr15	ENCODE	exon	41906470	41906608	.	+	.	Parent=gene716
chr15	ENCODE	exon	41907455	41907856	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41907587	41907856	.	+	0	Parent=gene716
chr15	ENCODE	exon	41914551	41914640	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41914551	41914640	.	+	0	Parent=gene716
chr15	ENCODE	exon	41915651	41915706	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41915651	41915706	.	+	0	Parent=gene716
chr15	ENCODE	exon	41919095	41919218	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41919095	41919218	.	+	1	Parent=gene716
chr15	ENCODE	exon	41921905	41922006	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41921905	41922006	.	+	0	Parent=gene716
chr15	ENCODE	exon	41922118	41922161	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41922118	41922161	.	+	0	Parent=gene716
chr15	ENCODE	exon	41923391	41923544	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41923391	41923544	.	+	1	Parent=gene716
chr15	ENCODE	exon	41930577	41930735	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41930577	41930735	.	+	0	Parent=gene716
chr15	ENCODE	exon	41936436	41936653	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41936436	41936653	.	+	0	Parent=gene716
chr15	ENCODE	exon	41938161	41938313	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41938161	41938313	.	+	1	Parent=gene716
chr15	ENCODE	exon	41940823	41940876	.	+	.	Parent=gene716
chr15	ENCODE	CDS	41940823	41940876	.	+	1	Parent=gene716
chr15	ENCODE	CDS	41945618	41945882	.	+	1	Parent=gene716
chr15	ENCODE	exon	41945618	41946508	.	+	.	Parent=gene716
###
chr15	ENCODE	gene	41906478	41922161	.	+	.	ID=gene717;Name=AC023356.1-003;name2=WDR76
chr15	ENCODE	exon	41906478	41906582	.	+	.	Parent=gene717
chr15	ENCODE	exon	41907565	41907856	.	+	.	Parent=gene717
chr15	ENCODE	CDS	41907587	41907856	.	+	0	Parent=gene717
chr15	ENCODE	exon	41914551	41914640	.	+	.	Parent=gene717
chr15	ENCODE	CDS	41914551	41914640	.	+	0	Parent=gene717
chr15	ENCODE	exon	41915651	41915706	.	+	.	Parent=gene717
chr15	ENCODE	CDS	41915651	41915706	.	+	0	Parent=gene717
chr15	ENCODE	exon	41919095	41919218	.	+	.	Parent=gene717
chr15	ENCODE	CDS	41919095	41919218	.	+	1	Parent=gene717
chr15	ENCODE	exon	41921905	41922006	.	+	.	Parent=gene717
chr15	ENCODE	CDS	41921905	41922006	.	+	0	Parent=gene717
chr15	ENCODE	exon	41922118	41922161	.	+	.	Parent=gene717
chr15	ENCODE	CDS	41922118	41922161	.	+	0	Parent=gene717
###
chr15	ENCODE	gene	41937997	41946508	.	+	.	ID=gene718;Name=AC023356.1-004;name2=WDR76
chr15	ENCODE	exon	41937997	41938070	.	+	.	Parent=gene718
chr15	ENCODE	exon	41938161	41938313	.	+	.	Parent=gene718
chr15	ENCODE	exon	41940823	41940876	.	+	.	Parent=gene718
chr15	ENCODE	exon	41945618	41946508	.	+	.	Parent=gene718
###
chr15	ENCODE	gene	41950254	42003799	.	-	.	ID=gene719;Name=AC023356.2-001;name2=FRMD5
chr15	ENCODE	exon	41950254	41953952	.	-	.	Parent=gene719
chr15	ENCODE	exon	41963193	41963299	.	-	.	Parent=gene719
chr15	ENCODE	exon	41964217	41964285	.	-	.	Parent=gene719
chr15	ENCODE	exon	41965171	41965245	.	-	.	Parent=gene719
chr15	ENCODE	exon	41967665	41967756	.	-	.	Parent=gene719
chr15	ENCODE	exon	41968299	41968362	.	-	.	Parent=gene719
chr15	ENCODE	exon	41971471	41971559	.	-	.	Parent=gene719
chr15	ENCODE	exon	41981665	41981752	.	-	.	Parent=gene719
chr15	ENCODE	exon	41985318	41985441	.	-	.	Parent=gene719
chr15	ENCODE	exon	41989372	41989469	.	-	.	Parent=gene719
chr15	ENCODE	exon	41998949	41999027	.	-	.	Parent=gene719
chr15	ENCODE	exon	41999257	41999299	.	-	.	Parent=gene719
chr15	ENCODE	exon	42003695	42003799	.	-	.	Parent=gene719
###
chr15	ENCODE	gene	41952765	42003799	.	-	.	ID=gene720;Name=AC023356.2-003;name2=FRMD5
chr15	ENCODE	exon	41952765	41953952	.	-	.	Parent=gene720
chr15	ENCODE	exon	41963193	41963299	.	-	.	Parent=gene720
chr15	ENCODE	exon	41964217	41964285	.	-	.	Parent=gene720
chr15	ENCODE	exon	41965158	41965245	.	-	.	Parent=gene720
chr15	ENCODE	exon	41967665	41967756	.	-	.	Parent=gene720
chr15	ENCODE	exon	41968299	41968362	.	-	.	Parent=gene720
chr15	ENCODE	exon	41971471	41971559	.	-	.	Parent=gene720
chr15	ENCODE	exon	41981665	41981752	.	-	.	Parent=gene720
chr15	ENCODE	exon	41985318	41985441	.	-	.	Parent=gene720
chr15	ENCODE	exon	41989372	41989469	.	-	.	Parent=gene720
chr15	ENCODE	exon	41998468	41998770	.	-	.	Parent=gene720
chr15	ENCODE	exon	41998949	41999027	.	-	.	Parent=gene720
chr15	ENCODE	exon	41999257	41999299	.	-	.	Parent=gene720
chr15	ENCODE	exon	42003695	42003799	.	-	.	Parent=gene720
###
chr15	ENCODE	gene	41952765	42003799	.	-	.	ID=gene721;Name=AC023356.2-006;name2=FRMD5
chr15	ENCODE	exon	41952765	41953429	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41953382	41953429	.	-	0	Parent=gene721
chr15	ENCODE	exon	41953609	41953952	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41953609	41953952	.	-	2	Parent=gene721
chr15	ENCODE	exon	41963193	41963299	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41963193	41963299	.	-	1	Parent=gene721
chr15	ENCODE	exon	41964217	41964285	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41964217	41964285	.	-	1	Parent=gene721
chr15	ENCODE	exon	41965171	41965245	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41965171	41965245	.	-	1	Parent=gene721
chr15	ENCODE	exon	41967665	41967756	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41967665	41967756	.	-	0	Parent=gene721
chr15	ENCODE	exon	41968299	41968362	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41968299	41968362	.	-	1	Parent=gene721
chr15	ENCODE	exon	41971471	41971559	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41971471	41971559	.	-	0	Parent=gene721
chr15	ENCODE	exon	41981665	41981752	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41981665	41981752	.	-	1	Parent=gene721
chr15	ENCODE	exon	41985318	41985441	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41985318	41985441	.	-	2	Parent=gene721
chr15	ENCODE	exon	41989372	41989469	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41989372	41989469	.	-	1	Parent=gene721
chr15	ENCODE	exon	41998949	41999027	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41998949	41999027	.	-	2	Parent=gene721
chr15	ENCODE	exon	41999257	41999299	.	-	.	Parent=gene721
chr15	ENCODE	CDS	41999257	41999299	.	-	0	Parent=gene721
chr15	ENCODE	exon	42003695	42003799	.	-	.	Parent=gene721
chr15	ENCODE	CDS	42003695	42003799	.	-	0	Parent=gene721
###
chr15	ENCODE	gene	41952765	42003799	.	-	.	ID=gene722;Name=AC023356.2-005;name2=FRMD5
chr15	ENCODE	exon	41952765	41953429	.	-	.	Parent=gene722
chr15	ENCODE	exon	41953609	41953952	.	-	.	Parent=gene722
chr15	ENCODE	exon	41963193	41963299	.	-	.	Parent=gene722
chr15	ENCODE	exon	41964217	41964285	.	-	.	Parent=gene722
chr15	ENCODE	exon	41965171	41965245	.	-	.	Parent=gene722
chr15	ENCODE	exon	41967665	41967756	.	-	.	Parent=gene722
chr15	ENCODE	exon	41968314	41968362	.	-	.	Parent=gene722
chr15	ENCODE	exon	41971471	41971559	.	-	.	Parent=gene722
chr15	ENCODE	exon	41981665	41981752	.	-	.	Parent=gene722
chr15	ENCODE	exon	41985318	41985441	.	-	.	Parent=gene722
chr15	ENCODE	exon	41989372	41989469	.	-	.	Parent=gene722
chr15	ENCODE	exon	41998949	41999027	.	-	.	Parent=gene722
chr15	ENCODE	exon	41999257	41999299	.	-	.	Parent=gene722
chr15	ENCODE	exon	42003695	42003799	.	-	.	Parent=gene722
###
chr15	ENCODE	gene	41952765	42003799	.	-	.	ID=gene723;Name=AC023356.2-002;name2=FRMD5
chr15	ENCODE	exon	41952765	41953952	.	-	.	Parent=gene723
chr15	ENCODE	exon	41963193	41963299	.	-	.	Parent=gene723
chr15	ENCODE	exon	41964217	41964285	.	-	.	Parent=gene723
chr15	ENCODE	exon	41965171	41965245	.	-	.	Parent=gene723
chr15	ENCODE	exon	41967665	41967756	.	-	.	Parent=gene723
chr15	ENCODE	exon	41968299	41968362	.	-	.	Parent=gene723
chr15	ENCODE	exon	41971471	41971559	.	-	.	Parent=gene723
chr15	ENCODE	exon	41981665	41981752	.	-	.	Parent=gene723
chr15	ENCODE	exon	41985318	41985441	.	-	.	Parent=gene723
chr15	ENCODE	exon	41989372	41989469	.	-	.	Parent=gene723
chr15	ENCODE	exon	41998949	41998993	.	-	.	Parent=gene723
chr15	ENCODE	exon	41999268	41999299	.	-	.	Parent=gene723
chr15	ENCODE	exon	42003695	42003799	.	-	.	Parent=gene723
###
chr15	ENCODE	gene	41952765	42003799	.	-	.	ID=gene724;Name=AC023356.2-004;name2=FRMD5
chr15	ENCODE	exon	41952765	41953952	.	-	.	Parent=gene724
chr15	ENCODE	exon	41963193	41963299	.	-	.	Parent=gene724
chr15	ENCODE	exon	41964217	41964285	.	-	.	Parent=gene724
chr15	ENCODE	exon	41965171	41965245	.	-	.	Parent=gene724
chr15	ENCODE	exon	41967665	41967756	.	-	.	Parent=gene724
chr15	ENCODE	exon	41968299	41968362	.	-	.	Parent=gene724
chr15	ENCODE	exon	41981665	41981752	.	-	.	Parent=gene724
chr15	ENCODE	exon	41985318	41985441	.	-	.	Parent=gene724
chr15	ENCODE	exon	41989372	41989469	.	-	.	Parent=gene724
chr15	ENCODE	exon	41997215	41997319	.	-	.	Parent=gene724
chr15	ENCODE	exon	41998468	41998770	.	-	.	Parent=gene724
chr15	ENCODE	exon	41998949	41999027	.	-	.	Parent=gene724
chr15	ENCODE	exon	41999257	41999299	.	-	.	Parent=gene724
chr15	ENCODE	exon	42003695	42003799	.	-	.	Parent=gene724
###
chr15	ENCODE	gene	41953850	41964596	.	-	.	ID=gene725;Name=AC023356.2-008;name2=FRMD5
chr15	ENCODE	exon	41953850	41953952	.	-	.	Parent=gene725
chr15	ENCODE	exon	41963193	41963299	.	-	.	Parent=gene725
chr15	ENCODE	exon	41964217	41964596	.	-	.	Parent=gene725
###
chr15	ENCODE	gene	41981404	41989417	.	-	.	ID=gene726;Name=AC023356.2-007;name2=FRMD5
chr15	ENCODE	exon	41981404	41981752	.	-	.	Parent=gene726
chr15	ENCODE	exon	41985318	41985441	.	-	.	Parent=gene726
chr15	ENCODE	exon	41989372	41989417	.	-	.	Parent=gene726
###
chr16	ENCODE	gene	4043	9448	.	-	.	ID=gene727;Name=Z84812.2-001;name2=Z84812.2
chr16	ENCODE	exon	4043	4511	.	-	.	Parent=gene727
chr16	ENCODE	CDS	4381	4511	.	-	2	Parent=gene727
chr16	ENCODE	exon	4652	4720	.	-	.	Parent=gene727
chr16	ENCODE	CDS	4652	4720	.	-	2	Parent=gene727
chr16	ENCODE	exon	5481	5633	.	-	.	Parent=gene727
chr16	ENCODE	CDS	5481	5633	.	-	2	Parent=gene727
chr16	ENCODE	exon	6290	6448	.	-	.	Parent=gene727
chr16	ENCODE	CDS	6290	6448	.	-	2	Parent=gene727
chr16	ENCODE	exon	6537	6738	.	-	.	Parent=gene727
chr16	ENCODE	CDS	6537	6738	.	-	0	Parent=gene727
chr16	ENCODE	exon	6916	7051	.	-	.	Parent=gene727
chr16	ENCODE	CDS	6916	7051	.	-	1	Parent=gene727
chr16	ENCODE	exon	7291	7427	.	-	.	Parent=gene727
chr16	ENCODE	CDS	7291	7427	.	-	0	Parent=gene727
chr16	ENCODE	exon	7604	7750	.	-	.	Parent=gene727
chr16	ENCODE	CDS	7604	7750	.	-	0	Parent=gene727
chr16	ENCODE	exon	7957	8068	.	-	.	Parent=gene727
chr16	ENCODE	CDS	7957	8068	.	-	1	Parent=gene727
chr16	ENCODE	CDS	8602	8789	.	-	0	Parent=gene727
chr16	ENCODE	exon	8602	9448	.	-	.	Parent=gene727
###
chr16	ENCODE	gene	4085	6383	.	-	.	ID=gene728;Name=Z84812.2-010;name2=Z84812.2
chr16	ENCODE	exon	4085	5633	.	-	.	Parent=gene728
chr16	ENCODE	exon	6290	6383	.	-	.	Parent=gene728
###
chr16	ENCODE	gene	4085	7083	.	-	.	ID=gene729;Name=Z84812.2-006;name2=Z84812.2
chr16	ENCODE	exon	4085	4720	.	-	.	Parent=gene729
chr16	ENCODE	exon	5481	5633	.	-	.	Parent=gene729
chr16	ENCODE	exon	6290	6448	.	-	.	Parent=gene729
chr16	ENCODE	exon	6541	6738	.	-	.	Parent=gene729
chr16	ENCODE	exon	6916	7083	.	-	.	Parent=gene729
###
chr16	ENCODE	gene	4085	8925	.	-	.	ID=gene730;Name=Z84812.2-004;name2=Z84812.2
chr16	ENCODE	exon	4085	4511	.	-	.	Parent=gene730
chr16	ENCODE	exon	4652	4720	.	-	.	Parent=gene730
chr16	ENCODE	exon	5481	5633	.	-	.	Parent=gene730
chr16	ENCODE	exon	6290	6448	.	-	.	Parent=gene730
chr16	ENCODE	exon	6541	6738	.	-	.	Parent=gene730
chr16	ENCODE	exon	6916	7427	.	-	.	Parent=gene730
chr16	ENCODE	exon	7604	7750	.	-	.	Parent=gene730
chr16	ENCODE	exon	7957	8058	.	-	.	Parent=gene730
chr16	ENCODE	exon	8190	8243	.	-	.	Parent=gene730
chr16	ENCODE	exon	8602	8925	.	-	.	Parent=gene730
###
chr16	ENCODE	gene	4085	9409	.	-	.	ID=gene731;Name=Z84812.2-003;name2=Z84812.2
chr16	ENCODE	exon	4085	4511	.	-	.	Parent=gene731
chr16	ENCODE	exon	4652	4720	.	-	.	Parent=gene731
chr16	ENCODE	exon	5481	5633	.	-	.	Parent=gene731
chr16	ENCODE	exon	6290	6448	.	-	.	Parent=gene731
chr16	ENCODE	exon	6541	6738	.	-	.	Parent=gene731
chr16	ENCODE	exon	6916	7427	.	-	.	Parent=gene731
chr16	ENCODE	exon	7604	7750	.	-	.	Parent=gene731
chr16	ENCODE	exon	7957	8055	.	-	.	Parent=gene731
chr16	ENCODE	exon	8602	9409	.	-	.	Parent=gene731
###
chr16	ENCODE	gene	4085	9452	.	-	.	ID=gene732;Name=Z84812.2-002;name2=Z84812.2
chr16	ENCODE	exon	4085	4511	.	-	.	Parent=gene732
chr16	ENCODE	exon	4652	4720	.	-	.	Parent=gene732
chr16	ENCODE	exon	5481	5633	.	-	.	Parent=gene732
chr16	ENCODE	exon	6290	6448	.	-	.	Parent=gene732
chr16	ENCODE	exon	6541	6738	.	-	.	Parent=gene732
chr16	ENCODE	exon	6916	7051	.	-	.	Parent=gene732
chr16	ENCODE	exon	7291	7427	.	-	.	Parent=gene732
chr16	ENCODE	exon	7604	7750	.	-	.	Parent=gene732
chr16	ENCODE	exon	7957	8055	.	-	.	Parent=gene732
chr16	ENCODE	exon	8602	9452	.	-	.	Parent=gene732
###
chr16	ENCODE	gene	4088	8422	.	-	.	ID=gene733;Name=Z84812.2-008;name2=Z84812.2
chr16	ENCODE	exon	4088	6448	.	-	.	Parent=gene733
chr16	ENCODE	exon	6541	8422	.	-	.	Parent=gene733
###
chr16	ENCODE	gene	4117	6241	.	-	.	ID=gene734;Name=Z84812.2-005;name2=Z84812.2
chr16	ENCODE	exon	4117	4720	.	-	.	Parent=gene734
chr16	ENCODE	exon	5481	6241	.	-	.	Parent=gene734
###
chr16	ENCODE	gene	4256	5022	.	-	.	ID=gene735;Name=Z84812.2-011;name2=Z84812.2
chr16	ENCODE	exon	4256	4511	.	-	.	Parent=gene735
chr16	ENCODE	exon	4652	5022	.	-	.	Parent=gene735
###
chr16	ENCODE	gene	5739	6975	.	-	.	ID=gene736;name2=Z84812.2;Name=Z84812.2-009
chr16	ENCODE	exon	5739	5993	.	-	.	Parent=gene736
chr16	ENCODE	exon	6290	6448	.	-	.	Parent=gene736
chr16	ENCODE	exon	6541	6738	.	-	.	Parent=gene736
chr16	ENCODE	exon	6916	6975	.	-	.	Parent=gene736
###
chr16	ENCODE	gene	7711	8508	.	-	.	ID=gene737;Name=Z84812.2-007;name2=Z84812.2
chr16	ENCODE	exon	7711	7750	.	-	.	Parent=gene737
chr16	ENCODE	exon	7957	8508	.	-	.	Parent=gene737
###
chr16	ENCODE	gene	12910	15123	.	+	.	ID=gene738;Name=Z84723.1-001;name2=Z84723.1
chr16	ENCODE	exon	12910	13085	.	+	.	Parent=gene738
chr16	ENCODE	CDS	12932	13085	.	+	0	Parent=gene738
chr16	ENCODE	CDS	14246	14283	.	+	2	Parent=gene738
chr16	ENCODE	exon	14246	15123	.	+	.	Parent=gene738
###
chr16	ENCODE	gene	36407	43628	.	-	.	ID=gene739;Name=Z69719.1-001;name2=POLR3K
chr16	ENCODE	exon	36407	37557	.	-	.	Parent=gene739
chr16	ENCODE	CDS	37430	37557	.	-	2	Parent=gene739
chr16	ENCODE	exon	41558	41645	.	-	.	Parent=gene739
chr16	ENCODE	CDS	41558	41645	.	-	0	Parent=gene739
chr16	ENCODE	CDS	43476	43586	.	-	0	Parent=gene739
chr16	ENCODE	exon	43476	43628	.	-	.	Parent=gene739
###
chr16	ENCODE	gene	37236	42142	.	-	.	ID=gene740;Name=Z69719.1-002;name2=POLR3K
chr16	ENCODE	exon	37236	37557	.	-	.	Parent=gene740
chr16	ENCODE	exon	41558	42142	.	-	.	Parent=gene740
###
chr16	ENCODE	gene	43010	47669	.	+	.	ID=gene741;Name=Z69719.2-001;name2=C16orf33
chr16	ENCODE	exon	43010	44058	.	+	.	Parent=gene741
chr16	ENCODE	CDS	44017	44058	.	+	0	Parent=gene741
chr16	ENCODE	exon	45459	45549	.	+	.	Parent=gene741
chr16	ENCODE	CDS	45459	45549	.	+	0	Parent=gene741
chr16	ENCODE	exon	45777	45882	.	+	.	Parent=gene741
chr16	ENCODE	CDS	45777	45882	.	+	2	Parent=gene741
chr16	ENCODE	exon	46539	46613	.	+	.	Parent=gene741
chr16	ENCODE	CDS	46539	46613	.	+	1	Parent=gene741
chr16	ENCODE	CDS	47086	47143	.	+	1	Parent=gene741
chr16	ENCODE	exon	47086	47669	.	+	.	Parent=gene741
###
chr16	ENCODE	gene	43864	47467	.	+	.	ID=gene742;Name=Z69719.2-003;name2=C16orf33
chr16	ENCODE	exon	43864	44058	.	+	.	Parent=gene742
chr16	ENCODE	exon	45766	45882	.	+	.	Parent=gene742
chr16	ENCODE	exon	46539	46613	.	+	.	Parent=gene742
chr16	ENCODE	exon	47086	47467	.	+	.	Parent=gene742
###
chr16	ENCODE	gene	43887	47372	.	+	.	ID=gene743;Name=Z69719.2-004;name2=C16orf33
chr16	ENCODE	exon	43887	44058	.	+	.	Parent=gene743
chr16	ENCODE	exon	45459	45549	.	+	.	Parent=gene743
chr16	ENCODE	exon	45777	45882	.	+	.	Parent=gene743
chr16	ENCODE	exon	46321	46420	.	+	.	Parent=gene743
chr16	ENCODE	exon	46539	46613	.	+	.	Parent=gene743
chr16	ENCODE	exon	47086	47372	.	+	.	Parent=gene743
###
chr16	ENCODE	gene	44960	47444	.	+	.	ID=gene744;Name=Z69719.2-002;name2=C16orf33
chr16	ENCODE	exon	44960	45549	.	+	.	Parent=gene744
chr16	ENCODE	exon	45777	45882	.	+	.	Parent=gene744
chr16	ENCODE	exon	46539	46613	.	+	.	Parent=gene744
chr16	ENCODE	exon	47086	47444	.	+	.	Parent=gene744
###
chr16	ENCODE	gene	45495	47453	.	+	.	ID=gene745;Name=Z69719.2-005;name2=C16orf33
chr16	ENCODE	exon	45495	45549	.	+	.	Parent=gene745
chr16	ENCODE	exon	45777	46613	.	+	.	Parent=gene745
chr16	ENCODE	exon	47086	47453	.	+	.	Parent=gene745
###
chr16	ENCODE	gene	48058	62629	.	-	.	ID=gene746;Name=Z69719.3-001;name2=RHBDF1
chr16	ENCODE	exon	48058	48758	.	-	.	Parent=gene746
chr16	ENCODE	CDS	48339	48758	.	-	0	Parent=gene746
chr16	ENCODE	exon	48972	49125	.	-	.	Parent=gene746
chr16	ENCODE	CDS	48972	49125	.	-	1	Parent=gene746
chr16	ENCODE	exon	49247	49347	.	-	.	Parent=gene746
chr16	ENCODE	CDS	49247	49347	.	-	0	Parent=gene746
chr16	ENCODE	exon	49417	49492	.	-	.	Parent=gene746
chr16	ENCODE	CDS	49417	49492	.	-	1	Parent=gene746
chr16	ENCODE	exon	49730	49824	.	-	.	Parent=gene746
chr16	ENCODE	CDS	49730	49824	.	-	0	Parent=gene746
chr16	ENCODE	exon	50214	50277	.	-	.	Parent=gene746
chr16	ENCODE	CDS	50214	50277	.	-	1	Parent=gene746
chr16	ENCODE	exon	50437	50537	.	-	.	Parent=gene746
chr16	ENCODE	CDS	50437	50537	.	-	0	Parent=gene746
chr16	ENCODE	exon	51118	51279	.	-	.	Parent=gene746
chr16	ENCODE	CDS	51118	51279	.	-	0	Parent=gene746
chr16	ENCODE	exon	51383	51457	.	-	.	Parent=gene746
chr16	ENCODE	CDS	51383	51457	.	-	0	Parent=gene746
chr16	ENCODE	exon	51583	51694	.	-	.	Parent=gene746
chr16	ENCODE	CDS	51583	51694	.	-	1	Parent=gene746
chr16	ENCODE	exon	51796	52050	.	-	.	Parent=gene746
chr16	ENCODE	CDS	51796	52050	.	-	1	Parent=gene746
chr16	ENCODE	exon	52536	52693	.	-	.	Parent=gene746
chr16	ENCODE	CDS	52536	52693	.	-	0	Parent=gene746
chr16	ENCODE	exon	52773	52895	.	-	.	Parent=gene746
chr16	ENCODE	CDS	52773	52895	.	-	0	Parent=gene746
chr16	ENCODE	exon	52971	53180	.	-	.	Parent=gene746
chr16	ENCODE	CDS	52971	53180	.	-	0	Parent=gene746
chr16	ENCODE	exon	53585	53798	.	-	.	Parent=gene746
chr16	ENCODE	CDS	53585	53798	.	-	1	Parent=gene746
chr16	ENCODE	exon	54697	54827	.	-	.	Parent=gene746
chr16	ENCODE	CDS	54697	54827	.	-	0	Parent=gene746
chr16	ENCODE	CDS	54897	55013	.	-	0	Parent=gene746
chr16	ENCODE	exon	54897	55037	.	-	.	Parent=gene746
chr16	ENCODE	exon	62511	62629	.	-	.	Parent=gene746
###
chr16	ENCODE	gene	48059	62593	.	-	.	ID=gene747;Name=Z69719.3-002;name2=RHBDF1
chr16	ENCODE	exon	48059	48758	.	-	.	Parent=gene747
chr16	ENCODE	exon	48972	49492	.	-	.	Parent=gene747
chr16	ENCODE	exon	49730	50277	.	-	.	Parent=gene747
chr16	ENCODE	exon	50437	51279	.	-	.	Parent=gene747
chr16	ENCODE	exon	51383	51457	.	-	.	Parent=gene747
chr16	ENCODE	exon	51583	51694	.	-	.	Parent=gene747
chr16	ENCODE	exon	51796	52050	.	-	.	Parent=gene747
chr16	ENCODE	exon	52536	52693	.	-	.	Parent=gene747
chr16	ENCODE	exon	52773	52895	.	-	.	Parent=gene747
chr16	ENCODE	exon	52971	53180	.	-	.	Parent=gene747
chr16	ENCODE	exon	53585	53798	.	-	.	Parent=gene747
chr16	ENCODE	exon	54697	54827	.	-	.	Parent=gene747
chr16	ENCODE	exon	54930	55037	.	-	.	Parent=gene747
chr16	ENCODE	exon	62511	62593	.	-	.	Parent=gene747
###
chr16	ENCODE	gene	48136	49760	.	-	.	ID=gene748;name2=RHBDF1;Name=Z69719.3-008
chr16	ENCODE	exon	48136	48758	.	-	.	Parent=gene748
chr16	ENCODE	CDS	48339	48758	.	-	1	Parent=gene748
chr16	ENCODE	exon	48972	49091	.	-	.	Parent=gene748
chr16	ENCODE	CDS	48972	49091	.	-	1	Parent=gene748
chr16	ENCODE	exon	49297	49347	.	-	.	Parent=gene748
chr16	ENCODE	CDS	49297	49347	.	-	1	Parent=gene748
chr16	ENCODE	exon	49417	49492	.	-	.	Parent=gene748
chr16	ENCODE	CDS	49417	49492	.	-	2	Parent=gene748
chr16	ENCODE	exon	49730	49760	.	-	.	Parent=gene748
chr16	ENCODE	CDS	49730	49760	.	-	0	Parent=gene748
###
chr16	ENCODE	gene	48972	50191	.	-	.	ID=gene749;Name=Z69719.3-007;name2=RHBDF1
chr16	ENCODE	exon	48972	49347	.	-	.	Parent=gene749
chr16	ENCODE	exon	49417	49492	.	-	.	Parent=gene749
chr16	ENCODE	exon	49730	50191	.	-	.	Parent=gene749
###
chr16	ENCODE	gene	49231	50678	.	-	.	ID=gene750;Name=Z69719.3-006;name2=RHBDF1
chr16	ENCODE	exon	49231	49492	.	-	.	Parent=gene750
chr16	ENCODE	exon	49730	50096	.	-	.	Parent=gene750
chr16	ENCODE	exon	50214	50277	.	-	.	Parent=gene750
chr16	ENCODE	exon	50437	50678	.	-	.	Parent=gene750
###
chr16	ENCODE	gene	51423	52204	.	-	.	ID=gene751;Name=Z69719.3-009;name2=RHBDF1
chr16	ENCODE	exon	51423	51457	.	-	.	Parent=gene751
chr16	ENCODE	exon	51583	51694	.	-	.	Parent=gene751
chr16	ENCODE	exon	51796	52204	.	-	.	Parent=gene751
###
chr16	ENCODE	gene	52971	55035	.	-	.	ID=gene752;Name=Z69719.3-005;name2=RHBDF1
chr16	ENCODE	exon	52971	53180	.	-	.	Parent=gene752
chr16	ENCODE	exon	53585	53920	.	-	.	Parent=gene752
chr16	ENCODE	exon	54697	54827	.	-	.	Parent=gene752
chr16	ENCODE	exon	54897	55035	.	-	.	Parent=gene752
###
chr16	ENCODE	gene	53035	62619	.	-	.	ID=gene753;Name=Z69719.3-003;name2=RHBDF1
chr16	ENCODE	exon	53035	53180	.	-	.	Parent=gene753
chr16	ENCODE	exon	53585	55037	.	-	.	Parent=gene753
chr16	ENCODE	exon	62511	62619	.	-	.	Parent=gene753
###
chr16	ENCODE	gene	53155	66354	.	-	.	ID=gene754;name2=RHBDF1;Name=Z69719.3-010
chr16	ENCODE	exon	53155	53180	.	-	.	Parent=gene754
chr16	ENCODE	CDS	53155	53180	.	-	0	Parent=gene754
chr16	ENCODE	exon	53585	53798	.	-	.	Parent=gene754
chr16	ENCODE	CDS	53585	53798	.	-	1	Parent=gene754
chr16	ENCODE	exon	54697	54827	.	-	.	Parent=gene754
chr16	ENCODE	CDS	54697	54827	.	-	0	Parent=gene754
chr16	ENCODE	CDS	54897	55013	.	-	0	Parent=gene754
chr16	ENCODE	exon	54897	55037	.	-	.	Parent=gene754
chr16	ENCODE	exon	66252	66354	.	-	.	Parent=gene754
###
chr16	ENCODE	gene	53585	62566	.	-	.	ID=gene755;Name=Z69719.3-004;name2=RHBDF1
chr16	ENCODE	exon	53585	53798	.	-	.	Parent=gene755
chr16	ENCODE	CDS	53585	53798	.	-	1	Parent=gene755
chr16	ENCODE	exon	54331	54438	.	-	.	Parent=gene755
chr16	ENCODE	CDS	54331	54438	.	-	1	Parent=gene755
chr16	ENCODE	exon	54697	54827	.	-	.	Parent=gene755
chr16	ENCODE	CDS	54697	54827	.	-	0	Parent=gene755
chr16	ENCODE	CDS	54897	55013	.	-	0	Parent=gene755
chr16	ENCODE	exon	54897	55037	.	-	.	Parent=gene755
chr16	ENCODE	exon	62514	62566	.	-	.	Parent=gene755
###
chr16	ENCODE	gene	54550	66340	.	-	.	ID=gene756;Name=Z69719.3-011;name2=RHBDF1
chr16	ENCODE	exon	54550	55037	.	-	.	Parent=gene756
chr16	ENCODE	exon	66252	66340	.	-	.	Parent=gene756
###
chr16	ENCODE	gene	67006	75683	.	+	.	ID=gene757;Name=Z69720.1-004;name2=MPG
chr16	ENCODE	exon	67006	67124	.	+	.	Parent=gene757
chr16	ENCODE	exon	69424	69699	.	+	.	Parent=gene757
chr16	ENCODE	CDS	69436	69699	.	+	0	Parent=gene757
chr16	ENCODE	exon	73051	73255	.	+	.	Parent=gene757
chr16	ENCODE	CDS	73051	73255	.	+	0	Parent=gene757
chr16	ENCODE	exon	75400	75683	.	+	.	Parent=gene757
chr16	ENCODE	CDS	75400	75683	.	+	2	Parent=gene757
###
chr16	ENCODE	gene	68062	75852	.	+	.	ID=gene758;name2=MPG;Name=Z69720.1-002
chr16	ENCODE	exon	68062	68332	.	+	.	Parent=gene758
chr16	ENCODE	CDS	68309	68332	.	+	0	Parent=gene758
chr16	ENCODE	exon	69424	69699	.	+	.	Parent=gene758
chr16	ENCODE	CDS	69424	69699	.	+	0	Parent=gene758
chr16	ENCODE	exon	73051	73255	.	+	.	Parent=gene758
chr16	ENCODE	CDS	73051	73255	.	+	0	Parent=gene758
chr16	ENCODE	CDS	75400	75776	.	+	2	Parent=gene758
chr16	ENCODE	exon	75400	75852	.	+	.	Parent=gene758
###
chr16	ENCODE	gene	68243	69843	.	+	.	ID=gene759;Name=Z69720.1-003;name2=MPG
chr16	ENCODE	exon	68243	68332	.	+	.	Parent=gene759
chr16	ENCODE	exon	69424	69843	.	+	.	Parent=gene759
###
chr16	ENCODE	gene	68256	75841	.	+	.	ID=gene760;Name=Z69720.1-001;name2=MPG
chr16	ENCODE	exon	68256	68332	.	+	.	Parent=gene760
chr16	ENCODE	exon	69138	69330	.	+	.	Parent=gene760
chr16	ENCODE	CDS	69292	69330	.	+	0	Parent=gene760
chr16	ENCODE	exon	69424	69699	.	+	.	Parent=gene760
chr16	ENCODE	CDS	69424	69699	.	+	0	Parent=gene760
chr16	ENCODE	exon	73051	73255	.	+	.	Parent=gene760
chr16	ENCODE	CDS	73051	73255	.	+	0	Parent=gene760
chr16	ENCODE	CDS	75400	75776	.	+	2	Parent=gene760
chr16	ENCODE	exon	75400	75841	.	+	.	Parent=gene760
###
chr16	ENCODE	gene	74273	81084	.	-	.	ID=gene761;Name=Z69666.1-005;name2=C16orf35
chr16	ENCODE	exon	74273	74594	.	-	.	Parent=gene761
chr16	ENCODE	exon	76667	76869	.	-	.	Parent=gene761
chr16	ENCODE	exon	78697	81084	.	-	.	Parent=gene761
###
chr16	ENCODE	gene	74273	128859	.	-	.	ID=gene762;Name=Z69666.1-001;name2=C16orf35
chr16	ENCODE	exon	74273	74594	.	-	.	Parent=gene762
chr16	ENCODE	exon	75820	76869	.	-	.	Parent=gene762
chr16	ENCODE	exon	78697	78773	.	-	.	Parent=gene762
chr16	ENCODE	exon	78776	78888	.	-	.	Parent=gene762
chr16	ENCODE	exon	79711	79900	.	-	.	Parent=gene762
chr16	ENCODE	exon	82594	82723	.	-	.	Parent=gene762
chr16	ENCODE	exon	83217	83323	.	-	.	Parent=gene762
chr16	ENCODE	exon	88143	88299	.	-	.	Parent=gene762
chr16	ENCODE	exon	90370	90507	.	-	.	Parent=gene762
chr16	ENCODE	exon	100523	100604	.	-	.	Parent=gene762
chr16	ENCODE	exon	102621	102774	.	-	.	Parent=gene762
chr16	ENCODE	exon	107300	107374	.	-	.	Parent=gene762
chr16	ENCODE	exon	109125	109254	.	-	.	Parent=gene762
chr16	ENCODE	exon	120521	120590	.	-	.	Parent=gene762
chr16	ENCODE	exon	128149	128333	.	-	.	Parent=gene762
chr16	ENCODE	exon	128641	128859	.	-	.	Parent=gene762
###
chr16	ENCODE	gene	75800	128511	.	-	.	ID=gene763;Name=Z69666.1-003;name2=C16orf35
chr16	ENCODE	exon	75800	76869	.	-	.	Parent=gene763
chr16	ENCODE	CDS	76704	76869	.	-	1	Parent=gene763
chr16	ENCODE	exon	78697	78773	.	-	.	Parent=gene763
chr16	ENCODE	CDS	78697	78773	.	-	0	Parent=gene763
chr16	ENCODE	exon	78776	78888	.	-	.	Parent=gene763
chr16	ENCODE	CDS	78776	78888	.	-	2	Parent=gene763
chr16	ENCODE	exon	79711	79900	.	-	.	Parent=gene763
chr16	ENCODE	CDS	79711	79900	.	-	0	Parent=gene763
chr16	ENCODE	exon	82594	82723	.	-	.	Parent=gene763
chr16	ENCODE	CDS	82594	82723	.	-	1	Parent=gene763
chr16	ENCODE	exon	83217	83323	.	-	.	Parent=gene763
chr16	ENCODE	CDS	83217	83323	.	-	0	Parent=gene763
chr16	ENCODE	exon	88143	88299	.	-	.	Parent=gene763
chr16	ENCODE	CDS	88143	88299	.	-	1	Parent=gene763
chr16	ENCODE	exon	90370	90507	.	-	.	Parent=gene763
chr16	ENCODE	CDS	90370	90507	.	-	1	Parent=gene763
chr16	ENCODE	exon	100523	100604	.	-	.	Parent=gene763
chr16	ENCODE	CDS	100523	100604	.	-	2	Parent=gene763
chr16	ENCODE	exon	102621	102774	.	-	.	Parent=gene763
chr16	ENCODE	CDS	102621	102774	.	-	0	Parent=gene763
chr16	ENCODE	exon	109125	109254	.	-	.	Parent=gene763
chr16	ENCODE	CDS	109125	109254	.	-	1	Parent=gene763
chr16	ENCODE	exon	120521	120590	.	-	.	Parent=gene763
chr16	ENCODE	CDS	120521	120590	.	-	2	Parent=gene763
chr16	ENCODE	CDS	128149	128266	.	-	0	Parent=gene763
chr16	ENCODE	exon	128149	128511	.	-	.	Parent=gene763
###
chr16	ENCODE	gene	75800	128669	.	-	.	ID=gene764;Name=Z69666.1-002;name2=C16orf35
chr16	ENCODE	exon	75800	76869	.	-	.	Parent=gene764
chr16	ENCODE	exon	78697	78773	.	-	.	Parent=gene764
chr16	ENCODE	exon	78776	78888	.	-	.	Parent=gene764
chr16	ENCODE	exon	79711	79900	.	-	.	Parent=gene764
chr16	ENCODE	exon	82594	82723	.	-	.	Parent=gene764
chr16	ENCODE	exon	83217	83323	.	-	.	Parent=gene764
chr16	ENCODE	exon	88143	88299	.	-	.	Parent=gene764
chr16	ENCODE	exon	90370	90507	.	-	.	Parent=gene764
chr16	ENCODE	exon	100523	100604	.	-	.	Parent=gene764
chr16	ENCODE	exon	102621	102774	.	-	.	Parent=gene764
chr16	ENCODE	exon	120521	120590	.	-	.	Parent=gene764
chr16	ENCODE	exon	128149	128669	.	-	.	Parent=gene764
###
chr16	ENCODE	gene	76696	128268	.	-	.	ID=gene765;Name=Z69666.1-004;name2=C16orf35
chr16	ENCODE	exon	76696	76869	.	-	.	Parent=gene765
chr16	ENCODE	exon	78697	78888	.	-	.	Parent=gene765
chr16	ENCODE	exon	79711	79900	.	-	.	Parent=gene765
chr16	ENCODE	exon	82594	82723	.	-	.	Parent=gene765
chr16	ENCODE	exon	83217	83323	.	-	.	Parent=gene765
chr16	ENCODE	exon	88143	88299	.	-	.	Parent=gene765
chr16	ENCODE	exon	90370	90507	.	-	.	Parent=gene765
chr16	ENCODE	exon	100523	100604	.	-	.	Parent=gene765
chr16	ENCODE	exon	102621	102774	.	-	.	Parent=gene765
chr16	ENCODE	exon	107300	107374	.	-	.	Parent=gene765
chr16	ENCODE	exon	120521	120590	.	-	.	Parent=gene765
chr16	ENCODE	exon	128149	128268	.	-	.	Parent=gene765
###
chr16	ENCODE	gene	76704	128266	.	-	.	ID=gene766;Name=Z69666.1-012;name2=C16orf35
chr16	ENCODE	exon	76704	76869	.	-	.	Parent=gene766
chr16	ENCODE	CDS	76704	76869	.	-	1	Parent=gene766
chr16	ENCODE	exon	78697	78773	.	-	.	Parent=gene766
chr16	ENCODE	CDS	78697	78773	.	-	0	Parent=gene766
chr16	ENCODE	exon	78776	78888	.	-	.	Parent=gene766
chr16	ENCODE	CDS	78776	78888	.	-	2	Parent=gene766
chr16	ENCODE	exon	79711	79900	.	-	.	Parent=gene766
chr16	ENCODE	CDS	79711	79900	.	-	0	Parent=gene766
chr16	ENCODE	exon	82594	82723	.	-	.	Parent=gene766
chr16	ENCODE	CDS	82594	82723	.	-	1	Parent=gene766
chr16	ENCODE	exon	83217	83323	.	-	.	Parent=gene766
chr16	ENCODE	CDS	83217	83323	.	-	0	Parent=gene766
chr16	ENCODE	exon	88143	88299	.	-	.	Parent=gene766
chr16	ENCODE	CDS	88143	88299	.	-	1	Parent=gene766
chr16	ENCODE	exon	90370	90507	.	-	.	Parent=gene766
chr16	ENCODE	CDS	90370	90507	.	-	1	Parent=gene766
chr16	ENCODE	exon	100523	100604	.	-	.	Parent=gene766
chr16	ENCODE	CDS	100523	100604	.	-	2	Parent=gene766
chr16	ENCODE	exon	102621	102774	.	-	.	Parent=gene766
chr16	ENCODE	CDS	102621	102774	.	-	0	Parent=gene766
chr16	ENCODE	exon	107300	107374	.	-	.	Parent=gene766
chr16	ENCODE	CDS	107300	107374	.	-	0	Parent=gene766
chr16	ENCODE	exon	109125	109254	.	-	.	Parent=gene766
chr16	ENCODE	CDS	109125	109254	.	-	1	Parent=gene766
chr16	ENCODE	exon	120521	120590	.	-	.	Parent=gene766
chr16	ENCODE	CDS	120521	120590	.	-	2	Parent=gene766
chr16	ENCODE	exon	128149	128266	.	-	.	Parent=gene766
chr16	ENCODE	CDS	128149	128266	.	-	0	Parent=gene766
###
chr16	ENCODE	gene	82789	88158	.	-	.	ID=gene767;Name=Z69666.1-009;name2=C16orf35
chr16	ENCODE	exon	82789	83323	.	-	.	Parent=gene767
chr16	ENCODE	exon	88143	88158	.	-	.	Parent=gene767
###
chr16	ENCODE	gene	83257	109404	.	-	.	ID=gene768;Name=Z69666.1-008;name2=C16orf35
chr16	ENCODE	exon	83257	83323	.	-	.	Parent=gene768
chr16	ENCODE	exon	88143	88299	.	-	.	Parent=gene768
chr16	ENCODE	exon	90370	90507	.	-	.	Parent=gene768
chr16	ENCODE	exon	100523	100604	.	-	.	Parent=gene768
chr16	ENCODE	exon	102621	102774	.	-	.	Parent=gene768
chr16	ENCODE	exon	107300	107374	.	-	.	Parent=gene768
chr16	ENCODE	exon	109125	109254	.	-	.	Parent=gene768
chr16	ENCODE	exon	109353	109404	.	-	.	Parent=gene768
###
chr16	ENCODE	gene	88228	128665	.	-	.	ID=gene769;Name=Z69666.1-010;name2=C16orf35
chr16	ENCODE	exon	88228	88299	.	-	.	Parent=gene769
chr16	ENCODE	exon	90370	90507	.	-	.	Parent=gene769
chr16	ENCODE	exon	100523	100604	.	-	.	Parent=gene769
chr16	ENCODE	exon	102621	102774	.	-	.	Parent=gene769
chr16	ENCODE	exon	107300	107374	.	-	.	Parent=gene769
chr16	ENCODE	exon	109125	109254	.	-	.	Parent=gene769
chr16	ENCODE	exon	113506	113544	.	-	.	Parent=gene769
chr16	ENCODE	exon	114936	115072	.	-	.	Parent=gene769
chr16	ENCODE	exon	120521	120590	.	-	.	Parent=gene769
chr16	ENCODE	exon	128641	128665	.	-	.	Parent=gene769
###
chr16	ENCODE	gene	100523	128676	.	-	.	ID=gene770;Name=Z69666.1-006;name2=C16orf35
chr16	ENCODE	exon	100523	100604	.	-	.	Parent=gene770
chr16	ENCODE	exon	102621	102774	.	-	.	Parent=gene770
chr16	ENCODE	exon	109125	109254	.	-	.	Parent=gene770
chr16	ENCODE	exon	114936	115072	.	-	.	Parent=gene770
chr16	ENCODE	exon	120521	120590	.	-	.	Parent=gene770
chr16	ENCODE	exon	128149	128333	.	-	.	Parent=gene770
chr16	ENCODE	exon	128641	128676	.	-	.	Parent=gene770
###
chr16	ENCODE	gene	102659	128334	.	-	.	ID=gene771;Name=Z69666.1-011;name2=C16orf35
chr16	ENCODE	exon	102659	102774	.	-	.	Parent=gene771
chr16	ENCODE	CDS	102659	102774	.	-	0	Parent=gene771
chr16	ENCODE	exon	107300	107374	.	-	.	Parent=gene771
chr16	ENCODE	CDS	107300	107374	.	-	0	Parent=gene771
chr16	ENCODE	exon	109125	109254	.	-	.	Parent=gene771
chr16	ENCODE	CDS	109125	109254	.	-	1	Parent=gene771
chr16	ENCODE	exon	113506	113544	.	-	.	Parent=gene771
chr16	ENCODE	CDS	113506	113544	.	-	1	Parent=gene771
chr16	ENCODE	exon	120521	120590	.	-	.	Parent=gene771
chr16	ENCODE	CDS	120521	120590	.	-	2	Parent=gene771
chr16	ENCODE	CDS	128149	128266	.	-	0	Parent=gene771
chr16	ENCODE	exon	128149	128334	.	-	.	Parent=gene771
###
chr16	ENCODE	gene	142686	144502	.	+	.	ID=gene772;Name=Z84721.1-001;name2=HBZ
chr16	ENCODE	exon	142686	143003	.	+	.	Parent=gene772
chr16	ENCODE	CDS	142909	143003	.	+	0	Parent=gene772
chr16	ENCODE	exon	143891	144095	.	+	.	Parent=gene772
chr16	ENCODE	CDS	143891	144095	.	+	1	Parent=gene772
chr16	ENCODE	CDS	144271	144399	.	+	0	Parent=gene772
chr16	ENCODE	exon	144271	144502	.	+	.	Parent=gene772
###
chr16	ENCODE	gene	143891	156760	.	+	.	ID=gene773;Name=Z84721.3-003;name2=HBM
chr16	ENCODE	exon	143891	144095	.	+	.	Parent=gene773
chr16	ENCODE	exon	156267	156471	.	+	.	Parent=gene773
chr16	ENCODE	exon	156579	156760	.	+	.	Parent=gene773
###
chr16	ENCODE	gene	154481	156760	.	+	.	ID=gene774;Name=Z84721.3-002;name2=HBM
chr16	ENCODE	exon	154481	154685	.	+	.	Parent=gene774
chr16	ENCODE	exon	156267	156471	.	+	.	Parent=gene774
chr16	ENCODE	exon	156579	156760	.	+	.	Parent=gene774
###
chr16	ENCODE	gene	155977	156767	.	+	.	ID=gene775;Name=Z84721.3-001;name2=HBM
chr16	ENCODE	exon	155977	156088	.	+	.	Parent=gene775
chr16	ENCODE	CDS	155997	156088	.	+	0	Parent=gene775
chr16	ENCODE	exon	156267	156471	.	+	.	Parent=gene775
chr16	ENCODE	CDS	156267	156471	.	+	1	Parent=gene775
chr16	ENCODE	CDS	156579	156707	.	+	0	Parent=gene775
chr16	ENCODE	exon	156579	156767	.	+	.	Parent=gene775
###
chr16	ENCODE	gene	162846	163709	.	+	.	ID=gene776;Name=Z84721.5-001;name2=HBA2
chr16	ENCODE	exon	162846	163006	.	+	.	Parent=gene776
chr16	ENCODE	CDS	162912	163006	.	+	0	Parent=gene776
chr16	ENCODE	exon	163124	163328	.	+	.	Parent=gene776
chr16	ENCODE	CDS	163124	163328	.	+	1	Parent=gene776
chr16	ENCODE	CDS	163471	163599	.	+	0	Parent=gene776
chr16	ENCODE	exon	163471	163709	.	+	.	Parent=gene776
###
chr16	ENCODE	gene	162889	163709	.	+	.	ID=gene777;Name=Z84721.5-002;name2=HBA2
chr16	ENCODE	exon	162889	162957	.	+	.	Parent=gene777
chr16	ENCODE	exon	163124	163328	.	+	.	Parent=gene777
chr16	ENCODE	CDS	163125	163328	.	+	0	Parent=gene777
chr16	ENCODE	CDS	163471	163599	.	+	0	Parent=gene777
chr16	ENCODE	exon	163471	163709	.	+	.	Parent=gene777
###
chr16	ENCODE	gene	162893	163674	.	+	.	ID=gene778;Name=Z84721.5-003;name2=HBA2
chr16	ENCODE	exon	162893	163328	.	+	.	Parent=gene778
chr16	ENCODE	exon	163471	163674	.	+	.	Parent=gene778
###
chr16	ENCODE	gene	162942	163655	.	+	.	ID=gene779;name2=HBA2;Name=Z84721.5-005
chr16	ENCODE	exon	162942	163006	.	+	.	Parent=gene779
chr16	ENCODE	exon	163124	163247	.	+	.	Parent=gene779
chr16	ENCODE	exon	163308	163328	.	+	.	Parent=gene779
chr16	ENCODE	exon	163471	163655	.	+	.	Parent=gene779
###
chr16	ENCODE	gene	162943	163462	.	+	.	ID=gene780;Name=Z84721.5-006;name2=HBA2
chr16	ENCODE	exon	162943	163006	.	+	.	Parent=gene780
chr16	ENCODE	exon	163124	163462	.	+	.	Parent=gene780
###
chr16	ENCODE	gene	166679	167521	.	+	.	ID=gene781;Name=Z84721.6-001;name2=HBA1
chr16	ENCODE	exon	166679	166810	.	+	.	Parent=gene781
chr16	ENCODE	CDS	166716	166810	.	+	0	Parent=gene781
chr16	ENCODE	exon	166928	167132	.	+	.	Parent=gene781
chr16	ENCODE	CDS	166928	167132	.	+	1	Parent=gene781
chr16	ENCODE	CDS	167282	167410	.	+	0	Parent=gene781
chr16	ENCODE	exon	167282	167521	.	+	.	Parent=gene781
###
chr16	ENCODE	gene	166697	167519	.	+	.	ID=gene782;Name=Z84721.6-002;name2=HBA1
chr16	ENCODE	exon	166697	167132	.	+	.	Parent=gene782
chr16	ENCODE	exon	167282	167519	.	+	.	Parent=gene782
###
chr16	ENCODE	gene	166702	167488	.	+	.	ID=gene783;Name=Z84721.6-003;name2=HBA1
chr16	ENCODE	exon	166702	166810	.	+	.	Parent=gene783
chr16	ENCODE	exon	166928	166967	.	+	.	Parent=gene783
chr16	ENCODE	exon	167121	167132	.	+	.	Parent=gene783
chr16	ENCODE	exon	167282	167488	.	+	.	Parent=gene783
###
chr16	ENCODE	gene	166703	167521	.	+	.	ID=gene784;Name=Z84721.6-006;name2=HBA1
chr16	ENCODE	exon	166703	166761	.	+	.	Parent=gene784
chr16	ENCODE	exon	166928	167132	.	+	.	Parent=gene784
chr16	ENCODE	CDS	166929	167132	.	+	0	Parent=gene784
chr16	ENCODE	CDS	167282	167410	.	+	0	Parent=gene784
chr16	ENCODE	exon	167282	167521	.	+	.	Parent=gene784
###
chr16	ENCODE	gene	166746	167498	.	+	.	ID=gene785;Name=Z84721.6-004;name2=HBA1
chr16	ENCODE	exon	166746	166810	.	+	.	Parent=gene785
chr16	ENCODE	exon	166928	167051	.	+	.	Parent=gene785
chr16	ENCODE	exon	167112	167132	.	+	.	Parent=gene785
chr16	ENCODE	exon	167282	167498	.	+	.	Parent=gene785
###
chr16	ENCODE	gene	166747	167273	.	+	.	ID=gene786;Name=Z84721.6-005;name2=HBA1
chr16	ENCODE	exon	166747	166810	.	+	.	Parent=gene786
chr16	ENCODE	exon	166928	167273	.	+	.	Parent=gene786
###
chr16	ENCODE	gene	170452	171180	.	+	.	ID=gene787;Name=Z84721.7-001;name2=HBQ1
chr16	ENCODE	exon	170452	170580	.	+	.	Parent=gene787
chr16	ENCODE	CDS	170486	170580	.	+	0	Parent=gene787
chr16	ENCODE	exon	170665	170869	.	+	.	Parent=gene787
chr16	ENCODE	CDS	170665	170869	.	+	1	Parent=gene787
chr16	ENCODE	CDS	170979	171107	.	+	0	Parent=gene787
chr16	ENCODE	exon	170979	171180	.	+	.	Parent=gene787
###
chr16	ENCODE	gene	178969	219439	.	-	.	ID=gene788;Name=LA16c-OS12.1-006;name2=LUC7L
chr16	ENCODE	exon	178969	179339	.	-	.	Parent=gene788
chr16	ENCODE	exon	179968	180135	.	-	.	Parent=gene788
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene788
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene788
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene788
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene788
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene788
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene788
chr16	ENCODE	exon	217242	217336	.	-	.	Parent=gene788
chr16	ENCODE	exon	217987	219439	.	-	.	Parent=gene788
###
chr16	ENCODE	gene	178969	219450	.	-	.	ID=gene789;Name=LA16c-OS12.1-003;name2=LUC7L
chr16	ENCODE	exon	178969	179339	.	-	.	Parent=gene789
chr16	ENCODE	CDS	179198	179339	.	-	1	Parent=gene789
chr16	ENCODE	exon	179968	180135	.	-	.	Parent=gene789
chr16	ENCODE	CDS	179968	180135	.	-	1	Parent=gene789
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene789
chr16	ENCODE	CDS	180541	180570	.	-	1	Parent=gene789
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene789
chr16	ENCODE	CDS	182927	183015	.	-	0	Parent=gene789
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene789
chr16	ENCODE	CDS	189062	189238	.	-	0	Parent=gene789
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene789
chr16	ENCODE	CDS	196004	196147	.	-	0	Parent=gene789
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene789
chr16	ENCODE	CDS	198078	198188	.	-	0	Parent=gene789
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene789
chr16	ENCODE	CDS	210649	210747	.	-	0	Parent=gene789
chr16	ENCODE	exon	217242	217336	.	-	.	Parent=gene789
chr16	ENCODE	CDS	217242	217336	.	-	2	Parent=gene789
chr16	ENCODE	CDS	219279	219339	.	-	0	Parent=gene789
chr16	ENCODE	exon	219279	219450	.	-	.	Parent=gene789
###
chr16	ENCODE	gene	178969	219463	.	-	.	ID=gene790;Name=LA16c-OS12.1-001;name2=LUC7L
chr16	ENCODE	exon	178969	180135	.	-	.	Parent=gene790
chr16	ENCODE	CDS	179964	180135	.	-	1	Parent=gene790
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene790
chr16	ENCODE	CDS	180541	180570	.	-	1	Parent=gene790
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene790
chr16	ENCODE	CDS	182927	183015	.	-	0	Parent=gene790
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene790
chr16	ENCODE	CDS	189062	189238	.	-	0	Parent=gene790
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene790
chr16	ENCODE	CDS	196004	196147	.	-	0	Parent=gene790
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene790
chr16	ENCODE	CDS	198078	198188	.	-	0	Parent=gene790
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene790
chr16	ENCODE	CDS	210649	210747	.	-	0	Parent=gene790
chr16	ENCODE	exon	217242	217336	.	-	.	Parent=gene790
chr16	ENCODE	CDS	217242	217336	.	-	2	Parent=gene790
chr16	ENCODE	CDS	219279	219339	.	-	0	Parent=gene790
chr16	ENCODE	exon	219279	219463	.	-	.	Parent=gene790
###
chr16	ENCODE	gene	178971	219463	.	-	.	ID=gene791;Name=LA16c-OS12.1-002;name2=LUC7L
chr16	ENCODE	exon	178971	179339	.	-	.	Parent=gene791
chr16	ENCODE	exon	179931	180135	.	-	.	Parent=gene791
chr16	ENCODE	CDS	179964	180135	.	-	1	Parent=gene791
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene791
chr16	ENCODE	CDS	180541	180570	.	-	1	Parent=gene791
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene791
chr16	ENCODE	CDS	182927	183015	.	-	0	Parent=gene791
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene791
chr16	ENCODE	CDS	189062	189238	.	-	0	Parent=gene791
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene791
chr16	ENCODE	CDS	196004	196147	.	-	0	Parent=gene791
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene791
chr16	ENCODE	CDS	198078	198188	.	-	0	Parent=gene791
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene791
chr16	ENCODE	CDS	210649	210747	.	-	0	Parent=gene791
chr16	ENCODE	exon	217242	217336	.	-	.	Parent=gene791
chr16	ENCODE	CDS	217242	217336	.	-	2	Parent=gene791
chr16	ENCODE	CDS	219279	219339	.	-	0	Parent=gene791
chr16	ENCODE	exon	219279	219463	.	-	.	Parent=gene791
###
chr16	ENCODE	gene	178990	180595	.	-	.	ID=gene792;Name=LA16c-OS12.1-017;name2=LUC7L
chr16	ENCODE	exon	178990	179339	.	-	.	Parent=gene792
chr16	ENCODE	exon	179968	180135	.	-	.	Parent=gene792
chr16	ENCODE	exon	180541	180595	.	-	.	Parent=gene792
###
chr16	ENCODE	gene	178990	196087	.	-	.	ID=gene793;Name=LA16c-OS12.1-016;name2=LUC7L
chr16	ENCODE	exon	178990	179339	.	-	.	Parent=gene793
chr16	ENCODE	CDS	179198	179339	.	-	1	Parent=gene793
chr16	ENCODE	exon	179968	180135	.	-	.	Parent=gene793
chr16	ENCODE	CDS	179968	180135	.	-	1	Parent=gene793
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene793
chr16	ENCODE	CDS	180541	180570	.	-	1	Parent=gene793
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene793
chr16	ENCODE	CDS	182927	183015	.	-	0	Parent=gene793
chr16	ENCODE	exon	196004	196087	.	-	.	Parent=gene793
chr16	ENCODE	CDS	196004	196087	.	-	0	Parent=gene793
###
chr16	ENCODE	gene	178990	219451	.	-	.	ID=gene794;Name=LA16c-OS12.1-005;name2=LUC7L
chr16	ENCODE	exon	178990	179339	.	-	.	Parent=gene794
chr16	ENCODE	exon	179968	180135	.	-	.	Parent=gene794
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene794
chr16	ENCODE	exon	180662	180802	.	-	.	Parent=gene794
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene794
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene794
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene794
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene794
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene794
chr16	ENCODE	exon	217242	218402	.	-	.	Parent=gene794
chr16	ENCODE	exon	219279	219451	.	-	.	Parent=gene794
###
chr16	ENCODE	gene	179098	199773	.	-	.	ID=gene795;Name=LA16c-OS12.1-008;name2=LUC7L
chr16	ENCODE	exon	179098	179339	.	-	.	Parent=gene795
chr16	ENCODE	exon	179968	180135	.	-	.	Parent=gene795
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene795
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene795
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene795
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene795
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene795
chr16	ENCODE	exon	198601	199773	.	-	.	Parent=gene795
###
chr16	ENCODE	gene	179115	180549	.	-	.	ID=gene796;Name=LA16c-OS12.1-018;name2=LUC7L
chr16	ENCODE	exon	179115	179339	.	-	.	Parent=gene796
chr16	ENCODE	exon	179947	180135	.	-	.	Parent=gene796
chr16	ENCODE	exon	180541	180549	.	-	.	Parent=gene796
###
chr16	ENCODE	gene	179896	217686	.	-	.	ID=gene797;Name=LA16c-OS12.1-007;name2=LUC7L
chr16	ENCODE	exon	179896	180135	.	-	.	Parent=gene797
chr16	ENCODE	CDS	179964	180135	.	-	1	Parent=gene797
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene797
chr16	ENCODE	CDS	180541	180570	.	-	1	Parent=gene797
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene797
chr16	ENCODE	CDS	182927	183015	.	-	0	Parent=gene797
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene797
chr16	ENCODE	CDS	189062	189238	.	-	0	Parent=gene797
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene797
chr16	ENCODE	CDS	196004	196147	.	-	0	Parent=gene797
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene797
chr16	ENCODE	CDS	198078	198188	.	-	0	Parent=gene797
chr16	ENCODE	CDS	210649	210744	.	-	0	Parent=gene797
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene797
chr16	ENCODE	exon	217242	217686	.	-	.	Parent=gene797
###
chr16	ENCODE	gene	179896	219434	.	-	.	ID=gene798;Name=LA16c-OS12.1-004;name2=LUC7L
chr16	ENCODE	exon	179896	180135	.	-	.	Parent=gene798
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene798
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene798
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene798
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene798
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene798
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene798
chr16	ENCODE	exon	217242	217336	.	-	.	Parent=gene798
chr16	ENCODE	exon	218333	218402	.	-	.	Parent=gene798
chr16	ENCODE	exon	219279	219434	.	-	.	Parent=gene798
###
chr16	ENCODE	gene	180001	198508	.	-	.	ID=gene799;Name=LA16c-OS12.1-014;name2=LUC7L
chr16	ENCODE	exon	180001	180135	.	-	.	Parent=gene799
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene799
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene799
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene799
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene799
chr16	ENCODE	exon	198078	198508	.	-	.	Parent=gene799
###
chr16	ENCODE	gene	180122	219374	.	-	.	ID=gene800;Name=LA16c-OS12.1-009;name2=LUC7L
chr16	ENCODE	exon	180122	180135	.	-	.	Parent=gene800
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene800
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene800
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene800
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene800
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene800
chr16	ENCODE	exon	198601	198664	.	-	.	Parent=gene800
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene800
chr16	ENCODE	exon	217242	217336	.	-	.	Parent=gene800
chr16	ENCODE	exon	218333	218402	.	-	.	Parent=gene800
chr16	ENCODE	exon	219279	219374	.	-	.	Parent=gene800
###
chr16	ENCODE	gene	180541	219422	.	-	.	ID=gene801;Name=LA16c-OS12.1-015;name2=LUC7L
chr16	ENCODE	exon	180541	180570	.	-	.	Parent=gene801
chr16	ENCODE	exon	182927	183015	.	-	.	Parent=gene801
chr16	ENCODE	exon	189062	189238	.	-	.	Parent=gene801
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene801
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene801
chr16	ENCODE	exon	219279	219422	.	-	.	Parent=gene801
###
chr16	ENCODE	gene	196004	217656	.	-	.	ID=gene802;Name=LA16c-OS12.1-012;name2=LUC7L
chr16	ENCODE	exon	196004	196147	.	-	.	Parent=gene802
chr16	ENCODE	exon	198078	198188	.	-	.	Parent=gene802
chr16	ENCODE	exon	198601	198664	.	-	.	Parent=gene802
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene802
chr16	ENCODE	exon	217242	217656	.	-	.	Parent=gene802
###
chr16	ENCODE	gene	198633	219142	.	-	.	ID=gene803;Name=LA16c-OS12.1-010;name2=LUC7L
chr16	ENCODE	exon	198633	198664	.	-	.	Parent=gene803
chr16	ENCODE	exon	210649	210747	.	-	.	Parent=gene803
chr16	ENCODE	exon	217242	217336	.	-	.	Parent=gene803
chr16	ENCODE	exon	218701	219142	.	-	.	Parent=gene803
###
chr16	ENCODE	gene	210171	217614	.	-	.	ID=gene804;Name=LA16c-OS12.1-013;name2=LUC7L
chr16	ENCODE	exon	210171	210747	.	-	.	Parent=gene804
chr16	ENCODE	exon	217242	217614	.	-	.	Parent=gene804
###
chr16	ENCODE	gene	218124	218990	.	-	.	ID=gene805;Name=LA16c-OS12.1-011;name2=LUC7L
chr16	ENCODE	exon	218124	218402	.	-	.	Parent=gene805
chr16	ENCODE	exon	218701	218990	.	-	.	Parent=gene805
###
chr16	ENCODE	gene	224546	256125	.	+	.	ID=gene806;name2=ITFG3;Name=AC004754.1-001
chr16	ENCODE	exon	224546	224857	.	+	.	Parent=gene806
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene806
chr16	ENCODE	exon	244381	244681	.	+	.	Parent=gene806
chr16	ENCODE	CDS	244414	244681	.	+	0	Parent=gene806
chr16	ENCODE	exon	249483	249599	.	+	.	Parent=gene806
chr16	ENCODE	CDS	249483	249599	.	+	2	Parent=gene806
chr16	ENCODE	exon	249969	250160	.	+	.	Parent=gene806
chr16	ENCODE	CDS	249969	250160	.	+	2	Parent=gene806
chr16	ENCODE	exon	251384	251514	.	+	.	Parent=gene806
chr16	ENCODE	CDS	251384	251514	.	+	2	Parent=gene806
chr16	ENCODE	exon	252093	252225	.	+	.	Parent=gene806
chr16	ENCODE	CDS	252093	252225	.	+	0	Parent=gene806
chr16	ENCODE	exon	252424	252553	.	+	.	Parent=gene806
chr16	ENCODE	CDS	252424	252553	.	+	2	Parent=gene806
chr16	ENCODE	exon	253262	253402	.	+	.	Parent=gene806
chr16	ENCODE	CDS	253262	253402	.	+	1	Parent=gene806
chr16	ENCODE	exon	253700	253775	.	+	.	Parent=gene806
chr16	ENCODE	CDS	253700	253775	.	+	1	Parent=gene806
chr16	ENCODE	exon	254016	254171	.	+	.	Parent=gene806
chr16	ENCODE	CDS	254016	254171	.	+	0	Parent=gene806
chr16	ENCODE	exon	254614	254716	.	+	.	Parent=gene806
chr16	ENCODE	CDS	254614	254716	.	+	0	Parent=gene806
chr16	ENCODE	CDS	254811	255022	.	+	2	Parent=gene806
chr16	ENCODE	exon	254811	256125	.	+	.	Parent=gene806
###
chr16	ENCODE	gene	224802	258971	.	+	.	ID=gene807;Name=AC004754.1-002;name2=ITFG3
chr16	ENCODE	exon	224802	224857	.	+	.	Parent=gene807
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene807
chr16	ENCODE	exon	244381	244681	.	+	.	Parent=gene807
chr16	ENCODE	CDS	244414	244681	.	+	0	Parent=gene807
chr16	ENCODE	exon	249483	249599	.	+	.	Parent=gene807
chr16	ENCODE	CDS	249483	249599	.	+	2	Parent=gene807
chr16	ENCODE	exon	249969	250160	.	+	.	Parent=gene807
chr16	ENCODE	CDS	249969	250160	.	+	2	Parent=gene807
chr16	ENCODE	exon	251384	251514	.	+	.	Parent=gene807
chr16	ENCODE	CDS	251384	251514	.	+	2	Parent=gene807
chr16	ENCODE	exon	252093	252225	.	+	.	Parent=gene807
chr16	ENCODE	CDS	252093	252225	.	+	0	Parent=gene807
chr16	ENCODE	exon	252424	252553	.	+	.	Parent=gene807
chr16	ENCODE	CDS	252424	252553	.	+	2	Parent=gene807
chr16	ENCODE	exon	253262	253402	.	+	.	Parent=gene807
chr16	ENCODE	CDS	253262	253402	.	+	1	Parent=gene807
chr16	ENCODE	exon	253700	253775	.	+	.	Parent=gene807
chr16	ENCODE	CDS	253700	253775	.	+	1	Parent=gene807
chr16	ENCODE	exon	254016	254171	.	+	.	Parent=gene807
chr16	ENCODE	CDS	254016	254171	.	+	0	Parent=gene807
chr16	ENCODE	exon	254614	254716	.	+	.	Parent=gene807
chr16	ENCODE	CDS	254614	254716	.	+	0	Parent=gene807
chr16	ENCODE	exon	254811	254908	.	+	.	Parent=gene807
chr16	ENCODE	CDS	254811	254908	.	+	2	Parent=gene807
chr16	ENCODE	CDS	258776	258853	.	+	0	Parent=gene807
chr16	ENCODE	exon	258776	258971	.	+	.	Parent=gene807
###
chr16	ENCODE	gene	224818	249521	.	+	.	ID=gene808;name2=ITFG3;Name=AC004754.1-017
chr16	ENCODE	exon	224818	224857	.	+	.	Parent=gene808
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene808
chr16	ENCODE	exon	243833	243929	.	+	.	Parent=gene808
chr16	ENCODE	exon	244381	244681	.	+	.	Parent=gene808
chr16	ENCODE	CDS	244414	244681	.	+	0	Parent=gene808
chr16	ENCODE	CDS	249483	249504	.	+	2	Parent=gene808
chr16	ENCODE	exon	249483	249521	.	+	.	Parent=gene808
###
chr16	ENCODE	gene	224827	244565	.	+	.	ID=gene809;Name=AC004754.1-005;name2=ITFG3
chr16	ENCODE	exon	224827	224857	.	+	.	Parent=gene809
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene809
chr16	ENCODE	exon	244329	244565	.	+	.	Parent=gene809
chr16	ENCODE	CDS	244414	244565	.	+	0	Parent=gene809
###
chr16	ENCODE	gene	224829	250003	.	+	.	ID=gene810;Name=AC004754.1-006;name2=ITFG3
chr16	ENCODE	exon	224829	224857	.	+	.	Parent=gene810
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene810
chr16	ENCODE	exon	244388	244681	.	+	.	Parent=gene810
chr16	ENCODE	CDS	244414	244681	.	+	0	Parent=gene810
chr16	ENCODE	exon	249483	249599	.	+	.	Parent=gene810
chr16	ENCODE	CDS	249483	249599	.	+	2	Parent=gene810
chr16	ENCODE	exon	249996	250003	.	+	.	Parent=gene810
chr16	ENCODE	CDS	249996	250003	.	+	2	Parent=gene810
###
chr16	ENCODE	gene	224830	244674	.	+	.	ID=gene811;Name=AC004754.1-007;name2=ITFG3
chr16	ENCODE	exon	224830	224857	.	+	.	Parent=gene811
chr16	ENCODE	exon	239549	239658	.	+	.	Parent=gene811
chr16	ENCODE	exon	244381	244674	.	+	.	Parent=gene811
chr16	ENCODE	CDS	244414	244674	.	+	0	Parent=gene811
###
chr16	ENCODE	gene	224834	251514	.	+	.	ID=gene812;Name=AC004754.1-004;name2=ITFG3
chr16	ENCODE	exon	224834	224857	.	+	.	Parent=gene812
chr16	ENCODE	exon	236957	237069	.	+	.	Parent=gene812
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene812
chr16	ENCODE	exon	244381	244681	.	+	.	Parent=gene812
chr16	ENCODE	CDS	244414	244681	.	+	0	Parent=gene812
chr16	ENCODE	exon	249483	249599	.	+	.	Parent=gene812
chr16	ENCODE	CDS	249483	249599	.	+	2	Parent=gene812
chr16	ENCODE	exon	249969	250160	.	+	.	Parent=gene812
chr16	ENCODE	CDS	249969	250160	.	+	2	Parent=gene812
chr16	ENCODE	exon	251384	251514	.	+	.	Parent=gene812
chr16	ENCODE	CDS	251384	251514	.	+	2	Parent=gene812
###
chr16	ENCODE	gene	224838	252139	.	+	.	ID=gene813;Name=AC004754.1-010;name2=ITFG3
chr16	ENCODE	exon	224838	224857	.	+	.	Parent=gene813
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene813
chr16	ENCODE	exon	244381	244681	.	+	.	Parent=gene813
chr16	ENCODE	CDS	244414	244681	.	+	0	Parent=gene813
chr16	ENCODE	exon	249483	249599	.	+	.	Parent=gene813
chr16	ENCODE	CDS	249483	249599	.	+	2	Parent=gene813
chr16	ENCODE	exon	249996	250160	.	+	.	Parent=gene813
chr16	ENCODE	CDS	249996	250160	.	+	2	Parent=gene813
chr16	ENCODE	exon	251384	251514	.	+	.	Parent=gene813
chr16	ENCODE	CDS	251384	251514	.	+	2	Parent=gene813
chr16	ENCODE	exon	252093	252139	.	+	.	Parent=gene813
chr16	ENCODE	CDS	252093	252139	.	+	0	Parent=gene813
###
chr16	ENCODE	gene	224844	251505	.	+	.	ID=gene814;Name=AC004754.1-009;name2=ITFG3
chr16	ENCODE	exon	224844	224857	.	+	.	Parent=gene814
chr16	ENCODE	exon	238244	238397	.	+	.	Parent=gene814
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene814
chr16	ENCODE	exon	244381	244681	.	+	.	Parent=gene814
chr16	ENCODE	CDS	244414	244681	.	+	0	Parent=gene814
chr16	ENCODE	exon	249483	249599	.	+	.	Parent=gene814
chr16	ENCODE	CDS	249483	249599	.	+	2	Parent=gene814
chr16	ENCODE	exon	249969	250160	.	+	.	Parent=gene814
chr16	ENCODE	CDS	249969	250160	.	+	2	Parent=gene814
chr16	ENCODE	exon	251384	251505	.	+	.	Parent=gene814
chr16	ENCODE	CDS	251384	251505	.	+	2	Parent=gene814
###
chr16	ENCODE	gene	224846	256120	.	+	.	ID=gene815;Name=AC004754.1-003;name2=ITFG3
chr16	ENCODE	exon	224846	224857	.	+	.	Parent=gene815
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene815
chr16	ENCODE	exon	244388	244681	.	+	.	Parent=gene815
chr16	ENCODE	CDS	244414	244681	.	+	0	Parent=gene815
chr16	ENCODE	exon	249483	249599	.	+	.	Parent=gene815
chr16	ENCODE	CDS	249483	249599	.	+	2	Parent=gene815
chr16	ENCODE	exon	249969	250160	.	+	.	Parent=gene815
chr16	ENCODE	CDS	249969	250160	.	+	2	Parent=gene815
chr16	ENCODE	exon	251384	251514	.	+	.	Parent=gene815
chr16	ENCODE	CDS	251384	251514	.	+	2	Parent=gene815
chr16	ENCODE	exon	252093	252225	.	+	.	Parent=gene815
chr16	ENCODE	CDS	252093	252225	.	+	0	Parent=gene815
chr16	ENCODE	exon	252424	252553	.	+	.	Parent=gene815
chr16	ENCODE	CDS	252424	252553	.	+	2	Parent=gene815
chr16	ENCODE	exon	253262	253402	.	+	.	Parent=gene815
chr16	ENCODE	CDS	253262	253402	.	+	1	Parent=gene815
chr16	ENCODE	exon	253700	253775	.	+	.	Parent=gene815
chr16	ENCODE	CDS	253700	253775	.	+	1	Parent=gene815
chr16	ENCODE	exon	254016	254171	.	+	.	Parent=gene815
chr16	ENCODE	CDS	254016	254171	.	+	0	Parent=gene815
chr16	ENCODE	exon	254614	254716	.	+	.	Parent=gene815
chr16	ENCODE	CDS	254614	254716	.	+	0	Parent=gene815
chr16	ENCODE	CDS	254811	255022	.	+	2	Parent=gene815
chr16	ENCODE	exon	254811	256120	.	+	.	Parent=gene815
###
chr16	ENCODE	gene	224847	250009	.	+	.	ID=gene816;Name=AC004754.1-016;name2=ITFG3
chr16	ENCODE	exon	224847	224857	.	+	.	Parent=gene816
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene816
chr16	ENCODE	exon	244381	244681	.	+	.	Parent=gene816
chr16	ENCODE	CDS	244414	244681	.	+	0	Parent=gene816
chr16	ENCODE	exon	249969	250009	.	+	.	Parent=gene816
chr16	ENCODE	CDS	249969	250009	.	+	2	Parent=gene816
###
chr16	ENCODE	gene	230188	244619	.	+	.	ID=gene817;name2=ITFG3;Name=AC004754.1-008
chr16	ENCODE	exon	230188	230276	.	+	.	Parent=gene817
chr16	ENCODE	exon	239549	239654	.	+	.	Parent=gene817
chr16	ENCODE	exon	243833	243929	.	+	.	Parent=gene817
chr16	ENCODE	exon	244329	244619	.	+	.	Parent=gene817
chr16	ENCODE	CDS	244414	244619	.	+	0	Parent=gene817
###
chr16	ENCODE	gene	244122	249520	.	+	.	ID=gene818;Name=AC004754.1-011;name2=ITFG3
chr16	ENCODE	exon	244122	244681	.	+	.	Parent=gene818
chr16	ENCODE	exon	249483	249520	.	+	.	Parent=gene818
###
chr16	ENCODE	gene	244628	250788	.	+	.	ID=gene819;Name=AC004754.1-013;name2=ITFG3
chr16	ENCODE	exon	244628	244681	.	+	.	Parent=gene819
chr16	ENCODE	CDS	244628	244681	.	+	0	Parent=gene819
chr16	ENCODE	exon	249483	249599	.	+	.	Parent=gene819
chr16	ENCODE	CDS	249483	249599	.	+	0	Parent=gene819
chr16	ENCODE	exon	249969	250160	.	+	.	Parent=gene819
chr16	ENCODE	CDS	249969	250160	.	+	0	Parent=gene819
chr16	ENCODE	CDS	250413	250753	.	+	0	Parent=gene819
chr16	ENCODE	exon	250413	250788	.	+	.	Parent=gene819
###
chr16	ENCODE	gene	251205	252244	.	+	.	ID=gene820;Name=AC004754.1-012;name2=ITFG3
chr16	ENCODE	exon	251205	251514	.	+	.	Parent=gene820
chr16	ENCODE	exon	252093	252244	.	+	.	Parent=gene820
###
chr16	ENCODE	gene	252508	255090	.	+	.	ID=gene821;Name=AC004754.1-014;name2=ITFG3
chr16	ENCODE	exon	252508	252553	.	+	.	Parent=gene821
chr16	ENCODE	CDS	252508	252553	.	+	0	Parent=gene821
chr16	ENCODE	exon	253262	253402	.	+	.	Parent=gene821
chr16	ENCODE	CDS	253262	253402	.	+	2	Parent=gene821
chr16	ENCODE	exon	253700	253775	.	+	.	Parent=gene821
chr16	ENCODE	CDS	253700	253775	.	+	2	Parent=gene821
chr16	ENCODE	exon	254614	254716	.	+	.	Parent=gene821
chr16	ENCODE	CDS	254614	254716	.	+	1	Parent=gene821
chr16	ENCODE	CDS	254811	255022	.	+	0	Parent=gene821
chr16	ENCODE	exon	254811	255090	.	+	.	Parent=gene821
###
chr16	ENCODE	gene	254624	256120	.	+	.	ID=gene822;Name=AC004754.1-015;name2=ITFG3
chr16	ENCODE	exon	254624	254716	.	+	.	Parent=gene822
chr16	ENCODE	exon	254811	254893	.	+	.	Parent=gene822
chr16	ENCODE	exon	255942	256120	.	+	.	Parent=gene822
###
chr16	ENCODE	gene	258301	265930	.	-	.	ID=gene823;Name=AC004754.2-001;name2=RGS11
chr16	ENCODE	exon	258301	259383	.	-	.	Parent=gene823
chr16	ENCODE	CDS	259269	259383	.	-	1	Parent=gene823
chr16	ENCODE	exon	259503	259585	.	-	.	Parent=gene823
chr16	ENCODE	CDS	259503	259585	.	-	0	Parent=gene823
chr16	ENCODE	exon	260523	260661	.	-	.	Parent=gene823
chr16	ENCODE	CDS	260523	260661	.	-	1	Parent=gene823
chr16	ENCODE	exon	260744	260831	.	-	.	Parent=gene823
chr16	ENCODE	CDS	260744	260831	.	-	2	Parent=gene823
chr16	ENCODE	exon	260984	261099	.	-	.	Parent=gene823
chr16	ENCODE	CDS	260984	261099	.	-	1	Parent=gene823
chr16	ENCODE	exon	261202	261315	.	-	.	Parent=gene823
chr16	ENCODE	CDS	261202	261315	.	-	1	Parent=gene823
chr16	ENCODE	exon	261399	261460	.	-	.	Parent=gene823
chr16	ENCODE	CDS	261399	261460	.	-	0	Parent=gene823
chr16	ENCODE	exon	261540	261569	.	-	.	Parent=gene823
chr16	ENCODE	CDS	261540	261569	.	-	0	Parent=gene823
chr16	ENCODE	exon	262863	262931	.	-	.	Parent=gene823
chr16	ENCODE	CDS	262863	262931	.	-	0	Parent=gene823
chr16	ENCODE	exon	263476	263557	.	-	.	Parent=gene823
chr16	ENCODE	CDS	263476	263557	.	-	1	Parent=gene823
chr16	ENCODE	exon	263761	263837	.	-	.	Parent=gene823
chr16	ENCODE	CDS	263761	263837	.	-	0	Parent=gene823
chr16	ENCODE	exon	264044	264102	.	-	.	Parent=gene823
chr16	ENCODE	CDS	264044	264102	.	-	2	Parent=gene823
chr16	ENCODE	exon	264215	264266	.	-	.	Parent=gene823
chr16	ENCODE	CDS	264215	264266	.	-	0	Parent=gene823
chr16	ENCODE	exon	264977	265083	.	-	.	Parent=gene823
chr16	ENCODE	CDS	264977	265083	.	-	2	Parent=gene823
chr16	ENCODE	exon	265284	265334	.	-	.	Parent=gene823
chr16	ENCODE	CDS	265284	265334	.	-	2	Parent=gene823
chr16	ENCODE	exon	265403	265499	.	-	.	Parent=gene823
chr16	ENCODE	CDS	265403	265499	.	-	0	Parent=gene823
chr16	ENCODE	CDS	265850	265912	.	-	0	Parent=gene823
chr16	ENCODE	exon	265850	265930	.	-	.	Parent=gene823
###
chr16	ENCODE	gene	258301	265941	.	-	.	ID=gene824;Name=AC004754.2-002;name2=RGS11
chr16	ENCODE	exon	258301	259383	.	-	.	Parent=gene824
chr16	ENCODE	exon	259503	259585	.	-	.	Parent=gene824
chr16	ENCODE	exon	260523	260661	.	-	.	Parent=gene824
chr16	ENCODE	exon	260744	260831	.	-	.	Parent=gene824
chr16	ENCODE	exon	260984	261099	.	-	.	Parent=gene824
chr16	ENCODE	exon	261202	261315	.	-	.	Parent=gene824
chr16	ENCODE	exon	261399	261460	.	-	.	Parent=gene824
chr16	ENCODE	exon	261540	261569	.	-	.	Parent=gene824
chr16	ENCODE	exon	263476	263557	.	-	.	Parent=gene824
chr16	ENCODE	exon	263761	263837	.	-	.	Parent=gene824
chr16	ENCODE	exon	264044	264102	.	-	.	Parent=gene824
chr16	ENCODE	exon	264215	264266	.	-	.	Parent=gene824
chr16	ENCODE	exon	265284	265334	.	-	.	Parent=gene824
chr16	ENCODE	exon	265403	265499	.	-	.	Parent=gene824
chr16	ENCODE	exon	265839	265941	.	-	.	Parent=gene824
###
chr16	ENCODE	gene	258311	265915	.	-	.	ID=gene825;Name=AC004754.2-003;name2=RGS11
chr16	ENCODE	exon	258311	259383	.	-	.	Parent=gene825
chr16	ENCODE	CDS	259269	259383	.	-	1	Parent=gene825
chr16	ENCODE	exon	259503	259585	.	-	.	Parent=gene825
chr16	ENCODE	CDS	259503	259585	.	-	0	Parent=gene825
chr16	ENCODE	exon	260523	260661	.	-	.	Parent=gene825
chr16	ENCODE	CDS	260523	260661	.	-	1	Parent=gene825
chr16	ENCODE	exon	260744	260831	.	-	.	Parent=gene825
chr16	ENCODE	CDS	260744	260831	.	-	2	Parent=gene825
chr16	ENCODE	exon	260984	261099	.	-	.	Parent=gene825
chr16	ENCODE	CDS	260984	261099	.	-	1	Parent=gene825
chr16	ENCODE	exon	261202	261315	.	-	.	Parent=gene825
chr16	ENCODE	CDS	261202	261315	.	-	1	Parent=gene825
chr16	ENCODE	exon	261399	261460	.	-	.	Parent=gene825
chr16	ENCODE	CDS	261399	261460	.	-	0	Parent=gene825
chr16	ENCODE	exon	261540	261569	.	-	.	Parent=gene825
chr16	ENCODE	CDS	261540	261569	.	-	0	Parent=gene825
chr16	ENCODE	exon	262863	262931	.	-	.	Parent=gene825
chr16	ENCODE	CDS	262863	262931	.	-	0	Parent=gene825
chr16	ENCODE	exon	263476	263557	.	-	.	Parent=gene825
chr16	ENCODE	CDS	263476	263557	.	-	1	Parent=gene825
chr16	ENCODE	exon	263761	263837	.	-	.	Parent=gene825
chr16	ENCODE	CDS	263761	263837	.	-	0	Parent=gene825
chr16	ENCODE	exon	264044	264102	.	-	.	Parent=gene825
chr16	ENCODE	CDS	264044	264102	.	-	2	Parent=gene825
chr16	ENCODE	exon	264215	264266	.	-	.	Parent=gene825
chr16	ENCODE	CDS	264215	264266	.	-	0	Parent=gene825
chr16	ENCODE	exon	264977	265083	.	-	.	Parent=gene825
chr16	ENCODE	CDS	264977	265083	.	-	2	Parent=gene825
chr16	ENCODE	exon	265284	265334	.	-	.	Parent=gene825
chr16	ENCODE	CDS	265284	265334	.	-	2	Parent=gene825
chr16	ENCODE	exon	265403	265499	.	-	.	Parent=gene825
chr16	ENCODE	CDS	265403	265499	.	-	0	Parent=gene825
chr16	ENCODE	exon	265839	265915	.	-	.	Parent=gene825
###
chr16	ENCODE	gene	258319	264957	.	-	.	ID=gene826;Name=AC004754.2-008;name2=RGS11
chr16	ENCODE	exon	258319	259383	.	-	.	Parent=gene826
chr16	ENCODE	exon	259503	259585	.	-	.	Parent=gene826
chr16	ENCODE	exon	260523	260661	.	-	.	Parent=gene826
chr16	ENCODE	exon	260744	260831	.	-	.	Parent=gene826
chr16	ENCODE	exon	260984	261099	.	-	.	Parent=gene826
chr16	ENCODE	exon	261202	262931	.	-	.	Parent=gene826
chr16	ENCODE	exon	263476	263557	.	-	.	Parent=gene826
chr16	ENCODE	exon	263761	263837	.	-	.	Parent=gene826
chr16	ENCODE	exon	264044	264957	.	-	.	Parent=gene826
###
chr16	ENCODE	gene	258727	272085	.	+	.	ID=gene827;Name=LA16c-314G4.1-006;name2=ARHGDIG
chr16	ENCODE	exon	258727	259005	.	+	.	Parent=gene827
chr16	ENCODE	CDS	258727	259005	.	+	0	Parent=gene827
chr16	ENCODE	exon	271747	271926	.	+	.	Parent=gene827
chr16	ENCODE	CDS	271747	271926	.	+	0	Parent=gene827
chr16	ENCODE	exon	272026	272085	.	+	.	Parent=gene827
chr16	ENCODE	CDS	272026	272085	.	+	0	Parent=gene827
###
chr16	ENCODE	gene	258727	272085	.	+	.	ID=gene828;Name=LA16c-314G4.1-005;name2=ARHGDIG
chr16	ENCODE	exon	258727	259005	.	+	.	Parent=gene828
chr16	ENCODE	CDS	258727	259005	.	+	0	Parent=gene828
chr16	ENCODE	exon	272026	272085	.	+	.	Parent=gene828
chr16	ENCODE	CDS	272026	272085	.	+	0	Parent=gene828
###
chr16	ENCODE	gene	258982	262183	.	+	.	ID=gene829;name2=ARHGDIG;Name=LA16c-314G4.1-007
chr16	ENCODE	exon	258982	259005	.	+	.	Parent=gene829
chr16	ENCODE	exon	261882	262183	.	+	.	Parent=gene829
###
chr16	ENCODE	gene	259269	265912	.	-	.	ID=gene830;Name=AC004754.2-004;name2=RGS11
chr16	ENCODE	exon	259269	259383	.	-	.	Parent=gene830
chr16	ENCODE	CDS	259269	259383	.	-	1	Parent=gene830
chr16	ENCODE	exon	259503	259585	.	-	.	Parent=gene830
chr16	ENCODE	CDS	259503	259585	.	-	0	Parent=gene830
chr16	ENCODE	exon	260523	260661	.	-	.	Parent=gene830
chr16	ENCODE	CDS	260523	260661	.	-	1	Parent=gene830
chr16	ENCODE	exon	260744	260831	.	-	.	Parent=gene830
chr16	ENCODE	CDS	260744	260831	.	-	2	Parent=gene830
chr16	ENCODE	exon	260984	261099	.	-	.	Parent=gene830
chr16	ENCODE	CDS	260984	261099	.	-	1	Parent=gene830
chr16	ENCODE	exon	261202	261315	.	-	.	Parent=gene830
chr16	ENCODE	CDS	261202	261315	.	-	1	Parent=gene830
chr16	ENCODE	exon	261399	261460	.	-	.	Parent=gene830
chr16	ENCODE	CDS	261399	261460	.	-	0	Parent=gene830
chr16	ENCODE	exon	261540	261569	.	-	.	Parent=gene830
chr16	ENCODE	CDS	261540	261569	.	-	0	Parent=gene830
chr16	ENCODE	exon	262863	262931	.	-	.	Parent=gene830
chr16	ENCODE	CDS	262863	262931	.	-	0	Parent=gene830
chr16	ENCODE	exon	263476	263557	.	-	.	Parent=gene830
chr16	ENCODE	CDS	263476	263557	.	-	1	Parent=gene830
chr16	ENCODE	exon	263761	263837	.	-	.	Parent=gene830
chr16	ENCODE	CDS	263761	263837	.	-	0	Parent=gene830
chr16	ENCODE	exon	264044	264102	.	-	.	Parent=gene830
chr16	ENCODE	CDS	264044	264102	.	-	2	Parent=gene830
chr16	ENCODE	exon	264958	265083	.	-	.	Parent=gene830
chr16	ENCODE	CDS	264958	265083	.	-	2	Parent=gene830
chr16	ENCODE	exon	265284	265334	.	-	.	Parent=gene830
chr16	ENCODE	CDS	265284	265334	.	-	2	Parent=gene830
chr16	ENCODE	exon	265403	265499	.	-	.	Parent=gene830
chr16	ENCODE	CDS	265403	265499	.	-	0	Parent=gene830
chr16	ENCODE	exon	265850	265912	.	-	.	Parent=gene830
chr16	ENCODE	CDS	265850	265912	.	-	0	Parent=gene830
###
chr16	ENCODE	gene	260647	264274	.	-	.	ID=gene831;Name=AC004754.2-007;name2=RGS11
chr16	ENCODE	exon	260647	260661	.	-	.	Parent=gene831
chr16	ENCODE	exon	260744	260831	.	-	.	Parent=gene831
chr16	ENCODE	exon	260984	261099	.	-	.	Parent=gene831
chr16	ENCODE	exon	261202	261315	.	-	.	Parent=gene831
chr16	ENCODE	exon	261399	261460	.	-	.	Parent=gene831
chr16	ENCODE	exon	261540	261569	.	-	.	Parent=gene831
chr16	ENCODE	exon	262863	262931	.	-	.	Parent=gene831
chr16	ENCODE	exon	263476	263557	.	-	.	Parent=gene831
chr16	ENCODE	exon	263761	263837	.	-	.	Parent=gene831
chr16	ENCODE	exon	264044	264102	.	-	.	Parent=gene831
chr16	ENCODE	exon	264215	264274	.	-	.	Parent=gene831
###
chr16	ENCODE	gene	261827	265981	.	-	.	ID=gene832;Name=AC004754.2-005;name2=RGS11
chr16	ENCODE	exon	261827	262494	.	-	.	Parent=gene832
chr16	ENCODE	exon	262863	262931	.	-	.	Parent=gene832
chr16	ENCODE	exon	263476	263557	.	-	.	Parent=gene832
chr16	ENCODE	exon	263761	263837	.	-	.	Parent=gene832
chr16	ENCODE	exon	264044	264102	.	-	.	Parent=gene832
chr16	ENCODE	exon	264215	265083	.	-	.	Parent=gene832
chr16	ENCODE	exon	265284	265334	.	-	.	Parent=gene832
chr16	ENCODE	exon	265403	265499	.	-	.	Parent=gene832
chr16	ENCODE	exon	265850	265981	.	-	.	Parent=gene832
###
chr16	ENCODE	gene	264940	265568	.	-	.	ID=gene833;Name=AC004754.2-006;name2=RGS11
chr16	ENCODE	exon	264940	265083	.	-	.	Parent=gene833
chr16	ENCODE	exon	265284	265334	.	-	.	Parent=gene833
chr16	ENCODE	exon	265403	265568	.	-	.	Parent=gene833
###
chr16	ENCODE	gene	270451	272689	.	+	.	ID=gene834;Name=LA16c-314G4.1-004;name2=ARHGDIG
chr16	ENCODE	exon	270451	270754	.	+	.	Parent=gene834
chr16	ENCODE	CDS	270682	270754	.	+	0	Parent=gene834
chr16	ENCODE	exon	271747	271926	.	+	.	Parent=gene834
chr16	ENCODE	CDS	271747	271926	.	+	2	Parent=gene834
chr16	ENCODE	exon	272026	272109	.	+	.	Parent=gene834
chr16	ENCODE	CDS	272026	272109	.	+	2	Parent=gene834
chr16	ENCODE	exon	272298	272356	.	+	.	Parent=gene834
chr16	ENCODE	CDS	272298	272356	.	+	2	Parent=gene834
chr16	ENCODE	exon	272468	272531	.	+	.	Parent=gene834
chr16	ENCODE	CDS	272468	272531	.	+	0	Parent=gene834
chr16	ENCODE	exon	272616	272689	.	+	.	Parent=gene834
chr16	ENCODE	CDS	272616	272689	.	+	2	Parent=gene834
###
chr16	ENCODE	gene	270607	273004	.	+	.	ID=gene835;name2=ARHGDIG;Name=LA16c-314G4.1-001
chr16	ENCODE	exon	270607	270754	.	+	.	Parent=gene835
chr16	ENCODE	CDS	270682	270754	.	+	0	Parent=gene835
chr16	ENCODE	exon	271747	271926	.	+	.	Parent=gene835
chr16	ENCODE	CDS	271747	271926	.	+	2	Parent=gene835
chr16	ENCODE	exon	272026	272109	.	+	.	Parent=gene835
chr16	ENCODE	CDS	272026	272109	.	+	2	Parent=gene835
chr16	ENCODE	exon	272298	272374	.	+	.	Parent=gene835
chr16	ENCODE	CDS	272298	272374	.	+	2	Parent=gene835
chr16	ENCODE	exon	272468	272531	.	+	.	Parent=gene835
chr16	ENCODE	CDS	272468	272531	.	+	0	Parent=gene835
chr16	ENCODE	CDS	272616	272815	.	+	2	Parent=gene835
chr16	ENCODE	exon	272616	273004	.	+	.	Parent=gene835
###
chr16	ENCODE	gene	270856	272811	.	+	.	ID=gene836;Name=LA16c-314G4.1-002;name2=ARHGDIG
chr16	ENCODE	exon	270856	270934	.	+	.	Parent=gene836
chr16	ENCODE	CDS	270856	270934	.	+	0	Parent=gene836
chr16	ENCODE	exon	271747	271926	.	+	.	Parent=gene836
chr16	ENCODE	CDS	271747	271926	.	+	2	Parent=gene836
chr16	ENCODE	exon	272026	272109	.	+	.	Parent=gene836
chr16	ENCODE	CDS	272026	272109	.	+	2	Parent=gene836
chr16	ENCODE	exon	272298	272374	.	+	.	Parent=gene836
chr16	ENCODE	CDS	272298	272374	.	+	2	Parent=gene836
chr16	ENCODE	exon	272468	272531	.	+	.	Parent=gene836
chr16	ENCODE	CDS	272468	272531	.	+	0	Parent=gene836
chr16	ENCODE	exon	272616	272811	.	+	.	Parent=gene836
chr16	ENCODE	CDS	272616	272811	.	+	2	Parent=gene836
###
chr16	ENCODE	gene	271083	272841	.	+	.	ID=gene837;Name=LA16c-314G4.1-003;name2=ARHGDIG
chr16	ENCODE	exon	271083	271926	.	+	.	Parent=gene837
chr16	ENCODE	exon	272049	272109	.	+	.	Parent=gene837
chr16	ENCODE	exon	272298	272374	.	+	.	Parent=gene837
chr16	ENCODE	exon	272468	272531	.	+	.	Parent=gene837
chr16	ENCODE	exon	272616	272841	.	+	.	Parent=gene837
###
chr16	ENCODE	gene	273153	277216	.	+	.	ID=gene838;Name=LA16c-314G4.2-001;name2=PDIA2
chr16	ENCODE	exon	273153	273369	.	+	.	Parent=gene838
chr16	ENCODE	CDS	273171	273369	.	+	0	Parent=gene838
chr16	ENCODE	exon	274388	274594	.	+	.	Parent=gene838
chr16	ENCODE	CDS	274388	274594	.	+	2	Parent=gene838
chr16	ENCODE	exon	274660	274793	.	+	.	Parent=gene838
chr16	ENCODE	CDS	274660	274793	.	+	2	Parent=gene838
chr16	ENCODE	exon	274879	275016	.	+	.	Parent=gene838
chr16	ENCODE	CDS	274879	275016	.	+	0	Parent=gene838
chr16	ENCODE	exon	275085	275201	.	+	.	Parent=gene838
chr16	ENCODE	CDS	275085	275201	.	+	0	Parent=gene838
chr16	ENCODE	exon	275313	275438	.	+	.	Parent=gene838
chr16	ENCODE	CDS	275313	275438	.	+	0	Parent=gene838
chr16	ENCODE	exon	275507	275704	.	+	.	Parent=gene838
chr16	ENCODE	CDS	275507	275704	.	+	0	Parent=gene838
chr16	ENCODE	exon	276354	276474	.	+	.	Parent=gene838
chr16	ENCODE	CDS	276354	276474	.	+	0	Parent=gene838
chr16	ENCODE	exon	276555	276736	.	+	.	Parent=gene838
chr16	ENCODE	CDS	276555	276736	.	+	2	Parent=gene838
chr16	ENCODE	exon	276836	276946	.	+	.	Parent=gene838
chr16	ENCODE	CDS	276836	276946	.	+	0	Parent=gene838
chr16	ENCODE	CDS	277070	277114	.	+	0	Parent=gene838
chr16	ENCODE	exon	277070	277216	.	+	.	Parent=gene838
###
chr16	ENCODE	gene	273165	277215	.	+	.	ID=gene839;Name=LA16c-314G4.2-002;name2=PDIA2
chr16	ENCODE	exon	273165	273369	.	+	.	Parent=gene839
chr16	ENCODE	exon	274388	274475	.	+	.	Parent=gene839
chr16	ENCODE	exon	274513	274594	.	+	.	Parent=gene839
chr16	ENCODE	exon	274660	274793	.	+	.	Parent=gene839
chr16	ENCODE	exon	274879	275016	.	+	.	Parent=gene839
chr16	ENCODE	exon	275085	275201	.	+	.	Parent=gene839
chr16	ENCODE	exon	275313	275438	.	+	.	Parent=gene839
chr16	ENCODE	exon	275507	275704	.	+	.	Parent=gene839
chr16	ENCODE	exon	276354	276474	.	+	.	Parent=gene839
chr16	ENCODE	exon	276555	276736	.	+	.	Parent=gene839
chr16	ENCODE	exon	276836	276946	.	+	.	Parent=gene839
chr16	ENCODE	exon	277070	277215	.	+	.	Parent=gene839
###
chr16	ENCODE	gene	273165	277215	.	+	.	ID=gene840;Name=LA16c-314G4.2-003;name2=PDIA2
chr16	ENCODE	exon	273165	273369	.	+	.	Parent=gene840
chr16	ENCODE	exon	274388	274793	.	+	.	Parent=gene840
chr16	ENCODE	exon	274879	275016	.	+	.	Parent=gene840
chr16	ENCODE	exon	275085	275201	.	+	.	Parent=gene840
chr16	ENCODE	exon	275313	275438	.	+	.	Parent=gene840
chr16	ENCODE	exon	275507	275704	.	+	.	Parent=gene840
chr16	ENCODE	exon	276354	276474	.	+	.	Parent=gene840
chr16	ENCODE	exon	276555	276736	.	+	.	Parent=gene840
chr16	ENCODE	exon	276836	276946	.	+	.	Parent=gene840
chr16	ENCODE	exon	277070	277215	.	+	.	Parent=gene840
###
chr16	ENCODE	gene	273181	275141	.	+	.	ID=gene841;Name=LA16c-314G4.2-005;name2=PDIA2
chr16	ENCODE	exon	273181	273369	.	+	.	Parent=gene841
chr16	ENCODE	CDS	273181	273369	.	+	0	Parent=gene841
chr16	ENCODE	exon	274388	274594	.	+	.	Parent=gene841
chr16	ENCODE	CDS	274388	274594	.	+	0	Parent=gene841
chr16	ENCODE	exon	274660	274793	.	+	.	Parent=gene841
chr16	ENCODE	CDS	274660	274793	.	+	0	Parent=gene841
chr16	ENCODE	exon	274924	275016	.	+	.	Parent=gene841
chr16	ENCODE	CDS	274924	275016	.	+	1	Parent=gene841
chr16	ENCODE	exon	275085	275141	.	+	.	Parent=gene841
chr16	ENCODE	CDS	275085	275141	.	+	1	Parent=gene841
###
chr16	ENCODE	gene	274153	277209	.	+	.	ID=gene842;Name=LA16c-314G4.2-004;name2=PDIA2
chr16	ENCODE	exon	274153	274594	.	+	.	Parent=gene842
chr16	ENCODE	exon	274660	274793	.	+	.	Parent=gene842
chr16	ENCODE	exon	274879	275704	.	+	.	Parent=gene842
chr16	ENCODE	exon	276354	276474	.	+	.	Parent=gene842
chr16	ENCODE	exon	276555	276736	.	+	.	Parent=gene842
chr16	ENCODE	exon	276836	276946	.	+	.	Parent=gene842
chr16	ENCODE	exon	277070	277209	.	+	.	Parent=gene842
###
chr16	ENCODE	gene	274876	275577	.	+	.	ID=gene843;Name=LA16c-314G4.2-006;name2=PDIA2
chr16	ENCODE	exon	274876	275016	.	+	.	Parent=gene843
chr16	ENCODE	exon	275085	275201	.	+	.	Parent=gene843
chr16	ENCODE	exon	275313	275434	.	+	.	Parent=gene843
chr16	ENCODE	exon	275507	275577	.	+	.	Parent=gene843
###
chr16	ENCODE	gene	275681	277216	.	+	.	ID=gene844;Name=LA16c-314G4.2-007;name2=PDIA2
chr16	ENCODE	exon	275681	275704	.	+	.	Parent=gene844
chr16	ENCODE	CDS	275681	275704	.	+	0	Parent=gene844
chr16	ENCODE	exon	276372	276474	.	+	.	Parent=gene844
chr16	ENCODE	CDS	276372	276474	.	+	0	Parent=gene844
chr16	ENCODE	exon	276555	276736	.	+	.	Parent=gene844
chr16	ENCODE	CDS	276555	276736	.	+	2	Parent=gene844
chr16	ENCODE	exon	276836	276946	.	+	.	Parent=gene844
chr16	ENCODE	CDS	276836	276946	.	+	0	Parent=gene844
chr16	ENCODE	CDS	277070	277114	.	+	0	Parent=gene844
chr16	ENCODE	exon	277070	277216	.	+	.	Parent=gene844
###
chr16	ENCODE	gene	277441	283533	.	-	.	ID=gene845;Name=LA16c-314G4.3-006;name2=AXIN1
chr16	ENCODE	exon	277441	277626	.	-	.	Parent=gene845
chr16	ENCODE	exon	279465	279608	.	-	.	Parent=gene845
chr16	ENCODE	exon	283489	283533	.	-	.	Parent=gene845
###
chr16	ENCODE	gene	277441	336323	.	-	.	ID=gene846;Name=LA16c-314G4.3-007;name2=AXIN1
chr16	ENCODE	exon	277441	278249	.	-	.	Parent=gene846
chr16	ENCODE	exon	279441	283719	.	-	.	Parent=gene846
chr16	ENCODE	exon	287057	287227	.	-	.	Parent=gene846
chr16	ENCODE	exon	287723	288252	.	-	.	Parent=gene846
chr16	ENCODE	exon	294305	294442	.	-	.	Parent=gene846
chr16	ENCODE	exon	299974	300070	.	-	.	Parent=gene846
chr16	ENCODE	exon	304544	304684	.	-	.	Parent=gene846
chr16	ENCODE	exon	336149	336323	.	-	.	Parent=gene846
###
chr16	ENCODE	gene	277441	342660	.	-	.	ID=gene847;Name=LA16c-314G4.3-001;name2=AXIN1
chr16	ENCODE	exon	277441	278249	.	-	.	Parent=gene847
chr16	ENCODE	CDS	278123	278249	.	-	1	Parent=gene847
chr16	ENCODE	exon	279441	279608	.	-	.	Parent=gene847
chr16	ENCODE	CDS	279441	279608	.	-	1	Parent=gene847
chr16	ENCODE	exon	281191	281298	.	-	.	Parent=gene847
chr16	ENCODE	CDS	281191	281298	.	-	1	Parent=gene847
chr16	ENCODE	exon	283489	283719	.	-	.	Parent=gene847
chr16	ENCODE	CDS	283489	283719	.	-	1	Parent=gene847
chr16	ENCODE	exon	287057	287227	.	-	.	Parent=gene847
chr16	ENCODE	CDS	287057	287227	.	-	1	Parent=gene847
chr16	ENCODE	exon	287723	288252	.	-	.	Parent=gene847
chr16	ENCODE	CDS	287723	288252	.	-	0	Parent=gene847
chr16	ENCODE	exon	294305	294442	.	-	.	Parent=gene847
chr16	ENCODE	CDS	294305	294442	.	-	0	Parent=gene847
chr16	ENCODE	exon	299974	300070	.	-	.	Parent=gene847
chr16	ENCODE	CDS	299974	300070	.	-	1	Parent=gene847
chr16	ENCODE	exon	304544	304684	.	-	.	Parent=gene847
chr16	ENCODE	CDS	304544	304684	.	-	1	Parent=gene847
chr16	ENCODE	CDS	336149	337026	.	-	0	Parent=gene847
chr16	ENCODE	exon	336149	337107	.	-	.	Parent=gene847
chr16	ENCODE	exon	342370	342660	.	-	.	Parent=gene847
###
chr16	ENCODE	gene	277442	342450	.	-	.	ID=gene848;Name=LA16c-314G4.3-002;name2=AXIN1
chr16	ENCODE	exon	277442	278249	.	-	.	Parent=gene848
chr16	ENCODE	CDS	278123	278249	.	-	1	Parent=gene848
chr16	ENCODE	exon	279441	279608	.	-	.	Parent=gene848
chr16	ENCODE	CDS	279441	279608	.	-	1	Parent=gene848
chr16	ENCODE	exon	283489	283719	.	-	.	Parent=gene848
chr16	ENCODE	CDS	283489	283719	.	-	1	Parent=gene848
chr16	ENCODE	exon	287057	287227	.	-	.	Parent=gene848
chr16	ENCODE	CDS	287057	287227	.	-	1	Parent=gene848
chr16	ENCODE	exon	287723	288252	.	-	.	Parent=gene848
chr16	ENCODE	CDS	287723	288252	.	-	0	Parent=gene848
chr16	ENCODE	exon	294305	294442	.	-	.	Parent=gene848
chr16	ENCODE	CDS	294305	294442	.	-	0	Parent=gene848
chr16	ENCODE	exon	299974	300070	.	-	.	Parent=gene848
chr16	ENCODE	CDS	299974	300070	.	-	1	Parent=gene848
chr16	ENCODE	exon	304544	304684	.	-	.	Parent=gene848
chr16	ENCODE	CDS	304544	304684	.	-	1	Parent=gene848
chr16	ENCODE	CDS	336149	337026	.	-	0	Parent=gene848
chr16	ENCODE	exon	336149	337107	.	-	.	Parent=gene848
chr16	ENCODE	exon	342370	342450	.	-	.	Parent=gene848
###
chr16	ENCODE	gene	278191	283537	.	-	.	ID=gene849;Name=LA16c-314G4.3-005;name2=AXIN1
chr16	ENCODE	exon	278191	278307	.	-	.	Parent=gene849
chr16	ENCODE	exon	279441	279608	.	-	.	Parent=gene849
chr16	ENCODE	exon	283489	283537	.	-	.	Parent=gene849
###
chr16	ENCODE	gene	287845	342674	.	-	.	ID=gene850;Name=LA16c-314G4.3-004;name2=AXIN1
chr16	ENCODE	exon	287845	288252	.	-	.	Parent=gene850
chr16	ENCODE	exon	294305	294442	.	-	.	Parent=gene850
chr16	ENCODE	exon	299974	300070	.	-	.	Parent=gene850
chr16	ENCODE	exon	304544	304684	.	-	.	Parent=gene850
chr16	ENCODE	exon	342370	342674	.	-	.	Parent=gene850
###
chr16	ENCODE	gene	356928	360569	.	-	.	ID=gene851;Name=Z97634.1-001;name2=MRPL28
chr16	ENCODE	exon	356928	357783	.	-	.	Parent=gene851
chr16	ENCODE	CDS	357676	357783	.	-	0	Parent=gene851
chr16	ENCODE	exon	358329	358415	.	-	.	Parent=gene851
chr16	ENCODE	CDS	358329	358415	.	-	0	Parent=gene851
chr16	ENCODE	exon	358502	358627	.	-	.	Parent=gene851
chr16	ENCODE	CDS	358502	358627	.	-	0	Parent=gene851
chr16	ENCODE	exon	359060	359221	.	-	.	Parent=gene851
chr16	ENCODE	CDS	359060	359221	.	-	0	Parent=gene851
chr16	ENCODE	CDS	359932	360219	.	-	0	Parent=gene851
chr16	ENCODE	exon	359932	360226	.	-	.	Parent=gene851
chr16	ENCODE	exon	360500	360569	.	-	.	Parent=gene851
###
chr16	ENCODE	gene	357395	360510	.	-	.	ID=gene852;Name=Z97634.1-004;name2=MRPL28
chr16	ENCODE	exon	357395	357783	.	-	.	Parent=gene852
chr16	ENCODE	exon	358329	358415	.	-	.	Parent=gene852
chr16	ENCODE	exon	358502	359221	.	-	.	Parent=gene852
chr16	ENCODE	exon	359932	360226	.	-	.	Parent=gene852
chr16	ENCODE	exon	360500	360510	.	-	.	Parent=gene852
###
chr16	ENCODE	gene	357395	360527	.	-	.	ID=gene853;name2=MRPL28;Name=Z97634.1-002
chr16	ENCODE	exon	357395	357783	.	-	.	Parent=gene853
chr16	ENCODE	exon	358329	358415	.	-	.	Parent=gene853
chr16	ENCODE	exon	358502	360226	.	-	.	Parent=gene853
chr16	ENCODE	exon	360500	360527	.	-	.	Parent=gene853
###
chr16	ENCODE	gene	357397	359804	.	-	.	ID=gene854;Name=Z97634.1-012;name2=MRPL28
chr16	ENCODE	exon	357397	357496	.	-	.	Parent=gene854
chr16	ENCODE	CDS	357411	357496	.	-	2	Parent=gene854
chr16	ENCODE	CDS	359595	359655	.	-	0	Parent=gene854
chr16	ENCODE	exon	359595	359804	.	-	.	Parent=gene854
###
chr16	ENCODE	gene	357397	360528	.	-	.	ID=gene855;Name=Z97634.1-006;name2=MRPL28
chr16	ENCODE	exon	357397	357783	.	-	.	Parent=gene855
chr16	ENCODE	CDS	357676	357783	.	-	0	Parent=gene855
chr16	ENCODE	exon	358329	358415	.	-	.	Parent=gene855
chr16	ENCODE	CDS	358329	358415	.	-	0	Parent=gene855
chr16	ENCODE	exon	358502	358636	.	-	.	Parent=gene855
chr16	ENCODE	CDS	358502	358636	.	-	0	Parent=gene855
chr16	ENCODE	exon	359069	359221	.	-	.	Parent=gene855
chr16	ENCODE	CDS	359069	359221	.	-	0	Parent=gene855
chr16	ENCODE	CDS	359932	360219	.	-	0	Parent=gene855
chr16	ENCODE	exon	359932	360226	.	-	.	Parent=gene855
chr16	ENCODE	exon	360500	360528	.	-	.	Parent=gene855
###
chr16	ENCODE	gene	357399	360226	.	-	.	ID=gene856;Name=Z97634.1-007;name2=MRPL28
chr16	ENCODE	exon	357399	357783	.	-	.	Parent=gene856
chr16	ENCODE	exon	358329	358415	.	-	.	Parent=gene856
chr16	ENCODE	exon	358502	359212	.	-	.	Parent=gene856
chr16	ENCODE	exon	359932	360226	.	-	.	Parent=gene856
###
chr16	ENCODE	gene	357410	360235	.	-	.	ID=gene857;Name=Z97634.1-005;name2=MRPL28
chr16	ENCODE	exon	357410	357783	.	-	.	Parent=gene857
chr16	ENCODE	CDS	357676	357783	.	-	0	Parent=gene857
chr16	ENCODE	exon	358329	358415	.	-	.	Parent=gene857
chr16	ENCODE	CDS	358329	358415	.	-	0	Parent=gene857
chr16	ENCODE	exon	358502	358627	.	-	.	Parent=gene857
chr16	ENCODE	CDS	358502	358627	.	-	0	Parent=gene857
chr16	ENCODE	exon	359060	359221	.	-	.	Parent=gene857
chr16	ENCODE	CDS	359060	359221	.	-	0	Parent=gene857
chr16	ENCODE	CDS	359932	360219	.	-	0	Parent=gene857
chr16	ENCODE	exon	359932	360235	.	-	.	Parent=gene857
###
chr16	ENCODE	gene	357428	360235	.	-	.	ID=gene858;Name=Z97634.1-003;name2=MRPL28
chr16	ENCODE	exon	357428	357783	.	-	.	Parent=gene858
chr16	ENCODE	exon	358329	358415	.	-	.	Parent=gene858
chr16	ENCODE	exon	358502	359221	.	-	.	Parent=gene858
chr16	ENCODE	exon	359932	360235	.	-	.	Parent=gene858
###
chr16	ENCODE	gene	357614	360510	.	-	.	ID=gene859;name2=MRPL28;Name=Z97634.1-008
chr16	ENCODE	exon	357614	357783	.	-	.	Parent=gene859
chr16	ENCODE	CDS	357676	357783	.	-	0	Parent=gene859
chr16	ENCODE	exon	358329	358415	.	-	.	Parent=gene859
chr16	ENCODE	CDS	358329	358415	.	-	0	Parent=gene859
chr16	ENCODE	exon	358502	358636	.	-	.	Parent=gene859
chr16	ENCODE	CDS	358502	358636	.	-	0	Parent=gene859
chr16	ENCODE	exon	359069	359221	.	-	.	Parent=gene859
chr16	ENCODE	CDS	359069	359221	.	-	0	Parent=gene859
chr16	ENCODE	CDS	359932	360219	.	-	0	Parent=gene859
chr16	ENCODE	exon	359932	360226	.	-	.	Parent=gene859
chr16	ENCODE	exon	360486	360510	.	-	.	Parent=gene859
###
chr16	ENCODE	gene	357725	360433	.	-	.	ID=gene860;Name=Z97634.1-010;name2=MRPL28
chr16	ENCODE	exon	357725	357783	.	-	.	Parent=gene860
chr16	ENCODE	CDS	357725	357783	.	-	0	Parent=gene860
chr16	ENCODE	exon	358329	358415	.	-	.	Parent=gene860
chr16	ENCODE	CDS	358329	358415	.	-	0	Parent=gene860
chr16	ENCODE	exon	358502	358636	.	-	.	Parent=gene860
chr16	ENCODE	CDS	358502	358636	.	-	0	Parent=gene860
chr16	ENCODE	exon	359069	359221	.	-	.	Parent=gene860
chr16	ENCODE	CDS	359069	359221	.	-	0	Parent=gene860
chr16	ENCODE	CDS	359932	360219	.	-	0	Parent=gene860
chr16	ENCODE	exon	359932	360226	.	-	.	Parent=gene860
chr16	ENCODE	exon	360363	360433	.	-	.	Parent=gene860
###
chr16	ENCODE	gene	358336	360503	.	-	.	ID=gene861;Name=Z97634.1-009;name2=MRPL28
chr16	ENCODE	exon	358336	358415	.	-	.	Parent=gene861
chr16	ENCODE	CDS	358336	358415	.	-	0	Parent=gene861
chr16	ENCODE	exon	358502	358636	.	-	.	Parent=gene861
chr16	ENCODE	CDS	358502	358636	.	-	0	Parent=gene861
chr16	ENCODE	exon	359069	359221	.	-	.	Parent=gene861
chr16	ENCODE	CDS	359069	359221	.	-	0	Parent=gene861
chr16	ENCODE	CDS	359932	360219	.	-	0	Parent=gene861
chr16	ENCODE	exon	359932	360226	.	-	.	Parent=gene861
chr16	ENCODE	exon	360445	360503	.	-	.	Parent=gene861
###
chr16	ENCODE	gene	358409	360339	.	-	.	ID=gene862;Name=Z97634.1-011;name2=MRPL28
chr16	ENCODE	exon	358409	358415	.	-	.	Parent=gene862
chr16	ENCODE	CDS	358409	358415	.	-	0	Parent=gene862
chr16	ENCODE	exon	358502	358636	.	-	.	Parent=gene862
chr16	ENCODE	CDS	358502	358636	.	-	0	Parent=gene862
chr16	ENCODE	exon	359069	359221	.	-	.	Parent=gene862
chr16	ENCODE	CDS	359069	359221	.	-	0	Parent=gene862
chr16	ENCODE	CDS	359932	360219	.	-	0	Parent=gene862
chr16	ENCODE	exon	359932	360226	.	-	.	Parent=gene862
chr16	ENCODE	exon	360311	360339	.	-	.	Parent=gene862
###
chr16	ENCODE	gene	360774	371983	.	-	.	ID=gene863;Name=Z97634.2-001;name2=TMEM8
chr16	ENCODE	exon	360774	362284	.	-	.	Parent=gene863
chr16	ENCODE	CDS	361988	362284	.	-	0	Parent=gene863
chr16	ENCODE	exon	362612	362728	.	-	.	Parent=gene863
chr16	ENCODE	CDS	362612	362728	.	-	0	Parent=gene863
chr16	ENCODE	exon	364006	364152	.	-	.	Parent=gene863
chr16	ENCODE	CDS	364006	364152	.	-	0	Parent=gene863
chr16	ENCODE	exon	364222	364400	.	-	.	Parent=gene863
chr16	ENCODE	CDS	364222	364400	.	-	2	Parent=gene863
chr16	ENCODE	exon	364757	364893	.	-	.	Parent=gene863
chr16	ENCODE	CDS	364757	364893	.	-	1	Parent=gene863
chr16	ENCODE	exon	365134	365257	.	-	.	Parent=gene863
chr16	ENCODE	CDS	365134	365257	.	-	2	Parent=gene863
chr16	ENCODE	exon	365346	365436	.	-	.	Parent=gene863
chr16	ENCODE	CDS	365346	365436	.	-	0	Parent=gene863
chr16	ENCODE	exon	366137	366456	.	-	.	Parent=gene863
chr16	ENCODE	CDS	366137	366456	.	-	2	Parent=gene863
chr16	ENCODE	exon	366545	366813	.	-	.	Parent=gene863
chr16	ENCODE	CDS	366545	366813	.	-	1	Parent=gene863
chr16	ENCODE	exon	367038	367165	.	-	.	Parent=gene863
chr16	ENCODE	CDS	367038	367165	.	-	0	Parent=gene863
chr16	ENCODE	exon	367379	367586	.	-	.	Parent=gene863
chr16	ENCODE	CDS	367379	367586	.	-	1	Parent=gene863
chr16	ENCODE	exon	367672	367849	.	-	.	Parent=gene863
chr16	ENCODE	CDS	367672	367849	.	-	2	Parent=gene863
chr16	ENCODE	CDS	371702	371822	.	-	0	Parent=gene863
chr16	ENCODE	exon	371702	371983	.	-	.	Parent=gene863
###
chr16	ENCODE	gene	361863	364852	.	-	.	ID=gene864;Name=Z97634.2-005;name2=TMEM8
chr16	ENCODE	exon	361863	362284	.	-	.	Parent=gene864
chr16	ENCODE	CDS	361988	362284	.	-	1	Parent=gene864
chr16	ENCODE	exon	364006	364152	.	-	.	Parent=gene864
chr16	ENCODE	CDS	364006	364152	.	-	1	Parent=gene864
chr16	ENCODE	exon	364222	364400	.	-	.	Parent=gene864
chr16	ENCODE	CDS	364222	364400	.	-	0	Parent=gene864
chr16	ENCODE	exon	364757	364852	.	-	.	Parent=gene864
chr16	ENCODE	CDS	364757	364852	.	-	0	Parent=gene864
###
chr16	ENCODE	gene	361865	371979	.	-	.	ID=gene865;Name=Z97634.2-002;name2=TMEM8
chr16	ENCODE	exon	361865	362284	.	-	.	Parent=gene865
chr16	ENCODE	exon	362612	362728	.	-	.	Parent=gene865
chr16	ENCODE	exon	364006	364152	.	-	.	Parent=gene865
chr16	ENCODE	exon	364222	364400	.	-	.	Parent=gene865
chr16	ENCODE	exon	364757	364893	.	-	.	Parent=gene865
chr16	ENCODE	exon	365134	365257	.	-	.	Parent=gene865
chr16	ENCODE	exon	365346	365436	.	-	.	Parent=gene865
chr16	ENCODE	exon	366137	366456	.	-	.	Parent=gene865
chr16	ENCODE	exon	366545	366813	.	-	.	Parent=gene865
chr16	ENCODE	exon	367038	367165	.	-	.	Parent=gene865
chr16	ENCODE	exon	367379	367586	.	-	.	Parent=gene865
chr16	ENCODE	exon	367672	367806	.	-	.	Parent=gene865
chr16	ENCODE	exon	371909	371979	.	-	.	Parent=gene865
###
chr16	ENCODE	gene	362417	365216	.	-	.	ID=gene866;Name=Z97634.2-006;name2=TMEM8
chr16	ENCODE	exon	362417	362728	.	-	.	Parent=gene866
chr16	ENCODE	exon	364006	364152	.	-	.	Parent=gene866
chr16	ENCODE	exon	364222	364400	.	-	.	Parent=gene866
chr16	ENCODE	exon	364757	364893	.	-	.	Parent=gene866
chr16	ENCODE	exon	365134	365216	.	-	.	Parent=gene866
###
chr16	ENCODE	gene	364006	365076	.	-	.	ID=gene867;Name=Z97634.2-004;name2=TMEM8
chr16	ENCODE	exon	364006	364152	.	-	.	Parent=gene867
chr16	ENCODE	exon	364222	364400	.	-	.	Parent=gene867
chr16	ENCODE	exon	364757	365076	.	-	.	Parent=gene867
###
chr16	ENCODE	gene	364810	366476	.	-	.	ID=gene868;Name=Z97634.2-003;name2=TMEM8
chr16	ENCODE	exon	364810	364893	.	-	.	Parent=gene868
chr16	ENCODE	exon	365134	365257	.	-	.	Parent=gene868
chr16	ENCODE	exon	365346	365436	.	-	.	Parent=gene868
chr16	ENCODE	exon	366137	366476	.	-	.	Parent=gene868
###
chr16	ENCODE	gene	366807	377000	.	-	.	ID=gene869;Name=Z97634.2-008;name2=TMEM8
chr16	ENCODE	exon	366807	366813	.	-	.	Parent=gene869
chr16	ENCODE	exon	367038	367165	.	-	.	Parent=gene869
chr16	ENCODE	exon	367379	367586	.	-	.	Parent=gene869
chr16	ENCODE	exon	374257	374397	.	-	.	Parent=gene869
chr16	ENCODE	exon	376898	377000	.	-	.	Parent=gene869
###
chr16	ENCODE	gene	367109	377114	.	-	.	ID=gene870;Name=Z97634.2-007;name2=TMEM8
chr16	ENCODE	exon	367109	367165	.	-	.	Parent=gene870
chr16	ENCODE	exon	367379	367586	.	-	.	Parent=gene870
chr16	ENCODE	exon	367672	367849	.	-	.	Parent=gene870
chr16	ENCODE	exon	374257	374397	.	-	.	Parent=gene870
chr16	ENCODE	exon	376898	377114	.	-	.	Parent=gene870
###
chr16	ENCODE	gene	386726	390747	.	+	.	ID=gene871;Name=Z97634.4-002;name2=NME4
chr16	ENCODE	exon	386726	387080	.	+	.	Parent=gene871
chr16	ENCODE	exon	388991	389124	.	+	.	Parent=gene871
chr16	ENCODE	CDS	389110	389124	.	+	0	Parent=gene871
chr16	ENCODE	exon	389380	389481	.	+	.	Parent=gene871
chr16	ENCODE	CDS	389380	389481	.	+	0	Parent=gene871
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene871
chr16	ENCODE	CDS	389628	389740	.	+	0	Parent=gene871
chr16	ENCODE	CDS	390220	390343	.	+	1	Parent=gene871
chr16	ENCODE	exon	390220	390747	.	+	.	Parent=gene871
###
chr16	ENCODE	gene	386770	389475	.	+	.	ID=gene872;Name=Z97634.4-005;name2=NME4
chr16	ENCODE	exon	386770	387080	.	+	.	Parent=gene872
chr16	ENCODE	exon	388209	388386	.	+	.	Parent=gene872
chr16	ENCODE	exon	388991	389124	.	+	.	Parent=gene872
chr16	ENCODE	CDS	389110	389124	.	+	0	Parent=gene872
chr16	ENCODE	exon	389380	389475	.	+	.	Parent=gene872
chr16	ENCODE	CDS	389380	389475	.	+	0	Parent=gene872
###
chr16	ENCODE	gene	387200	390735	.	+	.	ID=gene873;Name=Z97634.4-006;name2=NME4
chr16	ENCODE	exon	387200	387314	.	+	.	Parent=gene873
chr16	ENCODE	exon	388209	388395	.	+	.	Parent=gene873
chr16	ENCODE	exon	388991	389124	.	+	.	Parent=gene873
chr16	ENCODE	exon	389380	389481	.	+	.	Parent=gene873
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene873
chr16	ENCODE	exon	390220	390735	.	+	.	Parent=gene873
###
chr16	ENCODE	gene	387201	400368	.	+	.	ID=gene874;Name=Z97634.4-0012;name2=NME4
chr16	ENCODE	exon	387201	387314	.	+	.	Parent=gene874
chr16	ENCODE	exon	388991	389124	.	+	.	Parent=gene874
chr16	ENCODE	exon	389380	389481	.	+	.	Parent=gene874
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene874
chr16	ENCODE	exon	390220	390295	.	+	.	Parent=gene874
chr16	ENCODE	exon	391948	392044	.	+	.	Parent=gene874
chr16	ENCODE	exon	394957	395025	.	+	.	Parent=gene874
chr16	ENCODE	exon	396347	396398	.	+	.	Parent=gene874
chr16	ENCODE	exon	396686	396778	.	+	.	Parent=gene874
chr16	ENCODE	exon	397426	397561	.	+	.	Parent=gene874
chr16	ENCODE	exon	400244	400368	.	+	.	Parent=gene874
###
chr16	ENCODE	gene	387209	390588	.	+	.	ID=gene875;Name=Z97634.4-007;name2=NME4
chr16	ENCODE	exon	387209	387314	.	+	.	Parent=gene875
chr16	ENCODE	exon	388991	389012	.	+	.	Parent=gene875
chr16	ENCODE	exon	389067	389124	.	+	.	Parent=gene875
chr16	ENCODE	exon	389380	389481	.	+	.	Parent=gene875
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene875
chr16	ENCODE	exon	390220	390588	.	+	.	Parent=gene875
###
chr16	ENCODE	gene	387209	390634	.	+	.	ID=gene876;Name=Z97634.4-003;name2=NME4
chr16	ENCODE	exon	387209	387314	.	+	.	Parent=gene876
chr16	ENCODE	exon	388209	389124	.	+	.	Parent=gene876
chr16	ENCODE	exon	389380	389481	.	+	.	Parent=gene876
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene876
chr16	ENCODE	exon	390220	390634	.	+	.	Parent=gene876
###
chr16	ENCODE	gene	387210	390507	.	+	.	ID=gene877;Name=Z97634.4-011;name2=NME4
chr16	ENCODE	exon	387210	387314	.	+	.	Parent=gene877
chr16	ENCODE	CDS	387224	387314	.	+	0	Parent=gene877
chr16	ENCODE	exon	387880	387903	.	+	.	Parent=gene877
chr16	ENCODE	CDS	387880	387903	.	+	2	Parent=gene877
chr16	ENCODE	exon	388991	389124	.	+	.	Parent=gene877
chr16	ENCODE	CDS	388991	389124	.	+	2	Parent=gene877
chr16	ENCODE	exon	389380	389481	.	+	.	Parent=gene877
chr16	ENCODE	CDS	389380	389481	.	+	0	Parent=gene877
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene877
chr16	ENCODE	CDS	389628	389740	.	+	0	Parent=gene877
chr16	ENCODE	CDS	390220	390343	.	+	1	Parent=gene877
chr16	ENCODE	exon	390220	390507	.	+	.	Parent=gene877
###
chr16	ENCODE	gene	387210	390760	.	+	.	ID=gene878;Name=Z97634.4-001;name2=NME4
chr16	ENCODE	exon	387210	387314	.	+	.	Parent=gene878
chr16	ENCODE	CDS	387224	387314	.	+	0	Parent=gene878
chr16	ENCODE	exon	388991	389124	.	+	.	Parent=gene878
chr16	ENCODE	CDS	388991	389124	.	+	2	Parent=gene878
chr16	ENCODE	exon	389380	389481	.	+	.	Parent=gene878
chr16	ENCODE	CDS	389380	389481	.	+	0	Parent=gene878
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene878
chr16	ENCODE	CDS	389628	389740	.	+	0	Parent=gene878
chr16	ENCODE	CDS	390220	390343	.	+	1	Parent=gene878
chr16	ENCODE	exon	390220	390760	.	+	.	Parent=gene878
###
chr16	ENCODE	gene	387238	390649	.	+	.	ID=gene879;Name=Z97634.4-009;name2=NME4
chr16	ENCODE	exon	387238	387314	.	+	.	Parent=gene879
chr16	ENCODE	CDS	387238	387314	.	+	0	Parent=gene879
chr16	ENCODE	exon	388991	389124	.	+	.	Parent=gene879
chr16	ENCODE	CDS	388991	389124	.	+	1	Parent=gene879
chr16	ENCODE	exon	389380	389481	.	+	.	Parent=gene879
chr16	ENCODE	CDS	389380	389481	.	+	2	Parent=gene879
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene879
chr16	ENCODE	CDS	389628	389740	.	+	2	Parent=gene879
chr16	ENCODE	CDS	390110	390191	.	+	0	Parent=gene879
chr16	ENCODE	exon	390110	390649	.	+	.	Parent=gene879
###
chr16	ENCODE	gene	387743	390417	.	+	.	ID=gene880;Name=Z97634.4-010;name2=NME4
chr16	ENCODE	exon	387743	388180	.	+	.	Parent=gene880
chr16	ENCODE	exon	388991	389124	.	+	.	Parent=gene880
chr16	ENCODE	exon	389380	389481	.	+	.	Parent=gene880
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene880
chr16	ENCODE	exon	390220	390417	.	+	.	Parent=gene880
###
chr16	ENCODE	gene	387774	402488	.	+	.	ID=gene881;Name=Z97634.4-0013;name2=NME4
chr16	ENCODE	exon	387774	387893	.	+	.	Parent=gene881
chr16	ENCODE	exon	394986	395025	.	+	.	Parent=gene881
chr16	ENCODE	exon	396347	396398	.	+	.	Parent=gene881
chr16	ENCODE	exon	397426	397561	.	+	.	Parent=gene881
chr16	ENCODE	exon	400244	400368	.	+	.	Parent=gene881
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene881
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene881
chr16	ENCODE	exon	401362	401579	.	+	.	Parent=gene881
chr16	ENCODE	exon	401891	402488	.	+	.	Parent=gene881
###
chr16	ENCODE	gene	388411	390750	.	+	.	ID=gene882;Name=Z97634.4-004;name2=NME4
chr16	ENCODE	exon	388411	389740	.	+	.	Parent=gene882
chr16	ENCODE	exon	390220	390750	.	+	.	Parent=gene882
###
chr16	ENCODE	gene	389048	389740	.	+	.	ID=gene883;Name=Z97634.4-008;name2=NME4
chr16	ENCODE	exon	389048	389124	.	+	.	Parent=gene883
chr16	ENCODE	exon	389296	389481	.	+	.	Parent=gene883
chr16	ENCODE	exon	389628	389740	.	+	.	Parent=gene883
###
chr16	ENCODE	gene	391827	402488	.	+	.	ID=gene884;Name=AL023881.1-001;name2=DECR2
chr16	ENCODE	exon	391827	392044	.	+	.	Parent=gene884
chr16	ENCODE	CDS	391965	392044	.	+	0	Parent=gene884
chr16	ENCODE	exon	394957	395025	.	+	.	Parent=gene884
chr16	ENCODE	CDS	394957	395025	.	+	1	Parent=gene884
chr16	ENCODE	exon	396347	396398	.	+	.	Parent=gene884
chr16	ENCODE	CDS	396347	396398	.	+	1	Parent=gene884
chr16	ENCODE	exon	397426	397561	.	+	.	Parent=gene884
chr16	ENCODE	CDS	397426	397561	.	+	0	Parent=gene884
chr16	ENCODE	exon	400244	400368	.	+	.	Parent=gene884
chr16	ENCODE	CDS	400244	400368	.	+	2	Parent=gene884
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene884
chr16	ENCODE	CDS	400692	400785	.	+	0	Parent=gene884
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene884
chr16	ENCODE	CDS	400973	401077	.	+	2	Parent=gene884
chr16	ENCODE	exon	401362	401579	.	+	.	Parent=gene884
chr16	ENCODE	CDS	401362	401579	.	+	2	Parent=gene884
chr16	ENCODE	exon	401891	402488	.	+	.	Parent=gene884
###
chr16	ENCODE	gene	391859	402371	.	+	.	ID=gene885;name2=DECR2;Name=AL023881.1-005
chr16	ENCODE	exon	391859	392044	.	+	.	Parent=gene885
chr16	ENCODE	exon	394957	395025	.	+	.	Parent=gene885
chr16	ENCODE	exon	396347	396398	.	+	.	Parent=gene885
chr16	ENCODE	exon	396686	397201	.	+	.	Parent=gene885
chr16	ENCODE	exon	397296	397561	.	+	.	Parent=gene885
chr16	ENCODE	exon	400244	400368	.	+	.	Parent=gene885
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene885
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene885
chr16	ENCODE	exon	401362	401579	.	+	.	Parent=gene885
chr16	ENCODE	exon	401891	402094	.	+	.	Parent=gene885
chr16	ENCODE	exon	402121	402371	.	+	.	Parent=gene885
###
chr16	ENCODE	gene	391883	401977	.	+	.	ID=gene886;Name=AL023881.1-008;name2=DECR2
chr16	ENCODE	exon	391883	392044	.	+	.	Parent=gene886
chr16	ENCODE	CDS	391965	392044	.	+	0	Parent=gene886
chr16	ENCODE	exon	394957	395025	.	+	.	Parent=gene886
chr16	ENCODE	CDS	394957	395025	.	+	1	Parent=gene886
chr16	ENCODE	exon	396347	396362	.	+	.	Parent=gene886
chr16	ENCODE	CDS	396347	396362	.	+	1	Parent=gene886
chr16	ENCODE	exon	397426	397561	.	+	.	Parent=gene886
chr16	ENCODE	CDS	397426	397561	.	+	0	Parent=gene886
chr16	ENCODE	exon	400244	400368	.	+	.	Parent=gene886
chr16	ENCODE	CDS	400244	400368	.	+	2	Parent=gene886
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene886
chr16	ENCODE	CDS	400692	400785	.	+	0	Parent=gene886
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene886
chr16	ENCODE	CDS	400973	401077	.	+	2	Parent=gene886
chr16	ENCODE	exon	401362	401579	.	+	.	Parent=gene886
chr16	ENCODE	CDS	401362	401579	.	+	2	Parent=gene886
chr16	ENCODE	exon	401891	401977	.	+	.	Parent=gene886
###
chr16	ENCODE	gene	391883	402467	.	+	.	ID=gene887;Name=AL023881.1-004;name2=DECR2
chr16	ENCODE	exon	391883	392044	.	+	.	Parent=gene887
chr16	ENCODE	exon	394957	395040	.	+	.	Parent=gene887
chr16	ENCODE	exon	397426	397561	.	+	.	Parent=gene887
chr16	ENCODE	exon	400244	400368	.	+	.	Parent=gene887
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene887
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene887
chr16	ENCODE	exon	401362	401579	.	+	.	Parent=gene887
chr16	ENCODE	exon	401891	402467	.	+	.	Parent=gene887
###
chr16	ENCODE	gene	391894	402371	.	+	.	ID=gene888;Name=AL023881.1-003;name2=DECR2
chr16	ENCODE	exon	391894	392044	.	+	.	Parent=gene888
chr16	ENCODE	exon	394957	395025	.	+	.	Parent=gene888
chr16	ENCODE	exon	395514	395666	.	+	.	Parent=gene888
chr16	ENCODE	exon	396347	396398	.	+	.	Parent=gene888
chr16	ENCODE	exon	397426	397561	.	+	.	Parent=gene888
chr16	ENCODE	exon	400210	400368	.	+	.	Parent=gene888
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene888
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene888
chr16	ENCODE	exon	401362	401579	.	+	.	Parent=gene888
chr16	ENCODE	exon	401891	402371	.	+	.	Parent=gene888
###
chr16	ENCODE	gene	391916	402488	.	+	.	ID=gene889;Name=AL023881.1-006;name2=DECR2
chr16	ENCODE	exon	391916	392044	.	+	.	Parent=gene889
chr16	ENCODE	exon	394957	395025	.	+	.	Parent=gene889
chr16	ENCODE	exon	396347	396398	.	+	.	Parent=gene889
chr16	ENCODE	exon	396686	396834	.	+	.	Parent=gene889
chr16	ENCODE	exon	396891	396953	.	+	.	Parent=gene889
chr16	ENCODE	exon	397426	397561	.	+	.	Parent=gene889
chr16	ENCODE	exon	400244	400368	.	+	.	Parent=gene889
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene889
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene889
chr16	ENCODE	exon	401362	401579	.	+	.	Parent=gene889
chr16	ENCODE	exon	401891	402488	.	+	.	Parent=gene889
###
chr16	ENCODE	gene	391927	401472	.	+	.	ID=gene890;Name=AL023881.1-009;name2=DECR2
chr16	ENCODE	exon	391927	392044	.	+	.	Parent=gene890
chr16	ENCODE	exon	394957	395025	.	+	.	Parent=gene890
chr16	ENCODE	exon	396347	396398	.	+	.	Parent=gene890
chr16	ENCODE	exon	396686	396953	.	+	.	Parent=gene890
chr16	ENCODE	exon	397426	397561	.	+	.	Parent=gene890
chr16	ENCODE	exon	400244	400368	.	+	.	Parent=gene890
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene890
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene890
chr16	ENCODE	exon	401362	401472	.	+	.	Parent=gene890
###
chr16	ENCODE	gene	392006	397172	.	+	.	ID=gene891;name2=DECR2;Name=AL023881.1-010
chr16	ENCODE	exon	392006	392044	.	+	.	Parent=gene891
chr16	ENCODE	exon	394957	395025	.	+	.	Parent=gene891
chr16	ENCODE	exon	396347	396834	.	+	.	Parent=gene891
chr16	ENCODE	exon	396891	397172	.	+	.	Parent=gene891
###
chr16	ENCODE	gene	396896	402488	.	+	.	ID=gene892;Name=AL023881.1-015;name2=DECR2
chr16	ENCODE	exon	396896	396953	.	+	.	Parent=gene892
chr16	ENCODE	exon	400244	400405	.	+	.	Parent=gene892
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene892
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene892
chr16	ENCODE	exon	401891	402488	.	+	.	Parent=gene892
###
chr16	ENCODE	gene	396947	400296	.	+	.	ID=gene893;Name=AL023881.1-012;name2=DECR2
chr16	ENCODE	exon	396947	397561	.	+	.	Parent=gene893
chr16	ENCODE	exon	400210	400296	.	+	.	Parent=gene893
###
chr16	ENCODE	gene	397428	401929	.	+	.	ID=gene894;Name=AL023881.1-014;name2=DECR2
chr16	ENCODE	exon	397428	397561	.	+	.	Parent=gene894
chr16	ENCODE	exon	400244	400405	.	+	.	Parent=gene894
chr16	ENCODE	exon	400692	400754	.	+	.	Parent=gene894
chr16	ENCODE	exon	400973	401077	.	+	.	Parent=gene894
chr16	ENCODE	exon	401362	401579	.	+	.	Parent=gene894
chr16	ENCODE	exon	401891	401929	.	+	.	Parent=gene894
###
chr16	ENCODE	gene	399600	402482	.	+	.	ID=gene895;name2=DECR2;Name=AL023881.1-007
chr16	ENCODE	exon	399600	400368	.	+	.	Parent=gene895
chr16	ENCODE	exon	400692	400785	.	+	.	Parent=gene895
chr16	ENCODE	exon	400973	401579	.	+	.	Parent=gene895
chr16	ENCODE	exon	401891	402482	.	+	.	Parent=gene895
###
chr16	ENCODE	gene	400113	401051	.	+	.	ID=gene896;Name=AL023881.1-013;name2=DECR2
chr16	ENCODE	exon	400113	400368	.	+	.	Parent=gene896
chr16	ENCODE	exon	400692	401051	.	+	.	Parent=gene896
###
chr16	ENCODE	gene	415620	495628	.	+	.	ID=gene897;Name=Z98882.1-001;name2=RAB11FIP3
chr16	ENCODE	exon	415620	416721	.	+	.	Parent=gene897
chr16	ENCODE	exon	451405	451498	.	+	.	Parent=gene897
chr16	ENCODE	exon	461296	461390	.	+	.	Parent=gene897
chr16	ENCODE	exon	472526	472737	.	+	.	Parent=gene897
chr16	ENCODE	exon	478852	479001	.	+	.	Parent=gene897
chr16	ENCODE	exon	486825	486860	.	+	.	Parent=gene897
chr16	ENCODE	exon	493005	493098	.	+	.	Parent=gene897
chr16	ENCODE	exon	495525	495628	.	+	.	Parent=gene897
###
chr16	ENCODE	gene	464870	495606	.	+	.	ID=gene898;Name=Z98882.1-002;name2=RAB11FIP3
chr16	ENCODE	exon	464870	465099	.	+	.	Parent=gene898
chr16	ENCODE	exon	472526	472737	.	+	.	Parent=gene898
chr16	ENCODE	CDS	472553	472737	.	+	0	Parent=gene898
chr16	ENCODE	exon	478852	479001	.	+	.	Parent=gene898
chr16	ENCODE	CDS	478852	479001	.	+	1	Parent=gene898
chr16	ENCODE	exon	486825	486860	.	+	.	Parent=gene898
chr16	ENCODE	CDS	486825	486860	.	+	1	Parent=gene898
chr16	ENCODE	exon	493005	493098	.	+	.	Parent=gene898
chr16	ENCODE	CDS	493005	493098	.	+	1	Parent=gene898
chr16	ENCODE	exon	495525	495606	.	+	.	Parent=gene898
chr16	ENCODE	CDS	495525	495606	.	+	0	Parent=gene898
###
chr16	ENCODE	gene	464925	479102	.	+	.	ID=gene899;Name=Z98882.1-008;name2=RAB11FIP3
chr16	ENCODE	exon	464925	465046	.	+	.	Parent=gene899
chr16	ENCODE	exon	472526	472737	.	+	.	Parent=gene899
chr16	ENCODE	exon	478852	479102	.	+	.	Parent=gene899
###
chr16	ENCODE	gene	464925	493064	.	+	.	ID=gene900;Name=Z98882.1-009;name2=RAB11FIP3
chr16	ENCODE	exon	464925	465046	.	+	.	Parent=gene900
chr16	ENCODE	CDS	465032	465046	.	+	0	Parent=gene900
chr16	ENCODE	exon	472526	472737	.	+	.	Parent=gene900
chr16	ENCODE	CDS	472526	472737	.	+	0	Parent=gene900
chr16	ENCODE	exon	478852	479001	.	+	.	Parent=gene900
chr16	ENCODE	CDS	478852	479001	.	+	1	Parent=gene900
chr16	ENCODE	exon	486825	486860	.	+	.	Parent=gene900
chr16	ENCODE	CDS	486825	486860	.	+	1	Parent=gene900
chr16	ENCODE	exon	493005	493064	.	+	.	Parent=gene900
chr16	ENCODE	CDS	493005	493064	.	+	1	Parent=gene900
###
chr16	ENCODE	gene	472658	487449	.	+	.	ID=gene901;Name=Z98882.1-004;name2=RAB11FIP3
chr16	ENCODE	exon	472658	472737	.	+	.	Parent=gene901
chr16	ENCODE	exon	478852	479001	.	+	.	Parent=gene901
chr16	ENCODE	exon	481135	481269	.	+	.	Parent=gene901
chr16	ENCODE	exon	486825	486860	.	+	.	Parent=gene901
chr16	ENCODE	exon	487293	487449	.	+	.	Parent=gene901
###
chr16	ENCODE	gene	478943	487159	.	+	.	ID=gene902;Name=Z98882.1-003;name2=RAB11FIP3
chr16	ENCODE	exon	478943	479001	.	+	.	Parent=gene902
chr16	ENCODE	exon	481135	481269	.	+	.	Parent=gene902
chr16	ENCODE	exon	486825	487159	.	+	.	Parent=gene902
###
chr16	ENCODE	gene	492751	495628	.	+	.	ID=gene903;Name=Z98882.1-005;name2=RAB11FIP3
chr16	ENCODE	exon	492751	493098	.	+	.	Parent=gene903
chr16	ENCODE	exon	495525	495628	.	+	.	Parent=gene903
###
chr16	ENCODE	gene	25805568	26055029	.	+	.	ID=gene904;Name=AC093511.1-002;name2=HS3ST4
chr16	ENCODE	exon	25805568	25805743	.	+	.	Parent=gene904
chr16	ENCODE	exon	26054434	26055029	.	+	.	Parent=gene904
###
chr16	ENCODE	gene	26054434	26056510	.	+	.	ID=gene905;Name=AC093511.1-001;name2=HS3ST4
chr16	ENCODE	exon	26054434	26056510	.	+	.	Parent=gene905
###
chr18	ENCODE	gene	23784928	24011408	.	-	.	ID=gene906;Name=AC110015.1-001;name2=CDH2
chr18	ENCODE	exon	23784928	23786321	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23786115	23786321	.	-	0	Parent=gene906
chr18	ENCODE	exon	23797319	23797483	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23797319	23797483	.	-	0	Parent=gene906
chr18	ENCODE	exon	23816906	23817045	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23816906	23817045	.	-	2	Parent=gene906
chr18	ENCODE	exon	23818962	23819195	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23818962	23819195	.	-	2	Parent=gene906
chr18	ENCODE	exon	23819490	23819723	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23819490	23819723	.	-	2	Parent=gene906
chr18	ENCODE	exon	23822486	23822628	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23822486	23822628	.	-	1	Parent=gene906
chr18	ENCODE	exon	23824059	23824312	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23824059	23824312	.	-	0	Parent=gene906
chr18	ENCODE	exon	23826617	23826802	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23826617	23826802	.	-	0	Parent=gene906
chr18	ENCODE	exon	23827462	23827599	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23827462	23827599	.	-	0	Parent=gene906
chr18	ENCODE	exon	23836959	23837131	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23836959	23837131	.	-	2	Parent=gene906
chr18	ENCODE	exon	23839811	23839955	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23839811	23839955	.	-	0	Parent=gene906
chr18	ENCODE	exon	23843679	23843834	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23843679	23843834	.	-	0	Parent=gene906
chr18	ENCODE	exon	23845808	23845954	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23845808	23845954	.	-	0	Parent=gene906
chr18	ENCODE	exon	23847645	23847871	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23847645	23847871	.	-	2	Parent=gene906
chr18	ENCODE	exon	23981635	23981746	.	-	.	Parent=gene906
chr18	ENCODE	CDS	23981635	23981746	.	-	0	Parent=gene906
chr18	ENCODE	CDS	24010925	24010984	.	-	0	Parent=gene906
chr18	ENCODE	exon	24010925	24011408	.	-	.	Parent=gene906
###
chr18	ENCODE	gene	23785043	23870547	.	-	.	ID=gene907;Name=AC110015.1-003;name2=CDH2
chr18	ENCODE	exon	23785043	23786321	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23786115	23786321	.	-	0	Parent=gene907
chr18	ENCODE	exon	23797319	23797483	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23797319	23797483	.	-	0	Parent=gene907
chr18	ENCODE	exon	23816906	23817045	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23816906	23817045	.	-	2	Parent=gene907
chr18	ENCODE	exon	23818962	23819195	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23818962	23819195	.	-	2	Parent=gene907
chr18	ENCODE	exon	23819490	23819723	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23819490	23819723	.	-	2	Parent=gene907
chr18	ENCODE	exon	23822486	23822628	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23822486	23822628	.	-	1	Parent=gene907
chr18	ENCODE	exon	23824059	23824312	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23824059	23824312	.	-	0	Parent=gene907
chr18	ENCODE	exon	23826617	23826802	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23826617	23826802	.	-	0	Parent=gene907
chr18	ENCODE	exon	23827462	23827599	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23827462	23827599	.	-	0	Parent=gene907
chr18	ENCODE	exon	23836959	23837131	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23836959	23837131	.	-	2	Parent=gene907
chr18	ENCODE	exon	23839811	23839955	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23839811	23839955	.	-	0	Parent=gene907
chr18	ENCODE	exon	23843679	23843834	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23843679	23843834	.	-	0	Parent=gene907
chr18	ENCODE	exon	23845808	23845954	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23845808	23845954	.	-	0	Parent=gene907
chr18	ENCODE	exon	23847645	23847871	.	-	.	Parent=gene907
chr18	ENCODE	CDS	23847645	23847871	.	-	2	Parent=gene907
chr18	ENCODE	CDS	23870432	23870510	.	-	0	Parent=gene907
chr18	ENCODE	exon	23870432	23870547	.	-	.	Parent=gene907
###
chr18	ENCODE	gene	23839932	23879558	.	-	.	ID=gene908;Name=AC110015.1-002;name2=CDH2
chr18	ENCODE	exon	23839932	23839955	.	-	.	Parent=gene908
chr18	ENCODE	CDS	23839932	23839955	.	-	0	Parent=gene908
chr18	ENCODE	exon	23843679	23843834	.	-	.	Parent=gene908
chr18	ENCODE	CDS	23843679	23843834	.	-	0	Parent=gene908
chr18	ENCODE	exon	23845808	23845954	.	-	.	Parent=gene908
chr18	ENCODE	CDS	23845808	23845954	.	-	0	Parent=gene908
chr18	ENCODE	exon	23847645	23847871	.	-	.	Parent=gene908
chr18	ENCODE	CDS	23847645	23847871	.	-	2	Parent=gene908
chr18	ENCODE	CDS	23879373	23879391	.	-	0	Parent=gene908
chr18	ENCODE	exon	23879373	23879558	.	-	.	Parent=gene908
###
chr18	ENCODE	gene	23843766	23931191	.	-	.	ID=gene909;Name=AC110015.1-005;name2=CDH2
chr18	ENCODE	exon	23843766	23843834	.	-	.	Parent=gene909
chr18	ENCODE	exon	23845808	23845954	.	-	.	Parent=gene909
chr18	ENCODE	exon	23847645	23847871	.	-	.	Parent=gene909
chr18	ENCODE	exon	23931025	23931191	.	-	.	Parent=gene909
###
chr18	ENCODE	gene	23845880	23993259	.	-	.	ID=gene910;Name=AC110015.1-004;name2=CDH2
chr18	ENCODE	exon	23845880	23845954	.	-	.	Parent=gene910
chr18	ENCODE	exon	23847645	23847871	.	-	.	Parent=gene910
chr18	ENCODE	exon	23981635	23981746	.	-	.	Parent=gene910
chr18	ENCODE	exon	23993111	23993259	.	-	.	Parent=gene910
###
chr18	ENCODE	gene	59412569	59416957	.	+	.	ID=gene911;Name=AC090307.1-002;name2=SERPINB13
chr18	ENCODE	exon	59412569	59412711	.	+	.	Parent=gene911
chr18	ENCODE	exon	59413243	59413398	.	+	.	Parent=gene911
chr18	ENCODE	exon	59415173	59416957	.	+	.	Parent=gene911
###
chr18	ENCODE	gene	59412569	59417413	.	+	.	ID=gene912;Name=AC090307.1-001;name2=SERPINB13
chr18	ENCODE	exon	59412569	59412711	.	+	.	Parent=gene912
chr18	ENCODE	exon	59413243	59413398	.	+	.	Parent=gene912
chr18	ENCODE	exon	59415173	59417413	.	+	.	Parent=gene912
###
chr18	ENCODE	gene	59413243	59422853	.	+	.	ID=gene913;name2=SERPINB13;Name=AC090307.1-004
chr18	ENCODE	exon	59413243	59413398	.	+	.	Parent=gene913
chr18	ENCODE	exon	59422154	59422853	.	+	.	Parent=gene913
###
chr18	ENCODE	gene	59455473	59462512	.	-	.	ID=gene914;Name=AC069356.2-001;name2=SERPINB4
chr18	ENCODE	exon	59455473	59456337	.	-	.	Parent=gene914
chr18	ENCODE	CDS	59455933	59456337	.	-	0	Parent=gene914
chr18	ENCODE	exon	59457399	59457554	.	-	.	Parent=gene914
chr18	ENCODE	CDS	59457399	59457554	.	-	0	Parent=gene914
chr18	ENCODE	exon	59457848	59457990	.	-	.	Parent=gene914
chr18	ENCODE	CDS	59457848	59457990	.	-	2	Parent=gene914
chr18	ENCODE	exon	59459088	59459205	.	-	.	Parent=gene914
chr18	ENCODE	CDS	59459088	59459205	.	-	0	Parent=gene914
chr18	ENCODE	exon	59459974	59460102	.	-	.	Parent=gene914
chr18	ENCODE	CDS	59459974	59460102	.	-	0	Parent=gene914
chr18	ENCODE	exon	59461375	59461431	.	-	.	Parent=gene914
chr18	ENCODE	CDS	59461375	59461431	.	-	0	Parent=gene914
chr18	ENCODE	CDS	59461627	59461791	.	-	0	Parent=gene914
chr18	ENCODE	exon	59461627	59461817	.	-	.	Parent=gene914
chr18	ENCODE	exon	59462423	59462512	.	-	.	Parent=gene914
###
chr18	ENCODE	gene	59455932	59461796	.	-	.	ID=gene915;Name=AC069356.2-002;name2=SERPINB4
chr18	ENCODE	exon	59455932	59456337	.	-	.	Parent=gene915
chr18	ENCODE	CDS	59455933	59456337	.	-	1	Parent=gene915
chr18	ENCODE	exon	59457399	59457491	.	-	.	Parent=gene915
chr18	ENCODE	CDS	59457399	59457491	.	-	1	Parent=gene915
chr18	ENCODE	exon	59457848	59457990	.	-	.	Parent=gene915
chr18	ENCODE	CDS	59457848	59457990	.	-	0	Parent=gene915
chr18	ENCODE	exon	59459088	59459205	.	-	.	Parent=gene915
chr18	ENCODE	CDS	59459088	59459205	.	-	1	Parent=gene915
chr18	ENCODE	exon	59459974	59460102	.	-	.	Parent=gene915
chr18	ENCODE	CDS	59459974	59460102	.	-	1	Parent=gene915
chr18	ENCODE	exon	59461375	59461431	.	-	.	Parent=gene915
chr18	ENCODE	CDS	59461375	59461431	.	-	1	Parent=gene915
chr18	ENCODE	exon	59461627	59461796	.	-	.	Parent=gene915
chr18	ENCODE	CDS	59461627	59461796	.	-	0	Parent=gene915
###
chr18	ENCODE	gene	59457403	59462470	.	-	.	ID=gene916;name2=SERPINB4;Name=AC069356.2-004
chr18	ENCODE	exon	59457403	59457554	.	-	.	Parent=gene916
chr18	ENCODE	CDS	59457403	59457554	.	-	0	Parent=gene916
chr18	ENCODE	exon	59457848	59457990	.	-	.	Parent=gene916
chr18	ENCODE	CDS	59457848	59457990	.	-	2	Parent=gene916
chr18	ENCODE	exon	59459088	59459205	.	-	.	Parent=gene916
chr18	ENCODE	CDS	59459088	59459205	.	-	0	Parent=gene916
chr18	ENCODE	exon	59461375	59461431	.	-	.	Parent=gene916
chr18	ENCODE	CDS	59461375	59461431	.	-	0	Parent=gene916
chr18	ENCODE	CDS	59461627	59461791	.	-	0	Parent=gene916
chr18	ENCODE	exon	59461627	59461817	.	-	.	Parent=gene916
chr18	ENCODE	exon	59462423	59462470	.	-	.	Parent=gene916
###
chr18	ENCODE	gene	59461111	59462469	.	-	.	ID=gene917;Name=AC069356.2-003;name2=SERPINB4
chr18	ENCODE	exon	59461111	59461431	.	-	.	Parent=gene917
chr18	ENCODE	exon	59461627	59461817	.	-	.	Parent=gene917
chr18	ENCODE	exon	59462423	59462469	.	-	.	Parent=gene917
###
chr18	ENCODE	gene	59473411	59480177	.	-	.	ID=gene918;Name=AC069356.1-001;name2=SERPINB3
chr18	ENCODE	exon	59473411	59474275	.	-	.	Parent=gene918
chr18	ENCODE	CDS	59473871	59474275	.	-	0	Parent=gene918
chr18	ENCODE	exon	59475045	59475200	.	-	.	Parent=gene918
chr18	ENCODE	CDS	59475045	59475200	.	-	0	Parent=gene918
chr18	ENCODE	exon	59475484	59475626	.	-	.	Parent=gene918
chr18	ENCODE	CDS	59475484	59475626	.	-	2	Parent=gene918
chr18	ENCODE	exon	59476727	59476844	.	-	.	Parent=gene918
chr18	ENCODE	CDS	59476727	59476844	.	-	0	Parent=gene918
chr18	ENCODE	exon	59477613	59477741	.	-	.	Parent=gene918
chr18	ENCODE	CDS	59477613	59477741	.	-	0	Parent=gene918
chr18	ENCODE	exon	59479014	59479070	.	-	.	Parent=gene918
chr18	ENCODE	CDS	59479014	59479070	.	-	0	Parent=gene918
chr18	ENCODE	CDS	59479266	59479430	.	-	0	Parent=gene918
chr18	ENCODE	exon	59479266	59479456	.	-	.	Parent=gene918
chr18	ENCODE	exon	59480060	59480177	.	-	.	Parent=gene918
###
chr18	ENCODE	gene	59473412	59480098	.	-	.	ID=gene919;Name=AC069356.1-002;name2=SERPINB3
chr18	ENCODE	exon	59473412	59474275	.	-	.	Parent=gene919
chr18	ENCODE	CDS	59473871	59474275	.	-	0	Parent=gene919
chr18	ENCODE	exon	59475484	59475626	.	-	.	Parent=gene919
chr18	ENCODE	CDS	59475484	59475626	.	-	2	Parent=gene919
chr18	ENCODE	exon	59476727	59476844	.	-	.	Parent=gene919
chr18	ENCODE	CDS	59476727	59476844	.	-	0	Parent=gene919
chr18	ENCODE	exon	59477613	59477741	.	-	.	Parent=gene919
chr18	ENCODE	CDS	59477613	59477741	.	-	0	Parent=gene919
chr18	ENCODE	exon	59479014	59479070	.	-	.	Parent=gene919
chr18	ENCODE	CDS	59479014	59479070	.	-	0	Parent=gene919
chr18	ENCODE	CDS	59479266	59479430	.	-	0	Parent=gene919
chr18	ENCODE	exon	59479266	59479456	.	-	.	Parent=gene919
chr18	ENCODE	exon	59480060	59480098	.	-	.	Parent=gene919
###
chr18	ENCODE	gene	59571149	59614526	.	+	.	ID=gene920;Name=AC072051.1-002;name2=SERPINB7
chr18	ENCODE	exon	59571149	59571334	.	+	.	Parent=gene920
chr18	ENCODE	exon	59600569	59600754	.	+	.	Parent=gene920
chr18	ENCODE	CDS	59600587	59600754	.	+	0	Parent=gene920
chr18	ENCODE	exon	59610607	59610657	.	+	.	Parent=gene920
chr18	ENCODE	CDS	59610607	59610657	.	+	0	Parent=gene920
chr18	ENCODE	exon	59611375	59611491	.	+	.	Parent=gene920
chr18	ENCODE	CDS	59611375	59611491	.	+	0	Parent=gene920
chr18	ENCODE	exon	59614480	59614526	.	+	.	Parent=gene920
chr18	ENCODE	CDS	59614480	59614526	.	+	0	Parent=gene920
###
chr18	ENCODE	gene	59593624	59623584	.	+	.	ID=gene921;Name=AC072051.1-001;name2=SERPINB7
chr18	ENCODE	exon	59593624	59593930	.	+	.	Parent=gene921
chr18	ENCODE	exon	59600569	59600754	.	+	.	Parent=gene921
chr18	ENCODE	CDS	59600587	59600754	.	+	0	Parent=gene921
chr18	ENCODE	exon	59610607	59610657	.	+	.	Parent=gene921
chr18	ENCODE	CDS	59610607	59610657	.	+	0	Parent=gene921
chr18	ENCODE	exon	59611375	59611491	.	+	.	Parent=gene921
chr18	ENCODE	CDS	59611375	59611491	.	+	0	Parent=gene921
chr18	ENCODE	exon	59614480	59614597	.	+	.	Parent=gene921
chr18	ENCODE	CDS	59614480	59614597	.	+	0	Parent=gene921
chr18	ENCODE	exon	59616818	59616960	.	+	.	Parent=gene921
chr18	ENCODE	CDS	59616818	59616960	.	+	2	Parent=gene921
chr18	ENCODE	exon	59619080	59619226	.	+	.	Parent=gene921
chr18	ENCODE	CDS	59619080	59619226	.	+	0	Parent=gene921
chr18	ENCODE	CDS	59622451	59622849	.	+	0	Parent=gene921
chr18	ENCODE	exon	59622451	59623584	.	+	.	Parent=gene921
###
chr18	ENCODE	gene	59595991	59616857	.	+	.	ID=gene922;name2=SERPINB7;Name=AC072051.1-004
chr18	ENCODE	exon	59595991	59596039	.	+	.	Parent=gene922
chr18	ENCODE	exon	59600569	59600754	.	+	.	Parent=gene922
chr18	ENCODE	CDS	59600587	59600754	.	+	0	Parent=gene922
chr18	ENCODE	exon	59610607	59610657	.	+	.	Parent=gene922
chr18	ENCODE	CDS	59610607	59610657	.	+	0	Parent=gene922
chr18	ENCODE	exon	59611375	59611491	.	+	.	Parent=gene922
chr18	ENCODE	CDS	59611375	59611491	.	+	0	Parent=gene922
chr18	ENCODE	exon	59614480	59614597	.	+	.	Parent=gene922
chr18	ENCODE	CDS	59614480	59614597	.	+	0	Parent=gene922
chr18	ENCODE	exon	59616818	59616857	.	+	.	Parent=gene922
chr18	ENCODE	CDS	59616818	59616857	.	+	2	Parent=gene922
###
chr18	ENCODE	gene	59596191	59614527	.	+	.	ID=gene923;Name=AC072051.1-005;name2=SERPINB7
chr18	ENCODE	exon	59596191	59596348	.	+	.	Parent=gene923
chr18	ENCODE	exon	59600569	59600754	.	+	.	Parent=gene923
chr18	ENCODE	CDS	59600587	59600754	.	+	0	Parent=gene923
chr18	ENCODE	exon	59610607	59610657	.	+	.	Parent=gene923
chr18	ENCODE	CDS	59610607	59610657	.	+	0	Parent=gene923
chr18	ENCODE	exon	59611375	59611491	.	+	.	Parent=gene923
chr18	ENCODE	CDS	59611375	59611491	.	+	0	Parent=gene923
chr18	ENCODE	exon	59614480	59614527	.	+	.	Parent=gene923
chr18	ENCODE	CDS	59614480	59614527	.	+	0	Parent=gene923
###
chr18	ENCODE	gene	59619580	59623496	.	+	.	ID=gene924;Name=AC072051.1-003;name2=SERPINB7
chr18	ENCODE	exon	59619580	59623496	.	+	.	Parent=gene924
###
chr18	ENCODE	gene	59689906	59715357	.	+	.	ID=gene925;Name=AC072051.2-005;name2=SERPINB2
chr18	ENCODE	exon	59689906	59690014	.	+	.	Parent=gene925
chr18	ENCODE	exon	59708052	59708309	.	+	.	Parent=gene925
chr18	ENCODE	exon	59709650	59709826	.	+	.	Parent=gene925
chr18	ENCODE	CDS	59709659	59709826	.	+	0	Parent=gene925
chr18	ENCODE	exon	59713478	59713597	.	+	.	Parent=gene925
chr18	ENCODE	CDS	59713478	59713597	.	+	0	Parent=gene925
chr18	ENCODE	exon	59715305	59715357	.	+	.	Parent=gene925
chr18	ENCODE	CDS	59715305	59715357	.	+	0	Parent=gene925
###
chr18	ENCODE	gene	59705914	59722104	.	+	.	ID=gene926;Name=AC072051.2-001;name2=SERPINB2
chr18	ENCODE	exon	59705914	59705984	.	+	.	Parent=gene926
chr18	ENCODE	exon	59709650	59709826	.	+	.	Parent=gene926
chr18	ENCODE	CDS	59709659	59709826	.	+	0	Parent=gene926
chr18	ENCODE	exon	59713478	59713597	.	+	.	Parent=gene926
chr18	ENCODE	CDS	59713478	59713597	.	+	0	Parent=gene926
chr18	ENCODE	exon	59715305	59715433	.	+	.	Parent=gene926
chr18	ENCODE	CDS	59715305	59715433	.	+	0	Parent=gene926
chr18	ENCODE	exon	59715941	59716058	.	+	.	Parent=gene926
chr18	ENCODE	CDS	59715941	59716058	.	+	0	Parent=gene926
chr18	ENCODE	exon	59719954	59720096	.	+	.	Parent=gene926
chr18	ENCODE	CDS	59719954	59720096	.	+	2	Parent=gene926
chr18	ENCODE	exon	59720618	59720782	.	+	.	Parent=gene926
chr18	ENCODE	CDS	59720618	59720782	.	+	0	Parent=gene926
chr18	ENCODE	CDS	59721115	59721519	.	+	0	Parent=gene926
chr18	ENCODE	exon	59721115	59722104	.	+	.	Parent=gene926
###
chr18	ENCODE	gene	59705973	59716006	.	+	.	ID=gene927;Name=AC072051.2-002;name2=SERPINB2
chr18	ENCODE	exon	59705973	59705984	.	+	.	Parent=gene927
chr18	ENCODE	exon	59708052	59708309	.	+	.	Parent=gene927
chr18	ENCODE	exon	59709650	59709826	.	+	.	Parent=gene927
chr18	ENCODE	CDS	59709659	59709826	.	+	0	Parent=gene927
chr18	ENCODE	exon	59713478	59713597	.	+	.	Parent=gene927
chr18	ENCODE	CDS	59713478	59713597	.	+	0	Parent=gene927
chr18	ENCODE	exon	59715305	59715433	.	+	.	Parent=gene927
chr18	ENCODE	CDS	59715305	59715433	.	+	0	Parent=gene927
chr18	ENCODE	exon	59715941	59716006	.	+	.	Parent=gene927
chr18	ENCODE	CDS	59715941	59716006	.	+	0	Parent=gene927
###
chr18	ENCODE	gene	59708771	59715414	.	+	.	ID=gene928;Name=AC072051.2-003;name2=SERPINB2
chr18	ENCODE	exon	59708771	59709114	.	+	.	Parent=gene928
chr18	ENCODE	exon	59709650	59709826	.	+	.	Parent=gene928
chr18	ENCODE	CDS	59709659	59709826	.	+	0	Parent=gene928
chr18	ENCODE	exon	59713478	59713597	.	+	.	Parent=gene928
chr18	ENCODE	CDS	59713478	59713597	.	+	0	Parent=gene928
chr18	ENCODE	exon	59715305	59715414	.	+	.	Parent=gene928
chr18	ENCODE	CDS	59715305	59715414	.	+	0	Parent=gene928
###
chr18	ENCODE	gene	59710831	59720767	.	+	.	ID=gene929;Name=AC072051.2-004;name2=SERPINB2
chr18	ENCODE	exon	59710831	59710954	.	+	.	Parent=gene929
chr18	ENCODE	exon	59713478	59713597	.	+	.	Parent=gene929
chr18	ENCODE	exon	59715305	59715433	.	+	.	Parent=gene929
chr18	ENCODE	exon	59715941	59716058	.	+	.	Parent=gene929
chr18	ENCODE	exon	59719954	59720096	.	+	.	Parent=gene929
chr18	ENCODE	exon	59720618	59720767	.	+	.	Parent=gene929
###
chr18	ENCODE	gene	59715388	59735704	.	+	.	ID=gene930;Name=AC009802.1-003;name2=SERPINB10
chr18	ENCODE	exon	59715388	59715433	.	+	.	Parent=gene930
chr18	ENCODE	CDS	59715388	59715433	.	+	0	Parent=gene930
chr18	ENCODE	exon	59715941	59716058	.	+	.	Parent=gene930
chr18	ENCODE	CDS	59715941	59716058	.	+	2	Parent=gene930
chr18	ENCODE	exon	59719954	59720096	.	+	.	Parent=gene930
chr18	ENCODE	CDS	59719954	59720096	.	+	1	Parent=gene930
chr18	ENCODE	exon	59720618	59720782	.	+	.	Parent=gene930
chr18	ENCODE	CDS	59720618	59720782	.	+	2	Parent=gene930
chr18	ENCODE	exon	59721115	59721189	.	+	.	Parent=gene930
chr18	ENCODE	CDS	59721115	59721189	.	+	2	Parent=gene930
chr18	ENCODE	exon	59733716	59733892	.	+	.	Parent=gene930
chr18	ENCODE	CDS	59733716	59733892	.	+	2	Parent=gene930
chr18	ENCODE	exon	59735670	59735704	.	+	.	Parent=gene930
chr18	ENCODE	CDS	59735670	59735704	.	+	2	Parent=gene930
###
chr18	ENCODE	gene	59715388	59735704	.	+	.	ID=gene931;Name=AC009802.1-002;name2=SERPINB10
chr18	ENCODE	exon	59715388	59715433	.	+	.	Parent=gene931
chr18	ENCODE	CDS	59715388	59715433	.	+	0	Parent=gene931
chr18	ENCODE	exon	59715941	59716058	.	+	.	Parent=gene931
chr18	ENCODE	CDS	59715941	59716058	.	+	2	Parent=gene931
chr18	ENCODE	exon	59719954	59720096	.	+	.	Parent=gene931
chr18	ENCODE	CDS	59719954	59720096	.	+	1	Parent=gene931
chr18	ENCODE	exon	59720618	59720782	.	+	.	Parent=gene931
chr18	ENCODE	CDS	59720618	59720782	.	+	2	Parent=gene931
chr18	ENCODE	exon	59721115	59721189	.	+	.	Parent=gene931
chr18	ENCODE	CDS	59721115	59721189	.	+	2	Parent=gene931
chr18	ENCODE	exon	59726174	59726254	.	+	.	Parent=gene931
chr18	ENCODE	CDS	59726174	59726254	.	+	2	Parent=gene931
chr18	ENCODE	exon	59733716	59733892	.	+	.	Parent=gene931
chr18	ENCODE	CDS	59733716	59733892	.	+	2	Parent=gene931
chr18	ENCODE	exon	59735670	59735704	.	+	.	Parent=gene931
chr18	ENCODE	CDS	59735670	59735704	.	+	2	Parent=gene931
###
chr18	ENCODE	gene	59726205	59754325	.	+	.	ID=gene932;Name=AC009802.1-001;name2=SERPINB10
chr18	ENCODE	exon	59726205	59726254	.	+	.	Parent=gene932
chr18	ENCODE	exon	59733716	59733892	.	+	.	Parent=gene932
chr18	ENCODE	CDS	59733725	59733892	.	+	0	Parent=gene932
chr18	ENCODE	exon	59735670	59735735	.	+	.	Parent=gene932
chr18	ENCODE	CDS	59735670	59735735	.	+	0	Parent=gene932
chr18	ENCODE	exon	59736179	59736316	.	+	.	Parent=gene932
chr18	ENCODE	CDS	59736179	59736316	.	+	0	Parent=gene932
chr18	ENCODE	exon	59738002	59738119	.	+	.	Parent=gene932
chr18	ENCODE	CDS	59738002	59738119	.	+	0	Parent=gene932
chr18	ENCODE	exon	59748259	59748401	.	+	.	Parent=gene932
chr18	ENCODE	CDS	59748259	59748401	.	+	2	Parent=gene932
chr18	ENCODE	exon	59751262	59751417	.	+	.	Parent=gene932
chr18	ENCODE	CDS	59751262	59751417	.	+	0	Parent=gene932
chr18	ENCODE	CDS	59753052	59753456	.	+	0	Parent=gene932
chr18	ENCODE	exon	59753052	59754325	.	+	.	Parent=gene932
###
chr18	ENCODE	gene	59767515	59778626	.	+	.	ID=gene933;name2=AC009802.2;Name=AC009802.2-001
chr18	ENCODE	exon	59767515	59767614	.	+	.	Parent=gene933
chr18	ENCODE	exon	59771568	59771741	.	+	.	Parent=gene933
chr18	ENCODE	CDS	59771670	59771741	.	+	0	Parent=gene933
chr18	ENCODE	exon	59772622	59772771	.	+	.	Parent=gene933
chr18	ENCODE	CDS	59772622	59772771	.	+	0	Parent=gene933
chr18	ENCODE	CDS	59778372	59778569	.	+	0	Parent=gene933
chr18	ENCODE	exon	59778372	59778626	.	+	.	Parent=gene933
###
chr18	ENCODE	gene	59767571	59799988	.	+	.	ID=gene934;Name=AC009802.2-002;name2=AC009802.2
chr18	ENCODE	exon	59767571	59767614	.	+	.	Parent=gene934
chr18	ENCODE	exon	59772622	59772771	.	+	.	Parent=gene934
chr18	ENCODE	exon	59778372	59778489	.	+	.	Parent=gene934
chr18	ENCODE	exon	59796513	59796690	.	+	.	Parent=gene934
chr18	ENCODE	exon	59798015	59798152	.	+	.	Parent=gene934
chr18	ENCODE	exon	59799935	59799988	.	+	.	Parent=gene934
###
chr18	ENCODE	gene	59778396	59787000	.	+	.	ID=gene935;Name=AC009802.2-003;name2=AC009802.2
chr18	ENCODE	exon	59778396	59778489	.	+	.	Parent=gene935
chr18	ENCODE	exon	59786552	59787000	.	+	.	Parent=gene935
###
chr18	ENCODE	gene	59788139	59807588	.	+	.	ID=gene936;Name=AC009802.3-001;name2=SERPINB8
chr18	ENCODE	exon	59788139	59788384	.	+	.	Parent=gene936
chr18	ENCODE	exon	59796513	59796690	.	+	.	Parent=gene936
chr18	ENCODE	CDS	59796523	59796690	.	+	0	Parent=gene936
chr18	ENCODE	exon	59798015	59798152	.	+	.	Parent=gene936
chr18	ENCODE	CDS	59798015	59798152	.	+	0	Parent=gene936
chr18	ENCODE	exon	59799935	59800052	.	+	.	Parent=gene936
chr18	ENCODE	CDS	59799935	59800052	.	+	0	Parent=gene936
chr18	ENCODE	exon	59801793	59801935	.	+	.	Parent=gene936
chr18	ENCODE	CDS	59801793	59801935	.	+	2	Parent=gene936
chr18	ENCODE	exon	59803307	59803459	.	+	.	Parent=gene936
chr18	ENCODE	CDS	59803307	59803459	.	+	0	Parent=gene936
chr18	ENCODE	CDS	59805088	59805492	.	+	0	Parent=gene936
chr18	ENCODE	exon	59805088	59807588	.	+	.	Parent=gene936
###
chr18	ENCODE	gene	59788333	59804867	.	+	.	ID=gene937;Name=AC009802.3-002;name2=SERPINB8
chr18	ENCODE	exon	59788333	59788384	.	+	.	Parent=gene937
chr18	ENCODE	exon	59796513	59796690	.	+	.	Parent=gene937
chr18	ENCODE	CDS	59796523	59796690	.	+	0	Parent=gene937
chr18	ENCODE	exon	59798015	59798152	.	+	.	Parent=gene937
chr18	ENCODE	CDS	59798015	59798152	.	+	0	Parent=gene937
chr18	ENCODE	exon	59799935	59800052	.	+	.	Parent=gene937
chr18	ENCODE	CDS	59799935	59800052	.	+	0	Parent=gene937
chr18	ENCODE	exon	59801793	59801935	.	+	.	Parent=gene937
chr18	ENCODE	CDS	59801793	59801935	.	+	2	Parent=gene937
chr18	ENCODE	exon	59803307	59803459	.	+	.	Parent=gene937
chr18	ENCODE	CDS	59803307	59803459	.	+	0	Parent=gene937
chr18	ENCODE	CDS	59804472	59804480	.	+	0	Parent=gene937
chr18	ENCODE	exon	59804472	59804867	.	+	.	Parent=gene937
###
chr18	ENCODE	gene	59788463	59800000	.	+	.	ID=gene938;Name=AC009802.3-005;name2=SERPINB8
chr18	ENCODE	exon	59788463	59788660	.	+	.	Parent=gene938
chr18	ENCODE	exon	59796513	59796690	.	+	.	Parent=gene938
chr18	ENCODE	CDS	59796523	59796690	.	+	0	Parent=gene938
chr18	ENCODE	exon	59798015	59798152	.	+	.	Parent=gene938
chr18	ENCODE	CDS	59798015	59798152	.	+	0	Parent=gene938
chr18	ENCODE	exon	59799935	59800000	.	+	.	Parent=gene938
chr18	ENCODE	CDS	59799935	59800000	.	+	0	Parent=gene938
###
chr18	ENCODE	gene	59788719	59801861	.	+	.	ID=gene939;Name=AC009802.3-006;name2=SERPINB8
chr18	ENCODE	exon	59788719	59788779	.	+	.	Parent=gene939
chr18	ENCODE	exon	59796513	59796690	.	+	.	Parent=gene939
chr18	ENCODE	CDS	59796523	59796690	.	+	0	Parent=gene939
chr18	ENCODE	exon	59798015	59798152	.	+	.	Parent=gene939
chr18	ENCODE	CDS	59798015	59798152	.	+	0	Parent=gene939
chr18	ENCODE	exon	59799935	59800052	.	+	.	Parent=gene939
chr18	ENCODE	CDS	59799935	59800052	.	+	0	Parent=gene939
chr18	ENCODE	exon	59801793	59801861	.	+	.	Parent=gene939
chr18	ENCODE	CDS	59801793	59801861	.	+	2	Parent=gene939
###
chr18	ENCODE	gene	59798022	59805610	.	+	.	ID=gene940;Name=AC009802.3-003;name2=SERPINB8
chr18	ENCODE	exon	59798022	59798152	.	+	.	Parent=gene940
chr18	ENCODE	CDS	59798022	59798152	.	+	0	Parent=gene940
chr18	ENCODE	exon	59799935	59800052	.	+	.	Parent=gene940
chr18	ENCODE	CDS	59799935	59800052	.	+	1	Parent=gene940
chr18	ENCODE	exon	59801793	59801935	.	+	.	Parent=gene940
chr18	ENCODE	CDS	59801793	59801935	.	+	0	Parent=gene940
chr18	ENCODE	exon	59803307	59803459	.	+	.	Parent=gene940
chr18	ENCODE	CDS	59803307	59803459	.	+	1	Parent=gene940
chr18	ENCODE	CDS	59805177	59805200	.	+	1	Parent=gene940
chr18	ENCODE	exon	59805177	59805610	.	+	.	Parent=gene940
###
chr18	ENCODE	gene	59803390	59823258	.	+	.	ID=gene941;Name=AC009802.3-004;name2=SERPINB8
chr18	ENCODE	exon	59803390	59803459	.	+	.	Parent=gene941
chr18	ENCODE	exon	59823033	59823258	.	+	.	Parent=gene941
###
chr19	ENCODE	gene	59061289	59069322	.	+	.	ID=gene942;Name=AC008440.4-004;name2=MYADM
chr19	ENCODE	exon	59061289	59061483	.	+	.	Parent=gene942
chr19	ENCODE	exon	59064820	59064904	.	+	.	Parent=gene942
chr19	ENCODE	exon	59068594	59069322	.	+	.	Parent=gene942
chr19	ENCODE	CDS	59068596	59069322	.	+	0	Parent=gene942
###
chr19	ENCODE	gene	59062949	59069160	.	+	.	ID=gene943;Name=AC008440.4-005;name2=MYADM
chr19	ENCODE	exon	59062949	59063009	.	+	.	Parent=gene943
chr19	ENCODE	exon	59064756	59064904	.	+	.	Parent=gene943
chr19	ENCODE	exon	59068594	59069160	.	+	.	Parent=gene943
chr19	ENCODE	CDS	59068596	59069160	.	+	0	Parent=gene943
###
chr19	ENCODE	gene	59062949	59069373	.	+	.	ID=gene944;Name=AC008440.4-006;name2=MYADM
chr19	ENCODE	exon	59062949	59063009	.	+	.	Parent=gene944
chr19	ENCODE	exon	59068594	59069373	.	+	.	Parent=gene944
chr19	ENCODE	CDS	59068596	59069373	.	+	0	Parent=gene944
###
chr19	ENCODE	gene	59062949	59071503	.	+	.	ID=gene945;name2=MYADM;Name=AC008440.4-001
chr19	ENCODE	exon	59062949	59063009	.	+	.	Parent=gene945
chr19	ENCODE	exon	59064820	59064904	.	+	.	Parent=gene945
chr19	ENCODE	exon	59068594	59071503	.	+	.	Parent=gene945
chr19	ENCODE	CDS	59068596	59069564	.	+	0	Parent=gene945
###
chr19	ENCODE	gene	59064472	59071501	.	+	.	ID=gene946;Name=AC008440.4-002;name2=MYADM
chr19	ENCODE	exon	59064472	59064664	.	+	.	Parent=gene946
chr19	ENCODE	exon	59064820	59064904	.	+	.	Parent=gene946
chr19	ENCODE	exon	59068594	59071501	.	+	.	Parent=gene946
chr19	ENCODE	CDS	59068596	59069564	.	+	0	Parent=gene946
###
chr19	ENCODE	gene	59064505	59069685	.	+	.	ID=gene947;Name=AC008440.4-003;name2=MYADM
chr19	ENCODE	exon	59064505	59064904	.	+	.	Parent=gene947
chr19	ENCODE	exon	59068594	59069685	.	+	.	Parent=gene947
chr19	ENCODE	CDS	59068596	59069564	.	+	0	Parent=gene947
###
chr19	ENCODE	gene	59074256	59084996	.	+	.	ID=gene948;Name=AC008440.6-004;name2=PRKCG
chr19	ENCODE	exon	59074256	59074446	.	+	.	Parent=gene948
chr19	ENCODE	exon	59077623	59077730	.	+	.	Parent=gene948
chr19	ENCODE	exon	59078229	59078260	.	+	.	Parent=gene948
chr19	ENCODE	exon	59079227	59079309	.	+	.	Parent=gene948
chr19	ENCODE	exon	59084704	59084815	.	+	.	Parent=gene948
chr19	ENCODE	exon	59084952	59084996	.	+	.	Parent=gene948
###
chr19	ENCODE	gene	59076850	59086893	.	+	.	ID=gene949;Name=AC008440.6-005;name2=PRKCG
chr19	ENCODE	exon	59076850	59076906	.	+	.	Parent=gene949
chr19	ENCODE	exon	59077623	59077730	.	+	.	Parent=gene949
chr19	ENCODE	exon	59078229	59078260	.	+	.	Parent=gene949
chr19	ENCODE	exon	59079227	59079309	.	+	.	Parent=gene949
chr19	ENCODE	exon	59084704	59084815	.	+	.	Parent=gene949
chr19	ENCODE	exon	59084952	59085083	.	+	.	Parent=gene949
chr19	ENCODE	exon	59086740	59086893	.	+	.	Parent=gene949
###
chr19	ENCODE	gene	59077279	59102718	.	+	.	ID=gene950;Name=AC008440.6-001;name2=PRKCG
chr19	ENCODE	exon	59077279	59077730	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59077561	59077730	.	+	0	Parent=gene950
chr19	ENCODE	exon	59078229	59078260	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59078229	59078260	.	+	1	Parent=gene950
chr19	ENCODE	exon	59079227	59079309	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59079227	59079309	.	+	2	Parent=gene950
chr19	ENCODE	exon	59084704	59084815	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59084704	59084815	.	+	0	Parent=gene950
chr19	ENCODE	exon	59084952	59085083	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59084952	59085083	.	+	2	Parent=gene950
chr19	ENCODE	exon	59086740	59086896	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59086740	59086896	.	+	2	Parent=gene950
chr19	ENCODE	exon	59087575	59087709	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59087575	59087709	.	+	1	Parent=gene950
chr19	ENCODE	exon	59088054	59088141	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59088054	59088141	.	+	1	Parent=gene950
chr19	ENCODE	exon	59088428	59088457	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59088428	59088457	.	+	0	Parent=gene950
chr19	ENCODE	exon	59093025	59093177	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59093025	59093177	.	+	0	Parent=gene950
chr19	ENCODE	exon	59093506	59093694	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59093506	59093694	.	+	0	Parent=gene950
chr19	ENCODE	exon	59095299	59095390	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59095299	59095390	.	+	0	Parent=gene950
chr19	ENCODE	exon	59095485	59095547	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59095485	59095547	.	+	1	Parent=gene950
chr19	ENCODE	exon	59095677	59095815	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59095677	59095815	.	+	1	Parent=gene950
chr19	ENCODE	exon	59098139	59098219	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59098139	59098219	.	+	0	Parent=gene950
chr19	ENCODE	exon	59099701	59099808	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59099701	59099808	.	+	0	Parent=gene950
chr19	ENCODE	exon	59101383	59101523	.	+	.	Parent=gene950
chr19	ENCODE	CDS	59101383	59101523	.	+	0	Parent=gene950
chr19	ENCODE	CDS	59101773	59101961	.	+	0	Parent=gene950
chr19	ENCODE	exon	59101773	59102718	.	+	.	Parent=gene950
###
chr19	ENCODE	gene	59077295	59085045	.	+	.	ID=gene951;Name=AC008440.6-006;name2=PRKCG
chr19	ENCODE	exon	59077295	59077425	.	+	.	Parent=gene951
chr19	ENCODE	CDS	59077295	59077425	.	+	0	Parent=gene951
chr19	ENCODE	exon	59077623	59077730	.	+	.	Parent=gene951
chr19	ENCODE	CDS	59077623	59077730	.	+	1	Parent=gene951
chr19	ENCODE	exon	59078229	59078260	.	+	.	Parent=gene951
chr19	ENCODE	CDS	59078229	59078260	.	+	1	Parent=gene951
chr19	ENCODE	exon	59079227	59079309	.	+	.	Parent=gene951
chr19	ENCODE	CDS	59079227	59079309	.	+	2	Parent=gene951
chr19	ENCODE	exon	59084704	59084815	.	+	.	Parent=gene951
chr19	ENCODE	CDS	59084704	59084815	.	+	0	Parent=gene951
chr19	ENCODE	exon	59084952	59085045	.	+	.	Parent=gene951
chr19	ENCODE	CDS	59084952	59085045	.	+	2	Parent=gene951
###
chr19	ENCODE	gene	59077366	59088469	.	+	.	ID=gene952;Name=AC008440.6-002;name2=PRKCG
chr19	ENCODE	exon	59077366	59077730	.	+	.	Parent=gene952
chr19	ENCODE	exon	59078229	59078260	.	+	.	Parent=gene952
chr19	ENCODE	exon	59079227	59079309	.	+	.	Parent=gene952
chr19	ENCODE	exon	59084704	59084815	.	+	.	Parent=gene952
chr19	ENCODE	exon	59084952	59085083	.	+	.	Parent=gene952
chr19	ENCODE	exon	59086740	59086896	.	+	.	Parent=gene952
chr19	ENCODE	exon	59087575	59087709	.	+	.	Parent=gene952
chr19	ENCODE	exon	59088054	59088141	.	+	.	Parent=gene952
chr19	ENCODE	exon	59088428	59088469	.	+	.	Parent=gene952
###
chr19	ENCODE	gene	59077531	59091127	.	+	.	ID=gene953;Name=AC008440.6-003;name2=PRKCG
chr19	ENCODE	exon	59077531	59077730	.	+	.	Parent=gene953
chr19	ENCODE	exon	59078229	59078260	.	+	.	Parent=gene953
chr19	ENCODE	exon	59079227	59079309	.	+	.	Parent=gene953
chr19	ENCODE	exon	59084704	59084815	.	+	.	Parent=gene953
chr19	ENCODE	exon	59084952	59085083	.	+	.	Parent=gene953
chr19	ENCODE	exon	59086740	59087709	.	+	.	Parent=gene953
chr19	ENCODE	exon	59088054	59088141	.	+	.	Parent=gene953
chr19	ENCODE	exon	59088428	59089165	.	+	.	Parent=gene953
chr19	ENCODE	exon	59091089	59091127	.	+	.	Parent=gene953
###
chr19	ENCODE	gene	59104401	59136659	.	+	.	ID=gene954;name2=CACNG7;Name=AC008440.7-003
chr19	ENCODE	exon	59104401	59104583	.	+	.	Parent=gene954
chr19	ENCODE	exon	59110431	59110571	.	+	.	Parent=gene954
chr19	ENCODE	exon	59136536	59136659	.	+	.	Parent=gene954
###
chr19	ENCODE	gene	59104401	59139007	.	+	.	ID=gene955;Name=AC008440.7-001;name2=CACNG7
chr19	ENCODE	exon	59104401	59104583	.	+	.	Parent=gene955
chr19	ENCODE	exon	59107869	59108093	.	+	.	Parent=gene955
chr19	ENCODE	CDS	59107898	59108093	.	+	0	Parent=gene955
chr19	ENCODE	exon	59109566	59109652	.	+	.	Parent=gene955
chr19	ENCODE	CDS	59109566	59109652	.	+	2	Parent=gene955
chr19	ENCODE	exon	59110431	59110571	.	+	.	Parent=gene955
chr19	ENCODE	CDS	59110431	59110571	.	+	2	Parent=gene955
chr19	ENCODE	exon	59136536	59136681	.	+	.	Parent=gene955
chr19	ENCODE	CDS	59136536	59136681	.	+	2	Parent=gene955
chr19	ENCODE	CDS	59137102	59137359	.	+	0	Parent=gene955
chr19	ENCODE	exon	59137102	59139007	.	+	.	Parent=gene955
###
chr19	ENCODE	gene	59107883	59136727	.	+	.	ID=gene956;Name=AC008440.7-002;name2=CACNG7
chr19	ENCODE	exon	59107883	59108093	.	+	.	Parent=gene956
chr19	ENCODE	CDS	59107898	59108093	.	+	0	Parent=gene956
chr19	ENCODE	exon	59109566	59109652	.	+	.	Parent=gene956
chr19	ENCODE	CDS	59109566	59109652	.	+	2	Parent=gene956
chr19	ENCODE	exon	59110431	59110571	.	+	.	Parent=gene956
chr19	ENCODE	CDS	59110431	59110571	.	+	2	Parent=gene956
chr19	ENCODE	CDS	59136536	59136708	.	+	2	Parent=gene956
chr19	ENCODE	exon	59136536	59136727	.	+	.	Parent=gene956
###
chr19	ENCODE	gene	59158106	59185281	.	+	.	ID=gene957;Name=AC008440.8-001;name2=CACNG8
chr19	ENCODE	exon	59158106	59158491	.	+	.	Parent=gene957
chr19	ENCODE	CDS	59158209	59158491	.	+	0	Parent=gene957
chr19	ENCODE	exon	59173212	59173295	.	+	.	Parent=gene957
chr19	ENCODE	CDS	59173212	59173295	.	+	2	Parent=gene957
chr19	ENCODE	exon	59174933	59175073	.	+	.	Parent=gene957
chr19	ENCODE	CDS	59174933	59175073	.	+	2	Parent=gene957
chr19	ENCODE	CDS	59177146	59177915	.	+	2	Parent=gene957
chr19	ENCODE	exon	59177146	59185281	.	+	.	Parent=gene957
###
chr19	ENCODE	gene	59187354	59207735	.	+	.	ID=gene958;Name=AC008440.9-001;name2=CACNG6
chr19	ENCODE	exon	59187354	59188274	.	+	.	Parent=gene958
chr19	ENCODE	CDS	59187944	59188274	.	+	0	Parent=gene958
chr19	ENCODE	exon	59193305	59193379	.	+	.	Parent=gene958
chr19	ENCODE	CDS	59193305	59193379	.	+	2	Parent=gene958
chr19	ENCODE	exon	59194700	59194837	.	+	.	Parent=gene958
chr19	ENCODE	CDS	59194700	59194837	.	+	2	Parent=gene958
chr19	ENCODE	CDS	59207017	59207255	.	+	2	Parent=gene958
chr19	ENCODE	exon	59207017	59207735	.	+	.	Parent=gene958
###
chr19	ENCODE	gene	59187944	59207255	.	+	.	ID=gene959;Name=AC008440.9-002;name2=CACNG6
chr19	ENCODE	exon	59187944	59188274	.	+	.	Parent=gene959
chr19	ENCODE	CDS	59187944	59188274	.	+	0	Parent=gene959
chr19	ENCODE	exon	59193305	59193379	.	+	.	Parent=gene959
chr19	ENCODE	CDS	59193305	59193379	.	+	2	Parent=gene959
chr19	ENCODE	exon	59207017	59207255	.	+	.	Parent=gene959
chr19	ENCODE	CDS	59207017	59207255	.	+	2	Parent=gene959
###
chr19	ENCODE	gene	59235891	59253489	.	-	.	ID=gene960;name2=VSTM1;Name=AC012314.1-003
chr19	ENCODE	exon	59235891	59236146	.	-	.	Parent=gene960
chr19	ENCODE	CDS	59236027	59236146	.	-	0	Parent=gene960
chr19	ENCODE	exon	59236845	59236882	.	-	.	Parent=gene960
chr19	ENCODE	CDS	59236845	59236882	.	-	2	Parent=gene960
chr19	ENCODE	exon	59236982	59237019	.	-	.	Parent=gene960
chr19	ENCODE	CDS	59236982	59237019	.	-	1	Parent=gene960
chr19	ENCODE	exon	59237235	59237262	.	-	.	Parent=gene960
chr19	ENCODE	CDS	59237235	59237262	.	-	2	Parent=gene960
chr19	ENCODE	exon	59246476	59246514	.	-	.	Parent=gene960
chr19	ENCODE	CDS	59246476	59246514	.	-	2	Parent=gene960
chr19	ENCODE	exon	59253372	59253489	.	-	.	Parent=gene960
chr19	ENCODE	CDS	59253372	59253489	.	-	0	Parent=gene960
###
chr19	ENCODE	gene	59235891	59259019	.	-	.	ID=gene961;Name=AC012314.1-001;name2=VSTM1
chr19	ENCODE	exon	59235891	59236146	.	-	.	Parent=gene961
chr19	ENCODE	CDS	59236027	59236146	.	-	0	Parent=gene961
chr19	ENCODE	exon	59236845	59236882	.	-	.	Parent=gene961
chr19	ENCODE	CDS	59236845	59236882	.	-	2	Parent=gene961
chr19	ENCODE	exon	59236982	59237019	.	-	.	Parent=gene961
chr19	ENCODE	CDS	59236982	59237019	.	-	1	Parent=gene961
chr19	ENCODE	exon	59237235	59237262	.	-	.	Parent=gene961
chr19	ENCODE	CDS	59237235	59237262	.	-	2	Parent=gene961
chr19	ENCODE	exon	59237343	59237435	.	-	.	Parent=gene961
chr19	ENCODE	CDS	59237343	59237435	.	-	2	Parent=gene961
chr19	ENCODE	exon	59246476	59246514	.	-	.	Parent=gene961
chr19	ENCODE	CDS	59246476	59246514	.	-	2	Parent=gene961
chr19	ENCODE	exon	59253372	59253656	.	-	.	Parent=gene961
chr19	ENCODE	CDS	59253372	59253656	.	-	2	Parent=gene961
chr19	ENCODE	exon	59253763	59253798	.	-	.	Parent=gene961
chr19	ENCODE	CDS	59253763	59253798	.	-	2	Parent=gene961
chr19	ENCODE	CDS	59258810	59258843	.	-	0	Parent=gene961
chr19	ENCODE	exon	59258810	59259019	.	-	.	Parent=gene961
###
chr19	ENCODE	gene	59235895	59259019	.	-	.	ID=gene962;Name=AC012314.1-002;name2=VSTM1
chr19	ENCODE	exon	59235895	59236146	.	-	.	Parent=gene962
chr19	ENCODE	exon	59236845	59236882	.	-	.	Parent=gene962
chr19	ENCODE	exon	59236982	59237019	.	-	.	Parent=gene962
chr19	ENCODE	exon	59237293	59237435	.	-	.	Parent=gene962
chr19	ENCODE	exon	59246476	59246514	.	-	.	Parent=gene962
chr19	ENCODE	exon	59253372	59253656	.	-	.	Parent=gene962
chr19	ENCODE	exon	59253763	59253798	.	-	.	Parent=gene962
chr19	ENCODE	exon	59258810	59259019	.	-	.	Parent=gene962
###
chr19	ENCODE	gene	59289745	59295895	.	-	.	ID=gene963;Name=AC012314.3-008;name2=OSCAR
chr19	ENCODE	exon	59289745	59291230	.	-	.	Parent=gene963
chr19	ENCODE	CDS	59290755	59291230	.	-	2	Parent=gene963
chr19	ENCODE	exon	59291961	59292263	.	-	.	Parent=gene963
chr19	ENCODE	CDS	59291961	59292263	.	-	2	Parent=gene963
chr19	ENCODE	exon	59295859	59295895	.	-	.	Parent=gene963
chr19	ENCODE	CDS	59295859	59295895	.	-	0	Parent=gene963
###
chr19	ENCODE	gene	59289747	59295895	.	-	.	ID=gene964;Name=AC012314.3-005;name2=OSCAR
chr19	ENCODE	exon	59289747	59290434	.	-	.	Parent=gene964
chr19	ENCODE	CDS	59290298	59290434	.	-	2	Parent=gene964
chr19	ENCODE	exon	59290949	59291230	.	-	.	Parent=gene964
chr19	ENCODE	CDS	59290949	59291230	.	-	2	Parent=gene964
chr19	ENCODE	exon	59291961	59292263	.	-	.	Parent=gene964
chr19	ENCODE	CDS	59291961	59292263	.	-	2	Parent=gene964
chr19	ENCODE	exon	59294693	59294704	.	-	.	Parent=gene964
chr19	ENCODE	CDS	59294693	59294704	.	-	2	Parent=gene964
chr19	ENCODE	exon	59294851	59294883	.	-	.	Parent=gene964
chr19	ENCODE	CDS	59294851	59294883	.	-	2	Parent=gene964
chr19	ENCODE	exon	59295859	59295895	.	-	.	Parent=gene964
chr19	ENCODE	CDS	59295859	59295895	.	-	0	Parent=gene964
###
chr19	ENCODE	gene	59289747	59295904	.	-	.	ID=gene965;Name=AC012314.3-003;name2=OSCAR
chr19	ENCODE	exon	59289747	59291202	.	-	.	Parent=gene965
chr19	ENCODE	exon	59291221	59291230	.	-	.	Parent=gene965
chr19	ENCODE	exon	59291961	59292263	.	-	.	Parent=gene965
chr19	ENCODE	exon	59294851	59294883	.	-	.	Parent=gene965
chr19	ENCODE	exon	59295859	59295904	.	-	.	Parent=gene965
###
chr19	ENCODE	gene	59289747	59295918	.	-	.	ID=gene966;Name=AC012314.3-002;name2=OSCAR
chr19	ENCODE	exon	59289747	59291230	.	-	.	Parent=gene966
chr19	ENCODE	CDS	59290755	59291230	.	-	2	Parent=gene966
chr19	ENCODE	exon	59291961	59292263	.	-	.	Parent=gene966
chr19	ENCODE	CDS	59291961	59292263	.	-	2	Parent=gene966
chr19	ENCODE	exon	59294693	59294704	.	-	.	Parent=gene966
chr19	ENCODE	CDS	59294693	59294704	.	-	2	Parent=gene966
chr19	ENCODE	exon	59294851	59294883	.	-	.	Parent=gene966
chr19	ENCODE	CDS	59294851	59294883	.	-	2	Parent=gene966
chr19	ENCODE	CDS	59295859	59295895	.	-	0	Parent=gene966
chr19	ENCODE	exon	59295859	59295918	.	-	.	Parent=gene966
###
chr19	ENCODE	gene	59289747	59295941	.	-	.	ID=gene967;Name=AC012314.3-004;name2=OSCAR
chr19	ENCODE	exon	59289747	59290434	.	-	.	Parent=gene967
chr19	ENCODE	CDS	59290298	59290434	.	-	2	Parent=gene967
chr19	ENCODE	exon	59290949	59291230	.	-	.	Parent=gene967
chr19	ENCODE	CDS	59290949	59291230	.	-	2	Parent=gene967
chr19	ENCODE	exon	59291961	59292263	.	-	.	Parent=gene967
chr19	ENCODE	CDS	59291961	59292263	.	-	2	Parent=gene967
chr19	ENCODE	exon	59294851	59294883	.	-	.	Parent=gene967
chr19	ENCODE	CDS	59294851	59294883	.	-	2	Parent=gene967
chr19	ENCODE	CDS	59295859	59295895	.	-	0	Parent=gene967
chr19	ENCODE	exon	59295859	59295941	.	-	.	Parent=gene967
###
chr19	ENCODE	gene	59289747	59295960	.	-	.	ID=gene968;name2=OSCAR;Name=AC012314.3-006
chr19	ENCODE	exon	59289747	59290434	.	-	.	Parent=gene968
chr19	ENCODE	CDS	59290298	59290434	.	-	2	Parent=gene968
chr19	ENCODE	exon	59290949	59291230	.	-	.	Parent=gene968
chr19	ENCODE	CDS	59290949	59291230	.	-	2	Parent=gene968
chr19	ENCODE	exon	59291961	59292263	.	-	.	Parent=gene968
chr19	ENCODE	CDS	59291961	59292263	.	-	2	Parent=gene968
chr19	ENCODE	CDS	59295859	59295895	.	-	0	Parent=gene968
chr19	ENCODE	exon	59295859	59295960	.	-	.	Parent=gene968
###
chr19	ENCODE	gene	59289747	59297812	.	-	.	ID=gene969;Name=AC012314.3-001;name2=OSCAR
chr19	ENCODE	exon	59289747	59291230	.	-	.	Parent=gene969
chr19	ENCODE	CDS	59290755	59291230	.	-	2	Parent=gene969
chr19	ENCODE	exon	59291961	59292263	.	-	.	Parent=gene969
chr19	ENCODE	CDS	59291961	59292263	.	-	2	Parent=gene969
chr19	ENCODE	exon	59294851	59294883	.	-	.	Parent=gene969
chr19	ENCODE	CDS	59294851	59294883	.	-	2	Parent=gene969
chr19	ENCODE	CDS	59295859	59295895	.	-	0	Parent=gene969
chr19	ENCODE	exon	59295859	59296054	.	-	.	Parent=gene969
chr19	ENCODE	exon	59297774	59297812	.	-	.	Parent=gene969
###
chr19	ENCODE	gene	59290851	59295944	.	-	.	ID=gene970;Name=AC012314.3-007;name2=OSCAR
chr19	ENCODE	exon	59290851	59291230	.	-	.	Parent=gene970
chr19	ENCODE	CDS	59290945	59291230	.	-	1	Parent=gene970
chr19	ENCODE	exon	59291961	59292090	.	-	.	Parent=gene970
chr19	ENCODE	CDS	59291961	59292090	.	-	2	Parent=gene970
chr19	ENCODE	exon	59294851	59294883	.	-	.	Parent=gene970
chr19	ENCODE	CDS	59294851	59294883	.	-	2	Parent=gene970
chr19	ENCODE	CDS	59295859	59295895	.	-	0	Parent=gene970
chr19	ENCODE	exon	59295859	59295944	.	-	.	Parent=gene970
###
chr19	ENCODE	gene	59297848	59302080	.	+	.	ID=gene971;Name=AC012314.4-003;name2=NDUFA3
chr19	ENCODE	exon	59297848	59298008	.	+	.	Parent=gene971
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene971
chr19	ENCODE	exon	59300716	59300822	.	+	.	Parent=gene971
chr19	ENCODE	exon	59301053	59301130	.	+	.	Parent=gene971
chr19	ENCODE	exon	59301472	59301565	.	+	.	Parent=gene971
chr19	ENCODE	exon	59301930	59302080	.	+	.	Parent=gene971
###
chr19	ENCODE	gene	59297941	59303823	.	+	.	ID=gene972;Name=AC012314.4-010;name2=NDUFA3
chr19	ENCODE	exon	59297941	59298008	.	+	.	Parent=gene972
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene972
chr19	ENCODE	exon	59301053	59301130	.	+	.	Parent=gene972
chr19	ENCODE	exon	59301930	59302097	.	+	.	Parent=gene972
chr19	ENCODE	exon	59303559	59303823	.	+	.	Parent=gene972
###
chr19	ENCODE	gene	59297957	59302687	.	+	.	ID=gene973;Name=AC012314.4-001;name2=NDUFA3
chr19	ENCODE	exon	59297957	59298008	.	+	.	Parent=gene973
chr19	ENCODE	CDS	59297999	59298008	.	+	0	Parent=gene973
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene973
chr19	ENCODE	CDS	59298234	59298308	.	+	2	Parent=gene973
chr19	ENCODE	exon	59301053	59301130	.	+	.	Parent=gene973
chr19	ENCODE	CDS	59301053	59301130	.	+	2	Parent=gene973
chr19	ENCODE	CDS	59301930	59302021	.	+	2	Parent=gene973
chr19	ENCODE	exon	59301930	59302687	.	+	.	Parent=gene973
###
chr19	ENCODE	gene	59297972	59302080	.	+	.	ID=gene974;Name=AC012314.4-004;name2=NDUFA3
chr19	ENCODE	exon	59297972	59298008	.	+	.	Parent=gene974
chr19	ENCODE	CDS	59297999	59298008	.	+	0	Parent=gene974
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene974
chr19	ENCODE	CDS	59298234	59298308	.	+	2	Parent=gene974
chr19	ENCODE	exon	59301053	59301130	.	+	.	Parent=gene974
chr19	ENCODE	CDS	59301053	59301130	.	+	2	Parent=gene974
chr19	ENCODE	CDS	59301472	59301527	.	+	2	Parent=gene974
chr19	ENCODE	exon	59301472	59301565	.	+	.	Parent=gene974
chr19	ENCODE	exon	59301930	59302080	.	+	.	Parent=gene974
###
chr19	ENCODE	gene	59297975	59301589	.	+	.	ID=gene975;Name=AC012314.4-007;name2=NDUFA3
chr19	ENCODE	exon	59297975	59298008	.	+	.	Parent=gene975
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene975
chr19	ENCODE	exon	59301053	59301589	.	+	.	Parent=gene975
###
chr19	ENCODE	gene	59297975	59302080	.	+	.	ID=gene976;name2=NDUFA3;Name=AC012314.4-002
chr19	ENCODE	exon	59297975	59298008	.	+	.	Parent=gene976
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene976
chr19	ENCODE	exon	59300716	59300822	.	+	.	Parent=gene976
chr19	ENCODE	exon	59301053	59301130	.	+	.	Parent=gene976
chr19	ENCODE	exon	59301930	59302080	.	+	.	Parent=gene976
###
chr19	ENCODE	gene	59297989	59302084	.	+	.	ID=gene977;Name=AC012314.4-005;name2=NDUFA3
chr19	ENCODE	exon	59297989	59298018	.	+	.	Parent=gene977
chr19	ENCODE	CDS	59297999	59298018	.	+	0	Parent=gene977
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene977
chr19	ENCODE	CDS	59298234	59298308	.	+	1	Parent=gene977
chr19	ENCODE	exon	59301053	59301130	.	+	.	Parent=gene977
chr19	ENCODE	CDS	59301053	59301130	.	+	1	Parent=gene977
chr19	ENCODE	CDS	59301930	59301942	.	+	1	Parent=gene977
chr19	ENCODE	exon	59301930	59302084	.	+	.	Parent=gene977
###
chr19	ENCODE	gene	59297989	59303652	.	+	.	ID=gene978;Name=AC012314.4-011;name2=NDUFA3
chr19	ENCODE	exon	59297989	59298008	.	+	.	Parent=gene978
chr19	ENCODE	CDS	59297999	59298008	.	+	0	Parent=gene978
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene978
chr19	ENCODE	CDS	59298234	59298308	.	+	2	Parent=gene978
chr19	ENCODE	exon	59301053	59301130	.	+	.	Parent=gene978
chr19	ENCODE	CDS	59301053	59301130	.	+	2	Parent=gene978
chr19	ENCODE	CDS	59303559	59303641	.	+	2	Parent=gene978
chr19	ENCODE	exon	59303559	59303652	.	+	.	Parent=gene978
###
chr19	ENCODE	gene	59298005	59302080	.	+	.	ID=gene979;Name=AC012314.4-006;name2=NDUFA3
chr19	ENCODE	exon	59298005	59298079	.	+	.	Parent=gene979
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene979
chr19	ENCODE	exon	59301053	59301130	.	+	.	Parent=gene979
chr19	ENCODE	exon	59301930	59302080	.	+	.	Parent=gene979
###
chr19	ENCODE	gene	59298234	59303846	.	+	.	ID=gene980;Name=AC012314.4-009;name2=NDUFA3
chr19	ENCODE	exon	59298234	59298308	.	+	.	Parent=gene980
chr19	ENCODE	exon	59301053	59301130	.	+	.	Parent=gene980
chr19	ENCODE	exon	59301472	59301565	.	+	.	Parent=gene980
chr19	ENCODE	exon	59301930	59302089	.	+	.	Parent=gene980
chr19	ENCODE	exon	59303559	59303846	.	+	.	Parent=gene980
###
chr19	ENCODE	gene	59301084	59302080	.	+	.	ID=gene981;Name=AC012314.4-008;name2=NDUFA3
chr19	ENCODE	exon	59301084	59301130	.	+	.	Parent=gene981
chr19	ENCODE	exon	59301472	59301565	.	+	.	Parent=gene981
chr19	ENCODE	exon	59301883	59302080	.	+	.	Parent=gene981
###
chr19	ENCODE	gene	59302082	59306710	.	+	.	ID=gene982;Name=AC012314.4-012;name2=NDUFA3
chr19	ENCODE	exon	59302082	59302137	.	+	.	Parent=gene982
chr19	ENCODE	exon	59303559	59303845	.	+	.	Parent=gene982
chr19	ENCODE	exon	59303947	59304001	.	+	.	Parent=gene982
chr19	ENCODE	exon	59306490	59306710	.	+	.	Parent=gene982
###
chr19	ENCODE	gene	59302132	59310867	.	-	.	ID=gene983;Name=AC012314.5-003;name2=TFPT
chr19	ENCODE	exon	59302132	59302288	.	-	.	Parent=gene983
chr19	ENCODE	CDS	59302169	59302288	.	-	0	Parent=gene983
chr19	ENCODE	exon	59303145	59303363	.	-	.	Parent=gene983
chr19	ENCODE	CDS	59303145	59303363	.	-	0	Parent=gene983
chr19	ENCODE	exon	59303445	59303514	.	-	.	Parent=gene983
chr19	ENCODE	CDS	59303445	59303514	.	-	1	Parent=gene983
chr19	ENCODE	exon	59305246	59305316	.	-	.	Parent=gene983
chr19	ENCODE	CDS	59305246	59305316	.	-	0	Parent=gene983
chr19	ENCODE	exon	59309634	59309892	.	-	.	Parent=gene983
chr19	ENCODE	CDS	59309634	59309892	.	-	1	Parent=gene983
chr19	ENCODE	CDS	59310439	59310461	.	-	0	Parent=gene983
chr19	ENCODE	exon	59310439	59310867	.	-	.	Parent=gene983
###
chr19	ENCODE	gene	59302139	59310266	.	-	.	ID=gene984;Name=AC012314.5-002;name2=TFPT
chr19	ENCODE	exon	59302139	59302288	.	-	.	Parent=gene984
chr19	ENCODE	CDS	59302169	59302288	.	-	0	Parent=gene984
chr19	ENCODE	exon	59303145	59303363	.	-	.	Parent=gene984
chr19	ENCODE	CDS	59303145	59303363	.	-	0	Parent=gene984
chr19	ENCODE	exon	59303445	59303514	.	-	.	Parent=gene984
chr19	ENCODE	CDS	59303445	59303514	.	-	1	Parent=gene984
chr19	ENCODE	exon	59305246	59305316	.	-	.	Parent=gene984
chr19	ENCODE	CDS	59305246	59305316	.	-	0	Parent=gene984
chr19	ENCODE	CDS	59309634	59309888	.	-	0	Parent=gene984
chr19	ENCODE	exon	59309634	59309892	.	-	.	Parent=gene984
chr19	ENCODE	exon	59310232	59310266	.	-	.	Parent=gene984
###
chr19	ENCODE	gene	59302139	59310480	.	-	.	ID=gene985;Name=AC012314.5-005;name2=TFPT
chr19	ENCODE	exon	59302139	59302288	.	-	.	Parent=gene985
chr19	ENCODE	exon	59303145	59303326	.	-	.	Parent=gene985
chr19	ENCODE	CDS	59303168	59303326	.	-	0	Parent=gene985
chr19	ENCODE	exon	59303445	59303514	.	-	.	Parent=gene985
chr19	ENCODE	CDS	59303445	59303514	.	-	1	Parent=gene985
chr19	ENCODE	exon	59305246	59305316	.	-	.	Parent=gene985
chr19	ENCODE	CDS	59305246	59305316	.	-	0	Parent=gene985
chr19	ENCODE	exon	59309634	59309892	.	-	.	Parent=gene985
chr19	ENCODE	CDS	59309634	59309892	.	-	1	Parent=gene985
chr19	ENCODE	CDS	59310439	59310461	.	-	0	Parent=gene985
chr19	ENCODE	exon	59310439	59310480	.	-	.	Parent=gene985
###
chr19	ENCODE	gene	59302139	59310625	.	-	.	ID=gene986;Name=AC012314.5-004;name2=TFPT
chr19	ENCODE	exon	59302139	59302288	.	-	.	Parent=gene986
chr19	ENCODE	exon	59303145	59303182	.	-	.	Parent=gene986
chr19	ENCODE	exon	59303356	59303363	.	-	.	Parent=gene986
chr19	ENCODE	exon	59303445	59303514	.	-	.	Parent=gene986
chr19	ENCODE	exon	59305246	59305316	.	-	.	Parent=gene986
chr19	ENCODE	exon	59309634	59309892	.	-	.	Parent=gene986
chr19	ENCODE	exon	59310439	59310625	.	-	.	Parent=gene986
###
chr19	ENCODE	gene	59302142	59310848	.	-	.	ID=gene987;Name=AC012314.5-001;name2=TFPT
chr19	ENCODE	exon	59302142	59302288	.	-	.	Parent=gene987
chr19	ENCODE	exon	59303145	59303363	.	-	.	Parent=gene987
chr19	ENCODE	exon	59303445	59303514	.	-	.	Parent=gene987
chr19	ENCODE	exon	59305246	59305316	.	-	.	Parent=gene987
chr19	ENCODE	exon	59309634	59309892	.	-	.	Parent=gene987
chr19	ENCODE	exon	59310439	59310597	.	-	.	Parent=gene987
chr19	ENCODE	exon	59310705	59310848	.	-	.	Parent=gene987
###
chr19	ENCODE	gene	59303666	59304048	.	+	.	ID=gene988;Name=AC012314.4-013;name2=NDUFA3
chr19	ENCODE	exon	59303666	59303845	.	+	.	Parent=gene988
chr19	ENCODE	exon	59303947	59304048	.	+	.	Parent=gene988
###
chr19	ENCODE	gene	59303823	59304376	.	+	.	ID=gene989;Name=AC012314.4-014;name2=NDUFA3
chr19	ENCODE	exon	59303823	59303845	.	+	.	Parent=gene989
chr19	ENCODE	exon	59303947	59304013	.	+	.	Parent=gene989
chr19	ENCODE	exon	59304201	59304376	.	+	.	Parent=gene989
###
chr19	ENCODE	gene	59310649	59326952	.	+	.	ID=gene990;Name=AC012314.7-001;name2=PRPF31
chr19	ENCODE	exon	59310649	59310989	.	+	.	Parent=gene990
chr19	ENCODE	exon	59313463	59313647	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59313471	59313647	.	+	0	Parent=gene990
chr19	ENCODE	exon	59313765	59313825	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59313765	59313825	.	+	0	Parent=gene990
chr19	ENCODE	exon	59317051	59317134	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59317051	59317134	.	+	2	Parent=gene990
chr19	ENCODE	exon	59317688	59317785	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59317688	59317785	.	+	2	Parent=gene990
chr19	ENCODE	exon	59318645	59318751	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59318645	59318751	.	+	0	Parent=gene990
chr19	ENCODE	exon	59318940	59319109	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59318940	59319109	.	+	1	Parent=gene990
chr19	ENCODE	exon	59319690	59319847	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59319690	59319847	.	+	2	Parent=gene990
chr19	ENCODE	exon	59321715	59321804	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59321715	59321804	.	+	0	Parent=gene990
chr19	ENCODE	exon	59323260	59323387	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59323260	59323387	.	+	0	Parent=gene990
chr19	ENCODE	exon	59323492	59323564	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59323492	59323564	.	+	1	Parent=gene990
chr19	ENCODE	exon	59324244	59324372	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59324244	59324372	.	+	0	Parent=gene990
chr19	ENCODE	exon	59324459	59324557	.	+	.	Parent=gene990
chr19	ENCODE	CDS	59324459	59324557	.	+	0	Parent=gene990
chr19	ENCODE	CDS	59326550	59326675	.	+	0	Parent=gene990
chr19	ENCODE	exon	59326550	59326952	.	+	.	Parent=gene990
###
chr19	ENCODE	gene	59310946	59319845	.	+	.	ID=gene991;Name=AC012314.7-005;name2=PRPF31
chr19	ENCODE	exon	59310946	59310989	.	+	.	Parent=gene991
chr19	ENCODE	exon	59313440	59313647	.	+	.	Parent=gene991
chr19	ENCODE	CDS	59313471	59313647	.	+	0	Parent=gene991
chr19	ENCODE	exon	59313765	59313825	.	+	.	Parent=gene991
chr19	ENCODE	CDS	59313765	59313825	.	+	0	Parent=gene991
chr19	ENCODE	exon	59317051	59317134	.	+	.	Parent=gene991
chr19	ENCODE	CDS	59317051	59317134	.	+	2	Parent=gene991
chr19	ENCODE	exon	59317688	59317785	.	+	.	Parent=gene991
chr19	ENCODE	CDS	59317688	59317785	.	+	2	Parent=gene991
chr19	ENCODE	exon	59318645	59318751	.	+	.	Parent=gene991
chr19	ENCODE	CDS	59318645	59318751	.	+	0	Parent=gene991
chr19	ENCODE	exon	59318940	59319109	.	+	.	Parent=gene991
chr19	ENCODE	CDS	59318940	59319109	.	+	1	Parent=gene991
chr19	ENCODE	exon	59319690	59319845	.	+	.	Parent=gene991
chr19	ENCODE	CDS	59319690	59319845	.	+	2	Parent=gene991
###
chr19	ENCODE	gene	59310963	59326955	.	+	.	ID=gene992;Name=AC012314.7-002;name2=PRPF31
chr19	ENCODE	exon	59310963	59310989	.	+	.	Parent=gene992
chr19	ENCODE	exon	59313463	59313647	.	+	.	Parent=gene992
chr19	ENCODE	CDS	59313471	59313647	.	+	0	Parent=gene992
chr19	ENCODE	exon	59313765	59313825	.	+	.	Parent=gene992
chr19	ENCODE	CDS	59313765	59313825	.	+	0	Parent=gene992
chr19	ENCODE	exon	59317051	59317134	.	+	.	Parent=gene992
chr19	ENCODE	CDS	59317051	59317134	.	+	2	Parent=gene992
chr19	ENCODE	exon	59317688	59317785	.	+	.	Parent=gene992
chr19	ENCODE	CDS	59317688	59317785	.	+	2	Parent=gene992
chr19	ENCODE	exon	59318645	59318751	.	+	.	Parent=gene992
chr19	ENCODE	CDS	59318645	59318751	.	+	0	Parent=gene992
chr19	ENCODE	exon	59318940	59319109	.	+	.	Parent=gene992
chr19	ENCODE	CDS	59318940	59319109	.	+	1	Parent=gene992
chr19	ENCODE	exon	59319690	59319847	.	+	.	Parent=gene992
chr19	ENCODE	CDS	59319690	59319847	.	+	2	Parent=gene992
chr19	ENCODE	exon	59321715	59321804	.	+	.	Parent=gene992
chr19	ENCODE	CDS	59321715	59321804	.	+	0	Parent=gene992
chr19	ENCODE	exon	59323260	59323303	.	+	.	Parent=gene992
chr19	ENCODE	CDS	59323260	59323303	.	+	0	Parent=gene992
chr19	ENCODE	CDS	59326574	59326679	.	+	1	Parent=gene992
chr19	ENCODE	exon	59326574	59326955	.	+	.	Parent=gene992
###
chr19	ENCODE	gene	59310967	59326834	.	+	.	ID=gene993;Name=AC012314.7-007;name2=PRPF31
chr19	ENCODE	exon	59310967	59310989	.	+	.	Parent=gene993
chr19	ENCODE	exon	59313463	59313551	.	+	.	Parent=gene993
chr19	ENCODE	exon	59324250	59324372	.	+	.	Parent=gene993
chr19	ENCODE	exon	59324459	59324557	.	+	.	Parent=gene993
chr19	ENCODE	exon	59326550	59326834	.	+	.	Parent=gene993
###
chr19	ENCODE	gene	59310971	59319821	.	+	.	ID=gene994;Name=AC012314.7-006;name2=PRPF31
chr19	ENCODE	exon	59310971	59310989	.	+	.	Parent=gene994
chr19	ENCODE	exon	59313433	59313647	.	+	.	Parent=gene994
chr19	ENCODE	CDS	59313471	59313647	.	+	0	Parent=gene994
chr19	ENCODE	exon	59313765	59313825	.	+	.	Parent=gene994
chr19	ENCODE	CDS	59313765	59313825	.	+	0	Parent=gene994
chr19	ENCODE	exon	59317051	59317134	.	+	.	Parent=gene994
chr19	ENCODE	CDS	59317051	59317134	.	+	2	Parent=gene994
chr19	ENCODE	exon	59317688	59317785	.	+	.	Parent=gene994
chr19	ENCODE	CDS	59317688	59317785	.	+	2	Parent=gene994
chr19	ENCODE	exon	59318645	59318751	.	+	.	Parent=gene994
chr19	ENCODE	CDS	59318645	59318751	.	+	0	Parent=gene994
chr19	ENCODE	exon	59318940	59319109	.	+	.	Parent=gene994
chr19	ENCODE	CDS	59318940	59319109	.	+	1	Parent=gene994
chr19	ENCODE	exon	59319690	59319821	.	+	.	Parent=gene994
chr19	ENCODE	CDS	59319690	59319821	.	+	2	Parent=gene994
###
chr19	ENCODE	gene	59311001	59319774	.	+	.	ID=gene995;name2=PRPF31;Name=AC012314.7-009
chr19	ENCODE	exon	59311001	59311064	.	+	.	Parent=gene995
chr19	ENCODE	exon	59313463	59313647	.	+	.	Parent=gene995
chr19	ENCODE	CDS	59313471	59313647	.	+	0	Parent=gene995
chr19	ENCODE	exon	59313765	59313825	.	+	.	Parent=gene995
chr19	ENCODE	CDS	59313765	59313825	.	+	0	Parent=gene995
chr19	ENCODE	exon	59317051	59317134	.	+	.	Parent=gene995
chr19	ENCODE	CDS	59317051	59317134	.	+	2	Parent=gene995
chr19	ENCODE	exon	59317688	59317785	.	+	.	Parent=gene995
chr19	ENCODE	CDS	59317688	59317785	.	+	2	Parent=gene995
chr19	ENCODE	exon	59318645	59318751	.	+	.	Parent=gene995
chr19	ENCODE	CDS	59318645	59318751	.	+	0	Parent=gene995
chr19	ENCODE	exon	59318940	59319109	.	+	.	Parent=gene995
chr19	ENCODE	CDS	59318940	59319109	.	+	1	Parent=gene995
chr19	ENCODE	exon	59319690	59319774	.	+	.	Parent=gene995
chr19	ENCODE	CDS	59319690	59319774	.	+	2	Parent=gene995
###
chr19	ENCODE	gene	59313463	59326952	.	+	.	ID=gene996;Name=AC012314.7-003;name2=PRPF31
chr19	ENCODE	exon	59313463	59313647	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59313471	59313647	.	+	0	Parent=gene996
chr19	ENCODE	exon	59313765	59313825	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59313765	59313825	.	+	0	Parent=gene996
chr19	ENCODE	exon	59317051	59317134	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59317051	59317134	.	+	2	Parent=gene996
chr19	ENCODE	exon	59317688	59317785	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59317688	59317785	.	+	2	Parent=gene996
chr19	ENCODE	exon	59318645	59318751	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59318645	59318751	.	+	0	Parent=gene996
chr19	ENCODE	exon	59318940	59319109	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59318940	59319109	.	+	1	Parent=gene996
chr19	ENCODE	exon	59319690	59319847	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59319690	59319847	.	+	2	Parent=gene996
chr19	ENCODE	exon	59321715	59321804	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59321715	59321804	.	+	0	Parent=gene996
chr19	ENCODE	exon	59323278	59323387	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59323278	59323387	.	+	0	Parent=gene996
chr19	ENCODE	exon	59323492	59323564	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59323492	59323564	.	+	1	Parent=gene996
chr19	ENCODE	exon	59324244	59324372	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59324244	59324372	.	+	0	Parent=gene996
chr19	ENCODE	exon	59324459	59324557	.	+	.	Parent=gene996
chr19	ENCODE	CDS	59324459	59324557	.	+	0	Parent=gene996
chr19	ENCODE	CDS	59326550	59326675	.	+	0	Parent=gene996
chr19	ENCODE	exon	59326550	59326952	.	+	.	Parent=gene996
###
chr19	ENCODE	gene	59313598	59314003	.	+	.	ID=gene997;Name=AC012314.7-010;name2=PRPF31
chr19	ENCODE	exon	59313598	59313647	.	+	.	Parent=gene997
chr19	ENCODE	exon	59313765	59314003	.	+	.	Parent=gene997
###
chr19	ENCODE	gene	59313601	59326952	.	+	.	ID=gene998;Name=AC012314.7-004;name2=PRPF31
chr19	ENCODE	exon	59313601	59313647	.	+	.	Parent=gene998
chr19	ENCODE	exon	59313765	59313825	.	+	.	Parent=gene998
chr19	ENCODE	exon	59317051	59317134	.	+	.	Parent=gene998
chr19	ENCODE	exon	59317688	59317785	.	+	.	Parent=gene998
chr19	ENCODE	exon	59318645	59318751	.	+	.	Parent=gene998
chr19	ENCODE	exon	59318940	59319109	.	+	.	Parent=gene998
chr19	ENCODE	exon	59319690	59319847	.	+	.	Parent=gene998
chr19	ENCODE	exon	59321715	59321804	.	+	.	Parent=gene998
chr19	ENCODE	exon	59323260	59323564	.	+	.	Parent=gene998
chr19	ENCODE	exon	59324244	59324557	.	+	.	Parent=gene998
chr19	ENCODE	exon	59326550	59326952	.	+	.	Parent=gene998
###
chr19	ENCODE	gene	59313805	59323384	.	+	.	ID=gene999;Name=AC012314.7-008;name2=PRPF31
chr19	ENCODE	exon	59313805	59313825	.	+	.	Parent=gene999
chr19	ENCODE	exon	59317051	59317134	.	+	.	Parent=gene999
chr19	ENCODE	exon	59317688	59317785	.	+	.	Parent=gene999
chr19	ENCODE	exon	59318645	59318751	.	+	.	Parent=gene999
chr19	ENCODE	exon	59318940	59319109	.	+	.	Parent=gene999
chr19	ENCODE	exon	59319690	59319847	.	+	.	Parent=gene999
chr19	ENCODE	exon	59321687	59321804	.	+	.	Parent=gene999
chr19	ENCODE	exon	59323260	59323384	.	+	.	Parent=gene999
###
chr19	ENCODE	gene	59324792	59326952	.	+	.	ID=gene1000;Name=AC012314.7-011;name2=PRPF31
chr19	ENCODE	exon	59324792	59325284	.	+	.	Parent=gene1000
chr19	ENCODE	exon	59325341	59326952	.	+	.	Parent=gene1000
###
chr19	ENCODE	gene	59333256	59351231	.	+	.	ID=gene1001;Name=AC012314.9-001;name2=CNOT3
chr19	ENCODE	exon	59333256	59333521	.	+	.	Parent=gene1001
chr19	ENCODE	exon	59338477	59338551	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59338527	59338551	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59338667	59338734	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59338667	59338734	.	+	2	Parent=gene1001
chr19	ENCODE	exon	59338990	59339064	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59338990	59339064	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59339208	59339297	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59339208	59339297	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59339554	59339682	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59339554	59339682	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59339785	59339880	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59339785	59339880	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59341146	59341365	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59341146	59341365	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59341458	59341591	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59341458	59341591	.	+	2	Parent=gene1001
chr19	ENCODE	exon	59342149	59342205	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59342149	59342205	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59343695	59344082	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59343695	59344082	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59344167	59344290	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59344167	59344290	.	+	2	Parent=gene1001
chr19	ENCODE	exon	59345107	59345305	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59345107	59345305	.	+	1	Parent=gene1001
chr19	ENCODE	exon	59347775	59347874	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59347775	59347874	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59347977	59348175	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59347977	59348175	.	+	2	Parent=gene1001
chr19	ENCODE	exon	59348416	59348548	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59348416	59348548	.	+	1	Parent=gene1001
chr19	ENCODE	exon	59349264	59349389	.	+	.	Parent=gene1001
chr19	ENCODE	CDS	59349264	59349389	.	+	0	Parent=gene1001
chr19	ENCODE	CDS	59350859	59350957	.	+	0	Parent=gene1001
chr19	ENCODE	exon	59350859	59351231	.	+	.	Parent=gene1001
###
chr19	ENCODE	gene	59333315	59351230	.	+	.	ID=gene1002;Name=AC012314.9-002;name2=CNOT3
chr19	ENCODE	exon	59333315	59333521	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59338477	59338551	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59338667	59338734	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59338990	59339064	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59339208	59339682	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59339785	59339880	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59341146	59341365	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59341458	59341591	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59342149	59342205	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59343695	59344082	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59344167	59344290	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59345107	59345305	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59347775	59347874	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59347977	59348175	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59348416	59348548	.	+	.	Parent=gene1002
chr19	ENCODE	exon	59349264	59351230	.	+	.	Parent=gene1002
###
chr19	ENCODE	gene	59336924	59351230	.	+	.	ID=gene1003;Name=AC012314.9-003;name2=CNOT3
chr19	ENCODE	exon	59336924	59338551	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59338667	59338734	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59338990	59339064	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59339208	59339297	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59339554	59339682	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59339785	59339880	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59341146	59341365	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59341458	59341591	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59342149	59342205	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59343695	59344082	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59344167	59344290	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59345107	59345305	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59347775	59347874	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59347977	59348175	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59348416	59348548	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59349264	59349389	.	+	.	Parent=gene1003
chr19	ENCODE	exon	59350859	59351230	.	+	.	Parent=gene1003
###
chr19	ENCODE	gene	59338477	59351258	.	+	.	ID=gene1004;name2=CNOT3;Name=AC012314.9-004
chr19	ENCODE	exon	59338477	59338551	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59338667	59338734	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59338990	59339064	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59339208	59339297	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59339554	59339682	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59339785	59339880	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59341146	59341365	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59341458	59341591	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59342149	59342205	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59343695	59344082	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59344167	59344290	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59345107	59345305	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59347775	59347874	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59347977	59348086	.	+	.	Parent=gene1004
chr19	ENCODE	exon	59351003	59351258	.	+	.	Parent=gene1004
###
chr19	ENCODE	gene	59339278	59344244	.	+	.	ID=gene1005;Name=AC012314.9-009;name2=CNOT3
chr19	ENCODE	exon	59339278	59339297	.	+	.	Parent=gene1005
chr19	ENCODE	CDS	59339278	59339297	.	+	0	Parent=gene1005
chr19	ENCODE	exon	59339554	59339682	.	+	.	Parent=gene1005
chr19	ENCODE	CDS	59339554	59339682	.	+	1	Parent=gene1005
chr19	ENCODE	exon	59339785	59339880	.	+	.	Parent=gene1005
chr19	ENCODE	CDS	59339785	59339880	.	+	1	Parent=gene1005
chr19	ENCODE	exon	59341143	59341365	.	+	.	Parent=gene1005
chr19	ENCODE	CDS	59341143	59341365	.	+	1	Parent=gene1005
chr19	ENCODE	exon	59341458	59341591	.	+	.	Parent=gene1005
chr19	ENCODE	CDS	59341458	59341591	.	+	0	Parent=gene1005
chr19	ENCODE	exon	59342149	59342205	.	+	.	Parent=gene1005
chr19	ENCODE	CDS	59342149	59342205	.	+	1	Parent=gene1005
chr19	ENCODE	exon	59343695	59344082	.	+	.	Parent=gene1005
chr19	ENCODE	CDS	59343695	59344082	.	+	1	Parent=gene1005
chr19	ENCODE	exon	59344167	59344244	.	+	.	Parent=gene1005
chr19	ENCODE	CDS	59344167	59344244	.	+	0	Parent=gene1005
###
chr19	ENCODE	gene	59339285	59351231	.	+	.	ID=gene1006;Name=AC012314.9-005;name2=CNOT3
chr19	ENCODE	exon	59339285	59339297	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59339554	59339682	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59339785	59339880	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59341090	59341365	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59341458	59341591	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59342149	59342205	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59343695	59344082	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59344167	59344290	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59345107	59345305	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59347775	59347874	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59347977	59348175	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59348416	59348548	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59348730	59348942	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59349046	59349389	.	+	.	Parent=gene1006
chr19	ENCODE	exon	59350859	59351231	.	+	.	Parent=gene1006
###
chr19	ENCODE	gene	59345107	59350004	.	+	.	ID=gene1007;Name=AC012314.9-006;name2=CNOT3
chr19	ENCODE	exon	59345107	59345305	.	+	.	Parent=gene1007
chr19	ENCODE	exon	59347775	59347874	.	+	.	Parent=gene1007
chr19	ENCODE	exon	59347977	59348175	.	+	.	Parent=gene1007
chr19	ENCODE	exon	59348416	59348548	.	+	.	Parent=gene1007
chr19	ENCODE	exon	59349264	59349389	.	+	.	Parent=gene1007
chr19	ENCODE	exon	59349493	59350004	.	+	.	Parent=gene1007
###
chr19	ENCODE	gene	59345277	59349368	.	+	.	ID=gene1008;Name=AC012314.9-010;name2=CNOT3
chr19	ENCODE	exon	59345277	59345305	.	+	.	Parent=gene1008
chr19	ENCODE	exon	59347775	59347874	.	+	.	Parent=gene1008
chr19	ENCODE	exon	59347977	59348175	.	+	.	Parent=gene1008
chr19	ENCODE	exon	59348416	59348548	.	+	.	Parent=gene1008
chr19	ENCODE	exon	59349046	59349368	.	+	.	Parent=gene1008
###
chr19	ENCODE	gene	59348552	59351231	.	+	.	ID=gene1009;Name=AC012314.9-007;name2=CNOT3
chr19	ENCODE	exon	59348552	59348631	.	+	.	Parent=gene1009
chr19	ENCODE	exon	59349264	59351231	.	+	.	Parent=gene1009
###
chr19	ENCODE	gene	59350711	59355432	.	-	.	ID=gene1010;Name=AC012314.10-001;name2=LENG1
chr19	ENCODE	exon	59350711	59351490	.	-	.	Parent=gene1010
chr19	ENCODE	CDS	59351271	59351490	.	-	1	Parent=gene1010
chr19	ENCODE	exon	59352313	59352575	.	-	.	Parent=gene1010
chr19	ENCODE	CDS	59352313	59352575	.	-	0	Parent=gene1010
chr19	ENCODE	exon	59353832	59354011	.	-	.	Parent=gene1010
chr19	ENCODE	CDS	59353832	59354011	.	-	0	Parent=gene1010
chr19	ENCODE	CDS	59355114	59355245	.	-	0	Parent=gene1010
chr19	ENCODE	exon	59355114	59355432	.	-	.	Parent=gene1010
###
chr19	ENCODE	gene	59355658	59356198	.	-	.	ID=gene1011;Name=AC012314.11-009;name2=TMC4
chr19	ENCODE	exon	59355658	59355923	.	-	.	Parent=gene1011
chr19	ENCODE	exon	59356016	59356198	.	-	.	Parent=gene1011
###
chr19	ENCODE	gene	59355658	59356521	.	-	.	ID=gene1012;Name=AC012314.11-007;name2=TMC4
chr19	ENCODE	exon	59355658	59355923	.	-	.	Parent=gene1012
chr19	ENCODE	exon	59356016	59356159	.	-	.	Parent=gene1012
chr19	ENCODE	exon	59356427	59356521	.	-	.	Parent=gene1012
###
chr19	ENCODE	gene	59355658	59360262	.	-	.	ID=gene1013;Name=AC012314.11-010;name2=TMC4
chr19	ENCODE	exon	59355658	59355923	.	-	.	Parent=gene1013
chr19	ENCODE	exon	59356016	59356094	.	-	.	Parent=gene1013
chr19	ENCODE	exon	59356427	59356582	.	-	.	Parent=gene1013
chr19	ENCODE	exon	59356679	59356809	.	-	.	Parent=gene1013
chr19	ENCODE	exon	59357650	59357833	.	-	.	Parent=gene1013
chr19	ENCODE	exon	59358218	59358315	.	-	.	Parent=gene1013
chr19	ENCODE	exon	59358578	59358704	.	-	.	Parent=gene1013
chr19	ENCODE	exon	59359197	59359431	.	-	.	Parent=gene1013
chr19	ENCODE	exon	59359980	59360262	.	-	.	Parent=gene1013
###
chr19	ENCODE	gene	59355658	59368677	.	-	.	ID=gene1014;Name=AC012314.11-001;name2=TMC4
chr19	ENCODE	exon	59355658	59355923	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59355855	59355923	.	-	0	Parent=gene1014
chr19	ENCODE	exon	59356016	59356094	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59356016	59356094	.	-	1	Parent=gene1014
chr19	ENCODE	exon	59356427	59356582	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59356427	59356582	.	-	1	Parent=gene1014
chr19	ENCODE	exon	59356679	59356809	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59356679	59356809	.	-	0	Parent=gene1014
chr19	ENCODE	exon	59357650	59357833	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59357650	59357833	.	-	1	Parent=gene1014
chr19	ENCODE	exon	59358218	59358315	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59358218	59358315	.	-	0	Parent=gene1014
chr19	ENCODE	exon	59358578	59358704	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59358578	59358704	.	-	1	Parent=gene1014
chr19	ENCODE	exon	59359268	59359431	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59359268	59359431	.	-	0	Parent=gene1014
chr19	ENCODE	exon	59359980	59360147	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59359980	59360147	.	-	0	Parent=gene1014
chr19	ENCODE	exon	59360965	59361112	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59360965	59361112	.	-	1	Parent=gene1014
chr19	ENCODE	exon	59363709	59363830	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59363709	59363830	.	-	0	Parent=gene1014
chr19	ENCODE	exon	59363986	59364218	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59363986	59364218	.	-	2	Parent=gene1014
chr19	ENCODE	exon	59365062	59365210	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59365062	59365210	.	-	1	Parent=gene1014
chr19	ENCODE	exon	59367451	59367664	.	-	.	Parent=gene1014
chr19	ENCODE	CDS	59367451	59367664	.	-	2	Parent=gene1014
chr19	ENCODE	CDS	59368546	59368624	.	-	0	Parent=gene1014
chr19	ENCODE	exon	59368546	59368677	.	-	.	Parent=gene1014
###
chr19	ENCODE	gene	59355714	59368756	.	-	.	ID=gene1015;Name=AC012314.11-011;name2=TMC4
chr19	ENCODE	exon	59355714	59355923	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59355855	59355923	.	-	0	Parent=gene1015
chr19	ENCODE	exon	59356016	59356094	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59356016	59356094	.	-	1	Parent=gene1015
chr19	ENCODE	exon	59356427	59356582	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59356427	59356582	.	-	1	Parent=gene1015
chr19	ENCODE	exon	59356679	59356809	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59356679	59356809	.	-	0	Parent=gene1015
chr19	ENCODE	exon	59357650	59357833	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59357650	59357833	.	-	1	Parent=gene1015
chr19	ENCODE	exon	59358218	59358315	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59358218	59358315	.	-	0	Parent=gene1015
chr19	ENCODE	exon	59358578	59358704	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59358578	59358704	.	-	1	Parent=gene1015
chr19	ENCODE	exon	59359268	59359431	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59359268	59359431	.	-	0	Parent=gene1015
chr19	ENCODE	exon	59359980	59360147	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59359980	59360147	.	-	0	Parent=gene1015
chr19	ENCODE	exon	59360965	59361112	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59360965	59361112	.	-	1	Parent=gene1015
chr19	ENCODE	exon	59363709	59363830	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59363709	59363830	.	-	0	Parent=gene1015
chr19	ENCODE	exon	59363986	59364218	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59363986	59364218	.	-	2	Parent=gene1015
chr19	ENCODE	exon	59365062	59365210	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59365062	59365210	.	-	1	Parent=gene1015
chr19	ENCODE	exon	59367451	59367682	.	-	.	Parent=gene1015
chr19	ENCODE	CDS	59367451	59367682	.	-	2	Parent=gene1015
chr19	ENCODE	CDS	59368546	59368624	.	-	0	Parent=gene1015
chr19	ENCODE	exon	59368546	59368756	.	-	.	Parent=gene1015
###
chr19	ENCODE	gene	59356886	59359025	.	-	.	ID=gene1016;Name=AC012314.11-005;name2=TMC4
chr19	ENCODE	exon	59356886	59358315	.	-	.	Parent=gene1016
chr19	ENCODE	exon	59358578	59359025	.	-	.	Parent=gene1016
###
chr19	ENCODE	gene	59357774	59358812	.	-	.	ID=gene1017;Name=AC012314.11-006;name2=TMC4
chr19	ENCODE	exon	59357774	59357833	.	-	.	Parent=gene1017
chr19	ENCODE	exon	59358218	59358315	.	-	.	Parent=gene1017
chr19	ENCODE	exon	59358578	59358812	.	-	.	Parent=gene1017
###
chr19	ENCODE	gene	59358653	59368666	.	-	.	ID=gene1018;Name=AC012314.11-003;name2=TMC4
chr19	ENCODE	exon	59358653	59358704	.	-	.	Parent=gene1018
chr19	ENCODE	exon	59365062	59365210	.	-	.	Parent=gene1018
chr19	ENCODE	exon	59367451	59367664	.	-	.	Parent=gene1018
chr19	ENCODE	exon	59368546	59368666	.	-	.	Parent=gene1018
###
chr19	ENCODE	gene	59360085	59368666	.	-	.	ID=gene1019;Name=AC012314.11-004;name2=TMC4
chr19	ENCODE	exon	59360085	59360147	.	-	.	Parent=gene1019
chr19	ENCODE	exon	59365062	59365210	.	-	.	Parent=gene1019
chr19	ENCODE	exon	59367451	59367664	.	-	.	Parent=gene1019
chr19	ENCODE	exon	59368546	59368666	.	-	.	Parent=gene1019
###
chr19	ENCODE	gene	59360098	59364020	.	-	.	ID=gene1020;Name=AC012314.11-008;name2=TMC4
chr19	ENCODE	exon	59360098	59360147	.	-	.	Parent=gene1020
chr19	ENCODE	exon	59360965	59361112	.	-	.	Parent=gene1020
chr19	ENCODE	exon	59363709	59364020	.	-	.	Parent=gene1020
###
chr19	ENCODE	gene	59363709	59368259	.	-	.	ID=gene1021;Name=AC012314.11-002;name2=TMC4
chr19	ENCODE	exon	59363709	59363830	.	-	.	Parent=gene1021
chr19	ENCODE	CDS	59363709	59363830	.	-	0	Parent=gene1021
chr19	ENCODE	exon	59363986	59364218	.	-	.	Parent=gene1021
chr19	ENCODE	CDS	59363986	59364218	.	-	2	Parent=gene1021
chr19	ENCODE	exon	59365062	59365210	.	-	.	Parent=gene1021
chr19	ENCODE	CDS	59365062	59365210	.	-	1	Parent=gene1021
chr19	ENCODE	CDS	59367451	59367473	.	-	0	Parent=gene1021
chr19	ENCODE	exon	59367451	59367664	.	-	.	Parent=gene1021
chr19	ENCODE	exon	59368221	59368259	.	-	.	Parent=gene1021
###
chr19	ENCODE	gene	59368921	59385106	.	-	.	ID=gene1022;name2=LENG4;Name=AC012314.12-007
chr19	ENCODE	exon	59368921	59369937	.	-	.	Parent=gene1022
chr19	ENCODE	exon	59374294	59374470	.	-	.	Parent=gene1022
chr19	ENCODE	exon	59376302	59376662	.	-	.	Parent=gene1022
chr19	ENCODE	exon	59379216	59379375	.	-	.	Parent=gene1022
chr19	ENCODE	exon	59383883	59384012	.	-	.	Parent=gene1022
chr19	ENCODE	exon	59384099	59384177	.	-	.	Parent=gene1022
chr19	ENCODE	exon	59385001	59385106	.	-	.	Parent=gene1022
###
chr19	ENCODE	gene	59368921	59385478	.	-	.	ID=gene1023;Name=AC012314.12-001;name2=LENG4
chr19	ENCODE	exon	59368921	59369937	.	-	.	Parent=gene1023
chr19	ENCODE	CDS	59369550	59369937	.	-	1	Parent=gene1023
chr19	ENCODE	exon	59374294	59374470	.	-	.	Parent=gene1023
chr19	ENCODE	CDS	59374294	59374470	.	-	1	Parent=gene1023
chr19	ENCODE	exon	59376302	59376662	.	-	.	Parent=gene1023
chr19	ENCODE	CDS	59376302	59376662	.	-	2	Parent=gene1023
chr19	ENCODE	exon	59379216	59379375	.	-	.	Parent=gene1023
chr19	ENCODE	CDS	59379216	59379375	.	-	0	Parent=gene1023
chr19	ENCODE	exon	59382855	59382981	.	-	.	Parent=gene1023
chr19	ENCODE	CDS	59382855	59382981	.	-	1	Parent=gene1023
chr19	ENCODE	exon	59383883	59384012	.	-	.	Parent=gene1023
chr19	ENCODE	CDS	59383883	59384012	.	-	2	Parent=gene1023
chr19	ENCODE	CDS	59384099	59384174	.	-	0	Parent=gene1023
chr19	ENCODE	exon	59384099	59384177	.	-	.	Parent=gene1023
chr19	ENCODE	exon	59385001	59385478	.	-	.	Parent=gene1023
###
chr19	ENCODE	gene	59368925	59376319	.	-	.	ID=gene1024;Name=AC012314.12-003;name2=LENG4
chr19	ENCODE	exon	59368925	59369937	.	-	.	Parent=gene1024
chr19	ENCODE	exon	59374294	59376319	.	-	.	Parent=gene1024
###
chr19	ENCODE	gene	59373866	59385335	.	-	.	ID=gene1025;Name=AC012314.12-002;name2=LENG4
chr19	ENCODE	exon	59373866	59374470	.	-	.	Parent=gene1025
chr19	ENCODE	CDS	59374290	59374470	.	-	1	Parent=gene1025
chr19	ENCODE	exon	59376302	59376662	.	-	.	Parent=gene1025
chr19	ENCODE	CDS	59376302	59376662	.	-	2	Parent=gene1025
chr19	ENCODE	exon	59379216	59379375	.	-	.	Parent=gene1025
chr19	ENCODE	CDS	59379216	59379375	.	-	0	Parent=gene1025
chr19	ENCODE	exon	59382855	59382981	.	-	.	Parent=gene1025
chr19	ENCODE	CDS	59382855	59382981	.	-	1	Parent=gene1025
chr19	ENCODE	exon	59383883	59384012	.	-	.	Parent=gene1025
chr19	ENCODE	CDS	59383883	59384012	.	-	2	Parent=gene1025
chr19	ENCODE	CDS	59384099	59384174	.	-	0	Parent=gene1025
chr19	ENCODE	exon	59384099	59384177	.	-	.	Parent=gene1025
chr19	ENCODE	exon	59385001	59385335	.	-	.	Parent=gene1025
###
chr19	ENCODE	gene	59375850	59379329	.	-	.	ID=gene1026;Name=AC012314.12-005;name2=LENG4
chr19	ENCODE	exon	59375850	59376662	.	-	.	Parent=gene1026
chr19	ENCODE	exon	59379216	59379329	.	-	.	Parent=gene1026
###
chr19	ENCODE	gene	59376388	59384958	.	-	.	ID=gene1027;Name=AC012314.12-004;name2=LENG4
chr19	ENCODE	exon	59376388	59376662	.	-	.	Parent=gene1027
chr19	ENCODE	CDS	59376388	59376662	.	-	2	Parent=gene1027
chr19	ENCODE	exon	59379216	59379375	.	-	.	Parent=gene1027
chr19	ENCODE	CDS	59379216	59379375	.	-	0	Parent=gene1027
chr19	ENCODE	exon	59382855	59382981	.	-	.	Parent=gene1027
chr19	ENCODE	CDS	59382855	59382981	.	-	1	Parent=gene1027
chr19	ENCODE	exon	59383883	59384012	.	-	.	Parent=gene1027
chr19	ENCODE	CDS	59383883	59384012	.	-	2	Parent=gene1027
chr19	ENCODE	CDS	59384099	59384174	.	-	0	Parent=gene1027
chr19	ENCODE	exon	59384099	59384177	.	-	.	Parent=gene1027
chr19	ENCODE	exon	59384854	59384958	.	-	.	Parent=gene1027
###
chr19	ENCODE	gene	59379216	59385212	.	-	.	ID=gene1028;Name=AC012314.12-006;name2=LENG4
chr19	ENCODE	exon	59379216	59379375	.	-	.	Parent=gene1028
chr19	ENCODE	exon	59382855	59382981	.	-	.	Parent=gene1028
chr19	ENCODE	exon	59383883	59384012	.	-	.	Parent=gene1028
chr19	ENCODE	exon	59385001	59385212	.	-	.	Parent=gene1028
###
chr19	ENCODE	gene	59385601	59388018	.	+	.	ID=gene1029;name2=TSEN34;Name=AC012314.13-006
chr19	ENCODE	exon	59385601	59385825	.	+	.	Parent=gene1029
chr19	ENCODE	exon	59387024	59387270	.	+	.	Parent=gene1029
chr19	ENCODE	CDS	59387028	59387270	.	+	0	Parent=gene1029
chr19	ENCODE	exon	59387384	59387627	.	+	.	Parent=gene1029
chr19	ENCODE	CDS	59387384	59387627	.	+	0	Parent=gene1029
chr19	ENCODE	exon	59387779	59388018	.	+	.	Parent=gene1029
chr19	ENCODE	CDS	59387779	59388018	.	+	2	Parent=gene1029
###
chr19	ENCODE	gene	59385931	59388036	.	+	.	ID=gene1030;Name=AC012314.13-005;name2=TSEN34
chr19	ENCODE	exon	59385931	59386034	.	+	.	Parent=gene1030
chr19	ENCODE	exon	59387024	59387270	.	+	.	Parent=gene1030
chr19	ENCODE	CDS	59387028	59387270	.	+	0	Parent=gene1030
chr19	ENCODE	exon	59387384	59387627	.	+	.	Parent=gene1030
chr19	ENCODE	CDS	59387384	59387627	.	+	0	Parent=gene1030
chr19	ENCODE	exon	59387779	59388036	.	+	.	Parent=gene1030
chr19	ENCODE	CDS	59387779	59388036	.	+	2	Parent=gene1030
###
chr19	ENCODE	gene	59385931	59389333	.	+	.	ID=gene1031;Name=AC012314.13-001;name2=TSEN34
chr19	ENCODE	exon	59385931	59386113	.	+	.	Parent=gene1031
chr19	ENCODE	exon	59387024	59387270	.	+	.	Parent=gene1031
chr19	ENCODE	CDS	59387028	59387270	.	+	0	Parent=gene1031
chr19	ENCODE	exon	59387384	59387627	.	+	.	Parent=gene1031
chr19	ENCODE	CDS	59387384	59387627	.	+	0	Parent=gene1031
chr19	ENCODE	exon	59387779	59388036	.	+	.	Parent=gene1031
chr19	ENCODE	CDS	59387779	59388036	.	+	2	Parent=gene1031
chr19	ENCODE	CDS	59388842	59389029	.	+	2	Parent=gene1031
chr19	ENCODE	exon	59388842	59389333	.	+	.	Parent=gene1031
###
chr19	ENCODE	gene	59386006	59389333	.	+	.	ID=gene1032;Name=AC012314.13-002;name2=TSEN34
chr19	ENCODE	exon	59386006	59387627	.	+	.	Parent=gene1032
chr19	ENCODE	exon	59387779	59388036	.	+	.	Parent=gene1032
chr19	ENCODE	exon	59388842	59389333	.	+	.	Parent=gene1032
###
chr19	ENCODE	gene	59386394	59389333	.	+	.	ID=gene1033;Name=AC012314.13-003;name2=TSEN34
chr19	ENCODE	exon	59386394	59386700	.	+	.	Parent=gene1033
chr19	ENCODE	exon	59387024	59387270	.	+	.	Parent=gene1033
chr19	ENCODE	CDS	59387028	59387270	.	+	0	Parent=gene1033
chr19	ENCODE	exon	59387384	59387627	.	+	.	Parent=gene1033
chr19	ENCODE	CDS	59387384	59387627	.	+	0	Parent=gene1033
chr19	ENCODE	exon	59387779	59388036	.	+	.	Parent=gene1033
chr19	ENCODE	CDS	59387779	59388036	.	+	2	Parent=gene1033
chr19	ENCODE	CDS	59388842	59389029	.	+	2	Parent=gene1033
chr19	ENCODE	exon	59388842	59389333	.	+	.	Parent=gene1033
###
chr19	ENCODE	gene	59386916	59389333	.	+	.	ID=gene1034;Name=AC012314.13-004;name2=TSEN34
chr19	ENCODE	exon	59386916	59387270	.	+	.	Parent=gene1034
chr19	ENCODE	CDS	59387028	59387270	.	+	0	Parent=gene1034
chr19	ENCODE	exon	59387384	59387627	.	+	.	Parent=gene1034
chr19	ENCODE	CDS	59387384	59387627	.	+	0	Parent=gene1034
chr19	ENCODE	exon	59387779	59388036	.	+	.	Parent=gene1034
chr19	ENCODE	CDS	59387779	59388036	.	+	2	Parent=gene1034
chr19	ENCODE	CDS	59388842	59389029	.	+	2	Parent=gene1034
chr19	ENCODE	exon	59388842	59389333	.	+	.	Parent=gene1034
###
chr19	ENCODE	gene	59396422	59403327	.	+	.	ID=gene1035;Name=AC012314.14-003;name2=RPS9
chr19	ENCODE	exon	59396422	59396568	.	+	.	Parent=gene1035
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1035
chr19	ENCODE	CDS	59396865	59396961	.	+	0	Parent=gene1035
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1035
chr19	ENCODE	CDS	59397167	59397289	.	+	2	Parent=gene1035
chr19	ENCODE	exon	59401956	59402142	.	+	.	Parent=gene1035
chr19	ENCODE	CDS	59401956	59402142	.	+	2	Parent=gene1035
chr19	ENCODE	CDS	59403078	59403255	.	+	1	Parent=gene1035
chr19	ENCODE	exon	59403078	59403327	.	+	.	Parent=gene1035
###
chr19	ENCODE	gene	59396489	59402527	.	+	.	ID=gene1036;Name=AC012314.14-008;name2=RPS9
chr19	ENCODE	exon	59396489	59396568	.	+	.	Parent=gene1036
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1036
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1036
chr19	ENCODE	exon	59401956	59402527	.	+	.	Parent=gene1036
###
chr19	ENCODE	gene	59396538	59444674	.	+	.	ID=gene1037;name2=RPS9;Name=AC012314.14-002
chr19	ENCODE	exon	59396538	59396568	.	+	.	Parent=gene1037
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1037
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1037
chr19	ENCODE	exon	59427429	59427624	.	+	.	Parent=gene1037
chr19	ENCODE	exon	59442763	59444674	.	+	.	Parent=gene1037
###
chr19	ENCODE	gene	59396551	59403202	.	+	.	ID=gene1038;Name=AC012314.14-009;name2=RPS9
chr19	ENCODE	exon	59396551	59396573	.	+	.	Parent=gene1038
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1038
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1038
chr19	ENCODE	exon	59401956	59402142	.	+	.	Parent=gene1038
chr19	ENCODE	exon	59402233	59402404	.	+	.	Parent=gene1038
chr19	ENCODE	exon	59403078	59403202	.	+	.	Parent=gene1038
###
chr19	ENCODE	gene	59396552	59403327	.	+	.	ID=gene1039;Name=AC012314.14-001;name2=RPS9
chr19	ENCODE	exon	59396552	59396641	.	+	.	Parent=gene1039
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1039
chr19	ENCODE	CDS	59396865	59396961	.	+	0	Parent=gene1039
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1039
chr19	ENCODE	CDS	59397167	59397289	.	+	2	Parent=gene1039
chr19	ENCODE	exon	59401956	59402142	.	+	.	Parent=gene1039
chr19	ENCODE	CDS	59401956	59402142	.	+	2	Parent=gene1039
chr19	ENCODE	CDS	59403078	59403255	.	+	1	Parent=gene1039
chr19	ENCODE	exon	59403078	59403327	.	+	.	Parent=gene1039
###
chr19	ENCODE	gene	59396552	59403327	.	+	.	ID=gene1040;Name=AC012314.14-006;name2=RPS9
chr19	ENCODE	exon	59396552	59396641	.	+	.	Parent=gene1040
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1040
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1040
chr19	ENCODE	exon	59401956	59402142	.	+	.	Parent=gene1040
chr19	ENCODE	exon	59402233	59403327	.	+	.	Parent=gene1040
###
chr19	ENCODE	gene	59396552	59403327	.	+	.	ID=gene1041;Name=AC012314.14-007;name2=RPS9
chr19	ENCODE	exon	59396552	59396641	.	+	.	Parent=gene1041
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1041
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1041
chr19	ENCODE	exon	59401956	59402142	.	+	.	Parent=gene1041
chr19	ENCODE	exon	59402233	59402404	.	+	.	Parent=gene1041
chr19	ENCODE	exon	59403078	59403327	.	+	.	Parent=gene1041
###
chr19	ENCODE	gene	59396554	59403327	.	+	.	ID=gene1042;Name=AC012314.14-012;name2=RPS9
chr19	ENCODE	exon	59396554	59396568	.	+	.	Parent=gene1042
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1042
chr19	ENCODE	CDS	59396865	59396961	.	+	0	Parent=gene1042
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1042
chr19	ENCODE	CDS	59397167	59397289	.	+	2	Parent=gene1042
chr19	ENCODE	CDS	59403078	59403097	.	+	2	Parent=gene1042
chr19	ENCODE	exon	59403078	59403327	.	+	.	Parent=gene1042
###
chr19	ENCODE	gene	59396559	59403324	.	+	.	ID=gene1043;name2=RPS9;Name=AC012314.14-005
chr19	ENCODE	exon	59396559	59396573	.	+	.	Parent=gene1043
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1043
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1043
chr19	ENCODE	exon	59401956	59402404	.	+	.	Parent=gene1043
chr19	ENCODE	exon	59403078	59403324	.	+	.	Parent=gene1043
###
chr19	ENCODE	gene	59396813	59403327	.	+	.	ID=gene1044;Name=AC012314.14-010;name2=RPS9
chr19	ENCODE	exon	59396813	59396961	.	+	.	Parent=gene1044
chr19	ENCODE	CDS	59396865	59396961	.	+	0	Parent=gene1044
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1044
chr19	ENCODE	CDS	59397167	59397289	.	+	2	Parent=gene1044
chr19	ENCODE	exon	59401956	59402142	.	+	.	Parent=gene1044
chr19	ENCODE	CDS	59401956	59402142	.	+	2	Parent=gene1044
chr19	ENCODE	CDS	59403078	59403255	.	+	1	Parent=gene1044
chr19	ENCODE	exon	59403078	59403327	.	+	.	Parent=gene1044
###
chr19	ENCODE	gene	59396840	59397688	.	+	.	ID=gene1045;Name=AC012314.14-011;name2=RPS9
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1045
chr19	ENCODE	exon	59397167	59397688	.	+	.	Parent=gene1045
###
chr19	ENCODE	gene	59396840	59403310	.	+	.	ID=gene1046;Name=AC012314.14-004;name2=RPS9
chr19	ENCODE	exon	59396840	59396961	.	+	.	Parent=gene1046
chr19	ENCODE	exon	59397167	59397289	.	+	.	Parent=gene1046
chr19	ENCODE	exon	59401956	59403310	.	+	.	Parent=gene1046
###
chr19	ENCODE	gene	59411959	59419190	.	-	.	ID=gene1047;Name=AC012314.15-001;name2=LILRB3
chr19	ENCODE	exon	59411959	59412920	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59412774	59412920	.	-	0	Parent=gene1047
chr19	ENCODE	exon	59413000	59413155	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59413000	59413155	.	-	0	Parent=gene1047
chr19	ENCODE	exon	59414042	59414094	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59414042	59414094	.	-	2	Parent=gene1047
chr19	ENCODE	exon	59414326	59414363	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59414326	59414363	.	-	1	Parent=gene1047
chr19	ENCODE	exon	59414444	59414519	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59414444	59414519	.	-	2	Parent=gene1047
chr19	ENCODE	exon	59414810	59414926	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59414810	59414926	.	-	2	Parent=gene1047
chr19	ENCODE	exon	59415837	59415887	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59415837	59415887	.	-	2	Parent=gene1047
chr19	ENCODE	exon	59416210	59416512	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59416210	59416512	.	-	2	Parent=gene1047
chr19	ENCODE	exon	59416767	59417063	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59416767	59417063	.	-	2	Parent=gene1047
chr19	ENCODE	exon	59417512	59417814	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59417512	59417814	.	-	2	Parent=gene1047
chr19	ENCODE	exon	59417962	59418246	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59417962	59418246	.	-	2	Parent=gene1047
chr19	ENCODE	exon	59418431	59418466	.	-	.	Parent=gene1047
chr19	ENCODE	CDS	59418431	59418466	.	-	2	Parent=gene1047
chr19	ENCODE	CDS	59418627	59418660	.	-	0	Parent=gene1047
chr19	ENCODE	exon	59418627	59418711	.	-	.	Parent=gene1047
chr19	ENCODE	exon	59419105	59419190	.	-	.	Parent=gene1047
###
chr19	ENCODE	gene	59412777	59413379	.	-	.	ID=gene1048;Name=AC012314.15-002;name2=LILRB3
chr19	ENCODE	exon	59412777	59412920	.	-	.	Parent=gene1048
chr19	ENCODE	exon	59413000	59413379	.	-	.	Parent=gene1048
###
chr19	ENCODE	gene	59414276	59415036	.	-	.	ID=gene1049;Name=AC012314.15-003;name2=LILRB3
chr19	ENCODE	exon	59414276	59414363	.	-	.	Parent=gene1049
chr19	ENCODE	exon	59414444	59414519	.	-	.	Parent=gene1049
chr19	ENCODE	exon	59414810	59415036	.	-	.	Parent=gene1049
###
chr19	ENCODE	gene	59417662	59418771	.	-	.	ID=gene1050;Name=AC012314.15-004;name2=LILRB3
chr19	ENCODE	exon	59417662	59417814	.	-	.	Parent=gene1050
chr19	ENCODE	exon	59417962	59418246	.	-	.	Parent=gene1050
chr19	ENCODE	exon	59418431	59418771	.	-	.	Parent=gene1050
###
chr19	ENCODE	gene	59417695	59418771	.	-	.	ID=gene1051;Name=AC012314.15-005;name2=LILRB3
chr19	ENCODE	exon	59417695	59417814	.	-	.	Parent=gene1051
chr19	ENCODE	CDS	59417695	59417814	.	-	2	Parent=gene1051
chr19	ENCODE	exon	59417962	59418246	.	-	.	Parent=gene1051
chr19	ENCODE	CDS	59417962	59418246	.	-	2	Parent=gene1051
chr19	ENCODE	exon	59418431	59418466	.	-	.	Parent=gene1051
chr19	ENCODE	CDS	59418431	59418466	.	-	2	Parent=gene1051
chr19	ENCODE	CDS	59418627	59418660	.	-	0	Parent=gene1051
chr19	ENCODE	exon	59418627	59418771	.	-	.	Parent=gene1051
###
chr19	ENCODE	gene	59432280	59438429	.	-	.	ID=gene1052;Name=AC010492.1-002;name2=LILRA6
chr19	ENCODE	exon	59432280	59432881	.	-	.	Parent=gene1052
chr19	ENCODE	exon	59434174	59434301	.	-	.	Parent=gene1052
chr19	ENCODE	exon	59434510	59434777	.	-	.	Parent=gene1052
chr19	ENCODE	exon	59435589	59435639	.	-	.	Parent=gene1052
chr19	ENCODE	exon	59435962	59436264	.	-	.	Parent=gene1052
chr19	ENCODE	exon	59436519	59436815	.	-	.	Parent=gene1052
chr19	ENCODE	exon	59437350	59437566	.	-	.	Parent=gene1052
chr19	ENCODE	exon	59437714	59437998	.	-	.	Parent=gene1052
chr19	ENCODE	exon	59438183	59438218	.	-	.	Parent=gene1052
chr19	ENCODE	exon	59438379	59438429	.	-	.	Parent=gene1052
###
chr19	ENCODE	gene	59434237	59438452	.	-	.	ID=gene1053;Name=AC010492.1-003;name2=LILRA6
chr19	ENCODE	exon	59434237	59434777	.	-	.	Parent=gene1053
chr19	ENCODE	CDS	59434641	59434777	.	-	2	Parent=gene1053
chr19	ENCODE	exon	59435589	59435639	.	-	.	Parent=gene1053
chr19	ENCODE	CDS	59435589	59435639	.	-	2	Parent=gene1053
chr19	ENCODE	exon	59435962	59436264	.	-	.	Parent=gene1053
chr19	ENCODE	CDS	59435962	59436264	.	-	2	Parent=gene1053
chr19	ENCODE	exon	59436519	59436815	.	-	.	Parent=gene1053
chr19	ENCODE	CDS	59436519	59436815	.	-	2	Parent=gene1053
chr19	ENCODE	exon	59437264	59437566	.	-	.	Parent=gene1053
chr19	ENCODE	CDS	59437264	59437566	.	-	2	Parent=gene1053
chr19	ENCODE	exon	59437714	59437998	.	-	.	Parent=gene1053
chr19	ENCODE	CDS	59437714	59437998	.	-	2	Parent=gene1053
chr19	ENCODE	exon	59438183	59438218	.	-	.	Parent=gene1053
chr19	ENCODE	CDS	59438183	59438218	.	-	2	Parent=gene1053
chr19	ENCODE	CDS	59438379	59438412	.	-	0	Parent=gene1053
chr19	ENCODE	exon	59438379	59438452	.	-	.	Parent=gene1053
###
chr19	ENCODE	gene	59434641	59438942	.	-	.	ID=gene1054;Name=AC010492.1-001;name2=LILRA6
chr19	ENCODE	exon	59434641	59434777	.	-	.	Parent=gene1054
chr19	ENCODE	CDS	59434641	59434777	.	-	2	Parent=gene1054
chr19	ENCODE	exon	59435962	59436264	.	-	.	Parent=gene1054
chr19	ENCODE	CDS	59435962	59436264	.	-	2	Parent=gene1054
chr19	ENCODE	exon	59436519	59436815	.	-	.	Parent=gene1054
chr19	ENCODE	CDS	59436519	59436815	.	-	2	Parent=gene1054
chr19	ENCODE	exon	59437264	59437566	.	-	.	Parent=gene1054
chr19	ENCODE	CDS	59437264	59437566	.	-	2	Parent=gene1054
chr19	ENCODE	exon	59437714	59437998	.	-	.	Parent=gene1054
chr19	ENCODE	CDS	59437714	59437998	.	-	2	Parent=gene1054
chr19	ENCODE	exon	59438183	59438218	.	-	.	Parent=gene1054
chr19	ENCODE	CDS	59438183	59438218	.	-	2	Parent=gene1054
chr19	ENCODE	CDS	59438379	59438412	.	-	0	Parent=gene1054
chr19	ENCODE	exon	59438379	59438463	.	-	.	Parent=gene1054
chr19	ENCODE	exon	59438857	59438942	.	-	.	Parent=gene1054
###
chr19	ENCODE	gene	59436726	59438433	.	-	.	ID=gene1055;Name=AC010492.1-004;name2=LILRA6
chr19	ENCODE	exon	59436726	59436815	.	-	.	Parent=gene1055
chr19	ENCODE	exon	59437264	59437566	.	-	.	Parent=gene1055
chr19	ENCODE	exon	59437714	59437998	.	-	.	Parent=gene1055
chr19	ENCODE	exon	59438183	59438433	.	-	.	Parent=gene1055
###
chr19	ENCODE	gene	59446075	59452976	.	-	.	ID=gene1056;Name=AC010492.3-001;name2=LILRB5
chr19	ENCODE	exon	59446075	59446608	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59446462	59446608	.	-	0	Parent=gene1056
chr19	ENCODE	exon	59447729	59447781	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59447729	59447781	.	-	2	Parent=gene1056
chr19	ENCODE	exon	59448041	59448078	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59448041	59448078	.	-	1	Parent=gene1056
chr19	ENCODE	exon	59448161	59448224	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59448161	59448224	.	-	2	Parent=gene1056
chr19	ENCODE	exon	59448546	59448662	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59448546	59448662	.	-	2	Parent=gene1056
chr19	ENCODE	exon	59449693	59449740	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59449693	59449740	.	-	2	Parent=gene1056
chr19	ENCODE	exon	59450040	59450090	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59450040	59450090	.	-	2	Parent=gene1056
chr19	ENCODE	exon	59450410	59450712	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59450410	59450712	.	-	2	Parent=gene1056
chr19	ENCODE	exon	59450961	59451257	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59450961	59451257	.	-	2	Parent=gene1056
chr19	ENCODE	exon	59451718	59452017	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59451718	59452017	.	-	2	Parent=gene1056
chr19	ENCODE	exon	59452164	59452448	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59452164	59452448	.	-	2	Parent=gene1056
chr19	ENCODE	exon	59452636	59452671	.	-	.	Parent=gene1056
chr19	ENCODE	CDS	59452636	59452671	.	-	2	Parent=gene1056
chr19	ENCODE	CDS	59452835	59452868	.	-	0	Parent=gene1056
chr19	ENCODE	exon	59452835	59452976	.	-	.	Parent=gene1056
###
chr19	ENCODE	gene	59446101	59452967	.	-	.	ID=gene1057;Name=AC010492.3-004;name2=LILRB5
chr19	ENCODE	exon	59446101	59446844	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59447729	59447781	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59448041	59448078	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59448161	59448224	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59448546	59449743	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59450040	59450090	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59450410	59450712	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59450961	59451257	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59451718	59452017	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59452164	59452332	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59452636	59452671	.	-	.	Parent=gene1057
chr19	ENCODE	exon	59452835	59452967	.	-	.	Parent=gene1057
###
chr19	ENCODE	gene	59446143	59452937	.	-	.	ID=gene1058;Name=AC010492.3-002;name2=LILRB5
chr19	ENCODE	exon	59446143	59446608	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59446462	59446608	.	-	0	Parent=gene1058
chr19	ENCODE	exon	59447729	59447781	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59447729	59447781	.	-	2	Parent=gene1058
chr19	ENCODE	exon	59448041	59448078	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59448041	59448078	.	-	1	Parent=gene1058
chr19	ENCODE	exon	59448161	59448224	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59448161	59448224	.	-	2	Parent=gene1058
chr19	ENCODE	exon	59448546	59448662	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59448546	59448662	.	-	2	Parent=gene1058
chr19	ENCODE	exon	59449693	59449743	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59449693	59449743	.	-	2	Parent=gene1058
chr19	ENCODE	exon	59450040	59450090	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59450040	59450090	.	-	2	Parent=gene1058
chr19	ENCODE	exon	59450410	59450712	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59450410	59450712	.	-	2	Parent=gene1058
chr19	ENCODE	exon	59450961	59451257	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59450961	59451257	.	-	2	Parent=gene1058
chr19	ENCODE	exon	59452164	59452448	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59452164	59452448	.	-	2	Parent=gene1058
chr19	ENCODE	exon	59452636	59452671	.	-	.	Parent=gene1058
chr19	ENCODE	CDS	59452636	59452671	.	-	2	Parent=gene1058
chr19	ENCODE	CDS	59452835	59452868	.	-	0	Parent=gene1058
chr19	ENCODE	exon	59452835	59452937	.	-	.	Parent=gene1058
###
chr19	ENCODE	gene	59446222	59452920	.	-	.	ID=gene1059;Name=AC010492.3-003;name2=LILRB5
chr19	ENCODE	exon	59446222	59450712	.	-	.	Parent=gene1059
chr19	ENCODE	exon	59450961	59451257	.	-	.	Parent=gene1059
chr19	ENCODE	exon	59452164	59452920	.	-	.	Parent=gene1059
###
chr19	ENCODE	gene	59446231	59452949	.	-	.	ID=gene1060;Name=AC010492.3-005;name2=LILRB5
chr19	ENCODE	exon	59446231	59446844	.	-	.	Parent=gene1060
chr19	ENCODE	exon	59447729	59447781	.	-	.	Parent=gene1060
chr19	ENCODE	exon	59448041	59448078	.	-	.	Parent=gene1060
chr19	ENCODE	exon	59448161	59448224	.	-	.	Parent=gene1060
chr19	ENCODE	exon	59448546	59449740	.	-	.	Parent=gene1060
chr19	ENCODE	exon	59450040	59450491	.	-	.	Parent=gene1060
chr19	ENCODE	exon	59452285	59452448	.	-	.	Parent=gene1060
chr19	ENCODE	exon	59452636	59452671	.	-	.	Parent=gene1060
chr19	ENCODE	exon	59452835	59452949	.	-	.	Parent=gene1060
###
chr19	ENCODE	gene	59469487	59476550	.	-	.	ID=gene1061;Name=AC010518.1-001;name2=LILRB2
chr19	ENCODE	exon	59469487	59470495	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59470349	59470495	.	-	0	Parent=gene1061
chr19	ENCODE	exon	59471617	59471669	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59471617	59471669	.	-	2	Parent=gene1061
chr19	ENCODE	exon	59471930	59471967	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59471930	59471967	.	-	1	Parent=gene1061
chr19	ENCODE	exon	59472047	59472122	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59472047	59472122	.	-	2	Parent=gene1061
chr19	ENCODE	exon	59472473	59472595	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59472473	59472595	.	-	2	Parent=gene1061
chr19	ENCODE	exon	59473216	59473263	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59473216	59473263	.	-	2	Parent=gene1061
chr19	ENCODE	exon	59473555	59473605	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59473555	59473605	.	-	2	Parent=gene1061
chr19	ENCODE	exon	59473926	59474228	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59473926	59474228	.	-	2	Parent=gene1061
chr19	ENCODE	exon	59474479	59474775	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59474479	59474775	.	-	2	Parent=gene1061
chr19	ENCODE	exon	59475012	59475314	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59475012	59475314	.	-	2	Parent=gene1061
chr19	ENCODE	exon	59475458	59475742	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59475458	59475742	.	-	2	Parent=gene1061
chr19	ENCODE	exon	59475931	59475966	.	-	.	Parent=gene1061
chr19	ENCODE	CDS	59475931	59475966	.	-	2	Parent=gene1061
chr19	ENCODE	CDS	59476130	59476163	.	-	0	Parent=gene1061
chr19	ENCODE	exon	59476130	59476211	.	-	.	Parent=gene1061
chr19	ENCODE	exon	59476471	59476550	.	-	.	Parent=gene1061
###
chr19	ENCODE	gene	59470018	59476851	.	-	.	ID=gene1062;Name=AC010518.1-004;name2=LILRB2
chr19	ENCODE	exon	59470018	59470495	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59470349	59470495	.	-	0	Parent=gene1062
chr19	ENCODE	exon	59471617	59471669	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59471617	59471669	.	-	2	Parent=gene1062
chr19	ENCODE	exon	59471930	59471967	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59471930	59471967	.	-	1	Parent=gene1062
chr19	ENCODE	exon	59472047	59472122	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59472047	59472122	.	-	2	Parent=gene1062
chr19	ENCODE	exon	59472473	59472595	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59472473	59472595	.	-	2	Parent=gene1062
chr19	ENCODE	exon	59473216	59473263	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59473216	59473263	.	-	2	Parent=gene1062
chr19	ENCODE	exon	59473555	59473605	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59473555	59473605	.	-	2	Parent=gene1062
chr19	ENCODE	exon	59473926	59474228	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59473926	59474228	.	-	2	Parent=gene1062
chr19	ENCODE	exon	59474479	59474775	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59474479	59474775	.	-	2	Parent=gene1062
chr19	ENCODE	exon	59475012	59475314	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59475012	59475314	.	-	2	Parent=gene1062
chr19	ENCODE	exon	59475458	59475742	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59475458	59475742	.	-	2	Parent=gene1062
chr19	ENCODE	exon	59475931	59475966	.	-	.	Parent=gene1062
chr19	ENCODE	CDS	59475931	59475966	.	-	2	Parent=gene1062
chr19	ENCODE	CDS	59476130	59476163	.	-	0	Parent=gene1062
chr19	ENCODE	exon	59476130	59476211	.	-	.	Parent=gene1062
chr19	ENCODE	exon	59476628	59476851	.	-	.	Parent=gene1062
###
chr19	ENCODE	gene	59470132	59474210	.	-	.	ID=gene1063;Name=AC010518.1-007;name2=LILRB2
chr19	ENCODE	exon	59470132	59470495	.	-	.	Parent=gene1063
chr19	ENCODE	exon	59471617	59471669	.	-	.	Parent=gene1063
chr19	ENCODE	exon	59471913	59471967	.	-	.	Parent=gene1063
chr19	ENCODE	exon	59472047	59472122	.	-	.	Parent=gene1063
chr19	ENCODE	exon	59472473	59472595	.	-	.	Parent=gene1063
chr19	ENCODE	exon	59473216	59473266	.	-	.	Parent=gene1063
chr19	ENCODE	exon	59473555	59473605	.	-	.	Parent=gene1063
chr19	ENCODE	exon	59473926	59474210	.	-	.	Parent=gene1063
###
chr19	ENCODE	gene	59470132	59476165	.	-	.	ID=gene1064;Name=AC010518.1-005;name2=LILRB2
chr19	ENCODE	exon	59470132	59470495	.	-	.	Parent=gene1064
chr19	ENCODE	exon	59471617	59471669	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59471658	59471669	.	-	0	Parent=gene1064
chr19	ENCODE	exon	59471930	59471967	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59471930	59471967	.	-	2	Parent=gene1064
chr19	ENCODE	exon	59472473	59472595	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59472473	59472595	.	-	2	Parent=gene1064
chr19	ENCODE	exon	59473216	59473266	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59473216	59473266	.	-	2	Parent=gene1064
chr19	ENCODE	exon	59473555	59473605	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59473555	59473605	.	-	2	Parent=gene1064
chr19	ENCODE	exon	59473926	59474228	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59473926	59474228	.	-	2	Parent=gene1064
chr19	ENCODE	exon	59474479	59474775	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59474479	59474775	.	-	2	Parent=gene1064
chr19	ENCODE	exon	59475012	59475314	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59475012	59475314	.	-	2	Parent=gene1064
chr19	ENCODE	exon	59475458	59475742	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59475458	59475742	.	-	2	Parent=gene1064
chr19	ENCODE	exon	59475931	59475966	.	-	.	Parent=gene1064
chr19	ENCODE	CDS	59475931	59475966	.	-	2	Parent=gene1064
chr19	ENCODE	CDS	59476130	59476163	.	-	0	Parent=gene1064
chr19	ENCODE	exon	59476130	59476165	.	-	.	Parent=gene1064
###
chr19	ENCODE	gene	59470132	59476764	.	-	.	ID=gene1065;Name=AC010518.1-002;name2=LILRB2
chr19	ENCODE	exon	59470132	59470495	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59471617	59471669	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59471930	59471967	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59472047	59472122	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59472473	59473266	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59473555	59473605	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59473926	59474228	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59474479	59474775	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59475012	59475314	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59475458	59475742	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59475931	59475966	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59476130	59476211	.	-	.	Parent=gene1065
chr19	ENCODE	exon	59476628	59476764	.	-	.	Parent=gene1065
###
chr19	ENCODE	gene	59470132	59476851	.	-	.	ID=gene1066;Name=AC010518.1-003;name2=LILRB2
chr19	ENCODE	exon	59470132	59470495	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59470349	59470495	.	-	0	Parent=gene1066
chr19	ENCODE	exon	59471617	59471669	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59471617	59471669	.	-	2	Parent=gene1066
chr19	ENCODE	exon	59471930	59471967	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59471930	59471967	.	-	1	Parent=gene1066
chr19	ENCODE	exon	59472047	59472122	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59472047	59472122	.	-	2	Parent=gene1066
chr19	ENCODE	exon	59472473	59472595	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59472473	59472595	.	-	2	Parent=gene1066
chr19	ENCODE	exon	59473216	59473266	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59473216	59473266	.	-	2	Parent=gene1066
chr19	ENCODE	exon	59473555	59473605	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59473555	59473605	.	-	2	Parent=gene1066
chr19	ENCODE	exon	59473926	59474228	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59473926	59474228	.	-	2	Parent=gene1066
chr19	ENCODE	exon	59474479	59474775	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59474479	59474775	.	-	2	Parent=gene1066
chr19	ENCODE	exon	59475012	59475314	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59475012	59475314	.	-	2	Parent=gene1066
chr19	ENCODE	exon	59475458	59475742	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59475458	59475742	.	-	2	Parent=gene1066
chr19	ENCODE	exon	59475931	59475966	.	-	.	Parent=gene1066
chr19	ENCODE	CDS	59475931	59475966	.	-	2	Parent=gene1066
chr19	ENCODE	CDS	59476130	59476163	.	-	0	Parent=gene1066
chr19	ENCODE	exon	59476130	59476211	.	-	.	Parent=gene1066
chr19	ENCODE	exon	59476628	59476851	.	-	.	Parent=gene1066
###
chr19	ENCODE	gene	59475517	59476128	.	-	.	ID=gene1067;Name=AC010518.1-008;name2=LILRB2
chr19	ENCODE	exon	59475517	59475742	.	-	.	Parent=gene1067
chr19	ENCODE	exon	59475931	59476128	.	-	.	Parent=gene1067
###
chr19	ENCODE	gene	59491666	59495985	.	-	.	ID=gene1068;Name=AC010518.2-002;name2=LILRA3
chr19	ENCODE	exon	59491666	59491916	.	-	.	Parent=gene1068
chr19	ENCODE	CDS	59491858	59491916	.	-	2	Parent=gene1068
chr19	ENCODE	exon	59493739	59494041	.	-	.	Parent=gene1068
chr19	ENCODE	CDS	59493739	59494041	.	-	2	Parent=gene1068
chr19	ENCODE	exon	59494295	59494591	.	-	.	Parent=gene1068
chr19	ENCODE	CDS	59494295	59494591	.	-	2	Parent=gene1068
chr19	ENCODE	exon	59495020	59495130	.	-	.	Parent=gene1068
chr19	ENCODE	CDS	59495020	59495130	.	-	2	Parent=gene1068
chr19	ENCODE	exon	59495278	59495565	.	-	.	Parent=gene1068
chr19	ENCODE	CDS	59495278	59495565	.	-	2	Parent=gene1068
chr19	ENCODE	exon	59495755	59495790	.	-	.	Parent=gene1068
chr19	ENCODE	CDS	59495755	59495790	.	-	2	Parent=gene1068
chr19	ENCODE	exon	59495952	59495985	.	-	.	Parent=gene1068
chr19	ENCODE	CDS	59495952	59495985	.	-	0	Parent=gene1068
###
chr19	ENCODE	gene	59491666	59496077	.	-	.	ID=gene1069;name2=LILRA3;Name=AC010518.2-001
chr19	ENCODE	exon	59491666	59491916	.	-	.	Parent=gene1069
chr19	ENCODE	CDS	59491858	59491916	.	-	2	Parent=gene1069
chr19	ENCODE	exon	59493739	59494041	.	-	.	Parent=gene1069
chr19	ENCODE	CDS	59493739	59494041	.	-	2	Parent=gene1069
chr19	ENCODE	exon	59494295	59494591	.	-	.	Parent=gene1069
chr19	ENCODE	CDS	59494295	59494591	.	-	2	Parent=gene1069
chr19	ENCODE	exon	59494828	59495130	.	-	.	Parent=gene1069
chr19	ENCODE	CDS	59494828	59495130	.	-	2	Parent=gene1069
chr19	ENCODE	exon	59495278	59495565	.	-	.	Parent=gene1069
chr19	ENCODE	CDS	59495278	59495565	.	-	2	Parent=gene1069
chr19	ENCODE	exon	59495755	59495790	.	-	.	Parent=gene1069
chr19	ENCODE	CDS	59495755	59495790	.	-	2	Parent=gene1069
chr19	ENCODE	CDS	59495952	59495985	.	-	0	Parent=gene1069
chr19	ENCODE	exon	59495952	59496077	.	-	.	Parent=gene1069
###
chr19	ENCODE	gene	59491666	59501764	.	-	.	ID=gene1070;Name=AC010518.2-003;name2=LILRA3
chr19	ENCODE	exon	59491666	59491916	.	-	.	Parent=gene1070
chr19	ENCODE	CDS	59491858	59491916	.	-	2	Parent=gene1070
chr19	ENCODE	exon	59493739	59494041	.	-	.	Parent=gene1070
chr19	ENCODE	CDS	59493739	59494041	.	-	2	Parent=gene1070
chr19	ENCODE	exon	59494295	59494591	.	-	.	Parent=gene1070
chr19	ENCODE	CDS	59494295	59494591	.	-	2	Parent=gene1070
chr19	ENCODE	exon	59494828	59495130	.	-	.	Parent=gene1070
chr19	ENCODE	CDS	59494828	59495130	.	-	2	Parent=gene1070
chr19	ENCODE	exon	59495278	59495565	.	-	.	Parent=gene1070
chr19	ENCODE	CDS	59495278	59495565	.	-	2	Parent=gene1070
chr19	ENCODE	exon	59495755	59495790	.	-	.	Parent=gene1070
chr19	ENCODE	CDS	59495755	59495790	.	-	2	Parent=gene1070
chr19	ENCODE	CDS	59495952	59495985	.	-	0	Parent=gene1070
chr19	ENCODE	exon	59495952	59496033	.	-	.	Parent=gene1070
chr19	ENCODE	exon	59496416	59496533	.	-	.	Parent=gene1070
chr19	ENCODE	exon	59496716	59496780	.	-	.	Parent=gene1070
chr19	ENCODE	exon	59501004	59501039	.	-	.	Parent=gene1070
chr19	ENCODE	exon	59501664	59501764	.	-	.	Parent=gene1070
###
chr19	ENCODE	gene	59510165	59516221	.	-	.	ID=gene1071;Name=AC008984.1-001;name2=LILRA5
chr19	ENCODE	exon	59510165	59510646	.	-	.	Parent=gene1071
chr19	ENCODE	CDS	59510510	59510646	.	-	2	Parent=gene1071
chr19	ENCODE	exon	59510795	59510845	.	-	.	Parent=gene1071
chr19	ENCODE	CDS	59510795	59510845	.	-	2	Parent=gene1071
chr19	ENCODE	exon	59514496	59514798	.	-	.	Parent=gene1071
chr19	ENCODE	CDS	59514496	59514798	.	-	2	Parent=gene1071
chr19	ENCODE	exon	59514946	59515230	.	-	.	Parent=gene1071
chr19	ENCODE	CDS	59514946	59515230	.	-	2	Parent=gene1071
chr19	ENCODE	exon	59515417	59515452	.	-	.	Parent=gene1071
chr19	ENCODE	CDS	59515417	59515452	.	-	2	Parent=gene1071
chr19	ENCODE	exon	59515619	59515703	.	-	.	Parent=gene1071
chr19	ENCODE	CDS	59515619	59515703	.	-	0	Parent=gene1071
chr19	ENCODE	CDS	59516099	59516101	.	-	0	Parent=gene1071
chr19	ENCODE	exon	59516099	59516221	.	-	.	Parent=gene1071
###
chr19	ENCODE	gene	59510349	59516156	.	-	.	ID=gene1072;Name=AC008984.1-002;name2=LILRA5
chr19	ENCODE	exon	59510349	59510646	.	-	.	Parent=gene1072
chr19	ENCODE	CDS	59510510	59510646	.	-	2	Parent=gene1072
chr19	ENCODE	exon	59510795	59510845	.	-	.	Parent=gene1072
chr19	ENCODE	CDS	59510795	59510845	.	-	2	Parent=gene1072
chr19	ENCODE	exon	59514496	59514798	.	-	.	Parent=gene1072
chr19	ENCODE	CDS	59514496	59514798	.	-	2	Parent=gene1072
chr19	ENCODE	exon	59514946	59515230	.	-	.	Parent=gene1072
chr19	ENCODE	CDS	59514946	59515230	.	-	2	Parent=gene1072
chr19	ENCODE	exon	59515619	59515703	.	-	.	Parent=gene1072
chr19	ENCODE	CDS	59515619	59515703	.	-	0	Parent=gene1072
chr19	ENCODE	CDS	59516099	59516101	.	-	0	Parent=gene1072
chr19	ENCODE	exon	59516099	59516156	.	-	.	Parent=gene1072
###
chr19	ENCODE	gene	59510556	59514745	.	-	.	ID=gene1073;Name=AC008984.1-005;name2=LILRA5
chr19	ENCODE	exon	59510556	59510845	.	-	.	Parent=gene1073
chr19	ENCODE	exon	59514496	59514745	.	-	.	Parent=gene1073
###
chr19	ENCODE	gene	59514247	59516173	.	-	.	ID=gene1074;Name=AC008984.1-004;name2=LILRA5
chr19	ENCODE	exon	59514247	59514798	.	-	.	Parent=gene1074
chr19	ENCODE	exon	59514946	59515230	.	-	.	Parent=gene1074
chr19	ENCODE	exon	59515619	59515703	.	-	.	Parent=gene1074
chr19	ENCODE	exon	59516099	59516173	.	-	.	Parent=gene1074
###
chr19	ENCODE	gene	59514365	59516180	.	-	.	ID=gene1075;Name=AC008984.1-003;name2=LILRA5
chr19	ENCODE	exon	59514365	59514798	.	-	.	Parent=gene1075
chr19	ENCODE	exon	59514946	59515230	.	-	.	Parent=gene1075
chr19	ENCODE	exon	59515417	59515452	.	-	.	Parent=gene1075
chr19	ENCODE	exon	59515619	59515703	.	-	.	Parent=gene1075
chr19	ENCODE	exon	59516099	59516180	.	-	.	Parent=gene1075
###
chr19	ENCODE	gene	59536268	59542233	.	-	.	ID=gene1076;Name=AC008984.3-001;name2=LILRA4
chr19	ENCODE	exon	59536268	59536848	.	-	.	Parent=gene1076
chr19	ENCODE	CDS	59536655	59536848	.	-	2	Parent=gene1076
chr19	ENCODE	exon	59536998	59537048	.	-	.	Parent=gene1076
chr19	ENCODE	CDS	59536998	59537048	.	-	2	Parent=gene1076
chr19	ENCODE	exon	59539924	59540226	.	-	.	Parent=gene1076
chr19	ENCODE	CDS	59539924	59540226	.	-	2	Parent=gene1076
chr19	ENCODE	exon	59540483	59540779	.	-	.	Parent=gene1076
chr19	ENCODE	CDS	59540483	59540779	.	-	2	Parent=gene1076
chr19	ENCODE	exon	59541019	59541318	.	-	.	Parent=gene1076
chr19	ENCODE	CDS	59541019	59541318	.	-	2	Parent=gene1076
chr19	ENCODE	exon	59541479	59541763	.	-	.	Parent=gene1076
chr19	ENCODE	CDS	59541479	59541763	.	-	2	Parent=gene1076
chr19	ENCODE	exon	59541949	59541984	.	-	.	Parent=gene1076
chr19	ENCODE	CDS	59541949	59541984	.	-	2	Parent=gene1076
chr19	ENCODE	CDS	59542143	59542176	.	-	0	Parent=gene1076
chr19	ENCODE	exon	59542143	59542233	.	-	.	Parent=gene1076
###
chr19	ENCODE	gene	59541295	59542188	.	-	.	ID=gene1077;Name=AC008984.3-002;name2=LILRA4
chr19	ENCODE	exon	59541295	59541318	.	-	.	Parent=gene1077
chr19	ENCODE	exon	59541479	59541763	.	-	.	Parent=gene1077
chr19	ENCODE	exon	59541949	59542188	.	-	.	Parent=gene1077
###
chr19	ENCODE	gene	59557074	59559433	.	-	.	ID=gene1078;Name=AC008746.1-008;name2=LAIR1
chr19	ENCODE	exon	59557074	59558835	.	-	.	Parent=gene1078
chr19	ENCODE	exon	59559375	59559433	.	-	.	Parent=gene1078
###
chr19	ENCODE	gene	59557174	59573977	.	-	.	ID=gene1079;Name=AC008746.1-005;name2=LAIR1
chr19	ENCODE	exon	59557174	59558835	.	-	.	Parent=gene1079
chr19	ENCODE	CDS	59558689	59558835	.	-	0	Parent=gene1079
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1079
chr19	ENCODE	CDS	59559375	59559427	.	-	2	Parent=gene1079
chr19	ENCODE	exon	59559651	59559688	.	-	.	Parent=gene1079
chr19	ENCODE	CDS	59559651	59559688	.	-	1	Parent=gene1079
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1079
chr19	ENCODE	CDS	59559777	59559819	.	-	2	Parent=gene1079
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1079
chr19	ENCODE	CDS	59559912	59560040	.	-	2	Parent=gene1079
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1079
chr19	ENCODE	CDS	59560349	59560387	.	-	2	Parent=gene1079
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1079
chr19	ENCODE	CDS	59563441	59563491	.	-	2	Parent=gene1079
chr19	ENCODE	exon	59564335	59564628	.	-	.	Parent=gene1079
chr19	ENCODE	CDS	59564335	59564628	.	-	2	Parent=gene1079
chr19	ENCODE	CDS	59573681	59573696	.	-	0	Parent=gene1079
chr19	ENCODE	exon	59573681	59573977	.	-	.	Parent=gene1079
###
chr19	ENCODE	gene	59558096	59560768	.	-	.	ID=gene1080;Name=AC008746.1-007;name2=LAIR1
chr19	ENCODE	exon	59558096	59558835	.	-	.	Parent=gene1080
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1080
chr19	ENCODE	exon	59559651	59559688	.	-	.	Parent=gene1080
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1080
chr19	ENCODE	exon	59559912	59560768	.	-	.	Parent=gene1080
###
chr19	ENCODE	gene	59558096	59568284	.	-	.	ID=gene1081;Name=AC008746.1-003;name2=LAIR1
chr19	ENCODE	exon	59558096	59558835	.	-	.	Parent=gene1081
chr19	ENCODE	CDS	59558689	59558835	.	-	0	Parent=gene1081
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1081
chr19	ENCODE	CDS	59559375	59559427	.	-	2	Parent=gene1081
chr19	ENCODE	exon	59559651	59559688	.	-	.	Parent=gene1081
chr19	ENCODE	CDS	59559651	59559688	.	-	1	Parent=gene1081
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1081
chr19	ENCODE	CDS	59559777	59559819	.	-	2	Parent=gene1081
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1081
chr19	ENCODE	CDS	59559912	59560040	.	-	2	Parent=gene1081
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1081
chr19	ENCODE	CDS	59560349	59560387	.	-	2	Parent=gene1081
chr19	ENCODE	exon	59564335	59564628	.	-	.	Parent=gene1081
chr19	ENCODE	CDS	59564335	59564628	.	-	2	Parent=gene1081
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1081
chr19	ENCODE	CDS	59567714	59567749	.	-	2	Parent=gene1081
chr19	ENCODE	CDS	59568190	59568223	.	-	0	Parent=gene1081
chr19	ENCODE	exon	59568190	59568284	.	-	.	Parent=gene1081
###
chr19	ENCODE	gene	59558096	59568376	.	-	.	ID=gene1082;Name=AC008746.1-001;name2=LAIR1
chr19	ENCODE	exon	59558096	59558835	.	-	.	Parent=gene1082
chr19	ENCODE	CDS	59558689	59558835	.	-	0	Parent=gene1082
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1082
chr19	ENCODE	CDS	59559375	59559427	.	-	2	Parent=gene1082
chr19	ENCODE	exon	59559651	59559688	.	-	.	Parent=gene1082
chr19	ENCODE	CDS	59559651	59559688	.	-	1	Parent=gene1082
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1082
chr19	ENCODE	CDS	59559777	59559819	.	-	2	Parent=gene1082
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1082
chr19	ENCODE	CDS	59559912	59560040	.	-	2	Parent=gene1082
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1082
chr19	ENCODE	CDS	59560349	59560387	.	-	2	Parent=gene1082
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1082
chr19	ENCODE	CDS	59563441	59563491	.	-	2	Parent=gene1082
chr19	ENCODE	exon	59564335	59564628	.	-	.	Parent=gene1082
chr19	ENCODE	CDS	59564335	59564628	.	-	2	Parent=gene1082
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1082
chr19	ENCODE	CDS	59567714	59567749	.	-	2	Parent=gene1082
chr19	ENCODE	CDS	59568190	59568223	.	-	0	Parent=gene1082
chr19	ENCODE	exon	59568190	59568376	.	-	.	Parent=gene1082
###
chr19	ENCODE	gene	59558096	59568414	.	-	.	ID=gene1083;Name=AC008746.1-002;name2=LAIR1
chr19	ENCODE	exon	59558096	59558835	.	-	.	Parent=gene1083
chr19	ENCODE	CDS	59558689	59558835	.	-	0	Parent=gene1083
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1083
chr19	ENCODE	CDS	59559375	59559427	.	-	2	Parent=gene1083
chr19	ENCODE	exon	59559651	59559688	.	-	.	Parent=gene1083
chr19	ENCODE	CDS	59559651	59559688	.	-	1	Parent=gene1083
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1083
chr19	ENCODE	CDS	59559777	59559819	.	-	2	Parent=gene1083
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1083
chr19	ENCODE	CDS	59559912	59560040	.	-	2	Parent=gene1083
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1083
chr19	ENCODE	CDS	59560349	59560387	.	-	2	Parent=gene1083
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1083
chr19	ENCODE	CDS	59563441	59563491	.	-	2	Parent=gene1083
chr19	ENCODE	exon	59564335	59564625	.	-	.	Parent=gene1083
chr19	ENCODE	CDS	59564335	59564625	.	-	2	Parent=gene1083
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1083
chr19	ENCODE	CDS	59567714	59567749	.	-	2	Parent=gene1083
chr19	ENCODE	CDS	59568190	59568223	.	-	0	Parent=gene1083
chr19	ENCODE	exon	59568190	59568414	.	-	.	Parent=gene1083
###
chr19	ENCODE	gene	59558622	59564612	.	-	.	ID=gene1084;Name=AC008746.1-013;name2=LAIR1
chr19	ENCODE	exon	59558622	59558835	.	-	.	Parent=gene1084
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1084
chr19	ENCODE	exon	59559651	59559819	.	-	.	Parent=gene1084
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1084
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1084
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1084
chr19	ENCODE	exon	59564429	59564612	.	-	.	Parent=gene1084
###
chr19	ENCODE	gene	59558679	59568289	.	-	.	ID=gene1085;Name=AC008746.1-009;name2=LAIR1
chr19	ENCODE	exon	59558679	59558835	.	-	.	Parent=gene1085
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1085
chr19	ENCODE	exon	59559651	59559688	.	-	.	Parent=gene1085
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1085
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1085
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1085
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1085
chr19	ENCODE	exon	59564429	59564628	.	-	.	Parent=gene1085
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1085
chr19	ENCODE	exon	59568190	59568289	.	-	.	Parent=gene1085
###
chr19	ENCODE	gene	59558688	59568226	.	-	.	ID=gene1086;Name=AC008746.1-004;name2=LAIR1
chr19	ENCODE	exon	59558688	59558835	.	-	.	Parent=gene1086
chr19	ENCODE	CDS	59558689	59558835	.	-	0	Parent=gene1086
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1086
chr19	ENCODE	CDS	59559375	59559427	.	-	2	Parent=gene1086
chr19	ENCODE	exon	59559651	59559688	.	-	.	Parent=gene1086
chr19	ENCODE	CDS	59559651	59559688	.	-	1	Parent=gene1086
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1086
chr19	ENCODE	CDS	59559777	59559819	.	-	2	Parent=gene1086
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1086
chr19	ENCODE	CDS	59559912	59560040	.	-	2	Parent=gene1086
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1086
chr19	ENCODE	CDS	59560349	59560387	.	-	2	Parent=gene1086
chr19	ENCODE	exon	59564335	59564625	.	-	.	Parent=gene1086
chr19	ENCODE	CDS	59564335	59564625	.	-	2	Parent=gene1086
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1086
chr19	ENCODE	CDS	59567714	59567749	.	-	2	Parent=gene1086
chr19	ENCODE	CDS	59568190	59568223	.	-	0	Parent=gene1086
chr19	ENCODE	exon	59568190	59568226	.	-	.	Parent=gene1086
###
chr19	ENCODE	gene	59558688	59568226	.	-	.	ID=gene1087;Name=AC008746.1-006;name2=LAIR1
chr19	ENCODE	exon	59558688	59558835	.	-	.	Parent=gene1087
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1087
chr19	ENCODE	exon	59559651	59559819	.	-	.	Parent=gene1087
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1087
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1087
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1087
chr19	ENCODE	exon	59564335	59564628	.	-	.	Parent=gene1087
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1087
chr19	ENCODE	exon	59568190	59568226	.	-	.	Parent=gene1087
###
chr19	ENCODE	gene	59558767	59568255	.	-	.	ID=gene1088;Name=AC008746.1-011;name2=LAIR1
chr19	ENCODE	exon	59558767	59558835	.	-	.	Parent=gene1088
chr19	ENCODE	exon	59559375	59559427	.	-	.	Parent=gene1088
chr19	ENCODE	exon	59559651	59559688	.	-	.	Parent=gene1088
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1088
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1088
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1088
chr19	ENCODE	exon	59563262	59563491	.	-	.	Parent=gene1088
chr19	ENCODE	exon	59564429	59564628	.	-	.	Parent=gene1088
chr19	ENCODE	exon	59567714	59567905	.	-	.	Parent=gene1088
chr19	ENCODE	exon	59568190	59568255	.	-	.	Parent=gene1088
###
chr19	ENCODE	gene	59559401	59568509	.	-	.	ID=gene1089;Name=AC008746.1-019;name2=LAIR1
chr19	ENCODE	exon	59559401	59559427	.	-	.	Parent=gene1089
chr19	ENCODE	exon	59559651	59559688	.	-	.	Parent=gene1089
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1089
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1089
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1089
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1089
chr19	ENCODE	exon	59564429	59564628	.	-	.	Parent=gene1089
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1089
chr19	ENCODE	exon	59568449	59568509	.	-	.	Parent=gene1089
###
chr19	ENCODE	gene	59559658	59568286	.	-	.	ID=gene1090;name2=LAIR1;Name=AC008746.1-010
chr19	ENCODE	exon	59559658	59559688	.	-	.	Parent=gene1090
chr19	ENCODE	exon	59559777	59559819	.	-	.	Parent=gene1090
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1090
chr19	ENCODE	exon	59560133	59560387	.	-	.	Parent=gene1090
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1090
chr19	ENCODE	exon	59564335	59564628	.	-	.	Parent=gene1090
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1090
chr19	ENCODE	exon	59568190	59568286	.	-	.	Parent=gene1090
###
chr19	ENCODE	gene	59559707	59561050	.	-	.	ID=gene1091;Name=AC008746.1-014;name2=LAIR1
chr19	ENCODE	exon	59559707	59559819	.	-	.	Parent=gene1091
chr19	ENCODE	exon	59559912	59560040	.	-	.	Parent=gene1091
chr19	ENCODE	exon	59560349	59561050	.	-	.	Parent=gene1091
###
chr19	ENCODE	gene	59559978	59568518	.	-	.	ID=gene1092;Name=AC008746.1-018;name2=LAIR1
chr19	ENCODE	exon	59559978	59560040	.	-	.	Parent=gene1092
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1092
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1092
chr19	ENCODE	exon	59564335	59564625	.	-	.	Parent=gene1092
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1092
chr19	ENCODE	exon	59568449	59568518	.	-	.	Parent=gene1092
###
chr19	ENCODE	gene	59560006	59568350	.	-	.	ID=gene1093;Name=AC008746.1-021;name2=LAIR1
chr19	ENCODE	exon	59560006	59560040	.	-	.	Parent=gene1093
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1093
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1093
chr19	ENCODE	exon	59564335	59564662	.	-	.	Parent=gene1093
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1093
chr19	ENCODE	exon	59568190	59568350	.	-	.	Parent=gene1093
###
chr19	ENCODE	gene	59560029	59568350	.	-	.	ID=gene1094;Name=AC008746.1-020;name2=LAIR1
chr19	ENCODE	exon	59560029	59560040	.	-	.	Parent=gene1094
chr19	ENCODE	exon	59560349	59560387	.	-	.	Parent=gene1094
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1094
chr19	ENCODE	exon	59564429	59564662	.	-	.	Parent=gene1094
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1094
chr19	ENCODE	exon	59568190	59568350	.	-	.	Parent=gene1094
###
chr19	ENCODE	gene	59561427	59564368	.	-	.	ID=gene1095;Name=AC008746.1-016;name2=LAIR1
chr19	ENCODE	exon	59561427	59562044	.	-	.	Parent=gene1095
chr19	ENCODE	CDS	59561890	59562044	.	-	2	Parent=gene1095
chr19	ENCODE	exon	59563441	59563491	.	-	.	Parent=gene1095
chr19	ENCODE	CDS	59563441	59563491	.	-	2	Parent=gene1095
chr19	ENCODE	exon	59564335	59564368	.	-	.	Parent=gene1095
chr19	ENCODE	CDS	59564335	59564368	.	-	0	Parent=gene1095
###
chr19	ENCODE	gene	59564114	59568533	.	-	.	ID=gene1096;name2=LAIR1;Name=AC008746.1-012
chr19	ENCODE	exon	59564114	59564153	.	-	.	Parent=gene1096
chr19	ENCODE	exon	59564335	59564628	.	-	.	Parent=gene1096
chr19	ENCODE	exon	59567714	59567905	.	-	.	Parent=gene1096
chr19	ENCODE	exon	59568190	59568533	.	-	.	Parent=gene1096
###
chr19	ENCODE	gene	59564219	59568268	.	-	.	ID=gene1097;Name=AC008746.1-023;name2=LAIR1
chr19	ENCODE	exon	59564219	59564662	.	-	.	Parent=gene1097
chr19	ENCODE	CDS	59564598	59564662	.	-	2	Parent=gene1097
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1097
chr19	ENCODE	CDS	59567714	59567749	.	-	2	Parent=gene1097
chr19	ENCODE	CDS	59568190	59568223	.	-	0	Parent=gene1097
chr19	ENCODE	exon	59568190	59568268	.	-	.	Parent=gene1097
###
chr19	ENCODE	gene	59564378	59568350	.	-	.	ID=gene1098;Name=AC008746.1-022;name2=LAIR1
chr19	ENCODE	exon	59564378	59564662	.	-	.	Parent=gene1098
chr19	ENCODE	exon	59567714	59567905	.	-	.	Parent=gene1098
chr19	ENCODE	exon	59568190	59568350	.	-	.	Parent=gene1098
###
chr19	ENCODE	gene	59564379	59572018	.	-	.	ID=gene1099;Name=AC008746.1-017;name2=LAIR1
chr19	ENCODE	exon	59564379	59564628	.	-	.	Parent=gene1099
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1099
chr19	ENCODE	exon	59571731	59572018	.	-	.	Parent=gene1099
###
chr19	ENCODE	gene	59564401	59573910	.	-	.	ID=gene1100;Name=AC008746.1-015;name2=LAIR1
chr19	ENCODE	exon	59564401	59564628	.	-	.	Parent=gene1100
chr19	ENCODE	CDS	59564401	59564628	.	-	2	Parent=gene1100
chr19	ENCODE	exon	59567714	59567749	.	-	.	Parent=gene1100
chr19	ENCODE	CDS	59567714	59567749	.	-	2	Parent=gene1100
chr19	ENCODE	CDS	59573681	59573696	.	-	0	Parent=gene1100
chr19	ENCODE	exon	59573681	59573910	.	-	.	Parent=gene1100
###
chr19	ENCODE	gene	59618185	59624317	.	+	.	ID=gene1101;Name=AC008746.2-010;name2=TTYH1
chr19	ENCODE	exon	59618185	59618280	.	+	.	Parent=gene1101
chr19	ENCODE	CDS	59618239	59618280	.	+	0	Parent=gene1101
chr19	ENCODE	exon	59622114	59622292	.	+	.	Parent=gene1101
chr19	ENCODE	CDS	59622114	59622292	.	+	0	Parent=gene1101
chr19	ENCODE	exon	59624263	59624317	.	+	.	Parent=gene1101
chr19	ENCODE	CDS	59624263	59624317	.	+	1	Parent=gene1101
###
chr19	ENCODE	gene	59618417	59639892	.	+	.	ID=gene1102;Name=AC008746.2-001;name2=TTYH1
chr19	ENCODE	exon	59618417	59618664	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59618539	59618664	.	+	0	Parent=gene1102
chr19	ENCODE	exon	59622114	59622292	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59622114	59622292	.	+	0	Parent=gene1102
chr19	ENCODE	exon	59624263	59624374	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59624263	59624374	.	+	1	Parent=gene1102
chr19	ENCODE	exon	59625176	59625396	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59625176	59625396	.	+	0	Parent=gene1102
chr19	ENCODE	exon	59629662	59629757	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59629662	59629757	.	+	1	Parent=gene1102
chr19	ENCODE	exon	59632297	59632369	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59632297	59632369	.	+	1	Parent=gene1102
chr19	ENCODE	exon	59632872	59632947	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59632872	59632947	.	+	0	Parent=gene1102
chr19	ENCODE	exon	59633540	59633595	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59633540	59633595	.	+	2	Parent=gene1102
chr19	ENCODE	exon	59633803	59633895	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59633803	59633895	.	+	0	Parent=gene1102
chr19	ENCODE	exon	59634089	59634181	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59634089	59634181	.	+	0	Parent=gene1102
chr19	ENCODE	exon	59638534	59638676	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59638534	59638676	.	+	0	Parent=gene1102
chr19	ENCODE	exon	59638820	59638865	.	+	.	Parent=gene1102
chr19	ENCODE	CDS	59638820	59638865	.	+	1	Parent=gene1102
chr19	ENCODE	CDS	59639080	59639121	.	+	0	Parent=gene1102
chr19	ENCODE	exon	59639080	59639163	.	+	.	Parent=gene1102
chr19	ENCODE	exon	59639325	59639892	.	+	.	Parent=gene1102
###
chr19	ENCODE	gene	59618436	59639711	.	+	.	ID=gene1103;Name=AC008746.2-002;name2=TTYH1
chr19	ENCODE	exon	59618436	59618664	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59618539	59618664	.	+	0	Parent=gene1103
chr19	ENCODE	exon	59622114	59622292	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59622114	59622292	.	+	0	Parent=gene1103
chr19	ENCODE	exon	59624263	59624374	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59624263	59624374	.	+	1	Parent=gene1103
chr19	ENCODE	exon	59625176	59625396	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59625176	59625396	.	+	0	Parent=gene1103
chr19	ENCODE	exon	59629662	59629757	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59629662	59629757	.	+	1	Parent=gene1103
chr19	ENCODE	exon	59632297	59632369	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59632297	59632369	.	+	1	Parent=gene1103
chr19	ENCODE	exon	59632872	59632947	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59632872	59632947	.	+	0	Parent=gene1103
chr19	ENCODE	exon	59633540	59633595	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59633540	59633595	.	+	2	Parent=gene1103
chr19	ENCODE	exon	59633803	59633895	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59633803	59633895	.	+	0	Parent=gene1103
chr19	ENCODE	exon	59634089	59634181	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59634089	59634181	.	+	0	Parent=gene1103
chr19	ENCODE	exon	59638534	59638676	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59638534	59638676	.	+	0	Parent=gene1103
chr19	ENCODE	exon	59638820	59638865	.	+	.	Parent=gene1103
chr19	ENCODE	CDS	59638820	59638865	.	+	1	Parent=gene1103
chr19	ENCODE	CDS	59639083	59639121	.	+	0	Parent=gene1103
chr19	ENCODE	exon	59639083	59639163	.	+	.	Parent=gene1103
chr19	ENCODE	exon	59639325	59639711	.	+	.	Parent=gene1103
###
chr19	ENCODE	gene	59618451	59629717	.	+	.	ID=gene1104;Name=AC008746.2-007;name2=TTYH1
chr19	ENCODE	exon	59618451	59618664	.	+	.	Parent=gene1104
chr19	ENCODE	CDS	59618539	59618664	.	+	0	Parent=gene1104
chr19	ENCODE	exon	59619042	59619052	.	+	.	Parent=gene1104
chr19	ENCODE	CDS	59619042	59619052	.	+	0	Parent=gene1104
chr19	ENCODE	exon	59619775	59619910	.	+	.	Parent=gene1104
chr19	ENCODE	CDS	59619775	59619910	.	+	1	Parent=gene1104
chr19	ENCODE	exon	59622114	59622292	.	+	.	Parent=gene1104
chr19	ENCODE	CDS	59622114	59622292	.	+	0	Parent=gene1104
chr19	ENCODE	exon	59624263	59624374	.	+	.	Parent=gene1104
chr19	ENCODE	CDS	59624263	59624374	.	+	1	Parent=gene1104
chr19	ENCODE	exon	59625176	59625396	.	+	.	Parent=gene1104
chr19	ENCODE	CDS	59625176	59625396	.	+	0	Parent=gene1104
chr19	ENCODE	exon	59629662	59629717	.	+	.	Parent=gene1104
chr19	ENCODE	CDS	59629662	59629717	.	+	1	Parent=gene1104
###
chr19	ENCODE	gene	59618496	59629757	.	+	.	ID=gene1105;Name=AC008746.2-008;name2=TTYH1
chr19	ENCODE	exon	59618496	59618664	.	+	.	Parent=gene1105
chr19	ENCODE	exon	59622114	59622292	.	+	.	Parent=gene1105
chr19	ENCODE	exon	59625176	59625396	.	+	.	Parent=gene1105
chr19	ENCODE	exon	59629662	59629757	.	+	.	Parent=gene1105
###
chr19	ENCODE	gene	59618498	59639711	.	+	.	ID=gene1106;name2=TTYH1;Name=AC008746.2-005
chr19	ENCODE	exon	59618498	59618664	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59619042	59619910	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59622114	59622292	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59624263	59624374	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59625176	59625396	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59629662	59629757	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59632297	59632369	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59632872	59632947	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59633540	59633595	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59633803	59633895	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59634089	59634181	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59638534	59638676	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59638820	59638865	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59639083	59639163	.	+	.	Parent=gene1106
chr19	ENCODE	exon	59639325	59639711	.	+	.	Parent=gene1106
###
chr19	ENCODE	gene	59618512	59639711	.	+	.	ID=gene1107;Name=AC008746.2-003;name2=TTYH1
chr19	ENCODE	exon	59618512	59618664	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59618539	59618664	.	+	0	Parent=gene1107
chr19	ENCODE	exon	59622114	59622292	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59622114	59622292	.	+	0	Parent=gene1107
chr19	ENCODE	exon	59624263	59624374	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59624263	59624374	.	+	1	Parent=gene1107
chr19	ENCODE	exon	59625176	59625396	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59625176	59625396	.	+	0	Parent=gene1107
chr19	ENCODE	exon	59629662	59629757	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59629662	59629757	.	+	1	Parent=gene1107
chr19	ENCODE	exon	59632297	59632369	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59632297	59632369	.	+	1	Parent=gene1107
chr19	ENCODE	exon	59632872	59632947	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59632872	59632947	.	+	0	Parent=gene1107
chr19	ENCODE	exon	59633540	59633595	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59633540	59633595	.	+	2	Parent=gene1107
chr19	ENCODE	exon	59633803	59633895	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59633803	59633895	.	+	0	Parent=gene1107
chr19	ENCODE	exon	59634089	59634181	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59634089	59634181	.	+	0	Parent=gene1107
chr19	ENCODE	exon	59638534	59638676	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59638534	59638676	.	+	0	Parent=gene1107
chr19	ENCODE	exon	59639083	59639163	.	+	.	Parent=gene1107
chr19	ENCODE	CDS	59639083	59639163	.	+	1	Parent=gene1107
chr19	ENCODE	CDS	59639325	59639358	.	+	1	Parent=gene1107
chr19	ENCODE	exon	59639325	59639711	.	+	.	Parent=gene1107
###
chr19	ENCODE	gene	59621248	59622522	.	+	.	ID=gene1108;Name=AC008746.2-011;name2=TTYH1
chr19	ENCODE	exon	59621248	59621698	.	+	.	Parent=gene1108
chr19	ENCODE	exon	59622114	59622292	.	+	.	Parent=gene1108
chr19	ENCODE	exon	59622437	59622522	.	+	.	Parent=gene1108
###
chr19	ENCODE	gene	59622182	59636702	.	+	.	ID=gene1109;Name=AC008746.2-006;name2=TTYH1
chr19	ENCODE	exon	59622182	59622528	.	+	.	Parent=gene1109
chr19	ENCODE	exon	59624263	59624374	.	+	.	Parent=gene1109
chr19	ENCODE	exon	59625185	59625396	.	+	.	Parent=gene1109
chr19	ENCODE	exon	59629662	59629757	.	+	.	Parent=gene1109
chr19	ENCODE	exon	59632297	59632369	.	+	.	Parent=gene1109
chr19	ENCODE	exon	59632872	59632947	.	+	.	Parent=gene1109
chr19	ENCODE	exon	59633540	59633595	.	+	.	Parent=gene1109
chr19	ENCODE	exon	59633803	59633895	.	+	.	Parent=gene1109
chr19	ENCODE	exon	59634089	59636702	.	+	.	Parent=gene1109
###
chr19	ENCODE	gene	59623654	59629722	.	+	.	ID=gene1110;Name=AC008746.2-013;name2=TTYH1
chr19	ENCODE	exon	59623654	59623818	.	+	.	Parent=gene1110
chr19	ENCODE	exon	59624263	59624374	.	+	.	Parent=gene1110
chr19	ENCODE	exon	59625176	59625396	.	+	.	Parent=gene1110
chr19	ENCODE	exon	59629662	59629722	.	+	.	Parent=gene1110
###
chr19	ENCODE	gene	59623685	59632343	.	+	.	ID=gene1111;Name=AC008746.2-012;name2=TTYH1
chr19	ENCODE	exon	59623685	59623787	.	+	.	Parent=gene1111
chr19	ENCODE	CDS	59623744	59623787	.	+	0	Parent=gene1111
chr19	ENCODE	exon	59624263	59624374	.	+	.	Parent=gene1111
chr19	ENCODE	CDS	59624263	59624374	.	+	1	Parent=gene1111
chr19	ENCODE	exon	59625176	59625396	.	+	.	Parent=gene1111
chr19	ENCODE	CDS	59625176	59625396	.	+	0	Parent=gene1111
chr19	ENCODE	exon	59629662	59629757	.	+	.	Parent=gene1111
chr19	ENCODE	CDS	59629662	59629757	.	+	1	Parent=gene1111
chr19	ENCODE	exon	59632297	59632343	.	+	.	Parent=gene1111
chr19	ENCODE	CDS	59632297	59632343	.	+	1	Parent=gene1111
###
chr19	ENCODE	gene	59629463	59639711	.	+	.	ID=gene1112;Name=AC008746.2-004;name2=TTYH1
chr19	ENCODE	exon	59629463	59629555	.	+	.	Parent=gene1112
chr19	ENCODE	CDS	59629554	59629555	.	+	0	Parent=gene1112
chr19	ENCODE	exon	59629662	59629757	.	+	.	Parent=gene1112
chr19	ENCODE	CDS	59629662	59629757	.	+	1	Parent=gene1112
chr19	ENCODE	exon	59632297	59632369	.	+	.	Parent=gene1112
chr19	ENCODE	CDS	59632297	59632369	.	+	1	Parent=gene1112
chr19	ENCODE	exon	59632872	59632947	.	+	.	Parent=gene1112
chr19	ENCODE	CDS	59632872	59632947	.	+	0	Parent=gene1112
chr19	ENCODE	exon	59633540	59633595	.	+	.	Parent=gene1112
chr19	ENCODE	CDS	59633540	59633595	.	+	2	Parent=gene1112
chr19	ENCODE	exon	59633803	59633895	.	+	.	Parent=gene1112
chr19	ENCODE	CDS	59633803	59633895	.	+	0	Parent=gene1112
chr19	ENCODE	exon	59634089	59634181	.	+	.	Parent=gene1112
chr19	ENCODE	CDS	59634089	59634181	.	+	0	Parent=gene1112
chr19	ENCODE	exon	59638534	59638676	.	+	.	Parent=gene1112
chr19	ENCODE	CDS	59638534	59638676	.	+	0	Parent=gene1112
chr19	ENCODE	exon	59638820	59638865	.	+	.	Parent=gene1112
chr19	ENCODE	CDS	59638820	59638865	.	+	1	Parent=gene1112
chr19	ENCODE	CDS	59639080	59639121	.	+	0	Parent=gene1112
chr19	ENCODE	exon	59639080	59639163	.	+	.	Parent=gene1112
chr19	ENCODE	exon	59639325	59639711	.	+	.	Parent=gene1112
###
chr19	ENCODE	gene	59633803	59639464	.	+	.	ID=gene1113;Name=AC008746.2-009;name2=TTYH1
chr19	ENCODE	exon	59633803	59633895	.	+	.	Parent=gene1113
chr19	ENCODE	exon	59634089	59634181	.	+	.	Parent=gene1113
chr19	ENCODE	exon	59638534	59638676	.	+	.	Parent=gene1113
chr19	ENCODE	exon	59638820	59638865	.	+	.	Parent=gene1113
chr19	ENCODE	exon	59639083	59639464	.	+	.	Parent=gene1113
###
chr19	ENCODE	gene	59637952	59639320	.	+	.	ID=gene1114;Name=AC008746.2-014;name2=TTYH1
chr19	ENCODE	exon	59637952	59638105	.	+	.	Parent=gene1114
chr19	ENCODE	exon	59638534	59638676	.	+	.	Parent=gene1114
chr19	ENCODE	exon	59638820	59638865	.	+	.	Parent=gene1114
chr19	ENCODE	exon	59639083	59639320	.	+	.	Parent=gene1114
###
chr19	ENCODE	gene	59638997	59639709	.	+	.	ID=gene1115;Name=AC008746.2-015;name2=TTYH1
chr19	ENCODE	exon	59638997	59639163	.	+	.	Parent=gene1115
chr19	ENCODE	exon	59639325	59639709	.	+	.	Parent=gene1115
###
chr19	ENCODE	gene	59651877	59665029	.	+	.	ID=gene1116;Name=AC008746.4-001;name2=LENG8
chr19	ENCODE	exon	59651877	59652300	.	+	.	Parent=gene1116
chr19	ENCODE	exon	59654279	59654371	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59654334	59654371	.	+	0	Parent=gene1116
chr19	ENCODE	exon	59655082	59655256	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59655082	59655256	.	+	1	Parent=gene1116
chr19	ENCODE	exon	59655642	59655743	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59655642	59655743	.	+	0	Parent=gene1116
chr19	ENCODE	exon	59656537	59656647	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59656537	59656647	.	+	0	Parent=gene1116
chr19	ENCODE	exon	59657421	59657673	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59657421	59657673	.	+	0	Parent=gene1116
chr19	ENCODE	exon	59657942	59658083	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59657942	59658083	.	+	2	Parent=gene1116
chr19	ENCODE	exon	59658355	59658558	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59658355	59658558	.	+	1	Parent=gene1116
chr19	ENCODE	exon	59658958	59659236	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59658958	59659236	.	+	1	Parent=gene1116
chr19	ENCODE	exon	59659316	59659456	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59659316	59659456	.	+	1	Parent=gene1116
chr19	ENCODE	exon	59659627	59659912	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59659627	59659912	.	+	1	Parent=gene1116
chr19	ENCODE	exon	59660738	59660839	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59660738	59660839	.	+	0	Parent=gene1116
chr19	ENCODE	exon	59660925	59660993	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59660925	59660993	.	+	0	Parent=gene1116
chr19	ENCODE	exon	59661094	59661223	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59661094	59661223	.	+	0	Parent=gene1116
chr19	ENCODE	exon	59661305	59661512	.	+	.	Parent=gene1116
chr19	ENCODE	CDS	59661305	59661512	.	+	2	Parent=gene1116
chr19	ENCODE	CDS	59663758	59663920	.	+	1	Parent=gene1116
chr19	ENCODE	exon	59663758	59665029	.	+	.	Parent=gene1116
###
chr19	ENCODE	gene	59652180	59658434	.	+	.	ID=gene1117;Name=AC008746.4-002;name2=LENG8
chr19	ENCODE	exon	59652180	59652296	.	+	.	Parent=gene1117
chr19	ENCODE	exon	59654279	59654371	.	+	.	Parent=gene1117
chr19	ENCODE	CDS	59654334	59654371	.	+	0	Parent=gene1117
chr19	ENCODE	exon	59655082	59655256	.	+	.	Parent=gene1117
chr19	ENCODE	CDS	59655082	59655256	.	+	1	Parent=gene1117
chr19	ENCODE	exon	59655642	59655743	.	+	.	Parent=gene1117
chr19	ENCODE	CDS	59655642	59655743	.	+	0	Parent=gene1117
chr19	ENCODE	exon	59656537	59656647	.	+	.	Parent=gene1117
chr19	ENCODE	CDS	59656537	59656647	.	+	0	Parent=gene1117
chr19	ENCODE	exon	59657421	59657673	.	+	.	Parent=gene1117
chr19	ENCODE	CDS	59657421	59657673	.	+	0	Parent=gene1117
chr19	ENCODE	exon	59657942	59658083	.	+	.	Parent=gene1117
chr19	ENCODE	CDS	59657942	59658083	.	+	2	Parent=gene1117
chr19	ENCODE	exon	59658355	59658434	.	+	.	Parent=gene1117
chr19	ENCODE	CDS	59658355	59658434	.	+	1	Parent=gene1117
###
chr19	ENCODE	gene	59652208	59665029	.	+	.	ID=gene1118;Name=AC008746.4-007;name2=LENG8
chr19	ENCODE	exon	59652208	59652296	.	+	.	Parent=gene1118
chr19	ENCODE	exon	59654279	59654371	.	+	.	Parent=gene1118
chr19	ENCODE	exon	59655082	59655156	.	+	.	Parent=gene1118
chr19	ENCODE	exon	59663869	59665029	.	+	.	Parent=gene1118
###
chr19	ENCODE	gene	59652214	59665012	.	+	.	ID=gene1119;Name=AC008746.4-008;name2=LENG8
chr19	ENCODE	exon	59652214	59652296	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59654279	59654371	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59655082	59655256	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59655642	59655743	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59657421	59657673	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59657942	59658083	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59658355	59658558	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59658958	59659236	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59659316	59659456	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59659627	59659912	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59660738	59660839	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59660925	59660993	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59661094	59661223	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59661305	59661564	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59664550	59664694	.	+	.	Parent=gene1119
chr19	ENCODE	exon	59664811	59665012	.	+	.	Parent=gene1119
###
chr19	ENCODE	gene	59652602	59655703	.	+	.	ID=gene1120;name2=LENG8;Name=AC008746.4-003
chr19	ENCODE	exon	59652602	59652734	.	+	.	Parent=gene1120
chr19	ENCODE	exon	59654279	59654371	.	+	.	Parent=gene1120
chr19	ENCODE	CDS	59654334	59654371	.	+	0	Parent=gene1120
chr19	ENCODE	exon	59655082	59655256	.	+	.	Parent=gene1120
chr19	ENCODE	CDS	59655082	59655256	.	+	1	Parent=gene1120
chr19	ENCODE	exon	59655642	59655703	.	+	.	Parent=gene1120
chr19	ENCODE	CDS	59655642	59655703	.	+	0	Parent=gene1120
###
chr19	ENCODE	gene	59654981	59656614	.	+	.	ID=gene1121;Name=AC008746.4-005;name2=LENG8
chr19	ENCODE	exon	59654981	59655256	.	+	.	Parent=gene1121
chr19	ENCODE	exon	59655642	59655743	.	+	.	Parent=gene1121
chr19	ENCODE	exon	59656537	59656614	.	+	.	Parent=gene1121
###
chr19	ENCODE	gene	59657441	59664392	.	+	.	ID=gene1122;Name=AC008746.4-004;name2=LENG8
chr19	ENCODE	exon	59657441	59657673	.	+	.	Parent=gene1122
chr19	ENCODE	CDS	59657441	59657673	.	+	0	Parent=gene1122
chr19	ENCODE	exon	59657942	59658083	.	+	.	Parent=gene1122
chr19	ENCODE	CDS	59657942	59658083	.	+	1	Parent=gene1122
chr19	ENCODE	exon	59658355	59658558	.	+	.	Parent=gene1122
chr19	ENCODE	CDS	59658355	59658558	.	+	0	Parent=gene1122
chr19	ENCODE	exon	59658958	59659236	.	+	.	Parent=gene1122
chr19	ENCODE	CDS	59658958	59659236	.	+	0	Parent=gene1122
chr19	ENCODE	exon	59659316	59659456	.	+	.	Parent=gene1122
chr19	ENCODE	CDS	59659316	59659456	.	+	0	Parent=gene1122
chr19	ENCODE	exon	59659627	59659912	.	+	.	Parent=gene1122
chr19	ENCODE	CDS	59659627	59659912	.	+	0	Parent=gene1122
chr19	ENCODE	exon	59660738	59660839	.	+	.	Parent=gene1122
chr19	ENCODE	CDS	59660738	59660839	.	+	2	Parent=gene1122
chr19	ENCODE	exon	59660925	59660993	.	+	.	Parent=gene1122
chr19	ENCODE	CDS	59660925	59660993	.	+	2	Parent=gene1122
chr19	ENCODE	exon	59661094	59661223	.	+	.	Parent=gene1122
chr19	ENCODE	CDS	59661094	59661223	.	+	2	Parent=gene1122
chr19	ENCODE	CDS	59661305	59661897	.	+	1	Parent=gene1122
chr19	ENCODE	exon	59661305	59664392	.	+	.	Parent=gene1122
###
chr19	ENCODE	gene	59661406	59664704	.	+	.	ID=gene1123;Name=AC008746.4-006;name2=LENG8
chr19	ENCODE	exon	59661406	59661512	.	+	.	Parent=gene1123
chr19	ENCODE	exon	59664218	59664704	.	+	.	Parent=gene1123
###
chr19	ENCODE	gene	59664788	59666706	.	-	.	ID=gene1124;Name=AC008746.6-001;name2=LENG9
chr19	ENCODE	exon	59664788	59666706	.	-	.	Parent=gene1124
chr19	ENCODE	CDS	59665082	59666521	.	-	0	Parent=gene1124
###
chr19	ENCODE	gene	59668022	59676223	.	-	.	ID=gene1125;Name=AC008746.7-001;name2=CDC42EP5
chr19	ENCODE	exon	59668022	59668543	.	-	.	Parent=gene1125
chr19	ENCODE	CDS	59668097	59668543	.	-	0	Parent=gene1125
chr19	ENCODE	exon	59674578	59674718	.	-	.	Parent=gene1125
chr19	ENCODE	exon	59676023	59676223	.	-	.	Parent=gene1125
###
chr19	ENCODE	gene	59674539	59676130	.	-	.	ID=gene1126;Name=AC008746.7-002;name2=CDC42EP5
chr19	ENCODE	exon	59674539	59674718	.	-	.	Parent=gene1126
chr19	ENCODE	exon	59676023	59676130	.	-	.	Parent=gene1126
###
chr19	ENCODE	gene	59700912	59711133	.	+	.	ID=gene1127;Name=AC008746.8-004;name2=LAIR2
chr19	ENCODE	exon	59700912	59701290	.	+	.	Parent=gene1127
chr19	ENCODE	CDS	59701275	59701290	.	+	0	Parent=gene1127
chr19	ENCODE	exon	59710918	59711133	.	+	.	Parent=gene1127
chr19	ENCODE	CDS	59710918	59711133	.	+	2	Parent=gene1127
###
chr19	ENCODE	gene	59700912	59711133	.	+	.	ID=gene1128;Name=AC008746.8-003;name2=LAIR2
chr19	ENCODE	exon	59700912	59701290	.	+	.	Parent=gene1128
chr19	ENCODE	CDS	59701275	59701290	.	+	0	Parent=gene1128
chr19	ENCODE	exon	59706728	59706763	.	+	.	Parent=gene1128
chr19	ENCODE	CDS	59706728	59706763	.	+	2	Parent=gene1128
chr19	ENCODE	exon	59710918	59711133	.	+	.	Parent=gene1128
chr19	ENCODE	CDS	59710918	59711133	.	+	2	Parent=gene1128
###
chr19	ENCODE	gene	59705825	59713709	.	+	.	ID=gene1129;Name=AC008746.8-001;name2=LAIR2
chr19	ENCODE	exon	59705825	59705980	.	+	.	Parent=gene1129
chr19	ENCODE	CDS	59705947	59705980	.	+	0	Parent=gene1129
chr19	ENCODE	exon	59706728	59706763	.	+	.	Parent=gene1129
chr19	ENCODE	CDS	59706728	59706763	.	+	2	Parent=gene1129
chr19	ENCODE	exon	59710918	59711211	.	+	.	Parent=gene1129
chr19	ENCODE	CDS	59710918	59711211	.	+	2	Parent=gene1129
chr19	ENCODE	exon	59712057	59712107	.	+	.	Parent=gene1129
chr19	ENCODE	CDS	59712057	59712107	.	+	2	Parent=gene1129
chr19	ENCODE	CDS	59713548	59713591	.	+	2	Parent=gene1129
chr19	ENCODE	exon	59713548	59713709	.	+	.	Parent=gene1129
###
chr19	ENCODE	gene	59705935	59713709	.	+	.	ID=gene1130;Name=AC008746.8-002;name2=LAIR2
chr19	ENCODE	exon	59705935	59705980	.	+	.	Parent=gene1130
chr19	ENCODE	CDS	59705947	59705980	.	+	0	Parent=gene1130
chr19	ENCODE	exon	59706728	59706763	.	+	.	Parent=gene1130
chr19	ENCODE	CDS	59706728	59706763	.	+	2	Parent=gene1130
chr19	ENCODE	exon	59710918	59711211	.	+	.	Parent=gene1130
chr19	ENCODE	CDS	59710918	59711211	.	+	2	Parent=gene1130
chr19	ENCODE	CDS	59713548	59713591	.	+	2	Parent=gene1130
chr19	ENCODE	exon	59713548	59713709	.	+	.	Parent=gene1130
###
chr19	ENCODE	gene	59735789	59748865	.	+	.	ID=gene1131;Name=AC009892.1-002;name2=KIR3DX1
chr19	ENCODE	exon	59735789	59735860	.	+	.	Parent=gene1131
chr19	ENCODE	CDS	59735827	59735860	.	+	0	Parent=gene1131
chr19	ENCODE	exon	59736074	59736109	.	+	.	Parent=gene1131
chr19	ENCODE	CDS	59736074	59736109	.	+	2	Parent=gene1131
chr19	ENCODE	exon	59736763	59737041	.	+	.	Parent=gene1131
chr19	ENCODE	CDS	59736763	59737041	.	+	2	Parent=gene1131
chr19	ENCODE	exon	59738617	59738922	.	+	.	Parent=gene1131
chr19	ENCODE	CDS	59738617	59738922	.	+	2	Parent=gene1131
chr19	ENCODE	exon	59739901	59740193	.	+	.	Parent=gene1131
chr19	ENCODE	CDS	59739901	59740193	.	+	2	Parent=gene1131
chr19	ENCODE	exon	59740996	59741046	.	+	.	Parent=gene1131
chr19	ENCODE	CDS	59740996	59741046	.	+	0	Parent=gene1131
chr19	ENCODE	exon	59746397	59746449	.	+	.	Parent=gene1131
chr19	ENCODE	CDS	59746397	59746449	.	+	0	Parent=gene1131
chr19	ENCODE	CDS	59746558	59746603	.	+	1	Parent=gene1131
chr19	ENCODE	exon	59746558	59748865	.	+	.	Parent=gene1131
###
chr19	ENCODE	gene	59738309	59748834	.	+	.	ID=gene1132;Name=AC009892.1-001;name2=KIR3DX1
chr19	ENCODE	exon	59738309	59738922	.	+	.	Parent=gene1132
chr19	ENCODE	exon	59739901	59740193	.	+	.	Parent=gene1132
chr19	ENCODE	exon	59740996	59741680	.	+	.	Parent=gene1132
chr19	ENCODE	exon	59746050	59748834	.	+	.	Parent=gene1132
###
chr19	ENCODE	gene	59776199	59778189	.	+	.	ID=gene1133;name2=LILRA2;Name=AC009892.3-005
chr19	ENCODE	exon	59776199	59776714	.	+	.	Parent=gene1133
chr19	ENCODE	exon	59777355	59777390	.	+	.	Parent=gene1133
chr19	ENCODE	exon	59777580	59777861	.	+	.	Parent=gene1133
chr19	ENCODE	exon	59778010	59778189	.	+	.	Parent=gene1133
###
chr19	ENCODE	gene	59776307	59779115	.	+	.	ID=gene1134;Name=AC009892.3-006;name2=LILRA2
chr19	ENCODE	exon	59776307	59776714	.	+	.	Parent=gene1134
chr19	ENCODE	exon	59776977	59777191	.	+	.	Parent=gene1134
chr19	ENCODE	CDS	59777158	59777191	.	+	0	Parent=gene1134
chr19	ENCODE	exon	59777355	59777390	.	+	.	Parent=gene1134
chr19	ENCODE	CDS	59777355	59777390	.	+	2	Parent=gene1134
chr19	ENCODE	exon	59777580	59777861	.	+	.	Parent=gene1134
chr19	ENCODE	CDS	59777580	59777861	.	+	2	Parent=gene1134
chr19	ENCODE	exon	59778010	59778312	.	+	.	Parent=gene1134
chr19	ENCODE	CDS	59778010	59778312	.	+	2	Parent=gene1134
chr19	ENCODE	exon	59778535	59778831	.	+	.	Parent=gene1134
chr19	ENCODE	CDS	59778535	59778831	.	+	2	Parent=gene1134
chr19	ENCODE	exon	59779086	59779115	.	+	.	Parent=gene1134
chr19	ENCODE	CDS	59779086	59779115	.	+	2	Parent=gene1134
###
chr19	ENCODE	gene	59776630	59790839	.	+	.	ID=gene1135;Name=AC009892.3-001;name2=LILRA2
chr19	ENCODE	exon	59776630	59776714	.	+	.	Parent=gene1135
chr19	ENCODE	exon	59777110	59777191	.	+	.	Parent=gene1135
chr19	ENCODE	CDS	59777158	59777191	.	+	0	Parent=gene1135
chr19	ENCODE	exon	59777355	59777390	.	+	.	Parent=gene1135
chr19	ENCODE	CDS	59777355	59777390	.	+	2	Parent=gene1135
chr19	ENCODE	exon	59777580	59777861	.	+	.	Parent=gene1135
chr19	ENCODE	CDS	59777580	59777861	.	+	2	Parent=gene1135
chr19	ENCODE	exon	59778010	59778312	.	+	.	Parent=gene1135
chr19	ENCODE	CDS	59778010	59778312	.	+	2	Parent=gene1135
chr19	ENCODE	exon	59778535	59778831	.	+	.	Parent=gene1135
chr19	ENCODE	CDS	59778535	59778831	.	+	2	Parent=gene1135
chr19	ENCODE	exon	59779086	59779388	.	+	.	Parent=gene1135
chr19	ENCODE	CDS	59779086	59779388	.	+	2	Parent=gene1135
chr19	ENCODE	exon	59790289	59790339	.	+	.	Parent=gene1135
chr19	ENCODE	CDS	59790289	59790339	.	+	2	Parent=gene1135
chr19	ENCODE	CDS	59790480	59790625	.	+	2	Parent=gene1135
chr19	ENCODE	exon	59790480	59790839	.	+	.	Parent=gene1135
###
chr19	ENCODE	gene	59777071	59790839	.	+	.	ID=gene1136;Name=AC009892.3-003;name2=LILRA2
chr19	ENCODE	exon	59777071	59777191	.	+	.	Parent=gene1136
chr19	ENCODE	CDS	59777158	59777191	.	+	0	Parent=gene1136
chr19	ENCODE	exon	59777355	59777390	.	+	.	Parent=gene1136
chr19	ENCODE	CDS	59777355	59777390	.	+	2	Parent=gene1136
chr19	ENCODE	exon	59777580	59777861	.	+	.	Parent=gene1136
chr19	ENCODE	CDS	59777580	59777861	.	+	2	Parent=gene1136
chr19	ENCODE	exon	59778010	59778312	.	+	.	Parent=gene1136
chr19	ENCODE	CDS	59778010	59778312	.	+	2	Parent=gene1136
chr19	ENCODE	exon	59778535	59778831	.	+	.	Parent=gene1136
chr19	ENCODE	CDS	59778535	59778831	.	+	2	Parent=gene1136
chr19	ENCODE	exon	59779086	59779388	.	+	.	Parent=gene1136
chr19	ENCODE	CDS	59779086	59779388	.	+	2	Parent=gene1136
chr19	ENCODE	CDS	59790480	59790625	.	+	2	Parent=gene1136
chr19	ENCODE	exon	59790480	59790839	.	+	.	Parent=gene1136
###
chr19	ENCODE	gene	59777120	59790674	.	+	.	ID=gene1137;Name=AC009892.3-002;name2=LILRA2
chr19	ENCODE	exon	59777120	59777191	.	+	.	Parent=gene1137
chr19	ENCODE	CDS	59777158	59777191	.	+	0	Parent=gene1137
chr19	ENCODE	exon	59777580	59777861	.	+	.	Parent=gene1137
chr19	ENCODE	CDS	59777580	59777861	.	+	2	Parent=gene1137
chr19	ENCODE	exon	59778010	59778312	.	+	.	Parent=gene1137
chr19	ENCODE	CDS	59778010	59778312	.	+	2	Parent=gene1137
chr19	ENCODE	exon	59778535	59778831	.	+	.	Parent=gene1137
chr19	ENCODE	CDS	59778535	59778831	.	+	2	Parent=gene1137
chr19	ENCODE	exon	59779086	59779388	.	+	.	Parent=gene1137
chr19	ENCODE	CDS	59779086	59779388	.	+	2	Parent=gene1137
chr19	ENCODE	CDS	59790480	59790625	.	+	2	Parent=gene1137
chr19	ENCODE	exon	59790480	59790674	.	+	.	Parent=gene1137
###
chr19	ENCODE	gene	59777158	59790674	.	+	.	ID=gene1138;Name=AC009892.3-004;name2=LILRA2
chr19	ENCODE	exon	59777158	59777191	.	+	.	Parent=gene1138
chr19	ENCODE	exon	59777355	59777390	.	+	.	Parent=gene1138
chr19	ENCODE	exon	59777580	59777829	.	+	.	Parent=gene1138
chr19	ENCODE	exon	59779243	59779388	.	+	.	Parent=gene1138
chr19	ENCODE	exon	59790480	59790674	.	+	.	Parent=gene1138
###
chr19	ENCODE	gene	59779351	59790826	.	+	.	ID=gene1139;Name=AC009892.3-007;name2=LILRA2
chr19	ENCODE	exon	59779351	59779388	.	+	.	Parent=gene1139
chr19	ENCODE	exon	59780744	59781002	.	+	.	Parent=gene1139
chr19	ENCODE	exon	59790480	59790826	.	+	.	Parent=gene1139
###
chr19	ENCODE	gene	59796859	59802997	.	+	.	ID=gene1140;Name=AC009892.4-005;name2=LILRA1
chr19	ENCODE	exon	59796859	59797058	.	+	.	Parent=gene1140
chr19	ENCODE	exon	59797718	59797753	.	+	.	Parent=gene1140
chr19	ENCODE	exon	59797942	59798229	.	+	.	Parent=gene1140
chr19	ENCODE	exon	59798377	59798679	.	+	.	Parent=gene1140
chr19	ENCODE	exon	59798916	59799212	.	+	.	Parent=gene1140
chr19	ENCODE	exon	59799466	59799768	.	+	.	Parent=gene1140
chr19	ENCODE	exon	59802513	59802997	.	+	.	Parent=gene1140
###
chr19	ENCODE	gene	59796859	59805154	.	+	.	ID=gene1141;Name=AC009892.4-003;name2=LILRA1
chr19	ENCODE	exon	59796859	59797058	.	+	.	Parent=gene1141
chr19	ENCODE	exon	59797718	59797753	.	+	.	Parent=gene1141
chr19	ENCODE	exon	59797942	59798229	.	+	.	Parent=gene1141
chr19	ENCODE	exon	59798377	59798679	.	+	.	Parent=gene1141
chr19	ENCODE	exon	59799032	59799212	.	+	.	Parent=gene1141
chr19	ENCODE	exon	59799466	59799768	.	+	.	Parent=gene1141
chr19	ENCODE	exon	59802513	59802563	.	+	.	Parent=gene1141
chr19	ENCODE	exon	59803789	59803827	.	+	.	Parent=gene1141
chr19	ENCODE	exon	59803976	59805154	.	+	.	Parent=gene1141
###
chr19	ENCODE	gene	59796925	59804352	.	+	.	ID=gene1142;Name=AC009892.4-001;name2=LILRA1
chr19	ENCODE	exon	59796925	59797058	.	+	.	Parent=gene1142
chr19	ENCODE	exon	59797474	59797555	.	+	.	Parent=gene1142
chr19	ENCODE	CDS	59797522	59797555	.	+	0	Parent=gene1142
chr19	ENCODE	exon	59797718	59797753	.	+	.	Parent=gene1142
chr19	ENCODE	CDS	59797718	59797753	.	+	2	Parent=gene1142
chr19	ENCODE	exon	59797942	59798229	.	+	.	Parent=gene1142
chr19	ENCODE	CDS	59797942	59798229	.	+	2	Parent=gene1142
chr19	ENCODE	exon	59798377	59798679	.	+	.	Parent=gene1142
chr19	ENCODE	CDS	59798377	59798679	.	+	2	Parent=gene1142
chr19	ENCODE	exon	59798916	59799212	.	+	.	Parent=gene1142
chr19	ENCODE	CDS	59798916	59799212	.	+	2	Parent=gene1142
chr19	ENCODE	exon	59799466	59799768	.	+	.	Parent=gene1142
chr19	ENCODE	CDS	59799466	59799768	.	+	2	Parent=gene1142
chr19	ENCODE	exon	59802513	59802563	.	+	.	Parent=gene1142
chr19	ENCODE	CDS	59802513	59802563	.	+	2	Parent=gene1142
chr19	ENCODE	exon	59803789	59803827	.	+	.	Parent=gene1142
chr19	ENCODE	CDS	59803789	59803827	.	+	2	Parent=gene1142
chr19	ENCODE	CDS	59803976	59804094	.	+	2	Parent=gene1142
chr19	ENCODE	exon	59803976	59804352	.	+	.	Parent=gene1142
###
chr19	ENCODE	gene	59796927	59802993	.	+	.	ID=gene1143;Name=AC009892.4-004;name2=LILRA1
chr19	ENCODE	exon	59796927	59797058	.	+	.	Parent=gene1143
chr19	ENCODE	exon	59797474	59797753	.	+	.	Parent=gene1143
chr19	ENCODE	exon	59797942	59798229	.	+	.	Parent=gene1143
chr19	ENCODE	exon	59798377	59798679	.	+	.	Parent=gene1143
chr19	ENCODE	exon	59798916	59799212	.	+	.	Parent=gene1143
chr19	ENCODE	exon	59799466	59799768	.	+	.	Parent=gene1143
chr19	ENCODE	exon	59802513	59802993	.	+	.	Parent=gene1143
###
chr19	ENCODE	gene	59796937	59805367	.	+	.	ID=gene1144;Name=AC009892.4-002;name2=LILRA1
chr19	ENCODE	exon	59796937	59797058	.	+	.	Parent=gene1144
chr19	ENCODE	exon	59797474	59797555	.	+	.	Parent=gene1144
chr19	ENCODE	CDS	59797522	59797555	.	+	0	Parent=gene1144
chr19	ENCODE	exon	59797718	59797753	.	+	.	Parent=gene1144
chr19	ENCODE	CDS	59797718	59797753	.	+	2	Parent=gene1144
chr19	ENCODE	exon	59797942	59798229	.	+	.	Parent=gene1144
chr19	ENCODE	CDS	59797942	59798229	.	+	2	Parent=gene1144
chr19	ENCODE	exon	59798377	59798679	.	+	.	Parent=gene1144
chr19	ENCODE	CDS	59798377	59798679	.	+	2	Parent=gene1144
chr19	ENCODE	exon	59802513	59802563	.	+	.	Parent=gene1144
chr19	ENCODE	CDS	59802513	59802563	.	+	2	Parent=gene1144
chr19	ENCODE	exon	59803789	59803827	.	+	.	Parent=gene1144
chr19	ENCODE	CDS	59803789	59803827	.	+	2	Parent=gene1144
chr19	ENCODE	CDS	59803976	59804094	.	+	2	Parent=gene1144
chr19	ENCODE	exon	59803976	59805367	.	+	.	Parent=gene1144
###
chr19	ENCODE	gene	59820424	59840791	.	+	.	ID=gene1145;Name=AC009892.6-002;name2=LILRB1
chr19	ENCODE	exon	59820424	59820615	.	+	.	Parent=gene1145
chr19	ENCODE	exon	59833780	59833896	.	+	.	Parent=gene1145
chr19	ENCODE	exon	59834289	59834370	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59834337	59834370	.	+	0	Parent=gene1145
chr19	ENCODE	exon	59834534	59834569	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59834534	59834569	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59834763	59835050	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59834763	59835050	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59835198	59835500	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59835198	59835500	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59835727	59836023	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59835727	59836023	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59836279	59836581	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59836279	59836581	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59836901	59836951	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59836901	59836951	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59837237	59837284	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59837237	59837284	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59837904	59838026	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59837904	59838026	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59838367	59838442	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59838367	59838442	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59838522	59838559	.	+	1	Parent=gene1145
chr19	ENCODE	exon	59838820	59838872	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59838820	59838872	.	+	2	Parent=gene1145
chr19	ENCODE	exon	59839760	59839915	.	+	.	Parent=gene1145
chr19	ENCODE	CDS	59839760	59839915	.	+	0	Parent=gene1145
chr19	ENCODE	CDS	59839995	59840141	.	+	0	Parent=gene1145
chr19	ENCODE	exon	59839995	59840791	.	+	.	Parent=gene1145
###
chr19	ENCODE	gene	59833673	59840791	.	+	.	ID=gene1146;Name=AC009892.6-001;name2=LILRB1
chr19	ENCODE	exon	59833673	59833896	.	+	.	Parent=gene1146
chr19	ENCODE	exon	59834289	59834370	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59834337	59834370	.	+	0	Parent=gene1146
chr19	ENCODE	exon	59834534	59834569	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59834534	59834569	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59834763	59835050	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59834763	59835050	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59835198	59835500	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59835198	59835500	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59835727	59836023	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59835727	59836023	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59836279	59836581	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59836279	59836581	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59836901	59836951	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59836901	59836951	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59837234	59837284	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59837234	59837284	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59837904	59838026	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59837904	59838026	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59838367	59838442	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59838367	59838442	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59838522	59838559	.	+	1	Parent=gene1146
chr19	ENCODE	exon	59838820	59838872	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59838820	59838872	.	+	2	Parent=gene1146
chr19	ENCODE	exon	59839760	59839915	.	+	.	Parent=gene1146
chr19	ENCODE	CDS	59839760	59839915	.	+	0	Parent=gene1146
chr19	ENCODE	CDS	59839995	59840141	.	+	0	Parent=gene1146
chr19	ENCODE	exon	59839995	59840791	.	+	.	Parent=gene1146
###
chr19	ENCODE	gene	59833775	59840791	.	+	.	ID=gene1147;name2=LILRB1;Name=AC009892.6-003
chr19	ENCODE	exon	59833775	59833896	.	+	.	Parent=gene1147
chr19	ENCODE	exon	59834289	59834370	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59834337	59834370	.	+	0	Parent=gene1147
chr19	ENCODE	exon	59834534	59834569	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59834534	59834569	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59834763	59835050	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59834763	59835050	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59835198	59835500	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59835198	59835500	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59835727	59836023	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59835727	59836023	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59836279	59836581	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59836279	59836581	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59836901	59836951	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59836901	59836951	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59837237	59837284	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59837237	59837284	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59837904	59838026	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59837904	59838026	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59838367	59838442	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59838367	59838442	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59838522	59838559	.	+	1	Parent=gene1147
chr19	ENCODE	exon	59838820	59838872	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59838820	59838872	.	+	2	Parent=gene1147
chr19	ENCODE	exon	59839757	59839915	.	+	.	Parent=gene1147
chr19	ENCODE	CDS	59839757	59839915	.	+	0	Parent=gene1147
chr19	ENCODE	CDS	59839995	59840141	.	+	0	Parent=gene1147
chr19	ENCODE	exon	59839995	59840791	.	+	.	Parent=gene1147
###
chr19	ENCODE	gene	59833896	59840453	.	+	.	ID=gene1148;name2=LILRB1;Name=AC009892.6-007
chr19	ENCODE	exon	59833896	59834370	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59834337	59834370	.	+	0	Parent=gene1148
chr19	ENCODE	exon	59834534	59834569	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59834534	59834569	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59834763	59835050	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59834763	59835050	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59835198	59835500	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59835198	59835500	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59835727	59836023	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59835727	59836023	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59836279	59836581	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59836279	59836581	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59836901	59836951	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59836901	59836951	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59837234	59837284	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59837234	59837284	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59837627	59837665	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59837627	59837665	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59837904	59838026	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59837904	59838026	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59838367	59838442	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59838367	59838442	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59838522	59838559	.	+	1	Parent=gene1148
chr19	ENCODE	exon	59838820	59838872	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59838820	59838872	.	+	2	Parent=gene1148
chr19	ENCODE	exon	59839757	59839915	.	+	.	Parent=gene1148
chr19	ENCODE	CDS	59839757	59839915	.	+	0	Parent=gene1148
chr19	ENCODE	CDS	59839995	59840141	.	+	0	Parent=gene1148
chr19	ENCODE	exon	59839995	59840453	.	+	.	Parent=gene1148
###
chr19	ENCODE	gene	59834337	59840339	.	+	.	ID=gene1149;name2=LILRB1;Name=AC009892.6-004
chr19	ENCODE	exon	59834337	59834370	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59834337	59834370	.	+	0	Parent=gene1149
chr19	ENCODE	exon	59834534	59834569	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59834534	59834569	.	+	2	Parent=gene1149
chr19	ENCODE	exon	59834763	59835050	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59834763	59835050	.	+	2	Parent=gene1149
chr19	ENCODE	exon	59835198	59835500	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59835198	59835500	.	+	2	Parent=gene1149
chr19	ENCODE	exon	59835727	59836023	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59835727	59836023	.	+	2	Parent=gene1149
chr19	ENCODE	exon	59836279	59836581	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59836279	59836581	.	+	2	Parent=gene1149
chr19	ENCODE	exon	59837234	59837284	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59837234	59837284	.	+	2	Parent=gene1149
chr19	ENCODE	exon	59837904	59838026	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59837904	59838026	.	+	2	Parent=gene1149
chr19	ENCODE	exon	59838367	59838442	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59838367	59838442	.	+	2	Parent=gene1149
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59838522	59838559	.	+	1	Parent=gene1149
chr19	ENCODE	exon	59838820	59838872	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59838820	59838872	.	+	2	Parent=gene1149
chr19	ENCODE	exon	59839760	59839915	.	+	.	Parent=gene1149
chr19	ENCODE	CDS	59839760	59839915	.	+	0	Parent=gene1149
chr19	ENCODE	CDS	59839995	59840141	.	+	0	Parent=gene1149
chr19	ENCODE	exon	59839995	59840339	.	+	.	Parent=gene1149
###
chr19	ENCODE	gene	59834337	59840339	.	+	.	ID=gene1150;Name=AC009892.6-006;name2=LILRB1
chr19	ENCODE	exon	59834337	59834370	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59834534	59834569	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59834763	59835050	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59835198	59835500	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59835727	59836023	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59836279	59836581	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59836901	59836951	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59837237	59837284	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59837904	59838026	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59838820	59838872	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59839760	59839915	.	+	.	Parent=gene1150
chr19	ENCODE	exon	59839995	59840339	.	+	.	Parent=gene1150
###
chr19	ENCODE	gene	59834337	59840339	.	+	.	ID=gene1151;Name=AC009892.6-005;name2=LILRB1
chr19	ENCODE	exon	59834337	59834370	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59834337	59834370	.	+	0	Parent=gene1151
chr19	ENCODE	exon	59834534	59834569	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59834534	59834569	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59834763	59835050	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59834763	59835050	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59835198	59835500	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59835198	59835500	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59835727	59836023	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59835727	59836023	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59836279	59836581	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59836279	59836581	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59836901	59836951	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59836901	59836951	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59837234	59837284	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59837234	59837284	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59837904	59838026	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59837904	59838026	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59838367	59838442	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59838367	59838442	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59838522	59838559	.	+	1	Parent=gene1151
chr19	ENCODE	exon	59838820	59838872	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59838820	59838872	.	+	2	Parent=gene1151
chr19	ENCODE	exon	59839757	59839915	.	+	.	Parent=gene1151
chr19	ENCODE	CDS	59839757	59839915	.	+	0	Parent=gene1151
chr19	ENCODE	CDS	59839995	59840141	.	+	0	Parent=gene1151
chr19	ENCODE	exon	59839995	59840339	.	+	.	Parent=gene1151
###
chr19	ENCODE	gene	59834525	59835318	.	+	.	ID=gene1152;Name=AC009892.6-009;name2=LILRB1
chr19	ENCODE	exon	59834525	59834569	.	+	.	Parent=gene1152
chr19	ENCODE	exon	59834763	59835050	.	+	.	Parent=gene1152
chr19	ENCODE	exon	59835198	59835318	.	+	.	Parent=gene1152
###
chr19	ENCODE	gene	59836389	59837446	.	+	.	ID=gene1153;Name=AC009892.6-010;name2=LILRB1
chr19	ENCODE	exon	59836389	59836581	.	+	.	Parent=gene1153
chr19	ENCODE	exon	59836901	59836951	.	+	.	Parent=gene1153
chr19	ENCODE	exon	59837234	59837446	.	+	.	Parent=gene1153
###
chr19	ENCODE	gene	59836406	59840791	.	+	.	ID=gene1154;Name=AC009892.6-008;name2=LILRB1
chr19	ENCODE	exon	59836406	59836507	.	+	.	Parent=gene1154
chr19	ENCODE	exon	59836901	59836951	.	+	.	Parent=gene1154
chr19	ENCODE	exon	59837234	59837284	.	+	.	Parent=gene1154
chr19	ENCODE	exon	59837851	59838026	.	+	.	Parent=gene1154
chr19	ENCODE	exon	59838367	59838442	.	+	.	Parent=gene1154
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1154
chr19	ENCODE	exon	59838820	59839915	.	+	.	Parent=gene1154
chr19	ENCODE	exon	59839995	59840791	.	+	.	Parent=gene1154
###
chr19	ENCODE	gene	59837634	59838879	.	+	.	ID=gene1155;Name=AC009892.6-012;name2=LILRB1
chr19	ENCODE	exon	59837634	59838026	.	+	.	Parent=gene1155
chr19	ENCODE	exon	59838367	59838442	.	+	.	Parent=gene1155
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1155
chr19	ENCODE	exon	59838820	59838879	.	+	.	Parent=gene1155
###
chr19	ENCODE	gene	59838156	59839368	.	+	.	ID=gene1156;Name=AC009892.6-011;name2=LILRB1
chr19	ENCODE	exon	59838156	59838442	.	+	.	Parent=gene1156
chr19	ENCODE	exon	59838522	59838559	.	+	.	Parent=gene1156
chr19	ENCODE	exon	59838820	59839368	.	+	.	Parent=gene1156
###
chr19	ENCODE	gene	59838985	59842155	.	-	.	ID=gene1157;name2=AC009892.10;Name=AC009892.10-001
chr19	ENCODE	exon	59838985	59839339	.	-	.	Parent=gene1157
chr19	ENCODE	CDS	59839184	59839339	.	-	0	Parent=gene1157
chr19	ENCODE	CDS	59841957	59842001	.	-	0	Parent=gene1157
chr19	ENCODE	exon	59841957	59842155	.	-	.	Parent=gene1157
###
chr19	ENCODE	gene	59847152	59852861	.	+	.	ID=gene1158;name2=LILRB4;Name=AC011515.1-011
chr19	ENCODE	exon	59847152	59847229	.	+	.	Parent=gene1158
chr19	ENCODE	exon	59851295	59852861	.	+	.	Parent=gene1158
###
chr19	ENCODE	gene	59847178	59867225	.	+	.	ID=gene1159;Name=AC011515.1-010;name2=LILRB4
chr19	ENCODE	exon	59847178	59847229	.	+	.	Parent=gene1159
chr19	ENCODE	exon	59866083	59866331	.	+	.	Parent=gene1159
chr19	ENCODE	CDS	59866298	59866331	.	+	0	Parent=gene1159
chr19	ENCODE	exon	59866802	59866837	.	+	.	Parent=gene1159
chr19	ENCODE	CDS	59866802	59866837	.	+	2	Parent=gene1159
chr19	ENCODE	exon	59867024	59867225	.	+	.	Parent=gene1159
chr19	ENCODE	CDS	59867024	59867225	.	+	2	Parent=gene1159
###
chr19	ENCODE	gene	59865391	59873622	.	+	.	ID=gene1160;Name=AC011515.1-001;name2=LILRB4
chr19	ENCODE	exon	59865391	59865451	.	+	.	Parent=gene1160
chr19	ENCODE	exon	59865772	59865810	.	+	.	Parent=gene1160
chr19	ENCODE	exon	59866083	59866331	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59866298	59866331	.	+	0	Parent=gene1160
chr19	ENCODE	exon	59866802	59866837	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59866802	59866837	.	+	2	Parent=gene1160
chr19	ENCODE	exon	59867024	59867308	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59867024	59867308	.	+	2	Parent=gene1160
chr19	ENCODE	exon	59867449	59867748	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59867449	59867748	.	+	2	Parent=gene1160
chr19	ENCODE	exon	59868062	59868112	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59868062	59868112	.	+	2	Parent=gene1160
chr19	ENCODE	exon	59868393	59868443	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59868393	59868443	.	+	2	Parent=gene1160
chr19	ENCODE	exon	59869078	59869194	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59869078	59869194	.	+	2	Parent=gene1160
chr19	ENCODE	exon	59869503	59869578	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59869503	59869578	.	+	2	Parent=gene1160
chr19	ENCODE	exon	59869662	59869699	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59869662	59869699	.	+	1	Parent=gene1160
chr19	ENCODE	exon	59869960	59870012	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59869960	59870012	.	+	2	Parent=gene1160
chr19	ENCODE	exon	59870898	59871056	.	+	.	Parent=gene1160
chr19	ENCODE	CDS	59870898	59871056	.	+	0	Parent=gene1160
chr19	ENCODE	CDS	59871136	59871282	.	+	0	Parent=gene1160
chr19	ENCODE	exon	59871136	59873622	.	+	.	Parent=gene1160
###
chr19	ENCODE	gene	59865421	59870962	.	+	.	ID=gene1161;Name=AC011515.1-005;name2=LILRB4
chr19	ENCODE	exon	59865421	59865451	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59865772	59865810	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59866083	59866331	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59867104	59867308	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59867449	59867748	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59868062	59868112	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59868393	59868443	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59869078	59869194	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59869503	59869578	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59869662	59869699	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59869960	59870012	.	+	.	Parent=gene1161
chr19	ENCODE	exon	59870901	59870962	.	+	.	Parent=gene1161
###
chr19	ENCODE	gene	59866259	59871660	.	+	.	ID=gene1162;Name=AC011515.1-002;name2=LILRB4
chr19	ENCODE	exon	59866259	59866331	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59866298	59866331	.	+	0	Parent=gene1162
chr19	ENCODE	exon	59866802	59866837	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59866802	59866837	.	+	2	Parent=gene1162
chr19	ENCODE	exon	59867024	59867308	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59867024	59867308	.	+	2	Parent=gene1162
chr19	ENCODE	exon	59867449	59867748	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59867449	59867748	.	+	2	Parent=gene1162
chr19	ENCODE	exon	59868062	59868112	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59868062	59868112	.	+	2	Parent=gene1162
chr19	ENCODE	exon	59868393	59868443	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59868393	59868443	.	+	2	Parent=gene1162
chr19	ENCODE	exon	59869078	59869194	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59869078	59869194	.	+	2	Parent=gene1162
chr19	ENCODE	exon	59869503	59869578	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59869503	59869578	.	+	2	Parent=gene1162
chr19	ENCODE	exon	59869662	59869699	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59869662	59869699	.	+	1	Parent=gene1162
chr19	ENCODE	exon	59869960	59870012	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59869960	59870012	.	+	2	Parent=gene1162
chr19	ENCODE	exon	59870901	59871056	.	+	.	Parent=gene1162
chr19	ENCODE	CDS	59870901	59871056	.	+	0	Parent=gene1162
chr19	ENCODE	CDS	59871136	59871282	.	+	0	Parent=gene1162
chr19	ENCODE	exon	59871136	59871660	.	+	.	Parent=gene1162
###
chr19	ENCODE	gene	59866262	59871660	.	+	.	ID=gene1163;Name=AC011515.1-004;name2=LILRB4
chr19	ENCODE	exon	59866262	59866331	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59866298	59866331	.	+	0	Parent=gene1163
chr19	ENCODE	exon	59866802	59866837	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59866802	59866837	.	+	2	Parent=gene1163
chr19	ENCODE	exon	59867024	59867308	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59867024	59867308	.	+	2	Parent=gene1163
chr19	ENCODE	exon	59867449	59867748	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59867449	59867748	.	+	2	Parent=gene1163
chr19	ENCODE	exon	59868062	59868112	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59868062	59868112	.	+	2	Parent=gene1163
chr19	ENCODE	exon	59868393	59868443	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59868393	59868443	.	+	2	Parent=gene1163
chr19	ENCODE	exon	59869078	59869194	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59869078	59869194	.	+	2	Parent=gene1163
chr19	ENCODE	exon	59869503	59869578	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59869503	59869578	.	+	2	Parent=gene1163
chr19	ENCODE	exon	59869662	59869699	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59869662	59869699	.	+	1	Parent=gene1163
chr19	ENCODE	exon	59869960	59870012	.	+	.	Parent=gene1163
chr19	ENCODE	CDS	59869960	59870012	.	+	2	Parent=gene1163
chr19	ENCODE	CDS	59871136	59871282	.	+	0	Parent=gene1163
chr19	ENCODE	exon	59871136	59871660	.	+	.	Parent=gene1163
###
chr19	ENCODE	gene	59866284	59871660	.	+	.	ID=gene1164;Name=AC011515.1-003;name2=LILRB4
chr19	ENCODE	exon	59866284	59866331	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59866298	59866331	.	+	0	Parent=gene1164
chr19	ENCODE	exon	59866802	59866837	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59866802	59866837	.	+	2	Parent=gene1164
chr19	ENCODE	exon	59867024	59867308	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59867024	59867308	.	+	2	Parent=gene1164
chr19	ENCODE	exon	59867449	59867748	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59867449	59867748	.	+	2	Parent=gene1164
chr19	ENCODE	exon	59868062	59868112	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59868062	59868112	.	+	2	Parent=gene1164
chr19	ENCODE	exon	59868393	59868443	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59868393	59868443	.	+	2	Parent=gene1164
chr19	ENCODE	exon	59869078	59869194	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59869078	59869194	.	+	2	Parent=gene1164
chr19	ENCODE	exon	59869503	59869578	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59869503	59869578	.	+	2	Parent=gene1164
chr19	ENCODE	exon	59869662	59869699	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59869662	59869699	.	+	1	Parent=gene1164
chr19	ENCODE	exon	59869957	59870012	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59869957	59870012	.	+	2	Parent=gene1164
chr19	ENCODE	exon	59870898	59871056	.	+	.	Parent=gene1164
chr19	ENCODE	CDS	59870898	59871056	.	+	0	Parent=gene1164
chr19	ENCODE	CDS	59871136	59871282	.	+	0	Parent=gene1164
chr19	ENCODE	exon	59871136	59871660	.	+	.	Parent=gene1164
###
chr19	ENCODE	gene	59866291	59871056	.	+	.	ID=gene1165;Name=AC011515.1-006;name2=LILRB4
chr19	ENCODE	exon	59866291	59866331	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59866298	59866331	.	+	0	Parent=gene1165
chr19	ENCODE	exon	59866802	59866837	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59866802	59866837	.	+	2	Parent=gene1165
chr19	ENCODE	exon	59867024	59867308	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59867024	59867308	.	+	2	Parent=gene1165
chr19	ENCODE	exon	59867449	59867748	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59867449	59867748	.	+	2	Parent=gene1165
chr19	ENCODE	exon	59868062	59868112	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59868062	59868112	.	+	2	Parent=gene1165
chr19	ENCODE	exon	59868396	59868443	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59868396	59868443	.	+	2	Parent=gene1165
chr19	ENCODE	exon	59869078	59869194	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59869078	59869194	.	+	2	Parent=gene1165
chr19	ENCODE	exon	59869503	59869578	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59869503	59869578	.	+	2	Parent=gene1165
chr19	ENCODE	exon	59869662	59869699	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59869662	59869699	.	+	1	Parent=gene1165
chr19	ENCODE	exon	59869960	59870012	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59869960	59870012	.	+	2	Parent=gene1165
chr19	ENCODE	exon	59870898	59871056	.	+	.	Parent=gene1165
chr19	ENCODE	CDS	59870898	59871056	.	+	0	Parent=gene1165
###
chr19	ENCODE	gene	59868393	59870301	.	+	.	ID=gene1166;Name=AC011515.1-008;name2=LILRB4
chr19	ENCODE	exon	59868393	59868443	.	+	.	Parent=gene1166
chr19	ENCODE	exon	59869078	59869194	.	+	.	Parent=gene1166
chr19	ENCODE	exon	59869503	59869578	.	+	.	Parent=gene1166
chr19	ENCODE	exon	59869662	59869699	.	+	.	Parent=gene1166
chr19	ENCODE	exon	59869957	59870012	.	+	.	Parent=gene1166
chr19	ENCODE	exon	59870106	59870301	.	+	.	Parent=gene1166
###
chr19	ENCODE	gene	59869061	59870653	.	+	.	ID=gene1167;Name=AC011515.1-007;name2=LILRB4
chr19	ENCODE	exon	59869061	59869194	.	+	.	Parent=gene1167
chr19	ENCODE	exon	59869503	59869578	.	+	.	Parent=gene1167
chr19	ENCODE	exon	59869662	59869699	.	+	.	Parent=gene1167
chr19	ENCODE	exon	59869957	59870653	.	+	.	Parent=gene1167
###
chr19	ENCODE	gene	59869549	59870301	.	+	.	ID=gene1168;Name=AC011515.1-009;name2=LILRB4
chr19	ENCODE	exon	59869549	59869578	.	+	.	Parent=gene1168
chr19	ENCODE	exon	59869662	59869719	.	+	.	Parent=gene1168
chr19	ENCODE	exon	59869960	59870301	.	+	.	Parent=gene1168
###
chr19	ENCODE	gene	59927796	59939815	.	+	.	ID=gene1169;Name=AC006293.2-001;name2=KIR3DL3
chr19	ENCODE	exon	59927796	59927847	.	+	.	Parent=gene1169
chr19	ENCODE	CDS	59927814	59927847	.	+	0	Parent=gene1169
chr19	ENCODE	exon	59928525	59928560	.	+	.	Parent=gene1169
chr19	ENCODE	CDS	59928525	59928560	.	+	2	Parent=gene1169
chr19	ENCODE	exon	59929331	59929615	.	+	.	Parent=gene1169
chr19	ENCODE	CDS	59929331	59929615	.	+	2	Parent=gene1169
chr19	ENCODE	exon	59930889	59931188	.	+	.	Parent=gene1169
chr19	ENCODE	CDS	59930889	59931188	.	+	2	Parent=gene1169
chr19	ENCODE	exon	59932771	59933064	.	+	.	Parent=gene1169
chr19	ENCODE	CDS	59932771	59933064	.	+	2	Parent=gene1169
chr19	ENCODE	exon	59938532	59938636	.	+	.	Parent=gene1169
chr19	ENCODE	CDS	59938532	59938636	.	+	2	Parent=gene1169
chr19	ENCODE	exon	59939099	59939151	.	+	.	Parent=gene1169
chr19	ENCODE	CDS	59939099	59939151	.	+	2	Parent=gene1169
chr19	ENCODE	CDS	59939250	59939375	.	+	0	Parent=gene1169
chr19	ENCODE	exon	59939250	59939815	.	+	.	Parent=gene1169
###
chr19	ENCODE	gene	59941792	59956316	.	+	.	ID=gene1170;Name=AC011501.1-001;name2=KIR2DL3
chr19	ENCODE	exon	59941792	59941856	.	+	.	Parent=gene1170
chr19	ENCODE	CDS	59941823	59941856	.	+	0	Parent=gene1170
chr19	ENCODE	exon	59942765	59942800	.	+	.	Parent=gene1170
chr19	ENCODE	CDS	59942765	59942800	.	+	2	Parent=gene1170
chr19	ENCODE	exon	59945238	59945537	.	+	.	Parent=gene1170
chr19	ENCODE	CDS	59945238	59945537	.	+	2	Parent=gene1170
chr19	ENCODE	exon	59947055	59947348	.	+	.	Parent=gene1170
chr19	ENCODE	CDS	59947055	59947348	.	+	2	Parent=gene1170
chr19	ENCODE	exon	59950599	59950649	.	+	.	Parent=gene1170
chr19	ENCODE	CDS	59950599	59950649	.	+	2	Parent=gene1170
chr19	ENCODE	exon	59954913	59955017	.	+	.	Parent=gene1170
chr19	ENCODE	CDS	59954913	59955017	.	+	2	Parent=gene1170
chr19	ENCODE	exon	59955480	59955532	.	+	.	Parent=gene1170
chr19	ENCODE	CDS	59955480	59955532	.	+	2	Parent=gene1170
chr19	ENCODE	CDS	59955631	59955783	.	+	0	Parent=gene1170
chr19	ENCODE	exon	59955631	59956316	.	+	.	Parent=gene1170
###
chr19	ENCODE	gene	59973075	59987310	.	+	.	ID=gene1171;Name=AC011501.3-001;name2=KIR2DL1
chr19	ENCODE	exon	59973075	59973148	.	+	.	Parent=gene1171
chr19	ENCODE	CDS	59973115	59973148	.	+	0	Parent=gene1171
chr19	ENCODE	exon	59974113	59974148	.	+	.	Parent=gene1171
chr19	ENCODE	CDS	59974113	59974148	.	+	2	Parent=gene1171
chr19	ENCODE	exon	59976597	59976896	.	+	.	Parent=gene1171
chr19	ENCODE	CDS	59976597	59976896	.	+	2	Parent=gene1171
chr19	ENCODE	exon	59978429	59978722	.	+	.	Parent=gene1171
chr19	ENCODE	CDS	59978429	59978722	.	+	2	Parent=gene1171
chr19	ENCODE	exon	59981876	59981926	.	+	.	Parent=gene1171
chr19	ENCODE	CDS	59981876	59981926	.	+	2	Parent=gene1171
chr19	ENCODE	exon	59986186	59986287	.	+	.	Parent=gene1171
chr19	ENCODE	CDS	59986186	59986287	.	+	2	Parent=gene1171
chr19	ENCODE	exon	59986750	59986802	.	+	.	Parent=gene1171
chr19	ENCODE	CDS	59986750	59986802	.	+	2	Parent=gene1171
chr19	ENCODE	CDS	59986901	59987077	.	+	0	Parent=gene1171
chr19	ENCODE	exon	59986901	59987310	.	+	.	Parent=gene1171
###
chr19	ENCODE	gene	59973089	59987129	.	+	.	ID=gene1172;name2=KIR2DL1;Name=AC011501.3-002
chr19	ENCODE	exon	59973089	59973148	.	+	.	Parent=gene1172
chr19	ENCODE	CDS	59973115	59973148	.	+	0	Parent=gene1172
chr19	ENCODE	exon	59974113	59974148	.	+	.	Parent=gene1172
chr19	ENCODE	CDS	59974113	59974148	.	+	2	Parent=gene1172
chr19	ENCODE	exon	59976597	59976896	.	+	.	Parent=gene1172
chr19	ENCODE	CDS	59976597	59976896	.	+	2	Parent=gene1172
chr19	ENCODE	exon	59978429	59978722	.	+	.	Parent=gene1172
chr19	ENCODE	CDS	59978429	59978722	.	+	2	Parent=gene1172
chr19	ENCODE	exon	59981876	59981926	.	+	.	Parent=gene1172
chr19	ENCODE	CDS	59981876	59981926	.	+	2	Parent=gene1172
chr19	ENCODE	exon	59983353	59983430	.	+	.	Parent=gene1172
chr19	ENCODE	CDS	59983353	59983430	.	+	2	Parent=gene1172
chr19	ENCODE	exon	59986186	59986287	.	+	.	Parent=gene1172
chr19	ENCODE	CDS	59986186	59986287	.	+	2	Parent=gene1172
chr19	ENCODE	exon	59986750	59986802	.	+	.	Parent=gene1172
chr19	ENCODE	CDS	59986750	59986802	.	+	2	Parent=gene1172
chr19	ENCODE	CDS	59986901	59987077	.	+	0	Parent=gene1172
chr19	ENCODE	exon	59986901	59987129	.	+	.	Parent=gene1172
###
chr19	ENCODE	gene	60006878	60017784	.	+	.	ID=gene1173;Name=AC011501.5-001;name2=KIR2DL4
chr19	ENCODE	exon	60006878	60006958	.	+	.	Parent=gene1173
chr19	ENCODE	CDS	60006919	60006958	.	+	0	Parent=gene1173
chr19	ENCODE	exon	60007158	60007193	.	+	.	Parent=gene1173
chr19	ENCODE	CDS	60007158	60007193	.	+	2	Parent=gene1173
chr19	ENCODE	exon	60008060	60008344	.	+	.	Parent=gene1173
chr19	ENCODE	CDS	60008060	60008344	.	+	2	Parent=gene1173
chr19	ENCODE	exon	60009218	60009511	.	+	.	Parent=gene1173
chr19	ENCODE	CDS	60009218	60009511	.	+	2	Parent=gene1173
chr19	ENCODE	exon	60012100	60012150	.	+	.	Parent=gene1173
chr19	ENCODE	CDS	60012100	60012150	.	+	2	Parent=gene1173
chr19	ENCODE	exon	60016392	60016495	.	+	.	Parent=gene1173
chr19	ENCODE	CDS	60016392	60016495	.	+	2	Parent=gene1173
chr19	ENCODE	CDS	60016957	60016968	.	+	0	Parent=gene1173
chr19	ENCODE	exon	60016957	60017009	.	+	.	Parent=gene1173
chr19	ENCODE	exon	60017109	60017784	.	+	.	Parent=gene1173
###
chr19	ENCODE	gene	60006907	60017784	.	+	.	ID=gene1174;Name=AC011501.5-005;name2=KIR2DL4
chr19	ENCODE	exon	60006907	60006958	.	+	.	Parent=gene1174
chr19	ENCODE	exon	60007158	60007193	.	+	.	Parent=gene1174
chr19	ENCODE	exon	60008060	60008344	.	+	.	Parent=gene1174
chr19	ENCODE	exon	60009218	60009511	.	+	.	Parent=gene1174
chr19	ENCODE	exon	60016392	60016495	.	+	.	Parent=gene1174
chr19	ENCODE	exon	60016957	60017009	.	+	.	Parent=gene1174
chr19	ENCODE	exon	60017109	60017784	.	+	.	Parent=gene1174
###
chr19	ENCODE	gene	60006907	60017784	.	+	.	ID=gene1175;Name=AC011501.5-002;name2=KIR2DL4
chr19	ENCODE	exon	60006907	60006958	.	+	.	Parent=gene1175
chr19	ENCODE	exon	60007158	60007193	.	+	.	Parent=gene1175
chr19	ENCODE	exon	60008060	60008344	.	+	.	Parent=gene1175
chr19	ENCODE	exon	60009218	60009511	.	+	.	Parent=gene1175
chr19	ENCODE	exon	60017109	60017784	.	+	.	Parent=gene1175
###
chr19	ENCODE	gene	60006907	60017784	.	+	.	ID=gene1176;Name=AC011501.5-003;name2=KIR2DL4
chr19	ENCODE	exon	60006907	60006958	.	+	.	Parent=gene1176
chr19	ENCODE	CDS	60006919	60006958	.	+	0	Parent=gene1176
chr19	ENCODE	exon	60007158	60007193	.	+	.	Parent=gene1176
chr19	ENCODE	CDS	60007158	60007193	.	+	2	Parent=gene1176
chr19	ENCODE	exon	60008060	60008344	.	+	.	Parent=gene1176
chr19	ENCODE	CDS	60008060	60008344	.	+	2	Parent=gene1176
chr19	ENCODE	exon	60009218	60009511	.	+	.	Parent=gene1176
chr19	ENCODE	CDS	60009218	60009511	.	+	2	Parent=gene1176
chr19	ENCODE	exon	60012100	60012150	.	+	.	Parent=gene1176
chr19	ENCODE	CDS	60012100	60012150	.	+	2	Parent=gene1176
chr19	ENCODE	exon	60016957	60017009	.	+	.	Parent=gene1176
chr19	ENCODE	CDS	60016957	60017009	.	+	2	Parent=gene1176
chr19	ENCODE	CDS	60017109	60017378	.	+	0	Parent=gene1176
chr19	ENCODE	exon	60017109	60017784	.	+	.	Parent=gene1176
###
chr19	ENCODE	gene	60006907	60017784	.	+	.	ID=gene1177;name2=KIR2DL4;Name=AC011501.5-004
chr19	ENCODE	exon	60006907	60006958	.	+	.	Parent=gene1177
chr19	ENCODE	CDS	60006919	60006958	.	+	0	Parent=gene1177
chr19	ENCODE	exon	60007158	60007193	.	+	.	Parent=gene1177
chr19	ENCODE	CDS	60007158	60007193	.	+	2	Parent=gene1177
chr19	ENCODE	exon	60008060	60008344	.	+	.	Parent=gene1177
chr19	ENCODE	CDS	60008060	60008344	.	+	2	Parent=gene1177
chr19	ENCODE	exon	60009218	60009511	.	+	.	Parent=gene1177
chr19	ENCODE	CDS	60009218	60009511	.	+	2	Parent=gene1177
chr19	ENCODE	exon	60016957	60017009	.	+	.	Parent=gene1177
chr19	ENCODE	CDS	60016957	60017009	.	+	2	Parent=gene1177
chr19	ENCODE	CDS	60017109	60017378	.	+	0	Parent=gene1177
chr19	ENCODE	exon	60017109	60017784	.	+	.	Parent=gene1177
###
chr19	ENCODE	gene	60006908	60017389	.	+	.	ID=gene1178;Name=AC011501.5-007;name2=KIR2DL4
chr19	ENCODE	exon	60006908	60006958	.	+	.	Parent=gene1178
chr19	ENCODE	CDS	60006919	60006958	.	+	0	Parent=gene1178
chr19	ENCODE	exon	60007158	60007193	.	+	.	Parent=gene1178
chr19	ENCODE	CDS	60007158	60007193	.	+	2	Parent=gene1178
chr19	ENCODE	exon	60009218	60009511	.	+	.	Parent=gene1178
chr19	ENCODE	CDS	60009218	60009511	.	+	2	Parent=gene1178
chr19	ENCODE	exon	60016957	60017009	.	+	.	Parent=gene1178
chr19	ENCODE	CDS	60016957	60017009	.	+	2	Parent=gene1178
chr19	ENCODE	CDS	60017109	60017378	.	+	0	Parent=gene1178
chr19	ENCODE	exon	60017109	60017389	.	+	.	Parent=gene1178
###
chr19	ENCODE	gene	60006919	60017660	.	+	.	ID=gene1179;Name=AC011501.5-006;name2=KIR2DL4
chr19	ENCODE	exon	60006919	60006958	.	+	.	Parent=gene1179
chr19	ENCODE	CDS	60006919	60006958	.	+	0	Parent=gene1179
chr19	ENCODE	exon	60007158	60007193	.	+	.	Parent=gene1179
chr19	ENCODE	CDS	60007158	60007193	.	+	2	Parent=gene1179
chr19	ENCODE	exon	60009218	60009511	.	+	.	Parent=gene1179
chr19	ENCODE	CDS	60009218	60009511	.	+	2	Parent=gene1179
chr19	ENCODE	exon	60012100	60012150	.	+	.	Parent=gene1179
chr19	ENCODE	CDS	60012100	60012150	.	+	2	Parent=gene1179
chr19	ENCODE	exon	60016957	60017009	.	+	.	Parent=gene1179
chr19	ENCODE	CDS	60016957	60017009	.	+	2	Parent=gene1179
chr19	ENCODE	CDS	60017109	60017378	.	+	0	Parent=gene1179
chr19	ENCODE	exon	60017109	60017660	.	+	.	Parent=gene1179
###
chr19	ENCODE	gene	60006919	60017784	.	+	.	ID=gene1180;name2=KIR2DL4;Name=AC011501.5-008
chr19	ENCODE	exon	60006919	60006958	.	+	.	Parent=gene1180
chr19	ENCODE	CDS	60006919	60006958	.	+	0	Parent=gene1180
chr19	ENCODE	exon	60007158	60007193	.	+	.	Parent=gene1180
chr19	ENCODE	CDS	60007158	60007193	.	+	2	Parent=gene1180
chr19	ENCODE	exon	60008060	60008344	.	+	.	Parent=gene1180
chr19	ENCODE	CDS	60008060	60008344	.	+	2	Parent=gene1180
chr19	ENCODE	exon	60009218	60009511	.	+	.	Parent=gene1180
chr19	ENCODE	CDS	60009218	60009511	.	+	2	Parent=gene1180
chr19	ENCODE	exon	60012100	60012150	.	+	.	Parent=gene1180
chr19	ENCODE	CDS	60012100	60012150	.	+	2	Parent=gene1180
chr19	ENCODE	exon	60016392	60016562	.	+	.	Parent=gene1180
chr19	ENCODE	CDS	60016392	60016562	.	+	2	Parent=gene1180
chr19	ENCODE	exon	60016957	60017009	.	+	.	Parent=gene1180
chr19	ENCODE	CDS	60016957	60017009	.	+	2	Parent=gene1180
chr19	ENCODE	CDS	60017109	60017378	.	+	0	Parent=gene1180
chr19	ENCODE	exon	60017109	60017784	.	+	.	Parent=gene1180
###
chr19	ENCODE	gene	60019735	60023279	.	+	.	ID=gene1181;Name=AC011501.6-001;name2=KIR3DL1
chr19	ENCODE	exon	60019735	60019801	.	+	.	Parent=gene1181
chr19	ENCODE	exon	60020801	60020836	.	+	.	Parent=gene1181
chr19	ENCODE	exon	60021582	60021866	.	+	.	Parent=gene1181
chr19	ENCODE	exon	60022980	60023279	.	+	.	Parent=gene1181
###
chr19	ENCODE	gene	60019754	60023279	.	+	.	ID=gene1182;Name=AC011501.6-003;name2=KIR3DL1
chr19	ENCODE	exon	60019754	60019801	.	+	.	Parent=gene1182
chr19	ENCODE	exon	60020801	60020836	.	+	.	Parent=gene1182
chr19	ENCODE	exon	60021582	60021866	.	+	.	Parent=gene1182
chr19	ENCODE	exon	60022980	60023279	.	+	.	Parent=gene1182
###
chr19	ENCODE	gene	60019757	60023279	.	+	.	ID=gene1183;Name=AC011501.6-002;name2=KIR3DL1
chr19	ENCODE	exon	60019757	60019801	.	+	.	Parent=gene1183
chr19	ENCODE	exon	60020801	60020836	.	+	.	Parent=gene1183
chr19	ENCODE	exon	60022980	60023279	.	+	.	Parent=gene1183
###
chr2	ENCODE	gene	118288456	118306185	.	+	.	ID=gene1184;Name=AC009404.1-001;name2=DDX18
chr2	ENCODE	exon	118288456	118288668	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118288584	118288668	.	+	0	Parent=gene1184
chr2	ENCODE	exon	118291250	118291534	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118291250	118291534	.	+	2	Parent=gene1184
chr2	ENCODE	exon	118293455	118293598	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118293455	118293598	.	+	2	Parent=gene1184
chr2	ENCODE	exon	118294967	118295102	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118294967	118295102	.	+	2	Parent=gene1184
chr2	ENCODE	exon	118295456	118295556	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118295456	118295556	.	+	1	Parent=gene1184
chr2	ENCODE	exon	118295668	118295867	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118295668	118295867	.	+	2	Parent=gene1184
chr2	ENCODE	exon	118295953	118296067	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118295953	118296067	.	+	0	Parent=gene1184
chr2	ENCODE	exon	118298375	118298514	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118298375	118298514	.	+	2	Parent=gene1184
chr2	ENCODE	exon	118298746	118298907	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118298746	118298907	.	+	0	Parent=gene1184
chr2	ENCODE	exon	118299253	118299405	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118299253	118299405	.	+	0	Parent=gene1184
chr2	ENCODE	exon	118300075	118300188	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118300075	118300188	.	+	0	Parent=gene1184
chr2	ENCODE	exon	118302755	118302811	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118302755	118302811	.	+	0	Parent=gene1184
chr2	ENCODE	exon	118303095	118303272	.	+	.	Parent=gene1184
chr2	ENCODE	CDS	118303095	118303272	.	+	0	Parent=gene1184
chr2	ENCODE	CDS	118304388	118304530	.	+	2	Parent=gene1184
chr2	ENCODE	exon	118304388	118306185	.	+	.	Parent=gene1184
###
chr2	ENCODE	gene	118288864	118298405	.	+	.	ID=gene1185;Name=AC009404.1-006;name2=DDX18
chr2	ENCODE	exon	118288864	118288898	.	+	.	Parent=gene1185
chr2	ENCODE	exon	118289494	118289529	.	+	.	Parent=gene1185
chr2	ENCODE	exon	118291250	118291534	.	+	.	Parent=gene1185
chr2	ENCODE	exon	118293455	118293598	.	+	.	Parent=gene1185
chr2	ENCODE	exon	118294967	118295102	.	+	.	Parent=gene1185
chr2	ENCODE	exon	118295456	118295556	.	+	.	Parent=gene1185
chr2	ENCODE	exon	118295668	118295867	.	+	.	Parent=gene1185
chr2	ENCODE	exon	118295953	118296067	.	+	.	Parent=gene1185
chr2	ENCODE	exon	118298375	118298405	.	+	.	Parent=gene1185
###
chr2	ENCODE	gene	118291328	118306178	.	+	.	ID=gene1186;name2=DDX18;Name=AC009404.1-007
chr2	ENCODE	exon	118291328	118291534	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118293455	118293598	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118294967	118295102	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118295456	118295556	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118295668	118295867	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118295953	118296067	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118298375	118298514	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118298746	118298907	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118299253	118299405	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118300075	118300188	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118302755	118302811	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118303095	118303272	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118304388	118304971	.	+	.	Parent=gene1186
chr2	ENCODE	exon	118305350	118306178	.	+	.	Parent=gene1186
###
chr2	ENCODE	gene	118295782	118296586	.	+	.	ID=gene1187;Name=AC009404.1-002;name2=DDX18
chr2	ENCODE	exon	118295782	118295867	.	+	.	Parent=gene1187
chr2	ENCODE	exon	118295953	118296586	.	+	.	Parent=gene1187
###
chr2	ENCODE	gene	118295953	118302771	.	+	.	ID=gene1188;Name=AC009404.1-003;name2=DDX18
chr2	ENCODE	exon	118295953	118296067	.	+	.	Parent=gene1188
chr2	ENCODE	CDS	118295953	118296067	.	+	0	Parent=gene1188
chr2	ENCODE	exon	118298375	118298514	.	+	.	Parent=gene1188
chr2	ENCODE	CDS	118298375	118298514	.	+	2	Parent=gene1188
chr2	ENCODE	exon	118298803	118298907	.	+	.	Parent=gene1188
chr2	ENCODE	CDS	118298803	118298907	.	+	0	Parent=gene1188
chr2	ENCODE	exon	118299253	118299405	.	+	.	Parent=gene1188
chr2	ENCODE	CDS	118299253	118299405	.	+	0	Parent=gene1188
chr2	ENCODE	exon	118300075	118300188	.	+	.	Parent=gene1188
chr2	ENCODE	CDS	118300075	118300188	.	+	0	Parent=gene1188
chr2	ENCODE	exon	118302755	118302771	.	+	.	Parent=gene1188
chr2	ENCODE	CDS	118302755	118302771	.	+	0	Parent=gene1188
###
chr2	ENCODE	gene	118298143	118306176	.	+	.	ID=gene1189;Name=AC009404.1-005;name2=DDX18
chr2	ENCODE	exon	118298143	118298514	.	+	.	Parent=gene1189
chr2	ENCODE	exon	118298746	118298907	.	+	.	Parent=gene1189
chr2	ENCODE	exon	118299253	118299405	.	+	.	Parent=gene1189
chr2	ENCODE	exon	118300075	118303272	.	+	.	Parent=gene1189
chr2	ENCODE	exon	118304388	118306176	.	+	.	Parent=gene1189
###
chr2	ENCODE	gene	118298803	118299789	.	+	.	ID=gene1190;Name=AC009404.1-004;name2=DDX18
chr2	ENCODE	exon	118298803	118298907	.	+	.	Parent=gene1190
chr2	ENCODE	exon	118299253	118299789	.	+	.	Parent=gene1190
###
chr2	ENCODE	gene	118389284	118487939	.	-	.	ID=gene1191;name2=CCDC93;Name=AC009404.6-001
chr2	ENCODE	exon	118389284	118394202	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118394149	118394202	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118404843	118404956	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118404843	118404956	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118409301	118409385	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118409301	118409385	.	-	1	Parent=gene1191
chr2	ENCODE	exon	118410508	118410545	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118410508	118410545	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118412835	118412917	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118412835	118412917	.	-	2	Parent=gene1191
chr2	ENCODE	exon	118414995	118415103	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118414995	118415103	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118417830	118417892	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118417830	118417892	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118419335	118419388	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118419335	118419388	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118420617	118420688	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118420617	118420688	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118421911	118421992	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118421911	118421992	.	-	1	Parent=gene1191
chr2	ENCODE	exon	118423128	118423201	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118423128	118423201	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118426179	118426241	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118426179	118426241	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118432171	118432287	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118432171	118432287	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118447714	118447800	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118447714	118447800	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118448656	118448706	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118448656	118448706	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118448994	118449086	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118448994	118449086	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118451800	118451836	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118451800	118451836	.	-	1	Parent=gene1191
chr2	ENCODE	exon	118459775	118459875	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118459775	118459875	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118469252	118469308	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118469252	118469308	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118470070	118470168	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118470070	118470168	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118474627	118474738	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118474627	118474738	.	-	1	Parent=gene1191
chr2	ENCODE	exon	118480528	118480622	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118480528	118480622	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118482351	118482464	.	-	.	Parent=gene1191
chr2	ENCODE	CDS	118482351	118482464	.	-	0	Parent=gene1191
chr2	ENCODE	CDS	118487760	118487801	.	-	0	Parent=gene1191
chr2	ENCODE	exon	118487760	118487939	.	-	.	Parent=gene1191
###
chr2	ENCODE	gene	118389284	118487939	.	-	.	ID=gene1192;Name=AC009404.6-010;name2=CCDC93
chr2	ENCODE	exon	118389284	118394202	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118394149	118394202	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118404843	118404956	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118404843	118404956	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118409301	118409385	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118409301	118409385	.	-	1	Parent=gene1192
chr2	ENCODE	exon	118410508	118410545	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118410508	118410545	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118412835	118412917	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118412835	118412917	.	-	2	Parent=gene1192
chr2	ENCODE	exon	118414995	118415103	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118414995	118415103	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118417830	118417892	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118417830	118417892	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118419335	118419388	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118419335	118419388	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118420617	118420688	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118420617	118420688	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118421911	118421992	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118421911	118421992	.	-	1	Parent=gene1192
chr2	ENCODE	exon	118423128	118423201	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118423128	118423201	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118426179	118426241	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118426179	118426241	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118432171	118432287	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118432171	118432287	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118447714	118447800	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118447714	118447800	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118448656	118448706	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118448656	118448706	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118448994	118449086	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118448994	118449086	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118451800	118451833	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118451800	118451833	.	-	1	Parent=gene1192
chr2	ENCODE	exon	118459775	118459875	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118459775	118459875	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118469252	118469308	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118469252	118469308	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118470070	118470168	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118470070	118470168	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118474627	118474738	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118474627	118474738	.	-	1	Parent=gene1192
chr2	ENCODE	exon	118480528	118480622	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118480528	118480622	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118482351	118482464	.	-	.	Parent=gene1192
chr2	ENCODE	CDS	118482351	118482464	.	-	0	Parent=gene1192
chr2	ENCODE	CDS	118487760	118487801	.	-	0	Parent=gene1192
chr2	ENCODE	exon	118487760	118487939	.	-	.	Parent=gene1192
###
chr2	ENCODE	gene	118389377	118390700	.	-	.	ID=gene1193;Name=AC009404.6-009;name2=CCDC93
chr2	ENCODE	exon	118389377	118390700	.	-	.	Parent=gene1193
###
chr2	ENCODE	gene	118394111	118421985	.	-	.	ID=gene1194;name2=CCDC93;Name=AC009404.6-005
chr2	ENCODE	exon	118394111	118394202	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118404843	118404956	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118409301	118409385	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118410508	118410545	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118412835	118412917	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118414995	118415103	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118417830	118417892	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118418539	118418603	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118419335	118419388	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118420617	118420688	.	-	.	Parent=gene1194
chr2	ENCODE	exon	118421911	118421985	.	-	.	Parent=gene1194
###
chr2	ENCODE	gene	118404849	118409644	.	-	.	ID=gene1195;name2=CCDC93;Name=AC009404.6-008
chr2	ENCODE	exon	118404849	118404956	.	-	.	Parent=gene1195
chr2	ENCODE	exon	118409301	118409644	.	-	.	Parent=gene1195
###
chr2	ENCODE	gene	118409304	118410707	.	-	.	ID=gene1196;Name=AC009404.6-007;name2=CCDC93
chr2	ENCODE	exon	118409304	118409385	.	-	.	Parent=gene1196
chr2	ENCODE	exon	118410508	118410707	.	-	.	Parent=gene1196
###
chr2	ENCODE	gene	118410318	118417886	.	-	.	ID=gene1197;name2=CCDC93;Name=AC009404.6-006
chr2	ENCODE	exon	118410318	118410545	.	-	.	Parent=gene1197
chr2	ENCODE	exon	118412835	118412917	.	-	.	Parent=gene1197
chr2	ENCODE	exon	118414995	118415103	.	-	.	Parent=gene1197
chr2	ENCODE	exon	118417830	118417886	.	-	.	Parent=gene1197
###
chr2	ENCODE	gene	118421839	118426218	.	-	.	ID=gene1198;Name=AC009404.6-004;name2=CCDC93
chr2	ENCODE	exon	118421839	118421992	.	-	.	Parent=gene1198
chr2	ENCODE	exon	118423128	118423201	.	-	.	Parent=gene1198
chr2	ENCODE	exon	118426179	118426218	.	-	.	Parent=gene1198
###
chr2	ENCODE	gene	118425295	118470095	.	-	.	ID=gene1199;Name=AC009404.6-003;name2=CCDC93
chr2	ENCODE	exon	118425295	118425507	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118425484	118425507	.	-	1	Parent=gene1199
chr2	ENCODE	exon	118426179	118426241	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118426179	118426241	.	-	1	Parent=gene1199
chr2	ENCODE	exon	118432171	118432284	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118432171	118432284	.	-	1	Parent=gene1199
chr2	ENCODE	exon	118447714	118447800	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118447714	118447800	.	-	1	Parent=gene1199
chr2	ENCODE	exon	118448656	118448706	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118448656	118448706	.	-	1	Parent=gene1199
chr2	ENCODE	exon	118448994	118449086	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118448994	118449086	.	-	1	Parent=gene1199
chr2	ENCODE	exon	118451800	118451836	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118451800	118451836	.	-	2	Parent=gene1199
chr2	ENCODE	exon	118459775	118459875	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118459775	118459875	.	-	1	Parent=gene1199
chr2	ENCODE	exon	118469252	118469308	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118469252	118469308	.	-	1	Parent=gene1199
chr2	ENCODE	exon	118470070	118470095	.	-	.	Parent=gene1199
chr2	ENCODE	CDS	118470070	118470095	.	-	0	Parent=gene1199
###
chr2	ENCODE	gene	118469258	118474943	.	-	.	ID=gene1200;Name=AC009404.6-002;name2=CCDC93
chr2	ENCODE	exon	118469258	118469308	.	-	.	Parent=gene1200
chr2	ENCODE	exon	118470070	118470168	.	-	.	Parent=gene1200
chr2	ENCODE	exon	118474627	118474943	.	-	.	Parent=gene1200
###
chr2	ENCODE	gene	220108604	220116959	.	+	.	ID=gene1201;Name=AC053503.5-002;name2=DES
chr2	ENCODE	exon	220108604	220108865	.	+	.	Parent=gene1201
chr2	ENCODE	exon	220108926	220109267	.	+	.	Parent=gene1201
chr2	ENCODE	exon	220110322	220110382	.	+	.	Parent=gene1201
chr2	ENCODE	exon	220110478	220110573	.	+	.	Parent=gene1201
chr2	ENCODE	exon	220110722	220110883	.	+	.	Parent=gene1201
chr2	ENCODE	exon	220111055	220111180	.	+	.	Parent=gene1201
chr2	ENCODE	exon	220111567	220111787	.	+	.	Parent=gene1201
chr2	ENCODE	exon	220114004	220114047	.	+	.	Parent=gene1201
chr2	ENCODE	exon	220115890	220115972	.	+	.	Parent=gene1201
chr2	ENCODE	exon	220116176	220116959	.	+	.	Parent=gene1201
###
chr2	ENCODE	gene	220108604	220116966	.	+	.	ID=gene1202;name2=DES;Name=AC053503.5-001
chr2	ENCODE	exon	220108604	220109267	.	+	.	Parent=gene1202
chr2	ENCODE	CDS	220108690	220109267	.	+	0	Parent=gene1202
chr2	ENCODE	exon	220110322	220110382	.	+	.	Parent=gene1202
chr2	ENCODE	CDS	220110322	220110382	.	+	1	Parent=gene1202
chr2	ENCODE	exon	220110478	220110573	.	+	.	Parent=gene1202
chr2	ENCODE	CDS	220110478	220110573	.	+	0	Parent=gene1202
chr2	ENCODE	exon	220110722	220110883	.	+	.	Parent=gene1202
chr2	ENCODE	CDS	220110722	220110883	.	+	0	Parent=gene1202
chr2	ENCODE	exon	220111055	220111180	.	+	.	Parent=gene1202
chr2	ENCODE	CDS	220111055	220111180	.	+	0	Parent=gene1202
chr2	ENCODE	exon	220111567	220111787	.	+	.	Parent=gene1202
chr2	ENCODE	CDS	220111567	220111787	.	+	0	Parent=gene1202
chr2	ENCODE	exon	220114004	220114047	.	+	.	Parent=gene1202
chr2	ENCODE	CDS	220114004	220114047	.	+	1	Parent=gene1202
chr2	ENCODE	exon	220115890	220115972	.	+	.	Parent=gene1202
chr2	ENCODE	CDS	220115890	220115972	.	+	2	Parent=gene1202
chr2	ENCODE	CDS	220116176	220116217	.	+	0	Parent=gene1202
chr2	ENCODE	exon	220116176	220116966	.	+	.	Parent=gene1202
###
chr2	ENCODE	gene	220108606	220116959	.	+	.	ID=gene1203;name2=DES;Name=AC053503.5-003
chr2	ENCODE	exon	220108606	220108723	.	+	.	Parent=gene1203
chr2	ENCODE	exon	220108928	220109267	.	+	.	Parent=gene1203
chr2	ENCODE	exon	220110322	220110382	.	+	.	Parent=gene1203
chr2	ENCODE	exon	220110478	220110573	.	+	.	Parent=gene1203
chr2	ENCODE	exon	220110722	220110883	.	+	.	Parent=gene1203
chr2	ENCODE	exon	220111055	220111180	.	+	.	Parent=gene1203
chr2	ENCODE	exon	220111567	220111787	.	+	.	Parent=gene1203
chr2	ENCODE	exon	220114004	220114047	.	+	.	Parent=gene1203
chr2	ENCODE	exon	220115890	220115972	.	+	.	Parent=gene1203
chr2	ENCODE	exon	220116176	220116959	.	+	.	Parent=gene1203
###
chr2	ENCODE	gene	220108609	220116964	.	+	.	ID=gene1204;Name=AC053503.5-004;name2=DES
chr2	ENCODE	exon	220108609	220108914	.	+	.	Parent=gene1204
chr2	ENCODE	exon	220109171	220109267	.	+	.	Parent=gene1204
chr2	ENCODE	exon	220110322	220110382	.	+	.	Parent=gene1204
chr2	ENCODE	exon	220110478	220110573	.	+	.	Parent=gene1204
chr2	ENCODE	exon	220110722	220110883	.	+	.	Parent=gene1204
chr2	ENCODE	exon	220111055	220111180	.	+	.	Parent=gene1204
chr2	ENCODE	exon	220111567	220111787	.	+	.	Parent=gene1204
chr2	ENCODE	exon	220114004	220114047	.	+	.	Parent=gene1204
chr2	ENCODE	exon	220115890	220115972	.	+	.	Parent=gene1204
chr2	ENCODE	exon	220116176	220116964	.	+	.	Parent=gene1204
###
chr2	ENCODE	gene	220108622	220111180	.	+	.	ID=gene1205;name2=DES;Name=AC053503.5-005
chr2	ENCODE	exon	220108622	220108719	.	+	.	Parent=gene1205
chr2	ENCODE	exon	220109071	220109267	.	+	.	Parent=gene1205
chr2	ENCODE	exon	220110322	220110382	.	+	.	Parent=gene1205
chr2	ENCODE	exon	220110478	220110573	.	+	.	Parent=gene1205
chr2	ENCODE	exon	220110722	220110883	.	+	.	Parent=gene1205
chr2	ENCODE	exon	220111055	220111180	.	+	.	Parent=gene1205
###
chr2	ENCODE	gene	220110272	220114047	.	+	.	ID=gene1206;Name=AC053503.5-006;name2=DES
chr2	ENCODE	exon	220110272	220110382	.	+	.	Parent=gene1206
chr2	ENCODE	exon	220110478	220110573	.	+	.	Parent=gene1206
chr2	ENCODE	exon	220110722	220110883	.	+	.	Parent=gene1206
chr2	ENCODE	exon	220111055	220111180	.	+	.	Parent=gene1206
chr2	ENCODE	exon	220111567	220111787	.	+	.	Parent=gene1206
chr2	ENCODE	exon	220114004	220114047	.	+	.	Parent=gene1206
###
chr2	ENCODE	gene	220110349	220114070	.	+	.	ID=gene1207;Name=AC053503.5-007;name2=DES
chr2	ENCODE	exon	220110349	220110382	.	+	.	Parent=gene1207
chr2	ENCODE	exon	220110478	220110573	.	+	.	Parent=gene1207
chr2	ENCODE	exon	220110722	220110883	.	+	.	Parent=gene1207
chr2	ENCODE	exon	220111055	220111180	.	+	.	Parent=gene1207
chr2	ENCODE	exon	220111567	220111787	.	+	.	Parent=gene1207
chr2	ENCODE	exon	220114004	220114070	.	+	.	Parent=gene1207
###
chr2	ENCODE	gene	220111174	220116961	.	+	.	ID=gene1208;Name=AC053503.5-009;name2=DES
chr2	ENCODE	exon	220111174	220111180	.	+	.	Parent=gene1208
chr2	ENCODE	exon	220111567	220111787	.	+	.	Parent=gene1208
chr2	ENCODE	exon	220114004	220114047	.	+	.	Parent=gene1208
chr2	ENCODE	exon	220115890	220115972	.	+	.	Parent=gene1208
chr2	ENCODE	exon	220116176	220116223	.	+	.	Parent=gene1208
chr2	ENCODE	exon	220116860	220116961	.	+	.	Parent=gene1208
###
chr2	ENCODE	gene	220115747	220116411	.	+	.	ID=gene1209;name2=DES;Name=AC053503.5-008
chr2	ENCODE	exon	220115747	220115972	.	+	.	Parent=gene1209
chr2	ENCODE	exon	220116176	220116411	.	+	.	Parent=gene1209
###
chr2	ENCODE	gene	220125073	220183859	.	+	.	ID=gene1210;Name=AC053503.7-004;name2=SPEG
chr2	ENCODE	exon	220125073	220125592	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220125205	220125592	.	+	0	Parent=gene1210
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220134880	220134969	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220135052	220135388	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220135052	220135388	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220138201	220139498	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220138201	220139498	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220141363	220141506	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220141363	220141506	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220141852	220142034	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220141852	220142034	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220152109	220152284	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220152525	220152613	.	+	0	Parent=gene1210
chr2	ENCODE	exon	220154660	220154835	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220154660	220154835	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220157401	220157661	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220157401	220157661	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220158805	220158963	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220158805	220158963	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220159086	220159275	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220159086	220159275	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220159383	220159606	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220159383	220159606	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220162095	220162214	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220162095	220162214	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220162454	220162558	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220162454	220162558	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220163117	220163323	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220163117	220163323	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220163731	220163854	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220163731	220163854	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220163955	220164130	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220163955	220164130	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220167097	220167209	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220167097	220167209	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220167504	220167672	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220167504	220167672	.	+	0	Parent=gene1210
chr2	ENCODE	exon	220167916	220168012	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220167916	220168012	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220168132	220168332	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220168132	220168332	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220169371	220169428	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220169371	220169428	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220170010	220170087	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220170010	220170087	.	+	0	Parent=gene1210
chr2	ENCODE	exon	220170189	220170367	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220170189	220170367	.	+	0	Parent=gene1210
chr2	ENCODE	exon	220170898	220170924	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220170898	220170924	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220171531	220171683	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220171531	220171683	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220171865	220171907	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220171865	220171907	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220173011	220173079	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220173011	220173079	.	+	0	Parent=gene1210
chr2	ENCODE	exon	220173325	220175299	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220173325	220175299	.	+	0	Parent=gene1210
chr2	ENCODE	exon	220175573	220175704	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220175573	220175704	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220178421	220178537	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220178421	220178537	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220178725	220178892	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220178725	220178892	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220179005	220179127	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220179005	220179127	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220179281	220179448	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220179281	220179448	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220179563	220180166	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220179563	220180166	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220180636	220180875	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220180636	220180875	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220180960	220181183	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220180960	220181183	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220182021	220182096	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220182021	220182096	.	+	2	Parent=gene1210
chr2	ENCODE	exon	220182338	220182487	.	+	.	Parent=gene1210
chr2	ENCODE	CDS	220182338	220182487	.	+	1	Parent=gene1210
chr2	ENCODE	CDS	220182821	220183013	.	+	1	Parent=gene1210
chr2	ENCODE	exon	220182821	220183859	.	+	.	Parent=gene1210
###
chr2	ENCODE	gene	220127502	220157088	.	+	.	ID=gene1211;Name=AC053503.7-001;name2=SPEG
chr2	ENCODE	exon	220127502	220127547	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220133335	220133864	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220135052	220135388	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220138201	220139498	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220141363	220141506	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220141852	220142034	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220154660	220154835	.	+	.	Parent=gene1211
chr2	ENCODE	exon	220156284	220157088	.	+	.	Parent=gene1211
###
chr2	ENCODE	gene	220131743	220138398	.	+	.	ID=gene1212;name2=SPEG;Name=AC053503.7-013
chr2	ENCODE	exon	220131743	220131821	.	+	.	Parent=gene1212
chr2	ENCODE	CDS	220131785	220131821	.	+	0	Parent=gene1212
chr2	ENCODE	exon	220133335	220133377	.	+	.	Parent=gene1212
chr2	ENCODE	CDS	220133335	220133377	.	+	2	Parent=gene1212
chr2	ENCODE	exon	220134252	220134286	.	+	.	Parent=gene1212
chr2	ENCODE	CDS	220134252	220134286	.	+	1	Parent=gene1212
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1212
chr2	ENCODE	CDS	220134880	220134969	.	+	2	Parent=gene1212
chr2	ENCODE	exon	220135052	220135211	.	+	.	Parent=gene1212
chr2	ENCODE	CDS	220135052	220135211	.	+	2	Parent=gene1212
chr2	ENCODE	exon	220138201	220138398	.	+	.	Parent=gene1212
chr2	ENCODE	CDS	220138201	220138398	.	+	1	Parent=gene1212
###
chr2	ENCODE	gene	220132243	220135071	.	+	.	ID=gene1213;Name=AC053503.7-016;name2=SPEG
chr2	ENCODE	exon	220132243	220132310	.	+	.	Parent=gene1213
chr2	ENCODE	exon	220133335	220133667	.	+	.	Parent=gene1213
chr2	ENCODE	exon	220134252	220134286	.	+	.	Parent=gene1213
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1213
chr2	ENCODE	exon	220135052	220135071	.	+	.	Parent=gene1213
###
chr2	ENCODE	gene	220132250	220138742	.	+	.	ID=gene1214;Name=AC053503.7-009;name2=SPEG
chr2	ENCODE	exon	220132250	220132310	.	+	.	Parent=gene1214
chr2	ENCODE	CDS	220132278	220132310	.	+	0	Parent=gene1214
chr2	ENCODE	exon	220133335	220133377	.	+	.	Parent=gene1214
chr2	ENCODE	CDS	220133335	220133377	.	+	0	Parent=gene1214
chr2	ENCODE	exon	220134257	220134286	.	+	.	Parent=gene1214
chr2	ENCODE	CDS	220134257	220134286	.	+	2	Parent=gene1214
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1214
chr2	ENCODE	CDS	220134880	220134969	.	+	2	Parent=gene1214
chr2	ENCODE	exon	220135052	220135211	.	+	.	Parent=gene1214
chr2	ENCODE	CDS	220135052	220135211	.	+	2	Parent=gene1214
chr2	ENCODE	exon	220138201	220138742	.	+	.	Parent=gene1214
chr2	ENCODE	CDS	220138201	220138742	.	+	1	Parent=gene1214
###
chr2	ENCODE	gene	220132272	220157087	.	+	.	ID=gene1215;Name=AC053503.7-014;name2=SPEG
chr2	ENCODE	exon	220132272	220132310	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220132278	220132310	.	+	0	Parent=gene1215
chr2	ENCODE	exon	220133335	220133377	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220133335	220133377	.	+	0	Parent=gene1215
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220134880	220134969	.	+	2	Parent=gene1215
chr2	ENCODE	exon	220135052	220135388	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220135052	220135388	.	+	2	Parent=gene1215
chr2	ENCODE	exon	220138201	220139498	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220138201	220139498	.	+	1	Parent=gene1215
chr2	ENCODE	exon	220141363	220141506	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220141363	220141506	.	+	2	Parent=gene1215
chr2	ENCODE	exon	220141852	220142034	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220141852	220142034	.	+	2	Parent=gene1215
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220152109	220152284	.	+	2	Parent=gene1215
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220152525	220152613	.	+	0	Parent=gene1215
chr2	ENCODE	exon	220154660	220154835	.	+	.	Parent=gene1215
chr2	ENCODE	CDS	220154660	220154835	.	+	1	Parent=gene1215
chr2	ENCODE	CDS	220156284	220156291	.	+	2	Parent=gene1215
chr2	ENCODE	exon	220156284	220157087	.	+	.	Parent=gene1215
###
chr2	ENCODE	gene	220132274	220138418	.	+	.	ID=gene1216;name2=SPEG;Name=AC053503.7-011
chr2	ENCODE	exon	220132274	220132310	.	+	.	Parent=gene1216
chr2	ENCODE	exon	220133335	220133377	.	+	.	Parent=gene1216
chr2	ENCODE	exon	220134252	220134286	.	+	.	Parent=gene1216
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1216
chr2	ENCODE	exon	220135052	220135211	.	+	.	Parent=gene1216
chr2	ENCODE	exon	220138201	220138418	.	+	.	Parent=gene1216
###
chr2	ENCODE	gene	220132276	220135142	.	+	.	ID=gene1217;Name=AC053503.7-015;name2=SPEG
chr2	ENCODE	exon	220132276	220132310	.	+	.	Parent=gene1217
chr2	ENCODE	exon	220133335	220133667	.	+	.	Parent=gene1217
chr2	ENCODE	exon	220134257	220134286	.	+	.	Parent=gene1217
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1217
chr2	ENCODE	exon	220135052	220135142	.	+	.	Parent=gene1217
###
chr2	ENCODE	gene	220133901	220157088	.	+	.	ID=gene1218;Name=AC053503.7-002;name2=SPEG
chr2	ENCODE	exon	220133901	220134286	.	+	.	Parent=gene1218
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1218
chr2	ENCODE	exon	220135052	220135388	.	+	.	Parent=gene1218
chr2	ENCODE	exon	220138201	220139498	.	+	.	Parent=gene1218
chr2	ENCODE	exon	220141363	220141506	.	+	.	Parent=gene1218
chr2	ENCODE	exon	220141852	220142034	.	+	.	Parent=gene1218
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1218
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1218
chr2	ENCODE	exon	220154660	220157088	.	+	.	Parent=gene1218
###
chr2	ENCODE	gene	220134880	220183855	.	+	.	ID=gene1219;Name=AC053503.7-003;name2=SPEG
chr2	ENCODE	exon	220134880	220134969	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220135052	220135388	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220138201	220139498	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220141363	220141506	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220141852	220142034	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220154660	220154835	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220157401	220157661	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220158805	220158963	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220159086	220159275	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220159383	220159606	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220162095	220162214	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220162454	220162558	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220163117	220163323	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220163731	220163854	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220163955	220164130	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220167097	220167209	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220167504	220167672	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220167916	220168012	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220168132	220168332	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220169371	220169428	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220170010	220170087	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220170189	220170367	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220170898	220170924	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220171531	220171683	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220171865	220171907	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220173011	220173079	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220173325	220175299	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220175573	220175704	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220178421	220178537	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220178725	220178892	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220179005	220179127	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220179281	220179448	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220179563	220180166	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220180636	220180875	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220180960	220181183	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220182021	220182096	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220182338	220182487	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220182821	220182827	.	+	.	Parent=gene1219
chr2	ENCODE	exon	220183805	220183855	.	+	.	Parent=gene1219
###
chr2	ENCODE	gene	220135778	220138622	.	+	.	ID=gene1220;Name=AC053503.7-018;name2=SPEG
chr2	ENCODE	exon	220135778	220135909	.	+	.	Parent=gene1220
chr2	ENCODE	exon	220138201	220138622	.	+	.	Parent=gene1220
###
chr2	ENCODE	gene	220135807	220138682	.	+	.	ID=gene1221;Name=AC053503.7-017;name2=SPEG
chr2	ENCODE	exon	220135807	220135914	.	+	.	Parent=gene1221
chr2	ENCODE	exon	220138201	220138682	.	+	.	Parent=gene1221
###
chr2	ENCODE	gene	220140897	220157088	.	+	.	ID=gene1222;name2=SPEG;Name=AC053503.7-005
chr2	ENCODE	exon	220140897	220141506	.	+	.	Parent=gene1222
chr2	ENCODE	exon	220141852	220142034	.	+	.	Parent=gene1222
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1222
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1222
chr2	ENCODE	exon	220154660	220157088	.	+	.	Parent=gene1222
###
chr2	ENCODE	gene	220141968	220154894	.	+	.	ID=gene1223;Name=AC053503.7-020;name2=SPEG
chr2	ENCODE	exon	220141968	220142034	.	+	.	Parent=gene1223
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1223
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1223
chr2	ENCODE	exon	220154660	220154894	.	+	.	Parent=gene1223
###
chr2	ENCODE	gene	220150993	220157068	.	+	.	ID=gene1224;Name=AC053503.7-006;name2=SPEG
chr2	ENCODE	exon	220150993	220151223	.	+	.	Parent=gene1224
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1224
chr2	ENCODE	CDS	220152216	220152284	.	+	0	Parent=gene1224
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1224
chr2	ENCODE	CDS	220152525	220152613	.	+	0	Parent=gene1224
chr2	ENCODE	exon	220154660	220154835	.	+	.	Parent=gene1224
chr2	ENCODE	CDS	220154660	220154835	.	+	1	Parent=gene1224
chr2	ENCODE	CDS	220156284	220156291	.	+	2	Parent=gene1224
chr2	ENCODE	exon	220156284	220157068	.	+	.	Parent=gene1224
###
chr2	ENCODE	gene	220151449	220154881	.	+	.	ID=gene1225;Name=AC053503.7-019;name2=SPEG
chr2	ENCODE	exon	220151449	220151527	.	+	.	Parent=gene1225
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1225
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1225
chr2	ENCODE	exon	220154660	220154881	.	+	.	Parent=gene1225
###
chr2	ENCODE	gene	220151467	220157088	.	+	.	ID=gene1226;Name=AC053503.7-012;name2=SPEG
chr2	ENCODE	exon	220151467	220152284	.	+	.	Parent=gene1226
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1226
chr2	ENCODE	exon	220154660	220154835	.	+	.	Parent=gene1226
chr2	ENCODE	exon	220156284	220157088	.	+	.	Parent=gene1226
###
chr2	ENCODE	gene	220151482	220156882	.	+	.	ID=gene1227;Name=AC053503.7-010;name2=SPEG
chr2	ENCODE	exon	220151482	220151527	.	+	.	Parent=gene1227
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1227
chr2	ENCODE	CDS	220152216	220152284	.	+	0	Parent=gene1227
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1227
chr2	ENCODE	CDS	220152525	220152613	.	+	0	Parent=gene1227
chr2	ENCODE	exon	220154660	220154835	.	+	.	Parent=gene1227
chr2	ENCODE	CDS	220154660	220154835	.	+	1	Parent=gene1227
chr2	ENCODE	CDS	220156284	220156291	.	+	2	Parent=gene1227
chr2	ENCODE	exon	220156284	220156882	.	+	.	Parent=gene1227
###
chr2	ENCODE	gene	220151612	220157089	.	+	.	ID=gene1228;Name=AC053503.7-007;name2=SPEG
chr2	ENCODE	exon	220151612	220151638	.	+	.	Parent=gene1228
chr2	ENCODE	exon	220152109	220152284	.	+	.	Parent=gene1228
chr2	ENCODE	CDS	220152216	220152284	.	+	0	Parent=gene1228
chr2	ENCODE	exon	220152525	220152613	.	+	.	Parent=gene1228
chr2	ENCODE	CDS	220152525	220152613	.	+	0	Parent=gene1228
chr2	ENCODE	exon	220154660	220154835	.	+	.	Parent=gene1228
chr2	ENCODE	CDS	220154660	220154835	.	+	1	Parent=gene1228
chr2	ENCODE	CDS	220156284	220156291	.	+	2	Parent=gene1228
chr2	ENCODE	exon	220156284	220157089	.	+	.	Parent=gene1228
###
chr2	ENCODE	gene	220161889	220164605	.	+	.	ID=gene1229;name2=SPEG;Name=AC053503.7-008
chr2	ENCODE	exon	220161889	220162558	.	+	.	Parent=gene1229
chr2	ENCODE	exon	220163117	220164605	.	+	.	Parent=gene1229
###
chr2	ENCODE	gene	220182094	220188471	.	+	.	ID=gene1230;Name=AC053503.7-021;name2=SPEG
chr2	ENCODE	exon	220182094	220182096	.	+	.	Parent=gene1230
chr2	ENCODE	CDS	220182094	220182096	.	+	0	Parent=gene1230
chr2	ENCODE	exon	220182338	220182487	.	+	.	Parent=gene1230
chr2	ENCODE	CDS	220182338	220182487	.	+	0	Parent=gene1230
chr2	ENCODE	exon	220182821	220182980	.	+	.	Parent=gene1230
chr2	ENCODE	CDS	220182821	220182980	.	+	0	Parent=gene1230
chr2	ENCODE	exon	220186582	220186709	.	+	.	Parent=gene1230
chr2	ENCODE	CDS	220186582	220186709	.	+	2	Parent=gene1230
chr2	ENCODE	exon	220187036	220187343	.	+	.	Parent=gene1230
chr2	ENCODE	CDS	220187036	220187343	.	+	0	Parent=gene1230
chr2	ENCODE	exon	220187947	220188088	.	+	.	Parent=gene1230
chr2	ENCODE	CDS	220187947	220188088	.	+	1	Parent=gene1230
chr2	ENCODE	CDS	220188278	220188416	.	+	0	Parent=gene1230
chr2	ENCODE	exon	220188278	220188471	.	+	.	Parent=gene1230
###
chr2	ENCODE	gene	220187918	220188514	.	+	.	ID=gene1231;name2=SPEG;Name=AC053503.7-022
chr2	ENCODE	exon	220187918	220188088	.	+	.	Parent=gene1231
chr2	ENCODE	exon	220188278	220188514	.	+	.	Parent=gene1231
###
chr2	ENCODE	gene	220189094	220197214	.	+	.	ID=gene1232;Name=AC053503.10-001;name2=GMPPA
chr2	ENCODE	exon	220189094	220189165	.	+	.	Parent=gene1232
chr2	ENCODE	exon	220190183	220190242	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220190203	220190242	.	+	0	Parent=gene1232
chr2	ENCODE	exon	220190348	220190445	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220190348	220190445	.	+	2	Parent=gene1232
chr2	ENCODE	exon	220191703	220191806	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220191703	220191806	.	+	0	Parent=gene1232
chr2	ENCODE	exon	220192078	220192264	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220192078	220192264	.	+	1	Parent=gene1232
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220192609	220192668	.	+	0	Parent=gene1232
chr2	ENCODE	exon	220194310	220194440	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220194310	220194440	.	+	0	Parent=gene1232
chr2	ENCODE	exon	220195455	220195589	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220195455	220195589	.	+	1	Parent=gene1232
chr2	ENCODE	exon	220195685	220195782	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220195685	220195782	.	+	1	Parent=gene1232
chr2	ENCODE	exon	220195942	220195988	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220195942	220195988	.	+	2	Parent=gene1232
chr2	ENCODE	exon	220196207	220196299	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220196207	220196299	.	+	0	Parent=gene1232
chr2	ENCODE	exon	220196481	220196649	.	+	.	Parent=gene1232
chr2	ENCODE	CDS	220196481	220196649	.	+	0	Parent=gene1232
chr2	ENCODE	CDS	220196925	220197025	.	+	2	Parent=gene1232
chr2	ENCODE	exon	220196925	220197214	.	+	.	Parent=gene1232
###
chr2	ENCODE	gene	220189111	220192668	.	+	.	ID=gene1233;name2=GMPPA;Name=AC053503.10-009
chr2	ENCODE	exon	220189111	220189165	.	+	.	Parent=gene1233
chr2	ENCODE	exon	220190183	220190242	.	+	.	Parent=gene1233
chr2	ENCODE	exon	220190348	220190445	.	+	.	Parent=gene1233
chr2	ENCODE	exon	220191703	220192264	.	+	.	Parent=gene1233
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1233
###
chr2	ENCODE	gene	220189115	220197162	.	+	.	ID=gene1234;Name=AC053503.10-002;name2=GMPPA
chr2	ENCODE	exon	220189115	220189165	.	+	.	Parent=gene1234
chr2	ENCODE	exon	220190183	220190242	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220190203	220190242	.	+	0	Parent=gene1234
chr2	ENCODE	exon	220190348	220190445	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220190348	220190445	.	+	2	Parent=gene1234
chr2	ENCODE	exon	220191703	220191806	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220191703	220191806	.	+	0	Parent=gene1234
chr2	ENCODE	exon	220192078	220192264	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220192078	220192264	.	+	1	Parent=gene1234
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220192609	220192668	.	+	0	Parent=gene1234
chr2	ENCODE	exon	220194310	220194440	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220194310	220194440	.	+	0	Parent=gene1234
chr2	ENCODE	exon	220195455	220195589	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220195455	220195589	.	+	1	Parent=gene1234
chr2	ENCODE	exon	220195685	220195988	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220195685	220195988	.	+	1	Parent=gene1234
chr2	ENCODE	exon	220196207	220196299	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220196207	220196299	.	+	0	Parent=gene1234
chr2	ENCODE	exon	220196481	220196649	.	+	.	Parent=gene1234
chr2	ENCODE	CDS	220196481	220196649	.	+	0	Parent=gene1234
chr2	ENCODE	CDS	220196925	220197025	.	+	2	Parent=gene1234
chr2	ENCODE	exon	220196925	220197162	.	+	.	Parent=gene1234
###
chr2	ENCODE	gene	220189128	220197215	.	+	.	ID=gene1235;Name=AC053503.10-003;name2=GMPPA
chr2	ENCODE	exon	220189128	220189481	.	+	.	Parent=gene1235
chr2	ENCODE	exon	220190188	220190242	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220190203	220190242	.	+	0	Parent=gene1235
chr2	ENCODE	exon	220190348	220190445	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220190348	220190445	.	+	2	Parent=gene1235
chr2	ENCODE	exon	220191703	220191806	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220191703	220191806	.	+	0	Parent=gene1235
chr2	ENCODE	exon	220192078	220192264	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220192078	220192264	.	+	1	Parent=gene1235
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220192609	220192668	.	+	0	Parent=gene1235
chr2	ENCODE	exon	220194310	220194440	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220194310	220194440	.	+	0	Parent=gene1235
chr2	ENCODE	exon	220195455	220195589	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220195455	220195589	.	+	1	Parent=gene1235
chr2	ENCODE	exon	220195685	220195782	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220195685	220195782	.	+	1	Parent=gene1235
chr2	ENCODE	exon	220195942	220195988	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220195942	220195988	.	+	2	Parent=gene1235
chr2	ENCODE	exon	220196207	220196299	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220196207	220196299	.	+	0	Parent=gene1235
chr2	ENCODE	exon	220196481	220196649	.	+	.	Parent=gene1235
chr2	ENCODE	CDS	220196481	220196649	.	+	0	Parent=gene1235
chr2	ENCODE	CDS	220196925	220197025	.	+	2	Parent=gene1235
chr2	ENCODE	exon	220196925	220197215	.	+	.	Parent=gene1235
###
chr2	ENCODE	gene	220189132	220197160	.	+	.	ID=gene1236;name2=GMPPA;Name=AC053503.10-005
chr2	ENCODE	exon	220189132	220189481	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220190188	220190242	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220190348	220190445	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220191703	220191806	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220192078	220192264	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220194310	220194440	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220195455	220195589	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220195685	220195782	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220195922	220195988	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220196207	220196299	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220196481	220196649	.	+	.	Parent=gene1236
chr2	ENCODE	exon	220196925	220197160	.	+	.	Parent=gene1236
###
chr2	ENCODE	gene	220189133	220197215	.	+	.	ID=gene1237;Name=AC053503.10-004;name2=GMPPA
chr2	ENCODE	exon	220189133	220189165	.	+	.	Parent=gene1237
chr2	ENCODE	exon	220190188	220190242	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220190203	220190242	.	+	0	Parent=gene1237
chr2	ENCODE	exon	220190348	220190445	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220190348	220190445	.	+	2	Parent=gene1237
chr2	ENCODE	exon	220191703	220191806	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220191703	220191806	.	+	0	Parent=gene1237
chr2	ENCODE	exon	220192078	220192264	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220192078	220192264	.	+	1	Parent=gene1237
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220192609	220192668	.	+	0	Parent=gene1237
chr2	ENCODE	exon	220194310	220194440	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220194310	220194440	.	+	0	Parent=gene1237
chr2	ENCODE	exon	220195455	220195589	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220195455	220195589	.	+	1	Parent=gene1237
chr2	ENCODE	exon	220195685	220195782	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220195685	220195782	.	+	1	Parent=gene1237
chr2	ENCODE	exon	220195942	220195988	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220195942	220195988	.	+	2	Parent=gene1237
chr2	ENCODE	exon	220196207	220196299	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220196207	220196299	.	+	0	Parent=gene1237
chr2	ENCODE	exon	220196481	220196649	.	+	.	Parent=gene1237
chr2	ENCODE	CDS	220196481	220196649	.	+	0	Parent=gene1237
chr2	ENCODE	CDS	220196925	220197025	.	+	2	Parent=gene1237
chr2	ENCODE	exon	220196925	220197215	.	+	.	Parent=gene1237
###
chr2	ENCODE	gene	220189134	220194311	.	+	.	ID=gene1238;Name=AC053503.10-006;name2=GMPPA
chr2	ENCODE	exon	220189134	220189481	.	+	.	Parent=gene1238
chr2	ENCODE	exon	220190183	220190242	.	+	.	Parent=gene1238
chr2	ENCODE	CDS	220190203	220190242	.	+	0	Parent=gene1238
chr2	ENCODE	exon	220190348	220190445	.	+	.	Parent=gene1238
chr2	ENCODE	CDS	220190348	220190445	.	+	2	Parent=gene1238
chr2	ENCODE	exon	220191703	220191806	.	+	.	Parent=gene1238
chr2	ENCODE	CDS	220191703	220191806	.	+	0	Parent=gene1238
chr2	ENCODE	exon	220192078	220192264	.	+	.	Parent=gene1238
chr2	ENCODE	CDS	220192078	220192264	.	+	1	Parent=gene1238
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1238
chr2	ENCODE	CDS	220192609	220192668	.	+	0	Parent=gene1238
chr2	ENCODE	exon	220194310	220194311	.	+	.	Parent=gene1238
chr2	ENCODE	CDS	220194310	220194311	.	+	0	Parent=gene1238
###
chr2	ENCODE	gene	220189136	220195782	.	+	.	ID=gene1239;Name=AC053503.10-008;name2=GMPPA
chr2	ENCODE	exon	220189136	220189165	.	+	.	Parent=gene1239
chr2	ENCODE	exon	220190405	220190445	.	+	.	Parent=gene1239
chr2	ENCODE	CDS	220190413	220190445	.	+	0	Parent=gene1239
chr2	ENCODE	exon	220191703	220191806	.	+	.	Parent=gene1239
chr2	ENCODE	CDS	220191703	220191806	.	+	0	Parent=gene1239
chr2	ENCODE	exon	220192078	220192264	.	+	.	Parent=gene1239
chr2	ENCODE	CDS	220192078	220192264	.	+	1	Parent=gene1239
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1239
chr2	ENCODE	CDS	220192609	220192668	.	+	0	Parent=gene1239
chr2	ENCODE	exon	220194310	220194440	.	+	.	Parent=gene1239
chr2	ENCODE	CDS	220194310	220194440	.	+	0	Parent=gene1239
chr2	ENCODE	exon	220195455	220195589	.	+	.	Parent=gene1239
chr2	ENCODE	CDS	220195455	220195589	.	+	1	Parent=gene1239
chr2	ENCODE	exon	220195685	220195782	.	+	.	Parent=gene1239
chr2	ENCODE	CDS	220195685	220195782	.	+	1	Parent=gene1239
###
chr2	ENCODE	gene	220189142	220197214	.	+	.	ID=gene1240;Name=AC053503.10-012;name2=GMPPA
chr2	ENCODE	exon	220189142	220189198	.	+	.	Parent=gene1240
chr2	ENCODE	exon	220190188	220190242	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220190203	220190242	.	+	0	Parent=gene1240
chr2	ENCODE	exon	220190348	220190445	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220190348	220190445	.	+	2	Parent=gene1240
chr2	ENCODE	exon	220191703	220191806	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220191703	220191806	.	+	0	Parent=gene1240
chr2	ENCODE	exon	220192078	220192264	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220192078	220192264	.	+	1	Parent=gene1240
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220192609	220192668	.	+	0	Parent=gene1240
chr2	ENCODE	exon	220194310	220194440	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220194310	220194440	.	+	0	Parent=gene1240
chr2	ENCODE	exon	220195455	220195589	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220195455	220195589	.	+	1	Parent=gene1240
chr2	ENCODE	exon	220195685	220195782	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220195685	220195782	.	+	1	Parent=gene1240
chr2	ENCODE	exon	220195942	220195988	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220195942	220195988	.	+	2	Parent=gene1240
chr2	ENCODE	exon	220196207	220196299	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220196207	220196299	.	+	0	Parent=gene1240
chr2	ENCODE	exon	220196481	220196649	.	+	.	Parent=gene1240
chr2	ENCODE	CDS	220196481	220196649	.	+	0	Parent=gene1240
chr2	ENCODE	CDS	220196925	220197025	.	+	2	Parent=gene1240
chr2	ENCODE	exon	220196925	220197214	.	+	.	Parent=gene1240
###
chr2	ENCODE	gene	220190002	220197214	.	+	.	ID=gene1241;Name=AC053503.10-013;name2=GMPPA
chr2	ENCODE	exon	220190002	220190242	.	+	.	Parent=gene1241
chr2	ENCODE	exon	220190348	220192264	.	+	.	Parent=gene1241
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1241
chr2	ENCODE	exon	220194310	220196299	.	+	.	Parent=gene1241
chr2	ENCODE	exon	220196481	220197214	.	+	.	Parent=gene1241
###
chr2	ENCODE	gene	220190171	220194468	.	+	.	ID=gene1242;name2=GMPPA;Name=AC053503.10-007
chr2	ENCODE	exon	220190171	220190242	.	+	.	Parent=gene1242
chr2	ENCODE	exon	220190348	220190445	.	+	.	Parent=gene1242
chr2	ENCODE	exon	220191703	220191806	.	+	.	Parent=gene1242
chr2	ENCODE	exon	220192078	220192264	.	+	.	Parent=gene1242
chr2	ENCODE	exon	220192609	220192668	.	+	.	Parent=gene1242
chr2	ENCODE	exon	220194310	220194468	.	+	.	Parent=gene1242
###
chr2	ENCODE	gene	220195952	220196921	.	+	.	ID=gene1243;Name=AC053503.10-011;name2=GMPPA
chr2	ENCODE	exon	220195952	220195988	.	+	.	Parent=gene1243
chr2	ENCODE	exon	220196207	220196299	.	+	.	Parent=gene1243
chr2	ENCODE	exon	220196481	220196921	.	+	.	Parent=gene1243
###
chr2	ENCODE	gene	220196167	220196649	.	+	.	ID=gene1244;Name=AC053503.10-010;name2=GMPPA
chr2	ENCODE	exon	220196167	220196299	.	+	.	Parent=gene1244
chr2	ENCODE	exon	220196481	220196649	.	+	.	Parent=gene1244
###
chr2	ENCODE	gene	220204397	220224285	.	+	.	ID=gene1245;Name=AC009955.2-004;name2=ACCN4
chr2	ENCODE	exon	220204397	220205533	.	+	.	Parent=gene1245
chr2	ENCODE	exon	220221985	220222129	.	+	.	Parent=gene1245
chr2	ENCODE	exon	220222228	220224285	.	+	.	Parent=gene1245
###
chr2	ENCODE	gene	220204557	220228999	.	+	.	ID=gene1246;Name=AC009955.2-001;name2=ACCN4
chr2	ENCODE	exon	220204557	220205533	.	+	.	Parent=gene1246
chr2	ENCODE	CDS	220204571	220205533	.	+	0	Parent=gene1246
chr2	ENCODE	exon	220221985	220222129	.	+	.	Parent=gene1246
chr2	ENCODE	CDS	220221985	220222129	.	+	0	Parent=gene1246
chr2	ENCODE	exon	220222228	220222355	.	+	.	Parent=gene1246
chr2	ENCODE	CDS	220222228	220222355	.	+	2	Parent=gene1246
chr2	ENCODE	exon	220222542	220222704	.	+	.	Parent=gene1246
chr2	ENCODE	CDS	220222542	220222704	.	+	0	Parent=gene1246
chr2	ENCODE	exon	220225398	220225551	.	+	.	Parent=gene1246
chr2	ENCODE	CDS	220225398	220225551	.	+	2	Parent=gene1246
chr2	ENCODE	exon	220227293	220227384	.	+	.	Parent=gene1246
chr2	ENCODE	CDS	220227293	220227384	.	+	1	Parent=gene1246
chr2	ENCODE	exon	220227469	220227548	.	+	.	Parent=gene1246
chr2	ENCODE	CDS	220227469	220227548	.	+	2	Parent=gene1246
chr2	ENCODE	exon	220227859	220227963	.	+	.	Parent=gene1246
chr2	ENCODE	CDS	220227859	220227963	.	+	0	Parent=gene1246
chr2	ENCODE	CDS	220228160	220228273	.	+	0	Parent=gene1246
chr2	ENCODE	exon	220228160	220228999	.	+	.	Parent=gene1246
###
chr2	ENCODE	gene	220204557	220228999	.	+	.	ID=gene1247;Name=AC009955.2-002;name2=ACCN4
chr2	ENCODE	exon	220204557	220205533	.	+	.	Parent=gene1247
chr2	ENCODE	CDS	220204571	220205533	.	+	0	Parent=gene1247
chr2	ENCODE	exon	220221985	220222129	.	+	.	Parent=gene1247
chr2	ENCODE	CDS	220221985	220222129	.	+	0	Parent=gene1247
chr2	ENCODE	exon	220222228	220222355	.	+	.	Parent=gene1247
chr2	ENCODE	CDS	220222228	220222355	.	+	2	Parent=gene1247
chr2	ENCODE	exon	220222542	220222704	.	+	.	Parent=gene1247
chr2	ENCODE	CDS	220222542	220222704	.	+	0	Parent=gene1247
chr2	ENCODE	exon	220223110	220223166	.	+	.	Parent=gene1247
chr2	ENCODE	CDS	220223110	220223166	.	+	2	Parent=gene1247
chr2	ENCODE	exon	220225398	220225551	.	+	.	Parent=gene1247
chr2	ENCODE	CDS	220225398	220225551	.	+	2	Parent=gene1247
chr2	ENCODE	exon	220227293	220227384	.	+	.	Parent=gene1247
chr2	ENCODE	CDS	220227293	220227384	.	+	1	Parent=gene1247
chr2	ENCODE	exon	220227469	220227548	.	+	.	Parent=gene1247
chr2	ENCODE	CDS	220227469	220227548	.	+	2	Parent=gene1247
chr2	ENCODE	exon	220227859	220227963	.	+	.	Parent=gene1247
chr2	ENCODE	CDS	220227859	220227963	.	+	0	Parent=gene1247
chr2	ENCODE	CDS	220228160	220228273	.	+	0	Parent=gene1247
chr2	ENCODE	exon	220228160	220228999	.	+	.	Parent=gene1247
###
chr2	ENCODE	gene	220207363	220228999	.	+	.	ID=gene1248;Name=AC009955.2-003;name2=ACCN4
chr2	ENCODE	exon	220207363	220207495	.	+	.	Parent=gene1248
chr2	ENCODE	exon	220221985	220222129	.	+	.	Parent=gene1248
chr2	ENCODE	exon	220222228	220222355	.	+	.	Parent=gene1248
chr2	ENCODE	exon	220222542	220222704	.	+	.	Parent=gene1248
chr2	ENCODE	exon	220223110	220223166	.	+	.	Parent=gene1248
chr2	ENCODE	exon	220225398	220225551	.	+	.	Parent=gene1248
chr2	ENCODE	exon	220227293	220227384	.	+	.	Parent=gene1248
chr2	ENCODE	exon	220227469	220228999	.	+	.	Parent=gene1248
###
chr2	ENCODE	gene	220207468	220223258	.	+	.	ID=gene1249;Name=AC009955.2-005;name2=ACCN4
chr2	ENCODE	exon	220207468	220207495	.	+	.	Parent=gene1249
chr2	ENCODE	exon	220221985	220222129	.	+	.	Parent=gene1249
chr2	ENCODE	exon	220222228	220222355	.	+	.	Parent=gene1249
chr2	ENCODE	exon	220222542	220222704	.	+	.	Parent=gene1249
chr2	ENCODE	exon	220223110	220223258	.	+	.	Parent=gene1249
###
chr2	ENCODE	gene	220229174	220234014	.	-	.	ID=gene1250;Name=AC009955.3-001;name2=CHPF
chr2	ENCODE	exon	220229174	220230869	.	-	.	Parent=gene1250
chr2	ENCODE	CDS	220229610	220230869	.	-	0	Parent=gene1250
chr2	ENCODE	exon	220231173	220231352	.	-	.	Parent=gene1250
chr2	ENCODE	CDS	220231173	220231352	.	-	0	Parent=gene1250
chr2	ENCODE	exon	220231843	220232416	.	-	.	Parent=gene1250
chr2	ENCODE	CDS	220231843	220232416	.	-	1	Parent=gene1250
chr2	ENCODE	CDS	220233452	220233765	.	-	0	Parent=gene1250
chr2	ENCODE	exon	220233452	220234014	.	-	.	Parent=gene1250
###
chr2	ENCODE	gene	220231687	220233800	.	-	.	ID=gene1251;Name=AC009955.3-002;name2=CHPF
chr2	ENCODE	exon	220231687	220232416	.	-	.	Parent=gene1251
chr2	ENCODE	CDS	220231834	220232416	.	-	1	Parent=gene1251
chr2	ENCODE	CDS	220233452	220233765	.	-	0	Parent=gene1251
chr2	ENCODE	exon	220233452	220233800	.	-	.	Parent=gene1251
###
chr2	ENCODE	gene	220233890	220240806	.	+	.	ID=gene1252;Name=AC009955.4-002;name2=AC009955.4
chr2	ENCODE	exon	220233890	220234238	.	+	.	Parent=gene1252
chr2	ENCODE	exon	220234373	220234604	.	+	.	Parent=gene1252
chr2	ENCODE	exon	220234951	220235120	.	+	.	Parent=gene1252
chr2	ENCODE	CDS	220234955	220235120	.	+	0	Parent=gene1252
chr2	ENCODE	exon	220237733	220238308	.	+	.	Parent=gene1252
chr2	ENCODE	CDS	220237733	220238308	.	+	2	Parent=gene1252
chr2	ENCODE	exon	220239379	220239581	.	+	.	Parent=gene1252
chr2	ENCODE	CDS	220239379	220239581	.	+	2	Parent=gene1252
chr2	ENCODE	CDS	220239944	220240081	.	+	0	Parent=gene1252
chr2	ENCODE	exon	220239944	220240806	.	+	.	Parent=gene1252
###
chr2	ENCODE	gene	220234233	220238247	.	+	.	ID=gene1253;Name=AC009955.4-003;name2=AC009955.4
chr2	ENCODE	exon	220234233	220234604	.	+	.	Parent=gene1253
chr2	ENCODE	exon	220234951	220235120	.	+	.	Parent=gene1253
chr2	ENCODE	CDS	220234955	220235120	.	+	0	Parent=gene1253
chr2	ENCODE	exon	220237733	220238247	.	+	.	Parent=gene1253
chr2	ENCODE	CDS	220237733	220238247	.	+	2	Parent=gene1253
###
chr2	ENCODE	gene	220234250	220240822	.	+	.	ID=gene1254;Name=AC009955.4-001;name2=AC009955.4
chr2	ENCODE	exon	220234250	220234604	.	+	.	Parent=gene1254
chr2	ENCODE	exon	220234916	220235120	.	+	.	Parent=gene1254
chr2	ENCODE	CDS	220234955	220235120	.	+	0	Parent=gene1254
chr2	ENCODE	exon	220237733	220238308	.	+	.	Parent=gene1254
chr2	ENCODE	CDS	220237733	220238308	.	+	2	Parent=gene1254
chr2	ENCODE	exon	220239379	220239581	.	+	.	Parent=gene1254
chr2	ENCODE	CDS	220239379	220239581	.	+	2	Parent=gene1254
chr2	ENCODE	CDS	220239944	220240081	.	+	0	Parent=gene1254
chr2	ENCODE	exon	220239944	220240822	.	+	.	Parent=gene1254
###
chr2	ENCODE	gene	220234277	220237776	.	+	.	ID=gene1255;Name=AC009955.4-004;name2=AC009955.4
chr2	ENCODE	exon	220234277	220234604	.	+	.	Parent=gene1255
chr2	ENCODE	CDS	220234314	220234604	.	+	0	Parent=gene1255
chr2	ENCODE	exon	220234988	220235120	.	+	.	Parent=gene1255
chr2	ENCODE	CDS	220234988	220235120	.	+	0	Parent=gene1255
chr2	ENCODE	exon	220237733	220237776	.	+	.	Parent=gene1255
chr2	ENCODE	CDS	220237733	220237776	.	+	2	Parent=gene1255
###
chr2	ENCODE	gene	220240956	220242616	.	-	.	ID=gene1256;name2=OBSL1;Name=AC009955.5-011
chr2	ENCODE	exon	220240956	220241069	.	-	.	Parent=gene1256
chr2	ENCODE	exon	220241756	220242025	.	-	.	Parent=gene1256
chr2	ENCODE	exon	220242339	220242616	.	-	.	Parent=gene1256
###
chr2	ENCODE	gene	220240956	220242941	.	-	.	ID=gene1257;Name=AC009955.5-012;name2=OBSL1
chr2	ENCODE	exon	220240956	220241095	.	-	.	Parent=gene1257
chr2	ENCODE	exon	220241756	220242025	.	-	.	Parent=gene1257
chr2	ENCODE	exon	220242339	220242443	.	-	.	Parent=gene1257
chr2	ENCODE	exon	220242763	220242941	.	-	.	Parent=gene1257
###
chr2	ENCODE	gene	220240956	220260966	.	-	.	ID=gene1258;Name=AC009955.5-004;name2=OBSL1
chr2	ENCODE	exon	220240956	220242025	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220242339	220242443	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220242763	220243251	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220246247	220246519	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220246805	220246950	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220247570	220247845	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220248050	220248337	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220249452	220249724	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220252629	220252901	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220253582	220253854	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220255469	220255741	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220257057	220257353	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220257500	220257802	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220257945	220258196	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220258282	220258551	.	-	.	Parent=gene1258
chr2	ENCODE	exon	220260448	220260966	.	-	.	Parent=gene1258
###
chr2	ENCODE	gene	220240983	220261468	.	-	.	ID=gene1259;Name=AC009955.5-001;name2=OBSL1
chr2	ENCODE	exon	220240983	220241069	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220241062	220241069	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220241756	220242025	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220241756	220242025	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220242339	220242443	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220242339	220242443	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220242763	220242924	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220242763	220242924	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220243095	220243251	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220243095	220243251	.	-	0	Parent=gene1259
chr2	ENCODE	exon	220243801	220243913	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220243801	220243913	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220244701	220244967	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220244701	220244967	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220246247	220246519	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220246247	220246519	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220246681	220246950	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220246681	220246950	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220248050	220248337	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220248050	220248337	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220248411	220248686	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220248411	220248686	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220249452	220249724	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220249452	220249724	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220252629	220252901	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220252629	220252901	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220253582	220253854	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220253582	220253854	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220255469	220255741	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220255469	220255741	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220257057	220257353	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220257057	220257353	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220257500	220257802	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220257500	220257802	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220257945	220258196	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220257945	220258196	.	-	2	Parent=gene1259
chr2	ENCODE	exon	220258282	220258551	.	-	.	Parent=gene1259
chr2	ENCODE	CDS	220258282	220258551	.	-	2	Parent=gene1259
chr2	ENCODE	CDS	220260448	220261459	.	-	0	Parent=gene1259
chr2	ENCODE	exon	220260448	220261468	.	-	.	Parent=gene1259
###
chr2	ENCODE	gene	220245990	220249658	.	-	.	ID=gene1260;Name=AC009955.5-005;name2=OBSL1
chr2	ENCODE	exon	220245990	220246519	.	-	.	Parent=gene1260
chr2	ENCODE	CDS	220246224	220246519	.	-	0	Parent=gene1260
chr2	ENCODE	exon	220246681	220246950	.	-	.	Parent=gene1260
chr2	ENCODE	CDS	220246681	220246950	.	-	0	Parent=gene1260
chr2	ENCODE	exon	220248050	220248337	.	-	.	Parent=gene1260
chr2	ENCODE	CDS	220248050	220248337	.	-	0	Parent=gene1260
chr2	ENCODE	exon	220248411	220248686	.	-	.	Parent=gene1260
chr2	ENCODE	CDS	220248411	220248686	.	-	0	Parent=gene1260
chr2	ENCODE	exon	220249452	220249658	.	-	.	Parent=gene1260
chr2	ENCODE	CDS	220249452	220249658	.	-	0	Parent=gene1260
###
chr2	ENCODE	gene	220246300	220248608	.	-	.	ID=gene1261;Name=AC009955.5-009;name2=OBSL1
chr2	ENCODE	exon	220246300	220246519	.	-	.	Parent=gene1261
chr2	ENCODE	CDS	220246300	220246519	.	-	0	Parent=gene1261
chr2	ENCODE	exon	220246681	220246950	.	-	.	Parent=gene1261
chr2	ENCODE	CDS	220246681	220246950	.	-	0	Parent=gene1261
chr2	ENCODE	exon	220247570	220247845	.	-	.	Parent=gene1261
chr2	ENCODE	CDS	220247570	220247845	.	-	0	Parent=gene1261
chr2	ENCODE	exon	220248050	220248337	.	-	.	Parent=gene1261
chr2	ENCODE	CDS	220248050	220248337	.	-	0	Parent=gene1261
chr2	ENCODE	exon	220248411	220248608	.	-	.	Parent=gene1261
chr2	ENCODE	CDS	220248411	220248608	.	-	0	Parent=gene1261
###
chr2	ENCODE	gene	220246469	220247254	.	-	.	ID=gene1262;Name=AC009955.5-010;name2=OBSL1
chr2	ENCODE	exon	220246469	220246519	.	-	.	Parent=gene1262
chr2	ENCODE	exon	220246681	220247254	.	-	.	Parent=gene1262
###
chr2	ENCODE	gene	220251949	220261516	.	-	.	ID=gene1263;Name=AC009955.5-002;name2=OBSL1
chr2	ENCODE	exon	220251949	220252235	.	-	.	Parent=gene1263
chr2	ENCODE	CDS	220252111	220252235	.	-	2	Parent=gene1263
chr2	ENCODE	exon	220252629	220252901	.	-	.	Parent=gene1263
chr2	ENCODE	CDS	220252629	220252901	.	-	2	Parent=gene1263
chr2	ENCODE	exon	220253582	220253854	.	-	.	Parent=gene1263
chr2	ENCODE	CDS	220253582	220253854	.	-	2	Parent=gene1263
chr2	ENCODE	exon	220255469	220255741	.	-	.	Parent=gene1263
chr2	ENCODE	CDS	220255469	220255741	.	-	2	Parent=gene1263
chr2	ENCODE	exon	220257057	220257353	.	-	.	Parent=gene1263
chr2	ENCODE	CDS	220257057	220257353	.	-	2	Parent=gene1263
chr2	ENCODE	exon	220257500	220257802	.	-	.	Parent=gene1263
chr2	ENCODE	CDS	220257500	220257802	.	-	2	Parent=gene1263
chr2	ENCODE	exon	220257945	220258196	.	-	.	Parent=gene1263
chr2	ENCODE	CDS	220257945	220258196	.	-	2	Parent=gene1263
chr2	ENCODE	exon	220258282	220258551	.	-	.	Parent=gene1263
chr2	ENCODE	CDS	220258282	220258551	.	-	2	Parent=gene1263
chr2	ENCODE	CDS	220260448	220261459	.	-	0	Parent=gene1263
chr2	ENCODE	exon	220260448	220261516	.	-	.	Parent=gene1263
###
chr2	ENCODE	gene	220251974	220261691	.	-	.	ID=gene1264;Name=AC009955.5-003;name2=OBSL1
chr2	ENCODE	exon	220251974	220252235	.	-	.	Parent=gene1264
chr2	ENCODE	CDS	220252111	220252235	.	-	2	Parent=gene1264
chr2	ENCODE	exon	220252629	220252901	.	-	.	Parent=gene1264
chr2	ENCODE	CDS	220252629	220252901	.	-	2	Parent=gene1264
chr2	ENCODE	exon	220253582	220253854	.	-	.	Parent=gene1264
chr2	ENCODE	CDS	220253582	220253854	.	-	2	Parent=gene1264
chr2	ENCODE	exon	220255469	220255741	.	-	.	Parent=gene1264
chr2	ENCODE	CDS	220255469	220255741	.	-	2	Parent=gene1264
chr2	ENCODE	exon	220257057	220257353	.	-	.	Parent=gene1264
chr2	ENCODE	CDS	220257057	220257353	.	-	2	Parent=gene1264
chr2	ENCODE	exon	220257500	220257802	.	-	.	Parent=gene1264
chr2	ENCODE	CDS	220257500	220257802	.	-	2	Parent=gene1264
chr2	ENCODE	exon	220257945	220258196	.	-	.	Parent=gene1264
chr2	ENCODE	CDS	220257945	220258196	.	-	2	Parent=gene1264
chr2	ENCODE	CDS	220258282	220258324	.	-	0	Parent=gene1264
chr2	ENCODE	exon	220258282	220258551	.	-	.	Parent=gene1264
chr2	ENCODE	exon	220261621	220261691	.	-	.	Parent=gene1264
###
chr2	ENCODE	gene	220253042	220255606	.	-	.	ID=gene1265;Name=AC009955.5-008;name2=OBSL1
chr2	ENCODE	exon	220253042	220253854	.	-	.	Parent=gene1265
chr2	ENCODE	exon	220255469	220255606	.	-	.	Parent=gene1265
###
chr2	ENCODE	gene	220258123	220261748	.	-	.	ID=gene1266;Name=AC009955.5-006;name2=OBSL1
chr2	ENCODE	exon	220258123	220258196	.	-	.	Parent=gene1266
chr2	ENCODE	exon	220258282	220258551	.	-	.	Parent=gene1266
chr2	ENCODE	exon	220260448	220260593	.	-	.	Parent=gene1266
chr2	ENCODE	exon	220261664	220261748	.	-	.	Parent=gene1266
###
chr2	ENCODE	gene	220259389	220265280	.	+	.	ID=gene1267;Name=AC009955.6-002;name2=INHA
chr2	ENCODE	exon	220259389	220259673	.	+	.	Parent=gene1267
chr2	ENCODE	exon	220264921	220265280	.	+	.	Parent=gene1267
###
chr2	ENCODE	gene	220260448	220261719	.	-	.	ID=gene1268;Name=AC009955.5-007;name2=OBSL1
chr2	ENCODE	exon	220260448	220260919	.	-	.	Parent=gene1268
chr2	ENCODE	exon	220261621	220261719	.	-	.	Parent=gene1268
###
chr2	ENCODE	gene	220260685	220262086	.	-	.	ID=gene1269;Name=AC009955.5-013;name2=OBSL1
chr2	ENCODE	exon	220260685	220260802	.	-	.	Parent=gene1269
chr2	ENCODE	exon	220261621	220262086	.	-	.	Parent=gene1269
###
chr2	ENCODE	gene	220262422	220265940	.	+	.	ID=gene1270;Name=AC009955.6-001;name2=INHA
chr2	ENCODE	exon	220262422	220262869	.	+	.	Parent=gene1270
chr2	ENCODE	CDS	220262602	220262869	.	+	0	Parent=gene1270
chr2	ENCODE	CDS	220264921	220265753	.	+	2	Parent=gene1270
chr2	ENCODE	exon	220264921	220265940	.	+	.	Parent=gene1270
###
chr2	ENCODE	gene	220288087	220306678	.	+	.	ID=gene1271;Name=AC009955.7-001;name2=STK11IP
chr2	ENCODE	exon	220288087	220288150	.	+	.	Parent=gene1271
chr2	ENCODE	exon	220288321	220288407	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220288347	220288407	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220291462	220291667	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220291462	220291667	.	+	2	Parent=gene1271
chr2	ENCODE	exon	220291868	220291942	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220291868	220291942	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220292215	220292310	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220292215	220292310	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220292695	220292802	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220292695	220292802	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220292932	220293003	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220292932	220293003	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220295835	220295961	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220295835	220295961	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220296183	220296286	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220296183	220296286	.	+	2	Parent=gene1271
chr2	ENCODE	exon	220296422	220296517	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220296422	220296517	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220296703	220296744	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220296703	220296744	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220296939	220297085	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220296939	220297085	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220297280	220297364	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220297280	220297364	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220298274	220298657	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220298274	220298657	.	+	2	Parent=gene1271
chr2	ENCODE	exon	220298810	220299015	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220298810	220299015	.	+	2	Parent=gene1271
chr2	ENCODE	exon	220299324	220299440	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220299324	220299440	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220299590	220299767	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220299590	220299767	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220301831	220302061	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220301831	220302061	.	+	2	Parent=gene1271
chr2	ENCODE	exon	220302182	220302285	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220302182	220302285	.	+	2	Parent=gene1271
chr2	ENCODE	exon	220303355	220303452	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220303355	220303452	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220303979	220304157	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220303979	220304157	.	+	1	Parent=gene1271
chr2	ENCODE	exon	220304388	220304469	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220304388	220304469	.	+	2	Parent=gene1271
chr2	ENCODE	exon	220304703	220304773	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220304703	220304773	.	+	1	Parent=gene1271
chr2	ENCODE	exon	220305321	220305568	.	+	.	Parent=gene1271
chr2	ENCODE	CDS	220305321	220305568	.	+	2	Parent=gene1271
chr2	ENCODE	CDS	220306271	220306420	.	+	0	Parent=gene1271
chr2	ENCODE	exon	220306271	220306678	.	+	.	Parent=gene1271
###
chr2	ENCODE	gene	220288098	220292067	.	+	.	ID=gene1272;Name=AC009955.7-015;name2=STK11IP
chr2	ENCODE	exon	220288098	220288150	.	+	.	Parent=gene1272
chr2	ENCODE	exon	220288321	220288407	.	+	.	Parent=gene1272
chr2	ENCODE	exon	220291462	220291667	.	+	.	Parent=gene1272
chr2	ENCODE	exon	220291868	220292067	.	+	.	Parent=gene1272
###
chr2	ENCODE	gene	220288321	220292310	.	+	.	ID=gene1273;Name=AC009955.7-004;name2=STK11IP
chr2	ENCODE	exon	220288321	220288407	.	+	.	Parent=gene1273
chr2	ENCODE	exon	220291462	220291781	.	+	.	Parent=gene1273
chr2	ENCODE	exon	220291868	220291942	.	+	.	Parent=gene1273
chr2	ENCODE	exon	220292215	220292310	.	+	.	Parent=gene1273
###
chr2	ENCODE	gene	220288366	220299933	.	+	.	ID=gene1274;name2=STK11IP;Name=AC009955.7-002
chr2	ENCODE	exon	220288366	220288407	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220291462	220291667	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220291868	220291942	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220292215	220292310	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220292695	220292802	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220292932	220293003	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220295835	220295961	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220296183	220296286	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220296422	220296517	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220296703	220296744	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220296939	220297085	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220297280	220297364	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220298274	220298657	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220298810	220299015	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220299324	220299440	.	+	.	Parent=gene1274
chr2	ENCODE	exon	220299590	220299933	.	+	.	Parent=gene1274
###
chr2	ENCODE	gene	220288394	220291886	.	+	.	ID=gene1275;Name=AC009955.7-012;name2=STK11IP
chr2	ENCODE	exon	220288394	220288549	.	+	.	Parent=gene1275
chr2	ENCODE	exon	220291462	220291667	.	+	.	Parent=gene1275
chr2	ENCODE	exon	220291868	220291886	.	+	.	Parent=gene1275
###
chr2	ENCODE	gene	220288421	220292936	.	+	.	ID=gene1276;Name=AC009955.7-013;name2=STK11IP
chr2	ENCODE	exon	220288421	220288504	.	+	.	Parent=gene1276
chr2	ENCODE	exon	220291462	220291667	.	+	.	Parent=gene1276
chr2	ENCODE	exon	220291868	220291942	.	+	.	Parent=gene1276
chr2	ENCODE	exon	220292215	220292310	.	+	.	Parent=gene1276
chr2	ENCODE	exon	220292695	220292802	.	+	.	Parent=gene1276
chr2	ENCODE	exon	220292932	220292936	.	+	.	Parent=gene1276
###
chr2	ENCODE	gene	220288670	220296285	.	+	.	ID=gene1277;name2=STK11IP;Name=AC009955.7-003
chr2	ENCODE	exon	220288670	220288736	.	+	.	Parent=gene1277
chr2	ENCODE	exon	220291462	220291667	.	+	.	Parent=gene1277
chr2	ENCODE	exon	220291868	220291942	.	+	.	Parent=gene1277
chr2	ENCODE	exon	220292215	220292310	.	+	.	Parent=gene1277
chr2	ENCODE	exon	220292695	220292802	.	+	.	Parent=gene1277
chr2	ENCODE	exon	220292932	220293003	.	+	.	Parent=gene1277
chr2	ENCODE	exon	220295835	220295961	.	+	.	Parent=gene1277
chr2	ENCODE	exon	220296183	220296285	.	+	.	Parent=gene1277
###
chr2	ENCODE	gene	220295734	220296860	.	+	.	ID=gene1278;name2=STK11IP;Name=AC009955.7-005
chr2	ENCODE	exon	220295734	220295961	.	+	.	Parent=gene1278
chr2	ENCODE	exon	220296183	220296286	.	+	.	Parent=gene1278
chr2	ENCODE	exon	220296422	220296860	.	+	.	Parent=gene1278
###
chr2	ENCODE	gene	220295756	220297084	.	+	.	ID=gene1279;Name=AC009955.7-006;name2=STK11IP
chr2	ENCODE	exon	220295756	220295961	.	+	.	Parent=gene1279
chr2	ENCODE	exon	220296183	220296286	.	+	.	Parent=gene1279
chr2	ENCODE	exon	220296422	220296517	.	+	.	Parent=gene1279
chr2	ENCODE	exon	220296703	220296744	.	+	.	Parent=gene1279
chr2	ENCODE	exon	220296939	220297084	.	+	.	Parent=gene1279
###
chr2	ENCODE	gene	220298625	220299699	.	+	.	ID=gene1280;Name=AC009955.7-014;name2=STK11IP
chr2	ENCODE	exon	220298625	220298657	.	+	.	Parent=gene1280
chr2	ENCODE	exon	220298810	220299015	.	+	.	Parent=gene1280
chr2	ENCODE	exon	220299324	220299699	.	+	.	Parent=gene1280
###
chr2	ENCODE	gene	220299373	220300353	.	+	.	ID=gene1281;Name=AC009955.7-007;name2=STK11IP
chr2	ENCODE	exon	220299373	220299440	.	+	.	Parent=gene1281
chr2	ENCODE	exon	220299590	220299767	.	+	.	Parent=gene1281
chr2	ENCODE	exon	220300295	220300353	.	+	.	Parent=gene1281
###
chr2	ENCODE	gene	220302270	220305429	.	+	.	ID=gene1282;Name=AC009955.7-009;name2=STK11IP
chr2	ENCODE	exon	220302270	220302285	.	+	.	Parent=gene1282
chr2	ENCODE	exon	220303355	220303452	.	+	.	Parent=gene1282
chr2	ENCODE	exon	220303979	220304157	.	+	.	Parent=gene1282
chr2	ENCODE	exon	220304388	220304469	.	+	.	Parent=gene1282
chr2	ENCODE	exon	220304703	220305098	.	+	.	Parent=gene1282
chr2	ENCODE	exon	220305321	220305429	.	+	.	Parent=gene1282
###
chr2	ENCODE	gene	220303278	220304947	.	+	.	ID=gene1283;Name=AC009955.7-008;name2=STK11IP
chr2	ENCODE	exon	220303278	220303452	.	+	.	Parent=gene1283
chr2	ENCODE	exon	220303979	220304157	.	+	.	Parent=gene1283
chr2	ENCODE	exon	220304388	220304469	.	+	.	Parent=gene1283
chr2	ENCODE	exon	220304703	220304947	.	+	.	Parent=gene1283
###
chr2	ENCODE	gene	220304143	220306222	.	+	.	ID=gene1284;name2=STK11IP;Name=AC009955.7-011
chr2	ENCODE	exon	220304143	220304157	.	+	.	Parent=gene1284
chr2	ENCODE	exon	220304388	220304469	.	+	.	Parent=gene1284
chr2	ENCODE	exon	220304703	220304773	.	+	.	Parent=gene1284
chr2	ENCODE	exon	220305321	220305568	.	+	.	Parent=gene1284
chr2	ENCODE	exon	220305934	220306222	.	+	.	Parent=gene1284
###
chr2	ENCODE	gene	220305033	220306439	.	+	.	ID=gene1285;Name=AC009955.7-010;name2=STK11IP
chr2	ENCODE	exon	220305033	220305568	.	+	.	Parent=gene1285
chr2	ENCODE	exon	220306271	220306439	.	+	.	Parent=gene1285
###
chr2	ENCODE	gene	220317554	220332198	.	+	.	ID=gene1286;Name=AC009955.9-009;name2=SLC4A3
chr2	ENCODE	exon	220317554	220317972	.	+	.	Parent=gene1286
chr2	ENCODE	exon	220318127	220318270	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220318220	220318270	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220318632	220318797	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220318632	220318797	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220319371	220319648	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220319371	220319648	.	+	2	Parent=gene1286
chr2	ENCODE	exon	220319807	220319922	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220319807	220319922	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220320380	220320579	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220320380	220320579	.	+	1	Parent=gene1286
chr2	ENCODE	exon	220322195	220322343	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220322195	220322343	.	+	2	Parent=gene1286
chr2	ENCODE	exon	220322489	220322669	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220322489	220322669	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220323101	220323236	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220323101	220323236	.	+	2	Parent=gene1286
chr2	ENCODE	exon	220323501	220323684	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220323501	220323684	.	+	1	Parent=gene1286
chr2	ENCODE	exon	220324107	220324206	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220324107	220324206	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220324647	220324831	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220324647	220324831	.	+	2	Parent=gene1286
chr2	ENCODE	exon	220325498	220325723	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220325498	220325723	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220325900	220326118	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220325900	220326118	.	+	2	Parent=gene1286
chr2	ENCODE	exon	220326529	220326677	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220326529	220326677	.	+	2	Parent=gene1286
chr2	ENCODE	exon	220326907	220327101	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220326907	220327101	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220327808	220328038	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220327808	220328038	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220328391	220328480	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220328391	220328480	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220328930	220329096	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220328930	220329096	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220329709	220329962	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220329709	220329962	.	+	1	Parent=gene1286
chr2	ENCODE	exon	220330657	220330826	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220330657	220330826	.	+	2	Parent=gene1286
chr2	ENCODE	exon	220331016	220331189	.	+	.	Parent=gene1286
chr2	ENCODE	CDS	220331016	220331189	.	+	0	Parent=gene1286
chr2	ENCODE	CDS	220331878	220331955	.	+	0	Parent=gene1286
chr2	ENCODE	exon	220331878	220332198	.	+	.	Parent=gene1286
###
chr2	ENCODE	gene	220317621	220332198	.	+	.	ID=gene1287;name2=SLC4A3;Name=AC009955.9-010
chr2	ENCODE	exon	220317621	220317719	.	+	.	Parent=gene1287
chr2	ENCODE	exon	220318127	220318270	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220318220	220318270	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220318632	220318797	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220318632	220318797	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220319371	220319648	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220319371	220319648	.	+	2	Parent=gene1287
chr2	ENCODE	exon	220319807	220319922	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220319807	220319922	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220320380	220320579	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220320380	220320579	.	+	1	Parent=gene1287
chr2	ENCODE	exon	220322195	220322343	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220322195	220322343	.	+	2	Parent=gene1287
chr2	ENCODE	exon	220322489	220322669	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220322489	220322669	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220323101	220323236	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220323101	220323236	.	+	2	Parent=gene1287
chr2	ENCODE	exon	220323501	220323684	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220323501	220323684	.	+	1	Parent=gene1287
chr2	ENCODE	exon	220324107	220324206	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220324107	220324206	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220324647	220324831	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220324647	220324831	.	+	2	Parent=gene1287
chr2	ENCODE	exon	220325498	220325723	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220325498	220325723	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220325900	220326118	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220325900	220326118	.	+	2	Parent=gene1287
chr2	ENCODE	exon	220326529	220326677	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220326529	220326677	.	+	2	Parent=gene1287
chr2	ENCODE	exon	220326907	220327101	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220326907	220327101	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220327808	220328038	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220327808	220328038	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220328391	220328480	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220328391	220328480	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220328930	220329096	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220328930	220329096	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220329709	220329962	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220329709	220329962	.	+	1	Parent=gene1287
chr2	ENCODE	exon	220330657	220330826	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220330657	220330826	.	+	2	Parent=gene1287
chr2	ENCODE	exon	220331016	220331189	.	+	.	Parent=gene1287
chr2	ENCODE	CDS	220331016	220331189	.	+	0	Parent=gene1287
chr2	ENCODE	CDS	220331878	220331955	.	+	0	Parent=gene1287
chr2	ENCODE	exon	220331878	220332198	.	+	.	Parent=gene1287
###
chr2	ENCODE	gene	220317792	220332207	.	+	.	ID=gene1288;Name=AC009955.9-001;name2=SLC4A3
chr2	ENCODE	exon	220317792	220317972	.	+	.	Parent=gene1288
chr2	ENCODE	exon	220318187	220318270	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220318220	220318270	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220318632	220318797	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220318632	220318797	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220319371	220319648	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220319371	220319648	.	+	2	Parent=gene1288
chr2	ENCODE	exon	220319807	220319922	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220319807	220319922	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220320299	220320579	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220320299	220320579	.	+	1	Parent=gene1288
chr2	ENCODE	exon	220322195	220322343	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220322195	220322343	.	+	2	Parent=gene1288
chr2	ENCODE	exon	220322489	220322669	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220322489	220322669	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220323101	220323236	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220323101	220323236	.	+	2	Parent=gene1288
chr2	ENCODE	exon	220323501	220323684	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220323501	220323684	.	+	1	Parent=gene1288
chr2	ENCODE	exon	220324107	220324206	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220324107	220324206	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220324647	220324831	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220324647	220324831	.	+	2	Parent=gene1288
chr2	ENCODE	exon	220325498	220325723	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220325498	220325723	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220325900	220326118	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220325900	220326118	.	+	2	Parent=gene1288
chr2	ENCODE	exon	220326529	220326677	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220326529	220326677	.	+	2	Parent=gene1288
chr2	ENCODE	exon	220326907	220327101	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220326907	220327101	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220327808	220328038	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220327808	220328038	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220328391	220328480	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220328391	220328480	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220328930	220329096	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220328930	220329096	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220329709	220329962	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220329709	220329962	.	+	1	Parent=gene1288
chr2	ENCODE	exon	220330657	220330826	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220330657	220330826	.	+	2	Parent=gene1288
chr2	ENCODE	exon	220331016	220331189	.	+	.	Parent=gene1288
chr2	ENCODE	CDS	220331016	220331189	.	+	0	Parent=gene1288
chr2	ENCODE	CDS	220331878	220331955	.	+	0	Parent=gene1288
chr2	ENCODE	exon	220331878	220332207	.	+	.	Parent=gene1288
###
chr2	ENCODE	gene	220317888	220332207	.	+	.	ID=gene1289;Name=AC009955.9-002;name2=SLC4A3
chr2	ENCODE	exon	220317888	220317972	.	+	.	Parent=gene1289
chr2	ENCODE	exon	220318187	220318270	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220318220	220318270	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220318632	220318797	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220318632	220318797	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220319371	220319648	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220319371	220319648	.	+	2	Parent=gene1289
chr2	ENCODE	exon	220319807	220319922	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220319807	220319922	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220320380	220320579	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220320380	220320579	.	+	1	Parent=gene1289
chr2	ENCODE	exon	220322195	220322343	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220322195	220322343	.	+	2	Parent=gene1289
chr2	ENCODE	exon	220322489	220322669	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220322489	220322669	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220323101	220323236	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220323101	220323236	.	+	2	Parent=gene1289
chr2	ENCODE	exon	220323501	220323684	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220323501	220323684	.	+	1	Parent=gene1289
chr2	ENCODE	exon	220324107	220324206	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220324107	220324206	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220324647	220324831	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220324647	220324831	.	+	2	Parent=gene1289
chr2	ENCODE	exon	220325498	220325723	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220325498	220325723	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220325900	220326118	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220325900	220326118	.	+	2	Parent=gene1289
chr2	ENCODE	exon	220326529	220326677	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220326529	220326677	.	+	2	Parent=gene1289
chr2	ENCODE	exon	220326907	220327101	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220326907	220327101	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220327808	220328038	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220327808	220328038	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220328391	220328480	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220328391	220328480	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220328930	220329096	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220328930	220329096	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220329709	220329962	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220329709	220329962	.	+	1	Parent=gene1289
chr2	ENCODE	exon	220330657	220330826	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220330657	220330826	.	+	2	Parent=gene1289
chr2	ENCODE	exon	220331016	220331189	.	+	.	Parent=gene1289
chr2	ENCODE	CDS	220331016	220331189	.	+	0	Parent=gene1289
chr2	ENCODE	CDS	220331878	220331955	.	+	0	Parent=gene1289
chr2	ENCODE	exon	220331878	220332207	.	+	.	Parent=gene1289
###
chr2	ENCODE	gene	220317927	220332207	.	+	.	ID=gene1290;Name=AC009955.9-007;name2=SLC4A3
chr2	ENCODE	exon	220317927	220317972	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220318127	220318270	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220318632	220318797	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220319371	220319648	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220319807	220319922	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220320299	220320579	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220322195	220322275	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220323203	220323236	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220323501	220323684	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220324107	220324206	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220324647	220324831	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220325498	220325723	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220325900	220326118	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220326529	220326677	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220326907	220327101	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220327808	220328038	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220328391	220328480	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220328930	220329096	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220329709	220329962	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220330657	220330826	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220331016	220331189	.	+	.	Parent=gene1290
chr2	ENCODE	exon	220331878	220332207	.	+	.	Parent=gene1290
###
chr2	ENCODE	gene	220318743	220322645	.	+	.	ID=gene1291;Name=AC009955.9-003;name2=SLC4A3
chr2	ENCODE	exon	220318743	220318993	.	+	.	Parent=gene1291
chr2	ENCODE	exon	220319371	220319648	.	+	.	Parent=gene1291
chr2	ENCODE	exon	220322195	220322343	.	+	.	Parent=gene1291
chr2	ENCODE	exon	220322489	220322645	.	+	.	Parent=gene1291
###
chr2	ENCODE	gene	220319193	220319590	.	+	.	ID=gene1292;Name=AC009955.9-006;name2=SLC4A3
chr2	ENCODE	exon	220319193	220319218	.	+	.	Parent=gene1292
chr2	ENCODE	exon	220319371	220319590	.	+	.	Parent=gene1292
###
chr2	ENCODE	gene	220321357	220323236	.	+	.	ID=gene1293;Name=AC009955.9-008;name2=SLC4A3
chr2	ENCODE	exon	220321357	220321682	.	+	.	Parent=gene1293
chr2	ENCODE	CDS	220321466	220321682	.	+	0	Parent=gene1293
chr2	ENCODE	exon	220322195	220322343	.	+	.	Parent=gene1293
chr2	ENCODE	CDS	220322195	220322343	.	+	2	Parent=gene1293
chr2	ENCODE	exon	220322489	220322669	.	+	.	Parent=gene1293
chr2	ENCODE	CDS	220322489	220322669	.	+	0	Parent=gene1293
chr2	ENCODE	exon	220323101	220323236	.	+	.	Parent=gene1293
chr2	ENCODE	CDS	220323101	220323236	.	+	2	Parent=gene1293
###
chr2	ENCODE	gene	220322630	220324671	.	+	.	ID=gene1294;Name=AC009955.9-004;name2=SLC4A3
chr2	ENCODE	exon	220322630	220322669	.	+	.	Parent=gene1294
chr2	ENCODE	exon	220323101	220323236	.	+	.	Parent=gene1294
chr2	ENCODE	exon	220323501	220323684	.	+	.	Parent=gene1294
chr2	ENCODE	exon	220324082	220324206	.	+	.	Parent=gene1294
chr2	ENCODE	exon	220324647	220324671	.	+	.	Parent=gene1294
###
chr2	ENCODE	gene	220323573	220326008	.	+	.	ID=gene1295;Name=AC009955.9-005;name2=SLC4A3
chr2	ENCODE	exon	220323573	220323684	.	+	.	Parent=gene1295
chr2	ENCODE	exon	220324107	220324206	.	+	.	Parent=gene1295
chr2	ENCODE	exon	220325498	220325723	.	+	.	Parent=gene1295
chr2	ENCODE	exon	220325900	220326008	.	+	.	Parent=gene1295
###
chr2	ENCODE	gene	234308291	234463956	.	+	.	ID=gene1296;Name=AC006985.6-001;name2=UGT1A8
chr2	ENCODE	exon	234308291	234309208	.	+	.	Parent=gene1296
chr2	ENCODE	CDS	234308354	234309208	.	+	0	Parent=gene1296
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1296
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1296
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1296
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1296
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1296
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1296
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1296
chr2	ENCODE	exon	234462908	234463956	.	+	.	Parent=gene1296
###
chr2	ENCODE	gene	234327100	234463951	.	+	.	ID=gene1297;Name=AC006985.7-001;name2=UGT1A10
chr2	ENCODE	exon	234327100	234328023	.	+	.	Parent=gene1297
chr2	ENCODE	CDS	234327169	234328023	.	+	0	Parent=gene1297
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1297
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1297
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1297
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1297
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1297
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1297
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1297
chr2	ENCODE	exon	234462908	234463951	.	+	.	Parent=gene1297
###
chr2	ENCODE	gene	234327148	234460925	.	+	.	ID=gene1298;Name=AC006985.7-002;name2=UGT1A10
chr2	ENCODE	exon	234327148	234328023	.	+	.	Parent=gene1298
chr2	ENCODE	CDS	234327169	234328023	.	+	0	Parent=gene1298
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1298
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1298
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1298
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1298
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1298
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1298
chr2	ENCODE	CDS	234460177	234460207	.	+	1	Parent=gene1298
chr2	ENCODE	exon	234460177	234460925	.	+	.	Parent=gene1298
###
chr2	ENCODE	gene	234362499	234463946	.	+	.	ID=gene1299;Name=AC006985.8-001;name2=UGT1A9
chr2	ENCODE	exon	234362499	234363435	.	+	.	Parent=gene1299
chr2	ENCODE	CDS	234362581	234363435	.	+	0	Parent=gene1299
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1299
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1299
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1299
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1299
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1299
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1299
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1299
chr2	ENCODE	exon	234462908	234463946	.	+	.	Parent=gene1299
###
chr2	ENCODE	gene	234372584	234463945	.	+	.	ID=gene1300;Name=AC006985.4-001;name2=UGT1A7
chr2	ENCODE	exon	234372584	234373438	.	+	.	Parent=gene1300
chr2	ENCODE	CDS	234372584	234373438	.	+	0	Parent=gene1300
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1300
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1300
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1300
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1300
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1300
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1300
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1300
chr2	ENCODE	exon	234462908	234463945	.	+	.	Parent=gene1300
###
chr2	ENCODE	gene	234373014	234382993	.	+	.	ID=gene1301;Name=AC006985.4-002;name2=UGT1A7
chr2	ENCODE	exon	234373014	234373438	.	+	.	Parent=gene1301
chr2	ENCODE	exon	234380545	234380550	.	+	.	Parent=gene1301
chr2	ENCODE	exon	234381166	234382993	.	+	.	Parent=gene1301
###
chr2	ENCODE	gene	234382253	234463314	.	+	.	ID=gene1302;Name=AC006985.9-003;name2=UGT1A6
chr2	ENCODE	exon	234382253	234382466	.	+	.	Parent=gene1302
chr2	ENCODE	exon	234384445	234384511	.	+	.	Parent=gene1302
chr2	ENCODE	CDS	234384452	234384511	.	+	0	Parent=gene1302
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1302
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1302
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1302
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1302
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1302
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1302
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1302
chr2	ENCODE	exon	234462908	234463314	.	+	.	Parent=gene1302
###
chr2	ENCODE	gene	234382290	234384217	.	+	.	ID=gene1303;Name=AC006985.9-007;name2=UGT1A6
chr2	ENCODE	exon	234382290	234382466	.	+	.	Parent=gene1303
chr2	ENCODE	exon	234383650	234384217	.	+	.	Parent=gene1303
chr2	ENCODE	CDS	234383651	234384217	.	+	0	Parent=gene1303
###
chr2	ENCODE	gene	234382348	234446997	.	+	.	ID=gene1304;Name=AC006985.9-002;name2=UGT1A6
chr2	ENCODE	exon	234382348	234382466	.	+	.	Parent=gene1304
chr2	ENCODE	exon	234384445	234384511	.	+	.	Parent=gene1304
chr2	ENCODE	exon	234445336	234446997	.	+	.	Parent=gene1304
###
chr2	ENCODE	gene	234382356	234463115	.	+	.	ID=gene1305;Name=AC006985.9-004;name2=UGT1A6
chr2	ENCODE	exon	234382356	234382466	.	+	.	Parent=gene1305
chr2	ENCODE	exon	234384445	234384511	.	+	.	Parent=gene1305
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1305
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1305
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1305
chr2	ENCODE	exon	234460177	234460310	.	+	.	Parent=gene1305
chr2	ENCODE	exon	234462908	234463115	.	+	.	Parent=gene1305
###
chr2	ENCODE	gene	234383512	234463946	.	+	.	ID=gene1306;Name=AC006985.9-001;name2=UGT1A6
chr2	ENCODE	exon	234383512	234384511	.	+	.	Parent=gene1306
chr2	ENCODE	CDS	234383651	234384511	.	+	0	Parent=gene1306
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1306
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1306
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1306
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1306
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1306
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1306
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1306
chr2	ENCODE	exon	234462908	234463946	.	+	.	Parent=gene1306
###
chr2	ENCODE	gene	234384311	234457805	.	+	.	ID=gene1307;Name=AC006985.9-008;name2=UGT1A6
chr2	ENCODE	exon	234384311	234384511	.	+	.	Parent=gene1307
chr2	ENCODE	exon	234408437	234408678	.	+	.	Parent=gene1307
chr2	ENCODE	exon	234457680	234457805	.	+	.	Parent=gene1307
###
chr2	ENCODE	gene	234384331	234404505	.	+	.	ID=gene1308;Name=AC006985.9-006;name2=UGT1A6
chr2	ENCODE	exon	234384331	234384511	.	+	.	Parent=gene1308
chr2	ENCODE	exon	234404015	234404505	.	+	.	Parent=gene1308
###
chr2	ENCODE	gene	234384338	234460347	.	+	.	ID=gene1309;Name=AC006985.9-005;name2=UGT1A6
chr2	ENCODE	exon	234384338	234384511	.	+	.	Parent=gene1309
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1309
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1309
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1309
chr2	ENCODE	exon	234460177	234460347	.	+	.	Parent=gene1309
###
chr2	ENCODE	gene	234403638	234463945	.	+	.	ID=gene1310;Name=AC006985.10-001;name2=UGT1A5
chr2	ENCODE	exon	234403638	234404504	.	+	.	Parent=gene1310
chr2	ENCODE	CDS	234403638	234404504	.	+	0	Parent=gene1310
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1310
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1310
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1310
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1310
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1310
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1310
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1310
chr2	ENCODE	exon	234462908	234463945	.	+	.	Parent=gene1310
###
chr2	ENCODE	gene	234409424	234463945	.	+	.	ID=gene1311;Name=AC006985.11-001;name2=UGT1A4
chr2	ENCODE	exon	234409424	234410333	.	+	.	Parent=gene1311
chr2	ENCODE	CDS	234409467	234410333	.	+	0	Parent=gene1311
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1311
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1311
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1311
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1311
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1311
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1311
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1311
chr2	ENCODE	exon	234462908	234463945	.	+	.	Parent=gene1311
###
chr2	ENCODE	gene	234409467	234463652	.	+	.	ID=gene1312;Name=AC006985.11-002;name2=UGT1A4
chr2	ENCODE	exon	234409467	234410333	.	+	.	Parent=gene1312
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1312
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1312
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1312
chr2	ENCODE	exon	234460177	234460310	.	+	.	Parent=gene1312
chr2	ENCODE	exon	234462908	234463652	.	+	.	Parent=gene1312
###
chr2	ENCODE	gene	234419754	234463945	.	+	.	ID=gene1313;Name=AC006985.12-001;name2=UGT1A3
chr2	ENCODE	exon	234419754	234420639	.	+	.	Parent=gene1313
chr2	ENCODE	CDS	234419773	234420639	.	+	0	Parent=gene1313
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1313
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1313
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1313
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1313
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1313
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1313
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1313
chr2	ENCODE	exon	234462908	234463945	.	+	.	Parent=gene1313
###
chr2	ENCODE	gene	234450894	234463945	.	+	.	ID=gene1314;Name=AC006985.13-001;name2=UGT1A1
chr2	ENCODE	exon	234450894	234451797	.	+	.	Parent=gene1314
chr2	ENCODE	CDS	234450934	234451797	.	+	0	Parent=gene1314
chr2	ENCODE	exon	234457680	234457811	.	+	.	Parent=gene1314
chr2	ENCODE	CDS	234457680	234457811	.	+	0	Parent=gene1314
chr2	ENCODE	exon	234458495	234458582	.	+	.	Parent=gene1314
chr2	ENCODE	CDS	234458495	234458582	.	+	0	Parent=gene1314
chr2	ENCODE	exon	234458866	234459085	.	+	.	Parent=gene1314
chr2	ENCODE	CDS	234458866	234459085	.	+	2	Parent=gene1314
chr2	ENCODE	CDS	234462908	234463205	.	+	1	Parent=gene1314
chr2	ENCODE	exon	234462908	234463945	.	+	.	Parent=gene1314
###
chr2	ENCODE	gene	234466370	234470428	.	+	.	ID=gene1315;Name=AC006985.5-006;name2=AC006985.5
chr2	ENCODE	exon	234466370	234466403	.	+	.	Parent=gene1315
chr2	ENCODE	exon	234469991	234470098	.	+	.	Parent=gene1315
chr2	ENCODE	CDS	234470005	234470098	.	+	0	Parent=gene1315
chr2	ENCODE	exon	234470317	234470428	.	+	.	Parent=gene1315
chr2	ENCODE	CDS	234470317	234470428	.	+	2	Parent=gene1315
###
chr2	ENCODE	gene	234466370	234470428	.	+	.	ID=gene1316;Name=AC006985.5-008;name2=AC006985.5
chr2	ENCODE	exon	234466370	234466403	.	+	.	Parent=gene1316
chr2	ENCODE	exon	234470317	234470428	.	+	.	Parent=gene1316
chr2	ENCODE	CDS	234470400	234470428	.	+	0	Parent=gene1316
###
chr2	ENCODE	gene	234466370	234470428	.	+	.	ID=gene1317;Name=AC006985.5-007;name2=AC006985.5
chr2	ENCODE	exon	234466370	234466403	.	+	.	Parent=gene1317
chr2	ENCODE	exon	234469993	234470098	.	+	.	Parent=gene1317
chr2	ENCODE	CDS	234470005	234470098	.	+	0	Parent=gene1317
chr2	ENCODE	exon	234470317	234470428	.	+	.	Parent=gene1317
chr2	ENCODE	CDS	234470317	234470428	.	+	2	Parent=gene1317
###
chr2	ENCODE	gene	234468900	234484463	.	+	.	ID=gene1318;name2=AC006985.5;Name=AC006985.5-002
chr2	ENCODE	exon	234468900	234469127	.	+	.	Parent=gene1318
chr2	ENCODE	exon	234469991	234470098	.	+	.	Parent=gene1318
chr2	ENCODE	exon	234470317	234470498	.	+	.	Parent=gene1318
chr2	ENCODE	exon	234484319	234484463	.	+	.	Parent=gene1318
###
chr2	ENCODE	gene	234468976	234524069	.	+	.	ID=gene1319;Name=AC006985.5-001;name2=AC006985.5
chr2	ENCODE	exon	234468976	234469127	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234469052	234469127	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234469991	234470098	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234469991	234470098	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234470317	234470498	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234470317	234470498	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234480143	234480274	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234480143	234480274	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234480498	234480660	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234480498	234480660	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234483442	234483540	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234483442	234483540	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234484319	234484470	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234484319	234484470	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234485009	234485152	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234485009	234485152	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234486299	234486391	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234486299	234486391	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234486613	234486691	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234486613	234486691	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234486846	234486959	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234486846	234486959	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234489420	234489496	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234489420	234489496	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234490426	234490545	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234490426	234490545	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234490851	234490961	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234490851	234490961	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234492814	234492961	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234492814	234492961	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234494094	234494134	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234494094	234494134	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234494697	234494838	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234494697	234494838	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234495141	234495193	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234495141	234495193	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234495650	234495757	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234495650	234495757	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234498069	234498188	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234498069	234498188	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234498379	234498501	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234498379	234498501	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234499772	234499924	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234499772	234499924	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234501440	234501562	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234501440	234501562	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234502526	234502605	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234502526	234502605	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234504316	234504424	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234504316	234504424	.	+	1	Parent=gene1319
chr2	ENCODE	exon	234505228	234505323	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234505228	234505323	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234507427	234507531	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234507427	234507531	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234508648	234508771	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234508648	234508771	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234509298	234509416	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234509298	234509416	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234509963	234510115	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234509963	234510115	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234510548	234510702	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234510548	234510702	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234512770	234512929	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234512770	234512929	.	+	1	Parent=gene1319
chr2	ENCODE	exon	234513009	234513202	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234513009	234513202	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234513527	234513664	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234513527	234513664	.	+	1	Parent=gene1319
chr2	ENCODE	exon	234514202	234514316	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234514202	234514316	.	+	1	Parent=gene1319
chr2	ENCODE	exon	234519276	234519425	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234519276	234519425	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234519536	234519718	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234519536	234519718	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234520266	234520421	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234520266	234520421	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234522055	234522186	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234522055	234522186	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234522823	234522925	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234522823	234522925	.	+	0	Parent=gene1319
chr2	ENCODE	exon	234523225	234523290	.	+	.	Parent=gene1319
chr2	ENCODE	CDS	234523225	234523290	.	+	2	Parent=gene1319
chr2	ENCODE	CDS	234523784	234523905	.	+	2	Parent=gene1319
chr2	ENCODE	exon	234523784	234524069	.	+	.	Parent=gene1319
###
chr2	ENCODE	gene	234486295	234493114	.	+	.	ID=gene1320;Name=AC006985.5-003;name2=AC006985.5
chr2	ENCODE	exon	234486295	234486391	.	+	.	Parent=gene1320
chr2	ENCODE	exon	234486613	234486691	.	+	.	Parent=gene1320
chr2	ENCODE	exon	234486846	234486959	.	+	.	Parent=gene1320
chr2	ENCODE	exon	234489420	234489496	.	+	.	Parent=gene1320
chr2	ENCODE	exon	234490426	234490545	.	+	.	Parent=gene1320
chr2	ENCODE	exon	234490851	234490961	.	+	.	Parent=gene1320
chr2	ENCODE	exon	234492814	234493114	.	+	.	Parent=gene1320
###
chr2	ENCODE	gene	234519201	234524064	.	+	.	ID=gene1321;name2=AC006985.5;Name=AC006985.5-005
chr2	ENCODE	exon	234519201	234519425	.	+	.	Parent=gene1321
chr2	ENCODE	exon	234519536	234519718	.	+	.	Parent=gene1321
chr2	ENCODE	exon	234520266	234520421	.	+	.	Parent=gene1321
chr2	ENCODE	exon	234522055	234522186	.	+	.	Parent=gene1321
chr2	ENCODE	exon	234522823	234522925	.	+	.	Parent=gene1321
chr2	ENCODE	exon	234523225	234523290	.	+	.	Parent=gene1321
chr2	ENCODE	exon	234523784	234524064	.	+	.	Parent=gene1321
###
chr2	ENCODE	gene	234524062	234531384	.	-	.	ID=gene1322;Name=AC005538.1-005;name2=AC005538.1
chr2	ENCODE	exon	234524062	234524378	.	-	.	Parent=gene1322
chr2	ENCODE	exon	234527924	234528298	.	-	.	Parent=gene1322
chr2	ENCODE	exon	234531255	234531384	.	-	.	Parent=gene1322
###
chr2	ENCODE	gene	234527486	234545212	.	-	.	ID=gene1323;Name=AC005538.1-001;name2=AC005538.1
chr2	ENCODE	exon	234527486	234528298	.	-	.	Parent=gene1323
chr2	ENCODE	CDS	234528223	234528298	.	-	1	Parent=gene1323
chr2	ENCODE	exon	234531255	234532851	.	-	.	Parent=gene1323
chr2	ENCODE	CDS	234531255	234532851	.	-	2	Parent=gene1323
chr2	ENCODE	exon	234534851	234534929	.	-	.	Parent=gene1323
chr2	ENCODE	CDS	234534851	234534929	.	-	0	Parent=gene1323
chr2	ENCODE	exon	234536374	234536466	.	-	.	Parent=gene1323
chr2	ENCODE	CDS	234536374	234536466	.	-	0	Parent=gene1323
chr2	ENCODE	exon	234538043	234538107	.	-	.	Parent=gene1323
chr2	ENCODE	CDS	234538043	234538107	.	-	2	Parent=gene1323
chr2	ENCODE	exon	234540409	234540505	.	-	.	Parent=gene1323
chr2	ENCODE	CDS	234540409	234540505	.	-	0	Parent=gene1323
chr2	ENCODE	exon	234543211	234543266	.	-	.	Parent=gene1323
chr2	ENCODE	CDS	234543211	234543266	.	-	2	Parent=gene1323
chr2	ENCODE	exon	234544490	234544556	.	-	.	Parent=gene1323
chr2	ENCODE	CDS	234544490	234544556	.	-	0	Parent=gene1323
chr2	ENCODE	CDS	234545030	234545146	.	-	0	Parent=gene1323
chr2	ENCODE	exon	234545030	234545212	.	-	.	Parent=gene1323
###
chr2	ENCODE	gene	234531652	234536409	.	-	.	ID=gene1324;Name=AC005538.1-004;name2=AC005538.1
chr2	ENCODE	exon	234531652	234531784	.	-	.	Parent=gene1324
chr2	ENCODE	exon	234532733	234532851	.	-	.	Parent=gene1324
chr2	ENCODE	exon	234534851	234534929	.	-	.	Parent=gene1324
chr2	ENCODE	exon	234536374	234536409	.	-	.	Parent=gene1324
###
chr2	ENCODE	gene	234532497	234545120	.	-	.	ID=gene1325;Name=AC005538.1-002;name2=AC005538.1
chr2	ENCODE	exon	234532497	234532851	.	-	.	Parent=gene1325
chr2	ENCODE	CDS	234532497	234532851	.	-	2	Parent=gene1325
chr2	ENCODE	exon	234534851	234534929	.	-	.	Parent=gene1325
chr2	ENCODE	CDS	234534851	234534929	.	-	0	Parent=gene1325
chr2	ENCODE	exon	234536374	234536466	.	-	.	Parent=gene1325
chr2	ENCODE	CDS	234536374	234536466	.	-	0	Parent=gene1325
chr2	ENCODE	exon	234538043	234538107	.	-	.	Parent=gene1325
chr2	ENCODE	CDS	234538043	234538107	.	-	2	Parent=gene1325
chr2	ENCODE	exon	234543211	234543266	.	-	.	Parent=gene1325
chr2	ENCODE	CDS	234543211	234543266	.	-	1	Parent=gene1325
chr2	ENCODE	exon	234544490	234544556	.	-	.	Parent=gene1325
chr2	ENCODE	CDS	234544490	234544556	.	-	2	Parent=gene1325
chr2	ENCODE	exon	234545030	234545120	.	-	.	Parent=gene1325
chr2	ENCODE	CDS	234545030	234545120	.	-	0	Parent=gene1325
###
chr2	ENCODE	gene	234534871	234536781	.	-	.	ID=gene1326;Name=AC005538.1-003;name2=AC005538.1
chr2	ENCODE	exon	234534871	234534929	.	-	.	Parent=gene1326
chr2	ENCODE	exon	234536374	234536781	.	-	.	Parent=gene1326
###
chr2	ENCODE	gene	234608043	234710166	.	+	.	ID=gene1327;Name=AC005538.4-001;name2=TRPM8
chr2	ENCODE	exon	234608043	234608077	.	+	.	Parent=gene1327
chr2	ENCODE	exon	234617178	234617299	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234617183	234617299	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234621313	234621386	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234621313	234621386	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234627997	234628153	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234627997	234628153	.	+	1	Parent=gene1327
chr2	ENCODE	exon	234629642	234629819	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234629642	234629819	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234633220	234633392	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234633220	234633392	.	+	2	Parent=gene1327
chr2	ENCODE	exon	234636500	234636674	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234636500	234636674	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234637732	234637799	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234637732	234637799	.	+	2	Parent=gene1327
chr2	ENCODE	exon	234640593	234640790	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234640593	234640790	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234644561	234644663	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234644561	234644663	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234645776	234645894	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234645776	234645894	.	+	2	Parent=gene1327
chr2	ENCODE	exon	234651420	234651710	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234651420	234651710	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234653926	234654021	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234653926	234654021	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234655272	234655401	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234655272	234655401	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234657254	234657399	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234657254	234657399	.	+	2	Parent=gene1327
chr2	ENCODE	exon	234660339	234660451	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234660339	234660451	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234660854	234661070	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234660854	234661070	.	+	1	Parent=gene1327
chr2	ENCODE	exon	234670832	234670923	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234670832	234670923	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234672418	234672559	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234672418	234672559	.	+	1	Parent=gene1327
chr2	ENCODE	exon	234673697	234673868	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234673697	234673868	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234676332	234676509	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234676332	234676509	.	+	2	Parent=gene1327
chr2	ENCODE	exon	234686970	234687160	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234686970	234687160	.	+	1	Parent=gene1327
chr2	ENCODE	exon	234697497	234697596	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234697497	234697596	.	+	2	Parent=gene1327
chr2	ENCODE	exon	234698714	234698747	.	+	.	Parent=gene1327
chr2	ENCODE	CDS	234698714	234698747	.	+	1	Parent=gene1327
chr2	ENCODE	CDS	234705206	234705256	.	+	0	Parent=gene1327
chr2	ENCODE	exon	234705206	234705298	.	+	.	Parent=gene1327
chr2	ENCODE	exon	234707943	234710166	.	+	.	Parent=gene1327
###
chr2	ENCODE	gene	234620361	234633633	.	+	.	ID=gene1328;name2=TRPM8;Name=AC005538.4-002
chr2	ENCODE	exon	234620361	234620395	.	+	.	Parent=gene1328
chr2	ENCODE	exon	234621313	234621386	.	+	.	Parent=gene1328
chr2	ENCODE	exon	234627951	234628153	.	+	.	Parent=gene1328
chr2	ENCODE	exon	234629642	234629819	.	+	.	Parent=gene1328
chr2	ENCODE	exon	234633220	234633633	.	+	.	Parent=gene1328
###
chr2	ENCODE	gene	234620387	234633523	.	+	.	ID=gene1329;Name=AC005538.4-003;name2=TRPM8
chr2	ENCODE	exon	234620387	234620395	.	+	.	Parent=gene1329
chr2	ENCODE	exon	234621313	234621386	.	+	.	Parent=gene1329
chr2	ENCODE	exon	234627997	234628153	.	+	.	Parent=gene1329
chr2	ENCODE	exon	234629642	234629819	.	+	.	Parent=gene1329
chr2	ENCODE	exon	234633220	234633523	.	+	.	Parent=gene1329
###
chr2	ENCODE	gene	234624385	234628094	.	+	.	ID=gene1330;Name=AC005538.4-009;name2=TRPM8
chr2	ENCODE	exon	234624385	234624601	.	+	.	Parent=gene1330
chr2	ENCODE	CDS	234624574	234624601	.	+	0	Parent=gene1330
chr2	ENCODE	exon	234627997	234628094	.	+	.	Parent=gene1330
chr2	ENCODE	CDS	234627997	234628094	.	+	2	Parent=gene1330
###
chr2	ENCODE	gene	234644353	234651568	.	+	.	ID=gene1331;Name=AC005538.4-012;name2=TRPM8
chr2	ENCODE	exon	234644353	234644663	.	+	.	Parent=gene1331
chr2	ENCODE	exon	234645776	234645894	.	+	.	Parent=gene1331
chr2	ENCODE	exon	234651420	234651568	.	+	.	Parent=gene1331
###
chr2	ENCODE	gene	234656626	234661183	.	+	.	ID=gene1332;Name=AC005538.4-004;name2=TRPM8
chr2	ENCODE	exon	234656626	234656771	.	+	.	Parent=gene1332
chr2	ENCODE	exon	234657254	234657399	.	+	.	Parent=gene1332
chr2	ENCODE	exon	234660339	234660451	.	+	.	Parent=gene1332
chr2	ENCODE	exon	234660854	234661183	.	+	.	Parent=gene1332
###
chr2	ENCODE	gene	234657279	234660556	.	+	.	ID=gene1333;Name=AC005538.4-005;name2=TRPM8
chr2	ENCODE	exon	234657279	234657399	.	+	.	Parent=gene1333
chr2	ENCODE	exon	234660339	234660556	.	+	.	Parent=gene1333
###
chr2	ENCODE	gene	234658806	234687160	.	+	.	ID=gene1334;Name=AC005538.4-010;name2=TRPM8
chr2	ENCODE	exon	234658806	234658931	.	+	.	Parent=gene1334
chr2	ENCODE	exon	234673697	234673868	.	+	.	Parent=gene1334
chr2	ENCODE	exon	234676332	234676509	.	+	.	Parent=gene1334
chr2	ENCODE	exon	234686970	234687160	.	+	.	Parent=gene1334
###
chr2	ENCODE	gene	234672452	234709082	.	+	.	ID=gene1335;Name=AC005538.4-006;name2=TRPM8
chr2	ENCODE	exon	234672452	234672559	.	+	.	Parent=gene1335
chr2	ENCODE	exon	234673697	234673995	.	+	.	Parent=gene1335
chr2	ENCODE	exon	234676332	234676509	.	+	.	Parent=gene1335
chr2	ENCODE	exon	234686970	234687160	.	+	.	Parent=gene1335
chr2	ENCODE	exon	234697497	234697596	.	+	.	Parent=gene1335
chr2	ENCODE	exon	234698714	234698747	.	+	.	Parent=gene1335
chr2	ENCODE	exon	234705206	234705298	.	+	.	Parent=gene1335
chr2	ENCODE	exon	234707943	234709082	.	+	.	Parent=gene1335
###
chr2	ENCODE	gene	234687115	234708334	.	+	.	ID=gene1336;Name=AC005538.4-008;name2=TRPM8
chr2	ENCODE	exon	234687115	234687160	.	+	.	Parent=gene1336
chr2	ENCODE	exon	234697497	234697596	.	+	.	Parent=gene1336
chr2	ENCODE	exon	234698714	234698747	.	+	.	Parent=gene1336
chr2	ENCODE	exon	234705206	234705280	.	+	.	Parent=gene1336
chr2	ENCODE	exon	234707978	234708334	.	+	.	Parent=gene1336
###
chr2	ENCODE	gene	234703869	234705331	.	+	.	ID=gene1337;Name=AC005538.4-011;name2=TRPM8
chr2	ENCODE	exon	234703869	234704430	.	+	.	Parent=gene1337
chr2	ENCODE	exon	234705206	234705331	.	+	.	Parent=gene1337
###
chr2	ENCODE	gene	234741323	234767774	.	+	.	ID=gene1338;Name=AC006037.1-002;name2=SPP2
chr2	ENCODE	exon	234741323	234741515	.	+	.	Parent=gene1338
chr2	ENCODE	CDS	234741431	234741515	.	+	0	Parent=gene1338
chr2	ENCODE	exon	234741615	234741739	.	+	.	Parent=gene1338
chr2	ENCODE	CDS	234741615	234741739	.	+	2	Parent=gene1338
chr2	ENCODE	exon	234749480	234749602	.	+	.	Parent=gene1338
chr2	ENCODE	CDS	234749480	234749602	.	+	0	Parent=gene1338
chr2	ENCODE	exon	234751013	234751123	.	+	.	Parent=gene1338
chr2	ENCODE	CDS	234751013	234751123	.	+	0	Parent=gene1338
chr2	ENCODE	exon	234757177	234757231	.	+	.	Parent=gene1338
chr2	ENCODE	CDS	234757177	234757231	.	+	0	Parent=gene1338
chr2	ENCODE	exon	234757868	234757918	.	+	.	Parent=gene1338
chr2	ENCODE	CDS	234757868	234757918	.	+	2	Parent=gene1338
chr2	ENCODE	CDS	234760572	234760657	.	+	2	Parent=gene1338
chr2	ENCODE	exon	234760572	234760667	.	+	.	Parent=gene1338
chr2	ENCODE	exon	234767669	234767774	.	+	.	Parent=gene1338
###
chr2	ENCODE	gene	234741343	234767778	.	+	.	ID=gene1339;Name=AC006037.1-001;name2=SPP2
chr2	ENCODE	exon	234741343	234741515	.	+	.	Parent=gene1339
chr2	ENCODE	CDS	234741431	234741515	.	+	0	Parent=gene1339
chr2	ENCODE	exon	234741615	234741739	.	+	.	Parent=gene1339
chr2	ENCODE	CDS	234741615	234741739	.	+	2	Parent=gene1339
chr2	ENCODE	exon	234749480	234749602	.	+	.	Parent=gene1339
chr2	ENCODE	CDS	234749480	234749602	.	+	0	Parent=gene1339
chr2	ENCODE	exon	234751013	234751123	.	+	.	Parent=gene1339
chr2	ENCODE	CDS	234751013	234751123	.	+	0	Parent=gene1339
chr2	ENCODE	exon	234757177	234757231	.	+	.	Parent=gene1339
chr2	ENCODE	CDS	234757177	234757231	.	+	0	Parent=gene1339
chr2	ENCODE	exon	234757868	234757918	.	+	.	Parent=gene1339
chr2	ENCODE	CDS	234757868	234757918	.	+	2	Parent=gene1339
chr2	ENCODE	CDS	234760572	234760657	.	+	2	Parent=gene1339
chr2	ENCODE	exon	234760572	234760667	.	+	.	Parent=gene1339
chr2	ENCODE	exon	234767489	234767778	.	+	.	Parent=gene1339
###
chr2	ENCODE	gene	234741481	234746922	.	+	.	ID=gene1340;Name=AC006037.1-003;name2=SPP2
chr2	ENCODE	exon	234741481	234741515	.	+	.	Parent=gene1340
chr2	ENCODE	exon	234741615	234741739	.	+	.	Parent=gene1340
chr2	ENCODE	exon	234746702	234746922	.	+	.	Parent=gene1340
###
chr20	ENCODE	gene	33305669	33328215	.	+	.	ID=gene1341;Name=RP4-614O4.10-001;name2=MMP24
chr20	ENCODE	exon	33305669	33305973	.	+	.	Parent=gene1341
chr20	ENCODE	exon	33315010	33315171	.	+	.	Parent=gene1341
chr20	ENCODE	exon	33318422	33318636	.	+	.	Parent=gene1341
chr20	ENCODE	exon	33320977	33321115	.	+	.	Parent=gene1341
chr20	ENCODE	exon	33322786	33323052	.	+	.	Parent=gene1341
chr20	ENCODE	exon	33325489	33328215	.	+	.	Parent=gene1341
###
chr20	ENCODE	gene	33330128	33335740	.	-	.	ID=gene1342;Name=RP4-614O4.1-007;name2=ITGB4BP
chr20	ENCODE	exon	33330128	33330423	.	-	.	Parent=gene1342
chr20	ENCODE	exon	33330783	33330964	.	-	.	Parent=gene1342
chr20	ENCODE	exon	33331159	33331335	.	-	.	Parent=gene1342
chr20	ENCODE	exon	33335598	33335740	.	-	.	Parent=gene1342
###
chr20	ENCODE	gene	33330128	33335932	.	-	.	ID=gene1343;Name=RP4-614O4.1-002;name2=ITGB4BP
chr20	ENCODE	exon	33330128	33330423	.	-	.	Parent=gene1343
chr20	ENCODE	CDS	33330414	33330423	.	-	1	Parent=gene1343
chr20	ENCODE	exon	33330783	33330964	.	-	.	Parent=gene1343
chr20	ENCODE	CDS	33330783	33330964	.	-	0	Parent=gene1343
chr20	ENCODE	exon	33331159	33331335	.	-	.	Parent=gene1343
chr20	ENCODE	CDS	33331159	33331335	.	-	0	Parent=gene1343
chr20	ENCODE	exon	33331871	33332046	.	-	.	Parent=gene1343
chr20	ENCODE	CDS	33331871	33332046	.	-	2	Parent=gene1343
chr20	ENCODE	exon	33335393	33335478	.	-	.	Parent=gene1343
chr20	ENCODE	CDS	33335393	33335478	.	-	1	Parent=gene1343
chr20	ENCODE	CDS	33335598	33335704	.	-	0	Parent=gene1343
chr20	ENCODE	exon	33335598	33335932	.	-	.	Parent=gene1343
###
chr20	ENCODE	gene	33330128	33335987	.	-	.	ID=gene1344;Name=RP4-614O4.1-005;name2=ITGB4BP
chr20	ENCODE	exon	33330128	33330423	.	-	.	Parent=gene1344
chr20	ENCODE	CDS	33330414	33330423	.	-	1	Parent=gene1344
chr20	ENCODE	exon	33330783	33330964	.	-	.	Parent=gene1344
chr20	ENCODE	CDS	33330783	33330964	.	-	0	Parent=gene1344
chr20	ENCODE	exon	33331159	33331335	.	-	.	Parent=gene1344
chr20	ENCODE	CDS	33331159	33331335	.	-	0	Parent=gene1344
chr20	ENCODE	CDS	33335393	33335704	.	-	0	Parent=gene1344
chr20	ENCODE	exon	33335393	33335709	.	-	.	Parent=gene1344
chr20	ENCODE	exon	33335943	33335987	.	-	.	Parent=gene1344
###
chr20	ENCODE	gene	33330128	33336021	.	-	.	ID=gene1345;name2=ITGB4BP;Name=RP4-614O4.1-003
chr20	ENCODE	exon	33330128	33330423	.	-	.	Parent=gene1345
chr20	ENCODE	exon	33330783	33330964	.	-	.	Parent=gene1345
chr20	ENCODE	exon	33331159	33331335	.	-	.	Parent=gene1345
chr20	ENCODE	exon	33335393	33335478	.	-	.	Parent=gene1345
chr20	ENCODE	exon	33335598	33335709	.	-	.	Parent=gene1345
chr20	ENCODE	exon	33335943	33336021	.	-	.	Parent=gene1345
###
chr20	ENCODE	gene	33330128	33336202	.	-	.	ID=gene1346;Name=RP4-614O4.1-001;name2=ITGB4BP
chr20	ENCODE	exon	33330128	33330423	.	-	.	Parent=gene1346
chr20	ENCODE	CDS	33330414	33330423	.	-	1	Parent=gene1346
chr20	ENCODE	exon	33330783	33330964	.	-	.	Parent=gene1346
chr20	ENCODE	CDS	33330783	33330964	.	-	0	Parent=gene1346
chr20	ENCODE	exon	33331159	33331335	.	-	.	Parent=gene1346
chr20	ENCODE	CDS	33331159	33331335	.	-	0	Parent=gene1346
chr20	ENCODE	exon	33331871	33332046	.	-	.	Parent=gene1346
chr20	ENCODE	CDS	33331871	33332046	.	-	2	Parent=gene1346
chr20	ENCODE	exon	33335393	33335478	.	-	.	Parent=gene1346
chr20	ENCODE	CDS	33335393	33335478	.	-	1	Parent=gene1346
chr20	ENCODE	CDS	33335598	33335704	.	-	0	Parent=gene1346
chr20	ENCODE	exon	33335598	33335709	.	-	.	Parent=gene1346
chr20	ENCODE	exon	33335943	33336202	.	-	.	Parent=gene1346
###
chr20	ENCODE	gene	33330957	33336003	.	-	.	ID=gene1347;Name=RP4-614O4.1-004;name2=ITGB4BP
chr20	ENCODE	exon	33330957	33330964	.	-	.	Parent=gene1347
chr20	ENCODE	exon	33331159	33331335	.	-	.	Parent=gene1347
chr20	ENCODE	exon	33331871	33332046	.	-	.	Parent=gene1347
chr20	ENCODE	exon	33335393	33335709	.	-	.	Parent=gene1347
chr20	ENCODE	exon	33335943	33336003	.	-	.	Parent=gene1347
###
chr20	ENCODE	gene	33331291	33335919	.	-	.	ID=gene1348;Name=RP4-614O4.1-006;name2=ITGB4BP
chr20	ENCODE	exon	33331291	33331335	.	-	.	Parent=gene1348
chr20	ENCODE	exon	33335393	33335478	.	-	.	Parent=gene1348
chr20	ENCODE	exon	33335598	33335919	.	-	.	Parent=gene1348
###
chr20	ENCODE	gene	33331915	33336202	.	-	.	ID=gene1349;Name=RP4-614O4.1-008;name2=ITGB4BP
chr20	ENCODE	exon	33331915	33332046	.	-	.	Parent=gene1349
chr20	ENCODE	CDS	33331915	33332046	.	-	2	Parent=gene1349
chr20	ENCODE	exon	33335393	33335478	.	-	.	Parent=gene1349
chr20	ENCODE	CDS	33335393	33335478	.	-	1	Parent=gene1349
chr20	ENCODE	CDS	33335598	33335704	.	-	0	Parent=gene1349
chr20	ENCODE	exon	33335598	33335709	.	-	.	Parent=gene1349
chr20	ENCODE	exon	33335982	33336202	.	-	.	Parent=gene1349
###
chr20	ENCODE	gene	33336948	33343618	.	-	.	ID=gene1350;Name=RP4-614O4.9-001;name2=FAM83C
chr20	ENCODE	exon	33336948	33339189	.	-	.	Parent=gene1350
chr20	ENCODE	CDS	33337752	33339189	.	-	1	Parent=gene1350
chr20	ENCODE	exon	33339678	33339802	.	-	.	Parent=gene1350
chr20	ENCODE	CDS	33339678	33339802	.	-	0	Parent=gene1350
chr20	ENCODE	exon	33340008	33340175	.	-	.	Parent=gene1350
chr20	ENCODE	CDS	33340008	33340175	.	-	0	Parent=gene1350
chr20	ENCODE	CDS	33343009	33343521	.	-	0	Parent=gene1350
chr20	ENCODE	exon	33343009	33343618	.	-	.	Parent=gene1350
###
chr20	ENCODE	gene	33336948	33343639	.	-	.	ID=gene1351;Name=RP4-614O4.9-002;name2=FAM83C
chr20	ENCODE	exon	33336948	33338723	.	-	.	Parent=gene1351
chr20	ENCODE	exon	33339719	33339802	.	-	.	Parent=gene1351
chr20	ENCODE	exon	33340008	33340175	.	-	.	Parent=gene1351
chr20	ENCODE	exon	33341620	33341692	.	-	.	Parent=gene1351
chr20	ENCODE	exon	33343009	33343639	.	-	.	Parent=gene1351
###
chr20	ENCODE	gene	33353783	33358299	.	-	.	ID=gene1352;Name=RP4-614O4.7-014;name2=C20orf44
chr20	ENCODE	exon	33353783	33355286	.	-	.	Parent=gene1352
chr20	ENCODE	exon	33357883	33358299	.	-	.	Parent=gene1352
###
chr20	ENCODE	gene	33353783	33463175	.	-	.	ID=gene1353;Name=RP4-614O4.7-002;name2=C20orf44
chr20	ENCODE	exon	33353783	33355286	.	-	.	Parent=gene1353
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1353
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1353
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1353
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1353
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1353
chr20	ENCODE	exon	33463157	33463175	.	-	.	Parent=gene1353
###
chr20	ENCODE	gene	33353783	33463180	.	-	.	ID=gene1354;Name=RP4-614O4.7-017;name2=C20orf44
chr20	ENCODE	exon	33353783	33355286	.	-	.	Parent=gene1354
chr20	ENCODE	CDS	33355152	33355286	.	-	0	Parent=gene1354
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1354
chr20	ENCODE	CDS	33357883	33357996	.	-	0	Parent=gene1354
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1354
chr20	ENCODE	CDS	33365905	33365982	.	-	0	Parent=gene1354
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1354
chr20	ENCODE	CDS	33398381	33398489	.	-	1	Parent=gene1354
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1354
chr20	ENCODE	CDS	33417774	33417831	.	-	2	Parent=gene1354
chr20	ENCODE	exon	33433143	33433242	.	-	.	Parent=gene1354
chr20	ENCODE	CDS	33433143	33433242	.	-	0	Parent=gene1354
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1354
chr20	ENCODE	CDS	33435255	33435350	.	-	0	Parent=gene1354
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1354
chr20	ENCODE	CDS	33445309	33445413	.	-	0	Parent=gene1354
chr20	ENCODE	exon	33463157	33463180	.	-	.	Parent=gene1354
chr20	ENCODE	CDS	33463157	33463180	.	-	0	Parent=gene1354
###
chr20	ENCODE	gene	33353783	33463187	.	-	.	ID=gene1355;Name=RP4-614O4.7-006;name2=C20orf44
chr20	ENCODE	exon	33353783	33355286	.	-	.	Parent=gene1355
chr20	ENCODE	CDS	33355152	33355286	.	-	0	Parent=gene1355
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1355
chr20	ENCODE	CDS	33357883	33357996	.	-	0	Parent=gene1355
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1355
chr20	ENCODE	CDS	33365905	33365982	.	-	0	Parent=gene1355
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1355
chr20	ENCODE	CDS	33433135	33433242	.	-	0	Parent=gene1355
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1355
chr20	ENCODE	CDS	33435255	33435350	.	-	0	Parent=gene1355
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1355
chr20	ENCODE	CDS	33445309	33445413	.	-	0	Parent=gene1355
chr20	ENCODE	CDS	33463157	33463180	.	-	0	Parent=gene1355
chr20	ENCODE	exon	33463157	33463187	.	-	.	Parent=gene1355
###
chr20	ENCODE	gene	33353783	33463190	.	-	.	ID=gene1356;Name=RP4-614O4.7-012;name2=C20orf44
chr20	ENCODE	exon	33353783	33355286	.	-	.	Parent=gene1356
chr20	ENCODE	CDS	33355152	33355286	.	-	0	Parent=gene1356
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1356
chr20	ENCODE	CDS	33357883	33357996	.	-	0	Parent=gene1356
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1356
chr20	ENCODE	CDS	33398381	33398489	.	-	1	Parent=gene1356
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1356
chr20	ENCODE	CDS	33417774	33417831	.	-	2	Parent=gene1356
chr20	ENCODE	exon	33425401	33425473	.	-	.	Parent=gene1356
chr20	ENCODE	CDS	33425401	33425473	.	-	0	Parent=gene1356
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1356
chr20	ENCODE	CDS	33433135	33433242	.	-	0	Parent=gene1356
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1356
chr20	ENCODE	CDS	33435255	33435350	.	-	0	Parent=gene1356
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1356
chr20	ENCODE	CDS	33445309	33445413	.	-	0	Parent=gene1356
chr20	ENCODE	CDS	33463157	33463180	.	-	0	Parent=gene1356
chr20	ENCODE	exon	33463157	33463190	.	-	.	Parent=gene1356
###
chr20	ENCODE	gene	33353783	33463190	.	-	.	ID=gene1357;Name=RP4-614O4.7-011;name2=C20orf44
chr20	ENCODE	exon	33353783	33355286	.	-	.	Parent=gene1357
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1357
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1357
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1357
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1357
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1357
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1357
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1357
chr20	ENCODE	exon	33460562	33460684	.	-	.	Parent=gene1357
chr20	ENCODE	exon	33463157	33463190	.	-	.	Parent=gene1357
###
chr20	ENCODE	gene	33353783	33463248	.	-	.	ID=gene1358;Name=RP4-614O4.7-018;name2=C20orf44
chr20	ENCODE	exon	33353783	33355286	.	-	.	Parent=gene1358
chr20	ENCODE	CDS	33355152	33355286	.	-	0	Parent=gene1358
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1358
chr20	ENCODE	CDS	33357883	33357996	.	-	0	Parent=gene1358
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1358
chr20	ENCODE	CDS	33365905	33365982	.	-	0	Parent=gene1358
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1358
chr20	ENCODE	CDS	33398381	33398489	.	-	1	Parent=gene1358
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1358
chr20	ENCODE	CDS	33417774	33417831	.	-	2	Parent=gene1358
chr20	ENCODE	exon	33425401	33425473	.	-	.	Parent=gene1358
chr20	ENCODE	CDS	33425401	33425473	.	-	0	Parent=gene1358
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1358
chr20	ENCODE	CDS	33445309	33445413	.	-	0	Parent=gene1358
chr20	ENCODE	CDS	33463157	33463180	.	-	0	Parent=gene1358
chr20	ENCODE	exon	33463157	33463248	.	-	.	Parent=gene1358
###
chr20	ENCODE	gene	33353783	33463358	.	-	.	ID=gene1359;Name=RP4-614O4.7-010;name2=C20orf44
chr20	ENCODE	exon	33353783	33355286	.	-	.	Parent=gene1359
chr20	ENCODE	CDS	33355152	33355286	.	-	0	Parent=gene1359
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1359
chr20	ENCODE	CDS	33357883	33357996	.	-	0	Parent=gene1359
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1359
chr20	ENCODE	CDS	33365905	33365982	.	-	0	Parent=gene1359
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1359
chr20	ENCODE	CDS	33398381	33398489	.	-	1	Parent=gene1359
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1359
chr20	ENCODE	CDS	33417774	33417831	.	-	2	Parent=gene1359
chr20	ENCODE	exon	33425401	33425473	.	-	.	Parent=gene1359
chr20	ENCODE	CDS	33425401	33425473	.	-	0	Parent=gene1359
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1359
chr20	ENCODE	CDS	33433135	33433242	.	-	0	Parent=gene1359
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1359
chr20	ENCODE	CDS	33435255	33435350	.	-	0	Parent=gene1359
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1359
chr20	ENCODE	CDS	33445309	33445413	.	-	0	Parent=gene1359
chr20	ENCODE	CDS	33463157	33463180	.	-	0	Parent=gene1359
chr20	ENCODE	exon	33463157	33463358	.	-	.	Parent=gene1359
###
chr20	ENCODE	gene	33354650	33463177	.	-	.	ID=gene1360;Name=RP4-614O4.7-009;name2=C20orf44
chr20	ENCODE	exon	33354650	33355286	.	-	.	Parent=gene1360
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1360
chr20	ENCODE	exon	33365905	33365924	.	-	.	Parent=gene1360
chr20	ENCODE	exon	33433201	33433242	.	-	.	Parent=gene1360
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1360
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1360
chr20	ENCODE	exon	33463157	33463177	.	-	.	Parent=gene1360
###
chr20	ENCODE	gene	33354671	33358272	.	-	.	ID=gene1361;name2=C20orf44;Name=RP4-614O4.7-015
chr20	ENCODE	exon	33354671	33355286	.	-	.	Parent=gene1361
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1361
chr20	ENCODE	exon	33358202	33358272	.	-	.	Parent=gene1361
###
chr20	ENCODE	gene	33355011	33355873	.	-	.	ID=gene1362;Name=RP4-614O4.7-019;name2=C20orf44
chr20	ENCODE	exon	33355011	33355286	.	-	.	Parent=gene1362
chr20	ENCODE	exon	33355844	33355873	.	-	.	Parent=gene1362
###
chr20	ENCODE	gene	33355188	33366653	.	-	.	ID=gene1363;name2=C20orf44;Name=RP4-614O4.7-020
chr20	ENCODE	exon	33355188	33355286	.	-	.	Parent=gene1363
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1363
chr20	ENCODE	exon	33365905	33365983	.	-	.	Parent=gene1363
chr20	ENCODE	exon	33366394	33366653	.	-	.	Parent=gene1363
###
chr20	ENCODE	gene	33355208	33463190	.	-	.	ID=gene1364;Name=RP4-614O4.7-003;name2=C20orf44
chr20	ENCODE	exon	33355208	33355286	.	-	.	Parent=gene1364
chr20	ENCODE	CDS	33355208	33355286	.	-	0	Parent=gene1364
chr20	ENCODE	exon	33357883	33357996	.	-	.	Parent=gene1364
chr20	ENCODE	CDS	33357883	33357996	.	-	0	Parent=gene1364
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1364
chr20	ENCODE	CDS	33365905	33365982	.	-	0	Parent=gene1364
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1364
chr20	ENCODE	CDS	33398381	33398489	.	-	1	Parent=gene1364
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1364
chr20	ENCODE	CDS	33417774	33417831	.	-	2	Parent=gene1364
chr20	ENCODE	exon	33425401	33425473	.	-	.	Parent=gene1364
chr20	ENCODE	CDS	33425401	33425473	.	-	0	Parent=gene1364
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1364
chr20	ENCODE	CDS	33433135	33433242	.	-	0	Parent=gene1364
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1364
chr20	ENCODE	CDS	33445309	33445413	.	-	0	Parent=gene1364
chr20	ENCODE	CDS	33463157	33463180	.	-	0	Parent=gene1364
chr20	ENCODE	exon	33463157	33463190	.	-	.	Parent=gene1364
###
chr20	ENCODE	gene	33357667	33398443	.	-	.	ID=gene1365;Name=RP4-614O4.7-008;name2=C20orf44
chr20	ENCODE	exon	33357667	33357996	.	-	.	Parent=gene1365
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1365
chr20	ENCODE	exon	33398381	33398443	.	-	.	Parent=gene1365
###
chr20	ENCODE	gene	33357890	33463187	.	-	.	ID=gene1366;Name=RP4-614O4.7-004;name2=C20orf44
chr20	ENCODE	exon	33357890	33357996	.	-	.	Parent=gene1366
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1366
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1366
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1366
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1366
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1366
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1366
chr20	ENCODE	exon	33463157	33463187	.	-	.	Parent=gene1366
###
chr20	ENCODE	gene	33357960	33463186	.	-	.	ID=gene1367;Name=RP4-614O4.7-007;name2=C20orf44
chr20	ENCODE	exon	33357960	33357996	.	-	.	Parent=gene1367
chr20	ENCODE	CDS	33357960	33357996	.	-	0	Parent=gene1367
chr20	ENCODE	exon	33365905	33365982	.	-	.	Parent=gene1367
chr20	ENCODE	CDS	33365905	33365982	.	-	0	Parent=gene1367
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1367
chr20	ENCODE	CDS	33398381	33398489	.	-	1	Parent=gene1367
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1367
chr20	ENCODE	CDS	33417774	33417831	.	-	2	Parent=gene1367
chr20	ENCODE	exon	33425401	33425473	.	-	.	Parent=gene1367
chr20	ENCODE	CDS	33425401	33425473	.	-	0	Parent=gene1367
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1367
chr20	ENCODE	CDS	33433135	33433242	.	-	0	Parent=gene1367
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1367
chr20	ENCODE	CDS	33435255	33435350	.	-	0	Parent=gene1367
chr20	ENCODE	exon	33443453	33443494	.	-	.	Parent=gene1367
chr20	ENCODE	CDS	33443453	33443494	.	-	0	Parent=gene1367
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1367
chr20	ENCODE	CDS	33445309	33445413	.	-	0	Parent=gene1367
chr20	ENCODE	CDS	33463157	33463180	.	-	0	Parent=gene1367
chr20	ENCODE	exon	33463157	33463186	.	-	.	Parent=gene1367
###
chr20	ENCODE	gene	33395327	33463191	.	-	.	ID=gene1368;Name=RP4-614O4.7-005;name2=C20orf44
chr20	ENCODE	exon	33395327	33398489	.	-	.	Parent=gene1368
chr20	ENCODE	CDS	33398288	33398489	.	-	1	Parent=gene1368
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1368
chr20	ENCODE	CDS	33417774	33417831	.	-	2	Parent=gene1368
chr20	ENCODE	exon	33425401	33425473	.	-	.	Parent=gene1368
chr20	ENCODE	CDS	33425401	33425473	.	-	0	Parent=gene1368
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1368
chr20	ENCODE	CDS	33433135	33433242	.	-	0	Parent=gene1368
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1368
chr20	ENCODE	CDS	33435255	33435350	.	-	0	Parent=gene1368
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1368
chr20	ENCODE	CDS	33445309	33445413	.	-	0	Parent=gene1368
chr20	ENCODE	CDS	33463157	33463180	.	-	0	Parent=gene1368
chr20	ENCODE	exon	33463157	33463191	.	-	.	Parent=gene1368
###
chr20	ENCODE	gene	33396933	33398406	.	-	.	ID=gene1369;Name=RP4-614O4.7-016;name2=C20orf44
chr20	ENCODE	exon	33396933	33397640	.	-	.	Parent=gene1369
chr20	ENCODE	exon	33397918	33397964	.	-	.	Parent=gene1369
chr20	ENCODE	exon	33398381	33398406	.	-	.	Parent=gene1369
###
chr20	ENCODE	gene	33397237	33463193	.	-	.	ID=gene1370;Name=RP4-614O4.7-001;name2=C20orf44
chr20	ENCODE	exon	33397237	33397640	.	-	.	Parent=gene1370
chr20	ENCODE	exon	33398381	33398489	.	-	.	Parent=gene1370
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1370
chr20	ENCODE	exon	33425401	33425473	.	-	.	Parent=gene1370
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1370
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1370
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1370
chr20	ENCODE	exon	33463157	33463193	.	-	.	Parent=gene1370
###
chr20	ENCODE	gene	33398484	33463190	.	-	.	ID=gene1371;Name=RP4-614O4.7-021;name2=C20orf44
chr20	ENCODE	exon	33398484	33398489	.	-	.	Parent=gene1371
chr20	ENCODE	exon	33417774	33417831	.	-	.	Parent=gene1371
chr20	ENCODE	exon	33425401	33425473	.	-	.	Parent=gene1371
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1371
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1371
chr20	ENCODE	exon	33435776	33435861	.	-	.	Parent=gene1371
chr20	ENCODE	CDS	33435841	33435861	.	-	0	Parent=gene1371
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1371
chr20	ENCODE	CDS	33445309	33445413	.	-	0	Parent=gene1371
chr20	ENCODE	CDS	33463157	33463180	.	-	0	Parent=gene1371
chr20	ENCODE	exon	33463157	33463190	.	-	.	Parent=gene1371
###
chr20	ENCODE	gene	33433135	33461372	.	-	.	ID=gene1372;Name=RP4-614O4.7-013;name2=C20orf44
chr20	ENCODE	exon	33433135	33433242	.	-	.	Parent=gene1372
chr20	ENCODE	exon	33435255	33435350	.	-	.	Parent=gene1372
chr20	ENCODE	exon	33445309	33445413	.	-	.	Parent=gene1372
chr20	ENCODE	exon	33461272	33461372	.	-	.	Parent=gene1372
###
chr20	ENCODE	gene	33484241	33486662	.	+	.	ID=gene1373;Name=RP3-477O4.13-001;name2=RP3-477O4.13
chr20	ENCODE	exon	33484241	33484375	.	+	.	Parent=gene1373
chr20	ENCODE	exon	33485064	33486662	.	+	.	Parent=gene1373
chr20	ENCODE	CDS	33485371	33486123	.	+	0	Parent=gene1373
###
chr20	ENCODE	gene	33484559	33489437	.	-	.	ID=gene1374;Name=RP3-477O4.6-002;name2=GDF5
chr20	ENCODE	exon	33484559	33485995	.	-	.	Parent=gene1374
chr20	ENCODE	CDS	33485121	33485995	.	-	2	Parent=gene1374
chr20	ENCODE	CDS	33488492	33489122	.	-	0	Parent=gene1374
chr20	ENCODE	exon	33488492	33489437	.	-	.	Parent=gene1374
###
chr20	ENCODE	gene	33484559	33505982	.	-	.	ID=gene1375;Name=RP3-477O4.6-001;name2=GDF5
chr20	ENCODE	exon	33484559	33485995	.	-	.	Parent=gene1375
chr20	ENCODE	CDS	33485121	33485995	.	-	2	Parent=gene1375
chr20	ENCODE	CDS	33488492	33489122	.	-	0	Parent=gene1375
chr20	ENCODE	exon	33488492	33489363	.	-	.	Parent=gene1375
chr20	ENCODE	exon	33492453	33492608	.	-	.	Parent=gene1375
chr20	ENCODE	exon	33505876	33505982	.	-	.	Parent=gene1375
###
chr20	ENCODE	gene	33506399	33517443	.	+	.	ID=gene1376;Name=RP3-477O4.2-002;name2=CEP250
chr20	ENCODE	exon	33506399	33506477	.	+	.	Parent=gene1376
chr20	ENCODE	exon	33509539	33509613	.	+	.	Parent=gene1376
chr20	ENCODE	exon	33511221	33511339	.	+	.	Parent=gene1376
chr20	ENCODE	exon	33513504	33513792	.	+	.	Parent=gene1376
chr20	ENCODE	CDS	33513607	33513792	.	+	0	Parent=gene1376
chr20	ENCODE	exon	33514814	33514870	.	+	.	Parent=gene1376
chr20	ENCODE	CDS	33514814	33514870	.	+	0	Parent=gene1376
chr20	ENCODE	exon	33516982	33517064	.	+	.	Parent=gene1376
chr20	ENCODE	CDS	33516982	33517064	.	+	0	Parent=gene1376
chr20	ENCODE	exon	33517278	33517443	.	+	.	Parent=gene1376
chr20	ENCODE	CDS	33517278	33517443	.	+	1	Parent=gene1376
###
chr20	ENCODE	gene	33506410	33517293	.	+	.	ID=gene1377;Name=RP3-477O4.2-003;name2=CEP250
chr20	ENCODE	exon	33506410	33506472	.	+	.	Parent=gene1377
chr20	ENCODE	exon	33509539	33509609	.	+	.	Parent=gene1377
chr20	ENCODE	exon	33511217	33511339	.	+	.	Parent=gene1377
chr20	ENCODE	exon	33513504	33513792	.	+	.	Parent=gene1377
chr20	ENCODE	CDS	33513607	33513792	.	+	0	Parent=gene1377
chr20	ENCODE	exon	33514814	33514870	.	+	.	Parent=gene1377
chr20	ENCODE	CDS	33514814	33514870	.	+	0	Parent=gene1377
chr20	ENCODE	exon	33516982	33517064	.	+	.	Parent=gene1377
chr20	ENCODE	CDS	33516982	33517064	.	+	0	Parent=gene1377
chr20	ENCODE	exon	33517278	33517293	.	+	.	Parent=gene1377
chr20	ENCODE	CDS	33517278	33517293	.	+	1	Parent=gene1377
###
chr20	ENCODE	gene	33506436	33513543	.	+	.	ID=gene1378;Name=RP3-477O4.2-007;name2=CEP250
chr20	ENCODE	exon	33506436	33506751	.	+	.	Parent=gene1378
chr20	ENCODE	exon	33509539	33509609	.	+	.	Parent=gene1378
chr20	ENCODE	exon	33511217	33511339	.	+	.	Parent=gene1378
chr20	ENCODE	exon	33513504	33513543	.	+	.	Parent=gene1378
###
chr20	ENCODE	gene	33506564	33563218	.	+	.	ID=gene1379;Name=RP3-477O4.2-001;name2=CEP250
chr20	ENCODE	exon	33506564	33506986	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33509539	33509609	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33511217	33511339	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33513504	33513792	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33514814	33514870	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33516982	33517064	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33517278	33517443	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33518205	33518311	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33518543	33518794	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33521129	33521225	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33523289	33523390	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33523912	33524070	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33524613	33524791	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33525109	33525291	.	+	.	Parent=gene1379
chr20	ENCODE	exon	33526741	33526885	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33526748	33526885	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33527688	33527834	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33527688	33527834	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33529110	33529340	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33529110	33529340	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33530470	33530663	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33530470	33530663	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33530885	33531012	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33530885	33531012	.	+	1	Parent=gene1379
chr20	ENCODE	exon	33531215	33531384	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33531215	33531384	.	+	2	Parent=gene1379
chr20	ENCODE	exon	33541877	33542044	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33541877	33542044	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33542452	33542586	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33542452	33542586	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33544670	33544813	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33544670	33544813	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33545765	33545898	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33545765	33545898	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33547820	33547958	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33547820	33547958	.	+	1	Parent=gene1379
chr20	ENCODE	exon	33548962	33549310	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33548962	33549310	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33549838	33549959	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33549838	33549959	.	+	2	Parent=gene1379
chr20	ENCODE	exon	33551292	33551412	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33551292	33551412	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33553086	33553207	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33553086	33553207	.	+	2	Parent=gene1379
chr20	ENCODE	exon	33553632	33556247	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33553632	33556247	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33558981	33559094	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33558981	33559094	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33559278	33559433	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33559278	33559433	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33560186	33560287	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33560186	33560287	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33561241	33561297	.	+	.	Parent=gene1379
chr20	ENCODE	CDS	33561241	33561297	.	+	0	Parent=gene1379
chr20	ENCODE	CDS	33562606	33562869	.	+	0	Parent=gene1379
chr20	ENCODE	exon	33562606	33563218	.	+	.	Parent=gene1379
###
chr20	ENCODE	gene	33506959	33521371	.	+	.	ID=gene1380;Name=RP3-477O4.2-006;name2=CEP250
chr20	ENCODE	exon	33506959	33506986	.	+	.	Parent=gene1380
chr20	ENCODE	exon	33509539	33509609	.	+	.	Parent=gene1380
chr20	ENCODE	exon	33511217	33511339	.	+	.	Parent=gene1380
chr20	ENCODE	exon	33513504	33513792	.	+	.	Parent=gene1380
chr20	ENCODE	exon	33514814	33514870	.	+	.	Parent=gene1380
chr20	ENCODE	exon	33516982	33517064	.	+	.	Parent=gene1380
chr20	ENCODE	exon	33517278	33517387	.	+	.	Parent=gene1380
chr20	ENCODE	exon	33518291	33518311	.	+	.	Parent=gene1380
chr20	ENCODE	exon	33518543	33518794	.	+	.	Parent=gene1380
chr20	ENCODE	exon	33521129	33521371	.	+	.	Parent=gene1380
###
chr20	ENCODE	gene	33517003	33518555	.	+	.	ID=gene1381;Name=RP3-477O4.2-008;name2=CEP250
chr20	ENCODE	exon	33517003	33517064	.	+	.	Parent=gene1381
chr20	ENCODE	exon	33517278	33517443	.	+	.	Parent=gene1381
chr20	ENCODE	exon	33518205	33518311	.	+	.	Parent=gene1381
chr20	ENCODE	exon	33518511	33518555	.	+	.	Parent=gene1381
###
chr20	ENCODE	gene	33521085	33524024	.	+	.	ID=gene1382;Name=RP3-477O4.2-009;name2=CEP250
chr20	ENCODE	exon	33521085	33521225	.	+	.	Parent=gene1382
chr20	ENCODE	exon	33523289	33523390	.	+	.	Parent=gene1382
chr20	ENCODE	exon	33523912	33524024	.	+	.	Parent=gene1382
###
chr20	ENCODE	gene	33525240	33529335	.	+	.	ID=gene1383;Name=RP3-477O4.2-010;name2=CEP250
chr20	ENCODE	exon	33525240	33525291	.	+	.	Parent=gene1383
chr20	ENCODE	CDS	33525240	33525291	.	+	0	Parent=gene1383
chr20	ENCODE	exon	33526033	33526091	.	+	.	Parent=gene1383
chr20	ENCODE	CDS	33526033	33526091	.	+	2	Parent=gene1383
chr20	ENCODE	exon	33526741	33526885	.	+	.	Parent=gene1383
chr20	ENCODE	CDS	33526741	33526885	.	+	0	Parent=gene1383
chr20	ENCODE	exon	33527688	33527834	.	+	.	Parent=gene1383
chr20	ENCODE	CDS	33527688	33527834	.	+	2	Parent=gene1383
chr20	ENCODE	exon	33529110	33529335	.	+	.	Parent=gene1383
chr20	ENCODE	CDS	33529110	33529335	.	+	2	Parent=gene1383
###
chr20	ENCODE	gene	33545619	33547880	.	+	.	ID=gene1384;Name=RP3-477O4.2-005;name2=CEP250
chr20	ENCODE	exon	33545619	33545898	.	+	.	Parent=gene1384
chr20	ENCODE	exon	33547820	33547880	.	+	.	Parent=gene1384
###
chr20	ENCODE	gene	33549052	33554046	.	+	.	ID=gene1385;Name=RP3-477O4.2-004;name2=CEP250
chr20	ENCODE	exon	33549052	33549310	.	+	.	Parent=gene1385
chr20	ENCODE	exon	33549838	33549959	.	+	.	Parent=gene1385
chr20	ENCODE	exon	33553086	33553207	.	+	.	Parent=gene1385
chr20	ENCODE	exon	33553632	33554046	.	+	.	Parent=gene1385
###
chr20	ENCODE	gene	33578213	33580862	.	-	.	ID=gene1386;Name=RP3-477O4.9-001;name2=C20orf173
chr20	ENCODE	exon	33578213	33578492	.	-	.	Parent=gene1386
chr20	ENCODE	exon	33579476	33579527	.	-	.	Parent=gene1386
chr20	ENCODE	CDS	33579501	33579527	.	-	0	Parent=gene1386
chr20	ENCODE	exon	33579694	33579787	.	-	.	Parent=gene1386
chr20	ENCODE	CDS	33579694	33579787	.	-	1	Parent=gene1386
chr20	ENCODE	CDS	33579944	33580272	.	-	0	Parent=gene1386
chr20	ENCODE	exon	33579944	33580490	.	-	.	Parent=gene1386
chr20	ENCODE	exon	33580802	33580862	.	-	.	Parent=gene1386
###
chr20	ENCODE	gene	33579971	33580891	.	-	.	ID=gene1387;Name=RP3-477O4.9-003;name2=C20orf173
chr20	ENCODE	exon	33579971	33580122	.	-	.	Parent=gene1387
chr20	ENCODE	CDS	33579971	33580122	.	-	0	Parent=gene1387
chr20	ENCODE	CDS	33580308	33580616	.	-	0	Parent=gene1387
chr20	ENCODE	exon	33580308	33580667	.	-	.	Parent=gene1387
chr20	ENCODE	exon	33580802	33580891	.	-	.	Parent=gene1387
###
chr20	ENCODE	gene	33579988	33580866	.	-	.	ID=gene1388;Name=RP3-477O4.9-002;name2=C20orf173
chr20	ENCODE	exon	33579988	33580122	.	-	.	Parent=gene1388
chr20	ENCODE	CDS	33579988	33580122	.	-	0	Parent=gene1388
chr20	ENCODE	CDS	33580308	33580367	.	-	0	Parent=gene1388
chr20	ENCODE	exon	33580308	33580490	.	-	.	Parent=gene1388
chr20	ENCODE	exon	33580802	33580866	.	-	.	Parent=gene1388
###
chr20	ENCODE	gene	33593184	33608819	.	+	.	ID=gene1389;Name=RP3-477O4.12-001;name2=ERGIC3
chr20	ENCODE	exon	33593184	33593348	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33593261	33593348	.	+	0	Parent=gene1389
chr20	ENCODE	exon	33593486	33593556	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33593486	33593556	.	+	2	Parent=gene1389
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33593676	33593763	.	+	0	Parent=gene1389
chr20	ENCODE	exon	33593985	33594104	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33593985	33594104	.	+	2	Parent=gene1389
chr20	ENCODE	exon	33598577	33598670	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33598577	33598670	.	+	2	Parent=gene1389
chr20	ENCODE	exon	33599676	33599841	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33599676	33599841	.	+	1	Parent=gene1389
chr20	ENCODE	exon	33599975	33600032	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33599975	33600032	.	+	0	Parent=gene1389
chr20	ENCODE	exon	33606229	33606260	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33606229	33606260	.	+	2	Parent=gene1389
chr20	ENCODE	exon	33607218	33607314	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33607218	33607314	.	+	0	Parent=gene1389
chr20	ENCODE	exon	33607392	33607456	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33607392	33607456	.	+	2	Parent=gene1389
chr20	ENCODE	exon	33608158	33608294	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33608158	33608294	.	+	0	Parent=gene1389
chr20	ENCODE	exon	33608379	33608434	.	+	.	Parent=gene1389
chr20	ENCODE	CDS	33608379	33608434	.	+	1	Parent=gene1389
chr20	ENCODE	CDS	33608610	33608689	.	+	2	Parent=gene1389
chr20	ENCODE	exon	33608610	33608819	.	+	.	Parent=gene1389
###
chr20	ENCODE	gene	33593201	33608819	.	+	.	ID=gene1390;Name=RP3-477O4.12-003;name2=ERGIC3
chr20	ENCODE	exon	33593201	33593348	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33593261	33593348	.	+	0	Parent=gene1390
chr20	ENCODE	exon	33593486	33593556	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33593486	33593556	.	+	2	Parent=gene1390
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33593676	33593763	.	+	0	Parent=gene1390
chr20	ENCODE	exon	33593985	33594104	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33593985	33594104	.	+	2	Parent=gene1390
chr20	ENCODE	exon	33598577	33598670	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33598577	33598670	.	+	2	Parent=gene1390
chr20	ENCODE	exon	33599676	33599841	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33599676	33599841	.	+	1	Parent=gene1390
chr20	ENCODE	exon	33599975	33600032	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33599975	33600032	.	+	0	Parent=gene1390
chr20	ENCODE	exon	33605557	33605571	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33605557	33605571	.	+	2	Parent=gene1390
chr20	ENCODE	exon	33606229	33606260	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33606229	33606260	.	+	2	Parent=gene1390
chr20	ENCODE	exon	33607218	33607314	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33607218	33607314	.	+	0	Parent=gene1390
chr20	ENCODE	exon	33607392	33607456	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33607392	33607456	.	+	2	Parent=gene1390
chr20	ENCODE	exon	33608158	33608294	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33608158	33608294	.	+	0	Parent=gene1390
chr20	ENCODE	exon	33608379	33608434	.	+	.	Parent=gene1390
chr20	ENCODE	CDS	33608379	33608434	.	+	1	Parent=gene1390
chr20	ENCODE	CDS	33608610	33608689	.	+	2	Parent=gene1390
chr20	ENCODE	exon	33608610	33608819	.	+	.	Parent=gene1390
###
chr20	ENCODE	gene	33593232	33600951	.	+	.	ID=gene1391;Name=RP3-477O4.12-004;name2=ERGIC3
chr20	ENCODE	exon	33593232	33593348	.	+	.	Parent=gene1391
chr20	ENCODE	exon	33593486	33593556	.	+	.	Parent=gene1391
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1391
chr20	ENCODE	exon	33593985	33594104	.	+	.	Parent=gene1391
chr20	ENCODE	exon	33598577	33598670	.	+	.	Parent=gene1391
chr20	ENCODE	exon	33599676	33599841	.	+	.	Parent=gene1391
chr20	ENCODE	exon	33599975	33600951	.	+	.	Parent=gene1391
###
chr20	ENCODE	gene	33593242	33594302	.	+	.	ID=gene1392;Name=RP3-477O4.12-018;name2=ERGIC3
chr20	ENCODE	exon	33593242	33593348	.	+	.	Parent=gene1392
chr20	ENCODE	exon	33593486	33593556	.	+	.	Parent=gene1392
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1392
chr20	ENCODE	exon	33593985	33594302	.	+	.	Parent=gene1392
###
chr20	ENCODE	gene	33593242	33598636	.	+	.	ID=gene1393;Name=RP3-477O4.12-010;name2=ERGIC3
chr20	ENCODE	exon	33593242	33593348	.	+	.	Parent=gene1393
chr20	ENCODE	exon	33593486	33593556	.	+	.	Parent=gene1393
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1393
chr20	ENCODE	exon	33593985	33594104	.	+	.	Parent=gene1393
chr20	ENCODE	exon	33594824	33594967	.	+	.	Parent=gene1393
chr20	ENCODE	exon	33598577	33598636	.	+	.	Parent=gene1393
###
chr20	ENCODE	gene	33593245	33596569	.	+	.	ID=gene1394;name2=ERGIC3;Name=RP3-477O4.12-005
chr20	ENCODE	exon	33593245	33593348	.	+	.	Parent=gene1394
chr20	ENCODE	exon	33593486	33593556	.	+	.	Parent=gene1394
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1394
chr20	ENCODE	exon	33593985	33596569	.	+	.	Parent=gene1394
###
chr20	ENCODE	gene	33593265	33608731	.	+	.	ID=gene1395;Name=RP3-477O4.12-006;name2=ERGIC3
chr20	ENCODE	exon	33593265	33593348	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33593265	33593348	.	+	0	Parent=gene1395
chr20	ENCODE	exon	33593486	33593556	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33593486	33593556	.	+	0	Parent=gene1395
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33593676	33593763	.	+	1	Parent=gene1395
chr20	ENCODE	exon	33593985	33594104	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33593985	33594104	.	+	0	Parent=gene1395
chr20	ENCODE	exon	33598577	33598670	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33598577	33598670	.	+	0	Parent=gene1395
chr20	ENCODE	exon	33599676	33599841	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33599676	33599841	.	+	2	Parent=gene1395
chr20	ENCODE	exon	33599975	33600032	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33599975	33600032	.	+	1	Parent=gene1395
chr20	ENCODE	exon	33600331	33600375	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33600331	33600375	.	+	0	Parent=gene1395
chr20	ENCODE	exon	33606229	33606260	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33606229	33606260	.	+	0	Parent=gene1395
chr20	ENCODE	exon	33607218	33607314	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33607218	33607314	.	+	1	Parent=gene1395
chr20	ENCODE	exon	33607392	33607456	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33607392	33607456	.	+	0	Parent=gene1395
chr20	ENCODE	exon	33608158	33608294	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33608158	33608294	.	+	1	Parent=gene1395
chr20	ENCODE	exon	33608379	33608434	.	+	.	Parent=gene1395
chr20	ENCODE	CDS	33608379	33608434	.	+	2	Parent=gene1395
chr20	ENCODE	CDS	33608610	33608689	.	+	0	Parent=gene1395
chr20	ENCODE	exon	33608610	33608731	.	+	.	Parent=gene1395
###
chr20	ENCODE	gene	33593272	33608819	.	+	.	ID=gene1396;Name=RP3-477O4.12-002;name2=ERGIC3
chr20	ENCODE	exon	33593272	33593348	.	+	.	Parent=gene1396
chr20	ENCODE	exon	33593486	33593510	.	+	.	Parent=gene1396
chr20	ENCODE	exon	33598640	33598670	.	+	.	Parent=gene1396
chr20	ENCODE	exon	33599676	33599841	.	+	.	Parent=gene1396
chr20	ENCODE	exon	33599975	33600032	.	+	.	Parent=gene1396
chr20	ENCODE	exon	33606229	33606260	.	+	.	Parent=gene1396
chr20	ENCODE	exon	33607218	33607314	.	+	.	Parent=gene1396
chr20	ENCODE	exon	33607392	33607456	.	+	.	Parent=gene1396
chr20	ENCODE	exon	33608158	33608244	.	+	.	Parent=gene1396
chr20	ENCODE	exon	33608629	33608819	.	+	.	Parent=gene1396
###
chr20	ENCODE	gene	33593279	33595072	.	+	.	ID=gene1397;Name=RP3-477O4.12-011;name2=ERGIC3
chr20	ENCODE	exon	33593279	33593348	.	+	.	Parent=gene1397
chr20	ENCODE	CDS	33593279	33593348	.	+	0	Parent=gene1397
chr20	ENCODE	exon	33593486	33593556	.	+	.	Parent=gene1397
chr20	ENCODE	CDS	33593486	33593556	.	+	2	Parent=gene1397
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1397
chr20	ENCODE	CDS	33593676	33593763	.	+	0	Parent=gene1397
chr20	ENCODE	exon	33593985	33594104	.	+	.	Parent=gene1397
chr20	ENCODE	CDS	33593985	33594104	.	+	2	Parent=gene1397
chr20	ENCODE	CDS	33594821	33594828	.	+	2	Parent=gene1397
chr20	ENCODE	exon	33594821	33595072	.	+	.	Parent=gene1397
###
chr20	ENCODE	gene	33593293	33608251	.	+	.	ID=gene1398;Name=RP3-477O4.12-017;name2=ERGIC3
chr20	ENCODE	exon	33593293	33593348	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33593293	33593348	.	+	0	Parent=gene1398
chr20	ENCODE	exon	33593486	33593556	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33593486	33593556	.	+	1	Parent=gene1398
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33593676	33593763	.	+	2	Parent=gene1398
chr20	ENCODE	exon	33593949	33594104	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33593949	33594104	.	+	1	Parent=gene1398
chr20	ENCODE	exon	33598577	33598670	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33598577	33598670	.	+	1	Parent=gene1398
chr20	ENCODE	exon	33599676	33599841	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33599676	33599841	.	+	0	Parent=gene1398
chr20	ENCODE	exon	33599975	33600032	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33599975	33600032	.	+	2	Parent=gene1398
chr20	ENCODE	exon	33606229	33606260	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33606229	33606260	.	+	1	Parent=gene1398
chr20	ENCODE	exon	33607218	33607314	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33607218	33607314	.	+	2	Parent=gene1398
chr20	ENCODE	exon	33607392	33607456	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33607392	33607456	.	+	1	Parent=gene1398
chr20	ENCODE	exon	33608158	33608251	.	+	.	Parent=gene1398
chr20	ENCODE	CDS	33608158	33608251	.	+	2	Parent=gene1398
###
chr20	ENCODE	gene	33593355	33600032	.	+	.	ID=gene1399;Name=RP3-477O4.12-012;name2=ERGIC3
chr20	ENCODE	exon	33593355	33593556	.	+	.	Parent=gene1399
chr20	ENCODE	exon	33593676	33593763	.	+	.	Parent=gene1399
chr20	ENCODE	exon	33593985	33594104	.	+	.	Parent=gene1399
chr20	ENCODE	exon	33598577	33598670	.	+	.	Parent=gene1399
chr20	ENCODE	exon	33599676	33599821	.	+	.	Parent=gene1399
chr20	ENCODE	exon	33599975	33600032	.	+	.	Parent=gene1399
###
chr20	ENCODE	gene	33593606	33607447	.	+	.	ID=gene1400;Name=RP3-477O4.12-013;name2=ERGIC3
chr20	ENCODE	exon	33593606	33593763	.	+	.	Parent=gene1400
chr20	ENCODE	exon	33593985	33594104	.	+	.	Parent=gene1400
chr20	ENCODE	exon	33598577	33598670	.	+	.	Parent=gene1400
chr20	ENCODE	exon	33599676	33599841	.	+	.	Parent=gene1400
chr20	ENCODE	exon	33599975	33600032	.	+	.	Parent=gene1400
chr20	ENCODE	exon	33606229	33606260	.	+	.	Parent=gene1400
chr20	ENCODE	exon	33607218	33607314	.	+	.	Parent=gene1400
chr20	ENCODE	exon	33607392	33607447	.	+	.	Parent=gene1400
###
chr20	ENCODE	gene	33598427	33600146	.	+	.	ID=gene1401;Name=RP3-477O4.12-019;name2=ERGIC3
chr20	ENCODE	exon	33598427	33598670	.	+	.	Parent=gene1401
chr20	ENCODE	exon	33599676	33599841	.	+	.	Parent=gene1401
chr20	ENCODE	exon	33599975	33600146	.	+	.	Parent=gene1401
###
chr20	ENCODE	gene	33598652	33607617	.	+	.	ID=gene1402;Name=RP3-477O4.12-014;name2=ERGIC3
chr20	ENCODE	exon	33598652	33598670	.	+	.	Parent=gene1402
chr20	ENCODE	exon	33599676	33599841	.	+	.	Parent=gene1402
chr20	ENCODE	exon	33599975	33600032	.	+	.	Parent=gene1402
chr20	ENCODE	exon	33606229	33606260	.	+	.	Parent=gene1402
chr20	ENCODE	exon	33607218	33607314	.	+	.	Parent=gene1402
chr20	ENCODE	exon	33607392	33607617	.	+	.	Parent=gene1402
###
chr20	ENCODE	gene	33606042	33608281	.	+	.	ID=gene1403;Name=RP3-477O4.12-020;name2=ERGIC3
chr20	ENCODE	exon	33606042	33606260	.	+	.	Parent=gene1403
chr20	ENCODE	exon	33607218	33607314	.	+	.	Parent=gene1403
chr20	ENCODE	exon	33607392	33607456	.	+	.	Parent=gene1403
chr20	ENCODE	exon	33608158	33608281	.	+	.	Parent=gene1403
###
chr20	ENCODE	gene	33606101	33607745	.	+	.	ID=gene1404;Name=RP3-477O4.12-021;name2=ERGIC3
chr20	ENCODE	exon	33606101	33606260	.	+	.	Parent=gene1404
chr20	ENCODE	exon	33607392	33607745	.	+	.	Parent=gene1404
###
chr20	ENCODE	gene	33607228	33608640	.	+	.	ID=gene1405;Name=RP3-477O4.12-008;name2=ERGIC3
chr20	ENCODE	exon	33607228	33607314	.	+	.	Parent=gene1405
chr20	ENCODE	CDS	33607228	33607314	.	+	0	Parent=gene1405
chr20	ENCODE	exon	33607392	33607456	.	+	.	Parent=gene1405
chr20	ENCODE	CDS	33607392	33607456	.	+	0	Parent=gene1405
chr20	ENCODE	exon	33608062	33608294	.	+	.	Parent=gene1405
chr20	ENCODE	CDS	33608062	33608294	.	+	1	Parent=gene1405
chr20	ENCODE	exon	33608379	33608434	.	+	.	Parent=gene1405
chr20	ENCODE	CDS	33608379	33608434	.	+	2	Parent=gene1405
chr20	ENCODE	exon	33608610	33608640	.	+	.	Parent=gene1405
chr20	ENCODE	CDS	33608610	33608640	.	+	0	Parent=gene1405
###
chr20	ENCODE	gene	33607280	33608818	.	+	.	ID=gene1406;Name=RP3-477O4.12-015;name2=ERGIC3
chr20	ENCODE	exon	33607280	33607314	.	+	.	Parent=gene1406
chr20	ENCODE	CDS	33607280	33607314	.	+	0	Parent=gene1406
chr20	ENCODE	exon	33607392	33607456	.	+	.	Parent=gene1406
chr20	ENCODE	CDS	33607392	33607456	.	+	1	Parent=gene1406
chr20	ENCODE	exon	33608140	33608294	.	+	.	Parent=gene1406
chr20	ENCODE	CDS	33608140	33608294	.	+	2	Parent=gene1406
chr20	ENCODE	exon	33608379	33608434	.	+	.	Parent=gene1406
chr20	ENCODE	CDS	33608379	33608434	.	+	0	Parent=gene1406
chr20	ENCODE	CDS	33608610	33608689	.	+	1	Parent=gene1406
chr20	ENCODE	exon	33608610	33608818	.	+	.	Parent=gene1406
###
chr20	ENCODE	gene	33607764	33608635	.	+	.	ID=gene1407;Name=RP3-477O4.12-009;name2=ERGIC3
chr20	ENCODE	exon	33607764	33607933	.	+	.	Parent=gene1407
chr20	ENCODE	exon	33608158	33608294	.	+	.	Parent=gene1407
chr20	ENCODE	exon	33608379	33608434	.	+	.	Parent=gene1407
chr20	ENCODE	exon	33608610	33608635	.	+	.	Parent=gene1407
###
chr20	ENCODE	gene	33607795	33608819	.	+	.	ID=gene1408;Name=RP3-477O4.12-016;name2=ERGIC3
chr20	ENCODE	exon	33607795	33608294	.	+	.	Parent=gene1408
chr20	ENCODE	exon	33608379	33608434	.	+	.	Parent=gene1408
chr20	ENCODE	exon	33608610	33608819	.	+	.	Parent=gene1408
###
chr20	ENCODE	gene	33609921	33615871	.	-	.	ID=gene1409;Name=RP3-477O4.7-006;name2=FER1L4
chr20	ENCODE	exon	33609921	33610236	.	-	.	Parent=gene1409
chr20	ENCODE	exon	33610340	33610440	.	-	.	Parent=gene1409
chr20	ENCODE	exon	33610525	33610808	.	-	.	Parent=gene1409
chr20	ENCODE	exon	33611304	33611545	.	-	.	Parent=gene1409
chr20	ENCODE	exon	33611721	33611819	.	-	.	Parent=gene1409
chr20	ENCODE	exon	33613033	33613118	.	-	.	Parent=gene1409
chr20	ENCODE	exon	33615036	33615871	.	-	.	Parent=gene1409
###
chr20	ENCODE	gene	33609921	33630266	.	-	.	ID=gene1410;Name=RP3-477O4.7-001;name2=FER1L4
chr20	ENCODE	exon	33609921	33610236	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33610340	33610440	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33610525	33610808	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33611344	33611545	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33611721	33611819	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33613033	33613118	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33615036	33616248	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33616430	33616557	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33627503	33627619	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33627717	33627854	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33627932	33628032	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33628122	33628164	.	-	.	Parent=gene1410
chr20	ENCODE	exon	33630172	33630266	.	-	.	Parent=gene1410
###
chr20	ENCODE	gene	33609921	33651008	.	-	.	ID=gene1411;Name=RP3-477O4.7-002;name2=FER1L4
chr20	ENCODE	exon	33609921	33610236	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33610340	33610440	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33610525	33611819	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33613033	33613118	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33615036	33616248	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33616430	33616557	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33618934	33618987	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33627503	33627619	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33627717	33627854	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33627932	33628032	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33628122	33628164	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33646813	33646929	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33647003	33647090	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33650350	33650450	.	-	.	Parent=gene1411
chr20	ENCODE	exon	33650902	33651008	.	-	.	Parent=gene1411
###
chr20	ENCODE	gene	33609926	33633951	.	-	.	ID=gene1412;Name=RP3-477O4.7-008;name2=FER1L4
chr20	ENCODE	exon	33609926	33610236	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33610340	33610440	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33610525	33610808	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33611304	33611819	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33613033	33613118	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33615036	33616248	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33616430	33616557	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33627503	33627619	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33627717	33627854	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33627988	33628032	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33628122	33628164	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33630172	33630303	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33630392	33630450	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33630594	33630792	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33633375	33633536	.	-	.	Parent=gene1412
chr20	ENCODE	exon	33633631	33633951	.	-	.	Parent=gene1412
###
chr20	ENCODE	gene	33609928	33635303	.	-	.	ID=gene1413;Name=RP3-477O4.7-009;name2=FER1L4
chr20	ENCODE	exon	33609928	33610236	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33610340	33610808	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33611304	33611545	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33611721	33611819	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33613033	33613118	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33613990	33614150	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33615036	33615190	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33616078	33616248	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33616430	33616557	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33627503	33627619	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33627717	33627854	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33627932	33628032	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33628122	33628164	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33630172	33630303	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33630392	33630450	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33630594	33630792	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33633375	33633536	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33633631	33633747	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33634175	33634348	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33634464	33634598	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33635022	33635146	.	-	.	Parent=gene1413
chr20	ENCODE	exon	33635276	33635303	.	-	.	Parent=gene1413
###
chr20	ENCODE	gene	33609928	33658898	.	-	.	ID=gene1414;name2=FER1L4;Name=RP3-477O4.7-010
chr20	ENCODE	exon	33609928	33610236	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33610050	33610236	.	-	1	Parent=gene1414
chr20	ENCODE	exon	33610340	33610440	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33610340	33610440	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33610525	33610808	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33610525	33610808	.	-	2	Parent=gene1414
chr20	ENCODE	exon	33611304	33611545	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33611304	33611545	.	-	1	Parent=gene1414
chr20	ENCODE	exon	33611721	33611819	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33611721	33611819	.	-	1	Parent=gene1414
chr20	ENCODE	exon	33613033	33613118	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33613033	33613118	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33613990	33614132	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33613990	33614132	.	-	2	Parent=gene1414
chr20	ENCODE	exon	33615036	33615190	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33615036	33615190	.	-	1	Parent=gene1414
chr20	ENCODE	exon	33616078	33616248	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33616078	33616248	.	-	1	Parent=gene1414
chr20	ENCODE	exon	33616430	33616557	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33616430	33616557	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33627503	33627619	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33627503	33627619	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33627717	33627854	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33627717	33627854	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33627932	33628032	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33627932	33628032	.	-	2	Parent=gene1414
chr20	ENCODE	exon	33628122	33628164	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33628122	33628164	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33630172	33630303	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33630172	33630303	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33630392	33630450	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33630392	33630450	.	-	2	Parent=gene1414
chr20	ENCODE	exon	33630594	33630792	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33630594	33630792	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33633375	33633536	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33633375	33633536	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33633631	33633747	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33633631	33633747	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33634175	33634348	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33634175	33634348	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33634464	33634598	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33634464	33634598	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33635022	33635146	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33635022	33635146	.	-	2	Parent=gene1414
chr20	ENCODE	exon	33635276	33635429	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33635276	33635429	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33636460	33636612	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33636460	33636612	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33646813	33646929	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33646813	33646929	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33647003	33647090	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33647003	33647090	.	-	1	Parent=gene1414
chr20	ENCODE	exon	33650350	33650450	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33650350	33650450	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33650902	33651022	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33650902	33651022	.	-	1	Parent=gene1414
chr20	ENCODE	exon	33651109	33651280	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33651109	33651280	.	-	2	Parent=gene1414
chr20	ENCODE	exon	33651449	33651557	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33651449	33651557	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33651899	33652260	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33651899	33652260	.	-	2	Parent=gene1414
chr20	ENCODE	exon	33652868	33653054	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33652868	33653054	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33653142	33653325	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33653142	33653325	.	-	1	Parent=gene1414
chr20	ENCODE	exon	33653443	33653602	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33653443	33653602	.	-	2	Parent=gene1414
chr20	ENCODE	exon	33653859	33653943	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33653859	33653943	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33654025	33654087	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33654025	33654087	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33654346	33654477	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33654346	33654477	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33654595	33654655	.	-	.	Parent=gene1414
chr20	ENCODE	CDS	33654595	33654655	.	-	1	Parent=gene1414
chr20	ENCODE	CDS	33655133	33655152	.	-	0	Parent=gene1414
chr20	ENCODE	exon	33655133	33655303	.	-	.	Parent=gene1414
chr20	ENCODE	exon	33655640	33655681	.	-	.	Parent=gene1414
chr20	ENCODE	exon	33655866	33655957	.	-	.	Parent=gene1414
chr20	ENCODE	exon	33657458	33657557	.	-	.	Parent=gene1414
chr20	ENCODE	exon	33657654	33657742	.	-	.	Parent=gene1414
chr20	ENCODE	exon	33658437	33658492	.	-	.	Parent=gene1414
chr20	ENCODE	exon	33658751	33658898	.	-	.	Parent=gene1414
###
chr20	ENCODE	gene	33627512	33630597	.	-	.	ID=gene1415;Name=RP3-477O4.7-003;name2=FER1L4
chr20	ENCODE	exon	33627512	33627619	.	-	.	Parent=gene1415
chr20	ENCODE	CDS	33627512	33627619	.	-	0	Parent=gene1415
chr20	ENCODE	exon	33627717	33627854	.	-	.	Parent=gene1415
chr20	ENCODE	CDS	33627717	33627854	.	-	0	Parent=gene1415
chr20	ENCODE	exon	33627932	33628032	.	-	.	Parent=gene1415
chr20	ENCODE	CDS	33627932	33628032	.	-	2	Parent=gene1415
chr20	ENCODE	exon	33628122	33628164	.	-	.	Parent=gene1415
chr20	ENCODE	CDS	33628122	33628164	.	-	0	Parent=gene1415
chr20	ENCODE	exon	33630392	33630450	.	-	.	Parent=gene1415
chr20	ENCODE	CDS	33630392	33630450	.	-	2	Parent=gene1415
chr20	ENCODE	exon	33630594	33630597	.	-	.	Parent=gene1415
chr20	ENCODE	CDS	33630594	33630597	.	-	0	Parent=gene1415
###
chr20	ENCODE	gene	33627566	33627922	.	-	.	ID=gene1416;Name=RP3-477O4.7-011;name2=FER1L4
chr20	ENCODE	exon	33627566	33627619	.	-	.	Parent=gene1416
chr20	ENCODE	exon	33627717	33627922	.	-	.	Parent=gene1416
###
chr20	ENCODE	gene	33633455	33636545	.	-	.	ID=gene1417;Name=RP3-477O4.7-004;name2=FER1L4
chr20	ENCODE	exon	33633455	33633536	.	-	.	Parent=gene1417
chr20	ENCODE	exon	33633631	33633747	.	-	.	Parent=gene1417
chr20	ENCODE	exon	33634464	33634598	.	-	.	Parent=gene1417
chr20	ENCODE	exon	33635276	33635429	.	-	.	Parent=gene1417
chr20	ENCODE	exon	33636460	33636545	.	-	.	Parent=gene1417
###
chr20	ENCODE	gene	33651047	33652110	.	-	.	ID=gene1418;Name=RP3-477O4.7-012;name2=FER1L4
chr20	ENCODE	exon	33651047	33651557	.	-	.	Parent=gene1418
chr20	ENCODE	exon	33651899	33652110	.	-	.	Parent=gene1418
###
chr20	ENCODE	gene	33652035	33656662	.	-	.	ID=gene1419;Name=RP3-477O4.7-013;name2=FER1L4
chr20	ENCODE	exon	33652035	33652260	.	-	.	Parent=gene1419
chr20	ENCODE	exon	33652868	33653054	.	-	.	Parent=gene1419
chr20	ENCODE	exon	33653142	33654087	.	-	.	Parent=gene1419
chr20	ENCODE	exon	33654346	33654477	.	-	.	Parent=gene1419
chr20	ENCODE	exon	33654595	33654655	.	-	.	Parent=gene1419
chr20	ENCODE	exon	33655133	33655303	.	-	.	Parent=gene1419
chr20	ENCODE	exon	33655640	33655681	.	-	.	Parent=gene1419
chr20	ENCODE	exon	33655866	33655957	.	-	.	Parent=gene1419
chr20	ENCODE	exon	33656438	33656662	.	-	.	Parent=gene1419
###
chr20	ENCODE	gene	33654440	33657795	.	-	.	ID=gene1420;Name=RP3-477O4.7-014;name2=FER1L4
chr20	ENCODE	exon	33654440	33654477	.	-	.	Parent=gene1420
chr20	ENCODE	exon	33654595	33654655	.	-	.	Parent=gene1420
chr20	ENCODE	exon	33655133	33655303	.	-	.	Parent=gene1420
chr20	ENCODE	exon	33655640	33655681	.	-	.	Parent=gene1420
chr20	ENCODE	exon	33655866	33655957	.	-	.	Parent=gene1420
chr20	ENCODE	exon	33657458	33657557	.	-	.	Parent=gene1420
chr20	ENCODE	exon	33657654	33657795	.	-	.	Parent=gene1420
###
chr20	ENCODE	gene	33655257	33658865	.	-	.	ID=gene1421;Name=RP3-477O4.7-015;name2=FER1L4
chr20	ENCODE	exon	33655257	33655303	.	-	.	Parent=gene1421
chr20	ENCODE	exon	33655640	33655681	.	-	.	Parent=gene1421
chr20	ENCODE	exon	33655866	33655957	.	-	.	Parent=gene1421
chr20	ENCODE	exon	33657458	33657557	.	-	.	Parent=gene1421
chr20	ENCODE	exon	33657654	33657742	.	-	.	Parent=gene1421
chr20	ENCODE	exon	33658437	33658502	.	-	.	Parent=gene1421
chr20	ENCODE	exon	33658751	33658865	.	-	.	Parent=gene1421
###
chr20	ENCODE	gene	33667228	33672385	.	+	.	ID=gene1422;Name=RP1-309K20.4-001;name2=SPAG4
chr20	ENCODE	exon	33667228	33667643	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33667340	33667643	.	+	0	Parent=gene1422
chr20	ENCODE	exon	33668472	33668576	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33668472	33668576	.	+	2	Parent=gene1422
chr20	ENCODE	exon	33668856	33668922	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33668856	33668922	.	+	2	Parent=gene1422
chr20	ENCODE	exon	33669115	33669176	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33669115	33669176	.	+	1	Parent=gene1422
chr20	ENCODE	exon	33669423	33669466	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33669423	33669466	.	+	2	Parent=gene1422
chr20	ENCODE	exon	33669786	33669811	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33669786	33669811	.	+	0	Parent=gene1422
chr20	ENCODE	exon	33669948	33670056	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33669948	33670056	.	+	1	Parent=gene1422
chr20	ENCODE	exon	33670259	33670334	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33670259	33670334	.	+	0	Parent=gene1422
chr20	ENCODE	exon	33670531	33670646	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33670531	33670646	.	+	2	Parent=gene1422
chr20	ENCODE	exon	33670915	33671082	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33670915	33671082	.	+	0	Parent=gene1422
chr20	ENCODE	exon	33672020	33672109	.	+	.	Parent=gene1422
chr20	ENCODE	CDS	33672020	33672109	.	+	0	Parent=gene1422
chr20	ENCODE	CDS	33672212	33672358	.	+	0	Parent=gene1422
chr20	ENCODE	exon	33672212	33672385	.	+	.	Parent=gene1422
###
chr20	ENCODE	gene	33668216	33670232	.	+	.	ID=gene1423;Name=RP1-309K20.4-003;name2=SPAG4
chr20	ENCODE	exon	33668216	33668576	.	+	.	Parent=gene1423
chr20	ENCODE	exon	33668856	33668922	.	+	.	Parent=gene1423
chr20	ENCODE	exon	33669115	33669176	.	+	.	Parent=gene1423
chr20	ENCODE	exon	33669423	33669466	.	+	.	Parent=gene1423
chr20	ENCODE	exon	33669786	33670232	.	+	.	Parent=gene1423
###
chr20	ENCODE	gene	33668360	33670188	.	+	.	ID=gene1424;Name=RP1-309K20.4-006;name2=SPAG4
chr20	ENCODE	exon	33668360	33668576	.	+	.	Parent=gene1424
chr20	ENCODE	exon	33668856	33668922	.	+	.	Parent=gene1424
chr20	ENCODE	exon	33670105	33670188	.	+	.	Parent=gene1424
###
chr20	ENCODE	gene	33668360	33671024	.	+	.	ID=gene1425;Name=RP1-309K20.4-002;name2=SPAG4
chr20	ENCODE	exon	33668360	33668576	.	+	.	Parent=gene1425
chr20	ENCODE	exon	33668856	33668922	.	+	.	Parent=gene1425
chr20	ENCODE	exon	33669115	33669176	.	+	.	Parent=gene1425
chr20	ENCODE	exon	33669423	33669466	.	+	.	Parent=gene1425
chr20	ENCODE	exon	33669786	33669811	.	+	.	Parent=gene1425
chr20	ENCODE	exon	33669948	33670056	.	+	.	Parent=gene1425
chr20	ENCODE	exon	33670259	33670334	.	+	.	Parent=gene1425
chr20	ENCODE	exon	33670531	33670646	.	+	.	Parent=gene1425
chr20	ENCODE	exon	33670915	33671024	.	+	.	Parent=gene1425
###
chr20	ENCODE	gene	33668382	33671072	.	+	.	ID=gene1426;Name=RP1-309K20.4-004;name2=SPAG4
chr20	ENCODE	exon	33668382	33668576	.	+	.	Parent=gene1426
chr20	ENCODE	exon	33668856	33669176	.	+	.	Parent=gene1426
chr20	ENCODE	exon	33669423	33669466	.	+	.	Parent=gene1426
chr20	ENCODE	exon	33669786	33670056	.	+	.	Parent=gene1426
chr20	ENCODE	exon	33670259	33670334	.	+	.	Parent=gene1426
chr20	ENCODE	exon	33670531	33670646	.	+	.	Parent=gene1426
chr20	ENCODE	exon	33670915	33671072	.	+	.	Parent=gene1426
###
chr20	ENCODE	gene	33669025	33672270	.	+	.	ID=gene1427;name2=SPAG4;Name=RP1-309K20.4-005
chr20	ENCODE	exon	33669025	33669176	.	+	.	Parent=gene1427
chr20	ENCODE	exon	33669786	33669811	.	+	.	Parent=gene1427
chr20	ENCODE	exon	33670259	33670334	.	+	.	Parent=gene1427
chr20	ENCODE	exon	33670531	33670646	.	+	.	Parent=gene1427
chr20	ENCODE	exon	33670915	33671082	.	+	.	Parent=gene1427
chr20	ENCODE	exon	33672020	33672109	.	+	.	Parent=gene1427
chr20	ENCODE	exon	33672212	33672270	.	+	.	Parent=gene1427
###
chr20	ENCODE	gene	33670921	33672385	.	+	.	ID=gene1428;Name=RP1-309K20.4-007;name2=SPAG4
chr20	ENCODE	exon	33670921	33671082	.	+	.	Parent=gene1428
chr20	ENCODE	CDS	33670921	33671082	.	+	0	Parent=gene1428
chr20	ENCODE	exon	33671993	33672109	.	+	.	Parent=gene1428
chr20	ENCODE	CDS	33671993	33672109	.	+	0	Parent=gene1428
chr20	ENCODE	CDS	33672212	33672358	.	+	0	Parent=gene1428
chr20	ENCODE	exon	33672212	33672385	.	+	.	Parent=gene1428
###
chr20	ENCODE	gene	33677367	33716222	.	-	.	ID=gene1429;Name=RP1-309K20.2-004;name2=CPNE1
chr20	ENCODE	exon	33677367	33677717	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33677577	33677717	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33677903	33678139	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33677903	33678139	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33678616	33678749	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33678616	33678749	.	-	2	Parent=gene1429
chr20	ENCODE	exon	33681775	33681826	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33681775	33681826	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33682077	33682131	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33682077	33682131	.	-	1	Parent=gene1429
chr20	ENCODE	exon	33682237	33682370	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33682237	33682370	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33682450	33682509	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33682604	33682690	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33682828	33682914	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33683024	33683113	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33683281	33683361	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33683499	33683570	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1429
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1429
chr20	ENCODE	exon	33706538	33706680	.	-	.	Parent=gene1429
chr20	ENCODE	exon	33710266	33710318	.	-	.	Parent=gene1429
chr20	ENCODE	exon	33716096	33716222	.	-	.	Parent=gene1429
###
chr20	ENCODE	gene	33677380	33678189	.	-	.	ID=gene1430;Name=RP1-309K20.2-018;name2=CPNE1
chr20	ENCODE	exon	33677380	33677717	.	-	.	Parent=gene1430
chr20	ENCODE	exon	33677903	33678189	.	-	.	Parent=gene1430
###
chr20	ENCODE	gene	33677380	33678676	.	-	.	ID=gene1431;Name=RP1-309K20.2-022;name2=CPNE1
chr20	ENCODE	exon	33677380	33678139	.	-	.	Parent=gene1431
chr20	ENCODE	exon	33678616	33678676	.	-	.	Parent=gene1431
###
chr20	ENCODE	gene	33677380	33678735	.	-	.	ID=gene1432;name2=CPNE1;Name=RP1-309K20.2-019
chr20	ENCODE	exon	33677380	33677717	.	-	.	Parent=gene1432
chr20	ENCODE	exon	33678071	33678162	.	-	.	Parent=gene1432
chr20	ENCODE	exon	33678616	33678735	.	-	.	Parent=gene1432
###
chr20	ENCODE	gene	33677380	33681792	.	-	.	ID=gene1433;Name=RP1-309K20.2-015;name2=CPNE1
chr20	ENCODE	exon	33677380	33677717	.	-	.	Parent=gene1433
chr20	ENCODE	CDS	33677485	33677717	.	-	0	Parent=gene1433
chr20	ENCODE	exon	33677899	33678139	.	-	.	Parent=gene1433
chr20	ENCODE	CDS	33677899	33678139	.	-	1	Parent=gene1433
chr20	ENCODE	exon	33678616	33678749	.	-	.	Parent=gene1433
chr20	ENCODE	CDS	33678616	33678749	.	-	0	Parent=gene1433
chr20	ENCODE	exon	33681775	33681792	.	-	.	Parent=gene1433
chr20	ENCODE	CDS	33681775	33681792	.	-	0	Parent=gene1433
###
chr20	ENCODE	gene	33677380	33705013	.	-	.	ID=gene1434;Name=RP1-309K20.2-005;name2=CPNE1
chr20	ENCODE	exon	33677380	33677717	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33677577	33677717	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33677903	33678139	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33677903	33678139	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33678616	33678749	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33678616	33678749	.	-	2	Parent=gene1434
chr20	ENCODE	exon	33681775	33681826	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33681775	33681826	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33682077	33682131	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33682077	33682131	.	-	1	Parent=gene1434
chr20	ENCODE	exon	33682237	33682370	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33682237	33682370	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33682450	33682509	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33682604	33682690	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33682828	33682914	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33683024	33683113	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33683281	33683361	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33683499	33683570	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1434
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1434
chr20	ENCODE	exon	33704864	33705013	.	-	.	Parent=gene1434
###
chr20	ENCODE	gene	33677394	33716197	.	-	.	ID=gene1435;Name=RP1-309K20.2-027;name2=CPNE1
chr20	ENCODE	exon	33677394	33677717	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33677903	33678139	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33678616	33678749	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33681775	33681826	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33682077	33682131	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33682237	33682370	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33683499	33683721	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1435
chr20	ENCODE	exon	33716096	33716197	.	-	.	Parent=gene1435
###
chr20	ENCODE	gene	33677422	33683890	.	-	.	ID=gene1436;Name=RP1-309K20.2-001;name2=CPNE1
chr20	ENCODE	exon	33677422	33677717	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33677903	33678139	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33678616	33678749	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33681775	33682370	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1436
chr20	ENCODE	exon	33683853	33683890	.	-	.	Parent=gene1436
###
chr20	ENCODE	gene	33677495	33716213	.	-	.	ID=gene1437;Name=RP1-309K20.2-028;name2=CPNE1
chr20	ENCODE	exon	33677495	33677717	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33677903	33678162	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33678616	33678749	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33681775	33681826	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33682077	33682131	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33682237	33682370	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1437
chr20	ENCODE	exon	33716138	33716213	.	-	.	Parent=gene1437
###
chr20	ENCODE	gene	33677588	33716292	.	-	.	ID=gene1438;Name=RP1-309K20.2-006;name2=CPNE1
chr20	ENCODE	exon	33677588	33677717	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33677903	33678136	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33678616	33678749	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33681775	33681826	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33682077	33682131	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33682237	33682370	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1438
chr20	ENCODE	exon	33716138	33716292	.	-	.	Parent=gene1438
###
chr20	ENCODE	gene	33678030	33678867	.	-	.	ID=gene1439;Name=RP1-309K20.2-003;name2=CPNE1
chr20	ENCODE	exon	33678030	33678139	.	-	.	Parent=gene1439
chr20	ENCODE	exon	33678616	33678867	.	-	.	Parent=gene1439
###
chr20	ENCODE	gene	33678621	33716268	.	-	.	ID=gene1440;Name=RP1-309K20.2-013;name2=CPNE1
chr20	ENCODE	exon	33678621	33678749	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33678621	33678749	.	-	2	Parent=gene1440
chr20	ENCODE	exon	33681775	33681826	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33681775	33681826	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33682077	33682131	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33682077	33682131	.	-	1	Parent=gene1440
chr20	ENCODE	exon	33682237	33682370	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33682237	33682370	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33682450	33682509	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33682604	33682690	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33682828	33682914	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33683024	33683113	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33683281	33683361	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1440
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1440
chr20	ENCODE	exon	33716096	33716268	.	-	.	Parent=gene1440
###
chr20	ENCODE	gene	33682244	33716219	.	-	.	ID=gene1441;Name=RP1-309K20.2-014;name2=CPNE1
chr20	ENCODE	exon	33682244	33682370	.	-	.	Parent=gene1441
chr20	ENCODE	CDS	33682244	33682370	.	-	0	Parent=gene1441
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1441
chr20	ENCODE	CDS	33682450	33682509	.	-	0	Parent=gene1441
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1441
chr20	ENCODE	CDS	33682604	33682690	.	-	0	Parent=gene1441
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1441
chr20	ENCODE	CDS	33682828	33682914	.	-	0	Parent=gene1441
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1441
chr20	ENCODE	CDS	33683024	33683113	.	-	0	Parent=gene1441
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1441
chr20	ENCODE	CDS	33683281	33683361	.	-	0	Parent=gene1441
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1441
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1441
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1441
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1441
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1441
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1441
chr20	ENCODE	exon	33716138	33716219	.	-	.	Parent=gene1441
###
chr20	ENCODE	gene	33682294	33683385	.	-	.	ID=gene1442;name2=CPNE1;Name=RP1-309K20.2-026
chr20	ENCODE	exon	33682294	33682370	.	-	.	Parent=gene1442
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1442
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1442
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1442
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1442
chr20	ENCODE	exon	33683281	33683385	.	-	.	Parent=gene1442
###
chr20	ENCODE	gene	33682319	33716252	.	-	.	ID=gene1443;name2=CPNE1;Name=RP1-309K20.2-007
chr20	ENCODE	exon	33682319	33682370	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33682319	33682370	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33682450	33682509	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33682450	33682509	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33682604	33682690	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33682604	33682690	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33682828	33682914	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33682828	33682914	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33683024	33683113	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33683281	33683361	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33683499	33683570	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1443
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1443
chr20	ENCODE	exon	33716096	33716252	.	-	.	Parent=gene1443
###
chr20	ENCODE	gene	33682830	33716199	.	-	.	ID=gene1444;Name=RP1-309K20.2-017;name2=CPNE1
chr20	ENCODE	exon	33682830	33682914	.	-	.	Parent=gene1444
chr20	ENCODE	CDS	33682830	33682914	.	-	0	Parent=gene1444
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1444
chr20	ENCODE	CDS	33683024	33683113	.	-	0	Parent=gene1444
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1444
chr20	ENCODE	CDS	33683281	33683361	.	-	0	Parent=gene1444
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1444
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1444
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1444
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1444
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1444
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1444
chr20	ENCODE	exon	33716096	33716199	.	-	.	Parent=gene1444
###
chr20	ENCODE	gene	33682848	33716268	.	-	.	ID=gene1445;Name=RP1-309K20.2-009;name2=CPNE1
chr20	ENCODE	exon	33682848	33682914	.	-	.	Parent=gene1445
chr20	ENCODE	CDS	33682848	33682914	.	-	0	Parent=gene1445
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1445
chr20	ENCODE	CDS	33683024	33683113	.	-	0	Parent=gene1445
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1445
chr20	ENCODE	CDS	33683281	33683361	.	-	0	Parent=gene1445
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1445
chr20	ENCODE	CDS	33683499	33683570	.	-	0	Parent=gene1445
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1445
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1445
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1445
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1445
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1445
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1445
chr20	ENCODE	exon	33716212	33716268	.	-	.	Parent=gene1445
###
chr20	ENCODE	gene	33682895	33716218	.	-	.	ID=gene1446;Name=RP1-309K20.2-025;name2=CPNE1
chr20	ENCODE	exon	33682895	33682914	.	-	.	Parent=gene1446
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1446
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1446
chr20	ENCODE	exon	33683499	33683584	.	-	.	Parent=gene1446
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1446
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1446
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1446
chr20	ENCODE	exon	33716096	33716218	.	-	.	Parent=gene1446
###
chr20	ENCODE	gene	33683024	33716236	.	-	.	ID=gene1447;name2=CPNE1;Name=RP1-309K20.2-008
chr20	ENCODE	exon	33683024	33683113	.	-	.	Parent=gene1447
chr20	ENCODE	CDS	33683024	33683113	.	-	0	Parent=gene1447
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1447
chr20	ENCODE	CDS	33683281	33683361	.	-	0	Parent=gene1447
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1447
chr20	ENCODE	CDS	33683499	33683570	.	-	0	Parent=gene1447
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1447
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1447
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1447
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1447
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1447
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1447
chr20	ENCODE	exon	33710266	33710318	.	-	.	Parent=gene1447
chr20	ENCODE	exon	33716096	33716236	.	-	.	Parent=gene1447
###
chr20	ENCODE	gene	33683046	33716236	.	-	.	ID=gene1448;Name=RP1-309K20.2-016;name2=CPNE1
chr20	ENCODE	exon	33683046	33683113	.	-	.	Parent=gene1448
chr20	ENCODE	CDS	33683046	33683113	.	-	0	Parent=gene1448
chr20	ENCODE	exon	33683281	33683361	.	-	.	Parent=gene1448
chr20	ENCODE	CDS	33683281	33683361	.	-	0	Parent=gene1448
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1448
chr20	ENCODE	CDS	33683499	33683570	.	-	0	Parent=gene1448
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1448
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1448
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1448
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1448
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1448
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1448
chr20	ENCODE	exon	33710266	33710350	.	-	.	Parent=gene1448
chr20	ENCODE	exon	33716096	33716236	.	-	.	Parent=gene1448
###
chr20	ENCODE	gene	33683062	33684001	.	-	.	ID=gene1449;Name=RP1-309K20.2-002;name2=CPNE1
chr20	ENCODE	exon	33683062	33683113	.	-	.	Parent=gene1449
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1449
chr20	ENCODE	exon	33683853	33684001	.	-	.	Parent=gene1449
###
chr20	ENCODE	gene	33683296	33716218	.	-	.	ID=gene1450;Name=RP1-309K20.2-012;name2=CPNE1
chr20	ENCODE	exon	33683296	33683361	.	-	.	Parent=gene1450
chr20	ENCODE	CDS	33683296	33683361	.	-	0	Parent=gene1450
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1450
chr20	ENCODE	CDS	33683499	33683570	.	-	0	Parent=gene1450
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1450
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1450
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1450
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1450
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1450
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1450
chr20	ENCODE	exon	33706538	33706680	.	-	.	Parent=gene1450
chr20	ENCODE	exon	33716138	33716218	.	-	.	Parent=gene1450
###
chr20	ENCODE	gene	33683333	33716225	.	-	.	ID=gene1451;Name=RP1-309K20.2-020;name2=CPNE1
chr20	ENCODE	exon	33683333	33683361	.	-	.	Parent=gene1451
chr20	ENCODE	CDS	33683333	33683361	.	-	0	Parent=gene1451
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1451
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1451
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1451
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1451
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1451
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1451
chr20	ENCODE	exon	33710266	33710318	.	-	.	Parent=gene1451
chr20	ENCODE	exon	33716096	33716225	.	-	.	Parent=gene1451
###
chr20	ENCODE	gene	33683499	33716237	.	-	.	ID=gene1452;Name=RP1-309K20.2-010;name2=CPNE1
chr20	ENCODE	exon	33683499	33683570	.	-	.	Parent=gene1452
chr20	ENCODE	CDS	33683499	33683570	.	-	0	Parent=gene1452
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1452
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1452
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1452
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1452
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1452
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1452
chr20	ENCODE	exon	33706538	33706680	.	-	.	Parent=gene1452
chr20	ENCODE	exon	33710266	33710350	.	-	.	Parent=gene1452
chr20	ENCODE	exon	33716096	33716237	.	-	.	Parent=gene1452
###
chr20	ENCODE	gene	33683546	33716173	.	-	.	ID=gene1453;Name=RP1-309K20.2-011;name2=CPNE1
chr20	ENCODE	exon	33683546	33683570	.	-	.	Parent=gene1453
chr20	ENCODE	CDS	33683546	33683570	.	-	0	Parent=gene1453
chr20	ENCODE	exon	33683647	33683721	.	-	.	Parent=gene1453
chr20	ENCODE	CDS	33683647	33683721	.	-	0	Parent=gene1453
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1453
chr20	ENCODE	CDS	33683853	33684032	.	-	0	Parent=gene1453
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1453
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1453
chr20	ENCODE	exon	33706538	33706680	.	-	.	Parent=gene1453
chr20	ENCODE	exon	33710266	33710350	.	-	.	Parent=gene1453
chr20	ENCODE	exon	33716138	33716173	.	-	.	Parent=gene1453
###
chr20	ENCODE	gene	33683676	33725736	.	-	.	ID=gene1454;Name=RP1-309K20.2-030;name2=CPNE1
chr20	ENCODE	exon	33683676	33683721	.	-	.	Parent=gene1454
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1454
chr20	ENCODE	exon	33706538	33706680	.	-	.	Parent=gene1454
chr20	ENCODE	exon	33710266	33710350	.	-	.	Parent=gene1454
chr20	ENCODE	exon	33724091	33724180	.	-	.	Parent=gene1454
chr20	ENCODE	exon	33724937	33724952	.	-	.	Parent=gene1454
chr20	ENCODE	exon	33725686	33725736	.	-	.	Parent=gene1454
###
chr20	ENCODE	gene	33683676	33725736	.	-	.	ID=gene1455;Name=RP1-309K20.2-031;name2=CPNE1
chr20	ENCODE	exon	33683676	33683721	.	-	.	Parent=gene1455
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1455
chr20	ENCODE	exon	33706538	33706680	.	-	.	Parent=gene1455
chr20	ENCODE	exon	33710266	33710350	.	-	.	Parent=gene1455
chr20	ENCODE	exon	33724091	33724180	.	-	.	Parent=gene1455
chr20	ENCODE	exon	33724937	33725020	.	-	.	Parent=gene1455
chr20	ENCODE	exon	33725686	33725736	.	-	.	Parent=gene1455
###
chr20	ENCODE	gene	33683676	33725880	.	-	.	ID=gene1456;name2=CPNE1;Name=RP1-309K20.2-029
chr20	ENCODE	exon	33683676	33683721	.	-	.	Parent=gene1456
chr20	ENCODE	exon	33683853	33684032	.	-	.	Parent=gene1456
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1456
chr20	ENCODE	exon	33706538	33706680	.	-	.	Parent=gene1456
chr20	ENCODE	exon	33710266	33710350	.	-	.	Parent=gene1456
chr20	ENCODE	exon	33724091	33724180	.	-	.	Parent=gene1456
chr20	ENCODE	exon	33724937	33725020	.	-	.	Parent=gene1456
chr20	ENCODE	exon	33725686	33725767	.	-	.	Parent=gene1456
chr20	ENCODE	exon	33725848	33725880	.	-	.	Parent=gene1456
###
chr20	ENCODE	gene	33683962	33715894	.	-	.	ID=gene1457;Name=RP1-309K20.2-021;name2=CPNE1
chr20	ENCODE	exon	33683962	33684032	.	-	.	Parent=gene1457
chr20	ENCODE	CDS	33683962	33684032	.	-	0	Parent=gene1457
chr20	ENCODE	exon	33684131	33684259	.	-	.	Parent=gene1457
chr20	ENCODE	CDS	33684131	33684259	.	-	0	Parent=gene1457
chr20	ENCODE	exon	33715695	33715894	.	-	.	Parent=gene1457
###
chr20	ENCODE	gene	33700261	33716252	.	-	.	ID=gene1458;name2=RBM12;Name=RP1-309K20.5-001
chr20	ENCODE	exon	33700261	33706680	.	-	.	Parent=gene1458
chr20	ENCODE	CDS	33703860	33706658	.	-	0	Parent=gene1458
chr20	ENCODE	exon	33710266	33710350	.	-	.	Parent=gene1458
chr20	ENCODE	exon	33716096	33716252	.	-	.	Parent=gene1458
###
chr20	ENCODE	gene	33701478	33716224	.	-	.	ID=gene1459;Name=RP1-309K20.5-003;name2=RBM12
chr20	ENCODE	exon	33701478	33706680	.	-	.	Parent=gene1459
chr20	ENCODE	CDS	33703860	33706658	.	-	0	Parent=gene1459
chr20	ENCODE	exon	33716096	33716224	.	-	.	Parent=gene1459
###
chr20	ENCODE	gene	33701662	33716236	.	-	.	ID=gene1460;Name=RP1-309K20.5-002;name2=RBM12
chr20	ENCODE	exon	33701662	33706680	.	-	.	Parent=gene1460
chr20	ENCODE	CDS	33703860	33706658	.	-	0	Parent=gene1460
chr20	ENCODE	exon	33710266	33710318	.	-	.	Parent=gene1460
chr20	ENCODE	exon	33716096	33716236	.	-	.	Parent=gene1460
###
chr20	ENCODE	gene	33705786	33716225	.	-	.	ID=gene1461;Name=RP1-309K20.5-004;name2=RBM12
chr20	ENCODE	CDS	33705786	33706658	.	-	0	Parent=gene1461
chr20	ENCODE	exon	33705786	33706680	.	-	.	Parent=gene1461
chr20	ENCODE	exon	33710266	33710350	.	-	.	Parent=gene1461
chr20	ENCODE	exon	33716138	33716225	.	-	.	Parent=gene1461
###
chr20	ENCODE	gene	33710266	33716236	.	-	.	ID=gene1462;Name=RP1-309K20.2-024;name2=CPNE1
chr20	ENCODE	exon	33710266	33710350	.	-	.	Parent=gene1462
chr20	ENCODE	exon	33715695	33716236	.	-	.	Parent=gene1462
###
chr20	ENCODE	gene	33720024	33750695	.	-	.	ID=gene1463;Name=RP1-309K20.1-001;name2=NFS1
chr20	ENCODE	exon	33720024	33721021	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33720958	33721021	.	-	1	Parent=gene1463
chr20	ENCODE	exon	33724091	33724180	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33724091	33724180	.	-	1	Parent=gene1463
chr20	ENCODE	exon	33724937	33725020	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33724937	33725020	.	-	1	Parent=gene1463
chr20	ENCODE	exon	33725686	33725767	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33725686	33725767	.	-	2	Parent=gene1463
chr20	ENCODE	exon	33725848	33725953	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33725848	33725953	.	-	0	Parent=gene1463
chr20	ENCODE	exon	33726381	33726538	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33726381	33726538	.	-	2	Parent=gene1463
chr20	ENCODE	exon	33732073	33732207	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33732073	33732207	.	-	2	Parent=gene1463
chr20	ENCODE	exon	33733224	33733317	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33733224	33733317	.	-	0	Parent=gene1463
chr20	ENCODE	exon	33741749	33741901	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33741749	33741901	.	-	0	Parent=gene1463
chr20	ENCODE	exon	33747713	33747796	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33747713	33747796	.	-	0	Parent=gene1463
chr20	ENCODE	exon	33749020	33749136	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33749020	33749136	.	-	0	Parent=gene1463
chr20	ENCODE	exon	33749817	33749926	.	-	.	Parent=gene1463
chr20	ENCODE	CDS	33749817	33749926	.	-	2	Parent=gene1463
chr20	ENCODE	CDS	33750528	33750624	.	-	0	Parent=gene1463
chr20	ENCODE	exon	33750528	33750695	.	-	.	Parent=gene1463
###
chr20	ENCODE	gene	33720035	33750525	.	-	.	ID=gene1464;Name=RP1-309K20.1-003;name2=NFS1
chr20	ENCODE	exon	33720035	33721021	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33720958	33721021	.	-	1	Parent=gene1464
chr20	ENCODE	exon	33724091	33724180	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33724091	33724180	.	-	1	Parent=gene1464
chr20	ENCODE	exon	33724937	33725020	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33724937	33725020	.	-	1	Parent=gene1464
chr20	ENCODE	exon	33725686	33725767	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33725686	33725767	.	-	2	Parent=gene1464
chr20	ENCODE	exon	33725848	33725953	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33725848	33725953	.	-	0	Parent=gene1464
chr20	ENCODE	exon	33726381	33726538	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33726381	33726538	.	-	2	Parent=gene1464
chr20	ENCODE	exon	33732073	33732207	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33732073	33732207	.	-	2	Parent=gene1464
chr20	ENCODE	exon	33733224	33733317	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33733224	33733317	.	-	0	Parent=gene1464
chr20	ENCODE	exon	33741749	33741901	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33741749	33741901	.	-	0	Parent=gene1464
chr20	ENCODE	exon	33747713	33747796	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33747713	33747796	.	-	0	Parent=gene1464
chr20	ENCODE	exon	33749020	33749136	.	-	.	Parent=gene1464
chr20	ENCODE	CDS	33749020	33749136	.	-	0	Parent=gene1464
chr20	ENCODE	CDS	33749817	33749843	.	-	0	Parent=gene1464
chr20	ENCODE	exon	33749817	33749926	.	-	.	Parent=gene1464
chr20	ENCODE	exon	33750081	33750525	.	-	.	Parent=gene1464
###
chr20	ENCODE	gene	33720300	33725402	.	-	.	ID=gene1465;Name=RP1-309K20.1-005;name2=NFS1
chr20	ENCODE	exon	33720300	33721021	.	-	.	Parent=gene1465
chr20	ENCODE	exon	33724091	33724180	.	-	.	Parent=gene1465
chr20	ENCODE	exon	33724937	33725020	.	-	.	Parent=gene1465
chr20	ENCODE	exon	33725322	33725402	.	-	.	Parent=gene1465
###
chr20	ENCODE	gene	33720300	33727522	.	-	.	ID=gene1466;Name=RP1-309K20.1-004;name2=NFS1
chr20	ENCODE	exon	33720300	33721021	.	-	.	Parent=gene1466
chr20	ENCODE	exon	33724091	33724180	.	-	.	Parent=gene1466
chr20	ENCODE	exon	33724937	33725020	.	-	.	Parent=gene1466
chr20	ENCODE	exon	33725686	33725767	.	-	.	Parent=gene1466
chr20	ENCODE	exon	33725848	33727522	.	-	.	Parent=gene1466
###
chr20	ENCODE	gene	33720319	33750685	.	-	.	ID=gene1467;Name=RP1-309K20.1-009;name2=NFS1
chr20	ENCODE	exon	33720319	33721021	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33720958	33721021	.	-	1	Parent=gene1467
chr20	ENCODE	exon	33724091	33724180	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33724091	33724180	.	-	1	Parent=gene1467
chr20	ENCODE	exon	33724937	33725020	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33724937	33725020	.	-	1	Parent=gene1467
chr20	ENCODE	exon	33725686	33725767	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33725686	33725767	.	-	2	Parent=gene1467
chr20	ENCODE	exon	33725848	33725953	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33725848	33725953	.	-	0	Parent=gene1467
chr20	ENCODE	exon	33726381	33726538	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33726381	33726538	.	-	2	Parent=gene1467
chr20	ENCODE	exon	33732073	33732207	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33732073	33732207	.	-	2	Parent=gene1467
chr20	ENCODE	exon	33733224	33733317	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33733224	33733317	.	-	0	Parent=gene1467
chr20	ENCODE	exon	33741749	33741901	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33741749	33741901	.	-	0	Parent=gene1467
chr20	ENCODE	exon	33747713	33747796	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33747713	33747796	.	-	0	Parent=gene1467
chr20	ENCODE	exon	33749020	33749136	.	-	.	Parent=gene1467
chr20	ENCODE	CDS	33749020	33749136	.	-	0	Parent=gene1467
chr20	ENCODE	CDS	33749817	33749843	.	-	0	Parent=gene1467
chr20	ENCODE	exon	33749817	33749926	.	-	.	Parent=gene1467
chr20	ENCODE	exon	33750646	33750685	.	-	.	Parent=gene1467
###
chr20	ENCODE	gene	33720329	33750691	.	-	.	ID=gene1468;Name=RP1-309K20.1-002;name2=NFS1
chr20	ENCODE	exon	33720329	33721021	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33724091	33724180	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33724937	33725020	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33725686	33725767	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33725848	33725953	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33732073	33732207	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33733224	33733317	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33741749	33741901	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33747713	33747796	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33749020	33749136	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33749817	33749926	.	-	.	Parent=gene1468
chr20	ENCODE	exon	33750646	33750691	.	-	.	Parent=gene1468
###
chr20	ENCODE	gene	33725094	33726134	.	-	.	ID=gene1469;Name=RP1-309K20.1-008;name2=NFS1
chr20	ENCODE	exon	33725094	33725767	.	-	.	Parent=gene1469
chr20	ENCODE	exon	33725848	33726134	.	-	.	Parent=gene1469
###
chr20	ENCODE	gene	33725867	33734127	.	-	.	ID=gene1470;Name=RP1-309K20.1-007;name2=NFS1
chr20	ENCODE	exon	33725867	33725953	.	-	.	Parent=gene1470
chr20	ENCODE	exon	33726381	33726538	.	-	.	Parent=gene1470
chr20	ENCODE	exon	33732073	33732207	.	-	.	Parent=gene1470
chr20	ENCODE	exon	33733224	33733317	.	-	.	Parent=gene1470
chr20	ENCODE	exon	33734000	33734127	.	-	.	Parent=gene1470
###
chr20	ENCODE	gene	33733301	33750688	.	-	.	ID=gene1471;Name=RP1-309K20.1-011;name2=NFS1
chr20	ENCODE	exon	33733301	33733317	.	-	.	Parent=gene1471
chr20	ENCODE	exon	33741749	33741901	.	-	.	Parent=gene1471
chr20	ENCODE	exon	33743585	33743706	.	-	.	Parent=gene1471
chr20	ENCODE	exon	33747713	33747796	.	-	.	Parent=gene1471
chr20	ENCODE	exon	33749020	33749136	.	-	.	Parent=gene1471
chr20	ENCODE	exon	33749817	33749926	.	-	.	Parent=gene1471
chr20	ENCODE	exon	33750646	33750688	.	-	.	Parent=gene1471
###
chr20	ENCODE	gene	33741749	33750688	.	-	.	ID=gene1472;Name=RP1-309K20.1-012;name2=NFS1
chr20	ENCODE	exon	33741749	33741901	.	-	.	Parent=gene1472
chr20	ENCODE	exon	33743585	33743706	.	-	.	Parent=gene1472
chr20	ENCODE	exon	33747713	33747796	.	-	.	Parent=gene1472
chr20	ENCODE	exon	33749020	33749136	.	-	.	Parent=gene1472
chr20	ENCODE	exon	33749817	33749926	.	-	.	Parent=gene1472
chr20	ENCODE	exon	33750528	33750688	.	-	.	Parent=gene1472
###
chr20	ENCODE	gene	33741807	33750525	.	-	.	ID=gene1473;Name=RP1-309K20.1-013;name2=NFS1
chr20	ENCODE	exon	33741807	33741901	.	-	.	Parent=gene1473
chr20	ENCODE	CDS	33741807	33741901	.	-	0	Parent=gene1473
chr20	ENCODE	exon	33747713	33747796	.	-	.	Parent=gene1473
chr20	ENCODE	CDS	33747713	33747796	.	-	0	Parent=gene1473
chr20	ENCODE	exon	33749020	33749136	.	-	.	Parent=gene1473
chr20	ENCODE	CDS	33749020	33749136	.	-	0	Parent=gene1473
chr20	ENCODE	CDS	33749817	33749843	.	-	0	Parent=gene1473
chr20	ENCODE	exon	33749817	33749926	.	-	.	Parent=gene1473
chr20	ENCODE	exon	33750381	33750525	.	-	.	Parent=gene1473
###
chr20	ENCODE	gene	33741862	33750691	.	-	.	ID=gene1474;Name=RP1-309K20.1-010;name2=NFS1
chr20	ENCODE	exon	33741862	33741901	.	-	.	Parent=gene1474
chr20	ENCODE	exon	33743585	33743632	.	-	.	Parent=gene1474
chr20	ENCODE	exon	33747713	33747796	.	-	.	Parent=gene1474
chr20	ENCODE	exon	33749020	33749136	.	-	.	Parent=gene1474
chr20	ENCODE	exon	33749817	33749926	.	-	.	Parent=gene1474
chr20	ENCODE	exon	33750528	33750691	.	-	.	Parent=gene1474
###
chr20	ENCODE	gene	33745908	33750640	.	-	.	ID=gene1475;Name=RP1-309K20.1-006;name2=NFS1
chr20	ENCODE	exon	33745908	33746221	.	-	.	Parent=gene1475
chr20	ENCODE	CDS	33746060	33746221	.	-	0	Parent=gene1475
chr20	ENCODE	exon	33747713	33747796	.	-	.	Parent=gene1475
chr20	ENCODE	CDS	33747713	33747796	.	-	0	Parent=gene1475
chr20	ENCODE	exon	33749020	33749136	.	-	.	Parent=gene1475
chr20	ENCODE	CDS	33749020	33749136	.	-	0	Parent=gene1475
chr20	ENCODE	exon	33749817	33749926	.	-	.	Parent=gene1475
chr20	ENCODE	CDS	33749817	33749926	.	-	2	Parent=gene1475
chr20	ENCODE	CDS	33750528	33750624	.	-	0	Parent=gene1475
chr20	ENCODE	exon	33750528	33750640	.	-	.	Parent=gene1475
###
chr20	ENCODE	gene	33750608	33752320	.	+	.	ID=gene1476;Name=RP11-353C18.54-003;name2=C20orf52
chr20	ENCODE	exon	33750608	33750787	.	+	.	Parent=gene1476
chr20	ENCODE	exon	33750969	33751099	.	+	.	Parent=gene1476
chr20	ENCODE	CDS	33750969	33751099	.	+	0	Parent=gene1476
chr20	ENCODE	CDS	33752134	33752242	.	+	1	Parent=gene1476
chr20	ENCODE	exon	33752134	33752320	.	+	.	Parent=gene1476
###
chr20	ENCODE	gene	33750689	33752320	.	+	.	ID=gene1477;name2=C20orf52;Name=RP11-353C18.54-001
chr20	ENCODE	exon	33750689	33750792	.	+	.	Parent=gene1477
chr20	ENCODE	exon	33750969	33751099	.	+	.	Parent=gene1477
chr20	ENCODE	CDS	33750969	33751099	.	+	0	Parent=gene1477
chr20	ENCODE	CDS	33752134	33752242	.	+	1	Parent=gene1477
chr20	ENCODE	exon	33752134	33752320	.	+	.	Parent=gene1477
###
chr20	ENCODE	gene	33750778	33752314	.	+	.	ID=gene1478;Name=RP11-353C18.54-004;name2=C20orf52
chr20	ENCODE	exon	33750778	33750792	.	+	.	Parent=gene1478
chr20	ENCODE	exon	33750969	33751099	.	+	.	Parent=gene1478
chr20	ENCODE	CDS	33750969	33751099	.	+	0	Parent=gene1478
chr20	ENCODE	CDS	33752111	33752159	.	+	1	Parent=gene1478
chr20	ENCODE	exon	33752111	33752314	.	+	.	Parent=gene1478
###
chr20	ENCODE	gene	33750787	33752316	.	+	.	ID=gene1479;Name=RP11-353C18.54-002;name2=C20orf52
chr20	ENCODE	exon	33750787	33751099	.	+	.	Parent=gene1479
chr20	ENCODE	CDS	33750969	33751099	.	+	0	Parent=gene1479
chr20	ENCODE	CDS	33752134	33752242	.	+	1	Parent=gene1479
chr20	ENCODE	exon	33752134	33752316	.	+	.	Parent=gene1479
###
chr20	ENCODE	gene	33754946	33790373	.	-	.	ID=gene1480;Name=RP11-353C18.2-009;name2=RBM39
chr20	ENCODE	exon	33754946	33755917	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33760560	33760592	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33768076	33768141	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1480
chr20	ENCODE	exon	33790304	33790373	.	-	.	Parent=gene1480
###
chr20	ENCODE	gene	33754946	33793287	.	-	.	ID=gene1481;Name=RP11-353C18.2-002;name2=RBM39
chr20	ENCODE	exon	33754946	33755917	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33755817	33755917	.	-	2	Parent=gene1481
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33756004	33756082	.	-	0	Parent=gene1481
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33756561	33756666	.	-	1	Parent=gene1481
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33758456	33758537	.	-	2	Parent=gene1481
chr20	ENCODE	exon	33760560	33760610	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33760560	33760610	.	-	2	Parent=gene1481
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33764355	33764432	.	-	2	Parent=gene1481
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33765521	33765725	.	-	0	Parent=gene1481
chr20	ENCODE	exon	33768076	33768141	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33768076	33768141	.	-	0	Parent=gene1481
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33773076	33773213	.	-	0	Parent=gene1481
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33775906	33776058	.	-	0	Parent=gene1481
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33776374	33776491	.	-	1	Parent=gene1481
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33780648	33780701	.	-	1	Parent=gene1481
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33780798	33780863	.	-	1	Parent=gene1481
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33783277	33783471	.	-	1	Parent=gene1481
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1481
chr20	ENCODE	CDS	33790304	33790353	.	-	0	Parent=gene1481
chr20	ENCODE	CDS	33792160	33792210	.	-	0	Parent=gene1481
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1481
chr20	ENCODE	exon	33793277	33793287	.	-	.	Parent=gene1481
###
chr20	ENCODE	gene	33754946	33793648	.	-	.	ID=gene1482;Name=RP11-353C18.2-001;name2=RBM39
chr20	ENCODE	exon	33754946	33755917	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33755817	33755917	.	-	2	Parent=gene1482
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33756004	33756082	.	-	0	Parent=gene1482
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33756561	33756666	.	-	1	Parent=gene1482
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33758456	33758537	.	-	2	Parent=gene1482
chr20	ENCODE	exon	33760560	33760592	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33760560	33760592	.	-	2	Parent=gene1482
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33764355	33764432	.	-	2	Parent=gene1482
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33765521	33765725	.	-	0	Parent=gene1482
chr20	ENCODE	exon	33768076	33768141	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33768076	33768141	.	-	0	Parent=gene1482
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33773076	33773213	.	-	0	Parent=gene1482
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33775906	33776058	.	-	0	Parent=gene1482
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33776374	33776491	.	-	1	Parent=gene1482
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33780648	33780701	.	-	1	Parent=gene1482
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33780798	33780863	.	-	1	Parent=gene1482
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33783277	33783471	.	-	1	Parent=gene1482
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1482
chr20	ENCODE	CDS	33790304	33790353	.	-	0	Parent=gene1482
chr20	ENCODE	CDS	33792160	33792210	.	-	0	Parent=gene1482
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1482
chr20	ENCODE	exon	33793277	33793648	.	-	.	Parent=gene1482
###
chr20	ENCODE	gene	33754947	33793557	.	-	.	ID=gene1483;Name=RP11-353C18.2-008;name2=RBM39
chr20	ENCODE	exon	33754947	33755917	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33759276	33759328	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33760560	33760592	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33768076	33768141	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1483
chr20	ENCODE	exon	33793277	33793557	.	-	.	Parent=gene1483
###
chr20	ENCODE	gene	33754947	33793610	.	-	.	ID=gene1484;Name=RP11-353C18.2-006;name2=RBM39
chr20	ENCODE	exon	33754947	33755917	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33760560	33760610	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33768076	33768141	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33791861	33791933	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1484
chr20	ENCODE	exon	33793277	33793610	.	-	.	Parent=gene1484
###
chr20	ENCODE	gene	33755662	33764539	.	-	.	ID=gene1485;Name=RP11-353C18.2-032;name2=RBM39
chr20	ENCODE	exon	33755662	33755917	.	-	.	Parent=gene1485
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1485
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1485
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1485
chr20	ENCODE	exon	33760560	33760610	.	-	.	Parent=gene1485
chr20	ENCODE	exon	33764355	33764539	.	-	.	Parent=gene1485
###
chr20	ENCODE	gene	33755662	33765587	.	-	.	ID=gene1486;Name=RP11-353C18.2-029;name2=RBM39
chr20	ENCODE	exon	33755662	33755917	.	-	.	Parent=gene1486
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1486
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1486
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1486
chr20	ENCODE	exon	33760560	33760645	.	-	.	Parent=gene1486
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1486
chr20	ENCODE	exon	33765521	33765587	.	-	.	Parent=gene1486
###
chr20	ENCODE	gene	33755662	33793584	.	-	.	ID=gene1487;Name=RP11-353C18.2-007;name2=RBM39
chr20	ENCODE	exon	33755662	33755917	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33760560	33760592	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33768076	33768141	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33791861	33791933	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1487
chr20	ENCODE	exon	33793277	33793584	.	-	.	Parent=gene1487
###
chr20	ENCODE	gene	33755662	33793592	.	-	.	ID=gene1488;Name=RP11-353C18.2-005;name2=RBM39
chr20	ENCODE	exon	33755662	33755917	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33760560	33760610	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33768076	33768141	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33785522	33785593	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1488
chr20	ENCODE	exon	33793277	33793592	.	-	.	Parent=gene1488
###
chr20	ENCODE	gene	33755664	33784142	.	-	.	ID=gene1489;Name=RP11-353C18.2-010;name2=RBM39
chr20	ENCODE	exon	33755664	33755917	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33760560	33760610	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33768076	33768141	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1489
chr20	ENCODE	exon	33783277	33784142	.	-	.	Parent=gene1489
###
chr20	ENCODE	gene	33755713	33758697	.	-	.	ID=gene1490;Name=RP11-353C18.2-033;name2=RBM39
chr20	ENCODE	exon	33755713	33755917	.	-	.	Parent=gene1490
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1490
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1490
chr20	ENCODE	exon	33758456	33758697	.	-	.	Parent=gene1490
###
chr20	ENCODE	gene	33755713	33759324	.	-	.	ID=gene1491;Name=RP11-353C18.2-011;name2=RBM39
chr20	ENCODE	exon	33755713	33755917	.	-	.	Parent=gene1491
chr20	ENCODE	exon	33756004	33756666	.	-	.	Parent=gene1491
chr20	ENCODE	exon	33758456	33759324	.	-	.	Parent=gene1491
###
chr20	ENCODE	gene	33755736	33756735	.	-	.	ID=gene1492;name2=RBM39;Name=RP11-353C18.2-034
chr20	ENCODE	exon	33755736	33755917	.	-	.	Parent=gene1492
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1492
chr20	ENCODE	exon	33756561	33756735	.	-	.	Parent=gene1492
###
chr20	ENCODE	gene	33755741	33764702	.	-	.	ID=gene1493;Name=RP11-353C18.2-031;name2=RBM39
chr20	ENCODE	exon	33755741	33755917	.	-	.	Parent=gene1493
chr20	ENCODE	exon	33756004	33756082	.	-	.	Parent=gene1493
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1493
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1493
chr20	ENCODE	exon	33760560	33760592	.	-	.	Parent=gene1493
chr20	ENCODE	exon	33764355	33764702	.	-	.	Parent=gene1493
###
chr20	ENCODE	gene	33756039	33780680	.	-	.	ID=gene1494;Name=RP11-353C18.2-035;name2=RBM39
chr20	ENCODE	exon	33756039	33756082	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33756039	33756082	.	-	2	Parent=gene1494
chr20	ENCODE	exon	33756561	33756666	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33756561	33756666	.	-	0	Parent=gene1494
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33758456	33758537	.	-	1	Parent=gene1494
chr20	ENCODE	exon	33760560	33760610	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33760560	33760610	.	-	1	Parent=gene1494
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33764355	33764432	.	-	1	Parent=gene1494
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33765521	33765725	.	-	2	Parent=gene1494
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33773076	33773213	.	-	2	Parent=gene1494
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33775906	33776058	.	-	2	Parent=gene1494
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33776374	33776491	.	-	0	Parent=gene1494
chr20	ENCODE	exon	33780648	33780680	.	-	.	Parent=gene1494
chr20	ENCODE	CDS	33780648	33780680	.	-	0	Parent=gene1494
###
chr20	ENCODE	gene	33756598	33764751	.	-	.	ID=gene1495;Name=RP11-353C18.2-027;name2=RBM39
chr20	ENCODE	exon	33756598	33756666	.	-	.	Parent=gene1495
chr20	ENCODE	exon	33758456	33758537	.	-	.	Parent=gene1495
chr20	ENCODE	exon	33760560	33760592	.	-	.	Parent=gene1495
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1495
chr20	ENCODE	exon	33764630	33764751	.	-	.	Parent=gene1495
###
chr20	ENCODE	gene	33760140	33764432	.	-	.	ID=gene1496;Name=RP11-353C18.2-030;name2=RBM39
chr20	ENCODE	exon	33760140	33760610	.	-	.	Parent=gene1496
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1496
###
chr20	ENCODE	gene	33760328	33761902	.	-	.	ID=gene1497;Name=RP11-353C18.2-041;name2=RBM39
chr20	ENCODE	exon	33760328	33760592	.	-	.	Parent=gene1497
chr20	ENCODE	exon	33761619	33761902	.	-	.	Parent=gene1497
###
chr20	ENCODE	gene	33760369	33768123	.	-	.	ID=gene1498;Name=RP11-353C18.2-028;name2=RBM39
chr20	ENCODE	exon	33760369	33760592	.	-	.	Parent=gene1498
chr20	ENCODE	exon	33764355	33764432	.	-	.	Parent=gene1498
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1498
chr20	ENCODE	exon	33768076	33768123	.	-	.	Parent=gene1498
###
chr20	ENCODE	gene	33764654	33776399	.	-	.	ID=gene1499;Name=RP11-353C18.2-040;name2=RBM39
chr20	ENCODE	exon	33764654	33764743	.	-	.	Parent=gene1499
chr20	ENCODE	exon	33765168	33765193	.	-	.	Parent=gene1499
chr20	ENCODE	exon	33765521	33765725	.	-	.	Parent=gene1499
chr20	ENCODE	exon	33768076	33768141	.	-	.	Parent=gene1499
chr20	ENCODE	exon	33773076	33773213	.	-	.	Parent=gene1499
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1499
chr20	ENCODE	exon	33776374	33776399	.	-	.	Parent=gene1499
###
chr20	ENCODE	gene	33765144	33765689	.	-	.	ID=gene1500;Name=RP11-353C18.2-036;name2=RBM39
chr20	ENCODE	exon	33765144	33765193	.	-	.	Parent=gene1500
chr20	ENCODE	exon	33765521	33765689	.	-	.	Parent=gene1500
###
chr20	ENCODE	gene	33773203	33793594	.	-	.	ID=gene1501;Name=RP11-353C18.2-020;name2=RBM39
chr20	ENCODE	exon	33773203	33773213	.	-	.	Parent=gene1501
chr20	ENCODE	CDS	33773203	33773213	.	-	0	Parent=gene1501
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1501
chr20	ENCODE	CDS	33775906	33776058	.	-	0	Parent=gene1501
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1501
chr20	ENCODE	CDS	33776374	33776491	.	-	1	Parent=gene1501
chr20	ENCODE	exon	33780648	33780698	.	-	.	Parent=gene1501
chr20	ENCODE	CDS	33780648	33780698	.	-	1	Parent=gene1501
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1501
chr20	ENCODE	CDS	33780798	33780863	.	-	1	Parent=gene1501
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1501
chr20	ENCODE	CDS	33783277	33783471	.	-	1	Parent=gene1501
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1501
chr20	ENCODE	CDS	33790304	33790353	.	-	0	Parent=gene1501
chr20	ENCODE	CDS	33792160	33792210	.	-	0	Parent=gene1501
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1501
chr20	ENCODE	exon	33793277	33793594	.	-	.	Parent=gene1501
###
chr20	ENCODE	gene	33775906	33793449	.	-	.	ID=gene1502;Name=RP11-353C18.2-017;name2=RBM39
chr20	ENCODE	exon	33775906	33776058	.	-	.	Parent=gene1502
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1502
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1502
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1502
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1502
chr20	ENCODE	exon	33785522	33785593	.	-	.	Parent=gene1502
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1502
chr20	ENCODE	exon	33791861	33791933	.	-	.	Parent=gene1502
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1502
chr20	ENCODE	exon	33793277	33793449	.	-	.	Parent=gene1502
###
chr20	ENCODE	gene	33775921	33793572	.	-	.	ID=gene1503;name2=RBM39;Name=RP11-353C18.2-015
chr20	ENCODE	exon	33775921	33776058	.	-	.	Parent=gene1503
chr20	ENCODE	CDS	33775921	33776058	.	-	0	Parent=gene1503
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1503
chr20	ENCODE	CDS	33776374	33776491	.	-	1	Parent=gene1503
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1503
chr20	ENCODE	CDS	33780648	33780701	.	-	1	Parent=gene1503
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1503
chr20	ENCODE	CDS	33783277	33783471	.	-	1	Parent=gene1503
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1503
chr20	ENCODE	CDS	33790304	33790353	.	-	0	Parent=gene1503
chr20	ENCODE	CDS	33792160	33792210	.	-	0	Parent=gene1503
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1503
chr20	ENCODE	exon	33793277	33793572	.	-	.	Parent=gene1503
###
chr20	ENCODE	gene	33776012	33792945	.	-	.	ID=gene1504;Name=RP11-353C18.2-018;name2=RBM39
chr20	ENCODE	exon	33776012	33776058	.	-	.	Parent=gene1504
chr20	ENCODE	CDS	33776012	33776058	.	-	0	Parent=gene1504
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1504
chr20	ENCODE	CDS	33776374	33776491	.	-	1	Parent=gene1504
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1504
chr20	ENCODE	CDS	33780648	33780701	.	-	1	Parent=gene1504
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1504
chr20	ENCODE	CDS	33780798	33780863	.	-	1	Parent=gene1504
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1504
chr20	ENCODE	CDS	33783277	33783471	.	-	1	Parent=gene1504
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1504
chr20	ENCODE	CDS	33790304	33790353	.	-	0	Parent=gene1504
chr20	ENCODE	CDS	33792160	33792210	.	-	0	Parent=gene1504
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1504
chr20	ENCODE	exon	33792824	33792945	.	-	.	Parent=gene1504
###
chr20	ENCODE	gene	33776051	33790924	.	-	.	ID=gene1505;Name=RP11-353C18.2-023;name2=RBM39
chr20	ENCODE	exon	33776051	33776058	.	-	.	Parent=gene1505
chr20	ENCODE	exon	33776374	33776491	.	-	.	Parent=gene1505
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1505
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1505
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1505
chr20	ENCODE	exon	33790304	33790924	.	-	.	Parent=gene1505
###
chr20	ENCODE	gene	33776401	33791933	.	-	.	ID=gene1506;Name=RP11-353C18.2-021;name2=RBM39
chr20	ENCODE	exon	33776401	33776491	.	-	.	Parent=gene1506
chr20	ENCODE	exon	33780648	33780698	.	-	.	Parent=gene1506
chr20	ENCODE	exon	33780798	33780863	.	-	.	Parent=gene1506
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1506
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1506
chr20	ENCODE	exon	33791861	33791933	.	-	.	Parent=gene1506
###
chr20	ENCODE	gene	33776460	33790619	.	-	.	ID=gene1507;Name=RP11-353C18.2-022;name2=RBM39
chr20	ENCODE	exon	33776460	33776491	.	-	.	Parent=gene1507
chr20	ENCODE	exon	33780648	33780701	.	-	.	Parent=gene1507
chr20	ENCODE	exon	33780798	33780887	.	-	.	Parent=gene1507
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1507
chr20	ENCODE	exon	33790304	33790619	.	-	.	Parent=gene1507
###
chr20	ENCODE	gene	33780658	33793294	.	-	.	ID=gene1508;name2=RBM39;Name=RP11-353C18.2-019
chr20	ENCODE	exon	33780658	33780698	.	-	.	Parent=gene1508
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1508
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1508
chr20	ENCODE	exon	33791861	33791933	.	-	.	Parent=gene1508
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1508
chr20	ENCODE	exon	33793277	33793294	.	-	.	Parent=gene1508
###
chr20	ENCODE	gene	33782696	33790476	.	-	.	ID=gene1509;name2=RBM39;Name=RP11-353C18.2-026
chr20	ENCODE	exon	33782696	33783471	.	-	.	Parent=gene1509
chr20	ENCODE	exon	33790304	33790476	.	-	.	Parent=gene1509
###
chr20	ENCODE	gene	33782696	33792173	.	-	.	ID=gene1510;Name=RP11-353C18.2-039;name2=RBM39
chr20	ENCODE	exon	33782696	33783471	.	-	.	Parent=gene1510
chr20	ENCODE	CDS	33783276	33783471	.	-	2	Parent=gene1510
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1510
chr20	ENCODE	CDS	33790304	33790353	.	-	1	Parent=gene1510
chr20	ENCODE	exon	33792160	33792173	.	-	.	Parent=gene1510
chr20	ENCODE	CDS	33792160	33792173	.	-	0	Parent=gene1510
###
chr20	ENCODE	gene	33783252	33793514	.	-	.	ID=gene1511;Name=RP11-353C18.2-016;name2=RBM39
chr20	ENCODE	exon	33783252	33783471	.	-	.	Parent=gene1511
chr20	ENCODE	exon	33785522	33785593	.	-	.	Parent=gene1511
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1511
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1511
chr20	ENCODE	exon	33793277	33793514	.	-	.	Parent=gene1511
###
chr20	ENCODE	gene	33783277	33792226	.	-	.	ID=gene1512;Name=RP11-353C18.2-038;name2=RBM39
chr20	ENCODE	exon	33783277	33783471	.	-	.	Parent=gene1512
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1512
chr20	ENCODE	exon	33792160	33792226	.	-	.	Parent=gene1512
###
chr20	ENCODE	gene	33783396	33790525	.	-	.	ID=gene1513;Name=RP11-353C18.2-025;name2=RBM39
chr20	ENCODE	exon	33783396	33783471	.	-	.	Parent=gene1513
chr20	ENCODE	exon	33785522	33785593	.	-	.	Parent=gene1513
chr20	ENCODE	exon	33790304	33790525	.	-	.	Parent=gene1513
###
chr20	ENCODE	gene	33785855	33793594	.	-	.	ID=gene1514;name2=RBM39;Name=RP11-353C18.2-012
chr20	ENCODE	exon	33785855	33786417	.	-	.	Parent=gene1514
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1514
chr20	ENCODE	exon	33791861	33791933	.	-	.	Parent=gene1514
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1514
chr20	ENCODE	exon	33793277	33793594	.	-	.	Parent=gene1514
###
chr20	ENCODE	gene	33786103	33787977	.	-	.	ID=gene1515;Name=RP11-353C18.2-037;name2=RBM39
chr20	ENCODE	exon	33786103	33786417	.	-	.	Parent=gene1515
chr20	ENCODE	exon	33787849	33787977	.	-	.	Parent=gene1515
###
chr20	ENCODE	gene	33786132	33793315	.	-	.	ID=gene1516;Name=RP11-353C18.2-024;name2=RBM39
chr20	ENCODE	exon	33786132	33786417	.	-	.	Parent=gene1516
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1516
chr20	ENCODE	exon	33790729	33790883	.	-	.	Parent=gene1516
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1516
chr20	ENCODE	exon	33793277	33793315	.	-	.	Parent=gene1516
###
chr20	ENCODE	gene	33786212	33793568	.	-	.	ID=gene1517;Name=RP11-353C18.2-013;name2=RBM39
chr20	ENCODE	exon	33786212	33786417	.	-	.	Parent=gene1517
chr20	ENCODE	CDS	33786231	33786417	.	-	1	Parent=gene1517
chr20	ENCODE	exon	33790304	33790353	.	-	.	Parent=gene1517
chr20	ENCODE	CDS	33790304	33790353	.	-	0	Parent=gene1517
chr20	ENCODE	CDS	33792160	33792210	.	-	0	Parent=gene1517
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1517
chr20	ENCODE	exon	33793277	33793568	.	-	.	Parent=gene1517
###
chr20	ENCODE	gene	33790564	33793557	.	-	.	ID=gene1518;Name=RP11-353C18.2-003;name2=RBM39
chr20	ENCODE	exon	33790564	33790883	.	-	.	Parent=gene1518
chr20	ENCODE	exon	33791861	33791933	.	-	.	Parent=gene1518
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1518
chr20	ENCODE	exon	33793277	33793557	.	-	.	Parent=gene1518
###
chr20	ENCODE	gene	33791435	33793574	.	-	.	ID=gene1519;Name=RP11-353C18.2-014;name2=RBM39
chr20	ENCODE	exon	33791435	33791933	.	-	.	Parent=gene1519
chr20	ENCODE	exon	33792160	33792223	.	-	.	Parent=gene1519
chr20	ENCODE	exon	33793277	33793574	.	-	.	Parent=gene1519
###
chr20	ENCODE	gene	33791547	33793600	.	-	.	ID=gene1520;Name=RP11-353C18.2-004;name2=RBM39
chr20	ENCODE	exon	33791547	33792223	.	-	.	Parent=gene1520
chr20	ENCODE	exon	33793277	33793600	.	-	.	Parent=gene1520
###
chr21	ENCODE	gene	32669578	32687206	.	-	.	ID=gene1521;Name=AP000266.110-001;name2=URB1
chr21	ENCODE	exon	32669578	32669663	.	-	.	Parent=gene1521
chr21	ENCODE	exon	32672625	32672721	.	-	.	Parent=gene1521
chr21	ENCODE	exon	32677602	32677734	.	-	.	Parent=gene1521
chr21	ENCODE	exon	32678493	32678644	.	-	.	Parent=gene1521
chr21	ENCODE	exon	32679725	32679864	.	-	.	Parent=gene1521
chr21	ENCODE	exon	32686949	32687206	.	-	.	Parent=gene1521
###
chr21	ENCODE	gene	32706185	32762234	.	+	.	ID=gene1522;Name=AP000272.65-004;name2=C21orf63
chr21	ENCODE	exon	32706185	32707192	.	+	.	Parent=gene1522
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene1522
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene1522
chr21	ENCODE	exon	32761875	32762234	.	+	.	Parent=gene1522
###
chr21	ENCODE	gene	32706221	32795636	.	+	.	ID=gene1523;Name=AP000272.65-009;name2=C21orf63
chr21	ENCODE	exon	32706221	32706372	.	+	.	Parent=gene1523
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene1523
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene1523
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene1523
chr21	ENCODE	exon	32795596	32795636	.	+	.	Parent=gene1523
###
chr21	ENCODE	gene	32706560	32809570	.	+	.	ID=gene1524;Name=AP000272.65-001;name2=C21orf63
chr21	ENCODE	exon	32706560	32707192	.	+	.	Parent=gene1524
chr21	ENCODE	CDS	32707033	32707192	.	+	0	Parent=gene1524
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene1524
chr21	ENCODE	CDS	32747491	32747687	.	+	2	Parent=gene1524
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene1524
chr21	ENCODE	CDS	32751776	32751899	.	+	0	Parent=gene1524
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene1524
chr21	ENCODE	CDS	32761875	32762027	.	+	2	Parent=gene1524
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene1524
chr21	ENCODE	CDS	32789208	32789351	.	+	2	Parent=gene1524
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene1524
chr21	ENCODE	CDS	32795596	32795676	.	+	2	Parent=gene1524
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene1524
chr21	ENCODE	CDS	32798107	32798196	.	+	2	Parent=gene1524
chr21	ENCODE	CDS	32808995	32809371	.	+	2	Parent=gene1524
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene1524
###
chr21	ENCODE	gene	32706616	32809570	.	+	.	ID=gene1525;Name=AP000272.65-007;name2=C21orf63
chr21	ENCODE	exon	32706616	32707192	.	+	.	Parent=gene1525
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene1525
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene1525
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene1525
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene1525
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene1525
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene1525
###
chr21	ENCODE	gene	32706616	32809570	.	+	.	ID=gene1526;Name=AP000272.65-005;name2=C21orf63
chr21	ENCODE	exon	32706616	32707192	.	+	.	Parent=gene1526
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene1526
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene1526
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene1526
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene1526
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene1526
###
chr21	ENCODE	gene	32706732	32809570	.	+	.	ID=gene1527;Name=AP000272.65-006;name2=C21orf63
chr21	ENCODE	exon	32706732	32707192	.	+	.	Parent=gene1527
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene1527
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene1527
chr21	ENCODE	exon	32795596	32795719	.	+	.	Parent=gene1527
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene1527
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene1527
###
chr21	ENCODE	gene	32706881	32809570	.	+	.	ID=gene1528;Name=AP000272.65-002;name2=C21orf63
chr21	ENCODE	exon	32706881	32707192	.	+	.	Parent=gene1528
chr21	ENCODE	CDS	32707033	32707192	.	+	0	Parent=gene1528
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene1528
chr21	ENCODE	CDS	32747491	32747687	.	+	2	Parent=gene1528
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene1528
chr21	ENCODE	CDS	32751776	32751899	.	+	0	Parent=gene1528
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene1528
chr21	ENCODE	CDS	32761875	32762027	.	+	2	Parent=gene1528
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene1528
chr21	ENCODE	CDS	32789208	32789351	.	+	2	Parent=gene1528
chr21	ENCODE	exon	32795596	32795667	.	+	.	Parent=gene1528
chr21	ENCODE	CDS	32795596	32795667	.	+	2	Parent=gene1528
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene1528
chr21	ENCODE	CDS	32798107	32798196	.	+	2	Parent=gene1528
chr21	ENCODE	CDS	32808995	32809371	.	+	2	Parent=gene1528
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene1528
###
chr21	ENCODE	gene	32706943	32727463	.	+	.	ID=gene1529;Name=AP000272.65-010;name2=C21orf63
chr21	ENCODE	exon	32706943	32707192	.	+	.	Parent=gene1529
chr21	ENCODE	exon	32727330	32727463	.	+	.	Parent=gene1529
###
chr21	ENCODE	gene	32722513	32789318	.	+	.	ID=gene1530;Name=AP000272.65-008;name2=C21orf63
chr21	ENCODE	exon	32722513	32722863	.	+	.	Parent=gene1530
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene1530
chr21	ENCODE	CDS	32747616	32747687	.	+	0	Parent=gene1530
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene1530
chr21	ENCODE	CDS	32751776	32751899	.	+	0	Parent=gene1530
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene1530
chr21	ENCODE	CDS	32761875	32762027	.	+	2	Parent=gene1530
chr21	ENCODE	exon	32789208	32789318	.	+	.	Parent=gene1530
chr21	ENCODE	CDS	32789208	32789318	.	+	2	Parent=gene1530
###
chr21	ENCODE	gene	32746364	32809570	.	+	.	ID=gene1531;Name=AP000272.65-003;name2=C21orf63
chr21	ENCODE	exon	32746364	32747687	.	+	.	Parent=gene1531
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene1531
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene1531
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene1531
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene1531
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene1531
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene1531
###
chr21	ENCODE	gene	32787834	32809061	.	+	.	ID=gene1532;Name=AP000272.65-011;name2=C21orf63
chr21	ENCODE	exon	32787834	32787943	.	+	.	Parent=gene1532
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene1532
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene1532
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene1532
chr21	ENCODE	exon	32808995	32809061	.	+	.	Parent=gene1532
###
chr21	ENCODE	gene	32789298	32809570	.	+	.	ID=gene1533;Name=AP000272.65-012;name2=C21orf63
chr21	ENCODE	exon	32789298	32789351	.	+	.	Parent=gene1533
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene1533
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene1533
###
chr21	ENCODE	gene	32870733	32879714	.	-	.	ID=gene1534;Name=AP000274.7-001;name2=TCP10L
chr21	ENCODE	exon	32870733	32871104	.	-	.	Parent=gene1534
chr21	ENCODE	CDS	32870955	32871104	.	-	0	Parent=gene1534
chr21	ENCODE	exon	32872875	32873012	.	-	.	Parent=gene1534
chr21	ENCODE	CDS	32872875	32873012	.	-	0	Parent=gene1534
chr21	ENCODE	exon	32876381	32876596	.	-	.	Parent=gene1534
chr21	ENCODE	CDS	32876381	32876596	.	-	0	Parent=gene1534
chr21	ENCODE	CDS	32878342	32878485	.	-	0	Parent=gene1534
chr21	ENCODE	exon	32878342	32878486	.	-	.	Parent=gene1534
chr21	ENCODE	exon	32879602	32879714	.	-	.	Parent=gene1534
###
chr21	ENCODE	gene	32870840	32876615	.	-	.	ID=gene1535;Name=AP000274.7-002;name2=TCP10L
chr21	ENCODE	exon	32870840	32871104	.	-	.	Parent=gene1535
chr21	ENCODE	exon	32871607	32871857	.	-	.	Parent=gene1535
chr21	ENCODE	exon	32872875	32873012	.	-	.	Parent=gene1535
chr21	ENCODE	exon	32876381	32876615	.	-	.	Parent=gene1535
###
chr21	ENCODE	gene	32870840	32879714	.	-	.	ID=gene1536;Name=AP000274.7-003;name2=TCP10L
chr21	ENCODE	exon	32870840	32871104	.	-	.	Parent=gene1536
chr21	ENCODE	exon	32872875	32873012	.	-	.	Parent=gene1536
chr21	ENCODE	exon	32876381	32876596	.	-	.	Parent=gene1536
chr21	ENCODE	exon	32879602	32879714	.	-	.	Parent=gene1536
###
chr21	ENCODE	gene	32873003	32906327	.	-	.	ID=gene1537;Name=AP000274.7-005;name2=TCP10L
chr21	ENCODE	exon	32873003	32873012	.	-	.	Parent=gene1537
chr21	ENCODE	CDS	32873003	32873012	.	-	1	Parent=gene1537
chr21	ENCODE	exon	32876381	32876596	.	-	.	Parent=gene1537
chr21	ENCODE	CDS	32876381	32876596	.	-	1	Parent=gene1537
chr21	ENCODE	exon	32896453	32896548	.	-	.	Parent=gene1537
chr21	ENCODE	CDS	32896453	32896548	.	-	1	Parent=gene1537
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene1537
chr21	ENCODE	CDS	32897342	32897473	.	-	1	Parent=gene1537
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene1537
chr21	ENCODE	CDS	32898306	32898464	.	-	1	Parent=gene1537
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene1537
chr21	ENCODE	CDS	32901830	32901897	.	-	0	Parent=gene1537
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene1537
chr21	ENCODE	CDS	32904019	32904186	.	-	0	Parent=gene1537
chr21	ENCODE	exon	32906286	32906327	.	-	.	Parent=gene1537
chr21	ENCODE	CDS	32906286	32906327	.	-	0	Parent=gene1537
###
chr21	ENCODE	gene	32873004	32906462	.	-	.	ID=gene1538;Name=AP000274.7-004;name2=TCP10L
chr21	ENCODE	exon	32873004	32873012	.	-	.	Parent=gene1538
chr21	ENCODE	CDS	32873004	32873012	.	-	0	Parent=gene1538
chr21	ENCODE	exon	32876381	32876596	.	-	.	Parent=gene1538
chr21	ENCODE	CDS	32876381	32876596	.	-	0	Parent=gene1538
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene1538
chr21	ENCODE	CDS	32897342	32897473	.	-	0	Parent=gene1538
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene1538
chr21	ENCODE	CDS	32898306	32898464	.	-	0	Parent=gene1538
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene1538
chr21	ENCODE	CDS	32901830	32901897	.	-	2	Parent=gene1538
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene1538
chr21	ENCODE	CDS	32904019	32904186	.	-	2	Parent=gene1538
chr21	ENCODE	CDS	32906286	32906424	.	-	0	Parent=gene1538
chr21	ENCODE	exon	32906286	32906462	.	-	.	Parent=gene1538
###
chr21	ENCODE	gene	32876405	32901879	.	-	.	ID=gene1539;Name=AP000274.7-006;name2=TCP10L
chr21	ENCODE	exon	32876405	32876596	.	-	.	Parent=gene1539
chr21	ENCODE	CDS	32876405	32876596	.	-	1	Parent=gene1539
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene1539
chr21	ENCODE	CDS	32898306	32898464	.	-	1	Parent=gene1539
chr21	ENCODE	exon	32901830	32901879	.	-	.	Parent=gene1539
chr21	ENCODE	CDS	32901830	32901879	.	-	0	Parent=gene1539
###
chr21	ENCODE	gene	32886260	32897418	.	-	.	ID=gene1540;Name=AP000275.61-005;name2=C21orf59
chr21	ENCODE	exon	32886260	32886599	.	-	.	Parent=gene1540
chr21	ENCODE	exon	32897342	32897418	.	-	.	Parent=gene1540
###
chr21	ENCODE	gene	32895848	32898452	.	-	.	ID=gene1541;Name=AP000275.61-006;name2=C21orf59
chr21	ENCODE	exon	32895848	32896154	.	-	.	Parent=gene1541
chr21	ENCODE	CDS	32896044	32896154	.	-	0	Parent=gene1541
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene1541
chr21	ENCODE	CDS	32897342	32897473	.	-	0	Parent=gene1541
chr21	ENCODE	exon	32898306	32898452	.	-	.	Parent=gene1541
chr21	ENCODE	CDS	32898306	32898452	.	-	0	Parent=gene1541
###
chr21	ENCODE	gene	32895848	32906767	.	-	.	ID=gene1542;name2=C21orf59;Name=AP000275.61-002
chr21	ENCODE	exon	32895848	32897473	.	-	.	Parent=gene1542
chr21	ENCODE	CDS	32897270	32897473	.	-	0	Parent=gene1542
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene1542
chr21	ENCODE	CDS	32898306	32898464	.	-	0	Parent=gene1542
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene1542
chr21	ENCODE	CDS	32901830	32901897	.	-	2	Parent=gene1542
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene1542
chr21	ENCODE	CDS	32904019	32904186	.	-	2	Parent=gene1542
chr21	ENCODE	CDS	32906286	32906424	.	-	0	Parent=gene1542
chr21	ENCODE	exon	32906286	32906767	.	-	.	Parent=gene1542
###
chr21	ENCODE	gene	32895848	32907047	.	-	.	ID=gene1543;Name=AP000275.61-001;name2=C21orf59
chr21	ENCODE	exon	32895848	32896154	.	-	.	Parent=gene1543
chr21	ENCODE	CDS	32896044	32896154	.	-	0	Parent=gene1543
chr21	ENCODE	exon	32896453	32896548	.	-	.	Parent=gene1543
chr21	ENCODE	CDS	32896453	32896548	.	-	0	Parent=gene1543
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene1543
chr21	ENCODE	CDS	32897342	32897473	.	-	0	Parent=gene1543
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene1543
chr21	ENCODE	CDS	32898306	32898464	.	-	0	Parent=gene1543
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene1543
chr21	ENCODE	CDS	32901830	32901897	.	-	2	Parent=gene1543
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene1543
chr21	ENCODE	CDS	32904019	32904186	.	-	2	Parent=gene1543
chr21	ENCODE	CDS	32906286	32906424	.	-	0	Parent=gene1543
chr21	ENCODE	exon	32906286	32907047	.	-	.	Parent=gene1543
###
chr21	ENCODE	gene	32895884	32898381	.	-	.	ID=gene1544;Name=AP000275.61-004;name2=C21orf59
chr21	ENCODE	exon	32895884	32896548	.	-	.	Parent=gene1544
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene1544
chr21	ENCODE	exon	32898306	32898381	.	-	.	Parent=gene1544
###
chr21	ENCODE	gene	32895966	32906784	.	-	.	ID=gene1545;Name=AP000275.61-003;name2=C21orf59
chr21	ENCODE	exon	32895966	32896154	.	-	.	Parent=gene1545
chr21	ENCODE	exon	32896453	32896548	.	-	.	Parent=gene1545
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene1545
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene1545
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene1545
chr21	ENCODE	exon	32906286	32906784	.	-	.	Parent=gene1545
###
chr21	ENCODE	gene	32895991	32898694	.	-	.	ID=gene1546;Name=AP000275.61-008;name2=C21orf59
chr21	ENCODE	exon	32895991	32897473	.	-	.	Parent=gene1546
chr21	ENCODE	exon	32898306	32898694	.	-	.	Parent=gene1546
###
chr21	ENCODE	gene	32897406	32906736	.	-	.	ID=gene1547;Name=AP000275.61-007;name2=C21orf59
chr21	ENCODE	exon	32897406	32897473	.	-	.	Parent=gene1547
chr21	ENCODE	CDS	32897406	32897473	.	-	0	Parent=gene1547
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene1547
chr21	ENCODE	CDS	32898306	32898464	.	-	0	Parent=gene1547
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene1547
chr21	ENCODE	CDS	32901830	32901897	.	-	2	Parent=gene1547
chr21	ENCODE	exon	32904019	32904135	.	-	.	Parent=gene1547
chr21	ENCODE	CDS	32904019	32904135	.	-	2	Parent=gene1547
chr21	ENCODE	CDS	32906286	32906424	.	-	0	Parent=gene1547
chr21	ENCODE	exon	32906286	32906736	.	-	.	Parent=gene1547
###
chr21	ENCODE	gene	32922944	33022105	.	-	.	ID=gene1548;Name=AP000275.63-003;name2=SYNJ1
chr21	ENCODE	exon	32922944	32925982	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32929042	32929065	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32933089	32933306	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32933852	32933960	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32936077	32936147	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32936276	32936314	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32939149	32939187	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32939827	32939891	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32939940	32939970	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32940574	32940783	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32944365	32944527	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32947469	32947547	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32950868	32951083	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32951184	32951301	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32951897	32952053	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32959094	32959252	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32960124	32960316	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32960614	32960754	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32964469	32964553	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32967521	32967712	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32970513	32970536	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32972826	32972982	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32975677	32975829	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32978219	32978300	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32979929	32980098	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32981159	32981255	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32982487	32982548	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32988409	32988492	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32989238	32989463	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene1548
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene1548
chr21	ENCODE	exon	33020954	33021099	.	-	.	Parent=gene1548
chr21	ENCODE	exon	33022019	33022105	.	-	.	Parent=gene1548
###
chr21	ENCODE	gene	32922945	33022183	.	-	.	ID=gene1549;Name=AP000275.63-001;name2=SYNJ1
chr21	ENCODE	exon	32922945	32925982	.	-	.	Parent=gene1549
chr21	ENCODE	exon	32929042	32929065	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32929045	32929065	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32933089	32933306	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32933089	32933306	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32933852	32933960	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32933852	32933960	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32936077	32936147	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32936077	32936147	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32936276	32936314	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32936276	32936314	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32937591	32937638	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32937591	32937638	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32939149	32939187	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32939149	32939187	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32939827	32939970	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32939827	32939970	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32940574	32940783	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32940574	32940783	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32944365	32944527	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32944365	32944527	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32947469	32947547	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32947469	32947547	.	-	1	Parent=gene1549
chr21	ENCODE	exon	32950868	32951083	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32950868	32951083	.	-	1	Parent=gene1549
chr21	ENCODE	exon	32951184	32951301	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32951184	32951301	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32951897	32952053	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32951897	32952053	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32959094	32959252	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32959094	32959252	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32960124	32960316	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32960124	32960316	.	-	1	Parent=gene1549
chr21	ENCODE	exon	32960614	32960754	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32960614	32960754	.	-	1	Parent=gene1549
chr21	ENCODE	exon	32964469	32964553	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32964469	32964553	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32967521	32967712	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32967521	32967712	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32970513	32970536	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32970513	32970536	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32972826	32972982	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32972826	32972982	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32975677	32975829	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32975677	32975829	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32978219	32978300	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32978219	32978300	.	-	1	Parent=gene1549
chr21	ENCODE	exon	32979929	32980098	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32979929	32980098	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32981159	32981255	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32981159	32981255	.	-	1	Parent=gene1549
chr21	ENCODE	exon	32982487	32982548	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32982487	32982548	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32988409	32988492	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32988409	32988492	.	-	0	Parent=gene1549
chr21	ENCODE	exon	32989238	32989463	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32989238	32989463	.	-	1	Parent=gene1549
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32994019	32994286	.	-	2	Parent=gene1549
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene1549
chr21	ENCODE	CDS	32996142	32996228	.	-	2	Parent=gene1549
chr21	ENCODE	CDS	33020954	33021077	.	-	0	Parent=gene1549
chr21	ENCODE	exon	33020954	33021099	.	-	.	Parent=gene1549
chr21	ENCODE	exon	33022128	33022183	.	-	.	Parent=gene1549
###
chr21	ENCODE	gene	32925171	33022148	.	-	.	ID=gene1550;Name=AP000275.63-004;name2=SYNJ1
chr21	ENCODE	exon	32925171	32925982	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32925176	32925982	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32933089	32933306	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32933089	32933306	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32933852	32933960	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32933852	32933960	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32936077	32936147	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32936077	32936147	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32936276	32936314	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32936276	32936314	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32937591	32937638	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32937591	32937638	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32939149	32939187	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32939149	32939187	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32939827	32939970	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32939827	32939970	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32940574	32940783	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32940574	32940783	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32944365	32944527	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32944365	32944527	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32947469	32947547	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32947469	32947547	.	-	1	Parent=gene1550
chr21	ENCODE	exon	32950868	32951083	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32950868	32951083	.	-	1	Parent=gene1550
chr21	ENCODE	exon	32951184	32951301	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32951184	32951301	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32951897	32952053	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32951897	32952053	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32959094	32959252	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32959094	32959252	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32960124	32960316	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32960124	32960316	.	-	1	Parent=gene1550
chr21	ENCODE	exon	32960614	32960754	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32960614	32960754	.	-	1	Parent=gene1550
chr21	ENCODE	exon	32964469	32964553	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32964469	32964553	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32967521	32967712	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32967521	32967712	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32970513	32970536	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32970513	32970536	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32972826	32972982	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32972826	32972982	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32975677	32975829	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32975677	32975829	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32978219	32978300	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32978219	32978300	.	-	1	Parent=gene1550
chr21	ENCODE	exon	32979929	32980098	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32979929	32980098	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32981159	32981255	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32981159	32981255	.	-	1	Parent=gene1550
chr21	ENCODE	exon	32982487	32982548	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32982487	32982548	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32988409	32988492	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32988409	32988492	.	-	0	Parent=gene1550
chr21	ENCODE	exon	32989238	32989463	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32989238	32989463	.	-	1	Parent=gene1550
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32994019	32994286	.	-	2	Parent=gene1550
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene1550
chr21	ENCODE	CDS	32996142	32996228	.	-	2	Parent=gene1550
chr21	ENCODE	CDS	33020954	33021077	.	-	0	Parent=gene1550
chr21	ENCODE	exon	33020954	33021099	.	-	.	Parent=gene1550
chr21	ENCODE	exon	33022128	33022148	.	-	.	Parent=gene1550
###
chr21	ENCODE	gene	32933195	32939900	.	-	.	ID=gene1551;Name=AP000275.63-008;name2=SYNJ1
chr21	ENCODE	exon	32933195	32933306	.	-	.	Parent=gene1551
chr21	ENCODE	CDS	32933195	32933306	.	-	1	Parent=gene1551
chr21	ENCODE	exon	32933852	32933960	.	-	.	Parent=gene1551
chr21	ENCODE	CDS	32933852	32933960	.	-	2	Parent=gene1551
chr21	ENCODE	exon	32936077	32936147	.	-	.	Parent=gene1551
chr21	ENCODE	CDS	32936077	32936147	.	-	1	Parent=gene1551
chr21	ENCODE	exon	32939827	32939900	.	-	.	Parent=gene1551
chr21	ENCODE	CDS	32939827	32939900	.	-	0	Parent=gene1551
###
chr21	ENCODE	gene	32944365	32948282	.	-	.	ID=gene1552;Name=AP000275.63-005;name2=SYNJ1
chr21	ENCODE	exon	32944365	32944527	.	-	.	Parent=gene1552
chr21	ENCODE	exon	32947469	32948282	.	-	.	Parent=gene1552
###
chr21	ENCODE	gene	32950872	32952742	.	-	.	ID=gene1553;Name=AP000275.63-007;name2=SYNJ1
chr21	ENCODE	exon	32950872	32951083	.	-	.	Parent=gene1553
chr21	ENCODE	exon	32951184	32951301	.	-	.	Parent=gene1553
chr21	ENCODE	exon	32951897	32952053	.	-	.	Parent=gene1553
chr21	ENCODE	exon	32952652	32952742	.	-	.	Parent=gene1553
###
chr21	ENCODE	gene	32960167	33022121	.	-	.	ID=gene1554;Name=AP000275.63-002;name2=SYNJ1
chr21	ENCODE	exon	32960167	32960316	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32960167	32960316	.	-	1	Parent=gene1554
chr21	ENCODE	exon	32960614	32960754	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32960614	32960754	.	-	1	Parent=gene1554
chr21	ENCODE	exon	32964469	32964553	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32964469	32964553	.	-	2	Parent=gene1554
chr21	ENCODE	exon	32967521	32967712	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32967521	32967712	.	-	2	Parent=gene1554
chr21	ENCODE	exon	32972826	32972991	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32972826	32972991	.	-	0	Parent=gene1554
chr21	ENCODE	exon	32975677	32975829	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32975677	32975829	.	-	0	Parent=gene1554
chr21	ENCODE	exon	32978219	32978300	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32978219	32978300	.	-	1	Parent=gene1554
chr21	ENCODE	exon	32979929	32980098	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32979929	32980098	.	-	0	Parent=gene1554
chr21	ENCODE	exon	32981159	32981255	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32981159	32981255	.	-	1	Parent=gene1554
chr21	ENCODE	exon	32982487	32982548	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32982487	32982548	.	-	0	Parent=gene1554
chr21	ENCODE	exon	32988409	32988492	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32988409	32988492	.	-	0	Parent=gene1554
chr21	ENCODE	exon	32989238	32989463	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32989238	32989463	.	-	1	Parent=gene1554
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32994019	32994286	.	-	2	Parent=gene1554
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene1554
chr21	ENCODE	CDS	32996142	32996228	.	-	2	Parent=gene1554
chr21	ENCODE	CDS	33020954	33021077	.	-	0	Parent=gene1554
chr21	ENCODE	exon	33020954	33021099	.	-	.	Parent=gene1554
chr21	ENCODE	exon	33022019	33022121	.	-	.	Parent=gene1554
###
chr21	ENCODE	gene	32989407	33021124	.	-	.	ID=gene1555;Name=AP000275.63-006;name2=SYNJ1
chr21	ENCODE	exon	32989407	32989463	.	-	.	Parent=gene1555
chr21	ENCODE	CDS	32989407	32989463	.	-	1	Parent=gene1555
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene1555
chr21	ENCODE	CDS	32994019	32994286	.	-	2	Parent=gene1555
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene1555
chr21	ENCODE	CDS	32996142	32996228	.	-	2	Parent=gene1555
chr21	ENCODE	CDS	33020954	33021077	.	-	0	Parent=gene1555
chr21	ENCODE	exon	33020954	33021124	.	-	.	Parent=gene1555
###
chr21	ENCODE	gene	33028081	33066040	.	-	.	ID=gene1556;name2=C21orf66;Name=AP000279.68-001
chr21	ENCODE	exon	33028081	33029249	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33029132	33029249	.	-	1	Parent=gene1556
chr21	ENCODE	exon	33031436	33031590	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33031436	33031590	.	-	0	Parent=gene1556
chr21	ENCODE	exon	33032355	33032501	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33032355	33032501	.	-	0	Parent=gene1556
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33037430	33037496	.	-	1	Parent=gene1556
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33037860	33037936	.	-	0	Parent=gene1556
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33038974	33039095	.	-	2	Parent=gene1556
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33039756	33039900	.	-	0	Parent=gene1556
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33042681	33042880	.	-	2	Parent=gene1556
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33045099	33045214	.	-	1	Parent=gene1556
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33045301	33045400	.	-	2	Parent=gene1556
chr21	ENCODE	exon	33049412	33049535	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33049412	33049535	.	-	0	Parent=gene1556
chr21	ENCODE	exon	33053262	33053451	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33053262	33053451	.	-	1	Parent=gene1556
chr21	ENCODE	exon	33053959	33054176	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33053959	33054176	.	-	0	Parent=gene1556
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33055241	33055344	.	-	2	Parent=gene1556
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33056278	33056499	.	-	2	Parent=gene1556
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33058530	33058706	.	-	2	Parent=gene1556
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene1556
chr21	ENCODE	CDS	33063996	33064124	.	-	2	Parent=gene1556
chr21	ENCODE	CDS	33065508	33065850	.	-	0	Parent=gene1556
chr21	ENCODE	exon	33065508	33066040	.	-	.	Parent=gene1556
###
chr21	ENCODE	gene	33028082	33050976	.	-	.	ID=gene1557;Name=AP000279.68-002;name2=C21orf66
chr21	ENCODE	exon	33028082	33029249	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33031436	33031590	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33032355	33032501	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene1557
chr21	ENCODE	exon	33049395	33050976	.	-	.	Parent=gene1557
###
chr21	ENCODE	gene	33029002	33065869	.	-	.	ID=gene1558;Name=AP000279.68-006;name2=C21orf66
chr21	ENCODE	exon	33029002	33029249	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33031436	33031590	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33032355	33032501	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33049395	33049535	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33053262	33053451	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33053959	33054176	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene1558
chr21	ENCODE	exon	33065508	33065869	.	-	.	Parent=gene1558
###
chr21	ENCODE	gene	33029008	33046306	.	-	.	ID=gene1559;name2=C21orf66;Name=AP000279.68-003
chr21	ENCODE	exon	33029008	33029249	.	-	.	Parent=gene1559
chr21	ENCODE	exon	33031436	33031590	.	-	.	Parent=gene1559
chr21	ENCODE	exon	33032355	33032501	.	-	.	Parent=gene1559
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene1559
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene1559
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene1559
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene1559
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene1559
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene1559
chr21	ENCODE	exon	33045301	33046306	.	-	.	Parent=gene1559
###
chr21	ENCODE	gene	33035575	33065850	.	-	.	ID=gene1560;Name=AP000279.68-005;name2=C21orf66
chr21	ENCODE	exon	33035575	33035804	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33035691	33035804	.	-	0	Parent=gene1560
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33037430	33037496	.	-	1	Parent=gene1560
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33037860	33037936	.	-	0	Parent=gene1560
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33038974	33039095	.	-	2	Parent=gene1560
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33039756	33039900	.	-	0	Parent=gene1560
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33042681	33042880	.	-	2	Parent=gene1560
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33045099	33045214	.	-	1	Parent=gene1560
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33045301	33045400	.	-	2	Parent=gene1560
chr21	ENCODE	exon	33049412	33049535	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33049412	33049535	.	-	0	Parent=gene1560
chr21	ENCODE	exon	33053262	33053451	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33053262	33053451	.	-	1	Parent=gene1560
chr21	ENCODE	exon	33053959	33054176	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33053959	33054176	.	-	0	Parent=gene1560
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33055241	33055344	.	-	2	Parent=gene1560
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33056278	33056499	.	-	2	Parent=gene1560
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33058530	33058706	.	-	2	Parent=gene1560
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33063996	33064124	.	-	2	Parent=gene1560
chr21	ENCODE	exon	33065508	33065850	.	-	.	Parent=gene1560
chr21	ENCODE	CDS	33065508	33065850	.	-	0	Parent=gene1560
###
chr21	ENCODE	gene	33035601	33037450	.	-	.	ID=gene1561;Name=AP000279.68-009;name2=C21orf66
chr21	ENCODE	exon	33035601	33035804	.	-	.	Parent=gene1561
chr21	ENCODE	exon	33036542	33036683	.	-	.	Parent=gene1561
chr21	ENCODE	exon	33037143	33037248	.	-	.	Parent=gene1561
chr21	ENCODE	exon	33037430	33037450	.	-	.	Parent=gene1561
###
chr21	ENCODE	gene	33042741	33049493	.	-	.	ID=gene1562;Name=AP000279.68-008;name2=C21orf66
chr21	ENCODE	exon	33042741	33042880	.	-	.	Parent=gene1562
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene1562
chr21	ENCODE	exon	33049395	33049493	.	-	.	Parent=gene1562
###
chr21	ENCODE	gene	33050524	33065850	.	-	.	ID=gene1563;Name=AP000279.68-004;name2=C21orf66
chr21	ENCODE	exon	33050524	33050550	.	-	.	Parent=gene1563
chr21	ENCODE	exon	33053262	33053451	.	-	.	Parent=gene1563
chr21	ENCODE	exon	33053959	33054176	.	-	.	Parent=gene1563
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene1563
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene1563
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene1563
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene1563
chr21	ENCODE	exon	33065508	33065850	.	-	.	Parent=gene1563
###
chr21	ENCODE	gene	33053584	33065974	.	-	.	ID=gene1564;Name=AP000279.68-007;name2=C21orf66
chr21	ENCODE	exon	33053584	33054176	.	-	.	Parent=gene1564
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene1564
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene1564
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene1564
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene1564
chr21	ENCODE	exon	33065508	33065974	.	-	.	Parent=gene1564
###
chr21	ENCODE	gene	33066282	33093149	.	+	.	ID=gene1565;name2=C21orf49;Name=AP000281.64-001
chr21	ENCODE	exon	33066282	33066490	.	+	.	Parent=gene1565
chr21	ENCODE	exon	33078979	33079101	.	+	.	Parent=gene1565
chr21	ENCODE	CDS	33079060	33079101	.	+	0	Parent=gene1565
chr21	ENCODE	exon	33082794	33082883	.	+	.	Parent=gene1565
chr21	ENCODE	CDS	33082794	33082883	.	+	0	Parent=gene1565
chr21	ENCODE	CDS	33091119	33091226	.	+	0	Parent=gene1565
chr21	ENCODE	exon	33091119	33093149	.	+	.	Parent=gene1565
###
chr21	ENCODE	gene	33066307	33091887	.	+	.	ID=gene1566;Name=AP000281.64-002;name2=C21orf49
chr21	ENCODE	exon	33066307	33066454	.	+	.	Parent=gene1566
chr21	ENCODE	exon	33091119	33091887	.	+	.	Parent=gene1566
###
chr21	ENCODE	gene	33066332	33187913	.	+	.	ID=gene1567;Name=AP000281.64-007;name2=C21orf49
chr21	ENCODE	exon	33066332	33066454	.	+	.	Parent=gene1567
chr21	ENCODE	exon	33078957	33079101	.	+	.	Parent=gene1567
chr21	ENCODE	exon	33180110	33180246	.	+	.	Parent=gene1567
chr21	ENCODE	exon	33187756	33187913	.	+	.	Parent=gene1567
###
chr21	ENCODE	gene	33066343	33146649	.	+	.	ID=gene1568;name2=C21orf49;Name=AP000281.64-004
chr21	ENCODE	exon	33066343	33066490	.	+	.	Parent=gene1568
chr21	ENCODE	exon	33078979	33079101	.	+	.	Parent=gene1568
chr21	ENCODE	exon	33145929	33146649	.	+	.	Parent=gene1568
###
chr21	ENCODE	gene	33066344	33091348	.	+	.	ID=gene1569;Name=AP000281.64-005;name2=C21orf49
chr21	ENCODE	exon	33066344	33066502	.	+	.	Parent=gene1569
chr21	ENCODE	exon	33078979	33079101	.	+	.	Parent=gene1569
chr21	ENCODE	CDS	33079060	33079101	.	+	0	Parent=gene1569
chr21	ENCODE	exon	33082794	33082883	.	+	.	Parent=gene1569
chr21	ENCODE	CDS	33082794	33082883	.	+	0	Parent=gene1569
chr21	ENCODE	CDS	33091119	33091226	.	+	0	Parent=gene1569
chr21	ENCODE	exon	33091119	33091348	.	+	.	Parent=gene1569
###
chr21	ENCODE	gene	33066356	33091626	.	+	.	ID=gene1570;Name=AP000281.64-003;name2=C21orf49
chr21	ENCODE	exon	33066356	33066490	.	+	.	Parent=gene1570
chr21	ENCODE	exon	33082794	33082883	.	+	.	Parent=gene1570
chr21	ENCODE	exon	33091119	33091626	.	+	.	Parent=gene1570
###
chr21	ENCODE	gene	33066370	33091274	.	+	.	ID=gene1571;name2=C21orf49;Name=AP000281.64-006
chr21	ENCODE	exon	33066370	33066490	.	+	.	Parent=gene1571
chr21	ENCODE	exon	33078979	33079101	.	+	.	Parent=gene1571
chr21	ENCODE	CDS	33079060	33079101	.	+	0	Parent=gene1571
chr21	ENCODE	CDS	33091119	33091226	.	+	0	Parent=gene1571
chr21	ENCODE	exon	33091119	33091274	.	+	.	Parent=gene1571
###
chr21	ENCODE	gene	33087746	33107923	.	-	.	ID=gene1572;Name=AP000280.67-001;name2=C21orf62
chr21	ENCODE	exon	33087746	33088666	.	-	.	Parent=gene1572
chr21	ENCODE	CDS	33087859	33088602	.	-	0	Parent=gene1572
chr21	ENCODE	exon	33104754	33104834	.	-	.	Parent=gene1572
chr21	ENCODE	exon	33107772	33107923	.	-	.	Parent=gene1572
###
chr21	ENCODE	gene	33087747	33107859	.	-	.	ID=gene1573;Name=AP000280.67-003;name2=C21orf62
chr21	ENCODE	exon	33087747	33088666	.	-	.	Parent=gene1573
chr21	ENCODE	CDS	33087859	33088602	.	-	0	Parent=gene1573
chr21	ENCODE	exon	33107772	33107859	.	-	.	Parent=gene1573
###
chr21	ENCODE	gene	33087867	33107869	.	-	.	ID=gene1574;Name=AP000280.67-004;name2=C21orf62
chr21	ENCODE	exon	33087867	33088564	.	-	.	Parent=gene1574
chr21	ENCODE	CDS	33087867	33088564	.	-	1	Parent=gene1574
chr21	ENCODE	exon	33104754	33104834	.	-	.	Parent=gene1574
chr21	ENCODE	CDS	33104754	33104834	.	-	1	Parent=gene1574
chr21	ENCODE	exon	33107772	33107869	.	-	.	Parent=gene1574
chr21	ENCODE	CDS	33107772	33107869	.	-	0	Parent=gene1574
###
chr21	ENCODE	gene	33087903	33107814	.	-	.	ID=gene1575;Name=AP000280.67-002;name2=C21orf62
chr21	ENCODE	CDS	33087903	33088602	.	-	0	Parent=gene1575
chr21	ENCODE	exon	33087903	33088666	.	-	.	Parent=gene1575
chr21	ENCODE	exon	33101822	33101896	.	-	.	Parent=gene1575
chr21	ENCODE	exon	33104754	33104834	.	-	.	Parent=gene1575
chr21	ENCODE	exon	33107772	33107814	.	-	.	Parent=gene1575
###
chr21	ENCODE	gene	33320023	33323374	.	+	.	ID=gene1576;Name=AP000287.4-001;name2=OLIG2
chr21	ENCODE	exon	33320023	33320204	.	+	.	Parent=gene1576
chr21	ENCODE	exon	33320979	33323374	.	+	.	Parent=gene1576
chr21	ENCODE	CDS	33321041	33322012	.	+	0	Parent=gene1576
###
chr21	ENCODE	gene	33320113	33321227	.	+	.	ID=gene1577;Name=AP000287.4-003;name2=OLIG2
chr21	ENCODE	exon	33320113	33320438	.	+	.	Parent=gene1577
chr21	ENCODE	exon	33320979	33321227	.	+	.	Parent=gene1577
chr21	ENCODE	CDS	33321041	33321227	.	+	0	Parent=gene1577
###
chr21	ENCODE	gene	33320113	33323374	.	+	.	ID=gene1578;name2=OLIG2;Name=AP000287.4-002
chr21	ENCODE	exon	33320113	33323374	.	+	.	Parent=gene1578
chr21	ENCODE	CDS	33321041	33322012	.	+	0	Parent=gene1578
###
chr21	ENCODE	gene	33364320	33366596	.	+	.	ID=gene1579;Name=AP000289.5-001;name2=OLIG1
chr21	ENCODE	exon	33364320	33366596	.	+	.	Parent=gene1579
chr21	ENCODE	CDS	33364423	33365238	.	+	0	Parent=gene1579
###
chr21	ENCODE	gene	33365141	33366589	.	+	.	ID=gene1580;Name=AP000289.5-002;name2=OLIG1
chr21	ENCODE	exon	33365141	33365861	.	+	.	Parent=gene1580
chr21	ENCODE	exon	33366228	33366589	.	+	.	Parent=gene1580
###
chr21	ENCODE	gene	33365844	33366589	.	+	.	ID=gene1581;Name=AP000289.5-003;name2=OLIG1
chr21	ENCODE	exon	33365844	33365881	.	+	.	Parent=gene1581
chr21	ENCODE	exon	33366228	33366589	.	+	.	Parent=gene1581
###
chr21	ENCODE	gene	33459646	33464824	.	-	.	ID=gene1582;Name=AP000290.56-001;name2=C21orf54
chr21	ENCODE	exon	33459646	33459867	.	-	.	Parent=gene1582
chr21	ENCODE	CDS	33459847	33459867	.	-	0	Parent=gene1582
chr21	ENCODE	exon	33462618	33462756	.	-	.	Parent=gene1582
chr21	ENCODE	CDS	33462618	33462756	.	-	1	Parent=gene1582
chr21	ENCODE	exon	33463871	33464008	.	-	.	Parent=gene1582
chr21	ENCODE	CDS	33463871	33464008	.	-	1	Parent=gene1582
chr21	ENCODE	CDS	33464316	33464344	.	-	0	Parent=gene1582
chr21	ENCODE	exon	33464316	33464426	.	-	.	Parent=gene1582
chr21	ENCODE	exon	33464739	33464824	.	-	.	Parent=gene1582
###
chr21	ENCODE	gene	33524076	33556931	.	+	.	ID=gene1583;Name=AP000295.6-004;name2=IFNAR2
chr21	ENCODE	exon	33524076	33524391	.	+	.	Parent=gene1583
chr21	ENCODE	exon	33536061	33536152	.	+	.	Parent=gene1583
chr21	ENCODE	CDS	33536098	33536152	.	+	0	Parent=gene1583
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene1583
chr21	ENCODE	CDS	33537848	33537889	.	+	2	Parent=gene1583
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene1583
chr21	ENCODE	CDS	33539126	33539249	.	+	2	Parent=gene1583
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene1583
chr21	ENCODE	CDS	33540893	33541065	.	+	1	Parent=gene1583
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene1583
chr21	ENCODE	CDS	33542884	33543029	.	+	2	Parent=gene1583
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1583
chr21	ENCODE	CDS	33546837	33547005	.	+	0	Parent=gene1583
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene1583
chr21	ENCODE	CDS	33554772	33554902	.	+	2	Parent=gene1583
chr21	ENCODE	CDS	33556736	33556891	.	+	0	Parent=gene1583
chr21	ENCODE	exon	33556736	33556931	.	+	.	Parent=gene1583
###
chr21	ENCODE	gene	33524084	33559839	.	+	.	ID=gene1584;Name=AP000295.6-001;name2=IFNAR2
chr21	ENCODE	exon	33524084	33524391	.	+	.	Parent=gene1584
chr21	ENCODE	exon	33536015	33536152	.	+	.	Parent=gene1584
chr21	ENCODE	CDS	33536098	33536152	.	+	0	Parent=gene1584
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene1584
chr21	ENCODE	CDS	33537848	33537889	.	+	2	Parent=gene1584
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene1584
chr21	ENCODE	CDS	33539126	33539249	.	+	2	Parent=gene1584
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene1584
chr21	ENCODE	CDS	33540893	33541065	.	+	1	Parent=gene1584
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene1584
chr21	ENCODE	CDS	33542884	33543029	.	+	2	Parent=gene1584
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1584
chr21	ENCODE	CDS	33546837	33547005	.	+	0	Parent=gene1584
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene1584
chr21	ENCODE	CDS	33554772	33554902	.	+	2	Parent=gene1584
chr21	ENCODE	CDS	33556736	33556891	.	+	0	Parent=gene1584
chr21	ENCODE	exon	33556736	33559839	.	+	.	Parent=gene1584
###
chr21	ENCODE	gene	33524149	33558700	.	+	.	ID=gene1585;Name=AP000295.6-002;name2=IFNAR2
chr21	ENCODE	exon	33524149	33524391	.	+	.	Parent=gene1585
chr21	ENCODE	exon	33536015	33536152	.	+	.	Parent=gene1585
chr21	ENCODE	CDS	33536098	33536152	.	+	0	Parent=gene1585
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene1585
chr21	ENCODE	CDS	33537848	33537889	.	+	2	Parent=gene1585
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene1585
chr21	ENCODE	CDS	33539126	33539249	.	+	2	Parent=gene1585
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene1585
chr21	ENCODE	CDS	33540893	33541065	.	+	1	Parent=gene1585
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene1585
chr21	ENCODE	CDS	33542884	33543029	.	+	2	Parent=gene1585
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1585
chr21	ENCODE	CDS	33546837	33547005	.	+	0	Parent=gene1585
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene1585
chr21	ENCODE	CDS	33554772	33554902	.	+	2	Parent=gene1585
chr21	ENCODE	CDS	33556968	33557675	.	+	0	Parent=gene1585
chr21	ENCODE	exon	33556968	33558700	.	+	.	Parent=gene1585
###
chr21	ENCODE	gene	33524234	33556897	.	+	.	ID=gene1586;Name=AP000295.6-005;name2=IFNAR2
chr21	ENCODE	exon	33524234	33524391	.	+	.	Parent=gene1586
chr21	ENCODE	exon	33536061	33536152	.	+	.	Parent=gene1586
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene1586
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene1586
chr21	ENCODE	exon	33539668	33539980	.	+	.	Parent=gene1586
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene1586
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene1586
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1586
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene1586
chr21	ENCODE	exon	33556736	33556897	.	+	.	Parent=gene1586
###
chr21	ENCODE	gene	33524311	33558700	.	+	.	ID=gene1587;Name=AP000295.6-003;name2=IFNAR2
chr21	ENCODE	exon	33524311	33524391	.	+	.	Parent=gene1587
chr21	ENCODE	exon	33536015	33536152	.	+	.	Parent=gene1587
chr21	ENCODE	CDS	33536098	33536152	.	+	0	Parent=gene1587
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene1587
chr21	ENCODE	CDS	33537848	33537889	.	+	2	Parent=gene1587
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene1587
chr21	ENCODE	CDS	33539126	33539249	.	+	2	Parent=gene1587
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene1587
chr21	ENCODE	CDS	33540893	33541065	.	+	1	Parent=gene1587
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene1587
chr21	ENCODE	CDS	33542884	33543029	.	+	2	Parent=gene1587
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1587
chr21	ENCODE	CDS	33546837	33547005	.	+	0	Parent=gene1587
chr21	ENCODE	CDS	33556968	33556978	.	+	2	Parent=gene1587
chr21	ENCODE	exon	33556968	33558700	.	+	.	Parent=gene1587
###
chr21	ENCODE	gene	33524316	33557030	.	+	.	ID=gene1588;Name=AP000295.6-006;name2=IFNAR2
chr21	ENCODE	exon	33524316	33524391	.	+	.	Parent=gene1588
chr21	ENCODE	exon	33536061	33536152	.	+	.	Parent=gene1588
chr21	ENCODE	CDS	33536098	33536152	.	+	0	Parent=gene1588
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene1588
chr21	ENCODE	CDS	33537848	33537889	.	+	2	Parent=gene1588
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene1588
chr21	ENCODE	CDS	33539126	33539249	.	+	2	Parent=gene1588
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene1588
chr21	ENCODE	CDS	33540893	33541065	.	+	1	Parent=gene1588
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene1588
chr21	ENCODE	CDS	33542884	33543029	.	+	2	Parent=gene1588
chr21	ENCODE	CDS	33546313	33546366	.	+	0	Parent=gene1588
chr21	ENCODE	exon	33546313	33546423	.	+	.	Parent=gene1588
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1588
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene1588
chr21	ENCODE	exon	33556968	33557030	.	+	.	Parent=gene1588
###
chr21	ENCODE	gene	33524357	33557030	.	+	.	ID=gene1589;Name=AP000295.6-009;name2=IFNAR2
chr21	ENCODE	exon	33524357	33524391	.	+	.	Parent=gene1589
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene1589
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene1589
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene1589
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1589
chr21	ENCODE	exon	33556968	33557030	.	+	.	Parent=gene1589
###
chr21	ENCODE	gene	33524357	33557030	.	+	.	ID=gene1590;Name=AP000295.6-010;name2=IFNAR2
chr21	ENCODE	exon	33524357	33524391	.	+	.	Parent=gene1590
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene1590
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene1590
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene1590
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1590
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene1590
chr21	ENCODE	exon	33556968	33557030	.	+	.	Parent=gene1590
###
chr21	ENCODE	gene	33524584	33543029	.	+	.	ID=gene1591;name2=IFNAR2;Name=AP000295.6-008
chr21	ENCODE	exon	33524584	33524732	.	+	.	Parent=gene1591
chr21	ENCODE	exon	33536061	33536152	.	+	.	Parent=gene1591
chr21	ENCODE	CDS	33536098	33536152	.	+	0	Parent=gene1591
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene1591
chr21	ENCODE	CDS	33537848	33537889	.	+	2	Parent=gene1591
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene1591
chr21	ENCODE	CDS	33539126	33539249	.	+	2	Parent=gene1591
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene1591
chr21	ENCODE	CDS	33540893	33541065	.	+	1	Parent=gene1591
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene1591
chr21	ENCODE	CDS	33542884	33543029	.	+	2	Parent=gene1591
###
chr21	ENCODE	gene	33542890	33577387	.	+	.	ID=gene1592;Name=AP000295.8-006;name2=IL10RB
chr21	ENCODE	exon	33542890	33543029	.	+	.	Parent=gene1592
chr21	ENCODE	CDS	33542890	33543029	.	+	0	Parent=gene1592
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1592
chr21	ENCODE	CDS	33546837	33547005	.	+	1	Parent=gene1592
chr21	ENCODE	exon	33562569	33562692	.	+	.	Parent=gene1592
chr21	ENCODE	CDS	33562569	33562692	.	+	0	Parent=gene1592
chr21	ENCODE	exon	33570771	33570928	.	+	.	Parent=gene1592
chr21	ENCODE	CDS	33570771	33570928	.	+	2	Parent=gene1592
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene1592
chr21	ENCODE	CDS	33573927	33574093	.	+	0	Parent=gene1592
chr21	ENCODE	exon	33577269	33577387	.	+	.	Parent=gene1592
chr21	ENCODE	CDS	33577269	33577387	.	+	1	Parent=gene1592
###
chr21	ENCODE	gene	33542890	33577387	.	+	.	ID=gene1593;Name=AP000295.8-007;name2=IL10RB
chr21	ENCODE	exon	33542890	33543029	.	+	.	Parent=gene1593
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1593
chr21	ENCODE	exon	33570771	33570928	.	+	.	Parent=gene1593
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene1593
chr21	ENCODE	exon	33577269	33577387	.	+	.	Parent=gene1593
###
chr21	ENCODE	gene	33542919	33556932	.	+	.	ID=gene1594;Name=AP000295.6-007;name2=IFNAR2
chr21	ENCODE	exon	33542919	33543029	.	+	.	Parent=gene1594
chr21	ENCODE	CDS	33542919	33543029	.	+	0	Parent=gene1594
chr21	ENCODE	CDS	33546313	33546366	.	+	0	Parent=gene1594
chr21	ENCODE	exon	33546313	33546423	.	+	.	Parent=gene1594
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene1594
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene1594
chr21	ENCODE	exon	33556736	33556932	.	+	.	Parent=gene1594
###
chr21	ENCODE	gene	33560533	33591409	.	+	.	ID=gene1595;Name=AP000295.8-001;name2=IL10RB
chr21	ENCODE	exon	33560533	33560689	.	+	.	Parent=gene1595
chr21	ENCODE	CDS	33560641	33560689	.	+	0	Parent=gene1595
chr21	ENCODE	exon	33562569	33562692	.	+	.	Parent=gene1595
chr21	ENCODE	CDS	33562569	33562692	.	+	2	Parent=gene1595
chr21	ENCODE	exon	33570771	33570928	.	+	.	Parent=gene1595
chr21	ENCODE	CDS	33570771	33570928	.	+	1	Parent=gene1595
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene1595
chr21	ENCODE	CDS	33573927	33574093	.	+	2	Parent=gene1595
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene1595
chr21	ENCODE	CDS	33577269	33577416	.	+	0	Parent=gene1595
chr21	ENCODE	exon	33582279	33582436	.	+	.	Parent=gene1595
chr21	ENCODE	CDS	33582279	33582436	.	+	2	Parent=gene1595
chr21	ENCODE	CDS	33590359	33590532	.	+	0	Parent=gene1595
chr21	ENCODE	exon	33590359	33591409	.	+	.	Parent=gene1595
###
chr21	ENCODE	gene	33560557	33590414	.	+	.	ID=gene1596;Name=AP000295.8-003;name2=IL10RB
chr21	ENCODE	exon	33560557	33560689	.	+	.	Parent=gene1596
chr21	ENCODE	exon	33562569	33562692	.	+	.	Parent=gene1596
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene1596
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene1596
chr21	ENCODE	exon	33582279	33582436	.	+	.	Parent=gene1596
chr21	ENCODE	exon	33590359	33590414	.	+	.	Parent=gene1596
###
chr21	ENCODE	gene	33562103	33591128	.	+	.	ID=gene1597;name2=IL10RB;Name=AP000295.8-002
chr21	ENCODE	exon	33562103	33562692	.	+	.	Parent=gene1597
chr21	ENCODE	exon	33570771	33570928	.	+	.	Parent=gene1597
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene1597
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene1597
chr21	ENCODE	exon	33582279	33582436	.	+	.	Parent=gene1597
chr21	ENCODE	exon	33590359	33591128	.	+	.	Parent=gene1597
###
chr21	ENCODE	gene	33562457	33582295	.	+	.	ID=gene1598;Name=AP000295.8-005;name2=IL10RB
chr21	ENCODE	exon	33562457	33562692	.	+	.	Parent=gene1598
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene1598
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene1598
chr21	ENCODE	exon	33582279	33582295	.	+	.	Parent=gene1598
###
chr21	ENCODE	gene	33570787	33590525	.	+	.	ID=gene1599;Name=AP000295.8-004;name2=IL10RB
chr21	ENCODE	exon	33570787	33570928	.	+	.	Parent=gene1599
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene1599
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene1599
chr21	ENCODE	exon	33582279	33582436	.	+	.	Parent=gene1599
chr21	ENCODE	exon	33588187	33588302	.	+	.	Parent=gene1599
chr21	ENCODE	exon	33590359	33590525	.	+	.	Parent=gene1599
###
chr21	ENCODE	gene	33618652	33629787	.	+	.	ID=gene1600;Name=AP000298.3-002;name2=IFNAR1
chr21	ENCODE	exon	33618652	33618813	.	+	.	Parent=gene1600
chr21	ENCODE	exon	33629700	33629787	.	+	.	Parent=gene1600
###
chr21	ENCODE	gene	33619079	33654038	.	+	.	ID=gene1601;Name=AP000298.3-001;name2=IFNAR1
chr21	ENCODE	exon	33619079	33619306	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33619231	33619306	.	+	0	Parent=gene1601
chr21	ENCODE	exon	33629700	33629823	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33629700	33629823	.	+	2	Parent=gene1601
chr21	ENCODE	exon	33635175	33635350	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33635175	33635350	.	+	1	Parent=gene1601
chr21	ENCODE	exon	33637444	33637598	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33637444	33637598	.	+	2	Parent=gene1601
chr21	ENCODE	exon	33637711	33637852	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33637711	33637852	.	+	0	Parent=gene1601
chr21	ENCODE	exon	33639422	33639536	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33639422	33639536	.	+	2	Parent=gene1601
chr21	ENCODE	exon	33643267	33643466	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33643267	33643466	.	+	1	Parent=gene1601
chr21	ENCODE	exon	33643565	33643719	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33643565	33643719	.	+	2	Parent=gene1601
chr21	ENCODE	exon	33646934	33647084	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33646934	33647084	.	+	0	Parent=gene1601
chr21	ENCODE	exon	33647814	33647959	.	+	.	Parent=gene1601
chr21	ENCODE	CDS	33647814	33647959	.	+	2	Parent=gene1601
chr21	ENCODE	CDS	33649492	33649725	.	+	0	Parent=gene1601
chr21	ENCODE	exon	33649492	33654038	.	+	.	Parent=gene1601
###
chr21	ENCODE	gene	33619148	33639453	.	+	.	ID=gene1602;Name=AP000298.3-003;name2=IFNAR1
chr21	ENCODE	exon	33619148	33619306	.	+	.	Parent=gene1602
chr21	ENCODE	CDS	33619231	33619306	.	+	0	Parent=gene1602
chr21	ENCODE	exon	33629700	33629823	.	+	.	Parent=gene1602
chr21	ENCODE	CDS	33629700	33629823	.	+	2	Parent=gene1602
chr21	ENCODE	exon	33635175	33635350	.	+	.	Parent=gene1602
chr21	ENCODE	CDS	33635175	33635350	.	+	1	Parent=gene1602
chr21	ENCODE	exon	33639422	33639453	.	+	.	Parent=gene1602
chr21	ENCODE	CDS	33639422	33639453	.	+	2	Parent=gene1602
###
chr21	ENCODE	gene	33679169	33709121	.	+	.	ID=gene1603;Name=AP000300.6-006;name2=IFNGR2
chr21	ENCODE	exon	33679169	33679203	.	+	.	Parent=gene1603
chr21	ENCODE	exon	33679392	33679560	.	+	.	Parent=gene1603
chr21	ENCODE	exon	33709065	33709121	.	+	.	Parent=gene1603
###
chr21	ENCODE	gene	33697072	33731698	.	+	.	ID=gene1604;Name=AP000300.6-001;name2=IFNGR2
chr21	ENCODE	exon	33697072	33697792	.	+	.	Parent=gene1604
chr21	ENCODE	CDS	33697720	33697792	.	+	0	Parent=gene1604
chr21	ENCODE	exon	33709065	33709197	.	+	.	Parent=gene1604
chr21	ENCODE	CDS	33709065	33709197	.	+	2	Parent=gene1604
chr21	ENCODE	exon	33715657	33715862	.	+	.	Parent=gene1604
chr21	ENCODE	CDS	33715657	33715862	.	+	1	Parent=gene1604
chr21	ENCODE	exon	33721061	33721209	.	+	.	Parent=gene1604
chr21	ENCODE	CDS	33721061	33721209	.	+	2	Parent=gene1604
chr21	ENCODE	exon	33726354	33726513	.	+	.	Parent=gene1604
chr21	ENCODE	CDS	33726354	33726513	.	+	0	Parent=gene1604
chr21	ENCODE	exon	33726891	33727048	.	+	.	Parent=gene1604
chr21	ENCODE	CDS	33726891	33727048	.	+	2	Parent=gene1604
chr21	ENCODE	CDS	33731005	33731139	.	+	0	Parent=gene1604
chr21	ENCODE	exon	33731005	33731698	.	+	.	Parent=gene1604
###
chr21	ENCODE	gene	33697603	33726393	.	+	.	ID=gene1605;Name=AP000300.6-003;name2=IFNGR2
chr21	ENCODE	exon	33697603	33697792	.	+	.	Parent=gene1605
chr21	ENCODE	exon	33705012	33705068	.	+	.	Parent=gene1605
chr21	ENCODE	exon	33705621	33705751	.	+	.	Parent=gene1605
chr21	ENCODE	exon	33709065	33709197	.	+	.	Parent=gene1605
chr21	ENCODE	exon	33715657	33715862	.	+	.	Parent=gene1605
chr21	ENCODE	exon	33721061	33721209	.	+	.	Parent=gene1605
chr21	ENCODE	exon	33726354	33726393	.	+	.	Parent=gene1605
###
chr21	ENCODE	gene	33697608	33731698	.	+	.	ID=gene1606;Name=AP000300.6-002;name2=IFNGR2
chr21	ENCODE	exon	33697608	33697792	.	+	.	Parent=gene1606
chr21	ENCODE	CDS	33697720	33697792	.	+	0	Parent=gene1606
chr21	ENCODE	exon	33705012	33705068	.	+	.	Parent=gene1606
chr21	ENCODE	CDS	33705012	33705068	.	+	2	Parent=gene1606
chr21	ENCODE	exon	33709065	33709197	.	+	.	Parent=gene1606
chr21	ENCODE	CDS	33709065	33709197	.	+	2	Parent=gene1606
chr21	ENCODE	exon	33715657	33715862	.	+	.	Parent=gene1606
chr21	ENCODE	CDS	33715657	33715862	.	+	1	Parent=gene1606
chr21	ENCODE	exon	33721061	33721209	.	+	.	Parent=gene1606
chr21	ENCODE	CDS	33721061	33721209	.	+	2	Parent=gene1606
chr21	ENCODE	exon	33726354	33726513	.	+	.	Parent=gene1606
chr21	ENCODE	CDS	33726354	33726513	.	+	0	Parent=gene1606
chr21	ENCODE	exon	33726891	33727048	.	+	.	Parent=gene1606
chr21	ENCODE	CDS	33726891	33727048	.	+	2	Parent=gene1606
chr21	ENCODE	CDS	33731005	33731139	.	+	0	Parent=gene1606
chr21	ENCODE	exon	33731005	33731698	.	+	.	Parent=gene1606
###
chr21	ENCODE	gene	33697617	33731121	.	+	.	ID=gene1607;Name=AP000300.6-004;name2=IFNGR2
chr21	ENCODE	exon	33697617	33697792	.	+	.	Parent=gene1607
chr21	ENCODE	exon	33715657	33715862	.	+	.	Parent=gene1607
chr21	ENCODE	exon	33721061	33721209	.	+	.	Parent=gene1607
chr21	ENCODE	exon	33726354	33726513	.	+	.	Parent=gene1607
chr21	ENCODE	exon	33726891	33727048	.	+	.	Parent=gene1607
chr21	ENCODE	exon	33731005	33731121	.	+	.	Parent=gene1607
###
chr21	ENCODE	gene	33726496	33773525	.	+	.	ID=gene1608;Name=AP000300.6-005;name2=IFNGR2
chr21	ENCODE	exon	33726496	33726513	.	+	.	Parent=gene1608
chr21	ENCODE	exon	33726891	33727048	.	+	.	Parent=gene1608
chr21	ENCODE	exon	33772975	33773525	.	+	.	Parent=gene1608
###
chr21	ENCODE	gene	33726662	33743141	.	-	.	ID=gene1609;name2=TMEM50B;Name=AP000300.7-009
chr21	ENCODE	exon	33726662	33726979	.	-	.	Parent=gene1609
chr21	ENCODE	exon	33731060	33731169	.	-	.	Parent=gene1609
chr21	ENCODE	exon	33733391	33733474	.	-	.	Parent=gene1609
chr21	ENCODE	exon	33742959	33743141	.	-	.	Parent=gene1609
###
chr21	ENCODE	gene	33726662	33774120	.	-	.	ID=gene1610;name2=TMEM50B;Name=AP000300.7-002
chr21	ENCODE	exon	33726662	33726979	.	-	.	Parent=gene1610
chr21	ENCODE	exon	33733391	33733474	.	-	.	Parent=gene1610
chr21	ENCODE	exon	33742959	33745040	.	-	.	Parent=gene1610
chr21	ENCODE	exon	33749904	33749961	.	-	.	Parent=gene1610
chr21	ENCODE	exon	33754590	33754682	.	-	.	Parent=gene1610
chr21	ENCODE	exon	33759519	33759586	.	-	.	Parent=gene1610
chr21	ENCODE	exon	33761187	33761299	.	-	.	Parent=gene1610
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene1610
chr21	ENCODE	exon	33774015	33774120	.	-	.	Parent=gene1610
###
chr21	ENCODE	gene	33726975	33743587	.	-	.	ID=gene1611;Name=AP000300.7-007;name2=TMEM50B
chr21	ENCODE	exon	33726975	33726979	.	-	.	Parent=gene1611
chr21	ENCODE	exon	33733391	33733474	.	-	.	Parent=gene1611
chr21	ENCODE	exon	33742959	33743056	.	-	.	Parent=gene1611
chr21	ENCODE	exon	33743411	33743587	.	-	.	Parent=gene1611
###
chr21	ENCODE	gene	33731061	33743366	.	-	.	ID=gene1612;Name=AP000300.7-008;name2=TMEM50B
chr21	ENCODE	exon	33731061	33731169	.	-	.	Parent=gene1612
chr21	ENCODE	exon	33733391	33733474	.	-	.	Parent=gene1612
chr21	ENCODE	exon	33741195	33741317	.	-	.	Parent=gene1612
chr21	ENCODE	exon	33742959	33743136	.	-	.	Parent=gene1612
chr21	ENCODE	exon	33743191	33743366	.	-	.	Parent=gene1612
###
chr21	ENCODE	gene	33743312	33774188	.	-	.	ID=gene1613;Name=AP000300.7-001;name2=TMEM50B
chr21	ENCODE	exon	33743312	33745040	.	-	.	Parent=gene1613
chr21	ENCODE	CDS	33744995	33745040	.	-	1	Parent=gene1613
chr21	ENCODE	exon	33749904	33749961	.	-	.	Parent=gene1613
chr21	ENCODE	CDS	33749904	33749961	.	-	2	Parent=gene1613
chr21	ENCODE	exon	33754590	33754682	.	-	.	Parent=gene1613
chr21	ENCODE	CDS	33754590	33754682	.	-	2	Parent=gene1613
chr21	ENCODE	exon	33759519	33759586	.	-	.	Parent=gene1613
chr21	ENCODE	CDS	33759519	33759586	.	-	1	Parent=gene1613
chr21	ENCODE	exon	33761187	33761299	.	-	.	Parent=gene1613
chr21	ENCODE	CDS	33761187	33761299	.	-	0	Parent=gene1613
chr21	ENCODE	CDS	33762964	33763062	.	-	0	Parent=gene1613
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene1613
chr21	ENCODE	exon	33774015	33774188	.	-	.	Parent=gene1613
###
chr21	ENCODE	gene	33744724	33774113	.	-	.	ID=gene1614;Name=AP000300.7-004;name2=TMEM50B
chr21	ENCODE	exon	33744724	33745040	.	-	.	Parent=gene1614
chr21	ENCODE	exon	33749904	33749961	.	-	.	Parent=gene1614
chr21	ENCODE	exon	33750181	33750274	.	-	.	Parent=gene1614
chr21	ENCODE	exon	33754590	33754682	.	-	.	Parent=gene1614
chr21	ENCODE	exon	33759519	33759586	.	-	.	Parent=gene1614
chr21	ENCODE	exon	33761187	33761299	.	-	.	Parent=gene1614
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene1614
chr21	ENCODE	exon	33774015	33774113	.	-	.	Parent=gene1614
###
chr21	ENCODE	gene	33759195	33761312	.	-	.	ID=gene1615;Name=AP000300.7-006;name2=TMEM50B
chr21	ENCODE	exon	33759195	33759586	.	-	.	Parent=gene1615
chr21	ENCODE	exon	33761187	33761312	.	-	.	Parent=gene1615
###
chr21	ENCODE	gene	33759555	33773466	.	-	.	ID=gene1616;name2=TMEM50B;Name=AP000300.7-005
chr21	ENCODE	exon	33759555	33759586	.	-	.	Parent=gene1616
chr21	ENCODE	CDS	33759555	33759586	.	-	1	Parent=gene1616
chr21	ENCODE	exon	33761187	33761299	.	-	.	Parent=gene1616
chr21	ENCODE	CDS	33761187	33761299	.	-	0	Parent=gene1616
chr21	ENCODE	CDS	33762964	33763062	.	-	0	Parent=gene1616
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene1616
chr21	ENCODE	exon	33763708	33763860	.	-	.	Parent=gene1616
chr21	ENCODE	exon	33773286	33773466	.	-	.	Parent=gene1616
###
chr21	ENCODE	gene	33761212	33775369	.	-	.	ID=gene1617;Name=AP000300.7-010;name2=TMEM50B
chr21	ENCODE	exon	33761212	33761299	.	-	.	Parent=gene1617
chr21	ENCODE	CDS	33761212	33761299	.	-	0	Parent=gene1617
chr21	ENCODE	CDS	33762964	33763062	.	-	0	Parent=gene1617
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene1617
chr21	ENCODE	exon	33775311	33775369	.	-	.	Parent=gene1617
###
chr21	ENCODE	gene	33762597	33774125	.	-	.	ID=gene1618;Name=AP000300.7-003;name2=TMEM50B
chr21	ENCODE	exon	33762597	33763103	.	-	.	Parent=gene1618
chr21	ENCODE	exon	33774015	33774125	.	-	.	Parent=gene1618
###
chr21	ENCODE	gene	33779707	33785650	.	-	.	ID=gene1619;Name=AP000302.59-003;name2=C21orf55
chr21	ENCODE	exon	33779707	33779932	.	-	.	Parent=gene1619
chr21	ENCODE	exon	33782006	33783601	.	-	.	Parent=gene1619
chr21	ENCODE	exon	33785243	33785650	.	-	.	Parent=gene1619
###
chr21	ENCODE	gene	33782367	33785897	.	-	.	ID=gene1620;Name=AP000302.59-002;name2=C21orf55
chr21	ENCODE	exon	33782367	33783601	.	-	.	Parent=gene1620
chr21	ENCODE	CDS	33782404	33783570	.	-	0	Parent=gene1620
chr21	ENCODE	exon	33785779	33785897	.	-	.	Parent=gene1620
###
chr21	ENCODE	gene	33782385	33785650	.	-	.	ID=gene1621;Name=AP000302.59-001;name2=C21orf55
chr21	ENCODE	exon	33782385	33783601	.	-	.	Parent=gene1621
chr21	ENCODE	CDS	33782404	33783570	.	-	0	Parent=gene1621
chr21	ENCODE	exon	33785243	33785650	.	-	.	Parent=gene1621
###
chr21	ENCODE	gene	33798108	33836314	.	-	.	ID=gene1622;Name=AP000302.60-003;name2=GART
chr21	ENCODE	exon	33798108	33798492	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33798301	33798492	.	-	0	Parent=gene1622
chr21	ENCODE	exon	33798589	33798704	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33798589	33798704	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33799738	33799879	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33799738	33799879	.	-	0	Parent=gene1622
chr21	ENCODE	exon	33800151	33800281	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33800151	33800281	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33803960	33804097	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33803960	33804097	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33805429	33805635	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33805429	33805635	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33811166	33811318	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33811166	33811318	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33811534	33811785	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33811534	33811785	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33814541	33814739	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33814541	33814739	.	-	0	Parent=gene1622
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33815083	33815192	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33816365	33816459	.	-	1	Parent=gene1622
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33818946	33819177	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33822343	33822511	.	-	0	Parent=gene1622
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33822695	33822780	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33823026	33823113	.	-	0	Parent=gene1622
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33824935	33825060	.	-	0	Parent=gene1622
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33825665	33825733	.	-	0	Parent=gene1622
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33826521	33826632	.	-	1	Parent=gene1622
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33828755	33828929	.	-	2	Parent=gene1622
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1622
chr21	ENCODE	CDS	33829401	33829496	.	-	2	Parent=gene1622
chr21	ENCODE	CDS	33833347	33833491	.	-	0	Parent=gene1622
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene1622
chr21	ENCODE	exon	33836241	33836314	.	-	.	Parent=gene1622
###
chr21	ENCODE	gene	33798108	33837018	.	-	.	ID=gene1623;Name=AP000302.60-001;name2=GART
chr21	ENCODE	exon	33798108	33798492	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33798301	33798492	.	-	0	Parent=gene1623
chr21	ENCODE	exon	33798589	33798704	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33798589	33798704	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33799738	33799879	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33799738	33799879	.	-	0	Parent=gene1623
chr21	ENCODE	exon	33800151	33800281	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33800151	33800281	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33803960	33804097	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33803960	33804097	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33805429	33805635	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33805429	33805635	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33811166	33811318	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33811166	33811318	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33811534	33811785	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33811534	33811785	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33814541	33814739	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33814541	33814739	.	-	0	Parent=gene1623
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33815083	33815192	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33816365	33816459	.	-	1	Parent=gene1623
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33818946	33819177	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33822343	33822511	.	-	0	Parent=gene1623
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33822695	33822780	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33823026	33823113	.	-	0	Parent=gene1623
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33824935	33825060	.	-	0	Parent=gene1623
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33825665	33825733	.	-	0	Parent=gene1623
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33826521	33826632	.	-	1	Parent=gene1623
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33828755	33828929	.	-	2	Parent=gene1623
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1623
chr21	ENCODE	CDS	33829401	33829496	.	-	2	Parent=gene1623
chr21	ENCODE	CDS	33833347	33833491	.	-	0	Parent=gene1623
chr21	ENCODE	exon	33833347	33833499	.	-	.	Parent=gene1623
chr21	ENCODE	exon	33836763	33837018	.	-	.	Parent=gene1623
###
chr21	ENCODE	gene	33798108	33837037	.	-	.	ID=gene1624;Name=AP000302.60-006;name2=GART
chr21	ENCODE	exon	33798108	33798492	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33798301	33798492	.	-	0	Parent=gene1624
chr21	ENCODE	exon	33798589	33798704	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33798589	33798704	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33799738	33799879	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33799738	33799879	.	-	0	Parent=gene1624
chr21	ENCODE	exon	33800151	33800281	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33800151	33800281	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33803960	33804097	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33803960	33804097	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33805429	33805635	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33805429	33805635	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33811166	33811318	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33811166	33811318	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33811534	33811785	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33811534	33811785	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33814541	33814739	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33814541	33814739	.	-	0	Parent=gene1624
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33815083	33815192	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33816365	33816459	.	-	1	Parent=gene1624
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33818946	33819177	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33822343	33822511	.	-	0	Parent=gene1624
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33822695	33822780	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33823026	33823113	.	-	0	Parent=gene1624
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33824935	33825060	.	-	0	Parent=gene1624
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33825665	33825733	.	-	0	Parent=gene1624
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33826521	33826632	.	-	1	Parent=gene1624
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33828755	33828929	.	-	2	Parent=gene1624
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1624
chr21	ENCODE	CDS	33829401	33829496	.	-	2	Parent=gene1624
chr21	ENCODE	CDS	33833347	33833491	.	-	0	Parent=gene1624
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene1624
chr21	ENCODE	exon	33836836	33837037	.	-	.	Parent=gene1624
###
chr21	ENCODE	gene	33798110	33837068	.	-	.	ID=gene1625;Name=AP000302.60-002;name2=GART
chr21	ENCODE	exon	33798110	33798492	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33798589	33798704	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33799738	33799879	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33800151	33800281	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33803960	33804097	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33805429	33805635	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33811166	33811318	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33811534	33811785	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33814541	33814739	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33822691	33822780	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene1625
chr21	ENCODE	exon	33836767	33837068	.	-	.	Parent=gene1625
###
chr21	ENCODE	gene	33800152	33805569	.	-	.	ID=gene1626;Name=AP000302.60-017;name2=GART
chr21	ENCODE	exon	33800152	33800257	.	-	.	Parent=gene1626
chr21	ENCODE	exon	33803991	33804097	.	-	.	Parent=gene1626
chr21	ENCODE	exon	33805429	33805569	.	-	.	Parent=gene1626
###
chr21	ENCODE	gene	33800217	33804510	.	-	.	ID=gene1627;Name=AP000302.60-018;name2=GART
chr21	ENCODE	exon	33800217	33800281	.	-	.	Parent=gene1627
chr21	ENCODE	exon	33803960	33804510	.	-	.	Parent=gene1627
###
chr21	ENCODE	gene	33803365	33805481	.	-	.	ID=gene1628;Name=AP000302.60-019;name2=GART
chr21	ENCODE	exon	33803365	33804097	.	-	.	Parent=gene1628
chr21	ENCODE	exon	33805429	33805481	.	-	.	Parent=gene1628
###
chr21	ENCODE	gene	33814699	33819005	.	-	.	ID=gene1629;name2=GART;Name=AP000302.60-005
chr21	ENCODE	exon	33814699	33814822	.	-	.	Parent=gene1629
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene1629
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene1629
chr21	ENCODE	exon	33818946	33819005	.	-	.	Parent=gene1629
###
chr21	ENCODE	gene	33816368	33822940	.	-	.	ID=gene1630;Name=AP000302.60-016;name2=GART
chr21	ENCODE	exon	33816368	33816459	.	-	.	Parent=gene1630
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene1630
chr21	ENCODE	exon	33822343	33822940	.	-	.	Parent=gene1630
###
chr21	ENCODE	gene	33818186	33836290	.	-	.	ID=gene1631;Name=AP000302.60-004;name2=GART
chr21	ENCODE	exon	33818186	33819177	.	-	.	Parent=gene1631
chr21	ENCODE	CDS	33818942	33819177	.	-	2	Parent=gene1631
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene1631
chr21	ENCODE	CDS	33822343	33822511	.	-	0	Parent=gene1631
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene1631
chr21	ENCODE	CDS	33822695	33822780	.	-	2	Parent=gene1631
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene1631
chr21	ENCODE	CDS	33823026	33823113	.	-	0	Parent=gene1631
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene1631
chr21	ENCODE	CDS	33824935	33825060	.	-	0	Parent=gene1631
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene1631
chr21	ENCODE	CDS	33825665	33825733	.	-	0	Parent=gene1631
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1631
chr21	ENCODE	CDS	33826521	33826632	.	-	1	Parent=gene1631
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene1631
chr21	ENCODE	CDS	33828755	33828929	.	-	2	Parent=gene1631
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1631
chr21	ENCODE	CDS	33829401	33829496	.	-	2	Parent=gene1631
chr21	ENCODE	CDS	33833347	33833491	.	-	0	Parent=gene1631
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene1631
chr21	ENCODE	exon	33836241	33836290	.	-	.	Parent=gene1631
###
chr21	ENCODE	gene	33822442	33828806	.	-	.	ID=gene1632;Name=AP000302.60-014;name2=GART
chr21	ENCODE	exon	33822442	33822511	.	-	.	Parent=gene1632
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene1632
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene1632
chr21	ENCODE	exon	33823743	33823944	.	-	.	Parent=gene1632
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene1632
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene1632
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1632
chr21	ENCODE	exon	33828755	33828806	.	-	.	Parent=gene1632
###
chr21	ENCODE	gene	33822739	33825458	.	-	.	ID=gene1633;Name=AP000302.60-015;name2=GART
chr21	ENCODE	exon	33822739	33822780	.	-	.	Parent=gene1633
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene1633
chr21	ENCODE	exon	33824935	33825458	.	-	.	Parent=gene1633
###
chr21	ENCODE	gene	33824886	33828855	.	-	.	ID=gene1634;Name=AP000302.60-012;name2=GART
chr21	ENCODE	exon	33824886	33825060	.	-	.	Parent=gene1634
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene1634
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1634
chr21	ENCODE	exon	33828755	33828855	.	-	.	Parent=gene1634
###
chr21	ENCODE	gene	33824935	33837667	.	-	.	ID=gene1635;Name=AP000302.60-007;name2=GART
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene1635
chr21	ENCODE	CDS	33824935	33825060	.	-	0	Parent=gene1635
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene1635
chr21	ENCODE	CDS	33825665	33825733	.	-	0	Parent=gene1635
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1635
chr21	ENCODE	CDS	33826521	33826632	.	-	1	Parent=gene1635
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene1635
chr21	ENCODE	CDS	33828755	33828929	.	-	2	Parent=gene1635
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1635
chr21	ENCODE	CDS	33829401	33829496	.	-	2	Parent=gene1635
chr21	ENCODE	CDS	33833347	33833491	.	-	0	Parent=gene1635
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene1635
chr21	ENCODE	exon	33837396	33837667	.	-	.	Parent=gene1635
###
chr21	ENCODE	gene	33824963	33836969	.	-	.	ID=gene1636;Name=AP000302.60-009;name2=GART
chr21	ENCODE	exon	33824963	33825060	.	-	.	Parent=gene1636
chr21	ENCODE	CDS	33824963	33825060	.	-	0	Parent=gene1636
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene1636
chr21	ENCODE	CDS	33825665	33825733	.	-	0	Parent=gene1636
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1636
chr21	ENCODE	CDS	33826521	33826632	.	-	1	Parent=gene1636
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene1636
chr21	ENCODE	CDS	33828755	33828929	.	-	2	Parent=gene1636
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1636
chr21	ENCODE	CDS	33829401	33829496	.	-	2	Parent=gene1636
chr21	ENCODE	CDS	33833347	33833491	.	-	0	Parent=gene1636
chr21	ENCODE	exon	33833347	33833499	.	-	.	Parent=gene1636
chr21	ENCODE	exon	33836836	33836969	.	-	.	Parent=gene1636
###
chr21	ENCODE	gene	33825512	33836255	.	-	.	ID=gene1637;Name=AP000302.60-011;name2=GART
chr21	ENCODE	exon	33825512	33825733	.	-	.	Parent=gene1637
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene1637
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene1637
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1637
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene1637
chr21	ENCODE	exon	33836241	33836255	.	-	.	Parent=gene1637
###
chr21	ENCODE	gene	33825949	33828848	.	-	.	ID=gene1638;Name=AP000302.60-013;name2=GART
chr21	ENCODE	exon	33825949	33826632	.	-	.	Parent=gene1638
chr21	ENCODE	exon	33828755	33828848	.	-	.	Parent=gene1638
###
chr21	ENCODE	gene	33828755	33836996	.	-	.	ID=gene1639;Name=AP000302.60-008;name2=GART
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene1639
chr21	ENCODE	CDS	33828755	33828929	.	-	2	Parent=gene1639
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1639
chr21	ENCODE	CDS	33829401	33829496	.	-	2	Parent=gene1639
chr21	ENCODE	CDS	33833347	33833491	.	-	0	Parent=gene1639
chr21	ENCODE	exon	33833347	33833499	.	-	.	Parent=gene1639
chr21	ENCODE	exon	33836724	33836996	.	-	.	Parent=gene1639
###
chr21	ENCODE	gene	33828763	33836539	.	-	.	ID=gene1640;Name=AP000302.60-010;name2=GART
chr21	ENCODE	exon	33828763	33828929	.	-	.	Parent=gene1640
chr21	ENCODE	CDS	33828763	33828929	.	-	2	Parent=gene1640
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene1640
chr21	ENCODE	CDS	33829401	33829496	.	-	2	Parent=gene1640
chr21	ENCODE	CDS	33833347	33833491	.	-	0	Parent=gene1640
chr21	ENCODE	exon	33833347	33833499	.	-	.	Parent=gene1640
chr21	ENCODE	exon	33836241	33836539	.	-	.	Parent=gene1640
###
chr21	ENCODE	gene	33836794	33871657	.	+	.	ID=gene1641;Name=AP000304.8-001;name2=SON
chr21	ENCODE	exon	33836794	33837345	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33837269	33837345	.	+	0	Parent=gene1641
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33840389	33840555	.	+	1	Parent=gene1641
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33843652	33849567	.	+	2	Parent=gene1641
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33851332	33851492	.	+	2	Parent=gene1641
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33853406	33853552	.	+	0	Parent=gene1641
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33853763	33853951	.	+	0	Parent=gene1641
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33861333	33861443	.	+	0	Parent=gene1641
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33863147	33863263	.	+	0	Parent=gene1641
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33867484	33867631	.	+	0	Parent=gene1641
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33869772	33869843	.	+	2	Parent=gene1641
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1641
chr21	ENCODE	CDS	33869954	33870069	.	+	2	Parent=gene1641
chr21	ENCODE	CDS	33870541	33870600	.	+	0	Parent=gene1641
chr21	ENCODE	exon	33870541	33871657	.	+	.	Parent=gene1641
###
chr21	ENCODE	gene	33837220	33871655	.	+	.	ID=gene1642;Name=AP000304.8-021;name2=SON
chr21	ENCODE	exon	33837220	33837345	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33843652	33845625	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33845746	33849567	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1642
chr21	ENCODE	exon	33870541	33871655	.	+	.	Parent=gene1642
###
chr21	ENCODE	gene	33837228	33840928	.	+	.	ID=gene1643;Name=AP000304.8-010;name2=SON
chr21	ENCODE	exon	33837228	33837345	.	+	.	Parent=gene1643
chr21	ENCODE	exon	33840389	33840928	.	+	.	Parent=gene1643
###
chr21	ENCODE	gene	33837228	33871657	.	+	.	ID=gene1644;Name=AP000304.8-002;name2=SON
chr21	ENCODE	exon	33837228	33837345	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33837269	33837345	.	+	0	Parent=gene1644
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33840389	33840555	.	+	1	Parent=gene1644
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33851332	33851492	.	+	2	Parent=gene1644
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33853406	33853552	.	+	0	Parent=gene1644
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33853763	33853951	.	+	0	Parent=gene1644
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33861333	33861443	.	+	0	Parent=gene1644
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33863147	33863263	.	+	0	Parent=gene1644
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33867484	33867631	.	+	0	Parent=gene1644
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33869772	33869843	.	+	2	Parent=gene1644
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1644
chr21	ENCODE	CDS	33869954	33870069	.	+	2	Parent=gene1644
chr21	ENCODE	CDS	33870541	33870600	.	+	0	Parent=gene1644
chr21	ENCODE	exon	33870541	33871657	.	+	.	Parent=gene1644
###
chr21	ENCODE	gene	33837240	33854843	.	+	.	ID=gene1645;Name=AP000304.8-003;name2=SON
chr21	ENCODE	exon	33837240	33837345	.	+	.	Parent=gene1645
chr21	ENCODE	CDS	33837269	33837345	.	+	0	Parent=gene1645
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene1645
chr21	ENCODE	CDS	33840389	33840555	.	+	1	Parent=gene1645
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene1645
chr21	ENCODE	CDS	33843652	33849567	.	+	2	Parent=gene1645
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1645
chr21	ENCODE	CDS	33851332	33851492	.	+	2	Parent=gene1645
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene1645
chr21	ENCODE	CDS	33853406	33853552	.	+	0	Parent=gene1645
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene1645
chr21	ENCODE	CDS	33853763	33853951	.	+	0	Parent=gene1645
chr21	ENCODE	CDS	33854053	33854307	.	+	0	Parent=gene1645
chr21	ENCODE	exon	33854053	33854843	.	+	.	Parent=gene1645
###
chr21	ENCODE	gene	33837240	33871657	.	+	.	ID=gene1646;Name=AP000304.8-005;name2=SON
chr21	ENCODE	exon	33837240	33837345	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33851722	33851844	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1646
chr21	ENCODE	exon	33870594	33871657	.	+	.	Parent=gene1646
###
chr21	ENCODE	gene	33837240	33871657	.	+	.	ID=gene1647;name2=SON;Name=AP000304.8-004
chr21	ENCODE	exon	33837240	33837345	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1647
chr21	ENCODE	exon	33870594	33871657	.	+	.	Parent=gene1647
###
chr21	ENCODE	gene	33837241	33853232	.	+	.	ID=gene1648;name2=SON;Name=AP000304.8-006
chr21	ENCODE	exon	33837241	33837345	.	+	.	Parent=gene1648
chr21	ENCODE	CDS	33837269	33837345	.	+	0	Parent=gene1648
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene1648
chr21	ENCODE	CDS	33840389	33840555	.	+	1	Parent=gene1648
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene1648
chr21	ENCODE	CDS	33843652	33849567	.	+	2	Parent=gene1648
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1648
chr21	ENCODE	CDS	33851332	33851492	.	+	2	Parent=gene1648
chr21	ENCODE	CDS	33851722	33851727	.	+	0	Parent=gene1648
chr21	ENCODE	exon	33851722	33853232	.	+	.	Parent=gene1648
###
chr21	ENCODE	gene	33837246	33841215	.	+	.	ID=gene1649;Name=AP000304.8-011;name2=SON
chr21	ENCODE	exon	33837246	33837345	.	+	.	Parent=gene1649
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene1649
chr21	ENCODE	exon	33841177	33841215	.	+	.	Parent=gene1649
###
chr21	ENCODE	gene	33843772	33871651	.	+	.	ID=gene1650;Name=AP000304.8-020;name2=SON
chr21	ENCODE	exon	33843772	33844416	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33849478	33849567	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1650
chr21	ENCODE	exon	33870594	33871651	.	+	.	Parent=gene1650
###
chr21	ENCODE	gene	33845060	33871657	.	+	.	ID=gene1651;Name=AP000304.8-007;name2=SON
chr21	ENCODE	exon	33845060	33845465	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33846424	33849567	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1651
chr21	ENCODE	exon	33870541	33871657	.	+	.	Parent=gene1651
###
chr21	ENCODE	gene	33849225	33861643	.	+	.	ID=gene1652;name2=SON;Name=AP000304.8-008
chr21	ENCODE	exon	33849225	33849567	.	+	.	Parent=gene1652
chr21	ENCODE	CDS	33849225	33849567	.	+	0	Parent=gene1652
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene1652
chr21	ENCODE	CDS	33851332	33851492	.	+	2	Parent=gene1652
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene1652
chr21	ENCODE	CDS	33853406	33853552	.	+	0	Parent=gene1652
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene1652
chr21	ENCODE	CDS	33853763	33853951	.	+	0	Parent=gene1652
chr21	ENCODE	CDS	33861333	33861524	.	+	0	Parent=gene1652
chr21	ENCODE	exon	33861333	33861643	.	+	.	Parent=gene1652
###
chr21	ENCODE	gene	33861355	33863459	.	+	.	ID=gene1653;Name=AP000304.8-012;name2=SON
chr21	ENCODE	exon	33861355	33861443	.	+	.	Parent=gene1653
chr21	ENCODE	exon	33863147	33863459	.	+	.	Parent=gene1653
###
chr21	ENCODE	gene	33861361	33870689	.	+	.	ID=gene1654;Name=AP000304.8-013;name2=SON
chr21	ENCODE	exon	33861361	33861443	.	+	.	Parent=gene1654
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene1654
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene1654
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1654
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1654
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1654
chr21	ENCODE	exon	33870541	33870689	.	+	.	Parent=gene1654
###
chr21	ENCODE	gene	33863952	33870660	.	+	.	ID=gene1655;Name=AP000304.8-019;name2=SON
chr21	ENCODE	exon	33863952	33864106	.	+	.	Parent=gene1655
chr21	ENCODE	exon	33865927	33865964	.	+	.	Parent=gene1655
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene1655
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1655
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1655
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1655
chr21	ENCODE	exon	33870594	33870660	.	+	.	Parent=gene1655
###
chr21	ENCODE	gene	33865911	33870623	.	+	.	ID=gene1656;name2=SON;Name=AP000304.8-017
chr21	ENCODE	exon	33865911	33865964	.	+	.	Parent=gene1656
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene1656
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1656
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1656
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1656
chr21	ENCODE	exon	33870594	33870623	.	+	.	Parent=gene1656
###
chr21	ENCODE	gene	33865911	33870645	.	+	.	ID=gene1657;Name=AP000304.8-018;name2=SON
chr21	ENCODE	exon	33865911	33865964	.	+	.	Parent=gene1657
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene1657
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1657
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1657
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1657
chr21	ENCODE	exon	33870541	33870645	.	+	.	Parent=gene1657
###
chr21	ENCODE	gene	33866389	33871657	.	+	.	ID=gene1658;Name=AP000304.8-009;name2=SON
chr21	ENCODE	exon	33866389	33866806	.	+	.	Parent=gene1658
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1658
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1658
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1658
chr21	ENCODE	exon	33870594	33871657	.	+	.	Parent=gene1658
###
chr21	ENCODE	gene	33866703	33871057	.	+	.	ID=gene1659;Name=AP000304.8-014;name2=SON
chr21	ENCODE	exon	33866703	33866806	.	+	.	Parent=gene1659
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene1659
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1659
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1659
chr21	ENCODE	exon	33870541	33871057	.	+	.	Parent=gene1659
###
chr21	ENCODE	gene	33867201	33870692	.	+	.	ID=gene1660;Name=AP000304.8-015;name2=SON
chr21	ENCODE	exon	33867201	33867631	.	+	.	Parent=gene1660
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1660
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1660
chr21	ENCODE	exon	33870541	33870692	.	+	.	Parent=gene1660
###
chr21	ENCODE	gene	33867390	33871158	.	+	.	ID=gene1661;Name=AP000304.8-016;name2=SON
chr21	ENCODE	exon	33867390	33867631	.	+	.	Parent=gene1661
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene1661
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene1661
chr21	ENCODE	exon	33870594	33871158	.	+	.	Parent=gene1661
###
chr21	ENCODE	gene	33869653	33882846	.	-	.	ID=gene1662;Name=AP000304.11-008;name2=DONSON
chr21	ENCODE	exon	33869653	33869984	.	-	.	Parent=gene1662
chr21	ENCODE	exon	33872475	33872620	.	-	.	Parent=gene1662
chr21	ENCODE	CDS	33872483	33872620	.	-	0	Parent=gene1662
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene1662
chr21	ENCODE	CDS	33873526	33873738	.	-	0	Parent=gene1662
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene1662
chr21	ENCODE	CDS	33875478	33875676	.	-	1	Parent=gene1662
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene1662
chr21	ENCODE	CDS	33876127	33876231	.	-	1	Parent=gene1662
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene1662
chr21	ENCODE	CDS	33876341	33876422	.	-	2	Parent=gene1662
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene1662
chr21	ENCODE	CDS	33877664	33877842	.	-	1	Parent=gene1662
chr21	ENCODE	exon	33878766	33878902	.	-	.	Parent=gene1662
chr21	ENCODE	CDS	33878766	33878902	.	-	0	Parent=gene1662
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene1662
chr21	ENCODE	CDS	33880154	33880357	.	-	0	Parent=gene1662
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene1662
chr21	ENCODE	CDS	33881698	33881778	.	-	0	Parent=gene1662
chr21	ENCODE	CDS	33882497	33882817	.	-	0	Parent=gene1662
chr21	ENCODE	exon	33882497	33882846	.	-	.	Parent=gene1662
###
chr21	ENCODE	gene	33871737	33882822	.	-	.	ID=gene1663;Name=AP000304.11-007;name2=DONSON
chr21	ENCODE	exon	33871737	33872620	.	-	.	Parent=gene1663
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene1663
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene1663
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene1663
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene1663
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene1663
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene1663
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene1663
chr21	ENCODE	exon	33882497	33882822	.	-	.	Parent=gene1663
###
chr21	ENCODE	gene	33872081	33882884	.	-	.	ID=gene1664;Name=AP000304.11-001;name2=DONSON
chr21	ENCODE	exon	33872081	33872620	.	-	.	Parent=gene1664
chr21	ENCODE	CDS	33872483	33872620	.	-	0	Parent=gene1664
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene1664
chr21	ENCODE	CDS	33873526	33873738	.	-	0	Parent=gene1664
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene1664
chr21	ENCODE	CDS	33875478	33875676	.	-	1	Parent=gene1664
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene1664
chr21	ENCODE	CDS	33876127	33876231	.	-	1	Parent=gene1664
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene1664
chr21	ENCODE	CDS	33876341	33876422	.	-	2	Parent=gene1664
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene1664
chr21	ENCODE	CDS	33877664	33877842	.	-	1	Parent=gene1664
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene1664
chr21	ENCODE	CDS	33878766	33878944	.	-	0	Parent=gene1664
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene1664
chr21	ENCODE	CDS	33880154	33880357	.	-	0	Parent=gene1664
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene1664
chr21	ENCODE	CDS	33881698	33881778	.	-	0	Parent=gene1664
chr21	ENCODE	CDS	33882497	33882817	.	-	0	Parent=gene1664
chr21	ENCODE	exon	33882497	33882884	.	-	.	Parent=gene1664
###
chr21	ENCODE	gene	33872081	33889641	.	-	.	ID=gene1665;Name=AP000304.11-003;name2=DONSON
chr21	ENCODE	exon	33872081	33872620	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33882497	33883137	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33884017	33884097	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33885338	33885547	.	-	.	Parent=gene1665
chr21	ENCODE	exon	33889532	33889641	.	-	.	Parent=gene1665
###
chr21	ENCODE	gene	33872093	33882846	.	-	.	ID=gene1666;Name=AP000304.11-004;name2=DONSON
chr21	ENCODE	exon	33872093	33872620	.	-	.	Parent=gene1666
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene1666
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene1666
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene1666
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene1666
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene1666
chr21	ENCODE	exon	33880154	33880236	.	-	.	Parent=gene1666
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene1666
chr21	ENCODE	exon	33882497	33882846	.	-	.	Parent=gene1666
###
chr21	ENCODE	gene	33872100	33873790	.	-	.	ID=gene1667;Name=AP000304.11-010;name2=DONSON
chr21	ENCODE	exon	33872100	33872620	.	-	.	Parent=gene1667
chr21	ENCODE	exon	33873526	33873790	.	-	.	Parent=gene1667
###
chr21	ENCODE	gene	33872118	33881778	.	-	.	ID=gene1668;Name=AP000304.11-006;name2=DONSON
chr21	ENCODE	exon	33872118	33872620	.	-	.	Parent=gene1668
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene1668
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene1668
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene1668
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene1668
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene1668
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene1668
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene1668
###
chr21	ENCODE	gene	33872118	33881778	.	-	.	ID=gene1669;Name=AP000304.11-005;name2=DONSON
chr21	ENCODE	exon	33872118	33872620	.	-	.	Parent=gene1669
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene1669
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene1669
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene1669
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene1669
###
chr21	ENCODE	gene	33872377	33882810	.	-	.	ID=gene1670;Name=AP000304.11-002;name2=DONSON
chr21	ENCODE	exon	33872377	33872620	.	-	.	Parent=gene1670
chr21	ENCODE	CDS	33872483	33872620	.	-	1	Parent=gene1670
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene1670
chr21	ENCODE	CDS	33873526	33873738	.	-	1	Parent=gene1670
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene1670
chr21	ENCODE	CDS	33875478	33875676	.	-	2	Parent=gene1670
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene1670
chr21	ENCODE	CDS	33876127	33876231	.	-	2	Parent=gene1670
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene1670
chr21	ENCODE	CDS	33876341	33876422	.	-	0	Parent=gene1670
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene1670
chr21	ENCODE	CDS	33877664	33877842	.	-	2	Parent=gene1670
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene1670
chr21	ENCODE	CDS	33878766	33878944	.	-	1	Parent=gene1670
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene1670
chr21	ENCODE	CDS	33880154	33880357	.	-	1	Parent=gene1670
chr21	ENCODE	exon	33882497	33882810	.	-	.	Parent=gene1670
chr21	ENCODE	CDS	33882497	33882810	.	-	0	Parent=gene1670
###
chr21	ENCODE	gene	33873700	33880334	.	-	.	ID=gene1671;Name=AP000304.11-009;name2=DONSON
chr21	ENCODE	exon	33873700	33873738	.	-	.	Parent=gene1671
chr21	ENCODE	CDS	33873700	33873738	.	-	2	Parent=gene1671
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene1671
chr21	ENCODE	CDS	33875478	33875676	.	-	0	Parent=gene1671
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene1671
chr21	ENCODE	CDS	33876127	33876231	.	-	0	Parent=gene1671
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene1671
chr21	ENCODE	CDS	33878766	33878944	.	-	2	Parent=gene1671
chr21	ENCODE	exon	33880154	33880334	.	-	.	Parent=gene1671
chr21	ENCODE	CDS	33880154	33880334	.	-	0	Parent=gene1671
###
chr21	ENCODE	gene	33875351	33876230	.	-	.	ID=gene1672;Name=AP000304.11-011;name2=DONSON
chr21	ENCODE	exon	33875351	33875676	.	-	.	Parent=gene1672
chr21	ENCODE	exon	33876127	33876230	.	-	.	Parent=gene1672
###
chr21	ENCODE	gene	33878863	34206505	.	-	.	ID=gene1673;Name=AP000304.11-012;name2=DONSON
chr21	ENCODE	exon	33878863	33878944	.	-	.	Parent=gene1673
chr21	ENCODE	CDS	33878863	33878944	.	-	2	Parent=gene1673
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene1673
chr21	ENCODE	CDS	33880154	33880357	.	-	2	Parent=gene1673
chr21	ENCODE	exon	34201515	34201627	.	-	.	Parent=gene1673
chr21	ENCODE	CDS	34201515	34201627	.	-	1	Parent=gene1673
chr21	ENCODE	exon	34203256	34203385	.	-	.	Parent=gene1673
chr21	ENCODE	CDS	34203256	34203385	.	-	2	Parent=gene1673
chr21	ENCODE	exon	34206463	34206505	.	-	.	Parent=gene1673
chr21	ENCODE	CDS	34206463	34206505	.	-	0	Parent=gene1673
###
chr21	ENCODE	gene	33883517	33935936	.	-	.	ID=gene1674;Name=AP000304.10-001;name2=CRYZL1
chr21	ENCODE	exon	33883517	33884097	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33883998	33884097	.	-	1	Parent=gene1674
chr21	ENCODE	exon	33885338	33885383	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33885338	33885383	.	-	2	Parent=gene1674
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33889907	33890012	.	-	0	Parent=gene1674
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33891456	33891577	.	-	2	Parent=gene1674
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33893326	33893424	.	-	2	Parent=gene1674
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33896410	33896521	.	-	0	Parent=gene1674
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33897580	33897713	.	-	2	Parent=gene1674
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33907714	33907782	.	-	2	Parent=gene1674
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33910882	33910926	.	-	2	Parent=gene1674
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33916172	33916244	.	-	0	Parent=gene1674
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1674
chr21	ENCODE	CDS	33918859	33918936	.	-	0	Parent=gene1674
chr21	ENCODE	CDS	33925662	33925727	.	-	0	Parent=gene1674
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene1674
chr21	ENCODE	exon	33935857	33935936	.	-	.	Parent=gene1674
###
chr21	ENCODE	gene	33883562	33936094	.	-	.	ID=gene1675;Name=AP000304.10-007;name2=CRYZL1
chr21	ENCODE	exon	33883562	33884097	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33883998	33884097	.	-	1	Parent=gene1675
chr21	ENCODE	exon	33885338	33885383	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33885338	33885383	.	-	2	Parent=gene1675
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33889907	33890012	.	-	0	Parent=gene1675
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33891456	33891577	.	-	2	Parent=gene1675
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33893326	33893424	.	-	2	Parent=gene1675
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33896410	33896521	.	-	0	Parent=gene1675
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33897580	33897713	.	-	2	Parent=gene1675
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33907714	33907782	.	-	2	Parent=gene1675
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33916172	33916244	.	-	0	Parent=gene1675
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1675
chr21	ENCODE	CDS	33918859	33918936	.	-	0	Parent=gene1675
chr21	ENCODE	CDS	33925662	33925727	.	-	0	Parent=gene1675
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene1675
chr21	ENCODE	exon	33935857	33936094	.	-	.	Parent=gene1675
###
chr21	ENCODE	gene	33883637	33885894	.	-	.	ID=gene1676;Name=AP000304.10-023;name2=CRYZL1
chr21	ENCODE	exon	33883637	33884097	.	-	.	Parent=gene1676
chr21	ENCODE	exon	33885338	33885894	.	-	.	Parent=gene1676
###
chr21	ENCODE	gene	33883643	33935923	.	-	.	ID=gene1677;Name=AP000304.10-002;name2=CRYZL1
chr21	ENCODE	exon	33883643	33884097	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33884083	33884097	.	-	0	Parent=gene1677
chr21	ENCODE	exon	33885338	33885387	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33885338	33885387	.	-	2	Parent=gene1677
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33889907	33890012	.	-	0	Parent=gene1677
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33891456	33891577	.	-	2	Parent=gene1677
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33893326	33893424	.	-	2	Parent=gene1677
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33896410	33896521	.	-	0	Parent=gene1677
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33897580	33897713	.	-	2	Parent=gene1677
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33907714	33907782	.	-	2	Parent=gene1677
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33910882	33910926	.	-	2	Parent=gene1677
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33916172	33916244	.	-	0	Parent=gene1677
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1677
chr21	ENCODE	CDS	33918859	33918936	.	-	0	Parent=gene1677
chr21	ENCODE	CDS	33925662	33925727	.	-	0	Parent=gene1677
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene1677
chr21	ENCODE	exon	33935857	33935923	.	-	.	Parent=gene1677
###
chr21	ENCODE	gene	33883644	33907736	.	-	.	ID=gene1678;Name=AP000304.10-009;name2=CRYZL1
chr21	ENCODE	exon	33883644	33884097	.	-	.	Parent=gene1678
chr21	ENCODE	exon	33885338	33885547	.	-	.	Parent=gene1678
chr21	ENCODE	exon	33889532	33889790	.	-	.	Parent=gene1678
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1678
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1678
chr21	ENCODE	exon	33893326	33893461	.	-	.	Parent=gene1678
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1678
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1678
chr21	ENCODE	exon	33907714	33907736	.	-	.	Parent=gene1678
###
chr21	ENCODE	gene	33883721	33893327	.	-	.	ID=gene1679;Name=AP000304.10-021;name2=CRYZL1
chr21	ENCODE	exon	33883721	33883981	.	-	.	Parent=gene1679
chr21	ENCODE	CDS	33883921	33883981	.	-	0	Parent=gene1679
chr21	ENCODE	exon	33885338	33885383	.	-	.	Parent=gene1679
chr21	ENCODE	CDS	33885338	33885383	.	-	1	Parent=gene1679
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1679
chr21	ENCODE	CDS	33889907	33890012	.	-	2	Parent=gene1679
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1679
chr21	ENCODE	CDS	33891456	33891577	.	-	1	Parent=gene1679
chr21	ENCODE	exon	33893326	33893327	.	-	.	Parent=gene1679
chr21	ENCODE	CDS	33893326	33893327	.	-	0	Parent=gene1679
###
chr21	ENCODE	gene	33883736	33891576	.	-	.	ID=gene1680;Name=AP000304.10-022;name2=CRYZL1
chr21	ENCODE	exon	33883736	33884097	.	-	.	Parent=gene1680
chr21	ENCODE	exon	33885338	33885404	.	-	.	Parent=gene1680
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1680
chr21	ENCODE	exon	33891456	33891576	.	-	.	Parent=gene1680
###
chr21	ENCODE	gene	33883945	33896441	.	-	.	ID=gene1681;Name=AP000304.10-019;name2=CRYZL1
chr21	ENCODE	exon	33883945	33884097	.	-	.	Parent=gene1681
chr21	ENCODE	exon	33885338	33885383	.	-	.	Parent=gene1681
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1681
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1681
chr21	ENCODE	exon	33893326	33893461	.	-	.	Parent=gene1681
chr21	ENCODE	exon	33896410	33896441	.	-	.	Parent=gene1681
###
chr21	ENCODE	gene	33888683	33935935	.	-	.	ID=gene1682;Name=AP000304.10-003;name2=CRYZL1
chr21	ENCODE	exon	33888683	33889790	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33889789	33889790	.	-	2	Parent=gene1682
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33889907	33890012	.	-	0	Parent=gene1682
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33891456	33891577	.	-	2	Parent=gene1682
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33893326	33893424	.	-	2	Parent=gene1682
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33896410	33896521	.	-	0	Parent=gene1682
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33897580	33897713	.	-	2	Parent=gene1682
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33907714	33907782	.	-	2	Parent=gene1682
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33910882	33910926	.	-	2	Parent=gene1682
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33916172	33916244	.	-	0	Parent=gene1682
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33918859	33918936	.	-	0	Parent=gene1682
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene1682
chr21	ENCODE	CDS	33925662	33925733	.	-	0	Parent=gene1682
chr21	ENCODE	CDS	33935355	33935420	.	-	0	Parent=gene1682
chr21	ENCODE	exon	33935355	33935481	.	-	.	Parent=gene1682
chr21	ENCODE	exon	33935857	33935935	.	-	.	Parent=gene1682
###
chr21	ENCODE	gene	33888819	33935917	.	-	.	ID=gene1683;Name=AP000304.10-006;name2=CRYZL1
chr21	ENCODE	exon	33888819	33889790	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33889905	33890012	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33893326	33893461	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene1683
chr21	ENCODE	exon	33935857	33935917	.	-	.	Parent=gene1683
###
chr21	ENCODE	gene	33888838	33936514	.	-	.	ID=gene1684;name2=CRYZL1;Name=AP000304.10-005
chr21	ENCODE	exon	33888838	33889790	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33893326	33893461	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene1684
chr21	ENCODE	exon	33935857	33936514	.	-	.	Parent=gene1684
###
chr21	ENCODE	gene	33889307	33916218	.	-	.	ID=gene1685;Name=AP000304.10-017;name2=CRYZL1
chr21	ENCODE	exon	33889307	33889704	.	-	.	Parent=gene1685
chr21	ENCODE	CDS	33889609	33889704	.	-	2	Parent=gene1685
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene1685
chr21	ENCODE	CDS	33891456	33891577	.	-	1	Parent=gene1685
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene1685
chr21	ENCODE	CDS	33893326	33893424	.	-	1	Parent=gene1685
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1685
chr21	ENCODE	CDS	33896410	33896521	.	-	2	Parent=gene1685
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1685
chr21	ENCODE	CDS	33897580	33897713	.	-	1	Parent=gene1685
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1685
chr21	ENCODE	CDS	33907714	33907782	.	-	1	Parent=gene1685
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1685
chr21	ENCODE	CDS	33910882	33910926	.	-	1	Parent=gene1685
chr21	ENCODE	exon	33916172	33916218	.	-	.	Parent=gene1685
chr21	ENCODE	CDS	33916172	33916218	.	-	0	Parent=gene1685
###
chr21	ENCODE	gene	33889513	33896432	.	-	.	ID=gene1686;Name=AP000304.10-020;name2=CRYZL1
chr21	ENCODE	exon	33889513	33889790	.	-	.	Parent=gene1686
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene1686
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene1686
chr21	ENCODE	exon	33896410	33896432	.	-	.	Parent=gene1686
###
chr21	ENCODE	gene	33890238	33897624	.	-	.	ID=gene1687;Name=AP000304.10-018;name2=CRYZL1
chr21	ENCODE	exon	33890238	33890389	.	-	.	Parent=gene1687
chr21	ENCODE	CDS	33890352	33890389	.	-	2	Parent=gene1687
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene1687
chr21	ENCODE	CDS	33893326	33893424	.	-	2	Parent=gene1687
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1687
chr21	ENCODE	CDS	33896410	33896521	.	-	0	Parent=gene1687
chr21	ENCODE	exon	33897580	33897624	.	-	.	Parent=gene1687
chr21	ENCODE	CDS	33897580	33897624	.	-	0	Parent=gene1687
###
chr21	ENCODE	gene	33893372	33935921	.	-	.	ID=gene1688;Name=AP000304.10-012;name2=CRYZL1
chr21	ENCODE	exon	33893372	33893424	.	-	.	Parent=gene1688
chr21	ENCODE	CDS	33893372	33893424	.	-	2	Parent=gene1688
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene1688
chr21	ENCODE	CDS	33896410	33896521	.	-	0	Parent=gene1688
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1688
chr21	ENCODE	CDS	33897580	33897713	.	-	2	Parent=gene1688
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1688
chr21	ENCODE	CDS	33907714	33907782	.	-	2	Parent=gene1688
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1688
chr21	ENCODE	CDS	33910882	33910926	.	-	2	Parent=gene1688
chr21	ENCODE	CDS	33916172	33916232	.	-	0	Parent=gene1688
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1688
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1688
chr21	ENCODE	exon	33935857	33935921	.	-	.	Parent=gene1688
###
chr21	ENCODE	gene	33896444	33927878	.	-	.	ID=gene1689;Name=AP000304.10-013;name2=CRYZL1
chr21	ENCODE	exon	33896444	33896521	.	-	.	Parent=gene1689
chr21	ENCODE	CDS	33896444	33896521	.	-	0	Parent=gene1689
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1689
chr21	ENCODE	CDS	33897580	33897713	.	-	2	Parent=gene1689
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1689
chr21	ENCODE	CDS	33907714	33907782	.	-	2	Parent=gene1689
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1689
chr21	ENCODE	CDS	33910882	33910926	.	-	2	Parent=gene1689
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1689
chr21	ENCODE	CDS	33916172	33916244	.	-	0	Parent=gene1689
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1689
chr21	ENCODE	CDS	33918859	33918936	.	-	0	Parent=gene1689
chr21	ENCODE	CDS	33925662	33925727	.	-	0	Parent=gene1689
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene1689
chr21	ENCODE	exon	33927822	33927878	.	-	.	Parent=gene1689
###
chr21	ENCODE	gene	33896508	33911352	.	-	.	ID=gene1690;Name=AP000304.10-015;name2=CRYZL1
chr21	ENCODE	exon	33896508	33896521	.	-	.	Parent=gene1690
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1690
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1690
chr21	ENCODE	exon	33910882	33911352	.	-	.	Parent=gene1690
###
chr21	ENCODE	gene	33896509	33935906	.	-	.	ID=gene1691;Name=AP000304.10-014;name2=CRYZL1
chr21	ENCODE	exon	33896509	33896521	.	-	.	Parent=gene1691
chr21	ENCODE	CDS	33896509	33896521	.	-	0	Parent=gene1691
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene1691
chr21	ENCODE	CDS	33897580	33897713	.	-	2	Parent=gene1691
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1691
chr21	ENCODE	CDS	33907714	33907782	.	-	2	Parent=gene1691
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1691
chr21	ENCODE	CDS	33910882	33910926	.	-	2	Parent=gene1691
chr21	ENCODE	CDS	33916172	33916232	.	-	0	Parent=gene1691
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1691
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1691
chr21	ENCODE	exon	33925662	33925703	.	-	.	Parent=gene1691
chr21	ENCODE	exon	33935857	33935906	.	-	.	Parent=gene1691
###
chr21	ENCODE	gene	33897332	33935896	.	-	.	ID=gene1692;Name=AP000304.10-016;name2=CRYZL1
chr21	ENCODE	exon	33897332	33897713	.	-	.	Parent=gene1692
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene1692
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1692
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1692
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1692
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene1692
chr21	ENCODE	exon	33935857	33935896	.	-	.	Parent=gene1692
###
chr21	ENCODE	gene	33910463	33935898	.	-	.	ID=gene1693;Name=AP000304.10-008;name2=CRYZL1
chr21	ENCODE	exon	33910463	33910779	.	-	.	Parent=gene1693
chr21	ENCODE	CDS	33910700	33910779	.	-	2	Parent=gene1693
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene1693
chr21	ENCODE	CDS	33910882	33910926	.	-	2	Parent=gene1693
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene1693
chr21	ENCODE	CDS	33916172	33916244	.	-	0	Parent=gene1693
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene1693
chr21	ENCODE	CDS	33918859	33918936	.	-	0	Parent=gene1693
chr21	ENCODE	CDS	33925662	33925727	.	-	0	Parent=gene1693
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene1693
chr21	ENCODE	exon	33935857	33935898	.	-	.	Parent=gene1693
###
chr21	ENCODE	gene	33925669	33938102	.	-	.	ID=gene1694;Name=AP000304.10-011;name2=CRYZL1
chr21	ENCODE	exon	33925669	33925733	.	-	.	Parent=gene1694
chr21	ENCODE	exon	33937548	33938102	.	-	.	Parent=gene1694
###
chr21	ENCODE	gene	33933921	33935897	.	-	.	ID=gene1695;Name=AP000304.10-004;name2=CRYZL1
chr21	ENCODE	exon	33933921	33934364	.	-	.	Parent=gene1695
chr21	ENCODE	CDS	33934356	33934364	.	-	0	Parent=gene1695
chr21	ENCODE	CDS	33935355	33935420	.	-	0	Parent=gene1695
chr21	ENCODE	exon	33935355	33935481	.	-	.	Parent=gene1695
chr21	ENCODE	exon	33935857	33935897	.	-	.	Parent=gene1695
###
chr21	ENCODE	gene	33936576	34088586	.	+	.	ID=gene1696;Name=AP000313.6-020;name2=ITSN1
chr21	ENCODE	exon	33936576	33936889	.	+	.	Parent=gene1696
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34013004	34013031	.	+	0	Parent=gene1696
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34015353	34015445	.	+	2	Parent=gene1696
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34016763	34016826	.	+	2	Parent=gene1696
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34029219	34029379	.	+	1	Parent=gene1696
chr21	ENCODE	exon	34044429	34044497	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34044429	34044497	.	+	2	Parent=gene1696
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34045985	34046081	.	+	2	Parent=gene1696
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34049472	34049572	.	+	1	Parent=gene1696
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34056097	34056160	.	+	2	Parent=gene1696
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34060049	34060186	.	+	1	Parent=gene1696
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34061887	34062002	.	+	1	Parent=gene1696
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34066235	34066497	.	+	2	Parent=gene1696
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34068903	34069052	.	+	0	Parent=gene1696
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34069142	34069282	.	+	0	Parent=gene1696
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34075635	34075722	.	+	0	Parent=gene1696
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34076168	34076307	.	+	2	Parent=gene1696
chr21	ENCODE	exon	34088515	34088586	.	+	.	Parent=gene1696
chr21	ENCODE	CDS	34088515	34088586	.	+	0	Parent=gene1696
###
chr21	ENCODE	gene	33936576	34131192	.	+	.	ID=gene1697;Name=AP000313.6-025;name2=ITSN1
chr21	ENCODE	exon	33936576	33936889	.	+	.	Parent=gene1697
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34013004	34013031	.	+	0	Parent=gene1697
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34015353	34015445	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34016763	34016826	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34029219	34029379	.	+	1	Parent=gene1697
chr21	ENCODE	exon	34044429	34044497	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34044429	34044497	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34045985	34046081	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34049472	34049572	.	+	1	Parent=gene1697
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34056097	34056160	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34060049	34060186	.	+	1	Parent=gene1697
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34061887	34062002	.	+	1	Parent=gene1697
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34066235	34066497	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34068903	34069052	.	+	0	Parent=gene1697
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34069142	34069282	.	+	0	Parent=gene1697
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34075635	34075722	.	+	0	Parent=gene1697
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34076168	34076307	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34088515	34088642	.	+	0	Parent=gene1697
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34091553	34091782	.	+	1	Parent=gene1697
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34093982	34094103	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34105149	34105396	.	+	0	Parent=gene1697
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34108087	34108246	.	+	1	Parent=gene1697
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34112441	34112646	.	+	0	Parent=gene1697
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34113415	34113497	.	+	1	Parent=gene1697
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34117661	34117827	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34120992	34121037	.	+	0	Parent=gene1697
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34123798	34123919	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34128481	34128598	.	+	0	Parent=gene1697
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1697
chr21	ENCODE	CDS	34130615	34130806	.	+	2	Parent=gene1697
chr21	ENCODE	CDS	34131161	34131162	.	+	2	Parent=gene1697
chr21	ENCODE	exon	34131161	34131192	.	+	.	Parent=gene1697
###
chr21	ENCODE	gene	33936628	34029379	.	+	.	ID=gene1698;Name=AP000313.6-033;name2=ITSN1
chr21	ENCODE	exon	33936628	33936889	.	+	.	Parent=gene1698
chr21	ENCODE	exon	33983497	33983558	.	+	.	Parent=gene1698
chr21	ENCODE	exon	34010606	34010730	.	+	.	Parent=gene1698
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1698
chr21	ENCODE	CDS	34013004	34013031	.	+	0	Parent=gene1698
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1698
chr21	ENCODE	CDS	34015353	34015445	.	+	2	Parent=gene1698
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1698
chr21	ENCODE	CDS	34016763	34016826	.	+	2	Parent=gene1698
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene1698
chr21	ENCODE	CDS	34029219	34029379	.	+	1	Parent=gene1698
###
chr21	ENCODE	gene	33936629	34016166	.	+	.	ID=gene1699;Name=AP000313.6-034;name2=ITSN1
chr21	ENCODE	exon	33936629	33936889	.	+	.	Parent=gene1699
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1699
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1699
chr21	ENCODE	exon	34016107	34016166	.	+	.	Parent=gene1699
###
chr21	ENCODE	gene	33936634	34194035	.	+	.	ID=gene1700;Name=AP000313.6-001;name2=ITSN1
chr21	ENCODE	exon	33936634	33936889	.	+	.	Parent=gene1700
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34013004	34013031	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34015353	34015445	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34016763	34016826	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34029219	34029379	.	+	1	Parent=gene1700
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34044318	34044497	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34045985	34046081	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34049472	34049572	.	+	1	Parent=gene1700
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34056097	34056160	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34060049	34060186	.	+	1	Parent=gene1700
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34061887	34062002	.	+	1	Parent=gene1700
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34066235	34066497	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34068903	34069052	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34069142	34069282	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34075635	34075722	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34076168	34076307	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34088515	34088642	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34091553	34091782	.	+	1	Parent=gene1700
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34093982	34094103	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34096604	34096618	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34096604	34096618	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34105149	34105396	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34108087	34108246	.	+	1	Parent=gene1700
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34112441	34112646	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34113415	34113497	.	+	1	Parent=gene1700
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34117661	34117827	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34120992	34121037	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34123798	34123919	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34128481	34128598	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34130615	34130806	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34150910	34151031	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34150910	34151031	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34152860	34152966	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34152860	34152966	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34159325	34159508	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34159325	34159508	.	+	1	Parent=gene1700
chr21	ENCODE	exon	34161407	34161505	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34161407	34161505	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34169528	34169695	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34169528	34169695	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34176417	34176629	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34176417	34176629	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34177724	34177845	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34177724	34177845	.	+	0	Parent=gene1700
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34179215	34179297	.	+	1	Parent=gene1700
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34179613	34179696	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34180461	34180634	.	+	.	Parent=gene1700
chr21	ENCODE	CDS	34180461	34180634	.	+	2	Parent=gene1700
chr21	ENCODE	CDS	34182326	34182474	.	+	2	Parent=gene1700
chr21	ENCODE	exon	34182326	34194035	.	+	.	Parent=gene1700
###
chr21	ENCODE	gene	33936654	34132668	.	+	.	ID=gene1701;Name=AP000313.6-002;name2=ITSN1
chr21	ENCODE	exon	33936654	33936889	.	+	.	Parent=gene1701
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34013004	34013031	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34015353	34015445	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34016763	34016826	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34029219	34029379	.	+	1	Parent=gene1701
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34044318	34044497	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34045985	34046081	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34049472	34049572	.	+	1	Parent=gene1701
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34056097	34056160	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34060049	34060186	.	+	1	Parent=gene1701
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34061887	34062002	.	+	1	Parent=gene1701
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34066235	34066497	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34068903	34069052	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34069142	34069282	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34075635	34075722	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34076168	34076307	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34088515	34088642	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34091553	34091782	.	+	1	Parent=gene1701
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34093982	34094103	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34096604	34096618	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34096604	34096618	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34105149	34105396	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34108087	34108246	.	+	1	Parent=gene1701
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34112441	34112646	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34113415	34113497	.	+	1	Parent=gene1701
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34117661	34117827	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34120992	34121037	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34123798	34123919	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34128481	34128598	.	+	0	Parent=gene1701
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1701
chr21	ENCODE	CDS	34130615	34130806	.	+	2	Parent=gene1701
chr21	ENCODE	CDS	34131161	34131162	.	+	2	Parent=gene1701
chr21	ENCODE	exon	34131161	34132668	.	+	.	Parent=gene1701
###
chr21	ENCODE	gene	33936659	34182782	.	+	.	ID=gene1702;Name=AP000313.6-023;name2=ITSN1
chr21	ENCODE	exon	33936659	33936889	.	+	.	Parent=gene1702
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34013004	34013031	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34015353	34015445	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34016763	34016826	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34029219	34029379	.	+	1	Parent=gene1702
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34044318	34044497	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34045985	34046081	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34049472	34049572	.	+	1	Parent=gene1702
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34056097	34056160	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34060049	34060186	.	+	1	Parent=gene1702
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34061887	34062002	.	+	1	Parent=gene1702
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34066235	34066497	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34068903	34069052	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34069142	34069282	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34075635	34075722	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34076168	34076307	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34088515	34088642	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34091553	34091782	.	+	1	Parent=gene1702
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34093982	34094103	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34105149	34105396	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34108087	34108246	.	+	1	Parent=gene1702
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34112441	34112646	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34113415	34113497	.	+	1	Parent=gene1702
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34117661	34117827	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34120992	34121037	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34123798	34123919	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34128481	34128598	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34130615	34130806	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34150910	34151031	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34150910	34151031	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34152860	34152966	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34152860	34152966	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34159325	34159508	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34159325	34159508	.	+	1	Parent=gene1702
chr21	ENCODE	exon	34161407	34161505	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34161407	34161505	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34169528	34169695	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34169528	34169695	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34176417	34176629	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34176417	34176629	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34177724	34177845	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34177724	34177845	.	+	0	Parent=gene1702
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34179215	34179297	.	+	1	Parent=gene1702
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34179613	34179696	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34180461	34180634	.	+	.	Parent=gene1702
chr21	ENCODE	CDS	34180461	34180634	.	+	2	Parent=gene1702
chr21	ENCODE	CDS	34182326	34182474	.	+	2	Parent=gene1702
chr21	ENCODE	exon	34182326	34182782	.	+	.	Parent=gene1702
###
chr21	ENCODE	gene	33936672	34132672	.	+	.	ID=gene1703;Name=AP000313.6-024;name2=ITSN1
chr21	ENCODE	exon	33936672	33936889	.	+	.	Parent=gene1703
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34013004	34013031	.	+	0	Parent=gene1703
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34015353	34015445	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34016763	34016826	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34029219	34029379	.	+	1	Parent=gene1703
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34044318	34044497	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34045985	34046081	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34049472	34049572	.	+	1	Parent=gene1703
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34056097	34056160	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34060049	34060186	.	+	1	Parent=gene1703
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34061887	34062002	.	+	1	Parent=gene1703
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34066235	34066497	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34068903	34069052	.	+	0	Parent=gene1703
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34069142	34069282	.	+	0	Parent=gene1703
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34075635	34075722	.	+	0	Parent=gene1703
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34076168	34076307	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34088515	34088642	.	+	0	Parent=gene1703
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34091553	34091782	.	+	1	Parent=gene1703
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34093982	34094103	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34105149	34105396	.	+	0	Parent=gene1703
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34108087	34108246	.	+	1	Parent=gene1703
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34112441	34112646	.	+	0	Parent=gene1703
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34113415	34113497	.	+	1	Parent=gene1703
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34117661	34117827	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34120992	34121037	.	+	0	Parent=gene1703
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34123798	34123919	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34128481	34128598	.	+	0	Parent=gene1703
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1703
chr21	ENCODE	CDS	34130615	34130806	.	+	2	Parent=gene1703
chr21	ENCODE	CDS	34131161	34131162	.	+	2	Parent=gene1703
chr21	ENCODE	exon	34131161	34132672	.	+	.	Parent=gene1703
###
chr21	ENCODE	gene	33936674	34132670	.	+	.	ID=gene1704;Name=AP000313.6-003;name2=ITSN1
chr21	ENCODE	exon	33936674	33936889	.	+	.	Parent=gene1704
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34013004	34013031	.	+	0	Parent=gene1704
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34015353	34015445	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34016763	34016826	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34029219	34029379	.	+	1	Parent=gene1704
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34044318	34044497	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34045985	34046081	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34049472	34049572	.	+	1	Parent=gene1704
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34056097	34056160	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34060049	34060186	.	+	1	Parent=gene1704
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34061887	34062002	.	+	1	Parent=gene1704
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34066235	34066497	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34068903	34069052	.	+	0	Parent=gene1704
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34069142	34069282	.	+	0	Parent=gene1704
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34075635	34075722	.	+	0	Parent=gene1704
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34076168	34076307	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34088515	34088642	.	+	0	Parent=gene1704
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34091553	34091782	.	+	1	Parent=gene1704
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34093982	34094103	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34105149	34105396	.	+	0	Parent=gene1704
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34108087	34108246	.	+	1	Parent=gene1704
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34112441	34112646	.	+	0	Parent=gene1704
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34113415	34113497	.	+	1	Parent=gene1704
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34123798	34123919	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34128481	34128598	.	+	0	Parent=gene1704
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1704
chr21	ENCODE	CDS	34130615	34130806	.	+	2	Parent=gene1704
chr21	ENCODE	CDS	34131161	34131162	.	+	2	Parent=gene1704
chr21	ENCODE	exon	34131161	34132670	.	+	.	Parent=gene1704
###
chr21	ENCODE	gene	33936718	34029268	.	+	.	ID=gene1705;Name=AP000313.6-032;name2=ITSN1
chr21	ENCODE	exon	33936718	33936889	.	+	.	Parent=gene1705
chr21	ENCODE	exon	33983497	33983558	.	+	.	Parent=gene1705
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene1705
chr21	ENCODE	CDS	34013004	34013031	.	+	0	Parent=gene1705
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene1705
chr21	ENCODE	CDS	34015353	34015445	.	+	2	Parent=gene1705
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1705
chr21	ENCODE	CDS	34016763	34016826	.	+	2	Parent=gene1705
chr21	ENCODE	exon	34029219	34029268	.	+	.	Parent=gene1705
chr21	ENCODE	CDS	34029219	34029268	.	+	1	Parent=gene1705
###
chr21	ENCODE	gene	34015412	34036947	.	+	.	ID=gene1706;Name=AP000313.6-018;name2=ITSN1
chr21	ENCODE	exon	34015412	34015445	.	+	.	Parent=gene1706
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene1706
chr21	ENCODE	exon	34029219	34030908	.	+	.	Parent=gene1706
chr21	ENCODE	exon	34034992	34035796	.	+	.	Parent=gene1706
chr21	ENCODE	exon	34036517	34036947	.	+	.	Parent=gene1706
###
chr21	ENCODE	gene	34029216	34029801	.	+	.	ID=gene1707;name2=ITSN1;Name=AP000313.6-017
chr21	ENCODE	exon	34029216	34029379	.	+	.	Parent=gene1707
chr21	ENCODE	CDS	34029216	34029379	.	+	0	Parent=gene1707
chr21	ENCODE	CDS	34029481	34029497	.	+	1	Parent=gene1707
chr21	ENCODE	exon	34029481	34029801	.	+	.	Parent=gene1707
###
chr21	ENCODE	gene	34044454	34132672	.	+	.	ID=gene1708;Name=AP000313.6-014;name2=ITSN1
chr21	ENCODE	exon	34044454	34044497	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34131161	34131197	.	+	.	Parent=gene1708
chr21	ENCODE	exon	34131420	34132672	.	+	.	Parent=gene1708
###
chr21	ENCODE	gene	34048358	34066474	.	+	.	ID=gene1709;Name=AP000313.6-019;name2=ITSN1
chr21	ENCODE	exon	34048358	34048397	.	+	.	Parent=gene1709
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene1709
chr21	ENCODE	exon	34050962	34051248	.	+	.	Parent=gene1709
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene1709
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene1709
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene1709
chr21	ENCODE	exon	34066235	34066474	.	+	.	Parent=gene1709
###
chr21	ENCODE	gene	34068537	34069253	.	+	.	ID=gene1710;Name=AP000313.6-021;name2=ITSN1
chr21	ENCODE	exon	34068537	34069052	.	+	.	Parent=gene1710
chr21	ENCODE	exon	34069142	34069253	.	+	.	Parent=gene1710
###
chr21	ENCODE	gene	34091728	34111568	.	+	.	ID=gene1711;Name=AP000313.6-029;name2=ITSN1
chr21	ENCODE	exon	34091728	34091782	.	+	.	Parent=gene1711
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene1711
chr21	ENCODE	exon	34096611	34096618	.	+	.	Parent=gene1711
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene1711
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene1711
chr21	ENCODE	exon	34111405	34111568	.	+	.	Parent=gene1711
###
chr21	ENCODE	gene	34094097	34111910	.	+	.	ID=gene1712;Name=AP000313.6-030;name2=ITSN1
chr21	ENCODE	exon	34094097	34094103	.	+	.	Parent=gene1712
chr21	ENCODE	CDS	34094097	34094103	.	+	0	Parent=gene1712
chr21	ENCODE	exon	34096604	34096618	.	+	.	Parent=gene1712
chr21	ENCODE	CDS	34096604	34096618	.	+	2	Parent=gene1712
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene1712
chr21	ENCODE	CDS	34105149	34105396	.	+	2	Parent=gene1712
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene1712
chr21	ENCODE	CDS	34108087	34108246	.	+	0	Parent=gene1712
chr21	ENCODE	CDS	34111405	34111755	.	+	2	Parent=gene1712
chr21	ENCODE	exon	34111405	34111910	.	+	.	Parent=gene1712
###
chr21	ENCODE	gene	34105378	34108681	.	+	.	ID=gene1713;Name=AP000313.6-035;name2=ITSN1
chr21	ENCODE	exon	34105378	34105396	.	+	.	Parent=gene1713
chr21	ENCODE	exon	34108087	34108681	.	+	.	Parent=gene1713
###
chr21	ENCODE	gene	34112200	34123203	.	+	.	ID=gene1714;Name=AP000313.6-007;name2=ITSN1
chr21	ENCODE	exon	34112200	34112646	.	+	.	Parent=gene1714
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1714
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene1714
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene1714
chr21	ENCODE	exon	34123142	34123203	.	+	.	Parent=gene1714
###
chr21	ENCODE	gene	34112557	34123203	.	+	.	ID=gene1715;name2=ITSN1;Name=AP000313.6-006
chr21	ENCODE	exon	34112557	34112646	.	+	.	Parent=gene1715
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1715
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene1715
chr21	ENCODE	exon	34123142	34123203	.	+	.	Parent=gene1715
###
chr21	ENCODE	gene	34112626	34123860	.	+	.	ID=gene1716;Name=AP000313.6-016;name2=ITSN1
chr21	ENCODE	exon	34112626	34112646	.	+	.	Parent=gene1716
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene1716
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene1716
chr21	ENCODE	exon	34123798	34123860	.	+	.	Parent=gene1716
###
chr21	ENCODE	gene	34120990	34128570	.	+	.	ID=gene1717;Name=AP000313.6-022;name2=ITSN1
chr21	ENCODE	exon	34120990	34121037	.	+	.	Parent=gene1717
chr21	ENCODE	exon	34123142	34123224	.	+	.	Parent=gene1717
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1717
chr21	ENCODE	exon	34128481	34128570	.	+	.	Parent=gene1717
###
chr21	ENCODE	gene	34123180	34131212	.	+	.	ID=gene1718;name2=ITSN1;Name=AP000313.6-010
chr21	ENCODE	exon	34123180	34123342	.	+	.	Parent=gene1718
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1718
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1718
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1718
chr21	ENCODE	exon	34131161	34131212	.	+	.	Parent=gene1718
###
chr21	ENCODE	gene	34123180	34131212	.	+	.	ID=gene1719;Name=AP000313.6-008;name2=ITSN1
chr21	ENCODE	exon	34123180	34123224	.	+	.	Parent=gene1719
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1719
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1719
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1719
chr21	ENCODE	exon	34131161	34131212	.	+	.	Parent=gene1719
###
chr21	ENCODE	gene	34123180	34131212	.	+	.	ID=gene1720;Name=AP000313.6-013;name2=ITSN1
chr21	ENCODE	exon	34123180	34123919	.	+	.	Parent=gene1720
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1720
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1720
chr21	ENCODE	exon	34131161	34131212	.	+	.	Parent=gene1720
###
chr21	ENCODE	gene	34123180	34150967	.	+	.	ID=gene1721;Name=AP000313.6-012;name2=ITSN1
chr21	ENCODE	exon	34123180	34123919	.	+	.	Parent=gene1721
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1721
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1721
chr21	ENCODE	exon	34150910	34150967	.	+	.	Parent=gene1721
###
chr21	ENCODE	gene	34123180	34150967	.	+	.	ID=gene1722;Name=AP000313.6-011;name2=ITSN1
chr21	ENCODE	exon	34123180	34123919	.	+	.	Parent=gene1722
chr21	ENCODE	exon	34150910	34150967	.	+	.	Parent=gene1722
###
chr21	ENCODE	gene	34123180	34150967	.	+	.	ID=gene1723;Name=AP000313.6-009;name2=ITSN1
chr21	ENCODE	exon	34123180	34123224	.	+	.	Parent=gene1723
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene1723
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene1723
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene1723
chr21	ENCODE	exon	34150910	34150967	.	+	.	Parent=gene1723
###
chr21	ENCODE	gene	34152871	34180528	.	+	.	ID=gene1724;name2=ITSN1;Name=AP000313.6-004
chr21	ENCODE	exon	34152871	34152966	.	+	.	Parent=gene1724
chr21	ENCODE	CDS	34152871	34152966	.	+	0	Parent=gene1724
chr21	ENCODE	exon	34159325	34159508	.	+	.	Parent=gene1724
chr21	ENCODE	CDS	34159325	34159508	.	+	0	Parent=gene1724
chr21	ENCODE	exon	34161407	34161505	.	+	.	Parent=gene1724
chr21	ENCODE	CDS	34161407	34161505	.	+	2	Parent=gene1724
chr21	ENCODE	exon	34176417	34176629	.	+	.	Parent=gene1724
chr21	ENCODE	CDS	34176417	34176629	.	+	2	Parent=gene1724
chr21	ENCODE	exon	34177724	34177845	.	+	.	Parent=gene1724
chr21	ENCODE	CDS	34177724	34177845	.	+	2	Parent=gene1724
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene1724
chr21	ENCODE	CDS	34179215	34179297	.	+	0	Parent=gene1724
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene1724
chr21	ENCODE	CDS	34179613	34179696	.	+	1	Parent=gene1724
chr21	ENCODE	exon	34180461	34180528	.	+	.	Parent=gene1724
chr21	ENCODE	CDS	34180461	34180528	.	+	1	Parent=gene1724
###
chr21	ENCODE	gene	34169532	34180551	.	+	.	ID=gene1725;Name=AP000313.6-031;name2=ITSN1
chr21	ENCODE	exon	34169532	34169695	.	+	.	Parent=gene1725
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene1725
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene1725
chr21	ENCODE	exon	34180461	34180551	.	+	.	Parent=gene1725
###
chr21	ENCODE	gene	34169534	34180528	.	+	.	ID=gene1726;Name=AP000313.6-005;name2=ITSN1
chr21	ENCODE	exon	34169534	34169695	.	+	.	Parent=gene1726
chr21	ENCODE	CDS	34169534	34169695	.	+	0	Parent=gene1726
chr21	ENCODE	exon	34177724	34177845	.	+	.	Parent=gene1726
chr21	ENCODE	CDS	34177724	34177845	.	+	0	Parent=gene1726
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene1726
chr21	ENCODE	CDS	34179215	34179297	.	+	1	Parent=gene1726
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene1726
chr21	ENCODE	CDS	34179613	34179696	.	+	2	Parent=gene1726
chr21	ENCODE	exon	34180461	34180528	.	+	.	Parent=gene1726
chr21	ENCODE	CDS	34180461	34180528	.	+	2	Parent=gene1726
###
chr21	ENCODE	gene	34197627	34199755	.	-	.	ID=gene1727;Name=AP000313.5-006;name2=ATP5O
chr21	ENCODE	exon	34197627	34197813	.	-	.	Parent=gene1727
chr21	ENCODE	exon	34198109	34198748	.	-	.	Parent=gene1727
chr21	ENCODE	exon	34198856	34199755	.	-	.	Parent=gene1727
###
chr21	ENCODE	gene	34197627	34209935	.	-	.	ID=gene1728;Name=AP000313.5-003;name2=ATP5O
chr21	ENCODE	exon	34197627	34197813	.	-	.	Parent=gene1728
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene1728
chr21	ENCODE	exon	34201515	34201627	.	-	.	Parent=gene1728
chr21	ENCODE	exon	34206463	34206573	.	-	.	Parent=gene1728
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene1728
chr21	ENCODE	exon	34209902	34209935	.	-	.	Parent=gene1728
###
chr21	ENCODE	gene	34197627	34209942	.	-	.	ID=gene1729;Name=AP000313.5-002;name2=ATP5O
chr21	ENCODE	exon	34197627	34197813	.	-	.	Parent=gene1729
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene1729
chr21	ENCODE	exon	34200623	34201627	.	-	.	Parent=gene1729
chr21	ENCODE	exon	34203256	34203385	.	-	.	Parent=gene1729
chr21	ENCODE	exon	34206463	34206573	.	-	.	Parent=gene1729
chr21	ENCODE	exon	34208624	34209942	.	-	.	Parent=gene1729
###
chr21	ENCODE	gene	34197627	34210154	.	-	.	ID=gene1730;Name=AP000313.5-001;name2=ATP5O
chr21	ENCODE	exon	34197627	34197813	.	-	.	Parent=gene1730
chr21	ENCODE	CDS	34197700	34197813	.	-	0	Parent=gene1730
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene1730
chr21	ENCODE	CDS	34198109	34198195	.	-	0	Parent=gene1730
chr21	ENCODE	exon	34201515	34201627	.	-	.	Parent=gene1730
chr21	ENCODE	CDS	34201515	34201627	.	-	2	Parent=gene1730
chr21	ENCODE	exon	34203256	34203385	.	-	.	Parent=gene1730
chr21	ENCODE	CDS	34203256	34203385	.	-	0	Parent=gene1730
chr21	ENCODE	exon	34206463	34206573	.	-	.	Parent=gene1730
chr21	ENCODE	CDS	34206463	34206573	.	-	0	Parent=gene1730
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene1730
chr21	ENCODE	CDS	34208624	34208674	.	-	0	Parent=gene1730
chr21	ENCODE	CDS	34209902	34209937	.	-	0	Parent=gene1730
chr21	ENCODE	exon	34209902	34210154	.	-	.	Parent=gene1730
###
chr21	ENCODE	gene	34197630	34201586	.	-	.	ID=gene1731;name2=ATP5O;Name=AP000313.5-009
chr21	ENCODE	exon	34197630	34197813	.	-	.	Parent=gene1731
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene1731
chr21	ENCODE	exon	34200623	34200674	.	-	.	Parent=gene1731
chr21	ENCODE	exon	34200902	34200968	.	-	.	Parent=gene1731
chr21	ENCODE	exon	34201515	34201586	.	-	.	Parent=gene1731
###
chr21	ENCODE	gene	34197630	34203269	.	-	.	ID=gene1732;name2=ATP5O;Name=AP000313.5-010
chr21	ENCODE	exon	34197630	34197830	.	-	.	Parent=gene1732
chr21	ENCODE	CDS	34197786	34197830	.	-	2	Parent=gene1732
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene1732
chr21	ENCODE	CDS	34198109	34198195	.	-	2	Parent=gene1732
chr21	ENCODE	exon	34201515	34201627	.	-	.	Parent=gene1732
chr21	ENCODE	CDS	34201515	34201627	.	-	1	Parent=gene1732
chr21	ENCODE	exon	34203256	34203269	.	-	.	Parent=gene1732
chr21	ENCODE	CDS	34203256	34203269	.	-	0	Parent=gene1732
###
chr21	ENCODE	gene	34202988	34209927	.	-	.	ID=gene1733;Name=AP000313.5-004;name2=ATP5O
chr21	ENCODE	exon	34202988	34203385	.	-	.	Parent=gene1733
chr21	ENCODE	exon	34206463	34206573	.	-	.	Parent=gene1733
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene1733
chr21	ENCODE	exon	34209902	34209927	.	-	.	Parent=gene1733
###
chr21	ENCODE	gene	34206541	34209898	.	-	.	ID=gene1734;Name=AP000313.5-007;name2=ATP5O
chr21	ENCODE	exon	34206541	34206573	.	-	.	Parent=gene1734
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene1734
chr21	ENCODE	exon	34209310	34209898	.	-	.	Parent=gene1734
###
chr21	ENCODE	gene	34206552	34209953	.	-	.	ID=gene1735;Name=AP000313.5-008;name2=ATP5O
chr21	ENCODE	exon	34206552	34206573	.	-	.	Parent=gene1735
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene1735
chr21	ENCODE	exon	34209558	34209953	.	-	.	Parent=gene1735
###
chr21	ENCODE	gene	39468565	39477647	.	-	.	ID=gene1736;Name=AF129408.12-001;name2=DSCR2
chr21	ENCODE	exon	39468565	39469460	.	-	.	Parent=gene1736
chr21	ENCODE	CDS	39469386	39469460	.	-	0	Parent=gene1736
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene1736
chr21	ENCODE	CDS	39471231	39471367	.	-	2	Parent=gene1736
chr21	ENCODE	exon	39472245	39472443	.	-	.	Parent=gene1736
chr21	ENCODE	CDS	39472245	39472443	.	-	0	Parent=gene1736
chr21	ENCODE	exon	39473720	39473782	.	-	.	Parent=gene1736
chr21	ENCODE	CDS	39473720	39473782	.	-	0	Parent=gene1736
chr21	ENCODE	exon	39474081	39474232	.	-	.	Parent=gene1736
chr21	ENCODE	CDS	39474081	39474232	.	-	2	Parent=gene1736
chr21	ENCODE	exon	39475568	39475674	.	-	.	Parent=gene1736
chr21	ENCODE	CDS	39475568	39475674	.	-	1	Parent=gene1736
chr21	ENCODE	CDS	39477048	39477181	.	-	0	Parent=gene1736
chr21	ENCODE	exon	39477048	39477647	.	-	.	Parent=gene1736
###
chr21	ENCODE	gene	39469254	39472616	.	-	.	ID=gene1737;Name=AF129408.12-004;name2=DSCR2
chr21	ENCODE	exon	39469254	39469460	.	-	.	Parent=gene1737
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene1737
chr21	ENCODE	exon	39472245	39472616	.	-	.	Parent=gene1737
###
chr21	ENCODE	gene	39469254	39474234	.	-	.	ID=gene1738;Name=AF129408.12-003;name2=DSCR2
chr21	ENCODE	exon	39469254	39469460	.	-	.	Parent=gene1738
chr21	ENCODE	CDS	39469386	39469460	.	-	2	Parent=gene1738
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene1738
chr21	ENCODE	CDS	39471231	39471367	.	-	1	Parent=gene1738
chr21	ENCODE	exon	39472245	39472314	.	-	.	Parent=gene1738
chr21	ENCODE	CDS	39472245	39472314	.	-	2	Parent=gene1738
chr21	ENCODE	exon	39474081	39474234	.	-	.	Parent=gene1738
chr21	ENCODE	CDS	39474081	39474234	.	-	0	Parent=gene1738
###
chr21	ENCODE	gene	39469384	39477083	.	-	.	ID=gene1739;Name=AF129408.12-005;name2=DSCR2
chr21	ENCODE	exon	39469384	39469460	.	-	.	Parent=gene1739
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene1739
chr21	ENCODE	exon	39472245	39472443	.	-	.	Parent=gene1739
chr21	ENCODE	exon	39473720	39473782	.	-	.	Parent=gene1739
chr21	ENCODE	exon	39474081	39474232	.	-	.	Parent=gene1739
chr21	ENCODE	exon	39475568	39475674	.	-	.	Parent=gene1739
chr21	ENCODE	exon	39476860	39477083	.	-	.	Parent=gene1739
###
chr21	ENCODE	gene	39469386	39477181	.	-	.	ID=gene1740;name2=DSCR2;Name=AF129408.12-006
chr21	ENCODE	exon	39469386	39469460	.	-	.	Parent=gene1740
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene1740
chr21	ENCODE	exon	39472245	39472443	.	-	.	Parent=gene1740
chr21	ENCODE	exon	39473720	39473782	.	-	.	Parent=gene1740
chr21	ENCODE	exon	39474081	39474232	.	-	.	Parent=gene1740
chr21	ENCODE	exon	39477048	39477181	.	-	.	Parent=gene1740
###
chr21	ENCODE	gene	39469386	39477284	.	-	.	ID=gene1741;Name=AF129408.12-002;name2=DSCR2
chr21	ENCODE	exon	39469386	39469460	.	-	.	Parent=gene1741
chr21	ENCODE	CDS	39469386	39469460	.	-	0	Parent=gene1741
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene1741
chr21	ENCODE	CDS	39471231	39471367	.	-	2	Parent=gene1741
chr21	ENCODE	exon	39472245	39472443	.	-	.	Parent=gene1741
chr21	ENCODE	CDS	39472245	39472443	.	-	0	Parent=gene1741
chr21	ENCODE	exon	39474081	39474232	.	-	.	Parent=gene1741
chr21	ENCODE	CDS	39474081	39474232	.	-	2	Parent=gene1741
chr21	ENCODE	exon	39475568	39475674	.	-	.	Parent=gene1741
chr21	ENCODE	CDS	39475568	39475674	.	-	1	Parent=gene1741
chr21	ENCODE	CDS	39477048	39477181	.	-	0	Parent=gene1741
chr21	ENCODE	exon	39477048	39477284	.	-	.	Parent=gene1741
###
chr21	ENCODE	gene	39477972	39607366	.	-	.	ID=gene1742;Name=AF129408.13-001;name2=BRWD1
chr21	ENCODE	exon	39477972	39481213	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39480822	39481213	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39490294	39491211	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39490294	39491211	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39492559	39493458	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39492559	39493458	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39494015	39494182	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39494015	39494182	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39496121	39496341	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39496121	39496341	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39499904	39500070	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39499904	39500070	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39503791	39503943	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39503791	39503943	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39504582	39504725	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39504582	39504725	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39506462	39506503	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39507277	39507349	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39509033	39509158	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39511948	39512068	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39511948	39512068	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39512301	39512456	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39512301	39512456	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39518204	39518265	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39518204	39518265	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39518882	39518993	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39518882	39518993	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39522296	39522378	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39522296	39522378	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39523108	39523232	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39523108	39523232	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39525973	39526080	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39525973	39526080	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39526169	39526294	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39526169	39526294	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39530391	39530580	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39530391	39530580	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39532275	39532369	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39541497	39541628	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39544592	39544685	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39549441	39549624	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39552283	39552468	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39558256	39558481	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39558687	39558815	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39563695	39563829	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39564079	39564229	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39568170	39568268	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39569969	39570009	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39571047	39571147	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39572539	39572609	.	-	1	Parent=gene1742
chr21	ENCODE	exon	39573944	39574044	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39573944	39574044	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39587607	39587828	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39587607	39587828	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39589539	39589699	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39589539	39589699	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39590061	39590159	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39590061	39590159	.	-	2	Parent=gene1742
chr21	ENCODE	exon	39592228	39592378	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39592228	39592378	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39606637	39606696	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39606637	39606696	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39606868	39606897	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39607037	39607095	.	-	.	Parent=gene1742
chr21	ENCODE	CDS	39607037	39607095	.	-	2	Parent=gene1742
chr21	ENCODE	CDS	39607239	39607287	.	-	0	Parent=gene1742
chr21	ENCODE	exon	39607239	39607366	.	-	.	Parent=gene1742
###
chr21	ENCODE	gene	39481042	39558737	.	-	.	ID=gene1743;Name=AF129408.13-009;name2=BRWD1
chr21	ENCODE	exon	39481042	39481213	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39490294	39491211	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39492559	39493458	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39494015	39494182	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39496121	39496341	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39499904	39500070	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39503791	39503943	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39504582	39504725	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39512325	39512456	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39518204	39518265	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39518882	39518993	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39522296	39522378	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39523108	39523232	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39525973	39526080	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39526169	39526294	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39530391	39530580	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene1743
chr21	ENCODE	exon	39558687	39558737	.	-	.	Parent=gene1743
###
chr21	ENCODE	gene	39484015	39607366	.	-	.	ID=gene1744;Name=AF129408.13-002;name2=BRWD1
chr21	ENCODE	exon	39484015	39491211	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39490055	39491211	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39492559	39493458	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39492559	39493458	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39494015	39494182	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39494015	39494182	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39496121	39496341	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39496121	39496341	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39499904	39500070	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39499904	39500070	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39503791	39503943	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39503791	39503943	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39504582	39504725	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39504582	39504725	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39506462	39506503	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39507277	39507349	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39509033	39509158	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39511948	39512068	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39511948	39512068	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39512301	39512456	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39512301	39512456	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39518204	39518265	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39518204	39518265	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39518882	39518993	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39518882	39518993	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39522296	39522378	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39522296	39522378	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39523108	39523232	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39523108	39523232	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39525973	39526080	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39525973	39526080	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39526169	39526294	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39526169	39526294	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39530391	39530580	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39530391	39530580	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39532275	39532369	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39541497	39541628	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39544592	39544685	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39549441	39549624	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39552283	39552468	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39558256	39558481	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39558687	39558815	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39563695	39563829	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39564079	39564229	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39568170	39568268	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39569969	39570009	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39571047	39571147	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39572539	39572609	.	-	1	Parent=gene1744
chr21	ENCODE	exon	39573944	39574044	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39573944	39574044	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39587607	39587828	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39587607	39587828	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39589539	39589699	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39589539	39589699	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39590061	39590159	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39590061	39590159	.	-	2	Parent=gene1744
chr21	ENCODE	exon	39592228	39592378	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39592228	39592378	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39606637	39606696	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39606637	39606696	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39606868	39606897	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39607037	39607095	.	-	.	Parent=gene1744
chr21	ENCODE	CDS	39607037	39607095	.	-	2	Parent=gene1744
chr21	ENCODE	CDS	39607239	39607287	.	-	0	Parent=gene1744
chr21	ENCODE	exon	39607239	39607366	.	-	.	Parent=gene1744
###
chr21	ENCODE	gene	39493215	39494292	.	-	.	ID=gene1745;Name=AF129408.13-007;name2=BRWD1
chr21	ENCODE	exon	39493215	39493458	.	-	.	Parent=gene1745
chr21	ENCODE	exon	39494015	39494292	.	-	.	Parent=gene1745
###
chr21	ENCODE	gene	39496162	39523188	.	-	.	ID=gene1746;Name=AF129408.13-010;name2=BRWD1
chr21	ENCODE	exon	39496162	39496341	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39496162	39496341	.	-	0	Parent=gene1746
chr21	ENCODE	exon	39499904	39500070	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39499904	39500070	.	-	2	Parent=gene1746
chr21	ENCODE	exon	39503791	39503943	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39503791	39503943	.	-	2	Parent=gene1746
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39506462	39506503	.	-	2	Parent=gene1746
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39507277	39507349	.	-	0	Parent=gene1746
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39509033	39509158	.	-	0	Parent=gene1746
chr21	ENCODE	exon	39511948	39512068	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39511948	39512068	.	-	1	Parent=gene1746
chr21	ENCODE	exon	39512301	39512456	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39512301	39512456	.	-	1	Parent=gene1746
chr21	ENCODE	exon	39518204	39518265	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39518204	39518265	.	-	0	Parent=gene1746
chr21	ENCODE	exon	39518882	39518993	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39518882	39518993	.	-	1	Parent=gene1746
chr21	ENCODE	exon	39522296	39522378	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39522296	39522378	.	-	0	Parent=gene1746
chr21	ENCODE	exon	39523108	39523188	.	-	.	Parent=gene1746
chr21	ENCODE	CDS	39523108	39523188	.	-	0	Parent=gene1746
###
chr21	ENCODE	gene	39503582	39512456	.	-	.	ID=gene1747;Name=AF129408.13-006;name2=BRWD1
chr21	ENCODE	exon	39503582	39503943	.	-	.	Parent=gene1747
chr21	ENCODE	exon	39504662	39504725	.	-	.	Parent=gene1747
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene1747
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene1747
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene1747
chr21	ENCODE	exon	39511948	39512068	.	-	.	Parent=gene1747
chr21	ENCODE	exon	39512301	39512456	.	-	.	Parent=gene1747
###
chr21	ENCODE	gene	39530514	39574009	.	-	.	ID=gene1748;name2=BRWD1;Name=AF129408.13-011
chr21	ENCODE	exon	39530514	39530580	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene1748
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene1748
###
chr21	ENCODE	gene	39530514	39574009	.	-	.	ID=gene1749;Name=AF129408.13-012;name2=BRWD1
chr21	ENCODE	exon	39530514	39530580	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39558256	39558360	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene1749
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene1749
###
chr21	ENCODE	gene	39530514	39574009	.	-	.	ID=gene1750;Name=AF129408.13-013;name2=BRWD1
chr21	ENCODE	exon	39530514	39530580	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39558782	39558815	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene1750
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene1750
###
chr21	ENCODE	gene	39530515	39574009	.	-	.	ID=gene1751;Name=AF129408.13-014;name2=BRWD1
chr21	ENCODE	exon	39530515	39530580	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39530515	39530580	.	-	0	Parent=gene1751
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39532275	39532369	.	-	2	Parent=gene1751
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39544592	39544685	.	-	0	Parent=gene1751
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39549441	39549624	.	-	1	Parent=gene1751
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39552283	39552468	.	-	1	Parent=gene1751
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39558256	39558481	.	-	2	Parent=gene1751
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39558687	39558815	.	-	2	Parent=gene1751
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39563695	39563829	.	-	2	Parent=gene1751
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39564079	39564229	.	-	0	Parent=gene1751
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39568170	39568268	.	-	0	Parent=gene1751
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39569969	39570009	.	-	2	Parent=gene1751
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39571047	39571147	.	-	1	Parent=gene1751
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39572539	39572609	.	-	0	Parent=gene1751
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene1751
chr21	ENCODE	CDS	39573944	39574009	.	-	0	Parent=gene1751
###
chr21	ENCODE	gene	39530515	39574009	.	-	.	ID=gene1752;name2=BRWD1;Name=AF129408.13-015
chr21	ENCODE	exon	39530515	39530580	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39549461	39549624	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene1752
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene1752
###
chr21	ENCODE	gene	39572293	39574003	.	-	.	ID=gene1753;Name=AF129408.13-003;name2=BRWD1
chr21	ENCODE	exon	39572293	39572609	.	-	.	Parent=gene1753
chr21	ENCODE	exon	39573944	39574003	.	-	.	Parent=gene1753
###
chr21	ENCODE	gene	39590233	39607438	.	-	.	ID=gene1754;Name=AF129408.13-004;name2=BRWD1
chr21	ENCODE	exon	39590233	39592378	.	-	.	Parent=gene1754
chr21	ENCODE	CDS	39592214	39592378	.	-	0	Parent=gene1754
chr21	ENCODE	exon	39606637	39606696	.	-	.	Parent=gene1754
chr21	ENCODE	CDS	39606637	39606696	.	-	0	Parent=gene1754
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene1754
chr21	ENCODE	CDS	39606868	39606897	.	-	0	Parent=gene1754
chr21	ENCODE	exon	39607037	39607095	.	-	.	Parent=gene1754
chr21	ENCODE	CDS	39607037	39607095	.	-	2	Parent=gene1754
chr21	ENCODE	CDS	39607239	39607287	.	-	0	Parent=gene1754
chr21	ENCODE	exon	39607239	39607438	.	-	.	Parent=gene1754
###
chr21	ENCODE	gene	39591886	39615355	.	-	.	ID=gene1755;Name=AF129408.13-008;name2=BRWD1
chr21	ENCODE	exon	39591886	39592378	.	-	.	Parent=gene1755
chr21	ENCODE	exon	39606637	39606696	.	-	.	Parent=gene1755
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene1755
chr21	ENCODE	exon	39607037	39607095	.	-	.	Parent=gene1755
chr21	ENCODE	exon	39614822	39615355	.	-	.	Parent=gene1755
###
chr21	ENCODE	gene	39606359	39607097	.	-	.	ID=gene1756;Name=AF129408.13-005;name2=BRWD1
chr21	ENCODE	exon	39606359	39606696	.	-	.	Parent=gene1756
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene1756
chr21	ENCODE	exon	39607037	39607097	.	-	.	Parent=gene1756
###
chr21	ENCODE	gene	39636111	39642787	.	-	.	ID=gene1757;Name=AF064861.91-004;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene1757
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1757
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene1757
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1757
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1757
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1757
chr21	ENCODE	exon	39642699	39642787	.	-	.	Parent=gene1757
###
chr21	ENCODE	gene	39636111	39642895	.	-	.	ID=gene1758;Name=AF064861.91-006;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene1758
chr21	ENCODE	exon	39638942	39642135	.	-	.	Parent=gene1758
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1758
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1758
chr21	ENCODE	exon	39642699	39642895	.	-	.	Parent=gene1758
###
chr21	ENCODE	gene	39636111	39642936	.	-	.	ID=gene1759;Name=AF064861.91-002;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene1759
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1759
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene1759
chr21	ENCODE	exon	39641175	39641274	.	-	.	Parent=gene1759
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1759
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1759
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1759
chr21	ENCODE	exon	39642699	39642936	.	-	.	Parent=gene1759
###
chr21	ENCODE	gene	39636111	39642996	.	-	.	ID=gene1760;Name=AF064861.91-001;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene1760
chr21	ENCODE	CDS	39636908	39636955	.	-	0	Parent=gene1760
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1760
chr21	ENCODE	CDS	39638942	39639070	.	-	0	Parent=gene1760
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1760
chr21	ENCODE	CDS	39642088	39642135	.	-	0	Parent=gene1760
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1760
chr21	ENCODE	CDS	39642218	39642247	.	-	0	Parent=gene1760
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1760
chr21	ENCODE	CDS	39642341	39642373	.	-	0	Parent=gene1760
chr21	ENCODE	CDS	39642699	39642713	.	-	0	Parent=gene1760
chr21	ENCODE	exon	39642699	39642996	.	-	.	Parent=gene1760
###
chr21	ENCODE	gene	39636111	39643140	.	-	.	ID=gene1761;Name=AF064861.91-003;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene1761
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1761
chr21	ENCODE	exon	39639626	39641088	.	-	.	Parent=gene1761
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene1761
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1761
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1761
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1761
chr21	ENCODE	exon	39643087	39643140	.	-	.	Parent=gene1761
###
chr21	ENCODE	gene	39636442	39642884	.	-	.	ID=gene1762;Name=AF064861.91-009;name2=HMGN1
chr21	ENCODE	exon	39636442	39636955	.	-	.	Parent=gene1762
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1762
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene1762
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1762
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1762
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1762
chr21	ENCODE	exon	39642699	39642884	.	-	.	Parent=gene1762
###
chr21	ENCODE	gene	39636488	39642849	.	-	.	ID=gene1763;Name=AF064861.91-018;name2=HMGN1
chr21	ENCODE	exon	39636488	39636955	.	-	.	Parent=gene1763
chr21	ENCODE	CDS	39636908	39636955	.	-	0	Parent=gene1763
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1763
chr21	ENCODE	CDS	39638942	39639070	.	-	0	Parent=gene1763
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1763
chr21	ENCODE	CDS	39642088	39642135	.	-	0	Parent=gene1763
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1763
chr21	ENCODE	CDS	39642341	39642373	.	-	0	Parent=gene1763
chr21	ENCODE	CDS	39642699	39642713	.	-	0	Parent=gene1763
chr21	ENCODE	exon	39642699	39642849	.	-	.	Parent=gene1763
###
chr21	ENCODE	gene	39636584	39642836	.	-	.	ID=gene1764;Name=AF064861.91-015;name2=HMGN1
chr21	ENCODE	exon	39636584	39636955	.	-	.	Parent=gene1764
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1764
chr21	ENCODE	exon	39641175	39641274	.	-	.	Parent=gene1764
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1764
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1764
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1764
chr21	ENCODE	exon	39642699	39642836	.	-	.	Parent=gene1764
###
chr21	ENCODE	gene	39636596	39642658	.	-	.	ID=gene1765;Name=AF064861.91-012;name2=HMGN1
chr21	ENCODE	exon	39636596	39636955	.	-	.	Parent=gene1765
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1765
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene1765
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1765
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1765
chr21	ENCODE	exon	39642341	39642658	.	-	.	Parent=gene1765
###
chr21	ENCODE	gene	39636600	39642419	.	-	.	ID=gene1766;Name=AF064861.91-008;name2=HMGN1
chr21	ENCODE	exon	39636600	39636955	.	-	.	Parent=gene1766
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1766
chr21	ENCODE	exon	39641043	39641088	.	-	.	Parent=gene1766
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene1766
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1766
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1766
chr21	ENCODE	exon	39642341	39642419	.	-	.	Parent=gene1766
###
chr21	ENCODE	gene	39636675	39643443	.	-	.	ID=gene1767;Name=AF064861.91-013;name2=HMGN1
chr21	ENCODE	exon	39636675	39636955	.	-	.	Parent=gene1767
chr21	ENCODE	CDS	39636908	39636955	.	-	0	Parent=gene1767
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1767
chr21	ENCODE	CDS	39638942	39639070	.	-	0	Parent=gene1767
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1767
chr21	ENCODE	CDS	39642088	39642135	.	-	0	Parent=gene1767
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1767
chr21	ENCODE	CDS	39642218	39642247	.	-	0	Parent=gene1767
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1767
chr21	ENCODE	CDS	39642341	39642373	.	-	0	Parent=gene1767
chr21	ENCODE	CDS	39643256	39643318	.	-	0	Parent=gene1767
chr21	ENCODE	exon	39643256	39643443	.	-	.	Parent=gene1767
###
chr21	ENCODE	gene	39636705	39642393	.	-	.	ID=gene1768;name2=HMGN1;Name=AF064861.91-021
chr21	ENCODE	exon	39636705	39636955	.	-	.	Parent=gene1768
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1768
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene1768
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene1768
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1768
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1768
chr21	ENCODE	exon	39642341	39642393	.	-	.	Parent=gene1768
###
chr21	ENCODE	gene	39636774	39642135	.	-	.	ID=gene1769;Name=AF064861.91-010;name2=HMGN1
chr21	ENCODE	exon	39636774	39636955	.	-	.	Parent=gene1769
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1769
chr21	ENCODE	exon	39641043	39641088	.	-	.	Parent=gene1769
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1769
###
chr21	ENCODE	gene	39636805	39642850	.	-	.	ID=gene1770;Name=AF064861.91-017;name2=HMGN1
chr21	ENCODE	exon	39636805	39636955	.	-	.	Parent=gene1770
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1770
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene1770
chr21	ENCODE	exon	39641043	39641088	.	-	.	Parent=gene1770
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene1770
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1770
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1770
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1770
chr21	ENCODE	exon	39642699	39642850	.	-	.	Parent=gene1770
###
chr21	ENCODE	gene	39636933	39642850	.	-	.	ID=gene1771;Name=AF064861.91-007;name2=HMGN1
chr21	ENCODE	exon	39636933	39636955	.	-	.	Parent=gene1771
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene1771
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1771
chr21	ENCODE	exon	39642218	39642373	.	-	.	Parent=gene1771
chr21	ENCODE	exon	39642699	39642850	.	-	.	Parent=gene1771
###
chr21	ENCODE	gene	39640943	39642863	.	-	.	ID=gene1772;Name=AF064861.91-016;name2=HMGN1
chr21	ENCODE	exon	39640943	39641088	.	-	.	Parent=gene1772
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene1772
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1772
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1772
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1772
chr21	ENCODE	exon	39642699	39642863	.	-	.	Parent=gene1772
###
chr21	ENCODE	gene	39641132	39642811	.	-	.	ID=gene1773;Name=AF064861.91-019;name2=HMGN1
chr21	ENCODE	exon	39641132	39641748	.	-	.	Parent=gene1773
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1773
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1773
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene1773
chr21	ENCODE	exon	39642699	39642811	.	-	.	Parent=gene1773
###
chr21	ENCODE	gene	39641288	39642416	.	-	.	ID=gene1774;Name=AF064861.91-020;name2=HMGN1
chr21	ENCODE	exon	39641288	39641748	.	-	.	Parent=gene1774
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene1774
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene1774
chr21	ENCODE	exon	39642341	39642416	.	-	.	Parent=gene1774
###
chr21	ENCODE	gene	39641791	39642816	.	-	.	ID=gene1775;Name=AF064861.91-014;name2=HMGN1
chr21	ENCODE	exon	39641791	39642373	.	-	.	Parent=gene1775
chr21	ENCODE	exon	39642699	39642816	.	-	.	Parent=gene1775
###
chr21	ENCODE	gene	39641861	39642850	.	-	.	ID=gene1776;Name=AF064861.91-005;name2=HMGN1
chr21	ENCODE	exon	39641861	39642135	.	-	.	Parent=gene1776
chr21	ENCODE	exon	39642218	39642373	.	-	.	Parent=gene1776
chr21	ENCODE	exon	39642699	39642850	.	-	.	Parent=gene1776
###
chr21	ENCODE	gene	39674040	39691685	.	+	.	ID=gene1777;Name=AF064861.92-001;name2=WRB
chr21	ENCODE	exon	39674040	39674282	.	+	.	Parent=gene1777
chr21	ENCODE	CDS	39674181	39674282	.	+	0	Parent=gene1777
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene1777
chr21	ENCODE	CDS	39684494	39684659	.	+	0	Parent=gene1777
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene1777
chr21	ENCODE	CDS	39685565	39685632	.	+	2	Parent=gene1777
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene1777
chr21	ENCODE	CDS	39686962	39687076	.	+	0	Parent=gene1777
chr21	ENCODE	CDS	39690662	39690735	.	+	2	Parent=gene1777
chr21	ENCODE	exon	39690662	39691685	.	+	.	Parent=gene1777
###
chr21	ENCODE	gene	39674190	39685842	.	+	.	ID=gene1778;Name=AF064861.92-005;name2=WRB
chr21	ENCODE	exon	39674190	39674282	.	+	.	Parent=gene1778
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene1778
chr21	ENCODE	exon	39685565	39685842	.	+	.	Parent=gene1778
###
chr21	ENCODE	gene	39674210	39685001	.	+	.	ID=gene1779;Name=AF064861.92-008;name2=WRB
chr21	ENCODE	exon	39674210	39674282	.	+	.	Parent=gene1779
chr21	ENCODE	exon	39684494	39685001	.	+	.	Parent=gene1779
###
chr21	ENCODE	gene	39674254	39690912	.	+	.	ID=gene1780;Name=AF064861.92-002;name2=WRB
chr21	ENCODE	exon	39674254	39674352	.	+	.	Parent=gene1780
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene1780
chr21	ENCODE	CDS	39684494	39684659	.	+	0	Parent=gene1780
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene1780
chr21	ENCODE	CDS	39685565	39685632	.	+	2	Parent=gene1780
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene1780
chr21	ENCODE	CDS	39686962	39687076	.	+	0	Parent=gene1780
chr21	ENCODE	CDS	39690662	39690735	.	+	2	Parent=gene1780
chr21	ENCODE	exon	39690662	39690912	.	+	.	Parent=gene1780
###
chr21	ENCODE	gene	39674283	39684599	.	+	.	ID=gene1781;Name=AF064861.92-003;name2=WRB
chr21	ENCODE	exon	39674283	39674717	.	+	.	Parent=gene1781
chr21	ENCODE	exon	39684494	39684599	.	+	.	Parent=gene1781
chr21	ENCODE	CDS	39684494	39684599	.	+	0	Parent=gene1781
###
chr21	ENCODE	gene	39679889	39687076	.	+	.	ID=gene1782;Name=AF064861.92-009;name2=WRB
chr21	ENCODE	exon	39679889	39680307	.	+	.	Parent=gene1782
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene1782
chr21	ENCODE	CDS	39684494	39684659	.	+	0	Parent=gene1782
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene1782
chr21	ENCODE	CDS	39685565	39685632	.	+	2	Parent=gene1782
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene1782
chr21	ENCODE	CDS	39686962	39687076	.	+	0	Parent=gene1782
###
chr21	ENCODE	gene	39681561	39691685	.	+	.	ID=gene1783;Name=AF064861.92-004;name2=WRB
chr21	ENCODE	exon	39681561	39681651	.	+	.	Parent=gene1783
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene1783
chr21	ENCODE	CDS	39684494	39684659	.	+	0	Parent=gene1783
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene1783
chr21	ENCODE	CDS	39685565	39685632	.	+	2	Parent=gene1783
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene1783
chr21	ENCODE	CDS	39686962	39687076	.	+	0	Parent=gene1783
chr21	ENCODE	CDS	39690662	39690735	.	+	2	Parent=gene1783
chr21	ENCODE	exon	39690662	39691685	.	+	.	Parent=gene1783
###
chr21	ENCODE	gene	39681587	39691050	.	+	.	ID=gene1784;Name=AF064861.92-006;name2=WRB
chr21	ENCODE	exon	39681587	39681651	.	+	.	Parent=gene1784
chr21	ENCODE	exon	39684494	39685272	.	+	.	Parent=gene1784
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene1784
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene1784
chr21	ENCODE	exon	39690662	39691050	.	+	.	Parent=gene1784
###
chr21	ENCODE	gene	39686692	39690900	.	+	.	ID=gene1785;name2=WRB;Name=AF064861.92-007
chr21	ENCODE	exon	39686692	39687076	.	+	.	Parent=gene1785
chr21	ENCODE	exon	39690662	39690900	.	+	.	Parent=gene1785
###
chr21	ENCODE	gene	39699640	39739573	.	-	.	ID=gene1786;Name=AF121781.16-001;name2=C21orf13
chr21	ENCODE	exon	39699640	39700408	.	-	.	Parent=gene1786
chr21	ENCODE	CDS	39699678	39700408	.	-	2	Parent=gene1786
chr21	ENCODE	exon	39703775	39703892	.	-	.	Parent=gene1786
chr21	ENCODE	CDS	39703775	39703892	.	-	0	Parent=gene1786
chr21	ENCODE	exon	39704060	39704163	.	-	.	Parent=gene1786
chr21	ENCODE	CDS	39704060	39704163	.	-	2	Parent=gene1786
chr21	ENCODE	exon	39705514	39705598	.	-	.	Parent=gene1786
chr21	ENCODE	CDS	39705514	39705598	.	-	0	Parent=gene1786
chr21	ENCODE	exon	39714502	39714639	.	-	.	Parent=gene1786
chr21	ENCODE	CDS	39714502	39714639	.	-	0	Parent=gene1786
chr21	ENCODE	exon	39716772	39717286	.	-	.	Parent=gene1786
chr21	ENCODE	CDS	39716772	39717286	.	-	2	Parent=gene1786
chr21	ENCODE	CDS	39721968	39722289	.	-	0	Parent=gene1786
chr21	ENCODE	exon	39721968	39722299	.	-	.	Parent=gene1786
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1786
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1786
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1786
chr21	ENCODE	exon	39739521	39739573	.	-	.	Parent=gene1786
###
chr21	ENCODE	gene	39699656	39739529	.	-	.	ID=gene1787;Name=AF121781.16-002;name2=C21orf13
chr21	ENCODE	exon	39699656	39700408	.	-	.	Parent=gene1787
chr21	ENCODE	CDS	39699678	39700408	.	-	2	Parent=gene1787
chr21	ENCODE	exon	39703775	39703892	.	-	.	Parent=gene1787
chr21	ENCODE	CDS	39703775	39703892	.	-	0	Parent=gene1787
chr21	ENCODE	exon	39704060	39704163	.	-	.	Parent=gene1787
chr21	ENCODE	CDS	39704060	39704163	.	-	2	Parent=gene1787
chr21	ENCODE	exon	39705514	39705598	.	-	.	Parent=gene1787
chr21	ENCODE	CDS	39705514	39705598	.	-	0	Parent=gene1787
chr21	ENCODE	exon	39714502	39714639	.	-	.	Parent=gene1787
chr21	ENCODE	CDS	39714502	39714639	.	-	0	Parent=gene1787
chr21	ENCODE	exon	39716772	39717286	.	-	.	Parent=gene1787
chr21	ENCODE	CDS	39716772	39717286	.	-	2	Parent=gene1787
chr21	ENCODE	CDS	39721968	39722289	.	-	0	Parent=gene1787
chr21	ENCODE	exon	39721968	39722299	.	-	.	Parent=gene1787
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1787
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1787
chr21	ENCODE	exon	39739246	39739529	.	-	.	Parent=gene1787
###
chr21	ENCODE	gene	39699774	39704943	.	-	.	ID=gene1788;name2=C21orf13;Name=AF121781.16-020
chr21	ENCODE	exon	39699774	39700408	.	-	.	Parent=gene1788
chr21	ENCODE	exon	39703775	39703892	.	-	.	Parent=gene1788
chr21	ENCODE	exon	39704060	39704163	.	-	.	Parent=gene1788
chr21	ENCODE	exon	39704829	39704943	.	-	.	Parent=gene1788
###
chr21	ENCODE	gene	39705514	39739548	.	-	.	ID=gene1789;Name=AF121781.16-016;name2=C21orf13
chr21	ENCODE	exon	39705514	39705598	.	-	.	Parent=gene1789
chr21	ENCODE	exon	39714502	39714639	.	-	.	Parent=gene1789
chr21	ENCODE	exon	39716772	39716879	.	-	.	Parent=gene1789
chr21	ENCODE	exon	39722984	39723007	.	-	.	Parent=gene1789
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1789
chr21	ENCODE	exon	39729893	39729963	.	-	.	Parent=gene1789
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1789
chr21	ENCODE	exon	39739521	39739548	.	-	.	Parent=gene1789
###
chr21	ENCODE	gene	39715860	39732732	.	-	.	ID=gene1790;Name=AF121781.16-005;name2=C21orf13
chr21	ENCODE	exon	39715860	39717704	.	-	.	Parent=gene1790
chr21	ENCODE	exon	39721214	39722299	.	-	.	Parent=gene1790
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1790
chr21	ENCODE	exon	39732480	39732732	.	-	.	Parent=gene1790
###
chr21	ENCODE	gene	39716208	39739573	.	-	.	ID=gene1791;Name=AF121781.16-006;name2=C21orf13
chr21	ENCODE	exon	39716208	39717286	.	-	.	Parent=gene1791
chr21	ENCODE	exon	39721968	39722299	.	-	.	Parent=gene1791
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1791
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1791
chr21	ENCODE	exon	39739521	39739573	.	-	.	Parent=gene1791
###
chr21	ENCODE	gene	39716208	39739601	.	-	.	ID=gene1792;Name=AF121781.16-003;name2=C21orf13
chr21	ENCODE	exon	39716208	39717286	.	-	.	Parent=gene1792
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1792
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1792
chr21	ENCODE	exon	39739521	39739601	.	-	.	Parent=gene1792
###
chr21	ENCODE	gene	39716784	39739557	.	-	.	ID=gene1793;Name=AF121781.16-021;name2=C21orf13
chr21	ENCODE	exon	39716784	39717286	.	-	.	Parent=gene1793
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1793
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1793
chr21	ENCODE	exon	39739521	39739557	.	-	.	Parent=gene1793
###
chr21	ENCODE	gene	39717036	39739571	.	-	.	ID=gene1794;Name=AF121781.16-007;name2=C21orf13
chr21	ENCODE	exon	39717036	39717286	.	-	.	Parent=gene1794
chr21	ENCODE	exon	39721555	39721701	.	-	.	Parent=gene1794
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1794
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1794
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1794
chr21	ENCODE	exon	39738440	39738541	.	-	.	Parent=gene1794
chr21	ENCODE	exon	39739521	39739571	.	-	.	Parent=gene1794
###
chr21	ENCODE	gene	39717041	39739556	.	-	.	ID=gene1795;Name=AF121781.16-019;name2=C21orf13
chr21	ENCODE	exon	39717041	39717286	.	-	.	Parent=gene1795
chr21	ENCODE	CDS	39717041	39717286	.	-	2	Parent=gene1795
chr21	ENCODE	CDS	39721968	39722289	.	-	0	Parent=gene1795
chr21	ENCODE	exon	39721968	39722299	.	-	.	Parent=gene1795
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1795
chr21	ENCODE	exon	39729216	39729338	.	-	.	Parent=gene1795
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1795
chr21	ENCODE	exon	39739521	39739556	.	-	.	Parent=gene1795
###
chr21	ENCODE	gene	39717216	39739529	.	-	.	ID=gene1796;Name=AF121781.16-012;name2=C21orf13
chr21	ENCODE	exon	39717216	39717286	.	-	.	Parent=gene1796
chr21	ENCODE	exon	39722927	39723190	.	-	.	Parent=gene1796
chr21	ENCODE	exon	39729216	39729338	.	-	.	Parent=gene1796
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1796
chr21	ENCODE	exon	39739246	39739529	.	-	.	Parent=gene1796
###
chr21	ENCODE	gene	39721967	39739574	.	-	.	ID=gene1797;Name=AF121781.16-014;name2=C21orf13
chr21	ENCODE	CDS	39721967	39722289	.	-	0	Parent=gene1797
chr21	ENCODE	exon	39721967	39722299	.	-	.	Parent=gene1797
chr21	ENCODE	exon	39722927	39723190	.	-	.	Parent=gene1797
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1797
chr21	ENCODE	exon	39739521	39739574	.	-	.	Parent=gene1797
###
chr21	ENCODE	gene	39722004	39739599	.	-	.	ID=gene1798;Name=AF121781.16-018;name2=C21orf13
chr21	ENCODE	CDS	39722004	39722289	.	-	0	Parent=gene1798
chr21	ENCODE	exon	39722004	39722299	.	-	.	Parent=gene1798
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1798
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1798
chr21	ENCODE	exon	39739521	39739599	.	-	.	Parent=gene1798
###
chr21	ENCODE	gene	39722006	39739515	.	-	.	ID=gene1799;Name=AF121781.16-009;name2=C21orf13
chr21	ENCODE	CDS	39722006	39722289	.	-	0	Parent=gene1799
chr21	ENCODE	exon	39722006	39722299	.	-	.	Parent=gene1799
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1799
chr21	ENCODE	exon	39732480	39732514	.	-	.	Parent=gene1799
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1799
chr21	ENCODE	exon	39738440	39738541	.	-	.	Parent=gene1799
chr21	ENCODE	exon	39739246	39739515	.	-	.	Parent=gene1799
###
chr21	ENCODE	gene	39722011	39739529	.	-	.	ID=gene1800;name2=C21orf13;Name=AF121781.16-013
chr21	ENCODE	CDS	39722011	39722289	.	-	0	Parent=gene1800
chr21	ENCODE	exon	39722011	39722299	.	-	.	Parent=gene1800
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1800
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1800
chr21	ENCODE	exon	39739246	39739529	.	-	.	Parent=gene1800
###
chr21	ENCODE	gene	39722081	39739565	.	-	.	ID=gene1801;Name=AF121781.16-010;name2=C21orf13
chr21	ENCODE	CDS	39722081	39722289	.	-	0	Parent=gene1801
chr21	ENCODE	exon	39722081	39722299	.	-	.	Parent=gene1801
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1801
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1801
chr21	ENCODE	exon	39733430	39733569	.	-	.	Parent=gene1801
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1801
chr21	ENCODE	exon	39739521	39739565	.	-	.	Parent=gene1801
###
chr21	ENCODE	gene	39722101	39739565	.	-	.	ID=gene1802;Name=AF121781.16-015;name2=C21orf13
chr21	ENCODE	CDS	39722101	39722289	.	-	0	Parent=gene1802
chr21	ENCODE	exon	39722101	39722299	.	-	.	Parent=gene1802
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene1802
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1802
chr21	ENCODE	exon	39729893	39729963	.	-	.	Parent=gene1802
chr21	ENCODE	exon	39733430	39733569	.	-	.	Parent=gene1802
chr21	ENCODE	exon	39739521	39739565	.	-	.	Parent=gene1802
###
chr21	ENCODE	gene	39722198	39739576	.	-	.	ID=gene1803;Name=AF121781.16-017;name2=C21orf13
chr21	ENCODE	CDS	39722198	39722289	.	-	0	Parent=gene1803
chr21	ENCODE	exon	39722198	39722299	.	-	.	Parent=gene1803
chr21	ENCODE	exon	39722927	39723190	.	-	.	Parent=gene1803
chr21	ENCODE	exon	39729216	39729338	.	-	.	Parent=gene1803
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1803
chr21	ENCODE	exon	39739521	39739576	.	-	.	Parent=gene1803
###
chr21	ENCODE	gene	39722258	39739548	.	-	.	ID=gene1804;Name=AF121781.16-008;name2=C21orf13
chr21	ENCODE	CDS	39722258	39722289	.	-	0	Parent=gene1804
chr21	ENCODE	exon	39722258	39722299	.	-	.	Parent=gene1804
chr21	ENCODE	exon	39722927	39723190	.	-	.	Parent=gene1804
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene1804
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene1804
chr21	ENCODE	exon	39738440	39738541	.	-	.	Parent=gene1804
chr21	ENCODE	exon	39739521	39739548	.	-	.	Parent=gene1804
###
chr21	ENCODE	gene	39737255	39739549	.	-	.	ID=gene1805;Name=AF121781.16-011;name2=C21orf13
chr21	ENCODE	exon	39737255	39737997	.	-	.	Parent=gene1805
chr21	ENCODE	exon	39739521	39739549	.	-	.	Parent=gene1805
###
chr21	ENCODE	gene	39739651	39739725	.	+	.	ID=gene1806;Name=AF121897.3-002;name2=SH3BGR
chr21	ENCODE	exon	39739651	39739725	.	+	.	Parent=gene1806
###
chr21	ENCODE	gene	39739651	39739725	.	+	.	ID=gene1807;Name=AF121897.3-003;name2=SH3BGR
chr21	ENCODE	exon	39739651	39739725	.	+	.	Parent=gene1807
###
chr21	ENCODE	gene	39739661	39739688	.	+	.	ID=gene1808;Name=AF121897.3-007;name2=SH3BGR
chr21	ENCODE	exon	39739661	39739688	.	+	.	Parent=gene1808
###
chr21	ENCODE	gene	39739671	39739877	.	+	.	ID=gene1809;Name=AF121897.3-004;name2=SH3BGR
chr21	ENCODE	exon	39739671	39739877	.	+	.	Parent=gene1809
###
chr21	ENCODE	gene	39739727	39739894	.	+	.	ID=gene1810;Name=AF121897.3-005;name2=SH3BGR
chr21	ENCODE	exon	39739727	39739894	.	+	.	Parent=gene1810
###
chr21	ENCODE	gene	39739738	39739877	.	+	.	ID=gene1811;Name=AF121897.3-006;name2=SH3BGR
chr21	ENCODE	exon	39739738	39739877	.	+	.	Parent=gene1811
###
chr22	ENCODE	gene	30131552	30143859	.	+	.	ID=gene1812;name2=DRG1;Name=RP11-247I13.1-004
chr22	ENCODE	exon	30131552	30131621	.	+	.	Parent=gene1812
chr22	ENCODE	exon	30140796	30140965	.	+	.	Parent=gene1812
chr22	ENCODE	exon	30141848	30141939	.	+	.	Parent=gene1812
chr22	ENCODE	exon	30143820	30143859	.	+	.	Parent=gene1812
###
chr22	ENCODE	gene	30131552	30143886	.	+	.	ID=gene1813;Name=RP11-247I13.1-002;name2=DRG1
chr22	ENCODE	exon	30131552	30131621	.	+	.	Parent=gene1813
chr22	ENCODE	exon	30140796	30140965	.	+	.	Parent=gene1813
chr22	ENCODE	exon	30141848	30141939	.	+	.	Parent=gene1813
chr22	ENCODE	exon	30143820	30143886	.	+	.	Parent=gene1813
###
chr22	ENCODE	gene	30131552	30154992	.	+	.	ID=gene1814;Name=RP11-247I13.1-001;name2=DRG1
chr22	ENCODE	exon	30131552	30131621	.	+	.	Parent=gene1814
chr22	ENCODE	exon	30140796	30140965	.	+	.	Parent=gene1814
chr22	ENCODE	exon	30143820	30143950	.	+	.	Parent=gene1814
chr22	ENCODE	exon	30147155	30147322	.	+	.	Parent=gene1814
chr22	ENCODE	exon	30147600	30147722	.	+	.	Parent=gene1814
chr22	ENCODE	exon	30154412	30154992	.	+	.	Parent=gene1814
###
chr22	ENCODE	gene	30147053	30154695	.	+	.	ID=gene1815;Name=RP11-247I13.1-003;name2=DRG1
chr22	ENCODE	exon	30147053	30147322	.	+	.	Parent=gene1815
chr22	ENCODE	exon	30147600	30147722	.	+	.	Parent=gene1815
chr22	ENCODE	exon	30154412	30154695	.	+	.	Parent=gene1815
###
chr22	ENCODE	gene	30159903	30210364	.	-	.	ID=gene1816;Name=RP11-247I13.2-001;name2=EIF4ENIF1
chr22	ENCODE	exon	30159903	30160661	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30160420	30160661	.	-	2	Parent=gene1816
chr22	ENCODE	exon	30161244	30161408	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30161244	30161408	.	-	2	Parent=gene1816
chr22	ENCODE	exon	30162314	30162658	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30162314	30162658	.	-	2	Parent=gene1816
chr22	ENCODE	exon	30163502	30163634	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30163502	30163634	.	-	0	Parent=gene1816
chr22	ENCODE	exon	30165146	30165230	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30165146	30165230	.	-	1	Parent=gene1816
chr22	ENCODE	exon	30167966	30168108	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30167966	30168108	.	-	0	Parent=gene1816
chr22	ENCODE	exon	30168693	30168772	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30168693	30168772	.	-	2	Parent=gene1816
chr22	ENCODE	exon	30169888	30170071	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30169888	30170071	.	-	0	Parent=gene1816
chr22	ENCODE	exon	30170829	30170900	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30170829	30170900	.	-	0	Parent=gene1816
chr22	ENCODE	exon	30174720	30174916	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30174720	30174916	.	-	2	Parent=gene1816
chr22	ENCODE	exon	30175676	30175855	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30175676	30175855	.	-	2	Parent=gene1816
chr22	ENCODE	exon	30176392	30176527	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30176392	30176527	.	-	0	Parent=gene1816
chr22	ENCODE	exon	30179015	30179190	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30179015	30179190	.	-	2	Parent=gene1816
chr22	ENCODE	exon	30188715	30188842	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30188715	30188842	.	-	1	Parent=gene1816
chr22	ENCODE	exon	30192384	30192457	.	-	.	Parent=gene1816
chr22	ENCODE	CDS	30192384	30192457	.	-	0	Parent=gene1816
chr22	ENCODE	CDS	30209163	30209258	.	-	0	Parent=gene1816
chr22	ENCODE	exon	30209163	30209285	.	-	.	Parent=gene1816
chr22	ENCODE	exon	30210234	30210364	.	-	.	Parent=gene1816
###
chr22	ENCODE	gene	30159905	30171800	.	-	.	ID=gene1817;Name=RP11-247I13.2-004;name2=EIF4ENIF1
chr22	ENCODE	exon	30159905	30160661	.	-	.	Parent=gene1817
chr22	ENCODE	exon	30161244	30161408	.	-	.	Parent=gene1817
chr22	ENCODE	exon	30162314	30162658	.	-	.	Parent=gene1817
chr22	ENCODE	exon	30163502	30163634	.	-	.	Parent=gene1817
chr22	ENCODE	exon	30165146	30165230	.	-	.	Parent=gene1817
chr22	ENCODE	exon	30167966	30168108	.	-	.	Parent=gene1817
chr22	ENCODE	exon	30168693	30168772	.	-	.	Parent=gene1817
chr22	ENCODE	exon	30169888	30170071	.	-	.	Parent=gene1817
chr22	ENCODE	exon	30170829	30171800	.	-	.	Parent=gene1817
###
chr22	ENCODE	gene	30159907	30210127	.	-	.	ID=gene1818;Name=RP11-247I13.2-003;name2=EIF4ENIF1
chr22	ENCODE	exon	30159907	30160661	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30160420	30160661	.	-	2	Parent=gene1818
chr22	ENCODE	exon	30161244	30161408	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30161244	30161408	.	-	2	Parent=gene1818
chr22	ENCODE	exon	30162314	30162658	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30162314	30162658	.	-	2	Parent=gene1818
chr22	ENCODE	exon	30163502	30163634	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30163502	30163634	.	-	0	Parent=gene1818
chr22	ENCODE	exon	30165146	30165230	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30165146	30165230	.	-	1	Parent=gene1818
chr22	ENCODE	exon	30167966	30168105	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30167966	30168105	.	-	0	Parent=gene1818
chr22	ENCODE	exon	30168693	30168772	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30168693	30168772	.	-	2	Parent=gene1818
chr22	ENCODE	exon	30169888	30170071	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30169888	30170071	.	-	0	Parent=gene1818
chr22	ENCODE	exon	30170829	30170900	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30170829	30170900	.	-	0	Parent=gene1818
chr22	ENCODE	exon	30174684	30174916	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30174684	30174916	.	-	2	Parent=gene1818
chr22	ENCODE	exon	30175676	30175855	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30175676	30175855	.	-	2	Parent=gene1818
chr22	ENCODE	exon	30176392	30176527	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30176392	30176527	.	-	0	Parent=gene1818
chr22	ENCODE	exon	30179015	30179190	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30179015	30179190	.	-	2	Parent=gene1818
chr22	ENCODE	exon	30183472	30183673	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30183472	30183673	.	-	0	Parent=gene1818
chr22	ENCODE	exon	30184221	30184507	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30184221	30184507	.	-	2	Parent=gene1818
chr22	ENCODE	exon	30188715	30188842	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30188715	30188842	.	-	1	Parent=gene1818
chr22	ENCODE	exon	30192384	30192457	.	-	.	Parent=gene1818
chr22	ENCODE	CDS	30192384	30192457	.	-	0	Parent=gene1818
chr22	ENCODE	CDS	30209163	30209258	.	-	0	Parent=gene1818
chr22	ENCODE	exon	30209163	30209285	.	-	.	Parent=gene1818
chr22	ENCODE	exon	30209931	30210127	.	-	.	Parent=gene1818
###
chr22	ENCODE	gene	30159909	30210281	.	-	.	ID=gene1819;Name=RP11-247I13.2-002;name2=EIF4ENIF1
chr22	ENCODE	exon	30159909	30160661	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30160420	30160661	.	-	2	Parent=gene1819
chr22	ENCODE	exon	30161244	30161408	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30161244	30161408	.	-	2	Parent=gene1819
chr22	ENCODE	exon	30162314	30162658	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30162314	30162658	.	-	2	Parent=gene1819
chr22	ENCODE	exon	30163502	30163634	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30163502	30163634	.	-	0	Parent=gene1819
chr22	ENCODE	exon	30165146	30165230	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30165146	30165230	.	-	1	Parent=gene1819
chr22	ENCODE	exon	30167966	30168105	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30167966	30168105	.	-	0	Parent=gene1819
chr22	ENCODE	exon	30168693	30168772	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30168693	30168772	.	-	2	Parent=gene1819
chr22	ENCODE	exon	30169888	30170071	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30169888	30170071	.	-	0	Parent=gene1819
chr22	ENCODE	exon	30170829	30170900	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30170829	30170900	.	-	0	Parent=gene1819
chr22	ENCODE	exon	30174684	30174916	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30174684	30174916	.	-	2	Parent=gene1819
chr22	ENCODE	exon	30175676	30175855	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30175676	30175855	.	-	2	Parent=gene1819
chr22	ENCODE	exon	30176392	30176527	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30176392	30176527	.	-	0	Parent=gene1819
chr22	ENCODE	exon	30179015	30179190	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30179015	30179190	.	-	2	Parent=gene1819
chr22	ENCODE	exon	30183472	30183673	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30183472	30183673	.	-	0	Parent=gene1819
chr22	ENCODE	exon	30184221	30184507	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30184221	30184507	.	-	2	Parent=gene1819
chr22	ENCODE	exon	30188715	30188842	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30188715	30188842	.	-	1	Parent=gene1819
chr22	ENCODE	exon	30192384	30192457	.	-	.	Parent=gene1819
chr22	ENCODE	CDS	30192384	30192457	.	-	0	Parent=gene1819
chr22	ENCODE	CDS	30209163	30209258	.	-	0	Parent=gene1819
chr22	ENCODE	exon	30209163	30209285	.	-	.	Parent=gene1819
chr22	ENCODE	exon	30210234	30210281	.	-	.	Parent=gene1819
###
chr22	ENCODE	gene	30159913	30209285	.	-	.	ID=gene1820;Name=RP11-247I13.2-005;name2=EIF4ENIF1
chr22	ENCODE	exon	30159913	30160661	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30160420	30160661	.	-	2	Parent=gene1820
chr22	ENCODE	exon	30161244	30161408	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30161244	30161408	.	-	2	Parent=gene1820
chr22	ENCODE	exon	30162314	30162658	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30162314	30162658	.	-	2	Parent=gene1820
chr22	ENCODE	exon	30163502	30163634	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30163502	30163634	.	-	0	Parent=gene1820
chr22	ENCODE	exon	30165146	30165230	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30165146	30165230	.	-	1	Parent=gene1820
chr22	ENCODE	exon	30167966	30168105	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30167966	30168105	.	-	0	Parent=gene1820
chr22	ENCODE	exon	30168693	30168772	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30168693	30168772	.	-	2	Parent=gene1820
chr22	ENCODE	exon	30169888	30170071	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30169888	30170071	.	-	0	Parent=gene1820
chr22	ENCODE	exon	30174684	30174916	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30174684	30174916	.	-	2	Parent=gene1820
chr22	ENCODE	exon	30175676	30175855	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30175676	30175855	.	-	2	Parent=gene1820
chr22	ENCODE	exon	30176392	30176527	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30176392	30176527	.	-	0	Parent=gene1820
chr22	ENCODE	exon	30179015	30179190	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30179015	30179190	.	-	2	Parent=gene1820
chr22	ENCODE	exon	30183472	30183673	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30183472	30183673	.	-	0	Parent=gene1820
chr22	ENCODE	exon	30184221	30184507	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30184221	30184507	.	-	2	Parent=gene1820
chr22	ENCODE	exon	30188715	30188842	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30188715	30188842	.	-	1	Parent=gene1820
chr22	ENCODE	exon	30192384	30192457	.	-	.	Parent=gene1820
chr22	ENCODE	CDS	30192384	30192457	.	-	0	Parent=gene1820
chr22	ENCODE	CDS	30209163	30209258	.	-	0	Parent=gene1820
chr22	ENCODE	exon	30209163	30209285	.	-	.	Parent=gene1820
###
chr22	ENCODE	gene	30162343	30169923	.	-	.	ID=gene1821;Name=RP11-247I13.2-007;name2=EIF4ENIF1
chr22	ENCODE	exon	30162343	30162658	.	-	.	Parent=gene1821
chr22	ENCODE	exon	30163502	30163634	.	-	.	Parent=gene1821
chr22	ENCODE	exon	30165146	30165230	.	-	.	Parent=gene1821
chr22	ENCODE	exon	30167478	30167548	.	-	.	Parent=gene1821
chr22	ENCODE	exon	30167966	30168105	.	-	.	Parent=gene1821
chr22	ENCODE	exon	30168693	30168772	.	-	.	Parent=gene1821
chr22	ENCODE	exon	30169888	30169923	.	-	.	Parent=gene1821
###
chr22	ENCODE	gene	30162575	30163959	.	-	.	ID=gene1822;Name=RP11-247I13.2-011;name2=EIF4ENIF1
chr22	ENCODE	exon	30162575	30162658	.	-	.	Parent=gene1822
chr22	ENCODE	exon	30163502	30163959	.	-	.	Parent=gene1822
###
chr22	ENCODE	gene	30164978	30170030	.	-	.	ID=gene1823;Name=RP11-247I13.2-010;name2=EIF4ENIF1
chr22	ENCODE	exon	30164978	30165230	.	-	.	Parent=gene1823
chr22	ENCODE	exon	30167966	30168108	.	-	.	Parent=gene1823
chr22	ENCODE	exon	30168693	30168772	.	-	.	Parent=gene1823
chr22	ENCODE	exon	30169888	30170030	.	-	.	Parent=gene1823
###
chr22	ENCODE	gene	30184240	30209782	.	-	.	ID=gene1824;Name=RP11-247I13.2-006;name2=EIF4ENIF1
chr22	ENCODE	exon	30184240	30184507	.	-	.	Parent=gene1824
chr22	ENCODE	CDS	30184240	30184507	.	-	2	Parent=gene1824
chr22	ENCODE	exon	30188715	30188842	.	-	.	Parent=gene1824
chr22	ENCODE	CDS	30188715	30188842	.	-	1	Parent=gene1824
chr22	ENCODE	exon	30192384	30192457	.	-	.	Parent=gene1824
chr22	ENCODE	CDS	30192384	30192457	.	-	0	Parent=gene1824
chr22	ENCODE	CDS	30209163	30209258	.	-	0	Parent=gene1824
chr22	ENCODE	exon	30209163	30209285	.	-	.	Parent=gene1824
chr22	ENCODE	exon	30209688	30209782	.	-	.	Parent=gene1824
###
chr22	ENCODE	gene	30188822	30210477	.	-	.	ID=gene1825;Name=RP11-247I13.2-009;name2=EIF4ENIF1
chr22	ENCODE	exon	30188822	30188842	.	-	.	Parent=gene1825
chr22	ENCODE	CDS	30188822	30188842	.	-	1	Parent=gene1825
chr22	ENCODE	exon	30192384	30192457	.	-	.	Parent=gene1825
chr22	ENCODE	CDS	30192384	30192457	.	-	0	Parent=gene1825
chr22	ENCODE	CDS	30209163	30209258	.	-	0	Parent=gene1825
chr22	ENCODE	exon	30209163	30209285	.	-	.	Parent=gene1825
chr22	ENCODE	exon	30210445	30210477	.	-	.	Parent=gene1825
###
chr22	ENCODE	gene	30188822	30216648	.	-	.	ID=gene1826;Name=RP11-247I13.2-008;name2=EIF4ENIF1
chr22	ENCODE	exon	30188822	30188842	.	-	.	Parent=gene1826
chr22	ENCODE	CDS	30188822	30188842	.	-	1	Parent=gene1826
chr22	ENCODE	exon	30192384	30192457	.	-	.	Parent=gene1826
chr22	ENCODE	CDS	30192384	30192457	.	-	0	Parent=gene1826
chr22	ENCODE	CDS	30209163	30209258	.	-	0	Parent=gene1826
chr22	ENCODE	exon	30209163	30209285	.	-	.	Parent=gene1826
chr22	ENCODE	exon	30216493	30216648	.	-	.	Parent=gene1826
###
chr22	ENCODE	gene	30209228	30249607	.	+	.	ID=gene1827;Name=RP5-858B16.1-016;name2=SFI1
chr22	ENCODE	exon	30209228	30209323	.	+	.	Parent=gene1827
chr22	ENCODE	exon	30228795	30228916	.	+	.	Parent=gene1827
chr22	ENCODE	exon	30249230	30249607	.	+	.	Parent=gene1827
###
chr22	ENCODE	gene	30216815	30339091	.	+	.	ID=gene1828;name2=SFI1;Name=RP5-858B16.1-001
chr22	ENCODE	exon	30216815	30217177	.	+	.	Parent=gene1828
chr22	ENCODE	exon	30228795	30228916	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30228825	30228916	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30249230	30249403	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30249230	30249403	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30251598	30251669	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30251598	30251669	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30267401	30267511	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30267401	30267511	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30270794	30270888	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30270794	30270888	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30277482	30277599	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30277482	30277599	.	+	2	Parent=gene1828
chr22	ENCODE	exon	30281830	30281932	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30281830	30281932	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30293598	30293754	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30293598	30293754	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30295771	30295932	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30295771	30295932	.	+	2	Parent=gene1828
chr22	ENCODE	exon	30298922	30298992	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30298922	30298992	.	+	2	Parent=gene1828
chr22	ENCODE	exon	30304415	30304512	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30304415	30304512	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30305608	30305674	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30305608	30305674	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30309987	30310117	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30309987	30310117	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30322752	30322833	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30322752	30322833	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30323147	30323325	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30323147	30323325	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30324284	30324359	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30324284	30324359	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30324849	30324944	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30324849	30324944	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30325409	30325485	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30325409	30325485	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30326868	30326970	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30326868	30326970	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30328477	30328573	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30328477	30328573	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30331683	30331843	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30331683	30331843	.	+	2	Parent=gene1828
chr22	ENCODE	exon	30332306	30332380	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30332306	30332380	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30333682	30333756	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30333682	30333756	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30333894	30334070	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30333894	30334070	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30334142	30334395	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30334142	30334395	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30335329	30335400	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30335329	30335400	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30335588	30335819	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30335588	30335819	.	+	1	Parent=gene1828
chr22	ENCODE	exon	30337285	30337417	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30337285	30337417	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30337540	30337618	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30337540	30337618	.	+	2	Parent=gene1828
chr22	ENCODE	exon	30338655	30338766	.	+	.	Parent=gene1828
chr22	ENCODE	CDS	30338655	30338766	.	+	1	Parent=gene1828
chr22	ENCODE	CDS	30338854	30338958	.	+	0	Parent=gene1828
chr22	ENCODE	exon	30338854	30339091	.	+	.	Parent=gene1828
###
chr22	ENCODE	gene	30217059	30251645	.	+	.	ID=gene1829;name2=SFI1;Name=RP5-858B16.1-017
chr22	ENCODE	exon	30217059	30217177	.	+	.	Parent=gene1829
chr22	ENCODE	exon	30228795	30228916	.	+	.	Parent=gene1829
chr22	ENCODE	exon	30249230	30249403	.	+	.	Parent=gene1829
chr22	ENCODE	exon	30251132	30251324	.	+	.	Parent=gene1829
chr22	ENCODE	exon	30251598	30251645	.	+	.	Parent=gene1829
###
chr22	ENCODE	gene	30217078	30339088	.	+	.	ID=gene1830;Name=RP5-858B16.1-014;name2=SFI1
chr22	ENCODE	exon	30217078	30217177	.	+	.	Parent=gene1830
chr22	ENCODE	exon	30228799	30228916	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30228825	30228916	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30267401	30267511	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30267401	30267511	.	+	1	Parent=gene1830
chr22	ENCODE	exon	30270794	30270888	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30270794	30270888	.	+	1	Parent=gene1830
chr22	ENCODE	exon	30277482	30277599	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30277482	30277599	.	+	2	Parent=gene1830
chr22	ENCODE	exon	30281830	30281932	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30281830	30281932	.	+	1	Parent=gene1830
chr22	ENCODE	exon	30293598	30293754	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30293598	30293754	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30295771	30295932	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30295771	30295932	.	+	2	Parent=gene1830
chr22	ENCODE	exon	30298922	30298992	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30298922	30298992	.	+	2	Parent=gene1830
chr22	ENCODE	exon	30300812	30300904	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30300812	30300904	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30304415	30304512	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30304415	30304512	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30305608	30305674	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30305608	30305674	.	+	1	Parent=gene1830
chr22	ENCODE	exon	30309987	30310117	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30309987	30310117	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30322752	30322833	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30322752	30322833	.	+	1	Parent=gene1830
chr22	ENCODE	exon	30323147	30323325	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30323147	30323325	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30324284	30324359	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30324284	30324359	.	+	1	Parent=gene1830
chr22	ENCODE	exon	30324849	30324944	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30324849	30324944	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30325409	30325485	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30325409	30325485	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30326868	30326970	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30326868	30326970	.	+	1	Parent=gene1830
chr22	ENCODE	exon	30328477	30328573	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30328477	30328573	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30331683	30331843	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30331683	30331843	.	+	2	Parent=gene1830
chr22	ENCODE	exon	30332306	30332380	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30332306	30332380	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30333682	30333756	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30333682	30333756	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30333894	30334070	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30333894	30334070	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30334142	30334395	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30334142	30334395	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30335329	30335400	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30335329	30335400	.	+	1	Parent=gene1830
chr22	ENCODE	exon	30335588	30335819	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30335588	30335819	.	+	1	Parent=gene1830
chr22	ENCODE	exon	30337285	30337417	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30337285	30337417	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30337540	30337618	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30337540	30337618	.	+	2	Parent=gene1830
chr22	ENCODE	exon	30338655	30338766	.	+	.	Parent=gene1830
chr22	ENCODE	CDS	30338655	30338766	.	+	1	Parent=gene1830
chr22	ENCODE	CDS	30338854	30338958	.	+	0	Parent=gene1830
chr22	ENCODE	exon	30338854	30339088	.	+	.	Parent=gene1830
###
chr22	ENCODE	gene	30217098	30249375	.	+	.	ID=gene1831;Name=RP5-858B16.1-015;name2=SFI1
chr22	ENCODE	exon	30217098	30217177	.	+	.	Parent=gene1831
chr22	ENCODE	exon	30217788	30217888	.	+	.	Parent=gene1831
chr22	ENCODE	exon	30228795	30228916	.	+	.	Parent=gene1831
chr22	ENCODE	CDS	30228825	30228916	.	+	0	Parent=gene1831
chr22	ENCODE	exon	30249230	30249375	.	+	.	Parent=gene1831
chr22	ENCODE	CDS	30249230	30249375	.	+	1	Parent=gene1831
###
chr22	ENCODE	gene	30217123	30339088	.	+	.	ID=gene1832;Name=RP5-858B16.1-002;name2=SFI1
chr22	ENCODE	exon	30217123	30217177	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30228795	30228916	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30249230	30249403	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30251598	30251669	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30267401	30267511	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30270794	30270888	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30277482	30277599	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30281830	30281932	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30293598	30293754	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30295771	30295932	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30298922	30298992	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30300812	30300904	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30304415	30304512	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30305608	30305674	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30309987	30310117	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30322752	30322833	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30323147	30323325	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30324849	30324944	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30325409	30326970	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30328477	30328573	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30331683	30331843	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30332306	30332380	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30333682	30333756	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30333894	30334070	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30334142	30334395	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30335329	30335400	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30335588	30335819	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30337285	30337417	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30337540	30337618	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30338655	30338766	.	+	.	Parent=gene1832
chr22	ENCODE	exon	30338854	30339088	.	+	.	Parent=gene1832
###
chr22	ENCODE	gene	30249360	30271217	.	+	.	ID=gene1833;Name=RP5-858B16.1-007;name2=SFI1
chr22	ENCODE	exon	30249360	30249403	.	+	.	Parent=gene1833
chr22	ENCODE	exon	30251598	30251669	.	+	.	Parent=gene1833
chr22	ENCODE	exon	30267401	30267511	.	+	.	Parent=gene1833
chr22	ENCODE	exon	30270794	30271217	.	+	.	Parent=gene1833
###
chr22	ENCODE	gene	30293303	30304474	.	+	.	ID=gene1834;Name=RP5-858B16.1-018;name2=SFI1
chr22	ENCODE	exon	30293303	30293754	.	+	.	Parent=gene1834
chr22	ENCODE	exon	30295771	30295932	.	+	.	Parent=gene1834
chr22	ENCODE	exon	30298922	30298992	.	+	.	Parent=gene1834
chr22	ENCODE	exon	30304415	30304474	.	+	.	Parent=gene1834
###
chr22	ENCODE	gene	30293517	30304417	.	+	.	ID=gene1835;Name=RP5-858B16.1-019;name2=SFI1
chr22	ENCODE	exon	30293517	30293754	.	+	.	Parent=gene1835
chr22	ENCODE	exon	30295771	30295932	.	+	.	Parent=gene1835
chr22	ENCODE	exon	30298922	30298992	.	+	.	Parent=gene1835
chr22	ENCODE	exon	30300812	30300904	.	+	.	Parent=gene1835
chr22	ENCODE	exon	30304415	30304417	.	+	.	Parent=gene1835
###
chr22	ENCODE	gene	30293714	30339087	.	+	.	ID=gene1836;Name=RP5-858B16.1-003;name2=SFI1
chr22	ENCODE	exon	30293714	30293754	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30295771	30295932	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30298922	30298992	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30300812	30300904	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30304415	30304512	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30305608	30305674	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30309987	30310117	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30322752	30322833	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30323147	30323325	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30328477	30328573	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30331683	30331843	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30332306	30332380	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30333682	30333756	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30333894	30334070	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30334142	30334395	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30335329	30335400	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30335588	30335819	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30337285	30337417	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30337540	30337618	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30338655	30338766	.	+	.	Parent=gene1836
chr22	ENCODE	exon	30338854	30339087	.	+	.	Parent=gene1836
###
chr22	ENCODE	gene	30298488	30305666	.	+	.	ID=gene1837;Name=RP5-858B16.1-020;name2=SFI1
chr22	ENCODE	exon	30298488	30298992	.	+	.	Parent=gene1837
chr22	ENCODE	exon	30304415	30304512	.	+	.	Parent=gene1837
chr22	ENCODE	exon	30305608	30305666	.	+	.	Parent=gene1837
###
chr22	ENCODE	gene	30300628	30304509	.	+	.	ID=gene1838;name2=SFI1;Name=RP5-858B16.1-008
chr22	ENCODE	exon	30300628	30300904	.	+	.	Parent=gene1838
chr22	ENCODE	exon	30304415	30304509	.	+	.	Parent=gene1838
###
chr22	ENCODE	gene	30304446	30308452	.	+	.	ID=gene1839;Name=RP5-858B16.1-009;name2=SFI1
chr22	ENCODE	exon	30304446	30304512	.	+	.	Parent=gene1839
chr22	ENCODE	exon	30305608	30305674	.	+	.	Parent=gene1839
chr22	ENCODE	exon	30307868	30308452	.	+	.	Parent=gene1839
###
chr22	ENCODE	gene	30324854	30327266	.	+	.	ID=gene1840;Name=RP5-858B16.1-010;name2=SFI1
chr22	ENCODE	exon	30324854	30324944	.	+	.	Parent=gene1840
chr22	ENCODE	exon	30325409	30325485	.	+	.	Parent=gene1840
chr22	ENCODE	exon	30326868	30327266	.	+	.	Parent=gene1840
###
chr22	ENCODE	gene	30325109	30332309	.	+	.	ID=gene1841;Name=RP5-858B16.1-021;name2=SFI1
chr22	ENCODE	exon	30325109	30325211	.	+	.	Parent=gene1841
chr22	ENCODE	exon	30325409	30325485	.	+	.	Parent=gene1841
chr22	ENCODE	exon	30326868	30326970	.	+	.	Parent=gene1841
chr22	ENCODE	exon	30328477	30328573	.	+	.	Parent=gene1841
chr22	ENCODE	exon	30331683	30331843	.	+	.	Parent=gene1841
chr22	ENCODE	exon	30332306	30332309	.	+	.	Parent=gene1841
###
chr22	ENCODE	gene	30328191	30332341	.	+	.	ID=gene1842;Name=RP5-858B16.1-022;name2=SFI1
chr22	ENCODE	exon	30328191	30328573	.	+	.	Parent=gene1842
chr22	ENCODE	exon	30331683	30331843	.	+	.	Parent=gene1842
chr22	ENCODE	exon	30332306	30332341	.	+	.	Parent=gene1842
###
chr22	ENCODE	gene	30332306	30332982	.	+	.	ID=gene1843;Name=RP5-858B16.1-011;name2=SFI1
chr22	ENCODE	exon	30332306	30332380	.	+	.	Parent=gene1843
chr22	ENCODE	exon	30332539	30332982	.	+	.	Parent=gene1843
###
chr22	ENCODE	gene	30333313	30334255	.	+	.	ID=gene1844;Name=RP5-858B16.1-012;name2=SFI1
chr22	ENCODE	exon	30333313	30333756	.	+	.	Parent=gene1844
chr22	ENCODE	exon	30333894	30334070	.	+	.	Parent=gene1844
chr22	ENCODE	exon	30334142	30334255	.	+	.	Parent=gene1844
###
chr22	ENCODE	gene	30334375	30339088	.	+	.	ID=gene1845;Name=RP5-858B16.1-013;name2=SFI1
chr22	ENCODE	exon	30334375	30334395	.	+	.	Parent=gene1845
chr22	ENCODE	exon	30335329	30335400	.	+	.	Parent=gene1845
chr22	ENCODE	exon	30335588	30335819	.	+	.	Parent=gene1845
chr22	ENCODE	exon	30337285	30337417	.	+	.	Parent=gene1845
chr22	ENCODE	exon	30338752	30338766	.	+	.	Parent=gene1845
chr22	ENCODE	exon	30338854	30339088	.	+	.	Parent=gene1845
###
chr22	ENCODE	gene	30334707	30339088	.	+	.	ID=gene1846;Name=RP5-858B16.1-004;name2=SFI1
chr22	ENCODE	exon	30334707	30335400	.	+	.	Parent=gene1846
chr22	ENCODE	exon	30335588	30335819	.	+	.	Parent=gene1846
chr22	ENCODE	exon	30337285	30337417	.	+	.	Parent=gene1846
chr22	ENCODE	exon	30337540	30337618	.	+	.	Parent=gene1846
chr22	ENCODE	exon	30338655	30338766	.	+	.	Parent=gene1846
chr22	ENCODE	exon	30338854	30339088	.	+	.	Parent=gene1846
###
chr22	ENCODE	gene	30334911	30339087	.	+	.	ID=gene1847;Name=RP5-858B16.1-006;name2=SFI1
chr22	ENCODE	exon	30334911	30337417	.	+	.	Parent=gene1847
chr22	ENCODE	exon	30337540	30337618	.	+	.	Parent=gene1847
chr22	ENCODE	exon	30338655	30339087	.	+	.	Parent=gene1847
###
chr22	ENCODE	gene	30334926	30339088	.	+	.	ID=gene1848;Name=RP5-858B16.1-005;name2=SFI1
chr22	ENCODE	exon	30334926	30335819	.	+	.	Parent=gene1848
chr22	ENCODE	exon	30337285	30337417	.	+	.	Parent=gene1848
chr22	ENCODE	exon	30337540	30337618	.	+	.	Parent=gene1848
chr22	ENCODE	exon	30338655	30338766	.	+	.	Parent=gene1848
chr22	ENCODE	exon	30338854	30339088	.	+	.	Parent=gene1848
###
chr22	ENCODE	gene	30339031	30348761	.	-	.	ID=gene1849;Name=RP5-858B16.2-007;name2=PISD
chr22	ENCODE	exon	30339031	30340376	.	-	.	Parent=gene1849
chr22	ENCODE	CDS	30340152	30340376	.	-	0	Parent=gene1849
chr22	ENCODE	exon	30341093	30341253	.	-	.	Parent=gene1849
chr22	ENCODE	CDS	30341093	30341253	.	-	2	Parent=gene1849
chr22	ENCODE	exon	30341536	30341682	.	-	.	Parent=gene1849
chr22	ENCODE	CDS	30341536	30341682	.	-	2	Parent=gene1849
chr22	ENCODE	exon	30341874	30342012	.	-	.	Parent=gene1849
chr22	ENCODE	CDS	30341874	30342012	.	-	0	Parent=gene1849
chr22	ENCODE	exon	30342189	30342425	.	-	.	Parent=gene1849
chr22	ENCODE	CDS	30342189	30342425	.	-	0	Parent=gene1849
chr22	ENCODE	exon	30344224	30344389	.	-	.	Parent=gene1849
chr22	ENCODE	CDS	30344224	30344389	.	-	1	Parent=gene1849
chr22	ENCODE	CDS	30346303	30346355	.	-	0	Parent=gene1849
chr22	ENCODE	exon	30346303	30346556	.	-	.	Parent=gene1849
chr22	ENCODE	exon	30348543	30348761	.	-	.	Parent=gene1849
###
chr22	ENCODE	gene	30339031	30382755	.	-	.	ID=gene1850;Name=RP5-858B16.2-002;name2=PISD
chr22	ENCODE	exon	30339031	30340376	.	-	.	Parent=gene1850
chr22	ENCODE	exon	30341093	30341253	.	-	.	Parent=gene1850
chr22	ENCODE	exon	30341536	30341682	.	-	.	Parent=gene1850
chr22	ENCODE	exon	30341874	30342425	.	-	.	Parent=gene1850
chr22	ENCODE	exon	30368641	30368816	.	-	.	Parent=gene1850
chr22	ENCODE	exon	30371239	30371318	.	-	.	Parent=gene1850
chr22	ENCODE	exon	30382684	30382755	.	-	.	Parent=gene1850
###
chr22	ENCODE	gene	30339099	30351402	.	-	.	ID=gene1851;Name=RP5-858B16.2-005;name2=PISD
chr22	ENCODE	exon	30339099	30340376	.	-	.	Parent=gene1851
chr22	ENCODE	exon	30341093	30341253	.	-	.	Parent=gene1851
chr22	ENCODE	exon	30341536	30342012	.	-	.	Parent=gene1851
chr22	ENCODE	exon	30342189	30342425	.	-	.	Parent=gene1851
chr22	ENCODE	exon	30344224	30344389	.	-	.	Parent=gene1851
chr22	ENCODE	exon	30351344	30351402	.	-	.	Parent=gene1851
###
chr22	ENCODE	gene	30339154	30351371	.	-	.	ID=gene1852;Name=RP5-858B16.2-006;name2=PISD
chr22	ENCODE	exon	30339154	30340376	.	-	.	Parent=gene1852
chr22	ENCODE	CDS	30340330	30340376	.	-	2	Parent=gene1852
chr22	ENCODE	exon	30341536	30341682	.	-	.	Parent=gene1852
chr22	ENCODE	CDS	30341536	30341682	.	-	2	Parent=gene1852
chr22	ENCODE	exon	30341874	30342012	.	-	.	Parent=gene1852
chr22	ENCODE	CDS	30341874	30342012	.	-	0	Parent=gene1852
chr22	ENCODE	exon	30342189	30342425	.	-	.	Parent=gene1852
chr22	ENCODE	CDS	30342189	30342425	.	-	0	Parent=gene1852
chr22	ENCODE	exon	30344224	30344389	.	-	.	Parent=gene1852
chr22	ENCODE	CDS	30344224	30344389	.	-	1	Parent=gene1852
chr22	ENCODE	CDS	30346303	30346355	.	-	0	Parent=gene1852
chr22	ENCODE	exon	30346303	30346556	.	-	.	Parent=gene1852
chr22	ENCODE	exon	30351344	30351371	.	-	.	Parent=gene1852
###
chr22	ENCODE	gene	30339433	30346557	.	-	.	ID=gene1853;Name=RP5-858B16.2-008;name2=PISD
chr22	ENCODE	exon	30339433	30340376	.	-	.	Parent=gene1853
chr22	ENCODE	exon	30341093	30341253	.	-	.	Parent=gene1853
chr22	ENCODE	exon	30341536	30341700	.	-	.	Parent=gene1853
chr22	ENCODE	exon	30346408	30346557	.	-	.	Parent=gene1853
###
chr22	ENCODE	gene	30339517	30382720	.	-	.	ID=gene1854;Name=RP5-858B16.2-004;name2=PISD
chr22	ENCODE	exon	30339517	30340376	.	-	.	Parent=gene1854
chr22	ENCODE	CDS	30340152	30340376	.	-	1	Parent=gene1854
chr22	ENCODE	exon	30341093	30341139	.	-	.	Parent=gene1854
chr22	ENCODE	CDS	30341093	30341139	.	-	0	Parent=gene1854
chr22	ENCODE	exon	30341536	30341682	.	-	.	Parent=gene1854
chr22	ENCODE	CDS	30341536	30341682	.	-	0	Parent=gene1854
chr22	ENCODE	exon	30341874	30342012	.	-	.	Parent=gene1854
chr22	ENCODE	CDS	30341874	30342012	.	-	1	Parent=gene1854
chr22	ENCODE	exon	30342189	30342425	.	-	.	Parent=gene1854
chr22	ENCODE	CDS	30342189	30342425	.	-	1	Parent=gene1854
chr22	ENCODE	exon	30368641	30368816	.	-	.	Parent=gene1854
chr22	ENCODE	CDS	30368641	30368816	.	-	0	Parent=gene1854
chr22	ENCODE	exon	30371239	30371318	.	-	.	Parent=gene1854
chr22	ENCODE	CDS	30371239	30371318	.	-	2	Parent=gene1854
chr22	ENCODE	exon	30382684	30382720	.	-	.	Parent=gene1854
chr22	ENCODE	CDS	30382684	30382720	.	-	0	Parent=gene1854
###
chr22	ENCODE	gene	30339643	30382972	.	-	.	ID=gene1855;name2=PISD;Name=RP5-858B16.2-001
chr22	ENCODE	exon	30339643	30340376	.	-	.	Parent=gene1855
chr22	ENCODE	CDS	30340152	30340376	.	-	0	Parent=gene1855
chr22	ENCODE	exon	30341093	30341253	.	-	.	Parent=gene1855
chr22	ENCODE	CDS	30341093	30341253	.	-	2	Parent=gene1855
chr22	ENCODE	exon	30341536	30341682	.	-	.	Parent=gene1855
chr22	ENCODE	CDS	30341536	30341682	.	-	2	Parent=gene1855
chr22	ENCODE	exon	30341874	30342012	.	-	.	Parent=gene1855
chr22	ENCODE	CDS	30341874	30342012	.	-	0	Parent=gene1855
chr22	ENCODE	exon	30342189	30342425	.	-	.	Parent=gene1855
chr22	ENCODE	CDS	30342189	30342425	.	-	0	Parent=gene1855
chr22	ENCODE	exon	30368641	30368816	.	-	.	Parent=gene1855
chr22	ENCODE	CDS	30368641	30368816	.	-	2	Parent=gene1855
chr22	ENCODE	exon	30371239	30371318	.	-	.	Parent=gene1855
chr22	ENCODE	CDS	30371239	30371318	.	-	1	Parent=gene1855
chr22	ENCODE	CDS	30382684	30382748	.	-	0	Parent=gene1855
chr22	ENCODE	exon	30382684	30382972	.	-	.	Parent=gene1855
###
chr22	ENCODE	gene	30339984	30382743	.	-	.	ID=gene1856;Name=RP5-858B16.2-003;name2=PISD
chr22	ENCODE	exon	30339984	30340376	.	-	.	Parent=gene1856
chr22	ENCODE	exon	30341093	30341253	.	-	.	Parent=gene1856
chr22	ENCODE	exon	30341536	30342425	.	-	.	Parent=gene1856
chr22	ENCODE	exon	30368641	30368816	.	-	.	Parent=gene1856
chr22	ENCODE	exon	30371239	30371318	.	-	.	Parent=gene1856
chr22	ENCODE	exon	30382684	30382743	.	-	.	Parent=gene1856
###
chr22	ENCODE	gene	30341093	30346326	.	-	.	ID=gene1857;Name=RP5-858B16.2-015;name2=PISD
chr22	ENCODE	exon	30341093	30341253	.	-	.	Parent=gene1857
chr22	ENCODE	exon	30341536	30341682	.	-	.	Parent=gene1857
chr22	ENCODE	exon	30341874	30342012	.	-	.	Parent=gene1857
chr22	ENCODE	exon	30342189	30342425	.	-	.	Parent=gene1857
chr22	ENCODE	exon	30344224	30344389	.	-	.	Parent=gene1857
chr22	ENCODE	exon	30346121	30346326	.	-	.	Parent=gene1857
###
chr22	ENCODE	gene	30341118	30358938	.	-	.	ID=gene1858;Name=RP5-858B16.2-011;name2=PISD
chr22	ENCODE	exon	30341118	30341253	.	-	.	Parent=gene1858
chr22	ENCODE	exon	30341536	30341682	.	-	.	Parent=gene1858
chr22	ENCODE	exon	30341874	30342012	.	-	.	Parent=gene1858
chr22	ENCODE	exon	30342189	30342425	.	-	.	Parent=gene1858
chr22	ENCODE	exon	30358906	30358938	.	-	.	Parent=gene1858
###
chr22	ENCODE	gene	30341594	30349522	.	-	.	ID=gene1859;Name=RP5-858B16.2-012;name2=PISD
chr22	ENCODE	exon	30341594	30341682	.	-	.	Parent=gene1859
chr22	ENCODE	CDS	30341594	30341682	.	-	2	Parent=gene1859
chr22	ENCODE	exon	30341874	30342012	.	-	.	Parent=gene1859
chr22	ENCODE	CDS	30341874	30342012	.	-	0	Parent=gene1859
chr22	ENCODE	exon	30342189	30342425	.	-	.	Parent=gene1859
chr22	ENCODE	CDS	30342189	30342425	.	-	0	Parent=gene1859
chr22	ENCODE	exon	30344224	30344389	.	-	.	Parent=gene1859
chr22	ENCODE	CDS	30344224	30344389	.	-	1	Parent=gene1859
chr22	ENCODE	CDS	30346303	30346355	.	-	0	Parent=gene1859
chr22	ENCODE	exon	30346303	30346556	.	-	.	Parent=gene1859
chr22	ENCODE	exon	30349393	30349522	.	-	.	Parent=gene1859
###
chr22	ENCODE	gene	30342402	30346834	.	-	.	ID=gene1860;Name=RP5-858B16.2-014;name2=PISD
chr22	ENCODE	exon	30342402	30342425	.	-	.	Parent=gene1860
chr22	ENCODE	CDS	30342402	30342425	.	-	0	Parent=gene1860
chr22	ENCODE	exon	30344224	30344389	.	-	.	Parent=gene1860
chr22	ENCODE	CDS	30344224	30344389	.	-	1	Parent=gene1860
chr22	ENCODE	CDS	30346303	30346355	.	-	0	Parent=gene1860
chr22	ENCODE	exon	30346303	30346834	.	-	.	Parent=gene1860
###
chr22	ENCODE	gene	30344224	30358945	.	-	.	ID=gene1861;Name=RP5-858B16.2-010;name2=PISD
chr22	ENCODE	exon	30344224	30344389	.	-	.	Parent=gene1861
chr22	ENCODE	CDS	30344224	30344389	.	-	1	Parent=gene1861
chr22	ENCODE	CDS	30346303	30346355	.	-	0	Parent=gene1861
chr22	ENCODE	exon	30346303	30346556	.	-	.	Parent=gene1861
chr22	ENCODE	exon	30358906	30358945	.	-	.	Parent=gene1861
###
chr22	ENCODE	gene	30344224	30358985	.	-	.	ID=gene1862;Name=RP5-858B16.2-009;name2=PISD
chr22	ENCODE	exon	30344224	30344389	.	-	.	Parent=gene1862
chr22	ENCODE	CDS	30344224	30344389	.	-	1	Parent=gene1862
chr22	ENCODE	CDS	30346303	30346355	.	-	0	Parent=gene1862
chr22	ENCODE	exon	30346303	30346556	.	-	.	Parent=gene1862
chr22	ENCODE	exon	30352723	30352831	.	-	.	Parent=gene1862
chr22	ENCODE	exon	30358906	30358985	.	-	.	Parent=gene1862
###
chr22	ENCODE	gene	30346362	30350546	.	-	.	ID=gene1863;Name=RP5-858B16.2-013;name2=PISD
chr22	ENCODE	exon	30346362	30346556	.	-	.	Parent=gene1863
chr22	ENCODE	exon	30348543	30348750	.	-	.	Parent=gene1863
chr22	ENCODE	exon	30349393	30349521	.	-	.	Parent=gene1863
chr22	ENCODE	exon	30350242	30350546	.	-	.	Parent=gene1863
###
chr22	ENCODE	gene	30396796	30433285	.	-	.	ID=gene1864;Name=RP4-694E4.2-003;name2=C22orf30
chr22	ENCODE	exon	30396796	30397558	.	-	.	Parent=gene1864
chr22	ENCODE	CDS	30397288	30397558	.	-	0	Parent=gene1864
chr22	ENCODE	exon	30408696	30408767	.	-	.	Parent=gene1864
chr22	ENCODE	CDS	30408696	30408767	.	-	0	Parent=gene1864
chr22	ENCODE	exon	30422196	30422302	.	-	.	Parent=gene1864
chr22	ENCODE	CDS	30422196	30422302	.	-	2	Parent=gene1864
chr22	ENCODE	exon	30424090	30424261	.	-	.	Parent=gene1864
chr22	ENCODE	CDS	30424090	30424261	.	-	0	Parent=gene1864
chr22	ENCODE	exon	30425195	30425266	.	-	.	Parent=gene1864
chr22	ENCODE	CDS	30425195	30425266	.	-	0	Parent=gene1864
chr22	ENCODE	exon	30432623	30433285	.	-	.	Parent=gene1864
chr22	ENCODE	CDS	30432623	30433285	.	-	0	Parent=gene1864
###
chr22	ENCODE	gene	30401887	30470671	.	-	.	ID=gene1865;Name=RP4-694E4.2-001;name2=C22orf30
chr22	ENCODE	exon	30401887	30406343	.	-	.	Parent=gene1865
chr22	ENCODE	CDS	30406067	30406343	.	-	1	Parent=gene1865
chr22	ENCODE	exon	30408696	30408767	.	-	.	Parent=gene1865
chr22	ENCODE	CDS	30408696	30408767	.	-	1	Parent=gene1865
chr22	ENCODE	exon	30422196	30422302	.	-	.	Parent=gene1865
chr22	ENCODE	CDS	30422196	30422302	.	-	0	Parent=gene1865
chr22	ENCODE	exon	30424090	30424261	.	-	.	Parent=gene1865
chr22	ENCODE	CDS	30424090	30424261	.	-	1	Parent=gene1865
chr22	ENCODE	exon	30425195	30425266	.	-	.	Parent=gene1865
chr22	ENCODE	CDS	30425195	30425266	.	-	1	Parent=gene1865
chr22	ENCODE	exon	30432623	30437831	.	-	.	Parent=gene1865
chr22	ENCODE	CDS	30432623	30437831	.	-	2	Parent=gene1865
chr22	ENCODE	exon	30446078	30446150	.	-	.	Parent=gene1865
chr22	ENCODE	CDS	30446078	30446150	.	-	0	Parent=gene1865
chr22	ENCODE	CDS	30458927	30459400	.	-	0	Parent=gene1865
chr22	ENCODE	exon	30458927	30459451	.	-	.	Parent=gene1865
chr22	ENCODE	exon	30470533	30470671	.	-	.	Parent=gene1865
###
chr22	ENCODE	gene	30401890	30424258	.	-	.	ID=gene1866;Name=RP4-694E4.2-004;name2=C22orf30
chr22	ENCODE	exon	30401890	30402674	.	-	.	Parent=gene1866
chr22	ENCODE	exon	30404169	30406343	.	-	.	Parent=gene1866
chr22	ENCODE	exon	30408696	30408767	.	-	.	Parent=gene1866
chr22	ENCODE	exon	30422196	30422302	.	-	.	Parent=gene1866
chr22	ENCODE	exon	30424090	30424258	.	-	.	Parent=gene1866
###
chr22	ENCODE	gene	30405582	30434385	.	-	.	ID=gene1867;Name=RP4-694E4.2-002;name2=C22orf30
chr22	ENCODE	exon	30405582	30406343	.	-	.	Parent=gene1867
chr22	ENCODE	exon	30408696	30408767	.	-	.	Parent=gene1867
chr22	ENCODE	exon	30424090	30424261	.	-	.	Parent=gene1867
chr22	ENCODE	exon	30425195	30425266	.	-	.	Parent=gene1867
chr22	ENCODE	exon	30432623	30434385	.	-	.	Parent=gene1867
###
chr22	ENCODE	gene	30424984	30432887	.	-	.	ID=gene1868;Name=RP4-694E4.2-006;name2=C22orf30
chr22	ENCODE	exon	30424984	30425266	.	-	.	Parent=gene1868
chr22	ENCODE	exon	30432623	30432887	.	-	.	Parent=gene1868
###
chr22	ENCODE	gene	30437267	30470612	.	-	.	ID=gene1869;Name=RP4-694E4.2-005;name2=C22orf30
chr22	ENCODE	exon	30437267	30437831	.	-	.	Parent=gene1869
chr22	ENCODE	exon	30446078	30446150	.	-	.	Parent=gene1869
chr22	ENCODE	exon	30470533	30470612	.	-	.	Parent=gene1869
###
chr22	ENCODE	gene	30446084	30470680	.	-	.	ID=gene1870;Name=RP4-694E4.2-007;name2=C22orf30
chr22	ENCODE	exon	30446084	30446150	.	-	.	Parent=gene1870
chr22	ENCODE	CDS	30446084	30446150	.	-	0	Parent=gene1870
chr22	ENCODE	CDS	30458927	30459400	.	-	0	Parent=gene1870
chr22	ENCODE	exon	30458927	30459451	.	-	.	Parent=gene1870
chr22	ENCODE	exon	30470612	30470680	.	-	.	Parent=gene1870
###
chr22	ENCODE	gene	30474498	30479164	.	+	.	ID=gene1871;Name=LL22NC03-113A11.1-012;name2=DEPDC5
chr22	ENCODE	exon	30474498	30474536	.	+	.	Parent=gene1871
chr22	ENCODE	exon	30475402	30475519	.	+	.	Parent=gene1871
chr22	ENCODE	CDS	30475462	30475519	.	+	0	Parent=gene1871
chr22	ENCODE	exon	30479086	30479164	.	+	.	Parent=gene1871
chr22	ENCODE	CDS	30479086	30479164	.	+	2	Parent=gene1871
###
chr22	ENCODE	gene	30474510	30476051	.	+	.	ID=gene1872;Name=LL22NC03-113A11.1-013;name2=DEPDC5
chr22	ENCODE	exon	30474510	30474536	.	+	.	Parent=gene1872
chr22	ENCODE	exon	30475402	30476051	.	+	.	Parent=gene1872
###
chr22	ENCODE	gene	30474519	30498677	.	+	.	ID=gene1873;Name=LL22NC03-113A11.1-014;name2=DEPDC5
chr22	ENCODE	exon	30474519	30474536	.	+	.	Parent=gene1873
chr22	ENCODE	exon	30475402	30475519	.	+	.	Parent=gene1873
chr22	ENCODE	exon	30479067	30479173	.	+	.	Parent=gene1873
chr22	ENCODE	exon	30481196	30481242	.	+	.	Parent=gene1873
chr22	ENCODE	exon	30485515	30485600	.	+	.	Parent=gene1873
chr22	ENCODE	exon	30487125	30487208	.	+	.	Parent=gene1873
chr22	ENCODE	exon	30489354	30489403	.	+	.	Parent=gene1873
chr22	ENCODE	exon	30498639	30498677	.	+	.	Parent=gene1873
###
chr22	ENCODE	gene	30474609	30536528	.	+	.	ID=gene1874;name2=DEPDC5;Name=LL22NC03-113A11.1-002
chr22	ENCODE	exon	30474609	30474704	.	+	.	Parent=gene1874
chr22	ENCODE	exon	30475402	30475519	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30475462	30475519	.	+	0	Parent=gene1874
chr22	ENCODE	exon	30479086	30479173	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30479086	30479173	.	+	2	Parent=gene1874
chr22	ENCODE	exon	30481196	30481242	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30481196	30481242	.	+	1	Parent=gene1874
chr22	ENCODE	exon	30485515	30485600	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30485515	30485600	.	+	2	Parent=gene1874
chr22	ENCODE	exon	30487125	30487208	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30487125	30487208	.	+	0	Parent=gene1874
chr22	ENCODE	exon	30489354	30489403	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30489354	30489403	.	+	0	Parent=gene1874
chr22	ENCODE	exon	30498639	30498708	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30498639	30498708	.	+	1	Parent=gene1874
chr22	ENCODE	exon	30504447	30504525	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30504447	30504525	.	+	0	Parent=gene1874
chr22	ENCODE	exon	30505354	30505415	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30505354	30505415	.	+	2	Parent=gene1874
chr22	ENCODE	exon	30512573	30512642	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30512573	30512642	.	+	0	Parent=gene1874
chr22	ENCODE	exon	30513285	30513357	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30513285	30513357	.	+	2	Parent=gene1874
chr22	ENCODE	exon	30518140	30518243	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30518140	30518243	.	+	1	Parent=gene1874
chr22	ENCODE	exon	30519122	30519196	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30519122	30519196	.	+	2	Parent=gene1874
chr22	ENCODE	exon	30523244	30523378	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30523244	30523378	.	+	2	Parent=gene1874
chr22	ENCODE	exon	30524702	30524763	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30524702	30524763	.	+	2	Parent=gene1874
chr22	ENCODE	exon	30525382	30525455	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30525382	30525455	.	+	0	Parent=gene1874
chr22	ENCODE	exon	30526662	30526731	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30526662	30526731	.	+	1	Parent=gene1874
chr22	ENCODE	exon	30530151	30530187	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30530151	30530187	.	+	0	Parent=gene1874
chr22	ENCODE	exon	30531061	30531181	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30531061	30531181	.	+	2	Parent=gene1874
chr22	ENCODE	exon	30535532	30535752	.	+	.	Parent=gene1874
chr22	ENCODE	CDS	30535532	30535752	.	+	1	Parent=gene1874
chr22	ENCODE	CDS	30535956	30535969	.	+	2	Parent=gene1874
chr22	ENCODE	exon	30535956	30536528	.	+	.	Parent=gene1874
###
chr22	ENCODE	gene	30475392	30627545	.	+	.	ID=gene1875;Name=LL22NC03-113A11.1-006;name2=DEPDC5
chr22	ENCODE	exon	30475392	30475519	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30475462	30475519	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30479086	30479173	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30479086	30479173	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30481196	30481242	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30481196	30481242	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30485515	30485600	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30485515	30485600	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30487125	30487208	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30487125	30487208	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30489354	30489403	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30489354	30489403	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30498639	30498708	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30498639	30498708	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30504447	30504525	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30504447	30504525	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30505354	30505415	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30505354	30505415	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30512573	30512642	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30512573	30512642	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30513285	30513357	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30513285	30513357	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30518140	30518243	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30518140	30518243	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30519122	30519196	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30519122	30519196	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30523244	30523378	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30523244	30523378	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30524702	30524763	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30524702	30524763	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30525382	30525455	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30525382	30525455	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30526662	30526731	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30526662	30526731	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30530151	30530187	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30530151	30530187	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30531061	30531181	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30531061	30531181	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30535532	30535752	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30535532	30535752	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30539562	30539765	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30539562	30539765	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30542042	30542177	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30542042	30542177	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30543233	30543330	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30543233	30543330	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30554455	30554520	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30554455	30554520	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30557539	30557695	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30557539	30557695	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30559225	30559385	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30559225	30559385	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30563635	30563752	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30563635	30563752	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30564185	30564352	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30564185	30564352	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30565558	30565777	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30565558	30565777	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30567374	30567507	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30567374	30567507	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30577985	30578093	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30577985	30578093	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30581908	30581973	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30581908	30581973	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30591130	30591284	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30591130	30591284	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30593795	30593872	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30593795	30593872	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30594813	30594945	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30594813	30594945	.	+	1	Parent=gene1875
chr22	ENCODE	exon	30596697	30596805	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30596697	30596805	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30600065	30600292	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30600065	30600292	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30614122	30614291	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30614122	30614291	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30618022	30618193	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30618022	30618193	.	+	0	Parent=gene1875
chr22	ENCODE	exon	30622282	30622342	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30622282	30622342	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30626524	30626606	.	+	.	Parent=gene1875
chr22	ENCODE	CDS	30626524	30626606	.	+	1	Parent=gene1875
chr22	ENCODE	CDS	30626745	30627037	.	+	2	Parent=gene1875
chr22	ENCODE	exon	30626745	30627545	.	+	.	Parent=gene1875
###
chr22	ENCODE	gene	30475402	30627438	.	+	.	ID=gene1876;Name=LL22NC03-113A11.1-004;name2=DEPDC5
chr22	ENCODE	exon	30475402	30475519	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30475462	30475519	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30479086	30479173	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30479086	30479173	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30481196	30481242	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30481196	30481242	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30485515	30485600	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30485515	30485600	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30487125	30487208	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30487125	30487208	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30489354	30489403	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30489354	30489403	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30498639	30498708	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30498639	30498708	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30504447	30504525	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30504447	30504525	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30505354	30505415	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30505354	30505415	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30512573	30512642	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30512573	30512642	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30513285	30513357	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30513285	30513357	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30518140	30518243	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30518140	30518243	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30519122	30519196	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30519122	30519196	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30523244	30523378	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30523244	30523378	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30524702	30524763	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30524702	30524763	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30525382	30525455	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30525382	30525455	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30526662	30526731	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30526662	30526731	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30530151	30530187	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30530151	30530187	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30531061	30531181	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30531061	30531181	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30535532	30535752	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30535532	30535752	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30539562	30539765	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30539562	30539765	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30542042	30542177	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30542042	30542177	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30543233	30543330	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30543233	30543330	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30554455	30554520	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30554455	30554520	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30557512	30557695	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30557512	30557695	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30559225	30559385	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30559225	30559385	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30563635	30563752	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30563635	30563752	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30564185	30564352	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30564185	30564352	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30565558	30565777	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30565558	30565777	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30567374	30567507	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30567374	30567507	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30577985	30578093	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30577985	30578093	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30581908	30581973	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30581908	30581973	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30591130	30591284	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30591130	30591284	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30593795	30593872	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30593795	30593872	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30594813	30594945	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30594813	30594945	.	+	1	Parent=gene1876
chr22	ENCODE	exon	30596697	30596805	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30596697	30596805	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30600065	30600292	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30600065	30600292	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30614122	30614291	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30614122	30614291	.	+	2	Parent=gene1876
chr22	ENCODE	exon	30618022	30618193	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30618022	30618193	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30626524	30626606	.	+	.	Parent=gene1876
chr22	ENCODE	CDS	30626524	30626606	.	+	2	Parent=gene1876
chr22	ENCODE	CDS	30626745	30626945	.	+	0	Parent=gene1876
chr22	ENCODE	exon	30626745	30627438	.	+	.	Parent=gene1876
###
chr22	ENCODE	gene	30475403	30627555	.	+	.	ID=gene1877;Name=LL22NC03-113A11.1-001;name2=DEPDC5
chr22	ENCODE	exon	30475403	30475519	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30475462	30475519	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30479086	30479173	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30479086	30479173	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30481196	30481242	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30481196	30481242	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30485515	30485600	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30485515	30485600	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30487125	30487208	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30487125	30487208	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30489354	30489403	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30489354	30489403	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30498639	30498708	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30498639	30498708	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30504447	30504525	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30504447	30504525	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30505354	30505415	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30505354	30505415	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30512573	30512642	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30512573	30512642	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30513285	30513357	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30513285	30513357	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30518140	30518243	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30518140	30518243	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30519122	30519196	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30519122	30519196	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30523244	30523378	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30523244	30523378	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30524702	30524763	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30524702	30524763	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30525382	30525455	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30525382	30525455	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30526662	30526731	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30526662	30526731	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30530151	30530187	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30530151	30530187	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30531061	30531181	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30531061	30531181	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30535532	30535752	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30535532	30535752	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30539562	30539765	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30539562	30539765	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30542042	30542177	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30542042	30542177	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30543233	30543330	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30543233	30543330	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30554455	30554520	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30554455	30554520	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30557539	30557695	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30557539	30557695	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30559225	30559385	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30559225	30559385	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30563635	30563752	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30563635	30563752	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30564185	30564352	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30564185	30564352	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30565558	30565777	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30565558	30565777	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30567374	30567507	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30567374	30567507	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30577985	30578093	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30577985	30578093	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30591130	30591284	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30591130	30591284	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30593795	30593872	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30593795	30593872	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30594813	30594945	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30594813	30594945	.	+	1	Parent=gene1877
chr22	ENCODE	exon	30596697	30596805	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30596697	30596805	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30600065	30600292	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30600065	30600292	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30614122	30614291	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30614122	30614291	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30618022	30618193	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30618022	30618193	.	+	0	Parent=gene1877
chr22	ENCODE	exon	30622282	30622342	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30622282	30622342	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30626524	30626606	.	+	.	Parent=gene1877
chr22	ENCODE	CDS	30626524	30626606	.	+	1	Parent=gene1877
chr22	ENCODE	CDS	30626745	30627037	.	+	2	Parent=gene1877
chr22	ENCODE	exon	30626745	30627555	.	+	.	Parent=gene1877
###
chr22	ENCODE	gene	30489392	30504798	.	+	.	ID=gene1878;Name=LL22NC03-113A11.1-007;name2=DEPDC5
chr22	ENCODE	exon	30489392	30489403	.	+	.	Parent=gene1878
chr22	ENCODE	CDS	30489392	30489403	.	+	0	Parent=gene1878
chr22	ENCODE	exon	30498639	30498708	.	+	.	Parent=gene1878
chr22	ENCODE	CDS	30498639	30498708	.	+	0	Parent=gene1878
chr22	ENCODE	CDS	30504447	30504545	.	+	2	Parent=gene1878
chr22	ENCODE	exon	30504447	30504798	.	+	.	Parent=gene1878
###
chr22	ENCODE	gene	30505365	30523278	.	+	.	ID=gene1879;Name=LL22NC03-113A11.1-008;name2=DEPDC5
chr22	ENCODE	exon	30505365	30505647	.	+	.	Parent=gene1879
chr22	ENCODE	exon	30512573	30512642	.	+	.	Parent=gene1879
chr22	ENCODE	exon	30513285	30513357	.	+	.	Parent=gene1879
chr22	ENCODE	exon	30518140	30518243	.	+	.	Parent=gene1879
chr22	ENCODE	exon	30519122	30519196	.	+	.	Parent=gene1879
chr22	ENCODE	exon	30523244	30523278	.	+	.	Parent=gene1879
###
chr22	ENCODE	gene	30513227	30524759	.	+	.	ID=gene1880;Name=LL22NC03-113A11.1-009;name2=DEPDC5
chr22	ENCODE	exon	30513227	30513357	.	+	.	Parent=gene1880
chr22	ENCODE	exon	30518140	30518243	.	+	.	Parent=gene1880
chr22	ENCODE	exon	30519122	30519196	.	+	.	Parent=gene1880
chr22	ENCODE	exon	30523244	30523378	.	+	.	Parent=gene1880
chr22	ENCODE	exon	30524702	30524759	.	+	.	Parent=gene1880
###
chr22	ENCODE	gene	30539606	30627538	.	+	.	ID=gene1881;Name=LL22NC03-113A11.1-003;name2=DEPDC5
chr22	ENCODE	exon	30539606	30539765	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30554455	30554520	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30557512	30557695	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30559225	30559385	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30563635	30563752	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30564185	30564352	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30565558	30565777	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30567374	30567507	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30577985	30578093	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30581908	30581973	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30591130	30591284	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30593795	30593872	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30594813	30594945	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30600065	30600292	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30614122	30614291	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30618022	30618193	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30622282	30622342	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30626524	30626606	.	+	.	Parent=gene1881
chr22	ENCODE	exon	30626745	30627538	.	+	.	Parent=gene1881
###
chr22	ENCODE	gene	30539704	30627549	.	+	.	ID=gene1882;name2=DEPDC5;Name=LL22NC03-113A11.1-005
chr22	ENCODE	exon	30539704	30539765	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30539704	30539765	.	+	0	Parent=gene1882
chr22	ENCODE	exon	30542042	30542177	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30542042	30542177	.	+	1	Parent=gene1882
chr22	ENCODE	exon	30543233	30543330	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30543233	30543330	.	+	0	Parent=gene1882
chr22	ENCODE	exon	30554455	30554520	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30554455	30554520	.	+	1	Parent=gene1882
chr22	ENCODE	exon	30557512	30557695	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30557512	30557695	.	+	1	Parent=gene1882
chr22	ENCODE	exon	30559225	30559385	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30559225	30559385	.	+	0	Parent=gene1882
chr22	ENCODE	exon	30563635	30563752	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30563635	30563752	.	+	1	Parent=gene1882
chr22	ENCODE	exon	30564185	30564352	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30564185	30564352	.	+	0	Parent=gene1882
chr22	ENCODE	exon	30565558	30565777	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30565558	30565777	.	+	0	Parent=gene1882
chr22	ENCODE	exon	30567374	30567507	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30567374	30567507	.	+	2	Parent=gene1882
chr22	ENCODE	exon	30577985	30578093	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30577985	30578093	.	+	0	Parent=gene1882
chr22	ENCODE	exon	30591130	30591284	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30591130	30591284	.	+	2	Parent=gene1882
chr22	ENCODE	exon	30593795	30593872	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30593795	30593872	.	+	0	Parent=gene1882
chr22	ENCODE	exon	30594813	30594945	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30594813	30594945	.	+	0	Parent=gene1882
chr22	ENCODE	exon	30596697	30596805	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30596697	30596805	.	+	2	Parent=gene1882
chr22	ENCODE	exon	30600065	30600292	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30600065	30600292	.	+	1	Parent=gene1882
chr22	ENCODE	exon	30614122	30614291	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30614122	30614291	.	+	1	Parent=gene1882
chr22	ENCODE	exon	30618022	30618193	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30618022	30618193	.	+	2	Parent=gene1882
chr22	ENCODE	exon	30622282	30622342	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30622282	30622342	.	+	1	Parent=gene1882
chr22	ENCODE	exon	30626524	30626606	.	+	.	Parent=gene1882
chr22	ENCODE	CDS	30626524	30626606	.	+	0	Parent=gene1882
chr22	ENCODE	CDS	30626745	30627037	.	+	1	Parent=gene1882
chr22	ENCODE	exon	30626745	30627549	.	+	.	Parent=gene1882
###
chr22	ENCODE	gene	30554389	30559261	.	+	.	ID=gene1883;Name=LL22NC03-113A11.1-015;name2=DEPDC5
chr22	ENCODE	exon	30554389	30554520	.	+	.	Parent=gene1883
chr22	ENCODE	exon	30557634	30557695	.	+	.	Parent=gene1883
chr22	ENCODE	exon	30559225	30559261	.	+	.	Parent=gene1883
###
chr22	ENCODE	gene	30554406	30564202	.	+	.	ID=gene1884;Name=LL22NC03-113A11.1-016;name2=DEPDC5
chr22	ENCODE	exon	30554406	30554520	.	+	.	Parent=gene1884
chr22	ENCODE	exon	30557539	30557695	.	+	.	Parent=gene1884
chr22	ENCODE	exon	30559225	30559385	.	+	.	Parent=gene1884
chr22	ENCODE	exon	30563635	30563752	.	+	.	Parent=gene1884
chr22	ENCODE	exon	30564185	30564202	.	+	.	Parent=gene1884
###
chr22	ENCODE	gene	30554458	30557854	.	+	.	ID=gene1885;Name=LL22NC03-113A11.1-010;name2=DEPDC5
chr22	ENCODE	exon	30554458	30554520	.	+	.	Parent=gene1885
chr22	ENCODE	exon	30557512	30557854	.	+	.	Parent=gene1885
###
chr22	ENCODE	gene	30557388	30564199	.	+	.	ID=gene1886;Name=LL22NC03-113A11.1-017;name2=DEPDC5
chr22	ENCODE	exon	30557388	30557695	.	+	.	Parent=gene1886
chr22	ENCODE	exon	30559225	30559385	.	+	.	Parent=gene1886
chr22	ENCODE	exon	30563635	30563752	.	+	.	Parent=gene1886
chr22	ENCODE	exon	30564185	30564199	.	+	.	Parent=gene1886
###
chr22	ENCODE	gene	30567479	30595983	.	+	.	ID=gene1887;Name=LL22NC03-113A11.1-019;name2=DEPDC5
chr22	ENCODE	exon	30567479	30567507	.	+	.	Parent=gene1887
chr22	ENCODE	exon	30577985	30578093	.	+	.	Parent=gene1887
chr22	ENCODE	exon	30591130	30591284	.	+	.	Parent=gene1887
chr22	ENCODE	exon	30593795	30593872	.	+	.	Parent=gene1887
chr22	ENCODE	exon	30594813	30594945	.	+	.	Parent=gene1887
chr22	ENCODE	exon	30595738	30595983	.	+	.	Parent=gene1887
###
chr22	ENCODE	gene	30594514	30600236	.	+	.	ID=gene1888;Name=LL22NC03-113A11.1-018;name2=DEPDC5
chr22	ENCODE	exon	30594514	30594945	.	+	.	Parent=gene1888
chr22	ENCODE	exon	30596697	30596805	.	+	.	Parent=gene1888
chr22	ENCODE	exon	30600065	30600236	.	+	.	Parent=gene1888
###
chr22	ENCODE	gene	30618175	30627552	.	+	.	ID=gene1889;name2=DEPDC5;Name=LL22NC03-113A11.1-011
chr22	ENCODE	exon	30618175	30618193	.	+	.	Parent=gene1889
chr22	ENCODE	exon	30622282	30622342	.	+	.	Parent=gene1889
chr22	ENCODE	exon	30627345	30627552	.	+	.	Parent=gene1889
###
chr22	ENCODE	gene	30654061	30665890	.	-	.	ID=gene1890;Name=LL22NC03-44A4.2-002;name2=C22orf24
chr22	ENCODE	exon	30654061	30654989	.	-	.	Parent=gene1890
chr22	ENCODE	CDS	30654658	30654989	.	-	2	Parent=gene1890
chr22	ENCODE	CDS	30658456	30658606	.	-	0	Parent=gene1890
chr22	ENCODE	exon	30658456	30658655	.	-	.	Parent=gene1890
chr22	ENCODE	exon	30665773	30665890	.	-	.	Parent=gene1890
###
chr22	ENCODE	gene	30654580	30666058	.	-	.	ID=gene1891;Name=LL22NC03-44A4.2-004;name2=C22orf24
chr22	ENCODE	exon	30654580	30654989	.	-	.	Parent=gene1891
chr22	ENCODE	exon	30658529	30658655	.	-	.	Parent=gene1891
chr22	ENCODE	exon	30665773	30666058	.	-	.	Parent=gene1891
###
chr22	ENCODE	gene	30654888	30658994	.	-	.	ID=gene1892;Name=LL22NC03-44A4.2-003;name2=C22orf24
chr22	ENCODE	exon	30654888	30654989	.	-	.	Parent=gene1892
chr22	ENCODE	exon	30658529	30658994	.	-	.	Parent=gene1892
###
chr22	ENCODE	gene	30665001	30678144	.	+	.	ID=gene1893;Name=LL22NC03-44A4.1-001;name2=YWHAH
chr22	ENCODE	exon	30665001	30665360	.	+	.	Parent=gene1893
chr22	ENCODE	CDS	30665274	30665360	.	+	0	Parent=gene1893
chr22	ENCODE	CDS	30676680	30677333	.	+	0	Parent=gene1893
chr22	ENCODE	exon	30676680	30678144	.	+	.	Parent=gene1893
###
chr22	ENCODE	gene	30665062	30677023	.	+	.	ID=gene1894;name2=YWHAH;Name=LL22NC03-44A4.1-005
chr22	ENCODE	exon	30665062	30665360	.	+	.	Parent=gene1894
chr22	ENCODE	exon	30666040	30666218	.	+	.	Parent=gene1894
chr22	ENCODE	exon	30676680	30677023	.	+	.	Parent=gene1894
###
chr22	ENCODE	gene	30665062	30678144	.	+	.	ID=gene1895;Name=LL22NC03-44A4.1-002;name2=YWHAH
chr22	ENCODE	exon	30665062	30665360	.	+	.	Parent=gene1895
chr22	ENCODE	CDS	30665274	30665360	.	+	0	Parent=gene1895
chr22	ENCODE	exon	30670849	30670963	.	+	.	Parent=gene1895
chr22	ENCODE	CDS	30670849	30670963	.	+	0	Parent=gene1895
chr22	ENCODE	CDS	30676680	30676696	.	+	2	Parent=gene1895
chr22	ENCODE	exon	30676680	30678144	.	+	.	Parent=gene1895
###
chr22	ENCODE	gene	30665506	30678144	.	+	.	ID=gene1896;Name=LL22NC03-44A4.1-003;name2=YWHAH
chr22	ENCODE	exon	30665506	30665775	.	+	.	Parent=gene1896
chr22	ENCODE	exon	30676680	30678144	.	+	.	Parent=gene1896
###
chr22	ENCODE	gene	30667963	30677117	.	+	.	ID=gene1897;Name=LL22NC03-44A4.1-004;name2=YWHAH
chr22	ENCODE	exon	30667963	30668026	.	+	.	Parent=gene1897
chr22	ENCODE	CDS	30667979	30668026	.	+	0	Parent=gene1897
chr22	ENCODE	exon	30676680	30677117	.	+	.	Parent=gene1897
chr22	ENCODE	CDS	30676680	30677117	.	+	0	Parent=gene1897
###
chr22	ENCODE	gene	30763573	30833570	.	+	.	ID=gene1898;name2=SLC5A1;Name=RP1-127L4.1-001
chr22	ENCODE	exon	30763573	30763957	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30763823	30763957	.	+	0	Parent=gene1898
chr22	ENCODE	exon	30770484	30770555	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30770484	30770555	.	+	0	Parent=gene1898
chr22	ENCODE	exon	30787476	30787580	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30787476	30787580	.	+	0	Parent=gene1898
chr22	ENCODE	exon	30788508	30788567	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30788508	30788567	.	+	0	Parent=gene1898
chr22	ENCODE	exon	30789037	30789141	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30789037	30789141	.	+	0	Parent=gene1898
chr22	ENCODE	exon	30802407	30802512	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30802407	30802512	.	+	0	Parent=gene1898
chr22	ENCODE	exon	30803615	30803695	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30803615	30803695	.	+	2	Parent=gene1898
chr22	ENCODE	exon	30804980	30805200	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30804980	30805200	.	+	2	Parent=gene1898
chr22	ENCODE	exon	30805441	30805576	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30805441	30805576	.	+	0	Parent=gene1898
chr22	ENCODE	exon	30806761	30806868	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30806761	30806868	.	+	2	Parent=gene1898
chr22	ENCODE	exon	30812153	30812303	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30812153	30812303	.	+	2	Parent=gene1898
chr22	ENCODE	exon	30819724	30819892	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30819724	30819892	.	+	1	Parent=gene1898
chr22	ENCODE	exon	30822563	30822778	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30822563	30822778	.	+	0	Parent=gene1898
chr22	ENCODE	exon	30825327	30825432	.	+	.	Parent=gene1898
chr22	ENCODE	CDS	30825327	30825432	.	+	0	Parent=gene1898
chr22	ENCODE	CDS	30830531	30830754	.	+	2	Parent=gene1898
chr22	ENCODE	exon	30830531	30833570	.	+	.	Parent=gene1898
###
chr22	ENCODE	gene	30803592	30806867	.	+	.	ID=gene1899;Name=RP1-127L4.1-003;name2=SLC5A1
chr22	ENCODE	exon	30803592	30803695	.	+	.	Parent=gene1899
chr22	ENCODE	exon	30804980	30805200	.	+	.	Parent=gene1899
chr22	ENCODE	exon	30805441	30805576	.	+	.	Parent=gene1899
chr22	ENCODE	exon	30806761	30806867	.	+	.	Parent=gene1899
###
chr22	ENCODE	gene	30805390	30822748	.	+	.	ID=gene1900;Name=RP1-127L4.1-002;name2=SLC5A1
chr22	ENCODE	exon	30805390	30805576	.	+	.	Parent=gene1900
chr22	ENCODE	exon	30806761	30806868	.	+	.	Parent=gene1900
chr22	ENCODE	exon	30812153	30812303	.	+	.	Parent=gene1900
chr22	ENCODE	exon	30819724	30819892	.	+	.	Parent=gene1900
chr22	ENCODE	exon	30822563	30822748	.	+	.	Parent=gene1900
###
chr22	ENCODE	gene	30869547	30879829	.	-	.	ID=gene1901;Name=RP1-127L4.6-001;name2=RP1-127L4.6
chr22	ENCODE	exon	30869547	30870154	.	-	.	Parent=gene1901
chr22	ENCODE	CDS	30870081	30870154	.	-	2	Parent=gene1901
chr22	ENCODE	exon	30870294	30870321	.	-	.	Parent=gene1901
chr22	ENCODE	CDS	30870294	30870321	.	-	0	Parent=gene1901
chr22	ENCODE	exon	30870860	30871020	.	-	.	Parent=gene1901
chr22	ENCODE	CDS	30870860	30871020	.	-	2	Parent=gene1901
chr22	ENCODE	exon	30871533	30871560	.	-	.	Parent=gene1901
chr22	ENCODE	CDS	30871533	30871560	.	-	0	Parent=gene1901
chr22	ENCODE	exon	30872028	30872092	.	-	.	Parent=gene1901
chr22	ENCODE	CDS	30872028	30872092	.	-	2	Parent=gene1901
chr22	ENCODE	exon	30872608	30872635	.	-	.	Parent=gene1901
chr22	ENCODE	CDS	30872608	30872635	.	-	0	Parent=gene1901
chr22	ENCODE	exon	30873103	30873167	.	-	.	Parent=gene1901
chr22	ENCODE	CDS	30873103	30873167	.	-	2	Parent=gene1901
chr22	ENCODE	exon	30874785	30874859	.	-	.	Parent=gene1901
chr22	ENCODE	CDS	30874785	30874859	.	-	2	Parent=gene1901
chr22	ENCODE	CDS	30879525	30879756	.	-	0	Parent=gene1901
chr22	ENCODE	exon	30879525	30879829	.	-	.	Parent=gene1901
###
chr22	ENCODE	gene	30869547	30879863	.	-	.	ID=gene1902;Name=RP1-127L4.6-002;name2=RP1-127L4.6
chr22	ENCODE	exon	30869547	30870154	.	-	.	Parent=gene1902
chr22	ENCODE	exon	30870294	30870321	.	-	.	Parent=gene1902
chr22	ENCODE	exon	30870860	30871560	.	-	.	Parent=gene1902
chr22	ENCODE	exon	30872028	30872092	.	-	.	Parent=gene1902
chr22	ENCODE	exon	30872608	30872635	.	-	.	Parent=gene1902
chr22	ENCODE	exon	30873103	30873167	.	-	.	Parent=gene1902
chr22	ENCODE	exon	30874785	30874859	.	-	.	Parent=gene1902
chr22	ENCODE	exon	30879525	30879863	.	-	.	Parent=gene1902
###
chr22	ENCODE	gene	30869721	30870467	.	-	.	ID=gene1903;Name=RP1-127L4.6-003;name2=RP1-127L4.6
chr22	ENCODE	exon	30869721	30870154	.	-	.	Parent=gene1903
chr22	ENCODE	exon	30870294	30870467	.	-	.	Parent=gene1903
###
chr22	ENCODE	gene	30910979	30924018	.	-	.	ID=gene1904;Name=RP1-90G24.3-001;name2=RFPL2
chr22	ENCODE	exon	30910979	30911893	.	-	.	Parent=gene1904
chr22	ENCODE	CDS	30911313	30911893	.	-	2	Parent=gene1904
chr22	ENCODE	exon	30913443	30913733	.	-	.	Parent=gene1904
chr22	ENCODE	CDS	30913443	30913733	.	-	2	Parent=gene1904
chr22	ENCODE	exon	30914886	30915031	.	-	.	Parent=gene1904
chr22	ENCODE	CDS	30914886	30915031	.	-	1	Parent=gene1904
chr22	ENCODE	CDS	30922874	30922992	.	-	0	Parent=gene1904
chr22	ENCODE	exon	30922874	30923091	.	-	.	Parent=gene1904
chr22	ENCODE	exon	30923182	30924018	.	-	.	Parent=gene1904
###
chr22	ENCODE	gene	30911245	30913942	.	-	.	ID=gene1905;Name=RP1-90G24.3-002;name2=RFPL2
chr22	ENCODE	exon	30911245	30911893	.	-	.	Parent=gene1905
chr22	ENCODE	exon	30913443	30913942	.	-	.	Parent=gene1905
###
chr22	ENCODE	gene	30939019	30975882	.	-	.	ID=gene1906;Name=RP1-90G24.9-001;name2=SLC5A4
chr22	ENCODE	exon	30939019	30939266	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30939055	30939266	.	-	2	Parent=gene1906
chr22	ENCODE	exon	30941461	30941563	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30941461	30941563	.	-	0	Parent=gene1906
chr22	ENCODE	exon	30944808	30945023	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30944808	30945023	.	-	0	Parent=gene1906
chr22	ENCODE	exon	30946196	30946364	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30946196	30946364	.	-	1	Parent=gene1906
chr22	ENCODE	exon	30949735	30949885	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30949735	30949885	.	-	2	Parent=gene1906
chr22	ENCODE	exon	30951509	30951616	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30951509	30951616	.	-	2	Parent=gene1906
chr22	ENCODE	exon	30953440	30953575	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30953440	30953575	.	-	0	Parent=gene1906
chr22	ENCODE	exon	30955414	30955634	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30955414	30955634	.	-	2	Parent=gene1906
chr22	ENCODE	exon	30957785	30957865	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30957785	30957865	.	-	2	Parent=gene1906
chr22	ENCODE	exon	30959526	30959631	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30959526	30959631	.	-	0	Parent=gene1906
chr22	ENCODE	exon	30967952	30968056	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30967952	30968056	.	-	0	Parent=gene1906
chr22	ENCODE	exon	30969284	30969343	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30969284	30969343	.	-	0	Parent=gene1906
chr22	ENCODE	exon	30972311	30972415	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30972311	30972415	.	-	0	Parent=gene1906
chr22	ENCODE	exon	30974683	30974754	.	-	.	Parent=gene1906
chr22	ENCODE	CDS	30974683	30974754	.	-	0	Parent=gene1906
chr22	ENCODE	CDS	30975736	30975870	.	-	0	Parent=gene1906
chr22	ENCODE	exon	30975736	30975882	.	-	.	Parent=gene1906
###
chr22	ENCODE	gene	31075426	31081702	.	+	.	ID=gene1907;Name=RP1-149A16.1-002;name2=RFPL3
chr22	ENCODE	exon	31075426	31075438	.	+	.	Parent=gene1907
chr22	ENCODE	exon	31078695	31078985	.	+	.	Parent=gene1907
chr22	ENCODE	CDS	31078700	31078985	.	+	0	Parent=gene1907
chr22	ENCODE	CDS	31080793	31081373	.	+	2	Parent=gene1907
chr22	ENCODE	exon	31080793	31081702	.	+	.	Parent=gene1907
###
chr22	ENCODE	gene	31075849	31081701	.	+	.	ID=gene1908;Name=RP1-149A16.1-003;name2=RFPL3
chr22	ENCODE	exon	31075849	31076043	.	+	.	Parent=gene1908
chr22	ENCODE	exon	31078127	31078985	.	+	.	Parent=gene1908
chr22	ENCODE	exon	31080793	31081701	.	+	.	Parent=gene1908
###
chr22	ENCODE	gene	31078408	31081702	.	+	.	ID=gene1909;Name=RP1-149A16.1-001;name2=RFPL3
chr22	ENCODE	exon	31078408	31078985	.	+	.	Parent=gene1909
chr22	ENCODE	CDS	31078613	31078985	.	+	0	Parent=gene1909
chr22	ENCODE	CDS	31080793	31081373	.	+	2	Parent=gene1909
chr22	ENCODE	exon	31080793	31081702	.	+	.	Parent=gene1909
###
chr22	ENCODE	gene	31080447	31091526	.	-	.	ID=gene1910;Name=RP1-149A16.4-002;name2=RFPL3S
chr22	ENCODE	exon	31080447	31081380	.	-	.	Parent=gene1910
chr22	ENCODE	CDS	31081295	31081380	.	-	2	Parent=gene1910
chr22	ENCODE	exon	31088231	31088255	.	-	.	Parent=gene1910
chr22	ENCODE	CDS	31088231	31088255	.	-	0	Parent=gene1910
chr22	ENCODE	exon	31089038	31089108	.	-	.	Parent=gene1910
chr22	ENCODE	CDS	31089038	31089108	.	-	2	Parent=gene1910
chr22	ENCODE	CDS	31091440	31091467	.	-	0	Parent=gene1910
chr22	ENCODE	exon	31091440	31091526	.	-	.	Parent=gene1910
###
chr22	ENCODE	gene	31080447	31091617	.	-	.	ID=gene1911;Name=RP1-149A16.4-001;name2=RFPL3S
chr22	ENCODE	exon	31080447	31081380	.	-	.	Parent=gene1911
chr22	ENCODE	CDS	31081295	31081380	.	-	2	Parent=gene1911
chr22	ENCODE	exon	31083513	31083599	.	-	.	Parent=gene1911
chr22	ENCODE	CDS	31083513	31083599	.	-	2	Parent=gene1911
chr22	ENCODE	exon	31088231	31088255	.	-	.	Parent=gene1911
chr22	ENCODE	CDS	31088231	31088255	.	-	0	Parent=gene1911
chr22	ENCODE	exon	31089038	31089108	.	-	.	Parent=gene1911
chr22	ENCODE	CDS	31089038	31089108	.	-	2	Parent=gene1911
chr22	ENCODE	CDS	31091440	31091467	.	-	0	Parent=gene1911
chr22	ENCODE	exon	31091440	31091617	.	-	.	Parent=gene1911
###
chr22	ENCODE	gene	31081193	31083658	.	-	.	ID=gene1912;Name=RP1-149A16.4-004;name2=RFPL3S
chr22	ENCODE	exon	31081193	31081380	.	-	.	Parent=gene1912
chr22	ENCODE	exon	31083513	31083658	.	-	.	Parent=gene1912
###
chr22	ENCODE	gene	31083342	31091540	.	-	.	ID=gene1913;Name=RP1-149A16.4-003;name2=RFPL3S
chr22	ENCODE	exon	31083342	31083599	.	-	.	Parent=gene1913
chr22	ENCODE	CDS	31083493	31083599	.	-	2	Parent=gene1913
chr22	ENCODE	exon	31088231	31088255	.	-	.	Parent=gene1913
chr22	ENCODE	CDS	31088231	31088255	.	-	0	Parent=gene1913
chr22	ENCODE	exon	31089038	31089108	.	-	.	Parent=gene1913
chr22	ENCODE	CDS	31089038	31089108	.	-	2	Parent=gene1913
chr22	ENCODE	CDS	31091440	31091467	.	-	0	Parent=gene1913
chr22	ENCODE	exon	31091440	31091540	.	-	.	Parent=gene1913
###
chr22	ENCODE	gene	31108123	31132796	.	-	.	ID=gene1914;Name=RP1-149A16.6-001;name2=C22orf28
chr22	ENCODE	exon	31108123	31108640	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31108533	31108640	.	-	0	Parent=gene1914
chr22	ENCODE	exon	31112781	31112900	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31112781	31112900	.	-	0	Parent=gene1914
chr22	ENCODE	exon	31114433	31114543	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31114433	31114543	.	-	0	Parent=gene1914
chr22	ENCODE	exon	31115567	31115755	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31115567	31115755	.	-	0	Parent=gene1914
chr22	ENCODE	exon	31116615	31116790	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31116615	31116790	.	-	2	Parent=gene1914
chr22	ENCODE	exon	31118482	31118641	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31118482	31118641	.	-	0	Parent=gene1914
chr22	ENCODE	exon	31120144	31120300	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31120144	31120300	.	-	1	Parent=gene1914
chr22	ENCODE	exon	31122288	31122444	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31122288	31122444	.	-	2	Parent=gene1914
chr22	ENCODE	exon	31127203	31127302	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31127203	31127302	.	-	0	Parent=gene1914
chr22	ENCODE	exon	31128716	31128783	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31128716	31128783	.	-	2	Parent=gene1914
chr22	ENCODE	exon	31129296	31129374	.	-	.	Parent=gene1914
chr22	ENCODE	CDS	31129296	31129374	.	-	0	Parent=gene1914
chr22	ENCODE	CDS	31132605	31132697	.	-	0	Parent=gene1914
chr22	ENCODE	exon	31132605	31132796	.	-	.	Parent=gene1914
###
chr22	ENCODE	gene	31108377	31122385	.	-	.	ID=gene1915;name2=C22orf28;Name=RP1-149A16.6-005
chr22	ENCODE	exon	31108377	31108640	.	-	.	Parent=gene1915
chr22	ENCODE	exon	31112781	31112884	.	-	.	Parent=gene1915
chr22	ENCODE	exon	31118548	31118641	.	-	.	Parent=gene1915
chr22	ENCODE	exon	31120144	31120300	.	-	.	Parent=gene1915
chr22	ENCODE	exon	31122288	31122385	.	-	.	Parent=gene1915
###
chr22	ENCODE	gene	31118489	31120526	.	-	.	ID=gene1916;Name=RP1-149A16.6-008;name2=C22orf28
chr22	ENCODE	exon	31118489	31118641	.	-	.	Parent=gene1916
chr22	ENCODE	exon	31120144	31120526	.	-	.	Parent=gene1916
###
chr22	ENCODE	gene	31118583	31128067	.	-	.	ID=gene1917;Name=RP1-149A16.6-006;name2=C22orf28
chr22	ENCODE	exon	31118583	31118641	.	-	.	Parent=gene1917
chr22	ENCODE	exon	31120144	31120300	.	-	.	Parent=gene1917
chr22	ENCODE	exon	31122288	31122444	.	-	.	Parent=gene1917
chr22	ENCODE	exon	31127203	31127302	.	-	.	Parent=gene1917
chr22	ENCODE	exon	31127947	31128067	.	-	.	Parent=gene1917
###
chr22	ENCODE	gene	31118589	31127950	.	-	.	ID=gene1918;Name=RP1-149A16.6-007;name2=C22orf28
chr22	ENCODE	exon	31118589	31118641	.	-	.	Parent=gene1918
chr22	ENCODE	exon	31120144	31120300	.	-	.	Parent=gene1918
chr22	ENCODE	exon	31122288	31122444	.	-	.	Parent=gene1918
chr22	ENCODE	exon	31127203	31127302	.	-	.	Parent=gene1918
chr22	ENCODE	exon	31127854	31127950	.	-	.	Parent=gene1918
###
chr22	ENCODE	gene	31122103	31132782	.	-	.	ID=gene1919;Name=RP1-149A16.6-004;name2=C22orf28
chr22	ENCODE	exon	31122103	31122444	.	-	.	Parent=gene1919
chr22	ENCODE	exon	31127203	31127302	.	-	.	Parent=gene1919
chr22	ENCODE	exon	31128716	31128783	.	-	.	Parent=gene1919
chr22	ENCODE	exon	31129296	31129374	.	-	.	Parent=gene1919
chr22	ENCODE	exon	31132605	31132782	.	-	.	Parent=gene1919
###
chr22	ENCODE	gene	31122385	31132789	.	-	.	ID=gene1920;Name=RP1-149A16.6-002;name2=C22orf28
chr22	ENCODE	exon	31122385	31122444	.	-	.	Parent=gene1920
chr22	ENCODE	exon	31127203	31127302	.	-	.	Parent=gene1920
chr22	ENCODE	exon	31129296	31129374	.	-	.	Parent=gene1920
chr22	ENCODE	exon	31132605	31132789	.	-	.	Parent=gene1920
###
chr22	ENCODE	gene	31128420	31132789	.	-	.	ID=gene1921;name2=C22orf28;Name=RP1-149A16.6-003
chr22	ENCODE	exon	31128420	31128783	.	-	.	Parent=gene1921
chr22	ENCODE	exon	31129296	31129374	.	-	.	Parent=gene1921
chr22	ENCODE	exon	31132605	31132789	.	-	.	Parent=gene1921
###
chr22	ENCODE	gene	31134388	31185025	.	-	.	ID=gene1922;Name=RP1-149A16.10-010;name2=BPIL2
chr22	ENCODE	exon	31134388	31134966	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31134844	31134966	.	-	0	Parent=gene1922
chr22	ENCODE	exon	31136456	31136532	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31136456	31136532	.	-	2	Parent=gene1922
chr22	ENCODE	exon	31137626	31137689	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31137626	31137689	.	-	0	Parent=gene1922
chr22	ENCODE	exon	31139903	31139945	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31139903	31139945	.	-	1	Parent=gene1922
chr22	ENCODE	exon	31151888	31151955	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31151888	31151955	.	-	0	Parent=gene1922
chr22	ENCODE	exon	31152914	31153084	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31152914	31153084	.	-	0	Parent=gene1922
chr22	ENCODE	exon	31154260	31154313	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31154260	31154313	.	-	0	Parent=gene1922
chr22	ENCODE	exon	31156245	31156421	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31156245	31156421	.	-	0	Parent=gene1922
chr22	ENCODE	exon	31158301	31158392	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31158301	31158392	.	-	2	Parent=gene1922
chr22	ENCODE	exon	31163212	31163272	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31163212	31163272	.	-	0	Parent=gene1922
chr22	ENCODE	exon	31166176	31166239	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31166176	31166239	.	-	1	Parent=gene1922
chr22	ENCODE	exon	31166382	31166537	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31166382	31166537	.	-	1	Parent=gene1922
chr22	ENCODE	exon	31167753	31167881	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31167753	31167881	.	-	1	Parent=gene1922
chr22	ENCODE	exon	31173924	31174044	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31173924	31174044	.	-	2	Parent=gene1922
chr22	ENCODE	exon	31177804	31177927	.	-	.	Parent=gene1922
chr22	ENCODE	CDS	31177804	31177927	.	-	0	Parent=gene1922
chr22	ENCODE	exon	31184915	31185025	.	-	.	Parent=gene1922
###
chr22	ENCODE	gene	31173875	31184990	.	-	.	ID=gene1923;name2=BPIL2;Name=RP1-149A16.10-011
chr22	ENCODE	exon	31173875	31174044	.	-	.	Parent=gene1923
chr22	ENCODE	CDS	31173920	31174044	.	-	2	Parent=gene1923
chr22	ENCODE	exon	31177804	31177927	.	-	.	Parent=gene1923
chr22	ENCODE	CDS	31177804	31177927	.	-	0	Parent=gene1923
chr22	ENCODE	exon	31182115	31182202	.	-	.	Parent=gene1923
chr22	ENCODE	exon	31184915	31184990	.	-	.	Parent=gene1923
###
chr22	ENCODE	gene	31195217	31219370	.	+	.	ID=gene1924;Name=LL22NC03-28H9.2-003;name2=FBXO7
chr22	ENCODE	exon	31195217	31195665	.	+	.	Parent=gene1924
chr22	ENCODE	exon	31204438	31204665	.	+	.	Parent=gene1924
chr22	ENCODE	exon	31205609	31205750	.	+	.	Parent=gene1924
chr22	ENCODE	exon	31208286	31208369	.	+	.	Parent=gene1924
chr22	ENCODE	exon	31211627	31211722	.	+	.	Parent=gene1924
chr22	ENCODE	exon	31213646	31213822	.	+	.	Parent=gene1924
chr22	ENCODE	exon	31216034	31216071	.	+	.	Parent=gene1924
chr22	ENCODE	exon	31218685	31219370	.	+	.	Parent=gene1924
###
chr22	ENCODE	gene	31195217	31219370	.	+	.	ID=gene1925;Name=LL22NC03-28H9.2-001;name2=FBXO7
chr22	ENCODE	exon	31195217	31195665	.	+	.	Parent=gene1925
chr22	ENCODE	CDS	31195544	31195665	.	+	0	Parent=gene1925
chr22	ENCODE	exon	31199522	31199816	.	+	.	Parent=gene1925
chr22	ENCODE	CDS	31199522	31199816	.	+	1	Parent=gene1925
chr22	ENCODE	exon	31204438	31204665	.	+	.	Parent=gene1925
chr22	ENCODE	CDS	31204438	31204665	.	+	0	Parent=gene1925
chr22	ENCODE	exon	31205609	31205750	.	+	.	Parent=gene1925
chr22	ENCODE	CDS	31205609	31205750	.	+	0	Parent=gene1925
chr22	ENCODE	exon	31208286	31208369	.	+	.	Parent=gene1925
chr22	ENCODE	CDS	31208286	31208369	.	+	2	Parent=gene1925
chr22	ENCODE	exon	31211627	31211722	.	+	.	Parent=gene1925
chr22	ENCODE	CDS	31211627	31211722	.	+	2	Parent=gene1925
chr22	ENCODE	exon	31213646	31213822	.	+	.	Parent=gene1925
chr22	ENCODE	CDS	31213646	31213822	.	+	2	Parent=gene1925
chr22	ENCODE	exon	31216034	31216071	.	+	.	Parent=gene1925
chr22	ENCODE	CDS	31216034	31216071	.	+	2	Parent=gene1925
chr22	ENCODE	CDS	31218685	31219071	.	+	0	Parent=gene1925
chr22	ENCODE	exon	31218685	31219370	.	+	.	Parent=gene1925
###
chr22	ENCODE	gene	31195339	31219370	.	+	.	ID=gene1926;name2=FBXO7;Name=LL22NC03-28H9.2-004
chr22	ENCODE	exon	31195339	31195665	.	+	.	Parent=gene1926
chr22	ENCODE	exon	31199674	31199816	.	+	.	Parent=gene1926
chr22	ENCODE	exon	31204438	31204665	.	+	.	Parent=gene1926
chr22	ENCODE	exon	31205609	31205750	.	+	.	Parent=gene1926
chr22	ENCODE	exon	31208286	31208369	.	+	.	Parent=gene1926
chr22	ENCODE	exon	31211627	31211722	.	+	.	Parent=gene1926
chr22	ENCODE	exon	31213646	31213822	.	+	.	Parent=gene1926
chr22	ENCODE	exon	31216034	31216071	.	+	.	Parent=gene1926
chr22	ENCODE	exon	31218685	31219370	.	+	.	Parent=gene1926
###
chr22	ENCODE	gene	31195556	31219370	.	+	.	ID=gene1927;Name=LL22NC03-28H9.2-005;name2=FBXO7
chr22	ENCODE	exon	31195556	31195665	.	+	.	Parent=gene1927
chr22	ENCODE	exon	31199674	31199816	.	+	.	Parent=gene1927
chr22	ENCODE	exon	31204438	31204665	.	+	.	Parent=gene1927
chr22	ENCODE	exon	31205609	31205750	.	+	.	Parent=gene1927
chr22	ENCODE	exon	31208286	31213822	.	+	.	Parent=gene1927
chr22	ENCODE	exon	31216034	31216071	.	+	.	Parent=gene1927
chr22	ENCODE	exon	31218685	31219370	.	+	.	Parent=gene1927
###
chr22	ENCODE	gene	31195778	31204646	.	+	.	ID=gene1928;Name=LL22NC03-28H9.2-006;name2=FBXO7
chr22	ENCODE	exon	31195778	31195939	.	+	.	Parent=gene1928
chr22	ENCODE	CDS	31195903	31195939	.	+	0	Parent=gene1928
chr22	ENCODE	exon	31199674	31199816	.	+	.	Parent=gene1928
chr22	ENCODE	CDS	31199674	31199816	.	+	2	Parent=gene1928
chr22	ENCODE	exon	31204438	31204646	.	+	.	Parent=gene1928
chr22	ENCODE	CDS	31204438	31204646	.	+	0	Parent=gene1928
###
chr22	ENCODE	gene	31195798	31219370	.	+	.	ID=gene1929;Name=LL22NC03-28H9.2-002;name2=FBXO7
chr22	ENCODE	exon	31195798	31195939	.	+	.	Parent=gene1929
chr22	ENCODE	exon	31199522	31199816	.	+	.	Parent=gene1929
chr22	ENCODE	CDS	31199742	31199816	.	+	0	Parent=gene1929
chr22	ENCODE	exon	31204438	31204665	.	+	.	Parent=gene1929
chr22	ENCODE	CDS	31204438	31204665	.	+	0	Parent=gene1929
chr22	ENCODE	exon	31205609	31205750	.	+	.	Parent=gene1929
chr22	ENCODE	CDS	31205609	31205750	.	+	0	Parent=gene1929
chr22	ENCODE	exon	31208286	31208369	.	+	.	Parent=gene1929
chr22	ENCODE	CDS	31208286	31208369	.	+	2	Parent=gene1929
chr22	ENCODE	exon	31211627	31211722	.	+	.	Parent=gene1929
chr22	ENCODE	CDS	31211627	31211722	.	+	2	Parent=gene1929
chr22	ENCODE	exon	31213646	31213822	.	+	.	Parent=gene1929
chr22	ENCODE	CDS	31213646	31213822	.	+	2	Parent=gene1929
chr22	ENCODE	exon	31216034	31216071	.	+	.	Parent=gene1929
chr22	ENCODE	CDS	31216034	31216071	.	+	2	Parent=gene1929
chr22	ENCODE	CDS	31218685	31219071	.	+	0	Parent=gene1929
chr22	ENCODE	exon	31218685	31219370	.	+	.	Parent=gene1929
###
chr22	ENCODE	gene	31196134	31204524	.	+	.	ID=gene1930;Name=LL22NC03-28H9.2-007;name2=FBXO7
chr22	ENCODE	exon	31196134	31196498	.	+	.	Parent=gene1930
chr22	ENCODE	exon	31199522	31199816	.	+	.	Parent=gene1930
chr22	ENCODE	CDS	31199742	31199816	.	+	0	Parent=gene1930
chr22	ENCODE	exon	31204438	31204524	.	+	.	Parent=gene1930
chr22	ENCODE	CDS	31204438	31204524	.	+	0	Parent=gene1930
###
chr22	ENCODE	gene	31198576	31199772	.	+	.	ID=gene1931;Name=LL22NC03-28H9.2-008;name2=FBXO7
chr22	ENCODE	exon	31198576	31198737	.	+	.	Parent=gene1931
chr22	ENCODE	exon	31199522	31199772	.	+	.	Parent=gene1931
###
chr22	ENCODE	gene	31207829	31211654	.	+	.	ID=gene1932;Name=LL22NC03-28H9.2-010;name2=FBXO7
chr22	ENCODE	exon	31207829	31208369	.	+	.	Parent=gene1932
chr22	ENCODE	exon	31211627	31211654	.	+	.	Parent=gene1932
###
chr22	ENCODE	gene	31207849	31219244	.	+	.	ID=gene1933;name2=FBXO7;Name=LL22NC03-28H9.2-009
chr22	ENCODE	exon	31207849	31207899	.	+	.	Parent=gene1933
chr22	ENCODE	exon	31208286	31208369	.	+	.	Parent=gene1933
chr22	ENCODE	exon	31211627	31211722	.	+	.	Parent=gene1933
chr22	ENCODE	exon	31213646	31213822	.	+	.	Parent=gene1933
chr22	ENCODE	exon	31216034	31216071	.	+	.	Parent=gene1933
chr22	ENCODE	exon	31218685	31219244	.	+	.	Parent=gene1933
###
chr22	ENCODE	gene	31233093	31778912	.	-	.	ID=gene1934;Name=LL22NC03-28H9.1-001;name2=SYN3
chr22	ENCODE	exon	31233093	31234365	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31234233	31234365	.	-	1	Parent=gene1934
chr22	ENCODE	exon	31238584	31238875	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31238584	31238875	.	-	2	Parent=gene1934
chr22	ENCODE	exon	31248459	31248546	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31248459	31248546	.	-	0	Parent=gene1934
chr22	ENCODE	exon	31249415	31249549	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31249415	31249549	.	-	0	Parent=gene1934
chr22	ENCODE	exon	31254333	31254435	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31254333	31254435	.	-	1	Parent=gene1934
chr22	ENCODE	exon	31258576	31258650	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31258576	31258650	.	-	1	Parent=gene1934
chr22	ENCODE	exon	31262111	31262253	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31262111	31262253	.	-	0	Parent=gene1934
chr22	ENCODE	exon	31317214	31317276	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31317214	31317276	.	-	0	Parent=gene1934
chr22	ENCODE	exon	31585456	31585545	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31585456	31585545	.	-	0	Parent=gene1934
chr22	ENCODE	exon	31589507	31589666	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31589507	31589666	.	-	1	Parent=gene1934
chr22	ENCODE	exon	31651929	31652020	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31651929	31652020	.	-	0	Parent=gene1934
chr22	ENCODE	exon	31701184	31701241	.	-	.	Parent=gene1934
chr22	ENCODE	CDS	31701184	31701241	.	-	1	Parent=gene1934
chr22	ENCODE	CDS	31726891	31727201	.	-	0	Parent=gene1934
chr22	ENCODE	exon	31726891	31727363	.	-	.	Parent=gene1934
chr22	ENCODE	exon	31778832	31778912	.	-	.	Parent=gene1934
###
chr22	ENCODE	gene	31234117	31249612	.	-	.	ID=gene1935;Name=LL22NC03-28H9.1-005;name2=SYN3
chr22	ENCODE	exon	31234117	31234365	.	-	.	Parent=gene1935
chr22	ENCODE	exon	31238584	31238875	.	-	.	Parent=gene1935
chr22	ENCODE	exon	31248459	31248546	.	-	.	Parent=gene1935
chr22	ENCODE	exon	31249415	31249612	.	-	.	Parent=gene1935
###
chr22	ENCODE	gene	31234216	31240227	.	-	.	ID=gene1936;Name=LL22NC03-28H9.1-007;name2=SYN3
chr22	ENCODE	exon	31234216	31234365	.	-	.	Parent=gene1936
chr22	ENCODE	exon	31238584	31238875	.	-	.	Parent=gene1936
chr22	ENCODE	exon	31239928	31240227	.	-	.	Parent=gene1936
###
chr22	ENCODE	gene	31234980	31249623	.	-	.	ID=gene1937;Name=LL22NC03-28H9.1-006;name2=SYN3
chr22	ENCODE	exon	31234980	31235191	.	-	.	Parent=gene1937
chr22	ENCODE	exon	31238584	31238875	.	-	.	Parent=gene1937
chr22	ENCODE	exon	31249415	31249623	.	-	.	Parent=gene1937
###
chr22	ENCODE	gene	31238734	31250729	.	-	.	ID=gene1938;Name=LL22NC03-28H9.1-004;name2=SYN3
chr22	ENCODE	exon	31238734	31238875	.	-	.	Parent=gene1938
chr22	ENCODE	exon	31248459	31248546	.	-	.	Parent=gene1938
chr22	ENCODE	exon	31249415	31249549	.	-	.	Parent=gene1938
chr22	ENCODE	exon	31250588	31250729	.	-	.	Parent=gene1938
###
chr22	ENCODE	gene	31350146	31589641	.	-	.	ID=gene1939;Name=LL22NC03-28H9.1-002;name2=SYN3
chr22	ENCODE	exon	31350146	31350408	.	-	.	Parent=gene1939
chr22	ENCODE	exon	31585456	31585545	.	-	.	Parent=gene1939
chr22	ENCODE	exon	31589507	31589641	.	-	.	Parent=gene1939
###
chr22	ENCODE	gene	31522241	31583584	.	+	.	ID=gene1940;Name=RP1-309I22.1-001;name2=TIMP3
chr22	ENCODE	exon	31522241	31522662	.	+	.	Parent=gene1940
chr22	ENCODE	CDS	31522542	31522662	.	+	0	Parent=gene1940
chr22	ENCODE	exon	31569993	31570075	.	+	.	Parent=gene1940
chr22	ENCODE	CDS	31569993	31570075	.	+	2	Parent=gene1940
chr22	ENCODE	exon	31577790	31577901	.	+	.	Parent=gene1940
chr22	ENCODE	CDS	31577790	31577901	.	+	0	Parent=gene1940
chr22	ENCODE	exon	31578558	31578679	.	+	.	Parent=gene1940
chr22	ENCODE	CDS	31578558	31578679	.	+	2	Parent=gene1940
chr22	ENCODE	CDS	31579721	31579918	.	+	0	Parent=gene1940
chr22	ENCODE	exon	31579721	31583584	.	+	.	Parent=gene1940
###
chr22	ENCODE	gene	31522260	31583584	.	+	.	ID=gene1941;Name=RP1-309I22.1-002;name2=TIMP3
chr22	ENCODE	exon	31522260	31522662	.	+	.	Parent=gene1941
chr22	ENCODE	CDS	31522542	31522662	.	+	0	Parent=gene1941
chr22	ENCODE	exon	31569993	31570075	.	+	.	Parent=gene1941
chr22	ENCODE	CDS	31569993	31570075	.	+	2	Parent=gene1941
chr22	ENCODE	exon	31577790	31577901	.	+	.	Parent=gene1941
chr22	ENCODE	CDS	31577790	31577901	.	+	0	Parent=gene1941
chr22	ENCODE	exon	31578558	31578654	.	+	.	Parent=gene1941
chr22	ENCODE	CDS	31578558	31578654	.	+	2	Parent=gene1941
chr22	ENCODE	CDS	31579689	31579890	.	+	1	Parent=gene1941
chr22	ENCODE	exon	31579689	31583584	.	+	.	Parent=gene1941
###
chr22	ENCODE	gene	31522260	31583584	.	+	.	ID=gene1942;Name=RP1-309I22.1-003;name2=TIMP3
chr22	ENCODE	exon	31522260	31522662	.	+	.	Parent=gene1942
chr22	ENCODE	exon	31569993	31570075	.	+	.	Parent=gene1942
chr22	ENCODE	exon	31577790	31577901	.	+	.	Parent=gene1942
chr22	ENCODE	exon	31578558	31578679	.	+	.	Parent=gene1942
chr22	ENCODE	exon	31579714	31583584	.	+	.	Parent=gene1942
###
chr22	ENCODE	gene	31585116	31589599	.	-	.	ID=gene1943;Name=LL22NC03-28H9.1-003;name2=SYN3
chr22	ENCODE	exon	31585116	31585545	.	-	.	Parent=gene1943
chr22	ENCODE	exon	31589507	31589599	.	-	.	Parent=gene1943
###
chr22	ENCODE	gene	31651534	31668118	.	-	.	ID=gene1944;Name=LL22NC03-28H9.1-010;name2=SYN3
chr22	ENCODE	exon	31651534	31652020	.	-	.	Parent=gene1944
chr22	ENCODE	exon	31668011	31668118	.	-	.	Parent=gene1944
###
chr22	ENCODE	gene	31701184	31778398	.	-	.	ID=gene1945;Name=LL22NC03-28H9.1-009;name2=SYN3
chr22	ENCODE	exon	31701184	31701241	.	-	.	Parent=gene1945
chr22	ENCODE	CDS	31701184	31701241	.	-	1	Parent=gene1945
chr22	ENCODE	CDS	31726891	31727201	.	-	0	Parent=gene1945
chr22	ENCODE	exon	31726891	31727363	.	-	.	Parent=gene1945
chr22	ENCODE	exon	31778075	31778398	.	-	.	Parent=gene1945
###
chr22	ENCODE	gene	31701212	31735068	.	-	.	ID=gene1946;Name=LL22NC03-28H9.1-008;name2=SYN3
chr22	ENCODE	exon	31701212	31701241	.	-	.	Parent=gene1946
chr22	ENCODE	CDS	31701212	31701241	.	-	1	Parent=gene1946
chr22	ENCODE	CDS	31726891	31727201	.	-	0	Parent=gene1946
chr22	ENCODE	exon	31726891	31727363	.	-	.	Parent=gene1946
chr22	ENCODE	exon	31734940	31735068	.	-	.	Parent=gene1946
###
chr5	ENCODE	gene	55887725	55937816	.	-	.	ID=gene1947;Name=AC022431.2-001;name2=AC022431.2
chr5	ENCODE	exon	55887725	55887771	.	-	.	Parent=gene1947
chr5	ENCODE	exon	55937606	55937816	.	-	.	Parent=gene1947
###
chr5	ENCODE	gene	56147158	56227736	.	+	.	ID=gene1948;Name=AC008937.1-001;name2=MAP3K1
chr5	ENCODE	exon	56147158	56147639	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56147158	56147639	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56188184	56188334	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56188184	56188334	.	+	1	Parent=gene1948
chr5	ENCODE	exon	56191299	56191499	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56191299	56191499	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56196318	56196518	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56196318	56196518	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56196924	56197040	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56196924	56197040	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56197413	56197561	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56197413	56197561	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56203494	56203615	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56203494	56203615	.	+	1	Parent=gene1948
chr5	ENCODE	exon	56204225	56204306	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56204225	56204306	.	+	2	Parent=gene1948
chr5	ENCODE	exon	56204409	56204589	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56204409	56204589	.	+	1	Parent=gene1948
chr5	ENCODE	exon	56206616	56206894	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56206616	56206894	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56210564	56210685	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56210564	56210685	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56212295	56212386	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56212295	56212386	.	+	1	Parent=gene1948
chr5	ENCODE	exon	56212667	56212856	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56212667	56212856	.	+	2	Parent=gene1948
chr5	ENCODE	exon	56213154	56214450	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56213154	56214450	.	+	1	Parent=gene1948
chr5	ENCODE	exon	56215111	56215263	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56215111	56215263	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56216248	56216410	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56216248	56216410	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56217516	56217647	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56217516	56217647	.	+	2	Parent=gene1948
chr5	ENCODE	exon	56218962	56219104	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56218962	56219104	.	+	2	Parent=gene1948
chr5	ENCODE	exon	56219810	56219941	.	+	.	Parent=gene1948
chr5	ENCODE	CDS	56219810	56219941	.	+	0	Parent=gene1948
chr5	ENCODE	CDS	56225115	56225264	.	+	0	Parent=gene1948
chr5	ENCODE	exon	56225115	56227736	.	+	.	Parent=gene1948
###
chr5	ENCODE	gene	56188289	56227665	.	+	.	ID=gene1949;name2=MAP3K1;Name=AC008937.1-003
chr5	ENCODE	exon	56188289	56188334	.	+	.	Parent=gene1949
chr5	ENCODE	exon	56191299	56191436	.	+	.	Parent=gene1949
chr5	ENCODE	exon	56227451	56227665	.	+	.	Parent=gene1949
###
chr5	ENCODE	gene	56217537	56227736	.	+	.	ID=gene1950;Name=AC008937.1-002;name2=MAP3K1
chr5	ENCODE	exon	56217537	56217647	.	+	.	Parent=gene1950
chr5	ENCODE	exon	56218962	56219941	.	+	.	Parent=gene1950
chr5	ENCODE	exon	56225115	56227736	.	+	.	Parent=gene1950
###
chr5	ENCODE	gene	56240844	56248528	.	+	.	ID=gene1951;Name=AC008937.4-003;name2=C5orf35
chr5	ENCODE	exon	56240844	56241044	.	+	.	Parent=gene1951
chr5	ENCODE	exon	56242893	56243120	.	+	.	Parent=gene1951
chr5	ENCODE	exon	56244595	56244718	.	+	.	Parent=gene1951
chr5	ENCODE	exon	56245458	56245573	.	+	.	Parent=gene1951
chr5	ENCODE	exon	56246445	56246550	.	+	.	Parent=gene1951
chr5	ENCODE	exon	56248399	56248528	.	+	.	Parent=gene1951
###
chr5	ENCODE	gene	56240844	56248819	.	+	.	ID=gene1952;Name=AC008937.4-001;name2=C5orf35
chr5	ENCODE	exon	56240844	56241327	.	+	.	Parent=gene1952
chr5	ENCODE	CDS	56241230	56241327	.	+	0	Parent=gene1952
chr5	ENCODE	exon	56242753	56243120	.	+	.	Parent=gene1952
chr5	ENCODE	CDS	56242753	56243120	.	+	1	Parent=gene1952
chr5	ENCODE	exon	56244595	56244718	.	+	.	Parent=gene1952
chr5	ENCODE	CDS	56244595	56244718	.	+	2	Parent=gene1952
chr5	ENCODE	exon	56245458	56245573	.	+	.	Parent=gene1952
chr5	ENCODE	CDS	56245458	56245573	.	+	1	Parent=gene1952
chr5	ENCODE	exon	56246445	56246550	.	+	.	Parent=gene1952
chr5	ENCODE	CDS	56246445	56246550	.	+	2	Parent=gene1952
chr5	ENCODE	CDS	56248399	56248486	.	+	1	Parent=gene1952
chr5	ENCODE	exon	56248399	56248819	.	+	.	Parent=gene1952
###
chr5	ENCODE	gene	56241177	56243172	.	+	.	ID=gene1953;name2=C5orf35;Name=AC008937.4-010
chr5	ENCODE	exon	56241177	56241327	.	+	.	Parent=gene1953
chr5	ENCODE	exon	56242753	56243172	.	+	.	Parent=gene1953
###
chr5	ENCODE	gene	56241199	56248932	.	+	.	ID=gene1954;Name=AC008937.4-002;name2=C5orf35
chr5	ENCODE	exon	56241199	56241327	.	+	.	Parent=gene1954
chr5	ENCODE	exon	56244595	56244718	.	+	.	Parent=gene1954
chr5	ENCODE	exon	56245458	56245573	.	+	.	Parent=gene1954
chr5	ENCODE	exon	56246445	56246550	.	+	.	Parent=gene1954
chr5	ENCODE	exon	56248399	56248932	.	+	.	Parent=gene1954
###
chr5	ENCODE	gene	56241208	56244700	.	+	.	ID=gene1955;Name=AC008937.4-008;name2=C5orf35
chr5	ENCODE	exon	56241208	56241327	.	+	.	Parent=gene1955
chr5	ENCODE	exon	56242753	56243086	.	+	.	Parent=gene1955
chr5	ENCODE	exon	56244595	56244700	.	+	.	Parent=gene1955
###
chr5	ENCODE	gene	56241644	56248503	.	+	.	ID=gene1956;name2=C5orf35;Name=AC008937.4-004
chr5	ENCODE	exon	56241644	56241978	.	+	.	Parent=gene1956
chr5	ENCODE	exon	56244595	56244718	.	+	.	Parent=gene1956
chr5	ENCODE	exon	56245458	56245573	.	+	.	Parent=gene1956
chr5	ENCODE	exon	56246445	56246550	.	+	.	Parent=gene1956
chr5	ENCODE	exon	56248399	56248503	.	+	.	Parent=gene1956
###
chr5	ENCODE	gene	56241671	56245561	.	+	.	ID=gene1957;Name=AC008937.4-005;name2=C5orf35
chr5	ENCODE	exon	56241671	56241978	.	+	.	Parent=gene1957
chr5	ENCODE	exon	56242626	56242695	.	+	.	Parent=gene1957
chr5	ENCODE	exon	56244595	56244718	.	+	.	Parent=gene1957
chr5	ENCODE	exon	56245458	56245561	.	+	.	Parent=gene1957
###
chr5	ENCODE	gene	56241689	56242879	.	+	.	ID=gene1958;Name=AC008937.4-006;name2=C5orf35
chr5	ENCODE	exon	56241689	56241978	.	+	.	Parent=gene1958
chr5	ENCODE	CDS	56241959	56241978	.	+	0	Parent=gene1958
chr5	ENCODE	exon	56242753	56242879	.	+	.	Parent=gene1958
chr5	ENCODE	CDS	56242753	56242879	.	+	1	Parent=gene1958
###
chr5	ENCODE	gene	56242361	56245566	.	+	.	ID=gene1959;Name=AC008937.4-009;name2=C5orf35
chr5	ENCODE	exon	56242361	56242506	.	+	.	Parent=gene1959
chr5	ENCODE	exon	56242626	56242695	.	+	.	Parent=gene1959
chr5	ENCODE	exon	56244595	56244718	.	+	.	Parent=gene1959
chr5	ENCODE	exon	56245458	56245566	.	+	.	Parent=gene1959
###
chr5	ENCODE	gene	56242496	56242879	.	+	.	ID=gene1960;Name=AC008937.4-007;name2=C5orf35
chr5	ENCODE	exon	56242496	56242879	.	+	.	Parent=gene1960
###
chr5	ENCODE	gene	56251186	56283702	.	-	.	ID=gene1961;Name=AC008937.5-003;name2=MIER3
chr5	ENCODE	exon	56251186	56255169	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56254712	56255169	.	-	2	Parent=gene1961
chr5	ENCODE	exon	56255275	56255417	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56255275	56255417	.	-	1	Parent=gene1961
chr5	ENCODE	exon	56255499	56255626	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56255499	56255626	.	-	0	Parent=gene1961
chr5	ENCODE	exon	56260351	56260445	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56260351	56260445	.	-	2	Parent=gene1961
chr5	ENCODE	exon	56262248	56262329	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56262248	56262329	.	-	0	Parent=gene1961
chr5	ENCODE	exon	56264831	56264982	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56264831	56264982	.	-	2	Parent=gene1961
chr5	ENCODE	exon	56267012	56267084	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56267012	56267084	.	-	0	Parent=gene1961
chr5	ENCODE	exon	56267250	56267335	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56267250	56267335	.	-	2	Parent=gene1961
chr5	ENCODE	exon	56269162	56269282	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56269162	56269282	.	-	0	Parent=gene1961
chr5	ENCODE	exon	56270467	56270601	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56270467	56270601	.	-	0	Parent=gene1961
chr5	ENCODE	exon	56278510	56278670	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56278510	56278670	.	-	2	Parent=gene1961
chr5	ENCODE	exon	56282212	56282236	.	-	.	Parent=gene1961
chr5	ENCODE	CDS	56282212	56282236	.	-	0	Parent=gene1961
chr5	ENCODE	CDS	56283678	56283686	.	-	0	Parent=gene1961
chr5	ENCODE	exon	56283678	56283702	.	-	.	Parent=gene1961
###
chr5	ENCODE	gene	56251187	56283709	.	-	.	ID=gene1962;name2=MIER3;Name=AC008937.5-001
chr5	ENCODE	exon	56251187	56255169	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56254712	56255169	.	-	2	Parent=gene1962
chr5	ENCODE	exon	56255275	56255417	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56255275	56255417	.	-	1	Parent=gene1962
chr5	ENCODE	exon	56255499	56255626	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56255499	56255626	.	-	0	Parent=gene1962
chr5	ENCODE	exon	56260351	56260442	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56260351	56260442	.	-	2	Parent=gene1962
chr5	ENCODE	exon	56262248	56262329	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56262248	56262329	.	-	0	Parent=gene1962
chr5	ENCODE	exon	56264831	56264982	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56264831	56264982	.	-	2	Parent=gene1962
chr5	ENCODE	exon	56267012	56267084	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56267012	56267084	.	-	0	Parent=gene1962
chr5	ENCODE	exon	56267250	56267335	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56267250	56267335	.	-	2	Parent=gene1962
chr5	ENCODE	exon	56269162	56269282	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56269162	56269282	.	-	0	Parent=gene1962
chr5	ENCODE	exon	56270467	56270601	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56270467	56270601	.	-	0	Parent=gene1962
chr5	ENCODE	exon	56278510	56278655	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56278510	56278655	.	-	2	Parent=gene1962
chr5	ENCODE	exon	56282212	56282236	.	-	.	Parent=gene1962
chr5	ENCODE	CDS	56282212	56282236	.	-	0	Parent=gene1962
chr5	ENCODE	CDS	56283678	56283686	.	-	0	Parent=gene1962
chr5	ENCODE	exon	56283678	56283709	.	-	.	Parent=gene1962
###
chr5	ENCODE	gene	56251188	56283697	.	-	.	ID=gene1963;Name=AC008937.5-004;name2=MIER3
chr5	ENCODE	exon	56251188	56255169	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56254712	56255169	.	-	2	Parent=gene1963
chr5	ENCODE	exon	56255275	56255417	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56255275	56255417	.	-	1	Parent=gene1963
chr5	ENCODE	exon	56255499	56255626	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56255499	56255626	.	-	0	Parent=gene1963
chr5	ENCODE	exon	56260351	56260445	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56260351	56260445	.	-	2	Parent=gene1963
chr5	ENCODE	exon	56262248	56262329	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56262248	56262329	.	-	0	Parent=gene1963
chr5	ENCODE	exon	56264831	56264982	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56264831	56264982	.	-	2	Parent=gene1963
chr5	ENCODE	exon	56267012	56267084	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56267012	56267084	.	-	0	Parent=gene1963
chr5	ENCODE	exon	56267250	56267335	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56267250	56267335	.	-	2	Parent=gene1963
chr5	ENCODE	exon	56269162	56269282	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56269162	56269282	.	-	0	Parent=gene1963
chr5	ENCODE	exon	56270467	56270601	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56270467	56270601	.	-	0	Parent=gene1963
chr5	ENCODE	exon	56278510	56278655	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56278510	56278655	.	-	2	Parent=gene1963
chr5	ENCODE	exon	56282212	56282236	.	-	.	Parent=gene1963
chr5	ENCODE	CDS	56282212	56282236	.	-	0	Parent=gene1963
chr5	ENCODE	CDS	56283678	56283686	.	-	0	Parent=gene1963
chr5	ENCODE	exon	56283678	56283697	.	-	.	Parent=gene1963
###
chr5	ENCODE	gene	56251188	56283706	.	-	.	ID=gene1964;Name=AC008937.5-002;name2=MIER3
chr5	ENCODE	exon	56251188	56255169	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56255275	56255417	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56255499	56255626	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56260351	56260445	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56262248	56262329	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56264831	56264982	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56267012	56267084	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56267250	56267335	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56269162	56269282	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56269880	56269922	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56270467	56270601	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56278510	56278655	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56282212	56282236	.	-	.	Parent=gene1964
chr5	ENCODE	exon	56283678	56283706	.	-	.	Parent=gene1964
###
chr5	ENCODE	gene	56254168	56272717	.	-	.	ID=gene1965;Name=AC008937.5-005;name2=MIER3
chr5	ENCODE	exon	56254168	56255169	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56255275	56255417	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56255499	56255626	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56260351	56260445	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56262248	56262329	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56264831	56264982	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56267012	56267084	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56267250	56267335	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56269162	56269282	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56270467	56270601	.	-	.	Parent=gene1965
chr5	ENCODE	exon	56272583	56272717	.	-	.	Parent=gene1965
###
chr5	ENCODE	gene	56267255	56283775	.	-	.	ID=gene1966;Name=AC008937.5-008;name2=MIER3
chr5	ENCODE	exon	56267255	56267335	.	-	.	Parent=gene1966
chr5	ENCODE	CDS	56267255	56267335	.	-	2	Parent=gene1966
chr5	ENCODE	exon	56269162	56269282	.	-	.	Parent=gene1966
chr5	ENCODE	CDS	56269162	56269282	.	-	0	Parent=gene1966
chr5	ENCODE	exon	56270467	56270601	.	-	.	Parent=gene1966
chr5	ENCODE	CDS	56270467	56270601	.	-	0	Parent=gene1966
chr5	ENCODE	CDS	56278510	56278608	.	-	0	Parent=gene1966
chr5	ENCODE	exon	56278510	56278655	.	-	.	Parent=gene1966
chr5	ENCODE	exon	56282212	56282236	.	-	.	Parent=gene1966
chr5	ENCODE	exon	56283695	56283775	.	-	.	Parent=gene1966
###
chr5	ENCODE	gene	56267328	56270555	.	-	.	ID=gene1967;Name=AC008937.5-007;name2=MIER3
chr5	ENCODE	exon	56267328	56267335	.	-	.	Parent=gene1967
chr5	ENCODE	exon	56268478	56268520	.	-	.	Parent=gene1967
chr5	ENCODE	exon	56269162	56269282	.	-	.	Parent=gene1967
chr5	ENCODE	exon	56269880	56269922	.	-	.	Parent=gene1967
chr5	ENCODE	exon	56270467	56270555	.	-	.	Parent=gene1967
###
chr5	ENCODE	gene	56270398	56283696	.	-	.	ID=gene1968;Name=AC008937.5-006;name2=MIER3
chr5	ENCODE	exon	56270398	56270601	.	-	.	Parent=gene1968
chr5	ENCODE	exon	56278510	56278655	.	-	.	Parent=gene1968
chr5	ENCODE	exon	56282212	56282236	.	-	.	Parent=gene1968
chr5	ENCODE	exon	56283678	56283696	.	-	.	Parent=gene1968
###
chr5	ENCODE	gene	56278615	56303259	.	-	.	ID=gene1969;Name=AC008937.5-010;name2=MIER3
chr5	ENCODE	exon	56278615	56278655	.	-	.	Parent=gene1969
chr5	ENCODE	exon	56282212	56282236	.	-	.	Parent=gene1969
chr5	ENCODE	exon	56303217	56303259	.	-	.	Parent=gene1969
###
chr5	ENCODE	gene	56278615	56303259	.	-	.	ID=gene1970;Name=AC008937.5-009;name2=MIER3
chr5	ENCODE	exon	56278615	56278655	.	-	.	Parent=gene1970
chr5	ENCODE	exon	56282212	56282236	.	-	.	Parent=gene1970
chr5	ENCODE	exon	56290970	56291104	.	-	.	Parent=gene1970
chr5	ENCODE	exon	56303217	56303259	.	-	.	Parent=gene1970
###
chr5	ENCODE	gene	56278615	56303259	.	-	.	ID=gene1971;Name=AC008937.5-011;name2=MIER3
chr5	ENCODE	exon	56278615	56278655	.	-	.	Parent=gene1971
chr5	ENCODE	CDS	56278615	56278655	.	-	2	Parent=gene1971
chr5	ENCODE	CDS	56290970	56291000	.	-	0	Parent=gene1971
chr5	ENCODE	exon	56290970	56291104	.	-	.	Parent=gene1971
chr5	ENCODE	exon	56303217	56303259	.	-	.	Parent=gene1971
###
chr5	ENCODE	gene	131285414	131285530	.	-	.	ID=gene1972;Name=AC034228.1-013;name2=ACSL6
chr5	ENCODE	exon	131285414	131285530	.	-	.	Parent=gene1972
###
chr5	ENCODE	gene	131285414	131308384	.	-	.	ID=gene1973;Name=AC034228.1-015;name2=ACSL6
chr5	ENCODE	exon	131285414	131285533	.	-	.	Parent=gene1973
chr5	ENCODE	exon	131297105	131297233	.	-	.	Parent=gene1973
chr5	ENCODE	exon	131306227	131306287	.	-	.	Parent=gene1973
chr5	ENCODE	exon	131308257	131308384	.	-	.	Parent=gene1973
###
chr5	ENCODE	gene	131285414	131357870	.	-	.	ID=gene1974;Name=AC034228.1-006;name2=ACSL6
chr5	ENCODE	exon	131285414	131285533	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131297105	131297233	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131306227	131306287	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131308257	131308344	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131308748	131308841	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131311176	131311254	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131323128	131323199	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131324112	131324213	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131326127	131326270	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131330008	131330124	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131331532	131331620	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131333720	131333792	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131335142	131335237	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131336316	131336450	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131336858	131336992	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131338350	131338427	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131340240	131340313	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131348999	131349050	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131350414	131350446	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131351640	131351818	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131352397	131352496	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131352999	131353100	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1974
chr5	ENCODE	exon	131357623	131357870	.	-	.	Parent=gene1974
###
chr5	ENCODE	gene	131313565	131375254	.	-	.	ID=gene1975;name2=ACSL6;Name=AC034228.1-001
chr5	ENCODE	exon	131313565	131317963	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131317826	131317963	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131323128	131323199	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131323128	131323199	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131324112	131324213	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131324112	131324213	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131326127	131326270	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131326127	131326270	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131330008	131330124	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131330008	131330124	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131331532	131331620	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131331532	131331620	.	-	2	Parent=gene1975
chr5	ENCODE	exon	131333720	131333792	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131333720	131333792	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131335142	131335237	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131335142	131335237	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131336316	131336450	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131336316	131336450	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131336858	131336992	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131336858	131336992	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131338485	131338562	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131338485	131338562	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131340240	131340313	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131340240	131340313	.	-	2	Parent=gene1975
chr5	ENCODE	exon	131348999	131349050	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131348999	131349050	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131350414	131350446	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131350414	131350446	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131351640	131351818	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131351640	131351818	.	-	2	Parent=gene1975
chr5	ENCODE	exon	131352397	131352496	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131352397	131352496	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131352999	131353100	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131352999	131353100	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1975
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131357623	131357843	.	-	.	Parent=gene1975
chr5	ENCODE	CDS	131357623	131357843	.	-	2	Parent=gene1975
chr5	ENCODE	CDS	131375097	131375145	.	-	0	Parent=gene1975
chr5	ENCODE	exon	131375097	131375254	.	-	.	Parent=gene1975
###
chr5	ENCODE	gene	131317490	131375482	.	-	.	ID=gene1976;Name=AC034228.1-003;name2=ACSL6
chr5	ENCODE	exon	131317490	131317963	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131317826	131317963	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131323128	131323199	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131323128	131323199	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131324112	131324213	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131324112	131324213	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131326127	131326270	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131326127	131326270	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131330008	131330124	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131330008	131330124	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131331532	131331620	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131331532	131331620	.	-	2	Parent=gene1976
chr5	ENCODE	exon	131333720	131333792	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131333720	131333792	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131335142	131335237	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131335142	131335237	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131336316	131336450	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131336316	131336450	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131336858	131336950	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131336858	131336950	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131340240	131340313	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131340240	131340313	.	-	2	Parent=gene1976
chr5	ENCODE	exon	131348999	131349050	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131348999	131349050	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131350414	131350446	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131350414	131350446	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131351640	131351818	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131351640	131351818	.	-	2	Parent=gene1976
chr5	ENCODE	exon	131352397	131352496	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131352397	131352496	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131352999	131353100	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131352999	131353100	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1976
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1976
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1976
chr5	ENCODE	CDS	131357728	131357817	.	-	0	Parent=gene1976
chr5	ENCODE	exon	131357728	131357843	.	-	.	Parent=gene1976
chr5	ENCODE	exon	131375413	131375482	.	-	.	Parent=gene1976
###
chr5	ENCODE	gene	131317494	131375205	.	-	.	ID=gene1977;Name=AC034228.1-009;name2=ACSL6
chr5	ENCODE	exon	131317494	131317963	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131317826	131317963	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131323128	131323199	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131323128	131323199	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131324112	131324213	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131324112	131324213	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131326127	131326270	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131326127	131326270	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131330008	131330124	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131330008	131330124	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131331532	131331620	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131331532	131331620	.	-	2	Parent=gene1977
chr5	ENCODE	exon	131333720	131333792	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131333720	131333792	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131335142	131335237	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131335142	131335237	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131336316	131336450	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131336316	131336450	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131336858	131336992	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131336858	131336992	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131338350	131338427	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131338350	131338427	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131340240	131340313	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131340240	131340313	.	-	2	Parent=gene1977
chr5	ENCODE	exon	131348999	131349050	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131348999	131349050	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131350414	131350446	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131350414	131350446	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131351640	131351818	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131351640	131351818	.	-	2	Parent=gene1977
chr5	ENCODE	exon	131352397	131352496	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131352397	131352496	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131352999	131353100	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131352999	131353100	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1977
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131357623	131357843	.	-	.	Parent=gene1977
chr5	ENCODE	CDS	131357623	131357843	.	-	2	Parent=gene1977
chr5	ENCODE	CDS	131375097	131375145	.	-	0	Parent=gene1977
chr5	ENCODE	exon	131375097	131375205	.	-	.	Parent=gene1977
###
chr5	ENCODE	gene	131317496	131337627	.	-	.	ID=gene1978;Name=AC034228.1-010;name2=ACSL6
chr5	ENCODE	exon	131317496	131317963	.	-	.	Parent=gene1978
chr5	ENCODE	exon	131323128	131323199	.	-	.	Parent=gene1978
chr5	ENCODE	exon	131324112	131324213	.	-	.	Parent=gene1978
chr5	ENCODE	exon	131326127	131326270	.	-	.	Parent=gene1978
chr5	ENCODE	exon	131330008	131330124	.	-	.	Parent=gene1978
chr5	ENCODE	exon	131331532	131331620	.	-	.	Parent=gene1978
chr5	ENCODE	exon	131333720	131333792	.	-	.	Parent=gene1978
chr5	ENCODE	exon	131335142	131335237	.	-	.	Parent=gene1978
chr5	ENCODE	exon	131336316	131336450	.	-	.	Parent=gene1978
chr5	ENCODE	exon	131336858	131337627	.	-	.	Parent=gene1978
###
chr5	ENCODE	gene	131317497	131375678	.	-	.	ID=gene1979;Name=AC034228.1-002;name2=ACSL6
chr5	ENCODE	exon	131317497	131317963	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131317826	131317963	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131323128	131323199	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131323128	131323199	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131324112	131324213	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131324112	131324213	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131326127	131326270	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131326127	131326270	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131330008	131330124	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131330008	131330124	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131331532	131331620	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131331532	131331620	.	-	2	Parent=gene1979
chr5	ENCODE	exon	131333720	131333792	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131333720	131333792	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131335142	131335237	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131335142	131335237	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131336316	131336450	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131336316	131336450	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131336858	131336992	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131336858	131336992	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131338485	131338562	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131338485	131338562	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131340240	131340313	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131340240	131340313	.	-	2	Parent=gene1979
chr5	ENCODE	exon	131348999	131349050	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131348999	131349050	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131350414	131350446	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131350414	131350446	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131351640	131351818	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131351640	131351818	.	-	2	Parent=gene1979
chr5	ENCODE	exon	131352397	131352496	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131352397	131352496	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131352999	131353100	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131352999	131353100	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1979
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131357623	131357843	.	-	.	Parent=gene1979
chr5	ENCODE	CDS	131357623	131357843	.	-	2	Parent=gene1979
chr5	ENCODE	CDS	131375506	131375512	.	-	0	Parent=gene1979
chr5	ENCODE	exon	131375506	131375678	.	-	.	Parent=gene1979
###
chr5	ENCODE	gene	131317499	131363216	.	-	.	ID=gene1980;Name=AC034228.1-008;name2=ACSL6
chr5	ENCODE	exon	131317499	131317963	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131317826	131317963	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131323128	131323199	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131323128	131323199	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131324112	131324213	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131324112	131324213	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131326127	131326270	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131326127	131326270	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131330008	131330124	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131330008	131330124	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131331532	131331620	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131331532	131331620	.	-	2	Parent=gene1980
chr5	ENCODE	exon	131333720	131333792	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131333720	131333792	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131335142	131335237	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131335142	131335237	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131336316	131336450	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131336316	131336450	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131336858	131336992	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131336858	131336992	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131338350	131338427	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131338350	131338427	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131340240	131340313	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131340240	131340313	.	-	2	Parent=gene1980
chr5	ENCODE	exon	131348999	131349050	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131348999	131349050	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131350414	131350446	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131350414	131350446	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131351640	131351818	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131351640	131351818	.	-	2	Parent=gene1980
chr5	ENCODE	exon	131352397	131352496	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131352397	131352496	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131352999	131353100	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131352999	131353100	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1980
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1980
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1980
chr5	ENCODE	CDS	131357623	131357817	.	-	0	Parent=gene1980
chr5	ENCODE	exon	131357623	131357843	.	-	.	Parent=gene1980
chr5	ENCODE	exon	131363006	131363216	.	-	.	Parent=gene1980
###
chr5	ENCODE	gene	131317526	131358171	.	-	.	ID=gene1981;Name=AC034228.1-004;name2=ACSL6
chr5	ENCODE	exon	131317526	131317963	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131317826	131317963	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131323128	131323199	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131323128	131323199	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131324112	131324213	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131324112	131324213	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131326127	131326270	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131326127	131326270	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131330008	131330124	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131330008	131330124	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131331532	131331620	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131331532	131331620	.	-	2	Parent=gene1981
chr5	ENCODE	exon	131333720	131333792	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131333720	131333792	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131335142	131335237	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131335142	131335237	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131336316	131336450	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131336316	131336450	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131336858	131336992	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131336858	131336992	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131338485	131338562	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131338485	131338562	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131340240	131340313	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131340240	131340313	.	-	2	Parent=gene1981
chr5	ENCODE	exon	131348999	131349050	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131348999	131349050	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131350414	131350446	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131350414	131350446	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131351640	131351818	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131351640	131351818	.	-	2	Parent=gene1981
chr5	ENCODE	exon	131352397	131352496	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131352397	131352496	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131352999	131353100	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131352999	131353100	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1981
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1981
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1981
chr5	ENCODE	CDS	131357623	131357817	.	-	0	Parent=gene1981
chr5	ENCODE	exon	131357623	131357843	.	-	.	Parent=gene1981
chr5	ENCODE	exon	131358044	131358171	.	-	.	Parent=gene1981
###
chr5	ENCODE	gene	131336379	131357845	.	-	.	ID=gene1982;Name=AC034228.1-005;name2=ACSL6
chr5	ENCODE	exon	131336379	131336450	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131336379	131336450	.	-	2	Parent=gene1982
chr5	ENCODE	exon	131336858	131336992	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131336858	131336992	.	-	2	Parent=gene1982
chr5	ENCODE	exon	131338350	131338427	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131338350	131338427	.	-	2	Parent=gene1982
chr5	ENCODE	exon	131340240	131340313	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131340240	131340313	.	-	1	Parent=gene1982
chr5	ENCODE	exon	131348999	131349050	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131348999	131349050	.	-	2	Parent=gene1982
chr5	ENCODE	exon	131350414	131350446	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131350414	131350446	.	-	2	Parent=gene1982
chr5	ENCODE	exon	131351640	131351818	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131351640	131351818	.	-	1	Parent=gene1982
chr5	ENCODE	exon	131352397	131352496	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131352397	131352496	.	-	2	Parent=gene1982
chr5	ENCODE	exon	131352999	131353100	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131352999	131353100	.	-	2	Parent=gene1982
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131353692	131353756	.	-	1	Parent=gene1982
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131354445	131354559	.	-	2	Parent=gene1982
chr5	ENCODE	exon	131357728	131357845	.	-	.	Parent=gene1982
chr5	ENCODE	CDS	131357728	131357845	.	-	0	Parent=gene1982
###
chr5	ENCODE	gene	131345451	131351682	.	-	.	ID=gene1983;Name=AC034228.1-007;name2=ACSL6
chr5	ENCODE	exon	131345451	131349050	.	-	.	Parent=gene1983
chr5	ENCODE	exon	131350414	131350446	.	-	.	Parent=gene1983
chr5	ENCODE	exon	131351640	131351682	.	-	.	Parent=gene1983
###
chr5	ENCODE	gene	131351757	131375495	.	-	.	ID=gene1984;Name=AC034228.1-011;name2=ACSL6
chr5	ENCODE	exon	131351757	131351818	.	-	.	Parent=gene1984
chr5	ENCODE	CDS	131351757	131351818	.	-	2	Parent=gene1984
chr5	ENCODE	exon	131352397	131352496	.	-	.	Parent=gene1984
chr5	ENCODE	CDS	131352397	131352496	.	-	0	Parent=gene1984
chr5	ENCODE	exon	131352999	131353100	.	-	.	Parent=gene1984
chr5	ENCODE	CDS	131352999	131353100	.	-	0	Parent=gene1984
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1984
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1984
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1984
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1984
chr5	ENCODE	CDS	131357623	131357817	.	-	0	Parent=gene1984
chr5	ENCODE	exon	131357623	131357843	.	-	.	Parent=gene1984
chr5	ENCODE	exon	131375362	131375495	.	-	.	Parent=gene1984
###
chr5	ENCODE	gene	131353018	131358293	.	-	.	ID=gene1985;Name=AC034228.1-012;name2=ACSL6
chr5	ENCODE	exon	131353018	131353100	.	-	.	Parent=gene1985
chr5	ENCODE	CDS	131353018	131353100	.	-	0	Parent=gene1985
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1985
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1985
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1985
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1985
chr5	ENCODE	CDS	131357623	131357817	.	-	0	Parent=gene1985
chr5	ENCODE	exon	131357623	131358293	.	-	.	Parent=gene1985
###
chr5	ENCODE	gene	131353072	131375769	.	-	.	ID=gene1986;Name=AC034228.1-017;name2=ACSL6
chr5	ENCODE	exon	131353072	131353100	.	-	.	Parent=gene1986
chr5	ENCODE	CDS	131353072	131353100	.	-	0	Parent=gene1986
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1986
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1986
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1986
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1986
chr5	ENCODE	CDS	131357728	131357817	.	-	0	Parent=gene1986
chr5	ENCODE	exon	131357728	131357843	.	-	.	Parent=gene1986
chr5	ENCODE	exon	131375681	131375769	.	-	.	Parent=gene1986
###
chr5	ENCODE	gene	131353072	131375769	.	-	.	ID=gene1987;name2=ACSL6;Name=AC034228.1-016
chr5	ENCODE	exon	131353072	131353100	.	-	.	Parent=gene1987
chr5	ENCODE	CDS	131353072	131353100	.	-	0	Parent=gene1987
chr5	ENCODE	exon	131353692	131353756	.	-	.	Parent=gene1987
chr5	ENCODE	CDS	131353692	131353756	.	-	2	Parent=gene1987
chr5	ENCODE	exon	131354445	131354559	.	-	.	Parent=gene1987
chr5	ENCODE	CDS	131354445	131354559	.	-	0	Parent=gene1987
chr5	ENCODE	CDS	131357623	131357817	.	-	0	Parent=gene1987
chr5	ENCODE	exon	131357623	131357843	.	-	.	Parent=gene1987
chr5	ENCODE	exon	131375681	131375769	.	-	.	Parent=gene1987
###
chr5	ENCODE	gene	131424121	131426796	.	+	.	ID=gene1988;Name=AC034228.5-001;name2=IL3
chr5	ENCODE	exon	131424121	131424460	.	+	.	Parent=gene1988
chr5	ENCODE	CDS	131424299	131424460	.	+	0	Parent=gene1988
chr5	ENCODE	exon	131424559	131424600	.	+	.	Parent=gene1988
chr5	ENCODE	CDS	131424559	131424600	.	+	0	Parent=gene1988
chr5	ENCODE	exon	131425904	131425993	.	+	.	Parent=gene1988
chr5	ENCODE	CDS	131425904	131425993	.	+	0	Parent=gene1988
chr5	ENCODE	exon	131426118	131426159	.	+	.	Parent=gene1988
chr5	ENCODE	CDS	131426118	131426159	.	+	0	Parent=gene1988
chr5	ENCODE	CDS	131426261	131426383	.	+	0	Parent=gene1988
chr5	ENCODE	exon	131426261	131426796	.	+	.	Parent=gene1988
###
chr5	ENCODE	gene	131437382	131439758	.	+	.	ID=gene1989;Name=AC034228.6-001;name2=CSF2
chr5	ENCODE	exon	131437382	131437574	.	+	.	Parent=gene1989
chr5	ENCODE	CDS	131437416	131437574	.	+	0	Parent=gene1989
chr5	ENCODE	exon	131437673	131437714	.	+	.	Parent=gene1989
chr5	ENCODE	CDS	131437673	131437714	.	+	0	Parent=gene1989
chr5	ENCODE	exon	131438402	131438527	.	+	.	Parent=gene1989
chr5	ENCODE	CDS	131438402	131438527	.	+	0	Parent=gene1989
chr5	ENCODE	CDS	131439337	131439444	.	+	0	Parent=gene1989
chr5	ENCODE	exon	131439337	131439758	.	+	.	Parent=gene1989
###
chr5	ENCODE	gene	131555430	131590655	.	-	.	ID=gene1990;Name=AC063976.5-001;name2=P4HA2
chr5	ENCODE	exon	131555430	131556672	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131556602	131556672	.	-	2	Parent=gene1990
chr5	ENCODE	exon	131558518	131558614	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131558518	131558614	.	-	0	Parent=gene1990
chr5	ENCODE	exon	131559004	131559072	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131559004	131559072	.	-	0	Parent=gene1990
chr5	ENCODE	exon	131561798	131561863	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131561798	131561863	.	-	0	Parent=gene1990
chr5	ENCODE	exon	131562471	131562524	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131562471	131562524	.	-	0	Parent=gene1990
chr5	ENCODE	exon	131567340	131567439	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131567340	131567439	.	-	1	Parent=gene1990
chr5	ENCODE	exon	131567674	131567744	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131567674	131567744	.	-	0	Parent=gene1990
chr5	ENCODE	exon	131571300	131571476	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131571300	131571476	.	-	0	Parent=gene1990
chr5	ENCODE	exon	131572730	131572923	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131572730	131572923	.	-	2	Parent=gene1990
chr5	ENCODE	exon	131573876	131574115	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131573876	131574115	.	-	2	Parent=gene1990
chr5	ENCODE	exon	131577508	131577645	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131577508	131577645	.	-	2	Parent=gene1990
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene1990
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene1990
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene1990
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene1990
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene1990
chr5	ENCODE	exon	131590289	131590655	.	-	.	Parent=gene1990
###
chr5	ENCODE	gene	131556202	131591411	.	-	.	ID=gene1991;Name=AC063976.5-004;name2=P4HA2
chr5	ENCODE	exon	131556202	131556672	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131556602	131556672	.	-	2	Parent=gene1991
chr5	ENCODE	exon	131558518	131558614	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131558518	131558614	.	-	0	Parent=gene1991
chr5	ENCODE	exon	131559004	131559072	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131559004	131559072	.	-	0	Parent=gene1991
chr5	ENCODE	exon	131561913	131561972	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131561913	131561972	.	-	0	Parent=gene1991
chr5	ENCODE	exon	131562471	131562524	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131562471	131562524	.	-	0	Parent=gene1991
chr5	ENCODE	exon	131567340	131567439	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131567340	131567439	.	-	1	Parent=gene1991
chr5	ENCODE	exon	131567674	131567744	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131567674	131567744	.	-	0	Parent=gene1991
chr5	ENCODE	exon	131571300	131571476	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131571300	131571476	.	-	0	Parent=gene1991
chr5	ENCODE	exon	131572730	131572923	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131572730	131572923	.	-	2	Parent=gene1991
chr5	ENCODE	exon	131573876	131574115	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131573876	131574115	.	-	2	Parent=gene1991
chr5	ENCODE	exon	131577508	131577645	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131577508	131577645	.	-	2	Parent=gene1991
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene1991
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene1991
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene1991
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene1991
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene1991
chr5	ENCODE	exon	131590678	131590850	.	-	.	Parent=gene1991
chr5	ENCODE	exon	131591382	131591411	.	-	.	Parent=gene1991
###
chr5	ENCODE	gene	131556202	131591449	.	-	.	ID=gene1992;Name=AC063976.5-003;name2=P4HA2
chr5	ENCODE	exon	131556202	131556672	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131556602	131556672	.	-	2	Parent=gene1992
chr5	ENCODE	exon	131558518	131558614	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131558518	131558614	.	-	0	Parent=gene1992
chr5	ENCODE	exon	131559004	131559072	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131559004	131559072	.	-	0	Parent=gene1992
chr5	ENCODE	exon	131561798	131561863	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131561798	131561863	.	-	0	Parent=gene1992
chr5	ENCODE	exon	131562471	131562524	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131562471	131562524	.	-	0	Parent=gene1992
chr5	ENCODE	exon	131567340	131567439	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131567340	131567439	.	-	1	Parent=gene1992
chr5	ENCODE	exon	131567674	131567744	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131567674	131567744	.	-	0	Parent=gene1992
chr5	ENCODE	exon	131571300	131571476	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131571300	131571476	.	-	0	Parent=gene1992
chr5	ENCODE	exon	131572730	131572923	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131572730	131572923	.	-	2	Parent=gene1992
chr5	ENCODE	exon	131573876	131574115	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131573876	131574115	.	-	2	Parent=gene1992
chr5	ENCODE	exon	131577508	131577645	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131577508	131577645	.	-	2	Parent=gene1992
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene1992
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene1992
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene1992
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene1992
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene1992
chr5	ENCODE	exon	131590678	131590813	.	-	.	Parent=gene1992
chr5	ENCODE	exon	131591382	131591449	.	-	.	Parent=gene1992
###
chr5	ENCODE	gene	131556202	131591674	.	-	.	ID=gene1993;Name=AC063976.5-002;name2=P4HA2
chr5	ENCODE	exon	131556202	131556672	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131556602	131556672	.	-	2	Parent=gene1993
chr5	ENCODE	exon	131558518	131558614	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131558518	131558614	.	-	0	Parent=gene1993
chr5	ENCODE	exon	131559004	131559072	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131559004	131559072	.	-	0	Parent=gene1993
chr5	ENCODE	exon	131561913	131561972	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131561913	131561972	.	-	0	Parent=gene1993
chr5	ENCODE	exon	131562471	131562524	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131562471	131562524	.	-	0	Parent=gene1993
chr5	ENCODE	exon	131567340	131567439	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131567340	131567439	.	-	1	Parent=gene1993
chr5	ENCODE	exon	131567674	131567744	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131567674	131567744	.	-	0	Parent=gene1993
chr5	ENCODE	exon	131571300	131571476	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131571300	131571476	.	-	0	Parent=gene1993
chr5	ENCODE	exon	131572730	131572923	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131572730	131572923	.	-	2	Parent=gene1993
chr5	ENCODE	exon	131573876	131574115	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131573876	131574115	.	-	2	Parent=gene1993
chr5	ENCODE	exon	131577508	131577645	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131577508	131577645	.	-	2	Parent=gene1993
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene1993
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene1993
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene1993
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene1993
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene1993
chr5	ENCODE	exon	131591382	131591674	.	-	.	Parent=gene1993
###
chr5	ENCODE	gene	131556263	131558850	.	-	.	ID=gene1994;Name=AC063976.5-007;name2=P4HA2
chr5	ENCODE	exon	131556263	131556672	.	-	.	Parent=gene1994
chr5	ENCODE	exon	131558518	131558850	.	-	.	Parent=gene1994
###
chr5	ENCODE	gene	131556633	131559322	.	-	.	ID=gene1995;Name=AC063976.5-008;name2=P4HA2
chr5	ENCODE	exon	131556633	131556672	.	-	.	Parent=gene1995
chr5	ENCODE	exon	131558518	131558614	.	-	.	Parent=gene1995
chr5	ENCODE	exon	131559004	131559322	.	-	.	Parent=gene1995
###
chr5	ENCODE	gene	131573972	131591386	.	-	.	ID=gene1996;Name=AC063976.5-010;name2=P4HA2
chr5	ENCODE	exon	131573972	131574115	.	-	.	Parent=gene1996
chr5	ENCODE	CDS	131573972	131574115	.	-	2	Parent=gene1996
chr5	ENCODE	exon	131577508	131577645	.	-	.	Parent=gene1996
chr5	ENCODE	CDS	131577508	131577645	.	-	2	Parent=gene1996
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene1996
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene1996
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene1996
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene1996
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene1996
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene1996
chr5	ENCODE	exon	131590678	131590813	.	-	.	Parent=gene1996
chr5	ENCODE	exon	131591131	131591386	.	-	.	Parent=gene1996
###
chr5	ENCODE	gene	131573973	131658863	.	-	.	ID=gene1997;Name=AC063976.5-014;name2=P4HA2
chr5	ENCODE	exon	131573973	131574115	.	-	.	Parent=gene1997
chr5	ENCODE	CDS	131573973	131574115	.	-	2	Parent=gene1997
chr5	ENCODE	exon	131577508	131577645	.	-	.	Parent=gene1997
chr5	ENCODE	CDS	131577508	131577645	.	-	2	Parent=gene1997
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene1997
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene1997
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene1997
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene1997
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene1997
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene1997
chr5	ENCODE	exon	131658770	131658863	.	-	.	Parent=gene1997
###
chr5	ENCODE	gene	131574033	131641447	.	-	.	ID=gene1998;Name=AC063976.5-015;name2=P4HA2
chr5	ENCODE	exon	131574033	131574115	.	-	.	Parent=gene1998
chr5	ENCODE	CDS	131574033	131574115	.	-	2	Parent=gene1998
chr5	ENCODE	exon	131577508	131577645	.	-	.	Parent=gene1998
chr5	ENCODE	CDS	131577508	131577645	.	-	2	Parent=gene1998
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene1998
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene1998
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene1998
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene1998
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene1998
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene1998
chr5	ENCODE	exon	131640934	131641080	.	-	.	Parent=gene1998
chr5	ENCODE	exon	131641299	131641447	.	-	.	Parent=gene1998
###
chr5	ENCODE	gene	131574082	131585683	.	-	.	ID=gene1999;Name=AC063976.5-017;name2=P4HA2
chr5	ENCODE	exon	131574082	131574115	.	-	.	Parent=gene1999
chr5	ENCODE	CDS	131574082	131574115	.	-	2	Parent=gene1999
chr5	ENCODE	exon	131577508	131577645	.	-	.	Parent=gene1999
chr5	ENCODE	CDS	131577508	131577645	.	-	2	Parent=gene1999
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene1999
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene1999
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene1999
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene1999
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene1999
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene1999
chr5	ENCODE	exon	131585637	131585683	.	-	.	Parent=gene1999
###
chr5	ENCODE	gene	131577516	131591431	.	-	.	ID=gene2000;Name=AC063976.5-005;name2=P4HA2
chr5	ENCODE	exon	131577516	131577645	.	-	.	Parent=gene2000
chr5	ENCODE	CDS	131577516	131577645	.	-	2	Parent=gene2000
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene2000
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene2000
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene2000
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene2000
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene2000
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene2000
chr5	ENCODE	exon	131590524	131590813	.	-	.	Parent=gene2000
chr5	ENCODE	exon	131591382	131591431	.	-	.	Parent=gene2000
###
chr5	ENCODE	gene	131577537	131590970	.	-	.	ID=gene2001;Name=AC063976.5-009;name2=P4HA2
chr5	ENCODE	exon	131577537	131577645	.	-	.	Parent=gene2001
chr5	ENCODE	CDS	131577537	131577645	.	-	2	Parent=gene2001
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene2001
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene2001
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene2001
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene2001
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene2001
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene2001
chr5	ENCODE	exon	131590678	131590970	.	-	.	Parent=gene2001
###
chr5	ENCODE	gene	131577633	131591427	.	-	.	ID=gene2002;Name=AC063976.5-016;name2=P4HA2
chr5	ENCODE	exon	131577633	131577645	.	-	.	Parent=gene2002
chr5	ENCODE	CDS	131577633	131577645	.	-	2	Parent=gene2002
chr5	ENCODE	exon	131580789	131580940	.	-	.	Parent=gene2002
chr5	ENCODE	CDS	131580789	131580940	.	-	1	Parent=gene2002
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene2002
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene2002
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene2002
chr5	ENCODE	exon	131582137	131582260	.	-	.	Parent=gene2002
chr5	ENCODE	exon	131590678	131590813	.	-	.	Parent=gene2002
chr5	ENCODE	exon	131591382	131591427	.	-	.	Parent=gene2002
###
chr5	ENCODE	gene	131580789	131590854	.	-	.	ID=gene2003;name2=P4HA2;Name=AC063976.5-006
chr5	ENCODE	exon	131580789	131581440	.	-	.	Parent=gene2003
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene2003
chr5	ENCODE	exon	131590678	131590854	.	-	.	Parent=gene2003
###
chr5	ENCODE	gene	131580815	131641192	.	-	.	ID=gene2004;Name=AC063976.5-011;name2=P4HA2
chr5	ENCODE	exon	131580815	131580940	.	-	.	Parent=gene2004
chr5	ENCODE	CDS	131580815	131580940	.	-	1	Parent=gene2004
chr5	ENCODE	exon	131581344	131581440	.	-	.	Parent=gene2004
chr5	ENCODE	CDS	131581344	131581440	.	-	2	Parent=gene2004
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene2004
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene2004
chr5	ENCODE	exon	131640934	131641192	.	-	.	Parent=gene2004
###
chr5	ENCODE	gene	131581371	131591850	.	-	.	ID=gene2005;Name=AC063976.5-018;name2=P4HA2
chr5	ENCODE	exon	131581371	131581440	.	-	.	Parent=gene2005
chr5	ENCODE	CDS	131581371	131581440	.	-	2	Parent=gene2005
chr5	ENCODE	CDS	131582137	131582218	.	-	0	Parent=gene2005
chr5	ENCODE	exon	131582137	131582236	.	-	.	Parent=gene2005
chr5	ENCODE	exon	131590678	131590813	.	-	.	Parent=gene2005
chr5	ENCODE	exon	131591730	131591850	.	-	.	Parent=gene2005
###
chr5	ENCODE	gene	131612499	131658907	.	-	.	ID=gene2006;Name=AC063976.5-013;name2=P4HA2
chr5	ENCODE	exon	131612499	131614548	.	-	.	Parent=gene2006
chr5	ENCODE	exon	131640934	131641080	.	-	.	Parent=gene2006
chr5	ENCODE	exon	131644374	131644546	.	-	.	Parent=gene2006
chr5	ENCODE	exon	131658770	131658907	.	-	.	Parent=gene2006
###
chr5	ENCODE	gene	131621263	131637046	.	+	.	ID=gene2007;name2=PDLIM4;Name=AC034220.2-001
chr5	ENCODE	exon	131621263	131621419	.	+	.	Parent=gene2007
chr5	ENCODE	CDS	131621327	131621419	.	+	0	Parent=gene2007
chr5	ENCODE	exon	131626201	131626352	.	+	.	Parent=gene2007
chr5	ENCODE	CDS	131626201	131626352	.	+	0	Parent=gene2007
chr5	ENCODE	exon	131630056	131630137	.	+	.	Parent=gene2007
chr5	ENCODE	CDS	131630056	131630137	.	+	1	Parent=gene2007
chr5	ENCODE	exon	131634507	131634685	.	+	.	Parent=gene2007
chr5	ENCODE	CDS	131634507	131634685	.	+	0	Parent=gene2007
chr5	ENCODE	exon	131634895	131635058	.	+	.	Parent=gene2007
chr5	ENCODE	CDS	131634895	131635058	.	+	1	Parent=gene2007
chr5	ENCODE	exon	131635383	131635500	.	+	.	Parent=gene2007
chr5	ENCODE	CDS	131635383	131635500	.	+	2	Parent=gene2007
chr5	ENCODE	CDS	131635617	131635821	.	+	1	Parent=gene2007
chr5	ENCODE	exon	131635617	131637046	.	+	.	Parent=gene2007
###
chr5	ENCODE	gene	131621288	131630353	.	+	.	ID=gene2008;name2=PDLIM4;Name=AC034220.2-007
chr5	ENCODE	exon	131621288	131621419	.	+	.	Parent=gene2008
chr5	ENCODE	exon	131626201	131626352	.	+	.	Parent=gene2008
chr5	ENCODE	exon	131630056	131630353	.	+	.	Parent=gene2008
###
chr5	ENCODE	gene	131621295	131635465	.	+	.	ID=gene2009;Name=AC034220.2-003;name2=PDLIM4
chr5	ENCODE	exon	131621295	131621419	.	+	.	Parent=gene2009
chr5	ENCODE	exon	131634507	131635465	.	+	.	Parent=gene2009
###
chr5	ENCODE	gene	131621299	131635924	.	+	.	ID=gene2010;name2=PDLIM4;Name=AC034220.2-002
chr5	ENCODE	exon	131621299	131621419	.	+	.	Parent=gene2010
chr5	ENCODE	CDS	131621327	131621419	.	+	0	Parent=gene2010
chr5	ENCODE	exon	131626201	131626352	.	+	.	Parent=gene2010
chr5	ENCODE	CDS	131626201	131626352	.	+	0	Parent=gene2010
chr5	ENCODE	exon	131630056	131630137	.	+	.	Parent=gene2010
chr5	ENCODE	CDS	131630056	131630137	.	+	1	Parent=gene2010
chr5	ENCODE	exon	131634507	131634685	.	+	.	Parent=gene2010
chr5	ENCODE	CDS	131634507	131634685	.	+	0	Parent=gene2010
chr5	ENCODE	exon	131634895	131635058	.	+	.	Parent=gene2010
chr5	ENCODE	CDS	131634895	131635058	.	+	1	Parent=gene2010
chr5	ENCODE	CDS	131635617	131635687	.	+	2	Parent=gene2010
chr5	ENCODE	exon	131635617	131635924	.	+	.	Parent=gene2010
###
chr5	ENCODE	gene	131625041	131634928	.	+	.	ID=gene2011;Name=AC034220.2-004;name2=PDLIM4
chr5	ENCODE	exon	131625041	131625131	.	+	.	Parent=gene2011
chr5	ENCODE	exon	131626201	131626352	.	+	.	Parent=gene2011
chr5	ENCODE	exon	131630056	131630137	.	+	.	Parent=gene2011
chr5	ENCODE	exon	131634507	131634685	.	+	.	Parent=gene2011
chr5	ENCODE	exon	131634895	131634928	.	+	.	Parent=gene2011
###
chr5	ENCODE	gene	131634024	131635425	.	+	.	ID=gene2012;Name=AC034220.2-005;name2=PDLIM4
chr5	ENCODE	exon	131634024	131634093	.	+	.	Parent=gene2012
chr5	ENCODE	exon	131634507	131634685	.	+	.	Parent=gene2012
chr5	ENCODE	exon	131634895	131635058	.	+	.	Parent=gene2012
chr5	ENCODE	exon	131635383	131635425	.	+	.	Parent=gene2012
###
chr5	ENCODE	gene	131634564	131635655	.	+	.	ID=gene2013;Name=AC034220.2-006;name2=PDLIM4
chr5	ENCODE	exon	131634564	131634685	.	+	.	Parent=gene2013
chr5	ENCODE	exon	131634895	131635500	.	+	.	Parent=gene2013
chr5	ENCODE	exon	131635617	131635655	.	+	.	Parent=gene2013
###
chr5	ENCODE	gene	131640801	131641514	.	-	.	ID=gene2014;Name=AC063976.5-012;name2=P4HA2
chr5	ENCODE	exon	131640801	131641080	.	-	.	Parent=gene2014
chr5	ENCODE	exon	131641299	131641514	.	-	.	Parent=gene2014
###
chr5	ENCODE	gene	131658035	131707798	.	+	.	ID=gene2015;Name=AC008599.1-001;name2=SLC22A4
chr5	ENCODE	exon	131658035	131658601	.	+	.	Parent=gene2015
chr5	ENCODE	CDS	131658209	131658601	.	+	0	Parent=gene2015
chr5	ENCODE	exon	131675753	131675856	.	+	.	Parent=gene2015
chr5	ENCODE	CDS	131675753	131675856	.	+	0	Parent=gene2015
chr5	ENCODE	exon	131677206	131677360	.	+	.	Parent=gene2015
chr5	ENCODE	CDS	131677206	131677360	.	+	1	Parent=gene2015
chr5	ENCODE	exon	131685776	131685947	.	+	.	Parent=gene2015
chr5	ENCODE	CDS	131685776	131685947	.	+	2	Parent=gene2015
chr5	ENCODE	exon	131690869	131690995	.	+	.	Parent=gene2015
chr5	ENCODE	CDS	131690869	131690995	.	+	1	Parent=gene2015
chr5	ENCODE	exon	131695348	131695442	.	+	.	Parent=gene2015
chr5	ENCODE	CDS	131695348	131695442	.	+	0	Parent=gene2015
chr5	ENCODE	exon	131698310	131698524	.	+	.	Parent=gene2015
chr5	ENCODE	CDS	131698310	131698524	.	+	1	Parent=gene2015
chr5	ENCODE	exon	131699410	131699592	.	+	.	Parent=gene2015
chr5	ENCODE	CDS	131699410	131699592	.	+	2	Parent=gene2015
chr5	ENCODE	exon	131704157	131704292	.	+	.	Parent=gene2015
chr5	ENCODE	CDS	131704157	131704292	.	+	2	Parent=gene2015
chr5	ENCODE	CDS	131707352	131707427	.	+	1	Parent=gene2015
chr5	ENCODE	exon	131707352	131707798	.	+	.	Parent=gene2015
###
chr5	ENCODE	gene	131659017	131684564	.	+	.	ID=gene2016;Name=AC008599.1-003;name2=SLC22A4
chr5	ENCODE	exon	131659017	131659213	.	+	.	Parent=gene2016
chr5	ENCODE	exon	131675753	131675856	.	+	.	Parent=gene2016
chr5	ENCODE	exon	131677206	131677360	.	+	.	Parent=gene2016
chr5	ENCODE	exon	131684457	131684564	.	+	.	Parent=gene2016
###
chr5	ENCODE	gene	131685776	131690977	.	+	.	ID=gene2017;Name=AC008599.1-002;name2=SLC22A4
chr5	ENCODE	exon	131685776	131685947	.	+	.	Parent=gene2017
chr5	ENCODE	exon	131688053	131688234	.	+	.	Parent=gene2017
chr5	ENCODE	exon	131690869	131690977	.	+	.	Parent=gene2017
###
chr5	ENCODE	gene	131733343	131759205	.	+	.	ID=gene2018;name2=SLC22A5;Name=AC118464.1-001
chr5	ENCODE	exon	131733343	131733956	.	+	.	Parent=gene2018
chr5	ENCODE	CDS	131733564	131733956	.	+	0	Parent=gene2018
chr5	ENCODE	exon	131741969	131742072	.	+	.	Parent=gene2018
chr5	ENCODE	CDS	131741969	131742072	.	+	0	Parent=gene2018
chr5	ENCODE	exon	131747738	131747892	.	+	.	Parent=gene2018
chr5	ENCODE	CDS	131747738	131747892	.	+	1	Parent=gene2018
chr5	ENCODE	exon	131748919	131749090	.	+	.	Parent=gene2018
chr5	ENCODE	CDS	131748919	131749090	.	+	2	Parent=gene2018
chr5	ENCODE	exon	131750616	131750742	.	+	.	Parent=gene2018
chr5	ENCODE	CDS	131750616	131750742	.	+	1	Parent=gene2018
chr5	ENCODE	exon	131752512	131752612	.	+	.	Parent=gene2018
chr5	ENCODE	CDS	131752512	131752612	.	+	0	Parent=gene2018
chr5	ENCODE	exon	131754281	131754495	.	+	.	Parent=gene2018
chr5	ENCODE	CDS	131754281	131754495	.	+	1	Parent=gene2018
chr5	ENCODE	exon	131756024	131756206	.	+	.	Parent=gene2018
chr5	ENCODE	CDS	131756024	131756206	.	+	2	Parent=gene2018
chr5	ENCODE	exon	131757267	131757402	.	+	.	Parent=gene2018
chr5	ENCODE	CDS	131757267	131757402	.	+	2	Parent=gene2018
chr5	ENCODE	CDS	131757776	131757863	.	+	1	Parent=gene2018
chr5	ENCODE	exon	131757776	131759205	.	+	.	Parent=gene2018
###
chr5	ENCODE	gene	131733867	131750742	.	+	.	ID=gene2019;Name=AC118464.1-004;name2=SLC22A5
chr5	ENCODE	exon	131733867	131733956	.	+	.	Parent=gene2019
chr5	ENCODE	CDS	131733867	131733956	.	+	0	Parent=gene2019
chr5	ENCODE	exon	131741755	131741826	.	+	.	Parent=gene2019
chr5	ENCODE	CDS	131741755	131741826	.	+	0	Parent=gene2019
chr5	ENCODE	exon	131741969	131742072	.	+	.	Parent=gene2019
chr5	ENCODE	CDS	131741969	131742072	.	+	0	Parent=gene2019
chr5	ENCODE	exon	131747738	131747892	.	+	.	Parent=gene2019
chr5	ENCODE	CDS	131747738	131747892	.	+	1	Parent=gene2019
chr5	ENCODE	exon	131748919	131749090	.	+	.	Parent=gene2019
chr5	ENCODE	CDS	131748919	131749090	.	+	2	Parent=gene2019
chr5	ENCODE	exon	131750616	131750742	.	+	.	Parent=gene2019
chr5	ENCODE	CDS	131750616	131750742	.	+	1	Parent=gene2019
###
chr5	ENCODE	gene	131739677	131759202	.	+	.	ID=gene2020;Name=AC118464.1-006;name2=SLC22A5
chr5	ENCODE	exon	131739677	131741826	.	+	.	Parent=gene2020
chr5	ENCODE	exon	131741969	131747892	.	+	.	Parent=gene2020
chr5	ENCODE	exon	131748919	131749090	.	+	.	Parent=gene2020
chr5	ENCODE	exon	131750616	131750742	.	+	.	Parent=gene2020
chr5	ENCODE	exon	131752512	131752612	.	+	.	Parent=gene2020
chr5	ENCODE	exon	131754281	131754495	.	+	.	Parent=gene2020
chr5	ENCODE	exon	131756024	131756206	.	+	.	Parent=gene2020
chr5	ENCODE	exon	131757267	131757402	.	+	.	Parent=gene2020
chr5	ENCODE	exon	131757776	131759202	.	+	.	Parent=gene2020
###
chr5	ENCODE	gene	131748919	131757406	.	+	.	ID=gene2021;Name=AC118464.1-002;name2=SLC22A5
chr5	ENCODE	exon	131748919	131749090	.	+	.	Parent=gene2021
chr5	ENCODE	exon	131750616	131750742	.	+	.	Parent=gene2021
chr5	ENCODE	exon	131752512	131752612	.	+	.	Parent=gene2021
chr5	ENCODE	exon	131754367	131754495	.	+	.	Parent=gene2021
chr5	ENCODE	exon	131756024	131756206	.	+	.	Parent=gene2021
chr5	ENCODE	exon	131757267	131757406	.	+	.	Parent=gene2021
###
chr5	ENCODE	gene	131751404	131757274	.	+	.	ID=gene2022;Name=AC118464.1-007;name2=SLC22A5
chr5	ENCODE	exon	131751404	131751457	.	+	.	Parent=gene2022
chr5	ENCODE	exon	131752512	131752612	.	+	.	Parent=gene2022
chr5	ENCODE	exon	131754281	131754495	.	+	.	Parent=gene2022
chr5	ENCODE	exon	131756024	131756206	.	+	.	Parent=gene2022
chr5	ENCODE	exon	131757267	131757274	.	+	.	Parent=gene2022
###
chr5	ENCODE	gene	131752502	131758343	.	+	.	ID=gene2023;name2=SLC22A5;Name=AC118464.1-005
chr5	ENCODE	exon	131752502	131752612	.	+	.	Parent=gene2023
chr5	ENCODE	exon	131756024	131756206	.	+	.	Parent=gene2023
chr5	ENCODE	exon	131757267	131757402	.	+	.	Parent=gene2023
chr5	ENCODE	exon	131757776	131758343	.	+	.	Parent=gene2023
###
chr5	ENCODE	gene	131752551	131759204	.	+	.	ID=gene2024;Name=AC118464.1-003;name2=SLC22A5
chr5	ENCODE	exon	131752551	131754495	.	+	.	Parent=gene2024
chr5	ENCODE	exon	131756024	131756206	.	+	.	Parent=gene2024
chr5	ENCODE	exon	131757267	131757402	.	+	.	Parent=gene2024
chr5	ENCODE	exon	131757776	131759204	.	+	.	Parent=gene2024
###
chr5	ENCODE	gene	131774227	131839635	.	+	.	ID=gene2025;Name=AC116366.4-002;name2=AC116366.4
chr5	ENCODE	exon	131774227	131774632	.	+	.	Parent=gene2025
chr5	ENCODE	exon	131783414	131783531	.	+	.	Parent=gene2025
chr5	ENCODE	CDS	131783484	131783531	.	+	0	Parent=gene2025
chr5	ENCODE	exon	131813241	131813280	.	+	.	Parent=gene2025
chr5	ENCODE	CDS	131813241	131813280	.	+	0	Parent=gene2025
chr5	ENCODE	CDS	131839258	131839523	.	+	2	Parent=gene2025
chr5	ENCODE	exon	131839258	131839635	.	+	.	Parent=gene2025
###
chr5	ENCODE	gene	131774572	131813582	.	+	.	ID=gene2026;Name=AC116366.4-004;name2=AC116366.4
chr5	ENCODE	exon	131774572	131774632	.	+	.	Parent=gene2026
chr5	ENCODE	exon	131783414	131783531	.	+	.	Parent=gene2026
chr5	ENCODE	exon	131813241	131813582	.	+	.	Parent=gene2026
###
chr5	ENCODE	gene	131774572	131825958	.	+	.	ID=gene2027;Name=AC116366.4-001;name2=AC116366.4
chr5	ENCODE	exon	131774572	131774632	.	+	.	Parent=gene2027
chr5	ENCODE	exon	131783414	131783531	.	+	.	Parent=gene2027
chr5	ENCODE	CDS	131783484	131783531	.	+	0	Parent=gene2027
chr5	ENCODE	exon	131813241	131813280	.	+	.	Parent=gene2027
chr5	ENCODE	CDS	131813241	131813280	.	+	0	Parent=gene2027
chr5	ENCODE	CDS	131824153	131824445	.	+	2	Parent=gene2027
chr5	ENCODE	exon	131824153	131825958	.	+	.	Parent=gene2027
###
chr5	ENCODE	gene	131774580	131821012	.	+	.	ID=gene2028;Name=AC116366.4-003;name2=AC116366.4
chr5	ENCODE	exon	131774580	131774632	.	+	.	Parent=gene2028
chr5	ENCODE	exon	131783414	131783531	.	+	.	Parent=gene2028
chr5	ENCODE	CDS	131783484	131783531	.	+	0	Parent=gene2028
chr5	ENCODE	exon	131813241	131813280	.	+	.	Parent=gene2028
chr5	ENCODE	CDS	131813241	131813280	.	+	0	Parent=gene2028
chr5	ENCODE	CDS	131820603	131820757	.	+	2	Parent=gene2028
chr5	ENCODE	exon	131820603	131821012	.	+	.	Parent=gene2028
###
chr5	ENCODE	gene	131774580	131834499	.	+	.	ID=gene2029;Name=AC116366.4-005;name2=AC116366.4
chr5	ENCODE	exon	131774580	131774632	.	+	.	Parent=gene2029
chr5	ENCODE	exon	131783414	131783531	.	+	.	Parent=gene2029
chr5	ENCODE	exon	131813241	131813280	.	+	.	Parent=gene2029
chr5	ENCODE	exon	131833631	131834499	.	+	.	Parent=gene2029
###
chr5	ENCODE	gene	131834123	131839601	.	+	.	ID=gene2030;Name=AC116366.4-006;name2=AC116366.4
chr5	ENCODE	exon	131834123	131834645	.	+	.	Parent=gene2030
chr5	ENCODE	exon	131839258	131839601	.	+	.	Parent=gene2030
###
chr5	ENCODE	gene	131845200	131854389	.	-	.	ID=gene2031;Name=AC116366.3-001;name2=IRF1
chr5	ENCODE	exon	131845200	131847666	.	-	.	Parent=gene2031
chr5	ENCODE	CDS	131847542	131847666	.	-	2	Parent=gene2031
chr5	ENCODE	exon	131847953	131848088	.	-	.	Parent=gene2031
chr5	ENCODE	CDS	131847953	131848088	.	-	0	Parent=gene2031
chr5	ENCODE	exon	131849258	131849307	.	-	.	Parent=gene2031
chr5	ENCODE	CDS	131849258	131849307	.	-	2	Parent=gene2031
chr5	ENCODE	exon	131849842	131849964	.	-	.	Parent=gene2031
chr5	ENCODE	CDS	131849842	131849964	.	-	2	Parent=gene2031
chr5	ENCODE	exon	131850148	131850277	.	-	.	Parent=gene2031
chr5	ENCODE	CDS	131850148	131850277	.	-	0	Parent=gene2031
chr5	ENCODE	exon	131850386	131850435	.	-	.	Parent=gene2031
chr5	ENCODE	CDS	131850386	131850435	.	-	2	Parent=gene2031
chr5	ENCODE	exon	131850545	131850721	.	-	.	Parent=gene2031
chr5	ENCODE	CDS	131850545	131850721	.	-	2	Parent=gene2031
chr5	ENCODE	exon	131851517	131851616	.	-	.	Parent=gene2031
chr5	ENCODE	CDS	131851517	131851616	.	-	0	Parent=gene2031
chr5	ENCODE	CDS	131852983	131853069	.	-	0	Parent=gene2031
chr5	ENCODE	exon	131852983	131853074	.	-	.	Parent=gene2031
chr5	ENCODE	exon	131854136	131854389	.	-	.	Parent=gene2031
###
chr5	ENCODE	gene	131846676	131852623	.	-	.	ID=gene2032;Name=AC116366.3-006;name2=IRF1
chr5	ENCODE	exon	131846676	131850721	.	-	.	Parent=gene2032
chr5	ENCODE	exon	131851517	131852623	.	-	.	Parent=gene2032
###
chr5	ENCODE	gene	131849258	131854368	.	-	.	ID=gene2033;Name=AC116366.3-002;name2=IRF1
chr5	ENCODE	exon	131849258	131849307	.	-	.	Parent=gene2033
chr5	ENCODE	CDS	131849258	131849307	.	-	2	Parent=gene2033
chr5	ENCODE	exon	131850148	131850277	.	-	.	Parent=gene2033
chr5	ENCODE	CDS	131850148	131850277	.	-	0	Parent=gene2033
chr5	ENCODE	exon	131850386	131850435	.	-	.	Parent=gene2033
chr5	ENCODE	CDS	131850386	131850435	.	-	2	Parent=gene2033
chr5	ENCODE	exon	131850545	131850721	.	-	.	Parent=gene2033
chr5	ENCODE	CDS	131850545	131850721	.	-	2	Parent=gene2033
chr5	ENCODE	exon	131851517	131851616	.	-	.	Parent=gene2033
chr5	ENCODE	CDS	131851517	131851616	.	-	0	Parent=gene2033
chr5	ENCODE	CDS	131852983	131853069	.	-	0	Parent=gene2033
chr5	ENCODE	exon	131852983	131853074	.	-	.	Parent=gene2033
chr5	ENCODE	exon	131854136	131854368	.	-	.	Parent=gene2033
###
chr5	ENCODE	gene	131849714	131854356	.	-	.	ID=gene2034;name2=IRF1;Name=AC116366.3-004
chr5	ENCODE	exon	131849714	131850277	.	-	.	Parent=gene2034
chr5	ENCODE	exon	131850386	131850435	.	-	.	Parent=gene2034
chr5	ENCODE	exon	131850545	131850721	.	-	.	Parent=gene2034
chr5	ENCODE	exon	131851517	131851643	.	-	.	Parent=gene2034
chr5	ENCODE	exon	131852983	131853074	.	-	.	Parent=gene2034
chr5	ENCODE	exon	131854136	131854356	.	-	.	Parent=gene2034
###
chr5	ENCODE	gene	131850208	131854358	.	-	.	ID=gene2035;Name=AC116366.3-003;name2=IRF1
chr5	ENCODE	exon	131850208	131850277	.	-	.	Parent=gene2035
chr5	ENCODE	exon	131850386	131850435	.	-	.	Parent=gene2035
chr5	ENCODE	exon	131850545	131850721	.	-	.	Parent=gene2035
chr5	ENCODE	exon	131854136	131854358	.	-	.	Parent=gene2035
###
chr5	ENCODE	gene	131850553	131853236	.	-	.	ID=gene2036;Name=AC116366.3-007;name2=IRF1
chr5	ENCODE	exon	131850553	131850721	.	-	.	Parent=gene2036
chr5	ENCODE	exon	131851517	131851616	.	-	.	Parent=gene2036
chr5	ENCODE	exon	131852983	131853236	.	-	.	Parent=gene2036
###
chr5	ENCODE	gene	131852262	131854345	.	-	.	ID=gene2037;Name=AC116366.3-005;name2=IRF1
chr5	ENCODE	exon	131852262	131853074	.	-	.	Parent=gene2037
chr5	ENCODE	exon	131854136	131854345	.	-	.	Parent=gene2037
###
chr5	ENCODE	gene	131905035	131907113	.	-	.	ID=gene2038;Name=AC116366.2-001;name2=IL5
chr5	ENCODE	exon	131905035	131905500	.	-	.	Parent=gene2038
chr5	ENCODE	CDS	131905402	131905500	.	-	0	Parent=gene2038
chr5	ENCODE	exon	131905606	131905734	.	-	.	Parent=gene2038
chr5	ENCODE	CDS	131905606	131905734	.	-	0	Parent=gene2038
chr5	ENCODE	exon	131906685	131906717	.	-	.	Parent=gene2038
chr5	ENCODE	CDS	131906685	131906717	.	-	0	Parent=gene2038
chr5	ENCODE	CDS	131906926	131907069	.	-	0	Parent=gene2038
chr5	ENCODE	exon	131906926	131907113	.	-	.	Parent=gene2038
###
chr5	ENCODE	gene	131905657	131907511	.	-	.	ID=gene2039;Name=AC116366.2-003;name2=IL5
chr5	ENCODE	exon	131905657	131905734	.	-	.	Parent=gene2039
chr5	ENCODE	exon	131906685	131907511	.	-	.	Parent=gene2039
###
chr5	ENCODE	gene	131905657	131920429	.	-	.	ID=gene2040;name2=IL5;Name=AC116366.2-002
chr5	ENCODE	exon	131905657	131905734	.	-	.	Parent=gene2040
chr5	ENCODE	CDS	131905657	131905734	.	-	0	Parent=gene2040
chr5	ENCODE	exon	131906685	131906717	.	-	.	Parent=gene2040
chr5	ENCODE	CDS	131906685	131906717	.	-	0	Parent=gene2040
chr5	ENCODE	CDS	131920265	131920306	.	-	0	Parent=gene2040
chr5	ENCODE	exon	131920265	131920429	.	-	.	Parent=gene2040
###
chr5	ENCODE	gene	131919610	131943498	.	+	.	ID=gene2041;Name=AC004041.1-006;name2=RAD50
chr5	ENCODE	exon	131919610	131920064	.	+	.	Parent=gene2041
chr5	ENCODE	exon	131922875	131922958	.	+	.	Parent=gene2041
chr5	ENCODE	exon	131939368	131939519	.	+	.	Parent=gene2041
chr5	ENCODE	CDS	131939452	131939519	.	+	0	Parent=gene2041
chr5	ENCODE	exon	131942908	131943093	.	+	.	Parent=gene2041
chr5	ENCODE	CDS	131942908	131943093	.	+	1	Parent=gene2041
chr5	ENCODE	exon	131943453	131943498	.	+	.	Parent=gene2041
chr5	ENCODE	CDS	131943453	131943498	.	+	1	Parent=gene2041
###
chr5	ENCODE	gene	131920529	132006067	.	+	.	ID=gene2042;Name=AC004041.1-002;name2=RAD50
chr5	ENCODE	exon	131920529	131921044	.	+	.	Parent=gene2042
chr5	ENCODE	exon	131922875	131922958	.	+	.	Parent=gene2042
chr5	ENCODE	exon	131939368	131939454	.	+	.	Parent=gene2042
chr5	ENCODE	exon	131942908	131943093	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131942960	131943093	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131943453	131943657	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131943453	131943657	.	+	1	Parent=gene2042
chr5	ENCODE	exon	131951153	131951281	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131951153	131951281	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131951515	131951680	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131951515	131951680	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131952278	131952471	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131952278	131952471	.	+	2	Parent=gene2042
chr5	ENCODE	exon	131953222	131953428	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131953222	131953428	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131954815	131954997	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131954815	131954997	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131955468	131955625	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131955468	131955625	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131958460	131958635	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131958460	131958635	.	+	1	Parent=gene2042
chr5	ENCODE	exon	131959164	131959401	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131959164	131959401	.	+	2	Parent=gene2042
chr5	ENCODE	exon	131966891	131967080	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131966891	131967080	.	+	1	Parent=gene2042
chr5	ENCODE	exon	131967511	131967637	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131967511	131967637	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131968397	131968590	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131968397	131968590	.	+	2	Parent=gene2042
chr5	ENCODE	exon	131972206	131972316	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131972206	131972316	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131972708	131972800	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131972708	131972800	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131972874	131972987	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131972874	131972987	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131979594	131979721	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131979594	131979721	.	+	0	Parent=gene2042
chr5	ENCODE	exon	131981661	131981885	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	131981661	131981885	.	+	1	Parent=gene2042
chr5	ENCODE	exon	132000706	132000791	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	132000706	132000791	.	+	1	Parent=gene2042
chr5	ENCODE	exon	132001672	132001814	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	132001672	132001814	.	+	2	Parent=gene2042
chr5	ENCODE	exon	132004263	132004396	.	+	.	Parent=gene2042
chr5	ENCODE	CDS	132004263	132004396	.	+	0	Parent=gene2042
chr5	ENCODE	CDS	132005769	132005955	.	+	1	Parent=gene2042
chr5	ENCODE	exon	132005769	132006067	.	+	.	Parent=gene2042
###
chr5	ENCODE	gene	131920529	132007651	.	+	.	ID=gene2043;Name=AC004041.1-001;name2=RAD50
chr5	ENCODE	exon	131920529	131921044	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131920916	131921044	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131922875	131922958	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131922875	131922958	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131939368	131939519	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131939368	131939519	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131942908	131943093	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131942908	131943093	.	+	1	Parent=gene2043
chr5	ENCODE	exon	131943453	131943657	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131943453	131943657	.	+	1	Parent=gene2043
chr5	ENCODE	exon	131951153	131951281	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131951153	131951281	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131951515	131951680	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131951515	131951680	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131952278	131952471	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131952278	131952471	.	+	2	Parent=gene2043
chr5	ENCODE	exon	131953222	131953428	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131953222	131953428	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131954815	131954997	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131954815	131954997	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131955468	131955625	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131955468	131955625	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131958460	131958635	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131958460	131958635	.	+	1	Parent=gene2043
chr5	ENCODE	exon	131959164	131959401	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131959164	131959401	.	+	2	Parent=gene2043
chr5	ENCODE	exon	131966891	131967080	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131966891	131967080	.	+	1	Parent=gene2043
chr5	ENCODE	exon	131967511	131967637	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131967511	131967637	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131968397	131968590	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131968397	131968590	.	+	2	Parent=gene2043
chr5	ENCODE	exon	131972206	131972316	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131972206	131972316	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131972708	131972800	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131972708	131972800	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131972874	131972987	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131972874	131972987	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131979594	131979721	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131979594	131979721	.	+	0	Parent=gene2043
chr5	ENCODE	exon	131981661	131981885	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	131981661	131981885	.	+	1	Parent=gene2043
chr5	ENCODE	exon	132000706	132000791	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	132000706	132000791	.	+	1	Parent=gene2043
chr5	ENCODE	exon	132001672	132001814	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	132001672	132001814	.	+	2	Parent=gene2043
chr5	ENCODE	exon	132004263	132004396	.	+	.	Parent=gene2043
chr5	ENCODE	CDS	132004263	132004396	.	+	0	Parent=gene2043
chr5	ENCODE	CDS	132005769	132005955	.	+	1	Parent=gene2043
chr5	ENCODE	exon	132005769	132007651	.	+	.	Parent=gene2043
###
chr5	ENCODE	gene	131920822	131959359	.	+	.	ID=gene2044;Name=AC004041.1-003;name2=RAD50
chr5	ENCODE	exon	131920822	131921044	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131920916	131921044	.	+	0	Parent=gene2044
chr5	ENCODE	exon	131922875	131922958	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131922875	131922958	.	+	0	Parent=gene2044
chr5	ENCODE	exon	131939368	131939519	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131939368	131939519	.	+	0	Parent=gene2044
chr5	ENCODE	exon	131942908	131943093	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131942908	131943093	.	+	1	Parent=gene2044
chr5	ENCODE	exon	131943453	131943657	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131943453	131943657	.	+	1	Parent=gene2044
chr5	ENCODE	exon	131951153	131951281	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131951153	131951281	.	+	0	Parent=gene2044
chr5	ENCODE	exon	131951515	131951680	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131951515	131951680	.	+	0	Parent=gene2044
chr5	ENCODE	exon	131952278	131952471	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131952278	131952471	.	+	2	Parent=gene2044
chr5	ENCODE	exon	131953222	131953428	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131953222	131953428	.	+	0	Parent=gene2044
chr5	ENCODE	exon	131955468	131955625	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131955468	131955625	.	+	0	Parent=gene2044
chr5	ENCODE	exon	131958460	131958635	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131958460	131958635	.	+	1	Parent=gene2044
chr5	ENCODE	exon	131959164	131959359	.	+	.	Parent=gene2044
chr5	ENCODE	CDS	131959164	131959359	.	+	2	Parent=gene2044
###
chr5	ENCODE	gene	131920822	131972930	.	+	.	ID=gene2045;name2=RAD50;Name=AC004041.1-004
chr5	ENCODE	exon	131920822	131921044	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131922875	131922958	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131939368	131939519	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131942908	131943093	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131943453	131943657	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131951153	131951281	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131951515	131951680	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131952278	131952471	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131953222	131953428	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131954815	131954997	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131958460	131958635	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131959164	131959401	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131966891	131967080	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131967511	131967637	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131968397	131968590	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131972206	131972316	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131972708	131972800	.	+	.	Parent=gene2045
chr5	ENCODE	exon	131972874	131972930	.	+	.	Parent=gene2045
###
chr5	ENCODE	gene	131943336	131952398	.	+	.	ID=gene2046;Name=AC004041.1-007;name2=RAD50
chr5	ENCODE	exon	131943336	131943657	.	+	.	Parent=gene2046
chr5	ENCODE	exon	131951153	131951281	.	+	.	Parent=gene2046
chr5	ENCODE	exon	131951515	131951680	.	+	.	Parent=gene2046
chr5	ENCODE	exon	131952278	131952398	.	+	.	Parent=gene2046
###
chr5	ENCODE	gene	131954868	131957118	.	+	.	ID=gene2047;Name=AC004041.1-005;name2=RAD50
chr5	ENCODE	exon	131954868	131954997	.	+	.	Parent=gene2047
chr5	ENCODE	exon	131955468	131955625	.	+	.	Parent=gene2047
chr5	ENCODE	exon	131956355	131957118	.	+	.	Parent=gene2047
###
chr5	ENCODE	gene	131958813	131966996	.	+	.	ID=gene2048;Name=AC004041.1-008;name2=RAD50
chr5	ENCODE	exon	131958813	131958864	.	+	.	Parent=gene2048
chr5	ENCODE	exon	131959164	131959401	.	+	.	Parent=gene2048
chr5	ENCODE	exon	131963653	131963729	.	+	.	Parent=gene2048
chr5	ENCODE	exon	131966891	131966996	.	+	.	Parent=gene2048
###
chr5	ENCODE	gene	131981862	132006772	.	+	.	ID=gene2049;Name=AC004041.1-009;name2=RAD50
chr5	ENCODE	exon	131981862	131981885	.	+	.	Parent=gene2049
chr5	ENCODE	CDS	131981862	131981885	.	+	0	Parent=gene2049
chr5	ENCODE	exon	132000706	132000791	.	+	.	Parent=gene2049
chr5	ENCODE	CDS	132000706	132000791	.	+	0	Parent=gene2049
chr5	ENCODE	exon	132001672	132001814	.	+	.	Parent=gene2049
chr5	ENCODE	CDS	132001672	132001814	.	+	1	Parent=gene2049
chr5	ENCODE	exon	132004263	132004396	.	+	.	Parent=gene2049
chr5	ENCODE	CDS	132004263	132004396	.	+	2	Parent=gene2049
chr5	ENCODE	CDS	132006596	132006680	.	+	0	Parent=gene2049
chr5	ENCODE	exon	132006596	132006772	.	+	.	Parent=gene2049
###
chr5	ENCODE	gene	132019854	132024141	.	+	.	ID=gene2050;name2=IL13;Name=AC004039.3-002
chr5	ENCODE	exon	132019854	132020221	.	+	.	Parent=gene2050
chr5	ENCODE	exon	132020657	132020835	.	+	.	Parent=gene2050
chr5	ENCODE	exon	132023009	132023062	.	+	.	Parent=gene2050
chr5	ENCODE	exon	132023315	132023419	.	+	.	Parent=gene2050
chr5	ENCODE	exon	132023766	132024141	.	+	.	Parent=gene2050
###
chr5	ENCODE	gene	132020115	132024205	.	+	.	ID=gene2051;Name=AC004039.3-004;name2=IL13
chr5	ENCODE	exon	132020115	132020221	.	+	.	Parent=gene2051
chr5	ENCODE	exon	132021881	132021951	.	+	.	Parent=gene2051
chr5	ENCODE	exon	132023009	132023062	.	+	.	Parent=gene2051
chr5	ENCODE	exon	132023315	132023419	.	+	.	Parent=gene2051
chr5	ENCODE	exon	132023766	132024205	.	+	.	Parent=gene2051
###
chr5	ENCODE	gene	132020127	132024294	.	+	.	ID=gene2052;Name=AC004039.3-003;name2=IL13
chr5	ENCODE	exon	132020127	132020221	.	+	.	Parent=gene2052
chr5	ENCODE	exon	132020657	132020835	.	+	.	Parent=gene2052
chr5	ENCODE	exon	132021881	132021951	.	+	.	Parent=gene2052
chr5	ENCODE	exon	132023009	132023062	.	+	.	Parent=gene2052
chr5	ENCODE	exon	132023315	132023419	.	+	.	Parent=gene2052
chr5	ENCODE	exon	132023766	132024294	.	+	.	Parent=gene2052
###
chr5	ENCODE	gene	132021764	132023923	.	+	.	ID=gene2053;Name=AC004039.3-005;name2=IL13
chr5	ENCODE	exon	132021764	132023062	.	+	.	Parent=gene2053
chr5	ENCODE	exon	132023315	132023419	.	+	.	Parent=gene2053
chr5	ENCODE	exon	132023766	132023923	.	+	.	Parent=gene2053
###
chr5	ENCODE	gene	132021764	132024701	.	+	.	ID=gene2054;Name=AC004039.3-001;name2=IL13
chr5	ENCODE	exon	132021764	132021951	.	+	.	Parent=gene2054
chr5	ENCODE	CDS	132021778	132021951	.	+	0	Parent=gene2054
chr5	ENCODE	exon	132023009	132023062	.	+	.	Parent=gene2054
chr5	ENCODE	CDS	132023009	132023062	.	+	0	Parent=gene2054
chr5	ENCODE	exon	132023315	132023419	.	+	.	Parent=gene2054
chr5	ENCODE	CDS	132023315	132023419	.	+	0	Parent=gene2054
chr5	ENCODE	CDS	132023766	132023873	.	+	0	Parent=gene2054
chr5	ENCODE	exon	132023766	132024701	.	+	.	Parent=gene2054
###
chr5	ENCODE	gene	132037577	132046267	.	+	.	ID=gene2055;Name=AC004039.4-001;name2=IL4
chr5	ENCODE	exon	132037577	132037776	.	+	.	Parent=gene2055
chr5	ENCODE	CDS	132037642	132037776	.	+	0	Parent=gene2055
chr5	ENCODE	exon	132038050	132038097	.	+	.	Parent=gene2055
chr5	ENCODE	CDS	132038050	132038097	.	+	0	Parent=gene2055
chr5	ENCODE	exon	132043305	132043481	.	+	.	Parent=gene2055
chr5	ENCODE	CDS	132043305	132043481	.	+	0	Parent=gene2055
chr5	ENCODE	CDS	132046077	132046178	.	+	0	Parent=gene2055
chr5	ENCODE	exon	132046077	132046267	.	+	.	Parent=gene2055
###
chr5	ENCODE	gene	132037642	132046178	.	+	.	ID=gene2056;Name=AC004039.4-002;name2=IL4
chr5	ENCODE	exon	132037642	132037776	.	+	.	Parent=gene2056
chr5	ENCODE	CDS	132037642	132037776	.	+	0	Parent=gene2056
chr5	ENCODE	exon	132043305	132043481	.	+	.	Parent=gene2056
chr5	ENCODE	CDS	132043305	132043481	.	+	0	Parent=gene2056
chr5	ENCODE	exon	132046077	132046178	.	+	.	Parent=gene2056
chr5	ENCODE	CDS	132046077	132046178	.	+	0	Parent=gene2056
###
chr5	ENCODE	gene	132037949	132043460	.	+	.	ID=gene2057;Name=AC004039.4-003;name2=IL4
chr5	ENCODE	exon	132037949	132038097	.	+	.	Parent=gene2057
chr5	ENCODE	exon	132043305	132043460	.	+	.	Parent=gene2057
###
chr5	ENCODE	gene	132056267	132101229	.	-	.	ID=gene2058;Name=AC004039.5-001;name2=KIF3A
chr5	ENCODE	exon	132056267	132060273	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132060225	132060273	.	-	1	Parent=gene2058
chr5	ENCODE	exon	132062762	132062886	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132062762	132062886	.	-	0	Parent=gene2058
chr5	ENCODE	exon	132063807	132063875	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132063807	132063875	.	-	0	Parent=gene2058
chr5	ENCODE	exon	132064238	132064291	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132064238	132064291	.	-	0	Parent=gene2058
chr5	ENCODE	exon	132065678	132065803	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132065678	132065803	.	-	0	Parent=gene2058
chr5	ENCODE	exon	132066149	132066259	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132066149	132066259	.	-	0	Parent=gene2058
chr5	ENCODE	exon	132066476	132066656	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132066476	132066656	.	-	1	Parent=gene2058
chr5	ENCODE	exon	132067054	132067210	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132067054	132067210	.	-	2	Parent=gene2058
chr5	ENCODE	exon	132074550	132074648	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132074550	132074648	.	-	2	Parent=gene2058
chr5	ENCODE	exon	132079348	132079522	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132079348	132079522	.	-	0	Parent=gene2058
chr5	ENCODE	exon	132079836	132080033	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132079836	132080033	.	-	0	Parent=gene2058
chr5	ENCODE	exon	132080436	132080575	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132080436	132080575	.	-	2	Parent=gene2058
chr5	ENCODE	exon	132084200	132084305	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132084200	132084305	.	-	0	Parent=gene2058
chr5	ENCODE	exon	132089719	132089803	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132089719	132089803	.	-	1	Parent=gene2058
chr5	ENCODE	exon	132089945	132090089	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132089945	132090089	.	-	2	Parent=gene2058
chr5	ENCODE	exon	132097796	132098069	.	-	.	Parent=gene2058
chr5	ENCODE	CDS	132097796	132098069	.	-	0	Parent=gene2058
chr5	ENCODE	CDS	132101005	132101010	.	-	0	Parent=gene2058
chr5	ENCODE	exon	132101005	132101229	.	-	.	Parent=gene2058
###
chr5	ENCODE	gene	132059221	132101163	.	-	.	ID=gene2059;Name=AC004039.5-002;name2=KIF3A
chr5	ENCODE	exon	132059221	132060273	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132060225	132060273	.	-	1	Parent=gene2059
chr5	ENCODE	exon	132062762	132062886	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132062762	132062886	.	-	0	Parent=gene2059
chr5	ENCODE	exon	132063807	132063875	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132063807	132063875	.	-	0	Parent=gene2059
chr5	ENCODE	exon	132064238	132064291	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132064238	132064291	.	-	0	Parent=gene2059
chr5	ENCODE	exon	132065678	132065803	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132065678	132065803	.	-	0	Parent=gene2059
chr5	ENCODE	exon	132066149	132066259	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132066149	132066259	.	-	0	Parent=gene2059
chr5	ENCODE	exon	132066476	132066656	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132066476	132066656	.	-	1	Parent=gene2059
chr5	ENCODE	exon	132067054	132067210	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132067054	132067210	.	-	2	Parent=gene2059
chr5	ENCODE	exon	132070042	132070050	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132070042	132070050	.	-	2	Parent=gene2059
chr5	ENCODE	exon	132074550	132074648	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132074550	132074648	.	-	2	Parent=gene2059
chr5	ENCODE	exon	132079348	132079522	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132079348	132079522	.	-	0	Parent=gene2059
chr5	ENCODE	exon	132079836	132080033	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132079836	132080033	.	-	0	Parent=gene2059
chr5	ENCODE	exon	132080436	132080575	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132080436	132080575	.	-	2	Parent=gene2059
chr5	ENCODE	exon	132084200	132084305	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132084200	132084305	.	-	0	Parent=gene2059
chr5	ENCODE	exon	132089719	132089803	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132089719	132089803	.	-	1	Parent=gene2059
chr5	ENCODE	exon	132089945	132090089	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132089945	132090089	.	-	2	Parent=gene2059
chr5	ENCODE	exon	132097796	132098069	.	-	.	Parent=gene2059
chr5	ENCODE	CDS	132097796	132098069	.	-	0	Parent=gene2059
chr5	ENCODE	CDS	132101005	132101010	.	-	0	Parent=gene2059
chr5	ENCODE	exon	132101005	132101163	.	-	.	Parent=gene2059
###
chr5	ENCODE	gene	132060045	132066625	.	-	.	ID=gene2060;Name=AC004039.5-006;name2=KIF3A
chr5	ENCODE	exon	132060045	132060273	.	-	.	Parent=gene2060
chr5	ENCODE	CDS	132060225	132060273	.	-	1	Parent=gene2060
chr5	ENCODE	exon	132062762	132062886	.	-	.	Parent=gene2060
chr5	ENCODE	CDS	132062762	132062886	.	-	0	Parent=gene2060
chr5	ENCODE	exon	132063807	132063875	.	-	.	Parent=gene2060
chr5	ENCODE	CDS	132063807	132063875	.	-	0	Parent=gene2060
chr5	ENCODE	exon	132064238	132064291	.	-	.	Parent=gene2060
chr5	ENCODE	CDS	132064238	132064291	.	-	0	Parent=gene2060
chr5	ENCODE	exon	132066149	132066259	.	-	.	Parent=gene2060
chr5	ENCODE	CDS	132066149	132066259	.	-	0	Parent=gene2060
chr5	ENCODE	exon	132066476	132066625	.	-	.	Parent=gene2060
chr5	ENCODE	CDS	132066476	132066625	.	-	0	Parent=gene2060
###
chr5	ENCODE	gene	132060139	132063071	.	-	.	ID=gene2061;Name=AC004039.5-004;name2=KIF3A
chr5	ENCODE	exon	132060139	132060273	.	-	.	Parent=gene2061
chr5	ENCODE	exon	132062762	132063071	.	-	.	Parent=gene2061
###
chr5	ENCODE	gene	132062810	132067210	.	-	.	ID=gene2062;Name=AC004039.5-003;name2=KIF3A
chr5	ENCODE	exon	132062810	132062886	.	-	.	Parent=gene2062
chr5	ENCODE	exon	132063807	132063875	.	-	.	Parent=gene2062
chr5	ENCODE	exon	132064238	132064291	.	-	.	Parent=gene2062
chr5	ENCODE	exon	132065678	132065803	.	-	.	Parent=gene2062
chr5	ENCODE	exon	132066149	132066195	.	-	.	Parent=gene2062
chr5	ENCODE	exon	132066509	132066656	.	-	.	Parent=gene2062
chr5	ENCODE	exon	132067054	132067210	.	-	.	Parent=gene2062
###
chr5	ENCODE	gene	132064127	132067201	.	-	.	ID=gene2063;Name=AC004039.5-005;name2=KIF3A
chr5	ENCODE	exon	132064127	132064291	.	-	.	Parent=gene2063
chr5	ENCODE	exon	132065678	132065803	.	-	.	Parent=gene2063
chr5	ENCODE	exon	132066149	132066259	.	-	.	Parent=gene2063
chr5	ENCODE	exon	132066476	132066656	.	-	.	Parent=gene2063
chr5	ENCODE	exon	132067054	132067201	.	-	.	Parent=gene2063
###
chr5	ENCODE	gene	132089719	132100519	.	-	.	ID=gene2064;Name=AC004039.5-007;name2=KIF3A
chr5	ENCODE	exon	132089719	132089803	.	-	.	Parent=gene2064
chr5	ENCODE	CDS	132089719	132089803	.	-	1	Parent=gene2064
chr5	ENCODE	exon	132089945	132090089	.	-	.	Parent=gene2064
chr5	ENCODE	CDS	132089945	132090089	.	-	2	Parent=gene2064
chr5	ENCODE	exon	132097796	132098069	.	-	.	Parent=gene2064
chr5	ENCODE	CDS	132097796	132098069	.	-	0	Parent=gene2064
chr5	ENCODE	CDS	132100366	132100368	.	-	0	Parent=gene2064
chr5	ENCODE	exon	132100366	132100519	.	-	.	Parent=gene2064
###
chr5	ENCODE	gene	132111036	132117755	.	+	.	ID=gene2065;Name=AC004775.1-001;name2=AC004775.1
chr5	ENCODE	exon	132111036	132111515	.	+	.	Parent=gene2065
chr5	ENCODE	CDS	132111087	132111515	.	+	0	Parent=gene2065
chr5	ENCODE	exon	132111938	132112066	.	+	.	Parent=gene2065
chr5	ENCODE	CDS	132111938	132112066	.	+	0	Parent=gene2065
chr5	ENCODE	exon	132112939	132113013	.	+	.	Parent=gene2065
chr5	ENCODE	CDS	132112939	132113013	.	+	0	Parent=gene2065
chr5	ENCODE	exon	132114448	132114588	.	+	.	Parent=gene2065
chr5	ENCODE	CDS	132114448	132114588	.	+	0	Parent=gene2065
chr5	ENCODE	exon	132115557	132115787	.	+	.	Parent=gene2065
chr5	ENCODE	CDS	132115557	132115787	.	+	0	Parent=gene2065
chr5	ENCODE	CDS	132116457	132116561	.	+	0	Parent=gene2065
chr5	ENCODE	exon	132116457	132117755	.	+	.	Parent=gene2065
###
chr5	ENCODE	gene	132112961	132114884	.	+	.	ID=gene2066;Name=AC004775.1-002;name2=AC004775.1
chr5	ENCODE	exon	132112961	132113013	.	+	.	Parent=gene2066
chr5	ENCODE	exon	132114448	132114884	.	+	.	Parent=gene2066
###
chr5	ENCODE	gene	132114408	132140966	.	-	.	ID=gene2067;Name=AC004775.2-002;name2=SEPT8
chr5	ENCODE	exon	132114408	132115772	.	-	.	Parent=gene2067
chr5	ENCODE	CDS	132115607	132115772	.	-	1	Parent=gene2067
chr5	ENCODE	exon	132124393	132124583	.	-	.	Parent=gene2067
chr5	ENCODE	CDS	132124393	132124583	.	-	0	Parent=gene2067
chr5	ENCODE	exon	132124724	132124856	.	-	.	Parent=gene2067
chr5	ENCODE	CDS	132124724	132124856	.	-	1	Parent=gene2067
chr5	ENCODE	exon	132125049	132125217	.	-	.	Parent=gene2067
chr5	ENCODE	CDS	132125049	132125217	.	-	2	Parent=gene2067
chr5	ENCODE	exon	132125391	132125487	.	-	.	Parent=gene2067
chr5	ENCODE	CDS	132125391	132125487	.	-	0	Parent=gene2067
chr5	ENCODE	exon	132126075	132126236	.	-	.	Parent=gene2067
chr5	ENCODE	CDS	132126075	132126236	.	-	0	Parent=gene2067
chr5	ENCODE	exon	132127297	132127483	.	-	.	Parent=gene2067
chr5	ENCODE	CDS	132127297	132127483	.	-	1	Parent=gene2067
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2067
chr5	ENCODE	CDS	132127815	132128010	.	-	2	Parent=gene2067
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2067
chr5	ENCODE	CDS	132129000	132129120	.	-	0	Parent=gene2067
chr5	ENCODE	CDS	132140699	132140728	.	-	0	Parent=gene2067
chr5	ENCODE	exon	132140699	132140966	.	-	.	Parent=gene2067
###
chr5	ENCODE	gene	132114531	132115602	.	+	.	ID=gene2068;name2=AC004775.1;Name=AC004775.1-003
chr5	ENCODE	exon	132114531	132114588	.	+	.	Parent=gene2068
chr5	ENCODE	exon	132115285	132115602	.	+	.	Parent=gene2068
###
chr5	ENCODE	gene	132115050	132124462	.	-	.	ID=gene2069;Name=AC004775.2-010;name2=SEPT8
chr5	ENCODE	exon	132115050	132115769	.	-	.	Parent=gene2069
chr5	ENCODE	exon	132124393	132124462	.	-	.	Parent=gene2069
###
chr5	ENCODE	gene	132117770	132140829	.	-	.	ID=gene2070;Name=AC004775.2-006;name2=SEPT8
chr5	ENCODE	exon	132117770	132118111	.	-	.	Parent=gene2070
chr5	ENCODE	CDS	132118009	132118111	.	-	1	Parent=gene2070
chr5	ENCODE	exon	132124393	132124583	.	-	.	Parent=gene2070
chr5	ENCODE	CDS	132124393	132124583	.	-	0	Parent=gene2070
chr5	ENCODE	exon	132124724	132124856	.	-	.	Parent=gene2070
chr5	ENCODE	CDS	132124724	132124856	.	-	1	Parent=gene2070
chr5	ENCODE	exon	132125049	132125217	.	-	.	Parent=gene2070
chr5	ENCODE	CDS	132125049	132125217	.	-	2	Parent=gene2070
chr5	ENCODE	exon	132125391	132125487	.	-	.	Parent=gene2070
chr5	ENCODE	CDS	132125391	132125487	.	-	0	Parent=gene2070
chr5	ENCODE	exon	132126075	132126236	.	-	.	Parent=gene2070
chr5	ENCODE	CDS	132126075	132126236	.	-	0	Parent=gene2070
chr5	ENCODE	exon	132127297	132127477	.	-	.	Parent=gene2070
chr5	ENCODE	CDS	132127297	132127477	.	-	1	Parent=gene2070
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2070
chr5	ENCODE	CDS	132127815	132128010	.	-	2	Parent=gene2070
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2070
chr5	ENCODE	CDS	132129000	132129120	.	-	0	Parent=gene2070
chr5	ENCODE	CDS	132140699	132140728	.	-	0	Parent=gene2070
chr5	ENCODE	exon	132140699	132140829	.	-	.	Parent=gene2070
###
chr5	ENCODE	gene	132119596	132141012	.	-	.	ID=gene2071;name2=SEPT8;Name=AC004775.2-003
chr5	ENCODE	exon	132119596	132122415	.	-	.	Parent=gene2071
chr5	ENCODE	CDS	132122412	132122415	.	-	1	Parent=gene2071
chr5	ENCODE	exon	132124393	132124583	.	-	.	Parent=gene2071
chr5	ENCODE	CDS	132124393	132124583	.	-	0	Parent=gene2071
chr5	ENCODE	exon	132124724	132124856	.	-	.	Parent=gene2071
chr5	ENCODE	CDS	132124724	132124856	.	-	1	Parent=gene2071
chr5	ENCODE	exon	132125049	132125217	.	-	.	Parent=gene2071
chr5	ENCODE	CDS	132125049	132125217	.	-	2	Parent=gene2071
chr5	ENCODE	exon	132125391	132125487	.	-	.	Parent=gene2071
chr5	ENCODE	CDS	132125391	132125487	.	-	0	Parent=gene2071
chr5	ENCODE	exon	132126075	132126236	.	-	.	Parent=gene2071
chr5	ENCODE	CDS	132126075	132126236	.	-	0	Parent=gene2071
chr5	ENCODE	exon	132127297	132127483	.	-	.	Parent=gene2071
chr5	ENCODE	CDS	132127297	132127483	.	-	1	Parent=gene2071
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2071
chr5	ENCODE	CDS	132127815	132128010	.	-	2	Parent=gene2071
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2071
chr5	ENCODE	CDS	132129000	132129120	.	-	0	Parent=gene2071
chr5	ENCODE	CDS	132140699	132140728	.	-	0	Parent=gene2071
chr5	ENCODE	exon	132140699	132141012	.	-	.	Parent=gene2071
###
chr5	ENCODE	gene	132119924	132140935	.	-	.	ID=gene2072;Name=AC004775.2-004;name2=SEPT8
chr5	ENCODE	exon	132119924	132122598	.	-	.	Parent=gene2072
chr5	ENCODE	CDS	132122592	132122598	.	-	1	Parent=gene2072
chr5	ENCODE	exon	132124393	132124583	.	-	.	Parent=gene2072
chr5	ENCODE	CDS	132124393	132124583	.	-	0	Parent=gene2072
chr5	ENCODE	exon	132124724	132124856	.	-	.	Parent=gene2072
chr5	ENCODE	CDS	132124724	132124856	.	-	1	Parent=gene2072
chr5	ENCODE	exon	132125049	132125217	.	-	.	Parent=gene2072
chr5	ENCODE	CDS	132125049	132125217	.	-	2	Parent=gene2072
chr5	ENCODE	exon	132125391	132125487	.	-	.	Parent=gene2072
chr5	ENCODE	CDS	132125391	132125487	.	-	0	Parent=gene2072
chr5	ENCODE	exon	132126075	132126236	.	-	.	Parent=gene2072
chr5	ENCODE	CDS	132126075	132126236	.	-	0	Parent=gene2072
chr5	ENCODE	exon	132127297	132127483	.	-	.	Parent=gene2072
chr5	ENCODE	CDS	132127297	132127483	.	-	1	Parent=gene2072
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2072
chr5	ENCODE	CDS	132127815	132128010	.	-	2	Parent=gene2072
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2072
chr5	ENCODE	CDS	132129000	132129120	.	-	0	Parent=gene2072
chr5	ENCODE	CDS	132140699	132140728	.	-	0	Parent=gene2072
chr5	ENCODE	exon	132140699	132140935	.	-	.	Parent=gene2072
###
chr5	ENCODE	gene	132121734	132141807	.	-	.	ID=gene2073;Name=AC004775.2-001;name2=SEPT8
chr5	ENCODE	exon	132121734	132122415	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132124393	132124583	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132124724	132124856	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132125049	132125217	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132125391	132125487	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132126075	132126236	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132127297	132127483	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132141267	132141485	.	-	.	Parent=gene2073
chr5	ENCODE	exon	132141676	132141807	.	-	.	Parent=gene2073
###
chr5	ENCODE	gene	132121735	132140852	.	-	.	ID=gene2074;Name=AC004775.2-005;name2=SEPT8
chr5	ENCODE	exon	132121735	132122147	.	-	.	Parent=gene2074
chr5	ENCODE	CDS	132122105	132122147	.	-	1	Parent=gene2074
chr5	ENCODE	exon	132124393	132124583	.	-	.	Parent=gene2074
chr5	ENCODE	CDS	132124393	132124583	.	-	0	Parent=gene2074
chr5	ENCODE	exon	132124724	132124856	.	-	.	Parent=gene2074
chr5	ENCODE	CDS	132124724	132124856	.	-	1	Parent=gene2074
chr5	ENCODE	exon	132125049	132125217	.	-	.	Parent=gene2074
chr5	ENCODE	CDS	132125049	132125217	.	-	2	Parent=gene2074
chr5	ENCODE	exon	132125391	132125487	.	-	.	Parent=gene2074
chr5	ENCODE	CDS	132125391	132125487	.	-	0	Parent=gene2074
chr5	ENCODE	exon	132126075	132126236	.	-	.	Parent=gene2074
chr5	ENCODE	CDS	132126075	132126236	.	-	0	Parent=gene2074
chr5	ENCODE	exon	132127297	132127477	.	-	.	Parent=gene2074
chr5	ENCODE	CDS	132127297	132127477	.	-	1	Parent=gene2074
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2074
chr5	ENCODE	CDS	132127815	132128010	.	-	2	Parent=gene2074
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2074
chr5	ENCODE	CDS	132129000	132129120	.	-	0	Parent=gene2074
chr5	ENCODE	CDS	132140699	132140728	.	-	0	Parent=gene2074
chr5	ENCODE	exon	132140699	132140852	.	-	.	Parent=gene2074
###
chr5	ENCODE	gene	132121791	132140811	.	-	.	ID=gene2075;Name=AC004775.2-007;name2=SEPT8
chr5	ENCODE	exon	132121791	132122147	.	-	.	Parent=gene2075
chr5	ENCODE	CDS	132122105	132122147	.	-	1	Parent=gene2075
chr5	ENCODE	exon	132124393	132124583	.	-	.	Parent=gene2075
chr5	ENCODE	CDS	132124393	132124583	.	-	0	Parent=gene2075
chr5	ENCODE	exon	132124724	132124856	.	-	.	Parent=gene2075
chr5	ENCODE	CDS	132124724	132124856	.	-	1	Parent=gene2075
chr5	ENCODE	exon	132125049	132125217	.	-	.	Parent=gene2075
chr5	ENCODE	CDS	132125049	132125217	.	-	2	Parent=gene2075
chr5	ENCODE	exon	132125391	132125487	.	-	.	Parent=gene2075
chr5	ENCODE	CDS	132125391	132125487	.	-	0	Parent=gene2075
chr5	ENCODE	exon	132126075	132126236	.	-	.	Parent=gene2075
chr5	ENCODE	CDS	132126075	132126236	.	-	0	Parent=gene2075
chr5	ENCODE	exon	132127297	132127483	.	-	.	Parent=gene2075
chr5	ENCODE	CDS	132127297	132127483	.	-	1	Parent=gene2075
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2075
chr5	ENCODE	CDS	132127815	132128010	.	-	2	Parent=gene2075
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2075
chr5	ENCODE	CDS	132129000	132129120	.	-	0	Parent=gene2075
chr5	ENCODE	CDS	132140699	132140728	.	-	0	Parent=gene2075
chr5	ENCODE	exon	132140699	132140811	.	-	.	Parent=gene2075
###
chr5	ENCODE	gene	132122192	132126083	.	-	.	ID=gene2076;Name=AC004775.2-011;name2=SEPT8
chr5	ENCODE	exon	132122192	132122415	.	-	.	Parent=gene2076
chr5	ENCODE	exon	132124393	132124583	.	-	.	Parent=gene2076
chr5	ENCODE	exon	132124724	132124856	.	-	.	Parent=gene2076
chr5	ENCODE	exon	132125049	132125089	.	-	.	Parent=gene2076
chr5	ENCODE	exon	132125443	132125487	.	-	.	Parent=gene2076
chr5	ENCODE	exon	132126075	132126083	.	-	.	Parent=gene2076
###
chr5	ENCODE	gene	132125092	132129065	.	-	.	ID=gene2077;Name=AC004775.2-009;name2=SEPT8
chr5	ENCODE	exon	132125092	132125217	.	-	.	Parent=gene2077
chr5	ENCODE	exon	132126075	132126236	.	-	.	Parent=gene2077
chr5	ENCODE	exon	132127297	132127483	.	-	.	Parent=gene2077
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2077
chr5	ENCODE	exon	132129000	132129065	.	-	.	Parent=gene2077
###
chr5	ENCODE	gene	132126128	132140830	.	-	.	ID=gene2078;name2=SEPT8;Name=AC004775.2-014
chr5	ENCODE	exon	132126128	132126236	.	-	.	Parent=gene2078
chr5	ENCODE	CDS	132126128	132126236	.	-	0	Parent=gene2078
chr5	ENCODE	exon	132127297	132127477	.	-	.	Parent=gene2078
chr5	ENCODE	CDS	132127297	132127477	.	-	1	Parent=gene2078
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2078
chr5	ENCODE	CDS	132127815	132128010	.	-	2	Parent=gene2078
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2078
chr5	ENCODE	CDS	132129000	132129120	.	-	0	Parent=gene2078
chr5	ENCODE	CDS	132140699	132140728	.	-	0	Parent=gene2078
chr5	ENCODE	exon	132140699	132140830	.	-	.	Parent=gene2078
###
chr5	ENCODE	gene	132126194	132139557	.	-	.	ID=gene2079;Name=AC004775.2-013;name2=SEPT8
chr5	ENCODE	exon	132126194	132126236	.	-	.	Parent=gene2079
chr5	ENCODE	exon	132127297	132127477	.	-	.	Parent=gene2079
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2079
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2079
chr5	ENCODE	exon	132139326	132139557	.	-	.	Parent=gene2079
###
chr5	ENCODE	gene	132127360	132141600	.	-	.	ID=gene2080;Name=AC004775.2-012;name2=SEPT8
chr5	ENCODE	exon	132127360	132127483	.	-	.	Parent=gene2080
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2080
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2080
chr5	ENCODE	exon	132141349	132141600	.	-	.	Parent=gene2080
###
chr5	ENCODE	gene	132127415	132170832	.	-	.	ID=gene2081;Name=AC004775.2-016;name2=SEPT8
chr5	ENCODE	exon	132127415	132127483	.	-	.	Parent=gene2081
chr5	ENCODE	exon	132127815	132128010	.	-	.	Parent=gene2081
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2081
chr5	ENCODE	exon	132170657	132170832	.	-	.	Parent=gene2081
###
chr5	ENCODE	gene	132127552	132140812	.	-	.	ID=gene2082;Name=AC004775.2-008;name2=SEPT8
chr5	ENCODE	exon	132127552	132128010	.	-	.	Parent=gene2082
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2082
chr5	ENCODE	exon	132140699	132140812	.	-	.	Parent=gene2082
###
chr5	ENCODE	gene	132127982	132140839	.	-	.	ID=gene2083;Name=AC004775.2-015;name2=SEPT8
chr5	ENCODE	exon	132127982	132128010	.	-	.	Parent=gene2083
chr5	ENCODE	exon	132129000	132129120	.	-	.	Parent=gene2083
chr5	ENCODE	exon	132137514	132137803	.	-	.	Parent=gene2083
chr5	ENCODE	exon	132140699	132140839	.	-	.	Parent=gene2083
###
chr5	ENCODE	gene	132177178	132180388	.	+	.	ID=gene2084;Name=AC004775.3-001;name2=ANKRD43
chr5	ENCODE	exon	132177178	132180388	.	+	.	Parent=gene2084
chr5	ENCODE	CDS	132177213	132178862	.	+	0	Parent=gene2084
###
chr5	ENCODE	gene	132185732	132189019	.	-	.	ID=gene2085;Name=AC004775.4-005;name2=SHROOM1
chr5	ENCODE	exon	132185732	132185798	.	-	.	Parent=gene2085
chr5	ENCODE	exon	132188327	132188412	.	-	.	Parent=gene2085
chr5	ENCODE	exon	132188609	132188664	.	-	.	Parent=gene2085
chr5	ENCODE	exon	132188754	132189019	.	-	.	Parent=gene2085
###
chr5	ENCODE	gene	132185732	132194489	.	-	.	ID=gene2086;Name=AC004775.4-001;name2=SHROOM1
chr5	ENCODE	exon	132185732	132186719	.	-	.	Parent=gene2086
chr5	ENCODE	CDS	132186387	132186719	.	-	0	Parent=gene2086
chr5	ENCODE	exon	132186841	132187113	.	-	.	Parent=gene2086
chr5	ENCODE	CDS	132186841	132187113	.	-	0	Parent=gene2086
chr5	ENCODE	exon	132187214	132187355	.	-	.	Parent=gene2086
chr5	ENCODE	CDS	132187214	132187355	.	-	1	Parent=gene2086
chr5	ENCODE	exon	132187441	132188010	.	-	.	Parent=gene2086
chr5	ENCODE	CDS	132187441	132188010	.	-	1	Parent=gene2086
chr5	ENCODE	exon	132188206	132188412	.	-	.	Parent=gene2086
chr5	ENCODE	CDS	132188206	132188412	.	-	1	Parent=gene2086
chr5	ENCODE	exon	132188609	132188664	.	-	.	Parent=gene2086
chr5	ENCODE	CDS	132188609	132188664	.	-	0	Parent=gene2086
chr5	ENCODE	CDS	132188754	132189731	.	-	0	Parent=gene2086
chr5	ENCODE	exon	132188754	132189773	.	-	.	Parent=gene2086
chr5	ENCODE	exon	132189868	132190178	.	-	.	Parent=gene2086
chr5	ENCODE	exon	132191052	132191198	.	-	.	Parent=gene2086
chr5	ENCODE	exon	132194185	132194489	.	-	.	Parent=gene2086
###
chr5	ENCODE	gene	132185911	132189901	.	-	.	ID=gene2087;Name=AC004775.4-002;name2=SHROOM1
chr5	ENCODE	exon	132185911	132186704	.	-	.	Parent=gene2087
chr5	ENCODE	CDS	132186387	132186704	.	-	0	Parent=gene2087
chr5	ENCODE	exon	132186841	132187113	.	-	.	Parent=gene2087
chr5	ENCODE	CDS	132186841	132187113	.	-	0	Parent=gene2087
chr5	ENCODE	exon	132187214	132187355	.	-	.	Parent=gene2087
chr5	ENCODE	CDS	132187214	132187355	.	-	1	Parent=gene2087
chr5	ENCODE	exon	132187441	132188010	.	-	.	Parent=gene2087
chr5	ENCODE	CDS	132187441	132188010	.	-	1	Parent=gene2087
chr5	ENCODE	exon	132188206	132188412	.	-	.	Parent=gene2087
chr5	ENCODE	CDS	132188206	132188412	.	-	1	Parent=gene2087
chr5	ENCODE	exon	132188609	132188664	.	-	.	Parent=gene2087
chr5	ENCODE	CDS	132188609	132188664	.	-	0	Parent=gene2087
chr5	ENCODE	CDS	132188754	132189731	.	-	0	Parent=gene2087
chr5	ENCODE	exon	132188754	132189901	.	-	.	Parent=gene2087
###
chr5	ENCODE	gene	132186387	132189731	.	-	.	ID=gene2088;Name=AC004775.4-007;name2=SHROOM1
chr5	ENCODE	exon	132186387	132186719	.	-	.	Parent=gene2088
chr5	ENCODE	CDS	132186387	132186719	.	-	0	Parent=gene2088
chr5	ENCODE	exon	132186841	132187113	.	-	.	Parent=gene2088
chr5	ENCODE	CDS	132186841	132187113	.	-	0	Parent=gene2088
chr5	ENCODE	exon	132187214	132187355	.	-	.	Parent=gene2088
chr5	ENCODE	CDS	132187214	132187355	.	-	1	Parent=gene2088
chr5	ENCODE	exon	132187441	132188010	.	-	.	Parent=gene2088
chr5	ENCODE	CDS	132187441	132188010	.	-	1	Parent=gene2088
chr5	ENCODE	exon	132188609	132188664	.	-	.	Parent=gene2088
chr5	ENCODE	CDS	132188609	132188664	.	-	0	Parent=gene2088
chr5	ENCODE	exon	132188754	132189731	.	-	.	Parent=gene2088
chr5	ENCODE	CDS	132188754	132189731	.	-	0	Parent=gene2088
###
chr5	ENCODE	gene	132186874	132187396	.	-	.	ID=gene2089;Name=AC004775.4-004;name2=SHROOM1
chr5	ENCODE	exon	132186874	132187113	.	-	.	Parent=gene2089
chr5	ENCODE	exon	132187214	132187396	.	-	.	Parent=gene2089
###
chr5	ENCODE	gene	132187630	132188207	.	-	.	ID=gene2090;Name=AC004775.4-006;name2=SHROOM1
chr5	ENCODE	exon	132187630	132187771	.	-	.	Parent=gene2090
chr5	ENCODE	exon	132187872	132188010	.	-	.	Parent=gene2090
chr5	ENCODE	exon	132188206	132188207	.	-	.	Parent=gene2090
###
chr5	ENCODE	gene	132188760	132194250	.	-	.	ID=gene2091;Name=AC004775.4-003;name2=SHROOM1
chr5	ENCODE	CDS	132188760	132189731	.	-	0	Parent=gene2091
chr5	ENCODE	exon	132188760	132189773	.	-	.	Parent=gene2091
chr5	ENCODE	exon	132194185	132194250	.	-	.	Parent=gene2091
###
chr5	ENCODE	gene	132224772	132230228	.	-	.	ID=gene2092;Name=AC004500.1-001;name2=GDF9
chr5	ENCODE	exon	132224772	132226147	.	-	.	Parent=gene2092
chr5	ENCODE	CDS	132225180	132226147	.	-	2	Parent=gene2092
chr5	ENCODE	CDS	132227728	132228124	.	-	0	Parent=gene2092
chr5	ENCODE	exon	132227728	132228952	.	-	.	Parent=gene2092
chr5	ENCODE	exon	132230190	132230228	.	-	.	Parent=gene2092
###
chr5	ENCODE	gene	132230151	132231622	.	+	.	ID=gene2093;Name=AC004500.2-001;name2=UQCRQ
chr5	ENCODE	exon	132230151	132230278	.	+	.	Parent=gene2093
chr5	ENCODE	exon	132230460	132230626	.	+	.	Parent=gene2093
chr5	ENCODE	CDS	132230473	132230626	.	+	0	Parent=gene2093
chr5	ENCODE	CDS	132231079	132231173	.	+	2	Parent=gene2093
chr5	ENCODE	exon	132231079	132231622	.	+	.	Parent=gene2093
###
chr5	ENCODE	gene	132230221	132231278	.	+	.	ID=gene2094;name2=UQCRQ;Name=AC004500.2-002
chr5	ENCODE	exon	132230221	132230282	.	+	.	Parent=gene2094
chr5	ENCODE	exon	132230460	132230626	.	+	.	Parent=gene2094
chr5	ENCODE	CDS	132230473	132230626	.	+	0	Parent=gene2094
chr5	ENCODE	CDS	132231079	132231173	.	+	2	Parent=gene2094
chr5	ENCODE	exon	132231079	132231278	.	+	.	Parent=gene2094
###
chr5	ENCODE	gene	132230224	132231278	.	+	.	ID=gene2095;Name=AC004500.2-003;name2=UQCRQ
chr5	ENCODE	exon	132230224	132230278	.	+	.	Parent=gene2095
chr5	ENCODE	exon	132230460	132231278	.	+	.	Parent=gene2095
###
chr5	ENCODE	gene	132230233	132231290	.	+	.	ID=gene2096;Name=AC004500.2-004;name2=UQCRQ
chr5	ENCODE	exon	132230233	132230278	.	+	.	Parent=gene2096
chr5	ENCODE	exon	132231079	132231290	.	+	.	Parent=gene2096
###
chr5	ENCODE	gene	132230237	132231274	.	+	.	ID=gene2097;Name=AC004500.2-005;name2=UQCRQ
chr5	ENCODE	exon	132230237	132230626	.	+	.	Parent=gene2097
chr5	ENCODE	CDS	132230473	132230626	.	+	0	Parent=gene2097
chr5	ENCODE	CDS	132231079	132231173	.	+	2	Parent=gene2097
chr5	ENCODE	exon	132231079	132231274	.	+	.	Parent=gene2097
###
chr5	ENCODE	gene	132230248	132230933	.	+	.	ID=gene2098;Name=AC004500.2-006;name2=UQCRQ
chr5	ENCODE	exon	132230248	132230282	.	+	.	Parent=gene2098
chr5	ENCODE	exon	132230460	132230933	.	+	.	Parent=gene2098
###
chr5	ENCODE	gene	132235913	132238637	.	+	.	ID=gene2099;Name=AC004500.3-001;name2=LEAP2
chr5	ENCODE	exon	132235913	132237342	.	+	.	Parent=gene2099
chr5	ENCODE	CDS	132237286	132237342	.	+	0	Parent=gene2099
chr5	ENCODE	exon	132237541	132237680	.	+	.	Parent=gene2099
chr5	ENCODE	CDS	132237541	132237680	.	+	0	Parent=gene2099
chr5	ENCODE	CDS	132238001	132238037	.	+	1	Parent=gene2099
chr5	ENCODE	exon	132238001	132238637	.	+	.	Parent=gene2099
###
chr5	ENCODE	gene	132237035	132238289	.	+	.	ID=gene2100;Name=AC004500.3-002;name2=LEAP2
chr5	ENCODE	exon	132237035	132237680	.	+	.	Parent=gene2100
chr5	ENCODE	exon	132238001	132238289	.	+	.	Parent=gene2100
###
chr5	ENCODE	gene	132237257	132238286	.	+	.	ID=gene2101;Name=AC004500.3-003;name2=LEAP2
chr5	ENCODE	exon	132237257	132237342	.	+	.	Parent=gene2101
chr5	ENCODE	exon	132237541	132237680	.	+	.	Parent=gene2101
chr5	ENCODE	exon	132238056	132238286	.	+	.	Parent=gene2101
###
chr5	ENCODE	gene	132238970	132267995	.	-	.	ID=gene2102;Name=AC004500.4-001;name2=AFF4
chr5	ENCODE	exon	132238970	132244777	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132246931	132247151	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132248667	132248710	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132249901	132249994	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132251112	132251183	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132251437	132251573	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132251688	132251751	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132252670	132252764	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132255755	132255995	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132256621	132256709	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132259914	132260831	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132261821	132261983	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132262695	132262732	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132263178	132263232	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132266033	132266078	.	-	.	Parent=gene2102
chr5	ENCODE	exon	132267959	132267995	.	-	.	Parent=gene2102
###
chr5	ENCODE	gene	132255408	132267995	.	-	.	ID=gene2103;Name=AC004500.4-004;name2=AC004500.4
chr5	ENCODE	exon	132255408	132255995	.	-	.	Parent=gene2103
chr5	ENCODE	exon	132256621	132256709	.	-	.	Parent=gene2103
chr5	ENCODE	exon	132259914	132260831	.	-	.	Parent=gene2103
chr5	ENCODE	exon	132261821	132261983	.	-	.	Parent=gene2103
chr5	ENCODE	exon	132262695	132262732	.	-	.	Parent=gene2103
chr5	ENCODE	exon	132263178	132263232	.	-	.	Parent=gene2103
chr5	ENCODE	exon	132266033	132266078	.	-	.	Parent=gene2103
chr5	ENCODE	exon	132267959	132267995	.	-	.	Parent=gene2103
###
chr5	ENCODE	gene	132260402	132264673	.	-	.	ID=gene2104;Name=AC004500.4-008;name2=AC004500.4
chr5	ENCODE	exon	132260402	132260831	.	-	.	Parent=gene2104
chr5	ENCODE	exon	132261821	132261983	.	-	.	Parent=gene2104
chr5	ENCODE	exon	132262695	132262732	.	-	.	Parent=gene2104
chr5	ENCODE	exon	132263178	132263232	.	-	.	Parent=gene2104
chr5	ENCODE	exon	132264463	132264673	.	-	.	Parent=gene2104
###
chr5	ENCODE	gene	132260795	132267995	.	-	.	ID=gene2105;Name=AC004500.4-006;name2=AC004500.4
chr5	ENCODE	exon	132260795	132260831	.	-	.	Parent=gene2105
chr5	ENCODE	exon	132262695	132262732	.	-	.	Parent=gene2105
chr5	ENCODE	exon	132263178	132263232	.	-	.	Parent=gene2105
chr5	ENCODE	exon	132266033	132266078	.	-	.	Parent=gene2105
chr5	ENCODE	exon	132267959	132267995	.	-	.	Parent=gene2105
###
chr5	ENCODE	gene	132260795	132267995	.	-	.	ID=gene2106;Name=AC004500.4-005;name2=AC004500.4
chr5	ENCODE	exon	132260795	132260831	.	-	.	Parent=gene2106
chr5	ENCODE	exon	132261821	132261983	.	-	.	Parent=gene2106
chr5	ENCODE	exon	132262695	132262732	.	-	.	Parent=gene2106
chr5	ENCODE	exon	132263178	132263232	.	-	.	Parent=gene2106
chr5	ENCODE	exon	132266033	132266078	.	-	.	Parent=gene2106
chr5	ENCODE	exon	132267959	132267995	.	-	.	Parent=gene2106
###
chr5	ENCODE	gene	132261874	132267995	.	-	.	ID=gene2107;Name=AC004500.4-007;name2=AC004500.4
chr5	ENCODE	exon	132261874	132261983	.	-	.	Parent=gene2107
chr5	ENCODE	exon	132262695	132262732	.	-	.	Parent=gene2107
chr5	ENCODE	exon	132263178	132263232	.	-	.	Parent=gene2107
chr5	ENCODE	exon	132266033	132266078	.	-	.	Parent=gene2107
chr5	ENCODE	exon	132267959	132267995	.	-	.	Parent=gene2107
###
chr5	ENCODE	gene	132267452	132267995	.	-	.	ID=gene2108;name2=AC004500.4;Name=AC004500.4-002
chr5	ENCODE	exon	132267452	132267771	.	-	.	Parent=gene2108
chr5	ENCODE	exon	132267959	132267995	.	-	.	Parent=gene2108
###
chr5	ENCODE	gene	141951927	141981091	.	-	.	ID=gene2109;Name=AC005370.1-001;name2=FGF1
chr5	ENCODE	exon	141951927	141955233	.	-	.	Parent=gene2109
chr5	ENCODE	CDS	141955039	141955233	.	-	0	Parent=gene2109
chr5	ENCODE	exon	141960451	141960554	.	-	.	Parent=gene2109
chr5	ENCODE	CDS	141960451	141960554	.	-	2	Parent=gene2109
chr5	ENCODE	CDS	141973708	141973876	.	-	0	Parent=gene2109
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2109
chr5	ENCODE	exon	141981046	141981091	.	-	.	Parent=gene2109
###
chr5	ENCODE	gene	141953118	142045421	.	-	.	ID=gene2110;name2=FGF1;Name=AC005370.1-008
chr5	ENCODE	exon	141953118	141955233	.	-	.	Parent=gene2110
chr5	ENCODE	CDS	141955039	141955233	.	-	0	Parent=gene2110
chr5	ENCODE	exon	141960451	141960554	.	-	.	Parent=gene2110
chr5	ENCODE	CDS	141960451	141960554	.	-	2	Parent=gene2110
chr5	ENCODE	CDS	141973708	141973876	.	-	0	Parent=gene2110
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2110
chr5	ENCODE	exon	142045263	142045421	.	-	.	Parent=gene2110
###
chr5	ENCODE	gene	141953592	142057467	.	-	.	ID=gene2111;Name=AC005370.1-005;name2=FGF1
chr5	ENCODE	exon	141953592	141954351	.	-	.	Parent=gene2111
chr5	ENCODE	exon	141973887	141973910	.	-	.	Parent=gene2111
chr5	ENCODE	exon	142057371	142057467	.	-	.	Parent=gene2111
###
chr5	ENCODE	gene	141954501	142046134	.	-	.	ID=gene2112;Name=AC005370.1-002;name2=FGF1
chr5	ENCODE	exon	141954501	141955233	.	-	.	Parent=gene2112
chr5	ENCODE	CDS	141955039	141955233	.	-	0	Parent=gene2112
chr5	ENCODE	exon	141960451	141960554	.	-	.	Parent=gene2112
chr5	ENCODE	CDS	141960451	141960554	.	-	2	Parent=gene2112
chr5	ENCODE	CDS	141973708	141973876	.	-	0	Parent=gene2112
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2112
chr5	ENCODE	exon	142045706	142046134	.	-	.	Parent=gene2112
###
chr5	ENCODE	gene	141954837	142045800	.	-	.	ID=gene2113;Name=AC005370.1-007;name2=FGF1
chr5	ENCODE	exon	141954837	141955233	.	-	.	Parent=gene2113
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2113
chr5	ENCODE	exon	142045706	142045800	.	-	.	Parent=gene2113
###
chr5	ENCODE	gene	141954910	142057801	.	-	.	ID=gene2114;name2=FGF1;Name=AC005370.1-003
chr5	ENCODE	exon	141954910	141955233	.	-	.	Parent=gene2114
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2114
chr5	ENCODE	exon	142057371	142057801	.	-	.	Parent=gene2114
###
chr5	ENCODE	gene	141954980	142057770	.	-	.	ID=gene2115;Name=AC005370.1-009;name2=FGF1
chr5	ENCODE	exon	141954980	141955233	.	-	.	Parent=gene2115
chr5	ENCODE	exon	141960451	141960549	.	-	.	Parent=gene2115
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2115
chr5	ENCODE	exon	142057371	142057464	.	-	.	Parent=gene2115
chr5	ENCODE	exon	142057662	142057770	.	-	.	Parent=gene2115
###
chr5	ENCODE	gene	141954980	142057801	.	-	.	ID=gene2116;Name=AC005370.1-012;name2=FGF1
chr5	ENCODE	exon	141954980	141955233	.	-	.	Parent=gene2116
chr5	ENCODE	exon	141960451	141960554	.	-	.	Parent=gene2116
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2116
chr5	ENCODE	exon	142057371	142057801	.	-	.	Parent=gene2116
###
chr5	ENCODE	gene	141954992	142057795	.	-	.	ID=gene2117;Name=AC005370.1-010;name2=FGF1
chr5	ENCODE	exon	141954992	141955233	.	-	.	Parent=gene2117
chr5	ENCODE	CDS	141955039	141955233	.	-	0	Parent=gene2117
chr5	ENCODE	exon	141960451	141960554	.	-	.	Parent=gene2117
chr5	ENCODE	CDS	141960451	141960554	.	-	2	Parent=gene2117
chr5	ENCODE	CDS	141973708	141973876	.	-	0	Parent=gene2117
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2117
chr5	ENCODE	exon	142057662	142057795	.	-	.	Parent=gene2117
###
chr5	ENCODE	gene	141954992	142057795	.	-	.	ID=gene2118;Name=AC005370.1-006;name2=FGF1
chr5	ENCODE	exon	141954992	141955233	.	-	.	Parent=gene2118
chr5	ENCODE	CDS	141955039	141955233	.	-	0	Parent=gene2118
chr5	ENCODE	exon	141960451	141960554	.	-	.	Parent=gene2118
chr5	ENCODE	CDS	141960451	141960554	.	-	2	Parent=gene2118
chr5	ENCODE	CDS	141973708	141973876	.	-	0	Parent=gene2118
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2118
chr5	ENCODE	exon	142057371	142057464	.	-	.	Parent=gene2118
chr5	ENCODE	exon	142057662	142057795	.	-	.	Parent=gene2118
###
chr5	ENCODE	gene	141954992	142057801	.	-	.	ID=gene2119;Name=AC005370.1-011;name2=FGF1
chr5	ENCODE	exon	141954992	141955233	.	-	.	Parent=gene2119
chr5	ENCODE	exon	141960451	141960554	.	-	.	Parent=gene2119
chr5	ENCODE	exon	142057757	142057801	.	-	.	Parent=gene2119
###
chr5	ENCODE	gene	141960549	142003950	.	-	.	ID=gene2120;Name=AC005370.1-004;name2=FGF1
chr5	ENCODE	exon	141960549	141960554	.	-	.	Parent=gene2120
chr5	ENCODE	CDS	141960549	141960554	.	-	2	Parent=gene2120
chr5	ENCODE	CDS	141973708	141973876	.	-	0	Parent=gene2120
chr5	ENCODE	exon	141973708	141973910	.	-	.	Parent=gene2120
chr5	ENCODE	exon	142003862	142003950	.	-	.	Parent=gene2120
###
chr5	ENCODE	gene	141973754	142045815	.	-	.	ID=gene2121;Name=AC005370.1-013;name2=FGF1
chr5	ENCODE	CDS	141973754	141973876	.	-	0	Parent=gene2121
chr5	ENCODE	exon	141973754	141973910	.	-	.	Parent=gene2121
chr5	ENCODE	exon	142039673	142039816	.	-	.	Parent=gene2121
chr5	ENCODE	exon	142040460	142040598	.	-	.	Parent=gene2121
chr5	ENCODE	exon	142045706	142045815	.	-	.	Parent=gene2121
###
chr5	ENCODE	gene	142130133	142373874	.	+	.	ID=gene2122;Name=AC012630.1-001;name2=ARHGAP26
chr5	ENCODE	exon	142130133	142130664	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142233149	142233244	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142234859	142234920	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142239123	142239194	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142245047	142245148	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142253987	142254097	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142261684	142261788	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142263289	142263418	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142267453	142267553	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142272948	142273042	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142291796	142291874	.	+	.	Parent=gene2122
chr5	ENCODE	exon	142373838	142373874	.	+	.	Parent=gene2122
###
chr5	ENCODE	gene	142130156	142373874	.	+	.	ID=gene2123;Name=AC012630.1-008;name2=ARHGAP26
chr5	ENCODE	exon	142130156	142130664	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142233149	142233244	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142234859	142234920	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142239123	142239194	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142245047	142245148	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142253987	142254097	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142261684	142261788	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142263289	142263418	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142267453	142267553	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142272948	142273042	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142291796	142291874	.	+	.	Parent=gene2123
chr5	ENCODE	exon	142373838	142373874	.	+	.	Parent=gene2123
###
chr5	ENCODE	gene	142132466	142254084	.	+	.	ID=gene2124;Name=AC012630.1-014;name2=ARHGAP26
chr5	ENCODE	exon	142132466	142132599	.	+	.	Parent=gene2124
chr5	ENCODE	CDS	142132530	142132599	.	+	0	Parent=gene2124
chr5	ENCODE	exon	142233149	142233244	.	+	.	Parent=gene2124
chr5	ENCODE	CDS	142233149	142233244	.	+	2	Parent=gene2124
chr5	ENCODE	exon	142234859	142234920	.	+	.	Parent=gene2124
chr5	ENCODE	CDS	142234859	142234920	.	+	2	Parent=gene2124
chr5	ENCODE	exon	142239123	142239194	.	+	.	Parent=gene2124
chr5	ENCODE	CDS	142239123	142239194	.	+	0	Parent=gene2124
chr5	ENCODE	exon	142245047	142245148	.	+	.	Parent=gene2124
chr5	ENCODE	CDS	142245047	142245148	.	+	0	Parent=gene2124
chr5	ENCODE	exon	142253987	142254084	.	+	.	Parent=gene2124
chr5	ENCODE	CDS	142253987	142254084	.	+	0	Parent=gene2124
###
chr5	ENCODE	gene	142234642	142261762	.	+	.	ID=gene2125;Name=AC012630.1-003;name2=ARHGAP26
chr5	ENCODE	exon	142234642	142234920	.	+	.	Parent=gene2125
chr5	ENCODE	CDS	142234837	142234920	.	+	0	Parent=gene2125
chr5	ENCODE	exon	142239123	142239194	.	+	.	Parent=gene2125
chr5	ENCODE	CDS	142239123	142239194	.	+	0	Parent=gene2125
chr5	ENCODE	exon	142245047	142245148	.	+	.	Parent=gene2125
chr5	ENCODE	CDS	142245047	142245148	.	+	0	Parent=gene2125
chr5	ENCODE	exon	142253987	142254097	.	+	.	Parent=gene2125
chr5	ENCODE	CDS	142253987	142254097	.	+	0	Parent=gene2125
chr5	ENCODE	exon	142261684	142261762	.	+	.	Parent=gene2125
chr5	ENCODE	CDS	142261684	142261762	.	+	0	Parent=gene2125
###
chr5	ENCODE	gene	142263289	142281863	.	+	.	ID=gene2126;Name=AC012630.1-017;name2=ARHGAP26
chr5	ENCODE	exon	142263289	142263418	.	+	.	Parent=gene2126
chr5	ENCODE	exon	142267453	142267553	.	+	.	Parent=gene2126
chr5	ENCODE	exon	142272948	142273042	.	+	.	Parent=gene2126
chr5	ENCODE	exon	142281280	142281863	.	+	.	Parent=gene2126
###
chr5	ENCODE	gene	142267071	142373874	.	+	.	ID=gene2127;Name=AC012630.1-015;name2=ARHGAP26
chr5	ENCODE	exon	142267071	142267257	.	+	.	Parent=gene2127
chr5	ENCODE	exon	142267453	142267553	.	+	.	Parent=gene2127
chr5	ENCODE	exon	142272948	142273042	.	+	.	Parent=gene2127
chr5	ENCODE	exon	142291796	142291874	.	+	.	Parent=gene2127
chr5	ENCODE	exon	142373838	142373874	.	+	.	Parent=gene2127
###
chr5	ENCODE	gene	142267110	142291874	.	+	.	ID=gene2128;Name=AC012630.1-016;name2=ARHGAP26
chr5	ENCODE	exon	142267110	142267257	.	+	.	Parent=gene2128
chr5	ENCODE	exon	142267453	142267553	.	+	.	Parent=gene2128
chr5	ENCODE	exon	142272948	142273042	.	+	.	Parent=gene2128
chr5	ENCODE	exon	142275291	142275433	.	+	.	Parent=gene2128
chr5	ENCODE	exon	142291796	142291874	.	+	.	Parent=gene2128
###
chr5	ENCODE	gene	142267327	142373874	.	+	.	ID=gene2129;Name=AC012630.1-004;name2=ARHGAP26
chr5	ENCODE	exon	142267327	142267553	.	+	.	Parent=gene2129
chr5	ENCODE	exon	142272948	142273042	.	+	.	Parent=gene2129
chr5	ENCODE	exon	142291796	142291874	.	+	.	Parent=gene2129
chr5	ENCODE	exon	142373838	142373874	.	+	.	Parent=gene2129
###
chr5	ENCODE	gene	142268471	142373874	.	+	.	ID=gene2130;name2=ARHGAP26;Name=AC012630.1-005
chr5	ENCODE	exon	142268471	142268631	.	+	.	Parent=gene2130
chr5	ENCODE	exon	142272948	142273042	.	+	.	Parent=gene2130
chr5	ENCODE	exon	142291796	142291874	.	+	.	Parent=gene2130
chr5	ENCODE	exon	142373838	142373874	.	+	.	Parent=gene2130
###
chr5	ENCODE	gene	142329080	142374051	.	+	.	ID=gene2131;Name=AC012630.1-002;name2=ARHGAP26
chr5	ENCODE	exon	142329080	142329157	.	+	.	Parent=gene2131
chr5	ENCODE	exon	142373838	142374051	.	+	.	Parent=gene2131
###
chr5	ENCODE	gene	142370494	142374155	.	+	.	ID=gene2132;Name=AC012630.1-006;name2=ARHGAP26
chr5	ENCODE	exon	142370494	142370731	.	+	.	Parent=gene2132
chr5	ENCODE	exon	142373838	142374155	.	+	.	Parent=gene2132
###
chr5	ENCODE	gene	142373838	142373874	.	+	.	ID=gene2133;Name=AC012630.1-007;name2=ARHGAP26
chr5	ENCODE	exon	142373838	142373874	.	+	.	Parent=gene2133
###
chr6	ENCODE	gene	41411371	41426574	.	+	.	ID=gene2134;Name=RP1-149M18.2-001;name2=NCR2
chr6	ENCODE	exon	41411371	41411644	.	+	.	Parent=gene2134
chr6	ENCODE	CDS	41411593	41411644	.	+	0	Parent=gene2134
chr6	ENCODE	exon	41411803	41412144	.	+	.	Parent=gene2134
chr6	ENCODE	CDS	41411803	41412144	.	+	2	Parent=gene2134
chr6	ENCODE	exon	41417510	41417645	.	+	.	Parent=gene2134
chr6	ENCODE	CDS	41417510	41417645	.	+	2	Parent=gene2134
chr6	ENCODE	exon	41417752	41417865	.	+	.	Parent=gene2134
chr6	ENCODE	CDS	41417752	41417865	.	+	1	Parent=gene2134
chr6	ENCODE	exon	41418634	41418740	.	+	.	Parent=gene2134
chr6	ENCODE	CDS	41418634	41418740	.	+	1	Parent=gene2134
chr6	ENCODE	CDS	41426394	41426419	.	+	2	Parent=gene2134
chr6	ENCODE	exon	41426394	41426574	.	+	.	Parent=gene2134
###
chr6	ENCODE	gene	41411505	41426603	.	+	.	ID=gene2135;name2=NCR2;Name=RP1-149M18.2-003
chr6	ENCODE	exon	41411505	41411644	.	+	.	Parent=gene2135
chr6	ENCODE	CDS	41411593	41411644	.	+	0	Parent=gene2135
chr6	ENCODE	exon	41411803	41412144	.	+	.	Parent=gene2135
chr6	ENCODE	CDS	41411803	41412144	.	+	2	Parent=gene2135
chr6	ENCODE	exon	41417510	41417645	.	+	.	Parent=gene2135
chr6	ENCODE	CDS	41417510	41417645	.	+	2	Parent=gene2135
chr6	ENCODE	exon	41417752	41417865	.	+	.	Parent=gene2135
chr6	ENCODE	CDS	41417752	41417865	.	+	1	Parent=gene2135
chr6	ENCODE	CDS	41426394	41426580	.	+	1	Parent=gene2135
chr6	ENCODE	exon	41426394	41426603	.	+	.	Parent=gene2135
###
chr6	ENCODE	gene	41411567	41426580	.	+	.	ID=gene2136;Name=RP1-149M18.2-002;name2=NCR2
chr6	ENCODE	exon	41411567	41411644	.	+	.	Parent=gene2136
chr6	ENCODE	CDS	41411593	41411644	.	+	0	Parent=gene2136
chr6	ENCODE	exon	41411803	41412144	.	+	.	Parent=gene2136
chr6	ENCODE	CDS	41411803	41412144	.	+	2	Parent=gene2136
chr6	ENCODE	exon	41417510	41417645	.	+	.	Parent=gene2136
chr6	ENCODE	CDS	41417510	41417645	.	+	2	Parent=gene2136
chr6	ENCODE	exon	41417716	41417865	.	+	.	Parent=gene2136
chr6	ENCODE	CDS	41417716	41417865	.	+	1	Parent=gene2136
chr6	ENCODE	exon	41418634	41418740	.	+	.	Parent=gene2136
chr6	ENCODE	CDS	41418634	41418740	.	+	1	Parent=gene2136
chr6	ENCODE	CDS	41426394	41426419	.	+	2	Parent=gene2136
chr6	ENCODE	exon	41426394	41426580	.	+	.	Parent=gene2136
###
chr6	ENCODE	gene	41578160	41595568	.	+	.	ID=gene2137;Name=RP11-328M4.3-002;name2=RP11-328M4.3
chr6	ENCODE	exon	41578160	41578327	.	+	.	Parent=gene2137
chr6	ENCODE	CDS	41578275	41578327	.	+	0	Parent=gene2137
chr6	ENCODE	exon	41578519	41578689	.	+	.	Parent=gene2137
chr6	ENCODE	CDS	41578519	41578689	.	+	1	Parent=gene2137
chr6	ENCODE	CDS	41595092	41595119	.	+	1	Parent=gene2137
chr6	ENCODE	exon	41595092	41595568	.	+	.	Parent=gene2137
###
chr6	ENCODE	gene	41594089	41595568	.	+	.	ID=gene2138;Name=RP11-328M4.3-001;name2=RP11-328M4.3
chr6	ENCODE	exon	41594089	41594271	.	+	.	Parent=gene2138
chr6	ENCODE	exon	41595092	41595568	.	+	.	Parent=gene2138
###
chr6	ENCODE	gene	41622142	41678100	.	+	.	ID=gene2139;Name=RP11-328M4.1-001;name2=FOXP4
chr6	ENCODE	exon	41622142	41622583	.	+	.	Parent=gene2139
chr6	ENCODE	exon	41641461	41641680	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41641477	41641680	.	+	0	Parent=gene2139
chr6	ENCODE	exon	41653702	41653797	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41653702	41653797	.	+	0	Parent=gene2139
chr6	ENCODE	exon	41660485	41660607	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41660485	41660607	.	+	0	Parent=gene2139
chr6	ENCODE	exon	41661147	41661233	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41661147	41661233	.	+	0	Parent=gene2139
chr6	ENCODE	exon	41662725	41662872	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41662725	41662872	.	+	0	Parent=gene2139
chr6	ENCODE	exon	41663018	41663228	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41663018	41663228	.	+	2	Parent=gene2139
chr6	ENCODE	exon	41663509	41663613	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41663509	41663613	.	+	1	Parent=gene2139
chr6	ENCODE	exon	41664360	41664447	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41664360	41664447	.	+	1	Parent=gene2139
chr6	ENCODE	exon	41665487	41665570	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41665487	41665570	.	+	0	Parent=gene2139
chr6	ENCODE	exon	41665715	41665886	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41665715	41665886	.	+	0	Parent=gene2139
chr6	ENCODE	exon	41665987	41666063	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41665987	41666063	.	+	2	Parent=gene2139
chr6	ENCODE	exon	41666937	41667038	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41666937	41667038	.	+	0	Parent=gene2139
chr6	ENCODE	exon	41670586	41670707	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41670586	41670707	.	+	0	Parent=gene2139
chr6	ENCODE	exon	41672892	41672958	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41672892	41672958	.	+	1	Parent=gene2139
chr6	ENCODE	exon	41673497	41673666	.	+	.	Parent=gene2139
chr6	ENCODE	CDS	41673497	41673666	.	+	0	Parent=gene2139
chr6	ENCODE	CDS	41674505	41674652	.	+	1	Parent=gene2139
chr6	ENCODE	exon	41674505	41678100	.	+	.	Parent=gene2139
###
chr6	ENCODE	gene	41622364	41675679	.	+	.	ID=gene2140;Name=RP11-328M4.1-003;name2=FOXP4
chr6	ENCODE	exon	41622364	41622583	.	+	.	Parent=gene2140
chr6	ENCODE	exon	41641461	41641680	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41641477	41641680	.	+	0	Parent=gene2140
chr6	ENCODE	exon	41653702	41653797	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41653702	41653797	.	+	0	Parent=gene2140
chr6	ENCODE	exon	41660485	41660607	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41660485	41660607	.	+	0	Parent=gene2140
chr6	ENCODE	exon	41661153	41661233	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41661153	41661233	.	+	0	Parent=gene2140
chr6	ENCODE	exon	41662725	41662872	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41662725	41662872	.	+	0	Parent=gene2140
chr6	ENCODE	exon	41663015	41663228	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41663015	41663228	.	+	2	Parent=gene2140
chr6	ENCODE	exon	41663509	41663613	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41663509	41663613	.	+	1	Parent=gene2140
chr6	ENCODE	exon	41664360	41664447	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41664360	41664447	.	+	1	Parent=gene2140
chr6	ENCODE	exon	41665487	41665570	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41665487	41665570	.	+	0	Parent=gene2140
chr6	ENCODE	exon	41665679	41665886	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41665679	41665886	.	+	0	Parent=gene2140
chr6	ENCODE	exon	41665987	41666063	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41665987	41666063	.	+	2	Parent=gene2140
chr6	ENCODE	exon	41666937	41667038	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41666937	41667038	.	+	0	Parent=gene2140
chr6	ENCODE	exon	41670586	41670707	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41670586	41670707	.	+	0	Parent=gene2140
chr6	ENCODE	exon	41672892	41672958	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41672892	41672958	.	+	1	Parent=gene2140
chr6	ENCODE	exon	41673497	41673666	.	+	.	Parent=gene2140
chr6	ENCODE	CDS	41673497	41673666	.	+	0	Parent=gene2140
chr6	ENCODE	CDS	41674505	41674652	.	+	1	Parent=gene2140
chr6	ENCODE	exon	41674505	41675679	.	+	.	Parent=gene2140
###
chr6	ENCODE	gene	41641465	41676342	.	+	.	ID=gene2141;Name=RP11-328M4.1-002;name2=FOXP4
chr6	ENCODE	exon	41641465	41641680	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41641477	41641680	.	+	0	Parent=gene2141
chr6	ENCODE	exon	41653702	41653797	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41653702	41653797	.	+	0	Parent=gene2141
chr6	ENCODE	exon	41660485	41660607	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41660485	41660607	.	+	0	Parent=gene2141
chr6	ENCODE	exon	41661147	41661233	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41661147	41661233	.	+	0	Parent=gene2141
chr6	ENCODE	exon	41662725	41662872	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41662725	41662872	.	+	0	Parent=gene2141
chr6	ENCODE	exon	41663015	41663228	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41663015	41663228	.	+	2	Parent=gene2141
chr6	ENCODE	exon	41663509	41663613	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41663509	41663613	.	+	1	Parent=gene2141
chr6	ENCODE	exon	41664360	41664447	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41664360	41664447	.	+	1	Parent=gene2141
chr6	ENCODE	exon	41665487	41665570	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41665487	41665570	.	+	0	Parent=gene2141
chr6	ENCODE	exon	41665679	41665886	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41665679	41665886	.	+	0	Parent=gene2141
chr6	ENCODE	exon	41665987	41666063	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41665987	41666063	.	+	2	Parent=gene2141
chr6	ENCODE	exon	41666937	41667038	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41666937	41667038	.	+	0	Parent=gene2141
chr6	ENCODE	exon	41670586	41670707	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41670586	41670707	.	+	0	Parent=gene2141
chr6	ENCODE	exon	41672892	41672958	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41672892	41672958	.	+	1	Parent=gene2141
chr6	ENCODE	exon	41673497	41673666	.	+	.	Parent=gene2141
chr6	ENCODE	CDS	41673497	41673666	.	+	0	Parent=gene2141
chr6	ENCODE	CDS	41674505	41674652	.	+	1	Parent=gene2141
chr6	ENCODE	exon	41674505	41676342	.	+	.	Parent=gene2141
###
chr6	ENCODE	gene	41645890	41660534	.	+	.	ID=gene2142;Name=RP11-328M4.1-004;name2=FOXP4
chr6	ENCODE	exon	41645890	41646110	.	+	.	Parent=gene2142
chr6	ENCODE	CDS	41645994	41646110	.	+	0	Parent=gene2142
chr6	ENCODE	exon	41653702	41653797	.	+	.	Parent=gene2142
chr6	ENCODE	CDS	41653702	41653797	.	+	0	Parent=gene2142
chr6	ENCODE	exon	41660485	41660534	.	+	.	Parent=gene2142
chr6	ENCODE	CDS	41660485	41660534	.	+	0	Parent=gene2142
###
chr6	ENCODE	gene	41663159	41675682	.	+	.	ID=gene2143;Name=RP11-328M4.1-005;name2=FOXP4
chr6	ENCODE	exon	41663159	41663228	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41663509	41663613	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41664360	41664447	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41665487	41665570	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41665715	41665886	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41665987	41666063	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41666937	41667038	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41670586	41670707	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41672892	41672958	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41673497	41673632	.	+	.	Parent=gene2143
chr6	ENCODE	exon	41675540	41675682	.	+	.	Parent=gene2143
###
chr6	ENCODE	gene	41712598	41729190	.	+	.	ID=gene2144;Name=RP4-696P19.1-005;name2=MDFI
chr6	ENCODE	exon	41712598	41712649	.	+	.	Parent=gene2144
chr6	ENCODE	exon	41714455	41714541	.	+	.	Parent=gene2144
chr6	ENCODE	CDS	41714466	41714541	.	+	0	Parent=gene2144
chr6	ENCODE	exon	41721842	41722024	.	+	.	Parent=gene2144
chr6	ENCODE	CDS	41721842	41722024	.	+	2	Parent=gene2144
chr6	ENCODE	exon	41725335	41725559	.	+	.	Parent=gene2144
chr6	ENCODE	CDS	41725335	41725559	.	+	2	Parent=gene2144
chr6	ENCODE	exon	41729035	41729190	.	+	.	Parent=gene2144
chr6	ENCODE	CDS	41729035	41729190	.	+	2	Parent=gene2144
###
chr6	ENCODE	gene	41712748	41729244	.	+	.	ID=gene2145;Name=RP4-696P19.1-003;name2=MDFI
chr6	ENCODE	exon	41712748	41712989	.	+	.	Parent=gene2145
chr6	ENCODE	exon	41713856	41714091	.	+	.	Parent=gene2145
chr6	ENCODE	exon	41714455	41714541	.	+	.	Parent=gene2145
chr6	ENCODE	CDS	41714466	41714541	.	+	0	Parent=gene2145
chr6	ENCODE	exon	41721842	41722024	.	+	.	Parent=gene2145
chr6	ENCODE	CDS	41721842	41722024	.	+	2	Parent=gene2145
chr6	ENCODE	exon	41725335	41725559	.	+	.	Parent=gene2145
chr6	ENCODE	CDS	41725335	41725559	.	+	2	Parent=gene2145
chr6	ENCODE	exon	41729035	41729244	.	+	.	Parent=gene2145
chr6	ENCODE	CDS	41729035	41729244	.	+	2	Parent=gene2145
###
chr6	ENCODE	gene	41712784	41729955	.	+	.	ID=gene2146;Name=RP4-696P19.1-008;name2=MDFI
chr6	ENCODE	exon	41712784	41712989	.	+	.	Parent=gene2146
chr6	ENCODE	exon	41714455	41714541	.	+	.	Parent=gene2146
chr6	ENCODE	CDS	41714466	41714541	.	+	0	Parent=gene2146
chr6	ENCODE	exon	41721842	41722024	.	+	.	Parent=gene2146
chr6	ENCODE	CDS	41721842	41722024	.	+	2	Parent=gene2146
chr6	ENCODE	exon	41725335	41725559	.	+	.	Parent=gene2146
chr6	ENCODE	CDS	41725335	41725559	.	+	2	Parent=gene2146
chr6	ENCODE	CDS	41729035	41729291	.	+	2	Parent=gene2146
chr6	ENCODE	exon	41729035	41729955	.	+	.	Parent=gene2146
###
chr6	ENCODE	gene	41714154	41725369	.	+	.	ID=gene2147;Name=RP4-696P19.1-009;name2=MDFI
chr6	ENCODE	exon	41714154	41714201	.	+	.	Parent=gene2147
chr6	ENCODE	exon	41714455	41714541	.	+	.	Parent=gene2147
chr6	ENCODE	CDS	41714466	41714541	.	+	0	Parent=gene2147
chr6	ENCODE	exon	41721842	41722024	.	+	.	Parent=gene2147
chr6	ENCODE	CDS	41721842	41722024	.	+	2	Parent=gene2147
chr6	ENCODE	exon	41725335	41725369	.	+	.	Parent=gene2147
chr6	ENCODE	CDS	41725335	41725369	.	+	2	Parent=gene2147
###
chr6	ENCODE	gene	41714163	41729962	.	+	.	ID=gene2148;Name=RP4-696P19.1-001;name2=MDFI
chr6	ENCODE	exon	41714163	41714368	.	+	.	Parent=gene2148
chr6	ENCODE	exon	41714455	41714541	.	+	.	Parent=gene2148
chr6	ENCODE	CDS	41714466	41714541	.	+	0	Parent=gene2148
chr6	ENCODE	exon	41721842	41722024	.	+	.	Parent=gene2148
chr6	ENCODE	CDS	41721842	41722024	.	+	2	Parent=gene2148
chr6	ENCODE	exon	41725335	41725559	.	+	.	Parent=gene2148
chr6	ENCODE	CDS	41725335	41725559	.	+	2	Parent=gene2148
chr6	ENCODE	CDS	41729035	41729291	.	+	2	Parent=gene2148
chr6	ENCODE	exon	41729035	41729962	.	+	.	Parent=gene2148
###
chr6	ENCODE	gene	41714193	41729355	.	+	.	ID=gene2149;name2=MDFI;Name=RP4-696P19.1-002
chr6	ENCODE	exon	41714193	41714368	.	+	.	Parent=gene2149
chr6	ENCODE	exon	41714455	41714541	.	+	.	Parent=gene2149
chr6	ENCODE	CDS	41714466	41714541	.	+	0	Parent=gene2149
chr6	ENCODE	exon	41725335	41725559	.	+	.	Parent=gene2149
chr6	ENCODE	CDS	41725335	41725559	.	+	2	Parent=gene2149
chr6	ENCODE	CDS	41729035	41729291	.	+	2	Parent=gene2149
chr6	ENCODE	exon	41729035	41729355	.	+	.	Parent=gene2149
###
chr6	ENCODE	gene	41714215	41725459	.	+	.	ID=gene2150;Name=RP4-696P19.1-006;name2=MDFI
chr6	ENCODE	exon	41714215	41714541	.	+	.	Parent=gene2150
chr6	ENCODE	CDS	41714466	41714541	.	+	0	Parent=gene2150
chr6	ENCODE	exon	41721842	41722024	.	+	.	Parent=gene2150
chr6	ENCODE	CDS	41721842	41722024	.	+	2	Parent=gene2150
chr6	ENCODE	exon	41725335	41725459	.	+	.	Parent=gene2150
chr6	ENCODE	CDS	41725335	41725459	.	+	2	Parent=gene2150
###
chr6	ENCODE	gene	41714243	41729160	.	+	.	ID=gene2151;Name=RP4-696P19.1-007;name2=MDFI
chr6	ENCODE	exon	41714243	41714541	.	+	.	Parent=gene2151
chr6	ENCODE	CDS	41714466	41714541	.	+	0	Parent=gene2151
chr6	ENCODE	exon	41725335	41725559	.	+	.	Parent=gene2151
chr6	ENCODE	CDS	41725335	41725559	.	+	2	Parent=gene2151
chr6	ENCODE	exon	41729035	41729160	.	+	.	Parent=gene2151
chr6	ENCODE	CDS	41729035	41729160	.	+	2	Parent=gene2151
###
chr6	ENCODE	gene	41721970	41725828	.	+	.	ID=gene2152;Name=RP4-696P19.1-004;name2=MDFI
chr6	ENCODE	exon	41721970	41722024	.	+	.	Parent=gene2152
chr6	ENCODE	exon	41725335	41725828	.	+	.	Parent=gene2152
###
chr6	ENCODE	gene	41759694	41766758	.	-	.	ID=gene2153;Name=RP4-696P19.3-003;name2=TFEB
chr6	ENCODE	exon	41759694	41760794	.	-	.	Parent=gene2153
chr6	ENCODE	CDS	41760315	41760794	.	-	0	Parent=gene2153
chr6	ENCODE	exon	41761806	41761953	.	-	.	Parent=gene2153
chr6	ENCODE	CDS	41761806	41761953	.	-	1	Parent=gene2153
chr6	ENCODE	exon	41762810	41762885	.	-	.	Parent=gene2153
chr6	ENCODE	CDS	41762810	41762885	.	-	2	Parent=gene2153
chr6	ENCODE	exon	41763469	41763525	.	-	.	Parent=gene2153
chr6	ENCODE	CDS	41763469	41763525	.	-	2	Parent=gene2153
chr6	ENCODE	exon	41763624	41763744	.	-	.	Parent=gene2153
chr6	ENCODE	CDS	41763624	41763744	.	-	0	Parent=gene2153
chr6	ENCODE	exon	41765447	41765527	.	-	.	Parent=gene2153
chr6	ENCODE	CDS	41765447	41765527	.	-	0	Parent=gene2153
chr6	ENCODE	exon	41766717	41766758	.	-	.	Parent=gene2153
chr6	ENCODE	CDS	41766717	41766758	.	-	0	Parent=gene2153
###
chr6	ENCODE	gene	41759694	41767192	.	-	.	ID=gene2154;Name=RP4-696P19.3-015;name2=TFEB
chr6	ENCODE	exon	41759694	41760794	.	-	.	Parent=gene2154
chr6	ENCODE	CDS	41760315	41760794	.	-	0	Parent=gene2154
chr6	ENCODE	exon	41761806	41761953	.	-	.	Parent=gene2154
chr6	ENCODE	CDS	41761806	41761953	.	-	1	Parent=gene2154
chr6	ENCODE	exon	41762810	41762885	.	-	.	Parent=gene2154
chr6	ENCODE	CDS	41762810	41762885	.	-	2	Parent=gene2154
chr6	ENCODE	exon	41763469	41763525	.	-	.	Parent=gene2154
chr6	ENCODE	CDS	41763469	41763525	.	-	2	Parent=gene2154
chr6	ENCODE	exon	41763624	41763744	.	-	.	Parent=gene2154
chr6	ENCODE	CDS	41763624	41763744	.	-	0	Parent=gene2154
chr6	ENCODE	exon	41765447	41765527	.	-	.	Parent=gene2154
chr6	ENCODE	CDS	41765447	41765527	.	-	0	Parent=gene2154
chr6	ENCODE	exon	41766379	41766633	.	-	.	Parent=gene2154
chr6	ENCODE	CDS	41766379	41766633	.	-	0	Parent=gene2154
chr6	ENCODE	CDS	41766717	41767130	.	-	0	Parent=gene2154
chr6	ENCODE	exon	41766717	41767192	.	-	.	Parent=gene2154
###
chr6	ENCODE	gene	41759694	41810776	.	-	.	ID=gene2155;Name=RP4-696P19.3-001;name2=TFEB
chr6	ENCODE	exon	41759694	41760794	.	-	.	Parent=gene2155
chr6	ENCODE	CDS	41760315	41760794	.	-	0	Parent=gene2155
chr6	ENCODE	exon	41761806	41761953	.	-	.	Parent=gene2155
chr6	ENCODE	CDS	41761806	41761953	.	-	1	Parent=gene2155
chr6	ENCODE	exon	41762810	41762885	.	-	.	Parent=gene2155
chr6	ENCODE	CDS	41762810	41762885	.	-	2	Parent=gene2155
chr6	ENCODE	exon	41763469	41763525	.	-	.	Parent=gene2155
chr6	ENCODE	CDS	41763469	41763525	.	-	2	Parent=gene2155
chr6	ENCODE	exon	41763624	41763744	.	-	.	Parent=gene2155
chr6	ENCODE	CDS	41763624	41763744	.	-	0	Parent=gene2155
chr6	ENCODE	exon	41765447	41765527	.	-	.	Parent=gene2155
chr6	ENCODE	CDS	41765447	41765527	.	-	0	Parent=gene2155
chr6	ENCODE	exon	41766379	41766633	.	-	.	Parent=gene2155
chr6	ENCODE	CDS	41766379	41766633	.	-	0	Parent=gene2155
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2155
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2155
chr6	ENCODE	exon	41808365	41808483	.	-	.	Parent=gene2155
chr6	ENCODE	exon	41810616	41810776	.	-	.	Parent=gene2155
###
chr6	ENCODE	gene	41759694	41811975	.	-	.	ID=gene2156;Name=RP4-696P19.3-010;name2=TFEB
chr6	ENCODE	exon	41759694	41760794	.	-	.	Parent=gene2156
chr6	ENCODE	CDS	41760315	41760794	.	-	0	Parent=gene2156
chr6	ENCODE	exon	41761806	41761953	.	-	.	Parent=gene2156
chr6	ENCODE	CDS	41761806	41761953	.	-	1	Parent=gene2156
chr6	ENCODE	exon	41762810	41762885	.	-	.	Parent=gene2156
chr6	ENCODE	CDS	41762810	41762885	.	-	2	Parent=gene2156
chr6	ENCODE	exon	41763469	41763525	.	-	.	Parent=gene2156
chr6	ENCODE	CDS	41763469	41763525	.	-	2	Parent=gene2156
chr6	ENCODE	exon	41763624	41763744	.	-	.	Parent=gene2156
chr6	ENCODE	CDS	41763624	41763744	.	-	0	Parent=gene2156
chr6	ENCODE	exon	41765447	41765527	.	-	.	Parent=gene2156
chr6	ENCODE	CDS	41765447	41765527	.	-	0	Parent=gene2156
chr6	ENCODE	exon	41766379	41766633	.	-	.	Parent=gene2156
chr6	ENCODE	CDS	41766379	41766633	.	-	0	Parent=gene2156
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2156
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2156
chr6	ENCODE	exon	41811862	41811975	.	-	.	Parent=gene2156
###
chr6	ENCODE	gene	41759696	41811324	.	-	.	ID=gene2157;Name=RP4-696P19.3-005;name2=TFEB
chr6	ENCODE	exon	41759696	41760794	.	-	.	Parent=gene2157
chr6	ENCODE	CDS	41760315	41760794	.	-	0	Parent=gene2157
chr6	ENCODE	exon	41761806	41761953	.	-	.	Parent=gene2157
chr6	ENCODE	CDS	41761806	41761953	.	-	1	Parent=gene2157
chr6	ENCODE	exon	41762810	41762885	.	-	.	Parent=gene2157
chr6	ENCODE	CDS	41762810	41762885	.	-	2	Parent=gene2157
chr6	ENCODE	exon	41763469	41763525	.	-	.	Parent=gene2157
chr6	ENCODE	CDS	41763469	41763525	.	-	2	Parent=gene2157
chr6	ENCODE	exon	41763624	41763744	.	-	.	Parent=gene2157
chr6	ENCODE	CDS	41763624	41763744	.	-	0	Parent=gene2157
chr6	ENCODE	exon	41765447	41765527	.	-	.	Parent=gene2157
chr6	ENCODE	CDS	41765447	41765527	.	-	0	Parent=gene2157
chr6	ENCODE	exon	41766379	41766633	.	-	.	Parent=gene2157
chr6	ENCODE	CDS	41766379	41766633	.	-	0	Parent=gene2157
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2157
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2157
chr6	ENCODE	exon	41811066	41811324	.	-	.	Parent=gene2157
###
chr6	ENCODE	gene	41762245	41809569	.	-	.	ID=gene2158;Name=RP4-696P19.3-004;name2=TFEB
chr6	ENCODE	exon	41762245	41762885	.	-	.	Parent=gene2158
chr6	ENCODE	CDS	41762806	41762885	.	-	2	Parent=gene2158
chr6	ENCODE	exon	41763469	41763525	.	-	.	Parent=gene2158
chr6	ENCODE	CDS	41763469	41763525	.	-	2	Parent=gene2158
chr6	ENCODE	exon	41763624	41763744	.	-	.	Parent=gene2158
chr6	ENCODE	CDS	41763624	41763744	.	-	0	Parent=gene2158
chr6	ENCODE	exon	41765447	41765527	.	-	.	Parent=gene2158
chr6	ENCODE	CDS	41765447	41765527	.	-	0	Parent=gene2158
chr6	ENCODE	exon	41766379	41766633	.	-	.	Parent=gene2158
chr6	ENCODE	CDS	41766379	41766633	.	-	0	Parent=gene2158
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2158
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2158
chr6	ENCODE	exon	41808365	41809569	.	-	.	Parent=gene2158
###
chr6	ENCODE	gene	41762810	41763916	.	-	.	ID=gene2159;name2=TFEB;Name=RP4-696P19.3-007
chr6	ENCODE	exon	41762810	41762885	.	-	.	Parent=gene2159
chr6	ENCODE	exon	41763469	41763916	.	-	.	Parent=gene2159
###
chr6	ENCODE	gene	41762810	41810117	.	-	.	ID=gene2160;Name=RP4-696P19.3-006;name2=TFEB
chr6	ENCODE	exon	41762810	41762885	.	-	.	Parent=gene2160
chr6	ENCODE	CDS	41762810	41762885	.	-	2	Parent=gene2160
chr6	ENCODE	exon	41763469	41763525	.	-	.	Parent=gene2160
chr6	ENCODE	CDS	41763469	41763525	.	-	2	Parent=gene2160
chr6	ENCODE	exon	41763624	41763744	.	-	.	Parent=gene2160
chr6	ENCODE	CDS	41763624	41763744	.	-	0	Parent=gene2160
chr6	ENCODE	exon	41765447	41765527	.	-	.	Parent=gene2160
chr6	ENCODE	CDS	41765447	41765527	.	-	0	Parent=gene2160
chr6	ENCODE	exon	41766379	41766633	.	-	.	Parent=gene2160
chr6	ENCODE	CDS	41766379	41766633	.	-	0	Parent=gene2160
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2160
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2160
chr6	ENCODE	exon	41810029	41810117	.	-	.	Parent=gene2160
###
chr6	ENCODE	gene	41762879	41799442	.	-	.	ID=gene2161;Name=RP4-696P19.3-008;name2=TFEB
chr6	ENCODE	exon	41762879	41762885	.	-	.	Parent=gene2161
chr6	ENCODE	CDS	41762879	41762885	.	-	2	Parent=gene2161
chr6	ENCODE	exon	41763469	41763525	.	-	.	Parent=gene2161
chr6	ENCODE	CDS	41763469	41763525	.	-	2	Parent=gene2161
chr6	ENCODE	exon	41763624	41763744	.	-	.	Parent=gene2161
chr6	ENCODE	CDS	41763624	41763744	.	-	0	Parent=gene2161
chr6	ENCODE	exon	41765447	41765527	.	-	.	Parent=gene2161
chr6	ENCODE	CDS	41765447	41765527	.	-	0	Parent=gene2161
chr6	ENCODE	exon	41766379	41766633	.	-	.	Parent=gene2161
chr6	ENCODE	CDS	41766379	41766633	.	-	0	Parent=gene2161
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2161
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2161
chr6	ENCODE	exon	41799177	41799442	.	-	.	Parent=gene2161
###
chr6	ENCODE	gene	41763626	41781656	.	-	.	ID=gene2162;Name=RP4-696P19.3-002;name2=TFEB
chr6	ENCODE	exon	41763626	41763744	.	-	.	Parent=gene2162
chr6	ENCODE	CDS	41763626	41763744	.	-	0	Parent=gene2162
chr6	ENCODE	exon	41765447	41765527	.	-	.	Parent=gene2162
chr6	ENCODE	CDS	41765447	41765527	.	-	0	Parent=gene2162
chr6	ENCODE	exon	41766379	41766633	.	-	.	Parent=gene2162
chr6	ENCODE	CDS	41766379	41766633	.	-	0	Parent=gene2162
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2162
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2162
chr6	ENCODE	exon	41781363	41781656	.	-	.	Parent=gene2162
###
chr6	ENCODE	gene	41766610	41809406	.	-	.	ID=gene2163;Name=RP4-696P19.3-014;name2=TFEB
chr6	ENCODE	exon	41766610	41766633	.	-	.	Parent=gene2163
chr6	ENCODE	CDS	41766610	41766633	.	-	0	Parent=gene2163
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2163
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2163
chr6	ENCODE	exon	41808365	41808455	.	-	.	Parent=gene2163
chr6	ENCODE	exon	41809380	41809406	.	-	.	Parent=gene2163
###
chr6	ENCODE	gene	41766717	41781656	.	-	.	ID=gene2164;Name=RP4-696P19.3-009;name2=TFEB
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2164
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2164
chr6	ENCODE	exon	41781363	41781468	.	-	.	Parent=gene2164
chr6	ENCODE	exon	41781633	41781656	.	-	.	Parent=gene2164
###
chr6	ENCODE	gene	41766717	41792987	.	-	.	ID=gene2165;Name=RP4-696P19.3-016;name2=TFEB
chr6	ENCODE	CDS	41766717	41766929	.	-	0	Parent=gene2165
chr6	ENCODE	exon	41766717	41766951	.	-	.	Parent=gene2165
chr6	ENCODE	exon	41792883	41792987	.	-	.	Parent=gene2165
###
chr6	ENCODE	gene	41766832	41810776	.	-	.	ID=gene2166;Name=RP4-696P19.3-011;name2=TFEB
chr6	ENCODE	CDS	41766832	41766929	.	-	0	Parent=gene2166
chr6	ENCODE	exon	41766832	41766951	.	-	.	Parent=gene2166
chr6	ENCODE	exon	41810616	41810776	.	-	.	Parent=gene2166
###
chr6	ENCODE	gene	41766894	41809544	.	-	.	ID=gene2167;Name=RP4-696P19.3-013;name2=TFEB
chr6	ENCODE	CDS	41766894	41766929	.	-	0	Parent=gene2167
chr6	ENCODE	exon	41766894	41766951	.	-	.	Parent=gene2167
chr6	ENCODE	exon	41809380	41809544	.	-	.	Parent=gene2167
###
chr6	ENCODE	gene	41766894	41809910	.	-	.	ID=gene2168;Name=RP4-696P19.3-012;name2=TFEB
chr6	ENCODE	CDS	41766894	41766929	.	-	0	Parent=gene2168
chr6	ENCODE	exon	41766894	41766951	.	-	.	Parent=gene2168
chr6	ENCODE	exon	41809801	41809910	.	-	.	Parent=gene2168
###
chr6	ENCODE	gene	41812427	41823113	.	-	.	ID=gene2169;Name=RP11-298J23.1-001;name2=PGC
chr6	ENCODE	exon	41812427	41812720	.	-	.	Parent=gene2169
chr6	ENCODE	CDS	41812568	41812720	.	-	0	Parent=gene2169
chr6	ENCODE	exon	41813446	41813544	.	-	.	Parent=gene2169
chr6	ENCODE	CDS	41813446	41813544	.	-	0	Parent=gene2169
chr6	ENCODE	exon	41815515	41815662	.	-	.	Parent=gene2169
chr6	ENCODE	CDS	41815515	41815662	.	-	1	Parent=gene2169
chr6	ENCODE	exon	41816207	41816326	.	-	.	Parent=gene2169
chr6	ENCODE	CDS	41816207	41816326	.	-	1	Parent=gene2169
chr6	ENCODE	exon	41818006	41818205	.	-	.	Parent=gene2169
chr6	ENCODE	CDS	41818006	41818205	.	-	0	Parent=gene2169
chr6	ENCODE	exon	41818987	41819105	.	-	.	Parent=gene2169
chr6	ENCODE	CDS	41818987	41819105	.	-	2	Parent=gene2169
chr6	ENCODE	exon	41820113	41820230	.	-	.	Parent=gene2169
chr6	ENCODE	CDS	41820113	41820230	.	-	0	Parent=gene2169
chr6	ENCODE	exon	41820374	41820524	.	-	.	Parent=gene2169
chr6	ENCODE	CDS	41820374	41820524	.	-	1	Parent=gene2169
chr6	ENCODE	CDS	41822992	41823050	.	-	0	Parent=gene2169
chr6	ENCODE	exon	41822992	41823113	.	-	.	Parent=gene2169
###
chr6	ENCODE	gene	41812428	41823099	.	-	.	ID=gene2170;Name=RP11-298J23.1-002;name2=PGC
chr6	ENCODE	exon	41812428	41812541	.	-	.	Parent=gene2170
chr6	ENCODE	exon	41820156	41820230	.	-	.	Parent=gene2170
chr6	ENCODE	exon	41820374	41820524	.	-	.	Parent=gene2170
chr6	ENCODE	exon	41822992	41823099	.	-	.	Parent=gene2170
###
chr6	ENCODE	gene	41816318	41823111	.	-	.	ID=gene2171;Name=RP11-298J23.1-003;name2=PGC
chr6	ENCODE	exon	41816318	41816326	.	-	.	Parent=gene2171
chr6	ENCODE	CDS	41816318	41816326	.	-	1	Parent=gene2171
chr6	ENCODE	exon	41818006	41818205	.	-	.	Parent=gene2171
chr6	ENCODE	CDS	41818006	41818205	.	-	0	Parent=gene2171
chr6	ENCODE	exon	41820374	41820524	.	-	.	Parent=gene2171
chr6	ENCODE	CDS	41820374	41820524	.	-	1	Parent=gene2171
chr6	ENCODE	CDS	41822992	41823050	.	-	0	Parent=gene2171
chr6	ENCODE	exon	41822992	41823111	.	-	.	Parent=gene2171
###
chr6	ENCODE	gene	41820195	41829825	.	-	.	ID=gene2172;Name=RP11-298J23.1-004;name2=PGC
chr6	ENCODE	exon	41820195	41820230	.	-	.	Parent=gene2172
chr6	ENCODE	CDS	41820195	41820230	.	-	0	Parent=gene2172
chr6	ENCODE	exon	41820374	41820524	.	-	.	Parent=gene2172
chr6	ENCODE	CDS	41820374	41820524	.	-	1	Parent=gene2172
chr6	ENCODE	CDS	41829614	41829684	.	-	0	Parent=gene2172
chr6	ENCODE	exon	41829614	41829825	.	-	.	Parent=gene2172
###
chr6	ENCODE	gene	41845892	41855616	.	-	.	ID=gene2173;name2=FRS3;Name=RP11-298J23.2-001
chr6	ENCODE	exon	41845892	41847249	.	-	.	Parent=gene2173
chr6	ENCODE	CDS	41846335	41847249	.	-	0	Parent=gene2173
chr6	ENCODE	exon	41847532	41847680	.	-	.	Parent=gene2173
chr6	ENCODE	CDS	41847532	41847680	.	-	2	Parent=gene2173
chr6	ENCODE	exon	41848514	41848675	.	-	.	Parent=gene2173
chr6	ENCODE	CDS	41848514	41848675	.	-	2	Parent=gene2173
chr6	ENCODE	exon	41851135	41851321	.	-	.	Parent=gene2173
chr6	ENCODE	CDS	41851135	41851321	.	-	0	Parent=gene2173
chr6	ENCODE	CDS	41852638	41852703	.	-	0	Parent=gene2173
chr6	ENCODE	exon	41852638	41852726	.	-	.	Parent=gene2173
chr6	ENCODE	exon	41853749	41853892	.	-	.	Parent=gene2173
chr6	ENCODE	exon	41855532	41855616	.	-	.	Parent=gene2173
###
chr6	ENCODE	gene	41848560	41856182	.	-	.	ID=gene2174;Name=RP11-298J23.2-004;name2=FRS3
chr6	ENCODE	exon	41848560	41848675	.	-	.	Parent=gene2174
chr6	ENCODE	CDS	41848560	41848675	.	-	2	Parent=gene2174
chr6	ENCODE	exon	41851135	41851321	.	-	.	Parent=gene2174
chr6	ENCODE	CDS	41851135	41851321	.	-	0	Parent=gene2174
chr6	ENCODE	CDS	41852638	41852703	.	-	0	Parent=gene2174
chr6	ENCODE	exon	41852638	41852726	.	-	.	Parent=gene2174
chr6	ENCODE	exon	41856101	41856182	.	-	.	Parent=gene2174
###
chr6	ENCODE	gene	41851279	41862258	.	-	.	ID=gene2175;Name=RP11-298J23.2-005;name2=FRS3
chr6	ENCODE	exon	41851279	41851321	.	-	.	Parent=gene2175
chr6	ENCODE	CDS	41851279	41851321	.	-	0	Parent=gene2175
chr6	ENCODE	CDS	41852638	41852703	.	-	0	Parent=gene2175
chr6	ENCODE	exon	41852638	41852726	.	-	.	Parent=gene2175
chr6	ENCODE	exon	41853749	41853892	.	-	.	Parent=gene2175
chr6	ENCODE	exon	41862209	41862258	.	-	.	Parent=gene2175
###
chr6	ENCODE	gene	41852135	41853892	.	-	.	ID=gene2176;Name=RP11-298J23.2-003;name2=FRS3
chr6	ENCODE	exon	41852135	41852338	.	-	.	Parent=gene2176
chr6	ENCODE	exon	41852638	41852726	.	-	.	Parent=gene2176
chr6	ENCODE	exon	41853201	41853543	.	-	.	Parent=gene2176
chr6	ENCODE	exon	41853749	41853892	.	-	.	Parent=gene2176
###
chr6	ENCODE	gene	41856065	41865857	.	+	.	ID=gene2177;Name=RP11-298J23.3-003;name2=C6orf49
chr6	ENCODE	exon	41856065	41856542	.	+	.	Parent=gene2177
chr6	ENCODE	exon	41857066	41857236	.	+	.	Parent=gene2177
chr6	ENCODE	exon	41859178	41859321	.	+	.	Parent=gene2177
chr6	ENCODE	exon	41859450	41859954	.	+	.	Parent=gene2177
chr6	ENCODE	exon	41860651	41860788	.	+	.	Parent=gene2177
chr6	ENCODE	exon	41861053	41861256	.	+	.	Parent=gene2177
chr6	ENCODE	exon	41861844	41862048	.	+	.	Parent=gene2177
chr6	ENCODE	exon	41862156	41863541	.	+	.	Parent=gene2177
chr6	ENCODE	exon	41864948	41865052	.	+	.	Parent=gene2177
chr6	ENCODE	exon	41865247	41865857	.	+	.	Parent=gene2177
###
chr6	ENCODE	gene	41856488	41865607	.	+	.	ID=gene2178;Name=RP11-298J23.3-004;name2=C6orf49
chr6	ENCODE	exon	41856488	41856542	.	+	.	Parent=gene2178
chr6	ENCODE	exon	41857066	41857236	.	+	.	Parent=gene2178
chr6	ENCODE	exon	41859178	41859954	.	+	.	Parent=gene2178
chr6	ENCODE	exon	41860651	41860788	.	+	.	Parent=gene2178
chr6	ENCODE	exon	41861053	41861256	.	+	.	Parent=gene2178
chr6	ENCODE	exon	41861844	41862048	.	+	.	Parent=gene2178
chr6	ENCODE	exon	41862478	41863541	.	+	.	Parent=gene2178
chr6	ENCODE	exon	41864948	41865052	.	+	.	Parent=gene2178
chr6	ENCODE	exon	41865284	41865607	.	+	.	Parent=gene2178
###
chr6	ENCODE	gene	41856662	41865611	.	+	.	ID=gene2179;Name=RP11-298J23.3-001;name2=C6orf49
chr6	ENCODE	exon	41856662	41857236	.	+	.	Parent=gene2179
chr6	ENCODE	exon	41859178	41859321	.	+	.	Parent=gene2179
chr6	ENCODE	exon	41859847	41859954	.	+	.	Parent=gene2179
chr6	ENCODE	exon	41860651	41860788	.	+	.	Parent=gene2179
chr6	ENCODE	exon	41861053	41861256	.	+	.	Parent=gene2179
chr6	ENCODE	exon	41861844	41862048	.	+	.	Parent=gene2179
chr6	ENCODE	exon	41862478	41863541	.	+	.	Parent=gene2179
chr6	ENCODE	exon	41864948	41865052	.	+	.	Parent=gene2179
chr6	ENCODE	exon	41865284	41865611	.	+	.	Parent=gene2179
###
chr6	ENCODE	gene	41859190	41862845	.	+	.	ID=gene2180;Name=RP11-298J23.3-006;name2=C6orf49
chr6	ENCODE	exon	41859190	41859321	.	+	.	Parent=gene2180
chr6	ENCODE	CDS	41859190	41859321	.	+	0	Parent=gene2180
chr6	ENCODE	exon	41859847	41859954	.	+	.	Parent=gene2180
chr6	ENCODE	CDS	41859847	41859954	.	+	0	Parent=gene2180
chr6	ENCODE	exon	41860651	41860788	.	+	.	Parent=gene2180
chr6	ENCODE	CDS	41860651	41860788	.	+	0	Parent=gene2180
chr6	ENCODE	exon	41861053	41861256	.	+	.	Parent=gene2180
chr6	ENCODE	CDS	41861053	41861256	.	+	0	Parent=gene2180
chr6	ENCODE	exon	41861844	41862048	.	+	.	Parent=gene2180
chr6	ENCODE	CDS	41861844	41862048	.	+	0	Parent=gene2180
chr6	ENCODE	exon	41862478	41862845	.	+	.	Parent=gene2180
chr6	ENCODE	CDS	41862478	41862845	.	+	2	Parent=gene2180
###
chr6	ENCODE	gene	41859835	41862427	.	+	.	ID=gene2181;Name=RP11-298J23.3-008;name2=C6orf49
chr6	ENCODE	exon	41859835	41859954	.	+	.	Parent=gene2181
chr6	ENCODE	CDS	41859835	41859954	.	+	0	Parent=gene2181
chr6	ENCODE	exon	41860651	41860788	.	+	.	Parent=gene2181
chr6	ENCODE	CDS	41860651	41860788	.	+	0	Parent=gene2181
chr6	ENCODE	exon	41861053	41861256	.	+	.	Parent=gene2181
chr6	ENCODE	CDS	41861053	41861256	.	+	0	Parent=gene2181
chr6	ENCODE	exon	41861844	41862048	.	+	.	Parent=gene2181
chr6	ENCODE	CDS	41861844	41862048	.	+	0	Parent=gene2181
chr6	ENCODE	exon	41862156	41862427	.	+	.	Parent=gene2181
chr6	ENCODE	CDS	41862156	41862427	.	+	2	Parent=gene2181
###
chr6	ENCODE	gene	41859835	41862845	.	+	.	ID=gene2182;name2=C6orf49;Name=RP11-298J23.3-007
chr6	ENCODE	exon	41859835	41859954	.	+	.	Parent=gene2182
chr6	ENCODE	CDS	41859835	41859954	.	+	0	Parent=gene2182
chr6	ENCODE	exon	41860651	41860788	.	+	.	Parent=gene2182
chr6	ENCODE	CDS	41860651	41860788	.	+	0	Parent=gene2182
chr6	ENCODE	exon	41861053	41861256	.	+	.	Parent=gene2182
chr6	ENCODE	CDS	41861053	41861256	.	+	0	Parent=gene2182
chr6	ENCODE	exon	41861844	41862048	.	+	.	Parent=gene2182
chr6	ENCODE	CDS	41861844	41862048	.	+	0	Parent=gene2182
chr6	ENCODE	exon	41862478	41862845	.	+	.	Parent=gene2182
chr6	ENCODE	CDS	41862478	41862845	.	+	2	Parent=gene2182
###
chr6	ENCODE	gene	41860508	41861137	.	+	.	ID=gene2183;Name=RP11-298J23.3-002;name2=C6orf49
chr6	ENCODE	exon	41860508	41860788	.	+	.	Parent=gene2183
chr6	ENCODE	exon	41861053	41861137	.	+	.	Parent=gene2183
###
chr6	ENCODE	gene	41860722	41862452	.	+	.	ID=gene2184;Name=RP11-298J23.3-005;name2=C6orf49
chr6	ENCODE	exon	41860722	41860788	.	+	.	Parent=gene2184
chr6	ENCODE	exon	41861053	41861256	.	+	.	Parent=gene2184
chr6	ENCODE	exon	41861844	41862452	.	+	.	Parent=gene2184
###
chr6	ENCODE	gene	41863378	41865614	.	+	.	ID=gene2185;Name=RP11-298J23.7-001;name2=RP11-298J23.7
chr6	ENCODE	exon	41863378	41863541	.	+	.	Parent=gene2185
chr6	ENCODE	CDS	41863414	41863541	.	+	0	Parent=gene2185
chr6	ENCODE	CDS	41864948	41865044	.	+	1	Parent=gene2185
chr6	ENCODE	exon	41864948	41865052	.	+	.	Parent=gene2185
chr6	ENCODE	exon	41865247	41865614	.	+	.	Parent=gene2185
###
chr6	ENCODE	gene	41863381	41865612	.	+	.	ID=gene2186;Name=RP11-298J23.7-002;name2=RP11-298J23.7
chr6	ENCODE	exon	41863381	41863541	.	+	.	Parent=gene2186
chr6	ENCODE	CDS	41863414	41863541	.	+	0	Parent=gene2186
chr6	ENCODE	CDS	41864948	41865044	.	+	1	Parent=gene2186
chr6	ENCODE	exon	41864948	41865052	.	+	.	Parent=gene2186
chr6	ENCODE	exon	41865284	41865612	.	+	.	Parent=gene2186
###
chr6	ENCODE	gene	41865612	41882699	.	-	.	ID=gene2187;Name=RP11-298J23.4-003;name2=USP49
chr6	ENCODE	exon	41865612	41872439	.	-	.	Parent=gene2187
chr6	ENCODE	CDS	41872249	41872439	.	-	2	Parent=gene2187
chr6	ENCODE	exon	41874440	41874645	.	-	.	Parent=gene2187
chr6	ENCODE	CDS	41874440	41874645	.	-	1	Parent=gene2187
chr6	ENCODE	exon	41875546	41875654	.	-	.	Parent=gene2187
chr6	ENCODE	CDS	41875546	41875654	.	-	2	Parent=gene2187
chr6	ENCODE	exon	41879522	41879726	.	-	.	Parent=gene2187
chr6	ENCODE	CDS	41879522	41879726	.	-	0	Parent=gene2187
chr6	ENCODE	exon	41881344	41882699	.	-	.	Parent=gene2187
chr6	ENCODE	CDS	41881344	41882699	.	-	0	Parent=gene2187
###
chr6	ENCODE	gene	41871236	41882727	.	-	.	ID=gene2188;Name=RP11-298J23.4-007;name2=USP49
chr6	ENCODE	exon	41871236	41872439	.	-	.	Parent=gene2188
chr6	ENCODE	exon	41874440	41874645	.	-	.	Parent=gene2188
chr6	ENCODE	exon	41875546	41875654	.	-	.	Parent=gene2188
chr6	ENCODE	exon	41879522	41879726	.	-	.	Parent=gene2188
chr6	ENCODE	exon	41881344	41882727	.	-	.	Parent=gene2188
###
chr6	ENCODE	gene	41872214	41882727	.	-	.	ID=gene2189;Name=RP11-298J23.4-002;name2=USP49
chr6	ENCODE	exon	41872214	41872439	.	-	.	Parent=gene2189
chr6	ENCODE	exon	41874591	41874645	.	-	.	Parent=gene2189
chr6	ENCODE	exon	41875546	41875654	.	-	.	Parent=gene2189
chr6	ENCODE	exon	41879522	41879726	.	-	.	Parent=gene2189
chr6	ENCODE	exon	41881344	41882727	.	-	.	Parent=gene2189
###
chr6	ENCODE	gene	41872393	41881461	.	-	.	ID=gene2190;Name=RP11-298J23.4-004;name2=USP49
chr6	ENCODE	exon	41872393	41872439	.	-	.	Parent=gene2190
chr6	ENCODE	exon	41874440	41874645	.	-	.	Parent=gene2190
chr6	ENCODE	exon	41875546	41875654	.	-	.	Parent=gene2190
chr6	ENCODE	exon	41881344	41881461	.	-	.	Parent=gene2190
###
chr6	ENCODE	gene	41873361	41882727	.	-	.	ID=gene2191;Name=RP11-298J23.4-001;name2=USP49
chr6	ENCODE	exon	41873361	41874645	.	-	.	Parent=gene2191
chr6	ENCODE	exon	41875546	41875654	.	-	.	Parent=gene2191
chr6	ENCODE	exon	41879522	41879726	.	-	.	Parent=gene2191
chr6	ENCODE	exon	41881344	41882727	.	-	.	Parent=gene2191
###
chr6	ENCODE	gene	41882587	41882727	.	-	.	ID=gene2192;Name=RP11-298J23.4-006;name2=USP49
chr6	ENCODE	exon	41882587	41882727	.	-	.	Parent=gene2192
###
chr6	ENCODE	gene	41882655	41882727	.	-	.	ID=gene2193;name2=USP49;Name=RP11-298J23.4-005
chr6	ENCODE	exon	41882655	41882727	.	-	.	Parent=gene2193
###
chr6	ENCODE	gene	73808380	73808631	.	+	.	ID=gene2194;Name=RP11-257K9.5-005;name2=KCNQ5
chr6	ENCODE	exon	73808380	73808631	.	+	.	Parent=gene2194
###
chr6	ENCODE	gene	73808380	73809705	.	+	.	ID=gene2195;name2=KCNQ5;Name=RP11-257K9.5-003
chr6	ENCODE	exon	73808380	73808506	.	+	.	Parent=gene2195
chr6	ENCODE	CDS	73808380	73808506	.	+	0	Parent=gene2195
chr6	ENCODE	CDS	73809512	73809657	.	+	2	Parent=gene2195
chr6	ENCODE	exon	73809512	73809705	.	+	.	Parent=gene2195
###
chr6	ENCODE	gene	73808380	73891094	.	+	.	ID=gene2196;Name=RP11-257K9.5-002;name2=KCNQ5
chr6	ENCODE	exon	73808380	73808506	.	+	.	Parent=gene2196
chr6	ENCODE	exon	73843766	73843941	.	+	.	Parent=gene2196
chr6	ENCODE	exon	73844206	73844331	.	+	.	Parent=gene2196
chr6	ENCODE	exon	73871701	73871811	.	+	.	Parent=gene2196
chr6	ENCODE	exon	73877752	73877847	.	+	.	Parent=gene2196
chr6	ENCODE	exon	73886927	73887021	.	+	.	Parent=gene2196
chr6	ENCODE	exon	73890930	73891094	.	+	.	Parent=gene2196
###
chr6	ENCODE	gene	73808380	73965292	.	+	.	ID=gene2197;Name=RP11-257K9.5-006;name2=KCNQ5
chr6	ENCODE	exon	73808380	73808506	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73843766	73843941	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73844206	73844331	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73871701	73871811	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73877752	73877847	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73886927	73887021	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73890930	73890956	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73896237	73896293	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73899865	73900085	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73936190	73936298	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73957017	73957148	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73959009	73959135	.	+	.	Parent=gene2197
chr6	ENCODE	exon	73960896	73965292	.	+	.	Parent=gene2197
###
chr6	ENCODE	gene	73808380	73965295	.	+	.	ID=gene2198;Name=RP11-257K9.5-001;name2=KCNQ5
chr6	ENCODE	exon	73808380	73808506	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73843766	73843941	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73844206	73844331	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73871701	73871811	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73877752	73877847	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73886927	73887021	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73890930	73890956	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73899865	73900085	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73936190	73936298	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73957017	73957148	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73959009	73959135	.	+	.	Parent=gene2198
chr6	ENCODE	exon	73960896	73965295	.	+	.	Parent=gene2198
###
chr6	ENCODE	gene	73887001	73900771	.	+	.	ID=gene2199;Name=RP11-257K9.5-004;name2=KCNQ5
chr6	ENCODE	exon	73887001	73887021	.	+	.	Parent=gene2199
chr6	ENCODE	CDS	73887001	73887021	.	+	0	Parent=gene2199
chr6	ENCODE	exon	73899865	73900085	.	+	.	Parent=gene2199
chr6	ENCODE	CDS	73899865	73900085	.	+	0	Parent=gene2199
chr6	ENCODE	CDS	73900365	73900414	.	+	1	Parent=gene2199
chr6	ENCODE	exon	73900365	73900771	.	+	.	Parent=gene2199
###
chr6	ENCODE	gene	73975314	74029640	.	-	.	ID=gene2200;Name=RP11-257K9.4-002;name2=C6orf148
chr6	ENCODE	exon	73975314	73975694	.	-	.	Parent=gene2200
chr6	ENCODE	exon	73976193	73976524	.	-	.	Parent=gene2200
chr6	ENCODE	exon	73982963	73983083	.	-	.	Parent=gene2200
chr6	ENCODE	exon	73990143	73990283	.	-	.	Parent=gene2200
chr6	ENCODE	exon	73990610	73990792	.	-	.	Parent=gene2200
chr6	ENCODE	exon	73991741	73991865	.	-	.	Parent=gene2200
chr6	ENCODE	exon	74008499	74008681	.	-	.	Parent=gene2200
chr6	ENCODE	exon	74008850	74008974	.	-	.	Parent=gene2200
chr6	ENCODE	exon	74029218	74029640	.	-	.	Parent=gene2200
###
chr6	ENCODE	gene	73989988	73991896	.	-	.	ID=gene2201;Name=RP11-257K9.7-001;name2=RP11-257K9.7
chr6	ENCODE	exon	73989988	73990283	.	-	.	Parent=gene2201
chr6	ENCODE	CDS	73990192	73990283	.	-	2	Parent=gene2201
chr6	ENCODE	exon	73990610	73990792	.	-	.	Parent=gene2201
chr6	ENCODE	CDS	73990610	73990792	.	-	2	Parent=gene2201
chr6	ENCODE	CDS	73991741	73991852	.	-	0	Parent=gene2201
chr6	ENCODE	exon	73991741	73991896	.	-	.	Parent=gene2201
###
chr6	ENCODE	gene	73990700	73992214	.	-	.	ID=gene2202;Name=RP11-257K9.7-002;name2=RP11-257K9.7
chr6	ENCODE	exon	73990700	73990792	.	-	.	Parent=gene2202
chr6	ENCODE	exon	73991741	73992214	.	-	.	Parent=gene2202
###
chr6	ENCODE	gene	74007758	74029628	.	-	.	ID=gene2203;name2=C6orf148;Name=RP11-257K9.4-001
chr6	ENCODE	exon	74007758	74008172	.	-	.	Parent=gene2203
chr6	ENCODE	CDS	74007973	74008172	.	-	2	Parent=gene2203
chr6	ENCODE	exon	74008499	74008681	.	-	.	Parent=gene2203
chr6	ENCODE	CDS	74008499	74008681	.	-	2	Parent=gene2203
chr6	ENCODE	CDS	74008850	74008961	.	-	0	Parent=gene2203
chr6	ENCODE	exon	74008850	74008974	.	-	.	Parent=gene2203
chr6	ENCODE	exon	74029218	74029628	.	-	.	Parent=gene2203
###
chr6	ENCODE	gene	74007758	74076659	.	-	.	ID=gene2204;Name=RP11-257K9.4-005;name2=C6orf148
chr6	ENCODE	exon	74007758	74008172	.	-	.	Parent=gene2204
chr6	ENCODE	CDS	74007973	74008172	.	-	2	Parent=gene2204
chr6	ENCODE	exon	74008499	74008681	.	-	.	Parent=gene2204
chr6	ENCODE	CDS	74008499	74008681	.	-	2	Parent=gene2204
chr6	ENCODE	exon	74008850	74008974	.	-	.	Parent=gene2204
chr6	ENCODE	CDS	74008850	74008974	.	-	1	Parent=gene2204
chr6	ENCODE	exon	74058442	74058484	.	-	.	Parent=gene2204
chr6	ENCODE	CDS	74058442	74058484	.	-	2	Parent=gene2204
chr6	ENCODE	CDS	74075996	74076158	.	-	0	Parent=gene2204
chr6	ENCODE	exon	74075996	74076659	.	-	.	Parent=gene2204
###
chr6	ENCODE	gene	74008499	74029616	.	-	.	ID=gene2205;Name=RP11-257K9.4-004;name2=C6orf148
chr6	ENCODE	exon	74008499	74008681	.	-	.	Parent=gene2205
chr6	ENCODE	CDS	74008499	74008681	.	-	2	Parent=gene2205
chr6	ENCODE	CDS	74008850	74008961	.	-	0	Parent=gene2205
chr6	ENCODE	exon	74008850	74008974	.	-	.	Parent=gene2205
chr6	ENCODE	exon	74029378	74029616	.	-	.	Parent=gene2205
###
chr6	ENCODE	gene	74040583	74076587	.	-	.	ID=gene2206;name2=RP11-398K22.8;Name=RP11-398K22.8-002
chr6	ENCODE	exon	74040583	74042000	.	-	.	Parent=gene2206
chr6	ENCODE	CDS	74041997	74042000	.	-	1	Parent=gene2206
chr6	ENCODE	exon	74058442	74058484	.	-	.	Parent=gene2206
chr6	ENCODE	CDS	74058442	74058484	.	-	2	Parent=gene2206
chr6	ENCODE	CDS	74075996	74076158	.	-	0	Parent=gene2206
chr6	ENCODE	exon	74075996	74076587	.	-	.	Parent=gene2206
###
chr6	ENCODE	gene	74041490	74076809	.	-	.	ID=gene2207;Name=RP11-398K22.8-001;name2=RP11-398K22.8
chr6	ENCODE	exon	74041490	74041603	.	-	.	Parent=gene2207
chr6	ENCODE	exon	74041858	74042000	.	-	.	Parent=gene2207
chr6	ENCODE	CDS	74041997	74042000	.	-	1	Parent=gene2207
chr6	ENCODE	exon	74058442	74058484	.	-	.	Parent=gene2207
chr6	ENCODE	CDS	74058442	74058484	.	-	2	Parent=gene2207
chr6	ENCODE	CDS	74075996	74076158	.	-	0	Parent=gene2207
chr6	ENCODE	exon	74075996	74076172	.	-	.	Parent=gene2207
chr6	ENCODE	exon	74076750	74076809	.	-	.	Parent=gene2207
###
chr6	ENCODE	gene	74119506	74120739	.	-	.	ID=gene2208;name2=RP11-398K22.7;Name=RP11-398K22.7-001
chr6	ENCODE	exon	74119506	74119822	.	-	.	Parent=gene2208
chr6	ENCODE	CDS	74119764	74119822	.	-	2	Parent=gene2208
chr6	ENCODE	exon	74120297	74120476	.	-	.	Parent=gene2208
chr6	ENCODE	CDS	74120297	74120476	.	-	2	Parent=gene2208
chr6	ENCODE	CDS	74120558	74120669	.	-	0	Parent=gene2208
chr6	ENCODE	exon	74120558	74120739	.	-	.	Parent=gene2208
###
chr6	ENCODE	gene	74129121	74130615	.	+	.	ID=gene2209;name2=RP11-398K22.4;Name=RP11-398K22.4-001
chr6	ENCODE	exon	74129121	74129342	.	+	.	Parent=gene2209
chr6	ENCODE	CDS	74129174	74129342	.	+	0	Parent=gene2209
chr6	ENCODE	exon	74129539	74129718	.	+	.	Parent=gene2209
chr6	ENCODE	CDS	74129539	74129718	.	+	2	Parent=gene2209
chr6	ENCODE	CDS	74130000	74130304	.	+	2	Parent=gene2209
chr6	ENCODE	exon	74130000	74130615	.	+	.	Parent=gene2209
###
chr6	ENCODE	gene	74134999	74161537	.	-	.	ID=gene2210;Name=RP11-398K22.11-001;name2=RP11-398K22.11
chr6	ENCODE	exon	74134999	74135307	.	-	.	Parent=gene2210
chr6	ENCODE	CDS	74135228	74135307	.	-	2	Parent=gene2210
chr6	ENCODE	exon	74135650	74135829	.	-	.	Parent=gene2210
chr6	ENCODE	CDS	74135650	74135829	.	-	2	Parent=gene2210
chr6	ENCODE	CDS	74160790	74160814	.	-	0	Parent=gene2210
chr6	ENCODE	exon	74160790	74160932	.	-	.	Parent=gene2210
chr6	ENCODE	exon	74161163	74161537	.	-	.	Parent=gene2210
###
chr6	ENCODE	gene	74135200	74136226	.	-	.	ID=gene2211;Name=RP11-398K22.11-003;name2=RP11-398K22.11
chr6	ENCODE	exon	74135200	74135307	.	-	.	Parent=gene2211
chr6	ENCODE	CDS	74135228	74135307	.	-	0	Parent=gene2211
chr6	ENCODE	exon	74135650	74135829	.	-	.	Parent=gene2211
chr6	ENCODE	CDS	74135650	74135829	.	-	0	Parent=gene2211
chr6	ENCODE	exon	74136047	74136226	.	-	.	Parent=gene2211
chr6	ENCODE	CDS	74136047	74136226	.	-	0	Parent=gene2211
###
chr6	ENCODE	gene	74135654	74161577	.	-	.	ID=gene2212;Name=RP11-398K22.11-002;name2=RP11-398K22.11
chr6	ENCODE	exon	74135654	74135829	.	-	.	Parent=gene2212
chr6	ENCODE	CDS	74135654	74135829	.	-	2	Parent=gene2212
chr6	ENCODE	CDS	74160790	74160814	.	-	0	Parent=gene2212
chr6	ENCODE	exon	74160790	74161577	.	-	.	Parent=gene2212
###
chr6	ENCODE	gene	74161192	74184013	.	+	.	ID=gene2213;Name=RP11-398K22.1-001;name2=DDX43
chr6	ENCODE	exon	74161192	74161599	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74161350	74161599	.	+	0	Parent=gene2213
chr6	ENCODE	exon	74164133	74164188	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74164133	74164188	.	+	2	Parent=gene2213
chr6	ENCODE	exon	74166678	74166807	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74166678	74166807	.	+	0	Parent=gene2213
chr6	ENCODE	exon	74168303	74168434	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74168303	74168434	.	+	2	Parent=gene2213
chr6	ENCODE	exon	74171134	74171215	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74171134	74171215	.	+	2	Parent=gene2213
chr6	ENCODE	exon	74172123	74172279	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74172123	74172279	.	+	1	Parent=gene2213
chr6	ENCODE	exon	74172808	74172926	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74172808	74172926	.	+	0	Parent=gene2213
chr6	ENCODE	exon	74173949	74174059	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74173949	74174059	.	+	1	Parent=gene2213
chr6	ENCODE	exon	74174404	74174545	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74174404	74174545	.	+	1	Parent=gene2213
chr6	ENCODE	exon	74175692	74175792	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74175692	74175792	.	+	0	Parent=gene2213
chr6	ENCODE	exon	74178649	74178736	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74178649	74178736	.	+	1	Parent=gene2213
chr6	ENCODE	exon	74180102	74180229	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74180102	74180229	.	+	0	Parent=gene2213
chr6	ENCODE	exon	74180414	74180523	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74180414	74180523	.	+	1	Parent=gene2213
chr6	ENCODE	exon	74180992	74181130	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74180992	74181130	.	+	2	Parent=gene2213
chr6	ENCODE	exon	74181941	74182028	.	+	.	Parent=gene2213
chr6	ENCODE	CDS	74181941	74182028	.	+	1	Parent=gene2213
chr6	ENCODE	CDS	74182557	74182670	.	+	0	Parent=gene2213
chr6	ENCODE	exon	74182557	74182695	.	+	.	Parent=gene2213
chr6	ENCODE	exon	74183631	74184013	.	+	.	Parent=gene2213
###
chr6	ENCODE	gene	74161338	74164438	.	+	.	ID=gene2214;Name=RP11-398K22.1-003;name2=DDX43
chr6	ENCODE	exon	74161338	74161599	.	+	.	Parent=gene2214
chr6	ENCODE	exon	74164133	74164438	.	+	.	Parent=gene2214
###
chr6	ENCODE	gene	74173409	74180451	.	+	.	ID=gene2215;Name=RP11-398K22.1-002;name2=DDX43
chr6	ENCODE	exon	74173409	74173452	.	+	.	Parent=gene2215
chr6	ENCODE	exon	74173949	74174059	.	+	.	Parent=gene2215
chr6	ENCODE	exon	74174404	74174545	.	+	.	Parent=gene2215
chr6	ENCODE	exon	74175692	74175792	.	+	.	Parent=gene2215
chr6	ENCODE	exon	74178649	74178736	.	+	.	Parent=gene2215
chr6	ENCODE	exon	74180102	74180229	.	+	.	Parent=gene2215
chr6	ENCODE	exon	74180414	74180451	.	+	.	Parent=gene2215
###
chr6	ENCODE	gene	74179959	74218703	.	-	.	ID=gene2216;Name=RP11-398K22.2-001;name2=C6orf150
chr6	ENCODE	exon	74179959	74180465	.	-	.	Parent=gene2216
chr6	ENCODE	CDS	74180454	74180465	.	-	0	Parent=gene2216
chr6	ENCODE	exon	74191908	74192022	.	-	.	Parent=gene2216
chr6	ENCODE	CDS	74191908	74192022	.	-	1	Parent=gene2216
chr6	ENCODE	exon	74195153	74195255	.	-	.	Parent=gene2216
chr6	ENCODE	CDS	74195153	74195255	.	-	2	Parent=gene2216
chr6	ENCODE	exon	74206653	74206889	.	-	.	Parent=gene2216
chr6	ENCODE	CDS	74206653	74206889	.	-	2	Parent=gene2216
chr6	ENCODE	exon	74211972	74212191	.	-	.	Parent=gene2216
chr6	ENCODE	CDS	74211972	74212191	.	-	0	Parent=gene2216
chr6	ENCODE	CDS	74217969	74218625	.	-	0	Parent=gene2216
chr6	ENCODE	exon	74217969	74218703	.	-	.	Parent=gene2216
###
chr6	ENCODE	gene	74190153	74218720	.	-	.	ID=gene2217;Name=RP11-398K22.2-002;name2=C6orf150
chr6	ENCODE	exon	74190153	74192022	.	-	.	Parent=gene2217
chr6	ENCODE	CDS	74191671	74192022	.	-	1	Parent=gene2217
chr6	ENCODE	exon	74195153	74195255	.	-	.	Parent=gene2217
chr6	ENCODE	CDS	74195153	74195255	.	-	2	Parent=gene2217
chr6	ENCODE	exon	74206653	74206889	.	-	.	Parent=gene2217
chr6	ENCODE	CDS	74206653	74206889	.	-	2	Parent=gene2217
chr6	ENCODE	exon	74211972	74212191	.	-	.	Parent=gene2217
chr6	ENCODE	CDS	74211972	74212191	.	-	0	Parent=gene2217
chr6	ENCODE	CDS	74217969	74218625	.	-	0	Parent=gene2217
chr6	ENCODE	exon	74217969	74218720	.	-	.	Parent=gene2217
###
chr6	ENCODE	gene	74191661	74218720	.	-	.	ID=gene2218;Name=RP11-398K22.2-004;name2=C6orf150
chr6	ENCODE	exon	74191661	74191971	.	-	.	Parent=gene2218
chr6	ENCODE	CDS	74191671	74191971	.	-	1	Parent=gene2218
chr6	ENCODE	exon	74195153	74195255	.	-	.	Parent=gene2218
chr6	ENCODE	CDS	74195153	74195255	.	-	2	Parent=gene2218
chr6	ENCODE	exon	74206653	74206889	.	-	.	Parent=gene2218
chr6	ENCODE	CDS	74206653	74206889	.	-	2	Parent=gene2218
chr6	ENCODE	exon	74211972	74212191	.	-	.	Parent=gene2218
chr6	ENCODE	CDS	74211972	74212191	.	-	0	Parent=gene2218
chr6	ENCODE	CDS	74217969	74218625	.	-	0	Parent=gene2218
chr6	ENCODE	exon	74217969	74218720	.	-	.	Parent=gene2218
###
chr6	ENCODE	gene	74206187	74212129	.	-	.	ID=gene2219;Name=RP11-398K22.2-003;name2=C6orf150
chr6	ENCODE	exon	74206187	74206889	.	-	.	Parent=gene2219
chr6	ENCODE	exon	74211972	74212129	.	-	.	Parent=gene2219
###
chr6	ENCODE	gene	74228022	74275680	.	+	.	ID=gene2220;Name=RP11-505P4.1-001;name2=MTO1
chr6	ENCODE	exon	74228022	74228515	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74228299	74228515	.	+	0	Parent=gene2220
chr6	ENCODE	exon	74232653	74232852	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74232653	74232852	.	+	2	Parent=gene2220
chr6	ENCODE	exon	74232933	74233050	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74232933	74233050	.	+	0	Parent=gene2220
chr6	ENCODE	exon	74239809	74240098	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74239809	74240098	.	+	2	Parent=gene2220
chr6	ENCODE	exon	74246176	74246288	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74246176	74246288	.	+	0	Parent=gene2220
chr6	ENCODE	exon	74246380	74246570	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74246380	74246570	.	+	1	Parent=gene2220
chr6	ENCODE	exon	74247119	74247249	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74247119	74247249	.	+	2	Parent=gene2220
chr6	ENCODE	exon	74248484	74248688	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74248484	74248688	.	+	0	Parent=gene2220
chr6	ENCODE	exon	74248893	74249064	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74248893	74249064	.	+	2	Parent=gene2220
chr6	ENCODE	exon	74258678	74258796	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74258678	74258796	.	+	1	Parent=gene2220
chr6	ENCODE	exon	74264180	74264340	.	+	.	Parent=gene2220
chr6	ENCODE	CDS	74264180	74264340	.	+	2	Parent=gene2220
chr6	ENCODE	CDS	74267018	74267179	.	+	0	Parent=gene2220
chr6	ENCODE	exon	74267018	74275680	.	+	.	Parent=gene2220
###
chr6	ENCODE	gene	74228190	74267367	.	+	.	ID=gene2221;Name=RP11-505P4.1-007;name2=MTO1
chr6	ENCODE	exon	74228190	74228238	.	+	.	Parent=gene2221
chr6	ENCODE	exon	74232653	74232852	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74232658	74232852	.	+	0	Parent=gene2221
chr6	ENCODE	exon	74232933	74233050	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74232933	74233050	.	+	0	Parent=gene2221
chr6	ENCODE	exon	74239809	74240098	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74239809	74240098	.	+	2	Parent=gene2221
chr6	ENCODE	exon	74246176	74246288	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74246176	74246288	.	+	0	Parent=gene2221
chr6	ENCODE	exon	74246380	74246570	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74246380	74246570	.	+	1	Parent=gene2221
chr6	ENCODE	exon	74246737	74246811	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74246737	74246811	.	+	2	Parent=gene2221
chr6	ENCODE	exon	74247119	74247249	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74247119	74247249	.	+	2	Parent=gene2221
chr6	ENCODE	exon	74248484	74248688	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74248484	74248688	.	+	0	Parent=gene2221
chr6	ENCODE	exon	74248893	74249064	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74248893	74249064	.	+	2	Parent=gene2221
chr6	ENCODE	exon	74258678	74258796	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74258678	74258796	.	+	1	Parent=gene2221
chr6	ENCODE	exon	74264180	74264340	.	+	.	Parent=gene2221
chr6	ENCODE	CDS	74264180	74264340	.	+	2	Parent=gene2221
chr6	ENCODE	CDS	74267018	74267179	.	+	0	Parent=gene2221
chr6	ENCODE	exon	74267018	74267367	.	+	.	Parent=gene2221
###
chr6	ENCODE	gene	74228209	74267540	.	+	.	ID=gene2222;Name=RP11-505P4.1-002;name2=MTO1
chr6	ENCODE	exon	74228209	74228515	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74232653	74232852	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74232933	74233050	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74239809	74240098	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74246176	74246570	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74247119	74247249	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74248484	74248688	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74248893	74249064	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74258678	74258796	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74264180	74264340	.	+	.	Parent=gene2222
chr6	ENCODE	exon	74267018	74267540	.	+	.	Parent=gene2222
###
chr6	ENCODE	gene	74228209	74267540	.	+	.	ID=gene2223;Name=RP11-505P4.1-005;name2=MTO1
chr6	ENCODE	exon	74228209	74228515	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74232653	74232852	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74232933	74233050	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74246176	74246288	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74246380	74246570	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74247119	74247249	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74248484	74248688	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74248893	74249064	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74258678	74258796	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74264180	74264340	.	+	.	Parent=gene2223
chr6	ENCODE	exon	74267018	74267540	.	+	.	Parent=gene2223
###
chr6	ENCODE	gene	74228209	74267896	.	+	.	ID=gene2224;Name=RP11-505P4.1-003;name2=MTO1
chr6	ENCODE	exon	74228209	74228515	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74228299	74228515	.	+	0	Parent=gene2224
chr6	ENCODE	exon	74232653	74232852	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74232653	74232852	.	+	2	Parent=gene2224
chr6	ENCODE	exon	74232933	74233050	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74232933	74233050	.	+	0	Parent=gene2224
chr6	ENCODE	exon	74239809	74240098	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74239809	74240098	.	+	2	Parent=gene2224
chr6	ENCODE	exon	74246176	74246288	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74246176	74246288	.	+	0	Parent=gene2224
chr6	ENCODE	exon	74246380	74246570	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74246380	74246570	.	+	1	Parent=gene2224
chr6	ENCODE	exon	74246737	74246811	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74246737	74246811	.	+	2	Parent=gene2224
chr6	ENCODE	exon	74247119	74247249	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74247119	74247249	.	+	2	Parent=gene2224
chr6	ENCODE	exon	74248484	74248688	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74248484	74248688	.	+	0	Parent=gene2224
chr6	ENCODE	exon	74248893	74249064	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74248893	74249064	.	+	2	Parent=gene2224
chr6	ENCODE	exon	74258678	74258796	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74258678	74258796	.	+	1	Parent=gene2224
chr6	ENCODE	exon	74264180	74264340	.	+	.	Parent=gene2224
chr6	ENCODE	CDS	74264180	74264340	.	+	2	Parent=gene2224
chr6	ENCODE	CDS	74267018	74267179	.	+	0	Parent=gene2224
chr6	ENCODE	exon	74267018	74267896	.	+	.	Parent=gene2224
###
chr6	ENCODE	gene	74228239	74267494	.	+	.	ID=gene2225;Name=RP11-505P4.1-004;name2=MTO1
chr6	ENCODE	exon	74228239	74228515	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74232653	74232852	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74232933	74233050	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74246176	74246288	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74246380	74246811	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74247119	74247249	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74248473	74248688	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74248893	74249064	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74258678	74258796	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74264180	74264340	.	+	.	Parent=gene2225
chr6	ENCODE	exon	74267018	74267494	.	+	.	Parent=gene2225
###
chr6	ENCODE	gene	74228528	74233032	.	+	.	ID=gene2226;Name=RP11-505P4.1-011;name2=MTO1
chr6	ENCODE	exon	74228528	74228617	.	+	.	Parent=gene2226
chr6	ENCODE	exon	74232653	74232852	.	+	.	Parent=gene2226
chr6	ENCODE	CDS	74232658	74232852	.	+	0	Parent=gene2226
chr6	ENCODE	exon	74232933	74233032	.	+	.	Parent=gene2226
chr6	ENCODE	CDS	74232933	74233032	.	+	0	Parent=gene2226
###
chr6	ENCODE	gene	74232707	74238239	.	+	.	ID=gene2227;Name=RP11-505P4.1-008;name2=MTO1
chr6	ENCODE	exon	74232707	74232852	.	+	.	Parent=gene2227
chr6	ENCODE	exon	74232933	74233050	.	+	.	Parent=gene2227
chr6	ENCODE	exon	74237904	74238239	.	+	.	Parent=gene2227
###
chr6	ENCODE	gene	74239997	74246615	.	+	.	ID=gene2228;Name=RP11-505P4.1-009;name2=MTO1
chr6	ENCODE	exon	74239997	74240098	.	+	.	Parent=gene2228
chr6	ENCODE	exon	74246176	74246288	.	+	.	Parent=gene2228
chr6	ENCODE	exon	74246380	74246615	.	+	.	Parent=gene2228
###
chr6	ENCODE	gene	74246444	74248978	.	+	.	ID=gene2229;name2=MTO1;Name=RP11-505P4.1-006
chr6	ENCODE	exon	74246444	74246570	.	+	.	Parent=gene2229
chr6	ENCODE	exon	74247119	74247249	.	+	.	Parent=gene2229
chr6	ENCODE	exon	74247445	74247560	.	+	.	Parent=gene2229
chr6	ENCODE	exon	74248484	74248688	.	+	.	Parent=gene2229
chr6	ENCODE	exon	74248893	74248978	.	+	.	Parent=gene2229
###
chr6	ENCODE	gene	74246610	74247472	.	+	.	ID=gene2230;Name=RP11-505P4.1-010;name2=MTO1
chr6	ENCODE	exon	74246610	74246811	.	+	.	Parent=gene2230
chr6	ENCODE	exon	74247119	74247249	.	+	.	Parent=gene2230
chr6	ENCODE	exon	74247445	74247472	.	+	.	Parent=gene2230
###
chr6	ENCODE	gene	74282194	74287462	.	-	.	ID=gene2231;name2=EEF1A1;Name=RP11-505P4.2-001
chr6	ENCODE	exon	74282194	74284378	.	-	.	Parent=gene2231
chr6	ENCODE	CDS	74284254	74284378	.	-	2	Parent=gene2231
chr6	ENCODE	exon	74284474	74284708	.	-	.	Parent=gene2231
chr6	ENCODE	CDS	74284474	74284708	.	-	0	Parent=gene2231
chr6	ENCODE	exon	74284798	74285054	.	-	.	Parent=gene2231
chr6	ENCODE	CDS	74284798	74285054	.	-	2	Parent=gene2231
chr6	ENCODE	exon	74285142	74285292	.	-	.	Parent=gene2231
chr6	ENCODE	CDS	74285142	74285292	.	-	0	Parent=gene2231
chr6	ENCODE	exon	74285376	74285672	.	-	.	Parent=gene2231
chr6	ENCODE	CDS	74285376	74285672	.	-	0	Parent=gene2231
chr6	ENCODE	exon	74285781	74285960	.	-	.	Parent=gene2231
chr6	ENCODE	CDS	74285781	74285960	.	-	0	Parent=gene2231
chr6	ENCODE	CDS	74286327	74286470	.	-	0	Parent=gene2231
chr6	ENCODE	exon	74286327	74287462	.	-	.	Parent=gene2231
###
chr6	ENCODE	gene	74283959	74285861	.	-	.	ID=gene2232;Name=RP11-505P4.2-014;name2=EEF1A1
chr6	ENCODE	exon	74283959	74284262	.	-	.	Parent=gene2232
chr6	ENCODE	exon	74285425	74285672	.	-	.	Parent=gene2232
chr6	ENCODE	exon	74285781	74285861	.	-	.	Parent=gene2232
###
chr6	ENCODE	gene	74283959	74287478	.	-	.	ID=gene2233;Name=RP11-505P4.2-013;name2=EEF1A1
chr6	ENCODE	exon	74283959	74284325	.	-	.	Parent=gene2233
chr6	ENCODE	exon	74285854	74285960	.	-	.	Parent=gene2233
chr6	ENCODE	exon	74286327	74286500	.	-	.	Parent=gene2233
chr6	ENCODE	exon	74287444	74287478	.	-	.	Parent=gene2233
###
chr6	ENCODE	gene	74283959	74288032	.	-	.	ID=gene2234;Name=RP11-505P4.2-009;name2=EEF1A1
chr6	ENCODE	exon	74283959	74284378	.	-	.	Parent=gene2234
chr6	ENCODE	CDS	74284254	74284378	.	-	2	Parent=gene2234
chr6	ENCODE	exon	74284474	74284708	.	-	.	Parent=gene2234
chr6	ENCODE	CDS	74284474	74284708	.	-	0	Parent=gene2234
chr6	ENCODE	exon	74284798	74285054	.	-	.	Parent=gene2234
chr6	ENCODE	CDS	74284798	74285054	.	-	2	Parent=gene2234
chr6	ENCODE	exon	74285142	74285292	.	-	.	Parent=gene2234
chr6	ENCODE	CDS	74285142	74285292	.	-	0	Parent=gene2234
chr6	ENCODE	exon	74285376	74285672	.	-	.	Parent=gene2234
chr6	ENCODE	CDS	74285376	74285672	.	-	0	Parent=gene2234
chr6	ENCODE	exon	74285781	74285960	.	-	.	Parent=gene2234
chr6	ENCODE	CDS	74285781	74285960	.	-	0	Parent=gene2234
chr6	ENCODE	CDS	74286327	74286470	.	-	0	Parent=gene2234
chr6	ENCODE	exon	74286327	74286500	.	-	.	Parent=gene2234
chr6	ENCODE	exon	74287444	74288032	.	-	.	Parent=gene2234
###
chr6	ENCODE	gene	74283960	74286455	.	-	.	ID=gene2235;Name=RP11-505P4.2-012;name2=EEF1A1
chr6	ENCODE	exon	74283960	74284378	.	-	.	Parent=gene2235
chr6	ENCODE	exon	74284474	74284552	.	-	.	Parent=gene2235
chr6	ENCODE	exon	74286339	74286455	.	-	.	Parent=gene2235
###
chr6	ENCODE	gene	74283962	74287476	.	-	.	ID=gene2236;name2=EEF1A1;Name=RP11-505P4.2-006
chr6	ENCODE	exon	74283962	74284378	.	-	.	Parent=gene2236
chr6	ENCODE	exon	74284474	74284518	.	-	.	Parent=gene2236
chr6	ENCODE	exon	74284812	74285054	.	-	.	Parent=gene2236
chr6	ENCODE	exon	74285142	74285292	.	-	.	Parent=gene2236
chr6	ENCODE	exon	74285376	74285672	.	-	.	Parent=gene2236
chr6	ENCODE	exon	74285781	74285960	.	-	.	Parent=gene2236
chr6	ENCODE	exon	74286327	74286500	.	-	.	Parent=gene2236
chr6	ENCODE	exon	74287444	74287476	.	-	.	Parent=gene2236
###
chr6	ENCODE	gene	74283962	74287476	.	-	.	ID=gene2237;Name=RP11-505P4.2-007;name2=EEF1A1
chr6	ENCODE	exon	74283962	74284378	.	-	.	Parent=gene2237
chr6	ENCODE	exon	74284474	74284708	.	-	.	Parent=gene2237
chr6	ENCODE	exon	74284798	74284818	.	-	.	Parent=gene2237
chr6	ENCODE	exon	74285478	74285672	.	-	.	Parent=gene2237
chr6	ENCODE	exon	74285781	74285960	.	-	.	Parent=gene2237
chr6	ENCODE	exon	74286327	74286500	.	-	.	Parent=gene2237
chr6	ENCODE	exon	74287444	74287476	.	-	.	Parent=gene2237
###
chr6	ENCODE	gene	74283963	74286503	.	-	.	ID=gene2238;name2=EEF1A1;Name=RP11-505P4.2-008
chr6	ENCODE	exon	74283963	74284378	.	-	.	Parent=gene2238
chr6	ENCODE	exon	74284474	74285054	.	-	.	Parent=gene2238
chr6	ENCODE	exon	74285142	74285292	.	-	.	Parent=gene2238
chr6	ENCODE	exon	74285376	74285672	.	-	.	Parent=gene2238
chr6	ENCODE	exon	74285781	74285960	.	-	.	Parent=gene2238
chr6	ENCODE	exon	74286327	74286503	.	-	.	Parent=gene2238
###
chr6	ENCODE	gene	74283965	74288165	.	-	.	ID=gene2239;name2=EEF1A1;Name=RP11-505P4.2-004
chr6	ENCODE	exon	74283965	74284378	.	-	.	Parent=gene2239
chr6	ENCODE	CDS	74284254	74284378	.	-	2	Parent=gene2239
chr6	ENCODE	exon	74284474	74284708	.	-	.	Parent=gene2239
chr6	ENCODE	CDS	74284474	74284708	.	-	0	Parent=gene2239
chr6	ENCODE	exon	74284798	74285054	.	-	.	Parent=gene2239
chr6	ENCODE	CDS	74284798	74285054	.	-	2	Parent=gene2239
chr6	ENCODE	exon	74285142	74285292	.	-	.	Parent=gene2239
chr6	ENCODE	CDS	74285142	74285292	.	-	0	Parent=gene2239
chr6	ENCODE	exon	74285376	74285672	.	-	.	Parent=gene2239
chr6	ENCODE	CDS	74285376	74285672	.	-	0	Parent=gene2239
chr6	ENCODE	exon	74285781	74285960	.	-	.	Parent=gene2239
chr6	ENCODE	CDS	74285781	74285960	.	-	0	Parent=gene2239
chr6	ENCODE	CDS	74286327	74286470	.	-	0	Parent=gene2239
chr6	ENCODE	exon	74286327	74286500	.	-	.	Parent=gene2239
chr6	ENCODE	exon	74287951	74288165	.	-	.	Parent=gene2239
###
chr6	ENCODE	gene	74284034	74286503	.	-	.	ID=gene2240;Name=RP11-505P4.2-005;name2=EEF1A1
chr6	ENCODE	exon	74284034	74284349	.	-	.	Parent=gene2240
chr6	ENCODE	exon	74285816	74285960	.	-	.	Parent=gene2240
chr6	ENCODE	exon	74286327	74286503	.	-	.	Parent=gene2240
###
chr6	ENCODE	gene	74284062	74286503	.	-	.	ID=gene2241;Name=RP11-505P4.2-010;name2=EEF1A1
chr6	ENCODE	exon	74284062	74284378	.	-	.	Parent=gene2241
chr6	ENCODE	exon	74284474	74284642	.	-	.	Parent=gene2241
chr6	ENCODE	exon	74286425	74286503	.	-	.	Parent=gene2241
###
chr6	ENCODE	gene	74285010	74286503	.	-	.	ID=gene2242;Name=RP11-505P4.2-002;name2=EEF1A1
chr6	ENCODE	exon	74285010	74285054	.	-	.	Parent=gene2242
chr6	ENCODE	exon	74285142	74285292	.	-	.	Parent=gene2242
chr6	ENCODE	exon	74285376	74285960	.	-	.	Parent=gene2242
chr6	ENCODE	exon	74286327	74286503	.	-	.	Parent=gene2242
###
chr6	ENCODE	gene	74285238	74286503	.	-	.	ID=gene2243;Name=RP11-505P4.2-011;name2=EEF1A1
chr6	ENCODE	exon	74285238	74285672	.	-	.	Parent=gene2243
chr6	ENCODE	exon	74285781	74285960	.	-	.	Parent=gene2243
chr6	ENCODE	exon	74286327	74286503	.	-	.	Parent=gene2243
###
chr6	ENCODE	gene	74285561	74288344	.	-	.	ID=gene2244;name2=EEF1A1;Name=RP11-505P4.2-015
chr6	ENCODE	exon	74285561	74285672	.	-	.	Parent=gene2244
chr6	ENCODE	CDS	74285561	74285672	.	-	0	Parent=gene2244
chr6	ENCODE	exon	74285781	74285960	.	-	.	Parent=gene2244
chr6	ENCODE	CDS	74285781	74285960	.	-	0	Parent=gene2244
chr6	ENCODE	CDS	74286327	74286470	.	-	0	Parent=gene2244
chr6	ENCODE	exon	74286327	74286500	.	-	.	Parent=gene2244
chr6	ENCODE	exon	74288176	74288344	.	-	.	Parent=gene2244
###
chr6	ENCODE	gene	74285785	74286500	.	-	.	ID=gene2245;Name=RP11-505P4.2-003;name2=EEF1A1
chr6	ENCODE	exon	74285785	74285960	.	-	.	Parent=gene2245
chr6	ENCODE	exon	74286327	74286500	.	-	.	Parent=gene2245
###
chr6	ENCODE	gene	108382481	108385939	.	-	.	ID=gene2246;Name=RP1-191J18.4-002;name2=SEC63
chr6	ENCODE	exon	108382481	108382663	.	-	.	Parent=gene2246
chr6	ENCODE	exon	108383862	108384003	.	-	.	Parent=gene2246
chr6	ENCODE	exon	108385783	108385939	.	-	.	Parent=gene2246
###
chr6	ENCODE	gene	108383862	108386008	.	-	.	ID=gene2247;Name=RP1-191J18.4-010;name2=SEC63
chr6	ENCODE	exon	108383862	108384003	.	-	.	Parent=gene2247
chr6	ENCODE	exon	108385783	108386008	.	-	.	Parent=gene2247
###
chr6	ENCODE	gene	108385119	108385237	.	-	.	ID=gene2248;Name=RP1-191J18.4-007;name2=SEC63
chr6	ENCODE	exon	108385119	108385237	.	-	.	Parent=gene2248
###
chr6	ENCODE	gene	108385783	108385828	.	-	.	ID=gene2249;Name=RP1-191J18.4-005;name2=SEC63
chr6	ENCODE	exon	108385783	108385828	.	-	.	Parent=gene2249
###
chr6	ENCODE	gene	108385783	108386086	.	-	.	ID=gene2250;name2=SEC63;Name=RP1-191J18.4-001
chr6	ENCODE	exon	108385783	108386086	.	-	.	Parent=gene2250
###
chr6	ENCODE	gene	108469306	108502634	.	-	.	ID=gene2251;Name=RP1-111B22.1-001;name2=OSTM1
chr6	ENCODE	exon	108469306	108472737	.	-	.	Parent=gene2251
chr6	ENCODE	CDS	108472682	108472737	.	-	2	Parent=gene2251
chr6	ENCODE	exon	108477150	108477315	.	-	.	Parent=gene2251
chr6	ENCODE	CDS	108477150	108477315	.	-	0	Parent=gene2251
chr6	ENCODE	exon	108478928	108479095	.	-	.	Parent=gene2251
chr6	ENCODE	CDS	108478928	108479095	.	-	0	Parent=gene2251
chr6	ENCODE	exon	108482387	108482484	.	-	.	Parent=gene2251
chr6	ENCODE	CDS	108482387	108482484	.	-	2	Parent=gene2251
chr6	ENCODE	exon	108492082	108492196	.	-	.	Parent=gene2251
chr6	ENCODE	CDS	108492082	108492196	.	-	0	Parent=gene2251
chr6	ENCODE	CDS	108502147	108502548	.	-	0	Parent=gene2251
chr6	ENCODE	exon	108502147	108502634	.	-	.	Parent=gene2251
###
chr6	ENCODE	gene	108469369	108472135	.	-	.	ID=gene2252;Name=RP1-111B22.1-003;name2=OSTM1
chr6	ENCODE	exon	108469369	108470161	.	-	.	Parent=gene2252
chr6	ENCODE	exon	108470464	108472135	.	-	.	Parent=gene2252
###
chr6	ENCODE	gene	108472276	108478963	.	-	.	ID=gene2253;Name=RP1-111B22.1-005;name2=OSTM1
chr6	ENCODE	exon	108472276	108472737	.	-	.	Parent=gene2253
chr6	ENCODE	exon	108477150	108477315	.	-	.	Parent=gene2253
chr6	ENCODE	exon	108477429	108477480	.	-	.	Parent=gene2253
chr6	ENCODE	exon	108478928	108478963	.	-	.	Parent=gene2253
###
chr6	ENCODE	gene	108472630	108477565	.	-	.	ID=gene2254;Name=RP1-111B22.1-004;name2=OSTM1
chr6	ENCODE	exon	108472630	108472737	.	-	.	Parent=gene2254
chr6	ENCODE	exon	108477150	108477315	.	-	.	Parent=gene2254
chr6	ENCODE	exon	108477429	108477565	.	-	.	Parent=gene2254
###
chr6	ENCODE	gene	108472728	108593737	.	-	.	ID=gene2255;Name=RP1-111B22.1-006;name2=OSTM1
chr6	ENCODE	exon	108472728	108472737	.	-	.	Parent=gene2255
chr6	ENCODE	CDS	108472728	108472737	.	-	1	Parent=gene2255
chr6	ENCODE	exon	108477152	108477315	.	-	.	Parent=gene2255
chr6	ENCODE	CDS	108477152	108477315	.	-	0	Parent=gene2255
chr6	ENCODE	exon	108478928	108479095	.	-	.	Parent=gene2255
chr6	ENCODE	CDS	108478928	108479095	.	-	0	Parent=gene2255
chr6	ENCODE	exon	108482387	108482484	.	-	.	Parent=gene2255
chr6	ENCODE	CDS	108482387	108482484	.	-	2	Parent=gene2255
chr6	ENCODE	CDS	108492082	108492157	.	-	0	Parent=gene2255
chr6	ENCODE	exon	108492082	108492196	.	-	.	Parent=gene2255
chr6	ENCODE	exon	108593464	108593601	.	-	.	Parent=gene2255
chr6	ENCODE	exon	108593709	108593737	.	-	.	Parent=gene2255
###
chr6	ENCODE	gene	108492082	108502638	.	-	.	ID=gene2256;Name=RP1-111B22.1-002;name2=OSTM1
chr6	ENCODE	exon	108492082	108492196	.	-	.	Parent=gene2256
chr6	ENCODE	exon	108501539	108501695	.	-	.	Parent=gene2256
chr6	ENCODE	exon	108502147	108502638	.	-	.	Parent=gene2256
###
chr6	ENCODE	gene	108550233	108593751	.	-	.	ID=gene2257;Name=RP1-111B22.1-007;name2=OSTM1
chr6	ENCODE	exon	108550233	108550611	.	-	.	Parent=gene2257
chr6	ENCODE	exon	108593464	108593601	.	-	.	Parent=gene2257
chr6	ENCODE	exon	108593709	108593751	.	-	.	Parent=gene2257
###
chr6	ENCODE	gene	108593955	108616706	.	+	.	ID=gene2258;Name=RP3-429G5.1-001;name2=NR2E1
chr6	ENCODE	exon	108593955	108594687	.	+	.	Parent=gene2258
chr6	ENCODE	CDS	108594663	108594687	.	+	0	Parent=gene2258
chr6	ENCODE	exon	108599355	108599500	.	+	.	Parent=gene2258
chr6	ENCODE	CDS	108599355	108599500	.	+	2	Parent=gene2258
chr6	ENCODE	exon	108602733	108602820	.	+	.	Parent=gene2258
chr6	ENCODE	CDS	108602733	108602820	.	+	0	Parent=gene2258
chr6	ENCODE	exon	108604400	108604635	.	+	.	Parent=gene2258
chr6	ENCODE	CDS	108604400	108604635	.	+	2	Parent=gene2258
chr6	ENCODE	exon	108605992	108606138	.	+	.	Parent=gene2258
chr6	ENCODE	CDS	108605992	108606138	.	+	0	Parent=gene2258
chr6	ENCODE	exon	108608220	108608316	.	+	.	Parent=gene2258
chr6	ENCODE	CDS	108608220	108608316	.	+	0	Parent=gene2258
chr6	ENCODE	exon	108608704	108608853	.	+	.	Parent=gene2258
chr6	ENCODE	CDS	108608704	108608853	.	+	2	Parent=gene2258
chr6	ENCODE	exon	108609443	108609548	.	+	.	Parent=gene2258
chr6	ENCODE	CDS	108609443	108609548	.	+	2	Parent=gene2258
chr6	ENCODE	CDS	108615198	108615360	.	+	1	Parent=gene2258
chr6	ENCODE	exon	108615198	108616706	.	+	.	Parent=gene2258
###
chr6	ENCODE	gene	108595920	108616699	.	+	.	ID=gene2259;Name=RP3-429G5.1-002;name2=NR2E1
chr6	ENCODE	exon	108595920	108596059	.	+	.	Parent=gene2259
chr6	ENCODE	CDS	108595924	108596059	.	+	0	Parent=gene2259
chr6	ENCODE	exon	108599355	108599500	.	+	.	Parent=gene2259
chr6	ENCODE	CDS	108599355	108599500	.	+	2	Parent=gene2259
chr6	ENCODE	exon	108602733	108602820	.	+	.	Parent=gene2259
chr6	ENCODE	CDS	108602733	108602820	.	+	0	Parent=gene2259
chr6	ENCODE	exon	108604400	108604635	.	+	.	Parent=gene2259
chr6	ENCODE	CDS	108604400	108604635	.	+	2	Parent=gene2259
chr6	ENCODE	exon	108605992	108606138	.	+	.	Parent=gene2259
chr6	ENCODE	CDS	108605992	108606138	.	+	0	Parent=gene2259
chr6	ENCODE	exon	108608220	108608316	.	+	.	Parent=gene2259
chr6	ENCODE	CDS	108608220	108608316	.	+	0	Parent=gene2259
chr6	ENCODE	exon	108608704	108608853	.	+	.	Parent=gene2259
chr6	ENCODE	CDS	108608704	108608853	.	+	2	Parent=gene2259
chr6	ENCODE	exon	108609443	108609548	.	+	.	Parent=gene2259
chr6	ENCODE	CDS	108609443	108609548	.	+	2	Parent=gene2259
chr6	ENCODE	CDS	108615198	108615360	.	+	1	Parent=gene2259
chr6	ENCODE	exon	108615198	108616699	.	+	.	Parent=gene2259
###
chr6	ENCODE	gene	108596660	108604523	.	+	.	ID=gene2260;Name=RP3-429G5.1-003;name2=NR2E1
chr6	ENCODE	exon	108596660	108596818	.	+	.	Parent=gene2260
chr6	ENCODE	exon	108599355	108599500	.	+	.	Parent=gene2260
chr6	ENCODE	exon	108602733	108602820	.	+	.	Parent=gene2260
chr6	ENCODE	CDS	108602808	108602820	.	+	0	Parent=gene2260
chr6	ENCODE	exon	108604400	108604523	.	+	.	Parent=gene2260
chr6	ENCODE	CDS	108604400	108604523	.	+	2	Parent=gene2260
###
chr6	ENCODE	gene	108604001	108606044	.	+	.	ID=gene2261;Name=RP3-429G5.1-004;name2=NR2E1
chr6	ENCODE	exon	108604001	108604222	.	+	.	Parent=gene2261
chr6	ENCODE	exon	108604400	108604635	.	+	.	Parent=gene2261
chr6	ENCODE	exon	108605992	108606044	.	+	.	Parent=gene2261
###
chr6	ENCODE	gene	108639119	108689157	.	-	.	ID=gene2262;Name=RP3-429G5.4-001;name2=SNX3
chr6	ENCODE	exon	108639119	108640151	.	-	.	Parent=gene2262
chr6	ENCODE	CDS	108640046	108640151	.	-	1	Parent=gene2262
chr6	ENCODE	exon	108642395	108642519	.	-	.	Parent=gene2262
chr6	ENCODE	CDS	108642395	108642519	.	-	0	Parent=gene2262
chr6	ENCODE	exon	108650847	108650942	.	-	.	Parent=gene2262
chr6	ENCODE	CDS	108650847	108650942	.	-	0	Parent=gene2262
chr6	ENCODE	CDS	108688657	108688818	.	-	0	Parent=gene2262
chr6	ENCODE	exon	108688657	108689157	.	-	.	Parent=gene2262
###
chr6	ENCODE	gene	108639410	108688861	.	-	.	ID=gene2263;Name=RP3-429G5.4-004;name2=SNX3
chr6	ENCODE	exon	108639410	108640151	.	-	.	Parent=gene2263
chr6	ENCODE	CDS	108640046	108640151	.	-	1	Parent=gene2263
chr6	ENCODE	exon	108642395	108642519	.	-	.	Parent=gene2263
chr6	ENCODE	CDS	108642395	108642519	.	-	0	Parent=gene2263
chr6	ENCODE	CDS	108688657	108688818	.	-	0	Parent=gene2263
chr6	ENCODE	exon	108688657	108688861	.	-	.	Parent=gene2263
###
chr6	ENCODE	gene	108639410	108689143	.	-	.	ID=gene2264;name2=SNX3;Name=RP3-429G5.4-002
chr6	ENCODE	exon	108639410	108640151	.	-	.	Parent=gene2264
chr6	ENCODE	exon	108642395	108642519	.	-	.	Parent=gene2264
chr6	ENCODE	exon	108650131	108650217	.	-	.	Parent=gene2264
chr6	ENCODE	exon	108650847	108650942	.	-	.	Parent=gene2264
chr6	ENCODE	exon	108688657	108689143	.	-	.	Parent=gene2264
###
chr6	ENCODE	gene	108639902	108689141	.	-	.	ID=gene2265;Name=RP3-429G5.4-003;name2=SNX3
chr6	ENCODE	exon	108639902	108640151	.	-	.	Parent=gene2265
chr6	ENCODE	CDS	108640046	108640151	.	-	1	Parent=gene2265
chr6	ENCODE	exon	108642395	108642519	.	-	.	Parent=gene2265
chr6	ENCODE	CDS	108642395	108642519	.	-	0	Parent=gene2265
chr6	ENCODE	exon	108650847	108650942	.	-	.	Parent=gene2265
chr6	ENCODE	CDS	108650847	108650942	.	-	0	Parent=gene2265
chr6	ENCODE	CDS	108688723	108688818	.	-	0	Parent=gene2265
chr6	ENCODE	exon	108688723	108689141	.	-	.	Parent=gene2265
###
chr6	ENCODE	gene	108722791	108829951	.	+	.	ID=gene2266;Name=RP3-479O19.1-001;name2=LACE1
chr6	ENCODE	exon	108722791	108723115	.	+	.	Parent=gene2266
chr6	ENCODE	exon	108751722	108751945	.	+	.	Parent=gene2266
chr6	ENCODE	exon	108774885	108774936	.	+	.	Parent=gene2266
chr6	ENCODE	exon	108783551	108783652	.	+	.	Parent=gene2266
chr6	ENCODE	exon	108784587	108784717	.	+	.	Parent=gene2266
chr6	ENCODE	exon	108794130	108794229	.	+	.	Parent=gene2266
chr6	ENCODE	exon	108829893	108829951	.	+	.	Parent=gene2266
###
chr6	ENCODE	gene	108722888	108774887	.	+	.	ID=gene2267;name2=LACE1;Name=RP3-479O19.1-004
chr6	ENCODE	exon	108722888	108723115	.	+	.	Parent=gene2267
chr6	ENCODE	exon	108751722	108751945	.	+	.	Parent=gene2267
chr6	ENCODE	exon	108772672	108772758	.	+	.	Parent=gene2267
chr6	ENCODE	exon	108774885	108774887	.	+	.	Parent=gene2267
###
chr6	ENCODE	gene	108723098	108829951	.	+	.	ID=gene2268;name2=LACE1;Name=RP3-479O19.1-006
chr6	ENCODE	exon	108723098	108723115	.	+	.	Parent=gene2268
chr6	ENCODE	exon	108783551	108783652	.	+	.	Parent=gene2268
chr6	ENCODE	exon	108784587	108784717	.	+	.	Parent=gene2268
chr6	ENCODE	exon	108794130	108794229	.	+	.	Parent=gene2268
chr6	ENCODE	exon	108829893	108829951	.	+	.	Parent=gene2268
###
chr6	ENCODE	gene	108723650	108784648	.	+	.	ID=gene2269;Name=RP3-479O19.1-007;name2=LACE1
chr6	ENCODE	exon	108723650	108723776	.	+	.	Parent=gene2269
chr6	ENCODE	exon	108747514	108747688	.	+	.	Parent=gene2269
chr6	ENCODE	CDS	108747649	108747688	.	+	0	Parent=gene2269
chr6	ENCODE	exon	108751722	108751945	.	+	.	Parent=gene2269
chr6	ENCODE	CDS	108751722	108751945	.	+	2	Parent=gene2269
chr6	ENCODE	exon	108774885	108774936	.	+	.	Parent=gene2269
chr6	ENCODE	CDS	108774885	108774936	.	+	0	Parent=gene2269
chr6	ENCODE	exon	108783551	108783652	.	+	.	Parent=gene2269
chr6	ENCODE	CDS	108783551	108783652	.	+	2	Parent=gene2269
chr6	ENCODE	exon	108784587	108784648	.	+	.	Parent=gene2269
chr6	ENCODE	CDS	108784587	108784648	.	+	2	Parent=gene2269
###
chr6	ENCODE	gene	108784587	108794229	.	+	.	ID=gene2270;Name=RP3-479O19.1-002;name2=LACE1
chr6	ENCODE	exon	108784587	108784717	.	+	.	Parent=gene2270
chr6	ENCODE	exon	108794130	108794229	.	+	.	Parent=gene2270
###
chr6	ENCODE	gene	132221501	132253675	.	+	.	ID=gene2271;Name=RP1-131F15.1-004;name2=ENPP1
chr6	ENCODE	exon	132221501	132221580	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132223220	132223339	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132224428	132224537	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132227339	132227404	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132227725	132227771	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132230851	132230959	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132232191	132232322	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132234903	132234934	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132235756	132235883	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132237101	132237170	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132238609	132238696	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132239825	132239994	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132241375	132241426	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132242713	132242867	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132245178	132245307	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132246527	132246607	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132247764	132247896	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132249395	132249557	.	+	.	Parent=gene2271
chr6	ENCODE	exon	132253174	132253675	.	+	.	Parent=gene2271
###
chr6	ENCODE	gene	132221501	132257988	.	+	.	ID=gene2272;name2=ENPP1;Name=RP1-131F15.1-001
chr6	ENCODE	exon	132221501	132221580	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132223220	132223339	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132224428	132224537	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132227339	132227404	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132227699	132227771	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132230851	132230959	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132232191	132232322	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132234903	132234934	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132235756	132235883	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132237101	132237170	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132238609	132238696	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132239825	132239994	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132241375	132241426	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132242713	132242867	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132245178	132245307	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132246527	132246607	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132247764	132247896	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132249395	132249557	.	+	.	Parent=gene2272
chr6	ENCODE	exon	132253174	132257988	.	+	.	Parent=gene2272
###
chr6	ENCODE	gene	132224443	132240690	.	+	.	ID=gene2273;name2=ENPP1;Name=RP1-131F15.1-002
chr6	ENCODE	exon	132224443	132224537	.	+	.	Parent=gene2273
chr6	ENCODE	exon	132227339	132227404	.	+	.	Parent=gene2273
chr6	ENCODE	exon	132227725	132227771	.	+	.	Parent=gene2273
chr6	ENCODE	exon	132230851	132230959	.	+	.	Parent=gene2273
chr6	ENCODE	exon	132232191	132232322	.	+	.	Parent=gene2273
chr6	ENCODE	exon	132234903	132234934	.	+	.	Parent=gene2273
chr6	ENCODE	exon	132235756	132235883	.	+	.	Parent=gene2273
chr6	ENCODE	exon	132237101	132237170	.	+	.	Parent=gene2273
chr6	ENCODE	exon	132238609	132238696	.	+	.	Parent=gene2273
chr6	ENCODE	exon	132239825	132240690	.	+	.	Parent=gene2273
###
chr6	ENCODE	gene	132311009	132314206	.	-	.	ID=gene2274;Name=RP11-69I8.1-001;name2=CTGF
chr6	ENCODE	exon	132311009	132312393	.	-	.	Parent=gene2274
chr6	ENCODE	CDS	132312097	132312393	.	-	0	Parent=gene2274
chr6	ENCODE	exon	132312782	132312993	.	-	.	Parent=gene2274
chr6	ENCODE	CDS	132312782	132312993	.	-	2	Parent=gene2274
chr6	ENCODE	exon	132313125	132313376	.	-	.	Parent=gene2274
chr6	ENCODE	CDS	132313125	132313376	.	-	2	Parent=gene2274
chr6	ENCODE	exon	132313603	132313825	.	-	.	Parent=gene2274
chr6	ENCODE	CDS	132313603	132313825	.	-	0	Parent=gene2274
chr6	ENCODE	CDS	132313940	132314005	.	-	0	Parent=gene2274
chr6	ENCODE	exon	132313940	132314206	.	-	.	Parent=gene2274
###
chr6	ENCODE	gene	132311012	132314205	.	-	.	ID=gene2275;Name=RP11-69I8.1-003;name2=CTGF
chr6	ENCODE	exon	132311012	132312390	.	-	.	Parent=gene2275
chr6	ENCODE	exon	132312782	132312993	.	-	.	Parent=gene2275
chr6	ENCODE	exon	132313125	132313376	.	-	.	Parent=gene2275
chr6	ENCODE	exon	132313603	132313726	.	-	.	Parent=gene2275
chr6	ENCODE	exon	132314050	132314205	.	-	.	Parent=gene2275
###
chr6	ENCODE	gene	132311014	132314206	.	-	.	ID=gene2276;Name=RP11-69I8.1-002;name2=CTGF
chr6	ENCODE	exon	132311014	132312393	.	-	.	Parent=gene2276
chr6	ENCODE	exon	132312782	132312993	.	-	.	Parent=gene2276
chr6	ENCODE	exon	132313125	132313376	.	-	.	Parent=gene2276
chr6	ENCODE	exon	132313603	132313717	.	-	.	Parent=gene2276
chr6	ENCODE	exon	132313976	132314206	.	-	.	Parent=gene2276
###
chr6	ENCODE	gene	132312060	132314203	.	-	.	ID=gene2277;name2=CTGF;Name=RP11-69I8.1-005
chr6	ENCODE	exon	132312060	132312393	.	-	.	Parent=gene2277
chr6	ENCODE	exon	132312782	132312993	.	-	.	Parent=gene2277
chr6	ENCODE	exon	132313125	132313224	.	-	.	Parent=gene2277
chr6	ENCODE	exon	132314001	132314203	.	-	.	Parent=gene2277
###
chr6	ENCODE	gene	132312319	132314205	.	-	.	ID=gene2278;Name=RP11-69I8.1-004;name2=CTGF
chr6	ENCODE	exon	132312319	132312393	.	-	.	Parent=gene2278
chr6	ENCODE	exon	132312782	132312993	.	-	.	Parent=gene2278
chr6	ENCODE	exon	132313125	132313376	.	-	.	Parent=gene2278
chr6	ENCODE	exon	132313603	132313675	.	-	.	Parent=gene2278
chr6	ENCODE	exon	132314163	132314205	.	-	.	Parent=gene2278
###
chr6	ENCODE	gene	132658887	132691426	.	-	.	ID=gene2279;Name=RP1-248E1.1-002;name2=MOXD1
chr6	ENCODE	exon	132658887	132660149	.	-	.	Parent=gene2279
chr6	ENCODE	exon	132660619	132660787	.	-	.	Parent=gene2279
chr6	ENCODE	exon	132678467	132678609	.	-	.	Parent=gene2279
chr6	ENCODE	exon	132683461	132683520	.	-	.	Parent=gene2279
chr6	ENCODE	exon	132685511	132685702	.	-	.	Parent=gene2279
chr6	ENCODE	exon	132686763	132686929	.	-	.	Parent=gene2279
chr6	ENCODE	exon	132690845	132690947	.	-	.	Parent=gene2279
chr6	ENCODE	exon	132691247	132691426	.	-	.	Parent=gene2279
###
chr6	ENCODE	gene	132658901	132691426	.	-	.	ID=gene2280;Name=RP1-248E1.1-001;name2=MOXD1
chr6	ENCODE	exon	132658901	132660149	.	-	.	Parent=gene2280
chr6	ENCODE	exon	132660619	132660787	.	-	.	Parent=gene2280
chr6	ENCODE	exon	132678467	132678609	.	-	.	Parent=gene2280
chr6	ENCODE	exon	132683461	132683520	.	-	.	Parent=gene2280
chr6	ENCODE	exon	132685511	132685702	.	-	.	Parent=gene2280
chr6	ENCODE	exon	132686763	132686929	.	-	.	Parent=gene2280
chr6	ENCODE	exon	132690845	132690947	.	-	.	Parent=gene2280
chr6	ENCODE	exon	132691247	132691426	.	-	.	Parent=gene2280
###
chr6	ENCODE	gene	132659751	132685609	.	-	.	ID=gene2281;Name=RP1-248E1.1-003;name2=MOXD1
chr6	ENCODE	exon	132659751	132660149	.	-	.	Parent=gene2281
chr6	ENCODE	exon	132660619	132660641	.	-	.	Parent=gene2281
chr6	ENCODE	exon	132685511	132685609	.	-	.	Parent=gene2281
###
chr6	ENCODE	gene	132678529	132687979	.	-	.	ID=gene2282;Name=RP1-248E1.1-004;name2=MOXD1
chr6	ENCODE	exon	132678529	132678609	.	-	.	Parent=gene2282
chr6	ENCODE	exon	132683461	132683520	.	-	.	Parent=gene2282
chr6	ENCODE	exon	132685511	132685702	.	-	.	Parent=gene2282
chr6	ENCODE	exon	132686763	132686929	.	-	.	Parent=gene2282
chr6	ENCODE	exon	132687912	132687979	.	-	.	Parent=gene2282
###
chr7	ENCODE	gene	26905852	26908833	.	-	.	ID=gene2283;Name=AC004079.5-001;name2=HOXA1
chr7	ENCODE	exon	26905852	26907654	.	-	.	Parent=gene2283
chr7	ENCODE	CDS	26907299	26907654	.	-	2	Parent=gene2283
chr7	ENCODE	CDS	26908120	26908771	.	-	0	Parent=gene2283
chr7	ENCODE	exon	26908120	26908833	.	-	.	Parent=gene2283
###
chr7	ENCODE	gene	26906162	26908833	.	-	.	ID=gene2284;Name=AC004079.5-002;name2=HOXA1
chr7	ENCODE	exon	26906162	26907654	.	-	.	Parent=gene2284
chr7	ENCODE	exon	26908120	26908214	.	-	.	Parent=gene2284
chr7	ENCODE	CDS	26908155	26908214	.	-	0	Parent=gene2284
chr7	ENCODE	CDS	26908418	26908771	.	-	0	Parent=gene2284
chr7	ENCODE	exon	26908418	26908833	.	-	.	Parent=gene2284
###
chr7	ENCODE	gene	26913216	26915545	.	-	.	ID=gene2285;Name=AC004079.1-001;name2=HOXA2
chr7	ENCODE	exon	26913216	26914324	.	-	.	Parent=gene2285
chr7	ENCODE	CDS	26913585	26914324	.	-	2	Parent=gene2285
chr7	ENCODE	CDS	26914969	26915359	.	-	0	Parent=gene2285
chr7	ENCODE	exon	26914969	26915545	.	-	.	Parent=gene2285
###
chr7	ENCODE	gene	26919043	26932454	.	-	.	ID=gene2286;Name=AC004079.3-003;name2=HOXA3
chr7	ENCODE	exon	26919043	26921579	.	-	.	Parent=gene2286
chr7	ENCODE	CDS	26920774	26921579	.	-	2	Parent=gene2286
chr7	ENCODE	CDS	26922974	26923499	.	-	0	Parent=gene2286
chr7	ENCODE	exon	26922974	26923619	.	-	.	Parent=gene2286
chr7	ENCODE	exon	26932375	26932454	.	-	.	Parent=gene2286
###
chr7	ENCODE	gene	26919871	26926856	.	-	.	ID=gene2287;Name=AC004079.3-002;name2=HOXA3
chr7	ENCODE	exon	26919871	26921579	.	-	.	Parent=gene2287
chr7	ENCODE	exon	26922974	26923135	.	-	.	Parent=gene2287
chr7	ENCODE	exon	26926777	26926856	.	-	.	Parent=gene2287
###
chr7	ENCODE	gene	26919871	26939879	.	-	.	ID=gene2288;Name=AC004079.3-001;name2=HOXA3
chr7	ENCODE	exon	26919871	26921579	.	-	.	Parent=gene2288
chr7	ENCODE	CDS	26920774	26921579	.	-	2	Parent=gene2288
chr7	ENCODE	CDS	26922974	26923499	.	-	0	Parent=gene2288
chr7	ENCODE	exon	26922974	26923619	.	-	.	Parent=gene2288
chr7	ENCODE	exon	26935418	26935501	.	-	.	Parent=gene2288
chr7	ENCODE	exon	26939745	26939879	.	-	.	Parent=gene2288
###
chr7	ENCODE	gene	26923247	26953065	.	-	.	ID=gene2289;Name=AC004079.3-005;name2=HOXA3
chr7	ENCODE	CDS	26923247	26923499	.	-	0	Parent=gene2289
chr7	ENCODE	exon	26923247	26923619	.	-	.	Parent=gene2289
chr7	ENCODE	exon	26935418	26935501	.	-	.	Parent=gene2289
chr7	ENCODE	exon	26952942	26953065	.	-	.	Parent=gene2289
###
chr7	ENCODE	gene	26923338	26926704	.	-	.	ID=gene2290;Name=AC004079.3-006;name2=HOXA3
chr7	ENCODE	CDS	26923338	26923499	.	-	0	Parent=gene2290
chr7	ENCODE	exon	26923338	26923619	.	-	.	Parent=gene2290
chr7	ENCODE	exon	26926484	26926704	.	-	.	Parent=gene2290
###
chr7	ENCODE	gene	26923550	26953067	.	-	.	ID=gene2291;Name=AC004079.3-004;name2=HOXA3
chr7	ENCODE	exon	26923550	26923619	.	-	.	Parent=gene2291
chr7	ENCODE	exon	26935418	26935501	.	-	.	Parent=gene2291
chr7	ENCODE	exon	26937293	26937408	.	-	.	Parent=gene2291
chr7	ENCODE	exon	26939745	26939929	.	-	.	Parent=gene2291
chr7	ENCODE	exon	26952942	26953067	.	-	.	Parent=gene2291
###
chr7	ENCODE	gene	26941366	26943658	.	-	.	ID=gene2292;name2=HOXA4;Name=AC004080.5-001
chr7	ENCODE	exon	26941366	26942430	.	-	.	Parent=gene2292
chr7	ENCODE	CDS	26942084	26942430	.	-	2	Parent=gene2292
chr7	ENCODE	CDS	26942977	26943592	.	-	0	Parent=gene2292
chr7	ENCODE	exon	26942977	26943658	.	-	.	Parent=gene2292
###
chr7	ENCODE	gene	26953911	26956703	.	-	.	ID=gene2293;Name=AC004080.7-001;name2=HOXA5
chr7	ENCODE	exon	26953911	26954944	.	-	.	Parent=gene2293
chr7	ENCODE	CDS	26954694	26954944	.	-	2	Parent=gene2293
chr7	ENCODE	CDS	26955905	26956466	.	-	0	Parent=gene2293
chr7	ENCODE	exon	26955905	26956703	.	-	.	Parent=gene2293
###
chr7	ENCODE	gene	26954666	26955634	.	-	.	ID=gene2294;Name=AC004080.7-002;name2=HOXA5
chr7	ENCODE	exon	26954666	26954944	.	-	.	Parent=gene2294
chr7	ENCODE	exon	26955585	26955634	.	-	.	Parent=gene2294
###
chr7	ENCODE	gene	26958255	26960717	.	-	.	ID=gene2295;Name=AC004080.2-003;name2=HOXA6
chr7	ENCODE	exon	26958255	26958776	.	-	.	Parent=gene2295
chr7	ENCODE	CDS	26958517	26958776	.	-	2	Parent=gene2295
chr7	ENCODE	CDS	26960167	26960608	.	-	0	Parent=gene2295
chr7	ENCODE	exon	26960167	26960717	.	-	.	Parent=gene2295
###
chr7	ENCODE	gene	26958255	26963462	.	-	.	ID=gene2296;Name=AC004080.2-001;name2=HOXA6
chr7	ENCODE	exon	26958255	26958776	.	-	.	Parent=gene2296
chr7	ENCODE	exon	26960167	26960428	.	-	.	Parent=gene2296
chr7	ENCODE	exon	26963167	26963462	.	-	.	Parent=gene2296
###
chr7	ENCODE	gene	26960179	26963836	.	-	.	ID=gene2297;Name=AC004080.2-002;name2=HOXA6
chr7	ENCODE	exon	26960179	26960281	.	-	.	Parent=gene2297
chr7	ENCODE	exon	26963167	26963836	.	-	.	Parent=gene2297
###
chr7	ENCODE	gene	26960225	26965457	.	-	.	ID=gene2298;Name=AC004080.2-004;name2=HOXA6
chr7	ENCODE	exon	26960225	26960281	.	-	.	Parent=gene2298
chr7	ENCODE	exon	26965147	26965457	.	-	.	Parent=gene2298
###
chr7	ENCODE	gene	26966575	26970795	.	-	.	ID=gene2299;Name=AC004080.3-002;name2=HOXA7
chr7	ENCODE	exon	26966575	26968081	.	-	.	Parent=gene2299
chr7	ENCODE	CDS	26967768	26968081	.	-	2	Parent=gene2299
chr7	ENCODE	CDS	26969026	26969404	.	-	0	Parent=gene2299
chr7	ENCODE	exon	26969026	26969613	.	-	.	Parent=gene2299
chr7	ENCODE	exon	26969977	26970147	.	-	.	Parent=gene2299
chr7	ENCODE	exon	26970683	26970795	.	-	.	Parent=gene2299
###
chr7	ENCODE	gene	26967642	26968863	.	-	.	ID=gene2300;Name=AC004080.3-001;name2=HOXA7
chr7	ENCODE	exon	26967642	26968081	.	-	.	Parent=gene2300
chr7	ENCODE	exon	26968826	26968863	.	-	.	Parent=gene2300
###
chr7	ENCODE	gene	26975297	26978369	.	-	.	ID=gene2301;Name=AC004080.4-001;name2=HOXA9
chr7	ENCODE	exon	26975297	26976700	.	-	.	Parent=gene2301
chr7	ENCODE	CDS	26976462	26976700	.	-	2	Parent=gene2301
chr7	ENCODE	CDS	26977737	26978316	.	-	0	Parent=gene2301
chr7	ENCODE	exon	26977737	26978369	.	-	.	Parent=gene2301
###
chr7	ENCODE	gene	26975459	26982303	.	-	.	ID=gene2302;Name=AC004080.4-002;name2=HOXA9
chr7	ENCODE	exon	26975459	26976700	.	-	.	Parent=gene2302
chr7	ENCODE	exon	26982153	26982303	.	-	.	Parent=gene2302
###
chr7	ENCODE	gene	26976166	26983357	.	-	.	ID=gene2303;Name=AC004080.4-004;name2=HOXA9
chr7	ENCODE	exon	26976166	26976700	.	-	.	Parent=gene2303
chr7	ENCODE	exon	26977737	26977826	.	-	.	Parent=gene2303
chr7	ENCODE	exon	26983290	26983357	.	-	.	Parent=gene2303
###
chr7	ENCODE	gene	26976380	26978385	.	-	.	ID=gene2304;Name=AC004080.4-005;name2=HOXA9
chr7	ENCODE	exon	26976380	26976700	.	-	.	Parent=gene2304
chr7	ENCODE	exon	26977737	26977826	.	-	.	Parent=gene2304
chr7	ENCODE	CDS	26977823	26977826	.	-	1	Parent=gene2304
chr7	ENCODE	CDS	26978000	26978316	.	-	0	Parent=gene2304
chr7	ENCODE	exon	26978000	26978385	.	-	.	Parent=gene2304
###
chr7	ENCODE	gene	26976523	26988039	.	-	.	ID=gene2305;Name=AC004080.4-006;name2=HOXA9
chr7	ENCODE	exon	26976523	26976700	.	-	.	Parent=gene2305
chr7	ENCODE	exon	26987561	26988039	.	-	.	Parent=gene2305
###
chr7	ENCODE	gene	26976541	26982596	.	-	.	ID=gene2306;Name=AC004080.4-003;name2=HOXA9
chr7	ENCODE	exon	26976541	26976700	.	-	.	Parent=gene2306
chr7	ENCODE	exon	26977737	26977826	.	-	.	Parent=gene2306
chr7	ENCODE	exon	26982326	26982596	.	-	.	Parent=gene2306
###
chr7	ENCODE	gene	26983450	26987163	.	-	.	ID=gene2307;Name=AC004080.9-001;name2=HOXA10
chr7	ENCODE	exon	26983450	26985032	.	-	.	Parent=gene2307
chr7	ENCODE	CDS	26984758	26985032	.	-	2	Parent=gene2307
chr7	ENCODE	CDS	26986208	26987114	.	-	0	Parent=gene2307
chr7	ENCODE	exon	26986208	26987163	.	-	.	Parent=gene2307
###
chr7	ENCODE	gene	26984092	26987154	.	-	.	ID=gene2308;name2=HOXA10;Name=AC004080.9-002
chr7	ENCODE	exon	26984092	26985032	.	-	.	Parent=gene2308
chr7	ENCODE	exon	26986208	26986473	.	-	.	Parent=gene2308
chr7	ENCODE	exon	26986788	26987154	.	-	.	Parent=gene2308
###
chr7	ENCODE	gene	26984092	26993120	.	-	.	ID=gene2309;Name=AC004080.9-003;name2=HOXA10
chr7	ENCODE	exon	26984092	26985032	.	-	.	Parent=gene2309
chr7	ENCODE	CDS	26984758	26985032	.	-	2	Parent=gene2309
chr7	ENCODE	CDS	26992505	26992514	.	-	0	Parent=gene2309
chr7	ENCODE	exon	26992505	26993120	.	-	.	Parent=gene2309
###
chr7	ENCODE	gene	26984237	26985822	.	-	.	ID=gene2310;Name=AC004080.9-006;name2=HOXA10
chr7	ENCODE	exon	26984237	26985032	.	-	.	Parent=gene2310
chr7	ENCODE	exon	26985677	26985822	.	-	.	Parent=gene2310
###
chr7	ENCODE	gene	26984322	26985748	.	-	.	ID=gene2311;name2=HOXA10;Name=AC004080.9-005
chr7	ENCODE	exon	26984322	26985032	.	-	.	Parent=gene2311
chr7	ENCODE	exon	26985273	26985748	.	-	.	Parent=gene2311
###
chr7	ENCODE	gene	26984636	26985748	.	-	.	ID=gene2312;Name=AC004080.9-004;name2=HOXA10
chr7	ENCODE	exon	26984636	26985032	.	-	.	Parent=gene2312
chr7	ENCODE	exon	26985423	26985748	.	-	.	Parent=gene2312
###
chr7	ENCODE	gene	26994016	26998075	.	-	.	ID=gene2313;Name=AC004080.6-001;name2=HOXA11
chr7	ENCODE	exon	26994016	26995887	.	-	.	Parent=gene2313
chr7	ENCODE	CDS	26995655	26995887	.	-	2	Parent=gene2313
chr7	ENCODE	CDS	26997295	26998003	.	-	0	Parent=gene2313
chr7	ENCODE	exon	26997295	26998075	.	-	.	Parent=gene2313
###
chr7	ENCODE	gene	26994369	26998082	.	-	.	ID=gene2314;Name=AC004080.6-002;name2=HOXA11
chr7	ENCODE	exon	26994369	26995887	.	-	.	Parent=gene2314
chr7	ENCODE	exon	26997295	26997844	.	-	.	Parent=gene2314
chr7	ENCODE	exon	26998015	26998082	.	-	.	Parent=gene2314
###
chr7	ENCODE	gene	27008262	27012965	.	-	.	ID=gene2315;Name=AC004080.10-001;name2=HOXA13
chr7	ENCODE	exon	27008262	27011301	.	-	.	Parent=gene2315
chr7	ENCODE	CDS	27011057	27011301	.	-	2	Parent=gene2315
chr7	ENCODE	CDS	27012015	27012936	.	-	0	Parent=gene2315
chr7	ENCODE	exon	27012015	27012965	.	-	.	Parent=gene2315
###
chr7	ENCODE	gene	27055524	27060691	.	+	.	ID=gene2316;Name=AC004080.8-001;name2=EVX1
chr7	ENCODE	exon	27055524	27056316	.	+	.	Parent=gene2316
chr7	ENCODE	CDS	27055890	27056316	.	+	0	Parent=gene2316
chr7	ENCODE	exon	27057907	27058163	.	+	.	Parent=gene2316
chr7	ENCODE	CDS	27057907	27058163	.	+	2	Parent=gene2316
chr7	ENCODE	CDS	27058745	27059284	.	+	0	Parent=gene2316
chr7	ENCODE	exon	27058745	27060691	.	+	.	Parent=gene2316
###
chr7	ENCODE	gene	89428340	89438792	.	+	.	ID=gene2317;Name=AC004969.1-001;name2=STEAP1
chr7	ENCODE	exon	89428340	89428508	.	+	.	Parent=gene2317
chr7	ENCODE	exon	89433723	89433837	.	+	.	Parent=gene2317
chr7	ENCODE	CDS	89433754	89433837	.	+	0	Parent=gene2317
chr7	ENCODE	exon	89434770	89435282	.	+	.	Parent=gene2317
chr7	ENCODE	CDS	89434770	89435282	.	+	0	Parent=gene2317
chr7	ENCODE	exon	89435879	89436043	.	+	.	Parent=gene2317
chr7	ENCODE	CDS	89435879	89436043	.	+	0	Parent=gene2317
chr7	ENCODE	CDS	89438442	89438699	.	+	0	Parent=gene2317
chr7	ENCODE	exon	89438442	89438792	.	+	.	Parent=gene2317
###
chr7	ENCODE	gene	89435231	89438794	.	+	.	ID=gene2318;Name=AC004969.1-002;name2=STEAP1
chr7	ENCODE	exon	89435231	89435282	.	+	.	Parent=gene2318
chr7	ENCODE	exon	89435879	89436043	.	+	.	Parent=gene2318
chr7	ENCODE	exon	89436939	89437075	.	+	.	Parent=gene2318
chr7	ENCODE	exon	89438442	89438794	.	+	.	Parent=gene2318
###
chr7	ENCODE	gene	89441555	89500988	.	+	.	ID=gene2319;Name=AC002064.1-009;name2=STEAP2
chr7	ENCODE	exon	89441555	89441878	.	+	.	Parent=gene2319
chr7	ENCODE	CDS	89441786	89441878	.	+	0	Parent=gene2319
chr7	ENCODE	exon	89499015	89499539	.	+	.	Parent=gene2319
chr7	ENCODE	CDS	89499015	89499539	.	+	0	Parent=gene2319
chr7	ENCODE	exon	89500936	89500988	.	+	.	Parent=gene2319
chr7	ENCODE	CDS	89500936	89500988	.	+	0	Parent=gene2319
###
chr7	ENCODE	gene	89483235	89485600	.	-	.	ID=gene2320;Name=AC002064.3-001;name2=AC002064.3
chr7	ENCODE	exon	89483235	89483903	.	-	.	Parent=gene2320
chr7	ENCODE	CDS	89483815	89483903	.	-	2	Parent=gene2320
chr7	ENCODE	CDS	89485265	89485400	.	-	0	Parent=gene2320
chr7	ENCODE	exon	89485265	89485600	.	-	.	Parent=gene2320
###
chr7	ENCODE	gene	89485651	89511596	.	+	.	ID=gene2321;Name=AC002064.1-001;name2=STEAP2
chr7	ENCODE	exon	89485651	89486010	.	+	.	Parent=gene2321
chr7	ENCODE	exon	89499015	89499539	.	+	.	Parent=gene2321
chr7	ENCODE	CDS	89499048	89499539	.	+	0	Parent=gene2321
chr7	ENCODE	exon	89500936	89501463	.	+	.	Parent=gene2321
chr7	ENCODE	CDS	89500936	89501463	.	+	0	Parent=gene2321
chr7	ENCODE	exon	89503837	89504001	.	+	.	Parent=gene2321
chr7	ENCODE	CDS	89503837	89504001	.	+	0	Parent=gene2321
chr7	ENCODE	CDS	89506302	89506589	.	+	0	Parent=gene2321
chr7	ENCODE	exon	89506302	89511596	.	+	.	Parent=gene2321
###
chr7	ENCODE	gene	89485709	89511643	.	+	.	ID=gene2322;Name=AC002064.1-002;name2=STEAP2
chr7	ENCODE	exon	89485709	89486010	.	+	.	Parent=gene2322
chr7	ENCODE	exon	89499015	89499539	.	+	.	Parent=gene2322
chr7	ENCODE	CDS	89499048	89499539	.	+	0	Parent=gene2322
chr7	ENCODE	exon	89500936	89501463	.	+	.	Parent=gene2322
chr7	ENCODE	CDS	89500936	89501463	.	+	0	Parent=gene2322
chr7	ENCODE	exon	89503837	89504001	.	+	.	Parent=gene2322
chr7	ENCODE	CDS	89503837	89504001	.	+	0	Parent=gene2322
chr7	ENCODE	exon	89506302	89506449	.	+	.	Parent=gene2322
chr7	ENCODE	CDS	89506302	89506449	.	+	0	Parent=gene2322
chr7	ENCODE	CDS	89510856	89510887	.	+	2	Parent=gene2322
chr7	ENCODE	exon	89510856	89511643	.	+	.	Parent=gene2322
###
chr7	ENCODE	gene	89485825	89511559	.	+	.	ID=gene2323;Name=AC002064.1-004;name2=STEAP2
chr7	ENCODE	exon	89485825	89485899	.	+	.	Parent=gene2323
chr7	ENCODE	exon	89486241	89486301	.	+	.	Parent=gene2323
chr7	ENCODE	exon	89499015	89499539	.	+	.	Parent=gene2323
chr7	ENCODE	CDS	89499048	89499539	.	+	0	Parent=gene2323
chr7	ENCODE	exon	89500936	89501463	.	+	.	Parent=gene2323
chr7	ENCODE	CDS	89500936	89501463	.	+	0	Parent=gene2323
chr7	ENCODE	exon	89503837	89504001	.	+	.	Parent=gene2323
chr7	ENCODE	CDS	89503837	89504001	.	+	0	Parent=gene2323
chr7	ENCODE	CDS	89506302	89506589	.	+	0	Parent=gene2323
chr7	ENCODE	exon	89506302	89511559	.	+	.	Parent=gene2323
###
chr7	ENCODE	gene	89485825	89511573	.	+	.	ID=gene2324;Name=AC002064.1-003;name2=STEAP2
chr7	ENCODE	exon	89485825	89485899	.	+	.	Parent=gene2324
chr7	ENCODE	exon	89486241	89486301	.	+	.	Parent=gene2324
chr7	ENCODE	exon	89499015	89499539	.	+	.	Parent=gene2324
chr7	ENCODE	CDS	89499048	89499539	.	+	0	Parent=gene2324
chr7	ENCODE	exon	89500936	89501463	.	+	.	Parent=gene2324
chr7	ENCODE	CDS	89500936	89501463	.	+	0	Parent=gene2324
chr7	ENCODE	exon	89503837	89504001	.	+	.	Parent=gene2324
chr7	ENCODE	CDS	89503837	89504001	.	+	0	Parent=gene2324
chr7	ENCODE	CDS	89510856	89510930	.	+	0	Parent=gene2324
chr7	ENCODE	exon	89510856	89511573	.	+	.	Parent=gene2324
###
chr7	ENCODE	gene	89485825	89511573	.	+	.	ID=gene2325;Name=AC002064.1-005;name2=STEAP2
chr7	ENCODE	exon	89485825	89485899	.	+	.	Parent=gene2325
chr7	ENCODE	exon	89486241	89486316	.	+	.	Parent=gene2325
chr7	ENCODE	exon	89499015	89499539	.	+	.	Parent=gene2325
chr7	ENCODE	CDS	89499048	89499539	.	+	0	Parent=gene2325
chr7	ENCODE	exon	89500936	89501463	.	+	.	Parent=gene2325
chr7	ENCODE	CDS	89500936	89501463	.	+	0	Parent=gene2325
chr7	ENCODE	exon	89503837	89504001	.	+	.	Parent=gene2325
chr7	ENCODE	CDS	89503837	89504001	.	+	0	Parent=gene2325
chr7	ENCODE	exon	89506302	89506449	.	+	.	Parent=gene2325
chr7	ENCODE	CDS	89506302	89506449	.	+	0	Parent=gene2325
chr7	ENCODE	CDS	89510856	89510887	.	+	2	Parent=gene2325
chr7	ENCODE	exon	89510856	89511573	.	+	.	Parent=gene2325
###
chr7	ENCODE	gene	89485838	89499311	.	+	.	ID=gene2326;Name=AC002064.1-007;name2=STEAP2
chr7	ENCODE	exon	89485838	89486010	.	+	.	Parent=gene2326
chr7	ENCODE	exon	89490460	89490568	.	+	.	Parent=gene2326
chr7	ENCODE	exon	89499015	89499311	.	+	.	Parent=gene2326
chr7	ENCODE	CDS	89499048	89499311	.	+	0	Parent=gene2326
###
chr7	ENCODE	gene	89487785	89511596	.	+	.	ID=gene2327;Name=AC002064.1-006;name2=STEAP2
chr7	ENCODE	exon	89487785	89487825	.	+	.	Parent=gene2327
chr7	ENCODE	exon	89490456	89490568	.	+	.	Parent=gene2327
chr7	ENCODE	exon	89499015	89499539	.	+	.	Parent=gene2327
chr7	ENCODE	CDS	89499048	89499539	.	+	0	Parent=gene2327
chr7	ENCODE	exon	89500936	89501463	.	+	.	Parent=gene2327
chr7	ENCODE	CDS	89500936	89501463	.	+	0	Parent=gene2327
chr7	ENCODE	exon	89503837	89504001	.	+	.	Parent=gene2327
chr7	ENCODE	CDS	89503837	89504001	.	+	0	Parent=gene2327
chr7	ENCODE	exon	89506302	89506449	.	+	.	Parent=gene2327
chr7	ENCODE	CDS	89506302	89506449	.	+	0	Parent=gene2327
chr7	ENCODE	CDS	89510856	89510887	.	+	2	Parent=gene2327
chr7	ENCODE	exon	89510856	89511596	.	+	.	Parent=gene2327
###
chr7	ENCODE	gene	89489239	89500998	.	+	.	ID=gene2328;Name=AC002064.1-008;name2=STEAP2
chr7	ENCODE	exon	89489239	89490568	.	+	.	Parent=gene2328
chr7	ENCODE	exon	89499015	89499539	.	+	.	Parent=gene2328
chr7	ENCODE	exon	89500936	89500998	.	+	.	Parent=gene2328
###
chr7	ENCODE	gene	89519150	89585028	.	+	.	ID=gene2329;Name=AC002064.2-001;name2=AC002064.2
chr7	ENCODE	exon	89519150	89519509	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89519390	89519509	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89529388	89529447	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89529388	89529447	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89532063	89532128	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89532063	89532128	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89535912	89536021	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89535912	89536021	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89539266	89539342	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89539266	89539342	.	+	1	Parent=gene2329
chr7	ENCODE	exon	89542251	89542349	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89542251	89542349	.	+	2	Parent=gene2329
chr7	ENCODE	exon	89545491	89545640	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89545491	89545640	.	+	2	Parent=gene2329
chr7	ENCODE	exon	89545746	89545923	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89545746	89545923	.	+	2	Parent=gene2329
chr7	ENCODE	exon	89547952	89548075	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89547952	89548075	.	+	1	Parent=gene2329
chr7	ENCODE	exon	89551038	89551086	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89551038	89551086	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89551178	89551299	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89551178	89551299	.	+	2	Parent=gene2329
chr7	ENCODE	exon	89553642	89553858	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89553642	89553858	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89556857	89557021	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89556857	89557021	.	+	2	Parent=gene2329
chr7	ENCODE	exon	89560246	89560364	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89560246	89560364	.	+	2	Parent=gene2329
chr7	ENCODE	exon	89562199	89562317	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89562199	89562317	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89571714	89571795	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89571714	89571795	.	+	1	Parent=gene2329
chr7	ENCODE	exon	89573832	89574024	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89573832	89574024	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89577934	89578071	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89577934	89578071	.	+	2	Parent=gene2329
chr7	ENCODE	exon	89578709	89578785	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89578709	89578785	.	+	2	Parent=gene2329
chr7	ENCODE	exon	89580866	89581063	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89580866	89581063	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89581733	89581819	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89581733	89581819	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89583228	89583332	.	+	.	Parent=gene2329
chr7	ENCODE	CDS	89583228	89583332	.	+	0	Parent=gene2329
chr7	ENCODE	CDS	89584033	89584203	.	+	0	Parent=gene2329
chr7	ENCODE	exon	89584033	89585028	.	+	.	Parent=gene2329
###
chr7	ENCODE	gene	89519160	89580870	.	+	.	ID=gene2330;Name=AC002064.2-004;name2=AC002064.2
chr7	ENCODE	exon	89519160	89519509	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89529388	89529447	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89532063	89532128	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89535912	89536021	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89542251	89542349	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89545491	89545640	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89545746	89545923	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89551038	89551086	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89551178	89551299	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89553642	89553858	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89556857	89557021	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89560246	89560364	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89562199	89562317	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89571714	89571795	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89573832	89574024	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89577934	89578071	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89578709	89578785	.	+	.	Parent=gene2330
chr7	ENCODE	exon	89580866	89580870	.	+	.	Parent=gene2330
###
chr7	ENCODE	gene	89519176	89578718	.	+	.	ID=gene2331;Name=AC002064.2-002;name2=AC002064.2
chr7	ENCODE	exon	89519176	89519509	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89529388	89529447	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89532063	89532128	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89535912	89536021	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89539266	89539342	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89542251	89542349	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89545491	89545640	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89547952	89548075	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89549986	89550117	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89551038	89551086	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89551178	89551299	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89553642	89553858	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89556857	89557021	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89560246	89560364	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89561467	89561714	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89562199	89562317	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89571714	89571795	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89573832	89574024	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89577934	89578071	.	+	.	Parent=gene2331
chr7	ENCODE	exon	89578709	89578718	.	+	.	Parent=gene2331
###
chr7	ENCODE	gene	89519181	89573969	.	+	.	ID=gene2332;Name=AC002064.2-005;name2=AC002064.2
chr7	ENCODE	exon	89519181	89519509	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89519390	89519509	.	+	0	Parent=gene2332
chr7	ENCODE	exon	89529388	89529447	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89529388	89529447	.	+	0	Parent=gene2332
chr7	ENCODE	exon	89532063	89532128	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89532063	89532128	.	+	0	Parent=gene2332
chr7	ENCODE	exon	89535912	89536021	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89535912	89536021	.	+	0	Parent=gene2332
chr7	ENCODE	exon	89539266	89539342	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89539266	89539342	.	+	1	Parent=gene2332
chr7	ENCODE	exon	89542251	89542349	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89542251	89542349	.	+	2	Parent=gene2332
chr7	ENCODE	exon	89545491	89545640	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89545491	89545640	.	+	2	Parent=gene2332
chr7	ENCODE	exon	89545746	89545923	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89545746	89545923	.	+	2	Parent=gene2332
chr7	ENCODE	exon	89547952	89548075	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89547952	89548075	.	+	1	Parent=gene2332
chr7	ENCODE	exon	89553642	89553858	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89553642	89553858	.	+	0	Parent=gene2332
chr7	ENCODE	exon	89556857	89557021	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89556857	89557021	.	+	2	Parent=gene2332
chr7	ENCODE	exon	89560246	89560364	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89560246	89560364	.	+	2	Parent=gene2332
chr7	ENCODE	exon	89562199	89562317	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89562199	89562317	.	+	0	Parent=gene2332
chr7	ENCODE	exon	89571714	89571795	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89571714	89571795	.	+	1	Parent=gene2332
chr7	ENCODE	exon	89573931	89573969	.	+	.	Parent=gene2332
chr7	ENCODE	CDS	89573931	89573969	.	+	0	Parent=gene2332
###
chr7	ENCODE	gene	89519390	89547959	.	+	.	ID=gene2333;name2=AC002064.2;Name=AC002064.2-003
chr7	ENCODE	exon	89519390	89519509	.	+	.	Parent=gene2333
chr7	ENCODE	exon	89529388	89529447	.	+	.	Parent=gene2333
chr7	ENCODE	exon	89532063	89532128	.	+	.	Parent=gene2333
chr7	ENCODE	exon	89535912	89536015	.	+	.	Parent=gene2333
chr7	ENCODE	exon	89539266	89539342	.	+	.	Parent=gene2333
chr7	ENCODE	exon	89542251	89542349	.	+	.	Parent=gene2333
chr7	ENCODE	exon	89545491	89545640	.	+	.	Parent=gene2333
chr7	ENCODE	exon	89547952	89547959	.	+	.	Parent=gene2333
###
chr7	ENCODE	gene	89545554	89546184	.	+	.	ID=gene2334;name2=AC002064.2;Name=AC002064.2-008
chr7	ENCODE	exon	89545554	89545640	.	+	.	Parent=gene2334
chr7	ENCODE	CDS	89545554	89545640	.	+	0	Parent=gene2334
chr7	ENCODE	CDS	89545746	89545927	.	+	0	Parent=gene2334
chr7	ENCODE	exon	89545746	89546184	.	+	.	Parent=gene2334
###
chr7	ENCODE	gene	89545868	89584353	.	+	.	ID=gene2335;Name=AC002064.2-006;name2=AC002064.2
chr7	ENCODE	exon	89545868	89545923	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89547952	89548075	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89551038	89551086	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89551178	89551299	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89553642	89553858	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89556857	89557021	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89560246	89560364	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89561467	89561714	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89562199	89562317	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89571714	89571795	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89573832	89578785	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89580866	89581063	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89581733	89581819	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89583228	89583332	.	+	.	Parent=gene2335
chr7	ENCODE	exon	89584033	89584353	.	+	.	Parent=gene2335
###
chr7	ENCODE	gene	89553738	89584255	.	+	.	ID=gene2336;Name=AC002064.2-007;name2=AC002064.2
chr7	ENCODE	exon	89553738	89553858	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89553738	89553858	.	+	0	Parent=gene2336
chr7	ENCODE	exon	89556857	89557021	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89556857	89557021	.	+	2	Parent=gene2336
chr7	ENCODE	exon	89560246	89560364	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89560246	89560364	.	+	2	Parent=gene2336
chr7	ENCODE	exon	89562199	89562317	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89562199	89562317	.	+	0	Parent=gene2336
chr7	ENCODE	exon	89571714	89571795	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89571714	89571795	.	+	1	Parent=gene2336
chr7	ENCODE	exon	89573832	89574024	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89573832	89574024	.	+	0	Parent=gene2336
chr7	ENCODE	exon	89578709	89578785	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89578709	89578785	.	+	2	Parent=gene2336
chr7	ENCODE	exon	89580866	89581063	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89580866	89581063	.	+	0	Parent=gene2336
chr7	ENCODE	exon	89581733	89581819	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89581733	89581819	.	+	0	Parent=gene2336
chr7	ENCODE	exon	89583228	89583332	.	+	.	Parent=gene2336
chr7	ENCODE	CDS	89583228	89583332	.	+	0	Parent=gene2336
chr7	ENCODE	CDS	89584033	89584203	.	+	0	Parent=gene2336
chr7	ENCODE	exon	89584033	89584255	.	+	.	Parent=gene2336
###
chr7	ENCODE	gene	89553754	89560414	.	+	.	ID=gene2337;Name=AC002064.2-009;name2=AC002064.2
chr7	ENCODE	exon	89553754	89553858	.	+	.	Parent=gene2337
chr7	ENCODE	exon	89556857	89557021	.	+	.	Parent=gene2337
chr7	ENCODE	exon	89560246	89560414	.	+	.	Parent=gene2337
###
chr7	ENCODE	gene	89578001	89584265	.	+	.	ID=gene2338;name2=AC002064.2;Name=AC002064.2-011
chr7	ENCODE	exon	89578001	89578071	.	+	.	Parent=gene2338
chr7	ENCODE	CDS	89578001	89578071	.	+	0	Parent=gene2338
chr7	ENCODE	exon	89578709	89578785	.	+	.	Parent=gene2338
chr7	ENCODE	CDS	89578709	89578785	.	+	1	Parent=gene2338
chr7	ENCODE	exon	89581733	89581819	.	+	.	Parent=gene2338
chr7	ENCODE	CDS	89581733	89581819	.	+	2	Parent=gene2338
chr7	ENCODE	exon	89583228	89583332	.	+	.	Parent=gene2338
chr7	ENCODE	CDS	89583228	89583332	.	+	2	Parent=gene2338
chr7	ENCODE	CDS	89584033	89584203	.	+	2	Parent=gene2338
chr7	ENCODE	exon	89584033	89584265	.	+	.	Parent=gene2338
###
chr7	ENCODE	gene	89581042	89584534	.	+	.	ID=gene2339;Name=AC002064.2-012;name2=AC002064.2
chr7	ENCODE	exon	89581042	89581063	.	+	.	Parent=gene2339
chr7	ENCODE	CDS	89581042	89581063	.	+	0	Parent=gene2339
chr7	ENCODE	exon	89581733	89581819	.	+	.	Parent=gene2339
chr7	ENCODE	CDS	89581733	89581819	.	+	2	Parent=gene2339
chr7	ENCODE	CDS	89584033	89584203	.	+	2	Parent=gene2339
chr7	ENCODE	exon	89584033	89584534	.	+	.	Parent=gene2339
###
chr7	ENCODE	gene	89614336	89651537	.	+	.	ID=gene2340;Name=AC006153.3-008;name2=AC006153.3
chr7	ENCODE	exon	89614336	89614489	.	+	.	Parent=gene2340
chr7	ENCODE	CDS	89614484	89614489	.	+	0	Parent=gene2340
chr7	ENCODE	exon	89626781	89626974	.	+	.	Parent=gene2340
chr7	ENCODE	CDS	89626781	89626974	.	+	0	Parent=gene2340
chr7	ENCODE	exon	89628423	89628514	.	+	.	Parent=gene2340
chr7	ENCODE	CDS	89628423	89628514	.	+	1	Parent=gene2340
chr7	ENCODE	exon	89629051	89629195	.	+	.	Parent=gene2340
chr7	ENCODE	CDS	89629051	89629195	.	+	2	Parent=gene2340
chr7	ENCODE	exon	89646120	89646193	.	+	.	Parent=gene2340
chr7	ENCODE	CDS	89646120	89646193	.	+	1	Parent=gene2340
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2340
chr7	ENCODE	CDS	89648267	89648319	.	+	2	Parent=gene2340
chr7	ENCODE	exon	89651472	89651537	.	+	.	Parent=gene2340
chr7	ENCODE	CDS	89651472	89651537	.	+	0	Parent=gene2340
###
chr7	ENCODE	gene	89614336	89651537	.	+	.	ID=gene2341;name2=AC006153.3;Name=AC006153.3-009
chr7	ENCODE	exon	89614336	89614489	.	+	.	Parent=gene2341
chr7	ENCODE	exon	89626781	89626974	.	+	.	Parent=gene2341
chr7	ENCODE	exon	89629051	89629195	.	+	.	Parent=gene2341
chr7	ENCODE	exon	89646120	89646193	.	+	.	Parent=gene2341
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2341
chr7	ENCODE	exon	89651472	89651537	.	+	.	Parent=gene2341
###
chr7	ENCODE	gene	89614336	89651537	.	+	.	ID=gene2342;Name=AC006153.3-010;name2=AC006153.3
chr7	ENCODE	exon	89614336	89614489	.	+	.	Parent=gene2342
chr7	ENCODE	CDS	89614484	89614489	.	+	0	Parent=gene2342
chr7	ENCODE	exon	89616210	89616287	.	+	.	Parent=gene2342
chr7	ENCODE	CDS	89616210	89616287	.	+	0	Parent=gene2342
chr7	ENCODE	exon	89626781	89626974	.	+	.	Parent=gene2342
chr7	ENCODE	CDS	89626781	89626974	.	+	0	Parent=gene2342
chr7	ENCODE	exon	89628423	89628514	.	+	.	Parent=gene2342
chr7	ENCODE	CDS	89628423	89628514	.	+	1	Parent=gene2342
chr7	ENCODE	exon	89629051	89629195	.	+	.	Parent=gene2342
chr7	ENCODE	CDS	89629051	89629195	.	+	2	Parent=gene2342
chr7	ENCODE	exon	89646120	89646193	.	+	.	Parent=gene2342
chr7	ENCODE	CDS	89646120	89646193	.	+	1	Parent=gene2342
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2342
chr7	ENCODE	CDS	89648267	89648319	.	+	2	Parent=gene2342
chr7	ENCODE	exon	89651472	89651537	.	+	.	Parent=gene2342
chr7	ENCODE	CDS	89651472	89651537	.	+	0	Parent=gene2342
###
chr7	ENCODE	gene	89614336	89651540	.	+	.	ID=gene2343;Name=AC006153.3-007;name2=AC006153.3
chr7	ENCODE	exon	89614336	89614489	.	+	.	Parent=gene2343
chr7	ENCODE	exon	89626781	89626974	.	+	.	Parent=gene2343
chr7	ENCODE	exon	89628423	89628514	.	+	.	Parent=gene2343
chr7	ENCODE	exon	89646120	89646193	.	+	.	Parent=gene2343
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2343
chr7	ENCODE	exon	89651472	89651540	.	+	.	Parent=gene2343
###
chr7	ENCODE	gene	89620600	89651534	.	+	.	ID=gene2344;Name=AC006153.3-006;name2=AC006153.3
chr7	ENCODE	exon	89620600	89620662	.	+	.	Parent=gene2344
chr7	ENCODE	exon	89626781	89626974	.	+	.	Parent=gene2344
chr7	ENCODE	exon	89628423	89628514	.	+	.	Parent=gene2344
chr7	ENCODE	exon	89629051	89629195	.	+	.	Parent=gene2344
chr7	ENCODE	exon	89646120	89646193	.	+	.	Parent=gene2344
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2344
chr7	ENCODE	exon	89651472	89651534	.	+	.	Parent=gene2344
###
chr7	ENCODE	gene	89620630	89659608	.	+	.	ID=gene2345;Name=AC006153.3-002;name2=GTPBP10
chr7	ENCODE	exon	89620630	89620739	.	+	.	Parent=gene2345
chr7	ENCODE	CDS	89620707	89620739	.	+	0	Parent=gene2345
chr7	ENCODE	exon	89626781	89626974	.	+	.	Parent=gene2345
chr7	ENCODE	CDS	89626781	89626974	.	+	0	Parent=gene2345
chr7	ENCODE	exon	89646120	89646193	.	+	.	Parent=gene2345
chr7	ENCODE	CDS	89646120	89646193	.	+	1	Parent=gene2345
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2345
chr7	ENCODE	CDS	89648267	89648319	.	+	2	Parent=gene2345
chr7	ENCODE	exon	89651472	89651579	.	+	.	Parent=gene2345
chr7	ENCODE	CDS	89651472	89651579	.	+	0	Parent=gene2345
chr7	ENCODE	exon	89652099	89652176	.	+	.	Parent=gene2345
chr7	ENCODE	CDS	89652099	89652176	.	+	0	Parent=gene2345
chr7	ENCODE	exon	89656921	89657044	.	+	.	Parent=gene2345
chr7	ENCODE	CDS	89656921	89657044	.	+	0	Parent=gene2345
chr7	ENCODE	CDS	89658857	89659119	.	+	2	Parent=gene2345
chr7	ENCODE	exon	89658857	89659608	.	+	.	Parent=gene2345
###
chr7	ENCODE	gene	89620641	89665420	.	+	.	ID=gene2346;Name=AC006153.3-001;name2=GTPBP10
chr7	ENCODE	exon	89620641	89620739	.	+	.	Parent=gene2346
chr7	ENCODE	CDS	89620707	89620739	.	+	0	Parent=gene2346
chr7	ENCODE	exon	89626781	89626974	.	+	.	Parent=gene2346
chr7	ENCODE	CDS	89626781	89626974	.	+	0	Parent=gene2346
chr7	ENCODE	exon	89628423	89628514	.	+	.	Parent=gene2346
chr7	ENCODE	CDS	89628423	89628514	.	+	1	Parent=gene2346
chr7	ENCODE	exon	89629051	89629195	.	+	.	Parent=gene2346
chr7	ENCODE	CDS	89629051	89629195	.	+	2	Parent=gene2346
chr7	ENCODE	exon	89646120	89646193	.	+	.	Parent=gene2346
chr7	ENCODE	CDS	89646120	89646193	.	+	1	Parent=gene2346
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2346
chr7	ENCODE	CDS	89648267	89648319	.	+	2	Parent=gene2346
chr7	ENCODE	exon	89651472	89651579	.	+	.	Parent=gene2346
chr7	ENCODE	CDS	89651472	89651579	.	+	0	Parent=gene2346
chr7	ENCODE	exon	89652099	89652176	.	+	.	Parent=gene2346
chr7	ENCODE	CDS	89652099	89652176	.	+	0	Parent=gene2346
chr7	ENCODE	exon	89656921	89657044	.	+	.	Parent=gene2346
chr7	ENCODE	CDS	89656921	89657044	.	+	0	Parent=gene2346
chr7	ENCODE	CDS	89658857	89659119	.	+	2	Parent=gene2346
chr7	ENCODE	exon	89658857	89665420	.	+	.	Parent=gene2346
###
chr7	ENCODE	gene	89620667	89627197	.	+	.	ID=gene2347;Name=AC006153.3-011;name2=GTPBP10
chr7	ENCODE	exon	89620667	89620739	.	+	.	Parent=gene2347
chr7	ENCODE	exon	89626781	89627197	.	+	.	Parent=gene2347
###
chr7	ENCODE	gene	89620688	89659126	.	+	.	ID=gene2348;Name=AC006153.3-003;name2=AC006153.3
chr7	ENCODE	exon	89620688	89620739	.	+	.	Parent=gene2348
chr7	ENCODE	exon	89626781	89626974	.	+	.	Parent=gene2348
chr7	ENCODE	exon	89628423	89628514	.	+	.	Parent=gene2348
chr7	ENCODE	exon	89629051	89629195	.	+	.	Parent=gene2348
chr7	ENCODE	exon	89646120	89646193	.	+	.	Parent=gene2348
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2348
chr7	ENCODE	exon	89651472	89651579	.	+	.	Parent=gene2348
chr7	ENCODE	exon	89652099	89652176	.	+	.	Parent=gene2348
chr7	ENCODE	exon	89656921	89656955	.	+	.	Parent=gene2348
chr7	ENCODE	exon	89658857	89659126	.	+	.	Parent=gene2348
###
chr7	ENCODE	gene	89620695	89651579	.	+	.	ID=gene2349;Name=AC006153.3-004;name2=AC006153.3
chr7	ENCODE	exon	89620695	89620739	.	+	.	Parent=gene2349
chr7	ENCODE	exon	89626781	89626974	.	+	.	Parent=gene2349
chr7	ENCODE	exon	89629051	89629195	.	+	.	Parent=gene2349
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2349
chr7	ENCODE	exon	89651472	89651579	.	+	.	Parent=gene2349
###
chr7	ENCODE	gene	89628493	89659041	.	+	.	ID=gene2350;Name=AC006153.3-005;name2=AC006153.3
chr7	ENCODE	exon	89628493	89628514	.	+	.	Parent=gene2350
chr7	ENCODE	exon	89629051	89629195	.	+	.	Parent=gene2350
chr7	ENCODE	exon	89648267	89648319	.	+	.	Parent=gene2350
chr7	ENCODE	exon	89651472	89651579	.	+	.	Parent=gene2350
chr7	ENCODE	exon	89652099	89652176	.	+	.	Parent=gene2350
chr7	ENCODE	exon	89656921	89657044	.	+	.	Parent=gene2350
chr7	ENCODE	exon	89658857	89659041	.	+	.	Parent=gene2350
###
chr7	ENCODE	gene	89657686	89687168	.	+	.	ID=gene2351;Name=AC006153.2-014;name2=CLDN12
chr7	ENCODE	exon	89657686	89657752	.	+	.	Parent=gene2351
chr7	ENCODE	exon	89658857	89659203	.	+	.	Parent=gene2351
chr7	ENCODE	exon	89679484	89679573	.	+	.	Parent=gene2351
chr7	ENCODE	exon	89686609	89687168	.	+	.	Parent=gene2351
###
chr7	ENCODE	gene	89657686	89687168	.	+	.	ID=gene2352;name2=CLDN12;Name=AC006153.2-015
chr7	ENCODE	exon	89657686	89657752	.	+	.	Parent=gene2352
chr7	ENCODE	exon	89658857	89659203	.	+	.	Parent=gene2352
chr7	ENCODE	exon	89679484	89679573	.	+	.	Parent=gene2352
chr7	ENCODE	exon	89685928	89686026	.	+	.	Parent=gene2352
chr7	ENCODE	exon	89686609	89687168	.	+	.	Parent=gene2352
###
chr7	ENCODE	gene	89677351	89689919	.	+	.	ID=gene2353;Name=AC006153.2-001;name2=CLDN12
chr7	ENCODE	exon	89677351	89677514	.	+	.	Parent=gene2353
chr7	ENCODE	exon	89679484	89679573	.	+	.	Parent=gene2353
chr7	ENCODE	exon	89686609	89689919	.	+	.	Parent=gene2353
chr7	ENCODE	CDS	89686642	89687376	.	+	0	Parent=gene2353
###
chr7	ENCODE	gene	89677399	89787356	.	+	.	ID=gene2354;Name=AC006153.2-003;name2=CLDN12
chr7	ENCODE	exon	89677399	89677514	.	+	.	Parent=gene2354
chr7	ENCODE	exon	89679484	89679577	.	+	.	Parent=gene2354
chr7	ENCODE	exon	89753193	89753239	.	+	.	Parent=gene2354
chr7	ENCODE	exon	89787243	89787356	.	+	.	Parent=gene2354
###
chr7	ENCODE	gene	89677403	89680045	.	+	.	ID=gene2355;Name=AC006153.2-004;name2=CLDN12
chr7	ENCODE	exon	89677403	89677514	.	+	.	Parent=gene2355
chr7	ENCODE	exon	89679484	89680045	.	+	.	Parent=gene2355
###
chr7	ENCODE	gene	89677413	89687203	.	+	.	ID=gene2356;Name=AC006153.2-013;name2=CLDN12
chr7	ENCODE	exon	89677413	89677514	.	+	.	Parent=gene2356
chr7	ENCODE	exon	89679484	89679577	.	+	.	Parent=gene2356
chr7	ENCODE	exon	89685972	89686026	.	+	.	Parent=gene2356
chr7	ENCODE	exon	89686609	89687203	.	+	.	Parent=gene2356
chr7	ENCODE	CDS	89686642	89687203	.	+	0	Parent=gene2356
###
chr7	ENCODE	gene	89677449	89768381	.	+	.	ID=gene2357;Name=AC006153.2-008;name2=CLDN12
chr7	ENCODE	exon	89677449	89677514	.	+	.	Parent=gene2357
chr7	ENCODE	exon	89679484	89679573	.	+	.	Parent=gene2357
chr7	ENCODE	exon	89740375	89740478	.	+	.	Parent=gene2357
chr7	ENCODE	exon	89743856	89743918	.	+	.	Parent=gene2357
chr7	ENCODE	exon	89753193	89753239	.	+	.	Parent=gene2357
chr7	ENCODE	exon	89768332	89768381	.	+	.	Parent=gene2357
###
chr7	ENCODE	gene	89677484	89787348	.	+	.	ID=gene2358;Name=AC006153.2-006;name2=CLDN12
chr7	ENCODE	exon	89677484	89677514	.	+	.	Parent=gene2358
chr7	ENCODE	exon	89679484	89679573	.	+	.	Parent=gene2358
chr7	ENCODE	exon	89753193	89753239	.	+	.	Parent=gene2358
chr7	ENCODE	exon	89768332	89768395	.	+	.	Parent=gene2358
chr7	ENCODE	exon	89787243	89787348	.	+	.	Parent=gene2358
###
chr7	ENCODE	gene	89677501	89683149	.	+	.	ID=gene2359;Name=AC006153.2-007;name2=CLDN12
chr7	ENCODE	exon	89677501	89677514	.	+	.	Parent=gene2359
chr7	ENCODE	exon	89679484	89679573	.	+	.	Parent=gene2359
chr7	ENCODE	exon	89682912	89683149	.	+	.	Parent=gene2359
###
chr7	ENCODE	gene	89677514	89689919	.	+	.	ID=gene2360;Name=AC006153.2-002;name2=CLDN12
chr7	ENCODE	exon	89677514	89677514	.	+	.	Parent=gene2360
chr7	ENCODE	exon	89679484	89679577	.	+	.	Parent=gene2360
chr7	ENCODE	exon	89686609	89689919	.	+	.	Parent=gene2360
chr7	ENCODE	CDS	89686642	89687376	.	+	0	Parent=gene2360
###
chr7	ENCODE	gene	89677532	89687020	.	+	.	ID=gene2361;Name=AC006153.2-005;name2=CLDN12
chr7	ENCODE	exon	89677532	89677647	.	+	.	Parent=gene2361
chr7	ENCODE	exon	89679484	89679573	.	+	.	Parent=gene2361
chr7	ENCODE	exon	89686609	89687020	.	+	.	Parent=gene2361
chr7	ENCODE	CDS	89686642	89687020	.	+	0	Parent=gene2361
###
chr7	ENCODE	gene	89679546	89787367	.	+	.	ID=gene2362;Name=AC006153.2-011;name2=CLDN12
chr7	ENCODE	exon	89679546	89679577	.	+	.	Parent=gene2362
chr7	ENCODE	exon	89753193	89753239	.	+	.	Parent=gene2362
chr7	ENCODE	exon	89761292	89761385	.	+	.	Parent=gene2362
chr7	ENCODE	exon	89762836	89762929	.	+	.	Parent=gene2362
chr7	ENCODE	exon	89766204	89766274	.	+	.	Parent=gene2362
chr7	ENCODE	exon	89768332	89768395	.	+	.	Parent=gene2362
chr7	ENCODE	exon	89787243	89787367	.	+	.	Parent=gene2362
###
chr7	ENCODE	gene	89737205	89744312	.	+	.	ID=gene2363;Name=AC006153.2-009;name2=CLDN12
chr7	ENCODE	exon	89737205	89737336	.	+	.	Parent=gene2363
chr7	ENCODE	exon	89740375	89740478	.	+	.	Parent=gene2363
chr7	ENCODE	exon	89743856	89744312	.	+	.	Parent=gene2363
###
chr7	ENCODE	gene	89740375	89787336	.	+	.	ID=gene2364;Name=AC006153.2-010;name2=CLDN12
chr7	ENCODE	exon	89740375	89740478	.	+	.	Parent=gene2364
chr7	ENCODE	exon	89753193	89753239	.	+	.	Parent=gene2364
chr7	ENCODE	exon	89768332	89768395	.	+	.	Parent=gene2364
chr7	ENCODE	exon	89787243	89787336	.	+	.	Parent=gene2364
###
chr7	ENCODE	gene	89740389	90064594	.	+	.	ID=gene2365;Name=AC084381.2-007;name2=PFTK1
chr7	ENCODE	exon	89740389	89740478	.	+	.	Parent=gene2365
chr7	ENCODE	exon	89753193	89753239	.	+	.	Parent=gene2365
chr7	ENCODE	exon	89768332	89768395	.	+	.	Parent=gene2365
chr7	ENCODE	exon	89837700	89837828	.	+	.	Parent=gene2365
chr7	ENCODE	exon	89878183	89878214	.	+	.	Parent=gene2365
chr7	ENCODE	exon	90000532	90000777	.	+	.	Parent=gene2365
chr7	ENCODE	exon	90021647	90021741	.	+	.	Parent=gene2365
chr7	ENCODE	exon	90064539	90064594	.	+	.	Parent=gene2365
###
chr7	ENCODE	gene	89768135	89787353	.	+	.	ID=gene2366;Name=AC006153.2-012;name2=CLDN12
chr7	ENCODE	exon	89768135	89768395	.	+	.	Parent=gene2366
chr7	ENCODE	exon	89787243	89787353	.	+	.	Parent=gene2366
###
chr7	ENCODE	gene	89837739	90064591	.	+	.	ID=gene2367;name2=PFTK1;Name=AC084381.2-009
chr7	ENCODE	exon	89837739	89837828	.	+	.	Parent=gene2367
chr7	ENCODE	exon	89878183	89878214	.	+	.	Parent=gene2367
chr7	ENCODE	exon	90064539	90064591	.	+	.	Parent=gene2367
###
chr7	ENCODE	gene	89837739	90064593	.	+	.	ID=gene2368;Name=AC084381.2-010;name2=PFTK1
chr7	ENCODE	exon	89837739	89837828	.	+	.	Parent=gene2368
chr7	ENCODE	exon	89878183	89878214	.	+	.	Parent=gene2368
chr7	ENCODE	exon	89940305	89940376	.	+	.	Parent=gene2368
chr7	ENCODE	exon	90000532	90000777	.	+	.	Parent=gene2368
chr7	ENCODE	exon	90021647	90021741	.	+	.	Parent=gene2368
chr7	ENCODE	exon	90064539	90064593	.	+	.	Parent=gene2368
###
chr7	ENCODE	gene	89837739	90064594	.	+	.	ID=gene2369;Name=AC084381.2-008;name2=PFTK1
chr7	ENCODE	exon	89837739	89837828	.	+	.	Parent=gene2369
chr7	ENCODE	exon	89878183	89878214	.	+	.	Parent=gene2369
chr7	ENCODE	exon	89882495	89882540	.	+	.	Parent=gene2369
chr7	ENCODE	exon	90000532	90000777	.	+	.	Parent=gene2369
chr7	ENCODE	exon	90021647	90021741	.	+	.	Parent=gene2369
chr7	ENCODE	exon	90064539	90064594	.	+	.	Parent=gene2369
###
chr7	ENCODE	gene	89837739	90064594	.	+	.	ID=gene2370;Name=AC084381.2-011;name2=PFTK1
chr7	ENCODE	exon	89837739	89837828	.	+	.	Parent=gene2370
chr7	ENCODE	exon	89878183	89878214	.	+	.	Parent=gene2370
chr7	ENCODE	exon	89882495	89882540	.	+	.	Parent=gene2370
chr7	ENCODE	exon	89990305	89990359	.	+	.	Parent=gene2370
chr7	ENCODE	exon	90000532	90000777	.	+	.	Parent=gene2370
chr7	ENCODE	exon	90021647	90021741	.	+	.	Parent=gene2370
chr7	ENCODE	exon	90064539	90064594	.	+	.	Parent=gene2370
###
chr7	ENCODE	gene	89870462	90484556	.	+	.	ID=gene2371;name2=PFTK1;Name=AC084381.2-001
chr7	ENCODE	exon	89870462	89870683	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	89870593	89870683	.	+	0	Parent=gene2371
chr7	ENCODE	exon	89878183	89878214	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	89878183	89878214	.	+	2	Parent=gene2371
chr7	ENCODE	exon	90000532	90000777	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90000532	90000777	.	+	0	Parent=gene2371
chr7	ENCODE	exon	90021647	90021741	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90021647	90021741	.	+	0	Parent=gene2371
chr7	ENCODE	exon	90064539	90064618	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90064539	90064618	.	+	1	Parent=gene2371
chr7	ENCODE	exon	90137141	90137235	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90137141	90137235	.	+	2	Parent=gene2371
chr7	ENCODE	exon	90173257	90173319	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90173257	90173319	.	+	0	Parent=gene2371
chr7	ENCODE	exon	90191567	90191690	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90191567	90191690	.	+	0	Parent=gene2371
chr7	ENCODE	exon	90229663	90229783	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90229663	90229783	.	+	2	Parent=gene2371
chr7	ENCODE	exon	90258114	90258207	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90258114	90258207	.	+	1	Parent=gene2371
chr7	ENCODE	exon	90319863	90319926	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90319863	90319926	.	+	0	Parent=gene2371
chr7	ENCODE	exon	90353398	90353446	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90353398	90353446	.	+	2	Parent=gene2371
chr7	ENCODE	exon	90386508	90386647	.	+	.	Parent=gene2371
chr7	ENCODE	CDS	90386508	90386647	.	+	1	Parent=gene2371
chr7	ENCODE	CDS	90392031	90392146	.	+	2	Parent=gene2371
chr7	ENCODE	exon	90392031	90392174	.	+	.	Parent=gene2371
chr7	ENCODE	exon	90481131	90484556	.	+	.	Parent=gene2371
###
chr7	ENCODE	gene	89983363	90484555	.	+	.	ID=gene2372;name2=PFTK1;Name=AC084381.2-002
chr7	ENCODE	exon	89983363	89983575	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	89983507	89983575	.	+	0	Parent=gene2372
chr7	ENCODE	exon	90000532	90000777	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90000532	90000777	.	+	0	Parent=gene2372
chr7	ENCODE	exon	90021647	90021741	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90021647	90021741	.	+	0	Parent=gene2372
chr7	ENCODE	exon	90064539	90064618	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90064539	90064618	.	+	1	Parent=gene2372
chr7	ENCODE	exon	90137141	90137235	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90137141	90137235	.	+	2	Parent=gene2372
chr7	ENCODE	exon	90173257	90173319	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90173257	90173319	.	+	0	Parent=gene2372
chr7	ENCODE	exon	90191567	90191690	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90191567	90191690	.	+	0	Parent=gene2372
chr7	ENCODE	exon	90229663	90229783	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90229663	90229783	.	+	2	Parent=gene2372
chr7	ENCODE	exon	90258114	90258207	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90258114	90258207	.	+	1	Parent=gene2372
chr7	ENCODE	exon	90319863	90319926	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90319863	90319926	.	+	0	Parent=gene2372
chr7	ENCODE	exon	90353398	90353446	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90353398	90353446	.	+	2	Parent=gene2372
chr7	ENCODE	exon	90386508	90386647	.	+	.	Parent=gene2372
chr7	ENCODE	CDS	90386508	90386647	.	+	1	Parent=gene2372
chr7	ENCODE	CDS	90392031	90392146	.	+	2	Parent=gene2372
chr7	ENCODE	exon	90392031	90392174	.	+	.	Parent=gene2372
chr7	ENCODE	exon	90481131	90484555	.	+	.	Parent=gene2372
###
chr7	ENCODE	gene	89983496	90484551	.	+	.	ID=gene2373;Name=AC084381.2-003;name2=PFTK1
chr7	ENCODE	exon	89983496	89983922	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90000532	90000777	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90021647	90021741	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90064539	90064618	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90137141	90137235	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90173257	90173319	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90191567	90191690	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90229663	90229783	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90258114	90258207	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90319863	90319926	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90353398	90353446	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90386508	90386647	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90392031	90392174	.	+	.	Parent=gene2373
chr7	ENCODE	exon	90481131	90484551	.	+	.	Parent=gene2373
###
chr7	ENCODE	gene	89983827	90229759	.	+	.	ID=gene2374;Name=AC084381.2-004;name2=PFTK1
chr7	ENCODE	exon	89983827	89983922	.	+	.	Parent=gene2374
chr7	ENCODE	exon	90000532	90000777	.	+	.	Parent=gene2374
chr7	ENCODE	exon	90064539	90064618	.	+	.	Parent=gene2374
chr7	ENCODE	exon	90137141	90137235	.	+	.	Parent=gene2374
chr7	ENCODE	exon	90173257	90173319	.	+	.	Parent=gene2374
chr7	ENCODE	exon	90191567	90191690	.	+	.	Parent=gene2374
chr7	ENCODE	exon	90229663	90229759	.	+	.	Parent=gene2374
###
chr7	ENCODE	gene	90000469	90064580	.	+	.	ID=gene2375;Name=AC084381.2-005;name2=PFTK1
chr7	ENCODE	exon	90000469	90000777	.	+	.	Parent=gene2375
chr7	ENCODE	exon	90021647	90021741	.	+	.	Parent=gene2375
chr7	ENCODE	exon	90064539	90064580	.	+	.	Parent=gene2375
###
chr7	ENCODE	gene	90098571	90229762	.	+	.	ID=gene2376;Name=AC084381.2-012;name2=PFTK1
chr7	ENCODE	exon	90098571	90098733	.	+	.	Parent=gene2376
chr7	ENCODE	exon	90137141	90137235	.	+	.	Parent=gene2376
chr7	ENCODE	exon	90173257	90173319	.	+	.	Parent=gene2376
chr7	ENCODE	exon	90191567	90191690	.	+	.	Parent=gene2376
chr7	ENCODE	exon	90229663	90229762	.	+	.	Parent=gene2376
###
chr7	ENCODE	gene	90229758	90253767	.	+	.	ID=gene2377;Name=AC084381.2-006;name2=PFTK1
chr7	ENCODE	exon	90229758	90229783	.	+	.	Parent=gene2377
chr7	ENCODE	exon	90253358	90253767	.	+	.	Parent=gene2377
###
chr7	ENCODE	gene	90538330	90542684	.	+	.	ID=gene2378;name2=FZD1;Name=AC084381.1-002
chr7	ENCODE	exon	90538330	90538879	.	+	.	Parent=gene2378
chr7	ENCODE	exon	90540488	90542684	.	+	.	Parent=gene2378
###
chr7	ENCODE	gene	90538330	90542763	.	+	.	ID=gene2379;Name=AC084381.1-001;name2=FZD1
chr7	ENCODE	exon	90538330	90542763	.	+	.	Parent=gene2379
chr7	ENCODE	CDS	90538847	90540790	.	+	0	Parent=gene2379
###
chr7	ENCODE	gene	113649061	113924106	.	+	.	ID=gene2380;Name=AC020606.1-001;name2=FOXP2
chr7	ENCODE	exon	113649061	113649366	.	+	.	Parent=gene2380
chr7	ENCODE	exon	113660508	113660685	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113660518	113660685	.	+	0	Parent=gene2380
chr7	ENCODE	exon	113768623	113768712	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113768623	113768712	.	+	0	Parent=gene2380
chr7	ENCODE	exon	113862546	113862683	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113862546	113862683	.	+	0	Parent=gene2380
chr7	ENCODE	exon	113863811	113864011	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113863811	113864011	.	+	0	Parent=gene2380
chr7	ENCODE	exon	113865534	113865711	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113865534	113865711	.	+	0	Parent=gene2380
chr7	ENCODE	exon	113876416	113876629	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113876416	113876629	.	+	2	Parent=gene2380
chr7	ENCODE	exon	113878691	113878795	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113878691	113878795	.	+	1	Parent=gene2380
chr7	ENCODE	exon	113886209	113886296	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113886209	113886296	.	+	1	Parent=gene2380
chr7	ENCODE	exon	113887932	113888015	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113887932	113888015	.	+	0	Parent=gene2380
chr7	ENCODE	exon	113892072	113892273	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113892072	113892273	.	+	0	Parent=gene2380
chr7	ENCODE	exon	113893362	113893438	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113893362	113893438	.	+	2	Parent=gene2380
chr7	ENCODE	exon	113893578	113893679	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113893578	113893679	.	+	0	Parent=gene2380
chr7	ENCODE	exon	113896071	113896192	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113896071	113896192	.	+	0	Parent=gene2380
chr7	ENCODE	exon	113897456	113897525	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113897456	113897525	.	+	1	Parent=gene2380
chr7	ENCODE	exon	113898279	113898442	.	+	.	Parent=gene2380
chr7	ENCODE	CDS	113898279	113898442	.	+	0	Parent=gene2380
chr7	ENCODE	CDS	113923788	113923932	.	+	1	Parent=gene2380
chr7	ENCODE	exon	113923788	113924106	.	+	.	Parent=gene2380
###
chr7	ENCODE	gene	113649064	113924151	.	+	.	ID=gene2381;name2=FOXP2;Name=AC020606.1-005
chr7	ENCODE	exon	113649064	113649366	.	+	.	Parent=gene2381
chr7	ENCODE	exon	113660508	113660685	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113660518	113660685	.	+	0	Parent=gene2381
chr7	ENCODE	exon	113768623	113768712	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113768623	113768712	.	+	0	Parent=gene2381
chr7	ENCODE	exon	113862546	113862683	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113862546	113862683	.	+	0	Parent=gene2381
chr7	ENCODE	exon	113863877	113864011	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113863877	113864011	.	+	0	Parent=gene2381
chr7	ENCODE	exon	113865537	113865711	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113865537	113865711	.	+	0	Parent=gene2381
chr7	ENCODE	exon	113876416	113876629	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113876416	113876629	.	+	2	Parent=gene2381
chr7	ENCODE	exon	113878691	113878795	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113878691	113878795	.	+	1	Parent=gene2381
chr7	ENCODE	exon	113886209	113886296	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113886209	113886296	.	+	1	Parent=gene2381
chr7	ENCODE	exon	113887932	113888015	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113887932	113888015	.	+	0	Parent=gene2381
chr7	ENCODE	exon	113892072	113892273	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113892072	113892273	.	+	0	Parent=gene2381
chr7	ENCODE	exon	113893362	113893438	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113893362	113893438	.	+	2	Parent=gene2381
chr7	ENCODE	exon	113893578	113893679	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113893578	113893679	.	+	0	Parent=gene2381
chr7	ENCODE	exon	113896071	113896192	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113896071	113896192	.	+	0	Parent=gene2381
chr7	ENCODE	exon	113897456	113897525	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113897456	113897525	.	+	1	Parent=gene2381
chr7	ENCODE	exon	113898279	113898442	.	+	.	Parent=gene2381
chr7	ENCODE	CDS	113898279	113898442	.	+	0	Parent=gene2381
chr7	ENCODE	CDS	113923788	113923932	.	+	1	Parent=gene2381
chr7	ENCODE	exon	113923788	113924151	.	+	.	Parent=gene2381
###
chr7	ENCODE	gene	113649325	113879836	.	+	.	ID=gene2382;Name=AC020606.1-010;name2=FOXP2
chr7	ENCODE	exon	113649325	113649366	.	+	.	Parent=gene2382
chr7	ENCODE	exon	113660508	113660685	.	+	.	Parent=gene2382
chr7	ENCODE	exon	113768623	113768712	.	+	.	Parent=gene2382
chr7	ENCODE	exon	113862546	113862683	.	+	.	Parent=gene2382
chr7	ENCODE	exon	113863811	113864011	.	+	.	Parent=gene2382
chr7	ENCODE	exon	113865534	113865711	.	+	.	Parent=gene2382
chr7	ENCODE	exon	113876416	113876629	.	+	.	Parent=gene2382
chr7	ENCODE	exon	113878691	113879836	.	+	.	Parent=gene2382
###
chr7	ENCODE	gene	113863576	113876589	.	+	.	ID=gene2383;Name=AC020606.1-013;name2=FOXP2
chr7	ENCODE	exon	113863576	113863793	.	+	.	Parent=gene2383
chr7	ENCODE	exon	113863847	113864011	.	+	.	Parent=gene2383
chr7	ENCODE	exon	113865534	113865711	.	+	.	Parent=gene2383
chr7	ENCODE	exon	113876416	113876589	.	+	.	Parent=gene2383
###
chr7	ENCODE	gene	113876416	113888149	.	+	.	ID=gene2384;Name=AC020606.1-011;name2=FOXP2
chr7	ENCODE	exon	113876416	113876629	.	+	.	Parent=gene2384
chr7	ENCODE	exon	113878691	113878795	.	+	.	Parent=gene2384
chr7	ENCODE	exon	113886209	113886296	.	+	.	Parent=gene2384
chr7	ENCODE	exon	113887932	113888149	.	+	.	Parent=gene2384
###
chr7	ENCODE	gene	113887876	113898383	.	+	.	ID=gene2385;Name=AC020606.1-012;name2=FOXP2
chr7	ENCODE	exon	113887876	113888015	.	+	.	Parent=gene2385
chr7	ENCODE	exon	113893362	113893438	.	+	.	Parent=gene2385
chr7	ENCODE	exon	113893578	113893679	.	+	.	Parent=gene2385
chr7	ENCODE	exon	113896071	113896192	.	+	.	Parent=gene2385
chr7	ENCODE	exon	113897456	113897472	.	+	.	Parent=gene2385
chr7	ENCODE	exon	113898280	113898383	.	+	.	Parent=gene2385
###
chr7	ENCODE	gene	114156160	114253207	.	+	.	ID=gene2386;Name=AC017003.2-001;name2=MDFIC
chr7	ENCODE	exon	114156160	114156642	.	+	.	Parent=gene2386
chr7	ENCODE	exon	114156933	114157133	.	+	.	Parent=gene2386
chr7	ENCODE	CDS	114157040	114157133	.	+	0	Parent=gene2386
chr7	ENCODE	exon	114176281	114176403	.	+	.	Parent=gene2386
chr7	ENCODE	CDS	114176281	114176403	.	+	2	Parent=gene2386
chr7	ENCODE	exon	114213512	114213787	.	+	.	Parent=gene2386
chr7	ENCODE	CDS	114213512	114213787	.	+	2	Parent=gene2386
chr7	ENCODE	CDS	114249693	114249940	.	+	2	Parent=gene2386
chr7	ENCODE	exon	114249693	114253207	.	+	.	Parent=gene2386
###
chr7	ENCODE	gene	114156567	114157671	.	+	.	ID=gene2387;Name=AC017003.2-003;name2=MDFIC
chr7	ENCODE	exon	114156567	114156642	.	+	.	Parent=gene2387
chr7	ENCODE	exon	114156933	114157133	.	+	.	Parent=gene2387
chr7	ENCODE	exon	114157465	114157671	.	+	.	Parent=gene2387
###
chr7	ENCODE	gene	114156860	114157664	.	+	.	ID=gene2388;Name=AC017003.2-002;name2=MDFIC
chr7	ENCODE	exon	114156860	114157133	.	+	.	Parent=gene2388
chr7	ENCODE	exon	114157465	114157664	.	+	.	Parent=gene2388
###
chr7	ENCODE	gene	114157070	114249966	.	+	.	ID=gene2389;Name=AC017003.2-005;name2=MDFIC
chr7	ENCODE	exon	114157070	114157133	.	+	.	Parent=gene2389
chr7	ENCODE	exon	114176281	114176403	.	+	.	Parent=gene2389
chr7	ENCODE	exon	114213512	114213787	.	+	.	Parent=gene2389
chr7	ENCODE	exon	114248468	114248538	.	+	.	Parent=gene2389
chr7	ENCODE	exon	114249693	114249966	.	+	.	Parent=gene2389
###
chr7	ENCODE	gene	114157082	114214090	.	+	.	ID=gene2390;Name=AC017003.2-004;name2=MDFIC
chr7	ENCODE	exon	114157082	114157133	.	+	.	Parent=gene2390
chr7	ENCODE	exon	114176281	114176403	.	+	.	Parent=gene2390
chr7	ENCODE	exon	114213512	114213787	.	+	.	Parent=gene2390
chr7	ENCODE	exon	114213895	114214090	.	+	.	Parent=gene2390
###
chr7	ENCODE	gene	115444498	115492788	.	+	.	ID=gene2391;Name=AC073130.2-001;name2=TES
chr7	ENCODE	exon	115444498	115444739	.	+	.	Parent=gene2391
chr7	ENCODE	CDS	115444713	115444739	.	+	0	Parent=gene2391
chr7	ENCODE	exon	115468539	115468624	.	+	.	Parent=gene2391
chr7	ENCODE	CDS	115468539	115468624	.	+	0	Parent=gene2391
chr7	ENCODE	exon	115483025	115483277	.	+	.	Parent=gene2391
chr7	ENCODE	CDS	115483025	115483277	.	+	1	Parent=gene2391
chr7	ENCODE	exon	115484166	115484501	.	+	.	Parent=gene2391
chr7	ENCODE	CDS	115484166	115484501	.	+	0	Parent=gene2391
chr7	ENCODE	exon	115485765	115485980	.	+	.	Parent=gene2391
chr7	ENCODE	CDS	115485765	115485980	.	+	0	Parent=gene2391
chr7	ENCODE	exon	115486323	115486481	.	+	.	Parent=gene2391
chr7	ENCODE	CDS	115486323	115486481	.	+	0	Parent=gene2391
chr7	ENCODE	CDS	115491299	115491487	.	+	0	Parent=gene2391
chr7	ENCODE	exon	115491299	115492788	.	+	.	Parent=gene2391
###
chr7	ENCODE	gene	115444566	115483430	.	+	.	ID=gene2392;Name=AC073130.2-007;name2=TES
chr7	ENCODE	exon	115444566	115444739	.	+	.	Parent=gene2392
chr7	ENCODE	exon	115483025	115483430	.	+	.	Parent=gene2392
###
chr7	ENCODE	gene	115456956	115483369	.	+	.	ID=gene2393;Name=AC073130.2-006;name2=TES
chr7	ENCODE	exon	115456956	115457031	.	+	.	Parent=gene2393
chr7	ENCODE	exon	115468539	115468624	.	+	.	Parent=gene2393
chr7	ENCODE	exon	115483025	115483369	.	+	.	Parent=gene2393
###
chr7	ENCODE	gene	115484440	115486743	.	+	.	ID=gene2394;Name=AC073130.2-005;name2=TES
chr7	ENCODE	exon	115484440	115484501	.	+	.	Parent=gene2394
chr7	ENCODE	exon	115485765	115485980	.	+	.	Parent=gene2394
chr7	ENCODE	exon	115486323	115486743	.	+	.	Parent=gene2394
###
chr7	ENCODE	gene	115485512	115491581	.	+	.	ID=gene2395;Name=AC073130.2-003;name2=TES
chr7	ENCODE	exon	115485512	115485980	.	+	.	Parent=gene2395
chr7	ENCODE	exon	115486323	115486481	.	+	.	Parent=gene2395
chr7	ENCODE	exon	115491299	115491581	.	+	.	Parent=gene2395
###
chr7	ENCODE	gene	115485756	115486585	.	+	.	ID=gene2396;Name=AC073130.2-004;name2=TES
chr7	ENCODE	exon	115485756	115485980	.	+	.	Parent=gene2396
chr7	ENCODE	exon	115486323	115486585	.	+	.	Parent=gene2396
###
chr7	ENCODE	gene	115522078	115740105	.	+	.	ID=gene2397;Name=AC006159.1-009;name2=CAV2
chr7	ENCODE	exon	115522078	115522119	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115550437	115550515	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115553646	115553764	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115556807	115556893	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115571125	115571186	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115573828	115573924	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115704049	115704094	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115731829	115731988	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115733249	115733346	.	+	.	Parent=gene2397
chr7	ENCODE	exon	115739976	115740105	.	+	.	Parent=gene2397
###
chr7	ENCODE	gene	115522078	115740108	.	+	.	ID=gene2398;Name=AC006159.1-016;name2=CAV2
chr7	ENCODE	exon	115522078	115522119	.	+	.	Parent=gene2398
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2398
chr7	ENCODE	exon	115550437	115550515	.	+	.	Parent=gene2398
chr7	ENCODE	exon	115553646	115553764	.	+	.	Parent=gene2398
chr7	ENCODE	exon	115556807	115556893	.	+	.	Parent=gene2398
chr7	ENCODE	exon	115573836	115573874	.	+	.	Parent=gene2398
chr7	ENCODE	exon	115740011	115740108	.	+	.	Parent=gene2398
###
chr7	ENCODE	gene	115522078	115740110	.	+	.	ID=gene2399;Name=AC006159.1-008;name2=CAV2
chr7	ENCODE	exon	115522078	115522119	.	+	.	Parent=gene2399
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2399
chr7	ENCODE	exon	115532462	115532514	.	+	.	Parent=gene2399
chr7	ENCODE	exon	115573828	115573959	.	+	.	Parent=gene2399
chr7	ENCODE	exon	115661327	115661491	.	+	.	Parent=gene2399
chr7	ENCODE	exon	115666964	115667124	.	+	.	Parent=gene2399
chr7	ENCODE	exon	115731774	115731988	.	+	.	Parent=gene2399
chr7	ENCODE	exon	115733249	115733346	.	+	.	Parent=gene2399
chr7	ENCODE	exon	115739976	115740110	.	+	.	Parent=gene2399
###
chr7	ENCODE	gene	115522078	115740110	.	+	.	ID=gene2400;Name=AC006159.1-012;name2=CAV2
chr7	ENCODE	exon	115522078	115522119	.	+	.	Parent=gene2400
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2400
chr7	ENCODE	exon	115550437	115550515	.	+	.	Parent=gene2400
chr7	ENCODE	exon	115553646	115553764	.	+	.	Parent=gene2400
chr7	ENCODE	exon	115556807	115556893	.	+	.	Parent=gene2400
chr7	ENCODE	exon	115557095	115557184	.	+	.	Parent=gene2400
chr7	ENCODE	exon	115571125	115571263	.	+	.	Parent=gene2400
chr7	ENCODE	exon	115740086	115740110	.	+	.	Parent=gene2400
###
chr7	ENCODE	gene	115522078	115740113	.	+	.	ID=gene2401;Name=AC006159.1-015;name2=CAV2
chr7	ENCODE	exon	115522078	115522119	.	+	.	Parent=gene2401
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2401
chr7	ENCODE	exon	115661327	115661491	.	+	.	Parent=gene2401
chr7	ENCODE	exon	115731774	115731988	.	+	.	Parent=gene2401
chr7	ENCODE	exon	115733249	115733346	.	+	.	Parent=gene2401
chr7	ENCODE	exon	115739976	115740113	.	+	.	Parent=gene2401
###
chr7	ENCODE	gene	115522078	115740113	.	+	.	ID=gene2402;Name=AC006159.1-010;name2=CAV2
chr7	ENCODE	exon	115522078	115522119	.	+	.	Parent=gene2402
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2402
chr7	ENCODE	exon	115731774	115731988	.	+	.	Parent=gene2402
chr7	ENCODE	exon	115733249	115733346	.	+	.	Parent=gene2402
chr7	ENCODE	exon	115733846	115733936	.	+	.	Parent=gene2402
chr7	ENCODE	exon	115734265	115734452	.	+	.	Parent=gene2402
chr7	ENCODE	exon	115739976	115740113	.	+	.	Parent=gene2402
###
chr7	ENCODE	gene	115522080	115740102	.	+	.	ID=gene2403;Name=AC006159.1-014;name2=CAV2
chr7	ENCODE	exon	115522080	115522119	.	+	.	Parent=gene2403
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2403
chr7	ENCODE	exon	115550437	115550515	.	+	.	Parent=gene2403
chr7	ENCODE	exon	115553646	115553764	.	+	.	Parent=gene2403
chr7	ENCODE	exon	115556807	115556893	.	+	.	Parent=gene2403
chr7	ENCODE	exon	115557095	115557184	.	+	.	Parent=gene2403
chr7	ENCODE	exon	115565590	115565781	.	+	.	Parent=gene2403
chr7	ENCODE	exon	115571125	115571263	.	+	.	Parent=gene2403
chr7	ENCODE	exon	115740086	115740102	.	+	.	Parent=gene2403
###
chr7	ENCODE	gene	115522085	115740113	.	+	.	ID=gene2404;Name=AC006159.1-013;name2=CAV2
chr7	ENCODE	exon	115522085	115522119	.	+	.	Parent=gene2404
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2404
chr7	ENCODE	exon	115550437	115550515	.	+	.	Parent=gene2404
chr7	ENCODE	exon	115553646	115553764	.	+	.	Parent=gene2404
chr7	ENCODE	exon	115739976	115740113	.	+	.	Parent=gene2404
###
chr7	ENCODE	gene	115522093	115740113	.	+	.	ID=gene2405;Name=AC006159.1-017;name2=CAV2
chr7	ENCODE	exon	115522093	115522119	.	+	.	Parent=gene2405
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2405
chr7	ENCODE	exon	115553646	115553764	.	+	.	Parent=gene2405
chr7	ENCODE	exon	115556807	115556893	.	+	.	Parent=gene2405
chr7	ENCODE	exon	115571125	115571263	.	+	.	Parent=gene2405
chr7	ENCODE	exon	115740086	115740113	.	+	.	Parent=gene2405
###
chr7	ENCODE	gene	115522095	115740110	.	+	.	ID=gene2406;Name=AC006159.1-011;name2=CAV2
chr7	ENCODE	exon	115522095	115522119	.	+	.	Parent=gene2406
chr7	ENCODE	exon	115523857	115524055	.	+	.	Parent=gene2406
chr7	ENCODE	exon	115550437	115550515	.	+	.	Parent=gene2406
chr7	ENCODE	exon	115553646	115553764	.	+	.	Parent=gene2406
chr7	ENCODE	exon	115556807	115556893	.	+	.	Parent=gene2406
chr7	ENCODE	exon	115571125	115571263	.	+	.	Parent=gene2406
chr7	ENCODE	exon	115740086	115740110	.	+	.	Parent=gene2406
###
chr7	ENCODE	gene	115523882	115740098	.	+	.	ID=gene2407;Name=AC006159.1-005;name2=CAV2
chr7	ENCODE	exon	115523882	115524055	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115587923	115588022	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115641417	115641485	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115654168	115654365	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115659769	115659908	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115661327	115661491	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115731774	115731988	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115733249	115733346	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115733846	115733936	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115734265	115734452	.	+	.	Parent=gene2407
chr7	ENCODE	exon	115739976	115740098	.	+	.	Parent=gene2407
###
chr7	ENCODE	gene	115523883	115740034	.	+	.	ID=gene2408;Name=AC006159.1-006;name2=CAV2
chr7	ENCODE	exon	115523883	115524055	.	+	.	Parent=gene2408
chr7	ENCODE	exon	115550437	115550515	.	+	.	Parent=gene2408
chr7	ENCODE	exon	115553646	115553764	.	+	.	Parent=gene2408
chr7	ENCODE	exon	115556807	115556893	.	+	.	Parent=gene2408
chr7	ENCODE	exon	115661327	115661491	.	+	.	Parent=gene2408
chr7	ENCODE	exon	115731774	115731988	.	+	.	Parent=gene2408
chr7	ENCODE	exon	115733249	115733346	.	+	.	Parent=gene2408
chr7	ENCODE	exon	115739976	115740034	.	+	.	Parent=gene2408
###
chr7	ENCODE	gene	115523883	115740113	.	+	.	ID=gene2409;Name=AC006159.1-004;name2=CAV2
chr7	ENCODE	exon	115523883	115524055	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115553646	115553764	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115556807	115556893	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115557095	115557184	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115571125	115571186	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115573828	115573924	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115641273	115641485	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115661327	115661491	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115731774	115731988	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115733249	115733346	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115733846	115733936	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115734265	115734452	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115734539	115734663	.	+	.	Parent=gene2409
chr7	ENCODE	exon	115739976	115740113	.	+	.	Parent=gene2409
###
chr7	ENCODE	gene	115523883	115740114	.	+	.	ID=gene2410;Name=AC006159.1-007;name2=CAV2
chr7	ENCODE	exon	115523883	115524055	.	+	.	Parent=gene2410
chr7	ENCODE	exon	115565590	115565781	.	+	.	Parent=gene2410
chr7	ENCODE	exon	115571125	115571263	.	+	.	Parent=gene2410
chr7	ENCODE	exon	115740086	115740114	.	+	.	Parent=gene2410
###
chr7	ENCODE	gene	115733247	115740263	.	+	.	ID=gene2411;Name=AC006159.1-003;name2=CAV2
chr7	ENCODE	exon	115733247	115733346	.	+	.	Parent=gene2411
chr7	ENCODE	CDS	115733312	115733346	.	+	0	Parent=gene2411
chr7	ENCODE	exon	115733846	115733936	.	+	.	Parent=gene2411
chr7	ENCODE	CDS	115733846	115733936	.	+	1	Parent=gene2411
chr7	ENCODE	exon	115734265	115734452	.	+	.	Parent=gene2411
chr7	ENCODE	CDS	115734265	115734452	.	+	0	Parent=gene2411
chr7	ENCODE	CDS	115739976	115740126	.	+	1	Parent=gene2411
chr7	ENCODE	exon	115739976	115740263	.	+	.	Parent=gene2411
###
chr7	ENCODE	gene	115733395	115742546	.	+	.	ID=gene2412;Name=AC006159.1-001;name2=CAV2
chr7	ENCODE	exon	115733395	115733936	.	+	.	Parent=gene2412
chr7	ENCODE	CDS	115733787	115733936	.	+	0	Parent=gene2412
chr7	ENCODE	exon	115734265	115734452	.	+	.	Parent=gene2412
chr7	ENCODE	CDS	115734265	115734452	.	+	0	Parent=gene2412
chr7	ENCODE	CDS	115739976	115740126	.	+	1	Parent=gene2412
chr7	ENCODE	exon	115739976	115742546	.	+	.	Parent=gene2412
###
chr7	ENCODE	gene	115733606	115740939	.	+	.	ID=gene2413;Name=AC006159.1-018;name2=CAV2
chr7	ENCODE	exon	115733606	115733936	.	+	.	Parent=gene2413
chr7	ENCODE	exon	115734265	115734283	.	+	.	Parent=gene2413
chr7	ENCODE	exon	115739976	115740939	.	+	.	Parent=gene2413
###
chr7	ENCODE	gene	115733787	115740559	.	+	.	ID=gene2414;Name=AC006159.1-019;name2=CAV2
chr7	ENCODE	exon	115733787	115733936	.	+	.	Parent=gene2414
chr7	ENCODE	CDS	115733787	115733936	.	+	0	Parent=gene2414
chr7	ENCODE	CDS	115739976	115740164	.	+	0	Parent=gene2414
chr7	ENCODE	exon	115739976	115740559	.	+	.	Parent=gene2414
###
chr7	ENCODE	gene	115734102	115740358	.	+	.	ID=gene2415;Name=AC006159.1-002;name2=CAV2
chr7	ENCODE	exon	115734102	115734452	.	+	.	Parent=gene2415
chr7	ENCODE	exon	115739976	115740358	.	+	.	Parent=gene2415
###
chr7	ENCODE	gene	115758790	115795181	.	+	.	ID=gene2416;Name=AC006159.2-001;name2=CAV1
chr7	ENCODE	exon	115758790	115759097	.	+	.	Parent=gene2416
chr7	ENCODE	CDS	115759068	115759097	.	+	0	Parent=gene2416
chr7	ENCODE	exon	115760530	115760694	.	+	.	Parent=gene2416
chr7	ENCODE	CDS	115760530	115760694	.	+	0	Parent=gene2416
chr7	ENCODE	CDS	115792951	115793292	.	+	0	Parent=gene2416
chr7	ENCODE	exon	115792951	115795181	.	+	.	Parent=gene2416
###
chr7	ENCODE	gene	115759014	115793641	.	+	.	ID=gene2417;name2=CAV1;Name=AC006159.2-002
chr7	ENCODE	exon	115759014	115759810	.	+	.	Parent=gene2417
chr7	ENCODE	exon	115760530	115760694	.	+	.	Parent=gene2417
chr7	ENCODE	exon	115792951	115793641	.	+	.	Parent=gene2417
###
chr7	ENCODE	gene	115759017	115761023	.	+	.	ID=gene2418;Name=AC006159.2-005;name2=CAV1
chr7	ENCODE	exon	115759017	115759097	.	+	.	Parent=gene2418
chr7	ENCODE	exon	115760530	115761023	.	+	.	Parent=gene2418
###
chr7	ENCODE	gene	115760282	115793050	.	+	.	ID=gene2419;name2=CAV1;Name=AC006159.2-004
chr7	ENCODE	exon	115760282	115760393	.	+	.	Parent=gene2419
chr7	ENCODE	exon	115760530	115760694	.	+	.	Parent=gene2419
chr7	ENCODE	CDS	115760593	115760694	.	+	0	Parent=gene2419
chr7	ENCODE	exon	115792951	115793050	.	+	.	Parent=gene2419
chr7	ENCODE	CDS	115792951	115793050	.	+	0	Parent=gene2419
###
chr7	ENCODE	gene	115760358	115793638	.	+	.	ID=gene2420;Name=AC006159.2-003;name2=CAV1
chr7	ENCODE	exon	115760358	115760694	.	+	.	Parent=gene2420
chr7	ENCODE	CDS	115760593	115760694	.	+	0	Parent=gene2420
chr7	ENCODE	CDS	115792951	115793292	.	+	0	Parent=gene2420
chr7	ENCODE	exon	115792951	115793638	.	+	.	Parent=gene2420
###
chr7	ENCODE	gene	115906410	116030347	.	+	.	ID=gene2421;Name=AC002543.3-001;name2=MET
chr7	ENCODE	exon	115906410	115906582	.	+	.	Parent=gene2421
chr7	ENCODE	exon	115933076	115934289	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115933090	115934289	.	+	0	Parent=gene2421
chr7	ENCODE	exon	115965673	115965864	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115965673	115965864	.	+	0	Parent=gene2421
chr7	ENCODE	exon	115973955	115974089	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115973955	115974089	.	+	0	Parent=gene2421
chr7	ENCODE	exon	115974857	115975030	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115974857	115975030	.	+	0	Parent=gene2421
chr7	ENCODE	exon	115989360	115989520	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115989360	115989520	.	+	0	Parent=gene2421
chr7	ENCODE	exon	115991442	115991544	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115991442	115991544	.	+	1	Parent=gene2421
chr7	ENCODE	exon	115991643	115991779	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115991643	115991779	.	+	0	Parent=gene2421
chr7	ENCODE	exon	115992464	115992625	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115992464	115992625	.	+	1	Parent=gene2421
chr7	ENCODE	exon	115993342	115993495	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115993342	115993495	.	+	1	Parent=gene2421
chr7	ENCODE	exon	115997055	115997273	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	115997055	115997273	.	+	0	Parent=gene2421
chr7	ENCODE	exon	116003650	116003796	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	116003650	116003796	.	+	0	Parent=gene2421
chr7	ENCODE	exon	116005503	116005659	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	116005503	116005659	.	+	0	Parent=gene2421
chr7	ENCODE	exon	116005854	116005994	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	116005854	116005994	.	+	2	Parent=gene2421
chr7	ENCODE	exon	116008886	116009116	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	116008886	116009116	.	+	2	Parent=gene2421
chr7	ENCODE	exon	116011394	116011474	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	116011394	116011474	.	+	2	Parent=gene2421
chr7	ENCODE	exon	116012781	116012962	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	116012781	116012962	.	+	2	Parent=gene2421
chr7	ENCODE	exon	116015993	116016102	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	116015993	116016102	.	+	0	Parent=gene2421
chr7	ENCODE	exon	116017309	116017474	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	116017309	116017474	.	+	1	Parent=gene2421
chr7	ENCODE	exon	116029660	116029796	.	+	.	Parent=gene2421
chr7	ENCODE	CDS	116029660	116029796	.	+	0	Parent=gene2421
chr7	ENCODE	CDS	116029892	116030129	.	+	1	Parent=gene2421
chr7	ENCODE	exon	116029892	116030347	.	+	.	Parent=gene2421
###
chr7	ENCODE	gene	115906410	116032391	.	+	.	ID=gene2422;Name=AC002543.3-002;name2=MET
chr7	ENCODE	exon	115906410	115906582	.	+	.	Parent=gene2422
chr7	ENCODE	exon	115933076	115934289	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115933090	115934289	.	+	0	Parent=gene2422
chr7	ENCODE	exon	115965673	115965864	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115965673	115965864	.	+	0	Parent=gene2422
chr7	ENCODE	exon	115973955	115974089	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115973955	115974089	.	+	0	Parent=gene2422
chr7	ENCODE	exon	115974857	115975030	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115974857	115975030	.	+	0	Parent=gene2422
chr7	ENCODE	exon	115989360	115989520	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115989360	115989520	.	+	0	Parent=gene2422
chr7	ENCODE	exon	115991442	115991544	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115991442	115991544	.	+	1	Parent=gene2422
chr7	ENCODE	exon	115991643	115991779	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115991643	115991779	.	+	0	Parent=gene2422
chr7	ENCODE	exon	115992464	115992625	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115992464	115992625	.	+	1	Parent=gene2422
chr7	ENCODE	exon	115993396	115993495	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115993396	115993495	.	+	1	Parent=gene2422
chr7	ENCODE	exon	115997055	115997273	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	115997055	115997273	.	+	0	Parent=gene2422
chr7	ENCODE	exon	116003650	116003796	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	116003650	116003796	.	+	0	Parent=gene2422
chr7	ENCODE	exon	116005503	116005659	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	116005503	116005659	.	+	0	Parent=gene2422
chr7	ENCODE	exon	116005854	116005994	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	116005854	116005994	.	+	2	Parent=gene2422
chr7	ENCODE	exon	116008886	116009116	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	116008886	116009116	.	+	2	Parent=gene2422
chr7	ENCODE	exon	116011394	116011474	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	116011394	116011474	.	+	2	Parent=gene2422
chr7	ENCODE	exon	116012781	116012962	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	116012781	116012962	.	+	2	Parent=gene2422
chr7	ENCODE	exon	116015993	116016102	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	116015993	116016102	.	+	0	Parent=gene2422
chr7	ENCODE	exon	116017309	116017474	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	116017309	116017474	.	+	1	Parent=gene2422
chr7	ENCODE	exon	116029660	116029796	.	+	.	Parent=gene2422
chr7	ENCODE	CDS	116029660	116029796	.	+	0	Parent=gene2422
chr7	ENCODE	CDS	116029892	116030129	.	+	1	Parent=gene2422
chr7	ENCODE	exon	116029892	116032391	.	+	.	Parent=gene2422
###
chr7	ENCODE	gene	115906411	115933604	.	+	.	ID=gene2423;Name=AC002543.3-005;name2=MET
chr7	ENCODE	exon	115906411	115906582	.	+	.	Parent=gene2423
chr7	ENCODE	exon	115929755	115929804	.	+	.	Parent=gene2423
chr7	ENCODE	exon	115933076	115933604	.	+	.	Parent=gene2423
chr7	ENCODE	CDS	115933090	115933604	.	+	0	Parent=gene2423
###
chr7	ENCODE	gene	115958151	115989419	.	+	.	ID=gene2424;Name=AC002543.3-003;name2=MET
chr7	ENCODE	exon	115958151	115958254	.	+	.	Parent=gene2424
chr7	ENCODE	exon	115958777	115958852	.	+	.	Parent=gene2424
chr7	ENCODE	exon	115965673	115965864	.	+	.	Parent=gene2424
chr7	ENCODE	exon	115973955	115974089	.	+	.	Parent=gene2424
chr7	ENCODE	exon	115974857	115975030	.	+	.	Parent=gene2424
chr7	ENCODE	exon	115989360	115989419	.	+	.	Parent=gene2424
###
chr7	ENCODE	gene	115992522	116003914	.	+	.	ID=gene2425;Name=AC002543.3-004;name2=MET
chr7	ENCODE	exon	115992522	115992625	.	+	.	Parent=gene2425
chr7	ENCODE	CDS	115992522	115992625	.	+	0	Parent=gene2425
chr7	ENCODE	exon	115993396	115993495	.	+	.	Parent=gene2425
chr7	ENCODE	CDS	115993396	115993495	.	+	1	Parent=gene2425
chr7	ENCODE	exon	115997055	115997273	.	+	.	Parent=gene2425
chr7	ENCODE	CDS	115997055	115997273	.	+	0	Parent=gene2425
chr7	ENCODE	CDS	116003650	116003871	.	+	0	Parent=gene2425
chr7	ENCODE	exon	116003650	116003914	.	+	.	Parent=gene2425
###
chr7	ENCODE	gene	116045075	116132791	.	+	.	ID=gene2426;Name=AC002543.1-010;name2=CAPZA2
chr7	ENCODE	exon	116045075	116045107	.	+	.	Parent=gene2426
chr7	ENCODE	exon	116095196	116095355	.	+	.	Parent=gene2426
chr7	ENCODE	exon	116122132	116122195	.	+	.	Parent=gene2426
chr7	ENCODE	exon	116126999	116127050	.	+	.	Parent=gene2426
chr7	ENCODE	exon	116132777	116132791	.	+	.	Parent=gene2426
###
chr7	ENCODE	gene	116045075	116132791	.	+	.	ID=gene2427;Name=AC002543.1-009;name2=CAPZA2
chr7	ENCODE	exon	116045075	116045107	.	+	.	Parent=gene2427
chr7	ENCODE	exon	116122132	116122195	.	+	.	Parent=gene2427
chr7	ENCODE	exon	116126999	116127050	.	+	.	Parent=gene2427
chr7	ENCODE	exon	116132777	116132791	.	+	.	Parent=gene2427
###
chr7	ENCODE	gene	116096517	116153266	.	+	.	ID=gene2428;Name=AC002543.1-002;name2=CAPZA2
chr7	ENCODE	exon	116096517	116096655	.	+	.	Parent=gene2428
chr7	ENCODE	CDS	116096617	116096655	.	+	0	Parent=gene2428
chr7	ENCODE	exon	116122132	116122195	.	+	.	Parent=gene2428
chr7	ENCODE	CDS	116122132	116122195	.	+	0	Parent=gene2428
chr7	ENCODE	exon	116126999	116127050	.	+	.	Parent=gene2428
chr7	ENCODE	CDS	116126999	116127050	.	+	2	Parent=gene2428
chr7	ENCODE	exon	116132777	116132840	.	+	.	Parent=gene2428
chr7	ENCODE	CDS	116132777	116132840	.	+	1	Parent=gene2428
chr7	ENCODE	exon	116138182	116138388	.	+	.	Parent=gene2428
chr7	ENCODE	CDS	116138182	116138388	.	+	0	Parent=gene2428
chr7	ENCODE	exon	116140268	116140347	.	+	.	Parent=gene2428
chr7	ENCODE	CDS	116140268	116140347	.	+	0	Parent=gene2428
chr7	ENCODE	exon	116144238	116144316	.	+	.	Parent=gene2428
chr7	ENCODE	CDS	116144238	116144316	.	+	1	Parent=gene2428
chr7	ENCODE	exon	116146074	116146145	.	+	.	Parent=gene2428
chr7	ENCODE	CDS	116146074	116146145	.	+	0	Parent=gene2428
chr7	ENCODE	exon	116150065	116150127	.	+	.	Parent=gene2428
chr7	ENCODE	CDS	116150065	116150127	.	+	0	Parent=gene2428
chr7	ENCODE	CDS	116151732	116151872	.	+	0	Parent=gene2428
chr7	ENCODE	exon	116151732	116153266	.	+	.	Parent=gene2428
###
chr7	ENCODE	gene	116096592	116150115	.	+	.	ID=gene2429;Name=AC002543.1-004;name2=CAPZA2
chr7	ENCODE	exon	116096592	116096655	.	+	.	Parent=gene2429
chr7	ENCODE	exon	116114072	116114152	.	+	.	Parent=gene2429
chr7	ENCODE	exon	116122132	116122195	.	+	.	Parent=gene2429
chr7	ENCODE	exon	116126999	116127050	.	+	.	Parent=gene2429
chr7	ENCODE	exon	116132777	116132840	.	+	.	Parent=gene2429
chr7	ENCODE	exon	116138182	116138388	.	+	.	Parent=gene2429
chr7	ENCODE	exon	116140268	116140347	.	+	.	Parent=gene2429
chr7	ENCODE	exon	116144238	116144316	.	+	.	Parent=gene2429
chr7	ENCODE	exon	116146074	116146145	.	+	.	Parent=gene2429
chr7	ENCODE	exon	116150065	116150115	.	+	.	Parent=gene2429
###
chr7	ENCODE	gene	116096605	116138759	.	+	.	ID=gene2430;Name=AC002543.1-006;name2=CAPZA2
chr7	ENCODE	exon	116096605	116096655	.	+	.	Parent=gene2430
chr7	ENCODE	exon	116122132	116122195	.	+	.	Parent=gene2430
chr7	ENCODE	exon	116126999	116127050	.	+	.	Parent=gene2430
chr7	ENCODE	exon	116132777	116132840	.	+	.	Parent=gene2430
chr7	ENCODE	exon	116138182	116138759	.	+	.	Parent=gene2430
###
chr7	ENCODE	gene	116096608	116122704	.	+	.	ID=gene2431;Name=AC002543.1-003;name2=CAPZA2
chr7	ENCODE	exon	116096608	116096655	.	+	.	Parent=gene2431
chr7	ENCODE	exon	116122132	116122704	.	+	.	Parent=gene2431
###
chr7	ENCODE	gene	116096609	116108295	.	+	.	ID=gene2432;Name=AC002543.1-007;name2=CAPZA2
chr7	ENCODE	exon	116096609	116096655	.	+	.	Parent=gene2432
chr7	ENCODE	exon	116107717	116108295	.	+	.	Parent=gene2432
###
chr7	ENCODE	gene	116096619	116140741	.	+	.	ID=gene2433;Name=AC002543.1-005;name2=CAPZA2
chr7	ENCODE	exon	116096619	116096655	.	+	.	Parent=gene2433
chr7	ENCODE	exon	116122132	116122195	.	+	.	Parent=gene2433
chr7	ENCODE	exon	116126999	116127050	.	+	.	Parent=gene2433
chr7	ENCODE	exon	116132777	116132840	.	+	.	Parent=gene2433
chr7	ENCODE	exon	116138182	116138388	.	+	.	Parent=gene2433
chr7	ENCODE	exon	116140268	116140741	.	+	.	Parent=gene2433
###
chr7	ENCODE	gene	116140347	116150127	.	+	.	ID=gene2434;Name=AC002543.1-011;name2=CAPZA2
chr7	ENCODE	exon	116140347	116143760	.	+	.	Parent=gene2434
chr7	ENCODE	exon	116144238	116144316	.	+	.	Parent=gene2434
chr7	ENCODE	exon	116146074	116146145	.	+	.	Parent=gene2434
chr7	ENCODE	exon	116150065	116150127	.	+	.	Parent=gene2434
###
chr7	ENCODE	gene	116149461	116151765	.	+	.	ID=gene2435;Name=AC002543.1-012;name2=CAPZA2
chr7	ENCODE	exon	116149461	116150127	.	+	.	Parent=gene2435
chr7	ENCODE	exon	116151732	116151765	.	+	.	Parent=gene2435
###
chr7	ENCODE	gene	116149461	116151765	.	+	.	ID=gene2436;Name=AC002543.1-008;name2=CAPZA2
chr7	ENCODE	exon	116149461	116150127	.	+	.	Parent=gene2436
chr7	ENCODE	exon	116151732	116151765	.	+	.	Parent=gene2436
###
chr7	ENCODE	gene	116187332	116457912	.	+	.	ID=gene2437;Name=AC003987.1-002;name2=ST7
chr7	ENCODE	exon	116187332	116187696	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116187546	116187696	.	+	0	Parent=gene2437
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116333767	116333849	.	+	2	Parent=gene2437
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116353566	116353725	.	+	0	Parent=gene2437
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116363798	116363852	.	+	2	Parent=gene2437
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116364496	116364611	.	+	1	Parent=gene2437
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116365890	116365965	.	+	2	Parent=gene2437
chr7	ENCODE	exon	116368129	116368197	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116368129	116368197	.	+	1	Parent=gene2437
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116370086	116370240	.	+	1	Parent=gene2437
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116372440	116372537	.	+	2	Parent=gene2437
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116404867	116404981	.	+	0	Parent=gene2437
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116423326	116423398	.	+	2	Parent=gene2437
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116424839	116424941	.	+	1	Parent=gene2437
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116443792	116443942	.	+	0	Parent=gene2437
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116453089	116453181	.	+	2	Parent=gene2437
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2437
chr7	ENCODE	CDS	116455928	116456067	.	+	2	Parent=gene2437
chr7	ENCODE	CDS	116456866	116456985	.	+	0	Parent=gene2437
chr7	ENCODE	exon	116456866	116457912	.	+	.	Parent=gene2437
###
chr7	ENCODE	gene	116187347	116464108	.	+	.	ID=gene2438;Name=AC003987.1-007;name2=ST7
chr7	ENCODE	exon	116187347	116187696	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116187546	116187696	.	+	0	Parent=gene2438
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116333767	116333849	.	+	2	Parent=gene2438
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116353566	116353725	.	+	0	Parent=gene2438
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116363798	116363852	.	+	2	Parent=gene2438
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116364496	116364611	.	+	1	Parent=gene2438
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116365890	116365965	.	+	2	Parent=gene2438
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116370086	116370240	.	+	1	Parent=gene2438
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116372440	116372537	.	+	2	Parent=gene2438
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116404867	116404981	.	+	0	Parent=gene2438
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116423326	116423398	.	+	2	Parent=gene2438
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116424839	116424941	.	+	1	Parent=gene2438
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116443792	116443942	.	+	0	Parent=gene2438
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116453089	116453181	.	+	2	Parent=gene2438
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2438
chr7	ENCODE	CDS	116455928	116456067	.	+	2	Parent=gene2438
chr7	ENCODE	CDS	116463767	116463862	.	+	0	Parent=gene2438
chr7	ENCODE	exon	116463767	116464108	.	+	.	Parent=gene2438
###
chr7	ENCODE	gene	116187352	116372537	.	+	.	ID=gene2439;Name=AC003987.1-015;name2=ST7
chr7	ENCODE	exon	116187352	116187696	.	+	.	Parent=gene2439
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2439
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2439
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2439
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2439
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2439
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2439
###
chr7	ENCODE	gene	116187384	116464108	.	+	.	ID=gene2440;Name=AC003987.1-001;name2=ST7
chr7	ENCODE	exon	116187384	116187696	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116187546	116187696	.	+	0	Parent=gene2440
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116333767	116333849	.	+	2	Parent=gene2440
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116353566	116353725	.	+	0	Parent=gene2440
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116363798	116363852	.	+	2	Parent=gene2440
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116364496	116364611	.	+	1	Parent=gene2440
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116365890	116365965	.	+	2	Parent=gene2440
chr7	ENCODE	exon	116368129	116368197	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116368129	116368197	.	+	1	Parent=gene2440
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116370086	116370240	.	+	1	Parent=gene2440
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116372440	116372537	.	+	2	Parent=gene2440
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116404867	116404981	.	+	0	Parent=gene2440
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116423326	116423398	.	+	2	Parent=gene2440
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116424839	116424941	.	+	1	Parent=gene2440
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116443792	116443942	.	+	0	Parent=gene2440
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116453089	116453181	.	+	2	Parent=gene2440
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2440
chr7	ENCODE	CDS	116455928	116456067	.	+	2	Parent=gene2440
chr7	ENCODE	CDS	116463767	116463862	.	+	0	Parent=gene2440
chr7	ENCODE	exon	116463767	116464108	.	+	.	Parent=gene2440
###
chr7	ENCODE	gene	116187384	116464108	.	+	.	ID=gene2441;Name=AC003987.1-014;name2=ST7
chr7	ENCODE	exon	116187384	116187696	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116187546	116187696	.	+	0	Parent=gene2441
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116333767	116333849	.	+	2	Parent=gene2441
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116353566	116353725	.	+	0	Parent=gene2441
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116363798	116363852	.	+	2	Parent=gene2441
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116364496	116364611	.	+	1	Parent=gene2441
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116365890	116365965	.	+	2	Parent=gene2441
chr7	ENCODE	exon	116368129	116368197	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116368129	116368197	.	+	1	Parent=gene2441
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116370086	116370240	.	+	1	Parent=gene2441
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116372440	116372537	.	+	2	Parent=gene2441
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116404867	116404981	.	+	0	Parent=gene2441
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116423326	116423398	.	+	2	Parent=gene2441
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116424839	116424941	.	+	1	Parent=gene2441
chr7	ENCODE	exon	116443792	116443927	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116443792	116443927	.	+	0	Parent=gene2441
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116453089	116453181	.	+	2	Parent=gene2441
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2441
chr7	ENCODE	CDS	116455928	116456067	.	+	2	Parent=gene2441
chr7	ENCODE	CDS	116463767	116463862	.	+	0	Parent=gene2441
chr7	ENCODE	exon	116463767	116464108	.	+	.	Parent=gene2441
###
chr7	ENCODE	gene	116187506	116464022	.	+	.	ID=gene2442;Name=AC003987.1-003;name2=ST7
chr7	ENCODE	exon	116187506	116187696	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116353566	116353675	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116353697	116353725	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2442
chr7	ENCODE	exon	116463767	116464022	.	+	.	Parent=gene2442
###
chr7	ENCODE	gene	116187904	116193822	.	+	.	ID=gene2443;Name=AC106873.3-001;name2=ST7OT4
chr7	ENCODE	exon	116187904	116188114	.	+	.	Parent=gene2443
chr7	ENCODE	exon	116188466	116188684	.	+	.	Parent=gene2443
chr7	ENCODE	exon	116188979	116189158	.	+	.	Parent=gene2443
chr7	ENCODE	CDS	116189090	116189158	.	+	0	Parent=gene2443
chr7	ENCODE	exon	116190428	116190728	.	+	.	Parent=gene2443
chr7	ENCODE	CDS	116190428	116190728	.	+	0	Parent=gene2443
chr7	ENCODE	CDS	116193158	116193297	.	+	2	Parent=gene2443
chr7	ENCODE	exon	116193158	116193822	.	+	.	Parent=gene2443
###
chr7	ENCODE	gene	116188244	116202579	.	+	.	ID=gene2444;Name=AC106873.3-002;name2=ST7OT4
chr7	ENCODE	exon	116188244	116188684	.	+	.	Parent=gene2444
chr7	ENCODE	exon	116188979	116189158	.	+	.	Parent=gene2444
chr7	ENCODE	exon	116192594	116192690	.	+	.	Parent=gene2444
chr7	ENCODE	exon	116202404	116202579	.	+	.	Parent=gene2444
###
chr7	ENCODE	gene	116188625	116202579	.	+	.	ID=gene2445;Name=AC106873.3-003;name2=ST7OT4
chr7	ENCODE	exon	116188625	116188684	.	+	.	Parent=gene2445
chr7	ENCODE	exon	116188979	116189158	.	+	.	Parent=gene2445
chr7	ENCODE	exon	116202404	116202579	.	+	.	Parent=gene2445
###
chr7	ENCODE	gene	116188979	116202579	.	+	.	ID=gene2446;name2=ST7OT4;Name=AC106873.3-004
chr7	ENCODE	exon	116188979	116189158	.	+	.	Parent=gene2446
chr7	ENCODE	CDS	116189090	116189158	.	+	0	Parent=gene2446
chr7	ENCODE	exon	116190428	116190728	.	+	.	Parent=gene2446
chr7	ENCODE	CDS	116190428	116190728	.	+	0	Parent=gene2446
chr7	ENCODE	exon	116192594	116192690	.	+	.	Parent=gene2446
chr7	ENCODE	CDS	116192594	116192690	.	+	2	Parent=gene2446
chr7	ENCODE	CDS	116202404	116202419	.	+	1	Parent=gene2446
chr7	ENCODE	exon	116202404	116202579	.	+	.	Parent=gene2446
###
chr7	ENCODE	gene	116199851	116201477	.	-	.	ID=gene2447;Name=AC106873.4-001;name2=AC106873.4
chr7	ENCODE	exon	116199851	116200127	.	-	.	Parent=gene2447
chr7	ENCODE	CDS	116200100	116200127	.	-	1	Parent=gene2447
chr7	ENCODE	CDS	116201296	116201426	.	-	0	Parent=gene2447
chr7	ENCODE	exon	116201296	116201477	.	-	.	Parent=gene2447
###
chr7	ENCODE	gene	116248893	116365930	.	+	.	ID=gene2448;Name=AC003987.1-016;name2=ST7
chr7	ENCODE	exon	116248893	116249019	.	+	.	Parent=gene2448
chr7	ENCODE	CDS	116249007	116249019	.	+	0	Parent=gene2448
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2448
chr7	ENCODE	CDS	116333767	116333849	.	+	2	Parent=gene2448
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2448
chr7	ENCODE	CDS	116353566	116353725	.	+	0	Parent=gene2448
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2448
chr7	ENCODE	CDS	116363798	116363852	.	+	2	Parent=gene2448
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2448
chr7	ENCODE	CDS	116364496	116364611	.	+	1	Parent=gene2448
chr7	ENCODE	exon	116365890	116365930	.	+	.	Parent=gene2448
chr7	ENCODE	CDS	116365890	116365930	.	+	2	Parent=gene2448
###
chr7	ENCODE	gene	116248941	116363814	.	+	.	ID=gene2449;Name=AC003987.1-019;name2=ST7
chr7	ENCODE	exon	116248941	116249019	.	+	.	Parent=gene2449
chr7	ENCODE	exon	116332618	116332820	.	+	.	Parent=gene2449
chr7	ENCODE	CDS	116332820	116332820	.	+	0	Parent=gene2449
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2449
chr7	ENCODE	CDS	116333767	116333849	.	+	2	Parent=gene2449
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2449
chr7	ENCODE	CDS	116353566	116353725	.	+	0	Parent=gene2449
chr7	ENCODE	exon	116363798	116363814	.	+	.	Parent=gene2449
chr7	ENCODE	CDS	116363798	116363814	.	+	2	Parent=gene2449
###
chr7	ENCODE	gene	116254189	116424937	.	+	.	ID=gene2450;Name=AC003987.1-011;name2=ST7
chr7	ENCODE	exon	116254189	116254634	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116368129	116368197	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116424138	116424273	.	+	.	Parent=gene2450
chr7	ENCODE	exon	116424839	116424937	.	+	.	Parent=gene2450
###
chr7	ENCODE	gene	116254189	116464108	.	+	.	ID=gene2451;Name=AC003987.1-012;name2=ST7
chr7	ENCODE	exon	116254189	116254634	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116368129	116370240	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116424138	116424273	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2451
chr7	ENCODE	exon	116463767	116464108	.	+	.	Parent=gene2451
###
chr7	ENCODE	gene	116254223	116464108	.	+	.	ID=gene2452;Name=AC003987.1-004;name2=ST7
chr7	ENCODE	exon	116254223	116254634	.	+	.	Parent=gene2452
chr7	ENCODE	exon	116332618	116332820	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116332820	116332820	.	+	0	Parent=gene2452
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116333767	116333849	.	+	2	Parent=gene2452
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116353566	116353725	.	+	0	Parent=gene2452
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116363798	116363852	.	+	2	Parent=gene2452
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116364496	116364611	.	+	1	Parent=gene2452
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116365890	116365965	.	+	2	Parent=gene2452
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116370086	116370240	.	+	1	Parent=gene2452
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116372440	116372537	.	+	2	Parent=gene2452
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116404867	116404981	.	+	0	Parent=gene2452
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116423326	116423398	.	+	2	Parent=gene2452
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116424839	116424941	.	+	1	Parent=gene2452
chr7	ENCODE	exon	116443792	116443927	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116443792	116443927	.	+	0	Parent=gene2452
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116453089	116453181	.	+	2	Parent=gene2452
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2452
chr7	ENCODE	CDS	116455928	116456067	.	+	2	Parent=gene2452
chr7	ENCODE	CDS	116463767	116463862	.	+	0	Parent=gene2452
chr7	ENCODE	exon	116463767	116464108	.	+	.	Parent=gene2452
###
chr7	ENCODE	gene	116254282	116464108	.	+	.	ID=gene2453;Name=AC003987.1-006;name2=ST7
chr7	ENCODE	exon	116254282	116254634	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116254613	116254634	.	+	0	Parent=gene2453
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116333767	116333849	.	+	2	Parent=gene2453
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116353566	116353725	.	+	0	Parent=gene2453
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116363798	116363852	.	+	2	Parent=gene2453
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116364496	116364611	.	+	1	Parent=gene2453
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116365890	116365965	.	+	2	Parent=gene2453
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116370086	116370240	.	+	1	Parent=gene2453
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116372440	116372537	.	+	2	Parent=gene2453
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116404867	116404981	.	+	0	Parent=gene2453
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116423326	116423398	.	+	2	Parent=gene2453
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116424839	116424941	.	+	1	Parent=gene2453
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116443792	116443942	.	+	0	Parent=gene2453
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116453089	116453181	.	+	2	Parent=gene2453
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2453
chr7	ENCODE	CDS	116455928	116456067	.	+	2	Parent=gene2453
chr7	ENCODE	CDS	116463767	116463862	.	+	0	Parent=gene2453
chr7	ENCODE	exon	116463767	116464108	.	+	.	Parent=gene2453
###
chr7	ENCODE	gene	116254282	116464108	.	+	.	ID=gene2454;Name=AC003987.1-005;name2=ST7
chr7	ENCODE	exon	116254282	116254634	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116254613	116254634	.	+	0	Parent=gene2454
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116333767	116333849	.	+	2	Parent=gene2454
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116353566	116353725	.	+	0	Parent=gene2454
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116363798	116363852	.	+	2	Parent=gene2454
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116364496	116364611	.	+	1	Parent=gene2454
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116365890	116365965	.	+	2	Parent=gene2454
chr7	ENCODE	exon	116368129	116368197	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116368129	116368197	.	+	1	Parent=gene2454
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116370086	116370240	.	+	1	Parent=gene2454
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116372440	116372537	.	+	2	Parent=gene2454
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116404867	116404981	.	+	0	Parent=gene2454
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116423326	116423398	.	+	2	Parent=gene2454
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116424839	116424941	.	+	1	Parent=gene2454
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116443792	116443942	.	+	0	Parent=gene2454
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116453089	116453181	.	+	2	Parent=gene2454
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2454
chr7	ENCODE	CDS	116455928	116456067	.	+	2	Parent=gene2454
chr7	ENCODE	CDS	116463767	116463862	.	+	0	Parent=gene2454
chr7	ENCODE	exon	116463767	116464108	.	+	.	Parent=gene2454
###
chr7	ENCODE	gene	116254420	116464108	.	+	.	ID=gene2455;Name=AC003987.1-013;name2=ST7
chr7	ENCODE	exon	116254420	116254634	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116368129	116370240	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2455
chr7	ENCODE	exon	116463767	116464108	.	+	.	Parent=gene2455
###
chr7	ENCODE	gene	116333767	116464108	.	+	.	ID=gene2456;name2=ST7;Name=AC003987.1-008
chr7	ENCODE	exon	116333767	116333849	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116353566	116353725	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116368129	116368197	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2456
chr7	ENCODE	exon	116463767	116464108	.	+	.	Parent=gene2456
###
chr7	ENCODE	gene	116353691	116432402	.	+	.	ID=gene2457;name2=ST7;Name=AC003987.1-009
chr7	ENCODE	exon	116353691	116353725	.	+	.	Parent=gene2457
chr7	ENCODE	exon	116363798	116363852	.	+	.	Parent=gene2457
chr7	ENCODE	exon	116364496	116364611	.	+	.	Parent=gene2457
chr7	ENCODE	exon	116365890	116365965	.	+	.	Parent=gene2457
chr7	ENCODE	exon	116370086	116370240	.	+	.	Parent=gene2457
chr7	ENCODE	exon	116372440	116372537	.	+	.	Parent=gene2457
chr7	ENCODE	exon	116404867	116404981	.	+	.	Parent=gene2457
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2457
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2457
chr7	ENCODE	exon	116432325	116432402	.	+	.	Parent=gene2457
###
chr7	ENCODE	gene	116407413	116443942	.	+	.	ID=gene2458;Name=AC003987.1-017;name2=ST7
chr7	ENCODE	exon	116407413	116407571	.	+	.	Parent=gene2458
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2458
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2458
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2458
###
chr7	ENCODE	gene	116416674	116456067	.	+	.	ID=gene2459;Name=AC003987.1-018;name2=ST7
chr7	ENCODE	exon	116416674	116416750	.	+	.	Parent=gene2459
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2459
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2459
chr7	ENCODE	exon	116425640	116425766	.	+	.	Parent=gene2459
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2459
chr7	ENCODE	exon	116453089	116453181	.	+	.	Parent=gene2459
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2459
###
chr7	ENCODE	gene	116416686	116453095	.	+	.	ID=gene2460;Name=AC003987.1-010;name2=ST7
chr7	ENCODE	exon	116416686	116416750	.	+	.	Parent=gene2460
chr7	ENCODE	exon	116418130	116418204	.	+	.	Parent=gene2460
chr7	ENCODE	exon	116423326	116423398	.	+	.	Parent=gene2460
chr7	ENCODE	exon	116424138	116424273	.	+	.	Parent=gene2460
chr7	ENCODE	exon	116424839	116424941	.	+	.	Parent=gene2460
chr7	ENCODE	exon	116425640	116425766	.	+	.	Parent=gene2460
chr7	ENCODE	exon	116432325	116432545	.	+	.	Parent=gene2460
chr7	ENCODE	exon	116433077	116433149	.	+	.	Parent=gene2460
chr7	ENCODE	exon	116443792	116443942	.	+	.	Parent=gene2460
chr7	ENCODE	exon	116453089	116453095	.	+	.	Parent=gene2460
###
chr7	ENCODE	gene	116453030	116457138	.	+	.	ID=gene2461;Name=AC003987.1-020;name2=ST7
chr7	ENCODE	exon	116453030	116453181	.	+	.	Parent=gene2461
chr7	ENCODE	exon	116455928	116456067	.	+	.	Parent=gene2461
chr7	ENCODE	exon	116456866	116457138	.	+	.	Parent=gene2461
###
chr7	ENCODE	gene	116510636	116557294	.	-	.	ID=gene2462;Name=AC006326.1-002;name2=WNT2
chr7	ENCODE	exon	116510636	116512389	.	-	.	Parent=gene2462
chr7	ENCODE	CDS	116512160	116512389	.	-	2	Parent=gene2462
chr7	ENCODE	exon	116531617	116531881	.	-	.	Parent=gene2462
chr7	ENCODE	CDS	116531617	116531881	.	-	0	Parent=gene2462
chr7	ENCODE	exon	116549076	116549353	.	-	.	Parent=gene2462
chr7	ENCODE	CDS	116549076	116549353	.	-	2	Parent=gene2462
chr7	ENCODE	exon	116554572	116554798	.	-	.	Parent=gene2462
chr7	ENCODE	CDS	116554572	116554798	.	-	1	Parent=gene2462
chr7	ENCODE	CDS	116556912	116556994	.	-	0	Parent=gene2462
chr7	ENCODE	exon	116556912	116557294	.	-	.	Parent=gene2462
###
chr7	ENCODE	gene	116597227	116661513	.	-	.	ID=gene2463;Name=AC002465.3-001;name2=ASZ1
chr7	ENCODE	exon	116597227	116597753	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116597601	116597753	.	-	0	Parent=gene2463
chr7	ENCODE	exon	116601357	116601470	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116601357	116601470	.	-	0	Parent=gene2463
chr7	ENCODE	exon	116602617	116602722	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116602617	116602722	.	-	1	Parent=gene2463
chr7	ENCODE	exon	116613943	116614052	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116613943	116614052	.	-	0	Parent=gene2463
chr7	ENCODE	exon	116615016	116615072	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116615016	116615072	.	-	0	Parent=gene2463
chr7	ENCODE	exon	116616074	116616149	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116616074	116616149	.	-	1	Parent=gene2463
chr7	ENCODE	exon	116616991	116617115	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116616991	116617115	.	-	0	Parent=gene2463
chr7	ENCODE	exon	116618731	116618865	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116618731	116618865	.	-	0	Parent=gene2463
chr7	ENCODE	exon	116619703	116619814	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116619703	116619814	.	-	1	Parent=gene2463
chr7	ENCODE	exon	116654168	116654279	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116654168	116654279	.	-	2	Parent=gene2463
chr7	ENCODE	exon	116656242	116656364	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116656242	116656364	.	-	2	Parent=gene2463
chr7	ENCODE	exon	116660841	116660940	.	-	.	Parent=gene2463
chr7	ENCODE	CDS	116660841	116660940	.	-	0	Parent=gene2463
chr7	ENCODE	CDS	116661361	116661465	.	-	0	Parent=gene2463
chr7	ENCODE	exon	116661361	116661513	.	-	.	Parent=gene2463
###
chr7	ENCODE	gene	116597313	116661503	.	-	.	ID=gene2464;Name=AC002465.3-003;name2=ASZ1
chr7	ENCODE	exon	116597313	116597753	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116601357	116602722	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116613943	116614052	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116615016	116615072	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116616074	116616149	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116616991	116617115	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116618731	116618865	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116619703	116619814	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116654168	116654279	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116656242	116656364	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116660841	116660940	.	-	.	Parent=gene2464
chr7	ENCODE	exon	116661361	116661503	.	-	.	Parent=gene2464
###
chr7	ENCODE	gene	116597320	116661510	.	-	.	ID=gene2465;Name=AC002465.3-002;name2=ASZ1
chr7	ENCODE	exon	116597320	116597753	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116601357	116602722	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116613943	116614052	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116615016	116615072	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116616074	116616149	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116616991	116617115	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116618731	116618865	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116619703	116619814	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116654168	116654279	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116660841	116660940	.	-	.	Parent=gene2465
chr7	ENCODE	exon	116661361	116661510	.	-	.	Parent=gene2465
###
chr7	ENCODE	gene	116616991	116661512	.	-	.	ID=gene2466;Name=AC002465.3-004;name2=ASZ1
chr7	ENCODE	exon	116616991	116617115	.	-	.	Parent=gene2466
chr7	ENCODE	exon	116618731	116618865	.	-	.	Parent=gene2466
chr7	ENCODE	exon	116654168	116654279	.	-	.	Parent=gene2466
chr7	ENCODE	exon	116656242	116656364	.	-	.	Parent=gene2466
chr7	ENCODE	exon	116660841	116660940	.	-	.	Parent=gene2466
chr7	ENCODE	exon	116661361	116661512	.	-	.	Parent=gene2466
###
chr7	ENCODE	gene	116656277	116662128	.	-	.	ID=gene2467;Name=AC002465.3-005;name2=ASZ1
chr7	ENCODE	exon	116656277	116656364	.	-	.	Parent=gene2467
chr7	ENCODE	CDS	116656277	116656364	.	-	2	Parent=gene2467
chr7	ENCODE	CDS	116660841	116660886	.	-	0	Parent=gene2467
chr7	ENCODE	exon	116660841	116660940	.	-	.	Parent=gene2467
chr7	ENCODE	exon	116662075	116662128	.	-	.	Parent=gene2467
###
chr7	ENCODE	gene	116699789	116738313	.	+	.	ID=gene2468;Name=AC000061.1-003;name2=CFTR
chr7	ENCODE	exon	116699789	116699836	.	+	.	Parent=gene2468
chr7	ENCODE	exon	116709696	116709813	.	+	.	Parent=gene2468
chr7	ENCODE	exon	116738258	116738313	.	+	.	Parent=gene2468
###
chr7	ENCODE	gene	116713309	116764983	.	+	.	ID=gene2469;Name=AC000061.1-004;name2=CFTR
chr7	ENCODE	exon	116713309	116713350	.	+	.	Parent=gene2469
chr7	ENCODE	exon	116713467	116713699	.	+	.	Parent=gene2469
chr7	ENCODE	exon	116738258	116738368	.	+	.	Parent=gene2469
chr7	ENCODE	exon	116743039	116743147	.	+	.	Parent=gene2469
chr7	ENCODE	CDS	116743118	116743147	.	+	0	Parent=gene2469
chr7	ENCODE	exon	116764904	116764983	.	+	.	Parent=gene2469
chr7	ENCODE	CDS	116764904	116764983	.	+	0	Parent=gene2469
###
chr7	ENCODE	gene	116713968	116902666	.	+	.	ID=gene2470;Name=AC000061.1-001;name2=CFTR
chr7	ENCODE	exon	116713968	116714152	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116714100	116714152	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116738258	116738368	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116738258	116738368	.	+	1	Parent=gene2470
chr7	ENCODE	exon	116743039	116743147	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116743039	116743147	.	+	1	Parent=gene2470
chr7	ENCODE	exon	116764904	116765119	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116764904	116765119	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116768281	116768370	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116768281	116768370	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116769253	116769416	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116769253	116769416	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116770553	116770678	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116770553	116770678	.	+	1	Parent=gene2470
chr7	ENCODE	exon	116774105	116774351	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116774105	116774351	.	+	1	Parent=gene2470
chr7	ENCODE	exon	116776021	116776113	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116776021	116776113	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116782646	116782828	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116782646	116782828	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116793469	116793660	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116793469	116793660	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116821744	116821838	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116821744	116821838	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116824358	116824444	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116824358	116824444	.	+	1	Parent=gene2470
chr7	ENCODE	exon	116825939	116826662	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116825939	116826662	.	+	1	Parent=gene2470
chr7	ENCODE	exon	116828935	116829063	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116828935	116829063	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116836831	116836868	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116836831	116836868	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116837537	116837787	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116837537	116837787	.	+	1	Parent=gene2470
chr7	ENCODE	exon	116840679	116840758	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116840679	116840758	.	+	2	Parent=gene2470
chr7	ENCODE	exon	116844524	116844674	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116844524	116844674	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116845586	116845813	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116845586	116845813	.	+	2	Parent=gene2470
chr7	ENCODE	exon	116848618	116848718	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116848618	116848718	.	+	2	Parent=gene2470
chr7	ENCODE	exon	116861527	116861775	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116861527	116861775	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116876443	116876598	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116876443	116876598	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116886847	116886936	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116886847	116886936	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116898693	116898865	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116898693	116898865	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116899464	116899569	.	+	.	Parent=gene2470
chr7	ENCODE	CDS	116899464	116899569	.	+	1	Parent=gene2470
chr7	ENCODE	CDS	116900913	116901113	.	+	0	Parent=gene2470
chr7	ENCODE	exon	116900913	116902666	.	+	.	Parent=gene2470
###
chr7	ENCODE	gene	116845622	116861915	.	+	.	ID=gene2471;Name=AC000061.1-002;name2=CFTR
chr7	ENCODE	exon	116845622	116845813	.	+	.	Parent=gene2471
chr7	ENCODE	exon	116848618	116848718	.	+	.	Parent=gene2471
chr7	ENCODE	exon	116861527	116861915	.	+	.	Parent=gene2471
###
chr7	ENCODE	gene	116944656	117107512	.	-	.	ID=gene2472;Name=AC004240.1-001;name2=CTTNBP2
chr7	ENCODE	exon	116944656	116945787	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116945542	116945787	.	-	0	Parent=gene2472
chr7	ENCODE	exon	116952023	116952124	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116952023	116952124	.	-	0	Parent=gene2472
chr7	ENCODE	exon	116953509	116953641	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116953509	116953641	.	-	1	Parent=gene2472
chr7	ENCODE	exon	116955072	116955135	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116955072	116955135	.	-	2	Parent=gene2472
chr7	ENCODE	exon	116958552	116958737	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116958552	116958737	.	-	2	Parent=gene2472
chr7	ENCODE	exon	116959057	116959262	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116959057	116959262	.	-	1	Parent=gene2472
chr7	ENCODE	exon	116962094	116962272	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116962094	116962272	.	-	0	Parent=gene2472
chr7	ENCODE	exon	116968918	116969105	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116968918	116969105	.	-	2	Parent=gene2472
chr7	ENCODE	exon	116969274	116969426	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116969274	116969426	.	-	2	Parent=gene2472
chr7	ENCODE	exon	116979836	116979935	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116979836	116979935	.	-	0	Parent=gene2472
chr7	ENCODE	exon	116980018	116980104	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116980018	116980104	.	-	0	Parent=gene2472
chr7	ENCODE	exon	116990560	116990639	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116990560	116990639	.	-	2	Parent=gene2472
chr7	ENCODE	exon	116991880	116991975	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116991880	116991975	.	-	2	Parent=gene2472
chr7	ENCODE	exon	116994440	116994715	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	116994440	116994715	.	-	2	Parent=gene2472
chr7	ENCODE	exon	117001064	117001181	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	117001064	117001181	.	-	0	Parent=gene2472
chr7	ENCODE	exon	117011516	117011770	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	117011516	117011770	.	-	0	Parent=gene2472
chr7	ENCODE	exon	117014446	117014596	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	117014446	117014596	.	-	1	Parent=gene2472
chr7	ENCODE	exon	117016867	117016966	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	117016867	117016966	.	-	2	Parent=gene2472
chr7	ENCODE	exon	117018256	117018459	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	117018256	117018459	.	-	2	Parent=gene2472
chr7	ENCODE	exon	117025133	117026786	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	117025133	117026786	.	-	0	Parent=gene2472
chr7	ENCODE	exon	117044770	117044994	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	117044770	117044994	.	-	0	Parent=gene2472
chr7	ENCODE	exon	117095214	117095321	.	-	.	Parent=gene2472
chr7	ENCODE	CDS	117095214	117095321	.	-	0	Parent=gene2472
chr7	ENCODE	CDS	117107340	117107420	.	-	0	Parent=gene2472
chr7	ENCODE	exon	117107340	117107512	.	-	.	Parent=gene2472
###
chr7	ENCODE	gene	116989377	116992117	.	-	.	ID=gene2473;Name=AC004240.1-005;name2=CTTNBP2
chr7	ENCODE	exon	116989377	116989579	.	-	.	Parent=gene2473
chr7	ENCODE	exon	116990560	116990639	.	-	.	Parent=gene2473
chr7	ENCODE	exon	116991880	116992117	.	-	.	Parent=gene2473
###
chr7	ENCODE	gene	116989385	116994525	.	-	.	ID=gene2474;Name=AC004240.1-004;name2=CTTNBP2
chr7	ENCODE	exon	116989385	116989579	.	-	.	Parent=gene2474
chr7	ENCODE	CDS	116989553	116989579	.	-	2	Parent=gene2474
chr7	ENCODE	exon	116990560	116990639	.	-	.	Parent=gene2474
chr7	ENCODE	CDS	116990560	116990639	.	-	1	Parent=gene2474
chr7	ENCODE	exon	116991880	116991975	.	-	.	Parent=gene2474
chr7	ENCODE	CDS	116991880	116991975	.	-	1	Parent=gene2474
chr7	ENCODE	exon	116994440	116994525	.	-	.	Parent=gene2474
chr7	ENCODE	CDS	116994440	116994525	.	-	0	Parent=gene2474
###
chr7	ENCODE	gene	117026591	117105643	.	-	.	ID=gene2475;Name=AC004240.1-002;name2=CTTNBP2
chr7	ENCODE	exon	117026591	117026786	.	-	.	Parent=gene2475
chr7	ENCODE	CDS	117026591	117026786	.	-	2	Parent=gene2475
chr7	ENCODE	exon	117044770	117044994	.	-	.	Parent=gene2475
chr7	ENCODE	CDS	117044770	117044994	.	-	2	Parent=gene2475
chr7	ENCODE	exon	117095214	117095321	.	-	.	Parent=gene2475
chr7	ENCODE	CDS	117095214	117095321	.	-	2	Parent=gene2475
chr7	ENCODE	exon	117105595	117105643	.	-	.	Parent=gene2475
chr7	ENCODE	CDS	117105595	117105643	.	-	0	Parent=gene2475
###
chr7	ENCODE	gene	117026601	117027610	.	-	.	ID=gene2476;Name=AC004240.1-003;name2=CTTNBP2
chr7	ENCODE	exon	117026601	117026786	.	-	.	Parent=gene2476
chr7	ENCODE	exon	117027418	117027610	.	-	.	Parent=gene2476
###
chr7	ENCODE	gene	117026667	117106225	.	-	.	ID=gene2477;Name=AC004240.1-006;name2=CTTNBP2
chr7	ENCODE	exon	117026667	117026786	.	-	.	Parent=gene2477
chr7	ENCODE	CDS	117026667	117026786	.	-	0	Parent=gene2477
chr7	ENCODE	exon	117044770	117044994	.	-	.	Parent=gene2477
chr7	ENCODE	CDS	117044770	117044994	.	-	0	Parent=gene2477
chr7	ENCODE	CDS	117095214	117095276	.	-	0	Parent=gene2477
chr7	ENCODE	exon	117095214	117095321	.	-	.	Parent=gene2477
chr7	ENCODE	exon	117106109	117106225	.	-	.	Parent=gene2477
###
chr7	ENCODE	gene	117044772	117108144	.	-	.	ID=gene2478;Name=AC004240.1-007;name2=CTTNBP2
chr7	ENCODE	exon	117044772	117044994	.	-	.	Parent=gene2478
chr7	ENCODE	CDS	117044772	117044994	.	-	0	Parent=gene2478
chr7	ENCODE	CDS	117095214	117095276	.	-	0	Parent=gene2478
chr7	ENCODE	exon	117095214	117095321	.	-	.	Parent=gene2478
chr7	ENCODE	exon	117108006	117108144	.	-	.	Parent=gene2478
###
chr7	ENCODE	gene	125672607	126487299	.	-	.	ID=gene2479;Name=AC000370.1-001;name2=GRM8
chr7	ENCODE	exon	125672607	125673173	.	-	.	Parent=gene2479
chr7	ENCODE	CDS	125673124	125673173	.	-	2	Parent=gene2479
chr7	ENCODE	exon	125680131	125680377	.	-	.	Parent=gene2479
chr7	ENCODE	CDS	125680131	125680377	.	-	0	Parent=gene2479
chr7	ENCODE	exon	125766957	125767892	.	-	.	Parent=gene2479
chr7	ENCODE	CDS	125766957	125767892	.	-	0	Parent=gene2479
chr7	ENCODE	exon	125843367	125843503	.	-	.	Parent=gene2479
chr7	ENCODE	CDS	125843367	125843503	.	-	2	Parent=gene2479
chr7	ENCODE	exon	126003870	126004070	.	-	.	Parent=gene2479
chr7	ENCODE	CDS	126003870	126004070	.	-	2	Parent=gene2479
chr7	ENCODE	exon	126136547	126136684	.	-	.	Parent=gene2479
chr7	ENCODE	CDS	126136547	126136684	.	-	2	Parent=gene2479
chr7	ENCODE	exon	126137977	126138131	.	-	.	Parent=gene2479
chr7	ENCODE	CDS	126137977	126138131	.	-	1	Parent=gene2479
chr7	ENCODE	exon	126138553	126138688	.	-	.	Parent=gene2479
chr7	ENCODE	CDS	126138553	126138688	.	-	2	Parent=gene2479
chr7	ENCODE	exon	126340501	126340717	.	-	.	Parent=gene2479
chr7	ENCODE	CDS	126340501	126340717	.	-	0	Parent=gene2479
chr7	ENCODE	CDS	126476700	126477209	.	-	0	Parent=gene2479
chr7	ENCODE	exon	126476700	126477520	.	-	.	Parent=gene2479
chr7	ENCODE	exon	126486802	126487299	.	-	.	Parent=gene2479
###
chr7	ENCODE	gene	125672620	126477224	.	-	.	ID=gene2480;Name=AC000370.1-002;name2=GRM8
chr7	ENCODE	exon	125672620	125673173	.	-	.	Parent=gene2480
chr7	ENCODE	exon	125680076	125680377	.	-	.	Parent=gene2480
chr7	ENCODE	CDS	125680081	125680377	.	-	0	Parent=gene2480
chr7	ENCODE	exon	125766957	125767892	.	-	.	Parent=gene2480
chr7	ENCODE	CDS	125766957	125767892	.	-	0	Parent=gene2480
chr7	ENCODE	exon	125843367	125843503	.	-	.	Parent=gene2480
chr7	ENCODE	CDS	125843367	125843503	.	-	2	Parent=gene2480
chr7	ENCODE	exon	126003870	126004070	.	-	.	Parent=gene2480
chr7	ENCODE	CDS	126003870	126004070	.	-	2	Parent=gene2480
chr7	ENCODE	exon	126136547	126136684	.	-	.	Parent=gene2480
chr7	ENCODE	CDS	126136547	126136684	.	-	2	Parent=gene2480
chr7	ENCODE	exon	126137977	126138131	.	-	.	Parent=gene2480
chr7	ENCODE	CDS	126137977	126138131	.	-	1	Parent=gene2480
chr7	ENCODE	exon	126138553	126138688	.	-	.	Parent=gene2480
chr7	ENCODE	CDS	126138553	126138688	.	-	2	Parent=gene2480
chr7	ENCODE	exon	126340501	126340717	.	-	.	Parent=gene2480
chr7	ENCODE	CDS	126340501	126340717	.	-	0	Parent=gene2480
chr7	ENCODE	CDS	126476700	126477209	.	-	0	Parent=gene2480
chr7	ENCODE	exon	126476700	126477224	.	-	.	Parent=gene2480
###
chr7	ENCODE	gene	125672633	125699304	.	-	.	ID=gene2481;Name=AC000370.1-007;name2=GRM8
chr7	ENCODE	exon	125672633	125673173	.	-	.	Parent=gene2481
chr7	ENCODE	exon	125680131	125680377	.	-	.	Parent=gene2481
chr7	ENCODE	exon	125681141	125681193	.	-	.	Parent=gene2481
chr7	ENCODE	exon	125699236	125699304	.	-	.	Parent=gene2481
###
chr7	ENCODE	gene	125672697	126477224	.	-	.	ID=gene2482;Name=AC000370.1-003;name2=GRM8
chr7	ENCODE	exon	125672697	125673173	.	-	.	Parent=gene2482
chr7	ENCODE	exon	125680131	125680377	.	-	.	Parent=gene2482
chr7	ENCODE	exon	125766957	125767892	.	-	.	Parent=gene2482
chr7	ENCODE	exon	125843367	125843503	.	-	.	Parent=gene2482
chr7	ENCODE	exon	125935762	125935832	.	-	.	Parent=gene2482
chr7	ENCODE	exon	126003870	126004070	.	-	.	Parent=gene2482
chr7	ENCODE	exon	126136547	126136684	.	-	.	Parent=gene2482
chr7	ENCODE	exon	126137977	126138131	.	-	.	Parent=gene2482
chr7	ENCODE	exon	126138553	126138688	.	-	.	Parent=gene2482
chr7	ENCODE	exon	126340501	126340717	.	-	.	Parent=gene2482
chr7	ENCODE	exon	126476700	126477224	.	-	.	Parent=gene2482
###
chr7	ENCODE	gene	125672698	125681193	.	-	.	ID=gene2483;Name=AC000370.1-008;name2=GRM8
chr7	ENCODE	exon	125672698	125673173	.	-	.	Parent=gene2483
chr7	ENCODE	exon	125680076	125680377	.	-	.	Parent=gene2483
chr7	ENCODE	exon	125681141	125681193	.	-	.	Parent=gene2483
###
chr7	ENCODE	gene	125767056	126346325	.	-	.	ID=gene2484;Name=AC000370.1-004;name2=GRM8
chr7	ENCODE	exon	125767056	125767783	.	-	.	Parent=gene2484
chr7	ENCODE	exon	125843499	125843503	.	-	.	Parent=gene2484
chr7	ENCODE	exon	125935762	125935832	.	-	.	Parent=gene2484
chr7	ENCODE	exon	126003870	126004070	.	-	.	Parent=gene2484
chr7	ENCODE	exon	126136547	126136684	.	-	.	Parent=gene2484
chr7	ENCODE	exon	126137977	126138131	.	-	.	Parent=gene2484
chr7	ENCODE	exon	126138553	126138688	.	-	.	Parent=gene2484
chr7	ENCODE	exon	126339301	126339375	.	-	.	Parent=gene2484
chr7	ENCODE	exon	126340501	126340717	.	-	.	Parent=gene2484
chr7	ENCODE	exon	126346174	126346325	.	-	.	Parent=gene2484
###
chr7	ENCODE	gene	126003926	126352277	.	-	.	ID=gene2485;Name=AC000370.1-009;name2=GRM8
chr7	ENCODE	exon	126003926	126004070	.	-	.	Parent=gene2485
chr7	ENCODE	exon	126136547	126136684	.	-	.	Parent=gene2485
chr7	ENCODE	exon	126137977	126138131	.	-	.	Parent=gene2485
chr7	ENCODE	exon	126138553	126138688	.	-	.	Parent=gene2485
chr7	ENCODE	exon	126340501	126340717	.	-	.	Parent=gene2485
chr7	ENCODE	exon	126352226	126352277	.	-	.	Parent=gene2485
###
chr7	ENCODE	gene	126138114	126485224	.	-	.	ID=gene2486;Name=AC000370.1-012;name2=GRM8
chr7	ENCODE	exon	126138114	126138131	.	-	.	Parent=gene2486
chr7	ENCODE	CDS	126138114	126138131	.	-	1	Parent=gene2486
chr7	ENCODE	exon	126138553	126138688	.	-	.	Parent=gene2486
chr7	ENCODE	CDS	126138553	126138688	.	-	2	Parent=gene2486
chr7	ENCODE	exon	126340501	126340717	.	-	.	Parent=gene2486
chr7	ENCODE	CDS	126340501	126340717	.	-	0	Parent=gene2486
chr7	ENCODE	CDS	126476700	126477209	.	-	0	Parent=gene2486
chr7	ENCODE	exon	126476700	126477520	.	-	.	Parent=gene2486
chr7	ENCODE	exon	126485170	126485224	.	-	.	Parent=gene2486
###
chr7	ENCODE	gene	126309970	126340657	.	-	.	ID=gene2487;name2=GRM8;Name=AC000370.1-006
chr7	ENCODE	exon	126309970	126310241	.	-	.	Parent=gene2487
chr7	ENCODE	exon	126340501	126340657	.	-	.	Parent=gene2487
###
chr7	ENCODE	gene	126318294	126329815	.	-	.	ID=gene2488;Name=AC000370.1-013;name2=GRM8
chr7	ENCODE	exon	126318294	126318420	.	-	.	Parent=gene2488
chr7	ENCODE	exon	126318696	126318794	.	-	.	Parent=gene2488
chr7	ENCODE	exon	126324914	126325018	.	-	.	Parent=gene2488
chr7	ENCODE	exon	126329670	126329815	.	-	.	Parent=gene2488
###
chr7	ENCODE	gene	126324928	126346291	.	-	.	ID=gene2489;Name=AC000370.1-005;name2=GRM8
chr7	ENCODE	exon	126324928	126325018	.	-	.	Parent=gene2489
chr7	ENCODE	exon	126339301	126339375	.	-	.	Parent=gene2489
chr7	ENCODE	exon	126340501	126340717	.	-	.	Parent=gene2489
chr7	ENCODE	exon	126345046	126345191	.	-	.	Parent=gene2489
chr7	ENCODE	exon	126346174	126346291	.	-	.	Parent=gene2489
###
chr7	ENCODE	gene	126477079	126486386	.	-	.	ID=gene2490;Name=AC000370.1-010;name2=GRM8
chr7	ENCODE	CDS	126477079	126477209	.	-	0	Parent=gene2490
chr7	ENCODE	exon	126477079	126477520	.	-	.	Parent=gene2490
chr7	ENCODE	exon	126486134	126486386	.	-	.	Parent=gene2490
###
chr7	ENCODE	gene	126477148	126485031	.	-	.	ID=gene2491;Name=AC000370.1-011;name2=GRM8
chr7	ENCODE	CDS	126477148	126477209	.	-	0	Parent=gene2491
chr7	ENCODE	exon	126477148	126477520	.	-	.	Parent=gene2491
chr7	ENCODE	exon	126484854	126485031	.	-	.	Parent=gene2491
###
chr7	ENCODE	gene	126580795	126607570	.	-	.	ID=gene2492;Name=AC000123.1-004;name2=ZNF800
chr7	ENCODE	exon	126580795	126582048	.	-	.	Parent=gene2492
chr7	ENCODE	exon	126607347	126607570	.	-	.	Parent=gene2492
###
chr7	ENCODE	gene	126604048	126626696	.	-	.	ID=gene2493;Name=AC000123.1-002;name2=ZNF800
chr7	ENCODE	exon	126604048	126605819	.	-	.	Parent=gene2493
chr7	ENCODE	CDS	126605819	126605819	.	-	1	Parent=gene2493
chr7	ENCODE	exon	126607347	126609039	.	-	.	Parent=gene2493
chr7	ENCODE	CDS	126607347	126609039	.	-	2	Parent=gene2493
chr7	ENCODE	exon	126611191	126611334	.	-	.	Parent=gene2493
chr7	ENCODE	CDS	126611191	126611334	.	-	2	Parent=gene2493
chr7	ENCODE	exon	126620065	126620160	.	-	.	Parent=gene2493
chr7	ENCODE	CDS	126620065	126620160	.	-	2	Parent=gene2493
chr7	ENCODE	CDS	126625502	126625562	.	-	0	Parent=gene2493
chr7	ENCODE	exon	126625502	126625620	.	-	.	Parent=gene2493
chr7	ENCODE	exon	126626163	126626696	.	-	.	Parent=gene2493
###
chr7	ENCODE	gene	126604304	126626699	.	-	.	ID=gene2494;Name=AC000123.1-001;name2=ZNF800
chr7	ENCODE	exon	126604304	126605819	.	-	.	Parent=gene2494
chr7	ENCODE	CDS	126605819	126605819	.	-	1	Parent=gene2494
chr7	ENCODE	exon	126607347	126609039	.	-	.	Parent=gene2494
chr7	ENCODE	CDS	126607347	126609039	.	-	2	Parent=gene2494
chr7	ENCODE	exon	126611191	126611334	.	-	.	Parent=gene2494
chr7	ENCODE	CDS	126611191	126611334	.	-	2	Parent=gene2494
chr7	ENCODE	exon	126620065	126620160	.	-	.	Parent=gene2494
chr7	ENCODE	CDS	126620065	126620160	.	-	2	Parent=gene2494
chr7	ENCODE	CDS	126625502	126625562	.	-	0	Parent=gene2494
chr7	ENCODE	exon	126625502	126625620	.	-	.	Parent=gene2494
chr7	ENCODE	exon	126626065	126626699	.	-	.	Parent=gene2494
###
chr7	ENCODE	gene	126604446	126626095	.	-	.	ID=gene2495;Name=AC000123.1-006;name2=ZNF800
chr7	ENCODE	exon	126604446	126604720	.	-	.	Parent=gene2495
chr7	ENCODE	exon	126611310	126611334	.	-	.	Parent=gene2495
chr7	ENCODE	exon	126620065	126620160	.	-	.	Parent=gene2495
chr7	ENCODE	exon	126625502	126625620	.	-	.	Parent=gene2495
chr7	ENCODE	exon	126626065	126626095	.	-	.	Parent=gene2495
###
chr7	ENCODE	gene	126605605	126626371	.	-	.	ID=gene2496;Name=AC000123.1-009;name2=ZNF800
chr7	ENCODE	exon	126605605	126605819	.	-	.	Parent=gene2496
chr7	ENCODE	CDS	126605819	126605819	.	-	1	Parent=gene2496
chr7	ENCODE	exon	126607347	126609039	.	-	.	Parent=gene2496
chr7	ENCODE	CDS	126607347	126609039	.	-	2	Parent=gene2496
chr7	ENCODE	exon	126611191	126611334	.	-	.	Parent=gene2496
chr7	ENCODE	CDS	126611191	126611334	.	-	2	Parent=gene2496
chr7	ENCODE	exon	126620065	126620160	.	-	.	Parent=gene2496
chr7	ENCODE	CDS	126620065	126620160	.	-	2	Parent=gene2496
chr7	ENCODE	CDS	126625502	126625562	.	-	0	Parent=gene2496
chr7	ENCODE	exon	126625502	126625620	.	-	.	Parent=gene2496
chr7	ENCODE	exon	126626264	126626371	.	-	.	Parent=gene2496
###
chr7	ENCODE	gene	126605706	126626723	.	-	.	ID=gene2497;Name=AC000123.1-003;name2=ZNF800
chr7	ENCODE	exon	126605706	126605819	.	-	.	Parent=gene2497
chr7	ENCODE	exon	126607347	126609039	.	-	.	Parent=gene2497
chr7	ENCODE	exon	126611191	126611334	.	-	.	Parent=gene2497
chr7	ENCODE	exon	126620065	126620185	.	-	.	Parent=gene2497
chr7	ENCODE	exon	126625502	126625620	.	-	.	Parent=gene2497
chr7	ENCODE	exon	126626065	126626723	.	-	.	Parent=gene2497
###
chr7	ENCODE	gene	126608615	126626723	.	-	.	ID=gene2498;Name=AC000123.1-007;name2=ZNF800
chr7	ENCODE	exon	126608615	126609039	.	-	.	Parent=gene2498
chr7	ENCODE	CDS	126608615	126609039	.	-	2	Parent=gene2498
chr7	ENCODE	exon	126611191	126611334	.	-	.	Parent=gene2498
chr7	ENCODE	CDS	126611191	126611334	.	-	2	Parent=gene2498
chr7	ENCODE	exon	126620065	126620160	.	-	.	Parent=gene2498
chr7	ENCODE	CDS	126620065	126620160	.	-	2	Parent=gene2498
chr7	ENCODE	CDS	126625502	126625562	.	-	0	Parent=gene2498
chr7	ENCODE	exon	126625502	126625620	.	-	.	Parent=gene2498
chr7	ENCODE	exon	126626553	126626723	.	-	.	Parent=gene2498
###
chr7	ENCODE	gene	126608951	126626123	.	-	.	ID=gene2499;Name=AC000123.1-005;name2=ZNF800
chr7	ENCODE	exon	126608951	126609039	.	-	.	Parent=gene2499
chr7	ENCODE	CDS	126608951	126609039	.	-	2	Parent=gene2499
chr7	ENCODE	exon	126611191	126611334	.	-	.	Parent=gene2499
chr7	ENCODE	CDS	126611191	126611334	.	-	2	Parent=gene2499
chr7	ENCODE	exon	126620065	126620160	.	-	.	Parent=gene2499
chr7	ENCODE	CDS	126620065	126620160	.	-	2	Parent=gene2499
chr7	ENCODE	CDS	126625502	126625562	.	-	0	Parent=gene2499
chr7	ENCODE	exon	126625502	126625620	.	-	.	Parent=gene2499
chr7	ENCODE	exon	126626070	126626123	.	-	.	Parent=gene2499
###
chr7	ENCODE	gene	126611196	126665929	.	-	.	ID=gene2500;Name=AC000123.1-008;name2=ZNF800
chr7	ENCODE	exon	126611196	126611334	.	-	.	Parent=gene2500
chr7	ENCODE	CDS	126611196	126611334	.	-	2	Parent=gene2500
chr7	ENCODE	exon	126620065	126620160	.	-	.	Parent=gene2500
chr7	ENCODE	CDS	126620065	126620160	.	-	2	Parent=gene2500
chr7	ENCODE	CDS	126625502	126625562	.	-	0	Parent=gene2500
chr7	ENCODE	exon	126625502	126625620	.	-	.	Parent=gene2500
chr7	ENCODE	exon	126665874	126665929	.	-	.	Parent=gene2500
###
chr7	ENCODE	gene	126814623	126819612	.	-	.	ID=gene2501;Name=AC000357.1-001;name2=GCC1
chr7	ENCODE	exon	126814623	126817314	.	-	.	Parent=gene2501
chr7	ENCODE	CDS	126816019	126817314	.	-	0	Parent=gene2501
chr7	ENCODE	CDS	126818156	126819187	.	-	0	Parent=gene2501
chr7	ENCODE	exon	126818156	126819612	.	-	.	Parent=gene2501
###
chr7	ENCODE	gene	126816825	126827611	.	-	.	ID=gene2502;Name=AC000357.1-002;name2=GCC1
chr7	ENCODE	exon	126816825	126817314	.	-	.	Parent=gene2502
chr7	ENCODE	exon	126823761	126823956	.	-	.	Parent=gene2502
chr7	ENCODE	exon	126827503	126827611	.	-	.	Parent=gene2502
###
chr7	ENCODE	gene	126822350	126825710	.	+	.	ID=gene2503;Name=AC000357.2-001;name2=ARF5
chr7	ENCODE	exon	126822350	126822570	.	+	.	Parent=gene2503
chr7	ENCODE	CDS	126822504	126822570	.	+	0	Parent=gene2503
chr7	ENCODE	exon	126823088	126823168	.	+	.	Parent=gene2503
chr7	ENCODE	CDS	126823088	126823168	.	+	2	Parent=gene2503
chr7	ENCODE	exon	126823490	126823599	.	+	.	Parent=gene2503
chr7	ENCODE	CDS	126823490	126823599	.	+	2	Parent=gene2503
chr7	ENCODE	exon	126824071	126824142	.	+	.	Parent=gene2503
chr7	ENCODE	CDS	126824071	126824142	.	+	0	Parent=gene2503
chr7	ENCODE	exon	126824968	126825093	.	+	.	Parent=gene2503
chr7	ENCODE	CDS	126824968	126825093	.	+	0	Parent=gene2503
chr7	ENCODE	CDS	126825218	126825304	.	+	0	Parent=gene2503
chr7	ENCODE	exon	126825218	126825710	.	+	.	Parent=gene2503
###
chr7	ENCODE	gene	126822391	126825686	.	+	.	ID=gene2504;Name=AC000357.2-002;name2=ARF5
chr7	ENCODE	exon	126822391	126822570	.	+	.	Parent=gene2504
chr7	ENCODE	exon	126823088	126823168	.	+	.	Parent=gene2504
chr7	ENCODE	exon	126823490	126824142	.	+	.	Parent=gene2504
chr7	ENCODE	exon	126824968	126825093	.	+	.	Parent=gene2504
chr7	ENCODE	exon	126825218	126825686	.	+	.	Parent=gene2504
###
chr7	ENCODE	gene	126822410	126823579	.	+	.	ID=gene2505;Name=AC000357.2-006;name2=ARF5
chr7	ENCODE	exon	126822410	126822805	.	+	.	Parent=gene2505
chr7	ENCODE	exon	126823088	126823168	.	+	.	Parent=gene2505
chr7	ENCODE	exon	126823490	126823579	.	+	.	Parent=gene2505
###
chr7	ENCODE	gene	126822418	126825117	.	+	.	ID=gene2506;Name=AC000357.2-003;name2=ARF5
chr7	ENCODE	exon	126822418	126822570	.	+	.	Parent=gene2506
chr7	ENCODE	exon	126823088	126823168	.	+	.	Parent=gene2506
chr7	ENCODE	exon	126823490	126823599	.	+	.	Parent=gene2506
chr7	ENCODE	exon	126824071	126824142	.	+	.	Parent=gene2506
chr7	ENCODE	exon	126824968	126825117	.	+	.	Parent=gene2506
###
chr7	ENCODE	gene	126823050	126823836	.	+	.	ID=gene2507;name2=ARF5;Name=AC000357.2-004
chr7	ENCODE	exon	126823050	126823168	.	+	.	Parent=gene2507
chr7	ENCODE	exon	126823490	126823836	.	+	.	Parent=gene2507
###
chr7	ENCODE	gene	126823613	126825042	.	+	.	ID=gene2508;Name=AC000357.2-005;name2=ARF5
chr7	ENCODE	exon	126823613	126823781	.	+	.	Parent=gene2508
chr7	ENCODE	exon	126824041	126824142	.	+	.	Parent=gene2508
chr7	ENCODE	exon	126824968	126825042	.	+	.	Parent=gene2508
###
chr7	ENCODE	gene	126825414	126829473	.	+	.	ID=gene2509;name2=FSCN3;Name=AC073934.3-005
chr7	ENCODE	exon	126825414	126825956	.	+	.	Parent=gene2509
chr7	ENCODE	exon	126829312	126829473	.	+	.	Parent=gene2509
###
chr7	ENCODE	gene	126825497	126827616	.	-	.	ID=gene2510;Name=AC000357.1-003;name2=GCC1
chr7	ENCODE	exon	126825497	126825723	.	-	.	Parent=gene2510
chr7	ENCODE	exon	126825818	126826009	.	-	.	Parent=gene2510
chr7	ENCODE	exon	126826134	126826242	.	-	.	Parent=gene2510
chr7	ENCODE	exon	126827503	126827616	.	-	.	Parent=gene2510
###
chr7	ENCODE	gene	126827640	126835803	.	+	.	ID=gene2511;Name=AC073934.3-001;name2=FSCN3
chr7	ENCODE	exon	126827640	126828002	.	+	.	Parent=gene2511
chr7	ENCODE	CDS	126827859	126828002	.	+	0	Parent=gene2511
chr7	ENCODE	exon	126829312	126830008	.	+	.	Parent=gene2511
chr7	ENCODE	CDS	126829312	126830008	.	+	0	Parent=gene2511
chr7	ENCODE	exon	126830333	126830451	.	+	.	Parent=gene2511
chr7	ENCODE	CDS	126830333	126830451	.	+	2	Parent=gene2511
chr7	ENCODE	exon	126832440	126832599	.	+	.	Parent=gene2511
chr7	ENCODE	CDS	126832440	126832599	.	+	0	Parent=gene2511
chr7	ENCODE	exon	126833386	126833556	.	+	.	Parent=gene2511
chr7	ENCODE	CDS	126833386	126833556	.	+	2	Parent=gene2511
chr7	ENCODE	exon	126834199	126834404	.	+	.	Parent=gene2511
chr7	ENCODE	CDS	126834199	126834404	.	+	2	Parent=gene2511
chr7	ENCODE	exon	126835628	126835803	.	+	.	Parent=gene2511
###
chr7	ENCODE	gene	126827733	126830335	.	+	.	ID=gene2512;Name=AC073934.3-002;name2=FSCN3
chr7	ENCODE	exon	126827733	126827757	.	+	.	Parent=gene2512
chr7	ENCODE	exon	126829312	126830008	.	+	.	Parent=gene2512
chr7	ENCODE	exon	126830333	126830335	.	+	.	Parent=gene2512
###
chr7	ENCODE	gene	126827747	126829490	.	+	.	ID=gene2513;Name=AC073934.3-003;name2=FSCN3
chr7	ENCODE	exon	126827747	126828002	.	+	.	Parent=gene2513
chr7	ENCODE	exon	126828499	126828579	.	+	.	Parent=gene2513
chr7	ENCODE	exon	126828785	126828964	.	+	.	Parent=gene2513
chr7	ENCODE	exon	126829312	126829490	.	+	.	Parent=gene2513
###
chr7	ENCODE	gene	126829446	126830623	.	+	.	ID=gene2514;Name=AC073934.3-004;name2=FSCN3
chr7	ENCODE	exon	126829446	126830008	.	+	.	Parent=gene2514
chr7	ENCODE	exon	126830333	126830623	.	+	.	Parent=gene2514
###
chr8	ENCODE	gene	118886142	119192762	.	-	.	ID=gene2515;Name=AC113188.1-004;name2=EXT1
chr8	ENCODE	exon	118886142	118886313	.	-	.	Parent=gene2515
chr8	ENCODE	exon	118888637	118888797	.	-	.	Parent=gene2515
chr8	ENCODE	exon	118894292	118894381	.	-	.	Parent=gene2515
chr8	ENCODE	exon	118899855	118899950	.	-	.	Parent=gene2515
chr8	ENCODE	exon	118901096	118901214	.	-	.	Parent=gene2515
chr8	ENCODE	exon	118903885	118904017	.	-	.	Parent=gene2515
chr8	ENCODE	exon	118911650	118911769	.	-	.	Parent=gene2515
chr8	ENCODE	exon	118916864	118916971	.	-	.	Parent=gene2515
chr8	ENCODE	exon	119192394	119192762	.	-	.	Parent=gene2515
###
chr8	ENCODE	gene	118886142	119192806	.	-	.	ID=gene2516;Name=AC113188.1-002;name2=EXT1
chr8	ENCODE	exon	118886142	118886313	.	-	.	Parent=gene2516
chr8	ENCODE	exon	118888637	118888797	.	-	.	Parent=gene2516
chr8	ENCODE	exon	118894292	118894381	.	-	.	Parent=gene2516
chr8	ENCODE	exon	118899855	118899880	.	-	.	Parent=gene2516
chr8	ENCODE	exon	119191651	119192806	.	-	.	Parent=gene2516
###
chr8	ENCODE	gene	118886142	119193119	.	-	.	ID=gene2517;Name=AC113188.1-001;name2=EXT1
chr8	ENCODE	exon	118886142	118886313	.	-	.	Parent=gene2517
chr8	ENCODE	exon	118888637	118888797	.	-	.	Parent=gene2517
chr8	ENCODE	exon	118894292	118894381	.	-	.	Parent=gene2517
chr8	ENCODE	exon	118899855	118899950	.	-	.	Parent=gene2517
chr8	ENCODE	exon	118901096	118901214	.	-	.	Parent=gene2517
chr8	ENCODE	exon	118903885	118904017	.	-	.	Parent=gene2517
chr8	ENCODE	exon	118911650	118911769	.	-	.	Parent=gene2517
chr8	ENCODE	exon	118916864	118916971	.	-	.	Parent=gene2517
chr8	ENCODE	exon	118918528	118918621	.	-	.	Parent=gene2517
chr8	ENCODE	exon	119191505	119193119	.	-	.	Parent=gene2517
###
chr8	ENCODE	gene	118911657	119191834	.	-	.	ID=gene2518;Name=AC113188.1-003;name2=EXT1
chr8	ENCODE	exon	118911657	118911769	.	-	.	Parent=gene2518
chr8	ENCODE	exon	118913019	118913073	.	-	.	Parent=gene2518
chr8	ENCODE	exon	118916864	118916971	.	-	.	Parent=gene2518
chr8	ENCODE	exon	118918528	118918621	.	-	.	Parent=gene2518
chr8	ENCODE	exon	119191505	119191834	.	-	.	Parent=gene2518
###
chr8	ENCODE	gene	119276307	119279152	.	-	.	ID=gene2519;Name=AC023590.2-005;name2=SAMD12
chr8	ENCODE	exon	119276307	119279152	.	-	.	Parent=gene2519
###
chr8	ENCODE	gene	119276307	119279152	.	-	.	ID=gene2520;Name=AC023590.2-003;name2=SAMD12
chr8	ENCODE	exon	119276307	119279152	.	-	.	Parent=gene2520
###
chr8	ENCODE	gene	119278740	119279152	.	-	.	ID=gene2521;Name=AC023590.2-004;name2=SAMD12
chr8	ENCODE	exon	119278740	119279152	.	-	.	Parent=gene2521
###
chr9	ENCODE	gene	128768701	128778478	.	+	.	ID=gene2522;Name=RP11-101E3.2-006;name2=PHYHD1
chr9	ENCODE	exon	128768701	128769029	.	+	.	Parent=gene2522
chr9	ENCODE	exon	128775615	128775690	.	+	.	Parent=gene2522
chr9	ENCODE	exon	128775844	128775891	.	+	.	Parent=gene2522
chr9	ENCODE	exon	128778281	128778336	.	+	.	Parent=gene2522
chr9	ENCODE	exon	128778416	128778478	.	+	.	Parent=gene2522
###
chr9	ENCODE	gene	128768871	128769029	.	+	.	ID=gene2523;Name=RP11-101E3.2-011;name2=PHYHD1
chr9	ENCODE	exon	128768871	128769029	.	+	.	Parent=gene2523
###
chr9	ENCODE	gene	128768871	128775621	.	+	.	ID=gene2524;Name=RP11-101E3.2-012;name2=PHYHD1
chr9	ENCODE	exon	128768871	128769029	.	+	.	Parent=gene2524
chr9	ENCODE	exon	128775615	128775621	.	+	.	Parent=gene2524
###
chr9	ENCODE	gene	128768871	128782275	.	+	.	ID=gene2525;Name=RP11-101E3.2-005;name2=PHYHD1
chr9	ENCODE	exon	128768871	128769029	.	+	.	Parent=gene2525
chr9	ENCODE	exon	128775615	128775690	.	+	.	Parent=gene2525
chr9	ENCODE	exon	128775844	128775891	.	+	.	Parent=gene2525
chr9	ENCODE	exon	128778281	128778336	.	+	.	Parent=gene2525
chr9	ENCODE	exon	128778416	128778478	.	+	.	Parent=gene2525
chr9	ENCODE	exon	128779590	128779611	.	+	.	Parent=gene2525
chr9	ENCODE	exon	128782202	128782275	.	+	.	Parent=gene2525
###
chr9	ENCODE	gene	128768871	128783404	.	+	.	ID=gene2526;name2=PHYHD1;Name=RP11-101E3.2-002
chr9	ENCODE	exon	128768871	128769029	.	+	.	Parent=gene2526
chr9	ENCODE	exon	128775615	128775690	.	+	.	Parent=gene2526
chr9	ENCODE	exon	128775844	128775891	.	+	.	Parent=gene2526
chr9	ENCODE	exon	128778281	128778336	.	+	.	Parent=gene2526
chr9	ENCODE	exon	128779590	128779611	.	+	.	Parent=gene2526
chr9	ENCODE	exon	128782202	128782330	.	+	.	Parent=gene2526
chr9	ENCODE	exon	128782432	128782548	.	+	.	Parent=gene2526
chr9	ENCODE	exon	128783278	128783404	.	+	.	Parent=gene2526
###
chr9	ENCODE	gene	128768871	128783870	.	+	.	ID=gene2527;name2=PHYHD1;Name=RP11-101E3.2-001
chr9	ENCODE	exon	128768871	128769029	.	+	.	Parent=gene2527
chr9	ENCODE	exon	128775615	128775690	.	+	.	Parent=gene2527
chr9	ENCODE	exon	128775844	128775891	.	+	.	Parent=gene2527
chr9	ENCODE	exon	128778281	128778336	.	+	.	Parent=gene2527
chr9	ENCODE	exon	128778416	128778478	.	+	.	Parent=gene2527
chr9	ENCODE	exon	128779590	128779611	.	+	.	Parent=gene2527
chr9	ENCODE	exon	128782202	128782330	.	+	.	Parent=gene2527
chr9	ENCODE	exon	128782432	128782548	.	+	.	Parent=gene2527
chr9	ENCODE	exon	128783278	128783404	.	+	.	Parent=gene2527
chr9	ENCODE	exon	128783501	128783870	.	+	.	Parent=gene2527
###
chr9	ENCODE	gene	128768871	128783870	.	+	.	ID=gene2528;Name=RP11-101E3.2-009;name2=PHYHD1
chr9	ENCODE	exon	128768871	128769029	.	+	.	Parent=gene2528
chr9	ENCODE	exon	128775615	128775690	.	+	.	Parent=gene2528
chr9	ENCODE	exon	128775844	128775891	.	+	.	Parent=gene2528
chr9	ENCODE	exon	128778281	128778336	.	+	.	Parent=gene2528
chr9	ENCODE	exon	128778416	128778478	.	+	.	Parent=gene2528
chr9	ENCODE	exon	128779590	128779777	.	+	.	Parent=gene2528
chr9	ENCODE	exon	128782202	128782330	.	+	.	Parent=gene2528
chr9	ENCODE	exon	128782432	128782548	.	+	.	Parent=gene2528
chr9	ENCODE	exon	128783278	128783404	.	+	.	Parent=gene2528
chr9	ENCODE	exon	128783501	128783870	.	+	.	Parent=gene2528
###
chr9	ENCODE	gene	128768871	128783871	.	+	.	ID=gene2529;Name=RP11-101E3.2-008;name2=PHYHD1
chr9	ENCODE	exon	128768871	128769029	.	+	.	Parent=gene2529
chr9	ENCODE	exon	128775615	128775690	.	+	.	Parent=gene2529
chr9	ENCODE	exon	128775844	128775891	.	+	.	Parent=gene2529
chr9	ENCODE	exon	128778281	128778336	.	+	.	Parent=gene2529
chr9	ENCODE	exon	128778416	128778478	.	+	.	Parent=gene2529
chr9	ENCODE	exon	128782202	128782330	.	+	.	Parent=gene2529
chr9	ENCODE	exon	128782432	128782548	.	+	.	Parent=gene2529
chr9	ENCODE	exon	128783278	128783404	.	+	.	Parent=gene2529
chr9	ENCODE	exon	128783501	128783871	.	+	.	Parent=gene2529
###
chr9	ENCODE	gene	128768879	128782542	.	+	.	ID=gene2530;Name=RP11-101E3.2-010;name2=PHYHD1
chr9	ENCODE	exon	128768879	128769029	.	+	.	Parent=gene2530
chr9	ENCODE	CDS	128768968	128769029	.	+	0	Parent=gene2530
chr9	ENCODE	exon	128775560	128775690	.	+	.	Parent=gene2530
chr9	ENCODE	CDS	128775560	128775690	.	+	1	Parent=gene2530
chr9	ENCODE	exon	128775844	128775891	.	+	.	Parent=gene2530
chr9	ENCODE	CDS	128775844	128775891	.	+	2	Parent=gene2530
chr9	ENCODE	exon	128778281	128778336	.	+	.	Parent=gene2530
chr9	ENCODE	CDS	128778281	128778336	.	+	2	Parent=gene2530
chr9	ENCODE	exon	128778416	128778478	.	+	.	Parent=gene2530
chr9	ENCODE	CDS	128778416	128778478	.	+	0	Parent=gene2530
chr9	ENCODE	exon	128779590	128779611	.	+	.	Parent=gene2530
chr9	ENCODE	CDS	128779590	128779611	.	+	0	Parent=gene2530
chr9	ENCODE	exon	128782202	128782330	.	+	.	Parent=gene2530
chr9	ENCODE	CDS	128782202	128782330	.	+	2	Parent=gene2530
chr9	ENCODE	exon	128782432	128782542	.	+	.	Parent=gene2530
chr9	ENCODE	CDS	128782432	128782542	.	+	2	Parent=gene2530
###
chr9	ENCODE	gene	128775858	128783871	.	+	.	ID=gene2531;Name=RP11-101E3.2-004;name2=PHYHD1
chr9	ENCODE	exon	128775858	128775891	.	+	.	Parent=gene2531
chr9	ENCODE	CDS	128775858	128775891	.	+	0	Parent=gene2531
chr9	ENCODE	exon	128778281	128778336	.	+	.	Parent=gene2531
chr9	ENCODE	CDS	128778281	128778336	.	+	2	Parent=gene2531
chr9	ENCODE	exon	128778416	128778478	.	+	.	Parent=gene2531
chr9	ENCODE	CDS	128778416	128778478	.	+	0	Parent=gene2531
chr9	ENCODE	exon	128782202	128782330	.	+	.	Parent=gene2531
chr9	ENCODE	CDS	128782202	128782330	.	+	0	Parent=gene2531
chr9	ENCODE	exon	128783278	128783404	.	+	.	Parent=gene2531
chr9	ENCODE	CDS	128783278	128783404	.	+	0	Parent=gene2531
chr9	ENCODE	CDS	128783501	128783586	.	+	2	Parent=gene2531
chr9	ENCODE	exon	128783501	128783871	.	+	.	Parent=gene2531
###
chr9	ENCODE	gene	128779582	128783871	.	+	.	ID=gene2532;Name=RP11-101E3.2-003;name2=PHYHD1
chr9	ENCODE	exon	128779582	128779611	.	+	.	Parent=gene2532
chr9	ENCODE	CDS	128779582	128779611	.	+	0	Parent=gene2532
chr9	ENCODE	exon	128782202	128782330	.	+	.	Parent=gene2532
chr9	ENCODE	CDS	128782202	128782330	.	+	0	Parent=gene2532
chr9	ENCODE	CDS	128783278	128783412	.	+	0	Parent=gene2532
chr9	ENCODE	exon	128783278	128783871	.	+	.	Parent=gene2532
###
chr9	ENCODE	gene	128782226	128783541	.	+	.	ID=gene2533;Name=RP11-101E3.2-007;name2=PHYHD1
chr9	ENCODE	exon	128782226	128782548	.	+	.	Parent=gene2533
chr9	ENCODE	exon	128783278	128783404	.	+	.	Parent=gene2533
chr9	ENCODE	exon	128783501	128783541	.	+	.	Parent=gene2533
###
chr9	ENCODE	gene	128783311	128798854	.	+	.	ID=gene2534;Name=RP11-167N5.2-009;name2=NUP188
chr9	ENCODE	exon	128783311	128783404	.	+	.	Parent=gene2534
chr9	ENCODE	CDS	128783311	128783404	.	+	0	Parent=gene2534
chr9	ENCODE	exon	128791022	128791076	.	+	.	Parent=gene2534
chr9	ENCODE	CDS	128791022	128791076	.	+	2	Parent=gene2534
chr9	ENCODE	exon	128794606	128794679	.	+	.	Parent=gene2534
chr9	ENCODE	CDS	128794606	128794679	.	+	1	Parent=gene2534
chr9	ENCODE	exon	128798183	128798267	.	+	.	Parent=gene2534
chr9	ENCODE	CDS	128798183	128798267	.	+	2	Parent=gene2534
chr9	ENCODE	exon	128798785	128798854	.	+	.	Parent=gene2534
chr9	ENCODE	CDS	128798785	128798854	.	+	1	Parent=gene2534
###
chr9	ENCODE	gene	128787363	128789452	.	-	.	ID=gene2535;Name=RP11-101E3.1-001;name2=TMEM15
chr9	ENCODE	exon	128787363	128789452	.	-	.	Parent=gene2535
chr9	ENCODE	CDS	128787520	128789136	.	-	0	Parent=gene2535
###
chr9	ENCODE	gene	128789532	128848929	.	+	.	ID=gene2536;Name=RP11-167N5.2-001;name2=NUP188
chr9	ENCODE	exon	128789532	128789584	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128789553	128789584	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128791022	128791076	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128791022	128791076	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128794606	128794679	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128794606	128794679	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128798183	128798267	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128798183	128798267	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128798785	128798865	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128798785	128798865	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128799843	128799887	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128799843	128799887	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128800635	128800727	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128800635	128800727	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128800848	128800967	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128800848	128800967	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128810339	128810550	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128810339	128810550	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128811233	128811347	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128811233	128811347	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128812591	128812791	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128812591	128812791	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128814993	128815082	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128814993	128815082	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128821095	128821160	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128821095	128821160	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128822439	128822558	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128822439	128822558	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128823097	128823223	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128823097	128823223	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128824382	128824534	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128824382	128824534	.	+	2	Parent=gene2536
chr9	ENCODE	exon	128824735	128824861	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128824735	128824861	.	+	2	Parent=gene2536
chr9	ENCODE	exon	128825126	128825213	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128825126	128825213	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128825307	128825383	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128825307	128825383	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128826733	128826847	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128826733	128826847	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128828391	128828511	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128828391	128828511	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128828642	128828708	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128828642	128828708	.	+	2	Parent=gene2536
chr9	ENCODE	exon	128829422	128829550	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128829422	128829550	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128829880	128830019	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128829880	128830019	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128831953	128832059	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128831953	128832059	.	+	2	Parent=gene2536
chr9	ENCODE	exon	128835030	128835236	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128835030	128835236	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128835358	128835527	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128835358	128835527	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128836206	128836275	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128836206	128836275	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128836689	128836756	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128836689	128836756	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128837152	128837347	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128837152	128837347	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128839984	128840061	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128839984	128840061	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128840371	128840456	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128840371	128840456	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128841005	128841150	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128841005	128841150	.	+	1	Parent=gene2536
chr9	ENCODE	exon	128841457	128841638	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128841457	128841638	.	+	2	Parent=gene2536
chr9	ENCODE	exon	128843362	128843562	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128843362	128843562	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128843717	128843809	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128843717	128843809	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128844650	128844808	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128844650	128844808	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128845150	128845287	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128845150	128845287	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128846980	128847054	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128846980	128847054	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128847136	128847363	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128847136	128847363	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128847478	128847609	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128847478	128847609	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128847883	128847956	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128847883	128847956	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128848072	128848201	.	+	.	Parent=gene2536
chr9	ENCODE	CDS	128848072	128848201	.	+	1	Parent=gene2536
chr9	ENCODE	CDS	128848335	128848511	.	+	0	Parent=gene2536
chr9	ENCODE	exon	128848335	128848929	.	+	.	Parent=gene2536
###
chr9	ENCODE	gene	128789850	128798844	.	+	.	ID=gene2537;Name=RP11-167N5.2-010;name2=NUP188
chr9	ENCODE	exon	128789850	128790461	.	+	.	Parent=gene2537
chr9	ENCODE	exon	128791022	128791076	.	+	.	Parent=gene2537
chr9	ENCODE	exon	128794606	128794679	.	+	.	Parent=gene2537
chr9	ENCODE	exon	128798183	128798267	.	+	.	Parent=gene2537
chr9	ENCODE	exon	128798785	128798844	.	+	.	Parent=gene2537
###
chr9	ENCODE	gene	128790792	128794728	.	+	.	ID=gene2538;Name=RP11-167N5.2-004;name2=NUP188
chr9	ENCODE	exon	128790792	128791076	.	+	.	Parent=gene2538
chr9	ENCODE	exon	128794606	128794728	.	+	.	Parent=gene2538
###
chr9	ENCODE	gene	128825347	128827095	.	+	.	ID=gene2539;Name=RP11-167N5.2-008;name2=NUP188
chr9	ENCODE	exon	128825347	128825383	.	+	.	Parent=gene2539
chr9	ENCODE	exon	128826733	128827095	.	+	.	Parent=gene2539
###
chr9	ENCODE	gene	128826804	128845826	.	+	.	ID=gene2540;Name=RP11-167N5.2-002;name2=NUP188
chr9	ENCODE	exon	128826804	128826847	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128828391	128828511	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128828642	128828708	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128829422	128829550	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128829880	128830019	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128831953	128832059	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128835030	128835236	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128835358	128835527	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128836206	128836275	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128836689	128836756	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128837152	128837347	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128839984	128840061	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128840371	128840456	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128841005	128841150	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128841457	128841638	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128843362	128843562	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128843717	128843809	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128844650	128844808	.	+	.	Parent=gene2540
chr9	ENCODE	exon	128845150	128845826	.	+	.	Parent=gene2540
###
chr9	ENCODE	gene	128828422	128835063	.	+	.	ID=gene2541;Name=RP11-167N5.2-005;name2=NUP188
chr9	ENCODE	exon	128828422	128828511	.	+	.	Parent=gene2541
chr9	ENCODE	exon	128828642	128828708	.	+	.	Parent=gene2541
chr9	ENCODE	exon	128829422	128829550	.	+	.	Parent=gene2541
chr9	ENCODE	exon	128829880	128830019	.	+	.	Parent=gene2541
chr9	ENCODE	exon	128831986	128832059	.	+	.	Parent=gene2541
chr9	ENCODE	exon	128835030	128835063	.	+	.	Parent=gene2541
###
chr9	ENCODE	gene	128834928	128836723	.	+	.	ID=gene2542;Name=RP11-167N5.2-011;name2=NUP188
chr9	ENCODE	exon	128834928	128835236	.	+	.	Parent=gene2542
chr9	ENCODE	exon	128835358	128835527	.	+	.	Parent=gene2542
chr9	ENCODE	exon	128836206	128836275	.	+	.	Parent=gene2542
chr9	ENCODE	exon	128836689	128836723	.	+	.	Parent=gene2542
###
chr9	ENCODE	gene	128836229	128837033	.	+	.	ID=gene2543;Name=RP11-167N5.2-006;name2=NUP188
chr9	ENCODE	exon	128836229	128836275	.	+	.	Parent=gene2543
chr9	ENCODE	exon	128836689	128837033	.	+	.	Parent=gene2543
###
chr9	ENCODE	gene	128836969	128840429	.	+	.	ID=gene2544;Name=RP11-167N5.2-003;name2=NUP188
chr9	ENCODE	exon	128836969	128837347	.	+	.	Parent=gene2544
chr9	ENCODE	exon	128839984	128840061	.	+	.	Parent=gene2544
chr9	ENCODE	exon	128840371	128840429	.	+	.	Parent=gene2544
###
chr9	ENCODE	gene	128841434	128843724	.	+	.	ID=gene2545;Name=RP11-167N5.2-012;name2=NUP188
chr9	ENCODE	exon	128841434	128841638	.	+	.	Parent=gene2545
chr9	ENCODE	exon	128843362	128843724	.	+	.	Parent=gene2545
###
chr9	ENCODE	gene	128848869	128870133	.	-	.	ID=gene2546;Name=RP11-167N5.3-001;name2=SH3GLB2
chr9	ENCODE	exon	128848869	128850624	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128850517	128850624	.	-	0	Parent=gene2546
chr9	ENCODE	exon	128850939	128851179	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128850939	128851179	.	-	1	Parent=gene2546
chr9	ENCODE	exon	128851604	128851704	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128851604	128851704	.	-	0	Parent=gene2546
chr9	ENCODE	exon	128851953	128852042	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128851953	128852042	.	-	0	Parent=gene2546
chr9	ENCODE	exon	128852503	128852526	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128852503	128852526	.	-	0	Parent=gene2546
chr9	ENCODE	exon	128854069	128854131	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128854069	128854131	.	-	0	Parent=gene2546
chr9	ENCODE	exon	128856244	128856336	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128856244	128856336	.	-	0	Parent=gene2546
chr9	ENCODE	exon	128856604	128856737	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128856604	128856737	.	-	2	Parent=gene2546
chr9	ENCODE	exon	128862924	128863052	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128862924	128863052	.	-	2	Parent=gene2546
chr9	ENCODE	exon	128864115	128864256	.	-	.	Parent=gene2546
chr9	ENCODE	CDS	128864115	128864256	.	-	0	Parent=gene2546
chr9	ENCODE	CDS	128869925	128869987	.	-	0	Parent=gene2546
chr9	ENCODE	exon	128869925	128870133	.	-	.	Parent=gene2546
###
chr9	ENCODE	gene	128849625	128853849	.	-	.	ID=gene2547;Name=RP11-167N5.3-003;name2=SH3GLB2
chr9	ENCODE	exon	128849625	128850624	.	-	.	Parent=gene2547
chr9	ENCODE	exon	128850939	128851179	.	-	.	Parent=gene2547
chr9	ENCODE	exon	128851286	128851300	.	-	.	Parent=gene2547
chr9	ENCODE	exon	128851604	128851704	.	-	.	Parent=gene2547
chr9	ENCODE	exon	128851953	128852042	.	-	.	Parent=gene2547
chr9	ENCODE	exon	128852503	128853849	.	-	.	Parent=gene2547
###
chr9	ENCODE	gene	128849867	128870047	.	-	.	ID=gene2548;Name=RP11-167N5.3-002;name2=SH3GLB2
chr9	ENCODE	exon	128849867	128849983	.	-	.	Parent=gene2548
chr9	ENCODE	exon	128850517	128850624	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128850517	128850624	.	-	0	Parent=gene2548
chr9	ENCODE	exon	128850939	128851179	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128850939	128851179	.	-	1	Parent=gene2548
chr9	ENCODE	exon	128851604	128851704	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128851604	128851704	.	-	0	Parent=gene2548
chr9	ENCODE	exon	128851953	128852042	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128851953	128852042	.	-	0	Parent=gene2548
chr9	ENCODE	exon	128852503	128852526	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128852503	128852526	.	-	0	Parent=gene2548
chr9	ENCODE	exon	128854069	128854131	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128854069	128854131	.	-	0	Parent=gene2548
chr9	ENCODE	exon	128856244	128856336	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128856244	128856336	.	-	0	Parent=gene2548
chr9	ENCODE	exon	128856604	128856737	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128856604	128856737	.	-	2	Parent=gene2548
chr9	ENCODE	exon	128862924	128863052	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128862924	128863052	.	-	2	Parent=gene2548
chr9	ENCODE	exon	128864115	128864256	.	-	.	Parent=gene2548
chr9	ENCODE	CDS	128864115	128864256	.	-	0	Parent=gene2548
chr9	ENCODE	CDS	128869925	128869987	.	-	0	Parent=gene2548
chr9	ENCODE	exon	128869925	128870047	.	-	.	Parent=gene2548
###
chr9	ENCODE	gene	128849872	128870112	.	-	.	ID=gene2549;Name=RP11-167N5.3-008;name2=SH3GLB2
chr9	ENCODE	exon	128849872	128850624	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128850517	128850624	.	-	0	Parent=gene2549
chr9	ENCODE	exon	128850939	128851179	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128850939	128851179	.	-	1	Parent=gene2549
chr9	ENCODE	exon	128851286	128851300	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128851286	128851300	.	-	1	Parent=gene2549
chr9	ENCODE	exon	128851604	128851704	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128851604	128851704	.	-	0	Parent=gene2549
chr9	ENCODE	exon	128851953	128852042	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128851953	128852042	.	-	0	Parent=gene2549
chr9	ENCODE	exon	128852503	128852526	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128852503	128852526	.	-	0	Parent=gene2549
chr9	ENCODE	exon	128854069	128854131	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128854069	128854131	.	-	0	Parent=gene2549
chr9	ENCODE	exon	128854841	128854852	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128854841	128854852	.	-	0	Parent=gene2549
chr9	ENCODE	exon	128856244	128856336	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128856244	128856336	.	-	0	Parent=gene2549
chr9	ENCODE	exon	128856604	128856737	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128856604	128856737	.	-	2	Parent=gene2549
chr9	ENCODE	exon	128862924	128863052	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128862924	128863052	.	-	2	Parent=gene2549
chr9	ENCODE	exon	128864115	128864256	.	-	.	Parent=gene2549
chr9	ENCODE	CDS	128864115	128864256	.	-	0	Parent=gene2549
chr9	ENCODE	CDS	128869925	128869987	.	-	0	Parent=gene2549
chr9	ENCODE	exon	128869925	128870112	.	-	.	Parent=gene2549
###
chr9	ENCODE	gene	128849970	128855783	.	-	.	ID=gene2550;Name=RP11-167N5.3-004;name2=SH3GLB2
chr9	ENCODE	exon	128849970	128850624	.	-	.	Parent=gene2550
chr9	ENCODE	exon	128850939	128851179	.	-	.	Parent=gene2550
chr9	ENCODE	exon	128851604	128851704	.	-	.	Parent=gene2550
chr9	ENCODE	exon	128851953	128855783	.	-	.	Parent=gene2550
###
chr9	ENCODE	gene	128851060	128870136	.	-	.	ID=gene2551;Name=RP11-167N5.3-005;name2=SH3GLB2
chr9	ENCODE	exon	128851060	128851179	.	-	.	Parent=gene2551
chr9	ENCODE	exon	128851604	128851704	.	-	.	Parent=gene2551
chr9	ENCODE	exon	128851953	128852042	.	-	.	Parent=gene2551
chr9	ENCODE	exon	128852503	128852526	.	-	.	Parent=gene2551
chr9	ENCODE	exon	128854069	128854131	.	-	.	Parent=gene2551
chr9	ENCODE	exon	128856244	128856336	.	-	.	Parent=gene2551
chr9	ENCODE	exon	128856604	128856737	.	-	.	Parent=gene2551
chr9	ENCODE	exon	128869925	128870136	.	-	.	Parent=gene2551
###
chr9	ENCODE	gene	128851569	128870128	.	-	.	ID=gene2552;Name=RP11-167N5.3-010;name2=SH3GLB2
chr9	ENCODE	exon	128851569	128851704	.	-	.	Parent=gene2552
chr9	ENCODE	exon	128851953	128852042	.	-	.	Parent=gene2552
chr9	ENCODE	exon	128852503	128852526	.	-	.	Parent=gene2552
chr9	ENCODE	exon	128854069	128854131	.	-	.	Parent=gene2552
chr9	ENCODE	exon	128856244	128856336	.	-	.	Parent=gene2552
chr9	ENCODE	exon	128856604	128856737	.	-	.	Parent=gene2552
chr9	ENCODE	exon	128862924	128863052	.	-	.	Parent=gene2552
chr9	ENCODE	exon	128864115	128864256	.	-	.	Parent=gene2552
chr9	ENCODE	exon	128869925	128870128	.	-	.	Parent=gene2552
###
chr9	ENCODE	gene	128853557	128856291	.	-	.	ID=gene2553;Name=RP11-167N5.3-009;name2=SH3GLB2
chr9	ENCODE	exon	128853557	128854131	.	-	.	Parent=gene2553
chr9	ENCODE	exon	128856244	128856291	.	-	.	Parent=gene2553
###
chr9	ENCODE	gene	128854063	128863044	.	-	.	ID=gene2554;Name=RP11-167N5.3-007;name2=SH3GLB2
chr9	ENCODE	exon	128854063	128854131	.	-	.	Parent=gene2554
chr9	ENCODE	exon	128856244	128856336	.	-	.	Parent=gene2554
chr9	ENCODE	exon	128856604	128856737	.	-	.	Parent=gene2554
chr9	ENCODE	exon	128857573	128857693	.	-	.	Parent=gene2554
chr9	ENCODE	exon	128862924	128863044	.	-	.	Parent=gene2554
###
chr9	ENCODE	gene	128856254	128870031	.	-	.	ID=gene2555;Name=RP11-167N5.3-006;name2=SH3GLB2
chr9	ENCODE	exon	128856254	128856336	.	-	.	Parent=gene2555
chr9	ENCODE	exon	128856604	128856737	.	-	.	Parent=gene2555
chr9	ENCODE	exon	128857573	128857697	.	-	.	Parent=gene2555
chr9	ENCODE	exon	128862924	128863052	.	-	.	Parent=gene2555
chr9	ENCODE	exon	128864115	128864256	.	-	.	Parent=gene2555
chr9	ENCODE	exon	128869925	128870031	.	-	.	Parent=gene2555
###
chr9	ENCODE	gene	128878454	128884233	.	+	.	ID=gene2556;Name=RP11-167N5.1-010;name2=FAM73B
chr9	ENCODE	exon	128878454	128878514	.	+	.	Parent=gene2556
chr9	ENCODE	exon	128882285	128882523	.	+	.	Parent=gene2556
chr9	ENCODE	exon	128883965	128884233	.	+	.	Parent=gene2556
###
chr9	ENCODE	gene	128878454	128889057	.	+	.	ID=gene2557;Name=RP11-167N5.1-007;name2=FAM73B
chr9	ENCODE	exon	128878454	128878514	.	+	.	Parent=gene2557
chr9	ENCODE	exon	128882285	128882523	.	+	.	Parent=gene2557
chr9	ENCODE	exon	128884137	128884347	.	+	.	Parent=gene2557
chr9	ENCODE	exon	128888938	128889057	.	+	.	Parent=gene2557
###
chr9	ENCODE	gene	128878477	128913904	.	+	.	ID=gene2558;Name=RP11-167N5.1-002;name2=FAM73B
chr9	ENCODE	exon	128878477	128878514	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128882285	128882523	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128884137	128884347	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128890260	128890372	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128891214	128891331	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128891660	128891796	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128893133	128893253	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128900987	128901104	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128902383	128902483	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128903064	128903179	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128905077	128905149	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128905378	128905464	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128909606	128909704	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128910031	128910808	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128910909	128910962	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128911682	128911798	.	+	.	Parent=gene2558
chr9	ENCODE	exon	128912080	128913904	.	+	.	Parent=gene2558
###
chr9	ENCODE	gene	128878479	128913904	.	+	.	ID=gene2559;Name=RP11-167N5.1-003;name2=FAM73B
chr9	ENCODE	exon	128878479	128878514	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128882285	128882523	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128884137	128884347	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128890260	128890372	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128891214	128891331	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128891660	128891796	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128900987	128901104	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128902383	128902483	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128903064	128903179	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128909606	128909704	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128909852	128910165	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128910909	128910962	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128911682	128911798	.	+	.	Parent=gene2559
chr9	ENCODE	exon	128912080	128913904	.	+	.	Parent=gene2559
###
chr9	ENCODE	gene	128878767	128913915	.	+	.	ID=gene2560;Name=RP11-167N5.1-001;name2=FAM73B
chr9	ENCODE	exon	128878767	128878849	.	+	.	Parent=gene2560
chr9	ENCODE	exon	128882285	128882523	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128882428	128882523	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128884137	128884347	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128884137	128884347	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128890260	128890372	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128890260	128890372	.	+	2	Parent=gene2560
chr9	ENCODE	exon	128891214	128891331	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128891214	128891331	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128891660	128891796	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128891660	128891796	.	+	2	Parent=gene2560
chr9	ENCODE	exon	128900987	128901104	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128900987	128901104	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128902383	128902483	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128902383	128902483	.	+	2	Parent=gene2560
chr9	ENCODE	exon	128903064	128903179	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128903064	128903179	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128905077	128905149	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128905077	128905149	.	+	1	Parent=gene2560
chr9	ENCODE	exon	128905378	128905464	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128905378	128905464	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128909606	128909704	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128909606	128909704	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128910031	128910165	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128910031	128910165	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128910909	128910962	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128910909	128910962	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128911682	128911798	.	+	.	Parent=gene2560
chr9	ENCODE	CDS	128911682	128911798	.	+	0	Parent=gene2560
chr9	ENCODE	CDS	128912080	128912286	.	+	0	Parent=gene2560
chr9	ENCODE	exon	128912080	128913915	.	+	.	Parent=gene2560
###
chr9	ENCODE	gene	128878828	128884339	.	+	.	ID=gene2561;Name=RP11-167N5.1-009;name2=FAM73B
chr9	ENCODE	exon	128878828	128878849	.	+	.	Parent=gene2561
chr9	ENCODE	exon	128881621	128881719	.	+	.	Parent=gene2561
chr9	ENCODE	exon	128882285	128882523	.	+	.	Parent=gene2561
chr9	ENCODE	CDS	128882428	128882523	.	+	0	Parent=gene2561
chr9	ENCODE	exon	128884137	128884339	.	+	.	Parent=gene2561
chr9	ENCODE	CDS	128884137	128884339	.	+	0	Parent=gene2561
###
chr9	ENCODE	gene	128902315	128910144	.	+	.	ID=gene2562;Name=RP11-167N5.1-011;name2=FAM73B
chr9	ENCODE	exon	128902315	128902483	.	+	.	Parent=gene2562
chr9	ENCODE	exon	128903064	128903179	.	+	.	Parent=gene2562
chr9	ENCODE	exon	128905378	128905464	.	+	.	Parent=gene2562
chr9	ENCODE	exon	128909606	128909704	.	+	.	Parent=gene2562
chr9	ENCODE	exon	128910031	128910144	.	+	.	Parent=gene2562
###
chr9	ENCODE	gene	128902385	128905463	.	+	.	ID=gene2563;Name=RP11-167N5.1-006;name2=FAM73B
chr9	ENCODE	exon	128902385	128902483	.	+	.	Parent=gene2563
chr9	ENCODE	exon	128903064	128903179	.	+	.	Parent=gene2563
chr9	ENCODE	exon	128905006	128905149	.	+	.	Parent=gene2563
chr9	ENCODE	exon	128905378	128905463	.	+	.	Parent=gene2563
###
chr9	ENCODE	gene	128903130	128909847	.	+	.	ID=gene2564;Name=RP11-167N5.1-005;name2=FAM73B
chr9	ENCODE	exon	128903130	128903179	.	+	.	Parent=gene2564
chr9	ENCODE	exon	128905077	128905149	.	+	.	Parent=gene2564
chr9	ENCODE	exon	128905378	128905464	.	+	.	Parent=gene2564
chr9	ENCODE	exon	128909606	128909847	.	+	.	Parent=gene2564
###
chr9	ENCODE	gene	128905120	128910928	.	+	.	ID=gene2565;Name=RP11-167N5.1-013;name2=FAM73B
chr9	ENCODE	exon	128905120	128905149	.	+	.	Parent=gene2565
chr9	ENCODE	exon	128905378	128905464	.	+	.	Parent=gene2565
chr9	ENCODE	exon	128909606	128909704	.	+	.	Parent=gene2565
chr9	ENCODE	exon	128909828	128910165	.	+	.	Parent=gene2565
chr9	ENCODE	exon	128910909	128910928	.	+	.	Parent=gene2565
###
chr9	ENCODE	gene	128909341	128910233	.	+	.	ID=gene2566;Name=RP11-167N5.1-012;name2=FAM73B
chr9	ENCODE	exon	128909341	128909704	.	+	.	Parent=gene2566
chr9	ENCODE	exon	128910031	128910233	.	+	.	Parent=gene2566
###
chr9	ENCODE	gene	128910767	128911767	.	+	.	ID=gene2567;Name=RP11-167N5.1-008;name2=FAM73B
chr9	ENCODE	exon	128910767	128910808	.	+	.	Parent=gene2567
chr9	ENCODE	exon	128910909	128911767	.	+	.	Parent=gene2567
###
chr9	ENCODE	gene	128911092	128913904	.	+	.	ID=gene2568;Name=RP11-167N5.1-004;name2=FAM73B
chr9	ENCODE	exon	128911092	128911798	.	+	.	Parent=gene2568
chr9	ENCODE	exon	128912080	128913904	.	+	.	Parent=gene2568
###
chr9	ENCODE	gene	128922933	128932268	.	+	.	ID=gene2569;Name=RP11-167N5.4-001;name2=DOLPP1
chr9	ENCODE	exon	128922933	128923040	.	+	.	Parent=gene2569
chr9	ENCODE	CDS	128922965	128923040	.	+	0	Parent=gene2569
chr9	ENCODE	exon	128926501	128926601	.	+	.	Parent=gene2569
chr9	ENCODE	CDS	128926501	128926601	.	+	2	Parent=gene2569
chr9	ENCODE	exon	128926856	128926940	.	+	.	Parent=gene2569
chr9	ENCODE	CDS	128926856	128926940	.	+	0	Parent=gene2569
chr9	ENCODE	exon	128927040	128927139	.	+	.	Parent=gene2569
chr9	ENCODE	CDS	128927040	128927139	.	+	2	Parent=gene2569
chr9	ENCODE	exon	128927351	128927449	.	+	.	Parent=gene2569
chr9	ENCODE	CDS	128927351	128927449	.	+	1	Parent=gene2569
chr9	ENCODE	exon	128927972	128928100	.	+	.	Parent=gene2569
chr9	ENCODE	CDS	128927972	128928100	.	+	1	Parent=gene2569
chr9	ENCODE	exon	128928542	128928631	.	+	.	Parent=gene2569
chr9	ENCODE	CDS	128928542	128928631	.	+	1	Parent=gene2569
chr9	ENCODE	CDS	128930804	128930840	.	+	1	Parent=gene2569
chr9	ENCODE	exon	128930804	128932268	.	+	.	Parent=gene2569
###
chr9	ENCODE	gene	128922967	128932271	.	+	.	ID=gene2570;Name=RP11-167N5.4-002;name2=DOLPP1
chr9	ENCODE	exon	128922967	128923040	.	+	.	Parent=gene2570
chr9	ENCODE	exon	128926501	128926601	.	+	.	Parent=gene2570
chr9	ENCODE	exon	128927040	128927139	.	+	.	Parent=gene2570
chr9	ENCODE	exon	128927351	128927449	.	+	.	Parent=gene2570
chr9	ENCODE	exon	128928542	128928631	.	+	.	Parent=gene2570
chr9	ENCODE	exon	128930804	128932271	.	+	.	Parent=gene2570
###
chr9	ENCODE	gene	128922969	128931188	.	+	.	ID=gene2571;Name=RP11-167N5.4-003;name2=DOLPP1
chr9	ENCODE	exon	128922969	128923040	.	+	.	Parent=gene2571
chr9	ENCODE	exon	128926501	128926601	.	+	.	Parent=gene2571
chr9	ENCODE	exon	128926856	128926940	.	+	.	Parent=gene2571
chr9	ENCODE	exon	128927040	128927139	.	+	.	Parent=gene2571
chr9	ENCODE	exon	128927351	128927449	.	+	.	Parent=gene2571
chr9	ENCODE	exon	128928542	128928631	.	+	.	Parent=gene2571
chr9	ENCODE	exon	128930804	128931188	.	+	.	Parent=gene2571
###
chr9	ENCODE	gene	128926432	128932268	.	+	.	ID=gene2572;Name=RP11-167N5.4-004;name2=DOLPP1
chr9	ENCODE	exon	128926432	128926601	.	+	.	Parent=gene2572
chr9	ENCODE	exon	128926856	128926940	.	+	.	Parent=gene2572
chr9	ENCODE	exon	128927040	128927139	.	+	.	Parent=gene2572
chr9	ENCODE	exon	128932074	128932268	.	+	.	Parent=gene2572
###
chr9	ENCODE	gene	128936643	128952637	.	-	.	ID=gene2573;Name=RP11-247A12.5-006;name2=CRAT
chr9	ENCODE	exon	128936643	128937445	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128937230	128937445	.	-	0	Parent=gene2573
chr9	ENCODE	exon	128937831	128937968	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128937831	128937968	.	-	0	Parent=gene2573
chr9	ENCODE	exon	128939083	128939145	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128939083	128939145	.	-	0	Parent=gene2573
chr9	ENCODE	exon	128939846	128939981	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128939846	128939981	.	-	1	Parent=gene2573
chr9	ENCODE	exon	128940082	128940204	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128940082	128940204	.	-	1	Parent=gene2573
chr9	ENCODE	exon	128940364	128940483	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128940364	128940483	.	-	1	Parent=gene2573
chr9	ENCODE	exon	128941699	128941799	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128941699	128941799	.	-	0	Parent=gene2573
chr9	ENCODE	exon	128942344	128942522	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128942344	128942522	.	-	2	Parent=gene2573
chr9	ENCODE	exon	128943716	128943890	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128943716	128943890	.	-	0	Parent=gene2573
chr9	ENCODE	exon	128944233	128944398	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128944233	128944398	.	-	1	Parent=gene2573
chr9	ENCODE	exon	128944846	128944899	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128944846	128944899	.	-	1	Parent=gene2573
chr9	ENCODE	exon	128946021	128946139	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128946021	128946139	.	-	0	Parent=gene2573
chr9	ENCODE	exon	128949647	128949910	.	-	.	Parent=gene2573
chr9	ENCODE	CDS	128949647	128949910	.	-	0	Parent=gene2573
chr9	ENCODE	CDS	128952316	128952342	.	-	0	Parent=gene2573
chr9	ENCODE	exon	128952316	128952637	.	-	.	Parent=gene2573
###
chr9	ENCODE	gene	128937039	128940204	.	-	.	ID=gene2574;Name=RP11-247A12.5-010;name2=CRAT
chr9	ENCODE	exon	128937039	128937445	.	-	.	Parent=gene2574
chr9	ENCODE	CDS	128937230	128937445	.	-	2	Parent=gene2574
chr9	ENCODE	exon	128937903	128937968	.	-	.	Parent=gene2574
chr9	ENCODE	CDS	128937903	128937968	.	-	2	Parent=gene2574
chr9	ENCODE	exon	128939083	128939145	.	-	.	Parent=gene2574
chr9	ENCODE	CDS	128939083	128939145	.	-	2	Parent=gene2574
chr9	ENCODE	exon	128939846	128939981	.	-	.	Parent=gene2574
chr9	ENCODE	CDS	128939846	128939981	.	-	0	Parent=gene2574
chr9	ENCODE	exon	128940082	128940204	.	-	.	Parent=gene2574
chr9	ENCODE	CDS	128940082	128940204	.	-	0	Parent=gene2574
###
chr9	ENCODE	gene	128943740	128953022	.	-	.	ID=gene2575;Name=RP11-247A12.5-003;name2=CRAT
chr9	ENCODE	exon	128943740	128943890	.	-	.	Parent=gene2575
chr9	ENCODE	exon	128944233	128944398	.	-	.	Parent=gene2575
chr9	ENCODE	exon	128944846	128944899	.	-	.	Parent=gene2575
chr9	ENCODE	exon	128949647	128949910	.	-	.	Parent=gene2575
chr9	ENCODE	exon	128952791	128953022	.	-	.	Parent=gene2575
###
chr9	ENCODE	gene	128944247	128952615	.	-	.	ID=gene2576;Name=RP11-247A12.5-002;name2=CRAT
chr9	ENCODE	exon	128944247	128944398	.	-	.	Parent=gene2576
chr9	ENCODE	exon	128944846	128944899	.	-	.	Parent=gene2576
chr9	ENCODE	exon	128946021	128946139	.	-	.	Parent=gene2576
chr9	ENCODE	exon	128949647	128949910	.	-	.	Parent=gene2576
chr9	ENCODE	exon	128951012	128951110	.	-	.	Parent=gene2576
chr9	ENCODE	exon	128952316	128952615	.	-	.	Parent=gene2576
###
chr9	ENCODE	gene	128944275	128950725	.	-	.	ID=gene2577;Name=RP11-247A12.5-007;name2=CRAT
chr9	ENCODE	exon	128944275	128944398	.	-	.	Parent=gene2577
chr9	ENCODE	CDS	128944275	128944398	.	-	1	Parent=gene2577
chr9	ENCODE	exon	128944846	128944899	.	-	.	Parent=gene2577
chr9	ENCODE	CDS	128944846	128944899	.	-	1	Parent=gene2577
chr9	ENCODE	exon	128946021	128946139	.	-	.	Parent=gene2577
chr9	ENCODE	CDS	128946021	128946139	.	-	0	Parent=gene2577
chr9	ENCODE	exon	128949647	128949910	.	-	.	Parent=gene2577
chr9	ENCODE	CDS	128949647	128949910	.	-	0	Parent=gene2577
chr9	ENCODE	CDS	128950596	128950625	.	-	0	Parent=gene2577
chr9	ENCODE	exon	128950596	128950725	.	-	.	Parent=gene2577
###
chr9	ENCODE	gene	128946030	128952602	.	-	.	ID=gene2578;Name=RP11-247A12.5-005;name2=CRAT
chr9	ENCODE	exon	128946030	128946139	.	-	.	Parent=gene2578
chr9	ENCODE	exon	128949647	128949910	.	-	.	Parent=gene2578
chr9	ENCODE	exon	128950241	128950311	.	-	.	Parent=gene2578
chr9	ENCODE	exon	128951012	128951110	.	-	.	Parent=gene2578
chr9	ENCODE	exon	128952316	128952602	.	-	.	Parent=gene2578
###
chr9	ENCODE	gene	128949167	128952544	.	-	.	ID=gene2579;Name=RP11-247A12.5-004;name2=CRAT
chr9	ENCODE	exon	128949167	128949910	.	-	.	Parent=gene2579
chr9	ENCODE	CDS	128949452	128949910	.	-	0	Parent=gene2579
chr9	ENCODE	CDS	128952316	128952342	.	-	0	Parent=gene2579
chr9	ENCODE	exon	128952316	128952544	.	-	.	Parent=gene2579
###
chr9	ENCODE	gene	128949709	128951109	.	-	.	ID=gene2580;Name=RP11-247A12.5-009;name2=CRAT
chr9	ENCODE	exon	128949709	128949910	.	-	.	Parent=gene2580
chr9	ENCODE	CDS	128949709	128949910	.	-	0	Parent=gene2580
chr9	ENCODE	CDS	128950596	128950625	.	-	0	Parent=gene2580
chr9	ENCODE	exon	128950596	128950736	.	-	.	Parent=gene2580
chr9	ENCODE	exon	128951012	128951109	.	-	.	Parent=gene2580
###
chr9	ENCODE	gene	128949782	128950849	.	-	.	ID=gene2581;Name=RP11-247A12.5-008;name2=CRAT
chr9	ENCODE	exon	128949782	128949910	.	-	.	Parent=gene2581
chr9	ENCODE	exon	128950732	128950849	.	-	.	Parent=gene2581
###
chr9	ENCODE	gene	128952783	128990777	.	+	.	ID=gene2582;Name=RP11-247A12.4-010;name2=PPP2R4
chr9	ENCODE	exon	128952783	128952865	.	+	.	Parent=gene2582
chr9	ENCODE	exon	128953305	128953464	.	+	.	Parent=gene2582
chr9	ENCODE	CDS	128953434	128953464	.	+	0	Parent=gene2582
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2582
chr9	ENCODE	CDS	128962346	128962443	.	+	2	Parent=gene2582
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2582
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2582
chr9	ENCODE	exon	128970818	128970943	.	+	.	Parent=gene2582
chr9	ENCODE	CDS	128970818	128970943	.	+	0	Parent=gene2582
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2582
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2582
chr9	ENCODE	exon	128976628	128976727	.	+	.	Parent=gene2582
chr9	ENCODE	CDS	128976628	128976727	.	+	2	Parent=gene2582
chr9	ENCODE	exon	128978304	128978428	.	+	.	Parent=gene2582
chr9	ENCODE	CDS	128978304	128978428	.	+	1	Parent=gene2582
chr9	ENCODE	exon	128979425	128979525	.	+	.	Parent=gene2582
chr9	ENCODE	CDS	128979425	128979525	.	+	2	Parent=gene2582
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2582
chr9	ENCODE	CDS	128984278	128984385	.	+	0	Parent=gene2582
chr9	ENCODE	CDS	128989220	128989297	.	+	0	Parent=gene2582
chr9	ENCODE	exon	128989220	128990777	.	+	.	Parent=gene2582
###
chr9	ENCODE	gene	128952797	128978389	.	+	.	ID=gene2583;Name=RP11-247A12.4-012;name2=PPP2R4
chr9	ENCODE	exon	128952797	128952865	.	+	.	Parent=gene2583
chr9	ENCODE	exon	128953305	128953464	.	+	.	Parent=gene2583
chr9	ENCODE	CDS	128953434	128953464	.	+	0	Parent=gene2583
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2583
chr9	ENCODE	CDS	128962346	128962443	.	+	2	Parent=gene2583
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2583
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2583
chr9	ENCODE	exon	128969797	128969901	.	+	.	Parent=gene2583
chr9	ENCODE	CDS	128969797	128969901	.	+	0	Parent=gene2583
chr9	ENCODE	exon	128970818	128970943	.	+	.	Parent=gene2583
chr9	ENCODE	CDS	128970818	128970943	.	+	0	Parent=gene2583
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2583
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2583
chr9	ENCODE	exon	128976628	128976727	.	+	.	Parent=gene2583
chr9	ENCODE	CDS	128976628	128976727	.	+	2	Parent=gene2583
chr9	ENCODE	exon	128978304	128978389	.	+	.	Parent=gene2583
chr9	ENCODE	CDS	128978304	128978389	.	+	1	Parent=gene2583
###
chr9	ENCODE	gene	128953151	128990779	.	+	.	ID=gene2584;Name=RP11-247A12.4-011;name2=PPP2R4
chr9	ENCODE	exon	128953151	128953464	.	+	.	Parent=gene2584
chr9	ENCODE	CDS	128953434	128953464	.	+	0	Parent=gene2584
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2584
chr9	ENCODE	CDS	128962346	128962443	.	+	2	Parent=gene2584
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2584
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2584
chr9	ENCODE	exon	128970818	128970943	.	+	.	Parent=gene2584
chr9	ENCODE	CDS	128970818	128970943	.	+	0	Parent=gene2584
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2584
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2584
chr9	ENCODE	exon	128976628	128976727	.	+	.	Parent=gene2584
chr9	ENCODE	CDS	128976628	128976727	.	+	2	Parent=gene2584
chr9	ENCODE	exon	128978304	128978428	.	+	.	Parent=gene2584
chr9	ENCODE	CDS	128978304	128978428	.	+	1	Parent=gene2584
chr9	ENCODE	exon	128979425	128979525	.	+	.	Parent=gene2584
chr9	ENCODE	CDS	128979425	128979525	.	+	2	Parent=gene2584
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2584
chr9	ENCODE	CDS	128984278	128984385	.	+	0	Parent=gene2584
chr9	ENCODE	CDS	128989220	128989297	.	+	0	Parent=gene2584
chr9	ENCODE	exon	128989220	128990779	.	+	.	Parent=gene2584
###
chr9	ENCODE	gene	128953169	128990779	.	+	.	ID=gene2585;Name=RP11-247A12.4-020;name2=PPP2R4
chr9	ENCODE	exon	128953169	128953464	.	+	.	Parent=gene2585
chr9	ENCODE	CDS	128953434	128953464	.	+	0	Parent=gene2585
chr9	ENCODE	exon	128962346	128962461	.	+	.	Parent=gene2585
chr9	ENCODE	CDS	128962346	128962461	.	+	2	Parent=gene2585
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2585
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2585
chr9	ENCODE	exon	128970818	128970943	.	+	.	Parent=gene2585
chr9	ENCODE	CDS	128970818	128970943	.	+	0	Parent=gene2585
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2585
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2585
chr9	ENCODE	exon	128976628	128976727	.	+	.	Parent=gene2585
chr9	ENCODE	CDS	128976628	128976727	.	+	2	Parent=gene2585
chr9	ENCODE	exon	128978304	128978428	.	+	.	Parent=gene2585
chr9	ENCODE	CDS	128978304	128978428	.	+	1	Parent=gene2585
chr9	ENCODE	exon	128979425	128979525	.	+	.	Parent=gene2585
chr9	ENCODE	CDS	128979425	128979525	.	+	2	Parent=gene2585
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2585
chr9	ENCODE	CDS	128984278	128984385	.	+	0	Parent=gene2585
chr9	ENCODE	CDS	128989220	128989297	.	+	0	Parent=gene2585
chr9	ENCODE	exon	128989220	128990779	.	+	.	Parent=gene2585
###
chr9	ENCODE	gene	128953242	128990779	.	+	.	ID=gene2586;name2=PPP2R4;Name=RP11-247A12.4-015
chr9	ENCODE	exon	128953242	128953464	.	+	.	Parent=gene2586
chr9	ENCODE	CDS	128953434	128953464	.	+	0	Parent=gene2586
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2586
chr9	ENCODE	CDS	128962346	128962443	.	+	2	Parent=gene2586
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2586
chr9	ENCODE	CDS	128984278	128984385	.	+	0	Parent=gene2586
chr9	ENCODE	CDS	128989220	128989297	.	+	0	Parent=gene2586
chr9	ENCODE	exon	128989220	128990779	.	+	.	Parent=gene2586
###
chr9	ENCODE	gene	128953246	128978399	.	+	.	ID=gene2587;Name=RP11-247A12.4-013;name2=PPP2R4
chr9	ENCODE	exon	128953246	128953464	.	+	.	Parent=gene2587
chr9	ENCODE	CDS	128953434	128953464	.	+	0	Parent=gene2587
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2587
chr9	ENCODE	CDS	128962346	128962443	.	+	2	Parent=gene2587
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2587
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2587
chr9	ENCODE	exon	128969797	128969901	.	+	.	Parent=gene2587
chr9	ENCODE	CDS	128969797	128969901	.	+	0	Parent=gene2587
chr9	ENCODE	exon	128970818	128970943	.	+	.	Parent=gene2587
chr9	ENCODE	CDS	128970818	128970943	.	+	0	Parent=gene2587
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2587
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2587
chr9	ENCODE	exon	128976628	128976727	.	+	.	Parent=gene2587
chr9	ENCODE	CDS	128976628	128976727	.	+	2	Parent=gene2587
chr9	ENCODE	exon	128978304	128978399	.	+	.	Parent=gene2587
chr9	ENCODE	CDS	128978304	128978399	.	+	1	Parent=gene2587
###
chr9	ENCODE	gene	128953247	128990779	.	+	.	ID=gene2588;Name=RP11-247A12.4-016;name2=PPP2R4
chr9	ENCODE	exon	128953247	128953464	.	+	.	Parent=gene2588
chr9	ENCODE	CDS	128953434	128953464	.	+	0	Parent=gene2588
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2588
chr9	ENCODE	CDS	128962346	128962443	.	+	2	Parent=gene2588
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2588
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2588
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2588
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2588
chr9	ENCODE	exon	128976628	128976727	.	+	.	Parent=gene2588
chr9	ENCODE	CDS	128976628	128976727	.	+	2	Parent=gene2588
chr9	ENCODE	exon	128978304	128978428	.	+	.	Parent=gene2588
chr9	ENCODE	CDS	128978304	128978428	.	+	1	Parent=gene2588
chr9	ENCODE	exon	128979425	128979525	.	+	.	Parent=gene2588
chr9	ENCODE	CDS	128979425	128979525	.	+	2	Parent=gene2588
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2588
chr9	ENCODE	CDS	128984278	128984385	.	+	0	Parent=gene2588
chr9	ENCODE	CDS	128989220	128989297	.	+	0	Parent=gene2588
chr9	ENCODE	exon	128989220	128990779	.	+	.	Parent=gene2588
###
chr9	ENCODE	gene	128953268	128976675	.	+	.	ID=gene2589;Name=RP11-247A12.4-009;name2=PPP2R4
chr9	ENCODE	exon	128953268	128953464	.	+	.	Parent=gene2589
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2589
chr9	ENCODE	exon	128969797	128969901	.	+	.	Parent=gene2589
chr9	ENCODE	exon	128970818	128970943	.	+	.	Parent=gene2589
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2589
chr9	ENCODE	exon	128976628	128976675	.	+	.	Parent=gene2589
###
chr9	ENCODE	gene	128953426	128978308	.	+	.	ID=gene2590;Name=RP11-247A12.4-008;name2=PPP2R4
chr9	ENCODE	exon	128953426	128953464	.	+	.	Parent=gene2590
chr9	ENCODE	CDS	128953434	128953464	.	+	0	Parent=gene2590
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2590
chr9	ENCODE	CDS	128962346	128962443	.	+	2	Parent=gene2590
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2590
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2590
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2590
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2590
chr9	ENCODE	exon	128976628	128976727	.	+	.	Parent=gene2590
chr9	ENCODE	CDS	128976628	128976727	.	+	2	Parent=gene2590
chr9	ENCODE	exon	128978304	128978308	.	+	.	Parent=gene2590
chr9	ENCODE	CDS	128978304	128978308	.	+	1	Parent=gene2590
###
chr9	ENCODE	gene	128953521	128984385	.	+	.	ID=gene2591;Name=RP11-247A12.4-017;name2=PPP2R4
chr9	ENCODE	exon	128953521	128953624	.	+	.	Parent=gene2591
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2591
chr9	ENCODE	CDS	128962420	128962443	.	+	0	Parent=gene2591
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2591
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2591
chr9	ENCODE	exon	128970818	128970943	.	+	.	Parent=gene2591
chr9	ENCODE	CDS	128970818	128970943	.	+	0	Parent=gene2591
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2591
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2591
chr9	ENCODE	exon	128976628	128976727	.	+	.	Parent=gene2591
chr9	ENCODE	CDS	128976628	128976727	.	+	2	Parent=gene2591
chr9	ENCODE	exon	128978304	128978428	.	+	.	Parent=gene2591
chr9	ENCODE	CDS	128978304	128978428	.	+	1	Parent=gene2591
chr9	ENCODE	exon	128979425	128979525	.	+	.	Parent=gene2591
chr9	ENCODE	CDS	128979425	128979525	.	+	2	Parent=gene2591
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2591
chr9	ENCODE	CDS	128984278	128984385	.	+	0	Parent=gene2591
###
chr9	ENCODE	gene	128953701	128976660	.	+	.	ID=gene2592;Name=RP11-247A12.4-018;name2=PPP2R4
chr9	ENCODE	exon	128953701	128953786	.	+	.	Parent=gene2592
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2592
chr9	ENCODE	CDS	128962420	128962443	.	+	0	Parent=gene2592
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2592
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2592
chr9	ENCODE	exon	128970818	128970943	.	+	.	Parent=gene2592
chr9	ENCODE	CDS	128970818	128970943	.	+	0	Parent=gene2592
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2592
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2592
chr9	ENCODE	exon	128976628	128976660	.	+	.	Parent=gene2592
chr9	ENCODE	CDS	128976628	128976660	.	+	2	Parent=gene2592
###
chr9	ENCODE	gene	128960855	128973472	.	+	.	ID=gene2593;Name=RP11-247A12.4-021;name2=PPP2R4
chr9	ENCODE	exon	128960855	128960974	.	+	.	Parent=gene2593
chr9	ENCODE	CDS	128960893	128960974	.	+	0	Parent=gene2593
chr9	ENCODE	exon	128962346	128962461	.	+	.	Parent=gene2593
chr9	ENCODE	CDS	128962346	128962461	.	+	2	Parent=gene2593
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2593
chr9	ENCODE	CDS	128964885	128964971	.	+	0	Parent=gene2593
chr9	ENCODE	exon	128970818	128970943	.	+	.	Parent=gene2593
chr9	ENCODE	CDS	128970818	128970943	.	+	0	Parent=gene2593
chr9	ENCODE	exon	128973355	128973472	.	+	.	Parent=gene2593
chr9	ENCODE	CDS	128973355	128973472	.	+	0	Parent=gene2593
###
chr9	ENCODE	gene	128961346	128970898	.	+	.	ID=gene2594;Name=RP11-247A12.4-019;name2=PPP2R4
chr9	ENCODE	exon	128961346	128961569	.	+	.	Parent=gene2594
chr9	ENCODE	exon	128962346	128962443	.	+	.	Parent=gene2594
chr9	ENCODE	exon	128964885	128964971	.	+	.	Parent=gene2594
chr9	ENCODE	exon	128970818	128970898	.	+	.	Parent=gene2594
###
chr9	ENCODE	gene	128978304	128979944	.	+	.	ID=gene2595;Name=RP11-247A12.4-022;name2=PPP2R4
chr9	ENCODE	exon	128978304	128978428	.	+	.	Parent=gene2595
chr9	ENCODE	CDS	128978304	128978428	.	+	0	Parent=gene2595
chr9	ENCODE	CDS	128979425	128979660	.	+	1	Parent=gene2595
chr9	ENCODE	exon	128979425	128979944	.	+	.	Parent=gene2595
###
chr9	ENCODE	gene	128978330	128984815	.	+	.	ID=gene2596;Name=RP11-247A12.4-001;name2=PPP2R4
chr9	ENCODE	exon	128978330	128978428	.	+	.	Parent=gene2596
chr9	ENCODE	exon	128979425	128979525	.	+	.	Parent=gene2596
chr9	ENCODE	exon	128984278	128984815	.	+	.	Parent=gene2596
###
chr9	ENCODE	gene	128981215	128989831	.	+	.	ID=gene2597;Name=RP11-247A12.4-002;name2=PPP2R4
chr9	ENCODE	exon	128981215	128981482	.	+	.	Parent=gene2597
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2597
chr9	ENCODE	exon	128989220	128989831	.	+	.	Parent=gene2597
###
chr9	ENCODE	gene	128981841	128985487	.	+	.	ID=gene2598;Name=RP11-247A12.4-023;name2=PPP2R4
chr9	ENCODE	exon	128981841	128981984	.	+	.	Parent=gene2598
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2598
chr9	ENCODE	exon	128985208	128985487	.	+	.	Parent=gene2598
###
chr9	ENCODE	gene	128981841	128990120	.	+	.	ID=gene2599;name2=PPP2R4;Name=RP11-247A12.4-003
chr9	ENCODE	exon	128981841	128981984	.	+	.	Parent=gene2599
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2599
chr9	ENCODE	exon	128989220	128990120	.	+	.	Parent=gene2599
###
chr9	ENCODE	gene	128981933	128984920	.	+	.	ID=gene2600;Name=RP11-247A12.4-024;name2=PPP2R4
chr9	ENCODE	exon	128981933	128981984	.	+	.	Parent=gene2600
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2600
chr9	ENCODE	exon	128984514	128984920	.	+	.	Parent=gene2600
###
chr9	ENCODE	gene	128981951	128984773	.	+	.	ID=gene2601;Name=RP11-247A12.4-004;name2=PPP2R4
chr9	ENCODE	exon	128981951	128981984	.	+	.	Parent=gene2601
chr9	ENCODE	exon	128984278	128984773	.	+	.	Parent=gene2601
###
chr9	ENCODE	gene	128983479	128989790	.	+	.	ID=gene2602;Name=RP11-247A12.4-005;name2=PPP2R4
chr9	ENCODE	exon	128983479	128983751	.	+	.	Parent=gene2602
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2602
chr9	ENCODE	exon	128989220	128989790	.	+	.	Parent=gene2602
###
chr9	ENCODE	gene	128983787	128989839	.	+	.	ID=gene2603;Name=RP11-247A12.4-006;name2=PPP2R4
chr9	ENCODE	exon	128983787	128983915	.	+	.	Parent=gene2603
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2603
chr9	ENCODE	exon	128989220	128989839	.	+	.	Parent=gene2603
###
chr9	ENCODE	gene	128983827	128989605	.	+	.	ID=gene2604;Name=RP11-247A12.4-014;name2=PPP2R4
chr9	ENCODE	exon	128983827	128983950	.	+	.	Parent=gene2604
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2604
chr9	ENCODE	exon	128989220	128989605	.	+	.	Parent=gene2604
###
chr9	ENCODE	gene	128983858	128989828	.	+	.	ID=gene2605;Name=RP11-247A12.4-007;name2=PPP2R4
chr9	ENCODE	exon	128983858	128984010	.	+	.	Parent=gene2605
chr9	ENCODE	exon	128984278	128984385	.	+	.	Parent=gene2605
chr9	ENCODE	exon	128989220	128989828	.	+	.	Parent=gene2605
###
chr9	ENCODE	gene	129017385	129020095	.	-	.	ID=gene2606;Name=RP11-247A12.3-001;name2=IER5L
chr9	ENCODE	exon	129017385	129020095	.	-	.	Parent=gene2606
chr9	ENCODE	CDS	129018671	129019885	.	-	0	Parent=gene2606
###
chrX	ENCODE	gene	122525028	122592422	.	-	.	ID=gene2607;Name=RP5-1189B24.5-002;name2=THOC2
chrX	ENCODE	exon	122525028	122525223	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122526492	122526664	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122527545	122527700	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122531055	122531147	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122545933	122546099	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122555406	122555539	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122556106	122556220	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122557066	122557136	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122562839	122562890	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122566243	122566334	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122572235	122572293	.	-	.	Parent=gene2607
chrX	ENCODE	exon	122592337	122592422	.	-	.	Parent=gene2607
###
chrX	ENCODE	gene	122525028	122592441	.	-	.	ID=gene2608;Name=RP5-1189B24.5-001;name2=THOC2
chrX	ENCODE	exon	122525028	122525223	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122526492	122526664	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122527545	122527700	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122531055	122531147	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122545933	122546099	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122555406	122555539	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122556106	122556227	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122557066	122557136	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122562839	122562890	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122566243	122566334	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122572235	122572293	.	-	.	Parent=gene2608
chrX	ENCODE	exon	122592337	122592441	.	-	.	Parent=gene2608
###
chrX	ENCODE	gene	122527694	122592422	.	-	.	ID=gene2609;Name=RP5-1189B24.5-017;name2=THOC2
chrX	ENCODE	exon	122527694	122527700	.	-	.	Parent=gene2609
chrX	ENCODE	exon	122531055	122531147	.	-	.	Parent=gene2609
chrX	ENCODE	exon	122545933	122546099	.	-	.	Parent=gene2609
chrX	ENCODE	exon	122555406	122555539	.	-	.	Parent=gene2609
chrX	ENCODE	exon	122556106	122556220	.	-	.	Parent=gene2609
chrX	ENCODE	exon	122557066	122557136	.	-	.	Parent=gene2609
chrX	ENCODE	exon	122562839	122562890	.	-	.	Parent=gene2609
chrX	ENCODE	exon	122566243	122566334	.	-	.	Parent=gene2609
chrX	ENCODE	exon	122572235	122572293	.	-	.	Parent=gene2609
chrX	ENCODE	exon	122592337	122592422	.	-	.	Parent=gene2609
###
chrX	ENCODE	gene	122557111	122572289	.	-	.	ID=gene2610;name2=THOC2;Name=RP5-1189B24.5-016
chrX	ENCODE	exon	122557111	122557136	.	-	.	Parent=gene2610
chrX	ENCODE	exon	122562839	122562890	.	-	.	Parent=gene2610
chrX	ENCODE	exon	122566239	122566334	.	-	.	Parent=gene2610
chrX	ENCODE	exon	122572235	122572289	.	-	.	Parent=gene2610
###
chrX	ENCODE	gene	122719109	122745096	.	+	.	ID=gene2611;Name=RP1-315G1.5-007;name2=BIRC4
chrX	ENCODE	exon	122719109	122719290	.	+	.	Parent=gene2611
chrX	ENCODE	exon	122719552	122719678	.	+	.	Parent=gene2611
chrX	ENCODE	exon	122745016	122745096	.	+	.	Parent=gene2611
chrX	ENCODE	CDS	122745048	122745096	.	+	0	Parent=gene2611
###
chrX	ENCODE	gene	122719149	122766405	.	+	.	ID=gene2612;Name=RP1-315G1.5-003;name2=BIRC4
chrX	ENCODE	exon	122719149	122719290	.	+	.	Parent=gene2612
chrX	ENCODE	exon	122748004	122748103	.	+	.	Parent=gene2612
chrX	ENCODE	exon	122750623	122750701	.	+	.	Parent=gene2612
chrX	ENCODE	exon	122752116	122752158	.	+	.	Parent=gene2612
chrX	ENCODE	exon	122759878	122760078	.	+	.	Parent=gene2612
chrX	ENCODE	exon	122766373	122766405	.	+	.	Parent=gene2612
###
chrX	ENCODE	gene	122719212	122759951	.	+	.	ID=gene2613;Name=RP1-315G1.5-008;name2=BIRC4
chrX	ENCODE	exon	122719212	122719290	.	+	.	Parent=gene2613
chrX	ENCODE	exon	122719552	122719678	.	+	.	Parent=gene2613
chrX	ENCODE	exon	122748004	122748103	.	+	.	Parent=gene2613
chrX	ENCODE	exon	122750623	122750694	.	+	.	Parent=gene2613
chrX	ENCODE	exon	122752116	122752158	.	+	.	Parent=gene2613
chrX	ENCODE	exon	122759878	122759951	.	+	.	Parent=gene2613
###
chrX	ENCODE	gene	122719262	122766636	.	+	.	ID=gene2614;Name=RP1-315G1.5-001;name2=BIRC4
chrX	ENCODE	exon	122719262	122719290	.	+	.	Parent=gene2614
chrX	ENCODE	exon	122719552	122719678	.	+	.	Parent=gene2614
chrX	ENCODE	exon	122748004	122748103	.	+	.	Parent=gene2614
chrX	ENCODE	exon	122752116	122752158	.	+	.	Parent=gene2614
chrX	ENCODE	exon	122759878	122760078	.	+	.	Parent=gene2614
chrX	ENCODE	exon	122766373	122766636	.	+	.	Parent=gene2614
###
chrX	ENCODE	gene	122719263	122745515	.	+	.	ID=gene2615;Name=RP1-315G1.5-005;name2=BIRC4
chrX	ENCODE	exon	122719263	122719290	.	+	.	Parent=gene2615
chrX	ENCODE	exon	122745016	122745515	.	+	.	Parent=gene2615
chrX	ENCODE	CDS	122745048	122745515	.	+	0	Parent=gene2615
###
chrX	ENCODE	gene	122719412	122773364	.	+	.	ID=gene2616;Name=RP1-315G1.5-002;name2=BIRC4
chrX	ENCODE	exon	122719412	122719678	.	+	.	Parent=gene2616
chrX	ENCODE	exon	122745016	122745924	.	+	.	Parent=gene2616
chrX	ENCODE	CDS	122745048	122745924	.	+	0	Parent=gene2616
chrX	ENCODE	exon	122748004	122748103	.	+	.	Parent=gene2616
chrX	ENCODE	CDS	122748004	122748103	.	+	2	Parent=gene2616
chrX	ENCODE	exon	122750623	122750701	.	+	.	Parent=gene2616
chrX	ENCODE	CDS	122750623	122750701	.	+	1	Parent=gene2616
chrX	ENCODE	exon	122752116	122752158	.	+	.	Parent=gene2616
chrX	ENCODE	CDS	122752116	122752158	.	+	0	Parent=gene2616
chrX	ENCODE	exon	122759878	122760078	.	+	.	Parent=gene2616
chrX	ENCODE	CDS	122759878	122760078	.	+	2	Parent=gene2616
chrX	ENCODE	CDS	122766373	122766566	.	+	2	Parent=gene2616
chrX	ENCODE	exon	122766373	122773364	.	+	.	Parent=gene2616
###
chrX	ENCODE	gene	122719580	122766383	.	+	.	ID=gene2617;Name=RP1-315G1.5-004;name2=BIRC4
chrX	ENCODE	exon	122719580	122719678	.	+	.	Parent=gene2617
chrX	ENCODE	exon	122748004	122748103	.	+	.	Parent=gene2617
chrX	ENCODE	exon	122750623	122750701	.	+	.	Parent=gene2617
chrX	ENCODE	exon	122752116	122752158	.	+	.	Parent=gene2617
chrX	ENCODE	exon	122759878	122760078	.	+	.	Parent=gene2617
chrX	ENCODE	exon	122766373	122766383	.	+	.	Parent=gene2617
###
chrX	ENCODE	gene	122719657	122773350	.	+	.	ID=gene2618;Name=RP1-315G1.5-009;name2=BIRC4
chrX	ENCODE	exon	122719657	122719930	.	+	.	Parent=gene2618
chrX	ENCODE	exon	122745016	122745924	.	+	.	Parent=gene2618
chrX	ENCODE	CDS	122745048	122745924	.	+	0	Parent=gene2618
chrX	ENCODE	exon	122748004	122748103	.	+	.	Parent=gene2618
chrX	ENCODE	CDS	122748004	122748103	.	+	2	Parent=gene2618
chrX	ENCODE	exon	122750623	122750701	.	+	.	Parent=gene2618
chrX	ENCODE	CDS	122750623	122750701	.	+	1	Parent=gene2618
chrX	ENCODE	exon	122752116	122752158	.	+	.	Parent=gene2618
chrX	ENCODE	CDS	122752116	122752158	.	+	0	Parent=gene2618
chrX	ENCODE	exon	122759878	122760078	.	+	.	Parent=gene2618
chrX	ENCODE	CDS	122759878	122760078	.	+	2	Parent=gene2618
chrX	ENCODE	CDS	122766373	122766566	.	+	2	Parent=gene2618
chrX	ENCODE	exon	122766373	122773350	.	+	.	Parent=gene2618
###
chrX	ENCODE	gene	122719839	122748068	.	+	.	ID=gene2619;Name=RP1-315G1.5-010;name2=BIRC4
chrX	ENCODE	exon	122719839	122719930	.	+	.	Parent=gene2619
chrX	ENCODE	exon	122748004	122748068	.	+	.	Parent=gene2619
###
chrX	ENCODE	gene	122772145	122773000	.	+	.	ID=gene2620;name2=BIRC4;Name=RP1-315G1.5-006
chrX	ENCODE	exon	122772145	122772401	.	+	.	Parent=gene2620
chrX	ENCODE	exon	122772630	122773000	.	+	.	Parent=gene2620
###
chrX	ENCODE	gene	122819597	122890433	.	+	.	ID=gene2621;name2=STAG2;Name=RP11-517O1.1-020
chrX	ENCODE	exon	122819597	122819673	.	+	.	Parent=gene2621
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2621
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2621
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2621
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2621
chrX	ENCODE	exon	122890346	122890433	.	+	.	Parent=gene2621
chrX	ENCODE	CDS	122890346	122890433	.	+	0	Parent=gene2621
###
chrX	ENCODE	gene	122819904	122922292	.	+	.	ID=gene2622;name2=STAG2;Name=RP11-517O1.1-002
chrX	ENCODE	exon	122819904	122820251	.	+	.	Parent=gene2622
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2622
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2622
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2622
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122896912	122897008	.	+	0	Parent=gene2622
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122901954	122902030	.	+	2	Parent=gene2622
chrX	ENCODE	exon	122904549	122904753	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122904549	122904753	.	+	0	Parent=gene2622
chrX	ENCODE	exon	122906739	122906890	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122906739	122906890	.	+	2	Parent=gene2622
chrX	ENCODE	exon	122908390	122908463	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122908390	122908463	.	+	0	Parent=gene2622
chrX	ENCODE	exon	122909571	122909694	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122909571	122909694	.	+	1	Parent=gene2622
chrX	ENCODE	exon	122910506	122910604	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122910506	122910604	.	+	0	Parent=gene2622
chrX	ENCODE	exon	122910700	122910779	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122910700	122910779	.	+	0	Parent=gene2622
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122915513	122915620	.	+	1	Parent=gene2622
chrX	ENCODE	exon	122917251	122917362	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122917251	122917362	.	+	1	Parent=gene2622
chrX	ENCODE	exon	122920609	122920726	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122920609	122920726	.	+	0	Parent=gene2622
chrX	ENCODE	exon	122921156	122921259	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122921156	122921259	.	+	2	Parent=gene2622
chrX	ENCODE	exon	122922287	122922292	.	+	.	Parent=gene2622
chrX	ENCODE	CDS	122922287	122922292	.	+	0	Parent=gene2622
###
chrX	ENCODE	gene	122819904	122960883	.	+	.	ID=gene2623;Name=RP11-517O1.1-006;name2=STAG2
chrX	ENCODE	exon	122819904	122820251	.	+	.	Parent=gene2623
chrX	ENCODE	exon	122880752	122880816	.	+	.	Parent=gene2623
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2623
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122896912	122897008	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122901954	122902030	.	+	2	Parent=gene2623
chrX	ENCODE	exon	122904549	122904753	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122904549	122904753	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122906739	122906890	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122906739	122906890	.	+	2	Parent=gene2623
chrX	ENCODE	exon	122908390	122908463	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122908390	122908463	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122909571	122909694	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122909571	122909694	.	+	1	Parent=gene2623
chrX	ENCODE	exon	122910506	122910604	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122910506	122910604	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122910700	122910779	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122910700	122910779	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122915513	122915620	.	+	1	Parent=gene2623
chrX	ENCODE	exon	122917251	122917362	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122917251	122917362	.	+	1	Parent=gene2623
chrX	ENCODE	exon	122920609	122920726	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122920609	122920726	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122921156	122921259	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122921156	122921259	.	+	2	Parent=gene2623
chrX	ENCODE	exon	122922287	122922379	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122922287	122922379	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122922501	122922590	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122922501	122922590	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122923233	122923436	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122923233	122923436	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122925261	122925331	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122925261	122925331	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122925560	122925647	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122925560	122925647	.	+	1	Parent=gene2623
chrX	ENCODE	exon	122925741	122925821	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122925741	122925821	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122927949	122928041	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122927949	122928041	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122930534	122930708	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122930534	122930708	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122935717	122935856	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122935717	122935856	.	+	2	Parent=gene2623
chrX	ENCODE	exon	122937342	122937443	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122937342	122937443	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122940765	122940913	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122940765	122940913	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122942806	122942934	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122942806	122942934	.	+	1	Parent=gene2623
chrX	ENCODE	exon	122945932	122946155	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122945932	122946155	.	+	1	Parent=gene2623
chrX	ENCODE	exon	122949960	122950149	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122949960	122950149	.	+	2	Parent=gene2623
chrX	ENCODE	exon	122950239	122950349	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122950239	122950349	.	+	1	Parent=gene2623
chrX	ENCODE	exon	122953403	122953529	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122953403	122953529	.	+	1	Parent=gene2623
chrX	ENCODE	exon	122954757	122954834	.	+	.	Parent=gene2623
chrX	ENCODE	CDS	122954757	122954834	.	+	0	Parent=gene2623
chrX	ENCODE	CDS	122959959	122959982	.	+	0	Parent=gene2623
chrX	ENCODE	exon	122959959	122960883	.	+	.	Parent=gene2623
###
chrX	ENCODE	gene	122819945	122922379	.	+	.	ID=gene2624;Name=RP11-517O1.1-009;name2=STAG2
chrX	ENCODE	exon	122819945	122820251	.	+	.	Parent=gene2624
chrX	ENCODE	exon	122881916	122881937	.	+	.	Parent=gene2624
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2624
chrX	ENCODE	exon	122917251	122917362	.	+	.	Parent=gene2624
chrX	ENCODE	exon	122920609	122920726	.	+	.	Parent=gene2624
chrX	ENCODE	exon	122921156	122921259	.	+	.	Parent=gene2624
chrX	ENCODE	exon	122922287	122922379	.	+	.	Parent=gene2624
###
chrX	ENCODE	gene	122820080	122863132	.	+	.	ID=gene2625;Name=RP11-517O1.1-010;name2=STAG2
chrX	ENCODE	exon	122820080	122820251	.	+	.	Parent=gene2625
chrX	ENCODE	exon	122862852	122863132	.	+	.	Parent=gene2625
###
chrX	ENCODE	gene	122820249	122885300	.	+	.	ID=gene2626;Name=RP11-517O1.1-007;name2=STAG2
chrX	ENCODE	exon	122820249	122820327	.	+	.	Parent=gene2626
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2626
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2626
chrX	ENCODE	exon	122885225	122885300	.	+	.	Parent=gene2626
chrX	ENCODE	CDS	122885225	122885300	.	+	1	Parent=gene2626
###
chrX	ENCODE	gene	122820699	122962041	.	+	.	ID=gene2627;Name=RP11-517O1.1-018;name2=STAG2
chrX	ENCODE	exon	122820699	122820820	.	+	.	Parent=gene2627
chrX	ENCODE	exon	122821171	122821241	.	+	.	Parent=gene2627
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2627
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122896912	122897008	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122901954	122902030	.	+	2	Parent=gene2627
chrX	ENCODE	exon	122904549	122904753	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122904549	122904753	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122906739	122906890	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122906739	122906890	.	+	2	Parent=gene2627
chrX	ENCODE	exon	122908390	122908463	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122908390	122908463	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122909571	122909694	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122909571	122909694	.	+	1	Parent=gene2627
chrX	ENCODE	exon	122910506	122910604	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122910506	122910604	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122910700	122910779	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122910700	122910779	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122915513	122915620	.	+	1	Parent=gene2627
chrX	ENCODE	exon	122917251	122917362	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122917251	122917362	.	+	1	Parent=gene2627
chrX	ENCODE	exon	122920609	122920726	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122920609	122920726	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122921156	122921259	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122921156	122921259	.	+	2	Parent=gene2627
chrX	ENCODE	exon	122922287	122922379	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122922287	122922379	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122922501	122922590	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122922501	122922590	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122923233	122923436	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122923233	122923436	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122925261	122925331	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122925261	122925331	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122925560	122925647	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122925560	122925647	.	+	1	Parent=gene2627
chrX	ENCODE	exon	122925741	122925821	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122925741	122925821	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122927949	122928041	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122927949	122928041	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122930534	122930708	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122930534	122930708	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122935717	122935856	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122935717	122935856	.	+	2	Parent=gene2627
chrX	ENCODE	exon	122937342	122937443	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122937342	122937443	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122940765	122940913	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122940765	122940913	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122942806	122942934	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122942806	122942934	.	+	1	Parent=gene2627
chrX	ENCODE	exon	122945932	122946155	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122945932	122946155	.	+	1	Parent=gene2627
chrX	ENCODE	exon	122949960	122950149	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122949960	122950149	.	+	2	Parent=gene2627
chrX	ENCODE	exon	122953403	122953529	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122953403	122953529	.	+	1	Parent=gene2627
chrX	ENCODE	exon	122954757	122954834	.	+	.	Parent=gene2627
chrX	ENCODE	CDS	122954757	122954834	.	+	0	Parent=gene2627
chrX	ENCODE	CDS	122959959	122959982	.	+	0	Parent=gene2627
chrX	ENCODE	exon	122959959	122962041	.	+	.	Parent=gene2627
###
chrX	ENCODE	gene	122820703	122902030	.	+	.	ID=gene2628;name2=STAG2;Name=RP11-517O1.1-011
chrX	ENCODE	exon	122820703	122820820	.	+	.	Parent=gene2628
chrX	ENCODE	exon	122880752	122880816	.	+	.	Parent=gene2628
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2628
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2628
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2628
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2628
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2628
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2628
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2628
chrX	ENCODE	CDS	122896912	122897008	.	+	0	Parent=gene2628
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2628
chrX	ENCODE	CDS	122901954	122902030	.	+	2	Parent=gene2628
###
chrX	ENCODE	gene	122821103	122962041	.	+	.	ID=gene2629;Name=RP11-517O1.1-001;name2=STAG2
chrX	ENCODE	exon	122821103	122821241	.	+	.	Parent=gene2629
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2629
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122896912	122897008	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122901954	122902030	.	+	2	Parent=gene2629
chrX	ENCODE	exon	122904549	122904753	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122904549	122904753	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122906739	122906890	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122906739	122906890	.	+	2	Parent=gene2629
chrX	ENCODE	exon	122908390	122908463	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122908390	122908463	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122909571	122909694	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122909571	122909694	.	+	1	Parent=gene2629
chrX	ENCODE	exon	122910506	122910604	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122910506	122910604	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122910700	122910779	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122910700	122910779	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122915513	122915620	.	+	1	Parent=gene2629
chrX	ENCODE	exon	122917251	122917362	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122917251	122917362	.	+	1	Parent=gene2629
chrX	ENCODE	exon	122920609	122920726	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122920609	122920726	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122921156	122921259	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122921156	122921259	.	+	2	Parent=gene2629
chrX	ENCODE	exon	122922287	122922379	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122922287	122922379	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122922501	122922590	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122922501	122922590	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122923233	122923436	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122923233	122923436	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122925261	122925331	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122925261	122925331	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122925560	122925647	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122925560	122925647	.	+	1	Parent=gene2629
chrX	ENCODE	exon	122925741	122925821	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122925741	122925821	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122927949	122928041	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122927949	122928041	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122930534	122930708	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122930534	122930708	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122935717	122935856	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122935717	122935856	.	+	2	Parent=gene2629
chrX	ENCODE	exon	122937342	122937443	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122937342	122937443	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122940765	122940913	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122940765	122940913	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122942806	122942934	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122942806	122942934	.	+	1	Parent=gene2629
chrX	ENCODE	exon	122945932	122946155	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122945932	122946155	.	+	1	Parent=gene2629
chrX	ENCODE	exon	122949960	122950149	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122949960	122950149	.	+	2	Parent=gene2629
chrX	ENCODE	exon	122953403	122953529	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122953403	122953529	.	+	1	Parent=gene2629
chrX	ENCODE	exon	122954757	122954834	.	+	.	Parent=gene2629
chrX	ENCODE	CDS	122954757	122954834	.	+	0	Parent=gene2629
chrX	ENCODE	CDS	122959959	122959982	.	+	0	Parent=gene2629
chrX	ENCODE	exon	122959959	122962041	.	+	.	Parent=gene2629
###
chrX	ENCODE	gene	122821123	122960287	.	+	.	ID=gene2630;Name=RP11-517O1.1-019;name2=STAG2
chrX	ENCODE	exon	122821123	122821241	.	+	.	Parent=gene2630
chrX	ENCODE	exon	122880752	122880816	.	+	.	Parent=gene2630
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2630
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122896912	122897008	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122901954	122902030	.	+	2	Parent=gene2630
chrX	ENCODE	exon	122904549	122904753	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122904549	122904753	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122906739	122906890	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122906739	122906890	.	+	2	Parent=gene2630
chrX	ENCODE	exon	122908390	122908463	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122908390	122908463	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122909571	122909694	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122909571	122909694	.	+	1	Parent=gene2630
chrX	ENCODE	exon	122910506	122910604	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122910506	122910604	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122910700	122910779	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122910700	122910779	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122915513	122915620	.	+	1	Parent=gene2630
chrX	ENCODE	exon	122917251	122917362	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122917251	122917362	.	+	1	Parent=gene2630
chrX	ENCODE	exon	122920609	122920726	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122920609	122920726	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122921156	122921259	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122921156	122921259	.	+	2	Parent=gene2630
chrX	ENCODE	exon	122922287	122922379	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122922287	122922379	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122922501	122922590	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122922501	122922590	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122923233	122923436	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122923233	122923436	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122925261	122925331	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122925261	122925331	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122925560	122925647	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122925560	122925647	.	+	1	Parent=gene2630
chrX	ENCODE	exon	122925741	122925821	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122925741	122925821	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122927949	122928041	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122927949	122928041	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122930534	122930708	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122930534	122930708	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122935717	122935856	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122935717	122935856	.	+	2	Parent=gene2630
chrX	ENCODE	exon	122937342	122937443	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122937342	122937443	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122940765	122940913	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122940765	122940913	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122942806	122942934	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122942806	122942934	.	+	1	Parent=gene2630
chrX	ENCODE	exon	122945932	122946155	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122945932	122946155	.	+	1	Parent=gene2630
chrX	ENCODE	exon	122949960	122950149	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122949960	122950149	.	+	2	Parent=gene2630
chrX	ENCODE	exon	122950239	122950349	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122950239	122950349	.	+	1	Parent=gene2630
chrX	ENCODE	exon	122953403	122953529	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122953403	122953529	.	+	1	Parent=gene2630
chrX	ENCODE	exon	122954757	122954834	.	+	.	Parent=gene2630
chrX	ENCODE	CDS	122954757	122954834	.	+	0	Parent=gene2630
chrX	ENCODE	CDS	122959959	122959982	.	+	0	Parent=gene2630
chrX	ENCODE	exon	122959959	122960287	.	+	.	Parent=gene2630
###
chrX	ENCODE	gene	122821124	122904593	.	+	.	ID=gene2631;Name=RP11-517O1.1-005;name2=STAG2
chrX	ENCODE	exon	122821124	122821241	.	+	.	Parent=gene2631
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2631
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2631
chrX	ENCODE	exon	122885950	122886072	.	+	.	Parent=gene2631
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2631
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2631
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2631
chrX	ENCODE	exon	122904549	122904593	.	+	.	Parent=gene2631
###
chrX	ENCODE	gene	122821124	122960287	.	+	.	ID=gene2632;Name=RP11-517O1.1-008;name2=STAG2
chrX	ENCODE	exon	122821124	122821241	.	+	.	Parent=gene2632
chrX	ENCODE	exon	122880752	122880816	.	+	.	Parent=gene2632
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2632
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122896912	122897008	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122901954	122902030	.	+	2	Parent=gene2632
chrX	ENCODE	exon	122904549	122904753	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122904549	122904753	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122906739	122906890	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122906739	122906890	.	+	2	Parent=gene2632
chrX	ENCODE	exon	122908390	122908463	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122908390	122908463	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122909571	122909694	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122909571	122909694	.	+	1	Parent=gene2632
chrX	ENCODE	exon	122910506	122910604	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122910506	122910604	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122910700	122910779	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122910700	122910779	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122915513	122915620	.	+	1	Parent=gene2632
chrX	ENCODE	exon	122917251	122917362	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122917251	122917362	.	+	1	Parent=gene2632
chrX	ENCODE	exon	122920609	122920726	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122920609	122920726	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122921156	122921259	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122921156	122921259	.	+	2	Parent=gene2632
chrX	ENCODE	exon	122922287	122922379	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122922287	122922379	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122922501	122922590	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122922501	122922590	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122923233	122923436	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122923233	122923436	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122925261	122925331	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122925261	122925331	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122925560	122925647	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122925560	122925647	.	+	1	Parent=gene2632
chrX	ENCODE	exon	122925741	122925821	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122925741	122925821	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122927949	122928041	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122927949	122928041	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122930534	122930708	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122930534	122930708	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122935717	122935856	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122935717	122935856	.	+	2	Parent=gene2632
chrX	ENCODE	exon	122937342	122937443	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122937342	122937443	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122940765	122940913	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122940765	122940913	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122942806	122942934	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122942806	122942934	.	+	1	Parent=gene2632
chrX	ENCODE	exon	122945932	122946155	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122945932	122946155	.	+	1	Parent=gene2632
chrX	ENCODE	exon	122949960	122950149	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122949960	122950149	.	+	2	Parent=gene2632
chrX	ENCODE	exon	122953403	122953529	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122953403	122953529	.	+	1	Parent=gene2632
chrX	ENCODE	exon	122954757	122954834	.	+	.	Parent=gene2632
chrX	ENCODE	CDS	122954757	122954834	.	+	0	Parent=gene2632
chrX	ENCODE	CDS	122959959	122959982	.	+	0	Parent=gene2632
chrX	ENCODE	exon	122959959	122960287	.	+	.	Parent=gene2632
###
chrX	ENCODE	gene	122821146	122942827	.	+	.	ID=gene2633;Name=RP11-517O1.1-003;name2=STAG2
chrX	ENCODE	exon	122821146	122821241	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122881916	122881958	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122917251	122917357	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122923358	122923436	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122925261	122925293	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122930687	122930708	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122935717	122935856	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122937342	122937443	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122940765	122940913	.	+	.	Parent=gene2633
chrX	ENCODE	exon	122942806	122942827	.	+	.	Parent=gene2633
###
chrX	ENCODE	gene	122821160	122923376	.	+	.	ID=gene2634;Name=RP11-517O1.1-012;name2=STAG2
chrX	ENCODE	exon	122821160	122821241	.	+	.	Parent=gene2634
chrX	ENCODE	exon	122881916	122881937	.	+	.	Parent=gene2634
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2634
chrX	ENCODE	exon	122917251	122917362	.	+	.	Parent=gene2634
chrX	ENCODE	exon	122920609	122920726	.	+	.	Parent=gene2634
chrX	ENCODE	exon	122921156	122921259	.	+	.	Parent=gene2634
chrX	ENCODE	exon	122922287	122922379	.	+	.	Parent=gene2634
chrX	ENCODE	exon	122922501	122922590	.	+	.	Parent=gene2634
chrX	ENCODE	exon	122923233	122923376	.	+	.	Parent=gene2634
###
chrX	ENCODE	gene	122821208	122922590	.	+	.	ID=gene2635;Name=RP11-517O1.1-015;name2=STAG2
chrX	ENCODE	exon	122821208	122821241	.	+	.	Parent=gene2635
chrX	ENCODE	exon	122821464	122821491	.	+	.	Parent=gene2635
chrX	ENCODE	exon	122881916	122881937	.	+	.	Parent=gene2635
chrX	ENCODE	exon	122915513	122915620	.	+	.	Parent=gene2635
chrX	ENCODE	exon	122917251	122917362	.	+	.	Parent=gene2635
chrX	ENCODE	exon	122920609	122920726	.	+	.	Parent=gene2635
chrX	ENCODE	exon	122921156	122921259	.	+	.	Parent=gene2635
chrX	ENCODE	exon	122922287	122922379	.	+	.	Parent=gene2635
chrX	ENCODE	exon	122922501	122922590	.	+	.	Parent=gene2635
###
chrX	ENCODE	gene	122821418	122904593	.	+	.	ID=gene2636;name2=STAG2;Name=RP11-517O1.1-014
chrX	ENCODE	exon	122821418	122821491	.	+	.	Parent=gene2636
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2636
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2636
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2636
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2636
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2636
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2636
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2636
chrX	ENCODE	CDS	122896912	122897008	.	+	0	Parent=gene2636
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2636
chrX	ENCODE	CDS	122901954	122902030	.	+	2	Parent=gene2636
chrX	ENCODE	exon	122904549	122904593	.	+	.	Parent=gene2636
chrX	ENCODE	CDS	122904549	122904593	.	+	0	Parent=gene2636
###
chrX	ENCODE	gene	122821479	122904709	.	+	.	ID=gene2637;Name=RP11-517O1.1-013;name2=STAG2
chrX	ENCODE	exon	122821479	122821491	.	+	.	Parent=gene2637
chrX	ENCODE	exon	122880752	122880816	.	+	.	Parent=gene2637
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2637
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2637
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2637
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2637
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2637
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2637
chrX	ENCODE	exon	122896912	122897008	.	+	.	Parent=gene2637
chrX	ENCODE	CDS	122896912	122897008	.	+	0	Parent=gene2637
chrX	ENCODE	exon	122901954	122902030	.	+	.	Parent=gene2637
chrX	ENCODE	CDS	122901954	122902030	.	+	2	Parent=gene2637
chrX	ENCODE	exon	122904549	122904709	.	+	.	Parent=gene2637
chrX	ENCODE	CDS	122904549	122904709	.	+	0	Parent=gene2637
###
chrX	ENCODE	gene	122822555	122896970	.	+	.	ID=gene2638;Name=RP11-517O1.1-017;name2=STAG2
chrX	ENCODE	exon	122822555	122822786	.	+	.	Parent=gene2638
chrX	ENCODE	exon	122881916	122882056	.	+	.	Parent=gene2638
chrX	ENCODE	CDS	122882013	122882056	.	+	0	Parent=gene2638
chrX	ENCODE	exon	122885225	122885303	.	+	.	Parent=gene2638
chrX	ENCODE	CDS	122885225	122885303	.	+	1	Parent=gene2638
chrX	ENCODE	exon	122890346	122890510	.	+	.	Parent=gene2638
chrX	ENCODE	CDS	122890346	122890510	.	+	0	Parent=gene2638
chrX	ENCODE	exon	122896912	122896970	.	+	.	Parent=gene2638
chrX	ENCODE	CDS	122896912	122896970	.	+	0	Parent=gene2638
###
chrX	ENCODE	gene	122953298	122954880	.	+	.	ID=gene2639;Name=RP11-517O1.1-016;name2=STAG2
chrX	ENCODE	exon	122953298	122953529	.	+	.	Parent=gene2639
chrX	ENCODE	exon	122954757	122954880	.	+	.	Parent=gene2639
###
chrX	ENCODE	gene	152647816	152672447	.	-	.	ID=gene2640;Name=U52111.6-001;name2=L1CAM
chrX	ENCODE	exon	152647816	152649196	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152648965	152649196	.	-	1	Parent=gene2640
chrX	ENCODE	exon	152649670	152649681	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152649670	152649681	.	-	1	Parent=gene2640
chrX	ENCODE	exon	152649779	152649851	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152649779	152649851	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152650185	152650319	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152650185	152650319	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152650624	152650779	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152650624	152650779	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152650887	152651006	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152650887	152651006	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152651123	152651296	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152651123	152651296	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152651390	152651512	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152651390	152651512	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152651601	152651802	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152651601	152651802	.	-	0	Parent=gene2640
chrX	ENCODE	exon	152652006	152652121	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152652006	152652121	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152652951	152653173	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152652951	152653173	.	-	0	Parent=gene2640
chrX	ENCODE	exon	152653356	152653426	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152653356	152653426	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152653658	152653855	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152653658	152653855	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152654102	152654212	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152654102	152654212	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152654300	152654424	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152654300	152654424	.	-	1	Parent=gene2640
chrX	ENCODE	exon	152654604	152654760	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152654604	152654760	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152654863	152655029	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152654863	152655029	.	-	1	Parent=gene2640
chrX	ENCODE	exon	152655143	152655254	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152655143	152655254	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152655822	152655965	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152655822	152655965	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152656105	152656236	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152656105	152656236	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152656358	152656542	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152656358	152656542	.	-	1	Parent=gene2640
chrX	ENCODE	exon	152656690	152656801	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152656690	152656801	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152657092	152657262	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152657092	152657262	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152657359	152657481	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152657359	152657481	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152658454	152658656	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152658454	152658656	.	-	1	Parent=gene2640
chrX	ENCODE	exon	152658894	152658999	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152658894	152658999	.	-	2	Parent=gene2640
chrX	ENCODE	exon	152659530	152659544	.	-	.	Parent=gene2640
chrX	ENCODE	CDS	152659530	152659544	.	-	2	Parent=gene2640
chrX	ENCODE	CDS	152662063	152662138	.	-	0	Parent=gene2640
chrX	ENCODE	exon	152662063	152662246	.	-	.	Parent=gene2640
chrX	ENCODE	exon	152672366	152672447	.	-	.	Parent=gene2640
###
chrX	ENCODE	gene	152648255	152672455	.	-	.	ID=gene2641;Name=U52111.6-006;name2=L1CAM
chrX	ENCODE	exon	152648255	152649196	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152648965	152649196	.	-	1	Parent=gene2641
chrX	ENCODE	exon	152649779	152649851	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152649779	152649851	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152650185	152650319	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152650185	152650319	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152650624	152650779	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152650624	152650779	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152650887	152651006	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152650887	152651006	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152651123	152651296	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152651123	152651296	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152651390	152651512	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152651390	152651512	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152651601	152651802	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152651601	152651802	.	-	0	Parent=gene2641
chrX	ENCODE	exon	152652006	152652121	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152652006	152652121	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152652951	152653173	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152652951	152653173	.	-	0	Parent=gene2641
chrX	ENCODE	exon	152653356	152653426	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152653356	152653426	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152653658	152653855	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152653658	152653855	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152654102	152654212	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152654102	152654212	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152654300	152654424	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152654300	152654424	.	-	1	Parent=gene2641
chrX	ENCODE	exon	152654604	152654760	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152654604	152654760	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152654863	152655029	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152654863	152655029	.	-	1	Parent=gene2641
chrX	ENCODE	exon	152655143	152655254	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152655143	152655254	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152655822	152655965	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152655822	152655965	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152656105	152656236	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152656105	152656236	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152656358	152656542	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152656358	152656542	.	-	1	Parent=gene2641
chrX	ENCODE	exon	152656690	152656801	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152656690	152656801	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152657092	152657262	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152657092	152657262	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152657359	152657481	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152657359	152657481	.	-	2	Parent=gene2641
chrX	ENCODE	exon	152658454	152658656	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152658454	152658656	.	-	1	Parent=gene2641
chrX	ENCODE	exon	152658894	152658999	.	-	.	Parent=gene2641
chrX	ENCODE	CDS	152658894	152658999	.	-	2	Parent=gene2641
chrX	ENCODE	CDS	152662063	152662138	.	-	0	Parent=gene2641
chrX	ENCODE	exon	152662063	152662246	.	-	.	Parent=gene2641
chrX	ENCODE	exon	152672366	152672455	.	-	.	Parent=gene2641
###
chrX	ENCODE	gene	152648735	152650780	.	-	.	ID=gene2642;Name=U52111.6-003;name2=L1CAM
chrX	ENCODE	exon	152648735	152649196	.	-	.	Parent=gene2642
chrX	ENCODE	CDS	152648965	152649196	.	-	1	Parent=gene2642
chrX	ENCODE	exon	152649779	152649851	.	-	.	Parent=gene2642
chrX	ENCODE	CDS	152649779	152649851	.	-	2	Parent=gene2642
chrX	ENCODE	exon	152650624	152650780	.	-	.	Parent=gene2642
chrX	ENCODE	CDS	152650624	152650780	.	-	0	Parent=gene2642
###
chrX	ENCODE	gene	152648850	152662149	.	-	.	ID=gene2643;Name=U52111.6-002;name2=L1CAM
chrX	ENCODE	exon	152648850	152649196	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152648965	152649196	.	-	1	Parent=gene2643
chrX	ENCODE	exon	152649779	152649851	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152649779	152649851	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152650185	152650319	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152650185	152650319	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152650624	152650779	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152650624	152650779	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152650887	152651006	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152650887	152651006	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152651123	152651296	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152651123	152651296	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152651390	152651512	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152651390	152651512	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152651601	152651802	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152651601	152651802	.	-	0	Parent=gene2643
chrX	ENCODE	exon	152652006	152652121	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152652006	152652121	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152652951	152653173	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152652951	152653173	.	-	0	Parent=gene2643
chrX	ENCODE	exon	152653356	152653426	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152653356	152653426	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152653658	152653855	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152653658	152653855	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152654102	152654212	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152654102	152654212	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152654300	152654424	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152654300	152654424	.	-	1	Parent=gene2643
chrX	ENCODE	exon	152654604	152654760	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152654604	152654760	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152654863	152655029	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152654863	152655029	.	-	1	Parent=gene2643
chrX	ENCODE	exon	152655143	152655254	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152655143	152655254	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152655822	152655965	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152655822	152655965	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152656105	152656236	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152656105	152656236	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152656358	152656542	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152656358	152656542	.	-	1	Parent=gene2643
chrX	ENCODE	exon	152656690	152656801	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152656690	152656801	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152657092	152657262	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152657092	152657262	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152657359	152657481	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152657359	152657481	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152658454	152658656	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152658454	152658656	.	-	1	Parent=gene2643
chrX	ENCODE	exon	152658894	152658999	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152658894	152658999	.	-	2	Parent=gene2643
chrX	ENCODE	exon	152659530	152659544	.	-	.	Parent=gene2643
chrX	ENCODE	CDS	152659530	152659544	.	-	2	Parent=gene2643
chrX	ENCODE	CDS	152662063	152662138	.	-	0	Parent=gene2643
chrX	ENCODE	exon	152662063	152662149	.	-	.	Parent=gene2643
###
chrX	ENCODE	gene	152649094	152650271	.	-	.	ID=gene2644;Name=U52111.6-015;name2=L1CAM
chrX	ENCODE	exon	152649094	152649196	.	-	.	Parent=gene2644
chrX	ENCODE	exon	152649670	152649681	.	-	.	Parent=gene2644
chrX	ENCODE	exon	152649779	152650271	.	-	.	Parent=gene2644
###
chrX	ENCODE	gene	152651266	152652217	.	-	.	ID=gene2645;Name=U52111.6-014;name2=L1CAM
chrX	ENCODE	exon	152651266	152651296	.	-	.	Parent=gene2645
chrX	ENCODE	exon	152651390	152651512	.	-	.	Parent=gene2645
chrX	ENCODE	exon	152651601	152651802	.	-	.	Parent=gene2645
chrX	ENCODE	exon	152652006	152652217	.	-	.	Parent=gene2645
###
chrX	ENCODE	gene	152653074	152654679	.	-	.	ID=gene2646;Name=U52111.6-007;name2=L1CAM
chrX	ENCODE	exon	152653074	152653173	.	-	.	Parent=gene2646
chrX	ENCODE	CDS	152653074	152653173	.	-	1	Parent=gene2646
chrX	ENCODE	exon	152653356	152653426	.	-	.	Parent=gene2646
chrX	ENCODE	CDS	152653356	152653426	.	-	0	Parent=gene2646
chrX	ENCODE	exon	152653658	152653855	.	-	.	Parent=gene2646
chrX	ENCODE	CDS	152653658	152653855	.	-	0	Parent=gene2646
chrX	ENCODE	exon	152654300	152654424	.	-	.	Parent=gene2646
chrX	ENCODE	CDS	152654300	152654424	.	-	2	Parent=gene2646
chrX	ENCODE	exon	152654604	152654679	.	-	.	Parent=gene2646
chrX	ENCODE	CDS	152654604	152654679	.	-	0	Parent=gene2646
###
chrX	ENCODE	gene	152653853	152654925	.	-	.	ID=gene2647;Name=U52111.6-013;name2=L1CAM
chrX	ENCODE	exon	152653853	152653855	.	-	.	Parent=gene2647
chrX	ENCODE	exon	152654102	152654212	.	-	.	Parent=gene2647
chrX	ENCODE	exon	152654300	152654424	.	-	.	Parent=gene2647
chrX	ENCODE	exon	152654604	152654925	.	-	.	Parent=gene2647
###
chrX	ENCODE	gene	152654709	152655474	.	-	.	ID=gene2648;Name=U52111.6-012;name2=L1CAM
chrX	ENCODE	exon	152654709	152654760	.	-	.	Parent=gene2648
chrX	ENCODE	exon	152654863	152655029	.	-	.	Parent=gene2648
chrX	ENCODE	exon	152655143	152655474	.	-	.	Parent=gene2648
###
chrX	ENCODE	gene	152657430	152662341	.	-	.	ID=gene2649;Name=U52111.6-011;name2=L1CAM
chrX	ENCODE	exon	152657430	152657481	.	-	.	Parent=gene2649
chrX	ENCODE	exon	152658454	152658656	.	-	.	Parent=gene2649
chrX	ENCODE	exon	152658894	152658999	.	-	.	Parent=gene2649
chrX	ENCODE	exon	152659530	152659544	.	-	.	Parent=gene2649
chrX	ENCODE	exon	152662063	152662341	.	-	.	Parent=gene2649
###
chrX	ENCODE	gene	152658523	152695524	.	-	.	ID=gene2650;Name=U52111.6-016;name2=L1CAM
chrX	ENCODE	exon	152658523	152658656	.	-	.	Parent=gene2650
chrX	ENCODE	exon	152658894	152658999	.	-	.	Parent=gene2650
chrX	ENCODE	exon	152659530	152659544	.	-	.	Parent=gene2650
chrX	ENCODE	exon	152662063	152662246	.	-	.	Parent=gene2650
chrX	ENCODE	exon	152695371	152695524	.	-	.	Parent=gene2650
###
chrX	ENCODE	gene	152658569	152672474	.	-	.	ID=gene2651;Name=U52111.6-008;name2=L1CAM
chrX	ENCODE	exon	152658569	152658656	.	-	.	Parent=gene2651
chrX	ENCODE	CDS	152658569	152658656	.	-	1	Parent=gene2651
chrX	ENCODE	exon	152658894	152658999	.	-	.	Parent=gene2651
chrX	ENCODE	CDS	152658894	152658999	.	-	2	Parent=gene2651
chrX	ENCODE	CDS	152662063	152662138	.	-	0	Parent=gene2651
chrX	ENCODE	exon	152662063	152662246	.	-	.	Parent=gene2651
chrX	ENCODE	exon	152666584	152666665	.	-	.	Parent=gene2651
chrX	ENCODE	exon	152672366	152672474	.	-	.	Parent=gene2651
###
chrX	ENCODE	gene	152658603	152662693	.	-	.	ID=gene2652;Name=U52111.6-010;name2=L1CAM
chrX	ENCODE	exon	152658603	152658656	.	-	.	Parent=gene2652
chrX	ENCODE	exon	152658894	152658999	.	-	.	Parent=gene2652
chrX	ENCODE	exon	152659530	152659544	.	-	.	Parent=gene2652
chrX	ENCODE	exon	152662063	152662246	.	-	.	Parent=gene2652
chrX	ENCODE	exon	152662416	152662693	.	-	.	Parent=gene2652
###
chrX	ENCODE	gene	152659251	152672443	.	-	.	ID=gene2653;Name=U52111.6-009;name2=L1CAM
chrX	ENCODE	exon	152659251	152659544	.	-	.	Parent=gene2653
chrX	ENCODE	exon	152662063	152662246	.	-	.	Parent=gene2653
chrX	ENCODE	exon	152672366	152672443	.	-	.	Parent=gene2653
###
chrX	ENCODE	gene	152666974	152675291	.	+	.	ID=gene2654;Name=U52112.12-001;name2=U52112.12
chrX	ENCODE	exon	152666974	152667020	.	+	.	Parent=gene2654
chrX	ENCODE	CDS	152666974	152667020	.	+	0	Parent=gene2654
chrX	ENCODE	exon	152670013	152670198	.	+	.	Parent=gene2654
chrX	ENCODE	CDS	152670013	152670198	.	+	1	Parent=gene2654
chrX	ENCODE	exon	152670250	152670574	.	+	.	Parent=gene2654
chrX	ENCODE	CDS	152670250	152670574	.	+	1	Parent=gene2654
chrX	ENCODE	exon	152671664	152671737	.	+	.	Parent=gene2654
chrX	ENCODE	CDS	152671664	152671737	.	+	0	Parent=gene2654
chrX	ENCODE	exon	152672109	152672278	.	+	.	Parent=gene2654
chrX	ENCODE	CDS	152672109	152672278	.	+	1	Parent=gene2654
chrX	ENCODE	exon	152673264	152673358	.	+	.	Parent=gene2654
chrX	ENCODE	CDS	152673264	152673358	.	+	2	Parent=gene2654
chrX	ENCODE	CDS	152674798	152674898	.	+	0	Parent=gene2654
chrX	ENCODE	exon	152674798	152675291	.	+	.	Parent=gene2654
###
chrX	ENCODE	gene	152670166	152672462	.	-	.	ID=gene2655;name2=L1CAM;Name=U52111.6-005
chrX	ENCODE	exon	152670166	152670807	.	-	.	Parent=gene2655
chrX	ENCODE	exon	152672366	152672462	.	-	.	Parent=gene2655
###
chrX	ENCODE	gene	152688832	152693466	.	+	.	ID=gene2656;name2=AVPR2;Name=U52112.2-002
chrX	ENCODE	exon	152688832	152689193	.	+	.	Parent=gene2656
chrX	ENCODE	exon	152691275	152691471	.	+	.	Parent=gene2656
chrX	ENCODE	exon	152692320	152692717	.	+	.	Parent=gene2656
chrX	ENCODE	exon	152692824	152693466	.	+	.	Parent=gene2656
###
chrX	ENCODE	gene	152691036	152693467	.	+	.	ID=gene2657;Name=U52112.2-001;name2=AVPR2
chrX	ENCODE	exon	152691036	152691072	.	+	.	Parent=gene2657
chrX	ENCODE	exon	152691275	152691471	.	+	.	Parent=gene2657
chrX	ENCODE	CDS	152691447	152691471	.	+	0	Parent=gene2657
chrX	ENCODE	exon	152691833	152692717	.	+	.	Parent=gene2657
chrX	ENCODE	CDS	152691833	152692717	.	+	2	Parent=gene2657
chrX	ENCODE	CDS	152692824	152693029	.	+	2	Parent=gene2657
chrX	ENCODE	exon	152692824	152693467	.	+	.	Parent=gene2657
###
chrX	ENCODE	gene	152691415	152693082	.	+	.	ID=gene2658;Name=U52112.2-003;name2=AVPR2
chrX	ENCODE	exon	152691415	152691471	.	+	.	Parent=gene2658
chrX	ENCODE	CDS	152691447	152691471	.	+	0	Parent=gene2658
chrX	ENCODE	CDS	152691833	152692737	.	+	2	Parent=gene2658
chrX	ENCODE	exon	152691833	152693082	.	+	.	Parent=gene2658
###
chrX	ENCODE	gene	152693668	152712555	.	-	.	ID=gene2659;Name=U52112.4-024;name2=ARHGAP4
chrX	ENCODE	exon	152693668	152694263	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152694030	152694263	.	-	0	Parent=gene2659
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152695371	152695470	.	-	1	Parent=gene2659
chrX	ENCODE	exon	152695744	152695836	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152695744	152695836	.	-	1	Parent=gene2659
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152696042	152696225	.	-	2	Parent=gene2659
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152696313	152696386	.	-	1	Parent=gene2659
chrX	ENCODE	exon	152696472	152696705	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152696472	152696705	.	-	1	Parent=gene2659
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152696807	152696912	.	-	2	Parent=gene2659
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152697001	152697135	.	-	2	Parent=gene2659
chrX	ENCODE	exon	152697223	152697300	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152697223	152697300	.	-	2	Parent=gene2659
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152697430	152697490	.	-	0	Parent=gene2659
chrX	ENCODE	exon	152699001	152699103	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152699001	152699103	.	-	1	Parent=gene2659
chrX	ENCODE	exon	152699325	152699352	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152699325	152699352	.	-	2	Parent=gene2659
chrX	ENCODE	exon	152699519	152699603	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152699519	152699603	.	-	0	Parent=gene2659
chrX	ENCODE	exon	152699710	152699901	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152699710	152699901	.	-	0	Parent=gene2659
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152700079	152700180	.	-	0	Parent=gene2659
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152707397	152707459	.	-	0	Parent=gene2659
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152707665	152707827	.	-	1	Parent=gene2659
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2659
chrX	ENCODE	CDS	152707905	152708109	.	-	2	Parent=gene2659
chrX	ENCODE	CDS	152712437	152712503	.	-	0	Parent=gene2659
chrX	ENCODE	exon	152712437	152712555	.	-	.	Parent=gene2659
###
chrX	ENCODE	gene	152693677	152712561	.	-	.	ID=gene2660;Name=U52112.4-001;name2=ARHGAP4
chrX	ENCODE	exon	152693677	152694263	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152694030	152694263	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152695371	152695470	.	-	1	Parent=gene2660
chrX	ENCODE	exon	152695744	152695836	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152695744	152695836	.	-	1	Parent=gene2660
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152696042	152696225	.	-	2	Parent=gene2660
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152696313	152696386	.	-	1	Parent=gene2660
chrX	ENCODE	exon	152696472	152696705	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152696472	152696705	.	-	1	Parent=gene2660
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152696807	152696912	.	-	2	Parent=gene2660
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152697001	152697135	.	-	2	Parent=gene2660
chrX	ENCODE	exon	152697223	152697300	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152697223	152697300	.	-	2	Parent=gene2660
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152697430	152697490	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152699001	152699103	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152699001	152699103	.	-	1	Parent=gene2660
chrX	ENCODE	exon	152699325	152699352	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152699325	152699352	.	-	2	Parent=gene2660
chrX	ENCODE	exon	152699519	152699603	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152699519	152699603	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152699710	152699901	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152699710	152699901	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152700079	152700180	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152705133	152705354	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152705133	152705354	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152705456	152705584	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152705868	152705987	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152705868	152705987	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152706927	152707109	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152706927	152707109	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152707397	152707459	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152707665	152707827	.	-	1	Parent=gene2660
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2660
chrX	ENCODE	CDS	152707905	152708109	.	-	2	Parent=gene2660
chrX	ENCODE	CDS	152712437	152712503	.	-	0	Parent=gene2660
chrX	ENCODE	exon	152712437	152712561	.	-	.	Parent=gene2660
###
chrX	ENCODE	gene	152693678	152712545	.	-	.	ID=gene2661;Name=U52112.4-003;name2=ARHGAP4
chrX	ENCODE	exon	152693678	152694263	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152694030	152694263	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152695371	152695470	.	-	1	Parent=gene2661
chrX	ENCODE	exon	152695744	152695836	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152695744	152695836	.	-	1	Parent=gene2661
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152696042	152696225	.	-	2	Parent=gene2661
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152696313	152696386	.	-	1	Parent=gene2661
chrX	ENCODE	exon	152696472	152696705	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152696472	152696705	.	-	1	Parent=gene2661
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152696807	152696912	.	-	2	Parent=gene2661
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152697001	152697135	.	-	2	Parent=gene2661
chrX	ENCODE	exon	152697223	152697300	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152697223	152697300	.	-	2	Parent=gene2661
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152697430	152697490	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152699001	152699103	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152699001	152699103	.	-	1	Parent=gene2661
chrX	ENCODE	exon	152699325	152699352	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152699325	152699352	.	-	2	Parent=gene2661
chrX	ENCODE	exon	152699519	152699603	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152699519	152699603	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152699710	152699901	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152699710	152699901	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152700079	152700180	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152705133	152705354	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152705133	152705354	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152705456	152705584	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152706927	152707109	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152706927	152707109	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152707397	152707459	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152707665	152707827	.	-	1	Parent=gene2661
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2661
chrX	ENCODE	CDS	152707905	152708109	.	-	2	Parent=gene2661
chrX	ENCODE	CDS	152712437	152712503	.	-	0	Parent=gene2661
chrX	ENCODE	exon	152712437	152712545	.	-	.	Parent=gene2661
###
chrX	ENCODE	gene	152693678	152712545	.	-	.	ID=gene2662;Name=U52112.4-002;name2=ARHGAP4
chrX	ENCODE	exon	152693678	152694263	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152695744	152695836	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152699001	152699103	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152699325	152699352	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152699519	152699603	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152699710	152699901	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152705133	152705354	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152706927	152707109	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2662
chrX	ENCODE	exon	152712437	152712545	.	-	.	Parent=gene2662
###
chrX	ENCODE	gene	152693716	152699038	.	-	.	ID=gene2663;Name=U52112.4-016;name2=ARHGAP4
chrX	ENCODE	exon	152693716	152694263	.	-	.	Parent=gene2663
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2663
chrX	ENCODE	exon	152695744	152695836	.	-	.	Parent=gene2663
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2663
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2663
chrX	ENCODE	exon	152696472	152696912	.	-	.	Parent=gene2663
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2663
chrX	ENCODE	exon	152697223	152697300	.	-	.	Parent=gene2663
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2663
chrX	ENCODE	exon	152699001	152699038	.	-	.	Parent=gene2663
###
chrX	ENCODE	gene	152693740	152695959	.	-	.	ID=gene2664;Name=U52112.4-006;name2=ARHGAP4
chrX	ENCODE	exon	152693740	152694263	.	-	.	Parent=gene2664
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2664
chrX	ENCODE	exon	152695744	152695959	.	-	.	Parent=gene2664
###
chrX	ENCODE	gene	152693755	152712545	.	-	.	ID=gene2665;name2=ARHGAP4;Name=U52112.4-011
chrX	ENCODE	exon	152693755	152694263	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152694030	152694263	.	-	0	Parent=gene2665
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152695371	152695470	.	-	1	Parent=gene2665
chrX	ENCODE	exon	152695744	152695836	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152695744	152695836	.	-	1	Parent=gene2665
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152696042	152696225	.	-	2	Parent=gene2665
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152696313	152696386	.	-	1	Parent=gene2665
chrX	ENCODE	exon	152696472	152696705	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152696472	152696705	.	-	1	Parent=gene2665
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152696807	152696912	.	-	2	Parent=gene2665
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152697001	152697135	.	-	2	Parent=gene2665
chrX	ENCODE	exon	152697223	152697300	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152697223	152697300	.	-	2	Parent=gene2665
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152697430	152697490	.	-	0	Parent=gene2665
chrX	ENCODE	exon	152699001	152699103	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152699001	152699103	.	-	1	Parent=gene2665
chrX	ENCODE	exon	152699325	152699352	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152699325	152699352	.	-	2	Parent=gene2665
chrX	ENCODE	exon	152699519	152699603	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152699519	152699603	.	-	0	Parent=gene2665
chrX	ENCODE	exon	152699710	152699901	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152699710	152699901	.	-	0	Parent=gene2665
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152700079	152700180	.	-	0	Parent=gene2665
chrX	ENCODE	exon	152705133	152705354	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152705133	152705354	.	-	0	Parent=gene2665
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152705456	152705584	.	-	0	Parent=gene2665
chrX	ENCODE	exon	152706927	152707109	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152706927	152707109	.	-	0	Parent=gene2665
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152707665	152707827	.	-	1	Parent=gene2665
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2665
chrX	ENCODE	CDS	152707905	152708109	.	-	2	Parent=gene2665
chrX	ENCODE	CDS	152712437	152712503	.	-	0	Parent=gene2665
chrX	ENCODE	exon	152712437	152712545	.	-	.	Parent=gene2665
###
chrX	ENCODE	gene	152693755	152712545	.	-	.	ID=gene2666;Name=U52112.4-012;name2=ARHGAP4
chrX	ENCODE	exon	152693755	152694263	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152695744	152695836	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152696472	152696705	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152697223	152697300	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152699001	152699103	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152699325	152699352	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152699519	152699901	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152705133	152705354	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2666
chrX	ENCODE	exon	152712437	152712545	.	-	.	Parent=gene2666
###
chrX	ENCODE	gene	152693755	152712545	.	-	.	ID=gene2667;Name=U52112.4-013;name2=ARHGAP4
chrX	ENCODE	exon	152693755	152694263	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152695744	152695836	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152696472	152696705	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152697223	152697300	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152699001	152699103	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152699325	152699352	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152699519	152699901	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2667
chrX	ENCODE	exon	152712437	152712545	.	-	.	Parent=gene2667
###
chrX	ENCODE	gene	152693770	152712606	.	-	.	ID=gene2668;Name=U52112.4-014;name2=ARHGAP4
chrX	ENCODE	exon	152693770	152694263	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152695371	152695470	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152695744	152695836	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152696472	152696705	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152697223	152697300	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152699001	152699103	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152699325	152699352	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152699519	152699603	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152699710	152699901	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152705133	152705354	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152706927	152707137	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2668
chrX	ENCODE	exon	152712437	152712606	.	-	.	Parent=gene2668
###
chrX	ENCODE	gene	152695769	152697402	.	-	.	ID=gene2669;Name=U52112.4-009;name2=ARHGAP4
chrX	ENCODE	exon	152695769	152695836	.	-	.	Parent=gene2669
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2669
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2669
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2669
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2669
chrX	ENCODE	exon	152697223	152697402	.	-	.	Parent=gene2669
###
chrX	ENCODE	gene	152695809	152697172	.	-	.	ID=gene2670;Name=U52112.4-008;name2=ARHGAP4
chrX	ENCODE	exon	152695809	152695836	.	-	.	Parent=gene2670
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2670
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2670
chrX	ENCODE	exon	152696472	152696705	.	-	.	Parent=gene2670
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2670
chrX	ENCODE	exon	152697001	152697172	.	-	.	Parent=gene2670
###
chrX	ENCODE	gene	152696042	152699086	.	-	.	ID=gene2671;Name=U52112.4-010;name2=ARHGAP4
chrX	ENCODE	exon	152696042	152696225	.	-	.	Parent=gene2671
chrX	ENCODE	CDS	152696042	152696225	.	-	0	Parent=gene2671
chrX	ENCODE	exon	152696313	152696386	.	-	.	Parent=gene2671
chrX	ENCODE	CDS	152696313	152696386	.	-	2	Parent=gene2671
chrX	ENCODE	exon	152696472	152696705	.	-	.	Parent=gene2671
chrX	ENCODE	CDS	152696472	152696705	.	-	2	Parent=gene2671
chrX	ENCODE	exon	152696807	152696912	.	-	.	Parent=gene2671
chrX	ENCODE	CDS	152696807	152696912	.	-	0	Parent=gene2671
chrX	ENCODE	exon	152697001	152697135	.	-	.	Parent=gene2671
chrX	ENCODE	CDS	152697001	152697135	.	-	0	Parent=gene2671
chrX	ENCODE	exon	152697430	152697490	.	-	.	Parent=gene2671
chrX	ENCODE	CDS	152697430	152697490	.	-	1	Parent=gene2671
chrX	ENCODE	exon	152699001	152699086	.	-	.	Parent=gene2671
chrX	ENCODE	CDS	152699001	152699086	.	-	0	Parent=gene2671
###
chrX	ENCODE	gene	152696120	152696820	.	-	.	ID=gene2672;Name=U52112.4-007;name2=ARHGAP4
chrX	ENCODE	exon	152696120	152696225	.	-	.	Parent=gene2672
chrX	ENCODE	exon	152696313	152696820	.	-	.	Parent=gene2672
###
chrX	ENCODE	gene	152699511	152721299	.	-	.	ID=gene2673;Name=U52112.4-022;name2=ARHGAP4
chrX	ENCODE	exon	152699511	152699901	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152705133	152705354	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152706927	152707109	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152718371	152718415	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152720243	152720301	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2673
chrX	ENCODE	exon	152721184	152721299	.	-	.	Parent=gene2673
###
chrX	ENCODE	gene	152699529	152706932	.	-	.	ID=gene2674;Name=U52112.4-005;name2=ARHGAP4
chrX	ENCODE	exon	152699529	152699603	.	-	.	Parent=gene2674
chrX	ENCODE	CDS	152699529	152699603	.	-	0	Parent=gene2674
chrX	ENCODE	exon	152699710	152699817	.	-	.	Parent=gene2674
chrX	ENCODE	CDS	152699710	152699817	.	-	0	Parent=gene2674
chrX	ENCODE	exon	152700079	152700180	.	-	.	Parent=gene2674
chrX	ENCODE	CDS	152700079	152700180	.	-	0	Parent=gene2674
chrX	ENCODE	exon	152705133	152705354	.	-	.	Parent=gene2674
chrX	ENCODE	CDS	152705133	152705354	.	-	0	Parent=gene2674
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2674
chrX	ENCODE	CDS	152705456	152705584	.	-	0	Parent=gene2674
chrX	ENCODE	exon	152706927	152706932	.	-	.	Parent=gene2674
chrX	ENCODE	CDS	152706927	152706932	.	-	0	Parent=gene2674
###
chrX	ENCODE	gene	152699825	152700554	.	-	.	ID=gene2675;name2=ARHGAP4;Name=U52112.4-023
chrX	ENCODE	exon	152699825	152699901	.	-	.	Parent=gene2675
chrX	ENCODE	exon	152700079	152700554	.	-	.	Parent=gene2675
###
chrX	ENCODE	gene	152705143	152713058	.	-	.	ID=gene2676;Name=U52112.4-015;name2=ARHGAP4
chrX	ENCODE	exon	152705143	152705354	.	-	.	Parent=gene2676
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2676
chrX	ENCODE	exon	152706927	152707109	.	-	.	Parent=gene2676
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2676
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2676
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2676
chrX	ENCODE	exon	152712891	152713058	.	-	.	Parent=gene2676
###
chrX	ENCODE	gene	152705241	152707704	.	-	.	ID=gene2677;Name=U52112.4-020;name2=ARHGAP4
chrX	ENCODE	exon	152705241	152705354	.	-	.	Parent=gene2677
chrX	ENCODE	CDS	152705241	152705354	.	-	2	Parent=gene2677
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2677
chrX	ENCODE	CDS	152705456	152705584	.	-	2	Parent=gene2677
chrX	ENCODE	exon	152705868	152705987	.	-	.	Parent=gene2677
chrX	ENCODE	CDS	152705868	152705987	.	-	2	Parent=gene2677
chrX	ENCODE	exon	152706927	152707109	.	-	.	Parent=gene2677
chrX	ENCODE	CDS	152706927	152707109	.	-	2	Parent=gene2677
chrX	ENCODE	exon	152707665	152707704	.	-	.	Parent=gene2677
chrX	ENCODE	CDS	152707665	152707704	.	-	0	Parent=gene2677
###
chrX	ENCODE	gene	152705263	152708548	.	-	.	ID=gene2678;Name=U52112.4-004;name2=ARHGAP4
chrX	ENCODE	exon	152705263	152705354	.	-	.	Parent=gene2678
chrX	ENCODE	exon	152705456	152705584	.	-	.	Parent=gene2678
chrX	ENCODE	exon	152706927	152707109	.	-	.	Parent=gene2678
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2678
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2678
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2678
chrX	ENCODE	exon	152708424	152708548	.	-	.	Parent=gene2678
###
chrX	ENCODE	gene	152706713	152707700	.	-	.	ID=gene2679;name2=ARHGAP4;Name=U52112.4-021
chrX	ENCODE	exon	152706713	152707109	.	-	.	Parent=gene2679
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2679
chrX	ENCODE	exon	152707665	152707700	.	-	.	Parent=gene2679
###
chrX	ENCODE	gene	152707009	152714720	.	-	.	ID=gene2680;Name=U52112.4-017;name2=ARHGAP4
chrX	ENCODE	exon	152707009	152707109	.	-	.	Parent=gene2680
chrX	ENCODE	CDS	152707009	152707109	.	-	0	Parent=gene2680
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2680
chrX	ENCODE	CDS	152707397	152707459	.	-	0	Parent=gene2680
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2680
chrX	ENCODE	CDS	152707665	152707827	.	-	1	Parent=gene2680
chrX	ENCODE	CDS	152707905	152708107	.	-	0	Parent=gene2680
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2680
chrX	ENCODE	exon	152714628	152714720	.	-	.	Parent=gene2680
###
chrX	ENCODE	gene	152707016	152713161	.	-	.	ID=gene2681;Name=U52112.4-019;name2=ARHGAP4
chrX	ENCODE	exon	152707016	152707109	.	-	.	Parent=gene2681
chrX	ENCODE	CDS	152707016	152707109	.	-	0	Parent=gene2681
chrX	ENCODE	exon	152707397	152707459	.	-	.	Parent=gene2681
chrX	ENCODE	CDS	152707397	152707459	.	-	0	Parent=gene2681
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2681
chrX	ENCODE	CDS	152707665	152707827	.	-	1	Parent=gene2681
chrX	ENCODE	CDS	152707905	152708107	.	-	0	Parent=gene2681
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2681
chrX	ENCODE	exon	152713117	152713161	.	-	.	Parent=gene2681
###
chrX	ENCODE	gene	152707040	152714655	.	-	.	ID=gene2682;Name=U52112.4-018;name2=ARHGAP4
chrX	ENCODE	exon	152707040	152707109	.	-	.	Parent=gene2682
chrX	ENCODE	exon	152707397	152707523	.	-	.	Parent=gene2682
chrX	ENCODE	exon	152707665	152707827	.	-	.	Parent=gene2682
chrX	ENCODE	exon	152707905	152708109	.	-	.	Parent=gene2682
chrX	ENCODE	exon	152714628	152714655	.	-	.	Parent=gene2682
###
chrX	ENCODE	gene	152715542	152721523	.	-	.	ID=gene2683;name2=ARD1;Name=U52112.1-001
chrX	ENCODE	exon	152715542	152716523	.	-	.	Parent=gene2683
chrX	ENCODE	CDS	152716287	152716523	.	-	0	Parent=gene2683
chrX	ENCODE	exon	152717063	152717147	.	-	.	Parent=gene2683
chrX	ENCODE	CDS	152717063	152717147	.	-	1	Parent=gene2683
chrX	ENCODE	exon	152718371	152718415	.	-	.	Parent=gene2683
chrX	ENCODE	CDS	152718371	152718415	.	-	1	Parent=gene2683
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2683
chrX	ENCODE	CDS	152718616	152718731	.	-	0	Parent=gene2683
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2683
chrX	ENCODE	CDS	152718839	152718884	.	-	1	Parent=gene2683
chrX	ENCODE	exon	152720243	152720301	.	-	.	Parent=gene2683
chrX	ENCODE	CDS	152720243	152720301	.	-	0	Parent=gene2683
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2683
chrX	ENCODE	CDS	152720677	152720775	.	-	0	Parent=gene2683
chrX	ENCODE	CDS	152721184	152721204	.	-	0	Parent=gene2683
chrX	ENCODE	exon	152721184	152721523	.	-	.	Parent=gene2683
###
chrX	ENCODE	gene	152716127	152717740	.	-	.	ID=gene2684;name2=ARD1;Name=U52112.1-004
chrX	ENCODE	exon	152716127	152716523	.	-	.	Parent=gene2684
chrX	ENCODE	exon	152717063	152717740	.	-	.	Parent=gene2684
###
chrX	ENCODE	gene	152716214	152721341	.	-	.	ID=gene2685;Name=U52112.1-012;name2=ARD1
chrX	ENCODE	exon	152716214	152716607	.	-	.	Parent=gene2685
chrX	ENCODE	CDS	152716569	152716607	.	-	0	Parent=gene2685
chrX	ENCODE	exon	152717063	152717147	.	-	.	Parent=gene2685
chrX	ENCODE	CDS	152717063	152717147	.	-	1	Parent=gene2685
chrX	ENCODE	exon	152718371	152718415	.	-	.	Parent=gene2685
chrX	ENCODE	CDS	152718371	152718415	.	-	1	Parent=gene2685
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2685
chrX	ENCODE	CDS	152718616	152718731	.	-	0	Parent=gene2685
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2685
chrX	ENCODE	CDS	152718839	152718884	.	-	1	Parent=gene2685
chrX	ENCODE	exon	152720243	152720301	.	-	.	Parent=gene2685
chrX	ENCODE	CDS	152720243	152720301	.	-	0	Parent=gene2685
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2685
chrX	ENCODE	CDS	152720677	152720775	.	-	0	Parent=gene2685
chrX	ENCODE	CDS	152721184	152721204	.	-	0	Parent=gene2685
chrX	ENCODE	exon	152721184	152721341	.	-	.	Parent=gene2685
###
chrX	ENCODE	gene	152716221	152721258	.	-	.	ID=gene2686;Name=U52112.1-015;name2=ARD1
chrX	ENCODE	exon	152716221	152716603	.	-	.	Parent=gene2686
chrX	ENCODE	CDS	152716520	152716603	.	-	0	Parent=gene2686
chrX	ENCODE	exon	152717063	152717147	.	-	.	Parent=gene2686
chrX	ENCODE	CDS	152717063	152717147	.	-	1	Parent=gene2686
chrX	ENCODE	exon	152718371	152718415	.	-	.	Parent=gene2686
chrX	ENCODE	CDS	152718371	152718415	.	-	1	Parent=gene2686
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2686
chrX	ENCODE	CDS	152718616	152718731	.	-	0	Parent=gene2686
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2686
chrX	ENCODE	CDS	152718839	152718884	.	-	1	Parent=gene2686
chrX	ENCODE	exon	152720243	152720301	.	-	.	Parent=gene2686
chrX	ENCODE	CDS	152720243	152720301	.	-	0	Parent=gene2686
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2686
chrX	ENCODE	CDS	152720677	152720775	.	-	0	Parent=gene2686
chrX	ENCODE	CDS	152721184	152721204	.	-	0	Parent=gene2686
chrX	ENCODE	exon	152721184	152721258	.	-	.	Parent=gene2686
###
chrX	ENCODE	gene	152716224	152721315	.	-	.	ID=gene2687;Name=U52112.1-002;name2=ARD1
chrX	ENCODE	exon	152716224	152716523	.	-	.	Parent=gene2687
chrX	ENCODE	CDS	152716287	152716523	.	-	0	Parent=gene2687
chrX	ENCODE	exon	152717063	152717147	.	-	.	Parent=gene2687
chrX	ENCODE	CDS	152717063	152717147	.	-	1	Parent=gene2687
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2687
chrX	ENCODE	CDS	152718616	152718731	.	-	0	Parent=gene2687
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2687
chrX	ENCODE	CDS	152718839	152718884	.	-	1	Parent=gene2687
chrX	ENCODE	exon	152720243	152720301	.	-	.	Parent=gene2687
chrX	ENCODE	CDS	152720243	152720301	.	-	0	Parent=gene2687
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2687
chrX	ENCODE	CDS	152720677	152720775	.	-	0	Parent=gene2687
chrX	ENCODE	CDS	152721184	152721204	.	-	0	Parent=gene2687
chrX	ENCODE	exon	152721184	152721315	.	-	.	Parent=gene2687
###
chrX	ENCODE	gene	152716226	152721315	.	-	.	ID=gene2688;Name=U52112.1-003;name2=ARD1
chrX	ENCODE	exon	152716226	152716523	.	-	.	Parent=gene2688
chrX	ENCODE	exon	152717063	152717147	.	-	.	Parent=gene2688
chrX	ENCODE	exon	152718371	152718731	.	-	.	Parent=gene2688
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2688
chrX	ENCODE	exon	152720243	152720301	.	-	.	Parent=gene2688
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2688
chrX	ENCODE	exon	152721184	152721315	.	-	.	Parent=gene2688
###
chrX	ENCODE	gene	152716341	152719282	.	-	.	ID=gene2689;Name=U52112.1-010;name2=ARD1
chrX	ENCODE	exon	152716341	152716523	.	-	.	Parent=gene2689
chrX	ENCODE	exon	152717063	152717147	.	-	.	Parent=gene2689
chrX	ENCODE	exon	152718371	152718415	.	-	.	Parent=gene2689
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2689
chrX	ENCODE	exon	152718839	152719282	.	-	.	Parent=gene2689
###
chrX	ENCODE	gene	152716376	152721085	.	-	.	ID=gene2690;Name=U52112.1-006;name2=ARD1
chrX	ENCODE	exon	152716376	152716523	.	-	.	Parent=gene2690
chrX	ENCODE	exon	152717063	152717147	.	-	.	Parent=gene2690
chrX	ENCODE	exon	152718371	152718415	.	-	.	Parent=gene2690
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2690
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2690
chrX	ENCODE	exon	152720243	152720301	.	-	.	Parent=gene2690
chrX	ENCODE	exon	152720677	152721085	.	-	.	Parent=gene2690
###
chrX	ENCODE	gene	152716505	152721315	.	-	.	ID=gene2691;Name=U52112.1-014;name2=ARD1
chrX	ENCODE	exon	152716505	152716523	.	-	.	Parent=gene2691
chrX	ENCODE	CDS	152716505	152716523	.	-	0	Parent=gene2691
chrX	ENCODE	exon	152717063	152717147	.	-	.	Parent=gene2691
chrX	ENCODE	CDS	152717063	152717147	.	-	1	Parent=gene2691
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2691
chrX	ENCODE	CDS	152718616	152718731	.	-	0	Parent=gene2691
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2691
chrX	ENCODE	CDS	152718839	152718884	.	-	1	Parent=gene2691
chrX	ENCODE	exon	152720261	152720301	.	-	.	Parent=gene2691
chrX	ENCODE	CDS	152720261	152720301	.	-	0	Parent=gene2691
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2691
chrX	ENCODE	CDS	152720677	152720775	.	-	0	Parent=gene2691
chrX	ENCODE	CDS	152721184	152721204	.	-	0	Parent=gene2691
chrX	ENCODE	exon	152721184	152721315	.	-	.	Parent=gene2691
###
chrX	ENCODE	gene	152716593	152718558	.	-	.	ID=gene2692;Name=U52112.1-009;name2=ARD1
chrX	ENCODE	exon	152716593	152717147	.	-	.	Parent=gene2692
chrX	ENCODE	exon	152718371	152718558	.	-	.	Parent=gene2692
###
chrX	ENCODE	gene	152717079	152721366	.	-	.	ID=gene2693;name2=ARD1;Name=U52112.1-013
chrX	ENCODE	exon	152717079	152717147	.	-	.	Parent=gene2693
chrX	ENCODE	CDS	152717079	152717147	.	-	1	Parent=gene2693
chrX	ENCODE	exon	152718371	152718415	.	-	.	Parent=gene2693
chrX	ENCODE	CDS	152718371	152718415	.	-	1	Parent=gene2693
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2693
chrX	ENCODE	CDS	152718616	152718731	.	-	0	Parent=gene2693
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2693
chrX	ENCODE	CDS	152718839	152718884	.	-	1	Parent=gene2693
chrX	ENCODE	exon	152720261	152720301	.	-	.	Parent=gene2693
chrX	ENCODE	CDS	152720261	152720301	.	-	0	Parent=gene2693
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2693
chrX	ENCODE	CDS	152720677	152720775	.	-	0	Parent=gene2693
chrX	ENCODE	CDS	152721184	152721204	.	-	0	Parent=gene2693
chrX	ENCODE	exon	152721184	152721366	.	-	.	Parent=gene2693
###
chrX	ENCODE	gene	152718071	152721380	.	-	.	ID=gene2694;Name=U52112.1-007;name2=ARD1
chrX	ENCODE	exon	152718071	152718731	.	-	.	Parent=gene2694
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2694
chrX	ENCODE	exon	152720243	152720301	.	-	.	Parent=gene2694
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2694
chrX	ENCODE	exon	152721184	152721380	.	-	.	Parent=gene2694
###
chrX	ENCODE	gene	152718254	152721315	.	-	.	ID=gene2695;Name=U52112.1-017;name2=ARD1
chrX	ENCODE	exon	152718254	152718281	.	-	.	Parent=gene2695
chrX	ENCODE	CDS	152718254	152718281	.	-	1	Parent=gene2695
chrX	ENCODE	exon	152718371	152718415	.	-	.	Parent=gene2695
chrX	ENCODE	CDS	152718371	152718415	.	-	1	Parent=gene2695
chrX	ENCODE	exon	152718616	152718731	.	-	.	Parent=gene2695
chrX	ENCODE	CDS	152718616	152718731	.	-	0	Parent=gene2695
chrX	ENCODE	exon	152718839	152718884	.	-	.	Parent=gene2695
chrX	ENCODE	CDS	152718839	152718884	.	-	1	Parent=gene2695
chrX	ENCODE	exon	152720243	152720301	.	-	.	Parent=gene2695
chrX	ENCODE	CDS	152720243	152720301	.	-	0	Parent=gene2695
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2695
chrX	ENCODE	CDS	152720677	152720775	.	-	0	Parent=gene2695
chrX	ENCODE	CDS	152721184	152721204	.	-	0	Parent=gene2695
chrX	ENCODE	exon	152721184	152721315	.	-	.	Parent=gene2695
###
chrX	ENCODE	gene	152718367	152719282	.	-	.	ID=gene2696;Name=U52112.1-005;name2=ARD1
chrX	ENCODE	exon	152718367	152718731	.	-	.	Parent=gene2696
chrX	ENCODE	exon	152718839	152719282	.	-	.	Parent=gene2696
###
chrX	ENCODE	gene	152719960	152721315	.	-	.	ID=gene2697;Name=U52112.1-016;name2=ARD1
chrX	ENCODE	exon	152719960	152720301	.	-	.	Parent=gene2697
chrX	ENCODE	exon	152720677	152720775	.	-	.	Parent=gene2697
chrX	ENCODE	exon	152721184	152721315	.	-	.	Parent=gene2697
###
chrX	ENCODE	gene	152720330	152721306	.	-	.	ID=gene2698;Name=U52112.1-008;name2=ARD1
chrX	ENCODE	exon	152720330	152720775	.	-	.	Parent=gene2698
chrX	ENCODE	exon	152721184	152721306	.	-	.	Parent=gene2698
###
chrX	ENCODE	gene	152721563	152730990	.	-	.	ID=gene2699;Name=U52112.5-001;name2=RENBP
chrX	ENCODE	exon	152721563	152721704	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152721586	152721704	.	-	2	Parent=gene2699
chrX	ENCODE	exon	152721789	152721876	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152721789	152721876	.	-	0	Parent=gene2699
chrX	ENCODE	exon	152726402	152726533	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152726402	152726533	.	-	0	Parent=gene2699
chrX	ENCODE	exon	152727778	152727953	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152727778	152727953	.	-	2	Parent=gene2699
chrX	ENCODE	exon	152728250	152728331	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152728250	152728331	.	-	0	Parent=gene2699
chrX	ENCODE	exon	152729154	152729378	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152729154	152729378	.	-	0	Parent=gene2699
chrX	ENCODE	exon	152729845	152730017	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152729845	152730017	.	-	2	Parent=gene2699
chrX	ENCODE	exon	152730194	152730269	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152730194	152730269	.	-	0	Parent=gene2699
chrX	ENCODE	exon	152730379	152730454	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152730379	152730454	.	-	1	Parent=gene2699
chrX	ENCODE	exon	152730608	152730717	.	-	.	Parent=gene2699
chrX	ENCODE	CDS	152730608	152730717	.	-	0	Parent=gene2699
chrX	ENCODE	CDS	152730883	152730909	.	-	0	Parent=gene2699
chrX	ENCODE	exon	152730883	152730990	.	-	.	Parent=gene2699
###
chrX	ENCODE	gene	152721575	152728269	.	-	.	ID=gene2700;name2=RENBP;Name=U52112.5-002
chrX	ENCODE	exon	152721575	152721704	.	-	.	Parent=gene2700
chrX	ENCODE	exon	152721789	152721876	.	-	.	Parent=gene2700
chrX	ENCODE	exon	152722304	152722405	.	-	.	Parent=gene2700
chrX	ENCODE	exon	152723392	152723488	.	-	.	Parent=gene2700
chrX	ENCODE	exon	152726402	152726533	.	-	.	Parent=gene2700
chrX	ENCODE	exon	152727778	152727953	.	-	.	Parent=gene2700
chrX	ENCODE	exon	152728250	152728269	.	-	.	Parent=gene2700
###
chrX	ENCODE	gene	152721583	152730986	.	-	.	ID=gene2701;Name=U52112.5-004;name2=RENBP
chrX	ENCODE	exon	152721583	152721704	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152721586	152721704	.	-	2	Parent=gene2701
chrX	ENCODE	exon	152721789	152721876	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152721789	152721876	.	-	0	Parent=gene2701
chrX	ENCODE	exon	152726402	152726533	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152726402	152726533	.	-	0	Parent=gene2701
chrX	ENCODE	exon	152727778	152727953	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152727778	152727953	.	-	2	Parent=gene2701
chrX	ENCODE	exon	152728250	152728331	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152728250	152728331	.	-	0	Parent=gene2701
chrX	ENCODE	exon	152729154	152729378	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152729154	152729378	.	-	0	Parent=gene2701
chrX	ENCODE	exon	152729845	152730017	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152729845	152730017	.	-	2	Parent=gene2701
chrX	ENCODE	exon	152730194	152730269	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152730194	152730269	.	-	0	Parent=gene2701
chrX	ENCODE	exon	152730421	152730454	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152730421	152730454	.	-	1	Parent=gene2701
chrX	ENCODE	exon	152730608	152730717	.	-	.	Parent=gene2701
chrX	ENCODE	CDS	152730608	152730717	.	-	0	Parent=gene2701
chrX	ENCODE	CDS	152730883	152730909	.	-	0	Parent=gene2701
chrX	ENCODE	exon	152730883	152730986	.	-	.	Parent=gene2701
###
chrX	ENCODE	gene	152721586	152730925	.	-	.	ID=gene2702;Name=U52112.5-009;name2=RENBP
chrX	ENCODE	exon	152721586	152721704	.	-	.	Parent=gene2702
chrX	ENCODE	CDS	152721586	152721704	.	-	2	Parent=gene2702
chrX	ENCODE	exon	152721789	152721876	.	-	.	Parent=gene2702
chrX	ENCODE	CDS	152721789	152721876	.	-	0	Parent=gene2702
chrX	ENCODE	exon	152726402	152726533	.	-	.	Parent=gene2702
chrX	ENCODE	CDS	152726402	152726533	.	-	0	Parent=gene2702
chrX	ENCODE	exon	152727778	152727953	.	-	.	Parent=gene2702
chrX	ENCODE	CDS	152727778	152727953	.	-	2	Parent=gene2702
chrX	ENCODE	exon	152728250	152728331	.	-	.	Parent=gene2702
chrX	ENCODE	CDS	152728250	152728331	.	-	0	Parent=gene2702
chrX	ENCODE	exon	152729154	152729378	.	-	.	Parent=gene2702
chrX	ENCODE	CDS	152729154	152729378	.	-	0	Parent=gene2702
chrX	ENCODE	exon	152729845	152730017	.	-	.	Parent=gene2702
chrX	ENCODE	CDS	152729845	152730017	.	-	2	Parent=gene2702
chrX	ENCODE	exon	152730194	152730269	.	-	.	Parent=gene2702
chrX	ENCODE	CDS	152730194	152730269	.	-	0	Parent=gene2702
chrX	ENCODE	exon	152730379	152730454	.	-	.	Parent=gene2702
chrX	ENCODE	CDS	152730379	152730454	.	-	1	Parent=gene2702
chrX	ENCODE	CDS	152730608	152730714	.	-	0	Parent=gene2702
chrX	ENCODE	exon	152730608	152730717	.	-	.	Parent=gene2702
chrX	ENCODE	exon	152730879	152730925	.	-	.	Parent=gene2702
###
chrX	ENCODE	gene	152721633	152726515	.	-	.	ID=gene2703;Name=U52112.5-003;name2=RENBP
chrX	ENCODE	exon	152721633	152721704	.	-	.	Parent=gene2703
chrX	ENCODE	CDS	152721633	152721704	.	-	2	Parent=gene2703
chrX	ENCODE	exon	152721789	152721876	.	-	.	Parent=gene2703
chrX	ENCODE	CDS	152721789	152721876	.	-	0	Parent=gene2703
chrX	ENCODE	exon	152722304	152722405	.	-	.	Parent=gene2703
chrX	ENCODE	CDS	152722304	152722405	.	-	0	Parent=gene2703
chrX	ENCODE	exon	152726402	152726515	.	-	.	Parent=gene2703
chrX	ENCODE	CDS	152726402	152726515	.	-	0	Parent=gene2703
###
chrX	ENCODE	gene	152722299	152730242	.	-	.	ID=gene2704;Name=U52112.5-005;name2=RENBP
chrX	ENCODE	exon	152722299	152722405	.	-	.	Parent=gene2704
chrX	ENCODE	exon	152726402	152726533	.	-	.	Parent=gene2704
chrX	ENCODE	exon	152727778	152727953	.	-	.	Parent=gene2704
chrX	ENCODE	exon	152729154	152729333	.	-	.	Parent=gene2704
chrX	ENCODE	exon	152729845	152730017	.	-	.	Parent=gene2704
chrX	ENCODE	exon	152730194	152730242	.	-	.	Parent=gene2704
###
chrX	ENCODE	gene	152728545	152729931	.	-	.	ID=gene2705;Name=U52112.5-007;name2=RENBP
chrX	ENCODE	exon	152728545	152728841	.	-	.	Parent=gene2705
chrX	ENCODE	exon	152729154	152729378	.	-	.	Parent=gene2705
chrX	ENCODE	exon	152729845	152729931	.	-	.	Parent=gene2705
###
chrX	ENCODE	gene	152729154	152730910	.	-	.	ID=gene2706;Name=U52112.5-008;name2=RENBP
chrX	ENCODE	exon	152729154	152729378	.	-	.	Parent=gene2706
chrX	ENCODE	exon	152729845	152730017	.	-	.	Parent=gene2706
chrX	ENCODE	exon	152730194	152730269	.	-	.	Parent=gene2706
chrX	ENCODE	exon	152730608	152730717	.	-	.	Parent=gene2706
chrX	ENCODE	exon	152730883	152730910	.	-	.	Parent=gene2706
###
chrX	ENCODE	gene	152729357	152730531	.	-	.	ID=gene2707;Name=U52112.5-006;name2=RENBP
chrX	ENCODE	exon	152729357	152729378	.	-	.	Parent=gene2707
chrX	ENCODE	exon	152729845	152730017	.	-	.	Parent=gene2707
chrX	ENCODE	exon	152730194	152730269	.	-	.	Parent=gene2707
chrX	ENCODE	exon	152730379	152730531	.	-	.	Parent=gene2707
###
chrX	ENCODE	gene	152729913	152730942	.	-	.	ID=gene2708;name2=RENBP;Name=U52112.5-010
chrX	ENCODE	exon	152729913	152730017	.	-	.	Parent=gene2708
chrX	ENCODE	exon	152730194	152730269	.	-	.	Parent=gene2708
chrX	ENCODE	exon	152730379	152730717	.	-	.	Parent=gene2708
chrX	ENCODE	exon	152730883	152730942	.	-	.	Parent=gene2708
###
chrX	ENCODE	gene	152733851	152758105	.	-	.	ID=gene2709;name2=HCFC1;Name=U52112.6-001
chrX	ENCODE	exon	152733851	152735684	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152735645	152735684	.	-	1	Parent=gene2709
chrX	ENCODE	exon	152735851	152735914	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152735851	152735914	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152736541	152736841	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152736541	152736841	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152737111	152737296	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152737111	152737296	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152737648	152737785	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152737648	152737785	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152737887	152738005	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152737887	152738005	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152738139	152738456	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152738139	152738456	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152738812	152739256	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152738812	152739256	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152739905	152740068	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152739905	152740068	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152740364	152741840	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152740364	152741840	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152742489	152742709	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152742489	152742709	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152742923	152743061	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152742923	152743061	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152743216	152743358	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152743216	152743358	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152743612	152743831	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152743612	152743831	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152744080	152744184	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152744080	152744184	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152744323	152744547	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152744323	152744547	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152744867	152745064	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152744867	152745064	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152745629	152745789	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152745629	152745789	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152746100	152746459	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152746100	152746459	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152746533	152746712	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152746533	152746712	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152747840	152747946	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152747840	152747946	.	-	1	Parent=gene2709
chrX	ENCODE	exon	152748520	152748604	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152748520	152748604	.	-	2	Parent=gene2709
chrX	ENCODE	exon	152749523	152749731	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152749523	152749731	.	-	1	Parent=gene2709
chrX	ENCODE	exon	152750422	152750582	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152750422	152750582	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152750876	152751024	.	-	.	Parent=gene2709
chrX	ENCODE	CDS	152750876	152751024	.	-	2	Parent=gene2709
chrX	ENCODE	CDS	152756946	152757138	.	-	0	Parent=gene2709
chrX	ENCODE	exon	152756946	152758105	.	-	.	Parent=gene2709
###
chrX	ENCODE	gene	152733855	152740419	.	-	.	ID=gene2710;Name=U52112.6-004;name2=HCFC1
chrX	ENCODE	exon	152733855	152735684	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152735645	152735684	.	-	0	Parent=gene2710
chrX	ENCODE	exon	152735851	152735914	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152735851	152735914	.	-	1	Parent=gene2710
chrX	ENCODE	exon	152736541	152736841	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152736541	152736841	.	-	2	Parent=gene2710
chrX	ENCODE	exon	152737111	152737296	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152737111	152737296	.	-	2	Parent=gene2710
chrX	ENCODE	exon	152737648	152737785	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152737648	152737785	.	-	2	Parent=gene2710
chrX	ENCODE	exon	152737887	152738005	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152737887	152738005	.	-	1	Parent=gene2710
chrX	ENCODE	exon	152738139	152738459	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152738139	152738459	.	-	1	Parent=gene2710
chrX	ENCODE	exon	152738812	152739256	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152738812	152739256	.	-	2	Parent=gene2710
chrX	ENCODE	exon	152739905	152740068	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152739905	152740068	.	-	1	Parent=gene2710
chrX	ENCODE	exon	152740364	152740419	.	-	.	Parent=gene2710
chrX	ENCODE	CDS	152740364	152740419	.	-	0	Parent=gene2710
###
chrX	ENCODE	gene	152733857	152757482	.	-	.	ID=gene2711;Name=U52112.6-003;name2=HCFC1
chrX	ENCODE	exon	152733857	152735684	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152735645	152735684	.	-	1	Parent=gene2711
chrX	ENCODE	exon	152735851	152735914	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152735851	152735914	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152736541	152736841	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152736541	152736841	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152737111	152737296	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152737111	152737296	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152737648	152737785	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152737648	152737785	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152737887	152738005	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152737887	152738005	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152738139	152738459	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152738139	152738459	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152738812	152739388	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152738812	152739388	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152739905	152740068	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152739905	152740068	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152740364	152741840	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152740364	152741840	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152742489	152742709	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152742489	152742709	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152742923	152743061	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152742923	152743061	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152743216	152743358	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152743216	152743358	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152743612	152743831	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152743612	152743831	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152744080	152744184	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152744080	152744184	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152744323	152744547	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152744323	152744547	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152744867	152745064	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152744867	152745064	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152745629	152745789	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152745629	152745789	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152746100	152746459	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152746100	152746459	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152746533	152746712	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152746533	152746712	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152747840	152747946	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152747840	152747946	.	-	1	Parent=gene2711
chrX	ENCODE	exon	152748520	152748604	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152748520	152748604	.	-	2	Parent=gene2711
chrX	ENCODE	exon	152749523	152749731	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152749523	152749731	.	-	1	Parent=gene2711
chrX	ENCODE	exon	152750422	152750582	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152750422	152750582	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152750876	152751024	.	-	.	Parent=gene2711
chrX	ENCODE	CDS	152750876	152751024	.	-	2	Parent=gene2711
chrX	ENCODE	CDS	152756946	152757138	.	-	0	Parent=gene2711
chrX	ENCODE	exon	152756946	152757482	.	-	.	Parent=gene2711
###
chrX	ENCODE	gene	152746307	152748565	.	-	.	ID=gene2712;Name=U52112.6-002;name2=HCFC1
chrX	ENCODE	exon	152746307	152746459	.	-	.	Parent=gene2712
chrX	ENCODE	exon	152746533	152746712	.	-	.	Parent=gene2712
chrX	ENCODE	exon	152748520	152748565	.	-	.	Parent=gene2712
###
chrX	ENCODE	gene	152758625	152769493	.	+	.	ID=gene2713;Name=U52112.11-001;name2=CXorf12
chrX	ENCODE	exon	152758625	152759158	.	+	.	Parent=gene2713
chrX	ENCODE	exon	152768148	152769493	.	+	.	Parent=gene2713
chrX	ENCODE	CDS	152768361	152769146	.	+	0	Parent=gene2713
###
chrX	ENCODE	gene	152759156	152768558	.	+	.	ID=gene2714;Name=U52112.11-003;name2=CXorf12
chrX	ENCODE	exon	152759156	152759184	.	+	.	Parent=gene2714
chrX	ENCODE	exon	152768148	152768558	.	+	.	Parent=gene2714
chrX	ENCODE	CDS	152768361	152768558	.	+	0	Parent=gene2714
###
chrX	ENCODE	gene	152766904	152768459	.	+	.	ID=gene2715;name2=CXorf12;Name=U52112.11-002
chrX	ENCODE	exon	152766904	152766921	.	+	.	Parent=gene2715
chrX	ENCODE	exon	152768148	152768459	.	+	.	Parent=gene2715
chrX	ENCODE	CDS	152768361	152768459	.	+	0	Parent=gene2715
###
chrX	ENCODE	gene	152796798	152806278	.	-	.	ID=gene2716;Name=U52112.3-012;name2=IRAK1
chrX	ENCODE	exon	152796798	152798215	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152798157	152798215	.	-	2	Parent=gene2716
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152798827	152798976	.	-	2	Parent=gene2716
chrX	ENCODE	exon	152799341	152799731	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152799341	152799731	.	-	0	Parent=gene2716
chrX	ENCODE	exon	152800340	152800576	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152800340	152800576	.	-	0	Parent=gene2716
chrX	ENCODE	exon	152802330	152802395	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152802330	152802395	.	-	0	Parent=gene2716
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152802735	152802942	.	-	1	Parent=gene2716
chrX	ENCODE	exon	152803247	152803365	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152803247	152803365	.	-	0	Parent=gene2716
chrX	ENCODE	exon	152804304	152804418	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152804304	152804418	.	-	1	Parent=gene2716
chrX	ENCODE	exon	152804589	152804653	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152804589	152804653	.	-	0	Parent=gene2716
chrX	ENCODE	exon	152804897	152805085	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152804897	152805085	.	-	0	Parent=gene2716
chrX	ENCODE	exon	152805273	152805376	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152805273	152805376	.	-	2	Parent=gene2716
chrX	ENCODE	exon	152805495	152805626	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152805495	152805626	.	-	2	Parent=gene2716
chrX	ENCODE	exon	152805729	152805896	.	-	.	Parent=gene2716
chrX	ENCODE	CDS	152805729	152805896	.	-	2	Parent=gene2716
chrX	ENCODE	CDS	152805975	152806110	.	-	0	Parent=gene2716
chrX	ENCODE	exon	152805975	152806278	.	-	.	Parent=gene2716
###
chrX	ENCODE	gene	152796804	152806174	.	-	.	ID=gene2717;Name=U52112.3-001;name2=IRAK1
chrX	ENCODE	exon	152796804	152798215	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152798157	152798215	.	-	2	Parent=gene2717
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152798827	152798976	.	-	2	Parent=gene2717
chrX	ENCODE	exon	152799341	152799731	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152799341	152799731	.	-	0	Parent=gene2717
chrX	ENCODE	exon	152802330	152802395	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152802330	152802395	.	-	0	Parent=gene2717
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152802735	152802942	.	-	1	Parent=gene2717
chrX	ENCODE	exon	152803247	152803365	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152803247	152803365	.	-	0	Parent=gene2717
chrX	ENCODE	exon	152804304	152804418	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152804304	152804418	.	-	1	Parent=gene2717
chrX	ENCODE	exon	152804589	152804653	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152804589	152804653	.	-	0	Parent=gene2717
chrX	ENCODE	exon	152804897	152805085	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152804897	152805085	.	-	0	Parent=gene2717
chrX	ENCODE	exon	152805273	152805376	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152805273	152805376	.	-	2	Parent=gene2717
chrX	ENCODE	exon	152805495	152805626	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152805495	152805626	.	-	2	Parent=gene2717
chrX	ENCODE	exon	152805729	152805896	.	-	.	Parent=gene2717
chrX	ENCODE	CDS	152805729	152805896	.	-	2	Parent=gene2717
chrX	ENCODE	CDS	152805975	152806110	.	-	0	Parent=gene2717
chrX	ENCODE	exon	152805975	152806174	.	-	.	Parent=gene2717
###
chrX	ENCODE	gene	152796805	152806188	.	-	.	ID=gene2718;Name=U52112.3-009;name2=IRAK1
chrX	ENCODE	exon	152796805	152798215	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152799341	152799641	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152800340	152800405	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152800452	152800576	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152802330	152802395	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152803247	152803365	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152804304	152804418	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152804589	152804653	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152804897	152805085	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152805273	152805376	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152805495	152805626	.	-	.	Parent=gene2718
chrX	ENCODE	exon	152805729	152806188	.	-	.	Parent=gene2718
###
chrX	ENCODE	gene	152796808	152804653	.	-	.	ID=gene2719;Name=U52112.3-007;name2=IRAK1
chrX	ENCODE	exon	152796808	152796975	.	-	.	Parent=gene2719
chrX	ENCODE	exon	152803298	152803365	.	-	.	Parent=gene2719
chrX	ENCODE	exon	152804304	152804418	.	-	.	Parent=gene2719
chrX	ENCODE	exon	152804589	152804653	.	-	.	Parent=gene2719
###
chrX	ENCODE	gene	152796818	152806098	.	-	.	ID=gene2720;Name=U52112.3-017;name2=IRAK1
chrX	ENCODE	exon	152796818	152797414	.	-	.	Parent=gene2720
chrX	ENCODE	CDS	152797238	152797414	.	-	0	Parent=gene2720
chrX	ENCODE	exon	152805273	152805376	.	-	.	Parent=gene2720
chrX	ENCODE	CDS	152805273	152805376	.	-	2	Parent=gene2720
chrX	ENCODE	exon	152805495	152805626	.	-	.	Parent=gene2720
chrX	ENCODE	CDS	152805495	152805626	.	-	2	Parent=gene2720
chrX	ENCODE	exon	152805729	152805896	.	-	.	Parent=gene2720
chrX	ENCODE	CDS	152805729	152805896	.	-	2	Parent=gene2720
chrX	ENCODE	exon	152805975	152806098	.	-	.	Parent=gene2720
chrX	ENCODE	CDS	152805975	152806098	.	-	0	Parent=gene2720
###
chrX	ENCODE	gene	152797020	152804945	.	-	.	ID=gene2721;name2=IRAK1;Name=U52112.3-019
chrX	ENCODE	exon	152797020	152797109	.	-	.	Parent=gene2721
chrX	ENCODE	exon	152802337	152802395	.	-	.	Parent=gene2721
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2721
chrX	ENCODE	exon	152803247	152803365	.	-	.	Parent=gene2721
chrX	ENCODE	exon	152804304	152804418	.	-	.	Parent=gene2721
chrX	ENCODE	exon	152804589	152804653	.	-	.	Parent=gene2721
chrX	ENCODE	exon	152804897	152804945	.	-	.	Parent=gene2721
###
chrX	ENCODE	gene	152797138	152806098	.	-	.	ID=gene2722;Name=U52112.3-015;name2=IRAK1
chrX	ENCODE	exon	152797138	152797429	.	-	.	Parent=gene2722
chrX	ENCODE	exon	152805291	152805376	.	-	.	Parent=gene2722
chrX	ENCODE	exon	152805495	152805626	.	-	.	Parent=gene2722
chrX	ENCODE	exon	152805729	152805896	.	-	.	Parent=gene2722
chrX	ENCODE	exon	152805975	152806098	.	-	.	Parent=gene2722
###
chrX	ENCODE	gene	152797861	152802371	.	-	.	ID=gene2723;Name=U52112.3-016;name2=IRAK1
chrX	ENCODE	exon	152797861	152798215	.	-	.	Parent=gene2723
chrX	ENCODE	CDS	152798006	152798215	.	-	0	Parent=gene2723
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2723
chrX	ENCODE	CDS	152798827	152798976	.	-	0	Parent=gene2723
chrX	ENCODE	exon	152800340	152800576	.	-	.	Parent=gene2723
chrX	ENCODE	CDS	152800340	152800576	.	-	0	Parent=gene2723
chrX	ENCODE	exon	152802330	152802371	.	-	.	Parent=gene2723
chrX	ENCODE	CDS	152802330	152802371	.	-	0	Parent=gene2723
###
chrX	ENCODE	gene	152797963	152806157	.	-	.	ID=gene2724;Name=U52112.3-014;name2=IRAK1
chrX	ENCODE	exon	152797963	152798215	.	-	.	Parent=gene2724
chrX	ENCODE	exon	152798827	152798964	.	-	.	Parent=gene2724
chrX	ENCODE	exon	152805636	152805896	.	-	.	Parent=gene2724
chrX	ENCODE	exon	152805975	152806157	.	-	.	Parent=gene2724
###
chrX	ENCODE	gene	152797986	152806195	.	-	.	ID=gene2725;Name=U52112.3-004;name2=IRAK1
chrX	ENCODE	exon	152797986	152798215	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152799341	152799731	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152800340	152800576	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152802330	152802395	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152803247	152803365	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152804589	152804653	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152804897	152805085	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152805273	152805376	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152805495	152805626	.	-	.	Parent=gene2725
chrX	ENCODE	exon	152805729	152806195	.	-	.	Parent=gene2725
###
chrX	ENCODE	gene	152798029	152800544	.	-	.	ID=gene2726;Name=U52112.3-010;name2=IRAK1
chrX	ENCODE	exon	152798029	152798215	.	-	.	Parent=gene2726
chrX	ENCODE	CDS	152798157	152798215	.	-	1	Parent=gene2726
chrX	ENCODE	exon	152799341	152799731	.	-	.	Parent=gene2726
chrX	ENCODE	CDS	152799341	152799731	.	-	2	Parent=gene2726
chrX	ENCODE	exon	152800340	152800544	.	-	.	Parent=gene2726
chrX	ENCODE	CDS	152800340	152800544	.	-	0	Parent=gene2726
###
chrX	ENCODE	gene	152798056	152802386	.	-	.	ID=gene2727;name2=IRAK1;Name=U52112.3-013
chrX	ENCODE	exon	152798056	152798215	.	-	.	Parent=gene2727
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2727
chrX	ENCODE	exon	152799341	152799731	.	-	.	Parent=gene2727
chrX	ENCODE	exon	152800340	152800406	.	-	.	Parent=gene2727
chrX	ENCODE	exon	152800452	152800576	.	-	.	Parent=gene2727
chrX	ENCODE	exon	152802330	152802386	.	-	.	Parent=gene2727
###
chrX	ENCODE	gene	152798056	152802858	.	-	.	ID=gene2728;Name=U52112.3-011;name2=IRAK1
chrX	ENCODE	exon	152798056	152798215	.	-	.	Parent=gene2728
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2728
chrX	ENCODE	exon	152799341	152799731	.	-	.	Parent=gene2728
chrX	ENCODE	exon	152800340	152800399	.	-	.	Parent=gene2728
chrX	ENCODE	exon	152800445	152800576	.	-	.	Parent=gene2728
chrX	ENCODE	exon	152802330	152802395	.	-	.	Parent=gene2728
chrX	ENCODE	exon	152802735	152802858	.	-	.	Parent=gene2728
###
chrX	ENCODE	gene	152798125	152803292	.	-	.	ID=gene2729;Name=U52112.3-003;name2=IRAK1
chrX	ENCODE	exon	152798125	152798215	.	-	.	Parent=gene2729
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2729
chrX	ENCODE	exon	152799341	152799641	.	-	.	Parent=gene2729
chrX	ENCODE	exon	152802330	152802395	.	-	.	Parent=gene2729
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2729
chrX	ENCODE	exon	152803247	152803292	.	-	.	Parent=gene2729
###
chrX	ENCODE	gene	152798135	152803333	.	-	.	ID=gene2730;name2=IRAK1;Name=U52112.3-008
chrX	ENCODE	exon	152798135	152798215	.	-	.	Parent=gene2730
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2730
chrX	ENCODE	exon	152799341	152799731	.	-	.	Parent=gene2730
chrX	ENCODE	exon	152800340	152800414	.	-	.	Parent=gene2730
chrX	ENCODE	exon	152800452	152800576	.	-	.	Parent=gene2730
chrX	ENCODE	exon	152802330	152802395	.	-	.	Parent=gene2730
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2730
chrX	ENCODE	exon	152803247	152803333	.	-	.	Parent=gene2730
###
chrX	ENCODE	gene	152798157	152806110	.	-	.	ID=gene2731;Name=U52112.3-020;name2=IRAK1
chrX	ENCODE	exon	152798157	152798215	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152798157	152798215	.	-	2	Parent=gene2731
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152798827	152798976	.	-	2	Parent=gene2731
chrX	ENCODE	exon	152799341	152799641	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152799341	152799641	.	-	0	Parent=gene2731
chrX	ENCODE	exon	152800340	152800576	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152800340	152800576	.	-	0	Parent=gene2731
chrX	ENCODE	exon	152802330	152802395	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152802330	152802395	.	-	0	Parent=gene2731
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152802735	152802942	.	-	1	Parent=gene2731
chrX	ENCODE	exon	152803247	152803365	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152803247	152803365	.	-	0	Parent=gene2731
chrX	ENCODE	exon	152804304	152804418	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152804304	152804418	.	-	1	Parent=gene2731
chrX	ENCODE	exon	152804589	152804653	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152804589	152804653	.	-	0	Parent=gene2731
chrX	ENCODE	exon	152804897	152805085	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152804897	152805085	.	-	0	Parent=gene2731
chrX	ENCODE	exon	152805273	152805376	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152805273	152805376	.	-	2	Parent=gene2731
chrX	ENCODE	exon	152805495	152805626	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152805495	152805626	.	-	2	Parent=gene2731
chrX	ENCODE	exon	152805729	152806110	.	-	.	Parent=gene2731
chrX	ENCODE	CDS	152805729	152806110	.	-	0	Parent=gene2731
###
chrX	ENCODE	gene	152798157	152806110	.	-	.	ID=gene2732;Name=U52112.3-002;name2=IRAK1
chrX	ENCODE	exon	152798157	152798215	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152798157	152798215	.	-	2	Parent=gene2732
chrX	ENCODE	exon	152798827	152798976	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152798827	152798976	.	-	2	Parent=gene2732
chrX	ENCODE	exon	152799341	152799641	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152799341	152799641	.	-	0	Parent=gene2732
chrX	ENCODE	exon	152800340	152800576	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152800340	152800576	.	-	0	Parent=gene2732
chrX	ENCODE	exon	152802330	152802395	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152802330	152802395	.	-	0	Parent=gene2732
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152802735	152802942	.	-	1	Parent=gene2732
chrX	ENCODE	exon	152803247	152803365	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152803247	152803365	.	-	0	Parent=gene2732
chrX	ENCODE	exon	152804304	152804418	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152804304	152804418	.	-	1	Parent=gene2732
chrX	ENCODE	exon	152804589	152804653	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152804589	152804653	.	-	0	Parent=gene2732
chrX	ENCODE	exon	152804897	152805085	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152804897	152805085	.	-	0	Parent=gene2732
chrX	ENCODE	exon	152805273	152805376	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152805273	152805376	.	-	2	Parent=gene2732
chrX	ENCODE	exon	152805495	152805626	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152805495	152805626	.	-	2	Parent=gene2732
chrX	ENCODE	exon	152805729	152805896	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152805729	152805896	.	-	2	Parent=gene2732
chrX	ENCODE	exon	152805975	152806110	.	-	.	Parent=gene2732
chrX	ENCODE	CDS	152805975	152806110	.	-	0	Parent=gene2732
###
chrX	ENCODE	gene	152799341	152804936	.	-	.	ID=gene2733;Name=U52112.3-005;name2=IRAK1
chrX	ENCODE	exon	152799341	152799731	.	-	.	Parent=gene2733
chrX	ENCODE	CDS	152799341	152799731	.	-	2	Parent=gene2733
chrX	ENCODE	exon	152800340	152800576	.	-	.	Parent=gene2733
chrX	ENCODE	CDS	152800340	152800576	.	-	2	Parent=gene2733
chrX	ENCODE	exon	152802735	152802942	.	-	.	Parent=gene2733
chrX	ENCODE	CDS	152802735	152802942	.	-	0	Parent=gene2733
chrX	ENCODE	exon	152803247	152803365	.	-	.	Parent=gene2733
chrX	ENCODE	CDS	152803247	152803365	.	-	2	Parent=gene2733
chrX	ENCODE	exon	152804304	152804418	.	-	.	Parent=gene2733
chrX	ENCODE	CDS	152804304	152804418	.	-	0	Parent=gene2733
chrX	ENCODE	exon	152804589	152804653	.	-	.	Parent=gene2733
chrX	ENCODE	CDS	152804589	152804653	.	-	2	Parent=gene2733
chrX	ENCODE	exon	152804897	152804936	.	-	.	Parent=gene2733
chrX	ENCODE	CDS	152804897	152804936	.	-	0	Parent=gene2733
###
chrX	ENCODE	gene	152799634	152800675	.	-	.	ID=gene2734;Name=U52112.3-006;name2=IRAK1
chrX	ENCODE	exon	152799634	152799731	.	-	.	Parent=gene2734
chrX	ENCODE	exon	152800340	152800675	.	-	.	Parent=gene2734
###
chrX	ENCODE	gene	152804644	152805243	.	-	.	ID=gene2735;Name=U52112.3-018;name2=IRAK1
chrX	ENCODE	exon	152804644	152804653	.	-	.	Parent=gene2735
chrX	ENCODE	exon	152804897	152805243	.	-	.	Parent=gene2735
###
chrX	ENCODE	gene	152807871	152884059	.	-	.	ID=gene2736;Name=AF030876.1-001;name2=MECP2
chrX	ENCODE	exon	152807871	152817748	.	-	.	Parent=gene2736
chrX	ENCODE	CDS	152816665	152817748	.	-	1	Parent=gene2736
chrX	ENCODE	exon	152818505	152818855	.	-	.	Parent=gene2736
chrX	ENCODE	CDS	152818505	152818855	.	-	1	Parent=gene2736
chrX	ENCODE	CDS	152878489	152878514	.	-	0	Parent=gene2736
chrX	ENCODE	exon	152878489	152878612	.	-	.	Parent=gene2736
chrX	ENCODE	exon	152883908	152884059	.	-	.	Parent=gene2736
###
chrX	ENCODE	gene	152816532	152884024	.	-	.	ID=gene2737;Name=AF030876.1-002;name2=MECP2
chrX	ENCODE	exon	152816532	152817748	.	-	.	Parent=gene2737
chrX	ENCODE	CDS	152816665	152817748	.	-	1	Parent=gene2737
chrX	ENCODE	exon	152818505	152818855	.	-	.	Parent=gene2737
chrX	ENCODE	CDS	152818505	152818855	.	-	1	Parent=gene2737
chrX	ENCODE	CDS	152883908	152883969	.	-	0	Parent=gene2737
chrX	ENCODE	exon	152883908	152884024	.	-	.	Parent=gene2737
###
chrX	ENCODE	gene	152817311	152883995	.	-	.	ID=gene2738;Name=AF030876.1-005;name2=MECP2
chrX	ENCODE	exon	152817311	152817584	.	-	.	Parent=gene2738
chrX	ENCODE	exon	152817694	152817748	.	-	.	Parent=gene2738
chrX	ENCODE	exon	152818505	152818855	.	-	.	Parent=gene2738
chrX	ENCODE	exon	152878489	152878612	.	-	.	Parent=gene2738
chrX	ENCODE	exon	152883908	152883995	.	-	.	Parent=gene2738
###
chrX	ENCODE	gene	152817567	152844068	.	-	.	ID=gene2739;Name=AF030876.1-004;name2=MECP2
chrX	ENCODE	exon	152817567	152817748	.	-	.	Parent=gene2739
chrX	ENCODE	exon	152818505	152818855	.	-	.	Parent=gene2739
chrX	ENCODE	exon	152843239	152843552	.	-	.	Parent=gene2739
chrX	ENCODE	exon	152844041	152844068	.	-	.	Parent=gene2739
###
chrX	ENCODE	gene	152817668	152883967	.	-	.	ID=gene2740;Name=AF030876.1-003;name2=MECP2
chrX	ENCODE	exon	152817668	152817748	.	-	.	Parent=gene2740
chrX	ENCODE	exon	152818505	152818855	.	-	.	Parent=gene2740
chrX	ENCODE	exon	152844697	152844864	.	-	.	Parent=gene2740
chrX	ENCODE	exon	152878489	152878612	.	-	.	Parent=gene2740
chrX	ENCODE	exon	152883908	152883967	.	-	.	Parent=gene2740
###
chrX	ENCODE	gene	152818671	152883283	.	-	.	ID=gene2741;Name=AF030876.1-006;name2=MECP2
chrX	ENCODE	exon	152818671	152818855	.	-	.	Parent=gene2741
chrX	ENCODE	exon	152883118	152883283	.	-	.	Parent=gene2741
###
chrX	ENCODE	gene	152818671	152923425	.	-	.	ID=gene2742;Name=AF030876.1-007;name2=MECP2
chrX	ENCODE	exon	152818671	152818855	.	-	.	Parent=gene2742
chrX	ENCODE	exon	152891096	152891353	.	-	.	Parent=gene2742
chrX	ENCODE	exon	152923379	152923425	.	-	.	Parent=gene2742
###
chrX	ENCODE	gene	152818731	152874356	.	-	.	ID=gene2743;Name=AF030876.1-009;name2=MECP2
chrX	ENCODE	exon	152818731	152818746	.	-	.	Parent=gene2743
chrX	ENCODE	exon	152873964	152874356	.	-	.	Parent=gene2743
###
chrX	ENCODE	gene	152818732	152820476	.	-	.	ID=gene2744;Name=AF030876.1-014;name2=MECP2
chrX	ENCODE	exon	152818732	152820476	.	-	.	Parent=gene2744
###
chrX	ENCODE	gene	152818732	152826401	.	-	.	ID=gene2745;Name=AF030876.1-013;name2=MECP2
chrX	ENCODE	exon	152818732	152818855	.	-	.	Parent=gene2745
chrX	ENCODE	exon	152826090	152826401	.	-	.	Parent=gene2745
###
chrX	ENCODE	gene	152818732	152835779	.	-	.	ID=gene2746;Name=AF030876.1-010;name2=MECP2
chrX	ENCODE	exon	152818732	152818855	.	-	.	Parent=gene2746
chrX	ENCODE	exon	152826090	152826201	.	-	.	Parent=gene2746
chrX	ENCODE	exon	152834815	152835779	.	-	.	Parent=gene2746
###
chrX	ENCODE	gene	152818732	152835779	.	-	.	ID=gene2747;Name=AF030876.1-012;name2=MECP2
chrX	ENCODE	exon	152818732	152818855	.	-	.	Parent=gene2747
chrX	ENCODE	exon	152826090	152826201	.	-	.	Parent=gene2747
chrX	ENCODE	exon	152834480	152834577	.	-	.	Parent=gene2747
chrX	ENCODE	exon	152834815	152835779	.	-	.	Parent=gene2747
###
chrX	ENCODE	gene	152818732	152835779	.	-	.	ID=gene2748;Name=AF030876.1-011;name2=MECP2
chrX	ENCODE	exon	152818732	152818855	.	-	.	Parent=gene2748
chrX	ENCODE	exon	152834815	152835779	.	-	.	Parent=gene2748
###
chrX	ENCODE	gene	152818732	152883283	.	-	.	ID=gene2749;Name=AF030876.1-008;name2=MECP2
chrX	ENCODE	exon	152818732	152818855	.	-	.	Parent=gene2749
chrX	ENCODE	CDS	152818732	152818855	.	-	1	Parent=gene2749
chrX	ENCODE	CDS	152878489	152878514	.	-	0	Parent=gene2749
chrX	ENCODE	exon	152878489	152878612	.	-	.	Parent=gene2749
chrX	ENCODE	exon	152883118	152883283	.	-	.	Parent=gene2749
###
chrX	ENCODE	gene	152930592	152945354	.	+	.	ID=gene2750;Name=Z68193.1-001;name2=OPN1LW
chrX	ENCODE	exon	152930592	152930716	.	+	.	Parent=gene2750
chrX	ENCODE	CDS	152930605	152930716	.	+	0	Parent=gene2750
chrX	ENCODE	exon	152936975	152937271	.	+	.	Parent=gene2750
chrX	ENCODE	CDS	152936975	152937271	.	+	2	Parent=gene2750
chrX	ENCODE	exon	152939260	152939428	.	+	.	Parent=gene2750
chrX	ENCODE	CDS	152939260	152939428	.	+	2	Parent=gene2750
chrX	ENCODE	exon	152940896	152941061	.	+	.	Parent=gene2750
chrX	ENCODE	CDS	152940896	152941061	.	+	1	Parent=gene2750
chrX	ENCODE	exon	152942616	152942855	.	+	.	Parent=gene2750
chrX	ENCODE	CDS	152942616	152942855	.	+	0	Parent=gene2750
chrX	ENCODE	CDS	152945138	152945248	.	+	0	Parent=gene2750
chrX	ENCODE	exon	152945138	152945354	.	+	.	Parent=gene2750
###
chrX	ENCODE	gene	152939262	152945345	.	+	.	ID=gene2751;Name=Z68193.1-002;name2=OPN1LW
chrX	ENCODE	exon	152939262	152939428	.	+	.	Parent=gene2751
chrX	ENCODE	CDS	152939262	152939428	.	+	0	Parent=gene2751
chrX	ENCODE	exon	152940896	152941061	.	+	.	Parent=gene2751
chrX	ENCODE	CDS	152940896	152941061	.	+	1	Parent=gene2751
chrX	ENCODE	exon	152942616	152942666	.	+	.	Parent=gene2751
chrX	ENCODE	CDS	152942616	152942666	.	+	0	Parent=gene2751
chrX	ENCODE	CDS	152945138	152945248	.	+	0	Parent=gene2751
chrX	ENCODE	exon	152945138	152945345	.	+	.	Parent=gene2751
###
chrX	ENCODE	gene	152945529	152966481	.	-	.	ID=gene2752;Name=Z68193.2-001;name2=CXorf2B
chrX	ENCODE	exon	152945529	152946035	.	-	.	Parent=gene2752
chrX	ENCODE	CDS	152945679	152946035	.	-	0	Parent=gene2752
chrX	ENCODE	exon	152946655	152946790	.	-	.	Parent=gene2752
chrX	ENCODE	CDS	152946655	152946790	.	-	1	Parent=gene2752
chrX	ENCODE	exon	152961957	152962684	.	-	.	Parent=gene2752
chrX	ENCODE	CDS	152961957	152962684	.	-	0	Parent=gene2752
chrX	ENCODE	CDS	152966382	152966393	.	-	0	Parent=gene2752
chrX	ENCODE	exon	152966382	152966481	.	-	.	Parent=gene2752
###
chrX	ENCODE	gene	152969001	152982480	.	+	.	ID=gene2753;Name=AC092402.1-001;name2=OPN1MW
chrX	ENCODE	exon	152969001	152969125	.	+	.	Parent=gene2753
chrX	ENCODE	CDS	152969014	152969125	.	+	0	Parent=gene2753
chrX	ENCODE	exon	152974106	152974402	.	+	.	Parent=gene2753
chrX	ENCODE	CDS	152974106	152974402	.	+	2	Parent=gene2753
chrX	ENCODE	exon	152976390	152976558	.	+	.	Parent=gene2753
chrX	ENCODE	CDS	152976390	152976558	.	+	2	Parent=gene2753
chrX	ENCODE	exon	152978026	152978191	.	+	.	Parent=gene2753
chrX	ENCODE	CDS	152978026	152978191	.	+	1	Parent=gene2753
chrX	ENCODE	exon	152979746	152979985	.	+	.	Parent=gene2753
chrX	ENCODE	CDS	152979746	152979985	.	+	0	Parent=gene2753
chrX	ENCODE	CDS	152982268	152982378	.	+	0	Parent=gene2753
chrX	ENCODE	exon	152982268	152982480	.	+	.	Parent=gene2753
###
chrX	ENCODE	gene	152976394	152982475	.	+	.	ID=gene2754;Name=AC092402.1-002;name2=OPN1MW
chrX	ENCODE	exon	152976394	152976558	.	+	.	Parent=gene2754
chrX	ENCODE	CDS	152976394	152976558	.	+	0	Parent=gene2754
chrX	ENCODE	exon	152978026	152978191	.	+	.	Parent=gene2754
chrX	ENCODE	CDS	152978026	152978191	.	+	0	Parent=gene2754
chrX	ENCODE	exon	152979746	152979796	.	+	.	Parent=gene2754
chrX	ENCODE	CDS	152979746	152979796	.	+	2	Parent=gene2754
chrX	ENCODE	CDS	152982268	152982378	.	+	2	Parent=gene2754
chrX	ENCODE	exon	152982268	152982475	.	+	.	Parent=gene2754
###
chrX	ENCODE	gene	152982659	153003602	.	-	.	ID=gene2755;name2=AC092402.4;Name=AC092402.4-001
chrX	ENCODE	exon	152982659	152983165	.	-	.	Parent=gene2755
chrX	ENCODE	CDS	152982809	152983165	.	-	0	Parent=gene2755
chrX	ENCODE	exon	152983785	152983920	.	-	.	Parent=gene2755
chrX	ENCODE	CDS	152983785	152983920	.	-	1	Parent=gene2755
chrX	ENCODE	exon	152999077	152999804	.	-	.	Parent=gene2755
chrX	ENCODE	CDS	152999077	152999804	.	-	0	Parent=gene2755
chrX	ENCODE	CDS	153003503	153003514	.	-	0	Parent=gene2755
chrX	ENCODE	exon	153003503	153003602	.	-	.	Parent=gene2755
###
chrX	ENCODE	gene	153006119	153019602	.	+	.	ID=gene2756;Name=AC092402.5-001;name2=AC092402.5
chrX	ENCODE	exon	153006119	153006243	.	+	.	Parent=gene2756
chrX	ENCODE	CDS	153006132	153006243	.	+	0	Parent=gene2756
chrX	ENCODE	exon	153011224	153011520	.	+	.	Parent=gene2756
chrX	ENCODE	CDS	153011224	153011520	.	+	2	Parent=gene2756
chrX	ENCODE	exon	153013508	153013676	.	+	.	Parent=gene2756
chrX	ENCODE	CDS	153013508	153013676	.	+	2	Parent=gene2756
chrX	ENCODE	exon	153015144	153015309	.	+	.	Parent=gene2756
chrX	ENCODE	CDS	153015144	153015309	.	+	1	Parent=gene2756
chrX	ENCODE	exon	153016864	153017103	.	+	.	Parent=gene2756
chrX	ENCODE	CDS	153016864	153017103	.	+	0	Parent=gene2756
chrX	ENCODE	CDS	153019386	153019496	.	+	0	Parent=gene2756
chrX	ENCODE	exon	153019386	153019602	.	+	.	Parent=gene2756
###
chrX	ENCODE	gene	153013512	153019593	.	+	.	ID=gene2757;Name=AC092402.5-002;name2=AC092402.5
chrX	ENCODE	exon	153013512	153013676	.	+	.	Parent=gene2757
chrX	ENCODE	CDS	153013512	153013676	.	+	0	Parent=gene2757
chrX	ENCODE	exon	153015144	153015309	.	+	.	Parent=gene2757
chrX	ENCODE	CDS	153015144	153015309	.	+	0	Parent=gene2757
chrX	ENCODE	exon	153016864	153016914	.	+	.	Parent=gene2757
chrX	ENCODE	CDS	153016864	153016914	.	+	2	Parent=gene2757
chrX	ENCODE	CDS	153019386	153019496	.	+	2	Parent=gene2757
chrX	ENCODE	exon	153019386	153019593	.	+	.	Parent=gene2757
###
chrX	ENCODE	gene	153019777	153044411	.	-	.	ID=gene2758;Name=AC092402.6-001;name2=CXorf2
chrX	ENCODE	exon	153019777	153020283	.	-	.	Parent=gene2758
chrX	ENCODE	CDS	153019927	153020283	.	-	0	Parent=gene2758
chrX	ENCODE	exon	153020903	153021038	.	-	.	Parent=gene2758
chrX	ENCODE	CDS	153020903	153021038	.	-	1	Parent=gene2758
chrX	ENCODE	exon	153036882	153037609	.	-	.	Parent=gene2758
chrX	ENCODE	CDS	153036882	153037609	.	-	0	Parent=gene2758
chrX	ENCODE	CDS	153041306	153041317	.	-	0	Parent=gene2758
chrX	ENCODE	exon	153041306	153041405	.	-	.	Parent=gene2758
chrX	ENCODE	exon	153044334	153044411	.	-	.	Parent=gene2758
###
chrX	ENCODE	gene	153019779	153044285	.	-	.	ID=gene2759;Name=AC092402.6-002;name2=CXorf2
chrX	ENCODE	exon	153019779	153020283	.	-	.	Parent=gene2759
chrX	ENCODE	CDS	153019927	153020283	.	-	0	Parent=gene2759
chrX	ENCODE	exon	153020903	153021038	.	-	.	Parent=gene2759
chrX	ENCODE	CDS	153020903	153021038	.	-	1	Parent=gene2759
chrX	ENCODE	exon	153036882	153037609	.	-	.	Parent=gene2759
chrX	ENCODE	CDS	153036882	153037609	.	-	0	Parent=gene2759
chrX	ENCODE	CDS	153041306	153041317	.	-	0	Parent=gene2759
chrX	ENCODE	exon	153041306	153041405	.	-	.	Parent=gene2759
chrX	ENCODE	exon	153044230	153044285	.	-	.	Parent=gene2759
###
chrX	ENCODE	gene	153037338	153044643	.	-	.	ID=gene2760;name2=CXorf2;Name=AC092402.6-003
chrX	ENCODE	exon	153037338	153037609	.	-	.	Parent=gene2760
chrX	ENCODE	CDS	153037338	153037609	.	-	0	Parent=gene2760
chrX	ENCODE	CDS	153038933	153038953	.	-	0	Parent=gene2760
chrX	ENCODE	exon	153038933	153039022	.	-	.	Parent=gene2760
chrX	ENCODE	exon	153041306	153041405	.	-	.	Parent=gene2760
chrX	ENCODE	exon	153044584	153044643	.	-	.	Parent=gene2760
###
chrX	ENCODE	gene	153044871	153079547	.	+	.	ID=gene2761;name2=TKTL1;Name=LL0XNC01-14B7.1-002
chrX	ENCODE	exon	153044871	153045193	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153045060	153045193	.	+	0	Parent=gene2761
chrX	ENCODE	exon	153054503	153054620	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153054503	153054620	.	+	1	Parent=gene2761
chrX	ENCODE	exon	153058544	153058641	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153058544	153058641	.	+	0	Parent=gene2761
chrX	ENCODE	exon	153060034	153060225	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153060034	153060225	.	+	1	Parent=gene2761
chrX	ENCODE	exon	153060309	153060436	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153060309	153060436	.	+	1	Parent=gene2761
chrX	ENCODE	exon	153061778	153061971	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153061778	153061971	.	+	2	Parent=gene2761
chrX	ENCODE	exon	153064370	153064534	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153064370	153064534	.	+	0	Parent=gene2761
chrX	ENCODE	exon	153069951	153070107	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153069951	153070107	.	+	0	Parent=gene2761
chrX	ENCODE	exon	153072400	153072530	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153072400	153072530	.	+	2	Parent=gene2761
chrX	ENCODE	exon	153074532	153074615	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153074532	153074615	.	+	0	Parent=gene2761
chrX	ENCODE	exon	153076784	153076880	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153076784	153076880	.	+	0	Parent=gene2761
chrX	ENCODE	exon	153077032	153077151	.	+	.	Parent=gene2761
chrX	ENCODE	CDS	153077032	153077151	.	+	2	Parent=gene2761
chrX	ENCODE	CDS	153078713	153078885	.	+	2	Parent=gene2761
chrX	ENCODE	exon	153078713	153079547	.	+	.	Parent=gene2761
###
chrX	ENCODE	gene	153054122	153060358	.	+	.	ID=gene2762;Name=LL0XNC01-14B7.1-005;name2=TKTL1
chrX	ENCODE	exon	153054122	153054285	.	+	.	Parent=gene2762
chrX	ENCODE	CDS	153054152	153054285	.	+	0	Parent=gene2762
chrX	ENCODE	exon	153054503	153054620	.	+	.	Parent=gene2762
chrX	ENCODE	CDS	153054503	153054620	.	+	1	Parent=gene2762
chrX	ENCODE	exon	153058544	153058641	.	+	.	Parent=gene2762
chrX	ENCODE	CDS	153058544	153058641	.	+	0	Parent=gene2762
chrX	ENCODE	exon	153060034	153060225	.	+	.	Parent=gene2762
chrX	ENCODE	CDS	153060034	153060225	.	+	1	Parent=gene2762
chrX	ENCODE	exon	153060309	153060358	.	+	.	Parent=gene2762
chrX	ENCODE	CDS	153060309	153060358	.	+	1	Parent=gene2762
###
chrX	ENCODE	gene	153054243	153060344	.	+	.	ID=gene2763;Name=LL0XNC01-14B7.1-006;name2=TKTL1
chrX	ENCODE	exon	153054243	153054323	.	+	.	Parent=gene2763
chrX	ENCODE	CDS	153054243	153054323	.	+	0	Parent=gene2763
chrX	ENCODE	exon	153054503	153054620	.	+	.	Parent=gene2763
chrX	ENCODE	CDS	153054503	153054620	.	+	0	Parent=gene2763
chrX	ENCODE	exon	153058544	153058641	.	+	.	Parent=gene2763
chrX	ENCODE	CDS	153058544	153058641	.	+	2	Parent=gene2763
chrX	ENCODE	exon	153060034	153060225	.	+	.	Parent=gene2763
chrX	ENCODE	CDS	153060034	153060225	.	+	0	Parent=gene2763
chrX	ENCODE	exon	153060309	153060344	.	+	.	Parent=gene2763
chrX	ENCODE	CDS	153060309	153060344	.	+	0	Parent=gene2763
###
chrX	ENCODE	gene	153054256	153079547	.	+	.	ID=gene2764;Name=LL0XNC01-14B7.1-001;name2=TKTL1
chrX	ENCODE	exon	153054256	153054620	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153054537	153054620	.	+	0	Parent=gene2764
chrX	ENCODE	exon	153058544	153058641	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153058544	153058641	.	+	0	Parent=gene2764
chrX	ENCODE	exon	153060034	153060225	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153060034	153060225	.	+	1	Parent=gene2764
chrX	ENCODE	exon	153060309	153060436	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153060309	153060436	.	+	1	Parent=gene2764
chrX	ENCODE	exon	153061778	153061971	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153061778	153061971	.	+	2	Parent=gene2764
chrX	ENCODE	exon	153064370	153064534	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153064370	153064534	.	+	0	Parent=gene2764
chrX	ENCODE	exon	153069951	153070107	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153069951	153070107	.	+	0	Parent=gene2764
chrX	ENCODE	exon	153072400	153072530	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153072400	153072530	.	+	2	Parent=gene2764
chrX	ENCODE	exon	153074532	153074615	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153074532	153074615	.	+	0	Parent=gene2764
chrX	ENCODE	exon	153076784	153076880	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153076784	153076880	.	+	0	Parent=gene2764
chrX	ENCODE	exon	153077032	153077151	.	+	.	Parent=gene2764
chrX	ENCODE	CDS	153077032	153077151	.	+	2	Parent=gene2764
chrX	ENCODE	CDS	153078713	153078885	.	+	2	Parent=gene2764
chrX	ENCODE	exon	153078713	153079547	.	+	.	Parent=gene2764
###
chrX	ENCODE	gene	153069498	153074578	.	+	.	ID=gene2765;Name=LL0XNC01-14B7.1-007;name2=TKTL1
chrX	ENCODE	exon	153069498	153069717	.	+	.	Parent=gene2765
chrX	ENCODE	exon	153069951	153070107	.	+	.	Parent=gene2765
chrX	ENCODE	exon	153072400	153072530	.	+	.	Parent=gene2765
chrX	ENCODE	exon	153074532	153074578	.	+	.	Parent=gene2765
###
chrX	ENCODE	gene	153076377	153077092	.	+	.	ID=gene2766;Name=LL0XNC01-14B7.1-004;name2=TKTL1
chrX	ENCODE	exon	153076377	153076880	.	+	.	Parent=gene2766
chrX	ENCODE	exon	153077032	153077092	.	+	.	Parent=gene2766
###
chrX	ENCODE	gene	153076569	153078885	.	+	.	ID=gene2767;Name=LL0XNC01-14B7.1-003;name2=TKTL1
chrX	ENCODE	exon	153076569	153076619	.	+	.	Parent=gene2767
chrX	ENCODE	CDS	153076569	153076619	.	+	0	Parent=gene2767
chrX	ENCODE	exon	153076784	153076880	.	+	.	Parent=gene2767
chrX	ENCODE	CDS	153076784	153076880	.	+	0	Parent=gene2767
chrX	ENCODE	exon	153077032	153077151	.	+	.	Parent=gene2767
chrX	ENCODE	CDS	153077032	153077151	.	+	2	Parent=gene2767
chrX	ENCODE	exon	153078713	153078885	.	+	.	Parent=gene2767
chrX	ENCODE	CDS	153078713	153078885	.	+	2	Parent=gene2767
###
chrX	ENCODE	gene	153097741	153120498	.	-	.	ID=gene2768;Name=XX-FW83128A1.1-001;name2=FLNA
chrX	ENCODE	exon	153097741	153098251	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153098064	153098251	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153098577	153098780	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153098577	153098780	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153098864	153099082	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153098864	153099082	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153099246	153099422	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153099246	153099422	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153100124	153100256	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153100124	153100256	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153100796	153100911	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153100796	153100911	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153101099	153101236	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153101099	153101236	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153101396	153101662	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153101396	153101662	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153101768	153101890	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153101768	153101890	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153101987	153102139	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153101987	153102139	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153102216	153102419	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153102216	153102419	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153102511	153102672	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153102511	153102672	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153102769	153102942	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153102769	153102942	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153103130	153103258	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153103130	153103258	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153103366	153103506	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153103366	153103506	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153103596	153103698	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153103596	153103698	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153103831	153103926	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153103831	153103926	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153104040	153104287	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153104040	153104287	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153106649	153106838	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153106649	153106838	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153107414	153107570	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153107414	153107570	.	-	1	Parent=gene2768
chrX	ENCODE	exon	153107660	153107783	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153107660	153107783	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153108199	153108369	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153108199	153108369	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153108461	153108621	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153108461	153108621	.	-	1	Parent=gene2768
chrX	ENCODE	exon	153108699	153108861	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153108699	153108861	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153108947	153109120	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153108947	153109120	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153109205	153109802	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153109205	153109802	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153110523	153110785	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153110523	153110785	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153110885	153111002	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153110885	153111002	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153111194	153111363	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153111194	153111363	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153111457	153111547	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153111457	153111547	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153111633	153111793	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153111633	153111793	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153111876	153111999	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153111876	153111999	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153113237	153113380	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153113237	153113380	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153113474	153113587	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153113474	153113587	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153113741	153113934	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153113741	153113934	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153114036	153114172	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153114036	153114172	.	-	1	Parent=gene2768
chrX	ENCODE	exon	153114351	153114474	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153114351	153114474	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153114564	153114701	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153114564	153114701	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153115239	153115439	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153115239	153115439	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153115523	153115685	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153115523	153115685	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153115777	153115854	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153115777	153115854	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153115947	153116065	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153115947	153116065	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153116612	153116759	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153116612	153116759	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153116856	153116953	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153116856	153116953	.	-	2	Parent=gene2768
chrX	ENCODE	exon	153117057	153117305	.	-	.	Parent=gene2768
chrX	ENCODE	CDS	153117057	153117305	.	-	2	Parent=gene2768
chrX	ENCODE	CDS	153120088	153120460	.	-	0	Parent=gene2768
chrX	ENCODE	exon	153120088	153120498	.	-	.	Parent=gene2768
###
chrX	ENCODE	gene	153097745	153102098	.	-	.	ID=gene2769;Name=XX-FW83128A1.1-017;name2=FLNA
chrX	ENCODE	exon	153097745	153098045	.	-	.	Parent=gene2769
chrX	ENCODE	exon	153102032	153102098	.	-	.	Parent=gene2769
###
chrX	ENCODE	gene	153097746	153102005	.	-	.	ID=gene2770;Name=XX-FW83128A1.1-018;name2=FLNA
chrX	ENCODE	exon	153097746	153097944	.	-	.	Parent=gene2770
chrX	ENCODE	exon	153101557	153101662	.	-	.	Parent=gene2770
chrX	ENCODE	exon	153101768	153101890	.	-	.	Parent=gene2770
chrX	ENCODE	exon	153101987	153102005	.	-	.	Parent=gene2770
###
chrX	ENCODE	gene	153097863	153108542	.	-	.	ID=gene2771;name2=FLNA;Name=XX-FW83128A1.1-004
chrX	ENCODE	exon	153097863	153098251	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153098577	153098780	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153098864	153099082	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153099246	153099422	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153100124	153100911	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153101099	153101236	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153101396	153101662	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153101768	153101890	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153101987	153102139	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153102216	153102419	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153102511	153102672	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153102769	153102942	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153103130	153103258	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153103366	153103506	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153103596	153103698	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153103831	153103926	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153104040	153104287	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153106649	153106660	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153108316	153108369	.	-	.	Parent=gene2771
chrX	ENCODE	exon	153108461	153108542	.	-	.	Parent=gene2771
###
chrX	ENCODE	gene	153097863	153108853	.	-	.	ID=gene2772;Name=XX-FW83128A1.1-003;name2=FLNA
chrX	ENCODE	exon	153097863	153098251	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153098577	153098780	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153098864	153099082	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153099246	153100911	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153101099	153101236	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153101396	153101662	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153101768	153101890	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153101987	153102139	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153102216	153102419	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153102511	153102672	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153102769	153102942	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153103130	153103258	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153103366	153103506	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153103596	153103698	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153103831	153103926	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153104040	153104287	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153106649	153106838	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153107414	153107570	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153107660	153107783	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153108199	153108369	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153108461	153108621	.	-	.	Parent=gene2772
chrX	ENCODE	exon	153108699	153108853	.	-	.	Parent=gene2772
###
chrX	ENCODE	gene	153097863	153123841	.	-	.	ID=gene2773;Name=XX-FW83128A1.1-002;name2=FLNA
chrX	ENCODE	exon	153097863	153098251	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153098064	153098251	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153098577	153098780	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153098577	153098780	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153098864	153099082	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153098864	153099082	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153099246	153099422	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153099246	153099422	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153100124	153100256	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153100124	153100256	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153100796	153100911	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153100796	153100911	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153101099	153101236	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153101099	153101236	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153101396	153101662	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153101396	153101662	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153101768	153101890	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153101768	153101890	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153101987	153102139	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153101987	153102139	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153102216	153102419	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153102216	153102419	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153102511	153102672	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153102511	153102672	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153102769	153102942	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153102769	153102942	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153103130	153103258	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153103130	153103258	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153103366	153103506	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153103366	153103506	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153103596	153103698	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153103596	153103698	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153103831	153103926	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153103831	153103926	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153104040	153104287	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153104040	153104287	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153106466	153106489	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153106466	153106489	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153106649	153106838	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153106649	153106838	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153107414	153107570	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153107414	153107570	.	-	1	Parent=gene2773
chrX	ENCODE	exon	153107660	153107783	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153107660	153107783	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153108199	153108369	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153108199	153108369	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153108461	153108621	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153108461	153108621	.	-	1	Parent=gene2773
chrX	ENCODE	exon	153108699	153108861	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153108699	153108861	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153108947	153109120	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153108947	153109120	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153109205	153109802	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153109205	153109802	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153110523	153110785	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153110523	153110785	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153110885	153111002	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153110885	153111002	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153111194	153111363	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153111194	153111363	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153111457	153111547	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153111457	153111547	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153111633	153111793	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153111633	153111793	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153111876	153111999	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153111876	153111999	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153113237	153113380	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153113237	153113380	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153113474	153113587	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153113474	153113587	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153113741	153113934	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153113741	153113934	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153114036	153114172	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153114036	153114172	.	-	1	Parent=gene2773
chrX	ENCODE	exon	153114351	153114474	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153114351	153114474	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153114564	153114701	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153114564	153114701	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153115239	153115439	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153115239	153115439	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153115523	153115685	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153115523	153115685	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153115777	153115854	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153115777	153115854	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153115947	153116065	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153115947	153116065	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153116612	153116759	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153116612	153116759	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153116856	153116953	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153116856	153116953	.	-	2	Parent=gene2773
chrX	ENCODE	exon	153117057	153117305	.	-	.	Parent=gene2773
chrX	ENCODE	CDS	153117057	153117305	.	-	2	Parent=gene2773
chrX	ENCODE	CDS	153120088	153120460	.	-	0	Parent=gene2773
chrX	ENCODE	exon	153120088	153120576	.	-	.	Parent=gene2773
chrX	ENCODE	exon	153123721	153123841	.	-	.	Parent=gene2773
###
chrX	ENCODE	gene	153097999	153120503	.	-	.	ID=gene2774;name2=FLNA;Name=XX-FW83128A1.1-010
chrX	ENCODE	exon	153097999	153098251	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153098064	153098251	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153098577	153098780	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153098577	153098780	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153098864	153099082	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153098864	153099082	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153099246	153099422	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153099246	153099422	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153100124	153100256	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153100124	153100256	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153100796	153100911	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153100796	153100911	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153101099	153101236	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153101099	153101236	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153101396	153101662	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153101396	153101662	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153101768	153101890	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153101768	153101890	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153101987	153102139	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153101987	153102139	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153102216	153102419	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153102216	153102419	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153102511	153102672	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153102511	153102672	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153102769	153102942	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153102769	153102942	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153103130	153103258	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153103130	153103258	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153103366	153103506	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153103366	153103506	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153103596	153103698	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153103596	153103698	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153104040	153104287	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153104040	153104287	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153106649	153106838	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153106649	153106838	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153107414	153107570	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153107414	153107570	.	-	1	Parent=gene2774
chrX	ENCODE	exon	153107660	153107783	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153107660	153107783	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153108199	153108369	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153108199	153108369	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153108461	153108621	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153108461	153108621	.	-	1	Parent=gene2774
chrX	ENCODE	exon	153108699	153108861	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153108699	153108861	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153108947	153109120	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153108947	153109120	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153109205	153109802	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153109205	153109802	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153110523	153110785	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153110523	153110785	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153110885	153111002	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153110885	153111002	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153111194	153111363	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153111194	153111363	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153111457	153111547	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153111457	153111547	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153111633	153111793	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153111633	153111793	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153111876	153111999	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153111876	153111999	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153113237	153113380	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153113237	153113380	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153113474	153113587	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153113474	153113587	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153113741	153113934	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153113741	153113934	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153114036	153114172	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153114036	153114172	.	-	1	Parent=gene2774
chrX	ENCODE	exon	153114351	153114474	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153114351	153114474	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153114564	153114701	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153114564	153114701	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153115239	153115439	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153115239	153115439	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153115523	153115685	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153115523	153115685	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153115777	153115854	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153115777	153115854	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153115947	153116065	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153115947	153116065	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153116612	153116759	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153116612	153116759	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153116856	153116953	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153116856	153116953	.	-	2	Parent=gene2774
chrX	ENCODE	exon	153117057	153117305	.	-	.	Parent=gene2774
chrX	ENCODE	CDS	153117057	153117305	.	-	2	Parent=gene2774
chrX	ENCODE	CDS	153120088	153120460	.	-	0	Parent=gene2774
chrX	ENCODE	exon	153120088	153120503	.	-	.	Parent=gene2774
###
chrX	ENCODE	gene	153098135	153100418	.	-	.	ID=gene2775;Name=XX-FW83128A1.1-008;name2=FLNA
chrX	ENCODE	exon	153098135	153098251	.	-	.	Parent=gene2775
chrX	ENCODE	exon	153098577	153098780	.	-	.	Parent=gene2775
chrX	ENCODE	exon	153098864	153099082	.	-	.	Parent=gene2775
chrX	ENCODE	exon	153099246	153099422	.	-	.	Parent=gene2775
chrX	ENCODE	exon	153100124	153100256	.	-	.	Parent=gene2775
chrX	ENCODE	exon	153100355	153100418	.	-	.	Parent=gene2775
###
chrX	ENCODE	gene	153098137	153099570	.	-	.	ID=gene2776;Name=XX-FW83128A1.1-009;name2=FLNA
chrX	ENCODE	exon	153098137	153098251	.	-	.	Parent=gene2776
chrX	ENCODE	exon	153098577	153098780	.	-	.	Parent=gene2776
chrX	ENCODE	exon	153098864	153099570	.	-	.	Parent=gene2776
###
chrX	ENCODE	gene	153099300	153109255	.	-	.	ID=gene2777;Name=XX-FW83128A1.1-014;name2=FLNA
chrX	ENCODE	exon	153099300	153099422	.	-	.	Parent=gene2777
chrX	ENCODE	exon	153100124	153100256	.	-	.	Parent=gene2777
chrX	ENCODE	exon	153100796	153100911	.	-	.	Parent=gene2777
chrX	ENCODE	exon	153101099	153101236	.	-	.	Parent=gene2777
chrX	ENCODE	exon	153101396	153101420	.	-	.	Parent=gene2777
chrX	ENCODE	exon	153109220	153109255	.	-	.	Parent=gene2777
###
chrX	ENCODE	gene	153100796	153102327	.	-	.	ID=gene2778;Name=XX-FW83128A1.1-016;name2=FLNA
chrX	ENCODE	exon	153100796	153100911	.	-	.	Parent=gene2778
chrX	ENCODE	CDS	153100796	153100911	.	-	2	Parent=gene2778
chrX	ENCODE	exon	153101099	153101236	.	-	.	Parent=gene2778
chrX	ENCODE	CDS	153101099	153101236	.	-	2	Parent=gene2778
chrX	ENCODE	exon	153101396	153101662	.	-	.	Parent=gene2778
chrX	ENCODE	CDS	153101396	153101662	.	-	2	Parent=gene2778
chrX	ENCODE	exon	153101987	153102139	.	-	.	Parent=gene2778
chrX	ENCODE	CDS	153101987	153102139	.	-	2	Parent=gene2778
chrX	ENCODE	exon	153102216	153102327	.	-	.	Parent=gene2778
chrX	ENCODE	CDS	153102216	153102327	.	-	0	Parent=gene2778
###
chrX	ENCODE	gene	153100943	153101998	.	-	.	ID=gene2779;Name=XX-FW83128A1.1-007;name2=FLNA
chrX	ENCODE	exon	153100943	153101236	.	-	.	Parent=gene2779
chrX	ENCODE	exon	153101396	153101662	.	-	.	Parent=gene2779
chrX	ENCODE	exon	153101768	153101890	.	-	.	Parent=gene2779
chrX	ENCODE	exon	153101987	153101998	.	-	.	Parent=gene2779
###
chrX	ENCODE	gene	153101768	153102813	.	-	.	ID=gene2780;Name=XX-FW83128A1.1-019;name2=FLNA
chrX	ENCODE	exon	153101768	153101890	.	-	.	Parent=gene2780
chrX	ENCODE	exon	153101987	153102139	.	-	.	Parent=gene2780
chrX	ENCODE	exon	153102216	153102436	.	-	.	Parent=gene2780
chrX	ENCODE	exon	153102511	153102672	.	-	.	Parent=gene2780
chrX	ENCODE	exon	153102769	153102813	.	-	.	Parent=gene2780
###
chrX	ENCODE	gene	153102511	153104104	.	-	.	ID=gene2781;Name=XX-FW83128A1.1-015;name2=FLNA
chrX	ENCODE	exon	153102511	153102672	.	-	.	Parent=gene2781
chrX	ENCODE	CDS	153102511	153102672	.	-	0	Parent=gene2781
chrX	ENCODE	exon	153103130	153103258	.	-	.	Parent=gene2781
chrX	ENCODE	CDS	153103130	153103258	.	-	0	Parent=gene2781
chrX	ENCODE	exon	153103366	153103506	.	-	.	Parent=gene2781
chrX	ENCODE	CDS	153103366	153103506	.	-	0	Parent=gene2781
chrX	ENCODE	exon	153103596	153103698	.	-	.	Parent=gene2781
chrX	ENCODE	CDS	153103596	153103698	.	-	1	Parent=gene2781
chrX	ENCODE	exon	153103831	153103926	.	-	.	Parent=gene2781
chrX	ENCODE	CDS	153103831	153103926	.	-	1	Parent=gene2781
chrX	ENCODE	exon	153104040	153104104	.	-	.	Parent=gene2781
chrX	ENCODE	CDS	153104040	153104104	.	-	0	Parent=gene2781
###
chrX	ENCODE	gene	153103245	153103895	.	-	.	ID=gene2782;Name=XX-FW83128A1.1-006;name2=FLNA
chrX	ENCODE	exon	153103245	153103506	.	-	.	Parent=gene2782
chrX	ENCODE	exon	153103596	153103698	.	-	.	Parent=gene2782
chrX	ENCODE	exon	153103831	153103895	.	-	.	Parent=gene2782
###
chrX	ENCODE	gene	153106756	153107879	.	-	.	ID=gene2783;Name=XX-FW83128A1.1-005;name2=FLNA
chrX	ENCODE	exon	153106756	153106838	.	-	.	Parent=gene2783
chrX	ENCODE	exon	153107414	153107570	.	-	.	Parent=gene2783
chrX	ENCODE	exon	153107660	153107879	.	-	.	Parent=gene2783
###
chrX	ENCODE	gene	153113847	153114422	.	-	.	ID=gene2784;Name=XX-FW83128A1.1-013;name2=FLNA
chrX	ENCODE	exon	153113847	153114172	.	-	.	Parent=gene2784
chrX	ENCODE	exon	153114351	153114422	.	-	.	Parent=gene2784
###
chrX	ENCODE	gene	153114639	153120424	.	-	.	ID=gene2785;Name=XX-FW83128A1.1-011;name2=FLNA
chrX	ENCODE	exon	153114639	153114701	.	-	.	Parent=gene2785
chrX	ENCODE	exon	153115239	153115436	.	-	.	Parent=gene2785
chrX	ENCODE	exon	153115523	153115662	.	-	.	Parent=gene2785
chrX	ENCODE	exon	153120327	153120424	.	-	.	Parent=gene2785
###
chrX	ENCODE	gene	153115976	153120339	.	-	.	ID=gene2786;Name=XX-FW83128A1.1-012;name2=FLNA
chrX	ENCODE	exon	153115976	153116065	.	-	.	Parent=gene2786
chrX	ENCODE	exon	153116612	153116759	.	-	.	Parent=gene2786
chrX	ENCODE	exon	153116856	153116953	.	-	.	Parent=gene2786
chrX	ENCODE	exon	153117057	153117068	.	-	.	Parent=gene2786
chrX	ENCODE	exon	153120177	153120339	.	-	.	Parent=gene2786
###
chrX	ENCODE	gene	153128404	153130730	.	+	.	ID=gene2787;Name=XX-FW88778H2.1-001;name2=EMD
chrX	ENCODE	exon	153128404	153128773	.	+	.	Parent=gene2787
chrX	ENCODE	CDS	153128692	153128773	.	+	0	Parent=gene2787
chrX	ENCODE	exon	153128897	153129001	.	+	.	Parent=gene2787
chrX	ENCODE	CDS	153128897	153129001	.	+	2	Parent=gene2787
chrX	ENCODE	exon	153129149	153129226	.	+	.	Parent=gene2787
chrX	ENCODE	CDS	153129149	153129226	.	+	2	Parent=gene2787
chrX	ENCODE	exon	153129441	153129574	.	+	.	Parent=gene2787
chrX	ENCODE	CDS	153129441	153129574	.	+	2	Parent=gene2787
chrX	ENCODE	exon	153129960	153130009	.	+	.	Parent=gene2787
chrX	ENCODE	CDS	153129960	153130009	.	+	0	Parent=gene2787
chrX	ENCODE	CDS	153130089	153130404	.	+	1	Parent=gene2787
chrX	ENCODE	exon	153130089	153130730	.	+	.	Parent=gene2787
###
chrX	ENCODE	gene	153128480	153130498	.	+	.	ID=gene2788;Name=XX-FW88778H2.1-010;name2=EMD
chrX	ENCODE	exon	153128480	153128773	.	+	.	Parent=gene2788
chrX	ENCODE	CDS	153128692	153128773	.	+	0	Parent=gene2788
chrX	ENCODE	exon	153129149	153129226	.	+	.	Parent=gene2788
chrX	ENCODE	CDS	153129149	153129226	.	+	2	Parent=gene2788
chrX	ENCODE	exon	153129441	153129574	.	+	.	Parent=gene2788
chrX	ENCODE	CDS	153129441	153129574	.	+	2	Parent=gene2788
chrX	ENCODE	exon	153129960	153130009	.	+	.	Parent=gene2788
chrX	ENCODE	CDS	153129960	153130009	.	+	0	Parent=gene2788
chrX	ENCODE	CDS	153130089	153130404	.	+	1	Parent=gene2788
chrX	ENCODE	exon	153130089	153130498	.	+	.	Parent=gene2788
###
chrX	ENCODE	gene	153128548	153130486	.	+	.	ID=gene2789;Name=XX-FW88778H2.1-003;name2=EMD
chrX	ENCODE	exon	153128548	153128773	.	+	.	Parent=gene2789
chrX	ENCODE	exon	153128897	153129001	.	+	.	Parent=gene2789
chrX	ENCODE	exon	153129149	153129574	.	+	.	Parent=gene2789
chrX	ENCODE	exon	153129960	153130486	.	+	.	Parent=gene2789
###
chrX	ENCODE	gene	153128568	153130490	.	+	.	ID=gene2790;name2=EMD;Name=XX-FW88778H2.1-007
chrX	ENCODE	exon	153128568	153128744	.	+	.	Parent=gene2790
chrX	ENCODE	exon	153128897	153129001	.	+	.	Parent=gene2790
chrX	ENCODE	exon	153129149	153129226	.	+	.	Parent=gene2790
chrX	ENCODE	exon	153129441	153129574	.	+	.	Parent=gene2790
chrX	ENCODE	exon	153129960	153130009	.	+	.	Parent=gene2790
chrX	ENCODE	exon	153130089	153130490	.	+	.	Parent=gene2790
###
chrX	ENCODE	gene	153128611	153130162	.	+	.	ID=gene2791;Name=XX-FW88778H2.1-006;name2=EMD
chrX	ENCODE	exon	153128611	153128773	.	+	.	Parent=gene2791
chrX	ENCODE	exon	153129149	153129574	.	+	.	Parent=gene2791
chrX	ENCODE	exon	153129960	153130162	.	+	.	Parent=gene2791
###
chrX	ENCODE	gene	153128635	153129669	.	+	.	ID=gene2792;Name=XX-FW88778H2.1-005;name2=EMD
chrX	ENCODE	exon	153128635	153128773	.	+	.	Parent=gene2792
chrX	ENCODE	exon	153128897	153129001	.	+	.	Parent=gene2792
chrX	ENCODE	exon	153129149	153129669	.	+	.	Parent=gene2792
###
chrX	ENCODE	gene	153128732	153130101	.	+	.	ID=gene2793;Name=XX-FW88778H2.1-008;name2=EMD
chrX	ENCODE	exon	153128732	153128773	.	+	.	Parent=gene2793
chrX	ENCODE	exon	153128897	153129001	.	+	.	Parent=gene2793
chrX	ENCODE	exon	153129149	153129226	.	+	.	Parent=gene2793
chrX	ENCODE	exon	153129441	153129574	.	+	.	Parent=gene2793
chrX	ENCODE	exon	153129960	153130101	.	+	.	Parent=gene2793
###
chrX	ENCODE	gene	153128832	153130488	.	+	.	ID=gene2794;name2=EMD;Name=XX-FW88778H2.1-009
chrX	ENCODE	exon	153128832	153129001	.	+	.	Parent=gene2794
chrX	ENCODE	exon	153129149	153129226	.	+	.	Parent=gene2794
chrX	ENCODE	exon	153129441	153129574	.	+	.	Parent=gene2794
chrX	ENCODE	exon	153129960	153130009	.	+	.	Parent=gene2794
chrX	ENCODE	exon	153130089	153130488	.	+	.	Parent=gene2794
###
chrX	ENCODE	gene	153129218	153130729	.	+	.	ID=gene2795;name2=EMD;Name=XX-FW88778H2.1-011
chrX	ENCODE	exon	153129218	153129226	.	+	.	Parent=gene2795
chrX	ENCODE	exon	153129441	153129574	.	+	.	Parent=gene2795
chrX	ENCODE	exon	153129960	153130009	.	+	.	Parent=gene2795
chrX	ENCODE	exon	153130089	153130105	.	+	.	Parent=gene2795
chrX	ENCODE	exon	153130282	153130729	.	+	.	Parent=gene2795
###
chrX	ENCODE	gene	153129772	153130650	.	+	.	ID=gene2796;Name=XX-FW88778H2.1-004;name2=EMD
chrX	ENCODE	exon	153129772	153130009	.	+	.	Parent=gene2796
chrX	ENCODE	exon	153130089	153130650	.	+	.	Parent=gene2796
###
chrX	ENCODE	gene	153147246	153149354	.	+	.	ID=gene2797;Name=XX-FW83563B9.1-004;name2=RPL10
chrX	ENCODE	exon	153147246	153147582	.	+	.	Parent=gene2797
chrX	ENCODE	exon	153147685	153147730	.	+	.	Parent=gene2797
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2797
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2797
chrX	ENCODE	exon	153148991	153149354	.	+	.	Parent=gene2797
###
chrX	ENCODE	gene	153147418	153150105	.	+	.	ID=gene2798;Name=XX-FW83563B9.1-008;name2=RPL10
chrX	ENCODE	exon	153147418	153147582	.	+	.	Parent=gene2798
chrX	ENCODE	exon	153147685	153147730	.	+	.	Parent=gene2798
chrX	ENCODE	CDS	153147708	153147730	.	+	0	Parent=gene2798
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2798
chrX	ENCODE	CDS	153148526	153148584	.	+	1	Parent=gene2798
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2798
chrX	ENCODE	CDS	153148675	153148782	.	+	2	Parent=gene2798
chrX	ENCODE	exon	153148991	153149129	.	+	.	Parent=gene2798
chrX	ENCODE	CDS	153148991	153149129	.	+	2	Parent=gene2798
chrX	ENCODE	exon	153149652	153149814	.	+	.	Parent=gene2798
chrX	ENCODE	CDS	153149652	153149814	.	+	1	Parent=gene2798
chrX	ENCODE	CDS	153149890	153150042	.	+	0	Parent=gene2798
chrX	ENCODE	exon	153149890	153150105	.	+	.	Parent=gene2798
###
chrX	ENCODE	gene	153147555	153149999	.	+	.	ID=gene2799;Name=XX-FW83563B9.1-015;name2=RPL10
chrX	ENCODE	exon	153147555	153147586	.	+	.	Parent=gene2799
chrX	ENCODE	exon	153147685	153147730	.	+	.	Parent=gene2799
chrX	ENCODE	CDS	153147708	153147730	.	+	0	Parent=gene2799
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2799
chrX	ENCODE	CDS	153148526	153148584	.	+	1	Parent=gene2799
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2799
chrX	ENCODE	CDS	153148675	153148782	.	+	2	Parent=gene2799
chrX	ENCODE	exon	153148991	153149129	.	+	.	Parent=gene2799
chrX	ENCODE	CDS	153148991	153149129	.	+	2	Parent=gene2799
chrX	ENCODE	exon	153149652	153149814	.	+	.	Parent=gene2799
chrX	ENCODE	CDS	153149652	153149814	.	+	1	Parent=gene2799
chrX	ENCODE	exon	153149890	153149999	.	+	.	Parent=gene2799
chrX	ENCODE	CDS	153149890	153149999	.	+	0	Parent=gene2799
###
chrX	ENCODE	gene	153147560	153151527	.	+	.	ID=gene2800;Name=XX-FW83563B9.1-001;name2=RPL10
chrX	ENCODE	exon	153147560	153147730	.	+	.	Parent=gene2800
chrX	ENCODE	CDS	153147708	153147730	.	+	0	Parent=gene2800
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2800
chrX	ENCODE	CDS	153148526	153148584	.	+	1	Parent=gene2800
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2800
chrX	ENCODE	CDS	153148675	153148782	.	+	2	Parent=gene2800
chrX	ENCODE	exon	153148991	153149129	.	+	.	Parent=gene2800
chrX	ENCODE	CDS	153148991	153149129	.	+	2	Parent=gene2800
chrX	ENCODE	exon	153149652	153149814	.	+	.	Parent=gene2800
chrX	ENCODE	CDS	153149652	153149814	.	+	1	Parent=gene2800
chrX	ENCODE	CDS	153149890	153150042	.	+	0	Parent=gene2800
chrX	ENCODE	exon	153149890	153151527	.	+	.	Parent=gene2800
###
chrX	ENCODE	gene	153147565	153150086	.	+	.	ID=gene2801;Name=XX-FW83563B9.1-006;name2=RPL10
chrX	ENCODE	exon	153147565	153147730	.	+	.	Parent=gene2801
chrX	ENCODE	exon	153148526	153148782	.	+	.	Parent=gene2801
chrX	ENCODE	exon	153148991	153150086	.	+	.	Parent=gene2801
###
chrX	ENCODE	gene	153147565	153150101	.	+	.	ID=gene2802;Name=XX-FW83563B9.1-007;name2=RPL10
chrX	ENCODE	exon	153147565	153147582	.	+	.	Parent=gene2802
chrX	ENCODE	exon	153147685	153150101	.	+	.	Parent=gene2802
###
chrX	ENCODE	gene	153147565	153150101	.	+	.	ID=gene2803;Name=XX-FW83563B9.1-005;name2=RPL10
chrX	ENCODE	exon	153147565	153147730	.	+	.	Parent=gene2803
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2803
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2803
chrX	ENCODE	exon	153148991	153149814	.	+	.	Parent=gene2803
chrX	ENCODE	exon	153149890	153150101	.	+	.	Parent=gene2803
###
chrX	ENCODE	gene	153147566	153150105	.	+	.	ID=gene2804;Name=XX-FW83563B9.1-009;name2=RPL10
chrX	ENCODE	exon	153147566	153147582	.	+	.	Parent=gene2804
chrX	ENCODE	exon	153147685	153147730	.	+	.	Parent=gene2804
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2804
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2804
chrX	ENCODE	exon	153148991	153149129	.	+	.	Parent=gene2804
chrX	ENCODE	exon	153149890	153150105	.	+	.	Parent=gene2804
###
chrX	ENCODE	gene	153147567	153150005	.	+	.	ID=gene2805;Name=XX-FW83563B9.1-010;name2=RPL10
chrX	ENCODE	exon	153147567	153147730	.	+	.	Parent=gene2805
chrX	ENCODE	exon	153148526	153148782	.	+	.	Parent=gene2805
chrX	ENCODE	exon	153148991	153149129	.	+	.	Parent=gene2805
chrX	ENCODE	exon	153149652	153149814	.	+	.	Parent=gene2805
chrX	ENCODE	exon	153149890	153150005	.	+	.	Parent=gene2805
###
chrX	ENCODE	gene	153147576	153150101	.	+	.	ID=gene2806;name2=RPL10;Name=XX-FW83563B9.1-003
chrX	ENCODE	exon	153147576	153147730	.	+	.	Parent=gene2806
chrX	ENCODE	exon	153148526	153150101	.	+	.	Parent=gene2806
###
chrX	ENCODE	gene	153147591	153150101	.	+	.	ID=gene2807;Name=XX-FW83563B9.1-002;name2=RPL10
chrX	ENCODE	exon	153147591	153148584	.	+	.	Parent=gene2807
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2807
chrX	ENCODE	exon	153148991	153150101	.	+	.	Parent=gene2807
###
chrX	ENCODE	gene	153147684	153150085	.	+	.	ID=gene2808;Name=XX-FW83563B9.1-013;name2=RPL10
chrX	ENCODE	exon	153147684	153147730	.	+	.	Parent=gene2808
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2808
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2808
chrX	ENCODE	exon	153148991	153150085	.	+	.	Parent=gene2808
###
chrX	ENCODE	gene	153147685	153150101	.	+	.	ID=gene2809;Name=XX-FW83563B9.1-012;name2=RPL10
chrX	ENCODE	exon	153147685	153147730	.	+	.	Parent=gene2809
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2809
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2809
chrX	ENCODE	exon	153148991	153149129	.	+	.	Parent=gene2809
chrX	ENCODE	exon	153149652	153150101	.	+	.	Parent=gene2809
###
chrX	ENCODE	gene	153148078	153150097	.	+	.	ID=gene2810;Name=XX-FW83563B9.1-011;name2=RPL10
chrX	ENCODE	exon	153148078	153148148	.	+	.	Parent=gene2810
chrX	ENCODE	CDS	153148078	153148148	.	+	0	Parent=gene2810
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2810
chrX	ENCODE	CDS	153148526	153148584	.	+	1	Parent=gene2810
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2810
chrX	ENCODE	CDS	153148675	153148782	.	+	2	Parent=gene2810
chrX	ENCODE	exon	153148991	153149129	.	+	.	Parent=gene2810
chrX	ENCODE	CDS	153148991	153149129	.	+	2	Parent=gene2810
chrX	ENCODE	exon	153149652	153149814	.	+	.	Parent=gene2810
chrX	ENCODE	CDS	153149652	153149814	.	+	1	Parent=gene2810
chrX	ENCODE	CDS	153149890	153150042	.	+	0	Parent=gene2810
chrX	ENCODE	exon	153149890	153150097	.	+	.	Parent=gene2810
###
chrX	ENCODE	gene	153148180	153150101	.	+	.	ID=gene2811;Name=XX-FW83563B9.1-014;name2=RPL10
chrX	ENCODE	exon	153148180	153148260	.	+	.	Parent=gene2811
chrX	ENCODE	exon	153148526	153148584	.	+	.	Parent=gene2811
chrX	ENCODE	exon	153148675	153148782	.	+	.	Parent=gene2811
chrX	ENCODE	exon	153148991	153149129	.	+	.	Parent=gene2811
chrX	ENCODE	exon	153149652	153149814	.	+	.	Parent=gene2811
chrX	ENCODE	exon	153149890	153150101	.	+	.	Parent=gene2811
###
chrX	ENCODE	gene	153150946	153158459	.	-	.	ID=gene2812;Name=XX-FW83563B9.2-006;name2=DNASE1L1
chrX	ENCODE	exon	153150946	153152029	.	-	.	Parent=gene2812
chrX	ENCODE	CDS	153151895	153152029	.	-	0	Parent=gene2812
chrX	ENCODE	exon	153152130	153152378	.	-	.	Parent=gene2812
chrX	ENCODE	CDS	153152130	153152378	.	-	0	Parent=gene2812
chrX	ENCODE	exon	153152457	153152569	.	-	.	Parent=gene2812
chrX	ENCODE	CDS	153152457	153152569	.	-	2	Parent=gene2812
chrX	ENCODE	exon	153152710	153152810	.	-	.	Parent=gene2812
chrX	ENCODE	CDS	153152710	153152810	.	-	1	Parent=gene2812
chrX	ENCODE	exon	153154016	153154102	.	-	.	Parent=gene2812
chrX	ENCODE	CDS	153154016	153154102	.	-	1	Parent=gene2812
chrX	ENCODE	exon	153154183	153154271	.	-	.	Parent=gene2812
chrX	ENCODE	CDS	153154183	153154271	.	-	0	Parent=gene2812
chrX	ENCODE	CDS	153154622	153154756	.	-	0	Parent=gene2812
chrX	ENCODE	exon	153154622	153154843	.	-	.	Parent=gene2812
chrX	ENCODE	exon	153158295	153158459	.	-	.	Parent=gene2812
###
chrX	ENCODE	gene	153150946	153158461	.	-	.	ID=gene2813;Name=XX-FW83563B9.2-002;name2=DNASE1L1
chrX	ENCODE	exon	153150946	153152029	.	-	.	Parent=gene2813
chrX	ENCODE	CDS	153151895	153152029	.	-	0	Parent=gene2813
chrX	ENCODE	exon	153152130	153152378	.	-	.	Parent=gene2813
chrX	ENCODE	CDS	153152130	153152378	.	-	0	Parent=gene2813
chrX	ENCODE	exon	153152457	153152569	.	-	.	Parent=gene2813
chrX	ENCODE	CDS	153152457	153152569	.	-	2	Parent=gene2813
chrX	ENCODE	exon	153152710	153152810	.	-	.	Parent=gene2813
chrX	ENCODE	CDS	153152710	153152810	.	-	1	Parent=gene2813
chrX	ENCODE	exon	153154016	153154102	.	-	.	Parent=gene2813
chrX	ENCODE	CDS	153154016	153154102	.	-	1	Parent=gene2813
chrX	ENCODE	exon	153154183	153154271	.	-	.	Parent=gene2813
chrX	ENCODE	CDS	153154183	153154271	.	-	0	Parent=gene2813
chrX	ENCODE	CDS	153154622	153154756	.	-	0	Parent=gene2813
chrX	ENCODE	exon	153154622	153154843	.	-	.	Parent=gene2813
chrX	ENCODE	exon	153157741	153158461	.	-	.	Parent=gene2813
###
chrX	ENCODE	gene	153150946	153159222	.	-	.	ID=gene2814;Name=XX-FW83563B9.2-001;name2=DNASE1L1
chrX	ENCODE	exon	153150946	153152029	.	-	.	Parent=gene2814
chrX	ENCODE	CDS	153151895	153152029	.	-	0	Parent=gene2814
chrX	ENCODE	exon	153152130	153152378	.	-	.	Parent=gene2814
chrX	ENCODE	CDS	153152130	153152378	.	-	0	Parent=gene2814
chrX	ENCODE	exon	153152457	153152569	.	-	.	Parent=gene2814
chrX	ENCODE	CDS	153152457	153152569	.	-	2	Parent=gene2814
chrX	ENCODE	exon	153152710	153152810	.	-	.	Parent=gene2814
chrX	ENCODE	CDS	153152710	153152810	.	-	1	Parent=gene2814
chrX	ENCODE	exon	153154016	153154102	.	-	.	Parent=gene2814
chrX	ENCODE	CDS	153154016	153154102	.	-	1	Parent=gene2814
chrX	ENCODE	exon	153154183	153154271	.	-	.	Parent=gene2814
chrX	ENCODE	CDS	153154183	153154271	.	-	0	Parent=gene2814
chrX	ENCODE	CDS	153154622	153154756	.	-	0	Parent=gene2814
chrX	ENCODE	exon	153154622	153154843	.	-	.	Parent=gene2814
chrX	ENCODE	exon	153158295	153158379	.	-	.	Parent=gene2814
chrX	ENCODE	exon	153158601	153159222	.	-	.	Parent=gene2814
###
chrX	ENCODE	gene	153150949	153161296	.	-	.	ID=gene2815;Name=XX-FW83563B9.2-004;name2=DNASE1L1
chrX	ENCODE	exon	153150949	153152029	.	-	.	Parent=gene2815
chrX	ENCODE	CDS	153151895	153152029	.	-	0	Parent=gene2815
chrX	ENCODE	exon	153152130	153152378	.	-	.	Parent=gene2815
chrX	ENCODE	CDS	153152130	153152378	.	-	0	Parent=gene2815
chrX	ENCODE	exon	153152457	153152569	.	-	.	Parent=gene2815
chrX	ENCODE	CDS	153152457	153152569	.	-	2	Parent=gene2815
chrX	ENCODE	exon	153152710	153152810	.	-	.	Parent=gene2815
chrX	ENCODE	CDS	153152710	153152810	.	-	1	Parent=gene2815
chrX	ENCODE	exon	153154016	153154102	.	-	.	Parent=gene2815
chrX	ENCODE	CDS	153154016	153154102	.	-	1	Parent=gene2815
chrX	ENCODE	exon	153154183	153154271	.	-	.	Parent=gene2815
chrX	ENCODE	CDS	153154183	153154271	.	-	0	Parent=gene2815
chrX	ENCODE	CDS	153154622	153154756	.	-	0	Parent=gene2815
chrX	ENCODE	exon	153154622	153154843	.	-	.	Parent=gene2815
chrX	ENCODE	exon	153158295	153158379	.	-	.	Parent=gene2815
chrX	ENCODE	exon	153161075	153161296	.	-	.	Parent=gene2815
###
chrX	ENCODE	gene	153151675	153152784	.	-	.	ID=gene2816;Name=XX-FW83563B9.2-007;name2=DNASE1L1
chrX	ENCODE	exon	153151675	153152378	.	-	.	Parent=gene2816
chrX	ENCODE	exon	153152457	153152569	.	-	.	Parent=gene2816
chrX	ENCODE	exon	153152710	153152784	.	-	.	Parent=gene2816
###
chrX	ENCODE	gene	153154016	153161266	.	-	.	ID=gene2817;Name=XX-FW83563B9.2-003;name2=DNASE1L1
chrX	ENCODE	exon	153154016	153154102	.	-	.	Parent=gene2817
chrX	ENCODE	CDS	153154016	153154102	.	-	1	Parent=gene2817
chrX	ENCODE	exon	153154183	153154271	.	-	.	Parent=gene2817
chrX	ENCODE	CDS	153154183	153154271	.	-	0	Parent=gene2817
chrX	ENCODE	CDS	153154622	153154756	.	-	0	Parent=gene2817
chrX	ENCODE	exon	153154622	153154843	.	-	.	Parent=gene2817
chrX	ENCODE	exon	153158295	153158379	.	-	.	Parent=gene2817
chrX	ENCODE	exon	153158601	153158858	.	-	.	Parent=gene2817
chrX	ENCODE	exon	153161075	153161266	.	-	.	Parent=gene2817
###
chrX	ENCODE	gene	153154677	153161273	.	-	.	ID=gene2818;Name=XX-FW83563B9.2-005;name2=DNASE1L1
chrX	ENCODE	CDS	153154677	153154756	.	-	0	Parent=gene2818
chrX	ENCODE	exon	153154677	153154843	.	-	.	Parent=gene2818
chrX	ENCODE	exon	153158295	153158379	.	-	.	Parent=gene2818
chrX	ENCODE	exon	153158601	153158996	.	-	.	Parent=gene2818
chrX	ENCODE	exon	153161075	153161273	.	-	.	Parent=gene2818
###
chrX	ENCODE	gene	153159152	153161264	.	-	.	ID=gene2819;Name=XX-FW83563B9.2-008;name2=DNASE1L1
chrX	ENCODE	exon	153159152	153159491	.	-	.	Parent=gene2819
chrX	ENCODE	exon	153159808	153160054	.	-	.	Parent=gene2819
chrX	ENCODE	exon	153161075	153161264	.	-	.	Parent=gene2819
###
chrX	ENCODE	gene	153160701	153170846	.	+	.	ID=gene2820;Name=XX-FW83563B9.3-010;name2=TAZ
chrX	ENCODE	exon	153160701	153161136	.	+	.	Parent=gene2820
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2820
chrX	ENCODE	exon	153162391	153162523	.	+	.	Parent=gene2820
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2820
chrX	ENCODE	exon	153168729	153169280	.	+	.	Parent=gene2820
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2820
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2820
chrX	ENCODE	exon	153170089	153170846	.	+	.	Parent=gene2820
###
chrX	ENCODE	gene	153160707	153169228	.	+	.	ID=gene2821;Name=XX-FW83563B9.3-014;name2=TAZ
chrX	ENCODE	exon	153160707	153161136	.	+	.	Parent=gene2821
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2821
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2821
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2821
chrX	ENCODE	exon	153168729	153168809	.	+	.	Parent=gene2821
chrX	ENCODE	exon	153168891	153169228	.	+	.	Parent=gene2821
###
chrX	ENCODE	gene	153160738	153170879	.	+	.	ID=gene2822;Name=XX-FW83563B9.3-004;name2=TAZ
chrX	ENCODE	exon	153160738	153161136	.	+	.	Parent=gene2822
chrX	ENCODE	CDS	153161028	153161136	.	+	0	Parent=gene2822
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2822
chrX	ENCODE	CDS	153161270	153161398	.	+	2	Parent=gene2822
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2822
chrX	ENCODE	CDS	153162391	153162436	.	+	2	Parent=gene2822
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2822
chrX	ENCODE	CDS	153162666	153162751	.	+	1	Parent=gene2822
chrX	ENCODE	exon	153168729	153168809	.	+	.	Parent=gene2822
chrX	ENCODE	CDS	153168729	153168809	.	+	2	Parent=gene2822
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2822
chrX	ENCODE	CDS	153169218	153169280	.	+	2	Parent=gene2822
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2822
chrX	ENCODE	CDS	153169398	153169450	.	+	2	Parent=gene2822
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2822
chrX	ENCODE	CDS	153169844	153169921	.	+	0	Parent=gene2822
chrX	ENCODE	CDS	153170089	153170190	.	+	0	Parent=gene2822
chrX	ENCODE	exon	153170089	153170879	.	+	.	Parent=gene2822
###
chrX	ENCODE	gene	153160739	153169259	.	+	.	ID=gene2823;Name=XX-FW83563B9.3-012;name2=TAZ
chrX	ENCODE	exon	153160739	153161190	.	+	.	Parent=gene2823
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2823
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2823
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2823
chrX	ENCODE	exon	153168729	153168809	.	+	.	Parent=gene2823
chrX	ENCODE	exon	153168891	153168932	.	+	.	Parent=gene2823
chrX	ENCODE	exon	153169218	153169259	.	+	.	Parent=gene2823
###
chrX	ENCODE	gene	153160739	153170906	.	+	.	ID=gene2824;Name=XX-FW83563B9.3-002;name2=TAZ
chrX	ENCODE	exon	153160739	153161136	.	+	.	Parent=gene2824
chrX	ENCODE	CDS	153161028	153161136	.	+	0	Parent=gene2824
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2824
chrX	ENCODE	CDS	153161270	153161398	.	+	2	Parent=gene2824
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2824
chrX	ENCODE	CDS	153162391	153162436	.	+	2	Parent=gene2824
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2824
chrX	ENCODE	CDS	153162666	153162751	.	+	1	Parent=gene2824
chrX	ENCODE	exon	153168729	153168809	.	+	.	Parent=gene2824
chrX	ENCODE	CDS	153168729	153168809	.	+	2	Parent=gene2824
chrX	ENCODE	exon	153168891	153168932	.	+	.	Parent=gene2824
chrX	ENCODE	CDS	153168891	153168932	.	+	2	Parent=gene2824
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2824
chrX	ENCODE	CDS	153169218	153169280	.	+	2	Parent=gene2824
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2824
chrX	ENCODE	CDS	153169398	153169450	.	+	2	Parent=gene2824
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2824
chrX	ENCODE	CDS	153169844	153169921	.	+	0	Parent=gene2824
chrX	ENCODE	CDS	153170089	153170190	.	+	0	Parent=gene2824
chrX	ENCODE	exon	153170089	153170906	.	+	.	Parent=gene2824
###
chrX	ENCODE	gene	153160739	153170912	.	+	.	ID=gene2825;name2=TAZ;Name=XX-FW83563B9.3-001
chrX	ENCODE	exon	153160739	153161136	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153161028	153161136	.	+	0	Parent=gene2825
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153161270	153161398	.	+	2	Parent=gene2825
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153162391	153162436	.	+	2	Parent=gene2825
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153162666	153162751	.	+	1	Parent=gene2825
chrX	ENCODE	exon	153163285	153163374	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153163285	153163374	.	+	2	Parent=gene2825
chrX	ENCODE	exon	153168729	153168809	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153168729	153168809	.	+	2	Parent=gene2825
chrX	ENCODE	exon	153168891	153168932	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153168891	153168932	.	+	2	Parent=gene2825
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153169218	153169280	.	+	2	Parent=gene2825
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153169398	153169450	.	+	2	Parent=gene2825
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2825
chrX	ENCODE	CDS	153169844	153169921	.	+	0	Parent=gene2825
chrX	ENCODE	CDS	153170089	153170190	.	+	0	Parent=gene2825
chrX	ENCODE	exon	153170089	153170912	.	+	.	Parent=gene2825
###
chrX	ENCODE	gene	153160742	153162853	.	+	.	ID=gene2826;name2=TAZ;Name=XX-FW83563B9.3-009
chrX	ENCODE	exon	153160742	153161136	.	+	.	Parent=gene2826
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2826
chrX	ENCODE	exon	153162391	153162853	.	+	.	Parent=gene2826
###
chrX	ENCODE	gene	153160744	153170912	.	+	.	ID=gene2827;Name=XX-FW83563B9.3-005;name2=TAZ
chrX	ENCODE	exon	153160744	153161136	.	+	.	Parent=gene2827
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2827
chrX	ENCODE	exon	153162391	153162542	.	+	.	Parent=gene2827
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2827
chrX	ENCODE	exon	153168729	153168809	.	+	.	Parent=gene2827
chrX	ENCODE	exon	153168891	153168932	.	+	.	Parent=gene2827
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2827
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2827
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2827
chrX	ENCODE	exon	153170089	153170912	.	+	.	Parent=gene2827
###
chrX	ENCODE	gene	153160745	153162751	.	+	.	ID=gene2828;Name=XX-FW83563B9.3-015;name2=TAZ
chrX	ENCODE	exon	153160745	153161136	.	+	.	Parent=gene2828
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2828
chrX	ENCODE	exon	153162391	153162554	.	+	.	Parent=gene2828
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2828
###
chrX	ENCODE	gene	153160757	153169870	.	+	.	ID=gene2829;Name=XX-FW83563B9.3-016;name2=TAZ
chrX	ENCODE	exon	153160757	153161136	.	+	.	Parent=gene2829
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2829
chrX	ENCODE	exon	153162391	153162523	.	+	.	Parent=gene2829
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2829
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2829
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2829
chrX	ENCODE	exon	153169844	153169870	.	+	.	Parent=gene2829
###
chrX	ENCODE	gene	153160768	153163372	.	+	.	ID=gene2830;Name=XX-FW83563B9.3-011;name2=TAZ
chrX	ENCODE	exon	153160768	153161190	.	+	.	Parent=gene2830
chrX	ENCODE	CDS	153161028	153161190	.	+	0	Parent=gene2830
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2830
chrX	ENCODE	CDS	153161270	153161398	.	+	2	Parent=gene2830
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2830
chrX	ENCODE	CDS	153162391	153162436	.	+	2	Parent=gene2830
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2830
chrX	ENCODE	CDS	153162666	153162751	.	+	1	Parent=gene2830
chrX	ENCODE	exon	153163285	153163372	.	+	.	Parent=gene2830
chrX	ENCODE	CDS	153163285	153163372	.	+	2	Parent=gene2830
###
chrX	ENCODE	gene	153160788	153170906	.	+	.	ID=gene2831;Name=XX-FW83563B9.3-003;name2=TAZ
chrX	ENCODE	exon	153160788	153161136	.	+	.	Parent=gene2831
chrX	ENCODE	CDS	153161028	153161136	.	+	0	Parent=gene2831
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2831
chrX	ENCODE	CDS	153161270	153161398	.	+	2	Parent=gene2831
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2831
chrX	ENCODE	CDS	153162391	153162436	.	+	2	Parent=gene2831
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2831
chrX	ENCODE	CDS	153162666	153162751	.	+	1	Parent=gene2831
chrX	ENCODE	exon	153163285	153163374	.	+	.	Parent=gene2831
chrX	ENCODE	CDS	153163285	153163374	.	+	2	Parent=gene2831
chrX	ENCODE	exon	153168729	153168809	.	+	.	Parent=gene2831
chrX	ENCODE	CDS	153168729	153168809	.	+	2	Parent=gene2831
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2831
chrX	ENCODE	CDS	153169218	153169280	.	+	2	Parent=gene2831
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2831
chrX	ENCODE	CDS	153169398	153169450	.	+	2	Parent=gene2831
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2831
chrX	ENCODE	CDS	153169844	153169921	.	+	0	Parent=gene2831
chrX	ENCODE	CDS	153170089	153170190	.	+	0	Parent=gene2831
chrX	ENCODE	exon	153170089	153170906	.	+	.	Parent=gene2831
###
chrX	ENCODE	gene	153160808	153161867	.	+	.	ID=gene2832;Name=XX-FW83563B9.3-017;name2=TAZ
chrX	ENCODE	exon	153160808	153161136	.	+	.	Parent=gene2832
chrX	ENCODE	exon	153161270	153161867	.	+	.	Parent=gene2832
###
chrX	ENCODE	gene	153160943	153170912	.	+	.	ID=gene2833;Name=XX-FW83563B9.3-006;name2=TAZ
chrX	ENCODE	exon	153160943	153161190	.	+	.	Parent=gene2833
chrX	ENCODE	CDS	153161028	153161190	.	+	0	Parent=gene2833
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2833
chrX	ENCODE	CDS	153162391	153162436	.	+	2	Parent=gene2833
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2833
chrX	ENCODE	CDS	153162666	153162751	.	+	1	Parent=gene2833
chrX	ENCODE	exon	153168729	153168809	.	+	.	Parent=gene2833
chrX	ENCODE	CDS	153168729	153168809	.	+	2	Parent=gene2833
chrX	ENCODE	exon	153169218	153169450	.	+	.	Parent=gene2833
chrX	ENCODE	CDS	153169218	153169450	.	+	2	Parent=gene2833
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2833
chrX	ENCODE	CDS	153169844	153169921	.	+	0	Parent=gene2833
chrX	ENCODE	CDS	153170089	153170190	.	+	0	Parent=gene2833
chrX	ENCODE	exon	153170089	153170912	.	+	.	Parent=gene2833
###
chrX	ENCODE	gene	153161028	153170190	.	+	.	ID=gene2834;Name=XX-FW83563B9.3-026;name2=TAZ
chrX	ENCODE	exon	153161028	153161136	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153161028	153161136	.	+	0	Parent=gene2834
chrX	ENCODE	exon	153161270	153161398	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153161270	153161398	.	+	2	Parent=gene2834
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153162391	153162436	.	+	2	Parent=gene2834
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153162666	153162751	.	+	1	Parent=gene2834
chrX	ENCODE	exon	153163285	153163374	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153163285	153163374	.	+	2	Parent=gene2834
chrX	ENCODE	exon	153168891	153168932	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153168891	153168932	.	+	2	Parent=gene2834
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153169218	153169280	.	+	2	Parent=gene2834
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153169398	153169450	.	+	2	Parent=gene2834
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153169844	153169921	.	+	0	Parent=gene2834
chrX	ENCODE	exon	153170089	153170190	.	+	.	Parent=gene2834
chrX	ENCODE	CDS	153170089	153170190	.	+	0	Parent=gene2834
###
chrX	ENCODE	gene	153161345	153170178	.	+	.	ID=gene2835;Name=XX-FW83563B9.3-018;name2=TAZ
chrX	ENCODE	exon	153161345	153161398	.	+	.	Parent=gene2835
chrX	ENCODE	exon	153162391	153162536	.	+	.	Parent=gene2835
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2835
chrX	ENCODE	exon	153163285	153163374	.	+	.	Parent=gene2835
chrX	ENCODE	exon	153168729	153168932	.	+	.	Parent=gene2835
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2835
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2835
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2835
chrX	ENCODE	exon	153170089	153170178	.	+	.	Parent=gene2835
###
chrX	ENCODE	gene	153161387	153168972	.	+	.	ID=gene2836;name2=TAZ;Name=XX-FW83563B9.3-021
chrX	ENCODE	exon	153161387	153161398	.	+	.	Parent=gene2836
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2836
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2836
chrX	ENCODE	exon	153168729	153168972	.	+	.	Parent=gene2836
###
chrX	ENCODE	gene	153161899	153169138	.	+	.	ID=gene2837;Name=XX-FW83563B9.3-019;name2=TAZ
chrX	ENCODE	exon	153161899	153162049	.	+	.	Parent=gene2837
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2837
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2837
chrX	ENCODE	exon	153163285	153163374	.	+	.	Parent=gene2837
chrX	ENCODE	exon	153168729	153169138	.	+	.	Parent=gene2837
###
chrX	ENCODE	gene	153161905	153162751	.	+	.	ID=gene2838;Name=XX-FW83563B9.3-013;name2=TAZ
chrX	ENCODE	exon	153161905	153162171	.	+	.	Parent=gene2838
chrX	ENCODE	exon	153162391	153162436	.	+	.	Parent=gene2838
chrX	ENCODE	exon	153162666	153162751	.	+	.	Parent=gene2838
###
chrX	ENCODE	gene	153162149	153169015	.	+	.	ID=gene2839;Name=XX-FW83563B9.3-007;name2=TAZ
chrX	ENCODE	exon	153162149	153162751	.	+	.	Parent=gene2839
chrX	ENCODE	exon	153168729	153169015	.	+	.	Parent=gene2839
###
chrX	ENCODE	gene	153162275	153163325	.	+	.	ID=gene2840;Name=XX-FW83563B9.3-020;name2=TAZ
chrX	ENCODE	exon	153162275	153162751	.	+	.	Parent=gene2840
chrX	ENCODE	exon	153163285	153163325	.	+	.	Parent=gene2840
###
chrX	ENCODE	gene	153162713	153169327	.	+	.	ID=gene2841;name2=TAZ;Name=XX-FW83563B9.3-022
chrX	ENCODE	exon	153162713	153162751	.	+	.	Parent=gene2841
chrX	ENCODE	exon	153168729	153168809	.	+	.	Parent=gene2841
chrX	ENCODE	exon	153168891	153168932	.	+	.	Parent=gene2841
chrX	ENCODE	exon	153169218	153169327	.	+	.	Parent=gene2841
###
chrX	ENCODE	gene	153167661	153170908	.	+	.	ID=gene2842;Name=XX-FW83563B9.3-008;name2=TAZ
chrX	ENCODE	exon	153167661	153168932	.	+	.	Parent=gene2842
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2842
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2842
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2842
chrX	ENCODE	exon	153170089	153170908	.	+	.	Parent=gene2842
###
chrX	ENCODE	gene	153168760	153170912	.	+	.	ID=gene2843;Name=XX-FW83563B9.3-025;name2=TAZ
chrX	ENCODE	exon	153168760	153168932	.	+	.	Parent=gene2843
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2843
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2843
chrX	ENCODE	exon	153169844	153169879	.	+	.	Parent=gene2843
chrX	ENCODE	exon	153170597	153170912	.	+	.	Parent=gene2843
###
chrX	ENCODE	gene	153168839	153170223	.	+	.	ID=gene2844;Name=XX-FW83563B9.3-023;name2=TAZ
chrX	ENCODE	exon	153168839	153168932	.	+	.	Parent=gene2844
chrX	ENCODE	exon	153169218	153169280	.	+	.	Parent=gene2844
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2844
chrX	ENCODE	exon	153169898	153169921	.	+	.	Parent=gene2844
chrX	ENCODE	exon	153170089	153170223	.	+	.	Parent=gene2844
###
chrX	ENCODE	gene	153169177	153170510	.	+	.	ID=gene2845;Name=XX-FW83563B9.3-024;name2=TAZ
chrX	ENCODE	exon	153169177	153169280	.	+	.	Parent=gene2845
chrX	ENCODE	exon	153169398	153169450	.	+	.	Parent=gene2845
chrX	ENCODE	exon	153169844	153169921	.	+	.	Parent=gene2845
chrX	ENCODE	exon	153170089	153170322	.	+	.	Parent=gene2845
chrX	ENCODE	exon	153170443	153170510	.	+	.	Parent=gene2845
###
chrX	ENCODE	gene	153177831	153183639	.	+	.	ID=gene2846;Name=XX-FW83563B9.4-001;name2=ATP6AP1
chrX	ENCODE	exon	153177831	153178046	.	+	.	Parent=gene2846
chrX	ENCODE	exon	153178241	153178367	.	+	.	Parent=gene2846
chrX	ENCODE	exon	153181023	153181097	.	+	.	Parent=gene2846
chrX	ENCODE	exon	153181459	153181652	.	+	.	Parent=gene2846
chrX	ENCODE	exon	153182124	153182164	.	+	.	Parent=gene2846
chrX	ENCODE	exon	153182828	153182913	.	+	.	Parent=gene2846
chrX	ENCODE	exon	153183401	153183639	.	+	.	Parent=gene2846
###
chrX	ENCODE	gene	153177838	153183639	.	+	.	ID=gene2847;Name=XX-FW83563B9.4-003;name2=ATP6AP1
chrX	ENCODE	exon	153177838	153178046	.	+	.	Parent=gene2847
chrX	ENCODE	exon	153178241	153178367	.	+	.	Parent=gene2847
chrX	ENCODE	exon	153181023	153181097	.	+	.	Parent=gene2847
chrX	ENCODE	exon	153181459	153181569	.	+	.	Parent=gene2847
chrX	ENCODE	exon	153183401	153183639	.	+	.	Parent=gene2847
###
chrX	ENCODE	gene	153177891	153183639	.	+	.	ID=gene2848;Name=XX-FW83563B9.4-002;name2=ATP6AP1
chrX	ENCODE	exon	153177891	153178046	.	+	.	Parent=gene2848
chrX	ENCODE	exon	153178241	153180850	.	+	.	Parent=gene2848
chrX	ENCODE	exon	153181023	153181097	.	+	.	Parent=gene2848
chrX	ENCODE	exon	153181459	153181652	.	+	.	Parent=gene2848
chrX	ENCODE	exon	153182124	153182164	.	+	.	Parent=gene2848
chrX	ENCODE	exon	153182828	153182913	.	+	.	Parent=gene2848
chrX	ENCODE	exon	153183401	153183639	.	+	.	Parent=gene2848
###
chrX	ENCODE	gene	153177934	153183639	.	+	.	ID=gene2849;Name=XX-FW83563B9.4-006;name2=ATP6AP1
chrX	ENCODE	exon	153177934	153178046	.	+	.	Parent=gene2849
chrX	ENCODE	exon	153178241	153178367	.	+	.	Parent=gene2849
chrX	ENCODE	exon	153181023	153181097	.	+	.	Parent=gene2849
chrX	ENCODE	exon	153182853	153182913	.	+	.	Parent=gene2849
chrX	ENCODE	exon	153183401	153183639	.	+	.	Parent=gene2849
###
chrX	ENCODE	gene	153178038	153183639	.	+	.	ID=gene2850;Name=XX-FW83563B9.4-004;name2=ATP6AP1
chrX	ENCODE	exon	153178038	153178367	.	+	.	Parent=gene2850
chrX	ENCODE	exon	153181023	153181097	.	+	.	Parent=gene2850
chrX	ENCODE	exon	153181459	153181652	.	+	.	Parent=gene2850
chrX	ENCODE	exon	153182124	153182164	.	+	.	Parent=gene2850
chrX	ENCODE	exon	153182828	153182913	.	+	.	Parent=gene2850
chrX	ENCODE	exon	153183401	153183639	.	+	.	Parent=gene2850
###
chrX	ENCODE	gene	153236208	153242706	.	+	.	ID=gene2851;Name=XX-FW81657B9.2-001;name2=FAM50A
chrX	ENCODE	exon	153236208	153236397	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153236287	153236397	.	+	0	Parent=gene2851
chrX	ENCODE	exon	153237685	153237769	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153237685	153237769	.	+	0	Parent=gene2851
chrX	ENCODE	exon	153237864	153237963	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153237864	153237963	.	+	2	Parent=gene2851
chrX	ENCODE	exon	153238467	153238612	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153238467	153238612	.	+	1	Parent=gene2851
chrX	ENCODE	exon	153240536	153240612	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153240536	153240612	.	+	2	Parent=gene2851
chrX	ENCODE	exon	153240742	153240808	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153240742	153240808	.	+	0	Parent=gene2851
chrX	ENCODE	exon	153240945	153241006	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153240945	153241006	.	+	2	Parent=gene2851
chrX	ENCODE	exon	153241273	153241349	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153241273	153241349	.	+	0	Parent=gene2851
chrX	ENCODE	exon	153241733	153241787	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153241733	153241787	.	+	1	Parent=gene2851
chrX	ENCODE	exon	153241935	153241983	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153241935	153241983	.	+	0	Parent=gene2851
chrX	ENCODE	exon	153242081	153242151	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153242081	153242151	.	+	2	Parent=gene2851
chrX	ENCODE	exon	153242261	153242371	.	+	.	Parent=gene2851
chrX	ENCODE	CDS	153242261	153242371	.	+	0	Parent=gene2851
chrX	ENCODE	CDS	153242476	153242484	.	+	0	Parent=gene2851
chrX	ENCODE	exon	153242476	153242706	.	+	.	Parent=gene2851
###
chrX	ENCODE	gene	153236511	153242151	.	+	.	ID=gene2852;Name=XX-FW81657B9.2-002;name2=FAM50A
chrX	ENCODE	exon	153236511	153236961	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153237685	153237769	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153237864	153237963	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153238467	153238612	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153240536	153240612	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153240742	153240808	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153240945	153241006	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153241273	153241349	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153241733	153241787	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153241935	153241983	.	+	.	Parent=gene2852
chrX	ENCODE	exon	153242081	153242151	.	+	.	Parent=gene2852
###
chrX	ENCODE	gene	153237495	153237934	.	+	.	ID=gene2853;Name=XX-FW81657B9.2-003;name2=FAM50A
chrX	ENCODE	exon	153237495	153237769	.	+	.	Parent=gene2853
chrX	ENCODE	exon	153237864	153237934	.	+	.	Parent=gene2853
###
chrX	ENCODE	gene	153238318	153241187	.	+	.	ID=gene2854;Name=XX-FW81657B9.2-004;name2=FAM50A
chrX	ENCODE	exon	153238318	153238612	.	+	.	Parent=gene2854
chrX	ENCODE	exon	153240536	153240612	.	+	.	Parent=gene2854
chrX	ENCODE	exon	153240742	153240808	.	+	.	Parent=gene2854
chrX	ENCODE	exon	153240945	153241187	.	+	.	Parent=gene2854
###
chrX	ENCODE	gene	153238467	153242706	.	+	.	ID=gene2855;name2=FAM50A;Name=XX-FW81657B9.2-005
chrX	ENCODE	exon	153238467	153238612	.	+	.	Parent=gene2855
chrX	ENCODE	exon	153240536	153240612	.	+	.	Parent=gene2855
chrX	ENCODE	exon	153240742	153240808	.	+	.	Parent=gene2855
chrX	ENCODE	exon	153240945	153241006	.	+	.	Parent=gene2855
chrX	ENCODE	exon	153241273	153241349	.	+	.	Parent=gene2855
chrX	ENCODE	exon	153241733	153241983	.	+	.	Parent=gene2855
chrX	ENCODE	exon	153242081	153242151	.	+	.	Parent=gene2855
chrX	ENCODE	exon	153242261	153242371	.	+	.	Parent=gene2855
chrX	ENCODE	exon	153242476	153242706	.	+	.	Parent=gene2855
###
chrX	ENCODE	gene	153241939	153242341	.	+	.	ID=gene2856;Name=XX-FW81657B9.2-006;name2=FAM50A
chrX	ENCODE	exon	153241939	153242151	.	+	.	Parent=gene2856
chrX	ENCODE	exon	153242261	153242341	.	+	.	Parent=gene2856
###
chrX	ENCODE	gene	153250325	153265693	.	+	.	ID=gene2857;name2=PLXNA3;Name=XX-FW81657B9.3-001
chrX	ENCODE	exon	153250325	153250472	.	+	.	Parent=gene2857
chrX	ENCODE	exon	153252201	153252821	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153252228	153252821	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153253143	153253682	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153253143	153253682	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153254172	153254354	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153254172	153254354	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153255438	153255566	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153255438	153255566	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153255637	153255737	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153255637	153255737	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153255998	153256121	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153255998	153256121	.	+	1	Parent=gene2857
chrX	ENCODE	exon	153256204	153256360	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153256204	153256360	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153256449	153256548	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153256449	153256548	.	+	2	Parent=gene2857
chrX	ENCODE	exon	153256801	153256915	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153256801	153256915	.	+	1	Parent=gene2857
chrX	ENCODE	exon	153257065	153257265	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153257065	153257265	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153257471	153257567	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153257471	153257567	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153257704	153257894	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153257704	153257894	.	+	2	Parent=gene2857
chrX	ENCODE	exon	153257982	153258127	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153257982	153258127	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153258197	153258317	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153258197	153258317	.	+	1	Parent=gene2857
chrX	ENCODE	exon	153258423	153258559	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153258423	153258559	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153258670	153258840	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153258670	153258840	.	+	1	Parent=gene2857
chrX	ENCODE	exon	153259104	153259197	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153259104	153259197	.	+	1	Parent=gene2857
chrX	ENCODE	exon	153259279	153259518	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153259279	153259518	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153259592	153259735	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153259592	153259735	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153259814	153260048	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153259814	153260048	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153260129	153260271	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153260129	153260271	.	+	2	Parent=gene2857
chrX	ENCODE	exon	153260350	153260606	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153260350	153260606	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153260710	153260776	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153260710	153260776	.	+	1	Parent=gene2857
chrX	ENCODE	exon	153260870	153261016	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153260870	153261016	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153261103	153261262	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153261103	153261262	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153261426	153261529	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153261426	153261529	.	+	2	Parent=gene2857
chrX	ENCODE	exon	153261735	153261831	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153261735	153261831	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153262024	153262214	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153262024	153262214	.	+	2	Parent=gene2857
chrX	ENCODE	exon	153262489	153262658	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153262489	153262658	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153263152	153263364	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153263152	153263364	.	+	1	Parent=gene2857
chrX	ENCODE	exon	153263535	153263685	.	+	.	Parent=gene2857
chrX	ENCODE	CDS	153263535	153263685	.	+	1	Parent=gene2857
chrX	ENCODE	CDS	153264637	153264732	.	+	0	Parent=gene2857
chrX	ENCODE	exon	153264637	153265693	.	+	.	Parent=gene2857
###
chrX	ENCODE	gene	153250328	153253418	.	+	.	ID=gene2858;Name=XX-FW81657B9.3-008;name2=PLXNA3
chrX	ENCODE	exon	153250328	153250472	.	+	.	Parent=gene2858
chrX	ENCODE	exon	153253143	153253418	.	+	.	Parent=gene2858
###
chrX	ENCODE	gene	153258138	153258812	.	+	.	ID=gene2859;Name=XX-FW81657B9.3-004;name2=PLXNA3
chrX	ENCODE	exon	153258138	153258317	.	+	.	Parent=gene2859
chrX	ENCODE	exon	153258423	153258559	.	+	.	Parent=gene2859
chrX	ENCODE	exon	153258670	153258812	.	+	.	Parent=gene2859
###
chrX	ENCODE	gene	153258466	153259222	.	+	.	ID=gene2860;Name=XX-FW81657B9.3-005;name2=PLXNA3
chrX	ENCODE	exon	153258466	153258559	.	+	.	Parent=gene2860
chrX	ENCODE	exon	153258670	153258840	.	+	.	Parent=gene2860
chrX	ENCODE	exon	153259104	153259222	.	+	.	Parent=gene2860
###
chrX	ENCODE	gene	153260664	153260916	.	+	.	ID=gene2861;Name=XX-FW81657B9.3-006;name2=PLXNA3
chrX	ENCODE	exon	153260664	153260776	.	+	.	Parent=gene2861
chrX	ENCODE	exon	153260870	153260916	.	+	.	Parent=gene2861
###
chrX	ENCODE	gene	153260708	153261397	.	+	.	ID=gene2862;Name=XX-FW81657B9.3-003;name2=PLXNA3
chrX	ENCODE	exon	153260708	153261016	.	+	.	Parent=gene2862
chrX	ENCODE	exon	153261103	153261397	.	+	.	Parent=gene2862
###
chrX	ENCODE	gene	153261129	153262755	.	+	.	ID=gene2863;Name=XX-FW81657B9.3-007;name2=PLXNA3
chrX	ENCODE	exon	153261129	153261262	.	+	.	Parent=gene2863
chrX	ENCODE	exon	153261426	153261529	.	+	.	Parent=gene2863
chrX	ENCODE	exon	153261735	153261831	.	+	.	Parent=gene2863
chrX	ENCODE	exon	153262024	153262214	.	+	.	Parent=gene2863
chrX	ENCODE	exon	153262489	153262755	.	+	.	Parent=gene2863
###
chrX	ENCODE	gene	153262894	153264743	.	+	.	ID=gene2864;Name=XX-FW81657B9.3-002;name2=PLXNA3
chrX	ENCODE	exon	153262894	153263364	.	+	.	Parent=gene2864
chrX	ENCODE	exon	153263535	153263685	.	+	.	Parent=gene2864
chrX	ENCODE	exon	153264637	153264743	.	+	.	Parent=gene2864
###
chrX	ENCODE	gene	153269812	153271300	.	-	.	ID=gene2865;Name=XX-FW81657B9.4-001;name2=LAGE3
chrX	ENCODE	exon	153269812	153270101	.	-	.	Parent=gene2865
chrX	ENCODE	CDS	153269987	153270101	.	-	1	Parent=gene2865
chrX	ENCODE	exon	153270326	153270454	.	-	.	Parent=gene2865
chrX	ENCODE	CDS	153270326	153270454	.	-	1	Parent=gene2865
chrX	ENCODE	CDS	153270771	153270958	.	-	0	Parent=gene2865
chrX	ENCODE	exon	153270771	153271300	.	-	.	Parent=gene2865
###
chrX	ENCODE	gene	153275760	153278704	.	-	.	ID=gene2866;Name=XX-FW89031B12.1-001;name2=UBL4
chrX	ENCODE	exon	153275760	153277692	.	-	.	Parent=gene2866
chrX	ENCODE	CDS	153277582	153277692	.	-	0	Parent=gene2866
chrX	ENCODE	exon	153277814	153278022	.	-	.	Parent=gene2866
chrX	ENCODE	CDS	153277814	153278022	.	-	2	Parent=gene2866
chrX	ENCODE	exon	153278271	153278376	.	-	.	Parent=gene2866
chrX	ENCODE	CDS	153278271	153278376	.	-	0	Parent=gene2866
chrX	ENCODE	CDS	153278580	153278627	.	-	0	Parent=gene2866
chrX	ENCODE	exon	153278580	153278704	.	-	.	Parent=gene2866
###
chrX	ENCODE	gene	153276326	153278655	.	-	.	ID=gene2867;Name=XX-FW89031B12.1-003;name2=UBL4
chrX	ENCODE	exon	153276326	153277692	.	-	.	Parent=gene2867
chrX	ENCODE	exon	153277814	153278022	.	-	.	Parent=gene2867
chrX	ENCODE	exon	153278580	153278655	.	-	.	Parent=gene2867
###
chrX	ENCODE	gene	153277236	153278658	.	-	.	ID=gene2868;Name=XX-FW89031B12.1-002;name2=UBL4
chrX	ENCODE	exon	153277236	153277505	.	-	.	Parent=gene2868
chrX	ENCODE	CDS	153277373	153277505	.	-	1	Parent=gene2868
chrX	ENCODE	exon	153277646	153277692	.	-	.	Parent=gene2868
chrX	ENCODE	CDS	153277646	153277692	.	-	0	Parent=gene2868
chrX	ENCODE	exon	153277814	153278022	.	-	.	Parent=gene2868
chrX	ENCODE	CDS	153277814	153278022	.	-	2	Parent=gene2868
chrX	ENCODE	exon	153278271	153278376	.	-	.	Parent=gene2868
chrX	ENCODE	CDS	153278271	153278376	.	-	0	Parent=gene2868
chrX	ENCODE	CDS	153278580	153278627	.	-	0	Parent=gene2868
chrX	ENCODE	exon	153278580	153278658	.	-	.	Parent=gene2868
###
chrX	ENCODE	gene	153277396	153278145	.	-	.	ID=gene2869;Name=XX-FW89031B12.1-004;name2=UBL4
chrX	ENCODE	exon	153277396	153277692	.	-	.	Parent=gene2869
chrX	ENCODE	exon	153277814	153278145	.	-	.	Parent=gene2869
###
chrX	ENCODE	gene	153277419	153278629	.	-	.	ID=gene2870;Name=XX-FW89031B12.1-005;name2=UBL4
chrX	ENCODE	exon	153277419	153277692	.	-	.	Parent=gene2870
chrX	ENCODE	exon	153277814	153278126	.	-	.	Parent=gene2870
chrX	ENCODE	exon	153278271	153278376	.	-	.	Parent=gene2870
chrX	ENCODE	exon	153278580	153278629	.	-	.	Parent=gene2870
###
chrX	ENCODE	gene	153279349	153282657	.	-	.	ID=gene2871;Name=XX-FW89031B12.2-001;name2=SLC10A3
chrX	ENCODE	exon	153279349	153280539	.	-	.	Parent=gene2871
chrX	ENCODE	CDS	153279550	153280539	.	-	0	Parent=gene2871
chrX	ENCODE	CDS	153280627	153280983	.	-	0	Parent=gene2871
chrX	ENCODE	exon	153280627	153281125	.	-	.	Parent=gene2871
chrX	ENCODE	exon	153282350	153282401	.	-	.	Parent=gene2871
chrX	ENCODE	exon	153282637	153282657	.	-	.	Parent=gene2871
###
chrX	ENCODE	gene	153279354	153282671	.	-	.	ID=gene2872;Name=XX-FW89031B12.2-004;name2=SLC10A3
chrX	ENCODE	exon	153279354	153281125	.	-	.	Parent=gene2872
chrX	ENCODE	CDS	153279550	153280983	.	-	0	Parent=gene2872
chrX	ENCODE	exon	153281985	153282070	.	-	.	Parent=gene2872
chrX	ENCODE	exon	153282637	153282671	.	-	.	Parent=gene2872
###
chrX	ENCODE	gene	153279386	153282706	.	-	.	ID=gene2873;Name=XX-FW89031B12.2-002;name2=SLC10A3
chrX	ENCODE	exon	153279386	153281125	.	-	.	Parent=gene2873
chrX	ENCODE	CDS	153279550	153280983	.	-	0	Parent=gene2873
chrX	ENCODE	exon	153282350	153282401	.	-	.	Parent=gene2873
chrX	ENCODE	exon	153282637	153282706	.	-	.	Parent=gene2873
###
chrX	ENCODE	gene	153280330	153282700	.	-	.	ID=gene2874;Name=XX-FW89031B12.2-003;name2=SLC10A3
chrX	ENCODE	CDS	153280330	153280983	.	-	0	Parent=gene2874
chrX	ENCODE	exon	153280330	153281125	.	-	.	Parent=gene2874
chrX	ENCODE	exon	153282350	153282700	.	-	.	Parent=gene2874
###
chrX	ENCODE	gene	153298194	153308264	.	-	.	ID=gene2875;Name=XX-FW89031B12.3-001;name2=FAM3A
chrX	ENCODE	exon	153298194	153298941	.	-	.	Parent=gene2875
chrX	ENCODE	CDS	153298846	153298941	.	-	0	Parent=gene2875
chrX	ENCODE	exon	153299238	153299364	.	-	.	Parent=gene2875
chrX	ENCODE	CDS	153299238	153299364	.	-	1	Parent=gene2875
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2875
chrX	ENCODE	CDS	153299441	153299525	.	-	2	Parent=gene2875
chrX	ENCODE	exon	153299846	153299896	.	-	.	Parent=gene2875
chrX	ENCODE	CDS	153299846	153299896	.	-	2	Parent=gene2875
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2875
chrX	ENCODE	CDS	153300324	153300382	.	-	1	Parent=gene2875
chrX	ENCODE	exon	153300509	153300632	.	-	.	Parent=gene2875
chrX	ENCODE	CDS	153300509	153300632	.	-	2	Parent=gene2875
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2875
chrX	ENCODE	CDS	153303885	153303908	.	-	2	Parent=gene2875
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2875
chrX	ENCODE	CDS	153304851	153304964	.	-	2	Parent=gene2875
chrX	ENCODE	CDS	153307788	153307800	.	-	0	Parent=gene2875
chrX	ENCODE	exon	153307788	153307840	.	-	.	Parent=gene2875
chrX	ENCODE	exon	153307938	153308264	.	-	.	Parent=gene2875
###
chrX	ENCODE	gene	153298206	153308144	.	-	.	ID=gene2876;Name=XX-FW89031B12.3-003;name2=FAM3A
chrX	ENCODE	exon	153298206	153298941	.	-	.	Parent=gene2876
chrX	ENCODE	CDS	153298846	153298941	.	-	0	Parent=gene2876
chrX	ENCODE	exon	153299238	153299364	.	-	.	Parent=gene2876
chrX	ENCODE	CDS	153299238	153299364	.	-	1	Parent=gene2876
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2876
chrX	ENCODE	CDS	153299441	153299525	.	-	2	Parent=gene2876
chrX	ENCODE	exon	153299846	153299896	.	-	.	Parent=gene2876
chrX	ENCODE	CDS	153299846	153299896	.	-	2	Parent=gene2876
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2876
chrX	ENCODE	CDS	153300324	153300382	.	-	1	Parent=gene2876
chrX	ENCODE	exon	153300509	153300632	.	-	.	Parent=gene2876
chrX	ENCODE	CDS	153300509	153300632	.	-	2	Parent=gene2876
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2876
chrX	ENCODE	CDS	153303885	153303908	.	-	2	Parent=gene2876
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2876
chrX	ENCODE	CDS	153304851	153304964	.	-	2	Parent=gene2876
chrX	ENCODE	CDS	153307788	153307800	.	-	0	Parent=gene2876
chrX	ENCODE	exon	153307788	153307840	.	-	.	Parent=gene2876
chrX	ENCODE	exon	153307997	153308144	.	-	.	Parent=gene2876
###
chrX	ENCODE	gene	153298206	153308267	.	-	.	ID=gene2877;Name=XX-FW89031B12.3-004;name2=FAM3A
chrX	ENCODE	exon	153298206	153298941	.	-	.	Parent=gene2877
chrX	ENCODE	CDS	153298846	153298941	.	-	0	Parent=gene2877
chrX	ENCODE	exon	153299238	153299364	.	-	.	Parent=gene2877
chrX	ENCODE	CDS	153299238	153299364	.	-	1	Parent=gene2877
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2877
chrX	ENCODE	CDS	153299441	153299525	.	-	2	Parent=gene2877
chrX	ENCODE	exon	153299846	153299896	.	-	.	Parent=gene2877
chrX	ENCODE	CDS	153299846	153299896	.	-	2	Parent=gene2877
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2877
chrX	ENCODE	CDS	153300324	153300382	.	-	1	Parent=gene2877
chrX	ENCODE	exon	153300509	153300632	.	-	.	Parent=gene2877
chrX	ENCODE	CDS	153300509	153300632	.	-	2	Parent=gene2877
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2877
chrX	ENCODE	CDS	153303885	153303908	.	-	2	Parent=gene2877
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2877
chrX	ENCODE	CDS	153304851	153304964	.	-	2	Parent=gene2877
chrX	ENCODE	CDS	153307788	153307800	.	-	0	Parent=gene2877
chrX	ENCODE	exon	153307788	153308267	.	-	.	Parent=gene2877
###
chrX	ENCODE	gene	153298206	153308270	.	-	.	ID=gene2878;Name=XX-FW89031B12.3-002;name2=FAM3A
chrX	ENCODE	exon	153298206	153298941	.	-	.	Parent=gene2878
chrX	ENCODE	exon	153299238	153299364	.	-	.	Parent=gene2878
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2878
chrX	ENCODE	exon	153299846	153299896	.	-	.	Parent=gene2878
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2878
chrX	ENCODE	exon	153300509	153300632	.	-	.	Parent=gene2878
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2878
chrX	ENCODE	exon	153304342	153304439	.	-	.	Parent=gene2878
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2878
chrX	ENCODE	exon	153307788	153308270	.	-	.	Parent=gene2878
###
chrX	ENCODE	gene	153298208	153303449	.	-	.	ID=gene2879;Name=XX-FW89031B12.3-005;name2=FAM3A
chrX	ENCODE	exon	153298208	153298941	.	-	.	Parent=gene2879
chrX	ENCODE	exon	153299238	153299364	.	-	.	Parent=gene2879
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2879
chrX	ENCODE	exon	153299846	153299896	.	-	.	Parent=gene2879
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2879
chrX	ENCODE	exon	153300509	153303449	.	-	.	Parent=gene2879
###
chrX	ENCODE	gene	153298239	153308270	.	-	.	ID=gene2880;Name=XX-FW89031B12.3-011;name2=FAM3A
chrX	ENCODE	exon	153298239	153298941	.	-	.	Parent=gene2880
chrX	ENCODE	exon	153299238	153299364	.	-	.	Parent=gene2880
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2880
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2880
chrX	ENCODE	exon	153300509	153300632	.	-	.	Parent=gene2880
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2880
chrX	ENCODE	exon	153304342	153304439	.	-	.	Parent=gene2880
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2880
chrX	ENCODE	exon	153307788	153308270	.	-	.	Parent=gene2880
###
chrX	ENCODE	gene	153298570	153308266	.	-	.	ID=gene2881;Name=XX-FW89031B12.3-012;name2=FAM3A
chrX	ENCODE	exon	153298570	153298941	.	-	.	Parent=gene2881
chrX	ENCODE	CDS	153298846	153298941	.	-	0	Parent=gene2881
chrX	ENCODE	exon	153299238	153299364	.	-	.	Parent=gene2881
chrX	ENCODE	CDS	153299238	153299364	.	-	1	Parent=gene2881
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2881
chrX	ENCODE	CDS	153299441	153299525	.	-	2	Parent=gene2881
chrX	ENCODE	exon	153299846	153299917	.	-	.	Parent=gene2881
chrX	ENCODE	CDS	153299846	153299917	.	-	2	Parent=gene2881
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2881
chrX	ENCODE	CDS	153300324	153300382	.	-	1	Parent=gene2881
chrX	ENCODE	exon	153300509	153300632	.	-	.	Parent=gene2881
chrX	ENCODE	CDS	153300509	153300632	.	-	2	Parent=gene2881
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2881
chrX	ENCODE	CDS	153303885	153303908	.	-	2	Parent=gene2881
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2881
chrX	ENCODE	CDS	153304851	153304964	.	-	2	Parent=gene2881
chrX	ENCODE	CDS	153307788	153307800	.	-	0	Parent=gene2881
chrX	ENCODE	exon	153307788	153307840	.	-	.	Parent=gene2881
chrX	ENCODE	exon	153307938	153308266	.	-	.	Parent=gene2881
###
chrX	ENCODE	gene	153298746	153299626	.	-	.	ID=gene2882;Name=XX-FW89031B12.3-010;name2=FAM3A
chrX	ENCODE	exon	153298746	153298941	.	-	.	Parent=gene2882
chrX	ENCODE	exon	153299238	153299626	.	-	.	Parent=gene2882
###
chrX	ENCODE	gene	153298890	153308188	.	-	.	ID=gene2883;Name=XX-FW89031B12.3-017;name2=FAM3A
chrX	ENCODE	exon	153298890	153298941	.	-	.	Parent=gene2883
chrX	ENCODE	CDS	153298890	153298941	.	-	0	Parent=gene2883
chrX	ENCODE	exon	153299238	153299364	.	-	.	Parent=gene2883
chrX	ENCODE	CDS	153299238	153299364	.	-	1	Parent=gene2883
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2883
chrX	ENCODE	CDS	153299441	153299525	.	-	2	Parent=gene2883
chrX	ENCODE	exon	153299846	153299896	.	-	.	Parent=gene2883
chrX	ENCODE	CDS	153299846	153299896	.	-	2	Parent=gene2883
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2883
chrX	ENCODE	CDS	153300324	153300382	.	-	1	Parent=gene2883
chrX	ENCODE	exon	153300509	153300632	.	-	.	Parent=gene2883
chrX	ENCODE	CDS	153300509	153300632	.	-	2	Parent=gene2883
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2883
chrX	ENCODE	CDS	153303885	153303908	.	-	2	Parent=gene2883
chrX	ENCODE	CDS	153307788	153307800	.	-	0	Parent=gene2883
chrX	ENCODE	exon	153307788	153307840	.	-	.	Parent=gene2883
chrX	ENCODE	exon	153307938	153308188	.	-	.	Parent=gene2883
###
chrX	ENCODE	gene	153299238	153308258	.	-	.	ID=gene2884;Name=XX-FW89031B12.3-007;name2=FAM3A
chrX	ENCODE	exon	153299238	153299364	.	-	.	Parent=gene2884
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2884
chrX	ENCODE	exon	153299846	153299896	.	-	.	Parent=gene2884
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2884
chrX	ENCODE	exon	153300509	153300632	.	-	.	Parent=gene2884
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2884
chrX	ENCODE	exon	153304342	153304439	.	-	.	Parent=gene2884
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2884
chrX	ENCODE	exon	153307788	153307840	.	-	.	Parent=gene2884
chrX	ENCODE	exon	153307938	153308258	.	-	.	Parent=gene2884
###
chrX	ENCODE	gene	153299282	153308243	.	-	.	ID=gene2885;Name=XX-FW89031B12.3-008;name2=FAM3A
chrX	ENCODE	exon	153299282	153299364	.	-	.	Parent=gene2885
chrX	ENCODE	exon	153299441	153299525	.	-	.	Parent=gene2885
chrX	ENCODE	exon	153299846	153299896	.	-	.	Parent=gene2885
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2885
chrX	ENCODE	exon	153300509	153300846	.	-	.	Parent=gene2885
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2885
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2885
chrX	ENCODE	exon	153307788	153307840	.	-	.	Parent=gene2885
chrX	ENCODE	exon	153307938	153308243	.	-	.	Parent=gene2885
###
chrX	ENCODE	gene	153299715	153307849	.	-	.	ID=gene2886;Name=XX-FW89031B12.3-013;name2=FAM3A
chrX	ENCODE	exon	153299715	153299896	.	-	.	Parent=gene2886
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2886
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2886
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2886
chrX	ENCODE	exon	153307788	153307849	.	-	.	Parent=gene2886
###
chrX	ENCODE	gene	153299846	153308265	.	-	.	ID=gene2887;Name=XX-FW89031B12.3-006;name2=FAM3A
chrX	ENCODE	exon	153299846	153299896	.	-	.	Parent=gene2887
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2887
chrX	ENCODE	exon	153300509	153300687	.	-	.	Parent=gene2887
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2887
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2887
chrX	ENCODE	exon	153307788	153308265	.	-	.	Parent=gene2887
###
chrX	ENCODE	gene	153300324	153308198	.	-	.	ID=gene2888;Name=XX-FW89031B12.3-009;name2=FAM3A
chrX	ENCODE	exon	153300324	153300382	.	-	.	Parent=gene2888
chrX	ENCODE	exon	153300509	153300846	.	-	.	Parent=gene2888
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2888
chrX	ENCODE	exon	153307788	153308198	.	-	.	Parent=gene2888
###
chrX	ENCODE	gene	153300351	153308193	.	-	.	ID=gene2889;Name=XX-FW89031B12.3-016;name2=FAM3A
chrX	ENCODE	exon	153300351	153300382	.	-	.	Parent=gene2889
chrX	ENCODE	exon	153300509	153300687	.	-	.	Parent=gene2889
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2889
chrX	ENCODE	exon	153304342	153304439	.	-	.	Parent=gene2889
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2889
chrX	ENCODE	exon	153307788	153308193	.	-	.	Parent=gene2889
###
chrX	ENCODE	gene	153300488	153308186	.	-	.	ID=gene2890;Name=XX-FW89031B12.3-019;name2=FAM3A
chrX	ENCODE	exon	153300488	153300632	.	-	.	Parent=gene2890
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2890
chrX	ENCODE	exon	153307788	153308186	.	-	.	Parent=gene2890
###
chrX	ENCODE	gene	153300607	153308237	.	-	.	ID=gene2891;Name=XX-FW89031B12.3-018;name2=FAM3A
chrX	ENCODE	exon	153300607	153300632	.	-	.	Parent=gene2891
chrX	ENCODE	CDS	153300607	153300632	.	-	2	Parent=gene2891
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2891
chrX	ENCODE	CDS	153303885	153303908	.	-	2	Parent=gene2891
chrX	ENCODE	CDS	153307788	153307800	.	-	0	Parent=gene2891
chrX	ENCODE	exon	153307788	153308237	.	-	.	Parent=gene2891
###
chrX	ENCODE	gene	153300804	153308193	.	-	.	ID=gene2892;Name=XX-FW89031B12.3-015;name2=FAM3A
chrX	ENCODE	exon	153300804	153300846	.	-	.	Parent=gene2892
chrX	ENCODE	exon	153303885	153303908	.	-	.	Parent=gene2892
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2892
chrX	ENCODE	exon	153307788	153308193	.	-	.	Parent=gene2892
###
chrX	ENCODE	gene	153303905	153308257	.	-	.	ID=gene2893;Name=XX-FW89031B12.3-014;name2=FAM3A
chrX	ENCODE	exon	153303905	153303908	.	-	.	Parent=gene2893
chrX	ENCODE	exon	153304342	153304459	.	-	.	Parent=gene2893
chrX	ENCODE	exon	153304851	153304964	.	-	.	Parent=gene2893
chrX	ENCODE	exon	153307788	153308257	.	-	.	Parent=gene2893
###
chrX	ENCODE	gene	153323310	153339173	.	-	.	ID=gene2894;Name=AF277315.16-001;name2=G6PD
chrX	ENCODE	exon	153323310	153324009	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153323919	153324009	.	-	1	Parent=gene2894
chrX	ENCODE	exon	153324107	153324199	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153324107	153324199	.	-	1	Parent=gene2894
chrX	ENCODE	exon	153324305	153324381	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153324305	153324381	.	-	0	Parent=gene2894
chrX	ENCODE	exon	153324486	153324721	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153324486	153324721	.	-	2	Parent=gene2894
chrX	ENCODE	exon	153324861	153325047	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153324861	153325047	.	-	0	Parent=gene2894
chrX	ENCODE	exon	153325495	153325588	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153325495	153325588	.	-	1	Parent=gene2894
chrX	ENCODE	exon	153325954	153326079	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153325954	153326079	.	-	1	Parent=gene2894
chrX	ENCODE	exon	153326257	153326415	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153326257	153326415	.	-	1	Parent=gene2894
chrX	ENCODE	exon	153327087	153327304	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153327087	153327304	.	-	0	Parent=gene2894
chrX	ENCODE	exon	153327856	153327964	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153327856	153327964	.	-	1	Parent=gene2894
chrX	ENCODE	exon	153328060	153328097	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153328060	153328097	.	-	0	Parent=gene2894
chrX	ENCODE	exon	153337955	153338082	.	-	.	Parent=gene2894
chrX	ENCODE	CDS	153337955	153338082	.	-	2	Parent=gene2894
chrX	ENCODE	CDS	153338708	153338789	.	-	0	Parent=gene2894
chrX	ENCODE	exon	153338708	153339173	.	-	.	Parent=gene2894
###
chrX	ENCODE	gene	153323919	153339491	.	-	.	ID=gene2895;Name=AF277315.16-006;name2=G6PD
chrX	ENCODE	exon	153323919	153324009	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153323919	153324009	.	-	1	Parent=gene2895
chrX	ENCODE	exon	153324107	153324199	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153324107	153324199	.	-	1	Parent=gene2895
chrX	ENCODE	exon	153324305	153324381	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153324305	153324381	.	-	0	Parent=gene2895
chrX	ENCODE	exon	153324486	153324721	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153324486	153324721	.	-	2	Parent=gene2895
chrX	ENCODE	exon	153324861	153325047	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153324861	153325047	.	-	0	Parent=gene2895
chrX	ENCODE	exon	153325495	153325588	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153325495	153325588	.	-	1	Parent=gene2895
chrX	ENCODE	exon	153325954	153326079	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153325954	153326079	.	-	1	Parent=gene2895
chrX	ENCODE	exon	153326257	153326415	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153326257	153326415	.	-	1	Parent=gene2895
chrX	ENCODE	exon	153327087	153327304	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153327087	153327304	.	-	0	Parent=gene2895
chrX	ENCODE	exon	153327856	153327964	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153327856	153327964	.	-	1	Parent=gene2895
chrX	ENCODE	exon	153328060	153328097	.	-	.	Parent=gene2895
chrX	ENCODE	CDS	153328060	153328097	.	-	0	Parent=gene2895
chrX	ENCODE	CDS	153337955	153338074	.	-	0	Parent=gene2895
chrX	ENCODE	exon	153337955	153338082	.	-	.	Parent=gene2895
chrX	ENCODE	exon	153339387	153339491	.	-	.	Parent=gene2895
###
chrX	ENCODE	gene	153323919	153339491	.	-	.	ID=gene2896;Name=AF277315.16-010;name2=G6PD
chrX	ENCODE	exon	153323919	153324009	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153323919	153324009	.	-	1	Parent=gene2896
chrX	ENCODE	exon	153324107	153324199	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153324107	153324199	.	-	1	Parent=gene2896
chrX	ENCODE	exon	153324305	153324381	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153324305	153324381	.	-	0	Parent=gene2896
chrX	ENCODE	exon	153324486	153324721	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153324486	153324721	.	-	2	Parent=gene2896
chrX	ENCODE	exon	153324861	153325047	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153324861	153325047	.	-	0	Parent=gene2896
chrX	ENCODE	exon	153325495	153325726	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153325495	153325726	.	-	1	Parent=gene2896
chrX	ENCODE	exon	153325954	153326079	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153325954	153326079	.	-	1	Parent=gene2896
chrX	ENCODE	exon	153326257	153326415	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153326257	153326415	.	-	1	Parent=gene2896
chrX	ENCODE	exon	153327087	153327304	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153327087	153327304	.	-	0	Parent=gene2896
chrX	ENCODE	exon	153327856	153327964	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153327856	153327964	.	-	1	Parent=gene2896
chrX	ENCODE	exon	153328060	153328097	.	-	.	Parent=gene2896
chrX	ENCODE	CDS	153328060	153328097	.	-	0	Parent=gene2896
chrX	ENCODE	CDS	153337955	153338074	.	-	0	Parent=gene2896
chrX	ENCODE	exon	153337955	153338082	.	-	.	Parent=gene2896
chrX	ENCODE	exon	153339387	153339491	.	-	.	Parent=gene2896
###
chrX	ENCODE	gene	153324002	153324993	.	-	.	ID=gene2897;Name=AF277315.16-009;name2=G6PD
chrX	ENCODE	exon	153324002	153324199	.	-	.	Parent=gene2897
chrX	ENCODE	exon	153324305	153324381	.	-	.	Parent=gene2897
chrX	ENCODE	exon	153324486	153324993	.	-	.	Parent=gene2897
###
chrX	ENCODE	gene	153324899	153338757	.	-	.	ID=gene2898;Name=AF277315.16-002;name2=G6PD
chrX	ENCODE	exon	153324899	153325047	.	-	.	Parent=gene2898
chrX	ENCODE	CDS	153324899	153325047	.	-	2	Parent=gene2898
chrX	ENCODE	exon	153325495	153325588	.	-	.	Parent=gene2898
chrX	ENCODE	CDS	153325495	153325588	.	-	0	Parent=gene2898
chrX	ENCODE	exon	153325954	153326079	.	-	.	Parent=gene2898
chrX	ENCODE	CDS	153325954	153326079	.	-	0	Parent=gene2898
chrX	ENCODE	exon	153326257	153326418	.	-	.	Parent=gene2898
chrX	ENCODE	CDS	153326257	153326418	.	-	0	Parent=gene2898
chrX	ENCODE	exon	153327087	153327304	.	-	.	Parent=gene2898
chrX	ENCODE	CDS	153327087	153327304	.	-	2	Parent=gene2898
chrX	ENCODE	exon	153327856	153327964	.	-	.	Parent=gene2898
chrX	ENCODE	CDS	153327856	153327964	.	-	0	Parent=gene2898
chrX	ENCODE	exon	153328060	153328097	.	-	.	Parent=gene2898
chrX	ENCODE	CDS	153328060	153328097	.	-	2	Parent=gene2898
chrX	ENCODE	exon	153337955	153338082	.	-	.	Parent=gene2898
chrX	ENCODE	CDS	153337955	153338082	.	-	1	Parent=gene2898
chrX	ENCODE	exon	153338708	153338757	.	-	.	Parent=gene2898
chrX	ENCODE	CDS	153338708	153338757	.	-	0	Parent=gene2898
###
chrX	ENCODE	gene	153324953	153339476	.	-	.	ID=gene2899;Name=AF277315.16-007;name2=G6PD
chrX	ENCODE	exon	153324953	153325047	.	-	.	Parent=gene2899
chrX	ENCODE	CDS	153324953	153325047	.	-	0	Parent=gene2899
chrX	ENCODE	exon	153325495	153325588	.	-	.	Parent=gene2899
chrX	ENCODE	CDS	153325495	153325588	.	-	1	Parent=gene2899
chrX	ENCODE	exon	153325954	153326079	.	-	.	Parent=gene2899
chrX	ENCODE	CDS	153325954	153326079	.	-	1	Parent=gene2899
chrX	ENCODE	exon	153326257	153326418	.	-	.	Parent=gene2899
chrX	ENCODE	CDS	153326257	153326418	.	-	1	Parent=gene2899
chrX	ENCODE	exon	153327087	153327304	.	-	.	Parent=gene2899
chrX	ENCODE	CDS	153327087	153327304	.	-	0	Parent=gene2899
chrX	ENCODE	exon	153327856	153327964	.	-	.	Parent=gene2899
chrX	ENCODE	CDS	153327856	153327964	.	-	1	Parent=gene2899
chrX	ENCODE	exon	153328060	153328097	.	-	.	Parent=gene2899
chrX	ENCODE	CDS	153328060	153328097	.	-	0	Parent=gene2899
chrX	ENCODE	CDS	153337955	153338074	.	-	0	Parent=gene2899
chrX	ENCODE	exon	153337955	153338078	.	-	.	Parent=gene2899
chrX	ENCODE	exon	153339387	153339476	.	-	.	Parent=gene2899
###
chrX	ENCODE	gene	153325236	153326112	.	-	.	ID=gene2900;name2=G6PD;Name=AF277315.16-008
chrX	ENCODE	exon	153325236	153325588	.	-	.	Parent=gene2900
chrX	ENCODE	exon	153325954	153326112	.	-	.	Parent=gene2900
###
chrX	ENCODE	gene	153325955	153338751	.	-	.	ID=gene2901;Name=AF277315.16-005;name2=G6PD
chrX	ENCODE	exon	153325955	153326079	.	-	.	Parent=gene2901
chrX	ENCODE	CDS	153325955	153326079	.	-	1	Parent=gene2901
chrX	ENCODE	exon	153326257	153326415	.	-	.	Parent=gene2901
chrX	ENCODE	CDS	153326257	153326415	.	-	1	Parent=gene2901
chrX	ENCODE	exon	153327087	153327304	.	-	.	Parent=gene2901
chrX	ENCODE	CDS	153327087	153327304	.	-	0	Parent=gene2901
chrX	ENCODE	exon	153327856	153327964	.	-	.	Parent=gene2901
chrX	ENCODE	CDS	153327856	153327964	.	-	1	Parent=gene2901
chrX	ENCODE	exon	153328060	153328097	.	-	.	Parent=gene2901
chrX	ENCODE	CDS	153328060	153328097	.	-	0	Parent=gene2901
chrX	ENCODE	exon	153337955	153338078	.	-	.	Parent=gene2901
chrX	ENCODE	CDS	153337955	153338078	.	-	1	Parent=gene2901
chrX	ENCODE	exon	153338708	153338751	.	-	.	Parent=gene2901
chrX	ENCODE	CDS	153338708	153338751	.	-	0	Parent=gene2901
###
chrX	ENCODE	gene	153326994	153338028	.	-	.	ID=gene2902;name2=G6PD;Name=AF277315.16-004
chrX	ENCODE	exon	153326994	153327304	.	-	.	Parent=gene2902
chrX	ENCODE	exon	153327856	153327964	.	-	.	Parent=gene2902
chrX	ENCODE	exon	153328060	153328097	.	-	.	Parent=gene2902
chrX	ENCODE	exon	153337955	153338028	.	-	.	Parent=gene2902
###
chrX	ENCODE	gene	153327645	153338028	.	-	.	ID=gene2903;Name=AF277315.16-003;name2=G6PD
chrX	ENCODE	exon	153327645	153327964	.	-	.	Parent=gene2903
chrX	ENCODE	exon	153328060	153328097	.	-	.	Parent=gene2903
chrX	ENCODE	exon	153337955	153338028	.	-	.	Parent=gene2903
###
chrX	ENCODE	gene	153333118	153353687	.	+	.	ID=gene2904;Name=AF277315.14-007;name2=IKBKG
chrX	ENCODE	exon	153333118	153333310	.	+	.	Parent=gene2904
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2904
chrX	ENCODE	CDS	153343922	153344108	.	+	0	Parent=gene2904
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2904
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2904
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2904
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2904
chrX	ENCODE	exon	153352326	153352478	.	+	.	Parent=gene2904
chrX	ENCODE	CDS	153352326	153352478	.	+	1	Parent=gene2904
chrX	ENCODE	exon	153353607	153353687	.	+	.	Parent=gene2904
chrX	ENCODE	CDS	153353607	153353687	.	+	1	Parent=gene2904
###
chrX	ENCODE	gene	153333174	153352424	.	+	.	ID=gene2905;Name=AF277315.14-008;name2=IKBKG
chrX	ENCODE	exon	153333174	153333310	.	+	.	Parent=gene2905
chrX	ENCODE	exon	153334201	153334371	.	+	.	Parent=gene2905
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2905
chrX	ENCODE	CDS	153343922	153344108	.	+	0	Parent=gene2905
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2905
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2905
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2905
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2905
chrX	ENCODE	exon	153352326	153352424	.	+	.	Parent=gene2905
chrX	ENCODE	CDS	153352326	153352424	.	+	1	Parent=gene2905
###
chrX	ENCODE	gene	153334163	153356952	.	+	.	ID=gene2906;Name=AF277315.14-002;name2=IKBKG
chrX	ENCODE	exon	153334163	153334371	.	+	.	Parent=gene2906
chrX	ENCODE	CDS	153334183	153334371	.	+	0	Parent=gene2906
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2906
chrX	ENCODE	CDS	153343907	153344108	.	+	0	Parent=gene2906
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2906
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2906
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2906
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2906
chrX	ENCODE	exon	153352326	153352478	.	+	.	Parent=gene2906
chrX	ENCODE	CDS	153352326	153352478	.	+	1	Parent=gene2906
chrX	ENCODE	exon	153353607	153353703	.	+	.	Parent=gene2906
chrX	ENCODE	CDS	153353607	153353703	.	+	1	Parent=gene2906
chrX	ENCODE	exon	153354729	153354872	.	+	.	Parent=gene2906
chrX	ENCODE	CDS	153354729	153354872	.	+	0	Parent=gene2906
chrX	ENCODE	exon	153355478	153355620	.	+	.	Parent=gene2906
chrX	ENCODE	CDS	153355478	153355620	.	+	0	Parent=gene2906
chrX	ENCODE	exon	153355878	153355939	.	+	.	Parent=gene2906
chrX	ENCODE	CDS	153355878	153355939	.	+	1	Parent=gene2906
chrX	ENCODE	CDS	153356238	153356380	.	+	2	Parent=gene2906
chrX	ENCODE	exon	153356238	153356952	.	+	.	Parent=gene2906
###
chrX	ENCODE	gene	153334182	153356952	.	+	.	ID=gene2907;Name=AF277315.14-003;name2=IKBKG
chrX	ENCODE	exon	153334182	153334306	.	+	.	Parent=gene2907
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2907
chrX	ENCODE	CDS	153343922	153344108	.	+	0	Parent=gene2907
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2907
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2907
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2907
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2907
chrX	ENCODE	exon	153352326	153352478	.	+	.	Parent=gene2907
chrX	ENCODE	CDS	153352326	153352478	.	+	1	Parent=gene2907
chrX	ENCODE	exon	153353607	153353703	.	+	.	Parent=gene2907
chrX	ENCODE	CDS	153353607	153353703	.	+	1	Parent=gene2907
chrX	ENCODE	exon	153354729	153354872	.	+	.	Parent=gene2907
chrX	ENCODE	CDS	153354729	153354872	.	+	0	Parent=gene2907
chrX	ENCODE	exon	153355478	153355620	.	+	.	Parent=gene2907
chrX	ENCODE	CDS	153355478	153355620	.	+	0	Parent=gene2907
chrX	ENCODE	exon	153355878	153355939	.	+	.	Parent=gene2907
chrX	ENCODE	CDS	153355878	153355939	.	+	1	Parent=gene2907
chrX	ENCODE	CDS	153356238	153356380	.	+	2	Parent=gene2907
chrX	ENCODE	exon	153356238	153356952	.	+	.	Parent=gene2907
###
chrX	ENCODE	gene	153337846	153350465	.	+	.	ID=gene2908;Name=AF277315.14-012;name2=IKBKG
chrX	ENCODE	exon	153337846	153338109	.	+	.	Parent=gene2908
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2908
chrX	ENCODE	CDS	153343922	153344108	.	+	0	Parent=gene2908
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2908
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2908
chrX	ENCODE	exon	153350451	153350465	.	+	.	Parent=gene2908
chrX	ENCODE	CDS	153350451	153350465	.	+	0	Parent=gene2908
###
chrX	ENCODE	gene	153339226	153356952	.	+	.	ID=gene2909;Name=AF277315.14-004;name2=IKBKG
chrX	ENCODE	exon	153339226	153339664	.	+	.	Parent=gene2909
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2909
chrX	ENCODE	CDS	153343922	153344108	.	+	0	Parent=gene2909
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2909
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2909
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2909
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2909
chrX	ENCODE	exon	153352326	153352478	.	+	.	Parent=gene2909
chrX	ENCODE	CDS	153352326	153352478	.	+	1	Parent=gene2909
chrX	ENCODE	exon	153353607	153353703	.	+	.	Parent=gene2909
chrX	ENCODE	CDS	153353607	153353703	.	+	1	Parent=gene2909
chrX	ENCODE	exon	153354729	153354872	.	+	.	Parent=gene2909
chrX	ENCODE	CDS	153354729	153354872	.	+	0	Parent=gene2909
chrX	ENCODE	exon	153355478	153355620	.	+	.	Parent=gene2909
chrX	ENCODE	CDS	153355478	153355620	.	+	0	Parent=gene2909
chrX	ENCODE	exon	153355878	153355939	.	+	.	Parent=gene2909
chrX	ENCODE	CDS	153355878	153355939	.	+	1	Parent=gene2909
chrX	ENCODE	CDS	153356238	153356380	.	+	2	Parent=gene2909
chrX	ENCODE	exon	153356238	153356952	.	+	.	Parent=gene2909
###
chrX	ENCODE	gene	153339278	153352430	.	+	.	ID=gene2910;Name=AF277315.14-009;name2=IKBKG
chrX	ENCODE	exon	153339278	153339554	.	+	.	Parent=gene2910
chrX	ENCODE	exon	153343930	153344108	.	+	.	Parent=gene2910
chrX	ENCODE	CDS	153343958	153344108	.	+	0	Parent=gene2910
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2910
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2910
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2910
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2910
chrX	ENCODE	exon	153352326	153352430	.	+	.	Parent=gene2910
chrX	ENCODE	CDS	153352326	153352430	.	+	1	Parent=gene2910
###
chrX	ENCODE	gene	153339553	153356897	.	+	.	ID=gene2911;name2=IKBKG;Name=AF277315.14-011
chrX	ENCODE	exon	153339553	153339664	.	+	.	Parent=gene2911
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2911
chrX	ENCODE	CDS	153343922	153344108	.	+	0	Parent=gene2911
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2911
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2911
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2911
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2911
chrX	ENCODE	exon	153353607	153353703	.	+	.	Parent=gene2911
chrX	ENCODE	CDS	153353607	153353703	.	+	1	Parent=gene2911
chrX	ENCODE	exon	153354729	153354872	.	+	.	Parent=gene2911
chrX	ENCODE	CDS	153354729	153354872	.	+	0	Parent=gene2911
chrX	ENCODE	exon	153355478	153355620	.	+	.	Parent=gene2911
chrX	ENCODE	CDS	153355478	153355620	.	+	0	Parent=gene2911
chrX	ENCODE	exon	153355878	153355939	.	+	.	Parent=gene2911
chrX	ENCODE	CDS	153355878	153355939	.	+	1	Parent=gene2911
chrX	ENCODE	CDS	153356238	153356380	.	+	2	Parent=gene2911
chrX	ENCODE	exon	153356238	153356897	.	+	.	Parent=gene2911
###
chrX	ENCODE	gene	153339557	153359508	.	+	.	ID=gene2912;Name=AF277315.14-014;name2=IKBKG
chrX	ENCODE	exon	153339557	153339664	.	+	.	Parent=gene2912
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2912
chrX	ENCODE	CDS	153343922	153344108	.	+	0	Parent=gene2912
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2912
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2912
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2912
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2912
chrX	ENCODE	exon	153352326	153352478	.	+	.	Parent=gene2912
chrX	ENCODE	CDS	153352326	153352478	.	+	1	Parent=gene2912
chrX	ENCODE	exon	153353607	153353682	.	+	.	Parent=gene2912
chrX	ENCODE	CDS	153353607	153353682	.	+	1	Parent=gene2912
chrX	ENCODE	exon	153354729	153354872	.	+	.	Parent=gene2912
chrX	ENCODE	CDS	153354729	153354872	.	+	0	Parent=gene2912
chrX	ENCODE	exon	153355478	153355620	.	+	.	Parent=gene2912
chrX	ENCODE	CDS	153355478	153355620	.	+	0	Parent=gene2912
chrX	ENCODE	exon	153355878	153355939	.	+	.	Parent=gene2912
chrX	ENCODE	CDS	153355878	153355939	.	+	1	Parent=gene2912
chrX	ENCODE	CDS	153356238	153356380	.	+	2	Parent=gene2912
chrX	ENCODE	exon	153356238	153359508	.	+	.	Parent=gene2912
###
chrX	ENCODE	gene	153339561	153356952	.	+	.	ID=gene2913;name2=IKBKG;Name=AF277315.14-006
chrX	ENCODE	exon	153339561	153339664	.	+	.	Parent=gene2913
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2913
chrX	ENCODE	CDS	153343922	153344108	.	+	0	Parent=gene2913
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2913
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2913
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2913
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2913
chrX	ENCODE	exon	153353607	153353703	.	+	.	Parent=gene2913
chrX	ENCODE	CDS	153353607	153353703	.	+	1	Parent=gene2913
chrX	ENCODE	exon	153355478	153355620	.	+	.	Parent=gene2913
chrX	ENCODE	CDS	153355478	153355620	.	+	0	Parent=gene2913
chrX	ENCODE	exon	153355878	153355939	.	+	.	Parent=gene2913
chrX	ENCODE	CDS	153355878	153355939	.	+	1	Parent=gene2913
chrX	ENCODE	CDS	153356238	153356380	.	+	2	Parent=gene2913
chrX	ENCODE	exon	153356238	153356952	.	+	.	Parent=gene2913
###
chrX	ENCODE	gene	153339609	153355560	.	+	.	ID=gene2914;name2=IKBKG;Name=AF277315.14-013
chrX	ENCODE	exon	153339609	153339664	.	+	.	Parent=gene2914
chrX	ENCODE	exon	153348212	153348295	.	+	.	Parent=gene2914
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2914
chrX	ENCODE	CDS	153350454	153350569	.	+	0	Parent=gene2914
chrX	ENCODE	exon	153352326	153352478	.	+	.	Parent=gene2914
chrX	ENCODE	CDS	153352326	153352478	.	+	1	Parent=gene2914
chrX	ENCODE	exon	153353607	153353682	.	+	.	Parent=gene2914
chrX	ENCODE	CDS	153353607	153353682	.	+	1	Parent=gene2914
chrX	ENCODE	exon	153354729	153354872	.	+	.	Parent=gene2914
chrX	ENCODE	CDS	153354729	153354872	.	+	0	Parent=gene2914
chrX	ENCODE	exon	153355478	153355560	.	+	.	Parent=gene2914
chrX	ENCODE	CDS	153355478	153355560	.	+	0	Parent=gene2914
###
chrX	ENCODE	gene	153339766	153356965	.	+	.	ID=gene2915;Name=AF277315.14-005;name2=IKBKG
chrX	ENCODE	exon	153339766	153340008	.	+	.	Parent=gene2915
chrX	ENCODE	exon	153343907	153344108	.	+	.	Parent=gene2915
chrX	ENCODE	CDS	153343922	153344108	.	+	0	Parent=gene2915
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2915
chrX	ENCODE	CDS	153348084	153348295	.	+	2	Parent=gene2915
chrX	ENCODE	exon	153350451	153350569	.	+	.	Parent=gene2915
chrX	ENCODE	CDS	153350451	153350569	.	+	0	Parent=gene2915
chrX	ENCODE	exon	153352326	153352478	.	+	.	Parent=gene2915
chrX	ENCODE	CDS	153352326	153352478	.	+	1	Parent=gene2915
chrX	ENCODE	exon	153353607	153353703	.	+	.	Parent=gene2915
chrX	ENCODE	CDS	153353607	153353703	.	+	1	Parent=gene2915
chrX	ENCODE	exon	153354729	153354872	.	+	.	Parent=gene2915
chrX	ENCODE	CDS	153354729	153354872	.	+	0	Parent=gene2915
chrX	ENCODE	exon	153355478	153355620	.	+	.	Parent=gene2915
chrX	ENCODE	CDS	153355478	153355620	.	+	0	Parent=gene2915
chrX	ENCODE	exon	153355878	153355939	.	+	.	Parent=gene2915
chrX	ENCODE	CDS	153355878	153355939	.	+	1	Parent=gene2915
chrX	ENCODE	CDS	153356238	153356380	.	+	2	Parent=gene2915
chrX	ENCODE	exon	153356238	153356965	.	+	.	Parent=gene2915
###
chrX	ENCODE	gene	153344090	153348779	.	+	.	ID=gene2916;Name=AF277315.14-010;name2=IKBKG
chrX	ENCODE	exon	153344090	153344108	.	+	.	Parent=gene2916
chrX	ENCODE	exon	153348084	153348295	.	+	.	Parent=gene2916
chrX	ENCODE	exon	153348459	153348779	.	+	.	Parent=gene2916
###
chrX	ENCODE	gene	153354317	153355902	.	+	.	ID=gene2917;Name=AF277315.14-001;name2=IKBKG
chrX	ENCODE	exon	153354317	153354872	.	+	.	Parent=gene2917
chrX	ENCODE	exon	153355478	153355620	.	+	.	Parent=gene2917
chrX	ENCODE	exon	153355878	153355902	.	+	.	Parent=gene2917
###
chrX	ENCODE	gene	153363183	153363895	.	+	.	ID=gene2918;Name=AF277315.18-001;name2=CXorf52
chrX	ENCODE	exon	153363183	153363895	.	+	.	Parent=gene2918
chrX	ENCODE	CDS	153363389	153363757	.	+	0	Parent=gene2918
###
chrX	ENCODE	gene	153377111	153378779	.	+	.	ID=gene2919;Name=AF277315.1-001;name2=CTAG1A
chrX	ENCODE	exon	153377111	153377443	.	+	.	Parent=gene2919
chrX	ENCODE	CDS	153377175	153377443	.	+	0	Parent=gene2919
chrX	ENCODE	CDS	153378115	153378352	.	+	1	Parent=gene2919
chrX	ENCODE	exon	153378115	153378779	.	+	.	Parent=gene2919
###
chrX	ENCODE	gene	153377122	153378778	.	+	.	ID=gene2920;Name=AF277315.1-002;name2=CTAG1A
chrX	ENCODE	exon	153377122	153377443	.	+	.	Parent=gene2920
chrX	ENCODE	CDS	153377175	153377443	.	+	0	Parent=gene2920
chrX	ENCODE	exon	153378115	153378249	.	+	.	Parent=gene2920
chrX	ENCODE	CDS	153378115	153378249	.	+	1	Parent=gene2920
chrX	ENCODE	CDS	153378489	153378627	.	+	1	Parent=gene2920
chrX	ENCODE	exon	153378489	153378778	.	+	.	Parent=gene2920
###
chrX	ENCODE	gene	153409569	153411226	.	-	.	ID=gene2921;Name=AF277315.7-002;name2=CTAG1B
chrX	ENCODE	exon	153409569	153409859	.	-	.	Parent=gene2921
chrX	ENCODE	CDS	153409721	153409859	.	-	1	Parent=gene2921
chrX	ENCODE	exon	153410099	153410233	.	-	.	Parent=gene2921
chrX	ENCODE	CDS	153410099	153410233	.	-	1	Parent=gene2921
chrX	ENCODE	CDS	153410905	153411173	.	-	0	Parent=gene2921
chrX	ENCODE	exon	153410905	153411226	.	-	.	Parent=gene2921
###
chrX	ENCODE	gene	153409569	153411237	.	-	.	ID=gene2922;Name=AF277315.7-001;name2=CTAG1B
chrX	ENCODE	exon	153409569	153410233	.	-	.	Parent=gene2922
chrX	ENCODE	CDS	153409996	153410233	.	-	1	Parent=gene2922
chrX	ENCODE	CDS	153410905	153411173	.	-	0	Parent=gene2922
chrX	ENCODE	exon	153410905	153411237	.	-	.	Parent=gene2922
###
chrX	ENCODE	gene	153424440	153425152	.	-	.	ID=gene2923;Name=AF277315.17-001;name2=AF277315.17
chrX	ENCODE	exon	153424440	153425152	.	-	.	Parent=gene2923
chrX	ENCODE	CDS	153424578	153424946	.	-	0	Parent=gene2923
###
chrX	ENCODE	gene	153443950	153445557	.	-	.	ID=gene2924;name2=CTAG2;Name=AF277315.2-001
chrX	ENCODE	exon	153443950	153444609	.	-	.	Parent=gene2924
chrX	ENCODE	CDS	153444246	153444609	.	-	1	Parent=gene2924
chrX	ENCODE	CDS	153445225	153445493	.	-	0	Parent=gene2924
chrX	ENCODE	exon	153445225	153445557	.	-	.	Parent=gene2924
###
chrX	ENCODE	gene	153443955	153445546	.	-	.	ID=gene2925;Name=AF277315.2-002;name2=CTAG2
chrX	ENCODE	exon	153443955	153444245	.	-	.	Parent=gene2925
chrX	ENCODE	CDS	153444107	153444245	.	-	1	Parent=gene2925
chrX	ENCODE	exon	153444475	153444609	.	-	.	Parent=gene2925
chrX	ENCODE	CDS	153444475	153444609	.	-	1	Parent=gene2925
chrX	ENCODE	CDS	153445225	153445493	.	-	0	Parent=gene2925
chrX	ENCODE	exon	153445225	153445546	.	-	.	Parent=gene2925
###
chrX	ENCODE	gene	153467233	153543562	.	-	.	ID=gene2926;Name=CTD-2173L12.1-003;name2=GAB3
chrX	ENCODE	exon	153467233	153470275	.	-	.	Parent=gene2926
chrX	ENCODE	exon	153472113	153472229	.	-	.	Parent=gene2926
chrX	ENCODE	exon	153487896	153487998	.	-	.	Parent=gene2926
chrX	ENCODE	exon	153489111	153489192	.	-	.	Parent=gene2926
chrX	ENCODE	exon	153491273	153491492	.	-	.	Parent=gene2926
chrX	ENCODE	exon	153491983	153492038	.	-	.	Parent=gene2926
chrX	ENCODE	exon	153505186	153505405	.	-	.	Parent=gene2926
chrX	ENCODE	exon	153508005	153508308	.	-	.	Parent=gene2926
chrX	ENCODE	exon	153543471	153543562	.	-	.	Parent=gene2926
###
chrX	ENCODE	gene	153467234	153543036	.	-	.	ID=gene2927;Name=CTD-2173L12.1-001;name2=GAB3
chrX	ENCODE	exon	153467234	153470275	.	-	.	Parent=gene2927
chrX	ENCODE	CDS	153470159	153470275	.	-	0	Parent=gene2927
chrX	ENCODE	exon	153472113	153472229	.	-	.	Parent=gene2927
chrX	ENCODE	CDS	153472113	153472229	.	-	0	Parent=gene2927
chrX	ENCODE	exon	153487896	153487998	.	-	.	Parent=gene2927
chrX	ENCODE	CDS	153487896	153487998	.	-	1	Parent=gene2927
chrX	ENCODE	exon	153489111	153489192	.	-	.	Parent=gene2927
chrX	ENCODE	CDS	153489111	153489192	.	-	2	Parent=gene2927
chrX	ENCODE	exon	153491273	153491492	.	-	.	Parent=gene2927
chrX	ENCODE	CDS	153491273	153491492	.	-	0	Parent=gene2927
chrX	ENCODE	exon	153491983	153492038	.	-	.	Parent=gene2927
chrX	ENCODE	CDS	153491983	153492038	.	-	2	Parent=gene2927
chrX	ENCODE	exon	153504208	153504680	.	-	.	Parent=gene2927
chrX	ENCODE	CDS	153504208	153504680	.	-	1	Parent=gene2927
chrX	ENCODE	exon	153505186	153505402	.	-	.	Parent=gene2927
chrX	ENCODE	CDS	153505186	153505402	.	-	2	Parent=gene2927
chrX	ENCODE	exon	153508005	153508308	.	-	.	Parent=gene2927
chrX	ENCODE	CDS	153508005	153508308	.	-	0	Parent=gene2927
chrX	ENCODE	CDS	153542933	153543004	.	-	0	Parent=gene2927
chrX	ENCODE	exon	153542933	153543036	.	-	.	Parent=gene2927
###
chrX	ENCODE	gene	153468150	153543052	.	-	.	ID=gene2928;Name=CTD-2173L12.1-002;name2=GAB3
chrX	ENCODE	exon	153468150	153470275	.	-	.	Parent=gene2928
chrX	ENCODE	CDS	153470159	153470275	.	-	0	Parent=gene2928
chrX	ENCODE	exon	153487896	153487998	.	-	.	Parent=gene2928
chrX	ENCODE	CDS	153487896	153487998	.	-	1	Parent=gene2928
chrX	ENCODE	exon	153489111	153489192	.	-	.	Parent=gene2928
chrX	ENCODE	CDS	153489111	153489192	.	-	2	Parent=gene2928
chrX	ENCODE	exon	153491273	153491492	.	-	.	Parent=gene2928
chrX	ENCODE	CDS	153491273	153491492	.	-	0	Parent=gene2928
chrX	ENCODE	exon	153491983	153492038	.	-	.	Parent=gene2928
chrX	ENCODE	CDS	153491983	153492038	.	-	2	Parent=gene2928
chrX	ENCODE	exon	153504208	153504680	.	-	.	Parent=gene2928
chrX	ENCODE	CDS	153504208	153504680	.	-	1	Parent=gene2928
chrX	ENCODE	exon	153505186	153505405	.	-	.	Parent=gene2928
chrX	ENCODE	CDS	153505186	153505405	.	-	2	Parent=gene2928
chrX	ENCODE	exon	153508005	153508308	.	-	.	Parent=gene2928
chrX	ENCODE	CDS	153508005	153508308	.	-	0	Parent=gene2928
chrX	ENCODE	CDS	153542933	153543004	.	-	0	Parent=gene2928
chrX	ENCODE	exon	153542933	153543052	.	-	.	Parent=gene2928
###
chrX	ENCODE	gene	153470959	153472200	.	-	.	ID=gene2929;Name=CTD-2173L12.1-004;name2=GAB3
chrX	ENCODE	exon	153470959	153471320	.	-	.	Parent=gene2929
chrX	ENCODE	CDS	153470959	153471320	.	-	2	Parent=gene2929
chrX	ENCODE	exon	153472113	153472200	.	-	.	Parent=gene2929
chrX	ENCODE	CDS	153472113	153472200	.	-	0	Parent=gene2929
###
chrX	ENCODE	gene	153554739	153569668	.	+	.	ID=gene2930;name2=DKC1;Name=RP11-115M6.2-001
chrX	ENCODE	exon	153554739	153554960	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153554945	153554960	.	+	0	Parent=gene2930
chrX	ENCODE	exon	153556878	153556945	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153556878	153556945	.	+	2	Parent=gene2930
chrX	ENCODE	exon	153557423	153557509	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153557423	153557509	.	+	0	Parent=gene2930
chrX	ENCODE	exon	153557886	153557977	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153557886	153557977	.	+	0	Parent=gene2930
chrX	ENCODE	exon	153558195	153558379	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153558195	153558379	.	+	1	Parent=gene2930
chrX	ENCODE	exon	153558976	153559040	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153558976	153559040	.	+	2	Parent=gene2930
chrX	ENCODE	exon	153559235	153559361	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153559235	153559361	.	+	0	Parent=gene2930
chrX	ENCODE	exon	153560281	153560411	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153560281	153560411	.	+	2	Parent=gene2930
chrX	ENCODE	exon	153561146	153561289	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153561146	153561289	.	+	0	Parent=gene2930
chrX	ENCODE	exon	153562738	153562858	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153562738	153562858	.	+	0	Parent=gene2930
chrX	ENCODE	exon	153565110	153565228	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153565110	153565228	.	+	2	Parent=gene2930
chrX	ENCODE	exon	153566581	153566684	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153566581	153566684	.	+	0	Parent=gene2930
chrX	ENCODE	exon	153567174	153567252	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153567174	153567252	.	+	1	Parent=gene2930
chrX	ENCODE	exon	153568166	153568303	.	+	.	Parent=gene2930
chrX	ENCODE	CDS	153568166	153568303	.	+	0	Parent=gene2930
chrX	ENCODE	CDS	153568778	153568846	.	+	0	Parent=gene2930
chrX	ENCODE	exon	153568778	153569668	.	+	.	Parent=gene2930
###
chrX	ENCODE	gene	153554831	153557334	.	+	.	ID=gene2931;Name=RP11-115M6.2-007;name2=DKC1
chrX	ENCODE	exon	153554831	153554960	.	+	.	Parent=gene2931
chrX	ENCODE	exon	153556878	153557334	.	+	.	Parent=gene2931
###
chrX	ENCODE	gene	153554870	153561270	.	+	.	ID=gene2932;Name=RP11-115M6.2-008;name2=DKC1
chrX	ENCODE	exon	153554870	153554960	.	+	.	Parent=gene2932
chrX	ENCODE	CDS	153554945	153554960	.	+	0	Parent=gene2932
chrX	ENCODE	exon	153556878	153556945	.	+	.	Parent=gene2932
chrX	ENCODE	CDS	153556878	153556945	.	+	2	Parent=gene2932
chrX	ENCODE	exon	153557423	153557509	.	+	.	Parent=gene2932
chrX	ENCODE	CDS	153557423	153557509	.	+	0	Parent=gene2932
chrX	ENCODE	exon	153557886	153557977	.	+	.	Parent=gene2932
chrX	ENCODE	CDS	153557886	153557977	.	+	0	Parent=gene2932
chrX	ENCODE	exon	153558195	153558379	.	+	.	Parent=gene2932
chrX	ENCODE	CDS	153558195	153558379	.	+	1	Parent=gene2932
chrX	ENCODE	exon	153558976	153559040	.	+	.	Parent=gene2932
chrX	ENCODE	CDS	153558976	153559040	.	+	2	Parent=gene2932
chrX	ENCODE	exon	153559235	153559361	.	+	.	Parent=gene2932
chrX	ENCODE	CDS	153559235	153559361	.	+	0	Parent=gene2932
chrX	ENCODE	exon	153560281	153560291	.	+	.	Parent=gene2932
chrX	ENCODE	CDS	153560281	153560291	.	+	2	Parent=gene2932
chrX	ENCODE	exon	153561146	153561270	.	+	.	Parent=gene2932
chrX	ENCODE	CDS	153561146	153561270	.	+	0	Parent=gene2932
###
chrX	ENCODE	gene	153554892	153558534	.	+	.	ID=gene2933;Name=RP11-115M6.2-009;name2=DKC1
chrX	ENCODE	exon	153554892	153554960	.	+	.	Parent=gene2933
chrX	ENCODE	exon	153556878	153556945	.	+	.	Parent=gene2933
chrX	ENCODE	exon	153557423	153557509	.	+	.	Parent=gene2933
chrX	ENCODE	exon	153557886	153557977	.	+	.	Parent=gene2933
chrX	ENCODE	exon	153558195	153558534	.	+	.	Parent=gene2933
###
chrX	ENCODE	gene	153556904	153561189	.	+	.	ID=gene2934;Name=RP11-115M6.2-012;name2=DKC1
chrX	ENCODE	exon	153556904	153556945	.	+	.	Parent=gene2934
chrX	ENCODE	exon	153557423	153557509	.	+	.	Parent=gene2934
chrX	ENCODE	exon	153557886	153557977	.	+	.	Parent=gene2934
chrX	ENCODE	exon	153558195	153558379	.	+	.	Parent=gene2934
chrX	ENCODE	exon	153559235	153559361	.	+	.	Parent=gene2934
chrX	ENCODE	exon	153560281	153560411	.	+	.	Parent=gene2934
chrX	ENCODE	exon	153561146	153561189	.	+	.	Parent=gene2934
###
chrX	ENCODE	gene	153556906	153560337	.	+	.	ID=gene2935;Name=RP11-115M6.2-010;name2=DKC1
chrX	ENCODE	exon	153556906	153556945	.	+	.	Parent=gene2935
chrX	ENCODE	CDS	153556906	153556945	.	+	0	Parent=gene2935
chrX	ENCODE	exon	153557423	153557509	.	+	.	Parent=gene2935
chrX	ENCODE	CDS	153557423	153557509	.	+	2	Parent=gene2935
chrX	ENCODE	exon	153557886	153557977	.	+	.	Parent=gene2935
chrX	ENCODE	CDS	153557886	153557977	.	+	2	Parent=gene2935
chrX	ENCODE	exon	153558195	153558379	.	+	.	Parent=gene2935
chrX	ENCODE	CDS	153558195	153558379	.	+	0	Parent=gene2935
chrX	ENCODE	exon	153558976	153559040	.	+	.	Parent=gene2935
chrX	ENCODE	CDS	153558976	153559040	.	+	1	Parent=gene2935
chrX	ENCODE	exon	153559235	153559361	.	+	.	Parent=gene2935
chrX	ENCODE	CDS	153559235	153559361	.	+	2	Parent=gene2935
chrX	ENCODE	exon	153560248	153560337	.	+	.	Parent=gene2935
chrX	ENCODE	CDS	153560248	153560337	.	+	1	Parent=gene2935
###
chrX	ENCODE	gene	153558995	153568239	.	+	.	ID=gene2936;Name=RP11-115M6.2-011;name2=DKC1
chrX	ENCODE	exon	153558995	153559040	.	+	.	Parent=gene2936
chrX	ENCODE	exon	153559235	153559361	.	+	.	Parent=gene2936
chrX	ENCODE	exon	153562738	153562858	.	+	.	Parent=gene2936
chrX	ENCODE	exon	153565110	153565228	.	+	.	Parent=gene2936
chrX	ENCODE	exon	153566581	153566684	.	+	.	Parent=gene2936
chrX	ENCODE	exon	153567174	153567252	.	+	.	Parent=gene2936
chrX	ENCODE	exon	153568166	153568239	.	+	.	Parent=gene2936
###
chrX	ENCODE	gene	153559360	153567252	.	+	.	ID=gene2937;Name=RP11-115M6.2-005;name2=DKC1
chrX	ENCODE	exon	153559360	153559361	.	+	.	Parent=gene2937
chrX	ENCODE	exon	153560281	153560411	.	+	.	Parent=gene2937
chrX	ENCODE	exon	153561146	153561289	.	+	.	Parent=gene2937
chrX	ENCODE	exon	153562738	153562858	.	+	.	Parent=gene2937
chrX	ENCODE	exon	153565110	153565228	.	+	.	Parent=gene2937
chrX	ENCODE	exon	153566581	153566684	.	+	.	Parent=gene2937
chrX	ENCODE	exon	153566765	153566823	.	+	.	Parent=gene2937
chrX	ENCODE	exon	153567174	153567252	.	+	.	Parent=gene2937
###
chrX	ENCODE	gene	153560003	153562855	.	+	.	ID=gene2938;Name=RP11-115M6.2-002;name2=DKC1
chrX	ENCODE	exon	153560003	153560411	.	+	.	Parent=gene2938
chrX	ENCODE	exon	153561146	153561289	.	+	.	Parent=gene2938
chrX	ENCODE	exon	153562738	153562855	.	+	.	Parent=gene2938
###
chrX	ENCODE	gene	153560522	153568240	.	+	.	ID=gene2939;Name=RP11-115M6.2-003;name2=DKC1
chrX	ENCODE	exon	153560522	153560781	.	+	.	Parent=gene2939
chrX	ENCODE	exon	153561146	153561289	.	+	.	Parent=gene2939
chrX	ENCODE	exon	153562738	153562858	.	+	.	Parent=gene2939
chrX	ENCODE	exon	153565110	153565228	.	+	.	Parent=gene2939
chrX	ENCODE	exon	153566581	153566684	.	+	.	Parent=gene2939
chrX	ENCODE	exon	153567174	153567252	.	+	.	Parent=gene2939
chrX	ENCODE	exon	153568166	153568240	.	+	.	Parent=gene2939
###
chrX	ENCODE	gene	153565123	153567293	.	+	.	ID=gene2940;Name=RP11-115M6.2-004;name2=DKC1
chrX	ENCODE	exon	153565123	153565228	.	+	.	Parent=gene2940
chrX	ENCODE	exon	153566581	153567293	.	+	.	Parent=gene2940
###
chrX	ENCODE	gene	153567098	153568890	.	+	.	ID=gene2941;Name=RP11-115M6.2-006;name2=DKC1
chrX	ENCODE	exon	153567098	153567252	.	+	.	Parent=gene2941
chrX	ENCODE	exon	153568166	153568303	.	+	.	Parent=gene2941
chrX	ENCODE	exon	153568778	153568890	.	+	.	Parent=gene2941
###
chrX	ENCODE	gene	153570663	153597487	.	-	.	ID=gene2942;Name=RP11-115M6.1-006;name2=MPP1
chrX	ENCODE	exon	153570663	153571332	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153571156	153571332	.	-	0	Parent=gene2942
chrX	ENCODE	exon	153573218	153573292	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153573218	153573292	.	-	0	Parent=gene2942
chrX	ENCODE	exon	153573579	153573781	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153573579	153573781	.	-	2	Parent=gene2942
chrX	ENCODE	exon	153575406	153575486	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153575406	153575486	.	-	2	Parent=gene2942
chrX	ENCODE	exon	153576007	153576087	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153576007	153576087	.	-	2	Parent=gene2942
chrX	ENCODE	exon	153577030	153577136	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153577030	153577136	.	-	1	Parent=gene2942
chrX	ENCODE	exon	153578183	153578379	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153578183	153578379	.	-	0	Parent=gene2942
chrX	ENCODE	exon	153581933	153582001	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153581933	153582001	.	-	0	Parent=gene2942
chrX	ENCODE	exon	153582962	153583047	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153582962	153583047	.	-	2	Parent=gene2942
chrX	ENCODE	exon	153583748	153583826	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153583748	153583826	.	-	0	Parent=gene2942
chrX	ENCODE	exon	153584121	153584264	.	-	.	Parent=gene2942
chrX	ENCODE	CDS	153584121	153584264	.	-	0	Parent=gene2942
chrX	ENCODE	CDS	153597251	153597352	.	-	0	Parent=gene2942
chrX	ENCODE	exon	153597251	153597487	.	-	.	Parent=gene2942
###
chrX	ENCODE	gene	153570665	153575213	.	-	.	ID=gene2943;Name=RP11-115M6.1-004;name2=MPP1
chrX	ENCODE	exon	153570665	153571332	.	-	.	Parent=gene2943
chrX	ENCODE	exon	153573218	153573292	.	-	.	Parent=gene2943
chrX	ENCODE	exon	153573579	153575213	.	-	.	Parent=gene2943
###
chrX	ENCODE	gene	153570702	153573575	.	-	.	ID=gene2944;Name=RP11-115M6.1-008;name2=MPP1
chrX	ENCODE	exon	153570702	153571332	.	-	.	Parent=gene2944
chrX	ENCODE	exon	153573218	153573575	.	-	.	Parent=gene2944
###
chrX	ENCODE	gene	153570705	153597435	.	-	.	ID=gene2945;Name=RP11-115M6.1-007;name2=MPP1
chrX	ENCODE	exon	153570705	153571332	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153573218	153573292	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153573579	153573781	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153575406	153575486	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153576007	153576087	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153577030	153577136	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153578183	153578379	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153581933	153582001	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153582962	153583047	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153583748	153583826	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153584121	153584264	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153596676	153596806	.	-	.	Parent=gene2945
chrX	ENCODE	exon	153597251	153597435	.	-	.	Parent=gene2945
###
chrX	ENCODE	gene	153571132	153597376	.	-	.	ID=gene2946;Name=RP11-115M6.1-009;name2=MPP1
chrX	ENCODE	exon	153571132	153571332	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153571156	153571332	.	-	0	Parent=gene2946
chrX	ENCODE	exon	153573218	153573292	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153573218	153573292	.	-	0	Parent=gene2946
chrX	ENCODE	exon	153573579	153573781	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153573579	153573781	.	-	2	Parent=gene2946
chrX	ENCODE	exon	153575406	153575486	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153575406	153575486	.	-	2	Parent=gene2946
chrX	ENCODE	exon	153576007	153576087	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153576007	153576087	.	-	2	Parent=gene2946
chrX	ENCODE	exon	153577030	153577136	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153577030	153577136	.	-	1	Parent=gene2946
chrX	ENCODE	exon	153578183	153578319	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153578183	153578319	.	-	0	Parent=gene2946
chrX	ENCODE	exon	153581933	153582001	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153581933	153582001	.	-	0	Parent=gene2946
chrX	ENCODE	exon	153582962	153583047	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153582962	153583047	.	-	2	Parent=gene2946
chrX	ENCODE	exon	153583748	153583826	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153583748	153583826	.	-	0	Parent=gene2946
chrX	ENCODE	exon	153584121	153584264	.	-	.	Parent=gene2946
chrX	ENCODE	CDS	153584121	153584264	.	-	0	Parent=gene2946
chrX	ENCODE	CDS	153597251	153597352	.	-	0	Parent=gene2946
chrX	ENCODE	exon	153597251	153597376	.	-	.	Parent=gene2946
###
chrX	ENCODE	gene	153573292	153597464	.	-	.	ID=gene2947;name2=MPP1;Name=RP11-115M6.1-011
chrX	ENCODE	exon	153573292	153573781	.	-	.	Parent=gene2947
chrX	ENCODE	exon	153575406	153575486	.	-	.	Parent=gene2947
chrX	ENCODE	exon	153576007	153576087	.	-	.	Parent=gene2947
chrX	ENCODE	exon	153577030	153577136	.	-	.	Parent=gene2947
chrX	ENCODE	exon	153578183	153578379	.	-	.	Parent=gene2947
chrX	ENCODE	exon	153597251	153597464	.	-	.	Parent=gene2947
###
chrX	ENCODE	gene	153574688	153597420	.	-	.	ID=gene2948;Name=RP11-115M6.1-014;name2=MPP1
chrX	ENCODE	exon	153574688	153575486	.	-	.	Parent=gene2948
chrX	ENCODE	exon	153597251	153597420	.	-	.	Parent=gene2948
###
chrX	ENCODE	gene	153575224	153578262	.	-	.	ID=gene2949;Name=RP11-115M6.1-018;name2=MPP1
chrX	ENCODE	exon	153575224	153575486	.	-	.	Parent=gene2949
chrX	ENCODE	exon	153576007	153576087	.	-	.	Parent=gene2949
chrX	ENCODE	exon	153577101	153577136	.	-	.	Parent=gene2949
chrX	ENCODE	exon	153578183	153578262	.	-	.	Parent=gene2949
###
chrX	ENCODE	gene	153575356	153591794	.	-	.	ID=gene2950;Name=RP11-115M6.1-015;name2=MPP1
chrX	ENCODE	exon	153575356	153575486	.	-	.	Parent=gene2950
chrX	ENCODE	exon	153576007	153576087	.	-	.	Parent=gene2950
chrX	ENCODE	exon	153577030	153577136	.	-	.	Parent=gene2950
chrX	ENCODE	exon	153578183	153578379	.	-	.	Parent=gene2950
chrX	ENCODE	exon	153591724	153591794	.	-	.	Parent=gene2950
###
chrX	ENCODE	gene	153575632	153578204	.	-	.	ID=gene2951;Name=RP11-115M6.1-019;name2=MPP1
chrX	ENCODE	exon	153575632	153576087	.	-	.	Parent=gene2951
chrX	ENCODE	exon	153577030	153577136	.	-	.	Parent=gene2951
chrX	ENCODE	exon	153578183	153578204	.	-	.	Parent=gene2951
###
chrX	ENCODE	gene	153576010	153612986	.	-	.	ID=gene2952;Name=RP11-115M6.1-016;name2=MPP1
chrX	ENCODE	exon	153576010	153576087	.	-	.	Parent=gene2952
chrX	ENCODE	CDS	153576010	153576087	.	-	2	Parent=gene2952
chrX	ENCODE	exon	153577030	153577136	.	-	.	Parent=gene2952
chrX	ENCODE	CDS	153577030	153577136	.	-	1	Parent=gene2952
chrX	ENCODE	exon	153578183	153578379	.	-	.	Parent=gene2952
chrX	ENCODE	CDS	153578183	153578379	.	-	0	Parent=gene2952
chrX	ENCODE	exon	153581933	153582001	.	-	.	Parent=gene2952
chrX	ENCODE	CDS	153581933	153582001	.	-	0	Parent=gene2952
chrX	ENCODE	exon	153582962	153583047	.	-	.	Parent=gene2952
chrX	ENCODE	CDS	153582962	153583047	.	-	2	Parent=gene2952
chrX	ENCODE	exon	153583748	153583826	.	-	.	Parent=gene2952
chrX	ENCODE	CDS	153583748	153583826	.	-	0	Parent=gene2952
chrX	ENCODE	CDS	153584121	153584228	.	-	0	Parent=gene2952
chrX	ENCODE	exon	153584121	153584264	.	-	.	Parent=gene2952
chrX	ENCODE	exon	153612953	153612986	.	-	.	Parent=gene2952
###
chrX	ENCODE	gene	153576680	153597456	.	-	.	ID=gene2953;Name=RP11-115M6.1-012;name2=MPP1
chrX	ENCODE	exon	153576680	153577136	.	-	.	Parent=gene2953
chrX	ENCODE	exon	153578183	153578379	.	-	.	Parent=gene2953
chrX	ENCODE	exon	153597251	153597456	.	-	.	Parent=gene2953
###
chrX	ENCODE	gene	153577036	153597464	.	-	.	ID=gene2954;Name=RP11-115M6.1-010;name2=MPP1
chrX	ENCODE	exon	153577036	153577136	.	-	.	Parent=gene2954
chrX	ENCODE	CDS	153577036	153577136	.	-	1	Parent=gene2954
chrX	ENCODE	exon	153578183	153578379	.	-	.	Parent=gene2954
chrX	ENCODE	CDS	153578183	153578379	.	-	0	Parent=gene2954
chrX	ENCODE	exon	153581933	153582001	.	-	.	Parent=gene2954
chrX	ENCODE	CDS	153581933	153582001	.	-	0	Parent=gene2954
chrX	ENCODE	CDS	153597251	153597352	.	-	0	Parent=gene2954
chrX	ENCODE	exon	153597251	153597464	.	-	.	Parent=gene2954
###
chrX	ENCODE	gene	153577063	153583174	.	-	.	ID=gene2955;Name=RP11-115M6.1-017;name2=MPP1
chrX	ENCODE	exon	153577063	153577136	.	-	.	Parent=gene2955
chrX	ENCODE	exon	153578183	153578379	.	-	.	Parent=gene2955
chrX	ENCODE	exon	153581933	153582001	.	-	.	Parent=gene2955
chrX	ENCODE	exon	153582962	153583174	.	-	.	Parent=gene2955
###
chrX	ENCODE	gene	153578193	153597506	.	-	.	ID=gene2956;Name=RP11-115M6.1-002;name2=MPP1
chrX	ENCODE	exon	153578193	153578379	.	-	.	Parent=gene2956
chrX	ENCODE	exon	153581933	153582001	.	-	.	Parent=gene2956
chrX	ENCODE	exon	153582962	153583047	.	-	.	Parent=gene2956
chrX	ENCODE	exon	153583748	153583826	.	-	.	Parent=gene2956
chrX	ENCODE	exon	153584121	153584264	.	-	.	Parent=gene2956
chrX	ENCODE	exon	153591724	153591872	.	-	.	Parent=gene2956
chrX	ENCODE	exon	153597251	153597506	.	-	.	Parent=gene2956
###
chrX	ENCODE	gene	153578345	153584401	.	-	.	ID=gene2957;Name=RP11-115M6.1-003;name2=MPP1
chrX	ENCODE	exon	153578345	153578379	.	-	.	Parent=gene2957
chrX	ENCODE	exon	153581933	153582001	.	-	.	Parent=gene2957
chrX	ENCODE	exon	153582962	153583047	.	-	.	Parent=gene2957
chrX	ENCODE	exon	153583748	153583826	.	-	.	Parent=gene2957
chrX	ENCODE	exon	153584121	153584401	.	-	.	Parent=gene2957
###
chrX	ENCODE	gene	153581968	153597477	.	-	.	ID=gene2958;Name=RP11-115M6.1-005;name2=MPP1
chrX	ENCODE	exon	153581968	153582001	.	-	.	Parent=gene2958
chrX	ENCODE	CDS	153581968	153582001	.	-	0	Parent=gene2958
chrX	ENCODE	exon	153582962	153583047	.	-	.	Parent=gene2958
chrX	ENCODE	CDS	153582962	153583047	.	-	2	Parent=gene2958
chrX	ENCODE	exon	153583748	153583826	.	-	.	Parent=gene2958
chrX	ENCODE	CDS	153583748	153583826	.	-	0	Parent=gene2958
chrX	ENCODE	exon	153584172	153584264	.	-	.	Parent=gene2958
chrX	ENCODE	CDS	153584172	153584264	.	-	0	Parent=gene2958
chrX	ENCODE	CDS	153597251	153597352	.	-	0	Parent=gene2958
chrX	ENCODE	exon	153597251	153597477	.	-	.	Parent=gene2958
###
chrX	ENCODE	gene	153583610	153597447	.	-	.	ID=gene2959;name2=MPP1;Name=RP11-115M6.1-013
chrX	ENCODE	exon	153583610	153583826	.	-	.	Parent=gene2959
chrX	ENCODE	exon	153584121	153584264	.	-	.	Parent=gene2959
chrX	ENCODE	exon	153597251	153597447	.	-	.	Parent=gene2959
###
chrX	ENCODE	gene	153583610	153597447	.	-	.	ID=gene2960;Name=RP11-115M6.1-001;name2=MPP1
chrX	ENCODE	exon	153583610	153583826	.	-	.	Parent=gene2960
chrX	ENCODE	exon	153584121	153584264	.	-	.	Parent=gene2960
chrX	ENCODE	exon	153597251	153597447	.	-	.	Parent=gene2960
###
chrX	ENCODE	gene	153608305	153609500	.	-	.	ID=gene2961;Name=RP11-115M6.4-001;name2=RP11-115M6.4
chrX	ENCODE	exon	153608305	153609500	.	-	.	Parent=gene2961
chrX	ENCODE	CDS	153609078	153609380	.	-	0	Parent=gene2961
###
chrX	ENCODE	gene	153615327	153624650	.	-	.	ID=gene2962;Name=RP11-115M6.5-001;name2=RP11-115M6.5
chrX	ENCODE	exon	153615327	153615761	.	-	.	Parent=gene2962
chrX	ENCODE	CDS	153615734	153615761	.	-	1	Parent=gene2962
chrX	ENCODE	exon	153621514	153621643	.	-	.	Parent=gene2962
chrX	ENCODE	CDS	153621514	153621643	.	-	2	Parent=gene2962
chrX	ENCODE	CDS	153622694	153622835	.	-	0	Parent=gene2962
chrX	ENCODE	exon	153622694	153622934	.	-	.	Parent=gene2962
chrX	ENCODE	exon	153624553	153624650	.	-	.	Parent=gene2962
###
chrX	ENCODE	gene	153622552	153626641	.	-	.	ID=gene2963;Name=RP11-115M6.5-002;name2=RP11-115M6.5
chrX	ENCODE	exon	153622552	153622934	.	-	.	Parent=gene2963
chrX	ENCODE	exon	153624553	153624662	.	-	.	Parent=gene2963
chrX	ENCODE	exon	153626542	153626641	.	-	.	Parent=gene2963
###
chrX	ENCODE	gene	153627767	153678296	.	-	.	ID=gene2964;Name=RP11-115M6.7-003;name2=F8
chrX	ENCODE	exon	153627767	153629731	.	-	.	Parent=gene2964
chrX	ENCODE	CDS	153629576	153629731	.	-	0	Parent=gene2964
chrX	ENCODE	exon	153652411	153652587	.	-	.	Parent=gene2964
chrX	ENCODE	CDS	153652411	153652587	.	-	0	Parent=gene2964
chrX	ENCODE	exon	153653697	153653845	.	-	.	Parent=gene2964
chrX	ENCODE	CDS	153653697	153653845	.	-	2	Parent=gene2964
chrX	ENCODE	exon	153655062	153655206	.	-	.	Parent=gene2964
chrX	ENCODE	CDS	153655062	153655206	.	-	0	Parent=gene2964
chrX	ENCODE	CDS	153678113	153678136	.	-	0	Parent=gene2964
chrX	ENCODE	exon	153678113	153678296	.	-	.	Parent=gene2964
###
chrX	ENCODE	gene	153627774	153814732	.	-	.	ID=gene2965;name2=F8;Name=RP11-115M6.7-001
chrX	ENCODE	exon	153627774	153629731	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153629576	153629731	.	-	0	Parent=gene2965
chrX	ENCODE	exon	153652411	153652587	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153652411	153652587	.	-	0	Parent=gene2965
chrX	ENCODE	exon	153653697	153653845	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153653697	153653845	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153655062	153655206	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153655062	153655206	.	-	0	Parent=gene2965
chrX	ENCODE	exon	153688056	153688211	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153688056	153688211	.	-	0	Parent=gene2965
chrX	ENCODE	exon	153691845	153691930	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153691845	153691930	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153693350	153693421	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153693350	153693421	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153694030	153694146	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153694030	153694146	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153695885	153696067	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153695885	153696067	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153696275	153696503	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153696275	153696503	.	-	0	Parent=gene2965
chrX	ENCODE	exon	153696790	153697002	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153696790	153697002	.	-	0	Parent=gene2965
chrX	ENCODE	exon	153698399	153698552	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153698399	153698552	.	-	1	Parent=gene2965
chrX	ENCODE	exon	153720550	153723655	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153720550	153723655	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153739677	153739886	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153739677	153739886	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153745871	153746021	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153745871	153746021	.	-	0	Parent=gene2965
chrX	ENCODE	exon	153748936	153749150	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153748936	153749150	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153753054	153753147	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153753054	153753147	.	-	0	Parent=gene2965
chrX	ENCODE	exon	153757949	153758120	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153757949	153758120	.	-	1	Parent=gene2965
chrX	ENCODE	exon	153758405	153758666	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153758405	153758666	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153761310	153761531	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153761310	153761531	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153776666	153776782	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153776666	153776782	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153779216	153779284	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153779216	153779284	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153784915	153785127	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153784915	153785127	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153788952	153789074	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153788952	153789074	.	-	2	Parent=gene2965
chrX	ENCODE	exon	153791458	153791579	.	-	.	Parent=gene2965
chrX	ENCODE	CDS	153791458	153791579	.	-	1	Parent=gene2965
chrX	ENCODE	CDS	153814389	153814531	.	-	0	Parent=gene2965
chrX	ENCODE	exon	153814389	153814732	.	-	.	Parent=gene2965
###
chrX	ENCODE	gene	153676951	153677537	.	+	.	ID=gene2966;Name=CTD-2183H9.1-001;name2=H2AFB1
chrX	ENCODE	exon	153676951	153677537	.	+	.	Parent=gene2966
chrX	ENCODE	CDS	153677029	153677376	.	+	0	Parent=gene2966
###
chrX	ENCODE	gene	153678328	153680040	.	+	.	ID=gene2967;Name=CTD-2183H9.2-001;name2=F8A1
chrX	ENCODE	exon	153678328	153680040	.	+	.	Parent=gene2967
chrX	ENCODE	CDS	153678354	153679469	.	+	0	Parent=gene2967
###
chrX	ENCODE	gene	153757757	153758495	.	-	.	ID=gene2968;Name=RP11-115M6.7-002;name2=F8
chrX	ENCODE	exon	153757757	153758120	.	-	.	Parent=gene2968
chrX	ENCODE	exon	153758405	153758495	.	-	.	Parent=gene2968
###
chrX	ENCODE	gene	153776680	153818919	.	-	.	ID=gene2969;Name=RP11-115M6.7-004;name2=F8
chrX	ENCODE	exon	153776680	153776782	.	-	.	Parent=gene2969
chrX	ENCODE	CDS	153776680	153776782	.	-	2	Parent=gene2969
chrX	ENCODE	exon	153779216	153779284	.	-	.	Parent=gene2969
chrX	ENCODE	CDS	153779216	153779284	.	-	2	Parent=gene2969
chrX	ENCODE	exon	153784915	153785127	.	-	.	Parent=gene2969
chrX	ENCODE	CDS	153784915	153785127	.	-	2	Parent=gene2969
chrX	ENCODE	exon	153788952	153789074	.	-	.	Parent=gene2969
chrX	ENCODE	CDS	153788952	153789074	.	-	2	Parent=gene2969
chrX	ENCODE	exon	153791458	153791579	.	-	.	Parent=gene2969
chrX	ENCODE	CDS	153791458	153791579	.	-	1	Parent=gene2969
chrX	ENCODE	CDS	153818759	153818796	.	-	0	Parent=gene2969
chrX	ENCODE	exon	153818759	153818919	.	-	.	Parent=gene2969
###
chrX	ENCODE	gene	153785004	153818847	.	-	.	ID=gene2970;Name=RP11-115M6.7-005;name2=F8
chrX	ENCODE	exon	153785004	153785127	.	-	.	Parent=gene2970
chrX	ENCODE	CDS	153785004	153785127	.	-	2	Parent=gene2970
chrX	ENCODE	exon	153788952	153789074	.	-	.	Parent=gene2970
chrX	ENCODE	CDS	153788952	153789074	.	-	2	Parent=gene2970
chrX	ENCODE	exon	153791458	153791579	.	-	.	Parent=gene2970
chrX	ENCODE	CDS	153791458	153791579	.	-	1	Parent=gene2970
chrX	ENCODE	exon	153814389	153814475	.	-	.	Parent=gene2970
chrX	ENCODE	CDS	153814389	153814475	.	-	1	Parent=gene2970
chrX	ENCODE	CDS	153818759	153818796	.	-	0	Parent=gene2970
chrX	ENCODE	exon	153818759	153818847	.	-	.	Parent=gene2970
###
chrX	ENCODE	gene	153817959	153843711	.	+	.	ID=gene2971;Name=GS1-273L24.1-003;name2=FUNDC2
chrX	ENCODE	exon	153817959	153818130	.	+	.	Parent=gene2971
chrX	ENCODE	exon	153818590	153818659	.	+	.	Parent=gene2971
chrX	ENCODE	exon	153825382	153825532	.	+	.	Parent=gene2971
chrX	ENCODE	exon	153838488	153838563	.	+	.	Parent=gene2971
chrX	ENCODE	exon	153843649	153843711	.	+	.	Parent=gene2971
###
chrX	ENCODE	gene	153818664	153852282	.	+	.	ID=gene2972;Name=GS1-273L24.1-001;name2=FUNDC2
chrX	ENCODE	exon	153818664	153819050	.	+	.	Parent=gene2972
chrX	ENCODE	CDS	153818918	153819050	.	+	0	Parent=gene2972
chrX	ENCODE	exon	153825382	153825532	.	+	.	Parent=gene2972
chrX	ENCODE	CDS	153825382	153825532	.	+	2	Parent=gene2972
chrX	ENCODE	exon	153838488	153838563	.	+	.	Parent=gene2972
chrX	ENCODE	CDS	153838488	153838563	.	+	1	Parent=gene2972
chrX	ENCODE	exon	153843649	153843780	.	+	.	Parent=gene2972
chrX	ENCODE	CDS	153843649	153843780	.	+	0	Parent=gene2972
chrX	ENCODE	CDS	153846574	153846651	.	+	0	Parent=gene2972
chrX	ENCODE	exon	153846574	153852282	.	+	.	Parent=gene2972
###
chrX	ENCODE	gene	153819132	153846660	.	+	.	ID=gene2973;Name=GS1-273L24.1-004;name2=FUNDC2
chrX	ENCODE	exon	153819132	153819351	.	+	.	Parent=gene2973
chrX	ENCODE	CDS	153819132	153819351	.	+	0	Parent=gene2973
chrX	ENCODE	exon	153825382	153825532	.	+	.	Parent=gene2973
chrX	ENCODE	CDS	153825382	153825532	.	+	2	Parent=gene2973
chrX	ENCODE	exon	153838488	153838563	.	+	.	Parent=gene2973
chrX	ENCODE	CDS	153838488	153838563	.	+	1	Parent=gene2973
chrX	ENCODE	exon	153843649	153843780	.	+	.	Parent=gene2973
chrX	ENCODE	CDS	153843649	153843780	.	+	0	Parent=gene2973
chrX	ENCODE	CDS	153846574	153846651	.	+	0	Parent=gene2973
chrX	ENCODE	exon	153846574	153846660	.	+	.	Parent=gene2973
###
chrX	ENCODE	gene	153824958	153846592	.	+	.	ID=gene2974;Name=GS1-273L24.1-005;name2=FUNDC2
chrX	ENCODE	exon	153824958	153825532	.	+	.	Parent=gene2974
chrX	ENCODE	exon	153843649	153843780	.	+	.	Parent=gene2974
chrX	ENCODE	exon	153846574	153846592	.	+	.	Parent=gene2974
###
chrX	ENCODE	gene	153825405	153847085	.	+	.	ID=gene2975;Name=GS1-273L24.1-006;name2=FUNDC2
chrX	ENCODE	exon	153825405	153825532	.	+	.	Parent=gene2975
chrX	ENCODE	exon	153838488	153838563	.	+	.	Parent=gene2975
chrX	ENCODE	exon	153839348	153839370	.	+	.	Parent=gene2975
chrX	ENCODE	exon	153843649	153843780	.	+	.	Parent=gene2975
chrX	ENCODE	exon	153846574	153847085	.	+	.	Parent=gene2975
###
chrX	ENCODE	gene	153839036	153846871	.	+	.	ID=gene2976;Name=GS1-273L24.1-007;name2=FUNDC2
chrX	ENCODE	exon	153839036	153839370	.	+	.	Parent=gene2976
chrX	ENCODE	exon	153843649	153843780	.	+	.	Parent=gene2976
chrX	ENCODE	exon	153846574	153846871	.	+	.	Parent=gene2976
###
chrX	ENCODE	gene	153841073	153847550	.	+	.	ID=gene2977;Name=GS1-273L24.1-002;name2=FUNDC2
chrX	ENCODE	exon	153841073	153843780	.	+	.	Parent=gene2977
chrX	ENCODE	exon	153846574	153847550	.	+	.	Parent=gene2977
###
chrX	ENCODE	gene	153853601	153857498	.	-	.	ID=gene2978;Name=GS1-273L24.4-005;name2=MTCP1
chrX	ENCODE	exon	153853601	153853970	.	-	.	Parent=gene2978
chrX	ENCODE	CDS	153853822	153853970	.	-	2	Parent=gene2978
chrX	ENCODE	CDS	153855945	153856002	.	-	0	Parent=gene2978
chrX	ENCODE	exon	153855945	153856012	.	-	.	Parent=gene2978
chrX	ENCODE	exon	153857465	153857498	.	-	.	Parent=gene2978
###
chrX	ENCODE	gene	153853601	153863341	.	-	.	ID=gene2979;Name=GS1-273L24.4-001;name2=MTCP1
chrX	ENCODE	exon	153853601	153853970	.	-	.	Parent=gene2979
chrX	ENCODE	CDS	153853822	153853970	.	-	2	Parent=gene2979
chrX	ENCODE	CDS	153855945	153856002	.	-	0	Parent=gene2979
chrX	ENCODE	exon	153855945	153856012	.	-	.	Parent=gene2979
chrX	ENCODE	exon	153862673	153863341	.	-	.	Parent=gene2979
###
chrX	ENCODE	gene	153853607	153857347	.	-	.	ID=gene2980;Name=GS1-273L24.4-004;name2=MTCP1
chrX	ENCODE	exon	153853607	153853970	.	-	.	Parent=gene2980
chrX	ENCODE	CDS	153853822	153853970	.	-	2	Parent=gene2980
chrX	ENCODE	CDS	153855945	153856002	.	-	0	Parent=gene2980
chrX	ENCODE	exon	153855945	153856012	.	-	.	Parent=gene2980
chrX	ENCODE	exon	153856916	153857347	.	-	.	Parent=gene2980
###
chrX	ENCODE	gene	153856013	153863205	.	-	.	ID=gene2981;name2=MTCP1;Name=GS1-273L24.4-002
chrX	ENCODE	exon	153856013	153857378	.	-	.	Parent=gene2981
chrX	ENCODE	exon	153857465	153857516	.	-	.	Parent=gene2981
chrX	ENCODE	CDS	153857469	153857516	.	-	0	Parent=gene2981
chrX	ENCODE	exon	153857598	153857768	.	-	.	Parent=gene2981
chrX	ENCODE	CDS	153857598	153857768	.	-	0	Parent=gene2981
chrX	ENCODE	CDS	153857885	153857989	.	-	0	Parent=gene2981
chrX	ENCODE	exon	153857885	153858036	.	-	.	Parent=gene2981
chrX	ENCODE	exon	153862673	153863205	.	-	.	Parent=gene2981
###
chrX	ENCODE	gene	153856907	153863115	.	-	.	ID=gene2982;Name=GS1-273L24.4-003;name2=MTCP1
chrX	ENCODE	exon	153856907	153857378	.	-	.	Parent=gene2982
chrX	ENCODE	exon	153857465	153857516	.	-	.	Parent=gene2982
chrX	ENCODE	exon	153857598	153857768	.	-	.	Parent=gene2982
chrX	ENCODE	exon	153862673	153863115	.	-	.	Parent=gene2982
###
chrX	ENCODE	gene	153857142	153939916	.	-	.	ID=gene2983;name2=MTCP1;Name=GS1-273L24.4-007
chrX	ENCODE	exon	153857142	153857378	.	-	.	Parent=gene2983
chrX	ENCODE	exon	153857465	153857516	.	-	.	Parent=gene2983
chrX	ENCODE	exon	153857598	153857768	.	-	.	Parent=gene2983
chrX	ENCODE	exon	153939639	153939916	.	-	.	Parent=gene2983
###
chrX	ENCODE	gene	153857300	153939754	.	-	.	ID=gene2984;name2=MTCP1;Name=GS1-273L24.4-006
chrX	ENCODE	exon	153857300	153857378	.	-	.	Parent=gene2984
chrX	ENCODE	exon	153857465	153857516	.	-	.	Parent=gene2984
chrX	ENCODE	CDS	153857469	153857516	.	-	0	Parent=gene2984
chrX	ENCODE	exon	153857598	153857768	.	-	.	Parent=gene2984
chrX	ENCODE	CDS	153857598	153857768	.	-	0	Parent=gene2984
chrX	ENCODE	CDS	153857885	153857989	.	-	0	Parent=gene2984
chrX	ENCODE	exon	153857885	153858036	.	-	.	Parent=gene2984
chrX	ENCODE	exon	153939639	153939754	.	-	.	Parent=gene2984
###
chrX	ENCODE	gene	153863399	153913297	.	+	.	ID=gene2985;Name=RP11-143H17.2-006;name2=BRCC3
chrX	ENCODE	exon	153863399	153863629	.	+	.	Parent=gene2985
chrX	ENCODE	CDS	153863507	153863629	.	+	0	Parent=gene2985
chrX	ENCODE	exon	153864306	153864322	.	+	.	Parent=gene2985
chrX	ENCODE	CDS	153864306	153864322	.	+	0	Parent=gene2985
chrX	ENCODE	exon	153865353	153865410	.	+	.	Parent=gene2985
chrX	ENCODE	CDS	153865353	153865410	.	+	1	Parent=gene2985
chrX	ENCODE	exon	153869149	153869268	.	+	.	Parent=gene2985
chrX	ENCODE	CDS	153869149	153869268	.	+	0	Parent=gene2985
chrX	ENCODE	exon	153870595	153870682	.	+	.	Parent=gene2985
chrX	ENCODE	CDS	153870595	153870682	.	+	0	Parent=gene2985
chrX	ENCODE	exon	153881242	153881330	.	+	.	Parent=gene2985
chrX	ENCODE	CDS	153881242	153881330	.	+	2	Parent=gene2985
chrX	ENCODE	exon	153882763	153882818	.	+	.	Parent=gene2985
chrX	ENCODE	CDS	153882763	153882818	.	+	0	Parent=gene2985
chrX	ENCODE	exon	153908036	153908167	.	+	.	Parent=gene2985
chrX	ENCODE	CDS	153908036	153908167	.	+	1	Parent=gene2985
chrX	ENCODE	exon	153908690	153908733	.	+	.	Parent=gene2985
chrX	ENCODE	CDS	153908690	153908733	.	+	1	Parent=gene2985
chrX	ENCODE	CDS	153911978	153912129	.	+	2	Parent=gene2985
chrX	ENCODE	exon	153911978	153912147	.	+	.	Parent=gene2985
chrX	ENCODE	exon	153913202	153913297	.	+	.	Parent=gene2985
###
chrX	ENCODE	gene	153863410	153914706	.	+	.	ID=gene2986;Name=RP11-143H17.2-002;name2=BRCC3
chrX	ENCODE	exon	153863410	153863629	.	+	.	Parent=gene2986
chrX	ENCODE	CDS	153863507	153863629	.	+	0	Parent=gene2986
chrX	ENCODE	exon	153864306	153864322	.	+	.	Parent=gene2986
chrX	ENCODE	CDS	153864306	153864322	.	+	0	Parent=gene2986
chrX	ENCODE	exon	153865356	153865410	.	+	.	Parent=gene2986
chrX	ENCODE	CDS	153865356	153865410	.	+	1	Parent=gene2986
chrX	ENCODE	exon	153869149	153869268	.	+	.	Parent=gene2986
chrX	ENCODE	CDS	153869149	153869268	.	+	0	Parent=gene2986
chrX	ENCODE	exon	153870595	153870682	.	+	.	Parent=gene2986
chrX	ENCODE	CDS	153870595	153870682	.	+	0	Parent=gene2986
chrX	ENCODE	exon	153881242	153881330	.	+	.	Parent=gene2986
chrX	ENCODE	CDS	153881242	153881330	.	+	2	Parent=gene2986
chrX	ENCODE	exon	153882763	153882818	.	+	.	Parent=gene2986
chrX	ENCODE	CDS	153882763	153882818	.	+	0	Parent=gene2986
chrX	ENCODE	exon	153908036	153908167	.	+	.	Parent=gene2986
chrX	ENCODE	CDS	153908036	153908167	.	+	1	Parent=gene2986
chrX	ENCODE	exon	153908690	153908733	.	+	.	Parent=gene2986
chrX	ENCODE	CDS	153908690	153908733	.	+	1	Parent=gene2986
chrX	ENCODE	CDS	153911978	153912129	.	+	2	Parent=gene2986
chrX	ENCODE	exon	153911978	153912147	.	+	.	Parent=gene2986
chrX	ENCODE	exon	153913202	153914706	.	+	.	Parent=gene2986
###
chrX	ENCODE	gene	153863478	153915051	.	+	.	ID=gene2987;Name=RP11-143H17.2-004;name2=BRCC3
chrX	ENCODE	exon	153863478	153863629	.	+	.	Parent=gene2987
chrX	ENCODE	CDS	153863507	153863629	.	+	0	Parent=gene2987
chrX	ENCODE	exon	153864306	153864322	.	+	.	Parent=gene2987
chrX	ENCODE	CDS	153864306	153864322	.	+	0	Parent=gene2987
chrX	ENCODE	exon	153865356	153865410	.	+	.	Parent=gene2987
chrX	ENCODE	CDS	153865356	153865410	.	+	1	Parent=gene2987
chrX	ENCODE	exon	153869149	153869268	.	+	.	Parent=gene2987
chrX	ENCODE	CDS	153869149	153869268	.	+	0	Parent=gene2987
chrX	ENCODE	exon	153870595	153870682	.	+	.	Parent=gene2987
chrX	ENCODE	CDS	153870595	153870682	.	+	0	Parent=gene2987
chrX	ENCODE	exon	153881242	153881330	.	+	.	Parent=gene2987
chrX	ENCODE	CDS	153881242	153881330	.	+	2	Parent=gene2987
chrX	ENCODE	exon	153882763	153882818	.	+	.	Parent=gene2987
chrX	ENCODE	CDS	153882763	153882818	.	+	0	Parent=gene2987
chrX	ENCODE	exon	153908690	153908733	.	+	.	Parent=gene2987
chrX	ENCODE	CDS	153908690	153908733	.	+	1	Parent=gene2987
chrX	ENCODE	CDS	153911978	153912129	.	+	2	Parent=gene2987
chrX	ENCODE	exon	153911978	153912147	.	+	.	Parent=gene2987
chrX	ENCODE	exon	153913202	153915051	.	+	.	Parent=gene2987
###
chrX	ENCODE	gene	153863482	153915053	.	+	.	ID=gene2988;Name=RP11-143H17.2-001;name2=BRCC3
chrX	ENCODE	exon	153863482	153863629	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153863507	153863629	.	+	0	Parent=gene2988
chrX	ENCODE	exon	153864306	153864322	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153864306	153864322	.	+	0	Parent=gene2988
chrX	ENCODE	exon	153865356	153865410	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153865356	153865410	.	+	1	Parent=gene2988
chrX	ENCODE	exon	153869149	153869268	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153869149	153869268	.	+	0	Parent=gene2988
chrX	ENCODE	exon	153870595	153870682	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153870595	153870682	.	+	0	Parent=gene2988
chrX	ENCODE	exon	153881242	153881330	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153881242	153881330	.	+	2	Parent=gene2988
chrX	ENCODE	exon	153882763	153882818	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153882763	153882818	.	+	0	Parent=gene2988
chrX	ENCODE	exon	153891294	153891368	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153891294	153891368	.	+	1	Parent=gene2988
chrX	ENCODE	exon	153908036	153908167	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153908036	153908167	.	+	1	Parent=gene2988
chrX	ENCODE	exon	153908690	153908733	.	+	.	Parent=gene2988
chrX	ENCODE	CDS	153908690	153908733	.	+	1	Parent=gene2988
chrX	ENCODE	CDS	153911978	153912129	.	+	2	Parent=gene2988
chrX	ENCODE	exon	153911978	153912147	.	+	.	Parent=gene2988
chrX	ENCODE	exon	153913202	153915053	.	+	.	Parent=gene2988
###
chrX	ENCODE	gene	153863497	153908162	.	+	.	ID=gene2989;Name=RP11-143H17.2-007;name2=BRCC3
chrX	ENCODE	exon	153863497	153863629	.	+	.	Parent=gene2989
chrX	ENCODE	CDS	153863507	153863629	.	+	0	Parent=gene2989
chrX	ENCODE	exon	153869149	153869268	.	+	.	Parent=gene2989
chrX	ENCODE	CDS	153869149	153869268	.	+	0	Parent=gene2989
chrX	ENCODE	exon	153870595	153870682	.	+	.	Parent=gene2989
chrX	ENCODE	CDS	153870595	153870682	.	+	0	Parent=gene2989
chrX	ENCODE	exon	153881242	153881330	.	+	.	Parent=gene2989
chrX	ENCODE	CDS	153881242	153881330	.	+	2	Parent=gene2989
chrX	ENCODE	exon	153882763	153882818	.	+	.	Parent=gene2989
chrX	ENCODE	CDS	153882763	153882818	.	+	0	Parent=gene2989
chrX	ENCODE	exon	153891294	153891368	.	+	.	Parent=gene2989
chrX	ENCODE	CDS	153891294	153891368	.	+	1	Parent=gene2989
chrX	ENCODE	exon	153908036	153908162	.	+	.	Parent=gene2989
chrX	ENCODE	CDS	153908036	153908162	.	+	1	Parent=gene2989
###
chrX	ENCODE	gene	153863511	153915015	.	+	.	ID=gene2990;Name=RP11-143H17.2-005;name2=BRCC3
chrX	ENCODE	exon	153863511	153863633	.	+	.	Parent=gene2990
chrX	ENCODE	exon	153865353	153865410	.	+	.	Parent=gene2990
chrX	ENCODE	exon	153869149	153869268	.	+	.	Parent=gene2990
chrX	ENCODE	exon	153870595	153870682	.	+	.	Parent=gene2990
chrX	ENCODE	exon	153881242	153881330	.	+	.	Parent=gene2990
chrX	ENCODE	exon	153882763	153882818	.	+	.	Parent=gene2990
chrX	ENCODE	exon	153908036	153908167	.	+	.	Parent=gene2990
chrX	ENCODE	exon	153908690	153908733	.	+	.	Parent=gene2990
chrX	ENCODE	exon	153911978	153912147	.	+	.	Parent=gene2990
chrX	ENCODE	exon	153913202	153915015	.	+	.	Parent=gene2990
###
chrX	ENCODE	gene	153865390	153870909	.	+	.	ID=gene2991;Name=RP11-143H17.2-003;name2=BRCC3
chrX	ENCODE	exon	153865390	153865410	.	+	.	Parent=gene2991
chrX	ENCODE	CDS	153865390	153865410	.	+	0	Parent=gene2991
chrX	ENCODE	exon	153869149	153869268	.	+	.	Parent=gene2991
chrX	ENCODE	CDS	153869149	153869268	.	+	0	Parent=gene2991
chrX	ENCODE	CDS	153870595	153870726	.	+	0	Parent=gene2991
chrX	ENCODE	exon	153870595	153870909	.	+	.	Parent=gene2991
###
genometools-1.5.1/testdata/encode_known_genes_Mar07.seqids000066400000000000000000000001601211610345200236640ustar00rootroot00000000000000chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr18
chr19
chr2
chr20
chr21
chr22
chr5
chr6
chr7
chr8
chr9
chrX
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BCgenometools-1.5.1/testdata/example_1.fa000066400000000000000000000062311211610345200200420ustar00rootroot00000000000000>seq1
CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCT
GTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCAC
GGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAG
TCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTC
AGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAA
CAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACC
AAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCT
CTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCA
ATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGC
AGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAAC
AACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACAC
ATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATAC
CATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCT
TTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTT
TCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAAT
GCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAAT
ACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGA
ACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTG
TGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTA
CGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAG
TCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGC
TTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTC
TCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTG
TTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGG
AGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATA
TTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTC
TCCCTCGTCTTCTTA
>seq2
TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAG
CTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCT
TATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTT
CAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAA
AAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTT
AGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATAC
ATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAG
GAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCAT
CAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATT
TTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTA
AGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATA
ATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAAT
TAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATA
AAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACC
TCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATA
GATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATT
AATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCA
AATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGT
AAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATAT
AACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAAT
ACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGAT
GATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTG
CGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATA
GCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAA
AAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAA
TTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGC
CAGAAAAAAATATTTACAGTAACT
genometools-1.5.1/testdata/example_1.fa.fai000066400000000000000000000000471211610345200205770ustar00rootroot00000000000000seq1	1575	6	60	61
seq2	1584	1614	60	61
genometools-1.5.1/testdata/example_1.sam.extract000066400000000000000000012663621211610345200217230ustar00rootroot00000000000000B7_591:4:96:693:509	73	seq1	36M	cactagtggctcattgtaaatgtgtggtttaactcg	<<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7
EAS54_65:7:152:368:113	73	seq1	35M	ctagtggctcattgtaaatgtgtggtttaactcgt	<<<<<<<<<<0<<<<655<<7<<<:9<<3/:<6):
EAS51_64:8:5:734:57	137	seq1	35M	agtggctcattgtaaatgtgtggtttaactcgtcc	<<<<<<<<<<<7;71<<;<;;<7;<<3;);3*8/5
B7_591:1:289:587:906	137	seq1	36M	gtggctcattgtaattttttgttttaactcttctct	(-&----,----)-)-),'--)---',+-,),''*,
EAS56_59:8:38:671:758	137	seq1	35M	gctcattgtaaatgtgtggtttaactcgtccatgg	<<<<<<<<<<<<<<<;<;7<<<<<<<<7<<;:<5%
EAS56_61:6:18:467:281	73	seq1	35M	attgtaaatgtgtggtttaactcgtccctggccca	<<<<<<<<;<<<8<<<<<;8:;6/686&;(16666
EAS114_28:5:296:340:699	137	seq1	36M	attgtaaatgtgtggtttaactcgtccatggcccag	<<<<<;<<<;<;<<<<<<<<<<<8<8<3<8;<;<0;
B7_597:6:194:894:408	73	seq1	35M	tgtaaatgtgtggtttaactcgtccattgcccagc	<<<<<<<<<7<<;<<<<;<<<7;;<<<*,;;572<
EAS188_4:8:12:628:973	89	seq1	35M	aaatgtgtggtttaactcgtccatggcccagcatt	==;=:;:;;:====;=;===:=======;==;===
EAS51_66:7:68:402:50	137	seq1	35M	gtgtggtttaactcgtccatggcccagcatttggg	<<<<<<<<<<<<<<:<<<9<6;9;;&697;7&<55
EAS114_30:6:298:115:564	137	seq1	35M	gtgtggtttaactcgtccatggcccagcattaggg	<<<<<<<<<<<<<;<<<;<<<;<<<;<:<<;;5;;
B7_591:3:188:662:155	73	seq1	36M	gtggtttaactcgtccatggcccagcattagggagc	<<<<<<<<<<<<<<<<<<:;<<<4<<+<<14991;4
EAS56_59:2:225:608:291	73	seq1	35M	tttaactcgtccatggcccagcattagggatctgt	<<<<<<<<<<<<<<8&<<<;6<9;;+2++(%59(<
EAS51_66:7:328:397:316	73	seq1	35M	ttaactcgtccatggcccagcattagggagctgtg	<<<<<<<<<<<<<6=<<<;<<5<<<+<15:'<;;4
EAS51_64:5:257:960:682	73	seq1	35M	aactcgtccatggcccagcattagggagctgtgga	<<<<<<<<<<<;<<<<<<<<<<<<<<<<<<9;;9<
EAS54_61:4:143:69:578	99	seq1	35M	gtacatggcccagcattagggagctgtggaccccg	===;=====48=844;=;+=5==*57,2+5&,5+5
EAS114_32:5:78:583:499	163	seq1	35M	tccatggcccagcattagggcgctgtggaccctgc	<<8;<<<<<<1<<-1<+8<<&;:555;5-*77/51
EAS1_93:7:252:171:323	163	seq1	35M	gcccagcattagggagctgtggaccctgcagcctg	<<<):<<<<<<<<<:<<<&5<<2<562<<<<-7--
B7_593:4:106:316:452	99	seq1	36M	cattagggagctgtggaccctgcagcctggctgttg	;<<;<<<<;<;;;;7;<;<<<;<<;<<;4:<<;+&+
B7_589:8:113:968:19	163	seq1	35M	attagggagctgtggaccctgcagcctggctgggg	<<<<;<;<<<<<<:;;;.;;<75;);;;<.2+(;5
EAS54_65:3:321:311:983	99	seq1	35M	ttagggagctgtggaccctgcagcctggctgtggg	<<<;<<<<<<<<+;;<47;<9;94430499<88+6
B7_591:6:155:12:674	163	seq1	36M	tagggagctgtggaccctgcagcctggctgtggggg	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<+:9-<<
EAS219_FC30151:7:51:1429:1043	163	seq1	35M	ctgtggaccctgcagcctggctgtggggggcgccg	<<<<<<<<<<<<<:<<<;<<<<:):;<;;-15)+1
B7_591:5:42:540:501	99	seq1	36M	tgtggaccctgcagcctggctgtgggggccgcagtg	<<<<<<<<<<<<<<<<<<<<<<.;<<<<,804,858
EAS192_3:5:223:142:410	99	seq1	35M	tgtggaccctgcagcctggctggggggggcgcagt	<<<<<<<<<<<<<<:<5<<2<<(<:<<<:5,((7(
EAS1_108:1:65:787:74	163	seq1	35M	gtggaccctgcagcctggctggggggggcacgggg	<<<<<8-82<2823;-<;822222888,*(2%2-2
EAS56_61:6:227:259:597	99	seq1	35M	gtggaccctgcagcctggctgtgggggccgcagtg	<<<<<<<<<<;;<<<6;8:68333;<8(8,1,$$+
EAS114_30:1:243:10:911	163	seq1	35M	ggaccctgcagcctggctgtgggggccgctgtggg	<<;<<<<<<<<<<7<<<<<7<<<<<:4<((<%;<+
EAS221_1:2:90:986:1224	163	seq1	35M	cctgcagcctggctgtgggggccgcagcgggtggg	<<:<<<<<<<<<<<<0<<<<<)<<63<+<<2'<-<
EAS54_67:3:175:730:949	163	seq1	35M	gcagcctggctgtgggggccgcagtggctgagggg	<<<<<<<<<<8<;<<<<<0(<<;;,<<7<4%7626
EAS54_65:8:76:493:708	99	seq1	35M	gcctggctgtgggggcaccagccgctgcggggggt	<<<<1<<1<;626<;<''+;-'';+2'+;;)6--+
EAS1_97:7:20:979:96	163	seq1	35M	ctgtgggggccgcagtggctgagggggggaggggc	<<<<<<;<<<<<7<<,<<,:;,<<<<17)++':.'
EAS114_26:3:284:261:124	163	seq1	35M	ctgtgggggccgcagtgggtgaggggtggaggggg	============'8====':=+====,=8,8'=++
EAS221_1:2:29:1486:672	99	seq1	35M	ctgtgggggccgcagtggctgaggggtgcagagcc	<<<<<<<<<<<<<;<;<<<<<;<<<<8;;;<8;-;
EAS188_7:2:218:877:489	163	seq1	35M	tgtgggggccgcagtggctgggggggggcgggcgg	<<<<<<<;<<<07640<2<9(<9<<&9%(<(6%%3
EAS51_64:7:242:862:732	73	seq1	35M	ggctgaggggtgcagagccgagtcacggggttgcc	<<<<<<<<<<<<<<<;<<<:<;+<3<::3<';:';
EAS51_64:7:242:862:732	133	seq1	*	gggtctatgtgaacaaaggcactaaacacagctgt	<<<<<<<<<<8<<<<<78<<<378<<<77755++2
EAS56_57:6:190:289:82	69	seq1	*	ctcaaggttgttgcaagggggtctatgtgaacaaa	<<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<;
EAS56_57:6:190:289:82	137	seq1	35M	aggggtgcagagccgagtcacggggttgccagcac	<<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2;
EAS51_64:3:190:727:308	99	seq1	35M	ggtgcagagccgagtcacggggttgccagcacagg	<<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844
EAS112_34:7:141:80:875	99	seq1	35M	agccgagtcacggggttgccagcacaggggcttaa	<<<<<<<<<<<<<<<<<<<<<<:<<8;<<8+7;-7
EAS219_FC30151:3:40:1128:1940	163	seq1	35M	ccgagtcacggggttgccagcacaggggcttaacc	<<<<<<<<<<<<<<<<<<<;<<5;;<<<9;;;;7:
EAS51_62:5:290:319:736	69	seq1	*	gttctcaaggttgttgcaagggggtctatgtgaac	<<<<<<:7:<.<<<<7<<.<.<<.9*<4<:<4%74
EAS51_62:5:290:319:736	137	seq1	35M	cgagtcacggggttgccagcacaggggcttaacct	==;=======7====6=;==:;;====66=::27:
B7_597:2:132:493:921	69	seq1	*	gttctcaaggttgttgcaagggggtctatgtgaac	<<<<<<<<<<<<<<<<<<<;<<<<77;0<;;6777
B7_597:2:132:493:921	137	seq1	35M	acggggttgccagcacaggggcttaacctctggtg	<<<<<<<<<<<<<<<<;<<<<<<<<;<<<<;;88:
EAS114_30:7:283:799:560	163	seq1	35M	ggggttgccagcacaggggcttaacctctggtgac	<<<<+<<<<8<<<+<<<<<;<<:07;8;7402447
EAS192_3:1:225:195:543	99	seq1	35M	ggttgccagcacaggggcttaacctctggtgactg	<<<<<<<<<<<<<<<<<<<<<<<9<<;::388998
B7_589:6:114:714:317	99	seq1	35M	tgccagcacaggggcttaacctctggtgactgcca	<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<5;<;
EAS114_39:1:70:147:84	163	seq1	35M	ccagcacaggggcttaacctctggtgactgccaga	<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;(5<<
EAS188_7:2:187:227:818	163	seq1	35M	cagcacaggggcttaacctctggtgactgccagag	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<3<;<<
EAS1_97:4:77:29:126	99	seq1	35M	gcacaggggcttaacctctggtgactgccagagct	<<<<<<<<<<3<<<<<<<;;;7<;<<449<-:977
EAS114_30:4:327:795:103	99	seq1	35M	acaggggcttaacctctggtgactgccagagctgc	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<;
EAS114_30:3:139:117:262	69	seq1	*	gttctcaaggttgttgcaagggggtctatgtgaac	<<<7<<<<<<<<<<<<<<<<<<<;<;<<<<<37;3
EAS114_30:3:139:117:262	137	seq1	35M	aggggcttaacctctggtgactgccagagctgctg	<<<<;<<<<<<<<<<<<<:<<<<<:<<8<<<<:<:
EAS219_FC30151:5:29:817:854	73	seq1	35M	aggggcttaacctctggtgactgccagagctgctg	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS219_FC30151:5:29:817:854	133	seq1	*	gttctcaaggttgttgcaagggggtttatgtgaac	<<<<<<<<<<<<<<<1..;:;;;;1%407)07&7.
EAS192_3:6:170:169:57	163	seq1	35M	ggcttgacctctggtgactgccagagctgctggcc	<<<<<;<<<<<<;<<<<<<<<<<<<:<<<<<;;+%
B7_595:4:84:802:737	99	seq1	35M	cttaacctctggtgactgccagagctgctggcaag	<<<<<<<<<<;9<9<<<;<<;73;<<<<<37;1+.
EAS188_4:7:78:583:670	163	seq1	35M	taacctctggtgactgccagagctgctggcaagct	<<<<<<<<<<;;;<;;<<<:7;5;<5;;<2--8-;
EAS51_64:3:90:435:691	99	seq1	35M	tctggtgactgccagagctgctggcaagctagagt	<<<<<<<<<<;<<<;<<<<:<<<;<81;<<1;784
EAS188_7:3:13:122:187	163	seq1	35M	gactgccagagctgctggcaagctagagtcccctt	<<<<<<<;<;<<<;<<<<:;6<<<<;;;;:<<%%<
EAS221_1:6:69:735:1915	99	seq1	35M	actgccagagctgctggcaagctagagtcccattt	<<<<<<<<;<<<<<<<<<;<<<<;<8<<<<;1:<<
EAS114_45:5:66:959:1311	163	seq1	35M	cagagctgctggcaagctagaggcccatctggagc	;;4;;;+;;;-01;;&-;;4;;&;;73)(&**274
EAS56_57:6:325:759:288	99	seq1	35M	gctgctggcaagctagagtcccatttggagcccct	8<;<<<<81<<<<<;<<;<<<;9<<<<1>><<<<
EAS51_66:4:240:264:231	121	seq1	35M	tgtaatgaaaactatatttatgctattcagttcta	9;,;;62<9<)29<<<;96<<<;<<7<<<<<<;<<
EAS51_66:4:240:264:231	181	seq1	*	caacagatcaagaaggaggggcaatggacgagtta	%15+5022))0&<<)0)+7:4+&<0<<:0<<<7<<
EAS1_93:7:14:426:613	99	seq1	35M	gtaatgaaaactatatttatgctattcagttctaa	======;=;==========;;==3=;==-=<;<;<
EAS1_93:2:173:995:93	163	seq1	35M	taatgaaaactatatttatgctattcagttctaaa	<<<<<<<<<<<<<<<<<<<7:<<<<;:<:<<<<:7
EAS51_64:6:195:348:703	163	seq1	35M	taatgaaaactatatttatgctattcagttctaaa	<<<<<<<;<<<<<;:<<<<<<<<<<<<:<1:<:7<
EAS1_108:2:62:879:264	163	seq1	35M	aatgaaaactatatttatgctattcagttctaaat	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<<
EAS54_61:4:83:452:970	99	seq1	35M	aatgaaaactatatttatgctattcagttctaaat	==========================;========
EAS218_1:2:64:1318:1711	99	seq1	35M	tgaaaactatatttatgctattcagttctaaatat	<<<<<<<<<<<<<<<<7<<<<<<<:<<<<<2<<<<
B7_589:8:113:968:19	83	seq1	35M	gaaaactatatttatgctattcagttctaaatata	8;<;8;9<<<<<<<9<:<<<<<<<<<;<<<<<<<<
EAS1_93:4:160:896:275	163	seq1	35M	aaaactatatttatgctattcagttctaaatatag	============<====<==<====<==<==;=:6
B7_591:6:181:191:418	163	seq1	36M	aaactatatttatgctattcagttctaaatatagaa	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<988
EAS114_28:7:242:354:637	99	seq1	36M	aactatatttatgctattcagttctaaatatagaaa	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<6<;;
B7_589:1:122:77:789	163	seq1	35M	actatatttatgctattcagttctaaatatagaaa	<<<:<4<<9<:7<<<:<<<7<<<<<<<<<<9<9<<
B7_591:5:42:540:501	147	seq1	36M	ctatatttatgctattcagttctaaatatagaaatt	;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
B7_591:6:155:12:674	83	seq1	36M	ctatatttatgctattcagttctaaatatagaaatt	;<<<<<<<<<<;<<<<;<<<<8<<<<<<<<<<<<<<
B7_593:4:106:316:452	147	seq1	36M	ctatatttatgctattcagttctaaatatagaaatt	:<<<<<;<<<<:<<:<<<<<<7<<<<<<<<<<<<<<
EAS139_19:5:89:525:113	163	seq1	40M	tatttatgctattcagttataaatatagaaattgaaacag	<1<7<6;+0;7;7'<70;-<7<:<:<<5<<:9<5:7:%:7
EAS54_65:3:321:311:983	147	seq1	35M	atttatgctattcagttctaaatatagaaattgaa	;;4;;<7<<<<<<77<<<<<<<<<<17<<<<<<<<
EAS54_65:8:76:493:708	147	seq1	35M	tttatgctattcagttctaaatatagaaattgaaa	5/)63.&1517(544(055(0454&7706566679
EAS54_71:2:125:628:79	163	seq1	35M	tttatgctattcagttctaaatatagaaattgaaa	==================<6<====<<:<==7;::
EAS114_32:5:78:583:499	83	seq1	35M	tttacgctattcagtactaaatatagaaattgaaa	&6&9774&<;67<44&-4<;<9<7<<<<<;<<<<<
EAS54_67:3:175:730:949	83	seq1	35M	ttatgctattcagttctaaatatagaaattgaaac	<<<<;+<<<<7<;<<;<<<<<<<<<<<<<<<<<<<
EAS114_45:1:84:275:1572	163	seq1	35M	ttatgctattcagttctaaatatagaaattgaaac	/6;;;4;;;;;;;;7;;4;.4;;;;;6;;;77077
EAS1_108:4:248:753:731	99	seq1	35M	tatgctattcagttctaaatatagaaattgaaaca	<<<<<<<<<<<8<<<<<<<<<<<<:<<<<&<:<.:
EAS114_45:1:9:1289:215	99	seq1	35M	tatgctattcagttctaaatatagaaattgaaaca	;;;;;;9;;;67;;;;;99;9;;;;;;;;977747
B7_595:7:188:802:71	163	seq1	35M	atgctattcagttctaaatatagaaattgaaacag	<<<<<<<<<;<<<<<9<<<:<<<:<<<<<<:<<<;
EAS1_93:7:252:171:323	83	seq1	35M	gctattcagttctaaatatagaaattgaaacagct	;8<;<=3=6==:====;;======;==========
EAS192_3:5:223:142:410	147	seq1	35M	ctattcagttctaaatatagaaattgaaacagctg	8;<<<;<<<<;<<<<<<;<;<<<<<<<<<<<<;<<
EAS114_30:1:243:10:911	83	seq1	35M	tattcagttctaaatatagaaattgaaacagctgt	;<;;;<4;9:<<<;<<;<<<<<;;<<<<<<<<<<<
EAS114_45:6:5:730:1436	163	seq1	35M	tattcagttctaaatatagaaattgaaacagctgt	;;;;;;;;;;;;;;;;;;8;;;;;8;;;;;67777
EAS139_19:2:57:1672:1890	121	seq1	40M	tattcagttctaaatatagaaattgaaacagctgtgttta	:;;;9<8;;*<<<<<<:<<<<<<<<1:<<<<<<<<<<<7<
EAS139_19:2:57:1672:1890	181	seq1	*	cccccccccccccccccagccactgcggcccccccagcca	-+)%)'-'+,,<066,))090+:&486083:5&&:<<5<0
EAS1_105:2:299:360:220	99	seq1	35M	attcagttctaaatatagaaattgaaacagctgtg	<<<<<<<9<9<<<<<<<<<<<<<<<<<5<;<0<<<
EAS221_1:2:24:1037:84	163	seq1	35M	ttcagttctaaatatagaaattgaaacagctgtgt	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<;:<57<
EAS1_105:3:86:823:683	163	seq1	35M	cagttctaaatatagaaattgaaacagctgtgttt	<<<<<<<<;<<<<<<<<<<<<<<<<<<<<;;9<<<
EAS56_53:4:130:568:978	99	seq1	35M	taaatatagaaattgaaacagctgtgtttagtgac	7<<;<<;<7<:;<7<<<<<<<<);4;+<7+3+%;<
EAS114_45:4:73:1208:495	163	seq1	35M	taaatatagaaattgaaacagctgtgtttagtgcc	;;;;;;;;;;;;;;;;;;;;;;;;5;;;;;37377
EAS1_97:7:264:642:506	99	seq1	35M	aaatatagaaattgaaacagctgtgtttattgtat	<<;<<<<<<;<<<;:;;:;;<<;<<<<;*+;*&.4
EAS114_28:5:104:350:749	163	seq1	36M	aaatatagaaattgaaacagctgtgtttagtgcctt	<<8<<<<<<<<<<<;<<<<<<<<0;<<<9;<85;;;
EAS56_61:6:227:259:597	147	seq1	35M	aatatagaaattgaaacagctgtgtttagtgcctt	<8<;2;9;<;;-92<;;;<;<<<<<<<<<<<<<<<
EAS112_32:7:113:809:364	99	seq1	35M	tatagaaattgaaacagctgtgtttagtgcctttg	<<<<<<<<<<<<<<<<<<<<<<<<<<7<;<;<<<4
EAS188_7:2:218:877:489	83	seq1	35M	tatagaaattgaaacagctgtgtttagtgcctttg	9<<<8<<<;<9<<<<<<<<<<;<<<<<<<<<<<<<
EAS1_97:7:20:979:96	83	seq1	35M	gaaattgaaacagctgtgtttagtgcctttgttca	'9996;(:;-<;1<<<<=<<<<=<<<<<<<<<<<<
EAS188_7:2:259:219:114	99	seq1	35M	gaaattgaaacagctgtgtttagtgcctttgttca	<<<<<<<<<<<<<<<;<<<<<<7<7<<<<<0<<9<
EAS114_39:6:13:1034:1144	99	seq1	35M	aattgaaacagctgtgtttagtgcctttgttcaca	<<<<<<<<<<<<<<<<<<<<<<<<3<<<;<<;<++
EAS221_1:2:29:1486:672	147	seq1	35M	aattgaaacagctgtgtttagtgcctttgttcaca	<<:<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<++
EAS139_11:7:46:695:738	163	seq1	35M	tgaaacagctgagtttagcgcctgtgttcacatag	<;<<<<;<<),&4<3<<7&7<0;)).3;79;7<;0
EAS139_11:8:26:1221:222	163	seq1	35M	aaacagctgtgtttagtgcctttgttcaaccccct	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS51_64:3:190:727:308	147	seq1	35M	acagctgtgtttagtgcctttgttcaacccccttg	;;<;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS114_26:3:284:261:124	83	seq1	35M	acagctgtgtttagtgcctttgttcaacccccttg	===27===.====&===========;;========
EAS112_34:7:141:80:875	147	seq1	35M	agctgtgtttagtgcctttgttcaacccccttgca	6/<;84<;<;<<<<<<5<<<<<<<<<<<<<<<<<<
EAS139_19:3:24:1135:563	163	seq1	40M	gctgtgtttagtgcctttgttcaacccccttgcaacaacc	<<<<:<<<<:1:<<<<<<.<<<<<<<<;<;;;43+:30::
EAS221_1:2:90:986:1224	83	seq1	35M	ctgtgtttagtgcctttgttcaacccccttgcaac	<7*37;;;;;;;9<<;<7<<<<<<<<<<<;;<<<<
EAS114_28:7:287:492:169	99	seq1	36M	gtgtttagtgcctttgttcaacccccttgcaacaac	<<<7<<<<<<<<<<<<<<<<<<<<<<<8;;<;6<<;
EAS218_4:1:48:9:409	99	seq1	18M5I12M	gtttagtgcctttgttcacatagacccccttgcaa	<<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<
EAS139_19:1:87:1222:878	163	seq1	40M	tatagggcctttgttcaaaccccttgcaacaaccttgaga	&+6<6&<:<<9<1112<<;)9227>>>>>>>>>>>>>;<>>>>><<>>>;<+<>=>>+==>>==<==<=8=><:;8/;7<<<<<<<<;<:<<<<
B7_591:2:240:603:890	83	seq1	36M	gctcccaagagggaaagctttcaacgcttctagcca	;+&+//&<<<<<<<<<<9<<<8<<<<9<<<<<<<<<
B7_591:7:129:956:115	163	seq1	36M	gctccccagagggaaagctttcaacgcttctagcca	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;877-
EAS56_53:4:168:528:288	83	seq1	35M	gctccccagagggaaagctttcaacgcttctagcc	8<%<31;<<;<;<<<<<<<;<<<<<<<<<<;<<<<
EAS56_65:8:275:851:240	147	seq1	35M	ccccagagggaaagctttcaacgtttctagccatt	66614/&3616630666&66666&66666868666
EAS188_7:6:205:873:464	147	seq1	35M	ccccagagggaaagctttcaacgcttctagccatt	<-((+:+;289<--;<;-;<:;;<<<;;<<<<<<<
EAS56_65:6:37:610:260	163	seq1	35M	ccagagggaaagctttcaacgcttctagccatttc	<<<;<;<<7<<<<<<<<<<<<<<;6<963;;;3;1
EAS192_3:7:93:945:176	147	seq1	35M	ccagagggaaagctttcaacgcttctagccatttc	6;;;8<<3<<8.<;6)<<<<<9<<<<<<<<<<<<<
B7_593:6:61:628:681	83	seq1	36M	cagagggaaagctttcaacgcttctagccatttctt	95<<<<<<<<;<<<<;<<<:<<;;<<<<<<<<<<<<
EAS56_65:7:288:552:440	83	seq1	35M	agagggaacgctttcaactcttctagccatttctt	9<<%'%<<.2<<<<<<<<5:<<<<<<<<<<<<<<<
EAS56_53:2:170:265:818	163	seq1	35M	gaggggaagctttcaacgcttctagcactttcttt	<<<<<(5/959<8.<9<8<<<2<&59&&:22:8+(
B7_595:2:251:121:479	83	seq1	35M	gggaaagctttcaacgcttctagccatttcttttg	<<<<<6'..663;&<<;<<9<<<9<<<<<<<<<<<
EAS221_1:8:67:1797:1931	147	seq1	35M	gggaaagctttcaacgcttctagccatttcttttg	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS1_103:2:226:302:758	83	seq1	35M	ggaaagctttcaacgcttctagccatttcttttgg	;<<<<9;<<<<<<<<<<7<<<<<<<<<<<<<<<<<
EAS114_32:2:163:618:570	83	seq1	35M	ggaaagctgtcaacgcttctagccatttcttttgg	<9774<88&:8<:8<8:8<8<<<<<;88<88<<<<
EAS1_97:3:73:292:429	99	seq1	35M	gaaagctttcaacgcttctagccatttctttttgc	<<<<<<<<<<7<<;<<<<<<<2<<<5<<<<<:%)<
EAS1_108:3:82:356:253	99	seq1	35M	gaaagctttcaacgcttctagccatttcttttggc	===================<========;===39=
EAS114_30:6:62:386:959	147	seq1	35M	aaaagctttcaacgcttctagccatttcttttggc	%;71131((<<6<92(+<1<<;<-3<8<<;<;;<<
EAS51_62:3:263:74:407	83	seq1	35M	aagctttcaacgcttctagccatttcttttggcat	;;88<::+;<)<5<<:<<<<<<<<<<<<<<<<<<<
B7_597:3:67:620:344	99	seq1	35M	agctttcaacgcttctagccatttcttttggcatt	<<<<2<:2<<<<<<7<<<<:<<*<<<<<<***3<<
B7_610:6:148:776:486	83	seq1	35M	agctttcaacgcttctagccatttcttttggcatt	;:<<<;<<;<<<<<;<<<<<<<<<<<<<<<<<<<<
EAS54_61:3:150:933:810	83	seq1	35M	agctttcaacgcttctagccatttcttttggcatt	:89===:=:=;;==;====================
EAS51_64:4:102:467:897	99	seq1	35M	gctttcaacgcttctagccatttcttttgtctttt	<<<<9<<<<9<2<<<&,/=====>=>=>>>=>>==>=>>>>>>
B7_595:3:297:637:86	83	seq1	35M	tctcagctaggggaacagggaggtgcactaatgcg	<:75<;<;;<<<<<<;;<<<<<<<<<<<<<<<<<<
EAS54_65:3:290:558:349	147	seq1	35M	tctcagctaggggaacagggaggtgcactaatgcg	2;2;;'5&;<<5<<;5/<<<<<7<<;+;<<+1<8<
EAS1_95:3:308:956:873	99	seq1	35M	ctcatctaggggaacagggaggtgcactaatgcgc	<<<<<<<<<<<<<;<;<;1<<<<<.<9<;<<<<+;
EAS51_78:7:147:64:416	147	seq1	35M	ctcatctaggggaacagggaggtgcactaatgcgc	/;49;:6<<<<<<<<<<<<<<<<<<<<<<<<<<<<
B7_593:4:30:812:345	163	seq1	36M	tcatctaggggaacagggaggtgcactaatgcgctc	<<<<<<<7<;<<7<;77;3<&0-;<5<;6<1'13<:
EAS54_73:7:134:243:630	163	seq1	35M	tcatctaggggaacagggaggcgcactaatgagct	<<<:<<<<::1:818;;&::<>.;
EAS54_81:2:31:98:804	147	seq1	35M	ctttactgtcataactatgaagagactattgccag	====;========7=====================
EAS1_103:2:235:805:373	163	seq1	35M	tttactgtcataactatgaagagactatttccaga	<<<<<<<<<<<<<<<<<<<<;<;<<<<<<;;<99;
EAS114_28:5:11:868:62	99	seq1	36M	tttactgtcataactatgaagagactattgccagat	<<<<<<<<<<<<<<<<<<<<:<<<;<<<<(7:7039
EAS54_81:2:280:512:316	163	seq1	35M	ttactgtcataactatgaagagactattgccagct	==<========6==4==6;;==:===;=2/:+8%6
EAS1_93:5:292:122:666	99	seq1	35M	tactgtcataactatgaagagactattgtcagatg	<<<<<<6<<<<<<<<8;<<<<<<<<<<3&9+;;(;
EAS56_53:1:23:403:981	99	seq1	35M	tactgtcataactatgaagagactattgccagatg	<8<<<;<<<<<<;<<<<<<8;<<<9<9,3;,6(91
EAS114_45:7:33:1566:588	99	seq1	35M	tactgtcataactatgaagagcctattgccagatg	<;.;;;;6;;;;6;;29;;;<+9;;;.3;;73797
EAS139_11:7:92:367:1495	83	seq1	35M	ctgtcataactatgaagagactattgccagatgaa	<8<88<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<
EAS220_1:8:38:1576:1923	83	seq1	35M	ctgtcataactatgaagagactattgccagatgaa	8;<98<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<
B7_595:7:190:481:295	163	seq1	35M	tcataactatgaagagactattgccagatgaacca	<<<<<<<<<<<<<<<<<<<<<<9<<<<<9<7<2::
EAS112_32:7:168:117:441	99	seq1	35M	tcataactatgaagagactattgccagatgaacca	<<3<<<<<<<<<<<<<<<<<<<+<<17;<;:<995
EAS54_73:3:239:796:221	163	seq1	35M	ataactatgaagagactattgccagctgacccccc	<<<7<<7<<7<<7<;<<<<<,;;,+'<+/+99%:'
EAS220_1:4:69:88:1154	147	seq1	35M	ataactatgaagagactattgccagatgaaccaca	<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS221_3:8:34:956:1309	99	seq1	35M	aactatgaagagactattgccagatgaaccacaca	<<<<<<7<<<<<<<<<<<6<<<<<<<<<<<:<8<8
EAS1_108:5:229:717:121	99	seq1	35M	actatgaagagactattgccagatgaaccacacac	=================<)=<4<0=.<<<71;41&
EAS219_1:1:67:191:668	99	seq1	35M	actatgaagagactattgccagatgaaccacacct	<<<<<<<<<<<<<<<<<6<<;<;<;<<<<<<6;%2
EAS51_64:3:309:303:278	163	seq1	35M	ctatgaagagactattgccagatgaaccacacatt	<<<<<<<<<<<<<<<<+<<+<<7<<<<<5<<<;;;
EAS221_1:8:60:1020:1259	99	seq1	35M	ctatgaagagactattgccagatgaaccacacatt	<;<<<<;<<<<<<<<<;<<<<<<<8<<<<<:<:<<
EAS218_4:7:89:1487:520	83	seq1	35M	tatgaagagactattgccagatgaaccacacatta	4;;/<<<<<:<;<;<<<<<<<<<<<<<<<<<<<<<
B7_610:4:15:805:420	163	seq1	35M	atgaagagactattcacatgtgaaccacacattta	;73;;;;67.;1<<+*.;*&<4947<&474&*9*(
EAS56_57:3:119:761:239	147	seq1	35M	tgaagagactattgccagatgaaccacacattaat	;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS112_34:7:142:457:584	99	seq1	35M	tgaagagactatttccagatgaaccacacattaat	<<<<<<<<<<<<<<<
EAS56_63:7:190:95:706	147	seq1	35M	ttgtgtccatgtacacacgctgtcctatgtactta	9;97437;<;;<<;<;<<<<<<;<<<<<<<<<<<<
B7_589:1:101:825:28	83	seq1	35M	tgtgtccatgtacacacgctgtcctatgtacttat	0;0'0;<<<<<<8<;<<<<;;3<<;;<<<8<<<<<
EAS51_66:4:188:460:1000	99	seq1	35M	gtgtccatgtacacacgctgtcctatgtacttatc	<<<<<<<<<<<<<<<<7<<;:4;44<;;:8;;9;;
EAS1_95:3:268:523:511	99	seq1	35M	tgtccatgtacacacgctgtcctatgtacttatca	<<<<<<<<<<<<<<<<<<<<;<<<<6<:9<<3<44
EAS114_28:6:54:263:585	99	seq1	36M	tgtccatgtacacacgctgtcctatgtacttatcat	<<<<<<<<<<<<<<<<<<<:;<<;<:;::<<;;:;4
EAS51_66:7:174:987:334	83	seq1	35M	gtccatgtacacacgctgtcctatgtacttatcat	,;<;;<<<&<<<1<<<<<<<<<<<<<;<<<<<<<<
EAS54_71:6:224:932:942	99	seq1	34M	gtccatgtacacacgctgtcctatgtacttatca	<<<<<<<<<<<<<<<<<<<<<<;<<<<7<<(;3,
EAS114_45:1:12:1296:358	99	seq1	35M	gtccatgtacacacgctgtcctatgtacttatcat	;;;6;7;7;;;;;7;9;;-*1;9;699/99/7477
EAS114_32:2:306:119:56	147	seq1	35M	tccatgtacacacgctgtcctatgtacttatcatg	;;;;;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS1_95:4:66:179:118	163	seq1	35M	ccatgtacacacgctgtcctatgtacttatcatga	<<<<<<<<<<<<<<<<<<<<<<<<<<:<<;<<6<<
EAS1_105:2:110:584:649	99	seq1	35M	ccatgtacacacgctgtcctatgtacttatcatga	<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<::<38
EAS218_1:4:28:315:310	163	seq1	35M	catgtacacacgctgtcctatgtacttatcatgac	<<<<<<<<<<<<<<<<<<<<<:<+.<<.<+7<*17
B7_595:7:242:4:593	147	seq1	35M	atatacacacgctgtcctatgtacttatcatgact	1.%55877+8+88808887+7;7;18:8;;;.&;8
EAS1_93:1:131:946:353	163	seq1	35M	tgtacacacgctgtcctatgtacttatcatgactc	<<<<<<<<<<<<<;<<<<;;<<<<<<<;<:52;<2
EAS221_1:4:4:1732:88	99	seq1	35M	tgtacacacgctgtcctatgtacttatcatgactc	<<<<<<<<<<<<<<<<<2<8;8<;<8;<2;2:<:<
B7_595:4:58:703:72	83	seq1	35M	gtacacacgctgtcctatgtacttatcatgactct	5&<<7;+95;7'6<<<<<.<<<<<;<<9<7<<<<<
EAS56_59:5:113:694:725	163	seq1	35M	gtacacacgctgtcctatgtacttatcatgactct	<<<<<<<<<<<<9<<<<<:<<<<<<<<<<:;;<;;
EAS56_65:5:278:848:765	147	seq1	35M	gtacacacgctgtcctatgtacttatcatgactct	7;;<;5<55<<;;<;<<<<<<<<<<<<<<<<<<<<
EAS56_57:6:234:787:12	163	seq1	35M	acacgctggcctatgtacttataatgactctatcc	<;<<<9<<&+9;3;<993;<9<+94;9&41;08%9
EAS218_1:4:15:856:340	147	seq1	35M	cacgctgtcctatgtacttatcatgactctatccc	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS51_62:2:258:266:101	163	seq1	35M	acgctgtcctatgtacttatcatgactctatccca	<<<<<<<<<<<<<<<<<<5<;,<-2<<<<;68<<6
EAS56_59:2:177:552:234	147	seq1	35M	acgctgtcctatgtacttatcatgactctatccca	::;:=;=99=====;;====;==========<===
EAS114_30:1:134:379:893	147	seq1	35M	cgctgtcctatgtacttatcatgactctatcccaa	7137::;<<<<<<<;<<<<<<<<<<;<<<<<<<<<
EAS1_105:8:256:404:584	147	seq1	35M	actgtcctatgtacttatcatgactctatcccaaa	&&326+23<3<<<+:<<<<<<
B7_595:3:57:735:151	99	seq1	35M	ctatcccaaattcccaattacgtcctatcttcttc	<<<<<<<<8<<8<:<<*<:<<<4<<<;,<<<<:<:
EAS54_81:8:142:858:903	147	seq1	35M	ctatcccaaattcccaattacgtcctatcttcttc	<<<<<;<<<<9<<<<<<<<<<<<<<<<<<<<<<<<
EAS56_57:7:247:522:670	83	seq1	35M	ctatcccaaattcccaattacgtcctatcttcttc	;;;9;:<<<<<;<<<<<<<<<<<<<<<<<<<<<<<
EAS139_19:3:75:732:442	99	seq1	40M	ctatcccaaattcccaattacgtcctatcttcttcttagg	<<<<<;<<<<<9<<<;<<;<<<5<<;8<<<<<<<<;:9%%
EAS1_99:7:183:645:699	99	seq1	35M	tatcccaaattcccaattacgtcctatcttcttct	<<9<9<<<<<<<<<;<<;<<*175;173<;;;<-/
EAS192_3:6:175:437:950	163	seq1	35M	ccaaattcccaattacgtcctatcttcttcttagg	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:59
EAS56_63:3:93:1002:845	83	seq1	35M	aattcccaattacgtcctatcttcttcttagggaa	<<::;;;<<<<<<<<<<<<<<<<;<<<<<<<<<<<
EAS51_62:6:50:542:881	163	seq1	35M	tcccaattacgtcctatcttcttcttaggtaagaa	<<<<<4<09<<9<<2<<<<<<<<<<<2/.&2<%<7
EAS1_99:3:118:851:285	83	seq1	35M	cccaattacgtcctatcttcttcttagggaagaac	3+7<<<;<;<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS219_1:1:67:191:668	147	seq1	35M	ccaattacgtcctatcttcttcttagggaagaaca	<<<<<7<<7<<<<<<<;<<<<<<<<<<<<<<<<<<
B7_595:7:166:203:416	83	seq1	35M	aattacgtcctatcttcttcttagggaagaacagc	<<<<<<<<::<<<<<<<<<;<<<<<<<<<<<<<<<
EAS114_45:2:15:1497:1530	99	seq1	35M	aattacgtcctatcttcttcttagggaagaacagc	0<;;;9;;86<;;;<<&<<.<<;)3;7;654-471
EAS56_65:8:206:563:262	83	seq1	35M	attacgtcctatcttcttcttagggaagaacagct	<<<<7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<7
EAS114_26:4:40:352:151	99	seq1	35M	attacgtcctatcttcttcttagggaagaacagct	<<<<<<<<<<<<<<<;<<9<<<<:<<<<;<99<3<
B7_593:7:67:302:762	99	seq1	36M	ttacgtcctatcttcttcttagggaagaacagctta	<<<<<<<<<<<<<<<<<<<<;;65;<-<;<:8<<<3
EAS1_97:5:84:927:843	147	seq1	35M	ttacgtcctatcttcttcttagggaagaacagctt	588;<:<<<<<<<6<<<<;<<<:/<<3<:;<*<<<
EAS1_99:5:147:479:41	163	seq1	35M	tacgtcctatcttcttcttagggaagaacagctta	<<<<<<<<<<<<<<<<<<<<::6<<;<<<;;9;;6
EAS1_105:3:329:177:267	83	seq1	35M	tacgtcctatcttcttcttagggaagaacagctta	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
B7_589:7:72:916:763	163	seq1	35M	gtcctatcttcttcttagggaagaacagcttaggt	==7>==9>=7=>=>>=>>
EAS54_65:4:91:267:655	147	seq1	35M	tgttgttggttttctgtttctttgtttgatttggt	;,:;5:<6:<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS221_1:2:91:856:504	99	seq1	35M	gttgttggttttctgtttctttgtttgatttggtt	<<<<<<<<<<<<<<7<<<<<<<7<<<&;<<<&&<&
EAS1_108:2:170:326:433	99	seq1	35M	ttgttggttttctgtttctttgtttgatttggtgg	=====<=9===:=<:==2=======2:===9==/5
EAS1_93:6:132:717:233	99	seq1	35M	tgttggttttctgtttctttgtttgatttggtgga	<<<<<<<<<<<<;<<<<<<<<<<<7<<<<&-<4<1
EAS139_19:1:14:420:712	99	seq1	40M	tgttggttttctgtttctttgtttgatttttttgaagaca	<<<<<<<<<<<<;<<<<<<<;<<<-;<<<&,<&*8111:6
EAS114_39:4:43:1047:1626	163	seq1	35M	gttggttttctgtttctttgtttgatttggtggaa	<<<<<<<<<<<<<<<<<<<:<<<:<<<<:+;-4:(
EAS114_45:2:20:413:1334	147	seq1	35M	ttggttttctgtttctttgtttgatttggtggaag	88878777;:;:1:;9;;;6;;;6;9;;;;;296;
EAS51_62:5:154:669:853	83	seq1	35M	tggttttctgtttctttgtttgatttggtggaaga	<::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
B7_610:7:117:857:942	99	seq1	35M	ggttttctgtttctttgtttgatttggtggaagac	<<<<<<<<<<<<<<<<<<<<<<<<<:6<;;7;9<;
EAS56_57:6:145:144:796	147	seq1	35M	ggttttctgtttctttgtttgatttggtggaagac	;<<<;<<<<<<<<<;<<<;<<<<<<<<<<<<<<<<
EAS114_32:6:88:162:587	147	seq1	35M	ggttttctgtttctttgtttgatttggtggaagac	386;;388-<8;<;68<<;;<;<6<<<8<<<<<<<
EAS221_1:8:73:108:1621	99	seq1	35M	gttttctgtttctttgtttgatttggtggaagaca	<<<<<<<<71<<<<<<<<<+<<<<70:0<9<<61<
EAS112_34:6:127:153:861	147	seq1	35M	ttttctgtttctttgtttgatttggtggaagacat	:;:6;9<<1;<<95<<<9<<<<<<<<<<<<<<<<<
EAS188_7:2:152:765:744	163	seq1	35M	ttttctgtttctttgtttgatttggtggaagacat	<<<<<<<<<<<<<<<<<<:<<<<<<<<&<7293<<
EAS54_73:3:313:827:992	147	seq1	35M	tgtttctttgtttgatttggtggaagacataatcc	'187:1'<75<.*<<:5<..<<*<<917<<7<<17
EAS51_64:3:7:268:263	121	seq1	35M	ttgcgttatttgagttggtggaagacataatccca	',)*&2<$7+<<<'<-<7<<<<<<<7<<7><>;>+>>/;>>=>=>=:>><>=<<==;)<=8;
EAS218_4:7:85:923:726	147	seq2	35M	gtaaagtaactgaacctatgagtcacaggtattcc	<:<<<%3<<1<<86<<-<<<<<<<<<<<<6<<1<<
EAS1_103:5:285:241:560	83	seq2	35M	taaagtaactgaacctatgagtcacaggtattcct	:<<<<;<<,<<<<5<<<<<<<<<<<<<<<<<<<<<
EAS114_30:6:41:461:436	163	seq2	35M	taaagtaactgaacctatgagtcacaggtattcct	<<<<<<<<<<<<<<<<<<<:<<<<<<<<;<;;;:;
EAS54_61:6:25:949:33	99	seq2	35M	aaagtaactgaacctatgagtcacaggtattcctg	=;===/8========*==&;6=&=&:=6&:=::67
EAS221_3:2:60:590:1760	99	seq2	35M	aaagtaactgaacctatgagtcacaggtattcctg	<:<<<<<2<<<<:<::<<<::<<<<<6<<<<<<<6
EAS114_45:6:86:693:234	163	seq2	35M	aagtaactgaacctatgagtcacaggtattcctga	;;;;;;;;;;;;;;;;9;;;;;;;;99;;&70777
EAS56_57:6:4:223:776	163	seq2	35M	agtaactgaacctatgagtcacaggtattcctgag	<<<<<<<<<<<<<<<<<<<<<<<<<9<<<:;<;2<
EAS114_39:3:88:84:1558	99	seq2	35M	agtaactgaacctatgagtcacaggtattcctgtg	<<;<<<<<<<<<<<<;;<<<<<<<::<<<<<<7&<
B7_597:2:168:829:88	163	seq2	35M	taactgaacctatgagtcacaggtattcctgagga	<<<<<<<<<<<<<<<<<<<<<<<6<<<<<<9;4;2
EAS114_28:1:168:389:889	147	seq2	36M	taactgaacctatgagtcacaggtattcctgaggaa	;<<;;56;==================8========8
EAS54_71:5:81:685:141	99	seq2	34M	actgaacctatgagtcacaggtattcctgaggaa	<<<<<<<<<<<<<<<<<<<<<;;<<;<<<',7,7
EAS139_19:4:26:1312:1400	99	seq2	40M	actgaacctatgagtcacaggtattcctgaggaaaaagaa	<<<<;<<<:<<:<;<:<<<;:;<<<<<<:<8<1;;:::88
EAS54_71:4:127:725:381	83	seq2	34M	tgaacctatgagtcacaggtattcctgaggaaaa	+<<.<<;<;<<<3;<;<<<<<<6<8;<<<<<<<1
EAS188_7:2:19:736:559	99	seq2	35M	tgaacctatgagtcacaggtattcctgaggaaaaa	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<<
EAS114_26:3:117:284:589	83	seq2	35M	gaacctatgagtcacaggtattcctgaggaaaaag	==8==;==================;==========
B7_610:5:120:596:847	163	seq2	35M	aacctatgagtcacaggtattcctgaggaaaaaga	<<<<<<<<<<<<<;<<<9<<<<<<<;:<62;58;2
B7_610:5:51:904:391	163	seq2	35M	acctatgagtcacaggtattcctgaggaaaaagaa	<<<<<<<<<<<<<<<<<;<<<<<;:;<2<6;;;;;
EAS139_11:8:96:1314:1448	163	seq2	35M	cctatgagtcacaggtattcctgaggaaaaataaa	<<<<<<<<<<<<<<<<<<<<<<<<5<4<<<<-<<<
EAS139_19:3:73:1158:535	163	seq2	40M	cctatgagtcacaggtattcctgaggaaaaagaaaaagtg	<<<<<<<<<<<<<<<<<<<<<<8<;;<<<<<9<<9::8:8
B7_591:2:223:583:968	147	seq2	36M	tatgaggcacaggtattcctgaggaaaaagaaaaag	1<';<<&%-:<<<<<:66%<<<<<<<<<<<<<<<<<
EAS1_97:3:160:173:889	163	seq2	35M	tatgagtcacaggtattcctgaggaaaaagaaaaa	<<<<<<<<<<<<<<<<<<<<;0<7<<;<<<;7<09
EAS114_39:1:28:350:895	83	seq2	35M	tatgagtcacaggtattcctgaggaaaaagaaaaa	:<;<<<:;<-<<<<<4;77<<<<<<<<<<<<<<<<
EAS56_53:4:45:707:147	163	seq2	35M	atgagtcacaggtattcctgaggaaaaagaaaaag	<<<<<<<<<<<<&<<<<:<<9<<<9<<<<75;;;<
EAS220_1:8:18:1757:95	99	seq2	35M	atgagtcgcaggtattcctgaggaaaaagaaaaag	<<<<<<<<<<<<<<<<<<<1<:<<<<<<:<<<;:<
EAS51_66:6:310:747:415	163	seq2	35M	tgagtcacaggtattcctgaggaaaaagaaaaagt	<<<<<<<<<<<<<<<<<<:<<<<<;<<<<<;<;<;
EAS114_28:2:114:938:216	147	seq2	36M	gagtcacaggtattcctgaggaaaaagaaaaagtga	<<<<7<6<<<<<<<6<<<<<<<<<<<<<<<<<<<<<
EAS1_93:1:179:629:513	163	seq2	35M	gtcacaggtattcctgaggaaaaagaaaaagtgag	<<<<<<<<<<<<<<<;<;<<<<<<<<<<<<<;<<<
EAS114_45:4:88:55:1187	99	seq2	35M	gtcacaggtattcctgaggaaaaagaaaaagtgag	;;<;;;<<99<<;;<;;;;;:;49;:;;;;87898
EAS51_62:5:119:38:945	99	seq2	35M	tcacaggtattcctgaggaaaaagaaaaagtgaga	<<<<<<<<<<<<<<<8<<<<<8<<<8<;<<7<:<<
EAS56_65:6:67:800:450	147	seq2	35M	tcacaggtattcctgaggaaaaagaaaaagtgaga	9-<9<;<<<<9;5<<<<<<<<<<<<<<<<<<<<<<
B7_610:5:102:915:87	147	seq2	35M	cacaggtattcctgaggaaaaagaaaaagtgagaa	;<8<;;<<<<7;<<<;<<<<<<<<<<<<<<<<<<<
EAS114_26:1:113:367:659	163	seq2	35M	cacaggtattcctgaggaaaaagaaaaagcgagaa	=9====8==========:=:=====9=:=&====5
EAS218_1:2:26:211:481	147	seq2	35M	cacaggtattcctgaggaaaaagaaaaagtgagaa	:<:<<<<<<9:5<<<<<<<<<<<<<<:<:<<<<<<
EAS219_FC30151:3:90:1906:1528	83	seq2	35M	cacaggtattcctgaggaaaaagaaaaagtgagaa	:<<<<<<<<<3:<<<<<<<<<<<<<<<<<<<<<<<
B7_591:2:13:100:876	163	seq2	36M	acagggattcctgaggaaaaagaaaaagtgagaagt	<8<<<*<2<7<<<6<<<<<<6<<8<<<<5<<<<4<9
EAS56_63:5:117:570:971	163	seq2	35M	acaggtattcctgaggaaaaagaaaaagtgagaag	<<<<<<<<<<<<<;;;<<<<6<7;9;<:;<;<;;<
EAS221_3:8:50:1203:1094	83	seq2	35M	acaggtattcctgaggaaaaagaaaaagtgagaag	<7<<<<<5:+63<<<<<<<<<<<<<<<<2<<<<<<
EAS54_67:6:107:395:312	83	seq2	35M	caggtattcctgaggaaaaagaaaaagtgagaagt	;<;;<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS54_73:3:29:833:612	83	seq2	35M	caggtattcctgaggaaaaagaaaaagtgagaagt	<<;<<<;<::<<<<<<<<<<<<<<<<<<<<<<<<<
B7_610:7:158:943:467	83	seq2	35M	aggtattcctgaggaaaaagaaaaagtgagaagtt	<:<<;;<:5<<<<<<<<<<<<<<<<<<;<<<;<<<
EAS56_59:2:201:768:529	163	seq2	35M	aggtattcctgaggaaaaagaaaaagtgagaagtt	==========================1=======;
EAS188_7:6:11:994:584	99	seq2	35M	ggtattcctgaggaaaaagaaaaagtgagaagttt	<<<<<<<<<<<7<<<<<<<<<<<<<6<<<<<<3<6
EAS56_57:2:206:873:186	83	seq2	35M	gtattcctgaggaaaaagaaaaagtgagaagtttg	;<<;--7<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS56_63:4:38:28:122	83	seq2	35M	gtattcctgaggaaaaagaaaaagtgagaagtttg	;9;9;-1<<<<<<<<<<<<<<<<<;<<<<<<<<<<
EAS1_93:5:66:372:343	83	seq2	35M	tattcctgaggaaaaagaaaaagtgagaagtttgg	;<1;89<<<<<;<9<<<<9<<<;8<9<;<<<<<;8
EAS1_97:3:277:144:848	83	seq2	35M	tattcctgaggaaaaagaaaaagtgagaagtttgg	<<<)63<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS139_19:6:21:1601:1666	83	seq2	40M	tattactgaggaaaaagaaaaagtgagaagtttggaaaaa	-;;3&1<<<<<<<<<<<<1<<<<<<<<<<<7<<<<<<<<=<<<<<<<<<<<<<<
EAS56_57:2:23:268:529	153	seq2	35M	tgaaagaggctcaaagaatgccaggaagatacatt	7;<<<<<<57;-<<<<<<:<77<<<<<<<;<;<<<
EAS114_26:2:315:219:7	153	seq2	35M	gaaagaggctcaaagaatgccaggaagatacattg	7==::<2=8<<<=====>888<=2=>==>,>,>>8
EAS192_3:4:63:5:870	83	seq2	35M	gaaagaggctcaaagaatgccaggaagatacattg	:<;<;<<<4:;<<<<<<<<<<<<<<<<<<<<<<<<
B7_591:5:243:557:560	163	seq2	36M	aaagaggctcaaagaatgccaggaagatacattgca	<<<<<<<9<<<<<<<<<<<<<<<<<<;<<89<<9<;
B7_593:2:270:430:269	163	seq2	36M	aaagaggctcaaagaatgccaggaagatacattgca	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;7;:
EAS51_66:6:284:442:747	89	seq2	35M	aaagaggctcaaagaatgccaggaagatacattgc	<;<<<<<:<;<<<<<<<<;<<<<<<<<<<<<<<<<
EAS218_4:7:71:31:1973	89	seq2	35M	aaagaggctcaaagaatgccaggaagatacattgc	<<<<<7<:<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS1_93:2:30:466:652	147	seq2	35M	aagaggctaaaagaatgccaggaagatacattgca	<<<<<;3;&<<<<<<<=============
EAS114_39:3:88:84:1558	147	seq2	35M	atcagactatctaaagtcaacatgaaggaaaaaaa	;;<<;<<;<<5<<<<<<;<<:<<<;<<<<<<;<<<
EAS56_59:2:201:768:529	83	seq2	35M	cagactatctaaagtcaacatgaaggaaaaaaatt	3<:<9<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<
B7_591:2:13:100:876	83	seq2	36M	agaatatataaagtcaacatgaaggaaaaaaattct	;9<$<<<$<<<<<<<<75<<<<<<<9<9<<<<<<<<
EAS139_11:4:26:137:1382	99	seq2	35M	agactatctaaagtcaacatgaaggaaaaaaattc	<<<<<<7<<<77<<<<<<<<<<<<<<<<<<<<
EAS56_59:1:93:490:901	83	seq2	35M	agaaaagcatacagtcatctataaaggaaatccca	<<<<<<<;<<<;<<<;<<;<<;<<<<<<<<<<<<<
EAS112_34:7:96:489:453	99	seq2	35M	agaaaagcatacagtcatctataaaggaaatccca	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;;;:
EAS114_26:6:46:13:880	147	seq2	35M	agaaaagcatacagtcatctataaaggaaatccca	=&====8==========0=================
EAS114_28:2:167:905:852	163	seq2	36M	agaaaagcatacagtcatctataaagaaaatcccat	<<<7<<<<<<<<<<<<<<:<:<<:::&.<:<66:3<
EAS219_FC30151:3:13:674:1717	163	seq2	35M	agaaaagcatgcagtcatctataaaggaaatccca	<<<<<<<<<<%<<<<<<<<<<<<<<<<<<<;:;;;
EAS51_62:7:196:511:896	83	seq2	35M	gaaaagcatacagtcatctataaaggaaatcccat	8<<<<<;<<<:<<<<<<<<<<<<<<<<<<<<<<<<
EAS56_53:1:154:118:488	163	seq2	35M	aaaagcatacagtcatctataaaggaaatcccatc	<<<<<<<<<<<<<<<<<<<<<<:7<<<<7<:;;::
EAS56_57:2:44:153:969	83	seq2	35M	aaaagcatacagtcatctataaaggaaatcccatc	<<5<:7<72<51<7<*79<<<<<5<<<<<<<<<2<
EAS114_28:4:215:246:640	99	seq2	36M	aaaagcatacagtcatctataaaggaaatcccatca	<<<<<<<<<<9<;<<<<<<<<<<9;<<<<<<3;<;3
EAS219_1:7:94:1655:1921	147	seq2	35M	aaaagcatacagtcatctataaaggaaatcccatc	<<<<;:===<==;<==<;================;
EAS221_1:6:60:1037:1146	147	seq2	35M	aaaagcatacagtcatctataaaggaaatcccatc	<<<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<<<
EAS56_65:1:23:536:229	99	seq2	35M	aaagcatacagtcatctataaaggaaatcccatca	<<<<<<<<<<<<<<<<<:<8<:<<;<<<<<<7<<<
EAS112_34:6:130:865:838	163	seq2	35M	aaagcatacagtcatctataaaggaaatcccatca	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;:<;3
EAS56_59:2:239:1001:406	99	seq2	35M	agcatacagtcatctataaaggaaatcccatcaga	<<<<<<7<<<<<<<<8<;<<<7<<<<36<<3<:33
EAS1_97:3:147:423:584	147	seq2	35M	gcatacagtcatctataaaggaaatcccatcagaa	27<;<3<<<+<<;<<<;;-4<<<<<;<<<<<<<<<
EAS1_99:1:187:715:521	83	seq2	35M	gcatacagtcatctataaaggaaatcccatcagaa	<7<:<9<<<<<<<<<;<<<<<<<<<<<<<<<<<<<
EAS54_67:3:172:196:746	99	seq2	35M	gcatacagtcatctataaaggaaatcccatcagaa	<<<<<<<<9<<<<9<<<<<<<<<;<<<<6<<<<;<
EAS54_71:3:267:821:860	83	seq2	34M	gcatacagtcatctataaaggaaatcccatcaga	$&<<<.<:;6<<;<<<<<<<<<<<<<<<<<<<<<
EAS56_61:7:7:682:201	83	seq2	35M	catacagtcatctataaaggaaatcccatcagaat	0:8;5<8<1:78<<<<<<<<<<<<:8<<2<<<<:<
B7_589:3:82:13:897	163	seq2	35M	atacagtcatctataaaggaaatcccagcagaata	<<<<;<<<<<<;<;<;5<51;<1<<<<%<<<<,58
EAS56_53:6:180:695:621	99	seq2	35M	atacagtcatctataaaggaaatcccatcagaata	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;::<<<
EAS56_57:2:158:909:321	83	seq2	35M	atacagtcatctataaaggaaatcccatcagaata	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS114_26:2:237:497:165	99	seq2	35M	tacagtcatctataaaggaaatcccatcagaataa	8===<8===========37=<===7=;7=8=====
EAS1_99:2:152:355:962	83	seq2	35M	cagtcatctataaaggaaatcccatcagaataaca	&<.9.<;+;<;<<<<<<<<<<::<<:<<<<<<<<<
EAS192_3:4:255:549:422	83	seq2	35M	aagtcatctataaaggaaatcccatcagaataaca	&<;;+<;4;<<<<<<<<<<<;<;<<;<<<<<<<<<
EAS220_1:4:100:20:1199	163	seq2	35M	cagtcatctataaaggaaatcccatcagaataaca	7<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<4<<
EAS54_67:5:71:408:741	163	seq2	35M	agtcatctataaaggaaatcccatcagaataacaa	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<
EAS51_66:5:285:395:450	147	seq2	35M	gtcatctataaaggaaatcccatcagaataacaat	8)3<8+;<)<<<<<<<<97:7<<<<<<<<<<<<<<
EAS54_73:3:4:854:140	99	seq2	35M	gtcatctataaaggaaatcccatcagaataacaat	<<<6<<<:<6<<<:36:<<<<3<<8:.6<38::4<
EAS56_59:6:227:657:95	147	seq2	35M	gtcatctataaaggaaatcccatcagaataacaat	;3;<);<<<<<<<<<<<<18<<<<<<<<<<<<<<<
EAS114_28:7:57:324:546	83	seq2	36M	gtcatctataaaggaaatcccatcagaataacaatg	;;5<;,<<<;;<<<<<<<97<<<<<<<<<<9<<<<<
EAS139_19:4:26:274:1078	83	seq2	40M	gtcatctataaaggaaatcccatcagaataacaatgggct	9:*:64<<;<<<<<<<<<;8;<<:<<<<<<<<<<<<<<<<
EAS188_7:6:107:636:642	163	seq2	35M	gtcatctataaaggaaatcccatcagaataacaat	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS54_81:7:226:869:36	147	seq2	35M	atatataaaggaaatcccatcagaataacaatggg	<0/)&<=,==4>4=>>=
EAS218_1:8:82:1540:77	163	seq2	35M	gaaataaagtcaagtctttcctgacaagcaaatgc	<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<:8
EAS54_67:3:172:196:746	147	seq2	35M	aaataaagtcaagtctttcctgacaagcaaatgct	<<<;><<+<<<<:<<<<2<;<<<;<<<<<<<<<<<
EAS54_73:7:97:892:419	163	seq2	35M	aataaagtcaagtctttcctgacaagcaaatgcta	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS192_3:4:312:915:751	147	seq2	35M	aataaagtcaagtctttcctgacaagcaaaagcta	<:-<<<99:::);:7<4;8<<<<<<<;<2<+8<;<
EAS1_93:4:325:352:67	163	seq2	35M	ataaagtcaagtctttcctgacaagcaaatgctaa	==================<========<=<;-===
EAS1_97:4:83:731:540	99	seq2	35M	taaagtcaagtctttcctgacaagcaaatgctaag	<<<<<<<<<;<<<<<<<<<<<<<:<7<*;&;<;;9
EAS188_7:5:74:329:459	163	seq2	35M	taaagtcaagtctttcctgacaagcaaatgctaag	<<<<<<<<<<<<<<<<<<<<<<<;<<;<<;9;599
EAS219_FC30151:3:13:674:1717	83	seq2	35M	taaagtcaagtctttcctgacaagcaaatgctaag	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS1_105:1:141:415:738	69	seq2	*	ttacctagttgctctgtagtctcaattaattgttt	<<<<<<<<<<<<<<<<<<<<<<<;<<<<<;<8<<<
EAS1_105:1:141:415:738	137	seq2	35M	aaagtcaagtctttcctgacaagcaaatgctaaga	<<<<<<<<<<<<<<<<<<<<<<:<<;<<;<<<<6:
EAS56_53:1:154:118:488	83	seq2	35M	aaagtcaagtctttcctgacaagcaaatgctaaga	<<<;58<<95:<<;<;<<<;<<<;;<<<<<<<<<<
EAS56_59:5:198:929:684	83	seq2	35M	aaagtcaagtctttcctgacaagcaaatgctaaga	<<;<<<<<:<<<<<<<<<<<<<<<<<;<<<<<<<<
EAS114_28:4:215:246:640	147	seq2	36M	aaagtcaagtctttcctgacaagcaaatgctaagat	;<<,<<<96<<:<:<9<6<97<<<<<9<<<<9<<9<
EAS1_103:2:234:167:381	83	seq2	35M	aagtcaagtctttcctgacaagcaaatgctaagat	<<;<;<<<<;<<<<7<<<<<<<<<<<<<<<<<<<<
EAS112_34:7:96:489:453	147	seq2	35M	aagtcaagtctttcctgacaagcaaatgctaagat	;<;;;<<<<5:<<:<<<<:<<<<<<<<<<<<<<<<
EAS1_93:3:79:879:15	99	seq2	35M	agtcaagtctttcctgacaagcaaatgctaagata	<<<<<<<<<<<<<<<<<<<<<<<<<<<<2<;<<1<
EAS56_53:2:59:286:290	147	seq2	35M	tcaagtctttcctgacaagcaaatgctaagataat	77<<<<7<<<97<<,7<<<;<<<;<9<<<<<<<<<
EAS1_95:5:263:511:936	99	seq2	35M	caagtctttcctgacaagcaaatgctaagataatt	<<<<<<<<<<<<<<<<<;<<<<<;<<:<:<<<<<<
EAS114_30:3:181:582:435	147	seq2	35M	caagtctttcctgacaagcaaatgctaagataatt	<<<<<<<<;<<<<<;<<4<<<<<<;<<<<<<<<<<
EAS188_7:6:107:636:642	83	seq2	35M	aagtctttcctgacaagcaaatgctaagataattc	<<<<<<<;<<<<<;<<<<<<<<<<<<<<<<<<<<<
EAS112_34:4:12:273:89	83	seq2	35M	agtctttcctgacaagcaaatgctaagataattca	<:737<288<<<7<<<<<<<<<:9<<<<<<<<<<<
EAS56_59:2:239:1001:406	147	seq2	35M	ctttcctgacaagcaaatgctaagataattcatca	0':.71;;:9==9=;====;=;=============
EAS188_4:7:96:899:106	147	seq2	35M	ttcctgacaagcaaatgctaagataattcatcatc	;;;;<<<<<<<;<<<<<<<<<<<<<<<<<<<<<<<
EAS54_65:6:67:56:806	147	seq2	35M	tcctgacaagcaaatgctaagataattcatcatca	844:8;7<88;8<<<<<<<<<<<<<<<<<<<<<<<
EAS54_67:5:71:408:741	83	seq2	35M	tcctgacaagcaaatgctaagataattcatcatca	;7;<;<0<<<<<<<<:;<<<<<<<<<<<<<<<<<<
EAS56_53:6:180:695:621	147	seq2	35M	tactgaaaagcaaatgctaagataattcatcatca	;&377<&<<;7<<<<<7<<<<<<<<<<<<<<<<<<
EAS114_30:6:49:656:507	147	seq2	35M	tcctgacaagcaaatgctaagataattcatcatca	%44;;<:<<;<;<<<<<<<<<<<<<<<<<<<<<<<
EAS54_73:3:4:854:140	147	seq2	35M	cctgacaagcaaatgctaagataattcatcatcac	:9':<;<<<;<<<;<<<<<<<<<<<<<<<<<<<<<
EAS139_19:1:85:1521:58	99	seq2	40M	ctgacaagcaaatgctaagataattcatcatcactaaacc	<<<<<<<<9<<<<<<<<<<<<<7<<<<<<<<<<<<;;:7:
EAS114_39:2:57:1064:925	137	seq2	35M	tgacaagcaaatgctaagataattcatcatcacta	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:<<<
EAS1_103:3:323:196:855	163	seq2	35M	acaagcaaatgctaagataattcatcatcactaaa	<<<<<<<7<<<<<<:<<<<<<<<<<<<<<<<<;7:
EAS54_67:5:117:33:262	163	seq2	35M	acaagcaaatgctaagataattcatcatcactaaa	<<<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;
EAS139_11:1:59:742:549	99	seq2	35M	acaagcaaatgctaagataattcatcatcactaaa	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<
EAS114_28:2:55:562:403	163	seq2	36M	caagcaaatgctaagataattcatcatcactaaacc	<<<<<<<<<<<<<<<<<<<<<;<<;<<<<<<<;<;:
EAS54_71:7:97:743:602	163	seq2	35M	aagcaaatgctaagataattcatcatcactaaacc	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<:
EAS114_28:2:167:905:852	83	seq2	36M	caaatgctaagataattcatcatcactaaaccagtc	+<<<9;7;<<+<<<<<39<;9<;9<<7<<<<<<<<<
EAS112_34:6:130:865:838	83	seq2	35M	aatgctaagataattcatcatcactaaaccagtcc	;<:84<<<4<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS219_1:1:60:1420:660	163	seq2	35M	aatgctaagataattcatcatcactaaaccagtcc	<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<8<<<<
B7_593:3:180:89:582	99	seq2	36M	atgctaagataattcatcatcactaaaccagtccta	<<<<<<<<<7<<<<<<<<<7<<<:<<<:<<::77:<
EAS1_99:1:86:871:319	147	seq2	35M	tgctaagataattcatcatcactaaaccagtccta	7;+1;<:<<<<<<<<;<<;<<9<<<<<<<<<<<<<
EAS56_57:2:236:841:20	83	seq2	35M	gctaagataattcatcatcactaaaccagtcctat	7;<<<;<<<<;;<<<<<<<<<<<<<<<<<<<<;<<
EAS51_62:2:133:8:379	83	seq2	35M	ataagataattcatcatcactaaaccagtcctata	&=========='==7==0=2====28===00====
EAS1_105:8:96:720:940	83	seq2	35M	taagataattcatcatcactaaaccagtcctataa	*<<<<;<<<9<<;,<;0<;<<<<<<<<<<<<<<<<
EAS56_57:5:71:994:576	99	seq2	35M	aagataattcatcatcactaaaccagtcctataag	<<<<<<<<<<<<<<<<<<<<<<<;<<5<<<<<<<<
EAS1_103:4:164:79:134	147	seq2	35M	agataattcatcatcactaaaccagtcctataaga	<;<;<<<;<<;<<<<<<<<<<<<<<<<<<<<<<<<
EAS139_19:6:78:1029:512	83	seq2	40M	agataattcatcatcactaaaccagtcctataagaaatgc	;;;;;<;;<<<.<<6;<<;<;8<<<<::<<<<<<<<;<<<
EAS1_93:1:214:784:690	147	seq2	35M	gataattcatcatcactaaaccagtcctataagaa	-<7<<7<:<<2<<<<;<<<<<;<<<<3<<<<<<<<
EAS220_1:4:6:1178:1105	99	seq2	35M	gataattcatcatcactaaaccagtcctataagaa	<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS1_99:7:171:196:287	83	seq2	35M	ataattcatcatcactaaaccagtcctataagaaa	<;;;98;<;&<;;<<<<<<<;<<<<<<<<<<<<<<
EAS114_28:1:220:801:282	99	seq2	36M	aattcatcatcactaaaccagtcctataagaaatgc	<<<<<<<<<<<<<<<<<<<<<;<+<;<<<<<::<<:
EAS221_1:2:73:955:728	163	seq2	35M	aattcatcatcactaaaccagtcctataagaaatg	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<<
EAS1_105:1:3:903:957	147	seq2	35M	attcatcatcactaaaccagtcctataagaaatgc	<%12<&<<<;<:<<<<<<<<<7<<<<<<<<<<<<<
EAS56_65:2:224:579:433	83	seq2	35M	ttcatcatcactaaaccagtcctataagaaatgct	'<08/8<+<>===>
EAS1_105:2:146:374:692	99	seq2	35M	aaatgctcaaaagaattgtaaaagtcaaaattaaa	<<<<<<<<<<<<<<<=>>>==>>===>==>
EAS1_108:6:159:493:275	99	seq2	35M	acaaaactcacaggttttataaaacaattaattga	=====3=============================
EAS139_11:1:81:1019:558	163	seq2	35M	acaaaactcacaggttttataaaacaattaattga	<<<<<<<<<<<6<<<<<<<<<<<<<<<<<<<<<7<
EAS51_62:7:162:195:761	163	seq2	18M4I13M	tcacaggttttataaaacaattaattgagactaca	<<<<<<<<<<<<<<<<<<<<<<<<<<;<:<<<<;;
B7_597:3:115:646:430	147	seq2	17M4I14M	cacaggttttataaaacaattaattgagactacag	5;5<;<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS114_30:6:243:209:110	163	seq2	17M4I14M	cacaggttttataaaacaattaattgagactacag	<<<<<;<;<<<;<<<<<<<<<<<;<:;<<:;;+85
EAS1_108:2:266:994:429	147	seq2	16M4I15M	acaggttttataaaacaattaattgagactacaga	<<<<<<<<<<<<<<<<
EAS139_19:1:85:1521:58	147	seq2	40M	aaattaacattacaacaggaacaaaacctcatatatcaat	:::86<<:<<8<<<<;<<8<<<<<<<<<<<<<<<;<<<<<
EAS188_7:4:164:719:947	99	seq2	35M	aaattaacattacaacaggaacaaaacctcatata	<<<<<<<<<<<<<<<<<<<;<<<<<<<<<;<<<<<
EAS219_1:1:50:257:341	163	seq2	35M	aaattaacattacaacaggaacaaaacctcatata	<<<<<<<<<<<<<<<<<<<<<<<<<<<<7<6<<<<
EAS54_67:5:117:33:262	83	seq2	35M	aattaacattacaacaggaacaaaacctcatatat	<<;;<<;<:8<7<<;<<<<<<<<<<<<<<<<<<<<
EAS218_1:8:90:706:1276	163	seq2	35M	aattaacattacaacaggaacaaaacctcatatat	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<:<:<
EAS1_108:2:116:966:193	163	seq2	35M	attaacattacaacaggaacaaaacctcatatatc	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<<
EAS139_11:1:59:742:549	147	seq2	35M	ttaacattacaacaggaacaaaacctcatatatca	-<<<3<<<<6<<6<<<<<6<<<<6<<<<<<<<<<<
EAS139_11:7:74:213:877	99	seq2	35M	ttaacattacaacaggaacaaaacctcatatatca	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
B7_610:3:85:219:371	163	seq2	35M	taacattacaacaggaacaaaacctcatatatcaa	<<<<<<<<<<<<<<<<<<<<<:<<<<<<<<<<;<;
EAS1_108:2:176:653:957	163	seq2	35M	acattacaacaggaacaaaacctcatatatcaata	????????????<==>=>=>=>>>==>>>=>>>
EAS139_19:5:57:366:844	83	seq2	40M	aaattcccccacttaagagatatagattggcagaacagat	;;;7:8&555<,;<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS114_32:3:236:475:254	163	seq2	35M	ttcccccacttaagagatatagattggcagaacag	<<<<<<<<<<<<<<<<<<<<<<<<<:::<:;>=>>>>==>=>>>==>=>=:=====;=:=6:::6
EAS218_1:2:10:686:1024	163	seq2	35M	acaagaaactcattaataaagacatgagttcaggt	<:<<<<:<<<<<<<<<<:<:<<<<<<<<<<<5<<<
EAS54_73:5:53:61:31	163	seq2	35M	aagaaactcattaataaagacatgagttcagataa	<<<7;<7<<<;7<;;<7<7<7<;5<73<<<;>588>9<>7:<0<9;
B7_589:2:30:644:942	99	seq2	35M	tatatcagataaagcacactttaaatcaacaacag	<<<<<<<<<<<<<<<<<<<<<<<9<<<<<<9;<9<
B7_591:2:123:924:645	83	seq2	36M	tatatcagataaagcacactttaaatcaacaacagt	;<<<<*<<<<<<<<8<<<<<><<<<<><<<<<<<<<<<<<<<
EAS51_62:4:308:614:911	99	seq2	35M	tgcgcttgtacttctaaatctataacaaaattaaa	<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<<<<8<
EAS54_65:3:155:541:234	83	seq2	35M	tgcgcttgtacttctaaatctataaaaaaattaaa	78;<7<<<<<<<<<<<<<<;<<<<<<<<<<;<<<<
EAS56_57:6:175:289:351	147	seq2	35M	tgcgcttgtacttctaaatctataaaaaaattaaa	9;;:+<<<<<;<<:<<<<<<<<<<<<<<<<<<<<<
B7_593:7:283:186:707	83	seq2	36M	cgcttgtacttctaaatctataacaaaattaaaatt	889;<7;<7<<7<<<<<7<<<<<<<<<<<<<<<<<<
EAS1_105:3:308:66:538	147	seq2	35M	cgcttgtacttctaaatctataacaaaattaaaat	996999;<9;<:<<<<<:<<7<<<<<<<<<<<<<<
EAS1_108:5:11:555:330	163	seq2	35M	cgcttgtacttctaaatctataaaaaaattaaaat	<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<4<;<
EAS51_66:7:84:411:336	73	seq2	35M	gcttgtacttctaaatctataaaaaaattaaaatt	<<<;<<<;<<<<<<<<<<<<:<<;<<<<<<;8<;<
EAS139_11:5:52:1278:1478	163	seq2	35M	gcttgtacttctaaatctataacaaaattaaaatt	<<<<<<<<<<<<<<9<<<<<<<<<<<<<<<<9<<<
EAS56_53:3:101:809:776	147	seq2	35M	gtacttctaaatctataaaaaaattaaaatttaac	<<<-<;7;<<<<:;<<<7<<<<<<<<<<<<<<<<<
EAS192_3:3:221:881:916	147	seq2	35M	taattctaaatctagaacaaaattaaaatttaaca	44%-4(5<;9/,:<68:1<:8<:<<84;<<<<<;<
EAS1_105:1:28:745:352	147	seq2	35M	cttctaaatctataacaaaattaaaatttaacaaa	4;;*;<<<;;<<<<<<<<<<<<<<<<<<<<<<<<<
EAS114_45:2:23:1754:796	99	seq2	35M	cttctaaatctataaaaaaattaaaatttaacaaa	;<<;<;<;<;<;<<;;;;;<<<<;;<<<<<97999
EAS1_97:2:96:419:327	147	seq2	35M	tctaaatctataacaaaattaaaatttaacaaaag	;1<<<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS1_97:4:274:287:423	163	seq2	35M	ctaaatctataaaaaaattaaaatttaacaaaagt	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;<<<
EAS219_1:7:35:392:2042	83	seq2	35M	ataaatctataaaaaaattaaaatttaacaaaagt	+<<<<4<>>>>;>>&>->9>9;4>->>>>,4>9>,<1>
EAS139_19:2:82:154:1333	99	seq2	40M	ttaaaatttaacaaaagtaaataaaacacacagctaaaac	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<;;<;;:;:
EAS188_7:1:290:286:763	99	seq2	35M	ttaaaatttaacaaaagtaaataaaacacatagct	<<<<<<<<<<<<<<<<7<<<<<<<<<<<<<<<8<<
EAS221_1:4:3:248:1491	73	seq2	35M	ttaaaatttaacaaaagtaaataaaacacatagct	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<:8:<
EAS114_39:3:6:1064:1805	99	seq2	35M	taaaatttaacaaaagtaaataaaacacatagcta	<<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<<<
B7_595:6:137:811:130	83	seq2	35M	aaaatttaacaaaagtaaataaaacacatagctaa	<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<<<<<
EAS1_108:1:155:809:543	83	seq2	35M	aaatttaacaaaagtaaataaaacacatagctaaa	<<<+0<<<9<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS56_63:3:41:468:459	99	seq2	35M	aaatttaacaaaagtaaataaaacacatagctaaa	<<<<<<<<<<<<<<<<<<<<<;<<<<<<<<<<;;7
EAS1_108:4:31:622:216	73	seq2	35M	atttaacaaaagtaaataaaacacatagctaaaac	<<<<<<<<<<<<<<<<<<<<<<<<<<<<8<<96<7
EAS54_71:8:105:854:975	163	seq2	35M	atttaacaaaagtaaataaaacacatagctaaaac	<<<<<<<<<<<<<<<<<<<<<<<<<<<7:<;;;;5
B7_610:7:26:749:174	147	seq2	35M	taacaaaagtaaataaaacacatagctaaaactaa	(<<)<<<<6<<<<<<<<<<&:<3<<<6<<<)<:<<
EAS56_57:6:21:553:57	147	seq2	35M	aacaaaagtaaataaaacacatagctaaaactaaa	<<+<<<<<<<<<;<<<<8<<<<<<8<<<<<;<<<<
EAS1_97:2:128:629:484	83	seq2	35M	aaaaaagtaaataaaacacatagctaaaactaaaa	:(::<<<<<<<<<<
B7_589:6:33:356:636	73	seq2	35M	tttttttcttttctctttttttttttttttttttt	<<<<<<<8;<<<<<<<<<<<<<7<<<<<<<;;3&3
EAS114_45:6:86:859:1779	137	seq2	35M	tttttttcatttctctttttttttttttttttttt	;;;;;;;;;;;;;;;;;;;;;;;;;;;8;;)7699
EAS54_71:8:105:854:975	83	seq2	33M	ttttttttttttttttttttttttttttttttg	<<<<;<:<<;<&<;<<<<<<<<<<<<<<<<<<<
EAS51_62:4:187:907:145	153	seq2	35M	tttcttctctctctttttttttttttttattgcat	<<<+;;,6<<<<6<<<<<<<<<<<<<<<<<<<<<<
EAS54_71:4:284:269:882	73	seq2	34M	tttcttttctcttttttttttttttgtttttgca	<;<<<<<8<7<8;<<<;<7<<<<<;272;73&&)
EAS56_63:4:141:9:811	137	seq2	35M	tttcttttctcctttttttttttttttttctacat	<<<;<<<<<<<;<;<:<<<;<<<<<<<<..));;.
EAS114_30:6:277:397:932	73	seq2	35M	tttcttttcacttttttttttttttttttttactt	<<<<<<<<<<<<<<<<<<<<<<<<<<<<:8(,0%(
EAS139_11:7:50:1229:1313	83	seq2	35M	ttttttcttttttttttttttttttttgcatgcca	<<<<,<&<7<<<<<<<<<<<<<<<<<<<<<<<<<<
EAS54_65:3:320:20:250	147	seq2	35M	tttttttttttttttttttttttgcatgccagaaa	+'''/<<<<7:;+<;::<<<;;<<<<<<<<<<<<<
EAS114_26:7:37:79:581	83	seq2	35M	tttttttttttttttttttttttcatgccagaaaa	3,,,===6===<===<;=====-============
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BCgenometools-1.5.1/testdata/example_1.sorted.bam.bai000066400000000000000000000002601211610345200222400ustar00rootroot00000000000000BAII52J525I2wJ2w2genometools-1.5.1/testdata/fail_arrow_width.style000066400000000000000000000047541211610345200222750ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = function(gn)
                    fail()    -- nonexistant call should fail here
                  end,
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_background_color.style000066400000000000000000000050021211610345200232440ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = function(gn)
                              fail()    -- nonexistant call should fail here
                            end,
  },
}
genometools-1.5.1/testdata/fail_block_caption_font_size.style000066400000000000000000000050251211610345200246230ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = function(gn)
                                fail()    -- nonexistant call should fail here
                              end,
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_block_caption_space.style000066400000000000000000000047731211610345200237270ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_collapse.style000066400000000000000000000050421211610345200215350ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_default_stroke_color.style000066400000000000000000000050021211610345200241400ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = function(gn)
                              fail()    -- nonexistant call should fail here
                            end,
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_fill.style000066400000000000000000000050111211610345200206550ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_group_by_parent.style000066400000000000000000000047211211610345200231350ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    group_by_parent    = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
  },
  -- Defines various format options for drawing.
  format =
  {
    max_num_lines       = 10,
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_max_capt_show_width.style000066400000000000000000000050441211610345200237700ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_max_num_lines.style000066400000000000000000000047251211610345200226000ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
  },
  -- Defines various format options for drawing.
  format =
  {
    max_num_lines      = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_max_show_width.style000066400000000000000000000050441211610345200227610ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_min_len_block.style000066400000000000000000000047321211610345200225330ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = function(gn)
                      fail()    -- nonexistant call should fail here
                    end,
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_ruler_text.style000066400000000000000000000047751211610345200221440ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = function(gn)
                        fail()    -- nonexistant call should fail here
                      end,
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_rulerfontsize.style000066400000000000000000000050151211610345200226460ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_rulerspace.style000066400000000000000000000047761211610345200221150ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_show_bar_height.style000066400000000000000000000047521211610345200230760ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = function(gn)
                   fail()    -- nonexistant call should fail here
                 end,
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_show_block_captions.style000066400000000000000000000050071211610345200237660ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = function(gn)
                            fail()    -- nonexistant call should fail here
                          end,
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_show_grid.style000066400000000000000000000047431211610345200217270ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = function(gn)
                  fail()    -- nonexistant call should fail here
                end,
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_show_margins.style000066400000000000000000000047311211610345200224370ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = function(gn)
                fail()    -- nonexistant call should fail here
              end,
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_show_track_captions.style000066400000000000000000000047771211610345200240150ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_split.style000066400000000000000000000047561211610345200211010ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines         = function()
                            fail()    -- nonexistant call should fail here
                          end,
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_stroke.style000066400000000000000000000047741211610345200212550ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_stroke_width.style000066400000000000000000000047711211610345200224510ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = function(gn)
                     fail()    -- nonexistant call should fail here
                   end,
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_style.style000066400000000000000000000050421211610345200210730ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_track_caption_font_size.style000066400000000000000000000050251211610345200246350ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = function(gn)
                                fail()    -- nonexistant call should fail here
                              end,
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_track_caption_space.style000066400000000000000000000047751211610345200237430ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = function(gn)
                            fail()    -- nonexistant call should fail here
                          end,
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_track_title_color.style000066400000000000000000000050001211610345200234300ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = function()
                              fail()    -- nonexistant call should fail here
                            end,
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_track_vspace.style000066400000000000000000000050021211610345200223740ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = function(gn)
                           fail()    -- nonexistant call should fail here
                         end,
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_unit.style000066400000000000000000000047451211610345200207230ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    -- max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = function(gn)
             fail()    -- nonexistant call should fail here
           end,
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fail_vspace.style000066400000000000000000000047471211610345200212270ustar00rootroot00000000000000style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=0.0, blue=0.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = function(gn)
                   fail()    -- nonexistant call should fail here
                 end,
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/fasta_seq.gff3000066400000000000000000000000531211610345200203700ustar00rootroot00000000000000##gff-version   3
##FASTA
>seq1
cttctgggcg
genometools-1.5.1/testdata/fastq_long.fastq000066400000000000000000003237621211610345200210670ustar00rootroot00000000000000@SRR015141.1 WICMT-SOLEXA_209LAAAXX_8_1_891_487 length=26
GAAACATTACCAGTTCTGTTTCATTT
+SRR015141.1 WICMT-SOLEXA_209LAAAXX_8_1_891_487 length=26
IIIIIIIIIIIIH"
@SRR015141.23 WICMT-SOLEXA_209LAAAXX_8_1_878_659 length=26
GGGCCTGGGGACCTAGGATGGTCAGA
+SRR015141.23 WICMT-SOLEXA_209LAAAXX_8_1_878_659 length=26
IIIIIIIIIIIAIIII<9II2I>;.;
@SRR015141.24 WICMT-SOLEXA_209LAAAXX_8_1_920_639 length=26
GTAATTTACCCATTACGGTGCATGAG
+SRR015141.24 WICMT-SOLEXA_209LAAAXX_8_1_920_639 length=26
IIIIIIIIIIIIIDIIII+IIII$I2
@SRR015141.25 WICMT-SOLEXA_209LAAAXX_8_1_913_678 length=26
GAGACAGATTCTTTCCTCTGATTTTC
+SRR015141.25 WICMT-SOLEXA_209LAAAXX_8_1_913_678 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.26 WICMT-SOLEXA_209LAAAXX_8_1_938_406 length=26
GGGTGGGGGTGGTGGAGTTGCGGGGG
+SRR015141.26 WICMT-SOLEXA_209LAAAXX_8_1_938_406 length=26
IIIIIIIIIII1"IIHGII,I7"&C#
@SRR015141.27 WICMT-SOLEXA_209LAAAXX_8_1_885_743 length=26
GAATTCATCTCTGGAAAATCTTATTA
+SRR015141.27 WICMT-SOLEXA_209LAAAXX_8_1_885_743 length=26
IIIIIIIIIIII?3HIEIIEIIAI-G
@SRR015141.28 WICMT-SOLEXA_209LAAAXX_8_1_886_705 length=26
GTGAGACAGTCCTTGGACCTTCACAT
+SRR015141.28 WICMT-SOLEXA_209LAAAXX_8_1_886_705 length=26
IIIIIIIIIIIAII9<,/EII(E6BI
@SRR015141.29 WICMT-SOLEXA_209LAAAXX_8_1_897_707 length=26
GAAGAGTTACTCTCAGATGATCCCAG
+SRR015141.29 WICMT-SOLEXA_209LAAAXX_8_1_897_707 length=26
IIIIIIIIIIIIIIIIIIIIIIIIID
@SRR015141.30 WICMT-SOLEXA_209LAAAXX_8_1_943_713 length=26
GATAATACTTTCTTTATAAATAATTT
+SRR015141.30 WICMT-SOLEXA_209LAAAXX_8_1_943_713 length=26
IIII%IIIIIIIIII#III1IIIIII
@SRR015141.31 WICMT-SOLEXA_209LAAAXX_8_1_943_458 length=26
GAAGATCAGCCTTAGTGCATGGTGAT
+SRR015141.31 WICMT-SOLEXA_209LAAAXX_8_1_943_458 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.32 WICMT-SOLEXA_209LAAAXX_8_1_920_509 length=26
GATGATTGTATGTTGGCACTTTCTCC
+SRR015141.32 WICMT-SOLEXA_209LAAAXX_8_1_920_509 length=26
IIIIIIIIIIIIII".IIIIICIIII
@SRR015141.33 WICMT-SOLEXA_209LAAAXX_8_1_920_626 length=26
GTGGAACAACAATATGAACTAACCAT
+SRR015141.33 WICMT-SOLEXA_209LAAAXX_8_1_920_626 length=26
IIIIIIIIIIIIIII)IIIIIIIIII
@SRR015141.34 WICMT-SOLEXA_209LAAAXX_8_1_920_588 length=26
GCAACTAATGTCTCGTTTCCTTCCTC
+SRR015141.34 WICMT-SOLEXA_209LAAAXX_8_1_920_588 length=26
IIIIIIIIIIIIIIIIIIIIIIIII<
@SRR015141.35 WICMT-SOLEXA_209LAAAXX_8_1_894_696 length=26
GAAGTCCTCAGCTGAGATGCAGTCAT
+SRR015141.35 WICMT-SOLEXA_209LAAAXX_8_1_894_696 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.36 WICMT-SOLEXA_209LAAAXX_8_1_915_879 length=26
TTTCGTAAGCTTTCTTGTATTCTATT
+SRR015141.36 WICMT-SOLEXA_209LAAAXX_8_1_915_879 length=26
IIIIIIIIIIIIIIIFIICIIII#II
@SRR015141.37 WICMT-SOLEXA_209LAAAXX_8_1_917_551 length=26
GTGAAAACCTTAGCCAGAAAAATACT
+SRR015141.37 WICMT-SOLEXA_209LAAAXX_8_1_917_551 length=26
IIIIIIIIIIII.III;IIIIIIIII
@SRR015141.38 WICMT-SOLEXA_209LAAAXX_8_1_882_423 length=26
GTCAGAGAAGGGAGAGAGGTTTGGTG
+SRR015141.38 WICMT-SOLEXA_209LAAAXX_8_1_882_423 length=26
IIIIIIIIIIIIIIIIIIIIII,AI)
@SRR015141.39 WICMT-SOLEXA_209LAAAXX_8_1_917_956 length=26
GGTCNNNNNNNNNNNNNNNNNNNNNN
+SRR015141.39 WICMT-SOLEXA_209LAAAXX_8_1_917_956 length=26
IIII!!!!!!!!!!!!!!!!!!!!!!
@SRR015141.40 WICMT-SOLEXA_209LAAAXX_8_1_878_554 length=26
GGATTTCTGAGTTTGATGTCAGCCTG
+SRR015141.40 WICMT-SOLEXA_209LAAAXX_8_1_878_554 length=26
IIIIIIIIIIIIII$I%;IEI#91I&
@SRR015141.41 WICMT-SOLEXA_209LAAAXX_8_1_925_433 length=26
GTTATGGCGCATGAATCCAAATCACA
+SRR015141.41 WICMT-SOLEXA_209LAAAXX_8_1_925_433 length=26
IIIIIIIIIIII.IIIIIIIIIIIII
@SRR015141.42 WICMT-SOLEXA_209LAAAXX_8_1_885_708 length=26
GGGAAAAGGCCCACTTATAGGACACA
+SRR015141.42 WICMT-SOLEXA_209LAAAXX_8_1_885_708 length=26
IIIIIIIIIIIIIIIIFIIIIG8A9/
@SRR015141.43 WICMT-SOLEXA_209LAAAXX_8_1_916_212 length=26
GACTCATGGGAAACGAATGTCTGTTT
+SRR015141.43 WICMT-SOLEXA_209LAAAXX_8_1_916_212 length=26
IIIIIIIIIIIIII9IIIIIIIIIII
@SRR015141.44 WICMT-SOLEXA_209LAAAXX_8_1_929_382 length=26
GACGTTGACAACGTGGAATAGGAGCA
+SRR015141.44 WICMT-SOLEXA_209LAAAXX_8_1_929_382 length=26
IIIIIIIIIIIIIIIIIIII3II&II
@SRR015141.45 WICMT-SOLEXA_209LAAAXX_8_1_926_500 length=26
GACTCTGAGTGAAACTCGGAGGCTCT
+SRR015141.45 WICMT-SOLEXA_209LAAAXX_8_1_926_500 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.46 WICMT-SOLEXA_209LAAAXX_8_1_880_600 length=26
TGGGTGTGACATGAAAAGGTTTTACC
+SRR015141.46 WICMT-SOLEXA_209LAAAXX_8_1_880_600 length=26
IIIIIIIIIIIIIIIII@)IIIIH9:
@SRR015141.47 WICMT-SOLEXA_209LAAAXX_8_1_882_542 length=26
GGTTCAAACTCAAATTCTTAGGCTTT
+SRR015141.47 WICMT-SOLEXA_209LAAAXX_8_1_882_542 length=26
IIIIIIIIIIIIIIIIIIII',BII+
@SRR015141.48 WICMT-SOLEXA_209LAAAXX_8_1_896_744 length=26
GGGTTTCTGGGTTAAAGGAGCCTGGC
+SRR015141.48 WICMT-SOLEXA_209LAAAXX_8_1_896_744 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.49 WICMT-SOLEXA_209LAAAXX_8_1_899_526 length=26
GGTCTCAACAGCCAGCGGCACCAAGT
+SRR015141.49 WICMT-SOLEXA_209LAAAXX_8_1_899_526 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.50 WICMT-SOLEXA_209LAAAXX_8_1_879_606 length=26
TACATTAAATAAATAAATAAATAAAT
+SRR015141.50 WICMT-SOLEXA_209LAAAXX_8_1_879_606 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.51 WICMT-SOLEXA_209LAAAXX_8_1_904_568 length=26
GGCTCACAGCACCTGGCTGCTTCTCA
+SRR015141.51 WICMT-SOLEXA_209LAAAXX_8_1_904_568 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.52 WICMT-SOLEXA_209LAAAXX_8_1_945_450 length=26
GAGAAATGCACACAAAAGGACCTGGA
+SRR015141.52 WICMT-SOLEXA_209LAAAXX_8_1_945_450 length=26
IIIIIIIIIIIIIIIIIIIIIIII.I
@SRR015141.53 WICMT-SOLEXA_209LAAAXX_8_1_882_471 length=26
GTTCAGCAAGATAATATAACAGTTGA
+SRR015141.53 WICMT-SOLEXA_209LAAAXX_8_1_882_471 length=26
IIIIIIIIIIIIIIIIIIIBI)$I':
@SRR015141.54 WICMT-SOLEXA_209LAAAXX_8_1_903_472 length=26
GAGTGCTCTATCTGCATGTACACCTG
+SRR015141.54 WICMT-SOLEXA_209LAAAXX_8_1_903_472 length=26
IIIIIIIIIIIIIIIIIIIIIIIII2
@SRR015141.55 WICMT-SOLEXA_209LAAAXX_8_1_895_668 length=26
GCTGGGCAGACATTGTGTTTTAAAGC
+SRR015141.55 WICMT-SOLEXA_209LAAAXX_8_1_895_668 length=26
IIIIIII-6III'II,I;:=II
@SRR015141.58 WICMT-SOLEXA_209LAAAXX_8_1_927_488 length=26
TCACGAGCGTTTGTGATTTCTCATCA
+SRR015141.58 WICMT-SOLEXA_209LAAAXX_8_1_927_488 length=26
IIIIIIIIIIIIIIIIII2IIIIIII
@SRR015141.59 WICMT-SOLEXA_209LAAAXX_8_1_917_350 length=26
AATTTTTTTAAGGAGCAGTTGTAATT
+SRR015141.59 WICMT-SOLEXA_209LAAAXX_8_1_917_350 length=26
IIIIIIIIIIIIIIIIIIIIIIII9I
@SRR015141.60 WICMT-SOLEXA_209LAAAXX_8_1_876_720 length=26
ACCAAGGTATCATTTAGAATAGTTTT
+SRR015141.60 WICMT-SOLEXA_209LAAAXX_8_1_876_720 length=26
IIIIIIIIIIIIII"F<9@I--I&II
@SRR015141.61 WICMT-SOLEXA_209LAAAXX_8_1_880_861 length=26
TCCTTCTAAGGTGATTGTTCTTTCTT
+SRR015141.61 WICMT-SOLEXA_209LAAAXX_8_1_880_861 length=26
IIIIIIIIIIIIIIIIII%II,I"II
@SRR015141.62 WICMT-SOLEXA_209LAAAXX_8_1_936_720 length=26
GGGGCATCTTCTGGATATATGCCCAT
+SRR015141.62 WICMT-SOLEXA_209LAAAXX_8_1_936_720 length=26
IIIIIIIIIIIIIIIIIIII5IIII'
@SRR015141.63 WICMT-SOLEXA_209LAAAXX_8_1_895_423 length=26
GTTGGCTGAGAGGAAAAAGCAGAGCT
+SRR015141.63 WICMT-SOLEXA_209LAAAXX_8_1_895_423 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.64 WICMT-SOLEXA_209LAAAXX_8_1_905_700 length=26
GGAAATGGCACTATTAGGTGGTGTGG
+SRR015141.64 WICMT-SOLEXA_209LAAAXX_8_1_905_700 length=26
IIIIIIIIIIIIIIIIIIIIIIIII>
@SRR015141.65 WICMT-SOLEXA_209LAAAXX_8_1_908_663 length=26
TCTGAGTATCTTCAGCAGATAGAGAT
+SRR015141.65 WICMT-SOLEXA_209LAAAXX_8_1_908_663 length=26
IIIIIIIIIII9IIIIIIIIIIIIII
@SRR015141.66 WICMT-SOLEXA_209LAAAXX_8_1_935_598 length=26
TGTAAAAGACATTGTAATTTGCTGCA
+SRR015141.66 WICMT-SOLEXA_209LAAAXX_8_1_935_598 length=26
IIIIIIIIIIIIIIIIIIII8II"IF
@SRR015141.67 WICMT-SOLEXA_209LAAAXX_8_1_901_549 length=26
GTGTGGGAATATTTTGCATTTTTTTT
+SRR015141.67 WICMT-SOLEXA_209LAAAXX_8_1_901_549 length=26
IIIIIIIIIIIIIII-IBIIIIIII5
@SRR015141.68 WICMT-SOLEXA_209LAAAXX_8_1_909_440 length=26
GTCTATCAGATAGTTATGATTCTTAA
+SRR015141.68 WICMT-SOLEXA_209LAAAXX_8_1_909_440 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.69 WICMT-SOLEXA_209LAAAXX_8_1_890_595 length=26
GTACTTGGAGTAAAGGCGTGCGTCAC
+SRR015141.69 WICMT-SOLEXA_209LAAAXX_8_1_890_595 length=26
III(IIIIII/IIII(+9I.08I0/-
@SRR015141.70 WICMT-SOLEXA_209LAAAXX_8_1_887_685 length=26
GGGCGGGGGTGGTATTTTAGGAGGCT
+SRR015141.70 WICMT-SOLEXA_209LAAAXX_8_1_887_685 length=26
IIIIIIIII5III
@SRR015141.116 WICMT-SOLEXA_209LAAAXX_8_1_909_857 length=26
GAACACTCACAGGTAACACATTTATT
+SRR015141.116 WICMT-SOLEXA_209LAAAXX_8_1_909_857 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.117 WICMT-SOLEXA_209LAAAXX_8_1_923_373 length=26
TCCTTTCTTATTCTCTTGTAATCATT
+SRR015141.117 WICMT-SOLEXA_209LAAAXX_8_1_923_373 length=26
IIIIIIIIII#IIIII.$IIIIIIII
@SRR015141.118 WICMT-SOLEXA_209LAAAXX_8_1_800_483 length=26
GTACTAGAAGGTGTTATGTTTACTAC
+SRR015141.118 WICMT-SOLEXA_209LAAAXX_8_1_800_483 length=26
IIICIIBIII@IIII2I+I?II?I'(
@SRR015141.119 WICMT-SOLEXA_209LAAAXX_8_1_937_561 length=26
GCTTTACCCGTGCTTCTTCCATTTAT
+SRR015141.119 WICMT-SOLEXA_209LAAAXX_8_1_937_561 length=26
ICII&&)IIIIIIIIIIIIIIII-HI
@SRR015141.120 WICMT-SOLEXA_209LAAAXX_8_1_930_907 length=26
TTCTGTGTGCATTTCTCATTTTTCTC
+SRR015141.120 WICMT-SOLEXA_209LAAAXX_8_1_930_907 length=26
IIIIIIIIIIIIIIIIIIIIIIII9I
@SRR015141.121 WICMT-SOLEXA_209LAAAXX_8_1_883_454 length=26
TAATTCCAGTTCTTCACAAACTATTC
+SRR015141.121 WICMT-SOLEXA_209LAAAXX_8_1_883_454 length=26
IIIIIIIIIIIEIIIIEIII5ICIIF
@SRR015141.122 WICMT-SOLEXA_209LAAAXX_8_1_905_398 length=26
TTTGAGCCTGAAGATTTTTTTGTGGT
+SRR015141.122 WICMT-SOLEXA_209LAAAXX_8_1_905_398 length=26
IIIIDI3IIIFAII@
@SRR015141.136 WICMT-SOLEXA_209LAAAXX_8_1_891_687 length=26
GTGGTTTTCTTCTAACGGGCAATGTT
+SRR015141.136 WICMT-SOLEXA_209LAAAXX_8_1_891_687 length=26
IIIIIIIIIII:IIIII
@SRR015141.152 WICMT-SOLEXA_209LAAAXX_8_1_847_718 length=26
GTCCAAGTTATCATTGTGTAGGTTTT
+SRR015141.152 WICMT-SOLEXA_209LAAAXX_8_1_847_718 length=26
IIIIIIIIIII;GIIII=IAI1)I+I
@SRR015141.153 WICMT-SOLEXA_209LAAAXX_8_1_908_513 length=26
GTGGATCTTTGCTCCCTAGAGTCCTT
+SRR015141.153 WICMT-SOLEXA_209LAAAXX_8_1_908_513 length=26
IIIIIIIIIIIII?&III&%,=IDII
@SRR015141.154 WICMT-SOLEXA_209LAAAXX_8_1_896_688 length=26
TAGCATTCTTAACAAAAACTGTTTAA
+SRR015141.154 WICMT-SOLEXA_209LAAAXX_8_1_896_688 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.155 WICMT-SOLEXA_209LAAAXX_8_1_914_470 length=26
GCATGTGTGTATGTTTTTATATATTT
+SRR015141.155 WICMT-SOLEXA_209LAAAXX_8_1_914_470 length=26
II;I:>IIIIIIII.IIIIIIIIIII
@SRR015141.156 WICMT-SOLEXA_209LAAAXX_8_1_759_678 length=26
GGGGGGTGCCTTTGGACCCTGTGCTG
+SRR015141.156 WICMT-SOLEXA_209LAAAXX_8_1_759_678 length=26
IIIIII,I'#*+&*I"III>I,%#I"
@SRR015141.157 WICMT-SOLEXA_209LAAAXX_8_1_909_364 length=26
TATCACACTCACGTACTGGAGTTCAT
+SRR015141.157 WICMT-SOLEXA_209LAAAXX_8_1_909_364 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.158 WICMT-SOLEXA_209LAAAXX_8_1_952_461 length=26
TTTGGGACTGGATCTCATTGTGTATT
+SRR015141.158 WICMT-SOLEXA_209LAAAXX_8_1_952_461 length=26
IIIIIIIIIIIIIIIIIIIII"I5'I
@SRR015141.159 WICMT-SOLEXA_209LAAAXX_8_1_904_679 length=26
GAGTCAGACAATGGAGCAACCAGTGG
+SRR015141.159 WICMT-SOLEXA_209LAAAXX_8_1_904_679 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.160 WICMT-SOLEXA_209LAAAXX_8_1_896_795 length=26
TCTTGCTATGTCCACACAGGGCTTCA
+SRR015141.160 WICMT-SOLEXA_209LAAAXX_8_1_896_795 length=26
IIIIIIIIIIIIIIIIIIII6I?%II
@SRR015141.161 WICMT-SOLEXA_209LAAAXX_8_1_885_350 length=26
TTATGAGATGGTTATTCTTGTCATTT
+SRR015141.161 WICMT-SOLEXA_209LAAAXX_8_1_885_350 length=26
II2IIIIIIII(:"3III.#I$II7I
@SRR015141.162 WICMT-SOLEXA_209LAAAXX_8_1_785_699 length=26
GCAGCCAAAACCTTTGTAGTGTTTTG
+SRR015141.162 WICMT-SOLEXA_209LAAAXX_8_1_785_699 length=26
IIIIIIIIIIIIIIIIIICI2I(#&1
@SRR015141.163 WICMT-SOLEXA_209LAAAXX_8_1_903_299 length=26
AAAGTCGGAAAGTGGATGTTTGTGTT
+SRR015141.163 WICMT-SOLEXA_209LAAAXX_8_1_903_299 length=26
IIII'IIIIIIIIIIIIIIII,IIII
@SRR015141.164 WICMT-SOLEXA_209LAAAXX_8_1_775_694 length=26
GTTTCTTTATTTTTTATCTTTTTTTT
+SRR015141.164 WICMT-SOLEXA_209LAAAXX_8_1_775_694 length=26
IIIIIIIIIIIIIIII()III)I$II
@SRR015141.165 WICMT-SOLEXA_209LAAAXX_8_1_903_375 length=26
GTAAGAACATTCTTGTGAATTTCAAT
+SRR015141.165 WICMT-SOLEXA_209LAAAXX_8_1_903_375 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.166 WICMT-SOLEXA_209LAAAXX_8_1_907_607 length=26
GACAAGGCTTTGGCCTGCAAGCCTTC
+SRR015141.166 WICMT-SOLEXA_209LAAAXX_8_1_907_607 length=26
IIIIIIIIIII=IIIIIIIIIIIIII
@SRR015141.167 WICMT-SOLEXA_209LAAAXX_8_1_956_500 length=26
GATGTCACACACCACCAGGCAGTTTA
+SRR015141.167 WICMT-SOLEXA_209LAAAXX_8_1_956_500 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.168 WICMT-SOLEXA_209LAAAXX_8_1_877_851 length=26
TCCCACTACGCCTCTTCCTAGCATAA
+SRR015141.168 WICMT-SOLEXA_209LAAAXX_8_1_877_851 length=26
III?I+IIII1IIIII/I$I9II+%$
@SRR015141.169 WICMT-SOLEXA_209LAAAXX_8_1_894_896 length=26
TGGGGTTTCTGAAACACGCACTTGGT
+SRR015141.169 WICMT-SOLEXA_209LAAAXX_8_1_894_896 length=26
IIIIIIIIIIIIIIIIIII8III,(I
@SRR015141.170 WICMT-SOLEXA_209LAAAXX_8_1_882_685 length=26
TTCTTGAAAGCTTTTTCTAACTTGTT
+SRR015141.170 WICMT-SOLEXA_209LAAAXX_8_1_882_685 length=26
I@I8II(.05@I-*I3&I2%$II0I+
@SRR015141.171 WICMT-SOLEXA_209LAAAXX_8_1_927_789 length=26
GTGTGTGTTCCATTTTTGAATCCATA
+SRR015141.171 WICMT-SOLEXA_209LAAAXX_8_1_927_789 length=26
IIIIIIIIIIIIIIIIIIIIIIII"I
@SRR015141.172 WICMT-SOLEXA_209LAAAXX_8_1_909_369 length=26
AAAACATTTTACAAAACCAAGTGGCA
+SRR015141.172 WICMT-SOLEXA_209LAAAXX_8_1_909_369 length=26
IIIIIIIIIIIIIIIIIIIIIII=II
@SRR015141.173 WICMT-SOLEXA_209LAAAXX_8_1_926_695 length=26
GGCATAGATAAATAACATGGAGGCTT
+SRR015141.173 WICMT-SOLEXA_209LAAAXX_8_1_926_695 length=26
IIIIIIIIIIIIIIIIIIIII7IIII
@SRR015141.174 WICMT-SOLEXA_209LAAAXX_8_1_886_579 length=26
AGCCTCAGGGAGAATGAGGAGAAATA
+SRR015141.174 WICMT-SOLEXA_209LAAAXX_8_1_886_579 length=26
IIIIIIIIII7I>HII:>5:<-F9I=
@SRR015141.175 WICMT-SOLEXA_209LAAAXX_8_1_910_379 length=26
GCTGAGGTACCTATTTACTTCATTAT
+SRR015141.175 WICMT-SOLEXA_209LAAAXX_8_1_910_379 length=26
IIIIIIIIIIIII"I%8"I>I.$=#
@SRR015141.177 WICMT-SOLEXA_209LAAAXX_8_1_913_768 length=26
GGATGATGCTGGAAGATCACCAGCCG
+SRR015141.177 WICMT-SOLEXA_209LAAAXX_8_1_913_768 length=26
IIIIIIIIIIIIIIIIIIIIII.II(
@SRR015141.178 WICMT-SOLEXA_209LAAAXX_8_1_903_243 length=26
GGAGATTCTTCTTTGATGGCACTTTT
+SRR015141.178 WICMT-SOLEXA_209LAAAXX_8_1_903_243 length=26
IIIIIIIIIIIIII*III0IIIIIII
@SRR015141.179 WICMT-SOLEXA_209LAAAXX_8_1_902_707 length=26
GGATAAACCTGGACACAAATGGTAAG
+SRR015141.179 WICMT-SOLEXA_209LAAAXX_8_1_902_707 length=26
IIIIIIIIIIIIIIIIIIIIIIIII"
@SRR015141.180 WICMT-SOLEXA_209LAAAXX_8_1_887_922 length=26
TTAAGGATATGAAACACTCCAACACC
+SRR015141.180 WICMT-SOLEXA_209LAAAXX_8_1_887_922 length=26
IIIIIIIIIIIIII,III)58I<.32
@SRR015141.181 WICMT-SOLEXA_209LAAAXX_8_1_903_337 length=26
GAATATGGCGAGAAAATTGAAAATCA
+SRR015141.181 WICMT-SOLEXA_209LAAAXX_8_1_903_337 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.182 WICMT-SOLEXA_209LAAAXX_8_1_899_871 length=26
GGGGAACTTGATTTTACATTATTTCA
+SRR015141.182 WICMT-SOLEXA_209LAAAXX_8_1_899_871 length=26
IIIIIIDIIIIIIIIIIIIIIIIIII
@SRR015141.183 WICMT-SOLEXA_209LAAAXX_8_1_919_393 length=26
GACAGGTGTACCTGAACGGACCCCAC
+SRR015141.183 WICMT-SOLEXA_209LAAAXX_8_1_919_393 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.184 WICMT-SOLEXA_209LAAAXX_8_1_926_888 length=26
TCCCGTGCAAGAGCAACCATTGCTTT
+SRR015141.184 WICMT-SOLEXA_209LAAAXX_8_1_926_888 length=26
IIIIIIIIIIIIIIIIIII"IIIIII
@SRR015141.185 WICMT-SOLEXA_209LAAAXX_8_1_947_680 length=26
GAAGTGGACAGTTCTGGGTTGTGCAG
+SRR015141.185 WICMT-SOLEXA_209LAAAXX_8_1_947_680 length=26
IIIIIIIIIIIIII&IIIIIII&II5
@SRR015141.186 WICMT-SOLEXA_209LAAAXX_8_1_882_515 length=26
GAAAGTCGGTGTTGTGAATATATTTA
+SRR015141.186 WICMT-SOLEXA_209LAAAXX_8_1_882_515 length=26
IAI;IIIIIIIIIIB"F.I9I%I?I-
@SRR015141.187 WICMT-SOLEXA_209LAAAXX_8_1_879_720 length=26
TCTGCCCTGTGTCTGCTTGGCAGGTT
+SRR015141.187 WICMT-SOLEXA_209LAAAXX_8_1_879_720 length=26
III4II:IFIIIIIIFII""1$/#BI
@SRR015141.188 WICMT-SOLEXA_209LAAAXX_8_1_927_741 length=26
GGGCAGAGGGTCAGCATGGGAACGCA
+SRR015141.188 WICMT-SOLEXA_209LAAAXX_8_1_927_741 length=26
IIIIIIIIIIIIIIIIIBIIIIIBII
@SRR015141.189 WICMT-SOLEXA_209LAAAXX_8_1_894_589 length=26
TCTCAAGAACATTTTCTGTTGATTCT
+SRR015141.189 WICMT-SOLEXA_209LAAAXX_8_1_894_589 length=26
IIIIIIIIIIIIIIIIIIII9IIIII
@SRR015141.190 WICMT-SOLEXA_209LAAAXX_8_1_901_447 length=26
GACTATTCTACAAATACAATAATTCC
+SRR015141.190 WICMT-SOLEXA_209LAAAXX_8_1_901_447 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.191 WICMT-SOLEXA_209LAAAXX_8_1_877_454 length=26
TTGGAGTGCTTTCCTGAATTGTTTCT
+SRR015141.191 WICMT-SOLEXA_209LAAAXX_8_1_877_454 length=26
IIIIIIIIIIIII7I459II&III3I
@SRR015141.192 WICMT-SOLEXA_209LAAAXX_8_1_932_881 length=26
TGGAATAATTCTTAAGTAATTTTTTA
+SRR015141.192 WICMT-SOLEXA_209LAAAXX_8_1_932_881 length=26
IIIIIIIE+4II/I0IIIIIIIIII4
@SRR015141.193 WICMT-SOLEXA_209LAAAXX_8_1_912_568 length=26
GCAGAGTCTAGACCACACACAAGCTT
+SRR015141.193 WICMT-SOLEXA_209LAAAXX_8_1_912_568 length=26
IIIIIIIIIIIIIIIIIIIIIIIII4
@SRR015141.194 WICMT-SOLEXA_209LAAAXX_8_1_898_723 length=26
AAGGACAGTGATCTGTGAAGAGATTA
+SRR015141.194 WICMT-SOLEXA_209LAAAXX_8_1_898_723 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.195 WICMT-SOLEXA_209LAAAXX_8_1_927_516 length=26
GCAACATCGTAGCAATCAAATCCATC
+SRR015141.195 WICMT-SOLEXA_209LAAAXX_8_1_927_516 length=26
IIIIIIIIIIIIIIIIIIIIIIIIIE
@SRR015141.196 WICMT-SOLEXA_209LAAAXX_8_1_889_702 length=26
AGACCAGCTGAAACAACTAGCCTCGT
+SRR015141.196 WICMT-SOLEXA_209LAAAXX_8_1_889_702 length=26
IIIIIIIIIIIIIIII9IIID8II.
@SRR015141.202 WICMT-SOLEXA_209LAAAXX_8_1_944_420 length=26
GAACTGCCTAACATCCTTGGCCATTT
+SRR015141.202 WICMT-SOLEXA_209LAAAXX_8_1_944_420 length=26
IIIIIIIIIIIIIIIIIII,IIII7%
@SRR015141.203 WICMT-SOLEXA_209LAAAXX_8_1_933_517 length=26
GACCTCCAGTCTAGGGGTGACTCAGT
+SRR015141.203 WICMT-SOLEXA_209LAAAXX_8_1_933_517 length=26
II2IIIIIIII22IIIII&I"III+I
@SRR015141.204 WICMT-SOLEXA_209LAAAXX_8_1_913_580 length=26
AGACCTGGGTCTAAAAGATCCAGCTG
+SRR015141.204 WICMT-SOLEXA_209LAAAXX_8_1_913_580 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.205 WICMT-SOLEXA_209LAAAXX_8_1_909_436 length=26
GCATATGAAAGGTGTATTCCTGGGCA
+SRR015141.205 WICMT-SOLEXA_209LAAAXX_8_1_909_436 length=26
IIIIIIIIIIIIIIIIIII:I&3"I>
@SRR015141.206 WICMT-SOLEXA_209LAAAXX_8_1_884_512 length=26
TTTACTCATTTGCTGATATACAAGTA
+SRR015141.206 WICMT-SOLEXA_209LAAAXX_8_1_884_512 length=26
IIIIIIIIIIIIII+III*I9:I(I:
@SRR015141.207 WICMT-SOLEXA_209LAAAXX_8_1_888_504 length=26
TGGTCTCTCGCTGTGTCTTTTTTTTC
+SRR015141.207 WICMT-SOLEXA_209LAAAXX_8_1_888_504 length=26
IIIIIIIII9IIII4IIIIIIIII2"
@SRR015141.208 WICMT-SOLEXA_209LAAAXX_8_1_928_437 length=26
GGTGGTGGTCACAACATGAGGAATTT
+SRR015141.208 WICMT-SOLEXA_209LAAAXX_8_1_928_437 length=26
IIIIIIIIIIIIII"IIFIIIIIGII
@SRR015141.209 WICMT-SOLEXA_209LAAAXX_8_1_903_423 length=26
GCAGTGTATCAATACTGACCTTTCCT
+SRR015141.209 WICMT-SOLEXA_209LAAAXX_8_1_903_423 length=26
IIIIIIIIIIIIII+IIIIIII)III
@SRR015141.210 WICMT-SOLEXA_209LAAAXX_8_1_877_493 length=26
TGTGGAAGGGGTTTTTTATTACTTTT
+SRR015141.210 WICMT-SOLEXA_209LAAAXX_8_1_877_493 length=26
CI;II$ID'III,I#I5(II+#"I"+
@SRR015141.211 WICMT-SOLEXA_209LAAAXX_8_1_898_748 length=26
GGGCTGTATAGTAGCAACCTTGTCTC
+SRR015141.211 WICMT-SOLEXA_209LAAAXX_8_1_898_748 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.212 WICMT-SOLEXA_209LAAAXX_8_1_884_976 length=26
GCNNNNNNNNNNNNNNNNNNNNNNNN
+SRR015141.212 WICMT-SOLEXA_209LAAAXX_8_1_884_976 length=26
II!!!!!!!!!!!!!!!!!!!!!!!!
@SRR015141.213 WICMT-SOLEXA_209LAAAXX_8_1_878_273 length=26
AACAGGTTCTTGATGTTTGTCATTTT
+SRR015141.213 WICMT-SOLEXA_209LAAAXX_8_1_878_273 length=26
III)II,5I#2.:I,II4&IFII)II
@SRR015141.214 WICMT-SOLEXA_209LAAAXX_8_1_903_340 length=26
CATACTTAACTGTGTCAGCTATAGTT
+SRR015141.214 WICMT-SOLEXA_209LAAAXX_8_1_903_340 length=26
IIIIIIIIIIIIIIIIIIIIIIE"I&
@SRR015141.215 WICMT-SOLEXA_209LAAAXX_8_1_908_261 length=26
ATTGCATTTAATAGGTGGTTTATTAA
+SRR015141.215 WICMT-SOLEXA_209LAAAXX_8_1_908_261 length=26
IIIIIIIII*IIIIIII.IIIIII(I
@SRR015141.216 WICMT-SOLEXA_209LAAAXX_8_1_891_564 length=26
TGTCAATCTTTCTCATAATTTTATTT
+SRR015141.216 WICMT-SOLEXA_209LAAAXX_8_1_891_564 length=26
IIIIIIIIIIIIIIIIBII$I(4II(
@SRR015141.217 WICMT-SOLEXA_209LAAAXX_8_1_765_690 length=26
GTGGGTTAAGTCTTTGGAGAAGAAAG
+SRR015141.217 WICMT-SOLEXA_209LAAAXX_8_1_765_690 length=26
IIII3II+<*@D#II"2)=5I.DD4"
@SRR015141.218 WICMT-SOLEXA_209LAAAXX_8_1_894_598 length=26
ATTCACCATCTAAATACTGCTCCCCG
+SRR015141.218 WICMT-SOLEXA_209LAAAXX_8_1_894_598 length=26
IIIIIIIIIIIIIIIIIIIII=III.
@SRR015141.219 WICMT-SOLEXA_209LAAAXX_8_1_877_619 length=26
GACCTGTGAGACCTACTCACATCAAT
+SRR015141.219 WICMT-SOLEXA_209LAAAXX_8_1_877_619 length=26
IIIIIIIIIIC670E?I9=7HII
@SRR015141.234 WICMT-SOLEXA_209LAAAXX_8_1_903_687 length=26
AGGTAAGAGAAATGGCTCCTTTTTTC
+SRR015141.234 WICMT-SOLEXA_209LAAAXX_8_1_903_687 length=26
IIIIIIIIIIIIIIIIIIIIIII.II
@SRR015141.235 WICMT-SOLEXA_209LAAAXX_8_1_904_683 length=26
TATTAATCAGTCATGAAAAGTGATTG
+SRR015141.235 WICMT-SOLEXA_209LAAAXX_8_1_904_683 length=26
IIIIIIIIIIIIIIAIII)IIIIIII
@SRR015141.236 WICMT-SOLEXA_209LAAAXX_8_1_891_796 length=26
GGTCTAAGAGACTGCTGATCCTCTTT
+SRR015141.236 WICMT-SOLEXA_209LAAAXX_8_1_891_796 length=26
IIIIIIIIIIIIIIII<3IHFI5III
@SRR015141.237 WICMT-SOLEXA_209LAAAXX_8_1_917_909 length=26
GTCAATGATGCCAATATGTGGAACAT
+SRR015141.237 WICMT-SOLEXA_209LAAAXX_8_1_917_909 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.238 WICMT-SOLEXA_209LAAAXX_8_1_878_626 length=26
TGCAGCTTACCCACGCCCACTGCAGA
+SRR015141.238 WICMT-SOLEXA_209LAAAXX_8_1_878_626 length=26
IIIIIIIIIIIIIIII>5D6ICE<07
@SRR015141.239 WICMT-SOLEXA_209LAAAXX_8_1_898_878 length=26
TCTGCCTCCAGGTACCTGCATAACCT
+SRR015141.239 WICMT-SOLEXA_209LAAAXX_8_1_898_878 length=26
IIIIIIIIIIIIIIIIIIIIIIII5I
@SRR015141.240 WICMT-SOLEXA_209LAAAXX_8_1_949_517 length=26
GCCTCGAACTCAAAAAGATCCACTCG
+SRR015141.240 WICMT-SOLEXA_209LAAAXX_8_1_949_517 length=26
IIIIIIIIIIIIIIIIIIIIIIIII>
@SRR015141.241 WICMT-SOLEXA_209LAAAXX_8_1_906_958 length=26
GCCNNNNNNNNNNNNNNNNNNNNNNN
+SRR015141.241 WICMT-SOLEXA_209LAAAXX_8_1_906_958 length=26
III!!!!!!!!!!!!!!!!!!!!!!!
@SRR015141.242 WICMT-SOLEXA_209LAAAXX_8_1_878_830 length=26
GATATCCAGCATGAAGGCTCTGCAGT
+SRR015141.242 WICMT-SOLEXA_209LAAAXX_8_1_878_830 length=26
IIIIII/IIII%(@I"")III)DI*-
@SRR015141.243 WICMT-SOLEXA_209LAAAXX_8_1_909_680 length=26
TATGCAGCAGTTGGAGAACTTTGGCT
+SRR015141.243 WICMT-SOLEXA_209LAAAXX_8_1_909_680 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.244 WICMT-SOLEXA_209LAAAXX_8_1_887_568 length=26
AGATCAGAAGTTCAAGGCCAAATCAG
+SRR015141.244 WICMT-SOLEXA_209LAAAXX_8_1_887_568 length=26
IIIIIIIIIIIIGII<);DIIIIEI&
@SRR015141.245 WICMT-SOLEXA_209LAAAXX_8_1_940_311 length=26
CATAGGTTTCTTTGCACATATTATTA
+SRR015141.245 WICMT-SOLEXA_209LAAAXX_8_1_940_311 length=26
IIIIIIIIIII"IIII1I$III*II'
@SRR015141.246 WICMT-SOLEXA_209LAAAXX_8_1_936_834 length=26
TCAATGACCTTTGCTCTCTGGCCCAT
+SRR015141.246 WICMT-SOLEXA_209LAAAXX_8_1_936_834 length=26
IIIIIIIIIIIIII;IIIII5IIIII
@SRR015141.247 WICMT-SOLEXA_209LAAAXX_8_1_935_573 length=26
AATACACACTTTAGGACGTGAAATAT
+SRR015141.247 WICMT-SOLEXA_209LAAAXX_8_1_935_573 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.248 WICMT-SOLEXA_209LAAAXX_8_1_907_322 length=26
ATGACGTGGAATATGGCAAGAAAACT
+SRR015141.248 WICMT-SOLEXA_209LAAAXX_8_1_907_322 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.249 WICMT-SOLEXA_209LAAAXX_8_1_894_432 length=26
TGATGCTCCCATCCTCTGCTGGTTTT
+SRR015141.249 WICMT-SOLEXA_209LAAAXX_8_1_894_432 length=26
IIIIIIIIIIIIIIIIIIIII"I$II
@SRR015141.250 WICMT-SOLEXA_209LAAAXX_8_1_951_749 length=26
GATGGCTTCATGGTCCCCAAGTGATT
+SRR015141.250 WICMT-SOLEXA_209LAAAXX_8_1_951_749 length=26
IIIIIIIIIII/IIIIIIIII#III"
@SRR015141.251 WICMT-SOLEXA_209LAAAXX_8_1_808_645 length=26
GGTCAACCCTAGAAGTATTCTTCCAT
+SRR015141.251 WICMT-SOLEXA_209LAAAXX_8_1_808_645 length=26
IIIIIIIIIIIIIIIIIII5II(/A"
@SRR015141.252 WICMT-SOLEXA_209LAAAXX_8_1_895_371 length=26
TTCCACCTTTTTCAGTTGTCCTCTCC
+SRR015141.252 WICMT-SOLEXA_209LAAAXX_8_1_895_371 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.253 WICMT-SOLEXA_209LAAAXX_8_1_896_517 length=26
GAACTCAATTACTCTGACCAAGATGT
+SRR015141.253 WICMT-SOLEXA_209LAAAXX_8_1_896_517 length=26
IIIIIIIIIIIIIIIIIIFIIIIII#
@SRR015141.254 WICMT-SOLEXA_209LAAAXX_8_1_915_852 length=26
TTAAAGTCAGAATGGTGCTTCTGACA
+SRR015141.254 WICMT-SOLEXA_209LAAAXX_8_1_915_852 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.255 WICMT-SOLEXA_209LAAAXX_8_1_885_503 length=26
GTGCAGAGCCCCCTGGGGGGCACTAC
+SRR015141.255 WICMT-SOLEXA_209LAAAXX_8_1_885_503 length=26
IIIIIIIIDII6.ICB7/,,6.0II#
@SRR015141.256 WICMT-SOLEXA_209LAAAXX_8_1_793_732 length=26
GTGGGGGGAGGGGAGCGGCAGAGATG
+SRR015141.256 WICMT-SOLEXA_209LAAAXX_8_1_793_732 length=26
IIIIIIIIII9I9IDA;I(F8'"";,
@SRR015141.257 WICMT-SOLEXA_209LAAAXX_8_1_910_895 length=26
TCCGACATTGAATAATAAGGTATATA
+SRR015141.257 WICMT-SOLEXA_209LAAAXX_8_1_910_895 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.258 WICMT-SOLEXA_209LAAAXX_8_1_908_579 length=26
TAGCTGTCTTCAGATATACTAGAAGA
+SRR015141.258 WICMT-SOLEXA_209LAAAXX_8_1_908_579 length=26
IIIIIIIIIIIIIIIGI%I'/IIII&
@SRR015141.259 WICMT-SOLEXA_209LAAAXX_8_1_927_359 length=26
ACCAGCGGGTGAAATACACCAAGGAC
+SRR015141.259 WICMT-SOLEXA_209LAAAXX_8_1_927_359 length=26
IIIIIIIIIIIIIIII"IIIIIIIII
@SRR015141.260 WICMT-SOLEXA_209LAAAXX_8_1_903_771 length=26
GACAGAGCTCCCTGTGGCACAAATGT
+SRR015141.260 WICMT-SOLEXA_209LAAAXX_8_1_903_771 length=26
IIIIIIIIIIIIIIIIIIIIIIIID-
@SRR015141.261 WICMT-SOLEXA_209LAAAXX_8_1_904_365 length=26
AGAAAGAACCTTACTCCTTGCTTAGG
+SRR015141.261 WICMT-SOLEXA_209LAAAXX_8_1_904_365 length=26
IIIIIIIIIIIIIIIIIIIIIIII+&
@SRR015141.262 WICMT-SOLEXA_209LAAAXX_8_1_892_532 length=26
TGGGTACACCAGAGAATTTATGTACA
+SRR015141.262 WICMT-SOLEXA_209LAAAXX_8_1_892_532 length=26
IIIIIIIIIIIII?IIIII:I$$+/#
@SRR015141.263 WICMT-SOLEXA_209LAAAXX_8_1_931_560 length=26
GCTTAGTCATTTATAGGTGAGAGTGC
+SRR015141.263 WICMT-SOLEXA_209LAAAXX_8_1_931_560 length=26
IIIIIIIIIIIIIIIIIIIIIIIIDI
@SRR015141.264 WICMT-SOLEXA_209LAAAXX_8_1_908_688 length=26
GCCAGTCAGGATATACCTATTTTAAG
+SRR015141.264 WICMT-SOLEXA_209LAAAXX_8_1_908_688 length=26
IIIIIIIII2I8II.III"IIII(II
@SRR015141.265 WICMT-SOLEXA_209LAAAXX_8_1_901_697 length=26
TAAATGTGTGGAAAGCCGCCTAGATT
+SRR015141.265 WICMT-SOLEXA_209LAAAXX_8_1_901_697 length=26
IIIIIIIIIIIIIIIII9IIIIIIII
@SRR015141.266 WICMT-SOLEXA_209LAAAXX_8_1_941_840 length=26
GGTTTTTAGTGATTTTTTAATTTTTC
+SRR015141.266 WICMT-SOLEXA_209LAAAXX_8_1_941_840 length=26
IIIIIIIIIIIIIIIIII'IIIIII5
@SRR015141.267 WICMT-SOLEXA_209LAAAXX_8_1_831_726 length=26
GGACCCTTCCAGGTATCTCTGGCTAT
+SRR015141.267 WICMT-SOLEXA_209LAAAXX_8_1_831_726 length=26
IIIIIIIIIIIIIIIIIIII.%CI9I
@SRR015141.268 WICMT-SOLEXA_209LAAAXX_8_1_635_696 length=26
GTGAGTGTCTCTGTTTGTTCTTAATT
+SRR015141.268 WICMT-SOLEXA_209LAAAXX_8_1_635_696 length=26
IIEI#"I?"-D'-I*I$I)'II<"IIII0
@SRR015141.291 WICMT-SOLEXA_209LAAAXX_8_1_940_515 length=26
TGACAGGAAAAGTATATTTCTGTCAT
+SRR015141.291 WICMT-SOLEXA_209LAAAXX_8_1_940_515 length=26
IIIIIIIIIII;IIIIII.I;:3I7)
@SRR015141.292 WICMT-SOLEXA_209LAAAXX_8_1_878_787 length=26
GAATTTTACGTAAGACTAATCTTTTA
+SRR015141.292 WICMT-SOLEXA_209LAAAXX_8_1_878_787 length=26
IIIIIIIIIIIII6I>IIIIIII?(&I(7I4%
@SRR015141.309 WICMT-SOLEXA_209LAAAXX_8_1_929_554 length=26
TTATTCTAAGATGTTAATTTTTTAAA
+SRR015141.309 WICMT-SOLEXA_209LAAAXX_8_1_929_554 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.310 WICMT-SOLEXA_209LAAAXX_8_1_814_712 length=26
GTTGGCCAACAGGGAAATAGCATTCA
+SRR015141.310 WICMT-SOLEXA_209LAAAXX_8_1_814_712 length=26
I1IIIIIIIC:=F"IIIIGI5III1;
@SRR015141.311 WICMT-SOLEXA_209LAAAXX_8_1_811_746 length=26
GAAAATGAGAAACATCCACTTGACGA
+SRR015141.311 WICMT-SOLEXA_209LAAAXX_8_1_811_746 length=26
IIIIIIIIIIIICIII:I5II?B0:9
@SRR015141.312 WICMT-SOLEXA_209LAAAXX_8_1_810_591 length=26
GGTTAGGGTGAGGTTAGGGTTAAGTT
+SRR015141.312 WICMT-SOLEXA_209LAAAXX_8_1_810_591 length=26
IIIIIIII7IIIIIII4I2III+3"I
@SRR015141.313 WICMT-SOLEXA_209LAAAXX_8_1_931_836 length=26
TATGCCCCTTGCGTGTTTGGCAAATT
+SRR015141.313 WICMT-SOLEXA_209LAAAXX_8_1_931_836 length=26
IIIIII(#II5*II0IIIII/I-III
@SRR015141.314 WICMT-SOLEXA_209LAAAXX_8_1_819_424 length=26
GGAAAGCAAACAGGAAGTCATGGCAC
+SRR015141.314 WICMT-SOLEXA_209LAAAXX_8_1_819_424 length=26
IIIIIIIIIIIIIIIIII>#II/IC$
@SRR015141.315 WICMT-SOLEXA_209LAAAXX_8_1_870_741 length=26
GGATGGAACACAGGGCCCTCAATTGT
+SRR015141.315 WICMT-SOLEXA_209LAAAXX_8_1_870_741 length=26
IIIIIIIIIIIIIII,III753I#-$
@SRR015141.316 WICMT-SOLEXA_209LAAAXX_8_1_884_113 length=26
TGTTTAAAAATGAACAGTGACAAAGT
+SRR015141.316 WICMT-SOLEXA_209LAAAXX_8_1_884_113 length=26
IIIIIIIIIIIIIIIIII2IIIIICI
@SRR015141.317 WICMT-SOLEXA_209LAAAXX_8_1_932_722 length=26
AGATGACTACTCACAAAAGCCCCCTC
+SRR015141.317 WICMT-SOLEXA_209LAAAXX_8_1_932_722 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.318 WICMT-SOLEXA_209LAAAXX_8_1_884_701 length=26
AAGCAGGAGTGAGAAGCCAGTCACAT
+SRR015141.318 WICMT-SOLEXA_209LAAAXX_8_1_884_701 length=26
IIIIIII@IIIEIDI7;CDAI0*.)I
@SRR015141.319 WICMT-SOLEXA_209LAAAXX_8_1_917_218 length=26
GGAGGTCAGTAGTCATGAAGGTCAGA
+SRR015141.319 WICMT-SOLEXA_209LAAAXX_8_1_917_218 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.320 WICMT-SOLEXA_209LAAAXX_8_1_762_719 length=26
GTAAGGAGAAAGTAAGAAAGACAACA
+SRR015141.320 WICMT-SOLEXA_209LAAAXX_8_1_762_719 length=26
IIIIIIIIIIIIIIIIIIFIIDI;-?
@SRR015141.321 WICMT-SOLEXA_209LAAAXX_8_1_773_676 length=26
GGCTGACCGTTTGGCACTGGGCAACC
+SRR015141.321 WICMT-SOLEXA_209LAAAXX_8_1_773_676 length=26
IIIIIIIIIIII@HFI5I/:)558*-
@SRR015141.322 WICMT-SOLEXA_209LAAAXX_8_1_910_811 length=26
GTCCAACGAGTATGTGCGTGCACACA
+SRR015141.322 WICMT-SOLEXA_209LAAAXX_8_1_910_811 length=26
IIIIIIIIIIIII;IIIIIIIIIIII
@SRR015141.323 WICMT-SOLEXA_209LAAAXX_8_1_547_913 length=26
GTGGATGTTTCTCATTTTCCATTATT
+SRR015141.323 WICMT-SOLEXA_209LAAAXX_8_1_547_913 length=26
IIIIIIIIIIII(+IIII%,/I-#II
@SRR015141.324 WICMT-SOLEXA_209LAAAXX_8_1_948_365 length=26
AGCAAAAATCTTGTTGAAATCATTTG
+SRR015141.324 WICMT-SOLEXA_209LAAAXX_8_1_948_365 length=26
I(-II.III)IIIEIIIII*IIIIII
@SRR015141.325 WICMT-SOLEXA_209LAAAXX_8_1_883_525 length=26
AAGCTGAACTCACATACATTATAACT
+SRR015141.325 WICMT-SOLEXA_209LAAAXX_8_1_883_525 length=26
IIIIIIIIIIIIHIII:IIIIIII56
@SRR015141.326 WICMT-SOLEXA_209LAAAXX_8_1_889_539 length=26
TTGGTAGAACTGTTTATGAAGTATTA
+SRR015141.326 WICMT-SOLEXA_209LAAAXX_8_1_889_539 length=26
IIIIIIIIIIIAIIII(8;I/#4II$
@SRR015141.327 WICMT-SOLEXA_209LAAAXX_8_1_922_269 length=26
AGCCCAATGTGGGTTGCAGAGATGTA
+SRR015141.327 WICMT-SOLEXA_209LAAAXX_8_1_922_269 length=26
I.I"I:IIIIIIIII7IIIIAI74III"+
@SRR015141.362 WICMT-SOLEXA_209LAAAXX_8_1_829_694 length=26
GATCTGTCTGCTGAGACTTGCTACCT
+SRR015141.362 WICMT-SOLEXA_209LAAAXX_8_1_829_694 length=26
IIIIIIIIIIII'D8G4II'II5+3I
@SRR015141.363 WICMT-SOLEXA_209LAAAXX_8_1_884_507 length=26
AATAATTCATATTAGTGAGAGACACT
+SRR015141.363 WICMT-SOLEXA_209LAAAXX_8_1_884_507 length=26
IIIII?I&I/"8=-&3I67<"I,'*I
@SRR015141.364 WICMT-SOLEXA_209LAAAXX_8_1_925_391 length=26
TTAACTCCTGAACTCAGAAGGGCTGT
+SRR015141.364 WICMT-SOLEXA_209LAAAXX_8_1_925_391 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.365 WICMT-SOLEXA_209LAAAXX_8_1_880_255 length=26
GGATTCATGGAAAGATAATGTGTGAA
+SRR015141.365 WICMT-SOLEXA_209LAAAXX_8_1_880_255 length=26
IIIIIIIIIIIIIIIIIIIII@I.>%
@SRR015141.366 WICMT-SOLEXA_209LAAAXX_8_1_831_862 length=26
GGATTATTTGGTTTCACATTTGCTTT
+SRR015141.366 WICMT-SOLEXA_209LAAAXX_8_1_831_862 length=26
IIIIIIIIIIIIIIIIII"II..III
@SRR015141.367 WICMT-SOLEXA_209LAAAXX_8_1_798_870 length=26
GAACCAGTTTAAGTGGAATGGCAAAG
+SRR015141.367 WICMT-SOLEXA_209LAAAXX_8_1_798_870 length=26
IIIIIIIIIIIIII5/III7+IIII$
@SRR015141.368 WICMT-SOLEXA_209LAAAXX_8_1_931_874 length=26
GTAATGCAAGTGGTGTCTAGGATGAA
+SRR015141.368 WICMT-SOLEXA_209LAAAXX_8_1_931_874 length=26
IIIIIIIIIII+=IIIII%I@II)?I
@SRR015141.369 WICMT-SOLEXA_209LAAAXX_8_1_929_225 length=26
ACGTTGCTGTTTGCCTGGTTCATTTT
+SRR015141.369 WICMT-SOLEXA_209LAAAXX_8_1_929_225 length=26
IIIIIIIIIIIIIIIII(IIIIIIII
@SRR015141.370 WICMT-SOLEXA_209LAAAXX_8_1_881_361 length=26
AAGCACCCACTCTCCGGTAGTAATCC
+SRR015141.370 WICMT-SOLEXA_209LAAAXX_8_1_881_361 length=26
IIIIIIIBIIIIIIA/III,#III<;
@SRR015141.371 WICMT-SOLEXA_209LAAAXX_8_1_920_223 length=26
CCAGGAATGTTATCTTTGCTTTTTTT
+SRR015141.371 WICMT-SOLEXA_209LAAAXX_8_1_920_223 length=26
IIIIIIIIIIIIIIIIIIIIIIIII;
@SRR015141.372 WICMT-SOLEXA_209LAAAXX_8_1_913_890 length=26
AATTTTACCCGAGTAATATTTTAACA
+SRR015141.372 WICMT-SOLEXA_209LAAAXX_8_1_913_890 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.373 WICMT-SOLEXA_209LAAAXX_8_1_795_633 length=26
GACGACTTGAAAAATGACGAAATCAC
+SRR015141.373 WICMT-SOLEXA_209LAAAXX_8_1_795_633 length=26
IIIIIIIIIIIIIIIIIIIIIII=I3
@SRR015141.374 WICMT-SOLEXA_209LAAAXX_8_1_894_202 length=26
ACTGAAGGACGTTGAATATGGCAAGA
+SRR015141.374 WICMT-SOLEXA_209LAAAXX_8_1_894_202 length=26
IIII9IIIIIIIII3IIII+$III:"
@SRR015141.375 WICMT-SOLEXA_209LAAAXX_8_1_898_262 length=26
CATGCCTCCTGGACATGGTCACCACT
+SRR015141.375 WICMT-SOLEXA_209LAAAXX_8_1_898_262 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.376 WICMT-SOLEXA_209LAAAXX_8_1_919_570 length=26
GTCGGGCTGCAGAAGCTGTGGGAGTG
+SRR015141.376 WICMT-SOLEXA_209LAAAXX_8_1_919_570 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.377 WICMT-SOLEXA_209LAAAXX_8_1_858_424 length=26
GTGATTTCGTCATTTTTCAAGTCTTC
+SRR015141.377 WICMT-SOLEXA_209LAAAXX_8_1_858_424 length=26
IIIIIIIIIIIIIIIIIIII'I3DI0
@SRR015141.378 WICMT-SOLEXA_209LAAAXX_8_1_927_567 length=26
TCAAGGACGTTTTTCCATTTGACCAT
+SRR015141.378 WICMT-SOLEXA_209LAAAXX_8_1_927_567 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.379 WICMT-SOLEXA_209LAAAXX_8_1_881_891 length=26
TCTAGGCCTGGCTGGTAGCTGCCCAC
+SRR015141.379 WICMT-SOLEXA_209LAAAXX_8_1_881_891 length=26
IIIIIIIIIIICIIII6I:I'>0I7#
@SRR015141.380 WICMT-SOLEXA_209LAAAXX_8_1_725_631 length=26
GTACAAATAACATGACCAAAAGGATC
+SRR015141.380 WICMT-SOLEXA_209LAAAXX_8_1_725_631 length=26
IIIIIIIIIIIIIIIIIIIII=2II7
@SRR015141.381 WICMT-SOLEXA_209LAAAXX_8_1_916_793 length=26
AAGCATTACATCATCACACTTCTTTT
+SRR015141.381 WICMT-SOLEXA_209LAAAXX_8_1_916_793 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.382 WICMT-SOLEXA_209LAAAXX_8_1_944_695 length=26
GGTCTGTATAGAGCCATACACTGCTC
+SRR015141.382 WICMT-SOLEXA_209LAAAXX_8_1_944_695 length=26
IIIIIIIIIIIIII8*"G4A;I+II,
@SRR015141.383 WICMT-SOLEXA_209LAAAXX_8_1_876_905 length=26
GAAGATCAAACCCAAGACATGGCAAG
+SRR015141.383 WICMT-SOLEXA_209LAAAXX_8_1_876_905 length=26
IIIIIIIIIIIIIII7IIII8@?II0
@SRR015141.384 WICMT-SOLEXA_209LAAAXX_8_1_894_327 length=26
ACGTATCCATTATGACTCTTAATATC
+SRR015141.384 WICMT-SOLEXA_209LAAAXX_8_1_894_327 length=26
I:I>I#I1II?IIII6III/IIIIII
@SRR015141.385 WICMT-SOLEXA_209LAAAXX_8_1_879_267 length=26
GAGGGTGTCTGTGTCAACTTCCCATT
+SRR015141.385 WICMT-SOLEXA_209LAAAXX_8_1_879_267 length=26
IIIIIIIIIIIIIIFDIFII8IIAII
@SRR015141.386 WICMT-SOLEXA_209LAAAXX_8_1_892_849 length=26
GAATTAAAAATGACCAGAACTTCTTT
+SRR015141.386 WICMT-SOLEXA_209LAAAXX_8_1_892_849 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.387 WICMT-SOLEXA_209LAAAXX_8_1_855_718 length=26
GAGGTGGTGAGGGAGAGCGATGACGA
+SRR015141.387 WICMT-SOLEXA_209LAAAXX_8_1_855_718 length=26
IIIIIIIIIEI7IDIAH0IAI3=:)$
@SRR015141.388 WICMT-SOLEXA_209LAAAXX_8_1_875_467 length=26
AGTCCTAATAAGAAGAAATGCTCTCA
+SRR015141.388 WICMT-SOLEXA_209LAAAXX_8_1_875_467 length=26
IIIIIIIIIIIBII*IIIII@I7I7I
@SRR015141.389 WICMT-SOLEXA_209LAAAXX_8_1_887_278 length=26
CATGTGTATGAAGTTTGTATTTTATC
+SRR015141.389 WICMT-SOLEXA_209LAAAXX_8_1_887_278 length=26
IIIIIIIIIIII0I&I;III:IGF68
@SRR015141.390 WICMT-SOLEXA_209LAAAXX_8_1_918_397 length=26
GGACTGAGGATCAGCTCCGCCTCCTG
+SRR015141.390 WICMT-SOLEXA_209LAAAXX_8_1_918_397 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.391 WICMT-SOLEXA_209LAAAXX_8_1_923_800 length=26
GCTTTCTTGTAGACACTGTTTTCCCT
+SRR015141.391 WICMT-SOLEXA_209LAAAXX_8_1_923_800 length=26
IIIIIIIIIII@IIIIIIIIII'I$I
@SRR015141.392 WICMT-SOLEXA_209LAAAXX_8_1_899_815 length=26
TCCCCGGGGCACACACTTTGCTTATC
+SRR015141.392 WICMT-SOLEXA_209LAAAXX_8_1_899_815 length=26
IIIIIIIIIIIIIIIIIIIIII$I&I
@SRR015141.393 WICMT-SOLEXA_209LAAAXX_8_1_903_347 length=26
AAAACCAGTCTAATACAAGGCCTGCT
+SRR015141.393 WICMT-SOLEXA_209LAAAXX_8_1_903_347 length=26
IIFIII>IIIIIIIIII(IIAIIIII
@SRR015141.394 WICMT-SOLEXA_209LAAAXX_8_1_929_175 length=26
GGCGAGAAAACTGAAAATCACGGAAA
+SRR015141.394 WICMT-SOLEXA_209LAAAXX_8_1_929_175 length=26
IIIIIIIIIIIIIIIIIIIIII-III
@SRR015141.395 WICMT-SOLEXA_209LAAAXX_8_1_808_675 length=26
GCAGTCAGTGCTCTTAGCCACTGAGC
+SRR015141.395 WICMT-SOLEXA_209LAAAXX_8_1_808_675 length=26
IIIIIIIIIIII@III%2HIII-<4#
@SRR015141.396 WICMT-SOLEXA_209LAAAXX_8_1_838_226 length=26
GTATTATTTTTAAGTCTCTATTGTAA
+SRR015141.396 WICMT-SOLEXA_209LAAAXX_8_1_838_226 length=26
IIIIIIIIIIIIIIIIIIII$I(",=
@SRR015141.397 WICMT-SOLEXA_209LAAAXX_8_1_863_733 length=26
GGATGGACATCTGTGGTGGATTCTTT
+SRR015141.397 WICMT-SOLEXA_209LAAAXX_8_1_863_733 length=26
II3II@.$9III*'A5I22$A*/I&(
@SRR015141.398 WICMT-SOLEXA_209LAAAXX_8_1_955_585 length=26
GTACTTCTTTCTTCTTTTTTTATTTT
+SRR015141.398 WICMT-SOLEXA_209LAAAXX_8_1_955_585 length=26
IIIIIIIIIIIII2I*IIIIIIIIII
@SRR015141.399 WICMT-SOLEXA_209LAAAXX_8_1_885_839 length=26
GCTCCCATAGATTCATGTGTTTTAAC
+SRR015141.399 WICMT-SOLEXA_209LAAAXX_8_1_885_839 length=26
IIIIIIIIGIIIIIIIAI'III&??/
@SRR015141.400 WICMT-SOLEXA_209LAAAXX_8_1_882_82 length=26
GGTTGATTTTAACCCCTGAGTTTGAT
+SRR015141.400 WICMT-SOLEXA_209LAAAXX_8_1_882_82 length=26
IIIIIIIIIIIIIIIIIIIHIIIDII
@SRR015141.401 WICMT-SOLEXA_209LAAAXX_8_1_944_730 length=26
GTCCTCTGGAAAAAGAGCCAGTACTC
+SRR015141.401 WICMT-SOLEXA_209LAAAXX_8_1_944_730 length=26
IIIIIIIIIIIIIIII'IIIIII1II
@SRR015141.402 WICMT-SOLEXA_209LAAAXX_8_1_920_348 length=26
TGAGACCCTATCACAGTAGTTCTCAA
+SRR015141.402 WICMT-SOLEXA_209LAAAXX_8_1_920_348 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.403 WICMT-SOLEXA_209LAAAXX_8_1_908_504 length=26
AGCATGGATCTGATTATAAGTCTATG
+SRR015141.403 WICMT-SOLEXA_209LAAAXX_8_1_908_504 length=26
IIIIII"IIIIIIIIII#IIIIIII+
@SRR015141.404 WICMT-SOLEXA_209LAAAXX_8_1_929_207 length=26
GGATTTGATGATTTCTCTTCAACTAA
+SRR015141.404 WICMT-SOLEXA_209LAAAXX_8_1_929_207 length=26
II(IIIII$$5III+I"I#II$,HII
@SRR015141.405 WICMT-SOLEXA_209LAAAXX_8_1_875_425 length=26
GCGAGGAAAACTGAAAAAGGTGGAAA
+SRR015141.405 WICMT-SOLEXA_209LAAAXX_8_1_875_425 length=26
IIIIIIIIIIIIIIIIIIIIIIBIII
@SRR015141.406 WICMT-SOLEXA_209LAAAXX_8_1_906_484 length=26
ATTAGATATTCTGATAGCAAATATCA
+SRR015141.406 WICMT-SOLEXA_209LAAAXX_8_1_906_484 length=26
IIIIIIIIIIIIIIIIIIIII.IIII
@SRR015141.407 WICMT-SOLEXA_209LAAAXX_8_1_797_649 length=26
GCTAGCCCTTTGTTTTGTGATTTTAT
+SRR015141.407 WICMT-SOLEXA_209LAAAXX_8_1_797_649 length=26
II,III$IHI(/)-II'-'37'I"G5
@SRR015141.408 WICMT-SOLEXA_209LAAAXX_8_1_894_572 length=26
CTCCCAGGCAGCTCATCTAACCTAAT
+SRR015141.408 WICMT-SOLEXA_209LAAAXX_8_1_894_572 length=26
IIIIIIIIIIIIIIIIIIII24IIII
@SRR015141.409 WICMT-SOLEXA_209LAAAXX_8_1_924_689 length=26
GCTCACAGTCATCTATAAGATGTTAC
+SRR015141.409 WICMT-SOLEXA_209LAAAXX_8_1_924_689 length=26
IIIIIIIIIIIIIIIIIIIII:0@II
@SRR015141.410 WICMT-SOLEXA_209LAAAXX_8_1_841_821 length=26
GGCTTGGAGATCCTTATCTTGATCTT
+SRR015141.410 WICMT-SOLEXA_209LAAAXX_8_1_841_821 length=26
IIIIIIIIIIIIIIIIIII%)IIIII
@SRR015141.411 WICMT-SOLEXA_209LAAAXX_8_1_944_925 length=26
TGTGGCTCAGGCTGAACCTGCATTCA
+SRR015141.411 WICMT-SOLEXA_209LAAAXX_8_1_944_925 length=26
IIIIIIIIIIIII0IIIIIFIIII(I
@SRR015141.412 WICMT-SOLEXA_209LAAAXX_8_1_900_911 length=26
CAGGTAATCGTTATTTGTTTTCTTGT
+SRR015141.412 WICMT-SOLEXA_209LAAAXX_8_1_900_911 length=26
.I39II@II+II(IIAIIIIIEII0I
@SRR015141.413 WICMT-SOLEXA_209LAAAXX_8_1_760_496 length=26
GTTGTTTGCTCATCTGTCTTCCTCCT
+SRR015141.413 WICMT-SOLEXA_209LAAAXX_8_1_760_496 length=26
IIIIIIIIIIIIIBI(IIIIE0I-&I
@SRR015141.414 WICMT-SOLEXA_209LAAAXX_8_1_909_553 length=26
TCAGGGCTTAAGCAGAGACTTTAAGA
+SRR015141.414 WICMT-SOLEXA_209LAAAXX_8_1_909_553 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.415 WICMT-SOLEXA_209LAAAXX_8_1_941_538 length=26
AATTCCCATGTTTCTTCTAATTTTAT
+SRR015141.415 WICMT-SOLEXA_209LAAAXX_8_1_941_538 length=26
IIIIIIIIIIIIIIIIIDIIIIIIII
@SRR015141.416 WICMT-SOLEXA_209LAAAXX_8_1_909_709 length=26
TTGGTGTACCCAGTTTGGATGGTTCA
+SRR015141.416 WICMT-SOLEXA_209LAAAXX_8_1_909_709 length=26
IIIIIIII"IIIIII)I'IIIIIIII
@SRR015141.417 WICMT-SOLEXA_209LAAAXX_8_1_709_701 length=26
GAATCTCAGGTGCAGAAGATTCCATA
+SRR015141.417 WICMT-SOLEXA_209LAAAXX_8_1_709_701 length=26
IIIIIIIIIIIIIIIIIIIIII5DII
@SRR015141.418 WICMT-SOLEXA_209LAAAXX_8_1_667_695 length=26
GTGAGCAGGTGGGCTAGCATTACTTG
+SRR015141.418 WICMT-SOLEXA_209LAAAXX_8_1_667_695 length=26
IIIIIIIII)III6II3;)II0"I""
@SRR015141.419 WICMT-SOLEXA_209LAAAXX_8_1_911_307 length=26
GACAGAGGGAGAATGAGGTCAGCCAG
+SRR015141.419 WICMT-SOLEXA_209LAAAXX_8_1_911_307 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.420 WICMT-SOLEXA_209LAAAXX_8_1_876_593 length=26
GTATGGCAGGAACATTTAGTATTATG
+SRR015141.420 WICMT-SOLEXA_209LAAAXX_8_1_876_593 length=26
I$IIII&"%I"-HII)6,"4"II=$#
@SRR015141.421 WICMT-SOLEXA_209LAAAXX_8_1_888_488 length=26
TGTTGTCTTCTTTCCCTTAGATTTTT
+SRR015141.421 WICMT-SOLEXA_209LAAAXX_8_1_888_488 length=26
IIIIIIIII/IID?-7II;6DIII1&
@SRR015141.422 WICMT-SOLEXA_209LAAAXX_8_1_849_618 length=26
GACATGATGTTTTTCTATACTGTTGT
+SRR015141.422 WICMT-SOLEXA_209LAAAXX_8_1_849_618 length=26
IIIIIIIII1IIII1)@II%I3I*&=
@SRR015141.423 WICMT-SOLEXA_209LAAAXX_8_1_898_176 length=26
AAACCTGGAACAAACTGGAAATCTCT
+SRR015141.423 WICMT-SOLEXA_209LAAAXX_8_1_898_176 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.424 WICMT-SOLEXA_209LAAAXX_8_1_915_459 length=26
TGAGGTACCTCACAGAGAGCTACCTG
+SRR015141.424 WICMT-SOLEXA_209LAAAXX_8_1_915_459 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.425 WICMT-SOLEXA_209LAAAXX_8_1_893_288 length=26
GGGTATCTAAGGTACTGAAGTCATTT
+SRR015141.425 WICMT-SOLEXA_209LAAAXX_8_1_893_288 length=26
II$8GIIIIIIIIIIIIII2=,IIII
@SRR015141.426 WICMT-SOLEXA_209LAAAXX_8_1_903_500 length=26
AATGAATGTGGTAAAGCCTTTGCATA
+SRR015141.426 WICMT-SOLEXA_209LAAAXX_8_1_903_500 length=26
IIIIIIIIIIIIIII.IIIIIIIIII
@SRR015141.427 WICMT-SOLEXA_209LAAAXX_8_1_891_336 length=26
TGAATCTTCCATGTGTGCCTGTATTT
+SRR015141.427 WICMT-SOLEXA_209LAAAXX_8_1_891_336 length=26
IIIIIIIIID'I1&*I+III?""FI/
@SRR015141.428 WICMT-SOLEXA_209LAAAXX_8_1_919_99 length=26
GGGTAATGTGCTATATGATTATATAC
+SRR015141.428 WICMT-SOLEXA_209LAAAXX_8_1_919_99 length=26
IIII%I*IIIIIIIII"%"III4I/$
@SRR015141.429 WICMT-SOLEXA_209LAAAXX_8_1_876_328 length=26
AGATCACTGTTTGCAGCCAGATCACT
+SRR015141.429 WICMT-SOLEXA_209LAAAXX_8_1_876_328 length=26
IIIIIIIIIIIIIIIIIDIIIIBIAI
@SRR015141.430 WICMT-SOLEXA_209LAAAXX_8_1_770_277 length=26
GGTTTTGGTTTTTTTTTTTTTTATTT
+SRR015141.430 WICMT-SOLEXA_209LAAAXX_8_1_770_277 length=26
IIIIIIIIIIIIIIIII+IIIIIIII
@SRR015141.431 WICMT-SOLEXA_209LAAAXX_8_1_864_413 length=26
GTTCTCCTGCCTCAGCTTCCCAAATA
+SRR015141.431 WICMT-SOLEXA_209LAAAXX_8_1_864_413 length=26
IIIIIIIIIIIIIIIIIIIIIIHIII
@SRR015141.432 WICMT-SOLEXA_209LAAAXX_8_1_923_585 length=26
ACAAAGAAGTAGGTGCTGGCTCCCAC
+SRR015141.432 WICMT-SOLEXA_209LAAAXX_8_1_923_585 length=26
IIII;IIIIIIIIIIIIIIIIIIIIC
@SRR015141.433 WICMT-SOLEXA_209LAAAXX_8_1_915_177 length=26
ACTCAGCCTCAGCCTGGGATAGTGCT
+SRR015141.433 WICMT-SOLEXA_209LAAAXX_8_1_915_177 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.434 WICMT-SOLEXA_209LAAAXX_8_1_920_886 length=26
GCGAAGGGAAGGGGATATTTCGGAAC
+SRR015141.434 WICMT-SOLEXA_209LAAAXX_8_1_920_886 length=26
I1I6IIIIIIIIIIII*:-I>I9+I0
@SRR015141.435 WICMT-SOLEXA_209LAAAXX_8_1_918_782 length=26
GTGTGGAAAAATCTTTGATTTTTATT
+SRR015141.435 WICMT-SOLEXA_209LAAAXX_8_1_918_782 length=26
IIIIIIIIIII2+II3IIIIIIBIII
@SRR015141.436 WICMT-SOLEXA_209LAAAXX_8_1_914_714 length=26
CGGCGGCAATTGTTGTATTTTCTCTT
+SRR015141.436 WICMT-SOLEXA_209LAAAXX_8_1_914_714 length=26
7III9III?6II)II%III*"=I%I1
@SRR015141.437 WICMT-SOLEXA_209LAAAXX_8_1_892_618 length=26
CTAAAATAGTTACAATGATTTATTAC
+SRR015141.437 WICMT-SOLEXA_209LAAAXX_8_1_892_618 length=26
IIBFI68*IEIIII"I3CII"(?I""
@SRR015141.438 WICMT-SOLEXA_209LAAAXX_8_1_947_603 length=26
TGGCAGCTTCTCGGAACTTTCCGCAT
+SRR015141.438 WICMT-SOLEXA_209LAAAXX_8_1_947_603 length=26
IIIIIIIIIIII6IIIII+III'IH9
@SRR015141.439 WICMT-SOLEXA_209LAAAXX_8_1_815_778 length=26
GGATGGACCATGTAGAGACTGCCATA
+SRR015141.439 WICMT-SOLEXA_209LAAAXX_8_1_815_778 length=26
IIIIIIIIIIIIIIII7IFII/7II@
@SRR015141.440 WICMT-SOLEXA_209LAAAXX_8_1_540_910 length=26
GAAAATGTGGTAAATCTACATAATGG
+SRR015141.440 WICMT-SOLEXA_209LAAAXX_8_1_540_910 length=26
IIIIIII.II%I%IIII#.$&?IB*"
@SRR015141.441 WICMT-SOLEXA_209LAAAXX_8_1_892_961 length=26
TCTNNNNNNNNNNNNNNNNNNNNNNN
+SRR015141.441 WICMT-SOLEXA_209LAAAXX_8_1_892_961 length=26
III!!!!!!!!!!!!!!!!!!!!!!!
@SRR015141.442 WICMT-SOLEXA_209LAAAXX_8_1_756_462 length=26
GATCATTTCTGTTCCTAACACATAGT
+SRR015141.442 WICMT-SOLEXA_209LAAAXX_8_1_756_462 length=26
IIIIIIIIIIIIII50*3II
@SRR015141.444 WICMT-SOLEXA_209LAAAXX_8_1_900_605 length=26
AATCTCTAGTCTCACCAGAGAGAGAA
+SRR015141.444 WICMT-SOLEXA_209LAAAXX_8_1_900_605 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.445 WICMT-SOLEXA_209LAAAXX_8_1_803_708 length=26
GGGCTTCTTGGATGGGAGCCTAGTTG
+SRR015141.445 WICMT-SOLEXA_209LAAAXX_8_1_803_708 length=26
IIIIIIIIIIIII,-2.,.II@0I$+
@SRR015141.446 WICMT-SOLEXA_209LAAAXX_8_1_789_680 length=26
GGCTGAGCTAAGTCAAGAAGACATCT
+SRR015141.446 WICMT-SOLEXA_209LAAAXX_8_1_789_680 length=26
IIIIIIIIIIIIIIIIIGI>IB8I?I
@SRR015141.447 WICMT-SOLEXA_209LAAAXX_8_1_937_229 length=26
GACCTTCCTGACGTCTCCAGGATGGA
+SRR015141.447 WICMT-SOLEXA_209LAAAXX_8_1_937_229 length=26
IIIIIIIIIIIIIIIIIIIIIIII3I
@SRR015141.448 WICMT-SOLEXA_209LAAAXX_8_1_762_886 length=26
GATGCCCCTCATCAGAGGAATGGATA
+SRR015141.448 WICMT-SOLEXA_209LAAAXX_8_1_762_886 length=26
IIIIIIIIIIIIII9I6FIII)-FIG
@SRR015141.449 WICMT-SOLEXA_209LAAAXX_8_1_914_737 length=26
AGCATGCATGGTTGGTACACTTTTGT
+SRR015141.449 WICMT-SOLEXA_209LAAAXX_8_1_914_737 length=26
IIIIIIIIIIIIIIIIIIIIIIIFII
@SRR015141.450 WICMT-SOLEXA_209LAAAXX_8_1_947_508 length=26
TATCTCAGGCTCCCGCCAGAACCTTC
+SRR015141.450 WICMT-SOLEXA_209LAAAXX_8_1_947_508 length=26
IIIIIIIIIIIIIIIIIIIIIIIII-
@SRR015141.451 WICMT-SOLEXA_209LAAAXX_8_1_911_164 length=26
GTAGGATTTGCCTTTTTGTTAAATAC
+SRR015141.451 WICMT-SOLEXA_209LAAAXX_8_1_911_164 length=26
IIIIIIIIIIIIIIIIIII&IIIIIG
@SRR015141.452 WICMT-SOLEXA_209LAAAXX_8_1_774_635 length=26
GAGCCTCATTCTTGCAGCGTCTCACC
+SRR015141.452 WICMT-SOLEXA_209LAAAXX_8_1_774_635 length=26
IIIIIIIIIIIII,B@",II%I6G%%
@SRR015141.453 WICMT-SOLEXA_209LAAAXX_8_1_905_708 length=26
AAGTGGATTTTTCTCATTCTCCATTA
+SRR015141.453 WICMT-SOLEXA_209LAAAXX_8_1_905_708 length=26
IIIIIIIIIIIIIIIIIIIIIIII.I
@SRR015141.454 WICMT-SOLEXA_209LAAAXX_8_1_884_657 length=26
CCATCTGCATTAGTGGCAAGTCTTAC
+SRR015141.454 WICMT-SOLEXA_209LAAAXX_8_1_884_657 length=26
IIIIIIIIIIIIIIA8CI<1I8IIIA
@SRR015141.455 WICMT-SOLEXA_209LAAAXX_8_1_903_877 length=26
ATGTCTTCCCCTTCATCAAGAAGTAT
+SRR015141.455 WICMT-SOLEXA_209LAAAXX_8_1_903_877 length=26
IIIIIIIIIIIIII$IIII.I1IIII
@SRR015141.456 WICMT-SOLEXA_209LAAAXX_8_1_965_658 length=26
GCCTCTAGTCTGAGCTTTTGAGTTTT
+SRR015141.456 WICMT-SOLEXA_209LAAAXX_8_1_965_658 length=26
IIIIIIIIIIIIIIIIII"II:IIII
@SRR015141.457 WICMT-SOLEXA_209LAAAXX_8_1_953_455 length=26
GCAGGTTAGAGTACTTTCTCCTTTTA
+SRR015141.457 WICMT-SOLEXA_209LAAAXX_8_1_953_455 length=26
IIIIIIIIIIIIIHII#III?I"II+
@SRR015141.458 WICMT-SOLEXA_209LAAAXX_8_1_810_650 length=26
GATAGGGGACTTGAATGTAGTATTCC
+SRR015141.458 WICMT-SOLEXA_209LAAAXX_8_1_810_650 length=26
IIIII%III2III%/III$B.6II"%
@SRR015141.459 WICMT-SOLEXA_209LAAAXX_8_1_931_656 length=26
TAAGACTTCAGCAATGAAGCTGCTTT
+SRR015141.459 WICMT-SOLEXA_209LAAAXX_8_1_931_656 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.460 WICMT-SOLEXA_209LAAAXX_8_1_807_426 length=26
GTCATCTACGGTCAAGGTGAACTAAT
+SRR015141.460 WICMT-SOLEXA_209LAAAXX_8_1_807_426 length=26
IIIIIII3IIII86#?9I?IDI&I1I
@SRR015141.461 WICMT-SOLEXA_209LAAAXX_8_1_658_723 length=26
GGTCATCAGACTGGCTTATATAAACA
+SRR015141.461 WICMT-SOLEXA_209LAAAXX_8_1_658_723 length=26
II7IIIIIIII$II7II2#H%II?)$
@SRR015141.462 WICMT-SOLEXA_209LAAAXX_8_1_802_477 length=26
GTTATAAACAGAAGAATTGCCAAGGA
+SRR015141.462 WICMT-SOLEXA_209LAAAXX_8_1_802_477 length=26
IIIIIIIIIIIIIIIIIID1AII(75
@SRR015141.463 WICMT-SOLEXA_209LAAAXX_8_1_762_449 length=26
GGAAGTTGTAGCCATAGGATTCTCAT
+SRR015141.463 WICMT-SOLEXA_209LAAAXX_8_1_762_449 length=26
IIIIIIIII9I0*FE7I8*II"I8)I
@SRR015141.464 WICMT-SOLEXA_209LAAAXX_8_1_523_879 length=26
GTGATTTCGTCATTTTTCAATTTGTC
+SRR015141.464 WICMT-SOLEXA_209LAAAXX_8_1_523_879 length=26
IIIIIIIIIIIIIIIII;IC*II&I"
@SRR015141.465 WICMT-SOLEXA_209LAAAXX_8_1_584_904 length=26
GTTTCCAAAACTTACTCACAGCACTT
+SRR015141.465 WICMT-SOLEXA_209LAAAXX_8_1_584_904 length=26
IIIIIDIIIII3$B"I/./0:"51II
@SRR015141.466 WICMT-SOLEXA_209LAAAXX_8_1_770_865 length=26
GCATGTGTTTGTTGGAGAACGGTTAA
+SRR015141.466 WICMT-SOLEXA_209LAAAXX_8_1_770_865 length=26
IIIIIIIIIIIII"5?-HIF(*II0'
@SRR015141.467 WICMT-SOLEXA_209LAAAXX_8_1_903_210 length=26
TACTCTTGGGAATATACCCAAAAGAT
+SRR015141.467 WICMT-SOLEXA_209LAAAXX_8_1_903_210 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.468 WICMT-SOLEXA_209LAAAXX_8_1_911_214 length=26
AGCCCCAACCGGACATCTCTGTGTAG
+SRR015141.468 WICMT-SOLEXA_209LAAAXX_8_1_911_214 length=26
IIIIIIIIIIIIIIIIIIIIII:II4
@SRR015141.469 WICMT-SOLEXA_209LAAAXX_8_1_931_854 length=26
TGAACTCAGGACCTCTGGAAGAGCAG
+SRR015141.469 WICMT-SOLEXA_209LAAAXX_8_1_931_854 length=26
IIIIIIIIIIIIIIIIIIII55I(I'HI6"1+E")$$
@SRR015141.489 WICMT-SOLEXA_209LAAAXX_8_1_925_896 length=26
GCAGAGCAGAAGGCGCTCTTGGATCT
+SRR015141.489 WICMT-SOLEXA_209LAAAXX_8_1_925_896 length=26
IIIIIIIIIIIIIII%IIIIIIDIHI
@SRR015141.490 WICMT-SOLEXA_209LAAAXX_8_1_733_766 length=26
GGATAAGGGCCAGATTGTAGCCACGT
+SRR015141.490 WICMT-SOLEXA_209LAAAXX_8_1_733_766 length=26
IIIIIIIIIIIIIIIIIIID6DH.3I
@SRR015141.491 WICMT-SOLEXA_209LAAAXX_8_1_888_398 length=26
GCTCTCTTCAGGGTGCCAAGCCTCAA
+SRR015141.491 WICMT-SOLEXA_209LAAAXX_8_1_888_398 length=26
IIIIIIIIIIIIIIIA;IIG9FI@III$I1IIIII#IAI&"
@SRR015141.498 WICMT-SOLEXA_209LAAAXX_8_1_737_613 length=26
GGTCAACTTCGGTGATGTTACCATTT
+SRR015141.498 WICMT-SOLEXA_209LAAAXX_8_1_737_613 length=26
IIIIII.>I1I'",I129'I"%.I:$
@SRR015141.499 WICMT-SOLEXA_209LAAAXX_8_1_824_729 length=26
GTAGGCAGCATACACCAGCTGATATG
+SRR015141.499 WICMT-SOLEXA_209LAAAXX_8_1_824_729 length=26
IIIIIIIIIIIII?7:=C2IF+I3I*
@SRR015141.500 WICMT-SOLEXA_209LAAAXX_8_1_899_895 length=26
GTAGGCGCCCACGGGGGTCCAGGTAT
+SRR015141.500 WICMT-SOLEXA_209LAAAXX_8_1_899_895 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.501 WICMT-SOLEXA_209LAAAXX_8_1_882_902 length=26
GCTCTTTGGATTACTTTGTTGCTTGC
+SRR015141.501 WICMT-SOLEXA_209LAAAXX_8_1_882_902 length=26
):IC-II>,ICIIII34&<+(@1I&,
@SRR015141.502 WICMT-SOLEXA_209LAAAXX_8_1_911_619 length=26
TAAGCTGGAGACCCTATACTGAAATA
+SRR015141.502 WICMT-SOLEXA_209LAAAXX_8_1_911_619 length=26
IBIIIIIIIIIIIII/IIIIIIIII+
@SRR015141.503 WICMT-SOLEXA_209LAAAXX_8_1_904_593 length=26
CCAGAAAAACCCAAGGAGGTTGTGCT
+SRR015141.503 WICMT-SOLEXA_209LAAAXX_8_1_904_593 length=26
IIIIIIIIIIIIIIIIIIIIIII=GI
@SRR015141.504 WICMT-SOLEXA_209LAAAXX_8_1_935_418 length=26
TGACAGACGGCCTCTACCTCAGAAGC
+SRR015141.504 WICMT-SOLEXA_209LAAAXX_8_1_935_418 length=26
IIIIIIIIII,IIIIIGIIIIIIIII
@SRR015141.505 WICMT-SOLEXA_209LAAAXX_8_1_896_623 length=26
AGTCTGGGTAGAGGAGTGGGCAGCAG
+SRR015141.505 WICMT-SOLEXA_209LAAAXX_8_1_896_623 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.506 WICMT-SOLEXA_209LAAAXX_8_1_893_129 length=26
GAGGAGGGCTGTGGATGTGAATACTC
+SRR015141.506 WICMT-SOLEXA_209LAAAXX_8_1_893_129 length=26
I*.III4I3IIIID5-@?I$+I-1I"
@SRR015141.507 WICMT-SOLEXA_209LAAAXX_8_1_528_921 length=26
GATAAGCCAACCGTGAGCCAGGTCAG
+SRR015141.507 WICMT-SOLEXA_209LAAAXX_8_1_528_921 length=26
IIIIIIIIIII;II7II9II5:+;25
@SRR015141.510 WICMT-SOLEXA_209LAAAXX_8_1_957_552 length=26
TGTACGCCCGACCTCCTGATCCCTGC
+SRR015141.510 WICMT-SOLEXA_209LAAAXX_8_1_957_552 length=26
IIIIIIIIIIIIII(IIIIIIIIII4
@SRR015141.511 WICMT-SOLEXA_209LAAAXX_8_1_905_890 length=26
CTTTTAAACCTGCTCACTTTTATCAC
+SRR015141.511 WICMT-SOLEXA_209LAAAXX_8_1_905_890 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.512 WICMT-SOLEXA_209LAAAXX_8_1_879_100 length=26
TTTGAGTTTAGGTCTTACTAAGTTAT
+SRR015141.512 WICMT-SOLEXA_209LAAAXX_8_1_879_100 length=26
IIIIIIIIIIIIIIII%GIII4III7
@SRR015141.513 WICMT-SOLEXA_209LAAAXX_8_1_790_881 length=26
GTCCTGGGCTGGCTGGCTTATTTTTT
+SRR015141.513 WICMT-SOLEXA_209LAAAXX_8_1_790_881 length=26
IIIIIIIIIIIIIII2HII/I$II>$
@SRR015141.514 WICMT-SOLEXA_209LAAAXX_8_1_876_219 length=26
TGTTAGAACCTTAGCTCAAAAGACAC
+SRR015141.514 WICMT-SOLEXA_209LAAAXX_8_1_876_219 length=26
IIIIIIIIIIIIIHBIIIGIIII>IB
@SRR015141.515 WICMT-SOLEXA_209LAAAXX_8_1_626_878 length=26
GTAAGGGGAAGTAGCTGACCCCTTGT
+SRR015141.515 WICMT-SOLEXA_209LAAAXX_8_1_626_878 length=26
IIIIIIIIIII#I2II*I;4/(II&)
@SRR015141.516 WICMT-SOLEXA_209LAAAXX_8_1_594_963 length=26
GGANNNNNNNNNNNNNNNNNNNNNNN
+SRR015141.516 WICMT-SOLEXA_209LAAAXX_8_1_594_963 length=26
II-!!!!!!!!!!!!!!!!!!!!!!!
@SRR015141.517 WICMT-SOLEXA_209LAAAXX_8_1_894_292 length=26
ATATGCATATAATTATTATTTTTCTT
+SRR015141.517 WICMT-SOLEXA_209LAAAXX_8_1_894_292 length=26
IIIIIIIIIIIIIIIIIII(IIH5I@
@SRR015141.518 WICMT-SOLEXA_209LAAAXX_8_1_715_713 length=26
GATGTCAGGAGTTATGCCTTCGCAAT
+SRR015141.518 WICMT-SOLEXA_209LAAAXX_8_1_715_713 length=26
IIIIIIIIIIIIIIIHAIII9+7ED#
@SRR015141.519 WICMT-SOLEXA_209LAAAXX_8_1_900_223 length=26
TGTGCCCCAGTGGTAGATTAAATGTG
+SRR015141.519 WICMT-SOLEXA_209LAAAXX_8_1_900_223 length=26
IIIIIIIIIIIIIIIII(II(IIIII
@SRR015141.520 WICMT-SOLEXA_209LAAAXX_8_1_903_582 length=26
CTTTGCTGTGATTCCCCGTGACACTT
+SRR015141.520 WICMT-SOLEXA_209LAAAXX_8_1_903_582 length=26
IIIIIIIIIIII9IIIIIIIIIIIII
@SRR015141.521 WICMT-SOLEXA_209LAAAXX_8_1_946_438 length=26
ACTGGCAGCAGAGTTTATATGTATTT
+SRR015141.521 WICMT-SOLEXA_209LAAAXX_8_1_946_438 length=26
=/IIIII"I%IIIIIIIII,HIIIII
@SRR015141.522 WICMT-SOLEXA_209LAAAXX_8_1_957_887 length=26
GGTGGAAAAGTTAGAAATGTCCACTG
+SRR015141.522 WICMT-SOLEXA_209LAAAXX_8_1_957_887 length=26
IIIIIIIIIIIIIIIIIIIIIIIIIG
@SRR015141.523 WICMT-SOLEXA_209LAAAXX_8_1_897_588 length=26
AACAACCCCTCTCTGCTTCTCAGGAC
+SRR015141.523 WICMT-SOLEXA_209LAAAXX_8_1_897_588 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.524 WICMT-SOLEXA_209LAAAXX_8_1_801_455 length=26
GCTGAGCCATCTCTCCAGACACCAAG
+SRR015141.524 WICMT-SOLEXA_209LAAAXX_8_1_801_455 length=26
IIIIIIIIIIIIIIIGIIIIIIDC>3
@SRR015141.525 WICMT-SOLEXA_209LAAAXX_8_1_910_287 length=26
GCACAGAGCCTAGAGCTTAGGTGGAA
+SRR015141.525 WICMT-SOLEXA_209LAAAXX_8_1_910_287 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.526 WICMT-SOLEXA_209LAAAXX_8_1_926_676 length=26
AATATGAATTGACTACATTTACATTC
+SRR015141.526 WICMT-SOLEXA_209LAAAXX_8_1_926_676 length=26
IIIIIIIIIIIIIIIIIIIIIIII*I
@SRR015141.527 WICMT-SOLEXA_209LAAAXX_8_1_901_363 length=26
GAGTTTGAGGCCAGCCTAGTCTACAA
+SRR015141.527 WICMT-SOLEXA_209LAAAXX_8_1_901_363 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.528 WICMT-SOLEXA_209LAAAXX_8_1_883_603 length=26
ATTTTGCCTCTGGTAGGCATCGCCAT
+SRR015141.528 WICMT-SOLEXA_209LAAAXX_8_1_883_603 length=26
IIIIIIIIIIII#II*#;>I<=875I
@SRR015141.529 WICMT-SOLEXA_209LAAAXX_8_1_870_223 length=26
GTTTGTTTCTTTGAGGAAAGATCTTG
+SRR015141.529 WICMT-SOLEXA_209LAAAXX_8_1_870_223 length=26
IIIIIIIIIIIIDI,AIIII>I.II1
@SRR015141.530 WICMT-SOLEXA_209LAAAXX_8_1_900_963 length=26
TAGNNNNNNNNNNNNNNNNNNNNNNN
+SRR015141.530 WICMT-SOLEXA_209LAAAXX_8_1_900_963 length=26
III!!!!!!!!!!!!!!!!!!!!!!!
@SRR015141.531 WICMT-SOLEXA_209LAAAXX_8_1_910_816 length=26
GAGGACATCAGATCTCATTACATATG
+SRR015141.531 WICMT-SOLEXA_209LAAAXX_8_1_910_816 length=26
IIIIIIIIIIIIIIIIIIII;IIIII
@SRR015141.532 WICMT-SOLEXA_209LAAAXX_8_1_773_723 length=26
GAAGGACCTGGAATATGGCGAGAAAA
+SRR015141.532 WICMT-SOLEXA_209LAAAXX_8_1_773_723 length=26
IIIIIIIIIIIIIIIIIIIIA+8,III5+D'
@SRR015141.538 WICMT-SOLEXA_209LAAAXX_8_1_802_633 length=26
GATACTTAGGTTTTCCATTCAACAGC
+SRR015141.538 WICMT-SOLEXA_209LAAAXX_8_1_802_633 length=26
IIIIIIIIIIIIII?8="I48;*6*(
@SRR015141.539 WICMT-SOLEXA_209LAAAXX_8_1_858_671 length=26
GTGTCTCCTTCCTAGCCTGGCTTCCA
+SRR015141.539 WICMT-SOLEXA_209LAAAXX_8_1_858_671 length=26
IIIIIIIIIIIIIIFI9IG1>II74.
@SRR015141.540 WICMT-SOLEXA_209LAAAXX_8_1_736_674 length=26
GTTGGCCATCAATGGGGAGTGTGGCC
+SRR015141.540 WICMT-SOLEXA_209LAAAXX_8_1_736_674 length=26
I(I'I*+I7
@SRR015141.550 WICMT-SOLEXA_209LAAAXX_8_1_929_290 length=26
ACCTTGGAGACTGAAGTCAGGCACAA
+SRR015141.550 WICMT-SOLEXA_209LAAAXX_8_1_929_290 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.551 WICMT-SOLEXA_209LAAAXX_8_1_876_749 length=26
GCAGGGTCTGGGAAACTAACCCTAAC
+SRR015141.551 WICMT-SOLEXA_209LAAAXX_8_1_876_749 length=26
IIIIIIIIIIIGIEI@?D=H=I4
@SRR015141.555 WICMT-SOLEXA_209LAAAXX_8_1_240_835 length=26
GAATATGGCAACAAAACTGAAAATCA
+SRR015141.555 WICMT-SOLEXA_209LAAAXX_8_1_240_835 length=26
IIIIIIIIIIIDIIIIGIIIIIII6B
@SRR015141.556 WICMT-SOLEXA_209LAAAXX_8_1_963_389 length=26
GGGCGCGTACGTGTATGTTTGTTTTT
+SRR015141.556 WICMT-SOLEXA_209LAAAXX_8_1_963_389 length=26
III8III35IIIIIIII=IIIIAIII
@SRR015141.557 WICMT-SOLEXA_209LAAAXX_8_1_928_305 length=26
ATGGGAAGGAATAGAGTCCACCTTTG
+SRR015141.557 WICMT-SOLEXA_209LAAAXX_8_1_928_305 length=26
IIIIIIIIIIIIIIIIIIIIIIIII(
@SRR015141.558 WICMT-SOLEXA_209LAAAXX_8_1_957_537 length=26
GTGATTGTGGATATATACTCAAAATT
+SRR015141.558 WICMT-SOLEXA_209LAAAXX_8_1_957_537 length=26
IIIIIIIIIIIII'IIIII**IIIII
@SRR015141.559 WICMT-SOLEXA_209LAAAXX_8_1_925_332 length=26
CAACACCAGTTACCATCAGAGTGTGG
+SRR015141.559 WICMT-SOLEXA_209LAAAXX_8_1_925_332 length=26
IIIIIIIIIIIIIIIIIIIIIIIIIE
@SRR015141.560 WICMT-SOLEXA_209LAAAXX_8_1_815_655 length=26
GCTATTTGAGGTTAGTATGTTTTGGT
+SRR015141.560 WICMT-SOLEXA_209LAAAXX_8_1_815_655 length=26
I2I+1III6II.I(&6&I&GCII'%=
@SRR015141.561 WICMT-SOLEXA_209LAAAXX_8_1_931_634 length=26
ACAAAGATCCCAAACCCTTTTTTTAT
+SRR015141.561 WICMT-SOLEXA_209LAAAXX_8_1_931_634 length=26
IIIIIIIIIIIIIIIIIIIIIIIII*
@SRR015141.562 WICMT-SOLEXA_209LAAAXX_8_1_947_416 length=26
GACCAGTATTGGCATTGGTATCAGGG
+SRR015141.562 WICMT-SOLEXA_209LAAAXX_8_1_947_416 length=26
IIIIIIIIIIIIIIIIIIIIIIII+I
@SRR015141.563 WICMT-SOLEXA_209LAAAXX_8_1_912_363 length=26
ACCATCACCACCCGGCCACAGACCAC
+SRR015141.563 WICMT-SOLEXA_209LAAAXX_8_1_912_363 length=26
IIIIIIIIIIIIIIIIIIIIIII=II
@SRR015141.564 WICMT-SOLEXA_209LAAAXX_8_1_867_459 length=26
GACGCCTCAGACGCTCTGAAGAGGCT
+SRR015141.564 WICMT-SOLEXA_209LAAAXX_8_1_867_459 length=26
IIIIIIIIIIIIIIIII9?I1A	I
@SRR015141.565 WICMT-SOLEXA_209LAAAXX_8_1_926_275 length=26
AAACTTGGACGGGTGTGTTTGAATAT
+SRR015141.565 WICMT-SOLEXA_209LAAAXX_8_1_926_275 length=26
1*D/II'III;$;IIIIIIIIIIII"
@SRR015141.566 WICMT-SOLEXA_209LAAAXX_8_1_903_827 length=26
GGATAAAGCAGTCCTCCCATGCATGC
+SRR015141.566 WICMT-SOLEXA_209LAAAXX_8_1_903_827 length=26
IIIIIIIIIIIIIIIIII'IICIIII
@SRR015141.567 WICMT-SOLEXA_209LAAAXX_8_1_892_770 length=26
GGGCTCTTGGGAGCTGCAGAAGGCTA
+SRR015141.567 WICMT-SOLEXA_209LAAAXX_8_1_892_770 length=26
IIIIIIIIIIIII>IIIIIIF*9.I1
@SRR015141.568 WICMT-SOLEXA_209LAAAXX_8_1_556_839 length=26
GAAATACAATCAAAAATAAATCCATA
+SRR015141.568 WICMT-SOLEXA_209LAAAXX_8_1_556_839 length=26
IIIIIIIIIIIIIIEIIIIII<.III
@SRR015141.569 WICMT-SOLEXA_209LAAAXX_8_1_615_936 length=26
GGTATTTTAGCTTNNNNNNNTTNNNN
+SRR015141.569 WICMT-SOLEXA_209LAAAXX_8_1_615_936 length=26
IIIIIIIIIIIII!!!!!!!I#!!!!
@SRR015141.570 WICMT-SOLEXA_209LAAAXX_8_1_879_327 length=26
TGGACAAGTACTACAGCTTATCCTCA
+SRR015141.570 WICMT-SOLEXA_209LAAAXX_8_1_879_327 length=26
IIIIIIIIIIIIIII?IIIIIIIIII
@SRR015141.571 WICMT-SOLEXA_209LAAAXX_8_1_750_853 length=26
GGTACTCACCCTTCACTCTAGGATAT
+SRR015141.571 WICMT-SOLEXA_209LAAAXX_8_1_750_853 length=26
IIIIIIIIIIIIIIIIIIII/-C)8I
@SRR015141.572 WICMT-SOLEXA_209LAAAXX_8_1_442_897 length=26
GACACAGGGAAGGGACTCAGATGCCA
+SRR015141.572 WICMT-SOLEXA_209LAAAXX_8_1_442_897 length=26
IIIIIIIIIIIIIII8I@I2II+,.I
@SRR015141.573 WICMT-SOLEXA_209LAAAXX_8_1_935_862 length=26
GAGGGCACTTGCCACCACAGGTTGTC
+SRR015141.573 WICMT-SOLEXA_209LAAAXX_8_1_935_862 length=26
IIIIIIIIIIIIIIIIIIIIIIIII9
@SRR015141.574 WICMT-SOLEXA_209LAAAXX_8_1_919_320 length=26
CCTCACGAGTCATATGCACTAGCTTT
+SRR015141.574 WICMT-SOLEXA_209LAAAXX_8_1_919_320 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.575 WICMT-SOLEXA_209LAAAXX_8_1_915_658 length=26
TGGAGACTTTGACAAAGTACTCTTTT
+SRR015141.575 WICMT-SOLEXA_209LAAAXX_8_1_915_658 length=26
IIIIIIIIIIIIIIIIIIIIIIIII?
@SRR015141.576 WICMT-SOLEXA_209LAAAXX_8_1_824_625 length=26
GACACACACACAAATATTACGAGAAC
+SRR015141.576 WICMT-SOLEXA_209LAAAXX_8_1_824_625 length=26
IIIIIIIIIIIIIIIIII;8I886I:
@SRR015141.577 WICMT-SOLEXA_209LAAAXX_8_1_912_408 length=26
AGAGGACCAAAAGTTCAGCTCCCAGC
+SRR015141.577 WICMT-SOLEXA_209LAAAXX_8_1_912_408 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.578 WICMT-SOLEXA_209LAAAXX_8_1_957_515 length=26
TGGGGGAAAGAGCGTCATTCTGTTTT
+SRR015141.578 WICMT-SOLEXA_209LAAAXX_8_1_957_515 length=26
IIIIIIIIIIIIIIIIIIIGIIIIII
@SRR015141.579 WICMT-SOLEXA_209LAAAXX_8_1_899_245 length=26
AAAACATCCACTTGTCGACTTGAAAT
+SRR015141.579 WICMT-SOLEXA_209LAAAXX_8_1_899_245 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.580 WICMT-SOLEXA_209LAAAXX_8_1_967_398 length=26
TTTCTCGCATAATTCCAGGTCCTTCT
+SRR015141.580 WICMT-SOLEXA_209LAAAXX_8_1_967_398 length=26
IIIIIIIIIIIIIIIIIBII'III%I
@SRR015141.581 WICMT-SOLEXA_209LAAAXX_8_1_897_504 length=26
AGAAAACCTCCATATCACAAGGTTCT
+SRR015141.581 WICMT-SOLEXA_209LAAAXX_8_1_897_504 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.582 WICMT-SOLEXA_209LAAAXX_8_1_811_757 length=26
TATACTAAAACTGGAATGATAAAGAA
+SRR015141.582 WICMT-SOLEXA_209LAAAXX_8_1_811_757 length=26
IIIIIIIIIIIIIIIII7IIIII8II
@SRR015141.583 WICMT-SOLEXA_209LAAAXX_8_1_650_728 length=26
GTTTCCGAACATTATCAAATTCCCAG
+SRR015141.583 WICMT-SOLEXA_209LAAAXX_8_1_650_728 length=26
IIIIIIIIIIIIIII5II=IIG08I3
@SRR015141.584 WICMT-SOLEXA_209LAAAXX_8_1_878_299 length=26
CAGGGGAAATCAGAACTTGCATCACA
+SRR015141.584 WICMT-SOLEXA_209LAAAXX_8_1_878_299 length=26
IIIIIIIIIIIIIIIIIIEIIIAI:;
@SRR015141.585 WICMT-SOLEXA_209LAAAXX_8_1_880_825 length=26
CCATATCCGGGGATCCATCCCATAAT
+SRR015141.585 WICMT-SOLEXA_209LAAAXX_8_1_880_825 length=26
IIIIIIIIIII4IIII)2II>AI#
@SRR015141.593 WICMT-SOLEXA_209LAAAXX_8_1_910_305 length=26
AGGCAACGCTGTAGATAGAAACCCTA
+SRR015141.593 WICMT-SOLEXA_209LAAAXX_8_1_910_305 length=26
III"IIIIIIIIIIIIIIIIIIIIII
@SRR015141.594 WICMT-SOLEXA_209LAAAXX_8_1_877_347 length=26
TCTAAGCAGACCTCTGAATGCCAGAT
+SRR015141.594 WICMT-SOLEXA_209LAAAXX_8_1_877_347 length=26
IIIIIIIIIIIIIIIIIII*III6II
@SRR015141.595 WICMT-SOLEXA_209LAAAXX_8_1_908_198 length=26
AGTCAAAGGAAAACCTGAAAGGCCAT
+SRR015141.595 WICMT-SOLEXA_209LAAAXX_8_1_908_198 length=26
IIIIIIIIIIIIIIIIIIIIIIIIII
@SRR015141.596 WICMT-SOLEXA_209LAAAXX_8_1_856_487 length=26
GTAAGCATCTCATCAGCCATTTCTTT
+SRR015141.596 WICMT-SOLEXA_209LAAAXX_8_1_856_487 length=26
IIIIIIIIGII;II4%H>@III-III
@SRR015141.597 WICMT-SOLEXA_209LAAAXX_8_1_775_855 length=26
GATTGAGTATAAAGACTATGTGCTTT
+SRR015141.597 WICMT-SOLEXA_209LAAAXX_8_1_775_855 length=26
I.IIIIIIIIIIIIIII2I/II&
@SRR015141.598 WICMT-SOLEXA_209LAAAXX_8_1_778_686 length=26
GGTCATGGTAAGTCTACCAGAAGCCT
+SRR015141.598 WICMT-SOLEXA_209LAAAXX_8_1_778_686 length=26
IIIIIIIIII0II>IE40IIHI,;*I
@SRR015141.599 WICMT-SOLEXA_209LAAAXX_8_1_850_934 length=26
GTCTGTACACATGTNNNNNTGTCNTN
+SRR015141.599 WICMT-SOLEXA_209LAAAXX_8_1_850_934 length=26
IIIIIIIIIIII5I!!!!!I,I#!I!
@SRR015141.600 WICMT-SOLEXA_209LAAAXX_8_1_809_940 length=26
GATGAGNNNAAGNNNNNNNNNNNNNN
+SRR015141.600 WICMT-SOLEXA_209LAAAXX_8_1_809_940 length=26
IIIIEI!!!IAI!!!!!!!!!!!!!!
@SRR015141.601 WICMT-SOLEXA_209LAAAXX_8_1_893_365 length=26
ACAGATTTCTCAGCAGTTCTCGGAAG
+SRR015141.601 WICMT-SOLEXA_209LAAAXX_8_1_893_365 length=26
IIIIIIIIIIIIIIIIIIII4F)8I*
@SRR015141.602 WICMT-SOLEXA_209LAAAXX_8_1_765_608 length=26
GGAGTCCTCCCATTAGCATCAGCTAG
+SRR015141.602 WICMT-SOLEXA_209LAAAXX_8_1_765_608 length=26
IIIIIIIIIII8IIII+;I4I22I.1
@SRR015141.603 WICMT-SOLEXA_209LAAAXX_8_1_939_904 length=26
GCCCATTCACTGCATCCCAGACAGGC
+SRR015141.603 WICMT-SOLEXA_209LAAAXX_8_1_939_904 length=26
IIIIIIIIIIIIIIIIIIIIIIIII0IIGIII?*HI3,IA'*I34
@SRR015141.612 WICMT-SOLEXA_209LAAAXX_8_1_800_591 length=26
GCCTGGAGTTTCAGGGAGAGCAGATC
+SRR015141.612 WICMT-SOLEXA_209LAAAXX_8_1_800_591 length=26
IIIIIIIIIII&>IIB?51H+9#F%%
@SRR015141.613 WICMT-SOLEXA_209LAAAXX_8_1_933_880 length=26
GTCCACAATGCCTGTGTAATATTTTC
+SRR015141.613 WICMT-SOLEXA_209LAAAXX_8_1_933_880 length=26
IIIIIIIIIII*IIIIIIIIIIIIID
@SRR015141.614 WICMT-SOLEXA_209LAAAXX_8_1_894_922 length=26
GCTCTGGGACACCTCCAACTGCTGCA
+SRR015141.614 WICMT-SOLEXA_209LAAAXX_8_1_894_922 length=26
IIIIIIIIIIIIIIIIIIIIIII3II
@SRR015141.615 WICMT-SOLEXA_209LAAAXX_8_1_896_191 length=26
GGAGCAGCACCGTCTCAAATGCAAGG
+SRR015141.615 WICMT-SOLEXA_209LAAAXX_8_1_896_191 length=26
IIII&IIIIII-IIIIIII'
@SRR015141.622 WICMT-SOLEXA_209LAAAXX_8_1_810_796 length=26
GAACTCAGTACCTTCAGAAGAGCAGT
+SRR015141.622 WICMT-SOLEXA_209LAAAXX_8_1_810_796 length=26
IIIIIIIIIIIIIIII1III?4foo
aaaacccc
genometools-1.5.1/testdata/foo_width4.fas000066400000000000000000000000171211610345200204140ustar00rootroot00000000000000>foo
aaaa
cccc
genometools-1.5.1/testdata/foobar.fas000066400000000000000000000000341211610345200176150ustar00rootroot00000000000000>foo
aaaacccc
>bar
ggggtttt
genometools-1.5.1/testdata/foofoo.fas000066400000000000000000000000341211610345200176340ustar00rootroot00000000000000>foo
aaaacccc
>foo
aaaacccc
genometools-1.5.1/testdata/foofoofoo.fas000066400000000000000000000000521211610345200203400ustar00rootroot00000000000000>foo
aaaacccc
>foo
aaaacccc
>foo
aaaacccc
genometools-1.5.1/testdata/foorcfoo.fas000066400000000000000000000000361211610345200201630ustar00rootroot00000000000000>foo
aaaacccc
>rcfoo
ggggtttt
genometools-1.5.1/testdata/foorcfoofoo.fas000066400000000000000000000000541211610345200206670ustar00rootroot00000000000000>foo
aaaacccc
>rcfoo
ggggtttt
>foo
aaaacccc
genometools-1.5.1/testdata/frompos.fas000066400000000000000000000000131211610345200200270ustar00rootroot00000000000000>
ccccgggg
genometools-1.5.1/testdata/genbank_test.gbk000066400000000000000000000031331211610345200210060ustar00rootroot00000000000000LOCUS       AF078689                 275 bp    mRNA    linear   EST 26-JUL-1999
DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
ORIGIN      
        1 antnnctacn ncnncnntnn cnncnatnna antanacnna tnntnntann aatnaaannc
       61 tanaancnnc nnanaantat ntnnataana aataacaaaa actnannnna tcatnaantt
      121 cttcnttata ttatantttt caatctnaat ttcaattccn ccnctcncct ttttcctctc
      181 cnccttttcc ntctctccna tctnctcccn ccnccnacct tntnatnatt atanctctna
      241 anntccatac aannatataa aaaaaaaaaa aaaaa
//
genometools-1.5.1/testdata/genbank_test1.gbk000066400000000000000000000047321211610345200210750ustar00rootroot00000000000000LOCUS       AF078689                 275 bp    mRNA    linear   EST 26-JUL-1999
DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
//
LOCUS       AF078689                 275 bp    mRNA    linear   EST 26-JUL-1999
DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
//
genometools-1.5.1/testdata/genbank_test2.fas000066400000000000000000000005741211610345200211040ustar00rootroot00000000000000>AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana cDNA clone IFA2, mRNA sequence.
antnnctacnncnncnntnncnncnatnnaantanacnnatnntnntannaatnaaannc
tanaancnncnnanaantatntnnataanaaataacaaaaactnannnnatcatnaantt
cttcnttatattatanttttcaatctnaatttcaattccnccnctcncctttttcctctc
cnccttttccntctctccnatctnctcccnccnccnaccttntnatnattatanctctna
anntccatacaannatataaaaaaaaaaaaaaaaa
genometools-1.5.1/testdata/genbank_test2.gbk000066400000000000000000000031441211610345200210720ustar00rootroot00000000000000foo bar

LOCUS       AF078689                 275 bp    mRNA    linear   EST 26-JUL-1999
DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
ORIGIN      
        1 antnnctacn ncnncnntnn cnncnatnna antanacnna tnntnntann aatnaaannc
       61 tanaancnnc nnanaantat ntnnataana aataacaaaa actnannnna tcatnaantt
      121 cttcnttata ttatantttt caatctnaat ttcaattccn ccnctcncct ttttcctctc
      181 cnccttttcc ntctctccna tctnctcccn ccnccnacct tntnatnatt atanctctna
      241 anntccatac aannatataa aaaaaaaaaa aaaaa
//
genometools-1.5.1/testdata/genbank_test3.gbk000066400000000000000000000030131211610345200210660ustar00rootroot00000000000000DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
ORIGIN      
        1 antnnctacn ncnncnntnn cnncnatnna antanacnna tnntnntann aatnaaannc
       61 tanaancnnc nnanaantat ntnnataana aataacaaaa actnannnna tcatnaantt
      121 cttcnttata ttatantttt caatctnaat ttcaattccn ccnctcncct ttttcctctc
      181 cnccttttcc ntctctccna tctnctcccn ccnccnacct tntnatnatt atanctctna
      241 anntccatac aannatataa aaaaaaaaaa aaaaa
//
genometools-1.5.1/testdata/genbank_test4.gbk000066400000000000000000000062631211610345200211010ustar00rootroot00000000000000LOCUS       AF078689                 275 bp    mRNA    linear   EST 26-JUL-1999
DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
ORIGIN      
        1 antnnctacn ncnncnntnn cnncnatnna antanacnna tnntnntann aatnaaannc
       61 tanaancnnc nnanaantat ntnnataana aataacaaaa actnannnna tcatnaantt
      121 cttcnttata ttatantttt caatctnaat ttcaattccn ccnctcncct ttttcctctc
      181 cnccttttcc ntctctccna tctnctcccn ccnccnacct tntnatnatt atanctctna
      241 anntccatac aannatataa aaaaaaaaaa aaaaa
LOCUS       AF078689                 275 bp    mRNA    linear   EST 26-JUL-1999
DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
ORIGIN      
        1 antnnctacn ncnncnntnn cnncnatnna antanacnna tnntnntann aatnaaannc
       61 tanaancnnc nnanaantat ntnnataana aataacaaaa actnannnna tcatnaantt
      121 cttcnttata ttatantttt caatctnaat ttcaattccn ccnctcncct ttttcctctc
      181 cnccttttcc ntctctccna tctnctcccn ccnccnacct tntnatnatt atanctctna
      241 anntccatac aannatataa aaaaaaaaaa aaaaa
//
genometools-1.5.1/testdata/genbank_test5.gbk000066400000000000000000000031321211610345200210720ustar00rootroot00000000000000LOCUS       AF078689                 275 bp    mRNA    linear   EST 26-JUL-1999
DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
ORIGIN      
        1 antnnctacn ncnncnntnn cnncnatnna antanacnna tnntnntann aatnaaannc
       61tanaancnnc nnanaantat ntnnataana aataacaaaa actnannnna tcatnaantt
      121 cttcnttata ttatantttt caatctnaat ttcaattccn ccnctcncct ttttcctctc
      181 cnccttttcc ntctctccna tctnctcccn ccnccnacct tntnatnatt atanctctna
      241 anntccatac aannatataa aaaaaaaaaa aaaaa
//
genometools-1.5.1/testdata/genbank_test6.gbk000066400000000000000000000031331211610345200210740ustar00rootroot00000000000000LOCUS       AF078689                 275 bp    mRNA    linear   EST 26-JUL-1999
DEFINITION  AF078689 Arabidopsis thaliana library (Tan K) Arabidopsis thaliana
            cDNA clone IFA2, mRNA sequence.
ACCESSION   AF078689
VERSION     AF078689.1  GI:5587835
KEYWORDS    EST.
SOURCE      Arabidopsis thaliana (thale cress)
  ORGANISM  Arabidopsis thaliana
            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
            Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
            rosids; eurosids II; Brassicales; Brassicaceae; Arabidopsis.
REFERENCE   1  (bases 1 to 275)
  AUTHORS   Zhao,D., Chen,D., Yang,C. and Zhai,Z.
  TITLE     Isolation of intermediate filament-like genes from Arabidopsis
  JOURNAL   Unpublished (1999)
COMMENT     Contact: Tan K
            Plant Development Biology
            Institute of Botany
            20 Nanxincun Xiangshan. Hai Dian, Beijing, 100871, P. R. China.
FEATURES             Location/Qualifiers
     source          1..275
                     /organism="Arabidopsis thaliana"
                     /mol_type="mRNA"
                     /db_xref="taxon:3702"
                     /clone="IFA2"
                     /clone_lib="Arabidopsis thaliana library (Tan K)"
ORIGIN      
          antnnctacn ncnncnntnn cnncnatnna antanacnna tnntnntann aatnaaannc
          tanaancnnc nnanaantat ntnnataana aataacaaaa actnannnna tcatnaantt
          cttcnttata ttatantttt caatctnaat ttcaattccn ccnctcncct ttttcctctc
          cnccttttcc ntctctccna tctnctcccn ccnccnacct tntnatnatt atanctctna
          anntccatac aannatataa aaaaaaaaaa aaaaa
//
genometools-1.5.1/testdata/genbank_test7.gbk000066400000000000000000000005521211610345200210770ustar00rootroot00000000000000LOCUS      Random140
DEFINITION  n140
ORIGIN     
      60 nnacancaaa cncaccaaac caanancnca cncnanaccc anccnnanna ancccnaacn
     120 aacnaaaaan ncnncnanan accnacanaa cannnnncnn caanacnacc nnaaccnaac
     140 ncanccancc naaaacaca                                             
//

LOCUS       Random18
DEFINITION  n18
ORIGIN      
       18 caaccaannc cnaanccc
//
genometools-1.5.1/testdata/genbank_test8.gbk000066400000000000000000000006671211610345200211070ustar00rootroot00000000000000LOCUS       Random
DEFINITION  Random
DEFINITION  bla
ORIGIN      
        1 nnacancaaa cncaccaaac caanancnca cncnanaccc anccnnanna ancccnaacn
       61 aacnaaaaan ncnncnanan accnacanaa cannnnncnn caanacnacc nnaaccnaac
      121 ncanccancc naaaacacac caaccaannc cnaanccccn ccnnccacna ncccnnnnnc
      181 nnacacaann acncacnnnc cnananacan nnccnnnanc acancaacna cacancaaca
      241 aacaaaccac caaccacccc acaacaacnn cannacnaca accnaccnca
//
genometools-1.5.1/testdata/genomediff/000077500000000000000000000000001211610345200177605ustar00rootroot00000000000000genometools-1.5.1/testdata/genomediff/000050_001_0.1_002-kr.out000066400000000000000000000001441211610345200231650ustar00rootroot000000000000002
S1         0 942 
S2         936 0 
2
S1         0.000000 0.127152 
S2         0.127152 0.000000 
genometools-1.5.1/testdata/genomediff/000050_001_0.1_002_S001.fas000066400000000000000000000000671211610345200232240ustar00rootroot00000000000000>S1
ATTTACCCTTAAAGCTTAATTGGGTGTACATCTTAGACCCCACCCGACTT
genometools-1.5.1/testdata/genomediff/000050_001_0.1_002_S002.fas000066400000000000000000000000671211610345200232250ustar00rootroot00000000000000>S2
ATTTACCCTTAAAGCTTAATTGGCAGAACATCTTAAATCCCACCCGACTT
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010-kr.out000066400000000000000000000031041211610345200231630ustar00rootroot0000000000000010
S1         0 1882 1082 2650 1082 1024 1882 1882 742 2650 
S2         1888 0 1580 1888 1580 1522 2650 2650 952 1888 
S3         1092 1584 0 1092 2650 2160 1584 1584 1422 1092 
S4         2650 1882 1082 0 1082 1024 1882 1882 742 2650 
S5         1092 1584 2650 1092 0 2160 1584 1584 1422 1092 
S6         1034 1526 2160 1034 2160 0 1526 1526 1172 1034 
S7         1888 2650 1580 1888 1580 1522 0 2650 952 1888 
S8         1888 2650 1580 1888 1580 1522 2650 0 952 1888 
S9         752 956 1422 752 1422 1172 956 956 0 752 
S10        2650 1882 1082 2650 1082 1024 1882 1882 742 0 
10
S1         0.000000 0.054530 0.105537 0.032124 0.105537 0.113021 0.054530 0.054530 0.174705 0.032124 
S2         0.054530 0.000000 0.067461 0.054530 0.067461 0.070496 0.032119 0.032119 0.124041 0.054530 
S3         0.105537 0.067461 0.000000 0.105537 0.032119 0.045429 0.067461 0.067461 0.076352 0.105537 
S4         0.032124 0.054530 0.105537 0.000000 0.105537 0.113021 0.054530 0.054530 0.174705 0.032124 
S5         0.105537 0.067461 0.032119 0.105537 0.000000 0.045429 0.067461 0.067461 0.076352 0.105537 
S6         0.113021 0.070496 0.045429 0.113021 0.045429 0.000000 0.070496 0.070496 0.095901 0.113021 
S7         0.054530 0.032119 0.067461 0.054530 0.067461 0.070496 0.000000 0.032119 0.124041 0.054530 
S8         0.054530 0.032119 0.067461 0.054530 0.067461 0.070496 0.032119 0.000000 0.124041 0.054530 
S9         0.174705 0.124041 0.076352 0.174705 0.076352 0.095901 0.124041 0.124041 0.000000 0.174705 
S10        0.032124 0.054530 0.105537 0.032124 0.105537 0.113021 0.054530 0.054530 0.174705 0.000000 
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S001.fas000066400000000000000000000000671211610345200232230ustar00rootroot00000000000000>S1
TATCTTATGGTCATGTGTCGGGTCGATACCGCCTGAAATAAACACTGTTG
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S002.fas000066400000000000000000000000671211610345200232240ustar00rootroot00000000000000>S2
TAACTTATTGTCATGTGTCGGGTCGATACCGCCTGAAATAAACACTGTTG
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S003.fas000066400000000000000000000000671211610345200232250ustar00rootroot00000000000000>S3
TAACTTATTGTCATGTGTCGGGTCGATACCGCCTGTAATAAACACTGTTG
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S004.fas000066400000000000000000000000671211610345200232260ustar00rootroot00000000000000>S4
TATCTTATGGTCATGTGTCGGGTCGATACCGCCTGAAATAAACACTGTTG
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S005.fas000066400000000000000000000000671211610345200232270ustar00rootroot00000000000000>S5
TAACTTATTGTCATGTGTCGGGTCGATACCGCCTGTAATAAACACTGTTG
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S006.fas000066400000000000000000000000671211610345200232300ustar00rootroot00000000000000>S6
TAACTTATTGTCATGTGTCGGGTCGATACCGCCTGTAATAAACAGTGTTG
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S007.fas000066400000000000000000000000671211610345200232310ustar00rootroot00000000000000>S7
TAACTTATTGTCATGTGTCGGGTCGATACCGCCTGAAATAAACACTGTTG
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S008.fas000066400000000000000000000000671211610345200232320ustar00rootroot00000000000000>S8
TAACTTATTGTCATGTGTCGGGTCGATACCGCCTGAAATAAACACTGTTG
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S009.fas000066400000000000000000000000671211610345200232330ustar00rootroot00000000000000>S9
TAACTTATTGTCATGTGTCCGGTCGATACCGCCTGTAATAAACACTGTTG
genometools-1.5.1/testdata/genomediff/000050_001_0.1_010_S010.fas000066400000000000000000000000701211610345200232150ustar00rootroot00000000000000>S10
TATCTTATGGTCATGTGTCGGGTCGATACCGCCTGAAATAAACACTGTTG
genometools-1.5.1/testdata/genomediff/000050_005_0.1_002_S001.fas000066400000000000000000000001321211610345200232210ustar00rootroot00000000000000>L1_S1
TGAGGGATTA
>L1_S2
TGTGGGATTA
>L1_S3
TGAGGGATTA
>L1_S4
TGAGGGATTA
>L1_S5
TGAGGGATTA
genometools-1.5.1/testdata/genomediff/000050_005_0.1_002_S002.fas000066400000000000000000000001321211610345200232220ustar00rootroot00000000000000>L2_S1
GCTCTGGTGC
>L2_S2
GCTCTTGTGC
>L2_S3
GCTCTTGTGC
>L2_S4
GCTCTTGTGC
>L2_S5
GCTCTTGTGC
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S001.fas000066400000000000000000000001321211610345200232200ustar00rootroot00000000000000>L1_S1
CCTACGAGCC
>L1_S2
TCTACGAGCC
>L1_S3
TCTACGAGCC
>L1_S4
CCTACGAGCC
>L1_S5
CCTACGAGCC
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S002.fas000066400000000000000000000001321211610345200232210ustar00rootroot00000000000000>L2_S1
TATTCTCTGG
>L2_S2
TATTCTCTGG
>L2_S3
TATTCTCCGG
>L2_S4
TATTCTCTGG
>L2_S5
TATTCTCTGG
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S003.fas000066400000000000000000000001321211610345200232220ustar00rootroot00000000000000>L3_S1
TTGGGGGTCA
>L3_S2
TTTGGGGTCA
>L3_S3
TTGGGGGTCA
>L3_S4
TTGGGGGTCA
>L3_S5
TTGGGGGTCA
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S004.fas000066400000000000000000000001321211610345200232230ustar00rootroot00000000000000>L4_S1
GGTGGTCCAC
>L4_S2
GGTGGTCCAC
>L4_S3
GGTGGTCCAC
>L4_S4
GGTGTTCCAC
>L4_S5
GGTGTTCCAC
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S005.fas000066400000000000000000000001321211610345200232240ustar00rootroot00000000000000>L5_S1
ACATGTAAGA
>L5_S2
ACATGTAAGA
>L5_S3
ACATGTAAGA
>L5_S4
ACATGTAAGA
>L5_S5
ACACGTAAGA
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S006.fas000066400000000000000000000001321211610345200232250ustar00rootroot00000000000000>L6_S1
CCTACTCATG
>L6_S2
CCTACTCATG
>L6_S3
CCTACTCATG
>L6_S4
CCTACGCATG
>L6_S5
CCTACGCATG
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S007.fas000066400000000000000000000001321211610345200232260ustar00rootroot00000000000000>L7_S1
GCTGGTATTG
>L7_S2
GCTGGTATTG
>L7_S3
GCTGGTATTG
>L7_S4
GCTGGTATTG
>L7_S5
GCTGGTAATG
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S008.fas000066400000000000000000000001321211610345200232270ustar00rootroot00000000000000>L8_S1
TTGCATTAAA
>L8_S2
CTGCATTAAA
>L8_S3
CTGCATTAAA
>L8_S4
CTGCATTAAA
>L8_S5
TTGCATTAAA
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S009.fas000066400000000000000000000001321211610345200232300ustar00rootroot00000000000000>L9_S1
GCGTAAAATC
>L9_S2
GCGTTAAATC
>L9_S3
GCGTAAAATC
>L9_S4
GCGTTAAATC
>L9_S5
GCGTAAAATC
genometools-1.5.1/testdata/genomediff/000050_005_0.1_010_S010.fas000066400000000000000000000001371211610345200232250ustar00rootroot00000000000000>L10_S1
AGTGGTATAG
>L10_S2
AGTGGTATAG
>L10_S3
AGTGGTATAG
>L10_S4
ACTGGTATAG
>L10_S5
AGTGGTATAG
genometools-1.5.1/testdata/genomediff/000100_001_0.1_002-kr.out000066400000000000000000000001461211610345200231630ustar00rootroot000000000000002
S1         0 1984 
S2         1968 0 
2
S1         0.000000 0.121848 
S2         0.121848 0.000000 
genometools-1.5.1/testdata/genomediff/000100_001_0.1_002_S001.fas000066400000000000000000000001521211610345200232130ustar00rootroot00000000000000>S1
TGTTGACTCAGAGAGAACTCCTTACGTTCGATGAGGTGTAAGAAATCCCCATTATCTCGGTTGTACCTAA
CGCGTCACTCACTACAATCATTGCTAATAA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_002_S002.fas000066400000000000000000000001521211610345200232140ustar00rootroot00000000000000>S2
TGTTGAATCAGAGCGAACTCCTTACGTTCGATGAGGTGCAAGAAATGCCCATTTTCACGGTTGTACCTAA
CGCGTCACTCACTAAATTCATTGCTTATAC
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010-kr.out000066400000000000000000000031241211610345200231610ustar00rootroot0000000000000010
S1         0 8458 2832 2704 5740 3120 2704 8458 2616 2730 
S2         8458 0 3476 3448 5140 3864 3448 10300 3360 2894 
S3         2840 3482 0 3534 2434 5400 3534 3482 3446 4600 
S4         2704 3448 3526 0 2702 6046 10300 3448 9916 4190 
S5         5728 5130 2416 2690 0 2704 2690 5130 2606 2316 
S6         3132 3874 5402 6056 2726 0 6056 3874 5968 7460 
S7         2704 3448 3526 10300 2702 6046 0 3448 9916 4190 
S8         8458 10300 3476 3448 5140 3864 3448 0 3360 2894 
S9         2616 3360 3438 9916 2618 5958 9916 3360 0 4102 
S10        2744 2910 4608 4208 2344 7466 4208 2910 4120 0 
10
S1         0.000000 0.022649 0.077857 0.082135 0.035918 0.069725 0.082135 0.022649 0.085410 0.081216 
S2         0.022649 0.000000 0.061779 0.062326 0.040493 0.055000 0.062326 0.016552 0.064169 0.075929 
S3         0.077857 0.061779 0.000000 0.060786 0.093909 0.038299 0.060786 0.061779 0.062525 0.045534 
S4         0.082135 0.062326 0.060786 0.000000 0.082634 0.033861 0.016552 0.062326 0.017770 0.050384 
S5         0.035918 0.040493 0.093909 0.082634 0.000000 0.082123 0.082634 0.040493 0.085758 0.098828 
S6         0.069725 0.055000 0.038299 0.033861 0.082123 0.000000 0.033861 0.055000 0.034412 0.026589 
S7         0.082135 0.062326 0.060786 0.016552 0.082634 0.033861 0.000000 0.062326 0.017770 0.050384 
S8         0.022649 0.016552 0.061779 0.062326 0.040493 0.055000 0.062326 0.000000 0.064169 0.075929 
S9         0.085410 0.064169 0.062525 0.017770 0.085758 0.034412 0.017770 0.064169 0.000000 0.051560 
S10        0.081216 0.075929 0.045534 0.050384 0.098828 0.026589 0.050384 0.075929 0.051560 0.000000 
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S001.fas000066400000000000000000000001521211610345200232120ustar00rootroot00000000000000>S1
TATGAGCCGCTAGTGCGCAGTGGGCGTGTATAGTTACAACTAAGCGAAACAGTTTAGATGAAGGAATTGG
CTGCACTAAAGGAACGCGCCACCCGTGGTA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S002.fas000066400000000000000000000001521211610345200232130ustar00rootroot00000000000000>S2
TATGTGCCGGTAGTGCGCAGTGGGCGTGTATAGTTACAACTAAGCGAAACAGTTTAGATGAAGGAATTGG
CTGCACTAAAGGAACGCGCCACCCGTGGTA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S003.fas000066400000000000000000000001521211610345200232140ustar00rootroot00000000000000>S3
TATGTGCCGGTAGTGCGCAGTGGGCGTGTATAGTTACAACAAAGCCAAACAGTTTAGATGAAGGACTTGG
CTGCACTAAAGGAACGCGCCACCCGTGGTA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S004.fas000066400000000000000000000001521211610345200232150ustar00rootroot00000000000000>S4
TATGTGCCGGTAGTGCGCAGTGGGCGTGTATAGTTACAACTAAGCCAAACAGTTTAGATGAAGGACTTGG
CAGTACTAAAGGAACGCGCCACCCGTGGTA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S005.fas000066400000000000000000000001521211610345200232160ustar00rootroot00000000000000>S5
TATGTGCCGCTAGTGCGCAGTGGGCGTGTATAGTTACAACTAAGCGAAACAGTTTAGATGAAGGAATTGG
CTGCCCTAAAGGAACGCGCCACCCGTGGTA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S006.fas000066400000000000000000000001521211610345200232170ustar00rootroot00000000000000>S6
TATGTGCCGGTAGTGCGCAGTGGGCGTGTATAGTTACAACTAAGCCAAACAGTTTAGATGAAGGACTTGG
CTGCACTAAAGGAACGCGCCACCCGTGGTA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S007.fas000066400000000000000000000001521211610345200232200ustar00rootroot00000000000000>S7
TATGTGCCGGTAGTGCGCAGTGGGCGTGTATAGTTACAACTAAGCCAAACAGTTTAGATGAAGGACTTGG
CAGTACTAAAGGAACGCGCCACCCGTGGTA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S008.fas000066400000000000000000000001521211610345200232210ustar00rootroot00000000000000>S8
TATGTGCCGGTAGTGCGCAGTGGGCGTGTATAGTTACAACTAAGCGAAACAGTTTAGATGAAGGAATTGG
CTGCACTAAAGGAACGCGCCACCCGTGGTA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S009.fas000066400000000000000000000001521211610345200232220ustar00rootroot00000000000000>S9
TATGTGCCGGTAGTGCGCAGTGGGCGTGTATAGTTACAACTAAGCCAAACAGTTTAGATGAAGGACTTGG
CAGTACTAAAGGAACGCGCCACCCGTGGAA
genometools-1.5.1/testdata/genomediff/000100_001_0.1_010_S010.fas000066400000000000000000000001531211610345200232130ustar00rootroot00000000000000>S10
TATGTGCCGGTAGTGCCCAGTGGGCGTGTATAGTTACAACTAAGCCAAACAGTTTAGATGAAGGACTTGG
CTGCACTAAAGGAACGCGCCACCCGTGGTA
genometools-1.5.1/testdata/genomediff/000100_005_0.1_002_S001.fas000066400000000000000000000002141211610345200232160ustar00rootroot00000000000000>L1_S1
TCAAGCCGATGAACGGCCAA
>L1_S2
TCAAGCCGATAAACGGCCAA
>L1_S3
TCAAGCCGATGAACGGCCAA
>L1_S4
TCAAGCCGATAAACGGCCCA
>L1_S5
TCAAGCCGATGAACGGCCAA
genometools-1.5.1/testdata/genomediff/000100_005_0.1_002_S002.fas000066400000000000000000000002141211610345200232170ustar00rootroot00000000000000>L2_S1
GTCCTTGGATAGGAGTCACA
>L2_S2
GTCCTTGGATAGGAGTCACA
>L2_S3
GTCCTCGGATAGGACTCACA
>L2_S4
GTCCTCGGATAGGACTCACA
>L2_S5
GTCCTCGGATAGGACTCACA
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S001.fas000066400000000000000000000002141211610345200232150ustar00rootroot00000000000000>L1_S1
CGTACCAGTTATTGTGACAA
>L1_S2
CGTACAAGTTATTGTGAAAA
>L1_S3
CGTACAAGTTATTGTGAAAA
>L1_S4
CGTACAAGTTATTGTGAAAA
>L1_S5
CGTACAAGTTATTGTGAAAA
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S002.fas000066400000000000000000000002141211610345200232160ustar00rootroot00000000000000>L2_S1
ATCAAATAACGGGTGCCCAT
>L2_S2
ATCAAATAACGGGTGCCCAT
>L2_S3
ATCAAATAACGGGTGCCCAT
>L2_S4
ATCAAATAACAGGTGTCCAT
>L2_S5
ATCAAATAACAGGTGTCCAT
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S003.fas000066400000000000000000000002141211610345200232170ustar00rootroot00000000000000>L3_S1
CCTTGTTGCTCCCTACATGG
>L3_S2
CCTTGTTGCTCCCTACATGG
>L3_S3
CCTTGTTGCTCCCTACATGG
>L3_S4
GCTTGTTGCTCCCTACATGG
>L3_S5
CCTGGTTGCTCCCTACATGG
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S004.fas000066400000000000000000000002141211610345200232200ustar00rootroot00000000000000>L4_S1
CCCAAGAGTATCGTTGGGAA
>L4_S2
CCCAAGAGTATCGTTTGGAA
>L4_S3
CCCAAGAGTATCGTTTGGTA
>L4_S4
CCCAAGAGTATCGTTTGGAA
>L4_S5
CCCAAGAGTATCGTTTGGTA
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S005.fas000066400000000000000000000002141211610345200232210ustar00rootroot00000000000000>L5_S1
TTAAACTACCGTCGATCGGA
>L5_S2
TTAAACTACCGTCGATCGGA
>L5_S3
TTAAATTACCGACGATCGGA
>L5_S4
TTAAATTACCGACGATCGGA
>L5_S5
TTAAACTACCGTCGATCGGA
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S006.fas000066400000000000000000000002141211610345200232220ustar00rootroot00000000000000>L6_S1
AGCCTACTGGTCTGTCCTGC
>L6_S2
AGCCTACTGGTCTGTCCTGC
>L6_S3
AGCCTACGGGTCTGTCCAGC
>L6_S4
AGCCTACGGGTCTGTCCAGC
>L6_S5
AGCCTACTGGTCTGTCCTGC
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S007.fas000066400000000000000000000002141211610345200232230ustar00rootroot00000000000000>L7_S1
GCTTGCCTGTTCACCACGTG
>L7_S2
GCTTGCCTGTTCACCACGTG
>L7_S3
GCTTGGCTGTTCACCACGTG
>L7_S4
GCTTCCCTGTTCACCACGTG
>L7_S5
GCTTGCCTGTTCACCACGTG
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S008.fas000066400000000000000000000002141211610345200232240ustar00rootroot00000000000000>L8_S1
GTCACGCTTTGGCACCCGCT
>L8_S2
GTCACGCTTTGGCACCCGCT
>L8_S3
GTCACGCTTTGGCACGCGCT
>L8_S4
GTCACGCGTTGGCACCCGCT
>L8_S5
GTCACGCTTTGGCACCCGCT
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S009.fas000066400000000000000000000002141211610345200232250ustar00rootroot00000000000000>L9_S1
GTTTAAGCATAGTTCACCAA
>L9_S2
GTTTAAGCATAGCTCATCAA
>L9_S3
GTTTAAGCATAGCTCACCAA
>L9_S4
GTTTAAGCATAGCTCACCAA
>L9_S5
GTTTAAGCATAGCTCACCAA
genometools-1.5.1/testdata/genomediff/000100_005_0.1_010_S010.fas000066400000000000000000000002211211610345200232130ustar00rootroot00000000000000>L10_S1
GGAATGAGAAAATACGGCCG
>L10_S2
GGAATGAGAAAATACGGCCG
>L10_S3
GCAATGAGAAAAAACGGCCG
>L10_S4
GGAATGAGAAAATACGGCCG
>L10_S5
GGAATGAGAAAATACGGCCG
genometools-1.5.1/testdata/genomediff/000150_001_0.1_002-kr.out000066400000000000000000000001461211610345200231700ustar00rootroot000000000000002
S1         0 2578 
S2         2528 0 
2
S1         0.000000 0.154497 
S2         0.154497 0.000000 
genometools-1.5.1/testdata/genomediff/000150_001_0.1_002_S001.fas000066400000000000000000000002351211610345200232220ustar00rootroot00000000000000>S1
GAATTGTTAGGTTATCGTGTCACTTGTTTACTCCCGACACTTGTTAATGCTTACAACCAGGAGCGACGCT
CTCTCGTAAATAACCACGCACCCCTCTAATCTCCCGACCTACACTGGAAGATCCATCCCTATAGCGTCAA
ATTTTGTAGC
genometools-1.5.1/testdata/genomediff/000150_001_0.1_002_S002.fas000066400000000000000000000002351211610345200232230ustar00rootroot00000000000000>S2
GAATTGTTGGGTTATCGTGCCACTTGTTTACTCCCGAGACTTGTTAATGCTTACAACCAGGTGCGACGCT
GTCTCGTAAATTACCACGTCCCCCTCTAATCTCCTGACCTACACTCGAGGACCGATCCCTATAGCGTCAA
ATATTGTATC
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010-kr.out000066400000000000000000000031421211610345200231660ustar00rootroot0000000000000010
S1         0 22950 4916 5820 4652 8318 11654 9736 22950 6568 
S2         22950 0 4916 5820 4652 8318 11654 9736 22950 6568 
S3         4952 4952 0 4302 3510 4994 5140 5634 4952 4372 
S4         5818 5818 4262 0 6812 7288 8212 6232 5818 15716 
S5         4630 4630 3452 6804 0 4298 5218 4782 4630 6854 
S6         8326 8326 4964 7304 4326 0 14236 8928 8326 8672 
S7         11658 11658 5102 8218 5240 14232 0 11324 11658 9586 
S8         9746 9746 5604 6244 4812 8926 11330 0 9746 7232 
S9         22950 22950 4916 5820 4652 8318 11654 9736 0 6568 
S10        6572 6572 4338 15722 6868 8668 9586 7226 6572 0 
10
S1         0.000000 0.011152 0.066279 0.054946 0.070961 0.037465 0.026294 0.031763 0.011152 0.048206 
S2         0.011152 0.000000 0.066279 0.054946 0.070961 0.037465 0.026294 0.031763 0.011152 0.048206 
S3         0.066279 0.066279 0.000000 0.078083 0.100727 0.065562 0.063555 0.057287 0.066279 0.076494 
S4         0.054946 0.054946 0.078083 0.000000 0.046396 0.043095 0.037978 0.051020 0.054946 0.018948 
S5         0.070961 0.070961 0.100727 0.046396 0.000000 0.077322 0.062016 0.068402 0.070961 0.046031 
S6         0.037465 0.037465 0.065562 0.043095 0.077322 0.000000 0.021194 0.034800 0.037465 0.035879 
S7         0.026294 0.026294 0.063555 0.037978 0.062016 0.021194 0.000000 0.027084 0.026294 0.032288 
S8         0.031763 0.031763 0.057287 0.051020 0.068402 0.034800 0.027084 0.000000 0.031763 0.043501 
S9         0.011152 0.011152 0.066279 0.054946 0.070961 0.037465 0.026294 0.031763 0.000000 0.048206 
S10        0.048206 0.048206 0.076494 0.018948 0.046031 0.035879 0.032288 0.043501 0.048206 0.000000 
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S001.fas000066400000000000000000000002351211610345200232210ustar00rootroot00000000000000>S1
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGGGCGACCCAGTGACCGGACGGCCTACCTTCCA
ATTGATCCGGACTAGCCCCATTACGAATTCGAAGGTCGGCTCTGTGCATAAGGGTAGAAACGCACCGCTT
TTTCACCTAA
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S002.fas000066400000000000000000000002351211610345200232220ustar00rootroot00000000000000>S2
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGGGCGACCCAGTGACCGGACGGCCTACCTTCCA
ATTGATCCGGACTAGCCCCATTACGAATTCGAAGGTCGGCTCTGTGCATAAGGGTAGAAACGCACCGCTT
TTTCACCTAA
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S003.fas000066400000000000000000000002351211610345200232230ustar00rootroot00000000000000>S3
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGGGTGACCCAGTGACCGGACGGCCTACCTTCCT
ATTGATCCAGATTAGCCCCATTACGAATTCGAAGGTCGGCTCTGTCCATAAGGGTAGAAACGCACCGCTT
TTTCTTCTAA
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S004.fas000066400000000000000000000002351211610345200232240ustar00rootroot00000000000000>S4
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGGGCGACCCAGTGGCCGGACGGCCTACCTTCCA
ATTGATCCGGATTAGCCCCATTACGAATTCGAAGGTCGGCTCTGTGCATAGGGGTAGAAAGGCACCGCTT
TTTCACCTAA
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S005.fas000066400000000000000000000002351211610345200232250ustar00rootroot00000000000000>S5
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGGGCGACCCAGTGGCCGGACGGCCTGCCTTCCA
ATTGATCCGGATTAGCCCCATTACGAAATCGAAGGTCGGCTCTGTGCATTAGGGTAGAAAGGCACCGCTT
TTTCACCTAA
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S006.fas000066400000000000000000000002351211610345200232260ustar00rootroot00000000000000>S6
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGAGCGACCCAGTGACCGGACGGCCTACCTTCCA
ATTGATCCGGATTAGCCCCATTACGAATTCGAAGGTCGGCTCTGTGCATAAGGGTAGAAACGCACCGCTT
TTTCACCTAA
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S007.fas000066400000000000000000000002351211610345200232270ustar00rootroot00000000000000>S7
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGGGCGACCCAGTGACCGGACGGCCTACCTTCCA
ATTGATCCGGATTAGCCCCATTACGAATTCGAAGGTCGGCTCTGTGCATAAGGGTAGAAACGCACCGCTT
TTTCACCTAA
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S008.fas000066400000000000000000000002351211610345200232300ustar00rootroot00000000000000>S8
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGGGCGACCCAGTGACCGGACGGCCTACCTTCCT
ATTGATCCGGATTAGCCCCATTACGAATTCGAAGGTCGGCTCTGTGCATAAGGGTAGAAACGCACCGCTT
TTTCACCTCA
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S009.fas000066400000000000000000000002351211610345200232310ustar00rootroot00000000000000>S9
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGGGCGACCCAGTGACCGGACGGCCTACCTTCCA
ATTGATCCGGACTAGCCCCATTACGAATTCGAAGGTCGGCTCTGTGCATAAGGGTAGAAACGCACCGCTT
TTTCACCTAA
genometools-1.5.1/testdata/genomediff/000150_001_0.1_010_S010.fas000066400000000000000000000002361211610345200232220ustar00rootroot00000000000000>S10
TTCGCATAACCCTTCTTCTAAGGTGACTCACGGAATAGGGCGACCCAGTGGCCGGACGGCCTACCTTCCA
ATTGATCCGGATTAGCCCCATTACGAATTCGAAGGTCGGCTCTGTGCATAAGGGTAGAAAGGCACCGCTT
TTTCACCTAA
genometools-1.5.1/testdata/genomediff/000150_005_0.1_002_S001.fas000066400000000000000000000002761211610345200232330ustar00rootroot00000000000000>L1_S1
ACAGCAATACCGGCGAAAGGACGTGCCGTA
>L1_S2
ACAGCAATACCGGCTAAAGGACGTGCCGTT
>L1_S3
ACAGCAATACCGGCTAAAGGACGTGCGGTT
>L1_S4
ACAGCAATACCGGCTAAAGGACGTGCGGTT
>L1_S5
ACAGCAATACCGGCTAAAGGACGTGCCGTT
genometools-1.5.1/testdata/genomediff/000150_005_0.1_002_S002.fas000066400000000000000000000002761211610345200232340ustar00rootroot00000000000000>L2_S1
GGACAATGAACTTTCATGGGATATTATGCA
>L2_S2
GGACAACGAACTTTCTTAGGATATTATGCA
>L2_S3
GGACAATGAACTTTCTTGGGATATTATGCA
>L2_S4
GGACAATGAACTTTCTTAGGATATTATGCA
>L2_S5
GGACAATGAACTTTCTTGGGATATTATGCA
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S001.fas000066400000000000000000000002761211610345200232320ustar00rootroot00000000000000>L1_S1
GCGCCATTACGAGACATACGGTACTAATTC
>L1_S2
GCGCCATTACGAGACATAGGGTACGAATTC
>L1_S3
GCGCCATTACGAGACATACGGTACTAATTC
>L1_S4
GCGCCATTACGAGACATAGGGTGCTAATTC
>L1_S5
GCGCCATTACGAGACATAGGGTACTAATTC
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S002.fas000066400000000000000000000002761211610345200232330ustar00rootroot00000000000000>L2_S1
CGATGCTACACTCGTCTTGGAGCCCAGTAC
>L2_S2
CGACGCAACACCCGTCTTGGAGCCCAGTAC
>L2_S3
CGACGCAACACCCGTCTTGGAGCCCAGTAC
>L2_S4
CGATGCTACACTCGTCTTGGAGCCCAGTAC
>L2_S5
CGATGCTACACTCGTCTTGGAGCCCAGTAC
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S003.fas000066400000000000000000000002761211610345200232340ustar00rootroot00000000000000>L3_S1
GCGCTGTGGTTCGCTCTCTGAGGTCTACCA
>L3_S2
GCGCAGTGGTTCGCTCTCTGAGGTCTACCA
>L3_S3
GCGCAGTGGTTCGCTCTCTGAGGTCTACCA
>L3_S4
GCGCAGTGGTTCGCTCTCTGAGGTCTTCCA
>L3_S5
GCGCAGAGGTTCGCTCTCTGAGGTCTACCA
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S004.fas000066400000000000000000000002761211610345200232350ustar00rootroot00000000000000>L4_S1
GATGGGAATAGGACTCGCGGGCGGTGTAGC
>L4_S2
GATGGGAATAGGACTCGCGGACGGTGTAGG
>L4_S3
GATGGGAATAGGACTCGCGGACGGTGTAGG
>L4_S4
GATGGGAATAGGACTCGCGGACGGTGTACC
>L4_S5
GATGGGAATAGGACTCGCGGACGGTGTAGG
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S005.fas000066400000000000000000000002761211610345200232360ustar00rootroot00000000000000>L5_S1
GTGCTTATGCCCCGATGACATTACATATGC
>L5_S2
CTGCTTATGGCCCGATGACATTACATATGC
>L5_S3
CTGCTTAGGGCCCGATGACATTACATATGC
>L5_S4
CTGCTTATGGCCCGATGACATTACATATGC
>L5_S5
GTGCTTATGCCCCGATGACATTACATATGC
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S006.fas000066400000000000000000000002761211610345200232370ustar00rootroot00000000000000>L6_S1
GGGGCGGGAGTAAAGCGGAGGGACGGAGCT
>L6_S2
GGGGCTGGAGTAAAGCGGAGGGACGGAGCT
>L6_S3
GGGGCTGGAGTAAAGCGGAGGGCCGGAGCT
>L6_S4
GGGGCGGGAGTAAAGCGGAGGGACGGAGCT
>L6_S5
GGGGCTGGAGTAAAGCGGAGGGACGTAGCT
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S007.fas000066400000000000000000000002761211610345200232400ustar00rootroot00000000000000>L7_S1
TACCATGGCCTGTAACCAACCCTCTAAGAG
>L7_S2
TACCATGGCCTGTAACCAACCCTCTTAGAG
>L7_S3
TACCATGGCCTGTAACCAACCCTCTAAGAG
>L7_S4
TACCATGGCCTGTAACAAACCCACTAAGAG
>L7_S5
TACCATGGCCTGTAACAAACCCACTAAGAG
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S008.fas000066400000000000000000000002761211610345200232410ustar00rootroot00000000000000>L8_S1
AGCAGTGAGCCTATAAAGCCGTATGCTCTG
>L8_S2
AGCATTGAGCCTTTAAAGCCGTATGCTCTG
>L8_S3
AGCAGTGAGCCTATAAAGCCGTATGCTCTG
>L8_S4
AGCATTGAGTCTTTAAAGCCGTATGCTCTG
>L8_S5
AGCAGTGAGCCTATAAAGCCGTATGCTCTG
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S009.fas000066400000000000000000000002761211610345200232420ustar00rootroot00000000000000>L9_S1
TACACACCTTAAAGTAGTCCTTGACGGATA
>L9_S2
TACAAACCTTAAAGTAGTCCCTGACAGATA
>L9_S3
TACACACCTTAAAGTAGTCCTTGACGGATA
>L9_S4
TACACACCTTAAAGTAGTCCCTGACGGATA
>L9_S5
TACACACCTTAAAGTAGTCCTTGACGGATA
genometools-1.5.1/testdata/genomediff/000150_005_0.1_010_S010.fas000066400000000000000000000003031211610345200232210ustar00rootroot00000000000000>L10_S1
AGCTACTTCGGGTCCTACTTTTCCATGATT
>L10_S2
AGCTACTTCGGGTCCTACTTTTCCATGATT
>L10_S3
AGCTACTTCGGGTCCTACTTTTCCATGATT
>L10_S4
AGCTACTTCGGGTCCTACTTTTCCATGATT
>L10_S5
ACCTACGTCGGGTGCTACTTTTCCATGATT
genometools-1.5.1/testdata/genomediff/testsuite000066400000000000000000000000231211610345200217270ustar00rootroot00000000000000000150_001_0.1_010
genometools-1.5.1/testdata/genomediff/unitfile1.lua000066400000000000000000000007401211610345200223640ustar00rootroot00000000000000--correct file
units = {
  genome1 = { "000150_001_0.1_010_S001.fas",
              "000150_001_0.1_010_S002.fas",
              "000150_001_0.1_010_S003.fas",
              "000150_001_0.1_010_S004.fas",
              "000150_001_0.1_010_S005.fas" },
  genome2 = { "000150_001_0.1_010_S006.fas",
              "000150_001_0.1_010_S007.fas",
              "000150_001_0.1_010_S008.fas",
              "000150_001_0.1_010_S009.fas",
              "000150_001_0.1_010_S010.fas" }
}
genometools-1.5.1/testdata/genomediff/unitfile2.lua000066400000000000000000000010051211610345200223600ustar00rootroot00000000000000-- double file in genome1 and genome2 should fail!
units = { 
  genome1 = { "000150_001_0.1_010_S001.fas",
              "000150_001_0.1_010_S002.fas",
              "000150_001_0.1_010_S003.fas",
              "000150_001_0.1_010_S004.fas",
              "000150_001_0.1_010_S005.fas" },
  genome2 = { "000150_001_0.1_010_S002.fas",
              "000150_001_0.1_010_S007.fas",
              "000150_001_0.1_010_S008.fas",
              "000150_001_0.1_010_S009.fas",
              "000150_001_0.1_010_S010.fas" }
}
genometools-1.5.1/testdata/genomediff/unitfile3.lua000066400000000000000000000006731211610345200223730ustar00rootroot00000000000000-- one file is missing
units = {
  genome1 = { "000150_001_0.1_010_S001.fas",
              "000150_001_0.1_010_S002.fas",
              "000150_001_0.1_010_S003.fas",
              "000150_001_0.1_010_S004.fas" },
  genome2 = { "000150_001_0.1_010_S006.fas",
              "000150_001_0.1_010_S007.fas",
              "000150_001_0.1_010_S008.fas",
              "000150_001_0.1_010_S009.fas",
              "000150_001_0.1_010_S010.fas" }
}
genometools-1.5.1/testdata/genomediff/unitfile4.lua000066400000000000000000000010051211610345200223620ustar00rootroot00000000000000-- file not in index
units = {
  genome1 = { "000150_001_0.1_010_S001.fas",
              "not_there.fas",
              "000150_001_0.1_010_S002.fas",
              "000150_001_0.1_010_S003.fas",
              "000150_001_0.1_010_S004.fas",
              "000150_001_0.1_010_S005.fas" },
  genome2 = { "000150_001_0.1_010_S006.fas",
              "000150_001_0.1_010_S007.fas",
              "000150_001_0.1_010_S008.fas",
              "000150_001_0.1_010_S009.fas",
              "000150_001_0.1_010_S010.fas" }
}
genometools-1.5.1/testdata/gff3_file_1_short.txt000066400000000000000000000011671211610345200217060ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00002;Parent=gene00001
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA00003;Parent=gene00001
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA00003
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA00001,mRNA00002
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA00001,mRNA00003
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA00001,mRNA00002,mRNA00003
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA00001,mRNA00002,mRNA00003
genometools-1.5.1/testdata/gff3_file_1_short_sorted.txt000066400000000000000000000010571211610345200232640ustar00rootroot00000000000000###
##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1,mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	gene	1000	9000	.	+	.	ID=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
genometools-1.5.1/testdata/gmap2gff3_prob.gmap000066400000000000000000000034271211610345200213270ustar00rootroot00000000000000>gi|22209069|gb|BC036470.1| Homo sapiens cadherin 2, type 1, N-cadherin (neuronal), mRNA (cDNA clone MGC:41765 IMAGE:5264944), complete cds
Paths (1):
  Path 1: query 2--4018 (4017 bp) => chr NA:20,789,928--20,563,762 (-226167 bp)
    cDNA direction: sense
    Genomic pos: encode_regions:20,789,928--20,563,762 (- strand)
    Accessions: ENr213:65,702--291,868 (out of 500000 bp)
    Number of exons: 16
    Coverage: 99.6 (query length: 4033 bp)
    Trimmed coverage: 100.0 (trimmed length: 4018 bp, trimmed region: 1..4018)
    Percent identity: 99.6 (4003 matches, 14 mismatches, 1 indels, 0 unknowns)
    Non-intron gaps: 0 openings, 0 bases in cdna; 1 openings, 1 bases in genome
    Translation: 3..2837 (944 aa)
    Amino acid changes: P1R [2], P202S [605], P475Q [1424], T492A [1475], V522M [1565], D667G [2000]

Alignments:
  Alignment for path 1:

    -NA:20789928-20789754  (2-176)   98% ->   ...29178...
    -NA:20760575-20760464  (177-288)   100% ->   ...133763...
    -NA:20626700-20626474  (289-515)   99% ->   ...1690...
    -NA:20624783-20624637  (516-662)   99% ->   ...1973...
    -NA:20622663-20622508  (663-818)   100% ->   ...3723...
    -NA:20618784-20618640  (819-963)   100% ->   ...2679...
    -NA:20615960-20615788  (964-1136)   100% ->   ...9359...
    -NA:20606428-20606291  (1137-1274)   100% ->   ...659...
    -NA:20605631-20605446  (1275-1460)   99% ->   ...2304...
    -NA:20603141-20602888  (1461-1714)   98% ->   ...1430...
    -NA:20601457-20601315  (1715-1857)   100% ->   ...2762...
    -NA:20598552-20598319  (1858-2091)   99% ->   ...294...
    -NA:20598024-20597791  (2092-2325)   99% ->   ...1916...
    -NA:20595874-20595735  (2326-2465)   100% ->   ...19422...
    -NA:20576312-20576148  (2466-2630)   99% ->   ...10997...
    -NA:20565150-20563762  (2631-4018)   99%

genometools-1.5.1/testdata/gmap2gff3_prob.out000066400000000000000000000017231211610345200212070ustar00rootroot00000000000000##gff-version   3
##sequence-region ENr213 20563762 20789928
ENr213	gmap	gene	20563762	20789928	.	-	.	ID=gene1
ENr213	gmap	exon	20789754	20789928	.	-	.	Parent=gene1
ENr213	gmap	exon	20760464	20760575	.	-	.	Parent=gene1
ENr213	gmap	exon	20626474	20626700	.	-	.	Parent=gene1
ENr213	gmap	exon	20624637	20624783	.	-	.	Parent=gene1
ENr213	gmap	exon	20622508	20622663	.	-	.	Parent=gene1
ENr213	gmap	exon	20618640	20618784	.	-	.	Parent=gene1
ENr213	gmap	exon	20615788	20615960	.	-	.	Parent=gene1
ENr213	gmap	exon	20606291	20606428	.	-	.	Parent=gene1
ENr213	gmap	exon	20605446	20605631	.	-	.	Parent=gene1
ENr213	gmap	exon	20602888	20603141	.	-	.	Parent=gene1
ENr213	gmap	exon	20601315	20601457	.	-	.	Parent=gene1
ENr213	gmap	exon	20598319	20598552	.	-	.	Parent=gene1
ENr213	gmap	exon	20597791	20598024	.	-	.	Parent=gene1
ENr213	gmap	exon	20595735	20595874	.	-	.	Parent=gene1
ENr213	gmap	exon	20576148	20576312	.	-	.	Parent=gene1
ENr213	gmap	exon	20563762	20565150	.	-	.	Parent=gene1
###
genometools-1.5.1/testdata/graphics_curve_test_coords.txt000066400000000000000000000034111211610345200240310ustar00rootroot000000000000000.252464995017
0.716618647975
0.83852191163
0.202045104845
0.682322663933
0.625222020058
0.0464627170919
0.492734099275
0.654170946759
0.438116845367
0.0264870130995
0.430784649214
0.78778849365
0.348824961841
0.103773357931
0.257709570123
0.23014191757
0.662081461976
0.219166988477
0.0540194033005
0.54875457577
0.00565834156609
0.321912792477
0.402201358964
0.330139923464
0.0292826637407
0.606652525416
0.559477125422
0.72900242578
0.184423871612
0.688571973222
0.0687212062229
0.944742395088
0.863826487571
0.551930189584
0.739601363475
0.269300385162
0.764335175928
0.437325266564
0.943464908586
0.919697953018
0.688069524851
0.355759601303
0.351355072497
0.130259609106
0.430024816487
0.352326305516
0.869812762779
0.952130989772
0.588517073104
0.46576596471
0.964169927055
0.674351493669
0.920811068874
0.894093170248
0.740538396554
0.839071476775
0.318254040324
0.504775279167
0.68327537007
0.246838393533
0.0722537150165
0.144005651683
0.523513216403
0.310615087258
0.609291526849
0.722830866929
0.444321122305
0.168699740012
0.98193385698
0.885837262411
0.774797127085
0.509025068478
0.266816134398
0.145493119599
0.0505351051504
0.485829240225
0.406962804646
0.243669183637
0.0438175910366
0.572172305413
0.086649699935
0.302807895428
0.702069476032
0.272007127656
0.966887090457
0.0755566399874
0.39672632104
0.272856207442
0.177205544617
0.994850549681
0.935342011844
0.890435332824
0.503080598578
0.188600735111
0.757298718726
0.588767547135
0.426300856701
0.446797036927
0.201569236252
0.677500844938
0.935258347902
0.589133015268
0.632577206141
0.884366783136
0.712853930128
0.701441659378
0.10350035832
0.765294727045
0.25596088855
0.296620166883
0.805385889229
0.689686748786
0.749523614437
0.533825839419
0.603982863779
0.110041882939
0.833757730072
0.0157582782621
0.318078355996
genometools-1.5.1/testdata/graphics_test.out000066400000000000000000000646001211610345200212530ustar00rootroot00000000000000















































  


  


  


  


  


  


  


  


  


  


  


  


  





  
  
  
  
  
  
  
  
  


  
  
  
  
  
  
  
  
  
  
  
  
  
  


  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  


  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
















































genometools-1.5.1/testdata/gt.supp000066400000000000000000000045161211610345200172060ustar00rootroot00000000000000{
   
   Memcheck:Cond
   fun:_tr_flush_block
   fun:deflate_slow
   fun:deflate
   fun:png_write_finish_row
}
{
   
   Memcheck:Cond
   fun:_tr_flush_block
   fun:deflate_slow
   fun:deflate
   fun:png_write_filtered_row
}
{
   
   Memcheck:Cond
   fun:longest_match
   fun:deflate_slow
   fun:deflate
   fun:do_flush
   fun:gzclose
   ...
}
{
   
   Memcheck:Cond
   fun:deflate_slow
   fun:deflate
   fun:gzclose
   ...
}
{
   
   Memcheck:Cond
   fun:longest_match
   fun:deflate_slow
   ...
   fun:gt_graphics_cairo_save_to_*
   ...
}
{
   
   Memcheck:Cond
   ...
   fun:deflate_slow
   fun:deflate
   ...
   obj:*lib/*libcairo*
   ...
}
{
   
   Memcheck:Cond
   fun:pthread_rwlock_init
   fun:gt_rwlock_new
   fun:gt_ma_init
   fun:gt_lib_init
   ...
}
{
   Fontconfig_static_data_problem
   Memcheck:Addr4
   ...
   fun:FcConfigParseAndLoad
   ...
}
{
   Fontconfig_static_data_problem
   Memcheck:Addr8
   ...
   fun:FcConfigParseAndLoad
   ...
}
{
   leak_within_pango1
   fun:*alloc
   ...
   fun:g_type_init_with_debug_flags
   fun:pango_cairo_font_map_new
}
{
   leak_within_pango3
   Memcheck:Leak
   fun:*alloc
   ...
   fun:g_get_language_names
   fun:g_thread_init_glib
   fun:g_type_init_with_debug_flags
   fun:pango_cairo_font_map_new
}
{
   leak_within_pango5
   Memcheck:Leak
   fun:*alloc
   ...
   fun:g_type_register_fundamental
   ...
   fun:g_type_init_with_debug_flags
   fun:pango_cairo_font_map_new
}
{
   leak_within_pango8
   Memcheck:Leak
   fun:*alloc
   ...
   fun:pango_find_map
}
{
   leak_within_pango13
   Memcheck:Leak
   fun:*alloc
   ...
   fun:pango_itemize_with_base_dir
}
{
   leak_within_pango15
   Memcheck:Leak
   fun:memalign
   ...
   fun:g_type_init_with_debug_flags
   fun:pango_cairo_font_map_new
}
{
   leak_within_pango18
   Memcheck:Leak
   fun:*alloc
   ...
   fun:pango_cairo_font_map_get_default
}
{
   leak_within_pango19
   Memcheck:Leak
   fun:*alloc
   ...
   obj:/usr/lib*/libpango*
}
{
   leak_within_pango20
   Memcheck:Leak
   fun:memalign
   ...
   obj:/usr/lib*/libpango*
}
{
   freetype_leak
   Memcheck:Leak
   fun:*alloc
   ...
   obj:*lib/libfreetype*
   ...
}
{
   cairo_catchall_static_leaks
   Memcheck:Leak
   fun:malloc
   ...
   obj:*lib/libcairo*
   ...
}
{
   fontconfig_leak
   Memcheck:Leak
   fun:*alloc
   ...
   obj:*lib/libfontconfig*
   ...
}
genometools-1.5.1/testdata/gt_bioseq_fail_1.fas000066400000000000000000000000001211610345200215250ustar00rootroot00000000000000genometools-1.5.1/testdata/gt_bioseq_fail_2.fas000066400000000000000000000000021211610345200215300ustar00rootroot00000000000000x
genometools-1.5.1/testdata/gt_bioseq_fail_3.fas000066400000000000000000000000021211610345200215310ustar00rootroot00000000000000>
genometools-1.5.1/testdata/gt_bioseq_fail_4.fas000066400000000000000000000000031211610345200215330ustar00rootroot00000000000000>d
genometools-1.5.1/testdata/gt_bioseq_fail_5.fas000066400000000000000000000000031211610345200215340ustar00rootroot00000000000000>

genometools-1.5.1/testdata/gt_bioseq_fail_6.fas000066400000000000000000000000041211610345200215360ustar00rootroot00000000000000>
>
genometools-1.5.1/testdata/gt_bioseq_fail_7.fas000066400000000000000000000000021211610345200215350ustar00rootroot00000000000000>dgenometools-1.5.1/testdata/gt_bioseq_seqlengthdistri.out000066400000000000000000000007611211610345200236570ustar00rootroot00000000000000sequence length distribution:
29: 1 (prob=0.0833,cumulative=0.0833)
75: 1 (prob=0.0833,cumulative=0.1667)
102: 1 (prob=0.0833,cumulative=0.2500)
111: 1 (prob=0.0833,cumulative=0.3333)
156: 1 (prob=0.0833,cumulative=0.4167)
296: 1 (prob=0.0833,cumulative=0.5000)
368: 1 (prob=0.0833,cumulative=0.5833)
480: 1 (prob=0.0833,cumulative=0.6667)
493: 1 (prob=0.0833,cumulative=0.7500)
889: 1 (prob=0.0833,cumulative=0.8333)
924: 1 (prob=0.0833,cumulative=0.9167)
1300: 1 (prob=0.0833,cumulative=1.0000)
genometools-1.5.1/testdata/gt_bioseq_succ_1.fas000066400000000000000000000000041211610345200215530ustar00rootroot00000000000000>
c
genometools-1.5.1/testdata/gt_bioseq_succ_2.fas000066400000000000000000000000101211610345200215510ustar00rootroot00000000000000>
c
>
c
genometools-1.5.1/testdata/gt_bioseq_succ_3.fas000066400000000000000000000040741211610345200215700ustar00rootroot00000000000000>gi|8690385|dbj|AV530102.1|AV530102 AV530102 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL58h01R 5', mRNA sequence
CTGGTTCGTTGCCGCCTTGCACGTTCCTTCTTCTTCCTTCTCTCCCCCCCATCTTATCTCTTTCCCCCCC
TTTACCCTAACCCTAATTTTCTTCGCCGTCCTCTCTTTTCTCTCTATCTAATTTCGTTCCCATATTCGAA
ATCTCTTACCTTTTATCTCCAGATCTTTTAGATCCGTAATTCCCTACTATTGATTATACCCAAACTTTTA
CTCTTATCTTCCTCGTTTGATTCTTATGCTTCCTTTTATGAATTGATTTCTTCATAAAGTCATCATCTTT
GGATTGAATTCGACTCATTAATCAATCCGTTAACCAATAACCACCTTGACAGTTTCTTCTCCGAGGATTC
CAGATTACAATTCTAGTGGAGCTGTAATTGGATTCAGATCTAACTCAAGTTAGTGTTACTGATGTGTCTA
TTGGATGCAATCGTGTAGTGATATTGAATATATTTCTGATGGGAGAAGGAACTATTTGTTTGGAGATGCC
AAAGGAAGAGAATGGTCAATTGAAAAGAGATA
>gi|8690380|dbj|AV530097.1|AV530097 AV530097 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL58e12R 5', mRNA sequence
GTCGTGAAGAATCCACTCAGTCCAAATTCTGGACAAGCAAACCTTAAAAGGAATATGGTATCTGAAAAGG
AAATTGATGCACCTTTGCAGATTGGAATTGTTCGTGTCTTTGAGCAACAAGGTATTGAAGCTCCTAGTGA
CGATGATGATTTTATTGAGGTAAGATCAAAAAGGCAAATGCTTAATGATCGCCGTGAACAGAGAGAAAAG
GAAATTAAAGAGAAGTCTCAGGCAGCCAAGGCATTCCGAAAACCTCGTTCAACTTTCCAGAACAATACTA
CTGCAGCCAGGTCCAACAGAAGCCCACCAGCTAGCCGAGCTGCGAACAATAAGCAGTTTAATCCAGTCTC
CAACAGACAGACGTTAGCCCCAATTGGCACACCTTCACCTAAAATAGATTCCCATGTTGATGAAAAATCT
GGGAGCAACAAGTCCACTCAGGAAAGTAGTGCTCTTCCAGTTATACCCAAAAATGATCAGAATCCAGCGT
CAGGTTTTGTATTCAGCAACAAAAATAAGGTTCTCGATAACAGTCATACACCTGTGGGGAC
>gi|8690379|dbj|AV530096.1|AV530096 AV530096 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL58e11R 5', mRNA sequence
CCAAAATCCTCAAAGAGAGACTATACTTCTCTCGGATCCTTCCTGATTTCAAAATTTCTTCAACCCACCA
GCAGCAGCAGCAGATGAAGAAGGTTAAACAGATTCGTGTCTTAAAGCCTTTCGATCTTCTCTCGGAAGAG
CTCGTCTTTATCATCCTTGACCTCATCTCTCCCAACCCTTCCGATCTCAAATCCTTCTCTCTTACTTGCA
AATCTTTCTACCAGCTCGAGTCCAAGCACCGCGGATCCTTAAAACCTCTCCGCTCCGACTATCTCCCTCG
CATCTTGACTCGTTACCGGAACACCACCGATCTCGATCTTACCTTCTGCCCGCGTGTCACTGACTACGCG
CTTAGCGTCGTTGGCTGTCTCTCCGGACCTACGCTTCGCTCCCTCGACCTCTCGCGCTCTGGCTCCTTCT
CCGCCGCGGGACTACTGCGATTGGCCCTCAAATGTGTCAATTTAGTCGAGATTGACCTGTCCAATGCGAC
GGAGATGAGAGACGCCGATGCTG
genometools-1.5.1/testdata/gt_bioseq_succ_3.gc000066400000000000000000000001431211610345200214010ustar00rootroot00000000000000showing GC-content for sequence file "-"
GC-content: 44.07% (AT-content: 55.93%, N-content: 0.00%)
genometools-1.5.1/testdata/gt_bioseq_succ_3.out1000066400000000000000000000012701211610345200217020ustar00rootroot00000000000000>gi|8690385|dbj|AV530102.1|AV530102 AV530102 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL58h01R 5', mRNA sequence
CTGGTTCGTTGCCGCCTTGCACGTTCCTTCTTCTTCCTTCTCTCCCCCCCATCTTATCTCTTTCCCCCCC
TTTACCCTAACCCTAATTTTCTTCGCCGTCCTCTCTTTTCTCTCTATCTAATTTCGTTCCCATATTCGAA
ATCTCTTACCTTTTATCTCCAGATCTTTTAGATCCGTAATTCCCTACTATTGATTATACCCAAACTTTTA
CTCTTATCTTCCTCGTTTGATTCTTATGCTTCCTTTTATGAATTGATTTCTTCATAAAGTCATCATCTTT
GGATTGAATTCGACTCATTAATCAATCCGTTAACCAATAACCACCTTGACAGTTTCTTCTCCGAGGATTC
CAGATTACAATTCTAGTGGAGCTGTAATTGGATTCAGATCTAACTCAAGTTAGTGTTACTGATGTGTCTA
TTGGATGCAATCGTGTAGTGATATTGAATATATTTCTGATGGGAGAAGGAACTATTTGTTTGGAGATGCC
AAAGGAAGAGAATGGTCAATTGAAAAGAGATA
genometools-1.5.1/testdata/gt_bioseq_succ_3.out2000066400000000000000000000013251211610345200217040ustar00rootroot00000000000000>gi|8690380|dbj|AV530097.1|AV530097 AV530097 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL58e12R 5', mRNA sequence
GTCGTGAAGAATCCACTCAGTCCAAATTCTGGACAAGCAAACCTTAAAAGGAATATGGTATCTGAAAAGG
AAATTGATGCACCTTTGCAGATTGGAATTGTTCGTGTCTTTGAGCAACAAGGTATTGAAGCTCCTAGTGA
CGATGATGATTTTATTGAGGTAAGATCAAAAAGGCAAATGCTTAATGATCGCCGTGAACAGAGAGAAAAG
GAAATTAAAGAGAAGTCTCAGGCAGCCAAGGCATTCCGAAAACCTCGTTCAACTTTCCAGAACAATACTA
CTGCAGCCAGGTCCAACAGAAGCCCACCAGCTAGCCGAGCTGCGAACAATAAGCAGTTTAATCCAGTCTC
CAACAGACAGACGTTAGCCCCAATTGGCACACCTTCACCTAAAATAGATTCCCATGTTGATGAAAAATCT
GGGAGCAACAAGTCCACTCAGGAAAGTAGTGCTCTTCCAGTTATACCCAAAAATGATCAGAATCCAGCGT
CAGGTTTTGTATTCAGCAACAAAAATAAGGTTCTCGATAACAGTCATACACCTGTGGGGAC
genometools-1.5.1/testdata/gt_bioseq_succ_3.out3000066400000000000000000000012571211610345200217110ustar00rootroot00000000000000>gi|8690379|dbj|AV530096.1|AV530096 AV530096 Arabidopsis thaliana aboveground organs two to six-week old Arabidopsis thaliana cDNA clone APZL58e11R 5', mRNA sequence
CCAAAATCCTCAAAGAGAGACTATACTTCTCTCGGATCCTTCCTGATTTCAAAATTTCTTCAACCCACCA
GCAGCAGCAGCAGATGAAGAAGGTTAAACAGATTCGTGTCTTAAAGCCTTTCGATCTTCTCTCGGAAGAG
CTCGTCTTTATCATCCTTGACCTCATCTCTCCCAACCCTTCCGATCTCAAATCCTTCTCTCTTACTTGCA
AATCTTTCTACCAGCTCGAGTCCAAGCACCGCGGATCCTTAAAACCTCTCCGCTCCGACTATCTCCCTCG
CATCTTGACTCGTTACCGGAACACCACCGATCTCGATCTTACCTTCTGCCCGCGTGTCACTGACTACGCG
CTTAGCGTCGTTGGCTGTCTCTCCGGACCTACGCTTCGCTCCCTCGACCTCTCGCGCTCTGGCTCCTTCT
CCGCCGCGGGACTACTGCGATTGGCCCTCAAATGTGTCAATTTAGTCGAGATTGACCTGTCCAATGCGAC
GGAGATGAGAGACGCCGATGCTG
genometools-1.5.1/testdata/gt_cds_descrange_multi.fas000066400000000000000000000000601211610345200230340ustar00rootroot00000000000000>dna:101..109
augggguag
>dna:201..209
augggguag
genometools-1.5.1/testdata/gt_cds_descrange_multi.in000066400000000000000000000003121211610345200226710ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 101 209
dna	.	gene	101	109	.	+	.	ID=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
###
dna	.	gene	201	209	.	+	.	ID=gene2
dna	.	exon	201	209	.	+	.	Parent=gene2
###
genometools-1.5.1/testdata/gt_cds_descrange_multi.out000066400000000000000000000004561211610345200231030ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 101 209
dna	.	gene	101	109	.	+	.	ID=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	gt cds	CDS	101	109	.	+	0	ID=CDS1;Parent=gene1
###
dna	.	gene	201	209	.	+	.	ID=gene2
dna	.	exon	201	209	.	+	.	Parent=gene2
dna	gt cds	CDS	201	209	.	+	0	ID=CDS2;Parent=gene2
###
genometools-1.5.1/testdata/gt_cds_descrange_multi_fail_1.fas000066400000000000000000000000471211610345200242540ustar00rootroot00000000000000>dna:101..109
augggguag
>dna
augggguag
genometools-1.5.1/testdata/gt_cds_descrange_multi_fail_2.fas000066400000000000000000000000471211610345200242550ustar00rootroot00000000000000>dna
augggguag
>dna:101..109
augggguag
genometools-1.5.1/testdata/gt_cds_descrange_wrong_id.fas000066400000000000000000000000301211610345200235070ustar00rootroot00000000000000>dns:101..109
augggguag
genometools-1.5.1/testdata/gt_cds_descrange_wrong_range.fas000066400000000000000000000000301211610345200242070ustar00rootroot00000000000000>dna:201..209
augggguag
genometools-1.5.1/testdata/gt_cds_nostartcodon_nofinalstopcodon.in000066400000000000000000000020271211610345200257050ustar00rootroot00000000000000##gff-version   3
##sequence-region   1877523 1 106973
1877523	gth	gene	30278	31355	.	+	.	ID=gene1
1877523	gth	mRNA	30278	31355	.	+	.	ID=mRNA1;Parent=gene1;Target=8690080 1 524 +
1877523	gth	exon	30278	30391	1	+	.	Parent=mRNA1
1877523	1877523	five_prime_cis_splice_site	30392	30393	0.985	+	.	Parent=mRNA1
1877523	1877523	three_prime_cis_splice_site	30475	30476	0.918	+	.	Parent=mRNA1
1877523	gth	exon	30477	30562	1	+	.	Parent=mRNA1
1877523	1877523	five_prime_cis_splice_site	30563	30564	0.938	+	.	Parent=mRNA1
1877523	1877523	three_prime_cis_splice_site	30656	30657	0.973	+	.	Parent=mRNA1
1877523	gth	exon	30658	30763	1	+	.	Parent=mRNA1
1877523	1877523	five_prime_cis_splice_site	30764	30765	0.996	+	.	Parent=mRNA1
1877523	1877523	three_prime_cis_splice_site	30988	30989	1	+	.	Parent=mRNA1
1877523	gth	exon	30990	31085	1	+	.	Parent=mRNA1
1877523	1877523	five_prime_cis_splice_site	31086	31087	0.644	+	.	Parent=mRNA1
1877523	1877523	three_prime_cis_splice_site	31232	31233	0.987	+	.	Parent=mRNA1
1877523	gth	exon	31234	31355	1	+	.	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_cds_nostartcodon_nofinalstopcodon.out000066400000000000000000000024711211610345200261110ustar00rootroot00000000000000##gff-version   3
##sequence-region   1877523 1 106973
1877523	gth	gene	30278	31355	.	+	.	ID=gene1
1877523	gth	mRNA	30278	31355	.	+	.	ID=mRNA1;Parent=gene1;Target=8690080 1 524 +
1877523	gth	exon	30278	30391	1	+	.	Parent=mRNA1
1877523	gt cds	CDS	30278	30391	.	+	0	ID=CDS1;Parent=mRNA1
1877523	1877523	five_prime_cis_splice_site	30392	30393	0.985	+	.	Parent=mRNA1
1877523	1877523	three_prime_cis_splice_site	30475	30476	0.918	+	.	Parent=mRNA1
1877523	gth	exon	30477	30562	1	+	.	Parent=mRNA1
1877523	gt cds	CDS	30477	30562	.	+	0	ID=CDS1;Parent=mRNA1
1877523	1877523	five_prime_cis_splice_site	30563	30564	0.938	+	.	Parent=mRNA1
1877523	1877523	three_prime_cis_splice_site	30656	30657	0.973	+	.	Parent=mRNA1
1877523	gth	exon	30658	30763	1	+	.	Parent=mRNA1
1877523	gt cds	CDS	30658	30763	.	+	1	ID=CDS1;Parent=mRNA1
1877523	1877523	five_prime_cis_splice_site	30764	30765	0.996	+	.	Parent=mRNA1
1877523	1877523	three_prime_cis_splice_site	30988	30989	1	+	.	Parent=mRNA1
1877523	gth	exon	30990	31085	1	+	.	Parent=mRNA1
1877523	gt cds	CDS	30990	31085	.	+	0	ID=CDS1;Parent=mRNA1
1877523	1877523	five_prime_cis_splice_site	31086	31087	0.644	+	.	Parent=mRNA1
1877523	1877523	three_prime_cis_splice_site	31232	31233	0.987	+	.	Parent=mRNA1
1877523	gt cds	CDS	31234	31353	.	+	0	ID=CDS1;Parent=mRNA1
1877523	gth	exon	31234	31355	1	+	.	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_cds_test_1.fas000066400000000000000000000000171211610345200210700ustar00rootroot00000000000000>dna
augggguag
genometools-1.5.1/testdata/gt_cds_test_1.in000066400000000000000000000001541211610345200207270ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 9
dna	.	gene	1	9	.	+	.	ID=gene1
dna	.	exon	1	9	.	+	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_1.out000066400000000000000000000002401211610345200211240ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 9
dna	.	gene	1	9	.	+	.	ID=gene1
dna	.	exon	1	9	.	+	.	Parent=gene1
dna	gt cds	CDS	1	9	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_10.fas000066400000000000000000000000201211610345200211420ustar00rootroot00000000000000>dna
ctaccccatt
genometools-1.5.1/testdata/gt_cds_test_10.in000066400000000000000000000001571211610345200210120ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 10
dna	.	gene	1	10	.	-	.	ID=gene1
dna	.	exon	1	10	.	-	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_10.out000066400000000000000000000002431211610345200212070ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 10
dna	.	gene	1	10	.	-	.	ID=gene1
dna	gt cds	CDS	1	9	.	-	0	ID=CDS1;Parent=gene1
dna	.	exon	1	10	.	-	.	Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_11.fas000066400000000000000000000000211211610345200211440ustar00rootroot00000000000000>dna
ctaccccattt
genometools-1.5.1/testdata/gt_cds_test_11.in000066400000000000000000000001571211610345200210130ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 11
dna	.	gene	1	11	.	-	.	ID=gene1
dna	.	exon	1	11	.	-	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_11.out000066400000000000000000000002431211610345200212100ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 11
dna	.	gene	1	11	.	-	.	ID=gene1
dna	gt cds	CDS	1	9	.	-	0	ID=CDS1;Parent=gene1
dna	.	exon	1	11	.	-	.	Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_12.fas000066400000000000000000000000321211610345200211470ustar00rootroot00000000000000>dna
ctacccnnnnnnnnccccat
genometools-1.5.1/testdata/gt_cds_test_12.in000066400000000000000000000002221211610345200210050ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 20
dna	.	gene	1	20	.	-	.	ID=gene1
dna	.	exon	1	6	.	-	.	Parent=gene1
dna	.	exon	15	20	.	-	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_12.out000066400000000000000000000003661211610345200212170ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 20
dna	.	gene	1	20	.	-	.	ID=gene1
dna	.	exon	1	6	.	-	.	Parent=gene1
dna	gt cds	CDS	1	6	.	-	0	ID=CDS1;Parent=gene1
dna	.	exon	15	20	.	-	.	Parent=gene1
dna	gt cds	CDS	15	20	.	-	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_13.fas000066400000000000000000000000251211610345200211520ustar00rootroot00000000000000>dna
augnnngggtttuag
genometools-1.5.1/testdata/gt_cds_test_13.in000066400000000000000000000002641211610345200210140ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 15
dna	.	gene	1	15	.	+	.	ID=gene1
dna	.	exon	1	3	.	+	.	Parent=gene1
dna	.	exon	7	9	.	+	.	Parent=gene1
dna	.	exon	13	15	.	+	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_13.out000066400000000000000000000005061211610345200212140ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 15
dna	.	gene	1	15	.	+	.	ID=gene1
dna	.	exon	1	3	.	+	.	Parent=gene1
dna	gt cds	CDS	1	3	.	+	0	ID=CDS1;Parent=gene1
dna	.	exon	7	9	.	+	.	Parent=gene1
dna	gt cds	CDS	7	9	.	+	0	ID=CDS1;Parent=gene1
dna	.	exon	13	15	.	+	.	Parent=gene1
dna	gt cds	CDS	13	15	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_14.fas000066400000000000000000000000251211610345200211530ustar00rootroot00000000000000>dna
ctaaaacccnnncat
genometools-1.5.1/testdata/gt_cds_test_14.in000066400000000000000000000002641211610345200210150ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 15
dna	.	gene	1	15	.	-	.	ID=gene1
dna	.	exon	1	3	.	-	.	Parent=gene1
dna	.	exon	7	9	.	-	.	Parent=gene1
dna	.	exon	13	15	.	-	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_14.out000066400000000000000000000005061211610345200212150ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 15
dna	.	gene	1	15	.	-	.	ID=gene1
dna	.	exon	1	3	.	-	.	Parent=gene1
dna	gt cds	CDS	1	3	.	-	0	ID=CDS1;Parent=gene1
dna	.	exon	7	9	.	-	.	Parent=gene1
dna	gt cds	CDS	7	9	.	-	0	ID=CDS1;Parent=gene1
dna	.	exon	13	15	.	-	.	Parent=gene1
dna	gt cds	CDS	13	15	.	-	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_2.fas000066400000000000000000000000201211610345200210630ustar00rootroot00000000000000>dna
aaugggguag
genometools-1.5.1/testdata/gt_cds_test_2.in000066400000000000000000000001571211610345200207330ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 10
dna	.	gene	1	10	.	+	.	ID=gene1
dna	.	exon	1	10	.	+	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_2.out000066400000000000000000000002441211610345200211310ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 10
dna	.	gene	1	10	.	+	.	ID=gene1
dna	.	exon	1	10	.	+	.	Parent=gene1
dna	gt cds	CDS	2	10	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_3.fas000066400000000000000000000000211211610345200210650ustar00rootroot00000000000000>dna
aaaugggguag
genometools-1.5.1/testdata/gt_cds_test_3.in000066400000000000000000000001571211610345200207340ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 11
dna	.	gene	1	11	.	+	.	ID=gene1
dna	.	exon	1	11	.	+	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_3.out000066400000000000000000000002441211610345200211320ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 11
dna	.	gene	1	11	.	+	.	ID=gene1
dna	.	exon	1	11	.	+	.	Parent=gene1
dna	gt cds	CDS	3	11	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_4.fas000066400000000000000000000000171211610345200210730ustar00rootroot00000000000000>dna
augggguag
genometools-1.5.1/testdata/gt_cds_test_4.in000066400000000000000000000002271211610345200207330ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 9
dna	.	gene	1	9	.	+	.	ID=gene1
dna	.	mRNA	1	9	.	+	.	ID=mRNA1;Parent=gene1
dna	.	exon	1	9	.	+	.	Parent=mRNA1
genometools-1.5.1/testdata/gt_cds_test_4.out000066400000000000000000000003131211610345200211300ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 9
dna	.	gene	1	9	.	+	.	ID=gene1
dna	.	mRNA	1	9	.	+	.	ID=mRNA1;Parent=gene1
dna	.	exon	1	9	.	+	.	Parent=mRNA1
dna	gt cds	CDS	1	9	.	+	0	ID=CDS1;Parent=mRNA1
###
genometools-1.5.1/testdata/gt_cds_test_5.fas000066400000000000000000000000201211610345200210660ustar00rootroot00000000000000>dna
aaugggguag
genometools-1.5.1/testdata/gt_cds_test_5.in000066400000000000000000000002331211610345200207310ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 10
dna	.	gene	1	10	.	+	.	ID=gene1
dna	.	mRNA	1	10	.	+	.	ID=mRNA1;Parent=gene1
dna	.	exon	1	10	.	+	.	Parent=mRNA1
genometools-1.5.1/testdata/gt_cds_test_5.out000066400000000000000000000003201211610345200211270ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 10
dna	.	gene	1	10	.	+	.	ID=gene1
dna	.	mRNA	1	10	.	+	.	ID=mRNA1;Parent=gene1
dna	.	exon	1	10	.	+	.	Parent=mRNA1
dna	gt cds	CDS	2	10	.	+	0	ID=CDS1;Parent=mRNA1
###
genometools-1.5.1/testdata/gt_cds_test_6.fas000066400000000000000000000000211211610345200210700ustar00rootroot00000000000000>dna
aaaugggguag
genometools-1.5.1/testdata/gt_cds_test_6.in000066400000000000000000000002331211610345200207320ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 11
dna	.	gene	1	11	.	+	.	ID=gene1
dna	.	mRNA	1	11	.	+	.	ID=mRNA1;Parent=gene1
dna	.	exon	1	11	.	+	.	Parent=mRNA1
genometools-1.5.1/testdata/gt_cds_test_6.out000066400000000000000000000003201211610345200211300ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 11
dna	.	gene	1	11	.	+	.	ID=gene1
dna	.	mRNA	1	11	.	+	.	ID=mRNA1;Parent=gene1
dna	.	exon	1	11	.	+	.	Parent=mRNA1
dna	gt cds	CDS	3	11	.	+	0	ID=CDS1;Parent=mRNA1
###
genometools-1.5.1/testdata/gt_cds_test_7.fas000066400000000000000000000000321211610345200210730ustar00rootroot00000000000000>dna
auggggnnnnnnnnggguag
genometools-1.5.1/testdata/gt_cds_test_7.in000066400000000000000000000002221211610345200207310ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 20
dna	.	gene	1	20	.	+	.	ID=gene1
dna	.	exon	1	6	.	+	.	Parent=gene1
dna	.	exon	15	20	.	+	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_7.out000066400000000000000000000003661211610345200211430ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 20
dna	.	gene	1	20	.	+	.	ID=gene1
dna	.	exon	1	6	.	+	.	Parent=gene1
dna	gt cds	CDS	1	6	.	+	0	ID=CDS1;Parent=gene1
dna	.	exon	15	20	.	+	.	Parent=gene1
dna	gt cds	CDS	15	20	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_8.fas000066400000000000000000000000441211610345200210770ustar00rootroot00000000000000>dna
ttttttttttauggggnnnnnnnnggguag
genometools-1.5.1/testdata/gt_cds_test_8.in000066400000000000000000000002261211610345200207360ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 11 30
dna	.	gene	11	30	.	+	.	ID=gene1
dna	.	exon	11	16	.	+	.	Parent=gene1
dna	.	exon	25	30	.	+	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_8.out000066400000000000000000000003741211610345200211430ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 11 30
dna	.	gene	11	30	.	+	.	ID=gene1
dna	.	exon	11	16	.	+	.	Parent=gene1
dna	gt cds	CDS	11	16	.	+	0	ID=CDS1;Parent=gene1
dna	.	exon	25	30	.	+	.	Parent=gene1
dna	gt cds	CDS	25	30	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_9.fas000066400000000000000000000000171211610345200211000ustar00rootroot00000000000000>dna
ctaccccat
genometools-1.5.1/testdata/gt_cds_test_9.in000066400000000000000000000001541211610345200207370ustar00rootroot00000000000000##gff-version   3
##sequence-region dna 1 9
dna	.	gene	1	9	.	-	.	ID=gene1
dna	.	exon	1	9	.	-	.	Parent=gene1
genometools-1.5.1/testdata/gt_cds_test_9.out000066400000000000000000000002401211610345200211340ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 1 9
dna	.	gene	1	9	.	-	.	ID=gene1
dna	.	exon	1	9	.	-	.	Parent=gene1
dna	gt cds	CDS	1	9	.	-	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_descrange.fas000066400000000000000000000000301211610345200226560ustar00rootroot00000000000000>dna:101..109
augggguag
genometools-1.5.1/testdata/gt_cds_test_descrange.in000066400000000000000000000001761211610345200225260ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 101 109
dna	.	gene	101	109	.	+	.	ID=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
###
genometools-1.5.1/testdata/gt_cds_test_descrange.out000066400000000000000000000002601211610345200227210ustar00rootroot00000000000000##gff-version   3
##sequence-region   dna 101 109
dna	.	gene	101	109	.	+	.	ID=gene1
dna	.	exon	101	109	.	+	.	Parent=gene1
dna	gt cds	CDS	101	109	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/gt_chseqids_test_1.chseqids000066400000000000000000000000601211610345200231520ustar00rootroot00000000000000chseqids = {
  seq1 = "chr1",
  seq2 = "chr2"
}
genometools-1.5.1/testdata/gt_chseqids_test_1.gff3000066400000000000000000000002201211610345200221720ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
##sequence-region   seq2 1 10000
seq1	.	gene	1000	9000	.	+	.	.
seq2	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_chseqids_test_1.out000066400000000000000000000002201211610345200221540ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr1 1 10000
##sequence-region   chr2 1 10000
chr1	.	gene	1000	9000	.	+	.	.
chr2	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_chseqids_test_2.chseqids000066400000000000000000000000601211610345200231530ustar00rootroot00000000000000chseqids = {
  seq1 = "chr1",
  seq2 = "chr1"
}
genometools-1.5.1/testdata/gt_chseqids_test_2.gff3000066400000000000000000000002201211610345200221730ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
##sequence-region   seq2 1 10000
seq1	.	gene	1000	2000	.	+	.	.
seq2	.	gene	3000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_chseqids_test_2.out000066400000000000000000000001571211610345200221660ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr1 1 10000
chr1	.	gene	1000	2000	.	+	.	.
chr1	.	gene	3000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_chseqids_test_3.chseqids000066400000000000000000000000401211610345200231520ustar00rootroot00000000000000chseqids = {
  seq1 = "chr1",
}
genometools-1.5.1/testdata/gt_chseqids_test_3.gff3000066400000000000000000000002201211610345200221740ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
##sequence-region   seq2 1 10000
seq1	.	gene	1000	9000	.	+	.	.
seq2	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_chseqids_test_4.chseqids000066400000000000000000000000361211610345200231600ustar00rootroot00000000000000chseqids = {
  seq = "chr",
}
genometools-1.5.1/testdata/gt_chseqids_test_4.gff3000066400000000000000000000001741211610345200222050ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 10000
seq	.	gene	1000	9000	.	+	.	ID=gene
seq	.	exon	1000	9000	.	+	.	Parent=gene
genometools-1.5.1/testdata/gt_chseqids_test_4.out000066400000000000000000000002021211610345200221570ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr 1 10000
chr	.	gene	1000	9000	.	+	.	ID=gene1
chr	.	exon	1000	9000	.	+	.	Parent=gene1
###
genometools-1.5.1/testdata/gt_chseqids_test_5.chseqids000066400000000000000000000000571211610345200231640ustar00rootroot00000000000000chseqids = {
  seq1 = "chr",
  seq2 = "chr",
}
genometools-1.5.1/testdata/gt_chseqids_test_5.gff3000066400000000000000000000003541211610345200222060ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
##sequence-region   seq2 1 10000
seq1	.	gene	1000	9000	.	+	.	ID=gene1
seq1	.	exon	1000	9000	.	+	.	Parent=gene1
seq2	.	gene	100	900	.	+	.	ID=gene2
seq2	.	exon	100	900	.	+	.	Parent=gene2
genometools-1.5.1/testdata/gt_chseqids_test_5.out000066400000000000000000000003161211610345200221660ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr 1 10000
chr	.	gene	1000	9000	.	+	.	ID=gene1
chr	.	exon	1000	9000	.	+	.	Parent=gene1
###
chr	.	gene	100	900	.	+	.	ID=gene2
chr	.	exon	100	900	.	+	.	Parent=gene2
###
genometools-1.5.1/testdata/gt_chseqids_test_5.sorted_out000066400000000000000000000003161211610345200235460ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr 1 10000
chr	.	gene	100	900	.	+	.	ID=gene1
chr	.	exon	100	900	.	+	.	Parent=gene1
###
chr	.	gene	1000	9000	.	+	.	ID=gene2
chr	.	exon	1000	9000	.	+	.	Parent=gene2
###
genometools-1.5.1/testdata/gt_chseqids_test_6.chseqids000066400000000000000000000000411211610345200231560ustar00rootroot00000000000000chseqids = {
  ENm001 = "chr7"
}
genometools-1.5.1/testdata/gt_chseqids_test_6.gff3000066400000000000000000000002761211610345200222120ustar00rootroot00000000000000##gff-version   3
##sequence-region   ENm001 115404472 2110371766
ENm001	gth	gene	115422568	117114462	0.766362	+	.	ID=gene1
###
ENm001	gth	gene	115422568	117114462	0.770928	+	.	ID=gene2
###
genometools-1.5.1/testdata/gt_chseqids_test_6.out000066400000000000000000000002341211610345200221660ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr7 115404472 2110371766
chr7	gth	gene	115422568	117114462	0.766	+	.	.
chr7	gth	gene	115422568	117114462	0.771	+	.	.
genometools-1.5.1/testdata/gt_csa_prob_1.debug000066400000000000000000000001041211610345200213620ustar00rootroot00000000000000debug: -from 5414975
debug: csa number_of_sas=2
debug: csa finished
genometools-1.5.1/testdata/gt_csa_prob_1.in000066400000000000000000000007461211610345200207160ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 10000000
NC_003070	gth	gene	5414975	5415790	0.998350	+	.	ID=gene1
NC_003070	gth	exon	5414975	5415294	0.996875	+	.	Parent=gene1
NC_003070	gth	exon	5415423	5415589	1.000000	+	.	Parent=gene1
NC_003070	gth	exon	5415672	5415790	1.000000	+	.	Parent=gene1
###
NC_003070	gth	gene	5415008	5415564	0.995338	+	.	ID=gene2
NC_003070	gth	exon	5415008	5415294	0.996516	+	.	Parent=gene2
NC_003070	gth	exon	5415423	5415564	0.992958	+	.	Parent=gene2
###
genometools-1.5.1/testdata/gt_csa_prob_1.out000066400000000000000000000005451211610345200211140ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 10000000
NC_003070	gt csa	gene	5414975	5415790	.	+	.	ID=gene1
NC_003070	gt csa	mRNA	5414975	5415790	.	+	.	ID=mRNA1;Parent=gene1
NC_003070	gt csa	exon	5414975	5415294	0.997	+	.	Parent=mRNA1
NC_003070	gt csa	exon	5415423	5415589	1	+	.	Parent=mRNA1
NC_003070	gt csa	exon	5415672	5415790	1	+	.	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_csa_prob_2.debug000066400000000000000000000002411211610345200213650ustar00rootroot00000000000000debug: process cluster
debug: -from 10472279
debug: csa number_of_sas=3
debug: csa finished
debug: -from 10478330
debug: csa number_of_sas=3
debug: csa finished
genometools-1.5.1/testdata/gt_csa_prob_2.in000066400000000000000000000016551211610345200207170ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 20000000
NC_003070	gth	gene	10472279	10475534	0.861423	+	.	ID=gene1
NC_003070	gth	exon	10472279	10472330	0.788462	+	.	Parent=gene1
NC_003070	gth	exon	10473721	10473759	0.666667	+	.	Parent=gene1
NC_003070	gth	exon	10475053	10475534	0.869295	+	.	Parent=gene1
###
NC_003070	gth	gene	10474921	10475416	1.000000	+	.	ID=gene2
NC_003070	gth	exon	10474921	10475416	1.000000	+	.	Parent=gene2
###
NC_003070	gth	gene	10475055	10475601	0.967093	+	.	ID=gene3
NC_003070	gth	exon	10475055	10475601	0.967093	+	.	Parent=gene3
###
NC_003070	gth	gene	10478330	10478934	0.995041	+	.	ID=gene4
NC_003070	gth	exon	10478330	10478934	0.995041	+	.	Parent=gene4
###
NC_003070	gth	gene	10478406	10478990	0.907692	+	.	ID=gene5
NC_003070	gth	exon	10478406	10478990	0.907692	+	.	Parent=gene5
###
NC_003070	gth	gene	10478515	10478896	0.955497	+	.	ID=gene6
NC_003070	gth	exon	10478515	10478896	0.955497	+	.	Parent=gene6
###
genometools-1.5.1/testdata/gt_csa_prob_2.out000066400000000000000000000012701211610345200211110ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 20000000
NC_003070	gt csa	gene	10472279	10475601	.	+	.	ID=gene1
NC_003070	gt csa	mRNA	10472279	10475601	.	+	.	ID=mRNA1;Parent=gene1
NC_003070	gt csa	exon	10472279	10472330	0.788	+	.	Parent=mRNA1
NC_003070	gt csa	exon	10473721	10473759	0.667	+	.	Parent=mRNA1
NC_003070	gt csa	exon	10475053	10475601	0.967	+	.	Parent=mRNA1
NC_003070	gt csa	mRNA	10474921	10475601	.	+	.	ID=mRNA2;Parent=gene1
NC_003070	gt csa	exon	10474921	10475601	0.967	+	.	Parent=mRNA2
###
NC_003070	gt csa	gene	10478330	10478990	.	+	.	ID=gene2
NC_003070	gt csa	mRNA	10478330	10478990	.	+	.	ID=mRNA3;Parent=gene2
NC_003070	gt csa	exon	10478330	10478990	0.908	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/gt_csa_prob_3.debug000066400000000000000000000002411211610345200213660ustar00rootroot00000000000000debug: process cluster
debug: -from 20552738
debug: csa number_of_sas=2
debug: csa finished
debug: -from 24280722
debug: csa number_of_sas=1
debug: csa finished
genometools-1.5.1/testdata/gt_csa_prob_3.in000066400000000000000000000007641211610345200207200ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 30000000
NC_003070	gth	gene	20552738	20552824	0.747126	+	.	ID=gene1
NC_003070	gth	exon	20552738	20552824	0.747126	+	.	Parent=gene1
###
NC_003070	gth	gene	20552738	20553188	0.780269	+	.	ID=gene2
NC_003070	gth	exon	20552738	20552824	0.747126	+	.	Parent=gene2
NC_003070	gth	exon	20553053	20553188	0.801471	+	.	Parent=gene2
###
NC_003070	gth	gene	24280722	24280936	0.804651	+	.	ID=gene3
NC_003070	gth	exon	24280722	24280936	0.804651	+	.	Parent=gene3
###
genometools-1.5.1/testdata/gt_csa_prob_3.out000066400000000000000000000007661211610345200211230ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 30000000
NC_003070	gt csa	gene	20552738	20553188	.	+	.	ID=gene1
NC_003070	gt csa	mRNA	20552738	20553188	.	+	.	ID=mRNA1;Parent=gene1
NC_003070	gt csa	exon	20552738	20552824	0.747	+	.	Parent=mRNA1
NC_003070	gt csa	exon	20553053	20553188	0.801	+	.	Parent=mRNA1
###
NC_003070	gt csa	gene	24280722	24280936	.	+	.	ID=gene2
NC_003070	gt csa	mRNA	24280722	24280936	.	+	.	ID=mRNA2;Parent=gene2
NC_003070	gt csa	exon	24280722	24280936	0.805	+	.	Parent=mRNA2
###
genometools-1.5.1/testdata/gt_csa_prob_4.debug000066400000000000000000000001051211610345200213660ustar00rootroot00000000000000debug: -from 10472279
debug: csa number_of_sas=3
debug: csa finished
genometools-1.5.1/testdata/gt_csa_prob_4.in000066400000000000000000000010631211610345200207120ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 20000000
NC_003070	gth	gene	10472279	10475534	0.861423	+	.	ID=gene1
NC_003070	gth	exon	10472279	10472330	0.788462	+	.	Parent=gene1
NC_003070	gth	exon	10473721	10473759	0.666667	+	.	Parent=gene1
NC_003070	gth	exon	10475053	10475534	0.869295	+	.	Parent=gene1
###
NC_003070	gth	gene	10472500	10472941	1.000000	+	.	ID=gene2
NC_003070	gth	exon	10472500	10472941	1.000000	+	.	Parent=gene2
###
NC_003070	gth	gene	10474921	10475416	1.000000	+	.	ID=gene3
NC_003070	gth	exon	10474921	10475416	1.000000	+	.	Parent=gene3
###
genometools-1.5.1/testdata/gt_csa_prob_4.out000066400000000000000000000011651211610345200211160ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 20000000
NC_003070	gt csa	gene	10472279	10475534	.	+	.	ID=gene1
NC_003070	gt csa	mRNA	10472279	10475534	.	+	.	ID=mRNA1;Parent=gene1
NC_003070	gt csa	exon	10472279	10472330	0.788	+	.	Parent=mRNA1
NC_003070	gt csa	exon	10473721	10473759	0.667	+	.	Parent=mRNA1
NC_003070	gt csa	exon	10475053	10475534	0.869	+	.	Parent=mRNA1
NC_003070	gt csa	mRNA	10472500	10472941	.	+	.	ID=mRNA2;Parent=gene1
NC_003070	gt csa	exon	10472500	10472941	1	+	.	Parent=mRNA2
NC_003070	gt csa	mRNA	10474921	10475416	.	+	.	ID=mRNA3;Parent=gene1
NC_003070	gt csa	exon	10474921	10475416	1	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/gt_csa_prob_5.in000066400000000000000000000037111211610345200207150ustar00rootroot00000000000000##gff-version   3
##sequence-region   ENm002 1 1000000
ENm002	ENCODE	gene	774908	816850	.	-	.	ID=gene1;Name=AC004039.5-002;name2=KIF3A
ENm002	ENCODE	exon	774908	775960	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	775912	775960	.	-	1	Parent=gene1
ENm002	ENCODE	exon	778449	778573	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	778449	778573	.	-	0	Parent=gene1
ENm002	ENCODE	exon	779494	779562	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	779494	779562	.	-	0	Parent=gene1
ENm002	ENCODE	exon	779925	779978	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	779925	779978	.	-	0	Parent=gene1
ENm002	ENCODE	exon	781365	781490	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	781365	781490	.	-	0	Parent=gene1
ENm002	ENCODE	exon	781836	781946	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	781836	781946	.	-	0	Parent=gene1
ENm002	ENCODE	exon	782163	782343	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	782163	782343	.	-	1	Parent=gene1
ENm002	ENCODE	exon	782741	782897	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	782741	782897	.	-	2	Parent=gene1
ENm002	ENCODE	exon	785729	785737	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	785729	785737	.	-	2	Parent=gene1
ENm002	ENCODE	exon	790237	790335	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	790237	790335	.	-	2	Parent=gene1
ENm002	ENCODE	exon	795035	795209	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	795035	795209	.	-	0	Parent=gene1
ENm002	ENCODE	exon	795523	795720	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	795523	795720	.	-	0	Parent=gene1
ENm002	ENCODE	exon	796123	796262	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	796123	796262	.	-	2	Parent=gene1
ENm002	ENCODE	exon	799887	799992	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	799887	799992	.	-	0	Parent=gene1
ENm002	ENCODE	exon	805406	805490	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	805406	805490	.	-	1	Parent=gene1
ENm002	ENCODE	exon	805632	805776	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	805632	805776	.	-	2	Parent=gene1
ENm002	ENCODE	exon	813483	813756	.	-	.	Parent=gene1
ENm002	ENCODE	CDS	813483	813756	.	-	0	Parent=gene1
ENm002	ENCODE	CDS	816692	816697	.	-	0	Parent=gene1
ENm002	ENCODE	exon	816692	816850	.	-	.	Parent=gene1
###
genometools-1.5.1/testdata/gt_csa_prob_5.out000066400000000000000000000021201211610345200211070ustar00rootroot00000000000000##gff-version   3
##sequence-region   ENm002 1 1000000
ENm002	gt csa	gene	774908	816850	.	-	.	ID=gene1
ENm002	gt csa	mRNA	774908	816850	.	-	.	ID=mRNA1;Parent=gene1
ENm002	gt csa	exon	774908	775960	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	778449	778573	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	779494	779562	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	779925	779978	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	781365	781490	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	781836	781946	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	782163	782343	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	782741	782897	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	785729	785737	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	790237	790335	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	795035	795209	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	795523	795720	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	796123	796262	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	799887	799992	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	805406	805490	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	805632	805776	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	813483	813756	.	-	.	Parent=mRNA1
ENm002	gt csa	exon	816692	816850	.	-	.	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_csa_prob_6.in000066400000000000000000000100541211610345200207140ustar00rootroot00000000000000##gff-version   3
##sequence-region   ENm002 1 1000000
ENm002	gth	gene	29252	90941	1.000	-	.	ID=gene1;Target=exon_1 1 6539 +
ENm002	gth	exon	29252	33650	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	33650	33651	0.997	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	38814	38815	0.896	-	.	Parent=gene1
ENm002	gth	exon	38815	38886	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	38886	38887	0.969	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	39798	39799	0.965	-	.	Parent=gene1
ENm002	gth	exon	39799	39900	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	39900	39901	0.000	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	41813	41814	0.991	-	.	Parent=gene1
ENm002	gth	exon	41814	41957	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	41957	41958	0.896	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	45694	45695	0.532	-	.	Parent=gene1
ENm002	gth	exon	45695	45811	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	45811	45812	0.950	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	47218	47219	0.655	-	.	Parent=gene1
ENm002	gth	exon	47219	47307	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	47307	47308	0.932	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	49406	49407	0.964	-	.	Parent=gene1
ENm002	gth	exon	49407	49479	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	49479	49480	0.985	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	50828	50829	0.201	-	.	Parent=gene1
ENm002	gth	exon	50829	50924	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	50924	50925	0.998	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	52002	52003	0.959	-	.	Parent=gene1
ENm002	gth	exon	52003	52137	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	52137	52138	0.864	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	52544	52545	0.999	-	.	Parent=gene1
ENm002	gth	exon	52545	52679	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	52679	52680	0.984	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	54171	54172	0.991	-	.	Parent=gene1
ENm002	gth	exon	54172	54249	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	54249	54250	0.831	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	55926	55927	0.557	-	.	Parent=gene1
ENm002	gth	exon	55927	56000	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	56000	56001	1.000	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	64685	64686	0.975	-	.	Parent=gene1
ENm002	gth	exon	64686	64737	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	64737	64738	0.973	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	66100	66101	0.847	-	.	Parent=gene1
ENm002	gth	exon	66101	66133	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	66133	66134	0.989	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	67326	67327	0.934	-	.	Parent=gene1
ENm002	gth	exon	67327	67505	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	67505	67506	0.901	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	68083	68084	0.995	-	.	Parent=gene1
ENm002	gth	exon	68084	68183	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	68183	68184	0.941	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	68685	68686	0.962	-	.	Parent=gene1
ENm002	gth	exon	68686	68787	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	68787	68788	0.762	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	69378	69379	0.974	-	.	Parent=gene1
ENm002	gth	exon	69379	69443	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	69443	69444	0.975	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	70131	70132	0.998	-	.	Parent=gene1
ENm002	gth	exon	70132	70246	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	70246	70247	0.831	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	73309	73310	0.916	-	.	Parent=gene1
ENm002	gth	exon	73310	73530	1.000	-	.	Parent=gene1
ENm002	gth	three_prime_cis_splice_site	73530	73531	0.992	-	.	Parent=gene1
ENm002	gth	five_prime_cis_splice_site	90783	90784	0.939	-	.	Parent=gene1
ENm002	gth	exon	90784	90941	1.000	-	.	Parent=gene1
###
genometools-1.5.1/testdata/gt_csa_prob_6.out000066400000000000000000000023251211610345200211170ustar00rootroot00000000000000##gff-version   3
##sequence-region   ENm002 1 1000000
ENm002	gt csa	gene	29252	90941	.	-	.	ID=gene1
ENm002	gt csa	mRNA	29252	90941	.	-	.	ID=mRNA1;Parent=gene1;Target=exon_1 1 6539 +
ENm002	gt csa	exon	29252	33650	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	38815	38886	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	39799	39900	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	41814	41957	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	45695	45811	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	47219	47307	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	49407	49479	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	50829	50924	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	52003	52137	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	52545	52679	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	54172	54249	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	55927	56000	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	64686	64737	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	66101	66133	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	67327	67505	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	68084	68183	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	68686	68787	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	69379	69443	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	70132	70246	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	73310	73530	1	-	.	Parent=mRNA1
ENm002	gt csa	exon	90784	90941	1	-	.	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_csa_test_1.in000066400000000000000000000002071211610345200207230ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	10000	19000	.	+	.	ID=gene2
ctg123	.	gene	1000	9000	.	+	.	ID=gene1
genometools-1.5.1/testdata/gt_encseq_eqlen_last_empty.fas000066400000000000000000000004311211610345200237430ustar00rootroot00000000000000>read_0
taaaatatttccattgtatcatagaagagt
>read_1
gttatgcagttagctggctggatgaattgg
>read_2
ggacgtcttcacgccggccacgtccatcga
>read_3
tcctgtaatcctagcactttgggaggccaa
>read_4
caccatcttggccagggtggtcttgaactc
>read_5
cacagaaagctgttgcaaagaccaacagtg
>read_6
cacggctgaacagcaggggctcctttgggg
>read_7
genometools-1.5.1/testdata/gt_eval_ltr_prob_1.out000066400000000000000000000002071211610345200221510ustar00rootroot00000000000000LTR_retrotransposon sensitivity:  59.06% (75/127) (missing LTRs: 46)
LTR_retrotransposon specificity:  82.42% (75/91) (wrong LTRs: 13)
genometools-1.5.1/testdata/gt_eval_ltr_prob_1.prediction000066400000000000000000001330441211610345200235100ustar00rootroot00000000000000##gff-version 3
##sequence-region seq0 1 22217931
# 2L 2L release:3 length:22217931bp Assembled 2L chromosome arm sequence md5:9e624e9793414e1ea0654b86db5f8c1d
seq0	LTRharvest	repeat_region	16487	19458	.	?	.	ID=RepeatReg0
seq0	LTRharvest	LTR_retrotransposon	16491	19454	.	?	.	ID=LTRret0;Parent=RepeatReg0
seq0	LTRharvest	long_terminal_repeat	16491	16628	.	?	.	ID=LTR0;Parent=LTRret0
seq0	LTRharvest	long_terminal_repeat	19312	19454	.	?	.	ID=LTR1;Parent=LTRret0
seq0	LTRharvest	target_site_duplication	16487	16490	.	?	.	ID=TSD0;Parent=RepeatReg0
seq0	LTRharvest	target_site_duplication	19455	19458	.	?	.	ID=TSD1;Parent=RepeatReg0
seq0	LTRharvest	repeat_region	13835290	13844390	.	?	.	ID=RepeatReg1
seq0	LTRharvest	LTR_retrotransposon	13835294	13844386	.	?	.	ID=LTRret1;Parent=RepeatReg1
seq0	LTRharvest	long_terminal_repeat	13835294	13835721	.	?	.	ID=LTR2;Parent=LTRret1
seq0	LTRharvest	long_terminal_repeat	13843955	13844386	.	?	.	ID=LTR3;Parent=LTRret1
seq0	LTRharvest	target_site_duplication	13835290	13835293	.	?	.	ID=TSD2;Parent=RepeatReg1
seq0	LTRharvest	target_site_duplication	13844387	13844390	.	?	.	ID=TSD3;Parent=RepeatReg1
seq0	LTRharvest	repeat_region	360552	367102	.	?	.	ID=RepeatReg2
seq0	LTRharvest	LTR_retrotransposon	360556	367098	.	?	.	ID=LTRret2;Parent=RepeatReg2
seq0	LTRharvest	long_terminal_repeat	360556	361259	.	?	.	ID=LTR4;Parent=LTRret2
seq0	LTRharvest	long_terminal_repeat	366393	367098	.	?	.	ID=LTR5;Parent=LTRret2
seq0	LTRharvest	target_site_duplication	360552	360555	.	?	.	ID=TSD4;Parent=RepeatReg2
seq0	LTRharvest	target_site_duplication	367099	367102	.	?	.	ID=TSD5;Parent=RepeatReg2
seq0	LTRharvest	repeat_region	6428216	6437343	.	?	.	ID=RepeatReg3
seq0	LTRharvest	LTR_retrotransposon	6428220	6437339	.	?	.	ID=LTRret3;Parent=RepeatReg3
seq0	LTRharvest	long_terminal_repeat	6428220	6428664	.	?	.	ID=LTR6;Parent=LTRret3
seq0	LTRharvest	long_terminal_repeat	6436901	6437339	.	?	.	ID=LTR7;Parent=LTRret3
seq0	LTRharvest	target_site_duplication	6428216	6428219	.	?	.	ID=TSD6;Parent=RepeatReg3
seq0	LTRharvest	target_site_duplication	6437340	6437343	.	?	.	ID=TSD7;Parent=RepeatReg3
seq0	LTRharvest	repeat_region	22116552	22123211	.	?	.	ID=RepeatReg4
seq0	LTRharvest	LTR_retrotransposon	22116556	22123207	.	?	.	ID=LTRret4;Parent=RepeatReg4
seq0	LTRharvest	long_terminal_repeat	22116556	22116842	.	?	.	ID=LTR8;Parent=LTRret4
seq0	LTRharvest	long_terminal_repeat	22122921	22123207	.	?	.	ID=LTR9;Parent=LTRret4
seq0	LTRharvest	target_site_duplication	22116552	22116555	.	?	.	ID=TSD8;Parent=RepeatReg4
seq0	LTRharvest	target_site_duplication	22123208	22123211	.	?	.	ID=TSD9;Parent=RepeatReg4
seq0	LTRharvest	repeat_region	12770724	12778118	.	?	.	ID=RepeatReg5
seq0	LTRharvest	LTR_retrotransposon	12770728	12778114	.	?	.	ID=LTRret5;Parent=RepeatReg5
seq0	LTRharvest	long_terminal_repeat	12770728	12771386	.	?	.	ID=LTR10;Parent=LTRret5
seq0	LTRharvest	long_terminal_repeat	12777456	12778114	.	?	.	ID=LTR11;Parent=LTRret5
seq0	LTRharvest	target_site_duplication	12770724	12770727	.	?	.	ID=TSD10;Parent=RepeatReg5
seq0	LTRharvest	target_site_duplication	12778115	12778118	.	?	.	ID=TSD11;Parent=RepeatReg5
seq0	LTRharvest	repeat_region	4173892	4176474	.	?	.	ID=RepeatReg6
seq0	LTRharvest	LTR_retrotransposon	4173896	4176470	.	?	.	ID=LTRret6;Parent=RepeatReg6
seq0	LTRharvest	long_terminal_repeat	4173896	4174171	.	?	.	ID=LTR12;Parent=LTRret6
seq0	LTRharvest	long_terminal_repeat	4176195	4176470	.	?	.	ID=LTR13;Parent=LTRret6
seq0	LTRharvest	target_site_duplication	4173892	4173895	.	?	.	ID=TSD12;Parent=RepeatReg6
seq0	LTRharvest	target_site_duplication	4176471	4176474	.	?	.	ID=TSD13;Parent=RepeatReg6
seq0	LTRharvest	repeat_region	21524999	21531419	.	?	.	ID=RepeatReg7
seq0	LTRharvest	LTR_retrotransposon	21525003	21531415	.	?	.	ID=LTRret7;Parent=RepeatReg7
seq0	LTRharvest	long_terminal_repeat	21525003	21525278	.	?	.	ID=LTR14;Parent=LTRret7
seq0	LTRharvest	long_terminal_repeat	21531140	21531415	.	?	.	ID=LTR15;Parent=LTRret7
seq0	LTRharvest	target_site_duplication	21524999	21525002	.	?	.	ID=TSD14;Parent=RepeatReg7
seq0	LTRharvest	target_site_duplication	21531416	21531419	.	?	.	ID=TSD15;Parent=RepeatReg7
seq0	LTRharvest	repeat_region	22062539	22067386	.	?	.	ID=RepeatReg8
seq0	LTRharvest	LTR_retrotransposon	22062543	22067382	.	?	.	ID=LTRret8;Parent=RepeatReg8
seq0	LTRharvest	long_terminal_repeat	22062543	22062706	.	?	.	ID=LTR16;Parent=LTRret8
seq0	LTRharvest	long_terminal_repeat	22067216	22067382	.	?	.	ID=LTR17;Parent=LTRret8
seq0	LTRharvest	target_site_duplication	22062539	22062542	.	?	.	ID=TSD16;Parent=RepeatReg8
seq0	LTRharvest	target_site_duplication	22067383	22067386	.	?	.	ID=TSD17;Parent=RepeatReg8
seq0	LTRharvest	repeat_region	8586747	8593751	.	?	.	ID=RepeatReg9
seq0	LTRharvest	LTR_retrotransposon	8586751	8593747	.	?	.	ID=LTRret9;Parent=RepeatReg9
seq0	LTRharvest	long_terminal_repeat	8586751	8587164	.	?	.	ID=LTR18;Parent=LTRret9
seq0	LTRharvest	long_terminal_repeat	8593334	8593747	.	?	.	ID=LTR19;Parent=LTRret9
seq0	LTRharvest	target_site_duplication	8586747	8586750	.	?	.	ID=TSD18;Parent=RepeatReg9
seq0	LTRharvest	target_site_duplication	8593748	8593751	.	?	.	ID=TSD19;Parent=RepeatReg9
seq0	LTRharvest	repeat_region	16131871	16138875	.	?	.	ID=RepeatReg10
seq0	LTRharvest	LTR_retrotransposon	16131875	16138871	.	?	.	ID=LTRret10;Parent=RepeatReg10
seq0	LTRharvest	long_terminal_repeat	16131875	16132289	.	?	.	ID=LTR20;Parent=LTRret10
seq0	LTRharvest	long_terminal_repeat	16138457	16138871	.	?	.	ID=LTR21;Parent=LTRret10
seq0	LTRharvest	target_site_duplication	16131871	16131874	.	?	.	ID=TSD20;Parent=RepeatReg10
seq0	LTRharvest	target_site_duplication	16138872	16138875	.	?	.	ID=TSD21;Parent=RepeatReg10
seq0	LTRharvest	repeat_region	15696860	15705658	.	?	.	ID=RepeatReg11
seq0	LTRharvest	LTR_retrotransposon	15696864	15705654	.	?	.	ID=LTRret11;Parent=RepeatReg11
seq0	LTRharvest	long_terminal_repeat	15696864	15697522	.	?	.	ID=LTR22;Parent=LTRret11
seq0	LTRharvest	long_terminal_repeat	15704996	15705654	.	?	.	ID=LTR23;Parent=LTRret11
seq0	LTRharvest	target_site_duplication	15696860	15696863	.	?	.	ID=TSD22;Parent=RepeatReg11
seq0	LTRharvest	target_site_duplication	15705655	15705658	.	?	.	ID=TSD23;Parent=RepeatReg11
seq0	LTRharvest	repeat_region	12056252	12063254	.	?	.	ID=RepeatReg12
seq0	LTRharvest	LTR_retrotransposon	12056256	12063250	.	?	.	ID=LTRret12;Parent=RepeatReg12
seq0	LTRharvest	long_terminal_repeat	12056256	12056669	.	?	.	ID=LTR24;Parent=LTRret12
seq0	LTRharvest	long_terminal_repeat	12062837	12063250	.	?	.	ID=LTR25;Parent=LTRret12
seq0	LTRharvest	target_site_duplication	12056252	12056255	.	?	.	ID=TSD24;Parent=RepeatReg12
seq0	LTRharvest	target_site_duplication	12063251	12063254	.	?	.	ID=TSD25;Parent=RepeatReg12
seq0	LTRharvest	repeat_region	2558156	2564174	.	?	.	ID=RepeatReg13
seq0	LTRharvest	LTR_retrotransposon	2558160	2564170	.	?	.	ID=LTRret13;Parent=RepeatReg13
seq0	LTRharvest	long_terminal_repeat	2558160	2558573	.	?	.	ID=LTR26;Parent=LTRret13
seq0	LTRharvest	long_terminal_repeat	2563757	2564170	.	?	.	ID=LTR27;Parent=LTRret13
seq0	LTRharvest	target_site_duplication	2558156	2558159	.	?	.	ID=TSD26;Parent=RepeatReg13
seq0	LTRharvest	target_site_duplication	2564171	2564174	.	?	.	ID=TSD27;Parent=RepeatReg13
seq0	LTRharvest	repeat_region	2765218	2771748	.	?	.	ID=RepeatReg14
seq0	LTRharvest	LTR_retrotransposon	2765222	2771744	.	?	.	ID=LTRret14;Parent=RepeatReg14
seq0	LTRharvest	long_terminal_repeat	2765222	2765635	.	?	.	ID=LTR28;Parent=LTRret14
seq0	LTRharvest	long_terminal_repeat	2771331	2771744	.	?	.	ID=LTR29;Parent=LTRret14
seq0	LTRharvest	target_site_duplication	2765218	2765221	.	?	.	ID=TSD28;Parent=RepeatReg14
seq0	LTRharvest	target_site_duplication	2771745	2771748	.	?	.	ID=TSD29;Parent=RepeatReg14
seq0	LTRharvest	repeat_region	10869003	10876009	.	?	.	ID=RepeatReg15
seq0	LTRharvest	LTR_retrotransposon	10869007	10876005	.	?	.	ID=LTRret15;Parent=RepeatReg15
seq0	LTRharvest	long_terminal_repeat	10869007	10869420	.	?	.	ID=LTR30;Parent=LTRret15
seq0	LTRharvest	long_terminal_repeat	10875592	10876005	.	?	.	ID=LTR31;Parent=LTRret15
seq0	LTRharvest	target_site_duplication	10869003	10869006	.	?	.	ID=TSD30;Parent=RepeatReg15
seq0	LTRharvest	target_site_duplication	10876006	10876009	.	?	.	ID=TSD31;Parent=RepeatReg15
seq0	LTRharvest	repeat_region	15564545	15571547	.	?	.	ID=RepeatReg16
seq0	LTRharvest	LTR_retrotransposon	15564549	15571543	.	?	.	ID=LTRret16;Parent=RepeatReg16
seq0	LTRharvest	long_terminal_repeat	15564549	15564962	.	?	.	ID=LTR32;Parent=LTRret16
seq0	LTRharvest	long_terminal_repeat	15571130	15571543	.	?	.	ID=LTR33;Parent=LTRret16
seq0	LTRharvest	target_site_duplication	15564545	15564548	.	?	.	ID=TSD32;Parent=RepeatReg16
seq0	LTRharvest	target_site_duplication	15571544	15571547	.	?	.	ID=TSD33;Parent=RepeatReg16
seq0	LTRharvest	repeat_region	19125504	19132489	.	?	.	ID=RepeatReg17
seq0	LTRharvest	LTR_retrotransposon	19125508	19132485	.	?	.	ID=LTRret17;Parent=RepeatReg17
seq0	LTRharvest	long_terminal_repeat	19125508	19125921	.	?	.	ID=LTR34;Parent=LTRret17
seq0	LTRharvest	long_terminal_repeat	19132072	19132485	.	?	.	ID=LTR35;Parent=LTRret17
seq0	LTRharvest	target_site_duplication	19125504	19125507	.	?	.	ID=TSD34;Parent=RepeatReg17
seq0	LTRharvest	target_site_duplication	19132486	19132489	.	?	.	ID=TSD35;Parent=RepeatReg17
seq0	LTRharvest	repeat_region	7969362	7976286	.	?	.	ID=RepeatReg18
seq0	LTRharvest	LTR_retrotransposon	7969366	7976282	.	?	.	ID=LTRret18;Parent=RepeatReg18
seq0	LTRharvest	long_terminal_repeat	7969366	7969778	.	?	.	ID=LTR36;Parent=LTRret18
seq0	LTRharvest	long_terminal_repeat	7975870	7976282	.	?	.	ID=LTR37;Parent=LTRret18
seq0	LTRharvest	target_site_duplication	7969362	7969365	.	?	.	ID=TSD36;Parent=RepeatReg18
seq0	LTRharvest	target_site_duplication	7976283	7976286	.	?	.	ID=TSD37;Parent=RepeatReg18
seq0	LTRharvest	repeat_region	6355416	6358288	.	?	.	ID=RepeatReg19
seq0	LTRharvest	LTR_retrotransposon	6355420	6358284	.	?	.	ID=LTRret19;Parent=RepeatReg19
seq0	LTRharvest	long_terminal_repeat	6355420	6355695	.	?	.	ID=LTR38;Parent=LTRret19
seq0	LTRharvest	long_terminal_repeat	6358000	6358284	.	?	.	ID=LTR39;Parent=LTRret19
seq0	LTRharvest	target_site_duplication	6355416	6355419	.	?	.	ID=TSD38;Parent=RepeatReg19
seq0	LTRharvest	target_site_duplication	6358285	6358288	.	?	.	ID=TSD39;Parent=RepeatReg19
seq0	LTRharvest	repeat_region	2104731	2112343	.	?	.	ID=RepeatReg20
seq0	LTRharvest	LTR_retrotransposon	2104735	2112339	.	?	.	ID=LTRret20;Parent=RepeatReg20
seq0	LTRharvest	long_terminal_repeat	2104735	2105252	.	?	.	ID=LTR40;Parent=LTRret20
seq0	LTRharvest	long_terminal_repeat	2111822	2112339	.	?	.	ID=LTR41;Parent=LTRret20
seq0	LTRharvest	target_site_duplication	2104731	2104734	.	?	.	ID=TSD40;Parent=RepeatReg20
seq0	LTRharvest	target_site_duplication	2112340	2112343	.	?	.	ID=TSD41;Parent=RepeatReg20
seq0	LTRharvest	repeat_region	17122465	17130082	.	?	.	ID=RepeatReg21
seq0	LTRharvest	LTR_retrotransposon	17122469	17130078	.	?	.	ID=LTRret21;Parent=RepeatReg21
seq0	LTRharvest	long_terminal_repeat	17122469	17122986	.	?	.	ID=LTR42;Parent=LTRret21
seq0	LTRharvest	long_terminal_repeat	17129561	17130078	.	?	.	ID=LTR43;Parent=LTRret21
seq0	LTRharvest	target_site_duplication	17122465	17122468	.	?	.	ID=TSD42;Parent=RepeatReg21
seq0	LTRharvest	target_site_duplication	17130079	17130082	.	?	.	ID=TSD43;Parent=RepeatReg21
seq0	LTRharvest	repeat_region	19635759	19643375	.	?	.	ID=RepeatReg22
seq0	LTRharvest	LTR_retrotransposon	19635763	19643371	.	?	.	ID=LTRret22;Parent=RepeatReg22
seq0	LTRharvest	long_terminal_repeat	19635763	19636280	.	?	.	ID=LTR44;Parent=LTRret22
seq0	LTRharvest	long_terminal_repeat	19642854	19643371	.	?	.	ID=LTR45;Parent=LTRret22
seq0	LTRharvest	target_site_duplication	19635759	19635762	.	?	.	ID=TSD44;Parent=RepeatReg22
seq0	LTRharvest	target_site_duplication	19643372	19643375	.	?	.	ID=TSD45;Parent=RepeatReg22
seq0	LTRharvest	repeat_region	4654445	4661975	.	?	.	ID=RepeatReg23
seq0	LTRharvest	LTR_retrotransposon	4654449	4661971	.	?	.	ID=LTRret23;Parent=RepeatReg23
seq0	LTRharvest	long_terminal_repeat	4654449	4654966	.	?	.	ID=LTR46;Parent=LTRret23
seq0	LTRharvest	long_terminal_repeat	4661454	4661971	.	?	.	ID=LTR47;Parent=LTRret23
seq0	LTRharvest	target_site_duplication	4654445	4654448	.	?	.	ID=TSD46;Parent=RepeatReg23
seq0	LTRharvest	target_site_duplication	4661972	4661975	.	?	.	ID=TSD47;Parent=RepeatReg23
seq0	LTRharvest	repeat_region	10585302	10592914	.	?	.	ID=RepeatReg24
seq0	LTRharvest	LTR_retrotransposon	10585306	10592910	.	?	.	ID=LTRret24;Parent=RepeatReg24
seq0	LTRharvest	long_terminal_repeat	10585306	10585823	.	?	.	ID=LTR48;Parent=LTRret24
seq0	LTRharvest	long_terminal_repeat	10592393	10592910	.	?	.	ID=LTR49;Parent=LTRret24
seq0	LTRharvest	target_site_duplication	10585302	10585305	.	?	.	ID=TSD48;Parent=RepeatReg24
seq0	LTRharvest	target_site_duplication	10592911	10592914	.	?	.	ID=TSD49;Parent=RepeatReg24
seq0	LTRharvest	repeat_region	3244114	3251629	.	?	.	ID=RepeatReg25
seq0	LTRharvest	LTR_retrotransposon	3244118	3251625	.	?	.	ID=LTRret25;Parent=RepeatReg25
seq0	LTRharvest	long_terminal_repeat	3244118	3244521	.	?	.	ID=LTR50;Parent=LTRret25
seq0	LTRharvest	long_terminal_repeat	3251218	3251625	.	?	.	ID=LTR51;Parent=LTRret25
seq0	LTRharvest	target_site_duplication	3244114	3244117	.	?	.	ID=TSD50;Parent=RepeatReg25
seq0	LTRharvest	target_site_duplication	3251626	3251629	.	?	.	ID=TSD51;Parent=RepeatReg25
seq0	LTRharvest	repeat_region	14962533	14970064	.	?	.	ID=RepeatReg26
seq0	LTRharvest	LTR_retrotransposon	14962537	14970060	.	?	.	ID=LTRret26;Parent=RepeatReg26
seq0	LTRharvest	long_terminal_repeat	14962537	14963054	.	?	.	ID=LTR52;Parent=LTRret26
seq0	LTRharvest	long_terminal_repeat	14969543	14970060	.	?	.	ID=LTR53;Parent=LTRret26
seq0	LTRharvest	target_site_duplication	14962533	14962536	.	?	.	ID=TSD52;Parent=RepeatReg26
seq0	LTRharvest	target_site_duplication	14970061	14970064	.	?	.	ID=TSD53;Parent=RepeatReg26
seq0	LTRharvest	repeat_region	20710029	20717869	.	?	.	ID=RepeatReg27
seq0	LTRharvest	LTR_retrotransposon	20710033	20717865	.	?	.	ID=LTRret27;Parent=RepeatReg27
seq0	LTRharvest	long_terminal_repeat	20710033	20710462	.	?	.	ID=LTR54;Parent=LTRret27
seq0	LTRharvest	long_terminal_repeat	20717416	20717865	.	?	.	ID=LTR55;Parent=LTRret27
seq0	LTRharvest	target_site_duplication	20710029	20710032	.	?	.	ID=TSD54;Parent=RepeatReg27
seq0	LTRharvest	target_site_duplication	20717866	20717869	.	?	.	ID=TSD55;Parent=RepeatReg27
seq0	LTRharvest	repeat_region	12547242	12554320	.	?	.	ID=RepeatReg28
seq0	LTRharvest	LTR_retrotransposon	12547246	12554316	.	?	.	ID=LTRret28;Parent=RepeatReg28
seq0	LTRharvest	long_terminal_repeat	12547246	12547512	.	?	.	ID=LTR56;Parent=LTRret28
seq0	LTRharvest	long_terminal_repeat	12554050	12554316	.	?	.	ID=LTR57;Parent=LTRret28
seq0	LTRharvest	target_site_duplication	12547242	12547245	.	?	.	ID=TSD56;Parent=RepeatReg28
seq0	LTRharvest	target_site_duplication	12554317	12554320	.	?	.	ID=TSD57;Parent=RepeatReg28
seq0	LTRharvest	repeat_region	6983714	6990783	.	?	.	ID=RepeatReg29
seq0	LTRharvest	LTR_retrotransposon	6983718	6990779	.	?	.	ID=LTRret29;Parent=RepeatReg29
seq0	LTRharvest	long_terminal_repeat	6983718	6983983	.	?	.	ID=LTR58;Parent=LTRret29
seq0	LTRharvest	long_terminal_repeat	6990514	6990779	.	?	.	ID=LTR59;Parent=LTRret29
seq0	LTRharvest	target_site_duplication	6983714	6983717	.	?	.	ID=TSD58;Parent=RepeatReg29
seq0	LTRharvest	target_site_duplication	6990780	6990783	.	?	.	ID=TSD59;Parent=RepeatReg29
seq0	LTRharvest	repeat_region	8715396	8723725	.	?	.	ID=RepeatReg30
seq0	LTRharvest	LTR_retrotransposon	8715400	8723721	.	?	.	ID=LTRret30;Parent=RepeatReg30
seq0	LTRharvest	long_terminal_repeat	8715400	8715818	.	?	.	ID=LTR60;Parent=LTRret30
seq0	LTRharvest	long_terminal_repeat	8723298	8723721	.	?	.	ID=LTR61;Parent=LTRret30
seq0	LTRharvest	target_site_duplication	8715396	8715399	.	?	.	ID=TSD60;Parent=RepeatReg30
seq0	LTRharvest	target_site_duplication	8723722	8723725	.	?	.	ID=TSD61;Parent=RepeatReg30
seq0	LTRharvest	repeat_region	13504460	13509716	.	?	.	ID=RepeatReg31
seq0	LTRharvest	LTR_retrotransposon	13504464	13509712	.	?	.	ID=LTRret31;Parent=RepeatReg31
seq0	LTRharvest	long_terminal_repeat	13504464	13504793	.	?	.	ID=LTR62;Parent=LTRret31
seq0	LTRharvest	long_terminal_repeat	13509383	13509712	.	?	.	ID=LTR63;Parent=LTRret31
seq0	LTRharvest	target_site_duplication	13504460	13504463	.	?	.	ID=TSD62;Parent=RepeatReg31
seq0	LTRharvest	target_site_duplication	13509713	13509716	.	?	.	ID=TSD63;Parent=RepeatReg31
seq0	LTRharvest	repeat_region	9966186	9973255	.	?	.	ID=RepeatReg32
seq0	LTRharvest	LTR_retrotransposon	9966190	9973251	.	?	.	ID=LTRret32;Parent=RepeatReg32
seq0	LTRharvest	long_terminal_repeat	9966190	9966458	.	?	.	ID=LTR64;Parent=LTRret32
seq0	LTRharvest	long_terminal_repeat	9972986	9973251	.	?	.	ID=LTR65;Parent=LTRret32
seq0	LTRharvest	target_site_duplication	9966186	9966189	.	?	.	ID=TSD64;Parent=RepeatReg32
seq0	LTRharvest	target_site_duplication	9973252	9973255	.	?	.	ID=TSD65;Parent=RepeatReg32
seq0	LTRharvest	repeat_region	16490098	16497162	.	?	.	ID=RepeatReg33
seq0	LTRharvest	LTR_retrotransposon	16490102	16497158	.	?	.	ID=LTRret33;Parent=RepeatReg33
seq0	LTRharvest	long_terminal_repeat	16490102	16490367	.	?	.	ID=LTR66;Parent=LTRret33
seq0	LTRharvest	long_terminal_repeat	16496893	16497158	.	?	.	ID=LTR67;Parent=LTRret33
seq0	LTRharvest	target_site_duplication	16490098	16490101	.	?	.	ID=TSD66;Parent=RepeatReg33
seq0	LTRharvest	target_site_duplication	16497159	16497162	.	?	.	ID=TSD67;Parent=RepeatReg33
seq0	LTRharvest	repeat_region	20377601	20382639	.	?	.	ID=RepeatReg34
seq0	LTRharvest	LTR_retrotransposon	20377605	20382635	.	?	.	ID=LTRret34;Parent=RepeatReg34
seq0	LTRharvest	long_terminal_repeat	20377605	20377883	.	?	.	ID=LTR68;Parent=LTRret34
seq0	LTRharvest	long_terminal_repeat	20382359	20382635	.	?	.	ID=LTR69;Parent=LTRret34
seq0	LTRharvest	target_site_duplication	20377601	20377604	.	?	.	ID=TSD68;Parent=RepeatReg34
seq0	LTRharvest	target_site_duplication	20382636	20382639	.	?	.	ID=TSD69;Parent=RepeatReg34
seq0	LTRharvest	repeat_region	19984001	19989027	.	?	.	ID=RepeatReg35
seq0	LTRharvest	LTR_retrotransposon	19984005	19989023	.	?	.	ID=LTRret35;Parent=RepeatReg35
seq0	LTRharvest	long_terminal_repeat	19984005	19984275	.	?	.	ID=LTR70;Parent=LTRret35
seq0	LTRharvest	long_terminal_repeat	19988751	19989023	.	?	.	ID=LTR71;Parent=LTRret35
seq0	LTRharvest	target_site_duplication	19984001	19984004	.	?	.	ID=TSD70;Parent=RepeatReg35
seq0	LTRharvest	target_site_duplication	19989024	19989027	.	?	.	ID=TSD71;Parent=RepeatReg35
seq0	LTRharvest	repeat_region	22102767	22105689	.	?	.	ID=RepeatReg36
seq0	LTRharvest	LTR_retrotransposon	22102771	22105685	.	?	.	ID=LTRret36;Parent=RepeatReg36
seq0	LTRharvest	long_terminal_repeat	22102771	22102903	.	?	.	ID=LTR72;Parent=LTRret36
seq0	LTRharvest	long_terminal_repeat	22105549	22105685	.	?	.	ID=LTR73;Parent=LTRret36
seq0	LTRharvest	target_site_duplication	22102767	22102770	.	?	.	ID=TSD72;Parent=RepeatReg36
seq0	LTRharvest	target_site_duplication	22105686	22105689	.	?	.	ID=TSD73;Parent=RepeatReg36
seq0	LTRharvest	repeat_region	21486364	21489620	.	?	.	ID=RepeatReg37
seq0	LTRharvest	LTR_retrotransposon	21486368	21489616	.	?	.	ID=LTRret37;Parent=RepeatReg37
seq0	LTRharvest	long_terminal_repeat	21486368	21486720	.	?	.	ID=LTR74;Parent=LTRret37
seq0	LTRharvest	long_terminal_repeat	21489269	21489616	.	?	.	ID=LTR75;Parent=LTRret37
seq0	LTRharvest	target_site_duplication	21486364	21486367	.	?	.	ID=TSD74;Parent=RepeatReg37
seq0	LTRharvest	target_site_duplication	21489617	21489620	.	?	.	ID=TSD75;Parent=RepeatReg37
seq0	LTRharvest	repeat_region	5165909	5172357	.	?	.	ID=RepeatReg38
seq0	LTRharvest	LTR_retrotransposon	5165913	5172353	.	?	.	ID=LTRret38;Parent=RepeatReg38
seq0	LTRharvest	long_terminal_repeat	5165913	5166527	.	?	.	ID=LTR76;Parent=LTRret38
seq0	LTRharvest	long_terminal_repeat	5171742	5172353	.	?	.	ID=LTR77;Parent=LTRret38
seq0	LTRharvest	target_site_duplication	5165909	5165912	.	?	.	ID=TSD76;Parent=RepeatReg38
seq0	LTRharvest	target_site_duplication	5172354	5172357	.	?	.	ID=TSD77;Parent=RepeatReg38
seq0	LTRharvest	repeat_region	21899579	21905022	.	?	.	ID=RepeatReg39
seq0	LTRharvest	LTR_retrotransposon	21899583	21905018	.	?	.	ID=LTRret39;Parent=RepeatReg39
seq0	LTRharvest	long_terminal_repeat	21899583	21900233	.	?	.	ID=LTR78;Parent=LTRret39
seq0	LTRharvest	long_terminal_repeat	21904363	21905018	.	?	.	ID=LTR79;Parent=LTRret39
seq0	LTRharvest	target_site_duplication	21899579	21899582	.	?	.	ID=TSD78;Parent=RepeatReg39
seq0	LTRharvest	target_site_duplication	21905019	21905022	.	?	.	ID=TSD79;Parent=RepeatReg39
seq0	LTRharvest	repeat_region	5	5205	.	?	.	ID=RepeatReg40
seq0	LTRharvest	LTR_retrotransposon	9	5201	.	?	.	ID=LTRret40;Parent=RepeatReg40
seq0	LTRharvest	long_terminal_repeat	9	627	.	?	.	ID=LTR80;Parent=LTRret40
seq0	LTRharvest	long_terminal_repeat	4581	5201	.	?	.	ID=LTR81;Parent=LTRret40
seq0	LTRharvest	target_site_duplication	5	8	.	?	.	ID=TSD80;Parent=RepeatReg40
seq0	LTRharvest	target_site_duplication	5202	5205	.	?	.	ID=TSD81;Parent=RepeatReg40
seq0	LTRharvest	repeat_region	16827055	16831986	.	?	.	ID=RepeatReg41
seq0	LTRharvest	LTR_retrotransposon	16827059	16831982	.	?	.	ID=LTRret41;Parent=RepeatReg41
seq0	LTRharvest	long_terminal_repeat	16827059	16827383	.	?	.	ID=LTR82;Parent=LTRret41
seq0	LTRharvest	long_terminal_repeat	16831664	16831982	.	?	.	ID=LTR83;Parent=LTRret41
seq0	LTRharvest	target_site_duplication	16827055	16827058	.	?	.	ID=TSD82;Parent=RepeatReg41
seq0	LTRharvest	target_site_duplication	16831983	16831986	.	?	.	ID=TSD83;Parent=RepeatReg41
seq0	LTRharvest	repeat_region	22209725	22216962	.	?	.	ID=RepeatReg42
seq0	LTRharvest	LTR_retrotransposon	22209729	22216958	.	?	.	ID=LTRret42;Parent=RepeatReg42
seq0	LTRharvest	long_terminal_repeat	22209729	22210140	.	?	.	ID=LTR84;Parent=LTRret42
seq0	LTRharvest	long_terminal_repeat	22216538	22216958	.	?	.	ID=LTR85;Parent=LTRret42
seq0	LTRharvest	target_site_duplication	22209725	22209728	.	?	.	ID=TSD84;Parent=RepeatReg42
seq0	LTRharvest	target_site_duplication	22216959	22216962	.	?	.	ID=TSD85;Parent=RepeatReg42
seq0	LTRharvest	repeat_region	21169130	21172063	.	?	.	ID=RepeatReg43
seq0	LTRharvest	LTR_retrotransposon	21169134	21172059	.	?	.	ID=LTRret43;Parent=RepeatReg43
seq0	LTRharvest	long_terminal_repeat	21169134	21169738	.	?	.	ID=LTR86;Parent=LTRret43
seq0	LTRharvest	long_terminal_repeat	21171448	21172059	.	?	.	ID=LTR87;Parent=LTRret43
seq0	LTRharvest	target_site_duplication	21169130	21169133	.	?	.	ID=TSD86;Parent=RepeatReg43
seq0	LTRharvest	target_site_duplication	21172060	21172063	.	?	.	ID=TSD87;Parent=RepeatReg43
seq0	LTRharvest	repeat_region	2286659	2291814	.	?	.	ID=RepeatReg44
seq0	LTRharvest	LTR_retrotransposon	2286663	2291810	.	?	.	ID=LTRret44;Parent=RepeatReg44
seq0	LTRharvest	long_terminal_repeat	2286663	2286939	.	?	.	ID=LTR88;Parent=LTRret44
seq0	LTRharvest	long_terminal_repeat	2291534	2291810	.	?	.	ID=LTR89;Parent=LTRret44
seq0	LTRharvest	target_site_duplication	2286659	2286662	.	?	.	ID=TSD88;Parent=RepeatReg44
seq0	LTRharvest	target_site_duplication	2291811	2291814	.	?	.	ID=TSD89;Parent=RepeatReg44
seq0	LTRharvest	repeat_region	14782014	14787167	.	?	.	ID=RepeatReg45
seq0	LTRharvest	LTR_retrotransposon	14782018	14787163	.	?	.	ID=LTRret45;Parent=RepeatReg45
seq0	LTRharvest	long_terminal_repeat	14782018	14782294	.	?	.	ID=LTR90;Parent=LTRret45
seq0	LTRharvest	long_terminal_repeat	14786884	14787163	.	?	.	ID=LTR91;Parent=LTRret45
seq0	LTRharvest	target_site_duplication	14782014	14782017	.	?	.	ID=TSD90;Parent=RepeatReg45
seq0	LTRharvest	target_site_duplication	14787164	14787167	.	?	.	ID=TSD91;Parent=RepeatReg45
seq0	LTRharvest	repeat_region	11552558	11557712	.	?	.	ID=RepeatReg46
seq0	LTRharvest	LTR_retrotransposon	11552562	11557708	.	?	.	ID=LTRret46;Parent=RepeatReg46
seq0	LTRharvest	long_terminal_repeat	11552562	11552838	.	?	.	ID=LTR92;Parent=LTRret46
seq0	LTRharvest	long_terminal_repeat	11557432	11557708	.	?	.	ID=LTR93;Parent=LTRret46
seq0	LTRharvest	target_site_duplication	11552558	11552561	.	?	.	ID=TSD92;Parent=RepeatReg46
seq0	LTRharvest	target_site_duplication	11557709	11557712	.	?	.	ID=TSD93;Parent=RepeatReg46
seq0	LTRharvest	repeat_region	11190070	11193184	.	?	.	ID=RepeatReg47
seq0	LTRharvest	LTR_retrotransposon	11190074	11193180	.	?	.	ID=LTRret47;Parent=RepeatReg47
seq0	LTRharvest	long_terminal_repeat	11190074	11190381	.	?	.	ID=LTR94;Parent=LTRret47
seq0	LTRharvest	long_terminal_repeat	11192895	11193180	.	?	.	ID=LTR95;Parent=LTRret47
seq0	LTRharvest	target_site_duplication	11190070	11190073	.	?	.	ID=TSD94;Parent=RepeatReg47
seq0	LTRharvest	target_site_duplication	11193181	11193184	.	?	.	ID=TSD95;Parent=RepeatReg47
seq0	LTRharvest	repeat_region	21010922	21019163	.	?	.	ID=RepeatReg48
seq0	LTRharvest	LTR_retrotransposon	21010926	21019159	.	?	.	ID=LTRret48;Parent=RepeatReg48
seq0	LTRharvest	long_terminal_repeat	21010926	21011356	.	?	.	ID=LTR96;Parent=LTRret48
seq0	LTRharvest	long_terminal_repeat	21018739	21019159	.	?	.	ID=LTR97;Parent=LTRret48
seq0	LTRharvest	target_site_duplication	21010922	21010925	.	?	.	ID=TSD96;Parent=RepeatReg48
seq0	LTRharvest	target_site_duplication	21019160	21019163	.	?	.	ID=TSD97;Parent=RepeatReg48
seq0	LTRharvest	repeat_region	22162396	22167448	.	?	.	ID=RepeatReg49
seq0	LTRharvest	LTR_retrotransposon	22162400	22167444	.	?	.	ID=LTRret49;Parent=RepeatReg49
seq0	LTRharvest	long_terminal_repeat	22162400	22162655	.	?	.	ID=LTR98;Parent=LTRret49
seq0	LTRharvest	long_terminal_repeat	22167177	22167444	.	?	.	ID=LTR99;Parent=LTRret49
seq0	LTRharvest	target_site_duplication	22162396	22162399	.	?	.	ID=TSD98;Parent=RepeatReg49
seq0	LTRharvest	target_site_duplication	22167445	22167448	.	?	.	ID=TSD99;Parent=RepeatReg49
seq0	LTRharvest	repeat_region	7727082	7733685	.	?	.	ID=RepeatReg50
seq0	LTRharvest	LTR_retrotransposon	7727086	7733681	.	?	.	ID=LTRret50;Parent=RepeatReg50
seq0	LTRharvest	long_terminal_repeat	7727086	7727530	.	?	.	ID=LTR100;Parent=LTRret50
seq0	LTRharvest	long_terminal_repeat	7733234	7733681	.	?	.	ID=LTR101;Parent=LTRret50
seq0	LTRharvest	target_site_duplication	7727082	7727085	.	?	.	ID=TSD100;Parent=RepeatReg50
seq0	LTRharvest	target_site_duplication	7733682	7733685	.	?	.	ID=TSD101;Parent=RepeatReg50
seq0	LTRharvest	repeat_region	1680693	1688108	.	?	.	ID=RepeatReg51
seq0	LTRharvest	LTR_retrotransposon	1680697	1688104	.	?	.	ID=LTRret51;Parent=RepeatReg51
seq0	LTRharvest	long_terminal_repeat	1680697	1681098	.	?	.	ID=LTR102;Parent=LTRret51
seq0	LTRharvest	long_terminal_repeat	1687704	1688104	.	?	.	ID=LTR103;Parent=LTRret51
seq0	LTRharvest	target_site_duplication	1680693	1680696	.	?	.	ID=TSD102;Parent=RepeatReg51
seq0	LTRharvest	target_site_duplication	1688105	1688108	.	?	.	ID=TSD103;Parent=RepeatReg51
seq0	LTRharvest	repeat_region	15424187	15431605	.	?	.	ID=RepeatReg52
seq0	LTRharvest	LTR_retrotransposon	15424191	15431601	.	?	.	ID=LTRret52;Parent=RepeatReg52
seq0	LTRharvest	long_terminal_repeat	15424191	15424595	.	?	.	ID=LTR104;Parent=LTRret52
seq0	LTRharvest	long_terminal_repeat	15431201	15431601	.	?	.	ID=LTR105;Parent=LTRret52
seq0	LTRharvest	target_site_duplication	15424187	15424190	.	?	.	ID=TSD104;Parent=RepeatReg52
seq0	LTRharvest	target_site_duplication	15431602	15431605	.	?	.	ID=TSD105;Parent=RepeatReg52
seq0	LTRharvest	repeat_region	11885842	11889161	.	?	.	ID=RepeatReg53
seq0	LTRharvest	LTR_retrotransposon	11885846	11889157	.	?	.	ID=LTRret53;Parent=RepeatReg53
seq0	LTRharvest	long_terminal_repeat	11885846	11886024	.	?	.	ID=LTR106;Parent=LTRret53
seq0	LTRharvest	long_terminal_repeat	11888986	11889157	.	?	.	ID=LTR107;Parent=LTRret53
seq0	LTRharvest	target_site_duplication	11885842	11885845	.	?	.	ID=TSD106;Parent=RepeatReg53
seq0	LTRharvest	target_site_duplication	11889158	11889161	.	?	.	ID=TSD107;Parent=RepeatReg53
seq0	LTRharvest	repeat_region	1221846	1229262	.	?	.	ID=RepeatReg54
seq0	LTRharvest	LTR_retrotransposon	1221850	1229258	.	?	.	ID=LTRret54;Parent=RepeatReg54
seq0	LTRharvest	long_terminal_repeat	1221850	1222248	.	?	.	ID=LTR108;Parent=LTRret54
seq0	LTRharvest	long_terminal_repeat	1228859	1229258	.	?	.	ID=LTR109;Parent=LTRret54
seq0	LTRharvest	target_site_duplication	1221846	1221849	.	?	.	ID=TSD108;Parent=RepeatReg54
seq0	LTRharvest	target_site_duplication	1229259	1229262	.	?	.	ID=TSD109;Parent=RepeatReg54
seq0	LTRharvest	repeat_region	11702429	11709847	.	?	.	ID=RepeatReg55
seq0	LTRharvest	LTR_retrotransposon	11702433	11709843	.	?	.	ID=LTRret55;Parent=RepeatReg55
seq0	LTRharvest	long_terminal_repeat	11702433	11702831	.	?	.	ID=LTR110;Parent=LTRret55
seq0	LTRharvest	long_terminal_repeat	11709444	11709843	.	?	.	ID=LTR111;Parent=LTRret55
seq0	LTRharvest	target_site_duplication	11702429	11702432	.	?	.	ID=TSD110;Parent=RepeatReg55
seq0	LTRharvest	target_site_duplication	11709844	11709847	.	?	.	ID=TSD111;Parent=RepeatReg55
seq0	LTRharvest	repeat_region	19325620	19333044	.	?	.	ID=RepeatReg56
seq0	LTRharvest	LTR_retrotransposon	19325624	19333040	.	?	.	ID=LTRret56;Parent=RepeatReg56
seq0	LTRharvest	long_terminal_repeat	19325624	19326024	.	?	.	ID=LTR112;Parent=LTRret56
seq0	LTRharvest	long_terminal_repeat	19332639	19333040	.	?	.	ID=LTR113;Parent=LTRret56
seq0	LTRharvest	target_site_duplication	19325620	19325623	.	?	.	ID=TSD112;Parent=RepeatReg56
seq0	LTRharvest	target_site_duplication	19333041	19333044	.	?	.	ID=TSD113;Parent=RepeatReg56
seq0	LTRharvest	repeat_region	22148779	22151273	.	?	.	ID=RepeatReg57
seq0	LTRharvest	LTR_retrotransposon	22148784	22151268	.	?	.	ID=LTRret57;Parent=RepeatReg57
seq0	LTRharvest	long_terminal_repeat	22148784	22148988	.	?	.	ID=LTR114;Parent=LTRret57
seq0	LTRharvest	long_terminal_repeat	22151064	22151268	.	?	.	ID=LTR115;Parent=LTRret57
seq0	LTRharvest	target_site_duplication	22148779	22148783	.	?	.	ID=TSD114;Parent=RepeatReg57
seq0	LTRharvest	target_site_duplication	22151269	22151273	.	?	.	ID=TSD115;Parent=RepeatReg57
seq0	LTRharvest	repeat_region	14624776	14633889	.	?	.	ID=RepeatReg58
seq0	LTRharvest	LTR_retrotransposon	14624780	14633885	.	?	.	ID=LTRret58;Parent=RepeatReg58
seq0	LTRharvest	long_terminal_repeat	14624780	14625208	.	?	.	ID=LTR116;Parent=LTRret58
seq0	LTRharvest	long_terminal_repeat	14633455	14633885	.	?	.	ID=LTR117;Parent=LTRret58
seq0	LTRharvest	target_site_duplication	14624776	14624779	.	?	.	ID=TSD116;Parent=RepeatReg58
seq0	LTRharvest	target_site_duplication	14633886	14633889	.	?	.	ID=TSD117;Parent=RepeatReg58
seq0	LTRharvest	repeat_region	21814824	21823958	.	?	.	ID=RepeatReg59
seq0	LTRharvest	LTR_retrotransposon	21814828	21823954	.	?	.	ID=LTRret59;Parent=RepeatReg59
seq0	LTRharvest	long_terminal_repeat	21814828	21815279	.	?	.	ID=LTR118;Parent=LTRret59
seq0	LTRharvest	long_terminal_repeat	21823492	21823954	.	?	.	ID=LTR119;Parent=LTRret59
seq0	LTRharvest	target_site_duplication	21814824	21814827	.	?	.	ID=TSD118;Parent=RepeatReg59
seq0	LTRharvest	target_site_duplication	21823955	21823958	.	?	.	ID=TSD119;Parent=RepeatReg59
seq0	LTRharvest	repeat_region	8992561	9000022	.	?	.	ID=RepeatReg60
seq0	LTRharvest	LTR_retrotransposon	8992566	9000017	.	?	.	ID=LTRret60;Parent=RepeatReg60
seq0	LTRharvest	long_terminal_repeat	8992566	8992993	.	?	.	ID=LTR120;Parent=LTRret60
seq0	LTRharvest	long_terminal_repeat	8999590	9000017	.	?	.	ID=LTR121;Parent=LTRret60
seq0	LTRharvest	target_site_duplication	8992561	8992565	.	?	.	ID=TSD120;Parent=RepeatReg60
seq0	LTRharvest	target_site_duplication	9000018	9000022	.	?	.	ID=TSD121;Parent=RepeatReg60
seq0	LTRharvest	repeat_region	688634	697625	.	?	.	ID=RepeatReg61
seq0	LTRharvest	LTR_retrotransposon	688639	697620	.	?	.	ID=LTRret61;Parent=RepeatReg61
seq0	LTRharvest	long_terminal_repeat	688639	689066	.	?	.	ID=LTR122;Parent=LTRret61
seq0	LTRharvest	long_terminal_repeat	697193	697620	.	?	.	ID=LTR123;Parent=LTRret61
seq0	LTRharvest	target_site_duplication	688634	688638	.	?	.	ID=TSD122;Parent=RepeatReg61
seq0	LTRharvest	target_site_duplication	697621	697625	.	?	.	ID=TSD123;Parent=RepeatReg61
seq0	LTRharvest	repeat_region	5819971	5828943	.	?	.	ID=RepeatReg62
seq0	LTRharvest	LTR_retrotransposon	5819975	5828939	.	?	.	ID=LTRret62;Parent=RepeatReg62
seq0	LTRharvest	long_terminal_repeat	5819975	5820419	.	?	.	ID=LTR124;Parent=LTRret62
seq0	LTRharvest	long_terminal_repeat	5828500	5828939	.	?	.	ID=LTR125;Parent=LTRret62
seq0	LTRharvest	target_site_duplication	5819971	5819974	.	?	.	ID=TSD124;Parent=RepeatReg62
seq0	LTRharvest	target_site_duplication	5828940	5828943	.	?	.	ID=TSD125;Parent=RepeatReg62
seq0	LTRharvest	repeat_region	998433	1007489	.	?	.	ID=RepeatReg63
seq0	LTRharvest	LTR_retrotransposon	998437	1007485	.	?	.	ID=LTRret63;Parent=RepeatReg63
seq0	LTRharvest	long_terminal_repeat	998437	998872	.	?	.	ID=LTR126;Parent=LTRret63
seq0	LTRharvest	long_terminal_repeat	1007049	1007485	.	?	.	ID=LTR127;Parent=LTRret63
seq0	LTRharvest	target_site_duplication	998433	998436	.	?	.	ID=TSD126;Parent=RepeatReg63
seq0	LTRharvest	target_site_duplication	1007486	1007489	.	?	.	ID=TSD127;Parent=RepeatReg63
seq0	LTRharvest	repeat_region	19681670	19690756	.	?	.	ID=RepeatReg64
seq0	LTRharvest	LTR_retrotransposon	19681674	19690752	.	?	.	ID=LTRret64;Parent=RepeatReg64
seq0	LTRharvest	long_terminal_repeat	19681674	19682102	.	?	.	ID=LTR128;Parent=LTRret64
seq0	LTRharvest	long_terminal_repeat	19690311	19690752	.	?	.	ID=LTR129;Parent=LTRret64
seq0	LTRharvest	target_site_duplication	19681670	19681673	.	?	.	ID=TSD128;Parent=RepeatReg64
seq0	LTRharvest	target_site_duplication	19690753	19690756	.	?	.	ID=TSD129;Parent=RepeatReg64
seq0	LTRharvest	repeat_region	10148766	10156202	.	?	.	ID=RepeatReg65
seq0	LTRharvest	LTR_retrotransposon	10148770	10156198	.	?	.	ID=LTRret65;Parent=RepeatReg65
seq0	LTRharvest	long_terminal_repeat	10148770	10149189	.	?	.	ID=LTR130;Parent=LTRret65
seq0	LTRharvest	long_terminal_repeat	10155776	10156198	.	?	.	ID=LTR131;Parent=LTRret65
seq0	LTRharvest	target_site_duplication	10148766	10148769	.	?	.	ID=TSD130;Parent=RepeatReg65
seq0	LTRharvest	target_site_duplication	10156199	10156202	.	?	.	ID=TSD131;Parent=RepeatReg65
seq0	LTRharvest	repeat_region	347937	355400	.	?	.	ID=RepeatReg66
seq0	LTRharvest	LTR_retrotransposon	347941	355396	.	?	.	ID=LTRret66;Parent=RepeatReg66
seq0	LTRharvest	long_terminal_repeat	347941	348364	.	?	.	ID=LTR132;Parent=LTRret66
seq0	LTRharvest	long_terminal_repeat	354968	355396	.	?	.	ID=LTR133;Parent=LTRret66
seq0	LTRharvest	target_site_duplication	347937	347940	.	?	.	ID=TSD132;Parent=RepeatReg66
seq0	LTRharvest	target_site_duplication	355397	355400	.	?	.	ID=TSD133;Parent=RepeatReg66
seq0	LTRharvest	repeat_region	20272953	20280372	.	?	.	ID=RepeatReg67
seq0	LTRharvest	LTR_retrotransposon	20272957	20280368	.	?	.	ID=LTRret67;Parent=RepeatReg67
seq0	LTRharvest	long_terminal_repeat	20272957	20273355	.	?	.	ID=LTR134;Parent=LTRret67
seq0	LTRharvest	long_terminal_repeat	20279970	20280368	.	?	.	ID=LTR135;Parent=LTRret67
seq0	LTRharvest	target_site_duplication	20272953	20272956	.	?	.	ID=TSD134;Parent=RepeatReg67
seq0	LTRharvest	target_site_duplication	20280369	20280372	.	?	.	ID=TSD135;Parent=RepeatReg67
seq0	LTRharvest	repeat_region	12922771	12930188	.	?	.	ID=RepeatReg68
seq0	LTRharvest	LTR_retrotransposon	12922775	12930184	.	?	.	ID=LTRret68;Parent=RepeatReg68
seq0	LTRharvest	long_terminal_repeat	12922775	12923173	.	?	.	ID=LTR136;Parent=LTRret68
seq0	LTRharvest	long_terminal_repeat	12929786	12930184	.	?	.	ID=LTR137;Parent=LTRret68
seq0	LTRharvest	target_site_duplication	12922771	12922774	.	?	.	ID=TSD136;Parent=RepeatReg68
seq0	LTRharvest	target_site_duplication	12930185	12930188	.	?	.	ID=TSD137;Parent=RepeatReg68
seq0	LTRharvest	repeat_region	11529506	11536858	.	?	.	ID=RepeatReg69
seq0	LTRharvest	LTR_retrotransposon	11529510	11536854	.	?	.	ID=LTRret69;Parent=RepeatReg69
seq0	LTRharvest	long_terminal_repeat	11529510	11530017	.	?	.	ID=LTR138;Parent=LTRret69
seq0	LTRharvest	long_terminal_repeat	11536348	11536854	.	?	.	ID=LTR139;Parent=LTRret69
seq0	LTRharvest	target_site_duplication	11529506	11529509	.	?	.	ID=TSD138;Parent=RepeatReg69
seq0	LTRharvest	target_site_duplication	11536855	11536858	.	?	.	ID=TSD139;Parent=RepeatReg69
seq0	LTRharvest	repeat_region	21387100	21394156	.	?	.	ID=RepeatReg70
seq0	LTRharvest	LTR_retrotransposon	21387104	21394152	.	?	.	ID=LTRret70;Parent=RepeatReg70
seq0	LTRharvest	long_terminal_repeat	21387104	21387878	.	?	.	ID=LTR140;Parent=LTRret70
seq0	LTRharvest	long_terminal_repeat	21393380	21394152	.	?	.	ID=LTR141;Parent=LTRret70
seq0	LTRharvest	target_site_duplication	21387100	21387103	.	?	.	ID=TSD140;Parent=RepeatReg70
seq0	LTRharvest	target_site_duplication	21394153	21394156	.	?	.	ID=TSD141;Parent=RepeatReg70
seq0	LTRharvest	repeat_region	6869036	6875208	.	?	.	ID=RepeatReg71
seq0	LTRharvest	LTR_retrotransposon	6869040	6875204	.	?	.	ID=LTRret71;Parent=RepeatReg71
seq0	LTRharvest	long_terminal_repeat	6869040	6869311	.	?	.	ID=LTR142;Parent=LTRret71
seq0	LTRharvest	long_terminal_repeat	6874938	6875204	.	?	.	ID=LTR143;Parent=LTRret71
seq0	LTRharvest	target_site_duplication	6869036	6869039	.	?	.	ID=TSD142;Parent=RepeatReg71
seq0	LTRharvest	target_site_duplication	6875205	6875208	.	?	.	ID=TSD143;Parent=RepeatReg71
seq0	LTRharvest	repeat_region	21317345	21324767	.	?	.	ID=RepeatReg72
seq0	LTRharvest	LTR_retrotransposon	21317349	21324763	.	?	.	ID=LTRret72;Parent=RepeatReg72
seq0	LTRharvest	long_terminal_repeat	21317349	21317747	.	?	.	ID=LTR144;Parent=LTRret72
seq0	LTRharvest	long_terminal_repeat	21324365	21324763	.	?	.	ID=LTR145;Parent=LTRret72
seq0	LTRharvest	target_site_duplication	21317345	21317348	.	?	.	ID=TSD144;Parent=RepeatReg72
seq0	LTRharvest	target_site_duplication	21324764	21324767	.	?	.	ID=TSD145;Parent=RepeatReg72
seq0	LTRharvest	repeat_region	20546012	20553430	.	?	.	ID=RepeatReg73
seq0	LTRharvest	LTR_retrotransposon	20546016	20553426	.	?	.	ID=LTRret73;Parent=RepeatReg73
seq0	LTRharvest	long_terminal_repeat	20546016	20546414	.	?	.	ID=LTR146;Parent=LTRret73
seq0	LTRharvest	long_terminal_repeat	20553028	20553426	.	?	.	ID=LTR147;Parent=LTRret73
seq0	LTRharvest	target_site_duplication	20546012	20546015	.	?	.	ID=TSD146;Parent=RepeatReg73
seq0	LTRharvest	target_site_duplication	20553427	20553430	.	?	.	ID=TSD147;Parent=RepeatReg73
seq0	LTRharvest	repeat_region	4594317	4601734	.	?	.	ID=RepeatReg74
seq0	LTRharvest	LTR_retrotransposon	4594321	4601730	.	?	.	ID=LTRret74;Parent=RepeatReg74
seq0	LTRharvest	long_terminal_repeat	4594321	4594788	.	?	.	ID=LTR148;Parent=LTRret74
seq0	LTRharvest	long_terminal_repeat	4601268	4601730	.	?	.	ID=LTR149;Parent=LTRret74
seq0	LTRharvest	target_site_duplication	4594317	4594320	.	?	.	ID=TSD148;Parent=RepeatReg74
seq0	LTRharvest	target_site_duplication	4601731	4601734	.	?	.	ID=TSD149;Parent=RepeatReg74
seq0	LTRharvest	repeat_region	3195359	3202738	.	?	.	ID=RepeatReg75
seq0	LTRharvest	LTR_retrotransposon	3195363	3202734	.	?	.	ID=LTRret75;Parent=RepeatReg75
seq0	LTRharvest	long_terminal_repeat	3195363	3195805	.	?	.	ID=LTR150;Parent=LTRret75
seq0	LTRharvest	long_terminal_repeat	3202277	3202734	.	?	.	ID=LTR151;Parent=LTRret75
seq0	LTRharvest	target_site_duplication	3195359	3195362	.	?	.	ID=TSD150;Parent=RepeatReg75
seq0	LTRharvest	target_site_duplication	3202735	3202738	.	?	.	ID=TSD151;Parent=RepeatReg75
seq0	LTRharvest	repeat_region	8444702	8453824	.	?	.	ID=RepeatReg76
seq0	LTRharvest	LTR_retrotransposon	8444707	8453819	.	?	.	ID=LTRret76;Parent=RepeatReg76
seq0	LTRharvest	long_terminal_repeat	8444707	8445135	.	?	.	ID=LTR152;Parent=LTRret76
seq0	LTRharvest	long_terminal_repeat	8453391	8453819	.	?	.	ID=LTR153;Parent=LTRret76
seq0	LTRharvest	target_site_duplication	8444702	8444706	.	?	.	ID=TSD152;Parent=RepeatReg76
seq0	LTRharvest	target_site_duplication	8453820	8453824	.	?	.	ID=TSD153;Parent=RepeatReg76
seq0	LTRharvest	repeat_region	978598	986207	.	?	.	ID=RepeatReg77
seq0	LTRharvest	LTR_retrotransposon	978602	986203	.	?	.	ID=LTRret77;Parent=RepeatReg77
seq0	LTRharvest	long_terminal_repeat	978602	979049	.	?	.	ID=LTR154;Parent=LTRret77
seq0	LTRharvest	long_terminal_repeat	985750	986203	.	?	.	ID=LTR155;Parent=LTRret77
seq0	LTRharvest	target_site_duplication	978598	978601	.	?	.	ID=TSD154;Parent=RepeatReg77
seq0	LTRharvest	target_site_duplication	986204	986207	.	?	.	ID=TSD155;Parent=RepeatReg77
seq0	LTRharvest	repeat_region	21430199	21437893	.	?	.	ID=RepeatReg78
seq0	LTRharvest	LTR_retrotransposon	21430203	21437889	.	?	.	ID=LTRret78;Parent=RepeatReg78
seq0	LTRharvest	long_terminal_repeat	21430203	21430631	.	?	.	ID=LTR156;Parent=LTRret78
seq0	LTRharvest	long_terminal_repeat	21437458	21437889	.	?	.	ID=LTR157;Parent=LTRret78
seq0	LTRharvest	target_site_duplication	21430199	21430202	.	?	.	ID=TSD156;Parent=RepeatReg78
seq0	LTRharvest	target_site_duplication	21437890	21437893	.	?	.	ID=TSD157;Parent=RepeatReg78
seq0	LTRharvest	repeat_region	10939403	10948569	.	?	.	ID=RepeatReg79
seq0	LTRharvest	LTR_retrotransposon	10939408	10948564	.	?	.	ID=LTRret79;Parent=RepeatReg79
seq0	LTRharvest	long_terminal_repeat	10939408	10939835	.	?	.	ID=LTR158;Parent=LTRret79
seq0	LTRharvest	long_terminal_repeat	10948137	10948564	.	?	.	ID=LTR159;Parent=LTRret79
seq0	LTRharvest	target_site_duplication	10939403	10939407	.	?	.	ID=TSD158;Parent=RepeatReg79
seq0	LTRharvest	target_site_duplication	10948565	10948569	.	?	.	ID=TSD159;Parent=RepeatReg79
seq0	LTRharvest	repeat_region	7335608	7342674	.	?	.	ID=RepeatReg80
seq0	LTRharvest	LTR_retrotransposon	7335612	7342670	.	?	.	ID=LTRret80;Parent=RepeatReg80
seq0	LTRharvest	long_terminal_repeat	7335612	7336049	.	?	.	ID=LTR160;Parent=LTRret80
seq0	LTRharvest	long_terminal_repeat	7342242	7342670	.	?	.	ID=LTR161;Parent=LTRret80
seq0	LTRharvest	target_site_duplication	7335608	7335611	.	?	.	ID=TSD160;Parent=RepeatReg80
seq0	LTRharvest	target_site_duplication	7342671	7342674	.	?	.	ID=TSD161;Parent=RepeatReg80
seq0	LTRharvest	repeat_region	18030009	18039107	.	?	.	ID=RepeatReg81
seq0	LTRharvest	LTR_retrotransposon	18030014	18039102	.	?	.	ID=LTRret81;Parent=RepeatReg81
seq0	LTRharvest	long_terminal_repeat	18030014	18030427	.	?	.	ID=LTR162;Parent=LTRret81
seq0	LTRharvest	long_terminal_repeat	18038689	18039102	.	?	.	ID=LTR163;Parent=LTRret81
seq0	LTRharvest	target_site_duplication	18030009	18030013	.	?	.	ID=TSD162;Parent=RepeatReg81
seq0	LTRharvest	target_site_duplication	18039103	18039107	.	?	.	ID=TSD163;Parent=RepeatReg81
seq0	LTRharvest	repeat_region	3642407	3647561	.	?	.	ID=RepeatReg82
seq0	LTRharvest	LTR_retrotransposon	3642412	3647556	.	?	.	ID=LTRret82;Parent=RepeatReg82
seq0	LTRharvest	long_terminal_repeat	3642412	3642687	.	?	.	ID=LTR164;Parent=LTRret82
seq0	LTRharvest	long_terminal_repeat	3647281	3647556	.	?	.	ID=LTR165;Parent=LTRret82
seq0	LTRharvest	target_site_duplication	3642407	3642411	.	?	.	ID=TSD164;Parent=RepeatReg82
seq0	LTRharvest	target_site_duplication	3647557	3647561	.	?	.	ID=TSD165;Parent=RepeatReg82
seq0	LTRharvest	repeat_region	8005895	8011050	.	?	.	ID=RepeatReg83
seq0	LTRharvest	LTR_retrotransposon	8005900	8011045	.	?	.	ID=LTRret83;Parent=RepeatReg83
seq0	LTRharvest	long_terminal_repeat	8005900	8006175	.	?	.	ID=LTR166;Parent=LTRret83
seq0	LTRharvest	long_terminal_repeat	8010770	8011045	.	?	.	ID=LTR167;Parent=LTRret83
seq0	LTRharvest	target_site_duplication	8005895	8005899	.	?	.	ID=TSD166;Parent=RepeatReg83
seq0	LTRharvest	target_site_duplication	8011046	8011050	.	?	.	ID=TSD167;Parent=RepeatReg83
seq0	LTRharvest	repeat_region	3065652	3070805	.	?	.	ID=RepeatReg84
seq0	LTRharvest	LTR_retrotransposon	3065656	3070801	.	?	.	ID=LTRret84;Parent=RepeatReg84
seq0	LTRharvest	long_terminal_repeat	3065656	3065937	.	?	.	ID=LTR168;Parent=LTRret84
seq0	LTRharvest	long_terminal_repeat	3070525	3070801	.	?	.	ID=LTR169;Parent=LTRret84
seq0	LTRharvest	target_site_duplication	3065652	3065655	.	?	.	ID=TSD168;Parent=RepeatReg84
seq0	LTRharvest	target_site_duplication	3070802	3070805	.	?	.	ID=TSD169;Parent=RepeatReg84
seq0	LTRharvest	repeat_region	20242518	20247671	.	?	.	ID=RepeatReg85
seq0	LTRharvest	LTR_retrotransposon	20242523	20247666	.	?	.	ID=LTRret85;Parent=RepeatReg85
seq0	LTRharvest	long_terminal_repeat	20242523	20242798	.	?	.	ID=LTR170;Parent=LTRret85
seq0	LTRharvest	long_terminal_repeat	20247391	20247666	.	?	.	ID=LTR171;Parent=LTRret85
seq0	LTRharvest	target_site_duplication	20242518	20242522	.	?	.	ID=TSD170;Parent=RepeatReg85
seq0	LTRharvest	target_site_duplication	20247667	20247671	.	?	.	ID=TSD171;Parent=RepeatReg85
seq0	LTRharvest	repeat_region	20137089	20142349	.	?	.	ID=RepeatReg86
seq0	LTRharvest	LTR_retrotransposon	20137093	20142345	.	?	.	ID=LTRret86;Parent=RepeatReg86
seq0	LTRharvest	long_terminal_repeat	20137093	20137368	.	?	.	ID=LTR172;Parent=LTRret86
seq0	LTRharvest	long_terminal_repeat	20142068	20142345	.	?	.	ID=LTR173;Parent=LTRret86
seq0	LTRharvest	target_site_duplication	20137089	20137092	.	?	.	ID=TSD172;Parent=RepeatReg86
seq0	LTRharvest	target_site_duplication	20142346	20142349	.	?	.	ID=TSD173;Parent=RepeatReg86
seq0	LTRharvest	repeat_region	16119297	16124455	.	?	.	ID=RepeatReg87
seq0	LTRharvest	LTR_retrotransposon	16119302	16124450	.	?	.	ID=LTRret87;Parent=RepeatReg87
seq0	LTRharvest	long_terminal_repeat	16119302	16119577	.	?	.	ID=LTR174;Parent=LTRret87
seq0	LTRharvest	long_terminal_repeat	16124175	16124450	.	?	.	ID=LTR175;Parent=LTRret87
seq0	LTRharvest	target_site_duplication	16119297	16119301	.	?	.	ID=TSD174;Parent=RepeatReg87
seq0	LTRharvest	target_site_duplication	16124451	16124455	.	?	.	ID=TSD175;Parent=RepeatReg87
seq0	LTRharvest	repeat_region	22034479	22039632	.	?	.	ID=RepeatReg88
seq0	LTRharvest	LTR_retrotransposon	22034484	22039627	.	?	.	ID=LTRret88;Parent=RepeatReg88
seq0	LTRharvest	long_terminal_repeat	22034484	22034759	.	?	.	ID=LTR176;Parent=LTRret88
seq0	LTRharvest	long_terminal_repeat	22039352	22039627	.	?	.	ID=LTR177;Parent=LTRret88
seq0	LTRharvest	target_site_duplication	22034479	22034483	.	?	.	ID=TSD176;Parent=RepeatReg88
seq0	LTRharvest	target_site_duplication	22039628	22039632	.	?	.	ID=TSD177;Parent=RepeatReg88
seq0	LTRharvest	repeat_region	17798056	17803210	.	?	.	ID=RepeatReg89
seq0	LTRharvest	LTR_retrotransposon	17798061	17803205	.	?	.	ID=LTRret89;Parent=RepeatReg89
seq0	LTRharvest	long_terminal_repeat	17798061	17798335	.	?	.	ID=LTR178;Parent=LTRret89
seq0	LTRharvest	long_terminal_repeat	17802931	17803205	.	?	.	ID=LTR179;Parent=LTRret89
seq0	LTRharvest	target_site_duplication	17798056	17798060	.	?	.	ID=TSD178;Parent=RepeatReg89
seq0	LTRharvest	target_site_duplication	17803206	17803210	.	?	.	ID=TSD179;Parent=RepeatReg89
seq0	LTRharvest	repeat_region	1802936	1808463	.	?	.	ID=RepeatReg90
seq0	LTRharvest	LTR_retrotransposon	1802940	1808459	.	?	.	ID=LTRret90;Parent=RepeatReg90
seq0	LTRharvest	long_terminal_repeat	1802940	1803212	.	?	.	ID=LTR180;Parent=LTRret90
seq0	LTRharvest	long_terminal_repeat	1808191	1808459	.	?	.	ID=LTR181;Parent=LTRret90
seq0	LTRharvest	target_site_duplication	1802936	1802939	.	?	.	ID=TSD180;Parent=RepeatReg90
seq0	LTRharvest	target_site_duplication	1808460	1808463	.	?	.	ID=TSD181;Parent=RepeatReg90
genometools-1.5.1/testdata/gt_eval_ltr_prob_1.reality000066400000000000000000000176471211610345200230330ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq0 1 22217931
seq0	Fruitfly	LTR_retrotransposon	347940	355382	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	688639	697620	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	978600	986177	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	998445	1007482	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	1221849	1229258	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	1303473	1303954	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	1680695	1688104	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	1713076	1713343	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	1802938	1808457	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	2104735	2112341	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	2286663	2291810	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	2558160	2564170	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	2765222	2771744	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	3065656	3070800	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	3195363	3202734	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	3244118	3251625	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	3642412	3647556	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	4173896	4176470	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	4594328	4601711	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	4654449	4661975	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	5819978	5828927	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	6355420	6358284	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	6419126	6423779	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	6423780	6428231	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	6428230	6437328	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	6869048	6875195	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	6983718	6990779	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	7335612	7342669	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	7540367	7542745	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	7969366	7976282	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	8005900	8011045	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	8444707	8453819	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	8586751	8593747	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	8715395	8723721	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	8992566	9000017	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	9966190	9973251	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	10148786	10156201	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	10585306	10592911	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	10869007	10876005	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	10939408	10948564	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	11529509	11536853	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	11552562	11557708	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	11702432	11709843	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	12056256	12063250	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	12547246	12554316	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	12770728	12778114	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	12922775	12930184	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	13438387	13439046	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	13504464	13509712	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	13835292	13844383	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	14624781	14633885	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	14782018	14787163	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	14962535	14970060	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	15424189	15431601	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	15564549	15571543	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	15661867	15662525	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	15662859	15664842	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	15696864	15699839	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	15701246	15705654	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	15804999	15807341	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	16119302	16124450	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	16131875	16138871	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	16490102	16497158	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	17122469	17130082	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	17798061	17803205	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	18030014	18039102	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	19125508	19132485	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	19325623	19333040	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	19630711	19635762	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	19635763	19643371	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	19643372	19646532	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	19651276	19652086	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	19681675	19690752	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	19984003	19989022	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20133886	20134160	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20135490	20135814	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20137094	20142345	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20143985	20144088	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20148441	20149279	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20150134	20150594	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20154138	20154859	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20154860	20162270	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20162270	20169186	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20169187	20169317	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20169316	20170809	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20170804	20171048	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20178952	20179192	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20241908	20242522	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20242523	20247666	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20247666	20252561	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20272957	20280368	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20377606	20382636	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20546016	20553426	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20605022	20605341	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20710045	20717862	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	20805605	20806264	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21010933	21019137	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21317349	21324763	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21372835	21373265	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21375980	21378558	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21383095	21383351	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21402852	21403334	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21430204	21437889	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21486368	21489615	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21525003	21531415	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21566520	21570614	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21814814	21823919	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21909869	21910105	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	21944136	21944820	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22015372	22015594	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22034484	22039627	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22049240	22049623	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22052309	22052654	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22116556	22123207	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22133407	22137517	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22140503	22144064	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22148784	22151268	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22155967	22156135	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22162400	22167445	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22167561	22167782	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22168147	22168625	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22169273	22169463	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22170878	22170980	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22207263	22209332	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22210048	22210140	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22214446	22214882	.	?	.	.
###
seq0	Fruitfly	LTR_retrotransposon	22214882	22217230	.	?	.	.
###
genometools-1.5.1/testdata/gt_eval_ltr_test_1.in000066400000000000000000001106621211610345200217740ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq0 1 230209
##sequence-region   seq1 1 813139
##sequence-region   seq10 1 666449
##sequence-region   seq11 1 1078173
##sequence-region   seq12 1 924431
##sequence-region   seq13 1 784331
##sequence-region   seq14 1 1091284
##sequence-region   seq15 1 948061
##sequence-region   seq2 1 315342
##sequence-region   seq3 1 1531975
##sequence-region   seq4 1 576871
##sequence-region   seq5 1 270149
##sequence-region   seq6 1 1090937
##sequence-region   seq7 1 562639
##sequence-region   seq8 1 439886
##sequence-region   seq9 1 745441
seq0	LTRharvest	repeat_region	160234	166168	.	?	.	ID=repeat_region1
seq0	LTRharvest	target_site_duplication	160234	160238	.	?	.	Parent=repeat_region1
seq0	LTRharvest	inverted_repeat	160239	160240	.	?	.	Parent=repeat_region1
seq0	LTRharvest	LTR_retrotransposon	160239	166163	.	?	.	ID=LTR_retrotransposon1;Parent=repeat_region1
seq0	LTRharvest	long_terminal_repeat	160239	160575	.	?	.	Parent=LTR_retrotransposon1
seq0	LTRharvest	long_terminal_repeat	165827	166163	.	?	.	Parent=LTR_retrotransposon1
seq0	LTRharvest	inverted_repeat	160574	160575	.	?	.	Parent=repeat_region1
seq0	LTRharvest	inverted_repeat	165827	165828	.	?	.	Parent=repeat_region1
seq0	LTRharvest	inverted_repeat	166162	166163	.	?	.	Parent=repeat_region1
seq0	LTRharvest	target_site_duplication	166164	166168	.	?	.	Parent=repeat_region1
###
seq1	LTRharvest	repeat_region	29627	35595	.	?	.	ID=repeat_region2
seq1	LTRharvest	target_site_duplication	29627	29631	.	?	.	Parent=repeat_region2
seq1	LTRharvest	inverted_repeat	29632	29633	.	?	.	Parent=repeat_region2
seq1	LTRharvest	LTR_retrotransposon	29632	35590	.	?	.	ID=LTR_retrotransposon2;Parent=repeat_region2
seq1	LTRharvest	long_terminal_repeat	29632	29963	.	?	.	Parent=LTR_retrotransposon2
seq1	LTRharvest	long_terminal_repeat	35259	35590	.	?	.	Parent=LTR_retrotransposon2
seq1	LTRharvest	inverted_repeat	29962	29963	.	?	.	Parent=repeat_region2
seq1	LTRharvest	inverted_repeat	35259	35260	.	?	.	Parent=repeat_region2
seq1	LTRharvest	inverted_repeat	35589	35590	.	?	.	Parent=repeat_region2
seq1	LTRharvest	target_site_duplication	35591	35595	.	?	.	Parent=repeat_region2
###
seq1	LTRharvest	repeat_region	220991	226916	.	?	.	ID=repeat_region3
seq1	LTRharvest	target_site_duplication	220991	220995	.	?	.	Parent=repeat_region3
seq1	LTRharvest	inverted_repeat	220996	220997	.	?	.	Parent=repeat_region3
seq1	LTRharvest	LTR_retrotransposon	220996	226911	.	?	.	ID=LTR_retrotransposon3;Parent=repeat_region3
seq1	LTRharvest	long_terminal_repeat	220996	221329	.	?	.	Parent=LTR_retrotransposon3
seq1	LTRharvest	long_terminal_repeat	226575	226911	.	?	.	Parent=LTR_retrotransposon3
seq1	LTRharvest	inverted_repeat	221328	221329	.	?	.	Parent=repeat_region3
seq1	LTRharvest	inverted_repeat	226575	226576	.	?	.	Parent=repeat_region3
seq1	LTRharvest	inverted_repeat	226910	226911	.	?	.	Parent=repeat_region3
seq1	LTRharvest	target_site_duplication	226912	226916	.	?	.	Parent=repeat_region3
###
seq1	LTRharvest	repeat_region	259527	265453	.	?	.	ID=repeat_region4
seq1	LTRharvest	target_site_duplication	259527	259531	.	?	.	Parent=repeat_region4
seq1	LTRharvest	inverted_repeat	259532	259533	.	?	.	Parent=repeat_region4
seq1	LTRharvest	LTR_retrotransposon	259532	265448	.	?	.	ID=LTR_retrotransposon4;Parent=repeat_region4
seq1	LTRharvest	long_terminal_repeat	259532	259863	.	?	.	Parent=LTR_retrotransposon4
seq1	LTRharvest	long_terminal_repeat	265117	265448	.	?	.	Parent=LTR_retrotransposon4
seq1	LTRharvest	inverted_repeat	259862	259863	.	?	.	Parent=repeat_region4
seq1	LTRharvest	inverted_repeat	265117	265118	.	?	.	Parent=repeat_region4
seq1	LTRharvest	inverted_repeat	265447	265448	.	?	.	Parent=repeat_region4
seq1	LTRharvest	target_site_duplication	265449	265453	.	?	.	Parent=repeat_region4
###
seq11	LTRharvest	repeat_region	215076	221011	.	?	.	ID=repeat_region5
seq11	LTRharvest	target_site_duplication	215076	215080	.	?	.	Parent=repeat_region5
seq11	LTRharvest	inverted_repeat	215081	215082	.	?	.	Parent=repeat_region5
seq11	LTRharvest	LTR_retrotransposon	215081	221006	.	?	.	ID=LTR_retrotransposon5;Parent=repeat_region5
seq11	LTRharvest	long_terminal_repeat	215081	215427	.	?	.	Parent=LTR_retrotransposon5
seq11	LTRharvest	long_terminal_repeat	220669	221006	.	?	.	Parent=LTR_retrotransposon5
seq11	LTRharvest	inverted_repeat	215426	215427	.	?	.	Parent=repeat_region5
seq11	LTRharvest	inverted_repeat	220669	220670	.	?	.	Parent=repeat_region5
seq11	LTRharvest	inverted_repeat	221005	221006	.	?	.	Parent=repeat_region5
seq11	LTRharvest	target_site_duplication	221007	221011	.	?	.	Parent=repeat_region5
###
seq11	LTRharvest	repeat_region	475970	481903	.	?	.	ID=repeat_region6
seq11	LTRharvest	target_site_duplication	475970	475974	.	?	.	Parent=repeat_region6
seq11	LTRharvest	inverted_repeat	475975	475976	.	?	.	Parent=repeat_region6
seq11	LTRharvest	LTR_retrotransposon	475975	481898	.	?	.	ID=LTR_retrotransposon6;Parent=repeat_region6
seq11	LTRharvest	long_terminal_repeat	475975	476311	.	?	.	Parent=LTR_retrotransposon6
seq11	LTRharvest	long_terminal_repeat	481562	481898	.	?	.	Parent=LTR_retrotransposon6
seq11	LTRharvest	inverted_repeat	476310	476311	.	?	.	Parent=repeat_region6
seq11	LTRharvest	inverted_repeat	481562	481563	.	?	.	Parent=repeat_region6
seq11	LTRharvest	inverted_repeat	481897	481898	.	?	.	Parent=repeat_region6
seq11	LTRharvest	target_site_duplication	481899	481903	.	?	.	Parent=repeat_region6
###
seq11	LTRharvest	repeat_region	593140	599067	.	?	.	ID=repeat_region7
seq11	LTRharvest	target_site_duplication	593140	593144	.	?	.	Parent=repeat_region7
seq11	LTRharvest	inverted_repeat	593145	593146	.	?	.	Parent=repeat_region7
seq11	LTRharvest	LTR_retrotransposon	593145	599062	.	?	.	ID=LTR_retrotransposon7;Parent=repeat_region7
seq11	LTRharvest	long_terminal_repeat	593145	593478	.	?	.	Parent=LTR_retrotransposon7
seq11	LTRharvest	long_terminal_repeat	598695	599062	.	?	.	Parent=LTR_retrotransposon7
seq11	LTRharvest	inverted_repeat	593477	593478	.	?	.	Parent=repeat_region7
seq11	LTRharvest	inverted_repeat	598695	598696	.	?	.	Parent=repeat_region7
seq11	LTRharvest	inverted_repeat	599061	599062	.	?	.	Parent=repeat_region7
seq11	LTRharvest	target_site_duplication	599063	599067	.	?	.	Parent=repeat_region7
###
seq11	LTRharvest	repeat_region	650819	656748	.	?	.	ID=repeat_region8
seq11	LTRharvest	target_site_duplication	650819	650823	.	?	.	Parent=repeat_region8
seq11	LTRharvest	inverted_repeat	650824	650825	.	?	.	Parent=repeat_region8
seq11	LTRharvest	LTR_retrotransposon	650824	656743	.	?	.	ID=LTR_retrotransposon8;Parent=repeat_region8
seq11	LTRharvest	long_terminal_repeat	650824	651157	.	?	.	Parent=LTR_retrotransposon8
seq11	LTRharvest	long_terminal_repeat	656401	656743	.	?	.	Parent=LTR_retrotransposon8
seq11	LTRharvest	inverted_repeat	651156	651157	.	?	.	Parent=repeat_region8
seq11	LTRharvest	inverted_repeat	656401	656402	.	?	.	Parent=repeat_region8
seq11	LTRharvest	inverted_repeat	656742	656743	.	?	.	Parent=repeat_region8
seq11	LTRharvest	target_site_duplication	656744	656748	.	?	.	Parent=repeat_region8
###
seq11	LTRharvest	repeat_region	941182	947150	.	?	.	ID=repeat_region9
seq11	LTRharvest	target_site_duplication	941182	941186	.	?	.	Parent=repeat_region9
seq11	LTRharvest	inverted_repeat	941187	941188	.	?	.	Parent=repeat_region9
seq11	LTRharvest	LTR_retrotransposon	941187	947145	.	?	.	ID=LTR_retrotransposon9;Parent=repeat_region9
seq11	LTRharvest	long_terminal_repeat	941187	941518	.	?	.	Parent=LTR_retrotransposon9
seq11	LTRharvest	long_terminal_repeat	946814	947145	.	?	.	Parent=LTR_retrotransposon9
seq11	LTRharvest	inverted_repeat	941517	941518	.	?	.	Parent=repeat_region9
seq11	LTRharvest	inverted_repeat	946814	946815	.	?	.	Parent=repeat_region9
seq11	LTRharvest	inverted_repeat	947144	947145	.	?	.	Parent=repeat_region9
seq11	LTRharvest	target_site_duplication	947146	947150	.	?	.	Parent=repeat_region9
###
seq12	LTRharvest	repeat_region	184165	190088	.	?	.	ID=repeat_region10
seq12	LTRharvest	target_site_duplication	184165	184169	.	?	.	Parent=repeat_region10
seq12	LTRharvest	inverted_repeat	184170	184171	.	?	.	Parent=repeat_region10
seq12	LTRharvest	LTR_retrotransposon	184170	190083	.	?	.	ID=LTR_retrotransposon10;Parent=repeat_region10
seq12	LTRharvest	long_terminal_repeat	184170	184501	.	?	.	Parent=LTR_retrotransposon10
seq12	LTRharvest	long_terminal_repeat	189752	190083	.	?	.	Parent=LTR_retrotransposon10
seq12	LTRharvest	inverted_repeat	184500	184501	.	?	.	Parent=repeat_region10
seq12	LTRharvest	inverted_repeat	189752	189753	.	?	.	Parent=repeat_region10
seq12	LTRharvest	inverted_repeat	190082	190083	.	?	.	Parent=repeat_region10
seq12	LTRharvest	target_site_duplication	190084	190088	.	?	.	Parent=repeat_region10
###
seq12	LTRharvest	repeat_region	356999	362922	.	?	.	ID=repeat_region11
seq12	LTRharvest	target_site_duplication	356999	357003	.	?	.	Parent=repeat_region11
seq12	LTRharvest	inverted_repeat	357004	357005	.	?	.	Parent=repeat_region11
seq12	LTRharvest	LTR_retrotransposon	357004	362917	.	?	.	ID=LTR_retrotransposon11;Parent=repeat_region11
seq12	LTRharvest	long_terminal_repeat	357004	357335	.	?	.	Parent=LTR_retrotransposon11
seq12	LTRharvest	long_terminal_repeat	362586	362917	.	?	.	Parent=LTR_retrotransposon11
seq12	LTRharvest	inverted_repeat	357334	357335	.	?	.	Parent=repeat_region11
seq12	LTRharvest	inverted_repeat	362586	362587	.	?	.	Parent=repeat_region11
seq12	LTRharvest	inverted_repeat	362916	362917	.	?	.	Parent=repeat_region11
seq12	LTRharvest	target_site_duplication	362918	362922	.	?	.	Parent=repeat_region11
###
seq12	LTRharvest	repeat_region	372691	378626	.	?	.	ID=repeat_region12
seq12	LTRharvest	target_site_duplication	372691	372695	.	?	.	Parent=repeat_region12
seq12	LTRharvest	inverted_repeat	372696	372697	.	?	.	Parent=repeat_region12
seq12	LTRharvest	LTR_retrotransposon	372696	378621	.	?	.	ID=LTR_retrotransposon12;Parent=repeat_region12
seq12	LTRharvest	long_terminal_repeat	372696	373033	.	?	.	Parent=LTR_retrotransposon12
seq12	LTRharvest	long_terminal_repeat	378284	378621	.	?	.	Parent=LTR_retrotransposon12
seq12	LTRharvest	inverted_repeat	373032	373033	.	?	.	Parent=repeat_region12
seq12	LTRharvest	inverted_repeat	378284	378285	.	?	.	Parent=repeat_region12
seq12	LTRharvest	inverted_repeat	378620	378621	.	?	.	Parent=repeat_region12
seq12	LTRharvest	target_site_duplication	378622	378626	.	?	.	Parent=repeat_region12
###
seq13	LTRharvest	repeat_region	96603	102526	.	?	.	ID=repeat_region13
seq13	LTRharvest	target_site_duplication	96603	96607	.	?	.	Parent=repeat_region13
seq13	LTRharvest	inverted_repeat	96608	96609	.	?	.	Parent=repeat_region13
seq13	LTRharvest	LTR_retrotransposon	96608	102521	.	?	.	ID=LTR_retrotransposon13;Parent=repeat_region13
seq13	LTRharvest	long_terminal_repeat	96608	96939	.	?	.	Parent=LTR_retrotransposon13
seq13	LTRharvest	long_terminal_repeat	102190	102521	.	?	.	Parent=LTR_retrotransposon13
seq13	LTRharvest	inverted_repeat	96938	96939	.	?	.	Parent=repeat_region13
seq13	LTRharvest	inverted_repeat	102190	102191	.	?	.	Parent=repeat_region13
seq13	LTRharvest	inverted_repeat	102520	102521	.	?	.	Parent=repeat_region13
seq13	LTRharvest	target_site_duplication	102522	102526	.	?	.	Parent=repeat_region13
###
seq13	LTRharvest	repeat_region	519156	525065	.	?	.	ID=repeat_region14
seq13	LTRharvest	target_site_duplication	519156	519160	.	?	.	Parent=repeat_region14
seq13	LTRharvest	inverted_repeat	519161	519162	.	?	.	Parent=repeat_region14
seq13	LTRharvest	LTR_retrotransposon	519161	525060	.	?	.	ID=LTR_retrotransposon14;Parent=repeat_region14
seq13	LTRharvest	long_terminal_repeat	519161	519494	.	?	.	Parent=LTR_retrotransposon14
seq13	LTRharvest	long_terminal_repeat	524727	525060	.	?	.	Parent=LTR_retrotransposon14
seq13	LTRharvest	inverted_repeat	519493	519494	.	?	.	Parent=repeat_region14
seq13	LTRharvest	inverted_repeat	524727	524728	.	?	.	Parent=repeat_region14
seq13	LTRharvest	inverted_repeat	525059	525060	.	?	.	Parent=repeat_region14
seq13	LTRharvest	target_site_duplication	525061	525065	.	?	.	Parent=repeat_region14
###
seq13	LTRharvest	repeat_region	562026	567995	.	?	.	ID=repeat_region15
seq13	LTRharvest	target_site_duplication	562026	562030	.	?	.	Parent=repeat_region15
seq13	LTRharvest	inverted_repeat	562031	562032	.	?	.	Parent=repeat_region15
seq13	LTRharvest	LTR_retrotransposon	562031	567990	.	?	.	ID=LTR_retrotransposon15;Parent=repeat_region15
seq13	LTRharvest	long_terminal_repeat	562031	562362	.	?	.	Parent=LTR_retrotransposon15
seq13	LTRharvest	long_terminal_repeat	567658	567990	.	?	.	Parent=LTR_retrotransposon15
seq13	LTRharvest	inverted_repeat	562361	562362	.	?	.	Parent=repeat_region15
seq13	LTRharvest	inverted_repeat	567658	567659	.	?	.	Parent=repeat_region15
seq13	LTRharvest	inverted_repeat	567989	567990	.	?	.	Parent=repeat_region15
seq13	LTRharvest	target_site_duplication	567991	567995	.	?	.	Parent=repeat_region15
###
seq14	LTRharvest	repeat_region	117697	123632	.	?	.	ID=repeat_region16
seq14	LTRharvest	target_site_duplication	117697	117701	.	?	.	Parent=repeat_region16
seq14	LTRharvest	inverted_repeat	117702	117703	.	?	.	Parent=repeat_region16
seq14	LTRharvest	LTR_retrotransposon	117702	123627	.	?	.	ID=LTR_retrotransposon16;Parent=repeat_region16
seq14	LTRharvest	long_terminal_repeat	117702	118028	.	?	.	Parent=LTR_retrotransposon16
seq14	LTRharvest	long_terminal_repeat	123290	123627	.	?	.	Parent=LTR_retrotransposon16
seq14	LTRharvest	inverted_repeat	118027	118028	.	?	.	Parent=repeat_region16
seq14	LTRharvest	inverted_repeat	123290	123291	.	?	.	Parent=repeat_region16
seq14	LTRharvest	inverted_repeat	123626	123627	.	?	.	Parent=repeat_region16
seq14	LTRharvest	target_site_duplication	123628	123632	.	?	.	Parent=repeat_region16
###
seq14	LTRharvest	repeat_region	594814	600737	.	?	.	ID=repeat_region17
seq14	LTRharvest	target_site_duplication	594814	594818	.	?	.	Parent=repeat_region17
seq14	LTRharvest	inverted_repeat	594819	594820	.	?	.	Parent=repeat_region17
seq14	LTRharvest	LTR_retrotransposon	594819	600732	.	?	.	ID=LTR_retrotransposon17;Parent=repeat_region17
seq14	LTRharvest	long_terminal_repeat	594819	595150	.	?	.	Parent=LTR_retrotransposon17
seq14	LTRharvest	long_terminal_repeat	600401	600732	.	?	.	Parent=LTR_retrotransposon17
seq14	LTRharvest	inverted_repeat	595149	595150	.	?	.	Parent=repeat_region17
seq14	LTRharvest	inverted_repeat	600401	600402	.	?	.	Parent=repeat_region17
seq14	LTRharvest	inverted_repeat	600731	600732	.	?	.	Parent=repeat_region17
seq14	LTRharvest	target_site_duplication	600733	600737	.	?	.	Parent=repeat_region17
###
seq14	LTRharvest	repeat_region	704057	710027	.	?	.	ID=repeat_region18
seq14	LTRharvest	target_site_duplication	704057	704061	.	?	.	Parent=repeat_region18
seq14	LTRharvest	inverted_repeat	704062	704063	.	?	.	Parent=repeat_region18
seq14	LTRharvest	LTR_retrotransposon	704062	710022	.	?	.	ID=LTR_retrotransposon18;Parent=repeat_region18
seq14	LTRharvest	long_terminal_repeat	704062	704394	.	?	.	Parent=LTR_retrotransposon18
seq14	LTRharvest	long_terminal_repeat	709690	710022	.	?	.	Parent=LTR_retrotransposon18
seq14	LTRharvest	inverted_repeat	704393	704394	.	?	.	Parent=repeat_region18
seq14	LTRharvest	inverted_repeat	709690	709691	.	?	.	Parent=repeat_region18
seq14	LTRharvest	inverted_repeat	710021	710022	.	?	.	Parent=repeat_region18
seq14	LTRharvest	target_site_duplication	710023	710027	.	?	.	Parent=repeat_region18
###
seq14	LTRharvest	repeat_region	970273	976241	.	?	.	ID=repeat_region19
seq14	LTRharvest	target_site_duplication	970273	970277	.	?	.	Parent=repeat_region19
seq14	LTRharvest	inverted_repeat	970278	970279	.	?	.	Parent=repeat_region19
seq14	LTRharvest	LTR_retrotransposon	970278	976236	.	?	.	ID=LTR_retrotransposon19;Parent=repeat_region19
seq14	LTRharvest	long_terminal_repeat	970278	970609	.	?	.	Parent=LTR_retrotransposon19
seq14	LTRharvest	long_terminal_repeat	975900	976236	.	?	.	Parent=LTR_retrotransposon19
seq14	LTRharvest	inverted_repeat	970608	970609	.	?	.	Parent=repeat_region19
seq14	LTRharvest	inverted_repeat	975900	975901	.	?	.	Parent=repeat_region19
seq14	LTRharvest	inverted_repeat	976235	976236	.	?	.	Parent=repeat_region19
seq14	LTRharvest	target_site_duplication	976237	976241	.	?	.	Parent=repeat_region19
###
seq15	LTRharvest	repeat_region	56447	62380	.	?	.	ID=repeat_region20
seq15	LTRharvest	target_site_duplication	56447	56451	.	?	.	Parent=repeat_region20
seq15	LTRharvest	inverted_repeat	56452	56453	.	?	.	Parent=repeat_region20
seq15	LTRharvest	LTR_retrotransposon	56452	62375	.	?	.	ID=LTR_retrotransposon20;Parent=repeat_region20
seq15	LTRharvest	long_terminal_repeat	56452	56788	.	?	.	Parent=LTR_retrotransposon20
seq15	LTRharvest	long_terminal_repeat	62039	62375	.	?	.	Parent=LTR_retrotransposon20
seq15	LTRharvest	inverted_repeat	56787	56788	.	?	.	Parent=repeat_region20
seq15	LTRharvest	inverted_repeat	62039	62040	.	?	.	Parent=repeat_region20
seq15	LTRharvest	inverted_repeat	62374	62375	.	?	.	Parent=repeat_region20
seq15	LTRharvest	target_site_duplication	62376	62380	.	?	.	Parent=repeat_region20
###
seq15	LTRharvest	repeat_region	436880	443112	.	?	.	ID=repeat_region21
seq15	LTRharvest	target_site_duplication	436880	436884	.	?	.	Parent=repeat_region21
seq15	LTRharvest	inverted_repeat	436885	436886	.	?	.	Parent=repeat_region21
seq15	LTRharvest	LTR_retrotransposon	436885	443107	.	?	.	ID=LTR_retrotransposon21;Parent=repeat_region21
seq15	LTRharvest	long_terminal_repeat	436885	437255	.	?	.	Parent=LTR_retrotransposon21
seq15	LTRharvest	long_terminal_repeat	442737	443107	.	?	.	Parent=LTR_retrotransposon21
seq15	LTRharvest	inverted_repeat	437254	437255	.	?	.	Parent=repeat_region21
seq15	LTRharvest	inverted_repeat	442737	442738	.	?	.	Parent=repeat_region21
seq15	LTRharvest	inverted_repeat	443106	443107	.	?	.	Parent=repeat_region21
seq15	LTRharvest	target_site_duplication	443108	443112	.	?	.	Parent=repeat_region21
###
seq15	LTRharvest	repeat_region	804635	810562	.	?	.	ID=repeat_region22
seq15	LTRharvest	target_site_duplication	804635	804639	.	?	.	Parent=repeat_region22
seq15	LTRharvest	inverted_repeat	804640	804641	.	?	.	Parent=repeat_region22
seq15	LTRharvest	LTR_retrotransposon	804640	810557	.	?	.	ID=LTR_retrotransposon22;Parent=repeat_region22
seq15	LTRharvest	long_terminal_repeat	804640	804973	.	?	.	Parent=LTR_retrotransposon22
seq15	LTRharvest	long_terminal_repeat	810224	810557	.	?	.	Parent=LTR_retrotransposon22
seq15	LTRharvest	inverted_repeat	804972	804973	.	?	.	Parent=repeat_region22
seq15	LTRharvest	inverted_repeat	810224	810225	.	?	.	Parent=repeat_region22
seq15	LTRharvest	inverted_repeat	810556	810557	.	?	.	Parent=repeat_region22
seq15	LTRharvest	target_site_duplication	810558	810562	.	?	.	Parent=repeat_region22
###
seq15	LTRharvest	repeat_region	844402	850340	.	?	.	ID=repeat_region23
seq15	LTRharvest	target_site_duplication	844402	844406	.	?	.	Parent=repeat_region23
seq15	LTRharvest	inverted_repeat	844407	844408	.	?	.	Parent=repeat_region23
seq15	LTRharvest	LTR_retrotransposon	844407	850335	.	?	.	ID=LTR_retrotransposon23;Parent=repeat_region23
seq15	LTRharvest	long_terminal_repeat	844407	844744	.	?	.	Parent=LTR_retrotransposon23
seq15	LTRharvest	long_terminal_repeat	849998	850335	.	?	.	Parent=LTR_retrotransposon23
seq15	LTRharvest	inverted_repeat	844743	844744	.	?	.	Parent=repeat_region23
seq15	LTRharvest	inverted_repeat	849998	849999	.	?	.	Parent=repeat_region23
seq15	LTRharvest	inverted_repeat	850334	850335	.	?	.	Parent=repeat_region23
seq15	LTRharvest	target_site_duplication	850336	850340	.	?	.	Parent=repeat_region23
###
seq15	LTRharvest	repeat_region	850619	856554	.	?	.	ID=repeat_region24
seq15	LTRharvest	target_site_duplication	850619	850623	.	?	.	Parent=repeat_region24
seq15	LTRharvest	inverted_repeat	850624	850625	.	?	.	Parent=repeat_region24
seq15	LTRharvest	LTR_retrotransposon	850624	856549	.	?	.	ID=LTR_retrotransposon24;Parent=repeat_region24
seq15	LTRharvest	long_terminal_repeat	850624	850961	.	?	.	Parent=LTR_retrotransposon24
seq15	LTRharvest	long_terminal_repeat	856212	856549	.	?	.	Parent=LTR_retrotransposon24
seq15	LTRharvest	inverted_repeat	850960	850961	.	?	.	Parent=repeat_region24
seq15	LTRharvest	inverted_repeat	856212	856213	.	?	.	Parent=repeat_region24
seq15	LTRharvest	inverted_repeat	856548	856549	.	?	.	Parent=repeat_region24
seq15	LTRharvest	target_site_duplication	856550	856554	.	?	.	Parent=repeat_region24
###
seq2	LTRharvest	repeat_region	84414	90385	.	?	.	ID=repeat_region25
seq2	LTRharvest	target_site_duplication	84414	84418	.	?	.	Parent=repeat_region25
seq2	LTRharvest	inverted_repeat	84419	84420	.	?	.	Parent=repeat_region25
seq2	LTRharvest	LTR_retrotransposon	84419	90380	.	?	.	ID=LTR_retrotransposon25;Parent=repeat_region25
seq2	LTRharvest	long_terminal_repeat	84419	84750	.	?	.	Parent=LTR_retrotransposon25
seq2	LTRharvest	long_terminal_repeat	90049	90380	.	?	.	Parent=LTR_retrotransposon25
seq2	LTRharvest	inverted_repeat	84749	84750	.	?	.	Parent=repeat_region25
seq2	LTRharvest	inverted_repeat	90049	90050	.	?	.	Parent=repeat_region25
seq2	LTRharvest	inverted_repeat	90379	90380	.	?	.	Parent=repeat_region25
seq2	LTRharvest	target_site_duplication	90381	90385	.	?	.	Parent=repeat_region25
###
seq3	LTRharvest	repeat_region	513723	519691	.	?	.	ID=repeat_region26
seq3	LTRharvest	target_site_duplication	513723	513727	.	?	.	Parent=repeat_region26
seq3	LTRharvest	inverted_repeat	513728	513729	.	?	.	Parent=repeat_region26
seq3	LTRharvest	LTR_retrotransposon	513728	519686	.	?	.	ID=LTR_retrotransposon26;Parent=repeat_region26
seq3	LTRharvest	long_terminal_repeat	513728	514059	.	?	.	Parent=LTR_retrotransposon26
seq3	LTRharvest	long_terminal_repeat	519366	519686	.	?	.	Parent=LTR_retrotransposon26
seq3	LTRharvest	inverted_repeat	514058	514059	.	?	.	Parent=repeat_region26
seq3	LTRharvest	inverted_repeat	519366	519367	.	?	.	Parent=repeat_region26
seq3	LTRharvest	inverted_repeat	519685	519686	.	?	.	Parent=repeat_region26
seq3	LTRharvest	target_site_duplication	519687	519691	.	?	.	Parent=repeat_region26
###
seq3	LTRharvest	repeat_region	645535	651462	.	?	.	ID=repeat_region27
seq3	LTRharvest	target_site_duplication	645535	645539	.	?	.	Parent=repeat_region27
seq3	LTRharvest	inverted_repeat	645540	645541	.	?	.	Parent=repeat_region27
seq3	LTRharvest	LTR_retrotransposon	645540	651457	.	?	.	ID=LTR_retrotransposon27;Parent=repeat_region27
seq3	LTRharvest	long_terminal_repeat	645540	645873	.	?	.	Parent=LTR_retrotransposon27
seq3	LTRharvest	long_terminal_repeat	651124	651457	.	?	.	Parent=LTR_retrotransposon27
seq3	LTRharvest	inverted_repeat	645872	645873	.	?	.	Parent=repeat_region27
seq3	LTRharvest	inverted_repeat	651124	651125	.	?	.	Parent=repeat_region27
seq3	LTRharvest	inverted_repeat	651456	651457	.	?	.	Parent=repeat_region27
seq3	LTRharvest	target_site_duplication	651458	651462	.	?	.	Parent=repeat_region27
###
seq3	LTRharvest	repeat_region	871853	877821	.	?	.	ID=repeat_region28
seq3	LTRharvest	target_site_duplication	871853	871857	.	?	.	Parent=repeat_region28
seq3	LTRharvest	inverted_repeat	871858	871859	.	?	.	Parent=repeat_region28
seq3	LTRharvest	LTR_retrotransposon	871858	877816	.	?	.	ID=LTR_retrotransposon28;Parent=repeat_region28
seq3	LTRharvest	long_terminal_repeat	871858	872189	.	?	.	Parent=LTR_retrotransposon28
seq3	LTRharvest	long_terminal_repeat	877476	877816	.	?	.	Parent=LTR_retrotransposon28
seq3	LTRharvest	inverted_repeat	872188	872189	.	?	.	Parent=repeat_region28
seq3	LTRharvest	inverted_repeat	877476	877477	.	?	.	Parent=repeat_region28
seq3	LTRharvest	inverted_repeat	877815	877816	.	?	.	Parent=repeat_region28
seq3	LTRharvest	target_site_duplication	877817	877821	.	?	.	Parent=repeat_region28
###
seq3	LTRharvest	repeat_region	878335	884262	.	?	.	ID=repeat_region29
seq3	LTRharvest	target_site_duplication	878335	878339	.	?	.	Parent=repeat_region29
seq3	LTRharvest	inverted_repeat	878340	878341	.	?	.	Parent=repeat_region29
seq3	LTRharvest	LTR_retrotransposon	878340	884257	.	?	.	ID=LTR_retrotransposon29;Parent=repeat_region29
seq3	LTRharvest	long_terminal_repeat	878340	878673	.	?	.	Parent=LTR_retrotransposon29
seq3	LTRharvest	long_terminal_repeat	883924	884257	.	?	.	Parent=LTR_retrotransposon29
seq3	LTRharvest	inverted_repeat	878672	878673	.	?	.	Parent=repeat_region29
seq3	LTRharvest	inverted_repeat	883924	883925	.	?	.	Parent=repeat_region29
seq3	LTRharvest	inverted_repeat	884256	884257	.	?	.	Parent=repeat_region29
seq3	LTRharvest	target_site_duplication	884258	884262	.	?	.	Parent=repeat_region29
###
seq3	LTRharvest	repeat_region	981202	987170	.	?	.	ID=repeat_region30
seq3	LTRharvest	target_site_duplication	981202	981206	.	?	.	Parent=repeat_region30
seq3	LTRharvest	inverted_repeat	981207	981208	.	?	.	Parent=repeat_region30
seq3	LTRharvest	LTR_retrotransposon	981207	987165	.	?	.	ID=LTR_retrotransposon30;Parent=repeat_region30
seq3	LTRharvest	long_terminal_repeat	981207	981538	.	?	.	Parent=LTR_retrotransposon30
seq3	LTRharvest	long_terminal_repeat	986834	987165	.	?	.	Parent=LTR_retrotransposon30
seq3	LTRharvest	inverted_repeat	981537	981538	.	?	.	Parent=repeat_region30
seq3	LTRharvest	inverted_repeat	986834	986835	.	?	.	Parent=repeat_region30
seq3	LTRharvest	inverted_repeat	987164	987165	.	?	.	Parent=repeat_region30
seq3	LTRharvest	target_site_duplication	987166	987170	.	?	.	Parent=repeat_region30
###
seq3	LTRharvest	repeat_region	987181	992683	.	?	.	ID=repeat_region31
seq3	LTRharvest	target_site_duplication	987181	987185	.	?	.	Parent=repeat_region31
seq3	LTRharvest	inverted_repeat	987186	987187	.	?	.	Parent=repeat_region31
seq3	LTRharvest	LTR_retrotransposon	987186	992678	.	?	.	ID=LTR_retrotransposon31;Parent=repeat_region31
seq3	LTRharvest	long_terminal_repeat	987186	987519	.	?	.	Parent=LTR_retrotransposon31
seq3	LTRharvest	long_terminal_repeat	992345	992678	.	?	.	Parent=LTR_retrotransposon31
seq3	LTRharvest	inverted_repeat	987518	987519	.	?	.	Parent=repeat_region31
seq3	LTRharvest	inverted_repeat	992345	992346	.	?	.	Parent=repeat_region31
seq3	LTRharvest	inverted_repeat	992677	992678	.	?	.	Parent=repeat_region31
seq3	LTRharvest	target_site_duplication	992679	992683	.	?	.	Parent=repeat_region31
###
seq3	LTRharvest	repeat_region	1095799	1101734	.	?	.	ID=repeat_region32
seq3	LTRharvest	target_site_duplication	1095799	1095803	.	?	.	Parent=repeat_region32
seq3	LTRharvest	inverted_repeat	1095804	1095805	.	?	.	Parent=repeat_region32
seq3	LTRharvest	LTR_retrotransposon	1095804	1101729	.	?	.	ID=LTR_retrotransposon32;Parent=repeat_region32
seq3	LTRharvest	long_terminal_repeat	1095804	1096141	.	?	.	Parent=LTR_retrotransposon32
seq3	LTRharvest	long_terminal_repeat	1101392	1101729	.	?	.	Parent=LTR_retrotransposon32
seq3	LTRharvest	inverted_repeat	1096140	1096141	.	?	.	Parent=repeat_region32
seq3	LTRharvest	inverted_repeat	1101392	1101393	.	?	.	Parent=repeat_region32
seq3	LTRharvest	inverted_repeat	1101728	1101729	.	?	.	Parent=repeat_region32
seq3	LTRharvest	target_site_duplication	1101730	1101734	.	?	.	Parent=repeat_region32
###
seq3	LTRharvest	repeat_region	1206733	1212660	.	?	.	ID=repeat_region33
seq3	LTRharvest	target_site_duplication	1206733	1206737	.	?	.	Parent=repeat_region33
seq3	LTRharvest	inverted_repeat	1206738	1206739	.	?	.	Parent=repeat_region33
seq3	LTRharvest	LTR_retrotransposon	1206738	1212655	.	?	.	ID=LTR_retrotransposon33;Parent=repeat_region33
seq3	LTRharvest	long_terminal_repeat	1206738	1207071	.	?	.	Parent=LTR_retrotransposon33
seq3	LTRharvest	long_terminal_repeat	1212322	1212655	.	?	.	Parent=LTR_retrotransposon33
seq3	LTRharvest	inverted_repeat	1207070	1207071	.	?	.	Parent=repeat_region33
seq3	LTRharvest	inverted_repeat	1212322	1212323	.	?	.	Parent=repeat_region33
seq3	LTRharvest	inverted_repeat	1212654	1212655	.	?	.	Parent=repeat_region33
seq3	LTRharvest	target_site_duplication	1212656	1212660	.	?	.	Parent=repeat_region33
###
seq4	LTRharvest	repeat_region	443389	449322	.	?	.	ID=repeat_region34
seq4	LTRharvest	target_site_duplication	443389	443393	.	?	.	Parent=repeat_region34
seq4	LTRharvest	inverted_repeat	443394	443395	.	?	.	Parent=repeat_region34
seq4	LTRharvest	LTR_retrotransposon	443394	449317	.	?	.	ID=LTR_retrotransposon34;Parent=repeat_region34
seq4	LTRharvest	long_terminal_repeat	443394	443735	.	?	.	Parent=LTR_retrotransposon34
seq4	LTRharvest	long_terminal_repeat	448981	449317	.	?	.	Parent=LTR_retrotransposon34
seq4	LTRharvest	inverted_repeat	443734	443735	.	?	.	Parent=repeat_region34
seq4	LTRharvest	inverted_repeat	448981	448982	.	?	.	Parent=repeat_region34
seq4	LTRharvest	inverted_repeat	449316	449317	.	?	.	Parent=repeat_region34
seq4	LTRharvest	target_site_duplication	449318	449322	.	?	.	Parent=repeat_region34
###
seq5	LTRharvest	repeat_region	137902	143870	.	?	.	ID=repeat_region35
seq5	LTRharvest	target_site_duplication	137902	137906	.	?	.	Parent=repeat_region35
seq5	LTRharvest	inverted_repeat	137907	137908	.	?	.	Parent=repeat_region35
seq5	LTRharvest	LTR_retrotransposon	137907	143865	.	?	.	ID=LTR_retrotransposon35;Parent=repeat_region35
seq5	LTRharvest	long_terminal_repeat	137907	138238	.	?	.	Parent=LTR_retrotransposon35
seq5	LTRharvest	long_terminal_repeat	143534	143865	.	?	.	Parent=LTR_retrotransposon35
seq5	LTRharvest	inverted_repeat	138237	138238	.	?	.	Parent=repeat_region35
seq5	LTRharvest	inverted_repeat	143534	143535	.	?	.	Parent=repeat_region35
seq5	LTRharvest	inverted_repeat	143864	143865	.	?	.	Parent=repeat_region35
seq5	LTRharvest	target_site_duplication	143866	143870	.	?	.	Parent=repeat_region35
###
seq6	LTRharvest	repeat_region	535749	541684	.	?	.	ID=repeat_region36
seq6	LTRharvest	target_site_duplication	535749	535753	.	?	.	Parent=repeat_region36
seq6	LTRharvest	inverted_repeat	535754	535755	.	?	.	Parent=repeat_region36
seq6	LTRharvest	LTR_retrotransposon	535754	541679	.	?	.	ID=LTR_retrotransposon36;Parent=repeat_region36
seq6	LTRharvest	long_terminal_repeat	535754	536091	.	?	.	Parent=LTR_retrotransposon36
seq6	LTRharvest	long_terminal_repeat	541342	541679	.	?	.	Parent=LTR_retrotransposon36
seq6	LTRharvest	inverted_repeat	536090	536091	.	?	.	Parent=repeat_region36
seq6	LTRharvest	inverted_repeat	541342	541343	.	?	.	Parent=repeat_region36
seq6	LTRharvest	inverted_repeat	541678	541679	.	?	.	Parent=repeat_region36
seq6	LTRharvest	target_site_duplication	541680	541684	.	?	.	Parent=repeat_region36
###
seq6	LTRharvest	repeat_region	561832	567759	.	?	.	ID=repeat_region37
seq6	LTRharvest	target_site_duplication	561832	561836	.	?	.	Parent=repeat_region37
seq6	LTRharvest	inverted_repeat	561837	561838	.	?	.	Parent=repeat_region37
seq6	LTRharvest	LTR_retrotransposon	561837	567754	.	?	.	ID=LTR_retrotransposon37;Parent=repeat_region37
seq6	LTRharvest	long_terminal_repeat	561837	562170	.	?	.	Parent=LTR_retrotransposon37
seq6	LTRharvest	long_terminal_repeat	567421	567754	.	?	.	Parent=LTR_retrotransposon37
seq6	LTRharvest	inverted_repeat	562169	562170	.	?	.	Parent=repeat_region37
seq6	LTRharvest	inverted_repeat	567421	567422	.	?	.	Parent=repeat_region37
seq6	LTRharvest	inverted_repeat	567753	567754	.	?	.	Parent=repeat_region37
seq6	LTRharvest	target_site_duplication	567755	567759	.	?	.	Parent=repeat_region37
###
seq6	LTRharvest	repeat_region	568730	574699	.	?	.	ID=repeat_region38
seq6	LTRharvest	target_site_duplication	568730	568734	.	?	.	Parent=repeat_region38
seq6	LTRharvest	inverted_repeat	568735	568736	.	?	.	Parent=repeat_region38
seq6	LTRharvest	LTR_retrotransposon	568735	574694	.	?	.	ID=LTR_retrotransposon38;Parent=repeat_region38
seq6	LTRharvest	long_terminal_repeat	568735	569066	.	?	.	Parent=LTR_retrotransposon38
seq6	LTRharvest	long_terminal_repeat	574363	574694	.	?	.	Parent=LTR_retrotransposon38
seq6	LTRharvest	inverted_repeat	569065	569066	.	?	.	Parent=repeat_region38
seq6	LTRharvest	inverted_repeat	574363	574364	.	?	.	Parent=repeat_region38
seq6	LTRharvest	inverted_repeat	574693	574694	.	?	.	Parent=repeat_region38
seq6	LTRharvest	target_site_duplication	574695	574699	.	?	.	Parent=repeat_region38
###
seq6	LTRharvest	repeat_region	707184	712544	.	?	.	ID=repeat_region39
seq6	LTRharvest	target_site_duplication	707184	707188	.	?	.	Parent=repeat_region39
seq6	LTRharvest	inverted_repeat	707189	707190	.	?	.	Parent=repeat_region39
seq6	LTRharvest	LTR_retrotransposon	707189	712539	.	?	.	ID=LTR_retrotransposon39;Parent=repeat_region39
seq6	LTRharvest	long_terminal_repeat	707189	707528	.	?	.	Parent=LTR_retrotransposon39
seq6	LTRharvest	long_terminal_repeat	712200	712539	.	?	.	Parent=LTR_retrotransposon39
seq6	LTRharvest	inverted_repeat	707527	707528	.	?	.	Parent=repeat_region39
seq6	LTRharvest	inverted_repeat	712200	712201	.	?	.	Parent=repeat_region39
seq6	LTRharvest	inverted_repeat	712538	712539	.	?	.	Parent=repeat_region39
seq6	LTRharvest	target_site_duplication	712540	712544	.	?	.	Parent=repeat_region39
###
seq6	LTRharvest	repeat_region	817382	823305	.	?	.	ID=repeat_region40
seq6	LTRharvest	target_site_duplication	817382	817386	.	?	.	Parent=repeat_region40
seq6	LTRharvest	inverted_repeat	817387	817388	.	?	.	Parent=repeat_region40
seq6	LTRharvest	LTR_retrotransposon	817387	823300	.	?	.	ID=LTR_retrotransposon40;Parent=repeat_region40
seq6	LTRharvest	long_terminal_repeat	817387	817718	.	?	.	Parent=LTR_retrotransposon40
seq6	LTRharvest	long_terminal_repeat	822969	823300	.	?	.	Parent=LTR_retrotransposon40
seq6	LTRharvest	inverted_repeat	817717	817718	.	?	.	Parent=repeat_region40
seq6	LTRharvest	inverted_repeat	822969	822970	.	?	.	Parent=repeat_region40
seq6	LTRharvest	inverted_repeat	823299	823300	.	?	.	Parent=repeat_region40
seq6	LTRharvest	target_site_duplication	823301	823305	.	?	.	Parent=repeat_region40
###
seq7	LTRharvest	repeat_region	85529	91761	.	?	.	ID=repeat_region41
seq7	LTRharvest	target_site_duplication	85529	85533	.	?	.	Parent=repeat_region41
seq7	LTRharvest	inverted_repeat	85534	85535	.	?	.	Parent=repeat_region41
seq7	LTRharvest	LTR_retrotransposon	85534	91756	.	?	.	ID=LTR_retrotransposon41;Parent=repeat_region41
seq7	LTRharvest	long_terminal_repeat	85534	85904	.	?	.	Parent=LTR_retrotransposon41
seq7	LTRharvest	long_terminal_repeat	91386	91756	.	?	.	Parent=LTR_retrotransposon41
seq7	LTRharvest	inverted_repeat	85903	85904	.	?	.	Parent=repeat_region41
seq7	LTRharvest	inverted_repeat	91386	91387	.	?	.	Parent=repeat_region41
seq7	LTRharvest	inverted_repeat	91755	91756	.	?	.	Parent=repeat_region41
seq7	LTRharvest	target_site_duplication	91757	91761	.	?	.	Parent=repeat_region41
###
seq7	LTRharvest	repeat_region	543600	549637	.	?	.	ID=repeat_region42
seq7	LTRharvest	target_site_duplication	543600	543604	.	?	.	Parent=repeat_region42
seq7	LTRharvest	inverted_repeat	543605	543606	.	?	.	Parent=repeat_region42
seq7	LTRharvest	LTR_retrotransposon	543605	549632	.	?	.	ID=LTR_retrotransposon42;Parent=repeat_region42
seq7	LTRharvest	long_terminal_repeat	543605	543936	.	?	.	Parent=LTR_retrotransposon42
seq7	LTRharvest	long_terminal_repeat	549301	549632	.	?	.	Parent=LTR_retrotransposon42
seq7	LTRharvest	inverted_repeat	543935	543936	.	?	.	Parent=repeat_region42
seq7	LTRharvest	inverted_repeat	549301	549302	.	?	.	Parent=repeat_region42
seq7	LTRharvest	inverted_repeat	549631	549632	.	?	.	Parent=repeat_region42
seq7	LTRharvest	target_site_duplication	549633	549637	.	?	.	Parent=repeat_region42
###
seq8	LTRharvest	repeat_region	205212	210649	.	?	.	ID=repeat_region43
seq8	LTRharvest	target_site_duplication	205212	205216	.	?	.	Parent=repeat_region43
seq8	LTRharvest	inverted_repeat	205217	205218	.	?	.	Parent=repeat_region43
seq8	LTRharvest	LTR_retrotransposon	205217	210644	.	?	.	ID=LTR_retrotransposon43;Parent=repeat_region43
seq8	LTRharvest	long_terminal_repeat	205217	205556	.	?	.	Parent=LTR_retrotransposon43
seq8	LTRharvest	long_terminal_repeat	210305	210644	.	?	.	Parent=LTR_retrotransposon43
seq8	LTRharvest	inverted_repeat	205555	205556	.	?	.	Parent=repeat_region43
seq8	LTRharvest	inverted_repeat	210305	210306	.	?	.	Parent=repeat_region43
seq8	LTRharvest	inverted_repeat	210643	210644	.	?	.	Parent=repeat_region43
seq8	LTRharvest	target_site_duplication	210645	210649	.	?	.	Parent=repeat_region43
###
seq9	LTRharvest	repeat_region	197239	203474	.	?	.	ID=repeat_region44
seq9	LTRharvest	target_site_duplication	197239	197243	.	?	.	Parent=repeat_region44
seq9	LTRharvest	inverted_repeat	197244	197245	.	?	.	Parent=repeat_region44
seq9	LTRharvest	LTR_retrotransposon	197244	203469	.	?	.	ID=LTR_retrotransposon44;Parent=repeat_region44
seq9	LTRharvest	long_terminal_repeat	197244	197614	.	?	.	Parent=LTR_retrotransposon44
seq9	LTRharvest	long_terminal_repeat	203099	203469	.	?	.	Parent=LTR_retrotransposon44
seq9	LTRharvest	inverted_repeat	197613	197614	.	?	.	Parent=repeat_region44
seq9	LTRharvest	inverted_repeat	203099	203100	.	?	.	Parent=repeat_region44
seq9	LTRharvest	inverted_repeat	203468	203469	.	?	.	Parent=repeat_region44
seq9	LTRharvest	target_site_duplication	203470	203474	.	?	.	Parent=repeat_region44
###
seq9	LTRharvest	repeat_region	472146	483665	.	?	.	ID=repeat_region45
seq9	LTRharvest	target_site_duplication	472146	472150	.	?	.	Parent=repeat_region45
seq9	LTRharvest	inverted_repeat	472151	472152	.	?	.	Parent=repeat_region45
seq9	LTRharvest	LTR_retrotransposon	472151	483660	.	?	.	ID=LTR_retrotransposon45;Parent=repeat_region45
seq9	LTRharvest	long_terminal_repeat	472151	472488	.	?	.	Parent=LTR_retrotransposon45
seq9	LTRharvest	long_terminal_repeat	483323	483660	.	?	.	Parent=LTR_retrotransposon45
seq9	LTRharvest	inverted_repeat	472487	472488	.	?	.	Parent=repeat_region45
seq9	LTRharvest	inverted_repeat	483323	483324	.	?	.	Parent=repeat_region45
seq9	LTRharvest	inverted_repeat	483659	483660	.	?	.	Parent=repeat_region45
seq9	LTRharvest	target_site_duplication	483661	483665	.	?	.	Parent=repeat_region45
###
genometools-1.5.1/testdata/gt_eval_ltr_test_1.out000066400000000000000000000002041211610345200221630ustar00rootroot00000000000000LTR_retrotransposon sensitivity: 100.00% (45/45) (missing LTRs: 0)
LTR_retrotransposon specificity: 100.00% (45/45) (wrong LTRs: 0)
genometools-1.5.1/testdata/gt_eval_ltr_test_2.out000066400000000000000000000002001211610345200221600ustar00rootroot00000000000000LTR_retrotransposon sensitivity: 100.00% (1/1) (missing LTRs: 0)
LTR_retrotransposon specificity: 100.00% (1/1) (wrong LTRs: 0)
genometools-1.5.1/testdata/gt_eval_ltr_test_2.prediction000066400000000000000000000002441211610345200235210ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	100	200	.	-	.	Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_ltr_test_2.reality000066400000000000000000000002441211610345200230320ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	100	200	.	-	.	Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_ltr_test_3.out000066400000000000000000000002001211610345200221610ustar00rootroot00000000000000LTR_retrotransposon sensitivity:  50.00% (1/2) (missing LTRs: 1)
LTR_retrotransposon specificity: 100.00% (1/1) (wrong LTRs: 0)
genometools-1.5.1/testdata/gt_eval_ltr_test_3.prediction000066400000000000000000000002541211610345200235230ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	100	200	.	-	.	ID=mRNA;Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_ltr_test_3.reality000066400000000000000000000004321211610345200230320ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region1
gDNA	.	LTR_retrotransposon	100	200	.	-	.	Parent=repeat_region1
gDNA	.	repeat_region	300	400	.	-	.	ID=repeat_region2
gDNA	.	LTR_retrotransposon	300	400	.	-	.	Parent=repeat_region2
genometools-1.5.1/testdata/gt_eval_ltr_test_4.out000066400000000000000000000002001211610345200221620ustar00rootroot00000000000000LTR_retrotransposon sensitivity: 100.00% (1/1) (missing LTRs: 0)
LTR_retrotransposon specificity:  50.00% (1/2) (wrong LTRs: 1)
genometools-1.5.1/testdata/gt_eval_ltr_test_4.prediction000066400000000000000000000004321211610345200235220ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region1
gDNA	.	LTR_retrotransposon	100	200	.	-	.	Parent=repeat_region1
gDNA	.	repeat_region	300	400	.	-	.	ID=repeat_region2
gDNA	.	LTR_retrotransposon	300	400	.	-	.	Parent=repeat_region2
genometools-1.5.1/testdata/gt_eval_ltr_test_4.reality000066400000000000000000000002541211610345200230350ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	100	200	.	-	.	ID=mRNA;Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_ltr_test_5.out000066400000000000000000000002001211610345200221630ustar00rootroot00000000000000LTR_retrotransposon sensitivity:   0.00% (0/1) (missing LTRs: 1)
LTR_retrotransposon specificity: 100.00% (0/0) (wrong LTRs: 0)
genometools-1.5.1/testdata/gt_eval_ltr_test_5.prediction000066400000000000000000000000621211610345200235220ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
genometools-1.5.1/testdata/gt_eval_ltr_test_5.reality000066400000000000000000000002441211610345200230350ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	100	200	.	-	.	Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_ltr_test_6.out000066400000000000000000000002001211610345200221640ustar00rootroot00000000000000LTR_retrotransposon sensitivity: 100.00% (0/0) (missing LTRs: 0)
LTR_retrotransposon specificity:   0.00% (0/1) (wrong LTRs: 1)
genometools-1.5.1/testdata/gt_eval_ltr_test_6.prediction000066400000000000000000000002441211610345200235250ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	100	200	.	-	.	Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_ltr_test_6.reality000066400000000000000000000000621211610345200230340ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
genometools-1.5.1/testdata/gt_eval_ltr_test_7.out000066400000000000000000000002001211610345200221650ustar00rootroot00000000000000LTR_retrotransposon sensitivity: 100.00% (1/1) (missing LTRs: 0)
LTR_retrotransposon specificity: 100.00% (1/1) (wrong LTRs: 0)
genometools-1.5.1/testdata/gt_eval_ltr_test_7.prediction000066400000000000000000000002421211610345200235240ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	80	220	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	80	220	.	-	.	Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_ltr_test_7.reality000066400000000000000000000002441211610345200230370ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	100	200	.	-	.	Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_ltr_test_8.out000066400000000000000000000002001211610345200221660ustar00rootroot00000000000000LTR_retrotransposon sensitivity:  50.00% (1/2) (missing LTRs: 1)
LTR_retrotransposon specificity: 100.00% (1/1) (wrong LTRs: 0)
genometools-1.5.1/testdata/gt_eval_ltr_test_8.prediction000066400000000000000000000002421211610345200235250ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	80	220	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	80	220	.	-	.	Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_ltr_test_8.reality000066400000000000000000000004321211610345200230370ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region1
gDNA	.	LTR_retrotransposon	100	200	.	-	.	Parent=repeat_region1
gDNA	.	repeat_region	300	400	.	-	.	ID=repeat_region2
gDNA	.	LTR_retrotransposon	300	400	.	-	.	Parent=repeat_region2
genometools-1.5.1/testdata/gt_eval_ltr_test_9.out000066400000000000000000000002001211610345200221670ustar00rootroot00000000000000LTR_retrotransposon sensitivity: 100.00% (1/1) (missing LTRs: 0)
LTR_retrotransposon specificity:  50.00% (1/2) (wrong LTRs: 1)
genometools-1.5.1/testdata/gt_eval_ltr_test_9.prediction000066400000000000000000000004301211610345200235250ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	80	220	.	-	.	ID=repeat_region1
gDNA	.	LTR_retrotransposon	80	220	.	-	.	Parent=repeat_region1
gDNA	.	repeat_region	300	400	.	-	.	ID=repeat_region2
gDNA	.	LTR_retrotransposon	300	400	.	-	.	Parent=repeat_region2
genometools-1.5.1/testdata/gt_eval_ltr_test_9.reality000066400000000000000000000002441211610345200230410ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	repeat_region	100	200	.	-	.	ID=repeat_region
gDNA	.	LTR_retrotransposon	100	200	.	-	.	Parent=repeat_region
genometools-1.5.1/testdata/gt_eval_prob_1.out000066400000000000000000000054341211610345200212770ustar00rootroot00000000000000gene sensitivity (mRNA level):   0.00% (0/7) (missing genes: 3)
gene specificity (mRNA level):   0.00% (0/4) (wrong genes: 2)
gene sensitivity (CDS level):   0.00% (0/7) (missing genes: 3)
gene specificity (CDS level):   0.00% (0/4) (wrong genes: 2)
mRNA sensitivity (mRNA level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (mRNA level): 100.00% (0/0) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (CDS level): 100.00% (0/0) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all):   0.00% (0/32)
exon specificity (mRNA level, all): 100.00% (0/0)
exon sensitivity (mRNA level, single):   0.00% (0/3)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial):   0.00% (0/4)
exon specificity (mRNA level, initial): 100.00% (0/0)
exon sensitivity (mRNA level, internal):   0.00% (0/21)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal):   0.00% (0/4)
exon specificity (mRNA level, terminal): 100.00% (0/0)
exon sensitivity (mRNA level, all, collapsed):   0.00% (0/18)
exon specificity (mRNA level, all, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, single, collapsed):   0.00% (0/2)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed):   0.00% (0/4)
exon specificity (mRNA level, initial, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, internal, collapsed):   0.00% (0/10)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed):   0.00% (0/2)
exon specificity (mRNA level, terminal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, all): 100.00% (0/0)
exon specificity (CDS level, all):   0.00% (0/13)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single):   0.00% (0/13)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (0/0)
exon specificity (CDS level, all, collapsed):   0.00% (0/13)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed):   0.00% (0/13)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
genometools-1.5.1/testdata/gt_eval_prob_1.out_swapped000066400000000000000000000054341211610345200230220ustar00rootroot00000000000000gene sensitivity (mRNA level):   0.00% (0/4) (missing genes: 2)
gene specificity (mRNA level):   0.00% (0/7) (wrong genes: 3)
gene sensitivity (CDS level):   0.00% (0/4) (missing genes: 2)
gene specificity (CDS level):   0.00% (0/7) (wrong genes: 3)
mRNA sensitivity (mRNA level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (mRNA level): 100.00% (0/0) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (CDS level): 100.00% (0/0) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (0/0)
exon specificity (mRNA level, all):   0.00% (0/32)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single):   0.00% (0/3)
exon sensitivity (mRNA level, initial): 100.00% (0/0)
exon specificity (mRNA level, initial):   0.00% (0/4)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal):   0.00% (0/21)
exon sensitivity (mRNA level, terminal): 100.00% (0/0)
exon specificity (mRNA level, terminal):   0.00% (0/4)
exon sensitivity (mRNA level, all, collapsed): 100.00% (0/0)
exon specificity (mRNA level, all, collapsed):   0.00% (0/18)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed):   0.00% (0/2)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (0/0)
exon specificity (mRNA level, initial, collapsed):   0.00% (0/4)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed):   0.00% (0/10)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, terminal, collapsed):   0.00% (0/2)
exon sensitivity (CDS level, all):   0.00% (0/13)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single):   0.00% (0/13)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed):   0.00% (0/13)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed):   0.00% (0/13)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
genometools-1.5.1/testdata/gt_eval_prob_1.prediction000066400000000000000000000027771211610345200226370ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr8 118886142 119354298
#
#
chr8	AUGUSTUS	CDS	118886142	118886313	.	-	1	 gene_id="g1";transcript_id="g1.t1"
chr8	AUGUSTUS	gene	118886142	118926734	1.000000	-	.	.
chr8	AUGUSTUS	transcript	118886142	118926734	.	-	.	.
chr8	AUGUSTUS	CDS	118888637	118888797	.	-	0	 gene_id="g1";transcript_id="g1.t1"
chr8	AUGUSTUS	CDS	118894292	118894381	.	-	0	 gene_id="g1";transcript_id="g1.t1"
chr8	AUGUSTUS	CDS	118899855	118899950	.	-	0	 gene_id="g1";transcript_id="g1.t1"
chr8	AUGUSTUS	CDS	118901096	118901214	.	-	2	 gene_id="g1";transcript_id="g1.t1"
chr8	AUGUSTUS	CDS	118903885	118904017	.	-	0	 gene_id="g1";transcript_id="g1.t1"
chr8	AUGUSTUS	CDS	118916864	118916971	.	-	0	 gene_id="g1";transcript_id="g1.t1"
chr8	AUGUSTUS	CDS	118918528	118918621	.	-	1	 gene_id="g1";transcript_id="g1.t1"
chr8	AUGUSTUS	CDS	118926685	118926734	.	-	0	 gene_id="g1";transcript_id="g1.t1"
chr8	AUGUSTUS	gene	119191501	119192466	1.000000	-	.	.
chr8	AUGUSTUS	transcript	119191501	119192466	.	-	.	.
chr8	AUGUSTUS	CDS	119191501	119192466	.	-	0	 gene_id="g2";transcript_id="g2.t1"
chr8	AUGUSTUS	CDS	119192825	119192837	.	+	0	 gene_id="g3";transcript_id="g3.t1"
chr8	AUGUSTUS	gene	119192825	119193688	1.000000	+	.	.
chr8	AUGUSTUS	transcript	119192825	119193688	.	+	.	.
chr8	AUGUSTUS	CDS	119193042	119193688	.	+	2	 gene_id="g3";transcript_id="g3.t1"
chr8	AUGUSTUS	gene	119353885	119354298	1.000000	-	.	.
chr8	AUGUSTUS	transcript	119353885	119354298	.	-	.	.
chr8	AUGUSTUS	CDS	119353885	119354298	.	-	0	 gene_id="g4";transcript_id="g4.t1"
genometools-1.5.1/testdata/gt_eval_prob_1.reality000066400000000000000000000046461211610345200221450ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr8 118886142 119279152
chr8	ENCODE	gene	118886142	119192762	.	-	.	ID=gene1;Name=AC113188.1-004;name2=EXT1
chr8	ENCODE	exon	118886142	118886313	.	-	.	Parent=gene1
chr8	ENCODE	exon	118888637	118888797	.	-	.	Parent=gene1
chr8	ENCODE	exon	118894292	118894381	.	-	.	Parent=gene1
chr8	ENCODE	exon	118899855	118899950	.	-	.	Parent=gene1
chr8	ENCODE	exon	118901096	118901214	.	-	.	Parent=gene1
chr8	ENCODE	exon	118903885	118904017	.	-	.	Parent=gene1
chr8	ENCODE	exon	118911650	118911769	.	-	.	Parent=gene1
chr8	ENCODE	exon	118916864	118916971	.	-	.	Parent=gene1
chr8	ENCODE	exon	119192394	119192762	.	-	.	Parent=gene1
###
chr8	ENCODE	gene	118886142	119192806	.	-	.	ID=gene2;Name=AC113188.1-002;name2=EXT1
chr8	ENCODE	exon	118886142	118886313	.	-	.	Parent=gene2
chr8	ENCODE	exon	118888637	118888797	.	-	.	Parent=gene2
chr8	ENCODE	exon	118894292	118894381	.	-	.	Parent=gene2
chr8	ENCODE	exon	118899855	118899880	.	-	.	Parent=gene2
chr8	ENCODE	exon	119191651	119192806	.	-	.	Parent=gene2
###
chr8	ENCODE	gene	118886142	119193119	.	-	.	ID=gene3;Name=AC113188.1-001;name2=EXT1
chr8	ENCODE	exon	118886142	118886313	.	-	.	Parent=gene3
chr8	ENCODE	exon	118888637	118888797	.	-	.	Parent=gene3
chr8	ENCODE	exon	118894292	118894381	.	-	.	Parent=gene3
chr8	ENCODE	exon	118899855	118899950	.	-	.	Parent=gene3
chr8	ENCODE	exon	118901096	118901214	.	-	.	Parent=gene3
chr8	ENCODE	exon	118903885	118904017	.	-	.	Parent=gene3
chr8	ENCODE	exon	118911650	118911769	.	-	.	Parent=gene3
chr8	ENCODE	exon	118916864	118916971	.	-	.	Parent=gene3
chr8	ENCODE	exon	118918528	118918621	.	-	.	Parent=gene3
chr8	ENCODE	exon	119191505	119193119	.	-	.	Parent=gene3
###
chr8	ENCODE	gene	118911657	119191834	.	-	.	ID=gene4;Name=AC113188.1-003;name2=EXT1
chr8	ENCODE	exon	118911657	118911769	.	-	.	Parent=gene4
chr8	ENCODE	exon	118913019	118913073	.	-	.	Parent=gene4
chr8	ENCODE	exon	118916864	118916971	.	-	.	Parent=gene4
chr8	ENCODE	exon	118918528	118918621	.	-	.	Parent=gene4
chr8	ENCODE	exon	119191505	119191834	.	-	.	Parent=gene4
###
chr8	ENCODE	gene	119276307	119279152	.	-	.	ID=gene5;Name=AC023590.2-005;name2=SAMD12
chr8	ENCODE	exon	119276307	119279152	.	-	.	Parent=gene5
###
chr8	ENCODE	gene	119276307	119279152	.	-	.	ID=gene6;Name=AC023590.2-003;name2=SAMD12
chr8	ENCODE	exon	119276307	119279152	.	-	.	Parent=gene6
###
chr8	ENCODE	gene	119278740	119279152	.	-	.	ID=gene7;Name=AC023590.2-004;name2=SAMD12
chr8	ENCODE	exon	119278740	119279152	.	-	.	Parent=gene7
###
genometools-1.5.1/testdata/gt_eval_test_1.in000066400000000000000000000414351211610345200211140ustar00rootroot00000000000000##gff-version   3
##sequence-region   ENm001 1 1500000
ENm001	gth	gene	63867	87012	1.000000	+	.	ID=gene1
ENm001	gth	exon	86827	87012	1.000000	+	.	Parent=gene1
ENm001	gth	exon	81851	82009	1.000000	+	.	Parent=gene1
ENm001	gth	exon	81293	81508	1.000000	+	.	Parent=gene1
ENm001	gth	exon	79694	80029	1.000000	+	.	Parent=gene1
ENm001	gth	exon	78553	78805	1.000000	+	.	Parent=gene1
ENm001	gth	exon	64067	64152	1.000000	+	.	Parent=gene1
ENm001	gth	exon	63867	63893	0.196078	+	.	Parent=gene1
###
ENm001	gth	gene	78298	87012	0.883554	+	.	ID=gene2
ENm001	gth	exon	86827	87012	0.960317	+	.	Parent=gene2
ENm001	gth	exon	81851	82009	0.938776	+	.	Parent=gene2
ENm001	gth	exon	81293	81508	0.899756	+	.	Parent=gene2
ENm001	gth	exon	79694	80029	0.810409	+	.	Parent=gene2
ENm001	gth	exon	78553	78805	0.883152	+	.	Parent=gene2
ENm001	gth	exon	78298	78301	1.000000	+	.	Parent=gene2
###
ENm001	gth	gene	286309	286912	0.663080	+	.	ID=gene3
ENm001	gth	exon	286309	286912	0.663080	+	.	Parent=gene3
###
ENm001	gth	gene	286309	287101	0.547515	+	.	ID=gene4
ENm001	gth	exon	287066	287101	0.223881	+	.	Parent=gene4
ENm001	gth	exon	286309	286974	0.547515	+	.	Parent=gene4
###
ENm001	gth	gene	329315	335651	1.000000	+	.	ID=gene5
ENm001	gth	exon	335504	335651	1.000000	+	.	Parent=gene5
ENm001	gth	exon	329793	329980	1.000000	+	.	Parent=gene5
ENm001	gth	exon	329315	329464	1.000000	+	.	Parent=gene5
###
ENm001	gth	gene	329315	335651	0.796171	+	.	ID=gene6
ENm001	gth	exon	335504	335651	0.900383	+	.	Parent=gene6
ENm001	gth	exon	329793	329980	0.715789	+	.	Parent=gene6
ENm001	gth	exon	329315	329451	0.809717	+	.	Parent=gene6
###
ENm001	gth	gene	329315	335651	0.795647	+	.	ID=gene7
ENm001	gth	exon	335504	335651	0.861660	+	.	Parent=gene7
ENm001	gth	exon	329793	329980	0.815790	+	.	Parent=gene7
ENm001	gth	exon	329315	329464	0.711111	+	.	Parent=gene7
###
ENm001	gth	gene	329315	335651	0.859504	+	.	ID=gene8
ENm001	gth	exon	335504	335651	0.896825	+	.	Parent=gene8
ENm001	gth	exon	329793	329980	0.852761	+	.	Parent=gene8
ENm001	gth	exon	329315	329458	0.832714	+	.	Parent=gene8
###
ENm001	gth	gene	356027	388817	0.810929	+	.	ID=gene9
ENm001	gth	exon	388479	388817	0.883275	+	.	Parent=gene9
ENm001	gth	exon	356027	356222	0.689150	+	.	Parent=gene9
###
ENm001	gth	gene	356028	388817	0.897489	+	.	ID=gene10
ENm001	gth	exon	388479	388817	0.941957	+	.	Parent=gene10
ENm001	gth	exon	356028	356222	0.821530	+	.	Parent=gene10
###
ENm001	gth	gene	356028	388817	0.900932	+	.	ID=gene11
ENm001	gth	exon	388479	388817	0.968379	+	.	Parent=gene11
ENm001	gth	exon	356028	356222	0.803977	+	.	Parent=gene11
###
ENm001	gth	gene	356028	388817	0.895961	+	.	ID=gene12
ENm001	gth	exon	388479	388817	0.959432	+	.	Parent=gene12
ENm001	gth	exon	356028	356222	0.799383	+	.	Parent=gene12
###
ENm001	gth	gene	356028	388817	0.900932	+	.	ID=gene13
ENm001	gth	exon	388479	388817	0.968379	+	.	Parent=gene13
ENm001	gth	exon	356028	356222	0.803977	+	.	Parent=gene13
###
ENm001	gth	gene	356028	388817	0.902720	+	.	ID=gene14
ENm001	gth	exon	388479	388817	0.950249	+	.	Parent=gene14
ENm001	gth	exon	356028	356222	0.821530	+	.	Parent=gene14
###
ENm001	gth	gene	356031	388817	0.938775	+	.	ID=gene15
ENm001	gth	exon	388479	388817	1.000000	+	.	Parent=gene15
ENm001	gth	exon	356031	356222	0.866142	+	.	Parent=gene15
###
ENm001	gth	gene	468516	468738	0.704600	+	.	ID=gene16
ENm001	gth	exon	468516	468738	0.704600	+	.	Parent=gene16
###
ENm001	gth	gene	468516	468738	0.730583	+	.	ID=gene17
ENm001	gth	exon	468516	468738	0.730583	+	.	Parent=gene17
###
ENm001	gth	gene	528618	625654	0.999442	+	.	ID=gene18
ENm001	gth	exon	625420	625654	1.000000	+	.	Parent=gene18
ENm001	gth	exon	625188	625324	0.981651	+	.	Parent=gene18
ENm001	gth	exon	612837	613002	1.000000	+	.	Parent=gene18
ENm001	gth	exon	611521	611630	1.000000	+	.	Parent=gene18
ENm001	gth	exon	608309	608490	1.000000	+	.	Parent=gene18
ENm001	gth	exon	606922	607002	1.000000	+	.	Parent=gene18
ENm001	gth	exon	604414	604644	1.000000	+	.	Parent=gene18
ENm001	gth	exon	601382	601522	1.000000	+	.	Parent=gene18
ENm001	gth	exon	601031	601187	1.000000	+	.	Parent=gene18
ENm001	gth	exon	599178	599324	1.000000	+	.	Parent=gene18
ENm001	gth	exon	592583	592801	1.000000	+	.	Parent=gene18
ENm001	gth	exon	588924	589023	1.000000	+	.	Parent=gene18
ENm001	gth	exon	587992	588153	1.000000	+	.	Parent=gene18
ENm001	gth	exon	587171	587307	1.000000	+	.	Parent=gene18
ENm001	gth	exon	586970	587072	1.000000	+	.	Parent=gene18
ENm001	gth	exon	584888	585048	1.000000	+	.	Parent=gene18
ENm001	gth	exon	570385	570558	1.000000	+	.	Parent=gene18
ENm001	gth	exon	569483	569617	1.000000	+	.	Parent=gene18
ENm001	gth	exon	561201	561392	1.000000	+	.	Parent=gene18
ENm001	gth	exon	528618	529817	1.000000	+	.	Parent=gene18
###
ENm001	gth	gene	620432	684293	0.991022	-	.	ID=gene19
ENm001	gth	exon	684144	684293	0.979167	-	.	Parent=gene19
ENm001	gth	exon	680427	680540	1.000000	-	.	Parent=gene19
ENm001	gth	exon	679175	679280	1.000000	-	.	Parent=gene19
ENm001	gth	exon	667845	667954	1.000000	-	.	Parent=gene19
ENm001	gth	exon	666825	666881	1.000000	-	.	Parent=gene19
ENm001	gth	exon	665748	665823	0.961538	-	.	Parent=gene19
ENm001	gth	exon	664782	664906	1.000000	-	.	Parent=gene19
ENm001	gth	exon	663032	663166	1.000000	-	.	Parent=gene19
ENm001	gth	exon	662083	662194	1.000000	-	.	Parent=gene19
ENm001	gth	exon	627618	627729	1.000000	-	.	Parent=gene19
ENm001	gth	exon	625533	625655	0.974468	-	.	Parent=gene19
ENm001	gth	exon	620957	621056	0.963235	-	.	Parent=gene19
ENm001	gth	exon	620432	620536	1.000000	-	.	Parent=gene19
###
ENm001	gth	gene	620432	684293	1.000000	-	.	ID=gene20
ENm001	gth	exon	684144	684293	1.000000	-	.	Parent=gene20
ENm001	gth	exon	680427	680540	1.000000	-	.	Parent=gene20
ENm001	gth	exon	679175	679280	1.000000	-	.	Parent=gene20
ENm001	gth	exon	667845	667954	1.000000	-	.	Parent=gene20
ENm001	gth	exon	666825	666881	1.000000	-	.	Parent=gene20
ENm001	gth	exon	665748	665823	1.000000	-	.	Parent=gene20
ENm001	gth	exon	664782	664906	1.000000	-	.	Parent=gene20
ENm001	gth	exon	663032	663166	1.000000	-	.	Parent=gene20
ENm001	gth	exon	662083	662194	1.000000	-	.	Parent=gene20
ENm001	gth	exon	627618	627729	1.000000	-	.	Parent=gene20
ENm001	gth	exon	625533	625655	1.000000	-	.	Parent=gene20
ENm001	gth	exon	620957	621056	1.000000	-	.	Parent=gene20
ENm001	gth	exon	620432	620536	1.000000	-	.	Parent=gene20
###
ENm001	gth	gene	625234	684293	0.808461	-	.	ID=gene21
ENm001	gth	exon	684144	684293	0.779468	-	.	Parent=gene21
ENm001	gth	exon	680427	680540	0.811518	-	.	Parent=gene21
ENm001	gth	exon	679175	679280	0.953608	-	.	Parent=gene21
ENm001	gth	exon	667797	667954	0.516484	-	.	Parent=gene21
ENm001	gth	exon	665748	665823	0.921053	-	.	Parent=gene21
ENm001	gth	exon	664782	664906	0.850000	-	.	Parent=gene21
ENm001	gth	exon	663032	663166	0.880184	-	.	Parent=gene21
ENm001	gth	exon	662083	662194	0.973684	-	.	Parent=gene21
ENm001	gth	exon	627618	627729	0.825581	-	.	Parent=gene21
ENm001	gth	exon	625500	625655	0.752508	-	.	Parent=gene21
ENm001	gth	exon	625234	625253	0.200000	-	.	Parent=gene21
###
ENm001	gth	gene	717619	747397	0.765398	+	.	ID=gene22
ENm001	gth	exon	747260	747397	1.000000	+	.	Parent=gene22
ENm001	gth	exon	745593	745655	0.962264	+	.	Parent=gene22
ENm001	gth	exon	741602	741673	1.000000	+	.	Parent=gene22
ENm001	gth	exon	739766	739844	0.947059	+	.	Parent=gene22
ENm001	gth	exon	735796	735875	0.953271	+	.	Parent=gene22
ENm001	gth	exon	733622	733916	0.577438	+	.	Parent=gene22
ENm001	gth	exon	717619	717748	0.530516	+	.	Parent=gene22
###
ENm001	gth	gene	717622	747397	0.876956	+	.	ID=gene23
ENm001	gth	exon	747260	747397	1.000000	+	.	Parent=gene23
ENm001	gth	exon	745593	745655	1.000000	+	.	Parent=gene23
ENm001	gth	exon	741602	741673	1.000000	+	.	Parent=gene23
ENm001	gth	exon	739766	739844	0.973510	+	.	Parent=gene23
ENm001	gth	exon	735796	735875	0.972222	+	.	Parent=gene23
ENm001	gth	exon	733710	733916	0.945161	+	.	Parent=gene23
ENm001	gth	exon	728305	728368	0.933333	+	.	Parent=gene23
ENm001	gth	exon	717622	717773	0.451737	+	.	Parent=gene23
###
ENm001	gth	gene	717622	747397	0.890370	+	.	ID=gene24
ENm001	gth	exon	747260	747397	1.000000	+	.	Parent=gene24
ENm001	gth	exon	745593	745655	1.000000	+	.	Parent=gene24
ENm001	gth	exon	741602	741673	1.000000	+	.	Parent=gene24
ENm001	gth	exon	739766	739844	1.000000	+	.	Parent=gene24
ENm001	gth	exon	735796	735875	1.000000	+	.	Parent=gene24
ENm001	gth	exon	733710	733916	1.000000	+	.	Parent=gene24
ENm001	gth	exon	728305	728368	0.933333	+	.	Parent=gene24
ENm001	gth	exon	717622	717773	0.451737	+	.	Parent=gene24
###
ENm001	gth	gene	717625	733850	0.712980	+	.	ID=gene25
ENm001	gth	exon	733710	733850	0.913043	+	.	Parent=gene25
ENm001	gth	exon	728305	728368	0.933333	+	.	Parent=gene25
ENm001	gth	exon	717625	717773	0.468000	+	.	Parent=gene25
###
ENm001	gth	gene	724903	769734	0.966519	-	.	ID=gene26
ENm001	gth	exon	769508	769734	0.953125	-	.	Parent=gene26
ENm001	gth	exon	750016	750280	0.975824	-	.	Parent=gene26
ENm001	gth	exon	732544	732821	0.973361	-	.	Parent=gene26
ENm001	gth	exon	727099	727325	0.971800	-	.	Parent=gene26
ENm001	gth	exon	724903	724985	0.944134	-	.	Parent=gene26
###
ENm001	gth	gene	724903	769734	1.000000	-	.	ID=gene27
ENm001	gth	exon	769508	769734	1.000000	-	.	Parent=gene27
ENm001	gth	exon	750016	750280	1.000000	-	.	Parent=gene27
ENm001	gth	exon	732544	732821	1.000000	-	.	Parent=gene27
ENm001	gth	exon	727099	727325	1.000000	-	.	Parent=gene27
ENm001	gth	exon	724903	724985	1.000000	-	.	Parent=gene27
###
ENm001	gth	gene	1333735	1496638	0.889211	+	.	ID=gene28
ENm001	gth	exon	1496441	1496638	0.739550	+	.	Parent=gene28
ENm001	gth	exon	1494992	1495097	0.902703	+	.	Parent=gene28
ENm001	gth	exon	1494221	1494393	1.000000	+	.	Parent=gene28
ENm001	gth	exon	1482375	1482464	1.000000	+	.	Parent=gene28
ENm001	gth	exon	1471971	1472126	0.965779	+	.	Parent=gene28
ENm001	gth	exon	1457055	1457303	0.849020	+	.	Parent=gene28
ENm001	gth	exon	1444146	1444246	0.976471	+	.	Parent=gene28
ENm001	gth	exon	1441114	1441341	1.000000	+	.	Parent=gene28
ENm001	gth	exon	1440052	1440202	0.846847	+	.	Parent=gene28
ENm001	gth	exon	1436207	1436286	0.969697	+	.	Parent=gene28
ENm001	gth	exon	1433027	1433315	0.740594	+	.	Parent=gene28
ENm001	gth	exon	1424463	1424591	0.882353	+	.	Parent=gene28
ENm001	gth	exon	1421467	1422190	0.835843	+	.	Parent=gene28
ENm001	gth	exon	1419886	1419972	1.000000	+	.	Parent=gene28
ENm001	gth	exon	1417272	1417366	0.974684	+	.	Parent=gene28
ENm001	gth	exon	1388997	1389188	0.951923	+	.	Parent=gene28
ENm001	gth	exon	1378174	1378356	0.843450	+	.	Parent=gene28
ENm001	gth	exon	1371549	1371641	0.968944	+	.	Parent=gene28
ENm001	gth	exon	1369633	1369879	0.977117	+	.	Parent=gene28
ENm001	gth	exon	1366081	1366206	0.957547	+	.	Parent=gene28
ENm001	gth	exon	1364781	1364944	0.851590	+	.	Parent=gene28
ENm001	gth	exon	1363809	1363898	1.000000	+	.	Parent=gene28
ENm001	gth	exon	1360432	1360647	0.986111	+	.	Parent=gene28
ENm001	gth	exon	1338567	1338675	0.967033	+	.	Parent=gene28
ENm001	gth	exon	1333735	1333896	0.682432	+	.	Parent=gene28
###
ENm001	gth	gene	1333735	1496638	0.962358	+	.	ID=gene29
ENm001	gth	exon	1496441	1496638	0.972050	+	.	Parent=gene29
ENm001	gth	exon	1494992	1495097	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1494221	1494393	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1482375	1482464	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1471971	1472126	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1457055	1457303	0.909091	+	.	Parent=gene29
ENm001	gth	exon	1444146	1444246	0.965035	+	.	Parent=gene29
ENm001	gth	exon	1441114	1441341	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1440052	1440202	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1436207	1436286	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1433027	1433315	0.828753	+	.	Parent=gene29
ENm001	gth	exon	1424463	1424591	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1421467	1422190	0.972794	+	.	Parent=gene29
ENm001	gth	exon	1419886	1419972	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1417272	1417366	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1388997	1389188	0.965649	+	.	Parent=gene29
ENm001	gth	exon	1378174	1378356	0.967213	+	.	Parent=gene29
ENm001	gth	exon	1371549	1371641	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1369633	1369879	0.989305	+	.	Parent=gene29
ENm001	gth	exon	1366081	1366206	0.981481	+	.	Parent=gene29
ENm001	gth	exon	1364781	1364944	0.989041	+	.	Parent=gene29
ENm001	gth	exon	1363809	1363898	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1360432	1360647	1.000000	+	.	Parent=gene29
ENm001	gth	exon	1338567	1338675	0.967033	+	.	Parent=gene29
ENm001	gth	exon	1333735	1333896	0.754777	+	.	Parent=gene29
###
ENm001	gth	gene	1333735	1496638	0.983471	+	.	ID=gene30
ENm001	gth	exon	1496441	1496638	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1494992	1495097	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1494221	1494393	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1482375	1482464	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1471971	1472126	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1457055	1457303	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1444146	1444246	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1441114	1441341	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1440052	1440202	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1436207	1436286	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1433027	1433315	0.873706	+	.	Parent=gene30
ENm001	gth	exon	1424463	1424591	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1421467	1422190	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1419886	1419972	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1417272	1417366	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1388997	1389188	0.984674	+	.	Parent=gene30
ENm001	gth	exon	1378174	1378356	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1371549	1371641	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1369633	1369879	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1366081	1366206	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1364781	1364944	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1363809	1363898	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1360432	1360647	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1338567	1338675	1.000000	+	.	Parent=gene30
ENm001	gth	exon	1333735	1333896	0.768987	+	.	Parent=gene30
###
ENm001	gth	gene	1333735	1496638	0.882760	+	.	ID=gene31
ENm001	gth	exon	1496441	1496638	0.739550	+	.	Parent=gene31
ENm001	gth	exon	1494992	1495097	0.862745	+	.	Parent=gene31
ENm001	gth	exon	1494221	1494393	0.982684	+	.	Parent=gene31
ENm001	gth	exon	1482375	1482464	0.966667	+	.	Parent=gene31
ENm001	gth	exon	1471971	1472126	0.965779	+	.	Parent=gene31
ENm001	gth	exon	1457055	1457303	0.846303	+	.	Parent=gene31
ENm001	gth	exon	1444146	1444246	0.976471	+	.	Parent=gene31
ENm001	gth	exon	1441114	1441341	0.968668	+	.	Parent=gene31
ENm001	gth	exon	1440052	1440202	0.859155	+	.	Parent=gene31
ENm001	gth	exon	1436207	1436286	0.939850	+	.	Parent=gene31
ENm001	gth	exon	1433027	1433315	0.755859	+	.	Parent=gene31
ENm001	gth	exon	1424463	1424591	0.882353	+	.	Parent=gene31
ENm001	gth	exon	1421467	1422190	0.829035	+	.	Parent=gene31
ENm001	gth	exon	1419886	1419972	1.000000	+	.	Parent=gene31
ENm001	gth	exon	1417272	1417366	0.972222	+	.	Parent=gene31
ENm001	gth	exon	1388997	1389188	0.914286	+	.	Parent=gene31
ENm001	gth	exon	1378174	1378356	0.860841	+	.	Parent=gene31
ENm001	gth	exon	1371549	1371641	0.943820	+	.	Parent=gene31
ENm001	gth	exon	1369633	1369879	0.977117	+	.	Parent=gene31
ENm001	gth	exon	1366081	1366206	0.930481	+	.	Parent=gene31
ENm001	gth	exon	1364781	1364944	0.899083	+	.	Parent=gene31
ENm001	gth	exon	1363809	1363898	0.963235	+	.	Parent=gene31
ENm001	gth	exon	1360432	1360647	0.986111	+	.	Parent=gene31
ENm001	gth	exon	1338567	1338675	0.967033	+	.	Parent=gene31
ENm001	gth	exon	1333735	1333896	0.668919	+	.	Parent=gene31
###
ENm001	gth	gene	1333738	1496638	0.906741	+	.	ID=gene32
ENm001	gth	exon	1496441	1496638	0.801282	+	.	Parent=gene32
ENm001	gth	exon	1494992	1495097	0.950276	+	.	Parent=gene32
ENm001	gth	exon	1494221	1494393	0.961864	+	.	Parent=gene32
ENm001	gth	exon	1482375	1482464	1.000000	+	.	Parent=gene32
ENm001	gth	exon	1471971	1472126	0.974895	+	.	Parent=gene32
ENm001	gth	exon	1457055	1457303	0.851852	+	.	Parent=gene32
ENm001	gth	exon	1444146	1444246	1.000000	+	.	Parent=gene32
ENm001	gth	exon	1441114	1441341	0.976982	+	.	Parent=gene32
ENm001	gth	exon	1440052	1440202	0.884445	+	.	Parent=gene32
ENm001	gth	exon	1436207	1436286	1.000000	+	.	Parent=gene32
ENm001	gth	exon	1433027	1433315	0.775701	+	.	Parent=gene32
ENm001	gth	exon	1424463	1424591	0.842391	+	.	Parent=gene32
ENm001	gth	exon	1421467	1422190	0.864656	+	.	Parent=gene32
ENm001	gth	exon	1419886	1419972	1.000000	+	.	Parent=gene32
ENm001	gth	exon	1417272	1417366	0.942029	+	.	Parent=gene32
ENm001	gth	exon	1388997	1389188	0.975936	+	.	Parent=gene32
ENm001	gth	exon	1378174	1378356	0.871257	+	.	Parent=gene32
ENm001	gth	exon	1371549	1371641	0.972973	+	.	Parent=gene32
ENm001	gth	exon	1369633	1369879	0.990338	+	.	Parent=gene32
ENm001	gth	exon	1366081	1366206	0.981481	+	.	Parent=gene32
ENm001	gth	exon	1364781	1364944	0.933884	+	.	Parent=gene32
ENm001	gth	exon	1360432	1360647	0.987805	+	.	Parent=gene32
ENm001	gth	exon	1338567	1338675	1.000000	+	.	Parent=gene32
ENm001	gth	exon	1333738	1333896	0.698842	+	.	Parent=gene32
###
ENm001	gth	gene	1421486	1422028	0.816017	+	.	ID=gene33
ENm001	gth	exon	1421486	1422028	0.816017	+	.	Parent=gene33
###
ENm001	gth	gene	1421501	1422028	0.933333	+	.	ID=gene34
ENm001	gth	exon	1421501	1422028	0.933333	+	.	Parent=gene34
###
genometools-1.5.1/testdata/gt_eval_test_1.out000066400000000000000000000061361211610345200213140ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (34/34) (missing genes: 0)
gene specificity (mRNA level): 100.00% (34/34) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (34/34) (missing genes: 0)
gene specificity (CDS level): 100.00% (34/34) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (mRNA level): 100.00% (0/0) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (CDS level): 100.00% (0/0) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (263/263)
exon specificity (mRNA level, all): 100.00% (263/263)
exon sensitivity (mRNA level, single): 100.00% (5/5)
exon specificity (mRNA level, single): 100.00% (5/5)
exon sensitivity (mRNA level, initial): 100.00% (29/29)
exon specificity (mRNA level, initial): 100.00% (29/29)
exon sensitivity (mRNA level, internal): 100.00% (200/200)
exon specificity (mRNA level, internal): 100.00% (200/200)
exon sensitivity (mRNA level, terminal): 100.00% (29/29)
exon specificity (mRNA level, terminal): 100.00% (29/29)
exon sensitivity (mRNA level, all, collapsed): 100.00% (102/102)
exon specificity (mRNA level, all, collapsed): 100.00% (102/102)
exon sensitivity (mRNA level, single, collapsed): 100.00% (4/4)
exon specificity (mRNA level, single, collapsed): 100.00% (4/4)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (17/17)
exon specificity (mRNA level, initial, collapsed): 100.00% (17/17)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (70/70)
exon specificity (mRNA level, internal, collapsed): 100.00% (70/70)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (11/11)
exon specificity (mRNA level, terminal, collapsed): 100.00% (11/11)
exon sensitivity (CDS level, all): 100.00% (0/0)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (0/0)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
nucleotide sensitivity (mRNA level): 100.00% (TP=15373/(TP=15373 + FN=0))
nucleotide specificity (mRNA level): 100.00% (TP=15373/(TP=15373 + FP=0))
nucleotide sensitivity (CDS level): 100.00% (TP=0/(TP=0 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=0/(TP=0 + FP=0))
genometools-1.5.1/testdata/gt_eval_test_10.in000066400000000000000000000000601211610345200211610ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 80
genometools-1.5.1/testdata/gt_eval_test_10.out000066400000000000000000000060321211610345200213670ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (0/0) (missing genes: 0)
gene specificity (mRNA level): 100.00% (0/0) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (0/0) (missing genes: 0)
gene specificity (CDS level): 100.00% (0/0) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (mRNA level): 100.00% (0/0) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (CDS level): 100.00% (0/0) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (0/0)
exon specificity (mRNA level, all): 100.00% (0/0)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial): 100.00% (0/0)
exon specificity (mRNA level, initial): 100.00% (0/0)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (0/0)
exon specificity (mRNA level, terminal): 100.00% (0/0)
exon sensitivity (mRNA level, all, collapsed): 100.00% (0/0)
exon specificity (mRNA level, all, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (0/0)
exon specificity (mRNA level, initial, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, terminal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, all): 100.00% (0/0)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (0/0)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
nucleotide sensitivity (mRNA level): 100.00% (TP=0/(TP=0 + FN=0))
nucleotide specificity (mRNA level): 100.00% (TP=0/(TP=0 + FP=0))
nucleotide sensitivity (CDS level): 100.00% (TP=0/(TP=0 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=0/(TP=0 + FP=0))
genometools-1.5.1/testdata/gt_eval_test_2.nuc000066400000000000000000000060401211610345200212650ustar00rootroot00000000000000gene sensitivity (mRNA level):   0.00% (0/1) (missing genes: 0)
gene specificity (mRNA level):   0.00% (0/1) (wrong genes: 0)
gene sensitivity (CDS level):   0.00% (0/1) (missing genes: 0)
gene specificity (CDS level):   0.00% (0/1) (wrong genes: 0)
mRNA sensitivity (mRNA level):   0.00% (0/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):   0.00% (0/1) (wrong mRNAs: 0)
mRNA sensitivity (CDS level):   0.00% (0/1) (missing mRNAs: 0)
mRNA specificity (CDS level):   0.00% (0/1) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all):  50.00% (1/2)
exon specificity (mRNA level, all):  50.00% (1/2)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial):   0.00% (0/1)
exon specificity (mRNA level, initial):   0.00% (0/1)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal):   0.00% (0/1)
exon specificity (mRNA level, terminal):   0.00% (0/1)
exon sensitivity (mRNA level, all, collapsed):  50.00% (1/2)
exon specificity (mRNA level, all, collapsed):  50.00% (1/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed):   0.00% (0/1)
exon specificity (mRNA level, initial, collapsed):   0.00% (0/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed):   0.00% (0/1)
exon specificity (mRNA level, terminal, collapsed):   0.00% (0/1)
exon sensitivity (CDS level, all): 100.00% (0/0)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (0/0)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
nucleotide sensitivity (mRNA level):  50.00% (TP=26/(TP=26 + FN=26))
nucleotide specificity (mRNA level):  33.77% (TP=26/(TP=26 + FP=51))
nucleotide sensitivity (CDS level): 100.00% (TP=0/(TP=0 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=0/(TP=0 + FP=0))
genometools-1.5.1/testdata/gt_eval_test_2.out000066400000000000000000000054241211610345200213140ustar00rootroot00000000000000gene sensitivity (mRNA level):   0.00% (0/1) (missing genes: 0)
gene specificity (mRNA level):   0.00% (0/1) (wrong genes: 0)
gene sensitivity (CDS level):   0.00% (0/1) (missing genes: 0)
gene specificity (CDS level):   0.00% (0/1) (wrong genes: 0)
mRNA sensitivity (mRNA level):   0.00% (0/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):   0.00% (0/1) (wrong mRNAs: 0)
mRNA sensitivity (CDS level):   0.00% (0/1) (missing mRNAs: 0)
mRNA specificity (CDS level):   0.00% (0/1) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all):  50.00% (1/2)
exon specificity (mRNA level, all):  50.00% (1/2)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial):   0.00% (0/1)
exon specificity (mRNA level, initial):   0.00% (0/1)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal):   0.00% (0/1)
exon specificity (mRNA level, terminal):   0.00% (0/1)
exon sensitivity (mRNA level, all, collapsed):  50.00% (1/2)
exon specificity (mRNA level, all, collapsed):  50.00% (1/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed):   0.00% (0/1)
exon specificity (mRNA level, initial, collapsed):   0.00% (0/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed):   0.00% (0/1)
exon specificity (mRNA level, terminal, collapsed):   0.00% (0/1)
exon sensitivity (CDS level, all): 100.00% (0/0)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (0/0)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
genometools-1.5.1/testdata/gt_eval_test_2.prediction000066400000000000000000000003161211610345200226400ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	175	300	.	-	.	ID=gene
gDNA	.	mRNA	175	300	.	-	.	ID=mRNA;Parent=gene
gDNA	.	exon	175	200	.	-	.	Parent=mRNA
gDNA	.	exon	250	300	.	-	.	Parent=mRNA
genometools-1.5.1/testdata/gt_eval_test_2.reality000066400000000000000000000003161211610345200221510ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA;Parent=gene
gDNA	.	exon	100	125	.	-	.	Parent=mRNA
gDNA	.	exon	175	200	.	-	.	Parent=mRNA
genometools-1.5.1/testdata/gt_eval_test_3.nuc000066400000000000000000000060331211610345200212700ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (0/0) (missing genes: 0)
gene specificity (mRNA level):   0.00% (0/1) (wrong genes: 1)
gene sensitivity (CDS level): 100.00% (0/0) (missing genes: 0)
gene specificity (CDS level):   0.00% (0/1) (wrong genes: 1)
mRNA sensitivity (mRNA level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (mRNA level):   0.00% (0/1) (wrong mRNAs: 1)
mRNA sensitivity (CDS level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (CDS level):   0.00% (0/1) (wrong mRNAs: 1)
exon sensitivity (mRNA level, all): 100.00% (0/0)
exon specificity (mRNA level, all):   0.00% (0/2)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial): 100.00% (0/0)
exon specificity (mRNA level, initial):   0.00% (0/1)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (0/0)
exon specificity (mRNA level, terminal):   0.00% (0/1)
exon sensitivity (mRNA level, all, collapsed): 100.00% (0/0)
exon specificity (mRNA level, all, collapsed):   0.00% (0/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (0/0)
exon specificity (mRNA level, initial, collapsed):   0.00% (0/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, terminal, collapsed):   0.00% (0/1)
exon sensitivity (CDS level, all): 100.00% (0/0)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (0/0)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
nucleotide sensitivity (mRNA level): 100.00% (TP=0/(TP=0 + FN=0))
nucleotide specificity (mRNA level):   0.00% (TP=0/(TP=0 + FP=77))
nucleotide sensitivity (CDS level): 100.00% (TP=0/(TP=0 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=0/(TP=0 + FP=0))
genometools-1.5.1/testdata/gt_eval_test_3.out000066400000000000000000000054241211610345200213150ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (0/0) (missing genes: 0)
gene specificity (mRNA level):   0.00% (0/1) (wrong genes: 1)
gene sensitivity (CDS level): 100.00% (0/0) (missing genes: 0)
gene specificity (CDS level):   0.00% (0/1) (wrong genes: 1)
mRNA sensitivity (mRNA level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (mRNA level):   0.00% (0/1) (wrong mRNAs: 1)
mRNA sensitivity (CDS level): 100.00% (0/0) (missing mRNAs: 0)
mRNA specificity (CDS level):   0.00% (0/1) (wrong mRNAs: 1)
exon sensitivity (mRNA level, all): 100.00% (0/0)
exon specificity (mRNA level, all):   0.00% (0/2)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial): 100.00% (0/0)
exon specificity (mRNA level, initial):   0.00% (0/1)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (0/0)
exon specificity (mRNA level, terminal):   0.00% (0/1)
exon sensitivity (mRNA level, all, collapsed): 100.00% (0/0)
exon specificity (mRNA level, all, collapsed):   0.00% (0/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (0/0)
exon specificity (mRNA level, initial, collapsed):   0.00% (0/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, terminal, collapsed):   0.00% (0/1)
exon sensitivity (CDS level, all): 100.00% (0/0)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (0/0)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
genometools-1.5.1/testdata/gt_eval_test_3.prediction000066400000000000000000000003161211610345200226410ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	175	300	.	-	.	ID=gene
gDNA	.	mRNA	175	300	.	-	.	ID=mRNA;Parent=gene
gDNA	.	exon	175	200	.	-	.	Parent=mRNA
gDNA	.	exon	250	300	.	-	.	Parent=mRNA
genometools-1.5.1/testdata/gt_eval_test_3.reality000066400000000000000000000000621211610345200221500ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
genometools-1.5.1/testdata/gt_eval_test_4.nuc000066400000000000000000000060331211610345200212710ustar00rootroot00000000000000gene sensitivity (mRNA level):   0.00% (0/1) (missing genes: 1)
gene specificity (mRNA level): 100.00% (0/0) (wrong genes: 0)
gene sensitivity (CDS level):   0.00% (0/1) (missing genes: 1)
gene specificity (CDS level): 100.00% (0/0) (wrong genes: 0)
mRNA sensitivity (mRNA level):   0.00% (0/1) (missing mRNAs: 1)
mRNA specificity (mRNA level): 100.00% (0/0) (wrong mRNAs: 0)
mRNA sensitivity (CDS level):   0.00% (0/1) (missing mRNAs: 1)
mRNA specificity (CDS level): 100.00% (0/0) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all):   0.00% (0/2)
exon specificity (mRNA level, all): 100.00% (0/0)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial):   0.00% (0/1)
exon specificity (mRNA level, initial): 100.00% (0/0)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal):   0.00% (0/1)
exon specificity (mRNA level, terminal): 100.00% (0/0)
exon sensitivity (mRNA level, all, collapsed):   0.00% (0/2)
exon specificity (mRNA level, all, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed):   0.00% (0/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed):   0.00% (0/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, all): 100.00% (0/0)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (0/0)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
nucleotide sensitivity (mRNA level):   0.00% (TP=0/(TP=0 + FN=52))
nucleotide specificity (mRNA level): 100.00% (TP=0/(TP=0 + FP=0))
nucleotide sensitivity (CDS level): 100.00% (TP=0/(TP=0 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=0/(TP=0 + FP=0))
genometools-1.5.1/testdata/gt_eval_test_4.out000066400000000000000000000054241211610345200213160ustar00rootroot00000000000000gene sensitivity (mRNA level):   0.00% (0/1) (missing genes: 1)
gene specificity (mRNA level): 100.00% (0/0) (wrong genes: 0)
gene sensitivity (CDS level):   0.00% (0/1) (missing genes: 1)
gene specificity (CDS level): 100.00% (0/0) (wrong genes: 0)
mRNA sensitivity (mRNA level):   0.00% (0/1) (missing mRNAs: 1)
mRNA specificity (mRNA level): 100.00% (0/0) (wrong mRNAs: 0)
mRNA sensitivity (CDS level):   0.00% (0/1) (missing mRNAs: 1)
mRNA specificity (CDS level): 100.00% (0/0) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all):   0.00% (0/2)
exon specificity (mRNA level, all): 100.00% (0/0)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial):   0.00% (0/1)
exon specificity (mRNA level, initial): 100.00% (0/0)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal):   0.00% (0/1)
exon specificity (mRNA level, terminal): 100.00% (0/0)
exon sensitivity (mRNA level, all, collapsed):   0.00% (0/2)
exon specificity (mRNA level, all, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed):   0.00% (0/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed):   0.00% (0/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, all): 100.00% (0/0)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (0/0)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
genometools-1.5.1/testdata/gt_eval_test_4.prediction000066400000000000000000000000621211610345200226400ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
genometools-1.5.1/testdata/gt_eval_test_4.reality000066400000000000000000000003161211610345200221530ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA;Parent=gene
gDNA	.	exon	100	125	.	-	.	Parent=mRNA
gDNA	.	exon	175	200	.	-	.	Parent=mRNA
genometools-1.5.1/testdata/gt_eval_test_5.nuc000066400000000000000000000060421211610345200212720ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (1/1) (missing genes: 0)
gene specificity (mRNA level):  50.00% (1/2) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (1/1) (missing genes: 0)
gene specificity (CDS level):  50.00% (1/2) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):  50.00% (1/2) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (CDS level):  50.00% (1/2) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (2/2)
exon specificity (mRNA level, all):  50.00% (2/4)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial): 100.00% (1/1)
exon specificity (mRNA level, initial):  50.00% (1/2)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (1/1)
exon specificity (mRNA level, terminal):  50.00% (1/2)
exon sensitivity (mRNA level, all, collapsed): 100.00% (2/2)
exon specificity (mRNA level, all, collapsed): 100.00% (2/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (1/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, all): 100.00% (2/2)
exon specificity (CDS level, all):  50.00% (2/4)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (1/1)
exon specificity (CDS level, initial):  50.00% (1/2)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (1/1)
exon specificity (CDS level, terminal):  50.00% (1/2)
exon sensitivity (CDS level, all, collapsed): 100.00% (2/2)
exon specificity (CDS level, all, collapsed): 100.00% (2/2)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (1/1)
exon specificity (CDS level, initial, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (1/1)
exon specificity (CDS level, terminal, collapsed): 100.00% (1/1)
nucleotide sensitivity (mRNA level): 100.00% (TP=52/(TP=52 + FN=0))
nucleotide specificity (mRNA level): 100.00% (TP=52/(TP=52 + FP=0))
nucleotide sensitivity (CDS level): 100.00% (TP=52/(TP=52 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=52/(TP=52 + FP=0))
genometools-1.5.1/testdata/gt_eval_test_5.out000066400000000000000000000054241211610345200213170ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (1/1) (missing genes: 0)
gene specificity (mRNA level):  50.00% (1/2) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (1/1) (missing genes: 0)
gene specificity (CDS level):  50.00% (1/2) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):  50.00% (1/2) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (CDS level):  50.00% (1/2) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (2/2)
exon specificity (mRNA level, all):  50.00% (2/4)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial): 100.00% (1/1)
exon specificity (mRNA level, initial):  50.00% (1/2)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (1/1)
exon specificity (mRNA level, terminal):  50.00% (1/2)
exon sensitivity (mRNA level, all, collapsed): 100.00% (2/2)
exon specificity (mRNA level, all, collapsed): 100.00% (2/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (1/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, all): 100.00% (2/2)
exon specificity (CDS level, all):  50.00% (2/4)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (1/1)
exon specificity (CDS level, initial):  50.00% (1/2)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (1/1)
exon specificity (CDS level, terminal):  50.00% (1/2)
exon sensitivity (CDS level, all, collapsed): 100.00% (2/2)
exon specificity (CDS level, all, collapsed): 100.00% (2/2)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (1/1)
exon specificity (CDS level, initial, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (1/1)
exon specificity (CDS level, terminal, collapsed): 100.00% (1/1)
genometools-1.5.1/testdata/gt_eval_test_5.prediction000066400000000000000000000010241211610345200226400ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene1
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA1;Parent=gene1
gDNA	.	exon	100	125	.	-	.	Parent=mRNA1
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA1
gDNA	.	exon	175	200	.	-	.	Parent=mRNA1
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA1
###
gDNA	.	gene	100	200	.	-	.	ID=gene2
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA2;Parent=gene2
gDNA	.	exon	100	125	.	-	.	Parent=mRNA2
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA2
gDNA	.	exon	175	200	.	-	.	Parent=mRNA2
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA2
###
genometools-1.5.1/testdata/gt_eval_test_5.reality000066400000000000000000000004431211610345200221550ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene1
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA1;Parent=gene1
gDNA	.	exon	100	125	.	-	.	Parent=mRNA1
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA1
gDNA	.	exon	175	200	.	-	.	Parent=mRNA1
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_eval_test_6.nuc000066400000000000000000000060421211610345200212730ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (1/1) (missing genes: 0)
gene specificity (mRNA level):  50.00% (1/2) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (1/1) (missing genes: 0)
gene specificity (CDS level):  50.00% (1/2) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):  50.00% (1/2) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (CDS level):  50.00% (1/2) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (2/2)
exon specificity (mRNA level, all):  50.00% (2/4)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial): 100.00% (1/1)
exon specificity (mRNA level, initial):  50.00% (1/2)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (1/1)
exon specificity (mRNA level, terminal):  50.00% (1/2)
exon sensitivity (mRNA level, all, collapsed): 100.00% (2/2)
exon specificity (mRNA level, all, collapsed): 100.00% (2/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (1/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, all): 100.00% (2/2)
exon specificity (CDS level, all):  50.00% (2/4)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (1/1)
exon specificity (CDS level, initial):  50.00% (1/2)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (1/1)
exon specificity (CDS level, terminal):  50.00% (1/2)
exon sensitivity (CDS level, all, collapsed): 100.00% (2/2)
exon specificity (CDS level, all, collapsed): 100.00% (2/2)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (1/1)
exon specificity (CDS level, initial, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (1/1)
exon specificity (CDS level, terminal, collapsed): 100.00% (1/1)
nucleotide sensitivity (mRNA level): 100.00% (TP=52/(TP=52 + FN=0))
nucleotide specificity (mRNA level): 100.00% (TP=52/(TP=52 + FP=0))
nucleotide sensitivity (CDS level): 100.00% (TP=52/(TP=52 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=52/(TP=52 + FP=0))
genometools-1.5.1/testdata/gt_eval_test_6.out000066400000000000000000000054241211610345200213200ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (1/1) (missing genes: 0)
gene specificity (mRNA level):  50.00% (1/2) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (1/1) (missing genes: 0)
gene specificity (CDS level):  50.00% (1/2) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):  50.00% (1/2) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (CDS level):  50.00% (1/2) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (2/2)
exon specificity (mRNA level, all):  50.00% (2/4)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial): 100.00% (1/1)
exon specificity (mRNA level, initial):  50.00% (1/2)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (1/1)
exon specificity (mRNA level, terminal):  50.00% (1/2)
exon sensitivity (mRNA level, all, collapsed): 100.00% (2/2)
exon specificity (mRNA level, all, collapsed): 100.00% (2/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (1/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, all): 100.00% (2/2)
exon specificity (CDS level, all):  50.00% (2/4)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial): 100.00% (1/1)
exon specificity (CDS level, initial):  50.00% (1/2)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (1/1)
exon specificity (CDS level, terminal):  50.00% (1/2)
exon sensitivity (CDS level, all, collapsed): 100.00% (2/2)
exon specificity (CDS level, all, collapsed): 100.00% (2/2)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed): 100.00% (1/1)
exon specificity (CDS level, initial, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (1/1)
exon specificity (CDS level, terminal, collapsed): 100.00% (1/1)
genometools-1.5.1/testdata/gt_eval_test_6.prediction000066400000000000000000000010241211610345200226410ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene1
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA1;Parent=gene1
gDNA	.	exon	100	125	.	-	.	Parent=mRNA1
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA1
gDNA	.	exon	175	200	.	-	.	Parent=mRNA1
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA1
###
gDNA	.	gene	100	210	.	-	.	ID=gene2
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA2;Parent=gene2
gDNA	.	exon	100	125	.	-	.	Parent=mRNA2
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA2
gDNA	.	exon	175	200	.	-	.	Parent=mRNA2
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA2
###
genometools-1.5.1/testdata/gt_eval_test_6.reality000066400000000000000000000004431211610345200221560ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene1
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA1;Parent=gene1
gDNA	.	exon	100	125	.	-	.	Parent=mRNA1
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA1
gDNA	.	exon	175	200	.	-	.	Parent=mRNA1
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_eval_test_7.nuc000066400000000000000000000060421211610345200212740ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (1/1) (missing genes: 0)
gene specificity (mRNA level):  50.00% (1/2) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (1/1) (missing genes: 0)
gene specificity (CDS level):  50.00% (1/2) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):  50.00% (1/2) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (CDS level):  50.00% (1/2) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (2/2)
exon specificity (mRNA level, all):  66.67% (2/3)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single):   0.00% (0/1)
exon sensitivity (mRNA level, initial): 100.00% (1/1)
exon specificity (mRNA level, initial): 100.00% (1/1)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (1/1)
exon specificity (mRNA level, terminal): 100.00% (1/1)
exon sensitivity (mRNA level, all, collapsed): 100.00% (2/2)
exon specificity (mRNA level, all, collapsed): 100.00% (2/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed):   0.00% (0/1)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (1/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, all): 100.00% (2/2)
exon specificity (CDS level, all):  66.67% (2/3)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single):   0.00% (0/1)
exon sensitivity (CDS level, initial): 100.00% (1/1)
exon specificity (CDS level, initial): 100.00% (1/1)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (1/1)
exon specificity (CDS level, terminal): 100.00% (1/1)
exon sensitivity (CDS level, all, collapsed): 100.00% (2/2)
exon specificity (CDS level, all, collapsed):  66.67% (2/3)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed):   0.00% (0/1)
exon sensitivity (CDS level, initial, collapsed): 100.00% (1/1)
exon specificity (CDS level, initial, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (1/1)
exon specificity (CDS level, terminal, collapsed): 100.00% (1/1)
nucleotide sensitivity (mRNA level): 100.00% (TP=52/(TP=52 + FN=0))
nucleotide specificity (mRNA level): 100.00% (TP=52/(TP=52 + FP=0))
nucleotide sensitivity (CDS level): 100.00% (TP=52/(TP=52 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=52/(TP=52 + FP=0))
genometools-1.5.1/testdata/gt_eval_test_7.out000066400000000000000000000054241211610345200213210ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (1/1) (missing genes: 0)
gene specificity (mRNA level):  50.00% (1/2) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (1/1) (missing genes: 0)
gene specificity (CDS level):  50.00% (1/2) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):  50.00% (1/2) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (CDS level):  50.00% (1/2) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (2/2)
exon specificity (mRNA level, all):  66.67% (2/3)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single):   0.00% (0/1)
exon sensitivity (mRNA level, initial): 100.00% (1/1)
exon specificity (mRNA level, initial): 100.00% (1/1)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (1/1)
exon specificity (mRNA level, terminal): 100.00% (1/1)
exon sensitivity (mRNA level, all, collapsed): 100.00% (2/2)
exon specificity (mRNA level, all, collapsed): 100.00% (2/2)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed):   0.00% (0/1)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (1/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, all): 100.00% (2/2)
exon specificity (CDS level, all):  66.67% (2/3)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single):   0.00% (0/1)
exon sensitivity (CDS level, initial): 100.00% (1/1)
exon specificity (CDS level, initial): 100.00% (1/1)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (1/1)
exon specificity (CDS level, terminal): 100.00% (1/1)
exon sensitivity (CDS level, all, collapsed): 100.00% (2/2)
exon specificity (CDS level, all, collapsed):  66.67% (2/3)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed):   0.00% (0/1)
exon sensitivity (CDS level, initial, collapsed): 100.00% (1/1)
exon specificity (CDS level, initial, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (1/1)
exon specificity (CDS level, terminal, collapsed): 100.00% (1/1)
genometools-1.5.1/testdata/gt_eval_test_7.prediction000066400000000000000000000007071211610345200226510ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	125	.	-	.	ID=gene1
gDNA	.	mRNA	100	125	.	-	.	ID=mRNA1;Parent=gene1
gDNA	.	CDS	100	120	.	-	0	Parent=mRNA1
gDNA	.	exon	100	125	.	-	.	Parent=mRNA1
###
gDNA	.	gene	100	200	.	-	.	ID=gene2
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA2;Parent=gene2
gDNA	.	exon	100	125	.	-	.	Parent=mRNA2
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA2
gDNA	.	exon	175	200	.	-	.	Parent=mRNA2
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA2
###
genometools-1.5.1/testdata/gt_eval_test_7.reality000066400000000000000000000004431211610345200221570ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene1
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA1;Parent=gene1
gDNA	.	exon	100	125	.	-	.	Parent=mRNA1
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA1
gDNA	.	exon	175	200	.	-	.	Parent=mRNA1
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_eval_test_8.nuc000066400000000000000000000060421211610345200212750ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (1/1) (missing genes: 0)
gene specificity (mRNA level):  50.00% (1/2) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (1/1) (missing genes: 0)
gene specificity (CDS level):  50.00% (1/2) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):  50.00% (1/2) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (CDS level):  50.00% (1/2) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (2/2)
exon specificity (mRNA level, all):  66.67% (2/3)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single):   0.00% (0/1)
exon sensitivity (mRNA level, initial): 100.00% (1/1)
exon specificity (mRNA level, initial): 100.00% (1/1)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (1/1)
exon specificity (mRNA level, terminal): 100.00% (1/1)
exon sensitivity (mRNA level, all, collapsed): 100.00% (2/2)
exon specificity (mRNA level, all, collapsed):  66.67% (2/3)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed):   0.00% (0/1)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (1/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, all): 100.00% (2/2)
exon specificity (CDS level, all):  66.67% (2/3)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single):   0.00% (0/1)
exon sensitivity (CDS level, initial): 100.00% (1/1)
exon specificity (CDS level, initial): 100.00% (1/1)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (1/1)
exon specificity (CDS level, terminal): 100.00% (1/1)
exon sensitivity (CDS level, all, collapsed): 100.00% (2/2)
exon specificity (CDS level, all, collapsed): 100.00% (2/2)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed):   0.00% (0/1)
exon sensitivity (CDS level, initial, collapsed): 100.00% (1/1)
exon specificity (CDS level, initial, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (1/1)
exon specificity (CDS level, terminal, collapsed): 100.00% (1/1)
nucleotide sensitivity (mRNA level): 100.00% (TP=52/(TP=52 + FN=0))
nucleotide specificity (mRNA level):  91.23% (TP=52/(TP=52 + FP=5))
nucleotide sensitivity (CDS level): 100.00% (TP=52/(TP=52 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=52/(TP=52 + FP=0))
genometools-1.5.1/testdata/gt_eval_test_8.out000066400000000000000000000054241211610345200213220ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (1/1) (missing genes: 0)
gene specificity (mRNA level):  50.00% (1/2) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (1/1) (missing genes: 0)
gene specificity (CDS level):  50.00% (1/2) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (mRNA level):  50.00% (1/2) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (CDS level):  50.00% (1/2) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (2/2)
exon specificity (mRNA level, all):  66.67% (2/3)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single):   0.00% (0/1)
exon sensitivity (mRNA level, initial): 100.00% (1/1)
exon specificity (mRNA level, initial): 100.00% (1/1)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (1/1)
exon specificity (mRNA level, terminal): 100.00% (1/1)
exon sensitivity (mRNA level, all, collapsed): 100.00% (2/2)
exon specificity (mRNA level, all, collapsed):  66.67% (2/3)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed):   0.00% (0/1)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (1/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, all): 100.00% (2/2)
exon specificity (CDS level, all):  66.67% (2/3)
exon sensitivity (CDS level, single): 100.00% (0/0)
exon specificity (CDS level, single):   0.00% (0/1)
exon sensitivity (CDS level, initial): 100.00% (1/1)
exon specificity (CDS level, initial): 100.00% (1/1)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (1/1)
exon specificity (CDS level, terminal): 100.00% (1/1)
exon sensitivity (CDS level, all, collapsed): 100.00% (2/2)
exon specificity (CDS level, all, collapsed): 100.00% (2/2)
exon sensitivity (CDS level, single, collapsed): 100.00% (0/0)
exon specificity (CDS level, single, collapsed):   0.00% (0/1)
exon sensitivity (CDS level, initial, collapsed): 100.00% (1/1)
exon specificity (CDS level, initial, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (1/1)
exon specificity (CDS level, terminal, collapsed): 100.00% (1/1)
genometools-1.5.1/testdata/gt_eval_test_8.prediction000066400000000000000000000007071211610345200226520ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	125	.	-	.	ID=gene1
gDNA	.	mRNA	100	125	.	-	.	ID=mRNA1;Parent=gene1
gDNA	.	CDS	100	125	.	-	0	Parent=mRNA1
gDNA	.	exon	100	130	.	-	.	Parent=mRNA1
###
gDNA	.	gene	100	200	.	-	.	ID=gene2
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA2;Parent=gene2
gDNA	.	exon	100	125	.	-	.	Parent=mRNA2
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA2
gDNA	.	exon	175	200	.	-	.	Parent=mRNA2
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA2
###
genometools-1.5.1/testdata/gt_eval_test_8.reality000066400000000000000000000004431211610345200221600ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene1
gDNA	.	mRNA	100	200	.	-	.	ID=mRNA1;Parent=gene1
gDNA	.	exon	100	125	.	-	.	Parent=mRNA1
gDNA	.	CDS	100	125	.	-	1	Parent=mRNA1
gDNA	.	exon	175	200	.	-	.	Parent=mRNA1
gDNA	.	CDS	175	200	.	-	0	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_eval_test_9.in000066400000000000000000000003611211610345200211150ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 80
gDNA	.	gene	10	20	.	-	.	ID=gene1
gDNA	.	mRNA	10	20	.	-	.	ID=mRNA1;Parent=gene1
gDNA	.	exon	10	20	.	-	.	Parent=mRNA1
gDNA	.	CDS	10	20	.	-	0	Parent=mRNA1
gDNA	.	exon	10	20	.	-	.	Parent=mRNA1
###
genometools-1.5.1/testdata/gt_eval_test_9.out000066400000000000000000000060421211610345200213200ustar00rootroot00000000000000gene sensitivity (mRNA level): 100.00% (1/1) (missing genes: 0)
gene specificity (mRNA level): 100.00% (1/1) (wrong genes: 0)
gene sensitivity (CDS level): 100.00% (1/1) (missing genes: 0)
gene specificity (CDS level): 100.00% (1/1) (wrong genes: 0)
mRNA sensitivity (mRNA level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (mRNA level): 100.00% (1/1) (wrong mRNAs: 0)
mRNA sensitivity (CDS level): 100.00% (1/1) (missing mRNAs: 0)
mRNA specificity (CDS level): 100.00% (1/1) (wrong mRNAs: 0)
exon sensitivity (mRNA level, all): 100.00% (2/2)
exon specificity (mRNA level, all): 100.00% (2/2)
exon sensitivity (mRNA level, single): 100.00% (0/0)
exon specificity (mRNA level, single): 100.00% (0/0)
exon sensitivity (mRNA level, initial): 100.00% (1/1)
exon specificity (mRNA level, initial): 100.00% (1/1)
exon sensitivity (mRNA level, internal): 100.00% (0/0)
exon specificity (mRNA level, internal): 100.00% (0/0)
exon sensitivity (mRNA level, terminal): 100.00% (1/1)
exon specificity (mRNA level, terminal): 100.00% (1/1)
exon sensitivity (mRNA level, all, collapsed): 100.00% (1/1)
exon specificity (mRNA level, all, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, single, collapsed): 100.00% (0/0)
exon specificity (mRNA level, single, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, initial, collapsed): 100.00% (1/1)
exon specificity (mRNA level, initial, collapsed): 100.00% (1/1)
exon sensitivity (mRNA level, internal, collapsed): 100.00% (0/0)
exon specificity (mRNA level, internal, collapsed): 100.00% (0/0)
exon sensitivity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon specificity (mRNA level, terminal, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, all): 100.00% (1/1)
exon specificity (CDS level, all): 100.00% (1/1)
exon sensitivity (CDS level, single): 100.00% (1/1)
exon specificity (CDS level, single): 100.00% (1/1)
exon sensitivity (CDS level, initial): 100.00% (0/0)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal): 100.00% (0/0)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal): 100.00% (0/0)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed): 100.00% (1/1)
exon specificity (CDS level, all, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, single, collapsed): 100.00% (1/1)
exon specificity (CDS level, single, collapsed): 100.00% (1/1)
exon sensitivity (CDS level, initial, collapsed): 100.00% (0/0)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed): 100.00% (0/0)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed): 100.00% (0/0)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
nucleotide sensitivity (mRNA level): 100.00% (TP=11/(TP=11 + FN=0))
nucleotide specificity (mRNA level): 100.00% (TP=11/(TP=11 + FP=0))
nucleotide sensitivity (CDS level): 100.00% (TP=11/(TP=11 + FN=0))
nucleotide specificity (CDS level): 100.00% (TP=11/(TP=11 + FP=0))
genometools-1.5.1/testdata/gt_evalviz_test.out000066400000000000000000000051741211610345200216260ustar00rootroot00000000000000gene sensitivity:                0.00% (0/291) (missing genes: 43)
gene specificity:                0.00% (0/23) (wrong genes: 0)
mRNA sensitivity:              100.00% (0/0) (missing mRNAs: 0)
mRNA specificity:                0.00% (0/268) (wrong mRNAs: 268)
exon sensitivity (mRNA level, all):  93.79% (1962/2092)
exon specificity (mRNA level, all):  94.83% (1962/2069)
exon sensitivity (mRNA level, single):  25.00% (2/8)
exon specificity (mRNA level, single):  66.67% (2/3)
exon sensitivity (mRNA level, initial):  86.22% (244/283)
exon specificity (mRNA level, initial):  92.08% (244/265)
exon sensitivity (mRNA level, internal):  96.05% (1458/1518)
exon specificity (mRNA level, internal):  94.92% (1458/1536)
exon sensitivity (mRNA level, terminal):  88.69% (251/283)
exon specificity (mRNA level, terminal):  94.72% (251/265)
exon sensitivity (mRNA level, all, collapsed):  90.68% (759/837)
exon specificity (mRNA level, all, collapsed):  95.95% (759/791)
exon sensitivity (mRNA level, single, collapsed):  28.57% (2/7)
exon specificity (mRNA level, single, collapsed):  66.67% (2/3)
exon sensitivity (mRNA level, initial, collapsed):  86.51% (218/252)
exon specificity (mRNA level, initial, collapsed):  95.20% (218/229)
exon sensitivity (mRNA level, internal, collapsed):  95.65% (330/345)
exon specificity (mRNA level, internal, collapsed):  94.29% (330/350)
exon sensitivity (mRNA level, terminal, collapsed):  88.48% (215/243)
exon specificity (mRNA level, terminal, collapsed):  97.73% (215/220)
exon sensitivity (CDS level, all):   0.00% (0/994)
exon specificity (CDS level, all): 100.00% (0/0)
exon sensitivity (CDS level, single):   0.00% (0/18)
exon specificity (CDS level, single): 100.00% (0/0)
exon sensitivity (CDS level, initial):   0.00% (0/102)
exon specificity (CDS level, initial): 100.00% (0/0)
exon sensitivity (CDS level, internal):   0.00% (0/772)
exon specificity (CDS level, internal): 100.00% (0/0)
exon sensitivity (CDS level, terminal):   0.00% (0/102)
exon specificity (CDS level, terminal): 100.00% (0/0)
exon sensitivity (CDS level, all, collapsed):   0.00% (0/382)
exon specificity (CDS level, all, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, single, collapsed):   0.00% (0/15)
exon specificity (CDS level, single, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, initial, collapsed):   0.00% (0/68)
exon specificity (CDS level, initial, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, internal, collapsed):   0.00% (0/246)
exon specificity (CDS level, internal, collapsed): 100.00% (0/0)
exon sensitivity (CDS level, terminal, collapsed):   0.00% (0/59)
exon specificity (CDS level, terminal, collapsed): 100.00% (0/0)
genometools-1.5.1/testdata/gt_evalviz_test.prediction000066400000000000000000007251771211610345200231730ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr21 1 4294967295
chr21	gth	gene	32669578	32687206	.	-	.	ID=gene1
chr21	gth	mRNA	32669578	32687206	.	-	.	ID=mRNA1;Parent=gene1
chr21	gth	exon	32669578	32669663	1.000000	-	.	Parent=mRNA1
chr21	.	intron	32669664	32672624	.	-	.	Parent=mRNA1
chr21	gth	exon	32672625	32672721	1.000000	-	.	Parent=mRNA1
chr21	.	intron	32672722	32677601	.	-	.	Parent=mRNA1
chr21	gth	exon	32677602	32677734	1.000000	-	.	Parent=mRNA1
chr21	.	intron	32677735	32678492	.	-	.	Parent=mRNA1
chr21	gth	exon	32678493	32678644	1.000000	-	.	Parent=mRNA1
chr21	.	intron	32678645	32679724	.	-	.	Parent=mRNA1
chr21	gth	exon	32679725	32679864	1.000000	-	.	Parent=mRNA1
chr21	.	intron	32679865	32686948	.	-	.	Parent=mRNA1
chr21	gth	exon	32686949	32687206	1.000000	-	.	Parent=mRNA1
###
chr21	gth	gene	32706185	32809570	.	+	.	ID=gene2
chr21	gth	mRNA	32706185	32762234	.	+	.	ID=mRNA2;Parent=gene2
chr21	gth	exon	32706185	32707192	1.000000	+	.	Parent=mRNA2
chr21	.	intron	32707193	32747490	.	+	.	Parent=mRNA2
chr21	gth	exon	32747491	32747687	1.000000	+	.	Parent=mRNA2
chr21	.	intron	32747688	32751775	.	+	.	Parent=mRNA2
chr21	gth	exon	32751776	32751899	1.000000	+	.	Parent=mRNA2
chr21	.	intron	32751900	32761874	.	+	.	Parent=mRNA2
chr21	gth	exon	32761875	32762234	1.000000	+	.	Parent=mRNA2
chr21	gth	mRNA	32706221	32795636	.	+	.	ID=mRNA3;Parent=gene2
chr21	gth	exon	32706221	32706372	1.000000	+	.	Parent=mRNA3
chr21	.	intron	32706373	32747490	.	+	.	Parent=mRNA3
chr21	gth	exon	32747491	32747687	1.000000	+	.	Parent=mRNA3
chr21	.	intron	32747688	32761874	.	+	.	Parent=mRNA3
chr21	gth	exon	32761875	32762027	1.000000	+	.	Parent=mRNA3
chr21	.	intron	32762028	32789207	.	+	.	Parent=mRNA3
chr21	gth	exon	32789208	32789351	1.000000	+	.	Parent=mRNA3
chr21	.	intron	32789352	32795595	.	+	.	Parent=mRNA3
chr21	gth	exon	32795596	32795636	1.000000	+	.	Parent=mRNA3
chr21	gth	mRNA	32706560	32809570	.	+	.	ID=mRNA4;Parent=gene2
chr21	gth	exon	32706560	32707192	1.000000	+	.	Parent=mRNA4
chr21	.	intron	32707193	32747490	.	+	.	Parent=mRNA4
chr21	gth	exon	32747491	32747687	1.000000	+	.	Parent=mRNA4
chr21	.	intron	32747688	32751775	.	+	.	Parent=mRNA4
chr21	gth	exon	32751776	32751899	1.000000	+	.	Parent=mRNA4
chr21	.	intron	32751900	32761874	.	+	.	Parent=mRNA4
chr21	gth	exon	32761875	32762027	1.000000	+	.	Parent=mRNA4
chr21	.	intron	32762028	32789207	.	+	.	Parent=mRNA4
chr21	gth	exon	32789208	32789351	1.000000	+	.	Parent=mRNA4
chr21	.	intron	32789352	32795595	.	+	.	Parent=mRNA4
chr21	gth	exon	32795596	32795676	1.000000	+	.	Parent=mRNA4
chr21	.	intron	32795677	32798106	.	+	.	Parent=mRNA4
chr21	gth	exon	32798107	32798196	1.000000	+	.	Parent=mRNA4
chr21	.	intron	32798197	32808994	.	+	.	Parent=mRNA4
chr21	gth	exon	32808995	32809570	1.000000	+	.	Parent=mRNA4
chr21	gth	mRNA	32706616	32809570	.	+	.	ID=mRNA5;Parent=gene2
chr21	gth	exon	32706616	32707192	1.000000	+	.	Parent=mRNA5
chr21	.	intron	32707193	32751775	.	+	.	Parent=mRNA5
chr21	gth	exon	32751776	32751899	1.000000	+	.	Parent=mRNA5
chr21	.	intron	32751900	32761874	.	+	.	Parent=mRNA5
chr21	gth	exon	32761875	32762027	1.000000	+	.	Parent=mRNA5
chr21	.	intron	32762028	32789207	.	+	.	Parent=mRNA5
chr21	gth	exon	32789208	32789351	1.000000	+	.	Parent=mRNA5
chr21	.	intron	32789352	32795595	.	+	.	Parent=mRNA5
chr21	gth	exon	32795596	32795676	1.000000	+	.	Parent=mRNA5
chr21	.	intron	32795677	32798106	.	+	.	Parent=mRNA5
chr21	gth	exon	32798107	32798196	1.000000	+	.	Parent=mRNA5
chr21	.	intron	32798197	32808994	.	+	.	Parent=mRNA5
chr21	gth	exon	32808995	32809570	1.000000	+	.	Parent=mRNA5
chr21	gth	mRNA	32706616	32809570	.	+	.	ID=mRNA6;Parent=gene2
chr21	gth	exon	32706616	32707192	1.000000	+	.	Parent=mRNA6
chr21	.	intron	32707193	32751775	.	+	.	Parent=mRNA6
chr21	gth	exon	32751776	32751899	1.000000	+	.	Parent=mRNA6
chr21	.	intron	32751900	32761874	.	+	.	Parent=mRNA6
chr21	gth	exon	32761875	32762027	1.000000	+	.	Parent=mRNA6
chr21	.	intron	32762028	32795595	.	+	.	Parent=mRNA6
chr21	gth	exon	32795596	32795676	1.000000	+	.	Parent=mRNA6
chr21	.	intron	32795677	32798106	.	+	.	Parent=mRNA6
chr21	gth	exon	32798107	32798196	1.000000	+	.	Parent=mRNA6
chr21	.	intron	32798197	32808994	.	+	.	Parent=mRNA6
chr21	gth	exon	32808995	32809570	1.000000	+	.	Parent=mRNA6
chr21	gth	mRNA	32706732	32809570	.	+	.	ID=mRNA7;Parent=gene2
chr21	gth	exon	32706732	32707192	1.000000	+	.	Parent=mRNA7
chr21	.	intron	32707193	32761874	.	+	.	Parent=mRNA7
chr21	gth	exon	32761875	32762027	1.000000	+	.	Parent=mRNA7
chr21	.	intron	32762028	32789207	.	+	.	Parent=mRNA7
chr21	gth	exon	32789208	32789351	1.000000	+	.	Parent=mRNA7
chr21	.	intron	32789352	32795595	.	+	.	Parent=mRNA7
chr21	gth	exon	32795596	32795719	1.000000	+	.	Parent=mRNA7
chr21	.	intron	32795720	32798106	.	+	.	Parent=mRNA7
chr21	gth	exon	32798107	32798196	1.000000	+	.	Parent=mRNA7
chr21	.	intron	32798197	32808994	.	+	.	Parent=mRNA7
chr21	gth	exon	32808995	32809570	1.000000	+	.	Parent=mRNA7
chr21	gth	mRNA	32706881	32809570	.	+	.	ID=mRNA8;Parent=gene2
chr21	gth	exon	32706881	32707192	1.000000	+	.	Parent=mRNA8
chr21	.	intron	32707193	32747490	.	+	.	Parent=mRNA8
chr21	gth	exon	32747491	32747687	1.000000	+	.	Parent=mRNA8
chr21	.	intron	32747688	32751775	.	+	.	Parent=mRNA8
chr21	gth	exon	32751776	32751899	1.000000	+	.	Parent=mRNA8
chr21	.	intron	32751900	32761874	.	+	.	Parent=mRNA8
chr21	gth	exon	32761875	32762027	1.000000	+	.	Parent=mRNA8
chr21	.	intron	32762028	32789207	.	+	.	Parent=mRNA8
chr21	gth	exon	32789208	32789351	1.000000	+	.	Parent=mRNA8
chr21	.	intron	32789352	32795595	.	+	.	Parent=mRNA8
chr21	gth	exon	32795596	32795667	1.000000	+	.	Parent=mRNA8
chr21	.	intron	32795668	32798106	.	+	.	Parent=mRNA8
chr21	gth	exon	32798107	32798196	1.000000	+	.	Parent=mRNA8
chr21	.	intron	32798197	32808994	.	+	.	Parent=mRNA8
chr21	gth	exon	32808995	32809570	1.000000	+	.	Parent=mRNA8
chr21	gth	mRNA	32706943	32727463	.	+	.	ID=mRNA9;Parent=gene2
chr21	gth	exon	32706943	32707192	1.000000	+	.	Parent=mRNA9
chr21	.	intron	32707193	32727329	.	+	.	Parent=mRNA9
chr21	gth	exon	32727330	32727463	1.000000	+	.	Parent=mRNA9
chr21	gth	mRNA	32722513	32809570	.	+	.	ID=mRNA10;Parent=gene2
chr21	gth	exon	32722513	32722863	1.000000	+	.	Parent=mRNA10
chr21	.	intron	32722864	32747490	.	+	.	Parent=mRNA10
chr21	gth	exon	32747491	32747687	1.000000	+	.	Parent=mRNA10
chr21	.	intron	32747688	32751775	.	+	.	Parent=mRNA10
chr21	gth	exon	32751776	32751899	1.000000	+	.	Parent=mRNA10
chr21	.	intron	32751900	32761874	.	+	.	Parent=mRNA10
chr21	gth	exon	32761875	32762027	1.000000	+	.	Parent=mRNA10
chr21	.	intron	32762028	32789207	.	+	.	Parent=mRNA10
chr21	gth	exon	32789208	32789351	1.000000	+	.	Parent=mRNA10
chr21	.	intron	32789352	32798106	.	+	.	Parent=mRNA10
chr21	gth	exon	32798107	32798196	1.000000	+	.	Parent=mRNA10
chr21	.	intron	32798197	32808994	.	+	.	Parent=mRNA10
chr21	gth	exon	32808995	32809570	1.000000	+	.	Parent=mRNA10
chr21	gth	mRNA	32746364	32809570	.	+	.	ID=mRNA11;Parent=gene2
chr21	gth	exon	32746364	32747687	1.000000	+	.	Parent=mRNA11
chr21	.	intron	32747688	32751775	.	+	.	Parent=mRNA11
chr21	gth	exon	32751776	32751899	1.000000	+	.	Parent=mRNA11
chr21	.	intron	32751900	32761874	.	+	.	Parent=mRNA11
chr21	gth	exon	32761875	32762027	1.000000	+	.	Parent=mRNA11
chr21	.	intron	32762028	32789207	.	+	.	Parent=mRNA11
chr21	gth	exon	32789208	32789351	1.000000	+	.	Parent=mRNA11
chr21	.	intron	32789352	32795595	.	+	.	Parent=mRNA11
chr21	gth	exon	32795596	32795676	1.000000	+	.	Parent=mRNA11
chr21	.	intron	32795677	32798106	.	+	.	Parent=mRNA11
chr21	gth	exon	32798107	32798196	1.000000	+	.	Parent=mRNA11
chr21	.	intron	32798197	32808994	.	+	.	Parent=mRNA11
chr21	gth	exon	32808995	32809570	1.000000	+	.	Parent=mRNA11
chr21	gth	mRNA	32787834	32809061	.	+	.	ID=mRNA12;Parent=gene2
chr21	gth	exon	32787834	32787943	1.000000	+	.	Parent=mRNA12
chr21	.	intron	32787944	32789207	.	+	.	Parent=mRNA12
chr21	gth	exon	32789208	32789351	1.000000	+	.	Parent=mRNA12
chr21	.	intron	32789352	32795595	.	+	.	Parent=mRNA12
chr21	gth	exon	32795596	32795676	1.000000	+	.	Parent=mRNA12
chr21	.	intron	32795677	32798106	.	+	.	Parent=mRNA12
chr21	gth	exon	32798107	32798196	1.000000	+	.	Parent=mRNA12
chr21	.	intron	32798197	32808994	.	+	.	Parent=mRNA12
chr21	gth	exon	32808995	32809061	1.000000	+	.	Parent=mRNA12
###
chr21	gth	gene	32870733	32907047	.	-	.	ID=gene3
chr21	gth	mRNA	32870733	32879714	.	-	.	ID=mRNA13;Parent=gene3
chr21	gth	exon	32870733	32871104	1.000000	-	.	Parent=mRNA13
chr21	.	intron	32871105	32872874	.	-	.	Parent=mRNA13
chr21	gth	exon	32872875	32873012	1.000000	-	.	Parent=mRNA13
chr21	.	intron	32873013	32876380	.	-	.	Parent=mRNA13
chr21	gth	exon	32876381	32876596	1.000000	-	.	Parent=mRNA13
chr21	.	intron	32876597	32878341	.	-	.	Parent=mRNA13
chr21	gth	exon	32878342	32878486	1.000000	-	.	Parent=mRNA13
chr21	.	intron	32878487	32879601	.	-	.	Parent=mRNA13
chr21	gth	exon	32879602	32879714	1.000000	-	.	Parent=mRNA13
chr21	gth	mRNA	32870840	32876615	.	-	.	ID=mRNA14;Parent=gene3
chr21	gth	exon	32870840	32871104	1.000000	-	.	Parent=mRNA14
chr21	.	intron	32871105	32871606	.	-	.	Parent=mRNA14
chr21	gth	exon	32871607	32871857	1.000000	-	.	Parent=mRNA14
chr21	.	intron	32871858	32872874	.	-	.	Parent=mRNA14
chr21	gth	exon	32872875	32873012	1.000000	-	.	Parent=mRNA14
chr21	.	intron	32873013	32876380	.	-	.	Parent=mRNA14
chr21	gth	exon	32876381	32876615	1.000000	-	.	Parent=mRNA14
chr21	gth	mRNA	32870840	32879714	.	-	.	ID=mRNA15;Parent=gene3
chr21	gth	exon	32870840	32871104	1.000000	-	.	Parent=mRNA15
chr21	.	intron	32871105	32872874	.	-	.	Parent=mRNA15
chr21	gth	exon	32872875	32873012	1.000000	-	.	Parent=mRNA15
chr21	.	intron	32873013	32876380	.	-	.	Parent=mRNA15
chr21	gth	exon	32876381	32876596	1.000000	-	.	Parent=mRNA15
chr21	.	intron	32876597	32879601	.	-	.	Parent=mRNA15
chr21	gth	exon	32879602	32879714	1.000000	-	.	Parent=mRNA15
chr21	gth	mRNA	32876381	32906327	.	-	.	ID=mRNA16;Parent=gene3
chr21	gth	exon	32876381	32876596	1.000000	-	.	Parent=mRNA16
chr21	.	intron	32876597	32896452	.	-	.	Parent=mRNA16
chr21	gth	exon	32896453	32896548	1.000000	-	.	Parent=mRNA16
chr21	.	intron	32896549	32897341	.	-	.	Parent=mRNA16
chr21	gth	exon	32897342	32897473	1.000000	-	.	Parent=mRNA16
chr21	.	intron	32897474	32898305	.	-	.	Parent=mRNA16
chr21	gth	exon	32898306	32898464	1.000000	-	.	Parent=mRNA16
chr21	.	intron	32898465	32901829	.	-	.	Parent=mRNA16
chr21	gth	exon	32901830	32901897	1.000000	-	.	Parent=mRNA16
chr21	.	intron	32901898	32904018	.	-	.	Parent=mRNA16
chr21	gth	exon	32904019	32904186	1.000000	-	.	Parent=mRNA16
chr21	.	intron	32904187	32906285	.	-	.	Parent=mRNA16
chr21	gth	exon	32906286	32906327	1.000000	-	.	Parent=mRNA16
chr21	gth	mRNA	32876381	32906462	.	-	.	ID=mRNA17;Parent=gene3
chr21	gth	exon	32876381	32876596	1.000000	-	.	Parent=mRNA17
chr21	.	intron	32876597	32897341	.	-	.	Parent=mRNA17
chr21	gth	exon	32897342	32897473	1.000000	-	.	Parent=mRNA17
chr21	.	intron	32897474	32898305	.	-	.	Parent=mRNA17
chr21	gth	exon	32898306	32898464	1.000000	-	.	Parent=mRNA17
chr21	.	intron	32898465	32901829	.	-	.	Parent=mRNA17
chr21	gth	exon	32901830	32901897	1.000000	-	.	Parent=mRNA17
chr21	.	intron	32901898	32904018	.	-	.	Parent=mRNA17
chr21	gth	exon	32904019	32904186	1.000000	-	.	Parent=mRNA17
chr21	.	intron	32904187	32906285	.	-	.	Parent=mRNA17
chr21	gth	exon	32906286	32906462	1.000000	-	.	Parent=mRNA17
chr21	gth	mRNA	32876405	32901879	.	-	.	ID=mRNA18;Parent=gene3
chr21	gth	exon	32876405	32876596	1.000000	-	.	Parent=mRNA18
chr21	.	intron	32876597	32898305	.	-	.	Parent=mRNA18
chr21	gth	exon	32898306	32898464	1.000000	-	.	Parent=mRNA18
chr21	.	intron	32898465	32901829	.	-	.	Parent=mRNA18
chr21	gth	exon	32901830	32901879	1.000000	-	.	Parent=mRNA18
chr21	gth	mRNA	32886260	32906736	.	-	.	ID=mRNA19;Parent=gene3
chr21	gth	exon	32886260	32886599	1.000000	-	.	Parent=mRNA19
chr21	.	intron	32886600	32897341	.	-	.	Parent=mRNA19
chr21	gth	exon	32897342	32897473	1.000000	-	.	Parent=mRNA19
chr21	.	intron	32897474	32898305	.	-	.	Parent=mRNA19
chr21	gth	exon	32898306	32898464	1.000000	-	.	Parent=mRNA19
chr21	.	intron	32898465	32901829	.	-	.	Parent=mRNA19
chr21	gth	exon	32901830	32901897	1.000000	-	.	Parent=mRNA19
chr21	.	intron	32901898	32904018	.	-	.	Parent=mRNA19
chr21	gth	exon	32904019	32904135	1.000000	-	.	Parent=mRNA19
chr21	.	intron	32904136	32906285	.	-	.	Parent=mRNA19
chr21	gth	exon	32906286	32906736	1.000000	-	.	Parent=mRNA19
chr21	gth	mRNA	32895848	32906736	.	-	.	ID=mRNA20;Parent=gene3
chr21	gth	exon	32895848	32896154	1.000000	-	.	Parent=mRNA20
chr21	.	intron	32896155	32897341	.	-	.	Parent=mRNA20
chr21	gth	exon	32897342	32897473	1.000000	-	.	Parent=mRNA20
chr21	.	intron	32897474	32898305	.	-	.	Parent=mRNA20
chr21	gth	exon	32898306	32898464	1.000000	-	.	Parent=mRNA20
chr21	.	intron	32898465	32901829	.	-	.	Parent=mRNA20
chr21	gth	exon	32901830	32901897	1.000000	-	.	Parent=mRNA20
chr21	.	intron	32901898	32904018	.	-	.	Parent=mRNA20
chr21	gth	exon	32904019	32904135	1.000000	-	.	Parent=mRNA20
chr21	.	intron	32904136	32906285	.	-	.	Parent=mRNA20
chr21	gth	exon	32906286	32906736	1.000000	-	.	Parent=mRNA20
chr21	gth	mRNA	32895848	32906767	.	-	.	ID=mRNA21;Parent=gene3
chr21	gth	exon	32895848	32897473	1.000000	-	.	Parent=mRNA21
chr21	.	intron	32897474	32898305	.	-	.	Parent=mRNA21
chr21	gth	exon	32898306	32898464	1.000000	-	.	Parent=mRNA21
chr21	.	intron	32898465	32901829	.	-	.	Parent=mRNA21
chr21	gth	exon	32901830	32901897	1.000000	-	.	Parent=mRNA21
chr21	.	intron	32901898	32904018	.	-	.	Parent=mRNA21
chr21	gth	exon	32904019	32904186	1.000000	-	.	Parent=mRNA21
chr21	.	intron	32904187	32906285	.	-	.	Parent=mRNA21
chr21	gth	exon	32906286	32906767	1.000000	-	.	Parent=mRNA21
chr21	gth	mRNA	32895848	32907047	.	-	.	ID=mRNA22;Parent=gene3
chr21	gth	exon	32895848	32896154	1.000000	-	.	Parent=mRNA22
chr21	.	intron	32896155	32896452	.	-	.	Parent=mRNA22
chr21	gth	exon	32896453	32896548	1.000000	-	.	Parent=mRNA22
chr21	.	intron	32896549	32897341	.	-	.	Parent=mRNA22
chr21	gth	exon	32897342	32897473	1.000000	-	.	Parent=mRNA22
chr21	.	intron	32897474	32898305	.	-	.	Parent=mRNA22
chr21	gth	exon	32898306	32898464	1.000000	-	.	Parent=mRNA22
chr21	.	intron	32898465	32901829	.	-	.	Parent=mRNA22
chr21	gth	exon	32901830	32901897	1.000000	-	.	Parent=mRNA22
chr21	.	intron	32901898	32904018	.	-	.	Parent=mRNA22
chr21	gth	exon	32904019	32904186	1.000000	-	.	Parent=mRNA22
chr21	.	intron	32904187	32906285	.	-	.	Parent=mRNA22
chr21	gth	exon	32906286	32907047	1.000000	-	.	Parent=mRNA22
chr21	gth	mRNA	32895884	32906736	.	-	.	ID=mRNA23;Parent=gene3
chr21	gth	exon	32895884	32896548	1.000000	-	.	Parent=mRNA23
chr21	.	intron	32896549	32897341	.	-	.	Parent=mRNA23
chr21	gth	exon	32897342	32897473	1.000000	-	.	Parent=mRNA23
chr21	.	intron	32897474	32898305	.	-	.	Parent=mRNA23
chr21	gth	exon	32898306	32898464	1.000000	-	.	Parent=mRNA23
chr21	.	intron	32898465	32901829	.	-	.	Parent=mRNA23
chr21	gth	exon	32901830	32901897	1.000000	-	.	Parent=mRNA23
chr21	.	intron	32901898	32904018	.	-	.	Parent=mRNA23
chr21	gth	exon	32904019	32904135	1.000000	-	.	Parent=mRNA23
chr21	.	intron	32904136	32906285	.	-	.	Parent=mRNA23
chr21	gth	exon	32906286	32906736	1.000000	-	.	Parent=mRNA23
chr21	gth	mRNA	32895966	32906784	.	-	.	ID=mRNA24;Parent=gene3
chr21	gth	exon	32895966	32896154	1.000000	-	.	Parent=mRNA24
chr21	.	intron	32896155	32896452	.	-	.	Parent=mRNA24
chr21	gth	exon	32896453	32896548	1.000000	-	.	Parent=mRNA24
chr21	.	intron	32896549	32897341	.	-	.	Parent=mRNA24
chr21	gth	exon	32897342	32897473	1.000000	-	.	Parent=mRNA24
chr21	.	intron	32897474	32898305	.	-	.	Parent=mRNA24
chr21	gth	exon	32898306	32898464	1.000000	-	.	Parent=mRNA24
chr21	.	intron	32898465	32904018	.	-	.	Parent=mRNA24
chr21	gth	exon	32904019	32904186	1.000000	-	.	Parent=mRNA24
chr21	.	intron	32904187	32906285	.	-	.	Parent=mRNA24
chr21	gth	exon	32906286	32906784	1.000000	-	.	Parent=mRNA24
chr21	gth	mRNA	32895991	32898694	.	-	.	ID=mRNA25;Parent=gene3
chr21	gth	exon	32895991	32897473	1.000000	-	.	Parent=mRNA25
chr21	.	intron	32897474	32898305	.	-	.	Parent=mRNA25
chr21	gth	exon	32898306	32898694	1.000000	-	.	Parent=mRNA25
###
chr21	gth	gene	32922944	33022183	.	-	.	ID=gene4
chr21	gth	mRNA	32922944	33022105	.	-	.	ID=mRNA26;Parent=gene4
chr21	gth	exon	32922944	32925982	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32925983	32929041	.	-	.	Parent=mRNA26
chr21	gth	exon	32929042	32929065	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32929066	32933088	.	-	.	Parent=mRNA26
chr21	gth	exon	32933089	32933306	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32933307	32933851	.	-	.	Parent=mRNA26
chr21	gth	exon	32933852	32933960	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32933961	32936076	.	-	.	Parent=mRNA26
chr21	gth	exon	32936077	32936147	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32936148	32936275	.	-	.	Parent=mRNA26
chr21	gth	exon	32936276	32936314	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32936315	32939148	.	-	.	Parent=mRNA26
chr21	gth	exon	32939149	32939187	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32939188	32939826	.	-	.	Parent=mRNA26
chr21	gth	exon	32939827	32939894	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32939895	32939942	.	-	.	Parent=mRNA26
chr21	gth	exon	32939943	32939970	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32939971	32940573	.	-	.	Parent=mRNA26
chr21	gth	exon	32940574	32940783	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32940784	32944364	.	-	.	Parent=mRNA26
chr21	gth	exon	32944365	32944527	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32944528	32947468	.	-	.	Parent=mRNA26
chr21	gth	exon	32947469	32947547	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32947548	32950867	.	-	.	Parent=mRNA26
chr21	gth	exon	32950868	32951083	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32951084	32951183	.	-	.	Parent=mRNA26
chr21	gth	exon	32951184	32951301	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32951302	32951896	.	-	.	Parent=mRNA26
chr21	gth	exon	32951897	32952053	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32952054	32959093	.	-	.	Parent=mRNA26
chr21	gth	exon	32959094	32959252	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32959253	32960123	.	-	.	Parent=mRNA26
chr21	gth	exon	32960124	32960316	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32960317	32960613	.	-	.	Parent=mRNA26
chr21	gth	exon	32960614	32960754	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32960755	32964468	.	-	.	Parent=mRNA26
chr21	gth	exon	32964469	32964553	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32964554	32967520	.	-	.	Parent=mRNA26
chr21	gth	exon	32967521	32967712	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32967713	32967727	.	-	.	Parent=mRNA26
chr21	gth	exon	32967728	32967743	0.500000	-	.	Parent=mRNA26
chr21	.	intron	32967744	32972773	.	-	.	Parent=mRNA26
chr21	gth	exon	32972774	32972782	0.555556	-	.	Parent=mRNA26
chr21	.	intron	32972783	32972825	.	-	.	Parent=mRNA26
chr21	gth	exon	32972826	32972982	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32972983	32975676	.	-	.	Parent=mRNA26
chr21	gth	exon	32975677	32975829	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32975830	32978218	.	-	.	Parent=mRNA26
chr21	gth	exon	32978219	32978300	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32978301	32979928	.	-	.	Parent=mRNA26
chr21	gth	exon	32979929	32980098	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32980099	32981158	.	-	.	Parent=mRNA26
chr21	gth	exon	32981159	32981255	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32981256	32982486	.	-	.	Parent=mRNA26
chr21	gth	exon	32982487	32982548	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32982549	32988408	.	-	.	Parent=mRNA26
chr21	gth	exon	32988409	32988492	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32988493	32989237	.	-	.	Parent=mRNA26
chr21	gth	exon	32989238	32989463	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32989464	32994018	.	-	.	Parent=mRNA26
chr21	gth	exon	32994019	32994286	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32994287	32996141	.	-	.	Parent=mRNA26
chr21	gth	exon	32996142	32996228	1.000000	-	.	Parent=mRNA26
chr21	.	intron	32996229	33020953	.	-	.	Parent=mRNA26
chr21	gth	exon	33020954	33021099	1.000000	-	.	Parent=mRNA26
chr21	.	intron	33021100	33022018	.	-	.	Parent=mRNA26
chr21	gth	exon	33022019	33022105	1.000000	-	.	Parent=mRNA26
chr21	gth	mRNA	32922945	33022183	.	-	.	ID=mRNA27;Parent=gene4
chr21	gth	exon	32922945	32925982	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32925983	32929041	.	-	.	Parent=mRNA27
chr21	gth	exon	32929042	32929065	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32929066	32933088	.	-	.	Parent=mRNA27
chr21	gth	exon	32933089	32933306	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32933307	32933851	.	-	.	Parent=mRNA27
chr21	gth	exon	32933852	32933960	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32933961	32936076	.	-	.	Parent=mRNA27
chr21	gth	exon	32936077	32936147	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32936148	32936275	.	-	.	Parent=mRNA27
chr21	gth	exon	32936276	32936314	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32936315	32937590	.	-	.	Parent=mRNA27
chr21	gth	exon	32937591	32937638	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32937639	32939148	.	-	.	Parent=mRNA27
chr21	gth	exon	32939149	32939187	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32939188	32939826	.	-	.	Parent=mRNA27
chr21	gth	exon	32939827	32939970	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32939971	32940573	.	-	.	Parent=mRNA27
chr21	gth	exon	32940574	32940783	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32940784	32944364	.	-	.	Parent=mRNA27
chr21	gth	exon	32944365	32944527	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32944528	32947468	.	-	.	Parent=mRNA27
chr21	gth	exon	32947469	32947547	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32947548	32950867	.	-	.	Parent=mRNA27
chr21	gth	exon	32950868	32951083	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32951084	32951183	.	-	.	Parent=mRNA27
chr21	gth	exon	32951184	32951301	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32951302	32951896	.	-	.	Parent=mRNA27
chr21	gth	exon	32951897	32952053	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32952054	32959093	.	-	.	Parent=mRNA27
chr21	gth	exon	32959094	32959252	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32959253	32960123	.	-	.	Parent=mRNA27
chr21	gth	exon	32960124	32960316	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32960317	32960613	.	-	.	Parent=mRNA27
chr21	gth	exon	32960614	32960754	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32960755	32964468	.	-	.	Parent=mRNA27
chr21	gth	exon	32964469	32964553	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32964554	32967520	.	-	.	Parent=mRNA27
chr21	gth	exon	32967521	32967712	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32967713	32967727	.	-	.	Parent=mRNA27
chr21	gth	exon	32967728	32967743	0.500000	-	.	Parent=mRNA27
chr21	.	intron	32967744	32972773	.	-	.	Parent=mRNA27
chr21	gth	exon	32972774	32972782	0.555556	-	.	Parent=mRNA27
chr21	.	intron	32972783	32972825	.	-	.	Parent=mRNA27
chr21	gth	exon	32972826	32972982	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32972983	32975676	.	-	.	Parent=mRNA27
chr21	gth	exon	32975677	32975829	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32975830	32978218	.	-	.	Parent=mRNA27
chr21	gth	exon	32978219	32978300	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32978301	32979928	.	-	.	Parent=mRNA27
chr21	gth	exon	32979929	32980098	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32980099	32981158	.	-	.	Parent=mRNA27
chr21	gth	exon	32981159	32981255	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32981256	32982486	.	-	.	Parent=mRNA27
chr21	gth	exon	32982487	32982548	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32982549	32988408	.	-	.	Parent=mRNA27
chr21	gth	exon	32988409	32988492	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32988493	32989237	.	-	.	Parent=mRNA27
chr21	gth	exon	32989238	32989463	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32989464	32994018	.	-	.	Parent=mRNA27
chr21	gth	exon	32994019	32994286	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32994287	32996141	.	-	.	Parent=mRNA27
chr21	gth	exon	32996142	32996228	1.000000	-	.	Parent=mRNA27
chr21	.	intron	32996229	33020953	.	-	.	Parent=mRNA27
chr21	gth	exon	33020954	33021099	1.000000	-	.	Parent=mRNA27
chr21	.	intron	33021100	33022127	.	-	.	Parent=mRNA27
chr21	gth	exon	33022128	33022183	1.000000	-	.	Parent=mRNA27
chr21	gth	mRNA	32925171	33022148	.	-	.	ID=mRNA28;Parent=gene4
chr21	gth	exon	32925171	32925982	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32925983	32933088	.	-	.	Parent=mRNA28
chr21	gth	exon	32933089	32933306	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32933307	32933851	.	-	.	Parent=mRNA28
chr21	gth	exon	32933852	32933960	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32933961	32936076	.	-	.	Parent=mRNA28
chr21	gth	exon	32936077	32936147	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32936148	32936275	.	-	.	Parent=mRNA28
chr21	gth	exon	32936276	32936314	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32936315	32937590	.	-	.	Parent=mRNA28
chr21	gth	exon	32937591	32937638	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32937639	32939148	.	-	.	Parent=mRNA28
chr21	gth	exon	32939149	32939187	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32939188	32939826	.	-	.	Parent=mRNA28
chr21	gth	exon	32939827	32939970	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32939971	32940573	.	-	.	Parent=mRNA28
chr21	gth	exon	32940574	32940783	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32940784	32944364	.	-	.	Parent=mRNA28
chr21	gth	exon	32944365	32944527	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32944528	32947468	.	-	.	Parent=mRNA28
chr21	gth	exon	32947469	32947547	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32947548	32950867	.	-	.	Parent=mRNA28
chr21	gth	exon	32950868	32951083	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32951084	32951183	.	-	.	Parent=mRNA28
chr21	gth	exon	32951184	32951301	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32951302	32951896	.	-	.	Parent=mRNA28
chr21	gth	exon	32951897	32952053	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32952054	32959093	.	-	.	Parent=mRNA28
chr21	gth	exon	32959094	32959252	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32959253	32960123	.	-	.	Parent=mRNA28
chr21	gth	exon	32960124	32960316	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32960317	32960613	.	-	.	Parent=mRNA28
chr21	gth	exon	32960614	32960754	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32960755	32964468	.	-	.	Parent=mRNA28
chr21	gth	exon	32964469	32964553	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32964554	32967520	.	-	.	Parent=mRNA28
chr21	gth	exon	32967521	32967712	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32967713	32967727	.	-	.	Parent=mRNA28
chr21	gth	exon	32967728	32967743	0.500000	-	.	Parent=mRNA28
chr21	.	intron	32967744	32972773	.	-	.	Parent=mRNA28
chr21	gth	exon	32972774	32972782	0.555556	-	.	Parent=mRNA28
chr21	.	intron	32972783	32972825	.	-	.	Parent=mRNA28
chr21	gth	exon	32972826	32972982	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32972983	32975676	.	-	.	Parent=mRNA28
chr21	gth	exon	32975677	32975829	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32975830	32978218	.	-	.	Parent=mRNA28
chr21	gth	exon	32978219	32978300	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32978301	32979928	.	-	.	Parent=mRNA28
chr21	gth	exon	32979929	32980098	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32980099	32981158	.	-	.	Parent=mRNA28
chr21	gth	exon	32981159	32981255	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32981256	32982486	.	-	.	Parent=mRNA28
chr21	gth	exon	32982487	32982548	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32982549	32988408	.	-	.	Parent=mRNA28
chr21	gth	exon	32988409	32988492	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32988493	32989237	.	-	.	Parent=mRNA28
chr21	gth	exon	32989238	32989463	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32989464	32994018	.	-	.	Parent=mRNA28
chr21	gth	exon	32994019	32994286	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32994287	32996141	.	-	.	Parent=mRNA28
chr21	gth	exon	32996142	32996228	1.000000	-	.	Parent=mRNA28
chr21	.	intron	32996229	33020953	.	-	.	Parent=mRNA28
chr21	gth	exon	33020954	33021099	1.000000	-	.	Parent=mRNA28
chr21	.	intron	33021100	33022127	.	-	.	Parent=mRNA28
chr21	gth	exon	33022128	33022148	1.000000	-	.	Parent=mRNA28
chr21	gth	mRNA	32933195	32939900	.	-	.	ID=mRNA29;Parent=gene4
chr21	gth	exon	32933195	32933306	1.000000	-	.	Parent=mRNA29
chr21	.	intron	32933307	32933851	.	-	.	Parent=mRNA29
chr21	gth	exon	32933852	32933960	1.000000	-	.	Parent=mRNA29
chr21	.	intron	32933961	32936076	.	-	.	Parent=mRNA29
chr21	gth	exon	32936077	32936147	1.000000	-	.	Parent=mRNA29
chr21	.	intron	32936148	32939826	.	-	.	Parent=mRNA29
chr21	gth	exon	32939827	32939900	1.000000	-	.	Parent=mRNA29
chr21	gth	mRNA	32944365	32948282	.	-	.	ID=mRNA30;Parent=gene4
chr21	gth	exon	32944365	32944527	1.000000	-	.	Parent=mRNA30
chr21	.	intron	32944528	32947468	.	-	.	Parent=mRNA30
chr21	gth	exon	32947469	32948282	1.000000	-	.	Parent=mRNA30
chr21	gth	mRNA	32950872	32952742	.	-	.	ID=mRNA31;Parent=gene4
chr21	gth	exon	32950872	32951083	1.000000	-	.	Parent=mRNA31
chr21	.	intron	32951084	32951183	.	-	.	Parent=mRNA31
chr21	gth	exon	32951184	32951301	1.000000	-	.	Parent=mRNA31
chr21	.	intron	32951302	32951896	.	-	.	Parent=mRNA31
chr21	gth	exon	32951897	32952053	1.000000	-	.	Parent=mRNA31
chr21	.	intron	32952054	32952651	.	-	.	Parent=mRNA31
chr21	gth	exon	32952652	32952742	1.000000	-	.	Parent=mRNA31
chr21	gth	mRNA	32960167	33022121	.	-	.	ID=mRNA32;Parent=gene4
chr21	gth	exon	32960167	32960316	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32960317	32960613	.	-	.	Parent=mRNA32
chr21	gth	exon	32960614	32960754	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32960755	32964468	.	-	.	Parent=mRNA32
chr21	gth	exon	32964469	32964553	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32964554	32967520	.	-	.	Parent=mRNA32
chr21	gth	exon	32967521	32967712	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32967713	32972825	.	-	.	Parent=mRNA32
chr21	gth	exon	32972826	32972991	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32972992	32975676	.	-	.	Parent=mRNA32
chr21	gth	exon	32975677	32975829	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32975830	32978218	.	-	.	Parent=mRNA32
chr21	gth	exon	32978219	32978300	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32978301	32979928	.	-	.	Parent=mRNA32
chr21	gth	exon	32979929	32980098	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32980099	32981158	.	-	.	Parent=mRNA32
chr21	gth	exon	32981159	32981255	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32981256	32982486	.	-	.	Parent=mRNA32
chr21	gth	exon	32982487	32982548	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32982549	32988408	.	-	.	Parent=mRNA32
chr21	gth	exon	32988409	32988492	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32988493	32989237	.	-	.	Parent=mRNA32
chr21	gth	exon	32989238	32989463	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32989464	32994018	.	-	.	Parent=mRNA32
chr21	gth	exon	32994019	32994286	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32994287	32996141	.	-	.	Parent=mRNA32
chr21	gth	exon	32996142	32996228	1.000000	-	.	Parent=mRNA32
chr21	.	intron	32996229	33020953	.	-	.	Parent=mRNA32
chr21	gth	exon	33020954	33021099	1.000000	-	.	Parent=mRNA32
chr21	.	intron	33021100	33022018	.	-	.	Parent=mRNA32
chr21	gth	exon	33022019	33022121	1.000000	-	.	Parent=mRNA32
chr21	gth	mRNA	32989407	33021124	.	-	.	ID=mRNA33;Parent=gene4
chr21	gth	exon	32989407	32989463	1.000000	-	.	Parent=mRNA33
chr21	.	intron	32989464	32994018	.	-	.	Parent=mRNA33
chr21	gth	exon	32994019	32994286	1.000000	-	.	Parent=mRNA33
chr21	.	intron	32994287	32996141	.	-	.	Parent=mRNA33
chr21	gth	exon	32996142	32996228	1.000000	-	.	Parent=mRNA33
chr21	.	intron	32996229	33020953	.	-	.	Parent=mRNA33
chr21	gth	exon	33020954	33021124	1.000000	-	.	Parent=mRNA33
###
chr21	gth	gene	33028081	33066040	.	-	.	ID=gene5
chr21	gth	mRNA	33028081	33066040	.	-	.	ID=mRNA34;Parent=gene5
chr21	gth	exon	33028081	33029249	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33029250	33031435	.	-	.	Parent=mRNA34
chr21	gth	exon	33031436	33031590	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33031591	33032354	.	-	.	Parent=mRNA34
chr21	gth	exon	33032355	33032501	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33032502	33037429	.	-	.	Parent=mRNA34
chr21	gth	exon	33037430	33037496	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33037497	33037859	.	-	.	Parent=mRNA34
chr21	gth	exon	33037860	33037936	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33037937	33038973	.	-	.	Parent=mRNA34
chr21	gth	exon	33038974	33039095	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33039096	33039755	.	-	.	Parent=mRNA34
chr21	gth	exon	33039756	33039900	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33039901	33042680	.	-	.	Parent=mRNA34
chr21	gth	exon	33042681	33042880	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33042881	33045098	.	-	.	Parent=mRNA34
chr21	gth	exon	33045099	33045214	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33045215	33045300	.	-	.	Parent=mRNA34
chr21	gth	exon	33045301	33045400	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33045401	33049411	.	-	.	Parent=mRNA34
chr21	gth	exon	33049412	33049535	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33049536	33053261	.	-	.	Parent=mRNA34
chr21	gth	exon	33053262	33053451	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33053452	33053958	.	-	.	Parent=mRNA34
chr21	gth	exon	33053959	33054176	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33054177	33055240	.	-	.	Parent=mRNA34
chr21	gth	exon	33055241	33055344	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33055345	33056277	.	-	.	Parent=mRNA34
chr21	gth	exon	33056278	33056499	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33056500	33058529	.	-	.	Parent=mRNA34
chr21	gth	exon	33058530	33058706	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33058707	33063995	.	-	.	Parent=mRNA34
chr21	gth	exon	33063996	33064124	1.000000	-	.	Parent=mRNA34
chr21	.	intron	33064125	33065507	.	-	.	Parent=mRNA34
chr21	gth	exon	33065508	33066040	1.000000	-	.	Parent=mRNA34
chr21	gth	mRNA	33028084	33050976	.	-	.	ID=mRNA35;Parent=gene5
chr21	gth	exon	33028084	33029249	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33029250	33031435	.	-	.	Parent=mRNA35
chr21	gth	exon	33031436	33031590	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33031591	33032354	.	-	.	Parent=mRNA35
chr21	gth	exon	33032355	33032501	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33032502	33037429	.	-	.	Parent=mRNA35
chr21	gth	exon	33037430	33037496	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33037497	33037859	.	-	.	Parent=mRNA35
chr21	gth	exon	33037860	33037936	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33037937	33038973	.	-	.	Parent=mRNA35
chr21	gth	exon	33038974	33039095	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33039096	33039755	.	-	.	Parent=mRNA35
chr21	gth	exon	33039756	33039900	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33039901	33042680	.	-	.	Parent=mRNA35
chr21	gth	exon	33042681	33042880	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33042881	33045098	.	-	.	Parent=mRNA35
chr21	gth	exon	33045099	33045214	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33045215	33045300	.	-	.	Parent=mRNA35
chr21	gth	exon	33045301	33045400	1.000000	-	.	Parent=mRNA35
chr21	.	intron	33045401	33049394	.	-	.	Parent=mRNA35
chr21	gth	exon	33049395	33050976	1.000000	-	.	Parent=mRNA35
chr21	gth	mRNA	33029002	33065869	.	-	.	ID=mRNA36;Parent=gene5
chr21	gth	exon	33029002	33029249	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33029250	33031435	.	-	.	Parent=mRNA36
chr21	gth	exon	33031436	33031590	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33031591	33032354	.	-	.	Parent=mRNA36
chr21	gth	exon	33032355	33032501	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33032502	33037429	.	-	.	Parent=mRNA36
chr21	gth	exon	33037430	33037496	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33037497	33037859	.	-	.	Parent=mRNA36
chr21	gth	exon	33037860	33037936	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33037937	33038973	.	-	.	Parent=mRNA36
chr21	gth	exon	33038974	33039095	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33039096	33039755	.	-	.	Parent=mRNA36
chr21	gth	exon	33039756	33039900	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33039901	33042680	.	-	.	Parent=mRNA36
chr21	gth	exon	33042681	33042880	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33042881	33045098	.	-	.	Parent=mRNA36
chr21	gth	exon	33045099	33045214	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33045215	33045300	.	-	.	Parent=mRNA36
chr21	gth	exon	33045301	33045400	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33045401	33049394	.	-	.	Parent=mRNA36
chr21	gth	exon	33049395	33049535	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33049536	33053261	.	-	.	Parent=mRNA36
chr21	gth	exon	33053262	33053451	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33053452	33053958	.	-	.	Parent=mRNA36
chr21	gth	exon	33053959	33054176	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33054177	33055240	.	-	.	Parent=mRNA36
chr21	gth	exon	33055241	33055344	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33055345	33056277	.	-	.	Parent=mRNA36
chr21	gth	exon	33056278	33056499	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33056500	33058529	.	-	.	Parent=mRNA36
chr21	gth	exon	33058530	33058706	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33058707	33063995	.	-	.	Parent=mRNA36
chr21	gth	exon	33063996	33064124	1.000000	-	.	Parent=mRNA36
chr21	.	intron	33064125	33065507	.	-	.	Parent=mRNA36
chr21	gth	exon	33065508	33065869	1.000000	-	.	Parent=mRNA36
chr21	gth	mRNA	33029008	33046306	.	-	.	ID=mRNA37;Parent=gene5
chr21	gth	exon	33029008	33029249	1.000000	-	.	Parent=mRNA37
chr21	.	intron	33029250	33031435	.	-	.	Parent=mRNA37
chr21	gth	exon	33031436	33031590	1.000000	-	.	Parent=mRNA37
chr21	.	intron	33031591	33032354	.	-	.	Parent=mRNA37
chr21	gth	exon	33032355	33032501	1.000000	-	.	Parent=mRNA37
chr21	.	intron	33032502	33037429	.	-	.	Parent=mRNA37
chr21	gth	exon	33037430	33037496	1.000000	-	.	Parent=mRNA37
chr21	.	intron	33037497	33037859	.	-	.	Parent=mRNA37
chr21	gth	exon	33037860	33037936	1.000000	-	.	Parent=mRNA37
chr21	.	intron	33037937	33038973	.	-	.	Parent=mRNA37
chr21	gth	exon	33038974	33039095	1.000000	-	.	Parent=mRNA37
chr21	.	intron	33039096	33039755	.	-	.	Parent=mRNA37
chr21	gth	exon	33039756	33039900	1.000000	-	.	Parent=mRNA37
chr21	.	intron	33039901	33042680	.	-	.	Parent=mRNA37
chr21	gth	exon	33042681	33042880	1.000000	-	.	Parent=mRNA37
chr21	.	intron	33042881	33045098	.	-	.	Parent=mRNA37
chr21	gth	exon	33045099	33045214	1.000000	-	.	Parent=mRNA37
chr21	.	intron	33045215	33045300	.	-	.	Parent=mRNA37
chr21	gth	exon	33045301	33046306	1.000000	-	.	Parent=mRNA37
chr21	gth	mRNA	33035575	33065850	.	-	.	ID=mRNA38;Parent=gene5
chr21	gth	exon	33035575	33035804	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33035805	33037429	.	-	.	Parent=mRNA38
chr21	gth	exon	33037430	33037496	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33037497	33037859	.	-	.	Parent=mRNA38
chr21	gth	exon	33037860	33037936	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33037937	33038973	.	-	.	Parent=mRNA38
chr21	gth	exon	33038974	33039095	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33039096	33039755	.	-	.	Parent=mRNA38
chr21	gth	exon	33039756	33039900	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33039901	33042680	.	-	.	Parent=mRNA38
chr21	gth	exon	33042681	33042880	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33042881	33045098	.	-	.	Parent=mRNA38
chr21	gth	exon	33045099	33045214	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33045215	33045300	.	-	.	Parent=mRNA38
chr21	gth	exon	33045301	33045400	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33045401	33049411	.	-	.	Parent=mRNA38
chr21	gth	exon	33049412	33049535	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33049536	33053261	.	-	.	Parent=mRNA38
chr21	gth	exon	33053262	33053451	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33053452	33053958	.	-	.	Parent=mRNA38
chr21	gth	exon	33053959	33054176	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33054177	33055240	.	-	.	Parent=mRNA38
chr21	gth	exon	33055241	33055344	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33055345	33056277	.	-	.	Parent=mRNA38
chr21	gth	exon	33056278	33056499	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33056500	33058529	.	-	.	Parent=mRNA38
chr21	gth	exon	33058530	33058706	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33058707	33063995	.	-	.	Parent=mRNA38
chr21	gth	exon	33063996	33064124	1.000000	-	.	Parent=mRNA38
chr21	.	intron	33064125	33065507	.	-	.	Parent=mRNA38
chr21	gth	exon	33065508	33065850	1.000000	-	.	Parent=mRNA38
chr21	gth	mRNA	33035601	33037450	.	-	.	ID=mRNA39;Parent=gene5
chr21	gth	exon	33035601	33035804	1.000000	-	.	Parent=mRNA39
chr21	.	intron	33035805	33036541	.	-	.	Parent=mRNA39
chr21	gth	exon	33036542	33036683	1.000000	-	.	Parent=mRNA39
chr21	.	intron	33036684	33037142	.	-	.	Parent=mRNA39
chr21	gth	exon	33037143	33037248	1.000000	-	.	Parent=mRNA39
chr21	.	intron	33037249	33037429	.	-	.	Parent=mRNA39
chr21	gth	exon	33037430	33037450	1.000000	-	.	Parent=mRNA39
chr21	gth	mRNA	33042741	33049493	.	-	.	ID=mRNA40;Parent=gene5
chr21	gth	exon	33042741	33042880	1.000000	-	.	Parent=mRNA40
chr21	.	intron	33042881	33045300	.	-	.	Parent=mRNA40
chr21	gth	exon	33045301	33045400	1.000000	-	.	Parent=mRNA40
chr21	.	intron	33045401	33049394	.	-	.	Parent=mRNA40
chr21	gth	exon	33049395	33049493	1.000000	-	.	Parent=mRNA40
chr21	gth	mRNA	33050524	33065850	.	-	.	ID=mRNA41;Parent=gene5
chr21	gth	exon	33050524	33050550	1.000000	-	.	Parent=mRNA41
chr21	.	intron	33050551	33053261	.	-	.	Parent=mRNA41
chr21	gth	exon	33053262	33053451	1.000000	-	.	Parent=mRNA41
chr21	.	intron	33053452	33053958	.	-	.	Parent=mRNA41
chr21	gth	exon	33053959	33054176	1.000000	-	.	Parent=mRNA41
chr21	.	intron	33054177	33055240	.	-	.	Parent=mRNA41
chr21	gth	exon	33055241	33055344	1.000000	-	.	Parent=mRNA41
chr21	.	intron	33055345	33056277	.	-	.	Parent=mRNA41
chr21	gth	exon	33056278	33056499	1.000000	-	.	Parent=mRNA41
chr21	.	intron	33056500	33058529	.	-	.	Parent=mRNA41
chr21	gth	exon	33058530	33058706	1.000000	-	.	Parent=mRNA41
chr21	.	intron	33058707	33063995	.	-	.	Parent=mRNA41
chr21	gth	exon	33063996	33064124	1.000000	-	.	Parent=mRNA41
chr21	.	intron	33064125	33065507	.	-	.	Parent=mRNA41
chr21	gth	exon	33065508	33065850	1.000000	-	.	Parent=mRNA41
chr21	gth	mRNA	33053584	33065974	.	-	.	ID=mRNA42;Parent=gene5
chr21	gth	exon	33053584	33054176	1.000000	-	.	Parent=mRNA42
chr21	.	intron	33054177	33055240	.	-	.	Parent=mRNA42
chr21	gth	exon	33055241	33055344	1.000000	-	.	Parent=mRNA42
chr21	.	intron	33055345	33056277	.	-	.	Parent=mRNA42
chr21	gth	exon	33056278	33056499	1.000000	-	.	Parent=mRNA42
chr21	.	intron	33056500	33058529	.	-	.	Parent=mRNA42
chr21	gth	exon	33058530	33058706	1.000000	-	.	Parent=mRNA42
chr21	.	intron	33058707	33063995	.	-	.	Parent=mRNA42
chr21	gth	exon	33063996	33064124	1.000000	-	.	Parent=mRNA42
chr21	.	intron	33064125	33065507	.	-	.	Parent=mRNA42
chr21	gth	exon	33065508	33065974	1.000000	-	.	Parent=mRNA42
###
chr21	gth	gene	33066282	33187913	.	+	.	ID=gene6
chr21	gth	mRNA	33066282	33093149	.	+	.	ID=mRNA43;Parent=gene6
chr21	gth	exon	33066282	33066490	1.000000	+	.	Parent=mRNA43
chr21	.	intron	33066491	33078978	.	+	.	Parent=mRNA43
chr21	gth	exon	33078979	33079101	1.000000	+	.	Parent=mRNA43
chr21	.	intron	33079102	33082793	.	+	.	Parent=mRNA43
chr21	gth	exon	33082794	33082883	1.000000	+	.	Parent=mRNA43
chr21	.	intron	33082884	33091118	.	+	.	Parent=mRNA43
chr21	gth	exon	33091119	33093149	1.000000	+	.	Parent=mRNA43
chr21	gth	mRNA	33066307	33091887	.	+	.	ID=mRNA44;Parent=gene6
chr21	gth	exon	33066307	33066454	1.000000	+	.	Parent=mRNA44
chr21	.	intron	33066455	33091118	.	+	.	Parent=mRNA44
chr21	gth	exon	33091119	33091887	1.000000	+	.	Parent=mRNA44
chr21	gth	mRNA	33066332	33187913	.	+	.	ID=mRNA45;Parent=gene6
chr21	gth	exon	33066332	33066454	1.000000	+	.	Parent=mRNA45
chr21	.	intron	33066455	33078956	.	+	.	Parent=mRNA45
chr21	gth	exon	33078957	33079101	1.000000	+	.	Parent=mRNA45
chr21	.	intron	33079102	33180109	.	+	.	Parent=mRNA45
chr21	gth	exon	33180110	33180246	1.000000	+	.	Parent=mRNA45
chr21	.	intron	33180247	33187755	.	+	.	Parent=mRNA45
chr21	gth	exon	33187756	33187913	1.000000	+	.	Parent=mRNA45
chr21	gth	mRNA	33066343	33146649	.	+	.	ID=mRNA46;Parent=gene6
chr21	gth	exon	33066343	33066490	1.000000	+	.	Parent=mRNA46
chr21	.	intron	33066491	33078978	.	+	.	Parent=mRNA46
chr21	gth	exon	33078979	33079101	1.000000	+	.	Parent=mRNA46
chr21	.	intron	33079102	33145928	.	+	.	Parent=mRNA46
chr21	gth	exon	33145929	33146649	1.000000	+	.	Parent=mRNA46
chr21	gth	mRNA	33066344	33091348	.	+	.	ID=mRNA47;Parent=gene6
chr21	gth	exon	33066344	33066502	1.000000	+	.	Parent=mRNA47
chr21	.	intron	33066503	33078978	.	+	.	Parent=mRNA47
chr21	gth	exon	33078979	33079101	1.000000	+	.	Parent=mRNA47
chr21	.	intron	33079102	33082793	.	+	.	Parent=mRNA47
chr21	gth	exon	33082794	33082883	1.000000	+	.	Parent=mRNA47
chr21	.	intron	33082884	33091118	.	+	.	Parent=mRNA47
chr21	gth	exon	33091119	33091348	1.000000	+	.	Parent=mRNA47
chr21	gth	mRNA	33066356	33091626	.	+	.	ID=mRNA48;Parent=gene6
chr21	gth	exon	33066356	33066490	1.000000	+	.	Parent=mRNA48
chr21	.	intron	33066491	33082793	.	+	.	Parent=mRNA48
chr21	gth	exon	33082794	33082883	1.000000	+	.	Parent=mRNA48
chr21	.	intron	33082884	33091118	.	+	.	Parent=mRNA48
chr21	gth	exon	33091119	33091626	1.000000	+	.	Parent=mRNA48
chr21	gth	mRNA	33066370	33091274	.	+	.	ID=mRNA49;Parent=gene6
chr21	gth	exon	33066370	33066490	1.000000	+	.	Parent=mRNA49
chr21	.	intron	33066491	33078978	.	+	.	Parent=mRNA49
chr21	gth	exon	33078979	33079101	1.000000	+	.	Parent=mRNA49
chr21	.	intron	33079102	33091118	.	+	.	Parent=mRNA49
chr21	gth	exon	33091119	33091274	1.000000	+	.	Parent=mRNA49
###
chr21	gth	gene	33087746	33107923	.	-	.	ID=gene7
chr21	gth	mRNA	33087746	33107923	.	-	.	ID=mRNA50;Parent=gene7
chr21	gth	exon	33087746	33088666	1.000000	-	.	Parent=mRNA50
chr21	.	intron	33088667	33104753	.	-	.	Parent=mRNA50
chr21	gth	exon	33104754	33104834	1.000000	-	.	Parent=mRNA50
chr21	.	intron	33104835	33107771	.	-	.	Parent=mRNA50
chr21	gth	exon	33107772	33107923	1.000000	-	.	Parent=mRNA50
chr21	gth	mRNA	33087747	33107859	.	-	.	ID=mRNA51;Parent=gene7
chr21	gth	exon	33087747	33088666	1.000000	-	.	Parent=mRNA51
chr21	.	intron	33088667	33107771	.	-	.	Parent=mRNA51
chr21	gth	exon	33107772	33107859	1.000000	-	.	Parent=mRNA51
chr21	gth	mRNA	33087867	33107869	.	-	.	ID=mRNA52;Parent=gene7
chr21	gth	exon	33087867	33088564	1.000000	-	.	Parent=mRNA52
chr21	.	intron	33088565	33104753	.	-	.	Parent=mRNA52
chr21	gth	exon	33104754	33104834	1.000000	-	.	Parent=mRNA52
chr21	.	intron	33104835	33107771	.	-	.	Parent=mRNA52
chr21	gth	exon	33107772	33107869	1.000000	-	.	Parent=mRNA52
chr21	gth	mRNA	33087903	33107814	.	-	.	ID=mRNA53;Parent=gene7
chr21	gth	exon	33087903	33088666	1.000000	-	.	Parent=mRNA53
chr21	.	intron	33088667	33101821	.	-	.	Parent=mRNA53
chr21	gth	exon	33101822	33101896	1.000000	-	.	Parent=mRNA53
chr21	.	intron	33101897	33104753	.	-	.	Parent=mRNA53
chr21	gth	exon	33104754	33104834	1.000000	-	.	Parent=mRNA53
chr21	.	intron	33104835	33107771	.	-	.	Parent=mRNA53
chr21	gth	exon	33107772	33107814	1.000000	-	.	Parent=mRNA53
###
chr21	gth	gene	33320023	33323374	.	+	.	ID=gene8
chr21	gth	mRNA	33320023	33323374	.	+	.	ID=mRNA54;Parent=gene8
chr21	gth	exon	33320023	33320204	1.000000	+	.	Parent=mRNA54
chr21	.	intron	33320205	33320978	.	+	.	Parent=mRNA54
chr21	gth	exon	33320979	33323374	1.000000	+	.	Parent=mRNA54
chr21	gth	mRNA	33320113	33321227	.	+	.	ID=mRNA55;Parent=gene8
chr21	gth	exon	33320113	33320438	1.000000	+	.	Parent=mRNA55
chr21	.	intron	33320439	33320978	.	+	.	Parent=mRNA55
chr21	gth	exon	33320979	33321227	1.000000	+	.	Parent=mRNA55
chr21	gth	mRNA	33320113	33323374	.	+	.	ID=mRNA56;Parent=gene8
chr21	gth	exon	33320113	33323374	1.000000	+	.	Parent=mRNA56
###
chr21	gth	gene	33364320	33366596	.	+	.	ID=gene9
chr21	gth	mRNA	33364320	33366596	.	+	.	ID=mRNA57;Parent=gene9
chr21	gth	exon	33364320	33366596	1.000000	+	.	Parent=mRNA57
chr21	gth	mRNA	33365141	33366589	.	+	.	ID=mRNA58;Parent=gene9
chr21	gth	exon	33365141	33365861	1.000000	+	.	Parent=mRNA58
chr21	.	intron	33365862	33366227	.	+	.	Parent=mRNA58
chr21	gth	exon	33366228	33366589	1.000000	+	.	Parent=mRNA58
chr21	gth	mRNA	33365844	33366589	.	+	.	ID=mRNA59;Parent=gene9
chr21	gth	exon	33365844	33365881	1.000000	+	.	Parent=mRNA59
chr21	.	intron	33365882	33366227	.	+	.	Parent=mRNA59
chr21	gth	exon	33366228	33366589	1.000000	+	.	Parent=mRNA59
###
chr21	gth	gene	33459646	33464824	.	-	.	ID=gene10
chr21	gth	mRNA	33459646	33464824	.	-	.	ID=mRNA60;Parent=gene10
chr21	gth	exon	33459646	33459867	1.000000	-	.	Parent=mRNA60
chr21	.	intron	33459868	33462617	.	-	.	Parent=mRNA60
chr21	gth	exon	33462618	33462756	1.000000	-	.	Parent=mRNA60
chr21	.	intron	33462757	33463870	.	-	.	Parent=mRNA60
chr21	gth	exon	33463871	33464008	1.000000	-	.	Parent=mRNA60
chr21	.	intron	33464009	33464315	.	-	.	Parent=mRNA60
chr21	gth	exon	33464316	33464426	1.000000	-	.	Parent=mRNA60
chr21	.	intron	33464427	33464738	.	-	.	Parent=mRNA60
chr21	gth	exon	33464739	33464824	1.000000	-	.	Parent=mRNA60
###
chr21	gth	gene	33524076	33591409	.	+	.	ID=gene11
chr21	gth	mRNA	33524076	33556931	.	+	.	ID=mRNA61;Parent=gene11
chr21	gth	exon	33524076	33524391	1.000000	+	.	Parent=mRNA61
chr21	.	intron	33524392	33536060	.	+	.	Parent=mRNA61
chr21	gth	exon	33536061	33536152	1.000000	+	.	Parent=mRNA61
chr21	.	intron	33536153	33536175	.	+	.	Parent=mRNA61
chr21	gth	exon	33536176	33536220	0.477778	+	.	Parent=mRNA61
chr21	.	intron	33536221	33539125	.	+	.	Parent=mRNA61
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA61
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA61
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA61
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA61
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA61
chr21	.	intron	33543030	33546836	.	+	.	Parent=mRNA61
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA61
chr21	.	intron	33547006	33554771	.	+	.	Parent=mRNA61
chr21	gth	exon	33554772	33554902	1.000000	+	.	Parent=mRNA61
chr21	.	intron	33554903	33556735	.	+	.	Parent=mRNA61
chr21	gth	exon	33556736	33556931	1.000000	+	.	Parent=mRNA61
chr21	gth	mRNA	33524084	33559839	.	+	.	ID=mRNA62;Parent=gene11
chr21	gth	exon	33524084	33524391	1.000000	+	.	Parent=mRNA62
chr21	.	intron	33524392	33536014	.	+	.	Parent=mRNA62
chr21	gth	exon	33536015	33536152	1.000000	+	.	Parent=mRNA62
chr21	.	intron	33536153	33536175	.	+	.	Parent=mRNA62
chr21	gth	exon	33536176	33536220	0.477778	+	.	Parent=mRNA62
chr21	.	intron	33536221	33539125	.	+	.	Parent=mRNA62
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA62
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA62
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA62
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA62
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA62
chr21	.	intron	33543030	33546836	.	+	.	Parent=mRNA62
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA62
chr21	.	intron	33547006	33554771	.	+	.	Parent=mRNA62
chr21	gth	exon	33554772	33554902	1.000000	+	.	Parent=mRNA62
chr21	.	intron	33554903	33556735	.	+	.	Parent=mRNA62
chr21	gth	exon	33556736	33559839	1.000000	+	.	Parent=mRNA62
chr21	gth	mRNA	33524149	33558700	.	+	.	ID=mRNA63;Parent=gene11
chr21	gth	exon	33524149	33524391	1.000000	+	.	Parent=mRNA63
chr21	.	intron	33524392	33536014	.	+	.	Parent=mRNA63
chr21	gth	exon	33536015	33536152	1.000000	+	.	Parent=mRNA63
chr21	.	intron	33536153	33536175	.	+	.	Parent=mRNA63
chr21	gth	exon	33536176	33536220	0.477778	+	.	Parent=mRNA63
chr21	.	intron	33536221	33539125	.	+	.	Parent=mRNA63
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA63
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA63
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA63
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA63
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA63
chr21	.	intron	33543030	33546836	.	+	.	Parent=mRNA63
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA63
chr21	.	intron	33547006	33554771	.	+	.	Parent=mRNA63
chr21	gth	exon	33554772	33554902	1.000000	+	.	Parent=mRNA63
chr21	.	intron	33554903	33556967	.	+	.	Parent=mRNA63
chr21	gth	exon	33556968	33558700	1.000000	+	.	Parent=mRNA63
chr21	gth	mRNA	33524234	33556897	.	+	.	ID=mRNA64;Parent=gene11
chr21	gth	exon	33524234	33524391	1.000000	+	.	Parent=mRNA64
chr21	.	intron	33524392	33536060	.	+	.	Parent=mRNA64
chr21	gth	exon	33536061	33536152	1.000000	+	.	Parent=mRNA64
chr21	.	intron	33536153	33536175	.	+	.	Parent=mRNA64
chr21	gth	exon	33536176	33536220	0.477778	+	.	Parent=mRNA64
chr21	.	intron	33536221	33539125	.	+	.	Parent=mRNA64
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA64
chr21	.	intron	33539250	33539667	.	+	.	Parent=mRNA64
chr21	gth	exon	33539668	33539980	1.000000	+	.	Parent=mRNA64
chr21	.	intron	33539981	33540892	.	+	.	Parent=mRNA64
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA64
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA64
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA64
chr21	.	intron	33543030	33546836	.	+	.	Parent=mRNA64
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA64
chr21	.	intron	33547006	33554771	.	+	.	Parent=mRNA64
chr21	gth	exon	33554772	33554902	1.000000	+	.	Parent=mRNA64
chr21	.	intron	33554903	33556735	.	+	.	Parent=mRNA64
chr21	gth	exon	33556736	33556897	1.000000	+	.	Parent=mRNA64
chr21	gth	mRNA	33524311	33558700	.	+	.	ID=mRNA65;Parent=gene11
chr21	gth	exon	33524311	33524391	1.000000	+	.	Parent=mRNA65
chr21	.	intron	33524392	33536014	.	+	.	Parent=mRNA65
chr21	gth	exon	33536015	33536152	1.000000	+	.	Parent=mRNA65
chr21	.	intron	33536153	33536175	.	+	.	Parent=mRNA65
chr21	gth	exon	33536176	33536220	0.477778	+	.	Parent=mRNA65
chr21	.	intron	33536221	33539125	.	+	.	Parent=mRNA65
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA65
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA65
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA65
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA65
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA65
chr21	.	intron	33543030	33546836	.	+	.	Parent=mRNA65
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA65
chr21	.	intron	33547006	33556967	.	+	.	Parent=mRNA65
chr21	gth	exon	33556968	33558700	1.000000	+	.	Parent=mRNA65
chr21	gth	mRNA	33524316	33557030	.	+	.	ID=mRNA66;Parent=gene11
chr21	gth	exon	33524316	33524391	1.000000	+	.	Parent=mRNA66
chr21	.	intron	33524392	33536060	.	+	.	Parent=mRNA66
chr21	gth	exon	33536061	33536152	1.000000	+	.	Parent=mRNA66
chr21	.	intron	33536153	33536175	.	+	.	Parent=mRNA66
chr21	gth	exon	33536176	33536220	0.477778	+	.	Parent=mRNA66
chr21	.	intron	33536221	33539125	.	+	.	Parent=mRNA66
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA66
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA66
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA66
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA66
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA66
chr21	.	intron	33543030	33546312	.	+	.	Parent=mRNA66
chr21	gth	exon	33546313	33546423	1.000000	+	.	Parent=mRNA66
chr21	.	intron	33546424	33546836	.	+	.	Parent=mRNA66
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA66
chr21	.	intron	33547006	33554771	.	+	.	Parent=mRNA66
chr21	gth	exon	33554772	33554902	1.000000	+	.	Parent=mRNA66
chr21	.	intron	33554903	33556967	.	+	.	Parent=mRNA66
chr21	gth	exon	33556968	33557030	1.000000	+	.	Parent=mRNA66
chr21	gth	mRNA	33524357	33557030	.	+	.	ID=mRNA67;Parent=gene11
chr21	gth	exon	33524357	33524391	1.000000	+	.	Parent=mRNA67
chr21	.	intron	33524392	33539125	.	+	.	Parent=mRNA67
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA67
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA67
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA67
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA67
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA67
chr21	.	intron	33543030	33546836	.	+	.	Parent=mRNA67
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA67
chr21	.	intron	33547006	33554771	.	+	.	Parent=mRNA67
chr21	gth	exon	33554772	33554902	1.000000	+	.	Parent=mRNA67
chr21	.	intron	33554903	33556967	.	+	.	Parent=mRNA67
chr21	gth	exon	33556968	33557030	1.000000	+	.	Parent=mRNA67
chr21	gth	mRNA	33524357	33557030	.	+	.	ID=mRNA68;Parent=gene11
chr21	gth	exon	33524357	33524391	1.000000	+	.	Parent=mRNA68
chr21	.	intron	33524392	33539125	.	+	.	Parent=mRNA68
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA68
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA68
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA68
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA68
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA68
chr21	.	intron	33543030	33546836	.	+	.	Parent=mRNA68
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA68
chr21	.	intron	33547006	33556967	.	+	.	Parent=mRNA68
chr21	gth	exon	33556968	33557030	1.000000	+	.	Parent=mRNA68
chr21	gth	mRNA	33524584	33556932	.	+	.	ID=mRNA69;Parent=gene11
chr21	gth	exon	33524584	33524732	1.000000	+	.	Parent=mRNA69
chr21	.	intron	33524733	33536060	.	+	.	Parent=mRNA69
chr21	gth	exon	33536061	33536152	1.000000	+	.	Parent=mRNA69
chr21	.	intron	33536153	33536175	.	+	.	Parent=mRNA69
chr21	gth	exon	33536176	33536220	0.477778	+	.	Parent=mRNA69
chr21	.	intron	33536221	33539125	.	+	.	Parent=mRNA69
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA69
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA69
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA69
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA69
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA69
chr21	.	intron	33543030	33546312	.	+	.	Parent=mRNA69
chr21	gth	exon	33546313	33546423	1.000000	+	.	Parent=mRNA69
chr21	.	intron	33546424	33546836	.	+	.	Parent=mRNA69
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA69
chr21	.	intron	33547006	33554771	.	+	.	Parent=mRNA69
chr21	gth	exon	33554772	33554902	1.000000	+	.	Parent=mRNA69
chr21	.	intron	33554903	33556735	.	+	.	Parent=mRNA69
chr21	gth	exon	33556736	33556932	1.000000	+	.	Parent=mRNA69
chr21	gth	mRNA	33524584	33590525	.	+	.	ID=mRNA70;Parent=gene11
chr21	gth	exon	33524584	33524732	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33524733	33536060	.	+	.	Parent=mRNA70
chr21	gth	exon	33536061	33536152	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33536153	33536175	.	+	.	Parent=mRNA70
chr21	gth	exon	33536176	33536220	0.477778	+	.	Parent=mRNA70
chr21	.	intron	33536221	33539125	.	+	.	Parent=mRNA70
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA70
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA70
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33543030	33546836	.	+	.	Parent=mRNA70
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33547006	33562568	.	+	.	Parent=mRNA70
chr21	gth	exon	33562569	33562692	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33562693	33570770	.	+	.	Parent=mRNA70
chr21	gth	exon	33570771	33570928	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33570929	33573926	.	+	.	Parent=mRNA70
chr21	gth	exon	33573927	33574093	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33574094	33577268	.	+	.	Parent=mRNA70
chr21	gth	exon	33577269	33577416	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33577417	33582278	.	+	.	Parent=mRNA70
chr21	gth	exon	33582279	33582436	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33582437	33588186	.	+	.	Parent=mRNA70
chr21	gth	exon	33588187	33588302	1.000000	+	.	Parent=mRNA70
chr21	.	intron	33588303	33590358	.	+	.	Parent=mRNA70
chr21	gth	exon	33590359	33590525	1.000000	+	.	Parent=mRNA70
chr21	gth	mRNA	33524584	33590525	.	+	.	ID=mRNA71;Parent=gene11
chr21	gth	exon	33524584	33524732	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33524733	33536060	.	+	.	Parent=mRNA71
chr21	gth	exon	33536061	33536152	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33536153	33536175	.	+	.	Parent=mRNA71
chr21	gth	exon	33536176	33536220	0.477778	+	.	Parent=mRNA71
chr21	.	intron	33536221	33539125	.	+	.	Parent=mRNA71
chr21	gth	exon	33539126	33539249	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33539250	33540892	.	+	.	Parent=mRNA71
chr21	gth	exon	33540893	33541065	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33541066	33542883	.	+	.	Parent=mRNA71
chr21	gth	exon	33542884	33543029	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33543030	33546836	.	+	.	Parent=mRNA71
chr21	gth	exon	33546837	33547005	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33547006	33570770	.	+	.	Parent=mRNA71
chr21	gth	exon	33570771	33570928	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33570929	33573926	.	+	.	Parent=mRNA71
chr21	gth	exon	33573927	33574093	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33574094	33577268	.	+	.	Parent=mRNA71
chr21	gth	exon	33577269	33577416	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33577417	33582278	.	+	.	Parent=mRNA71
chr21	gth	exon	33582279	33582436	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33582437	33588186	.	+	.	Parent=mRNA71
chr21	gth	exon	33588187	33588302	1.000000	+	.	Parent=mRNA71
chr21	.	intron	33588303	33590358	.	+	.	Parent=mRNA71
chr21	gth	exon	33590359	33590525	1.000000	+	.	Parent=mRNA71
chr21	gth	mRNA	33560533	33591409	.	+	.	ID=mRNA72;Parent=gene11
chr21	gth	exon	33560533	33560689	1.000000	+	.	Parent=mRNA72
chr21	.	intron	33560690	33562568	.	+	.	Parent=mRNA72
chr21	gth	exon	33562569	33562692	1.000000	+	.	Parent=mRNA72
chr21	.	intron	33562693	33570770	.	+	.	Parent=mRNA72
chr21	gth	exon	33570771	33570928	1.000000	+	.	Parent=mRNA72
chr21	.	intron	33570929	33573926	.	+	.	Parent=mRNA72
chr21	gth	exon	33573927	33574093	1.000000	+	.	Parent=mRNA72
chr21	.	intron	33574094	33577268	.	+	.	Parent=mRNA72
chr21	gth	exon	33577269	33577416	1.000000	+	.	Parent=mRNA72
chr21	.	intron	33577417	33582278	.	+	.	Parent=mRNA72
chr21	gth	exon	33582279	33582436	1.000000	+	.	Parent=mRNA72
chr21	.	intron	33582437	33590358	.	+	.	Parent=mRNA72
chr21	gth	exon	33590359	33591409	1.000000	+	.	Parent=mRNA72
chr21	gth	mRNA	33560557	33590414	.	+	.	ID=mRNA73;Parent=gene11
chr21	gth	exon	33560557	33560689	1.000000	+	.	Parent=mRNA73
chr21	.	intron	33560690	33562568	.	+	.	Parent=mRNA73
chr21	gth	exon	33562569	33562692	1.000000	+	.	Parent=mRNA73
chr21	.	intron	33562693	33573926	.	+	.	Parent=mRNA73
chr21	gth	exon	33573927	33574093	1.000000	+	.	Parent=mRNA73
chr21	.	intron	33574094	33577268	.	+	.	Parent=mRNA73
chr21	gth	exon	33577269	33577416	1.000000	+	.	Parent=mRNA73
chr21	.	intron	33577417	33582278	.	+	.	Parent=mRNA73
chr21	gth	exon	33582279	33582436	1.000000	+	.	Parent=mRNA73
chr21	.	intron	33582437	33590358	.	+	.	Parent=mRNA73
chr21	gth	exon	33590359	33590414	1.000000	+	.	Parent=mRNA73
chr21	gth	mRNA	33562103	33591128	.	+	.	ID=mRNA74;Parent=gene11
chr21	gth	exon	33562103	33562692	1.000000	+	.	Parent=mRNA74
chr21	.	intron	33562693	33570770	.	+	.	Parent=mRNA74
chr21	gth	exon	33570771	33570928	1.000000	+	.	Parent=mRNA74
chr21	.	intron	33570929	33573926	.	+	.	Parent=mRNA74
chr21	gth	exon	33573927	33574093	1.000000	+	.	Parent=mRNA74
chr21	.	intron	33574094	33577268	.	+	.	Parent=mRNA74
chr21	gth	exon	33577269	33577416	1.000000	+	.	Parent=mRNA74
chr21	.	intron	33577417	33582278	.	+	.	Parent=mRNA74
chr21	gth	exon	33582279	33582436	1.000000	+	.	Parent=mRNA74
chr21	.	intron	33582437	33590358	.	+	.	Parent=mRNA74
chr21	gth	exon	33590359	33591128	1.000000	+	.	Parent=mRNA74
chr21	gth	mRNA	33562457	33582295	.	+	.	ID=mRNA75;Parent=gene11
chr21	gth	exon	33562457	33562692	1.000000	+	.	Parent=mRNA75
chr21	.	intron	33562693	33573926	.	+	.	Parent=mRNA75
chr21	gth	exon	33573927	33574093	1.000000	+	.	Parent=mRNA75
chr21	.	intron	33574094	33577268	.	+	.	Parent=mRNA75
chr21	gth	exon	33577269	33577416	1.000000	+	.	Parent=mRNA75
chr21	.	intron	33577417	33582278	.	+	.	Parent=mRNA75
chr21	gth	exon	33582279	33582295	1.000000	+	.	Parent=mRNA75
###
chr21	gth	gene	33618652	33654038	.	+	.	ID=gene12
chr21	gth	mRNA	33618652	33629787	.	+	.	ID=mRNA76;Parent=gene12
chr21	gth	exon	33618652	33618813	1.000000	+	.	Parent=mRNA76
chr21	.	intron	33618814	33629699	.	+	.	Parent=mRNA76
chr21	gth	exon	33629700	33629787	1.000000	+	.	Parent=mRNA76
chr21	gth	mRNA	33619079	33654038	.	+	.	ID=mRNA77;Parent=gene12
chr21	gth	exon	33619079	33619306	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33619307	33629699	.	+	.	Parent=mRNA77
chr21	gth	exon	33629700	33629823	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33629824	33635174	.	+	.	Parent=mRNA77
chr21	gth	exon	33635175	33635350	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33635351	33637443	.	+	.	Parent=mRNA77
chr21	gth	exon	33637444	33637598	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33637599	33637710	.	+	.	Parent=mRNA77
chr21	gth	exon	33637711	33637852	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33637853	33639421	.	+	.	Parent=mRNA77
chr21	gth	exon	33639422	33639536	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33639537	33643266	.	+	.	Parent=mRNA77
chr21	gth	exon	33643267	33643466	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33643467	33643564	.	+	.	Parent=mRNA77
chr21	gth	exon	33643565	33643719	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33643720	33646933	.	+	.	Parent=mRNA77
chr21	gth	exon	33646934	33647084	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33647085	33647813	.	+	.	Parent=mRNA77
chr21	gth	exon	33647814	33647959	1.000000	+	.	Parent=mRNA77
chr21	.	intron	33647960	33649491	.	+	.	Parent=mRNA77
chr21	gth	exon	33649492	33654038	1.000000	+	.	Parent=mRNA77
chr21	gth	mRNA	33619148	33639453	.	+	.	ID=mRNA78;Parent=gene12
chr21	gth	exon	33619148	33619306	1.000000	+	.	Parent=mRNA78
chr21	.	intron	33619307	33629699	.	+	.	Parent=mRNA78
chr21	gth	exon	33629700	33629823	1.000000	+	.	Parent=mRNA78
chr21	.	intron	33629824	33635174	.	+	.	Parent=mRNA78
chr21	gth	exon	33635175	33635350	1.000000	+	.	Parent=mRNA78
chr21	.	intron	33635351	33639421	.	+	.	Parent=mRNA78
chr21	gth	exon	33639422	33639453	1.000000	+	.	Parent=mRNA78
###
chr21	gth	gene	33679169	33773525	.	+	.	ID=gene13
chr21	gth	mRNA	33679169	33709121	.	+	.	ID=mRNA79;Parent=gene13
chr21	gth	exon	33679169	33679203	1.000000	+	.	Parent=mRNA79
chr21	.	intron	33679204	33679391	.	+	.	Parent=mRNA79
chr21	gth	exon	33679392	33679560	1.000000	+	.	Parent=mRNA79
chr21	.	intron	33679561	33709064	.	+	.	Parent=mRNA79
chr21	gth	exon	33709065	33709121	1.000000	+	.	Parent=mRNA79
chr21	gth	mRNA	33697072	33731698	.	+	.	ID=mRNA80;Parent=gene13
chr21	gth	exon	33697072	33697792	1.000000	+	.	Parent=mRNA80
chr21	.	intron	33697793	33709064	.	+	.	Parent=mRNA80
chr21	gth	exon	33709065	33709197	1.000000	+	.	Parent=mRNA80
chr21	.	intron	33709198	33715656	.	+	.	Parent=mRNA80
chr21	gth	exon	33715657	33715862	1.000000	+	.	Parent=mRNA80
chr21	.	intron	33715863	33721060	.	+	.	Parent=mRNA80
chr21	gth	exon	33721061	33721209	1.000000	+	.	Parent=mRNA80
chr21	.	intron	33721210	33726353	.	+	.	Parent=mRNA80
chr21	gth	exon	33726354	33726513	1.000000	+	.	Parent=mRNA80
chr21	.	intron	33726514	33726890	.	+	.	Parent=mRNA80
chr21	gth	exon	33726891	33727048	1.000000	+	.	Parent=mRNA80
chr21	.	intron	33727049	33731004	.	+	.	Parent=mRNA80
chr21	gth	exon	33731005	33731698	1.000000	+	.	Parent=mRNA80
chr21	gth	mRNA	33697603	33726393	.	+	.	ID=mRNA81;Parent=gene13
chr21	gth	exon	33697603	33697792	1.000000	+	.	Parent=mRNA81
chr21	.	intron	33697793	33705011	.	+	.	Parent=mRNA81
chr21	gth	exon	33705012	33705068	1.000000	+	.	Parent=mRNA81
chr21	.	intron	33705069	33705620	.	+	.	Parent=mRNA81
chr21	gth	exon	33705621	33705751	1.000000	+	.	Parent=mRNA81
chr21	.	intron	33705752	33709064	.	+	.	Parent=mRNA81
chr21	gth	exon	33709065	33709197	1.000000	+	.	Parent=mRNA81
chr21	.	intron	33709198	33715656	.	+	.	Parent=mRNA81
chr21	gth	exon	33715657	33715862	1.000000	+	.	Parent=mRNA81
chr21	.	intron	33715863	33721060	.	+	.	Parent=mRNA81
chr21	gth	exon	33721061	33721209	1.000000	+	.	Parent=mRNA81
chr21	.	intron	33721210	33726353	.	+	.	Parent=mRNA81
chr21	gth	exon	33726354	33726393	1.000000	+	.	Parent=mRNA81
chr21	gth	mRNA	33697608	33731698	.	+	.	ID=mRNA82;Parent=gene13
chr21	gth	exon	33697608	33697792	1.000000	+	.	Parent=mRNA82
chr21	.	intron	33697793	33705011	.	+	.	Parent=mRNA82
chr21	gth	exon	33705012	33705068	1.000000	+	.	Parent=mRNA82
chr21	.	intron	33705069	33709064	.	+	.	Parent=mRNA82
chr21	gth	exon	33709065	33709197	1.000000	+	.	Parent=mRNA82
chr21	.	intron	33709198	33715656	.	+	.	Parent=mRNA82
chr21	gth	exon	33715657	33715862	1.000000	+	.	Parent=mRNA82
chr21	.	intron	33715863	33721060	.	+	.	Parent=mRNA82
chr21	gth	exon	33721061	33721209	1.000000	+	.	Parent=mRNA82
chr21	.	intron	33721210	33726353	.	+	.	Parent=mRNA82
chr21	gth	exon	33726354	33726513	1.000000	+	.	Parent=mRNA82
chr21	.	intron	33726514	33726890	.	+	.	Parent=mRNA82
chr21	gth	exon	33726891	33727048	1.000000	+	.	Parent=mRNA82
chr21	.	intron	33727049	33731004	.	+	.	Parent=mRNA82
chr21	gth	exon	33731005	33731698	1.000000	+	.	Parent=mRNA82
chr21	gth	mRNA	33697617	33731121	.	+	.	ID=mRNA83;Parent=gene13
chr21	gth	exon	33697617	33697792	1.000000	+	.	Parent=mRNA83
chr21	.	intron	33697793	33715656	.	+	.	Parent=mRNA83
chr21	gth	exon	33715657	33715862	1.000000	+	.	Parent=mRNA83
chr21	.	intron	33715863	33721060	.	+	.	Parent=mRNA83
chr21	gth	exon	33721061	33721209	1.000000	+	.	Parent=mRNA83
chr21	.	intron	33721210	33726353	.	+	.	Parent=mRNA83
chr21	gth	exon	33726354	33726513	1.000000	+	.	Parent=mRNA83
chr21	.	intron	33726514	33726890	.	+	.	Parent=mRNA83
chr21	gth	exon	33726891	33727048	1.000000	+	.	Parent=mRNA83
chr21	.	intron	33727049	33731004	.	+	.	Parent=mRNA83
chr21	gth	exon	33731005	33731121	1.000000	+	.	Parent=mRNA83
chr21	gth	mRNA	33726891	33773525	.	+	.	ID=mRNA84;Parent=gene13
chr21	gth	exon	33726891	33727048	1.000000	+	.	Parent=mRNA84
chr21	.	intron	33727049	33772974	.	+	.	Parent=mRNA84
chr21	gth	exon	33772975	33773525	1.000000	+	.	Parent=mRNA84
###
chr21	gth	gene	33726662	33775369	.	-	.	ID=gene14
chr21	gth	mRNA	33726662	33743141	.	-	.	ID=mRNA85;Parent=gene14
chr21	gth	exon	33726662	33726979	1.000000	-	.	Parent=mRNA85
chr21	.	intron	33726980	33731059	.	-	.	Parent=mRNA85
chr21	gth	exon	33731060	33731169	1.000000	-	.	Parent=mRNA85
chr21	.	intron	33731170	33733390	.	-	.	Parent=mRNA85
chr21	gth	exon	33733391	33733474	1.000000	-	.	Parent=mRNA85
chr21	.	intron	33733475	33742958	.	-	.	Parent=mRNA85
chr21	gth	exon	33742959	33743141	1.000000	-	.	Parent=mRNA85
chr21	gth	mRNA	33726662	33774188	.	-	.	ID=mRNA86;Parent=gene14
chr21	gth	exon	33726662	33726979	1.000000	-	.	Parent=mRNA86
chr21	.	intron	33726980	33733390	.	-	.	Parent=mRNA86
chr21	gth	exon	33733391	33733474	1.000000	-	.	Parent=mRNA86
chr21	.	intron	33733475	33742958	.	-	.	Parent=mRNA86
chr21	gth	exon	33742959	33745040	1.000000	-	.	Parent=mRNA86
chr21	.	intron	33745041	33749903	.	-	.	Parent=mRNA86
chr21	gth	exon	33749904	33749961	1.000000	-	.	Parent=mRNA86
chr21	.	intron	33749962	33754589	.	-	.	Parent=mRNA86
chr21	gth	exon	33754590	33754682	1.000000	-	.	Parent=mRNA86
chr21	.	intron	33754683	33759518	.	-	.	Parent=mRNA86
chr21	gth	exon	33759519	33759586	1.000000	-	.	Parent=mRNA86
chr21	.	intron	33759587	33761186	.	-	.	Parent=mRNA86
chr21	gth	exon	33761187	33761299	1.000000	-	.	Parent=mRNA86
chr21	.	intron	33761300	33762963	.	-	.	Parent=mRNA86
chr21	gth	exon	33762964	33763103	1.000000	-	.	Parent=mRNA86
chr21	.	intron	33763104	33774014	.	-	.	Parent=mRNA86
chr21	gth	exon	33774015	33774188	1.000000	-	.	Parent=mRNA86
chr21	gth	mRNA	33731061	33774188	.	-	.	ID=mRNA87;Parent=gene14
chr21	gth	exon	33731061	33731169	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33731170	33733390	.	-	.	Parent=mRNA87
chr21	gth	exon	33733391	33733474	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33733475	33741194	.	-	.	Parent=mRNA87
chr21	gth	exon	33741195	33741317	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33741318	33742958	.	-	.	Parent=mRNA87
chr21	gth	exon	33742959	33743136	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33743137	33743190	.	-	.	Parent=mRNA87
chr21	gth	exon	33743191	33745040	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33745041	33749903	.	-	.	Parent=mRNA87
chr21	gth	exon	33749904	33749961	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33749962	33754589	.	-	.	Parent=mRNA87
chr21	gth	exon	33754590	33754682	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33754683	33759518	.	-	.	Parent=mRNA87
chr21	gth	exon	33759519	33759586	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33759587	33761186	.	-	.	Parent=mRNA87
chr21	gth	exon	33761187	33761299	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33761300	33762963	.	-	.	Parent=mRNA87
chr21	gth	exon	33762964	33763103	1.000000	-	.	Parent=mRNA87
chr21	.	intron	33763104	33774014	.	-	.	Parent=mRNA87
chr21	gth	exon	33774015	33774188	1.000000	-	.	Parent=mRNA87
chr21	gth	mRNA	33733331	33743587	.	-	.	ID=mRNA88;Parent=gene14
chr21	gth	exon	33733331	33733335	0.600000	-	.	Parent=mRNA88
chr21	.	intron	33733336	33733390	.	-	.	Parent=mRNA88
chr21	gth	exon	33733391	33733474	1.000000	-	.	Parent=mRNA88
chr21	.	intron	33733475	33742958	.	-	.	Parent=mRNA88
chr21	gth	exon	33742959	33743056	1.000000	-	.	Parent=mRNA88
chr21	.	intron	33743057	33743410	.	-	.	Parent=mRNA88
chr21	gth	exon	33743411	33743587	1.000000	-	.	Parent=mRNA88
chr21	gth	mRNA	33744724	33774113	.	-	.	ID=mRNA89;Parent=gene14
chr21	gth	exon	33744724	33745040	1.000000	-	.	Parent=mRNA89
chr21	.	intron	33745041	33749903	.	-	.	Parent=mRNA89
chr21	gth	exon	33749904	33749961	1.000000	-	.	Parent=mRNA89
chr21	.	intron	33749962	33750180	.	-	.	Parent=mRNA89
chr21	gth	exon	33750181	33750274	1.000000	-	.	Parent=mRNA89
chr21	.	intron	33750275	33754589	.	-	.	Parent=mRNA89
chr21	gth	exon	33754590	33754682	1.000000	-	.	Parent=mRNA89
chr21	.	intron	33754683	33759518	.	-	.	Parent=mRNA89
chr21	gth	exon	33759519	33759586	1.000000	-	.	Parent=mRNA89
chr21	.	intron	33759587	33761186	.	-	.	Parent=mRNA89
chr21	gth	exon	33761187	33761299	1.000000	-	.	Parent=mRNA89
chr21	.	intron	33761300	33762963	.	-	.	Parent=mRNA89
chr21	gth	exon	33762964	33763103	1.000000	-	.	Parent=mRNA89
chr21	.	intron	33763104	33774014	.	-	.	Parent=mRNA89
chr21	gth	exon	33774015	33774113	1.000000	-	.	Parent=mRNA89
chr21	gth	mRNA	33759195	33761312	.	-	.	ID=mRNA90;Parent=gene14
chr21	gth	exon	33759195	33759586	1.000000	-	.	Parent=mRNA90
chr21	.	intron	33759587	33761186	.	-	.	Parent=mRNA90
chr21	gth	exon	33761187	33761312	1.000000	-	.	Parent=mRNA90
chr21	gth	mRNA	33759555	33773466	.	-	.	ID=mRNA91;Parent=gene14
chr21	gth	exon	33759555	33759586	1.000000	-	.	Parent=mRNA91
chr21	.	intron	33759587	33761186	.	-	.	Parent=mRNA91
chr21	gth	exon	33761187	33761299	1.000000	-	.	Parent=mRNA91
chr21	.	intron	33761300	33762963	.	-	.	Parent=mRNA91
chr21	gth	exon	33762964	33763103	1.000000	-	.	Parent=mRNA91
chr21	.	intron	33763104	33763707	.	-	.	Parent=mRNA91
chr21	gth	exon	33763708	33763860	1.000000	-	.	Parent=mRNA91
chr21	.	intron	33763861	33773285	.	-	.	Parent=mRNA91
chr21	gth	exon	33773286	33773466	1.000000	-	.	Parent=mRNA91
chr21	gth	mRNA	33761212	33775369	.	-	.	ID=mRNA92;Parent=gene14
chr21	gth	exon	33761212	33761299	1.000000	-	.	Parent=mRNA92
chr21	.	intron	33761300	33762963	.	-	.	Parent=mRNA92
chr21	gth	exon	33762964	33763103	1.000000	-	.	Parent=mRNA92
chr21	.	intron	33763104	33775310	.	-	.	Parent=mRNA92
chr21	gth	exon	33775311	33775369	1.000000	-	.	Parent=mRNA92
chr21	gth	mRNA	33762597	33774125	.	-	.	ID=mRNA93;Parent=gene14
chr21	gth	exon	33762597	33763103	1.000000	-	.	Parent=mRNA93
chr21	.	intron	33763104	33774014	.	-	.	Parent=mRNA93
chr21	gth	exon	33774015	33774125	1.000000	-	.	Parent=mRNA93
###
chr21	gth	gene	33779707	33785897	.	-	.	ID=gene15
chr21	gth	mRNA	33779707	33785650	.	-	.	ID=mRNA94;Parent=gene15
chr21	gth	exon	33779707	33779934	1.000000	-	.	Parent=mRNA94
chr21	.	intron	33779935	33782007	.	-	.	Parent=mRNA94
chr21	gth	exon	33782008	33783601	1.000000	-	.	Parent=mRNA94
chr21	.	intron	33783602	33785242	.	-	.	Parent=mRNA94
chr21	gth	exon	33785243	33785650	1.000000	-	.	Parent=mRNA94
chr21	gth	mRNA	33782367	33785897	.	-	.	ID=mRNA95;Parent=gene15
chr21	gth	exon	33782367	33783601	1.000000	-	.	Parent=mRNA95
chr21	.	intron	33783602	33785778	.	-	.	Parent=mRNA95
chr21	gth	exon	33785779	33785897	1.000000	-	.	Parent=mRNA95
###
chr21	gth	gene	33798108	33837667	.	-	.	ID=gene16
chr21	gth	mRNA	33798108	33836314	.	-	.	ID=mRNA96;Parent=gene16
chr21	gth	exon	33798108	33798492	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33798493	33798588	.	-	.	Parent=mRNA96
chr21	gth	exon	33798589	33798704	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33798705	33799737	.	-	.	Parent=mRNA96
chr21	gth	exon	33799738	33799879	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33799880	33800150	.	-	.	Parent=mRNA96
chr21	gth	exon	33800151	33800281	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33800282	33803959	.	-	.	Parent=mRNA96
chr21	gth	exon	33803960	33804097	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33804098	33805428	.	-	.	Parent=mRNA96
chr21	gth	exon	33805429	33805635	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33805636	33811165	.	-	.	Parent=mRNA96
chr21	gth	exon	33811166	33811318	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33811319	33811533	.	-	.	Parent=mRNA96
chr21	gth	exon	33811534	33811785	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33811786	33814540	.	-	.	Parent=mRNA96
chr21	gth	exon	33814541	33814739	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33814740	33815082	.	-	.	Parent=mRNA96
chr21	gth	exon	33815083	33815192	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33815193	33816364	.	-	.	Parent=mRNA96
chr21	gth	exon	33816365	33816459	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33816460	33818945	.	-	.	Parent=mRNA96
chr21	gth	exon	33818946	33819177	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33819178	33822342	.	-	.	Parent=mRNA96
chr21	gth	exon	33822343	33822511	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33822512	33822694	.	-	.	Parent=mRNA96
chr21	gth	exon	33822695	33822780	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33822781	33823025	.	-	.	Parent=mRNA96
chr21	gth	exon	33823026	33823113	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33823114	33824934	.	-	.	Parent=mRNA96
chr21	gth	exon	33824935	33825060	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA96
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA96
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA96
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA96
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA96
chr21	gth	exon	33833347	33833532	1.000000	-	.	Parent=mRNA96
chr21	.	intron	33833533	33836240	.	-	.	Parent=mRNA96
chr21	gth	exon	33836241	33836314	1.000000	-	.	Parent=mRNA96
chr21	gth	mRNA	33798108	33837018	.	-	.	ID=mRNA97;Parent=gene16
chr21	gth	exon	33798108	33798492	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33798493	33798588	.	-	.	Parent=mRNA97
chr21	gth	exon	33798589	33798704	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33798705	33799737	.	-	.	Parent=mRNA97
chr21	gth	exon	33799738	33799879	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33799880	33800150	.	-	.	Parent=mRNA97
chr21	gth	exon	33800151	33800281	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33800282	33803959	.	-	.	Parent=mRNA97
chr21	gth	exon	33803960	33804097	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33804098	33805428	.	-	.	Parent=mRNA97
chr21	gth	exon	33805429	33805635	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33805636	33811165	.	-	.	Parent=mRNA97
chr21	gth	exon	33811166	33811318	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33811319	33811533	.	-	.	Parent=mRNA97
chr21	gth	exon	33811534	33811785	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33811786	33814540	.	-	.	Parent=mRNA97
chr21	gth	exon	33814541	33814739	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33814740	33815082	.	-	.	Parent=mRNA97
chr21	gth	exon	33815083	33815192	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33815193	33816364	.	-	.	Parent=mRNA97
chr21	gth	exon	33816365	33816459	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33816460	33818945	.	-	.	Parent=mRNA97
chr21	gth	exon	33818946	33819177	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33819178	33822342	.	-	.	Parent=mRNA97
chr21	gth	exon	33822343	33822511	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33822512	33822694	.	-	.	Parent=mRNA97
chr21	gth	exon	33822695	33822780	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33822781	33823025	.	-	.	Parent=mRNA97
chr21	gth	exon	33823026	33823113	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33823114	33824934	.	-	.	Parent=mRNA97
chr21	gth	exon	33824935	33825060	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA97
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA97
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA97
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA97
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA97
chr21	gth	exon	33833347	33833499	1.000000	-	.	Parent=mRNA97
chr21	.	intron	33833500	33836762	.	-	.	Parent=mRNA97
chr21	gth	exon	33836763	33837018	1.000000	-	.	Parent=mRNA97
chr21	gth	mRNA	33798108	33837037	.	-	.	ID=mRNA98;Parent=gene16
chr21	gth	exon	33798108	33798492	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33798493	33798588	.	-	.	Parent=mRNA98
chr21	gth	exon	33798589	33798704	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33798705	33799737	.	-	.	Parent=mRNA98
chr21	gth	exon	33799738	33799879	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33799880	33800150	.	-	.	Parent=mRNA98
chr21	gth	exon	33800151	33800281	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33800282	33803959	.	-	.	Parent=mRNA98
chr21	gth	exon	33803960	33804097	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33804098	33805428	.	-	.	Parent=mRNA98
chr21	gth	exon	33805429	33805635	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33805636	33811165	.	-	.	Parent=mRNA98
chr21	gth	exon	33811166	33811318	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33811319	33811533	.	-	.	Parent=mRNA98
chr21	gth	exon	33811534	33811785	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33811786	33814540	.	-	.	Parent=mRNA98
chr21	gth	exon	33814541	33814739	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33814740	33815082	.	-	.	Parent=mRNA98
chr21	gth	exon	33815083	33815192	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33815193	33816364	.	-	.	Parent=mRNA98
chr21	gth	exon	33816365	33816459	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33816460	33818945	.	-	.	Parent=mRNA98
chr21	gth	exon	33818946	33819177	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33819178	33822342	.	-	.	Parent=mRNA98
chr21	gth	exon	33822343	33822511	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33822512	33822694	.	-	.	Parent=mRNA98
chr21	gth	exon	33822695	33822780	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33822781	33823025	.	-	.	Parent=mRNA98
chr21	gth	exon	33823026	33823113	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33823114	33824934	.	-	.	Parent=mRNA98
chr21	gth	exon	33824935	33825060	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA98
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA98
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA98
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA98
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA98
chr21	gth	exon	33833347	33833532	1.000000	-	.	Parent=mRNA98
chr21	.	intron	33833533	33836835	.	-	.	Parent=mRNA98
chr21	gth	exon	33836836	33837037	1.000000	-	.	Parent=mRNA98
chr21	gth	mRNA	33798110	33837068	.	-	.	ID=mRNA99;Parent=gene16
chr21	gth	exon	33798110	33798492	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33798493	33798588	.	-	.	Parent=mRNA99
chr21	gth	exon	33798589	33798704	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33798705	33799737	.	-	.	Parent=mRNA99
chr21	gth	exon	33799738	33799879	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33799880	33800150	.	-	.	Parent=mRNA99
chr21	gth	exon	33800151	33800281	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33800282	33803959	.	-	.	Parent=mRNA99
chr21	gth	exon	33803960	33804097	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33804098	33805428	.	-	.	Parent=mRNA99
chr21	gth	exon	33805429	33805635	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33805636	33811165	.	-	.	Parent=mRNA99
chr21	gth	exon	33811166	33811318	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33811319	33811533	.	-	.	Parent=mRNA99
chr21	gth	exon	33811534	33811785	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33811786	33814540	.	-	.	Parent=mRNA99
chr21	gth	exon	33814541	33814739	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33814740	33815082	.	-	.	Parent=mRNA99
chr21	gth	exon	33815083	33815192	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33815193	33816364	.	-	.	Parent=mRNA99
chr21	gth	exon	33816365	33816459	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33816460	33818945	.	-	.	Parent=mRNA99
chr21	gth	exon	33818946	33819177	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33819178	33822342	.	-	.	Parent=mRNA99
chr21	gth	exon	33822343	33822511	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33822512	33822690	.	-	.	Parent=mRNA99
chr21	gth	exon	33822691	33822780	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33822781	33823025	.	-	.	Parent=mRNA99
chr21	gth	exon	33823026	33823113	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33823114	33824934	.	-	.	Parent=mRNA99
chr21	gth	exon	33824935	33825060	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA99
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA99
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA99
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA99
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA99
chr21	gth	exon	33833347	33833532	1.000000	-	.	Parent=mRNA99
chr21	.	intron	33833533	33836766	.	-	.	Parent=mRNA99
chr21	gth	exon	33836767	33837068	1.000000	-	.	Parent=mRNA99
chr21	gth	mRNA	33800152	33805569	.	-	.	ID=mRNA100;Parent=gene16
chr21	gth	exon	33800152	33800257	1.000000	-	.	Parent=mRNA100
chr21	.	intron	33800258	33803990	.	-	.	Parent=mRNA100
chr21	gth	exon	33803991	33804097	1.000000	-	.	Parent=mRNA100
chr21	.	intron	33804098	33805428	.	-	.	Parent=mRNA100
chr21	gth	exon	33805429	33805569	1.000000	-	.	Parent=mRNA100
chr21	gth	mRNA	33800217	33804510	.	-	.	ID=mRNA101;Parent=gene16
chr21	gth	exon	33800217	33800281	1.000000	-	.	Parent=mRNA101
chr21	.	intron	33800282	33803959	.	-	.	Parent=mRNA101
chr21	gth	exon	33803960	33804510	1.000000	-	.	Parent=mRNA101
chr21	gth	mRNA	33803365	33805481	.	-	.	ID=mRNA102;Parent=gene16
chr21	gth	exon	33803365	33804097	1.000000	-	.	Parent=mRNA102
chr21	.	intron	33804098	33805428	.	-	.	Parent=mRNA102
chr21	gth	exon	33805429	33805481	1.000000	-	.	Parent=mRNA102
chr21	gth	mRNA	33814699	33822940	.	-	.	ID=mRNA103;Parent=gene16
chr21	gth	exon	33814699	33814822	1.000000	-	.	Parent=mRNA103
chr21	.	intron	33814823	33815082	.	-	.	Parent=mRNA103
chr21	gth	exon	33815083	33815192	1.000000	-	.	Parent=mRNA103
chr21	.	intron	33815193	33816364	.	-	.	Parent=mRNA103
chr21	gth	exon	33816365	33816459	1.000000	-	.	Parent=mRNA103
chr21	.	intron	33816460	33818945	.	-	.	Parent=mRNA103
chr21	gth	exon	33818946	33819177	1.000000	-	.	Parent=mRNA103
chr21	.	intron	33819178	33822342	.	-	.	Parent=mRNA103
chr21	gth	exon	33822343	33822940	1.000000	-	.	Parent=mRNA103
chr21	gth	mRNA	33818186	33836290	.	-	.	ID=mRNA104;Parent=gene16
chr21	gth	exon	33818186	33819177	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33819178	33822342	.	-	.	Parent=mRNA104
chr21	gth	exon	33822343	33822511	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33822512	33822694	.	-	.	Parent=mRNA104
chr21	gth	exon	33822695	33822780	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33822781	33823025	.	-	.	Parent=mRNA104
chr21	gth	exon	33823026	33823113	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33823114	33824934	.	-	.	Parent=mRNA104
chr21	gth	exon	33824935	33825060	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA104
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA104
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA104
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA104
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA104
chr21	gth	exon	33833347	33833532	1.000000	-	.	Parent=mRNA104
chr21	.	intron	33833533	33836240	.	-	.	Parent=mRNA104
chr21	gth	exon	33836241	33836290	1.000000	-	.	Parent=mRNA104
chr21	gth	mRNA	33822442	33836539	.	-	.	ID=mRNA105;Parent=gene16
chr21	gth	exon	33822442	33822511	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33822512	33822694	.	-	.	Parent=mRNA105
chr21	gth	exon	33822695	33822780	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33822781	33823025	.	-	.	Parent=mRNA105
chr21	gth	exon	33823026	33823113	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33823114	33823742	.	-	.	Parent=mRNA105
chr21	gth	exon	33823743	33823944	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33823945	33824934	.	-	.	Parent=mRNA105
chr21	gth	exon	33824935	33825060	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA105
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA105
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA105
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA105
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA105
chr21	gth	exon	33833347	33833499	1.000000	-	.	Parent=mRNA105
chr21	.	intron	33833500	33836240	.	-	.	Parent=mRNA105
chr21	gth	exon	33836241	33836539	1.000000	-	.	Parent=mRNA105
chr21	gth	mRNA	33822739	33825458	.	-	.	ID=mRNA106;Parent=gene16
chr21	gth	exon	33822739	33822780	1.000000	-	.	Parent=mRNA106
chr21	.	intron	33822781	33823025	.	-	.	Parent=mRNA106
chr21	gth	exon	33823026	33823113	1.000000	-	.	Parent=mRNA106
chr21	.	intron	33823114	33824934	.	-	.	Parent=mRNA106
chr21	gth	exon	33824935	33825458	1.000000	-	.	Parent=mRNA106
chr21	gth	mRNA	33824886	33836539	.	-	.	ID=mRNA107;Parent=gene16
chr21	gth	exon	33824886	33825060	1.000000	-	.	Parent=mRNA107
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA107
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA107
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA107
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA107
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA107
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA107
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA107
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA107
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA107
chr21	gth	exon	33833347	33833499	1.000000	-	.	Parent=mRNA107
chr21	.	intron	33833500	33836240	.	-	.	Parent=mRNA107
chr21	gth	exon	33836241	33836539	1.000000	-	.	Parent=mRNA107
chr21	gth	mRNA	33824886	33836969	.	-	.	ID=mRNA108;Parent=gene16
chr21	gth	exon	33824886	33825060	1.000000	-	.	Parent=mRNA108
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA108
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA108
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA108
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA108
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA108
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA108
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA108
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA108
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA108
chr21	gth	exon	33833347	33833499	1.000000	-	.	Parent=mRNA108
chr21	.	intron	33833500	33836835	.	-	.	Parent=mRNA108
chr21	gth	exon	33836836	33836969	1.000000	-	.	Parent=mRNA108
chr21	gth	mRNA	33824886	33836996	.	-	.	ID=mRNA109;Parent=gene16
chr21	gth	exon	33824886	33825060	1.000000	-	.	Parent=mRNA109
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA109
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA109
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA109
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA109
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA109
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA109
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA109
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA109
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA109
chr21	gth	exon	33833347	33833499	1.000000	-	.	Parent=mRNA109
chr21	.	intron	33833500	33836723	.	-	.	Parent=mRNA109
chr21	gth	exon	33836724	33836996	1.000000	-	.	Parent=mRNA109
chr21	gth	mRNA	33824886	33837667	.	-	.	ID=mRNA110;Parent=gene16
chr21	gth	exon	33824886	33825060	1.000000	-	.	Parent=mRNA110
chr21	.	intron	33825061	33825664	.	-	.	Parent=mRNA110
chr21	gth	exon	33825665	33825733	1.000000	-	.	Parent=mRNA110
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA110
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA110
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA110
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA110
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA110
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA110
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA110
chr21	gth	exon	33833347	33833532	1.000000	-	.	Parent=mRNA110
chr21	.	intron	33833533	33837395	.	-	.	Parent=mRNA110
chr21	gth	exon	33837396	33837667	1.000000	-	.	Parent=mRNA110
chr21	gth	mRNA	33825512	33833532	.	-	.	ID=mRNA111;Parent=gene16
chr21	gth	exon	33825512	33825733	1.000000	-	.	Parent=mRNA111
chr21	.	intron	33825734	33826520	.	-	.	Parent=mRNA111
chr21	gth	exon	33826521	33826632	1.000000	-	.	Parent=mRNA111
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA111
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA111
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA111
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA111
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA111
chr21	gth	exon	33833347	33833532	1.000000	-	.	Parent=mRNA111
chr21	gth	mRNA	33825949	33836539	.	-	.	ID=mRNA112;Parent=gene16
chr21	gth	exon	33825949	33826632	1.000000	-	.	Parent=mRNA112
chr21	.	intron	33826633	33828754	.	-	.	Parent=mRNA112
chr21	gth	exon	33828755	33828929	1.000000	-	.	Parent=mRNA112
chr21	.	intron	33828930	33829400	.	-	.	Parent=mRNA112
chr21	gth	exon	33829401	33829496	1.000000	-	.	Parent=mRNA112
chr21	.	intron	33829497	33833346	.	-	.	Parent=mRNA112
chr21	gth	exon	33833347	33833499	1.000000	-	.	Parent=mRNA112
chr21	.	intron	33833500	33836240	.	-	.	Parent=mRNA112
chr21	gth	exon	33836241	33836539	1.000000	-	.	Parent=mRNA112
###
chr21	gth	gene	33836794	33871657	.	+	.	ID=gene17
chr21	gth	mRNA	33836794	33871657	.	+	.	ID=mRNA113;Parent=gene17
chr21	gth	exon	33836794	33837345	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33837346	33840388	.	+	.	Parent=mRNA113
chr21	gth	exon	33840389	33840555	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33840556	33843651	.	+	.	Parent=mRNA113
chr21	gth	exon	33843652	33849567	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33849568	33851331	.	+	.	Parent=mRNA113
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33851493	33853405	.	+	.	Parent=mRNA113
chr21	gth	exon	33853406	33853552	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33853553	33853762	.	+	.	Parent=mRNA113
chr21	gth	exon	33853763	33853951	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33853952	33861332	.	+	.	Parent=mRNA113
chr21	gth	exon	33861333	33861443	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33861444	33863146	.	+	.	Parent=mRNA113
chr21	gth	exon	33863147	33863263	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33863264	33867483	.	+	.	Parent=mRNA113
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA113
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA113
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA113
chr21	.	intron	33870070	33870540	.	+	.	Parent=mRNA113
chr21	gth	exon	33870541	33871657	1.000000	+	.	Parent=mRNA113
chr21	gth	mRNA	33837220	33871655	.	+	.	ID=mRNA114;Parent=gene17
chr21	gth	exon	33837220	33837345	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33837346	33840388	.	+	.	Parent=mRNA114
chr21	gth	exon	33840389	33840555	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33840556	33843651	.	+	.	Parent=mRNA114
chr21	gth	exon	33843652	33845641	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33845642	33845761	.	+	.	Parent=mRNA114
chr21	gth	exon	33845762	33849567	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33849568	33851331	.	+	.	Parent=mRNA114
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33851493	33853405	.	+	.	Parent=mRNA114
chr21	gth	exon	33853406	33853552	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33853553	33853762	.	+	.	Parent=mRNA114
chr21	gth	exon	33853763	33853951	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33853952	33861332	.	+	.	Parent=mRNA114
chr21	gth	exon	33861333	33861443	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33861444	33863146	.	+	.	Parent=mRNA114
chr21	gth	exon	33863147	33863263	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33863264	33867483	.	+	.	Parent=mRNA114
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA114
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA114
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA114
chr21	.	intron	33870070	33870540	.	+	.	Parent=mRNA114
chr21	gth	exon	33870541	33871655	1.000000	+	.	Parent=mRNA114
chr21	gth	mRNA	33837228	33840928	.	+	.	ID=mRNA115;Parent=gene17
chr21	gth	exon	33837228	33837345	1.000000	+	.	Parent=mRNA115
chr21	.	intron	33837346	33840388	.	+	.	Parent=mRNA115
chr21	gth	exon	33840389	33840928	1.000000	+	.	Parent=mRNA115
chr21	gth	mRNA	33837228	33871657	.	+	.	ID=mRNA116;Parent=gene17
chr21	gth	exon	33837228	33837345	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33837346	33840388	.	+	.	Parent=mRNA116
chr21	gth	exon	33840389	33840555	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33840556	33851331	.	+	.	Parent=mRNA116
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33851493	33853405	.	+	.	Parent=mRNA116
chr21	gth	exon	33853406	33853552	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33853553	33853762	.	+	.	Parent=mRNA116
chr21	gth	exon	33853763	33853951	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33853952	33861332	.	+	.	Parent=mRNA116
chr21	gth	exon	33861333	33861443	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33861444	33863146	.	+	.	Parent=mRNA116
chr21	gth	exon	33863147	33863263	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33863264	33867483	.	+	.	Parent=mRNA116
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA116
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA116
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA116
chr21	.	intron	33870070	33870540	.	+	.	Parent=mRNA116
chr21	gth	exon	33870541	33871657	1.000000	+	.	Parent=mRNA116
chr21	gth	mRNA	33837240	33854843	.	+	.	ID=mRNA117;Parent=gene17
chr21	gth	exon	33837240	33837345	1.000000	+	.	Parent=mRNA117
chr21	.	intron	33837346	33840388	.	+	.	Parent=mRNA117
chr21	gth	exon	33840389	33840555	1.000000	+	.	Parent=mRNA117
chr21	.	intron	33840556	33843651	.	+	.	Parent=mRNA117
chr21	gth	exon	33843652	33849567	1.000000	+	.	Parent=mRNA117
chr21	.	intron	33849568	33851331	.	+	.	Parent=mRNA117
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA117
chr21	.	intron	33851493	33853405	.	+	.	Parent=mRNA117
chr21	gth	exon	33853406	33853552	1.000000	+	.	Parent=mRNA117
chr21	.	intron	33853553	33853762	.	+	.	Parent=mRNA117
chr21	gth	exon	33853763	33853951	1.000000	+	.	Parent=mRNA117
chr21	.	intron	33853952	33854052	.	+	.	Parent=mRNA117
chr21	gth	exon	33854053	33854843	1.000000	+	.	Parent=mRNA117
chr21	gth	mRNA	33837240	33871657	.	+	.	ID=mRNA118;Parent=gene17
chr21	gth	exon	33837240	33837345	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33837346	33840388	.	+	.	Parent=mRNA118
chr21	gth	exon	33840389	33840555	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33840556	33843651	.	+	.	Parent=mRNA118
chr21	gth	exon	33843652	33849567	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33849568	33851331	.	+	.	Parent=mRNA118
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33851493	33851721	.	+	.	Parent=mRNA118
chr21	gth	exon	33851722	33851844	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33851845	33853405	.	+	.	Parent=mRNA118
chr21	gth	exon	33853406	33853552	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33853553	33853762	.	+	.	Parent=mRNA118
chr21	gth	exon	33853763	33853951	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33853952	33861332	.	+	.	Parent=mRNA118
chr21	gth	exon	33861333	33861443	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33861444	33863146	.	+	.	Parent=mRNA118
chr21	gth	exon	33863147	33863263	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33863264	33867483	.	+	.	Parent=mRNA118
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA118
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA118
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA118
chr21	.	intron	33870070	33870593	.	+	.	Parent=mRNA118
chr21	gth	exon	33870594	33871657	1.000000	+	.	Parent=mRNA118
chr21	gth	mRNA	33837240	33871657	.	+	.	ID=mRNA119;Parent=gene17
chr21	gth	exon	33837240	33837345	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33837346	33840388	.	+	.	Parent=mRNA119
chr21	gth	exon	33840389	33840555	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33840556	33843651	.	+	.	Parent=mRNA119
chr21	gth	exon	33843652	33849567	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33849568	33851331	.	+	.	Parent=mRNA119
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33851493	33853405	.	+	.	Parent=mRNA119
chr21	gth	exon	33853406	33853552	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33853553	33853762	.	+	.	Parent=mRNA119
chr21	gth	exon	33853763	33853951	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33853952	33861332	.	+	.	Parent=mRNA119
chr21	gth	exon	33861333	33861443	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33861444	33863146	.	+	.	Parent=mRNA119
chr21	gth	exon	33863147	33863263	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33863264	33866726	.	+	.	Parent=mRNA119
chr21	gth	exon	33866727	33866806	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33866807	33867483	.	+	.	Parent=mRNA119
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA119
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA119
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA119
chr21	.	intron	33870070	33870593	.	+	.	Parent=mRNA119
chr21	gth	exon	33870594	33871657	1.000000	+	.	Parent=mRNA119
chr21	gth	mRNA	33837241	33853232	.	+	.	ID=mRNA120;Parent=gene17
chr21	gth	exon	33837241	33837345	1.000000	+	.	Parent=mRNA120
chr21	.	intron	33837346	33840388	.	+	.	Parent=mRNA120
chr21	gth	exon	33840389	33840555	1.000000	+	.	Parent=mRNA120
chr21	.	intron	33840556	33843651	.	+	.	Parent=mRNA120
chr21	gth	exon	33843652	33849567	1.000000	+	.	Parent=mRNA120
chr21	.	intron	33849568	33851331	.	+	.	Parent=mRNA120
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA120
chr21	.	intron	33851493	33851721	.	+	.	Parent=mRNA120
chr21	gth	exon	33851722	33853232	1.000000	+	.	Parent=mRNA120
chr21	gth	mRNA	33837246	33841215	.	+	.	ID=mRNA121;Parent=gene17
chr21	gth	exon	33837246	33837345	1.000000	+	.	Parent=mRNA121
chr21	.	intron	33837346	33840388	.	+	.	Parent=mRNA121
chr21	gth	exon	33840389	33840555	1.000000	+	.	Parent=mRNA121
chr21	.	intron	33840556	33841176	.	+	.	Parent=mRNA121
chr21	gth	exon	33841177	33841215	1.000000	+	.	Parent=mRNA121
chr21	gth	mRNA	33843772	33871651	.	+	.	ID=mRNA122;Parent=gene17
chr21	gth	exon	33843772	33844420	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33844421	33849481	.	+	.	Parent=mRNA122
chr21	gth	exon	33849482	33849567	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33849568	33851331	.	+	.	Parent=mRNA122
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33851493	33853405	.	+	.	Parent=mRNA122
chr21	gth	exon	33853406	33853552	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33853553	33853762	.	+	.	Parent=mRNA122
chr21	gth	exon	33853763	33853951	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33853952	33861332	.	+	.	Parent=mRNA122
chr21	gth	exon	33861333	33861443	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33861444	33863146	.	+	.	Parent=mRNA122
chr21	gth	exon	33863147	33863263	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33863264	33867483	.	+	.	Parent=mRNA122
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA122
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA122
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA122
chr21	.	intron	33870070	33870593	.	+	.	Parent=mRNA122
chr21	gth	exon	33870594	33871651	1.000000	+	.	Parent=mRNA122
chr21	gth	mRNA	33845060	33871657	.	+	.	ID=mRNA123;Parent=gene17
chr21	gth	exon	33845060	33845465	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33845466	33846423	.	+	.	Parent=mRNA123
chr21	gth	exon	33846424	33849567	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33849568	33851331	.	+	.	Parent=mRNA123
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33851493	33853405	.	+	.	Parent=mRNA123
chr21	gth	exon	33853406	33853552	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33853553	33853762	.	+	.	Parent=mRNA123
chr21	gth	exon	33853763	33853951	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33853952	33861332	.	+	.	Parent=mRNA123
chr21	gth	exon	33861333	33861443	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33861444	33863146	.	+	.	Parent=mRNA123
chr21	gth	exon	33863147	33863263	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33863264	33867483	.	+	.	Parent=mRNA123
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA123
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA123
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA123
chr21	.	intron	33870070	33870540	.	+	.	Parent=mRNA123
chr21	gth	exon	33870541	33871657	1.000000	+	.	Parent=mRNA123
chr21	gth	mRNA	33849225	33861643	.	+	.	ID=mRNA124;Parent=gene17
chr21	gth	exon	33849225	33849567	1.000000	+	.	Parent=mRNA124
chr21	.	intron	33849568	33851331	.	+	.	Parent=mRNA124
chr21	gth	exon	33851332	33851492	1.000000	+	.	Parent=mRNA124
chr21	.	intron	33851493	33853405	.	+	.	Parent=mRNA124
chr21	gth	exon	33853406	33853552	1.000000	+	.	Parent=mRNA124
chr21	.	intron	33853553	33853762	.	+	.	Parent=mRNA124
chr21	gth	exon	33853763	33853951	1.000000	+	.	Parent=mRNA124
chr21	.	intron	33853952	33861332	.	+	.	Parent=mRNA124
chr21	gth	exon	33861333	33861643	1.000000	+	.	Parent=mRNA124
chr21	gth	mRNA	33861355	33863459	.	+	.	ID=mRNA125;Parent=gene17
chr21	gth	exon	33861355	33861443	1.000000	+	.	Parent=mRNA125
chr21	.	intron	33861444	33863146	.	+	.	Parent=mRNA125
chr21	gth	exon	33863147	33863459	1.000000	+	.	Parent=mRNA125
chr21	gth	mRNA	33861361	33870689	.	+	.	ID=mRNA126;Parent=gene17
chr21	gth	exon	33861361	33861443	1.000000	+	.	Parent=mRNA126
chr21	.	intron	33861444	33863146	.	+	.	Parent=mRNA126
chr21	gth	exon	33863147	33863263	1.000000	+	.	Parent=mRNA126
chr21	.	intron	33863264	33866726	.	+	.	Parent=mRNA126
chr21	gth	exon	33866727	33866806	1.000000	+	.	Parent=mRNA126
chr21	.	intron	33866807	33867483	.	+	.	Parent=mRNA126
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA126
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA126
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA126
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA126
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA126
chr21	.	intron	33870070	33870540	.	+	.	Parent=mRNA126
chr21	gth	exon	33870541	33870689	1.000000	+	.	Parent=mRNA126
chr21	gth	mRNA	33863952	33870660	.	+	.	ID=mRNA127;Parent=gene17
chr21	gth	exon	33863952	33864106	1.000000	+	.	Parent=mRNA127
chr21	.	intron	33864107	33865926	.	+	.	Parent=mRNA127
chr21	gth	exon	33865927	33865964	1.000000	+	.	Parent=mRNA127
chr21	.	intron	33865965	33866726	.	+	.	Parent=mRNA127
chr21	gth	exon	33866727	33866806	1.000000	+	.	Parent=mRNA127
chr21	.	intron	33866807	33867483	.	+	.	Parent=mRNA127
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA127
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA127
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA127
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA127
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA127
chr21	.	intron	33870070	33870593	.	+	.	Parent=mRNA127
chr21	gth	exon	33870594	33870660	1.000000	+	.	Parent=mRNA127
chr21	gth	mRNA	33865911	33870623	.	+	.	ID=mRNA128;Parent=gene17
chr21	gth	exon	33865911	33865964	1.000000	+	.	Parent=mRNA128
chr21	.	intron	33865965	33866726	.	+	.	Parent=mRNA128
chr21	gth	exon	33866727	33866806	1.000000	+	.	Parent=mRNA128
chr21	.	intron	33866807	33867483	.	+	.	Parent=mRNA128
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA128
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA128
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA128
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA128
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA128
chr21	.	intron	33870070	33870593	.	+	.	Parent=mRNA128
chr21	gth	exon	33870594	33870623	1.000000	+	.	Parent=mRNA128
chr21	gth	mRNA	33865911	33870645	.	+	.	ID=mRNA129;Parent=gene17
chr21	gth	exon	33865911	33865964	1.000000	+	.	Parent=mRNA129
chr21	.	intron	33865965	33866726	.	+	.	Parent=mRNA129
chr21	gth	exon	33866727	33866806	1.000000	+	.	Parent=mRNA129
chr21	.	intron	33866807	33867483	.	+	.	Parent=mRNA129
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA129
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA129
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA129
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA129
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA129
chr21	.	intron	33870070	33870540	.	+	.	Parent=mRNA129
chr21	gth	exon	33870541	33870645	1.000000	+	.	Parent=mRNA129
chr21	gth	mRNA	33866389	33871657	.	+	.	ID=mRNA130;Parent=gene17
chr21	gth	exon	33866389	33866806	1.000000	+	.	Parent=mRNA130
chr21	.	intron	33866807	33867483	.	+	.	Parent=mRNA130
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA130
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA130
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA130
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA130
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA130
chr21	.	intron	33870070	33870593	.	+	.	Parent=mRNA130
chr21	gth	exon	33870594	33871657	1.000000	+	.	Parent=mRNA130
chr21	gth	mRNA	33866703	33871057	.	+	.	ID=mRNA131;Parent=gene17
chr21	gth	exon	33866703	33866806	1.000000	+	.	Parent=mRNA131
chr21	.	intron	33866807	33867483	.	+	.	Parent=mRNA131
chr21	gth	exon	33867484	33867631	1.000000	+	.	Parent=mRNA131
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA131
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA131
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA131
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA131
chr21	.	intron	33870070	33870540	.	+	.	Parent=mRNA131
chr21	gth	exon	33870541	33871057	1.000000	+	.	Parent=mRNA131
chr21	gth	mRNA	33867201	33870692	.	+	.	ID=mRNA132;Parent=gene17
chr21	gth	exon	33867201	33867631	1.000000	+	.	Parent=mRNA132
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA132
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA132
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA132
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA132
chr21	.	intron	33870070	33870540	.	+	.	Parent=mRNA132
chr21	gth	exon	33870541	33870692	1.000000	+	.	Parent=mRNA132
chr21	gth	mRNA	33867390	33871158	.	+	.	ID=mRNA133;Parent=gene17
chr21	gth	exon	33867390	33867631	1.000000	+	.	Parent=mRNA133
chr21	.	intron	33867632	33869771	.	+	.	Parent=mRNA133
chr21	gth	exon	33869772	33869843	1.000000	+	.	Parent=mRNA133
chr21	.	intron	33869844	33869953	.	+	.	Parent=mRNA133
chr21	gth	exon	33869954	33870069	1.000000	+	.	Parent=mRNA133
chr21	.	intron	33870070	33870593	.	+	.	Parent=mRNA133
chr21	gth	exon	33870594	33871158	1.000000	+	.	Parent=mRNA133
###
chr21	gth	gene	33869653	34210154	.	-	.	ID=gene18
chr21	gth	mRNA	33869653	33882846	.	-	.	ID=mRNA134;Parent=gene18
chr21	gth	exon	33869653	33869984	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33869985	33872474	.	-	.	Parent=mRNA134
chr21	gth	exon	33872475	33872620	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33872621	33873525	.	-	.	Parent=mRNA134
chr21	gth	exon	33873526	33873738	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33873739	33875477	.	-	.	Parent=mRNA134
chr21	gth	exon	33875478	33875676	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33875677	33876126	.	-	.	Parent=mRNA134
chr21	gth	exon	33876127	33876231	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33876232	33876340	.	-	.	Parent=mRNA134
chr21	gth	exon	33876341	33876422	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33876423	33877663	.	-	.	Parent=mRNA134
chr21	gth	exon	33877664	33877842	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33877843	33878765	.	-	.	Parent=mRNA134
chr21	gth	exon	33878766	33878902	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33878903	33880153	.	-	.	Parent=mRNA134
chr21	gth	exon	33880154	33880357	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33880358	33881697	.	-	.	Parent=mRNA134
chr21	gth	exon	33881698	33881778	1.000000	-	.	Parent=mRNA134
chr21	.	intron	33881779	33882496	.	-	.	Parent=mRNA134
chr21	gth	exon	33882497	33882846	1.000000	-	.	Parent=mRNA134
chr21	gth	mRNA	33871737	33882822	.	-	.	ID=mRNA135;Parent=gene18
chr21	gth	exon	33871737	33872620	1.000000	-	.	Parent=mRNA135
chr21	.	intron	33872621	33873525	.	-	.	Parent=mRNA135
chr21	gth	exon	33873526	33873738	1.000000	-	.	Parent=mRNA135
chr21	.	intron	33873739	33875477	.	-	.	Parent=mRNA135
chr21	gth	exon	33875478	33875676	1.000000	-	.	Parent=mRNA135
chr21	.	intron	33875677	33876126	.	-	.	Parent=mRNA135
chr21	gth	exon	33876127	33876231	1.000000	-	.	Parent=mRNA135
chr21	.	intron	33876232	33876340	.	-	.	Parent=mRNA135
chr21	gth	exon	33876341	33876422	1.000000	-	.	Parent=mRNA135
chr21	.	intron	33876423	33877663	.	-	.	Parent=mRNA135
chr21	gth	exon	33877664	33877842	1.000000	-	.	Parent=mRNA135
chr21	.	intron	33877843	33880153	.	-	.	Parent=mRNA135
chr21	gth	exon	33880154	33880357	1.000000	-	.	Parent=mRNA135
chr21	.	intron	33880358	33881697	.	-	.	Parent=mRNA135
chr21	gth	exon	33881698	33881778	1.000000	-	.	Parent=mRNA135
chr21	.	intron	33881779	33882496	.	-	.	Parent=mRNA135
chr21	gth	exon	33882497	33882822	1.000000	-	.	Parent=mRNA135
chr21	gth	mRNA	33872081	33889641	.	-	.	ID=mRNA136;Parent=gene18
chr21	gth	exon	33872081	33872620	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33872621	33873525	.	-	.	Parent=mRNA136
chr21	gth	exon	33873526	33873738	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33873739	33875477	.	-	.	Parent=mRNA136
chr21	gth	exon	33875478	33875676	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33875677	33876126	.	-	.	Parent=mRNA136
chr21	gth	exon	33876127	33876231	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33876232	33876340	.	-	.	Parent=mRNA136
chr21	gth	exon	33876341	33876422	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33876423	33877663	.	-	.	Parent=mRNA136
chr21	gth	exon	33877664	33877842	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33877843	33878765	.	-	.	Parent=mRNA136
chr21	gth	exon	33878766	33878944	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33878945	33880153	.	-	.	Parent=mRNA136
chr21	gth	exon	33880154	33880357	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33880358	33881697	.	-	.	Parent=mRNA136
chr21	gth	exon	33881698	33881778	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33881779	33882496	.	-	.	Parent=mRNA136
chr21	gth	exon	33882497	33883137	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33883138	33884016	.	-	.	Parent=mRNA136
chr21	gth	exon	33884017	33884097	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33884098	33885337	.	-	.	Parent=mRNA136
chr21	gth	exon	33885338	33885547	1.000000	-	.	Parent=mRNA136
chr21	.	intron	33885548	33889531	.	-	.	Parent=mRNA136
chr21	gth	exon	33889532	33889641	1.000000	-	.	Parent=mRNA136
chr21	gth	mRNA	33872093	33882846	.	-	.	ID=mRNA137;Parent=gene18
chr21	gth	exon	33872093	33872620	1.000000	-	.	Parent=mRNA137
chr21	.	intron	33872621	33873525	.	-	.	Parent=mRNA137
chr21	gth	exon	33873526	33873738	1.000000	-	.	Parent=mRNA137
chr21	.	intron	33873739	33875477	.	-	.	Parent=mRNA137
chr21	gth	exon	33875478	33875676	1.000000	-	.	Parent=mRNA137
chr21	.	intron	33875677	33876126	.	-	.	Parent=mRNA137
chr21	gth	exon	33876127	33876231	1.000000	-	.	Parent=mRNA137
chr21	.	intron	33876232	33876340	.	-	.	Parent=mRNA137
chr21	gth	exon	33876341	33876422	1.000000	-	.	Parent=mRNA137
chr21	.	intron	33876423	33878765	.	-	.	Parent=mRNA137
chr21	gth	exon	33878766	33878944	1.000000	-	.	Parent=mRNA137
chr21	.	intron	33878945	33880153	.	-	.	Parent=mRNA137
chr21	gth	exon	33880154	33880236	1.000000	-	.	Parent=mRNA137
chr21	.	intron	33880237	33881697	.	-	.	Parent=mRNA137
chr21	gth	exon	33881698	33881778	1.000000	-	.	Parent=mRNA137
chr21	.	intron	33881779	33882496	.	-	.	Parent=mRNA137
chr21	gth	exon	33882497	33882846	1.000000	-	.	Parent=mRNA137
chr21	gth	mRNA	33872100	33873790	.	-	.	ID=mRNA138;Parent=gene18
chr21	gth	exon	33872100	33872620	1.000000	-	.	Parent=mRNA138
chr21	.	intron	33872621	33873525	.	-	.	Parent=mRNA138
chr21	gth	exon	33873526	33873790	1.000000	-	.	Parent=mRNA138
chr21	gth	mRNA	33872118	33881778	.	-	.	ID=mRNA139;Parent=gene18
chr21	gth	exon	33872118	33872620	1.000000	-	.	Parent=mRNA139
chr21	.	intron	33872621	33873525	.	-	.	Parent=mRNA139
chr21	gth	exon	33873526	33873738	1.000000	-	.	Parent=mRNA139
chr21	.	intron	33873739	33875477	.	-	.	Parent=mRNA139
chr21	gth	exon	33875478	33875676	1.000000	-	.	Parent=mRNA139
chr21	.	intron	33875677	33876126	.	-	.	Parent=mRNA139
chr21	gth	exon	33876127	33876231	1.000000	-	.	Parent=mRNA139
chr21	.	intron	33876232	33876340	.	-	.	Parent=mRNA139
chr21	gth	exon	33876341	33876422	1.000000	-	.	Parent=mRNA139
chr21	.	intron	33876423	33878765	.	-	.	Parent=mRNA139
chr21	gth	exon	33878766	33878944	1.000000	-	.	Parent=mRNA139
chr21	.	intron	33878945	33880153	.	-	.	Parent=mRNA139
chr21	gth	exon	33880154	33880357	1.000000	-	.	Parent=mRNA139
chr21	.	intron	33880358	33881697	.	-	.	Parent=mRNA139
chr21	gth	exon	33881698	33881778	1.000000	-	.	Parent=mRNA139
chr21	gth	mRNA	33872118	33881778	.	-	.	ID=mRNA140;Parent=gene18
chr21	gth	exon	33872118	33872620	1.000000	-	.	Parent=mRNA140
chr21	.	intron	33872621	33873525	.	-	.	Parent=mRNA140
chr21	gth	exon	33873526	33873738	1.000000	-	.	Parent=mRNA140
chr21	.	intron	33873739	33878765	.	-	.	Parent=mRNA140
chr21	gth	exon	33878766	33878944	1.000000	-	.	Parent=mRNA140
chr21	.	intron	33878945	33880153	.	-	.	Parent=mRNA140
chr21	gth	exon	33880154	33880357	1.000000	-	.	Parent=mRNA140
chr21	.	intron	33880358	33881697	.	-	.	Parent=mRNA140
chr21	gth	exon	33881698	33881778	1.000000	-	.	Parent=mRNA140
chr21	gth	mRNA	33872377	33882810	.	-	.	ID=mRNA141;Parent=gene18
chr21	gth	exon	33872377	33872620	1.000000	-	.	Parent=mRNA141
chr21	.	intron	33872621	33873525	.	-	.	Parent=mRNA141
chr21	gth	exon	33873526	33873738	1.000000	-	.	Parent=mRNA141
chr21	.	intron	33873739	33875477	.	-	.	Parent=mRNA141
chr21	gth	exon	33875478	33875676	1.000000	-	.	Parent=mRNA141
chr21	.	intron	33875677	33876126	.	-	.	Parent=mRNA141
chr21	gth	exon	33876127	33876231	1.000000	-	.	Parent=mRNA141
chr21	.	intron	33876232	33876340	.	-	.	Parent=mRNA141
chr21	gth	exon	33876341	33876422	1.000000	-	.	Parent=mRNA141
chr21	.	intron	33876423	33877663	.	-	.	Parent=mRNA141
chr21	gth	exon	33877664	33877842	1.000000	-	.	Parent=mRNA141
chr21	.	intron	33877843	33878765	.	-	.	Parent=mRNA141
chr21	gth	exon	33878766	33878944	1.000000	-	.	Parent=mRNA141
chr21	.	intron	33878945	33880153	.	-	.	Parent=mRNA141
chr21	gth	exon	33880154	33880357	1.000000	-	.	Parent=mRNA141
chr21	.	intron	33880358	33882496	.	-	.	Parent=mRNA141
chr21	gth	exon	33882497	33882810	1.000000	-	.	Parent=mRNA141
chr21	gth	mRNA	33873700	34206505	.	-	.	ID=mRNA142;Parent=gene18
chr21	gth	exon	33873700	33873738	1.000000	-	.	Parent=mRNA142
chr21	.	intron	33873739	33875477	.	-	.	Parent=mRNA142
chr21	gth	exon	33875478	33875676	1.000000	-	.	Parent=mRNA142
chr21	.	intron	33875677	33876126	.	-	.	Parent=mRNA142
chr21	gth	exon	33876127	33876231	1.000000	-	.	Parent=mRNA142
chr21	.	intron	33876232	33878765	.	-	.	Parent=mRNA142
chr21	gth	exon	33878766	33878944	1.000000	-	.	Parent=mRNA142
chr21	.	intron	33878945	33880153	.	-	.	Parent=mRNA142
chr21	gth	exon	33880154	33880357	1.000000	-	.	Parent=mRNA142
chr21	.	intron	33880358	34201514	.	-	.	Parent=mRNA142
chr21	gth	exon	34201515	34201627	1.000000	-	.	Parent=mRNA142
chr21	.	intron	34201628	34203255	.	-	.	Parent=mRNA142
chr21	gth	exon	34203256	34203385	1.000000	-	.	Parent=mRNA142
chr21	.	intron	34203386	34206462	.	-	.	Parent=mRNA142
chr21	gth	exon	34206463	34206505	1.000000	-	.	Parent=mRNA142
chr21	gth	mRNA	33875351	33876230	.	-	.	ID=mRNA143;Parent=gene18
chr21	gth	exon	33875351	33875676	1.000000	-	.	Parent=mRNA143
chr21	.	intron	33875677	33876126	.	-	.	Parent=mRNA143
chr21	gth	exon	33876127	33876230	1.000000	-	.	Parent=mRNA143
chr21	gth	mRNA	33883517	33935936	.	-	.	ID=mRNA144;Parent=gene18
chr21	gth	exon	33883517	33884097	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33884098	33885337	.	-	.	Parent=mRNA144
chr21	gth	exon	33885338	33885383	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33885384	33889906	.	-	.	Parent=mRNA144
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA144
chr21	gth	exon	33891456	33891577	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33891578	33893325	.	-	.	Parent=mRNA144
chr21	gth	exon	33893326	33893424	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33893425	33896409	.	-	.	Parent=mRNA144
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA144
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA144
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA144
chr21	gth	exon	33910882	33910926	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33910927	33916171	.	-	.	Parent=mRNA144
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA144
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA144
chr21	gth	exon	33925662	33925733	1.000000	-	.	Parent=mRNA144
chr21	.	intron	33925734	33935856	.	-	.	Parent=mRNA144
chr21	gth	exon	33935857	33935936	1.000000	-	.	Parent=mRNA144
chr21	gth	mRNA	33883562	33936094	.	-	.	ID=mRNA145;Parent=gene18
chr21	gth	exon	33883562	33884097	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33884098	33885337	.	-	.	Parent=mRNA145
chr21	gth	exon	33885338	33885383	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33885384	33889906	.	-	.	Parent=mRNA145
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA145
chr21	gth	exon	33891456	33891577	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33891578	33893325	.	-	.	Parent=mRNA145
chr21	gth	exon	33893326	33893424	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33893425	33896409	.	-	.	Parent=mRNA145
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA145
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA145
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33907783	33916171	.	-	.	Parent=mRNA145
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA145
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA145
chr21	gth	exon	33925662	33925733	1.000000	-	.	Parent=mRNA145
chr21	.	intron	33925734	33935856	.	-	.	Parent=mRNA145
chr21	gth	exon	33935857	33936094	1.000000	-	.	Parent=mRNA145
chr21	gth	mRNA	33883637	33885894	.	-	.	ID=mRNA146;Parent=gene18
chr21	gth	exon	33883637	33884097	1.000000	-	.	Parent=mRNA146
chr21	.	intron	33884098	33885337	.	-	.	Parent=mRNA146
chr21	gth	exon	33885338	33885894	1.000000	-	.	Parent=mRNA146
chr21	gth	mRNA	33883643	33935923	.	-	.	ID=mRNA147;Parent=gene18
chr21	gth	exon	33883643	33884097	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33884098	33885337	.	-	.	Parent=mRNA147
chr21	gth	exon	33885338	33885387	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33885388	33889906	.	-	.	Parent=mRNA147
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA147
chr21	gth	exon	33891456	33891577	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33891578	33893325	.	-	.	Parent=mRNA147
chr21	gth	exon	33893326	33893424	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33893425	33896409	.	-	.	Parent=mRNA147
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA147
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA147
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA147
chr21	gth	exon	33910882	33910926	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33910927	33916171	.	-	.	Parent=mRNA147
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA147
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA147
chr21	gth	exon	33925662	33925733	1.000000	-	.	Parent=mRNA147
chr21	.	intron	33925734	33935856	.	-	.	Parent=mRNA147
chr21	gth	exon	33935857	33935923	1.000000	-	.	Parent=mRNA147
chr21	gth	mRNA	33883644	33911352	.	-	.	ID=mRNA148;Parent=gene18
chr21	gth	exon	33883644	33884097	1.000000	-	.	Parent=mRNA148
chr21	.	intron	33884098	33885337	.	-	.	Parent=mRNA148
chr21	gth	exon	33885338	33885547	1.000000	-	.	Parent=mRNA148
chr21	.	intron	33885548	33889531	.	-	.	Parent=mRNA148
chr21	gth	exon	33889532	33889790	1.000000	-	.	Parent=mRNA148
chr21	.	intron	33889791	33889906	.	-	.	Parent=mRNA148
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA148
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA148
chr21	gth	exon	33891456	33891577	1.000000	-	.	Parent=mRNA148
chr21	.	intron	33891578	33893325	.	-	.	Parent=mRNA148
chr21	gth	exon	33893326	33893461	1.000000	-	.	Parent=mRNA148
chr21	.	intron	33893462	33896409	.	-	.	Parent=mRNA148
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA148
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA148
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA148
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA148
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA148
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA148
chr21	gth	exon	33910882	33911352	1.000000	-	.	Parent=mRNA148
chr21	gth	mRNA	33883721	33891579	.	-	.	ID=mRNA149;Parent=gene18
chr21	gth	exon	33883721	33883981	1.000000	-	.	Parent=mRNA149
chr21	.	intron	33883982	33885337	.	-	.	Parent=mRNA149
chr21	gth	exon	33885338	33885383	1.000000	-	.	Parent=mRNA149
chr21	.	intron	33885384	33889906	.	-	.	Parent=mRNA149
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA149
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA149
chr21	gth	exon	33891456	33891579	1.000000	-	.	Parent=mRNA149
chr21	gth	mRNA	33883736	33891576	.	-	.	ID=mRNA150;Parent=gene18
chr21	gth	exon	33883736	33884097	1.000000	-	.	Parent=mRNA150
chr21	.	intron	33884098	33885337	.	-	.	Parent=mRNA150
chr21	gth	exon	33885338	33885404	1.000000	-	.	Parent=mRNA150
chr21	.	intron	33885405	33889906	.	-	.	Parent=mRNA150
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA150
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA150
chr21	gth	exon	33891456	33891576	1.000000	-	.	Parent=mRNA150
chr21	gth	mRNA	33883945	33896441	.	-	.	ID=mRNA151;Parent=gene18
chr21	gth	exon	33883945	33884097	1.000000	-	.	Parent=mRNA151
chr21	.	intron	33884098	33885337	.	-	.	Parent=mRNA151
chr21	gth	exon	33885338	33885383	1.000000	-	.	Parent=mRNA151
chr21	.	intron	33885384	33889906	.	-	.	Parent=mRNA151
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA151
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA151
chr21	gth	exon	33891456	33891577	1.000000	-	.	Parent=mRNA151
chr21	.	intron	33891578	33893325	.	-	.	Parent=mRNA151
chr21	gth	exon	33893326	33893461	1.000000	-	.	Parent=mRNA151
chr21	.	intron	33893462	33896409	.	-	.	Parent=mRNA151
chr21	gth	exon	33896410	33896441	1.000000	-	.	Parent=mRNA151
chr21	gth	mRNA	33888683	33935935	.	-	.	ID=mRNA152;Parent=gene18
chr21	gth	exon	33888683	33889790	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33889791	33889906	.	-	.	Parent=mRNA152
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA152
chr21	gth	exon	33891456	33891577	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33891578	33893325	.	-	.	Parent=mRNA152
chr21	gth	exon	33893326	33893424	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33893425	33896409	.	-	.	Parent=mRNA152
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA152
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA152
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA152
chr21	gth	exon	33910882	33910926	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33910927	33916171	.	-	.	Parent=mRNA152
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA152
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA152
chr21	gth	exon	33925662	33925733	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33925734	33935354	.	-	.	Parent=mRNA152
chr21	gth	exon	33935355	33935481	1.000000	-	.	Parent=mRNA152
chr21	.	intron	33935482	33935856	.	-	.	Parent=mRNA152
chr21	gth	exon	33935857	33935935	1.000000	-	.	Parent=mRNA152
chr21	gth	mRNA	33888819	33935917	.	-	.	ID=mRNA153;Parent=gene18
chr21	gth	exon	33888819	33889792	0.998973	-	.	Parent=mRNA153
chr21	.	intron	33889793	33889906	.	-	.	Parent=mRNA153
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA153
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA153
chr21	gth	exon	33891456	33891577	1.000000	-	.	Parent=mRNA153
chr21	.	intron	33891578	33893325	.	-	.	Parent=mRNA153
chr21	gth	exon	33893326	33893461	1.000000	-	.	Parent=mRNA153
chr21	.	intron	33893462	33896409	.	-	.	Parent=mRNA153
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA153
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA153
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA153
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA153
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA153
chr21	.	intron	33907783	33916171	.	-	.	Parent=mRNA153
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA153
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA153
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA153
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA153
chr21	gth	exon	33925662	33925733	1.000000	-	.	Parent=mRNA153
chr21	.	intron	33925734	33935856	.	-	.	Parent=mRNA153
chr21	gth	exon	33935857	33935917	1.000000	-	.	Parent=mRNA153
chr21	gth	mRNA	33888838	33936514	.	-	.	ID=mRNA154;Parent=gene18
chr21	gth	exon	33888838	33889790	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33889791	33889906	.	-	.	Parent=mRNA154
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33890013	33891455	.	-	.	Parent=mRNA154
chr21	gth	exon	33891456	33891577	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33891578	33893325	.	-	.	Parent=mRNA154
chr21	gth	exon	33893326	33893461	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33893462	33896409	.	-	.	Parent=mRNA154
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA154
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA154
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA154
chr21	gth	exon	33910882	33910926	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33910927	33916171	.	-	.	Parent=mRNA154
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA154
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA154
chr21	gth	exon	33925662	33925733	1.000000	-	.	Parent=mRNA154
chr21	.	intron	33925734	33935856	.	-	.	Parent=mRNA154
chr21	gth	exon	33935857	33936514	1.000000	-	.	Parent=mRNA154
chr21	gth	mRNA	33889307	33927878	.	-	.	ID=mRNA155;Parent=gene18
chr21	gth	exon	33889307	33889704	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33889705	33891455	.	-	.	Parent=mRNA155
chr21	gth	exon	33891456	33891577	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33891578	33893325	.	-	.	Parent=mRNA155
chr21	gth	exon	33893326	33893424	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33893425	33896409	.	-	.	Parent=mRNA155
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA155
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA155
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA155
chr21	gth	exon	33910882	33910926	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33910927	33916171	.	-	.	Parent=mRNA155
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA155
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA155
chr21	gth	exon	33925662	33925733	1.000000	-	.	Parent=mRNA155
chr21	.	intron	33925734	33927821	.	-	.	Parent=mRNA155
chr21	gth	exon	33927822	33927878	1.000000	-	.	Parent=mRNA155
chr21	gth	mRNA	33889513	33935921	.	-	.	ID=mRNA156;Parent=gene18
chr21	gth	exon	33889513	33889790	1.000000	-	.	Parent=mRNA156
chr21	.	intron	33889791	33889906	.	-	.	Parent=mRNA156
chr21	gth	exon	33889907	33890012	1.000000	-	.	Parent=mRNA156
chr21	.	intron	33890013	33893325	.	-	.	Parent=mRNA156
chr21	gth	exon	33893326	33893424	1.000000	-	.	Parent=mRNA156
chr21	.	intron	33893425	33896409	.	-	.	Parent=mRNA156
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA156
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA156
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA156
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA156
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA156
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA156
chr21	gth	exon	33910882	33910926	1.000000	-	.	Parent=mRNA156
chr21	.	intron	33910927	33916171	.	-	.	Parent=mRNA156
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA156
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA156
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA156
chr21	.	intron	33918937	33935856	.	-	.	Parent=mRNA156
chr21	gth	exon	33935857	33935921	1.000000	-	.	Parent=mRNA156
chr21	gth	mRNA	33890238	33911352	.	-	.	ID=mRNA157;Parent=gene18
chr21	gth	exon	33890238	33890389	1.000000	-	.	Parent=mRNA157
chr21	.	intron	33890390	33893325	.	-	.	Parent=mRNA157
chr21	gth	exon	33893326	33893424	1.000000	-	.	Parent=mRNA157
chr21	.	intron	33893425	33896409	.	-	.	Parent=mRNA157
chr21	gth	exon	33896410	33896521	1.000000	-	.	Parent=mRNA157
chr21	.	intron	33896522	33897579	.	-	.	Parent=mRNA157
chr21	gth	exon	33897580	33897713	1.000000	-	.	Parent=mRNA157
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA157
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA157
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA157
chr21	gth	exon	33910882	33911352	1.000000	-	.	Parent=mRNA157
chr21	gth	mRNA	33897332	33935896	.	-	.	ID=mRNA158;Parent=gene18
chr21	gth	exon	33897332	33897713	1.000000	-	.	Parent=mRNA158
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA158
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA158
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA158
chr21	gth	exon	33910882	33910926	1.000000	-	.	Parent=mRNA158
chr21	.	intron	33910927	33916171	.	-	.	Parent=mRNA158
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA158
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA158
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA158
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA158
chr21	gth	exon	33925662	33925733	1.000000	-	.	Parent=mRNA158
chr21	.	intron	33925734	33935856	.	-	.	Parent=mRNA158
chr21	gth	exon	33935857	33935896	1.000000	-	.	Parent=mRNA158
chr21	gth	mRNA	33897567	33935906	.	-	.	ID=mRNA159;Parent=gene18
chr21	gth	exon	33897567	33897713	0.952381	-	.	Parent=mRNA159
chr21	.	intron	33897714	33907713	.	-	.	Parent=mRNA159
chr21	gth	exon	33907714	33907782	1.000000	-	.	Parent=mRNA159
chr21	.	intron	33907783	33910881	.	-	.	Parent=mRNA159
chr21	gth	exon	33910882	33910926	1.000000	-	.	Parent=mRNA159
chr21	.	intron	33910927	33916171	.	-	.	Parent=mRNA159
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA159
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA159
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA159
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA159
chr21	gth	exon	33925662	33925703	1.000000	-	.	Parent=mRNA159
chr21	.	intron	33925704	33935856	.	-	.	Parent=mRNA159
chr21	gth	exon	33935857	33935906	1.000000	-	.	Parent=mRNA159
chr21	gth	mRNA	33910463	33935898	.	-	.	ID=mRNA160;Parent=gene18
chr21	gth	exon	33910463	33910779	1.000000	-	.	Parent=mRNA160
chr21	.	intron	33910780	33910881	.	-	.	Parent=mRNA160
chr21	gth	exon	33910882	33910926	1.000000	-	.	Parent=mRNA160
chr21	.	intron	33910927	33916171	.	-	.	Parent=mRNA160
chr21	gth	exon	33916172	33916244	1.000000	-	.	Parent=mRNA160
chr21	.	intron	33916245	33918858	.	-	.	Parent=mRNA160
chr21	gth	exon	33918859	33918936	1.000000	-	.	Parent=mRNA160
chr21	.	intron	33918937	33925661	.	-	.	Parent=mRNA160
chr21	gth	exon	33925662	33925733	1.000000	-	.	Parent=mRNA160
chr21	.	intron	33925734	33935856	.	-	.	Parent=mRNA160
chr21	gth	exon	33935857	33935898	1.000000	-	.	Parent=mRNA160
chr21	gth	mRNA	33925669	33938102	.	-	.	ID=mRNA161;Parent=gene18
chr21	gth	exon	33925669	33925733	1.000000	-	.	Parent=mRNA161
chr21	.	intron	33925734	33937547	.	-	.	Parent=mRNA161
chr21	gth	exon	33937548	33938102	1.000000	-	.	Parent=mRNA161
chr21	gth	mRNA	33933921	33935897	.	-	.	ID=mRNA162;Parent=gene18
chr21	gth	exon	33933921	33934364	1.000000	-	.	Parent=mRNA162
chr21	.	intron	33934365	33935354	.	-	.	Parent=mRNA162
chr21	gth	exon	33935355	33935481	1.000000	-	.	Parent=mRNA162
chr21	.	intron	33935482	33935856	.	-	.	Parent=mRNA162
chr21	gth	exon	33935857	33935897	1.000000	-	.	Parent=mRNA162
chr21	gth	mRNA	34197627	34199755	.	-	.	ID=mRNA163;Parent=gene18
chr21	gth	exon	34197627	34197813	1.000000	-	.	Parent=mRNA163
chr21	.	intron	34197814	34198108	.	-	.	Parent=mRNA163
chr21	gth	exon	34198109	34198746	1.000000	-	.	Parent=mRNA163
chr21	.	intron	34198747	34198853	.	-	.	Parent=mRNA163
chr21	gth	exon	34198854	34199755	0.998891	-	.	Parent=mRNA163
chr21	gth	mRNA	34197627	34209935	.	-	.	ID=mRNA164;Parent=gene18
chr21	gth	exon	34197627	34197813	1.000000	-	.	Parent=mRNA164
chr21	.	intron	34197814	34198108	.	-	.	Parent=mRNA164
chr21	gth	exon	34198109	34198195	1.000000	-	.	Parent=mRNA164
chr21	.	intron	34198196	34201514	.	-	.	Parent=mRNA164
chr21	gth	exon	34201515	34201627	1.000000	-	.	Parent=mRNA164
chr21	.	intron	34201628	34206462	.	-	.	Parent=mRNA164
chr21	gth	exon	34206463	34206573	1.000000	-	.	Parent=mRNA164
chr21	.	intron	34206574	34208623	.	-	.	Parent=mRNA164
chr21	gth	exon	34208624	34208674	1.000000	-	.	Parent=mRNA164
chr21	.	intron	34208675	34209901	.	-	.	Parent=mRNA164
chr21	gth	exon	34209902	34209935	1.000000	-	.	Parent=mRNA164
chr21	gth	mRNA	34197627	34209942	.	-	.	ID=mRNA165;Parent=gene18
chr21	gth	exon	34197627	34197813	1.000000	-	.	Parent=mRNA165
chr21	.	intron	34197814	34198108	.	-	.	Parent=mRNA165
chr21	gth	exon	34198109	34198195	1.000000	-	.	Parent=mRNA165
chr21	.	intron	34198196	34200622	.	-	.	Parent=mRNA165
chr21	gth	exon	34200623	34201627	1.000000	-	.	Parent=mRNA165
chr21	.	intron	34201628	34203255	.	-	.	Parent=mRNA165
chr21	gth	exon	34203256	34203385	1.000000	-	.	Parent=mRNA165
chr21	.	intron	34203386	34206462	.	-	.	Parent=mRNA165
chr21	gth	exon	34206463	34206573	1.000000	-	.	Parent=mRNA165
chr21	.	intron	34206574	34208623	.	-	.	Parent=mRNA165
chr21	gth	exon	34208624	34209942	1.000000	-	.	Parent=mRNA165
chr21	gth	mRNA	34197627	34210154	.	-	.	ID=mRNA166;Parent=gene18
chr21	gth	exon	34197627	34197813	1.000000	-	.	Parent=mRNA166
chr21	.	intron	34197814	34198108	.	-	.	Parent=mRNA166
chr21	gth	exon	34198109	34198195	1.000000	-	.	Parent=mRNA166
chr21	.	intron	34198196	34201514	.	-	.	Parent=mRNA166
chr21	gth	exon	34201515	34201627	1.000000	-	.	Parent=mRNA166
chr21	.	intron	34201628	34203255	.	-	.	Parent=mRNA166
chr21	gth	exon	34203256	34203385	1.000000	-	.	Parent=mRNA166
chr21	.	intron	34203386	34206462	.	-	.	Parent=mRNA166
chr21	gth	exon	34206463	34206573	1.000000	-	.	Parent=mRNA166
chr21	.	intron	34206574	34208623	.	-	.	Parent=mRNA166
chr21	gth	exon	34208624	34208674	1.000000	-	.	Parent=mRNA166
chr21	.	intron	34208675	34209901	.	-	.	Parent=mRNA166
chr21	gth	exon	34209902	34210154	1.000000	-	.	Parent=mRNA166
chr21	gth	mRNA	34197630	34201586	.	-	.	ID=mRNA167;Parent=gene18
chr21	gth	exon	34197630	34197813	1.000000	-	.	Parent=mRNA167
chr21	.	intron	34197814	34198108	.	-	.	Parent=mRNA167
chr21	gth	exon	34198109	34198195	1.000000	-	.	Parent=mRNA167
chr21	.	intron	34198196	34200622	.	-	.	Parent=mRNA167
chr21	gth	exon	34200623	34200674	1.000000	-	.	Parent=mRNA167
chr21	.	intron	34200675	34200901	.	-	.	Parent=mRNA167
chr21	gth	exon	34200902	34200968	1.000000	-	.	Parent=mRNA167
chr21	.	intron	34200969	34201514	.	-	.	Parent=mRNA167
chr21	gth	exon	34201515	34201586	1.000000	-	.	Parent=mRNA167
chr21	gth	mRNA	34197630	34201627	.	-	.	ID=mRNA168;Parent=gene18
chr21	gth	exon	34197630	34197830	1.000000	-	.	Parent=mRNA168
chr21	.	intron	34197831	34198108	.	-	.	Parent=mRNA168
chr21	gth	exon	34198109	34198195	1.000000	-	.	Parent=mRNA168
chr21	.	intron	34198196	34201514	.	-	.	Parent=mRNA168
chr21	gth	exon	34201515	34201627	1.000000	-	.	Parent=mRNA168
chr21	gth	mRNA	34202988	34209927	.	-	.	ID=mRNA169;Parent=gene18
chr21	gth	exon	34202988	34203385	1.000000	-	.	Parent=mRNA169
chr21	.	intron	34203386	34206462	.	-	.	Parent=mRNA169
chr21	gth	exon	34206463	34206573	1.000000	-	.	Parent=mRNA169
chr21	.	intron	34206574	34208623	.	-	.	Parent=mRNA169
chr21	gth	exon	34208624	34208674	1.000000	-	.	Parent=mRNA169
chr21	.	intron	34208675	34209901	.	-	.	Parent=mRNA169
chr21	gth	exon	34209902	34209927	1.000000	-	.	Parent=mRNA169
chr21	gth	mRNA	34206541	34209898	.	-	.	ID=mRNA170;Parent=gene18
chr21	gth	exon	34206541	34206573	1.000000	-	.	Parent=mRNA170
chr21	.	intron	34206574	34208623	.	-	.	Parent=mRNA170
chr21	gth	exon	34208624	34208674	1.000000	-	.	Parent=mRNA170
chr21	.	intron	34208675	34209309	.	-	.	Parent=mRNA170
chr21	gth	exon	34209310	34209898	1.000000	-	.	Parent=mRNA170
chr21	gth	mRNA	34206552	34209953	.	-	.	ID=mRNA171;Parent=gene18
chr21	gth	exon	34206552	34206573	1.000000	-	.	Parent=mRNA171
chr21	.	intron	34206574	34208623	.	-	.	Parent=mRNA171
chr21	gth	exon	34208624	34208674	1.000000	-	.	Parent=mRNA171
chr21	.	intron	34208675	34209557	.	-	.	Parent=mRNA171
chr21	gth	exon	34209558	34209953	1.000000	-	.	Parent=mRNA171
###
chr21	gth	gene	33936576	34194035	.	+	.	ID=gene19
chr21	gth	mRNA	33936576	34131192	.	+	.	ID=mRNA172;Parent=gene19
chr21	gth	exon	33936576	33936889	1.000000	+	.	Parent=mRNA172
chr21	.	intron	33936890	34012971	.	+	.	Parent=mRNA172
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA172
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34015446	34016762	.	+	.	Parent=mRNA172
chr21	gth	exon	34016763	34016826	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34016827	34029218	.	+	.	Parent=mRNA172
chr21	gth	exon	34029219	34029379	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34029380	34044428	.	+	.	Parent=mRNA172
chr21	gth	exon	34044429	34044497	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34044498	34045984	.	+	.	Parent=mRNA172
chr21	gth	exon	34045985	34046081	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34046082	34049471	.	+	.	Parent=mRNA172
chr21	gth	exon	34049472	34049572	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34049573	34056096	.	+	.	Parent=mRNA172
chr21	gth	exon	34056097	34056160	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34056161	34060048	.	+	.	Parent=mRNA172
chr21	gth	exon	34060049	34060186	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34060187	34061886	.	+	.	Parent=mRNA172
chr21	gth	exon	34061887	34062002	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34062003	34066234	.	+	.	Parent=mRNA172
chr21	gth	exon	34066235	34066497	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34066498	34068902	.	+	.	Parent=mRNA172
chr21	gth	exon	34068903	34069052	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34069053	34069141	.	+	.	Parent=mRNA172
chr21	gth	exon	34069142	34069282	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34069283	34075634	.	+	.	Parent=mRNA172
chr21	gth	exon	34075635	34075722	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34075723	34076167	.	+	.	Parent=mRNA172
chr21	gth	exon	34076168	34076307	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34076308	34088514	.	+	.	Parent=mRNA172
chr21	gth	exon	34088515	34088642	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34088643	34091552	.	+	.	Parent=mRNA172
chr21	gth	exon	34091553	34091782	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34091783	34093981	.	+	.	Parent=mRNA172
chr21	gth	exon	34093982	34094103	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34094104	34105148	.	+	.	Parent=mRNA172
chr21	gth	exon	34105149	34105396	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34105397	34108086	.	+	.	Parent=mRNA172
chr21	gth	exon	34108087	34108246	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34108247	34112440	.	+	.	Parent=mRNA172
chr21	gth	exon	34112441	34112646	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA172
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34113498	34117660	.	+	.	Parent=mRNA172
chr21	gth	exon	34117661	34117827	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34117828	34120991	.	+	.	Parent=mRNA172
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34121038	34123797	.	+	.	Parent=mRNA172
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA172
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA172
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA172
chr21	.	intron	34130807	34131160	.	+	.	Parent=mRNA172
chr21	gth	exon	34131161	34131192	1.000000	+	.	Parent=mRNA172
chr21	gth	mRNA	33936576	34132672	.	+	.	ID=mRNA173;Parent=gene19
chr21	gth	exon	33936576	33936889	1.000000	+	.	Parent=mRNA173
chr21	.	intron	33936890	34012971	.	+	.	Parent=mRNA173
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA173
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34015446	34016762	.	+	.	Parent=mRNA173
chr21	gth	exon	34016763	34016826	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34016827	34029218	.	+	.	Parent=mRNA173
chr21	gth	exon	34029219	34029379	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34029380	34044428	.	+	.	Parent=mRNA173
chr21	gth	exon	34044429	34044497	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34044498	34045984	.	+	.	Parent=mRNA173
chr21	gth	exon	34045985	34046081	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34046082	34049471	.	+	.	Parent=mRNA173
chr21	gth	exon	34049472	34049572	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34049573	34056096	.	+	.	Parent=mRNA173
chr21	gth	exon	34056097	34056160	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34056161	34060048	.	+	.	Parent=mRNA173
chr21	gth	exon	34060049	34060186	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34060187	34061886	.	+	.	Parent=mRNA173
chr21	gth	exon	34061887	34062002	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34062003	34066234	.	+	.	Parent=mRNA173
chr21	gth	exon	34066235	34066497	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34066498	34068902	.	+	.	Parent=mRNA173
chr21	gth	exon	34068903	34069052	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34069053	34069141	.	+	.	Parent=mRNA173
chr21	gth	exon	34069142	34069282	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34069283	34075634	.	+	.	Parent=mRNA173
chr21	gth	exon	34075635	34075722	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34075723	34076167	.	+	.	Parent=mRNA173
chr21	gth	exon	34076168	34076307	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34076308	34088514	.	+	.	Parent=mRNA173
chr21	gth	exon	34088515	34088642	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34088643	34091552	.	+	.	Parent=mRNA173
chr21	gth	exon	34091553	34091782	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34091783	34093981	.	+	.	Parent=mRNA173
chr21	gth	exon	34093982	34094103	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34094104	34105148	.	+	.	Parent=mRNA173
chr21	gth	exon	34105149	34105396	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34105397	34108086	.	+	.	Parent=mRNA173
chr21	gth	exon	34108087	34108246	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34108247	34112440	.	+	.	Parent=mRNA173
chr21	gth	exon	34112441	34112646	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA173
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34113498	34123797	.	+	.	Parent=mRNA173
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA173
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA173
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34130807	34131160	.	+	.	Parent=mRNA173
chr21	gth	exon	34131161	34131197	1.000000	+	.	Parent=mRNA173
chr21	.	intron	34131198	34131419	.	+	.	Parent=mRNA173
chr21	gth	exon	34131420	34132672	1.000000	+	.	Parent=mRNA173
chr21	gth	mRNA	33936628	34036947	.	+	.	ID=mRNA174;Parent=gene19
chr21	gth	exon	33936628	33936889	1.000000	+	.	Parent=mRNA174
chr21	.	intron	33936890	33983496	.	+	.	Parent=mRNA174
chr21	gth	exon	33983497	33983558	1.000000	+	.	Parent=mRNA174
chr21	.	intron	33983559	34010605	.	+	.	Parent=mRNA174
chr21	gth	exon	34010606	34010730	1.000000	+	.	Parent=mRNA174
chr21	.	intron	34010731	34012971	.	+	.	Parent=mRNA174
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA174
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA174
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA174
chr21	.	intron	34015446	34016762	.	+	.	Parent=mRNA174
chr21	gth	exon	34016763	34016826	1.000000	+	.	Parent=mRNA174
chr21	.	intron	34016827	34029218	.	+	.	Parent=mRNA174
chr21	gth	exon	34029219	34030908	1.000000	+	.	Parent=mRNA174
chr21	.	intron	34030909	34034991	.	+	.	Parent=mRNA174
chr21	gth	exon	34034992	34035796	1.000000	+	.	Parent=mRNA174
chr21	.	intron	34035797	34036516	.	+	.	Parent=mRNA174
chr21	gth	exon	34036517	34036947	1.000000	+	.	Parent=mRNA174
chr21	gth	mRNA	33936629	34016166	.	+	.	ID=mRNA175;Parent=gene19
chr21	gth	exon	33936629	33936889	1.000000	+	.	Parent=mRNA175
chr21	.	intron	33936890	34012971	.	+	.	Parent=mRNA175
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA175
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA175
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA175
chr21	.	intron	34015446	34016106	.	+	.	Parent=mRNA175
chr21	gth	exon	34016107	34016166	1.000000	+	.	Parent=mRNA175
chr21	gth	mRNA	33936634	34194035	.	+	.	ID=mRNA176;Parent=gene19
chr21	gth	exon	33936634	33936889	1.000000	+	.	Parent=mRNA176
chr21	.	intron	33936890	34012971	.	+	.	Parent=mRNA176
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA176
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34015446	34016762	.	+	.	Parent=mRNA176
chr21	gth	exon	34016763	34016826	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34016827	34029218	.	+	.	Parent=mRNA176
chr21	gth	exon	34029219	34029379	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34029380	34044317	.	+	.	Parent=mRNA176
chr21	gth	exon	34044318	34044497	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34044498	34045984	.	+	.	Parent=mRNA176
chr21	gth	exon	34045985	34046081	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34046082	34049471	.	+	.	Parent=mRNA176
chr21	gth	exon	34049472	34049572	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34049573	34056096	.	+	.	Parent=mRNA176
chr21	gth	exon	34056097	34056160	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34056161	34060048	.	+	.	Parent=mRNA176
chr21	gth	exon	34060049	34060186	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34060187	34061886	.	+	.	Parent=mRNA176
chr21	gth	exon	34061887	34062002	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34062003	34066234	.	+	.	Parent=mRNA176
chr21	gth	exon	34066235	34066497	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34066498	34068902	.	+	.	Parent=mRNA176
chr21	gth	exon	34068903	34069052	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34069053	34069141	.	+	.	Parent=mRNA176
chr21	gth	exon	34069142	34069282	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34069283	34075634	.	+	.	Parent=mRNA176
chr21	gth	exon	34075635	34075722	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34075723	34076167	.	+	.	Parent=mRNA176
chr21	gth	exon	34076168	34076307	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34076308	34088514	.	+	.	Parent=mRNA176
chr21	gth	exon	34088515	34088642	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34088643	34091552	.	+	.	Parent=mRNA176
chr21	gth	exon	34091553	34091782	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34091783	34093981	.	+	.	Parent=mRNA176
chr21	gth	exon	34093982	34094118	0.927007	+	.	Parent=mRNA176
chr21	.	intron	34094119	34105148	.	+	.	Parent=mRNA176
chr21	gth	exon	34105149	34105396	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34105397	34108086	.	+	.	Parent=mRNA176
chr21	gth	exon	34108087	34108246	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34108247	34112440	.	+	.	Parent=mRNA176
chr21	gth	exon	34112441	34112646	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA176
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34113498	34117660	.	+	.	Parent=mRNA176
chr21	gth	exon	34117661	34117827	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34117828	34120991	.	+	.	Parent=mRNA176
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34121038	34123797	.	+	.	Parent=mRNA176
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA176
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA176
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34130807	34150909	.	+	.	Parent=mRNA176
chr21	gth	exon	34150910	34151031	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34151032	34152859	.	+	.	Parent=mRNA176
chr21	gth	exon	34152860	34152966	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34152967	34159324	.	+	.	Parent=mRNA176
chr21	gth	exon	34159325	34159508	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34159509	34161406	.	+	.	Parent=mRNA176
chr21	gth	exon	34161407	34161505	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34161506	34169527	.	+	.	Parent=mRNA176
chr21	gth	exon	34169528	34169695	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34169696	34176416	.	+	.	Parent=mRNA176
chr21	gth	exon	34176417	34176629	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34176630	34177723	.	+	.	Parent=mRNA176
chr21	gth	exon	34177724	34177845	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34177846	34179214	.	+	.	Parent=mRNA176
chr21	gth	exon	34179215	34179297	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34179298	34179612	.	+	.	Parent=mRNA176
chr21	gth	exon	34179613	34179696	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34179697	34180460	.	+	.	Parent=mRNA176
chr21	gth	exon	34180461	34180634	1.000000	+	.	Parent=mRNA176
chr21	.	intron	34180635	34182325	.	+	.	Parent=mRNA176
chr21	gth	exon	34182326	34194035	1.000000	+	.	Parent=mRNA176
chr21	gth	mRNA	33936654	34132668	.	+	.	ID=mRNA177;Parent=gene19
chr21	gth	exon	33936654	33936889	1.000000	+	.	Parent=mRNA177
chr21	.	intron	33936890	34012971	.	+	.	Parent=mRNA177
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA177
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34015446	34016762	.	+	.	Parent=mRNA177
chr21	gth	exon	34016763	34016826	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34016827	34029218	.	+	.	Parent=mRNA177
chr21	gth	exon	34029219	34029379	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34029380	34044317	.	+	.	Parent=mRNA177
chr21	gth	exon	34044318	34044497	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34044498	34045984	.	+	.	Parent=mRNA177
chr21	gth	exon	34045985	34046081	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34046082	34049471	.	+	.	Parent=mRNA177
chr21	gth	exon	34049472	34049572	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34049573	34056096	.	+	.	Parent=mRNA177
chr21	gth	exon	34056097	34056160	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34056161	34060048	.	+	.	Parent=mRNA177
chr21	gth	exon	34060049	34060186	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34060187	34061886	.	+	.	Parent=mRNA177
chr21	gth	exon	34061887	34062002	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34062003	34066234	.	+	.	Parent=mRNA177
chr21	gth	exon	34066235	34066497	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34066498	34068902	.	+	.	Parent=mRNA177
chr21	gth	exon	34068903	34069052	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34069053	34069141	.	+	.	Parent=mRNA177
chr21	gth	exon	34069142	34069282	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34069283	34075634	.	+	.	Parent=mRNA177
chr21	gth	exon	34075635	34075722	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34075723	34076167	.	+	.	Parent=mRNA177
chr21	gth	exon	34076168	34076307	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34076308	34088514	.	+	.	Parent=mRNA177
chr21	gth	exon	34088515	34088642	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34088643	34091552	.	+	.	Parent=mRNA177
chr21	gth	exon	34091553	34091782	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34091783	34093981	.	+	.	Parent=mRNA177
chr21	gth	exon	34093982	34094118	0.927007	+	.	Parent=mRNA177
chr21	.	intron	34094119	34105148	.	+	.	Parent=mRNA177
chr21	gth	exon	34105149	34105396	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34105397	34108086	.	+	.	Parent=mRNA177
chr21	gth	exon	34108087	34108246	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34108247	34112440	.	+	.	Parent=mRNA177
chr21	gth	exon	34112441	34112646	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA177
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34113498	34117660	.	+	.	Parent=mRNA177
chr21	gth	exon	34117661	34117827	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34117828	34120991	.	+	.	Parent=mRNA177
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34121038	34123797	.	+	.	Parent=mRNA177
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA177
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA177
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA177
chr21	.	intron	34130807	34131160	.	+	.	Parent=mRNA177
chr21	gth	exon	34131161	34132668	1.000000	+	.	Parent=mRNA177
chr21	gth	mRNA	33936659	34182782	.	+	.	ID=mRNA178;Parent=gene19
chr21	gth	exon	33936659	33936889	1.000000	+	.	Parent=mRNA178
chr21	.	intron	33936890	34012971	.	+	.	Parent=mRNA178
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA178
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34015446	34016762	.	+	.	Parent=mRNA178
chr21	gth	exon	34016763	34016826	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34016827	34029218	.	+	.	Parent=mRNA178
chr21	gth	exon	34029219	34029379	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34029380	34044317	.	+	.	Parent=mRNA178
chr21	gth	exon	34044318	34044497	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34044498	34045984	.	+	.	Parent=mRNA178
chr21	gth	exon	34045985	34046081	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34046082	34049471	.	+	.	Parent=mRNA178
chr21	gth	exon	34049472	34049572	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34049573	34056096	.	+	.	Parent=mRNA178
chr21	gth	exon	34056097	34056160	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34056161	34060048	.	+	.	Parent=mRNA178
chr21	gth	exon	34060049	34060186	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34060187	34061886	.	+	.	Parent=mRNA178
chr21	gth	exon	34061887	34062002	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34062003	34066234	.	+	.	Parent=mRNA178
chr21	gth	exon	34066235	34066497	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34066498	34068902	.	+	.	Parent=mRNA178
chr21	gth	exon	34068903	34069052	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34069053	34069141	.	+	.	Parent=mRNA178
chr21	gth	exon	34069142	34069282	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34069283	34075634	.	+	.	Parent=mRNA178
chr21	gth	exon	34075635	34075722	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34075723	34076167	.	+	.	Parent=mRNA178
chr21	gth	exon	34076168	34076307	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34076308	34088514	.	+	.	Parent=mRNA178
chr21	gth	exon	34088515	34088642	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34088643	34091552	.	+	.	Parent=mRNA178
chr21	gth	exon	34091553	34091782	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34091783	34093981	.	+	.	Parent=mRNA178
chr21	gth	exon	34093982	34094103	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34094104	34105148	.	+	.	Parent=mRNA178
chr21	gth	exon	34105149	34105396	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34105397	34108086	.	+	.	Parent=mRNA178
chr21	gth	exon	34108087	34108246	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34108247	34112440	.	+	.	Parent=mRNA178
chr21	gth	exon	34112441	34112646	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA178
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34113498	34117660	.	+	.	Parent=mRNA178
chr21	gth	exon	34117661	34117827	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34117828	34120991	.	+	.	Parent=mRNA178
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34121038	34123797	.	+	.	Parent=mRNA178
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA178
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA178
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34130807	34150909	.	+	.	Parent=mRNA178
chr21	gth	exon	34150910	34151031	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34151032	34152859	.	+	.	Parent=mRNA178
chr21	gth	exon	34152860	34152966	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34152967	34159324	.	+	.	Parent=mRNA178
chr21	gth	exon	34159325	34159508	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34159509	34161406	.	+	.	Parent=mRNA178
chr21	gth	exon	34161407	34161505	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34161506	34169527	.	+	.	Parent=mRNA178
chr21	gth	exon	34169528	34169695	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34169696	34176416	.	+	.	Parent=mRNA178
chr21	gth	exon	34176417	34176629	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34176630	34177723	.	+	.	Parent=mRNA178
chr21	gth	exon	34177724	34177845	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34177846	34179214	.	+	.	Parent=mRNA178
chr21	gth	exon	34179215	34179297	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34179298	34179612	.	+	.	Parent=mRNA178
chr21	gth	exon	34179613	34179696	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34179697	34180460	.	+	.	Parent=mRNA178
chr21	gth	exon	34180461	34180634	1.000000	+	.	Parent=mRNA178
chr21	.	intron	34180635	34182325	.	+	.	Parent=mRNA178
chr21	gth	exon	34182326	34182782	1.000000	+	.	Parent=mRNA178
chr21	gth	mRNA	33936672	34132672	.	+	.	ID=mRNA179;Parent=gene19
chr21	gth	exon	33936672	33936889	1.000000	+	.	Parent=mRNA179
chr21	.	intron	33936890	34012971	.	+	.	Parent=mRNA179
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA179
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34015446	34016762	.	+	.	Parent=mRNA179
chr21	gth	exon	34016763	34016826	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34016827	34029218	.	+	.	Parent=mRNA179
chr21	gth	exon	34029219	34029379	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34029380	34044317	.	+	.	Parent=mRNA179
chr21	gth	exon	34044318	34044497	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34044498	34045984	.	+	.	Parent=mRNA179
chr21	gth	exon	34045985	34046081	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34046082	34049471	.	+	.	Parent=mRNA179
chr21	gth	exon	34049472	34049572	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34049573	34056096	.	+	.	Parent=mRNA179
chr21	gth	exon	34056097	34056160	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34056161	34060048	.	+	.	Parent=mRNA179
chr21	gth	exon	34060049	34060186	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34060187	34061886	.	+	.	Parent=mRNA179
chr21	gth	exon	34061887	34062002	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34062003	34066234	.	+	.	Parent=mRNA179
chr21	gth	exon	34066235	34066497	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34066498	34068902	.	+	.	Parent=mRNA179
chr21	gth	exon	34068903	34069052	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34069053	34069141	.	+	.	Parent=mRNA179
chr21	gth	exon	34069142	34069282	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34069283	34075634	.	+	.	Parent=mRNA179
chr21	gth	exon	34075635	34075722	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34075723	34076167	.	+	.	Parent=mRNA179
chr21	gth	exon	34076168	34076307	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34076308	34088514	.	+	.	Parent=mRNA179
chr21	gth	exon	34088515	34088642	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34088643	34091552	.	+	.	Parent=mRNA179
chr21	gth	exon	34091553	34091782	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34091783	34093981	.	+	.	Parent=mRNA179
chr21	gth	exon	34093982	34094103	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34094104	34105148	.	+	.	Parent=mRNA179
chr21	gth	exon	34105149	34105396	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34105397	34108086	.	+	.	Parent=mRNA179
chr21	gth	exon	34108087	34108246	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34108247	34112440	.	+	.	Parent=mRNA179
chr21	gth	exon	34112441	34112646	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA179
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34113498	34117660	.	+	.	Parent=mRNA179
chr21	gth	exon	34117661	34117827	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34117828	34120991	.	+	.	Parent=mRNA179
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34121038	34123797	.	+	.	Parent=mRNA179
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA179
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA179
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA179
chr21	.	intron	34130807	34131160	.	+	.	Parent=mRNA179
chr21	gth	exon	34131161	34132672	1.000000	+	.	Parent=mRNA179
chr21	gth	mRNA	33936674	34132670	.	+	.	ID=mRNA180;Parent=gene19
chr21	gth	exon	33936674	33936889	1.000000	+	.	Parent=mRNA180
chr21	.	intron	33936890	34012971	.	+	.	Parent=mRNA180
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA180
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34015446	34016762	.	+	.	Parent=mRNA180
chr21	gth	exon	34016763	34016826	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34016827	34029218	.	+	.	Parent=mRNA180
chr21	gth	exon	34029219	34029379	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34029380	34044317	.	+	.	Parent=mRNA180
chr21	gth	exon	34044318	34044497	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34044498	34045984	.	+	.	Parent=mRNA180
chr21	gth	exon	34045985	34046081	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34046082	34049471	.	+	.	Parent=mRNA180
chr21	gth	exon	34049472	34049572	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34049573	34056096	.	+	.	Parent=mRNA180
chr21	gth	exon	34056097	34056160	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34056161	34060048	.	+	.	Parent=mRNA180
chr21	gth	exon	34060049	34060186	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34060187	34061886	.	+	.	Parent=mRNA180
chr21	gth	exon	34061887	34062002	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34062003	34066234	.	+	.	Parent=mRNA180
chr21	gth	exon	34066235	34066497	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34066498	34068902	.	+	.	Parent=mRNA180
chr21	gth	exon	34068903	34069052	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34069053	34069141	.	+	.	Parent=mRNA180
chr21	gth	exon	34069142	34069282	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34069283	34075634	.	+	.	Parent=mRNA180
chr21	gth	exon	34075635	34075722	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34075723	34076167	.	+	.	Parent=mRNA180
chr21	gth	exon	34076168	34076307	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34076308	34088514	.	+	.	Parent=mRNA180
chr21	gth	exon	34088515	34088642	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34088643	34091552	.	+	.	Parent=mRNA180
chr21	gth	exon	34091553	34091782	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34091783	34093981	.	+	.	Parent=mRNA180
chr21	gth	exon	34093982	34094103	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34094104	34105148	.	+	.	Parent=mRNA180
chr21	gth	exon	34105149	34105396	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34105397	34108086	.	+	.	Parent=mRNA180
chr21	gth	exon	34108087	34108246	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34108247	34112440	.	+	.	Parent=mRNA180
chr21	gth	exon	34112441	34112646	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA180
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34113498	34123797	.	+	.	Parent=mRNA180
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA180
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA180
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA180
chr21	.	intron	34130807	34131160	.	+	.	Parent=mRNA180
chr21	gth	exon	34131161	34132670	1.000000	+	.	Parent=mRNA180
chr21	gth	mRNA	33936718	34036947	.	+	.	ID=mRNA181;Parent=gene19
chr21	gth	exon	33936718	33936889	1.000000	+	.	Parent=mRNA181
chr21	.	intron	33936890	33983496	.	+	.	Parent=mRNA181
chr21	gth	exon	33983497	33983558	1.000000	+	.	Parent=mRNA181
chr21	.	intron	33983559	34012971	.	+	.	Parent=mRNA181
chr21	gth	exon	34012972	34013031	1.000000	+	.	Parent=mRNA181
chr21	.	intron	34013032	34015352	.	+	.	Parent=mRNA181
chr21	gth	exon	34015353	34015445	1.000000	+	.	Parent=mRNA181
chr21	.	intron	34015446	34016762	.	+	.	Parent=mRNA181
chr21	gth	exon	34016763	34016826	1.000000	+	.	Parent=mRNA181
chr21	.	intron	34016827	34029218	.	+	.	Parent=mRNA181
chr21	gth	exon	34029219	34030908	1.000000	+	.	Parent=mRNA181
chr21	.	intron	34030909	34034991	.	+	.	Parent=mRNA181
chr21	gth	exon	34034992	34035796	1.000000	+	.	Parent=mRNA181
chr21	.	intron	34035797	34036516	.	+	.	Parent=mRNA181
chr21	gth	exon	34036517	34036947	1.000000	+	.	Parent=mRNA181
chr21	gth	mRNA	34029216	34029801	.	+	.	ID=mRNA182;Parent=gene19
chr21	gth	exon	34029216	34029379	1.000000	+	.	Parent=mRNA182
chr21	.	intron	34029380	34029480	.	+	.	Parent=mRNA182
chr21	gth	exon	34029481	34029801	1.000000	+	.	Parent=mRNA182
chr21	gth	mRNA	34048358	34066474	.	+	.	ID=mRNA183;Parent=gene19
chr21	gth	exon	34048358	34048397	1.000000	+	.	Parent=mRNA183
chr21	.	intron	34048398	34049471	.	+	.	Parent=mRNA183
chr21	gth	exon	34049472	34049572	1.000000	+	.	Parent=mRNA183
chr21	.	intron	34049573	34050961	.	+	.	Parent=mRNA183
chr21	gth	exon	34050962	34051248	1.000000	+	.	Parent=mRNA183
chr21	.	intron	34051249	34056096	.	+	.	Parent=mRNA183
chr21	gth	exon	34056097	34056160	1.000000	+	.	Parent=mRNA183
chr21	.	intron	34056161	34060048	.	+	.	Parent=mRNA183
chr21	gth	exon	34060049	34060186	1.000000	+	.	Parent=mRNA183
chr21	.	intron	34060187	34061886	.	+	.	Parent=mRNA183
chr21	gth	exon	34061887	34062002	1.000000	+	.	Parent=mRNA183
chr21	.	intron	34062003	34066234	.	+	.	Parent=mRNA183
chr21	gth	exon	34066235	34066474	1.000000	+	.	Parent=mRNA183
chr21	gth	mRNA	34068537	34069253	.	+	.	ID=mRNA184;Parent=gene19
chr21	gth	exon	34068537	34069052	1.000000	+	.	Parent=mRNA184
chr21	.	intron	34069053	34069141	.	+	.	Parent=mRNA184
chr21	gth	exon	34069142	34069253	1.000000	+	.	Parent=mRNA184
chr21	gth	mRNA	34091728	34111910	.	+	.	ID=mRNA185;Parent=gene19
chr21	gth	exon	34091728	34091782	1.000000	+	.	Parent=mRNA185
chr21	.	intron	34091783	34093981	.	+	.	Parent=mRNA185
chr21	gth	exon	34093982	34094103	1.000000	+	.	Parent=mRNA185
chr21	.	intron	34094104	34105106	.	+	.	Parent=mRNA185
chr21	gth	exon	34105107	34105116	0.600000	+	.	Parent=mRNA185
chr21	.	intron	34105117	34105148	.	+	.	Parent=mRNA185
chr21	gth	exon	34105149	34105396	1.000000	+	.	Parent=mRNA185
chr21	.	intron	34105397	34108086	.	+	.	Parent=mRNA185
chr21	gth	exon	34108087	34108246	1.000000	+	.	Parent=mRNA185
chr21	.	intron	34108247	34111404	.	+	.	Parent=mRNA185
chr21	gth	exon	34111405	34111910	1.000000	+	.	Parent=mRNA185
chr21	gth	mRNA	34105378	34108681	.	+	.	ID=mRNA186;Parent=gene19
chr21	gth	exon	34105378	34105396	1.000000	+	.	Parent=mRNA186
chr21	.	intron	34105397	34108086	.	+	.	Parent=mRNA186
chr21	gth	exon	34108087	34108681	1.000000	+	.	Parent=mRNA186
chr21	gth	mRNA	34112200	34150967	.	+	.	ID=mRNA187;Parent=gene19
chr21	gth	exon	34112200	34112646	1.000000	+	.	Parent=mRNA187
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA187
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA187
chr21	.	intron	34113498	34117660	.	+	.	Parent=mRNA187
chr21	gth	exon	34117661	34117827	1.000000	+	.	Parent=mRNA187
chr21	.	intron	34117828	34120991	.	+	.	Parent=mRNA187
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA187
chr21	.	intron	34121038	34123141	.	+	.	Parent=mRNA187
chr21	gth	exon	34123142	34123224	1.000000	+	.	Parent=mRNA187
chr21	.	intron	34123225	34123797	.	+	.	Parent=mRNA187
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA187
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA187
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA187
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA187
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA187
chr21	.	intron	34130807	34150909	.	+	.	Parent=mRNA187
chr21	gth	exon	34150910	34150967	1.000000	+	.	Parent=mRNA187
chr21	gth	mRNA	34112557	34131212	.	+	.	ID=mRNA188;Parent=gene19
chr21	gth	exon	34112557	34112646	1.000000	+	.	Parent=mRNA188
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA188
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA188
chr21	.	intron	34113498	34120991	.	+	.	Parent=mRNA188
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA188
chr21	.	intron	34121038	34123141	.	+	.	Parent=mRNA188
chr21	gth	exon	34123142	34123919	1.000000	+	.	Parent=mRNA188
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA188
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA188
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA188
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA188
chr21	.	intron	34130807	34131160	.	+	.	Parent=mRNA188
chr21	gth	exon	34131161	34131212	1.000000	+	.	Parent=mRNA188
chr21	gth	mRNA	34112557	34131212	.	+	.	ID=mRNA189;Parent=gene19
chr21	gth	exon	34112557	34112646	1.000000	+	.	Parent=mRNA189
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA189
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA189
chr21	.	intron	34113498	34120991	.	+	.	Parent=mRNA189
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA189
chr21	.	intron	34121038	34123141	.	+	.	Parent=mRNA189
chr21	gth	exon	34123142	34123342	1.000000	+	.	Parent=mRNA189
chr21	.	intron	34123343	34123797	.	+	.	Parent=mRNA189
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA189
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA189
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA189
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA189
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA189
chr21	.	intron	34130807	34131160	.	+	.	Parent=mRNA189
chr21	gth	exon	34131161	34131212	1.000000	+	.	Parent=mRNA189
chr21	gth	mRNA	34112557	34150967	.	+	.	ID=mRNA190;Parent=gene19
chr21	gth	exon	34112557	34112646	1.000000	+	.	Parent=mRNA190
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA190
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA190
chr21	.	intron	34113498	34120991	.	+	.	Parent=mRNA190
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA190
chr21	.	intron	34121038	34123141	.	+	.	Parent=mRNA190
chr21	gth	exon	34123142	34123919	1.000000	+	.	Parent=mRNA190
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA190
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA190
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA190
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA190
chr21	.	intron	34130807	34150909	.	+	.	Parent=mRNA190
chr21	gth	exon	34150910	34150967	1.000000	+	.	Parent=mRNA190
chr21	gth	mRNA	34112557	34150967	.	+	.	ID=mRNA191;Parent=gene19
chr21	gth	exon	34112557	34112646	1.000000	+	.	Parent=mRNA191
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA191
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA191
chr21	.	intron	34113498	34120991	.	+	.	Parent=mRNA191
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA191
chr21	.	intron	34121038	34123141	.	+	.	Parent=mRNA191
chr21	gth	exon	34123142	34123919	1.000000	+	.	Parent=mRNA191
chr21	.	intron	34123920	34150909	.	+	.	Parent=mRNA191
chr21	gth	exon	34150910	34150967	1.000000	+	.	Parent=mRNA191
chr21	gth	mRNA	34112626	34123860	.	+	.	ID=mRNA192;Parent=gene19
chr21	gth	exon	34112626	34112646	1.000000	+	.	Parent=mRNA192
chr21	.	intron	34112647	34113414	.	+	.	Parent=mRNA192
chr21	gth	exon	34113415	34113497	1.000000	+	.	Parent=mRNA192
chr21	.	intron	34113498	34120991	.	+	.	Parent=mRNA192
chr21	gth	exon	34120992	34121037	1.000000	+	.	Parent=mRNA192
chr21	.	intron	34121038	34123797	.	+	.	Parent=mRNA192
chr21	gth	exon	34123798	34123860	1.000000	+	.	Parent=mRNA192
chr21	gth	mRNA	34120990	34131212	.	+	.	ID=mRNA193;Parent=gene19
chr21	gth	exon	34120990	34121037	1.000000	+	.	Parent=mRNA193
chr21	.	intron	34121038	34123141	.	+	.	Parent=mRNA193
chr21	gth	exon	34123142	34123224	1.000000	+	.	Parent=mRNA193
chr21	.	intron	34123225	34123797	.	+	.	Parent=mRNA193
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA193
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA193
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA193
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA193
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA193
chr21	.	intron	34130807	34131160	.	+	.	Parent=mRNA193
chr21	gth	exon	34131161	34131212	1.000000	+	.	Parent=mRNA193
chr21	gth	mRNA	34120990	34150967	.	+	.	ID=mRNA194;Parent=gene19
chr21	gth	exon	34120990	34121037	1.000000	+	.	Parent=mRNA194
chr21	.	intron	34121038	34123141	.	+	.	Parent=mRNA194
chr21	gth	exon	34123142	34123224	1.000000	+	.	Parent=mRNA194
chr21	.	intron	34123225	34123797	.	+	.	Parent=mRNA194
chr21	gth	exon	34123798	34123919	1.000000	+	.	Parent=mRNA194
chr21	.	intron	34123920	34128480	.	+	.	Parent=mRNA194
chr21	gth	exon	34128481	34128598	1.000000	+	.	Parent=mRNA194
chr21	.	intron	34128599	34130614	.	+	.	Parent=mRNA194
chr21	gth	exon	34130615	34130806	1.000000	+	.	Parent=mRNA194
chr21	.	intron	34130807	34150909	.	+	.	Parent=mRNA194
chr21	gth	exon	34150910	34150967	1.000000	+	.	Parent=mRNA194
chr21	gth	mRNA	34152871	34180528	.	+	.	ID=mRNA195;Parent=gene19
chr21	gth	exon	34152871	34152966	1.000000	+	.	Parent=mRNA195
chr21	.	intron	34152967	34159324	.	+	.	Parent=mRNA195
chr21	gth	exon	34159325	34159508	1.000000	+	.	Parent=mRNA195
chr21	.	intron	34159509	34161406	.	+	.	Parent=mRNA195
chr21	gth	exon	34161407	34161505	1.000000	+	.	Parent=mRNA195
chr21	.	intron	34161506	34176416	.	+	.	Parent=mRNA195
chr21	gth	exon	34176417	34176629	1.000000	+	.	Parent=mRNA195
chr21	.	intron	34176630	34177723	.	+	.	Parent=mRNA195
chr21	gth	exon	34177724	34177845	1.000000	+	.	Parent=mRNA195
chr21	.	intron	34177846	34179214	.	+	.	Parent=mRNA195
chr21	gth	exon	34179215	34179297	1.000000	+	.	Parent=mRNA195
chr21	.	intron	34179298	34179612	.	+	.	Parent=mRNA195
chr21	gth	exon	34179613	34179696	1.000000	+	.	Parent=mRNA195
chr21	.	intron	34179697	34180460	.	+	.	Parent=mRNA195
chr21	gth	exon	34180461	34180528	1.000000	+	.	Parent=mRNA195
chr21	gth	mRNA	34169532	34180551	.	+	.	ID=mRNA196;Parent=gene19
chr21	gth	exon	34169532	34169695	1.000000	+	.	Parent=mRNA196
chr21	.	intron	34169696	34179214	.	+	.	Parent=mRNA196
chr21	gth	exon	34179215	34179297	1.000000	+	.	Parent=mRNA196
chr21	.	intron	34179298	34179612	.	+	.	Parent=mRNA196
chr21	gth	exon	34179613	34179696	1.000000	+	.	Parent=mRNA196
chr21	.	intron	34179697	34180460	.	+	.	Parent=mRNA196
chr21	gth	exon	34180461	34180551	1.000000	+	.	Parent=mRNA196
chr21	gth	mRNA	34169534	34180528	.	+	.	ID=mRNA197;Parent=gene19
chr21	gth	exon	34169534	34169695	1.000000	+	.	Parent=mRNA197
chr21	.	intron	34169696	34177723	.	+	.	Parent=mRNA197
chr21	gth	exon	34177724	34177845	1.000000	+	.	Parent=mRNA197
chr21	.	intron	34177846	34179214	.	+	.	Parent=mRNA197
chr21	gth	exon	34179215	34179297	1.000000	+	.	Parent=mRNA197
chr21	.	intron	34179298	34179612	.	+	.	Parent=mRNA197
chr21	gth	exon	34179613	34179696	1.000000	+	.	Parent=mRNA197
chr21	.	intron	34179697	34180460	.	+	.	Parent=mRNA197
chr21	gth	exon	34180461	34180528	1.000000	+	.	Parent=mRNA197
###
chr21	gth	gene	39013395	39647224	.	-	.	ID=gene20
chr21	gth	mRNA	39013395	39647224	.	-	.	ID=mRNA198;Parent=gene20
chr21	gth	exon	39013395	39013432	0.736842	-	.	Parent=mRNA198
chr21	.	intron	39013433	39013624	.	-	.	Parent=mRNA198
chr21	gth	exon	39013625	39013666	0.952381	-	.	Parent=mRNA198
chr21	.	intron	39013667	39234091	.	-	.	Parent=mRNA198
chr21	gth	exon	39234092	39234281	0.863158	-	.	Parent=mRNA198
chr21	.	intron	39234282	39647177	.	-	.	Parent=mRNA198
chr21	gth	exon	39647178	39647224	0.893617	-	.	Parent=mRNA198
chr21	gth	mRNA	39468565	39477647	.	-	.	ID=mRNA199;Parent=gene20
chr21	gth	exon	39468565	39469460	1.000000	-	.	Parent=mRNA199
chr21	.	intron	39469461	39471230	.	-	.	Parent=mRNA199
chr21	gth	exon	39471231	39471367	1.000000	-	.	Parent=mRNA199
chr21	.	intron	39471368	39472244	.	-	.	Parent=mRNA199
chr21	gth	exon	39472245	39472443	1.000000	-	.	Parent=mRNA199
chr21	.	intron	39472444	39473719	.	-	.	Parent=mRNA199
chr21	gth	exon	39473720	39473782	1.000000	-	.	Parent=mRNA199
chr21	.	intron	39473783	39474080	.	-	.	Parent=mRNA199
chr21	gth	exon	39474081	39474232	1.000000	-	.	Parent=mRNA199
chr21	.	intron	39474233	39475567	.	-	.	Parent=mRNA199
chr21	gth	exon	39475568	39475674	1.000000	-	.	Parent=mRNA199
chr21	.	intron	39475675	39477047	.	-	.	Parent=mRNA199
chr21	gth	exon	39477048	39477647	1.000000	-	.	Parent=mRNA199
chr21	gth	mRNA	39469254	39472616	.	-	.	ID=mRNA200;Parent=gene20
chr21	gth	exon	39469254	39469460	1.000000	-	.	Parent=mRNA200
chr21	.	intron	39469461	39471230	.	-	.	Parent=mRNA200
chr21	gth	exon	39471231	39471367	1.000000	-	.	Parent=mRNA200
chr21	.	intron	39471368	39472244	.	-	.	Parent=mRNA200
chr21	gth	exon	39472245	39472616	1.000000	-	.	Parent=mRNA200
chr21	gth	mRNA	39469254	39474234	.	-	.	ID=mRNA201;Parent=gene20
chr21	gth	exon	39469254	39469460	1.000000	-	.	Parent=mRNA201
chr21	.	intron	39469461	39471230	.	-	.	Parent=mRNA201
chr21	gth	exon	39471231	39471367	1.000000	-	.	Parent=mRNA201
chr21	.	intron	39471368	39472244	.	-	.	Parent=mRNA201
chr21	gth	exon	39472245	39472314	1.000000	-	.	Parent=mRNA201
chr21	.	intron	39472315	39474080	.	-	.	Parent=mRNA201
chr21	gth	exon	39474081	39474234	1.000000	-	.	Parent=mRNA201
chr21	gth	mRNA	39469384	39477083	.	-	.	ID=mRNA202;Parent=gene20
chr21	gth	exon	39469384	39469460	1.000000	-	.	Parent=mRNA202
chr21	.	intron	39469461	39471230	.	-	.	Parent=mRNA202
chr21	gth	exon	39471231	39471367	1.000000	-	.	Parent=mRNA202
chr21	.	intron	39471368	39472244	.	-	.	Parent=mRNA202
chr21	gth	exon	39472245	39472443	1.000000	-	.	Parent=mRNA202
chr21	.	intron	39472444	39473719	.	-	.	Parent=mRNA202
chr21	gth	exon	39473720	39473782	1.000000	-	.	Parent=mRNA202
chr21	.	intron	39473783	39474080	.	-	.	Parent=mRNA202
chr21	gth	exon	39474081	39474232	1.000000	-	.	Parent=mRNA202
chr21	.	intron	39474233	39475567	.	-	.	Parent=mRNA202
chr21	gth	exon	39475568	39475674	1.000000	-	.	Parent=mRNA202
chr21	.	intron	39475675	39476859	.	-	.	Parent=mRNA202
chr21	gth	exon	39476860	39477083	1.000000	-	.	Parent=mRNA202
chr21	gth	mRNA	39469386	39477181	.	-	.	ID=mRNA203;Parent=gene20
chr21	gth	exon	39469386	39469460	1.000000	-	.	Parent=mRNA203
chr21	.	intron	39469461	39471230	.	-	.	Parent=mRNA203
chr21	gth	exon	39471231	39471367	1.000000	-	.	Parent=mRNA203
chr21	.	intron	39471368	39472244	.	-	.	Parent=mRNA203
chr21	gth	exon	39472245	39472443	1.000000	-	.	Parent=mRNA203
chr21	.	intron	39472444	39473719	.	-	.	Parent=mRNA203
chr21	gth	exon	39473720	39473782	1.000000	-	.	Parent=mRNA203
chr21	.	intron	39473783	39474080	.	-	.	Parent=mRNA203
chr21	gth	exon	39474081	39474232	1.000000	-	.	Parent=mRNA203
chr21	.	intron	39474233	39477047	.	-	.	Parent=mRNA203
chr21	gth	exon	39477048	39477181	1.000000	-	.	Parent=mRNA203
chr21	gth	mRNA	39469386	39477284	.	-	.	ID=mRNA204;Parent=gene20
chr21	gth	exon	39469386	39469460	1.000000	-	.	Parent=mRNA204
chr21	.	intron	39469461	39471230	.	-	.	Parent=mRNA204
chr21	gth	exon	39471231	39471367	1.000000	-	.	Parent=mRNA204
chr21	.	intron	39471368	39472244	.	-	.	Parent=mRNA204
chr21	gth	exon	39472245	39472443	1.000000	-	.	Parent=mRNA204
chr21	.	intron	39472444	39474080	.	-	.	Parent=mRNA204
chr21	gth	exon	39474081	39474232	1.000000	-	.	Parent=mRNA204
chr21	.	intron	39474233	39475567	.	-	.	Parent=mRNA204
chr21	gth	exon	39475568	39475674	1.000000	-	.	Parent=mRNA204
chr21	.	intron	39475675	39477047	.	-	.	Parent=mRNA204
chr21	gth	exon	39477048	39477284	1.000000	-	.	Parent=mRNA204
chr21	gth	mRNA	39477972	39607366	.	-	.	ID=mRNA205;Parent=gene20
chr21	gth	exon	39477972	39481213	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39481214	39490293	.	-	.	Parent=mRNA205
chr21	gth	exon	39490294	39491211	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39491212	39492558	.	-	.	Parent=mRNA205
chr21	gth	exon	39492559	39493458	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39493459	39494014	.	-	.	Parent=mRNA205
chr21	gth	exon	39494015	39494182	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39494183	39496120	.	-	.	Parent=mRNA205
chr21	gth	exon	39496121	39496341	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39496342	39499903	.	-	.	Parent=mRNA205
chr21	gth	exon	39499904	39500070	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39500071	39503790	.	-	.	Parent=mRNA205
chr21	gth	exon	39503791	39503943	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39503944	39504581	.	-	.	Parent=mRNA205
chr21	gth	exon	39504582	39504725	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39504726	39506461	.	-	.	Parent=mRNA205
chr21	gth	exon	39506462	39506503	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39506504	39507276	.	-	.	Parent=mRNA205
chr21	gth	exon	39507277	39507349	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39507350	39509032	.	-	.	Parent=mRNA205
chr21	gth	exon	39509033	39509158	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39509159	39511947	.	-	.	Parent=mRNA205
chr21	gth	exon	39511948	39512068	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39512069	39512300	.	-	.	Parent=mRNA205
chr21	gth	exon	39512301	39512456	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39512457	39518203	.	-	.	Parent=mRNA205
chr21	gth	exon	39518204	39518265	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39518266	39518881	.	-	.	Parent=mRNA205
chr21	gth	exon	39518882	39518993	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39518994	39522295	.	-	.	Parent=mRNA205
chr21	gth	exon	39522296	39522378	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39522379	39523107	.	-	.	Parent=mRNA205
chr21	gth	exon	39523108	39523232	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39523233	39525972	.	-	.	Parent=mRNA205
chr21	gth	exon	39525973	39526080	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39526081	39526168	.	-	.	Parent=mRNA205
chr21	gth	exon	39526169	39526294	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39526295	39530390	.	-	.	Parent=mRNA205
chr21	gth	exon	39530391	39530580	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39530581	39532274	.	-	.	Parent=mRNA205
chr21	gth	exon	39532275	39532369	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39532370	39541496	.	-	.	Parent=mRNA205
chr21	gth	exon	39541497	39541628	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39541629	39544591	.	-	.	Parent=mRNA205
chr21	gth	exon	39544592	39544685	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39544686	39549440	.	-	.	Parent=mRNA205
chr21	gth	exon	39549441	39549624	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39549625	39552282	.	-	.	Parent=mRNA205
chr21	gth	exon	39552283	39552468	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39552469	39558255	.	-	.	Parent=mRNA205
chr21	gth	exon	39558256	39558481	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39558482	39558686	.	-	.	Parent=mRNA205
chr21	gth	exon	39558687	39558815	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39558816	39563694	.	-	.	Parent=mRNA205
chr21	gth	exon	39563695	39563829	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39563830	39564078	.	-	.	Parent=mRNA205
chr21	gth	exon	39564079	39564229	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39564230	39568169	.	-	.	Parent=mRNA205
chr21	gth	exon	39568170	39568268	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39568269	39569968	.	-	.	Parent=mRNA205
chr21	gth	exon	39569969	39570009	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39570010	39571046	.	-	.	Parent=mRNA205
chr21	gth	exon	39571047	39571147	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39571148	39572538	.	-	.	Parent=mRNA205
chr21	gth	exon	39572539	39572609	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39572610	39573943	.	-	.	Parent=mRNA205
chr21	gth	exon	39573944	39574044	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39574045	39587606	.	-	.	Parent=mRNA205
chr21	gth	exon	39587607	39587828	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39587829	39589538	.	-	.	Parent=mRNA205
chr21	gth	exon	39589539	39589699	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39589700	39590060	.	-	.	Parent=mRNA205
chr21	gth	exon	39590061	39590159	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39590160	39592227	.	-	.	Parent=mRNA205
chr21	gth	exon	39592228	39592378	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39592379	39606636	.	-	.	Parent=mRNA205
chr21	gth	exon	39606637	39606696	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39606697	39606867	.	-	.	Parent=mRNA205
chr21	gth	exon	39606868	39606897	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39606898	39607036	.	-	.	Parent=mRNA205
chr21	gth	exon	39607037	39607095	1.000000	-	.	Parent=mRNA205
chr21	.	intron	39607096	39607238	.	-	.	Parent=mRNA205
chr21	gth	exon	39607239	39607366	1.000000	-	.	Parent=mRNA205
chr21	gth	mRNA	39481042	39558737	.	-	.	ID=mRNA206;Parent=gene20
chr21	gth	exon	39481042	39481213	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39481214	39490293	.	-	.	Parent=mRNA206
chr21	gth	exon	39490294	39491211	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39491212	39492558	.	-	.	Parent=mRNA206
chr21	gth	exon	39492559	39493458	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39493459	39494014	.	-	.	Parent=mRNA206
chr21	gth	exon	39494015	39494182	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39494183	39496120	.	-	.	Parent=mRNA206
chr21	gth	exon	39496121	39496341	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39496342	39499903	.	-	.	Parent=mRNA206
chr21	gth	exon	39499904	39500070	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39500071	39503790	.	-	.	Parent=mRNA206
chr21	gth	exon	39503791	39503943	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39503944	39504581	.	-	.	Parent=mRNA206
chr21	gth	exon	39504582	39504725	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39504726	39506461	.	-	.	Parent=mRNA206
chr21	gth	exon	39506462	39506503	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39506504	39507276	.	-	.	Parent=mRNA206
chr21	gth	exon	39507277	39507349	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39507350	39509032	.	-	.	Parent=mRNA206
chr21	gth	exon	39509033	39509158	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39509159	39512324	.	-	.	Parent=mRNA206
chr21	gth	exon	39512325	39512456	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39512457	39518203	.	-	.	Parent=mRNA206
chr21	gth	exon	39518204	39518265	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39518266	39518881	.	-	.	Parent=mRNA206
chr21	gth	exon	39518882	39518993	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39518994	39522295	.	-	.	Parent=mRNA206
chr21	gth	exon	39522296	39522378	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39522379	39523107	.	-	.	Parent=mRNA206
chr21	gth	exon	39523108	39523232	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39523233	39525972	.	-	.	Parent=mRNA206
chr21	gth	exon	39525973	39526080	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39526081	39526168	.	-	.	Parent=mRNA206
chr21	gth	exon	39526169	39526294	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39526295	39530390	.	-	.	Parent=mRNA206
chr21	gth	exon	39530391	39530580	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39530581	39532274	.	-	.	Parent=mRNA206
chr21	gth	exon	39532275	39532369	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39532370	39541496	.	-	.	Parent=mRNA206
chr21	gth	exon	39541497	39541628	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39541629	39544591	.	-	.	Parent=mRNA206
chr21	gth	exon	39544592	39544685	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39544686	39549440	.	-	.	Parent=mRNA206
chr21	gth	exon	39549441	39549624	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39549625	39552282	.	-	.	Parent=mRNA206
chr21	gth	exon	39552283	39552468	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39552469	39558255	.	-	.	Parent=mRNA206
chr21	gth	exon	39558256	39558481	1.000000	-	.	Parent=mRNA206
chr21	.	intron	39558482	39558686	.	-	.	Parent=mRNA206
chr21	gth	exon	39558687	39558737	1.000000	-	.	Parent=mRNA206
chr21	gth	mRNA	39484015	39607366	.	-	.	ID=mRNA207;Parent=gene20
chr21	gth	exon	39484015	39491211	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39491212	39492558	.	-	.	Parent=mRNA207
chr21	gth	exon	39492559	39493458	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39493459	39494014	.	-	.	Parent=mRNA207
chr21	gth	exon	39494015	39494182	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39494183	39496120	.	-	.	Parent=mRNA207
chr21	gth	exon	39496121	39496341	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39496342	39499903	.	-	.	Parent=mRNA207
chr21	gth	exon	39499904	39500070	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39500071	39503790	.	-	.	Parent=mRNA207
chr21	gth	exon	39503791	39503943	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39503944	39504581	.	-	.	Parent=mRNA207
chr21	gth	exon	39504582	39504725	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39504726	39506461	.	-	.	Parent=mRNA207
chr21	gth	exon	39506462	39506503	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39506504	39507276	.	-	.	Parent=mRNA207
chr21	gth	exon	39507277	39507349	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39507350	39509032	.	-	.	Parent=mRNA207
chr21	gth	exon	39509033	39509158	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39509159	39511947	.	-	.	Parent=mRNA207
chr21	gth	exon	39511948	39512068	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39512069	39512300	.	-	.	Parent=mRNA207
chr21	gth	exon	39512301	39512456	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39512457	39518203	.	-	.	Parent=mRNA207
chr21	gth	exon	39518204	39518265	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39518266	39518881	.	-	.	Parent=mRNA207
chr21	gth	exon	39518882	39518993	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39518994	39522295	.	-	.	Parent=mRNA207
chr21	gth	exon	39522296	39522378	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39522379	39523107	.	-	.	Parent=mRNA207
chr21	gth	exon	39523108	39523232	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39523233	39525972	.	-	.	Parent=mRNA207
chr21	gth	exon	39525973	39526080	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39526081	39526168	.	-	.	Parent=mRNA207
chr21	gth	exon	39526169	39526294	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39526295	39530390	.	-	.	Parent=mRNA207
chr21	gth	exon	39530391	39530580	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39530581	39532274	.	-	.	Parent=mRNA207
chr21	gth	exon	39532275	39532369	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39532370	39541496	.	-	.	Parent=mRNA207
chr21	gth	exon	39541497	39541628	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39541629	39544591	.	-	.	Parent=mRNA207
chr21	gth	exon	39544592	39544685	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39544686	39549440	.	-	.	Parent=mRNA207
chr21	gth	exon	39549441	39549624	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39549625	39552282	.	-	.	Parent=mRNA207
chr21	gth	exon	39552283	39552468	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39552469	39558255	.	-	.	Parent=mRNA207
chr21	gth	exon	39558256	39558481	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39558482	39558686	.	-	.	Parent=mRNA207
chr21	gth	exon	39558687	39558815	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39558816	39563694	.	-	.	Parent=mRNA207
chr21	gth	exon	39563695	39563829	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39563830	39564078	.	-	.	Parent=mRNA207
chr21	gth	exon	39564079	39564229	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39564230	39568169	.	-	.	Parent=mRNA207
chr21	gth	exon	39568170	39568268	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39568269	39569968	.	-	.	Parent=mRNA207
chr21	gth	exon	39569969	39570009	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39570010	39571046	.	-	.	Parent=mRNA207
chr21	gth	exon	39571047	39571147	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39571148	39572538	.	-	.	Parent=mRNA207
chr21	gth	exon	39572539	39572609	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39572610	39573943	.	-	.	Parent=mRNA207
chr21	gth	exon	39573944	39574044	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39574045	39587606	.	-	.	Parent=mRNA207
chr21	gth	exon	39587607	39587828	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39587829	39589538	.	-	.	Parent=mRNA207
chr21	gth	exon	39589539	39589699	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39589700	39590060	.	-	.	Parent=mRNA207
chr21	gth	exon	39590061	39590159	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39590160	39592227	.	-	.	Parent=mRNA207
chr21	gth	exon	39592228	39592378	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39592379	39606636	.	-	.	Parent=mRNA207
chr21	gth	exon	39606637	39606696	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39606697	39606867	.	-	.	Parent=mRNA207
chr21	gth	exon	39606868	39606897	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39606898	39607036	.	-	.	Parent=mRNA207
chr21	gth	exon	39607037	39607095	1.000000	-	.	Parent=mRNA207
chr21	.	intron	39607096	39607238	.	-	.	Parent=mRNA207
chr21	gth	exon	39607239	39607366	1.000000	-	.	Parent=mRNA207
chr21	gth	mRNA	39493215	39494292	.	-	.	ID=mRNA208;Parent=gene20
chr21	gth	exon	39493215	39493458	1.000000	-	.	Parent=mRNA208
chr21	.	intron	39493459	39494014	.	-	.	Parent=mRNA208
chr21	gth	exon	39494015	39494292	1.000000	-	.	Parent=mRNA208
chr21	gth	mRNA	39496162	39523188	.	-	.	ID=mRNA209;Parent=gene20
chr21	gth	exon	39496162	39496341	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39496342	39499903	.	-	.	Parent=mRNA209
chr21	gth	exon	39499904	39500070	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39500071	39503790	.	-	.	Parent=mRNA209
chr21	gth	exon	39503791	39503943	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39503944	39506461	.	-	.	Parent=mRNA209
chr21	gth	exon	39506462	39506503	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39506504	39507276	.	-	.	Parent=mRNA209
chr21	gth	exon	39507277	39507349	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39507350	39509032	.	-	.	Parent=mRNA209
chr21	gth	exon	39509033	39509158	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39509159	39511947	.	-	.	Parent=mRNA209
chr21	gth	exon	39511948	39512068	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39512069	39512300	.	-	.	Parent=mRNA209
chr21	gth	exon	39512301	39512456	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39512457	39518203	.	-	.	Parent=mRNA209
chr21	gth	exon	39518204	39518265	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39518266	39518881	.	-	.	Parent=mRNA209
chr21	gth	exon	39518882	39518993	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39518994	39522295	.	-	.	Parent=mRNA209
chr21	gth	exon	39522296	39522378	1.000000	-	.	Parent=mRNA209
chr21	.	intron	39522379	39523107	.	-	.	Parent=mRNA209
chr21	gth	exon	39523108	39523188	1.000000	-	.	Parent=mRNA209
chr21	gth	mRNA	39503582	39512456	.	-	.	ID=mRNA210;Parent=gene20
chr21	gth	exon	39503582	39503943	1.000000	-	.	Parent=mRNA210
chr21	.	intron	39503944	39504661	.	-	.	Parent=mRNA210
chr21	gth	exon	39504662	39504725	1.000000	-	.	Parent=mRNA210
chr21	.	intron	39504726	39506461	.	-	.	Parent=mRNA210
chr21	gth	exon	39506462	39506503	1.000000	-	.	Parent=mRNA210
chr21	.	intron	39506504	39507276	.	-	.	Parent=mRNA210
chr21	gth	exon	39507277	39507349	1.000000	-	.	Parent=mRNA210
chr21	.	intron	39507350	39509032	.	-	.	Parent=mRNA210
chr21	gth	exon	39509033	39509158	1.000000	-	.	Parent=mRNA210
chr21	.	intron	39509159	39511947	.	-	.	Parent=mRNA210
chr21	gth	exon	39511948	39512068	1.000000	-	.	Parent=mRNA210
chr21	.	intron	39512069	39512300	.	-	.	Parent=mRNA210
chr21	gth	exon	39512301	39512456	1.000000	-	.	Parent=mRNA210
chr21	gth	mRNA	39530514	39574009	.	-	.	ID=mRNA211;Parent=gene20
chr21	gth	exon	39530514	39530580	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39530581	39532274	.	-	.	Parent=mRNA211
chr21	gth	exon	39532275	39532369	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39532370	39541496	.	-	.	Parent=mRNA211
chr21	gth	exon	39541497	39541628	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39541629	39544591	.	-	.	Parent=mRNA211
chr21	gth	exon	39544592	39544685	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39544686	39552282	.	-	.	Parent=mRNA211
chr21	gth	exon	39552283	39552468	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39552469	39558255	.	-	.	Parent=mRNA211
chr21	gth	exon	39558256	39558481	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39558482	39558686	.	-	.	Parent=mRNA211
chr21	gth	exon	39558687	39558815	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39558816	39563694	.	-	.	Parent=mRNA211
chr21	gth	exon	39563695	39563829	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39563830	39564078	.	-	.	Parent=mRNA211
chr21	gth	exon	39564079	39564229	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39564230	39568169	.	-	.	Parent=mRNA211
chr21	gth	exon	39568170	39568268	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39568269	39569968	.	-	.	Parent=mRNA211
chr21	gth	exon	39569969	39570009	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39570010	39571046	.	-	.	Parent=mRNA211
chr21	gth	exon	39571047	39571147	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39571148	39572538	.	-	.	Parent=mRNA211
chr21	gth	exon	39572539	39572609	1.000000	-	.	Parent=mRNA211
chr21	.	intron	39572610	39573943	.	-	.	Parent=mRNA211
chr21	gth	exon	39573944	39574009	1.000000	-	.	Parent=mRNA211
chr21	gth	mRNA	39530514	39574009	.	-	.	ID=mRNA212;Parent=gene20
chr21	gth	exon	39530514	39530580	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39530581	39532274	.	-	.	Parent=mRNA212
chr21	gth	exon	39532275	39532369	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39532370	39541496	.	-	.	Parent=mRNA212
chr21	gth	exon	39541497	39541628	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39541629	39544591	.	-	.	Parent=mRNA212
chr21	gth	exon	39544592	39544685	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39544686	39549440	.	-	.	Parent=mRNA212
chr21	gth	exon	39549441	39549624	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39549625	39552282	.	-	.	Parent=mRNA212
chr21	gth	exon	39552283	39552468	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39552469	39558255	.	-	.	Parent=mRNA212
chr21	gth	exon	39558256	39558360	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39558361	39558686	.	-	.	Parent=mRNA212
chr21	gth	exon	39558687	39558815	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39558816	39563694	.	-	.	Parent=mRNA212
chr21	gth	exon	39563695	39563829	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39563830	39564078	.	-	.	Parent=mRNA212
chr21	gth	exon	39564079	39564229	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39564230	39568169	.	-	.	Parent=mRNA212
chr21	gth	exon	39568170	39568268	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39568269	39569968	.	-	.	Parent=mRNA212
chr21	gth	exon	39569969	39570009	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39570010	39571046	.	-	.	Parent=mRNA212
chr21	gth	exon	39571047	39571147	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39571148	39572538	.	-	.	Parent=mRNA212
chr21	gth	exon	39572539	39572609	1.000000	-	.	Parent=mRNA212
chr21	.	intron	39572610	39573943	.	-	.	Parent=mRNA212
chr21	gth	exon	39573944	39574009	1.000000	-	.	Parent=mRNA212
chr21	gth	mRNA	39530514	39574009	.	-	.	ID=mRNA213;Parent=gene20
chr21	gth	exon	39530514	39530580	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39530581	39532274	.	-	.	Parent=mRNA213
chr21	gth	exon	39532275	39532369	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39532370	39541496	.	-	.	Parent=mRNA213
chr21	gth	exon	39541497	39541628	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39541629	39544591	.	-	.	Parent=mRNA213
chr21	gth	exon	39544592	39544685	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39544686	39549440	.	-	.	Parent=mRNA213
chr21	gth	exon	39549441	39549624	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39549625	39552282	.	-	.	Parent=mRNA213
chr21	gth	exon	39552283	39552468	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39552469	39558255	.	-	.	Parent=mRNA213
chr21	gth	exon	39558256	39558481	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39558482	39558781	.	-	.	Parent=mRNA213
chr21	gth	exon	39558782	39558815	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39558816	39563694	.	-	.	Parent=mRNA213
chr21	gth	exon	39563695	39563829	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39563830	39564078	.	-	.	Parent=mRNA213
chr21	gth	exon	39564079	39564229	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39564230	39568169	.	-	.	Parent=mRNA213
chr21	gth	exon	39568170	39568268	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39568269	39569968	.	-	.	Parent=mRNA213
chr21	gth	exon	39569969	39570009	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39570010	39571046	.	-	.	Parent=mRNA213
chr21	gth	exon	39571047	39571147	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39571148	39572538	.	-	.	Parent=mRNA213
chr21	gth	exon	39572539	39572609	1.000000	-	.	Parent=mRNA213
chr21	.	intron	39572610	39573943	.	-	.	Parent=mRNA213
chr21	gth	exon	39573944	39574009	1.000000	-	.	Parent=mRNA213
chr21	gth	mRNA	39530515	39574009	.	-	.	ID=mRNA214;Parent=gene20
chr21	gth	exon	39530515	39530580	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39530581	39532274	.	-	.	Parent=mRNA214
chr21	gth	exon	39532275	39532369	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39532370	39544591	.	-	.	Parent=mRNA214
chr21	gth	exon	39544592	39544685	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39544686	39549440	.	-	.	Parent=mRNA214
chr21	gth	exon	39549441	39549624	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39549625	39552282	.	-	.	Parent=mRNA214
chr21	gth	exon	39552283	39552468	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39552469	39558255	.	-	.	Parent=mRNA214
chr21	gth	exon	39558256	39558481	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39558482	39558686	.	-	.	Parent=mRNA214
chr21	gth	exon	39558687	39558815	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39558816	39563694	.	-	.	Parent=mRNA214
chr21	gth	exon	39563695	39563829	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39563830	39564078	.	-	.	Parent=mRNA214
chr21	gth	exon	39564079	39564229	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39564230	39568169	.	-	.	Parent=mRNA214
chr21	gth	exon	39568170	39568268	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39568269	39569968	.	-	.	Parent=mRNA214
chr21	gth	exon	39569969	39570009	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39570010	39571046	.	-	.	Parent=mRNA214
chr21	gth	exon	39571047	39571147	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39571148	39572538	.	-	.	Parent=mRNA214
chr21	gth	exon	39572539	39572609	1.000000	-	.	Parent=mRNA214
chr21	.	intron	39572610	39573943	.	-	.	Parent=mRNA214
chr21	gth	exon	39573944	39574009	1.000000	-	.	Parent=mRNA214
chr21	gth	mRNA	39530515	39574009	.	-	.	ID=mRNA215;Parent=gene20
chr21	gth	exon	39530515	39530580	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39530581	39532274	.	-	.	Parent=mRNA215
chr21	gth	exon	39532275	39532369	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39532370	39541496	.	-	.	Parent=mRNA215
chr21	gth	exon	39541497	39541628	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39541629	39544591	.	-	.	Parent=mRNA215
chr21	gth	exon	39544592	39544685	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39544686	39549460	.	-	.	Parent=mRNA215
chr21	gth	exon	39549461	39549624	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39549625	39552282	.	-	.	Parent=mRNA215
chr21	gth	exon	39552283	39552468	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39552469	39558255	.	-	.	Parent=mRNA215
chr21	gth	exon	39558256	39558481	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39558482	39558686	.	-	.	Parent=mRNA215
chr21	gth	exon	39558687	39558815	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39558816	39563694	.	-	.	Parent=mRNA215
chr21	gth	exon	39563695	39563829	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39563830	39564078	.	-	.	Parent=mRNA215
chr21	gth	exon	39564079	39564229	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39564230	39568169	.	-	.	Parent=mRNA215
chr21	gth	exon	39568170	39568268	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39568269	39569968	.	-	.	Parent=mRNA215
chr21	gth	exon	39569969	39570009	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39570010	39571046	.	-	.	Parent=mRNA215
chr21	gth	exon	39571047	39571147	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39571148	39572538	.	-	.	Parent=mRNA215
chr21	gth	exon	39572539	39572609	1.000000	-	.	Parent=mRNA215
chr21	.	intron	39572610	39573943	.	-	.	Parent=mRNA215
chr21	gth	exon	39573944	39574009	1.000000	-	.	Parent=mRNA215
chr21	gth	mRNA	39572293	39574003	.	-	.	ID=mRNA216;Parent=gene20
chr21	gth	exon	39572293	39572609	1.000000	-	.	Parent=mRNA216
chr21	.	intron	39572610	39573943	.	-	.	Parent=mRNA216
chr21	gth	exon	39573944	39574003	1.000000	-	.	Parent=mRNA216
chr21	gth	mRNA	39590233	39607438	.	-	.	ID=mRNA217;Parent=gene20
chr21	gth	exon	39590233	39592378	1.000000	-	.	Parent=mRNA217
chr21	.	intron	39592379	39606636	.	-	.	Parent=mRNA217
chr21	gth	exon	39606637	39606696	1.000000	-	.	Parent=mRNA217
chr21	.	intron	39606697	39606867	.	-	.	Parent=mRNA217
chr21	gth	exon	39606868	39606897	1.000000	-	.	Parent=mRNA217
chr21	.	intron	39606898	39607036	.	-	.	Parent=mRNA217
chr21	gth	exon	39607037	39607095	1.000000	-	.	Parent=mRNA217
chr21	.	intron	39607096	39607238	.	-	.	Parent=mRNA217
chr21	gth	exon	39607239	39607438	1.000000	-	.	Parent=mRNA217
chr21	gth	mRNA	39591886	39615355	.	-	.	ID=mRNA218;Parent=gene20
chr21	gth	exon	39591886	39592378	1.000000	-	.	Parent=mRNA218
chr21	.	intron	39592379	39606636	.	-	.	Parent=mRNA218
chr21	gth	exon	39606637	39606696	1.000000	-	.	Parent=mRNA218
chr21	.	intron	39606697	39606867	.	-	.	Parent=mRNA218
chr21	gth	exon	39606868	39606897	1.000000	-	.	Parent=mRNA218
chr21	.	intron	39606898	39607036	.	-	.	Parent=mRNA218
chr21	gth	exon	39607037	39607095	1.000000	-	.	Parent=mRNA218
chr21	.	intron	39607096	39614821	.	-	.	Parent=mRNA218
chr21	gth	exon	39614822	39615355	1.000000	-	.	Parent=mRNA218
chr21	gth	mRNA	39606359	39607097	.	-	.	ID=mRNA219;Parent=gene20
chr21	gth	exon	39606359	39606696	1.000000	-	.	Parent=mRNA219
chr21	.	intron	39606697	39606867	.	-	.	Parent=mRNA219
chr21	gth	exon	39606868	39606897	1.000000	-	.	Parent=mRNA219
chr21	.	intron	39606898	39607036	.	-	.	Parent=mRNA219
chr21	gth	exon	39607037	39607097	1.000000	-	.	Parent=mRNA219
chr21	gth	mRNA	39636111	39642787	.	-	.	ID=mRNA220;Parent=gene20
chr21	gth	exon	39636111	39636955	1.000000	-	.	Parent=mRNA220
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA220
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA220
chr21	.	intron	39639071	39639625	.	-	.	Parent=mRNA220
chr21	gth	exon	39639626	39639754	1.000000	-	.	Parent=mRNA220
chr21	.	intron	39639755	39642087	.	-	.	Parent=mRNA220
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA220
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA220
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA220
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA220
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA220
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA220
chr21	gth	exon	39642699	39642787	1.000000	-	.	Parent=mRNA220
chr21	gth	mRNA	39636111	39642895	.	-	.	ID=mRNA221;Parent=gene20
chr21	gth	exon	39636111	39636955	1.000000	-	.	Parent=mRNA221
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA221
chr21	gth	exon	39638942	39642135	1.000000	-	.	Parent=mRNA221
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA221
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA221
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA221
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA221
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA221
chr21	gth	exon	39642699	39642895	1.000000	-	.	Parent=mRNA221
chr21	gth	mRNA	39636111	39642936	.	-	.	ID=mRNA222;Parent=gene20
chr21	gth	exon	39636111	39636955	1.000000	-	.	Parent=mRNA222
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA222
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA222
chr21	.	intron	39639071	39639625	.	-	.	Parent=mRNA222
chr21	gth	exon	39639626	39639754	1.000000	-	.	Parent=mRNA222
chr21	.	intron	39639755	39641174	.	-	.	Parent=mRNA222
chr21	gth	exon	39641175	39641274	1.000000	-	.	Parent=mRNA222
chr21	.	intron	39641275	39642087	.	-	.	Parent=mRNA222
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA222
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA222
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA222
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA222
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA222
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA222
chr21	gth	exon	39642699	39642936	1.000000	-	.	Parent=mRNA222
chr21	gth	mRNA	39636111	39642996	.	-	.	ID=mRNA223;Parent=gene20
chr21	gth	exon	39636111	39636955	1.000000	-	.	Parent=mRNA223
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA223
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA223
chr21	.	intron	39639071	39642087	.	-	.	Parent=mRNA223
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA223
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA223
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA223
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA223
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA223
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA223
chr21	gth	exon	39642699	39642996	1.000000	-	.	Parent=mRNA223
chr21	gth	mRNA	39636111	39643140	.	-	.	ID=mRNA224;Parent=gene20
chr21	gth	exon	39636111	39636955	1.000000	-	.	Parent=mRNA224
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA224
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA224
chr21	.	intron	39639071	39639625	.	-	.	Parent=mRNA224
chr21	gth	exon	39639626	39641088	1.000000	-	.	Parent=mRNA224
chr21	.	intron	39641089	39641174	.	-	.	Parent=mRNA224
chr21	gth	exon	39641175	39641279	1.000000	-	.	Parent=mRNA224
chr21	.	intron	39641280	39642087	.	-	.	Parent=mRNA224
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA224
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA224
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA224
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA224
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA224
chr21	.	intron	39642374	39643086	.	-	.	Parent=mRNA224
chr21	gth	exon	39643087	39643140	1.000000	-	.	Parent=mRNA224
chr21	gth	mRNA	39636442	39642884	.	-	.	ID=mRNA225;Parent=gene20
chr21	gth	exon	39636442	39636955	1.000000	-	.	Parent=mRNA225
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA225
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA225
chr21	.	intron	39639071	39641174	.	-	.	Parent=mRNA225
chr21	gth	exon	39641175	39641279	1.000000	-	.	Parent=mRNA225
chr21	.	intron	39641280	39642087	.	-	.	Parent=mRNA225
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA225
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA225
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA225
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA225
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA225
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA225
chr21	gth	exon	39642699	39642884	1.000000	-	.	Parent=mRNA225
chr21	gth	mRNA	39636488	39642849	.	-	.	ID=mRNA226;Parent=gene20
chr21	gth	exon	39636488	39636955	1.000000	-	.	Parent=mRNA226
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA226
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA226
chr21	.	intron	39639071	39642087	.	-	.	Parent=mRNA226
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA226
chr21	.	intron	39642136	39642340	.	-	.	Parent=mRNA226
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA226
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA226
chr21	gth	exon	39642699	39642849	1.000000	-	.	Parent=mRNA226
chr21	gth	mRNA	39636584	39642836	.	-	.	ID=mRNA227;Parent=gene20
chr21	gth	exon	39636584	39636955	1.000000	-	.	Parent=mRNA227
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA227
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA227
chr21	.	intron	39639071	39641174	.	-	.	Parent=mRNA227
chr21	gth	exon	39641175	39641274	1.000000	-	.	Parent=mRNA227
chr21	.	intron	39641275	39642087	.	-	.	Parent=mRNA227
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA227
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA227
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA227
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA227
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA227
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA227
chr21	gth	exon	39642699	39642836	1.000000	-	.	Parent=mRNA227
chr21	gth	mRNA	39636596	39642658	.	-	.	ID=mRNA228;Parent=gene20
chr21	gth	exon	39636596	39636955	1.000000	-	.	Parent=mRNA228
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA228
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA228
chr21	.	intron	39639071	39639625	.	-	.	Parent=mRNA228
chr21	gth	exon	39639626	39639754	1.000000	-	.	Parent=mRNA228
chr21	.	intron	39639755	39642087	.	-	.	Parent=mRNA228
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA228
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA228
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA228
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA228
chr21	gth	exon	39642341	39642658	1.000000	-	.	Parent=mRNA228
chr21	gth	mRNA	39636600	39642419	.	-	.	ID=mRNA229;Parent=gene20
chr21	gth	exon	39636600	39636955	1.000000	-	.	Parent=mRNA229
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA229
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA229
chr21	.	intron	39639071	39641042	.	-	.	Parent=mRNA229
chr21	gth	exon	39641043	39641088	1.000000	-	.	Parent=mRNA229
chr21	.	intron	39641089	39641174	.	-	.	Parent=mRNA229
chr21	gth	exon	39641175	39641279	1.000000	-	.	Parent=mRNA229
chr21	.	intron	39641280	39642087	.	-	.	Parent=mRNA229
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA229
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA229
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA229
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA229
chr21	gth	exon	39642341	39642419	1.000000	-	.	Parent=mRNA229
chr21	gth	mRNA	39636675	39643443	.	-	.	ID=mRNA230;Parent=gene20
chr21	gth	exon	39636675	39636955	1.000000	-	.	Parent=mRNA230
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA230
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA230
chr21	.	intron	39639071	39642087	.	-	.	Parent=mRNA230
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA230
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA230
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA230
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA230
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA230
chr21	.	intron	39642374	39643255	.	-	.	Parent=mRNA230
chr21	gth	exon	39643256	39643443	1.000000	-	.	Parent=mRNA230
chr21	gth	mRNA	39636705	39642393	.	-	.	ID=mRNA231;Parent=gene20
chr21	gth	exon	39636705	39636955	1.000000	-	.	Parent=mRNA231
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA231
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA231
chr21	.	intron	39639071	39639625	.	-	.	Parent=mRNA231
chr21	gth	exon	39639626	39639754	1.000000	-	.	Parent=mRNA231
chr21	.	intron	39639755	39641174	.	-	.	Parent=mRNA231
chr21	gth	exon	39641175	39641279	1.000000	-	.	Parent=mRNA231
chr21	.	intron	39641280	39642087	.	-	.	Parent=mRNA231
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA231
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA231
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA231
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA231
chr21	gth	exon	39642341	39642393	1.000000	-	.	Parent=mRNA231
chr21	gth	mRNA	39636774	39642135	.	-	.	ID=mRNA232;Parent=gene20
chr21	gth	exon	39636774	39636955	1.000000	-	.	Parent=mRNA232
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA232
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA232
chr21	.	intron	39639071	39641042	.	-	.	Parent=mRNA232
chr21	gth	exon	39641043	39641088	1.000000	-	.	Parent=mRNA232
chr21	.	intron	39641089	39642087	.	-	.	Parent=mRNA232
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA232
chr21	gth	mRNA	39636805	39642850	.	-	.	ID=mRNA233;Parent=gene20
chr21	gth	exon	39636805	39636955	1.000000	-	.	Parent=mRNA233
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA233
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA233
chr21	.	intron	39639071	39639625	.	-	.	Parent=mRNA233
chr21	gth	exon	39639626	39639754	1.000000	-	.	Parent=mRNA233
chr21	.	intron	39639755	39641042	.	-	.	Parent=mRNA233
chr21	gth	exon	39641043	39641088	1.000000	-	.	Parent=mRNA233
chr21	.	intron	39641089	39641174	.	-	.	Parent=mRNA233
chr21	gth	exon	39641175	39641279	1.000000	-	.	Parent=mRNA233
chr21	.	intron	39641280	39642087	.	-	.	Parent=mRNA233
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA233
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA233
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA233
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA233
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA233
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA233
chr21	gth	exon	39642699	39642850	1.000000	-	.	Parent=mRNA233
chr21	gth	mRNA	39636933	39642850	.	-	.	ID=mRNA234;Parent=gene20
chr21	gth	exon	39636933	39636955	1.000000	-	.	Parent=mRNA234
chr21	.	intron	39636956	39638941	.	-	.	Parent=mRNA234
chr21	gth	exon	39638942	39639070	1.000000	-	.	Parent=mRNA234
chr21	.	intron	39639071	39642087	.	-	.	Parent=mRNA234
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA234
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA234
chr21	gth	exon	39642218	39642373	1.000000	-	.	Parent=mRNA234
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA234
chr21	gth	exon	39642699	39642850	1.000000	-	.	Parent=mRNA234
chr21	gth	mRNA	39640943	39642863	.	-	.	ID=mRNA235;Parent=gene20
chr21	gth	exon	39640943	39641088	1.000000	-	.	Parent=mRNA235
chr21	.	intron	39641089	39641174	.	-	.	Parent=mRNA235
chr21	gth	exon	39641175	39641279	1.000000	-	.	Parent=mRNA235
chr21	.	intron	39641280	39642087	.	-	.	Parent=mRNA235
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA235
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA235
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA235
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA235
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA235
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA235
chr21	gth	exon	39642699	39642863	1.000000	-	.	Parent=mRNA235
chr21	gth	mRNA	39641132	39642811	.	-	.	ID=mRNA236;Parent=gene20
chr21	gth	exon	39641132	39641748	1.000000	-	.	Parent=mRNA236
chr21	.	intron	39641749	39642087	.	-	.	Parent=mRNA236
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA236
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA236
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA236
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA236
chr21	gth	exon	39642341	39642373	1.000000	-	.	Parent=mRNA236
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA236
chr21	gth	exon	39642699	39642811	1.000000	-	.	Parent=mRNA236
chr21	gth	mRNA	39641288	39642416	.	-	.	ID=mRNA237;Parent=gene20
chr21	gth	exon	39641288	39641748	1.000000	-	.	Parent=mRNA237
chr21	.	intron	39641749	39642087	.	-	.	Parent=mRNA237
chr21	gth	exon	39642088	39642135	1.000000	-	.	Parent=mRNA237
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA237
chr21	gth	exon	39642218	39642247	1.000000	-	.	Parent=mRNA237
chr21	.	intron	39642248	39642340	.	-	.	Parent=mRNA237
chr21	gth	exon	39642341	39642416	1.000000	-	.	Parent=mRNA237
chr21	gth	mRNA	39641791	39642816	.	-	.	ID=mRNA238;Parent=gene20
chr21	gth	exon	39641791	39642373	1.000000	-	.	Parent=mRNA238
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA238
chr21	gth	exon	39642699	39642816	1.000000	-	.	Parent=mRNA238
chr21	gth	mRNA	39641861	39642850	.	-	.	ID=mRNA239;Parent=gene20
chr21	gth	exon	39641861	39642135	1.000000	-	.	Parent=mRNA239
chr21	.	intron	39642136	39642217	.	-	.	Parent=mRNA239
chr21	gth	exon	39642218	39642373	1.000000	-	.	Parent=mRNA239
chr21	.	intron	39642374	39642698	.	-	.	Parent=mRNA239
chr21	gth	exon	39642699	39642850	1.000000	-	.	Parent=mRNA239
###
chr21	gth	gene	39674040	39691685	.	+	.	ID=gene21
chr21	gth	mRNA	39674040	39691685	.	+	.	ID=mRNA240;Parent=gene21
chr21	gth	exon	39674040	39674282	1.000000	+	.	Parent=mRNA240
chr21	.	intron	39674283	39684493	.	+	.	Parent=mRNA240
chr21	gth	exon	39684494	39684659	1.000000	+	.	Parent=mRNA240
chr21	.	intron	39684660	39685564	.	+	.	Parent=mRNA240
chr21	gth	exon	39685565	39685632	1.000000	+	.	Parent=mRNA240
chr21	.	intron	39685633	39686961	.	+	.	Parent=mRNA240
chr21	gth	exon	39686962	39687076	1.000000	+	.	Parent=mRNA240
chr21	.	intron	39687077	39690661	.	+	.	Parent=mRNA240
chr21	gth	exon	39690662	39691685	1.000000	+	.	Parent=mRNA240
chr21	gth	mRNA	39674190	39685842	.	+	.	ID=mRNA241;Parent=gene21
chr21	gth	exon	39674190	39674282	1.000000	+	.	Parent=mRNA241
chr21	.	intron	39674283	39684493	.	+	.	Parent=mRNA241
chr21	gth	exon	39684494	39684659	1.000000	+	.	Parent=mRNA241
chr21	.	intron	39684660	39685564	.	+	.	Parent=mRNA241
chr21	gth	exon	39685565	39685842	1.000000	+	.	Parent=mRNA241
chr21	gth	mRNA	39674210	39685001	.	+	.	ID=mRNA242;Parent=gene21
chr21	gth	exon	39674210	39674282	1.000000	+	.	Parent=mRNA242
chr21	.	intron	39674283	39684493	.	+	.	Parent=mRNA242
chr21	gth	exon	39684494	39685001	1.000000	+	.	Parent=mRNA242
chr21	gth	mRNA	39674254	39690912	.	+	.	ID=mRNA243;Parent=gene21
chr21	gth	exon	39674254	39674352	1.000000	+	.	Parent=mRNA243
chr21	.	intron	39674353	39684493	.	+	.	Parent=mRNA243
chr21	gth	exon	39684494	39684659	1.000000	+	.	Parent=mRNA243
chr21	.	intron	39684660	39685564	.	+	.	Parent=mRNA243
chr21	gth	exon	39685565	39685632	1.000000	+	.	Parent=mRNA243
chr21	.	intron	39685633	39686961	.	+	.	Parent=mRNA243
chr21	gth	exon	39686962	39687076	1.000000	+	.	Parent=mRNA243
chr21	.	intron	39687077	39690661	.	+	.	Parent=mRNA243
chr21	gth	exon	39690662	39690912	1.000000	+	.	Parent=mRNA243
chr21	gth	mRNA	39674283	39684599	.	+	.	ID=mRNA244;Parent=gene21
chr21	gth	exon	39674283	39674717	1.000000	+	.	Parent=mRNA244
chr21	.	intron	39674718	39684493	.	+	.	Parent=mRNA244
chr21	gth	exon	39684494	39684599	1.000000	+	.	Parent=mRNA244
chr21	gth	mRNA	39679889	39687076	.	+	.	ID=mRNA245;Parent=gene21
chr21	gth	exon	39679889	39680307	1.000000	+	.	Parent=mRNA245
chr21	.	intron	39680308	39684493	.	+	.	Parent=mRNA245
chr21	gth	exon	39684494	39684659	1.000000	+	.	Parent=mRNA245
chr21	.	intron	39684660	39685564	.	+	.	Parent=mRNA245
chr21	gth	exon	39685565	39685632	1.000000	+	.	Parent=mRNA245
chr21	.	intron	39685633	39686961	.	+	.	Parent=mRNA245
chr21	gth	exon	39686962	39687076	1.000000	+	.	Parent=mRNA245
chr21	gth	mRNA	39681561	39691685	.	+	.	ID=mRNA246;Parent=gene21
chr21	gth	exon	39681561	39681651	1.000000	+	.	Parent=mRNA246
chr21	.	intron	39681652	39684493	.	+	.	Parent=mRNA246
chr21	gth	exon	39684494	39684659	1.000000	+	.	Parent=mRNA246
chr21	.	intron	39684660	39685564	.	+	.	Parent=mRNA246
chr21	gth	exon	39685565	39685632	1.000000	+	.	Parent=mRNA246
chr21	.	intron	39685633	39686961	.	+	.	Parent=mRNA246
chr21	gth	exon	39686962	39687076	1.000000	+	.	Parent=mRNA246
chr21	.	intron	39687077	39690661	.	+	.	Parent=mRNA246
chr21	gth	exon	39690662	39691685	1.000000	+	.	Parent=mRNA246
chr21	gth	mRNA	39681587	39691050	.	+	.	ID=mRNA247;Parent=gene21
chr21	gth	exon	39681587	39681651	1.000000	+	.	Parent=mRNA247
chr21	.	intron	39681652	39684493	.	+	.	Parent=mRNA247
chr21	gth	exon	39684494	39685272	1.000000	+	.	Parent=mRNA247
chr21	.	intron	39685273	39685564	.	+	.	Parent=mRNA247
chr21	gth	exon	39685565	39685632	1.000000	+	.	Parent=mRNA247
chr21	.	intron	39685633	39686961	.	+	.	Parent=mRNA247
chr21	gth	exon	39686962	39687076	1.000000	+	.	Parent=mRNA247
chr21	.	intron	39687077	39690661	.	+	.	Parent=mRNA247
chr21	gth	exon	39690662	39691050	1.000000	+	.	Parent=mRNA247
chr21	gth	mRNA	39686692	39690900	.	+	.	ID=mRNA248;Parent=gene21
chr21	gth	exon	39686692	39687076	1.000000	+	.	Parent=mRNA248
chr21	.	intron	39687077	39690661	.	+	.	Parent=mRNA248
chr21	gth	exon	39690662	39690900	1.000000	+	.	Parent=mRNA248
###
chr21	gth	gene	39699640	39739601	.	-	.	ID=gene22
chr21	gth	mRNA	39699640	39739573	.	-	.	ID=mRNA249;Parent=gene22
chr21	gth	exon	39699640	39700408	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39700409	39703774	.	-	.	Parent=mRNA249
chr21	gth	exon	39703775	39703892	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39703893	39704059	.	-	.	Parent=mRNA249
chr21	gth	exon	39704060	39704163	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39704164	39705513	.	-	.	Parent=mRNA249
chr21	gth	exon	39705514	39705598	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39705599	39714501	.	-	.	Parent=mRNA249
chr21	gth	exon	39714502	39714639	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39714640	39716771	.	-	.	Parent=mRNA249
chr21	gth	exon	39716772	39717286	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39717287	39721967	.	-	.	Parent=mRNA249
chr21	gth	exon	39721968	39722299	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA249
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39723008	39729215	.	-	.	Parent=mRNA249
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39729370	39737930	.	-	.	Parent=mRNA249
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA249
chr21	.	intron	39737998	39739520	.	-	.	Parent=mRNA249
chr21	gth	exon	39739521	39739573	1.000000	-	.	Parent=mRNA249
chr21	gth	mRNA	39699656	39739529	.	-	.	ID=mRNA250;Parent=gene22
chr21	gth	exon	39699656	39700408	1.000000	-	.	Parent=mRNA250
chr21	.	intron	39700409	39703774	.	-	.	Parent=mRNA250
chr21	gth	exon	39703775	39703892	1.000000	-	.	Parent=mRNA250
chr21	.	intron	39703893	39704059	.	-	.	Parent=mRNA250
chr21	gth	exon	39704060	39704163	1.000000	-	.	Parent=mRNA250
chr21	.	intron	39704164	39705513	.	-	.	Parent=mRNA250
chr21	gth	exon	39705514	39705598	1.000000	-	.	Parent=mRNA250
chr21	.	intron	39705599	39714501	.	-	.	Parent=mRNA250
chr21	gth	exon	39714502	39714639	1.000000	-	.	Parent=mRNA250
chr21	.	intron	39714640	39716771	.	-	.	Parent=mRNA250
chr21	gth	exon	39716772	39717286	1.000000	-	.	Parent=mRNA250
chr21	.	intron	39717287	39721967	.	-	.	Parent=mRNA250
chr21	gth	exon	39721968	39722299	1.000000	-	.	Parent=mRNA250
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA250
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA250
chr21	.	intron	39723008	39729215	.	-	.	Parent=mRNA250
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA250
chr21	.	intron	39729370	39739245	.	-	.	Parent=mRNA250
chr21	gth	exon	39739246	39739529	1.000000	-	.	Parent=mRNA250
chr21	gth	mRNA	39699774	39704943	.	-	.	ID=mRNA251;Parent=gene22
chr21	gth	exon	39699774	39700408	1.000000	-	.	Parent=mRNA251
chr21	.	intron	39700409	39703774	.	-	.	Parent=mRNA251
chr21	gth	exon	39703775	39703892	1.000000	-	.	Parent=mRNA251
chr21	.	intron	39703893	39704059	.	-	.	Parent=mRNA251
chr21	gth	exon	39704060	39704163	1.000000	-	.	Parent=mRNA251
chr21	.	intron	39704164	39704828	.	-	.	Parent=mRNA251
chr21	gth	exon	39704829	39704943	1.000000	-	.	Parent=mRNA251
chr21	gth	mRNA	39705514	39739548	.	-	.	ID=mRNA252;Parent=gene22
chr21	gth	exon	39705514	39705598	1.000000	-	.	Parent=mRNA252
chr21	.	intron	39705599	39714501	.	-	.	Parent=mRNA252
chr21	gth	exon	39714502	39714639	1.000000	-	.	Parent=mRNA252
chr21	.	intron	39714640	39716771	.	-	.	Parent=mRNA252
chr21	gth	exon	39716772	39716882	0.990991	-	.	Parent=mRNA252
chr21	.	intron	39716883	39729127	.	-	.	Parent=mRNA252
chr21	gth	exon	39729128	39729148	0.523810	-	.	Parent=mRNA252
chr21	.	intron	39729149	39729215	.	-	.	Parent=mRNA252
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA252
chr21	.	intron	39729370	39729892	.	-	.	Parent=mRNA252
chr21	gth	exon	39729893	39729963	1.000000	-	.	Parent=mRNA252
chr21	.	intron	39729964	39737930	.	-	.	Parent=mRNA252
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA252
chr21	.	intron	39737998	39739520	.	-	.	Parent=mRNA252
chr21	gth	exon	39739521	39739548	1.000000	-	.	Parent=mRNA252
chr21	gth	mRNA	39715860	39732732	.	-	.	ID=mRNA253;Parent=gene22
chr21	gth	exon	39715860	39717714	0.999461	-	.	Parent=mRNA253
chr21	.	intron	39717715	39721222	.	-	.	Parent=mRNA253
chr21	gth	exon	39721223	39722299	1.000000	-	.	Parent=mRNA253
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA253
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA253
chr21	.	intron	39723008	39732479	.	-	.	Parent=mRNA253
chr21	gth	exon	39732480	39732732	1.000000	-	.	Parent=mRNA253
chr21	gth	mRNA	39716208	39739573	.	-	.	ID=mRNA254;Parent=gene22
chr21	gth	exon	39716208	39717286	1.000000	-	.	Parent=mRNA254
chr21	.	intron	39717287	39721967	.	-	.	Parent=mRNA254
chr21	gth	exon	39721968	39722299	1.000000	-	.	Parent=mRNA254
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA254
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA254
chr21	.	intron	39723008	39729215	.	-	.	Parent=mRNA254
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA254
chr21	.	intron	39729370	39739520	.	-	.	Parent=mRNA254
chr21	gth	exon	39739521	39739573	1.000000	-	.	Parent=mRNA254
chr21	gth	mRNA	39716208	39739601	.	-	.	ID=mRNA255;Parent=gene22
chr21	gth	exon	39716208	39717286	1.000000	-	.	Parent=mRNA255
chr21	.	intron	39717287	39722926	.	-	.	Parent=mRNA255
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA255
chr21	.	intron	39723008	39737930	.	-	.	Parent=mRNA255
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA255
chr21	.	intron	39737998	39739520	.	-	.	Parent=mRNA255
chr21	gth	exon	39739521	39739601	1.000000	-	.	Parent=mRNA255
chr21	gth	mRNA	39716784	39739557	.	-	.	ID=mRNA256;Parent=gene22
chr21	gth	exon	39716784	39717286	1.000000	-	.	Parent=mRNA256
chr21	.	intron	39717287	39722926	.	-	.	Parent=mRNA256
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA256
chr21	.	intron	39723008	39729215	.	-	.	Parent=mRNA256
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA256
chr21	.	intron	39729370	39739520	.	-	.	Parent=mRNA256
chr21	gth	exon	39739521	39739557	1.000000	-	.	Parent=mRNA256
chr21	gth	mRNA	39717036	39739571	.	-	.	ID=mRNA257;Parent=gene22
chr21	gth	exon	39717036	39717286	1.000000	-	.	Parent=mRNA257
chr21	.	intron	39717287	39721554	.	-	.	Parent=mRNA257
chr21	gth	exon	39721555	39721701	1.000000	-	.	Parent=mRNA257
chr21	.	intron	39721702	39722926	.	-	.	Parent=mRNA257
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA257
chr21	.	intron	39723008	39729215	.	-	.	Parent=mRNA257
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA257
chr21	.	intron	39729370	39737930	.	-	.	Parent=mRNA257
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA257
chr21	.	intron	39737998	39738439	.	-	.	Parent=mRNA257
chr21	gth	exon	39738440	39738541	1.000000	-	.	Parent=mRNA257
chr21	.	intron	39738542	39739520	.	-	.	Parent=mRNA257
chr21	gth	exon	39739521	39739571	1.000000	-	.	Parent=mRNA257
chr21	gth	mRNA	39717041	39739556	.	-	.	ID=mRNA258;Parent=gene22
chr21	gth	exon	39717041	39717286	1.000000	-	.	Parent=mRNA258
chr21	.	intron	39717287	39721967	.	-	.	Parent=mRNA258
chr21	gth	exon	39721968	39722299	1.000000	-	.	Parent=mRNA258
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA258
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA258
chr21	.	intron	39723008	39729215	.	-	.	Parent=mRNA258
chr21	gth	exon	39729216	39729338	1.000000	-	.	Parent=mRNA258
chr21	.	intron	39729339	39737930	.	-	.	Parent=mRNA258
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA258
chr21	.	intron	39737998	39739520	.	-	.	Parent=mRNA258
chr21	gth	exon	39739521	39739556	1.000000	-	.	Parent=mRNA258
chr21	gth	mRNA	39717216	39739529	.	-	.	ID=mRNA259;Parent=gene22
chr21	gth	exon	39717216	39717286	1.000000	-	.	Parent=mRNA259
chr21	.	intron	39717287	39722926	.	-	.	Parent=mRNA259
chr21	gth	exon	39722927	39723190	1.000000	-	.	Parent=mRNA259
chr21	.	intron	39723191	39729215	.	-	.	Parent=mRNA259
chr21	gth	exon	39729216	39729338	1.000000	-	.	Parent=mRNA259
chr21	.	intron	39729339	39737930	.	-	.	Parent=mRNA259
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA259
chr21	.	intron	39737998	39739245	.	-	.	Parent=mRNA259
chr21	gth	exon	39739246	39739529	1.000000	-	.	Parent=mRNA259
chr21	gth	mRNA	39721968	39739574	.	-	.	ID=mRNA260;Parent=gene22
chr21	gth	exon	39721968	39722299	1.000000	-	.	Parent=mRNA260
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA260
chr21	gth	exon	39722927	39723190	1.000000	-	.	Parent=mRNA260
chr21	.	intron	39723191	39729215	.	-	.	Parent=mRNA260
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA260
chr21	.	intron	39729370	39739520	.	-	.	Parent=mRNA260
chr21	gth	exon	39739521	39739574	1.000000	-	.	Parent=mRNA260
chr21	gth	mRNA	39722004	39739599	.	-	.	ID=mRNA261;Parent=gene22
chr21	gth	exon	39722004	39722299	1.000000	-	.	Parent=mRNA261
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA261
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA261
chr21	.	intron	39723008	39737930	.	-	.	Parent=mRNA261
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA261
chr21	.	intron	39737998	39739520	.	-	.	Parent=mRNA261
chr21	gth	exon	39739521	39739599	1.000000	-	.	Parent=mRNA261
chr21	gth	mRNA	39722006	39739515	.	-	.	ID=mRNA262;Parent=gene22
chr21	gth	exon	39722006	39722299	1.000000	-	.	Parent=mRNA262
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA262
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA262
chr21	.	intron	39723008	39732479	.	-	.	Parent=mRNA262
chr21	gth	exon	39732480	39732514	1.000000	-	.	Parent=mRNA262
chr21	.	intron	39732515	39737930	.	-	.	Parent=mRNA262
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA262
chr21	.	intron	39737998	39738439	.	-	.	Parent=mRNA262
chr21	gth	exon	39738440	39738541	1.000000	-	.	Parent=mRNA262
chr21	.	intron	39738542	39739245	.	-	.	Parent=mRNA262
chr21	gth	exon	39739246	39739515	1.000000	-	.	Parent=mRNA262
chr21	gth	mRNA	39722081	39739565	.	-	.	ID=mRNA263;Parent=gene22
chr21	gth	exon	39722081	39722299	1.000000	-	.	Parent=mRNA263
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA263
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA263
chr21	.	intron	39723008	39729215	.	-	.	Parent=mRNA263
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA263
chr21	.	intron	39729370	39733429	.	-	.	Parent=mRNA263
chr21	gth	exon	39733430	39733569	1.000000	-	.	Parent=mRNA263
chr21	.	intron	39733570	39737930	.	-	.	Parent=mRNA263
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA263
chr21	.	intron	39737998	39739520	.	-	.	Parent=mRNA263
chr21	gth	exon	39739521	39739565	1.000000	-	.	Parent=mRNA263
chr21	gth	mRNA	39722101	39739565	.	-	.	ID=mRNA264;Parent=gene22
chr21	gth	exon	39722101	39722299	1.000000	-	.	Parent=mRNA264
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA264
chr21	gth	exon	39722927	39723007	1.000000	-	.	Parent=mRNA264
chr21	.	intron	39723008	39729215	.	-	.	Parent=mRNA264
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA264
chr21	.	intron	39729370	39729892	.	-	.	Parent=mRNA264
chr21	gth	exon	39729893	39729963	1.000000	-	.	Parent=mRNA264
chr21	.	intron	39729964	39733429	.	-	.	Parent=mRNA264
chr21	gth	exon	39733430	39733569	1.000000	-	.	Parent=mRNA264
chr21	.	intron	39733570	39739520	.	-	.	Parent=mRNA264
chr21	gth	exon	39739521	39739565	1.000000	-	.	Parent=mRNA264
chr21	gth	mRNA	39722198	39739576	.	-	.	ID=mRNA265;Parent=gene22
chr21	gth	exon	39722198	39722299	1.000000	-	.	Parent=mRNA265
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA265
chr21	gth	exon	39722927	39723190	1.000000	-	.	Parent=mRNA265
chr21	.	intron	39723191	39729215	.	-	.	Parent=mRNA265
chr21	gth	exon	39729216	39729338	1.000000	-	.	Parent=mRNA265
chr21	.	intron	39729339	39737930	.	-	.	Parent=mRNA265
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA265
chr21	.	intron	39737998	39739520	.	-	.	Parent=mRNA265
chr21	gth	exon	39739521	39739576	1.000000	-	.	Parent=mRNA265
chr21	gth	mRNA	39722258	39739548	.	-	.	ID=mRNA266;Parent=gene22
chr21	gth	exon	39722258	39722299	1.000000	-	.	Parent=mRNA266
chr21	.	intron	39722300	39722926	.	-	.	Parent=mRNA266
chr21	gth	exon	39722927	39723190	1.000000	-	.	Parent=mRNA266
chr21	.	intron	39723191	39729215	.	-	.	Parent=mRNA266
chr21	gth	exon	39729216	39729369	1.000000	-	.	Parent=mRNA266
chr21	.	intron	39729370	39737930	.	-	.	Parent=mRNA266
chr21	gth	exon	39737931	39737997	1.000000	-	.	Parent=mRNA266
chr21	.	intron	39737998	39738439	.	-	.	Parent=mRNA266
chr21	gth	exon	39738440	39738541	1.000000	-	.	Parent=mRNA266
chr21	.	intron	39738542	39739520	.	-	.	Parent=mRNA266
chr21	gth	exon	39739521	39739548	1.000000	-	.	Parent=mRNA266
chr21	gth	mRNA	39737255	39739549	.	-	.	ID=mRNA267;Parent=gene22
chr21	gth	exon	39737255	39737997	1.000000	-	.	Parent=mRNA267
chr21	.	intron	39737998	39739520	.	-	.	Parent=mRNA267
chr21	gth	exon	39739521	39739549	1.000000	-	.	Parent=mRNA267
###
chr21	gth	gene	39739651	39739894	.	+	.	ID=gene23
chr21	gth	mRNA	39739651	39739894	.	+	.	ID=mRNA268;Parent=gene23
chr21	gth	exon	39739651	39739894	1.000000	+	.	Parent=mRNA268
###
genometools-1.5.1/testdata/gt_evalviz_test.reality000066400000000000000000011035671211610345200224760ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr21 32669578 39739894
chr21	ENCODE	gene	32669578	32687206	.	-	.	ID=gene1;Name=AP000266.110-001;name2=URB1
chr21	ENCODE	exon	32669578	32669663	.	-	.	Parent=gene1
chr21	.	intron	32669664	32672624	.	-	.	Parent=gene1
chr21	ENCODE	exon	32672625	32672721	.	-	.	Parent=gene1
chr21	.	intron	32672722	32677601	.	-	.	Parent=gene1
chr21	ENCODE	exon	32677602	32677734	.	-	.	Parent=gene1
chr21	.	intron	32677735	32678492	.	-	.	Parent=gene1
chr21	ENCODE	exon	32678493	32678644	.	-	.	Parent=gene1
chr21	.	intron	32678645	32679724	.	-	.	Parent=gene1
chr21	ENCODE	exon	32679725	32679864	.	-	.	Parent=gene1
chr21	.	intron	32679865	32686948	.	-	.	Parent=gene1
chr21	ENCODE	exon	32686949	32687206	.	-	.	Parent=gene1
###
chr21	ENCODE	gene	32706185	32762234	.	+	.	ID=gene2;Name=AP000272.65-004;name2=C21orf63
chr21	ENCODE	exon	32706185	32707192	.	+	.	Parent=gene2
chr21	.	intron	32707193	32747490	.	+	.	Parent=gene2
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene2
chr21	.	intron	32747688	32751775	.	+	.	Parent=gene2
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene2
chr21	.	intron	32751900	32761874	.	+	.	Parent=gene2
chr21	ENCODE	exon	32761875	32762234	.	+	.	Parent=gene2
###
chr21	ENCODE	gene	32706221	32795636	.	+	.	ID=gene3;Name=AP000272.65-009;name2=C21orf63
chr21	ENCODE	exon	32706221	32706372	.	+	.	Parent=gene3
chr21	.	intron	32706373	32747490	.	+	.	Parent=gene3
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene3
chr21	.	intron	32747688	32761874	.	+	.	Parent=gene3
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene3
chr21	.	intron	32762028	32789207	.	+	.	Parent=gene3
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene3
chr21	.	intron	32789352	32795595	.	+	.	Parent=gene3
chr21	ENCODE	exon	32795596	32795636	.	+	.	Parent=gene3
###
chr21	ENCODE	gene	32706560	32809570	.	+	.	ID=gene4;Name=AP000272.65-001;name2=C21orf63
chr21	ENCODE	exon	32706560	32707192	.	+	.	Parent=gene4
chr21	ENCODE	CDS	32707033	32707192	.	+	.	Parent=gene4
chr21	.	intron	32707193	32747490	.	+	.	Parent=gene4
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene4
chr21	ENCODE	CDS	32747491	32747687	.	+	.	Parent=gene4
chr21	.	intron	32747688	32751775	.	+	.	Parent=gene4
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene4
chr21	ENCODE	CDS	32751776	32751899	.	+	.	Parent=gene4
chr21	.	intron	32751900	32761874	.	+	.	Parent=gene4
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene4
chr21	ENCODE	CDS	32761875	32762027	.	+	.	Parent=gene4
chr21	.	intron	32762028	32789207	.	+	.	Parent=gene4
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene4
chr21	ENCODE	CDS	32789208	32789351	.	+	.	Parent=gene4
chr21	.	intron	32789352	32795595	.	+	.	Parent=gene4
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene4
chr21	ENCODE	CDS	32795596	32795676	.	+	.	Parent=gene4
chr21	.	intron	32795677	32798106	.	+	.	Parent=gene4
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene4
chr21	ENCODE	CDS	32798107	32798196	.	+	.	Parent=gene4
chr21	.	intron	32798197	32808994	.	+	.	Parent=gene4
chr21	ENCODE	CDS	32808995	32809371	.	+	.	Parent=gene4
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene4
###
chr21	ENCODE	gene	32706616	32809570	.	+	.	ID=gene5;Name=AP000272.65-007;name2=C21orf63
chr21	ENCODE	exon	32706616	32707192	.	+	.	Parent=gene5
chr21	.	intron	32707193	32751775	.	+	.	Parent=gene5
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene5
chr21	.	intron	32751900	32761874	.	+	.	Parent=gene5
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene5
chr21	.	intron	32762028	32789207	.	+	.	Parent=gene5
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene5
chr21	.	intron	32789352	32795595	.	+	.	Parent=gene5
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene5
chr21	.	intron	32795677	32798106	.	+	.	Parent=gene5
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene5
chr21	.	intron	32798197	32808994	.	+	.	Parent=gene5
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene5
###
chr21	ENCODE	gene	32706616	32809570	.	+	.	ID=gene6;Name=AP000272.65-005;name2=C21orf63
chr21	ENCODE	exon	32706616	32707192	.	+	.	Parent=gene6
chr21	.	intron	32707193	32751775	.	+	.	Parent=gene6
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene6
chr21	.	intron	32751900	32761874	.	+	.	Parent=gene6
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene6
chr21	.	intron	32762028	32795595	.	+	.	Parent=gene6
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene6
chr21	.	intron	32795677	32798106	.	+	.	Parent=gene6
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene6
chr21	.	intron	32798197	32808994	.	+	.	Parent=gene6
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene6
###
chr21	ENCODE	gene	32706732	32809570	.	+	.	ID=gene7;Name=AP000272.65-006;name2=C21orf63
chr21	ENCODE	exon	32706732	32707192	.	+	.	Parent=gene7
chr21	.	intron	32707193	32761874	.	+	.	Parent=gene7
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene7
chr21	.	intron	32762028	32789207	.	+	.	Parent=gene7
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene7
chr21	.	intron	32789352	32795595	.	+	.	Parent=gene7
chr21	ENCODE	exon	32795596	32795719	.	+	.	Parent=gene7
chr21	.	intron	32795720	32798106	.	+	.	Parent=gene7
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene7
chr21	.	intron	32798197	32808994	.	+	.	Parent=gene7
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene7
###
chr21	ENCODE	gene	32706881	32809570	.	+	.	ID=gene8;Name=AP000272.65-002;name2=C21orf63
chr21	ENCODE	exon	32706881	32707192	.	+	.	Parent=gene8
chr21	ENCODE	CDS	32707033	32707192	.	+	.	Parent=gene8
chr21	.	intron	32707193	32747490	.	+	.	Parent=gene8
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene8
chr21	ENCODE	CDS	32747491	32747687	.	+	.	Parent=gene8
chr21	.	intron	32747688	32751775	.	+	.	Parent=gene8
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene8
chr21	ENCODE	CDS	32751776	32751899	.	+	.	Parent=gene8
chr21	.	intron	32751900	32761874	.	+	.	Parent=gene8
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene8
chr21	ENCODE	CDS	32761875	32762027	.	+	.	Parent=gene8
chr21	.	intron	32762028	32789207	.	+	.	Parent=gene8
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene8
chr21	ENCODE	CDS	32789208	32789351	.	+	.	Parent=gene8
chr21	.	intron	32789352	32795595	.	+	.	Parent=gene8
chr21	ENCODE	exon	32795596	32795667	.	+	.	Parent=gene8
chr21	ENCODE	CDS	32795596	32795667	.	+	.	Parent=gene8
chr21	.	intron	32795668	32798106	.	+	.	Parent=gene8
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene8
chr21	ENCODE	CDS	32798107	32798196	.	+	.	Parent=gene8
chr21	.	intron	32798197	32808994	.	+	.	Parent=gene8
chr21	ENCODE	CDS	32808995	32809371	.	+	.	Parent=gene8
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene8
###
chr21	ENCODE	gene	32706943	32727463	.	+	.	ID=gene9;Name=AP000272.65-010;name2=C21orf63
chr21	ENCODE	exon	32706943	32707192	.	+	.	Parent=gene9
chr21	.	intron	32707193	32727329	.	+	.	Parent=gene9
chr21	ENCODE	exon	32727330	32727463	.	+	.	Parent=gene9
###
chr21	ENCODE	gene	32722513	32789318	.	+	.	ID=gene10;Name=AP000272.65-008;name2=C21orf63
chr21	ENCODE	exon	32722513	32722863	.	+	.	Parent=gene10
chr21	.	intron	32722864	32747490	.	+	.	Parent=gene10
chr21	ENCODE	exon	32747491	32747687	.	+	.	Parent=gene10
chr21	ENCODE	CDS	32747616	32747687	.	+	.	Parent=gene10
chr21	.	intron	32747688	32751775	.	+	.	Parent=gene10
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene10
chr21	ENCODE	CDS	32751776	32751899	.	+	.	Parent=gene10
chr21	.	intron	32751900	32761874	.	+	.	Parent=gene10
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene10
chr21	ENCODE	CDS	32761875	32762027	.	+	.	Parent=gene10
chr21	.	intron	32762028	32789207	.	+	.	Parent=gene10
chr21	ENCODE	exon	32789208	32789318	.	+	.	Parent=gene10
chr21	ENCODE	CDS	32789208	32789318	.	+	.	Parent=gene10
###
chr21	ENCODE	gene	32746364	32809570	.	+	.	ID=gene11;Name=AP000272.65-003;name2=C21orf63
chr21	ENCODE	exon	32746364	32747687	.	+	.	Parent=gene11
chr21	.	intron	32747688	32751775	.	+	.	Parent=gene11
chr21	ENCODE	exon	32751776	32751899	.	+	.	Parent=gene11
chr21	.	intron	32751900	32761874	.	+	.	Parent=gene11
chr21	ENCODE	exon	32761875	32762027	.	+	.	Parent=gene11
chr21	.	intron	32762028	32789207	.	+	.	Parent=gene11
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene11
chr21	.	intron	32789352	32795595	.	+	.	Parent=gene11
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene11
chr21	.	intron	32795677	32798106	.	+	.	Parent=gene11
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene11
chr21	.	intron	32798197	32808994	.	+	.	Parent=gene11
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene11
###
chr21	ENCODE	gene	32787834	32809061	.	+	.	ID=gene12;Name=AP000272.65-011;name2=C21orf63
chr21	ENCODE	exon	32787834	32787943	.	+	.	Parent=gene12
chr21	.	intron	32787944	32789207	.	+	.	Parent=gene12
chr21	ENCODE	exon	32789208	32789351	.	+	.	Parent=gene12
chr21	.	intron	32789352	32795595	.	+	.	Parent=gene12
chr21	ENCODE	exon	32795596	32795676	.	+	.	Parent=gene12
chr21	.	intron	32795677	32798106	.	+	.	Parent=gene12
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene12
chr21	.	intron	32798197	32808994	.	+	.	Parent=gene12
chr21	ENCODE	exon	32808995	32809061	.	+	.	Parent=gene12
###
chr21	ENCODE	gene	32789298	32809570	.	+	.	ID=gene13;Name=AP000272.65-012;name2=C21orf63
chr21	ENCODE	exon	32789298	32789351	.	+	.	Parent=gene13
chr21	.	intron	32789352	32798106	.	+	.	Parent=gene13
chr21	ENCODE	exon	32798107	32798196	.	+	.	Parent=gene13
chr21	.	intron	32798197	32808994	.	+	.	Parent=gene13
chr21	ENCODE	exon	32808995	32809570	.	+	.	Parent=gene13
###
chr21	ENCODE	gene	32870733	32879714	.	-	.	ID=gene14;Name=AP000274.7-001;name2=TCP10L
chr21	ENCODE	exon	32870733	32871104	.	-	.	Parent=gene14
chr21	ENCODE	CDS	32870955	32871104	.	-	.	Parent=gene14
chr21	.	intron	32871105	32872874	.	-	.	Parent=gene14
chr21	ENCODE	exon	32872875	32873012	.	-	.	Parent=gene14
chr21	ENCODE	CDS	32872875	32873012	.	-	.	Parent=gene14
chr21	.	intron	32873013	32876380	.	-	.	Parent=gene14
chr21	ENCODE	exon	32876381	32876596	.	-	.	Parent=gene14
chr21	ENCODE	CDS	32876381	32876596	.	-	.	Parent=gene14
chr21	.	intron	32876597	32878341	.	-	.	Parent=gene14
chr21	ENCODE	CDS	32878342	32878485	.	-	.	Parent=gene14
chr21	ENCODE	exon	32878342	32878486	.	-	.	Parent=gene14
chr21	.	intron	32878487	32879601	.	-	.	Parent=gene14
chr21	ENCODE	exon	32879602	32879714	.	-	.	Parent=gene14
###
chr21	ENCODE	gene	32870840	32876615	.	-	.	ID=gene15;Name=AP000274.7-002;name2=TCP10L
chr21	ENCODE	exon	32870840	32871104	.	-	.	Parent=gene15
chr21	.	intron	32871105	32871606	.	-	.	Parent=gene15
chr21	ENCODE	exon	32871607	32871857	.	-	.	Parent=gene15
chr21	.	intron	32871858	32872874	.	-	.	Parent=gene15
chr21	ENCODE	exon	32872875	32873012	.	-	.	Parent=gene15
chr21	.	intron	32873013	32876380	.	-	.	Parent=gene15
chr21	ENCODE	exon	32876381	32876615	.	-	.	Parent=gene15
###
chr21	ENCODE	gene	32870840	32879714	.	-	.	ID=gene16;Name=AP000274.7-003;name2=TCP10L
chr21	ENCODE	exon	32870840	32871104	.	-	.	Parent=gene16
chr21	.	intron	32871105	32872874	.	-	.	Parent=gene16
chr21	ENCODE	exon	32872875	32873012	.	-	.	Parent=gene16
chr21	.	intron	32873013	32876380	.	-	.	Parent=gene16
chr21	ENCODE	exon	32876381	32876596	.	-	.	Parent=gene16
chr21	.	intron	32876597	32879601	.	-	.	Parent=gene16
chr21	ENCODE	exon	32879602	32879714	.	-	.	Parent=gene16
###
chr21	ENCODE	gene	32873003	32906327	.	-	.	ID=gene17;Name=AP000274.7-005;name2=TCP10L
chr21	ENCODE	exon	32873003	32873012	.	-	.	Parent=gene17
chr21	ENCODE	CDS	32873003	32873012	.	-	.	Parent=gene17
chr21	.	intron	32873013	32876380	.	-	.	Parent=gene17
chr21	ENCODE	exon	32876381	32876596	.	-	.	Parent=gene17
chr21	ENCODE	CDS	32876381	32876596	.	-	.	Parent=gene17
chr21	.	intron	32876597	32896452	.	-	.	Parent=gene17
chr21	ENCODE	exon	32896453	32896548	.	-	.	Parent=gene17
chr21	ENCODE	CDS	32896453	32896548	.	-	.	Parent=gene17
chr21	.	intron	32896549	32897341	.	-	.	Parent=gene17
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene17
chr21	ENCODE	CDS	32897342	32897473	.	-	.	Parent=gene17
chr21	.	intron	32897474	32898305	.	-	.	Parent=gene17
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene17
chr21	ENCODE	CDS	32898306	32898464	.	-	.	Parent=gene17
chr21	.	intron	32898465	32901829	.	-	.	Parent=gene17
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene17
chr21	ENCODE	CDS	32901830	32901897	.	-	.	Parent=gene17
chr21	.	intron	32901898	32904018	.	-	.	Parent=gene17
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene17
chr21	ENCODE	CDS	32904019	32904186	.	-	.	Parent=gene17
chr21	.	intron	32904187	32906285	.	-	.	Parent=gene17
chr21	ENCODE	exon	32906286	32906327	.	-	.	Parent=gene17
chr21	ENCODE	CDS	32906286	32906327	.	-	.	Parent=gene17
###
chr21	ENCODE	gene	32873004	32906462	.	-	.	ID=gene18;Name=AP000274.7-004;name2=TCP10L
chr21	ENCODE	exon	32873004	32873012	.	-	.	Parent=gene18
chr21	ENCODE	CDS	32873004	32873012	.	-	.	Parent=gene18
chr21	.	intron	32873013	32876380	.	-	.	Parent=gene18
chr21	ENCODE	exon	32876381	32876596	.	-	.	Parent=gene18
chr21	ENCODE	CDS	32876381	32876596	.	-	.	Parent=gene18
chr21	.	intron	32876597	32897341	.	-	.	Parent=gene18
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene18
chr21	ENCODE	CDS	32897342	32897473	.	-	.	Parent=gene18
chr21	.	intron	32897474	32898305	.	-	.	Parent=gene18
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene18
chr21	ENCODE	CDS	32898306	32898464	.	-	.	Parent=gene18
chr21	.	intron	32898465	32901829	.	-	.	Parent=gene18
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene18
chr21	ENCODE	CDS	32901830	32901897	.	-	.	Parent=gene18
chr21	.	intron	32901898	32904018	.	-	.	Parent=gene18
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene18
chr21	ENCODE	CDS	32904019	32904186	.	-	.	Parent=gene18
chr21	.	intron	32904187	32906285	.	-	.	Parent=gene18
chr21	ENCODE	CDS	32906286	32906424	.	-	.	Parent=gene18
chr21	ENCODE	exon	32906286	32906462	.	-	.	Parent=gene18
###
chr21	ENCODE	gene	32876405	32901879	.	-	.	ID=gene19;Name=AP000274.7-006;name2=TCP10L
chr21	ENCODE	exon	32876405	32876596	.	-	.	Parent=gene19
chr21	ENCODE	CDS	32876405	32876596	.	-	.	Parent=gene19
chr21	.	intron	32876597	32898305	.	-	.	Parent=gene19
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene19
chr21	ENCODE	CDS	32898306	32898464	.	-	.	Parent=gene19
chr21	.	intron	32898465	32901829	.	-	.	Parent=gene19
chr21	ENCODE	exon	32901830	32901879	.	-	.	Parent=gene19
chr21	ENCODE	CDS	32901830	32901879	.	-	.	Parent=gene19
###
chr21	ENCODE	gene	32886260	32897418	.	-	.	ID=gene20;Name=AP000275.61-005;name2=C21orf59
chr21	ENCODE	exon	32886260	32886599	.	-	.	Parent=gene20
chr21	.	intron	32886600	32897341	.	-	.	Parent=gene20
chr21	ENCODE	exon	32897342	32897418	.	-	.	Parent=gene20
###
chr21	ENCODE	gene	32895848	32898452	.	-	.	ID=gene21;Name=AP000275.61-006;name2=C21orf59
chr21	ENCODE	exon	32895848	32896154	.	-	.	Parent=gene21
chr21	ENCODE	CDS	32896044	32896154	.	-	.	Parent=gene21
chr21	.	intron	32896155	32897341	.	-	.	Parent=gene21
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene21
chr21	ENCODE	CDS	32897342	32897473	.	-	.	Parent=gene21
chr21	.	intron	32897474	32898305	.	-	.	Parent=gene21
chr21	ENCODE	exon	32898306	32898452	.	-	.	Parent=gene21
chr21	ENCODE	CDS	32898306	32898452	.	-	.	Parent=gene21
###
chr21	ENCODE	gene	32895848	32906767	.	-	.	ID=gene22;Name=AP000275.61-002;name2=C21orf59
chr21	ENCODE	exon	32895848	32897473	.	-	.	Parent=gene22
chr21	ENCODE	CDS	32897270	32897473	.	-	.	Parent=gene22
chr21	.	intron	32897474	32898305	.	-	.	Parent=gene22
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene22
chr21	ENCODE	CDS	32898306	32898464	.	-	.	Parent=gene22
chr21	.	intron	32898465	32901829	.	-	.	Parent=gene22
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene22
chr21	ENCODE	CDS	32901830	32901897	.	-	.	Parent=gene22
chr21	.	intron	32901898	32904018	.	-	.	Parent=gene22
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene22
chr21	ENCODE	CDS	32904019	32904186	.	-	.	Parent=gene22
chr21	.	intron	32904187	32906285	.	-	.	Parent=gene22
chr21	ENCODE	CDS	32906286	32906424	.	-	.	Parent=gene22
chr21	ENCODE	exon	32906286	32906767	.	-	.	Parent=gene22
###
chr21	ENCODE	gene	32895848	32907047	.	-	.	ID=gene23;Name=AP000275.61-001;name2=C21orf59
chr21	ENCODE	exon	32895848	32896154	.	-	.	Parent=gene23
chr21	ENCODE	CDS	32896044	32896154	.	-	.	Parent=gene23
chr21	.	intron	32896155	32896452	.	-	.	Parent=gene23
chr21	ENCODE	exon	32896453	32896548	.	-	.	Parent=gene23
chr21	ENCODE	CDS	32896453	32896548	.	-	.	Parent=gene23
chr21	.	intron	32896549	32897341	.	-	.	Parent=gene23
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene23
chr21	ENCODE	CDS	32897342	32897473	.	-	.	Parent=gene23
chr21	.	intron	32897474	32898305	.	-	.	Parent=gene23
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene23
chr21	ENCODE	CDS	32898306	32898464	.	-	.	Parent=gene23
chr21	.	intron	32898465	32901829	.	-	.	Parent=gene23
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene23
chr21	ENCODE	CDS	32901830	32901897	.	-	.	Parent=gene23
chr21	.	intron	32901898	32904018	.	-	.	Parent=gene23
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene23
chr21	ENCODE	CDS	32904019	32904186	.	-	.	Parent=gene23
chr21	.	intron	32904187	32906285	.	-	.	Parent=gene23
chr21	ENCODE	CDS	32906286	32906424	.	-	.	Parent=gene23
chr21	ENCODE	exon	32906286	32907047	.	-	.	Parent=gene23
###
chr21	ENCODE	gene	32895884	32898381	.	-	.	ID=gene24;Name=AP000275.61-004;name2=C21orf59
chr21	ENCODE	exon	32895884	32896548	.	-	.	Parent=gene24
chr21	.	intron	32896549	32897341	.	-	.	Parent=gene24
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene24
chr21	.	intron	32897474	32898305	.	-	.	Parent=gene24
chr21	ENCODE	exon	32898306	32898381	.	-	.	Parent=gene24
###
chr21	ENCODE	gene	32895966	32906784	.	-	.	ID=gene25;Name=AP000275.61-003;name2=C21orf59
chr21	ENCODE	exon	32895966	32896154	.	-	.	Parent=gene25
chr21	.	intron	32896155	32896452	.	-	.	Parent=gene25
chr21	ENCODE	exon	32896453	32896548	.	-	.	Parent=gene25
chr21	.	intron	32896549	32897341	.	-	.	Parent=gene25
chr21	ENCODE	exon	32897342	32897473	.	-	.	Parent=gene25
chr21	.	intron	32897474	32898305	.	-	.	Parent=gene25
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene25
chr21	.	intron	32898465	32904018	.	-	.	Parent=gene25
chr21	ENCODE	exon	32904019	32904186	.	-	.	Parent=gene25
chr21	.	intron	32904187	32906285	.	-	.	Parent=gene25
chr21	ENCODE	exon	32906286	32906784	.	-	.	Parent=gene25
###
chr21	ENCODE	gene	32895991	32898694	.	-	.	ID=gene26;Name=AP000275.61-008;name2=C21orf59
chr21	ENCODE	exon	32895991	32897473	.	-	.	Parent=gene26
chr21	.	intron	32897474	32898305	.	-	.	Parent=gene26
chr21	ENCODE	exon	32898306	32898694	.	-	.	Parent=gene26
###
chr21	ENCODE	gene	32897406	32906736	.	-	.	ID=gene27;Name=AP000275.61-007;name2=C21orf59
chr21	ENCODE	exon	32897406	32897473	.	-	.	Parent=gene27
chr21	ENCODE	CDS	32897406	32897473	.	-	.	Parent=gene27
chr21	.	intron	32897474	32898305	.	-	.	Parent=gene27
chr21	ENCODE	exon	32898306	32898464	.	-	.	Parent=gene27
chr21	ENCODE	CDS	32898306	32898464	.	-	.	Parent=gene27
chr21	.	intron	32898465	32901829	.	-	.	Parent=gene27
chr21	ENCODE	exon	32901830	32901897	.	-	.	Parent=gene27
chr21	ENCODE	CDS	32901830	32901897	.	-	.	Parent=gene27
chr21	.	intron	32901898	32904018	.	-	.	Parent=gene27
chr21	ENCODE	exon	32904019	32904135	.	-	.	Parent=gene27
chr21	ENCODE	CDS	32904019	32904135	.	-	.	Parent=gene27
chr21	.	intron	32904136	32906285	.	-	.	Parent=gene27
chr21	ENCODE	CDS	32906286	32906424	.	-	.	Parent=gene27
chr21	ENCODE	exon	32906286	32906736	.	-	.	Parent=gene27
###
chr21	ENCODE	gene	32922944	33022105	.	-	.	ID=gene28;Name=AP000275.63-003;name2=SYNJ1
chr21	ENCODE	exon	32922944	32925982	.	-	.	Parent=gene28
chr21	.	intron	32925983	32929041	.	-	.	Parent=gene28
chr21	ENCODE	exon	32929042	32929065	.	-	.	Parent=gene28
chr21	.	intron	32929066	32933088	.	-	.	Parent=gene28
chr21	ENCODE	exon	32933089	32933306	.	-	.	Parent=gene28
chr21	.	intron	32933307	32933851	.	-	.	Parent=gene28
chr21	ENCODE	exon	32933852	32933960	.	-	.	Parent=gene28
chr21	.	intron	32933961	32936076	.	-	.	Parent=gene28
chr21	ENCODE	exon	32936077	32936147	.	-	.	Parent=gene28
chr21	.	intron	32936148	32936275	.	-	.	Parent=gene28
chr21	ENCODE	exon	32936276	32936314	.	-	.	Parent=gene28
chr21	.	intron	32936315	32939148	.	-	.	Parent=gene28
chr21	ENCODE	exon	32939149	32939187	.	-	.	Parent=gene28
chr21	.	intron	32939188	32939826	.	-	.	Parent=gene28
chr21	ENCODE	exon	32939827	32939891	.	-	.	Parent=gene28
chr21	.	intron	32939892	32939939	.	-	.	Parent=gene28
chr21	ENCODE	exon	32939940	32939970	.	-	.	Parent=gene28
chr21	.	intron	32939971	32940573	.	-	.	Parent=gene28
chr21	ENCODE	exon	32940574	32940783	.	-	.	Parent=gene28
chr21	.	intron	32940784	32944364	.	-	.	Parent=gene28
chr21	ENCODE	exon	32944365	32944527	.	-	.	Parent=gene28
chr21	.	intron	32944528	32947468	.	-	.	Parent=gene28
chr21	ENCODE	exon	32947469	32947547	.	-	.	Parent=gene28
chr21	.	intron	32947548	32950867	.	-	.	Parent=gene28
chr21	ENCODE	exon	32950868	32951083	.	-	.	Parent=gene28
chr21	.	intron	32951084	32951183	.	-	.	Parent=gene28
chr21	ENCODE	exon	32951184	32951301	.	-	.	Parent=gene28
chr21	.	intron	32951302	32951896	.	-	.	Parent=gene28
chr21	ENCODE	exon	32951897	32952053	.	-	.	Parent=gene28
chr21	.	intron	32952054	32959093	.	-	.	Parent=gene28
chr21	ENCODE	exon	32959094	32959252	.	-	.	Parent=gene28
chr21	.	intron	32959253	32960123	.	-	.	Parent=gene28
chr21	ENCODE	exon	32960124	32960316	.	-	.	Parent=gene28
chr21	.	intron	32960317	32960613	.	-	.	Parent=gene28
chr21	ENCODE	exon	32960614	32960754	.	-	.	Parent=gene28
chr21	.	intron	32960755	32964468	.	-	.	Parent=gene28
chr21	ENCODE	exon	32964469	32964553	.	-	.	Parent=gene28
chr21	.	intron	32964554	32967520	.	-	.	Parent=gene28
chr21	ENCODE	exon	32967521	32967712	.	-	.	Parent=gene28
chr21	.	intron	32967713	32970512	.	-	.	Parent=gene28
chr21	ENCODE	exon	32970513	32970536	.	-	.	Parent=gene28
chr21	.	intron	32970537	32972825	.	-	.	Parent=gene28
chr21	ENCODE	exon	32972826	32972982	.	-	.	Parent=gene28
chr21	.	intron	32972983	32975676	.	-	.	Parent=gene28
chr21	ENCODE	exon	32975677	32975829	.	-	.	Parent=gene28
chr21	.	intron	32975830	32978218	.	-	.	Parent=gene28
chr21	ENCODE	exon	32978219	32978300	.	-	.	Parent=gene28
chr21	.	intron	32978301	32979928	.	-	.	Parent=gene28
chr21	ENCODE	exon	32979929	32980098	.	-	.	Parent=gene28
chr21	.	intron	32980099	32981158	.	-	.	Parent=gene28
chr21	ENCODE	exon	32981159	32981255	.	-	.	Parent=gene28
chr21	.	intron	32981256	32982486	.	-	.	Parent=gene28
chr21	ENCODE	exon	32982487	32982548	.	-	.	Parent=gene28
chr21	.	intron	32982549	32988408	.	-	.	Parent=gene28
chr21	ENCODE	exon	32988409	32988492	.	-	.	Parent=gene28
chr21	.	intron	32988493	32989237	.	-	.	Parent=gene28
chr21	ENCODE	exon	32989238	32989463	.	-	.	Parent=gene28
chr21	.	intron	32989464	32994018	.	-	.	Parent=gene28
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene28
chr21	.	intron	32994287	32996141	.	-	.	Parent=gene28
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene28
chr21	.	intron	32996229	33020953	.	-	.	Parent=gene28
chr21	ENCODE	exon	33020954	33021099	.	-	.	Parent=gene28
chr21	.	intron	33021100	33022018	.	-	.	Parent=gene28
chr21	ENCODE	exon	33022019	33022105	.	-	.	Parent=gene28
###
chr21	ENCODE	gene	32922945	33022183	.	-	.	ID=gene29;Name=AP000275.63-001;name2=SYNJ1
chr21	ENCODE	exon	32922945	32925982	.	-	.	Parent=gene29
chr21	.	intron	32925983	32929041	.	-	.	Parent=gene29
chr21	ENCODE	exon	32929042	32929065	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32929045	32929065	.	-	.	Parent=gene29
chr21	.	intron	32929066	32933088	.	-	.	Parent=gene29
chr21	ENCODE	exon	32933089	32933306	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32933089	32933306	.	-	.	Parent=gene29
chr21	.	intron	32933307	32933851	.	-	.	Parent=gene29
chr21	ENCODE	exon	32933852	32933960	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32933852	32933960	.	-	.	Parent=gene29
chr21	.	intron	32933961	32936076	.	-	.	Parent=gene29
chr21	ENCODE	exon	32936077	32936147	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32936077	32936147	.	-	.	Parent=gene29
chr21	.	intron	32936148	32936275	.	-	.	Parent=gene29
chr21	ENCODE	exon	32936276	32936314	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32936276	32936314	.	-	.	Parent=gene29
chr21	.	intron	32936315	32937590	.	-	.	Parent=gene29
chr21	ENCODE	exon	32937591	32937638	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32937591	32937638	.	-	.	Parent=gene29
chr21	.	intron	32937639	32939148	.	-	.	Parent=gene29
chr21	ENCODE	exon	32939149	32939187	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32939149	32939187	.	-	.	Parent=gene29
chr21	.	intron	32939188	32939826	.	-	.	Parent=gene29
chr21	ENCODE	exon	32939827	32939970	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32939827	32939970	.	-	.	Parent=gene29
chr21	.	intron	32939971	32940573	.	-	.	Parent=gene29
chr21	ENCODE	exon	32940574	32940783	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32940574	32940783	.	-	.	Parent=gene29
chr21	.	intron	32940784	32944364	.	-	.	Parent=gene29
chr21	ENCODE	exon	32944365	32944527	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32944365	32944527	.	-	.	Parent=gene29
chr21	.	intron	32944528	32947468	.	-	.	Parent=gene29
chr21	ENCODE	exon	32947469	32947547	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32947469	32947547	.	-	.	Parent=gene29
chr21	.	intron	32947548	32950867	.	-	.	Parent=gene29
chr21	ENCODE	exon	32950868	32951083	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32950868	32951083	.	-	.	Parent=gene29
chr21	.	intron	32951084	32951183	.	-	.	Parent=gene29
chr21	ENCODE	exon	32951184	32951301	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32951184	32951301	.	-	.	Parent=gene29
chr21	.	intron	32951302	32951896	.	-	.	Parent=gene29
chr21	ENCODE	exon	32951897	32952053	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32951897	32952053	.	-	.	Parent=gene29
chr21	.	intron	32952054	32959093	.	-	.	Parent=gene29
chr21	ENCODE	exon	32959094	32959252	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32959094	32959252	.	-	.	Parent=gene29
chr21	.	intron	32959253	32960123	.	-	.	Parent=gene29
chr21	ENCODE	exon	32960124	32960316	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32960124	32960316	.	-	.	Parent=gene29
chr21	.	intron	32960317	32960613	.	-	.	Parent=gene29
chr21	ENCODE	exon	32960614	32960754	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32960614	32960754	.	-	.	Parent=gene29
chr21	.	intron	32960755	32964468	.	-	.	Parent=gene29
chr21	ENCODE	exon	32964469	32964553	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32964469	32964553	.	-	.	Parent=gene29
chr21	.	intron	32964554	32967520	.	-	.	Parent=gene29
chr21	ENCODE	exon	32967521	32967712	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32967521	32967712	.	-	.	Parent=gene29
chr21	.	intron	32967713	32970512	.	-	.	Parent=gene29
chr21	ENCODE	exon	32970513	32970536	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32970513	32970536	.	-	.	Parent=gene29
chr21	.	intron	32970537	32972825	.	-	.	Parent=gene29
chr21	ENCODE	exon	32972826	32972982	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32972826	32972982	.	-	.	Parent=gene29
chr21	.	intron	32972983	32975676	.	-	.	Parent=gene29
chr21	ENCODE	exon	32975677	32975829	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32975677	32975829	.	-	.	Parent=gene29
chr21	.	intron	32975830	32978218	.	-	.	Parent=gene29
chr21	ENCODE	exon	32978219	32978300	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32978219	32978300	.	-	.	Parent=gene29
chr21	.	intron	32978301	32979928	.	-	.	Parent=gene29
chr21	ENCODE	exon	32979929	32980098	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32979929	32980098	.	-	.	Parent=gene29
chr21	.	intron	32980099	32981158	.	-	.	Parent=gene29
chr21	ENCODE	exon	32981159	32981255	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32981159	32981255	.	-	.	Parent=gene29
chr21	.	intron	32981256	32982486	.	-	.	Parent=gene29
chr21	ENCODE	exon	32982487	32982548	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32982487	32982548	.	-	.	Parent=gene29
chr21	.	intron	32982549	32988408	.	-	.	Parent=gene29
chr21	ENCODE	exon	32988409	32988492	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32988409	32988492	.	-	.	Parent=gene29
chr21	.	intron	32988493	32989237	.	-	.	Parent=gene29
chr21	ENCODE	exon	32989238	32989463	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32989238	32989463	.	-	.	Parent=gene29
chr21	.	intron	32989464	32994018	.	-	.	Parent=gene29
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32994019	32994286	.	-	.	Parent=gene29
chr21	.	intron	32994287	32996141	.	-	.	Parent=gene29
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene29
chr21	ENCODE	CDS	32996142	32996228	.	-	.	Parent=gene29
chr21	.	intron	32996229	33020953	.	-	.	Parent=gene29
chr21	ENCODE	CDS	33020954	33021077	.	-	.	Parent=gene29
chr21	ENCODE	exon	33020954	33021099	.	-	.	Parent=gene29
chr21	.	intron	33021100	33022127	.	-	.	Parent=gene29
chr21	ENCODE	exon	33022128	33022183	.	-	.	Parent=gene29
###
chr21	ENCODE	gene	32925171	33022148	.	-	.	ID=gene30;Name=AP000275.63-004;name2=SYNJ1
chr21	ENCODE	exon	32925171	32925982	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32925176	32925982	.	-	.	Parent=gene30
chr21	.	intron	32925983	32933088	.	-	.	Parent=gene30
chr21	ENCODE	exon	32933089	32933306	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32933089	32933306	.	-	.	Parent=gene30
chr21	.	intron	32933307	32933851	.	-	.	Parent=gene30
chr21	ENCODE	exon	32933852	32933960	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32933852	32933960	.	-	.	Parent=gene30
chr21	.	intron	32933961	32936076	.	-	.	Parent=gene30
chr21	ENCODE	exon	32936077	32936147	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32936077	32936147	.	-	.	Parent=gene30
chr21	.	intron	32936148	32936275	.	-	.	Parent=gene30
chr21	ENCODE	exon	32936276	32936314	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32936276	32936314	.	-	.	Parent=gene30
chr21	.	intron	32936315	32937590	.	-	.	Parent=gene30
chr21	ENCODE	exon	32937591	32937638	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32937591	32937638	.	-	.	Parent=gene30
chr21	.	intron	32937639	32939148	.	-	.	Parent=gene30
chr21	ENCODE	exon	32939149	32939187	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32939149	32939187	.	-	.	Parent=gene30
chr21	.	intron	32939188	32939826	.	-	.	Parent=gene30
chr21	ENCODE	exon	32939827	32939970	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32939827	32939970	.	-	.	Parent=gene30
chr21	.	intron	32939971	32940573	.	-	.	Parent=gene30
chr21	ENCODE	exon	32940574	32940783	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32940574	32940783	.	-	.	Parent=gene30
chr21	.	intron	32940784	32944364	.	-	.	Parent=gene30
chr21	ENCODE	exon	32944365	32944527	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32944365	32944527	.	-	.	Parent=gene30
chr21	.	intron	32944528	32947468	.	-	.	Parent=gene30
chr21	ENCODE	exon	32947469	32947547	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32947469	32947547	.	-	.	Parent=gene30
chr21	.	intron	32947548	32950867	.	-	.	Parent=gene30
chr21	ENCODE	exon	32950868	32951083	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32950868	32951083	.	-	.	Parent=gene30
chr21	.	intron	32951084	32951183	.	-	.	Parent=gene30
chr21	ENCODE	exon	32951184	32951301	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32951184	32951301	.	-	.	Parent=gene30
chr21	.	intron	32951302	32951896	.	-	.	Parent=gene30
chr21	ENCODE	exon	32951897	32952053	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32951897	32952053	.	-	.	Parent=gene30
chr21	.	intron	32952054	32959093	.	-	.	Parent=gene30
chr21	ENCODE	exon	32959094	32959252	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32959094	32959252	.	-	.	Parent=gene30
chr21	.	intron	32959253	32960123	.	-	.	Parent=gene30
chr21	ENCODE	exon	32960124	32960316	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32960124	32960316	.	-	.	Parent=gene30
chr21	.	intron	32960317	32960613	.	-	.	Parent=gene30
chr21	ENCODE	exon	32960614	32960754	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32960614	32960754	.	-	.	Parent=gene30
chr21	.	intron	32960755	32964468	.	-	.	Parent=gene30
chr21	ENCODE	exon	32964469	32964553	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32964469	32964553	.	-	.	Parent=gene30
chr21	.	intron	32964554	32967520	.	-	.	Parent=gene30
chr21	ENCODE	exon	32967521	32967712	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32967521	32967712	.	-	.	Parent=gene30
chr21	.	intron	32967713	32970512	.	-	.	Parent=gene30
chr21	ENCODE	exon	32970513	32970536	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32970513	32970536	.	-	.	Parent=gene30
chr21	.	intron	32970537	32972825	.	-	.	Parent=gene30
chr21	ENCODE	exon	32972826	32972982	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32972826	32972982	.	-	.	Parent=gene30
chr21	.	intron	32972983	32975676	.	-	.	Parent=gene30
chr21	ENCODE	exon	32975677	32975829	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32975677	32975829	.	-	.	Parent=gene30
chr21	.	intron	32975830	32978218	.	-	.	Parent=gene30
chr21	ENCODE	exon	32978219	32978300	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32978219	32978300	.	-	.	Parent=gene30
chr21	.	intron	32978301	32979928	.	-	.	Parent=gene30
chr21	ENCODE	exon	32979929	32980098	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32979929	32980098	.	-	.	Parent=gene30
chr21	.	intron	32980099	32981158	.	-	.	Parent=gene30
chr21	ENCODE	exon	32981159	32981255	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32981159	32981255	.	-	.	Parent=gene30
chr21	.	intron	32981256	32982486	.	-	.	Parent=gene30
chr21	ENCODE	exon	32982487	32982548	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32982487	32982548	.	-	.	Parent=gene30
chr21	.	intron	32982549	32988408	.	-	.	Parent=gene30
chr21	ENCODE	exon	32988409	32988492	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32988409	32988492	.	-	.	Parent=gene30
chr21	.	intron	32988493	32989237	.	-	.	Parent=gene30
chr21	ENCODE	exon	32989238	32989463	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32989238	32989463	.	-	.	Parent=gene30
chr21	.	intron	32989464	32994018	.	-	.	Parent=gene30
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32994019	32994286	.	-	.	Parent=gene30
chr21	.	intron	32994287	32996141	.	-	.	Parent=gene30
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene30
chr21	ENCODE	CDS	32996142	32996228	.	-	.	Parent=gene30
chr21	.	intron	32996229	33020953	.	-	.	Parent=gene30
chr21	ENCODE	CDS	33020954	33021077	.	-	.	Parent=gene30
chr21	ENCODE	exon	33020954	33021099	.	-	.	Parent=gene30
chr21	.	intron	33021100	33022127	.	-	.	Parent=gene30
chr21	ENCODE	exon	33022128	33022148	.	-	.	Parent=gene30
###
chr21	ENCODE	gene	32933195	32939900	.	-	.	ID=gene31;Name=AP000275.63-008;name2=SYNJ1
chr21	ENCODE	exon	32933195	32933306	.	-	.	Parent=gene31
chr21	ENCODE	CDS	32933195	32933306	.	-	.	Parent=gene31
chr21	.	intron	32933307	32933851	.	-	.	Parent=gene31
chr21	ENCODE	exon	32933852	32933960	.	-	.	Parent=gene31
chr21	ENCODE	CDS	32933852	32933960	.	-	.	Parent=gene31
chr21	.	intron	32933961	32936076	.	-	.	Parent=gene31
chr21	ENCODE	exon	32936077	32936147	.	-	.	Parent=gene31
chr21	ENCODE	CDS	32936077	32936147	.	-	.	Parent=gene31
chr21	.	intron	32936148	32939826	.	-	.	Parent=gene31
chr21	ENCODE	exon	32939827	32939900	.	-	.	Parent=gene31
chr21	ENCODE	CDS	32939827	32939900	.	-	.	Parent=gene31
###
chr21	ENCODE	gene	32944365	32948282	.	-	.	ID=gene32;Name=AP000275.63-005;name2=SYNJ1
chr21	ENCODE	exon	32944365	32944527	.	-	.	Parent=gene32
chr21	.	intron	32944528	32947468	.	-	.	Parent=gene32
chr21	ENCODE	exon	32947469	32948282	.	-	.	Parent=gene32
###
chr21	ENCODE	gene	32950872	32952742	.	-	.	ID=gene33;Name=AP000275.63-007;name2=SYNJ1
chr21	ENCODE	exon	32950872	32951083	.	-	.	Parent=gene33
chr21	.	intron	32951084	32951183	.	-	.	Parent=gene33
chr21	ENCODE	exon	32951184	32951301	.	-	.	Parent=gene33
chr21	.	intron	32951302	32951896	.	-	.	Parent=gene33
chr21	ENCODE	exon	32951897	32952053	.	-	.	Parent=gene33
chr21	.	intron	32952054	32952651	.	-	.	Parent=gene33
chr21	ENCODE	exon	32952652	32952742	.	-	.	Parent=gene33
###
chr21	ENCODE	gene	32960167	33022121	.	-	.	ID=gene34;Name=AP000275.63-002;name2=SYNJ1
chr21	ENCODE	exon	32960167	32960316	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32960167	32960316	.	-	.	Parent=gene34
chr21	.	intron	32960317	32960613	.	-	.	Parent=gene34
chr21	ENCODE	exon	32960614	32960754	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32960614	32960754	.	-	.	Parent=gene34
chr21	.	intron	32960755	32964468	.	-	.	Parent=gene34
chr21	ENCODE	exon	32964469	32964553	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32964469	32964553	.	-	.	Parent=gene34
chr21	.	intron	32964554	32967520	.	-	.	Parent=gene34
chr21	ENCODE	exon	32967521	32967712	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32967521	32967712	.	-	.	Parent=gene34
chr21	.	intron	32967713	32972825	.	-	.	Parent=gene34
chr21	ENCODE	exon	32972826	32972991	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32972826	32972991	.	-	.	Parent=gene34
chr21	.	intron	32972992	32975676	.	-	.	Parent=gene34
chr21	ENCODE	exon	32975677	32975829	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32975677	32975829	.	-	.	Parent=gene34
chr21	.	intron	32975830	32978218	.	-	.	Parent=gene34
chr21	ENCODE	exon	32978219	32978300	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32978219	32978300	.	-	.	Parent=gene34
chr21	.	intron	32978301	32979928	.	-	.	Parent=gene34
chr21	ENCODE	exon	32979929	32980098	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32979929	32980098	.	-	.	Parent=gene34
chr21	.	intron	32980099	32981158	.	-	.	Parent=gene34
chr21	ENCODE	exon	32981159	32981255	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32981159	32981255	.	-	.	Parent=gene34
chr21	.	intron	32981256	32982486	.	-	.	Parent=gene34
chr21	ENCODE	exon	32982487	32982548	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32982487	32982548	.	-	.	Parent=gene34
chr21	.	intron	32982549	32988408	.	-	.	Parent=gene34
chr21	ENCODE	exon	32988409	32988492	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32988409	32988492	.	-	.	Parent=gene34
chr21	.	intron	32988493	32989237	.	-	.	Parent=gene34
chr21	ENCODE	exon	32989238	32989463	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32989238	32989463	.	-	.	Parent=gene34
chr21	.	intron	32989464	32994018	.	-	.	Parent=gene34
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32994019	32994286	.	-	.	Parent=gene34
chr21	.	intron	32994287	32996141	.	-	.	Parent=gene34
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene34
chr21	ENCODE	CDS	32996142	32996228	.	-	.	Parent=gene34
chr21	.	intron	32996229	33020953	.	-	.	Parent=gene34
chr21	ENCODE	CDS	33020954	33021077	.	-	.	Parent=gene34
chr21	ENCODE	exon	33020954	33021099	.	-	.	Parent=gene34
chr21	.	intron	33021100	33022018	.	-	.	Parent=gene34
chr21	ENCODE	exon	33022019	33022121	.	-	.	Parent=gene34
###
chr21	ENCODE	gene	32989407	33021124	.	-	.	ID=gene35;Name=AP000275.63-006;name2=SYNJ1
chr21	ENCODE	exon	32989407	32989463	.	-	.	Parent=gene35
chr21	ENCODE	CDS	32989407	32989463	.	-	.	Parent=gene35
chr21	.	intron	32989464	32994018	.	-	.	Parent=gene35
chr21	ENCODE	exon	32994019	32994286	.	-	.	Parent=gene35
chr21	ENCODE	CDS	32994019	32994286	.	-	.	Parent=gene35
chr21	.	intron	32994287	32996141	.	-	.	Parent=gene35
chr21	ENCODE	exon	32996142	32996228	.	-	.	Parent=gene35
chr21	ENCODE	CDS	32996142	32996228	.	-	.	Parent=gene35
chr21	.	intron	32996229	33020953	.	-	.	Parent=gene35
chr21	ENCODE	CDS	33020954	33021077	.	-	.	Parent=gene35
chr21	ENCODE	exon	33020954	33021124	.	-	.	Parent=gene35
###
chr21	ENCODE	gene	33028081	33066040	.	-	.	ID=gene36;Name=AP000279.68-001;name2=C21orf66
chr21	ENCODE	exon	33028081	33029249	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33029132	33029249	.	-	.	Parent=gene36
chr21	.	intron	33029250	33031435	.	-	.	Parent=gene36
chr21	ENCODE	exon	33031436	33031590	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33031436	33031590	.	-	.	Parent=gene36
chr21	.	intron	33031591	33032354	.	-	.	Parent=gene36
chr21	ENCODE	exon	33032355	33032501	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33032355	33032501	.	-	.	Parent=gene36
chr21	.	intron	33032502	33037429	.	-	.	Parent=gene36
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33037430	33037496	.	-	.	Parent=gene36
chr21	.	intron	33037497	33037859	.	-	.	Parent=gene36
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33037860	33037936	.	-	.	Parent=gene36
chr21	.	intron	33037937	33038973	.	-	.	Parent=gene36
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33038974	33039095	.	-	.	Parent=gene36
chr21	.	intron	33039096	33039755	.	-	.	Parent=gene36
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33039756	33039900	.	-	.	Parent=gene36
chr21	.	intron	33039901	33042680	.	-	.	Parent=gene36
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33042681	33042880	.	-	.	Parent=gene36
chr21	.	intron	33042881	33045098	.	-	.	Parent=gene36
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33045099	33045214	.	-	.	Parent=gene36
chr21	.	intron	33045215	33045300	.	-	.	Parent=gene36
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33045301	33045400	.	-	.	Parent=gene36
chr21	.	intron	33045401	33049411	.	-	.	Parent=gene36
chr21	ENCODE	exon	33049412	33049535	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33049412	33049535	.	-	.	Parent=gene36
chr21	.	intron	33049536	33053261	.	-	.	Parent=gene36
chr21	ENCODE	exon	33053262	33053451	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33053262	33053451	.	-	.	Parent=gene36
chr21	.	intron	33053452	33053958	.	-	.	Parent=gene36
chr21	ENCODE	exon	33053959	33054176	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33053959	33054176	.	-	.	Parent=gene36
chr21	.	intron	33054177	33055240	.	-	.	Parent=gene36
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33055241	33055344	.	-	.	Parent=gene36
chr21	.	intron	33055345	33056277	.	-	.	Parent=gene36
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33056278	33056499	.	-	.	Parent=gene36
chr21	.	intron	33056500	33058529	.	-	.	Parent=gene36
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33058530	33058706	.	-	.	Parent=gene36
chr21	.	intron	33058707	33063995	.	-	.	Parent=gene36
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33063996	33064124	.	-	.	Parent=gene36
chr21	.	intron	33064125	33065507	.	-	.	Parent=gene36
chr21	ENCODE	CDS	33065508	33065850	.	-	.	Parent=gene36
chr21	ENCODE	exon	33065508	33066040	.	-	.	Parent=gene36
###
chr21	ENCODE	gene	33028082	33050976	.	-	.	ID=gene37;Name=AP000279.68-002;name2=C21orf66
chr21	ENCODE	exon	33028082	33029249	.	-	.	Parent=gene37
chr21	.	intron	33029250	33031435	.	-	.	Parent=gene37
chr21	ENCODE	exon	33031436	33031590	.	-	.	Parent=gene37
chr21	.	intron	33031591	33032354	.	-	.	Parent=gene37
chr21	ENCODE	exon	33032355	33032501	.	-	.	Parent=gene37
chr21	.	intron	33032502	33037429	.	-	.	Parent=gene37
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene37
chr21	.	intron	33037497	33037859	.	-	.	Parent=gene37
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene37
chr21	.	intron	33037937	33038973	.	-	.	Parent=gene37
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene37
chr21	.	intron	33039096	33039755	.	-	.	Parent=gene37
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene37
chr21	.	intron	33039901	33042680	.	-	.	Parent=gene37
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene37
chr21	.	intron	33042881	33045098	.	-	.	Parent=gene37
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene37
chr21	.	intron	33045215	33045300	.	-	.	Parent=gene37
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene37
chr21	.	intron	33045401	33049394	.	-	.	Parent=gene37
chr21	ENCODE	exon	33049395	33050976	.	-	.	Parent=gene37
###
chr21	ENCODE	gene	33029002	33065869	.	-	.	ID=gene38;Name=AP000279.68-006;name2=C21orf66
chr21	ENCODE	exon	33029002	33029249	.	-	.	Parent=gene38
chr21	.	intron	33029250	33031435	.	-	.	Parent=gene38
chr21	ENCODE	exon	33031436	33031590	.	-	.	Parent=gene38
chr21	.	intron	33031591	33032354	.	-	.	Parent=gene38
chr21	ENCODE	exon	33032355	33032501	.	-	.	Parent=gene38
chr21	.	intron	33032502	33037429	.	-	.	Parent=gene38
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene38
chr21	.	intron	33037497	33037859	.	-	.	Parent=gene38
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene38
chr21	.	intron	33037937	33038973	.	-	.	Parent=gene38
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene38
chr21	.	intron	33039096	33039755	.	-	.	Parent=gene38
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene38
chr21	.	intron	33039901	33042680	.	-	.	Parent=gene38
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene38
chr21	.	intron	33042881	33045098	.	-	.	Parent=gene38
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene38
chr21	.	intron	33045215	33045300	.	-	.	Parent=gene38
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene38
chr21	.	intron	33045401	33049394	.	-	.	Parent=gene38
chr21	ENCODE	exon	33049395	33049535	.	-	.	Parent=gene38
chr21	.	intron	33049536	33053261	.	-	.	Parent=gene38
chr21	ENCODE	exon	33053262	33053451	.	-	.	Parent=gene38
chr21	.	intron	33053452	33053958	.	-	.	Parent=gene38
chr21	ENCODE	exon	33053959	33054176	.	-	.	Parent=gene38
chr21	.	intron	33054177	33055240	.	-	.	Parent=gene38
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene38
chr21	.	intron	33055345	33056277	.	-	.	Parent=gene38
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene38
chr21	.	intron	33056500	33058529	.	-	.	Parent=gene38
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene38
chr21	.	intron	33058707	33063995	.	-	.	Parent=gene38
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene38
chr21	.	intron	33064125	33065507	.	-	.	Parent=gene38
chr21	ENCODE	exon	33065508	33065869	.	-	.	Parent=gene38
###
chr21	ENCODE	gene	33029008	33046306	.	-	.	ID=gene39;Name=AP000279.68-003;name2=C21orf66
chr21	ENCODE	exon	33029008	33029249	.	-	.	Parent=gene39
chr21	.	intron	33029250	33031435	.	-	.	Parent=gene39
chr21	ENCODE	exon	33031436	33031590	.	-	.	Parent=gene39
chr21	.	intron	33031591	33032354	.	-	.	Parent=gene39
chr21	ENCODE	exon	33032355	33032501	.	-	.	Parent=gene39
chr21	.	intron	33032502	33037429	.	-	.	Parent=gene39
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene39
chr21	.	intron	33037497	33037859	.	-	.	Parent=gene39
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene39
chr21	.	intron	33037937	33038973	.	-	.	Parent=gene39
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene39
chr21	.	intron	33039096	33039755	.	-	.	Parent=gene39
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene39
chr21	.	intron	33039901	33042680	.	-	.	Parent=gene39
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene39
chr21	.	intron	33042881	33045098	.	-	.	Parent=gene39
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene39
chr21	.	intron	33045215	33045300	.	-	.	Parent=gene39
chr21	ENCODE	exon	33045301	33046306	.	-	.	Parent=gene39
###
chr21	ENCODE	gene	33035575	33065850	.	-	.	ID=gene40;Name=AP000279.68-005;name2=C21orf66
chr21	ENCODE	exon	33035575	33035804	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33035691	33035804	.	-	.	Parent=gene40
chr21	.	intron	33035805	33037429	.	-	.	Parent=gene40
chr21	ENCODE	exon	33037430	33037496	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33037430	33037496	.	-	.	Parent=gene40
chr21	.	intron	33037497	33037859	.	-	.	Parent=gene40
chr21	ENCODE	exon	33037860	33037936	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33037860	33037936	.	-	.	Parent=gene40
chr21	.	intron	33037937	33038973	.	-	.	Parent=gene40
chr21	ENCODE	exon	33038974	33039095	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33038974	33039095	.	-	.	Parent=gene40
chr21	.	intron	33039096	33039755	.	-	.	Parent=gene40
chr21	ENCODE	exon	33039756	33039900	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33039756	33039900	.	-	.	Parent=gene40
chr21	.	intron	33039901	33042680	.	-	.	Parent=gene40
chr21	ENCODE	exon	33042681	33042880	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33042681	33042880	.	-	.	Parent=gene40
chr21	.	intron	33042881	33045098	.	-	.	Parent=gene40
chr21	ENCODE	exon	33045099	33045214	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33045099	33045214	.	-	.	Parent=gene40
chr21	.	intron	33045215	33045300	.	-	.	Parent=gene40
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33045301	33045400	.	-	.	Parent=gene40
chr21	.	intron	33045401	33049411	.	-	.	Parent=gene40
chr21	ENCODE	exon	33049412	33049535	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33049412	33049535	.	-	.	Parent=gene40
chr21	.	intron	33049536	33053261	.	-	.	Parent=gene40
chr21	ENCODE	exon	33053262	33053451	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33053262	33053451	.	-	.	Parent=gene40
chr21	.	intron	33053452	33053958	.	-	.	Parent=gene40
chr21	ENCODE	exon	33053959	33054176	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33053959	33054176	.	-	.	Parent=gene40
chr21	.	intron	33054177	33055240	.	-	.	Parent=gene40
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33055241	33055344	.	-	.	Parent=gene40
chr21	.	intron	33055345	33056277	.	-	.	Parent=gene40
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33056278	33056499	.	-	.	Parent=gene40
chr21	.	intron	33056500	33058529	.	-	.	Parent=gene40
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33058530	33058706	.	-	.	Parent=gene40
chr21	.	intron	33058707	33063995	.	-	.	Parent=gene40
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33063996	33064124	.	-	.	Parent=gene40
chr21	.	intron	33064125	33065507	.	-	.	Parent=gene40
chr21	ENCODE	exon	33065508	33065850	.	-	.	Parent=gene40
chr21	ENCODE	CDS	33065508	33065850	.	-	.	Parent=gene40
###
chr21	ENCODE	gene	33035601	33037450	.	-	.	ID=gene41;Name=AP000279.68-009;name2=C21orf66
chr21	ENCODE	exon	33035601	33035804	.	-	.	Parent=gene41
chr21	.	intron	33035805	33036541	.	-	.	Parent=gene41
chr21	ENCODE	exon	33036542	33036683	.	-	.	Parent=gene41
chr21	.	intron	33036684	33037142	.	-	.	Parent=gene41
chr21	ENCODE	exon	33037143	33037248	.	-	.	Parent=gene41
chr21	.	intron	33037249	33037429	.	-	.	Parent=gene41
chr21	ENCODE	exon	33037430	33037450	.	-	.	Parent=gene41
###
chr21	ENCODE	gene	33042741	33049493	.	-	.	ID=gene42;Name=AP000279.68-008;name2=C21orf66
chr21	ENCODE	exon	33042741	33042880	.	-	.	Parent=gene42
chr21	.	intron	33042881	33045300	.	-	.	Parent=gene42
chr21	ENCODE	exon	33045301	33045400	.	-	.	Parent=gene42
chr21	.	intron	33045401	33049394	.	-	.	Parent=gene42
chr21	ENCODE	exon	33049395	33049493	.	-	.	Parent=gene42
###
chr21	ENCODE	gene	33050524	33065850	.	-	.	ID=gene43;Name=AP000279.68-004;name2=C21orf66
chr21	ENCODE	exon	33050524	33050550	.	-	.	Parent=gene43
chr21	.	intron	33050551	33053261	.	-	.	Parent=gene43
chr21	ENCODE	exon	33053262	33053451	.	-	.	Parent=gene43
chr21	.	intron	33053452	33053958	.	-	.	Parent=gene43
chr21	ENCODE	exon	33053959	33054176	.	-	.	Parent=gene43
chr21	.	intron	33054177	33055240	.	-	.	Parent=gene43
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene43
chr21	.	intron	33055345	33056277	.	-	.	Parent=gene43
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene43
chr21	.	intron	33056500	33058529	.	-	.	Parent=gene43
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene43
chr21	.	intron	33058707	33063995	.	-	.	Parent=gene43
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene43
chr21	.	intron	33064125	33065507	.	-	.	Parent=gene43
chr21	ENCODE	exon	33065508	33065850	.	-	.	Parent=gene43
###
chr21	ENCODE	gene	33053584	33065974	.	-	.	ID=gene44;Name=AP000279.68-007;name2=C21orf66
chr21	ENCODE	exon	33053584	33054176	.	-	.	Parent=gene44
chr21	.	intron	33054177	33055240	.	-	.	Parent=gene44
chr21	ENCODE	exon	33055241	33055344	.	-	.	Parent=gene44
chr21	.	intron	33055345	33056277	.	-	.	Parent=gene44
chr21	ENCODE	exon	33056278	33056499	.	-	.	Parent=gene44
chr21	.	intron	33056500	33058529	.	-	.	Parent=gene44
chr21	ENCODE	exon	33058530	33058706	.	-	.	Parent=gene44
chr21	.	intron	33058707	33063995	.	-	.	Parent=gene44
chr21	ENCODE	exon	33063996	33064124	.	-	.	Parent=gene44
chr21	.	intron	33064125	33065507	.	-	.	Parent=gene44
chr21	ENCODE	exon	33065508	33065974	.	-	.	Parent=gene44
###
chr21	ENCODE	gene	33066282	33093149	.	+	.	ID=gene45;Name=AP000281.64-001;name2=C21orf49
chr21	ENCODE	exon	33066282	33066490	.	+	.	Parent=gene45
chr21	.	intron	33066491	33078978	.	+	.	Parent=gene45
chr21	ENCODE	exon	33078979	33079101	.	+	.	Parent=gene45
chr21	ENCODE	CDS	33079060	33079101	.	+	.	Parent=gene45
chr21	.	intron	33079102	33082793	.	+	.	Parent=gene45
chr21	ENCODE	exon	33082794	33082883	.	+	.	Parent=gene45
chr21	ENCODE	CDS	33082794	33082883	.	+	.	Parent=gene45
chr21	.	intron	33082884	33091118	.	+	.	Parent=gene45
chr21	ENCODE	CDS	33091119	33091226	.	+	.	Parent=gene45
chr21	ENCODE	exon	33091119	33093149	.	+	.	Parent=gene45
###
chr21	ENCODE	gene	33066307	33091887	.	+	.	ID=gene46;Name=AP000281.64-002;name2=C21orf49
chr21	ENCODE	exon	33066307	33066454	.	+	.	Parent=gene46
chr21	.	intron	33066455	33091118	.	+	.	Parent=gene46
chr21	ENCODE	exon	33091119	33091887	.	+	.	Parent=gene46
###
chr21	ENCODE	gene	33066332	33187913	.	+	.	ID=gene47;Name=AP000281.64-007;name2=C21orf49
chr21	ENCODE	exon	33066332	33066454	.	+	.	Parent=gene47
chr21	.	intron	33066455	33078956	.	+	.	Parent=gene47
chr21	ENCODE	exon	33078957	33079101	.	+	.	Parent=gene47
chr21	.	intron	33079102	33180109	.	+	.	Parent=gene47
chr21	ENCODE	exon	33180110	33180246	.	+	.	Parent=gene47
chr21	.	intron	33180247	33187755	.	+	.	Parent=gene47
chr21	ENCODE	exon	33187756	33187913	.	+	.	Parent=gene47
###
chr21	ENCODE	gene	33066343	33146649	.	+	.	ID=gene48;Name=AP000281.64-004;name2=C21orf49
chr21	ENCODE	exon	33066343	33066490	.	+	.	Parent=gene48
chr21	.	intron	33066491	33078978	.	+	.	Parent=gene48
chr21	ENCODE	exon	33078979	33079101	.	+	.	Parent=gene48
chr21	.	intron	33079102	33145928	.	+	.	Parent=gene48
chr21	ENCODE	exon	33145929	33146649	.	+	.	Parent=gene48
###
chr21	ENCODE	gene	33066344	33091348	.	+	.	ID=gene49;Name=AP000281.64-005;name2=C21orf49
chr21	ENCODE	exon	33066344	33066502	.	+	.	Parent=gene49
chr21	.	intron	33066503	33078978	.	+	.	Parent=gene49
chr21	ENCODE	exon	33078979	33079101	.	+	.	Parent=gene49
chr21	ENCODE	CDS	33079060	33079101	.	+	.	Parent=gene49
chr21	.	intron	33079102	33082793	.	+	.	Parent=gene49
chr21	ENCODE	exon	33082794	33082883	.	+	.	Parent=gene49
chr21	ENCODE	CDS	33082794	33082883	.	+	.	Parent=gene49
chr21	.	intron	33082884	33091118	.	+	.	Parent=gene49
chr21	ENCODE	CDS	33091119	33091226	.	+	.	Parent=gene49
chr21	ENCODE	exon	33091119	33091348	.	+	.	Parent=gene49
###
chr21	ENCODE	gene	33066356	33091626	.	+	.	ID=gene50;Name=AP000281.64-003;name2=C21orf49
chr21	ENCODE	exon	33066356	33066490	.	+	.	Parent=gene50
chr21	.	intron	33066491	33082793	.	+	.	Parent=gene50
chr21	ENCODE	exon	33082794	33082883	.	+	.	Parent=gene50
chr21	.	intron	33082884	33091118	.	+	.	Parent=gene50
chr21	ENCODE	exon	33091119	33091626	.	+	.	Parent=gene50
###
chr21	ENCODE	gene	33066370	33091274	.	+	.	ID=gene51;Name=AP000281.64-006;name2=C21orf49
chr21	ENCODE	exon	33066370	33066490	.	+	.	Parent=gene51
chr21	.	intron	33066491	33078978	.	+	.	Parent=gene51
chr21	ENCODE	exon	33078979	33079101	.	+	.	Parent=gene51
chr21	ENCODE	CDS	33079060	33079101	.	+	.	Parent=gene51
chr21	.	intron	33079102	33091118	.	+	.	Parent=gene51
chr21	ENCODE	CDS	33091119	33091226	.	+	.	Parent=gene51
chr21	ENCODE	exon	33091119	33091274	.	+	.	Parent=gene51
###
chr21	ENCODE	gene	33087746	33107923	.	-	.	ID=gene52;Name=AP000280.67-001;name2=C21orf62
chr21	ENCODE	exon	33087746	33088666	.	-	.	Parent=gene52
chr21	ENCODE	CDS	33087859	33088602	.	-	.	Parent=gene52
chr21	.	intron	33088667	33104753	.	-	.	Parent=gene52
chr21	ENCODE	exon	33104754	33104834	.	-	.	Parent=gene52
chr21	.	intron	33104835	33107771	.	-	.	Parent=gene52
chr21	ENCODE	exon	33107772	33107923	.	-	.	Parent=gene52
###
chr21	ENCODE	gene	33087747	33107859	.	-	.	ID=gene53;Name=AP000280.67-003;name2=C21orf62
chr21	ENCODE	exon	33087747	33088666	.	-	.	Parent=gene53
chr21	ENCODE	CDS	33087859	33088602	.	-	.	Parent=gene53
chr21	.	intron	33088667	33107771	.	-	.	Parent=gene53
chr21	ENCODE	exon	33107772	33107859	.	-	.	Parent=gene53
###
chr21	ENCODE	gene	33087867	33107869	.	-	.	ID=gene54;Name=AP000280.67-004;name2=C21orf62
chr21	ENCODE	exon	33087867	33088564	.	-	.	Parent=gene54
chr21	ENCODE	CDS	33087867	33088564	.	-	.	Parent=gene54
chr21	.	intron	33088565	33104753	.	-	.	Parent=gene54
chr21	ENCODE	exon	33104754	33104834	.	-	.	Parent=gene54
chr21	ENCODE	CDS	33104754	33104834	.	-	.	Parent=gene54
chr21	.	intron	33104835	33107771	.	-	.	Parent=gene54
chr21	ENCODE	exon	33107772	33107869	.	-	.	Parent=gene54
chr21	ENCODE	CDS	33107772	33107869	.	-	.	Parent=gene54
###
chr21	ENCODE	gene	33087903	33107814	.	-	.	ID=gene55;Name=AP000280.67-002;name2=C21orf62
chr21	ENCODE	CDS	33087903	33088602	.	-	.	Parent=gene55
chr21	ENCODE	exon	33087903	33088666	.	-	.	Parent=gene55
chr21	.	intron	33088667	33101821	.	-	.	Parent=gene55
chr21	ENCODE	exon	33101822	33101896	.	-	.	Parent=gene55
chr21	.	intron	33101897	33104753	.	-	.	Parent=gene55
chr21	ENCODE	exon	33104754	33104834	.	-	.	Parent=gene55
chr21	.	intron	33104835	33107771	.	-	.	Parent=gene55
chr21	ENCODE	exon	33107772	33107814	.	-	.	Parent=gene55
###
chr21	ENCODE	gene	33320023	33323374	.	+	.	ID=gene56;Name=AP000287.4-001;name2=OLIG2
chr21	ENCODE	exon	33320023	33320204	.	+	.	Parent=gene56
chr21	.	intron	33320205	33320978	.	+	.	Parent=gene56
chr21	ENCODE	exon	33320979	33323374	.	+	.	Parent=gene56
chr21	ENCODE	CDS	33321041	33322012	.	+	.	Parent=gene56
###
chr21	ENCODE	gene	33320113	33321227	.	+	.	ID=gene57;Name=AP000287.4-003;name2=OLIG2
chr21	ENCODE	exon	33320113	33320438	.	+	.	Parent=gene57
chr21	.	intron	33320439	33320978	.	+	.	Parent=gene57
chr21	ENCODE	exon	33320979	33321227	.	+	.	Parent=gene57
chr21	ENCODE	CDS	33321041	33321227	.	+	.	Parent=gene57
###
chr21	ENCODE	gene	33320113	33323374	.	+	.	ID=gene58;Name=AP000287.4-002;name2=OLIG2
chr21	ENCODE	exon	33320113	33323374	.	+	.	Parent=gene58
chr21	ENCODE	CDS	33321041	33322012	.	+	.	Parent=gene58
###
chr21	ENCODE	gene	33364320	33366596	.	+	.	ID=gene59;Name=AP000289.5-001;name2=OLIG1
chr21	ENCODE	exon	33364320	33366596	.	+	.	Parent=gene59
chr21	ENCODE	CDS	33364423	33365238	.	+	.	Parent=gene59
###
chr21	ENCODE	gene	33365141	33366589	.	+	.	ID=gene60;Name=AP000289.5-002;name2=OLIG1
chr21	ENCODE	exon	33365141	33365861	.	+	.	Parent=gene60
chr21	.	intron	33365862	33366227	.	+	.	Parent=gene60
chr21	ENCODE	exon	33366228	33366589	.	+	.	Parent=gene60
###
chr21	ENCODE	gene	33365844	33366589	.	+	.	ID=gene61;Name=AP000289.5-003;name2=OLIG1
chr21	ENCODE	exon	33365844	33365881	.	+	.	Parent=gene61
chr21	.	intron	33365882	33366227	.	+	.	Parent=gene61
chr21	ENCODE	exon	33366228	33366589	.	+	.	Parent=gene61
###
chr21	ENCODE	gene	33459646	33464824	.	-	.	ID=gene62;Name=AP000290.56-001;name2=C21orf54
chr21	ENCODE	exon	33459646	33459867	.	-	.	Parent=gene62
chr21	ENCODE	CDS	33459847	33459867	.	-	.	Parent=gene62
chr21	.	intron	33459868	33462617	.	-	.	Parent=gene62
chr21	ENCODE	exon	33462618	33462756	.	-	.	Parent=gene62
chr21	ENCODE	CDS	33462618	33462756	.	-	.	Parent=gene62
chr21	.	intron	33462757	33463870	.	-	.	Parent=gene62
chr21	ENCODE	exon	33463871	33464008	.	-	.	Parent=gene62
chr21	ENCODE	CDS	33463871	33464008	.	-	.	Parent=gene62
chr21	.	intron	33464009	33464315	.	-	.	Parent=gene62
chr21	ENCODE	CDS	33464316	33464344	.	-	.	Parent=gene62
chr21	ENCODE	exon	33464316	33464426	.	-	.	Parent=gene62
chr21	.	intron	33464427	33464738	.	-	.	Parent=gene62
chr21	ENCODE	exon	33464739	33464824	.	-	.	Parent=gene62
###
chr21	ENCODE	gene	33524076	33556931	.	+	.	ID=gene63;Name=AP000295.6-004;name2=IFNAR2
chr21	ENCODE	exon	33524076	33524391	.	+	.	Parent=gene63
chr21	.	intron	33524392	33536060	.	+	.	Parent=gene63
chr21	ENCODE	exon	33536061	33536152	.	+	.	Parent=gene63
chr21	ENCODE	CDS	33536098	33536152	.	+	.	Parent=gene63
chr21	.	intron	33536153	33537847	.	+	.	Parent=gene63
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene63
chr21	ENCODE	CDS	33537848	33537889	.	+	.	Parent=gene63
chr21	.	intron	33537890	33539125	.	+	.	Parent=gene63
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene63
chr21	ENCODE	CDS	33539126	33539249	.	+	.	Parent=gene63
chr21	.	intron	33539250	33540892	.	+	.	Parent=gene63
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene63
chr21	ENCODE	CDS	33540893	33541065	.	+	.	Parent=gene63
chr21	.	intron	33541066	33542883	.	+	.	Parent=gene63
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene63
chr21	ENCODE	CDS	33542884	33543029	.	+	.	Parent=gene63
chr21	.	intron	33543030	33546836	.	+	.	Parent=gene63
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene63
chr21	ENCODE	CDS	33546837	33547005	.	+	.	Parent=gene63
chr21	.	intron	33547006	33554771	.	+	.	Parent=gene63
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene63
chr21	ENCODE	CDS	33554772	33554902	.	+	.	Parent=gene63
chr21	.	intron	33554903	33556735	.	+	.	Parent=gene63
chr21	ENCODE	CDS	33556736	33556891	.	+	.	Parent=gene63
chr21	ENCODE	exon	33556736	33556931	.	+	.	Parent=gene63
###
chr21	ENCODE	gene	33524084	33559839	.	+	.	ID=gene64;Name=AP000295.6-001;name2=IFNAR2
chr21	ENCODE	exon	33524084	33524391	.	+	.	Parent=gene64
chr21	.	intron	33524392	33536014	.	+	.	Parent=gene64
chr21	ENCODE	exon	33536015	33536152	.	+	.	Parent=gene64
chr21	ENCODE	CDS	33536098	33536152	.	+	.	Parent=gene64
chr21	.	intron	33536153	33537847	.	+	.	Parent=gene64
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene64
chr21	ENCODE	CDS	33537848	33537889	.	+	.	Parent=gene64
chr21	.	intron	33537890	33539125	.	+	.	Parent=gene64
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene64
chr21	ENCODE	CDS	33539126	33539249	.	+	.	Parent=gene64
chr21	.	intron	33539250	33540892	.	+	.	Parent=gene64
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene64
chr21	ENCODE	CDS	33540893	33541065	.	+	.	Parent=gene64
chr21	.	intron	33541066	33542883	.	+	.	Parent=gene64
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene64
chr21	ENCODE	CDS	33542884	33543029	.	+	.	Parent=gene64
chr21	.	intron	33543030	33546836	.	+	.	Parent=gene64
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene64
chr21	ENCODE	CDS	33546837	33547005	.	+	.	Parent=gene64
chr21	.	intron	33547006	33554771	.	+	.	Parent=gene64
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene64
chr21	ENCODE	CDS	33554772	33554902	.	+	.	Parent=gene64
chr21	.	intron	33554903	33556735	.	+	.	Parent=gene64
chr21	ENCODE	CDS	33556736	33556891	.	+	.	Parent=gene64
chr21	ENCODE	exon	33556736	33559839	.	+	.	Parent=gene64
###
chr21	ENCODE	gene	33524149	33558700	.	+	.	ID=gene65;Name=AP000295.6-002;name2=IFNAR2
chr21	ENCODE	exon	33524149	33524391	.	+	.	Parent=gene65
chr21	.	intron	33524392	33536014	.	+	.	Parent=gene65
chr21	ENCODE	exon	33536015	33536152	.	+	.	Parent=gene65
chr21	ENCODE	CDS	33536098	33536152	.	+	.	Parent=gene65
chr21	.	intron	33536153	33537847	.	+	.	Parent=gene65
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene65
chr21	ENCODE	CDS	33537848	33537889	.	+	.	Parent=gene65
chr21	.	intron	33537890	33539125	.	+	.	Parent=gene65
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene65
chr21	ENCODE	CDS	33539126	33539249	.	+	.	Parent=gene65
chr21	.	intron	33539250	33540892	.	+	.	Parent=gene65
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene65
chr21	ENCODE	CDS	33540893	33541065	.	+	.	Parent=gene65
chr21	.	intron	33541066	33542883	.	+	.	Parent=gene65
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene65
chr21	ENCODE	CDS	33542884	33543029	.	+	.	Parent=gene65
chr21	.	intron	33543030	33546836	.	+	.	Parent=gene65
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene65
chr21	ENCODE	CDS	33546837	33547005	.	+	.	Parent=gene65
chr21	.	intron	33547006	33554771	.	+	.	Parent=gene65
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene65
chr21	ENCODE	CDS	33554772	33554902	.	+	.	Parent=gene65
chr21	.	intron	33554903	33556967	.	+	.	Parent=gene65
chr21	ENCODE	CDS	33556968	33557675	.	+	.	Parent=gene65
chr21	ENCODE	exon	33556968	33558700	.	+	.	Parent=gene65
###
chr21	ENCODE	gene	33524234	33556897	.	+	.	ID=gene66;Name=AP000295.6-005;name2=IFNAR2
chr21	ENCODE	exon	33524234	33524391	.	+	.	Parent=gene66
chr21	.	intron	33524392	33536060	.	+	.	Parent=gene66
chr21	ENCODE	exon	33536061	33536152	.	+	.	Parent=gene66
chr21	.	intron	33536153	33537847	.	+	.	Parent=gene66
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene66
chr21	.	intron	33537890	33539125	.	+	.	Parent=gene66
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene66
chr21	.	intron	33539250	33539667	.	+	.	Parent=gene66
chr21	ENCODE	exon	33539668	33539980	.	+	.	Parent=gene66
chr21	.	intron	33539981	33540892	.	+	.	Parent=gene66
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene66
chr21	.	intron	33541066	33542883	.	+	.	Parent=gene66
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene66
chr21	.	intron	33543030	33546836	.	+	.	Parent=gene66
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene66
chr21	.	intron	33547006	33554771	.	+	.	Parent=gene66
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene66
chr21	.	intron	33554903	33556735	.	+	.	Parent=gene66
chr21	ENCODE	exon	33556736	33556897	.	+	.	Parent=gene66
###
chr21	ENCODE	gene	33524311	33558700	.	+	.	ID=gene67;Name=AP000295.6-003;name2=IFNAR2
chr21	ENCODE	exon	33524311	33524391	.	+	.	Parent=gene67
chr21	.	intron	33524392	33536014	.	+	.	Parent=gene67
chr21	ENCODE	exon	33536015	33536152	.	+	.	Parent=gene67
chr21	ENCODE	CDS	33536098	33536152	.	+	.	Parent=gene67
chr21	.	intron	33536153	33537847	.	+	.	Parent=gene67
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene67
chr21	ENCODE	CDS	33537848	33537889	.	+	.	Parent=gene67
chr21	.	intron	33537890	33539125	.	+	.	Parent=gene67
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene67
chr21	ENCODE	CDS	33539126	33539249	.	+	.	Parent=gene67
chr21	.	intron	33539250	33540892	.	+	.	Parent=gene67
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene67
chr21	ENCODE	CDS	33540893	33541065	.	+	.	Parent=gene67
chr21	.	intron	33541066	33542883	.	+	.	Parent=gene67
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene67
chr21	ENCODE	CDS	33542884	33543029	.	+	.	Parent=gene67
chr21	.	intron	33543030	33546836	.	+	.	Parent=gene67
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene67
chr21	ENCODE	CDS	33546837	33547005	.	+	.	Parent=gene67
chr21	.	intron	33547006	33556967	.	+	.	Parent=gene67
chr21	ENCODE	CDS	33556968	33556978	.	+	.	Parent=gene67
chr21	ENCODE	exon	33556968	33558700	.	+	.	Parent=gene67
###
chr21	ENCODE	gene	33524316	33557030	.	+	.	ID=gene68;Name=AP000295.6-006;name2=IFNAR2
chr21	ENCODE	exon	33524316	33524391	.	+	.	Parent=gene68
chr21	.	intron	33524392	33536060	.	+	.	Parent=gene68
chr21	ENCODE	exon	33536061	33536152	.	+	.	Parent=gene68
chr21	ENCODE	CDS	33536098	33536152	.	+	.	Parent=gene68
chr21	.	intron	33536153	33537847	.	+	.	Parent=gene68
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene68
chr21	ENCODE	CDS	33537848	33537889	.	+	.	Parent=gene68
chr21	.	intron	33537890	33539125	.	+	.	Parent=gene68
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene68
chr21	ENCODE	CDS	33539126	33539249	.	+	.	Parent=gene68
chr21	.	intron	33539250	33540892	.	+	.	Parent=gene68
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene68
chr21	ENCODE	CDS	33540893	33541065	.	+	.	Parent=gene68
chr21	.	intron	33541066	33542883	.	+	.	Parent=gene68
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene68
chr21	ENCODE	CDS	33542884	33543029	.	+	.	Parent=gene68
chr21	.	intron	33543030	33546312	.	+	.	Parent=gene68
chr21	ENCODE	CDS	33546313	33546366	.	+	.	Parent=gene68
chr21	ENCODE	exon	33546313	33546423	.	+	.	Parent=gene68
chr21	.	intron	33546424	33546836	.	+	.	Parent=gene68
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene68
chr21	.	intron	33547006	33554771	.	+	.	Parent=gene68
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene68
chr21	.	intron	33554903	33556967	.	+	.	Parent=gene68
chr21	ENCODE	exon	33556968	33557030	.	+	.	Parent=gene68
###
chr21	ENCODE	gene	33524357	33557030	.	+	.	ID=gene69;Name=AP000295.6-009;name2=IFNAR2
chr21	ENCODE	exon	33524357	33524391	.	+	.	Parent=gene69
chr21	.	intron	33524392	33539125	.	+	.	Parent=gene69
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene69
chr21	.	intron	33539250	33540892	.	+	.	Parent=gene69
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene69
chr21	.	intron	33541066	33542883	.	+	.	Parent=gene69
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene69
chr21	.	intron	33543030	33546836	.	+	.	Parent=gene69
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene69
chr21	.	intron	33547006	33556967	.	+	.	Parent=gene69
chr21	ENCODE	exon	33556968	33557030	.	+	.	Parent=gene69
###
chr21	ENCODE	gene	33524357	33557030	.	+	.	ID=gene70;Name=AP000295.6-010;name2=IFNAR2
chr21	ENCODE	exon	33524357	33524391	.	+	.	Parent=gene70
chr21	.	intron	33524392	33539125	.	+	.	Parent=gene70
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene70
chr21	.	intron	33539250	33540892	.	+	.	Parent=gene70
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene70
chr21	.	intron	33541066	33542883	.	+	.	Parent=gene70
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene70
chr21	.	intron	33543030	33546836	.	+	.	Parent=gene70
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene70
chr21	.	intron	33547006	33554771	.	+	.	Parent=gene70
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene70
chr21	.	intron	33554903	33556967	.	+	.	Parent=gene70
chr21	ENCODE	exon	33556968	33557030	.	+	.	Parent=gene70
###
chr21	ENCODE	gene	33524584	33543029	.	+	.	ID=gene71;Name=AP000295.6-008;name2=IFNAR2
chr21	ENCODE	exon	33524584	33524732	.	+	.	Parent=gene71
chr21	.	intron	33524733	33536060	.	+	.	Parent=gene71
chr21	ENCODE	exon	33536061	33536152	.	+	.	Parent=gene71
chr21	ENCODE	CDS	33536098	33536152	.	+	.	Parent=gene71
chr21	.	intron	33536153	33537847	.	+	.	Parent=gene71
chr21	ENCODE	exon	33537848	33537889	.	+	.	Parent=gene71
chr21	ENCODE	CDS	33537848	33537889	.	+	.	Parent=gene71
chr21	.	intron	33537890	33539125	.	+	.	Parent=gene71
chr21	ENCODE	exon	33539126	33539249	.	+	.	Parent=gene71
chr21	ENCODE	CDS	33539126	33539249	.	+	.	Parent=gene71
chr21	.	intron	33539250	33540892	.	+	.	Parent=gene71
chr21	ENCODE	exon	33540893	33541065	.	+	.	Parent=gene71
chr21	ENCODE	CDS	33540893	33541065	.	+	.	Parent=gene71
chr21	.	intron	33541066	33542883	.	+	.	Parent=gene71
chr21	ENCODE	exon	33542884	33543029	.	+	.	Parent=gene71
chr21	ENCODE	CDS	33542884	33543029	.	+	.	Parent=gene71
###
chr21	ENCODE	gene	33542890	33577387	.	+	.	ID=gene72;Name=AP000295.8-006;name2=IL10RB
chr21	ENCODE	exon	33542890	33543029	.	+	.	Parent=gene72
chr21	ENCODE	CDS	33542890	33543029	.	+	.	Parent=gene72
chr21	.	intron	33543030	33546836	.	+	.	Parent=gene72
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene72
chr21	ENCODE	CDS	33546837	33547005	.	+	.	Parent=gene72
chr21	.	intron	33547006	33562568	.	+	.	Parent=gene72
chr21	ENCODE	exon	33562569	33562692	.	+	.	Parent=gene72
chr21	ENCODE	CDS	33562569	33562692	.	+	.	Parent=gene72
chr21	.	intron	33562693	33570770	.	+	.	Parent=gene72
chr21	ENCODE	exon	33570771	33570928	.	+	.	Parent=gene72
chr21	ENCODE	CDS	33570771	33570928	.	+	.	Parent=gene72
chr21	.	intron	33570929	33573926	.	+	.	Parent=gene72
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene72
chr21	ENCODE	CDS	33573927	33574093	.	+	.	Parent=gene72
chr21	.	intron	33574094	33577268	.	+	.	Parent=gene72
chr21	ENCODE	exon	33577269	33577387	.	+	.	Parent=gene72
chr21	ENCODE	CDS	33577269	33577387	.	+	.	Parent=gene72
###
chr21	ENCODE	gene	33542890	33577387	.	+	.	ID=gene73;Name=AP000295.8-007;name2=IL10RB
chr21	ENCODE	exon	33542890	33543029	.	+	.	Parent=gene73
chr21	.	intron	33543030	33546836	.	+	.	Parent=gene73
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene73
chr21	.	intron	33547006	33570770	.	+	.	Parent=gene73
chr21	ENCODE	exon	33570771	33570928	.	+	.	Parent=gene73
chr21	.	intron	33570929	33573926	.	+	.	Parent=gene73
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene73
chr21	.	intron	33574094	33577268	.	+	.	Parent=gene73
chr21	ENCODE	exon	33577269	33577387	.	+	.	Parent=gene73
###
chr21	ENCODE	gene	33542919	33556932	.	+	.	ID=gene74;Name=AP000295.6-007;name2=IFNAR2
chr21	ENCODE	exon	33542919	33543029	.	+	.	Parent=gene74
chr21	ENCODE	CDS	33542919	33543029	.	+	.	Parent=gene74
chr21	.	intron	33543030	33546312	.	+	.	Parent=gene74
chr21	ENCODE	CDS	33546313	33546366	.	+	.	Parent=gene74
chr21	ENCODE	exon	33546313	33546423	.	+	.	Parent=gene74
chr21	.	intron	33546424	33546836	.	+	.	Parent=gene74
chr21	ENCODE	exon	33546837	33547005	.	+	.	Parent=gene74
chr21	.	intron	33547006	33554771	.	+	.	Parent=gene74
chr21	ENCODE	exon	33554772	33554902	.	+	.	Parent=gene74
chr21	.	intron	33554903	33556735	.	+	.	Parent=gene74
chr21	ENCODE	exon	33556736	33556932	.	+	.	Parent=gene74
###
chr21	ENCODE	gene	33560533	33591409	.	+	.	ID=gene75;Name=AP000295.8-001;name2=IL10RB
chr21	ENCODE	exon	33560533	33560689	.	+	.	Parent=gene75
chr21	ENCODE	CDS	33560641	33560689	.	+	.	Parent=gene75
chr21	.	intron	33560690	33562568	.	+	.	Parent=gene75
chr21	ENCODE	exon	33562569	33562692	.	+	.	Parent=gene75
chr21	ENCODE	CDS	33562569	33562692	.	+	.	Parent=gene75
chr21	.	intron	33562693	33570770	.	+	.	Parent=gene75
chr21	ENCODE	exon	33570771	33570928	.	+	.	Parent=gene75
chr21	ENCODE	CDS	33570771	33570928	.	+	.	Parent=gene75
chr21	.	intron	33570929	33573926	.	+	.	Parent=gene75
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene75
chr21	ENCODE	CDS	33573927	33574093	.	+	.	Parent=gene75
chr21	.	intron	33574094	33577268	.	+	.	Parent=gene75
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene75
chr21	ENCODE	CDS	33577269	33577416	.	+	.	Parent=gene75
chr21	.	intron	33577417	33582278	.	+	.	Parent=gene75
chr21	ENCODE	exon	33582279	33582436	.	+	.	Parent=gene75
chr21	ENCODE	CDS	33582279	33582436	.	+	.	Parent=gene75
chr21	.	intron	33582437	33590358	.	+	.	Parent=gene75
chr21	ENCODE	CDS	33590359	33590532	.	+	.	Parent=gene75
chr21	ENCODE	exon	33590359	33591409	.	+	.	Parent=gene75
###
chr21	ENCODE	gene	33560557	33590414	.	+	.	ID=gene76;Name=AP000295.8-003;name2=IL10RB
chr21	ENCODE	exon	33560557	33560689	.	+	.	Parent=gene76
chr21	.	intron	33560690	33562568	.	+	.	Parent=gene76
chr21	ENCODE	exon	33562569	33562692	.	+	.	Parent=gene76
chr21	.	intron	33562693	33573926	.	+	.	Parent=gene76
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene76
chr21	.	intron	33574094	33577268	.	+	.	Parent=gene76
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene76
chr21	.	intron	33577417	33582278	.	+	.	Parent=gene76
chr21	ENCODE	exon	33582279	33582436	.	+	.	Parent=gene76
chr21	.	intron	33582437	33590358	.	+	.	Parent=gene76
chr21	ENCODE	exon	33590359	33590414	.	+	.	Parent=gene76
###
chr21	ENCODE	gene	33562103	33591128	.	+	.	ID=gene77;Name=AP000295.8-002;name2=IL10RB
chr21	ENCODE	exon	33562103	33562692	.	+	.	Parent=gene77
chr21	.	intron	33562693	33570770	.	+	.	Parent=gene77
chr21	ENCODE	exon	33570771	33570928	.	+	.	Parent=gene77
chr21	.	intron	33570929	33573926	.	+	.	Parent=gene77
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene77
chr21	.	intron	33574094	33577268	.	+	.	Parent=gene77
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene77
chr21	.	intron	33577417	33582278	.	+	.	Parent=gene77
chr21	ENCODE	exon	33582279	33582436	.	+	.	Parent=gene77
chr21	.	intron	33582437	33590358	.	+	.	Parent=gene77
chr21	ENCODE	exon	33590359	33591128	.	+	.	Parent=gene77
###
chr21	ENCODE	gene	33562457	33582295	.	+	.	ID=gene78;Name=AP000295.8-005;name2=IL10RB
chr21	ENCODE	exon	33562457	33562692	.	+	.	Parent=gene78
chr21	.	intron	33562693	33573926	.	+	.	Parent=gene78
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene78
chr21	.	intron	33574094	33577268	.	+	.	Parent=gene78
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene78
chr21	.	intron	33577417	33582278	.	+	.	Parent=gene78
chr21	ENCODE	exon	33582279	33582295	.	+	.	Parent=gene78
###
chr21	ENCODE	gene	33570787	33590525	.	+	.	ID=gene79;Name=AP000295.8-004;name2=IL10RB
chr21	ENCODE	exon	33570787	33570928	.	+	.	Parent=gene79
chr21	.	intron	33570929	33573926	.	+	.	Parent=gene79
chr21	ENCODE	exon	33573927	33574093	.	+	.	Parent=gene79
chr21	.	intron	33574094	33577268	.	+	.	Parent=gene79
chr21	ENCODE	exon	33577269	33577416	.	+	.	Parent=gene79
chr21	.	intron	33577417	33582278	.	+	.	Parent=gene79
chr21	ENCODE	exon	33582279	33582436	.	+	.	Parent=gene79
chr21	.	intron	33582437	33588186	.	+	.	Parent=gene79
chr21	ENCODE	exon	33588187	33588302	.	+	.	Parent=gene79
chr21	.	intron	33588303	33590358	.	+	.	Parent=gene79
chr21	ENCODE	exon	33590359	33590525	.	+	.	Parent=gene79
###
chr21	ENCODE	gene	33618652	33629787	.	+	.	ID=gene80;Name=AP000298.3-002;name2=IFNAR1
chr21	ENCODE	exon	33618652	33618813	.	+	.	Parent=gene80
chr21	.	intron	33618814	33629699	.	+	.	Parent=gene80
chr21	ENCODE	exon	33629700	33629787	.	+	.	Parent=gene80
###
chr21	ENCODE	gene	33619079	33654038	.	+	.	ID=gene81;Name=AP000298.3-001;name2=IFNAR1
chr21	ENCODE	exon	33619079	33619306	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33619231	33619306	.	+	.	Parent=gene81
chr21	.	intron	33619307	33629699	.	+	.	Parent=gene81
chr21	ENCODE	exon	33629700	33629823	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33629700	33629823	.	+	.	Parent=gene81
chr21	.	intron	33629824	33635174	.	+	.	Parent=gene81
chr21	ENCODE	exon	33635175	33635350	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33635175	33635350	.	+	.	Parent=gene81
chr21	.	intron	33635351	33637443	.	+	.	Parent=gene81
chr21	ENCODE	exon	33637444	33637598	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33637444	33637598	.	+	.	Parent=gene81
chr21	.	intron	33637599	33637710	.	+	.	Parent=gene81
chr21	ENCODE	exon	33637711	33637852	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33637711	33637852	.	+	.	Parent=gene81
chr21	.	intron	33637853	33639421	.	+	.	Parent=gene81
chr21	ENCODE	exon	33639422	33639536	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33639422	33639536	.	+	.	Parent=gene81
chr21	.	intron	33639537	33643266	.	+	.	Parent=gene81
chr21	ENCODE	exon	33643267	33643466	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33643267	33643466	.	+	.	Parent=gene81
chr21	.	intron	33643467	33643564	.	+	.	Parent=gene81
chr21	ENCODE	exon	33643565	33643719	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33643565	33643719	.	+	.	Parent=gene81
chr21	.	intron	33643720	33646933	.	+	.	Parent=gene81
chr21	ENCODE	exon	33646934	33647084	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33646934	33647084	.	+	.	Parent=gene81
chr21	.	intron	33647085	33647813	.	+	.	Parent=gene81
chr21	ENCODE	exon	33647814	33647959	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33647814	33647959	.	+	.	Parent=gene81
chr21	.	intron	33647960	33649491	.	+	.	Parent=gene81
chr21	ENCODE	CDS	33649492	33649725	.	+	.	Parent=gene81
chr21	ENCODE	exon	33649492	33654038	.	+	.	Parent=gene81
###
chr21	ENCODE	gene	33619148	33639453	.	+	.	ID=gene82;Name=AP000298.3-003;name2=IFNAR1
chr21	ENCODE	exon	33619148	33619306	.	+	.	Parent=gene82
chr21	ENCODE	CDS	33619231	33619306	.	+	.	Parent=gene82
chr21	.	intron	33619307	33629699	.	+	.	Parent=gene82
chr21	ENCODE	exon	33629700	33629823	.	+	.	Parent=gene82
chr21	ENCODE	CDS	33629700	33629823	.	+	.	Parent=gene82
chr21	.	intron	33629824	33635174	.	+	.	Parent=gene82
chr21	ENCODE	exon	33635175	33635350	.	+	.	Parent=gene82
chr21	ENCODE	CDS	33635175	33635350	.	+	.	Parent=gene82
chr21	.	intron	33635351	33639421	.	+	.	Parent=gene82
chr21	ENCODE	exon	33639422	33639453	.	+	.	Parent=gene82
chr21	ENCODE	CDS	33639422	33639453	.	+	.	Parent=gene82
###
chr21	ENCODE	gene	33679169	33709121	.	+	.	ID=gene83;Name=AP000300.6-006;name2=IFNGR2
chr21	ENCODE	exon	33679169	33679203	.	+	.	Parent=gene83
chr21	.	intron	33679204	33679391	.	+	.	Parent=gene83
chr21	ENCODE	exon	33679392	33679560	.	+	.	Parent=gene83
chr21	.	intron	33679561	33709064	.	+	.	Parent=gene83
chr21	ENCODE	exon	33709065	33709121	.	+	.	Parent=gene83
###
chr21	ENCODE	gene	33697072	33731698	.	+	.	ID=gene84;Name=AP000300.6-001;name2=IFNGR2
chr21	ENCODE	exon	33697072	33697792	.	+	.	Parent=gene84
chr21	ENCODE	CDS	33697720	33697792	.	+	.	Parent=gene84
chr21	.	intron	33697793	33709064	.	+	.	Parent=gene84
chr21	ENCODE	exon	33709065	33709197	.	+	.	Parent=gene84
chr21	ENCODE	CDS	33709065	33709197	.	+	.	Parent=gene84
chr21	.	intron	33709198	33715656	.	+	.	Parent=gene84
chr21	ENCODE	exon	33715657	33715862	.	+	.	Parent=gene84
chr21	ENCODE	CDS	33715657	33715862	.	+	.	Parent=gene84
chr21	.	intron	33715863	33721060	.	+	.	Parent=gene84
chr21	ENCODE	exon	33721061	33721209	.	+	.	Parent=gene84
chr21	ENCODE	CDS	33721061	33721209	.	+	.	Parent=gene84
chr21	.	intron	33721210	33726353	.	+	.	Parent=gene84
chr21	ENCODE	exon	33726354	33726513	.	+	.	Parent=gene84
chr21	ENCODE	CDS	33726354	33726513	.	+	.	Parent=gene84
chr21	.	intron	33726514	33726890	.	+	.	Parent=gene84
chr21	ENCODE	exon	33726891	33727048	.	+	.	Parent=gene84
chr21	ENCODE	CDS	33726891	33727048	.	+	.	Parent=gene84
chr21	.	intron	33727049	33731004	.	+	.	Parent=gene84
chr21	ENCODE	CDS	33731005	33731139	.	+	.	Parent=gene84
chr21	ENCODE	exon	33731005	33731698	.	+	.	Parent=gene84
###
chr21	ENCODE	gene	33697603	33726393	.	+	.	ID=gene85;Name=AP000300.6-003;name2=IFNGR2
chr21	ENCODE	exon	33697603	33697792	.	+	.	Parent=gene85
chr21	.	intron	33697793	33705011	.	+	.	Parent=gene85
chr21	ENCODE	exon	33705012	33705068	.	+	.	Parent=gene85
chr21	.	intron	33705069	33705620	.	+	.	Parent=gene85
chr21	ENCODE	exon	33705621	33705751	.	+	.	Parent=gene85
chr21	.	intron	33705752	33709064	.	+	.	Parent=gene85
chr21	ENCODE	exon	33709065	33709197	.	+	.	Parent=gene85
chr21	.	intron	33709198	33715656	.	+	.	Parent=gene85
chr21	ENCODE	exon	33715657	33715862	.	+	.	Parent=gene85
chr21	.	intron	33715863	33721060	.	+	.	Parent=gene85
chr21	ENCODE	exon	33721061	33721209	.	+	.	Parent=gene85
chr21	.	intron	33721210	33726353	.	+	.	Parent=gene85
chr21	ENCODE	exon	33726354	33726393	.	+	.	Parent=gene85
###
chr21	ENCODE	gene	33697608	33731698	.	+	.	ID=gene86;Name=AP000300.6-002;name2=IFNGR2
chr21	ENCODE	exon	33697608	33697792	.	+	.	Parent=gene86
chr21	ENCODE	CDS	33697720	33697792	.	+	.	Parent=gene86
chr21	.	intron	33697793	33705011	.	+	.	Parent=gene86
chr21	ENCODE	exon	33705012	33705068	.	+	.	Parent=gene86
chr21	ENCODE	CDS	33705012	33705068	.	+	.	Parent=gene86
chr21	.	intron	33705069	33709064	.	+	.	Parent=gene86
chr21	ENCODE	exon	33709065	33709197	.	+	.	Parent=gene86
chr21	ENCODE	CDS	33709065	33709197	.	+	.	Parent=gene86
chr21	.	intron	33709198	33715656	.	+	.	Parent=gene86
chr21	ENCODE	exon	33715657	33715862	.	+	.	Parent=gene86
chr21	ENCODE	CDS	33715657	33715862	.	+	.	Parent=gene86
chr21	.	intron	33715863	33721060	.	+	.	Parent=gene86
chr21	ENCODE	exon	33721061	33721209	.	+	.	Parent=gene86
chr21	ENCODE	CDS	33721061	33721209	.	+	.	Parent=gene86
chr21	.	intron	33721210	33726353	.	+	.	Parent=gene86
chr21	ENCODE	exon	33726354	33726513	.	+	.	Parent=gene86
chr21	ENCODE	CDS	33726354	33726513	.	+	.	Parent=gene86
chr21	.	intron	33726514	33726890	.	+	.	Parent=gene86
chr21	ENCODE	exon	33726891	33727048	.	+	.	Parent=gene86
chr21	ENCODE	CDS	33726891	33727048	.	+	.	Parent=gene86
chr21	.	intron	33727049	33731004	.	+	.	Parent=gene86
chr21	ENCODE	CDS	33731005	33731139	.	+	.	Parent=gene86
chr21	ENCODE	exon	33731005	33731698	.	+	.	Parent=gene86
###
chr21	ENCODE	gene	33697617	33731121	.	+	.	ID=gene87;Name=AP000300.6-004;name2=IFNGR2
chr21	ENCODE	exon	33697617	33697792	.	+	.	Parent=gene87
chr21	.	intron	33697793	33715656	.	+	.	Parent=gene87
chr21	ENCODE	exon	33715657	33715862	.	+	.	Parent=gene87
chr21	.	intron	33715863	33721060	.	+	.	Parent=gene87
chr21	ENCODE	exon	33721061	33721209	.	+	.	Parent=gene87
chr21	.	intron	33721210	33726353	.	+	.	Parent=gene87
chr21	ENCODE	exon	33726354	33726513	.	+	.	Parent=gene87
chr21	.	intron	33726514	33726890	.	+	.	Parent=gene87
chr21	ENCODE	exon	33726891	33727048	.	+	.	Parent=gene87
chr21	.	intron	33727049	33731004	.	+	.	Parent=gene87
chr21	ENCODE	exon	33731005	33731121	.	+	.	Parent=gene87
###
chr21	ENCODE	gene	33726496	33773525	.	+	.	ID=gene88;Name=AP000300.6-005;name2=IFNGR2
chr21	ENCODE	exon	33726496	33726513	.	+	.	Parent=gene88
chr21	.	intron	33726514	33726890	.	+	.	Parent=gene88
chr21	ENCODE	exon	33726891	33727048	.	+	.	Parent=gene88
chr21	.	intron	33727049	33772974	.	+	.	Parent=gene88
chr21	ENCODE	exon	33772975	33773525	.	+	.	Parent=gene88
###
chr21	ENCODE	gene	33726662	33743141	.	-	.	ID=gene89;Name=AP000300.7-009;name2=TMEM50B
chr21	ENCODE	exon	33726662	33726979	.	-	.	Parent=gene89
chr21	.	intron	33726980	33731059	.	-	.	Parent=gene89
chr21	ENCODE	exon	33731060	33731169	.	-	.	Parent=gene89
chr21	.	intron	33731170	33733390	.	-	.	Parent=gene89
chr21	ENCODE	exon	33733391	33733474	.	-	.	Parent=gene89
chr21	.	intron	33733475	33742958	.	-	.	Parent=gene89
chr21	ENCODE	exon	33742959	33743141	.	-	.	Parent=gene89
###
chr21	ENCODE	gene	33726662	33774120	.	-	.	ID=gene90;Name=AP000300.7-002;name2=TMEM50B
chr21	ENCODE	exon	33726662	33726979	.	-	.	Parent=gene90
chr21	.	intron	33726980	33733390	.	-	.	Parent=gene90
chr21	ENCODE	exon	33733391	33733474	.	-	.	Parent=gene90
chr21	.	intron	33733475	33742958	.	-	.	Parent=gene90
chr21	ENCODE	exon	33742959	33745040	.	-	.	Parent=gene90
chr21	.	intron	33745041	33749903	.	-	.	Parent=gene90
chr21	ENCODE	exon	33749904	33749961	.	-	.	Parent=gene90
chr21	.	intron	33749962	33754589	.	-	.	Parent=gene90
chr21	ENCODE	exon	33754590	33754682	.	-	.	Parent=gene90
chr21	.	intron	33754683	33759518	.	-	.	Parent=gene90
chr21	ENCODE	exon	33759519	33759586	.	-	.	Parent=gene90
chr21	.	intron	33759587	33761186	.	-	.	Parent=gene90
chr21	ENCODE	exon	33761187	33761299	.	-	.	Parent=gene90
chr21	.	intron	33761300	33762963	.	-	.	Parent=gene90
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene90
chr21	.	intron	33763104	33774014	.	-	.	Parent=gene90
chr21	ENCODE	exon	33774015	33774120	.	-	.	Parent=gene90
###
chr21	ENCODE	gene	33726975	33743587	.	-	.	ID=gene91;Name=AP000300.7-007;name2=TMEM50B
chr21	ENCODE	exon	33726975	33726979	.	-	.	Parent=gene91
chr21	.	intron	33726980	33733390	.	-	.	Parent=gene91
chr21	ENCODE	exon	33733391	33733474	.	-	.	Parent=gene91
chr21	.	intron	33733475	33742958	.	-	.	Parent=gene91
chr21	ENCODE	exon	33742959	33743056	.	-	.	Parent=gene91
chr21	.	intron	33743057	33743410	.	-	.	Parent=gene91
chr21	ENCODE	exon	33743411	33743587	.	-	.	Parent=gene91
###
chr21	ENCODE	gene	33731061	33743366	.	-	.	ID=gene92;Name=AP000300.7-008;name2=TMEM50B
chr21	ENCODE	exon	33731061	33731169	.	-	.	Parent=gene92
chr21	.	intron	33731170	33733390	.	-	.	Parent=gene92
chr21	ENCODE	exon	33733391	33733474	.	-	.	Parent=gene92
chr21	.	intron	33733475	33741194	.	-	.	Parent=gene92
chr21	ENCODE	exon	33741195	33741317	.	-	.	Parent=gene92
chr21	.	intron	33741318	33742958	.	-	.	Parent=gene92
chr21	ENCODE	exon	33742959	33743136	.	-	.	Parent=gene92
chr21	.	intron	33743137	33743190	.	-	.	Parent=gene92
chr21	ENCODE	exon	33743191	33743366	.	-	.	Parent=gene92
###
chr21	ENCODE	gene	33743312	33774188	.	-	.	ID=gene93;Name=AP000300.7-001;name2=TMEM50B
chr21	ENCODE	exon	33743312	33745040	.	-	.	Parent=gene93
chr21	ENCODE	CDS	33744995	33745040	.	-	.	Parent=gene93
chr21	.	intron	33745041	33749903	.	-	.	Parent=gene93
chr21	ENCODE	exon	33749904	33749961	.	-	.	Parent=gene93
chr21	ENCODE	CDS	33749904	33749961	.	-	.	Parent=gene93
chr21	.	intron	33749962	33754589	.	-	.	Parent=gene93
chr21	ENCODE	exon	33754590	33754682	.	-	.	Parent=gene93
chr21	ENCODE	CDS	33754590	33754682	.	-	.	Parent=gene93
chr21	.	intron	33754683	33759518	.	-	.	Parent=gene93
chr21	ENCODE	exon	33759519	33759586	.	-	.	Parent=gene93
chr21	ENCODE	CDS	33759519	33759586	.	-	.	Parent=gene93
chr21	.	intron	33759587	33761186	.	-	.	Parent=gene93
chr21	ENCODE	exon	33761187	33761299	.	-	.	Parent=gene93
chr21	ENCODE	CDS	33761187	33761299	.	-	.	Parent=gene93
chr21	.	intron	33761300	33762963	.	-	.	Parent=gene93
chr21	ENCODE	CDS	33762964	33763062	.	-	.	Parent=gene93
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene93
chr21	.	intron	33763104	33774014	.	-	.	Parent=gene93
chr21	ENCODE	exon	33774015	33774188	.	-	.	Parent=gene93
###
chr21	ENCODE	gene	33744724	33774113	.	-	.	ID=gene94;Name=AP000300.7-004;name2=TMEM50B
chr21	ENCODE	exon	33744724	33745040	.	-	.	Parent=gene94
chr21	.	intron	33745041	33749903	.	-	.	Parent=gene94
chr21	ENCODE	exon	33749904	33749961	.	-	.	Parent=gene94
chr21	.	intron	33749962	33750180	.	-	.	Parent=gene94
chr21	ENCODE	exon	33750181	33750274	.	-	.	Parent=gene94
chr21	.	intron	33750275	33754589	.	-	.	Parent=gene94
chr21	ENCODE	exon	33754590	33754682	.	-	.	Parent=gene94
chr21	.	intron	33754683	33759518	.	-	.	Parent=gene94
chr21	ENCODE	exon	33759519	33759586	.	-	.	Parent=gene94
chr21	.	intron	33759587	33761186	.	-	.	Parent=gene94
chr21	ENCODE	exon	33761187	33761299	.	-	.	Parent=gene94
chr21	.	intron	33761300	33762963	.	-	.	Parent=gene94
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene94
chr21	.	intron	33763104	33774014	.	-	.	Parent=gene94
chr21	ENCODE	exon	33774015	33774113	.	-	.	Parent=gene94
###
chr21	ENCODE	gene	33759195	33761312	.	-	.	ID=gene95;Name=AP000300.7-006;name2=TMEM50B
chr21	ENCODE	exon	33759195	33759586	.	-	.	Parent=gene95
chr21	.	intron	33759587	33761186	.	-	.	Parent=gene95
chr21	ENCODE	exon	33761187	33761312	.	-	.	Parent=gene95
###
chr21	ENCODE	gene	33759555	33773466	.	-	.	ID=gene96;Name=AP000300.7-005;name2=TMEM50B
chr21	ENCODE	exon	33759555	33759586	.	-	.	Parent=gene96
chr21	ENCODE	CDS	33759555	33759586	.	-	.	Parent=gene96
chr21	.	intron	33759587	33761186	.	-	.	Parent=gene96
chr21	ENCODE	exon	33761187	33761299	.	-	.	Parent=gene96
chr21	ENCODE	CDS	33761187	33761299	.	-	.	Parent=gene96
chr21	.	intron	33761300	33762963	.	-	.	Parent=gene96
chr21	ENCODE	CDS	33762964	33763062	.	-	.	Parent=gene96
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene96
chr21	.	intron	33763104	33763707	.	-	.	Parent=gene96
chr21	ENCODE	exon	33763708	33763860	.	-	.	Parent=gene96
chr21	.	intron	33763861	33773285	.	-	.	Parent=gene96
chr21	ENCODE	exon	33773286	33773466	.	-	.	Parent=gene96
###
chr21	ENCODE	gene	33761212	33775369	.	-	.	ID=gene97;Name=AP000300.7-010;name2=TMEM50B
chr21	ENCODE	exon	33761212	33761299	.	-	.	Parent=gene97
chr21	ENCODE	CDS	33761212	33761299	.	-	.	Parent=gene97
chr21	.	intron	33761300	33762963	.	-	.	Parent=gene97
chr21	ENCODE	CDS	33762964	33763062	.	-	.	Parent=gene97
chr21	ENCODE	exon	33762964	33763103	.	-	.	Parent=gene97
chr21	.	intron	33763104	33775310	.	-	.	Parent=gene97
chr21	ENCODE	exon	33775311	33775369	.	-	.	Parent=gene97
###
chr21	ENCODE	gene	33762597	33774125	.	-	.	ID=gene98;Name=AP000300.7-003;name2=TMEM50B
chr21	ENCODE	exon	33762597	33763103	.	-	.	Parent=gene98
chr21	.	intron	33763104	33774014	.	-	.	Parent=gene98
chr21	ENCODE	exon	33774015	33774125	.	-	.	Parent=gene98
###
chr21	ENCODE	gene	33779707	33785650	.	-	.	ID=gene99;Name=AP000302.59-003;name2=C21orf55
chr21	ENCODE	exon	33779707	33779932	.	-	.	Parent=gene99
chr21	.	intron	33779933	33782005	.	-	.	Parent=gene99
chr21	ENCODE	exon	33782006	33783601	.	-	.	Parent=gene99
chr21	.	intron	33783602	33785242	.	-	.	Parent=gene99
chr21	ENCODE	exon	33785243	33785650	.	-	.	Parent=gene99
###
chr21	ENCODE	gene	33782367	33785897	.	-	.	ID=gene100;Name=AP000302.59-002;name2=C21orf55
chr21	ENCODE	exon	33782367	33783601	.	-	.	Parent=gene100
chr21	ENCODE	CDS	33782404	33783570	.	-	.	Parent=gene100
chr21	.	intron	33783602	33785778	.	-	.	Parent=gene100
chr21	ENCODE	exon	33785779	33785897	.	-	.	Parent=gene100
###
chr21	ENCODE	gene	33782385	33785650	.	-	.	ID=gene101;Name=AP000302.59-001;name2=C21orf55
chr21	ENCODE	exon	33782385	33783601	.	-	.	Parent=gene101
chr21	ENCODE	CDS	33782404	33783570	.	-	.	Parent=gene101
chr21	.	intron	33783602	33785242	.	-	.	Parent=gene101
chr21	ENCODE	exon	33785243	33785650	.	-	.	Parent=gene101
###
chr21	ENCODE	gene	33798108	33836314	.	-	.	ID=gene102;Name=AP000302.60-003;name2=GART
chr21	ENCODE	exon	33798108	33798492	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33798301	33798492	.	-	.	Parent=gene102
chr21	.	intron	33798493	33798588	.	-	.	Parent=gene102
chr21	ENCODE	exon	33798589	33798704	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33798589	33798704	.	-	.	Parent=gene102
chr21	.	intron	33798705	33799737	.	-	.	Parent=gene102
chr21	ENCODE	exon	33799738	33799879	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33799738	33799879	.	-	.	Parent=gene102
chr21	.	intron	33799880	33800150	.	-	.	Parent=gene102
chr21	ENCODE	exon	33800151	33800281	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33800151	33800281	.	-	.	Parent=gene102
chr21	.	intron	33800282	33803959	.	-	.	Parent=gene102
chr21	ENCODE	exon	33803960	33804097	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33803960	33804097	.	-	.	Parent=gene102
chr21	.	intron	33804098	33805428	.	-	.	Parent=gene102
chr21	ENCODE	exon	33805429	33805635	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33805429	33805635	.	-	.	Parent=gene102
chr21	.	intron	33805636	33811165	.	-	.	Parent=gene102
chr21	ENCODE	exon	33811166	33811318	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33811166	33811318	.	-	.	Parent=gene102
chr21	.	intron	33811319	33811533	.	-	.	Parent=gene102
chr21	ENCODE	exon	33811534	33811785	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33811534	33811785	.	-	.	Parent=gene102
chr21	.	intron	33811786	33814540	.	-	.	Parent=gene102
chr21	ENCODE	exon	33814541	33814739	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33814541	33814739	.	-	.	Parent=gene102
chr21	.	intron	33814740	33815082	.	-	.	Parent=gene102
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33815083	33815192	.	-	.	Parent=gene102
chr21	.	intron	33815193	33816364	.	-	.	Parent=gene102
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33816365	33816459	.	-	.	Parent=gene102
chr21	.	intron	33816460	33818945	.	-	.	Parent=gene102
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33818946	33819177	.	-	.	Parent=gene102
chr21	.	intron	33819178	33822342	.	-	.	Parent=gene102
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33822343	33822511	.	-	.	Parent=gene102
chr21	.	intron	33822512	33822694	.	-	.	Parent=gene102
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33822695	33822780	.	-	.	Parent=gene102
chr21	.	intron	33822781	33823025	.	-	.	Parent=gene102
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33823026	33823113	.	-	.	Parent=gene102
chr21	.	intron	33823114	33824934	.	-	.	Parent=gene102
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33824935	33825060	.	-	.	Parent=gene102
chr21	.	intron	33825061	33825664	.	-	.	Parent=gene102
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33825665	33825733	.	-	.	Parent=gene102
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene102
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33826521	33826632	.	-	.	Parent=gene102
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene102
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33828755	33828929	.	-	.	Parent=gene102
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene102
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33829401	33829496	.	-	.	Parent=gene102
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene102
chr21	ENCODE	CDS	33833347	33833491	.	-	.	Parent=gene102
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene102
chr21	.	intron	33833533	33836240	.	-	.	Parent=gene102
chr21	ENCODE	exon	33836241	33836314	.	-	.	Parent=gene102
###
chr21	ENCODE	gene	33798108	33837018	.	-	.	ID=gene103;Name=AP000302.60-001;name2=GART
chr21	ENCODE	exon	33798108	33798492	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33798301	33798492	.	-	.	Parent=gene103
chr21	.	intron	33798493	33798588	.	-	.	Parent=gene103
chr21	ENCODE	exon	33798589	33798704	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33798589	33798704	.	-	.	Parent=gene103
chr21	.	intron	33798705	33799737	.	-	.	Parent=gene103
chr21	ENCODE	exon	33799738	33799879	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33799738	33799879	.	-	.	Parent=gene103
chr21	.	intron	33799880	33800150	.	-	.	Parent=gene103
chr21	ENCODE	exon	33800151	33800281	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33800151	33800281	.	-	.	Parent=gene103
chr21	.	intron	33800282	33803959	.	-	.	Parent=gene103
chr21	ENCODE	exon	33803960	33804097	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33803960	33804097	.	-	.	Parent=gene103
chr21	.	intron	33804098	33805428	.	-	.	Parent=gene103
chr21	ENCODE	exon	33805429	33805635	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33805429	33805635	.	-	.	Parent=gene103
chr21	.	intron	33805636	33811165	.	-	.	Parent=gene103
chr21	ENCODE	exon	33811166	33811318	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33811166	33811318	.	-	.	Parent=gene103
chr21	.	intron	33811319	33811533	.	-	.	Parent=gene103
chr21	ENCODE	exon	33811534	33811785	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33811534	33811785	.	-	.	Parent=gene103
chr21	.	intron	33811786	33814540	.	-	.	Parent=gene103
chr21	ENCODE	exon	33814541	33814739	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33814541	33814739	.	-	.	Parent=gene103
chr21	.	intron	33814740	33815082	.	-	.	Parent=gene103
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33815083	33815192	.	-	.	Parent=gene103
chr21	.	intron	33815193	33816364	.	-	.	Parent=gene103
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33816365	33816459	.	-	.	Parent=gene103
chr21	.	intron	33816460	33818945	.	-	.	Parent=gene103
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33818946	33819177	.	-	.	Parent=gene103
chr21	.	intron	33819178	33822342	.	-	.	Parent=gene103
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33822343	33822511	.	-	.	Parent=gene103
chr21	.	intron	33822512	33822694	.	-	.	Parent=gene103
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33822695	33822780	.	-	.	Parent=gene103
chr21	.	intron	33822781	33823025	.	-	.	Parent=gene103
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33823026	33823113	.	-	.	Parent=gene103
chr21	.	intron	33823114	33824934	.	-	.	Parent=gene103
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33824935	33825060	.	-	.	Parent=gene103
chr21	.	intron	33825061	33825664	.	-	.	Parent=gene103
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33825665	33825733	.	-	.	Parent=gene103
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene103
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33826521	33826632	.	-	.	Parent=gene103
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene103
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33828755	33828929	.	-	.	Parent=gene103
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene103
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33829401	33829496	.	-	.	Parent=gene103
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene103
chr21	ENCODE	CDS	33833347	33833491	.	-	.	Parent=gene103
chr21	ENCODE	exon	33833347	33833499	.	-	.	Parent=gene103
chr21	.	intron	33833500	33836762	.	-	.	Parent=gene103
chr21	ENCODE	exon	33836763	33837018	.	-	.	Parent=gene103
###
chr21	ENCODE	gene	33798108	33837037	.	-	.	ID=gene104;Name=AP000302.60-006;name2=GART
chr21	ENCODE	exon	33798108	33798492	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33798301	33798492	.	-	.	Parent=gene104
chr21	.	intron	33798493	33798588	.	-	.	Parent=gene104
chr21	ENCODE	exon	33798589	33798704	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33798589	33798704	.	-	.	Parent=gene104
chr21	.	intron	33798705	33799737	.	-	.	Parent=gene104
chr21	ENCODE	exon	33799738	33799879	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33799738	33799879	.	-	.	Parent=gene104
chr21	.	intron	33799880	33800150	.	-	.	Parent=gene104
chr21	ENCODE	exon	33800151	33800281	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33800151	33800281	.	-	.	Parent=gene104
chr21	.	intron	33800282	33803959	.	-	.	Parent=gene104
chr21	ENCODE	exon	33803960	33804097	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33803960	33804097	.	-	.	Parent=gene104
chr21	.	intron	33804098	33805428	.	-	.	Parent=gene104
chr21	ENCODE	exon	33805429	33805635	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33805429	33805635	.	-	.	Parent=gene104
chr21	.	intron	33805636	33811165	.	-	.	Parent=gene104
chr21	ENCODE	exon	33811166	33811318	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33811166	33811318	.	-	.	Parent=gene104
chr21	.	intron	33811319	33811533	.	-	.	Parent=gene104
chr21	ENCODE	exon	33811534	33811785	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33811534	33811785	.	-	.	Parent=gene104
chr21	.	intron	33811786	33814540	.	-	.	Parent=gene104
chr21	ENCODE	exon	33814541	33814739	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33814541	33814739	.	-	.	Parent=gene104
chr21	.	intron	33814740	33815082	.	-	.	Parent=gene104
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33815083	33815192	.	-	.	Parent=gene104
chr21	.	intron	33815193	33816364	.	-	.	Parent=gene104
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33816365	33816459	.	-	.	Parent=gene104
chr21	.	intron	33816460	33818945	.	-	.	Parent=gene104
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33818946	33819177	.	-	.	Parent=gene104
chr21	.	intron	33819178	33822342	.	-	.	Parent=gene104
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33822343	33822511	.	-	.	Parent=gene104
chr21	.	intron	33822512	33822694	.	-	.	Parent=gene104
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33822695	33822780	.	-	.	Parent=gene104
chr21	.	intron	33822781	33823025	.	-	.	Parent=gene104
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33823026	33823113	.	-	.	Parent=gene104
chr21	.	intron	33823114	33824934	.	-	.	Parent=gene104
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33824935	33825060	.	-	.	Parent=gene104
chr21	.	intron	33825061	33825664	.	-	.	Parent=gene104
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33825665	33825733	.	-	.	Parent=gene104
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene104
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33826521	33826632	.	-	.	Parent=gene104
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene104
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33828755	33828929	.	-	.	Parent=gene104
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene104
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33829401	33829496	.	-	.	Parent=gene104
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene104
chr21	ENCODE	CDS	33833347	33833491	.	-	.	Parent=gene104
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene104
chr21	.	intron	33833533	33836835	.	-	.	Parent=gene104
chr21	ENCODE	exon	33836836	33837037	.	-	.	Parent=gene104
###
chr21	ENCODE	gene	33798110	33837068	.	-	.	ID=gene105;Name=AP000302.60-002;name2=GART
chr21	ENCODE	exon	33798110	33798492	.	-	.	Parent=gene105
chr21	.	intron	33798493	33798588	.	-	.	Parent=gene105
chr21	ENCODE	exon	33798589	33798704	.	-	.	Parent=gene105
chr21	.	intron	33798705	33799737	.	-	.	Parent=gene105
chr21	ENCODE	exon	33799738	33799879	.	-	.	Parent=gene105
chr21	.	intron	33799880	33800150	.	-	.	Parent=gene105
chr21	ENCODE	exon	33800151	33800281	.	-	.	Parent=gene105
chr21	.	intron	33800282	33803959	.	-	.	Parent=gene105
chr21	ENCODE	exon	33803960	33804097	.	-	.	Parent=gene105
chr21	.	intron	33804098	33805428	.	-	.	Parent=gene105
chr21	ENCODE	exon	33805429	33805635	.	-	.	Parent=gene105
chr21	.	intron	33805636	33811165	.	-	.	Parent=gene105
chr21	ENCODE	exon	33811166	33811318	.	-	.	Parent=gene105
chr21	.	intron	33811319	33811533	.	-	.	Parent=gene105
chr21	ENCODE	exon	33811534	33811785	.	-	.	Parent=gene105
chr21	.	intron	33811786	33814540	.	-	.	Parent=gene105
chr21	ENCODE	exon	33814541	33814739	.	-	.	Parent=gene105
chr21	.	intron	33814740	33815082	.	-	.	Parent=gene105
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene105
chr21	.	intron	33815193	33816364	.	-	.	Parent=gene105
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene105
chr21	.	intron	33816460	33818945	.	-	.	Parent=gene105
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene105
chr21	.	intron	33819178	33822342	.	-	.	Parent=gene105
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene105
chr21	.	intron	33822512	33822690	.	-	.	Parent=gene105
chr21	ENCODE	exon	33822691	33822780	.	-	.	Parent=gene105
chr21	.	intron	33822781	33823025	.	-	.	Parent=gene105
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene105
chr21	.	intron	33823114	33824934	.	-	.	Parent=gene105
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene105
chr21	.	intron	33825061	33825664	.	-	.	Parent=gene105
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene105
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene105
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene105
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene105
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene105
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene105
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene105
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene105
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene105
chr21	.	intron	33833533	33836766	.	-	.	Parent=gene105
chr21	ENCODE	exon	33836767	33837068	.	-	.	Parent=gene105
###
chr21	ENCODE	gene	33800152	33805569	.	-	.	ID=gene106;Name=AP000302.60-017;name2=GART
chr21	ENCODE	exon	33800152	33800257	.	-	.	Parent=gene106
chr21	.	intron	33800258	33803990	.	-	.	Parent=gene106
chr21	ENCODE	exon	33803991	33804097	.	-	.	Parent=gene106
chr21	.	intron	33804098	33805428	.	-	.	Parent=gene106
chr21	ENCODE	exon	33805429	33805569	.	-	.	Parent=gene106
###
chr21	ENCODE	gene	33800217	33804510	.	-	.	ID=gene107;Name=AP000302.60-018;name2=GART
chr21	ENCODE	exon	33800217	33800281	.	-	.	Parent=gene107
chr21	.	intron	33800282	33803959	.	-	.	Parent=gene107
chr21	ENCODE	exon	33803960	33804510	.	-	.	Parent=gene107
###
chr21	ENCODE	gene	33803365	33805481	.	-	.	ID=gene108;Name=AP000302.60-019;name2=GART
chr21	ENCODE	exon	33803365	33804097	.	-	.	Parent=gene108
chr21	.	intron	33804098	33805428	.	-	.	Parent=gene108
chr21	ENCODE	exon	33805429	33805481	.	-	.	Parent=gene108
###
chr21	ENCODE	gene	33814699	33819005	.	-	.	ID=gene109;Name=AP000302.60-005;name2=GART
chr21	ENCODE	exon	33814699	33814822	.	-	.	Parent=gene109
chr21	.	intron	33814823	33815082	.	-	.	Parent=gene109
chr21	ENCODE	exon	33815083	33815192	.	-	.	Parent=gene109
chr21	.	intron	33815193	33816364	.	-	.	Parent=gene109
chr21	ENCODE	exon	33816365	33816459	.	-	.	Parent=gene109
chr21	.	intron	33816460	33818945	.	-	.	Parent=gene109
chr21	ENCODE	exon	33818946	33819005	.	-	.	Parent=gene109
###
chr21	ENCODE	gene	33816368	33822940	.	-	.	ID=gene110;Name=AP000302.60-016;name2=GART
chr21	ENCODE	exon	33816368	33816459	.	-	.	Parent=gene110
chr21	.	intron	33816460	33818945	.	-	.	Parent=gene110
chr21	ENCODE	exon	33818946	33819177	.	-	.	Parent=gene110
chr21	.	intron	33819178	33822342	.	-	.	Parent=gene110
chr21	ENCODE	exon	33822343	33822940	.	-	.	Parent=gene110
###
chr21	ENCODE	gene	33818186	33836290	.	-	.	ID=gene111;Name=AP000302.60-004;name2=GART
chr21	ENCODE	exon	33818186	33819177	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33818942	33819177	.	-	.	Parent=gene111
chr21	.	intron	33819178	33822342	.	-	.	Parent=gene111
chr21	ENCODE	exon	33822343	33822511	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33822343	33822511	.	-	.	Parent=gene111
chr21	.	intron	33822512	33822694	.	-	.	Parent=gene111
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33822695	33822780	.	-	.	Parent=gene111
chr21	.	intron	33822781	33823025	.	-	.	Parent=gene111
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33823026	33823113	.	-	.	Parent=gene111
chr21	.	intron	33823114	33824934	.	-	.	Parent=gene111
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33824935	33825060	.	-	.	Parent=gene111
chr21	.	intron	33825061	33825664	.	-	.	Parent=gene111
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33825665	33825733	.	-	.	Parent=gene111
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene111
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33826521	33826632	.	-	.	Parent=gene111
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene111
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33828755	33828929	.	-	.	Parent=gene111
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene111
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33829401	33829496	.	-	.	Parent=gene111
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene111
chr21	ENCODE	CDS	33833347	33833491	.	-	.	Parent=gene111
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene111
chr21	.	intron	33833533	33836240	.	-	.	Parent=gene111
chr21	ENCODE	exon	33836241	33836290	.	-	.	Parent=gene111
###
chr21	ENCODE	gene	33822442	33828806	.	-	.	ID=gene112;Name=AP000302.60-014;name2=GART
chr21	ENCODE	exon	33822442	33822511	.	-	.	Parent=gene112
chr21	.	intron	33822512	33822694	.	-	.	Parent=gene112
chr21	ENCODE	exon	33822695	33822780	.	-	.	Parent=gene112
chr21	.	intron	33822781	33823025	.	-	.	Parent=gene112
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene112
chr21	.	intron	33823114	33823742	.	-	.	Parent=gene112
chr21	ENCODE	exon	33823743	33823944	.	-	.	Parent=gene112
chr21	.	intron	33823945	33824934	.	-	.	Parent=gene112
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene112
chr21	.	intron	33825061	33825664	.	-	.	Parent=gene112
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene112
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene112
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene112
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene112
chr21	ENCODE	exon	33828755	33828806	.	-	.	Parent=gene112
###
chr21	ENCODE	gene	33822739	33825458	.	-	.	ID=gene113;Name=AP000302.60-015;name2=GART
chr21	ENCODE	exon	33822739	33822780	.	-	.	Parent=gene113
chr21	.	intron	33822781	33823025	.	-	.	Parent=gene113
chr21	ENCODE	exon	33823026	33823113	.	-	.	Parent=gene113
chr21	.	intron	33823114	33824934	.	-	.	Parent=gene113
chr21	ENCODE	exon	33824935	33825458	.	-	.	Parent=gene113
###
chr21	ENCODE	gene	33824886	33828855	.	-	.	ID=gene114;Name=AP000302.60-012;name2=GART
chr21	ENCODE	exon	33824886	33825060	.	-	.	Parent=gene114
chr21	.	intron	33825061	33825664	.	-	.	Parent=gene114
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene114
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene114
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene114
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene114
chr21	ENCODE	exon	33828755	33828855	.	-	.	Parent=gene114
###
chr21	ENCODE	gene	33824935	33837667	.	-	.	ID=gene115;Name=AP000302.60-007;name2=GART
chr21	ENCODE	exon	33824935	33825060	.	-	.	Parent=gene115
chr21	ENCODE	CDS	33824935	33825060	.	-	.	Parent=gene115
chr21	.	intron	33825061	33825664	.	-	.	Parent=gene115
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene115
chr21	ENCODE	CDS	33825665	33825733	.	-	.	Parent=gene115
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene115
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene115
chr21	ENCODE	CDS	33826521	33826632	.	-	.	Parent=gene115
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene115
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene115
chr21	ENCODE	CDS	33828755	33828929	.	-	.	Parent=gene115
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene115
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene115
chr21	ENCODE	CDS	33829401	33829496	.	-	.	Parent=gene115
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene115
chr21	ENCODE	CDS	33833347	33833491	.	-	.	Parent=gene115
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene115
chr21	.	intron	33833533	33837395	.	-	.	Parent=gene115
chr21	ENCODE	exon	33837396	33837667	.	-	.	Parent=gene115
###
chr21	ENCODE	gene	33824963	33836969	.	-	.	ID=gene116;Name=AP000302.60-009;name2=GART
chr21	ENCODE	exon	33824963	33825060	.	-	.	Parent=gene116
chr21	ENCODE	CDS	33824963	33825060	.	-	.	Parent=gene116
chr21	.	intron	33825061	33825664	.	-	.	Parent=gene116
chr21	ENCODE	exon	33825665	33825733	.	-	.	Parent=gene116
chr21	ENCODE	CDS	33825665	33825733	.	-	.	Parent=gene116
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene116
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene116
chr21	ENCODE	CDS	33826521	33826632	.	-	.	Parent=gene116
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene116
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene116
chr21	ENCODE	CDS	33828755	33828929	.	-	.	Parent=gene116
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene116
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene116
chr21	ENCODE	CDS	33829401	33829496	.	-	.	Parent=gene116
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene116
chr21	ENCODE	CDS	33833347	33833491	.	-	.	Parent=gene116
chr21	ENCODE	exon	33833347	33833499	.	-	.	Parent=gene116
chr21	.	intron	33833500	33836835	.	-	.	Parent=gene116
chr21	ENCODE	exon	33836836	33836969	.	-	.	Parent=gene116
###
chr21	ENCODE	gene	33825512	33836255	.	-	.	ID=gene117;Name=AP000302.60-011;name2=GART
chr21	ENCODE	exon	33825512	33825733	.	-	.	Parent=gene117
chr21	.	intron	33825734	33826520	.	-	.	Parent=gene117
chr21	ENCODE	exon	33826521	33826632	.	-	.	Parent=gene117
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene117
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene117
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene117
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene117
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene117
chr21	ENCODE	exon	33833347	33833532	.	-	.	Parent=gene117
chr21	.	intron	33833533	33836240	.	-	.	Parent=gene117
chr21	ENCODE	exon	33836241	33836255	.	-	.	Parent=gene117
###
chr21	ENCODE	gene	33825949	33828848	.	-	.	ID=gene118;Name=AP000302.60-013;name2=GART
chr21	ENCODE	exon	33825949	33826632	.	-	.	Parent=gene118
chr21	.	intron	33826633	33828754	.	-	.	Parent=gene118
chr21	ENCODE	exon	33828755	33828848	.	-	.	Parent=gene118
###
chr21	ENCODE	gene	33828755	33836996	.	-	.	ID=gene119;Name=AP000302.60-008;name2=GART
chr21	ENCODE	exon	33828755	33828929	.	-	.	Parent=gene119
chr21	ENCODE	CDS	33828755	33828929	.	-	.	Parent=gene119
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene119
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene119
chr21	ENCODE	CDS	33829401	33829496	.	-	.	Parent=gene119
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene119
chr21	ENCODE	CDS	33833347	33833491	.	-	.	Parent=gene119
chr21	ENCODE	exon	33833347	33833499	.	-	.	Parent=gene119
chr21	.	intron	33833500	33836723	.	-	.	Parent=gene119
chr21	ENCODE	exon	33836724	33836996	.	-	.	Parent=gene119
###
chr21	ENCODE	gene	33828763	33836539	.	-	.	ID=gene120;Name=AP000302.60-010;name2=GART
chr21	ENCODE	exon	33828763	33828929	.	-	.	Parent=gene120
chr21	ENCODE	CDS	33828763	33828929	.	-	.	Parent=gene120
chr21	.	intron	33828930	33829400	.	-	.	Parent=gene120
chr21	ENCODE	exon	33829401	33829496	.	-	.	Parent=gene120
chr21	ENCODE	CDS	33829401	33829496	.	-	.	Parent=gene120
chr21	.	intron	33829497	33833346	.	-	.	Parent=gene120
chr21	ENCODE	CDS	33833347	33833491	.	-	.	Parent=gene120
chr21	ENCODE	exon	33833347	33833499	.	-	.	Parent=gene120
chr21	.	intron	33833500	33836240	.	-	.	Parent=gene120
chr21	ENCODE	exon	33836241	33836539	.	-	.	Parent=gene120
###
chr21	ENCODE	gene	33836794	33871657	.	+	.	ID=gene121;Name=AP000304.8-001;name2=SON
chr21	ENCODE	exon	33836794	33837345	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33837269	33837345	.	+	.	Parent=gene121
chr21	.	intron	33837346	33840388	.	+	.	Parent=gene121
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33840389	33840555	.	+	.	Parent=gene121
chr21	.	intron	33840556	33843651	.	+	.	Parent=gene121
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33843652	33849567	.	+	.	Parent=gene121
chr21	.	intron	33849568	33851331	.	+	.	Parent=gene121
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33851332	33851492	.	+	.	Parent=gene121
chr21	.	intron	33851493	33853405	.	+	.	Parent=gene121
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33853406	33853552	.	+	.	Parent=gene121
chr21	.	intron	33853553	33853762	.	+	.	Parent=gene121
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33853763	33853951	.	+	.	Parent=gene121
chr21	.	intron	33853952	33861332	.	+	.	Parent=gene121
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33861333	33861443	.	+	.	Parent=gene121
chr21	.	intron	33861444	33863146	.	+	.	Parent=gene121
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33863147	33863263	.	+	.	Parent=gene121
chr21	.	intron	33863264	33867483	.	+	.	Parent=gene121
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33867484	33867631	.	+	.	Parent=gene121
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene121
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33869772	33869843	.	+	.	Parent=gene121
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene121
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33869954	33870069	.	+	.	Parent=gene121
chr21	.	intron	33870070	33870540	.	+	.	Parent=gene121
chr21	ENCODE	CDS	33870541	33870600	.	+	.	Parent=gene121
chr21	ENCODE	exon	33870541	33871657	.	+	.	Parent=gene121
###
chr21	ENCODE	gene	33837220	33871655	.	+	.	ID=gene122;Name=AP000304.8-021;name2=SON
chr21	ENCODE	exon	33837220	33837345	.	+	.	Parent=gene122
chr21	.	intron	33837346	33840388	.	+	.	Parent=gene122
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene122
chr21	.	intron	33840556	33843651	.	+	.	Parent=gene122
chr21	ENCODE	exon	33843652	33845625	.	+	.	Parent=gene122
chr21	.	intron	33845626	33845745	.	+	.	Parent=gene122
chr21	ENCODE	exon	33845746	33849567	.	+	.	Parent=gene122
chr21	.	intron	33849568	33851331	.	+	.	Parent=gene122
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene122
chr21	.	intron	33851493	33853405	.	+	.	Parent=gene122
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene122
chr21	.	intron	33853553	33853762	.	+	.	Parent=gene122
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene122
chr21	.	intron	33853952	33861332	.	+	.	Parent=gene122
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene122
chr21	.	intron	33861444	33863146	.	+	.	Parent=gene122
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene122
chr21	.	intron	33863264	33867483	.	+	.	Parent=gene122
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene122
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene122
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene122
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene122
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene122
chr21	.	intron	33870070	33870540	.	+	.	Parent=gene122
chr21	ENCODE	exon	33870541	33871655	.	+	.	Parent=gene122
###
chr21	ENCODE	gene	33837228	33840928	.	+	.	ID=gene123;Name=AP000304.8-010;name2=SON
chr21	ENCODE	exon	33837228	33837345	.	+	.	Parent=gene123
chr21	.	intron	33837346	33840388	.	+	.	Parent=gene123
chr21	ENCODE	exon	33840389	33840928	.	+	.	Parent=gene123
###
chr21	ENCODE	gene	33837228	33871657	.	+	.	ID=gene124;Name=AP000304.8-002;name2=SON
chr21	ENCODE	exon	33837228	33837345	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33837269	33837345	.	+	.	Parent=gene124
chr21	.	intron	33837346	33840388	.	+	.	Parent=gene124
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33840389	33840555	.	+	.	Parent=gene124
chr21	.	intron	33840556	33851331	.	+	.	Parent=gene124
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33851332	33851492	.	+	.	Parent=gene124
chr21	.	intron	33851493	33853405	.	+	.	Parent=gene124
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33853406	33853552	.	+	.	Parent=gene124
chr21	.	intron	33853553	33853762	.	+	.	Parent=gene124
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33853763	33853951	.	+	.	Parent=gene124
chr21	.	intron	33853952	33861332	.	+	.	Parent=gene124
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33861333	33861443	.	+	.	Parent=gene124
chr21	.	intron	33861444	33863146	.	+	.	Parent=gene124
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33863147	33863263	.	+	.	Parent=gene124
chr21	.	intron	33863264	33867483	.	+	.	Parent=gene124
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33867484	33867631	.	+	.	Parent=gene124
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene124
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33869772	33869843	.	+	.	Parent=gene124
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene124
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33869954	33870069	.	+	.	Parent=gene124
chr21	.	intron	33870070	33870540	.	+	.	Parent=gene124
chr21	ENCODE	CDS	33870541	33870600	.	+	.	Parent=gene124
chr21	ENCODE	exon	33870541	33871657	.	+	.	Parent=gene124
###
chr21	ENCODE	gene	33837240	33854843	.	+	.	ID=gene125;Name=AP000304.8-003;name2=SON
chr21	ENCODE	exon	33837240	33837345	.	+	.	Parent=gene125
chr21	ENCODE	CDS	33837269	33837345	.	+	.	Parent=gene125
chr21	.	intron	33837346	33840388	.	+	.	Parent=gene125
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene125
chr21	ENCODE	CDS	33840389	33840555	.	+	.	Parent=gene125
chr21	.	intron	33840556	33843651	.	+	.	Parent=gene125
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene125
chr21	ENCODE	CDS	33843652	33849567	.	+	.	Parent=gene125
chr21	.	intron	33849568	33851331	.	+	.	Parent=gene125
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene125
chr21	ENCODE	CDS	33851332	33851492	.	+	.	Parent=gene125
chr21	.	intron	33851493	33853405	.	+	.	Parent=gene125
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene125
chr21	ENCODE	CDS	33853406	33853552	.	+	.	Parent=gene125
chr21	.	intron	33853553	33853762	.	+	.	Parent=gene125
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene125
chr21	ENCODE	CDS	33853763	33853951	.	+	.	Parent=gene125
chr21	.	intron	33853952	33854052	.	+	.	Parent=gene125
chr21	ENCODE	CDS	33854053	33854307	.	+	.	Parent=gene125
chr21	ENCODE	exon	33854053	33854843	.	+	.	Parent=gene125
###
chr21	ENCODE	gene	33837240	33871657	.	+	.	ID=gene126;Name=AP000304.8-005;name2=SON
chr21	ENCODE	exon	33837240	33837345	.	+	.	Parent=gene126
chr21	.	intron	33837346	33840388	.	+	.	Parent=gene126
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene126
chr21	.	intron	33840556	33843651	.	+	.	Parent=gene126
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene126
chr21	.	intron	33849568	33851331	.	+	.	Parent=gene126
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene126
chr21	.	intron	33851493	33851721	.	+	.	Parent=gene126
chr21	ENCODE	exon	33851722	33851844	.	+	.	Parent=gene126
chr21	.	intron	33851845	33853405	.	+	.	Parent=gene126
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene126
chr21	.	intron	33853553	33853762	.	+	.	Parent=gene126
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene126
chr21	.	intron	33853952	33861332	.	+	.	Parent=gene126
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene126
chr21	.	intron	33861444	33863146	.	+	.	Parent=gene126
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene126
chr21	.	intron	33863264	33867483	.	+	.	Parent=gene126
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene126
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene126
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene126
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene126
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene126
chr21	.	intron	33870070	33870593	.	+	.	Parent=gene126
chr21	ENCODE	exon	33870594	33871657	.	+	.	Parent=gene126
###
chr21	ENCODE	gene	33837240	33871657	.	+	.	ID=gene127;Name=AP000304.8-004;name2=SON
chr21	ENCODE	exon	33837240	33837345	.	+	.	Parent=gene127
chr21	.	intron	33837346	33840388	.	+	.	Parent=gene127
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene127
chr21	.	intron	33840556	33843651	.	+	.	Parent=gene127
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene127
chr21	.	intron	33849568	33851331	.	+	.	Parent=gene127
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene127
chr21	.	intron	33851493	33853405	.	+	.	Parent=gene127
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene127
chr21	.	intron	33853553	33853762	.	+	.	Parent=gene127
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene127
chr21	.	intron	33853952	33861332	.	+	.	Parent=gene127
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene127
chr21	.	intron	33861444	33863146	.	+	.	Parent=gene127
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene127
chr21	.	intron	33863264	33866726	.	+	.	Parent=gene127
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene127
chr21	.	intron	33866807	33867483	.	+	.	Parent=gene127
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene127
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene127
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene127
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene127
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene127
chr21	.	intron	33870070	33870593	.	+	.	Parent=gene127
chr21	ENCODE	exon	33870594	33871657	.	+	.	Parent=gene127
###
chr21	ENCODE	gene	33837241	33853232	.	+	.	ID=gene128;Name=AP000304.8-006;name2=SON
chr21	ENCODE	exon	33837241	33837345	.	+	.	Parent=gene128
chr21	ENCODE	CDS	33837269	33837345	.	+	.	Parent=gene128
chr21	.	intron	33837346	33840388	.	+	.	Parent=gene128
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene128
chr21	ENCODE	CDS	33840389	33840555	.	+	.	Parent=gene128
chr21	.	intron	33840556	33843651	.	+	.	Parent=gene128
chr21	ENCODE	exon	33843652	33849567	.	+	.	Parent=gene128
chr21	ENCODE	CDS	33843652	33849567	.	+	.	Parent=gene128
chr21	.	intron	33849568	33851331	.	+	.	Parent=gene128
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene128
chr21	ENCODE	CDS	33851332	33851492	.	+	.	Parent=gene128
chr21	.	intron	33851493	33851721	.	+	.	Parent=gene128
chr21	ENCODE	CDS	33851722	33851727	.	+	.	Parent=gene128
chr21	ENCODE	exon	33851722	33853232	.	+	.	Parent=gene128
###
chr21	ENCODE	gene	33837246	33841215	.	+	.	ID=gene129;Name=AP000304.8-011;name2=SON
chr21	ENCODE	exon	33837246	33837345	.	+	.	Parent=gene129
chr21	.	intron	33837346	33840388	.	+	.	Parent=gene129
chr21	ENCODE	exon	33840389	33840555	.	+	.	Parent=gene129
chr21	.	intron	33840556	33841176	.	+	.	Parent=gene129
chr21	ENCODE	exon	33841177	33841215	.	+	.	Parent=gene129
###
chr21	ENCODE	gene	33843772	33871651	.	+	.	ID=gene130;Name=AP000304.8-020;name2=SON
chr21	ENCODE	exon	33843772	33844416	.	+	.	Parent=gene130
chr21	.	intron	33844417	33849477	.	+	.	Parent=gene130
chr21	ENCODE	exon	33849478	33849567	.	+	.	Parent=gene130
chr21	.	intron	33849568	33851331	.	+	.	Parent=gene130
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene130
chr21	.	intron	33851493	33853405	.	+	.	Parent=gene130
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene130
chr21	.	intron	33853553	33853762	.	+	.	Parent=gene130
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene130
chr21	.	intron	33853952	33861332	.	+	.	Parent=gene130
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene130
chr21	.	intron	33861444	33863146	.	+	.	Parent=gene130
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene130
chr21	.	intron	33863264	33867483	.	+	.	Parent=gene130
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene130
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene130
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene130
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene130
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene130
chr21	.	intron	33870070	33870593	.	+	.	Parent=gene130
chr21	ENCODE	exon	33870594	33871651	.	+	.	Parent=gene130
###
chr21	ENCODE	gene	33845060	33871657	.	+	.	ID=gene131;Name=AP000304.8-007;name2=SON
chr21	ENCODE	exon	33845060	33845465	.	+	.	Parent=gene131
chr21	.	intron	33845466	33846423	.	+	.	Parent=gene131
chr21	ENCODE	exon	33846424	33849567	.	+	.	Parent=gene131
chr21	.	intron	33849568	33851331	.	+	.	Parent=gene131
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene131
chr21	.	intron	33851493	33853405	.	+	.	Parent=gene131
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene131
chr21	.	intron	33853553	33853762	.	+	.	Parent=gene131
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene131
chr21	.	intron	33853952	33861332	.	+	.	Parent=gene131
chr21	ENCODE	exon	33861333	33861443	.	+	.	Parent=gene131
chr21	.	intron	33861444	33863146	.	+	.	Parent=gene131
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene131
chr21	.	intron	33863264	33867483	.	+	.	Parent=gene131
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene131
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene131
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene131
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene131
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene131
chr21	.	intron	33870070	33870540	.	+	.	Parent=gene131
chr21	ENCODE	exon	33870541	33871657	.	+	.	Parent=gene131
###
chr21	ENCODE	gene	33849225	33861643	.	+	.	ID=gene132;Name=AP000304.8-008;name2=SON
chr21	ENCODE	exon	33849225	33849567	.	+	.	Parent=gene132
chr21	ENCODE	CDS	33849225	33849567	.	+	.	Parent=gene132
chr21	.	intron	33849568	33851331	.	+	.	Parent=gene132
chr21	ENCODE	exon	33851332	33851492	.	+	.	Parent=gene132
chr21	ENCODE	CDS	33851332	33851492	.	+	.	Parent=gene132
chr21	.	intron	33851493	33853405	.	+	.	Parent=gene132
chr21	ENCODE	exon	33853406	33853552	.	+	.	Parent=gene132
chr21	ENCODE	CDS	33853406	33853552	.	+	.	Parent=gene132
chr21	.	intron	33853553	33853762	.	+	.	Parent=gene132
chr21	ENCODE	exon	33853763	33853951	.	+	.	Parent=gene132
chr21	ENCODE	CDS	33853763	33853951	.	+	.	Parent=gene132
chr21	.	intron	33853952	33861332	.	+	.	Parent=gene132
chr21	ENCODE	CDS	33861333	33861524	.	+	.	Parent=gene132
chr21	ENCODE	exon	33861333	33861643	.	+	.	Parent=gene132
###
chr21	ENCODE	gene	33861355	33863459	.	+	.	ID=gene133;Name=AP000304.8-012;name2=SON
chr21	ENCODE	exon	33861355	33861443	.	+	.	Parent=gene133
chr21	.	intron	33861444	33863146	.	+	.	Parent=gene133
chr21	ENCODE	exon	33863147	33863459	.	+	.	Parent=gene133
###
chr21	ENCODE	gene	33861361	33870689	.	+	.	ID=gene134;Name=AP000304.8-013;name2=SON
chr21	ENCODE	exon	33861361	33861443	.	+	.	Parent=gene134
chr21	.	intron	33861444	33863146	.	+	.	Parent=gene134
chr21	ENCODE	exon	33863147	33863263	.	+	.	Parent=gene134
chr21	.	intron	33863264	33866726	.	+	.	Parent=gene134
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene134
chr21	.	intron	33866807	33867483	.	+	.	Parent=gene134
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene134
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene134
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene134
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene134
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene134
chr21	.	intron	33870070	33870540	.	+	.	Parent=gene134
chr21	ENCODE	exon	33870541	33870689	.	+	.	Parent=gene134
###
chr21	ENCODE	gene	33863952	33870660	.	+	.	ID=gene135;Name=AP000304.8-019;name2=SON
chr21	ENCODE	exon	33863952	33864106	.	+	.	Parent=gene135
chr21	.	intron	33864107	33865926	.	+	.	Parent=gene135
chr21	ENCODE	exon	33865927	33865964	.	+	.	Parent=gene135
chr21	.	intron	33865965	33866726	.	+	.	Parent=gene135
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene135
chr21	.	intron	33866807	33867483	.	+	.	Parent=gene135
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene135
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene135
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene135
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene135
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene135
chr21	.	intron	33870070	33870593	.	+	.	Parent=gene135
chr21	ENCODE	exon	33870594	33870660	.	+	.	Parent=gene135
###
chr21	ENCODE	gene	33865911	33870623	.	+	.	ID=gene136;Name=AP000304.8-017;name2=SON
chr21	ENCODE	exon	33865911	33865964	.	+	.	Parent=gene136
chr21	.	intron	33865965	33866726	.	+	.	Parent=gene136
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene136
chr21	.	intron	33866807	33867483	.	+	.	Parent=gene136
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene136
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene136
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene136
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene136
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene136
chr21	.	intron	33870070	33870593	.	+	.	Parent=gene136
chr21	ENCODE	exon	33870594	33870623	.	+	.	Parent=gene136
###
chr21	ENCODE	gene	33865911	33870645	.	+	.	ID=gene137;Name=AP000304.8-018;name2=SON
chr21	ENCODE	exon	33865911	33865964	.	+	.	Parent=gene137
chr21	.	intron	33865965	33866726	.	+	.	Parent=gene137
chr21	ENCODE	exon	33866727	33866806	.	+	.	Parent=gene137
chr21	.	intron	33866807	33867483	.	+	.	Parent=gene137
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene137
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene137
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene137
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene137
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene137
chr21	.	intron	33870070	33870540	.	+	.	Parent=gene137
chr21	ENCODE	exon	33870541	33870645	.	+	.	Parent=gene137
###
chr21	ENCODE	gene	33866389	33871657	.	+	.	ID=gene138;Name=AP000304.8-009;name2=SON
chr21	ENCODE	exon	33866389	33866806	.	+	.	Parent=gene138
chr21	.	intron	33866807	33867483	.	+	.	Parent=gene138
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene138
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene138
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene138
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene138
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene138
chr21	.	intron	33870070	33870593	.	+	.	Parent=gene138
chr21	ENCODE	exon	33870594	33871657	.	+	.	Parent=gene138
###
chr21	ENCODE	gene	33866703	33871057	.	+	.	ID=gene139;Name=AP000304.8-014;name2=SON
chr21	ENCODE	exon	33866703	33866806	.	+	.	Parent=gene139
chr21	.	intron	33866807	33867483	.	+	.	Parent=gene139
chr21	ENCODE	exon	33867484	33867631	.	+	.	Parent=gene139
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene139
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene139
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene139
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene139
chr21	.	intron	33870070	33870540	.	+	.	Parent=gene139
chr21	ENCODE	exon	33870541	33871057	.	+	.	Parent=gene139
###
chr21	ENCODE	gene	33867201	33870692	.	+	.	ID=gene140;Name=AP000304.8-015;name2=SON
chr21	ENCODE	exon	33867201	33867631	.	+	.	Parent=gene140
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene140
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene140
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene140
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene140
chr21	.	intron	33870070	33870540	.	+	.	Parent=gene140
chr21	ENCODE	exon	33870541	33870692	.	+	.	Parent=gene140
###
chr21	ENCODE	gene	33867390	33871158	.	+	.	ID=gene141;Name=AP000304.8-016;name2=SON
chr21	ENCODE	exon	33867390	33867631	.	+	.	Parent=gene141
chr21	.	intron	33867632	33869771	.	+	.	Parent=gene141
chr21	ENCODE	exon	33869772	33869843	.	+	.	Parent=gene141
chr21	.	intron	33869844	33869953	.	+	.	Parent=gene141
chr21	ENCODE	exon	33869954	33870069	.	+	.	Parent=gene141
chr21	.	intron	33870070	33870593	.	+	.	Parent=gene141
chr21	ENCODE	exon	33870594	33871158	.	+	.	Parent=gene141
###
chr21	ENCODE	gene	33869653	33882846	.	-	.	ID=gene142;Name=AP000304.11-008;name2=DONSON
chr21	ENCODE	exon	33869653	33869984	.	-	.	Parent=gene142
chr21	.	intron	33869985	33872474	.	-	.	Parent=gene142
chr21	ENCODE	exon	33872475	33872620	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33872483	33872620	.	-	.	Parent=gene142
chr21	.	intron	33872621	33873525	.	-	.	Parent=gene142
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33873526	33873738	.	-	.	Parent=gene142
chr21	.	intron	33873739	33875477	.	-	.	Parent=gene142
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33875478	33875676	.	-	.	Parent=gene142
chr21	.	intron	33875677	33876126	.	-	.	Parent=gene142
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33876127	33876231	.	-	.	Parent=gene142
chr21	.	intron	33876232	33876340	.	-	.	Parent=gene142
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33876341	33876422	.	-	.	Parent=gene142
chr21	.	intron	33876423	33877663	.	-	.	Parent=gene142
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33877664	33877842	.	-	.	Parent=gene142
chr21	.	intron	33877843	33878765	.	-	.	Parent=gene142
chr21	ENCODE	exon	33878766	33878902	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33878766	33878902	.	-	.	Parent=gene142
chr21	.	intron	33878903	33880153	.	-	.	Parent=gene142
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33880154	33880357	.	-	.	Parent=gene142
chr21	.	intron	33880358	33881697	.	-	.	Parent=gene142
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33881698	33881778	.	-	.	Parent=gene142
chr21	.	intron	33881779	33882496	.	-	.	Parent=gene142
chr21	ENCODE	CDS	33882497	33882817	.	-	.	Parent=gene142
chr21	ENCODE	exon	33882497	33882846	.	-	.	Parent=gene142
###
chr21	ENCODE	gene	33871737	33882822	.	-	.	ID=gene143;Name=AP000304.11-007;name2=DONSON
chr21	ENCODE	exon	33871737	33872620	.	-	.	Parent=gene143
chr21	.	intron	33872621	33873525	.	-	.	Parent=gene143
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene143
chr21	.	intron	33873739	33875477	.	-	.	Parent=gene143
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene143
chr21	.	intron	33875677	33876126	.	-	.	Parent=gene143
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene143
chr21	.	intron	33876232	33876340	.	-	.	Parent=gene143
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene143
chr21	.	intron	33876423	33877663	.	-	.	Parent=gene143
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene143
chr21	.	intron	33877843	33880153	.	-	.	Parent=gene143
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene143
chr21	.	intron	33880358	33881697	.	-	.	Parent=gene143
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene143
chr21	.	intron	33881779	33882496	.	-	.	Parent=gene143
chr21	ENCODE	exon	33882497	33882822	.	-	.	Parent=gene143
###
chr21	ENCODE	gene	33872081	33882884	.	-	.	ID=gene144;Name=AP000304.11-001;name2=DONSON
chr21	ENCODE	exon	33872081	33872620	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33872483	33872620	.	-	.	Parent=gene144
chr21	.	intron	33872621	33873525	.	-	.	Parent=gene144
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33873526	33873738	.	-	.	Parent=gene144
chr21	.	intron	33873739	33875477	.	-	.	Parent=gene144
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33875478	33875676	.	-	.	Parent=gene144
chr21	.	intron	33875677	33876126	.	-	.	Parent=gene144
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33876127	33876231	.	-	.	Parent=gene144
chr21	.	intron	33876232	33876340	.	-	.	Parent=gene144
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33876341	33876422	.	-	.	Parent=gene144
chr21	.	intron	33876423	33877663	.	-	.	Parent=gene144
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33877664	33877842	.	-	.	Parent=gene144
chr21	.	intron	33877843	33878765	.	-	.	Parent=gene144
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33878766	33878944	.	-	.	Parent=gene144
chr21	.	intron	33878945	33880153	.	-	.	Parent=gene144
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33880154	33880357	.	-	.	Parent=gene144
chr21	.	intron	33880358	33881697	.	-	.	Parent=gene144
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33881698	33881778	.	-	.	Parent=gene144
chr21	.	intron	33881779	33882496	.	-	.	Parent=gene144
chr21	ENCODE	CDS	33882497	33882817	.	-	.	Parent=gene144
chr21	ENCODE	exon	33882497	33882884	.	-	.	Parent=gene144
###
chr21	ENCODE	gene	33872081	33889641	.	-	.	ID=gene145;Name=AP000304.11-003;name2=DONSON
chr21	ENCODE	exon	33872081	33872620	.	-	.	Parent=gene145
chr21	.	intron	33872621	33873525	.	-	.	Parent=gene145
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene145
chr21	.	intron	33873739	33875477	.	-	.	Parent=gene145
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene145
chr21	.	intron	33875677	33876126	.	-	.	Parent=gene145
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene145
chr21	.	intron	33876232	33876340	.	-	.	Parent=gene145
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene145
chr21	.	intron	33876423	33877663	.	-	.	Parent=gene145
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene145
chr21	.	intron	33877843	33878765	.	-	.	Parent=gene145
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene145
chr21	.	intron	33878945	33880153	.	-	.	Parent=gene145
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene145
chr21	.	intron	33880358	33881697	.	-	.	Parent=gene145
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene145
chr21	.	intron	33881779	33882496	.	-	.	Parent=gene145
chr21	ENCODE	exon	33882497	33883137	.	-	.	Parent=gene145
chr21	.	intron	33883138	33884016	.	-	.	Parent=gene145
chr21	ENCODE	exon	33884017	33884097	.	-	.	Parent=gene145
chr21	.	intron	33884098	33885337	.	-	.	Parent=gene145
chr21	ENCODE	exon	33885338	33885547	.	-	.	Parent=gene145
chr21	.	intron	33885548	33889531	.	-	.	Parent=gene145
chr21	ENCODE	exon	33889532	33889641	.	-	.	Parent=gene145
###
chr21	ENCODE	gene	33872093	33882846	.	-	.	ID=gene146;Name=AP000304.11-004;name2=DONSON
chr21	ENCODE	exon	33872093	33872620	.	-	.	Parent=gene146
chr21	.	intron	33872621	33873525	.	-	.	Parent=gene146
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene146
chr21	.	intron	33873739	33875477	.	-	.	Parent=gene146
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene146
chr21	.	intron	33875677	33876126	.	-	.	Parent=gene146
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene146
chr21	.	intron	33876232	33876340	.	-	.	Parent=gene146
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene146
chr21	.	intron	33876423	33878765	.	-	.	Parent=gene146
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene146
chr21	.	intron	33878945	33880153	.	-	.	Parent=gene146
chr21	ENCODE	exon	33880154	33880236	.	-	.	Parent=gene146
chr21	.	intron	33880237	33881697	.	-	.	Parent=gene146
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene146
chr21	.	intron	33881779	33882496	.	-	.	Parent=gene146
chr21	ENCODE	exon	33882497	33882846	.	-	.	Parent=gene146
###
chr21	ENCODE	gene	33872100	33873790	.	-	.	ID=gene147;Name=AP000304.11-010;name2=DONSON
chr21	ENCODE	exon	33872100	33872620	.	-	.	Parent=gene147
chr21	.	intron	33872621	33873525	.	-	.	Parent=gene147
chr21	ENCODE	exon	33873526	33873790	.	-	.	Parent=gene147
###
chr21	ENCODE	gene	33872118	33881778	.	-	.	ID=gene148;Name=AP000304.11-006;name2=DONSON
chr21	ENCODE	exon	33872118	33872620	.	-	.	Parent=gene148
chr21	.	intron	33872621	33873525	.	-	.	Parent=gene148
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene148
chr21	.	intron	33873739	33875477	.	-	.	Parent=gene148
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene148
chr21	.	intron	33875677	33876126	.	-	.	Parent=gene148
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene148
chr21	.	intron	33876232	33876340	.	-	.	Parent=gene148
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene148
chr21	.	intron	33876423	33878765	.	-	.	Parent=gene148
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene148
chr21	.	intron	33878945	33880153	.	-	.	Parent=gene148
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene148
chr21	.	intron	33880358	33881697	.	-	.	Parent=gene148
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene148
###
chr21	ENCODE	gene	33872118	33881778	.	-	.	ID=gene149;Name=AP000304.11-005;name2=DONSON
chr21	ENCODE	exon	33872118	33872620	.	-	.	Parent=gene149
chr21	.	intron	33872621	33873525	.	-	.	Parent=gene149
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene149
chr21	.	intron	33873739	33878765	.	-	.	Parent=gene149
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene149
chr21	.	intron	33878945	33880153	.	-	.	Parent=gene149
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene149
chr21	.	intron	33880358	33881697	.	-	.	Parent=gene149
chr21	ENCODE	exon	33881698	33881778	.	-	.	Parent=gene149
###
chr21	ENCODE	gene	33872377	33882810	.	-	.	ID=gene150;Name=AP000304.11-002;name2=DONSON
chr21	ENCODE	exon	33872377	33872620	.	-	.	Parent=gene150
chr21	ENCODE	CDS	33872483	33872620	.	-	.	Parent=gene150
chr21	.	intron	33872621	33873525	.	-	.	Parent=gene150
chr21	ENCODE	exon	33873526	33873738	.	-	.	Parent=gene150
chr21	ENCODE	CDS	33873526	33873738	.	-	.	Parent=gene150
chr21	.	intron	33873739	33875477	.	-	.	Parent=gene150
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene150
chr21	ENCODE	CDS	33875478	33875676	.	-	.	Parent=gene150
chr21	.	intron	33875677	33876126	.	-	.	Parent=gene150
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene150
chr21	ENCODE	CDS	33876127	33876231	.	-	.	Parent=gene150
chr21	.	intron	33876232	33876340	.	-	.	Parent=gene150
chr21	ENCODE	exon	33876341	33876422	.	-	.	Parent=gene150
chr21	ENCODE	CDS	33876341	33876422	.	-	.	Parent=gene150
chr21	.	intron	33876423	33877663	.	-	.	Parent=gene150
chr21	ENCODE	exon	33877664	33877842	.	-	.	Parent=gene150
chr21	ENCODE	CDS	33877664	33877842	.	-	.	Parent=gene150
chr21	.	intron	33877843	33878765	.	-	.	Parent=gene150
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene150
chr21	ENCODE	CDS	33878766	33878944	.	-	.	Parent=gene150
chr21	.	intron	33878945	33880153	.	-	.	Parent=gene150
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene150
chr21	ENCODE	CDS	33880154	33880357	.	-	.	Parent=gene150
chr21	.	intron	33880358	33882496	.	-	.	Parent=gene150
chr21	ENCODE	exon	33882497	33882810	.	-	.	Parent=gene150
chr21	ENCODE	CDS	33882497	33882810	.	-	.	Parent=gene150
###
chr21	ENCODE	gene	33873700	33880334	.	-	.	ID=gene151;Name=AP000304.11-009;name2=DONSON
chr21	ENCODE	exon	33873700	33873738	.	-	.	Parent=gene151
chr21	ENCODE	CDS	33873700	33873738	.	-	.	Parent=gene151
chr21	.	intron	33873739	33875477	.	-	.	Parent=gene151
chr21	ENCODE	exon	33875478	33875676	.	-	.	Parent=gene151
chr21	ENCODE	CDS	33875478	33875676	.	-	.	Parent=gene151
chr21	.	intron	33875677	33876126	.	-	.	Parent=gene151
chr21	ENCODE	exon	33876127	33876231	.	-	.	Parent=gene151
chr21	ENCODE	CDS	33876127	33876231	.	-	.	Parent=gene151
chr21	.	intron	33876232	33878765	.	-	.	Parent=gene151
chr21	ENCODE	exon	33878766	33878944	.	-	.	Parent=gene151
chr21	ENCODE	CDS	33878766	33878944	.	-	.	Parent=gene151
chr21	.	intron	33878945	33880153	.	-	.	Parent=gene151
chr21	ENCODE	exon	33880154	33880334	.	-	.	Parent=gene151
chr21	ENCODE	CDS	33880154	33880334	.	-	.	Parent=gene151
###
chr21	ENCODE	gene	33875351	33876230	.	-	.	ID=gene152;Name=AP000304.11-011;name2=DONSON
chr21	ENCODE	exon	33875351	33875676	.	-	.	Parent=gene152
chr21	.	intron	33875677	33876126	.	-	.	Parent=gene152
chr21	ENCODE	exon	33876127	33876230	.	-	.	Parent=gene152
###
chr21	ENCODE	gene	33878863	34206505	.	-	.	ID=gene153;Name=AP000304.11-012;name2=DONSON
chr21	ENCODE	exon	33878863	33878944	.	-	.	Parent=gene153
chr21	ENCODE	CDS	33878863	33878944	.	-	.	Parent=gene153
chr21	.	intron	33878945	33880153	.	-	.	Parent=gene153
chr21	ENCODE	exon	33880154	33880357	.	-	.	Parent=gene153
chr21	ENCODE	CDS	33880154	33880357	.	-	.	Parent=gene153
chr21	.	intron	33880358	34201514	.	-	.	Parent=gene153
chr21	ENCODE	exon	34201515	34201627	.	-	.	Parent=gene153
chr21	ENCODE	CDS	34201515	34201627	.	-	.	Parent=gene153
chr21	.	intron	34201628	34203255	.	-	.	Parent=gene153
chr21	ENCODE	exon	34203256	34203385	.	-	.	Parent=gene153
chr21	ENCODE	CDS	34203256	34203385	.	-	.	Parent=gene153
chr21	.	intron	34203386	34206462	.	-	.	Parent=gene153
chr21	ENCODE	exon	34206463	34206505	.	-	.	Parent=gene153
chr21	ENCODE	CDS	34206463	34206505	.	-	.	Parent=gene153
###
chr21	ENCODE	gene	33883517	33935936	.	-	.	ID=gene154;Name=AP000304.10-001;name2=CRYZL1
chr21	ENCODE	exon	33883517	33884097	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33883998	33884097	.	-	.	Parent=gene154
chr21	.	intron	33884098	33885337	.	-	.	Parent=gene154
chr21	ENCODE	exon	33885338	33885383	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33885338	33885383	.	-	.	Parent=gene154
chr21	.	intron	33885384	33889906	.	-	.	Parent=gene154
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33889907	33890012	.	-	.	Parent=gene154
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene154
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33891456	33891577	.	-	.	Parent=gene154
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene154
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33893326	33893424	.	-	.	Parent=gene154
chr21	.	intron	33893425	33896409	.	-	.	Parent=gene154
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33896410	33896521	.	-	.	Parent=gene154
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene154
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33897580	33897713	.	-	.	Parent=gene154
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene154
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33907714	33907782	.	-	.	Parent=gene154
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene154
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33910882	33910926	.	-	.	Parent=gene154
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene154
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33916172	33916244	.	-	.	Parent=gene154
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene154
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33918859	33918936	.	-	.	Parent=gene154
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene154
chr21	ENCODE	CDS	33925662	33925727	.	-	.	Parent=gene154
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene154
chr21	.	intron	33925734	33935856	.	-	.	Parent=gene154
chr21	ENCODE	exon	33935857	33935936	.	-	.	Parent=gene154
###
chr21	ENCODE	gene	33883562	33936094	.	-	.	ID=gene155;Name=AP000304.10-007;name2=CRYZL1
chr21	ENCODE	exon	33883562	33884097	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33883998	33884097	.	-	.	Parent=gene155
chr21	.	intron	33884098	33885337	.	-	.	Parent=gene155
chr21	ENCODE	exon	33885338	33885383	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33885338	33885383	.	-	.	Parent=gene155
chr21	.	intron	33885384	33889906	.	-	.	Parent=gene155
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33889907	33890012	.	-	.	Parent=gene155
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene155
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33891456	33891577	.	-	.	Parent=gene155
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene155
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33893326	33893424	.	-	.	Parent=gene155
chr21	.	intron	33893425	33896409	.	-	.	Parent=gene155
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33896410	33896521	.	-	.	Parent=gene155
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene155
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33897580	33897713	.	-	.	Parent=gene155
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene155
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33907714	33907782	.	-	.	Parent=gene155
chr21	.	intron	33907783	33916171	.	-	.	Parent=gene155
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33916172	33916244	.	-	.	Parent=gene155
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene155
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33918859	33918936	.	-	.	Parent=gene155
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene155
chr21	ENCODE	CDS	33925662	33925727	.	-	.	Parent=gene155
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene155
chr21	.	intron	33925734	33935856	.	-	.	Parent=gene155
chr21	ENCODE	exon	33935857	33936094	.	-	.	Parent=gene155
###
chr21	ENCODE	gene	33883637	33885894	.	-	.	ID=gene156;Name=AP000304.10-023;name2=CRYZL1
chr21	ENCODE	exon	33883637	33884097	.	-	.	Parent=gene156
chr21	.	intron	33884098	33885337	.	-	.	Parent=gene156
chr21	ENCODE	exon	33885338	33885894	.	-	.	Parent=gene156
###
chr21	ENCODE	gene	33883643	33935923	.	-	.	ID=gene157;Name=AP000304.10-002;name2=CRYZL1
chr21	ENCODE	exon	33883643	33884097	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33884083	33884097	.	-	.	Parent=gene157
chr21	.	intron	33884098	33885337	.	-	.	Parent=gene157
chr21	ENCODE	exon	33885338	33885387	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33885338	33885387	.	-	.	Parent=gene157
chr21	.	intron	33885388	33889906	.	-	.	Parent=gene157
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33889907	33890012	.	-	.	Parent=gene157
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene157
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33891456	33891577	.	-	.	Parent=gene157
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene157
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33893326	33893424	.	-	.	Parent=gene157
chr21	.	intron	33893425	33896409	.	-	.	Parent=gene157
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33896410	33896521	.	-	.	Parent=gene157
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene157
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33897580	33897713	.	-	.	Parent=gene157
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene157
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33907714	33907782	.	-	.	Parent=gene157
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene157
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33910882	33910926	.	-	.	Parent=gene157
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene157
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33916172	33916244	.	-	.	Parent=gene157
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene157
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33918859	33918936	.	-	.	Parent=gene157
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene157
chr21	ENCODE	CDS	33925662	33925727	.	-	.	Parent=gene157
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene157
chr21	.	intron	33925734	33935856	.	-	.	Parent=gene157
chr21	ENCODE	exon	33935857	33935923	.	-	.	Parent=gene157
###
chr21	ENCODE	gene	33883644	33907736	.	-	.	ID=gene158;Name=AP000304.10-009;name2=CRYZL1
chr21	ENCODE	exon	33883644	33884097	.	-	.	Parent=gene158
chr21	.	intron	33884098	33885337	.	-	.	Parent=gene158
chr21	ENCODE	exon	33885338	33885547	.	-	.	Parent=gene158
chr21	.	intron	33885548	33889531	.	-	.	Parent=gene158
chr21	ENCODE	exon	33889532	33889790	.	-	.	Parent=gene158
chr21	.	intron	33889791	33889906	.	-	.	Parent=gene158
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene158
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene158
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene158
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene158
chr21	ENCODE	exon	33893326	33893461	.	-	.	Parent=gene158
chr21	.	intron	33893462	33896409	.	-	.	Parent=gene158
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene158
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene158
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene158
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene158
chr21	ENCODE	exon	33907714	33907736	.	-	.	Parent=gene158
###
chr21	ENCODE	gene	33883721	33893327	.	-	.	ID=gene159;Name=AP000304.10-021;name2=CRYZL1
chr21	ENCODE	exon	33883721	33883981	.	-	.	Parent=gene159
chr21	ENCODE	CDS	33883921	33883981	.	-	.	Parent=gene159
chr21	.	intron	33883982	33885337	.	-	.	Parent=gene159
chr21	ENCODE	exon	33885338	33885383	.	-	.	Parent=gene159
chr21	ENCODE	CDS	33885338	33885383	.	-	.	Parent=gene159
chr21	.	intron	33885384	33889906	.	-	.	Parent=gene159
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene159
chr21	ENCODE	CDS	33889907	33890012	.	-	.	Parent=gene159
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene159
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene159
chr21	ENCODE	CDS	33891456	33891577	.	-	.	Parent=gene159
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene159
chr21	ENCODE	exon	33893326	33893327	.	-	.	Parent=gene159
chr21	ENCODE	CDS	33893326	33893327	.	-	.	Parent=gene159
###
chr21	ENCODE	gene	33883736	33891576	.	-	.	ID=gene160;Name=AP000304.10-022;name2=CRYZL1
chr21	ENCODE	exon	33883736	33884097	.	-	.	Parent=gene160
chr21	.	intron	33884098	33885337	.	-	.	Parent=gene160
chr21	ENCODE	exon	33885338	33885404	.	-	.	Parent=gene160
chr21	.	intron	33885405	33889906	.	-	.	Parent=gene160
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene160
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene160
chr21	ENCODE	exon	33891456	33891576	.	-	.	Parent=gene160
###
chr21	ENCODE	gene	33883945	33896441	.	-	.	ID=gene161;Name=AP000304.10-019;name2=CRYZL1
chr21	ENCODE	exon	33883945	33884097	.	-	.	Parent=gene161
chr21	.	intron	33884098	33885337	.	-	.	Parent=gene161
chr21	ENCODE	exon	33885338	33885383	.	-	.	Parent=gene161
chr21	.	intron	33885384	33889906	.	-	.	Parent=gene161
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene161
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene161
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene161
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene161
chr21	ENCODE	exon	33893326	33893461	.	-	.	Parent=gene161
chr21	.	intron	33893462	33896409	.	-	.	Parent=gene161
chr21	ENCODE	exon	33896410	33896441	.	-	.	Parent=gene161
###
chr21	ENCODE	gene	33888683	33935935	.	-	.	ID=gene162;Name=AP000304.10-003;name2=CRYZL1
chr21	ENCODE	exon	33888683	33889790	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33889789	33889790	.	-	.	Parent=gene162
chr21	.	intron	33889791	33889906	.	-	.	Parent=gene162
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33889907	33890012	.	-	.	Parent=gene162
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene162
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33891456	33891577	.	-	.	Parent=gene162
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene162
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33893326	33893424	.	-	.	Parent=gene162
chr21	.	intron	33893425	33896409	.	-	.	Parent=gene162
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33896410	33896521	.	-	.	Parent=gene162
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene162
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33897580	33897713	.	-	.	Parent=gene162
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene162
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33907714	33907782	.	-	.	Parent=gene162
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene162
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33910882	33910926	.	-	.	Parent=gene162
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene162
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33916172	33916244	.	-	.	Parent=gene162
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene162
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33918859	33918936	.	-	.	Parent=gene162
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene162
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33925662	33925733	.	-	.	Parent=gene162
chr21	.	intron	33925734	33935354	.	-	.	Parent=gene162
chr21	ENCODE	CDS	33935355	33935420	.	-	.	Parent=gene162
chr21	ENCODE	exon	33935355	33935481	.	-	.	Parent=gene162
chr21	.	intron	33935482	33935856	.	-	.	Parent=gene162
chr21	ENCODE	exon	33935857	33935935	.	-	.	Parent=gene162
###
chr21	ENCODE	gene	33888819	33935917	.	-	.	ID=gene163;Name=AP000304.10-006;name2=CRYZL1
chr21	ENCODE	exon	33888819	33889790	.	-	.	Parent=gene163
chr21	.	intron	33889791	33889904	.	-	.	Parent=gene163
chr21	ENCODE	exon	33889905	33890012	.	-	.	Parent=gene163
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene163
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene163
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene163
chr21	ENCODE	exon	33893326	33893461	.	-	.	Parent=gene163
chr21	.	intron	33893462	33896409	.	-	.	Parent=gene163
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene163
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene163
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene163
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene163
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene163
chr21	.	intron	33907783	33916171	.	-	.	Parent=gene163
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene163
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene163
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene163
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene163
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene163
chr21	.	intron	33925734	33935856	.	-	.	Parent=gene163
chr21	ENCODE	exon	33935857	33935917	.	-	.	Parent=gene163
###
chr21	ENCODE	gene	33888838	33936514	.	-	.	ID=gene164;Name=AP000304.10-005;name2=CRYZL1
chr21	ENCODE	exon	33888838	33889790	.	-	.	Parent=gene164
chr21	.	intron	33889791	33889906	.	-	.	Parent=gene164
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene164
chr21	.	intron	33890013	33891455	.	-	.	Parent=gene164
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene164
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene164
chr21	ENCODE	exon	33893326	33893461	.	-	.	Parent=gene164
chr21	.	intron	33893462	33896409	.	-	.	Parent=gene164
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene164
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene164
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene164
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene164
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene164
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene164
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene164
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene164
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene164
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene164
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene164
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene164
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene164
chr21	.	intron	33925734	33935856	.	-	.	Parent=gene164
chr21	ENCODE	exon	33935857	33936514	.	-	.	Parent=gene164
###
chr21	ENCODE	gene	33889307	33916218	.	-	.	ID=gene165;Name=AP000304.10-017;name2=CRYZL1
chr21	ENCODE	exon	33889307	33889704	.	-	.	Parent=gene165
chr21	ENCODE	CDS	33889609	33889704	.	-	.	Parent=gene165
chr21	.	intron	33889705	33891455	.	-	.	Parent=gene165
chr21	ENCODE	exon	33891456	33891577	.	-	.	Parent=gene165
chr21	ENCODE	CDS	33891456	33891577	.	-	.	Parent=gene165
chr21	.	intron	33891578	33893325	.	-	.	Parent=gene165
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene165
chr21	ENCODE	CDS	33893326	33893424	.	-	.	Parent=gene165
chr21	.	intron	33893425	33896409	.	-	.	Parent=gene165
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene165
chr21	ENCODE	CDS	33896410	33896521	.	-	.	Parent=gene165
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene165
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene165
chr21	ENCODE	CDS	33897580	33897713	.	-	.	Parent=gene165
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene165
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene165
chr21	ENCODE	CDS	33907714	33907782	.	-	.	Parent=gene165
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene165
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene165
chr21	ENCODE	CDS	33910882	33910926	.	-	.	Parent=gene165
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene165
chr21	ENCODE	exon	33916172	33916218	.	-	.	Parent=gene165
chr21	ENCODE	CDS	33916172	33916218	.	-	.	Parent=gene165
###
chr21	ENCODE	gene	33889513	33896432	.	-	.	ID=gene166;Name=AP000304.10-020;name2=CRYZL1
chr21	ENCODE	exon	33889513	33889790	.	-	.	Parent=gene166
chr21	.	intron	33889791	33889906	.	-	.	Parent=gene166
chr21	ENCODE	exon	33889907	33890012	.	-	.	Parent=gene166
chr21	.	intron	33890013	33893325	.	-	.	Parent=gene166
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene166
chr21	.	intron	33893425	33896409	.	-	.	Parent=gene166
chr21	ENCODE	exon	33896410	33896432	.	-	.	Parent=gene166
###
chr21	ENCODE	gene	33890238	33897624	.	-	.	ID=gene167;Name=AP000304.10-018;name2=CRYZL1
chr21	ENCODE	exon	33890238	33890389	.	-	.	Parent=gene167
chr21	ENCODE	CDS	33890352	33890389	.	-	.	Parent=gene167
chr21	.	intron	33890390	33893325	.	-	.	Parent=gene167
chr21	ENCODE	exon	33893326	33893424	.	-	.	Parent=gene167
chr21	ENCODE	CDS	33893326	33893424	.	-	.	Parent=gene167
chr21	.	intron	33893425	33896409	.	-	.	Parent=gene167
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene167
chr21	ENCODE	CDS	33896410	33896521	.	-	.	Parent=gene167
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene167
chr21	ENCODE	exon	33897580	33897624	.	-	.	Parent=gene167
chr21	ENCODE	CDS	33897580	33897624	.	-	.	Parent=gene167
###
chr21	ENCODE	gene	33893372	33935921	.	-	.	ID=gene168;Name=AP000304.10-012;name2=CRYZL1
chr21	ENCODE	exon	33893372	33893424	.	-	.	Parent=gene168
chr21	ENCODE	CDS	33893372	33893424	.	-	.	Parent=gene168
chr21	.	intron	33893425	33896409	.	-	.	Parent=gene168
chr21	ENCODE	exon	33896410	33896521	.	-	.	Parent=gene168
chr21	ENCODE	CDS	33896410	33896521	.	-	.	Parent=gene168
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene168
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene168
chr21	ENCODE	CDS	33897580	33897713	.	-	.	Parent=gene168
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene168
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene168
chr21	ENCODE	CDS	33907714	33907782	.	-	.	Parent=gene168
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene168
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene168
chr21	ENCODE	CDS	33910882	33910926	.	-	.	Parent=gene168
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene168
chr21	ENCODE	CDS	33916172	33916232	.	-	.	Parent=gene168
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene168
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene168
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene168
chr21	.	intron	33918937	33935856	.	-	.	Parent=gene168
chr21	ENCODE	exon	33935857	33935921	.	-	.	Parent=gene168
###
chr21	ENCODE	gene	33896444	33927878	.	-	.	ID=gene169;Name=AP000304.10-013;name2=CRYZL1
chr21	ENCODE	exon	33896444	33896521	.	-	.	Parent=gene169
chr21	ENCODE	CDS	33896444	33896521	.	-	.	Parent=gene169
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene169
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene169
chr21	ENCODE	CDS	33897580	33897713	.	-	.	Parent=gene169
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene169
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene169
chr21	ENCODE	CDS	33907714	33907782	.	-	.	Parent=gene169
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene169
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene169
chr21	ENCODE	CDS	33910882	33910926	.	-	.	Parent=gene169
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene169
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene169
chr21	ENCODE	CDS	33916172	33916244	.	-	.	Parent=gene169
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene169
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene169
chr21	ENCODE	CDS	33918859	33918936	.	-	.	Parent=gene169
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene169
chr21	ENCODE	CDS	33925662	33925727	.	-	.	Parent=gene169
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene169
chr21	.	intron	33925734	33927821	.	-	.	Parent=gene169
chr21	ENCODE	exon	33927822	33927878	.	-	.	Parent=gene169
###
chr21	ENCODE	gene	33896508	33911352	.	-	.	ID=gene170;Name=AP000304.10-015;name2=CRYZL1
chr21	ENCODE	exon	33896508	33896521	.	-	.	Parent=gene170
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene170
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene170
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene170
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene170
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene170
chr21	ENCODE	exon	33910882	33911352	.	-	.	Parent=gene170
###
chr21	ENCODE	gene	33896509	33935906	.	-	.	ID=gene171;Name=AP000304.10-014;name2=CRYZL1
chr21	ENCODE	exon	33896509	33896521	.	-	.	Parent=gene171
chr21	ENCODE	CDS	33896509	33896521	.	-	.	Parent=gene171
chr21	.	intron	33896522	33897579	.	-	.	Parent=gene171
chr21	ENCODE	exon	33897580	33897713	.	-	.	Parent=gene171
chr21	ENCODE	CDS	33897580	33897713	.	-	.	Parent=gene171
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene171
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene171
chr21	ENCODE	CDS	33907714	33907782	.	-	.	Parent=gene171
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene171
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene171
chr21	ENCODE	CDS	33910882	33910926	.	-	.	Parent=gene171
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene171
chr21	ENCODE	CDS	33916172	33916232	.	-	.	Parent=gene171
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene171
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene171
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene171
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene171
chr21	ENCODE	exon	33925662	33925703	.	-	.	Parent=gene171
chr21	.	intron	33925704	33935856	.	-	.	Parent=gene171
chr21	ENCODE	exon	33935857	33935906	.	-	.	Parent=gene171
###
chr21	ENCODE	gene	33897332	33935896	.	-	.	ID=gene172;Name=AP000304.10-016;name2=CRYZL1
chr21	ENCODE	exon	33897332	33897713	.	-	.	Parent=gene172
chr21	.	intron	33897714	33907713	.	-	.	Parent=gene172
chr21	ENCODE	exon	33907714	33907782	.	-	.	Parent=gene172
chr21	.	intron	33907783	33910881	.	-	.	Parent=gene172
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene172
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene172
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene172
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene172
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene172
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene172
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene172
chr21	.	intron	33925734	33935856	.	-	.	Parent=gene172
chr21	ENCODE	exon	33935857	33935896	.	-	.	Parent=gene172
###
chr21	ENCODE	gene	33910463	33935898	.	-	.	ID=gene173;Name=AP000304.10-008;name2=CRYZL1
chr21	ENCODE	exon	33910463	33910779	.	-	.	Parent=gene173
chr21	ENCODE	CDS	33910700	33910779	.	-	.	Parent=gene173
chr21	.	intron	33910780	33910881	.	-	.	Parent=gene173
chr21	ENCODE	exon	33910882	33910926	.	-	.	Parent=gene173
chr21	ENCODE	CDS	33910882	33910926	.	-	.	Parent=gene173
chr21	.	intron	33910927	33916171	.	-	.	Parent=gene173
chr21	ENCODE	exon	33916172	33916244	.	-	.	Parent=gene173
chr21	ENCODE	CDS	33916172	33916244	.	-	.	Parent=gene173
chr21	.	intron	33916245	33918858	.	-	.	Parent=gene173
chr21	ENCODE	exon	33918859	33918936	.	-	.	Parent=gene173
chr21	ENCODE	CDS	33918859	33918936	.	-	.	Parent=gene173
chr21	.	intron	33918937	33925661	.	-	.	Parent=gene173
chr21	ENCODE	CDS	33925662	33925727	.	-	.	Parent=gene173
chr21	ENCODE	exon	33925662	33925733	.	-	.	Parent=gene173
chr21	.	intron	33925734	33935856	.	-	.	Parent=gene173
chr21	ENCODE	exon	33935857	33935898	.	-	.	Parent=gene173
###
chr21	ENCODE	gene	33925669	33938102	.	-	.	ID=gene174;Name=AP000304.10-011;name2=CRYZL1
chr21	ENCODE	exon	33925669	33925733	.	-	.	Parent=gene174
chr21	.	intron	33925734	33937547	.	-	.	Parent=gene174
chr21	ENCODE	exon	33937548	33938102	.	-	.	Parent=gene174
###
chr21	ENCODE	gene	33933921	33935897	.	-	.	ID=gene175;Name=AP000304.10-004;name2=CRYZL1
chr21	ENCODE	exon	33933921	33934364	.	-	.	Parent=gene175
chr21	ENCODE	CDS	33934356	33934364	.	-	.	Parent=gene175
chr21	.	intron	33934365	33935354	.	-	.	Parent=gene175
chr21	ENCODE	CDS	33935355	33935420	.	-	.	Parent=gene175
chr21	ENCODE	exon	33935355	33935481	.	-	.	Parent=gene175
chr21	.	intron	33935482	33935856	.	-	.	Parent=gene175
chr21	ENCODE	exon	33935857	33935897	.	-	.	Parent=gene175
###
chr21	ENCODE	gene	33936576	34088586	.	+	.	ID=gene176;Name=AP000313.6-020;name2=ITSN1
chr21	ENCODE	exon	33936576	33936889	.	+	.	Parent=gene176
chr21	.	intron	33936890	34012971	.	+	.	Parent=gene176
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34013004	34013031	.	+	.	Parent=gene176
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene176
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34015353	34015445	.	+	.	Parent=gene176
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene176
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34016763	34016826	.	+	.	Parent=gene176
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene176
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34029219	34029379	.	+	.	Parent=gene176
chr21	.	intron	34029380	34044428	.	+	.	Parent=gene176
chr21	ENCODE	exon	34044429	34044497	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34044429	34044497	.	+	.	Parent=gene176
chr21	.	intron	34044498	34045984	.	+	.	Parent=gene176
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34045985	34046081	.	+	.	Parent=gene176
chr21	.	intron	34046082	34049471	.	+	.	Parent=gene176
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34049472	34049572	.	+	.	Parent=gene176
chr21	.	intron	34049573	34056096	.	+	.	Parent=gene176
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34056097	34056160	.	+	.	Parent=gene176
chr21	.	intron	34056161	34060048	.	+	.	Parent=gene176
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34060049	34060186	.	+	.	Parent=gene176
chr21	.	intron	34060187	34061886	.	+	.	Parent=gene176
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34061887	34062002	.	+	.	Parent=gene176
chr21	.	intron	34062003	34066234	.	+	.	Parent=gene176
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34066235	34066497	.	+	.	Parent=gene176
chr21	.	intron	34066498	34068902	.	+	.	Parent=gene176
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34068903	34069052	.	+	.	Parent=gene176
chr21	.	intron	34069053	34069141	.	+	.	Parent=gene176
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34069142	34069282	.	+	.	Parent=gene176
chr21	.	intron	34069283	34075634	.	+	.	Parent=gene176
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34075635	34075722	.	+	.	Parent=gene176
chr21	.	intron	34075723	34076167	.	+	.	Parent=gene176
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34076168	34076307	.	+	.	Parent=gene176
chr21	.	intron	34076308	34088514	.	+	.	Parent=gene176
chr21	ENCODE	exon	34088515	34088586	.	+	.	Parent=gene176
chr21	ENCODE	CDS	34088515	34088586	.	+	.	Parent=gene176
###
chr21	ENCODE	gene	33936576	34131192	.	+	.	ID=gene177;Name=AP000313.6-025;name2=ITSN1
chr21	ENCODE	exon	33936576	33936889	.	+	.	Parent=gene177
chr21	.	intron	33936890	34012971	.	+	.	Parent=gene177
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34013004	34013031	.	+	.	Parent=gene177
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene177
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34015353	34015445	.	+	.	Parent=gene177
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene177
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34016763	34016826	.	+	.	Parent=gene177
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene177
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34029219	34029379	.	+	.	Parent=gene177
chr21	.	intron	34029380	34044428	.	+	.	Parent=gene177
chr21	ENCODE	exon	34044429	34044497	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34044429	34044497	.	+	.	Parent=gene177
chr21	.	intron	34044498	34045984	.	+	.	Parent=gene177
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34045985	34046081	.	+	.	Parent=gene177
chr21	.	intron	34046082	34049471	.	+	.	Parent=gene177
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34049472	34049572	.	+	.	Parent=gene177
chr21	.	intron	34049573	34056096	.	+	.	Parent=gene177
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34056097	34056160	.	+	.	Parent=gene177
chr21	.	intron	34056161	34060048	.	+	.	Parent=gene177
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34060049	34060186	.	+	.	Parent=gene177
chr21	.	intron	34060187	34061886	.	+	.	Parent=gene177
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34061887	34062002	.	+	.	Parent=gene177
chr21	.	intron	34062003	34066234	.	+	.	Parent=gene177
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34066235	34066497	.	+	.	Parent=gene177
chr21	.	intron	34066498	34068902	.	+	.	Parent=gene177
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34068903	34069052	.	+	.	Parent=gene177
chr21	.	intron	34069053	34069141	.	+	.	Parent=gene177
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34069142	34069282	.	+	.	Parent=gene177
chr21	.	intron	34069283	34075634	.	+	.	Parent=gene177
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34075635	34075722	.	+	.	Parent=gene177
chr21	.	intron	34075723	34076167	.	+	.	Parent=gene177
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34076168	34076307	.	+	.	Parent=gene177
chr21	.	intron	34076308	34088514	.	+	.	Parent=gene177
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34088515	34088642	.	+	.	Parent=gene177
chr21	.	intron	34088643	34091552	.	+	.	Parent=gene177
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34091553	34091782	.	+	.	Parent=gene177
chr21	.	intron	34091783	34093981	.	+	.	Parent=gene177
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34093982	34094103	.	+	.	Parent=gene177
chr21	.	intron	34094104	34105148	.	+	.	Parent=gene177
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34105149	34105396	.	+	.	Parent=gene177
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene177
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34108087	34108246	.	+	.	Parent=gene177
chr21	.	intron	34108247	34112440	.	+	.	Parent=gene177
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34112441	34112646	.	+	.	Parent=gene177
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene177
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34113415	34113497	.	+	.	Parent=gene177
chr21	.	intron	34113498	34117660	.	+	.	Parent=gene177
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34117661	34117827	.	+	.	Parent=gene177
chr21	.	intron	34117828	34120991	.	+	.	Parent=gene177
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34120992	34121037	.	+	.	Parent=gene177
chr21	.	intron	34121038	34123797	.	+	.	Parent=gene177
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34123798	34123919	.	+	.	Parent=gene177
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene177
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34128481	34128598	.	+	.	Parent=gene177
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene177
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34130615	34130806	.	+	.	Parent=gene177
chr21	.	intron	34130807	34131160	.	+	.	Parent=gene177
chr21	ENCODE	CDS	34131161	34131162	.	+	.	Parent=gene177
chr21	ENCODE	exon	34131161	34131192	.	+	.	Parent=gene177
###
chr21	ENCODE	gene	33936628	34029379	.	+	.	ID=gene178;Name=AP000313.6-033;name2=ITSN1
chr21	ENCODE	exon	33936628	33936889	.	+	.	Parent=gene178
chr21	.	intron	33936890	33983496	.	+	.	Parent=gene178
chr21	ENCODE	exon	33983497	33983558	.	+	.	Parent=gene178
chr21	.	intron	33983559	34010605	.	+	.	Parent=gene178
chr21	ENCODE	exon	34010606	34010730	.	+	.	Parent=gene178
chr21	.	intron	34010731	34012971	.	+	.	Parent=gene178
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene178
chr21	ENCODE	CDS	34013004	34013031	.	+	.	Parent=gene178
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene178
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene178
chr21	ENCODE	CDS	34015353	34015445	.	+	.	Parent=gene178
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene178
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene178
chr21	ENCODE	CDS	34016763	34016826	.	+	.	Parent=gene178
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene178
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene178
chr21	ENCODE	CDS	34029219	34029379	.	+	.	Parent=gene178
###
chr21	ENCODE	gene	33936629	34016166	.	+	.	ID=gene179;Name=AP000313.6-034;name2=ITSN1
chr21	ENCODE	exon	33936629	33936889	.	+	.	Parent=gene179
chr21	.	intron	33936890	34012971	.	+	.	Parent=gene179
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene179
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene179
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene179
chr21	.	intron	34015446	34016106	.	+	.	Parent=gene179
chr21	ENCODE	exon	34016107	34016166	.	+	.	Parent=gene179
###
chr21	ENCODE	gene	33936634	34194035	.	+	.	ID=gene180;Name=AP000313.6-001;name2=ITSN1
chr21	ENCODE	exon	33936634	33936889	.	+	.	Parent=gene180
chr21	.	intron	33936890	34012971	.	+	.	Parent=gene180
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34013004	34013031	.	+	.	Parent=gene180
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene180
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34015353	34015445	.	+	.	Parent=gene180
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene180
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34016763	34016826	.	+	.	Parent=gene180
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene180
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34029219	34029379	.	+	.	Parent=gene180
chr21	.	intron	34029380	34044317	.	+	.	Parent=gene180
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34044318	34044497	.	+	.	Parent=gene180
chr21	.	intron	34044498	34045984	.	+	.	Parent=gene180
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34045985	34046081	.	+	.	Parent=gene180
chr21	.	intron	34046082	34049471	.	+	.	Parent=gene180
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34049472	34049572	.	+	.	Parent=gene180
chr21	.	intron	34049573	34056096	.	+	.	Parent=gene180
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34056097	34056160	.	+	.	Parent=gene180
chr21	.	intron	34056161	34060048	.	+	.	Parent=gene180
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34060049	34060186	.	+	.	Parent=gene180
chr21	.	intron	34060187	34061886	.	+	.	Parent=gene180
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34061887	34062002	.	+	.	Parent=gene180
chr21	.	intron	34062003	34066234	.	+	.	Parent=gene180
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34066235	34066497	.	+	.	Parent=gene180
chr21	.	intron	34066498	34068902	.	+	.	Parent=gene180
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34068903	34069052	.	+	.	Parent=gene180
chr21	.	intron	34069053	34069141	.	+	.	Parent=gene180
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34069142	34069282	.	+	.	Parent=gene180
chr21	.	intron	34069283	34075634	.	+	.	Parent=gene180
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34075635	34075722	.	+	.	Parent=gene180
chr21	.	intron	34075723	34076167	.	+	.	Parent=gene180
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34076168	34076307	.	+	.	Parent=gene180
chr21	.	intron	34076308	34088514	.	+	.	Parent=gene180
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34088515	34088642	.	+	.	Parent=gene180
chr21	.	intron	34088643	34091552	.	+	.	Parent=gene180
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34091553	34091782	.	+	.	Parent=gene180
chr21	.	intron	34091783	34093981	.	+	.	Parent=gene180
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34093982	34094103	.	+	.	Parent=gene180
chr21	.	intron	34094104	34096603	.	+	.	Parent=gene180
chr21	ENCODE	exon	34096604	34096618	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34096604	34096618	.	+	.	Parent=gene180
chr21	.	intron	34096619	34105148	.	+	.	Parent=gene180
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34105149	34105396	.	+	.	Parent=gene180
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene180
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34108087	34108246	.	+	.	Parent=gene180
chr21	.	intron	34108247	34112440	.	+	.	Parent=gene180
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34112441	34112646	.	+	.	Parent=gene180
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene180
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34113415	34113497	.	+	.	Parent=gene180
chr21	.	intron	34113498	34117660	.	+	.	Parent=gene180
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34117661	34117827	.	+	.	Parent=gene180
chr21	.	intron	34117828	34120991	.	+	.	Parent=gene180
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34120992	34121037	.	+	.	Parent=gene180
chr21	.	intron	34121038	34123797	.	+	.	Parent=gene180
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34123798	34123919	.	+	.	Parent=gene180
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene180
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34128481	34128598	.	+	.	Parent=gene180
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene180
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34130615	34130806	.	+	.	Parent=gene180
chr21	.	intron	34130807	34150909	.	+	.	Parent=gene180
chr21	ENCODE	exon	34150910	34151031	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34150910	34151031	.	+	.	Parent=gene180
chr21	.	intron	34151032	34152859	.	+	.	Parent=gene180
chr21	ENCODE	exon	34152860	34152966	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34152860	34152966	.	+	.	Parent=gene180
chr21	.	intron	34152967	34159324	.	+	.	Parent=gene180
chr21	ENCODE	exon	34159325	34159508	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34159325	34159508	.	+	.	Parent=gene180
chr21	.	intron	34159509	34161406	.	+	.	Parent=gene180
chr21	ENCODE	exon	34161407	34161505	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34161407	34161505	.	+	.	Parent=gene180
chr21	.	intron	34161506	34169527	.	+	.	Parent=gene180
chr21	ENCODE	exon	34169528	34169695	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34169528	34169695	.	+	.	Parent=gene180
chr21	.	intron	34169696	34176416	.	+	.	Parent=gene180
chr21	ENCODE	exon	34176417	34176629	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34176417	34176629	.	+	.	Parent=gene180
chr21	.	intron	34176630	34177723	.	+	.	Parent=gene180
chr21	ENCODE	exon	34177724	34177845	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34177724	34177845	.	+	.	Parent=gene180
chr21	.	intron	34177846	34179214	.	+	.	Parent=gene180
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34179215	34179297	.	+	.	Parent=gene180
chr21	.	intron	34179298	34179612	.	+	.	Parent=gene180
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34179613	34179696	.	+	.	Parent=gene180
chr21	.	intron	34179697	34180460	.	+	.	Parent=gene180
chr21	ENCODE	exon	34180461	34180634	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34180461	34180634	.	+	.	Parent=gene180
chr21	.	intron	34180635	34182325	.	+	.	Parent=gene180
chr21	ENCODE	CDS	34182326	34182474	.	+	.	Parent=gene180
chr21	ENCODE	exon	34182326	34194035	.	+	.	Parent=gene180
###
chr21	ENCODE	gene	33936654	34132668	.	+	.	ID=gene181;Name=AP000313.6-002;name2=ITSN1
chr21	ENCODE	exon	33936654	33936889	.	+	.	Parent=gene181
chr21	.	intron	33936890	34012971	.	+	.	Parent=gene181
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34013004	34013031	.	+	.	Parent=gene181
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene181
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34015353	34015445	.	+	.	Parent=gene181
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene181
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34016763	34016826	.	+	.	Parent=gene181
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene181
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34029219	34029379	.	+	.	Parent=gene181
chr21	.	intron	34029380	34044317	.	+	.	Parent=gene181
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34044318	34044497	.	+	.	Parent=gene181
chr21	.	intron	34044498	34045984	.	+	.	Parent=gene181
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34045985	34046081	.	+	.	Parent=gene181
chr21	.	intron	34046082	34049471	.	+	.	Parent=gene181
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34049472	34049572	.	+	.	Parent=gene181
chr21	.	intron	34049573	34056096	.	+	.	Parent=gene181
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34056097	34056160	.	+	.	Parent=gene181
chr21	.	intron	34056161	34060048	.	+	.	Parent=gene181
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34060049	34060186	.	+	.	Parent=gene181
chr21	.	intron	34060187	34061886	.	+	.	Parent=gene181
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34061887	34062002	.	+	.	Parent=gene181
chr21	.	intron	34062003	34066234	.	+	.	Parent=gene181
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34066235	34066497	.	+	.	Parent=gene181
chr21	.	intron	34066498	34068902	.	+	.	Parent=gene181
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34068903	34069052	.	+	.	Parent=gene181
chr21	.	intron	34069053	34069141	.	+	.	Parent=gene181
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34069142	34069282	.	+	.	Parent=gene181
chr21	.	intron	34069283	34075634	.	+	.	Parent=gene181
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34075635	34075722	.	+	.	Parent=gene181
chr21	.	intron	34075723	34076167	.	+	.	Parent=gene181
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34076168	34076307	.	+	.	Parent=gene181
chr21	.	intron	34076308	34088514	.	+	.	Parent=gene181
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34088515	34088642	.	+	.	Parent=gene181
chr21	.	intron	34088643	34091552	.	+	.	Parent=gene181
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34091553	34091782	.	+	.	Parent=gene181
chr21	.	intron	34091783	34093981	.	+	.	Parent=gene181
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34093982	34094103	.	+	.	Parent=gene181
chr21	.	intron	34094104	34096603	.	+	.	Parent=gene181
chr21	ENCODE	exon	34096604	34096618	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34096604	34096618	.	+	.	Parent=gene181
chr21	.	intron	34096619	34105148	.	+	.	Parent=gene181
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34105149	34105396	.	+	.	Parent=gene181
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene181
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34108087	34108246	.	+	.	Parent=gene181
chr21	.	intron	34108247	34112440	.	+	.	Parent=gene181
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34112441	34112646	.	+	.	Parent=gene181
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene181
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34113415	34113497	.	+	.	Parent=gene181
chr21	.	intron	34113498	34117660	.	+	.	Parent=gene181
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34117661	34117827	.	+	.	Parent=gene181
chr21	.	intron	34117828	34120991	.	+	.	Parent=gene181
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34120992	34121037	.	+	.	Parent=gene181
chr21	.	intron	34121038	34123797	.	+	.	Parent=gene181
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34123798	34123919	.	+	.	Parent=gene181
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene181
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34128481	34128598	.	+	.	Parent=gene181
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene181
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34130615	34130806	.	+	.	Parent=gene181
chr21	.	intron	34130807	34131160	.	+	.	Parent=gene181
chr21	ENCODE	CDS	34131161	34131162	.	+	.	Parent=gene181
chr21	ENCODE	exon	34131161	34132668	.	+	.	Parent=gene181
###
chr21	ENCODE	gene	33936659	34182782	.	+	.	ID=gene182;Name=AP000313.6-023;name2=ITSN1
chr21	ENCODE	exon	33936659	33936889	.	+	.	Parent=gene182
chr21	.	intron	33936890	34012971	.	+	.	Parent=gene182
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34013004	34013031	.	+	.	Parent=gene182
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene182
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34015353	34015445	.	+	.	Parent=gene182
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene182
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34016763	34016826	.	+	.	Parent=gene182
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene182
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34029219	34029379	.	+	.	Parent=gene182
chr21	.	intron	34029380	34044317	.	+	.	Parent=gene182
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34044318	34044497	.	+	.	Parent=gene182
chr21	.	intron	34044498	34045984	.	+	.	Parent=gene182
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34045985	34046081	.	+	.	Parent=gene182
chr21	.	intron	34046082	34049471	.	+	.	Parent=gene182
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34049472	34049572	.	+	.	Parent=gene182
chr21	.	intron	34049573	34056096	.	+	.	Parent=gene182
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34056097	34056160	.	+	.	Parent=gene182
chr21	.	intron	34056161	34060048	.	+	.	Parent=gene182
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34060049	34060186	.	+	.	Parent=gene182
chr21	.	intron	34060187	34061886	.	+	.	Parent=gene182
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34061887	34062002	.	+	.	Parent=gene182
chr21	.	intron	34062003	34066234	.	+	.	Parent=gene182
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34066235	34066497	.	+	.	Parent=gene182
chr21	.	intron	34066498	34068902	.	+	.	Parent=gene182
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34068903	34069052	.	+	.	Parent=gene182
chr21	.	intron	34069053	34069141	.	+	.	Parent=gene182
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34069142	34069282	.	+	.	Parent=gene182
chr21	.	intron	34069283	34075634	.	+	.	Parent=gene182
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34075635	34075722	.	+	.	Parent=gene182
chr21	.	intron	34075723	34076167	.	+	.	Parent=gene182
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34076168	34076307	.	+	.	Parent=gene182
chr21	.	intron	34076308	34088514	.	+	.	Parent=gene182
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34088515	34088642	.	+	.	Parent=gene182
chr21	.	intron	34088643	34091552	.	+	.	Parent=gene182
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34091553	34091782	.	+	.	Parent=gene182
chr21	.	intron	34091783	34093981	.	+	.	Parent=gene182
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34093982	34094103	.	+	.	Parent=gene182
chr21	.	intron	34094104	34105148	.	+	.	Parent=gene182
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34105149	34105396	.	+	.	Parent=gene182
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene182
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34108087	34108246	.	+	.	Parent=gene182
chr21	.	intron	34108247	34112440	.	+	.	Parent=gene182
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34112441	34112646	.	+	.	Parent=gene182
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene182
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34113415	34113497	.	+	.	Parent=gene182
chr21	.	intron	34113498	34117660	.	+	.	Parent=gene182
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34117661	34117827	.	+	.	Parent=gene182
chr21	.	intron	34117828	34120991	.	+	.	Parent=gene182
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34120992	34121037	.	+	.	Parent=gene182
chr21	.	intron	34121038	34123797	.	+	.	Parent=gene182
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34123798	34123919	.	+	.	Parent=gene182
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene182
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34128481	34128598	.	+	.	Parent=gene182
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene182
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34130615	34130806	.	+	.	Parent=gene182
chr21	.	intron	34130807	34150909	.	+	.	Parent=gene182
chr21	ENCODE	exon	34150910	34151031	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34150910	34151031	.	+	.	Parent=gene182
chr21	.	intron	34151032	34152859	.	+	.	Parent=gene182
chr21	ENCODE	exon	34152860	34152966	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34152860	34152966	.	+	.	Parent=gene182
chr21	.	intron	34152967	34159324	.	+	.	Parent=gene182
chr21	ENCODE	exon	34159325	34159508	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34159325	34159508	.	+	.	Parent=gene182
chr21	.	intron	34159509	34161406	.	+	.	Parent=gene182
chr21	ENCODE	exon	34161407	34161505	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34161407	34161505	.	+	.	Parent=gene182
chr21	.	intron	34161506	34169527	.	+	.	Parent=gene182
chr21	ENCODE	exon	34169528	34169695	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34169528	34169695	.	+	.	Parent=gene182
chr21	.	intron	34169696	34176416	.	+	.	Parent=gene182
chr21	ENCODE	exon	34176417	34176629	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34176417	34176629	.	+	.	Parent=gene182
chr21	.	intron	34176630	34177723	.	+	.	Parent=gene182
chr21	ENCODE	exon	34177724	34177845	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34177724	34177845	.	+	.	Parent=gene182
chr21	.	intron	34177846	34179214	.	+	.	Parent=gene182
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34179215	34179297	.	+	.	Parent=gene182
chr21	.	intron	34179298	34179612	.	+	.	Parent=gene182
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34179613	34179696	.	+	.	Parent=gene182
chr21	.	intron	34179697	34180460	.	+	.	Parent=gene182
chr21	ENCODE	exon	34180461	34180634	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34180461	34180634	.	+	.	Parent=gene182
chr21	.	intron	34180635	34182325	.	+	.	Parent=gene182
chr21	ENCODE	CDS	34182326	34182474	.	+	.	Parent=gene182
chr21	ENCODE	exon	34182326	34182782	.	+	.	Parent=gene182
###
chr21	ENCODE	gene	33936672	34132672	.	+	.	ID=gene183;Name=AP000313.6-024;name2=ITSN1
chr21	ENCODE	exon	33936672	33936889	.	+	.	Parent=gene183
chr21	.	intron	33936890	34012971	.	+	.	Parent=gene183
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34013004	34013031	.	+	.	Parent=gene183
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene183
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34015353	34015445	.	+	.	Parent=gene183
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene183
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34016763	34016826	.	+	.	Parent=gene183
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene183
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34029219	34029379	.	+	.	Parent=gene183
chr21	.	intron	34029380	34044317	.	+	.	Parent=gene183
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34044318	34044497	.	+	.	Parent=gene183
chr21	.	intron	34044498	34045984	.	+	.	Parent=gene183
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34045985	34046081	.	+	.	Parent=gene183
chr21	.	intron	34046082	34049471	.	+	.	Parent=gene183
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34049472	34049572	.	+	.	Parent=gene183
chr21	.	intron	34049573	34056096	.	+	.	Parent=gene183
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34056097	34056160	.	+	.	Parent=gene183
chr21	.	intron	34056161	34060048	.	+	.	Parent=gene183
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34060049	34060186	.	+	.	Parent=gene183
chr21	.	intron	34060187	34061886	.	+	.	Parent=gene183
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34061887	34062002	.	+	.	Parent=gene183
chr21	.	intron	34062003	34066234	.	+	.	Parent=gene183
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34066235	34066497	.	+	.	Parent=gene183
chr21	.	intron	34066498	34068902	.	+	.	Parent=gene183
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34068903	34069052	.	+	.	Parent=gene183
chr21	.	intron	34069053	34069141	.	+	.	Parent=gene183
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34069142	34069282	.	+	.	Parent=gene183
chr21	.	intron	34069283	34075634	.	+	.	Parent=gene183
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34075635	34075722	.	+	.	Parent=gene183
chr21	.	intron	34075723	34076167	.	+	.	Parent=gene183
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34076168	34076307	.	+	.	Parent=gene183
chr21	.	intron	34076308	34088514	.	+	.	Parent=gene183
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34088515	34088642	.	+	.	Parent=gene183
chr21	.	intron	34088643	34091552	.	+	.	Parent=gene183
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34091553	34091782	.	+	.	Parent=gene183
chr21	.	intron	34091783	34093981	.	+	.	Parent=gene183
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34093982	34094103	.	+	.	Parent=gene183
chr21	.	intron	34094104	34105148	.	+	.	Parent=gene183
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34105149	34105396	.	+	.	Parent=gene183
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene183
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34108087	34108246	.	+	.	Parent=gene183
chr21	.	intron	34108247	34112440	.	+	.	Parent=gene183
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34112441	34112646	.	+	.	Parent=gene183
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene183
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34113415	34113497	.	+	.	Parent=gene183
chr21	.	intron	34113498	34117660	.	+	.	Parent=gene183
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34117661	34117827	.	+	.	Parent=gene183
chr21	.	intron	34117828	34120991	.	+	.	Parent=gene183
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34120992	34121037	.	+	.	Parent=gene183
chr21	.	intron	34121038	34123797	.	+	.	Parent=gene183
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34123798	34123919	.	+	.	Parent=gene183
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene183
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34128481	34128598	.	+	.	Parent=gene183
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene183
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34130615	34130806	.	+	.	Parent=gene183
chr21	.	intron	34130807	34131160	.	+	.	Parent=gene183
chr21	ENCODE	CDS	34131161	34131162	.	+	.	Parent=gene183
chr21	ENCODE	exon	34131161	34132672	.	+	.	Parent=gene183
###
chr21	ENCODE	gene	33936674	34132670	.	+	.	ID=gene184;Name=AP000313.6-003;name2=ITSN1
chr21	ENCODE	exon	33936674	33936889	.	+	.	Parent=gene184
chr21	.	intron	33936890	34012971	.	+	.	Parent=gene184
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34013004	34013031	.	+	.	Parent=gene184
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene184
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34015353	34015445	.	+	.	Parent=gene184
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene184
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34016763	34016826	.	+	.	Parent=gene184
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene184
chr21	ENCODE	exon	34029219	34029379	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34029219	34029379	.	+	.	Parent=gene184
chr21	.	intron	34029380	34044317	.	+	.	Parent=gene184
chr21	ENCODE	exon	34044318	34044497	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34044318	34044497	.	+	.	Parent=gene184
chr21	.	intron	34044498	34045984	.	+	.	Parent=gene184
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34045985	34046081	.	+	.	Parent=gene184
chr21	.	intron	34046082	34049471	.	+	.	Parent=gene184
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34049472	34049572	.	+	.	Parent=gene184
chr21	.	intron	34049573	34056096	.	+	.	Parent=gene184
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34056097	34056160	.	+	.	Parent=gene184
chr21	.	intron	34056161	34060048	.	+	.	Parent=gene184
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34060049	34060186	.	+	.	Parent=gene184
chr21	.	intron	34060187	34061886	.	+	.	Parent=gene184
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34061887	34062002	.	+	.	Parent=gene184
chr21	.	intron	34062003	34066234	.	+	.	Parent=gene184
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34066235	34066497	.	+	.	Parent=gene184
chr21	.	intron	34066498	34068902	.	+	.	Parent=gene184
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34068903	34069052	.	+	.	Parent=gene184
chr21	.	intron	34069053	34069141	.	+	.	Parent=gene184
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34069142	34069282	.	+	.	Parent=gene184
chr21	.	intron	34069283	34075634	.	+	.	Parent=gene184
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34075635	34075722	.	+	.	Parent=gene184
chr21	.	intron	34075723	34076167	.	+	.	Parent=gene184
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34076168	34076307	.	+	.	Parent=gene184
chr21	.	intron	34076308	34088514	.	+	.	Parent=gene184
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34088515	34088642	.	+	.	Parent=gene184
chr21	.	intron	34088643	34091552	.	+	.	Parent=gene184
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34091553	34091782	.	+	.	Parent=gene184
chr21	.	intron	34091783	34093981	.	+	.	Parent=gene184
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34093982	34094103	.	+	.	Parent=gene184
chr21	.	intron	34094104	34105148	.	+	.	Parent=gene184
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34105149	34105396	.	+	.	Parent=gene184
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene184
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34108087	34108246	.	+	.	Parent=gene184
chr21	.	intron	34108247	34112440	.	+	.	Parent=gene184
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34112441	34112646	.	+	.	Parent=gene184
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene184
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34113415	34113497	.	+	.	Parent=gene184
chr21	.	intron	34113498	34123797	.	+	.	Parent=gene184
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34123798	34123919	.	+	.	Parent=gene184
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene184
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34128481	34128598	.	+	.	Parent=gene184
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene184
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34130615	34130806	.	+	.	Parent=gene184
chr21	.	intron	34130807	34131160	.	+	.	Parent=gene184
chr21	ENCODE	CDS	34131161	34131162	.	+	.	Parent=gene184
chr21	ENCODE	exon	34131161	34132670	.	+	.	Parent=gene184
###
chr21	ENCODE	gene	33936718	34029268	.	+	.	ID=gene185;Name=AP000313.6-032;name2=ITSN1
chr21	ENCODE	exon	33936718	33936889	.	+	.	Parent=gene185
chr21	.	intron	33936890	33983496	.	+	.	Parent=gene185
chr21	ENCODE	exon	33983497	33983558	.	+	.	Parent=gene185
chr21	.	intron	33983559	34012971	.	+	.	Parent=gene185
chr21	ENCODE	exon	34012972	34013031	.	+	.	Parent=gene185
chr21	ENCODE	CDS	34013004	34013031	.	+	.	Parent=gene185
chr21	.	intron	34013032	34015352	.	+	.	Parent=gene185
chr21	ENCODE	exon	34015353	34015445	.	+	.	Parent=gene185
chr21	ENCODE	CDS	34015353	34015445	.	+	.	Parent=gene185
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene185
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene185
chr21	ENCODE	CDS	34016763	34016826	.	+	.	Parent=gene185
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene185
chr21	ENCODE	exon	34029219	34029268	.	+	.	Parent=gene185
chr21	ENCODE	CDS	34029219	34029268	.	+	.	Parent=gene185
###
chr21	ENCODE	gene	34015412	34036947	.	+	.	ID=gene186;Name=AP000313.6-018;name2=ITSN1
chr21	ENCODE	exon	34015412	34015445	.	+	.	Parent=gene186
chr21	.	intron	34015446	34016762	.	+	.	Parent=gene186
chr21	ENCODE	exon	34016763	34016826	.	+	.	Parent=gene186
chr21	.	intron	34016827	34029218	.	+	.	Parent=gene186
chr21	ENCODE	exon	34029219	34030908	.	+	.	Parent=gene186
chr21	.	intron	34030909	34034991	.	+	.	Parent=gene186
chr21	ENCODE	exon	34034992	34035796	.	+	.	Parent=gene186
chr21	.	intron	34035797	34036516	.	+	.	Parent=gene186
chr21	ENCODE	exon	34036517	34036947	.	+	.	Parent=gene186
###
chr21	ENCODE	gene	34029216	34029801	.	+	.	ID=gene187;Name=AP000313.6-017;name2=ITSN1
chr21	ENCODE	exon	34029216	34029379	.	+	.	Parent=gene187
chr21	ENCODE	CDS	34029216	34029379	.	+	.	Parent=gene187
chr21	.	intron	34029380	34029480	.	+	.	Parent=gene187
chr21	ENCODE	CDS	34029481	34029497	.	+	.	Parent=gene187
chr21	ENCODE	exon	34029481	34029801	.	+	.	Parent=gene187
###
chr21	ENCODE	gene	34044454	34132672	.	+	.	ID=gene188;Name=AP000313.6-014;name2=ITSN1
chr21	ENCODE	exon	34044454	34044497	.	+	.	Parent=gene188
chr21	.	intron	34044498	34045984	.	+	.	Parent=gene188
chr21	ENCODE	exon	34045985	34046081	.	+	.	Parent=gene188
chr21	.	intron	34046082	34049471	.	+	.	Parent=gene188
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene188
chr21	.	intron	34049573	34056096	.	+	.	Parent=gene188
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene188
chr21	.	intron	34056161	34060048	.	+	.	Parent=gene188
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene188
chr21	.	intron	34060187	34061886	.	+	.	Parent=gene188
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene188
chr21	.	intron	34062003	34066234	.	+	.	Parent=gene188
chr21	ENCODE	exon	34066235	34066497	.	+	.	Parent=gene188
chr21	.	intron	34066498	34068902	.	+	.	Parent=gene188
chr21	ENCODE	exon	34068903	34069052	.	+	.	Parent=gene188
chr21	.	intron	34069053	34069141	.	+	.	Parent=gene188
chr21	ENCODE	exon	34069142	34069282	.	+	.	Parent=gene188
chr21	.	intron	34069283	34075634	.	+	.	Parent=gene188
chr21	ENCODE	exon	34075635	34075722	.	+	.	Parent=gene188
chr21	.	intron	34075723	34076167	.	+	.	Parent=gene188
chr21	ENCODE	exon	34076168	34076307	.	+	.	Parent=gene188
chr21	.	intron	34076308	34088514	.	+	.	Parent=gene188
chr21	ENCODE	exon	34088515	34088642	.	+	.	Parent=gene188
chr21	.	intron	34088643	34091552	.	+	.	Parent=gene188
chr21	ENCODE	exon	34091553	34091782	.	+	.	Parent=gene188
chr21	.	intron	34091783	34093981	.	+	.	Parent=gene188
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene188
chr21	.	intron	34094104	34105148	.	+	.	Parent=gene188
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene188
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene188
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene188
chr21	.	intron	34108247	34112440	.	+	.	Parent=gene188
chr21	ENCODE	exon	34112441	34112646	.	+	.	Parent=gene188
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene188
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene188
chr21	.	intron	34113498	34123797	.	+	.	Parent=gene188
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene188
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene188
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene188
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene188
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene188
chr21	.	intron	34130807	34131160	.	+	.	Parent=gene188
chr21	ENCODE	exon	34131161	34131197	.	+	.	Parent=gene188
chr21	.	intron	34131198	34131419	.	+	.	Parent=gene188
chr21	ENCODE	exon	34131420	34132672	.	+	.	Parent=gene188
###
chr21	ENCODE	gene	34048358	34066474	.	+	.	ID=gene189;Name=AP000313.6-019;name2=ITSN1
chr21	ENCODE	exon	34048358	34048397	.	+	.	Parent=gene189
chr21	.	intron	34048398	34049471	.	+	.	Parent=gene189
chr21	ENCODE	exon	34049472	34049572	.	+	.	Parent=gene189
chr21	.	intron	34049573	34050961	.	+	.	Parent=gene189
chr21	ENCODE	exon	34050962	34051248	.	+	.	Parent=gene189
chr21	.	intron	34051249	34056096	.	+	.	Parent=gene189
chr21	ENCODE	exon	34056097	34056160	.	+	.	Parent=gene189
chr21	.	intron	34056161	34060048	.	+	.	Parent=gene189
chr21	ENCODE	exon	34060049	34060186	.	+	.	Parent=gene189
chr21	.	intron	34060187	34061886	.	+	.	Parent=gene189
chr21	ENCODE	exon	34061887	34062002	.	+	.	Parent=gene189
chr21	.	intron	34062003	34066234	.	+	.	Parent=gene189
chr21	ENCODE	exon	34066235	34066474	.	+	.	Parent=gene189
###
chr21	ENCODE	gene	34068537	34069253	.	+	.	ID=gene190;Name=AP000313.6-021;name2=ITSN1
chr21	ENCODE	exon	34068537	34069052	.	+	.	Parent=gene190
chr21	.	intron	34069053	34069141	.	+	.	Parent=gene190
chr21	ENCODE	exon	34069142	34069253	.	+	.	Parent=gene190
###
chr21	ENCODE	gene	34091728	34111568	.	+	.	ID=gene191;Name=AP000313.6-029;name2=ITSN1
chr21	ENCODE	exon	34091728	34091782	.	+	.	Parent=gene191
chr21	.	intron	34091783	34093981	.	+	.	Parent=gene191
chr21	ENCODE	exon	34093982	34094103	.	+	.	Parent=gene191
chr21	.	intron	34094104	34096610	.	+	.	Parent=gene191
chr21	ENCODE	exon	34096611	34096618	.	+	.	Parent=gene191
chr21	.	intron	34096619	34105148	.	+	.	Parent=gene191
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene191
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene191
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene191
chr21	.	intron	34108247	34111404	.	+	.	Parent=gene191
chr21	ENCODE	exon	34111405	34111568	.	+	.	Parent=gene191
###
chr21	ENCODE	gene	34094097	34111910	.	+	.	ID=gene192;Name=AP000313.6-030;name2=ITSN1
chr21	ENCODE	exon	34094097	34094103	.	+	.	Parent=gene192
chr21	ENCODE	CDS	34094097	34094103	.	+	.	Parent=gene192
chr21	.	intron	34094104	34096603	.	+	.	Parent=gene192
chr21	ENCODE	exon	34096604	34096618	.	+	.	Parent=gene192
chr21	ENCODE	CDS	34096604	34096618	.	+	.	Parent=gene192
chr21	.	intron	34096619	34105148	.	+	.	Parent=gene192
chr21	ENCODE	exon	34105149	34105396	.	+	.	Parent=gene192
chr21	ENCODE	CDS	34105149	34105396	.	+	.	Parent=gene192
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene192
chr21	ENCODE	exon	34108087	34108246	.	+	.	Parent=gene192
chr21	ENCODE	CDS	34108087	34108246	.	+	.	Parent=gene192
chr21	.	intron	34108247	34111404	.	+	.	Parent=gene192
chr21	ENCODE	CDS	34111405	34111755	.	+	.	Parent=gene192
chr21	ENCODE	exon	34111405	34111910	.	+	.	Parent=gene192
###
chr21	ENCODE	gene	34105378	34108681	.	+	.	ID=gene193;Name=AP000313.6-035;name2=ITSN1
chr21	ENCODE	exon	34105378	34105396	.	+	.	Parent=gene193
chr21	.	intron	34105397	34108086	.	+	.	Parent=gene193
chr21	ENCODE	exon	34108087	34108681	.	+	.	Parent=gene193
###
chr21	ENCODE	gene	34112200	34123203	.	+	.	ID=gene194;Name=AP000313.6-007;name2=ITSN1
chr21	ENCODE	exon	34112200	34112646	.	+	.	Parent=gene194
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene194
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene194
chr21	.	intron	34113498	34117660	.	+	.	Parent=gene194
chr21	ENCODE	exon	34117661	34117827	.	+	.	Parent=gene194
chr21	.	intron	34117828	34120991	.	+	.	Parent=gene194
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene194
chr21	.	intron	34121038	34123141	.	+	.	Parent=gene194
chr21	ENCODE	exon	34123142	34123203	.	+	.	Parent=gene194
###
chr21	ENCODE	gene	34112557	34123203	.	+	.	ID=gene195;Name=AP000313.6-006;name2=ITSN1
chr21	ENCODE	exon	34112557	34112646	.	+	.	Parent=gene195
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene195
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene195
chr21	.	intron	34113498	34120991	.	+	.	Parent=gene195
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene195
chr21	.	intron	34121038	34123141	.	+	.	Parent=gene195
chr21	ENCODE	exon	34123142	34123203	.	+	.	Parent=gene195
###
chr21	ENCODE	gene	34112626	34123860	.	+	.	ID=gene196;Name=AP000313.6-016;name2=ITSN1
chr21	ENCODE	exon	34112626	34112646	.	+	.	Parent=gene196
chr21	.	intron	34112647	34113414	.	+	.	Parent=gene196
chr21	ENCODE	exon	34113415	34113497	.	+	.	Parent=gene196
chr21	.	intron	34113498	34120991	.	+	.	Parent=gene196
chr21	ENCODE	exon	34120992	34121037	.	+	.	Parent=gene196
chr21	.	intron	34121038	34123797	.	+	.	Parent=gene196
chr21	ENCODE	exon	34123798	34123860	.	+	.	Parent=gene196
###
chr21	ENCODE	gene	34120990	34128570	.	+	.	ID=gene197;Name=AP000313.6-022;name2=ITSN1
chr21	ENCODE	exon	34120990	34121037	.	+	.	Parent=gene197
chr21	.	intron	34121038	34123141	.	+	.	Parent=gene197
chr21	ENCODE	exon	34123142	34123224	.	+	.	Parent=gene197
chr21	.	intron	34123225	34123797	.	+	.	Parent=gene197
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene197
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene197
chr21	ENCODE	exon	34128481	34128570	.	+	.	Parent=gene197
###
chr21	ENCODE	gene	34123180	34131212	.	+	.	ID=gene198;Name=AP000313.6-010;name2=ITSN1
chr21	ENCODE	exon	34123180	34123342	.	+	.	Parent=gene198
chr21	.	intron	34123343	34123797	.	+	.	Parent=gene198
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene198
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene198
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene198
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene198
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene198
chr21	.	intron	34130807	34131160	.	+	.	Parent=gene198
chr21	ENCODE	exon	34131161	34131212	.	+	.	Parent=gene198
###
chr21	ENCODE	gene	34123180	34131212	.	+	.	ID=gene199;Name=AP000313.6-008;name2=ITSN1
chr21	ENCODE	exon	34123180	34123224	.	+	.	Parent=gene199
chr21	.	intron	34123225	34123797	.	+	.	Parent=gene199
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene199
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene199
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene199
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene199
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene199
chr21	.	intron	34130807	34131160	.	+	.	Parent=gene199
chr21	ENCODE	exon	34131161	34131212	.	+	.	Parent=gene199
###
chr21	ENCODE	gene	34123180	34131212	.	+	.	ID=gene200;Name=AP000313.6-013;name2=ITSN1
chr21	ENCODE	exon	34123180	34123919	.	+	.	Parent=gene200
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene200
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene200
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene200
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene200
chr21	.	intron	34130807	34131160	.	+	.	Parent=gene200
chr21	ENCODE	exon	34131161	34131212	.	+	.	Parent=gene200
###
chr21	ENCODE	gene	34123180	34150967	.	+	.	ID=gene201;Name=AP000313.6-012;name2=ITSN1
chr21	ENCODE	exon	34123180	34123919	.	+	.	Parent=gene201
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene201
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene201
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene201
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene201
chr21	.	intron	34130807	34150909	.	+	.	Parent=gene201
chr21	ENCODE	exon	34150910	34150967	.	+	.	Parent=gene201
###
chr21	ENCODE	gene	34123180	34150967	.	+	.	ID=gene202;Name=AP000313.6-011;name2=ITSN1
chr21	ENCODE	exon	34123180	34123919	.	+	.	Parent=gene202
chr21	.	intron	34123920	34150909	.	+	.	Parent=gene202
chr21	ENCODE	exon	34150910	34150967	.	+	.	Parent=gene202
###
chr21	ENCODE	gene	34123180	34150967	.	+	.	ID=gene203;Name=AP000313.6-009;name2=ITSN1
chr21	ENCODE	exon	34123180	34123224	.	+	.	Parent=gene203
chr21	.	intron	34123225	34123797	.	+	.	Parent=gene203
chr21	ENCODE	exon	34123798	34123919	.	+	.	Parent=gene203
chr21	.	intron	34123920	34128480	.	+	.	Parent=gene203
chr21	ENCODE	exon	34128481	34128598	.	+	.	Parent=gene203
chr21	.	intron	34128599	34130614	.	+	.	Parent=gene203
chr21	ENCODE	exon	34130615	34130806	.	+	.	Parent=gene203
chr21	.	intron	34130807	34150909	.	+	.	Parent=gene203
chr21	ENCODE	exon	34150910	34150967	.	+	.	Parent=gene203
###
chr21	ENCODE	gene	34152871	34180528	.	+	.	ID=gene204;Name=AP000313.6-004;name2=ITSN1
chr21	ENCODE	exon	34152871	34152966	.	+	.	Parent=gene204
chr21	ENCODE	CDS	34152871	34152966	.	+	.	Parent=gene204
chr21	.	intron	34152967	34159324	.	+	.	Parent=gene204
chr21	ENCODE	exon	34159325	34159508	.	+	.	Parent=gene204
chr21	ENCODE	CDS	34159325	34159508	.	+	.	Parent=gene204
chr21	.	intron	34159509	34161406	.	+	.	Parent=gene204
chr21	ENCODE	exon	34161407	34161505	.	+	.	Parent=gene204
chr21	ENCODE	CDS	34161407	34161505	.	+	.	Parent=gene204
chr21	.	intron	34161506	34176416	.	+	.	Parent=gene204
chr21	ENCODE	exon	34176417	34176629	.	+	.	Parent=gene204
chr21	ENCODE	CDS	34176417	34176629	.	+	.	Parent=gene204
chr21	.	intron	34176630	34177723	.	+	.	Parent=gene204
chr21	ENCODE	exon	34177724	34177845	.	+	.	Parent=gene204
chr21	ENCODE	CDS	34177724	34177845	.	+	.	Parent=gene204
chr21	.	intron	34177846	34179214	.	+	.	Parent=gene204
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene204
chr21	ENCODE	CDS	34179215	34179297	.	+	.	Parent=gene204
chr21	.	intron	34179298	34179612	.	+	.	Parent=gene204
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene204
chr21	ENCODE	CDS	34179613	34179696	.	+	.	Parent=gene204
chr21	.	intron	34179697	34180460	.	+	.	Parent=gene204
chr21	ENCODE	exon	34180461	34180528	.	+	.	Parent=gene204
chr21	ENCODE	CDS	34180461	34180528	.	+	.	Parent=gene204
###
chr21	ENCODE	gene	34169532	34180551	.	+	.	ID=gene205;Name=AP000313.6-031;name2=ITSN1
chr21	ENCODE	exon	34169532	34169695	.	+	.	Parent=gene205
chr21	.	intron	34169696	34179214	.	+	.	Parent=gene205
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene205
chr21	.	intron	34179298	34179612	.	+	.	Parent=gene205
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene205
chr21	.	intron	34179697	34180460	.	+	.	Parent=gene205
chr21	ENCODE	exon	34180461	34180551	.	+	.	Parent=gene205
###
chr21	ENCODE	gene	34169534	34180528	.	+	.	ID=gene206;Name=AP000313.6-005;name2=ITSN1
chr21	ENCODE	exon	34169534	34169695	.	+	.	Parent=gene206
chr21	ENCODE	CDS	34169534	34169695	.	+	.	Parent=gene206
chr21	.	intron	34169696	34177723	.	+	.	Parent=gene206
chr21	ENCODE	exon	34177724	34177845	.	+	.	Parent=gene206
chr21	ENCODE	CDS	34177724	34177845	.	+	.	Parent=gene206
chr21	.	intron	34177846	34179214	.	+	.	Parent=gene206
chr21	ENCODE	exon	34179215	34179297	.	+	.	Parent=gene206
chr21	ENCODE	CDS	34179215	34179297	.	+	.	Parent=gene206
chr21	.	intron	34179298	34179612	.	+	.	Parent=gene206
chr21	ENCODE	exon	34179613	34179696	.	+	.	Parent=gene206
chr21	ENCODE	CDS	34179613	34179696	.	+	.	Parent=gene206
chr21	.	intron	34179697	34180460	.	+	.	Parent=gene206
chr21	ENCODE	exon	34180461	34180528	.	+	.	Parent=gene206
chr21	ENCODE	CDS	34180461	34180528	.	+	.	Parent=gene206
###
chr21	ENCODE	gene	34197627	34199755	.	-	.	ID=gene207;Name=AP000313.5-006;name2=ATP5O
chr21	ENCODE	exon	34197627	34197813	.	-	.	Parent=gene207
chr21	.	intron	34197814	34198108	.	-	.	Parent=gene207
chr21	ENCODE	exon	34198109	34198748	.	-	.	Parent=gene207
chr21	.	intron	34198749	34198855	.	-	.	Parent=gene207
chr21	ENCODE	exon	34198856	34199755	.	-	.	Parent=gene207
###
chr21	ENCODE	gene	34197627	34209935	.	-	.	ID=gene208;Name=AP000313.5-003;name2=ATP5O
chr21	ENCODE	exon	34197627	34197813	.	-	.	Parent=gene208
chr21	.	intron	34197814	34198108	.	-	.	Parent=gene208
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene208
chr21	.	intron	34198196	34201514	.	-	.	Parent=gene208
chr21	ENCODE	exon	34201515	34201627	.	-	.	Parent=gene208
chr21	.	intron	34201628	34206462	.	-	.	Parent=gene208
chr21	ENCODE	exon	34206463	34206573	.	-	.	Parent=gene208
chr21	.	intron	34206574	34208623	.	-	.	Parent=gene208
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene208
chr21	.	intron	34208675	34209901	.	-	.	Parent=gene208
chr21	ENCODE	exon	34209902	34209935	.	-	.	Parent=gene208
###
chr21	ENCODE	gene	34197627	34209942	.	-	.	ID=gene209;Name=AP000313.5-002;name2=ATP5O
chr21	ENCODE	exon	34197627	34197813	.	-	.	Parent=gene209
chr21	.	intron	34197814	34198108	.	-	.	Parent=gene209
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene209
chr21	.	intron	34198196	34200622	.	-	.	Parent=gene209
chr21	ENCODE	exon	34200623	34201627	.	-	.	Parent=gene209
chr21	.	intron	34201628	34203255	.	-	.	Parent=gene209
chr21	ENCODE	exon	34203256	34203385	.	-	.	Parent=gene209
chr21	.	intron	34203386	34206462	.	-	.	Parent=gene209
chr21	ENCODE	exon	34206463	34206573	.	-	.	Parent=gene209
chr21	.	intron	34206574	34208623	.	-	.	Parent=gene209
chr21	ENCODE	exon	34208624	34209942	.	-	.	Parent=gene209
###
chr21	ENCODE	gene	34197627	34210154	.	-	.	ID=gene210;Name=AP000313.5-001;name2=ATP5O
chr21	ENCODE	exon	34197627	34197813	.	-	.	Parent=gene210
chr21	ENCODE	CDS	34197700	34197813	.	-	.	Parent=gene210
chr21	.	intron	34197814	34198108	.	-	.	Parent=gene210
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene210
chr21	ENCODE	CDS	34198109	34198195	.	-	.	Parent=gene210
chr21	.	intron	34198196	34201514	.	-	.	Parent=gene210
chr21	ENCODE	exon	34201515	34201627	.	-	.	Parent=gene210
chr21	ENCODE	CDS	34201515	34201627	.	-	.	Parent=gene210
chr21	.	intron	34201628	34203255	.	-	.	Parent=gene210
chr21	ENCODE	exon	34203256	34203385	.	-	.	Parent=gene210
chr21	ENCODE	CDS	34203256	34203385	.	-	.	Parent=gene210
chr21	.	intron	34203386	34206462	.	-	.	Parent=gene210
chr21	ENCODE	exon	34206463	34206573	.	-	.	Parent=gene210
chr21	ENCODE	CDS	34206463	34206573	.	-	.	Parent=gene210
chr21	.	intron	34206574	34208623	.	-	.	Parent=gene210
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene210
chr21	ENCODE	CDS	34208624	34208674	.	-	.	Parent=gene210
chr21	.	intron	34208675	34209901	.	-	.	Parent=gene210
chr21	ENCODE	CDS	34209902	34209937	.	-	.	Parent=gene210
chr21	ENCODE	exon	34209902	34210154	.	-	.	Parent=gene210
###
chr21	ENCODE	gene	34197630	34201586	.	-	.	ID=gene211;Name=AP000313.5-009;name2=ATP5O
chr21	ENCODE	exon	34197630	34197813	.	-	.	Parent=gene211
chr21	.	intron	34197814	34198108	.	-	.	Parent=gene211
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene211
chr21	.	intron	34198196	34200622	.	-	.	Parent=gene211
chr21	ENCODE	exon	34200623	34200674	.	-	.	Parent=gene211
chr21	.	intron	34200675	34200901	.	-	.	Parent=gene211
chr21	ENCODE	exon	34200902	34200968	.	-	.	Parent=gene211
chr21	.	intron	34200969	34201514	.	-	.	Parent=gene211
chr21	ENCODE	exon	34201515	34201586	.	-	.	Parent=gene211
###
chr21	ENCODE	gene	34197630	34203269	.	-	.	ID=gene212;Name=AP000313.5-010;name2=ATP5O
chr21	ENCODE	exon	34197630	34197830	.	-	.	Parent=gene212
chr21	ENCODE	CDS	34197786	34197830	.	-	.	Parent=gene212
chr21	.	intron	34197831	34198108	.	-	.	Parent=gene212
chr21	ENCODE	exon	34198109	34198195	.	-	.	Parent=gene212
chr21	ENCODE	CDS	34198109	34198195	.	-	.	Parent=gene212
chr21	.	intron	34198196	34201514	.	-	.	Parent=gene212
chr21	ENCODE	exon	34201515	34201627	.	-	.	Parent=gene212
chr21	ENCODE	CDS	34201515	34201627	.	-	.	Parent=gene212
chr21	.	intron	34201628	34203255	.	-	.	Parent=gene212
chr21	ENCODE	exon	34203256	34203269	.	-	.	Parent=gene212
chr21	ENCODE	CDS	34203256	34203269	.	-	.	Parent=gene212
###
chr21	ENCODE	gene	34202988	34209927	.	-	.	ID=gene213;Name=AP000313.5-004;name2=ATP5O
chr21	ENCODE	exon	34202988	34203385	.	-	.	Parent=gene213
chr21	.	intron	34203386	34206462	.	-	.	Parent=gene213
chr21	ENCODE	exon	34206463	34206573	.	-	.	Parent=gene213
chr21	.	intron	34206574	34208623	.	-	.	Parent=gene213
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene213
chr21	.	intron	34208675	34209901	.	-	.	Parent=gene213
chr21	ENCODE	exon	34209902	34209927	.	-	.	Parent=gene213
###
chr21	ENCODE	gene	34206541	34209898	.	-	.	ID=gene214;Name=AP000313.5-007;name2=ATP5O
chr21	ENCODE	exon	34206541	34206573	.	-	.	Parent=gene214
chr21	.	intron	34206574	34208623	.	-	.	Parent=gene214
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene214
chr21	.	intron	34208675	34209309	.	-	.	Parent=gene214
chr21	ENCODE	exon	34209310	34209898	.	-	.	Parent=gene214
###
chr21	ENCODE	gene	34206552	34209953	.	-	.	ID=gene215;Name=AP000313.5-008;name2=ATP5O
chr21	ENCODE	exon	34206552	34206573	.	-	.	Parent=gene215
chr21	.	intron	34206574	34208623	.	-	.	Parent=gene215
chr21	ENCODE	exon	34208624	34208674	.	-	.	Parent=gene215
chr21	.	intron	34208675	34209557	.	-	.	Parent=gene215
chr21	ENCODE	exon	34209558	34209953	.	-	.	Parent=gene215
###
chr21	ENCODE	gene	39468565	39477647	.	-	.	ID=gene216;Name=AF129408.12-001;name2=DSCR2
chr21	ENCODE	exon	39468565	39469460	.	-	.	Parent=gene216
chr21	ENCODE	CDS	39469386	39469460	.	-	.	Parent=gene216
chr21	.	intron	39469461	39471230	.	-	.	Parent=gene216
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene216
chr21	ENCODE	CDS	39471231	39471367	.	-	.	Parent=gene216
chr21	.	intron	39471368	39472244	.	-	.	Parent=gene216
chr21	ENCODE	exon	39472245	39472443	.	-	.	Parent=gene216
chr21	ENCODE	CDS	39472245	39472443	.	-	.	Parent=gene216
chr21	.	intron	39472444	39473719	.	-	.	Parent=gene216
chr21	ENCODE	exon	39473720	39473782	.	-	.	Parent=gene216
chr21	ENCODE	CDS	39473720	39473782	.	-	.	Parent=gene216
chr21	.	intron	39473783	39474080	.	-	.	Parent=gene216
chr21	ENCODE	exon	39474081	39474232	.	-	.	Parent=gene216
chr21	ENCODE	CDS	39474081	39474232	.	-	.	Parent=gene216
chr21	.	intron	39474233	39475567	.	-	.	Parent=gene216
chr21	ENCODE	exon	39475568	39475674	.	-	.	Parent=gene216
chr21	ENCODE	CDS	39475568	39475674	.	-	.	Parent=gene216
chr21	.	intron	39475675	39477047	.	-	.	Parent=gene216
chr21	ENCODE	CDS	39477048	39477181	.	-	.	Parent=gene216
chr21	ENCODE	exon	39477048	39477647	.	-	.	Parent=gene216
###
chr21	ENCODE	gene	39469254	39472616	.	-	.	ID=gene217;Name=AF129408.12-004;name2=DSCR2
chr21	ENCODE	exon	39469254	39469460	.	-	.	Parent=gene217
chr21	.	intron	39469461	39471230	.	-	.	Parent=gene217
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene217
chr21	.	intron	39471368	39472244	.	-	.	Parent=gene217
chr21	ENCODE	exon	39472245	39472616	.	-	.	Parent=gene217
###
chr21	ENCODE	gene	39469254	39474234	.	-	.	ID=gene218;Name=AF129408.12-003;name2=DSCR2
chr21	ENCODE	exon	39469254	39469460	.	-	.	Parent=gene218
chr21	ENCODE	CDS	39469386	39469460	.	-	.	Parent=gene218
chr21	.	intron	39469461	39471230	.	-	.	Parent=gene218
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene218
chr21	ENCODE	CDS	39471231	39471367	.	-	.	Parent=gene218
chr21	.	intron	39471368	39472244	.	-	.	Parent=gene218
chr21	ENCODE	exon	39472245	39472314	.	-	.	Parent=gene218
chr21	ENCODE	CDS	39472245	39472314	.	-	.	Parent=gene218
chr21	.	intron	39472315	39474080	.	-	.	Parent=gene218
chr21	ENCODE	exon	39474081	39474234	.	-	.	Parent=gene218
chr21	ENCODE	CDS	39474081	39474234	.	-	.	Parent=gene218
###
chr21	ENCODE	gene	39469384	39477083	.	-	.	ID=gene219;Name=AF129408.12-005;name2=DSCR2
chr21	ENCODE	exon	39469384	39469460	.	-	.	Parent=gene219
chr21	.	intron	39469461	39471230	.	-	.	Parent=gene219
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene219
chr21	.	intron	39471368	39472244	.	-	.	Parent=gene219
chr21	ENCODE	exon	39472245	39472443	.	-	.	Parent=gene219
chr21	.	intron	39472444	39473719	.	-	.	Parent=gene219
chr21	ENCODE	exon	39473720	39473782	.	-	.	Parent=gene219
chr21	.	intron	39473783	39474080	.	-	.	Parent=gene219
chr21	ENCODE	exon	39474081	39474232	.	-	.	Parent=gene219
chr21	.	intron	39474233	39475567	.	-	.	Parent=gene219
chr21	ENCODE	exon	39475568	39475674	.	-	.	Parent=gene219
chr21	.	intron	39475675	39476859	.	-	.	Parent=gene219
chr21	ENCODE	exon	39476860	39477083	.	-	.	Parent=gene219
###
chr21	ENCODE	gene	39469386	39477181	.	-	.	ID=gene220;Name=AF129408.12-006;name2=DSCR2
chr21	ENCODE	exon	39469386	39469460	.	-	.	Parent=gene220
chr21	.	intron	39469461	39471230	.	-	.	Parent=gene220
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene220
chr21	.	intron	39471368	39472244	.	-	.	Parent=gene220
chr21	ENCODE	exon	39472245	39472443	.	-	.	Parent=gene220
chr21	.	intron	39472444	39473719	.	-	.	Parent=gene220
chr21	ENCODE	exon	39473720	39473782	.	-	.	Parent=gene220
chr21	.	intron	39473783	39474080	.	-	.	Parent=gene220
chr21	ENCODE	exon	39474081	39474232	.	-	.	Parent=gene220
chr21	.	intron	39474233	39477047	.	-	.	Parent=gene220
chr21	ENCODE	exon	39477048	39477181	.	-	.	Parent=gene220
###
chr21	ENCODE	gene	39469386	39477284	.	-	.	ID=gene221;Name=AF129408.12-002;name2=DSCR2
chr21	ENCODE	exon	39469386	39469460	.	-	.	Parent=gene221
chr21	ENCODE	CDS	39469386	39469460	.	-	.	Parent=gene221
chr21	.	intron	39469461	39471230	.	-	.	Parent=gene221
chr21	ENCODE	exon	39471231	39471367	.	-	.	Parent=gene221
chr21	ENCODE	CDS	39471231	39471367	.	-	.	Parent=gene221
chr21	.	intron	39471368	39472244	.	-	.	Parent=gene221
chr21	ENCODE	exon	39472245	39472443	.	-	.	Parent=gene221
chr21	ENCODE	CDS	39472245	39472443	.	-	.	Parent=gene221
chr21	.	intron	39472444	39474080	.	-	.	Parent=gene221
chr21	ENCODE	exon	39474081	39474232	.	-	.	Parent=gene221
chr21	ENCODE	CDS	39474081	39474232	.	-	.	Parent=gene221
chr21	.	intron	39474233	39475567	.	-	.	Parent=gene221
chr21	ENCODE	exon	39475568	39475674	.	-	.	Parent=gene221
chr21	ENCODE	CDS	39475568	39475674	.	-	.	Parent=gene221
chr21	.	intron	39475675	39477047	.	-	.	Parent=gene221
chr21	ENCODE	CDS	39477048	39477181	.	-	.	Parent=gene221
chr21	ENCODE	exon	39477048	39477284	.	-	.	Parent=gene221
###
chr21	ENCODE	gene	39477972	39607366	.	-	.	ID=gene222;Name=AF129408.13-001;name2=BRWD1
chr21	ENCODE	exon	39477972	39481213	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39480822	39481213	.	-	.	Parent=gene222
chr21	.	intron	39481214	39490293	.	-	.	Parent=gene222
chr21	ENCODE	exon	39490294	39491211	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39490294	39491211	.	-	.	Parent=gene222
chr21	.	intron	39491212	39492558	.	-	.	Parent=gene222
chr21	ENCODE	exon	39492559	39493458	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39492559	39493458	.	-	.	Parent=gene222
chr21	.	intron	39493459	39494014	.	-	.	Parent=gene222
chr21	ENCODE	exon	39494015	39494182	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39494015	39494182	.	-	.	Parent=gene222
chr21	.	intron	39494183	39496120	.	-	.	Parent=gene222
chr21	ENCODE	exon	39496121	39496341	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39496121	39496341	.	-	.	Parent=gene222
chr21	.	intron	39496342	39499903	.	-	.	Parent=gene222
chr21	ENCODE	exon	39499904	39500070	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39499904	39500070	.	-	.	Parent=gene222
chr21	.	intron	39500071	39503790	.	-	.	Parent=gene222
chr21	ENCODE	exon	39503791	39503943	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39503791	39503943	.	-	.	Parent=gene222
chr21	.	intron	39503944	39504581	.	-	.	Parent=gene222
chr21	ENCODE	exon	39504582	39504725	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39504582	39504725	.	-	.	Parent=gene222
chr21	.	intron	39504726	39506461	.	-	.	Parent=gene222
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39506462	39506503	.	-	.	Parent=gene222
chr21	.	intron	39506504	39507276	.	-	.	Parent=gene222
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39507277	39507349	.	-	.	Parent=gene222
chr21	.	intron	39507350	39509032	.	-	.	Parent=gene222
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39509033	39509158	.	-	.	Parent=gene222
chr21	.	intron	39509159	39511947	.	-	.	Parent=gene222
chr21	ENCODE	exon	39511948	39512068	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39511948	39512068	.	-	.	Parent=gene222
chr21	.	intron	39512069	39512300	.	-	.	Parent=gene222
chr21	ENCODE	exon	39512301	39512456	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39512301	39512456	.	-	.	Parent=gene222
chr21	.	intron	39512457	39518203	.	-	.	Parent=gene222
chr21	ENCODE	exon	39518204	39518265	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39518204	39518265	.	-	.	Parent=gene222
chr21	.	intron	39518266	39518881	.	-	.	Parent=gene222
chr21	ENCODE	exon	39518882	39518993	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39518882	39518993	.	-	.	Parent=gene222
chr21	.	intron	39518994	39522295	.	-	.	Parent=gene222
chr21	ENCODE	exon	39522296	39522378	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39522296	39522378	.	-	.	Parent=gene222
chr21	.	intron	39522379	39523107	.	-	.	Parent=gene222
chr21	ENCODE	exon	39523108	39523232	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39523108	39523232	.	-	.	Parent=gene222
chr21	.	intron	39523233	39525972	.	-	.	Parent=gene222
chr21	ENCODE	exon	39525973	39526080	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39525973	39526080	.	-	.	Parent=gene222
chr21	.	intron	39526081	39526168	.	-	.	Parent=gene222
chr21	ENCODE	exon	39526169	39526294	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39526169	39526294	.	-	.	Parent=gene222
chr21	.	intron	39526295	39530390	.	-	.	Parent=gene222
chr21	ENCODE	exon	39530391	39530580	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39530391	39530580	.	-	.	Parent=gene222
chr21	.	intron	39530581	39532274	.	-	.	Parent=gene222
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39532275	39532369	.	-	.	Parent=gene222
chr21	.	intron	39532370	39541496	.	-	.	Parent=gene222
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39541497	39541628	.	-	.	Parent=gene222
chr21	.	intron	39541629	39544591	.	-	.	Parent=gene222
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39544592	39544685	.	-	.	Parent=gene222
chr21	.	intron	39544686	39549440	.	-	.	Parent=gene222
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39549441	39549624	.	-	.	Parent=gene222
chr21	.	intron	39549625	39552282	.	-	.	Parent=gene222
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39552283	39552468	.	-	.	Parent=gene222
chr21	.	intron	39552469	39558255	.	-	.	Parent=gene222
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39558256	39558481	.	-	.	Parent=gene222
chr21	.	intron	39558482	39558686	.	-	.	Parent=gene222
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39558687	39558815	.	-	.	Parent=gene222
chr21	.	intron	39558816	39563694	.	-	.	Parent=gene222
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39563695	39563829	.	-	.	Parent=gene222
chr21	.	intron	39563830	39564078	.	-	.	Parent=gene222
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39564079	39564229	.	-	.	Parent=gene222
chr21	.	intron	39564230	39568169	.	-	.	Parent=gene222
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39568170	39568268	.	-	.	Parent=gene222
chr21	.	intron	39568269	39569968	.	-	.	Parent=gene222
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39569969	39570009	.	-	.	Parent=gene222
chr21	.	intron	39570010	39571046	.	-	.	Parent=gene222
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39571047	39571147	.	-	.	Parent=gene222
chr21	.	intron	39571148	39572538	.	-	.	Parent=gene222
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39572539	39572609	.	-	.	Parent=gene222
chr21	.	intron	39572610	39573943	.	-	.	Parent=gene222
chr21	ENCODE	exon	39573944	39574044	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39573944	39574044	.	-	.	Parent=gene222
chr21	.	intron	39574045	39587606	.	-	.	Parent=gene222
chr21	ENCODE	exon	39587607	39587828	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39587607	39587828	.	-	.	Parent=gene222
chr21	.	intron	39587829	39589538	.	-	.	Parent=gene222
chr21	ENCODE	exon	39589539	39589699	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39589539	39589699	.	-	.	Parent=gene222
chr21	.	intron	39589700	39590060	.	-	.	Parent=gene222
chr21	ENCODE	exon	39590061	39590159	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39590061	39590159	.	-	.	Parent=gene222
chr21	.	intron	39590160	39592227	.	-	.	Parent=gene222
chr21	ENCODE	exon	39592228	39592378	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39592228	39592378	.	-	.	Parent=gene222
chr21	.	intron	39592379	39606636	.	-	.	Parent=gene222
chr21	ENCODE	exon	39606637	39606696	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39606637	39606696	.	-	.	Parent=gene222
chr21	.	intron	39606697	39606867	.	-	.	Parent=gene222
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39606868	39606897	.	-	.	Parent=gene222
chr21	.	intron	39606898	39607036	.	-	.	Parent=gene222
chr21	ENCODE	exon	39607037	39607095	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39607037	39607095	.	-	.	Parent=gene222
chr21	.	intron	39607096	39607238	.	-	.	Parent=gene222
chr21	ENCODE	CDS	39607239	39607287	.	-	.	Parent=gene222
chr21	ENCODE	exon	39607239	39607366	.	-	.	Parent=gene222
###
chr21	ENCODE	gene	39481042	39558737	.	-	.	ID=gene223;Name=AF129408.13-009;name2=BRWD1
chr21	ENCODE	exon	39481042	39481213	.	-	.	Parent=gene223
chr21	.	intron	39481214	39490293	.	-	.	Parent=gene223
chr21	ENCODE	exon	39490294	39491211	.	-	.	Parent=gene223
chr21	.	intron	39491212	39492558	.	-	.	Parent=gene223
chr21	ENCODE	exon	39492559	39493458	.	-	.	Parent=gene223
chr21	.	intron	39493459	39494014	.	-	.	Parent=gene223
chr21	ENCODE	exon	39494015	39494182	.	-	.	Parent=gene223
chr21	.	intron	39494183	39496120	.	-	.	Parent=gene223
chr21	ENCODE	exon	39496121	39496341	.	-	.	Parent=gene223
chr21	.	intron	39496342	39499903	.	-	.	Parent=gene223
chr21	ENCODE	exon	39499904	39500070	.	-	.	Parent=gene223
chr21	.	intron	39500071	39503790	.	-	.	Parent=gene223
chr21	ENCODE	exon	39503791	39503943	.	-	.	Parent=gene223
chr21	.	intron	39503944	39504581	.	-	.	Parent=gene223
chr21	ENCODE	exon	39504582	39504725	.	-	.	Parent=gene223
chr21	.	intron	39504726	39506461	.	-	.	Parent=gene223
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene223
chr21	.	intron	39506504	39507276	.	-	.	Parent=gene223
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene223
chr21	.	intron	39507350	39509032	.	-	.	Parent=gene223
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene223
chr21	.	intron	39509159	39512324	.	-	.	Parent=gene223
chr21	ENCODE	exon	39512325	39512456	.	-	.	Parent=gene223
chr21	.	intron	39512457	39518203	.	-	.	Parent=gene223
chr21	ENCODE	exon	39518204	39518265	.	-	.	Parent=gene223
chr21	.	intron	39518266	39518881	.	-	.	Parent=gene223
chr21	ENCODE	exon	39518882	39518993	.	-	.	Parent=gene223
chr21	.	intron	39518994	39522295	.	-	.	Parent=gene223
chr21	ENCODE	exon	39522296	39522378	.	-	.	Parent=gene223
chr21	.	intron	39522379	39523107	.	-	.	Parent=gene223
chr21	ENCODE	exon	39523108	39523232	.	-	.	Parent=gene223
chr21	.	intron	39523233	39525972	.	-	.	Parent=gene223
chr21	ENCODE	exon	39525973	39526080	.	-	.	Parent=gene223
chr21	.	intron	39526081	39526168	.	-	.	Parent=gene223
chr21	ENCODE	exon	39526169	39526294	.	-	.	Parent=gene223
chr21	.	intron	39526295	39530390	.	-	.	Parent=gene223
chr21	ENCODE	exon	39530391	39530580	.	-	.	Parent=gene223
chr21	.	intron	39530581	39532274	.	-	.	Parent=gene223
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene223
chr21	.	intron	39532370	39541496	.	-	.	Parent=gene223
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene223
chr21	.	intron	39541629	39544591	.	-	.	Parent=gene223
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene223
chr21	.	intron	39544686	39549440	.	-	.	Parent=gene223
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene223
chr21	.	intron	39549625	39552282	.	-	.	Parent=gene223
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene223
chr21	.	intron	39552469	39558255	.	-	.	Parent=gene223
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene223
chr21	.	intron	39558482	39558686	.	-	.	Parent=gene223
chr21	ENCODE	exon	39558687	39558737	.	-	.	Parent=gene223
###
chr21	ENCODE	gene	39484015	39607366	.	-	.	ID=gene224;Name=AF129408.13-002;name2=BRWD1
chr21	ENCODE	exon	39484015	39491211	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39490055	39491211	.	-	.	Parent=gene224
chr21	.	intron	39491212	39492558	.	-	.	Parent=gene224
chr21	ENCODE	exon	39492559	39493458	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39492559	39493458	.	-	.	Parent=gene224
chr21	.	intron	39493459	39494014	.	-	.	Parent=gene224
chr21	ENCODE	exon	39494015	39494182	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39494015	39494182	.	-	.	Parent=gene224
chr21	.	intron	39494183	39496120	.	-	.	Parent=gene224
chr21	ENCODE	exon	39496121	39496341	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39496121	39496341	.	-	.	Parent=gene224
chr21	.	intron	39496342	39499903	.	-	.	Parent=gene224
chr21	ENCODE	exon	39499904	39500070	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39499904	39500070	.	-	.	Parent=gene224
chr21	.	intron	39500071	39503790	.	-	.	Parent=gene224
chr21	ENCODE	exon	39503791	39503943	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39503791	39503943	.	-	.	Parent=gene224
chr21	.	intron	39503944	39504581	.	-	.	Parent=gene224
chr21	ENCODE	exon	39504582	39504725	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39504582	39504725	.	-	.	Parent=gene224
chr21	.	intron	39504726	39506461	.	-	.	Parent=gene224
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39506462	39506503	.	-	.	Parent=gene224
chr21	.	intron	39506504	39507276	.	-	.	Parent=gene224
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39507277	39507349	.	-	.	Parent=gene224
chr21	.	intron	39507350	39509032	.	-	.	Parent=gene224
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39509033	39509158	.	-	.	Parent=gene224
chr21	.	intron	39509159	39511947	.	-	.	Parent=gene224
chr21	ENCODE	exon	39511948	39512068	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39511948	39512068	.	-	.	Parent=gene224
chr21	.	intron	39512069	39512300	.	-	.	Parent=gene224
chr21	ENCODE	exon	39512301	39512456	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39512301	39512456	.	-	.	Parent=gene224
chr21	.	intron	39512457	39518203	.	-	.	Parent=gene224
chr21	ENCODE	exon	39518204	39518265	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39518204	39518265	.	-	.	Parent=gene224
chr21	.	intron	39518266	39518881	.	-	.	Parent=gene224
chr21	ENCODE	exon	39518882	39518993	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39518882	39518993	.	-	.	Parent=gene224
chr21	.	intron	39518994	39522295	.	-	.	Parent=gene224
chr21	ENCODE	exon	39522296	39522378	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39522296	39522378	.	-	.	Parent=gene224
chr21	.	intron	39522379	39523107	.	-	.	Parent=gene224
chr21	ENCODE	exon	39523108	39523232	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39523108	39523232	.	-	.	Parent=gene224
chr21	.	intron	39523233	39525972	.	-	.	Parent=gene224
chr21	ENCODE	exon	39525973	39526080	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39525973	39526080	.	-	.	Parent=gene224
chr21	.	intron	39526081	39526168	.	-	.	Parent=gene224
chr21	ENCODE	exon	39526169	39526294	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39526169	39526294	.	-	.	Parent=gene224
chr21	.	intron	39526295	39530390	.	-	.	Parent=gene224
chr21	ENCODE	exon	39530391	39530580	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39530391	39530580	.	-	.	Parent=gene224
chr21	.	intron	39530581	39532274	.	-	.	Parent=gene224
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39532275	39532369	.	-	.	Parent=gene224
chr21	.	intron	39532370	39541496	.	-	.	Parent=gene224
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39541497	39541628	.	-	.	Parent=gene224
chr21	.	intron	39541629	39544591	.	-	.	Parent=gene224
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39544592	39544685	.	-	.	Parent=gene224
chr21	.	intron	39544686	39549440	.	-	.	Parent=gene224
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39549441	39549624	.	-	.	Parent=gene224
chr21	.	intron	39549625	39552282	.	-	.	Parent=gene224
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39552283	39552468	.	-	.	Parent=gene224
chr21	.	intron	39552469	39558255	.	-	.	Parent=gene224
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39558256	39558481	.	-	.	Parent=gene224
chr21	.	intron	39558482	39558686	.	-	.	Parent=gene224
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39558687	39558815	.	-	.	Parent=gene224
chr21	.	intron	39558816	39563694	.	-	.	Parent=gene224
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39563695	39563829	.	-	.	Parent=gene224
chr21	.	intron	39563830	39564078	.	-	.	Parent=gene224
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39564079	39564229	.	-	.	Parent=gene224
chr21	.	intron	39564230	39568169	.	-	.	Parent=gene224
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39568170	39568268	.	-	.	Parent=gene224
chr21	.	intron	39568269	39569968	.	-	.	Parent=gene224
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39569969	39570009	.	-	.	Parent=gene224
chr21	.	intron	39570010	39571046	.	-	.	Parent=gene224
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39571047	39571147	.	-	.	Parent=gene224
chr21	.	intron	39571148	39572538	.	-	.	Parent=gene224
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39572539	39572609	.	-	.	Parent=gene224
chr21	.	intron	39572610	39573943	.	-	.	Parent=gene224
chr21	ENCODE	exon	39573944	39574044	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39573944	39574044	.	-	.	Parent=gene224
chr21	.	intron	39574045	39587606	.	-	.	Parent=gene224
chr21	ENCODE	exon	39587607	39587828	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39587607	39587828	.	-	.	Parent=gene224
chr21	.	intron	39587829	39589538	.	-	.	Parent=gene224
chr21	ENCODE	exon	39589539	39589699	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39589539	39589699	.	-	.	Parent=gene224
chr21	.	intron	39589700	39590060	.	-	.	Parent=gene224
chr21	ENCODE	exon	39590061	39590159	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39590061	39590159	.	-	.	Parent=gene224
chr21	.	intron	39590160	39592227	.	-	.	Parent=gene224
chr21	ENCODE	exon	39592228	39592378	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39592228	39592378	.	-	.	Parent=gene224
chr21	.	intron	39592379	39606636	.	-	.	Parent=gene224
chr21	ENCODE	exon	39606637	39606696	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39606637	39606696	.	-	.	Parent=gene224
chr21	.	intron	39606697	39606867	.	-	.	Parent=gene224
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39606868	39606897	.	-	.	Parent=gene224
chr21	.	intron	39606898	39607036	.	-	.	Parent=gene224
chr21	ENCODE	exon	39607037	39607095	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39607037	39607095	.	-	.	Parent=gene224
chr21	.	intron	39607096	39607238	.	-	.	Parent=gene224
chr21	ENCODE	CDS	39607239	39607287	.	-	.	Parent=gene224
chr21	ENCODE	exon	39607239	39607366	.	-	.	Parent=gene224
###
chr21	ENCODE	gene	39493215	39494292	.	-	.	ID=gene225;Name=AF129408.13-007;name2=BRWD1
chr21	ENCODE	exon	39493215	39493458	.	-	.	Parent=gene225
chr21	.	intron	39493459	39494014	.	-	.	Parent=gene225
chr21	ENCODE	exon	39494015	39494292	.	-	.	Parent=gene225
###
chr21	ENCODE	gene	39496162	39523188	.	-	.	ID=gene226;Name=AF129408.13-010;name2=BRWD1
chr21	ENCODE	exon	39496162	39496341	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39496162	39496341	.	-	.	Parent=gene226
chr21	.	intron	39496342	39499903	.	-	.	Parent=gene226
chr21	ENCODE	exon	39499904	39500070	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39499904	39500070	.	-	.	Parent=gene226
chr21	.	intron	39500071	39503790	.	-	.	Parent=gene226
chr21	ENCODE	exon	39503791	39503943	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39503791	39503943	.	-	.	Parent=gene226
chr21	.	intron	39503944	39506461	.	-	.	Parent=gene226
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39506462	39506503	.	-	.	Parent=gene226
chr21	.	intron	39506504	39507276	.	-	.	Parent=gene226
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39507277	39507349	.	-	.	Parent=gene226
chr21	.	intron	39507350	39509032	.	-	.	Parent=gene226
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39509033	39509158	.	-	.	Parent=gene226
chr21	.	intron	39509159	39511947	.	-	.	Parent=gene226
chr21	ENCODE	exon	39511948	39512068	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39511948	39512068	.	-	.	Parent=gene226
chr21	.	intron	39512069	39512300	.	-	.	Parent=gene226
chr21	ENCODE	exon	39512301	39512456	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39512301	39512456	.	-	.	Parent=gene226
chr21	.	intron	39512457	39518203	.	-	.	Parent=gene226
chr21	ENCODE	exon	39518204	39518265	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39518204	39518265	.	-	.	Parent=gene226
chr21	.	intron	39518266	39518881	.	-	.	Parent=gene226
chr21	ENCODE	exon	39518882	39518993	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39518882	39518993	.	-	.	Parent=gene226
chr21	.	intron	39518994	39522295	.	-	.	Parent=gene226
chr21	ENCODE	exon	39522296	39522378	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39522296	39522378	.	-	.	Parent=gene226
chr21	.	intron	39522379	39523107	.	-	.	Parent=gene226
chr21	ENCODE	exon	39523108	39523188	.	-	.	Parent=gene226
chr21	ENCODE	CDS	39523108	39523188	.	-	.	Parent=gene226
###
chr21	ENCODE	gene	39503582	39512456	.	-	.	ID=gene227;Name=AF129408.13-006;name2=BRWD1
chr21	ENCODE	exon	39503582	39503943	.	-	.	Parent=gene227
chr21	.	intron	39503944	39504661	.	-	.	Parent=gene227
chr21	ENCODE	exon	39504662	39504725	.	-	.	Parent=gene227
chr21	.	intron	39504726	39506461	.	-	.	Parent=gene227
chr21	ENCODE	exon	39506462	39506503	.	-	.	Parent=gene227
chr21	.	intron	39506504	39507276	.	-	.	Parent=gene227
chr21	ENCODE	exon	39507277	39507349	.	-	.	Parent=gene227
chr21	.	intron	39507350	39509032	.	-	.	Parent=gene227
chr21	ENCODE	exon	39509033	39509158	.	-	.	Parent=gene227
chr21	.	intron	39509159	39511947	.	-	.	Parent=gene227
chr21	ENCODE	exon	39511948	39512068	.	-	.	Parent=gene227
chr21	.	intron	39512069	39512300	.	-	.	Parent=gene227
chr21	ENCODE	exon	39512301	39512456	.	-	.	Parent=gene227
###
chr21	ENCODE	gene	39530514	39574009	.	-	.	ID=gene228;Name=AF129408.13-011;name2=BRWD1
chr21	ENCODE	exon	39530514	39530580	.	-	.	Parent=gene228
chr21	.	intron	39530581	39532274	.	-	.	Parent=gene228
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene228
chr21	.	intron	39532370	39541496	.	-	.	Parent=gene228
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene228
chr21	.	intron	39541629	39544591	.	-	.	Parent=gene228
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene228
chr21	.	intron	39544686	39552282	.	-	.	Parent=gene228
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene228
chr21	.	intron	39552469	39558255	.	-	.	Parent=gene228
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene228
chr21	.	intron	39558482	39558686	.	-	.	Parent=gene228
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene228
chr21	.	intron	39558816	39563694	.	-	.	Parent=gene228
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene228
chr21	.	intron	39563830	39564078	.	-	.	Parent=gene228
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene228
chr21	.	intron	39564230	39568169	.	-	.	Parent=gene228
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene228
chr21	.	intron	39568269	39569968	.	-	.	Parent=gene228
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene228
chr21	.	intron	39570010	39571046	.	-	.	Parent=gene228
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene228
chr21	.	intron	39571148	39572538	.	-	.	Parent=gene228
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene228
chr21	.	intron	39572610	39573943	.	-	.	Parent=gene228
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene228
###
chr21	ENCODE	gene	39530514	39574009	.	-	.	ID=gene229;Name=AF129408.13-012;name2=BRWD1
chr21	ENCODE	exon	39530514	39530580	.	-	.	Parent=gene229
chr21	.	intron	39530581	39532274	.	-	.	Parent=gene229
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene229
chr21	.	intron	39532370	39541496	.	-	.	Parent=gene229
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene229
chr21	.	intron	39541629	39544591	.	-	.	Parent=gene229
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene229
chr21	.	intron	39544686	39549440	.	-	.	Parent=gene229
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene229
chr21	.	intron	39549625	39552282	.	-	.	Parent=gene229
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene229
chr21	.	intron	39552469	39558255	.	-	.	Parent=gene229
chr21	ENCODE	exon	39558256	39558360	.	-	.	Parent=gene229
chr21	.	intron	39558361	39558686	.	-	.	Parent=gene229
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene229
chr21	.	intron	39558816	39563694	.	-	.	Parent=gene229
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene229
chr21	.	intron	39563830	39564078	.	-	.	Parent=gene229
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene229
chr21	.	intron	39564230	39568169	.	-	.	Parent=gene229
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene229
chr21	.	intron	39568269	39569968	.	-	.	Parent=gene229
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene229
chr21	.	intron	39570010	39571046	.	-	.	Parent=gene229
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene229
chr21	.	intron	39571148	39572538	.	-	.	Parent=gene229
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene229
chr21	.	intron	39572610	39573943	.	-	.	Parent=gene229
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene229
###
chr21	ENCODE	gene	39530514	39574009	.	-	.	ID=gene230;Name=AF129408.13-013;name2=BRWD1
chr21	ENCODE	exon	39530514	39530580	.	-	.	Parent=gene230
chr21	.	intron	39530581	39532274	.	-	.	Parent=gene230
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene230
chr21	.	intron	39532370	39541496	.	-	.	Parent=gene230
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene230
chr21	.	intron	39541629	39544591	.	-	.	Parent=gene230
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene230
chr21	.	intron	39544686	39549440	.	-	.	Parent=gene230
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene230
chr21	.	intron	39549625	39552282	.	-	.	Parent=gene230
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene230
chr21	.	intron	39552469	39558255	.	-	.	Parent=gene230
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene230
chr21	.	intron	39558482	39558781	.	-	.	Parent=gene230
chr21	ENCODE	exon	39558782	39558815	.	-	.	Parent=gene230
chr21	.	intron	39558816	39563694	.	-	.	Parent=gene230
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene230
chr21	.	intron	39563830	39564078	.	-	.	Parent=gene230
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene230
chr21	.	intron	39564230	39568169	.	-	.	Parent=gene230
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene230
chr21	.	intron	39568269	39569968	.	-	.	Parent=gene230
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene230
chr21	.	intron	39570010	39571046	.	-	.	Parent=gene230
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene230
chr21	.	intron	39571148	39572538	.	-	.	Parent=gene230
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene230
chr21	.	intron	39572610	39573943	.	-	.	Parent=gene230
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene230
###
chr21	ENCODE	gene	39530515	39574009	.	-	.	ID=gene231;Name=AF129408.13-014;name2=BRWD1
chr21	ENCODE	exon	39530515	39530580	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39530515	39530580	.	-	.	Parent=gene231
chr21	.	intron	39530581	39532274	.	-	.	Parent=gene231
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39532275	39532369	.	-	.	Parent=gene231
chr21	.	intron	39532370	39544591	.	-	.	Parent=gene231
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39544592	39544685	.	-	.	Parent=gene231
chr21	.	intron	39544686	39549440	.	-	.	Parent=gene231
chr21	ENCODE	exon	39549441	39549624	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39549441	39549624	.	-	.	Parent=gene231
chr21	.	intron	39549625	39552282	.	-	.	Parent=gene231
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39552283	39552468	.	-	.	Parent=gene231
chr21	.	intron	39552469	39558255	.	-	.	Parent=gene231
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39558256	39558481	.	-	.	Parent=gene231
chr21	.	intron	39558482	39558686	.	-	.	Parent=gene231
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39558687	39558815	.	-	.	Parent=gene231
chr21	.	intron	39558816	39563694	.	-	.	Parent=gene231
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39563695	39563829	.	-	.	Parent=gene231
chr21	.	intron	39563830	39564078	.	-	.	Parent=gene231
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39564079	39564229	.	-	.	Parent=gene231
chr21	.	intron	39564230	39568169	.	-	.	Parent=gene231
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39568170	39568268	.	-	.	Parent=gene231
chr21	.	intron	39568269	39569968	.	-	.	Parent=gene231
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39569969	39570009	.	-	.	Parent=gene231
chr21	.	intron	39570010	39571046	.	-	.	Parent=gene231
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39571047	39571147	.	-	.	Parent=gene231
chr21	.	intron	39571148	39572538	.	-	.	Parent=gene231
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39572539	39572609	.	-	.	Parent=gene231
chr21	.	intron	39572610	39573943	.	-	.	Parent=gene231
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene231
chr21	ENCODE	CDS	39573944	39574009	.	-	.	Parent=gene231
###
chr21	ENCODE	gene	39530515	39574009	.	-	.	ID=gene232;Name=AF129408.13-015;name2=BRWD1
chr21	ENCODE	exon	39530515	39530580	.	-	.	Parent=gene232
chr21	.	intron	39530581	39532274	.	-	.	Parent=gene232
chr21	ENCODE	exon	39532275	39532369	.	-	.	Parent=gene232
chr21	.	intron	39532370	39541496	.	-	.	Parent=gene232
chr21	ENCODE	exon	39541497	39541628	.	-	.	Parent=gene232
chr21	.	intron	39541629	39544591	.	-	.	Parent=gene232
chr21	ENCODE	exon	39544592	39544685	.	-	.	Parent=gene232
chr21	.	intron	39544686	39549460	.	-	.	Parent=gene232
chr21	ENCODE	exon	39549461	39549624	.	-	.	Parent=gene232
chr21	.	intron	39549625	39552282	.	-	.	Parent=gene232
chr21	ENCODE	exon	39552283	39552468	.	-	.	Parent=gene232
chr21	.	intron	39552469	39558255	.	-	.	Parent=gene232
chr21	ENCODE	exon	39558256	39558481	.	-	.	Parent=gene232
chr21	.	intron	39558482	39558686	.	-	.	Parent=gene232
chr21	ENCODE	exon	39558687	39558815	.	-	.	Parent=gene232
chr21	.	intron	39558816	39563694	.	-	.	Parent=gene232
chr21	ENCODE	exon	39563695	39563829	.	-	.	Parent=gene232
chr21	.	intron	39563830	39564078	.	-	.	Parent=gene232
chr21	ENCODE	exon	39564079	39564229	.	-	.	Parent=gene232
chr21	.	intron	39564230	39568169	.	-	.	Parent=gene232
chr21	ENCODE	exon	39568170	39568268	.	-	.	Parent=gene232
chr21	.	intron	39568269	39569968	.	-	.	Parent=gene232
chr21	ENCODE	exon	39569969	39570009	.	-	.	Parent=gene232
chr21	.	intron	39570010	39571046	.	-	.	Parent=gene232
chr21	ENCODE	exon	39571047	39571147	.	-	.	Parent=gene232
chr21	.	intron	39571148	39572538	.	-	.	Parent=gene232
chr21	ENCODE	exon	39572539	39572609	.	-	.	Parent=gene232
chr21	.	intron	39572610	39573943	.	-	.	Parent=gene232
chr21	ENCODE	exon	39573944	39574009	.	-	.	Parent=gene232
###
chr21	ENCODE	gene	39572293	39574003	.	-	.	ID=gene233;Name=AF129408.13-003;name2=BRWD1
chr21	ENCODE	exon	39572293	39572609	.	-	.	Parent=gene233
chr21	.	intron	39572610	39573943	.	-	.	Parent=gene233
chr21	ENCODE	exon	39573944	39574003	.	-	.	Parent=gene233
###
chr21	ENCODE	gene	39590233	39607438	.	-	.	ID=gene234;Name=AF129408.13-004;name2=BRWD1
chr21	ENCODE	exon	39590233	39592378	.	-	.	Parent=gene234
chr21	ENCODE	CDS	39592214	39592378	.	-	.	Parent=gene234
chr21	.	intron	39592379	39606636	.	-	.	Parent=gene234
chr21	ENCODE	exon	39606637	39606696	.	-	.	Parent=gene234
chr21	ENCODE	CDS	39606637	39606696	.	-	.	Parent=gene234
chr21	.	intron	39606697	39606867	.	-	.	Parent=gene234
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene234
chr21	ENCODE	CDS	39606868	39606897	.	-	.	Parent=gene234
chr21	.	intron	39606898	39607036	.	-	.	Parent=gene234
chr21	ENCODE	exon	39607037	39607095	.	-	.	Parent=gene234
chr21	ENCODE	CDS	39607037	39607095	.	-	.	Parent=gene234
chr21	.	intron	39607096	39607238	.	-	.	Parent=gene234
chr21	ENCODE	CDS	39607239	39607287	.	-	.	Parent=gene234
chr21	ENCODE	exon	39607239	39607438	.	-	.	Parent=gene234
###
chr21	ENCODE	gene	39591886	39615355	.	-	.	ID=gene235;Name=AF129408.13-008;name2=BRWD1
chr21	ENCODE	exon	39591886	39592378	.	-	.	Parent=gene235
chr21	.	intron	39592379	39606636	.	-	.	Parent=gene235
chr21	ENCODE	exon	39606637	39606696	.	-	.	Parent=gene235
chr21	.	intron	39606697	39606867	.	-	.	Parent=gene235
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene235
chr21	.	intron	39606898	39607036	.	-	.	Parent=gene235
chr21	ENCODE	exon	39607037	39607095	.	-	.	Parent=gene235
chr21	.	intron	39607096	39614821	.	-	.	Parent=gene235
chr21	ENCODE	exon	39614822	39615355	.	-	.	Parent=gene235
###
chr21	ENCODE	gene	39606359	39607097	.	-	.	ID=gene236;Name=AF129408.13-005;name2=BRWD1
chr21	ENCODE	exon	39606359	39606696	.	-	.	Parent=gene236
chr21	.	intron	39606697	39606867	.	-	.	Parent=gene236
chr21	ENCODE	exon	39606868	39606897	.	-	.	Parent=gene236
chr21	.	intron	39606898	39607036	.	-	.	Parent=gene236
chr21	ENCODE	exon	39607037	39607097	.	-	.	Parent=gene236
###
chr21	ENCODE	gene	39636111	39642787	.	-	.	ID=gene237;Name=AF064861.91-004;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene237
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene237
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene237
chr21	.	intron	39639071	39639625	.	-	.	Parent=gene237
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene237
chr21	.	intron	39639755	39642087	.	-	.	Parent=gene237
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene237
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene237
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene237
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene237
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene237
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene237
chr21	ENCODE	exon	39642699	39642787	.	-	.	Parent=gene237
###
chr21	ENCODE	gene	39636111	39642895	.	-	.	ID=gene238;Name=AF064861.91-006;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene238
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene238
chr21	ENCODE	exon	39638942	39642135	.	-	.	Parent=gene238
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene238
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene238
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene238
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene238
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene238
chr21	ENCODE	exon	39642699	39642895	.	-	.	Parent=gene238
###
chr21	ENCODE	gene	39636111	39642936	.	-	.	ID=gene239;Name=AF064861.91-002;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene239
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene239
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene239
chr21	.	intron	39639071	39639625	.	-	.	Parent=gene239
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene239
chr21	.	intron	39639755	39641174	.	-	.	Parent=gene239
chr21	ENCODE	exon	39641175	39641274	.	-	.	Parent=gene239
chr21	.	intron	39641275	39642087	.	-	.	Parent=gene239
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene239
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene239
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene239
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene239
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene239
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene239
chr21	ENCODE	exon	39642699	39642936	.	-	.	Parent=gene239
###
chr21	ENCODE	gene	39636111	39642996	.	-	.	ID=gene240;Name=AF064861.91-001;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene240
chr21	ENCODE	CDS	39636908	39636955	.	-	.	Parent=gene240
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene240
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene240
chr21	ENCODE	CDS	39638942	39639070	.	-	.	Parent=gene240
chr21	.	intron	39639071	39642087	.	-	.	Parent=gene240
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene240
chr21	ENCODE	CDS	39642088	39642135	.	-	.	Parent=gene240
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene240
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene240
chr21	ENCODE	CDS	39642218	39642247	.	-	.	Parent=gene240
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene240
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene240
chr21	ENCODE	CDS	39642341	39642373	.	-	.	Parent=gene240
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene240
chr21	ENCODE	CDS	39642699	39642713	.	-	.	Parent=gene240
chr21	ENCODE	exon	39642699	39642996	.	-	.	Parent=gene240
###
chr21	ENCODE	gene	39636111	39643140	.	-	.	ID=gene241;Name=AF064861.91-003;name2=HMGN1
chr21	ENCODE	exon	39636111	39636955	.	-	.	Parent=gene241
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene241
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene241
chr21	.	intron	39639071	39639625	.	-	.	Parent=gene241
chr21	ENCODE	exon	39639626	39641088	.	-	.	Parent=gene241
chr21	.	intron	39641089	39641174	.	-	.	Parent=gene241
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene241
chr21	.	intron	39641280	39642087	.	-	.	Parent=gene241
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene241
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene241
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene241
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene241
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene241
chr21	.	intron	39642374	39643086	.	-	.	Parent=gene241
chr21	ENCODE	exon	39643087	39643140	.	-	.	Parent=gene241
###
chr21	ENCODE	gene	39636442	39642884	.	-	.	ID=gene242;Name=AF064861.91-009;name2=HMGN1
chr21	ENCODE	exon	39636442	39636955	.	-	.	Parent=gene242
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene242
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene242
chr21	.	intron	39639071	39641174	.	-	.	Parent=gene242
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene242
chr21	.	intron	39641280	39642087	.	-	.	Parent=gene242
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene242
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene242
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene242
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene242
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene242
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene242
chr21	ENCODE	exon	39642699	39642884	.	-	.	Parent=gene242
###
chr21	ENCODE	gene	39636488	39642849	.	-	.	ID=gene243;Name=AF064861.91-018;name2=HMGN1
chr21	ENCODE	exon	39636488	39636955	.	-	.	Parent=gene243
chr21	ENCODE	CDS	39636908	39636955	.	-	.	Parent=gene243
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene243
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene243
chr21	ENCODE	CDS	39638942	39639070	.	-	.	Parent=gene243
chr21	.	intron	39639071	39642087	.	-	.	Parent=gene243
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene243
chr21	ENCODE	CDS	39642088	39642135	.	-	.	Parent=gene243
chr21	.	intron	39642136	39642340	.	-	.	Parent=gene243
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene243
chr21	ENCODE	CDS	39642341	39642373	.	-	.	Parent=gene243
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene243
chr21	ENCODE	CDS	39642699	39642713	.	-	.	Parent=gene243
chr21	ENCODE	exon	39642699	39642849	.	-	.	Parent=gene243
###
chr21	ENCODE	gene	39636584	39642836	.	-	.	ID=gene244;Name=AF064861.91-015;name2=HMGN1
chr21	ENCODE	exon	39636584	39636955	.	-	.	Parent=gene244
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene244
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene244
chr21	.	intron	39639071	39641174	.	-	.	Parent=gene244
chr21	ENCODE	exon	39641175	39641274	.	-	.	Parent=gene244
chr21	.	intron	39641275	39642087	.	-	.	Parent=gene244
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene244
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene244
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene244
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene244
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene244
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene244
chr21	ENCODE	exon	39642699	39642836	.	-	.	Parent=gene244
###
chr21	ENCODE	gene	39636596	39642658	.	-	.	ID=gene245;Name=AF064861.91-012;name2=HMGN1
chr21	ENCODE	exon	39636596	39636955	.	-	.	Parent=gene245
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene245
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene245
chr21	.	intron	39639071	39639625	.	-	.	Parent=gene245
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene245
chr21	.	intron	39639755	39642087	.	-	.	Parent=gene245
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene245
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene245
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene245
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene245
chr21	ENCODE	exon	39642341	39642658	.	-	.	Parent=gene245
###
chr21	ENCODE	gene	39636600	39642419	.	-	.	ID=gene246;Name=AF064861.91-008;name2=HMGN1
chr21	ENCODE	exon	39636600	39636955	.	-	.	Parent=gene246
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene246
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene246
chr21	.	intron	39639071	39641042	.	-	.	Parent=gene246
chr21	ENCODE	exon	39641043	39641088	.	-	.	Parent=gene246
chr21	.	intron	39641089	39641174	.	-	.	Parent=gene246
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene246
chr21	.	intron	39641280	39642087	.	-	.	Parent=gene246
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene246
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene246
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene246
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene246
chr21	ENCODE	exon	39642341	39642419	.	-	.	Parent=gene246
###
chr21	ENCODE	gene	39636675	39643443	.	-	.	ID=gene247;Name=AF064861.91-013;name2=HMGN1
chr21	ENCODE	exon	39636675	39636955	.	-	.	Parent=gene247
chr21	ENCODE	CDS	39636908	39636955	.	-	.	Parent=gene247
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene247
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene247
chr21	ENCODE	CDS	39638942	39639070	.	-	.	Parent=gene247
chr21	.	intron	39639071	39642087	.	-	.	Parent=gene247
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene247
chr21	ENCODE	CDS	39642088	39642135	.	-	.	Parent=gene247
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene247
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene247
chr21	ENCODE	CDS	39642218	39642247	.	-	.	Parent=gene247
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene247
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene247
chr21	ENCODE	CDS	39642341	39642373	.	-	.	Parent=gene247
chr21	.	intron	39642374	39643255	.	-	.	Parent=gene247
chr21	ENCODE	CDS	39643256	39643318	.	-	.	Parent=gene247
chr21	ENCODE	exon	39643256	39643443	.	-	.	Parent=gene247
###
chr21	ENCODE	gene	39636705	39642393	.	-	.	ID=gene248;Name=AF064861.91-021;name2=HMGN1
chr21	ENCODE	exon	39636705	39636955	.	-	.	Parent=gene248
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene248
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene248
chr21	.	intron	39639071	39639625	.	-	.	Parent=gene248
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene248
chr21	.	intron	39639755	39641174	.	-	.	Parent=gene248
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene248
chr21	.	intron	39641280	39642087	.	-	.	Parent=gene248
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene248
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene248
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene248
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene248
chr21	ENCODE	exon	39642341	39642393	.	-	.	Parent=gene248
###
chr21	ENCODE	gene	39636774	39642135	.	-	.	ID=gene249;Name=AF064861.91-010;name2=HMGN1
chr21	ENCODE	exon	39636774	39636955	.	-	.	Parent=gene249
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene249
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene249
chr21	.	intron	39639071	39641042	.	-	.	Parent=gene249
chr21	ENCODE	exon	39641043	39641088	.	-	.	Parent=gene249
chr21	.	intron	39641089	39642087	.	-	.	Parent=gene249
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene249
###
chr21	ENCODE	gene	39636805	39642850	.	-	.	ID=gene250;Name=AF064861.91-017;name2=HMGN1
chr21	ENCODE	exon	39636805	39636955	.	-	.	Parent=gene250
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene250
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene250
chr21	.	intron	39639071	39639625	.	-	.	Parent=gene250
chr21	ENCODE	exon	39639626	39639754	.	-	.	Parent=gene250
chr21	.	intron	39639755	39641042	.	-	.	Parent=gene250
chr21	ENCODE	exon	39641043	39641088	.	-	.	Parent=gene250
chr21	.	intron	39641089	39641174	.	-	.	Parent=gene250
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene250
chr21	.	intron	39641280	39642087	.	-	.	Parent=gene250
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene250
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene250
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene250
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene250
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene250
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene250
chr21	ENCODE	exon	39642699	39642850	.	-	.	Parent=gene250
###
chr21	ENCODE	gene	39636933	39642850	.	-	.	ID=gene251;Name=AF064861.91-007;name2=HMGN1
chr21	ENCODE	exon	39636933	39636955	.	-	.	Parent=gene251
chr21	.	intron	39636956	39638941	.	-	.	Parent=gene251
chr21	ENCODE	exon	39638942	39639070	.	-	.	Parent=gene251
chr21	.	intron	39639071	39642087	.	-	.	Parent=gene251
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene251
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene251
chr21	ENCODE	exon	39642218	39642373	.	-	.	Parent=gene251
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene251
chr21	ENCODE	exon	39642699	39642850	.	-	.	Parent=gene251
###
chr21	ENCODE	gene	39640943	39642863	.	-	.	ID=gene252;Name=AF064861.91-016;name2=HMGN1
chr21	ENCODE	exon	39640943	39641088	.	-	.	Parent=gene252
chr21	.	intron	39641089	39641174	.	-	.	Parent=gene252
chr21	ENCODE	exon	39641175	39641279	.	-	.	Parent=gene252
chr21	.	intron	39641280	39642087	.	-	.	Parent=gene252
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene252
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene252
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene252
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene252
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene252
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene252
chr21	ENCODE	exon	39642699	39642863	.	-	.	Parent=gene252
###
chr21	ENCODE	gene	39641132	39642811	.	-	.	ID=gene253;Name=AF064861.91-019;name2=HMGN1
chr21	ENCODE	exon	39641132	39641748	.	-	.	Parent=gene253
chr21	.	intron	39641749	39642087	.	-	.	Parent=gene253
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene253
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene253
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene253
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene253
chr21	ENCODE	exon	39642341	39642373	.	-	.	Parent=gene253
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene253
chr21	ENCODE	exon	39642699	39642811	.	-	.	Parent=gene253
###
chr21	ENCODE	gene	39641288	39642416	.	-	.	ID=gene254;Name=AF064861.91-020;name2=HMGN1
chr21	ENCODE	exon	39641288	39641748	.	-	.	Parent=gene254
chr21	.	intron	39641749	39642087	.	-	.	Parent=gene254
chr21	ENCODE	exon	39642088	39642135	.	-	.	Parent=gene254
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene254
chr21	ENCODE	exon	39642218	39642247	.	-	.	Parent=gene254
chr21	.	intron	39642248	39642340	.	-	.	Parent=gene254
chr21	ENCODE	exon	39642341	39642416	.	-	.	Parent=gene254
###
chr21	ENCODE	gene	39641791	39642816	.	-	.	ID=gene255;Name=AF064861.91-014;name2=HMGN1
chr21	ENCODE	exon	39641791	39642373	.	-	.	Parent=gene255
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene255
chr21	ENCODE	exon	39642699	39642816	.	-	.	Parent=gene255
###
chr21	ENCODE	gene	39641861	39642850	.	-	.	ID=gene256;Name=AF064861.91-005;name2=HMGN1
chr21	ENCODE	exon	39641861	39642135	.	-	.	Parent=gene256
chr21	.	intron	39642136	39642217	.	-	.	Parent=gene256
chr21	ENCODE	exon	39642218	39642373	.	-	.	Parent=gene256
chr21	.	intron	39642374	39642698	.	-	.	Parent=gene256
chr21	ENCODE	exon	39642699	39642850	.	-	.	Parent=gene256
###
chr21	ENCODE	gene	39674040	39691685	.	+	.	ID=gene257;Name=AF064861.92-001;name2=WRB
chr21	ENCODE	exon	39674040	39674282	.	+	.	Parent=gene257
chr21	ENCODE	CDS	39674181	39674282	.	+	.	Parent=gene257
chr21	.	intron	39674283	39684493	.	+	.	Parent=gene257
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene257
chr21	ENCODE	CDS	39684494	39684659	.	+	.	Parent=gene257
chr21	.	intron	39684660	39685564	.	+	.	Parent=gene257
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene257
chr21	ENCODE	CDS	39685565	39685632	.	+	.	Parent=gene257
chr21	.	intron	39685633	39686961	.	+	.	Parent=gene257
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene257
chr21	ENCODE	CDS	39686962	39687076	.	+	.	Parent=gene257
chr21	.	intron	39687077	39690661	.	+	.	Parent=gene257
chr21	ENCODE	CDS	39690662	39690735	.	+	.	Parent=gene257
chr21	ENCODE	exon	39690662	39691685	.	+	.	Parent=gene257
###
chr21	ENCODE	gene	39674190	39685842	.	+	.	ID=gene258;Name=AF064861.92-005;name2=WRB
chr21	ENCODE	exon	39674190	39674282	.	+	.	Parent=gene258
chr21	.	intron	39674283	39684493	.	+	.	Parent=gene258
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene258
chr21	.	intron	39684660	39685564	.	+	.	Parent=gene258
chr21	ENCODE	exon	39685565	39685842	.	+	.	Parent=gene258
###
chr21	ENCODE	gene	39674210	39685001	.	+	.	ID=gene259;Name=AF064861.92-008;name2=WRB
chr21	ENCODE	exon	39674210	39674282	.	+	.	Parent=gene259
chr21	.	intron	39674283	39684493	.	+	.	Parent=gene259
chr21	ENCODE	exon	39684494	39685001	.	+	.	Parent=gene259
###
chr21	ENCODE	gene	39674254	39690912	.	+	.	ID=gene260;Name=AF064861.92-002;name2=WRB
chr21	ENCODE	exon	39674254	39674352	.	+	.	Parent=gene260
chr21	.	intron	39674353	39684493	.	+	.	Parent=gene260
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene260
chr21	ENCODE	CDS	39684494	39684659	.	+	.	Parent=gene260
chr21	.	intron	39684660	39685564	.	+	.	Parent=gene260
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene260
chr21	ENCODE	CDS	39685565	39685632	.	+	.	Parent=gene260
chr21	.	intron	39685633	39686961	.	+	.	Parent=gene260
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene260
chr21	ENCODE	CDS	39686962	39687076	.	+	.	Parent=gene260
chr21	.	intron	39687077	39690661	.	+	.	Parent=gene260
chr21	ENCODE	CDS	39690662	39690735	.	+	.	Parent=gene260
chr21	ENCODE	exon	39690662	39690912	.	+	.	Parent=gene260
###
chr21	ENCODE	gene	39674283	39684599	.	+	.	ID=gene261;Name=AF064861.92-003;name2=WRB
chr21	ENCODE	exon	39674283	39674717	.	+	.	Parent=gene261
chr21	.	intron	39674718	39684493	.	+	.	Parent=gene261
chr21	ENCODE	exon	39684494	39684599	.	+	.	Parent=gene261
chr21	ENCODE	CDS	39684494	39684599	.	+	.	Parent=gene261
###
chr21	ENCODE	gene	39679889	39687076	.	+	.	ID=gene262;Name=AF064861.92-009;name2=WRB
chr21	ENCODE	exon	39679889	39680307	.	+	.	Parent=gene262
chr21	.	intron	39680308	39684493	.	+	.	Parent=gene262
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene262
chr21	ENCODE	CDS	39684494	39684659	.	+	.	Parent=gene262
chr21	.	intron	39684660	39685564	.	+	.	Parent=gene262
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene262
chr21	ENCODE	CDS	39685565	39685632	.	+	.	Parent=gene262
chr21	.	intron	39685633	39686961	.	+	.	Parent=gene262
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene262
chr21	ENCODE	CDS	39686962	39687076	.	+	.	Parent=gene262
###
chr21	ENCODE	gene	39681561	39691685	.	+	.	ID=gene263;Name=AF064861.92-004;name2=WRB
chr21	ENCODE	exon	39681561	39681651	.	+	.	Parent=gene263
chr21	.	intron	39681652	39684493	.	+	.	Parent=gene263
chr21	ENCODE	exon	39684494	39684659	.	+	.	Parent=gene263
chr21	ENCODE	CDS	39684494	39684659	.	+	.	Parent=gene263
chr21	.	intron	39684660	39685564	.	+	.	Parent=gene263
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene263
chr21	ENCODE	CDS	39685565	39685632	.	+	.	Parent=gene263
chr21	.	intron	39685633	39686961	.	+	.	Parent=gene263
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene263
chr21	ENCODE	CDS	39686962	39687076	.	+	.	Parent=gene263
chr21	.	intron	39687077	39690661	.	+	.	Parent=gene263
chr21	ENCODE	CDS	39690662	39690735	.	+	.	Parent=gene263
chr21	ENCODE	exon	39690662	39691685	.	+	.	Parent=gene263
###
chr21	ENCODE	gene	39681587	39691050	.	+	.	ID=gene264;Name=AF064861.92-006;name2=WRB
chr21	ENCODE	exon	39681587	39681651	.	+	.	Parent=gene264
chr21	.	intron	39681652	39684493	.	+	.	Parent=gene264
chr21	ENCODE	exon	39684494	39685272	.	+	.	Parent=gene264
chr21	.	intron	39685273	39685564	.	+	.	Parent=gene264
chr21	ENCODE	exon	39685565	39685632	.	+	.	Parent=gene264
chr21	.	intron	39685633	39686961	.	+	.	Parent=gene264
chr21	ENCODE	exon	39686962	39687076	.	+	.	Parent=gene264
chr21	.	intron	39687077	39690661	.	+	.	Parent=gene264
chr21	ENCODE	exon	39690662	39691050	.	+	.	Parent=gene264
###
chr21	ENCODE	gene	39686692	39690900	.	+	.	ID=gene265;Name=AF064861.92-007;name2=WRB
chr21	ENCODE	exon	39686692	39687076	.	+	.	Parent=gene265
chr21	.	intron	39687077	39690661	.	+	.	Parent=gene265
chr21	ENCODE	exon	39690662	39690900	.	+	.	Parent=gene265
###
chr21	ENCODE	gene	39699640	39739573	.	-	.	ID=gene266;Name=AF121781.16-001;name2=C21orf13
chr21	ENCODE	exon	39699640	39700408	.	-	.	Parent=gene266
chr21	ENCODE	CDS	39699678	39700408	.	-	.	Parent=gene266
chr21	.	intron	39700409	39703774	.	-	.	Parent=gene266
chr21	ENCODE	exon	39703775	39703892	.	-	.	Parent=gene266
chr21	ENCODE	CDS	39703775	39703892	.	-	.	Parent=gene266
chr21	.	intron	39703893	39704059	.	-	.	Parent=gene266
chr21	ENCODE	exon	39704060	39704163	.	-	.	Parent=gene266
chr21	ENCODE	CDS	39704060	39704163	.	-	.	Parent=gene266
chr21	.	intron	39704164	39705513	.	-	.	Parent=gene266
chr21	ENCODE	exon	39705514	39705598	.	-	.	Parent=gene266
chr21	ENCODE	CDS	39705514	39705598	.	-	.	Parent=gene266
chr21	.	intron	39705599	39714501	.	-	.	Parent=gene266
chr21	ENCODE	exon	39714502	39714639	.	-	.	Parent=gene266
chr21	ENCODE	CDS	39714502	39714639	.	-	.	Parent=gene266
chr21	.	intron	39714640	39716771	.	-	.	Parent=gene266
chr21	ENCODE	exon	39716772	39717286	.	-	.	Parent=gene266
chr21	ENCODE	CDS	39716772	39717286	.	-	.	Parent=gene266
chr21	.	intron	39717287	39721967	.	-	.	Parent=gene266
chr21	ENCODE	CDS	39721968	39722289	.	-	.	Parent=gene266
chr21	ENCODE	exon	39721968	39722299	.	-	.	Parent=gene266
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene266
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene266
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene266
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene266
chr21	.	intron	39729370	39737930	.	-	.	Parent=gene266
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene266
chr21	.	intron	39737998	39739520	.	-	.	Parent=gene266
chr21	ENCODE	exon	39739521	39739573	.	-	.	Parent=gene266
###
chr21	ENCODE	gene	39699656	39739529	.	-	.	ID=gene267;Name=AF121781.16-002;name2=C21orf13
chr21	ENCODE	exon	39699656	39700408	.	-	.	Parent=gene267
chr21	ENCODE	CDS	39699678	39700408	.	-	.	Parent=gene267
chr21	.	intron	39700409	39703774	.	-	.	Parent=gene267
chr21	ENCODE	exon	39703775	39703892	.	-	.	Parent=gene267
chr21	ENCODE	CDS	39703775	39703892	.	-	.	Parent=gene267
chr21	.	intron	39703893	39704059	.	-	.	Parent=gene267
chr21	ENCODE	exon	39704060	39704163	.	-	.	Parent=gene267
chr21	ENCODE	CDS	39704060	39704163	.	-	.	Parent=gene267
chr21	.	intron	39704164	39705513	.	-	.	Parent=gene267
chr21	ENCODE	exon	39705514	39705598	.	-	.	Parent=gene267
chr21	ENCODE	CDS	39705514	39705598	.	-	.	Parent=gene267
chr21	.	intron	39705599	39714501	.	-	.	Parent=gene267
chr21	ENCODE	exon	39714502	39714639	.	-	.	Parent=gene267
chr21	ENCODE	CDS	39714502	39714639	.	-	.	Parent=gene267
chr21	.	intron	39714640	39716771	.	-	.	Parent=gene267
chr21	ENCODE	exon	39716772	39717286	.	-	.	Parent=gene267
chr21	ENCODE	CDS	39716772	39717286	.	-	.	Parent=gene267
chr21	.	intron	39717287	39721967	.	-	.	Parent=gene267
chr21	ENCODE	CDS	39721968	39722289	.	-	.	Parent=gene267
chr21	ENCODE	exon	39721968	39722299	.	-	.	Parent=gene267
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene267
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene267
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene267
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene267
chr21	.	intron	39729370	39739245	.	-	.	Parent=gene267
chr21	ENCODE	exon	39739246	39739529	.	-	.	Parent=gene267
###
chr21	ENCODE	gene	39699774	39704943	.	-	.	ID=gene268;Name=AF121781.16-020;name2=C21orf13
chr21	ENCODE	exon	39699774	39700408	.	-	.	Parent=gene268
chr21	.	intron	39700409	39703774	.	-	.	Parent=gene268
chr21	ENCODE	exon	39703775	39703892	.	-	.	Parent=gene268
chr21	.	intron	39703893	39704059	.	-	.	Parent=gene268
chr21	ENCODE	exon	39704060	39704163	.	-	.	Parent=gene268
chr21	.	intron	39704164	39704828	.	-	.	Parent=gene268
chr21	ENCODE	exon	39704829	39704943	.	-	.	Parent=gene268
###
chr21	ENCODE	gene	39705514	39739548	.	-	.	ID=gene269;Name=AF121781.16-016;name2=C21orf13
chr21	ENCODE	exon	39705514	39705598	.	-	.	Parent=gene269
chr21	.	intron	39705599	39714501	.	-	.	Parent=gene269
chr21	ENCODE	exon	39714502	39714639	.	-	.	Parent=gene269
chr21	.	intron	39714640	39716771	.	-	.	Parent=gene269
chr21	ENCODE	exon	39716772	39716879	.	-	.	Parent=gene269
chr21	.	intron	39716880	39722983	.	-	.	Parent=gene269
chr21	ENCODE	exon	39722984	39723007	.	-	.	Parent=gene269
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene269
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene269
chr21	.	intron	39729370	39729892	.	-	.	Parent=gene269
chr21	ENCODE	exon	39729893	39729963	.	-	.	Parent=gene269
chr21	.	intron	39729964	39737930	.	-	.	Parent=gene269
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene269
chr21	.	intron	39737998	39739520	.	-	.	Parent=gene269
chr21	ENCODE	exon	39739521	39739548	.	-	.	Parent=gene269
###
chr21	ENCODE	gene	39715860	39732732	.	-	.	ID=gene270;Name=AF121781.16-005;name2=C21orf13
chr21	ENCODE	exon	39715860	39717704	.	-	.	Parent=gene270
chr21	.	intron	39717705	39721213	.	-	.	Parent=gene270
chr21	ENCODE	exon	39721214	39722299	.	-	.	Parent=gene270
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene270
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene270
chr21	.	intron	39723008	39732479	.	-	.	Parent=gene270
chr21	ENCODE	exon	39732480	39732732	.	-	.	Parent=gene270
###
chr21	ENCODE	gene	39716208	39739573	.	-	.	ID=gene271;Name=AF121781.16-006;name2=C21orf13
chr21	ENCODE	exon	39716208	39717286	.	-	.	Parent=gene271
chr21	.	intron	39717287	39721967	.	-	.	Parent=gene271
chr21	ENCODE	exon	39721968	39722299	.	-	.	Parent=gene271
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene271
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene271
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene271
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene271
chr21	.	intron	39729370	39739520	.	-	.	Parent=gene271
chr21	ENCODE	exon	39739521	39739573	.	-	.	Parent=gene271
###
chr21	ENCODE	gene	39716208	39739601	.	-	.	ID=gene272;Name=AF121781.16-003;name2=C21orf13
chr21	ENCODE	exon	39716208	39717286	.	-	.	Parent=gene272
chr21	.	intron	39717287	39722926	.	-	.	Parent=gene272
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene272
chr21	.	intron	39723008	39737930	.	-	.	Parent=gene272
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene272
chr21	.	intron	39737998	39739520	.	-	.	Parent=gene272
chr21	ENCODE	exon	39739521	39739601	.	-	.	Parent=gene272
###
chr21	ENCODE	gene	39716784	39739557	.	-	.	ID=gene273;Name=AF121781.16-021;name2=C21orf13
chr21	ENCODE	exon	39716784	39717286	.	-	.	Parent=gene273
chr21	.	intron	39717287	39722926	.	-	.	Parent=gene273
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene273
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene273
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene273
chr21	.	intron	39729370	39739520	.	-	.	Parent=gene273
chr21	ENCODE	exon	39739521	39739557	.	-	.	Parent=gene273
###
chr21	ENCODE	gene	39717036	39739571	.	-	.	ID=gene274;Name=AF121781.16-007;name2=C21orf13
chr21	ENCODE	exon	39717036	39717286	.	-	.	Parent=gene274
chr21	.	intron	39717287	39721554	.	-	.	Parent=gene274
chr21	ENCODE	exon	39721555	39721701	.	-	.	Parent=gene274
chr21	.	intron	39721702	39722926	.	-	.	Parent=gene274
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene274
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene274
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene274
chr21	.	intron	39729370	39737930	.	-	.	Parent=gene274
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene274
chr21	.	intron	39737998	39738439	.	-	.	Parent=gene274
chr21	ENCODE	exon	39738440	39738541	.	-	.	Parent=gene274
chr21	.	intron	39738542	39739520	.	-	.	Parent=gene274
chr21	ENCODE	exon	39739521	39739571	.	-	.	Parent=gene274
###
chr21	ENCODE	gene	39717041	39739556	.	-	.	ID=gene275;Name=AF121781.16-019;name2=C21orf13
chr21	ENCODE	exon	39717041	39717286	.	-	.	Parent=gene275
chr21	ENCODE	CDS	39717041	39717286	.	-	.	Parent=gene275
chr21	.	intron	39717287	39721967	.	-	.	Parent=gene275
chr21	ENCODE	CDS	39721968	39722289	.	-	.	Parent=gene275
chr21	ENCODE	exon	39721968	39722299	.	-	.	Parent=gene275
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene275
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene275
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene275
chr21	ENCODE	exon	39729216	39729338	.	-	.	Parent=gene275
chr21	.	intron	39729339	39737930	.	-	.	Parent=gene275
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene275
chr21	.	intron	39737998	39739520	.	-	.	Parent=gene275
chr21	ENCODE	exon	39739521	39739556	.	-	.	Parent=gene275
###
chr21	ENCODE	gene	39717216	39739529	.	-	.	ID=gene276;Name=AF121781.16-012;name2=C21orf13
chr21	ENCODE	exon	39717216	39717286	.	-	.	Parent=gene276
chr21	.	intron	39717287	39722926	.	-	.	Parent=gene276
chr21	ENCODE	exon	39722927	39723190	.	-	.	Parent=gene276
chr21	.	intron	39723191	39729215	.	-	.	Parent=gene276
chr21	ENCODE	exon	39729216	39729338	.	-	.	Parent=gene276
chr21	.	intron	39729339	39737930	.	-	.	Parent=gene276
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene276
chr21	.	intron	39737998	39739245	.	-	.	Parent=gene276
chr21	ENCODE	exon	39739246	39739529	.	-	.	Parent=gene276
###
chr21	ENCODE	gene	39721967	39739574	.	-	.	ID=gene277;Name=AF121781.16-014;name2=C21orf13
chr21	ENCODE	CDS	39721967	39722289	.	-	.	Parent=gene277
chr21	ENCODE	exon	39721967	39722299	.	-	.	Parent=gene277
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene277
chr21	ENCODE	exon	39722927	39723190	.	-	.	Parent=gene277
chr21	.	intron	39723191	39729215	.	-	.	Parent=gene277
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene277
chr21	.	intron	39729370	39739520	.	-	.	Parent=gene277
chr21	ENCODE	exon	39739521	39739574	.	-	.	Parent=gene277
###
chr21	ENCODE	gene	39722004	39739599	.	-	.	ID=gene278;Name=AF121781.16-018;name2=C21orf13
chr21	ENCODE	CDS	39722004	39722289	.	-	.	Parent=gene278
chr21	ENCODE	exon	39722004	39722299	.	-	.	Parent=gene278
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene278
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene278
chr21	.	intron	39723008	39737930	.	-	.	Parent=gene278
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene278
chr21	.	intron	39737998	39739520	.	-	.	Parent=gene278
chr21	ENCODE	exon	39739521	39739599	.	-	.	Parent=gene278
###
chr21	ENCODE	gene	39722006	39739515	.	-	.	ID=gene279;Name=AF121781.16-009;name2=C21orf13
chr21	ENCODE	CDS	39722006	39722289	.	-	.	Parent=gene279
chr21	ENCODE	exon	39722006	39722299	.	-	.	Parent=gene279
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene279
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene279
chr21	.	intron	39723008	39732479	.	-	.	Parent=gene279
chr21	ENCODE	exon	39732480	39732514	.	-	.	Parent=gene279
chr21	.	intron	39732515	39737930	.	-	.	Parent=gene279
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene279
chr21	.	intron	39737998	39738439	.	-	.	Parent=gene279
chr21	ENCODE	exon	39738440	39738541	.	-	.	Parent=gene279
chr21	.	intron	39738542	39739245	.	-	.	Parent=gene279
chr21	ENCODE	exon	39739246	39739515	.	-	.	Parent=gene279
###
chr21	ENCODE	gene	39722011	39739529	.	-	.	ID=gene280;Name=AF121781.16-013;name2=C21orf13
chr21	ENCODE	CDS	39722011	39722289	.	-	.	Parent=gene280
chr21	ENCODE	exon	39722011	39722299	.	-	.	Parent=gene280
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene280
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene280
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene280
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene280
chr21	.	intron	39729370	39739245	.	-	.	Parent=gene280
chr21	ENCODE	exon	39739246	39739529	.	-	.	Parent=gene280
###
chr21	ENCODE	gene	39722081	39739565	.	-	.	ID=gene281;Name=AF121781.16-010;name2=C21orf13
chr21	ENCODE	CDS	39722081	39722289	.	-	.	Parent=gene281
chr21	ENCODE	exon	39722081	39722299	.	-	.	Parent=gene281
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene281
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene281
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene281
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene281
chr21	.	intron	39729370	39733429	.	-	.	Parent=gene281
chr21	ENCODE	exon	39733430	39733569	.	-	.	Parent=gene281
chr21	.	intron	39733570	39737930	.	-	.	Parent=gene281
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene281
chr21	.	intron	39737998	39739520	.	-	.	Parent=gene281
chr21	ENCODE	exon	39739521	39739565	.	-	.	Parent=gene281
###
chr21	ENCODE	gene	39722101	39739565	.	-	.	ID=gene282;Name=AF121781.16-015;name2=C21orf13
chr21	ENCODE	CDS	39722101	39722289	.	-	.	Parent=gene282
chr21	ENCODE	exon	39722101	39722299	.	-	.	Parent=gene282
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene282
chr21	ENCODE	exon	39722927	39723007	.	-	.	Parent=gene282
chr21	.	intron	39723008	39729215	.	-	.	Parent=gene282
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene282
chr21	.	intron	39729370	39729892	.	-	.	Parent=gene282
chr21	ENCODE	exon	39729893	39729963	.	-	.	Parent=gene282
chr21	.	intron	39729964	39733429	.	-	.	Parent=gene282
chr21	ENCODE	exon	39733430	39733569	.	-	.	Parent=gene282
chr21	.	intron	39733570	39739520	.	-	.	Parent=gene282
chr21	ENCODE	exon	39739521	39739565	.	-	.	Parent=gene282
###
chr21	ENCODE	gene	39722198	39739576	.	-	.	ID=gene283;Name=AF121781.16-017;name2=C21orf13
chr21	ENCODE	CDS	39722198	39722289	.	-	.	Parent=gene283
chr21	ENCODE	exon	39722198	39722299	.	-	.	Parent=gene283
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene283
chr21	ENCODE	exon	39722927	39723190	.	-	.	Parent=gene283
chr21	.	intron	39723191	39729215	.	-	.	Parent=gene283
chr21	ENCODE	exon	39729216	39729338	.	-	.	Parent=gene283
chr21	.	intron	39729339	39737930	.	-	.	Parent=gene283
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene283
chr21	.	intron	39737998	39739520	.	-	.	Parent=gene283
chr21	ENCODE	exon	39739521	39739576	.	-	.	Parent=gene283
###
chr21	ENCODE	gene	39722258	39739548	.	-	.	ID=gene284;Name=AF121781.16-008;name2=C21orf13
chr21	ENCODE	CDS	39722258	39722289	.	-	.	Parent=gene284
chr21	ENCODE	exon	39722258	39722299	.	-	.	Parent=gene284
chr21	.	intron	39722300	39722926	.	-	.	Parent=gene284
chr21	ENCODE	exon	39722927	39723190	.	-	.	Parent=gene284
chr21	.	intron	39723191	39729215	.	-	.	Parent=gene284
chr21	ENCODE	exon	39729216	39729369	.	-	.	Parent=gene284
chr21	.	intron	39729370	39737930	.	-	.	Parent=gene284
chr21	ENCODE	exon	39737931	39737997	.	-	.	Parent=gene284
chr21	.	intron	39737998	39738439	.	-	.	Parent=gene284
chr21	ENCODE	exon	39738440	39738541	.	-	.	Parent=gene284
chr21	.	intron	39738542	39739520	.	-	.	Parent=gene284
chr21	ENCODE	exon	39739521	39739548	.	-	.	Parent=gene284
###
chr21	ENCODE	gene	39737255	39739549	.	-	.	ID=gene285;Name=AF121781.16-011;name2=C21orf13
chr21	ENCODE	exon	39737255	39737997	.	-	.	Parent=gene285
chr21	.	intron	39737998	39739520	.	-	.	Parent=gene285
chr21	ENCODE	exon	39739521	39739549	.	-	.	Parent=gene285
###
chr21	ENCODE	gene	39739651	39739725	.	+	.	ID=gene286;Name=AF121897.3-002;name2=SH3BGR
chr21	ENCODE	exon	39739651	39739725	.	+	.	Parent=gene286
###
chr21	ENCODE	gene	39739651	39739725	.	+	.	ID=gene287;Name=AF121897.3-003;name2=SH3BGR
chr21	ENCODE	exon	39739651	39739725	.	+	.	Parent=gene287
###
chr21	ENCODE	gene	39739661	39739688	.	+	.	ID=gene288;Name=AF121897.3-007;name2=SH3BGR
chr21	ENCODE	exon	39739661	39739688	.	+	.	Parent=gene288
###
chr21	ENCODE	gene	39739671	39739877	.	+	.	ID=gene289;Name=AF121897.3-004;name2=SH3BGR
chr21	ENCODE	exon	39739671	39739877	.	+	.	Parent=gene289
###
chr21	ENCODE	gene	39739727	39739894	.	+	.	ID=gene290;Name=AF121897.3-005;name2=SH3BGR
chr21	ENCODE	exon	39739727	39739894	.	+	.	Parent=gene290
###
chr21	ENCODE	gene	39739738	39739877	.	+	.	ID=gene291;Name=AF121897.3-006;name2=SH3BGR
chr21	ENCODE	exon	39739738	39739877	.	+	.	Parent=gene291
###
genometools-1.5.1/testdata/gt_extractfeat_mappings.fas000066400000000000000000000006511211610345200232540ustar00rootroot00000000000000>foo
AAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
>bar
GCTGATCGCTGACCGGCCGCGCGTTTTTTTTTTTTTTTTTTTTTTTTTCGATCGCGCATCGGGCATTTTTTTTTTTTACCGACCCCCCCCCCCAAAAAAA
>baz
AATAAAAAAACCCCCCCCCCCCCCCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCAAAAAAAAAACCCCCTTTTTTTTTTTTCCCCCANN
>quux
TTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGAAAAAAAATTTTTTTTTTTTTTTTTTTNNNNGGCTGGGGGGG
genometools-1.5.1/testdata/gt_extractfeat_mappings.gff3000066400000000000000000000003441211610345200233270ustar00rootroot00000000000000##gff-version   3
##sequence-region bar 1 100
##sequence-region baz 1 100
##sequence-region foo 1 100
##sequence-region quux 1 100
bar	.	gene	1	10	.	.	.	.
baz	.	gene	1	10	.	.	.	.
foo	.	gene	1	10	.	.	.	.
quux	.	gene	1	10	.	.	.	.
genometools-1.5.1/testdata/gt_extractfeat_mappings.md5.gff3000066400000000000000000000010241211610345200240070ustar00rootroot00000000000000##gff-version   3
##sequence-region   md5:9448bcca4c03ff54d1384378051e2a89:bar 1 100
##sequence-region   md5:99d681c067dc0429579ac0f192c2d8c8:quux 1 100
##sequence-region   md5:a39f549be076d51150511e802807cf51:foo 1 100
##sequence-region   md5:acff2b1574e4418ecdd8b31111c7bb7a:baz 1 100
md5:9448bcca4c03ff54d1384378051e2a89:bar	.	gene	1	10	.	.	.	.
md5:99d681c067dc0429579ac0f192c2d8c8:quux	.	gene	1	10	.	.	.	.
md5:a39f549be076d51150511e802807cf51:foo	.	gene	1	10	.	.	.	.
md5:acff2b1574e4418ecdd8b31111c7bb7a:baz	.	gene	1	10	.	.	.	.
genometools-1.5.1/testdata/gt_extractfeat_mappings_md5.fas000066400000000000000000000001141211610345200240130ustar00rootroot00000000000000>gene_1
GCTGATCGCT
>gene_2
TTTTTTTTTT
>gene_3
AAAAAAAAAA
>gene_4
AATAAAAAAA
genometools-1.5.1/testdata/gt_extractfeat_mappings_ref.fas000066400000000000000000000001141211610345200241020ustar00rootroot00000000000000>gene_1
GCTGATCGCT
>gene_2
AATAAAAAAA
>gene_3
AAAAAAAAAA
>gene_4
TTTTTTTTTT
genometools-1.5.1/testdata/gt_extractfeat_mappings_ref.md5.fas000066400000000000000000000001141211610345200245660ustar00rootroot00000000000000>gene_1
GCTGATCGCT
>gene_2
TTTTTTTTTT
>gene_3
AAAAAAAAAA
>gene_4
AATAAAAAAA
genometools-1.5.1/testdata/gt_extractfeat_mappings_sep1.fas000066400000000000000000000003251211610345200242020ustar00rootroot00000000000000>baz
AATAAAAAAACCCCCCCCCCCCCCCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCAAAAAAAAAACCCCCTTTTTTTTTTTTCCCCCANN
>quux
TTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGAAAAAAAATTTTTTTTTTTTTTTTTTTNNNNGGCTGGGGGGG
genometools-1.5.1/testdata/gt_extractfeat_mappings_sep2.fas000066400000000000000000000003241211610345200242020ustar00rootroot00000000000000>foo
AAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
>bar
GCTGATCGCTGACCGGCCGCGCGTTTTTTTTTTTTTTTTTTTTTTTTTCGATCGCGCATCGGGCATTTTTTTTTTTTACCGACCCCCCCCCCCAAAAAAA
genometools-1.5.1/testdata/gt_extractfeat_mappings_seprm.lua000066400000000000000000000002041211610345200244640ustar00rootroot00000000000000function mapping(sequence_region)
  return os.getenv("GT_TESTDATA").."gt_extractfeat_mappings_seprm_"..sequence_region..".fas"
end

genometools-1.5.1/testdata/gt_extractfeat_mappings_seprm_bar.fas000066400000000000000000000001521211610345200253020ustar00rootroot00000000000000>bar
GCTGATCGCTGACCGGCCGCGCGTTTTTTTTTTTTTTTTTTTTTTTTTCGATCGCGCATCGGGCATTTTTTTTTTTTACCGACCCCCCCCCCCAAAAAAA
genometools-1.5.1/testdata/gt_extractfeat_mappings_seprm_baz.fas000066400000000000000000000001521211610345200253120ustar00rootroot00000000000000>baz
AATAAAAAAACCCCCCCCCCCCCCCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCAAAAAAAAAACCCCCTTTTTTTTTTTTCCCCCANN
genometools-1.5.1/testdata/gt_extractfeat_mappings_seprm_foo.fas000066400000000000000000000001521211610345200253210ustar00rootroot00000000000000>foo
AAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
genometools-1.5.1/testdata/gt_extractfeat_mappings_seprm_quux.fas000066400000000000000000000001531211610345200255410ustar00rootroot00000000000000>quux
TTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGAAAAAAAATTTTTTTTTTTTTTTTTTTNNNNGGCTGGGGGGG
genometools-1.5.1/testdata/gt_extractfeat_seqid.fas000066400000000000000000000005521211610345200225430ustar00rootroot00000000000000>CDS_1 (joined) [seqid md5:063b1024d68e26716b7f38caf958316f]
GACACAGGACTTCGGGATCTTGGGCAGCTGGAACAAGATCTTGTTTTTGGAGATGCAGGTGCCAAGGACGTTATCAACTTTCTGAGGACGAATCAGGACACAAACCCGGAAAACAAATTACGGCTTTTGATGATTTATGCAACAGTGTACCCCGAGAAGTTTGAAGGTGACAAGGGTGTGAAGCTAATGCAGCTTGCTAGATTATCACCTGTGGATATGAAGGTTATAAGCAACATGCAATTGATAGCTGGATCCCCAGAAAACAAAGCTAAGTCCGGTAGTTTCTCCCTCAAATTTGAC
genometools-1.5.1/testdata/gt_extractfeat_seqid_target.fas000066400000000000000000000006341211610345200241120ustar00rootroot00000000000000>CDS_1 (joined) [seqid md5:063b1024d68e26716b7f38caf958316f] [target IDs md5:14c0ff5e76ef8ac009fdcc923f701356]
GACACAGGACTTCGGGATCTTGGGCAGCTGGAACAAGATCTTGTTTTTGGAGATGCAGGTGCCAAGGACGTTATCAACTTTCTGAGGACGAATCAGGACACAAACCCGGAAAACAAATTACGGCTTTTGATGATTTATGCAACAGTGTACCCCGAGAAGTTTGAAGGTGACAAGGGTGTGAAGCTAATGCAGCTTGCTAGATTATCACCTGTGGATATGAAGGTTATAAGCAACATGCAATTGATAGCTGGATCCCCAGAAAACAAAGCTAAGTCCGGTAGTTTCTCCCTCAAATTTGAC
genometools-1.5.1/testdata/gt_extractfeat_seqid_target.gff3000066400000000000000000000043071211610345200241670ustar00rootroot00000000000000##gff-version   3
##sequence-region   md5:063b1024d68e26716b7f38caf958316f 1 106973
md5:063b1024d68e26716b7f38caf958316f	gth	gene	1074	1540	.	+	.	ID=gene1
md5:063b1024d68e26716b7f38caf958316f	gth	mRNA	1074	1540	.	+	.	ID=mRNA1;Parent=gene1;Target=md5:14c0ff5e76ef8ac009fdcc923f701356 1 303 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	1074	1171	1	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	gth	CDS	1076	1171	.	+	0	ID=CDS1;Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	md5:063b1024d68e26716b7f38caf958316f	five_prime_cis_splice_site	1172	1173	0.866	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	md5:063b1024d68e26716b7f38caf958316f	three_prime_cis_splice_site	1257	1258	0.994	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	gth	exon	1259	1354	1	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	gth	CDS	1259	1354	.	+	0	ID=CDS1;Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	md5:063b1024d68e26716b7f38caf958316f	five_prime_cis_splice_site	1355	1356	5e-05	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	md5:063b1024d68e26716b7f38caf958316f	three_prime_cis_splice_site	1430	1431	0.745	+	.	Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	gth	CDS	1432	1539	.	+	0	ID=CDS1;Parent=mRNA1
md5:063b1024d68e26716b7f38caf958316f	gth	exon	1432	1540	1	+	.	Parent=mRNA1
###
md5:063b1024d68e26716b7f38caf958316f	gth	gene	2779	3506	.	+	.	ID=gene2
md5:063b1024d68e26716b7f38caf958316f	gth	mRNA	2779	3506	.	+	.	ID=mRNA2;Parent=gene2;Target=md5:527995da853a37f9c47e616ce237d523 1 337 +,md5:a9dcd316817972a94c0af505715b10bc 1 426 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	2779	2801	0.696	+	.	Parent=mRNA2
md5:063b1024d68e26716b7f38caf958316f	md5:063b1024d68e26716b7f38caf958316f	five_prime_cis_splice_site	2802	2803	0.459	+	.	Parent=mRNA2
md5:063b1024d68e26716b7f38caf958316f	md5:063b1024d68e26716b7f38caf958316f	three_prime_cis_splice_site	3041	3042	1e-06	+	.	Parent=mRNA2
md5:063b1024d68e26716b7f38caf958316f	gth	exon	3043	3506	0.974	+	.	Parent=mRNA2
md5:063b1024d68e26716b7f38caf958316f	gth	mRNA	3025	3506	.	+	.	ID=mRNA3;Parent=gene2;Target=md5:f1a0d426e93585553b21aa1a47aa2970 1 327 +,md5:a9dcd316817972a94c0af505715b10bc 1 426 +
md5:063b1024d68e26716b7f38caf958316f	gth	exon	3025	3506	0.974	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/gt_extractfeat_succ_1.fas000066400000000000000000000001521211610345200226070ustar00rootroot00000000000000>foo
AAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
genometools-1.5.1/testdata/gt_extractfeat_succ_1.fas.gz000066400000000000000000000000711211610345200232260ustar00rootroot00000000000000^Egt_extractfeat_succ_1.fasKrg.jgenometools-1.5.1/testdata/gt_extractfeat_succ_1.gff3000066400000000000000000000001061211610345200226620ustar00rootroot00000000000000##gff-version   3
##sequence-region foo 1 100
foo	.	gene	1	10	.	.	.	.
genometools-1.5.1/testdata/gt_extractfeat_succ_1.out000066400000000000000000000000231211610345200226420ustar00rootroot00000000000000>gene_1
AAAAAAAAAA
genometools-1.5.1/testdata/gt_extractfeat_succ_2.fas000066400000000000000000000001521211610345200226100ustar00rootroot00000000000000>foo
AAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
genometools-1.5.1/testdata/gt_extractfeat_succ_2.gff3000066400000000000000000000002721211610345200226670ustar00rootroot00000000000000##gff-version   3
##sequence-region foo 1 100
foo	.	gene	1	100	.	.	.	ID=gene1
foo	.	exon	1	10	.	.	.	Parent=gene1
foo	.	exon	41	50	.	.	.	Parent=gene1
foo	.	exon	91	100	.	.	.	Parent=gene1
genometools-1.5.1/testdata/gt_extractfeat_succ_2.out1000066400000000000000000000001551211610345200227320ustar00rootroot00000000000000>gene_1
AAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
genometools-1.5.1/testdata/gt_extractfeat_succ_2.out2000066400000000000000000000000711211610345200227300ustar00rootroot00000000000000>exon_1
AAAAAAAAAA
>exon_2
GGGGGGGGGG
>exon_3
CCCCCCCCCC
genometools-1.5.1/testdata/gt_extractfeat_succ_2.out3000066400000000000000000000000601211610345200227270ustar00rootroot00000000000000>exon_1 (joined)
AAAAAAAAAAGGGGGGGGGGCCCCCCCCCC
genometools-1.5.1/testdata/gt_extractfeat_succ_3.fas000066400000000000000000000001521211610345200226110ustar00rootroot00000000000000>foo
AAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
genometools-1.5.1/testdata/gt_extractfeat_succ_3.gff3000066400000000000000000000004761211610345200226760ustar00rootroot00000000000000##gff-version   3
##sequence-region   foo 1 100
foo	.	gene	1	100	.	.	.	ID=gene1
foo	.	mRNA	1	50	.	.	.	ID=mRNA1;Parent=gene1
foo	.	exon	1	10	.	.	.	Parent=mRNA1
foo	.	exon	41	50	.	.	.	Parent=mRNA1
foo	.	mRNA	41	100	.	.	.	ID=mRNA2;Parent=gene1
foo	.	exon	41	50	.	.	.	Parent=mRNA2
foo	.	exon	91	100	.	.	.	Parent=mRNA2
###
genometools-1.5.1/testdata/gt_extractfeat_succ_3.out000066400000000000000000000001141211610345200226450ustar00rootroot00000000000000>exon_1 (joined)
AAAAAAAAAAGGGGGGGGGG
>exon_2 (joined)
GGGGGGGGGGCCCCCCCCCC
genometools-1.5.1/testdata/gt_extractfeat_target.fas000066400000000000000000000034721211610345200227300ustar00rootroot00000000000000>mRNA_1 (joined) [target IDs md5:14c0ff5e76ef8ac009fdcc923f701356]
GAGACACAGGACTTCGGGATCTTGGGCAGCTGGAACAAGATCTTGTTTTTGGAGATGCAGGTGCCAAGGACGTTATCAACTTTCTGAGGACGAATCAGGTGAATAAGTTTGAAACATGACAAAAAAAACTTGATAGCCGCATTGATTTAGTGTTTGAAATGACACATCATGTATTTAAAATGCAGGACACAAACCCGGAAAACAAATTACGGCTTTTGATGATTTATGCAACAGTGTACCCCGAGAAGTTTGAAGGTGACAAGGGTGTGAAGCTAATGCAGGTAGCTTTTCGTGTGATAGAGACCCCTTGTAATGCATGGAACAACTTGCTAAACAAATACTGCATTTATGTTATCAGCTTGCTAGATTATCACCTGTGGATATGAAGGTTATAAGCAACATGCAATTGATAGCTGGATCCCCAGAAAACAAAGCTAAGTCCGGTAGTTTCTCCCTCAAATTTGACG
>mRNA_2 (joined) [target IDs md5:527995da853a37f9c47e616ce237d523,md5:a9dcd316817972a94c0af505715b10bc]
CCTTATTTTTTTTCTTCATATGGGTCATTTGGTTCATACTCTATATACTTTTGTGTCACAATTTAACTCTATATATTAGTCTCTACGTCGACTTAATGGAAAAAGTGAAGATGATAGCTTCTAATTTGCTTTATTTATTTATAAACTTTTGGCTATTATTGATTCTTCTGATGTAAGTTAATTTTAAGTTTCGAGTTATATAGCAATCGTTAAGTTGGCAAAAGATTTTAACCCTCGAGACTTTTTGGACAACAAAACGCAAATATGATAGAGCGGAAGCTCATTAAAAAATCGTTTTAGAGCAATGTCACCAAACAAAGAAAATCCATTTCCCAATAAAAAAACAACGAATATAAAATTCGATTATATATTTACCATCAACCACTTAACAGACCACAAAATGAAGGCTGTTTACGGATTCAACACAGATTAACGGGTATGTATGTATGATCTAGGCAACGGTGGTGGTGGGACCAGGATAAGCAGGAAGAGTCATGATCCGCTTGTCTACAACTGGACCTCCCACAGTGAAATGGTACAGACTCTGAAAGCTAGAGTCATTAATCCCCAGAACCTCGTGCACTGGATCATCGAAATAGCACCCAATCCCGGTTGCTGAGATCCCCATTGCGTGTGCTTCCAGGTACAAAACTTGTCCAACAACACCCGTCTCCCAGAACAGTCGAGGGTACATCCATGAGCCCTTCTCCCGCAGTGCTGGTTCAAACGGACAACAAAACGCAAATATGATAGAGCGGAAGCTCATTAAAAAATCGTTTTAGAGCAATGTCACCAAACAAAGAAAATCCATTTCCCAATAAAAAAACAACGAATATAAAATTCGATTATATATTTACCATCAACCACTTAACAGACCACAAAATGAAGGCTGTTTACGGATTCAACACAGATTAACGGGTATGTATGTATGATCTAGGCAACGGTGGTGGTGGGACCAGGATAAGCAGGAAGAGTCATGATCCGCTTGTCTACAACTGGACCTCCCACAGTGAAATGGTACAGACTCTGAAAGCTAGAGTCATTAATCCCCAGAACCTCGTGCACTGGATCATCGAAATAGCACCCAATCCCGGTTGCTGAGATCCCCATTGCGTGTGCTTCCAGGTACAAAACTTGTCCAACAACACCCGTCTCCCAGAACAGTCGAGGGTACATCCATGAGCCCTTCTCCCGCAGTGCTGGTTCAAAC
genometools-1.5.1/testdata/gt_fingerprint_extract.out000066400000000000000000000001521211610345200231570ustar00rootroot00000000000000>SQ;8720010
TTTTTTTTTTTTTTTTTCCTGACAAAACCCCAAGACTCAATTTAATCAATCCTCAAATTTACATGATACCAACGTAATGGGAGCTTAAAAATA
genometools-1.5.1/testdata/gt_gff3_addintrons_overlapping_exons.gff3000066400000000000000000000353201211610345200260150ustar00rootroot00000000000000##gff-version 3
##sequence-region chr6_ssto_hap7 1832076 30559309
chr6_ssto_hap7	.	gene	1832076	30559309	.	+	.	ID=ABCF1;Name=ABCF1
chr6_ssto_hap7	.	mRNA	1832076	30559309	.	+	.	ID=NM_001025091;Parent=ABCF1;Name=NM_001025091
chr6_ssto_hap7	.	mRNA	1832076	30559309	.	+	.	ID=NM_001090;Parent=ABCF1;Name=NM_001090
chr6_ssto_hap7	.	exon	1832076	1832243	.	+	.	ID=exon1;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1832805	1832972	.	+	.	ID=exon2;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1838094	1838140	.	+	.	ID=exon3;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1838503	1838598	.	+	.	ID=exon4;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1838761	1838887	.	+	.	ID=exon5;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1838825	1838871	.	+	.	ID=exon6;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1839033	1839070	.	+	.	ID=exon7;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1839155	1839262	.	+	.	ID=exon8;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1839234	1839329	.	+	.	ID=exon9;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1839492	1839618	.	+	.	ID=exon10;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1839764	1839801	.	+	.	ID=exon11;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1839886	1839993	.	+	.	ID=exon12;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1840616	1840690	.	+	.	ID=exon13;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1841090	1841203	.	+	.	ID=exon14;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1841348	1841422	.	+	.	ID=exon15;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1841822	1841935	.	+	.	ID=exon16;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1843079	1843192	.	+	.	ID=exon17;Parent=NM_001025091
chr6_ssto_hap7	.	exon	1843751	1843873	.	+	.	ID=exon18;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1843812	1843925	.	+	.	ID=exon19;Parent=NM_001025091
chr6_ssto_hap7	.	exon	1844293	1844393	.	+	.	ID=exon20;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1844484	1844606	.	+	.	ID=exon21;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1844490	1844575	.	+	.	ID=exon22;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1844877	1845016	.	+	.	ID=exon23;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1845026	1845126	.	+	.	ID=exon24;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1845103	1845251	.	+	.	ID=exon25;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1845223	1845308	.	+	.	ID=exon26;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1845610	1845749	.	+	.	ID=exon27;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1845836	1845984	.	+	.	ID=exon28;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1845945	1846028	.	+	.	ID=exon29;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1846243	1846367	.	+	.	ID=exon30;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1846564	1846676	.	+	.	ID=exon31;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1846678	1846761	.	+	.	ID=exon32;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1846819	1846990	.	+	.	ID=exon33;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1846976	1847100	.	+	.	ID=exon34;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1847159	1847233	.	+	.	ID=exon35;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1847297	1847409	.	+	.	ID=exon36;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1847326	1847396	.	+	.	ID=exon37;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1847552	1847723	.	+	.	ID=exon38;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1847892	1847966	.	+	.	ID=exon39;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1848059	1848129	.	+	.	ID=exon40;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1850366	1850398	.	+	.	ID=exon41;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1850484	1850652	.	+	.	ID=exon42;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1850827	1850891	.	+	.	ID=exon43;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1850984	1851056	.	+	.	ID=exon44;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1851099	1851131	.	+	.	ID=exon45;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1851213	1852211	.	+	.	ID=exon46;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1851217	1851385	.	+	.	ID=exon47;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1851560	1851624	.	+	.	ID=exon48;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1851717	1851789	.	+	.	ID=exon49;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1851946	1852944	.	+	.	ID=exon50;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1871448	1871615	.	+	.	ID=exon51;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1877467	1877513	.	+	.	ID=exon52;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1877876	1877971	.	+	.	ID=exon53;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1878134	1878260	.	+	.	ID=exon54;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1878406	1878443	.	+	.	ID=exon55;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1878528	1878635	.	+	.	ID=exon56;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1879990	1880064	.	+	.	ID=exon57;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1880464	1880577	.	+	.	ID=exon58;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1882453	1882566	.	+	.	ID=exon59;Parent=NM_001025091
chr6_ssto_hap7	.	exon	1883125	1883247	.	+	.	ID=exon60;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1883667	1883767	.	+	.	ID=exon61;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1883864	1883949	.	+	.	ID=exon62;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1884251	1884390	.	+	.	ID=exon63;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1884477	1884625	.	+	.	ID=exon64;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1885319	1885402	.	+	.	ID=exon65;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1885617	1885741	.	+	.	ID=exon66;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1885938	1886050	.	+	.	ID=exon67;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1886193	1886364	.	+	.	ID=exon68;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1886533	1886607	.	+	.	ID=exon69;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1886700	1886770	.	+	.	ID=exon70;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1887242	1887409	.	+	.	ID=exon71;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1889741	1889773	.	+	.	ID=exon72;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1889859	1890027	.	+	.	ID=exon73;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1890202	1890266	.	+	.	ID=exon74;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1890359	1890431	.	+	.	ID=exon75;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1890588	1891586	.	+	.	ID=exon76;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1893258	1893304	.	+	.	ID=exon77;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1893667	1893762	.	+	.	ID=exon78;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1893925	1894051	.	+	.	ID=exon79;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1894197	1894234	.	+	.	ID=exon80;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1894319	1894426	.	+	.	ID=exon81;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1895780	1895854	.	+	.	ID=exon82;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1896255	1896368	.	+	.	ID=exon83;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1898243	1898356	.	+	.	ID=exon84;Parent=NM_001025091
chr6_ssto_hap7	.	exon	1898915	1899037	.	+	.	ID=exon85;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1899457	1899557	.	+	.	ID=exon86;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1899654	1899739	.	+	.	ID=exon87;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1900041	1900180	.	+	.	ID=exon88;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1900267	1900415	.	+	.	ID=exon89;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1901109	1901192	.	+	.	ID=exon90;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1901407	1901531	.	+	.	ID=exon91;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1901728	1901840	.	+	.	ID=exon92;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1901983	1902154	.	+	.	ID=exon93;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1902323	1902397	.	+	.	ID=exon94;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1902490	1902560	.	+	.	ID=exon95;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1905537	1905569	.	+	.	ID=exon96;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1905655	1905823	.	+	.	ID=exon97;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1905998	1906062	.	+	.	ID=exon98;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1906155	1906227	.	+	.	ID=exon99;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1906384	1907381	.	+	.	ID=exon100;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1921024	1921191	.	+	.	ID=exon101;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1927040	1927086	.	+	.	ID=exon102;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1927449	1927544	.	+	.	ID=exon103;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1927707	1927833	.	+	.	ID=exon104;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1927979	1928016	.	+	.	ID=exon105;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1928101	1928208	.	+	.	ID=exon106;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1929562	1929636	.	+	.	ID=exon107;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1930037	1930150	.	+	.	ID=exon108;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1932025	1932138	.	+	.	ID=exon109;Parent=NM_001025091
chr6_ssto_hap7	.	exon	1932697	1932819	.	+	.	ID=exon110;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1933239	1933339	.	+	.	ID=exon111;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1933436	1933521	.	+	.	ID=exon112;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1933823	1933962	.	+	.	ID=exon113;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1934049	1934197	.	+	.	ID=exon114;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1934891	1934974	.	+	.	ID=exon115;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1935189	1935313	.	+	.	ID=exon116;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1935510	1935622	.	+	.	ID=exon117;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1935765	1935936	.	+	.	ID=exon118;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1936105	1936179	.	+	.	ID=exon119;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1936272	1936342	.	+	.	ID=exon120;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1939319	1939351	.	+	.	ID=exon121;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1939437	1939605	.	+	.	ID=exon122;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1939780	1939844	.	+	.	ID=exon123;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1939937	1940009	.	+	.	ID=exon124;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	1940166	1941163	.	+	.	ID=exon125;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2051221	2051388	.	+	.	ID=exon126;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2057238	2057284	.	+	.	ID=exon127;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2057647	2057742	.	+	.	ID=exon128;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2057905	2058031	.	+	.	ID=exon129;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2058177	2058214	.	+	.	ID=exon130;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2058299	2058406	.	+	.	ID=exon131;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2059761	2059835	.	+	.	ID=exon132;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2060235	2060348	.	+	.	ID=exon133;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2062224	2062337	.	+	.	ID=exon134;Parent=NM_001025091
chr6_ssto_hap7	.	exon	2062896	2063018	.	+	.	ID=exon135;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2063438	2063538	.	+	.	ID=exon136;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2063635	2063720	.	+	.	ID=exon137;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2064022	2064161	.	+	.	ID=exon138;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2064248	2064396	.	+	.	ID=exon139;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2065090	2065173	.	+	.	ID=exon140;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2065388	2065512	.	+	.	ID=exon141;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2065709	2065821	.	+	.	ID=exon142;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2065964	2066135	.	+	.	ID=exon143;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2066304	2066378	.	+	.	ID=exon144;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2066471	2066541	.	+	.	ID=exon145;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2069511	2069543	.	+	.	ID=exon146;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2069629	2069797	.	+	.	ID=exon147;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2069972	2070036	.	+	.	ID=exon148;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2070129	2070201	.	+	.	ID=exon149;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	2070358	2071356	.	+	.	ID=exon150;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30539170	30539337	.	+	.	ID=exon151;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30545186	30545232	.	+	.	ID=exon152;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30545595	30545690	.	+	.	ID=exon153;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30545853	30545979	.	+	.	ID=exon154;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30546125	30546162	.	+	.	ID=exon155;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30546247	30546354	.	+	.	ID=exon156;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30547708	30547782	.	+	.	ID=exon157;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30548183	30548296	.	+	.	ID=exon158;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30550171	30550284	.	+	.	ID=exon159;Parent=NM_001025091
chr6_ssto_hap7	.	exon	30550843	30550965	.	+	.	ID=exon160;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30551385	30551485	.	+	.	ID=exon161;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30551582	30551667	.	+	.	ID=exon162;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30551969	30552108	.	+	.	ID=exon163;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30552195	30552343	.	+	.	ID=exon164;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30553037	30553120	.	+	.	ID=exon165;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30553335	30553459	.	+	.	ID=exon166;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30553656	30553768	.	+	.	ID=exon167;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30553911	30554082	.	+	.	ID=exon168;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30554251	30554325	.	+	.	ID=exon169;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30554418	30554488	.	+	.	ID=exon170;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30557465	30557497	.	+	.	ID=exon171;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30557583	30557751	.	+	.	ID=exon172;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30557926	30557990	.	+	.	ID=exon173;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30558083	30558155	.	+	.	ID=exon174;Parent=NM_001090,NM_001025091
chr6_ssto_hap7	.	exon	30558312	30559309	.	+	.	ID=exon175;Parent=NM_001090,NM_001025091
genometools-1.5.1/testdata/gt_gff3_addintrons_overlapping_exons_with_introns.gff3000066400000000000000000000727651211610345200306420ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr6_ssto_hap7 1832076 30559309
chr6_ssto_hap7	.	gene	1832076	30559309	.	+	.	ID=gene1;Name=ABCF1
chr6_ssto_hap7	.	mRNA	1832076	30559309	.	+	.	ID=mRNA1;Parent=gene1;Name=NM_001025091
chr6_ssto_hap7	.	intron	1832244	1832804	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1832973	1838093	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1838141	1838502	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1838599	1838760	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1838888	1839032	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1839071	1839154	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1839263	1839491	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1839619	1839763	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1839802	1839885	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1839994	1840615	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1840691	1841089	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1841204	1841347	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1841423	1841821	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1841936	1843078	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	exon	1843079	1843192	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1843193	1843750	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	exon	1843812	1843925	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1843874	1844292	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1844394	1844483	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1844607	1844876	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1845017	1845025	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1845127	1845222	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1845309	1845609	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1845750	1845835	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1845985	1846242	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1846368	1846563	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1846677	1846677	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1846762	1846818	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1846991	1847158	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1847234	1847296	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1847410	1847551	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1847724	1847891	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1847967	1848058	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1848130	1850365	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1850399	1850483	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1850653	1850826	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1850892	1850983	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1851057	1851098	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1851132	1851212	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1852212	1871447	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1871616	1877466	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1877514	1877875	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1877972	1878133	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1878261	1878405	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1878444	1878527	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1878636	1879989	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1880065	1880463	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1880578	1882452	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	exon	1882453	1882566	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1882567	1883124	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1883248	1883666	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1883768	1883863	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1883950	1884250	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1884391	1884476	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1884626	1885318	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1885403	1885616	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1885742	1885937	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1886051	1886192	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1886365	1886532	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1886608	1886699	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1886771	1887241	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1887410	1889740	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1889774	1889858	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1890028	1890201	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1890267	1890358	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1890432	1890587	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1891587	1893257	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1893305	1893666	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1893763	1893924	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1894052	1894196	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1894235	1894318	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1894427	1895779	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1895855	1896254	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1896369	1898242	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	exon	1898243	1898356	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1898357	1898914	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1899038	1899456	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1899558	1899653	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1899740	1900040	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1900181	1900266	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1900416	1901108	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1901193	1901406	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1901532	1901727	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1901841	1901982	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1902155	1902322	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1902398	1902489	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1902561	1905536	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1905570	1905654	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1905824	1905997	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1906063	1906154	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1906228	1906383	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1907382	1921023	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1921192	1927039	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1927087	1927448	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1927545	1927706	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1927834	1927978	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1928017	1928100	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1928209	1929561	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1929637	1930036	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1930151	1932024	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	exon	1932025	1932138	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1932139	1932696	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1932820	1933238	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1933340	1933435	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1933522	1933822	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1933963	1934048	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1934198	1934890	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1934975	1935188	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1935314	1935509	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1935623	1935764	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1935937	1936104	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1936180	1936271	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1936343	1939318	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1939352	1939436	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1939606	1939779	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1939845	1939936	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1940010	1940165	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	1941164	2051220	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2051389	2057237	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2057285	2057646	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2057743	2057904	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2058032	2058176	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2058215	2058298	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2058407	2059760	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2059836	2060234	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2060349	2062223	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	exon	2062224	2062337	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2062338	2062895	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2063019	2063437	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2063539	2063634	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2063721	2064021	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2064162	2064247	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2064397	2065089	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2065174	2065387	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2065513	2065708	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2065822	2065963	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2066136	2066303	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2066379	2066470	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2066542	2069510	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2069544	2069628	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2069798	2069971	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2070037	2070128	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2070202	2070357	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	2071357	30539169	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30539338	30545185	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30545233	30545594	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30545691	30545852	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30545980	30546124	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30546163	30546246	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30546355	30547707	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30547783	30548182	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30548297	30550170	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	exon	30550171	30550284	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30550285	30550842	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30550966	30551384	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30551486	30551581	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30551668	30551968	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30552109	30552194	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30552344	30553036	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30553121	30553334	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30553460	30553655	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30553769	30553910	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30554083	30554250	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30554326	30554417	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30554489	30557464	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30557498	30557582	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30557752	30557925	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30557991	30558082	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	intron	30558156	30558311	.	+	.	Parent=mRNA1
chr6_ssto_hap7	.	mRNA	1832076	30559309	.	+	.	ID=mRNA2;Parent=gene1;Name=NM_001090
chr6_ssto_hap7	.	exon	1832076	1832243	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1832244	1832804	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1832805	1832972	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1832973	1838093	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1838094	1838140	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1838141	1838502	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1838503	1838598	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1838599	1838760	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1838761	1838887	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1838825	1838871	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1838888	1839032	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1839033	1839070	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1839071	1839154	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1839155	1839262	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1839234	1839329	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1839263	1839491	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1839492	1839618	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1839619	1839763	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1839764	1839801	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1839802	1839885	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1839886	1839993	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1839994	1840615	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1840616	1840690	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1840691	1841089	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1841090	1841203	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1841204	1841347	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1841348	1841422	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1841423	1841821	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1841822	1841935	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1841936	1843750	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1843751	1843873	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1843874	1844292	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1844293	1844393	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1844394	1844483	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1844484	1844606	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1844490	1844575	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1844607	1844876	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1844877	1845016	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1845017	1845025	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1845026	1845126	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1845103	1845251	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1845127	1845222	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1845223	1845308	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1845309	1845609	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1845610	1845749	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1845750	1845835	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1845836	1845984	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1845945	1846028	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1845985	1846242	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1846243	1846367	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1846368	1846563	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1846564	1846676	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1846677	1846677	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1846678	1846761	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1846762	1846818	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1846819	1846990	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1846976	1847100	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1846991	1847158	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1847159	1847233	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1847234	1847296	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1847297	1847409	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1847326	1847396	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1847410	1847551	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1847552	1847723	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1847724	1847891	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1847892	1847966	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1847967	1848058	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1848059	1848129	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1848130	1850365	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1850366	1850398	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1850399	1850483	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1850484	1850652	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1850653	1850826	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1850827	1850891	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1850892	1850983	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1850984	1851056	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1851057	1851098	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1851099	1851131	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1851132	1851212	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1851213	1852211	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1851217	1851385	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1851560	1851624	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1851717	1851789	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	exon	1851946	1852944	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1852212	1871447	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1871448	1871615	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1871616	1877466	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1877467	1877513	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1877514	1877875	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1877876	1877971	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1877972	1878133	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1878134	1878260	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1878261	1878405	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1878406	1878443	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1878444	1878527	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1878528	1878635	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1878636	1879989	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1879990	1880064	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1880065	1880463	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1880464	1880577	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1880578	1883124	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1883125	1883247	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1883248	1883666	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1883667	1883767	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1883768	1883863	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1883864	1883949	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1883950	1884250	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1884251	1884390	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1884391	1884476	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1884477	1884625	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1884626	1885318	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1885319	1885402	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1885403	1885616	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1885617	1885741	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1885742	1885937	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1885938	1886050	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1886051	1886192	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1886193	1886364	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1886365	1886532	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1886533	1886607	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1886608	1886699	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1886700	1886770	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1886771	1887241	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1887242	1887409	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1887410	1889740	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1889741	1889773	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1889774	1889858	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1889859	1890027	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1890028	1890201	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1890202	1890266	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1890267	1890358	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1890359	1890431	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1890432	1890587	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1890588	1891586	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1891587	1893257	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1893258	1893304	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1893305	1893666	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1893667	1893762	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1893763	1893924	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1893925	1894051	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1894052	1894196	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1894197	1894234	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1894235	1894318	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1894319	1894426	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1894427	1895779	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1895780	1895854	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1895855	1896254	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1896255	1896368	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1896369	1898914	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1898915	1899037	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1899038	1899456	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1899457	1899557	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1899558	1899653	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1899654	1899739	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1899740	1900040	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1900041	1900180	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1900181	1900266	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1900267	1900415	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1900416	1901108	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1901109	1901192	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1901193	1901406	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1901407	1901531	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1901532	1901727	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1901728	1901840	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1901841	1901982	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1901983	1902154	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1902155	1902322	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1902323	1902397	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1902398	1902489	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1902490	1902560	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1902561	1905536	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1905537	1905569	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1905570	1905654	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1905655	1905823	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1905824	1905997	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1905998	1906062	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1906063	1906154	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1906155	1906227	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1906228	1906383	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1906384	1907381	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1907382	1921023	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1921024	1921191	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1921192	1927039	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1927040	1927086	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1927087	1927448	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1927449	1927544	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1927545	1927706	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1927707	1927833	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1927834	1927978	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1927979	1928016	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1928017	1928100	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1928101	1928208	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1928209	1929561	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1929562	1929636	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1929637	1930036	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1930037	1930150	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1930151	1932696	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1932697	1932819	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1932820	1933238	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1933239	1933339	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1933340	1933435	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1933436	1933521	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1933522	1933822	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1933823	1933962	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1933963	1934048	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1934049	1934197	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1934198	1934890	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1934891	1934974	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1934975	1935188	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1935189	1935313	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1935314	1935509	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1935510	1935622	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1935623	1935764	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1935765	1935936	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1935937	1936104	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1936105	1936179	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1936180	1936271	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1936272	1936342	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1936343	1939318	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1939319	1939351	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1939352	1939436	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1939437	1939605	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1939606	1939779	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1939780	1939844	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1939845	1939936	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1939937	1940009	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1940010	1940165	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	1940166	1941163	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	1941164	2051220	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2051221	2051388	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2051389	2057237	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2057238	2057284	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2057285	2057646	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2057647	2057742	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2057743	2057904	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2057905	2058031	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2058032	2058176	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2058177	2058214	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2058215	2058298	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2058299	2058406	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2058407	2059760	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2059761	2059835	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2059836	2060234	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2060235	2060348	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2060349	2062895	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2062896	2063018	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2063019	2063437	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2063438	2063538	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2063539	2063634	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2063635	2063720	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2063721	2064021	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2064022	2064161	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2064162	2064247	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2064248	2064396	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2064397	2065089	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2065090	2065173	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2065174	2065387	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2065388	2065512	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2065513	2065708	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2065709	2065821	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2065822	2065963	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2065964	2066135	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2066136	2066303	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2066304	2066378	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2066379	2066470	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2066471	2066541	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2066542	2069510	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2069511	2069543	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2069544	2069628	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2069629	2069797	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2069798	2069971	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2069972	2070036	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2070037	2070128	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2070129	2070201	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2070202	2070357	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	2070358	2071356	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	2071357	30539169	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30539170	30539337	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30539338	30545185	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30545186	30545232	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30545233	30545594	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30545595	30545690	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30545691	30545852	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30545853	30545979	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30545980	30546124	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30546125	30546162	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30546163	30546246	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30546247	30546354	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30546355	30547707	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30547708	30547782	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30547783	30548182	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30548183	30548296	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30548297	30550842	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30550843	30550965	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30550966	30551384	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30551385	30551485	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30551486	30551581	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30551582	30551667	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30551668	30551968	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30551969	30552108	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30552109	30552194	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30552195	30552343	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30552344	30553036	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30553037	30553120	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30553121	30553334	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30553335	30553459	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30553460	30553655	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30553656	30553768	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30553769	30553910	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30553911	30554082	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30554083	30554250	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30554251	30554325	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30554326	30554417	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30554418	30554488	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30554489	30557464	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30557465	30557497	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30557498	30557582	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30557583	30557751	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30557752	30557925	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30557926	30557990	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30557991	30558082	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30558083	30558155	.	+	.	Parent=mRNA1,mRNA2
chr6_ssto_hap7	.	intron	30558156	30558311	.	+	.	Parent=mRNA2
chr6_ssto_hap7	.	exon	30558312	30559309	.	+	.	Parent=mRNA1,mRNA2
###
genometools-1.5.1/testdata/gt_gff3_fail_1.gff3000066400000000000000000000001341211610345200211540ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
##sequence-region   ctg123 1 1497228
genometools-1.5.1/testdata/gt_gff3_illegal_feature_start.gff3000066400000000000000000000001111211610345200243550ustar00rootroot00000000000000##gff-version   3
##sequence-region   sr 1 1000
sr	.	gene	0	1000	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_illegal_region_start.gff3000066400000000000000000000001111211610345200242050ustar00rootroot00000000000000##gff-version   3
##sequence-region   sr 0 1000
sr	.	gene	1	1000	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_offset_test.gff3000066400000000000000000000002241211610345200223460ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1000 9000
##sequence-region   seq2 1000 9000
seq1	.	gene	1000	9000	.	+	.	.
seq2	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_offset_test.out-1000066400000000000000000000002201211610345200224620ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 999 8999
##sequence-region   seq2 999 8999
seq1	.	gene	999	8999	.	+	.	.
seq2	.	gene	999	8999	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_offset_test.out-999000066400000000000000000000002101211610345200226530ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 8001
##sequence-region   seq2 1 8001
seq1	.	gene	1	8001	.	+	.	.
seq2	.	gene	1	8001	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_offset_test.out1000000066400000000000000000000002301211610345200226260ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 2000 10000
##sequence-region   seq2 2000 10000
seq1	.	gene	2000	10000	.	+	.	.
seq2	.	gene	2000	10000	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_offsetfile_test.gff3000066400000000000000000000002201211610345200232020ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
##sequence-region   seq2 1 10000
seq1	.	gene	1000	9000	.	+	.	.
seq2	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_offsetfile_test.offsetfile000066400000000000000000000000521211610345200245060ustar00rootroot00000000000000offsets = {
  seq1 = 1000,
  seq2 = 500
}
genometools-1.5.1/testdata/gt_gff3_offsetfile_test.out000066400000000000000000000002261211610345200231720ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1001 11000
##sequence-region   seq2 501 10500
seq1	.	gene	2000	10000	.	+	.	.
seq2	.	gene	1500	9500	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_prob_1.gff3000066400000000000000000000017461211610345200212150ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 4294967295
NC_003070	gth	gene	5842386	5842719	.	+	.	ID=gene485
NC_003070	gth	mRNA	5842386	5842719	.	+	.	ID=mRNA517;Parent=gene485
NC_003070	gth	exon	5842386	5842719	0.934132	+	.	Parent=mRNA517
###
# the following mRNA refers to an undefined gene
NC_003070	gth	mRNA	5869883	5872798	.	+	.	ID=mRNA520;Parent=gene488
NC_003070	gth	exon	5869883	5870106	0.812500	+	.	Parent=mRNA520
NC_003070	gth	exon	5872420	5872515	0.781250	+	.	Parent=mRNA520
NC_003070	gth	exon	5872601	5872798	0.742424	+	.	Parent=mRNA520
NC_003070	gth	mRNA	5869902	5870107	.	+	.	ID=mRNA521;Parent=gene488
NC_003070	gth	exon	5869902	5870107	0.766990	+	.	Parent=mRNA521
###
NC_003070	gth	gene	5870624	5871356	.	-	.	ID=gene489
NC_003070	gth	mRNA	5870624	5871356	.	-	.	ID=mRNA522;Parent=gene489
NC_003070	gth	exon	5870624	5870822	1.000000	-	.	Parent=mRNA522
NC_003070	gth	exon	5870939	5871023	0.976471	-	.	Parent=mRNA522
NC_003070	gth	exon	5871121	5871356	0.775424	-	.	Parent=mRNA522
###
genometools-1.5.1/testdata/gt_gff3_prob_10.in000066400000000000000000000016211211610345200210460ustar00rootroot00000000000000##gff-version   3
#
#
### gene g1
chr8	AUGUSTUS	gene	3922	44514	1	-	.	ID=g1
chr8	AUGUSTUS	CDS	3922	4093	.	-	1	Parent=g1
chr8	AUGUSTUS	CDS	6417	6577	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	12072	12161	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	17635	17730	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	18876	18994	.	-	2	Parent=g1
chr8	AUGUSTUS	CDS	21665	21797	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	34644	34751	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	36308	36401	.	-	1	Parent=g1
chr8	AUGUSTUS	CDS	44465	44514	.	-	0	Parent=g1
### end gene g1
### gene g2
chr8	AUGUSTUS	gene	309281	310246	1	-	.	ID=g2
chr8	AUGUSTUS	CDS	309281	310246	.	-	0	Parent=g2
### end gene g2
### gene g3
chr8	AUGUSTUS	gene	310605	311468	1	+	.	ID=g3
chr8	AUGUSTUS	CDS	310605	310617	.	+	0	Parent=g3
chr8	AUGUSTUS	CDS	310822	311468	.	+	2	Parent=g3
### end gene g3
### gene g4
chr8	AUGUSTUS	gene	471665	472078	1	-	.	ID=g4
chr8	AUGUSTUS	CDS	471665	472078	.	-	0	Parent=g4
### end gene g4
genometools-1.5.1/testdata/gt_gff3_prob_10.out000066400000000000000000000016111211610345200212460ustar00rootroot00000000000000##gff-version   3
#
#
##sequence-region   chr8 3922 472078
chr8	AUGUSTUS	gene	3922	44514	1	-	.	ID=gene1
chr8	AUGUSTUS	CDS	3922	4093	.	-	1	Parent=gene1
chr8	AUGUSTUS	CDS	6417	6577	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	12072	12161	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	17635	17730	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	18876	18994	.	-	2	Parent=gene1
chr8	AUGUSTUS	CDS	21665	21797	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	34644	34751	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	36308	36401	.	-	1	Parent=gene1
chr8	AUGUSTUS	CDS	44465	44514	.	-	0	Parent=gene1
###
chr8	AUGUSTUS	gene	309281	310246	1	-	.	ID=gene2
chr8	AUGUSTUS	CDS	309281	310246	.	-	0	Parent=gene2
###
chr8	AUGUSTUS	gene	310605	311468	1	+	.	ID=gene3
chr8	AUGUSTUS	CDS	310605	310617	.	+	0	Parent=gene3
chr8	AUGUSTUS	CDS	310822	311468	.	+	2	Parent=gene3
###
chr8	AUGUSTUS	gene	471665	472078	1	-	.	ID=gene4
chr8	AUGUSTUS	CDS	471665	472078	.	-	0	Parent=gene4
###
genometools-1.5.1/testdata/gt_gff3_prob_11.in000066400000000000000000000021461211610345200210520ustar00rootroot00000000000000##gff-version   3
#
#
### gene g1
chr8	AUGUSTUS	gene	3922	44514	1	-	.	ID=g1
chr8	AUGUSTUS	transcript	3922	44514	.	-	.	ID=g1.t1
chr8	AUGUSTUS	CDS	3922	4093	.	-	1	Parent=g1
chr8	AUGUSTUS	CDS	6417	6577	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	12072	12161	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	17635	17730	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	18876	18994	.	-	2	Parent=g1
chr8	AUGUSTUS	CDS	21665	21797	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	34644	34751	.	-	0	Parent=g1
chr8	AUGUSTUS	CDS	36308	36401	.	-	1	Parent=g1
chr8	AUGUSTUS	CDS	44465	44514	.	-	0	Parent=g1
### end gene g1
### gene g2
chr8	AUGUSTUS	gene	309281	310246	1	-	.	ID=g2
chr8	AUGUSTUS	transcript	309281	310246	.	-	.	ID=g2.t1
chr8	AUGUSTUS	CDS	309281	310246	.	-	0	Parent=g2
### end gene g2
### gene g3
chr8	AUGUSTUS	gene	310605	311468	1	+	.	ID=g3
chr8	AUGUSTUS	transcript	310605	311468	.	+	.	ID=g3.t1
chr8	AUGUSTUS	CDS	310605	310617	.	+	0	Parent=g3
chr8	AUGUSTUS	CDS	310822	311468	.	+	2	Parent=g3
### end gene g3
### gene g4
chr8	AUGUSTUS	gene	471665	472078	1	-	.	ID=g4
chr8	AUGUSTUS	transcript	471665	472078	.	-	.	ID=g4.t1
chr8	AUGUSTUS	CDS	471665	472078	.	-	0	Parent=g4
### end gene g4
genometools-1.5.1/testdata/gt_gff3_prob_11.out000066400000000000000000000021021211610345200212430ustar00rootroot00000000000000##gff-version   3
#
#
##sequence-region   chr8 3922 472078
chr8	AUGUSTUS	gene	3922	44514	1	-	.	ID=gene1
chr8	AUGUSTUS	CDS	3922	4093	.	-	1	Parent=gene1
chr8	AUGUSTUS	CDS	6417	6577	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	12072	12161	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	17635	17730	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	18876	18994	.	-	2	Parent=gene1
chr8	AUGUSTUS	CDS	21665	21797	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	34644	34751	.	-	0	Parent=gene1
chr8	AUGUSTUS	CDS	36308	36401	.	-	1	Parent=gene1
chr8	AUGUSTUS	CDS	44465	44514	.	-	0	Parent=gene1
###
chr8	AUGUSTUS	transcript	3922	44514	.	-	.	.
chr8	AUGUSTUS	gene	309281	310246	1	-	.	ID=gene2
chr8	AUGUSTUS	CDS	309281	310246	.	-	0	Parent=gene2
###
chr8	AUGUSTUS	transcript	309281	310246	.	-	.	.
chr8	AUGUSTUS	gene	310605	311468	1	+	.	ID=gene3
chr8	AUGUSTUS	CDS	310605	310617	.	+	0	Parent=gene3
chr8	AUGUSTUS	CDS	310822	311468	.	+	2	Parent=gene3
###
chr8	AUGUSTUS	transcript	310605	311468	.	+	.	.
chr8	AUGUSTUS	gene	471665	472078	1	-	.	ID=gene4
chr8	AUGUSTUS	CDS	471665	472078	.	-	0	Parent=gene4
###
chr8	AUGUSTUS	transcript	471665	472078	.	-	.	.
genometools-1.5.1/testdata/gt_gff3_prob_12.gff3000066400000000000000000000004421211610345200212670ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001;Name=EDEN
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001
ctg123	.	CDS	1201	1500	.	+	0	ID=cds000001;Parent=mRNA00001
###
ctg123	.	CDS	3000	3902	.	+	0	ID=cds000001;Parent=mRNA00001
genometools-1.5.1/testdata/gt_gff3_prob_13.gff3000066400000000000000000000011621211610345200212700ustar00rootroot00000000000000Chr1	TAIR10	gene	52239	54692	.	+	.	ID=AT1G01110;Note=protein_coding_gene;Name=AT1G01110
Chr1	TAIR10	mRNA	52869	54685	.	+	.	ID=AT1G01110.1;Parent=AT1G01110;Name=AT1G01110.1;Index=1
Chr1	TAIR10	protein	53022	54494	.	+	.	ID=AT1G01110.1-Protein;Name=AT1G01110.1;Derives_from=AT1G01110.1
Chr1	TAIR10	CDS	53022	53183	.	+	0	Parent=AT1G01110.1,AT1G01110.1-Protein;
Chr1	TAIR10	mRNA	52239	54692	.	+	.	ID=AT1G01110.2;Parent=AT1G01110;Name=AT1G01110.2;Index=1
Chr1	TAIR10	protein	52239	54494	.	+	.	ID=AT1G01110.2-Protein;Name=AT1G01110.2;Derives_from=AT1G01110.2
Chr1	TAIR10	CDS	52239	52346	.	+	0	Parent=AT1G01110.2,AT1G01110.2-Protein;
genometools-1.5.1/testdata/gt_gff3_prob_2.in000066400000000000000000000011321211610345200207640ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 10000000
# 1 comment
#1  comment
# a comment
#a comment
# z comment
#z comment
# A comment
#A comment
# Z comment
#Z comment
NC_003070	gth	gene	5414975	5415790	0.998350	+	.	ID=gene1
NC_003070	gth	exon	5414975	5415294	0.996875	+	.	Parent=gene1
NC_003070	gth	exon	5415423	5415589	1.000000	+	.	Parent=gene1
NC_003070	gth	exon	5415672	5415790	1.000000	+	.	Parent=gene1
###
NC_003070	gth	gene	5415008	5415564	0.995338	+	.	ID=gene2
NC_003070	gth	exon	5415008	5415294	0.996516	+	.	Parent=gene2
NC_003070	gth	exon	5415423	5415564	0.992958	+	.	Parent=gene2
###
genometools-1.5.1/testdata/gt_gff3_prob_2.out000066400000000000000000000010751211610345200211730ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 10000000
# 1 comment
#1  comment
# a comment
#a comment
# z comment
#z comment
# A comment
#A comment
# Z comment
#Z comment
NC_003070	gth	gene	5414975	5415790	0.998	+	.	ID=gene1
NC_003070	gth	exon	5414975	5415294	0.997	+	.	Parent=gene1
NC_003070	gth	exon	5415423	5415589	1	+	.	Parent=gene1
NC_003070	gth	exon	5415672	5415790	1	+	.	Parent=gene1
###
NC_003070	gth	gene	5415008	5415564	0.995	+	.	ID=gene2
NC_003070	gth	exon	5415008	5415294	0.997	+	.	Parent=gene2
NC_003070	gth	exon	5415423	5415564	0.993	+	.	Parent=gene2
###
genometools-1.5.1/testdata/gt_gff3_prob_3.gff3000066400000000000000000000021211211610345200212030ustar00rootroot00000000000000##gff-version   3
##sequence-region   ENm001 40027 1703041
ENm001	.	gene	328776	338075	.	+	.	ID=gene1
ENm001	.	mRNA	328776	335792	.	+	.	ID=mRNA1;Parent=gene1
ENm001	VEGA_Known	exon	328776	328875	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	328841	328875	.	+	0	Parent=mRNA1
ENm001	VEGA_Known	CDS	329375	329465	.	+	1	Parent=mRNA1
ENm001	VEGA_Known	exon	329375	329465	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	329794	329981	.	+	0	Parent=mRNA1
ENm001	VEGA_Known	exon	329794	329981	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	335505	335652	.	+	1	Parent=mRNA1
ENm001	VEGA_Known	exon	335505	335792	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	335653	335655	.	+	0	Parent=mRNA1
ENm001	.	mRNA	328924	338075	.	+	.	ID=mRNA2;Parent=gene1
ENm001	VEGA_Known	exon	328924	329465	.	+	.	Parent=mRNA2
ENm001	VEGA_Known	CDS	329316	329465	.	+	0	Parent=mRNA2
ENm001	VEGA_Known	CDS	329794	329981	.	+	0	Parent=mRNA2
ENm001	VEGA_Known	exon	329794	329981	.	+	.	Parent=mRNA2
ENm001	VEGA_Known	CDS	335505	335652	.	+	1	Parent=mRNA2
ENm001	VEGA_Known	exon	335505	338075	.	+	.	Parent=mRNA2
ENm001	VEGA_Known	CDS	335653	335655	.	+	0	Parent=mRNA2
###
genometools-1.5.1/testdata/gt_gff3_prob_4.gff3000066400000000000000000000004361211610345200212130ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001;Name=EDEN
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001
ctg123	.	CDS	1201	1500	.	+	0	ID=cds000001;Parent=mRNA00001
ctg123	.	CDS	3000	3902	.	+	0	ID=cds000001;Parent=mRNA00001
genometools-1.5.1/testdata/gt_gff3_prob_5.in000066400000000000000000001050421211610345200207740ustar00rootroot00000000000000##gff-version   3
##sequence-region   ENm001 40027 1703041
ENm001	.	gene	1540185	1703041	.	-	.	ID=gene1
ENm001	.	mRNA	1540185	1703041	.	-	.	ID=mRNA1;Parent=gene1
ENm001	VEGA_Known	exon	1540185	1541316	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1541071	1541073	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	CDS	1541074	1541316	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	CDS	1547552	1547653	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1547552	1547653	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1549038	1549170	.	-	1	Parent=mRNA1
ENm001	VEGA_Known	exon	1549038	1549170	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1550601	1550664	.	-	2	Parent=mRNA1
ENm001	VEGA_Known	exon	1550601	1550664	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1554081	1554266	.	-	2	Parent=mRNA1
ENm001	VEGA_Known	exon	1554081	1554266	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1554586	1554791	.	-	1	Parent=mRNA1
ENm001	VEGA_Known	exon	1554586	1554791	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1557623	1557801	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1557623	1557801	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1564447	1564634	.	-	2	Parent=mRNA1
ENm001	VEGA_Known	exon	1564447	1564634	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1564803	1564955	.	-	2	Parent=mRNA1
ENm001	VEGA_Known	exon	1564803	1564955	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1575365	1575464	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1575365	1575464	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1575547	1575633	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1575547	1575633	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1586089	1586168	.	-	2	Parent=mRNA1
ENm001	VEGA_Known	exon	1586089	1586168	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1587409	1587504	.	-	2	Parent=mRNA1
ENm001	VEGA_Known	exon	1587409	1587504	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1589969	1590244	.	-	2	Parent=mRNA1
ENm001	VEGA_Known	exon	1589969	1590244	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1596593	1596710	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1596593	1596710	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1607045	1607299	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1607045	1607299	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1609975	1610125	.	-	1	Parent=mRNA1
ENm001	VEGA_Known	exon	1609975	1610125	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1612396	1612495	.	-	2	Parent=mRNA1
ENm001	VEGA_Known	exon	1612396	1612495	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1613785	1613988	.	-	2	Parent=mRNA1
ENm001	VEGA_Known	exon	1613785	1613988	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1620662	1622315	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1620662	1622315	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1640299	1640523	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1640299	1640523	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1690743	1690850	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1690743	1690850	.	-	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	1702869	1702949	.	-	0	Parent=mRNA1
ENm001	VEGA_Known	exon	1702869	1703041	.	-	.	Parent=mRNA1
ENm001	.	mRNA	1622120	1701172	.	-	.	ID=mRNA2;Parent=gene1
ENm001	VEGA_Known	CDS	1622120	1622315	.	-	0	Parent=mRNA2
ENm001	VEGA_Known	exon	1622120	1622315	.	-	.	Parent=mRNA2
ENm001	VEGA_Known	CDS	1640299	1640523	.	-	0	Parent=mRNA2
ENm001	VEGA_Known	exon	1640299	1640523	.	-	.	Parent=mRNA2
ENm001	VEGA_Known	CDS	1690743	1690805	.	-	0	Parent=mRNA2
ENm001	VEGA_Known	exon	1690743	1690850	.	-	.	Parent=mRNA2
ENm001	VEGA_Known	exon	1701124	1701172	.	-	.	Parent=mRNA2
###
ENm001	.	gene	1192756	1257031	.	-	.	ID=gene2
ENm001	.	mRNA	1192756	1257031	.	-	.	ID=mRNA3;Parent=gene2
ENm001	VEGA_Known	exon	1192756	1193282	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1193130	1193132	.	-	0	Parent=mRNA3
ENm001	VEGA_Known	CDS	1193133	1193282	.	-	0	Parent=mRNA3
ENm001	VEGA_Known	CDS	1196886	1196999	.	-	0	Parent=mRNA3
ENm001	VEGA_Known	exon	1196886	1196999	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1198146	1198251	.	-	1	Parent=mRNA3
ENm001	VEGA_Known	exon	1198146	1198251	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1209472	1209581	.	-	0	Parent=mRNA3
ENm001	VEGA_Known	exon	1209472	1209581	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1210545	1210601	.	-	0	Parent=mRNA3
ENm001	VEGA_Known	exon	1210545	1210601	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1211603	1211678	.	-	1	Parent=mRNA3
ENm001	VEGA_Known	exon	1211603	1211678	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1212520	1212644	.	-	0	Parent=mRNA3
ENm001	VEGA_Known	exon	1212520	1212644	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1214260	1214394	.	-	0	Parent=mRNA3
ENm001	VEGA_Known	exon	1214260	1214394	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1215232	1215343	.	-	1	Parent=mRNA3
ENm001	VEGA_Known	exon	1215232	1215343	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1249697	1249808	.	-	2	Parent=mRNA3
ENm001	VEGA_Known	exon	1249697	1249808	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1251771	1251893	.	-	2	Parent=mRNA3
ENm001	VEGA_Known	exon	1251771	1251893	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1256370	1256469	.	-	0	Parent=mRNA3
ENm001	VEGA_Known	exon	1256370	1256469	.	-	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	1256890	1256994	.	-	0	Parent=mRNA3
ENm001	VEGA_Known	exon	1256890	1257031	.	-	.	Parent=mRNA3
###
ENm001	.	gene	692046	748795	.	+	.	ID=gene3
ENm001	.	mRNA	692046	748795	.	+	.	ID=mRNA4;Parent=gene3
ENm001	VEGA_Known	exon	692046	692184	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	692146	692184	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	CDS	717661	717724	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	exon	717661	717724	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	722528	722579	.	+	2	Parent=mRNA4
ENm001	VEGA_Known	exon	722528	722579	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	728306	728369	.	+	1	Parent=mRNA4
ENm001	VEGA_Known	exon	728306	728369	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	733711	733917	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	exon	733711	733917	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	735797	735876	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	exon	735797	735876	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	739767	739845	.	+	1	Parent=mRNA4
ENm001	VEGA_Known	exon	739767	739845	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	741603	741674	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	exon	741603	741674	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	745594	745656	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	exon	745594	745656	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	747261	747398	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	exon	747261	748795	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	747399	747401	.	+	0	Parent=mRNA4
ENm001	.	mRNA	692121	745644	.	+	.	ID=mRNA5;Parent=gene3
ENm001	VEGA_Known	exon	692121	692184	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	exon	709601	709681	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	709676	709681	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	CDS	717661	717724	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	717661	717724	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	722528	722579	.	+	2	Parent=mRNA5
ENm001	VEGA_Known	exon	722528	722579	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	728306	728369	.	+	1	Parent=mRNA5
ENm001	VEGA_Known	exon	728306	728369	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	733711	733917	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	733711	733917	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	735797	735876	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	735797	735876	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	739767	739845	.	+	1	Parent=mRNA5
ENm001	VEGA_Known	exon	739767	739845	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	741603	741674	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	741603	741674	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	745594	745644	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	745594	745644	.	+	.	Parent=mRNA5
###
ENm001	.	gene	501939	627920	.	+	.	ID=gene4
ENm001	.	mRNA	501939	625876	.	+	.	ID=mRNA6;Parent=gene4
ENm001	VEGA_Known	exon	501939	502111	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	exon	528605	529818	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	528721	529818	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	CDS	561202	561393	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	561202	561393	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	569484	569618	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	569484	569618	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	570386	570559	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	570386	570559	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	584889	585049	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	584889	585049	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	586971	587073	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	586971	587073	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	587172	587308	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	587172	587308	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	587993	588154	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	587993	588154	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	588871	589024	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	588871	589024	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	592584	592802	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	592584	592802	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	599179	599325	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	599179	599325	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	601032	601188	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	601032	601188	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	601383	601523	.	+	2	Parent=mRNA6
ENm001	VEGA_Known	exon	601383	601523	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	604415	604645	.	+	2	Parent=mRNA6
ENm001	VEGA_Known	exon	604415	604645	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	606923	607003	.	+	2	Parent=mRNA6
ENm001	VEGA_Known	exon	606923	607003	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	608310	608491	.	+	2	Parent=mRNA6
ENm001	VEGA_Known	exon	608310	608491	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	611522	611631	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	611522	611631	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	612838	613003	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	612838	613003	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	625189	625325	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	625189	625325	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	625421	625655	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	625421	625876	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	625656	625658	.	+	0	Parent=mRNA6
ENm001	.	mRNA	501939	627920	.	+	.	ID=mRNA7;Parent=gene4
ENm001	VEGA_Known	exon	501939	502111	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	exon	528605	529818	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	528721	529818	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	CDS	561202	561393	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	561202	561393	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	569484	569618	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	569484	569618	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	570386	570559	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	570386	570559	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	584889	585049	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	584889	585049	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	586971	587073	.	+	1	Parent=mRNA7
ENm001	VEGA_Known	exon	586971	587073	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	587172	587308	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	587172	587308	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	587993	588154	.	+	1	Parent=mRNA7
ENm001	VEGA_Known	exon	587993	588154	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	588925	589024	.	+	1	Parent=mRNA7
ENm001	VEGA_Known	exon	588925	589024	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	592584	592802	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	592584	592802	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	599179	599325	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	599179	599325	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	601032	601188	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	601032	601188	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	601383	601523	.	+	2	Parent=mRNA7
ENm001	VEGA_Known	exon	601383	601523	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	604415	604645	.	+	2	Parent=mRNA7
ENm001	VEGA_Known	exon	604415	604645	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	606923	607003	.	+	2	Parent=mRNA7
ENm001	VEGA_Known	exon	606923	607003	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	608310	608491	.	+	2	Parent=mRNA7
ENm001	VEGA_Known	exon	608310	608491	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	611522	611631	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	611522	611631	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	612838	613003	.	+	1	Parent=mRNA7
ENm001	VEGA_Known	exon	612838	613003	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	625189	625325	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	625189	625325	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	625421	625655	.	+	1	Parent=mRNA7
ENm001	VEGA_Known	exon	625421	627920	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	625656	625658	.	+	0	Parent=mRNA7
###
ENm001	.	gene	1309497	1498195	.	+	.	ID=gene5
ENm001	.	mRNA	1309497	1498195	.	+	.	ID=mRNA8;Parent=gene5
ENm001	VEGA_Known	exon	1309497	1309681	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1309629	1309681	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	CDS	1333787	1333897	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	1333787	1333897	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1338568	1338676	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	1338568	1338676	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1360433	1360648	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1360433	1360648	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1363810	1363899	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1363810	1363899	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1364782	1364945	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1364782	1364945	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1366082	1366207	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	1366082	1366207	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1369634	1369880	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	1369634	1369880	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1371550	1371642	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1371550	1371642	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1378175	1378357	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1378175	1378357	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1388998	1389189	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1388998	1389189	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1417273	1417367	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1417273	1417367	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1419887	1419973	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	1419887	1419973	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1421468	1422191	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	1421468	1422191	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1424464	1424592	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1424464	1424592	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1432360	1432397	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1432360	1432397	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1433066	1433316	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	1433066	1433316	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1436208	1436287	.	+	2	Parent=mRNA8
ENm001	VEGA_Known	exon	1436208	1436287	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1440053	1440203	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1440053	1440203	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1441115	1441342	.	+	2	Parent=mRNA8
ENm001	VEGA_Known	exon	1441115	1441342	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1444147	1444247	.	+	2	Parent=mRNA8
ENm001	VEGA_Known	exon	1444147	1444247	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1457056	1457304	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1457056	1457304	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1471972	1472127	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1471972	1472127	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1482376	1482465	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1482376	1482465	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1494222	1494394	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1494222	1494394	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1494993	1495098	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	1494993	1495098	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1496442	1496639	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	1496442	1498195	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	1496640	1496642	.	+	0	Parent=mRNA8
###
ENm001	.	gene	40027	88317	.	+	.	ID=gene6
ENm001	.	mRNA	40027	88317	.	+	.	ID=mRNA9;Parent=gene6
ENm001	VEGA_Known	exon	40027	40268	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	40242	40268	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	CDS	64068	64153	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	exon	64068	64153	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	78554	78806	.	+	1	Parent=mRNA9
ENm001	VEGA_Known	exon	78554	78806	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	79695	80030	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	exon	79695	80030	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	81294	81509	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	exon	81294	81509	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	81852	82010	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	exon	81852	82010	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	86828	87013	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	exon	86828	88317	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	87014	87016	.	+	0	Parent=mRNA9
###
ENm001	.	gene	1106165	1152823	.	-	.	ID=gene7
ENm001	.	mRNA	1106165	1152823	.	-	.	ID=mRNA10;Parent=gene7
ENm001	VEGA_Known	exon	1106165	1107918	.	-	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1107689	1107691	.	-	0	Parent=mRNA10
ENm001	VEGA_Known	CDS	1107692	1107918	.	-	2	Parent=mRNA10
ENm001	VEGA_Known	CDS	1127146	1127410	.	-	0	Parent=mRNA10
ENm001	VEGA_Known	exon	1127146	1127410	.	-	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1144605	1144882	.	-	2	Parent=mRNA10
ENm001	VEGA_Known	exon	1144605	1144882	.	-	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1150101	1150327	.	-	1	Parent=mRNA10
ENm001	VEGA_Known	exon	1150101	1150327	.	-	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1152441	1152523	.	-	0	Parent=mRNA10
ENm001	VEGA_Known	exon	1152441	1152823	.	-	.	Parent=mRNA10
###
ENm001	.	gene	328776	338075	.	+	.	ID=gene8
ENm001	.	mRNA	328776	335792	.	+	.	ID=mRNA11;Parent=gene8
ENm001	VEGA_Known	exon	328776	328875	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	328841	328875	.	+	0	Parent=mRNA11
ENm001	VEGA_Known	CDS	329375	329465	.	+	1	Parent=mRNA11
ENm001	VEGA_Known	exon	329375	329465	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	329794	329981	.	+	0	Parent=mRNA11
ENm001	VEGA_Known	exon	329794	329981	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	335505	335652	.	+	1	Parent=mRNA11
ENm001	VEGA_Known	exon	335505	335792	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	335653	335655	.	+	0	Parent=mRNA11
ENm001	.	mRNA	328924	338075	.	+	.	ID=mRNA12;Parent=gene8
ENm001	VEGA_Known	exon	328924	329465	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	329316	329465	.	+	0	Parent=mRNA12
ENm001	VEGA_Known	CDS	329794	329981	.	+	0	Parent=mRNA12
ENm001	VEGA_Known	exon	329794	329981	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	335505	335652	.	+	1	Parent=mRNA12
ENm001	VEGA_Known	exon	335505	338075	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	335653	335655	.	+	0	Parent=mRNA12
###
ENm001	.	gene	354319	390710	.	+	.	ID=gene9
ENm001	.	mRNA	354319	390710	.	+	.	ID=mRNA13;Parent=gene9
ENm001	VEGA_Known	exon	354319	354626	.	+	.	Parent=mRNA13
ENm001	VEGA_Known	CDS	354597	354626	.	+	0	Parent=mRNA13
ENm001	VEGA_Known	CDS	356059	356223	.	+	0	Parent=mRNA13
ENm001	VEGA_Known	exon	356059	356223	.	+	.	Parent=mRNA13
ENm001	VEGA_Known	CDS	388480	388818	.	+	0	Parent=mRNA13
ENm001	VEGA_Known	exon	388480	390710	.	+	.	Parent=mRNA13
ENm001	VEGA_Known	CDS	388819	388821	.	+	0	Parent=mRNA13
###
ENm001	.	gene	782861	1059637	.	+	.	ID=gene10
ENm001	.	mRNA	782861	1053441	.	+	.	ID=mRNA14;Parent=gene10
ENm001	VEGA_Known	exon	782861	783225	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	783075	783225	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA14
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	963658	963726	.	+	1	Parent=mRNA14
ENm001	VEGA_Known	exon	963658	963726	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA14
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA14
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1052395	1052511	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	exon	1052395	1053441	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1052512	1052514	.	+	0	Parent=mRNA14
ENm001	.	mRNA	782876	1059637	.	+	.	ID=mRNA15;Parent=gene10
ENm001	VEGA_Known	exon	782876	783225	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	783075	783225	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA15
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA15
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA15
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA15
ENm001	.	mRNA	782913	1059637	.	+	.	ID=mRNA16;Parent=gene10
ENm001	VEGA_Known	exon	782913	783225	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	783075	783225	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA16
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	963658	963726	.	+	1	Parent=mRNA16
ENm001	VEGA_Known	exon	963658	963726	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA16
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA16
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA16
ENm001	.	mRNA	782913	1059637	.	+	.	ID=mRNA17;Parent=gene10
ENm001	VEGA_Known	exon	782913	783225	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	783075	783225	.	+	0	Parent=mRNA17
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA17
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA17
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	963658	963726	.	+	1	Parent=mRNA17
ENm001	VEGA_Known	exon	963658	963726	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA17
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA17
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA17
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1039321	1039456	.	+	0	Parent=mRNA17
ENm001	VEGA_Known	exon	1039321	1039456	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA17
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA17
ENm001	.	mRNA	844422	961459	.	+	.	ID=mRNA18;Parent=gene10
ENm001	VEGA_Known	exon	844422	844548	.	+	.	Parent=mRNA18
ENm001	VEGA_Known	CDS	844536	844548	.	+	0	Parent=mRNA18
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA18
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA18
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA18
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA18
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA18
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA18
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA18
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA18
ENm001	VEGA_Known	CDS	961419	961459	.	+	2	Parent=mRNA18
ENm001	VEGA_Known	exon	961419	961459	.	+	.	Parent=mRNA18
ENm001	.	mRNA	849752	1059637	.	+	.	ID=mRNA19;Parent=gene10
ENm001	VEGA_Known	exon	849752	850163	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	exon	928147	928349	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	928349	928349	.	+	0	Parent=mRNA19
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA19
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA19
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA19
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA19
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA19
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA19
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA19
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA19
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA19
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA19
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	1039321	1039456	.	+	0	Parent=mRNA19
ENm001	VEGA_Known	exon	1039321	1039456	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA19
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA19
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA19
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA19
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA19
ENm001	.	mRNA	849811	1059637	.	+	.	ID=mRNA20;Parent=gene10
ENm001	VEGA_Known	exon	849811	850163	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	850142	850163	.	+	0	Parent=mRNA20
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA20
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA20
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA20
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA20
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA20
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA20
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA20
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA20
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA20
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA20
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA20
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA20
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA20
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA20
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA20
ENm001	.	mRNA	849811	1059637	.	+	.	ID=mRNA21;Parent=gene10
ENm001	VEGA_Known	exon	849811	850163	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	850142	850163	.	+	0	Parent=mRNA21
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA21
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA21
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA21
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA21
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA21
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	963658	963726	.	+	1	Parent=mRNA21
ENm001	VEGA_Known	exon	963658	963726	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA21
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA21
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA21
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA21
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA21
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA21
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA21
ENm001	.	mRNA	949220	1027931	.	+	.	ID=mRNA22;Parent=gene10
ENm001	VEGA_Known	exon	949220	949254	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	949221	949254	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA22
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA22
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA22
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA22
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1027854	1027865	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1027854	1027931	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1027866	1027868	.	+	0	Parent=mRNA22
###
ENm001	.	gene	783433	798108	.	+	.	ID=gene11
ENm001	.	mRNA	783433	789351	.	+	.	ID=mRNA23;Parent=gene11
ENm001	VEGA_Novel_CDS	exon	783433	783643	.	+	.	Parent=mRNA23
ENm001	VEGA_Novel_CDS	exon	783995	784213	.	+	.	Parent=mRNA23
ENm001	VEGA_Novel_CDS	exon	784508	784687	.	+	.	Parent=mRNA23
ENm001	VEGA_Novel_CDS	CDS	784619	784687	.	+	0	Parent=mRNA23
ENm001	VEGA_Novel_CDS	CDS	785957	786257	.	+	0	Parent=mRNA23
ENm001	VEGA_Novel_CDS	exon	785957	786257	.	+	.	Parent=mRNA23
ENm001	VEGA_Novel_CDS	CDS	788687	788823	.	+	2	Parent=mRNA23
ENm001	VEGA_Novel_CDS	exon	788687	789351	.	+	.	Parent=mRNA23
ENm001	VEGA_Novel_CDS	CDS	788824	788826	.	+	0	Parent=mRNA23
ENm001	.	mRNA	784508	798108	.	+	.	ID=mRNA24;Parent=gene11
ENm001	VEGA_Novel_CDS	exon	784508	784687	.	+	.	Parent=mRNA24
ENm001	VEGA_Novel_CDS	CDS	784619	784687	.	+	0	Parent=mRNA24
ENm001	VEGA_Novel_CDS	CDS	785957	786257	.	+	0	Parent=mRNA24
ENm001	VEGA_Novel_CDS	exon	785957	786257	.	+	.	Parent=mRNA24
ENm001	VEGA_Novel_CDS	CDS	788123	788219	.	+	2	Parent=mRNA24
ENm001	VEGA_Novel_CDS	exon	788123	788219	.	+	.	Parent=mRNA24
ENm001	VEGA_Novel_CDS	CDS	797933	797945	.	+	1	Parent=mRNA24
ENm001	VEGA_Novel_CDS	exon	797933	798108	.	+	.	Parent=mRNA24
ENm001	VEGA_Novel_CDS	CDS	797946	797948	.	+	0	Parent=mRNA24
###
genometools-1.5.1/testdata/gt_gff3_prob_5.out000066400000000000000000001051521211610345200211770ustar00rootroot00000000000000##gff-version   3
##sequence-region   ENm001 40027 1703041
ENm001	.	gene	40027	88317	.	+	.	ID=gene1
ENm001	.	mRNA	40027	88317	.	+	.	ID=mRNA1;Parent=gene1
ENm001	VEGA_Known	exon	40027	40268	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	40242	40268	.	+	0	Parent=mRNA1
ENm001	VEGA_Known	CDS	64068	64153	.	+	0	Parent=mRNA1
ENm001	VEGA_Known	exon	64068	64153	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	78554	78806	.	+	1	Parent=mRNA1
ENm001	VEGA_Known	exon	78554	78806	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	79695	80030	.	+	0	Parent=mRNA1
ENm001	VEGA_Known	exon	79695	80030	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	81294	81509	.	+	0	Parent=mRNA1
ENm001	VEGA_Known	exon	81294	81509	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	81852	82010	.	+	0	Parent=mRNA1
ENm001	VEGA_Known	exon	81852	82010	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	86828	87013	.	+	0	Parent=mRNA1
ENm001	VEGA_Known	exon	86828	88317	.	+	.	Parent=mRNA1
ENm001	VEGA_Known	CDS	87014	87016	.	+	0	Parent=mRNA1
###
ENm001	.	gene	328776	338075	.	+	.	ID=gene2
ENm001	.	mRNA	328776	335792	.	+	.	ID=mRNA2;Parent=gene2
ENm001	VEGA_Known	exon	328776	328875	.	+	.	Parent=mRNA2
ENm001	VEGA_Known	CDS	328841	328875	.	+	0	Parent=mRNA2
ENm001	VEGA_Known	CDS	329375	329465	.	+	1	Parent=mRNA2
ENm001	VEGA_Known	exon	329375	329465	.	+	.	Parent=mRNA2
ENm001	VEGA_Known	CDS	329794	329981	.	+	0	Parent=mRNA2
ENm001	VEGA_Known	exon	329794	329981	.	+	.	Parent=mRNA2
ENm001	VEGA_Known	CDS	335505	335652	.	+	1	Parent=mRNA2
ENm001	VEGA_Known	exon	335505	335792	.	+	.	Parent=mRNA2
ENm001	VEGA_Known	CDS	335653	335655	.	+	0	Parent=mRNA2
ENm001	.	mRNA	328924	338075	.	+	.	ID=mRNA3;Parent=gene2
ENm001	VEGA_Known	exon	328924	329465	.	+	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	329316	329465	.	+	0	Parent=mRNA3
ENm001	VEGA_Known	CDS	329794	329981	.	+	0	Parent=mRNA3
ENm001	VEGA_Known	exon	329794	329981	.	+	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	335505	335652	.	+	1	Parent=mRNA3
ENm001	VEGA_Known	exon	335505	338075	.	+	.	Parent=mRNA3
ENm001	VEGA_Known	CDS	335653	335655	.	+	0	Parent=mRNA3
###
ENm001	.	gene	354319	390710	.	+	.	ID=gene3
ENm001	.	mRNA	354319	390710	.	+	.	ID=mRNA4;Parent=gene3
ENm001	VEGA_Known	exon	354319	354626	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	354597	354626	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	CDS	356059	356223	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	exon	356059	356223	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	388480	388818	.	+	0	Parent=mRNA4
ENm001	VEGA_Known	exon	388480	390710	.	+	.	Parent=mRNA4
ENm001	VEGA_Known	CDS	388819	388821	.	+	0	Parent=mRNA4
###
ENm001	.	gene	501939	627920	.	+	.	ID=gene4
ENm001	.	mRNA	501939	625876	.	+	.	ID=mRNA5;Parent=gene4
ENm001	VEGA_Known	exon	501939	502111	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	exon	528605	529818	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	528721	529818	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	CDS	561202	561393	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	561202	561393	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	569484	569618	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	569484	569618	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	570386	570559	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	570386	570559	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	584889	585049	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	584889	585049	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	586971	587073	.	+	1	Parent=mRNA5
ENm001	VEGA_Known	exon	586971	587073	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	587172	587308	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	587172	587308	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	587993	588154	.	+	1	Parent=mRNA5
ENm001	VEGA_Known	exon	587993	588154	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	588871	589024	.	+	1	Parent=mRNA5
ENm001	VEGA_Known	exon	588871	589024	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	592584	592802	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	592584	592802	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	599179	599325	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	599179	599325	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	601032	601188	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	601032	601188	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	601383	601523	.	+	2	Parent=mRNA5
ENm001	VEGA_Known	exon	601383	601523	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	604415	604645	.	+	2	Parent=mRNA5
ENm001	VEGA_Known	exon	604415	604645	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	606923	607003	.	+	2	Parent=mRNA5
ENm001	VEGA_Known	exon	606923	607003	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	608310	608491	.	+	2	Parent=mRNA5
ENm001	VEGA_Known	exon	608310	608491	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	611522	611631	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	611522	611631	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	612838	613003	.	+	1	Parent=mRNA5
ENm001	VEGA_Known	exon	612838	613003	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	625189	625325	.	+	0	Parent=mRNA5
ENm001	VEGA_Known	exon	625189	625325	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	625421	625655	.	+	1	Parent=mRNA5
ENm001	VEGA_Known	exon	625421	625876	.	+	.	Parent=mRNA5
ENm001	VEGA_Known	CDS	625656	625658	.	+	0	Parent=mRNA5
ENm001	.	mRNA	501939	627920	.	+	.	ID=mRNA6;Parent=gene4
ENm001	VEGA_Known	exon	501939	502111	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	exon	528605	529818	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	528721	529818	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	CDS	561202	561393	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	561202	561393	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	569484	569618	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	569484	569618	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	570386	570559	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	570386	570559	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	584889	585049	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	584889	585049	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	586971	587073	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	586971	587073	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	587172	587308	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	587172	587308	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	587993	588154	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	587993	588154	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	588925	589024	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	588925	589024	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	592584	592802	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	592584	592802	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	599179	599325	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	599179	599325	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	601032	601188	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	601032	601188	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	601383	601523	.	+	2	Parent=mRNA6
ENm001	VEGA_Known	exon	601383	601523	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	604415	604645	.	+	2	Parent=mRNA6
ENm001	VEGA_Known	exon	604415	604645	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	606923	607003	.	+	2	Parent=mRNA6
ENm001	VEGA_Known	exon	606923	607003	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	608310	608491	.	+	2	Parent=mRNA6
ENm001	VEGA_Known	exon	608310	608491	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	611522	611631	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	611522	611631	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	612838	613003	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	612838	613003	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	625189	625325	.	+	0	Parent=mRNA6
ENm001	VEGA_Known	exon	625189	625325	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	625421	625655	.	+	1	Parent=mRNA6
ENm001	VEGA_Known	exon	625421	627920	.	+	.	Parent=mRNA6
ENm001	VEGA_Known	CDS	625656	625658	.	+	0	Parent=mRNA6
###
ENm001	.	gene	692046	748795	.	+	.	ID=gene5
ENm001	.	mRNA	692046	748795	.	+	.	ID=mRNA7;Parent=gene5
ENm001	VEGA_Known	exon	692046	692184	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	692146	692184	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	CDS	717661	717724	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	717661	717724	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	722528	722579	.	+	2	Parent=mRNA7
ENm001	VEGA_Known	exon	722528	722579	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	728306	728369	.	+	1	Parent=mRNA7
ENm001	VEGA_Known	exon	728306	728369	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	733711	733917	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	733711	733917	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	735797	735876	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	735797	735876	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	739767	739845	.	+	1	Parent=mRNA7
ENm001	VEGA_Known	exon	739767	739845	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	741603	741674	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	741603	741674	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	745594	745656	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	745594	745656	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	747261	747398	.	+	0	Parent=mRNA7
ENm001	VEGA_Known	exon	747261	748795	.	+	.	Parent=mRNA7
ENm001	VEGA_Known	CDS	747399	747401	.	+	0	Parent=mRNA7
ENm001	.	mRNA	692121	745644	.	+	.	ID=mRNA8;Parent=gene5
ENm001	VEGA_Known	exon	692121	692184	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	exon	709601	709681	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	709676	709681	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	CDS	717661	717724	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	717661	717724	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	722528	722579	.	+	2	Parent=mRNA8
ENm001	VEGA_Known	exon	722528	722579	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	728306	728369	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	728306	728369	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	733711	733917	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	733711	733917	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	735797	735876	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	735797	735876	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	739767	739845	.	+	1	Parent=mRNA8
ENm001	VEGA_Known	exon	739767	739845	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	741603	741674	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	741603	741674	.	+	.	Parent=mRNA8
ENm001	VEGA_Known	CDS	745594	745644	.	+	0	Parent=mRNA8
ENm001	VEGA_Known	exon	745594	745644	.	+	.	Parent=mRNA8
###
ENm001	.	gene	782861	1059637	.	+	.	ID=gene6
ENm001	.	mRNA	782861	1053441	.	+	.	ID=mRNA9;Parent=gene6
ENm001	VEGA_Known	exon	782861	783225	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	783075	783225	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA9
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA9
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA9
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA9
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	963658	963726	.	+	1	Parent=mRNA9
ENm001	VEGA_Known	exon	963658	963726	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA9
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA9
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA9
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA9
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA9
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA9
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	1052395	1052511	.	+	0	Parent=mRNA9
ENm001	VEGA_Known	exon	1052395	1053441	.	+	.	Parent=mRNA9
ENm001	VEGA_Known	CDS	1052512	1052514	.	+	0	Parent=mRNA9
ENm001	.	mRNA	782876	1059637	.	+	.	ID=mRNA10;Parent=gene6
ENm001	VEGA_Known	exon	782876	783225	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	783075	783225	.	+	0	Parent=mRNA10
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA10
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA10
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA10
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA10
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA10
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA10
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA10
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA10
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA10
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA10
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA10
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA10
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA10
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA10
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA10
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA10
ENm001	.	mRNA	782913	1059637	.	+	.	ID=mRNA11;Parent=gene6
ENm001	VEGA_Known	exon	782913	783225	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	783075	783225	.	+	0	Parent=mRNA11
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA11
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA11
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA11
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA11
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA11
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	963658	963726	.	+	1	Parent=mRNA11
ENm001	VEGA_Known	exon	963658	963726	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA11
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA11
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA11
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA11
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA11
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA11
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA11
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA11
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA11
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA11
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA11
ENm001	.	mRNA	782913	1059637	.	+	.	ID=mRNA12;Parent=gene6
ENm001	VEGA_Known	exon	782913	783225	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	783075	783225	.	+	0	Parent=mRNA12
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA12
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA12
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA12
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA12
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA12
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	963658	963726	.	+	1	Parent=mRNA12
ENm001	VEGA_Known	exon	963658	963726	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA12
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA12
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA12
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA12
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA12
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	1039321	1039456	.	+	0	Parent=mRNA12
ENm001	VEGA_Known	exon	1039321	1039456	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA12
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA12
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA12
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA12
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA12
ENm001	.	mRNA	844422	961459	.	+	.	ID=mRNA13;Parent=gene6
ENm001	VEGA_Known	exon	844422	844548	.	+	.	Parent=mRNA13
ENm001	VEGA_Known	CDS	844536	844548	.	+	0	Parent=mRNA13
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA13
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA13
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA13
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA13
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA13
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA13
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA13
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA13
ENm001	VEGA_Known	CDS	961419	961459	.	+	2	Parent=mRNA13
ENm001	VEGA_Known	exon	961419	961459	.	+	.	Parent=mRNA13
ENm001	.	mRNA	849752	1059637	.	+	.	ID=mRNA14;Parent=gene6
ENm001	VEGA_Known	exon	849752	850163	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	exon	928147	928349	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	928349	928349	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA14
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA14
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA14
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1039321	1039456	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	exon	1039321	1039456	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA14
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA14
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA14
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA14
ENm001	.	mRNA	849811	1059637	.	+	.	ID=mRNA15;Parent=gene6
ENm001	VEGA_Known	exon	849811	850163	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	850142	850163	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA15
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA15
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA15
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA15
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA15
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA15
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA15
ENm001	.	mRNA	849811	1059637	.	+	.	ID=mRNA16;Parent=gene6
ENm001	VEGA_Known	exon	849811	850163	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	850142	850163	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	CDS	929296	929378	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	929296	929378	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	949095	949254	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	exon	949095	949254	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA16
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	963658	963726	.	+	1	Parent=mRNA16
ENm001	VEGA_Known	exon	963658	963726	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA16
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA16
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1039321	1039471	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	exon	1039321	1039471	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1048618	1048710	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	1048618	1048710	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1051457	1051596	.	+	2	Parent=mRNA16
ENm001	VEGA_Known	exon	1051457	1051596	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1059296	1059388	.	+	0	Parent=mRNA16
ENm001	VEGA_Known	exon	1059296	1059637	.	+	.	Parent=mRNA16
ENm001	VEGA_Known	CDS	1059389	1059391	.	+	0	Parent=mRNA16
ENm001	.	mRNA	949220	1027931	.	+	.	ID=mRNA17;Parent=gene6
ENm001	VEGA_Known	exon	949220	949254	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	949221	949254	.	+	0	Parent=mRNA17
ENm001	VEGA_Known	CDS	959327	959381	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	959327	959381	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	960025	960140	.	+	1	Parent=mRNA17
ENm001	VEGA_Known	exon	960025	960140	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	961419	961494	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	961419	961494	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	965615	965769	.	+	1	Parent=mRNA17
ENm001	VEGA_Known	exon	965615	965769	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	967969	968066	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	967969	968066	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1000396	1000510	.	+	0	Parent=mRNA17
ENm001	VEGA_Known	exon	1000396	1000510	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1018855	1018927	.	+	2	Parent=mRNA17
ENm001	VEGA_Known	exon	1018855	1018927	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1020368	1020470	.	+	1	Parent=mRNA17
ENm001	VEGA_Known	exon	1020368	1020470	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1027854	1027865	.	+	0	Parent=mRNA17
ENm001	VEGA_Known	exon	1027854	1027931	.	+	.	Parent=mRNA17
ENm001	VEGA_Known	CDS	1027866	1027868	.	+	0	Parent=mRNA17
###
ENm001	.	gene	783433	798108	.	+	.	ID=gene7
ENm001	.	mRNA	783433	789351	.	+	.	ID=mRNA18;Parent=gene7
ENm001	VEGA_Novel_CDS	exon	783433	783643	.	+	.	Parent=mRNA18
ENm001	VEGA_Novel_CDS	exon	783995	784213	.	+	.	Parent=mRNA18
ENm001	VEGA_Novel_CDS	exon	784508	784687	.	+	.	Parent=mRNA18
ENm001	VEGA_Novel_CDS	CDS	784619	784687	.	+	0	Parent=mRNA18
ENm001	VEGA_Novel_CDS	CDS	785957	786257	.	+	0	Parent=mRNA18
ENm001	VEGA_Novel_CDS	exon	785957	786257	.	+	.	Parent=mRNA18
ENm001	VEGA_Novel_CDS	CDS	788687	788823	.	+	2	Parent=mRNA18
ENm001	VEGA_Novel_CDS	exon	788687	789351	.	+	.	Parent=mRNA18
ENm001	VEGA_Novel_CDS	CDS	788824	788826	.	+	0	Parent=mRNA18
ENm001	.	mRNA	784508	798108	.	+	.	ID=mRNA19;Parent=gene7
ENm001	VEGA_Novel_CDS	exon	784508	784687	.	+	.	Parent=mRNA19
ENm001	VEGA_Novel_CDS	CDS	784619	784687	.	+	0	Parent=mRNA19
ENm001	VEGA_Novel_CDS	CDS	785957	786257	.	+	0	Parent=mRNA19
ENm001	VEGA_Novel_CDS	exon	785957	786257	.	+	.	Parent=mRNA19
ENm001	VEGA_Novel_CDS	CDS	788123	788219	.	+	2	Parent=mRNA19
ENm001	VEGA_Novel_CDS	exon	788123	788219	.	+	.	Parent=mRNA19
ENm001	VEGA_Novel_CDS	CDS	797933	797945	.	+	1	Parent=mRNA19
ENm001	VEGA_Novel_CDS	exon	797933	798108	.	+	.	Parent=mRNA19
ENm001	VEGA_Novel_CDS	CDS	797946	797948	.	+	0	Parent=mRNA19
###
ENm001	.	gene	1106165	1152823	.	-	.	ID=gene8
ENm001	.	mRNA	1106165	1152823	.	-	.	ID=mRNA20;Parent=gene8
ENm001	VEGA_Known	exon	1106165	1107918	.	-	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1107689	1107691	.	-	0	Parent=mRNA20
ENm001	VEGA_Known	CDS	1107692	1107918	.	-	2	Parent=mRNA20
ENm001	VEGA_Known	CDS	1127146	1127410	.	-	0	Parent=mRNA20
ENm001	VEGA_Known	exon	1127146	1127410	.	-	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1144605	1144882	.	-	2	Parent=mRNA20
ENm001	VEGA_Known	exon	1144605	1144882	.	-	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1150101	1150327	.	-	1	Parent=mRNA20
ENm001	VEGA_Known	exon	1150101	1150327	.	-	.	Parent=mRNA20
ENm001	VEGA_Known	CDS	1152441	1152523	.	-	0	Parent=mRNA20
ENm001	VEGA_Known	exon	1152441	1152823	.	-	.	Parent=mRNA20
###
ENm001	.	gene	1192756	1257031	.	-	.	ID=gene9
ENm001	.	mRNA	1192756	1257031	.	-	.	ID=mRNA21;Parent=gene9
ENm001	VEGA_Known	exon	1192756	1193282	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1193130	1193132	.	-	0	Parent=mRNA21
ENm001	VEGA_Known	CDS	1193133	1193282	.	-	0	Parent=mRNA21
ENm001	VEGA_Known	CDS	1196886	1196999	.	-	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1196886	1196999	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1198146	1198251	.	-	1	Parent=mRNA21
ENm001	VEGA_Known	exon	1198146	1198251	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1209472	1209581	.	-	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1209472	1209581	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1210545	1210601	.	-	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1210545	1210601	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1211603	1211678	.	-	1	Parent=mRNA21
ENm001	VEGA_Known	exon	1211603	1211678	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1212520	1212644	.	-	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1212520	1212644	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1214260	1214394	.	-	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1214260	1214394	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1215232	1215343	.	-	1	Parent=mRNA21
ENm001	VEGA_Known	exon	1215232	1215343	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1249697	1249808	.	-	2	Parent=mRNA21
ENm001	VEGA_Known	exon	1249697	1249808	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1251771	1251893	.	-	2	Parent=mRNA21
ENm001	VEGA_Known	exon	1251771	1251893	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1256370	1256469	.	-	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1256370	1256469	.	-	.	Parent=mRNA21
ENm001	VEGA_Known	CDS	1256890	1256994	.	-	0	Parent=mRNA21
ENm001	VEGA_Known	exon	1256890	1257031	.	-	.	Parent=mRNA21
###
ENm001	.	gene	1309497	1498195	.	+	.	ID=gene10
ENm001	.	mRNA	1309497	1498195	.	+	.	ID=mRNA22;Parent=gene10
ENm001	VEGA_Known	exon	1309497	1309681	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1309629	1309681	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	CDS	1333787	1333897	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	1333787	1333897	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1338568	1338676	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	1338568	1338676	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1360433	1360648	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1360433	1360648	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1363810	1363899	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1363810	1363899	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1364782	1364945	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1364782	1364945	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1366082	1366207	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	1366082	1366207	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1369634	1369880	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	1369634	1369880	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1371550	1371642	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1371550	1371642	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1378175	1378357	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1378175	1378357	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1388998	1389189	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1388998	1389189	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1417273	1417367	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1417273	1417367	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1419887	1419973	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	1419887	1419973	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1421468	1422191	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	1421468	1422191	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1424464	1424592	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1424464	1424592	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1432360	1432397	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1432360	1432397	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1433066	1433316	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	1433066	1433316	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1436208	1436287	.	+	2	Parent=mRNA22
ENm001	VEGA_Known	exon	1436208	1436287	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1440053	1440203	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1440053	1440203	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1441115	1441342	.	+	2	Parent=mRNA22
ENm001	VEGA_Known	exon	1441115	1441342	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1444147	1444247	.	+	2	Parent=mRNA22
ENm001	VEGA_Known	exon	1444147	1444247	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1457056	1457304	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1457056	1457304	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1471972	1472127	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1471972	1472127	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1482376	1482465	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1482376	1482465	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1494222	1494394	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1494222	1494394	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1494993	1495098	.	+	1	Parent=mRNA22
ENm001	VEGA_Known	exon	1494993	1495098	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1496442	1496639	.	+	0	Parent=mRNA22
ENm001	VEGA_Known	exon	1496442	1498195	.	+	.	Parent=mRNA22
ENm001	VEGA_Known	CDS	1496640	1496642	.	+	0	Parent=mRNA22
###
ENm001	.	gene	1540185	1703041	.	-	.	ID=gene11
ENm001	.	mRNA	1540185	1703041	.	-	.	ID=mRNA23;Parent=gene11
ENm001	VEGA_Known	exon	1540185	1541316	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1541071	1541073	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	CDS	1541074	1541316	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	CDS	1547552	1547653	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1547552	1547653	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1549038	1549170	.	-	1	Parent=mRNA23
ENm001	VEGA_Known	exon	1549038	1549170	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1550601	1550664	.	-	2	Parent=mRNA23
ENm001	VEGA_Known	exon	1550601	1550664	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1554081	1554266	.	-	2	Parent=mRNA23
ENm001	VEGA_Known	exon	1554081	1554266	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1554586	1554791	.	-	1	Parent=mRNA23
ENm001	VEGA_Known	exon	1554586	1554791	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1557623	1557801	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1557623	1557801	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1564447	1564634	.	-	2	Parent=mRNA23
ENm001	VEGA_Known	exon	1564447	1564634	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1564803	1564955	.	-	2	Parent=mRNA23
ENm001	VEGA_Known	exon	1564803	1564955	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1575365	1575464	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1575365	1575464	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1575547	1575633	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1575547	1575633	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1586089	1586168	.	-	2	Parent=mRNA23
ENm001	VEGA_Known	exon	1586089	1586168	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1587409	1587504	.	-	2	Parent=mRNA23
ENm001	VEGA_Known	exon	1587409	1587504	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1589969	1590244	.	-	2	Parent=mRNA23
ENm001	VEGA_Known	exon	1589969	1590244	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1596593	1596710	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1596593	1596710	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1607045	1607299	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1607045	1607299	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1609975	1610125	.	-	1	Parent=mRNA23
ENm001	VEGA_Known	exon	1609975	1610125	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1612396	1612495	.	-	2	Parent=mRNA23
ENm001	VEGA_Known	exon	1612396	1612495	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1613785	1613988	.	-	2	Parent=mRNA23
ENm001	VEGA_Known	exon	1613785	1613988	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1620662	1622315	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1620662	1622315	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1640299	1640523	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1640299	1640523	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1690743	1690850	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1690743	1690850	.	-	.	Parent=mRNA23
ENm001	VEGA_Known	CDS	1702869	1702949	.	-	0	Parent=mRNA23
ENm001	VEGA_Known	exon	1702869	1703041	.	-	.	Parent=mRNA23
ENm001	.	mRNA	1622120	1701172	.	-	.	ID=mRNA24;Parent=gene11
ENm001	VEGA_Known	CDS	1622120	1622315	.	-	0	Parent=mRNA24
ENm001	VEGA_Known	exon	1622120	1622315	.	-	.	Parent=mRNA24
ENm001	VEGA_Known	CDS	1640299	1640523	.	-	0	Parent=mRNA24
ENm001	VEGA_Known	exon	1640299	1640523	.	-	.	Parent=mRNA24
ENm001	VEGA_Known	CDS	1690743	1690805	.	-	0	Parent=mRNA24
ENm001	VEGA_Known	exon	1690743	1690850	.	-	.	Parent=mRNA24
ENm001	VEGA_Known	exon	1701124	1701172	.	-	.	Parent=mRNA24
###
genometools-1.5.1/testdata/gt_gff3_prob_6.in000066400000000000000000000034021211610345200207720ustar00rootroot00000000000000##gff-version   3
##sequence-region chrX 122459947 153939754
chrX	ENCODE	gene	122459947	122480545	.	-	.	ID=gene1;Name=RP5-1189B24.5-003;name2=THOC2
chrX	ENCODE	exon	122459947	122460724	.	-	.	Parent=gene1
chrX	ENCODE	exon	122470304	122470349	.	-	.	Parent=gene1
chrX	ENCODE	exon	122470826	122470902	.	-	.	Parent=gene1
chrX	ENCODE	exon	122472785	122472942	.	-	.	Parent=gene1
chrX	ENCODE	exon	122473025	122473094	.	-	.	Parent=gene1
chrX	ENCODE	exon	122473438	122473575	.	-	.	Parent=gene1
chrX	ENCODE	exon	122478787	122478822	.	-	.	Parent=gene1
chrX	ENCODE	exon	122480293	122480351	.	-	.	Parent=gene1
chrX	ENCODE	exon	122480543	122480545	.	-	.	Parent=gene1
chrX	ENCODE	gene	122459955	122482231	.	-	.	ID=gene2;Name=RP5-1189B24.5-009;name2=THOC2
chrX	ENCODE	exon	122459955	122463134	.	-	.	Parent=gene2
chrX	ENCODE	exon	122470304	122470349	.	-	.	Parent=gene2
chrX	ENCODE	CDS	122470324	122470349	.	-	.
Parent=gene2
chrX	ENCODE	exon	122470826	122470902	.	-	.	Parent=gene2
chrX	ENCODE	CDS	122470826	122470902	.	-	.
Parent=gene2
chrX	ENCODE	exon	122472785	122472942	.	-	.	Parent=gene2
chrX	ENCODE	CDS	122472785	122472942	.	-	.
Parent=gene2
chrX	ENCODE	exon	122473025	122473094	.	-	.	Parent=gene2
chrX	ENCODE	CDS	122473025	122473094	.	-	.
Parent=gene2
chrX	ENCODE	exon	122473438	122473575	.	-	.	Parent=gene2
chrX	ENCODE	CDS	122473438	122473575	.	-	.
Parent=gene2
chrX	ENCODE	exon	122478787	122478903	.	-	.	Parent=gene2
chrX	ENCODE	CDS	122478787	122478903	.	-	.
Parent=gene2
chrX	ENCODE	exon	122480293	122480351	.	-	.	Parent=gene2
chrX	ENCODE	CDS	122480293	122480351	.	-	.
Parent=gene2
chrX	ENCODE	exon	122480543	122480973	.	-	.	Parent=gene2
chrX	ENCODE	CDS	122480543	122480973	.	-	.
Parent=gene2
chrX	ENCODE	exon	122482144	122482231	.	-	.	Parent=gene2
chrX	ENCODE	CDS	122482144	122482231	.	-	.
Parent=gene2
genometools-1.5.1/testdata/gt_gff3_prob_7.in000066400000000000000000000033341211610345200207770ustar00rootroot00000000000000##gff-version 3
##sequence-region seq0 1 135606
# CH478465
seq0	Genbank	LTR_retrotransposon	3874	4142	.	?	.	ID=LTRret0
seq0	Genbank	LTR_retrotransposon	57759	59137	.	?	.	ID=LTRret1
seq0	Genbank	LTR_retrotransposon	58703	63379	.	?	.	ID=LTRret2
seq0	Genbank	LTR_retrotransposon	63362	63799	.	?	.	ID=LTRret3
seq0	Genbank	LTR_retrotransposon	63793	64472	.	?	.	ID=LTRret4
seq0	Genbank	LTR_retrotransposon	82889	83299	.	?	.	ID=LTRret5
seq0	Genbank	LTR_retrotransposon	83296	84549	.	?	.	ID=LTRret6
seq0	Genbank	LTR_retrotransposon	84542	87203	.	?	.	ID=LTRret7
seq0	Genbank	LTR_retrotransposon	119186	123973	.	?	.	ID=LTRret8
##sequence-region seq1 1 163182
# CH478464
seq1	Genbank	LTR_retrotransposon	67057	67156	.	?	.	ID=LTRret9
seq1	Genbank	LTR_retrotransposon	74405	74533	.	?	.	ID=LTRret10
seq1	Genbank	LTR_retrotransposon	74817	74954	.	?	.	ID=LTRret11
seq1	Genbank	LTR_retrotransposon	83694	84311	.	?	.	ID=LTRret12
seq1	Genbank	LTR_retrotransposon	106946	107130	.	?	.	ID=LTRret13
seq1	Genbank	LTR_retrotransposon	114751	115665	.	?	.	ID=LTRret14
seq1	Genbank	LTR_retrotransposon	117806	117952	.	?	.	ID=LTRret15
seq1	Genbank	LTR_retrotransposon	121320	121492	.	?	.	ID=LTRret16
seq1	Genbank	LTR_retrotransposon	129429	129553	.	?	.	ID=LTRret17
seq1	Genbank	LTR_retrotransposon	129536	129703	.	?	.	ID=LTRret18
seq1	Genbank	LTR_retrotransposon	129694	129847	.	?	.	ID=LTRret19
seq1	Genbank	LTR_retrotransposon	138908	139082	.	?	.	ID=LTRret20
seq1	Genbank	LTR_retrotransposon	147916	148117	.	?	.	ID=LTRret21
seq1	Genbank	LTR_retrotransposon	149265	149964	.	?	.	ID=LTRret22
seq1	Genbank	LTR_retrotransposon	153048	153242	.	?	.	ID=LTRret23
seq1	Genbank	LTR_retrotransposon	153232	153342	.	?	.	ID=LTRret24
seq1	Genbank	LTR_retrotransposon	153809	154103	.	?	.	ID=LTRret25
genometools-1.5.1/testdata/gt_gff3_prob_7.sorted000066400000000000000000000027501211610345200216720ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq0 1 135606
##sequence-region   seq1 1 163182
# CH478465
# CH478464
seq0	Genbank	LTR_retrotransposon	3874	4142	.	?	.	.
seq0	Genbank	LTR_retrotransposon	57759	59137	.	?	.	.
seq0	Genbank	LTR_retrotransposon	58703	63379	.	?	.	.
seq0	Genbank	LTR_retrotransposon	63362	63799	.	?	.	.
seq0	Genbank	LTR_retrotransposon	63793	64472	.	?	.	.
seq0	Genbank	LTR_retrotransposon	82889	83299	.	?	.	.
seq0	Genbank	LTR_retrotransposon	83296	84549	.	?	.	.
seq0	Genbank	LTR_retrotransposon	84542	87203	.	?	.	.
seq0	Genbank	LTR_retrotransposon	119186	123973	.	?	.	.
seq1	Genbank	LTR_retrotransposon	67057	67156	.	?	.	.
seq1	Genbank	LTR_retrotransposon	74405	74533	.	?	.	.
seq1	Genbank	LTR_retrotransposon	74817	74954	.	?	.	.
seq1	Genbank	LTR_retrotransposon	83694	84311	.	?	.	.
seq1	Genbank	LTR_retrotransposon	106946	107130	.	?	.	.
seq1	Genbank	LTR_retrotransposon	114751	115665	.	?	.	.
seq1	Genbank	LTR_retrotransposon	117806	117952	.	?	.	.
seq1	Genbank	LTR_retrotransposon	121320	121492	.	?	.	.
seq1	Genbank	LTR_retrotransposon	129429	129553	.	?	.	.
seq1	Genbank	LTR_retrotransposon	129536	129703	.	?	.	.
seq1	Genbank	LTR_retrotransposon	129694	129847	.	?	.	.
seq1	Genbank	LTR_retrotransposon	138908	139082	.	?	.	.
seq1	Genbank	LTR_retrotransposon	147916	148117	.	?	.	.
seq1	Genbank	LTR_retrotransposon	149265	149964	.	?	.	.
seq1	Genbank	LTR_retrotransposon	153048	153242	.	?	.	.
seq1	Genbank	LTR_retrotransposon	153232	153342	.	?	.	.
seq1	Genbank	LTR_retrotransposon	153809	154103	.	?	.	.
genometools-1.5.1/testdata/gt_gff3_prob_7.unsorted000066400000000000000000000027501211610345200222350ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq0 1 135606
# CH478465
seq0	Genbank	LTR_retrotransposon	3874	4142	.	?	.	.
seq0	Genbank	LTR_retrotransposon	57759	59137	.	?	.	.
seq0	Genbank	LTR_retrotransposon	58703	63379	.	?	.	.
seq0	Genbank	LTR_retrotransposon	63362	63799	.	?	.	.
seq0	Genbank	LTR_retrotransposon	63793	64472	.	?	.	.
seq0	Genbank	LTR_retrotransposon	82889	83299	.	?	.	.
seq0	Genbank	LTR_retrotransposon	83296	84549	.	?	.	.
seq0	Genbank	LTR_retrotransposon	84542	87203	.	?	.	.
seq0	Genbank	LTR_retrotransposon	119186	123973	.	?	.	.
##sequence-region   seq1 1 163182
# CH478464
seq1	Genbank	LTR_retrotransposon	67057	67156	.	?	.	.
seq1	Genbank	LTR_retrotransposon	74405	74533	.	?	.	.
seq1	Genbank	LTR_retrotransposon	74817	74954	.	?	.	.
seq1	Genbank	LTR_retrotransposon	83694	84311	.	?	.	.
seq1	Genbank	LTR_retrotransposon	106946	107130	.	?	.	.
seq1	Genbank	LTR_retrotransposon	114751	115665	.	?	.	.
seq1	Genbank	LTR_retrotransposon	117806	117952	.	?	.	.
seq1	Genbank	LTR_retrotransposon	121320	121492	.	?	.	.
seq1	Genbank	LTR_retrotransposon	129429	129553	.	?	.	.
seq1	Genbank	LTR_retrotransposon	129536	129703	.	?	.	.
seq1	Genbank	LTR_retrotransposon	129694	129847	.	?	.	.
seq1	Genbank	LTR_retrotransposon	138908	139082	.	?	.	.
seq1	Genbank	LTR_retrotransposon	147916	148117	.	?	.	.
seq1	Genbank	LTR_retrotransposon	149265	149964	.	?	.	.
seq1	Genbank	LTR_retrotransposon	153048	153242	.	?	.	.
seq1	Genbank	LTR_retrotransposon	153232	153342	.	?	.	.
seq1	Genbank	LTR_retrotransposon	153809	154103	.	?	.	.
genometools-1.5.1/testdata/gt_gff3_prob_8.in000066400000000000000000000002401211610345200207710ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene
##sequence-region   cause_prob 1 1000
gDNA	.	exon	100	200	.	-	.	Parent=gene
genometools-1.5.1/testdata/gt_gff3_prob_8.out000066400000000000000000000002461211610345200212000ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene1
gDNA	.	exon	100	200	.	-	.	Parent=gene1
###
##sequence-region   cause_prob 1 1000
genometools-1.5.1/testdata/gt_gff3_prob_9.in000066400000000000000000000002071211610345200207750ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene
# cause prob
gDNA	.	exon	100	200	.	-	.	Parent=gene
genometools-1.5.1/testdata/gt_gff3_prob_9.out000066400000000000000000000002151211610345200211750ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	gene	100	200	.	-	.	ID=gene1
gDNA	.	exon	100	200	.	-	.	Parent=gene1
###
# cause prob
genometools-1.5.1/testdata/gt_gff3_range_check.gff3000066400000000000000000000001171211610345200222530ustar00rootroot00000000000000##gff-version   3
##sequence-region   sr 1000 2000
sr	.	gene	1000	2001	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_range_check2.gff3000066400000000000000000000001161211610345200223340ustar00rootroot00000000000000##gff-version   3
##sequence-region   sr 1000 2000
sr	.	gene	900	2000	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_range_check3.gff3000066400000000000000000000001161211610345200223350ustar00rootroot00000000000000##gff-version   3
##sequence-region   sr 1000 2000
sr	.	gene	900	2001	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_test_1.in000066400000000000000000000002071211610345200210020ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1
ctg123	.	gene	10000	19000	.	+	.	ID=gene2
genometools-1.5.1/testdata/gt_gff3_test_1.out000066400000000000000000000001771211610345200212110ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	
###
ctg123	.	gene	10000	19000	.	+	.	
###
genometools-1.5.1/testdata/gt_gff3_test_10.gff3000066400000000000000000000001001211610345200212710ustar00rootroot00000000000000##gff-version   3
##sequence-region testregion 1 2
testregion	.
genometools-1.5.1/testdata/gt_gff3_test_11.gff3000066400000000000000000000001421211610345200213000ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	geNe	1000	9000	.	+	.	ID=gene00001
genometools-1.5.1/testdata/gt_gff3_test_12.gff3000066400000000000000000000001561211610345200213060ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001;ID=gene0001
genometools-1.5.1/testdata/gt_gff3_test_13.gff3000066400000000000000000000001531211610345200213040ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001=gene0001
genometools-1.5.1/testdata/gt_gff3_test_14.gff3000066400000000000000000000002401211610345200213020ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene00001=bla
genometools-1.5.1/testdata/gt_gff3_test_15.gff3000066400000000000000000000001421211610345200213040ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
CTG123	.	gene	1000	9000	.	+	.	ID=gene00001
genometools-1.5.1/testdata/gt_gff3_test_15.out000066400000000000000000000001741211610345200212730ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
##sequence-region   CTG123 1000 9000
CTG123	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_test_16.gff3000066400000000000000000000001271211610345200213100ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_test_17.gff3000066400000000000000000000000751211610345200213130ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
##foo
genometools-1.5.1/testdata/gt_gff3_test_18.gff3000066400000000000000000000001371211610345200213130ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	Name=EDEN
genometools-1.5.1/testdata/gt_gff3_test_19.gff3000066400000000000000000000000201211610345200213030ustar00rootroot00000000000000##gff-version 3
genometools-1.5.1/testdata/gt_gff3_test_2.gff3000066400000000000000000000000221211610345200212150ustar00rootroot00000000000000##gff-versIon   3
genometools-1.5.1/testdata/gt_gff3_test_20.gff3000066400000000000000000000000201211610345200212730ustar00rootroot00000000000000##gff-version X
genometools-1.5.1/testdata/gt_gff3_test_21.gff3000066400000000000000000000000201211610345200212740ustar00rootroot00000000000000##gff-version 2
genometools-1.5.1/testdata/gt_gff3_test_22.gff3000066400000000000000000000010571211610345200213100ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1,mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1,mRNA2,mRNA3
###
genometools-1.5.1/testdata/gt_gff3_test_23.gff3000066400000000000000000000004121211610345200213030ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	LTR_retrotransposon	100	200	.	-	.	.
gDNA	.	LTR_retrotransposon	300	400	.	-	.	.
gDNA	.	LTR_retrotransposon	500	600	.	-	.	.
gDNA	.	LTR_retrotransposon	700	800	.	-	.	.
gDNA	.	LTR_retrotransposon	900	1000	.	-	.	.
genometools-1.5.1/testdata/gt_gff3_test_24.gff3000066400000000000000000000004501211610345200213060ustar00rootroot00000000000000##gff-version   3
##sequence-region   gDNA 1 1000
gDNA	.	LTR_retrotransposon	100	200	.	-	.	ID=LTR1
gDNA	.	LTR_retrotransposon	300	400	.	-	.	ID=LTR2
gDNA	.	LTR_retrotransposon	500	600	.	-	.	ID=LTR3
gDNA	.	LTR_retrotransposon	700	800	.	-	.	ID=LTR4
gDNA	.	LTR_retrotransposon	900	1000	.	-	.	ID=LTR5
genometools-1.5.1/testdata/gt_gff3_test_25.gff3000066400000000000000000000001521211610345200213060ustar00rootroot00000000000000##gff-version   3
CTG123	.	gene	1000	9000	.	+	.	ID=gene00001
CTG123	.	gene	10000	11000	.	+	.	ID=gene00002
genometools-1.5.1/testdata/gt_gff3_test_25.out000066400000000000000000000001721211610345200212720ustar00rootroot00000000000000##gff-version   3
##sequence-region   CTG123 1000 11000
CTG123	.	gene	1000	9000	.	+	.	.
CTG123	.	gene	10000	11000	.	+	.	.
genometools-1.5.1/testdata/gt_gff3_test_26.gff3000066400000000000000000000001101211610345200213010ustar00rootroot00000000000000##gff-version   3
CTG123	.	gene	1000	9000	.	+	.	ID=gene00001;Parent=nil
genometools-1.5.1/testdata/gt_gff3_test_27.gff3000066400000000000000000000001361211610345200213120ustar00rootroot00000000000000##gff-version   3
CTG123	.	gene	1000	9000	.	+	.	ID=gene00001
##sequence-region CTG123 1 10000
genometools-1.5.1/testdata/gt_gff3_test_3.gff3000066400000000000000000000000231211610345200212170ustar00rootroot00000000000000##gff-version   3

genometools-1.5.1/testdata/gt_gff3_test_4.gff3000066400000000000000000000000441211610345200212230ustar00rootroot00000000000000##gff-version   3
##sequence-region
genometools-1.5.1/testdata/gt_gff3_test_5.gff3000066400000000000000000000000571211610345200212300ustar00rootroot00000000000000##gff-version   3
##sequence-region testregion
genometools-1.5.1/testdata/gt_gff3_test_6.gff3000066400000000000000000000000621211610345200212250ustar00rootroot00000000000000##gff-version   3
##sequence-region testregion  1
genometools-1.5.1/testdata/gt_gff3_test_7.gff3000066400000000000000000000000611211610345200212250ustar00rootroot00000000000000##gff-version   3
##sequence-region testregion x
genometools-1.5.1/testdata/gt_gff3_test_8.gff3000066400000000000000000000000631211610345200212300ustar00rootroot00000000000000##gff-version   3
##sequence-region testregion 1 x
genometools-1.5.1/testdata/gt_gff3_test_9.gff3000066400000000000000000000000631211610345200212310ustar00rootroot00000000000000##gff-version   3
##sequence-region testregion 2 1
genometools-1.5.1/testdata/gt_gff3_undefined_range.gff3000066400000000000000000000004451211610345200231430ustar00rootroot00000000000000##gff-version 3
##sequence-region NG_017013.1 1 26144
NG_017013.1	annotation	remark	.	.	.	.	.	comment=foo
NG_017013.1	feature	STS	23478	24350	.	+	.	db_xref=UniSTS%3A277840;standard_name=TP53_278
NG_017013.1	feature	STS	23999	24075	.	+	.	db_xref=UniSTS%3A59997;standard_name=WI-20715;gene=TP53
genometools-1.5.1/testdata/gt_gff3_undefined_range_parent.gff3000066400000000000000000000004671211610345200245200ustar00rootroot00000000000000##gff-version 3
##sequence-region NG_017013.1 1 26144
NG_017013.1	annotation	remark	.	.	.	.	.	comment=foo;ID=bar
NG_017013.1	feature	STS	23478	24350	.	+	.	db_xref=UniSTS%3A277840;standard_name=TP53_278;Parent=bar
NG_017013.1	feature	STS	23999	24075	.	+	.	db_xref=UniSTS%3A59997;standard_name=WI-20715;gene=TP53
genometools-1.5.1/testdata/gt_gff3_undefined_range_tidy.gff3000066400000000000000000000003651211610345200241750ustar00rootroot00000000000000##gff-version   3
##sequence-region   NG_017013.1 1 26144
NG_017013.1	feature	STS	23478	24350	.	+	.	db_xref=UniSTS%3A277840;standard_name=TP53_278
NG_017013.1	feature	STS	23999	24075	.	+	.	db_xref=UniSTS%3A59997;standard_name=WI-20715;gene=TP53
genometools-1.5.1/testdata/gt_gtf_to_gff3_test.gff3000066400000000000000000000215521211610345200223510ustar00rootroot00000000000000##gff-version   3
##sequence-region   Hs.22.ENST00000216085.2 27980398 27986169
##sequence-region   Hs.16.ENST00000219207.1 57024629 57053191
##sequence-region   Hs.1.ENST00000289753.1 19137760 19152035
##sequence-region   Hs.2.ENST00000233735.1 79305643 79308243
##sequence-region   Hs.3.ENST00000302762.1 156827614 156853401
##sequence-region   Hs.19.ENST00000301452.1 6246725 6273562
##sequence-region   Hs.5.ENST00000194152.1 140484730 140488350
##sequence-region   Hs.1.ENST00000294816.1 161868957 162021049
##sequence-region   Hs.22.ENST00000249079.1 36582572 36592644
Hs.2.ENST00000233735.1	.	gene	79305643	79308243	.	+	.	ID=gene1
Hs.2.ENST00000233735.1	.	mRNA	79305643	79308243	.	+	.	ID=mRNA1;Parent=gene1
Hs.2.ENST00000233735.1	EnsEMBL	exon	79305643	79305759	.	+	.	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79305696	79305759	.	+	0	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	exon	79306396	79306514	.	+	.	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79306396	79306514	.	+	2	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	exon	79306822	79306959	.	+	.	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79306822	79306959	.	+	0	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	exon	79307675	79307786	.	+	.	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79307675	79307786	.	+	0	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79307982	79308046	.	+	2	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	exon	79307982	79308243	.	+	.	Parent=mRNA1
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79308047	79308049	.	+	0	Parent=mRNA1
###
Hs.22.ENST00000249079.1	.	gene	36582572	36592644	.	-	.	ID=gene2
Hs.22.ENST00000249079.1	.	mRNA	36582572	36592644	.	-	.	ID=mRNA2;Parent=gene2
Hs.22.ENST00000249079.1	EnsEMBL	exon	36582572	36583292	.	-	.	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36583221	36583223	.	-	0	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36583224	36583292	.	-	0	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	exon	36583463	36583563	.	-	.	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36583463	36583563	.	-	2	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	exon	36584088	36584219	.	-	.	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36584088	36584219	.	-	2	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	exon	36586327	36586509	.	-	.	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36586327	36586509	.	-	2	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	exon	36590506	36590568	.	-	.	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36590506	36590568	.	-	2	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36592093	36592195	.	-	0	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	exon	36592093	36592204	.	-	.	Parent=mRNA2
Hs.22.ENST00000249079.1	EnsEMBL	exon	36592395	36592644	.	-	.	Parent=mRNA2
###
Hs.1.ENST00000289753.1	.	gene	19137760	19152035	.	+	.	ID=gene3
Hs.1.ENST00000289753.1	.	mRNA	19137760	19152035	.	+	.	ID=mRNA3;Parent=gene3
Hs.1.ENST00000289753.1	EnsEMBL	exon	19137760	19138940	.	+	.	Parent=mRNA3
Hs.1.ENST00000289753.1	EnsEMBL	CDS	19138227	19138940	.	+	0	Parent=mRNA3
Hs.1.ENST00000289753.1	EnsEMBL	exon	19151040	19151198	.	+	.	Parent=mRNA3
Hs.1.ENST00000289753.1	EnsEMBL	CDS	19151040	19151198	.	+	0	Parent=mRNA3
Hs.1.ENST00000289753.1	EnsEMBL	CDS	19151392	19151838	.	+	0	Parent=mRNA3
Hs.1.ENST00000289753.1	EnsEMBL	exon	19151392	19152035	.	+	.	Parent=mRNA3
Hs.1.ENST00000289753.1	EnsEMBL	CDS	19151839	19151841	.	+	0	Parent=mRNA3
###
Hs.16.ENST00000219207.1	.	gene	57024629	57053191	.	-	.	ID=gene4
Hs.16.ENST00000219207.1	.	mRNA	57024629	57053191	.	-	.	ID=mRNA4;Parent=gene4
Hs.16.ENST00000219207.1	EnsEMBL	exon	57024629	57025561	.	-	.	Parent=mRNA4
Hs.16.ENST00000219207.1	EnsEMBL	CDS	57025445	57025447	.	-	0	Parent=mRNA4
Hs.16.ENST00000219207.1	EnsEMBL	CDS	57025448	57025561	.	-	0	Parent=mRNA4
Hs.16.ENST00000219207.1	EnsEMBL	exon	57026994	57027116	.	-	.	Parent=mRNA4
Hs.16.ENST00000219207.1	EnsEMBL	CDS	57026994	57027116	.	-	0	Parent=mRNA4
Hs.16.ENST00000219207.1	EnsEMBL	exon	57030429	57030602	.	-	.	Parent=mRNA4
Hs.16.ENST00000219207.1	EnsEMBL	CDS	57030429	57030602	.	-	0	Parent=mRNA4
Hs.16.ENST00000219207.1	EnsEMBL	CDS	57052938	57053072	.	-	0	Parent=mRNA4
Hs.16.ENST00000219207.1	EnsEMBL	exon	57052938	57053191	.	-	.	Parent=mRNA4
###
Hs.3.ENST00000302762.1	.	gene	156827614	156853401	.	-	.	ID=gene5
Hs.3.ENST00000302762.1	.	mRNA	156827614	156853401	.	-	.	ID=mRNA5;Parent=gene5
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156827614	156827616	.	-	0	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	exon	156827614	156827781	.	-	.	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156827617	156827781	.	-	0	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	exon	156829092	156829307	.	-	.	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156829092	156829307	.	-	0	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	exon	156832872	156832989	.	-	.	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156832872	156832989	.	-	1	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	exon	156833261	156833445	.	-	.	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156833261	156833445	.	-	0	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	exon	156841836	156842023	.	-	.	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156841836	156842023	.	-	2	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	exon	156852627	156853401	.	-	.	Parent=mRNA5
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156852627	156853401	.	-	0	Parent=mRNA5
###
Hs.19.ENST00000301452.1	.	gene	6246725	6273562	.	-	.	ID=gene6
Hs.19.ENST00000301452.1	.	mRNA	6246725	6273562	.	-	.	ID=mRNA6;Parent=gene6
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6246725	6246727	.	-	0	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	exon	6246725	6246893	.	-	.	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6246728	6246893	.	-	1	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	exon	6247164	6247301	.	-	.	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6247164	6247301	.	-	1	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	exon	6249708	6249845	.	-	.	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6249708	6249845	.	-	1	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	exon	6252160	6252301	.	-	.	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6252160	6252301	.	-	2	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	exon	6252396	6252510	.	-	.	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6252396	6252510	.	-	0	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	exon	6273470	6273562	.	-	.	Parent=mRNA6
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6273470	6273562	.	-	0	Parent=mRNA6
###
Hs.22.ENST00000216085.2	.	gene	27980398	27986169	.	-	.	ID=gene7
Hs.22.ENST00000216085.2	.	mRNA	27980398	27986169	.	-	.	ID=mRNA7;Parent=gene7
Hs.22.ENST00000216085.2	EnsEMBL	exon	27980398	27980780	.	-	.	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27980603	27980605	.	-	0	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27980606	27980780	.	-	1	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	exon	27980869	27981156	.	-	.	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27980869	27981156	.	-	1	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	exon	27981245	27981407	.	-	.	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27981245	27981407	.	-	2	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	exon	27984378	27984761	.	-	.	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27984378	27984761	.	-	2	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	exon	27986022	27986169	.	-	.	Parent=mRNA7
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27986022	27986169	.	-	0	Parent=mRNA7
###
Hs.5.ENST00000194152.1	.	gene	140484730	140488350	.	+	.	ID=gene8
Hs.5.ENST00000194152.1	.	mRNA	140484730	140488350	.	+	.	ID=mRNA8;Parent=gene8
Hs.5.ENST00000194152.1	EnsEMBL	CDS	140484730	140487114	.	+	0	Parent=mRNA8
Hs.5.ENST00000194152.1	EnsEMBL	exon	140484730	140488350	.	+	.	Parent=mRNA8
Hs.5.ENST00000194152.1	EnsEMBL	CDS	140487115	140487117	.	+	0	Parent=mRNA8
###
Hs.1.ENST00000294816.1	.	gene	161868957	162021049	.	-	.	ID=gene9
Hs.1.ENST00000294816.1	.	mRNA	161868957	162021049	.	-	.	ID=mRNA9;Parent=gene9
Hs.1.ENST00000294816.1	EnsEMBL	exon	161868957	161869309	.	-	.	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161869149	161869151	.	-	0	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161869152	161869309	.	-	2	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	exon	161871133	161871303	.	-	.	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161871133	161871303	.	-	2	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	exon	161873332	161873401	.	-	.	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161873332	161873401	.	-	0	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	exon	161875968	161876045	.	-	.	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161875968	161876045	.	-	0	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	exon	161878910	161879082	.	-	.	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161878910	161879082	.	-	2	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	exon	161914677	161914909	.	-	.	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161914677	161914909	.	-	1	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	exon	162018345	162018531	.	-	.	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	CDS	162018345	162018531	.	-	2	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	CDS	162020753	162020828	.	-	0	Parent=mRNA9
Hs.1.ENST00000294816.1	EnsEMBL	exon	162020753	162021049	.	-	.	Parent=mRNA9
###
genometools-1.5.1/testdata/gt_gtf_to_gff3_test.gtf000066400000000000000000000403641211610345200223060ustar00rootroot00000000000000Hs.3.ENST00000302762.1	EnsEMBL	exon	156852627	156853401	.	-	.	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001330091.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156852627	156853401	.	-	0	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001330091.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	start_codon	156853399	156853401	.	-	0	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001330091.1";
Hs.3.ENST00000302762.1	EnsEMBL	exon	156841836	156842023	.	-	.	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001182133.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156841836	156842023	.	-	2	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001182133.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	exon	156833261	156833445	.	-	.	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001169591.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156833261	156833445	.	-	0	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001169591.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	exon	156832872	156832989	.	-	.	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001169581.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156832872	156832989	.	-	1	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001169581.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	exon	156829092	156829307	.	-	.	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001169576.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156829092	156829307	.	-	0	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001169576.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	exon	156827614	156827781	.	-	.	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001318604.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	CDS	156827617	156827781	.	-	0	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001318604.1"; 
Hs.3.ENST00000302762.1	EnsEMBL	stop_codon	156827614	156827616	.	-	0	gene_id "ENSG00000169359.2"; transcript_id "ENST00000302762.1"; exon_id "ENSE00001318604.1";
Hs.22.ENST00000216085.2	EnsEMBL	exon	27986022	27986169	.	-	.	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000879709.2"; 
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27986022	27986169	.	-	0	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000879709.2"; 
Hs.22.ENST00000216085.2	EnsEMBL	start_codon	27986167	27986169	.	-	0	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000879709.2";
Hs.22.ENST00000216085.2	EnsEMBL	exon	27984378	27984761	.	-	.	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000652009.1"; 
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27984378	27984761	.	-	2	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000652009.1"; 
Hs.22.ENST00000216085.2	EnsEMBL	exon	27981245	27981407	.	-	.	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000652008.1"; 
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27981245	27981407	.	-	2	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000652008.1"; 
Hs.22.ENST00000216085.2	EnsEMBL	exon	27980869	27981156	.	-	.	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000652007.1"; 
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27980869	27981156	.	-	1	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000652007.1"; 
Hs.22.ENST00000216085.2	EnsEMBL	exon	27980398	27980780	.	-	.	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000879708.1"; 
Hs.22.ENST00000216085.2	EnsEMBL	CDS	27980606	27980780	.	-	1	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000879708.1"; 
Hs.22.ENST00000216085.2	EnsEMBL	stop_codon	27980603	27980605	.	-	0	gene_id "ENSG00000100263.2"; transcript_id "ENST00000216085.2"; exon_id "ENSE00000879708.1";
Hs.1.ENST00000289753.1	EnsEMBL	exon	19137760	19138940	.	+	.	gene_id "ENSG00000158748.1"; transcript_id "ENST00000289753.1"; exon_id "ENSE00001040779.1"; 
Hs.1.ENST00000289753.1	EnsEMBL	CDS	19138227	19138940	.	+	0	gene_id "ENSG00000158748.1"; transcript_id "ENST00000289753.1"; exon_id "ENSE00001040779.1"; 
Hs.1.ENST00000289753.1	EnsEMBL	start_codon	19138227	19138229	.	+	0	gene_id "ENSG00000158748.1"; transcript_id "ENST00000289753.1"; exon_id "ENSE00001040779.1";
Hs.1.ENST00000289753.1	EnsEMBL	exon	19151040	19151198	.	+	.	gene_id "ENSG00000158748.1"; transcript_id "ENST00000289753.1"; exon_id "ENSE00001040777.1"; 
Hs.1.ENST00000289753.1	EnsEMBL	CDS	19151040	19151198	.	+	0	gene_id "ENSG00000158748.1"; transcript_id "ENST00000289753.1"; exon_id "ENSE00001040777.1"; 
Hs.1.ENST00000289753.1	EnsEMBL	exon	19151392	19152035	.	+	.	gene_id "ENSG00000158748.1"; transcript_id "ENST00000289753.1"; exon_id "ENSE00001263964.2"; 
Hs.1.ENST00000289753.1	EnsEMBL	CDS	19151392	19151838	.	+	0	gene_id "ENSG00000158748.1"; transcript_id "ENST00000289753.1"; exon_id "ENSE00001263964.2"; 
Hs.1.ENST00000289753.1	EnsEMBL	stop_codon	19151839	19151841	.	+	0	gene_id "ENSG00000158748.1"; transcript_id "ENST00000289753.1"; exon_id "ENSE00001263964.2";
Hs.19.ENST00000301452.1	EnsEMBL	exon	6273470	6273562	.	-	.	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001312002.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6273470	6273562	.	-	0	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001312002.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	start_codon	6273560	6273562	.	-	0	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001312002.1";
Hs.19.ENST00000301452.1	EnsEMBL	exon	6252396	6252510	.	-	.	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001116785.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6252396	6252510	.	-	0	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001116785.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	exon	6252160	6252301	.	-	.	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001116786.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6252160	6252301	.	-	2	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001116786.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	exon	6249708	6249845	.	-	.	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001160540.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6249708	6249845	.	-	1	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001160540.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	exon	6247164	6247301	.	-	.	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001160535.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6247164	6247301	.	-	1	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001160535.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	exon	6246725	6246893	.	-	.	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001160559.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	CDS	6246728	6246893	.	-	1	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001160559.1"; 
Hs.19.ENST00000301452.1	EnsEMBL	stop_codon	6246725	6246727	.	-	0	gene_id "ENSG00000167769.1"; transcript_id "ENST00000301452.1"; exon_id "ENSE00001160559.1";
Hs.16.ENST00000219207.1	EnsEMBL	exon	57052938	57053191	.	-	.	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00001165318.1"; 
Hs.16.ENST00000219207.1	EnsEMBL	CDS	57052938	57053072	.	-	0	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00001165318.1"; 
Hs.16.ENST00000219207.1	EnsEMBL	start_codon	57053070	57053072	.	-	0	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00001165318.1";
Hs.16.ENST00000219207.1	EnsEMBL	exon	57030429	57030602	.	-	.	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00000852888.1"; 
Hs.16.ENST00000219207.1	EnsEMBL	CDS	57030429	57030602	.	-	0	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00000852888.1"; 
Hs.16.ENST00000219207.1	EnsEMBL	exon	57026994	57027116	.	-	.	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00000685165.1"; 
Hs.16.ENST00000219207.1	EnsEMBL	CDS	57026994	57027116	.	-	0	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00000685165.1"; 
Hs.16.ENST00000219207.1	EnsEMBL	exon	57024629	57025561	.	-	.	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00001165312.1"; 
Hs.16.ENST00000219207.1	EnsEMBL	CDS	57025448	57025561	.	-	0	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00001165312.1"; 
Hs.16.ENST00000219207.1	EnsEMBL	stop_codon	57025445	57025447	.	-	0	gene_id "ENSG00000102934.1"; transcript_id "ENST00000219207.1"; exon_id "ENSE00001165312.1";
Hs.1.ENST00000294816.1	EnsEMBL	exon	162020753	162021049	.	-	.	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001291550.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	CDS	162020753	162020828	.	-	0	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001291550.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	start_codon	162020826	162020828	.	-	0	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001291550.1";
Hs.1.ENST00000294816.1	EnsEMBL	exon	162018345	162018531	.	-	.	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158610.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	CDS	162018345	162018531	.	-	2	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158610.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	exon	161914677	161914909	.	-	.	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158602.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161914677	161914909	.	-	1	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158602.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	exon	161878910	161879082	.	-	.	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001068374.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161878910	161879082	.	-	2	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001068374.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	exon	161875968	161876045	.	-	.	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158587.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161875968	161876045	.	-	0	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158587.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	exon	161873332	161873401	.	-	.	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158579.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161873332	161873401	.	-	0	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158579.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	exon	161871133	161871303	.	-	.	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158569.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161871133	161871303	.	-	2	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001158569.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	exon	161868957	161869309	.	-	.	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001324656.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	CDS	161869152	161869309	.	-	2	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001324656.1"; 
Hs.1.ENST00000294816.1	EnsEMBL	stop_codon	161869149	161869151	.	-	0	gene_id "ENSG00000162761.1"; transcript_id "ENST00000294816.1"; exon_id "ENSE00001324656.1";
Hs.22.ENST00000249079.1	EnsEMBL	exon	36592395	36592644	.	-	.	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00001047894.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	exon	36592093	36592204	.	-	.	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880244.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36592093	36592195	.	-	0	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880244.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	start_codon	36592193	36592195	.	-	0	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880244.1";
Hs.22.ENST00000249079.1	EnsEMBL	exon	36590506	36590568	.	-	.	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880243.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36590506	36590568	.	-	2	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880243.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	exon	36586327	36586509	.	-	.	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880242.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36586327	36586509	.	-	2	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880242.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	exon	36584088	36584219	.	-	.	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880241.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36584088	36584219	.	-	2	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880241.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	exon	36583463	36583563	.	-	.	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880240.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36583463	36583563	.	-	2	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880240.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	exon	36582572	36583292	.	-	.	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880239.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	CDS	36583224	36583292	.	-	0	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880239.1"; 
Hs.22.ENST00000249079.1	EnsEMBL	stop_codon	36583221	36583223	.	-	0	gene_id "ENSG00000128346.1"; transcript_id "ENST00000249079.1"; exon_id "ENSE00000880239.1";
Hs.2.ENST00000233735.1	EnsEMBL	exon	79305643	79305759	.	+	.	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00001124716.2"; 
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79305696	79305759	.	+	0	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00001124716.2"; 
Hs.2.ENST00000233735.1	EnsEMBL	start_codon	79305696	79305698	.	+	0	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00001124716.2";
Hs.2.ENST00000233735.1	EnsEMBL	exon	79306396	79306514	.	+	.	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00001124706.1"; 
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79306396	79306514	.	+	2	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00001124706.1"; 
Hs.2.ENST00000233735.1	EnsEMBL	exon	79306822	79306959	.	+	.	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00001124699.1"; 
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79306822	79306959	.	+	0	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00001124699.1"; 
Hs.2.ENST00000233735.1	EnsEMBL	exon	79307675	79307786	.	+	.	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00001124693.1"; 
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79307675	79307786	.	+	0	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00001124693.1"; 
Hs.2.ENST00000233735.1	EnsEMBL	exon	79307982	79308243	.	+	.	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00000846820.2"; 
Hs.2.ENST00000233735.1	EnsEMBL	CDS	79307982	79308046	.	+	2	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00000846820.2"; 
Hs.2.ENST00000233735.1	EnsEMBL	stop_codon	79308047	79308049	.	+	0	gene_id "ENSG00000115386.2"; transcript_id "ENST00000233735.1"; exon_id "ENSE00000846820.2";
Hs.5.ENST00000194152.1	EnsEMBL	exon	140484730	140488350	.	+	.	gene_id "ENSG00000081818.1"; transcript_id "ENST00000194152.1"; exon_id "ENSE00000527102.1"; 
Hs.5.ENST00000194152.1	EnsEMBL	CDS	140484730	140487114	.	+	0	gene_id "ENSG00000081818.1"; transcript_id "ENST00000194152.1"; exon_id "ENSE00000527102.1"; 
Hs.5.ENST00000194152.1	EnsEMBL	start_codon	140484730	140484732	.	+	0	gene_id "ENSG00000081818.1"; transcript_id "ENST00000194152.1"; exon_id "ENSE00000527102.1";
Hs.5.ENST00000194152.1	EnsEMBL	stop_codon	140487115	140487117	.	+	0	gene_id "ENSG00000081818.1"; transcript_id "ENST00000194152.1"; exon_id "ENSE00000527102.1";
genometools-1.5.1/testdata/gt_merge_prob_1.in1000066400000000000000000000001271211610345200213210ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_merge_prob_1.in2000066400000000000000000000001311211610345200213150ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	10000	11000	.	+	.	.
genometools-1.5.1/testdata/gt_merge_prob_1.out000066400000000000000000000001711211610345200214400ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	.
ctg123	.	gene	10000	11000	.	+	.	.
genometools-1.5.1/testdata/gt_merge_prob_2.in1000066400000000000000000000001351211610345200213210ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 10000 1497228
ctg123	.	gene	10000	11000	.	+	.	.
genometools-1.5.1/testdata/gt_merge_prob_2.in2000066400000000000000000000001271211610345200213230ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/gt_merge_prob_2.out000066400000000000000000000001711211610345200214410ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	.
ctg123	.	gene	10000	11000	.	+	.	.
genometools-1.5.1/testdata/gt_mmapandread_test_1.in000066400000000000000000000000021211610345200224170ustar00rootroot000000000000001
genometools-1.5.1/testdata/gt_mmapandread_test_2.in000066400000000000000000000000001211610345200224160ustar00rootroot00000000000000genometools-1.5.1/testdata/gt_mmapandread_test_3.in000066400000000000000000000000011211610345200224200ustar00rootroot00000000000000genometools-1.5.1/testdata/gt_mmapandread_test_4.in000066400000000000000000000000001211610345200224200ustar00rootroot00000000000000genometools-1.5.1/testdata/gt_mutate_test_1.fas000066400000000000000000000237321211610345200216270ustar00rootroot00000000000000>
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genometools-1.5.1/testdata/gt_mutate_test_2.fas000066400000000000000000000237321211610345200216300ustar00rootroot00000000000000>
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genometools-1.5.1/testdata/gt_mutate_test_2.out000066400000000000000000000234551211610345200216700ustar00rootroot00000000000000> [mutated with rate 1]
ttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttgtttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttcttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttcttcttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttt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tttt
genometools-1.5.1/testdata/gt_mutate_test_both.out000066400000000000000000000471121211610345200224570ustar00rootroot00000000000000> [mutated with rate 2]
aaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaagaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaataaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaatataaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaataaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaataaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
> [mutated with rate 2]
tttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttgtttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttgtttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttgttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttcttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttctttttttttttttttttgtttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttcttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttatttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttatttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttctttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttatttttttttttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttgtttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcctttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttttttttttttctttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttcttttttttttttttttatttttttttttttttttatttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttgtttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttcttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttcttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttttttttatttttttttttttttttttttttttttttttttttttttttttccttttttttttttttttttttttttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttattttattttttttttttattttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttattttttttttttttttttttcttttttttttttttttttttttttttttattttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttctttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttgttttttttttttttattttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttatttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttcttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttgtttttttttttttttttttttttttttttttttttttttttttttttttatttttttgttttatttttttttttttttttttttttttttttttttttttttttttttttttttttgttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttt
genometools-1.5.1/testdata/gt_regioncov_test_1.out000066400000000000000000000141671211610345200223630ustar00rootroot00000000000000chr1:
147971134, 147980870
147983498, 148035085
148040252, 148053028
148065573, 148077454
148077486, 148113264
148126189, 148132906
148149851, 148158282
148185083, 148187493
148188273, 148245014
148296059, 148324241
148325854, 148369132
148397614, 148468994
chr10:
55232537, 55643814
chr11:
1710216, 1741798
1806113, 1815327
1816795, 1819484
1830776, 1870073
1897368, 1916512
1925084, 1962328
2106918, 2139147
2141735, 2149683
2246301, 2249421
2273451, 2296006
4745076, 4970235
4976789, 4977736
5024332, 5025267
5036456, 5037433
5109498, 5110448
5128815, 5164188
5177541, 5178506
5203270, 5207201
5210484, 5213176
5225889, 5227698
5230996, 5623595
5641363, 5663200
5667495, 5715297
5732547, 5732587
63973122, 63975702
64079674, 64096923
64114689, 64126396
64130222, 64247236
64250959, 64269504
64270437, 64284345
64288654, 64302834
64313185, 64327289
64327564, 64335342
64347435, 64368617
64375690, 64412344
64418594, 64438548
116124096, 116148914
116151036, 116151802
116153646, 116163976
116165293, 116168337
116196629, 116199232
116205632, 116208998
116211677, 116213876
116219328, 116332990
130745583, 131036335
chr12:
38629559, 38786158
38876813, 39049354
39073464, 39125713
chr13:
29419740, 29422625
29674767, 29779621
112349359, 112386812
112392644, 112589483
112604510, 112802054
112808106, 112822996
112825129, 112832621
chr14:
98705377, 98807614
98933836, 98950024
chr15:
41520749, 41590218
41590448, 41611110
41612952, 41747608
41772376, 41778712
41825882, 41882533
41883982, 41904292
41906453, 41947909
41950254, 42003799
chr16:
4043, 9452
12910, 15123
36407, 47669
48058, 66354
67006, 128859
142686, 156767
162846, 163709
166679, 167521
170452, 171180
178969, 219463
224546, 273004
273153, 277216
277441, 342674
356928, 360569
360774, 377114
386726, 402488
415620, 495628
25805568, 26056510
chr18:
23784928, 24011408
59412569, 59422853
59455473, 59462512
59473411, 59480177
59571149, 59623584
59689906, 59754325
59767515, 59823258
chr19:
59061289, 59071503
59074256, 59102718
59104401, 59139007
59158106, 59185281
59187354, 59207735
59235891, 59259019
59289745, 59297812
59297848, 59326955
59333256, 59355432
59355658, 59368756
59368921, 59385478
59385601, 59389333
59396422, 59444674
59446075, 59452976
59469487, 59476851
59491666, 59501764
59510165, 59516221
59536268, 59542233
59557074, 59573977
59618185, 59639892
59651877, 59666706
59668022, 59676223
59700912, 59713709
59735789, 59748865
59776199, 59790839
59796859, 59805367
59820424, 59842155
59847152, 59873622
59927796, 59939815
59941792, 59956316
59973075, 59987310
60006878, 60017784
60019735, 60023279
chr2:
118288456, 118306185
118389284, 118487939
220108604, 220116966
220125073, 220188514
220189094, 220197215
220204397, 220228999
220229174, 220240822
220240956, 220265940
220288087, 220306678
220317554, 220332207
234308291, 234463956
234466370, 234545212
234608043, 234710166
234741323, 234767778
chr20:
33305669, 33328215
33330128, 33336202
33336948, 33343639
33353783, 33463358
33484241, 33505982
33506399, 33563218
33578213, 33580891
33593184, 33608819
33609921, 33658898
33667228, 33672385
33677367, 33752320
33754946, 33793648
chr21:
32669578, 32687206
32706185, 32809570
32870733, 32907047
32922944, 33022183
33028081, 33066040
33066282, 33187913
33320023, 33323374
33364320, 33366596
33459646, 33464824
33524076, 33591409
33618652, 33654038
33679169, 33775369
33779707, 33785897
33798108, 34210154
39468565, 39477647
39477972, 39615355
39636111, 39643443
39674040, 39691685
39699640, 39739601
39739651, 39739894
chr22:
30131552, 30154992
30159903, 30382972
30396796, 30470680
30474498, 30627555
30654061, 30678144
30763573, 30833570
30869547, 30879863
30910979, 30924018
30939019, 30975882
31075426, 31091617
31108123, 31132796
31134388, 31185025
31195217, 31219370
31233093, 31778912
chr5:
55887725, 55937816
56147158, 56227736
56240844, 56248932
56251186, 56303259
131285414, 131375769
131424121, 131426796
131437382, 131439758
131555430, 131707798
131733343, 131759205
131774227, 131839635
131845200, 131854389
131905035, 132007651
132019854, 132024701
132037577, 132046267
132056267, 132101229
132111036, 132170832
132177178, 132180388
132185732, 132194489
132224772, 132231622
132235913, 132238637
132238970, 132267995
141951927, 142057801
142130133, 142374155
chr6:
41411371, 41426603
41578160, 41595568
41622142, 41678100
41712598, 41729962
41759694, 41811975
41812427, 41829825
41845892, 41882727
73808380, 73965295
73975314, 74076809
74119506, 74120739
74129121, 74130615
74134999, 74218720
74228022, 74275680
74282194, 74288344
108382481, 108386086
108469306, 108593751
108593955, 108616706
108639119, 108689157
108722791, 108829951
132221501, 132257988
132311009, 132314206
132658887, 132691426
chr7:
26905852, 26908833
26913216, 26915545
26919043, 26953067
26953911, 26956703
26958255, 26965457
26966575, 26970795
26975297, 26993120
26994016, 26998082
27008262, 27012965
27055524, 27060691
89428340, 89438794
89441555, 89511643
89519150, 89585028
89614336, 90484556
90538330, 90542763
113649061, 113924151
114156160, 114253207
115444498, 115492788
115522078, 115742546
115758790, 115795181
115906410, 116032391
116045075, 116153266
116187332, 116464108
116510636, 116557294
116597227, 116662128
116699789, 116902666
116944656, 117108144
125672607, 126487299
126580795, 126665929
126814623, 126835803
chr8:
118886142, 119193119
119276307, 119279152
chr9:
128768701, 128870136
128878454, 128913915
128922933, 128932271
128936643, 128990779
129017385, 129020095
chrX:
122525028, 122592441
122719109, 122773364
122819597, 122962041
152647816, 152721523
152721563, 152730990
152733851, 152758105
152758625, 152769493
152796798, 152806278
152807871, 152923425
152930592, 152945354
152945529, 152966481
152969001, 152982480
152982659, 153003602
153006119, 153019602
153019777, 153044643
153044871, 153079547
153097741, 153123841
153128404, 153130730
153147246, 153170912
153177831, 153183639
153236208, 153242706
153250325, 153265693
153269812, 153271300
153275760, 153278704
153279349, 153282706
153298194, 153308270
153323310, 153359508
153363183, 153363895
153377111, 153378779
153409569, 153411237
153424440, 153425152
153443950, 153445557
153467233, 153543562
153554739, 153569668
153570663, 153612986
153615327, 153626641
153627767, 153852282
153853601, 153939916
genometools-1.5.1/testdata/gt_regioncov_test_2.out000066400000000000000000000017231211610345200223560ustar00rootroot00000000000000chr1:
147971134, 148468994
chr10:
55232537, 55643814
chr11:
1710216, 2296006
4745076, 5732587
63973122, 64438548
116124096, 116332990
130745583, 131036335
chr12:
38629559, 39125713
chr13:
29419740, 29422625
29674767, 29779621
112349359, 112832621
chr14:
98705377, 98950024
chr15:
41520749, 42003799
chr16:
4043, 495628
25805568, 26056510
chr18:
23784928, 24011408
59412569, 59823258
chr19:
59061289, 60023279
chr2:
118288456, 118487939
220108604, 220332207
234308291, 234767778
chr20:
33305669, 33793648
chr21:
32669578, 34210154
39468565, 39739894
chr22:
30131552, 31778912
chr5:
55887725, 56303259
131285414, 132267995
141951927, 142374155
chr6:
41411371, 41882727
73808380, 74288344
108382481, 108829951
132221501, 132314206
132658887, 132691426
chr7:
26905852, 27060691
89428340, 90542763
113649061, 113924151
114156160, 114253207
115444498, 117108144
125672607, 126835803
chr8:
118886142, 119279152
chr9:
128768701, 129020095
chrX:
122525028, 122962041
152647816, 153939916
genometools-1.5.1/testdata/gt_select_encode.out000066400000000000000000000002151211610345200216720ustar00rootroot00000000000000parsed genome node DAGs: 1352
sequence regions: 20 (total length: 713365500)
genes: 1332
protein-coding genes: 1332
exons: 10938
CDSs: 10072
genometools-1.5.1/testdata/gt_select_test.out000066400000000000000000000000671211610345200214210ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
genometools-1.5.1/testdata/gt_select_test_contain.1000-8999000066400000000000000000000000671211610345200233250ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1000 8999
genometools-1.5.1/testdata/gt_select_test_contain.1000-9000000066400000000000000000000014171211610345200232730ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1000 9000
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/gt_select_test_contain.1001-9000000066400000000000000000000000671211610345200232740ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1001 9000
genometools-1.5.1/testdata/gt_seqlensort_test.fas000066400000000000000000000007141211610345200223020ustar00rootroot00000000000000>first
aaaaaaaaaaaaaaaaaa
>second
gggggggagagagagagc
>third
ttttttatatatatatcg
>fourth
acgtag
>5th
caccac
>6th
caca
>7th
cacaca
>8th
cacacacacacacggtgtgtgtgttgttgtttttttttttttttttcagtcatgctagctagctagctagctagtcgatcgtagctagctag
>ninth
cagttgctagtgcgtgtgcatgcgatgtcgtagctagctagtgtgtagctagctagtttatatattatatatatattatatatattatat
>the tenth sequence
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
>11th
aaaaaaaaaaaaaaaaaa
genometools-1.5.1/testdata/gt_seqlensort_test_sorted.fas000066400000000000000000000006171211610345200236640ustar00rootroot00000000000000>
caca
>
acgtag
>
caccac
>
cacaca
>
aaaaaaaaaaaaaaaaaa
>
gggggggagagagagagc
>
ttttttatatatatatcg
>
aaaaaaaaaaaaaaaaaa
>
cagttgctagtgcgtgtgcatgcgatgtcgtagctagctagtgtgtagctagctagtttatatattatatatatattatatatattatat
>
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
>
cacacacacacacggtgtgtgtgttgttgtttttttttttttttttcagtcatgctagctagctagctagctagtcgatcgtagctagctag
genometools-1.5.1/testdata/gt_seqorder_test.fas000066400000000000000000000001621211610345200217240ustar00rootroot00000000000000>0
aan
>1
at
>2
ta
>3
ag
>4
gg
>5
ca
>6
at
>7
tt
>8
ac
>9
cg
>10
ga
>11
a
>12
aaa
>13
aaaa
>14
aa
>15
aan
>16
ana
genometools-1.5.1/testdata/gt_seqorder_test_revsort.fas000066400000000000000000000001621211610345200235100ustar00rootroot00000000000000>7
tt
>2
ta
>4
gg
>10
ga
>9
cg
>5
ca
>16
ana
>11
a
>6
at
>1
at
>3
ag
>8
ac
>15
aan
>14
aa
>0
aan
>12
aaa
>13
aaaa
genometools-1.5.1/testdata/gt_seqorder_test_sort.fas000066400000000000000000000001621211610345200227730ustar00rootroot00000000000000>13
aaaa
>12
aaa
>0
aan
>14
aa
>15
aan
>8
ac
>3
ag
>1
at
>6
at
>11
a
>16
ana
>5
ca
>9
cg
>10
ga
>4
gg
>2
ta
>7
tt
genometools-1.5.1/testdata/gt_sketch_multiline_without_parent.gff3000066400000000000000000000007271211610345200256230ustar00rootroot00000000000000##gff-version 3
##sequence-region ctg123 1 1497228
ctg123	.	CDS	1201	1500	.	+	0	ID=cds00001;Name=edenprotein.1
ctg123	.	CDS	3000	3902	.	+	0	ID=cds00001;Name=edenprotein.1
ctg123	.	CDS	5000	5500	.	+	0	ID=cds00001;Name=edenprotein.1
ctg123	.	CDS	7000	7600	.	+	0	ID=cds00001;Name=edenprotein.1
ctg123	.	CDS	1201	1500	.	+	0	ID=cds00002;Name=edenprotein.2
ctg123	.	CDS	5000	5500	.	+	0	ID=cds00002;Name=edenprotein.2
ctg123	.	CDS	7000	7600	.	+	0	ID=cds00002;Name=edenprotein.2
genometools-1.5.1/testdata/gt_sketch_textwidth.gff3000066400000000000000000000004761211610345200225120ustar00rootroot00000000000000##gff-version 3
##sequence-region ctg123 1 1497228
ctg123	.	gene	1000	2000	.	+	0	ID=g00001;Name=thisisalongname
ctg123	.	gene	2001	3000	.	+	0	ID=g00002;Name=anotherlongname
ctg123	.	gene	3001	4000	.	+	0	ID=g00003;Name=stillanotherlonglonglonglonglonglonglongname
ctg123	.	gene	4001	5000	.	+	0	ID=g00004;Name=shortname
genometools-1.5.1/testdata/gt_sketch_textwidth_0.recmaps000066400000000000000000000001241211610345200235240ustar00rootroot0000000000000030,90,215,106, gene
215,90,400,106, gene
400,90,585,106, gene
585,132,770,148, gene
genometools-1.5.1/testdata/gt_sketch_textwidth_1.recmaps000066400000000000000000000001231211610345200235240ustar00rootroot0000000000000030,90,90,106, gene
150,90,210,106, gene
90,132,150,148, gene
210,132,270,148, gene
genometools-1.5.1/testdata/gt_sketch_textwidth_2.recmaps000066400000000000000000000001271211610345200235310ustar00rootroot0000000000000030,102,215,118, gene
400,102,585,118, gene
215,154,400,170, gene
585,154,770,170, gene
genometools-1.5.1/testdata/gt_splicesiteinfo_prob_1.gff3000066400000000000000000000001711211610345200233770ustar00rootroot00000000000000##gff-version 3
##sequence-region seq 1 16
seq	.	gene	1	16	.	+	.	ID=gene
seq	.	exon	1	4	.	+	.	.
seq	.	exon	13	16	.	+	.	.
genometools-1.5.1/testdata/gt_splicesiteinfo_test_1.fas000066400000000000000000000000071211610345200233360ustar00rootroot00000000000000>
gtag
genometools-1.5.1/testdata/gt_splicesiteinfo_test_1.gff3000066400000000000000000000001031211610345200234070ustar00rootroot00000000000000##gff-version 3
##sequence-region seq 1 4
seq	.	intron	1	4	.	+	.	.
genometools-1.5.1/testdata/gt_splicesiteinfo_test_1.out000066400000000000000000000003061211610345200233760ustar00rootroot00000000000000splice site distribution (for introns >= 4bp)
gt-ag: 100.00% (n=1)

donor site distribution (for introns >= 4bp)
gt: 100.00% (n=1)

acceptor site distribution (for introns >= 4bp)
ag: 100.00% (n=1)
genometools-1.5.1/testdata/gt_splicesiteinfo_test_2.fas000066400000000000000000000000071211610345200233370ustar00rootroot00000000000000>
ctac
genometools-1.5.1/testdata/gt_splicesiteinfo_test_2.gff3000066400000000000000000000001031211610345200234100ustar00rootroot00000000000000##gff-version 3
##sequence-region seq 1 4
seq	.	intron	1	4	.	-	.	.
genometools-1.5.1/testdata/gt_splicesiteinfo_test_2.out000066400000000000000000000003061211610345200233770ustar00rootroot00000000000000splice site distribution (for introns >= 4bp)
gt-ag: 100.00% (n=1)

donor site distribution (for introns >= 4bp)
gt: 100.00% (n=1)

acceptor site distribution (for introns >= 4bp)
ag: 100.00% (n=1)
genometools-1.5.1/testdata/gt_splicesiteinfo_test_3.gff3000066400000000000000000000001031211610345200234110ustar00rootroot00000000000000##gff-version 3
##sequence-region seq 1 4
seq	.	intron	1	4	.	?	.	.
genometools-1.5.1/testdata/gt_splicesiteinfo_test_4.fas000066400000000000000000000000171211610345200233420ustar00rootroot00000000000000>
gtaggtaggcag
genometools-1.5.1/testdata/gt_splicesiteinfo_test_4.gff3000066400000000000000000000001671211610345200234240ustar00rootroot00000000000000##gff-version 3
##sequence-region seq 1 12
seq	.	intron	1	4	.	+	.	.
seq	.	intron	5	8	.	+	.	.
seq	.	intron	9	12	.	+	.	.
genometools-1.5.1/testdata/gt_splicesiteinfo_test_4.out000066400000000000000000000003551211610345200234050ustar00rootroot00000000000000splice site distribution (for introns >= 4bp)
gc-ag:  33.33% (n=1)
gt-ag:  66.67% (n=2)

donor site distribution (for introns >= 4bp)
gc:  33.33% (n=1)
gt:  66.67% (n=2)

acceptor site distribution (for introns >= 4bp)
ag: 100.00% (n=3)
genometools-1.5.1/testdata/gt_splicesiteinfo_test_5.fas000066400000000000000000000000231211610345200233400ustar00rootroot00000000000000>
nnnngtnnnnagnnnn
genometools-1.5.1/testdata/gt_splicesiteinfo_test_5.gff3000066400000000000000000000002151211610345200234170ustar00rootroot00000000000000##gff-version 3
##sequence-region seq 1 16
seq	.	gene	1	16	.	+	.	ID=gene
seq	.	exon	1	4	.	+	.	Parent=gene
seq	.	exon	13	16	.	+	.	Parent=gene
genometools-1.5.1/testdata/gt_splicesiteinfo_test_5.out000066400000000000000000000003061211610345200234020ustar00rootroot00000000000000splice site distribution (for introns >= 4bp)
gt-ag: 100.00% (n=1)

donor site distribution (for introns >= 4bp)
gt: 100.00% (n=1)

acceptor site distribution (for introns >= 4bp)
ag: 100.00% (n=1)
genometools-1.5.1/testdata/gt_splicesiteinfo_test_6.gff3000066400000000000000000000001031211610345200234140ustar00rootroot00000000000000##gff-version 3
##sequence-region seq 1 4
seq	.	intron	1	4	.	+	.	.
genometools-1.5.1/testdata/gt_splicesiteinfo_test_6.mapping000066400000000000000000000000341211610345200242250ustar00rootroot00000000000000mapping = {
  foo = "bar"
}
genometools-1.5.1/testdata/gt_stat_cdslengthdistri.out000066400000000000000000000003441211610345200233260ustar00rootroot00000000000000parsed genome node DAGs: 5
sequence regions: 1 (total length: 1497228)
multi-features: 1
genes: 1
protein-coding genes: 1
mRNAs: 1
protein-coding mRNAs: 1
CDSs: 4
CDS length distribution:
2305: 1 (prob=1.0000,cumulative=1.0000)
genometools-1.5.1/testdata/gt_stat_exonnumberdistri_encode.out000066400000000000000000000035541211610345200250600ustar00rootroot00000000000000parsed genome node DAGs: 3011
sequence regions: 20 (total length: 713365500)
genes: 2991
protein-coding genes: 1332
exons: 20154
CDSs: 10072
exon number distribution:
1: 70 (prob=0.0234,cumulative=0.0234)
2: 413 (prob=0.1381,cumulative=0.1615)
3: 462 (prob=0.1545,cumulative=0.3159)
4: 403 (prob=0.1347,cumulative=0.4507)
5: 365 (prob=0.1220,cumulative=0.5727)
6: 248 (prob=0.0829,cumulative=0.6556)
7: 188 (prob=0.0629,cumulative=0.7185)
8: 139 (prob=0.0465,cumulative=0.7650)
9: 116 (prob=0.0388,cumulative=0.8037)
10: 109 (prob=0.0364,cumulative=0.8402)
11: 71 (prob=0.0237,cumulative=0.8639)
12: 49 (prob=0.0164,cumulative=0.8803)
13: 65 (prob=0.0217,cumulative=0.9020)
14: 48 (prob=0.0160,cumulative=0.9181)
15: 34 (prob=0.0114,cumulative=0.9295)
16: 32 (prob=0.0107,cumulative=0.9402)
17: 29 (prob=0.0097,cumulative=0.9498)
18: 17 (prob=0.0057,cumulative=0.9555)
19: 9 (prob=0.0030,cumulative=0.9585)
20: 10 (prob=0.0033,cumulative=0.9619)
21: 12 (prob=0.0040,cumulative=0.9659)
22: 12 (prob=0.0040,cumulative=0.9699)
23: 11 (prob=0.0037,cumulative=0.9736)
24: 5 (prob=0.0017,cumulative=0.9753)
25: 5 (prob=0.0017,cumulative=0.9769)
26: 6 (prob=0.0020,cumulative=0.9789)
27: 10 (prob=0.0033,cumulative=0.9823)
28: 3 (prob=0.0010,cumulative=0.9833)
29: 6 (prob=0.0020,cumulative=0.9853)
30: 8 (prob=0.0027,cumulative=0.9880)
31: 3 (prob=0.0010,cumulative=0.9890)
32: 4 (prob=0.0013,cumulative=0.9903)
33: 4 (prob=0.0013,cumulative=0.9916)
34: 2 (prob=0.0007,cumulative=0.9923)
35: 3 (prob=0.0010,cumulative=0.9933)
37: 2 (prob=0.0007,cumulative=0.9940)
39: 1 (prob=0.0003,cumulative=0.9943)
40: 3 (prob=0.0010,cumulative=0.9953)
41: 5 (prob=0.0017,cumulative=0.9970)
42: 3 (prob=0.0010,cumulative=0.9980)
44: 1 (prob=0.0003,cumulative=0.9983)
45: 2 (prob=0.0007,cumulative=0.9990)
46: 1 (prob=0.0003,cumulative=0.9993)
48: 1 (prob=0.0003,cumulative=0.9997)
51: 1 (prob=0.0003,cumulative=1.0000)
genometools-1.5.1/testdata/gt_stat_exonnumberdistri_standard.out000066400000000000000000000003071211610345200254140ustar00rootroot00000000000000parsed genome node DAGs: 2
sequence regions: 1 (total length: 1497228)
genes: 1
mRNAs: 3
exons: 11
exon number distribution:
3: 1 (prob=0.3333,cumulative=0.3333)
4: 2 (prob=0.6667,cumulative=1.0000)
genometools-1.5.1/testdata/gt_stat_source.out000066400000000000000000000001671211610345200214370ustar00rootroot00000000000000parsed genome node DAGs: 2
sequence regions: 1 (total length: 1497228)
genes: 1
mRNAs: 3
exons: 11
used source tags:
.
genometools-1.5.1/testdata/gt_stat_test_1.out000066400000000000000000000001431211610345200213300ustar00rootroot00000000000000parsed genome node DAGs: 2
sequence regions: 1 (total length: 1497228)
genes: 1
mRNAs: 3
exons: 11
genometools-1.5.1/testdata/gt_stat_test_2.out000066400000000000000000000002451211610345200213340ustar00rootroot00000000000000parsed genome node DAGs: 2
sequence regions: 1 (total length: 1497228)
genes: 1
mRNAs: 3
exons: 11
gene length distribution:
8001: 1 (prob=1.0000,cumulative=1.0000)
genometools-1.5.1/testdata/gt_stat_test_3.out000066400000000000000000000005011211610345200213300ustar00rootroot00000000000000parsed genome node DAGs: 2
sequence regions: 1 (total length: 1497228)
genes: 1
mRNAs: 3
exons: 11
exon length distribution:
201: 1 (prob=0.0909,cumulative=0.0909)
451: 2 (prob=0.1818,cumulative=0.2727)
501: 3 (prob=0.2727,cumulative=0.5455)
903: 2 (prob=0.1818,cumulative=0.7273)
2001: 3 (prob=0.2727,cumulative=1.0000)
genometools-1.5.1/testdata/gt_stat_test_4.out000066400000000000000000000003671211610345200213430ustar00rootroot00000000000000parsed genome node DAGs: 2
sequence regions: 1 (total length: 1497228)
genes: 1
mRNAs: 3
exons: 11
intron length distribution:
1097: 2 (prob=0.2500,cumulative=0.2500)
1499: 5 (prob=0.6250,cumulative=0.8750)
3499: 1 (prob=0.1250,cumulative=1.0000)
genometools-1.5.1/testdata/gt_stat_test_5.out000066400000000000000000000002421211610345200213340ustar00rootroot00000000000000parsed genome node DAGs: 2
sequence regions: 1 (total length: 1497228)
genes: 1
mRNAs: 3
exons: 11
gene score distribution:
50: 1 (prob=1.0000,cumulative=1.0000)
genometools-1.5.1/testdata/gt_stat_test_6.out000066400000000000000000000001431211610345200213350ustar00rootroot00000000000000parsed genome node DAGs: 61
sequence regions: 16 (total length: 12069317)
LTR_retrotransposons: 45
genometools-1.5.1/testdata/gt_translate.in000066400000000000000000000000131211610345200206660ustar00rootroot00000000000000gattacatag
genometools-1.5.1/testdata/gt_translate.out000066400000000000000000000000431211610345200210720ustar00rootroot00000000000000frame1: DYI
frame2: IT*
frame3: LH
genometools-1.5.1/testdata/gt_uniq_test_1.gff3000066400000000000000000000001451211610345200213510ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	.	+	.	.
seq	.	gene	1	1000	.	+	.	.
genometools-1.5.1/testdata/gt_uniq_test_1.out000066400000000000000000000001131211610345200213260ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	.	+	.	.
genometools-1.5.1/testdata/gt_uniq_test_2.gff3000066400000000000000000000001451211610345200213520ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	.	+	.	.
seq	.	gene	1	1000	.	-	.	.
genometools-1.5.1/testdata/gt_uniq_test_2.out000066400000000000000000000001451211610345200213340ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	.	+	.	.
seq	.	gene	1	1000	.	-	.	.
genometools-1.5.1/testdata/gt_uniq_test_3.gff3000066400000000000000000000001511211610345200213500ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	1.0	+	.	.
seq	.	gene	1	1000	0.5	+	.	.
genometools-1.5.1/testdata/gt_uniq_test_3.out000066400000000000000000000001131211610345200213300ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	1	+	.	.
genometools-1.5.1/testdata/gt_uniq_test_4.gff3000066400000000000000000000001511211610345200213510ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	0.5	+	.	.
seq	.	gene	1	1000	1.0	+	.	.
genometools-1.5.1/testdata/gt_uniq_test_4.out000066400000000000000000000001131211610345200213310ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	1	+	.	.
genometools-1.5.1/testdata/gt_uniq_test_5.gff3000066400000000000000000000002051211610345200213520ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	0.5	+	.	.
seq	.	gene	1	1000	1.0	+	.	.
seq	.	gene	1	1000	0.4	+	.	.
genometools-1.5.1/testdata/gt_uniq_test_5.out000066400000000000000000000001131211610345200213320ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	1	+	.	.
genometools-1.5.1/testdata/gt_uniq_test_6.gff3000066400000000000000000000027551211610345200213670ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.500000	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
ctg123	.	gene	1000	9000	0.500000	+	.	ID=gene2
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene2
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA4;Parent=gene2
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA4
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA4
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA4
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA4
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA5;Parent=gene2
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA5
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA5
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA5
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA6;Parent=gene2
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA6
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA6
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA6
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA6
###
genometools-1.5.1/testdata/gt_uniq_test_6.out000066400000000000000000000014171211610345200213430ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/gt_view.sh000066400000000000000000000013311211610345200176530ustar00rootroot00000000000000#!/bin/sh -ex

gt view -force png_devel_1.png png_devel_1.gff3
gt view -force png_devel_2.png png_devel_2.gff3
gt view -force png_devel_3.png png_devel_3.gff3
gt view -force png_devel_4.png png_devel_4.gff3
gt view -force png_devel_5.png png_devel_5.gff3
gt view -force png_devel_6.png png_devel_6.gff3
gt view -force png_devel_7.png png_devel_7.gff3
gt view -start 190000 -end 199000 -force png_devel_8.png png_devel_8.gff3
gt view -start 190000 -end 199000 -force png_devel_9.png png_devel_9.gff3
gt view -start 190000 -end 199000 -force png_devel_10.png png_devel_10.gff3
gt view -start 190000 -end 199000 -force png_devel_11.png png_devel_11.gff3
gt view -start 5867900 -end 5872900 -force png_devel_12.png png_devel_12.gff3
genometools-1.5.1/testdata/gt_view_prob_1.gff3000066400000000000000000000000201211610345200213220ustar00rootroot00000000000000##gff-version 3
genometools-1.5.1/testdata/gt_view_prob_2.gff3000066400000000000000000000000671211610345200213360ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
genometools-1.5.1/testdata/gtpython/000077500000000000000000000000001211610345200175315ustar00rootroot00000000000000genometools-1.5.1/testdata/gtpython/block_stuff.py000066400000000000000000000041071211610345200224060ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re


class TestFailedError(Exception):

    pass


def testfunc(bl):
    b = Block(bl)
    print "%s %s %s %d" % (b.get_type(), b.get_strand(), b.get_range(),
                           b.get_size())
    if not b.get_top_level_feature():
        raise TestFailedError
    return b.get_type()


if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_file\n")
        sys.stderr.write("Test the TrackSelector callback and Block bindings.")
        sys.exit(1)

    genome_stream = GFF3InStream((sys.argv)[1])

  # instantiate index object

    feature_index = FeatureIndexMemory()
    genome_stream = FeatureStream(genome_stream, feature_index)

    feature = genome_stream.next_tree()
    while feature:
        feature = genome_stream.next_tree()

    seqid = feature_index.get_first_seqid()
    range = feature_index.get_range_for_seqid(seqid)

    style = Style()
    diagram = Diagram.from_index(feature_index, seqid, range, style)
    diagram.set_track_selector_func(testfunc)

    layout = Layout(diagram, 800, style)
    height = layout.get_height()

genometools-1.5.1/testdata/gtpython/feature_node.py000066400000000000000000000054731211610345200225540ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re


class TestFailedError(Exception):

    pass


if __name__ == "__main__":
    fn = FeatureNode.create_new("test", "type", 100, 500, "+")
    fn.add_attribute("test", "testval")
    fn.add_attribute("test2", "testval2")
    if fn.score_is_defined():
        raise TestFailedError
    fn.set_score(2)
    if not fn.score_is_defined():
        raise TestFailedError
    if fn.get_score() != 2:
        raise TestFailedError
    fn.unset_score()
    if fn.score_is_defined():
        raise TestFailedError
    if fn.has_type("foo"):
        raise TestFailedError
    if not fn.has_type("type"):
        raise TestFailedError
    if not fn.get_type() == "type":
        raise TestFailedError
    fn.set_type("foo")
    if not fn.has_type("foo"):
        raise TestFailedError
    if not fn.get_type() == "foo":
        raise TestFailedError
    if not fn.get_strand() == "+":
        raise TestFailedError
    fn2 = FeatureNode.create_new("test", "type2", 200, 300, "+")
    fn.add_child(fn2)
    num_attrs = 0
    for (tag, val) in fn.each_attribute():
        if not val == fn.get_attribute(tag):
            raise TestFailedError
        num_attrs += 1
    if not num_attrs == 2:
        raise TestFailedError
    if fn.get_phase() != 3:  #undefined
        raise TestFailedError
    fn.set_phase(0)
    if fn.get_phase() != 0:  #zero
        raise TestFailedError

    fni = FeatureNodeIteratorDepthFirst(fn)
    num_features = 0
    tfn = fni.next()
    while tfn:
        num_features += 1
        tfn = fni.next()
    if num_features != 2:
        raise TestFailedError

    fn3 = FeatureNode.create_new("test", "type3", 250, 300, "+")
    fn.add_child(fn3)
    fni = FeatureNodeIteratorDepthFirst(fn)
    num_features = 0
    tfn = fni.next()
    while tfn:
        num_features += 1
        tfn = fni.next()
    if num_features != 3:
        raise TestFailedError
genometools-1.5.1/testdata/gtpython/feature_stuff.py000066400000000000000000000044031211610345200227460ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re


class TestFailedError(Exception):

    pass


if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_file\n")
        sys.stderr.write('Test the FeatureIndex and FeatureStream bindings on GFF3_file.')
        sys.exit(1)

    genome_stream = GFF3InStream((sys.argv)[1])

  # try to instantiate an interface -> should fail

    try:
        feature_index = FeatureIndex()
    except NotImplementedError:
        pass
    else:
        raise

  # instantiate index object

    feature_index = FeatureIndexMemory()
    genome_stream = FeatureStream(genome_stream, feature_index)

    feature = genome_stream.next_tree()
    while feature:
        feature = genome_stream.next_tree()

    seqid = feature_index.get_first_seqid()
    features = feature_index.get_features_for_seqid(seqid)
    if not features:
        raise TestFailedError

    rng = feature_index.get_range_for_seqid(seqid)
    features_r = feature_index.get_features_for_range(rng.start, rng.end,
            seqid)

    if not len(features) == len(features_r):
        raise TestFailedError

    gff3_visitor = GFF3Visitor()

    for feature in features:
        feature.accept(gff3_visitor)
        if not isinstance(feature, FeatureNode):
            raise TestFailedError
genometools-1.5.1/testdata/gtpython/feature_stuff_db.py000066400000000000000000000041051211610345200234120ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008-2012 Sascha Steinbiss 
# Copyright (c) 2008-2012 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re


class TestFailedError(Exception):

    pass


if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_db\n")
        sys.stderr.write('Test the FeatureIndex bindings on GFF3_db.\n')
        sys.exit(1)

  # try to instantiate an interface -> should fail

    try:
        feature_index = FeatureIndex()
    except NotImplementedError:
        pass
    else:
        raise

    rdb = RDBSqlite(sys.argv[1])
    adbs = AnnoDBGFFLike()

    feature_index = adbs.get_feature_index(rdb)
    seqid = feature_index.get_first_seqid()
    features = feature_index.get_features_for_seqid(seqid)
    if not features:
        raise TestFailedError

    rng = feature_index.get_range_for_seqid(seqid)
    features_r = feature_index.get_features_for_range(rng.start, rng.end,
            seqid)

    if not len(features) == len(features_r):
        raise TestFailedError

    gff3_visitor = GFF3Visitor()

    for feature in features:
        feature.accept(gff3_visitor)
        if not isinstance(feature, FeatureNode):
            raise TestFailedError
genometools-1.5.1/testdata/gtpython/genome_visitor.py000066400000000000000000000026361211610345200231430ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re

if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_file\n")
        sys.stderr.write("Parse and output the given GFF3 file.")
        sys.exit(1)

    genome_stream = GFF3InStream((sys.argv)[1])
    gff3_visitor = GFF3Visitor()
    feature = genome_stream.next_tree()
    while feature:
        feature.accept(gff3_visitor)
        feature = genome_stream.next_tree()
genometools-1.5.1/testdata/gtpython/gff3.py000066400000000000000000000025701211610345200207340ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re

if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_file\n")
        sys.stderr.write("Parse and output the given GFF3 file.")
        sys.exit(1)

    in_stream = GFF3InStream((sys.argv)[1])
    out_stream = GFF3OutStream(in_stream)
    feature = out_stream.next_tree()
    while feature:
        feature = out_stream.next_tree()
genometools-1.5.1/testdata/gtpython/graphics_stuff.py000066400000000000000000000073631211610345200231230ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys


class TestFailedError(Exception):

    pass


if __name__ == "__main__":
    if len(sys.argv) != 3:
        sys.stderr.write("Usage: " + (sys.argv)[0] +
                         " curve_coords PNG_file\n")
        sys.stderr.write("Tests drawing functions in the Graphics object.\n")
        sys.exit(1)
    g = GraphicsCairoSVG(700, 800)

    g.draw_text(300, 20, "draw_text")
    g.draw_text_right(300, 40, "draw_text_left")
    g.draw_text_centered(300, 60, "draw_text_centered")
    g.draw_colored_text(300, 80, Color(1, 0, 0, 0.7),
                        "draw_colored_text")
    g.set_margins(20, 30)
    if g.get_image_height() != 800:
        raise TestFailedError
    if g.get_image_width() != 700:
        raise TestFailedError
    if g.get_xmargins() != 20:
        raise TestFailedError
    if g.get_ymargins() != 30:
        raise TestFailedError

    g.draw_horizontal_line(150, 100, Color(0, 0, 0, 0.3), 300, 5.5)
    g.draw_vertical_line(200, 70, Color(1, 0, 0, 0.3), 100, 3.5)
    g.draw_box(
        150,
        120,
        300,
        30,
        Color(0, 1, 0, 0.2),
        ARROW_LEFT,
        20,
        2,
        Color(0, 0, 0, 1),
        False,
        )
    g.draw_box(
        150,
        170,
        300,
        20,
        Color(0, 1, 1, 0.2),
        ARROW_RIGHT,
        20,
        1,
        Color(0, 0, 0, 1),
        False,
        )
    g.draw_box(
        150,
        210,
        300,
        20,
        Color(1, 0, 0, 0.2),
        ARROW_BOTH,
        20,
        1,
        Color(0, 0, 0, 1),
        False,
        )
    g.draw_box(
        300,
        250,
        20,
        20,
        Color(1, 0, 0, 0.2),
        ARROW_BOTH,
        20,
        1,
        Color(0, 0, 0, 1),
        False,
        )
    g.draw_box(
        150,
        290,
        300,
        20,
        Color(1, 0, 0, 0.2),
        ARROW_NONE,
        20,
        1,
        Color(0, 0, 0, 1),
        False,
        )
    g.draw_dashes(159, 340, 90, 20, ARROW_RIGHT, 20, 1, Color(0, 0, 0, 1))
    g.draw_dashes(359, 340, 60, 20, ARROW_LEFT, 20, 1, Color(0, 0, 0, 1))
    g.draw_dashes(59, 340, 60, 20, ARROW_NONE, 20, 1, Color(0, 0, 0, 1))
    g.draw_dashes(559, 340, 60, 20, ARROW_BOTH, 20, 1, Color(0, 0, 0, 1))
    g.draw_caret(159, 390, 90, 20, ARROW_RIGHT, 20, 1, Color(0, 0, 0, 1))
    g.draw_caret(359, 390, 60, 20, ARROW_LEFT, 20, 1, Color(0, 0, 0, 1))
    g.draw_caret(59, 390, 60, 20, ARROW_NONE, 20, 1, Color(0, 0, 0, 1))
    g.draw_caret(559, 390, 60, 20, ARROW_BOTH, 20, 1, Color(0, 0, 0, 1))

    from random import random
    data = []
    ndata = 0
    f = open((sys.argv)[1])
    for line in f:
        data.append(float(line))
        ndata += 1
    g.draw_curve_data(20, 430, Color(0, 0, 1, .6), data, ndata, Range(0,
                      1), 40)

    g.to_file((sys.argv)[2])
genometools-1.5.1/testdata/gtpython/show_recmaps.py000066400000000000000000000040041211610345200225730ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re

if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_file\n")
        sys.stderr.write("Show RecMaps of GFF3 annotation file.")
        sys.exit(1)

    in_stream = GFF3InStream((sys.argv)[1])
    feature_index = FeatureIndexMemory()
    feature_stream = FeatureStream(in_stream, feature_index)
    gn = feature_stream.next_tree()

  # fill feature index

    while gn:
        gn = feature_stream.next_tree()

    seqid = feature_index.get_first_seqid()
    range = feature_index.get_range_for_seqid(seqid)

    style = Style()
    diagram = Diagram.from_index(feature_index, seqid, range, style)
    layout = Layout(diagram, 700, style)
    height = layout.get_height()
    image_info = ImageInfo()
    canvas = CanvasCairoFile(style, 800, height, image_info)
    layout.sketch(canvas)
    canvas.to_file("foo1.png")

    for (x1, y1, x2, y2, gn) in image_info.each_hotspot():
        print "x1=%d, y1=%d, x2=%d, y2=%d, gn.type=%s" % (x1, y1, x2, y2,
                gn.get_type())
genometools-1.5.1/testdata/gtpython/show_seqids.py000066400000000000000000000030531211610345200224340ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re

if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_file\n")
        sys.stderr.write("Show sequence ids contained in GFF3 annotation file.")
        sys.exit(1)

    in_stream = GFF3InStream((sys.argv)[1])
    feature_index = FeatureIndexMemory()
    feature_stream = FeatureStream(in_stream, feature_index)
    gn = feature_stream.next_tree()

  # fill feature index

    while gn:
        gn = feature_stream.next_tree()

    seqids = feature_index.get_seqids()
    for seqid in seqids:
        print seqid
genometools-1.5.1/testdata/gtpython/sketch-failures.py000066400000000000000000000064511211610345200232020ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from ctypes import ArgumentError
from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re


class TestFailedError(Exception):

    pass


if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_file\n")
        sys.stderr.write("Test failures in GFF3 annotation file.")
        sys.exit(1)

    feature_index = FeatureIndexMemory()
    feature_index.add_gff3file((sys.argv)[1])

    seqid = feature_index.get_first_seqid()
    range = feature_index.get_range_for_seqid(seqid)

    style = Style()
    style.set_num("format", "margins", 40)

  # check error reporting in the Diagram class

    try:
        diagram = Diagram.from_index(feature_index, "nonexist", range,
                style)
    except GTError, strerr:
        if -1 == str(strerr).find("feature index does not contain "):
            raise TestFailedError
    else:
        raise TestFailedError
    try:
        diagram = Diagram.from_index(feature_index, seqid, range, 42)
    except ArgumentError, strerr:
        if -1 == str(strerr).find("must be a Style"):
            raise TestFailedError
    else:
        raise TestFailedError
    try:
        diagram = Diagram.from_index(feature_index, seqid, 42, style)
    except AttributeError, strerr:
        if -1 == str(strerr).find("object has no attribute 'start'"):
            raise TestFailedError
    else:
        raise TestFailedError
    try:
        diagram = Diagram.from_index(42, seqid, range, style)
    except ArgumentError, strerr:
        if -1 == str(strerr).find("must be a FeatureIndex"):
            raise TestFailedError
    else:
        raise TestFailedError
    diagram = Diagram.from_index(feature_index, seqid, range, style)

  # check error reporting in the Layout class

    try:
        layout = Layout(diagram, 70, style)
    except GTError, strerr:
        if -1 == str(strerr).find("layout width must at least be twice"):
            raise TestFailedError
    else:
        raise TestFailedError
    layout = Layout(diagram, 700, style)
    height = layout.get_height()

  # check error reporting in the CanvasCairoFile class

    try:
        canvas = CanvasCairoFile(12, 700, height, None)
    except ArgumentError, strerr:
        if -1 == str(strerr).find("must be a Style"):
            raise TestFailedError
    else:
        raise TestFailedError
    canvas = CanvasCairoFile(style, 700, height, None)
genometools-1.5.1/testdata/gtpython/sketch.py000066400000000000000000000036271211610345200213740ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re

if __name__ == "__main__":
    if len(sys.argv) != 3:
        sys.stderr.write("Usage: " + (sys.argv)[0] +
                         " PNG_file GFF3_file\n")
        sys.stderr.write("Create PNG representation of GFF3 annotation file.")
        sys.exit(1)

    pngfile = (sys.argv)[1]
    in_stream = GFF3InStream((sys.argv)[2])
    feature_index = FeatureIndexMemory()
    feature_stream = FeatureStream(in_stream, feature_index)
    gn = feature_stream.next_tree()

  # fill feature index

    while gn:
        gn = feature_stream.next_tree()

    seqid = feature_index.get_first_seqid()
    range = feature_index.get_range_for_seqid(seqid)

    style = Style()
    diagram = Diagram.from_index(feature_index, seqid, range, style)
    layout = Layout(diagram, 700, style)
    height = layout.get_height()
    ii = ImageInfo()
    canvas = CanvasCairoFile(style, 700, height, ii)
    layout.sketch(canvas)
    canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtpython/sketch_parsed_with_invalid_ordering.py000066400000000000000000000023351211610345200273570ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-

from gt.annotationsketch import *
from gt.core.gtrange import Range
import sys

if __name__ == "__main__":
    if len(sys.argv) != 4:
        sys.stderr.write("Usage: " + (sys.argv)[0] +
                         " Style_file PNG_file GFF3_file\n")
        sys.stderr.write("Create PNG representation of GFF3 annotation file.")
        sys.exit(1)

    pngfile = (sys.argv)[2]

  # load style file

    style = Style()
    style.load_file((sys.argv)[1])

  # create feature index

    feature_index = FeatureIndexMemory()

  # add GFF3 file to index

    feature_index.add_gff3file((sys.argv)[3])

  # create diagram for first sequence ID in feature index

    seqid = feature_index.get_first_seqid()
    range = feature_index.get_range_for_seqid(seqid)
    diagram = Diagram.from_index(feature_index, seqid, range, style)

  # create layout

    layout = Layout(diagram, 600, style)
    height = layout.get_height()

  # set alternative ordering function

    layout.set_track_ordering_func(lambda s1, s2: "not_a_number")

  # create canvas

    canvas = CanvasCairoFile(style, 600, height)

  # sketch layout on canvas

    layout.sketch(canvas)

  # write canvas to file

    canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtpython/sketch_parsed_with_invalid_ordering_2.py000066400000000000000000000023231211610345200275750ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-

from gt.annotationsketch import *
from gt.core.gtrange import Range
import sys

if __name__ == "__main__":
    if len(sys.argv) != 4:
        sys.stderr.write("Usage: " + (sys.argv)[0] +
                         " Style_file PNG_file GFF3_file\n")
        sys.stderr.write("Create PNG representation of GFF3 annotation file.")
        sys.exit(1)

    pngfile = (sys.argv)[2]

  # load style file

    style = Style()
    style.load_file((sys.argv)[1])

  # create feature index

    feature_index = FeatureIndexMemory()

  # add GFF3 file to index

    feature_index.add_gff3file((sys.argv)[3])

  # create diagram for first sequence ID in feature index

    seqid = feature_index.get_first_seqid()
    range = feature_index.get_range_for_seqid(seqid)
    diagram = Diagram.from_index(feature_index, seqid, range, style)

  # create layout

    layout = Layout(diagram, 600, style)
    height = layout.get_height()

  # set alternative ordering function

    layout.set_track_ordering_func(lambda s1, s2: None)

  # create canvas

    canvas = CanvasCairoFile(style, 600, height)

  # sketch layout on canvas

    layout.sketch(canvas)

  # write canvas to file

    canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtpython/sketch_parsed_with_ordering.py000066400000000000000000000023341211610345200256500ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-

from gt.annotationsketch import *
from gt.core.gtrange import Range
import sys

if __name__ == "__main__":
    if len(sys.argv) != 4:
        sys.stderr.write("Usage: " + (sys.argv)[0] +
                         " Style_file PNG_file GFF3_file\n")
        sys.stderr.write("Create PNG representation of GFF3 annotation file.")
        sys.exit(1)

    pngfile = (sys.argv)[2]

  # load style file

    style = Style()
    style.load_file((sys.argv)[1])

  # create feature index

    feature_index = FeatureIndexMemory()

  # add GFF3 file to index

    feature_index.add_gff3file((sys.argv)[3])

  # create diagram for first sequence ID in feature index

    seqid = feature_index.get_first_seqid()
    range = feature_index.get_range_for_seqid(seqid)
    diagram = Diagram.from_index(feature_index, seqid, range, style)

  # create layout

    layout = Layout(diagram, 600, style)
    height = layout.get_height()

  # set alternative ordering function

    layout.set_track_ordering_func(lambda s1, s2: cmp(s1,s2)*-1)

  # create canvas

    canvas = CanvasCairoFile(style, 600, height)

  # sketch layout on canvas

    layout.sketch(canvas)

  # write canvas to file

    canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtpython/sketch_simple.py000066400000000000000000000033501211610345200227360ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re

if __name__ == "__main__":
    if len(sys.argv) != 3:
        sys.stderr.write("Usage: " + (sys.argv)[0] +
                         " PNG_file GFF3_file\n")
        sys.stderr.write("Create PNG representation of GFF3 annotation file.")
        sys.exit(1)

    pngfile = (sys.argv)[1]
    gff3file = (sys.argv)[2]
    feature_index = FeatureIndexMemory()
    feature_index.add_gff3file(gff3file)

    seqid = feature_index.get_first_seqid()
    range = feature_index.get_range_for_seqid(seqid)

    style = Style()
    diagram = Diagram.from_index(feature_index, seqid, range, style)
    layout = Layout(diagram, 700, style)
    height = layout.get_height()
    canvas = CanvasCairoFile(style, 700, height)
    layout.sketch(canvas)
    canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtpython/sketch_stream.py000066400000000000000000000040761211610345200227460ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re

if __name__ == "__main__":
    if len(sys.argv) != 3:
        sys.stderr.write("Usage: " + (sys.argv)[0] +
                         " PNG_file GFF3_file\n")
        sys.stderr.write("Create PNG representation of GFF3 annotation file (adds introns).")
        sys.exit(1)

    pngfile = (sys.argv)[1]
    in_stream = GFF3InStream((sys.argv)[2])
    add_introns_stream = AddIntronsStream(in_stream)
    feature_index = FeatureIndexMemory()
    feature_stream = FeatureStream(add_introns_stream, feature_index)
    gn = feature_stream.next_tree()

  # fill feature index

    while gn:
        gn = feature_stream.next_tree()

    seqid = feature_index.get_first_seqid()
    range = feature_index.get_range_for_seqid(seqid)

    style = Style()
    diagram = Diagram.from_index(feature_index, seqid, range, style)
    layout = Layout(diagram, 700, style)
    height = layout.get_height()
    ii = ImageInfo()
    canvas = CanvasCairoFile(style, 700, height, ii)
    layout.sketch(canvas)

    pngstream = canvas.to_stream()
    outfile = open(pngfile, "w")
    outfile.write(pngstream)
    outfile.close()
genometools-1.5.1/testdata/gtpython/style.py000066400000000000000000000122721211610345200212470ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys


class TestFailedException(Exception):

    pass


if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " style_file")
        sys.stderr.write("Load style_file and test style bindings.")
        sys.exit(1)

    stylefile = (sys.argv)[1]

  # create new style object

    style = Style()

  # load style file

    style.load_file(stylefile)

  # clone style file

    clone = style.clone()
    if not clone:
        raise TestFailedException

  # get color

    color = style.get_color("exon", "fill")
    if not color:
        raise TestFailedException

  # set color

    color = Color(0.3, 0.4, 0.3)
    style.set_color("exon", "fill", color)
    color2 = style.get_color("exon", "fill")
    if color2.red != color.red and color2.green != color.green and \
        color2.blue != color.blue:
        raise TestFailedException

  # unset color

    style.unset("exon", "fill")
    color2 = style.get_color("exon", "fill")
    if color2:
        raise TestFailedException

  # get undefined color

    color = style.get_color("undefined", "undefined")
    if color:
        raise TestFailedException

  # get string

    string = style.get_cstr("exon", "style")
    if string != "box":
        raise TestFailedException

  # set string

    style.set_cstr("exon", "style", "line")
    string = style.get_cstr("exon", "style")
    if string != "line":
        raise TestFailedException

  # unset string

    style.unset("exon", "style")
    string = style.get_cstr("exon", "style")
    if string:
        raise TestFailedException

  # get undefined string

    string = style.get_cstr("undefined", "undefined")
    if string:
        raise TestFailedException

  # get number

    num = style.get_num("format", "margins")
    if num != 30:
        raise TestFailedException

  # set number

    style.set_num("format", "margins", 20)
    num = style.get_num("format", "margins")
    if num != 20:
        raise TestFailedException

  # unset number

    style.unset("format", "margins")
    None
    num = style.get_num("format", "margins")
    if num:
        raise TestFailedException

  #get undefined number

    num = style.get_num("undefined", "undefined")
    if num:
        raise TestFailedException

  # get boolean

    bool = style.get_bool("format", "show_grid")
    if bool == False:
        raise TestFailedException

  # get undefined boolean

    bool = style.get_bool("undefined", "undefined")
    if not bool == None:
        raise TestFailedException

  # set boolean

    style.set_bool("format", "show_grid", False)
    bool = style.get_bool("format", "show_grid")
    if bool:
        raise TestFailedException

  # unset boolean

    style.unset("format", "show_grid")
    bool = style.get_bool("format", "show_grid")
    if not bool == None:
        raise TestFailedException

  # serialise style to Lua code

    style.set_num("format", "margins", 20)
    style.set_bool("format", "show_grid", True)
    color = Color(0.3, 0.4, 0.3)
    style.set_color("exon", "fill", color)
    luacode = style.to_str()
    if luacode == None or len(luacode) == 0:
        raise TestFailedException

  # load style from Lua code

    style.load_str(luacode)
    num = style.get_num("format", "margins")
    if num != 20:
        raise TestFailedException
    bool = style.get_bool("format", "show_grid")
    if not bool:
        raise TestFailedException
    color2 = style.get_color("exon", "fill")
    if color2.red != color.red and color2.green != color.green and \
        color2.blue != color.blue:
        raise TestFailedException

  # clone style from existing copy

    style2 = style.clone()
    num = style2.get_num("format", "margins")
    if num != 20:
        raise TestFailedException
    bool = style2.get_bool("format", "show_grid")
    if not bool:
        raise TestFailedException
    color2 = style2.get_color("exon", "fill")
    if color2.red != color.red and color2.green != color.green and \
        color2.blue != color.blue:
        raise TestFailedException
    style2.set_num("format", "margins", 30)
    if style2.get_num("format", "margins") != 30:
        raise TestFailedException
    if style.get_num("format", "margins") == style2.get_num("format",
            "margins"):
        raise TestFailedException
genometools-1.5.1/testdata/gtpython/style_serialize.py000066400000000000000000000026461211610345200233220ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2010 Sascha Steinbiss 
# Copyright (c) 2010 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys


class TestFailedException(Exception):

    pass


if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " style_file")
        sys.stderr.write("Load style_file and test style bindings.")
        sys.exit(1)

    stylefile = (sys.argv)[1]

  # create new style object

    style = Style()

  # load style file

    style.load_file(stylefile)

  # serialise style to Lua code

    style.to_str()
genometools-1.5.1/testdata/gtpython/unicode_strings.py000066400000000000000000000044631211610345200233110ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
from gt.annotationsketch.custom_track import CustomTrack
from gt.core.gtrange import Range
import sys


class GeneRegion(object):
    """Represents a gene region"""

    def __init__(self, start, end):
        self.start = start
        self.end = end

class BetterGeneRegion(GeneRegion):
    """Has even more info and inherits from GeneRegion"""
    def __init__(self, start, end, chromosome, strand):
        GeneRegion.__init__(self, start, end)
        self.chromosome = chromosome
        self.strand = strand

if __name__ == "__main__":
    if len(sys.argv) != 3:
        sys.stderr.write("Usage: " + (sys.argv)[0] +
                         " style_file PNG_file\n")
        sys.exit(1)

    nodes = []

    # construct a gene on the forward strand with two exons
    G = BetterGeneRegion(113558120L, 113578742L, 'chr7', '+')
    seqid = G.chromosome


    gene = FeatureNode.create_new(unicode(seqid),
                                  "gene",
                                   #100,
                                   #900,
                                   G.start,
                                   G.end,
                                   "+")
    gene.add_attribute("Name", u"Testcase™ あがぃいぅ".encode("utf-8"))

    nodes.append(gene)

    exon = FeatureNode.create_new(seqid, "exon", 100, 200, "+")
    gene.add_child(exon)
    intron = FeatureNode.create_new(seqid, "intron", 201, 799, "+")
    gene.add_child(intron)
    exon = FeatureNode.create_new(seqid, "exon", 800, 900, "+")
    gene.add_child(exon)

  # construct a single-exon gene on the reverse strand
  # (within the intron of the forward strand gene)

    reverse_gene = FeatureNode.create_new(seqid, "gene", 400, 600, "-")
    reverse_exon = FeatureNode.create_new(seqid, "exon", 400, 600, "-")
    reverse_gene.add_child(reverse_exon)

    nodes.append(reverse_gene)

    pngfile = (sys.argv)[2]

    style = Style()
    style.load_file((sys.argv)[1])

    diagram = Diagram.from_array(nodes, Range(G.start, G.end),
                                 style)

    layout = Layout(diagram, 600, style)
    height = layout.get_height()
    canvas = CanvasCairoFile(style, 600, height)
    layout.sketch(canvas)

    canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtpython/used_types.py000066400000000000000000000026361211610345200222760ustar00rootroot00000000000000#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

from gt.core import *
from gt.extended import *
from gt.annotationsketch import *
import sys
import re

if __name__ == "__main__":
    if len(sys.argv) != 2:
        sys.stderr.write("Usage: " + (sys.argv)[0] + " GFF3_file\n")
        sys.stderr.write("Parse and output the types used in GFF3_file.")
        sys.exit(1)

    in_stream = GFF3InStream((sys.argv)[1])
    gn = in_stream.next_tree()

  # fill feature index

    while gn:
        gn = in_stream.next_tree()

    for type in in_stream.get_used_types():
        print type
genometools-1.5.1/testdata/gtruby/000077500000000000000000000000001211610345200171715ustar00rootroot00000000000000genometools-1.5.1/testdata/gtruby/block_stuff.rb000066400000000000000000000035501211610345200220220ustar00rootroot00000000000000#
# Copyright (c) 2007 Gordon Gremme 
# Copyright (c) 2007 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for FeatureIndex and FeatureStream classes

require 'gtruby'

testcallback = Proc.new { |block, data|
  r = block.get_range
  puts "#{block.get_type} #{block.get_strand} (#{r.begin}L, #{r.end}L) " + \
       "#{block.get_size}"
  block.get_type
}

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} GFF3_file"
  STDERR.puts "Test the FeatureIndex and FeatureStream bindings on GFF3 file."
  exit(1)
end

gff3file = ARGV[0]

# set up the feature stream
genome_stream = GT::GFF3InStream.new(gff3file)

# instantiate index object
feature_index = GT::FeatureIndexMemory.new()
genome_stream = GT::FeatureStream.new(genome_stream, feature_index)

feature = genome_stream.next_tree()
while (feature) do
  feature = genome_stream.next_tree()
end

seqid = feature_index.get_first_seqid()
range = feature_index.get_range_for_seqid(seqid)

style = GT::Style.new()
diagram = GT::Diagram.from_index(feature_index, seqid, range, style)
diagram.set_track_selector_func(testcallback)
layout = GT::Layout.new(diagram, 700, style)
genometools-1.5.1/testdata/gtruby/custom_stuff.rb000066400000000000000000000050321211610345200222370ustar00rootroot00000000000000#
# Copyright (c) 2009 Sascha Steinbiss 
# Copyright (c) 2009 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} GFF3_file"
  STDERR.puts "Test the custom stream bindings on GFF3 file."
  exit(1)
end

module GT
  class PrinterStream < CustomStream
    def initialize(instream, types)
      super()
      @types = types
      @instream = instream
      @visitor = PrinterVisitor.new(@types)
    end

    def next
      node = @instream.next_tree
      node.accept(@visitor) if node
      node
    end
  end

  class PrinterVisitor < CustomVisitor
    def initialize(types)
      super()
      @types = types
    end

    def visit_feature_node(fn)
      fn.traverse_dfs do |node|
        @types.push(node.get_type)
        @types.uniq!
        rng = node.get_range
        puts "#{node.get_source} #{node.get_type} #{rng.begin} #{rng.end}"
        attribs = []
        node.each_attribute do |k,v|
           attribs.push("#{k}=#{v}")
        end
        puts attribs.sort.join(',')
      end
      0
    end
  end

  class ErrorStream < CustomStream
    def initialize
      super
    end

    def next
      raise "foo"
    end
  end

  class IncompleteStream < CustomStream
    def initialize
      super
    end
  end
end

gff3file = ARGV[0]

types = []
is = GT::GFF3InStream.new(gff3file)
ps = GT::PrinterStream.new(is, types)
while ps.next_tree do
end

raise unless types.include?("gene")
raise unless types.include?("mRNA")
raise unless types.include?("TF_binding_site")
raise unless types.include?("exon")
raise unless types.include?("CDS")

es = GT::ErrorStream.new()
begin
  while es.next_tree do
  end
rescue GT::GTError
  # exception expected
else
  raise
end

begin
  is = GT::IncompleteStream.new
rescue GT::GTError
  # exception expected
else
  raise
end
genometools-1.5.1/testdata/gtruby/custom_visitor.rb000066400000000000000000000042171211610345200226130ustar00rootroot00000000000000#
# Copyright (c) 2012 Sascha Steinbiss 
# Copyright (c) 2012 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'

module GT
  class TestVisitor < CustomVisitor
    attr_reader :sn, :en, :rn, :cn, :fn, :mn

    def initialize
      super()
      @sn = nil
      @en = nil
      @rn = nil
      @cn = nil
      @fn = nil
      @mn = nil
    end

    def visit_feature_node(fn)
      @fn = fn
      0
    end

    def visit_sequence_node(sn)
      @sn = sn
      0
    end

    def visit_comment_node(cn)
      @cn = cn
      0
    end

    def visit_region_node(rn)
      @rn = rn
      0
    end

    def visit_meta_node(mn)
      @mn = mn
      0
    end

    def visit_eof_node(en)
      @en = en
      0
    end
  end
end

fn = GT::FeatureNode.create("foo", "gene", 100, 10000, "+")
cn = GT::CommentNode.create("comment")
rn = GT::RegionNode.create("foo", 100, 2000)
sn = GT::SequenceNode.create("foo", "AGATATAGA")
en = GT::EOFNode.create
mn = GT::MetaNode.create("foo", "bar")

v = GT::TestVisitor.new

raise unless v.sn.nil?
sn.accept(v)
raise if v.sn.nil? or v.sn != sn

raise unless v.cn.nil?
cn.accept(v)
raise if v.cn.nil? or v.cn != cn

raise unless v.fn.nil?
fn.accept(v)
raise if v.fn.nil? or v.fn != fn

raise unless v.en.nil?
en.accept(v)
raise if v.en.nil? or v.en != en

raise unless v.rn.nil?
rn.accept(v)
raise if v.rn.nil? or v.rn != rn

raise unless v.mn.nil?
mn.accept(v)
raise if v.mn.nil? or v.mn != mn
genometools-1.5.1/testdata/gtruby/encseq.rb000066400000000000000000000231111211610345200207720ustar00rootroot00000000000000#
# Copyright (c) 2010 Sascha Steinbiss 
# Copyright (c) 2010 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'
require 'tempfile'

@dnaseqfile = Tempfile.new('dnaseq')
@aaseqfile = Tempfile.new('aaseq')
@dseq1 = "agtccagctgtcagctagcgggcccgatgatatttt"
@dseq2 = "gtgctgtac"
@dseq3 = "gtacagcac"
@dseq4 = "aaaatatcatcgggcccgctagctgacagctggact"
@dnaseqfile.write(">seq1\n#{@dseq1}\n")
@dnaseqfile.write(">seq2\n#{@dseq2}\n")
@aaseq1 = "MVHFTAEEKAAVTSLWSKMNVEEAGGEALG"
@aaseq2 = "KMNAVE"
@aaseqfile.write(">seq1\n#{@aaseq1}\n")
@aaseqfile.write(">seq2\n#{@aaseq2}\n")
@dnaseqfile.flush
@aaseqfile.flush
@idxsuffixes = ['esq','des','ssp','sds']

def create_es(indexname)
  GT::EncseqEncoder.new.encode([@dnaseqfile.path], indexname)
end

def create_es_protein(indexname)
  GT::EncseqEncoder.new.encode([@aaseqfile.path], indexname)
end
      
def create_mem
    a= GT::Alphabet.create_dna
    eb = GT::EncseqBuilder.create(a)
    eb.enable_description_support
    eb.enable_multiseq_support
    eb.add_string(@dseq1, 'seq1')
    eb.add_string(@dseq2, 'seq2')
    eb.build
end

def create_mem_protein
    a = GT::Alphabet.create_protein
    eb = GT::EncseqBuilder.create(a)
    eb.enable_description_support
    eb.enable_multiseq_support
    eb.add_string(@aaseq1, 'seq1')
    eb.add_string(@aaseq2, 'seq2')
    eb.build
end

def delete_idx(indexname)
    @idxsuffixes.each do |suf|
      File.unlink(indexname+"."+suf)
    end
end

val = create_es("foo")
@idxsuffixes.each do |suf|
  raise if !File.exists?("foo.#{suf}")
end
delete_idx("foo")

create_es("foo_mapped")
el = GT::EncseqLoader.new
es = el.load("foo_mapped")
raise if not es 
delete_idx("foo_mapped")

el = GT::EncseqLoader.new
begin
  el.load("foo_fail")
  raise
rescue
  # pass
end

def run_test_num_seqs(es)
  raise unless es.num_of_sequences == 2
  if es.alphabet.is_dna? then
    es.mirror
    raise unless es.num_of_sequences == 4
    es.unmirror
  end
end

def run_test_num_files(es)
  raise unless es.num_of_files == 1
  if es.alphabet.is_dna? then
    es.mirror
    raise unless es.num_of_files == 1
    es.unmirror
  end
end

def run_test_num_files_mem(es)
  raise unless es.num_of_files == 1
  if es.alphabet.is_dna? then
    es.mirror
    raise unless es.num_of_files == 1
    es.unmirror
  end
end

def run_test_descriptions(es)
  begin
    es.description(2)
    raise
  rescue
    #pass
  end
  raise unless es.description(0) == "seq1"
  raise unless es.description(1) == "seq2"
  if es.alphabet.is_dna? then
    es.mirror
    begin
      es.description(5)
      raise
    rescue
      #pass
    end
    raise unless es.description(3) == "seq1"
    raise unless es.description(2) == "seq2"
    es.unmirror
  end
end

def run_test_total_length(es)
  raise unless es.total_length == 46
  es.mirror
  raise unless es.total_length == 93
  es.unmirror
end

def run_test_total_length_protein(es)
  raise unless es.total_length == 37
end

def run_test_get_encoded_char(es, seq1, seq2, seq3=nil, seq4=nil)
  a = es.alphabet
  0.upto(seq1.length-1) do |i|
    encchar = es.get_encoded_char(i, GT::READMODE_FORWARD)
    raise unless a.decode(encchar) ==  seq1[i].chr
  end
  (seq2.length-1).downto(0) do |i|
    encchar = es.get_encoded_char(seq2.length-1-i, GT::READMODE_REVERSE)
    raise unless a.decode(encchar) == seq2[i].chr
  end
  if a.is_dna? then
    es.mirror
    0.upto(seq3.length-1) do |i|
      encchar = es.get_encoded_char(47+i, GT::READMODE_FORWARD)
      raise unless a.decode(encchar) ==  seq3[i].chr
    end
    (seq4.length-1).downto(0) do |i|
      encchar = es.get_encoded_char(seq4.length-1-i, GT::READMODE_REVERSE)
      raise unless a.decode(encchar) == seq4[i].chr
    end
    es.unmirror
  end
end

def run_test_seq_startpos(es)
  raise unless es.seqstartpos(0) == 0
  raise unless es.seqstartpos(1) == 37
  es.mirror
  raise unless es.seqstartpos(2) == 47
  raise unless es.seqstartpos(3) == 57
  es.unmirror
end

def run_test_seq_startpos_protein(es)
  raise unless es.seqstartpos(0) == 0
  raise unless es.seqstartpos(1) == 31
end

def run_test_seq_length(es)
  raise unless es.seqlength(0) == 36
  raise unless es.seqlength(1) == 9
  es.mirror
  raise unless es.seqlength(3) == 36
  raise unless es.seqlength(2) == 9
  es.unmirror
end

def run_test_file_length(es)
  raise "#{es.effective_filelength(0)} != 46" \
    unless es.effective_filelength(0) == 46
end

def run_test_seq_length_protein(es)
  raise unless es.seqlength(0) == 30
  raise unless es.seqlength(1) == 6
end

def run_test_file_length_protein(es)
  raise "#{es.effective_filelength(0)} != 37" \
    unless es.effective_filelength(0) == 37
end
  
def run_test_seq_substr_encoded(es, seq1, seq2, seq3=nil, seq4=nil)
  start = 3
  stop = 13
  res = es.extract_encoded(start, stop)
  a = es.alphabet()
  start.upto(stop) do |i|
    raise unless a.decode(res[i-start]) == seq1[i].chr
  end
  start = 0
  stop = 5
  spos = es.seqstartpos(1)
  res = es.extract_encoded(start+spos, stop+spos)
  start.upto(stop) do |i|
    raise unless a.decode(res[i-start]) == seq2[i].chr
  end
  if a.is_dna? then
    es.mirror
    spos = es.seqstartpos(2)
    start = 3
    stop = 8
    res = es.extract_encoded(start+spos, stop+spos)
    a = es.alphabet()
    start.upto(stop) do |i|
      raise unless a.decode(res[i-start]) == seq3[i].chr
    end
    start = 0
    stop = 5
    spos = es.seqstartpos(3)
    res = es.extract_encoded(start+spos, stop+spos)
    start.upto(stop) do |i|
      raise unless a.decode(res[i-start]) == seq4[i].chr
    end
    es.unmirror
  end
end

def run_test_seq_substr_plain(es, seq1, seq2, seq3=nil, seq4=nil)
  start = 3
  stop = 13
  raise unless es.extract_decoded(start, stop) == seq1[start..(stop)]
  start = 0
  stop = 5
  spos = es.seqstartpos(1)
  raise unless es.extract_decoded(spos+start, spos+stop) == seq2[start..(stop)]
  if es.alphabet.is_dna? then
    es.mirror
    spos = es.seqstartpos(2)
    start = 3
    stop = 8
    raise unless es.extract_decoded(start+spos, stop+spos) == seq3[start..(stop)]
    start = 0
    stop = 5
    spos = es.seqstartpos(3)
    raise unless es.extract_decoded(start+spos, stop+spos) == seq4[start..(stop)]
    es.unmirror
  end
end

def run_test_seq_substr_sequential(es, seq1, seq2, seq3=nil, seq4=nil)
  start = 3
  stop = 13
  er = es.create_reader_with_readmode(GT::READMODE_FORWARD, start)
  a = es.alphabet()
  start.upto(stop) do |i|
    raise unless a.decode(er.next_encoded_char) == seq1[i].chr
  end
  start = es.seqstartpos(1)
  stop = start + 5
  er = es.create_reader_with_readmode(GT::READMODE_FORWARD, start)
  0.upto(stop-start) do |i|
    encchar = a.decode(er.next_encoded_char)
    seqchar = seq2[i].chr
    raise unless encchar == seqchar
  end
  if a.is_dna? then
    es.mirror
    start = es.seqstartpos(2)
    stop = start + 5
    er = es.create_reader_with_readmode(GT::READMODE_FORWARD, start)
    0.upto(stop-start) do |i|
      encchar = a.decode(er.next_encoded_char)
      seqchar = seq3[i].chr
      raise unless encchar == seqchar
    end
    start = es.seqstartpos(3)
    stop = start + 5
    er = es.create_reader_with_readmode(GT::READMODE_FORWARD, start)
    0.upto(stop-start) do |i|
      encchar = a.decode(er.next_encoded_char)
      seqchar = seq4[i].chr
      raise unless encchar == seqchar
    end
    es.unmirror
  end
end

create_es("foo")
el = GT::EncseqLoader.new
es = el.load("foo")
run_test_descriptions(es)
run_test_get_encoded_char(es, @dseq1, @dseq2, @dseq3, @dseq4)
run_test_num_seqs(es)
run_test_num_files(es)
run_test_seq_length(es)
run_test_seq_startpos(es)
run_test_file_length(es)
run_test_seq_substr_encoded(es, @dseq1, @dseq2, @dseq3, @dseq4)
run_test_seq_substr_plain(es, @dseq1, @dseq2, @dseq3, @dseq4)
run_test_seq_substr_sequential(es, @dseq1, @dseq2, @dseq3, @dseq4)
run_test_total_length(es)
delete_idx("foo")
es = create_mem
run_test_descriptions(es)
run_test_get_encoded_char(es, @dseq1, @dseq2, @dseq3, @dseq4)
run_test_num_seqs(es)
run_test_num_files_mem(es)
run_test_seq_length(es)
run_test_seq_substr_encoded(es, @dseq1, @dseq2, @dseq3, @dseq4)
run_test_seq_substr_plain(es, @dseq1, @dseq2, @dseq3, @dseq4)
run_test_seq_substr_sequential(es, @dseq1, @dseq2, @dseq3, @dseq4)
run_test_total_length(es)

create_es_protein("foo")
el = GT::EncseqLoader.new
es = el.load("foo")
run_test_descriptions(es)
run_test_get_encoded_char(es,@aaseq1,@aaseq2)
run_test_num_seqs(es)
run_test_num_files(es)
run_test_seq_startpos_protein(es)
run_test_file_length_protein(es)
run_test_seq_length_protein(es)
run_test_seq_substr_encoded(es,@aaseq1,@aaseq2)
run_test_seq_substr_plain(es,@aaseq1,@aaseq2)
run_test_seq_substr_sequential(es,@aaseq1,@aaseq2)
run_test_total_length_protein(es)
delete_idx("foo")
es = create_mem_protein
run_test_descriptions(es)
run_test_get_encoded_char(es,@aaseq1,@aaseq2)
run_test_num_seqs(es)
run_test_num_files_mem(es)
run_test_seq_length_protein(es)
run_test_seq_substr_encoded(es,@aaseq1,@aaseq2)
run_test_seq_substr_plain(es,@aaseq1,@aaseq2)
run_test_seq_substr_sequential(es,@aaseq1,@aaseq2)
run_test_total_length_protein(es)
genometools-1.5.1/testdata/gtruby/feature_node.rb000066400000000000000000000054461211610345200221670ustar00rootroot00000000000000#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'


class TestFailedError < Exception
end

fn = GT::FeatureNode.create("test", "type", 100, 500, "+")
fn.add_attribute("test","testval")
fn.add_attribute("test2","testval2")
if fn.score_is_defined? then
  raise TestFailedError
end
fn.set_score(2)
if !fn.score_is_defined? then
  raise TestFailedError
end
if fn.get_score != 2 then
  raise TestFailedError
end
fn.unset_score()
if fn.score_is_defined? then
  raise TestFailedError
end
if fn.has_type?("foo") then
  raise TestFailedError
end
if !fn.has_type?("type") then
  raise TestFailedError
end
if !fn.get_strand == "+" then
  raise TestFailedError
end
fn2 = GT::FeatureNode.create("test", "type2", 200,300,"+")
fn.add_child(fn2)
num_attrs = 0
fn.each_attribute do |tag, val|
  if val != fn.get_attribute(tag) then
    raise TestFailedError
  end
  num_attrs += 1
end
if !num_attrs == 2 then
  raise TestFailedError
end
if fn.get_phase != 3 then   #undefined
  raise TestFailedError
end
fn.set_phase(0)
if fn.get_phase != 0 then   #zero
  raise TestFailedError
end
if fn.get_filename != "generated" then
  raise TestFailedError
end

begin
  fn.add_child(GT::FeatureNode.create("nottest", "foo", 100, 200, "+"))
rescue GT::GTError => msg
  # expect exception
else
  raise TestFailedError
end

fni = GT::FeatureNodeIteratorDepthFirst.new(fn)
num_features = 0
tfn = fni.next
while tfn do
  num_features += 1
  tfn = fni.next
end
if num_features != 2 then
  raise TestFailedError
end

fn3 = GT::FeatureNode.create("test", "type3", 250, 300,"+")
fn.add_child(fn3)
fni = GT::FeatureNodeIteratorDepthFirst.new(fn)
num_features = 0
tfn = fni.next
while tfn do
  num_features += 1
  tfn = fni.next
end
if num_features != 3 then
  raise TestFailedError
end

types = []
fn.traverse_dfs do |tfn|
  types.push(tfn.get_type())
end
if types != ["type", "type2", "type3"] then
  raise TestFailedError
end

types = []
fn.traverse_direct do |tfn|
  types.push(tfn.get_type())
end
if types != ["type2", "type3"] then
  raise TestFailedError
end
genometools-1.5.1/testdata/gtruby/feature_stuff.rb000066400000000000000000000037431211610345200223670ustar00rootroot00000000000000#
# Copyright (c) 2007 Gordon Gremme 
# Copyright (c) 2007 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for FeatureIndex and FeatureStream classes

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} GFF3_file"
  STDERR.puts "Test the FeatureIndex and FeatureStream bindings on GFF3 file."
  exit(1)
end


gff3file = ARGV[0]

# set up the feature stream
genome_stream = GT::GFF3InStream.new(gff3file)

# try to instantiate an interface
begin
  feature_index = GT::FeatureIndex.new()
rescue NotImplementedError => e
  raise unless /GT::FeatureIndex implementation/.match(e)
else
  raise
end

# instantiate index object
feature_index = GT::FeatureIndexMemory.new()
genome_stream = GT::FeatureStream.new(genome_stream, feature_index)

feature = genome_stream.next_tree()
while (feature) do
  feature = genome_stream.next_tree()
end

seqid = feature_index.get_first_seqid()
features = feature_index.get_features_for_seqid(seqid)
raise if not features

rng = feature_index.get_range_for_seqid(seqid)
features_r = feature_index.get_features_for_range(rng.start, rng.end, seqid)
raise unless features.length == features_r.length

gff3_visitor = GT::GFF3Visitor.new()

features.each do |feature|
  feature.accept(gff3_visitor)
end
genometools-1.5.1/testdata/gtruby/feature_stuff_db.rb000066400000000000000000000031001211610345200230170ustar00rootroot00000000000000#
# Copyright (c) 2012 Sascha Steinbiss 
# Copyright (c) 2012 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for the database-backed feature stores

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} GFF3_db"
  STDERR.puts "Test the FeatureIndex bindings on GFF-like db."
  exit(1)
end

gffdb = ARGV[0]

rdb = GT::RDBSqlite.new(gffdb)
adb = GT::AnnoDBGFFlike.new()
feature_index = adb.get_feature_index(rdb)

seqid = feature_index.get_first_seqid()
features = feature_index.get_features_for_seqid(seqid)
raise if not features

rng = feature_index.get_range_for_seqid(seqid)
features_r = feature_index.get_features_for_range(rng.start, rng.end, seqid)
raise unless features.length == features_r.length

gff3_visitor = GT::GFF3Visitor.new()

features.each do |feature|
  feature.accept(gff3_visitor)
end
genometools-1.5.1/testdata/gtruby/genome_visitor.rb000066400000000000000000000023301211610345200225450ustar00rootroot00000000000000#
# Copyright (c) 2007 Gordon Gremme 
# Copyright (c) 2007 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for the GFF3 GenomeVisitor (similar to gff3 tool)

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} GFF3_file"
  STDERR.puts "Parse and output the given GFF3_file."
  exit(1)
end

gff3file = ARGV[0]

gs = GT::GFF3InStream.new(gff3file)
gv = GT::GFF3Visitor.new()
gn = gs.next_tree()
while gn do
  gn.accept(gv)
  gn = gs.next_tree()
end
genometools-1.5.1/testdata/gtruby/gff3.rb000066400000000000000000000023621211610345200203460ustar00rootroot00000000000000#
# Copyright (c) 2007 Gordon Gremme 
# Copyright (c) 2007 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for the GFF3 output stream (similar to gff3 tool)

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} GFF3_file"
  STDERR.puts "Parse and output the given GFF3_file."
  exit(1)
end

gff3file = ARGV[0]

in_stream = GT::GFF3InStream.new(gff3file)
out_stream = GT::GFF3OutStream.new(in_stream)
gn = out_stream.next_tree()
while gn do
  gn = out_stream.next_tree()
end
genometools-1.5.1/testdata/gtruby/graphics_stuff.rb000066400000000000000000000055721211610345200225360ustar00rootroot00000000000000#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'

if ARGV.size != 2 then
  STDERR.puts "Usage: #{$0} curve_coords PNG_file"
  STDERR.puts "Tests drawing functions in the Graphics object."
  exit(1)
end

g = GT::GraphicsCairoSVG.new(700, 800)

black = [0,0,0,1].pack('dddd').to_ptr
black2 = [0,0,0,0.7].pack('dddd').to_ptr
red = [1,0,0,0.2].pack('dddd').to_ptr
red2 = [1,0,0,0.3].pack('dddd').to_ptr
grey1 = [0,0,0,0.3].pack('dddd').to_ptr
green = [0,1,0,0.2].pack('dddd').to_ptr
lastcol = [0,1,1,0.2].pack('dddd').to_ptr
blue = [0,0,1,0.6].pack('dddd').to_ptr

g.draw_text(300, 20, "draw_text")
g.draw_text_right(300, 40, "draw_text_left")
g.draw_text_centered(300, 60, "draw_text_centered")
g.draw_colored_text(300, 80, red, "draw_colored_text")
g.set_margins(20, 30)
raise if g.get_image_height() != 800
raise if g.get_image_width() != 700
raise if g.get_xmargins() != 20
raise if g.get_ymargins() != 30

g.draw_horizontal_line(150, 100, grey1, 300, 5.5)
g.draw_vertical_line(200, 70, red2, 100, 3.5)
g.draw_box(150, 120, 300, 30, green, GT::ARROW_LEFT,  20, 2, \
           black, false)
g.draw_box(150, 170, 300, 20, lastcol, GT::ARROW_RIGHT, 20, 1, \
           black, false)
g.draw_box(150, 210, 300, 20, red, GT::ARROW_BOTH,  20, 1, \
           black, false)
g.draw_box(300, 250,  20, 20, red, GT::ARROW_BOTH,  20, 1, \
           black, false)
g.draw_box(150, 290, 300, 20, red, GT::ARROW_NONE,  20, 1, \
           black, false)
g.draw_dashes(159, 340, 90, 20, GT::ARROW_RIGHT, 20, 1, black)
g.draw_dashes(359, 340, 60, 20, GT::ARROW_LEFT, 20, 1, black)
g.draw_dashes(59, 340, 60, 20, GT::ARROW_NONE, 20, 1, black)
g.draw_dashes(559, 340, 60, 20, GT::ARROW_BOTH, 20, 1, black)
g.draw_caret(159, 390, 90, 20, GT::ARROW_RIGHT, 20, 1, black)
g.draw_caret(359, 390, 60, 20, GT::ARROW_LEFT, 20, 1, black)
g.draw_caret(59, 390, 60, 20, GT::ARROW_NONE, 20, 1, black)
g.draw_caret(559, 390, 60, 20, GT::ARROW_BOTH, 20, 1, black)

data = []
File.open(ARGV[0]) do |file|
  file.each_line do |l|
    data.push(l.to_f)
  end
end
g.draw_curve_data(20, 430, blue, data, data.length, 0, 1, 40)

g.to_file(ARGV[1])
genometools-1.5.1/testdata/gtruby/node_types.rb000066400000000000000000000052061211610345200216720ustar00rootroot00000000000000#
# Copyright (c) 2009 Sascha Steinbiss 
# Copyright (c) 2009 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'

class TestFailedError < Exception
end

# test CommentNodes
cn  = GT::CommentNode.create("Comment")
cn2 = GT::CommentNode.create(333)

unless cn.get_comment == "Comment"
  raise(TestFailedError, "CommentNode.get_comment")
end
unless cn2.get_comment == "333"
  raise(TestFailedError, "CommentNode.get_comment")
end

# test SequenceNodes
SEQUENCE = 'AGATATAGA'
DESC = 'testdesc'
begin
  sn = GT::SequenceNode.create("foo")
rescue ArgumentError
  # expected
else
  raise(TestFailedError, "no failure on not enough arguments")
end
sn = GT::SequenceNode.create(DESC, SEQUENCE)
unless sn.get_description == 'testdesc'
  raise(TestFailedError, "SequenceNode.get_description")
end
unless (seq = sn.get_sequence) == 'AGATATAGA'
  raise(TestFailedError, "SequenceNode.get_sequence")
end
unless sn.get_sequence_length == 9
  raise(TestFailedError, "SequenceNode.get_sequence_length")
end
unless sn.get_sequence_length == seq.length
  raise(TestFailedError, "SequenceNode.get_sequence_length")
end

# test RegionNodes
begin
  rn = GT::RegionNode.create("foo", 100, 50)
rescue ArgumentError
  # expected
else
  raise(TestFailedError, "no failure on start > stop")
end
# does not have any exposed methods yet (see _api.h)

# test MetaNodes
cn  = GT::MetaNode.create("directive", "data")
cn2 = GT::MetaNode.create(333, 444)

unless cn.get_directive == "directive"
  raise(TestFailedError, "MetaNode.get_directive")
end
unless cn2.get_directive == "333"
  raise(TestFailedError, "CommentNode.get_directive")
end
unless cn.get_data == "data"
  raise(TestFailedError, "MetaNode.get_data")
end
unless cn2.get_data == "444"
  raise(TestFailedError, "CommentNode.get_data")
end

# test EOFNodes
rn = GT::EOFNode.create()
if rn.nil? then
  raise(TestFailedError, "EOFNode.create")
end
# does not have any exposed methods yet (see _api.h)
genometools-1.5.1/testdata/gtruby/range.rb000066400000000000000000000042071211610345200206150ustar00rootroot00000000000000#
# Copyright (c) 2010 Sascha Steinbiss 
# Copyright (c) 2010 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'

def assert_raises
  begin
    yield
    raise
  rescue GT::GTError, ArgumentError => e
    #pass
  end
end

assert_raises do
  GT::Range.new()
end

assert_raises do
  GT::Range.new(1)
end

assert_raises do
  GT::Range.new(1, nil)
end

assert_raises do
  GT::Range.new(nil, 1)
end

assert_raises do
  GT::Range.new(20, 1)
end

assert_raises do
  GT::Range.new(-1, 1)
end

assert_raises do
  GT::Range.new(1, -1)
end

assert_raises do
  GT::Range.new(-1, -1)
end

assert_raises do
  GT::Range.new(-1, -2)
end

raise unless !GT::Range.new(1, 2).nil?
raise unless !GT::Range.new(1, 1).nil?

rng = GT::Range.new(100, 200)

assert_raises do
  rng.start = 300
end

assert_raises do
  rng.start = -100
end

assert_raises do
  rng.end = 50
end

assert_raises do
  rng.end = -350
end

rng.start = 50
raise unless rng.start == 50
rng.start = 150
raise unless rng.start == 150

rng.end = 250
raise unless rng.end == 250
rng.end = 151
raise unless rng.end == 151
rng.end = 150
raise unless rng.end == 150

assert_raises do
  rng.set(1)
end

assert_raises do
  rng.set(1, nil)
end

assert_raises do
  rng.set(nil, 1)
end

assert_raises do
  rng.set(20, 1)
end

assert_raises do
  rng.set(-1, 1)
end

assert_raises do
  rng.set(1, -1)
end

assert_raises do
  rng.set(-1, -1)
end

assert_raises do
  rng.set(-1, -2)
end
genometools-1.5.1/testdata/gtruby/show_recmaps.rb000066400000000000000000000034641211610345200222170ustar00rootroot00000000000000#
# Copyright (c) 2008 Gordon Gremme 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for libgtview

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} PNG_file GFF3_file"
  STDERR.puts "Show RecMaps of GFF3 annotation file."
  exit(1)
end

gff3file = ARGV[0]

in_stream = GT::GFF3InStream.new(gff3file)
feature_index = GT::FeatureIndexMemory.new()
feature_stream = GT::FeatureStream.new(in_stream, feature_index)
gn = feature_stream.next_tree()
# fill feature index
while (gn) do
  gn = feature_stream.next_tree()
end

seqid = feature_index.get_first_seqid()
range = feature_index.get_range_for_seqid(seqid)

style = GT::Style.new()
diagram = GT::Diagram.from_index(feature_index, seqid, range, style)
layout = GT::Layout.new(diagram, 700, style)
ii = GT::ImageInfo.new()
image_info = GT::ImageInfo.new()
canvas = GT::CanvasCairoFile.new(style, 800, layout.get_height, image_info)
layout.sketch(canvas)

image_info.each_hotspot do |x1, y1, x2, y2, gn|
  puts "x1=#{x1}, y1=#{y1}, x2=#{x2}, y2=#{y2}, gn.type=#{gn.get_type}"
end
genometools-1.5.1/testdata/gtruby/show_seqids.rb000066400000000000000000000026111211610345200220460ustar00rootroot00000000000000#
# Copyright (c) 2007 Gordon Gremme 
# Copyright (c) 2007 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing some Ruby bindings for FeatureIndex

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} GFF3_file"
  STDERR.puts "Show sequence ids contained in GFF3 annotation file."
  exit(1)
end


gff3file = ARGV[0]

in_stream = GT::GFF3InStream.new(gff3file)
feature_index = GT::FeatureIndexMemory.new()
feature_stream = GT::FeatureStream.new(in_stream, feature_index)
gn = feature_stream.next_tree()
# fill feature index
while (gn) do
  gn = feature_stream.next_tree()
end

seqids = feature_index.get_seqids()
seqids.each { |seqid| puts seqid }
genometools-1.5.1/testdata/gtruby/sketch-failures.rb000066400000000000000000000042641211610345200226150ustar00rootroot00000000000000#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} GFF3_file"
  exit(1)
end

class TestFailedError < Exception
end

feature_index = GT::FeatureIndexMemory.new()
feature_index.add_gff3file(ARGV[0])

seqid = feature_index.get_first_seqid()
range = feature_index.get_range_for_seqid(seqid)

style = GT::Style.new()
style.set_num("format","margins",100)

begin
  diagram = GT::Diagram.from_index(feature_index, "nonexist", range, style)
rescue GT::GTError => msg
    raise if !/feature index does not contain the given sequence id/.match(msg)
else
  raise TestFailedError
end
begin
  diagram = GT::Diagram.from_index(nil, seqid, range, style)
rescue
  # exception expected
else
  raise TestFailedError
end
begin
  diagram = GT::Diagram.from_index(feature_index, seqid, nil, style)
rescue
  # exception expected
else
  raise TestFailedError
end
begin
  diagram = GT::Diagram.from_index(feature_index, seqid, range, "Dd")
rescue
  # exception expected
else
  raise TestFailedError
end
diagram = GT::Diagram.from_index(feature_index, seqid, range, style)

begin
  layout = GT::Layout.new(diagram, 70, style)
rescue GT::GTError => msg
  raise if !/layout width must at least be twice the x-margin/.match(msg)
else
  raise TestFailedError
end
layout = GT::Layout.new(diagram, 700, style)

canvas = GT::CanvasCairoFile.new(style, 700, layout.get_height, nil)
genometools-1.5.1/testdata/gtruby/sketch.rb000066400000000000000000000033641211610345200210050ustar00rootroot00000000000000#
# Copyright (c) 2007-2008 Gordon Gremme 
# Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for AnnotationSketch (similar to the sketch tool)

require 'gtruby'

if ARGV.size != 2 then
  STDERR.puts "Usage: #{$0} PNG_file GFF3_file"
  STDERR.puts "Create PNG representation of GFF3 annotation file."
  exit(1)
end

pngfile  = ARGV[0]
gff3file = ARGV[1]

in_stream = GT::GFF3InStream.new(gff3file)
feature_index = GT::FeatureIndexMemory.new()
feature_stream = GT::FeatureStream.new(in_stream, feature_index)
gn = feature_stream.next_tree()
# fill feature index
while (gn) do
  gn = feature_stream.next_tree()
end

seqid = feature_index.get_first_seqid()
range = feature_index.get_range_for_seqid(seqid)

style = GT::Style.new()
diagram = GT::Diagram.from_index(feature_index, seqid, range, style)
layout = GT::Layout.new(diagram, 700, style)
ii = GT::ImageInfo.new()
canvas = GT::CanvasCairoFile.new(style, 700, layout.get_height, ii)
layout.sketch(canvas)
canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtruby/sketch_parsed_with_invalid_ordering.rb000066400000000000000000000020351211610345200267670ustar00rootroot00000000000000require 'gtruby'

if ARGV.size != 3 then
  STDERR.puts "Usage: #{$0} style_file PNG_file GFF3_file"
  STDERR.puts "Create PNG representation of GFF3 annotation file."
  exit(1)
end

(stylefile, pngfile, gff3file) = ARGV

# load style file
style = GT::Style.new()
style.load_file(stylefile)

# create feature index
feature_index = GT::FeatureIndexMemory.new()

# add GFF3 file to index
feature_index.add_gff3file(gff3file)

# create diagram for first sequence ID in feature index
seqid = feature_index.get_first_seqid()
range = feature_index.get_range_for_seqid(seqid)
diagram = GT::Diagram.from_index(feature_index, seqid, range, style)

# create layout for given width
layout = GT::Layout.new(diagram, 800, style)

# set a track ordering comparator function
layout.set_track_ordering_func(lambda { |s1, s2| return "not_a_number" })

# create canvas with given width and computed height
canvas = GT::CanvasCairoFile.new(style, 800, layout.get_height, nil)

# sketch layout on canvas
layout.sketch(canvas)

# write canvas to file
canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtruby/sketch_parsed_with_invalid_ordering_2.rb000066400000000000000000000020221211610345200272040ustar00rootroot00000000000000require 'gtruby'

if ARGV.size != 3 then
  STDERR.puts "Usage: #{$0} style_file PNG_file GFF3_file"
  STDERR.puts "Create PNG representation of GFF3 annotation file."
  exit(1)
end

(stylefile, pngfile, gff3file) = ARGV

# load style file
style = GT::Style.new()
style.load_file(stylefile)

# create feature index
feature_index = GT::FeatureIndexMemory.new()

# add GFF3 file to index
feature_index.add_gff3file(gff3file)

# create diagram for first sequence ID in feature index
seqid = feature_index.get_first_seqid()
range = feature_index.get_range_for_seqid(seqid)
diagram = GT::Diagram.from_index(feature_index, seqid, range, style)

# create layout for given width
layout = GT::Layout.new(diagram, 800, style)

# set a track ordering comparator function
layout.set_track_ordering_func(lambda { |s1, s2| return nil })

# create canvas with given width and computed height
canvas = GT::CanvasCairoFile.new(style, 800, layout.get_height, nil)

# sketch layout on canvas
layout.sketch(canvas)

# write canvas to file
canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtruby/sketch_parsed_with_ordering.rb000066400000000000000000000020311211610345200252550ustar00rootroot00000000000000require 'gtruby'

if ARGV.size != 3 then
  STDERR.puts "Usage: #{$0} style_file PNG_file GFF3_file"
  STDERR.puts "Create PNG representation of GFF3 annotation file."
  exit(1)
end

(stylefile, pngfile, gff3file) = ARGV

# load style file
style = GT::Style.new()
style.load_file(stylefile)

# create feature index
feature_index = GT::FeatureIndexMemory.new()

# add GFF3 file to index
feature_index.add_gff3file(gff3file)

# create diagram for first sequence ID in feature index
seqid = feature_index.get_first_seqid()
range = feature_index.get_range_for_seqid(seqid)
diagram = GT::Diagram.from_index(feature_index, seqid, range, style)

# create layout for given width
layout = GT::Layout.new(diagram, 800, style)

# set a track ordering comparator function
layout.set_track_ordering_func(lambda { |s1, s2|  return s2 <=> s1 })

# create canvas with given width and computed height
canvas = GT::CanvasCairoFile.new(style, 800, layout.get_height, nil)

# sketch layout on canvas
layout.sketch(canvas)

# write canvas to file
canvas.to_file(pngfile)
genometools-1.5.1/testdata/gtruby/sketch_stream.rb000066400000000000000000000040151211610345200223520ustar00rootroot00000000000000#
# Copyright (c) 2007-2008 Gordon Gremme 
# Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for AnnotationSketch (similar to the sketch tool)

require 'gtruby'

if ARGV.size != 2 then
  STDERR.puts "Usage: #{$0} PNG_file GFF3_file"
  STDERR.puts "Create PNG representation of GFF3 annotation file (adds introns)."
  exit(1)
end


pngfile  = ARGV[0]
gff3file = ARGV[1]

in_stream = GT::GFF3InStream.new(gff3file)

# add introns
add_introns_stream = GT::AddIntronsStream.new(in_stream)
in_stream = add_introns_stream

feature_index = GT::FeatureIndexMemory.new()
feature_stream = GT::FeatureStream.new(in_stream, feature_index)
gn = feature_stream.next_tree()
# fill feature index
while (gn) do
  gn = feature_stream.next_tree()
  if !gn.nil? and gn.get_filename != gff3file then
    raise TestFailedError
  end
end

seqid = feature_index.get_first_seqid()
range = feature_index.get_range_for_seqid(seqid)

style = GT::Style.new()
diagram = GT::Diagram.from_index(feature_index, seqid, range, style)
layout = GT::Layout.new(diagram, 700, style)
ii = GT::ImageInfo.new()
canvas = GT::CanvasCairoFile.new(style, 700, layout.get_height, ii)
layout.sketch(canvas)

pngstream = canvas.to_stream
outfile = File.new(pngfile, "w")
outfile.write(pngstream)
outfile.close
genometools-1.5.1/testdata/gtruby/style.rb000066400000000000000000000100141211610345200206520ustar00rootroot00000000000000#
# Copyright (c) 2008 Gordon Gremme 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for the style object

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} style_file"
  STDERR.puts "Load style_file and test style bindings."
  exit(1)
end

stylefile = ARGV[0]

# create new style object
style = GT::Style.new()

# load style file
style.load_file(stylefile)

# clone style file
clone = style.clone
raise if not clone

# get color
color = style.get_color("exon", "fill")
raise if not color

# set color
color = GT::Color.malloc
color.red   = 0.3
color.green = 0.4
color.blue  = 0.3
style.set_color("exon", "fill", color)
color2 = style.get_color("exon", "fill")
raise if color2.red != color.red \
  and color2.green != color.green \
  and color2.blue != color.blue

# unset color
style.unset("exon", "fill")
color2 = style.get_color("exon", "fill")
raise if not color2.nil?

# get undefined color
color = style.get_color("undefined", "undefined")
raise if not color.nil?

# get string
str = style.get_cstr("exon", "style")
raise if str != "box"

# set string
style.set_cstr("exon", "style", "line")
str = style.get_cstr("exon", "style")
raise if str != "line"

# unset string
style.unset("exon", "style")
str = style.get_cstr("exon", "style")
raise if not str.nil?

# get undefined string
str = style.get_cstr("undefined", "undefined")
raise if not str.nil?

# get number
num = style.get_num("format", "margins")
raise if num != 30

# set number
style.set_num("format", "margins", 20)
num = style.get_num("format", "margins")
raise if num != 20

# unset number
style.unset("format", "margins");
num = style.get_num("format", "margins")
raise if not num.nil?

#get undefined number
num = style.get_num("undefined", "undefined")
raise if not num.nil?

# get boolean
bool = style.get_bool("format", "show_grid")
raise if not bool

# get undefined boolean
bool = style.get_bool("undefined", "undefined")
raise if not bool.nil?

# set boolean
style.set_bool("format", "show_grid", false)
bool = style.get_bool("format", "show_grid")
raise if bool

# unset boolean
style.unset("format", "show_grid")
bool = style.get_bool("format", "show_grid")
raise if not bool.nil?

# serialise style to Lua code
style.set_num("format", "margins", 20)
style.set_bool("format", "show_grid", true)
color = GT::Color.malloc
color.red   = 0.3
color.green = 0.4
color.blue  = 0.3
style.set_color("exon", "fill", color)
luacode = style.to_str
raise if luacode.nil? or luacode.length == 0

# load style from Lua code
style.load_str(luacode)
num = style.get_num("format", "margins")
raise if num != 20
bool = style.get_bool("format", "show_grid")
raise if not bool
color2 = style.get_color("exon", "fill")
raise if color2.red != color.red \
  and color2.green != color.green \
  and color2.blue != color.blue

# clone style from existing copy
style2 = style.clone
num = style2.get_num("format", "margins")
raise if num != 20
bool = style2.get_bool("format", "show_grid")
raise if not bool
color2 = style2.get_color("exon", "fill")
raise if color2.red != color.red \
  and color2.green != color.green \
  and color2.blue != color.blue
style2.set_num("format", "margins", 30)
raise if style2.get_num("format", "margins") != 30
raise if style.get_num("format", "margins")\
           == style2.get_num("format", "margins")
genometools-1.5.1/testdata/gtruby/style_serialize.rb000066400000000000000000000022221211610345200227230ustar00rootroot00000000000000#
# Copyright (c) 2010 Sascha Steinbiss 
# Copyright (c) 2010 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} style_file"
  STDERR.puts "Load style_file and test style bindings."
  exit(1)
end

stylefile = ARGV[0]

# create new style object
style = GT::Style.new()

# load style file
style.load_file(stylefile)

# serialise to Lua code

style.to_str
genometools-1.5.1/testdata/gtruby/type_checker.rb000066400000000000000000000030011211610345200221550ustar00rootroot00000000000000#
# Copyright (c) 2012 Sascha Steinbiss 
# Copyright (c) 2012 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} OBO_file"
  STDERR.puts "Test the type checker Ruby bindings using ."
  exit(1)
end

obofile = ARGV[0]

begin
  tc = GT::TypeChecker.new
rescue NotImplementedError => msg
  # expect exception
else
  raise TestFailedError
end

tc = GT::TypeCheckerBuiltin.new
raise unless tc.is_valid?("gene")
raise if tc.is_valid?("foo")

tc = GT::TypeCheckerOBO.new(obofile)
raise unless tc.is_valid?("gene")
raise unless tc.is_valid?("processed_transcript")
raise if tc.is_valid?("foo")

begin
  tc = GT::TypeCheckerOBO.new("fooo")
rescue GT::GTError => msg
  # expect exception
else
  raise TestFailedError
end
genometools-1.5.1/testdata/gtruby/used_types.rb000066400000000000000000000024331211610345200217040ustar00rootroot00000000000000#
# Copyright (c) 2008 Gordon Gremme 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# testing the Ruby bindings for the GFF3 output stream (similar to gff3 tool)

require 'gtruby'

if ARGV.size != 1 then
  STDERR.puts "Usage: #{$0} GFF3_file"
  STDERR.puts "Parse and output the types used in GFF3_file."
  exit(1)
end

gff3file = ARGV[0]

in_stream = GT::GFF3InStream.new(gff3file)
gn = in_stream.next_tree()
while gn do
  gn = in_stream.next_tree()
end

used_types = in_stream.get_used_types
used_types.each do |type|
  puts type
end
genometools-1.5.1/testdata/gtscripts/000077500000000000000000000000001211610345200176775ustar00rootroot00000000000000genometools-1.5.1/testdata/gtscripts/arg.lua000066400000000000000000000017601211610345200211570ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the arg table

io.write(string.format("arg[0]=%s\n", arg[0]))
for i,v in ipairs(arg) do
  io.write(string.format("arg[%d]=%s\n", i, v))
end
genometools-1.5.1/testdata/gtscripts/bittab.lua000066400000000000000000000040311211610345200216450ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the Bittab class

-- testing gt.bittab_new
b = gt.bittab_new(10)
rval, err = pcall(gt.bittab_new, 0)
assert(not rval)
assert(string.find(err, "must be > 0"))

-- testing bittab:set_bit
b:set_bit(1)
rval, err = pcall(b.set_bit, b, 10)
assert(not rval)
assert(string.find(err, "bit number too large"))
rval, err = pcall(b.set_bit, a, 1)
assert(not rval)
assert(string.find(err, "bittab expected"))

-- testing bittab:unset_bit
b:unset_bit(1);
rval, err = pcall(b.unset_bit, b, 10)
assert(not rval)
assert(string.find(err, "bit number too large"))

-- testing bittab:complement
src = gt.bittab_new(10)
src:set_bit(5)
src:set_bit(7)
prob = gt.bittab_new(11)
b:complement(src)
rval, err = pcall(b.complement, b, prob)
assert(not rval)
assert(string.find(err, "bittabs have different sizes"))

-- testing bittab:equal
b:equal(src)
rval, err = pcall(b.equal, b, prob)
assert(not rval)
assert(string.find(err, "bittabs have different sizes"))

-- testing bittab:and_equal and bittab:bit_is_set
a = gt.bittab_new(100)
b = gt.bittab_new(100)
a:set_bit(0)
a:set_bit(50)
b:set_bit(50)
b:set_bit(99)
a:and_equal(b)
assert(not a:bit_is_set(0))
assert(a:bit_is_set(50))
assert(not a:bit_is_set(99))
genometools-1.5.1/testdata/gtscripts/cds_stream.lua000066400000000000000000000030051211610345200225240ustar00rootroot00000000000000--[[
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the CSAStream binding

function usage()
  io.stderr:write(string.format("Usage: %s Fasta_file GFF3_file\n", arg[0]))
  io.stderr:write("Add CDS features to exon features given in GFF3_file.\n")
  os.exit(1)
end

if #arg == 2 then
  fasta_file = arg[1]
  gff3file = arg[2]
else
  usage()
end

in_stream = gt.gff3_in_stream_new_sorted(gff3file)
region_mapping = gt.region_mapping_new_seqfile(fasta_file)
cds_stream = gt.cds_stream_new(in_stream, region_mapping)
out_stream = gt.gff3_out_stream_new(cds_stream)
in_stream = nil;
cds_stream = nil;
collectgarbage() -- being nasty

gn = out_stream:next_tree()
while (gn) do
  gn = out_stream:next_tree()
end
genometools-1.5.1/testdata/gtscripts/csa_stream.lua000066400000000000000000000027071211610345200225310ustar00rootroot00000000000000--[[
  Copyright (c) 2008 Gordon Gremme 
  Copyright (c) 2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the CSAStream binding

function usage()
  io.stderr:write(string.format("Usage: %s GFF3_file\n", arg[0]))
  io.stderr:write("Replace spliced alignments with computed consensus " ..
                  "spliced alignments.\n")
  os.exit(1)
end

if #arg == 1 then
  gff3file = arg[1]
else
  usage()
end

in_stream = gt.gff3_in_stream_new_sorted(gff3file)
csa_stream = gt.csa_stream_new(in_stream, 300)
out_stream = gt.gff3_out_stream_new(csa_stream)
in_stream = nil;
csa_stream = nil;
collectgarbage() -- being nasty

gn = out_stream:next_tree()
while (gn) do
  gn = out_stream:next_tree()
end
genometools-1.5.1/testdata/gtscripts/encseq.lua000066400000000000000000000165201211610345200216640ustar00rootroot00000000000000--[[
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the Encseq class

dnaseqfile = arg[1].."/lua_dnaseq.fas"
aaseqfile = arg[1].."/lua_aaseq.fas"
dseq1 = "agtccagctgtcagctagcgggcccgatgatatttt"
dseq2 = "gtgctgtac"
aaseq1 = "MVHFTAEEKAAVTSLWSKMNVEEAGGEALG"
aaseq2 = "KMNAVE"
idxsuffixes = {'esq','des','ssp','sds','al1'}

function run_test_num_seqs(es)
  assert(es:num_of_sequences() == 2)
end

function run_test_num_files(es)
  assert(es:num_of_files() == 1)
end

function run_test_descriptions(es)
  rval, err = pcall(GenomeTools_encseq.description, es, 2)
  assert(not rval)
  assert(string.find(err, "cannot exceed number of sequences"))
end

function run_test_total_length(es)
  assert(es:total_length() == 46)
end

function run_test_total_length_protein(es)
  assert(es:total_length() == 37)
end

function run_test_get_encoded_char(es, seq1, seq2)
  local a = es:alphabet()
  for i=1,seq1:len() do
    assert(a:decode(es:get_encoded_char(i-1, 0)) == seq1:sub(i,i))
    assert(es:get_decoded_char(i-1, 0) == seq1:sub(i,i))
  end
  for i=seq2:len(),1,-1 do
    assert(a:decode(es:get_encoded_char(seq2:len()-i, 1)) == seq2:sub(i,i))
    assert(es:get_decoded_char(seq2:len()-i, 1) == seq2:sub(i,i))
  end
  rval, err = pcall(GenomeTools_encseq.get_encoded_char, es, 100, 0)
  assert(not rval)
  assert(string.find(err, "cannot exceed"))
end

function run_test_seq_startpos(es)
  assert(es:seqstartpos(0) == 0)
  assert(es:seqstartpos(1) == 37)
  rval, err = pcall(GenomeTools_encseq.seqstartpos, es, 2)
  assert(not rval)
  assert(string.find(err, "cannot exceed number of sequences"))
end

function run_test_seq_startpos_protein(es)
  assert(es:seqstartpos(0) == 0)
  assert(es:seqstartpos(1) == 31)
  rval, err = pcall(GenomeTools_encseq.seqstartpos, es, 2)
  assert(not rval)
  assert(string.find(err, "cannot exceed number of sequences"))
end

function run_test_seq_length(es)
  assert(es:seqlength(0) == 36)
  assert(es:seqlength(1) == 9)
  rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
  assert(not rval)
  assert(string.find(err, "cannot exceed number of sequences"))
end

function run_test_seq_length_protein(es)
  assert(es:seqlength(0) == 30)
  assert(es:seqlength(1) == 6)
  rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
  assert(not rval)
  assert(string.find(err, "cannot exceed number of sequences"))
end

function run_test_file_length(es)
  assert(es:effective_filelength(0) == 46)
  rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
  assert(not rval)
  assert(string.find(err, "cannot exceed"))
end

function run_test_file_length_protein(es)
  assert(es:effective_filelength(0) == 37)
  rval, err = pcall(GenomeTools_encseq.seqlength, es, 2)
  assert(not rval)
  assert(string.find(err, "cannot exceed"))
end

function run_test_seq_substr_encoded(es, seq1, seq2)
  start = 3
  stop = 13
  res = es:extract_encoded(start, stop)
  a = es:alphabet()
  for i=start,stop do
    assert(a:decode(res[i-start+1]) == seq1:sub(i+1,i+1))
  end
  start = es:seqstartpos(1)
  stop = start + 4
  res = es:extract_encoded(start, stop)
  for i=start,stop do
    assert(a:decode(res[i-start+1]) == seq2:sub(i-start+1,i-start+1))
  end
  rval, err = pcall(GenomeTools_encseq.extract_encoded, es, 3, 1)
  assert(not rval)
  assert(string.find(err, "range endposition"))
  rval, err = pcall(GenomeTools_encseq.extract_encoded, es, 300, 500)
  assert(not rval)
  assert(string.find(err, "cannot exceed"))
  
end

function run_test_seq_substr_decoded(es, seq1, seq2)
  start = 3
  stop = 13
  res = es:extract_decoded(start, stop)
  a = es:alphabet()
  assert(res == seq1:sub(start+1,stop+1))
  start = es:seqstartpos(1)
  stop = start + 4
  res = es:extract_decoded(start, stop)
  assert(res == seq2:sub(1,5))
  rval, err = pcall(GenomeTools_encseq.extract_decoded, es, 3, 1)
  assert(not rval)
  assert(string.find(err, "range endposition"))
  rval, err = pcall(GenomeTools_encseq.extract_decoded, es, 300, 500)
  assert(not rval)
  assert(string.find(err, "cannot exceed"))
end

function run_test_seq_substr_sequential(es, seq1, seq2)
  start = 3
  stop = 13
  er = es:create_reader_with_readmode(0, start)
  a = es:alphabet()
  for i=start,stop do
    assert(a:decode(er:next_encoded_char()) == seq1:sub(i+1,i+1))
  end
  start = es:seqstartpos(1)
  stop = start + 4
  er = es:create_reader_with_readmode(0, start)
  for i=start,stop do
    encchar = a:decode(er:next_encoded_char())
    seqchar = seq2:sub(i-start+1, i-start+1)
    assert(encchar == seqchar)
  end
  rval, err = pcall(GenomeTools_encseq.create_reader_with_readmode, es, 0, 300)
  assert(not rval)
  assert(string.find(err, "cannot exceed"))
end    

ee = gt.encseq_encoder_new()
ee:encode({dnaseqfile}, "dnaseqfile")
ee:encode({aaseqfile}, "aaseqfile")

el = gt.encseq_loader_new()
es = el:load("dnaseqfile")
run_test_descriptions(es)
run_test_num_seqs(es)
run_test_total_length(es)
run_test_num_files(es)
run_test_get_encoded_char(es, dseq1, dseq2)
run_test_seq_length(es)
run_test_seq_startpos(es)
run_test_file_length(es)
run_test_seq_substr_encoded(es, dseq1, dseq2)
run_test_seq_substr_decoded(es, dseq1, dseq2)
run_test_seq_substr_sequential(es, dseq1, dseq2)
a = gt.alphabet_new_dna()
eb = gt.encseq_builder_new(a)
eb:enable_multiseq_support()
eb:add_string(dseq1, "seq1")
eb:add_string(dseq2, "seq2")
es = eb:build()
run_test_descriptions(es)
run_test_num_seqs(es)
run_test_total_length(es)
run_test_num_files(es)
run_test_get_encoded_char(es, dseq1, dseq2)
run_test_seq_length(es)
run_test_seq_startpos(es)
run_test_file_length(es)
run_test_seq_substr_encoded(es, dseq1, dseq2)
run_test_seq_substr_decoded(es, dseq1, dseq2)
run_test_seq_substr_sequential(es, dseq1, dseq2)

es = el:load("aaseqfile")
run_test_descriptions(es)
run_test_num_seqs(es)
run_test_total_length_protein(es)
run_test_num_files(es)
run_test_get_encoded_char(es, aaseq1, aaseq2)
run_test_seq_length_protein(es)
run_test_seq_startpos_protein(es)
run_test_file_length_protein(es)
run_test_seq_substr_encoded(es, aaseq1, aaseq2)
run_test_seq_substr_decoded(es, aaseq1, aaseq2)
run_test_seq_substr_sequential(es, aaseq1, aaseq2)

a = gt.alphabet_new_protein()
eb = gt.encseq_builder_new(a)
eb:enable_multiseq_support()
eb:add_string(aaseq1, "seq1")
eb:add_string(aaseq2, "seq2")
es = eb:build()
run_test_descriptions(es)
run_test_num_seqs(es)
run_test_total_length_protein(es)
run_test_num_files(es)
run_test_get_encoded_char(es, aaseq1, aaseq2)
run_test_seq_length_protein(es)
run_test_seq_startpos_protein(es)
run_test_file_length_protein(es)
run_test_seq_substr_encoded(es, aaseq1, aaseq2)
run_test_seq_substr_decoded(es, aaseq1, aaseq2)
run_test_seq_substr_sequential(es, aaseq1, aaseq2)
genometools-1.5.1/testdata/gtscripts/feature_stuff.lua000066400000000000000000000044241211610345200232500ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for FeatureIndex and FeatureStream classes

function usage()
io.stderr:write(string.format("Usage: %s testdata_dir\n", arg[0]))
  io.stderr:write("Test the FeatureIndex and FeatureStream bindings.\n")
  os.exit(1)
end


if #arg == 1 then
  testdata = arg[1]
else
  usage()
end

-- set up the feature stream
genome_stream = gt.gff3_in_stream_new_sorted(testdata.."/gff3_file_1_short.txt")
feature_index = gt.feature_index_memory_new()
genome_stream = gt.feature_stream_new(genome_stream, feature_index)
collectgarbage()

feature = genome_stream:next_tree()
while (feature) do
  feature = genome_stream:next_tree()
end

features = feature_index:get_features_for_seqid("ctg123")
assert(features)
gff3_visitor = gt.gff3_visitor_new()

for i,feature in ipairs(features) do
  feature:accept(gff3_visitor)
end

range = gt.range_new(1, 100)

-- more tests
fi    = gt.feature_index_memory_new()
sr    = gt.region_node_new("chr1", 1, 100)
gf    = gt.feature_node_new("chr1", "gene", 1, 100 , "+")
rval, err = pcall(GenomeTools_feature_index.add_feature_node, fi, nil)
assert(not rval)
assert(string.find(err, "genome_node expected"))
rval, err = pcall(GenomeTools_feature_index.add_region_node, fi, nil)
assert(not rval)
assert(string.find(err, "genome_node expected"))
rval, err = pcall(GenomeTools_feature_index.add_region_node, fi, gf)
assert(not rval)
assert(string.find(err, "not a region node"))
fi:add_region_node(sr)
fi:add_feature_node(gf)
genometools-1.5.1/testdata/gtscripts/filter_metadata_test_all_strings.lua000066400000000000000000000003071211610345200271670ustar00rootroot00000000000000name        = "name"
author      = "author"
version     = "1.0"
email       = "email@example.com"
short_descr = "short description"
description = "description"

function filter(gn)
  return true
end
genometools-1.5.1/testdata/gtscripts/filter_metadata_test_author_function.lua000066400000000000000000000003651211610345200300610ustar00rootroot00000000000000function name()
  return "name"
end

function author()
  str = "author"
  return str
end

version     = "1.0"
email       = "email@example.com"
short_descr = "short description"
description = "description"

function filter(gn)
  return true
end
genometools-1.5.1/testdata/gtscripts/filter_metadata_test_description_function.lua000066400000000000000000000005241211610345200310770ustar00rootroot00000000000000function name()
  return "name"
end

function author()
  str = "author"
  return str
end

version = function()
  return "1.0"
end

function email()
  return "email" .. "@" .. "example.com"
end

function short_descr()
  return "short description"
end

function description()
  return "description"
end

function filter(gn)
  return true
end
genometools-1.5.1/testdata/gtscripts/filter_metadata_test_email_function.lua000066400000000000000000000004471211610345200276470ustar00rootroot00000000000000function name()
  return "name"
end

function author()
  str = "author"
  return str
end

version = function()
  return "1.0"
end

function email()
  return "email" .. "@" .. "example.com"
end

short_descr = "short description"
description = "description"

function filter(gn)
  return true
end
genometools-1.5.1/testdata/gtscripts/filter_metadata_test_error_function.lua000066400000000000000000000005351211610345200277070ustar00rootroot00000000000000function name()
  return "name"
end

function author()
  str = "author"
  barf()
  return str
end

version = function()
  return "1.0"
end

function email()
  return "email" .. "@" .. "example.com"
end

function short_descr()
  return "short description"
end

function description()
  return "description"
end

function filter(gn)
  return true
end
genometools-1.5.1/testdata/gtscripts/filter_metadata_test_name_function.lua000066400000000000000000000003271211610345200274750ustar00rootroot00000000000000function name()
  return "name"
end

author      = "author"
version     = "1.0"
email       = "email@example.com"
short_descr = "short description"
description = "description"

function filter(gn)
  return true
end
genometools-1.5.1/testdata/gtscripts/filter_metadata_test_short_description_function.lua000066400000000000000000000005241211610345200323160ustar00rootroot00000000000000function name()
  return "name"
end

function author()
  str = "author"
  return str
end

version = function()
  return "1.0"
end

function email()
  return "email" .. "@" .. "example.com"
end

function short_descr()
  return "short description"
end

function description()
  return "description"
end

function filter(gn)
  return true
end
genometools-1.5.1/testdata/gtscripts/filter_metadata_test_version_function.lua000066400000000000000000000004121211610345200302350ustar00rootroot00000000000000function name()
  return "name"
end

function author()
  str = "author"
  return str
end

version = function()
  return "1.0"
end

email       = "email@example.com"
short_descr = "short description"
description = "description"

function filter(gn)
  return true
end
genometools-1.5.1/testdata/gtscripts/filter_test_LTR.lua000066400000000000000000000016761211610345200234610ustar00rootroot00000000000000name        = "LTR node type filter"
author      = "Sascha Kastens"
version     = "1.0"
email       = "sascha.kastens@studium.uni-hamburg.de"
short_descr = "Select nodes with two long terminal repeats."
description = "Selects a node if it contains a node of type " ..
              "LTR_retrotransposon with two child nodes of type " ..
              "long_terminal_repeat."

function filter(gn)
  target = "LTR_retrotransposon"
  subtarget = "long_terminal_repeat"
  gfi = gt.feature_node_iterator_new(gn)

  curnode = gfi:next()
  found_target = false;
  count = 0

  while not(curnode == nil) do
    if (curnode:get_type() == target) then
      found_target = true
    elseif ((found_target == true) and (curnode:get_type() == subtarget)) then
      count = count + 1
    end
    curnode = gfi:next()
  end

  if ((found_target == true) and (count == 2)) then
    return false
  elseif found_target == false then
    return false
  end

  return true
end
genometools-1.5.1/testdata/gtscripts/filter_test_frame_attribute.lua000066400000000000000000000012301211610345200261570ustar00rootroot00000000000000name        = "ORF filter w/o frame"
author      = "Sascha Kastens"
version     = "1.0"
email       = "sascha.kastens@studium.uni-hamburg.de"
short_descr = "Selects nodes with ORF frame information."
description = "Selects a node if it contains a node of type " ..
              "reading_frame with frame information."

function filter(gn)
  gfi = gt.feature_node_iterator_new(gn)

  target = "reading_frame"

  curnode = gfi:next()
  count = 0

  while not(curnode == nil) do

    if (curnode:get_type() == target) then
      if (curnode:get_attribute("frame") == nil) then
        return true
      end
    end
    curnode = gfi:next()
  end

  return false
end
genometools-1.5.1/testdata/gtscripts/filter_test_nodetype.lua000066400000000000000000000007241211610345200246400ustar00rootroot00000000000000name        = "Name here"
author      = "Sascha Kastens"
version     = "1.0"
email       = "sascha.kastens@studium.uni-hamburg.de"
short_descr = "Short description here."
description = "Description here"
			    
function filter(gn)
  target = "exon"
  gfi = gt.feature_node_iterator_new(gn)

  curnode = gfi:next()

  while not(curnode == nil) do

    if (curnode:get_type() == target) then
      return false
    end
    curnode = gfi:next()
  end

  return true
end
genometools-1.5.1/testdata/gtscripts/filter_test_orf_pos_strand.lua000066400000000000000000000011161211610345200260270ustar00rootroot00000000000000name        = "Name here"
author      = "Sascha Kastens"
version     = "1.0"
email       = "sascha.kastens@studium.uni-hamburg.de"
short_descr = "Short description here."
description = "Description here"

function filter(gn)
  target = "reading_frame"
  gfi = gt.feature_node_iterator_new(gn)

  curnode = gfi:next()
  count = 0

  while not(curnode == nil) do

    if (curnode:get_type() == target) then
      if (curnode:get_strand() == '+') then
        count = count + 1
      end
    end
    curnode = gfi:next()
  end

  if (count >= 2) then
    return false
  end

  return true
end
genometools-1.5.1/testdata/gtscripts/filter_test_orflength.lua000066400000000000000000000011321211610345200247730ustar00rootroot00000000000000name        = "Name here"
author      = "Sascha Kastens"
version     = "1.0"
email       = "sascha.kastens@studium.uni-hamburg.de"
short_descr = "Short description here."
description = "Description here"

function filter(gn)
  target = "reading_frame"
  gfi = gt.feature_node_iterator_new(gn)

  curnode = gfi:next()

  while not(curnode == nil) do

    if (curnode:get_type() == target) then
      rng = curnode:get_range()
      length = rng:get_end() - rng:get_start() + 1
      if not((length % 3) == 0) then
        return true
      end
    end
    curnode = gfi:next()
  end

  return false
end
genometools-1.5.1/testdata/gtscripts/filter_test_syntax_fail.lua000066400000000000000000000007121211610345200253270ustar00rootroot00000000000000name        = "Name here"
author      = "Sascha Kastens"
version     = "1.0"
email       = "sascha.kastens@studium.uni-hamburg.de"
short_descr = "Short description here."
description = "Description here"

function filter(gn)
  target = "exon"
  gfi = gt.feature_node_iterator_new(gn)

  curnode = gfi:next()

  whie not(curnode == nil) do

    if (curnode:get_type() == target) then
      return false
    end
    curnode = gfi:next()
  end

  ret true

end
genometools-1.5.1/testdata/gtscripts/filter_test_wrong_function_name.lua000066400000000000000000000007331211610345200270520ustar00rootroot00000000000000name        = "Name here"
author      = "Sascha Kastens"
version     = "1.0"
email       = "sascha.kastens@studium.uni-hamburg.de"
short_descr = "Short description here."
description = "Description here"

function wrong_function_name(gn)
  target = "exon"
  gfi = gt.feature_node_iterator_new(gn)

  curnode = gfi:next()

  while not(curnode == nil) do

    if (curnode:get_type() == target) then
      return false
    end
    curnode = gfi:next()
  end

  return true

end
genometools-1.5.1/testdata/gtscripts/filter_test_wrong_nodetype.lua000066400000000000000000000007141211610345200260530ustar00rootroot00000000000000name        = "Name here"
author      = "Sascha Kastens"
version     = "1.0"
email       = "sascha.kastens@studium.uni-hamburg.de"
short_descr = "Short description here."
description = "Description here"

function filter(gn)
  target = "xon"
  gfi = gt.feature_node_iterator_new(gn)

  curnode = gfi:next()

  while not(curnode == nil) do

    if (curnode:get_type() == target) then
      return false
    end
    curnode = gfi:next()
  end

  return true
end
genometools-1.5.1/testdata/gtscripts/genome_node.lua000066400000000000000000000071101211610345200226600ustar00rootroot00000000000000--[[
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the GenomeNode interface

function count_children(parent)
  count = 0
  gfi = gt.feature_node_iterator_new(parent)
  curnode = gfi:next()
  while not(curnode == nil) do
      count = count + 1
      curnode = gfi:next()
  end
  return count
end

-- testing gt.feature_node_new
range = gt.range_new(1, 100)
rval, err = pcall(gt.feature_node_new, nil, nil, range:get_start(), range:get_end(), "+")
assert(not rval)
rval, err = pcall(gt.feature_node_new, "seqid", nil, range:get_start(), range:get_end(), "+")
assert(not rval)
rval, err = pcall(gt.feature_node_new, "seqid", "gene", "test", "+")
assert(not rval)
rval, err = pcall(gt.feature_node_new, "seqid", "gene", range:get_start(), range:get_end(), "plus")
assert(not rval)
assert(string.find(err, "strand string must have length 1"))
rval, err = pcall(gt.feature_node_new, "seqid", "gene", range:get_start(), range:get_end(), "p")
assert(not rval)
assert(string.find(err, "invalid strand"))
gn = gt.feature_node_new("seqid", "gene", range:get_start(), range:get_end(), "+")
assert(not gn:is_marked())
gn:mark()
assert(gn:is_marked())

parent = gt.feature_node_new("seqid", "gene", range:get_start(), range:get_end(), "+")
child  = gt.feature_node_new("seqid", "exon", range:get_start(), range:get_end(), "+")
parent:add_child(child)
assert(not parent:is_marked(parent))
assert(not parent:contains_marked(parent))
child:mark()
child  = nil; collectgarbage() -- being nasty
assert(not parent:is_marked(parent))
assert(parent:contains_marked(parent))

-- testing genome_node:get_filename
rval, fn = pcall(gn.get_filename, gn)
assert(rval)
assert(string.find(fn, "^generated$"))

-- testing genome_node:remove_leaf
-- testing removal of leaves which are direct children
parent = gt.feature_node_new("seqid", "gene", range:get_start(), range:get_end(), "+")
child  = gt.feature_node_new("seqid", "exon", range:get_start(), range:get_end(), "+")
parent:add_child(child)
child  = gt.feature_node_new("seqid", "exon", range:get_start(), range:get_end(), "+")
parent:add_child(child)
assert(count_children(parent) == 3)
parent:remove_leaf(child)
assert(count_children(parent) == 2)
parent:add_child(child)
assert(count_children(parent) == 3)
-- testing removal of leaves which are non-direct children
newchild = gt.feature_node_new("seqid", "exon", range:get_start(), range:get_end(), "+")
child:add_child(newchild)
assert(count_children(parent) == 4)
parent:remove_leaf(newchild)
assert(count_children(parent) == 3)

-- testing gt.region_node_new
range = gt.range_new(1, 100)
rval, err = pcall(gt.region_node_new, nil, range:get_start(), range:get_end())
assert(not rval)
rval, err = pcall(gt.region_node_new, "chr1", "test")
assert(not rval)
gn = gt.region_node_new("chr1", range:get_start(), range:get_end())
genometools-1.5.1/testdata/gtscripts/genome_stream.lua000066400000000000000000000035041211610345200232310ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the GenomeStream interface

function usage()
  io.stderr:write(string.format("Usage: %s testdata_dir\n", arg[0]))
  io.stderr:write("Test the GenomeStream bindings.\n")
  os.exit(1)
end

if arg[1] then
  testdata = arg[1]
else
  usage()
end

-- testing gt.gff3_in_stream_new_sorted
rval, err = pcall(gt.gff3_in_stream_new_sorted, "undefined")
assert(not rval)
assert(string.find(err, "does not exist"))

-- test correct file
gs = gt.gff3_in_stream_new_sorted(testdata.."/gff3_file_1_short.txt")
gn = gs:next_tree()
while (gn) do
  -- do something with the node...
  gn = gs:next_tree()
end

-- test corrupt file
gs = gt.gff3_in_stream_new_sorted(testdata.."/gt_gff3_fail_1.gff3")
rval, err = pcall(gs.next_tree, gs)
assert(not rval)
assert(string.find(err, "already been defined"))

-- test unsorted file
gs = gt.gff3_in_stream_new_sorted(testdata.."/unsorted_gff3_file.txt")
rval, err = pcall(gs.next_tree, gs)
assert(not rval)
assert(string.find(err, "is not sorted"))
genometools-1.5.1/testdata/gtscripts/genome_visitor.lua000066400000000000000000000024361211610345200234400ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the GFF3 GenomeVisitor (similar to the gff3
-- tool)

function usage()
  io.stderr:write(string.format("Usage: %s GFF3_file\n", arg[0]))
  io.stderr:write("Parse and output the given GFF3_file.\n")
  os.exit(1)
end

if #arg == 1 then
  gff3file = arg[1]
else
  usage()
end

gs = gt.gff3_in_stream_new_sorted(gff3file)
gv = gt.gff3_visitor_new()
gn = gs:next_tree()
while (gn) do
  gn:accept(gv)
  gn = gs:next_tree()
end
genometools-1.5.1/testdata/gtscripts/gff3.lua000066400000000000000000000025521211610345200212330ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the GFF3 output stream (similar to the gff3
-- tool)

function usage()
  io.stderr:write(string.format("Usage: %s GFF3_file\n", arg[0]))
  io.stderr:write("Parse and output the given GFF3_file.\n")
  os.exit(1)
end

if #arg == 1 then
  gff3file = arg[1]
else
  usage()
end

in_stream = gt.gff3_in_stream_new_sorted(gff3file)
out_stream = gt.gff3_out_stream_new(in_stream)
in_stream = nil; collectgarbage() -- being nasty
gn = out_stream:next_tree()
while (gn) do
  gn = out_stream:next_tree()
end
genometools-1.5.1/testdata/gtscripts/ii_fail.lua000066400000000000000000000032721211610345200220020ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for AnnotationSketch (similar to the sketch tool)

function usage()
  io.stderr:write(string.format("Usage: %s GFF3_file\n", arg[0]))
  io.stderr:write("Try to create PNG representation of GFF3 annotation file.\n")
  os.exit(1)
end

if #arg == 1 then
  gff3file = arg[1]
else
  usage()
end

in_stream = gt.gff3_in_stream_new_sorted(gff3file)
feature_index = gt.feature_index_memory_new()
feature_stream = gt.feature_stream_new(in_stream, feature_index)
in_stream = nil; collectgarbage() -- being nasty
gn = feature_stream:next_tree()
-- fill feature index
while (gn) do
  gn = feature_stream:next_tree()
end

seqid = feature_index:get_first_seqid()
range = feature_index:get_range_for_seqid(seqid)

ii = {}

diagram = gt.diagram_new(feature_index, seqid, range)
canvas = gt.canvas_cairo_file_new_png(800, 200, ii)
diagram:sketch(canvas)
genometools-1.5.1/testdata/gtscripts/mathsupport.lua000066400000000000000000000017361211610345200227770ustar00rootroot00000000000000--[[
  Copyright (c) 2011 Sascha Steinbiss 
  Copyright (c) 2011 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the mathsupport module
-- must be called with seed 12345

assert(gt.rand_max(100000) == 90441)
genometools-1.5.1/testdata/gtscripts/memleak.lua000066400000000000000000000022031211610345200220120ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

function usage()
  io.stderr:write(string.format("Usage: %s GFF3_file\n", arg[0]))
  os.exit(1)
end

if #arg == 1 then
  gff3file = arg[1]
else
  usage()
end

in_stream = gt.gff3_in_stream_new_sorted(gff3file)
gff3_visitor = gt.gff3_visitor_new()
gn = in_stream:next_tree()
gn:accept(gff3_visitor)
genometools-1.5.1/testdata/gtscripts/range.lua000066400000000000000000000023651211610345200215040ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the Range class

range = gt.range_new(1, 1000)
assert(range:get_start() == 1)
assert(range:get_end() == 1000)

rval, err = pcall(gt.range_new, 1000, 1)
assert(not rval)
assert(string.find(err, "must be <= endpos"))

ranges = {}
for i = 1, 100 do
  range = gt.range_new(i, i+1)
  table.insert(ranges, range)
end
ranges = gt.ranges_sort(ranges)
assert(gt.ranges_are_sorted(ranges))
genometools-1.5.1/testdata/gtscripts/recmap.lua000066400000000000000000000037331211610345200216570ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for AnnotationSketch (similar to the sketch tool)

function usage()
  io.stderr:write(string.format("Usage: %s PNG_file GFF3_file\n", arg[0]))
  io.stderr:write("Create PNG representation of GFF3 annotation file.\n")
  os.exit(1)
end

if #arg == 1 then
  gff3file = arg[1]
else
  usage()
end

in_stream = gt.gff3_in_stream_new_sorted(gff3file)
feature_index = gt.feature_index_memory_new()
feature_stream = gt.feature_stream_new(in_stream, feature_index)
in_stream = nil; collectgarbage() -- being nasty
gn = feature_stream:next_tree()
-- fill feature index
while (gn) do
  gn = feature_stream:next_tree()
end

seqid = feature_index:get_first_seqid()
range = feature_index:get_range_for_seqid(seqid)

ii = gt.imageinfo_new()

diagram = gt.diagram_new(feature_index, seqid, range)
layout = gt.layout_new(diagram, 800)
height = layout:get_height()
canvas = gt.canvas_cairo_file_new_png(800, height, ii)
layout:sketch(canvas)
if #(ii:get_recmaps()) ~= 16 then
  os.exit(1)
end
for _,v in pairs(ii:get_recmaps()) do
    print(string.format("%.0f,%.0f,%.0f,%.0f, %s",v.nw_x, v.nw_y, v.se_x, v.se_y, v.feature_ref:get_type()))
end

genometools-1.5.1/testdata/gtscripts/require_gtlua.lua000066400000000000000000000016541211610345200232600ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- test if gtdata/modules has been added correctly to package.path
require 'gtlua'
genometools-1.5.1/testdata/gtscripts/scorematrix2c.lua000066400000000000000000000034141211610345200231710ustar00rootroot00000000000000--[[
  Copyright (c) 2007-2009 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the ScoreMatrix class

function usage()
  io.stderr:write(string.format("Usage: %s score_matrix_file\n", arg[0]))
  io.stderr:write("Parse protein score_matrix_file and show it as C program.\n")
  os.exit(1)
end

if #arg == 1 then
  score_matrix_file = arg[1]
else
  usage()
end

protein_alpha = gt.alphabet_new_protein()
score_matrix = gt.score_matrix_new_read_protein(score_matrix_file)
assert(protein_alpha:size() == score_matrix:get_dimension())

print("#include \n")
print("int main(int argc, char *argv[])")
print("{")
print("  int score_matrix[CHAR_MAX][CHAR_MAX] = {{0}};")
for idx1 = 0, score_matrix:get_dimension()-1 do
  for idx2 = 0, score_matrix:get_dimension()-1 do
    print(string.format("  score_matrix['%s']['%s'] = %d;",
          protein_alpha:decode(idx1), protein_alpha:decode(idx2),
          score_matrix:get_score(idx1, idx2)))
  end
end
print("  return 0;")
print("}")
genometools-1.5.1/testdata/gtscripts/scorematrix2stdout.lua000066400000000000000000000040111211610345200242630ustar00rootroot00000000000000--[[
  Copyright (c) 2009 Gordon Gremme 

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for the ScoreMatrix class

function usage()
  io.stderr:write(string.format("Usage: %s score_matrix_file\n", arg[0]))
  io.stderr:write("Parse score_matrix_file and show it on stdout.\n")
  os.exit(1)
end

if #arg == 1 then
  score_matrix_file = arg[1]
else
  usage()
end

blast_alphabet = gt.alphabet_new_empty()
blast_alphabet:add_mapping('A')
blast_alphabet:add_mapping('R')
blast_alphabet:add_mapping('N')
blast_alphabet:add_mapping('D')
blast_alphabet:add_mapping('C')
blast_alphabet:add_mapping('Q')
blast_alphabet:add_mapping('E')
blast_alphabet:add_mapping('G')
blast_alphabet:add_mapping('H')
blast_alphabet:add_mapping('I')
blast_alphabet:add_mapping('L')
blast_alphabet:add_mapping('K')
blast_alphabet:add_mapping('M')
blast_alphabet:add_mapping('F')
blast_alphabet:add_mapping('P')
blast_alphabet:add_mapping('S')
blast_alphabet:add_mapping('T')
blast_alphabet:add_mapping('W')
blast_alphabet:add_mapping('Y')
blast_alphabet:add_mapping('V')
blast_alphabet:add_mapping('B')
blast_alphabet:add_mapping('Z')
blast_alphabet:add_mapping('X')
blast_alphabet:add_wildcard('*')

blast_matrix = gt.score_matrix_new_read(score_matrix_file, blast_alphabet)
assert(blast_alphabet:size() == blast_matrix:get_dimension())

blast_matrix:show()
genometools-1.5.1/testdata/gtscripts/show_seqids.lua000066400000000000000000000027201211610345200227330ustar00rootroot00000000000000--[[
  Copyright (c) 2007 Gordon Gremme 
  Copyright (c) 2007 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing some Lua bindings for FeatureIndex

function usage()
io.stderr:write(string.format("Usage: %s GFF3_file\n", arg[0]))
  io.stderr:write("Show sequence ids contained in GFF3 annotation file.\n")
  os.exit(1)
end


if #arg == 1 then
  gff3file = arg[1]
else
  usage()
end

in_stream = gt.gff3_in_stream_new_sorted(gff3file)
feature_index = gt.feature_index_memory_new()
feature_stream = gt.feature_stream_new(in_stream, feature_index)
gn = feature_stream:next_tree()
-- fill feature index
while (gn) do
  gn = feature_stream:next_tree()
end

seqids = feature_index:get_seqids()
for _, v in ipairs(seqids) do
  print(v)
end
genometools-1.5.1/testdata/gtscripts/sketch.lua000066400000000000000000000040761211610345200216720ustar00rootroot00000000000000--[[
  Copyright (c) 2007-2008 Gordon Gremme 
  Copyright (c) 2007-2008 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

-- testing the Lua bindings for AnnotationSketch (similar to the sketch tool)

function usage()
  io.stderr:write(string.format("Usage: %s PNG_file GFF3_file\n", arg[0]))
  io.stderr:write("Create PNG representation of GFF3 annotation file.\n")
  os.exit(1)
end

if #arg == 2 then
  pngfile  = arg[1]
  gff3file = arg[2]
else
  usage()
end

in_stream = gt.gff3_in_stream_new_sorted(gff3file)
feature_index = gt.feature_index_memory_new()
feature_stream = gt.feature_stream_new(in_stream, feature_index)
in_stream = nil; collectgarbage() -- being nasty
gn = feature_stream:next_tree()
-- fill feature index
while (gn) do
  gn = feature_stream:next_tree()
end

seqid = feature_index:get_first_seqid()
range = feature_index:get_range_for_seqid(seqid)

ii = gt.imageinfo_new()

diagram = gt.diagram_new(feature_index, seqid, range)
layout = gt.layout_new(diagram, 800)
height = layout:get_height()
canvas = gt.canvas_cairo_file_new_png(800, height, ii)
-- nil as ImageInfo parameter must be ok
canvas2 = gt.canvas_cairo_file_new_png(800, height, nil)

-- test sketching with image info
layout:sketch(canvas)
canvas:to_file(pngfile)
if #(ii:get_recmaps()) ~= 16 then
  os.exit(1)
end

-- and without
layout:sketch(canvas2)
canvas2:to_file(pngfile)
genometools-1.5.1/testdata/header.gff3000066400000000000000000000000221211610345200176460ustar00rootroot00000000000000##gff-version   3
genometools-1.5.1/testdata/header_3_1_21.gff3000066400000000000000000000000271211610345200206170ustar00rootroot00000000000000##gff-version   3.1.21
genometools-1.5.1/testdata/hop/000077500000000000000000000000001211610345200164435ustar00rootroot00000000000000genometools-1.5.1/testdata/hop/10reads.fastq000066400000000000000000000036141211610345200207460ustar00rootroot00000000000000@126
TCCACCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTTCACCGCCGG
+
000KNGI8CKN/'5+.B(7L3<('BHI=2,D&*GCIFF()DJ9A.N.-LH223/A491C+K@AI)09ICDN
@127
ATTACCGGCGGTGAAAACCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAG
+
00@<-(GC=629<6HCD*;L*9>/I5'E94)@14CE=C)@)/.J*7J9F/@J9,*L:C++/52758*AN-.K*'L6*+4E9K4+B3G>2DL<:IJ8/=A97I><,&)G03L3,A:N>MBI8.K6@G&@:3J
@131
GATCACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAAAAGGCGAACTGGTGGTGCTTGGACGCA
+
00H-<.K+1+3,F)D'N;M@:47GH)E80M
@133
TATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTTTCACCGCCGGTAATGAAAAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTC
+
00000I708'.@;.'=*J<*-BJCI2+-:0*5-3I&>&*4BEH4J+=79L4KN69+F9G.(3>:)=61+5LM3(
@137
GGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTCATTACCGGCGGTGAAACCTGCCATCA
+
I?7H+0F&510-4(<8C>);:E'C,4AHKAD*AD>GN3,*;A(9<=8:IM):ADKE@/'HE28+/?LG(D0*6?62(I>FE1H026N(8EE0=GH9?>FMA6LEJE,E:5<875=;4MG1>1=LFC?FF.EN/B'EBJ&+)3EE3*6BC7?M9::26;-HN?F5/D+I9;22D3NEJ'6'>,N,Dsomegenome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC
TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT
CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG
CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATAC
CGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGG
CGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGA
ATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTC
TACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGG
TAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATAT
CAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG
GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA
TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG
GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA
AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC
CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG
GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT
TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG
CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA
AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT
GCCCGCAGAGTTTAACGCCGAGGGGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGAT
CTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATG
AAGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA
AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC
AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC
ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG
TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG
CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT
CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC
GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC
GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC
AAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTC
ATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCT
ACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAG
CGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCC
GACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGG
GCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC
GCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGC
CTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTA
TTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGT
CGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTC
GGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGA
CCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCT
CTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACT
GTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCGTTTGATGATGAAGAACTGA
AAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACATCAGCCGTTTGCTGGCGCAGATTTGCTACTA
CTTTGAAGCTGTTGCGCAGCTGCCGCAGGAGACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAAC
TTCGGCGATTTGACGGCGGGTCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGA
CCAACGTGAACGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGAC
GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAA
ATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGT
TAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAA
TCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATT
CTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATC
TGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAA
AGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCAT
CGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATC
TATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTC
CCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCG
ACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA
genometools-1.5.1/testdata/hop/hop_10reads.fastq000066400000000000000000000036041211610345200216130ustar00rootroot00000000000000@126
tccacccgccgtattgcggcaagccgcattccggctgatcacatggtgctgatggcaggtttcaccgccgg
+
000KJNGI8CKN/'5+.B(7L3<('BHI=2,D&*GCIFF()DJ9A.N.-LH223/A491C+KAI)09ICDN
@127
attaccggcggtgaaacctgccatcagcaccatgtgatcagccggaatgcggcttgccgcaatacggcgggtggactcag
+
00@<-(GC=629/I5'E94)@14CE=C)@)/.J*7J9F/@J9,*L:C++/52758*AN-.K*'L6*+4E9K4+B3G>2DL<:IJ8/=A97I><,&)G03L3,A:N>MBI8.K6@G&@:3J
@131
gatcacatggtgctgatggcaggtttcaccgccggtaatgaaaaaggcgaactggtggtgcttggacgca
+
00H-&*4BEH4J+=79L469+F9G.(3>:)+5LM3(
@137
ggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttcattaccggcggtgaaacctgccatca
+
I?7H+0F&510-4(<8C>);:E'C,4AHKAD*AD>GN3,*;A(9<=8:IM):ADKE@/'HE2;;;8+/?LG(D0*6?62(I>FE1H026N(8EE0=GH9?<>FMA6LEJE,E:5<875=;4MG1>1=LFC?FF.EN/B'EBJ&+)3EE3*6BC7?M9::26;-5/D+I9;22D3NEJ'6'>,N,D/I5'E94)@14CE=C)@)/.J*7J9F/@J9,*L:C++/52758*AN-.K*'L6*+4E9K4+B3G>2DL<:IJ8/=A97I><,&)G03L3,A:N>MBI8.K6@G&@:3J
@131
gatcacatggtgctgatggcaggtttcaccgccggtaatgaaaaaggcgaactggtggtgcttggacgca
+
00H-&*4BEH4J+=79L469+F9G.(3>:)+5LM3(
@137
ggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttcattaccggcggtgaaacctgccatca
+
I?7H+0F&510-4(<8C>);:E'C,4AHKAD*AD>GN3,*;A(9<=8:IM):ADKE@/'HE2;;;8+/?LG(D0*6?62(I>FE1H026N(8EE0=GH9?<>FMA6LEJE,E:5<875=;4MG1>1=LFC?FF.EN/B'EBJ&+)3EE3*6BC7?M9::26;-5/D+I9;22D3NEJ'6'>,N,D,BKN:6784B>;IAB':=;@-/6N:B,=J0+FG30)C6'CL.<+K<:
@142
gtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
+
00L=)H.405GF+=C-:A2<)>/>E>D4BE&+B:AK27>09
@143
acgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccg
+
0009F7HI90:/4GN2B&M59,*AM(0&60N&3F?3L=7EF7NMJ?N8N-.?2*0,<)0D2<&)8BJ*?LCL
@144
cgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccacca
+
000&C*&5GMB4=5F'LHH@)9=3J9G+3L(+FEJEC)>2:D(I/N',
@145
cgaactggtggtgcttggacgcaacggttccgactactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggacgttgacggggggt
+
0000IDD:);6.2JB:/3LKL3E7-2)'+3&.5J2(:6*;J4(D@C*>;NA;?;(AA7@*>K2J:1IHG&;F(7,.:'F;MK&2E.B=3-*(G-C9B:818I2J=@-
@146
tagaccccgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttt
+
00000-E6)/08HCK.;>I;?)*AN.5KCL/IHJB-3(83M;E4,I6ML65'JH/K5.7>8;B0'D
@149
cgcaggtatagaccccgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
+
0000+899@+,1HCGG2-M19*FE85BI:)5=953E4>)02&*'B@B'JB>BL/2+;,+'.5C,8;AHA+)2L?9*C4(;ABAA1@-6(/)61F2)2)DDD:5F,NGHB
@151
aacggttccgactactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggacgttgacggggtctatacctgcgacccgcgtcaggtgccg
+
000).K7JA0F29G5(;H:,?3N:A9NI&F8)>15L1<@5A7?JJ5.HBA1NB58='3BA(@:HDE&+0>)A*.<,'(77H&GG0/2L8(8<8'NN6F.:2+40*?/-3FN
@152
gcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccga
+
00/C+K;>474J:N,K0ECELMC++HE-*N7M+.DHH-=8AABJK8-C&-+-8)B5@.34DN/:1@8J;,)-.225E:BMN
@160
catcgcttcctggtaggacatcgacttcaacaacctcgcatcgggcacctgacgcgggtcgcaggtatagaccccgtcaacgtccgtccaaatctc
+
00000(75E,/5><-379KCL7D@3?JJB&)+G1K.HLK48?F1AG/5D:);'E:M6AEBIH>E70?:IN'D@-,GJ/N00FEC;/()=>@AI=D*
@162
tggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctt
+
00000/60K<.C;/E?7N:NG?&FDHD/J6?J25.*0:<4*/@N./JM'=:N:I-)19I,):'79N/>F?GA.898KJ>H:/6'?BIM31,M9HC@BHCC?C.NNG9',
@166
ttgacggggtctatacctgcgacccgcgtcaggtgcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctttcctacttcgg
+
0H(1;<1>(.83L>99474AE<2MC4./'J6;JL<7J.D?/=,//)I<,.;I(41'@AC&,<27H2:87G<&5NM)43&K372?MM97
@168
gcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctttcctacttcggcgctaaagttct
+
0;&6GM3<,86-2CL-2GH&(,KL>-9MFIG887I;F5@LL/FKH+&:17CB+9NF9,8/L9@<**EC,6M355/5KH+E4;KGH-I?@6(70AE;F.,D4F@GJ>-+4BEL&=J**1-:+@.3C&>DE;C&I/>85J)A';,L5:?A/I3<8F*.DJNC9C:-E
@172
tctggaactgggcgatgggggtaatggtgcgggggtgaagaactttagcgccgaagtaggaaagctccatcgcttcctggtaggacatcgacttcaacaacctcgca
+
0001??5DC7).//M7M5/;;12?N>7K))-5?0M(73HMFF:FI(/*=K:,='G+A7B6'4DILK0-DK@+>HI>A>N/0>GIEJD(3=6761:'>2B/@8/E
@177
agcgtacctggtgcttgaggatttccggtatttttaatcaggcaagggatctggaactgggcgatgg
+
000=7722(3?,M'..)E':EGCE(N'@K4/&>6&'C)1-/A;&:;-6&CM*74F)GGI/&5<3CE0+>4-5H,D7JF.-F(07>3?D:8=HL?
@185
caccaggtacgctcattggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctga
+
0005,B6(1MJ*9;+LB<=FIEKFG1E+@5BE-947?C2A8'H6<7G&8N2+14-0&A;7=?E*>FF'M
@188
ctcattggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctgaataacatggcaat
+
JIF22>.NJ0/45N.BB1*A&.M+,)E)2;:<.HA:1>1A52JMM80;I*E8@&AB1I:CJ
@189
gaacattgccatgttattcagattggaaatgcccttgaccggtaattcgtcttcatcacggctggcaccaatgagcgtacct
+
B1>7904BE&HG/K/3K9(9B.=J=G/G;<47-5*-9CFIA?((F5IJ:0CKLF8D?3FC759A(6=2618(7;EG2,/.LN=C)A97(2*K)E((*,G5D?*C-N4??DME&I6KL9M/1@6J?MF9F&D6/0(5FJ4K,;F0=M4A;=?1AN*:+N3+*J=?B1;)6&4:K9(,11IN7G-N1H35>GBBF0*3*'7'D>
@192
ccttcatccccggaccagaaacgctgaacattgccatgttattcagattggaaatgcccttgaccggtaattcgtcttcatcacggctggca
+
0E=;)>.K6)E;DEJI'(JF2@C1.=A+112CJCL&G?48>08LA(:0EK)JN0:A);@J;5(M&5GF37HDDHMF
@195
tggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctgaataacatggcaatgttcagcgtttctggtccggggatgaaagggatggtcggcatggc
+
00000)72BLGB>;:(/)&>@(39-N5F5>DL@H<>4C6J3N5KM76GN41/4D7)NM@N+,E)8,H7*I?*
@201
atgttcagcgtttctggtccggggatgaaagggatggtcggcatggcggcgcgcgtctttgcagc
+
0000:*NEE?65I4H;1+A/2;1*-H:=55FK.=,2&@1NH0N@>IC/6
@205
ggatggtcggcatggcggcgcgcgtctttgcagcgatgtcacgcgcccgtatttccgtggtgctgattacgc
+
?-E>9B;BJ7/51BA?:N70>+(:-?42:;N;7:-;@8IA.90.*
@207
agatgattgcgtaatcagcaccacggaaatacgggcgcgtgacatcgctgcaaagacgcgcgccgccatgccgaccatccctttcatcccccc
+
00=2G+8I>9(MFL8+20KIH6,7<*=69JH76+0MMB8;1+JDI''2:JB9=:F65<370I24K0A+LI
@210
gtcggcatggcggcgcgcgtctttgcagcgatgtcacgcgcccgtatttccgtggtgctgattacgcaatcatcttccgaatacagcatcagt
+
00K9EH2066:6B;;84DN9K=B9'9K2L?LH-'&FE.,&GMH0'';.(ML21:B<)2,F7F:@3;35->+NHMIC=7HK*I*1,55A3:1CN6,F?;'*=?(-))=-=A179M9C)M@@8B/=GD*J*5H&>9=L>;/0HB1)3GJ=)C:M&5DFAF;;8I2.0/-48*1:+@FK
@214
gcgcccgtatttccgtggtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaa
+
00*6C)6CJ1KCB@537DNHD=:'7I=7-62>0KB@9'HH/,;KNC;LA6@,,DI+9&+1L.934D?&B:*IMMB:73KKE=9L>3275,1-B;)MA8*
@216
gtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaatgcaggaagagttctacct
+
00000@K9(,DHFC0'+8(NC4F50H000D165&F/2M3GE?*A38?<>/:=A89(G0+-9L,'.'AHHAE((IE'9/?,')9E.253@3:EGG3J'--J,
@218
agcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaatgcaggaagagttctacctggaa
+
9(D-C320J22CKGGM;:48BA@A6?A4BKD-;5(3,J1CI87KA66>/?)&NG44;3A-1@2)*D:(9*2-09F
@219
ctccagtaagccttctttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcgctttgtggaacgcagaaactgatgctgtattcggaagatgattg
+
00>2B93(B?'7A,?A?@AMBJ;'&&.('?C,2;)2G4&CH82+166BLG>08JJHK30E*?69@-L51>K4,=-6'N(D7.-KI4E;,)+C?.()835);A6G77J7@849
@221
gccgttccgtcactgccagcggctccagtaagccttctttcagttccaggtagaactcttcctgca
+
00+(45D(>E;K+F=DH('H/D/';L&AF9F?*:J9AAJ35>G161--4'KIDE5,1C@??2(BD<
@223
tggccagccgttccgtcactgccagcggctccagtaagccttctttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcgctttgtggaacgca
+
00.IN9DJ'D;214><*69F3808DB(>GB+NEC4G7N19@=;E>A?3J0,@>NA55I+52>129J,GK)J4+G39'36NJJF9?8C?9:4'M0=6+E?5359,=G;K6,)F
@224
ataatggccagccgttccgtcactgccagcggctccagtaagccttctttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcg
+
0000FB5(>B0..-,6I,NA-J,>@I868,19H+/@F/N&.KCK>7C:B.(A:>2))<
@225
gcaggaagagttctacctggaactgaaagaaggcttactggagccgctggcagtgacggaacggctggccattatctcggt
+
E<,4@0B551<40I&:B>@54=;>+/,GAKAI9I&4139F&=:5)<3EEE3N))N2L6BHD':'*N2;AM<,17@5D)(@2
@227
aggtgcgcataccatcacctaccaccgagataatggccagccgttccgtcactgccagcggctccagta
+
2-@L-;1J.12J(<=G/5+FB5>*J6E;*=M&6M=-)17NDMK/*-,
@232
tgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaagaatttcgccgagatcccacgcaaggtgcgcataccatcacct
+
09CG+5)&7D80)D.M,07F=:==)A1'-*B(NC&B29NFB,?'HB4D,D1N20/9C@,>D:,'*2'A(01I>,?9@
@237
aattctttgccgcactggcccgcgccaatatcaacattgtcgccattgctcagggatcttctgaacgctcaatctctgtc
+
0157B=7C<<=MI/,(IB(F&<,N,56BLAM-JD-4I*M)C@E85LFAI+6AM9AAA&31*0N;I-MA'*KB6ELF@I,J
@238
cacgacagagattgagcgttcagaagatccctgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaagaatttcgccgaga
+
00(0A1L=+=A*+D8L16L&MMGH8K6/12?HH9@,3JH=*BA*8>>.5/,:7B<*G:+E+N?FIA9JD<6?5@?03,*<(*69889;2DEC
@239
ttaccacgacagagattgagcgttcagaagatccctgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaag
+
0000HD2NG95*B=N-='>60/M(BG=N4D9'4K7D2((E;@/?=0/=2)8J2ACK3B4C:;NN,/AK(3?H05M73&:&9;=
@240
caatatcaacattgtcgccattgctcagggatcttctgaacgctcaatctctgtcgtggtaaataac
+
00000=6G+NN&HM'>NC2C3D/+1F(FN=7D<345)@<**?;39?K7*'13EG@/7=J0N*H7I=.
@242
cagggatcttctgaacgctcaatctctgtcgtggtaaataacgatgatgcgaccactggcgtgcg
+
000007:?G*5843,G99L:3&*(
@245
gatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacgacagagattgagcgttcagaagatccct
+
000034E0J1)H=4FLJ6,9=6?>:M65EL+-ND-FGJ5515I-9+5AI)D69N:IF<;=5J:8N9:2I5D5J<+
@246
agcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacgacagagattgagcg
+
00BK,K4E-L>(L9''64A6@HH>>/)G&J20.JLI5&'J@8;2A&I,
@249
atcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacgacagagattgagcgttcagaagatc
+
09.'A&1&JAG@/A7I0J'01EB)F-I9I<7(M33,D>G-15'F&&'<>L-(5G?320(.+BC.8'+7L31GGI6G.247I933L9)>>'A.
@251
cctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacg
+
000,J=KE?;C-CD6AH@23+J@&8?3E1@8=JI./<=,>95.-8?0K/*>CF?L@)@*0E&GAAH&I.5>
@252
taacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttat
+
8@NMID/I)'8JKA26KH@K@2A7&?HH028&=:/6?H897F?2E=;D2+F6AAGM@*G13LKE<(
@253
tcagggatcttctgaacgctcaatctctgtcgtggtaaataacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcg
+
000;N3C2/@<'71NE1J<5B<-LID0H*,+N)G)E,4)=3-:?L;-2/(M56:LI1*:N.(AE9H96LJ6A=D1(:&N;0-:A>A0.JE1MM5LL@GG
@255
cacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacgacagagattgag
+
0000H<+'A4A.DG-<;.A.-HJ/7;5H=?KC8I0,5MH;2.F?=:0C,K4&9,4/)@JFHE8,H.&)G,I6:CN25BKDFM1+7/658=-M>H
@256
acgatgatgcgaccactggcgtgcgcgttactctcagatgctgttcaataccgatcaggttatcgaagtgtt
+
F+B11,?-9I:)@60;,KMKG&F'3@?.=9N)H/,BE-3/JF4?&?9B/8*:36.4746=<9D>?DH.D22J92N;>(J+7H6<9*
@258
atgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcgaagtgtttgtgattggcgtcggtggcgttggcgg
+
H-=2FK3C7*H7.9@&H:F4LD=(;+&.&I<3E87J,M+K+;1C2D-(=IIA47I-E46N;G7:E528K,0L1*-I?3/NG77H);&?*@+N=?
@259
ctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgt
+
=.I;NB,<<.JI/FK.,'J7ACL+NK=NH.2FM)5;9;7NBNL:,KB/)3MB6-0L:-5E-F>DJNEJ@,@63&04H?78E;B?G2DEGJMNJN.'8:8;3;F2C+'I17:0C
@260
atgctgttcaataccgatcaggttatcgaagtgtttgtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaa
+
000'9K5(G4<*/4A0BI3@19/KFD@.J>MMA96/-G6,2*/LCB-941HFK56=5L,29)8AI942(,/L5@+5KJI?/@;53(93B9B1:?J2=FN;B&@>.032/:M+1B52L=,/*DB=2'G7I<.J2;8H:*I>;GNNC@9G-='LKD;F'6E
@263
ttcagccagctttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcggtattga
+
0000;;0KD2-D-1L0)/M1@A3>,9@DE-4)DB-@*C>6=,?GK)J8J4.)2C47&9M1.N0='1D(>FBM65ID,1=);FB7D.7GDI1>+I1/L
@264
tcttcagccagctttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcg
+
000,?86K-E'/*60I@=2HGKM:)JDK'>C07HF.?;?)K+:A;))F3=NL)*D.LM1AB,N70-+78E2J&M(.*&D@'A-G)3.AF>1J
@265
gtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaaagctggctgaaga
+
000('9@7C:L8M/L7H//A-M:(-@FH.G255MD0M+;:1(DLJCH<.C,9+1N<-F=9*NG5:A)I31
@268
ccgcagacacgtaagtcgatatgtttattcttcagccagctttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgcca
+
6CEBI5GFJ'61D(8:C7C7F6K>M,6+&9N*36J,*?0;E/G6?3
@271
agcaactgaagcgtcagcaaagctggctgaagaataaacatatcgacttacgtgtctgcggtgttgccaactcgaaggctct
+
7;<,(;)=H?(?G4854*5;/N*4KA?'AJ;6BL'@:F*M)8@JH,HH10EJ('&C';.*0E:'()@'(DFHDM)G)F5-8@
@272
aacagagccttcgagttggcaacaccgcagacacgtaagtcgatatgtttattcttcagccagctttgctgacgcttcagttgctccagca
+
00C5,7FH=828;ILNJ(6A44DC&9L3<7&N>B)6'2,J2/KFI0N.=D7FA7IAH6'6H/N&(()FF&F-'E5&L7L6E,,*JI/+9&@83C/KJIC*IK)5*2H662+N
@276
cgctgctggagcaactgaagcgtcagcaaagctggctgaagaataaacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaa
+
000),<+H(F48.:M?0656FJNH,.2@@A(2ED'IB8.92,:9KH7>5E7'5J?M&)))?:31.M--5;=B+J=F00&7@.9)6I3@<)@>?3G:2AD.63=/F+:87<.7.=F
@278
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggc
+
D4.BA)670:MAL;'J'(;0FA)4I80'0M2+IK0?1IJ)47>*1/=CC54=/>3BNC8=0>B;.7;7?>C'I4(6)L4E-2HB(5'N::3KFN,?9/D)DC4=4J,*,>DFL2'+G@@;/K,4*H1(A16?.?0DBDE
@282
gtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactg
+
<+?)=L7@N2FGJE>>+ED1J9B5;KFEIE&//)4*3C.A8H?3C0C:GC)33<*8NKL(@@@46AEJK)J
@283
cgccagttcttcctgccagttttccagattaaggccatgtacattggtgagcagagccttcgagttggcaacaccgcagacacgtaagtcgatatgttattc
+
;6LC2@7?.DL*;+254=H4I12B.'3(6>5=3A=39N7D/6)5IG5G(F(C2A9@;DC'=:(3,8>LA33J5<95,,H@:.A=A''-I9;C0=;A*+)72.
@284
aacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
(4-*2>G*04M8:)C@+E10IEE,0/C6EL08=9,.)NC5,I:)+7'&82'JML;/.4GHCC?G,11I3IDGI/(==1KLM'?1C:5=6DG8=-BHN=
@285
gtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
00?>EBFI>5M/C&,@N5*8@J4FKLA404/4;N&'2B3,G>CM8)4*:.F7;@EHL*F/>;A@).AEB:/23)J60L)M7BI
@286
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgc
+
HJ=;;.*.?21LN)496-(((I5/N(BI50>F.A=5L/6.8779K''4*9:L6>:/5H'.6L1@1G+7BD7L:K.N6*04&>F7>E'B)D02=(I7E,6C94B.(.?K8;>/G>,6FK83:C8GH62>J&E0/NF>C3&*+E:EM;&41N?9L2'9,MH-)I382>L3/GLCJ&-,(;72.+H2;?8@8,H*A)@-?@7D5MLD6L/GE
@292
aagcgcccgagattaaacggctctttggcttgcgccagttcttcctgccagttttccagattaaggc
+
00080M28+8MB;2JHLG,9D6/&7)H'-/GJJF@CL<*3K2)I*??>*4LFAF:(HGF:32KKJ1.
@296
cgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgcaagccaaagagccgtttaatctcgggcgcttaattcgcctcgtgaaaaa
+
000>G&?F4,:>GD-)ILN;-7>(97FNC5C.@I;3JE(00101<0K1;K'7F;M9?4DL.K15C/L<=K9F3>A33.,D'27<,26BH5E?'H++3C5,>H/MCE95K=6J
@297
agatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagttcttcctgccagttttccagatt
+
00000N(?)2GEJG++2N=BM&/=LAKKN10H*DNF='CFE+H*'(MG+MEJ00M&',1AEJC3D4;;.B/GJ=J7E53J?JDI1'(7(
@302
tgaccgggttcagcagatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagtt
+
0003F,*/BBJ3&6J@H:=-6F&68(-@F06DCFIG(KMD;N::BI3?I4)4B*:81ID;:/BL-1CNHM0B)@/=C3IJ&*L-=L&G4;'.*9>?ND=
@307
gctggaagtgcagtcaacaatgaccgggttcagcagatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagtt
+
003/+-/0D?>+N3EB,FL?2?/(8ENEH5AMB3;:I..0==/9H'H;BJNH(8@/+6CN6C1DA)IG83H'G+*)H901,1F;:M4&'E=CNC.:@'1:8
@310
cgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggttcagcagatgatattctttcacgagg
+
00000LF<9+;FH?*5-1L.9L5(4(N=-8FD(J36A*/1<0I*.=B=)'1D.88/5.+:-KG
@311
tcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggttcagcagatgatattctttcacgaggcgaattaagcgcccgaga
+
:+.L6E@3@B*@8=+LK?G'31K/I7=*NJ<0*0M,J52GAB4'B,75:KDIJ6>'E*9N/7M9+2:E3/E)N@<73'F)0/NJ?D&BEB?>G5IBJ7+,/'K363CA;EJ
@312
taatctcgggcgcttaattcgcctcgtgaaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaa
+
:+.&G>&6*C/10)3A@.LLA&0HC-J485;.866L+F@A/(H.-(F@N11:39;FAFHHH9BK2FG<==HJ7;GA34ADJM*7C.FK*'&/<*C.EM0=6:A=G&M,;CI:?9J
@314
gtgacaacgtggaaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagt
+
0@7;:C8=N09FG&690M:*62E;KLKIHKI8D:BC6:L35H<&@NG@@297?(&+4H2(-@A>?
@315
cctcgtgaaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaaggtttccacgttgtcacgc
+
00B02H9:9*1+?G,.+(I@5/8AD>:=9?==N'/(,(GHBD2=I&71A9>GE57K3*27+.D:4=6?=G(=>2HM3D=89?*0IANL850*=33>(11II'C-JIJ*01J2:;E348F&MMC1/>('FDA.**>83GIM;-MM03@EH'5=F(=D*2/A(@(BFG9L@+KA@28I@@:G>FL'@8*N;K(>
@318
ttgttcggcgtgacaacgtggaaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggttcagcagatgatattc
+
00C23M,&E&&B)-AIJ*6EE.N=03613*6((MCE@2B(@F7KJALE3JKM2H5(.K*I4,H,6(:(&N2L
@319
ccaggcagtggcggatcaatatgccgacttcctgcgcgaaggtttccacgttgtcacgccgaacaaaaaggccaacacctcgtcg
+
0K5H6J?-95J1H0:BC4<.7>6J1'NA,)MC5B+9+49GJ+MN:G;F7F:K1E;J(?BBB8L5MMC:(8*B0?48EJ'
@320
tatgccgacttcctgcgcgaagtttttccacgttgtcacgccgaacaaaaaggccaacacctcgtcgat
+
000F922=>G>+'I(&D=>=5'2'09)H@I,BG;9>6/EF/C,:56GM-5(1.)AK@+555'*L&.@A&(F5D,*9FN
@327
aaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgac
+
0B+>C)3E7&.K3J=-)3L*:./6H,=>2KL?6A07L(.90?&33(N5:1LN'8L>.MFL'ANDLHHBB&,4)':,3L:8MG9/80<-H39L3BIILDC?HL8>L*;J./G.9M6);?8K28+3GN:&86FKE>D=@CN;NF//)*31J;(/*K
@330
tccagccccaacgttggtgtcatagaggaatttacgccgcgatttttccgccgcataacgcaactgatggtagtaatccatcgacgagg
+
00(D/=FAA*G/33;G><185L0,AA)F7BM@4G-?-IMGL?7<@A3&3KF&)A6,GC2?*;D5487L'JL.7'M45G0E'475(219>
@331
gtcacgccgaacaaaaaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgacaccaacgttggggctggat
+
0/,-+B+)BFI;?L;H/.'54>,))-C2'3;(*)3)/,;-.-K26,K7+30CN,+0M=/@B1E>H?(/((NMJ)H6&,BD59,)=<;M22K4,J99(7I22DM'N)+FJ,EK2C-
@332
ataaccggtaatccagccccaacgttggtgtcatagaggaatttacgccgcgatttttccgccgcataacgcaactgatggtagtaatcc
+
00))A'4G@091GL3AK(@8L428=7:-?*C1+E-96.6D@;02-??NK/N7+N1???JC)MM&K400A,1J0-*I(C7G?F+/).0K08=4/-AJB4:=4K'(5,G='?8HN92+,(+B)(B1AKI>=9;;CBEEEE.H7+1C8&576=DH/-J)763>8ML1L5+(?*+4EG0?:CJGN:@50):('/(:028IG57M
@338
aaccagaaagaatgccggagaacttcatcaattcatcacctgcattgagcagattttgcaggttctcaataaccggtaatcca
+
NG/BH9-AAFB@,E@'3E908.&:'/NM'KLH12'K?:*/;-7:A:KA=D494:>DC>*18.K;DAB@K'LH66'<.7B8?LN>09&(FB1;@27&AN*'<'7&;:2L898853::7>HCGN&+I4?+92?(@J17K@4G.L):6
@341
aacctgcaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttagacgaag
+
000M8KAM-LKDEB697+)-NJ9.@>/2MG6,D:1LB;<*?JJ&&)2B89)NEJ.DCI(&<,IN)F?0,&.'B,6E8I<;JE,,H@57*=N'7I=4A
@343
aaaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttagacgaaggcatg
+
000F8:+G4;'N054J?&G.>':12@6231-75J86N99G
@344
tctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttcgacgaaggcatgagtttctc
+
0CHA87M&MN?L0.?+'2GL/+++E)LH,4.C68D:7F=7J6?1/F2I.@H&)&-:.,&317G5-MLC/3BMG=HC469.+.6)>.F/H=BF259I.+LF'5/6@8B2:>L4441AN4-()AD(E0>*0C2344A6*6:DL*3N,)&.774L(E,6CE-D(&B(C6NIM29DB/A8M:ME49GK.64HEJ
@352
tcatctcgcgggtccggttcggtataacccatttcccgcgccagcgtggtcgcctcggagaaactcatgccttcgtctaacttgccgaagatataagaa
+
00I88:5('DG1G@D'/);:1;-A>I.D30BA7<3+;@F137=8J07?2:H@M,E>4)HNAHJGE3?,)L45*N,BFA(-9JC&=<(-DG/M8>>I6'?
@353
gacgaaggcatgagtttctccaggcgaccacgctggcgcgggaaatgggttataccgaaccggacccgcgagatgatctttctggtatggatgtg
+
000*26+>(/G0843C71'F?2IC6*M1CKGK)L/(;H@>0L1?2;C(7,B.3C0H>47>MK:0@CGL0,:+D3A5,-KL1I>@-;<0,4C@(-L
@355
gcgccacatccataccagaaagatcatctcgcgggtccggttcggtataacccatttcccgcgccagcgtggtcgcctcggagaaactc
+
0000-)-D*<1J(1A*JD?-6M*9*9H0J.&?-9DK/EKF09N<.:DA.L)6,9C;IDH&-?(-:KB;5(/0&;*9A:JA>C2LD4H1'
@362
caggttcaatttcaatatccgccagctccagttcacgtcccgtttcacgagcgagaatcaatagtttacgcgccacatccataccagaaagatcatctcgcgggtccggttcg
+
000-?/?2.?(48,@5F5F<;'I=9J7A6?2C,9,JGIN;CA8I3JL---IB'L45I(3B
@363
taaactctgcgggcagcacaggttcaatttcaatatccgccagctccagttcacgtcccgtttcacg
+
0HNE7HJ7A865'-9.E/N57A4=HHII&IB2;2B:K<&/':.(BKL6F&/3C2FJKF1&;//48J?
@366
cgccacgcgcgcggcaaagagatcgtcgagttgtgacagattcgccataagcggcaacatcaccctcggcg
+
9;,*HFG+)'-4=&I/(&+,F93K1F69&21CL:>B7L5B4-CGC2K(EHB8G>0+N-N=C+E=:G=L.:G
@367
gtgatgttgccgcttttatggcgaatctgtcacaactcgacatctctttgccgcgccgtggcgaaggcccgtgatgaaggaa
+
000F:G@43?K*3.E<>-62N:)=<(K37G>B10@C+*G03AG>8)?3CI89A<A8=>68/
@368
gttaacgccgagggtgatgttgccgctttttttatggcgaatctgtcacaactcgacgatctctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgct
+
000G@&?2*MI;G+,H5'F,'(2>791F'@3,:K4&9=G85G/FM=9).(48@BK(857,1G??N7DJ&L>E+<(A5LGC7+);;8+>)7MD6>E2M.0&7H'@4<
@369
gtcacaactcgacgatctctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgctatgttgg
+
000F/6LM1;2:*0IK'J()HF3.8.4-9K<4@FA7*25G)C;?7;B3H*:&@B?K<=
@371
atcttcatcaatattgccaacatagcgcaaaacttttccttcatcacgggccttcgccacgcgcgcggcaa
+
0-DME>MB8>/M=03M<*K)0:M:5L9=7>BH85'*N+G>/HN0(>:720;5B)7>-?=?C)6>CM&,K1J
@375
ccgtgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgt
+
0-34)/7<.+14;E8B;)I
@376
tgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttc
+
7+@5EJ:6,G:E5;FFAKDL&4HB'><)E*;BL*CL-H=8D+*BG'C5LH)*/'D+6+E?E&MNI2D><*9;57<2/476J?@+C(4
@378
catttttcactttgaacagcggatcattaccatccacttcggcaatcttcacgcggcagacgccatcttcatcaatattgccaac
+
00DCDD7+>8ILFJ)@&J5@.LJ/918(?4G'7G*=.8H(1A-I2-@G;--+)>KF'IC-&M,D83='?HM=B>83L;LGFJM,:
@379
gatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttcaagtgaaatggcgaaaacgccctggccttctatag
+
KL.)M0-BLBJ:+8HJ<8?G9&GH&6?ID>K1CA=8=/MDC14/==,9<)
@383
atccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccagggcgttttcgccatttttcactttgaacagcggatc
+
I(&D<=H4@I7;I4HJ(&*GC36='8643N?):NM-,3.('=G.<-B.JIF/),-4;+K;72<44>*)D<@)DG98MD=@&GF9??K3I2E5-6/C@G4?<(E(D6&E
@386
aacgtcattgcccgcaccatatccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccagggcgt
+
EE)?9N:F(K+F8:,6@-FLB030A6;LN30*I?.M0;49J&B<,,+K>'>AKKH(:7-;=/8G6)N:.*;*3C,629NKGBAA;(*;:J<
@389
atagccactattatcagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctg
+
0000-;(G/(AI))FNNN;-M.38=((C>*-G1C,7A:-HC5@.60(.:43A-3@GC'E44''>42&-M=6C:K+C>NHI@:?8
@391
actattatcagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctg
+
00JI-0318GFGDGD6@G'MF=?/M3*K@,B?.*F6.2H44D5D04KK7.=6F:AHFE)7L2F6(I+1;CB52@LF)'N3*F?
@392
acgtagcagatcagcaaagacaccggcagctgtaacgtcattgcccgcaccatatccgcgcagtaccaacggcagcggc
+
26@1;L<.C63JBC?-<4'&J*(;):B1:/MEKAD+J'H&>')0D:65+05D@0+C34;0D6>CG>I?M0H1)EG&L3I
@393
cagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctgctacgtaccctct
+
0'.*;)E'&>CN*<->,:C>L7GL(:E;@/E7DF1M(-?F11L@)JEA>AJIM*D-*:8/:M)9&LMCKD/@,:6/E26@.(
@397
cgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctgctacgtaccctctcatggaagttaggagtctgacatggttaa
+
000M)G+7HK0?2DA+G/=B(=9C7@9'6ALMF):&9'9><0AI5M/-K?
@405
gcaccatcaacaggtgtcaccgccgccccgagcacatcaaacccgacgctcatattggcactggaagccggggcataaactttaaccatgtcagactcctaac
+
-+7G(>JI9+JN=C/=.+9.:=
@406
caatgcaccatcaacaggtgtcaccgccgccccgagcacatcaaacccgacgctcatattggcactggaagccggggcataaactttaac
+
000000N00/6-8:BI703(,II+.GN'E=L+K/2;>8),4+=;BNI.D8438J?K&B/D,L@((5<8J55*E:(A3/D6H6/'KC2I24
@410
gttgatgtgctcggggcggcggtgacacctgttgatggtgcattgctcggagatgtagtcacggttgaggcggc
+
-M?,<00)N4NB/+<(N):@(N=&J70)8'&BE/)76?8>*4>F<,>FHC:&6G>K/A)5LEF388IMJID2',
@411
tgaatgtctctgccgcctcaaccgtgactacatctaaaagcaatgcaccatcaacaggtgtcaccgccgccccgagc
+
0D*;E.5??='*?F/61()JJ4A)>ILL8M>5/?4=C?L5'4>:/*&.=5+'I8=MK;*9@/E(,9.=/KDF<
@413
aggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtca
+
CE.?+L00>)4897JM'0II.5FE61I76*1NDDF9AA39GDB,G)84K52+E4=D,'G@I2CIM*+,=()K==,:L(<@4GKA8GFNA7?6@L<9D=/
@415
cctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcactctcaacaacctcggacgctt
+
(;G5<107,F078J8H7D'61*C?-L63H9=M8:9N6;JD+;ELK-.)*3D&,&D30627NA<>L'DE/(L;',>:&K*/,;E-&
@417
cgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatc
+
D()C0:AG;.GKM;?K>@,.-@?1<2:=KC*N>8LL?./HN-M;&L34L34B.04)&H*F+F0
@418
tgcattgctcggagatgtagtcacggttgacgcggcagagacattcagtctcaacaacctcggacgctttgccgat
+
(EADDA@KE'::2J,,,-,J;:J)88EJD;CA6C)JF.+B:D3M*?C*B>:ID:AGD5
@419
tatcggcaaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtcaccgccgccccgagcac
+
02KE';3@29EB3;G5/NGN4*JG,E/K0L56.BH'4L8K9A4,8LK?&+D-7CMB30L)8))N.17N:IJ&AA*6M>:076ECJG,L9&D&)M1@L??(4:57+C*3,><9/6&(0)M>1NB;IA4D0F5?+B:@,B9/AM:CN)0J=3+E>LC,'E&B)K'N/658:4/II,&05/22@'554+L&).FD9-:<&+/+@;&.=H:C9KBJ4.8@7G.)6
@424
tctgacggcagcttatcggcaaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccg
+
16=E=JI&&:;9I:>MKI=;,8?*+G-96A;;17@4G?C:+:/E6/HJKICDI@:H=5N4NB?>H+/J5?M6;>===AI,=
@425
acctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaa
+
09BCJMF0D609&=GCB0D1F(.;-AGAH);;742KJ(6I-0.AFF>;IBFI2';
@426
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaa
+
6IE4EJ';/F5.<6A(B.BL8613)3'CBD,:I6=7?/72;3AN&+23B8524+'(J'&9E3K3C1GHBL&'02(/9ECD>/5+(*3=HHF/?)&
@432
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttatcagtg
+
00:2'.)(>@:A.E'I:C=?:,J@:2,GC4.=G930>*0N&5<)JM@5K-)0.>B+L9/J)/CKK68C7@I(D'H/A<56/IND7?'DMHGIN@AJ1&<01/?(/8-4&
@439
gacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttatcagtgctgggagcgtttttgccaggaactgg
+
0000:;(A;&)/HD62;)?AD&1)+2=JJA,06KF++1:(J+1BJ-*B5;<83&7/?/+B)NB88<+&LMD.&80B,:FGNF*B0*'IJ':K>+8MI<71BE-0
@441
ttccagggtcatcgccactggaatttgcttacccagttcctggcaaaaacgctcccagcactgataa
+
0+=1=>ENA5:&5BJ-C9'AM(71(;1HJK18=8))-EN9+JJL&2;9A54(A2I48N8NC.JFJ)055NCD(+0GA9&.3HJB(@A34
@446
gccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccgatcggcatattcttttccagggtcatc
+
000B4BE62..C@8C8CD':1N3K1AK6;A)E(54?FE?(7J7=89-0NK>B;HG?FEE0N>IAKH86NEDC23(7<,
@448
tcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccgatcggcatattctttc
+
00A/I<1?NIJC=.BCBL;C@95:=L*7'*9J6)6+=+J=.LMI?B*)?L)7FA.5+*(>E0@+837*G4,4
@449
cagtgttcattcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccg
+
:>-752F,6IAD*E+B7KN-KF)(?,@)L&>CD/*1?(CF&.9(D&/=34:D?,8/3L**+1E56.
@450
atgccgatcggttcgggcttaggctccagtgcctgttcggtggtcgcggcgctgatggcgatgaatgaacactgcggcaagccgc
+
@C/CMMN=B:7,D9JJJJ.NDE(=LGI8D10.85ABI4=GF)?J(G8N&.N@H58J@?JMN;7K<*MM64>?M/3643,H?:-+E8?5&>.2H;249B4A2A8G<81?C*J?+N;8>C)2((-,;2F,7'/4+3-1,N/.JK0/7B.2(&J/-H9D*GF'+H,6CH'D1A+D&<(50:0:+,J>.A3.,<;.+3@2JJJL&I*)0'2>*:K3HHL9;9,GB.-A-;AC'+139I/D5
    0HK=1-BA5M)I>'/+-'<2+3@9@N
@460
gacactcgtttgctggctttgatgggcgagctggaaggccgtatctccgcagcattcattacgacaacgtggca
+
F/7D44J/0+88=3E2;K2IN&I,'F22=1:B(@JM9/L)K<:GNI<7F==
@461
acggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagctcgcccatcaaagccagcaaacgagtgtcattaagcggcttgccgcagtgttcattcatcgc
+
000000;GI(CM-9>':JK5NE5A..=0'I+?>7AJ>I'..H)/<2/M44(@,-<2=+F2/8A?5'M;BI5I'-&E:./7&ELAKGEB*01
@463
gatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcgg
+
M>:9-EJ-;8-;H@KH+-4JH:71KI8.==6NJLKF.<+5/550.*LH')NNEB+@4GL95L/&:8C=9
@464
gatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgc
+
005/6)HH;25-2A*.I*?M&FN&FF=4FB4?(G/8'53+=?DJA*;I*+MB88&KF?L:?6/:E(*24I?)
@466
tttgctggctttgatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
+
00D4BA4;'C2I&9&6+N:<4E5*3;AI+L&-JLE)5N(6&&5>@56+8E0K>E?1<*F1-;4@2/9/<)/:-+M)-0B6-C4M3,/36=I1?3B=>+M;MG8.?@IC/AK7GA3H/882<,IN(0*'BA.0@:,0?8<,I@@@5GB
@468
gaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
+
,I9,N/=HDIAE?E'5J:+-<)6I&*@;0<(64D*N9N2-88.82)-:26H41M9&M3H=+=9C88)K8(A9FA:
@469
tcttcgatcatcaactgcataccaccgagaaaacacggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagct
+
2;/7/H2LI,@=I0F4?)H'?=+6DIIFM*;-=3.*7+F6-(I&208M/*8E/3E/(
@471
ggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatcgaagaaaacgacatcatcagcc
+
;7/C*014+A077F,7FN0MH(.L==F5I4=?:>)C(('91K??:-M1
@472
gcacttgctggctgatgatgtcgttttcttcgatcatcaactgcataccaccgagaaaacacggtgccacgttgtcgtaatgaatgctgccggagatacggcct
+
00-'D51D321KIMJ9(C(3>E<'/9M(=?8)4G+0;=@F<+DNG;(*;+?3@?<,?MEN?,:J1+L(E8B==6D1FM4;:MA?D3AG((N?M96I'1&K62M
@476
ttaatccccggatacgccagcacccacagccactcatcaaaccctggcacttgctggctgatgatgtcgt
+
*;08G&-M05KH)EMK0H/F5:'&-IAM8:/*3FH1N@6E=<&J,'?CFC'.&*FK@3E+@MD&:1*D7-
@477
tatgcagttgatgatcgaagaaaacgacatcatcagccagcaagtgccagggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctc
+
0H;(K51G('3C.4JA.-5)((')?8K0>8>M-13;67N:?M(3E:JHE.'*/C(;F1HK13=+KC5*2
@479
aatagccctggcttctgccgtcgagactttaatccccggatacgccagcacccacagccactcatcaaaacc
+
000>4LL@*'&DJ8))CF@5AI/A,=>?AD-/1H<=@>A6CE;7KN67IⅅLJI(19GL,+()2@GB/(;
@485
gccagggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctcgacggcagaagccagggctattttaccggcgcagtatcgccgccaggattgcattg
+
000;+IH<<(GEH6C&'.2&-K5?.=GN?,20&(GC546H>>??=<.G-LN70*J?I8:M)9K9JMNECN-64.89&B
@487
aagtctcgacggcagaagccagggctattttaccggcgcagtatcgccgccaggattgcattgcgcacgg
+
00M=/KA;DLN<'=5>-=;.D7+C+L-E0A07)+GINN61,G9C@)<&F?&)INLEI@)KI)=M57L7I=
@494
ccgccaggattgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgag
+
00+4NA>EB>)M4ED=//J:7F=5F.++@FE;&;JN6)?0-B2GJ)6G/9IE&LK9CJ<=N&&@LJ95F.*7M
@495
gcagaagccagggctattttaccggcgcagtatcgccgccaggattgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagc
+
0*5LIK.B26>0L+)2&>4/.A?864:)B1F'E,12)J(+I6BK?M6.A889+G(::=()MAIB5K70//5:)3095D@DH4IIFJ(L'L:'MFH*3IHEL8NC&0E.?@8BN>D;5<+89>N=6=II10C(
@498
attgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatg
+
0000D'1='0.G8(,N)H/5:,:8;.<1;:KFK5)6JME;0)?FE+(5D<;1L'I01?E+<=N;L,/7L;17I.INEJ8;?,E
@499
ttttttaccggcgcagtatcgccgccaggattgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaa
+
000000F92/J:2<:H+&BL&/I*?L28K2*EJ9F-GKE:HE))7:M4M@6;1+MC:<2A9G()78AMC5B26H7JC,396&L5,B@MC4,JA,FJ@HH8*H+K8+&*1<02.5
@500
acggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaac
+
I,4BF,8&)D(:H>5.73(0*6B81<2A?I;;L1F;,:8IK:H@D976@M>7GCI)M,.''ML?*;CJ4-7+*J/NK4&GC(-NAE?5K
@501
caggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacc
+
0:?;DH,&A);B)51H+L0(H7&@)=NKK?A?CH7IJBA//./IJ7B,9N2A>JI**B>56A?3-E&B>J64*>AM
@502
ttccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacgg
+
009G>7BD9-?CE??)&C*>KCF6+@L/J8>A;9'I<-5)*6?6H,F.(B0I4M&4//+K5J,/4;
@503
aaccgttcacggtagggttcagcgataacatctttcatcagcttcgcggcaagctcaggctgacgggaatagcaggc
+
000059*90,N&524C,GG2+8H8I;
@508
gccggaagcctggcagtaaccgttcacggtagggttcagcgataacatctttcatcagcttcgcggcaagctc
+
00,13@83646HB?6=4M(>8EK6:+2M5E)I+->N=1.87HN7I>91D&,)2;+7G-+AKCKN8.F67A;F-
@509
tcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcagg
+
0009BF4&4/B(<&L+482LKAK1H40@72I.>M-G31,(53?C'?G82A)LLI/GB+*4CC1L;88B:'L)+@=8CJ1G7>+
@510
tattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggc
+
)G=CK;N0+GG'.4L*G6M*>7EKDHB+()N:N8H)&G(MDI:-/),,3:.F9175:8=JGJF'?CD&'3MH&0L*C>0D6MN23E5')E9&
@512
cgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
+
0000G'';'B4IF>DMI6;FJHFH9NI>F(N-I.2.G=@?/7I?JAC79+GA;3'),9LEF?&CM;(@(8G6=I'63E;2,HJD,F8CCC44G3;.
@513
tcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
+
0.'7J6,H@C22HGB>M.(?*64@643&81@C,=->N+(7/(3K-@8+FLNG,?E/J---GD6=*.>.&9'/AJN1&6N@(&F@JJBEJC67+F
@514
ccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggttcagcgataacatctttcatcagcttcgcggcaagctcaggc
+
00).I04?EK;)B)/62:/<0F/.:/:KB1+888+7=/59DCHN'N:E,KA=@/L/;G*//E6?;NINL*,*
@515
gaaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcggt
+
000&=K.@)>:J>83G'3(/4:4JH8@7,-N5@//K;)//C&>7D@N:7L=.M*M*=D)2K/=@7(
@517
ttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggttcagcgataacatct
+
.;G3C3-ELJ(E4)@1&4&,<,JM5JLAL-91?-(H@LA
@519
gcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggtccagcgataac
+
0000(30DNE&&-A+9C4G>@I026)JAM0=ID,;L@?;I149L6/;?,8:.':GA+'B@(2L);3A.B?+E81K@,2.@;?>C5E5;9*'>K7M6562*AI&9C?G
@523
gttactgccaggcttccggcaggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttg
+
000I>)+E-,73G@,8:,&J:F32>,M=BK+,J/G7F+FADHF&N;7GCB0*&A49D)A2K*83NMC;M,4@.67?NN/5)(B
@524
gagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttca
+
*KGBF=M78LN86MGA2KG2L3K:,259M9+B.HI8DD+?GC0H@J4;&NN0E2B9C)J(8KCC*&/>:I:)36-6M<@BA:*/@7&-&62,M>E.L38BM
@525
aggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttgttcgctctgtgtgacaagc
+
0K>*K?65**&=<-A.3NB6>K&FE2.>8J&865,D22I??L/;A@(.LJ&<0C9<7**M,/A4,@I>CH;BFM/94+K':.C:BH<
@526
gaacggttactgccaggcttccggcaggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttgttcgctctgtgtgacaagccgg
+
MN@B@JGKMN'/CGKL:288B*A,1?)?*)'.4I7CB@A014@097<@8?0L3G(J9J?/CJM+*9=N>7HN=<&J?'J3'KH@)=F>(318>D2CM7
@529
ctgggcggtttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctg
+
009H69>L9@@A?2B11AD'9>K-L9466DG0<)BA(6?-0+8HJ=L7=A54IN?L+J/B(/1B0)>J@KEKD(@0J0=K*'+'7J>3/H@=/5(*/&;8GE0149)I23A-D
@530
atctccggctccggcccgaccttgttcgctctgtgtgacaagccggaaaccgcccagcgcgttgccgactggttgg
+
0.'N3.159A)IM3,ED'.JNJ(47087<4.23M+&@,':.&0G4-F&FKE026G*
@531
ccggctccggcccgaccttgttcgctctgtgtgacaagccggaaaccgcccagcgcgttgccgactggttgg
+
*(=1BNE1;7JJJ-+:GH:)G,K>1>GC1,DA:BD(DE(/A:MMN.:IL/?7AA)//?MI@E>K7NNJD;2:
@532
cttacccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcg
+
>FM2)*)+H+@;A1265=02HN0;/J?9;42(03;E(0/B/DE@*MD5(C'L&0D9;3,-IA4-C6&L9HE?(DB)83/7KGM7H>C'IN'7N@6@,-<(9:65A
@534
tcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacaga
+
0&)IH*;-44?:,(:L.CB+131('0J)&*A@BA8*:''CK-F;&>>@)A'B:5+':*L7)0=G*:JMG&A9
@537
acaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctggcggttttccggcttgtcacacagagcgaacaaggtcgggccggagccggagat
+
000L?GN7:3+G:23G=4;C=EL=,B9B+&<+&L/@71=+*JF-9>-&=HH@71*80)7J-275F1-(=,K=<)6,'9'EM@@KF?,;-,AAI0GFKB?;6B::3,L&
@543
tccagtactcgtgcgcccgccgtatccagccggcaaatatgaacaaaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctgggcggtttccggctt
+
00000G(?/BM6I?(3L@*/CK-L15<)GJ;18NF-93K322;<7+-)44@J+:N&;:27GE+>9>'43I8D+(&>AK2@LI'N(018*(9B/2B70=59C0572A043B>*G
@545
atatttgccggctggatacggcgggcgcacgagtactggaaaactaaatgaaactctacaatctgaaagatcacaac
+
0>8*0H9K1@?,?'*LH>BC'85'D7C;&F5E@E(&?(892B&L@*D&G6JCH*;HK7?K4J-5,?2DKE46C/492'B&,D0LA..;70
@568
gccgagaggatcttcgcactgcgggtgacaaaatccagcttcagcatctcatcaatttcagtcaggctgaattccggcaggtcgtgcggaaaaaacagcccctgatttttgc
+
00000008B>?&N46C1A8?M*@/05=J@)L+'H'C--LC(96I&5--6-//I6-=9/:)+J:@
@574
attgatgagatgctgaagctggattttgtcacccgcagtgcgaagatcctctcggcgtttattggtgatgaaatcccac
+
000244B-G>.J)66J572:'J?@M0CFKH6*KNG0=G@J1>CL?+N<+(MK(:<7=,0HG43B;'8@05>FKF2/('B
@579
cgccgcgcgcacgcgctcttccaggatttcctgtgggatttcatcaccaataaacgccgagaggatcttcgcactgcgggtg
+
000BF1M1LDJ&<&E(61G/&EKKJ.&'&?6+034A:EK>1*68&==D'>:,-FNI,7/2M-(2=L8,,(A8:;@/4F80:,
@580
aggcaaacgccgcgcgcacgcgctcttccaggatttcctgtgggatttcatcaccaataaacgccgagaggatcttcgcactgcgggtgacaaaatcc
+
000000F087'8F'L))8(9E7CEM)&GCD'G9LM+?889)'&3?-/M<3F9M,*0N3BH?*.2F?(5H');J0;3:A;41N*
@585
ttcaacattggcgaccggagccgggaaggcaaacgccgcgcgcacgcgctcttccaggatttcct
+
4B'JJG@F<4)*,.3<3/'H(G)??HN*:NA5;85GC)NL55?EK?<);0?G>2-;MHL5MCD4;
@586
accgacatcgctttcaacattggcgaccggagccgggaaggcaaacgccgcgcgcacgcgctcttccaggatttcctgtg
+
000/HAK45(2.B/@<(F:0M51IIIJ'=B719F6KN0I'D4J(3K&M&61K+::+.+(+A)N&3DC<4;,+=+4C))=K8=A'3.I
@595
cgccgaaatctttaaatgccagcgttggcccgtggaacaattccagacaaccgacatcgctttcaacattggcgaccggagccg
+
073)029H2GCNG41/DK5F6G7M+6ENN7BI31+6+@4B<<*K*-IHA;(:9D=E'IJM*7HNA:9AKJJ',+6K76:3?=8,
@597
ttcccggctccggtcgccaatgttgaaagcgatgtcggttgtctggaattgttccacgggccaacgctggcatttaaagatttcggcggtcgctttatggcacaaa
+
00-4&)3K/=>(5;J970N'42M-,&I--/AJ+NF;=N>B8(L1D6))BK)E0DI'@147JAHE3.2)@3MED80;8CA@2.I9A7.;<1@>>I=FE
@599
tcagcatttgtgccataaagcgaccgccgaaatctttaaatgccagcgttggcccgtggaacaattccagacaacc
+
000HD:*JIG&@3JGE0'KEBFNI0@.5:6)/(L;?)==IN&A=/>6B9;70:NM2*G003J-/E(:8;-C,<8+L
@600
tgttccacgggccaacgctggcatttaaagatttcggcggtcgctttatggcacaaatgctgaccca
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00&?G/KFED9-H69=3'1.5>9+HCF*D.@.37H'EB2C27A&F95&2(LC7G6JN(51BB,:@N?AA'@2H;I
@620
aaaaaccgtagaaagcatgagccactgccgctccggtatcaccggaggtcgcggtcagaatggtcactggcttatcacc
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00(G,LB?09*=B2;0I'6I:9J1>C&I=3&+29/-;8+.@C*7=G>*3CH8-0.50*E>9
@621
agtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtta
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F585):=+&LK(2&B'&7*&>&+LG<4B(?064L9H9@?NC64-?8AJ/*
@622
ggtgataagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaa
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000D6N=+MLCA,8C6*@C<)G6C10A+/><7H*?@-:NFD;79HCC@G7DC=J=*==C=<&5-ADAN:,@8:CHNMK1HM1-+9;9B:9)I8M'>6NF>/>76D*;)EF?70?L.402
@625
aagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaatgtgaaagtggt
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0000J/K97G4=;HD*N@J5:D77C13@&A'8/*:<;.D?1)>IC5)A)>?;7@BB.3GH;D3G9:IL=D8536CE0D/(1
@627
tgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaatgtgaaagtggttatcctctatccacgaggcaaaaaatc
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0008:L07J+//;KAM&7N1(3D(&9+HA5'7L6E/.6G4)?L8//,-5L7N8'7N*KA>7)8EL?C';E7H07./:8863EA>&5CJD&<5;K8&G?,3&D8/(B<'BIF=N?L/H*-/(K0E6AF:M?0@
@635
tacggtttaccgaatgtgaaagtggttatcctctatccacgaggcaaaatcagtccactgcaagaaaaactgttctgtacattgggcggca
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00H/N8K&2.KM?B8K0MF@55F)H914DM,4MME>E*6M)'<3'J,AMHBMB';@,KD*E*@FD(+DCE78*=?D4,*8658<8AM6M51
@639
gcaatcagtccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatt
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7NF3C,);'(8+*8>N<)?'4=MDMN
@642
ccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatttcgatgcct
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00;H=)->D-F(IN5J-6N)-+@*25KB8M>3(.,;6(>E+A/)/N9)'*L0ED&*4B0/C8(&)-42DJ+@;ALM
@646
aaaaaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatttcgatgcctgtcaggcgctggtgaagc
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0000ILN23K'II,EG586K*>9NJ00GM:@2B(10=74:6,MI/N&>/L)H?,1EG?C5/E,2AH::3==6.:GCE&/MA//)2)(//H6'M;>BC49
@656
gccagcaaacggctgatgttaatcgagttagccgagtttaaccctagcgccactttcagttcttcatcatcaaacgcctgctt
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000A(CL'97D(=>N&9).??2J8F81AD0N3,BG.7M>H3-'&@,9FK&&:@<=BDC:NK:6KM66;33?5MIJ-HE6?=:C3<.&70,H0(H56N@/B4GH
@667
tgttgcgcagctgccgcaggagacgcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgatttgacggcgggtctgctggcgaagtca
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FK,F8EL@4(F2M91>NE->B/A/I=CD777+'4D'(,4FME;J=''64:;D23>;K*J'H-H-9'.BMAI8/6I-I)
@668
gcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgatttgacggcgggtctgctggcgaagtcact
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00.31N9/)B1012LB:K6:K+C@<6LI,?FJ3J+3:(65(9EMC8>35A.-02..M-/G?48:M:8L*0B-F+(
@671
tcggtgccaagcggaaacttcggcgatttgacggcgggtctgctggcgaagtcactcggtctgccggtgaaacgttttattgctgcgaccaa
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000<.N:FN*7E<9(C;0JAE>(I2D3=*J9?KMG&MM-?7-&(GH,JF71=,=6IE&;'B-DBCCDADL:K1CLAD>&+IAI&D'2=B@'/
@673
tttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaaacgtttcaccggcagaccgagtgacttcgccagcagacccgcc
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0000D6(+*6-)):=166@/&&'55<+-;&DJ@AC&3FCNF27K671DLEFFFE7I@BG)>:1IL1)8,,9IMGI';I@+N?E@I3G2(4LCK>&98JL:CD'
@674
gagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaacg
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00B:C@9CAB=B(&4>F*)GB-JA-='&8<0<4=GE0-(DE:3B@+EDDLIF/;@JJ('ME.F*(84CK)=1A(&-JK
@678
tccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtg
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0?-*(?-,.'AF3:1:0I';.D7+(02N-DA/,822/5I)&,B-@72.*B:.C19,L+JH0:=2>'/
@679
cgtccatcgcgttggataacgtcgcctgagtcgctttttggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacg
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00B1>2+08HL)LB<>+83M(NNH9?H)6090A<77=IG0DKNJ.:'J)357D>+4F'H4&.2:?4>'-(6L;=+2LB+57:JB@:-7(FHB
@681
ttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggca
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0000:7:<'=H*/:/<&D5D92;E*3*4E?51?0K9E.50>D=M1.G*.-A84E--H@7A2H*/9G+61KH1'F//(E+&K<2KM
@682
gttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttggggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgtt
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0000&0A3+4G:*3+.4M+BI:0I9&:/>>J,1='EAD:24B'C5+,:1)89=ML=C-&H&(GG*=A4*?3;4KL<0=F2'L3F'LI./J,0.H:I48579
@683
ccgtgccacgtttcctgcacgacggtcagtggtcacccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccg
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*EG85/5G;+?0N8N=)1L9E472N.ILF>/@G:H4-<;:*GH5;F96B9)'*3E65-B7HGK3BH)98N'=I2FM/<)G4>EA7+@LI=*.6/30::
@684
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcg
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007-8)KG?1:>N2HG?KJ5?>1BK0137;L'H:J7KD1JI/:L'3@G1';AM8NDI-B-;>HC?G86(;9.-C*,M8*4>3?76,&@BEC;C&J?E9&-K1DEMEB
@685
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtgg
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0D9N2C5EG*1>6JBH1?0B(.N(0;LLJ&=0E5E=.+E'LL:&;2M?GIK(3)+A'>2M8<*,9=6)H.?&NC-E:&B7A/NAAB66A4@:CC368
@686
cacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatc
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0000,BI4C;6C*D..L9+,&+&@:=32IG:>-9JB4GL+NI@G))@*J56E5::=+&'9B8:MM.?AANAAH>83@CA)GE596:M?7M6.-?@71>.AG-KE?.L?
@687
gataccgtgccacgtttcctgcacgacggtcagtggtcacccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccgcgtgtggaa
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0G=IJDI'=DI/MI0)762*8:(/DN9C,&3K*;'9@*37;K8;&(K+B/39<&NI=27(C>,M4M4.E+8-NJ;*;A4J=D>>4N0K3,(,(4>DMK9.D8?;(G.&?3C
@688
gcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgag
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0M6.41&KH/A*A/&C/B1,5-?=5G;IC:2''+2@B>F&3)JEFN;00K1&46D4E)C/IDG
@689
gttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcg
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003*61(@174CI3JK9+2<>C0;?B&M<6A)9-BB-@4-G,D1((:.E,'B-4K,)6=3?EB(A6.@4'/C)(6I5-HF=C**HA>(/'<+/>4NB&/87'KD@+DC:H1?9;LHA@54LD6-K'I@*K5J+'KGF=*);9=)'GKG>@50J.7F2>-7',8@D?H,3<
@693
cccagctctttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcg
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00+:EF,'>KD,H'LG.'&4(5.=B=1C/1GH&(<*6I=BK8-,88<';N:NJ14&JI;*M<33/*
@694
ggctgcataacccagctctttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgt
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00000.+J'M94D@FCK=@7;?A?H97'1D/.14-+8K/:5:NNFC,M>IM@=68NMK739@CE@3IFKMH185LI2M:.@H-&'M
@696
cattgtctgttgcgtggtttcatcatccacggctgcataacccagctctttcagttgccagattttgcggcgga
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003K*M+LID6'BH87J523-G6DFI4(<&-B>7)58MI45=>K/8;3C(3+@5
@697
tggccgcgtgtggaagagttgttccgccgcaaaatctggcaactgaaagagctgggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgt
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00000-6JGGB+15&(A58/41C7*&6.0L?;8K2K5,,1501'+1-99:8JD,@3/B03A+N3AN/42+H>-:C;L)75'>3JAAI.F@0H::D;)8@+-2:**9<+MCG-;?K.(.+D
@705
atctggcaactgaaagagctgggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgtgagttaaaagaactgggctacacttcggagccgcac
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0(50@?=7C&M+,6.2-LH7B>BD1NC?.I*3K4>NL<&A/6(M'(/5>8':I8C28.?=;H*4KH+:78A8?*9D':?0?A,2>J>L7<;D=0+7D.=24@JD8
@710
ggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagcccagttcttttaactcacgcattgtctgttgcgtggtttcat
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000'?@4ECE'9&3>?8?C)3)HJ0H.-.GK/*G(M6=.F5G>E7'1);)'1&E14-;?'D69L*8G4=GH&+8E<=5/:34'B1G@0-+;2-*G=H&;H&.>
@711
gcctggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagcccagttcttttaactcacgcattgtctgttgc
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0000I>1K/*E)M*3,4.E7D?29F:D055I.@7LH*D19&-.B;A&5086<&*:+&25I-H&/M9A1:H,<3GK,)*NL.0L6>CB,5/3<)*?G'
@712
aactgggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaat
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@714
ctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcacc
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::L4G)+K/5@IHFB7D+?+&&'0=J0:G(J;=D-,J1EL.B6NA*87:?J;MIEG:711D>;,6MF>'@)/6EC(42?0'C98?F=H;LA1?/B(?<--L<,EII'H:/H;J(5+2A9,J)F;
@716
tcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgtt
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&B.?MEMIDDF6/&046?M5'1,9:G14A9H;F*.C/=DACNI'27&>/?29:CH@G>..M<01-HMD7-67/2CM'=(I)CG(1L(C2FFH0G98@1?E&7CE.85.995H721L;>IIB-18,I2)AH6
@719
ctggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatt
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00,,5*H9G(15@9L/*?E.'?FH37DI)>*@;1-@&)/(7-*L*E*33(@?M4NL@KHM(2&L7'5D6LJ4N<2DE37L9/L>;?3HJBD.DE/3/G'4HF;JH'=-:
@724
gcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtgga
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0G;DN&CI)B73D)(E)>DNM6(E.)'I>B;3)B-MKJ<.:*H,*0D@/'/)LE;*38>G&.(=5F:F/KM4A.K+I:LF2L7
@725
cacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtggaagc
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0003&@;+:8/'@:E<2.GJ.+?CFI.M0E.3E?&D>GD::?&:'(85=,J1710CA67*3E=M9J0@D0'.@>GD4'*-;.CAMH8:)J/E+'+L.@J6.:H6HAN
@728
ttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtggaagcgattctcggtgaaacgttggatctgccaaaagagctggcagaa
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0000.9FBM*8*8B)58I;=.J?5A16.K@)*-N=I>'@HC96+.AJ)NC?K*/CC60,1G1):N&18.;M''7JHC0/,1*1;2)E0/6D@4'0'+:=2N>B9:+G('1&
@730
ggcgaaaattaaagagagcgtggaagcgattctcggtgaaacgttggatctgccaaaagagctggcagaacgtgctgatttaccc
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000&K+@L:AK+G8<&5(:44(J:')L-8>&E(/394EN6-;N/F;;-1<.9,919&4HM(0?<:FA:H-*>3B5I*:J,:?13>
@731
gttggatctgccaaaagagctggcagaacgtgctgatttacccttgctttcacataatctgcccgc
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000000'?=CAHA-MIGKA3(*-14IIJ,:LH+9.5;M<4H:K/ME'@@CJC-;CAD6AD6
@743
attgagataatgaatagattttactgatgattcatcatcaatttacgcaacgcagcaaaatcggcggg
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00-0DN?GG'C:<>@H')+>''D89MML;K,,L;4.457>,HJI;7L?M67G>BN/BN:36*KJ+@HB
@747
aatctattcattatctcaatcaggccggggttgcttttatgcagcccggcttttttatgaagaaattatggagaaaa
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00000<6:)LAM')E67&=4N'4,93JMF&*55&7E-&?B+>@A,G/02:BG1I8DHALD.'&>+5'460LL(L7&;
@755
tatccggagattactcgatgagaacggcggttgttattctccgcaatcctaatctctaagttaccgcatttattgagaatttctc
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L2DB85E-9;,41'03=?+=>5)4@2=8D>GI5B7.M3D.'2=&60)4HI1.&LIH3*6N.4/N4'A,1,.CN--)2DMH.;4/.
@756
tgcggtaacttagagattaggattgcggagaataacaaccgccgttctcatcgagtaatctccggatatcg
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8=3GA+MK'C./E/*<)I968-J,&CH89I+)&>'/H>@:EH&5*/>D101>8L-I;F.?8K'CN3G&?.4
@759
ctccttttatcattgcccgttatgggtcgatatccggagattactcgatgagaacggcggttgttattc
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05+KB?/I5'E94)@14CE=C)@)/.J*7J9F/@J9,*L:C++/52758*AN-.K*'L6*+4E9K4+B3G>2DL<:IJ8/=A97I><,&)G03L3,A:N>MBI8.K6@G&@:3J
@131
gatcacatggtgctgatggcaggtttcaccgccggtaatgaaaaaggcgaactggtggtgcttggacgca
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00H-&*4BEH4J+=79L469+F9G.(3>:)=61+5LM3(
@137
ggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttcattaccggcggtgaaacctgccatca
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I?7H+0F&510-4(<8C>);:E'C,4AHKAD*AD>GN3,*;A(9<=8:IM):ADKE@/'HE2;;;8+/?LG(D0*6?62(I>FE1H026N(8EE0=GH9?>FMA6LEJE,E:5<875=;4MG1>1=LFC?FF.EN/B'EBJ&+)3EE3*6BC7?M9::26;-5/D+I9;22D3NEJ'6'>,N,D,BKN:6784B>;IAB':=;@-/6N:B,=J0+FG30)C6'CL.<'+K<:
@142
gtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
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00L=)H.405GF+=C-:A2<)>/>E>D4BE&+B:AK27>09
@143
acgtccgtccaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccg
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0009F7HI90:/GN2B&M59,*AM(0&60N&3F?3L=7EF7NMJ?N8N-.?2*0,<)0D2<&)8BJ*?LCL
@144
cgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccacca
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000&C*&5GMB4=5F'LHH@)9=3J9G+3L(+FEJEC)>2:D(I/N',
@145
cgaactggtggtgcttggacgcaacggttccgactactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggacgttgacggggggt
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0000IDD:);6.2JB:/3LKL3E7-2)'+3&.5J2(:6*;J4(D@C*>;NA;?;(AA7@*>K2J:1IHG&;F(7,.:'F;MK&2E.B=3-*(G-C9B:818I2J=@-
@146
tagaccccgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttt
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00000-E6)/08HCK.;>I;?)*AN.5KCL/IHJB-3(83M;E4,I6ML65'JH/K5.7>8;B0'D
@149
cgcaggtatagaccccccgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
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0000+899@+,1>9HCGG2-M19*FE85BI:)5=953E4>)02&*'B@B'JB>BL/2+;,+'.5C,8;AHA+)2L?9*C4(;ABAA1@-6(/)61F2)2)DDD:5F,NGHB
@151
aacggttccgactactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggacgttgacggtctatacctgcgacccgcgtcaggtgccg
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000).K7JA0F29G5(;H:,?3N:A9NI&F8)>15L1<@5A7?JJ5.HBA1NB58='3BA(@:HDE&+0>)A*.<,'(H&GG0/2L8(8<8'NN6F.:2+40*?/-3FN
@152
gcggtgctggctgcctgtttacgcgccgattgttgcgagattggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccga
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00/C+K;>474J:N,K0ECELMC++HE-*N7M+.DHH-=8ABJK8-C&-+-8)B5@.34DN/:1@8J;,)-.225E:BMN
@160
catcgcttcctggtaggacatcgacttcaacaacctcgcatcggggggcacctgacgcgggtcgcaggtatagaccccgtcaacgtccgtccaaatctc
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00000(75E,/5><-379KCL7D@3?JJB&)+G1K.HLK48?>9>F1AG/5D:);'E:M6AEBIH>E70?:IN'D@-,GJ/N00FEC;/()=>@AI=D*
@162
tggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccccccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctt
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00000/60K<.C;/E?7N:NG?&FDHD/J6?J25.*0:<4*/@N./JM'=:N:I)19I,):'79N/>F?GA.898KJ>H:/6'?BIM31,M9HC@BHCC?C.NNG9',
@166
ttgacggggtctatacctgcgacccgcgtcaggtgcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagcttttcctacttcgg
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0H(1;<1>(.83L>99474AE<2MC4./'J6;JL<7J.D?/=,//)I<,.;I(41'@AC&,<27H2:87G<&5NM)432&K372?MM97
@168
gcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctttcctacttcggcgctaaagttct
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0;&6GM3<,86-2CL-2GH&(,KL>-9MFIG887I;F5@LL/FKH+&:17CB+9NF9,8/L9@<**EC,6M355/5KH+E4;KGH-I?@6(70AE;F.,D4F@GJ>-+4BEL&=J**1-:+@.3C&>DE;C&I/>85J)A';,L5:?A/I3<8F*.DJNC9C:-E
@172
tctggaactgggcgatgggtaatggtgcggggggggtgaagaactttagcgccgaagtaggaaagctccatcgcttcctggtaggacatcgacttcaacaacctcgca
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0001??5DC7).//M7M5/12?N>79-/K))-5?0M(73HMFF:FI(/*=K:,='G+A7B6'4DILK0-DK@+>HI>A>N/0>GIEJD(3=6761:'>2B/@8/E
@177
agcgtacctggtgcttgaggattccggtatttttaatcaggcaagggatctggaactgggcgatgg
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000=7722(3?,M'..)E':EGC(N'@K4/&>6&'C)1-/9477G'@.?9-;+:DE94,=N?H,
@184
tccagatcccttgcctgattaaaaataccggaaatcctcaagcaccaggtacgctcattggtgccagccgtgatgaagacgaattaccggtcaaggggcattcca
+
000**925<9L,(MEJ9'B7@H>A;&:;-6&CM*74F)GGI/&5<3CE0+>4-5H,D7JF.-F(07>3??D8=HL?
@185
caccaggtacgctcattggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctga
+
0005,B6(1MJ*9;+LB<=FIEKFG1E+@5BE-947?C2A8'H6<7G&8N2+14-0&A;7=?E*>FF'M
@188
ctcattggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctgaataacatggcaat
+
JIF22>.NJ0/45N.BB1*A&.M+,)E)2;:<.HA:1>1A52JMM80;I*E8@&AB1I:CJ
@189
gaacattgccatgttattcagattggaaatgcccttgaccggtaattcgtcttcatcacggctggcaccaatgagcgtacct
+
B1>7904BE&HG/K/3K9(9B.=J=G/G;<47-5*-9CFIA?((F5IJ:0CKLF8D?3FC759A(6=2618(7;EG2,/.LN=C)A97(2*K)E((*,G5D?*C-N4??DME&I6KL9M/1@6J?M9F&D6/0(5FJ4K,;F0=M4A;=?1AN*:+N3+*J=?B1;)6&4:K9(,11IN7G-N1H35>GBBF0*3*'7'D>
@192
ccttcatccccggaccagaaacgctgaacattgccatgttattcagattggaaatgcccttgaccggtaattcgtcttcatcacggctggca
+
0E=;)>.K6)E;DEJI'(JF2@C1.=A+112CJCL&G?48>08LA(:0EK)JN0:A);@J;5(M&5GF37HDDHMF
@195
tggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctgaataacatggcaatgttcagcgtttctggtccggggatgaaaggggatggtcggcatggc
+
00000)72BLGB>;:(/)&>@(39-N5F5>DL@H<>4C6J3N5KM76GN41/4D7)NM;@N+,E)8,H7*I?*
@201
atgttcagcgtttctggtccggggatgaaagggatggtcggcatggcggcgcgcgtcttttgcagc
+
0000:*NEE?65I4H;1+A/2;1*-H:=55FK.=,2&@1NH0N@D>IC/6
@205
ggatggtcggcatggcggcgcgcgtctttgcagcgatgtcacgcgccgtatttccgtggtgctgattacgc
+
?-E>9B;BJ7/51BA?:N0>+(:-?42:;N;7:-;@8IA.90.*
@207
agatgattgcgtaatcagcaccacggaatacgggcgcgtgacatcgctgcaaagacgcgcgccgccatgccgaccatccctttcatcccccc
+
00=2G+8I>9(MFL8+20KIH6,7<*=6JH76+0MMB8;1+JDI''2:JB9=:F65<370I24K0A+LI
@210
gtcggcatggcggcgcgcgtctttgcagcgatgtcacgcgcccgtatttccgtggtgctgattacgcaatcatcttccgaatacagcatcagt
+
00K9EH2066:6B;;84DN9K=B9'9K2L?LH-'&FE.,&GMH0'';.(ML21:B<)2,F7F:@3;35->+NHMIC=7HK*I*1,55A3:1CN6,F?;'*=?(-))=-=A179M9C)M@@8B/=GD*J*5H&>9=L>;/0HB1)3GJ=)C:M&5DFAF;;8I2.0/-48*1:+@FK
@214
gcgcccgtattttccgtggtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaa
+
00*6C)6CJ1KC(B@537DNHD=:'7I=7-62>0KB@9'HH/,;KNC;LA6@,,DI+9&+1L.934D?&B:*IMMB:73KKE=9L>3275,1-B;)MA8*
@216
gtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaatgcaggaagagttctacct
+
00000@K9(,DHFC0'+8(NC4F50H000D165&F/2M3GE?*A38?<>/:=A89(G0+-9L,'.'AHHAE((IE'9/?,')9E.253@3:EGG3J'--J,
@218
agcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaatgcaggaagagttctacctggaa
+
9(D-C320J22CKGGM;:48BA@A6?A4BKD-;5(3,J1CI87KA66>/?)&NG44;3A-1@2)*D:(9*2-09F
@219
ctccagtaagccttcttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcgctttgtggaacgcagaaactgatgctgtattcggaagatgattg
+
00>2B93(B?'7A,?A?AMBJ;'&&.('?C,2;)2G4&CH82+166BLG>08JJHK30E*?69@-L51>K4,=-6'N(D7.-KI4E;,)+CA6G77J7@849
@221
gccgttccgtcactgccagcggctccagtaagccttctttcagttccaggtagaactcttcctgca
+
00+(45D(>E;K+F=DH('H/D/';L&AF9F?*:J9AAJ35>G161--4'KIDE5,1C@??2(BD<
@223
tggccagccgttccgtcactgccagcggctccagtaagccttctttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcgctttgtggaacgca
+
00.IN9DJ'D;214><*69F3808DB(>GB+NEC4G7N19@=;E>A?3J0,@>NA55I+52>129J,GK)J4+G39'36NJJF9?8C?9:4'M0=6+E?5359,=G;K6,)F
@224
ataatggccagccgttccgtcactgccagcggctccagtaagccttcttttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcg
+
0000FB5(>B0..-,6I,NA-J,>@I868,19H+/@F/N&.KCK>7C:B.(A:>2))<
@225
gcaggaagagttctacctggaactgaaagaaggcttactggagccgctggcagtgacggaacggctggccattatctcggt
+
E<,4@0B551<40I&:B>@54=;>+/,GAKAI9I&4139F&=:5)<3EEE3N))N2L6BHD':'*N2;AM<,17@5D)(@2
@227
aggtgcgcataccatcacctaccaccgagataatggccagccgttccgtcactgccagcggctccagta
+
2-@L-;1J.12J(<=G/5+FB5>*J6E;*=M&6M=-)17NDMK/*-,
@232
tgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaagaatttcgccgagatcccacgcaaggtgcgcataccatcacct
+
09CG+5)&7D80)D.M,07F=:==)A1'-*B(NC&B29NFB,?'HB4D,D1N20/9C@,>D:,'*2'A(01I>,?9@
@237
aattctttgccgcactggcccgcgccaatatcaacattgtcgccattgctcaggggatcttctgaacgctcaatctctgtc
+
0157B=7C<<=MI/,(IB(F&<,N,56BLAM-JD-4I*M)C@E85LFAI+6AM9AJAA&31*0N;I-MA'*KB6ELF@I,J
@238
cacgacagagattgagcgttcagaagatccctgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaagaatttcgccgaga
+
00(0A1L=+=A*+D8L16L&MMGH8K6/12?HH9@,3JH=*BA*8>>.5/,:7B<*G:+E+N?FIA9JD<6?5@?03,*<(*69889;2DEC
@239
ttaccacgacagagattgagcgttcagaagatcccctgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaag
+
0000HD2NG95*B=N-='>60/M(BG=N4D9'H4K7D2((E;@/?=0/=2)8J2ACK3B4C:;NN,/AK(3?H05M73&:&9;=
@240
caatatcaacattgtcgccattgctcagggatcttctgaacgctcaatctctgtcgtggtaaaaataac
+
00000=6G+NN&HM'>NC2C3D/+1F(FN=7D<345)@<**?;39?K7*'13EG@/7=J0N*HF?7I=.
@242
cagggatcttctgaacgctcaatctctgtcgtggtaaaaataacgatgatgcgaccactggcgtgcg
+
000007:?G*5843,G99L:3&*(
@245
gatgagtaacgcgcacgccagtggtcgcatcatcgttattttttaccacgacagagattgagcgttcagaagatccct
+
000034E0J1)H=4FLJ6,9=6?>:M65EL+-ND-FGJ1'(5515I-9+5AI)D69N:IF<;=5J:8N9:2I5D5J<+
@246
agcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttttaccacgacagagattgagcg
+
00BK,K4E-L>(L9''64A6@HH>/)G&J20.JLI5&'J@8;2A&I,
@249
atcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttattaccacgacagagattgagcgttcagaagatc
+
09.'A&1&JAG@/A7I0J'01EB)F-I9I<7(M33,D>G-15'F&&'<>L-(5G?320(.BC.8'+7L31GGI6G.247I933L9)>>'A.
@251
cctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttattttttaccacg
+
000,J=KE?;C-CD6AH@23+J@&8?3E1@8=JI./<=,>95.-8?0K/*>CF?L@)@*0E&JC5GAAH&I.5>
@252
taacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttat
+
8@NMID/I)'8JKA26KH@K@2A7&?HH028&=:/6?H897F?2E=;D2+F6AAGM@*G13LKE<(
@253
tcagggatcttctgaacgctcaatctctgtcgtggtaaaaaataacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcg
+
000;N3C2/@<'71NE1J<5B<-LID0H*,+N)G)E,4)@/4=3-:?L;-2/(M56:LI1*:N.(AE9H96LJ6A=D1(:&N;0-:A>A0.JE1MM5LL@GG
@255
cacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttattttaccacgacagagattgag
+
0000H<+'A4A.DG-<;.A.-HJ/7;5H=?KC8I0,5MH;2.F?=:0C,K4&9,4/)@JFHE8,H.&)G,I6:1CN25BKDFM1+7/658=-M>H
@256
acgatgatgcgaccactggcgtgcgcgttactctcagatgctgttcaataccgatcaggttatcgaagtgtt
+
F+B11,?-9I:)@60;,KMKG&F'3@?.=9N)H/,BE-3/JF4?&?9B/8*:36.4746=<9D>?DH.D22J92N;>(J+7H6<9*
@258
atgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcgaagtgtttgtgattggcgtcggtggcgttggcgg
+
H-=2FK3C7*H7.9@&H:F4LD=(;+&.&I<3E87J,M+K+;1C2D-(=IIA47I-E46N;G7:E528K,0L1*-I?3/NG77H);&?*@+N=?
@259
ctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgt
+
=.I;NB,<<.JI/FK.,'J7ACL+NK=NH.2FM)5;9;7NBNL:,KB/)3MB6-0L:-5E-F>DJNEJ@,@63&04H?78E;B?G2DEGJMNJN.'8:8;3;F2C+'I17:0C
@260
atgctgttcaataccgatcaggttatcgaagtgtttgtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaa
+
000'9K5(G4<*/4A0BI3@19/KFD@.J>MMA96/-G6,2*/LCB-941HFK56=5L,29)8AI942(,/L5@+5KJI?/@;53(93B9B1:?J2=FN;B&@>.032/:M+1B52L=,/*DB=2'G7I<.J2;8H:*I>;GNNC@9G-=M'LKD;F'6E
@263
ttcagccagcttttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcggtattga
+
0000;;0KD2'-D-1L0)/M1@A3>,9@DE-4)DB-@*C>6=,?GK)J8J4.)2C47&9M1.N0='1D(>FBM65ID,1=);FB7D.7GDI1>+I1/L
@264
tcttcagccagcttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcg
+
000,?86K-E'/*6I@=2HGKM:)JDK'>C07HF.?;?)K+:A;))F3=NL)*D.LM1AB,N70-+78E2J&M(.*&D@'A-G)3.AF>1J
@265
gtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaaagctggctgaaga
+
000('9@7C:L8M/L7H//A-M:(-@FH.G255MD0M+;:1(DLJCH<.C,9+1N<-F=9*NG5:A)I31
@268
ccgcagacacgtaagtcgatatgtttattcttcagccagctttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgcca
+
6CEBI5GFJ'61D(8:C7C7F6K>M,6+&9N*36J,*?0;E/G6?3
@271
agcaactgaagcgtcagcaaagctggctgaagaataacatatcgacttacgtgtctgcggtgttgccaactcgaaggctct
+
7;<,(;)=H?(?G4854*5;/N*4KA?'AJ;6BL':F*M)8@JH,HH10EJ('&C';.*0E:'()@'(DFHDM)G)F5-8@
@272
aacagagccttcgagttggcaacaccgcagacacgtaagtcgatatgtttattcttcagccagctttgctgacgcttcagttgctccagca
+
00C5,7FH=828;ILNJ(6A44DC&9L3<7&N>B)6'2,J2/KFI0N.=D7FA7IAH6'6H/N&(()FAFF&F-'E5&L7L6E,,*JI/+9&@83C/KJIC*IK)5*2H662+N
@276
cgctgctggagcaactgaagcgtcagcaaagctggctgaagaataaaaaacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaa
+
000),<+H(F48.:M?0656FJNH,.2@@A(2ED'IB8.92,:9KH7@5B>5E7'5J?M&)))?:31.M--5;=B+J=F00&7@.9)6I3@<)@>?3G:2AD.63=/F+:87<.7.=F
@278
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggc
+
D4.BA)670:MAL;'J'(;0FA)4I80'0M2+IK0?1IJ)47>*1/=CC54=/>3BNC8=0>B;.7;7?>C'I4(6)L4E-2HB(5'N::3KFN,?9/D)DC4=4J,*,>DFL2'+G@@;/K,4*H1(A16?.?0DBDE
@282
gtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactg
+
<+?)=L7@N2FGJE>>+ED1J9B5;KFEIE&//)4*3C.A8H?3C0C:GC)33<*8NKL(@@@46AEJK)J
@283
cgccagttcttcctgccagttttccagattaaggccatgtacattggtgagcagagccttcgagttggcaacaccgcagacacgtaagtcgatatgttattc
+
;6LC2@7?.DL*;+254=H4I12B.'3(6>5=3A=39N7D/6)5IG5G(F(C2A9@;DC'=:(3,8>LA33J5<95,,H@:.A=A''-I9;C0=;A*+)72.
@284
aacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
(4-*2>G*04M8:)C@+E10IEE,0/C6EL08=9,.)NC5,I:)+7'&82'JML;/.4GHCC?G,11I3IDGI/(==1KLM'?1C:5=6DG8=-BHN=
@285
gtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
00?>EBFI>5M/C&,@N5*8@J4FKLA404/4;N&'2B3,G>CM8)4*:.F7;@EHL*F/>;A@).AEB:/23)J60L)M7BI
@286
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgc
+
HJ=;;.*.?21LN)496-(((I5/N(BI50>F.A=5L/6.8779K''4*9:L6>:/5H'.6L1@1G+7BD7L:K.N6*04&>F7>E'B)D02=(I7E,6C94B.(.?K8;>/G>,6FK83:C8GH62>J&E0/NF>C3&*+E:EM;&41N?9L2'9,MH-)I382>L3/GLCJ&-,(;72.+H2?8@8,H*A)@-?@7D5MLD6L/GE
@292
aagcgccccgagattaaacggctctttggcttgcgccagttcttcctgccagttttccagattaaggc
+
00080)M28+8MB;2JHLG,9D6/&7)H'-/GJJF@CL<*3K2)I*??>*4LFAF:(HGF:32KKJ1.
@296
cgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgcaagccaaaagagccgtttaatctcgggcgcttaattcgcctcgtgaaaaa
+
000>G&?F4,:>GD-)ILN;-7>(97FNC5C.@I;3JE(00101<0K1;K'7F;M9?4DL.K15C/L<=K9.F3>A33.,D'27<,26BH5E?'H++3C5,>H/MCE95K=6J
@297
agatgatattcttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagttcttcctgccagttttccagatt
+
00000N(?)2GEJ++2N=BM&/=LAKKN10H*DNF='CFE+H*'(MG+MEJ00M&',1AEJC3D4;;.B/GJ=J7E53J?JDI1'(7(
@302
tgaccgggttcagcagatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagtt
+
0003F,*/BBJ3&6J@H:=-6F&68(-@F06DCFIG(KMD;N::BI3?I4)4B*:8H1ID;:/BL-1CNHM0B)@/=C3IJ&*L-=L&G4;'.*9>?ND=
@307
gctggaagtgcagtcaacaatgaccggggttcagcagatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagtt
+
003/+-/0D?>+N3EB,FL?2?/(85ENEH5AMB3;:I..0==/9H'H;BJNH(8@/+6CN6C1DA)IG83H'G+*)H901,1F;:M4&'E=CNC.:@'1:8
@310
cgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggggggttcagcagatgatattctttcacgagg
+
00000LF<9+;FH?*5-1L.9L5(4(N=-8FD(.A&&J36A*/1<0I*.=B=)'1D.88/5.+:-KG
@311
tcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccggttcagcagatgatattctttcacgaggcgaattaagcgcccgaga
+
:+.L6E@3@B*@8=+LK?G'31K/I7=*NJ<0*0M,J52GAB4'B,75:KDIJ6>'E*9N/7M9+:E3/E)N@<73'F)0/NJ?D&BEB?>G5IBJ7+,/'K363CA;EJ
@312
taatctcgggcgcttaattcgcctcgtgaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaa
+
:+.&G>&6*C/10)3A@.LLA&0HC-J45;.866L+F@A/(H.-(F@N11:39;FAFHHH9BK2FG<==HJ7;GA34ADJM*7C.FK*'&/<*C.EM0=6:A=G&M,;CI:?9J
@314
gtgacaacgtggaaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagt
+
0@7;:C8=N09FG&690M:*62E;KLKIHKI8D:BC6:L35H<&@NG@@297?(&+4H2(-@A>?
@315
cctcgtgaaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaaggtttccacgttgtcacgc
+
00B02H9:9*1+?G,.+(I@5/8AD>:=9?==N'/(,(GHBD2=I&71A9>GE57K3*27+.D:4=6?=G(=>2HM3D=89?*0IANL850*=33>(11II'C-JIJ*01J2:;E348F&MMC1/>('FDA.**>83GIM;-MM03@EH'5=F(=D*2/A(@(BFG9L@+KA@28I@@:G>FL'@8*N;K(>
@318
ttgttcggcgtgacaacgtggaaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggttcagcagatgatattc
+
00C23M,&E&&B)-AIJ*6EE.N=03613*6((MCE@2B(@F7KJALE3JKM2H5(.K*I4,H,6(:(&N2L
@319
ccaggcagtggcggatcaatatgccgacttcctgcgcgaaggtttccacgttgtcacgccgaacaaggccaacacctcgtcg
+
0K5H6J?-95J1H0:BC4<.7>6J1'NA,)MC5B+9+49GJ+MN:G;F7F:K1E;J(?8L5MMC:(8*B0?48EJ'
@320
tatgccgacttcctgcgcgaagtttttccacgttgtcacgccgaacaaaaaggccaacacctcgtcgat
+
000F922=>G>+'I(&D=>=5'2'09)H@I,BG;9>6/EF/C,:56GM-5(1.)AK@+555'*L&.@A&(F5D,*9FN
@327
aaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgac
+
0B+>C)3E7&.K3J=-)3L*:./6H,=>2KL?6A07L(.90?&33(N5:1LN'8L>.MFL'ANDLHHBB&,4)':,3L:8MG9/80<-H39L3BIILDC?HL8>L*;J./G.9M);?8K28+3GN:&86FKE>D=@CN;NF//)*31J;(/*K
@330
tccagccccaacgttggtgtcatagaggaatttacgccgcgatttttccgccgcataacgcaactgatggtagtaatccatcgacgagg
+
00(D/=FAA*G/33;G><185L0,AA)F7BM@4G-?-IMGL?7<@A3&3KF&)A6,GC2?*;D5487L'JL.7'M45G0E'475(219>
@331
gtcacgccgaacaaaaaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgacaccaacgttggggctggat
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0/,-+B+)BFI;?L;H/.'54>,))-C2'3;(*)3)/,;-.-K26,K7+30CN,+0M=/@B1E>H?(/((NMJ)H6&,BD59,)=<;M22K4,J99(7I22DM'N)+FJ,EK2C-
@332
ataaccggtaatccagcccccaacgttggtgtcatagaggaatttacgccgcgatttttccgccgcataacgcaactgatggtagtaatcc
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00))A'4G@091GL3A=K(@8L428=7:-?*C1+E-96.6D@;02-??NK/N7+N1???JC)MM&K400A,1J0-*I(C7G?F+/).0K08=4/-AJB4:=4K'(5,G='?8HN92+,(+B)(B1AKI>=9;;CBEEEE.H7+1C8&576=DH/-J)763>8ML1L5+(?*+4EG0?:CJGN:@50):('/(:028IG57M
@338
aaccagaaagaatgccggagaacttcatcaattcatcacctgcattgagcagattttgcaggttctcaataaccggtaatcca
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NG/BH9-AAFB@,E@'3E908.&:'/NM'KLH12'K?:*/;-7:A:KA=D494:>DC>*18.K;DAB@K'LH66'<.7B8?LN>09&(FB1;@27&AN*'<'7&;:2L898853::7>HCGN&+I4?+92?(@J17K@4G.L):6
@341
aacctgcaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttagacgaag
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000M8KAM-LKDEB697+)-NJ9.@>/2MG6,D:1LB;<*?JJ&&)2B89)NEJ.DCI(&<,IN)F?0,&.'B,6E8I<;JE,,H@57*=N'7I=4A
@343
aaaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgcttttcttatatcttcggcaagttagacgaaggcatg
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000F8:+G4;'N054J?&G.>':12@6231-75J86N99G
@344
tctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttcgacgaaggcatgagttctc
+
0CHA87M&MN?L0.?+'2GL/+++E)LH,4.C68D:7F=7J6?1/F2I.@H&)&-:.,&317G5-MLC/3BMG=HC469.+.6)>.F/H=BF259I.+LF'5/6@8B2>L4441AN4-()AD(E0>*0C2344A6*6:DL*3N,)&.774L(E,6CE-D(&B(C6NIM29DB/A8M:ME49GK.64HEJ
@352
tcatctcgcgggtccggttcggtataaccccccattcccgcgccagcgtggtcgcctcggagaaactcatgccttcgtctaacttgccgaagatataagaa
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00I88:5('DG1G@D'/);:1;-A>I.J:'D30BA73+;@F137=8J07?2:H@M,E>4)HNAHJGE3?,)L45*N,BFA(-9JC&=<(-DG/M8>>I6'?
@353
gacgaaggcatgagtttctccaggcgaccacgctggcgcgggaaatgggttataccgaaccggacccgcgagatgatctttctggtatggatgtg
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000*26+>(/G0843C71'F?2IC6*M1CKGK)L/(;H@>0L1?2;C(7,B.3C0H>47>MK:0@CGL0,:+D3A5,-KL1I>@-;<0,4C@(-L
@355
gcgccacatccataccagaaaaagatcatctcgcgggtccggttcggtataacccatttcccgcgccagcgtggtcgcctcggagaaactc
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0000-)-D*<1J(1A*JDLH?-6M*9*9H0J.&?-9DK/EKF09N<.:DA.L)6,9C;IDH&-?(-:KB;5(/0&;*9A:JA>C2LD4H1'
@362
caggttcaatttcaatatccgccagctccagttcacgtcccgtttcacgagcgagaatcaatagttttacgcgccacatccataccagaaagatcatctcgcgggtccggttcg
+
000-?/?2.?(/48,@5F5F<;'I=9J7A6?2C,9,JGIN;CA8I3JL---IB'L45I(3B
@363
taaactctgcgggcagcacaggttcaatttcaatatccgccagctccagttcacgtcccgtttcacg
+
0HNE7HJ7A865'-9.E/N57A4=HHII&IB2;2B:K<&/':.(BKL6F&/3C2FJKF1&;//48J?
@366
cgccacgcgcgcggcaaagagatcgtcgagttgtgacagattcgccataagcggcaacatcaccctcggcg
+
9;,*HFG+)'-4=&I/(&+,F93K1F69&21CL:>B7L5B4-CGC2K(EHB8G>0+N-N=C+E=:G=L.:G
@367
gtgatgttgccgcttttatggcgaatctgtcacaactcgacatctctttgccgcgccgtggcgaaggcccgtgatgaaggaa
+
000F:G@43?K*3.E<>-62N:)=<(K37G>B10@C+*G03AG>8)?3CI89A<A8=>68/
@368
gttaacgccgagggtgatgttgccgctttttttatggcgaatctgtcacaactcgacgatctctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgct
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000G@&?2*MI;G+,H5'F,'(2>791F'@3,:K4&9=G85G/FM=9).(48@BK(857,1G??N7DJ&L>E+<(A5LGC7+);;8+>)7MD6>E2M.0&7H'@4<
@369
gtcacaactcgacgatctctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgctatgttgg
+
000F/6LM1;2:*0IK'J()HF3.8.4-9K<4@FA7*25G)C;?7;B3H*:&@B?K<=
@371
atcttcatcaatattgccaacatagcgcaaaacttttccttcatcacgggccttcgccacgcgcgcggcaa
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0-DME>MB8>/M=03M<*K)0:M:5L9=7>BH85'*N+G>/HN0(>:720;5B)7>-?=?C)6>CM&,K1J
@375
ccgtgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgt
+
0-34)/7<.+14;E8B;)I
@376
tgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttc
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7+@5EJ:6,G:E5;FFAKDL&4HB'><)E*;BL*CL-H=8D+*BG'C5LH)*/'D+6+E?E&MNI2D><*9;57<2/476J?@+C(4
@378
catttttcactttgaacagcggatcattaccatccacttcggcaatcttcacgcggcagacgccatcttcatcaatattgccaac
+
00DCDD7+>8ILFJ)@&J5@.LJ/918(?4G'7G*=.8H(1A-I2-@G;--+)>KF'IC-&M,D83='?HM=B>83L;LGFJM,:
@379
gatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttcaagtgaaatggcgaaaacgccctggccttctatag
+
KL.)M0-BLBJ:+8HJ<8?G9&GH&6?ID>K1CA=8=/MDC14/==,9<)
@383
atccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccaggcgttttcgccatttttcactttgaacagcggatc
+
I(&D<=H4@I7;I4HJ(&*GC36='8643N?):NM-,3.('=G.<-B.JIF/)-4;+K;72<44>*)D<@)DG98MD=&GF9??K3I2E5-6/C@G4?<(E(D6&E
@386
aacgtcattgcccgcaccatatccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccagggcgt
+
EE)?9N:F(K+F8:,6@-FLB030A6;LN30*I?.M0;49J&B<,,+K>'>AKKH(:7-;=/8G6)N:.*;*3C,629NKGBAA;(*;:J<
@389
atagccactattatcagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctg
+
0000-;(G/(AI))FNNN;-M.38=((C>*-G1C,7A:-HC5@.60(.:43A-3@GC'E44''>42&-M=6C:K+C>NHI@:?8
@391
actattatcagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctg
+
00JI-0318GFGDGD6@G'MF=?/M3*K@,B?.*F6.2H44D5D04KK7.=6F:AHFE)7L2F6(I+1;CB52@LF)'N3*F?
@392
acgtagcagatcagcaagacaccggcagctgtaacgtcattgcccgcaccatatccgcgcagtaccaacggcagcggc
+
26@1;L<.C63JBC?-<'&J*(;):B1:/MEKAD+J'H&>')0D:65+05D@0+C34;0D6>CG>I?M0H1)EG&L3I
@393
cagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctgctacgtaccctct
+
0'.*;)E'&>CN*<->,:C>L7GL(:E;@/E7DF1M(-?F11L@)JEA>AJIM*D-*:8/:M)9&LMCKD/@,:6/E26@.(
@397
cgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctgctacgtaccctctcatggaagttaggagtctgacatggttaa
+
000M)G+7HK0?2DA+G/=B(=9C7@9'6ALMF):&9'9><0AI5M/-K?
@405
gcaccatcaacaggtgtcaccgccgccgagcacatcaacccgacgctcatattggcactggaagccggggcataaactttaaccatgtcagactcctaac
+
-+7G(>JI9+JN=C/=.+9.:=
@406
caatgcaccatcaacaggtgtcaccgccgccccccgagcacatcaaacccgacgctcatattggcactggaagccggggcataaactttaac
+
000000N00/6-8:BI703(,II+.GN'EE6=L+K/2;>8),4+=;BNI.D8438J?K&B/D,L@((5<8J55*E:(A3/D6H6/'KC2I24
@410
gttgatgtgctcggggcggcggtgacacctgttgatggtgcattgctcggagatgtagtcacggttgaggcggc
+
-M?,<00)N4NB/+<(N):@(N=&J70)8'&BE/)76?8>*4>F<,>FHC:&6G>K/A)5LEF388IMJID2',
@411
tgaatgtctctgccgcctcaaccgtgactacatctaaaagcaatgcaccatcaacaggtgtcaccgccgccccgagc
+
0D*;E.5??='*?F/61()JJ4A)>ILL8M>5/?4=C?L5'4>:/*&.=5+'I8=MK;*9@/E(,9.=/KDF<
@413
aggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtca
+
CE.?+L00>)4897JM'0II.5FE61I76*1NDDF9AA39GDB,G)84K52+E4=D,'G@I2CIM*+,=()K==,:L(<@4GKA8GFNA7?6@L<9D=/
@415
cctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcactctcaacaacctcggacgctt
+
(;G5<107,F078J8H7D'61*C?-L63H9=M8:9N6;JD+;ELK-.)*3D&,&D30627NA<>L'DE/(L;',>:&K*/,;E-&
@417
cgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatc
+
D()C0:AG;.GKM;?K>@,.-@?1<2:=KC*N>8LL?./HN-M;&L34L34B.04)&H*F+F0
@418
tgcattgctcggagatgtagtcacggttgacgcggcagagacattcagtctcaacaacctcggacgctttgccgat
+
(EADDA@KE'::2J,,,-,J;:J)88EJD;CA6C)JF.+B:D3M*?C*B>:ID:AGD5
@419
tatcggcaaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtcaccgccgccccgagcac
+
02KE';3@29EB3;G5/NGN4*JG,E/K0L56.BH'4L8K9A4,8LK?&+D-7CMB30L)8))N.17N:IJ&AA*6M>:076ECJG,L9&D&)M1@L??(4:57+C*3,><9/6&(0)M>1NB;IA4D0F5?+B:@,B9/AM:CN)0J=3+E>LC,'E&B)K'N/658:4/II,&05/22@'554+L&).FD9-:<&+/+@;&.=H:C9KBJ4.8@7G.)6
@424
tctgacggcagcttatcggcaaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccg
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16=E=JI&&:;9I:>MKI=;,8?*+G-96A;;17@4G?C:+:/E6/HJKICDI@:H=5N4NB?>H+/J5?M6;>===AI,=
@425
acctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaa
+
09BCJMF0D609&=GCB0D1F(.;-AGAH);;742KJ(6I-0.AFF>;IBFI2';
@426
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaa
+
6IE4EJ';/F5.<6A(B.BL8613)3'CBD,:I6=7?/72;3AN&+23B8524+'(J'&9E3K3C1GHBL&'02(/9ECD>/5+(*3=HHF/?)&
@432
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacgggaaatatcgttatcagtg
+
00:2'.)(>@:A.E'I:C=?:,J@:2,GC4.=G930>*0N&5<)JM@5K-)0.>B+L9/J)/CKK68C7@I(D'H/A<56/IND7?'DMHIN@AJ1&<1/?(/8-4&
@439
gacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttatcagtgctgggagcgtttttgccaggaactgg
+
0000:;(A;&)/HD62;)?AD&1)+2=JJA,06KF++1:(J+1BJ-*B5;<83&7/?/+B)NB88<+&LMD.&80B,:FGNF*B0*'IJ':K>+8MI<71BE-0
@441
ttccagggtcatcgccactggaattttgcttacccagttcctggcaaaaacgctcccagcactgataa
+
0+=1=>ENA5:&5BJ-C9'AM(7<1(;1HJK18=8))-EN9+JJL&2;9A54(A2I48N8NC.JFJ)055NCD(+0GA9&.3HJB(@A34
@446
gccatcagcgccgcgaccaccgaacaggcactggagcctaagccccgaaccgatcggcatattcttttccagggtcatc
+
000B4BE62..C@8C8CD':1N3K1AK6;A)E(54?FE?(7J77=89-0NK>B;HG?FEE0N>IAKH86NEDC23(7<,
@448
tcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccgatcggcatattctttc
+
00A/I<1?NIJC=.BCBL;C@95:=L*7'*9J6)6+=+J=.LMI?B*)?L)7FA.5+*(>E0@+837*G4,4
@449
cagtgttcattcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccg
+
:>-752F,6IAD*E+B7KN-KF)(?,@)L&>CD/*1?(CF&.9(D&/=34:D?,8/3L**+1E56.
@450
atgccgatcggttcgggcttaggctccagtgcctgttcggtggtcgcggcgctgatggcgatgaatgaacactgcggcaagccgc
+
@C/CMMN=B:7,D9JJJJ.NDE(=LGI8D10.85ABI4=GF)?J(G8N&.N@H58J@?JMN;7K<*MM64>?M/3643,H?:-+E8?5&>.2H;249B4A2A8G<81?C*J?+N;8>C)2((-,;2F,7'/4+3-1,N/.JK0/7B.2(&J/-H9D*GF'+H,6CH'D1A+D&<(50:0:+,J>.A3.,<;.+3@2JIJJL&I*)0'2>*:K3HHL9;9,GB.-A-;AC'+139I/D5
    0HK=1-BA5M)I>'/+-'<2+3@9@N
@460
gacactcgtttgctggctttgatgggcgagctggaaggccgtatctccgcagcattcattacgacaacgtggca
+
F/7D44J/0+88=3E2;K2IN&I,'F22=1:B(@JM9/L)K<:GNI<7F==
@461
acggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagctcgcccatcaaagccagcaaacgagtgtcattaagcggcttgccgcagtgttcattcatcgc
+
000000;GI(CM-9>':JK5NE5A..=0'I+?>7AJ>I'..H)/<2/M44(@,-<2=+F2/8A?5'M;BI5I'-&E:./7&ELAKGEB*01
@463
gatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgtttctcgg
+
M>:9-EJ-;8-;H@KH+-4JH:71KI8.==6NJLKF.<+5/550.*LH')NNEB+@4GL9L/&:8C=9
@464
gatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgc
+
005/6)HH;25-2A*.I*?M&FN&FF=4FB4?(G/8'53+=?DJA*;I*+MB88&KF?L:?6/:E(*24I?)
@466
tttgctggctttgatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
+
00D4BA4;'C2I&9&6+N:<4E5*3;AI+L&-JLE)5N(6&&5>@56+8E0K>E?1<*F1-;4@2/9/<)/:-+M)-0B6-C4M3,/36=I1?3B=>+M;MG8.?@IC/AK7GA3H/882<,IN(0*'BA.0@:,0?8<,I@@@5GB
@468
gaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
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,I9,N/=HDIAE?E'5J:+-<)6I&*@;0<(64D*N9N2-88.82)-:26H41M9&M3H=+=9C88)K8(A9FA:
@469
tcttcgatcatcaactgcataccaccgagaaaacacggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagct
+
2;/7/H2LI,@=I0F4?)H'?=+6DIIFM*;-=3.*7+F6-(I&208M/*8E/3E/(
@471
ggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatcgaagaaacgacatcatcagcc
+
;7/C*014+A077F,7FN0MH(.L==F5I4?:>)C(('91K??:-M1
@472
gcacttgctggctgatgatgtcgttttttcttcgatcatcaactgcataccaccgagaaaacacggtgccacgttgtcgtaatgaatgctgccggagatacggcct
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00-'D51D321KIMJ9(C(3)0>E<'/9M(=?8)4G+0;=@F<+DNG;(*;+?3@?<,?MEN?,:J1+L(E8B==6D1FM4;:MA?D3AG.C(((N?M96I'1&K62M
@476
ttaatccccggatacgccagcacccacagccactcatcaaaccctggcacttgctggctgatgatgtcgt
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*;08G&-M05KH)EMK0H/F5:'&-IAM8:/*3FH1N@6E=<&J,'?CFC'.&*FK@3E+@MD&:1*D7-
@477
tatgcagttgatgatcgaagaaaacgacatcatcagccagcaagtgccagggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctc
+
0H;(K51G('3C.4JA.-5)((')?8K0>8>M-13;67N:?M(3E:JHE.'*/C(;F1HK13=+KC5*2
@479
aatagcccctggcttctgccgtcgagactttaatccccggatacgccagcacccacagccactcatcaaaacc
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000>4GLL@*'&DJ8))CF@5AI/A,=>?AD-/1H<=@>A6CE;7KN67IⅅLJI(19GL,+()2@GB/(;
@485
gccagggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctcgacggcagaagccaggctattttaccggcgcagtatcgccgccaggattgcattg
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000;+IH<<(GEH6C&'.2&-K5?.=GN?,20&(GC46H>>??=<.G-LN70*J?I8:M)9K9JMNECN-64.89&B
@487
aagtctcgacggcagaagccagggctattttttaccggcgcagtatcgccgccaggattgcattgcgcacgg
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00M=/KA;DLN<'=5>-=;.D7+C+L-E0A0,57)+GINN61,G9C@)<&F?&)INLEI@)KI)=M57L7I=
@494
ccgccaggattgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgag
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00+4NA>EB>)M4ED=//J:7F=5F.++@FE;&;JN6)?0-B2GJ)6G/9IE&LK9CJ<=N&&@LJ95F.*7M
@495
gcagaagccagggctattttaccggcgcagtatcgccgccaggattgcattgcgcacggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagc
+
0*5LIK.B26>0L+)2&>4/.A?864:)B1F'E,12)J(+I6BK?M6.A889+G(::=()MAIB5K70//5:)3095D@DH4IIFJ(L'L:'MFH*3IHEL8NC&0E.?@8BN>D;5<+89>N=6=II10C(
@498
attgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatg
+
0000D'1='0.G8(,N)H/5:,:8;.<1;:KFK5)6JME;0)?FE+(5D<;1L'I01?E+<=N;L,/7L;17I.INEJ8;?,E
@499
ttttttaccggcgcagtatcgccgccaggattgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattccccccgtcagcctgagcttgccgcgaagctgatgaa
+
000000F92/J:2<:H+&BL&/I*?L28K2*EJ9F-GKE:HE))7:M4M@6;1+MC:<2A9G()78AMC5B26H7JC,396&L2MN5,B@MC4,JA,FJ@HH8*H+K8+&*1<02.5
@500
acggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaac
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I,4BF,8&)D(:H>5.73(0*6B81<2A?I;;L1F;,:8IK:H@D976@M>7GCI)M,.''ML?*;CJ4-7+*J/NK4&GC(-NAE?5K
@501
caggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacc
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0:?;DH,&A);B)51H+L0(H7&@)=NKK?A?CH7IJBA//./IJ7B,9N2A>JI**B>56A?3-E&B>J64*>AM
@502
ttccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacgg
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009G>7BD9-?CE??)&C*>KCF6+@L/J8>A;9'I<-5)*6?6H,F.(B0I4M&4//+K5J,/4;
@503
aaccgttcacggtagggggttcagcgataacatctttcatcagcttcgcggcaagctcaggctgacgggaatagcaggc
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000059*90,N&525=4C,GG2+8H8I;
@508
gccggaagcctggcagtaaccgttcacggtagggggttcagcgataacatctttcatcagcttcgcggcaagctc
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00,13@83646HB?6=4M(>8EK6:+2M5E)H(I+->N=1.87HN7I>91D&,)2;+7G-+AKCKN8.F67A;F-
@509
tcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcagg
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0009BF4&4/B(<&L+482LKAK1H40@72I.>M-G31,(53?C'?G82A)LLI/GB+*4CC1L;88B:'L)+@=8CJ1G7>+
@510
tattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggc
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)G=CK;N0+GG'.4L*G6M*>7EKDHB+()N:N8H)&G(MDI:-/),,3:.F9175:8=JGJF'?CD&'3MH&0L*C>0D6MN23E5')E9&
@512
cgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
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0000G'';'B4IF>DMI6;FJHFH9NI>F(N-I.2.G=@?/7I?JAC7+GA;3'),9LEF?&CM;(@(8G6=I'63E;2,HJD,F8CCC44G3;.
@513
tcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
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0.'7J6,H@C22HGB>M.(?*64@643&81@C,=->N+(7/(3K-@+FLNG,?E/J---GD6=*.>.&9'/AJN1&6N@(&F@JJBEJC67+F
@514
ccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtaggttcagcgataacatctttcatcagcttcgcggcaagctcaggc
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00).I04?EK;)B)/62:/<0F/.:/:K1+888+7=/59DCHN'N:E,KA=@/L/;G*//E6?;NINL*,*
@515
gaaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcggt
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000&=K.@)>:J>83G'3(/4:4JH8@7,-N5@//K;)//C&>7D@N:7L=.M*M*=D)2K/=@7(
@517
ttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggttcagcgataacatct
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.;G3C3-ELJ(E4)@1&4&,<,JM5JLAL-91?-(H@LA
@519
gcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggtccagcgataac
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0000(30DNE&&-A+9C4G>@I026)JAM0=ID,;L@?;I149L6/;?,8:.':GA+'B@(2L);3A.B?+E81K@,2.@;?>C5E5;9*'>K7M6562*AI&9C?G
@523
gttactgccaggcttccggcaggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttg
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000I>)+E-,73G@,8:,&J:F32>,M=BK+,J/G7F+FADHF&N;7GCB0*&A49D)A2K*83NMC;M,4@.67?NN/5)(B
@524
gagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttca
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*KGBF=M78LN86MGA2KG2L3K:,259M9+B.HI8DD+?GC0H@J4;&NN0E2B9C)J(8KCC*&/>:I:)36-6M<@BA:*/@7&-&62,M>E.L38BM
@525
aggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttgttcgctctgtgtgacaagc
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0K>*K?65**&=<-A.3NB6>K&FE2.>8J&865,D22I??L/;A@(.LJ&<0C9<7**M,/A4,@I>CH;BFM/94+K':.C:BH<
@526
gaacggttactgccaggcttccggcaggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggccgaccttgttcgctctgtgtgacaagccgg
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MN@B@JGKMN'/CGKL:288B*A,1?)?*)'.4I7CB@A014@097<@8?0L3G(J9J?/CJM+*9=N>7HN=<&J?'J3'KH@)=F>(318>D2CM7
@529
ctgggcggtttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctg
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009H69>L9@@A?2B11AD'9>K-L9466DG0<)BA(6?-0+8HJ=L7=A54IN?L+J/B(/1B0)>J@KEKD(@0J0=K*'+'7J>3/H@=/5(*/&;8GE0149)I23A-D
@530
atctccggctccggcccgaccttgttcgctctgtgtgacaagccggaaccgcccagcgcgttgccgactggttgg
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0.'N3.159A)IM3,ED'.JNJ(47087<4.23M+&@,':.&0G4-F&FKE026G*
@531
ccggctccggcccgaccttgttcgctctgtgtgacaagccggaaccgcccagcgcgttgccgactggttgg
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*(=1BNE1;7JJJ-+:GH:)G,K>1>GC1,DA:BD(DE(/A:MN.:IL/?7AA)//?MI@E>K7NNJD;2:
@532
cttacccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcg
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>FM2)*)+H+@;A1265=02HN0;/J?9;42(03;E(0/B/DE@*MD5(C'L&0D9;3,-IA4-C6&L9HE?(DB)83/7KGM7H>C'IN'7N@6@,-<(9:65A
@534
tcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacaga
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0&)IH*;-44?:,(:L.CB+131('0J)&*A@BA8*:''CK-F;&>>@)A'B:5+':*L7)0=G*:JMG&A9
@537
acaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctggcggttttccggcttgtcacacagagcgaacaaggtcgggccggagccggagat
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000L?GN7:3+G:23G=4;C=EL=,B9B+&<+&L/@71=+*JF-9>-&=HH@71*80)7J-275F1-(=,K=<)6,'9'EM@@KF?,;-,AAI0GFKB?;6B::3,L&
@543
tccagtactcgtgcgcccgccgtatccagccggcaaatatgaacaaaaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctggcggtttccggctt
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00000G(?/BM6I?(3L@*/CK-L15<)GJ;18NF-93K322;9>'43I8D+(&>AK2@LI'N(018*(9B/2B70=5C0572A043B>*G
@545
atatttgccggctggatacggcgggcgcacgagtactggaaaactaaatgaaactctacaatctgaaagatcacaac
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0>8*0H9K1@?,?'*LH>BC'85'D7C;&F5E@GE(&?(892B&L@*D&G6JCH*;HK7?K4J-5,?2DKE46C/492'B&,D0LA..;70
@568
gccgagaggatcttcgcactgcgggtgacaaaatccagcttcagcatctcatcaatttcagtcaggctgaattccggcaggtcgtgcggaaaaaaaacagcccctgatttttgc
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00000008B>?&N462C1A8?M*@/05=J@)L+'H'C--LC(96I&5--6-//I6-=9/:)+J:@
@574
attgatgagatgctgaagctggattttgtcacccgcagtgcgaagatcctctcggcgttttttattggtgatgaaatcccac
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000244B-G>.J)66J572:'J?@M0CFKH6*KNG0=G@J1>CL?+N<+(MK(:<7=,0H:)4G43B;'8@05>FKF2/('B
@579
cgccgcgcgcacgcgctcttccaggattttcctgtgggatttcatcaccaataaacgccgagaggatcttcgcactgcgggtg
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000BF1M1LDJ&<&E(61G/&EKKJ.H&'&?6+034A:EK>1*68&==D'>:,-FNI,7/2M-(2=L8,,(A8:;@/4F80:,
@580
aggcaaacgccgcgcgcacgcgctcttccaggatttcctgtggattttttcatcaccaataaacgccgagaggatcttcgcactgcgggtgacaaaatcc
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000000F087'8F'L))8(9E7CEM)&GCD'G9LM+?889)'&3?-/M<3F9M,*0N3BH?*.2F?(5H');J0;3:A;41N*
@585
ttcaacattggcgaccggagccgggaaggcaaacgccgcgcgcacgcgctcttccaggatttcct
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4B'JJG@F<4)*,.3<3/'H(G)??HN*:NA5;85GC)NL55?EK?<);0?G>2-;MHL5MCD4;
@586
accgacatcgcttttcaacattggcgaccggagccgggaaggcaaacgccgcgcgcacgcgctcttccaggatttcctgtg
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000/HAK45(2K.B/@<(F:0M51IIIJ'=B719F6KN0I'D4J(3K&M&61K+::+.+(+A)N&3DC<4;,+=+4C))=K8=A'3.I
@595
cgccgaaatctttaaatgccagcgttggcccgtggaacaattccagacaaccgacatcgctttcaacattggcgaccggagccg
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073)029H2GCNG41/DK5F6G7M+6ENN7BI31+6+@4B<<*K*-IHA;(:9D=E'IJM*7HNA:9AKJJ',+6K76:3?=8,
@597
ttcccggctccggtcgccaatgttgaaagcgatgtcggttgtctggaattgttccacggggggccaacgctggcatttaagatttcggcggtcgctttatggcacaaa
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00-4&)3K/=>(5;J970N'42M-,&I--/AJ+NF;=N>B8(L1D6))BK)E0DI'@147JAHE3.2)@3MED80;8CA@2.I9A7.;<1@>>I=FE
@599
tcagcatttttgtgccataaagcgaccgccgaaatctttaaatgccagcgttggcccgtggaacaattccagacaacc
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000HD::C*JIG&@3JGE0'KEBFNI0@.5:6)/(L;?)==IN&A=/>6B9;70:NM2*G003J-/E(:8;-C,<8+L
@600
tgttccacgggccaacgctggcatttaaagatttcggcggtcgctttatggcacaaatgctgaccca
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00&?G/KFED9-H69=3'1.5>9+HCF*D.@.37H'EB2C27A&F95&2(LC7G6JN(51BB,:@N?AA'@2H;I
@620
aaaaaccgtagaaagcatgagccactgccgctccggtatcaccggaggtcgcggtcagaatggtcactggcttatcacc
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00(G,LB?09*=B2;0I'6I:9J1>C&I=3&+29/-;8+.@C*7=G>*3CH8-0.50*E>9
@621
agtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtta
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F585):=+&LK(2&B'&7*&>&+LG<4B(?064L9H9@?NC64-?8AJ/*
@622
ggtgataagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaa
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000D6N=+MLCA,8C6*@C<)G6C10A+/><7H*?@-:NFD;79HCC@G7DC=J=*==C=<&5-ADAN:,@8:CHNMK1HM1-+9;9B:9)I8M'>6NF>/>76D*;)EF?0?L.402
@625
aagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggttaccgaatgtgaaagtggt
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0000J/K97G4=;HD*N@J5:D77C13@&A'8/*:<;.D?1)>IC5)A)>?;7@BB.3GHD3G9:IL=D8536CE0D/(1
@627
tgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaatgtgaaagtggttatcctctatccacgaggcaaaaaatc
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0008:L07J+//;KAM&7N1(3D(&9+HA5'7L6E/.6G4)?L8//,-5L7N8'7N*KA>7)8EL?C';E7H07./:8863EA>&5CJD&<5;K8&G?,3&D8/(B<'BIF=N?L/H*-/(K0E6AF:M?0@
@635
tacggtttaccgaatgtgaaagtggttatcctctatccacgaggcaaaatcagtccactgcaagaaaaactgttctgtacattggcggca
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00H/N8K&2.KM?B8K0MF@55F)H914DM,4MME>E*6M)'<3'J,AMHBMB';@,KD*E*@FD(+DCE78*=?D4,*86588AM6M51
@639
gcaatcagtccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatt
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7NF3C,);'(8+*8>N<)?'4=MDMN
@642
ccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatttcgatgcct
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00;H=)->D-F(IN5J-6N)-+@*25KB8M>3(.,;6(>E+A/)/N9)'*L0ED&*4B0/C8(&)-42DJ+@;ALM
@646
aaaaaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatttcgatgcctgtcaggcgctggtgaagc
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0000ILN23K'II,EG586K*>9NJ00GM:@2B(10=74:6,MI/N&>/L)H?,1EG?C5/E,2AH::3==6.:GCE&/MA//)2)(//H6'M;>BC49
@656
gccagcaacggctgatgttaatcgagttagccgagtttaaccctagcgccactttcagttcttcatcatcaaacgcctgctt
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000A(CL'7D(=>N&9).??2J8F81AD0N3,BG.7M>H3-'&@,9FK&&:@<=BDC:NK:6KM66;33?5MIJ-HE6?=:MC3<.&70,H0(H56N@/B4GH
@667
tgttgcgcagctgccgcaggagacgcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtca
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FK,F8EL@4(F2M91>NE->B/A/I=CD777+'4D'(,4FME;J=''64:D23>;K*J'H-H-9'.BMAI8/6I-I)
@668
gcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtcact
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00.31N9/)B1012LB:K6:K+C@<6LI,?FJ3J+3:(65(9EMC>35A.-02..M-/G?48:M:8L*0B-F+(
@671
tcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtcactcggtctgccggtgaaacgttttattgctgcgaccaa
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000<.N:FN*7E<9(C;0JAE>(I2D=*J9?KMG&MM-?7-&(GH,JF71=,=6IE&;'B-DBCCDADL:K1CLAD>&+IAI&D'2=B@'/
@673
tttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaaacgtttcaccggcagaccgagtgacttcgccagcagacccgcc
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0000D6(+*6-)):=166@/&&'55<+-;&DJ@AC&3FCNF27K671DLEFFFE7I@BG)>:1IL1)8,,9IMGI';I@+N?E@I3G2(4LCK>&98JL:CD'
@674
gagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaacg
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00B:C@9CAB=B(&4>F*)GB-JA-='&8<0<4=GE0-(DE:3B@+EDDLIF/;@JJ('ME.F*(84CK)=1A(&-JK
@678
tccatcgcgttggataacgtcgcctgagtcgcttggtgaccactgaccgtcgtgcaggaaacgtg
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0?-*(?-,.'AF3:1:0I';.D7+(02N-DA/,8/5I)&,B-@72.*B:.C19,L+JH0:=2>'/
@679
cgtccatcgcgttggataacgtcgcctgagtcgctttttggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacg
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00B1>2+08HL)LB<>+83M(NNH9?H)6090A<77=IG0DKNJ.:'J)357D>+F'H4&.2:?4>'-(6L;=+2LB+57:JB@:-7(FHB
@681
ttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttttgggtgaccactgaccgtcgtgcaggaaacgtggca
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0000:7:<'=H*/:/<&D5D92;E*3*4E?51?0K9E.50>D=M1.GJ3D*.-A84E--H@7A2H*/9G+61KH1'F//(E+&K<2KM
@682
gttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttggggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgtt
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0000&0A3+4G:*3+.4M+BI:0I9&:/>>J,1='EAD:24B'C5+,:1)89=ML=C-&H&(GG*=A4*?3;4KL<0=F2'L3F'LI./J,0.H:I48579
@683
ccgtgccacgtttcctgcacgacggtcagtggtcaccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccg
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*EG85/5G;+?0N8N=)1L9E472N.ILF>/@G:H-<;:*GH5;F96B9)'*3E65-B7HGK3BH)98N'=I2FM/<)G4>EA7+@LI=*.6/30::
@684
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcg
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007-8)KG?1:>N2HG?KJ5?>1BK0137;L'H:J7KD1JI/:L'3@G1';AM8NDI-B-;>H?G86(;9.-C*,M8*4>3?76,&@BEC;C&J?E9&-K1DEMEB
@685
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttgggtgaccactgaccgtcgtgcaggaaacgtgg
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0D9N2C5EG*1>6JBH1?0B(.N(0;LLJ&=0E5E=.+E'LL:&;2M?GIK(3)+A'>2M8'<*,9=6)H.?&NC-E:&B7A/NAAB66A4@:CC368
@686
cacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatc
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0000,BI4C;6C*D..L9+,&+&@:=32IG:>-9JB4GL+NI@G))@*J56E5::=+&'9B8:MM.?AANAAH>83@CA)GE596:M?7M6.-?@71>.AG-KE?.L?
@687
gataccgtgccacgtttcctgcacgacggtcagtggtcaccccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccgcgtgtggaa
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0G=IJDI'=DI/MI0)762*8:(/DN9C,&3K*;'9@*37;KJ8;&(K+B/39<&NI=27(C>,M4M4.E+8-NJ;*;A4J=D>>4N0K3,(,(4>DMK9.D8?;(G.&?3C
@688
gcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgag
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0M6.41&KH/A*A/&C/B1,5-?=5G;IC:2''+2@B>F&3)JEFN;00K1&46D4E)C/IDG
@689
gttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcg
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003*61(@174CI3JK9+2<>C0;?B&M<6A)9-BB-@4-G,D1((:.E,'B-4K,)6=3?EB(A6.@4'/C)(6I5-HF=C**HA>(/'<+/>4NB&/87'KD@+DC:H1?9;LHA@54LD6-K'I@*K5J+'KGF=*);9=)'GKG>@50J.7F2>-7',8@D?H,3<
@693
cccagctcttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcg
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00+:EF,'>K,H'LG.'&4(5.=B=1C/1GH&(<*6I=BK8-,88<';N:NJ14&JI;*M<33/*
@694
ggctgcataacccagctctttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgt
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00000.+J'M94D@FCK=@7;?A?H97'1D/.14-+8K/:5:NNFC,M>IM@=68NMK739@CE@3IFKMH185LI2M:.@H-&'M
@696
cattgtctgttgcgtggttcatcatccacggctgcataacccagctctttcagttgccagattttgcggcgga
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003K*M+LID6'BH87J52-G6DFI4(<&-B>7)58MI45=>K/8;3C(3+@5
@697
tggccgcgtgtggaagagttgttccgccgcaaaatctggcaactgaaagagctggggggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgt
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00000-6JGGB+15&(A58/41C7*&6.0L?;8K2K5,,1501'+1-99:8JD,@3FM,/B03A+N3AN/42+H>-:C;L)75'>3JAAI.F@0H::D;)8@+-2:**9<+MCG-;?K.(.+D
@705
atctggcaactgaaagagctgggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgtgagttaaaagaactggctacacttcggagccgcac
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0(50@?=7C&M+,6.2-LH7B>BD1NC?.I*3K4>NL<&A/6(M'(/5>8':I8C28.?=;H*4KH+:78A8?*9D':?0?A,2>J>L7<;D=0+7D.=24@JD8
@710
ggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagccccagttcttttaactcacgcattgtctgttgcgtggtttcat
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000'?@4ECE'9&3>?8?C)3)HJ0H.-.GK/*G(M6=.F5G>E7'1);)'1&E14-;?'9D69L*8G4=GH&+8E<=5/:34'B1G@0-+;2-*G=H&;H&.>
@711
gcctggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagcccagttcttttaactcacgcattgtctgttgc
+
0000I>1K/*E)M*3,4.E7D?29F:D055I.@7LH*D19&-.B;A&5086<&*:+&25I-H&/M9A1:H,<3GK,)*NL.0L6>CB,5/3<)*?G'
@712
aactgggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaat
+
+MA=307EN--&4?.J1A8NF''+.;DILL.&9E+KH4A+;E1M2L98+>+9,G&KB5D';,4>L7G26I&1
@714
ctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcacc
+
::L4G)+K/5@IHFB7D+?+&&'0=J0:G(J;=D-,J1EL.B6NA*87:?J;MIEG:711D>;,6MF>'@)/6EC(42?0'C98?F=H;LA1?/B(?<--L<,EII'H:/H;J(5+2A9,J)F;
@716
tcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgtt
+
&B.?MEMIDDF6/&046?M5'1,9:G14A9H;F*.C/=DACNI'27&>/?29:CH@G>..M<01-HMD7-67/2CM'=(I)CG(1L(C2FFH0G98@1?E&7CE.85.995H721L;>IIB-18,I2)AH6
@719
ctggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatt
+
00,,5*H9G(15@9L/*?E.'?FH37DI)>*@;1-@&)/(7-*L*E*33(@?M4NL@KHM(2&L7'5D6LJ4N<2DE37L9/L>;?3HJBD.DE/3/G'4HF;JH'=-:
@724
gcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtgga
+
0G;DN&CI)B73D)(E)>DNM6(E.)'I>B;3)B-MKJ<.:*H,*0D@/'/)LE;*38>G&.(=5F:F/KM4A.K+I:LF2L7
@725
cacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtggaagc
+
0003&@;+:8/'@:E<2.GJ.+?CFI.M0E.3E?&D>GD::?&:'(85=,J1710CA67*3E=M9J0@D0'.@>GD4'*-;.CAMH8:)J/E+'+L.@J6.:H6HAN
@728
ttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtggaagcgattctcggtgaaaacgttggatctgccaaaagagctggcagaa
+
0000.9FBM*8*8B)58I;=.J?5A16.K@)*-N=I>'@HC96+.AJ)NC?K*/CC60,1G1):(N&18.;M''7JHC0/,1*1;2)E0/6D@4'0'+:=2N>B9:+G('1&
@730
ggcgaaaattaaagagagcgtggaagcgattctcggtgaaacgttggatctgccaaaagagctggcagaacgtgctgatttttaccc
+
000&K+@L:AK+G8<&5(:44(J:')L-8>&E(/394EN6-;N/F;;-1<.9,919&4HM(0?<:FA:H-*>3B5I*:J,:.G?13>
@731
gttggatctgccaaaagagctggcagaacgtgctgatttacccttgctttttcacataatctgcccgc
+
000000'?=CAHA-MIGKA3(*-14IJ,:LH+9.5;M<4H:K/ME'@@CJC-;CAD6AD6
@743
attgagataatgaatagattttactgatgattcatcatcaattacgcaacgcagcaaaatcggcggg
+
00-0DN?GG'C:<>@H')+>''D89MML;K,,L;4.457>,HJ;7L?M67G>BN/BN:36*KJ+@HB
@747
aatctattcattatctcaatcaggccgggggttgcttttttatgcagcccggcttttttatgaagaaattatggagaaaa
+
00000<6:)LAM')E67&=4N'4,93JMFK&*55&7E-&&H?B+>@A,G/02:BG1I8DHALD.'&>+5'460LL(L7&;
@755
tatccggagattactcgatgagaacggcggttgttattctccgcaatcctaatctctaagttaccgcattattgagaattctc
+
L2DB85E-9;,41'03=?+=>5)4@2=8D>GI5B7.M3D.'2=&60)4HI1.&LIH3*6N.4/N4'A,1,CN--)2DMH.4/.
@756
tgcggtaacttagagattaggattgcggagaataacaaccgccgttctcatcgagtaatctccggatatcg
+
8=3GA+MK'C./E/*<)I968-J,&CH89I+)&>'/H>@:EH&5*/>D101>8L-I;F.?8K'CN3G&?.4
@759
ctcctttatcattgccccgttatgggtcgatatccggagattactcgatgagaacggcggttgttattc
+
05+KB?/I5'E94)@14CE=C)@)/.J*7J9F/@J9,*L:C++/52758*AN-.K*'L6*+4E9K4+B3G>2DL<:IJ8/=A97I><,&)G03L3,A:N>MBI8.K6@G&@:3J
@131
gatcacatggtgctgatggcaggtttcaccgccggtaatgaaaaaggcgaactggtggtgcttggacgca
+
00H-&*4BEH4J+=79L4KN69+F9G.(3>:)+5LM3(
@137
ggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttcattaccggcggtgaaacctgccatca
+
I?7H+0F&510-4(<8C>);:E'C,4AHKAD*AD>GN3,*;A(9<=8:IM):ADKE@/'HE2;;;8+/?LG(D0*6?62(I>FE1H026N(8EE0=GH9?>FMA6LEJE,E:5<875=;4MG1>1=LFC?FF.EN/B'EBJ&+)3EE3*6BC7?M9::26;-5/D+I9;22D3NEJ'6'>,N,D,BKN:6784B>;IAB':;@-/6N:B,=J0+FG30)C6'CL.<'+K<:
@142
gtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
+
00L=)H.405GF+=C-:A2<)>/>E>D4BE&+B:AK27>09
@143
acgtccgtccaatctcgcaacaatcggcgcgtaaaaaacaggcagccagcaccgcagcagagtagtcggaaccg
+
0009F7HI90:/GN2B&M59,*AM(0&60N&37>)F?3L=7EF7NMJ?N8N-.?2*0,<)0D2<&)8BJ*?LCL
@144
cgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccacca
+
000&C*&5GMB4=5F'LHH@)9=3J9G+3L(+FEJEC)>2:D(I/N',
@145
cgaactggtggtgcttggacgcaacggttccgactactctgctgcggtgctggctgcctgttacgcgccgattgttgcgagatttggacggacgttgacggggggt
+
0000IDD:);6.2JB:/3LKL3E7-2)'+3&.5J2(:6*;J4(D@C*>;NA;?;(AA7@*K2J:1IHG&;F(7,.:'F;MK&2E.B=3-*(G-C9B:818I2J=@-
@146
tagaccccgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttt
+
00000-E6)/08HCK.;>I;?)*AN.5KCL/IHJB-3(83M;E4,I6ML65'JH/K5.7>8;B0'D
@149
cgcaggtatagaccccgtcaacgtccgtccaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
+
0000+899@+,1HCGG2-M19*FE85BI:)5=53E4>)02&*'B@B'JB>BL/2+;,+'.5C,8;AHA+)2L?9*C4(;ABAA1@-6(/)61F2)2)DDD:5F,NGHB
@151
aacggttccgactactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttttggacggacgttgacggggtctatacctgcgacccgcgtcaggtgccg
+
000).K7JA0F29G5(;H:,?3N:A9NI&F8)>15L1<@5A7?JJ5.HBA1NB58='3BA(@:H>&DE&+0>)A*.<,'(77H&GG0/2L8(8<8'NN6F.:2+40*?/-3FN
@152
gcggtgctggctgcctgtttttacgcgccgattgttgcgagattggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccga
+
00/C+K;>474J:N,K0ECE;DLMC++HE-*N7M+.DHH-=8ABJK8-C&-+-8)B@.34DN/:1@8J;,)-.225E:BMN
@160
catcgcttcctggtaggacatcgacttcaacaacctcgcatcggggggcacctgacgcggtcgcaggtatagaccccgtcaacgtccgtccaaatctc
+
00000(75E,/5><-379KCL7D@3?JJB&)+G1K.HLK48?>9>F1AG/5D:);'E:M6EBIH>E70?:IN'D@-,GJ/N00FEC;/()=>@AI=D*
@162
tggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccccccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctt
+
00000/60K<.C;/E?7N:NG?&FDHD/J6?J25.*0:<4*/@N./JM'=:N:I)19I,):'79N/>F?GA.898KJ>H:/6'?BIM31,M9HC@BHCC?C.NNG9',
@166
ttgacggggtctatacctgcgacccgcgtcaggtgcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagcttttcctacttcgg
+
0H(1;<1>(.83L>99474AE<2MC4./'J6;JL<7J.D?/=,//)I<,.;I(41'@AC&,<27H2:87G<&5NM)432&K372?MM97
@168
gcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctttcctacttcggcgctaagttct
+
0;&6GM3<,86-2CL-2GH&(,KL>-9MFIG887I;F5@LL/FKH+&:17CB+9NF9,8/L9@<**E,6M355/5KH+E4;KGH-I?@6(70AE;F.,D4F@GJ>-+4BEL&=J**1-:+@.3C&>DE;C&I/>85J)A';,L5:?A/I3<8F*.DJNC9C:-E
@172
tctggaactgggcgatgggtaatggtgcggggggggtgaagaactttagcgccgaagtaggaaagctccatcgcttcctggtaggacatcgacttcaacaacctcgca
+
0001??5DC7).//M7M5/12?N>79-/K))-5?0M(73HMFF:FI(/*=K:,='G+A7B6'4DILK0-DK@+>HI>A>N/0>GIEJD(3=6761:'>2B/@8/E
@177
agcgtacctggtgcttgaggattccggtatttttaatcaggcaagggggatctggaactgggcgatgg
+
000=7722(3?,M'..)E':EGC(N'@K4/&>6&'C)1-/A;&:;-6&CM*74F)GGI/&5<3CE0+>4-5H,D7JF.-F(07>3??D8=HL?
@185
caccaggtacgctcattggtgccagccgtgatgaagacgaattaccggtcaaggggcatttccaatctga
+
0005,B6(1MJ*9;+LB<=FIEKFG1E+@5BE-947?C2A8'H6<7G&8N2+14-90&A;7=?E*>FF'M
@188
ctcattggtgccagccgtgatgaagacgaattaccggtcaagggcattccaatctgaataacatggcaat
+
JIF22>.NJ0/45N.BB1*A&.M+,)E)2;:<.HA:1>1A52JMM80;I*E8@&AB1I:CJ
@189
gaacattgccatgttattcagattggaatgcccttgaccggtaattcgtcttcatcacggctggcaccaatgagcgtacct
+
B1>7904BE&HG/K/3K9(9B.=J=G/G<47-5*-9CFIA?((F5IJ:0CKLF8D?3FC759F.A(6=2618(7;EG2,/.LN=C)A97(2*K)E((*,G5D?*C-N4??DME&I6KL9M/1@6J?M9FF(&D6/0(5FJ4K,;F0=M4A;=?1AN*:+N3+*J=?B1;)6&4:K9(,11IN7G-N1H35>GBBF0*3*'7'D>
@192
ccttcatccccggaccagaaacgctgaacattgccatgttattcagattggaaatgcccttgaccggtaattcgtcttcatcacggctggca
+
0E=;)>.K6)E;DEJI'(JF2@C1.=A+112CJCL&G?48>08LA(:0EK)JN0:A);@J;5(M&5GF37HDDHMF
@195
tggtgccagccgtgatgaagacgaattaccggtcaagggcattttttccaatctgaataacatggcaatgttcagcgtttctggtccggggatgaaaggggatggtcggcatggc
+
00000)72BLGB>;:(/)&>@((?&39-N5F5>DL@H<>4C6J3N5KM76GN41/4D7)NM;@N+,E)8,H7*I?*
@201
atgttcagcgtttctggtccggggatgaaagggatggtcggcatggcggcgcgcgtcttttgcagc
+
0000:*NEE?65I4H;1+A/2;1*-H:=55FK.=,2&@1NH0N@D>IC/6
@205
ggatggtcggcatggcggcgcgcgtcttgcagcgatgtcacgcgccgtatttccgtggtgctgattacgc
+
?-E>9B;BJ7/51BA?:N0>+(:-?42:;N;7:-;@8IA.90.*
@207
agatgattgcgtaatcagcaccacggaatacggcgcgtgacatcgctgcaaagacgcgcgccgccatgccgaccatccctttcatcccccc
+
00=2G+8I>9(MFL8+20KIH6,7<*=6JH76+MMB8;1+JDI''2:JB9=:F65<370I24K0A+LI
@210
gtcggcatggcggcgcgcgtcttgcagcgatgtcacgcgcccgtatttccgtggtgctgattacgcaatcatcttccgaatacagcatcagt
+
00K9EH2066:6B;;84DN9KB9'9K2L?LH-'&FE.,&GMH0'';.(ML21:B<)2,F7F:@3;35->+NHMIC=7HK*I*1,55A3:1CN6,F?;'5*=?(-))=-=A179M9C)M@@8B/=GD*J*5H&>9=L>;/0HB1)3GJ=)C:M&5DFAF;;8I2.0/-48*1:+@FK
@214
gcgccgtattttccgtggtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaa
+
00*C)6CJ1KC(B@537DNHD=:'7I=7-62>0KB@9'HH/,;KNC;LA6@,,DI+9&+1L.934D?&B:*IMMB:73KKE=9L>3275,1-B;)MA8*
@216
gtgctgattacgcaatcatcttccgaatacagcatcagttttttttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaatgcaggaagagttctacct
+
00000@K9(,DHFC0'+8(NC4F50H000D165&F/2M3GE9=6:3?*A38?<>/:=A89(G0+-9L,'.'AHHAE((IE'9/?,')9E.253@3:EGG3J'--J,
@218
agcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacggcaatgcaggaagagttctacctggaa
+
9(D-C320J22CKGGM;:48BA@A6?A4BKD-;5(3,J1CI87KA6>/?)&NG44;3A-1@2)*D:(9*2-09F
@219
ctccagtaagccttcttcagttccaggtagaactcttcctgcattgccgttcagctcgcacacagtcgctttgtggaacgcagaaactgatgctgtattcggaagatgattg
+
00>2B93(B?'7A,?A?AMBJ;'&&.('?C,2;)2G4&CH82+166BL>08JJHK30E*?69@-L51>K4,=-6'N(D7.-KI4E;,)+CA6G77J7@849
@221
gccgttccgtcactgccagcggctccagtaagccttctttttcagttccaggtagaactcttcctgca
+
00+(45D(>E;K+F=DH('H/D/';L&AF9F?*:J9A(0AJ35>G161--4'KIDE5,1C@??2(BD<
@223
tggccagccgttccgtcactgccagcggctccagtaagccttcttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcgctttgtggaacgca
+
00.IN9DJ'D;214><*69F3808DB(>GB+NEC4G7N19@=;E>?3J0,@>NA55I+52>129J,GK)J4+G39'36NJJF9?8C?9:4'M0=6+E?5359,=G;K6,)F
@224
ataatggccagccgttccgtcactgccagcggctccagtaagccttcttttcagttccaggtagaactcttcctgcattgccccccgttcagctcgcacacagtcg
+
0000FB5(>B0..-,6I,NA-J,>@I868,19H+/05C@F/N&.KCK>7C:B.(A:>2))<
@225
gcaggaagagttctacctggaactgaaagaaggcttactggagccgctggcagtgacggaacggctggccattatctcggt
+
E<,4@0B551<40I&:B>@54=;>+/,GAKAI9I&4139F&=:5)<3EEE3N))N2L6BHD':'*N2;AM<,17@5D)(@2
@227
aggtgcgcataccatcacctaccaccgagataatggccagccgttccgtcactgccagcggctccagta
+
2-@L-;1J.12J(<=G/5+FB5>*J6E;*=M&6M=-)17NDMK/*-,
@232
tgagcaatggcgacaatgttgatattggcgcggccagtgcggcaaagaatttcgccgagatcccacgcaaggtgcgcataccatcacct
+
09CG+5)&7D80)D.M,07F=:==)A1'-*B(NC&B29NFB,?'HB4D,D1N20/9C@,>D:,'*2'A(01I>,?9@
@237
aattcttgccgcactggcccgcgccaatatcaacattgtcgccattgctcaggggatcttctgaacgctcaatctctgtc
+
0157B7C<<=MI/,(IB(F&<,N,56BLAM-JD-4I*M)C@E85LFAI+6AM9AJAA&31*0N;I-MA'*KB6ELF@I,J
@238
cacgacagagattgagcgttcagaagatccctgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaaagaatttcgccgaga
+
00(0A1L=+=A*+D8L16L&MMGH8K6/12?HH9@,3JH=*BA*8>>.5/,:7B<*G:+E+N?FIA9JD<6?5@?.03,*<(*69889;2DEC
@239
ttaccacgacagagattgagcgttcagaagatcccctgagcaatggcgacaatgttgatattggcgcggggggccagtgcggcaaag
+
0000HD2NG95*B=N-='>60/M(BG=N4D9'H4K7D2((E;@/?=0/=2)8J2ACK3B4C:;NN,/D.@AK(3?H05M73&:&9;=
@240
caatatcaacattgtcgccattgctcagggatcttctgaacgctcaatctctgtcgtggtaaaaataac
+
00000=6G+NN&HM'>NC2C3D/+1F(FN=7D<345)@<**?;39?K7*'13EG@/7=J0N*HF?7I=.
@242
caggatcttctgaacgctcaatctctgtcgtggtaaaaataacgatgatgcgaccactggcgtgcg
+
00007:?G*5843,G99L:3&*(
@245
gatgagtaacgcgcacgccagtggtcgcatcatcgttattttttaccacgacagagattgagcgttcagaagatccct
+
000034E0J1)H=4FLJ6,9=6?>:M65EL+-ND-FGJ1'(5515I-9+5AI)D69N:IF<;=5J:8N9:2I5D5J<+
@246
agcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttttaccacgacagagattgagcg
+
00BK,K4E-L>(L9''64A6@HH>/)G&J20.JLI5&'J@8;2A&I,
@249
atcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttattaccacgacagagattgagcgttcagaagatc
+
09.'A&1&JAG@/A7I0J'01EB)F-I9I<7(M33,D>G-15'F&&'<>L-(5G?320(.BC.8'+7L31GGI6G.247I933L9)>>'A.
@251
cctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttattttttaccacg
+
000,J=KE?;C-CD6AH@23+J@&8?3E1@8=JI./<=,>95.-8?0K/*>CF?L@)@*0E&JC5GAAH&I.5>
@252
taacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttat
+
8@NMID/I)'8JKA26KH@K@2A7&?HH028&=:/6?H897F?2E=;D2+F6AAGM@*G13LKE<(
@253
tcagggatcttctgaacgctcaatctctgtcgtggtaaaaaataacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcg
+
000;N3C2/@<'71NE1J<5B<-LID0H*,+N)G)E,4)@/4=3-:?L;-2/(M56:LI1*:N.(AE9H96LJ6A=D1(:&N;0-:A>A0.JE1MM5LL@GG
@255
cacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttattttaccacgacagagattgag
+
0000H<+'A4A.DG-<;.A.-HJ/7;5H=?KC8I0,5MH;2.F?=:0C,K4&9,4/)@JFHE8,H.&)G,I6:1CN25BKDFM1+7/658=-M>H
@256
acgatgatgcgaccactggcgtgcgcgttactctcagatgctgttcaataccgatcaggttatcgaagtgtt
+
F+B11,?-9I:)@60;,KMKG&F'3@?.=9N)H/,BE-3/JF4?&?9B/8*:36.4746=<9D>?DH.D22J92N;>(J+7H6<9*
@258
atgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcgaagtgttgtgattggcgtcggtggcgttggcgg
+
H-=2FK3C7*H7.9@&H:F4LD=(;+&.&I<3E87J,M+K+;1C2D-(=IIA47I-E46N;G7:E28K,0L1*-I?3/NG77H);&?*@+N=?
@259
ctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgt
+
=.I;NB,<<.JI/FK.,'J7ACL+NK=NH.2FM)5;9;7NBNL:,KB/)3MB6-0L:-5E-F>DJNEJ@,@63&04H?78E;B?G2DEGJMNJN.'8:8;3;F2C+'I17:0C
@260
atgctgttcaataccgatcaggttatcgaagtgtttttgtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaa
+
000'9K5(G4<*/4A0BI3@19/KFD@.J>MMA96/A;-G6,2*/LCB-941HFK56=5L,29)8AI942(,/L5@+5KJI?/@;53(93BB1:?J2=FN;B&@>.032/:M+1B52L=,/*DB=2'G7I<.J2;8H:*I>;GNNC@9G-=M'LKD;F'6E
@263
ttcagccagcttttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaaaaacacttcgataacctgatcggtattga
+
0000;;0KD2'-D-1L0)/M1@A3>,9@DE-4)DB-@*C>6=,?GK)J8J4.)2C47&9M1.N0='1D(*FBM65ID,1=);FB7D.7GDI1>+I1/L
@264
tcttcagccagcttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaaaaacacttcgataacctgatcg
+
000,?86K-E'/*6I@=2HGKM:)JDK'>C07HF.?;?)K+:A;))F3=NL)*D.LM1AB,N70-+78E?LE2J&M(.*&D@'A-G)3.AF>1J
@265
gtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaaaaagctggctgaaga
+
000('9@7C:L8M/L7H//A-M:(-@FH.G255MD0M+;:1(DLJCH<.C,9+1N<-F38=9*NG5:A)I31
@268
ccgcagacacgtaagtcgatatgtttattcttcagccagctttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgcca
+
6CEBI5GFJ'61D(8:C7C7F6K>M,6+&9N*36J,*?0;E/G6?3
@271
agcaactgaagcgtcagcaagctggctgaagaataacatatcgacttacgtgtctgcggtgttgccaactcgaaggctct
+
7;<,(;)=H?(?G4854*;/N*4KA?'AJ;6BL':F*M)8@JH,HH10EJ('&C';.*0E:'()@'(DFHDM)G)F5-8@
@272
aacagagccttcgagttggcaacaccgcagacacgtaagtcgatatgtttattcttcagccagctttttgctgacgcttcagttgctccagca
+
00C5,7FH=828;ILNJ(6A44DC&9L3<7&N>B)6'2,J2/KFI0N.D7FA7IAH6'6H/N&(()FAFF&F-'E5&L7L6E,,*JI/+9&@83C/KJIC*IK)5*2H662+N
@276
cgctgctggagcaactgaagcgtcagcaagctggctgaagaataaaaaacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaa
+
000),<+H(F48.:M?0656FJNH,.2@A(2ED'IB8.92,:9KH7@5B>5E7'5J?M&)))?:31.M--5;=B+J=F00&7@.9)6I3@<)@>?3G:2AD.63=/F+:87<.7.=F
@278
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggc
+
D4.BA)670:MAL;'J'(;0FA)4I80'0M2+IK0?1IJ)47>*1/=CC54=/>3BNC8=0>B;.7;7?>C'I4(6)L4E-2HB(5'N::3KFN,?9/D)DC4=4J,*,>DFL2'+G@@;/K,224*H1(A16?.?0DBDE
@282
gtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactg
+
<+?)=L7@N2FGJE>>+ED1J9B5;KFEIE&//)4*3C.A8H?3C0C:GC)33<*8NKL(@@@46AEJK)J
@283
cgccagttcttcctgccagttttccagattaaggccatgtacattggtgagcagagccttcgagttggcaacaccgcagacacgtaagtcgatatgttattc
+
;6LC2@7?.DL*;+254=H4I12B.'3(6>5=3A=39N7D/6)5IG5G(F(C2A9@;DC'=:(3,8>LA33J5<95,,H@:.A=A''-I9;C0=;A*+)72.
@284
aacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
(4-*2>G*04M8:)C@+E10IEE,0/C6EL08=9,.)NC5,I:)+7'&82'JML;/.4GHCC?G,11I3IDGI/(==1KLM'?1C:5=6DG8=-BHN=
@285
gtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
00?>EBFI>5M/C&,@N5*8@J4FKLA404/4;N&'2B3,G>CM8)4*:.F7;@EHL*F/>;A@).AEB:/23)J60L)M7BI
@286
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgc
+
HJ=;;.*.?21LN)496-(((I5/N(BI50>F.A=5L/6.8779K''4*9:L6>:/5H'.6L1@1G+7BD7L:K.N6*04&>F7>E'B)D02=(I7E,6C94B.(.?K8;>/G>,6FK83:C8GH62>J&E0/NF>C3&*+E:EM;&41N?9L2'9,MH-)I382>L3/GLCJ&-,(;72.+H2?8@8,H*A)@-?@7D5MLD6L/GE
@292
aagcgccccgagattaaaacggctctttggcttgcgccagttcttcctgccagttttccagattaaggc
+
00080)M28+8MB;2=JHLG,9D6/&7)H'-/GJJF@CL<*3K2)I*??>*4LFAF:(HGF:32KKJ1.
@296
cgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgcaagccaaaagagccgtttaatctcgggcgcttaattcgcctcgtgaaaaa
+
000>G&?F4,:>GD-)ILN;-7>(97FNC5C.@I;3JE(00101<0K1;K'7F;M9?4DL.K15C/L<=K9.F3>A33.,D'27<,26BH5E?'H++3C5,>H/MCE95K=6J
@297
agatgatattcttcacgaggcgaattaagcgccccccgagattaaacggctctttggcttgcgccagttcttcctgccagttttccagatt
+
00000N(?)2GEJ++2N=BM&/=LAKKN10H(H;*DNF='CFE+H*'(MG+MEJ00M&',1AEJC3D4;;.B/GJ=J7E53J?JDI1'(7(
@302
tgaccgggttcagcagatgatattctttcacgaggcgaattaagcgcccgagattaaaaacggctctttggcttgcgccagtt
+
0003F,*/BBJ3&6J@H:=-6F&68(-@F06DCFIG(KMD;N::BI3?I4)4B*:8H1ID;:/BL-1CNHM0B)@/=C3IJ&*L-=L&G4;'.*9>?ND=
@307
gctggaagtgcagtcaacaatgaccggggttcagcagatgatattcttttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagtt
+
003/+-/0D?>+N3EB,FL?2?/(85ENEH5AMB3;:I..0==/9HE'H;BJNH(8@/+6CN6C1DA)IG83H'G+*)H901,1F;:M4&'E=CNC.:@'1:8
@310
cgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggggggttcagcagatgatattcttttcacgagg
+
00000LF<9+;FH?*5-1L.9L5(4(N=-8FD(.A&&J36A*/1<0I*.=B=)'1D.+88/5.+:-KG
@311
tcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccggttcagcagatgatattcttcacgaggcgaattaagcgcccgaga
+
:+.L6E@3@B*@8=+LK?G'31K/I7=*NJ<0*0M,J52GAB4'B,75:KDIJ6>'E*9N/7M9+:E3/E)N@<73'F)0/NJ?&BEB?>G5IBJ7+,/'K363CA;EJ
@312
taatctcggcgcttaattcgcctcgtgaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaa
+
:+.&G>&*C/10)3A@.LLA&0HC-J45;.866L+F@A/(H.-(F@N11:39;FAFHHH9BK2FG<==HJ7;GA34ADJM*7C.FK*'&/<*C.EM0=6:A=G&M,;CI:?9J
@314
gtgacaacgtggaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagt
+
0@7;:C8=N09FG&90M:*62E;KLKIHKI8D:BC6:L35H<&@NG@@297?(&+4H2(-@A>?
@315
cctcgtgaaaaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaaggtttccacgttgtcacgc
+
00B02H9:9*A@1+?G,.+(I@5/8AD>:=9?==N'/(,(GHBD2=I&71A9>GE57K3*27+.D:4=6?=G(=>2HM3D=89?*0IANL850*=3>(11II'C-JIJ*01J2:;E348F&MMC1/>('FDA.**>83GIM;-MM03@EH'5=F(=D*2/A(@(BFG9L@+KA@28I@@:G>FL'@8*N;K(>
@318
ttgttcggcgtgacaacgtggaaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggttcagcagatgatattc
+
00C23M,&E&&B)-AIJ*6EE.N=03613*6((MCE@2B(@F7KJALE3JKM2H5(.K*I4,H,6(:(&N2L
@319
ccaggcagtggcggatcaatatgccgacttcctgcgcgaaggttttccacgttgtcacgccgaacaaaaaggccaacacctcgtcg
+
0K5H6J?-95J1H0:BC4<.7>6J1'NA,)MC5B+9+49GJ+MN:G;F7F:K1E;J(?BBB8L5MMC:(8*B0?48EJ'
@320
tatgccgacttcctgcgcgaagtttttccacgttgtcacgccgaacaaaaaggccaacacctcgtcgat
+
000F922=>G>+'I(&D=>=5'2'09)H@I,BG;9>6/EF/C,:56GM-5(1.)AK@+555'*L&.@A&(F5D,*9FN
@327
aaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgac
+
0B+>C)3E7&.K3J=-)3L*:./6H,=>2KL?6A07L(.90?&33(N5:1LN'8L>.MFL'ANDLHHBB&,4)':,3L:8MG9/80<-H39L3BIILDC?HL8>L*;J./G.9M);?8K28+3GN:&86FKE>D=@CN;NF//)*31J;(/*K
@330
tccagccccaacgttggtgtcatagaggaatttacgccgcgatttttccgccgcataacgcaactgatggtagtaatccatcgacgagg
+
00(D/=FAA*G/33;G><185L0,AA)F7BM@4G-?-IMGL?7<@A3&3KF&)A6,GC2?*;D5487L'JL.7'M45G0E'475(219>
@331
gtcacgccgaacaaaaaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgacaccaacgttggggctggat
+
0/,-+B+)BFI;?L;H/.'54>,))-C2'3;(*)3)/,;-.-K26,K7+30CN,+0M=/@B1E>H?(/((NMJ)H6&,BD59,)=<;M22K4,J99(7I22DM'N)+FJ,EK2C-
@332
ataaccggtaatccagcccccaacgttggtgtcatagaggaatttacgccgcgatttttccgccgcataacgcaactgatggtagtaatcc
+
00))A'4G@091GL3A=K(@8L428=7:-?*C1+E-96.6D@;02-??NK/N7+N1???JC)MM&K400A,1J0-*I(C7G?F+/).0K08=4/-AJB4:=4K'(5,G='?8HN92+,(+B)(B1AKI>=9;;CBEEEE.H7+1C8&576=DH/-J)763>8ML1L5+(?*+4EG0?:CJGN:@50):('/(:028IG57M
@338
aaccagaaagaatgccggagaacttcatcaattcatcacctgcattgagcagattttgcaggttctcaataaccggtaatcca
+
NG/BH9-AAFB@,E@'3E908.&:'/NM'KLH12'K?:*/;-7:A:KA=D494:>DC>*18.K;DAB@K'LH66'<.7B8?LN>09&(FB1;@27&AN*'<'7&;:2L898853::7>HCGN&+I4?+92?(@J17K@4G.L):6
@341
aacctgcaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttagacgaag
+
000M8KAM-LKDEB697+)-NJ9.@>/2MG6,D:1LB;<*?JJ&&)2B89)NEJ.DCI(&<,IN)F?0,&.'B,6E8I<;JE,,H@57*=N'7I=4A
@343
aaaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattcttctggttcgcttttcttatatcttcggcaagttagacgaaggcatg
+
000F8:+G4;'N054J?&G.>':12@6231-75J86N99G
@344
tctgctcaatgcaggtgatgaattgatgaagttctccggcattcttttctggttcgctttcttatatcttcggcaagttcgacgaaggcatgagttctc
+
0CHA87M&MN?L0.?+'2GL/+++E)LH,4.C68D:7F=7J6?1/F<)ICLKCE7H&,.7;JKF*.A;A4-'E4&'(;(LL+7@/+6G)H@3D18*+F,
@347
gtggtcgcctcggagaactcatgccttcgtctaacttgccgaagatataagaaagcgaaccagaaagaatgccggagaacttcatcaattcatcacctgcattga
+
00;:>2I.@H&)&-:.,&317G5-MLC/3BMG=HC469.+.6)>.F/H=BF259I.+LF'5/6@8B2>L4441AN4-()AD(E0>*0C2344A6*6:DL*3N,)&.774L(E,6CE-D(&B(C6NIM29DB/A8M:ME49GK.64HEJ
@352
tcatctcgcgggtccggttcggtataaccccccattccgcgccagcgtggtcgcctcggagaaactcatgccttcgtctaacttgccgaagatataagaa
+
00I88:5('DG1G@D'/);:1;-A>I.J:'D30BA7+;@F137=8J07?2:H@M,E>4)HNAHJGE3?,)L45*N,BFA(-9JC&=<(-DG/M8>>I6'?
@353
gacgaaggcatgagtttctccaggcgaccacgctggcgcggaaatgggttataccgaaccggacccgcgagatgatctttctggtatggatgtg
+
000*26+>(/G0843C71'F?2IC6*M1CKGK)L/(;H@0L1?2;C(7,B.3C0H>47>MK:0@CGL0,:+D3A5,-KL1I>@-;<0,4C@(-L
@355
gcgccacatccataccagaaaaagatcatctcgcgggtccggttcggtataacccatttcccgcgccagcgtggtcgcctcggagaaaactc
+
0000-)-D*<1J(1A*JDLH?-6M*9*9H0J.&?-9DK/EKF09N<.:DA.L)6,9C;IDH&-?(-:KB;5(/0&;*9A:JA>C2:LD4H1'
@362
caggttcaatttcaatatccgccagctccagttcacgtcccgtttcacgagcgagaatcaatagttttacgcgccacatccataccagaaagatcatctcgcggggtccggttcg
+
000-?/?2.?(/48,@5F5F<;'I=9J7A6?2C,9,JGIN;CA8I3JL-I--IB'L45I(3B
@363
taaactctgcgggcagcacaggttcaatttcaatatccgccagctccagttcacgtcccgtttcacg
+
0HNE7HJ7A865'-9.E/N57A4=HHII&IB2;2B:K<&/':.(BKL6F&/3C2FJKF1&;//48J?
@366
cgccacgcgcgcggcaaagagatcgtcgagttgtgacagattcgccataagcggcaacatcaccctcggcg
+
9;,*HFG+)'-4=&I/(&+,F93K1F69&21CL:>B7L5B4-CGC2K(EHB8G>0+N-N=C+E=:G=L.:G
@367
gtgatgttgccgcttttatggcgaatctgtcacaactcgacatctctttgccgcgccgtggcgaaggcccgtgatgaaggaa
+
000F:G@43?K*3.E<>-62N:)=<(K37G>B10@C+*G03AG>8)?3CI89A<A8=>68/
@368
gttaacgccgagggtgatgttgccgctttttttatggcgaatctgtcacaactcgacgatctctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgct
+
000G@&?2*MI;G+,H5'F,'(2>791F'@3,:K4&9=G85G/FM=9).(48@BK(857,1G??N7DJ&L>E+<(A5LGC7+);;8+>)7MD6>E2M.0&7H'@4<
@369
gtcacaactcgacgatctctttttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgctatgttgg
+
000F/6LM1;2:*0IK'J()HFFE3.8.4-9K<4@FA7*25G)C;?7;B3H*:&@B?K<=
@371
atcttcatcaatattgccaacatagcgcaaaacttttccttcatcacgggccttcgccacgcgcgcggcaa
+
0-DME>MB8>/M=03M<*K)0:M:5L9=7>BH85'*N+G>/HN0(>:720;5B)7>-?=?C)6>CM&,K1J
@375
ccgtgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgt
+
0-34)/7<.+14;E8B;)I
@376
tgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttc
+
7+@5EJ:6,G:E5;FFAKDL&4HB'><)E*;BL*CL-H=8D+*BG'C5LH)*/'D+6+E?E&MNI2D><*9;57<2/476J?@+C(4
@378
catttttcactttgaacagcggatcattaccatccacttcggcaatcttcacgcggcagacgccatcttcatcaatattgccaac
+
00DCDD7+>8ILFJ)@&J5@.LJ/918(?4G'7G*=.8H(1A-I2-@G;--+)>KF'IC-&M,D83='?HM=B>83L;LGFJM,:
@379
gatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttcaagtgaaatggcgaaaacgccctggccttctatag
+
KL.)M0-BLBJ:+8HJ<8?G9&GH&6?ID>K1CA=8=/MDC14/==,9<)
@383
atccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccaggcgttttcgccatttttcactttgaacagcggatc
+
I(&D<=H4@I7;I4HJ(&*GC36='8643N?):NM-,3.('=G.<-B.JIF/)-4;+K;72<44>*)D<@)DG98MD=&GF9??K3I2E5-6/C@G4?<(E(D6&E
@386
aacgtcattgccgcaccatatccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccagggcgt
+
EE)?9N:F(K+F:,6@-FLB030A6;LN30*I?.M0;49J&B<,,+K>'>AKKH(:7-;=/8G6)N:.*;*3C,629NKGBAA;(*;:J<
@389
atagccactattatcagccgctgccgttggtactgcgcggatatggtgcggggcaatgacgttacagctgccggtgtctttgctg
+
0000-;(G/(AI))FNNN;-M.38=((C>*-G1C,7A:-HC5@.60(.:43AG-3@GC'E44''>42&-M=6C:K+C>NHI@:?8
@391
actattatcagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttttgctgatctg
+
00JI-0318GFGDGD6@G'MF=?/M3*K@,B?.*F6.2H44D5D04KK7.=6F:AHFE)7L2F6(I+1;CB52@?-LF)'N3*F?
@392
acgtagcagatcagcaagacaccggcagctgtaacgtcattgccgcaccatatccgcgcagtaccaacggcagcggc
+
26@1;L<.C63JBC?-<'&J*(;):B1:/MEKAD+J'H&>')0D65+05D@0+C34;0D6>CG>I?M0H1)EG&L3I
@393
cagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtcttgctgatctgctacgtaccctct
+
0'.*;)E'&>CN*<->,:C>L7GL(:E;@/E7DF1M(-?F11L@)JEA>AJIM*D-*:8/:M)&LMCKD/@,:6/E26@.(
@397
cgttggtactgcgcggatatggtgcgggggcaatgacgttacagctgccggtgtctttgctgatctgctacgtaccctctcatggaagttaggagtctgacatggttaa
+
000M)G+7HK0?2DA+G/=B(=9C7@9'6ALMF):&9'9><0AI5M/-K?
@405
gcaccatcaacaggtgtcaccgccgccccgagcacatcaaccgacgctcatattggcactggaagccggggcataaactttaaccatgtcagactcctaac
+
-+7G(>JI9+JN=C/=.+9.:=
@406
caatgcaccatcaacaggtgtcaccgccgccccccgagcacatcaaacccgacgctcatattggcactggaagccggggcataaactttaac
+
000000N00/6-8:BI703(,II+.GN'EE6=L+K/2;>8),4+=;BNI.D8438J?K&B/D,L@((5<8J55*E:(A3/D6H6/'KC2I24
@410
gttgatgtgctcggggcggcggtgacacctgttgatggtgcattgctcggagatgtagtcacggttgaggcggc
+
-M?,<00)N4NB/+<(N):@(N=&J70)8'&BE/)76?8>*4>F<,>FHC:&6G>K/A)5LEF388IMJID2',
@411
tgaatgtctctgccgcctcaaccgtgactacatctaaaagcaatgcaccatcaacaggtgtcaccgccgccccgagc
+
0D*;E.5??='*?F/61()JJ4A)>ILL8M>5/?4=C?L5'4>:/*&.=5+'I8=MK;*9@/E(,9.=/KDF<
@413
aggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtca
+
CE.?+L00>)4897JM'0II.5FE61I76*1NDDF9AA39GDB,G)84K52+E4=D,'G@I2CIM*+,=()K==,:L(<@4GKA8GFNA7?6@L<9D=/
@415
cctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcactctcaacaacctcggacgctt
+
(;G5<107,F078J8H7D'61*C?-L63H9=M8:9N6;JD+;ELK-.)*3D&,&D30627NA<>L'DE/(L;',>:&K*/,;E-&
@417
cgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatc
+
D()C0:AG;.GKM;?K>@,.-@?1<2:=KC*N>8LL?./HN-M;&L34L34B.04)&H*F+F0
@418
tgcattgctcggagatgtagtcacggttgacgcggcagagacattcagtctcaacaacctcggacgctttgccgat
+
(EADDA@KE'::2J,,,-,J;:J)88EJD;CA6C)JF.+B:D3M*?C*B>:ID:AGD5
@419
tatcggcaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtcaccgccgccccgagcac
+
02KE';3@2EB3;G5/NGN4*JG,E/K0L56.BH'4L8K9A4,8LK?&+D-7CMB30L)8))N.17N:IJ&AA*6M>:076ECJG,L9&D&)M1@L??(4:57+C*3,><9/6&(0)M>1NB;IA4D0F5?+B:@,B9/AM:CN)0J=3+E>LC,'E&B)K'N/658:4/II,&05/22@'554+L&).FD9-:<&+/+@;&.DI/=H:C9KBJ4.8@7G.)6
@424
tctgacggcagcttatcggcaaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccg
+
16=E=JI&&:;9I:>MKI=;,8?*+G-96A;;17@4G?C:+:/E6/HJKICDI@:H=5N4NB?>H+/J5?M6;>===AI,=
@425
acctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgcttttgccgataagctgccgtcagaa
+
09BCJMF0D609&=GCB0D1F(.;-AGAH);;74G2KJ(6I-0.AFF>;IBFI2';
@426
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaa
+
6IE4EJ';/F5.<6A(B.BL8613)3'CBD,:I6=7?/72;3AN&+23B8524+'(J'&9E3K3C1GHBL&'02(/9ECD>/5H&+(*3=HHF/?)&
@432
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacggaaaatatcgttatcagtg
+
00:2'.)(>@:A.E'I:C=?:,J@:2,GC4.=G930>*0N&5<)JM@5K-)0.>B+L9/J)/CKK68C7@I(D'H/A<56/IND7?'DMGIN@AJ1&<1/?(/8-4&
@439
gacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttatcagtgctgggagcgtttttgccaggaactgg
+
0000:;(A;&)/HD62;)?AD&1)+2=JJA,06KF++1:(J+1BJ-*B5;<83&7/?/+B)NB88<+&LMD.&80B,:FGNF*B0*'IJ':K>+8MI<71BE-0
@441
ttccagggtcatcgccactggaattttgcttacccagttcctggcaaaaacgctcccagcactgataa
+
0+=1=>ENA5:&5BJ-C9'AM(7<1(;1HJK18=8))-EN9+JJL&2;9A54(A2I48N8NC.JFJ)055NCD(+0GA9&.3HJB(@A34
@446
gccatcagcgccgcgaccaccgaacaggcactggagcctaagccccgaaccgatcggcatattcttttccagggtcatc
+
000B4BE62..C@8C8CD':1N3K1AK6;A)E(54?FE?(7J77=89-0NK>B;HG?FEE0N>IAKH86NEDC23(7<,
@448
tcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccgatcggcatattctttc
+
00A/I<1?NIJC=.BCBL;C@95:=L*7'*9J6)6+=+J=.LMI?B*)?L)7FA.5+*(>E0@+837*G4,4
@449
cagtgttcattcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccg
+
:>-752F,6IAD*E+B7KN-KF)(?,@)L&>CD/*1?(CF&.9(D&/=34:D?,8/3L**+1E56.
@450
atgccgatcggttcggcttaggctccagtgcctgttcggtggtcgcggcgctgatggcgatgaatgaacactgcggcaagccgc
+
@C/CMMN=B:7,D9JJJ.NDE(=LGI8D10.85ABI4=GF)?J(G8N&.N@H58J@?JMN;7K<*MM64>?M/3643,H?:-+E8?5&>.2H;249B4A2A8G<81?C*J?+N;8>C)2((-,;2F,7'/4+3-1,N/.JK0/7B.2(&J/-H9D*GF'+H,6CH'D1A+D&<(0:0:+,J>.A3.,<;3.+3@2JIJJL&I*)0'2>*:K3HHL9;9,GB.-A-;AC'+139I/D5
    0HK=1-BA5M)I>'/+-'<2+3@9@N
@460
gacactcgtttgctggctttgatgggcgagctggaaggccgtatctccgcagcattcattacgacaacgtggca
+
F/7D44J/0+88=3E2;K2IN&I,'F22=1:B(@JM9/L)K<:GNI<7F==
@461
acggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagctcgcccatcaaagccagcaaacgagtgtcattaagcggcttgccgcagtgttcattcatcgc
+
000000;GI(CM-9>':JK5NE5A..=0'I+?>7AJ>I'..H)/<2/M44(@,-<2=+F2/8A?5'M;BI5I'-&E:./7&ELAKGEB*01
@463
gatggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcgg
+
M>:-EJ-;8-;H@KH+-4JH:71KI8.==6NJLKF.<+5/550.*LH')NNEB+@4GL95L/&:8C=9
@464
gatgggggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgc
+
005/6)F9HH;25-2A*.I*?M&FN&FF=4FB4?(G/8'53+=?DJA*;I*+MB88&KF?L:?6/:E(*24I?)
@466
tttgctggcttttgatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
+
00D4BA4;'C2I&9&6+N:<4E5*3;AI+L&-JLE)5N(6&&5>@56+8E0K>E?1<*F1-;4@2/9/<)/:-+M)-0B6-C4M3,/36=I1?3B=>+M;MG8.?@IC/AK7GA3H/882<,IN(0*'BA.0@:,0?8<,I@@@5GB
@468
gaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
+
,I9,N/=HDIAE?E'5J:+-<)6I&*@;0<(64D*N9N2-88.82)-:26H41M9&M3H=+=9C88)K8(A9FA:
@469
tcttcgatcatcaactgcataccaccgagaaaacacggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagct
+
2;/7/H2LI,@=I0F4?)H'?=+6DIIFM*;-=3.*7+F6-(I&208M/*8E/3E/(
@471
ggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatcgaagaaacgacatcatcagcc
+
;7/C*014+A077F,7FN0MH(.L==F5I4?:>)C(('91K??:-M1
@472
gcacttgctggctgatgatgtcgttttttcttcgatcatcaactgcataccaccgagaaaacacggtgccacgttgtcgtaatgaatgctgccggagatacggcct
+
00-'D51D321KIMJ9(C(3)0>E<'/9M(=?8)4G+0;=@F<+DNG;(*;+?3@?<,?MEN?,:J1+L(E8B==6D1FM4;:MA?D3AG.C(((N?M96I'1&K62M
@476
ttaatccccggatacgccagcacccacagccactcatcaaccctggcacttgctggctgatgatgtcgt
+
*;08G&-M05KH)EMK0H/F5:'&-IAM8:/*3FH1N@6E<&J,'?CFC'.&*FK@3E+@MD&:1*D7-
@477
tatgcagttgatgatcgaagaaaacgacatcatcagccagcaagtgccagggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctc
+
0H;(K51G('3C.4JA.-5)((')?8K0>8>M-13;67N:?M(3E:JHE.'*/C(;F1HK13=+KC5*2
@479
aatagcccctggcttctgccgtcgagactttaatccccggatacgccagcacccacagccactcatcaaaacc
+
000>4GLL@*'&DJ8))CF@5AI/A,=>?AD-/1H<=@>A6CE;7KN67IⅅLJI(19GL,+()2@GB/(;
@485
gccagggtttttgatgagtggctgtgggtgctggcgtatccggggattaaagtctcgacggcagaagccaggctattttaccggcgcagtatcgccgccaggattgcattg
+
000;+IH<<(/>GEH6C&'.2&-K5?.=GN?,20&(GC46H>>??=<.G-LN70*J?I8:M)9K9JMNECN-64.89&B
@487
aagtctcgacggcagaagccaggctattttaccggcgcagtatcgccgccaggattgcattgcgcacgg
+
00M=/KA;DLN<'=5>-=;.D+C+L-E0A07)+GINN61,G9C@)<&F?&)INLEI@)KI)=M57L7I=
@494
ccgccaggattgcattgcgcacggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgag
+
00+4NA>EB>)M4ED=//J:7F5F.++@FE;&;JN6)?0-B2GJ)6G/9IE&LK9CJ<=N&&@LJ95F.*7M
@495
gcagaagccaggctattttaccggcgcagtatcgccgccaggattgcattgcgcacggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagc
+
0*5LIK.B260L+)2&>4/.A?864:)B1F'E,12)J(+I6BK?M6.A889+G(::=()MAIB5K70//5:)3095D@DH4IIFJ+(L'L:'MFH*3IHEL8NC&0E.?@8BN>D;5<+89>N=6=II10C(
@498
attgcattgcgcacggggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatg
+
0000D'1='0.G8(,N)'H/5:,:8;.<1;:KFK5)6JME;0)?FE+(5D<;1L'I01?E+<=N;L,/7L;17I.INEJ8;?,E
@499
ttttttaccggcgcagtatcgccgccaggattgcattgcgcacggggcgacatctggcaggcttcattcacgcctgctattccccccgtcagcctgagcttgccgcgaagctgatgaa
+
000000F92/J:2<:H+&BL&/I*?L28K2*EJ9F-GKE:HE))7:,M4M@6;1+MC:<2A9G()78AMC5B26H7JC,396&L2MN5,B@MC4,JA,FJ@HH8*H+K8+&*1<02.5
@500
acggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaac
+
I,4BF,8&)D(:H>5.73(0*6B81<2A?I;;L1F;,:8IK:H@D976@M>7GCI)M,.''ML?*;CJ4-7+*J/NK4&GC(-NAE?5K
@501
caggcttcattcacgcctgctattccccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacc
+
0:?;DH,&A);B)51H+L0(H7&@)=NDKK?A?CH7IJBA//./IJ7B,9N2A>JI**B>56A?3-E&B>J64*>AM
@502
ttccgtcagcctgagcttgccgcgaagctgatgaaaaagatgttatcgctgaaccctaccgtgaacgg
+
009G>7BD9-?CE??)&C*>KCF6+@L/J8>A;9'IB8<-5)*6?6H,F.(B0I4M&4//+K5J,/4;
@503
aaccgttcacggtagggggttcagcgataacatctttcatcagcttcgcggcaagctcaggctgacggggaatagcaggc
+
000059*90,N&525=4C,GG2+8H8I;
@508
gccggaagcctggcagtaaccgttcacggtagggggttcagcgataacatcttcatcagcttcgcggcaagctc
+
00,13@83646HB?6=4M(>8EK6:+2M5E)H(I+->N=1.87HN7I>91D&,2;+7G-+AKCKN8.F67A;F-
@509
tcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacccctaccgtgaacggttactgccaggcttccggcagg
+
0009BF4&4/B(<&L+482LKAK1H40@72I.>M-G31,(53?C'?G826A)LLI/GB+*4CC1L;88B:'L)+@=8CJ1G7>+
@510
tattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacctaccgtgaacggttactgccaggcttccggcaggc
+
)G=CK;N0+GG'.4L*G6M*>7EKDHB+()N:N8H)&G(MDI:-/),,3:.F915:8=JGJF'?CD&'3MH&0L*C>0D6MN23E5')E9&
@512
cgtcagcctgagcttgccgcgaagctgatgaaaaaaagatgttatcgctgaacctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
+
0000G'';'B4IF>DMI6;FJHFH9NI>F(N-I>EHH.2.G=@?/7I?JAC7+GA;3'),9LEF?&CM;(@(8G6=I'63E;2,HJD,F8CCC44G3;.
@513
tcagcctgagcttgccgcgaagctgatgaagatgttatcgctgaacctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
+
0.'7J6,H@C22HGB>M.(?*64@643&1@C,=->N+(7/(3K-@+FLNG,?E/J---GD6=*.>.&9'/AJN1&6N@(&F@JJBEJC67+F
@514
ccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtaggttcagcgataacatcttcatcagcttcgcggcaagctcaggc
+
00).I04?EK;)B)/62:/<0F/.:/:K1+888+7=/59DCHN'NE,KA=@/L/;G*//E6?;NINL*,*
@515
gaaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcggt
+
000&=K.@)>:J>83G'3(/4:4JH8.@7,-N5@//K;)//C&>7D@N:7L=.M*M*=D)2K/=@7(
@517
ttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggttcagcgataacatct
+
.;G3C3-ELJ(E4)@1&4&,<,JM5JLAL-91?-(H@LA
@519
gcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtaggggggtccagcgataac
+
0000(30DNE&&-A+9C4G>@I026)JAM0=ID,;L@?;I149L6/;?,8:.':GA+'B@(2L);3A.B?+E81K@,2.@;?>C5E5;9*'>KJ*7M6562*AI&9C?G
@523
gttactgccaggcttccggcaggcgcggcaggcggtcgcggaaaaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttg
+
000I>)+E-,73G@,8:,&J:F32>,M=BK+,J/G7F+FADHF<@1@?(L>&N;7GCB0*&A49D)A2K*83NMC;M,4@.67?NN/5)(B
@524
gagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttca
+
*KGBF=M78LN86MGA2KG2L3K:,259M9+B.HI8DD+?GC0H@J4;&NN0E2B9C)J(8KCC*&/>:I:)36-6M<@BA:*/@7&-&62,M>E.L38BM
@525
aggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggccccgaccttgttcgctctgtgtgacaagc
+
0K>*K?65**&=<-A.3NB6>K&FE2.>8J&865,D22I??L/;A@(.LJ&<0C9<7**M,4/A4,@I>CH;BFM/94+K':.C:BH<
@526
gaacggttactgccaggcttccggcaggcgcggcaggcggtcgcggaatcggcgcggtagcgagcggtatctccggctccggccgaccttgttcgctctgtgtgacaagccgg
+
MN@B@JGKMN'/CGKL:288B*A,1?)?*)'.4I7CB@A014@097<@8?0L3G(J9J?/CJM+*9=N>7HN=<&J?'J3'KH@)=F>(318>D2CM7
@529
ctgggcggttttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctg
+
009H69>LL9@@A?2B11AD'9>K-L9466DG0<)BA(6?-0+8HJ=L7=A54IN?L+J/B(/1B0)>J@KEKD(@0J0=K*'+'7J>3/H@=/5(*/&;8GE0149)I23A-D
@530
atctccggctccggccccgaccttgttcgctctgtgtgacaagccggaaccgcccagcgcgttgccgactggttgg
+
0.'N3.159A)IM3,ED<'.JNJ(47087<4.23M+&@,':.&0G4-F&FKE026G*
@531
ccggctccggccgaccttgttcgctctgtgtgacaagccggaaccgcccagcgcgttgccgactggttgg
+
*(=1BNE1;7JJ-+:GH:)G,K>1>GC1,DA:BD(DE(/A:MN.:IL/?7AA)//?MI@E>K7NNJD;2:
@532
cttaccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcg
+
>FM2)*+H+@;A1265=02HN0;/J?9;42(03;E(0/B/DE@*MD5(C'L&0D9;3,-IA4-C6&L9HE?(DB)83/7KGM7H>C'IN'7N@6@,-<(9:65A
@534
tcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacaga
+
0&)IH*;-44?:,(:L.CB+131('0J)&*A@BA8*:''CK-F;&>>@)A'B:5+':*L7)0=G*:JMG&A9
@537
acaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctggcggttttccggcttgtcacacagagcgaacaaggtcgggccggagccggagat
+
000L?GN7:3+G:23G=4;C=EL=,B9B+&<+&L/@71=+*JF-9>-&=HH@71*80)7J-275F1-(=,K=<)6,'9'EM@@KF?,;-,AAI0GFKB?;6B::3,L&
@543
tccagtactcgtgcgcccgccgtatccagccggcaaatatgaacaaaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctggcggtttttccggctt
+
00000G(?/BM6I?(3L@*/CK-L15<)GJ;18NF-93K322;<7+-)44@J+:N&;:27GE+>9>'43I8D+(&>AK2@LI'N(018*(9B/2B70=5C059K72A043B>*G
@545
atatttgccggctggatacggcggcgcacgagtactggaaaactaaatgaaactctacaatctgaaagatcacaac
+
0>8*0H9K1@?,?'*LH>BC'8'D7C;&F5E@GE(&?(892B&L@*D&G6JCH*;HK7?K4J-,?2DKE46C/492'B&,D0LA..;70
@568
gccgagaggatcttcgcactgcgggtgacaaaatccagcttcagcatctcatcaatttcagtcaggctgaattccggcaggtcgtgcggaaaaaaaacagcccctgatttttgc
+
00000008B>?&N462C1A8?M*@/05=J@)L+'H'C--LC(96I&5--6-//I6-=9/:)+J:@
@574
attgatgagatgctgaagctggattttgtcacccgcagtgcgaagatcctctcggcgttttttattggtgatgaaatcccac
+
000244B-G>.J)66J572:'J?@M0CFKH6*KNG0=G@J1>CL?+N<+(MK(:<7=,0H:)4G43B;'8@05>FKF2/('B
@579
cgccgcgcgcacgcgctcttccaggattttcctgtggatttcatcaccaataaacgccgagaggatcttcgcactgcgggtg
+
000BF1M1LDJ&<&E(61G/&EKKJ.H&'&?6+034AEK>1*68&==D'>:,-FNI,7/2M-(2=L8,,(A8:;@/4F80:,
@580
aggcaaacgccgcgcgcacgcgctcttccaggatttcctgtggattttttcatcaccaataaacgccgagaggatcttcgcactgcggggtgacaaaatcc
+
000000F087'8F'L))8(9E7CEM)&GCD'G9LM+?889)'&3?-/M<3F9M,*0N3BH?*.2F?(5H+');J0;3:A;41N*
@585
ttcaacattggcgaccggagccgggaaggcaacgccgcgcgcacgcgctcttccaggatttcct
+
4B'JJG@F<4)*,.3<3/'H(G)??HN*:NA585GC)NL55?EK?<);0?G>2-;MHL5MCD4;
@586
accgacatcgcttttcaacattggcgaccggagccgggaaggcaaacgccgcgcgcacgcgctcttccaggattcctgtg
+
000/HAK45(2K.B/@<(F:0M51IIIJ'=B719F6KN0I'D4J(3K&M&61K+::+.+(+A)N&3DC<4;,+=+4C))=K8=A'3.I
@595
cgccgaaaatctttaaatgccagcgttggcccgtggaacaattccagacaaccgacatcgctttcaacattggcgaccggagccg
+
073)0F29H2GCNG41/DK5F6G7M+6ENN7BI31+6+@4B<<*K*-IHA;(:9D=E'IJM*7HNA:9AKJJ',+6K76:3?=8,
@597
ttccggctccggtcgccaatgttgaaagcgatgtcggttgtctggaattgttccacggggggccaacgctggcatttaagatttcggcggtcgctttatggcacaaa
+
004&)3K/=>(5;J970N'42M-,&I--/AJ+NF;=N>B8(L1D6))BK)E0DI'@147JAHE3.2)@3MED80;8CA@2.I9A7.;<1@>>I=FE
@599
tcagcatttttgtgccataaagcgaccgccgaatctttaaatgccagcgttggcccgtggaacaattccagacaacc
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000HD::C*JIG&@3JGE0'KEBFNI0@.5:6)(L;?)==IN&A=/>6B9;70:NM2*G003J-/E(:8;-C,<8+L
@600
tgttccacggggccaacgctggcatttaaagatttcggcggtcgctttatggcacaaatgctgaccca
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00&?G/KFED9-H69=3'1.5>9+HCF*D.@.3H'EB2C27A&F95&2(LC7G6JN(51BB,:@N?AA'@2H;I
@620
aaaaaccgtagaaagcatgagccactgccgctccggtatcaccggaggtcgcggtcagaatggtcactggcttatcacc
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00(G,LB?09*=B2;0I'6I:9J1>C&I=3&+29/-;8+.@C*7=G>*3CH8-0.50*E>9
@621
agtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtta
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F585):=+&LK(2&B'&7*&>&+LG<4B(?064L9H9@?NC64-?8AJ/*
@622
ggtgataagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggttttaccgaa
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000D6N=+MLCA,8C6*@C<)G6C10A+/><7H*?@-:NFD;79HCC@G7DC=J=*==C=<&5-ADAN:,@8:CHNMK1HM1-+9;9B:)I8M'>6NF>/>76D*;)EF?0?L.402
@625
aagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgcttctacggttaccgaatgtgaaagtggt
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0000J/K97G4=;HD*N@J5:D77C13@&A'8/*:<;.D?1)>IC5)A)>?7@BB.3GHD3G9:IL=D8536CE0D/(1
@627
tgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaatgtgaaagtggttatcctctatccacgaggcaaaaaatc
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0008:L07J+//;KAM&7N1(3D(&9+HA5'7L6E/.6G4)?L8//,-5L7N8'7N*KA>7)8EL?C';E7H07./:8863EA>&5CJD&<5;K8&G?,3&D8/(B<'BIF=N0.*?L/H*-/(K0E6AF:M?0@
@635
tacggttaccgaatgtgaaagtggttatcctctatccacgaggcaaaatcagtccactgcaagaaaaactgttctgtacattggcggca
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00H/NK&2.KM?B8K0MF@55F)H914DM,4MME>E*6M)'<3'J,AMHBMB';@,KD*E*@FD(+DCE78*=?D4,*86588AM6M51
@639
gcaatcagtccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatt
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7NF3C,);'(8+*8>N<)?'4=MDMN
@642
ccactgcaagaaaaactgttctgtacattggggcggcaatatcgaaactgttgccatcgacggcgatttcgatgcct
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00;H=)->D-F(IN5J-6N)-+@*25KB8M>3/(.,;6(>E+A/)/N9)'*L0ED&*4B0/C8(&)-42DJ+@;ALM
@646
aaaaaaaaactgttctgtacattgggcggcaatatcgaactgttgccatcgacggcgatttcgatgcctgtcaggcgctggtgaagc
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0000ILN23K'II,EG586K*>9NJ00GM:@2B(10=4:6,MI/N&>/L)H?,1EG?C5/E,2AH::3==6.:GCE&/MA//)2)(//H6'M;>BC49
@656
gccagcaacggctgatgttaatcgagttagccgagttttttaaccctagcgccactttcagttcttcatcatcaaacgcctgctt
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000A(CL'7D(=>N&9).??2J8F81AD0N3,BG.:>07M>H3-'&@,9FK&&:@<=BDC:NK:6KM66;33?5MIJ-HE6?=:MC3<.&70,H0(H56N@/B4GH
@667
tgttgcgcagctgccgcaggagacgcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtca
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FK,F8EL@4(F2M91>NE->B/A/I=CD777+'4D'(,4FME;J=''64:D23>;K*J'H-H-9'.BMAI8/6I-I)
@668
gcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgattgacggcggggtctgctggcgaagtcact
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00.31N9/)B1012LB:K6:K+C@<6LI,?FJ3J+3:(65(9EMC>35A.-02..MB-/G?48:M:8L*0B-F+(
@671
tcggtgccaagcggaaacttcggcgattgacggcggggggtctgctggcgaagtcactcggtctgccggtgaaacgttttattgctgcgaccaa
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000<.N:FN*7E<9(C;0JAE>(I2D=*J9?KMG&MM93F-?7-&(GH,JF71=,=6IE&;'B-DBCCDADL:K1CLAD>&+IAI&D'2=B@'/
@673
tttgggggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaaacgtttcaccggcagaccgagtgacttcgccagcagacccgcc
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000000D6(+*6-)):=166@/&&'55<+-;&DJ@AC&3FCNF27K671DLEFFFE7I@BG)>:1IL1)8,,9IMGI';I@+N?E@I3G2(4LCK>&98JL:CD'
@674
gagtcgcttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaacg
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00B:C@9CA=B(&4>F*)GB-JA-='&8<0<4=GE0-(DE:3B@+EDDLIF/;@JJ('ME.F*(84CK)=1A(&-JK
@678
tccatcgcgttggataacgtcgcctgagtcgcttggtgaccactgaccgtcgtgcaggaaaacgtg
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0?-*(?-,.'AF3:1:0I';.D7+(02N-DA/,8/5I)&,B-@72.*B:.C19,L+JH(0:=2>'/
@679
cgtccatcgcgttggataacgtcgcctgagtcgctttttggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacg
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00B1>2+08HL)LB<>+83M(NNH9?H)6090A<77=IG0DKNJ.:'J)357D>+F'H4&.2:?4>'-(6L;=+2LB+57:J@:-7(FHB
@681
ttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttttgggtgaccactgaccgtcgtgcaggaaaacgtggca
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0000:7:<'=H*/:/<&D5D92;E*3*4E?51?0K9E.50>D=M1.GJ3D*.-A84E--H@7A2H*/9G+61KH1'F/G/(E+&K<2KM
@682
gttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttggggtgaccactgaccgtcgtgcaggaaaaacgtggcacggtatcgtt
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0000&0A3+4G:*3+.4M+BI:0I9&:/>>J,1='EAD:24B'C5+,:1)89=ML=C-&H&(GG*=A4*?3;4KL<0=F2''=L3F'LI./J,0.H:I48579
@683
ccgtgccacgttcctgcacgacggtcagtggtcaccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccg
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@684
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcg
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007-8)KG?1:>N2HG?KJ5?>1BK0137;L'H:J7KD1JI/:L'3@G1';AM8NDI-B-;>HG86(;9.-C*,M8*4>3?76,&@BEC;C&J?E9&-K1DEMEB
@685
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttgggtgaccactgaccgtcgtgcaggaacgtgg
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0D9N2C5EG*1>6JBH1?0B(.N(0;LLJ&=0E5E=.+E'LL:&;2M?GIK(3)+A'>2M8'<*,9=6)H.?&NC-E:&B7A/NAAB66A4@CC368
@686
cacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatc
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0000,BI4C;6C*D..L9+,&+&@:=32IG:>-9JB4GL+NI@G))@*J56E5::=+&'9B8:+0MM.?AANAAH>83@CA)GE596:M?7M6.-?@71>.AG-KE?.L?
@687
gataccgtgccacgttcctgcacgacggtcagtggtcaccccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccgcgtgtggaa
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0G=IJDI'=DI/MI)762*8:(/DN9C,&3K*;'9@*37;KJ8;&(K+B/39<&NI=27(C>,M4M4.E+8-NJ;*;A4J=D>>4N0K3,(,(4>DMK9.D8?;(G.&?3C
@688
gcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgag
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0M6.41&KH/A*A/&C/B1,5-?=5G;IC:2''+2@B>F&3)JEFN;00K1&46D4E)C/IDG
@689
gttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcg
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003*61(@174CI3JK9+2<>C0;?B&M<6A)9-BB-@4-G,D1((:.E,'B-4K,)6=3?EB(A6.@4'/C)(6I5-HF=C**HA>(/'<+/>4NB&/87'KD@+DC:H1?9;LHA@54LD6-K'I@*K5J+'KGF=*);9=)'GKG>@50J.7F2>-7',8@D?EH,3<
@693
cccagctcttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcg
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00+:EF,'>K,H'LG.'&4(5.=B=1C/1GH&(<*6I=BK8-,88<';N:NJ14&JI;*M<33/*
@694
ggctgcataacccccagctctttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgt
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00000.+J'M?E94D@FCK=@7;?A?H97'1D/.14-+8K/:5:NNFC,M>IM@=68NMK739@CE@3IFKMH185LI2M:.@H-&'M
@696
cattgtctgttgcgtggttcatcatccacggctgcataaccccagctctttcagttgccagattttgcggcgga
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003K*M+LID6'BH87J527-G6DFI4(<&-B>7)58MI45=>K/8;3C(3+@5
@697
tggccgcgtgtggaagagttgttccgccgcaaaatctggcaactgaaagagctggggggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgt
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00000-6JGGB+15&(A58/41C7*&6.0L?;8K2K5,,1501'+1-99:8JD,@3FM,/B03A+N3AN/42+H>-:C;L)75'>3JAAI.F@0H::D;)8@+-2:**9<+MCG-;?K.(.+D
@705
atctggcaactgaaagagctgggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgtgagttaaaagaactggctacacttcggagccgcac
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0(50@?=7C&M+,6.2-LH7B>BD1NC?.I*3K4>NL<&A/6(M'(/5>8':I8C28.?=;H*4KH+:78A8?*9D':?0?A,2>J>L7<;D=0+7D.=24@JD8
@710
ggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagccccagttcttttaactcacgcattgtctgttgcgtggtttcat
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000'?@4ECE'9&3>?8?C)3)HJ0H.-.GK/*G(M6=.F5G>E7'1);)'1&E14-;?'9D69L*8G4=GH&+8E<=5/:34'B1G@0-+;2-*G=H&;H&.>
@711
gcctggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagcccccccagttcttttaactcacgcattgtctgttgc
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0000I>1K/*E)M*3,4.E7D?29F:D055I.@7LH*D19&-.B;A&5086<&*:+&25I-H&//1D,M9A1:H,<3GK,)*NL.0L6>CB,5/3<)*?G'
@712
aactggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaat
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@714
ctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcacc
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::L4G)+K/5@IHFB7D+?+&&'0=J0:G(J;=D-,J1EL.B6NA*87:?J;MIEG:711D>;,6MF>'@)/6EC(42?0'C98?F=H;LA1?/B(?<--L<,EII'H:/HJ(5+2A9,J)F;
@716
tcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgtt
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&B.?MEMIDDF6/&046?M5'1,9:G14A9H;F*.C/=DACNI'27&>/?29:CH@G>..M<01-HMD7-67/2CM'=(I)CG(1L(C2FFH0G98@1?E&7CE.85.995H721L;>IIB-18,I2)AH6
@719
ctggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatt
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00,,5*H9G(15@9L/*?E.'?FH37DI)>*@;1-@&)/(7-*L*E*33(@?M4NL@KHM(2&L7'5D6LJ4N<2DE37L9/L>;?3HJBD.DE/3/G'4HF;JH'=-:
@724
gcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaatttaaagagagcgtgga
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0G;DN&CI)B73D)(E)>DNM6(E.)'I>B;3)B-MKJ<.:*H,*0D@/'/)LE;*38>G&.(5F:F/KM4A.K+I:LF2L7
@725
cacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatttaaaagagagcgtggaagc
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0003&@;+:8/'@:E<2.GJ.+?CFI.M0E.3E?&D>GD::?&:'(85=,J1710CA67*3E=M9J0@D0'.@>GD4'*-;.CAMH8:)J/E+;'+L.@J6.:H6HAN
@728
ttgttcctcggcaccgcgcatccggcgaaaaatttaaagagagcgtggaagcgattctcggtgaaaacgttggatctgccaaaagagctggcagaa
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0000.9FBM*8*8B)58I;=.J?5A16.K@41)*-N=I>'@HC96+.AJ)NC?K*/CC60,1G1):(N&18.;M''7JHC0/,1*1;2)E0/6D@4'0'+:=2N>B9:+G('1&
@730
ggcgaaaattaaagagagcgtggaagcgattctcggtgaaacgttggatctgccaaaagagctggcagaacgtgctgatttttaccc
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000&K+@L:AK+G8<&5(:44(J:')L-8>&E(/394EN6-;N/F;;-1<.9,919&4HM(0?<:FA:H-*>3B5I*:J,:.G?13>
@731
gttggatctgccaaaagagctggcagaacgtgctgatttacccttgctttttcacataatctgcccgc
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000000'?=CAHA-MIGKA3(*-14IJ,:LH+9.5;M<4H:K/ME'@@CJC-;CAD6AD6
@743
attgagataatgaatagattttactgatgattcatcatcaattacgcaacgcagcaaaatcggcggg
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00-0DN?GG'C:<>@H')+>''D89MML;K,,L;4.457>,HJ;7L?M67G>BN/BN:36*KJ+@HB
@747
aatctattcattatctcaatcaggccgggggttgcttttttatgcagcccggcttttttatgaagaaattatggagaaaa
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00000<6:)LAM')E67&=4N'4,93JMFK&*55&7E-&&H?B+>@A,G/02:BG1I8DHALD.'&>+5'460LL(L7&;
@755
tatccggagattactcgatgagaacggcggttgttattctccgcaatcctaatctctaagttaccgcattattgagaattctc
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L2DB85E-9;,41'03=?+=>5)4@2=8D>GI5B7.M3D.'2=&60)4HI1.&LIH3*6N.4/N4'A,1,CN--)2DMH.4/.
@756
tgcggtaacttagagattaggattgcggagaataacaaccgccgttctcatcgagtaatctccggatatcg
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8=3GA+MK'C./E/*<)I968-J,&CH89I+)&>'/H>@:EH&5*/>D101>8L-I;F.?8K'CN3G&?.4
@759
ctcctttatcattgccccgttatgggtcgatatccggagattactcgatgagaacggcggttgttattc
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05+KB?/I5'E94)@14CE=C)@)/.J*7J9F/@J9,*L:C++/52758*AN-.K*'L6*+4E9K4+B3G>2DL<:IJ8/=A97I><,&)G03L3,A:N>MBI8.K6@G&@:3J
@131
gatcacatggtgctgatggcaggtttcaccgccggtaatgaaaaaggcgaactggtggtgcttggacgca
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00H-&*4BEH4J+=79L469+F9G.(3>:)+5LM3(
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ggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttcattaccggcggtgaaacctgccatca
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I?7H+0F&510-4(<8C>);:E'C,4AHKAD*AD>GN3,*;A(9<=8:IM):ADKE@/'HE2;;;8+/?LG(D0*6?62(I>FE1H026N(8EE0=GH9?<>FMA6LEJE,E:5<875=;4MG1>1=LFC?FF.EN/B'EBJ&+)3EE3*6BC7?M9::26;-5/D+I9;22D3NEJ'6'>,N,D,BKN:6784B>;IAB':=;@-/6N:B,=J0+FG30)C6'CL.<+K<:
@142
gtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
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00L=)H.405GF+=C-:A2<)>/>E>D4BE&+B:AK27>09
@143
acgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccg
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0009F7HI90:/4GN2B&M59,*AM(0&60N&3F?3L=7EF7NMJ?N8N-.?2*0,<)0D2<&)8BJ*?LCL
@144
cgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccacca
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000&C*&5GMB4=5F'LHH@)9=3J9G+3L(+FEJEC)>2:D(I/N',
@145
cgaactggtggtgcttggacgcaacggttccgactactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggacgttgacggggggt
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0000IDD:);6.2JB:/3LKL3E7-2)'+3&.5J2(:6*;J4(D@C*>;NA;?;(AA7@*>K2J:1IHG&;F(7,.:'F;MK&2E.B=3-*(G-C9B:818I2J=@-
@146
tagaccccgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttt
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00000-E6)/08HCK.;>I;?)*AN.5KCL/IHJB-3(83M;E4,I6ML65'JH/K5.7>8;B0'D
@149
cgcaggtatagaccccgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
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0000+899@+,1HCGG2-M19*FE85BI:)5=953E4>)02&*'B@B'JB>BL/2+;,+'.5C,8;AHA+)2L?9*C4(;ABAA1@-6(/)61F2)2)DDD:5F,NGHB
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aacggttccgactactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggacgttgacggggtctatacctgcgacccgcgtcaggtgccg
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000).K7JA0F29G5(;H:,?3N:A9NI&F8)>15L1<@5A7?JJ5.HBA1NB58='3BA(@:HDE&+0>)A*.<,'(77H&GG0/2L8(8<8'NN6F.:2+40*?/-3FN
@152
gcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccga
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00/C+K;>474J:N,K0ECELMC++HE-*N7M+.DHH-=8AABJK8-C&-+-8)B5@.34DN/:1@8J;,)-.225E:BMN
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catcgcttcctggtaggacatcgacttcaacaacctcgcatcgggcacctgacgcgggtcgcaggtatagaccccgtcaacgtccgtccaaatctc
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00000(75E,/5><-379KCL7D@3?JJB&)+G1K.HLK48?F1AG/5D:);'E:M6AEBIH>E70?:IN'D@-,GJ/N00FEC;/()=>@AI=D*
@162
tggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctt
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00000/60K<.C;/E?7N:NG?&FDHD/J6?J25.*0:<4*/@N./JM'=:N:I-)19I,):'79N/>F?GA.898KJ>H:/6'?BIM31,M9HC@BHCC?C.NNG9',
@166
ttgacggggtctatacctgcgacccgcgtcaggtgcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctttcctacttcgg
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0H(1;<1>(.83L>99474AE<2MC4./'J6;JL<7J.D?/=,//)I<,.;I(41'@AC&,<27H2:87G<&5NM)43&K372?MM97
@168
gcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctttcctacttcggcgctaaagttct
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0;&6GM3<,86-2CL-2GH&(,KL>-9MFIG887I;F5@LL/FKH+&:17CB+9NF9,8/L9@<**EC,6M355/5KH+E4;KGH-I?@6(70AE;F.,D4F@GJ>-+4BEL&=J**1-:+@.3C&>DE;C&I/>85J)A';,L5:?A/I3<8F*.DJNC9C:-E
@172
tctggaactgggcgatgggtaatggtgcggggggggtgaagaactttagcgccgaagtaggaaagctccatcgcttcctggtaggacatcgacttcaacaacctcgca
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0001??5DC7).//M7M5/12?N>79-/K))-5?0M(73HMFF:FI(/*=K:,='G+A7B6'4DILK0-DK@+>HI>A>N/0>GIEJD(3=6761:'>2B/@8/E
@177
agcgtacctggtgcttgaggatttccggtatttttaatcaggcaagggatctggaactgggcgatgg
+
000=7722(3?,M'..)E':EGCE(N'@K4/&>6&'C)1-/A;&:;-6&CM*74F)GGI/&5<3CE0+>4-5H,D7JF.-F(07>3?D:8=HL?
@185
caccaggtacgctcattggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctga
+
0005,B6(1MJ*9;+LB<=FIEKFG1E+@5BE-947?C2A8'H6<7G&8N2+14-0&A;7=?E*>FF'M
@188
ctcattggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctgaataacatggcaat
+
JIF22>.NJ0/45N.BB1*A&.M+,)E)2;:<.HA:1>1A52JMM80;I*E8@&AB1I:CJ
@189
gaacattgccatgttattcagattggaaatgcccttgaccggtaattcgtcttcatcacggctggcaccaatgagcgtacct
+
B1>7904BE&HG/K/3K9(9B.=J=G/G;<47-5*-9CFIA?((F5IJ:0CKLF8D?3FC759A(6=2618(7;EG2,/.LN=C)A97(2*K)E((*,G5D?*C-N4??DME&I6KL9M/1@6J?MF9F&D6/0(5FJ4K,;F0=M4A;=?1AN*:+N3+*J=?B1;)6&4:K9(,11IN7G-N1H35>GBBF0*3*'7'D>
@192
ccttcatccccggaccagaaacgctgaacattgccatgttattcagattggaaatgcccttgaccggtaattcgtcttcatcacggctggca
+
0E=;)>.K6)E;DEJI'(JF2@C1.=A+112CJCL&G?48>08LA(:0EK)JN0:A);@J;5(M&5GF37HDDHMF
@195
tggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctgaataacatggcaatgttcagcgtttctggtccggggatgaaagggatggtcggcatggc
+
00000)72BLGB>;:(/)&>@(39-N5F5>DL@H<>4C6J3N5KM76GN41/4D7)NM@N+,E)8,H7*I?*
@201
atgttcagcgtttctggtccggggatgaaagggatggtcggcatggcggcgcgcgtctttgcagc
+
0000:*NEE?65I4H;1+A/2;1*-H:=55FK.=,2&@1NH0N@>IC/6
@205
ggatggtcggcatggcggcgcgcgtctttgcagcgatgtcacgcgcccgtatttccgtggtgctgattacgc
+
?-E>9B;BJ7/51BA?:N70>+(:-?42:;N;7:-;@8IA.90.*
@207
agatgattgcgtaatcagcaccacggaaatacgggcgcgtgacatcgctgcaaagacgcgcgccgccatgccgaccatccctttcatcccccc
+
00=2G+8I>9(MFL8+20KIH6,7<*=69JH76+0MMB8;1+JDI''2:JB9=:F65<370I24K0A+LI
@210
gtcggcatggcggcgcgcgtctttgcagcgatgtcacgcgcccgtatttccgtggtgctgattacgcaatcatcttccgaatacagcatcagt
+
00K9EH2066:6B;;84DN9K=B9'9K2L?LH-'&FE.,&GMH0'';.(ML21:B<)2,F7F:@3;35->+NHMIC=7HK*I*1,55A3:1CN6,F?;'*=?(-))=-=A179M9C)M@@8B/=GD*J*5H&>9=L>;/0HB1)3GJ=)C:M&5DFAF;;8I2.0/-48*1:+@FK
@214
gcgcccgtatttccgtggtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaa
+
00*6C)6CJ1KCB@537DNHD=:'7I=7-62>0KB@9'HH/,;KNC;LA6@,,DI+9&+1L.934D?&B:*IMMB:73KKE=9L>3275,1-B;)MA8*
@216
gtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaatgcaggaagagttctacct
+
00000@K9(,DHFC0'+8(NC4F50H000D165&F/2M3GE?*A38?<>/:=A89(G0+-9L,'.'AHHAE((IE'9/?,')9E.253@3:EGG3J'--J,
@218
agcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaatgcaggaagagttctacctggaa
+
9(D-C320J22CKGGM;:48BA@A6?A4BKD-;5(3,J1CI87KA66>/?)&NG44;3A-1@2)*D:(9*2-09F
@219
ctccagtaagccttctttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcgctttgtggaacgcagaaactgatgctgtattcggaagatgattg
+
00>2B93(B?'7A,?A?@AMBJ;'&&.('?C,2;)2G4&CH82+166BLG>08JJHK30E*?69@-L51>K4,=-6'N(D7.-KI4E;,)+C?.()835);A6G77J7@849
@221
gccgttccgtcactgccagcggctccagtaagccttctttcagttccaggtagaactcttcctgca
+
00+(45D(>E;K+F=DH('H/D/';L&AF9F?*:J9AAJ35>G161--4'KIDE5,1C@??2(BD<
@223
tggccagccgttccgtcactgccagcggctccagtaagccttctttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcgctttgtggaacgca
+
00.IN9DJ'D;214><*69F3808DB(>GB+NEC4G7N19@=;E>A?3J0,@>NA55I+52>129J,GK)J4+G39'36NJJF9?8C?9:4'M0=6+E?5359,=G;K6,)F
@224
ataatggccagccgttccgtcactgccagcggctccagtaagccttctttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcg
+
0000FB5(>B0..-,6I,NA-J,>@I868,19H+/@F/N&.KCK>7C:B.(A:>2))<
@225
gcaggaagagttctacctggaactgaaagaaggcttactggagccgctggcagtgacggaacggctggccattatctcggt
+
E<,4@0B551<40I&:B>@54=;>+/,GAKAI9I&4139F&=:5)<3EEE3N))N2L6BHD':'*N2;AM<,17@5D)(@2
@227
aggtgcgcataccatcacctaccaccgagataatggccagccgttccgtcactgccagcggctccagta
+
2-@L-;1J.12J(<=G/5+FB5>*J6E;*=M&6M=-)17NDMK/*-,
@232
tgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaagaatttcgccgagatcccacgcaaggtgcgcataccatcacct
+
09CG+5)&7D80)D.M,07F=:==)A1'-*B(NC&B29NFB,?'HB4D,D1N20/9C@,>D:,'*2'A(01I>,?9@
@237
aattctttgccgcactggcccgcgccaatatcaacattgtcgccattgctcagggatcttctgaacgctcaatctctgtc
+
0157B=7C<<=MI/,(IB(F&<,N,56BLAM-JD-4I*M)C@E85LFAI+6AM9AAA&31*0N;I-MA'*KB6ELF@I,J
@238
cacgacagagattgagcgttcagaagatccctgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaagaatttcgccgaga
+
00(0A1L=+=A*+D8L16L&MMGH8K6/12?HH9@,3JH=*BA*8>>.5/,:7B<*G:+E+N?FIA9JD<6?5@?03,*<(*69889;2DEC
@239
ttaccacgacagagattgagcgttcagaagatccctgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaag
+
0000HD2NG95*B=N-='>60/M(BG=N4D9'4K7D2((E;@/?=0/=2)8J2ACK3B4C:;NN,/AK(3?H05M73&:&9;=
@240
caatatcaacattgtcgccattgctcagggatcttctgaacgctcaatctctgtcgtggtaaataac
+
00000=6G+NN&HM'>NC2C3D/+1F(FN=7D<345)@<**?;39?K7*'13EG@/7=J0N*H7I=.
@242
cagggatcttctgaacgctcaatctctgtcgtggtaaataacgatgatgcgaccactggcgtgcg
+
000007:?G*5843,G99L:3&*(
@245
gatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacgacagagattgagcgttcagaagatccct
+
000034E0J1)H=4FLJ6,9=6?>:M65EL+-ND-FGJ5515I-9+5AI)D69N:IF<;=5J:8N9:2I5D5J<+
@246
agcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacgacagagattgagcg
+
00BK,K4E-L>(L9''64A6@HH>>/)G&J20.JLI5&'J@8;2A&I,
@249
atcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacgacagagattgagcgttcagaagatc
+
09.'A&1&JAG@/A7I0J'01EB)F-I9I<7(M33,D>G-15'F&&'<>L-(5G?320(.+BC.8'+7L31GGI6G.247I933L9)>>'A.
@251
cctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacg
+
000,J=KE?;C-CD6AH@23+J@&8?3E1@8=JI./<=,>95.-8?0K/*>CF?L@)@*0E&GAAH&I.5>
@252
taacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttat
+
8@NMID/I)'8JKA26KH@K@2A7&?HH028&=:/6?H897F?2E=;D2+F6AAGM@*G13LKE<(
@253
tcagggatcttctgaacgctcaatctctgtcgtggtaaataacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcg
+
000;N3C2/@<'71NE1J<5B<-LID0H*,+N)G)E,4)=3-:?L;-2/(M56:LI1*:N.(AE9H96LJ6A=D1(:&N;0-:A>A0.JE1MM5LL@GG
@255
cacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttaccacgacagagattgag
+
0000H<+'A4A.DG-<;.A.-HJ/7;5H=?KC8I0,5MH;2.F?=:0C,K4&9,4/)@JFHE8,H.&)G,I6:CN25BKDFM1+7/658=-M>H
@256
acgatgatgcgaccactggcgtgcgcgttactctcagatgctgttcaataccgatcaggttatcgaagtgtt
+
F+B11,?-9I:)@60;,KMKG&F'3@?.=9N)H/,BE-3/JF4?&?9B/8*:36.4746=<9D>?DH.D22J92N;>(J+7H6<9*
@258
atgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcgaagtgtttgtgattggcgtcggtggcgttggcgg
+
H-=2FK3C7*H7.9@&H:F4LD=(;+&.&I<3E87J,M+K+;1C2D-(=IIA47I-E46N;G7:E528K,0L1*-I?3/NG77H);&?*@+N=?
@259
ctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgt
+
=.I;NB,<<.JI/FK.,'J7ACL+NK=NH.2FM)5;9;7NBNL:,KB/)3MB6-0L:-5E-F>DJNEJ@,@63&04H?78E;B?G2DEGJMNJN.'8:8;3;F2C+'I17:0C
@260
atgctgttcaataccgatcaggttatcgaagtgtttgtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaa
+
000'9K5(G4<*/4A0BI3@19/KFD@.J>MMA96/-G6,2*/LCB-941HFK56=5L,29)8AI942(,/L5@+5KJI?/@;53(93B9B1:?J2=FN;B&@>.032/:M+1B52L=,/*DB=2'G7I<.J2;8H:*I>;GNNC@9G-='LKD;F'6E
@263
ttcagccagctttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcggtattga
+
0000;;0KD2-D-1L0)/M1@A3>,9@DE-4)DB-@*C>6=,?GK)J8J4.)2C47&9M1.N0='1D(>FBM65ID,1=);FB7D.7GDI1>+I1/L
@264
tcttcagccagctttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcg
+
000,?86K-E'/*60I@=2HGKM:)JDK'>C07HF.?;?)K+:A;))F3=NL)*D.LM1AB,N70-+78E2J&M(.*&D@'A-G)3.AF>1J
@265
gtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaaagctggctgaaga
+
000('9@7C:L8M/L7H//A-M:(-@FH.G255MD0M+;:1(DLJCH<.C,9+1N<-F=9*NG5:A)I31
@268
ccgcagacacgtaagtcgatatgtttattcttcagccagctttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgcca
+
6CEBI5GFJ'61D(8:C7C7F6K>M,6+&9N*36J,*?0;E/G6?3
@271
agcaactgaagcgtcagcaaagctggctgaagaataaacatatcgacttacgtgtctgcggtgttgccaactcgaaggctct
+
7;<,(;)=H?(?G4854*5;/N*4KA?'AJ;6BL'@:F*M)8@JH,HH10EJ('&C';.*0E:'()@'(DFHDM)G)F5-8@
@272
aacagagccttcgagttggcaacaccgcagacacgtaagtcgatatgtttattcttcagccagctttgctgacgcttcagttgctccagca
+
00C5,7FH=828;ILNJ(6A44DC&9L3<7&N>B)6'2,J2/KFI0N.=D7FA7IAH6'6H/N&(()FF&F-'E5&L7L6E,,*JI/+9&@83C/KJIC*IK)5*2H662+N
@276
cgctgctggagcaactgaagcgtcagcaaagctggctgaagaataaacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaa
+
000),<+H(F48.:M?0656FJNH,.2@@A(2ED'IB8.92,:9KH7>5E7'5J?M&)))?:31.M--5;=B+J=F00&7@.9)6I3@<)@>?3G:2AD.63=/F+:87<.7.=F
@278
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggc
+
D4.BA)670:MAL;'J'(;0FA)4I80'0M2+IK0?1IJ)47>*1/=CC54=/>3BNC8=0>B;.7;7?>C'I4(6)L4E-2HB(5'N::3KFN,?9/D)DC4=4J,*,>DFL2'+G@@;/K,4*H1(A16?.?0DBDE
@282
gtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactg
+
<+?)=L7@N2FGJE>>+ED1J9B5;KFEIE&//)4*3C.A8H?3C0C:GC)33<*8NKL(@@@46AEJK)J
@283
cgccagttcttcctgccagttttccagattaaggccatgtacattggtgagcagagccttcgagttggcaacaccgcagacacgtaagtcgatatgttattc
+
;6LC2@7?.DL*;+254=H4I12B.'3(6>5=3A=39N7D/6)5IG5G(F(C2A9@;DC'=:(3,8>LA33J5<95,,H@:.A=A''-I9;C0=;A*+)72.
@284
aacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
(4-*2>G*04M8:)C@+E10IEE,0/C6EL08=9,.)NC5,I:)+7'&82'JML;/.4GHCC?G,11I3IDGI/(==1KLM'?1C:5=6DG8=-BHN=
@285
gtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
00?>EBFI>5M/C&,@N5*8@J4FKLA404/4;N&'2B3,G>CM8)4*:.F7;@EHL*F/>;A@).AEB:/23)J60L)M7BI
@286
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgc
+
HJ=;;.*.?21LN)496-(((I5/N(BI50>F.A=5L/6.8779K''4*9:L6>:/5H'.6L1@1G+7BD7L:K.N6*04&>F7>E'B)D02=(I7E,6C94B.(.?K8;>/G>,6FK83:C8GH62>J&E0/NF>C3&*+E:EM;&41N?9L2'9,MH-)I382>L3/GLCJ&-,(;72.+H2;?8@8,H*A)@-?@7D5MLD6L/GE
@292
aagcgcccgagattaaacggctctttggcttgcgccagttcttcctgccagttttccagattaaggc
+
00080M28+8MB;2JHLG,9D6/&7)H'-/GJJF@CL<*3K2)I*??>*4LFAF:(HGF:32KKJ1.
@296
cgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcgcaagccaaagagccgtttaatctcgggcgcttaattcgcctcgtgaaaaa
+
000>G&?F4,:>GD-)ILN;-7>(97FNC5C.@I;3JE(00101<0K1;K'7F;M9?4DL.K15C/L<=K9F3>A33.,D'27<,26BH5E?'H++3C5,>H/MCE95K=6J
@297
agatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagttcttcctgccagttttccagatt
+
00000N(?)2GEJG++2N=BM&/=LAKKN10H*DNF='CFE+H*'(MG+MEJ00M&',1AEJC3D4;;.B/GJ=J7E53J?JDI1'(7(
@302
tgaccgggttcagcagatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagtt
+
0003F,*/BBJ3&6J@H:=-6F&68(-@F06DCFIG(KMD;N::BI3?I4)4B*:81ID;:/BL-1CNHM0B)@/=C3IJ&*L-=L&G4;'.*9>?ND=
@307
gctggaagtgcagtcaacaatgaccgggttcagcagatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagtt
+
003/+-/0D?>+N3EB,FL?2?/(8ENEH5AMB3;:I..0==/9H'H;BJNH(8@/+6CN6C1DA)IG83H'G+*)H901,1F;:M4&'E=CNC.:@'1:8
@310
cgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggttcagcagatgatattctttcacgagg
+
00000LF<9+;FH?*5-1L.9L5(4(N=-8FD(J36A*/1<0I*.=B=)'1D.88/5.+:-KG
@311
tcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggttcagcagatgatattctttcacgaggcgaattaagcgcccgaga
+
:+.L6E@3@B*@8=+LK?G'31K/I7=*NJ<0*0M,J52GAB4'B,75:KDIJ6>'E*9N/7M9+2:E3/E)N@<73'F)0/NJ?D&BEB?>G5IBJ7+,/'K363CA;EJ
@312
taatctcgggcgcttaattcgcctcgtgaaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaa
+
:+.&G>&6*C/10)3A@.LLA&0HC-J485;.866L+F@A/(H.-(F@N11:39;FAFHHH9BK2FG<==HJ7;GA34ADJM*7C.FK*'&/<*C.EM0=6:A=G&M,;CI:?9J
@314
gtgacaacgtggaaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagt
+
0@7;:C8=N09FG&690M:*62E;KLKIHKI8D:BC6:L35H<&@NG@@297?(&+4H2(-@A>?
@315
cctcgtgaaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaaggtttccacgttgtcacgc
+
00B02H9:9*1+?G,.+(I@5/8AD>:=9?==N'/(,(GHBD2=I&71A9>GE57K3*27+.D:4=6?=G(=>2HM3D=89?*0IANL850*=33>(11II'C-JIJ*01J2:;E348F&MMC1/>('FDA.**>83GIM;-MM03@EH'5=F(=D*2/A(@(BFG9L@+KA@28I@@:G>FL'@8*N;K(>
@318
ttgttcggcgtgacaacgtggaaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggttcagcagatgatattc
+
00C23M,&E&&B)-AIJ*6EE.N=03613*6((MCE@2B(@F7KJALE3JKM2H5(.K*I4,H,6(:(&N2L
@319
ccaggcagtggcggatcaatatgccgacttcctgcgcgaaggtttccacgttgtcacgccgaacaaaaaggccaacacctcgtcg
+
0K5H6J?-95J1H0:BC4<.7>6J1'NA,)MC5B+9+49GJ+MN:G;F7F:K1E;J(?BBB8L5MMC:(8*B0?48EJ'
@320
tatgccgacttcctgcgcgaagtttttccacgttgtcacgccgaacaaaaaggccaacacctcgtcgat
+
000F922=>G>+'I(&D=>=5'2'09)H@I,BG;9>6/EF/C,:56GM-5(1.)AK@+555'*L&.@A&(F5D,*9FN
@327
aaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgac
+
0B+>C)3E7&.K3J=-)3L*:./6H,=>2KL?6A07L(.90?&33(N5:1LN'8L>.MFL'ANDLHHBB&,4)':,3L:8MG9/80<-H39L3BIILDC?HL8>L*;J./G.9M6);?8K28+3GN:&86FKE>D=@CN;NF//)*31J;(/*K
@330
tccagccccaacgttggtgtcatagaggaatttacgccgcgatttttccgccgcataacgcaactgatggtagtaatccatcgacgagg
+
00(D/=FAA*G/33;G><185L0,AA)F7BM@4G-?-IMGL?7<@A3&3KF&)A6,GC2?*;D5487L'JL.7'M45G0E'475(219>
@331
gtcacgccgaacaaaaaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgacaccaacgttggggctggat
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0/,-+B+)BFI;?L;H/.'54>,))-C2'3;(*)3)/,;-.-K26,K7+30CN,+0M=/@B1E>H?(/((NMJ)H6&,BD59,)=<;M22K4,J99(7I22DM'N)+FJ,EK2C-
@332
ataaccggtaatccagccccaacgttggtgtcatagaggaatttacgccgcgatttttccgccgcataacgcaactgatggtagtaatcc
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00))A'4G@091GL3AK(@8L428=7:-?*C1+E-96.6D@;02-??NK/N7+N1???JC)MM&K400A,1J0-*I(C7G?F+/).0K08=4/-AJB4:=4K'(5,G='?8HN92+,(+B)(B1AKI>=9;;CBEEEE.H7+1C8&576=DH/-J)763>8ML1L5+(?*+4EG0?:CJGN:@50):('/(:028IG57M
@338
aaccagaaagaatgccggagaacttcatcaattcatcacctgcattgagcagattttgcaggttctcaataaccggtaatcca
+
NG/BH9-AAFB@,E@'3E908.&:'/NM'KLH12'K?:*/;-7:A:KA=D494:>DC>*18.K;DAB@K'LH66'<.7B8?LN>09&(FB1;@27&AN*'<'7&;:2L898853::7>HCGN&+I4?+92?(@J17K@4G.L):6
@341
aacctgcaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttagacgaag
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000M8KAM-LKDEB697+)-NJ9.@>/2MG6,D:1LB;<*?JJ&&)2B89)NEJ.DCI(&<,IN)F?0,&.'B,6E8I<;JE,,H@57*=N'7I=4A
@343
aaaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttagacgaaggcatg
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000F8:+G4;'N054J?&G.>':12@6231-75J86N99G
@344
tctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttcgacgaaggcatgagtttctc
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0CHA87M&MN?L0.?+'2GL/+++E)LH,4.C68D:7F=7J6?1/F2I.@H&)&-:.,&317G5-MLC/3BMG=HC469.+.6)>.F/H=BF259I.+LF'5/6@8B2:>L4441AN4-()AD(E0>*0C2344A6*6:DL*3N,)&.774L(E,6CE-D(&B(C6NIM29DB/A8M:ME49GK.64HEJ
@352
tcatctcgcgggtccggttcggtataacccatttcccgcgccagcgtggtcgcctcggagaaactcatgccttcgtctaacttgccgaagatataagaa
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00I88:5('DG1G@D'/);:1;-A>I.D30BA7<3+;@F137=8J07?2:H@M,E>4)HNAHJGE3?,)L45*N,BFA(-9JC&=<(-DG/M8>>I6'?
@353
gacgaaggcatgagtttctccaggcgaccacgctggcgcgggaaatgggttataccgaaccggacccgcgagatgatctttctggtatggatgtg
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000*26+>(/G0843C71'F?2IC6*M1CKGK)L/(;H@>0L1?2;C(7,B.3C0H>47>MK:0@CGL0,:+D3A5,-KL1I>@-;<0,4C@(-L
@355
gcgccacatccataccagaaagatcatctcgcgggtccggttcggtataacccatttcccgcgccagcgtggtcgcctcggagaaactc
+
0000-)-D*<1J(1A*JD?-6M*9*9H0J.&?-9DK/EKF09N<.:DA.L)6,9C;IDH&-?(-:KB;5(/0&;*9A:JA>C2LD4H1'
@362
caggttcaatttcaatatccgccagctccagttcacgtcccgtttcacgagcgagaatcaatagttttacgcgccacatccataccagaaagatcatctcgcgggtccggttcg
+
000-?/?2.?(/48,@5F5F<;'I=9J7A6?2C,9,JGIN;CA8I3JL---IB'L45I(3B
@363
taaactctgcgggcagcacaggttcaatttcaatatccgccagctccagttcacgtcccgtttcacg
+
0HNE7HJ7A865'-9.E/N57A4=HHII&IB2;2B:K<&/':.(BKL6F&/3C2FJKF1&;//48J?
@366
cgccacgcgcgcggcaaagagatcgtcgagttgtgacagattcgccataagcggcaacatcaccctcggcg
+
9;,*HFG+)'-4=&I/(&+,F93K1F69&21CL:>B7L5B4-CGC2K(EHB8G>0+N-N=C+E=:G=L.:G
@367
gtgatgttgccgcttttatggcgaatctgtcacaactcgacatctctttgccgcgccgtggcgaaggcccgtgatgaaggaa
+
000F:G@43?K*3.E<>-62N:)=<(K37G>B10@C+*G03AG>8)?3CI89A<A8=>68/
@368
gttaacgccgagggtgatgttgccgctttttttatggcgaatctgtcacaactcgacgatctctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgct
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000G@&?2*MI;G+,H5'F,'(2>791F'@3,:K4&9=G85G/FM=9).(48@BK(857,1G??N7DJ&L>E+<(A5LGC7+);;8+>)7MD6>E2M.0&7H'@4<
@369
gtcacaactcgacgatctctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgctatgttgg
+
000F/6LM1;2:*0IK'J()HF3.8.4-9K<4@FA7*25G)C;?7;B3H*:&@B?K<=
@371
atcttcatcaatattgccaacatagcgcaaaacttttccttcatcacgggccttcgccacgcgcgcggcaa
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0-DME>MB8>/M=03M<*K)0:M:5L9=7>BH85'*N+G>/HN0(>:720;5B)7>-?=?C)6>CM&,K1J
@375
ccgtgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgt
+
0-34)/7<.+14;E8B;)I
@376
tgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttc
+
7+@5EJ:6,G:E5;FFAKDL&4HB'><)E*;BL*CL-H=8D+*BG'C5LH)*/'D+6+E?E&MNI2D><*9;57<2/476J?@+C(4
@378
catttttcactttgaacagcggatcattaccatccacttcggcaatcttcacgcggcagacgccatcttcatcaatattgccaac
+
00DCDD7+>8ILFJ)@&J5@.LJ/918(?4G'7G*=.8H(1A-I2-@G;--+)>KF'IC-&M,D83='?HM=B>83L;LGFJM,:
@379
gatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttcaagtgaaatggcgaaaacgccctggccttctatag
+
KL.)M0-BLBJ:+8HJ<8?G9&GH&6?ID>K1CA=8=/MDC14/==,9<)
@383
atccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccagggcgttttcgccatttttcactttgaacagcggatc
+
I(&D<=H4@I7;I4HJ(&*GC36='8643N?):NM-,3.('=G.<-B.JIF/),-4;+K;72<44>*)D<@)DG98MD=@&GF9??K3I2E5-6/C@G4?<(E(D6&E
@386
aacgtcattgcccgcaccatatccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccagggcgt
+
EE)?9N:F(K+F8:,6@-FLB030A6;LN30*I?.M0;49J&B<,,+K>'>AKKH(:7-;=/8G6)N:.*;*3C,629NKGBAA;(*;:J<
@389
atagccactattatcagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctg
+
0000-;(G/(AI))FNNN;-M.38=((C>*-G1C,7A:-HC5@.60(.:43A-3@GC'E44''>42&-M=6C:K+C>NHI@:?8
@391
actattatcagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctg
+
00JI-0318GFGDGD6@G'MF=?/M3*K@,B?.*F6.2H44D5D04KK7.=6F:AHFE)7L2F6(I+1;CB52@LF)'N3*F?
@392
acgtagcagatcagcaaagacaccggcagctgtaacgtcattgcccgcaccatatccgcgcagtaccaacggcagcggc
+
26@1;L<.C63JBC?-<4'&J*(;):B1:/MEKAD+J'H&>')0D:65+05D@0+C34;0D6>CG>I?M0H1)EG&L3I
@393
cagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctgctacgtaccctct
+
0'.*;)E'&>CN*<->,:C>L7GL(:E;@/E7DF1M(-?F11L@)JEA>AJIM*D-*:8/:M)9&LMCKD/@,:6/E26@.(
@397
cgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctgctacgtaccctctcatggaagttaggagtctgacatggttaa
+
000M)G+7HK0?2DA+G/=B(=9C7@9'6ALMF):&9'9><0AI5M/-K?
@405
gcaccatcaacaggtgtcaccgccgccccgagcacatcaaacccgacgctcatattggcactggaagccggggcataaactttaaccatgtcagactcctaac
+
-+7G(>JI9+JN=C/=.+9.:=
@406
caatgcaccatcaacaggtgtcaccgccgccccgagcacatcaaacccgacgctcatattggcactggaagccggggcataaactttaac
+
000000N00/6-8:BI703(,II+.GN'E=L+K/2;>8),4+=;BNI.D8438J?K&B/D,L@((5<8J55*E:(A3/D6H6/'KC2I24
@410
gttgatgtgctcggggcggcggtgacacctgttgatggtgcattgctcggagatgtagtcacggttgaggcggc
+
-M?,<00)N4NB/+<(N):@(N=&J70)8'&BE/)76?8>*4>F<,>FHC:&6G>K/A)5LEF388IMJID2',
@411
tgaatgtctctgccgcctcaaccgtgactacatctaaaagcaatgcaccatcaacaggtgtcaccgccgccccgagc
+
0D*;E.5??='*?F/61()JJ4A)>ILL8M>5/?4=C?L5'4>:/*&.=5+'I8=MK;*9@/E(,9.=/KDF<
@413
aggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtca
+
CE.?+L00>)4897JM'0II.5FE61I76*1NDDF9AA39GDB,G)84K52+E4=D,'G@I2CIM*+,=()K==,:L(<@4GKA8GFNA7?6@L<9D=/
@415
cctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcactctcaacaacctcggacgctt
+
(;G5<107,F078J8H7D'61*C?-L63H9=M8:9N6;JD+;ELK-.)*3D&,&D30627NA<>L'DE/(L;',>:&K*/,;E-&
@417
cgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatc
+
D()C0:AG;.GKM;?K>@,.-@?1<2:=KC*N>8LL?./HN-M;&L34L34B.04)&H*F+F0
@418
tgcattgctcggagatgtagtcacggttgacgcggcagagacattcagtctcaacaacctcggacgctttgccgat
+
(EADDA@KE'::2J,,,-,J;:J)88EJD;CA6C)JF.+B:D3M*?C*B>:ID:AGD5
@419
tatcggcaaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtcaccgccgccccgagcac
+
02KE';3@29EB3;G5/NGN4*JG,E/K0L56.BH'4L8K9A4,8LK?&+D-7CMB30L)8))N.17N:IJ&AA*6M>:076ECJG,L9&D&)M1@L??(4:57+C*3,><9/6&(0)M>1NB;IA4D0F5?+B:@,B9/AM:CN)0J=3+E>LC,'E&B)K'N/658:4/II,&05/22@'554+L&).FD9-:<&+/+@;&.=H:C9KBJ4.8@7G.)6
@424
tctgacggcagcttatcggcaaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccg
+
16=E=JI&&:;9I:>MKI=;,8?*+G-96A;;17@4G?C:+:/E6/HJKICDI@:H=5N4NB?>H+/J5?M6;>===AI,=
@425
acctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaa
+
09BCJMF0D609&=GCB0D1F(.;-AGAH);;742KJ(6I-0.AFF>;IBFI2';
@426
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaa
+
6IE4EJ';/F5.<6A(B.BL8613)3'CBD,:I6=7?/72;3AN&+23B8524+'(J'&9E3K3C1GHBL&'02(/9ECD>/5+(*3=HHF/?)&
@432
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttatcagtg
+
00:2'.)(>@:A.E'I:C=?:,J@:2,GC4.=G930>*0N&5<)JM@5K-)0.>B+L9/J)/CKK68C7@I(D'H/A<56/IND7?'DMHGIN@AJ1&<01/?(/8-4&
@439
gacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttatcagtgctgggagcgtttttgccaggaactgg
+
0000:;(A;&)/HD62;)?AD&1)+2=JJA,06KF++1:(J+1BJ-*B5;<83&7/?/+B)NB88<+&LMD.&80B,:FGNF*B0*'IJ':K>+8MI<71BE-0
@441
ttccagggtcatcgccactggaattttgcttacccagttcctggcaaaaacgctcccagcactgataa
+
0+=1=>ENA5:&5BJ-C9'AM(7<1(;1HJK18=8))-EN9+JJL&2;9A54(A2I48N8NC.JFJ)055NCD(+0GA9&.3HJB(@A34
@446
gccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccgatcggcatattcttttccagggtcatc
+
000B4BE62..C@8C8CD':1N3K1AK6;A)E(54?FE?(7J7=89-0NK>B;HG?FEE0N>IAKH86NEDC23(7<,
@448
tcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccgatcggcatattctttc
+
00A/I<1?NIJC=.BCBL;C@95:=L*7'*9J6)6+=+J=.LMI?B*)?L)7FA.5+*(>E0@+837*G4,4
@449
cagtgttcattcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccg
+
:>-752F,6IAD*E+B7KN-KF)(?,@)L&>CD/*1?(CF&.9(D&/=34:D?,8/3L**+1E56.
@450
atgccgatcggttcgggcttaggctccagtgcctgttcggtggtcgcggcgctgatggcgatgaatgaacactgcggcaagccgc
+
@C/CMMN=B:7,D9JJJJ.NDE(=LGI8D10.85ABI4=GF)?J(G8N&.N@H58J@?JMN;7K<*MM64>?M/3643,H?:-+E8?5&>.2H;249B4A2A8G<81?C*J?+N;8>C)2((-,;2F,7'/4+3-1,N/.JK0/7B.2(&J/-H9D*GF'+H,6CH'D1A+D&<(50:0:+,J>.A3.,<;.+3@2JJJL&I*)0'2>*:K3HHL9;9,GB.-A-;AC'+139I/D5
    0HK=1-BA5M)I>'/+-'<2+3@9@N
@460
gacactcgtttgctggctttgatgggcgagctggaaggccgtatctccgcagcattcattacgacaacgtggca
+
F/7D44J/0+88=3E2;K2IN&I,'F22=1:B(@JM9/L)K<:GNI<7F==
@461
acggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagctcgcccatcaaagccagcaaacgagtgtcattaagcggcttgccgcagtgttcattcatcgc
+
000000;GI(CM-9>':JK5NE5A..=0'I+?>7AJ>I'..H)/<2/M44(@,-<2=+F2/8A?5'M;BI5I'-&E:./7&ELAKGEB*01
@463
gatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcgg
+
M>:9-EJ-;8-;H@KH+-4JH:71KI8.==6NJLKF.<+5/550.*LH')NNEB+@4GL95L/&:8C=9
@464
gatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgc
+
005/6)HH;25-2A*.I*?M&FN&FF=4FB4?(G/8'53+=?DJA*;I*+MB88&KF?L:?6/:E(*24I?)
@466
tttgctggctttgatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
+
00D4BA4;'C2I&9&6+N:<4E5*3;AI+L&-JLE)5N(6&&5>@56+8E0K>E?1<*F1-;4@2/9/<)/:-+M)-0B6-C4M3,/36=I1?3B=>+M;MG8.?@IC/AK7GA3H/882<,IN(0*'BA.0@:,0?8<,I@@@5GB
@468
gaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
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,I9,N/=HDIAE?E'5J:+-<)6I&*@;0<(64D*N9N2-88.82)-:26H41M9&M3H=+=9C88)K8(A9FA:
@469
tcttcgatcatcaactgcataccaccgagaaaacacggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagct
+
2;/7/H2LI,@=I0F4?)H'?=+6DIIFM*;-=3.*7+F6-(I&208M/*8E/3E/(
@471
ggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatcgaagaaaacgacatcatcagcc
+
;7/C*014+A077F,7FN0MH(.L==F5I4=?:>)C(('91K??:-M1
@472
gcacttgctggctgatgatgtcgttttcttcgatcatcaactgcataccaccgagaaaacacggtgccacgttgtcgtaatgaatgctgccggagatacggcct
+
00-'D51D321KIMJ9(C(3>E<'/9M(=?8)4G+0;=@F<+DNG;(*;+?3@?<,?MEN?,:J1+L(E8B==6D1FM4;:MA?D3AG((N?M96I'1&K62M
@476
ttaatccccggatacgccagcacccacagccactcatcaaaccctggcacttgctggctgatgatgtcgt
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*;08G&-M05KH)EMK0H/F5:'&-IAM8:/*3FH1N@6E=<&J,'?CFC'.&*FK@3E+@MD&:1*D7-
@477
tatgcagttgatgatcgaagaaaacgacatcatcagccagcaagtgccagggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctc
+
0H;(K51G('3C.4JA.-5)((')?8K0>8>M-13;67N:?M(3E:JHE.'*/C(;F1HK13=+KC5*2
@479
aatagccctggcttctgccgtcgagactttaatccccggatacgccagcacccacagccactcatcaaaacc
+
000>4LL@*'&DJ8))CF@5AI/A,=>?AD-/1H<=@>A6CE;7KN67IⅅLJI(19GL,+()2@GB/(;
@485
gccagggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctcgacggcagaagccagggctattttaccggcgcagtatcgccgccaggattgcattg
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000;+IH<<(GEH6C&'.2&-K5?.=GN?,20&(GC546H>>??=<.G-LN70*J?I8:M)9K9JMNECN-64.89&B
@487
aagtctcgacggcagaagccagggctattttaccggcgcagtatcgccgccaggattgcattgcgcacgg
+
00M=/KA;DLN<'=5>-=;.D7+C+L-E0A07)+GINN61,G9C@)<&F?&)INLEI@)KI)=M57L7I=
@494
ccgccaggattgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgag
+
00+4NA>EB>)M4ED=//J:7F=5F.++@FE;&;JN6)?0-B2GJ)6G/9IE&LK9CJ<=N&&@LJ95F.*7M
@495
gcagaagccagggctattttaccggcgcagtatcgccgccaggattgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagc
+
0*5LIK.B26>0L+)2&>4/.A?864:)B1F'E,12)J(+I6BK?M6.A889+G(::=()MAIB5K70//5:)3095D@DH4IIFJ(L'L:'MFH*3IHEL8NC&0E.?@8BN>D;5<+89>N=6=II10C(
@498
attgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatg
+
0000D'1='0.G8(,N)H/5:,:8;.<1;:KFK5)6JME;0)?FE+(5D<;1L'I01?E+<=N;L,/7L;17I.INEJ8;?,E
@499
ttttttaccggcgcagtatcgccgccaggattgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaa
+
000000F92/J:2<:H+&BL&/I*?L28K2*EJ9F-GKE:HE))7:M4M@6;1+MC:<2A9G()78AMC5B26H7JC,396&L5,B@MC4,JA,FJ@HH8*H+K8+&*1<02.5
@500
acggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaac
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I,4BF,8&)D(:H>5.73(0*6B81<2A?I;;L1F;,:8IK:H@D976@M>7GCI)M,.''ML?*;CJ4-7+*J/NK4&GC(-NAE?5K
@501
caggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacc
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0:?;DH,&A);B)51H+L0(H7&@)=NKK?A?CH7IJBA//./IJ7B,9N2A>JI**B>56A?3-E&B>J64*>AM
@502
ttccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacgg
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009G>7BD9-?CE??)&C*>KCF6+@L/J8>A;9'I<-5)*6?6H,F.(B0I4M&4//+K5J,/4;
@503
aaccgttcacggtagggttcagcgataacatctttcatcagcttcgcggcaagctcaggctgacgggaatagcaggc
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000059*90,N&524C,GG2+8H8I;
@508
gccggaagcctggcagtaaccgttcacggtagggttcagcgataacatctttcatcagcttcgcggcaagctc
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00,13@83646HB?6=4M(>8EK6:+2M5E)I+->N=1.87HN7I>91D&,)2;+7G-+AKCKN8.F67A;F-
@509
tcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcagg
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0009BF4&4/B(<&L+482LKAK1H40@72I.>M-G31,(53?C'?G82A)LLI/GB+*4CC1L;88B:'L)+@=8CJ1G7>+
@510
tattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggc
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)G=CK;N0+GG'.4L*G6M*>7EKDHB+()N:N8H)&G(MDI:-/),,3:.F9175:8=JGJF'?CD&'3MH&0L*C>0D6MN23E5')E9&
@512
cgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
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0000G'';'B4IF>DMI6;FJHFH9NI>F(N-I.2.G=@?/7I?JAC79+GA;3'),9LEF?&CM;(@(8G6=I'63E;2,HJD,F8CCC44G3;.
@513
tcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
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0.'7J6,H@C22HGB>M.(?*64@643&81@C,=->N+(7/(3K-@8+FLNG,?E/J---GD6=*.>.&9'/AJN1&6N@(&F@JJBEJC67+F
@514
ccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggttcagcgataacatctttcatcagcttcgcggcaagctcaggc
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00).I04?EK;)B)/62:/<0F/.:/:KB1+888+7=/59DCHN'N:E,KA=@/L/;G*//E6?;NINL*,*
@515
gaaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcggt
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000&=K.@)>:J>83G'3(/4:4JH8@7,-N5@//K;)//C&>7D@N:7L=.M*M*=D)2K/=@7(
@517
ttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggttcagcgataacatct
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.;G3C3-ELJ(E4)@1&4&,<,JM5JLAL-91?-(H@LA
@519
gcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggtccagcgataac
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0000(30DNE&&-A+9C4G>@I026)JAM0=ID,;L@?;I149L6/;?,8:.':GA+'B@(2L);3A.B?+E81K@,2.@;?>C5E5;9*'>K7M6562*AI&9C?G
@523
gttactgccaggcttccggcaggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttg
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000I>)+E-,73G@,8:,&J:F32>,M=BK+,J/G7F+FADHF&N;7GCB0*&A49D)A2K*83NMC;M,4@.67?NN/5)(B
@524
gagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttca
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*KGBF=M78LN86MGA2KG2L3K:,259M9+B.HI8DD+?GC0H@J4;&NN0E2B9C)J(8KCC*&/>:I:)36-6M<@BA:*/@7&-&62,M>E.L38BM
@525
aggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttgttcgctctgtgtgacaagc
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0K>*K?65**&=<-A.3NB6>K&FE2.>8J&865,D22I??L/;A@(.LJ&<0C9<7**M,/A4,@I>CH;BFM/94+K':.C:BH<
@526
gaacggttactgccaggcttccggcaggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttgttcgctctgtgtgacaagccgg
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MN@B@JGKMN'/CGKL:288B*A,1?)?*)'.4I7CB@A014@097<@8?0L3G(J9J?/CJM+*9=N>7HN=<&J?'J3'KH@)=F>(318>D2CM7
@529
ctgggcggtttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctg
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009H69>L9@@A?2B11AD'9>K-L9466DG0<)BA(6?-0+8HJ=L7=A54IN?L+J/B(/1B0)>J@KEKD(@0J0=K*'+'7J>3/H@=/5(*/&;8GE0149)I23A-D
@530
atctccggctccggcccgaccttgttcgctctgtgtgacaagccggaaaccgcccagcgcgttgccgactggttgg
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0.'N3.159A)IM3,ED'.JNJ(47087<4.23M+&@,':.&0G4-F&FKE026G*
@531
ccggctccggcccgaccttgttcgctctgtgtgacaagccggaaaccgcccagcgcgttgccgactggttgg
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*(=1BNE1;7JJJ-+:GH:)G,K>1>GC1,DA:BD(DE(/A:MMN.:IL/?7AA)//?MI@E>K7NNJD;2:
@532
cttacccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcg
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>FM2)*)+H+@;A1265=02HN0;/J?9;42(03;E(0/B/DE@*MD5(C'L&0D9;3,-IA4-C6&L9HE?(DB)83/7KGM7H>C'IN'7N@6@,-<(9:65A
@534
tcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacaga
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0&)IH*;-44?:,(:L.CB+131('0J)&*A@BA8*:''CK-F;&>>@)A'B:5+':*L7)0=G*:JMG&A9
@537
acaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctggcggttttccggcttgtcacacagagcgaacaaggtcgggccggagccggagat
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000L?GN7:3+G:23G=4;C=EL=,B9B+&<+&L/@71=+*JF-9>-&=HH@71*80)7J-275F1-(=,K=<)6,'9'EM@@KF?,;-,AAI0GFKB?;6B::3,L&
@543
tccagtactcgtgcgcccgccgtatccagccggcaaatatgaacaaaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctgggcggtttccggctt
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00000G(?/BM6I?(3L@*/CK-L15<)GJ;18NF-93K322;<7+-)44@J+:N&;:27GE+>9>'43I8D+(&>AK2@LI'N(018*(9B/2B70=59C0572A043B>*G
@545
atatttgccggctggatacggcgggcgcacgagtactggaaaactaaatgaaactctacaatctgaaagatcacaac
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0>8*0H9K1@?,?'*LH>BC'85'D7C;&F5E@E(&?(892B&L@*D&G6JCH*;HK7?K4J-5,?2DKE46C/492'B&,D0LA..;70
@568
gccgagaggatcttcgcactgcgggtgacaaaatccagcttcagcatctcatcaatttcagtcaggctgaattccggcaggtcgtgcggaaaaaaaacagcccctgatttttgc
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00000008B>?&N46C1A8?M*@/05=J@)L+'H'C--LC(96I&5--6-//I6-=9/:)+J:@
@574
attgatgagatgctgaagctggattttgtcacccgcagtgcgaagatcctctcggcgtttattggtgatgaaatcccac
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000244B-G>.J)66J572:'J?@M0CFKH6*KNG0=G@J1>CL?+N<+(MK(:<7=,0HG43B;'8@05>FKF2/('B
@579
cgccgcgcgcacgcgctcttccaggatttcctgtgggatttcatcaccaataaacgccgagaggatcttcgcactgcgggtg
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000BF1M1LDJ&<&E(61G/&EKKJ.&'&?6+034A:EK>1*68&==D'>:,-FNI,7/2M-(2=L8,,(A8:;@/4F80:,
@580
aggcaaacgccgcgcgcacgcgctcttccaggatttcctgtgggatttcatcaccaataaacgccgagaggatcttcgcactgcgggtgacaaaatcc
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000000F087'8F'L))8(9E7CEM)&GCD'G9LM+?889)'&3?-/M<3F9M,*0N3BH?*.2F?(5H');J0;3:A;41N*
@585
ttcaacattggcgaccggagccgggaaggcaaacgccgcgcgcacgcgctcttccaggatttcct
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4B'JJG@F<4)*,.3<3/'H(G)??HN*:NA5;85GC)NL55?EK?<);0?G>2-;MHL5MCD4;
@586
accgacatcgctttcaacattggcgaccggagccgggaaggcaaacgccgcgcgcacgcgctcttccaggatttcctgtg
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000/HAK45(2.B/@<(F:0M51IIIJ'=B719F6KN0I'D4J(3K&M&61K+::+.+(+A)N&3DC<4;,+=+4C))=K8=A'3.I
@595
cgccgaaatctttaaatgccagcgttggcccgtggaacaattccagacaaccgacatcgctttcaacattggcgaccggagccg
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073)029H2GCNG41/DK5F6G7M+6ENN7BI31+6+@4B<<*K*-IHA;(:9D=E'IJM*7HNA:9AKJJ',+6K76:3?=8,
@597
ttcccggctccggtcgccaatgttgaaagcgatgtcggttgtctggaattgttccacgggccaacgctggcatttaaagatttcggcggtcgctttatggcacaaa
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00-4&)3K/=>(5;J970N'42M-,&I--/AJ+NF;=N>B8(L1D6))BK)E0DI'@147JAHE3.2)@3MED80;8CA@2.I9A7.;<1@>>I=FE
@599
tcagcatttgtgccataaagcgaccgccgaaatctttaaatgccagcgttggcccgtggaacaattccagacaacc
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000HD:*JIG&@3JGE0'KEBFNI0@.5:6)/(L;?)==IN&A=/>6B9;70:NM2*G003J-/E(:8;-C,<8+L
@600
tgttccacgggccaacgctggcatttaaagatttcggcggtcgctttatggcacaaatgctgaccca
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00&?G/KFED9-H69=3'1.5>9+HCF*D.@.37H'EB2C27A&F95&2(LC7G6JN(51BB,:@N?AA'@2H;I
@620
aaaaaccgtagaaagcatgagccactgccgctccggtatcaccggaggtcgcggtcagaatggtcactggcttatcacc
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00(G,LB?09*=B2;0I'6I:9J1>C&I=3&+29/-;8+.@C*7=G>*3CH8-0.50*E>9
@621
agtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtta
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F585):=+&LK(2&B'&7*&>&+LG<4B(?064L9H9@?NC64-?8AJ/*
@622
ggtgataagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaa
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000D6N=+MLCA,8C6*@C<)G6C10A+/><7H*?@-:NFD;79HCC@G7DC=J=*==C=<&5-ADAN:,@8:CHNMK1HM1-+9;9B:9)I8M'>6NF>/>76D*;)EF?70?L.402
@625
aagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaatgtgaaagtggt
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0000J/K97G4=;HD*N@J5:D77C13@&A'8/*:<;.D?1)>IC5)A)>?;7@BB.3GH;D3G9:IL=D8536CE0D/(1
@627
tgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaatgtgaaagtggttatcctctatccacgaggcaaaaaatc
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0008:L07J+//;KAM&7N1(3D(&9+HA5'7L6E/.6G4)?L8//,-5L7N8'7N*KA>7)8EL?C';E7H07./:8863EA>&5CJD&<5;K8&G?,3&D8/(B<'BIF=N?L/H*-/(K0E6AF:M?0@
@635
tacggtttaccgaatgtgaaagtggttatcctctatccacgaggcaaaatcagtccactgcaagaaaaactgttctgtacattgggcggca
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00H/N8K&2.KM?B8K0MF@55F)H914DM,4MME>E*6M)'<3'J,AMHBMB';@,KD*E*@FD(+DCE78*=?D4,*8658<8AM6M51
@639
gcaatcagtccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatt
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7NF3C,);'(8+*8>N<)?'4=MDMN
@642
ccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatttcgatgcct
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00;H=)->D-F(IN5J-6N)-+@*25KB8M>3(.,;6(>E+A/)/N9)'*L0ED&*4B0/C8(&)-42DJ+@;ALM
@646
aaaaaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatttcgatgcctgtcaggcgctggtgaagc
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0000ILN23K'II,EG586K*>9NJ00GM:@2B(10=74:6,MI/N&>/L)H?,1EG?C5/E,2AH::3==6.:GCE&/MA//)2)(//H6'M;>BC49
@656
gccagcaaacggctgatgttaatcgagttagccgagtttaaccctagcgccactttcagttcttcatcatcaaacgcctgctt
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000A(CL'97D(=>N&9).??2J8F81AD0N3,BG.7M>H3-'&@,9FK&&:@<=BDC:NK:6KM66;33?5MIJ-HE6?=:C3<.&70,H0(H56N@/B4GH
@667
tgttgcgcagctgccgcaggagacgcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtca
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FK,F8EL@4(F2M91>NE->B/A/I=CD777+'4D'(,4FME;J=''64:D23>;K*J'H-H-9'.BMAI8/6I-I)
@668
gcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtcact
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00.31N9/)B1012LB:K6:K+C@<6LI,?FJ3J+3:(65(9EMC>35A.-02..M-/G?48:M:8L*0B-F+(
@671
tcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtcactcggtctgccggtgaaacgttttattgctgcgaccaa
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000<.N:FN*7E<9(C;0JAE>(I2D=*J9?KMG&MM-?7-&(GH,JF71=,=6IE&;'B-DBCCDADL:K1CLAD>&+IAI&D'2=B@'/
@673
tttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaaacgtttcaccggcagaccgagtgacttcgccagcagacccgcc
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0000D6(+*6-)):=166@/&&'55<+-;&DJ@AC&3FCNF27K671DLEFFFE7I@BG)>:1IL1)8,,9IMGI';I@+N?E@I3G2(4LCK>&98JL:CD'
@674
gagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaacg
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00B:C@9CAB=B(&4>F*)GB-JA-='&8<0<4=GE0-(DE:3B@+EDDLIF/;@JJ('ME.F*(84CK)=1A(&-JK
@678
tccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtg
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0?-*(?-,.'AF3:1:0I';.D7+(02N-DA/,822/5I)&,B-@72.*B:.C19,L+JH0:=2>'/
@679
cgtccatcgcgttggataacgtcgcctgagtcgctttttggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacg
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00B1>2+08HL)LB<>+83M(NNH9?H)6090A<77=IG0DKNJ.:'J)357D>+4F'H4&.2:?4>'-(6L;=+2LB+57:JB@:-7(FHB
@681
ttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggca
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0000:7:<'=H*/:/<&D5D92;E*3*4E?51?0K9E.50>D=M1.G*.-A84E--H@7A2H*/9G+61KH1'F//(E+&K<2KM
@682
gttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttggggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgtt
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0000&0A3+4G:*3+.4M+BI:0I9&:/>>J,1='EAD:24B'C5+,:1)89=ML=C-&H&(GG*=A4*?3;4KL<0=F2'L3F'LI./J,0.H:I48579
@683
ccgtgccacgtttcctgcacgacggtcagtggtcacccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccg
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*EG85/5G;+?0N8N=)1L9E472N.ILF>/@G:H4-<;:*GH5;F96B9)'*3E65-B7HGK3BH)98N'=I2FM/<)G4>EA7+@LI=*.6/30::
@684
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcg
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007-8)KG?1:>N2HG?KJ5?>1BK0137;L'H:J7KD1JI/:L'3@G1';AM8NDI-B-;>HC?G86(;9.-C*,M8*4>3?76,&@BEC;C&J?E9&-K1DEMEB
@685
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtgg
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0D9N2C5EG*1>6JBH1?0B(.N(0;LLJ&=0E5E=.+E'LL:&;2M?GIK(3)+A'>2M8<*,9=6)H.?&NC-E:&B7A/NAAB66A4@:CC368
@686
cacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatc
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0000,BI4C;6C*D..L9+,&+&@:=32IG:>-9JB4GL+NI@G))@*J56E5::=+&'9B8:MM.?AANAAH>83@CA)GE596:M?7M6.-?@71>.AG-KE?.L?
@687
gataccgtgccacgtttcctgcacgacggtcagtggtcacccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccgcgtgtggaa
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0G=IJDI'=DI/MI0)762*8:(/DN9C,&3K*;'9@*37;K8;&(K+B/39<&NI=27(C>,M4M4.E+8-NJ;*;A4J=D>>4N0K3,(,(4>DMK9.D8?;(G.&?3C
@688
gcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgag
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0M6.41&KH/A*A/&C/B1,5-?=5G;IC:2''+2@B>F&3)JEFN;00K1&46D4E)C/IDG
@689
gttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcg
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003*61(@174CI3JK9+2<>C0;?B&M<6A)9-BB-@4-G,D1((:.E,'B-4K,)6=3?EB(A6.@4'/C)(6I5-HF=C**HA>(/'<+/>4NB&/87'KD@+DC:H1?9;LHA@54LD6-K'I@*K5J+'KGF=*);9=)'GKG>@50J.7F2>-7',8@D?H,3<
@693
cccagctctttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcg
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00+:EF,'>KD,H'LG.'&4(5.=B=1C/1GH&(<*6I=BK8-,88<';N:NJ14&JI;*M<33/*
@694
ggctgcataacccagctctttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgt
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00000.+J'M94D@FCK=@7;?A?H97'1D/.14-+8K/:5:NNFC,M>IM@=68NMK739@CE@3IFKMH185LI2M:.@H-&'M
@696
cattgtctgttgcgtggtttcatcatccacggctgcataacccagctctttcagttgccagattttgcggcgga
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003K*M+LID6'BH87J523-G6DFI4(<&-B>7)58MI45=>K/8;3C(3+@5
@697
tggccgcgtgtggaagagttgttccgccgcaaaatctggcaactgaaagagctgggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgt
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00000-6JGGB+15&(A58/41C7*&6.0L?;8K2K5,,1501'+1-99:8JD,@3/B03A+N3AN/42+H>-:C;L)75'>3JAAI.F@0H::D;)8@+-2:**9<+MCG-;?K.(.+D
@705
atctggcaactgaaagagctgggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgtgagttaaaagaactgggctacacttcggagccgcac
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0(50@?=7C&M+,6.2-LH7B>BD1NC?.I*3K4>NL<&A/6(M'(/5>8':I8C28.?=;H*4KH+:78A8?*9D':?0?A,2>J>L7<;D=0+7D.=24@JD8
@710
ggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagcccagttcttttaactcacgcattgtctgttgcgtggtttcat
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000'?@4ECE'9&3>?8?C)3)HJ0H.-.GK/*G(M6=.F5G>E7'1);)'1&E14-;?'D69L*8G4=GH&+8E<=5/:34'B1G@0-+;2-*G=H&;H&.>
@711
gcctggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagcccagttcttttaactcacgcattgtctgttgc
+
0000I>1K/*E)M*3,4.E7D?29F:D055I.@7LH*D19&-.B;A&5086<&*:+&25I-H&/M9A1:H,<3GK,)*NL.0L6>CB,5/3<)*?G'
@712
aactgggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaat
+
+MA=307EN--&4?.J1A8NF''+.;DILL.&9E+KH4A+;E1M2L98+>+9,G&KB5D';,4>L7G26I&1
@714
ctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcacc
+
::L4G)+K/5@IHFB7D+?+&&'0=J0:G(J;=D-,J1EL.B6NA*87:?J;MIEG:711D>;,6MF>'@)/6EC(42?0'C98?F=H;LA1?/B(?<--L<,EII'H:/H;J(5+2A9,J)F;
@716
tcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgtt
+
&B.?MEMIDDF6/&046?M5'1,9:G14A9H;F*.C/=DACNI'27&>/?29:CH@G>..M<01-HMD7-67/2CM'=(I)CG(1L(C2FFH0G98@1?E&7CE.85.995H721L;>IIB-18,I2)AH6
@719
ctggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatt
+
00,,5*H9G(15@9L/*?E.'?FH37DI)>*@;1-@&)/(7-*L*E*33(@?M4NL@KHM(2&L7'5D6LJ4N<2DE37L9/L>;?3HJBD.DE/3/G'4HF;JH'=-:
@724
gcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtgga
+
0G;DN&CI)B73D)(E)>DNM6(E.)'I>B;3)B-MKJ<.:*H,*0D@/'/)LE;*38>G&.(=5F:F/KM4A.K+I:LF2L7
@725
cacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtggaagc
+
0003&@;+:8/'@:E<2.GJ.+?CFI.M0E.3E?&D>GD::?&:'(85=,J1710CA67*3E=M9J0@D0'.@>GD4'*-;.CAMH8:)J/E+'+L.@J6.:H6HAN
@728
ttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtggaagcgattctcggtgaaacgttggatctgccaaaagagctggcagaa
+
0000.9FBM*8*8B)58I;=.J?5A16.K@)*-N=I>'@HC96+.AJ)NC?K*/CC60,1G1):N&18.;M''7JHC0/,1*1;2)E0/6D@4'0'+:=2N>B9:+G('1&
@730
ggcgaaaattaaagagagcgtggaagcgattctcggtgaaacgttggatctgccaaaagagctggcagaacgtgctgatttaccc
+
000&K+@L:AK+G8<&5(:44(J:')L-8>&E(/394EN6-;N/F;;-1<.9,919&4HM(0?<:FA:H-*>3B5I*:J,:?13>
@731
gttggatctgccaaaagagctggcagaacgtgctgatttacccttgctttcacataatctgcccgc
+
000000'?=CAHA-MIGKA3(*-14IIJ,:LH+9.5;M<4H:K/ME'@@CJC-;CAD6AD6
@743
attgagataatgaatagattttactgatgattcatcatcaattacgcaacgcagcaaaatcggcggg
+
00-0DN?GG'C:<>@H')+>''D89MML;K,,L;4.457>,HJ;7L?M67G>BN/BN:36*KJ+@HB
@747
aatctattcattatctcaatcaggccgggggttgcttttttatgcagcccggcttttttatgaagaaattatggagaaaa
+
00000<6:)LAM')E67&=4N'4,93JMFK&*55&7E-&&H?B+>@A,G/02:BG1I8DHALD.'&>+5'460LL(L7&;
@755
tatccggagattactcgatgagaacggcggttgttattctccgcaatcctaatctctaagttaccgcattattgagaattctc
+
L2DB85E-9;,41'03=?+=>5)4@2=8D>GI5B7.M3D.'2=&60)4HI1.&LIH3*6N.4/N4'A,1,CN--)2DMH.4/.
@756
tgcggtaacttagagattaggattgcggagaataacaaccgccgttctcatcgagtaatctccggatatcg
+
8=3GA+MK'C./E/*<)I968-J,&CH89I+)&>'/H>@:EH&5*/>D101>8L-I;F.?8K'CN3G&?.4
@759
ctcctttatcattgccccgttatgggtcgatatccggagattactcgatgagaacggcggttgttattc
+
05+KB?'@HC96+.AJ)NC?K*/CC60,1G1):N&18.;M''7JHC0/,1*1;2)E0/6D@4'0'+:=2N>B9:+G('1&
@730
ggcgaaaattaaagagagcgtggaagcgattctcggtgaaacgttggatctgccaaaagagctggcagaacgtgctgatttaccc
+
000&K+@L:AK+G8<&5(:44(J:')L-8>&E(/394EN6-;N/F;;-1<.9,919&4HM(0?<:FA:H-*>3B5I*:J,:?13>
@731
gttggatctgccaaaagagctggcagaacgtgctgatttacccttgctttcacataatctgcccgc
+
000000'?=CAHA-MIGKA3(*-14IIJ,:LH+9.5;M<4H:K/ME'@@CJC-;CAD6AD6
@743
attgagataatgaatagattttactgatgattcatcatcaatttacgcaacgcagcaaaatcggcggg
+
00-0DN?GG'C:<>@H')+>''D89MML;K,,L;4.457>,HJI;7L?M67G>BN/BN:36*KJ+@HB
@747
aatctattcattatctcaatcaggccggggttgcttttatgcagcccggcttttttatgaagaaattatggagaaaa
+
00000<6:)LAM')E67&=4N'4,93JMF&*55&7E-&?B+>@A,G/02:BG1I8DHALD.'&>+5'460LL(L7&;
@755
tatccggagattactcgatgagaacggcggttgttattctccgcaatcctaatctctaagttaccgcatttattgagaatttctc
+
L2DB85E-9;,41'03=?+=>5)4@2=8D>GI5B7.M3D.'2=&60)4HI1.&LIH3*6N.4/N4'A,1,.CN--)2DMH.;4/.
@756
tgcggtaacttagagattaggattgcggagaataacaaccgccgttctcatcgagtaatctccggatatcg
+
8=3GA+MK'C./E/*<)I968-J,&CH89I+)&>'/H>@:EH&5*/>D101>8L-I;F.?8K'CN3G&?.4
@759
ctccttttatcattgcccgttatgggtcgatatccggagattactcgatgagaacggcggttgttattc
+
05+KB?/I5'E94)@14CE=C)@)/.J*7J9F/@J9,*L:C++/52758*AN-.K*'L6*+4E9K4+B3G>2DL<:IJ8/=A97I><,&)G03L3,A:N>MBI8.K6@G&@:3J
@131
gatcacatggtgctgatggcaggtttcaccgccggtaatgaaaaaggcgaactggtggtgcttggacgca
+
00H-&*4BEH4J+=79L469+F9G.(3>:)=61+5LM3(
@137
ggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgccttcattaccggcggtgaaacctgccatca
+
I?7H+0F&510-4(<8C>);:E'C,4AHKAD*AD>GN3,*;A(9<=8:IM):ADKE@/'HE28+/?LG(D0*6?62(I>FE1H026N(8EE0=GH9?>FMA6LEJE,E:5<875=;4MG1>1=LFC?FF.EN/B'EBJ&+)3EE3*6BC7?M9::26;-5/D+I9;22D3NEJ'6'>,N,D,BKN:6784B>;IAB':;@-/6N:B,=J0+FG30)C6'CL.<+K<:
@142
gtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
+
00L=)H.405GF+=C-:A2<)>/>E>D4BE&+B:AK27>09
@143
acgtccgtccaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccg
+
0009F7HI90:/GN2B&M59,*AM(0&60N&3F?3L=7EF7NMJ?N8N-.?2*0,<)0D2<&)8BJ*?LCL
@144
cgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccacca
+
000&C*&5GMB4=5F'LHH@)9=3J9G+3L(+FEJEC)>2:D(I/N',
@145
cgaactggtggtgcttggacgcaacggttccgactactctgctgcggtgctggctgcctgttacgcgccgattgttgcgagatttggacggacgttgacggggggt
+
0000IDD:);6.2JB:/3LKL3E7-2)'+3&.5J2(:6*;J4(D@C*>;NA;?;(AA7@*K2J:1IHG&;F(7,.:'F;MK&2E.B=3-*(G-C9B:818I2J=@-
@146
tagaccccgtcaacgtccgtccaaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagcaccaccagttcgcctttttt
+
00000-E6)/08HCK.;>I;?)*AN.5KCL/IHJB-3(83M;E4,I6ML65'JH/K5.7>8;B0'D
@149
cgcaggtatagaccccgtcaacgtccgtccaatctcgcaacaatcggcgcgtaaacaggcagccagcaccgcagcagagtagtcggaaccgttgcgtccaagca
+
0000+899@+,1HCGG2-M19*FE85BI:)5=53E4>)02&*'B@B'JB>BL/2+;,+'.5C,8;AHA+)2L?9*C4(;ABAA1@-6(/)61F2)2)DDD:5F,NGHB
@151
aacggttccgactactctgctgcggtgctggctgcctgtttacgcgccgattgttgcgagatttggacggacgttgacggtctatacctgcgacccgcgtcaggtgccg
+
000).K7JA0F29G5(;H:,?3N:A9NI&F8)>15L1<@5A7?JJ5.HBA1NB58='3BA(@:HDE&+0>)A*.<,'(H&GG0/2L8(8<8'NN6F.:2+40*?/-3FN
@152
gcggtgctggctgcctgtttacgcgccgattgttgcgagattggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccga
+
00/C+K;>474J:N,K0ECELMC++HE-*N7M+.DHH-=8ABJK8-C&-+-8)B@.34DN/:1@8J;,)-.225E:BMN
@160
catcgcttcctggtaggacatcgacttcaacaacctcgcatcgggcacctgacgcggtcgcaggtatagaccccgtcaacgtccgtccaaatctc
+
00000(75E,/5><-379KCL7D@3?JJB&)+G1K.HLK48?F1AG/5D:);'E:M6EBIH>E70?:IN'D@-,GJ/N00FEC;/()=>@AI=D*
@162
tggacggacgttgacggggtctatacctgcgacccgcgtcaggtgcccccccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctt
+
00000/60K<.C;/E?7N:NG?&FDHD/J6?J25.*0:<4*/@N./JM'=:N:I)19I,):'79N/>F?GA.898KJ>H:/6'?BIM31,M9HC@BHCC?C.NNG9',
@166
ttgacggtctatacctgcgacccgcgtcaggtgcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctttcctacttcgg
+
0H(1;C61L'+F>1>(.83L>99474AE<2MC4./'J6;JL<7J.D?/=,//)I<,.;I(41'@AC&,<27H2:87G<&5NM)43&K372?MM97
@168
gcccgatgcgaggttgttgaagtcgatgtcctaccaggaagcgatggagctttcctacttcggcgctaagttct
+
0;&6GM3<,86-2CL-2GH&(,KL>-9MFIG887I;F5@LL/FKH+&:17CB+9NF9,8/L9@<**E,6M355/5KH+E4;KGH-I?@6(70AE;F.,D4F@GJ>-+4BEL&=J**1-:+@.3C&>DE;C&I/>85J)A';,L5:?A/I3<8F*.DJNC9C:-E
@172
tctggaactgggcgatgggtaatggtgcggggggggtgaagaactttagcgccgaagtaggaaagctccatcgcttcctggtaggacatcgacttcaacaacctcgca
+
0001??5DC7).//M7M5/12?N>79-/K))-5?0M(73HMFF:FI(/*=K:,='G+A7B6'4DILK0-DK@+>HI>A>N/0>GIEJD(3=6761:'>2B/@8/E
@177
agcgtacctggtgcttgaggattccggtatttttaatcaggcaagggatctggaactgggcgatgg
+
000=7722(3?,M'..)E':EGC(N'@K4/&>6&'C)1-/9477G'@.?9-;+:DE94,=N?H,
@184
tccagatcccttgcctgattaaaaataccggaaatcctcaagcaccaggtacgctcattggtgccagccgtgatgaagacgaattaccggtcaaggggcattcca
+
000**925<9L,(MEJ9'B7@H>A;&:;-6&CM*74F)GGI/&5<3CE0+>4-5H,D7JF.-F(07>3??D8=HL?
@185
caccaggtacgctcattggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctga
+
0005,B6(1MJ*9;+LB<=FIEKFG1E+@5BE-947?C2A8'H6<7G&8N2+14-0&A;7=?E*>FF'M
@188
ctcattggtgccagccgtgatgaagacgaattaccggtcaagggcattccaatctgaataacatggcaat
+
JIF22>.NJ0/45N.BB1*A&.M+,)E)2;:<.HA:1>1A52JMM80;I*E8@&AB1I:CJ
@189
gaacattgccatgttattcagattggaatgcccttgaccggtaattcgtcttcatcacggctggcaccaatgagcgtacct
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B1>7904BE&HG/K/3K9(9B.=J=G/G<47-5*-9CFIA?((F5IJ:0CKLF8D?3FC759A(6=2618(7;EG2,/.LN=C)A97(2*K)E((*,G5D?*C-N4??DME&I6KL9M/1@6J?M9F&D6/0(5FJ4K,;F0=M4A;=?1AN*:+N3+*J=?B1;)6&4:K9(,11IN7G-N1H35>GBBF0*3*'7'D>
@192
ccttcatccccggaccagaaacgctgaacattgccatgttattcagattggaaatgcccttgaccggtaattcgtcttcatcacggctggca
+
0E=;)>.K6)E;DEJI'(JF2@C1.=A+112CJCL&G?48>08LA(:0EK)JN0:A);@J;5(M&5GF37HDDHMF
@195
tggtgccagccgtgatgaagacgaattaccggtcaagggcatttccaatctgaataacatggcaatgttcagcgtttctggtccggggatgaaaggggatggtcggcatggc
+
00000)72BLGB>;:(/)&>@(39-N5F5>DL@H<>4C6J3N5KM76GN41/4D7)NM;@N+,E)8,H7*I?*
@201
atgttcagcgtttctggtccggggatgaaagggatggtcggcatggcggcgcgcgtcttttgcagc
+
0000:*NEE?65I4H;1+A/2;1*-H:=55FK.=,2&@1NH0N@D>IC/6
@205
ggatggtcggcatggcggcgcgcgtcttgcagcgatgtcacgcgccgtatttccgtggtgctgattacgc
+
?-E>9B;BJ7/51BA?:N0>+(:-?42:;N;7:-;@8IA.90.*
@207
agatgattgcgtaatcagcaccacggaatacggcgcgtgacatcgctgcaaagacgcgcgccgccatgccgaccatccctttcatcccccc
+
00=2G+8I>9(MFL8+20KIH6,7<*=6JH76+MMB8;1+JDI''2:JB9=:F65<370I24K0A+LI
@210
gtcggcatggcggcgcgcgtcttgcagcgatgtcacgcgcccgtatttccgtggtgctgattacgcaatcatcttccgaatacagcatcagt
+
00K9EH2066:6B;;84DN9KB9'9K2L?LH-'&FE.,&GMH0'';.(ML21:B<)2,F7F:@3;35->+NHMIC=7HK*I*1,55A3:1CN6,F?;'*=?(-))=-=A179M9C)M@@8B/=GD*J*5H&>9=L>;/0HB1)3GJ=)C:M&5DFAF;;8I2.0/-48*1:+@FK
@214
gcgccgtatttccgtggtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaa
+
00*C)6CJ1KCB@537DNHD=:'7I=7-62>0KB@9'HH/,;KNC;LA6@,,DI+9&+1L.934D?&B:*IMMB:73KKE=9L>3275,1-B;)MA8*
@216
gtgctgattacgcaatcatcttccgaatacagcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacgggcaatgcaggaagagttctacct
+
00000@K9(,DHFC0'+8(NC4F50H000D165&F/2M3GE?*A38?<>/:=A89(G0+-9L,'.'AHHAE((IE'9/?,')9E.253@3:EGG3J'--J,
@218
agcatcagtttctgcgttccacaaagcgactgtgtgcgagctgaacggcaatgcaggaagagttctacctggaa
+
9(D-C320J22CKGGM;:48BA@A6?A4BKD-;5(3,J1CI87KA6>/?)&NG44;3A-1@2)*D:(9*2-09F
@219
ctccagtaagccttcttcagttccaggtagaactcttcctgcattgccgttcagctcgcacacagtcgctttgtggaacgcagaaactgatgctgtattcggaagatgattg
+
00>2B93(B?'7A,?A?AMBJ;'&&.('?C,2;)2G4&CH82+166BL>08JJHK30E*?69@-L51>K4,=-6'N(D7.-KI4E;,)+CA6G77J7@849
@221
gccgttccgtcactgccagcggctccagtaagccttctttcagttccaggtagaactcttcctgca
+
00+(45D(>E;K+F=DH('H/D/';L&AF9F?*:J9AAJ35>G161--4'KIDE5,1C@??2(BD<
@223
tggccagccgttccgtcactgccagcggctccagtaagccttcttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcgctttgtggaacgca
+
00.IN9DJ'D;214><*69F3808DB(>GB+NEC4G7N19@=;E>?3J0,@>NA55I+52>129J,GK)J4+G39'36NJJF9?8C?9:4'M0=6+E?5359,=G;K6,)F
@224
ataatggccagccgttccgtcactgccagcggctccagtaagccttcttttcagttccaggtagaactcttcctgcattgcccgttcagctcgcacacagtcg
+
0000FB5(>B0..-,6I,NA-J,>@I868,19H+/@F/N&.KCK>7C:B.(A:>2))<
@225
gcaggaagagttctacctggaactgaaagaaggcttactggagccgctggcagtgacggaacggctggccattatctcggt
+
E<,4@0B551<40I&:B>@54=;>+/,GAKAI9I&4139F&=:5)<3EEE3N))N2L6BHD':'*N2;AM<,17@5D)(@2
@227
aggtgcgcataccatcacctaccaccgagataatggccagccgttccgtcactgccagcggctccagta
+
2-@L-;1J.12J(<=G/5+FB5>*J6E;*=M&6M=-)17NDMK/*-,
@232
tgagcaatggcgacaatgttgatattggcgcggccagtgcggcaaagaatttcgccgagatcccacgcaaggtgcgcataccatcacct
+
09CG+5)&7D80)D.M,07F=:==)A1'-*B(NC&B29NFB,?'HB4D,D1N20/9C@,>D:,'*2'A(01I>,?9@
@237
aattcttgccgcactggcccgcgccaatatcaacattgtcgccattgctcagggatcttctgaacgctcaatctctgtc
+
0157B7C<<=MI/,(IB(F&<,N,56BLAM-JD-4I*M)C@E85LFAI+6AM9AAA&31*0N;I-MA'*KB6ELF@I,J
@238
cacgacagagattgagcgttcagaagatccctgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaagaatttcgccgaga
+
00(0A1L=+=A*+D8L16L&MMGH8K6/12?HH9@,3JH=*BA*8>>.5/,:7B<*G:+E+N?FIA9JD<6?5@?03,*<(*69889;2DEC
@239
ttaccacgacagagattgagcgttcagaagatcccctgagcaatggcgacaatgttgatattggcgcgggccagtgcggcaaag
+
0000HD2NG95*B=N-='>60/M(BG=N4D9'H4K7D2((E;@/?=0/=2)8J2ACK3B4C:;NN,/AK(3?H05M73&:&9;=
@240
caatatcaacattgtcgccattgctcagggatcttctgaacgctcaatctctgtcgtggtaaaaataac
+
00000=6G+NN&HM'>NC2C3D/+1F(FN=7D<345)@<**?;39?K7*'13EG@/7=J0N*HF?7I=.
@242
caggatcttctgaacgctcaatctctgtcgtggtaaaaataacgatgatgcgaccactggcgtgcg
+
00007:?G*5843,G99L:3&*(
@245
gatgagtaacgcgcacgccagtggtcgcatcatcgttattttttaccacgacagagattgagcgttcagaagatccct
+
000034E0J1)H=4FLJ6,9=6?>:M65EL+-ND-FGJ1'(5515I-9+5AI)D69N:IF<;=5J:8N9:2I5D5J<+
@246
agcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttatttttaccacgacagagattgagcg
+
00BK,K4E-L>(L9''64A6@HH>/)G&J20.JLI5&'J@8;2A&I,
@249
atcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttattaccacgacagagattgagcgttcagaagatc
+
09.'A&1&JAG@/A7I0J'01EB)F-I9I<7(M33,D>G-15'F&&'<>L-(5G?320(.BC.8'+7L31GGI6G.247I933L9)>>'A.
@251
cctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttattttttaccacg
+
000,J=KE?;C-CD6AH@23+J@&8?3E1@8=JI./<=,>95.-8?0K/*>CF?L@)@*0E&JC5GAAH&I.5>
@252
taacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttat
+
8@NMID/I)'8JKA26KH@K@2A7&?HH028&=:/6?H897F?2E=;D2+F6AAGM@*G13LKE<(
@253
tcagggatcttctgaacgctcaatctctgtcgtggtaaaaaataacgatgatgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcg
+
000;N3C2/@<'71NE1J<5B<-LID0H*,+N)G)E,4)@/4=3-:?L;-2/(M56:LI1*:N.(AE9H96LJ6A=D1(:&N;0-:A>A0.JE1MM5LL@GG
@255
cacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgttattttaccacgacagagattgag
+
0000H<+'A4A.DG-<;.A.-HJ/7;5H=?KC8I0,5MH;2.F?=:0C,K4&9,4/)@JFHE8,H.&)G,I6:1CN25BKDFM1+7/658=-M>H
@256
acgatgatgcgaccactggcgtgcgcgttactctcagatgctgttcaataccgatcaggttatcgaagtgtt
+
F+B11,?-9I:)@60;,KMKG&F'3@?.=9N)H/,BE-3/JF4?&?9B/8*:36.4746=<9D>?DH.D22J92N;>(J+7H6<9*
@258
atgcgaccactggcgtgcgcgttactcatcagatgctgttcaataccgatcaggttatcgaagtgttgtgattggcgtcggtggcgttggcgg
+
H-=2FK3C7*H7.9@&H:F4LD=(;+&.&I<3E87J,M+K+;1C2D-(=IIA47I-E46N;G7:E28K,0L1*-I?3/NG77H);&?*@+N=?
@259
ctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcggtattgaacagcatctgatgagtaacgcgcacgccagtggtcgcatcatcgt
+
=.I;NB,<<.JI/FK.,'J7ACL+NK=NH.2FM)5;9;7NBNL:,KB/)3MB6-0L:-5E-F>DJNEJ@,@63&04H?78E;B?G2DEGJMNJN.'8:8;3;F2C+'I17:0C
@260
atgctgttcaataccgatcaggttatcgaagtgtttgtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaa
+
000'9K5(G4<*/4A0BI3@19/KFD@.J>MMA96/-G6,2*/LCB-941HFK56=5L,29)8AI942(,/L5@+5KJI?/@;53(93BB1:?J2=FN;B&@>.032/:M+1B52L=,/*DB=2'G7I<.J2;8H:*I>;GNNC@9G-='LKD;F'6E
@263
ttcagccagcttttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcggtattga
+
0000;;0KD2'-D-1L0)/M1@A3>,9@DE-4)DB-@*C>6=,?GK)J8J4.)2C47&9M1.N0='1D(>FBM65ID,1=);FB7D.7GDI1>+I1/L
@264
tcttcagccagcttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgccaatcacaaacacttcgataacctgatcg
+
000,?86K-E'/*6I@=2HGKM:)JDK'>C07HF.?;?)K+:A;))F3=NL)*D.LM1AB,N70-+78E2J&M(.*&D@'A-G)3.AF>1J
@265
gtgattggcgtcggtggcgttggcggtgcgctgctggagcaactgaagcgtcagcaaagctggctgaaga
+
000('9@7C:L8M/L7H//A-M:(-@FH.G255MD0M+;:1(DLJCH<.C,9+1N<-F=9*NG5:A)I31
@268
ccgcagacacgtaagtcgatatgtttattcttcagccagctttgctgacgcttcagttgctccagcagcgcaccgccaacgccaccgacgcca
+
6CEBI5GFJ'61D(8:C7C7F6K>M,6+&9N*36J,*?0;E/G6?3
@271
agcaactgaagcgtcagcaagctggctgaagaataacatatcgacttacgtgtctgcggtgttgccaactcgaaggctct
+
7;<,(;)=H?(?G4854*;/N*4KA?'AJ;6BL':F*M)8@JH,HH10EJ('&C';.*0E:'()@'(DFHDM)G)F5-8@
@272
aacagagccttcgagttggcaacaccgcagacacgtaagtcgatatgtttattcttcagccagctttgctgacgcttcagttgctccagca
+
00C5,7FH=828;ILNJ(6A44DC&9L3<7&N>B)6'2,J2/KFI0N.D7FA7IAH6'6H/N&(()FF&F-'E5&L7L6E,,*JI/+9&@83C/KJIC*IK)5*2H662+N
@276
cgctgctggagcaactgaagcgtcagcaagctggctgaagaataaacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaa
+
000),<+H(F48.:M?0656FJNH,.2@A(2ED'IB8.92,:9KH7>5E7'5J?M&)))?:31.M--5;=B+J=F00&7@.9)6I3@<)@>?3G:2AD.63=/F+:87<.7.=F
@278
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggc
+
D4.BA)670:MAL;'J'(;0FA)4I80'0M2+IK0?1IJ)47>*1/=CC54=/>3BNC8=0>B;.7;7?>C'I4(6)L4E-2HB(5'N::3KFN,?9/D)DC4=4J,*,>DFL2'+G@@;/K,4*H1(A16?.?0DBDE
@282
gtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaactggcaggaagaactg
+
<+?)=L7@N2FGJE>>+ED1J9B5;KFEIE&//)4*3C.A8H?3C0C:GC)<*8NKL(@@@46AEJK)J
@283
cgccagttcttcctgccagttttccagattaaggccatgtacattggtgagcagagccttcgagttggcaacaccgcagacacgtaagtcgatatgttattc
+
;6LC2@7?.DL*;+254=H4I12B.'3(6>5=3A=39N7D/6)5IG5G(F(C2A9@;DC'=:(3,8>LA33J5<95,,H@:.A=A''-I9;C0=;A*+)72.
@284
aacatatcgacttacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
(4-*2>G*04M8:)C@+E10IEE,0/C6EL08=9,.)NC5,I:)+7'&82'JML;/.4GHCC?G,11I3IDGI/(==1KLM'?1C:5=6DG8=-BHN=
@285
gtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaaaactggcaggaagaactggcg
+
00?>EBFI>5M/C&,@N5*8@J4FKLA404/4;N&'2B3,G>CM8)4*:.F7;@EHL*F/>;A@).AEB:/23)J60L)M7BI
@286
tacgtgtctgcggtgttgccaactcgaaggctctgctcaccaatgtacatggccttaatctggaactggcaggaagaactggcgc
+
HJ=;;.*.?21LN)496-(((I5/N(BI50>F.A=5L/6.8779K''4*9:L6>:/5H'.6L1@1G+7BD7L:K.N6*04&>F7>E'B)D02=(I7E,6C94B.(.?K8;>/G>,6FK83:C8GH62>J&E0/NF>C3&*+E:EM;&41N?9L2'9,MH-)I382>L3/GLCJ&-,(;72.+H2?8@8,H*A)@-?@7D5MLD6L/GE
@292
aagcgccccgagattaaacggctctttggcttgcgccagttcttcctgccagttttccagattaaggc
+
00080)M28+8MB;2JHLG,9D6/&7)H'-/GJJF@CL<*3K2)I*??>*4LFAF:(HGF:32KKJ1.
@296
cgaaggctctgctcaccaatgtacatggccttaatctggaactggcaggaagaactggcgcaagccaaagagccgtttaatctcgggcgcttaattcgcctcgtgaaaaa
+
000>G&?F4,:>GD-)ILN;-7>(97FNC5C.@I;3JE(101<0K1;K'7F;M9?4DL.K15C/L<=K9F3>A33.,D'27<,26BH5E?'H++3C5,>H/MCE95K=6J
@297
agatgatattcttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagttcttcctgccagttttccagatt
+
00000N(?)2GEJ++2N=BM&/=LAKKN10H*DNF='CFE+H*'(MG+MEJ00M&',1AEJC3D4;;.B/GJ=J7E53J?JDI1'(7(
@302
tgaccgggttcagcagatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagtt
+
0003F,*/BBJ3&6J@H:=-6F&68(-@F06DCFIG(KMD;N::BI3?I4)4B*:81ID;:/BL-1CNHM0B)@/=C3IJ&*L-=L&G4;'.*9>?ND=
@307
gctggaagtgcagtcaacaatgaccggggttcagcagatgatattctttcacgaggcgaattaagcgcccgagattaaacggctctttggcttgcgccagtt
+
003/+-/0D?>+N3EB,FL?2?/(85ENEH5AMB3;:I..0==/9H'H;BJNH(8@/+6CN6C1DA)IG83H'G+*)H901,1F;:M4&'E=CNC.:@'1:8
@310
cgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggggggttcagcagatgatattctttcacgagg
+
00000LF<9+;FH?*5-1L.9L5(4(N=-8FD(.A&&J36A*/1<0I*.=B=)'1D.88/5.+:-KG
@311
tcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccggttcagcagatgatattcttcacgaggcgaattaagcgcccgaga
+
:+.L6E@3@B*@8=+LK?G'31K/I7=*NJ<0*0M,J52GAB4'B,75:KDIJ6>'E*9N/7M9+:E3/E)N@<73'F)0/NJ?&BEB?>G5IBJ7+,/'K363CA;EJ
@312
taatctcggcgcttaattcgcctcgtgaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaa
+
:+.&G>&*C/10)3A@.LLA&0HC-J45;.866L+F@A/(H.-(F@N11:39;FAFHHH9BK2FG<==HJ7;GA34ADJM*7C.FK*'&/<*C.EM0=6:A=G&M,;CI:?9J
@314
gtgacaacgtggaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagt
+
0@7;:C8=N09FG&90M:*62E;KLKIHKI8D:BC6:L35H<&@NG@@297?(&+4H2(-@A>?
@315
cctcgtgaaagaatatcatctgctgaacccggtcattgttgactgcacttccagccaggcagtggcggatcaatatgccgacttcctgcgcgaaggtttccacgttgtcacgc
+
00B02H9:9*1+?G,.+(I@5/8AD>:=9?==N'/(,(GHBD2=I&71A9>GE57K3*27+.D:4=6?=G(=>2HM3D=89?*0IANL850*=3>(11II'C-JIJ*01J2:;E348F&MMC1/>('FDA.**>83GIM;-MM03@EH'5=F(=D*2/A(@(BFG9L@+KA@28I@@:G>FL'@8*N;K(>
@318
ttgttcggcgtgacaacgtggaaaccttcgcgcaggaagtcggcatattgatccgccactgcctggctggaagtgcagtcaacaatgaccgggttcagcagatgatattc
+
00C23M,&E&&B)-AIJ*6EE.N=03613*6((MCE@2B(@F7KJALE3JKM2H5(.K*I4,H,6(:(&N2L
@319
ccaggcagtggcggatcaatatgccgacttcctgcgcgaaggtttccacgttgtcacgccgaacaaggccaacacctcgtcg
+
0K5H6J?-95J1H0:BC4<.7>6J1'NA,)MC5B+9+49GJ+MN:G;F7F:K1E;J(?8L5MMC:(8*B0?48EJ'
@320
tatgccgacttcctgcgcgaagtttttccacgttgtcacgccgaacaaaaaggccaacacctcgtcgat
+
000F922=>G>+'I(&D=>=5'2'09)H@I,BG;9>6/EF/C,:56GM-5(1.)AK@+'*L&.@A&(F5D,*9FN
@327
aaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgac
+
0B+>C)3E7&.K3J=-)3L*:./6H,=>2KL?6A07L(.90?&33(N5:1LN'8L>.MFL'ANDLHHBB&,4)':,3L:8MG9/80<-H39L3BIILDC?HL8>L*;J./G.9M);?8K28+3GN:&86FKE>D=@CN;NF//)*31J;(/*K
@330
tccagccaacgttggtgtcatagaggaatttacgccgcgatttttccgccgcataacgcaactgatggtagtaatccatcgacgagg
+
00(D/=F*G/33;G><185L0,AA)F7BM@4G-?-IMGL?7<@A3&3KF&)A6,GC2?*;D5487L'JL.7'M45G0E'475(219>
@331
gtcacgccgaacaaaaaggccaacacctcgtcgatggattactaccatcagttgcgttatgcggcggaaaaatcgcggcgtaaattcctctatgacaccaacgttggggctggat
+
0/,-+B+)BFI;?L;H/.'54>,))-C2'3;(*)3)/,;-.-K26,K7+30CN,+0M=/@B1E>H?(/((NMJ)H6&,BD59,)=<;M22K4,J99(7I22DM'N)+FJ,EK2C-
@332
ataaccggtaatccagccccaacgttggtgtcatagaggaatttacgccgcgattccgccgcataacgcaactgatggtagtaatcc
+
00))A'4G@091GL3AK(@8L428=7:-?*C1+E-96.6D@;02-??NK/N7+N1JC)MM&K400A,1J0-*I(C7G?F+/).0K08=4/-AJB4:=4K'(5,G='?8HN92+,(+B)(B1AKI>=9CBEEEE.H7+1C8&576=DH/-J)763>8ML1L5+(?*+4EG0?:CJGN:@50):('/(:028IG57M
@338
aaccagaaagaatgccggagaacttcatcaattcatcacctgcattgagcagattttgcaggttctcaataaccggtaatcca
+
NG/BH9-AAFB@,E@'3E908.&:'/NM'KLH12'K?:*/;-7:A:KA=D494:>DC>*18.K;DAB@K'LH66'<.7B8?LN>09&(FB1;@27&AN*'<'7&;:2L8953::7>HCGN&+I4?+92?(@J17K@4G.L):6
@341
aacctgcaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttagacgaag
+
000M8KAM-LKDEB697+)-NJ9.@>/2MG6,D:1LB;<*?JJ&&)2B89)NEJ.DCI(&<,IN)F?0,&.'B,6E8I<;JE,,H@57*=N'7I=4A
@343
aaaaaatctgctcaatgcaggtgatgaattgatgaagttctccggcattcttctggttcgctttcttatatcttcggcaagttagacgaaggcatg
+
000F8:+G4;'N054J?&G.>':12@6231-75J86N99G
@344
tctgctcaatgcaggtgatgaattgatgaagttctccggcattctttctggttcgctttcttatatcttcggcaagttcgacgaaggcatgagttctc
+
0CHA87M&MN?L0.?+'2GL/+++E)LH,4.C68D:7F=7J6?1/F2I.@H&)&-:.,&317G5-MLC/3BMG=HC469.+.6)>.F/H=BF259I.+LF'5/6@8B2>L4441AN4-()AD(E0>*0C2344A6*6:DL*3N,)&.774L(E,6CE-D(&B(C6NIM29DB/A8M:ME49GK.64HEJ
@352
tcatctcgcgggtccggttcggtataacccattccgcgccagcgtggtcgcctcggagaaactcatgccttcgtctaacttgccgaagatataagaa
+
00I88:5('DG1G@D'/);:1;-A>I.D30BA7+;@F137=8J07?2:H@M,E>4)HNAHJGE3?,)L45*N,BFA(-9JC&=<(-DG/M8>>I6'?
@353
gacgaaggcatgagtttctccaggcgaccacgctggcgcggaaatgggttataccgaaccggacccgcgagatgatctttctggtatggatgtg
+
000*26+>(/G0843C71'F?2IC6*M1CKGK)L/(;H@0L1?2;C(7,B.3C0H>47>MK:0@CGL0,:+D3A5,-KL1I>@-;<0,4C@(-L
@355
gcgccacatccataccagaaaaagatcatctcgcgggtccggttcggtataacccatttcccgcgccagcgtggtcgcctcggagaaactc
+
0000-)-D*<1J(1A*JDLH?-6M*9*9H0J.&?-9DK/EKF09N<.:DA.L)6,9C;IDH&-?(-:KB;5(/0&;*9A:JA>C2LD4H1'
@362
caggttcaatttcaatatccgccagctccagttcacgtcccgtttcacgagcgagaatcaatagttttacgcgccacatccataccagaaagatcatctcgcgggtccggttcg
+
000-?/?2.?(/48,@5F5F<;'I=9J7A6?2C,9,JGIN;CA8I3JL---IB'L45I(3B
@363
taaactctgcgggcagcacaggttcaatttcaatatccgccagctccagttcacgtcccgtttcacg
+
0HNE7HJ7A865'-9.E/N57A4=HHII&IB2;2B:K<&/':.(BKL6F&/3C2FJKF1&;//48J?
@366
cgccacgcgcgcggcaaagagatcgtcgagttgtgacagattcgccataagcggcaacatcaccctcggcg
+
9;,*HFG+)'-4=&I/(&+,F93K1F69&21CL:>B7L5B4-CGC2K(EHB8G>0+N-N=C+E=:G=L.:G
@367
gtgatgttgccgcttttatggcgaatctgtcacaactcgacatctctttgccgcgccgtggcgaaggcccgtgatgaaggaa
+
000F:G@43?K*3.E<>-62N:)=<(K37G>B10@C+*G03AG>8)?3CI89A<A8=>68/
@368
gttaacgccgagggtgatgttgccgctttttttatggcgaatctgtcacaactcgacgatctctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgct
+
000G@&?2*MI;G+,H5'F,'(2>791F'@3,:K4&9=G85G/FM=9).(48@BK(857,1G??N7DJ&L>E+<(A5LGC7+);;8+>)7MD6>E2M.0&7H'@4<
@369
gtcacaactcgacgatctctttgccgcgcgcgtggcgaaggcccgtgatgaaggaaaagttttgcgctatgttgg
+
000F/6LM1;2:*0IK'J()HF3.8.4-9K<4@FA7*25G)C;?7;B3H*:&@B?K<=
@371
atcttcatcaatattgccaacatagcgcaaaacttttccttcatcacgggccttcgccacgcgcgcggcaa
+
0-DME>MB8>/M=03M<*K)0:M:5L9=7>BH85'*N+G>/HN0(>:720;5B)7>-?=?C)6>CM&,K1J
@375
ccgtgatgaaggaaaagttttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgt
+
0-34)/7<.+14;E8B;)I
@376
tgatgaaggaaaagttgcgctatgttggcaatattgatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttc
+
7+@5EJ:6,G:E5;AKDL&4HB'><)E*;BL*CL-H=8D+*BG'C5LH)*/'D+6+E?E&MNI2D><*9;57<2/476J?@+C(4
@378
catttttcactttgaacagcggatcattaccatccacttcggcaatcttcacgcggcagacgccatcttcatcaatattgccaac
+
00DCDD7+>8ILFJ)@&J5@.LJ/918(?4G'7G*=.8H(1A-I2-@G;--+)>KF'IC-&M,D83='?HM=B>83L;LGFJM,:
@379
gatgaagatggcgtctgccgcgtgaagattgccgaagtggatggtaatgatccgctgttcaagtgaaatggcgaaaacgccctggccttctatag
+
KL.)M0-BLBJ:+8HJ<8?G9&GH&6?ID>K1CA=8=/MDC14/==,9<)
@383
atccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccaggcgttttcgccatttttcactttgaacagcggatc
+
I(&D<=H4@I7;I4HJ(&*GC36='8643N?):NM-,3.('=G.<-B.JIF/)-4;+K;72<44>*)D<@)DG98MD=&GF9K3I2E5-6/C@G4?<(E(D6&E
@386
aacgtcattgccgcaccatatccgcgcagtaccaacggcagcggctgataatagtggctatagaaggccagggcgt
+
EE)?9N:F(K+F:,6@-FLB030A6;LN30*I?.M0;49J&B<,,+K>'>AKKH(:7-;=/8G6)N:.*;*3C,629NKGBAA;(*;:J<
@389
atagccactattatcagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctg
+
0000-;(G/(AI))FNNN;-M.38=((C>*-G1C,7A:-HC5@.60(.:43A-3@GC'E44''>42&-M=6C:K+C>NHI@:?8
@391
actattatcagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctg
+
00JI-0318GFGDGD6@G'MF=?/M3*K@,B?.*F6.2H44D5D04KK7.=6F:AHFE)7L2F6(I+1;CB52@LF)'N3*F?
@392
acgtagcagatcagcaagacaccggcagctgtaacgtcattgccgcaccatatccgcgcagtaccaacggcagcggc
+
26@1;L<.C63JBC?-<'&J*(;):B1:/MEKAD+J'H&>')0D65+05D@0+C34;0D6>CG>I?M0H1)EG&L3I
@393
cagccgctgccgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtcttgctgatctgctacgtaccctct
+
0'.*;)E'&>CN*<->,:C>L7GL(:E;@/E7DF1M(-?F11L@)JEA>AJIM*D-*:8/:M)&LMCKD/@,:6/E26@.(
@397
cgttggtactgcgcggatatggtgcgggcaatgacgttacagctgccggtgtctttgctgatctgctacgtaccctctcatggaagttaggagtctgacatggttaa
+
000M)G+7HK0?2DA+G/=B(=9C7@9'6ALMF):&9'9><0AI5M/-K?
@405
gcaccatcaacaggtgtcaccgccgccgagcacatcaaccgacgctcatattggcactggaagccggggcataaactttaaccatgtcagactcctaac
+
-+7G(>JI9+JN=C/=.+9.:=
@406
caatgcaccatcaacaggtgtcaccgccgccccccgagcacatcaaacccgacgctcatattggcactggaagccggggcataaactttaac
+
000000N00/6-8:BI703(,II+.GN'EE6=L+K/2;>8),4+=;BNI.D8438J?K&B/D,L@((5<8J55*E:(A3/D6H6/'KC2I24
@410
gttgatgtgctcggggcggcggtgacacctgttgatggtgcattgctcggagatgtagtcacggttgaggcggc
+
-M?,<00)N4NB/+<(N):@(N=&J70)8'&BE/)76?8>*4>F<,>FHC:&6G>K/A)5LEF388IMJID2',
@411
tgaatgtctctgccgcctcaaccgtgactacatctaaaagcaatgcaccatcaacaggtgtcaccgccgccccgagc
+
0D*;E.5??='*?F/61()JJ4A)>ILL8M>5/?4=C?L5'4>:/*&.=5+'I8=MK;*9@/E(,9.=/KDF<
@413
aggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtca
+
CE.?+L00>)4897JM'0II.5FE61I76*1NDDF9AA39GDB,G)84K52+E4=D,'G@I2CIM*+,=()K==,:L(<@4GKA8GFNA7?6@L<9D=/
@415
cctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcactctcaacaacctcggacgctt
+
(;G5<107,F078J8H7D'61*C?-L63H9=M8:9N6;JD+;ELK-.)*3D&,&D30627NA<>L'DE/(L;',>:&K*/,;E-&
@417
cgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatc
+
D()C0:AG;.GKM;?K>@,.-@?1<2:=KC*N>8LL?./HN-M;&L34L34B.04)&H*F+F0
@418
tgcattgctcggagatgtagtcacggttgacgcggcagagacattcagtctcaacaacctcggacgctttgccgat
+
(EADDA@KE'::2J,,,-,J;:J)88EJD;CA6C)JF.+B:D3M*?C*B>:ID:AGD5
@419
tatcggcaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccgagcaatgcaccatcaacaggtgtcaccgccgccccgagcac
+
02KE';3@2EB3;G5/NGN4*JG,E/K0L56.BH'4L8K9A4,8LK?&+D-7CMB30L)8))N.17N:IJ&AA*6M>:076ECJG,L9&D&)M1@L??(4:57+C*3,><9/6&(0)M>1NB;IA4D0F5?+B:@,B9/AM:CN)0J=3+E>LC,'E&B)K'N/658:4/II,&05/22@'554+L&).FD9-:<&+/+@;&.=H:C9KBJ4.8@7G.)6
@424
tctgacggcagcttatcggcaaagcgtccgaggttgttgagactgaatgtctctgccgcctcaaccgtgactacatctccg
+
16=E=JI&&:;9I:>MKI=;,8?*+G-96A;;17@4G?C:+:/E6/HJKICDI@:H=5N4NB?>H+/J5?M6;>===AI,=
@425
acctgttgatggtgcattgctcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaa
+
09BCJMF0D609&=GCB0D1F(.;-AGAH);;742KJ(6I-0.AFF>;IBFI2';
@426
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaa
+
6IE4EJ';/F5.<6A(B.BL8613)3'CBD,:I6=7?/72;3AN&+23B8524+'(J'&9E3K3C1GHBL&'02(/9ECD>/5+(*3=HHF/?)&
@432
tcggagatgtagtcacggttgaggcggcagagacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacggaaaatatcgttatcagtg
+
00:2'.)(>@:A.E'I:C=?:,J@:2,GC4.=G930>*0N&5<)JM@5K-)0.>B+L9/J)/CKK68C7@I(D'H/A<56/IND7?'DMGIN@AJ1&<1/?(/8-4&
@439
gacattcagtctcaacaacctcggacgctttgccgataagctgccgtcagaaccacgggaaaatatcgtttatcagtgctgggagcgtttttgccaggaactgg
+
0000:;(A;&)/HD62;)?AD&1)+2=JJA,06KF++1:(J+1BJ-*B5;<83&7/?/+B)NB88<+&LMD.&80B,:FGNF*B0*'IJ':K>+8MI<71BE-0
@441
ttccagggtcatcgccactggaattttgcttacccagttcctggcaaaaacgctcccagcactgataa
+
0+=1=>ENA5:&5BJ-C9'AM(7<1(;1HJK18=8))-EN9+JJL&2;9A54(A2I48N8NC.JFJ)055NCD(+0GA9&.3HJB(@A34
@446
gccatcagcgccgcgaccaccgaacaggcactggagcctaagccccgaaccgatcggcatattcttttccagggtcatc
+
000B4BE62..C@8C8CD':1N3K1AK6;A)E(54?FE?(7J77=89-0NK>B;HG?FEE0N>IAKH86NEDC23(7<,
@448
tcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccgatcggcatattctttc
+
00A/I<1?NIJC=.BCBL;C@95:=L*7'*9J6)6+=+J=.LMI?B*)?L)7FA.5+*(>E0@+837*G4,4
@449
cagtgttcattcatcgccatcagcgccgcgaccaccgaacaggcactggagcctaagcccgaaccg
+
:>-752F,6IAD*E+B7KN-KF)(?,@)L&>CD/*1?(CF&.9(D&/=34:D?,8/3L**+1E56.
@450
atgccgatcggttcggcttaggctccagtgcctgttcggtggtcgcggcgctgatggcgatgaatgaacactgcggcaagccgc
+
@C/CMMN=B:7,D9JJJ.NDE(=LGI8D10.85ABI4=GF)?J(G8N&.N@H58J@?JMN;7K<*MM64>?M/3643,H?:-+E8?5&>.2H;249B4A2A8G<81?C*J?+N;8>C)2((-,;2F,7'/4+3-1,N/.JK0/7B.2(&J/-H9D*GF'+H,6CH'D1A+D&<(0:0:+,J>.A3.,<;.+3@2JIJJL&I*)0'2>*:K3HHL9;9,GB.-A-;AC'+139I/D5
    0HK=1-BA5M)I>'/+-'<2+3@9@N
@460
gacactcgtttgctggctttgatgggcgagctggaaggccgtatctccgcagcattcattacgacaacgtggca
+
F/7D44J/0+88=3E2;K2IN&I,'F22=1:B(@JM9/L)K<:GNI<7F==
@461
acggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagctcgcccatcaaagccagcaaacgagtgtcattaagcggcttgccgcagtgttcattcatcgc
+
000000;GI(CM-9>':JK5NE5A..=0'I+?>7AJ>I'..H)/<2/M44(@,-<2=+F2/8A?5'M;BI5I'-&E:./7&ELAKGEB*01
@463
gatggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcgg
+
M>:-EJ-;8-;H@KH+-4JH:71KI8.==6NJLKF.<+5/550.*LH')NNEB+@4GL95L/&:8C=9
@464
gatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgc
+
005/6)HH;25-2A*.I*?M&FN&FF=4FB4?(G/8'53+=?DJA*;I*+MB&KF?L:?6/:E(*24I?)
@466
tttgctggctttgatgggcgagctggaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
+
00D4BA4;'C2I&9&6+N:<4E5*3;AI+L&-JLE)5N(6&&5>@56+8E0K>E?1<*F1-;4@2/9/<)/:-+M)-0B6-C4M3,/36=I1?3B=>+M;MG8.?@IC/AK7GA3H/882<,IN(0*'BA.0@:,0?8<,I@@@5GB
@468
gaaggccgtatctccggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatc
+
,I9,N/=HDIAE?E'5J:+-<)6I&*@;0<(64D*N9N2-88.82)-:26H41M9&M3H=+=9C88)K8(A9FA:
@469
tcttcgatcatcaactgcataccaccgagaaaacacggtgccacgttgtcgtaatgaatgctgccggagatacggccttccagct
+
2;/7/H2LI,@=I0F4?)H'?=+6DIIFM*;-=3.*7+F6-(I&208M/*8E/3E/(
@471
ggcagcattcattacgacaacgtggcaccgtgttttctcggtggtatgcagttgatgatcgaagaaacgacatcatcagcc
+
;7/C*014+A077F,7FN0MH(.L==F5I4?:>)C(('91K??:-M1
@472
gcacttgctggctgatgatgtcgttttcttcgatcatcaactgcataccaccgagaacacggtgccacgttgtcgtaatgaatgctgccggagatacggcct
+
00-'D51D321KIMJ9(C(3>E<'/9M(=?8)4G+0;=@F<+DNG;(*;+?3@?<,?MEN?,:J1+L(E8B==6D1FM4;:MA?D3AG.C(((N?M96I'1&K62M
@476
ttaatccccggatacgccagcacccacagccactcatcaaccctggcacttgctggctgatgatgtcgt
+
*;08G&-M05KH)EMK0H/F5:'&-IAM8:/*3FH1N@6E<&J,'?CFC'.&*FK@3E+@MD&:1*D7-
@477
tatgcagttgatgatcgaagaacgacatcatcagccagcaagtgccagggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctc
+
0H;(K51G('3C.4JA.-5)')?8K0>8>M-13;67N:?M(3E:JHE.'*/C(;F1HK13=+KC5*2
@479
aatagcccctggcttctgccgtcgagactttaatccccggatacgccagcacccacagccactcatcaaaacc
+
000>4GLL@*'&DJ8))CF@5AI/A,=>?AD-/1H<=@>A6CE;7KN67IⅅLJI(19GL,+()2@GB/(;
@485
gccagggtttgatgagtggctgtgggtgctggcgtatccggggattaaagtctcgacggcagaagccaggctattttaccggcgcagtatcgccgccaggattgcattg
+
000;+IH<<(GEH6C&'.2&-K5?.=GN?,20&(GC46H>>??=<.G-LN70*J?I8:M)9K9JMNECN-64.89&B
@487
aagtctcgacggcagaagccaggctattttaccggcgcagtatcgccgccaggattgcattgcgcacgg
+
00M=/KA;DLN<'=5>-=;.D+C+L-E0A07)+GINN61,G9C@)<&F?&)INLEI@)KI)=M57L7I=
@494
ccgccaggattgcattgcgcacggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgag
+
00+4NA>EB>)M4ED=//J:7F5F.++@FE;&;JN6)?0-B2GJ)6G/9IE&LK9CJ<=N&&@LJ95F.*7M
@495
gcagaagccaggctattttaccggcgcagtatcgccgccaggattgcattgcgcacggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagc
+
0*5LIK.B260L+)2&>4/.A?864:)B1F'E,12)J(+I6BK?M6.A889+G(::=()MAIB5K70//5:)3095D@DH4IIFJ(L'L:'MFH*3IHEL8NC&0E.?@8BN>D;5<+89>N=6=II10C(
@498
attgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatg
+
0000D'1='0.G8(,N)H/5:,:8;.<1;:KFK5)6JME;0)?FE+(5D<;1L'I01?E+<=N;L,/7L;17I.INEJ8;?,E
@499
ttttttaccggcgcagtatcgccgccaggattgcattgcgcacgggcgacatctggcaggcttcattcacgcctgctattccccccgtcagcctgagcttgccgcgaagctgatgaa
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000000F92/J:2<:H+&BL&/I*?L28K2*EJ9F-GKE:HE))7:M4M@6;1+MC:<2A9G()78AMC5B26H7JC,396&L2MN5,B@MC4,JA,FJ@HH8*H+K8+&*1<02.5
@500
acggcgacatctggcaggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaac
+
I,4BF,8&)D(:H>5.73(0*6B81<2A?I;;L1F;,:8IK:H@D976@M>7GCI)M,.''ML?*;CJ4-7+*J/NK4&GC(-NAE?5K
@501
caggcttcattcacgcctgctattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacc
+
0:?;DH,&A);B)51H+L0(H7&@)=NKK?A?CH7IJBA//./IJ7B,9N2A>JI**B>56A?3-E&B>J64*>AM
@502
ttccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacgg
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009G>7BD9-?CE??)&C*>KCF6+@L/J8>A;9'I<-5)*6?6H,F.(B0I4M&4//+K5J,/4;
@503
aaccgttcacggtagggggttcagcgataacatctttcatcagcttcgcggcaagctcaggctgacgggaatagcaggc
+
000059*90,N&525=4C,GG2+8H8I;
@508
gccggaagcctggcagtaaccgttcacggtagggttcagcgataacatcttcatcagcttcgcggcaagctc
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00,13@83646HB?6=4M(>8EK6:+2M5E)I+->N=1.87HN7I>91D&,2;+7G-+AKCKN8.F67A;F-
@509
tcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcagg
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0009BF4&4/B(<&L+482LKAK1H40@72I.>M-G31,(53?C'?G82A)LLI/GB+*4CC1L;88B:'L)+@=8CJ1G7>+
@510
tattcccgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacctaccgtgaacggttactgccaggcttccggcaggc
+
)G=CK;N0+GG'.4L*G6M*>7EKDHB+()N:N8H)&G(MDI:-/),,3:.F915:8=JGJF'?CD&'3MH&0L*C>0D6MN23E5')E9&
@512
cgtcagcctgagcttgccgcgaagctgatgaaagatgttatcgctgaacctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
+
0000G'';'B4IF>DMI6;FJHFH9NI>F(N-I.2.G=@?/7I?JAC7+GA;3'),9LEF?&CM;(@(8G6=I'63E;2,HJD,F8CCC44G3;.
@513
tcagcctgagcttgccgcgaagctgatgaagatgttatcgctgaacctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcg
+
0.'7J6,H@C22HGB>M.(?*64@643&1@C,=->N+(7/(3K-@+FLNG,?E/J---GD6=*.>.&9'/AJN1&6N@(&F@JJBEJC67+F
@514
ccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtaggttcagcgataacatcttcatcagcttcgcggcaagctcaggc
+
00).I04?EK;)B)/62:/<0F/.:/:K1+888+7=/59DCHN'NE,KA=@/L/;G*//E6?;NINL*,*
@515
gaaaagatgttatcgctgaaccctaccgtgaacggttactgccaggcttccggcaggcgcggcaggcggt
+
000&=K.@)>:J>83G'3(/4:4JH8@7,-N5@//K;)//C&>7D@N:7L=.M*M*=D)2K/=@7(
@517
ttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggttcagcgataacatct
+
.;G3C3-ELJ(E4)@1&4&,<,JM5JLAL-91?-(H@LA
@519
gcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttcacggtagggtccagcgataac
+
0000(30DNE&&-A+9C4G>@I026)JAM0=ID,;L@?;I149L6/;?,8:.':GA+'B@(2L);3A.B?+E81K@,2.@;?>C5E5;9*'>K7M6562*AI&9C?G
@523
gttactgccaggcttccggcaggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttg
+
000I>)+E-,73G@,8:,&J:F32>,M=BK+,J/G7F+FADHF&N;7GCB0*&A49D)A2K*83NMC;M,4@.67?NN/5)(B
@524
gagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctggcagtaaccgttca
+
*KGBF=M78LN86MGA2KG2L3K:,259M9+B.HI8DD+?GC0H@J4;&NN0E2B9C)J(8KCC*&/>:I:)36-6M<@BA:*/@7&-&62,M>E.L38BM
@525
aggcgcggcaggcggtcgcggaaatcggcgcggtagcgagcggtatctccggctccggcccgaccttgttcgctctgtgtgacaagc
+
0K>*K?65**&=<-A.3NB6>K&FE2.>8J&865,D22I??L/;A@(.LJ&<0C9<7**M,/A4,@I>CH;BFM/94+K':.C:BH<
@526
gaacggttactgccaggcttccggcaggcgcggcaggcggtcgcggaatcggcgcggtagcgagcggtatctccggctccggccgaccttgttcgctctgtgtgacaagccgg
+
MN@B@JGKMN'/CGKL:288B*A,1?)?*)'.4I7CB@A014@097<@8?0L3G(J9J?/CJM+*9=N>7HN=<&J?'J3'KH@)=F>(318>D2CM7
@529
ctgggcggtttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcgaccgcctgccgcgcctgccggaagcctg
+
009H69>L9@@A?2B11AD'9>K-L9466DG0<)BA(6?-0+8HJ=L7=A54IN?L+J/B(/1B0)>J@KEKD(@0J0=K*'+'7J>3/H@=/5(*/&;8GE0149)I23A-D
@530
atctccggctccggcccgaccttgttcgctctgtgtgacaagccggaaccgcccagcgcgttgccgactggttgg
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0.'N3.159A)IM3,ED'.JNJ(47087<4.23M+&@,':.&0G4-F&FKE026G*
@531
ccggctccggccgaccttgttcgctctgtgtgacaagccggaaccgcccagcgcgttgccgactggttgg
+
*(=1BNE1;7JJ-+:GH:)G,K>1>GC1,DA:BD(DE(/A:MN.:IL/?7AA)//?MI@E>K7NNJD;2:
@532
cttaccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacagagcgaacaaggtcgggccggagccggagataccgctcgctaccgcgccgatttccgcg
+
>FM2)*+H+@;A1265=02HN0;/J?9;42(03;E(0/B/DE@*MD5(C'L&0D9;3,-IA4-C6&L9HE?(DB)83/7KGM7H>C'IN'7N@6@,-<(9:65A
@534
tcctgattgcaggtagttcttacccaaccagtcggcaacgcgctgggcggtttccggcttgtcacacaga
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0&)IH*;-?:,(:L.CB+131('0J)&*A@BA8*:''CK-F;&>>@)A'B:5+':*L7)0=G*:JMG&A9
@537
acaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctggcggttttccggcttgtcacacagagcgaacaaggtcgggccggagccggagat
+
000L?GN7:3+G:23G=4;C=EL=,B9B+&<+&L/@71=+*JF-9>-&=HH@71*80)7J-275F1-(=,K=<)6,'9'EM@@KF?,;-,AAI0GFKB?;6B::3,L&
@543
tccagtactcgtgcgcccgccgtatccagccggcaaatatgaacaaaaaccttcctgattttgcaggtagttcttacccaaccagtcggcaacgcgctggcggtttccggctt
+
00000G(?/BM6I?(3L@*/CK-L15<)GJ;18NF-93K322;9>'43I8D+(&>AK2@LI'N(018*(9B/2B70=5C0572A043B>*G
@545
atatttgccggctggatacggcggcgcacgagtactggaaaactaaatgaaactctacaatctgaaagatcacaac
+
0>8*0H9K1@?,?'*LH>BC'8'D7C;&F5E@GE(&?(892B&L@*D&G6JCH*;HK7?K4J-,?2DKE46C/492'B&,D0LA..;70
@568
gccgagaggatcttcgcactgcgggtgacaaaatccagcttcagcatctcatcaatttcagtcaggctgaattccggcaggtcgtgcggaaaaaaaacagcccctgatttttgc
+
00000008B>?&N462C1A8?M*@/05=J@)L+'H'C--LC(96I&5--6-//I6-=9/:)+J:@
@574
attgatgagatgctgaagctggattttgtcacccgcagtgcgaagatcctctcggcgttttttattggtgatgaaatcccac
+
000244B-G>.J)66J572:'J?@M0CFKH6*KNG0=G@J1>CL?+N<+(MK(:<7=,0H:)4G43B;'8@05>FKF2/('B
@579
cgccgcgcgcacgcgctcttccaggatttcctgtggatttcatcaccaataaacgccgagaggatcttcgcactgcgggtg
+
000BF1M1LDJ&<&E(61G/&EKKJ.&'&?6+034AEK>1*68&==D'>:,-FNI,7/2M-(2=L8,,(A8:;@/4F80:,
@580
aggcaaacgccgcgcgcacgcgctcttccaggatttcctgtggattttttcatcaccaataaacgccgagaggatcttcgcactgcgggtgacaaaatcc
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000000F087'8F'L))8(9E7CEM)&GCD'G9LM+?889)'&3?-/M<3F9M,*0N3BH?*.2F?(5H');J0;3:A;41N*
@585
ttcaacattggcgaccggagccgggaaggcaacgccgcgcgcacgcgctcttccaggatttcct
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4B'JJG@F<4)*,.3<3/'H(G)??HN*:NA585GC)NL55?EK?<);0?G>2-;MHL5MCD4;
@586
accgacatcgctttcaacattggcgaccggagccgggaaggcaaacgccgcgcgcacgcgctcttccaggattcctgtg
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000/HAK45(2.B/@<(F:0M51IIIJ'=B719F6KN0I'D4J(3K&M&61K+::+.+(+A)N&3DC<4;,+=+4C))=K8=A'3.I
@595
cgccgaaatctttaaatgccagcgttggcccgtggaacaattccagacaaccgacatcgctttcaacattggcgaccggagccg
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073)029H2GCNG41/DK5F6G7M+6ENN7BI31+6+@4B<<*K*-IHA;(:9D=E'IJM*7HNA:9AKJJ',+6K76:3?=8,
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ttccggctccggtcgccaatgttgaaagcgatgtcggttgtctggaattgttccacgggccaacgctggcatttaagatttcggcggtcgctttatggcacaaa
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004&)3K/=>(5;J970N'42M-,&I--/AJ+NF;=N>B8(L1D6))BK)E0DI'@147JAHE3.2)@3MED80;8CA@2.I9A7.;<1@>>I=FE
@599
tcagcatttgtgccataaagcgaccgccgaatctttaaatgccagcgttggcccgtggaacaattccagacaacc
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000HD:*JIG&@3JGE0'KEBFNI0@.5:6)(L;?)==IN&A=/>6B9;70:NM2*G003J-/E(:8;-C,<8+L
@600
tgttccacgggccaacgctggcatttaaagatttcggcggtcgctttatggcacaaatgctgaccca
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00&?G/KFED9-H69=3'1.5>9+HCF*D.@.3H'EB2C27A&F95&2(LC7G6JN(51BB,:@N?AA'@2H;I
@620
aaaaaccgtagaaagcatgagccactgccgctccggtatcaccggaggtcgcggtcagaatggtcactggcttatcacc
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00(G,LB?09*=B2;0I'6I:9J1>C&I=3&+29/-;8+.@C*7=G>*3CH8-0.50*E>9
@621
agtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtta
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F585):=+&LK(2&B'&7*&>&+LG<4B(?064L9H9@?NC64-?8AJ/*
@622
ggtgataagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaa
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000D6N=+MLCA,8C6*@C<)G6C10A+/><7H*?@-:NFD;79HCC@G7DC=J=*==C=<&5-ADAN:,@8:CHNMK1HM1-+9;9B:)I8M'>6NF>/>76D*;)EF?0?L.402
@625
aagccagtgaccattctgaccgcgacctccggtgataccggagcggcagtggctcatgcttctacggttaccgaatgtgaaagtggt
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0000J/K97G4=;HD*N@J5:D77C13@&A'8/*:<;.D?1)>IC5)A)>?7@BB.3GHD3G9:IL=D8536CE0D/(1
@627
tgaccgcgacctccggtgataccggagcggcagtggctcatgctttctacggtttaccgaatgtgaaagtggttatcctctatccacgaggcaaaaaatc
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0008:L07J+//;KAM&7N1(3D(&9+HA5'7L6E/.6G4)?L8//,-5L7N8'7N*KA>7)8EL?C';E7H07./:8863EA>&5CJD&<5;K8&G?,3&D8/(B<'BIF=N?L/H*-/(K0E6AF:M?0@
@635
tacggttaccgaatgtgaaagtggttatcctctatccacgaggcaaaatcagtccactgcaagaaaaactgttctgtacattggcggca
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00H/NK&2.KM?B8K0MF@55F)H914DM,4MME>E*6M)'<3'J,AMHBMB';@,KD*E*@FD(+DCE78*=?D4,*86588AM6M51
@639
gcaatcagtccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatt
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7NF3C,);'(8+*8>N<)?'4=MDMN
@642
ccactgcaagaaaaactgttctgtacattgggcggcaatatcgaaactgttgccatcgacggcgatttcgatgcct
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00;H=)->D-F(IN5J-6N)-+@*25KB8M>3(.,;6(>E+A/)/N9)'*L0ED&*4B0/C8(&)-42DJ+@;ALM
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aaaaaaaaactgttctgtacattgggcggcaatatcgaactgttgccatcgacggcgatttcgatgcctgtcaggcgctggtgaagc
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0000ILN23K'II,EG586K*>9NJ00GM:@2B(10=4:6,MI/N&>/L)H?,1EG?C5/E,2AH::3==6.:GCE&/MA//)2)(//H6'M;>BC49
@656
gccagcaacggctgatgttaatcgagttagccgagtttaaccctagcgccactttcagttcttcatcatcaaacgcctgctt
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000A(CL'7D(=>N&9).??2J8F81AD0N3,BG.7M>H3-'&@,9FK&&:@<=BDC:NK:6KM66;33?5MIJ-HE6?=:MC3<.&70,H0(H56N@/B4GH
@667
tgttgcgcagctgccgcaggagacgcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtca
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FK,F8EL@4(F2M91>NE->B/A/I=CD777+'4D'(,4FME;J=''64:D23>;K*J'H-H-9'.BMAI8/6I-I)
@668
gcgcaaccagctggttgtctcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtcact
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00.31N9/)B1012LB:K6:K+C@<6LI,?FJ3J+3:(65(9EMC>35A.-02..M-/G?48:M:8L*0B-F+(
@671
tcggtgccaagcggaaacttcggcgattgacggcgggtctgctggcgaagtcactcggtctgccggtgaaacgttttattgctgcgaccaa
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000<.N:FN*7E<9(C;0JAE>(I2D=*J9?KMG&MM-?7-&(GH,JF71=,=6IE&;'B-DBCCDADL:K1CLAD>&+IAI&D'2=B@'/
@673
tttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaaacgtttcaccggcagaccgagtgacttcgccagcagacccgcc
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0000D6(+*6-)):=166@/&&'55<+-;&DJ@AC&3FCNF27K671DLEFFFE7I@BG)>:1IL1)8,,9IMGI';I@+N?E@I3G2(4LCK>&98JL:CD'
@674
gagtcgcttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacgttggtcgcagcaataaacg
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00B:C@9CA=B(&4>F*)GB-JA-='&8<0<4=GE0-(DE:3B@+EDDLIF/;@JJ('ME.F*(84CK)=1A(&-JK
@678
tccatcgcgttggataacgtcgcctgagtcgcttggtgaccactgaccgtcgtgcaggaaacgtg
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0?-*(?-,.'AF3:1:0I';.D7+(02N-DA/,8/5I)&,B-@72.*B:.C19,L+JH0:=2>'/
@679
cgtccatcgcgttggataacgtcgcctgagtcgctttttggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgttcacg
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00B1>2+08HL)LB<>+83M(NNH9?H)6090A<77=IG0DKNJ.:'J)357D>+F'H4&.2:?4>'-(6L;=+2LB+57:J@:-7(FHB
@681
ttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttttgggtgaccactgaccgtcgtgcaggaaacgtggca
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0000:7:<'=H*/:/<&D5D92;E*3*4E?51?0K9E.50>D=M1.GJ3D*.-A84E--H@7A2H*/9G+61KH1'F//(E+&K<2KM
@682
gttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttttggggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcgtt
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0000&0A3+4G:*3+.4M+BI:0I9&:/>>J,1='EAD:24B'C5+,:1)89=ML=C-&H&(GG*=A4*?3;4KL<0=F2'L3F'LI./J,0.H:I48579
@683
ccgtgccacgttcctgcacgacggtcagtggtcaccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccg
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*EG85/5G;+0N8N=)1L9E472N.ILF>/@G:H-<;:*GH5;F96B9)'*3E65-B7HGK3BH)98N'=I2FM/<)G4>EA7+@LI=*.6/30::
@684
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgcttggtgaccactgaccgtcgtgcaggaaacgtggcacggtatcg
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007-8)KG?1:>N2HG?KJ5?>1BK0137;L'H:J7KD1JI/:L'3@G1';AM8NDI-B-;>HG86(;9.-C*,M8*4>3?76,&@BEC;C&J?E9&-K1DEMEB
@685
cacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaacgtgg
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0D9N2C5EG*1>6JBH1?0B(.N(0;LLJ&=0E5E=.+E'LL:&;2M?GIK(3)+A'>2M8<*,9=6)H.?&NC-E:&B7A/NAAB66A4@CC368
@686
cacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgagtcgctttgggtgaccactgaccgtcgtgcaggaaacgtggcacggtatc
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0000,BI4C;6C*D..L9+,&+&@:=32IG:>-9JB4GL+NI@G))@*J56E5::=+&'9B8:MM.?AANAAH>83@CA)GE596:M?7M6.-?@71>.AG-KE?.L?
@687
gataccgtgccacgttcctgcacgacggtcagtggtcacccaaagcgactcaggcgacgttatccaacgcgatggacgtgagtcagccgaacaactggccgcgtgtggaa
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0G=IJDI'=DI/MI)762*8:(/DN9C,&3K*;'9@*37;K8;&(K+B/39<&NI=27(C>,M4M4.E+8-NJ;*;A4J=D>>4N0K3,(,(4>DMK9.D8?;(G.&?3C
@688
gcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcgcctgag
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0M6.41&KH/A*A/&C/B1,5-?=5G;IC:2''+2@B>F&3)JEFN;00K1&46D4E)C/IDG
@689
gttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcgttggataacgtcg
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003*61(@174CI3JK9+2<>C0;?B&M<6A)9-BB-@4-G,D1((:.E,'B-4K,)6=3?EB(A6.@4'/C)(6I5-HF=C**HA>(/'<+/>4NB&/87'KD@+DC:H1?9;LHA@54LD6-K'I@*K5J+'KGF=*);9=)'GKG>@50J.7F2>-7',8@D?H,3<
@693
cccagctcttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgtccatcgcg
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00+:EF,'>K,H'LG.'&4(5.=B=1C/1GH&(<*6I=BK8-,88<';N:NJ14&JI;*M<33/*
@694
ggctgcataacccagctctttcagttgccagattttgcggcggaacaactcttccacacgcggccagttgttcggctgactcacgt
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00000.+J'M94D@FCK=@7;?A?H97'1D/.14-+8K/:5:NNFC,M>IM@=68NMK739@CE@3IFKMH185LI2M:.@H-&'M
@696
cattgtctgttgcgtggttcatcatccacggctgcataacccagctctttcagttgccagattttgcggcgga
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003K*M+LID6'BH87J52-G6DFI4(<&-B>7)58MI45=>K/8;3C(3+@5
@697
tggccgcgtgtggaagagttgttccgccgcaaaatctggcaactgaaagagctggggggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgt
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00000-6JGGB+15&(A58/41C7*&6.0L?;8K2K5,,1501'+1-99:8JD,@3FM,/B03A+N3AN/42+H>-:C;L)75'>3JAAI.F@0H::D;)8@+-2:**9<+MCG-;?K.(.+D
@705
atctggcaactgaaagagctgggttatgcagccgtggatgatgaaaccacgcaacagacaatgcgtgagttaagaactggctacacttcggagccgcac
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0(50@?=7C&M+,6.2-LH7B>BD1NC?.I*3K4>NL<&A/6(M'(/5>8':I8C28.?=;H*4KH+:78A8?*9D':?0?A,2>J>L7<;D=0+7D.=24@JD8
@710
ggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagccccagttcttttaactcacgcattgtctgttgcgtggtttcat
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000'?@4ECE'9&3>?8?C)3)HJ0H.-.GK/*G(M6=.F5G>E7'1);)'1&E14-;?'9D69L*8G4=GH&+8E<=5/:34'B1G@0-+;2-*G=H&;H&.>
@711
gcctggattcaactgatcacgcagcgcacgataagctacggcagcgtgcggctccgaagtgtagcccagttcttttaactcacgcattgtctgttgc
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0000I>1K/*E)M*3,4.E7D?29F:D055I.@7LH*D19&-.B;A&5086<&*:+&25I-H&/M9A1:H,<3GK,)*NL.0L6>CB,5/3<)*?G'
@712
aactggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaat
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ctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcacc
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::L4G)+K/5@IHFB7D+?+&&'0=J0:G(J;=D-,J1EL.B6NA*87:?J;MIEG:711D>;,6MF>'@)/6EC(42?0'C98?F=H;LA1?/B(?<--L<,EII'H:/HJ(5+2A9,J)F;
@716
tcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgtt
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&B.?MEMIDDF6/&046?M5'1,9:G14A9H;F*.C/=DACNI'27&>/?29:CH@G>..M<01-HMD7-67/2CM'=(I)CG(1L(C2FFH0G98@1?E&7CE.85.995H721L;>IIB-18,I2)AH6
@719
ctggctacacttcggagccgcacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatt
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00,,5*H9G(15@9L/*?E.'?FH37DI)>*@;1-@&)/(7-*L*E*33(@?M4NL@KHM(2&L7'5D6LJ4N<2DE37L9/L>;?3HJBD.DE/3/G'4HF;JH'=-:
@724
gcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaatttaaagagagcgtgga
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0G;DN&CI)B73D)(E)>DNM6(E.)'I>B;3)B-MKJ<.:*H,*0D@/'/)LE;*38>G&.(5F:F/KM4A.K+I:LF2L7
@725
cacgctgccgtagcttatcgtgcgctgcgtgatcagttgaatccaggcgaatatggcttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtggaagc
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0003&@;+:8/'@:E<2.GJ.+?CFI.M0E.3E?&D>GD::?&:'(85=,J1710CA67*3E=M9J0@D0'.@>GD4'*-;.CAMH8:)J/E+'+L.@J6.:H6HAN
@728
ttgttcctcggcaccgcgcatccggcgaaatttaaagagagcgtggaagcgattctcggtgaaaacgttggatctgccaaaagagctggcagaa
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0000.9FBM*8*8B)58I;=.J?5A16.K@)*-N=I>'@HC96+.AJ)NC?K*/CC60,1G1):(N&18.;M''7JHC0/,1*1;2)E0/6D@4'0'+:=2N>B9:+G('1&
@730
ggcgaaaattaaagagagcgtggaagcgattctcggtgaaacgttggatctgccaaaagagctggcagaacgtgctgatttttaccc
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000&K+@L:AK+G8<&5(:44(J:')L-8>&E(/394EN6-;N/F;;-1<.9,919&4HM(0?<:FA:H-*>3B5I*:J,:.G?13>
@731
gttggatctgccaaaagagctggcagaacgtgctgatttacccttgctttttcacataatctgcccgc
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000000'?=CAHA-MIGKA3(*-14IJ,:LH+9.5;M<4H:K/ME'@@CJC-;CAD6AD6
@743
attgagataatgaatagattttactgatgattcatcatcaattacgcaacgcagcaaaatcggcggg
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00-0DN?GG'C:<>@H')+>''D89MML;K,,L;4.457>,HJ;7L?M67G>BN/BN:36*KJ+@HB
@747
aatctattcattatctcaatcaggccgggggttgcttttttatgcagcccggcttttttatgaagaaattatggagaaaa
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00000<6:)LAM')E67&=4N'4,93JMFK&*55&7E-&&H?B+>@A,G/02:BG1I8DHALD.'&>+5'460LL(L7&;
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tatccggagattactcgatgagaacggcggttgttattctccgcaatcctaatctctaagttaccgcattattgagaattctc
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L2DB85E-9;,41'03=?+=>5)4@2=8D>GI5B7.M3D.'2=&60)4HI1.&LIH3*6N.4/N4'A,1,CN--)2DMH.4/.
@756
tgcggtaacttagagattaggattgcggagaataacaaccgccgttctcatcgagtaatctccggatatcg
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8=3GA+MK'C./E/*<)I968-J,&CH89I+)&>'/H>@:EH&5*/>D101>8L-I;F.?8K'CN3G&?.4
@759
ctcctttatcattgccccgttatgggtcgatatccggagattactcgatgagaacggcggttgttattc
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=D6+1:L)DG<@6K.8IBM>N:A,3L30G)&,<>I79A=/8JI:G3B+4K9E4+*6>D8G:E;N1+);KK,MM9*L;*DCH6<926=CG(-<@00	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:80
126	0	somegenome	844	37	4M1D54M1I12M	*	0	0	TCCACCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTTCACCGCCGG	000KNGI8CKN/'5+.B(7L3<('BHI=2,D&*GCIFF()DJ9A.N.-LH223/A491C+K@AI)09ICDN	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:4^C66
133	0	somegenome	855	37	48M2I17M3I37M	*	0	0	TATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTTTCACCGCCGGTAATGAAAAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTC	00000I708'.@;.'=*J<*-BJCI2+-:0*5-3I&>&*4BEH4J+=79L4KN69+F9G.(3>:)=61+5<.K+1+3,F)D'N;M@:47GH)E80M	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:70
135	0	somegenome	887	37	16M2I17M2D56M	*	0	0	TGGTGCTGATGGCAGGTTTTTCACCGCCGGTAATGAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCT	000'=0L-)+32L-.1(.:-:43&'3N:/G56E-M9F+7);D(8278=M@96A()6DC8C*J9(&H,)KD3?@/'8*1,CND*@59>LM3(	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:33^AA56
137	16	somegenome	893	37	27M3D62M	*	0	0	TGATGGCAGGTTTCACCGCCGGTAATGAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCC	?I(26?6*0D(GL?/+82EH'/@EKDA:)MI:8=<9(A;*,3NG>DA*DAKHA4,C'E:;)>C8<(4-015&F0+H7?I	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:3	MD:Z:27^AAA62
139	16	somegenome	904	37	16M4I67M1D23M	*	0	0	TTCACCGCCGGTAATGAAAAAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTACGCGCCGATTGTTGCGAGAT	/:B<'6'JEN3D22;9I+D/5F?NH-;62::9M?7CB6*3EE3)+&JBE'B/NE.FF?CFL=1>1GM4;=578<5:E,EJEL6AMF>?9HG=0EE8(>77(K4<'D0000	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:5	MD:Z:83^T23
146	16	somegenome	919	37	108M1D7M	*	0	0	AAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGTCTA	D'0B>,.@=)NMLN;'NI41IB.2LBI975I<;8>7.5K/HJ'56LM6I,4E;M38(3-BJHI/LC>;9@2;?'*HB/'2'14D.'D;.KCH80/)E-00000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:1	MD:Z:0G107^G7
140	16	somegenome	926	37	61M1D24M	*	0	0	GCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTACGCGCCGATTGTTGCGAGATT	+7CH>21.N/1&D&)M6'.9<3C2.+N62F23H&?+3M*6B+MCCH:6&5??6'5F00	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:61^T24
141	0	somegenome	926	37	61M1D22M1I7M	*	0	0	GCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTACGCGCCGATTGTTGCGAGATTTTGGAC	0*1A+,8:1DF&D1NL1B&M3'?,BKN:6784B>;IAB':;@-/6N:B,=J0+FG30)C6'CL.<'+K<:	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:61^T29
145	0	somegenome	927	37	60M1D46M	*	0	0	CGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGGGT	0000IDD:);6.2JB:/3LKL3E7-2)'+3&.5J2(:6*;J4(D@C*>;NA;?;(AA7@*K2J:1IHG&;F(7,.:'F;MK&2E.B=3-*(G-C9B:818I2J=@-	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:2	XO:i:1	XG:i:1	MD:Z:60^T43T0C1
144	16	somegenome	932	37	55M1I41M	*	0	0	TGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACG	,'N/I(D:2>/,770MJ&D<>)CEJEF+(L3+G9J3=9)@HHL>(M18,J9K/*=63(&?H*(0'M5.K99MH.72KA:B+&EB4D>E>/>)<2A:-C=+FG5>?.B8F&GA=C)E,/4)JH7F5C+@M,9))A,))83D<04.H)=L00	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:79
149	16	somegenome	938	37	72M1D16M2I16M	*	0	0	TGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTGGACGGACGTTGACGGGGGGTCTATACCTGCG	;I<:DDD)2)2F16)/(6-@1AABA;(4C*9?L2)+AHA;8,C5.'+,;+2/LB>BJ'B@B'*&20)>4E35=5):IB58EF*91M-2GGCH9>1,+@998+0000	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:72^T32
151	0	somegenome	949	37	61M2I17M2D31M	*	0	0	AACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTTTGGACGGACGTTGACGGTCTATACCTGCGACCCGCGTCAGGTGCCG	000).K7JA0F29G5(;H:,?3N:A9NI&F8)>15L1<@5A7?JJ5.HBA1NB58='3BA(@:H>&DE&+0>)A*.<,'(H&GG0/2L8(8<8'NN6F.:2+40*?/-3FN	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:1	XO:i:2	XG:i:4	MD:Z:78^GG30C0
143	16	somegenome	951	37	36M3I23M1D12M	*	0	0	CGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTTTTACGCGCCGATTGTTGCGAGATTGGACGGACGT	LCL?*JB8)&<2D0)<,0*2?.-N8N?JMN7FE7=L3?F)>73&N06&0(MA*,95M&B2NG/:09IH7F9000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:59^T12
150	16	somegenome	958	37	52M1D16M2D17M	*	0	0	GACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTGGACGGACGTTGACGGTCTATACCTGCGACC	BHGN,F5>-GIJH/1KK1=,DD;I=H&A+4(@CIHJH0:;6L,GA.''53(=M+50I/46<=ND9&MD1F98/KLE?0=3&H51D	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:52^T16^GG17
152	0	somegenome	970	37	17M2I23M1D51M	*	0	0	GCGGTGCTGGCTGCCTGTTTTTACGCGCCGATTGTTGCGAGATTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGA	00/C+K;>474J:N,K0ECE;DLMC++HE-*N7M+.DHH-=8ABJK8-C&-*0:<4*/@N./JM'=:N:I)19I,):'79N/>F?GA.898KJ>H:/6'?BIM31,M9HC@BHCC?C.NNG9',	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:29^G29^C54
160	16	somegenome	1006	37	38M1D12M3I45M	*	0	0	GAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCGCGTCAGGTGCCCCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATG	*D=IA@>=)(/;CEF00N/JG,-@D'NI:?07E>HIBE6M:E';):D5/GA1F>9>?84KLH.K1G+)&BJJ?3@D7LCK973-<>5/,E57(00000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:38^C57
162	0	somegenome	1012	37	15M1D29M4I51M	*	0	0	TGGACGGACGTTGACGGGTCTATACCTGCGACCCGCGTCAGGTGCCCCCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTT	00000/60K<.C;/E7N:NG?&FDHD/J6?J25.=C,/I&C;ED>&C3.@+:-1**J=&LEB4+->JG@F4D,.F;EA07(6@?I-HGK;4E+HK5/553M6,>52E**I4=+D65G0LB00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:114
166	0	somegenome	1022	37	5M2D77M1I13M	*	0	0	TTGACGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTTCCTACTTCGG	0H(1;C61L'+F>1>(.83L>99474AE<2MC4./'J6;JL<7J.D?/=,//)I<,.;I(41'@AC&,<27H2:87G<&5NM)432&K372?MM97	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:5^GG90
168	0	somegenome	1056	37	67M1D7M	*	0	0	GCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAGTTCT	0;&6GM3<,86-2CL-2GH&(,KL>-9MFIG887I;F5@LL/FKH+&:17CB+9NF9,8/L9@<**E':1676=3(DJEIG>0/N>A>IH>+@KD-0KLID4'6B7A+G'=,:K=*/(IF:FFMH37(M0?5-))K/-97>I<>N?21/5M7M//.)7CD5??1000	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:5	MD:Z:86^CC19
177	16	somegenome	1151	37	19M2I24M1D23M	*	0	0	CCATCGCCCAGTTCCAGATCCCCCTTGCCTGATTAAAAATACCGGAATCCTCAAGCACCAGGTACGCT	2K.M,B.K+H6CH/6(EDGILH0C2BK&/4K@'N(CGE:'E)..'M,?3(2277=000	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:43^A23
181	0	somegenome	1155	37	28M3D58M	*	0	0	CGCCCAGTTCCAGATCCCTTGCCTGATTAATACCGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACG	000.LH5:G/+<26C&DF=5HL4-.36E'AA<@5;&;*-FNHL)0;)@EL(9GFI7I/4064DNA+07&3JL);&5L4(7'J@B&I	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:3	MD:Z:28^AAA58
184	0	somegenome	1163	37	20M1D73M1I5M1D5M	*	0	0	TCCAGATCCCTTGCCTGATTAAAATACCGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGGCATTCCA	000**925<9L,(MEJ9'B7H>A;&:;-6&CM*74F)GGI/&5<3CE0+>4-5H,D7JF.-F(07>3??D8=HL?	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:20^A78^T5
182	16	somegenome	1164	37	6M1I13M1I77M	*	0	0	CCAGATCCCCTTGCCTGATTAAAAAATACCGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGC	,H?N=,49E(D:+;-9?.@'G7749>'HN6&H?+'7/:+(89M8&;J/52*D5&4(8:?G62+A&@0:F8D?3FC759F.A(6=2618(7;EG2,/.LN=C)A97(2*K)E((*,G5D?*C-N4??DME&ID'7'*3*0FBBG>53H1N-G7NI11,(9K:4&6);1B?=J*+3N+:*NA1?=;A4M=0F;,K4JF5(0/6D&(FF9M?J6@1/M9LK6>J6L+=)35FJH.5A:@&=JD&000	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:75^T37
185	0	somegenome	1205	37	52M1I17M	*	0	0	CACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGGCATTTCCAATCTGA	0005,B6(1MJ*9;+LB<=FIEKFG1E+@5BE-947?C2A8'H6<7G&8N2+14-90&A;7=?E*>FF'M	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:69
189	16	somegenome	1209	37	53M1D28M	*	0	0	AGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTCCAATCTGAATAACATGGCAATGTTC	A;C1-C@2IG:*-?+@;&41;;LK52IE1B	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:53^T28
188	0	somegenome	1216	37	46M1D24M	*	0	0	CTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTCCAATCTGAATAACATGGCAAT	JIF22>.NJ0/45N.BB1*A&.M+,)E)2;:<.HA:1>1A52JMM80;I*E8@&AB1I:CJ	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:46^T24
195	0	somegenome	1221	37	41M3I53M1I17M	*	0	0	TGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTTTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGGATGGTCGGCATGGC	00000)72BLGB>;:(/)&>@((?&39-N5F5>DL@H<>4C6J3N5KM76GN41/4D7)NM;@N+,E)8,H7*I?*	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:111
192	16	somegenome	1224	37	92M	*	0	0	TGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAGG	FMHDDH73FG5&M(5;J@;)A:>D4'K3M+)LJ(4=D<0NJ)KE0:(AL80>84?G&LCJC211+A=.1C@2FJ('IJED;E)6K.>);=E0	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:90A1
201	0	somegenome	1285	37	20M1D36M1I8M	*	0	0	ATGTTCAGCGTTTCTGGTCCGGGATGAAAGGGATGGTCGGCATGGCGGCGCGCGTCTTTTGCAGC	0000:*NEE?65I4H;1+A/;1*-H:=55FK.=,2&@1NH0N@D>IC/6	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:20^G44
207	16	somegenome	1303	37	58M1D5M1D28M	*	0	0	GGGGGGATGAAAGGGATGGTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCGTATTCCGTGGTGCTGATTACGCAATCATCT	IL+A0>3=33)-9+'<;9@M)++/B8DI8+G2=00	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:2	XO:i:2	XG:i:2	MD:Z:0C0C56^C5^T28
205	0	somegenome	1316	37	26M1D18M1D26M	*	0	0	GGATGGTCGGCATGGCGGCGCGCGTCTTGCAGCGATGTCACGCGCCGTATTTCCGTGGTGCTGATTACGC	?-E>9B;BJ7/51BA?:N0>+(:-?42:;N;7:-;@8IA.90.*	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:26^T18^C26
210	0	somegenome	1321	37	21M1D71M	*	0	0	GTCGGCATGGCGGCGCGCGTCTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGT	00K9EH2066:6B;;84DN9KB9'9K2L?LH-'&FE.,&GMH0'';.(ML21:B<)2,F7F:@3;35->+NHMIC=7HK*I*1,55A3:1CN6,F?;'5*=?(-))=-=A179M9C)M@@8B/=GD*J*5H&>9=L>;/0HB1)3GJ=)C:M&5DFAF;;8I2.0/-48*1:+@FK	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:98
214	0	somegenome	1358	37	3M1D5M1I90M	*	0	0	GCGCCGTATTTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAA	00*C)6CJ1KC(B@537DNHD=:'7I=7-62>0KB@9'HH/,;KNC;LA6@,,DI+9&+1L.934D?&B:*IMMB:73KKE=9L>3275,1-B;)MA8*	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:3^C95
216	0	somegenome	1375	37	38M5I63M	*	0	0	GTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGTTTTTTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCT	00000@K9(,DHFC0'+8(NC4F50H000D165&F/2M3GE9=6:3?*A38?<>/:=A89(G0+-9L,'.'AHHAE((IE'9/?,')9E.253@3:EGG3J'--J,	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:5	MD:Z:101
219	16	somegenome	1387	37	64M1D31M1D17M	*	0	0	CAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAGAAGGCTTACTGGAG	ND+9GGL6FK7L(L+<3+1./15L-@96?*E03KHJJ80>LB661+28HC&4G2);2,C?'(.&&';JBMA?A?,A7'?B(39B2>00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:64^G31^A17
218	0	somegenome	1405	37	46M1D28M	*	0	0	AGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGCAATGCAGGAAGAGTTCTACCTGGAA	9(D-C320J22CKGGM;:48BA@A6?A4BKD-;5(3,J1CI87KA6>/?)&NG44;3A-1@2)*D:(9*2-09F	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:46^G28
220	16	somegenome	1411	37	40M1D31M1D38M	*	0	0	AGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGG	948@7J77G6A>'18)BI40'3J*A=)(@5<0(0.&86@6I++'.4H3.D=7/:KL(;,+E<;)538)(.?25+I55AN>@,0J3?>E;=@91N7G4CEN+BG>(BD8083F96*<>412;D'JD9NI.00	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:66^A45
224	16	somegenome	1431	37	20M3I32M1I50M	*	0	0	CGACTGTGTGCGAGCTGAACGGGGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTAT	<))2>:A(.B:C7>KCK.&N/F@C50/+H91,868I@>,J-AN,I6,-..0B>(5>BCM?CFI79@;D0GBJBG@8KDJ(,+EK@5.2,71;2BG4@IL53JA0(A9J:*?F9FA&L;'/D/H'(HD=F+K;E>(D54(+00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:66
225	0	somegenome	1458	37	81M	*	0	0	GCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGT	E<,4@0B551<40I&:B>@54=;>+/,GAKAI9I&4139F&=:5)<3EEE3N))N2L6BHD':'*N2;AM<,17@5D)(@2	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:81
227	16	somegenome	1493	37	69M	*	0	0	TACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCT	,-*/KMDN71)-=M6&>85NC=HNK'.79,/+282.F5BF+5/G=<(J21.J1;-L@-2	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:69
232	16	somegenome	1542	37	56M1D33M	*	0	0	AGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCGCGCCAATATCAACATTGTCGCCATTGCTCA	@9?,>I10(A'2*',:D>,@C9/02N1D,D4BH'?,BFN92B&CN(B*-'1A)==>*)D;4):(&K<:=F70,M.D)08D7&)5+GC90	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:56^C33
238	16	somegenome	1571	37	14M1I78M	*	0	0	TCTCGGCGAAATTCTTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTG	CED2;98896*(<*,30.?@5?6>8*AB*=HJ3,@9HH?21/6K8HGMM&L61L8D+*A=+=L1A0(00	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:92
237	0	somegenome	1580	37	5M1D46M1I28M	*	0	0	AATTCTTGCCGCACTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGGATCTTCTGAACGCTCAATCTCTGTC	0157B7C<<=MI/,(IB(F&<,N,56BLAM-JD-4I*M)C@E85LFAI+6AM9AJAA&31*0N;I-MA'*KB6ELF@I,J	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:5^T74
239	16	somegenome	1584	37	14M3I34M1I35M	*	0	0	CTTTGCCGCACTGGCCCCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAA	=;9&:&37M50H?3(KA@.D/,NN;:C4B3KCA2J8)2=/0=?/@;E((2D7K4H'9D4N=GB(M/06>'=-N=B*59GN2DH0000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:83
243	0	somegenome	1604	37	28M1D32M2I35M	*	0	0	CCAATATCAACATTGTCGCCATTGCTCAGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAAAATAACGATGATGCGACCACTGGCGTGCGCGTTA	00')H5K4H,8LE12H-'+/2?I,-AN/G99L:3&*(	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:28^G67
240	0	somegenome	1605	37	60M2I7M	*	0	0	CAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAAAATAAC	00000=6G+NN&HM'>NC2C3D/+1F(FN=7D<345)@<**?;39?K7*'13EG@/7=J0N*HF?7I=.	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:67
247	16	somegenome	1618	37	14M1D32M1I51M	*	0	0	GTCGCCATTGCTCAGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTT	0:;,AFD-:+J(9A2*)7*6B(/6K6ADK/3E,3;7A=4GI*J8:.,N*E/HB:N&;L+CN1D6.F-F0F':.49J6A6B2,0*//A10LJ000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:14^G83
253	0	somegenome	1629	37	36M3I71M	*	0	0	TCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAAAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCG	000;N3C2/@<'71NE1J<5B<-LID0H*,+N)G)E,4)@/4=3-:?L;-2/(M56:LI1*:N.(AE9H96LJ6A=D1(:&N;0-:A>A0.JE1MM5LL@GG	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:3	MD:Z:107
242	0	somegenome	1630	37	2M1D32M2I30M	*	0	0	CAGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAAAATAACGATGATGCGACCACTGGCGTGCG	00007:?G*5843,?6=9,6JLF4=H)1J0E430000	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:3	MD:Z:75
249	16	somegenome	1634	37	31M1D60M	*	0	0	GATCTTCTGAACGCTCAATCTCTGTCGTGGTAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGAT	.A'>>)9L339I742.G6IGG13L7+'8.CB.(023?G5(-L><'&&F'51-G>D,33M(7>4)2@M'ED<&9'&7)9*IJC/+-6M3N(1@)2?:)9D((4@-(:.6+)2K;0	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:23^A54
246	16	somegenome	1645	37	20M2I48M	*	0	0	CGCTCAATCTCTGTCGTGGTAAAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCT	.G02/*AL-E4K,KB00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:68
255	16	somegenome	1647	37	18M1I76M	*	0	0	CTCAATCTCTGTCGTGGTAAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG	H>M-=856/7+1MFDKB52NC1:6I,G)&.H,8EHFJ@)/4,9&4K,C0:=?F.2;HM5,0I8CK?=H5;7/JH-.A.;<-GD.A4A'+DH.D22J92N;>(J+7H6<9*	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:10^A104
251	16	somegenome	1659	37	6M3I65M	*	0	0	CGTGGTAAAAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGG	>5.I&HAAG5CJ&E0*@)@L?FC>*/K0?8-.59>,=?F-E5-:L0-6BM3)/BK,:LNBN7;9;5)MF2.HN=KN+LCA7J',.KF/IJ.<<,BN;I.=	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:113
258	0	somegenome	1676	37	65M1D28M	*	0	0	ATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTGTGATTGGCGTCGGTGGCGTTGGCGG	H-=2FK3C7*H7.9@&H:F4LD=(;+&.&I<3E87J,M+K+;1C2D-(=IIA47I-E46N;G7:E28K,0L1*-I?3/NG77H);&?*@+N=?	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:65^T28
260	0	somegenome	1708	37	33M2I60M	*	0	0	ATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA	000'9K5(G4<*/4A0BI3@19/KFD@.J>MMA96/A;-G6,2*/LCB-941HFK56=5L,29)8AI942(,/L5@+5KJI?/@;53(93BB1:?J2=FN;B&@>.032/:M+1B52L=,/*DB=2'G7I<.J2;8H:*I>;GNNC@9G-=M'LKD;F'6E	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:33^T69
261	0	somegenome	1709	37	32M1D57M2I6M	*	0	0	TGCTGTTCAATACCGATCAGGTTATCGAAGTGTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAAAGCT	000/K4H&(MN,0'+:&=5F0@-:B@AM)(A1IDG7.D7BF;)=1,DI56MBF>L<*(D1'=0N.1M9&74C2).4J8J)KG?,=6>C*@-BD)4-ED@9,>3A@1M/)0L1-D-'2DK0;;0000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:97
264	16	somegenome	1722	37	19M3I58M1D14M	*	0	0	CGATCAGGTTATCGAAGTGTTTTTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAGCTGGCTGAAGA	J1>FA.3)G-A'@D&*.(M&J2EL?E87+-07N,BA1ML.D*)LN=3F));A:+K)?;?.FH70C>'KDJ):MKGH2=@I6*/'E-K68?,000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:77^A14
265	0	somegenome	1744	37	55M2I15M	*	0	0	GTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAAAGCTGGCTGAAGA	000('9@7C:L8M/L7H//A-M:(-@FH.G255MD0M+;:1(DLJCH<.C,9+1N<-F38=9*NG5:A)I31	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:70
268	16	somegenome	1749	37	93M	*	0	0	TGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGG	&?50.LB;23&D2KD;29M+.*8.-FLC@M/L-1A1'+LN?'LK)J4=68'-4J(D9L.C+539C@=E6NBGHJ&-:G&AI*;0*;-9+NK6F7C7C:8(D16'JFG>8C40,,94N)5F/L'.64J:DJ4@4&@I05=C('2D+0C	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:60^A24^GT11
276	0	somegenome	1772	37	27M1D16M3I71M	*	0	0	CGCTGCTGGAGCAACTGAAGCGTCAGCAAGCTGGCTGAAGAATAAAAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAA	000),<+H(F48.:M?0656FJNH,.2@A(2ED'IB8.92,:9KH7@5B>5E7'5J?M&)))?:31.M--5;=B+J=F00&7@.9)6I3@<)@>?3G:2AD.63=/F+:87<.7.=F	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:27^A87
272	16	somegenome	1775	37	24M2I67M	*	0	0	TGCTGGAGCAACTGAAGCGTCAGCAAAAAGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGTT	9'0/E6*@B60/9?3N9D.C;EJ4+76K.E89N&7<3L9&CD44A6(JNLI;828=HF7,5C00	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:2	MD:Z:89C1
274	0	somegenome	1775	37	24M1D16M2I60M	*	0	0	TGCTGGAGCAACTGAAGCGTCAGCAAGCTGGCTGAAGAATAAAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTA	0*216ML?J*M(=8N8&>KFI0N.D7FA7IAH6'6H/N&(()FAFF&F-'E5&L7L6E,,*JI/+9&@83C/KJIC*IK)5*2H662+N	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:13^A67
281	16	somegenome	1803	37	13M2I76M2I18M	*	0	0	CTGGCTGAAGAATAAAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAAAAACTGGCAGGAAGAAC	EDBD0?.?61A(1H*422,K/;@@G+'2LFD>,*,J4=4CD)D/9?,NFK3::N'5(BH2-E4L)6(4I'C>?7;7.;B>0>E(@A1&?E(0&<=0)F<*19/5I<20000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:107
283	16	somegenome	1813	23	102M	*	0	0	GAATAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCG	.27)+*A;=0C;9I-''A=A.:@H,,59<5J33AL>8,3(:='CD;@9A2C(F(G5GI5)6/D7N93=A3=5>6(3'.B21I4H=452+;*LD.?7@2CL6;	XT:A:U	NM:i:3	X0:i:1	X1:i:1	XM:i:3	XO:i:0	XG:i:0	MD:Z:0A1T0A98	XA:Z:somegenome,-1812,4M1D98M,1;
284	0	somegenome	1817	37	75M1D22M	*	0	0	AACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAACTGGCAGGAAGAACTGGCG	(4-*2>G*04M8:)C@+E10IEE,0/C6EL08=9,.)NC5,I:)+7'&82'JML;/.4GHCC?G,11I3IDGI/(=1KLM'?1C:5=6DG8=-BHN=	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:75^A22
288	16	somegenome	1827	37	65M2I34M	*	0	0	CTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGA	AKB/E135&*&.40=*G974@C6EA@J@1I9H/2L<4&;ME:E+*&3C>FN/0E&J>26HG8C:3>22K&&-KB*,9G7&KD01:5L/6.8779K''4*9:L6>:/5H'.6L1@1G+7BD7L:K.N6*04&>F7>E'B)D02=(IE,6C94B.(.?K8;>/G>,6FK8*1/=CC54=/>3BNC8=F.A=EBFI>5M/C&,@N5*8@J4FKLA404/4;N&'2B3,G>CM8)4*:.F7;@EHL*F/;A@).AEB:/23)J60L)M7BI	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:60^A22
291	0	somegenome	1833	37	59M2D27M1D24M	*	0	0	TGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAACTGGCAGGAAGAACTGGCGCAAGCCAAGAGCCGTTTAATCTCGGGCGCT	'LA0=M/&=,I75JLH7MDH?1-6>1N?9L2'9,MH-)I382>L3/GLCJ&-,(;72.+H2?8@8,H*A)@-?@7D5MLD6L/GE	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:59^AA27^A24
280	16	somegenome	1835	37	57M1D12M	*	0	0	TCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAACTGGCAGGA	1H*)FD(NF19B(F708AD+GA<.LKAJ*2:1*36N:)/+/:KL).;J78?E5=.1@A/(JG8612&32	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:57^A12
282	0	somegenome	1841	37	51M2D18M	*	0	0	GTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAACTGGCAGGAAGAACTG	<+?)=L7@N2FGJE>>+ED1J9B5;KFEIE&//)4*3C.A8H?3C0C:GC)<*8NKL(@@@46AEJK)J	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:51^AA18
296	0	somegenome	1853	37	39M2D27M1I44M	*	0	0	CGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAACTGGCAGGAAGAACTGGCGCAAGCCAAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAAA	000>G&?F4,:>GD-)ILN;-7>(97FNC5C.@I;3JE(101<0K1;K'7F;M9?4DL.K15C/L<=K9.F3>A33.,D'27<,26BH5E?'H++3C5,>H/MCE95K=6J	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:1	XO:i:2	XG:i:3	MD:Z:39^AA69G1
292	16	somegenome	1880	37	50M1I9M1I8M	*	0	0	GCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTTAATCTCGGGGCGCTT	.1JKK23:FGH(:FAFL4*>??*I)2K3*?D0/-+/300	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:101
306	0	somegenome	1908	37	22M1D29M1I46M	*	0	0	ACTGGCGCAAGCCAAAGAGCCGTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCA	00BCKCG(KMD;N::BI3?I4)4B*:8H1ID;:/BL-1CNHM0B)@/=C3IJ&*L-=L&G4;'.*9>?ND=	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:22^T75
312	0	somegenome	1932	37	7M1D20M1D86M	*	0	0	TAATCTCGGCGCTTAATTCGCCTCGTGAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAA	:+.&G>&*C/10)3A@.LLA&0HC-J45;.866L+F@A/(H.-(F@N11:39;FAFHHH9BK2FG<==HJ7;GA34ADJM*7C.FK*'&/<*C.EM0=6:A=G&M,;CI:?9J	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:7^G20^A86
311	16	somegenome	1935	37	25M1D19M1D65M	*	0	0	TCTCGGGCGCTTAATTCGCCTCGTGAAGAATATCATCTGCTGAACCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGA	JE;AC363K'/,+7JBI5G>?BEB&?JN/0)F'37<@N)E/3E:+9M7/N9*E'>6JIDK:57,B'4BAG25J,M0*0(7M1-<3(8;&ID83K''/:7.B?A<8-=N(4(5L9.L1-5*?HF;+9:=9?==N'/(,(GHBD2=I&71A93=*058LNAI0*?98=D3MH2>=(G=?6=4:D.+72*3K75EG>>?*'+-@.L'CM<&D-CCLH5M9*AG+GM)1CF';16D(4'6:21K<6*JIA-)B&&E&,M32C00	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:110
317	16	somegenome	1984	37	85M	*	0	0	GTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGA	>(K;N*8@'LF>G:@@I82@AK+@L9GFB(@(A/2*D=(F=5'HE@30MM-;MIG38>**.ADF'(>/1CMM&F843E;>+M&)8	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:85
314	16	somegenome	1999	37	50M1D14M	*	0	0	ACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTCCACGTTGTCAC	?>A@-(2H4+&(?792@@GN@&6J1'NA,)MC5B+9+49GJ+MN:G;F7F:K1E;J(?8L5MMC:(8*B0?48EJ'	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:64^AAA18
320	0	somegenome	2026	37	22M1I23M1I23M	*	0	0	TATGCCGACTTCCTGCGCGAAGTTTTTCCACGTTGTCACGCCGAACAAAAAAGGCCAACACCTCGTCGAT	000F922=>G>+'I(&D=>=5'2'09)H@I,BG;9>6/EF/C,:5(8,A=8NC*2K*I@L*.MH??,))-C2'3;(*)3)/,;-.-K26,K7+30CN,+0M=/@B1E>H?(/((NMJ)H6&,BD59,)=<;M22K4,J99(7I22DM'N)+FJ,EK2C-	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:12^A102
328	0	somegenome	2062	37	9M2I55M1D39M	*	0	0	ACGCCGAACAAAAAAAGGCCAACACCTCGTCGATGGATTACTACCATCAGTTGCGTTATGCGGCGGAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGG	0000&6>MFL'AND7CLHHBB&,4)':,3L:8MG9/80<-H39L3BIILDC?HL8>L*;J./G.9M);?8K28+3GN:&86FKE>D=@CN;NF//)*31J;(/*K	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:64^A39
327	0	somegenome	2074	37	81M	*	0	0	AAGGCCAACACCTCGTCGATGGATTACTACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGAC	0B+>C)3E7&.K3J=-)3L*:./6H,=>2KL?6A07L(.90?&33(N5:1LN'8L>.912(574'E0G54M'7.LJ'L7845D;*?2CG,6A)&FK3&3A@<7?LGMI-?-G4@MB7F)AA,0L581<>G;33/G*F=/D(00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:80^GG7
332	16	somegenome	2094	37	32M3D35M1I20M	*	0	0	GGATTACTACCATCAGTTGCGTTATGCGGCGGAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGGCTGGATTACCGGTTAT	LAF99I<0J1,>F.F/*B8/-*I(C7G?F+/).0K08=4/-AJB4:=4K'(5,G='?8HN92+,(367)J-/HD=675&8C1+7H.EEEEBC9=>IKA1B()B+>/;,E/<,2@LH3	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:2	MD:Z:0A67^AA25
339	16	somegenome	2162	37	33M2D61M1D4M1D1M	*	0	0	TTGGGGCTGGATTACCGGTTATTGAGAACCTGCAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTTTCTT	6:)L.G4@K71J@(?29+?4I+&NGCH>7::3598L2:;&7'<'*NA&72@;1BF(&90>NL?8B7.<'66>K=:8;3NKCCN)9:6;(ME?B.-J500	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:33^AA61^C2A1^A1
338	16	somegenome	2169	37	83M	*	0	0	TGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCTGGTT	/27+(M2/I?CD>:494D=AK:A:7-;/*:?K'21HLK'MN/':&.809E3'@E,@BFAA-9HB/GN	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:83
341	0	somegenome	2188	37	7M1I90M	*	0	0	AACCTGCAAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAG	000M8KAM-LK.DEB697+)-NJ9.@>/2MG6,D:1LB;<*?JJ&&)2B89)NEJ.DCI(&<,IN)F?0,&.'B,6E8I<;JE,,H@57*=N'7I=4A	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:97
343	0	somegenome	2193	37	50M1D11M1I35M	*	0	0	AAAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTCTGGTTCGCTTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATG	000F8:+G4;'N054J?&G.>':12@6231-75J86N99G	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:2	XO:i:2	XG:i:2	MD:Z:0G0C48^T46
344	0	somegenome	2199	37	44M1I49M1D4M1S	*	0	0	TCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTCGACGAAGGCATGAGTTCTC	0CHA87M&MN?L0.?+'2GL/+++E)LH,4.C68D:7F=7J6?1/F<)ICLKCE7H&,.7;JKF*.A;A4-'E4&'(;(LL+7@/+6G)H@3D18*+F,	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:4	XO:i:1	XG:i:1	MD:Z:78A14^T4
347	16	somegenome	2204	37	88M1D17M	*	0	0	TCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTCTCCGAGGCGACCAC	(L9G'23+96*6)L19M;*,A,+)M5=L&)29M)6.+.964CH=GMB3/CLM-5G713&,.:-&)&>/HC6+-HDKB:;00	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:88^T17
348	16	somegenome	2243	37	12M1D36M1D25M	*	0	0	TTTCTGGTTCGCTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTCTCCGAGGCGACCACGCTGGCGC	3LL416<5HB;,K+',&7N5++/<432C0*>0E(DA)(-4NA1444L>2B8@6/5'FL+.I952>A&AC5-:+	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:12^T36^T25
352	16	somegenome	2256	37	64M2D3M3I30M	*	0	0	TTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGAATGGGGGGTTATACCGAACCGGACCCGCGAGATGA	?'6I>>8M/GD-(<=&CJ9-(AFB,N*54L),?3EGJHANH)4>E,M@H:2?70J8=731F@;+7AB03D':J.I>A-;1:;)/'D@G1GD'(5:88I00	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:4	XO:i:1	XG:i:1	MD:Z:64^GA33
350	16	somegenome	2260	37	58M2I7M1I23M	*	0	0	TATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGGGGAATGGGGTTATACCGAACCGGACCCGC	JEH46.KG94EM:M8A/BD92MIN6C(B&(D-EC6,E(L477.&),N3*LD:6*6A4>+(8BM6I'(/G0843C71'F?2IC6*M1CKGK)L/(;H@0L1?2;C(7,B.3C0H>47>MK:0@CGL0,:+D3A5,-KL1I>@-;<0,4C@(-L	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:21^G18^G55
355	16	somegenome	2289	37	3M1I65M2I21M	*	0	0	GAGTTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTTTCTGGTATGGATGTGGCGC	'1H4DL:2C>AJ:A9*;&0/(5;BK:-(?-&HDI;C9,6)L.AD:.(:)H;D0E<-?26(M'=*ACI7F3:I0A2L.B&,MC*&6HL1')<)2JBBE-62N:)=<(K37G>B10@C+*G03AG>8)?3CI89A<A8=>68/	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:41^G15^G26
369	0	somegenome	2505	37	19M2I56M	*	0	0	GTCACAACTCGACGATCTCTTTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGG	000F/6LM1;2:*0IK'J()HFFE3.8.4-9K<4@FA7*25G)C;?7;B3H*:&@B?K<=	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:75
371	16	somegenome	2525	37	71M	*	0	0	TTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAGAT	J1K,&MC>6)C?=?->7)B5;027:>(0NH/>G+N*'58HB>7=9L5:M:0)K*8BM>EMD-0	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:69G0C0
375	0	somegenome	2547	37	17M1I29M3I49M	*	0	0	CCGTGATGAAGGAAAAGTTTTTGCGCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGT	0-34)/7<.+14;E8B;)I	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:95
376	0	somegenome	2550	37	14M2D27M3I51M	*	0	0	TGATGAAGGAAAAGTTGCGCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTC	7+@5EJ:6,G:E5;AKDL&4HB'><)E*;BL*CL-H=8D+*BG'C5LH)*/'D+6+E?E&MNI2D><*9;57<2/476B=MH?'=38D,M&-CI'FK>)+--;G@-2I-A1(H8.=*G7'G4?(819/JL.@5J&@)JFLI8>+7DDCD000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:82
383	16	somegenome	2632	37	28M1D5M1D53M	*	0	0	GATCCGCTGTTCAAAGTGAAAAATGGCGAAACGCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGAT	*33C0LA0;D62,4K@<-F<)*>44<27K+;4-)/FIJ.B-<.G='(.3,-MN:)?N3468'=63CG*&(JH4I;7I@4H=;C,&56CL('(JI=@5D36K<2.-+4&,=B&?&:-)/A+J<,I@AEI'>K+,,/A1H;00*K-IJF20;2BE/2LI.3440F:K8*;D+6@F:-F,+&K-C300	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:74^G29
386	16	somegenome	2663	37	64M1D12M	*	0	0	ACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGCAATGACGTT	?M0KMD7A+E?3EEFF0GJE.*J+2@4(MBFLJ,-G<94;0M.?I*03NL;6A030BLF-@6,:F+K(F:N9?)EE	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:64^G12
389	0	somegenome	2678	37	49M1I35M	*	0	0	ATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCTG	0000-;(G/(AI))FNNN;-M.38=((C>*-G1C,7A:-HC5@.60(.:43AG-3@GC'E44''>42&-M=6C:K+C>NHI@:?8	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:84
391	0	somegenome	2684	37	71M2I12M	*	0	0	ACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTTTGCTGATCTG	00JI-0318GFGDGD6@G'MF=?/M3*K@,B?.*F6.2H44D5D04KK7.=6F:AHFE)7L2F6(I+1;CB52@?-LF)'N3*F?	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:83
393	0	somegenome	2692	37	63M1D24M	*	0	0	CAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTGCTGATCTGCTACGTACCCTCT	0'.*;)E'&>CN*<->,:C>L7GL(:E;@/E7DF1M(-?F11L@)JEA>AJIM*D-*:8/:M)&LMCKD/@,:6/E26@.(	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:63^T24
392	16	somegenome	2694	37	33M1D27M1D17M	*	0	0	GCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGCAATGACGTTACAGCTGCCGGTGTCTTGCTGATCTGCTACGT	I3L&GE)1H0M?I>GC>6D0;43C+0@D50+56D0)'>&H'J+DAKEM/:1B:);(*J&'<-?CBJ36C.-MNCJK0K9IK6I.:)84=FD79'9&:)FMLA6'9@7C9=(B=/G+AD2?0KH7+>L1ANI,51CJEEN=.A1+M.000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:40^A73
405	16	somegenome	2787	37	61M2D11M2D27M	*	0	0	GTTAGGAGTCTGACATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGTTGATGTGCTCGGCGGCGGTGACACCTGTTGATGGTGC	=:.>6D30E@7C1*A-6EC8A3?960AE/38.@+0&GK(AI'A.?7=6=(6*:GG@&<(F8E,18@MGD;N=*'N1AHK<9+.=/C=NJ+9IJ>(G7+-	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:61^GT11^GG27
406	16	somegenome	2804	37	13M3I44M2I33M	*	0	0	GTTAAAGTTTATGCCCCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGGGCGGCGGTGACACCTGTTGATGGTGCATTG	42I2CK'/6H6D/3A(:71&E*55J8<5((@L,D/B&K?J8348D.INB;=+4,)8>;2/K+L=6EE'NG.+II,(307IB:8-6/00N000000	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:5	MD:Z:90
410	0	somegenome	2849	37	12M1D61M	*	0	0	GTTGATGTGCTCGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGC	-M?,<00)N4NB+<(N):@(N=&J70)8'&BE/)76?8>*4>F<,>FHC:&6G>K/A)5LEF388IMJID2',	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:1	MD:Z:0T11^G61
419	16	somegenome	2855	37	99M1D9M	*	0	0	GTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTGCCGATA	F4CL202;AMM6*AA&JI:N71.N))8)L03>:*I7'D<(E/@9*;KM=8I'+5=.&*/:>4'5L?C=4?/5>M8LLI>)A4JJ)(16/F?*'=??5.E;*D0	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:0	XG:i:0	MD:Z:39C0G0G35
422	0	somegenome	2861	37	112M	*	0	0	TCGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGT	)?4:5<.(<7&:.GD41C67.FK8449NE4N<4)>00L+?.EC	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:76
414	16	somegenome	2871	37	84M	*	0	0	TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAAGAACCTCGGACGCT	/=D9H:I7FBJ50BLF5GK6GAG+?82?C<'G;-	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:70C13
420	16	somegenome	2873	37	81M1D11M	*	0	0	ACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTGCCGATAAG	2?:G/M&9I6*K..6+MG6.L@HHHN'2M65,A@E<;BLKE<0(&6/9<>,3*C+75:4(??L@1M)&D&9L,G>9,KL9=7D2E43FD+GG	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:81^T11
425	0	somegenome	2875	37	79M1I24M	*	0	0	ACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTTGCCGATAAGCTGCCGTCAGAA	09BCJMF0D609&=GCB0D1F(.;-AGAH);;74G2KJ(6I-0.AFF>;IBFI2';	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:103
415	0	somegenome	2876	37	80M	*	0	0	CCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCACTCTCAACAACCTCGGACGCTT	(;G5<107,F078J8H7D'61*C?-L63H9=M8:9N6;JD+;ELK-.)*3D&,&D30627NA<>L'DE/(L;',>:&K*/,;E-&	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:31^A41
417	16	somegenome	2882	37	71M	*	0	0	GATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACG	0F+F*H&)40.B43L43L&;M-NH/.?LL8>N*>2()J0AK?;MKG.;GA:0C)(D	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:71
421	0	somegenome	2882	37	72M1D11M	*	0	0	GATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTGCCGATAAG	;1@=>)M>1NB;IA4D0F5?+B:@,B9/AM:CN)0J=3+E>LCM*?C*B>:ID:AGD5	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:30G45
430	0	somegenome	2889	37	65M2I28M1D16M	*	0	0	CATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTTTGCCGATAAGCTGCCGTCAGAACCACGGAAAATATCGTTTAT	00C9=6K//GD1:,2-954'0FJ,CK=C89179,BL)(2L-GBM;C:7;?6G0&MH6CLFNN3>D>/5H&+(*3=HHF/?)&	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:93^G16
423	0	somegenome	2892	37	62M3I20M	*	0	0	TGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTTTTGCCGATAAGCTGCCGTC	0005G1EFG+AM,L,>,'E&B)K'N/658:4/II,&05/22@'554+L&).FD9-:<&+/+@;&.DI/=H:C9KBJ4.8@7G.)6	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:3	MD:Z:82
426	0	somegenome	2895	37	83M	*	0	0	TCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAA	6IE4EJ';/F5.<6A(B.BL8613)3'CBD,:I6=7?/72;3AN&+23B8524+'(J'&9E3K3C1GHBL&'02(/9EC@:A.E'I:C=?:,J@:2,GC4.=G930>*0N&5<)JM@5K-)0.>B+L9/J)/CKK68C7@I(D'H/A<56/IND7?'DMIN@AJ1&<1/?(/8-4&	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:89^GA8^T9
424	16	somegenome	2896	37	81M	*	0	0	CGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGA	=,IA===>;6M?5J/+H>?BN4N5=H:@IDCIKJH/6E/:+:C?G4@71;;A69-G+*?8,;=IKM>:I9;:&&IJ=E=61	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:81
439	0	somegenome	2926	37	59M5I45M	*	0	0	GACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAAAAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGG	0000:;(A;&)/HD62;)?AD&1)+2=JJA,06KF++1:(J+1BJ-*B5;<83&7/?/+B)NB>22M<88<+&LMD.&80B,:FGNF*B0*'IJ':K>+8MI<71BE-0	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:5	MD:Z:104
429	0	somegenome	2930	37	24M1D27M3I16M	*	0	0	TTCAGTCTCAACAACCTCGGACGCTTGCCGATAAGCTGCCGTCAGAACCACGGGGGGAAAATATCGTTTA	0000@38,(8LG039-*F=E5(6?(I*'=(6FD'D5&?J<4G'N@1@6D-M?=1=+0	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:67
445	0	somegenome	3040	37	14M1D27M1I30M	*	0	0	TCCAGTGGCGATGACCTGGAAAAGAATATGCCGATCGGTTCGGGGCTTAGGCTCCAGTGCCTGTTCGGTGGT	0KE-JDJ@.@&9N(A17*@;H-B8*/ELCN7G)1+G;9<=D6E=@'+>)055NCD(+0GA9&.3HJB(@A34	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:14^C57
446	16	somegenome	3049	37	11M1I22M1I45M	*	0	0	GATGACCCTGGAAAAAGAATATGCCGATCGGTTCGGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGC	,<7(32CDEN68HKA@I>N0EEF?GH;B>KN0-98=77J7(?EF?45(E)A;6KA1K3N1:'DC8C8@C..26EB4B000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:78
448	16	somegenome	3060	37	72M	*	0	0	GAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGA	4,4G*738+@0E>(*+5.AF7)L?)*B?IML.=J+=+6)6J9*'7*L=:59@C;LBCB.=CJIN?1?M/3643,H?:&L)@,?()FK-NK7B+E*DAI6,F257->:	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:66
451	16	somegenome	3079	37	74M	*	0	0	TCGGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGC	3<7H+E5:<,++/D?ND;=43?/<>8;N+?J*C?18&5?8E+->1&.HB3@EC:0000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:1T0C71
452	0	somegenome	3083	37	72M	*	0	0	GGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTT	D>C)2((-,;2F,7'/4+3-1,N/.JK0/7B.2(&J/-H9D*GF'+H,6CH'D1A+D&<(0:0:+,J>.A357J/?5L)CHL:3;-G=CJA7>?+I'0=..A5EN5KJ:'>9-MC(IG;000000	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:112
459	16	somegenome	3131	37	35M1D8M1I55M	*	0	0	AATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTGCTGGCTTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTG	N@9@3+2<'-+/'>I)M5AB-1=KH0>4CH0*9-/IF<*(+*N956=0CDI;,L<1H-E.*G.JLC,(2(+/*-&0):12/):=-?3J=@K:BN?J000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:35^T63
458	16	somegenome	3138	37	37M2I6M1I48M	*	0	0	ACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTTTGATGGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGT	@2IC4C1D5:)6B;-@*:K5E';==*D14?.KN'E'CDL0I0M2+-2:2NC/,DN5@HALMEBG7B;LM:C)+5E@06J@'4'6CC:G/00000	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:91
456	0	somegenome	3145	37	30M1I6M1I46M	*	0	0	CAAGCCGCTTAATGACACTCGTTTGCTGGCTTTTGATGGGGCGAGCTGGAACGCCGTATCTCCGGCAGCATTCATTACGACAAC	0075N??+-GF=/110GD801FE*H=(>3.,<;3.+3@2JIJJL&I*)0'2>*:K3HHL9;9,GB.-A-;AC'+139I/D5
    2IN&I,'F22=1:B(@JM9/L)K<:GNI<7F==	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:48^G26
466	0	somegenome	3166	37	9M1I91M	*	0	0	TTTGCTGGCTTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATC	00D4BA4;'C2I&9&6+N:<4E5*3;AI+L&-JLE)5N(6&&5>@56+8E0K>E?1<*F1-;4@2/9/<)/:-+M)-0:-EJ-;8-;H@KH+-4JH:71KI8.==6NJLKF.<+5/550.*LH')NNEB+@4GL9L/&:8C=9	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:3^G56^T8
464	0	somegenome	3178	37	3M2I74M	*	0	0	GATGGGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGC	005/6)F9HH;25-2A*.I*?M&FN&F208M/*8E/3E/(	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:56^T37
465	0	somegenome	3183	37	55M2D18M	*	0	0	GCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTCTCGGTGGTATGCAGT	&GA4&/DN8MF=4FB4?(G/8'53+=?DJA*;I*+MB&KF?L:?6/:E(*24I?)	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:55^TT18
469	16	somegenome	3186	37	85M	*	0	0	AGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGA	I/?JB@2=&01E2A?0L.EI.=FB9N8H&3+)M';;M?.H<&I(-6F+7*.3=-;*MFIID6+=?'H)?4F0I=@,IL2H/7/;2	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:85
467	0	somegenome	3189	37	49M1I28M	*	0	0	TGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTTCTCGGTGGTATGCAGTTGATGATC	000C19H>B6-C4M3,/36=I1?3B=>+M;MG8.?@IC/AK7GA3H/882<,I/N(0*'BA.0@:,0?8<,I@@@5GB	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:77
468	0	somegenome	3191	37	47M1D27M	*	0	0	GAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTCTCGGTGGTATGCAGTTGATGATC	,I9,N/=HDIAE?E'5J:+-<)6I&*@;0<(64D*N9N2-88.82)-26H41M9&M3H=+=9C88)K8(A9FA:	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:47^T27
472	16	somegenome	3193	37	45M2D30M2I27M	*	0	0	AGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAAAACGACATCATCAGCCAGCAAGTGC	IE*BE<@=;0+G>?M6+F9IAC,H<(5H7JI25.@.MN))E5M-H29(815.J&23L,)D5;?'E<4)8?=(M9/'0)3(C(9J>?F<+DNG;(*;+?3@?<,?MEN?,:J1+L(E8B==6D1FM4;:MA?D3AG.C(((N?M96I'1&K62M	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:34^T78
471	0	somegenome	3206	37	32M1D31M1D17M	*	0	0	GGCAGCATTCATTACGACAACGTGGCACCGTGTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAACGACATCATCAGCC	;7/C*014+A077F,7FN0MH(.L==F5I4?:>)C(('91K??:-M1	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:32^T31^A17
477	0	somegenome	3250	37	20M2D77M	*	0	0	TATGCAGTTGATGATCGAAGAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTC	0H;(K51G('3C.4JA.-5)')?8K0>8>M-13;67N:?M(3E:JHE.'*/C(;F1HK13=+KC5*2	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:20^AA77
476	16	somegenome	3273	37	29M1D40M	*	0	0	ACGACATCATCAGCCAGCAAGTGCCAGGGTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAA	-7D*1:&DM@+E3@KF*&.'CFC?',J&GEH6C&'.2&-K5?.=GN?,20&(GC46H>>??=<.G-LN70*J?I8:M)9K9JMNECN-64.89&B	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:68^G41
479	16	somegenome	3299	37	35M1D28M1I8M	*	0	0	GGTTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGATTAAAGTCTCGACGGCAGAAGCCAGGGGCTATT	;(/BG@2)(+,LG91(IJL;DD&I76NK7;EC6A>=
    =,A/IA5@FC))8JD&'*@LLG4>000	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:1	XO:i:2	XG:i:2	MD:Z:2G32^G36
487	0	somegenome	3342	37	21M1D5M2I43M	*	0	0	AAGTCTCGACGGCAGAAGCCAGGCTATTTTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGG	00M=/KA;DLN<'=5>-=;.D+C+L-E0A0,57)+GINN61,G9C@)<&F?&)INLEI@)KI)=M57L7I=	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:21^G48
495	0	somegenome	3353	37	10M1D46M1D51M	*	0	0	GCAGAAGCCAGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGC	0*5LIK.B260L+)2&>4/.A?864:)B1F'E,12)J(+I6BK?M6.A889+G98+<5;D>NB8@?.E0&CN8LEHI3*HFM':L'L(+JFII4HD@D5903):5//07K5BIAM)(=::(>@0@'L?KBK.20(K.?F4,<:.@N4AE/G0	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:80^C29
499	0	somegenome	3367	37	43M1I37M3I34M	*	0	0	TTTTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA	000000F92/J:2<:H+&BL&/I*?L28K2*EJ9F-GKE:HE))7:,M4M@6;1+MC:<2A9G()78AMC5B26H7JC,396&L2MN5,B@MC4,JA,FJ@HH8*H+K8+&*1<02.5	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:1	XO:i:2	XG:i:4	MD:Z:1A112
494	0	somegenome	3388	37	22M1D50M	*	0	0	CCGCCAGGATTGCATTGCGCACGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAG	00+4NA>EB>)M4ED=//J:7F5F.++@FE;&;JN6)?0-B2GJ)6G/9IE&LK9CJ<=N&&@LJ95F.*7M	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:22^G50
498	0	somegenome	3396	37	14M1I69M	*	0	0	ATTGCATTGCGCACGGGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATG	0000D'1='0.G8(,N)'H/5:,:8;.<1;:KFK5)6JME;0)?FE+(5D<;1L'I01?E+<=N;L,/7L;17I.INEJ8;?,E	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:83
500	0	somegenome	3409	37	89M	*	0	0	ACGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAAC	I,4BF,8&)D(:H>5.73(0*6B81<2A?I;;L1F;,:8IK:H@D976@M>7GCI)M,.''ML?*;CJ4-7+*J/NK4&GC(-NAE?5K	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:0C0G87
501	0	somegenome	3423	37	24M1I52M	*	0	0	CAGGCTTCATTCACGCCTGCTATTCCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACC	0:?;DH,&A);B)51H+L0(H7&@)=NDKK?A?CH7IJBA//./IJ7B,9N2A>JI**B>56A?3-E&B>J64*>AM	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:76
503	16	somegenome	3437	37	10M1I50M2I17M	*	0	0	GCCTGCTATTCCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCCCTACCGTGAACGGTT	ELJ7IL9FIA=7EKDHB+()N:N8H)&G(MDI:-/),,3:.F915:8=JGJF'?CD&'3MH&0L*C>0D6MN23E5')E9&	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:54^C37
502	0	somegenome	3446	37	33M2I33M	*	0	0	TTCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAAAGATGTTATCGCTGAACCCTACCGTGAACGG	009G>7BD9-?CE??)&C*>KCF6+@L/J8>A;9'IB8<-5)*6?6H,F.(B0I4M&4//+K5J,/4;	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:2	MD:Z:1C64
504	0	somegenome	3449	37	30M2I18M2I17M	*	0	0	CGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAAAGATGTTATCGCTGAACCCCCTACCGTGAACGGTT	000000G7A30LH0;:BI,LL='FD<852:-5D,C102E,?M43GNDMI6;FJHFH9NI>F(N-I>EHH.2.G=@?/7I?JAC7+GA;3'),9LEF?&CM;(@(8G6=I'63E;2,HJD,F8CCC44G3;.	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:5	MD:Z:48^C47
509	0	somegenome	3451	37	46M1I37M	*	0	0	TCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGG	0009BF4&4/B(<&L+482LKAK1H40@72I.>M-G31,(53?C'?G826A)LLI/GB+*4CC1L;88B:'L)+@=8CJ1G7>+	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:83
513	0	somegenome	3451	37	28M1D17M1D47M	*	0	0	TCAGCCTGAGCTTGCCGCGAAGCTGATGAAGATGTTATCGCTGAACCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCG	0.'7J6,H@C22HGB>M.(?*64@643&1@C,=->N+(7/(3K-@+FLNG,?E/J---GD6=*.>.&9'/AJN1&6N@(&F@JJBEJC67+F	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:28^A17^C47
514	16	somegenome	3454	37	25M1D17M1D48M	*	0	0	GCCTGAGCTTGCCGCGAAGCTGATGAAGATGTTATCGCTGAACCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGG	*,*LNIN;?6E//*G;/L/@=AK,EN'NHCD95/=7+888+1K:/:./F0&)A,DKB&/@@--'.NLBGG2+8H8I;	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:39^C26
508	16	somegenome	3458	37	21M1D17M2I34M	*	0	0	GAGCTTGCCGCGAAGCTGATGAAGATGTTATCGCTGAACCCCCTACCGTGAACGGTTACTGCCAGGCTTCCGGC	-F;A76F.8NKCKA+-G7+;2,&D19>I7NH78.1=N>-+I(H)E5M2+:6KE8>(M4=6?BH64638@31,00	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:21^A51
516	16	somegenome	3460	37	37M1I51M	*	0	0	GCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTC	(7@=/K2)D=*M*M.=L7:N@D7>&C//);K//@5N-,7@.8HJ4:4/(3'G38>>6B4?LK@HCH.<1(85'8D;.8@<30*EHI-'0	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:88
515	0	somegenome	3477	37	70M	*	0	0	GAAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGT	000&=K.@)>:J29?'@DGH5I+*G*0&B8'IB,K.JM2IGG4C9+A-&&END03(0000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:3	MD:Z:10A66
521	0	somegenome	3504	37	48M2I17M	*	0	0	GTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAAAATCGGCGCGGTAGCG	00K93->8:.':GA+'B@(2L);3A.B?+E81K@,2.@;?>C5E5;9*'>KJ*7M6562*AI&9C?G	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:65
524	16	somegenome	3505	37	101M	*	0	0	TGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTC	MB83L.E>M,26&-&7@/*:AB@/&*CCK8(J)C9B2E0NN&;4J@H0CG?+DD8IH.B+9M952,:K3L2GK2AGM68NL87M=FBGK*	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:101
526	0	somegenome	3506	37	46M1D36M1D31M	*	0	0	GAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCGACCTTGTTCGCTCTGTGTGACAAGCCGG	MN@B@JGKMN'/CGKL:288B*A,1?)?*)'.4I7CB@)+E-,73G@,8:,&J:F32>,M=BK+,J/G7F+FADHF<@1@?(L>&N;7GCB0*&A49D)A2K*83NMC;M,4@.67?NN/5)(B	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:3	MD:Z:88
529	16	somegenome	3519	37	102M1I11M	*	0	0	CAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAAACCGCCCAG	D-A32I)9410EG8;&/*(5/=@H/3>J7'+'*K=0J0@(DKEK@J>)0B1/(B/J+L?NI45A=7L=JH8+0-?6(AB)<0GD6649L-K>9'DA11B2?A@@9LL>96H900	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:113
525	0	somegenome	3531	37	58M1I29M	*	0	0	AGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCCGACCTTGTTCGCTCTGTGTGACAAGC	0K>*K?65**&=<-A.3NB6>K&FE2.>8J&865,D22I??L/;A@(.LJ&<0C9<7**M,4/A4,@I>CH;BFM/94+K':.C:BH<	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:87
528	16	somegenome	3542	37	79M1I8M	*	0	0	GCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAAACCGCC	7MC2D>813(>F=)@HK'3J'?J&<=NH7>N=9*+MJC/?>'I?<;,7K4D5&E@;5/G(6IG0	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:87
532	16	somegenome	3547	37	102M1D6M	*	0	0	CGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGTAAG	A56:9(<-,@6@N7'NI'C>H7MGK7/38)BD(?EH9L&6>.K	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:102^G6
530	0	somegenome	3575	37	14M1I32M1D29M	*	0	0	ATCTCCGGCTCCGGCCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAACCGCCCAGCGCGTTGCCGACTGGTTGG	0.'N3.159A)IM3,ED<'.JNJ(47087<4.23M+&@,':.&0G4-F&FKE026G*	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:46^A29
537	16	somegenome	3575	37	108M	*	0	0	ATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAAACCGCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTGT	&L,3::B6;?BKFG0IAA,-;,?FK@@ME'9',6)<=K,=(-1F572-J7)08*17@HH=&->9-FJ*+=17@/L&+<&+B9B,=LE=C;4=G32:G+3:7NG?L000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:4	XO:i:0	XG:i:0	MD:Z:49C1G0C53T1
531	0	somegenome	3579	37	10M1D31M1D29M	*	0	0	CCGGCTCCGGCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAACCGCCCAGCGCGTTGCCGACTGGTTGG	*(=1BNE1;7JJ-+:GH:)G,K>1>GC1,DA:BD(DE(/A:MN.:IL/?7AA)//?MI@E>K7NNJD;2:	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:10^C31^A29
534	16	somegenome	3604	37	62M2D8M	*	0	0	TCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAATCAGGA	9A&GMJ:*G=0)7L*:'+5:B'A)@>>&;F-KC'':*8AB@A*&)J0'(131+BC.L:(,:?-;*HI)&0	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:62^AA8
543	16	somegenome	3614	37	7M2I6M1D51M1I48M	*	0	0	AAGCCGGAAAAACCGCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGA	G*>B340A27K950C5=07B2/B9(*810(N'IL@2KA>&(+D8I34'>9>+EG72:;&N:+J@44)-+7B<;223K39-FN81;JG)<51L-KC/*@L3(?I6MB/?(G00000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:3	XO:i:2	XG:i:2	MD:Z:13^C99
545	0	somegenome	3687	37	22M1D54M	*	0	0	ATATTTGCCGGCTGGATACGGCGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAAC	0>8*0H9K1@?,?'*LH>BC'8'D7(00000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:76
551	16	somegenome	3702	37	94M2D5M	*	0	0	ATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGCGCAAGCCGTAACCCAGGTTG	4I?&LCNDJ18+I=3I<@L&B298>H&3===H<(>AL85MDICI4+D@'C=L-3G*?GF<;)GDL*LCNG7&70=K29G,.4;+NJ&;.C4*N(C-300	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:94^GG5
561	16	somegenome	3804	37	17M2I64M	*	0	0	AAAAAAATCAGGGGCTGTTTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATT	I<++4&1IL,(@@BJJ0L2H7:'8KAAA7,H*,(N9G;B80000000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:112
562	0	somegenome	3822	37	36M1D26M	*	0	0	TGTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAATTGATGAGATGCTGAAGCTGGATT	0)IE2E:M+LJ93)-<3>*D&G6JCH*;HK7?K4J-,?2DKE46C/492'B&,D0LA..;70	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:1	MD:Z:1T34^A26
572	16	somegenome	3845	37	38M1D7M1I39M	*	0	0	TTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTGTCACCCCGCAGTGCGAAGATCCTCTCGGCGTTTATTGGTGATG	@:J+):/9=-6I//-6--5&I69(CL--C'H'+L)@J=0/@*M?8A1C264>MC(IG/++0NB6-@'G+&+LLNFDC(+.,)A00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:38^T46
574	0	somegenome	3860	37	23M1D33M3I22M	*	0	0	ATTGATGAGATGCTGAAGCTGGATTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTTTTATTGGTGATGAAATCCCAC	000244B-G>.J)66J572:'J?M0CFKH6*KNG0=G@J1>CL?+N<+(MK(:<7=,0H:)4G43B;'8@05>FKF2/('B	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:23^T55
580	16	somegenome	3880	37	11M1I39M3I4M1D43M	*	0	0	GGATTTTGTCACCCCGCAGTGCGAAGATCCTCTCGGCGTTTATTGGTGATGAAAAAATCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCT	*N14;A:3;0J;)'+H5(?F2.*?HB3N0*,M9F3=@L3LI;0+G?EH*H'D==&86*1>KEA430+6?&'&H.JKKE&/G16(E&<&JDL1M1FB000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:45^C36
586	16	somegenome	3936	37	6M1D59M1I14M	*	0	0	CACAGGAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAAGCGATGTCGGT	2KF,A32DD&=3:MD&H,;/E/=2<6)76C<4D'I0NK6F917B='JIII15M0:F>N(CB<(<@/B.K2(54KAH/000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:6^A73
585	16	somegenome	3939	37	32M1D32M	*	0	0	AGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAA	;4DCM5LHM;-2>G?0;)(5;J970N'42M-,&I--/AJ+NF;=N>B8(L1D6))BK)E0DI'@147JAHE3.2)J(3K&M&61K+::+.+(+A)N&3DC<4;,+=+4C))=K8=A'3.I	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:74
595	16	somegenome	3981	37	76M1I8M	*	0	0	CGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTTCGGCG	,8=?3:67K6+,'JJKA9:ANH7*MJI'E=D9:(;AHI-*K*<>@1<;.7A9I.2@AC8;08DEM3@>5DN'C;E9;447&(HHA)-NKK:(NN=*)B192<=G.-)(4=-H<=60&+GF+;6-F+E.)9;0000	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:94
599	16	somegenome	4013	37	44M1D22M2I9M	*	0	0	GGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTCGGCGGTCGCTTTATGGCACAAAAATGCTGA	L+8<,C-;8:(E/-J300G*2MN:07;9B6>/=A&NI==)?;L()6:5.@0INFBEK'0EGJ3@&GIJ*C::DH000	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:44^T31
600	0	somegenome	4026	37	8M1I59M	*	0	0	TGTTCCACGGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCA	00&?G/KFED9-H69=3'1.5>9+HCF*D.@.3H'EB2C27A&F95&2(LC7G&>1+/B?AG3EK5:<<9K>)AK.4(N4N00-AE8N=ADAN:,@8:CHNMK1HM1-+9;9B:)I8M'>6NF>/>76D*;)EF?0?L.402	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:2	XO:i:2	XG:i:2	MD:Z:0C0G65^T21^A7
620	16	somegenome	4100	37	79M	*	0	0	GGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTTT	9>E*05.0-8HC3*>G=7*C@.+8;-/92+&3=I&C>1J9:I6'I0;2B=*90?BL>2C&?N@C2<)'=5?CE<,G(00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:77A0C0
622	0	somegenome	4100	37	74M1I9M	*	0	0	GGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTTACCGAA	000D6N=+MLCA,8C6*@C<)G6C10A+/><7H*?@-:NFD;79HCC@G7DC=J=*==C=<&5-1&D?@421B7D+-:.L(9<--+LHHJ.;JF)N2DA0JA(':+700	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:66
625	0	somegenome	4106	37	59M1D8M1D20M	*	0	0	AAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTCTACGGTTACCGAATGTGAAAGTGGT	0000J/K97G4=;HD*N@J5:D77C13@&A'8/*:<;.D?1)>IC5)A)>?7@BB.3GHD3G9:IL=D8536CE0D/(1	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:59^T8^T20
621	0	somegenome	4111	37	66M	*	0	0	AGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTA	F585):=+&LK(2&B'&7*&>&+LG<4B(?064L9H9@?NC64-?8AJ/*	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:65T0
627	0	somegenome	4122	23	100M	*	0	0	TGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAAAATC	0008:L07J+//;KAM&7N1(3D(&9+HA5'7L6E/.6G4)?L8//,-5L7N8'7N*KA>7)8EL?C';E7H07./:8863EA>0*G8):@F4',KF5&A1269-JBH<9=MI50?-'@5=L)/?CB-,99=0E1000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:84^A20
632	16	somegenome	4160	37	54M2I19M2D18M	*	0	0	CATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAAAATCAGTCCACTGCAAGAAACTGTTCTGTACATTG	..2+'2FL6.15;E*6M)'<3'J,AMHBMB';@,KD*E*@FD(+DCE78*=?D4,*86588AM6M51	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:5^T77^G7
639	0	somegenome	4214	37	76M	*	0	0	GCAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATT	7NF3C,);'(8+*8>N<)?'4=MDMN	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:0A0A74
642	0	somegenome	4223	37	29M1I47M	*	0	0	CCACTGCAAGAAAAACTGTTCTGTACATTGGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCT	00;H=)->D-F(IN5J-6N)-+@*25KB8M>3/(.,;6(>E+A/)/N9)'*L0ED&*4B0/C8(&)-42DJ+@;ALM	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:76
647	16	somegenome	4223	37	10M1D54M4I32M	*	0	0	CCACTGCAAGAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTTTTTCGATGCCTGTCAGGCGCTGGTGAAGCAGG	94CB>;M'6H/()>8HAH<2)//AM/&ECG:.>?.+GI8'?E?+G4+I<6==3::HA2>JA7I2G.'=;(-&/1J3I7;E++MLD1F7(*3/='<00000	XT:A:U	NM:i:5	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:5	MD:Z:10^A86
646	0	somegenome	4229	37	37M1D50M	*	0	0	AAAAAAAAACTGTTCTGTACATTGGGCGGCAATATCGAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGC	0000ILN23K'II,EG586K*>9NJ00GM:@2B(10=4:6,MI/N&>/L)H?,1EG?C5/E,M70>:.GB,3N0DA18F8J2??.)9&N>=(D7'LC(A000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:74^T8
663	0	somegenome	4341	37	11M1D94M	*	0	0	AAGTGGCGCTAGGTTAAACTCGGCTAACTCGATTAACATCAGCCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGAGACGCG	0;<1B1+?@M,KBA+?5C1(9.JL?JB2M=55N,)).?&@'BB9&)JB<*.;@:1FFCIJ-HE6?=:MC3<.&70,H0(H56N@/B4GH	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:78
667	0	somegenome	4420	37	69M1D27M	*	0	0	TGTTGCGCAGCTGCCGCAGGAGACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTGACGGCGGGTCTGCTGGCGAAGTCA	FK,F8EL@4(F2M91>NE->B/A/I=CD777+'4D'(,4FME;J=''64:D23>;K*J'H-H-9'.BMAI8/6I-I)	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:69^T27
668	0	somegenome	4444	37	45M1D8M1I21M	*	0	0	GCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTGACGGCGGGGTCTGCTGGCGAAGTCACT	00.31N9/)B1012LB:K6:K+C@<6LI,?FJ3J+3:(65(9EMC>35A.-02..MB-/G?48:M:8L*0B-F+(	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:45^T29
671	0	somegenome	4463	37	26M1D8M3I57M	*	0	0	TCGGTGCCAAGCGGAAACTTCGGCGATTGACGGCGGGGGGTCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAA	000<.N:FN*7E<9(C;0JAE>(I2D=*J9?KMG&MM93F-?7-&(GH,JF71=,=6IE&;'B-DBCCDADL:K1CLAD>&+IAI&D'2=B@'/	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:26^T65
673	16	somegenome	4495	37	106M2I6M	*	0	0	GGCGGGTCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAACGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCCCAAA	'DC:LJ89&>KCL4(2G3I@E>C-L(FNJ)GB@I7EFFFELD176K72FNCF3&CA@JD&;-+<55'&&/@661=:))-6*+(6D000000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:112
674	16	somegenome	4536	37	68M1D9M	*	0	0	CGTTTATTGCTGCGACCAACGTGAACGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAGCGACTC	KJ-&(A1=)KC48(*F.EM'(JJ@;/FILDDE+@B3:ED(-0EG=4<0<8&'=-AJ-BG)*F>4&(B=AC9@C:B00	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:2	XO:i:1	XG:i:1	MD:Z:0G0T66^A9
679	16	somegenome	4555	37	48M1I38M	*	0	0	CGTGAACGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCAAAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACG	2MNF*@I39K*776@631-059/IBC'&-J'4?EA:G:=)*:M3KC<0GI=771B00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:1	MD:Z:48C37
682	16	somegenome	4559	37	17M2I28M2I54M	*	0	0	AACGATACCGTGCCACGTTTTTCCTGCACGACGGTCAGTGGTCACCCCAAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAAC	97584I:H.0,J/.IL'F3L=''2F=0>/:&9I0:IB+M4.+3*:G4+3A0&0000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:4	MD:Z:99
684	16	somegenome	4561	37	42M2D63M	*	0	0	CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTG	BEMED1K-&9E?J&C;CEB@&,67?3>4*8M,*C-.9;(68GH>;-B-IDN8MA;'1G@3'L:/IJ1DK7J:H'L;7310KB1>?5JK?GH2N>:1?GK)8-700	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:42^CA63
686	16	somegenome	4562	37	42M2I66M	*	0	0	GATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTG	?L.?EK-GA.>17@?-.6M7?M:695EG)AC@38>HAANAA?.MM0+:8B9'&+=::5E65J*@))G@IN+LG4BJ9->:GI23=:@&+&,+9L..D*C6;C4IB,0000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:108
687	0	somegenome	4562	37	14M1D24M1I72M	*	0	0	GATACCGTGCCACGTTCCTGCACGACGGTCAGTGGTCACCCCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAA	0G=IJDI'=DI/MI)762*8:(/DN9C,&3K*;'9@*37;KJ8;&(K+B/39<&NI=27(C>,M4M4.E+8-NJ;*;A4J=D>>4N0K3,(,(4>DMK9.D8?;(G.&?3C	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:14^T96
683	0	somegenome	4566	37	10M1D24M1D62M	*	0	0	CCGTGCCACGTTCCTGCACGACGGTCAGTGGTCACCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCG	*EG85/5G;+0N8N=)1L9E472N.ILF>/@G:H-<;:*GH5;F96B9)'*3E65-B7HGK3BH)98N'=I2FM/<)G4>EA7+@LI=*.6/30::	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:10^T24^C62
680	16	somegenome	4568	37	8M1D27M1D48M	*	0	0	GTGCCACGTTCCTGCACGACGGTCAGTGGTCACCCAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGA	BHF(7-:@J:75+BL2+=;L6(-'>4?:2.&4H'F+>D753)>9**34MLF:/B*57;88MKHI+:IDCL=00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:8^T27^A48
681	16	somegenome	4569	37	7M1I28M3I50M	*	0	0	TGCCACGTTTTCCTGCACGACGGTCAGTGGTCACCCAAAAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAA	MK205.E9K0?15?E4*3*E;29D5D&'A+)3(KIG?M2;&:LL'E+.=E5E0=&JLL;0(N.(B0?1HBJ6>1*GE5C2N9D0	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:5^T91
678	16	somegenome	4572	37	4M1I27M2D34M	*	0	0	CACGTTTTCCTGCACGACGGTCAGTGGTCACCAAGCGACTCAGGCGACGTTATCCAACGCGATGGA	/'>2=:0(HJ+L,91C.:B*.27@-B,&)I5/8,/AD-N20(+7D.;'I0:1:3FA'.,-?(*-?0	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:31^CA34
692	0	somegenome	4608	37	95M1I7M	*	0	0	CGACTCAGGCGACGTAATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAAGAGC	0'J;-5?&*K5/A;0,>A>(/'<+/>4NB&/87'KD@+DC:H1?9;LHA@54LD6-K'I@*K5J+'KGF=*);9=)'GKG>@50J.7F2>-7',8@D?EH,3<	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:1	XO:i:1	XG:i:1	MD:Z:15T86
688	16	somegenome	4611	37	74M	*	0	0	CTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGC	GDI/C)E4D64&1K00;NFEJ)3&F>B@2+''2:CI;G5=?-5,1B/C>'D+N(7-3N<&/A*A/HK&14.6M0	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:74
690	16	somegenome	4611	37	77M1D14M	*	0	0	CTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAATCTGGCAACTG	/<@10()1?C,3EB.1*M(&.C6+&<-89K22EJ7G9++BE365L442@J-6E22A--F004J3ECNLL00	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:77^A14
689	16	somegenome	4617	37	71M2I13M	*	0	0	CGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAAAATCTGGCAAC	2<@7@)M1BDA7J+HB<.6A(BE?3=6),K4-B',E.:((1D,G-4@-BB-9)A6<2+9KJ3IC47H/1@(16*300	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:84
693	16	somegenome	4630	37	58M1I15M1D10M	*	0	0	CGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAAATCTGGCAACTGAAGAGCTGGG	*/33J',FE:+00	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:73^A10
694	16	somegenome	4638	37	73M2I13M	*	0	0	ACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGGGTTATGCAGCC	M'&-H@.:M2IL581HMKFI3@EC@937KMN86=@MI>M,CFNN:5:/K8+-41./D1'79H?A?;7@=KCF@D49E?M'J+.00000	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:86
697	0	somegenome	4658	37	30M1D22M3I46M	*	0	0	TGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAATCTGGCAACTGAAAGAGCTGGGGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGT	00000-6JGGB+15&(A58/41C7*&6.0L;8K2K5,,1501'+1-99:8JD,@3FM,/B03A+N3AN/42+H>-:C;L)75'>3JAAI.F=54IM85)7>B-&<(4IFD6G-7>?B@<(L'.-G(:+(3B+E<25J78HB'6DIL+M*K300	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:54^A19
700	16	somegenome	4682	37	52M2I35M4D1M	*	0	0	CGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAAAACCACGCAACAGACAATGCGTGAGTTAAAAAAAG	D+.(.K?;-GCM+>&3MK<<9**:2-+@8);D::H0@>=.CLH'K+-4=NF,324182I@*18;H2DK7?/)<61FH6:=+394000000	XT:A:U	NM:i:7	X0:i:1	X1:i:0	XM:i:2	XO:i:1	XG:i:2	MD:Z:84G2^CTGG1
705	0	somegenome	4691	37	71M2D7M1D21M	*	0	0	ATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAGAACTGGCTACACTTCGGAGCCGCAC	0(50@?=7C&M+,6.2-LH7B>BD1NC?.I*3K4>NL<&A/6(M'(/5>8':I8C28.?=;H*4KH+:78A8?*9D':?0?A,2>J>L7<;D=0+7D.=24@JD8	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:112
710	16	somegenome	4731	37	31M2I9M1I63M	*	0	0	ATGAAACCACGCAACAGACAATGCGTGAGTTAAAAAAGAACTGGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCC	>.&H;&H=G*-2;+-0@G1B'43:/5=G5F.=6M(G*/KG.-.H0JH)3)C?8?>3&9'ECE4@?'000	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:3	MD:Z:103
711	16	somegenome	4741	37	30M4I67M	*	0	0	GCAACAGACAATGCGTGAGTTAAAAGAACTGGGGGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGC	'G?*)<3/5,BC>6L0.LN*),KG3<,H:1A9M,D1//&H-I52&+:*&<6805&A;B.-&91D*HL7@.I550D:F92?D7E.4,3*M)E*/K1>I0000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:4	MD:Z:97
713	0	somegenome	4749	37	13M1I90M	*	0	0	CAATGCGTGAGTTAAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTT	002J6)C@&/BG=:JBM79GKAJ72')BGM+9-I1539J1A8NF''+.;DILL.&9E+KH4A+;E1M2L98+>+9,G&KB5D';,4>L7G26I&1	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:103
715	16	somegenome	4759	37	12M1D96M	*	0	0	GTTAAAAGAACTGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCAT	;F)J,9A2+5(JH/:H'IIE,FM6,;>D117:GEIM;J?:78*AN6B.LE1J,-D=;J>6N=F:@;76@;E00	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:12^G96
712	0	somegenome	4767	37	4M1D70M	*	0	0	AACTGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAAT	+MA=07EN--&4?.*@;1-@&)/(7-*L*E*33(@?M4NL@KHM(2&L7'5D6LJ4N<2DE37L9/L>;?3HJBD.DE/3/G'4HF;JH'=-:	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:2	XO:i:0	XG:i:0	MD:Z:0T0G107
714	0	somegenome	4774	37	88M	*	0	0	CTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC	::L4G)+K/5@IHFB7D+?+&&'0=J0:G(/?29:CH@G>..M<01-HMD7-67/2CM'=(I)CG(1L(C2FFH0G98@1?E&7CE.85.995H721L;>IIB-18,I2)AH6	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:91
717	0	somegenome	4789	37	66M	*	0	0	GCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCT	L(8@/0-G)=M1M?I?/=;49D)4/L55;CB3,A:GD23//J,(&03IJ*7GD::?&:'(85=,J1710CA67*3E=M9J0@D0'.@>GD4'*-;.CAMH8:)J/E+;'+L.@J6.:H6HAN	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:107
724	0	somegenome	4802	37	72M1D19M	*	0	0	GCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAATTTAAAGAGAGCGTGGA	0G;DN&CI)B73D)(E)>DNM6(E.)'I>B;3)B-MKJ<.:*H,*0D@/'/)LE;*38>G&.(5F:F/KM4A.K+I:LF2L7	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:72^A19
728	0	somegenome	4847	37	27M2I34M1I32M	*	0	0	TTGTTCCTCGGCACCGCGCATCCGGCGAAAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAAACGTTGGATCTGCCAAAAGAGCTGGCAGAA	0000.9FBM*8*8B)58I;=.J?5A16.K@41)*-N=I>'@HC96+.AJ)NC?K*/CC60,1G1):(N&18.;M''7JHC0/&E(/394EN6-;N/F;;-1<.9,99&4HM(0?<:FA:H-*>3B5I*:J,:.G?13>	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:1	XO:i:2	XG:i:3	MD:Z:7T46^A30
729	16	somegenome	4873	37	35M1D15M2I17M	*	0	0	GAAAATTAAAGAGAGCGTGGAAGCGATTCTCGGTGAACGTTGGATCTGCCAAAAAAGAGCTGGCAGAAC	&1'(G+:9B>N2=:+'0'4@D6/0E)2;1*1,>2L6)F56)BNE=.30/K8K4@-GD9,LHN53<:000	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:1	XO:i:2	XG:i:3	MD:Z:4T30^A32
731	0	somegenome	4912	37	12M1D34M2I19M	*	0	0	GTTGGATCTGCCAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTTTCACATAATCTGCCCGC	000000'?=CAH-MIGKA3(*-14IJ,:LH+9.5;M<4H:K/ME'@@CJC-;CAD6AD6	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:0	XO:i:2	XG:i:2	MD:Z:29^T35
743	16	somegenome	4973	37	24M1D43M	*	0	0	CCCGCCGATTTTGCTGCGTTGCGTAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT	BH@+JK*63:NB/NB>G76M?L7;JH,>754.4;L,,K;LMM98D''>+)'H@><:C'GG?ND0-00	XT:A:U	NM:i:1	X0:i:1	X1:i:0	XM:i:0	XO:i:1	XG:i:1	MD:Z:24^A43
747	0	somegenome	5021	37	26M1I8M2I43M	*	0	0	AATCTATTCATTATCTCAATCAGGCCGGGGGTTGCTTTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAA	00000<6:)LAM')E67&=4N'4,93JMFK&*55&7E-&&H?B+>@A,G/02:BG1I8DHALD.'&>+5'460LL(L7&;	XT:A:U	NM:i:4	X0:i:1	X1:i:0	XM:i:1	XO:i:2	XG:i:3	MD:Z:29T47
755	16	somegenome	5114	37	1S2M1D10M1D70M	*	0	0	GAGAATTCTCAATAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATA	./4.HMD2)--NC,1,A'4N/4.N6*3HIL&.1IH4)06&=2'.D3M.7B5IG>D8=2@4)5>=+?=30'14,;9-E58BD2L	XT:A:U	NM:i:2	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:2^A10^A70
756	0	somegenome	5130	37	71M	*	0	0	TGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCG	8=3GA+MK'C./E/*<)I968-J,&CH89I+)&>'/H>@:EH&5*/>D101>8L-I;F.?8K'CN3G&?.4	XT:A:U	NM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:71
759	16	somegenome	5159	37	51M1I10M1D7M	*	0	0	GAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGGCAATGATAAAGGAG	K?)EC,&D+I?BM.F&6<'&8/4,G<'=?DK(?8D4E6N-F;L)NDB7L5B4-CGC2K(EHB8G>0+N-N=C+E=:G=L.:G
368	4	*	0	0	*	*	0	0	GTTAACGCCGAGGGTGATGTTGCCGCTTTTTTTATGGCGAATCTGTCACAACTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCT	000G@&?2*MI;G+,H5'F,'(2>791F'@3,:K4&9=G85G/FM=9).(48@BK(857,1G??N7DJ&L>E+<(A5LGC7+);;8+>)7MD6>E2M.0&7H'@4<
377	4	*	0	0	*	*	0	0	GCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAGTGAAT	)NJ*+J&NKK@)A7A>J?@+C(4
379	4	*	0	0	*	*	0	0	GATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAGTGAAATGGCGAAAACGCCCTGGCCTTCTATAG	KL.)M0-BLBJ:+8HJ<8?G9&GH&6?ID>K1CA=8=/MDC14/==,9<)
genometools-1.5.1/testdata/hop/map2.bam000066400000000000000000000051371211610345200177710ustar00rootroot00000000000000BCesreb``p*MMO>~V\.VI剜~`*@LPZf20UYBC	ˋ,Wkfnu]3[=i܄␕s](.\L7
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Nich[c0ktlR\Xd^4(HΩNBCgenometools-1.5.1/testdata/hop/other10reads.fastq000066400000000000000000000030741211610345200220100ustar00rootroot00000000000000@728
TTGTTCCTCGGCACCGCGCATCCGGCGAAAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAAACGTTGGATCTGCCAAAAGAGCTGGCAGAA
+
0000.9FBM*8*8B)58I;=.J?5A16.K@41)*-N=I>'@HC96+.AJ)NC?K*/CC60,1G1):(N&18.;M''7JHC0/,1*1;2)E0/6D@4'0'+:=2N>B9:+G('1&
@730
GGCGAAAATTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAGAGCTGGCAGAACGTGCTGATTTTTACCC
+
000&K+@L:AK+G8<&5(:44(J:')L-8>&E(/394EN6-;N/F;;-1<.9,99&4HM(0?<:FA:H-*>3B5I*:J,:.G?13>
@731
GTTGGATCTGCCAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTTTCACATAATCTGCCCGC
+
000000'?=CAH-MIGKA3(*-14IJ,:LH+9.5;M<4H:K/ME'@@CJC-;CAD6AD6
@743
ATTGAGATAATGAATAGATTTTACTGATGATTCATCATCAATTACGCAACGCAGCAAAATCGGCGGG
+
00-0DN?GG'C:<>@H')+>''D89MML;K,,L;4.457>,HJ;7L?M67G>BN/BN:36*KJ+@HB
@747
AATCTATTCATTATCTCAATCAGGCCGGGGGTTGCTTTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAA
+
00000<6:)LAM')E67&=4N'4,93JMFK&*55&7E-&&H?B+>@A,G/02:BG1I8DHALD.'&>+5'460LL(L7&;
@755
TATCCGGAGATTACTCGATGAGAACGGCGGTTGTTATTCTCCGCAATCCTAATCTCTAAGTTACCGCATTATTGAGAATTCTC
+
L2DB85E-9;,41'03=?+=>5)4@2=8D>GI5B7.M3D.'2=&60)4HI1.&LIH3*6N.4/N4'A,1,CN--)2DMH.4/.
@756
TGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCG
+
8=3GA+MK'C./E/*<)I968-J,&CH89I+)&>'/H>@:EH&5*/>D101>8L-I;F.?8K'CN3G&?.4
@759
CTCCTTTATCATTGCCCCGTTATGGGTCGATATCCGGAGATTACTCGATGAGAACGGCGGTTGTTATTC
+
05+KB?/I5'E94)@14CE=C)@)/.J*7J9F/@J9,*L:C++/52758*AN-.K*'L6*+4E9K4+B3G>2DL<:IJ8/=A97I><,&)G03L3,A:N>MBI8.K6@G&@:3J
@131
GATCACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAAAAGGCGAACTGGTGGTGCTTGGACGCA
+
00H-<.K+1+3,F)D'N;M@:47GH)E80M
@133
TATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTTTCACCGCCGGTAATGAAAAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTC
+
00000I708'.@;.'=*J<*-BJCI2+-:0*5-3I&>&*4BEH4J+=79L4KN69+F9G.(3>:)=61+5LM3(
@137
GGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTCATTACCGGCGGTGAAACCTGCCATCA
+
I?7H+0F&510-4(<8C>);:E'C,4AHKAD*AD>GN3,*;A(9<=8:IM):ADKE@/'HE28+/?LG(D0*6?62(I>FE1H026N(8EE0=GH9?>FMA6LEJE,E:5<875=;4MG1>1=LFC?FF.EN/B'EBJ&+)3EE3*6BC7?M9::26;-HN?F5/D+I9;22D3NEJ'6'>,N,D,BKN:6784B>;IAB':;@-/6N:B,=J0+FG30)C6'CL.<'+K<:
@142
GTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCA
+
00L=)H.405GF+=C-:A2<)>/>E>D4BE&+B:AK27>09
@143
ACGTCCGTCCAATCTCGCAACAATCGGCGCGTAAAAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCG
+
0009F7HI90:/GN2B&M59,*AM(0&60N&37>)F?3L=7EF7NMJ?N8N-.?2*0,<)0D2<&)8BJ*?LCL
@144
CGTCAACGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCA
+
000&C*&5GMB4=5F'LHH@)9=3J9G+3L(+FEJEC)>2:D(I/N',
@145
CGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGGGT
+
0000IDD:);6.2JB:/3LKL3E7-2)'+3&.5J2(:6*;J4(D@C*>;NA;?;(AA7@*K2J:1IHG&;F(7,.:'F;MK&2E.B=3-*(G-C9B:818I2J=@-
@146
TAGACCCGTCAACGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTTTTT
+
00000-E)/08HCK.;>I;?)*AN.5KCL/IHJB-3(83M;E4,I6ML65'JH/K5.7>8;B0'D
@149
CGCAGGTATAGACCCCCCGTCAACGTCCGTCCAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCA
+
0000+899@+,1>9HCGG2-M19*FE85BI:)5=53E4>)02&*'B@B'JB>BL/2+;,+'.5C,8;AHA+)2L?9*C4(;ABAA1@-6(/)61F2)2)DDD:5F,NGHB
@151
AACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTTTGGACGGACGTTGACGGTCTATACCTGCGACCCGCGTCAGGTGCCG
+
000).K7JA0F29G5(;H:,?3N:A9NI&F8)>15L1<@5A7?JJ5.HBA1NB58='3BA(@:H>&DE&+0>)A*.<,'(H&GG0/2L8(8<8'NN6F.:2+40*?/-3FN
@152
GCGGTGCTGGCTGCCTGTTTTTACGCGCCGATTGTTGCGAGATTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGA
+
00/C+K;>474J:N,K0ECE;DLMC++HE-*N7M+.DHH-=8ABJK8-C&-+-8)B@.34DN/:1@8J;,)-.225E:BMN
@160
CATCGCTTCCTGGTAGGACATCGACTTCAACAACCTCGCATCGGGGGGCACCTGACGCGGTCGCAGGTATAGACCCCGTCAACGTCCGTCCAAATCTC
+
00000(75E,/5><-379KCL7D@3?JJB&)+G1K.HLK48?>9>F1AG/5D:);'E:M6EBIH>E70?:IN'D@-,GJ/N00FEC;/()=>@AI=D*
@162
TGGACGGACGTTGACGGGTCTATACCTGCGACCCGCGTCAGGTGCCCCCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTT
+
00000/60K<.C;/E7N:NG?&FDHD/J6?J25.*0:<4*/@N./JM'=:N:I)19I,):'79N/>F?GA.898KJ>H:/6'?BIM31,M9HC@BHCC?C.NNG9',
@166
TTGACGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTTCCTACTTCGG
+
0H(1;C61L'+F>1>(.83L>99474AE<2MC4./'J6;JL<7J.D?/=,//)I<,.;I(41'@AC&,<27H2:87G<&5NM)432&K372?MM97
@168
GCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAGTTCT
+
0;&6GM3<,86-2CL-2GH&(,KL>-9MFIG887I;F5@LL/FKH+&:17CB+9NF9,8/L9@<**E,6M355/5KH+E4;KGH-I?@6(70AE;F.,D4F@GJ>-+4BEL&=J**1-:+@.3C&>DE;C&I/>85J)A';,L5:?A/I3<8F*.DJNC9C:-E
@172
TCTGGAACTGGGCGATGGGTAATGGTGCGGGGGGGGTGAAGAACTTTAGCGCCGAAGTAGGAAAGCTCCATCGCTTCCTGGTAGGACATCGACTTCAACAACCTCGCA
+
0001??5DC7).//M7M5/12?N>79-/K))-5?0M(73HMFF:FI(/*=K:,='G+A7B6'4DILK0-DK@+>HI>A>N/0>GIEJD(3=6761:'>2B/@8/E
@177
AGCGTACCTGGTGCTTGAGGATTCCGGTATTTTTAATCAGGCAAGGGGGATCTGGAACTGGGCGATGG
+
000=7722(3?,M'..)E':EGC(N'@K4/&>6&'C)1-/9477G'@.?9-;+:D(E94,=N?H,
@184
TCCAGATCCCTTGCCTGATTAAAATACCGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGGCATTCCA
+
000**925<9L,(MEJ9'B7H>A;&:;-6&CM*74F)GGI/&5<3CE0+>4-5H,D7JF.-F(07>3??D8=HL?
@185
CACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGGCATTTCCAATCTGA
+
0005,B6(1MJ*9;+LB<=FIEKFG1E+@5BE-947?C2A8'H6<7G&8N2+14-90&A;7=?E*>FF'M
@188
CTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTCCAATCTGAATAACATGGCAAT
+
JIF22>.NJ0/45N.BB1*A&.M+,)E)2;:<.HA:1>1A52JMM80;I*E8@&AB1I:CJ
@189
GAACATTGCCATGTTATTCAGATTGGAATGCCCTTGACCGGTAATTCGTCTTCATCACGGCTGGCACCAATGAGCGTACCT
+
B1>7904BE&HG/K/3K9(9B.=J=G/G<47-5*-9CFIA?((F5IJ:0CKLF8D?3FC759F.A(6=2618(7;EG2,/.LN=C)A97(2*K)E((*,G5D?*C-N4??DME&I6KL9M/1@6J?M9FF(&D6/0(5FJ4K,;F0=M4A;=?1AN*:+N3+*J=?B1;)6&4:K9(,11IN7G-N1H35>GBBF0*3*'7'D>
@192
CCTTCATCCCCGGACCAGAAACGCTGAACATTGCCATGTTATTCAGATTGGAAATGCCCTTGACCGGTAATTCGTCTTCATCACGGCTGGCA
+
0E=;)>.K6)E;DEJI'(JF2@C1.=A+112CJCL&G?48>08LA(:0EK)JN0:A);@J;5(M&5GF37HDDHMF
@195
TGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTTTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGGATGGTCGGCATGGC
+
00000)72BLGB>;:(/)&>@((?&39-N5F5>DL@H<>4C6J3N5KM76GN41/4D7)NM;@N+,E)8,H7*I?*
@201
ATGTTCAGCGTTTCTGGTCCGGGATGAAAGGGATGGTCGGCATGGCGGCGCGCGTCTTTTGCAGC
+
0000:*NEE?65I4H;1+A/;1*-H:=55FK.=,2&@1NH0N@D>IC/6
@205
GGATGGTCGGCATGGCGGCGCGCGTCTTGCAGCGATGTCACGCGCCGTATTTCCGTGGTGCTGATTACGC
+
?-E>9B;BJ7/51BA?:N0>+(:-?42:;N;7:-;@8IA.90.*
@207
AGATGATTGCGTAATCAGCACCACGGAATACGGCGCGTGACATCGCTGCAAAGACGCGCGCCGCCATGCCGACCATCCCTTTCATCCCCCC
+
00=2G+8I>9(MFL8+20KIH6,7<*=6JH76+MMB8;1+JDI''2:JB9=:F65<370I24K0A+LI
@210
GTCGGCATGGCGGCGCGCGTCTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGT
+
00K9EH2066:6B;;84DN9KB9'9K2L?LH-'&FE.,&GMH0'';.(ML21:B<)2,F7F:@3;35->+NHMIC=7HK*I*1,55A3:1CN6,F?;'5*=?(-))=-=A179M9C)M@@8B/=GD*J*5H&>9=L>;/0HB1)3GJ=)C:M&5DFAF;;8I2.0/-48*1:+@FK
@214
GCGCCGTATTTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAA
+
00*C)6CJ1KC(B@537DNHD=:'7I=7-62>0KB@9'HH/,;KNC;LA6@,,DI+9&+1L.934D?&B:*IMMB:73KKE=9L>3275,1-B;)MA8*
@216
GTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGTTTTTTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCT
+
00000@K9(,DHFC0'+8(NC4F50H000D165&F/2M3GE9=6:3?*A38?<>/:=A89(G0+-9L,'.'AHHAE((IE'9/?,')9E.253@3:EGG3J'--J,
@218
AGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGCAATGCAGGAAGAGTTCTACCTGGAA
+
9(D-C320J22CKGGM;:48BA@A6?A4BKD-;5(3,J1CI87KA6>/?)&NG44;3A-1@2)*D:(9*2-09F
@219
CTCCAGTAAGCCTTCTTCAGTTCCAGGTAGAACTCTTCCTGCATTGCCGTTCAGCTCGCACACAGTCGCTTTGTGGAACGCAGAAACTGATGCTGTATTCGGAAGATGATTG
+
00>2B93(B?'7A,?A?AMBJ;'&&.('?C,2;)2G4&CH82+166BL>08JJHK30E*?69@-L51>K4,=-6'N(D7.-KI4E;,)+CA6G77J7@849
@221
GCCGTTCCGTCACTGCCAGCGGCTCCAGTAAGCCTTCTTTTTCAGTTCCAGGTAGAACTCTTCCTGCA
+
00+(45D(>E;K+F=DH('H/D/';L&AF9F?*:J9A(0AJ35>G161--4'KIDE5,1C@??2(BD<
@223
TGGCCAGCCGTTCCGTCACTGCCAGCGGCTCCAGTAAGCCTTCTTCAGTTCCAGGTAGAACTCTTCCTGCATTGCCCGTTCAGCTCGCACACAGTCGCTTTGTGGAACGCA
+
00.IN9DJ'D;214><*69F3808DB(>GB+NEC4G7N19@=;E>?3J0,@>NA55I+52>129J,GK)J4+G39'36NJJF9?8C?9:4'M0=6+E?5359,=G;K6,)F
@224
ATAATGGCCAGCCGTTCCGTCACTGCCAGCGGCTCCAGTAAGCCTTCTTTTCAGTTCCAGGTAGAACTCTTCCTGCATTGCCCCCCGTTCAGCTCGCACACAGTCG
+
0000FB5(>B0..-,6I,NA-J,>@I868,19H+/05C@F/N&.KCK>7C:B.(A:>2))<
@225
GCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGT
+
E<,4@0B551<40I&:B>@54=;>+/,GAKAI9I&4139F&=:5)<3EEE3N))N2L6BHD':'*N2;AM<,17@5D)(@2
@227
AGGTGCGCATACCATCACCTACCACCGAGATAATGGCCAGCCGTTCCGTCACTGCCAGCGGCTCCAGTA
+
2-@L-;1J.12J(<=G/5+FB5>*J6E;*=M&6M=-)17NDMK/*-,
@232
TGAGCAATGGCGACAATGTTGATATTGGCGCGGCCAGTGCGGCAAAGAATTTCGCCGAGATCCCACGCAAGGTGCGCATACCATCACCT
+
09CG+5)&7D80)D.M,07F=:==)A1'-*B(NC&B29NFB,?'HB4D,D1N20/9C@,>D:,'*2'A(01I>,?9@
@237
AATTCTTGCCGCACTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGGATCTTCTGAACGCTCAATCTCTGTC
+
0157B7C<<=MI/,(IB(F&<,N,56BLAM-JD-4I*M)C@E85LFAI+6AM9AJAA&31*0N;I-MA'*KB6ELF@I,J
@238
CACGACAGAGATTGAGCGTTCAGAAGATCCCTGAGCAATGGCGACAATGTTGATATTGGCGCGGGCCAGTGCGGCAAAAGAATTTCGCCGAGA
+
00(0A1L=+=A*+D8L16L&MMGH8K6/12?HH9@,3JH=*BA*8>>.5/,:7B<*G:+E+N?FIA9JD<6?5@?.03,*<(*69889;2DEC
@239
TTACCACGACAGAGATTGAGCGTTCAGAAGATCCCCTGAGCAATGGCGACAATGTTGATATTGGCGCGGGGGGCCAGTGCGGCAAAG
+
0000HD2NG95*B=N-='>60/M(BG=N4D9'H4K7D2((E;@/?=0/=2)8J2ACK3B4C:;NN,/D.@AK(3?H05M73&:&9;=
@240
CAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAAAATAAC
+
00000=6G+NN&HM'>NC2C3D/+1F(FN=7D<345)@<**?;39?K7*'13EG@/7=J0N*HF?7I=.
@242
CAGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAAAATAACGATGATGCGACCACTGGCGTGCG
+
00007:?G*5843,G99L:3&*(
@245
GATGAGTAACGCGCACGCCAGTGGTCGCATCATCGTTATTTTTTACCACGACAGAGATTGAGCGTTCAGAAGATCCCT
+
000034E0J1)H=4FLJ6,9=6?>:M65EL+-ND-FGJ1'(5515I-9+5AI)D69N:IF<;=5J:8N9:2I5D5J<+
@246
AGCATCTGATGAGTAACGCGCACGCCAGTGGTCGCATCATCGTTATTTTTACCACGACAGAGATTGAGCG
+
00BK,K4E-L>(L9''64A6@HH>/)G&J20.JLI5&'J@8;2A&I,
@249
ATCGGTATTGAACAGCATCTGATGAGTAACGCGCACGCCAGTGGTCGCATCATCGTTATTACCACGACAGAGATTGAGCGTTCAGAAGATC
+
09.'A&1&JAG@/A7I0J'01EB)F-I9I<7(M33,D>G-15'F&&'<>L-(5G?320(.BC.8'+7L31GGI6G.247I933L9)>>'A.
@251
CCTGATCGGTATTGAACAGCATCTGATGAGTAACGCGCACGCCAGTGGTCGCATCATCGTTATTTTTTACCACG
+
000,J=KE?;C-CD6AH@23+J@&8?3E1@8=JI./<=,>95.-8?0K/*>CF?L@)@*0E&JC5GAAH&I.5>
@252
TAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTAT
+
8@NMID/I)'8JKA26KH@K@2A7&?HH028&=:/6?H897F?2E=;D2+F6AAGM@*G13LKE<(
@253
TCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAAAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCG
+
000;N3C2/@<'71NE1J<5B<-LID0H*,+N)G)E,4)@/4=3-:?L;-2/(M56:LI1*:N.(AE9H96LJ6A=D1(:&N;0-:A>A0.JE1MM5LL@GG
@255
CACTTCGATAACCTGATCGGTATTGAACAGCATCTGATGAGTAACGCGCACGCCAGTGGTCGCATCATCGTTATTTTACCACGACAGAGATTGAG
+
0000H<+'A4A.DG-<;.A.-HJ/7;5H=?KC8I0,5MH;2.F?=:0C,K4&9,4/)@JFHE8,H.&)G,I6:1CN25BKDFM1+7/658=-M>H
@256
ACGATGATGCGACCACTGGCGTGCGCGTTACTCTCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTT
+
F+B11,?-9I:)@60;,KMKG&F'3@?.=9N)H/,BE-3/JF4?&?9B/8*:36.4746=<9D>?DH.D22J92N;>(J+7H6<9*
@258
ATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTGTGATTGGCGTCGGTGGCGTTGGCGG
+
H-=2FK3C7*H7.9@&H:F4LD=(;+&.&I<3E87J,M+K+;1C2D-(=IIA47I-E46N;G7:E28K,0L1*-I?3/NG77H);&?*@+N=?
@259
CTCCAGCAGCGCACCGCCAACGCCACCGACGCCAATCACAAACACTTCGATAACCTGATCGGTATTGAACAGCATCTGATGAGTAACGCGCACGCCAGTGGTCGCATCATCGT
+
=.I;NB,<<.JI/FK.,'J7ACL+NK=NH.2FM)5;9;7NBNL:,KB/)3MB6-0L:-5E-F>DJNEJ@,@63&04H?78E;B?G2DEGJMNJN.'8:8;3;F2C+'I17:0C
@260
ATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
+
000'9K5(G4<*/4A0BI3@19/KFD@.J>MMA96/A;-G6,2*/LCB-941HFK56=5L,29)8AI942(,/L5@+5KJI?/@;53(93BB1:?J2=FN;B&@>.032/:M+1B52L=,/*DB=2'G7I<.J2;8H:*I>;GNNC@9G-=M'LKD;F'6E
@263
TTCAGCCAGCTTTTGCTGACGCTTCAGTTGCTCCAGCAGCGCACCGCCAACGCCACCGACGCCAATCACAAAAAACACTTCGATAACCTGATCGGTATTGA
+
0000;;0KD2'-D-1L0)/M1@A3>,9@DE-4)DB-@*C>6=,?GK)J8J4.)2C47&9M1.N0='1D(*FBM65ID,1=);FB7D.7GDI1>+I1/L
@264
TCTTCAGCCAGCTTGCTGACGCTTCAGTTGCTCCAGCAGCGCACCGCCAACGCCACCGACGCCAATCACAAAAAACACTTCGATAACCTGATCG
+
000,?86K-E'/*6I@=2HGKM:)JDK'>C07HF.?;?)K+:A;))F3=NL)*D.LM1AB,N70-+78E?LE2J&M(.*&D@'A-G)3.AF>1J
@265
GTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAAAGCTGGCTGAAGA
+
000('9@7C:L8M/L7H//A-M:(-@FH.G255MD0M+;:1(DLJCH<.C,9+1N<-F38=9*NG5:A)I31
@268
CCGCAGACACGTAAGTCGATATGTTTATTCTTCAGCCAGCTTTGCTGACGCTTCAGTTGCTCCAGCAGCGCACCGCCAACGCCACCGACGCCA
+
6CEBI5GFJ'61D(8:C7C7F6K>M,6+&9N*36J,*?0;E/G6?3
@271
AGCAACTGAAGCGTCAGCAAGCTGGCTGAAGAATAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCT
+
7;<,(;)=H?(?G4854*;/N*4KA?'AJ;6BL':F*M)8@JH,HH10EJ('&C';.*0E:'()@'(DFHDM)G)F5-8@
@272
AACAGAGCCTTCGAGTTGGCAACACCGCAGACACGTAAGTCGATATGTTTATTCTTCAGCCAGCTTTTTGCTGACGCTTCAGTTGCTCCAGCA
+
00C5,7FH=828;ILNJ(6A44DC&9L3<7&N>B)6'2,J2/KFI0N.D7FA7IAH6'6H/N&(()FAFF&F-'E5&L7L6E,,*JI/+9&@83C/KJIC*IK)5*2H662+N
@276
CGCTGCTGGAGCAACTGAAGCGTCAGCAAGCTGGCTGAAGAATAAAAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAA
+
000),<+H(F48.:M?0656FJNH,.2@A(2ED'IB8.92,:9KH7@5B>5E7'5J?M&)))?:31.M--5;=B+J=F00&7@.9)6I3@<)@>?3G:2AD.63=/F+:87<.7.=F
@278
TACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAACTGGC
+
D4.BA)670:MAL;'J'(;0FA)4I80'0M2+IK0?1IJ)47>*1/=CC54=/>3BNC8=0>B;.7;7?>C'I4(6)L4E-2HB(5'N::3KFN,?9/D)DC4=4J,*,>DFL2'+G@@;/K,224*H1(A16?.?0DBDE
@282
GTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAACTGGCAGGAAGAACTG
+
<+?)=L7@N2FGJE>>+ED1J9B5;KFEIE&//)4*3C.A8H?3C0C:GC)<*8NKL(@@@46AEJK)J
@283
CGCCAGTTCTTCCTGCCAGTTTTCCAGATTAAGGCCATGTACATTGGTGAGCAGAGCCTTCGAGTTGGCAACACCGCAGACACGTAAGTCGATATGTTATTC
+
;6LC2@7?.DL*;+254=H4I12B.'3(6>5=3A=39N7D/6)5IG5G(F(C2A9@;DC'=:(3,8>LA33J5<95,,H@:.A=A''-I9;C0=;A*+)72.
@284
AACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAACTGGCAGGAAGAACTGGCG
+
(4-*2>G*04M8:)C@+E10IEE,0/C6EL08=9,.)NC5,I:)+7'&82'JML;/.4GHCC?G,11I3IDGI/(=1KLM'?1C:5=6DG8=-BHN=
@285
GTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAACTGGCAGGAAGAACTGGCG
+
00?>EBFI>5M/C&,@N5*8@J4FKLA404/4;N&'2B3,G>CM8)4*:.F7;@EHL*F/;A@).AEB:/23)J60L)M7BI
@286
TACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAACTGGCAGGAAGAACTGGCGC
+
HJ=;;.*.?21LN)496-(((I5/N(BI50>F.A=5L/6.8779K''4*9:L6>:/5H'.6L1@1G+7BD7L:K.N6*04&>F7>E'B)D02=(IE,6C94B.(.?K8;>/G>,6FK83:C8GH62>J&E0/NF>C3&*+E:EM;&41N?9L2'9,MH-)I382>L3/GLCJ&-,(;72.+H2?8@8,H*A)@-?@7D5MLD6L/GE
@292
AAGCGCCCCGAGATTAAAACGGCTCTTTGGCTTGCGCCAGTTCTTCCTGCCAGTTTTCCAGATTAAGGC
+
00080)M28+8MB;2=JHLG,9D6/&7)H'-/GJJF@CL<*3K2)I*??>*4LFAF:(HGF:32KKJ1.
@296
CGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAACTGGCAGGAAGAACTGGCGCAAGCCAAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAAA
+
000>G&?F4,:>GD-)ILN;-7>(97FNC5C.@I;3JE(101<0K1;K'7F;M9?4DL.K15C/L<=K9.F3>A33.,D'27<,26BH5E?'H++3C5,>H/MCE95K=6J
@297
AGATGATATTCTTCACGAGGCGAATTAAGCGCCCCCCGAGATTAAACGGCTCTTTGGCTTGCGCCAGTTCTTCCTGCCAGTTTTCCAGATT
+
00000N(?)2GEJ++2N=BM&/=LAKKN10H(H;*DNF='CFE+H*'(MG+MEJ00M&',1AEJC3D4;;.B/GJ=J7E53J?JDI1'(7(
@302
TGACCGGGTTCAGCAGATGATATTCTTTCACGAGGCGAATTAAGCGCCCGAGATTAAAAACGGCTCTTTGGCTTGCGCCAGTT
+
0003F,*/BBJ3&6J@H:=-6F&68(-@F06DCFIG(KMD;N::BI3?I4)4B*:8H1ID;:/BL-1CNHM0B)@/=C3IJ&*L-=L&G4;'.*9>?ND=
@307
GCTGGAAGTGCAGTCAACAATGACCGGGGTTCAGCAGATGATATTCTTTTCACGAGGCGAATTAAGCGCCCGAGATTAAACGGCTCTTTGGCTTGCGCCAGTT
+
003/+-/0D?>+N3EB,FL?2?/(85ENEH5AMB3;:I..0==/9HE'H;BJNH(8@/+6CN6C1DA)IG83H'G+*)H901,1F;:M4&'E=CNC.:@'1:8
@310
CGCAGGAAGTCGGCATATTGATCCGCCACTGCCTGGCTGGAAGTGCAGTCAACAATGACCGGGGGGGTTCAGCAGATGATATTCTTTTCACGAGG
+
00000LF<9+;FH?*5-1L.9L5(4(N=-8FD(.A&&J36A*/1<0I*.=B=)'1D.+88/5.+:-KG
@311
TCGCGCAGGAAGTCGGCATATTGATCCGCCACTGCCTGGCTGGAAGTGCAGTCAACAATGACCGGTTCAGCAGATGATATTCTTCACGAGGCGAATTAAGCGCCCGAGA
+
:+.L6E@3@B*@8=+LK?G'31K/I7=*NJ<0*0M,J52GAB4'B,75:KDIJ6>'E*9N/7M9+:E3/E)N@<73'F)0/NJ?&BEB?>G5IBJ7+,/'K363CA;EJ
@312
TAATCTCGGCGCTTAATTCGCCTCGTGAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAA
+
:+.&G>&*C/10)3A@.LLA&0HC-J45;.866L+F@A/(H.-(F@N11:39;FAFHHH9BK2FG<==HJ7;GA34ADJM*7C.FK*'&/<*C.EM0=6:A=G&M,;CI:?9J
@314
GTGACAACGTGGAACCTTCGCGCAGGAAGTCGGCATATTGATCCGCCACTGCCTGGCTGGAAGT
+
0@7;:C8=N09FG&90M:*62E;KLKIHKI8D:BC6:L35H<&@NG@@297?(&+4H2(-@A>?
@315
CCTCGTGAAAAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGC
+
00B02H9:9*A@1+?G,.+(I@5/8AD>:=9?==N'/(,(GHBD2=I&71A9>GE57K3*27+.D:4=6?=G(=>2HM3D=89?*0IANL850*=3>(11II'C-JIJ*01J2:;E348F&MMC1/>('FDA.**>83GIM;-MM03@EH'5=F(=D*2/A(@(BFG9L@+KA@28I@@:G>FL'@8*N;K(>
@318
TTGTTCGGCGTGACAACGTGGAAACCTTCGCGCAGGAAGTCGGCATATTGATCCGCCACTGCCTGGCTGGAAGTGCAGTCAACAATGACCGGGTTCAGCAGATGATATTC
+
00C23M,&E&&B)-AIJ*6EE.N=03613*6((MCE@2B(@F7KJALE3JKM2H5(.K*I4,H,6(:(&N2L
@319
CCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTTCCACGTTGTCACGCCGAACAAGGCCAACACCTCGTCG
+
0K5H6J?-95J1H0:BC4<.7>6J1'NA,)MC5B+9+49GJ+MN:G;F7F:K1E;J(?8L5MMC:(8*B0?48EJ'
@320
TATGCCGACTTCCTGCGCGAAGTTTTTCCACGTTGTCACGCCGAACAAAAAAGGCCAACACCTCGTCGAT
+
000F922=>G>+'I(&D=>=5'2'09)H@I,BG;9>6/EF/C,:56GM-5(1.)AK@+'*L&.@A&(F5D,*9FN
@327
AAGGCCAACACCTCGTCGATGGATTACTACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGAC
+
0B+>C)3E7&.K3J=-)3L*:./6H,=>2KL?6A07L(.90?&33(N5:1LN'8L>.MFL'AND7CLHHBB&,4)':,3L:8MG9/80<-H39L3BIILDC?HL8>L*;J./G.9M);?8K28+3GN:&86FKE>D=@CN;NF//)*31J;(/*K
@330
TCCAGCCAACGTTGGTGTCATAGAGGAATTTACGCCGCGATTTTTCCGCCGCATAACGCAACTGATGGTAGTAATCCATCGACGAGG
+
00(D/=F*G/33;G><185L0,AA)F7BM@4G-?-IMGL?7<@A3&3KF&)A6,GC2?*;D5487L'JL.7'M45G0E'475(219>
@331
GTCACGCCGAACAAAAGGCCAACACCTCGTCGATGGATTACTACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTGGAT
+
0/,-+B+)BFI;L;H/.'54>,))-C2'3;(*)3)/,;-.-K26,K7+30CN,+0M=/@B1E>H?(/((NMJ)H6&,BD59,)=<;M22K4,J99(7I22DM'N)+FJ,EK2C-
@332
ATAACCGGTAATCCAGCCCCCAACGTTGGTGTCATAGAGGAATTTACGCCGCGATTCCGCCGCATAACGCAACTGATGGTAGTAATCC
+
00))A'4G@091GL3A=K(@8L428=7:-?*C1+E-96.6D@;02-??NK/N7+N1JC)MM&K400A,1J0-*I(C7G?F+/).0K08=4/-AJB4:=4K'(5,G='?8HN92+,(+B)(B1AKI>=9CBEEEE.H7+1C8&576=DH/-J)763>8ML1L5+(?*+4EG0?:CJGN:@50):('/(:028IG57M
@338
AACCAGAAAGAATGCCGGAGAACTTCATCAATTCATCACCTGCATTGAGCAGATTTTGCAGGTTCTCAATAACCGGTAATCCA
+
NG/BH9-AAFB@,E@'3E908.&:'/NM'KLH12'K?:*/;-7:A:KA=D494:>DC>*18.K;DAB@K'LH66'<.7B8?LN>09&(FB1;@27&AN*'<'7&;:2L8953::7>HCGN&+I4?+92?(@J17K@4G.L):6
@341
AACCTGCAAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAG
+
000M8KAM-LK.DEB697+)-NJ9.@>/2MG6,D:1LB;<*?JJ&&)2B89)NEJ.DCI(&<,IN)F?0,&.'B,6E8I<;JE,,H@57*=N'7I=4A
@343
AAAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTCTGGTTCGCTTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATG
+
000F8:+G4;'N054J?&G.>':12@6231-75J86N99G
@344
TCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTCGACGAAGGCATGAGTTCTC
+
0CHA87M&MN?L0.?+'2GL/+++E)LH,4.C68D:7F=7J6?1/F<)ICLKCE7H&,.7;JKF*.A;A4-'E4&'(;(LL+7@/+6G)H@3D18*+F,
@347
GTGGTCGCCTCGGAGAACTCATGCCTTCGTCTAACTTGCCGAAGATATAAGAAAGCGAACCAGAAAGAATGCCGGAGAACTTCATCAATTCATCACCTGCATTGA
+
00;:>2I.@H&)&-:.,&317G5-MLC/3BMG=HC469.+.6)>.F/H=BF259I.+LF'5/6@8B2>L4441AN4-()AD(E0>*0C2344A6*6:DL*3N,)&.774L(E,6CE-D(&B(C6NIM29DB/A8M:ME49GK.64HEJ
@352
TCATCTCGCGGGTCCGGTTCGGTATAACCCCCCATTCCGCGCCAGCGTGGTCGCCTCGGAGAAACTCATGCCTTCGTCTAACTTGCCGAAGATATAAGAA
+
00I88:5('DG1G@D'/);:1;-A>I.J:'D30BA7+;@F137=8J07?2:H@M,E>4)HNAHJGE3?,)L45*N,BFA(-9JC&=<(-DG/M8>>I6'?
@353
GACGAAGGCATGAGTTTCTCCAGGCGACCACGCTGGCGCGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTG
+
000*26+>(/G0843C71'F?2IC6*M1CKGK)L/(;H@0L1?2;C(7,B.3C0H>47>MK:0@CGL0,:+D3A5,-KL1I>@-;<0,4C@(-L
@355
GCGCCACATCCATACCAGAAAAAGATCATCTCGCGGGTCCGGTTCGGTATAACCCATTTCCCGCGCCAGCGTGGTCGCCTCGGAGAAAACTC
+
0000-)-D*<1J(1A*JDLH?-6M*9*9H0J.&?-9DK/EKF09N<.:DA.L)6,9C;IDH&-?(-:KB;5(/0&;*9A:JA>C2:LD4H1'
@362
CAGGTTCAATTTCAATATCCGCCAGCTCCAGTTCACGTCCCGTTTCACGAGCGAGAATCAATAGTTTTACGCGCCACATCCATACCAGAAAGATCATCTCGCGGGGTCCGGTTCG
+
000-?/?2.?(/48,@5F5F<;'I=9J7A6?2C,9,JGIN;CA8I3JL-I--IB'L45I(3B
@363
TAAACTCTGCGGGCAGCACAGGTTCAATTTCAATATCCGCCAGCTCCAGTTCACGTCCCGTTTCACG
+
0HNE7HJ7A865'-9.E/N57A4=HHII&IB2;2B:K<&/':.(BKL6F&/3C2FJKF1&;//48J?
@366
CGCCACGCGCGCGGCAAAGAGATCGTCGAGTTGTGACAGATTCGCCATAAGCGGCAACATCACCCTCGGCG
+
9;,*HFG+)'-4=&I/(&+,F93K1F69&21CL:>B7L5B4-CGC2K(EHB8G>0+N-N=C+E=:G=L.:G
@367
GTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACATCTCTTTGCCGCGCCGTGGCGAAGGCCCGTGATGAAGGAA
+
000F:G@43?K*3.E<>-62N:)=<(K37G>B10@C+*G03AG>8)?3CI89A<A8=>68/
@368
GTTAACGCCGAGGGTGATGTTGCCGCTTTTTTTATGGCGAATCTGTCACAACTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCT
+
000G@&?2*MI;G+,H5'F,'(2>791F'@3,:K4&9=G85G/FM=9).(48@BK(857,1G??N7DJ&L>E+<(A5LGC7+);;8+>)7MD6>E2M.0&7H'@4<
@369
GTCACAACTCGACGATCTCTTTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGG
+
000F/6LM1;2:*0IK'J()HFFE3.8.4-9K<4@FA7*25G)C;?7;B3H*:&@B?K<=
@371
ATCTTCATCAATATTGCCAACATAGCGCAAAACTTTTCCTTCATCACGGGCCTTCGCCACGCGCGCGGCAA
+
0-DME>MB8>/M=03M<*K)0:M:5L9=7>BH85'*N+G>/HN0(>:720;5B)7>-?=?C)6>CM&,K1J
@375
CCGTGATGAAGGAAAAGTTTTTGCGCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGT
+
0-34)/7<.+14;E8B;)I
@376
TGATGAAGGAAAAGTTGCGCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTC
+
7+@5EJ:6,G:E5;AKDL&4HB'><)E*;BL*CL-H=8D+*BG'C5LH)*/'D+6+E?E&MNI2D><*9;57<2/476J?@+C(4
@378
CATTTTTTCACTTTGAACAGCGGATCATTACCATCCACTTCGGCAATCTTCACGCGGCAGACGCCATCTTCATCAATATTGCCAAC
+
000DCDD7+>8ILFJ)@&J5@.LJ/918(?4G'7G*=.8H(1A-I2-@G;--+)>KF'IC-&M,D83='?HM=B>83L;LGFJM,:
@379
GATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAGTGAAATGGCGAAAACGCCCTGGCCTTCTATAG
+
KL.)M0-BLBJ:+8HJ<8?G9&GH&6?ID>K1CA=8=/MDC14/==,9<)
@383
ATCCGCGCAGTACCAACGGCAGCGGCTGATAATAGTGGCTATAGAAGGCCAGGCGTTTCGCCATTTTTCACTTTGAACAGCGGATC
+
I(&D<=H4@I7;I4HJ(&*GC36='8643N?):NM-,3.('=G.<-B.JIF/)-4;+K72<44>*)D<@)DG98MD=&GF9K3I2E5-6/C@G4?<(E(D6&E
@386
AACGTCATTGCCGCACCATATCCGCGCAGTACCAACGGCAGCGGCTGATAATAGTGGCTATAGAAGGCCAGGGCGT
+
EE)?9N:F(K+F:,6@-FLB030A6;LN30*I?.M0;49J&B<,,+K>'>AKKH(:7-;=/8G6)N:.*;*3C,629NK8'GBAA;(*;:J<
@389
ATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCTG
+
0000-;(G/(AI))FNNN;-M.38=((C>*-G1C,7A:-HC5@.60(.:43AG-3@GC'E44''>42&-M=6C:K+C>NHI@:?8
@391
ACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTTTGCTGATCTG
+
00JI-0318GFGDGD6@G'MF=?/M3*K@,B?.*F6.2H44D5D04KK7.=6F:AHFE)7L2F6(I+1;CB52@?-LF)'N3*F?
@392
ACGTAGCAGATCAGCAAGACACCGGCAGCTGTAACGTCATTGCCGCACCATATCCGCGCAGTACCAACGGCAGCGGC
+
26@1;L<.C63JBC?-<'&J*(;):B1:/MEKAD+J'H&>')0D65+05D@0+C34;0D6>CG>I?M0H1)EG&L3I
@393
CAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTGCTGATCTGCTACGTACCCTCT
+
0'.*;)E'&>CN*<->,:C>L7GL(:E;@/E7DF1M(-?F11L@)JEA>AJIM*D-*:8/:M)&LMCKD/@,:6/E26@.(
@397
CGTTGGTACTGCGCGGATATGGTGCGGGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAA
+
000M)G+7HK0?2DA+G/=B(=9C7@9'6ALMF):&9'9><0AI5M/-K?
@405
GCACCATCAACAGGTGTCACCGCCGCCGAGCACATCAACCGACGCTCATATTGGCACTGGAAGCCGGGGCATAAACTTTAACCATGTCAGACTCCTAAC
+
-+7G(>JI9+JN=C/=.+9.:=
@406
CAATGCACCATCAACAGGTGTCACCGCCGCCCCCCGAGCACATCAAACCCGACGCTCATATTGGCACTGGAAGCCGGGGGGGCATAAACTTTAAC
+
000000N00/6-8:BI703(,II+.GN'EE6=L+K/2;>8),4+=;BNI.D8438J?K&B/D,L@((5<8J55*E&17:(A3/D6H6/'KC2I24
@410
GTTGATGTGCTCGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGC
+
-M?,<00)N4NB+<(N):@(N=&J70)8'&BE/)76?8>*4>F<,>FHC:&6G>K/A)5LEF388IMJID2',
@411
TGAATGTCTCTGCCGCCTCAACCGTGACTACATCTAAAAGCAATGCACCATCAACAGGTGTCACCGCCGCCCCGAGC
+
0D*;E.5??='*?F/61()JJ4A)>ILL8M>5/?4=C?L5'4>:/*&.=5+'I8=MK;*9@/E(,9.=/KDF<
@413
AGGTTGTTGAGACTGAATGTCTCTGCCGCCTCAACCGTGACTACATCTCCGAGCAATGCACCATCAACAGGTGTCA
+
CE.?+L00>)4897JM'0II.5FE61I76*1NDDF9AA39GDB,G)84K52+E4=D,'G@I2CIM*+,=()K==,:L(<@4GKA8GFNA7?6@L<9D=/
@415
CCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCACTCTCAACAACCTCGGACGCTT
+
(;G5<107,F078J8H7D'61*C?-L63H9=M8:9N6;JD+;ELK-.)*3D&,&D30627NA<>L'DE/(L;',>:&K*/,;E-&
@417
CGTCCGAGGTTGTTGAGACTGAATGTCTCTGCCGCCTCAACCGTGACTACATCTCCGAGCAATGCACCATC
+
D()C0:AG;.GKM;?K>@,.-@?1<2:=KC*N>8LL?./HN-M;&L34L34B.04)&H*F+F0
@418
TGCATTGCTCGGAGATGTAGTCACGGTTGACGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGAT
+
(EADDA@KE'::2J,,,-,J;:J)88EJD;CA6C)JF.+B:D3M*?C*B>:ID:AGD5
@419
TATCGGCAAGCGTCCGAGGTTGTTGAGACTGAATGTCTCTGCCGCCTCAACCGTGACTACATCTCCGAGCAATGCACCATCAACAGGTGTCACCGCCGCCCCGAGCAC
+
02KE';3@2EB3;G5/NGN4*JG,E/K0L56.BH'4L8K9A4,8LK?&+D-7CMB30L)8))N.17N:IJ&AA*6M>:076ECJG,L9&D&)M1@L??(4:57+C*3,><9/6&(0)M>1NB;IA4D0F5?+B:@,B9/AM:CN)0J=3+E>LC,'E&B)K'N/658:4/II,&05/22@'554+L&).FD9-:<&+/+@;&.DI/=H:C9KBJ4.8@7G.)6
@424
TCTGACGGCAGCTTATCGGCAAAGCGTCCGAGGTTGTTGAGACTGAATGTCTCTGCCGCCTCAACCGTGACTACATCTCCG
+
16=E=JI&&:;9I:>MKI=;,8?*+G-96A;;17@4G?C:+:/E6/HJKICDI@:H=5N4NB?>H+/J5?M6;>===AI,=
@425
ACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTTGCCGATAAGCTGCCGTCAGAA
+
09BCJMF0D609&=GCB0D1F(.;-AGAH);;74G2KJ(6I-0.AFF>;IBFI2';
@426
TCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAA
+
6IE4EJ';/F5.<6A(B.BL8613)3'CBD,:I6=7?/72;3AN&+23B8524+'(J'&9E3K3C1GHBL&'02(/9ECD>/5H&+(*3=HHF/?)&
@432
TCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGAAATATCGTTATCAGTG
+
00:2'.)(>@:A.E'I:C=?:,J@:2,GC4.=G930>*0N&5<)JM@5K-)0.>B+L9/J)/CKK68C7@I(D'H/A<56/IND7?'DMIN@AJ1&<1/?(/8-4&
@439
GACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAAAAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGG
+
0000:;(A;&)/HD62;)?AD&1)+2=JJA,06KF++1:(J+1BJ-*B5;<83&7/?/+B)NB>22M<88<+&LMD.&80B,:FGNF*B0*'IJ':K>+8MI<71BE-0
@441
TTCCAGGGTCATCGCCACTGGAATTTTGCTTACCCAGTTCCTGGCAAAAACGCTCCCAGCACTGATAA
+
0+=1=>ENA5:&5BJ-C9'AM(7<1(;1HJK18=8))-EN9+JJL&2;9A54(A2I48N8NC.JFJ)055NCD(+0GA9&.3HJB(@A34
@446
GCCATCAGCGCCGCGACCACCGAACAGGCACTGGAGCCTAAGCCCCGAACCGATCGGCATATTCTTTTTCCAGGGTCATC
+
000B4BE62..C@8C8CD':1N3K1AK6;A)E(54?FE?(7J77=89-0NK>B;HG?FEE0N>I@AKH86NEDC23(7<,
@448
TCATCGCCATCAGCGCCGCGACCACCGAACAGGCACTGGAGCCTAAGCCCGAACCGATCGGCATATTCTTTC
+
00A/I<1?NIJC=.BCBL;C@95:=L*7'*9J6)6+=+J=.LMI?B*)?L)7FA.5+*(>E0@+837*G4,4
@449
CAGTGTTCATTCATCGCCATCAGCGCCGCGACCACCGAACAGGCACTGGAGCCTAAGCCCGAACCG
+
:>-752F,6IAD*E+B7KN-KF)(?,@)L&>CD/*1?(CF&.9(D&/=34:D?,8/3L**+1E56.
@450
ATGCCGATCGGTTCGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGC
+
@C/CMMN=B:7,D9JJJ.NDE(=LGI8D10.85ABI4=GF)?J(G8N&.N@H58J@?JMN;7K<*MM64>?M/3643,H?:-+E8?5&>.2H;249B4A2A8G<81?C*J?+N;8>C)2((-,;2F,7'/4+3-1,N/.JK0/7B.2(&J/-H9D*GF'+H,6CH'D1A+D&<(0:0:+,J>.A3.,<;3.+3@2JIJJL&I*)0'2>*:K3HHL9;9,GB.-A-;AC'+139I/D5
    0HK=1-BA5M)I>'/+-'<2+3@9@N
@460
GACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGCAGCATTCATTACGACAACGTGGCA
+
F/7D44J/0+88=3E2;K2IN&I,'F22=1:B(@JM9/L)K<:GNI<7F==
@461
ACGGTGCCACGTTGTCGTAATGAATGCTGCCGGAGATACGGCCTTCCAGCTCGCCCATCAAAGCCAGCAAACGAGTGTCATTAAGCGGCTTGCCGCAGTGTTCATTCATCGC
+
000000;GI(CM-9>':JK5NE5A..=0'I+?>7AJ>I'..H)/<2/M44(@,-<2=+F2/8A?5'M;BI5I'-&E:./7&ELAKGEB*01
@463
GATGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTCTCGG
+
M>:-EJ-;8-;H@KH+-4JH:71KI8.==6NJLKF.<+5/550.*LH')NNEB+@4GL9L/&:8C=9
@464
GATGGGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGC
+
005/6)F9HH;25-2A*.I*?M&FN&FF=4FB4?(G/8'53+=?DJA*;I*+MB&KF?L:?6/:E(*24I?)
@466
TTTGCTGGCTTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATC
+
00D4BA4;'C2I&9&6+N:<4E5*3;AI+L&-JLE)5N(6&&5>@56+8E0K>E?1<*F1-;4@2/9/<)/:-+M)-0B6-C4M3,/36=I1?3B=>+M;MG8.?@IC/AK7GA3H/882<,I/N(0*'BA.0@:,0?8<,I@@@5GB
@468
GAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTCTCGGTGGTATGCAGTTGATGATC
+
,I9,N/=HDIAE?E'5J:+-<)6I&*@;0<(64D*N9N2-88.82)-26H41M9&M3H=+=9C88)K8(A9FA:
@469
TCTTCGATCATCAACTGCATACCACCGAGAAAACACGGTGCCACGTTGTCGTAATGAATGCTGCCGGAGATACGGCCTTCCAGCT
+
2;/7/H2LI,@=I0F4?)H'?=+6DIIFM*;-=3.*7+F6-(I&208M/*8E/3E/(
@471
GGCAGCATTCATTACGACAACGTGGCACCGTGTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAACGACATCATCAGCC
+
;7/C*014+A077F,7FN0MH(.L==F5I4?:>)C(('91K??:-M1
@472
GCACTTGCTGGCTGATGATGTCGTTTTTTCTTCGATCATCAACTGCATACCACCGAGAACACGGTGCCACGTTGTCGTAATGAATGCTGCCGGAGATACGGCCT
+
00-'D51D321KIMJ9(C(3)0>E<'/9M(=?8)4G+0;=@F<+DNG;(*;+?3@?<,?MEN?,:J1+L(E8B==6D1FM4;:MA?D3AG.C(((N?M96I'1&K62M
@476
TTAATCCCCGGATACGCCAGCACCCACAGCCACTCATCAACCCTGGCACTTGCTGGCTGATGATGTCGT
+
*;08G&-M05KH)EMK0H/F5:'&-IAM8:/*3FH1N@6E<&J,'?CFC'.&*FK@3E+@MD&:1*D7-
@477
TATGCAGTTGATGATCGAAGAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTC
+
0H;(K51G('3C.4JA.-5)')?8K0>8>M-13;67N:?M(3E:JHE.'*/C(;F1HK13=+KC5*2
@479
AATAGCCCCTGGCTTCTGCCGTCGAGACTTTAATCCCGGATACGCCAGCACCCACAGCCACTCATCAAAACC
+
000>4GLL@*'&DJ8))CF@5AI/A,=>?AD-/1H<=>A6CE;7KN67IⅅLJI(19GL,+()2@GB/(;
@485
GCCAGGGTTTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGCCAGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTG
+
000;+IH<<(/>GEH6C&'.2&-K5?.=GN?,20&(GC46H>>??=<.G-LN70*J?I8:M)9K9JMNECN-64.89&B
@487
AAGTCTCGACGGCAGAAGCCAGGCTATTTTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGG
+
00M=/KA;DLN<'=5>-=;.D+C+L-E0A0,57)+GINN61,G9C@)<&F?&)INLEI@)KI)=M57L7I=
@494
CCGCCAGGATTGCATTGCGCACGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAG
+
00+4NA>EB>)M4ED=//J:7F5F.++@FE;&;JN6)?0-B2GJ)6G/9IE&LK9CJ<=N&&@LJ95F.*7M
@495
GCAGAAGCCAGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGC
+
0*5LIK.B260L+)2&>4/.A?864:)B1F'E,12)J(+I6BK?M6.A889+G(::=()MAIB5K70//5:)3095D@DH4IIFJ+(L'L:'MFH*3IHEL8NC&0E.?@8BN>D;5<+89>N=6=II10C(
@498
ATTGCATTGCGCACGGGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATG
+
0000D'1='0.G8(,N)'H/5:,:8;.<1;:KFK5)6JME;0)?FE+(5D<;1L'I01?E+<=N;L,/7L;17I.INEJ8;?,E
@499
TTTTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA
+
000000F92/J:2<:H+&BL&/I*?L28K2*EJ9F-GKE:HE))7:,M4M@6;1+MC:<2A9G()78AMC5B26H7JC,396&L2MN5,B@MC4,JA,FJ@HH8*H+K8+&*1<02.5
@500
ACGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAAC
+
I,4BF,8&)D(:H>5.73(0*6B81<2A?I;;L1F;,:8IK:H@D976@M>7GCI)M,.''ML?*;CJ4-7+*J/NK4&GC(-NAE?5K
@501
CAGGCTTCATTCACGCCTGCTATTCCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACC
+
0:?;DH,&A);B)51H+L0(H7&@)=NDKK?A?CH7IJBA//./IJ7B,9N2A>JI**B>56A?3-E&B>J64*>AM
@502
TTCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAAAGATGTTATCGCTGAACCCTACCGTGAACGG
+
009G>7BD9-?CE??)&C*>KCF6+@L/J8>A;9'IB8<-5)*6?6H,F.(B0I4M&4//+K5J,/4;
@503
AACCGTTCACGGTAGGGGGTTCAGCGATAACATCTTTCATCAGCTTCGCGGCAAGCTCAGGCTGACGGGGAATAGCAGGC
+
000059*90,N&525=4C,GG2+8H8I;
@508
GCCGGAAGCCTGGCAGTAACCGTTCACGGTAGGGGGTTCAGCGATAACATCTTCATCAGCTTCGCGGCAAGCTC
+
00,13@83646HB?6=4M(>8EK6:+2M5E)H(I+->N=1.87HN7I>91D&,2;+7G-+AKCKN8.F67A;F-
@509
TCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGG
+
0009BF4&4/B(<&L+482LKAK1H40@72I.>M-G31,(53?C'?G826A)LLI/GB+*4CC1L;88B:'L)+@=8CJ1G7>+
@510
TATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGC
+
)G=CK;N0+GG'.4L*G6M*>7EKDHB+()N:N8H)&G(MDI:-/),,3:.F915:8=JGJF'?CD&'3MH&0L*C>0D6MN23E5')E9&
@512
CGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAAAAAGATGTTATCGCTGAACCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCG
+
0000G'';'B4IF>DMI6;FJHFH9NI>F(N-I>EHH.2.G=@?/7I?JAC7+GA;3'),9LEF?&CM;(@(8G6=I'63E;2,HJD,F8CCC44G3;.
@513
TCAGCCTGAGCTTGCCGCGAAGCTGATGAAGATGTTATCGCTGAACCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCG
+
0.'7J6,H@C22HGB>M.(?*64@643&1@C,=->N+(7/(3K-@+FLNG,?E/J---GD6=*.>.&9'/AJN1&6N@(&F@JJBEJC67+F
@514
CCGCCTGCCGCGCCTGCCGGAAGCCTGGCAGTAACCGTTCACGGTAGGTTCAGCGATAACATCTTCATCAGCTTCGCGGCAAGCTCAGGC
+
00).I04?EK;)B)/62:/<0F/.:/:K1+888+7=/59DCHN'NE,KA=@/L/;G*//E6?;NINL*,*
@515
GAAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGT
+
000&=K.@)>:J>83G'3(/4:4JH8.@7,-N5@//K;)//C&>7D@N:7L=.M*M*=D)2K/=@7(
@517
TTCCGCGACCGCCTGCCGCGCCTGCCGGAAGCCTGGCAGTAACCGTTCACGGTAGGGTTCAGCGATAACATCT
+
.;G3C3-ELJ(E4)@1&4&,<,JM5JLAL-91?-(H@LA
@519
GCGCCGATTTCCGCGACCGCCTGCCGCGCCTGCCGGAAGCCTGGCAGTAACCGTTCACGGTAGGGGGGTCCAGCGATAAC
+
0000(30DNE&&-A+9C4G>@I026)JAM0=ID,;L@?;I149L6/;?,8:.':GA+'B@(2L);3A.B?+E81K@,2.@;?>C5E5;9*'>KJ*7M6562*AI&9C?G
@523
GTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAAAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTG
+
000I>)+E-,73G@,8:,&J:F32>,M=BK+,J/G7F+FADHF<@1@?(L>&N;7GCB0*&A49D)A2K*83NMC;M,4@.67?NN/5)(B
@524
GAGCGAACAAGGTCGGGCCGGAGCCGGAGATACCGCTCGCTACCGCGCCGATTTCCGCGACCGCCTGCCGCGCCTGCCGGAAGCCTGGCAGTAACCGTTCA
+
*KGBF=M78LN86MGA2KG2L3K:,259M9+B.HI8DD+?GC0H@J4;&NN0E2B9C)J(8KCC*&/>:I:)36-6M<@BA:*/@7&-&62,M>E.L38BM
@525
AGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCCGACCTTGTTCGCTCTGTGTGACAAGC
+
0K>*K?65**&=<-A.3NB6>K&FE2.>8J&865,D22I??L/;A@(.LJ&<0C9<7**M,4/A4,@I>CH;BFM/94+K':.C:BH<
@526
GAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCGACCTTGTTCGCTCTGTGTGACAAGCCGG
+
MN@B@JGKMN'/CGKL:288B*A,1?)?*)'.4I7CB@A014@097<@8?0L3G(J9J?/CJM+*9=N>7HN=<&J?'J3'KH@)=F>(318>D2CM7
@529
CTGGGCGGTTTTCCGGCTTGTCACACAGAGCGAACAAGGTCGGGCCGGAGCCGGAGATACCGCTCGCTACCGCGCCGATTTCCGCGACCGCCTGCCGCGCCTGCCGGAAGCCTG
+
009H69>LL9@@A?2B11AD'9>K-L9466DG0<)BA(6?-0+8HJ=L7=A54IN?L+J/B(/1B0)>J@KEKD(@0J0=K*'+'7J>3/H@=/5(*/&;8GE0149)I23A-D
@530
ATCTCCGGCTCCGGCCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAACCGCCCAGCGCGTTGCCGACTGGTTGG
+
0.'N3.159A)IM3,ED<'.JNJ(47087<4.23M+&@,':.&0G4-F&FKE026G*
@531
CCGGCTCCGGCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAACCGCCCAGCGCGTTGCCGACTGGTTGG
+
*(=1BNE1;7JJ-+:GH:)G,K>1>GC1,DA:BD(DE(/A:MN.:IL/?7AA)//?MI@E>K7NNJD;2:
@532
CTTACCAACCAGTCGGCAACGCGCTGGGCGGTTTCCGGCTTGTCACACAGAGCGAACAAGGTCGGGCCGGAGCCGGAGATACCGCTCGCTACCGCGCCGATTTCCGCG
+
>FM2)*+H+@;A1265=02HN0;/J?9;42(03;E(0/B/DE@*MD5(C'L&0D9;3,-IA4-C6&L9HE?(DB)83/7KGM7H>C'IN'7N@6@,-<(9:65A
@534
TCCTGATTGCAGGTAGTTCTTACCCAACCAGTCGGCAACGCGCTGGGCGGTTTCCGGCTTGTCACACAGA
+
0&)IH*;-?:,(:L.CB+131('0J)&*A@BA8*:''CK-F;&>>@)A'B:5+':*L7)0=G*:JMG&A9
@537
ACAACCTTCCTGATTTTGCAGGTAGTTCTTACCCAACCAGTCGGCAACGCGCTGGCGGTTTTCCGGCTTGTCACACAGAGCGAACAAGGTCGGGCCGGAGCCGGAGAT
+
000L?GN7:3+G:23G=4;C=EL=,B9B+&<+&L/@71=+*JF-9>-&=HH@71*80)7J-275F1-(=,K=<)6,'9'EM@@KF?,;-,AAI0GFKB?;6B::3,L&
@543
TCCAGTACTCGTGCGCCCGCCGTATCCAGCCGGCAAATATGAACAAAAACCTTCCTGATTTTGCAGGTAGTTCTTACCCAACCAGTCGGCAACGCGCTGGCGGTTTTTCCGGCTT
+
00000G(?/BM6I?(3L@*/CK-L15<)GJ;18NF-93K322;9>'43I8D+(&>AK2@LI'N(018*(9B/2B70=5C059K72A043B>*G
@545
ATATTTGCCGGCTGGATACGGCGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAAC
+
0>8*0H9K1@?,?'*LH>BC'8'D7C;&F5E@GE(&?(892B&L@*D&G6JCH*;HK7?K4J-,?2DKE46C/492'B&,D0LA..;70
@568
GCCGAGAGGATCTTCGCACTGCGGGTGACAAAATCCAGCTTCAGCATCTCATCAATTTCAGTCAGGCTGAATTCCGGCAGGTCGTGCGGAAAAAAAACAGCCCCTGATTTTTGC
+
00000008B>?&N462C1A8?M*@/0=J@)L+'H'C--LC(96I&5--6-//I6-=9/:)+J:@
@574
ATTGATGAGATGCTGAAGCTGGATTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTTTTATTGGTGATGAAATCCCAC
+
000244B-G>.J)66J572:'J?M0CFKH6*KNG0=G@J1>CL?+N<+(MK(:<7=,0H:)4G43B;'8@05>FKF2/('B
@579
CGCCGCGCGCACGCGCTCTTCCAGGATTTTCCTGTGGATTTCATCACCAATAAACGCCGAGAGGATCTTCGCACTGCGGGTG
+
000BF1M1LDJ&<&E(61G/&EKKJ.H&'&?6+034AEK>1*68&==D'>:,-FNI,7/2M-(2=L8,,(A8:;@/4F80:,
@580
AGGCAAACGCCGCGCGCACGCGCTCTTCCAGGATTTCCTGTGGATTTTTTCATCACCAATAAACGCCGAGAGGATCTTCGCACTGCGGGGTGACAAAATCC
+
000000F087'8F'L))8(9E7CEM)&GCD'G9LM+?889)'&3?-/M<3F9M,*0N3BH?*.2F?(5H+');J0;3:A;41N*
@585
TTCAACATTGGCGACCGGAGCCGGGAAGGCAACGCCGCGCGCACGCGCTCTTCCAGGATTTCCT
+
4B'JJG@F<4)*,.3<3/'H(G)??HN*:NA585GC)NL55?EK?<);0?G>2-;MHL5MCD4;
@586
ACCGACATCGCTTTTCAACATTGGCGACCGGAGCCGGGAAGGCAAACGCCGCGCGCACGCGCTCTTCCAGGATTCCTGTG
+
000/HAK45(2K.B/@<(F:0M51IIIJ'=B719F6KN0I'D4J(3K&M&61K+::+.+(+A)N&3DC<4;,+=+4C))=K8=A'3.I
@595
CGCCGAAAATCTTTAAATGCCAGCGTTGGCCCGTGGAACAATTCCAGACAACCGACATCGCTTTCAACATTGGCGACCGGAGCCG
+
073)0F29H2GCNG41/DK5F6G7M+6ENN7BI31+6+@4B<<*K*-IHA;(:9D=E'IJM*7HNA:9AKJJ',+6K76:3?=8,
@597
TTCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGGGGCCAACGCTGGCATTTAAGATTTCGGCGGTCGCTTTATGGCACAAA
+
004&)3K/=>(5;J970N'42M-,&I--/AJ+NF;=N>B8(L1D6))BK)E0DI'@147JAHE3.2)@3MED80;8CA@2.I9A7.;<1@>>I=FE
@599
TCAGCATTTTTGTGCCATAAAGCGACCGCCGAATCTTTAAATGCCAGCGTTGGCCCGTGGAACAATTCCAGACAACC
+
000HD::C*JIG&@3JGE0'KEBFNI0@.5:6)(L;?)==IN&A=/>6B9;70:NM2*G003J-/E(:8;-C,<8+L
@600
TGTTCCACGGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCA
+
00&?G/KFED9-H69=3'1.5>9+HCF*D.@.3H'EB2C27A&F95&2(LC7G6JN(51BB,:@N?AA'@2H;I
@620
AAAAACCGTAGAAAGCATGAGCCACTGCCGCTCCGGTATCACCGGAGGTCGCGGTCAGAATGGTCACTGGCTTATCACC
+
00(G,LB?09*=B2;0I'6I:9J1>C&I=3&+29/-;8+.@C*7=G>*3CH8-0.50*E>9
@621
AGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTA
+
F585):=+&LK(2&B'&7*&>&+LG<4B(?064L9H9@?NC64-?8AJ/*
@622
GGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTTACCGAA
+
000D6N=+MLCA,8C6*@C<)G6C10A+/><7H*?@-:NFD;79HCC@G7DC=J=*==C=<&5-ADAN:,@8:CHNMK1HM1-+9;9B:)I8M'>6NF>/>76D*;)EF?0?L.402
@625
AAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTCTACGGTTACCGAATGTGAAAGTGGT
+
0000J/K97G4=;HD*N@J5:D77C13@&A'8/*:<;.D?1)>IC5)A)>?7@BB.3GHD3G9:IL=D8536CE0D/(1
@627
TGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAAAATC
+
0008:L07J+//;KAM&7N1(3D(&9+HA5'7L6E/.6G4)?L8//,-5L7N8'7N*KA>7)8EL?C';E7H07./:8863EA>&5CJD&<5;K8&G?,3&D8/(B<'BIF=N0.*?L/H*-/(K0E6AF:M?0@
@635
TACGGTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGCGGCA
+
00H/NK&2.KM?B8K0MF@55F)H914DM,4MME>E*6M)'<3'J,AMHBMB';@,KD*E*@FD(+DCE78*=?D4,*86588AM6M51
@639
GCAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATT
+
7NF3C,);'(8+*8>N<)?'4=MDMN
@642
CCACTGCAAGAAAAACTGTTCTGTACATTGGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCT
+
00;H=)->D-F(IN5J-6N)-+@*25KB8M>3/(.,;6(>E+A/)/N9)'*L0ED&*4B0/C8(&)-42DJ+@;ALM
@646
AAAAAAAAACTGTTCTGTACATTGGGCGGCAATATCGAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGC
+
0000ILN23K'II,EG586K*>9NJ00GM:@2B(10=4:6,MI/N&>/L)H?,1EG?C5/E,2AH::3==6.:GCE&/MA//)2)(/H6'M;>BC49
@656
GCCAGCAACGGCTGATGTTAATCGAGTTAGCCGAGTTTTTTAACCCTAGCGCCACTTTCAGTTCTTCATCATCAAACGCCTGCTT
+
000A(CL'7D(=>N&9).??2J8F81AD0N3,BG.:>07M>H3-'&@,9FK&&:@<=BDC:NK:6KM66;33?5MIJ-HE6?=:MC3<.&70,H0(H56N@/B4GH
@667
TGTTGCGCAGCTGCCGCAGGAGACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTGACGGCGGGTCTGCTGGCGAAGTCA
+
FK,F8EL@4(F2M91>NE->B/A/I=CD777+'4D'(,4FME;J=''64:D23>;K*J'H-H-9'.BMAI8/6I-I)
@668
GCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTGACGGCGGGGTCTGCTGGCGAAGTCACT
+
00.31N9/)B1012LB:K6:K+C@<6LI,?FJ3J+3:(65(9EMC>35A.-02..MB-/G?48:M:8L*0B-F+(
@671
TCGGTGCCAAGCGGAAACTTCGGCGATTGACGGCGGGGGGTCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAA
+
000<.N:FN*7E<9(C;0JAE>(I2D=*J9?KMG&MM93F-?7-&(GH,JF71=,=6IE&;'B-DBCCDADL:K1CLAD>&+IAI&D'2=B@'/
@673
TTTGGGGGTGACCACTGACCGTCGTGCAGGAAACGTGGCACGGTATCGTTCACGTTGGTCGCAGCAATAAAACGTTTCACCGGCAGACCGAGTGACTTCGCCAGCAGACCCGCC
+
000000D6(+*6-)):=166@/&&'55<+-;&DJ@AC&3FCNF27K671DLEFFFE7I@BG)>:1IL1)8,,9IMGI';I@+N?E@I3G2(4LCK>&98JL:CD'
@674
GAGTCGCTTGGGTGACCACTGACCGTCGTGCAGGAAACGTGGCACGGTATCGTTCACGTTGGTCGCAGCAATAAACG
+
00B:C@9CA=B(&4>F*)GB-JA-='&8<0<4=GE0-(DE:3B@+EDDLIF/;@JJ('ME.F*(84CK)=1A(&-JK
@678
TCCATCGCGTTGGATAACGTCGCCTGAGTCGCTTGGTGACCACTGACCGTCGTGCAGGAAAACGTG
+
0?-*(?-,.'AF3:1:0I';.D7+(02N-DA/,8/5I)&,B-@72.*B:.C19,L+JH(0:=2>'/
@679
CGTCCATCGCGTTGGATAACGTCGCCTGAGTCGCTTTTTGGTGACCACTGACCGTCGTGCAGGAAACGTGGCACGGTATCGTTCACG
+
00B1>2+08HL)LB<>+83M(NNH9?H)6090A<77=IG0DKNJ.:'J)357D>+F'H4&.2:?4>'-(6L;=+2LB+57:J@:-7(FHB
@681
TTCGGCTGACTCACGTCCATCGCGTTGGATAACGTCGCCTGAGTCGCTTTTTTGGGTGACCACTGACCGTCGTGCAGGAAAACGTGGCA
+
0000:7:<'=H*/:/<&D5D92;E*3*4E?51?0K9E.50>D=M1.GJ3D*.-A84E--H@7A2H*/9G+61KH1'F/G/(E+&K<2KM
@682
GTTGTTCGGCTGACTCACGTCCATCGCGTTGGATAACGTCGCCTGAGTCGCTTTTGGGGTGACCACTGACCGTCGTGCAGGAAAAACGTGGCACGGTATCGTT
+
0000&0A3+4G:*3+.4M+BI:0I9&:/>>J,1='EAD:24B'C5+,:1)89=ML=C-&H&(GG*=A4*?3;4KL<0=F2''=L3F'LI./J,0.H:I48579
@683
CCGTGCCACGTTCCTGCACGACGGTCAGTGGTCACCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCG
+
*EG85/5G;+0N8N=)1L9E472N.ILF>/@G:H-<;:*GH5;F96B9)'*3E65-B7HGK3BH)98N'=I2FM/<)G4>EA7+@LI=*.6/30::
@684
CACGCGGCCAGTTGTTCGGCTGACTCACGTCCATCGCGTTGGATAACGTCGCCTGAGTCGCTTGGTGACCACTGACCGTCGTGCAGGAAACGTGGCACGGTATCG
+
007-8)KG?1:>N2HG?KJ5?>1BK0137;L'H:J7KD1JI/:L'3@G1';AM8NDI-B-;>HG86(;9.-C*,M8*4>3?76,&@BEC;C&J?E9&-K1DEMEB
@685
CACGCGGCCAGTTGTTCGGCTGACTCACGTCCATCGCGTTGGATAACGTCGCCTGAGTCGCTTTTGGGTGACCACTGACCGTCGTGCAGGAACGTGG
+
0D9N2C5EG*1>6JBH1?0B(.N(0;LLJ&=0E5E=.+E'LL:&;2M?GIK(3)+A'>2M8'<*,9=6)H.?&NC-E:&B7A/NAAB66A4@CC368
@686
CACACGCGGCCAGTTGTTCGGCTGACTCACGTCCATCGCGTTGGATAACGTCGCCTGAGTCGCTTTTTGGGTGACCACTGACCGTCGTGCAGGAAACGTGGCACGGTATC
+
0000,BI4C;6C*D..L9+,&+&@:=32IG:>-9JB4GL+NI@G))@*J56E5::=+&'9B8:+0MM.?AANAAH>83@CA)GE596:M?7M6.-?@71>.AG-KE?.L?
@687
GATACCGTGCCACGTTCCTGCACGACGGTCAGTGGTCACCCCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAA
+
0G=IJDI'=DI/MI)762*8:(/DN9C,&3K*;'9@*37;KJ8;&(K+B/39<&NI=27(C>,M4M4.E+8-NJ;*;A4J=D>>4N0K3,(,(4>DMK9.D8?;(G.&?3C
@688
GCGGAACAACTCTTCCACACGCGGCCAGTTGTTCGGCTGACTCACGTCCATCGCGTTGGATAACGTCGCCTGAG
+
0M6.41&KH/A*A/&C/B1,5-?=5G;IC:2''+2@B>F&3)JEFN;00K1&46D4E)C/IDG
@689
GTTGCCAGATTTTTTGCGGCGGAACAACTCTTCCACACGCGGCCAGTTGTTCGGCTGACTCACGTCCATCGCGTTGGATAACGTCG
+
003*61(@1/H74CI3JK9+2<>C0;?B&M<6A)9-BB-@4-G,D1((:.E,'B-4K,)6=3?EB(A6.@4'/C)(6I5-HF=C**HA>(/'<+/>4NB&/87'KD@+DC:H1?9;LHA@54LD6-K'I@*K5J+'KGF=*);9=)'GKG>@50J.7F2>-7',8@D?EH,3<
@693
CCCAGCTCTTCAGTTGCCAGATTTTTGCGGCGGAACAACTCTTCCACACGCGGCCAGTTGTTCGGCTGACTCACGTCCATCGCG
+
00+:EF,'>K,H'LG.'&4(5*.=B=1C/1GH&(<*6I=BK8-,88<';N:NJ14&JI;*M<33/*
@694
GGCTGCATAACCCCCAGCTCTTTCAGTTGCCAGATTTTGCGGCGGAACAACTCTTCCACACGCGGCCAGTTGTTCGGCTGACTCACGT
+
00000.+J'M?E94D@FCK=@7;?A?H97'1D/.14-+8K/:5:NNFC,M>IM@=68NMK739@CE@3IFKMH185LI2M:.@H-&'M
@696
CATTGTCTGTTGCGTGGTTCATCATCCACGGCTGCATAACCCCAGCTCTTTCAGTTGCCAGATTTTGCGGCGGA
+
003K*M+LID6'BH87J527-G6DFI4(<&-B>7)58MI45=>K/8;3C(3+@5
@697
TGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAATCTGGCAACTGAAAGAGCTGGGGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGT
+
00000-6JGGB+15&(A58/41C7*&6.0L;8K2K5,,1501'+1-99:8JD,@3FM,/B03A+N3AN/42+H>-:C;L)75'>3JAAI.F@0H::D;)8@+-2:**9<+MCG-;?K.(.+D
@705
ATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAGAACTGGCTACACTTCGGAGCCGCAC
+
0(50@?=7C&M+,6.2-LH7B>BD1NC?.I*3K4>NL<&A/6(M'(/5>8':I8C28.?=;H*4KH+:78A8?*9D':?0?A,2>J>L7<;D=0+7D.=24@JD8
@710
GGATTCAACTGATCACGCAGCGCACGATAAGCTACGGCAGCGTGCGGCTCCGAAGTGTAGCCCCAGTTCTTTTTTAACTCACGCATTGTCTGTTGCGTGGTTTCAT
+
000'?@4ECE'9&3>?8?C)3)HJ0H.-.GK/*G(M6=.F5G>E7'1);)'1&E14-;?'9D69L*8G4J,=GH&+8E<=5/:34'B1G@0-+;2-*G=H&;H&.>
@711
GCCTGGATTCAACTGATCACGCAGCGCACGATAAGCTACGGCAGCGTGCGGCTCCGAAGTGTAGCCCCCCCAGTTCTTTTAACTCACGCATTGTCTGTTGC
+
0000I>1K/*E)M*3,4.E7D?29F:D055I.@7LH*D19&-.B;A&5086<&*:+&25I-H&//1D,M9A1:H,<3GK,)*NL.0L6>CB,5/3<)*?G'
@712
AACTGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAAT
+
+MA=07EN--&4?.J1A8NF''+.;DILL.&9E+KH4A+;E1M2L98+>+9,G&KB5D';,4>L7G26I&1
@714
CTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACC
+
::L4G)+K/5@IHFB7D+?+&&'0=J0:G(J;=D-,J1EL.B6NA*87:?J;MIEG:711D>;,6MF>'@)/6EC(42?0'C98?F=H;LA1?/B(?<--L<,EII'H:/HJ(5+2A9,J)F;
@716
TCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTT
+
&B.?MEMIDDF6/&046?M5'1,9:G14A9H;F*.C/=DACNI'27&>/?29:CH@G>..M<01-HMD7-67/2CM'=(I)CG(1L(C2FFH0G98@1?E&7CE.85.995H721L;>IIB-18,I2)AH6
@719
CTGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATT
+
00,,5*H9G(15@9L/*?E.'?FH37DI)>*@;1-@&)/(7-*L*E*33(@?M4NL@KHM(2&L7'5D6LJ4N<2DE37L9/L>;?3HJBD.DE/3/G'4HF;JH'=-:
@724
GCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAATTTAAAGAGAGCGTGGA
+
0G;DN&CI)B73D)(E)>DNM6(E.)'I>B;3)B-MKJ<.:*H,*0D@/'/)LE;*38>G&.(5F:F/KM4A.K+I:LF2L7
@725
CACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAAAAGAGAGCGTGGAAGC
+
0003&@;+:8/'@:E<2.GJ.+?CFI.M0E.3E?&D>GD::?&:'(85=,J1710CA67*3E=M9J0@D0'.@>GD4'*-;.CAMH8:)J/E+;'+L.@J6.:H6HAN
@728
TTGTTCCTCGGCACCGCGCATCCGGCGAAAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAAACGTTGGATCTGCCAAAAGAGCTGGCAGAA
+
0000.9FBM*8*8B)58I;=.J?5A16.K@41)*-N=I>'@HC96+.AJ)NC?K*/CC60,1G1):(N&18.;M''7JHC0/,1*1;2)E0/6D@4'0'+:=2N>B9:+G('1&
@730
GGCGAAAATTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAGAGCTGGCAGAACGTGCTGATTTTTACCC
+
000&K+@L:AK+G8<&5(:44(J:')L-8>&E(/394EN6-;N/F;;-1<.9,99&4HM(0?<:FA:H-*>3B5I*:J,:.G?13>
@731
GTTGGATCTGCCAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTTTCACATAATCTGCCCGC
+
000000'?=CAH-MIGKA3(*-14IJ,:LH+9.5;M<4H:K/ME'@@CJC-;CAD6AD6
@743
ATTGAGATAATGAATAGATTTTACTGATGATTCATCATCAATTACGCAACGCAGCAAAATCGGCGGG
+
00-0DN?GG'C:<>@H')+>''D89MML;K,,L;4.457>,HJ;7L?M67G>BN/BN:36*KJ+@HB
@747
AATCTATTCATTATCTCAATCAGGCCGGGGGTTGCTTTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAA
+
00000<6:)LAM')E67&=4N'4,93JMFK&*55&7E-&&H?B+>@A,G/02:BG1I8DHALD.'&>+5'460LL(L7&;
@755
TATCCGGAGATTACTCGATGAGAACGGCGGTTGTTATTCTCCGCAATCCTAATCTCTAAGTTACCGCATTATTGAGAATTCTC
+
L2DB85E-9;,41'03=?+=>5)4@2=8D>GI5B7.M3D.'2=&60)4HI1.&LIH3*6N.4/N4'A,1,CN--)2DMH.4/.
@756
TGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCG
+
8=3GA+MK'C./E/*<)I968-J,&CH89I+)&>'/H>@:EH&5*/>D101>8L-I;F.?8K'CN3G&?.4
@759
CTCCTTTATCATTGCCCCGTTATGGGTCGATATCCGGAGATTACTCGATGAGAACGGCGGTTGTTATTC
+
05+KB?$?)_ë\}r~>q6|(IPZ!Z_g2ËtЫ9=8ϸN{ArjF9н-|ARS9*O	v:J-Ԗs4'VZF@QlG3-cq;5j&hM*TۤDR?:̈́|Ȣ,IaIP-Ap./A=*gҕ575TA}0mf;7*$hB:sT!Dmwaʃ>[o`e\smallgenome
cgatcgatcgatcgatgctagctagctagcttatatatatgagggggcatgctagctagcgcatgcggcggcgcgatcgatcgtagctagctagtcgtagggcc
genometools-1.5.1/testdata/identity_score_matrix000066400000000000000000000022001211610345200222020ustar00rootroot00000000000000  A R N D C Q E G H I L K M F P S T W Y V B Z X
A 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
R 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
N 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
D 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
C 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Q 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
E 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
G 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
H 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
I 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
L 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
K 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
M 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
F 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
P 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
S 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
T 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
W 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
Y 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
V 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
Z 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
genometools-1.5.1/testdata/illegal_is_circular_value.gff3000066400000000000000000000001421211610345200236050ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	.	+	.	ID=gene1;Is_circular=xxx
genometools-1.5.1/testdata/illegal_uppercase_attribute.gff3000066400000000000000000000001401211610345200241620ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	.	+	.	ID=gene1;Undefined=xxx
genometools-1.5.1/testdata/inconsistent_sequence_ids.gff3000066400000000000000000000001671211610345200236770ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	.	+	.	ID=gene
undef	.	exon	1	1000	.	+	.	Parent=gene
genometools-1.5.1/testdata/is_circular_example.gff3000066400000000000000000000003561211610345200224420ustar00rootroot00000000000000##gff-version 3
# organism Enterobacteria phage f1
# Note Bacteriophage f1, complete genome.
J02448	GenBank	region	1	6407	.	+	.	ID=J02448;Name=J02448;Is_circular=true;
J02448	GenBank	CDS	6006	7238	.	+	0	ID=geneII;Name=II;Note=protein II;
genometools-1.5.1/testdata/is_circular_example_with_sequence_region.gff3000066400000000000000000000003741211610345200267300ustar00rootroot00000000000000##gff-version   3
# organism Enterobacteria phage f1
# Note Bacteriophage f1, complete genome.
##sequence-region   J02448 1 6407
J02448	GenBank	region	1	6407	.	+	.	Name=J02448;Is_circular=true
J02448	GenBank	CDS	6006	7238	.	+	0	Name=II;Note=protein II
genometools-1.5.1/testdata/lua_aaseq.fas000066400000000000000000000000621211610345200203010ustar00rootroot00000000000000>seq1
MVHFTAEEKAAVTSLWSKMNVEEAGGEALG
>seq2
KMNAVE
genometools-1.5.1/testdata/lua_dnaseq.fas000066400000000000000000000000731211610345200204640ustar00rootroot00000000000000>seq1
agtccagctgtcagctagcgggcccgatgatatttt
>seq2
gtgctgtac
genometools-1.5.1/testdata/marker.fas000066400000000000000000000015561211610345200176400ustar00rootroot00000000000000>gnl|dbSNP|rs1327328|allelePos=201|totalLen=701|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=127
GTAAAAGATA AAAGTTCCAC TACAATGGAG GAATAATATC CATCGATTTT TTTCACAGAG
GATGTCTGTC GTTCTTAAAA CTCAGCTTTT TATTACTTCC AAGTCATGCT AGTATTTATC
TTATTCTGTT TACATTTGTA TTGATATGAC CAGTGTAGCT AGGAAAATGT GAACACATGT
AAGAATGTAA CTTTAGGCTG
Y
GAAACTGGAA GCAGAAATTC TGTGATGCAA GAGTCACATT TTTTCAAATG TATTCccatg
tgtcattaag tcttaagatg ccatcgattg taagacagac cattattata ggtaatacta
agaaaTTTTT AAATGCAGCT TATTAAAAGT GAATCACTTG AAAGACACCT TAAATATAAA
AACTATACAC AACAAAGTTA AGGGAATATC ATAAATAATG GAAAATTGTT TTCAAATAAA
TGTTAATatt tctaccagaa atgcatcaga ggaccaggtt ctatttgtcc atcccaatag
tagaggttgt ctcactttaa ttttggccaa tcttttcagt gtataattgt gtttctttgt
agctatattt acatttttct tcttactgat gaattaaagc ataccttcac atgtgtatta
gtcattcatg tttcctcttc tgtgggttat acattttctt taacacactt ttattgacat
agttgttccc ttactgttTT
genometools-1.5.1/testdata/marker.out000066400000000000000000000000271211610345200176660ustar00rootroot00000000000000>
TACAATGGAGGAATAATATC
genometools-1.5.1/testdata/matchtool_blast.db000066400000000000000000000316711211610345200213530ustar00rootroot00000000000000>gi|321400135|ref|NG_001764.3| Mus musculus olfactory receptor 400, pseudogene 1 (Olfr400-ps1) on chromosome 11
ATCACTTTTAAAACTATTTCTTTATGTGCACTATTTTATTATTACATCAATTAAAGGGATCAAAAGGAAG
AGAGAGAATGAGATGAGTTCCTCTTTTAAGAATTATAATTCCATGTTTTCCAGCAGCTATGATTTAAATT
TCTTCAATTCACTGAGAGGTCTTGCTATTTTCCTCCATATGTGTATCTTTAAATGAACTCATGCAGCCAA
AGCTGAGAGCCAATGAAACCACTGTTACTGAGTTCATACGCCTAGGTTTGATGGAGACACCAGAGATGTG
GCCAGTTGTCTTCATACTCTTCCTCTTAGATTATATGACTACAGTTTAGGGTAATTTGAGCATCCTAGCC
TACTGTCTTGGTGGAACCCAAACTGCACACCCCCATGTACTTCTTCCTGAGGAATCTGTCACTGATGGAT
GTGGGGTGCATCAGTGTCACTATTCCCTCCATGTTGGGTCGGCTCTTAGTCCACAAACCTACAATTCCAA
ATGGAGACTGCCTCACACAGCTCTTCTTCTTTCCTCTGCTGGCTGGGGTTGACTGATTTCTGTTGACAGC
CATGGCTAATGAGCGCTTCCTGGCCATCTGCCCCTCACTTGTACCCTCCTTCAGCCTAGGCAGACTGGTT
CAGACCGTTCACCACTGAGGCTGGGCCACCTGCTGTGCTGCTTCTCAACACTCCCCTTTGATGTTACACT
GCCTGCCACCTGCCCTGAGGCCGAACTGGTTCTCCAAGATTTGCCAGAGTTTGTTACAAACTGTGAATTT
GGCGAGTTTCTGCTAAAAGGCTGTTCTGAAAATTTCACATCTCTACATCAAGAAACTTGATGTGACTGGG
GATGAGCTTCCCTCTTTATAAGCACAGATTTTATTATTAAACACTTGAACCTTGAACAGACTAGCATGTC
TTGGTTCCATTATTTCTGTACTCACCTAGATTCCCCCTTCTCTTTCAGCTCCAAGATGCCTCCCAGGCTC
GAACCCAGACATGAGAGCTGCAGGCTGGCCCCAACAAGTTTGCACCCAACGTGGGACCTGGGAATGGCAA
AAGATGCTGGAAGAAACACTGCTGGTATGGAGCTCCACGGATAGGAAAAAATTAGAAAATTTGTACTGGA
ACACGGAGAAGCTGTGGTACAGTCTGAGCTGGAACAGCATGCTAACCCATGTGCTGGATTCGCTCAGGTT
CAGCAGTGATATCAGGATCTAGGAACACTACAGGCAGTCGGCCGCAGCTTCCAGAAGCTGCTTTTTAGGC
GAAAGGAATAAGGGTTTAAAAGAATGAACAGGTGGATGGCCGCAGTCAGAAACTGCATCAAGCGGGAGGA
AAGTTGGGTTTTGAAACTCTCCCAGAGACAGAGAGAAACGGGGATGCCCTGCTTTATTCTCTCTGGGCCC
TACAGAAGAAGTTCTCTGCCCTCTTTTTGTTTTTGTCTAAGGTCTTGTCTAATGTCTGGTGCACTGGTCT
GTTCATGTGTTCAACTCATGTGTGTTCGTGTCTTCTCATCTGAATGACTGAATGTTCTGTTTCATGTTGG
AAAATAAAAGATGGCTAAAACTTTCTCTGCTGGTATAGCAAAGCTGAGAGTGGCTCACACTTTGACTGAG
AATCAGGCACAGCAGGAGGGCTCCTGCTAGAAAAACTGTTTCTTAAGAAAGGGAATCTGCAGCCTCATGG
ATTTGGGGTGAAAAAGCTGATAGATGGTTTTTTCCTAAGAAAATTCTCTGTATTTGTGATTATTGCGTTT
AGCTAATGACAAAGTGCTTTTTATTTTATAATTAGAGCTAGAAAAATTAAAATTCTCTGATTGGTCTAAG
TGTAGCCGCTTCGTTTGGTATCAGCTCATAAGTTATTGGTTAGGATTAAATAATTGTAACATCGGTAACA
GAAGGTTAGCCTTAAGTTGGCAACTCAGGAGTCTTTTCAAACACATGGCATAAGCGGGCCAAAAAACTGG
GCCTCCTAAGATTCTTCTAGCTGAGATAATATTTAATGTGATTCTTATCCTAGAAAGTAAATTTAAAGAA
AAGATTTAAAGCAATGTCTCTTTAATGAAGCATTAAAGCTTGCACTGTCATGCATTCATGGGTATAAATT
GGCAGCCAAATCTTGCAATGTGGTAGTGAAGATTTAATGTTGATTCTAAAGTGATATATTGCTTTGAAAT
TGGGTATTGCTTTCCCAAGGCTGTAGATATTATTCTAACGTTGCATAAGAAACTTAAAAATCATAGTTAA
AAATTGCCAGTGTTCCTTTAAGTGCAGCTGGCAGTTTGATTGCAAATTTAAGATTTTATACTCACCCATA
TATTGTTAATTAAGATAATTACAAGAGTAATCATCTTATGAGAGCACTAACACAGCTCTCTGTGGCTATA
CAGCCATACAAAGCTCAGGGTAGCCTCAGCGAGGTTTGTGTGACTTTCTTTTGTTTTGCAAACAGTATGC
CTAAGGAAGTTCTTGAAACTTGCCTCTCCTTGCCTCTCAAGGGAAGTTACTTTAAATCTTTGCTCTAACA
CAGGCGCTTTTAAGTTCTGGGGAGTAACTGTTGCTCCAGAAAAGATTCAGAGGCAATATATTTTTAATTC
TTATGGTTTTAGTTTACTACAGAAGGCTTTGCAGAAAATAAAGAAAGCATTTATAATTGTTATCAATTAT
AATCAATGGTAATTAAATATTAGCTGCCCATTTTAGTTAATGGTTATTAAATGTGCCCACAGCAACTCTT
TAGCAGGCTGCATTGTGACTAAGGGTGTGAAATCCTTAGCTGTCATTAAGCTAACCCTAAGCCTAGCTGC
TTTATCTTTACTGTAAACATTTATCTGGTTCCTGTAGTCCTTTTGAAGTCATTCCTTTGTTTCCTGTCAG
GTAACTTGAATGTACTTTGCCTGCTGTGACTTCCTGCCCCCTTTATTTTCTGTATTCTTTGGCAAGAGAA
AACATTATTTGTTTTCTGCTGCTGGCTGCTGCGGGGCGGGGCCTTGAGGCACACAGATTTTCCTGAGCAT
GGTGGCTCAGAAGGCTGTCAGAAAGCTGGTGGCTTTGTAGCAAACTCAGGAGAGGGCCATGCTCACCATT
GCCCCCATGAGACTCCACCCATCCCCGCCTGGGTAGCCATATTTTTCCACGCTAAGACTCGGGGTGCTCT
GCCACTTGGGCTTTCTAGCCTACAACAGATTGGGCCACCTTCAGCCTCTTCCGCCTGAGAAGAAGGCCGA
GGGTGGGCAAGGCCGAGGTAGCGCTCACCTCAAAACACAGTTTCAGCATCCTATTAAAACTGCTATGGTG
CTAATAAAGAATTGTAAGATAAATTCGTATATTTTAGAAAACTTACAACAAAAATTGTGTTTTAAAAACC
GACTAAGTGTCTGTTCCTTGTTCCAAACAGCAATTAATTTGGTAATTACAGATCTATTGCATACCATCAT
TTTGAATAAAATTGACAATCATTATCCCAAAGATAAGTTAAAAATTTGTTTTTATGCATGCTTCTGTATC
TTCTATAAATTCATGCATGCATGCATTCCACTTACTGTGTTTAAAAACAACCCCTCTATGGGAAATGAGT
AAATGTGAATTAGATCACACGTTTATTCTTTTGAGTTTCCTCCTGTTTCAGCACAGATAATTAAGTTGTG
TGCTGTAGATGGTGTTTTAAAATGCTGAACAATCAAACCTTAATTTGTATATTAATAGTCAATATTATAT
CTCAGAGCTCACAATTGCTTAAGATTGTTCGTCCCTTCTCAAATTTGCAATTGCTTATGTATATACAACT
CATAAGTAAAAATGCTAGATTTATGTCTCAGGCAGTCTATAGGTCCTACATATAAGATAGATTGGATATA
TAATCTCGTTCTTTATATATTCAAAACAGTTATGGTTTAAGATAATATTTTAGTATTCTTGGAAATTGTG
CATGTCAAATTGTAAAAAATTCTTTGCTCTTAGTGTCCTAGGTTACTACTTGTTTCCAAATAATAGTGTT
AATTCTTGAGGACTTATACTTAATAAAATGCTGCAAATAAATACTCTTATTTCTGATTTAATAAATAAAT
AAATTATACACATGTGACTATTAATAACTTGTCAAGCTTTCTAGTTACAACTGCTCTTTAAGAGAAACAA
TTAAAAGTGCAATTAGTCACTGCCCATGTTACATTAAAACTGACTATAACAGTCAAGTATTTAGATGTCA
ACAAATTATTAATTCTCAAGAACAAGGTATTGTGGAACTTTAAAACTTTAGCTTCTTAAAAGACAAAGAA
GGGGGAAATTATATCCCCGTGCATATTATTTAATGTATTCCCATTCACATTATTTAAATCATACTTTTAT
TTTAGAATTTTGAAATTTAGATGTCAAAGAACTTAATAAATGCCTTATATTATCTTAAAAGGATCTACTT
ATTGGCATATGGCTTGATCCTGAACAGCTACCTTATTAGGAAAGGAAAAAGCATAGGTTCTCTCCACAGA
AGCATGATGGCTAATTCATGTGACAAGCTGACAGGTGAGTTTGCTCAGTGCCCTGACTGTAGTGACAAGG
AAGCTGAATTGGGCACATGTTTTCGACCCATCCTTGCTTGCCATTTTTCCAGTTTAGACAAGCAAAGCTG
CCTTGCTTCAAGCTTTTTAACTTTATGGTAAAAAGAACATCAGAGACTGTGTAATCTGACTTAGAAAGAT
TAGTCATATAATAGAGTTATAATGATTCTTCTCTTTCCTTCAATGTGACCAGTTATTCTAACTCAATCTT
AGACTGGTCTAGTACTAATTCCAATATTAGAGATACCTATTAAAGATAGCTAAAAATCTTAATTACCTAG
CAAAGTTAATTTGGAGCACAGTCTCCACTTCCAGAGAATCTCTGGCTTTTCTGCTAATCCTCAAAGCCAG
ATCCCCACACCGGGAGGCCAGAGCCTGAGTTTGATTGTTGCTAATTTGCAACTGAATAAAGTACCTGGGC
TTCCACAAAGAAGCTTTTATACTGTTGTTTTTCACTGCCCCACCTTTGTTTCTCAAGCAGGTCAGCCATT
CTTTTCAGCCTGACTACAGGAGATGTAAAGCCTCACCTCCAACAGTGCAGATGGCAGTTATTAATCTTCA
TAAAGAAGCATTTTAAGTACATATTGTGGCCTTCATCTGATTTGGGAATAAGGTGTGCTATGAGGGCCGG
TTAGTCAATGACGGACAACCAGATTTCGGAGCCATAACAATCTAAGACAGAGGTACATGCCAAAAGGCCA
TGGCTGTTGATAACACACCACAGAACCATGTTTGTGTGAAATATAACACAAACTAGCTGCATGTAGCCTC
CAAGACAGAATTAGATGGTTCGGGAAAATCTGAGATCCTAAGGCAGGCACGGCCGCCAGCCACCATAACT
CCCAGGCAAGACTATAGAGCATAAATAAATTTTATGCCTCAGTCCAGTTTTTTTAATATTATTTAAAGGG
GGGAAAATGTACCTCCTTCAGCCTAGGCAGGCTGGTTCAGACCATTCACCACTGAGGCTAGGCCACCTGC
TACCCACCTAGATTCCCTCTTCTCTTTCAGCTCCAAGATGCCTCCCAGACTCGAACCCAGCCTCAACACT
CATTTACAGCACCCAAATGAACCACACCATCCAGAGGATCTTGGTGGCCTCATCGTGGGTTTGTTCCTTC
AGCAGTGTACTTACTCATACTGTGGCCATATCCACACTTCACTTCTGTGGTCTCAATGTGGTCAATAACT
TCTACTGTGACCTGCCTCAGCTCTTCCAACTGTCCTGCTCCACTACCCAGCTAAATGAGCTGCTGCTCTT
TGCAGTAGGTTTCCTAATGACAGAAACCTCCATGGCACTCATTTTTACCTTTTACATCTATGGGGCAGTT
GCAATTCTGCAAATCCGCTCTGCTGAAGGCAGGTAGAAAGCCTTCTCCACATACAGCTCTCACCTCACTG
TGGTTGCCATATTCTATGGCACAGGTATCTTTGCCTACATGAGTCTCAGGTCCATCAAACTTTCTGATAA
TGATAAAGCTATTGGGATTTTCAACACTGATGATCAACCCCATGCTAAACCCACTCATCTACAGTCTCAG
AAACCCTGATGTGCAGGCTGCCCTCTGGAAGGTACTCACAGGGAAACAGCTATCACATTGAGACCTCAAA
GCTTCTTCCACCTATTTCTTCTAAAACTAAAGCTGTATATTAAGGTTTCCTGTGGTTCAACACTAGAACA
AATTGTTCAACATTGTTTCCAATGAGAAATGTTATGATGGAAAAGAGCTTCCCTCAATTATCATCTGCTG
AATGTTTTAATTTTTTGAAAGAGAGGAATTTGTAATCTAAACATTTAAATA
>gi|321400152|ref|NM_001025241.3| Mus musculus Ssty2 family member (LOC434960), mRNA
GGAGGTGCTAGAATCCATTCAAGGAGCTCAAATCTGTTTAGCATAGTCTTCTTCACCTGCTCAGAAGTTC
TCGTAGAGAAGAGTCTTGGTCCAGCATTCACTCCCAACCCATAACCATTGCCCATCAGGAATTCATATAT
ATGACAGAGGCAACAGCATTGTGTCTGGTGTAAACGGGCAAGATCTTCAGTCCCAGGCAATGAGCAAGTA
TGATATTTGAAGGGAATGGAAGCCACAAGACAGTGTGATCTACCACAACAGGTCTACAGCCAGGTAGAAG
ACAATACATCTGAAGAGTCTGAGCATGACATCACTCAAGAAGAAGAGTAGGAGGAAGCCTTCTTCCCAGG
CCCTGGGGAATATTGTTGGCTGCAGAATTTCTCATGGGTGGAAGGAAGGTAATGAGCCTGTCACCCATTG
GAAGGCCATCATTCTAGGTCAACTGCCAACAAACCCTTCTCTTTATTTGGTGAAGTATGACGGAATTGAC
AGTGTCTACGGACAGGAGCTCCACAGCGATGAGAGGATTTTAAATCTTAAGGTCTTGCCTCACAAAGTAG
TTTTTCCTCAGGTGAGGGATGTCCACCTCGCAGGCGCACTGGTTGGCAGAGAGGTACAACACAAATTTGA
GGGGAAAGATGGCTCTGAGGACAACTGGAGTGGGATGGTGCTAGCCCAGGTGCCATTCTTACAGGACTAT
TTTTACATTTCCTACAAGAAGGATCCGGTCCTCTACGTCTATCAGCTCCTGGATGACTACAAGGAAGGTA
ACCTCCACATCATTCCAGAGACCCCTCTGGCTGAGGCGAGATCAGGTGATGACAATGACTTCTTAATAGG
TTCCTGGGTGCAGTACACCAGAGATGATGGATCCAAAAAGTTCGGAAAGGTTGTTTACAAAGTTCTAGCC
AATTCTACTGTGTACTTTATCAAATTTCTCGGTGACCTCCATATCTATGTCTATACTCTGGTGTCAAATA
TCACTTAAATTTAAAAAAATCACAAAGTACAGAAATGTAAACTTATAGGATTGAAAAAAAATGTTTGTTT
TCCTGTGTTGGGTACCTATGGGTCTTTGACAACCTCAGTATCTTTGTCAATAAAATTTGTTTTGTTCTAA
AAA
>gi|321400062|ref|NM_001202523.1| Homo sapiens discoidin domain receptor tyrosine kinase 1 (DDR1), transcript variant 6, mRNA
AGTGCGGAGGAACTGAGCCCCGGGAGGAGGTGCTCCTGTGCAGCCCCACTGAGTCAGCTCATCTATCGCC
TGCCCTCCACCTGGCCAGTCCCTGCGGGCATCTAACTGCTAAGCCTCCGCTCAGCCAACACCCAGTTGGT
CAGTCTGGTCACAGTCCAGCAAAAAGAGGGACTGCCACTCTAACCCACCAGTGACACCACTCTTCCCGGC
TGGATGGTCAATTAGCTCTGGCATGAGAGAATGTCACTGCCGAGATGCTGCCCCCACCCCCTTAGGCCCG
AGGGATCAGGAGCTATGGGACCAGAGGCCCTGTCATCTTTACTGCTGCTGCTCTTGGTGGCAAGTGGAGA
TGCTGACATGAAGGGACATTTTGATCCTGCCAAGTGCCGCTATGCCCTGGGCATGCAGGACCGGACCATC
CCAGACAGTGACATCTCTGCTTCCAGCTCCTGGTCAGATTCCACTGCCGCCCGCCACAGCAGGTTGGAGA
GCAGTGACGGGGATGGGGCCTGGTGCCCCGCAGGGTCGGTGTTTCCCAAGGAGGAGGAGTACTTGCAGGT
GGATCTACAACGACTGCACCTGGTGGCTCTGGTGGGCACCCAGGGACGGCATGCCGGGGGCCTGGGCAAG
GAGTTCTCCCGGAGCTACCGGCTGCGTTACTCCCGGGATGGTCGCCGCTGGATGGGCTGGAAGGACCGCT
GGGGTCAGGAGGTGATCTCAGGCAATGAGGACCCTGAGGGAGTGGTGCTGAAGGACCTTGGGCCCCCCAT
GGTTGCCCGACTGGTTCGCTTCTACCCCCGGGCTGACCGGGTCATGAGCGTCTGTCTGCGGGTAGAGCTC
TATGGCTGCCTCTGGAGGGATGGACTCCTGTCTTACACCGCCCCTGTGGGGCAGACAATGTATTTATCTG
AGGCCGTGTACCTCAACGACTCCACCTATGACGGACATACCGTGGGCGGACTGCAGTATGGGGGTCTGGG
CCAGCTGGCAGATGGTGTGGTGGGGCTGGATGACTTTAGGAAGAGTCAGGAGCTGCGGGTCTGGCCAGGC
TATGACTATGTGGGATGGAGCAACCACAGCTTCTCCAGTGGCTATGTGGAGATGGAGTTTGAGTTTGACC
GGCTGAGGGCCTTCCAGGCTATGCAGGTCCACTGTAACAACATGCACACGCTGGGAGCCCGTCTGCCTGG
CGGGGTGGAATGTCGCTTCCGGCGTGGCCCTGCCATGGCCTGGGAGGGGGAGCCCATGCGCCACAACCTA
GGGGGCAACCTGGGGGACCCCAGAGCCCGGGCTGTCTCAGTGCCCCTTGGCGGCCGTGTGGCTCGCTTTC
TGCAGTGCCGCTTCCTCTTTGCGGGGCCCTGGTTACTCTTCAGCGAAATCTCCTTCATCTCTGATGTGGT
GAACAATTCCTCTCCGGCACTGGGAGGCACCTTCCCGCCAGCCCCCTGGTGGCCGCCTGGCCCACCTCCC
ACCAACTTCAGCAGCTTGGAGCTGGAGCCCAGAGGCCAGCAGCCCGTGGCCAAGGCCGAGGGGAGCCCGA
CCGCCATCCTCATCGGCTGCCTGGTGGCCATCATCCTGCTCCTGCTGCTCATCATTGCCCTCATGCTCTG
GCGGCTGCACTGGCGCAGGCTCCTCAGCAAGGCTGAACGGAGGGTGTTGGAAGAGGAGCTGACGGTTCAC
CTCTCTGTCCCTGGGGACACTATCCTCATCAACAACCGCCCAGGTCCTAGAGAGCCACCCCCGTACCAGG
AGCCCCGGCCTCGTGGGAATCCGCCCCACTCCGCTCCCTGTGTCCCCAATGGCTCTGCCTACAGTGGGGA
CTATATGGAGCCTGAGAAGCCAGGCGCCCCGCTTCTGCCCCCACCTCCCCAGAACAGCGTCCCCCATTAT
GCCGAGGCTGACATTGTTACCCTGCAGGGCGTCACCGGGGGCAACACCTATGCTGTGCCTGCACTGCCCC
CAGGGGCAGTCGGGGATGGGCCCCCCAGAGTGGATTTCCCTCGATCTCGACTCCGCTTCAAGGAGAAGCT
TGGCGAGGGCCAGTTTGGGGAGGTGCACCTGTGTGAGGTCGACAGCCCTCAAGATCTGGTTAGTCTTGAT
TTCCCCCTTAATGTGCGTAAGGGACACCCTTTGCTGGTAGCTGTCAAGATCTTACGGCCAGATGCCACCA
AGAATGCCAGGAATGATTTCCTGAAAGAGGTGAAGATCATGTCGAGGCTCAAGGACCCAAACATCATTCG
GCTGCTGGGCGTGTGTGTGCAGGACGACCCCCTCTGCATGATTACTGACTACATGGAGAACGGCGACCTC
AACCAGTTCCTCAGTGCCCACCAGCTGGAGGACAAGGCAGCCGAGGGGGCCCCTGGGGACGGGCAGGCTG
CGCAGGGGCCCACCATCAGCTACCCAATGCTGCTGCATGTGGCAGCCCAGATCGCCTCCGGCATGCGCTA
TCTGGCCACACTCAACTTTGTACATCGGGACCTGGCCACGCGGAACTGCCTAGTTGGGGAAAATTTCACC
ATCAAAATCGCAGACTTTGGCATGAGCCGGAACCTCTATGCTGGGGACTATTACCGTGTGCAGGGCCGGG
CAGTGCTGCCCATCCGCTGGATGGCCTGGGAGTGCATCCTCATGGGGAAGTTCACGACTGCGAGTGACGT
GTGGGCCTTTGGTGTGACCCTGTGGGAGGTGCTGATGCTCTGTAGGGCCCAGCCCTTTGGGCAGCTCACC
GACGAGCAGGTCATCGAGAACGCGGGGGAGTTCTTCCGGGACCAGGGCCGGCAGGTGTACCTGTCCCGGC
CGCCTGCCTGCCCGCAGGGCCTATATGAGCTGATGCTTCGGTGCTGGAGCCGGGAGTCTGAGCAGCGACC
ACCCTTTTCCCAGCTGCATCGGTTCCTGGCAGAGGATGCACTCAACACGGTGTGAATCACACATCCAGCT
GCCCCTCCCTCAGGGAGCGATCCAGGGGAAGCCAGTGACACTAAAACAAGAGGACACAATGGCACCTCTG
CCCTTCCCCTCCCGACAGCCCATCACCTCTAATAGAGGCAGTGAGACTGCAGGTGGGCTGGGCCCACCCA
GGGAGCTGATGCCCCTTCTCCCCTTCCTGGACACACTCTCATGTCCCCTTCCTGTTCTTCCTTCCTAGAA
GCCCCTGTCGCCCACCCAGCTGGTCCTGTGGATGGGATCCTCTCCACCCTCCTCTAGCCATCCCTTGGGG
AAGGGTGGGGAGAAATATAGGATAGACACTGGACATGGCCCATTGGAGCACCTGGGCCCCACTGGACAAC
ACTGATTCCTGGAGAGGTGGCTGCGCCCCCAGCTTCTCTCTCCCTGTCACACACTGGACCCCACTGGCTG
AGAATCTGGGGGTGAGGAGGACAAGAAGGAGAGGAAAATGTTTCCTTGTGCCTGCTCCTGTACTTGTCCT
CAGCTTGGGCTTCTTCCTCCTCCATCACCTGAAACACTGGACCTGGGGGTAGCCCCGCCCCAGCCCTCAG
TCACCCCCACTTCCCACTTGCAGTCTTGTAGCTAGAACTTCTCTAAGCCTATACGTTTCTGTGGAGTAAA
TATTGGGATTGGGGGGAAAGAGGGAGCAACGGCCCATAGCCTTGGGGTTGGACATCTCTAGTGTAGCTGC
CACATTGATTTTTCTATAATCACTTGGGGTTTGTACATTTTTGGGGGGAGAGACACAGATTTTTACACTA
ATATATGGACCTAGCTTGAGGCAATTTTAATCCCCTGCACTAGGCAGGTAATAATAAAGGTTGAGTTTTC
CACAAAAAAAAAAAAAAAAAA
>gi|321267542|ref|NM_001202506.1| Danio rerio brain specific kinase 146-like (LOC791840), mRNA
GCAGCGGAGAGACAGGATGATGATGATTATGATTATGATGATAATGATGAAGATGAGGATAATTATGTGA
TATCTGTATGTGATTTATCCACCGGGGGAACAGCGGAGATTCACGGGAGCGGTTTAACGTATTGTGAGGC
TGTCTGTGGGCCAGGATGAGCTCGTCTCCGGTGGTTTCCCATGACATTCTGGAGGAGCTGCAGCTCTACA
CCGCTCAGAACCTGGAGAAGCTGGAGGTCAATAAATACTATGAGGTGATCCGGGAGCTCGGGAAGGGCAC
TTACGGGAAGGTGGACCTCGTCATTCATAAGATCAGAGGTAGCAAAATGGCTCTGAAGTTTCTGAAGAAG
AAAAGCACCAAGCTGAAGAGCTTCTTGCGGGAGTACAGCATCTCTCTCTATCTCTCTCCATGTCCCTTCA
TCATCAACATGTTCGGCATCGCCTTTGAGACAGACGAGTATTATGTGTTTGCGCAGGAATACGCTCCTTC
TGGGGACCTGTTTGACATCATTCCACCACAGGTGGGTCTGCCAGAGCCGGTGGCGAAGCGCTGTGTGCAT
CAGGTGGCCATCGCTCTCGAATACCTGCACTCCAAAAAACTGGTGCACCGAGACATCAAACCCGAGAACA
TCCTAATCTTCGACAAGGAGTGCCGTAAGGTCAAGCTGTCAGACTTCGGGATGGCGCGGCGCGCCGGTTC
ACCGGTCAAGCGTGTTAGCGGCACAATCCCATACACGGCTCCAGAACTCTGCGATACGTCCAAACACGAC
GGCTTCTGCGTGGACTACAGCACCGATGTGTGGGCGTTCGGAGTGCTGCTGTTCTGCATGCTAACCGGGA
ACTTTCCATGGGAAAAAGCGATGCCGTCTGATACTTTCTACGAGGAGTTTGTGCGCTGGCAGAAGCGGCG
GACGGGTGCGGTTCCGTCACAATGGCGTCGATTTACAGACGAATCCCTGCGCATGTTTCGAAAGCTCCTA
GCATTGGAGCAGGAACGCAGATGCAGCGTCAAGGAGGTTTTCGCACATTTAGGCCACCGCTGGATGCTTG
ATGGAACTAGCGGAAACCATCATCAATCCGTGCTCAACTCTTCATCAGAGGAAGACGAATTGCTTGTGGA
TCGTATGAAGCAGCAGACCTTATCTCCGACAGCTAACACGAGCAATGCTATTGAGCCCGGATCGGCTAAC
CACTTCACATCTGTGTCCACCAATAGCTCGGTGTCTTCCACTAACAGCTATGAGCGTTCGGCTAGAGACA
GTCCTCCGACTAGCAGGATCCTGGTCACGACGCCTATAGAAATCTGCGTCTAAATGCACAGCTGATGAAA
TTAACATGCGCACAAGCTGACGCACACTCCTGTGA
genometools-1.5.1/testdata/matchtool_blast.match000066400000000000000000041440711211610345200220650ustar00rootroot00000000000000# BLASTN 2.2.24+
# Query:  test.2
# Database: /home/stud2009/skastens/Downloads/ncbi-blast-2.2.24+/bin/bla.fas
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 27 hits found
test.2	test	100.00	210	0	0	1	210	351	560	2e-111	 388
test.2	test	100.00	210	0	0	211	420	1121	1330	2e-111	 388
test.2	test	86.96	23	2	1	397	419	154	175	0.053	25.1
test.2	test	93.75	16	1	0	184	199	1429	1414	0.053	25.1
test.2	test	85.00	20	3	0	36	55	1450	1431	0.68	21.4
test.2	test	81.48	27	3	2	336	361	1571	1596	0.68	21.4
test.2	test	100.00	10	0	0	34	43	393	384	2.5	19.6
test.2	test	100.00	10	0	0	109	118	1027	1036	2.5	19.6
test.2	test	100.00	10	0	0	249	258	1168	1159	2.5	19.6
test.2	test	100.00	10	0	0	305	314	1224	1215	2.5	19.6
test.2	test	100.00	10	0	0	274	283	1801	1792	2.5	19.6
test.2	test	92.86	14	0	1	45	57	1915	1902	2.5	19.6
test.2	test	92.31	13	1	0	385	397	1979	1991	2.5	19.6
test.2	test	100.00	10	0	0	205	214	2010	2001	2.5	19.6
test.2	test	100.00	10	0	0	102	111	2693	2684	2.5	19.6
test.2	test	100.00	10	0	0	66	75	4550	4559	2.5	19.6
test.2	test	84.21	19	2	1	125	143	18	1	8.9	17.7
test.2	test	100.00	9	0	0	150	158	649	657	8.9	17.7
test.2	test	91.67	12	1	0	17	28	825	814	8.9	17.7
test.2	test	100.00	9	0	0	152	160	1010	1002	8.9	17.7
test.2	test	100.00	9	0	0	375	383	1014	1006	8.9	17.7
test.2	test	91.67	12	1	0	111	122	1035	1046	8.9	17.7
test.2	test	87.50	16	1	1	231	245	1500	1515	8.9	17.7
test.2	test	100.00	9	0	0	190	198	2102	2110	8.9	17.7
test.2	test	100.00	9	0	0	49	57	3437	3445	8.9	17.7
test.2	test	100.00	9	0	0	45	53	3481	3473	8.9	17.7
test.2	test	100.00	9	0	0	25	33	4286	4294	8.9	17.7
# BLAST processed 1 queries
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  210     0       0       211     420     1121    1330    2e-111   388
test.2  test    86.96   23      2       1       397     419     154     175     0.053   25.1
test.2  test    93.75   16      1       0       184     199     1429    1414    0.053   25.1
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    81.48   27      3       2       336     361     1571    1596    0.68    21.4
test.2  test    100.00  10      0       0       34      43      393     384     2.5     19.6
test.2  test    100.00  10      0       0       109     118     1027    1036    2.5     19.6
test.2  test    100.00  10      0       0       249     258     1168    1159    2.5     19.6
test.2  test    100.00  10      0       0       305     314     1224    1215    2.5     19.6
test.2  test    100.00  10      0       0       274     283     1801    1792    2.5     19.6
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    100.00  9       0       0       375     383     1014    1006    8.9     17.7
test.2  test    91.67   12      1       0       111     122     1035    1046    8.9     17.7
test.2  test    87.50   16      1       1       231     245     1500    1515    8.9     17.7
test.2  test    100.00  9       0       0       190     198     2102    2110    8.9     17.7
test.2  test    100.00  9       0       0       49      57      3437    3445    8.9     17.7
test.2  test    100.00  9       0       0       152     160     1010    1002    8.9     17.7
test.2  test    85.00   20      3       0       36      55      1450    1431    0.68    21.4
test.2  test    92.86   14      0       1       45      57      1915    1902    2.5     19.6
test.2  test    92.31   13      1       0       385     397     1979    1991    2.5     19.6
test.2  test    100.00  10      0       0       205     214     2010    2001    2.5     19.6
test.2  test    100.00  10      0       0       102     111     2693    2684    2.5     19.6
test.2  test    100.00  10      0       0       66      75      4550    4559    2.5     19.6
test.2  test    84.21   19      2       1       125     143     18      1       8.9     17.7
test.2  test    100.00  9       0       0       150     158     649     657     8.9     17.7
test.2  test    91.67   12      1       0       17      28      825     814     8.9     17.7
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7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#je9'X|9wi[xoY6-m]Mrc٧"99,\長[rao@4@Z}yҎdyKhB-K\{xu0IO[y˙0/6Gn-xo-yKK\rYnY.ss:k@c(bhe)c^6DE'̭\罖V(*"
7,3a.49s#*AKeќs{-ϭ\QQTEE$n.Ygsՙ\hs0FTyˢ9oq#jeP1P9genometools-1.5.1/testdata/matchtool_blast.out000066400000000000000000017440621211610345200216030ustar00rootroot00000000000000query	dbname2	q.startpos	d.startpos	q.endpos	d.endpos	bit score	evalue	ali length
test.2	test	1	351	210	560	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	45	3473	53	3481	17.700	8.9	9
test.2	test	25	4286	33	4294	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	211	1121	420	1330	388.000	2e-111	210
test.2	test	397	154	419	175	25.100	0.053	23
test.2	test	184	1414	199	1429	25.100	0.053	16
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	336	1571	361	1596	21.400	0.68	27
test.2	test	34	384	43	393	19.600	2.5	10
test.2	test	109	1027	118	1036	19.600	2.5	10
test.2	test	249	1159	258	1168	19.600	2.5	10
test.2	test	305	1215	314	1224	19.600	2.5	10
test.2	test	274	1792	283	1801	19.600	2.5	10
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	375	1006	383	1014	17.700	8.9	9
test.2	test	111	1035	122	1046	17.700	8.9	12
test.2	test	231	1500	245	1515	17.700	8.9	16
test.2	test	190	2102	198	2110	17.700	8.9	9
test.2	test	49	3437	57	3445	17.700	8.9	9
test.2	test	152	1002	160	1010	17.700	8.9	9
test.2	test	36	1431	55	1450	21.400	0.68	20
test.2	test	45	1902	57	1915	19.600	2.5	14
test.2	test	385	1979	397	1991	19.600	2.5	13
test.2	test	205	2001	214	2010	19.600	2.5	10
test.2	test	102	2684	111	2693	19.600	2.5	10
test.2	test	66	4550	75	4559	19.600	2.5	10
test.2	test	125	1	143	18	17.700	8.9	19
test.2	test	150	649	158	657	17.700	8.9	9
test.2	test	17	814	28	825	17.700	8.9	12
genometools-1.5.1/testdata/matchtool_blast_corrupt.match000066400000000000000000000024531211610345200236340ustar00rootroot00000000000000gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	13	0	0	1218	1230	118	106	0.29	25.7
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	13	0	0	922	934	2847	2835	0.29	25.7
i|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	92.86	14	1	0	1153	1166	34	47	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	82.61	23	4	0	630	652	200	222	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	88.24	17	2	0	648	664	567	551	4.1	21.8
broken file
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	11	0	0	386	396	670	680	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	11	0	0	891	901	2948	2938	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	92.86	14	1	0	783	796	4891	4878	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321267542|ref|NM_001202506.1|	100.00	11	0	0	781	791	151	161	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321267542|ref|NM_001202506.1|	100.00	11	0	0	644	654	336	326	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400062|ref|NM_001202523.1|	100.00	11	0	0	725	735	2311	2301	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400062|ref|NM_001202523.1|	100.00	11	0	0	761	771	2406	2416	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400152|ref|NM_001025241.3|	100.00	11	0	0	643	653	649	639	4.1	21.8
genometools-1.5.1/testdata/matchtool_blast_empty.match000066400000000000000000000000001211610345200232560ustar00rootroot00000000000000genometools-1.5.1/testdata/matchtool_blast_empty.out000066400000000000000000000001221211610345200227760ustar00rootroot00000000000000query	dbname2	q.startpos	d.startpos	q.endpos	d.endpos	bit score	evalue	ali length
genometools-1.5.1/testdata/matchtool_blast_neg.match000066400000000000000000000024411211610345200227040ustar00rootroot00000000000000gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	13	0	0	1218	1230	118	106	0.29	25.7
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	13	0	0	922	934	2847	2835	0.29	25.7
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	92.86	14	1	0	1153	1166	34	47	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	82.61	23	4	0	630	652	200	222	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	88.24	17	2	0	648	664	567	551	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	11	0	0	386	396	670	680	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	11	0	0	891	901	2948	-2938	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	92.86	14	1	0	783	796	4891	4878	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321267542|ref|NM_001202506.1|	100.00	11	0	0	781	791	151	161	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321267542|ref|NM_001202506.1|	100.00	11	0	0	644	654	336	326	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400062|ref|NM_001202523.1|	100.00	11	0	0	725	735	2311	2301	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400062|ref|NM_001202523.1|	100.00	11	0	0	761	771	2406	2416	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400152|ref|NM_001025241.3|	100.00	11	0	0	643	653	649	639	4.1	21.8
genometools-1.5.1/testdata/matchtool_blast_too_few.match000066400000000000000000000024021211610345200235720ustar00rootroot00000000000000gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	13	0	0	1218	1230	118	106	0.29	25.7
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	13	0	0	922	934	2847	2835	0.29	25.7
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	92.86	14	1	0	1153	1166	34	47	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	82.61	23	4	0	630	652	200	222	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	88.24	17	2	0	648	664	567	551	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	11	0	0	386	396	670	680	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	11	0	0	891	901	2948	2938	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	92.86	14	1	0	783	796	4891	4878	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321267542|ref|NM_001202506.1|	100.00	11	0	0	781	791	151	161	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321267542|ref|NM_001202506.1|	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400062|ref|NM_001202523.1|	100.00	11	0	0	725	735	2311	2301	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400062|ref|NM_001202523.1|	100.00	11	0	0	761	771	2406	2416	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400152|ref|NM_001025241.3|	100.00	11	0	0	643	653	649	639	4.1	21.8
genometools-1.5.1/testdata/matchtool_blast_too_many.match000066400000000000000000000024521211610345200237620ustar00rootroot00000000000000gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	13	0	0	1218	1230	118	106	0.29	25.7
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	13	0	0	922	934	2847	2835	0.29	25.7
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	92.86	14	1	0	1153	1166	34	47	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	82.61	23	4	0	630	652	200	222	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	88.24	17	2	0	648	664	567	551	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	11	0	0	386	396	670	680	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	100.00	11	0	0	891	901	2948	2938	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400135|ref|NG_001764.3|	92.86	14	1	0	783	796	4891	4878	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321267542|ref|NM_001202506.1|	100.00	11	0	0	781	791	151	161	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321267542|ref|NM_001202506.1|	100.00	11	0	0	644	654	336	326	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400062|ref|NM_001202523.1|	100.00	11	0	0	725	735	2311	2301	4.1	21.8	1234	1234
gi|321267505|ref|NM_200010.2|	gi|321400062|ref|NM_001202523.1|	100.00	11	0	0	761	771	2406	2416	4.1	21.8
gi|321267505|ref|NM_200010.2|	gi|321400152|ref|NM_001025241.3|	100.00	11	0	0	643	653	649	639	4.1	21.8
genometools-1.5.1/testdata/matchtool_blastalln.out000066400000000000000000000030641211610345200224370ustar00rootroot00000000000000query	dbname2	q.startpos	d.startpos	q.endpos	d.endpos	bit score	evalue	ali length
GT_PARSER_TEST	gi|321400062|ref|NM_001202523.1|	281	1191	1330	2240	2081.000	0	1050
GT_PARSER_TEST	gi|321400062|ref|NM_001202523.1|	1412	1088	1423	1077	24.300	0.89	12
GT_PARSER_TEST	gi|321400062|ref|NM_001202523.1|	315	2611	326	2622	24.300	0.89	12
GT_PARSER_TEST	gi|321400062|ref|NM_001202523.1|	945	258	955	268	22.300	3.5	11
GT_PARSER_TEST	gi|321400062|ref|NM_001202523.1|	1253	342	1263	332	22.300	3.5	11
GT_PARSER_TEST	gi|321400062|ref|NM_001202523.1|	1067	759	1077	769	22.300	3.5	11
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	1	421	280	700	555.000	1e-160	280
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	185	5472	244	5531	95.600	3e-22	60
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	606	3223	621	3238	24.300	0.89	16
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	1031	1624	1041	1614	22.300	3.5	11
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	955	2544	965	2534	22.300	3.5	11
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	612	3213	622	3223	22.300	3.5	11
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	1189	4279	1199	4269	22.300	3.5	11
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	136	5257	146	5247	22.300	3.5	11
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	398	5378	408	5368	22.300	3.5	11
GT_PARSER_TEST	gi|321267542|ref|NM_001202506.1|	1331	141	1458	268	254.000	5e-70	128
GT_PARSER_TEST	gi|321267542|ref|NM_001202506.1|	1385	206	1396	195	24.300	0.89	12
GT_PARSER_TEST	gi|321267542|ref|NM_001202506.1|	939	908	949	898	22.300	3.5	11
GT_PARSER_TEST	gi|321400152|ref|NM_001025241.3|	91	327	101	317	22.300	3.5	11
genometools-1.5.1/testdata/matchtool_blastallp.out000066400000000000000000000012101211610345200224300ustar00rootroot00000000000000query	dbname2	q.startpos	d.startpos	q.endpos	d.endpos	bit score	evalue	ali length
gi|159663|gb|AAA29374.1|	gi|160797|gb|AAA29796.1|	18	18	315	317	398.000	5e-115	300
gi|159663|gb|AAA29374.1|	gi|160797|gb|AAA29796.1|	21	170	167	318	140.000	2e-37	149
gi|159663|gb|AAA29374.1|	gi|157386153|gb|ABV52468.1|	274	397	313	440	17.300	2.3	44
gi|159663|gb|AAA29374.1|	gi|157386153|gb|ABV52468.1|	71	509	86	524	16.500	4.6	16
gi|159663|gb|AAA29374.1|	gi|157386153|gb|ABV52468.1|	44	8	83	47	16.500	4.8	42
gi|159663|gb|AAA29374.1|	gi|157386153|gb|ABV52468.1|	150	70	162	82	16.200	6	13
gi|159663|gb|AAA29374.1|	gi|157386153|gb|ABV52468.1|	193	8	232	47	15.400	10	40
genometools-1.5.1/testdata/matchtool_blastn.db000066400000000000000000000316711211610345200215310ustar00rootroot00000000000000>gi|321400135|ref|NG_001764.3| Mus musculus olfactory receptor 400, pseudogene 1 (Olfr400-ps1) on chromosome 11
ATCACTTTTAAAACTATTTCTTTATGTGCACTATTTTATTATTACATCAATTAAAGGGATCAAAAGGAAG
AGAGAGAATGAGATGAGTTCCTCTTTTAAGAATTATAATTCCATGTTTTCCAGCAGCTATGATTTAAATT
TCTTCAATTCACTGAGAGGTCTTGCTATTTTCCTCCATATGTGTATCTTTAAATGAACTCATGCAGCCAA
AGCTGAGAGCCAATGAAACCACTGTTACTGAGTTCATACGCCTAGGTTTGATGGAGACACCAGAGATGTG
GCCAGTTGTCTTCATACTCTTCCTCTTAGATTATATGACTACAGTTTAGGGTAATTTGAGCATCCTAGCC
TACTGTCTTGGTGGAACCCAAACTGCACACCCCCATGTACTTCTTCCTGAGGAATCTGTCACTGATGGAT
GTGGGGTGCATCAGTGTCACTATTCCCTCCATGTTGGGTCGGCTCTTAGTCCACAAACCTACAATTCCAA
ATGGAGACTGCCTCACACAGCTCTTCTTCTTTCCTCTGCTGGCTGGGGTTGACTGATTTCTGTTGACAGC
CATGGCTAATGAGCGCTTCCTGGCCATCTGCCCCTCACTTGTACCCTCCTTCAGCCTAGGCAGACTGGTT
CAGACCGTTCACCACTGAGGCTGGGCCACCTGCTGTGCTGCTTCTCAACACTCCCCTTTGATGTTACACT
GCCTGCCACCTGCCCTGAGGCCGAACTGGTTCTCCAAGATTTGCCAGAGTTTGTTACAAACTGTGAATTT
GGCGAGTTTCTGCTAAAAGGCTGTTCTGAAAATTTCACATCTCTACATCAAGAAACTTGATGTGACTGGG
GATGAGCTTCCCTCTTTATAAGCACAGATTTTATTATTAAACACTTGAACCTTGAACAGACTAGCATGTC
TTGGTTCCATTATTTCTGTACTCACCTAGATTCCCCCTTCTCTTTCAGCTCCAAGATGCCTCCCAGGCTC
GAACCCAGACATGAGAGCTGCAGGCTGGCCCCAACAAGTTTGCACCCAACGTGGGACCTGGGAATGGCAA
AAGATGCTGGAAGAAACACTGCTGGTATGGAGCTCCACGGATAGGAAAAAATTAGAAAATTTGTACTGGA
ACACGGAGAAGCTGTGGTACAGTCTGAGCTGGAACAGCATGCTAACCCATGTGCTGGATTCGCTCAGGTT
CAGCAGTGATATCAGGATCTAGGAACACTACAGGCAGTCGGCCGCAGCTTCCAGAAGCTGCTTTTTAGGC
GAAAGGAATAAGGGTTTAAAAGAATGAACAGGTGGATGGCCGCAGTCAGAAACTGCATCAAGCGGGAGGA
AAGTTGGGTTTTGAAACTCTCCCAGAGACAGAGAGAAACGGGGATGCCCTGCTTTATTCTCTCTGGGCCC
TACAGAAGAAGTTCTCTGCCCTCTTTTTGTTTTTGTCTAAGGTCTTGTCTAATGTCTGGTGCACTGGTCT
GTTCATGTGTTCAACTCATGTGTGTTCGTGTCTTCTCATCTGAATGACTGAATGTTCTGTTTCATGTTGG
AAAATAAAAGATGGCTAAAACTTTCTCTGCTGGTATAGCAAAGCTGAGAGTGGCTCACACTTTGACTGAG
AATCAGGCACAGCAGGAGGGCTCCTGCTAGAAAAACTGTTTCTTAAGAAAGGGAATCTGCAGCCTCATGG
ATTTGGGGTGAAAAAGCTGATAGATGGTTTTTTCCTAAGAAAATTCTCTGTATTTGTGATTATTGCGTTT
AGCTAATGACAAAGTGCTTTTTATTTTATAATTAGAGCTAGAAAAATTAAAATTCTCTGATTGGTCTAAG
TGTAGCCGCTTCGTTTGGTATCAGCTCATAAGTTATTGGTTAGGATTAAATAATTGTAACATCGGTAACA
GAAGGTTAGCCTTAAGTTGGCAACTCAGGAGTCTTTTCAAACACATGGCATAAGCGGGCCAAAAAACTGG
GCCTCCTAAGATTCTTCTAGCTGAGATAATATTTAATGTGATTCTTATCCTAGAAAGTAAATTTAAAGAA
AAGATTTAAAGCAATGTCTCTTTAATGAAGCATTAAAGCTTGCACTGTCATGCATTCATGGGTATAAATT
GGCAGCCAAATCTTGCAATGTGGTAGTGAAGATTTAATGTTGATTCTAAAGTGATATATTGCTTTGAAAT
TGGGTATTGCTTTCCCAAGGCTGTAGATATTATTCTAACGTTGCATAAGAAACTTAAAAATCATAGTTAA
AAATTGCCAGTGTTCCTTTAAGTGCAGCTGGCAGTTTGATTGCAAATTTAAGATTTTATACTCACCCATA
TATTGTTAATTAAGATAATTACAAGAGTAATCATCTTATGAGAGCACTAACACAGCTCTCTGTGGCTATA
CAGCCATACAAAGCTCAGGGTAGCCTCAGCGAGGTTTGTGTGACTTTCTTTTGTTTTGCAAACAGTATGC
CTAAGGAAGTTCTTGAAACTTGCCTCTCCTTGCCTCTCAAGGGAAGTTACTTTAAATCTTTGCTCTAACA
CAGGCGCTTTTAAGTTCTGGGGAGTAACTGTTGCTCCAGAAAAGATTCAGAGGCAATATATTTTTAATTC
TTATGGTTTTAGTTTACTACAGAAGGCTTTGCAGAAAATAAAGAAAGCATTTATAATTGTTATCAATTAT
AATCAATGGTAATTAAATATTAGCTGCCCATTTTAGTTAATGGTTATTAAATGTGCCCACAGCAACTCTT
TAGCAGGCTGCATTGTGACTAAGGGTGTGAAATCCTTAGCTGTCATTAAGCTAACCCTAAGCCTAGCTGC
TTTATCTTTACTGTAAACATTTATCTGGTTCCTGTAGTCCTTTTGAAGTCATTCCTTTGTTTCCTGTCAG
GTAACTTGAATGTACTTTGCCTGCTGTGACTTCCTGCCCCCTTTATTTTCTGTATTCTTTGGCAAGAGAA
AACATTATTTGTTTTCTGCTGCTGGCTGCTGCGGGGCGGGGCCTTGAGGCACACAGATTTTCCTGAGCAT
GGTGGCTCAGAAGGCTGTCAGAAAGCTGGTGGCTTTGTAGCAAACTCAGGAGAGGGCCATGCTCACCATT
GCCCCCATGAGACTCCACCCATCCCCGCCTGGGTAGCCATATTTTTCCACGCTAAGACTCGGGGTGCTCT
GCCACTTGGGCTTTCTAGCCTACAACAGATTGGGCCACCTTCAGCCTCTTCCGCCTGAGAAGAAGGCCGA
GGGTGGGCAAGGCCGAGGTAGCGCTCACCTCAAAACACAGTTTCAGCATCCTATTAAAACTGCTATGGTG
CTAATAAAGAATTGTAAGATAAATTCGTATATTTTAGAAAACTTACAACAAAAATTGTGTTTTAAAAACC
GACTAAGTGTCTGTTCCTTGTTCCAAACAGCAATTAATTTGGTAATTACAGATCTATTGCATACCATCAT
TTTGAATAAAATTGACAATCATTATCCCAAAGATAAGTTAAAAATTTGTTTTTATGCATGCTTCTGTATC
TTCTATAAATTCATGCATGCATGCATTCCACTTACTGTGTTTAAAAACAACCCCTCTATGGGAAATGAGT
AAATGTGAATTAGATCACACGTTTATTCTTTTGAGTTTCCTCCTGTTTCAGCACAGATAATTAAGTTGTG
TGCTGTAGATGGTGTTTTAAAATGCTGAACAATCAAACCTTAATTTGTATATTAATAGTCAATATTATAT
CTCAGAGCTCACAATTGCTTAAGATTGTTCGTCCCTTCTCAAATTTGCAATTGCTTATGTATATACAACT
CATAAGTAAAAATGCTAGATTTATGTCTCAGGCAGTCTATAGGTCCTACATATAAGATAGATTGGATATA
TAATCTCGTTCTTTATATATTCAAAACAGTTATGGTTTAAGATAATATTTTAGTATTCTTGGAAATTGTG
CATGTCAAATTGTAAAAAATTCTTTGCTCTTAGTGTCCTAGGTTACTACTTGTTTCCAAATAATAGTGTT
AATTCTTGAGGACTTATACTTAATAAAATGCTGCAAATAAATACTCTTATTTCTGATTTAATAAATAAAT
AAATTATACACATGTGACTATTAATAACTTGTCAAGCTTTCTAGTTACAACTGCTCTTTAAGAGAAACAA
TTAAAAGTGCAATTAGTCACTGCCCATGTTACATTAAAACTGACTATAACAGTCAAGTATTTAGATGTCA
ACAAATTATTAATTCTCAAGAACAAGGTATTGTGGAACTTTAAAACTTTAGCTTCTTAAAAGACAAAGAA
GGGGGAAATTATATCCCCGTGCATATTATTTAATGTATTCCCATTCACATTATTTAAATCATACTTTTAT
TTTAGAATTTTGAAATTTAGATGTCAAAGAACTTAATAAATGCCTTATATTATCTTAAAAGGATCTACTT
ATTGGCATATGGCTTGATCCTGAACAGCTACCTTATTAGGAAAGGAAAAAGCATAGGTTCTCTCCACAGA
AGCATGATGGCTAATTCATGTGACAAGCTGACAGGTGAGTTTGCTCAGTGCCCTGACTGTAGTGACAAGG
AAGCTGAATTGGGCACATGTTTTCGACCCATCCTTGCTTGCCATTTTTCCAGTTTAGACAAGCAAAGCTG
CCTTGCTTCAAGCTTTTTAACTTTATGGTAAAAAGAACATCAGAGACTGTGTAATCTGACTTAGAAAGAT
TAGTCATATAATAGAGTTATAATGATTCTTCTCTTTCCTTCAATGTGACCAGTTATTCTAACTCAATCTT
AGACTGGTCTAGTACTAATTCCAATATTAGAGATACCTATTAAAGATAGCTAAAAATCTTAATTACCTAG
CAAAGTTAATTTGGAGCACAGTCTCCACTTCCAGAGAATCTCTGGCTTTTCTGCTAATCCTCAAAGCCAG
ATCCCCACACCGGGAGGCCAGAGCCTGAGTTTGATTGTTGCTAATTTGCAACTGAATAAAGTACCTGGGC
TTCCACAAAGAAGCTTTTATACTGTTGTTTTTCACTGCCCCACCTTTGTTTCTCAAGCAGGTCAGCCATT
CTTTTCAGCCTGACTACAGGAGATGTAAAGCCTCACCTCCAACAGTGCAGATGGCAGTTATTAATCTTCA
TAAAGAAGCATTTTAAGTACATATTGTGGCCTTCATCTGATTTGGGAATAAGGTGTGCTATGAGGGCCGG
TTAGTCAATGACGGACAACCAGATTTCGGAGCCATAACAATCTAAGACAGAGGTACATGCCAAAAGGCCA
TGGCTGTTGATAACACACCACAGAACCATGTTTGTGTGAAATATAACACAAACTAGCTGCATGTAGCCTC
CAAGACAGAATTAGATGGTTCGGGAAAATCTGAGATCCTAAGGCAGGCACGGCCGCCAGCCACCATAACT
CCCAGGCAAGACTATAGAGCATAAATAAATTTTATGCCTCAGTCCAGTTTTTTTAATATTATTTAAAGGG
GGGAAAATGTACCTCCTTCAGCCTAGGCAGGCTGGTTCAGACCATTCACCACTGAGGCTAGGCCACCTGC
TACCCACCTAGATTCCCTCTTCTCTTTCAGCTCCAAGATGCCTCCCAGACTCGAACCCAGCCTCAACACT
CATTTACAGCACCCAAATGAACCACACCATCCAGAGGATCTTGGTGGCCTCATCGTGGGTTTGTTCCTTC
AGCAGTGTACTTACTCATACTGTGGCCATATCCACACTTCACTTCTGTGGTCTCAATGTGGTCAATAACT
TCTACTGTGACCTGCCTCAGCTCTTCCAACTGTCCTGCTCCACTACCCAGCTAAATGAGCTGCTGCTCTT
TGCAGTAGGTTTCCTAATGACAGAAACCTCCATGGCACTCATTTTTACCTTTTACATCTATGGGGCAGTT
GCAATTCTGCAAATCCGCTCTGCTGAAGGCAGGTAGAAAGCCTTCTCCACATACAGCTCTCACCTCACTG
TGGTTGCCATATTCTATGGCACAGGTATCTTTGCCTACATGAGTCTCAGGTCCATCAAACTTTCTGATAA
TGATAAAGCTATTGGGATTTTCAACACTGATGATCAACCCCATGCTAAACCCACTCATCTACAGTCTCAG
AAACCCTGATGTGCAGGCTGCCCTCTGGAAGGTACTCACAGGGAAACAGCTATCACATTGAGACCTCAAA
GCTTCTTCCACCTATTTCTTCTAAAACTAAAGCTGTATATTAAGGTTTCCTGTGGTTCAACACTAGAACA
AATTGTTCAACATTGTTTCCAATGAGAAATGTTATGATGGAAAAGAGCTTCCCTCAATTATCATCTGCTG
AATGTTTTAATTTTTTGAAAGAGAGGAATTTGTAATCTAAACATTTAAATA
>gi|321400152|ref|NM_001025241.3| Mus musculus Ssty2 family member (LOC434960), mRNA
GGAGGTGCTAGAATCCATTCAAGGAGCTCAAATCTGTTTAGCATAGTCTTCTTCACCTGCTCAGAAGTTC
TCGTAGAGAAGAGTCTTGGTCCAGCATTCACTCCCAACCCATAACCATTGCCCATCAGGAATTCATATAT
ATGACAGAGGCAACAGCATTGTGTCTGGTGTAAACGGGCAAGATCTTCAGTCCCAGGCAATGAGCAAGTA
TGATATTTGAAGGGAATGGAAGCCACAAGACAGTGTGATCTACCACAACAGGTCTACAGCCAGGTAGAAG
ACAATACATCTGAAGAGTCTGAGCATGACATCACTCAAGAAGAAGAGTAGGAGGAAGCCTTCTTCCCAGG
CCCTGGGGAATATTGTTGGCTGCAGAATTTCTCATGGGTGGAAGGAAGGTAATGAGCCTGTCACCCATTG
GAAGGCCATCATTCTAGGTCAACTGCCAACAAACCCTTCTCTTTATTTGGTGAAGTATGACGGAATTGAC
AGTGTCTACGGACAGGAGCTCCACAGCGATGAGAGGATTTTAAATCTTAAGGTCTTGCCTCACAAAGTAG
TTTTTCCTCAGGTGAGGGATGTCCACCTCGCAGGCGCACTGGTTGGCAGAGAGGTACAACACAAATTTGA
GGGGAAAGATGGCTCTGAGGACAACTGGAGTGGGATGGTGCTAGCCCAGGTGCCATTCTTACAGGACTAT
TTTTACATTTCCTACAAGAAGGATCCGGTCCTCTACGTCTATCAGCTCCTGGATGACTACAAGGAAGGTA
ACCTCCACATCATTCCAGAGACCCCTCTGGCTGAGGCGAGATCAGGTGATGACAATGACTTCTTAATAGG
TTCCTGGGTGCAGTACACCAGAGATGATGGATCCAAAAAGTTCGGAAAGGTTGTTTACAAAGTTCTAGCC
AATTCTACTGTGTACTTTATCAAATTTCTCGGTGACCTCCATATCTATGTCTATACTCTGGTGTCAAATA
TCACTTAAATTTAAAAAAATCACAAAGTACAGAAATGTAAACTTATAGGATTGAAAAAAAATGTTTGTTT
TCCTGTGTTGGGTACCTATGGGTCTTTGACAACCTCAGTATCTTTGTCAATAAAATTTGTTTTGTTCTAA
AAA
>gi|321400062|ref|NM_001202523.1| Homo sapiens discoidin domain receptor tyrosine kinase 1 (DDR1), transcript variant 6, mRNA
AGTGCGGAGGAACTGAGCCCCGGGAGGAGGTGCTCCTGTGCAGCCCCACTGAGTCAGCTCATCTATCGCC
TGCCCTCCACCTGGCCAGTCCCTGCGGGCATCTAACTGCTAAGCCTCCGCTCAGCCAACACCCAGTTGGT
CAGTCTGGTCACAGTCCAGCAAAAAGAGGGACTGCCACTCTAACCCACCAGTGACACCACTCTTCCCGGC
TGGATGGTCAATTAGCTCTGGCATGAGAGAATGTCACTGCCGAGATGCTGCCCCCACCCCCTTAGGCCCG
AGGGATCAGGAGCTATGGGACCAGAGGCCCTGTCATCTTTACTGCTGCTGCTCTTGGTGGCAAGTGGAGA
TGCTGACATGAAGGGACATTTTGATCCTGCCAAGTGCCGCTATGCCCTGGGCATGCAGGACCGGACCATC
CCAGACAGTGACATCTCTGCTTCCAGCTCCTGGTCAGATTCCACTGCCGCCCGCCACAGCAGGTTGGAGA
GCAGTGACGGGGATGGGGCCTGGTGCCCCGCAGGGTCGGTGTTTCCCAAGGAGGAGGAGTACTTGCAGGT
GGATCTACAACGACTGCACCTGGTGGCTCTGGTGGGCACCCAGGGACGGCATGCCGGGGGCCTGGGCAAG
GAGTTCTCCCGGAGCTACCGGCTGCGTTACTCCCGGGATGGTCGCCGCTGGATGGGCTGGAAGGACCGCT
GGGGTCAGGAGGTGATCTCAGGCAATGAGGACCCTGAGGGAGTGGTGCTGAAGGACCTTGGGCCCCCCAT
GGTTGCCCGACTGGTTCGCTTCTACCCCCGGGCTGACCGGGTCATGAGCGTCTGTCTGCGGGTAGAGCTC
TATGGCTGCCTCTGGAGGGATGGACTCCTGTCTTACACCGCCCCTGTGGGGCAGACAATGTATTTATCTG
AGGCCGTGTACCTCAACGACTCCACCTATGACGGACATACCGTGGGCGGACTGCAGTATGGGGGTCTGGG
CCAGCTGGCAGATGGTGTGGTGGGGCTGGATGACTTTAGGAAGAGTCAGGAGCTGCGGGTCTGGCCAGGC
TATGACTATGTGGGATGGAGCAACCACAGCTTCTCCAGTGGCTATGTGGAGATGGAGTTTGAGTTTGACC
GGCTGAGGGCCTTCCAGGCTATGCAGGTCCACTGTAACAACATGCACACGCTGGGAGCCCGTCTGCCTGG
CGGGGTGGAATGTCGCTTCCGGCGTGGCCCTGCCATGGCCTGGGAGGGGGAGCCCATGCGCCACAACCTA
GGGGGCAACCTGGGGGACCCCAGAGCCCGGGCTGTCTCAGTGCCCCTTGGCGGCCGTGTGGCTCGCTTTC
TGCAGTGCCGCTTCCTCTTTGCGGGGCCCTGGTTACTCTTCAGCGAAATCTCCTTCATCTCTGATGTGGT
GAACAATTCCTCTCCGGCACTGGGAGGCACCTTCCCGCCAGCCCCCTGGTGGCCGCCTGGCCCACCTCCC
ACCAACTTCAGCAGCTTGGAGCTGGAGCCCAGAGGCCAGCAGCCCGTGGCCAAGGCCGAGGGGAGCCCGA
CCGCCATCCTCATCGGCTGCCTGGTGGCCATCATCCTGCTCCTGCTGCTCATCATTGCCCTCATGCTCTG
GCGGCTGCACTGGCGCAGGCTCCTCAGCAAGGCTGAACGGAGGGTGTTGGAAGAGGAGCTGACGGTTCAC
CTCTCTGTCCCTGGGGACACTATCCTCATCAACAACCGCCCAGGTCCTAGAGAGCCACCCCCGTACCAGG
AGCCCCGGCCTCGTGGGAATCCGCCCCACTCCGCTCCCTGTGTCCCCAATGGCTCTGCCTACAGTGGGGA
CTATATGGAGCCTGAGAAGCCAGGCGCCCCGCTTCTGCCCCCACCTCCCCAGAACAGCGTCCCCCATTAT
GCCGAGGCTGACATTGTTACCCTGCAGGGCGTCACCGGGGGCAACACCTATGCTGTGCCTGCACTGCCCC
CAGGGGCAGTCGGGGATGGGCCCCCCAGAGTGGATTTCCCTCGATCTCGACTCCGCTTCAAGGAGAAGCT
TGGCGAGGGCCAGTTTGGGGAGGTGCACCTGTGTGAGGTCGACAGCCCTCAAGATCTGGTTAGTCTTGAT
TTCCCCCTTAATGTGCGTAAGGGACACCCTTTGCTGGTAGCTGTCAAGATCTTACGGCCAGATGCCACCA
AGAATGCCAGGAATGATTTCCTGAAAGAGGTGAAGATCATGTCGAGGCTCAAGGACCCAAACATCATTCG
GCTGCTGGGCGTGTGTGTGCAGGACGACCCCCTCTGCATGATTACTGACTACATGGAGAACGGCGACCTC
AACCAGTTCCTCAGTGCCCACCAGCTGGAGGACAAGGCAGCCGAGGGGGCCCCTGGGGACGGGCAGGCTG
CGCAGGGGCCCACCATCAGCTACCCAATGCTGCTGCATGTGGCAGCCCAGATCGCCTCCGGCATGCGCTA
TCTGGCCACACTCAACTTTGTACATCGGGACCTGGCCACGCGGAACTGCCTAGTTGGGGAAAATTTCACC
ATCAAAATCGCAGACTTTGGCATGAGCCGGAACCTCTATGCTGGGGACTATTACCGTGTGCAGGGCCGGG
CAGTGCTGCCCATCCGCTGGATGGCCTGGGAGTGCATCCTCATGGGGAAGTTCACGACTGCGAGTGACGT
GTGGGCCTTTGGTGTGACCCTGTGGGAGGTGCTGATGCTCTGTAGGGCCCAGCCCTTTGGGCAGCTCACC
GACGAGCAGGTCATCGAGAACGCGGGGGAGTTCTTCCGGGACCAGGGCCGGCAGGTGTACCTGTCCCGGC
CGCCTGCCTGCCCGCAGGGCCTATATGAGCTGATGCTTCGGTGCTGGAGCCGGGAGTCTGAGCAGCGACC
ACCCTTTTCCCAGCTGCATCGGTTCCTGGCAGAGGATGCACTCAACACGGTGTGAATCACACATCCAGCT
GCCCCTCCCTCAGGGAGCGATCCAGGGGAAGCCAGTGACACTAAAACAAGAGGACACAATGGCACCTCTG
CCCTTCCCCTCCCGACAGCCCATCACCTCTAATAGAGGCAGTGAGACTGCAGGTGGGCTGGGCCCACCCA
GGGAGCTGATGCCCCTTCTCCCCTTCCTGGACACACTCTCATGTCCCCTTCCTGTTCTTCCTTCCTAGAA
GCCCCTGTCGCCCACCCAGCTGGTCCTGTGGATGGGATCCTCTCCACCCTCCTCTAGCCATCCCTTGGGG
AAGGGTGGGGAGAAATATAGGATAGACACTGGACATGGCCCATTGGAGCACCTGGGCCCCACTGGACAAC
ACTGATTCCTGGAGAGGTGGCTGCGCCCCCAGCTTCTCTCTCCCTGTCACACACTGGACCCCACTGGCTG
AGAATCTGGGGGTGAGGAGGACAAGAAGGAGAGGAAAATGTTTCCTTGTGCCTGCTCCTGTACTTGTCCT
CAGCTTGGGCTTCTTCCTCCTCCATCACCTGAAACACTGGACCTGGGGGTAGCCCCGCCCCAGCCCTCAG
TCACCCCCACTTCCCACTTGCAGTCTTGTAGCTAGAACTTCTCTAAGCCTATACGTTTCTGTGGAGTAAA
TATTGGGATTGGGGGGAAAGAGGGAGCAACGGCCCATAGCCTTGGGGTTGGACATCTCTAGTGTAGCTGC
CACATTGATTTTTCTATAATCACTTGGGGTTTGTACATTTTTGGGGGGAGAGACACAGATTTTTACACTA
ATATATGGACCTAGCTTGAGGCAATTTTAATCCCCTGCACTAGGCAGGTAATAATAAAGGTTGAGTTTTC
CACAAAAAAAAAAAAAAAAAA
>gi|321267542|ref|NM_001202506.1| Danio rerio brain specific kinase 146-like (LOC791840), mRNA
GCAGCGGAGAGACAGGATGATGATGATTATGATTATGATGATAATGATGAAGATGAGGATAATTATGTGA
TATCTGTATGTGATTTATCCACCGGGGGAACAGCGGAGATTCACGGGAGCGGTTTAACGTATTGTGAGGC
TGTCTGTGGGCCAGGATGAGCTCGTCTCCGGTGGTTTCCCATGACATTCTGGAGGAGCTGCAGCTCTACA
CCGCTCAGAACCTGGAGAAGCTGGAGGTCAATAAATACTATGAGGTGATCCGGGAGCTCGGGAAGGGCAC
TTACGGGAAGGTGGACCTCGTCATTCATAAGATCAGAGGTAGCAAAATGGCTCTGAAGTTTCTGAAGAAG
AAAAGCACCAAGCTGAAGAGCTTCTTGCGGGAGTACAGCATCTCTCTCTATCTCTCTCCATGTCCCTTCA
TCATCAACATGTTCGGCATCGCCTTTGAGACAGACGAGTATTATGTGTTTGCGCAGGAATACGCTCCTTC
TGGGGACCTGTTTGACATCATTCCACCACAGGTGGGTCTGCCAGAGCCGGTGGCGAAGCGCTGTGTGCAT
CAGGTGGCCATCGCTCTCGAATACCTGCACTCCAAAAAACTGGTGCACCGAGACATCAAACCCGAGAACA
TCCTAATCTTCGACAAGGAGTGCCGTAAGGTCAAGCTGTCAGACTTCGGGATGGCGCGGCGCGCCGGTTC
ACCGGTCAAGCGTGTTAGCGGCACAATCCCATACACGGCTCCAGAACTCTGCGATACGTCCAAACACGAC
GGCTTCTGCGTGGACTACAGCACCGATGTGTGGGCGTTCGGAGTGCTGCTGTTCTGCATGCTAACCGGGA
ACTTTCCATGGGAAAAAGCGATGCCGTCTGATACTTTCTACGAGGAGTTTGTGCGCTGGCAGAAGCGGCG
GACGGGTGCGGTTCCGTCACAATGGCGTCGATTTACAGACGAATCCCTGCGCATGTTTCGAAAGCTCCTA
GCATTGGAGCAGGAACGCAGATGCAGCGTCAAGGAGGTTTTCGCACATTTAGGCCACCGCTGGATGCTTG
ATGGAACTAGCGGAAACCATCATCAATCCGTGCTCAACTCTTCATCAGAGGAAGACGAATTGCTTGTGGA
TCGTATGAAGCAGCAGACCTTATCTCCGACAGCTAACACGAGCAATGCTATTGAGCCCGGATCGGCTAAC
CACTTCACATCTGTGTCCACCAATAGCTCGGTGTCTTCCACTAACAGCTATGAGCGTTCGGCTAGAGACA
GTCCTCCGACTAGCAGGATCCTGGTCACGACGCCTATAGAAATCTGCGTCTAAATGCACAGCTGATGAAA
TTAACATGCGCACAAGCTGACGCACACTCCTGTGA
genometools-1.5.1/testdata/matchtool_blastn.out000066400000000000000000000005071211610345200217450ustar00rootroot00000000000000query	dbname2	q.startpos	d.startpos	q.endpos	d.endpos	bit score	evalue	ali length
GT_PARSER_TEST	gi|321400062|ref|NM_001202523.1|	281	1191	1341	2250	1941.000	0	1062
GT_PARSER_TEST	gi|321400135|ref|NG_001764.3|	1	421	280	700	518.000	2e-149	280
GT_PARSER_TEST	gi|321267542|ref|NM_001202506.1|	1331	141	1458	268	237.000	6e-65	128
genometools-1.5.1/testdata/matchtool_blastn.query000066400000000000000000000027361211610345200223110ustar00rootroot00000000000000>GT_PARSER_TEST BLASTN
GTGGGGTGCATCAGTGTCACTATTCCCTCCATGTTGGGTCGGCTCTTAGTCCACAAACCTACAATTCCAA
ATGGAGACTGCCTCACACAGCTCTTCTTCTTTCCTCTGCTGGCTGGGGTTGACTGATTTCTGTTGACAGC
CATGGCTAATGAGCGCTTCCTGGCCATCTGCCCCTCACTTGTACCCTCCTTCAGCCTAGGCAGACTGGTT
CAGACCGTTCACCACTGAGGCTGGGCCACCTGCTGTGCTGCTTCTCAACACTCCCCTTTGATGTTACACT
CGGGGTGGAATGTCGCTTCCGGCGTGGCCCTGCCATGGCCTGGGAGGGGGAGCCCATGCGCCACAACCTA
GGGGGCAACCTGGGGGACCCCAGAGCCCGGGCTGTCTCAGTGCCCCTTGGCGGCCGTGTGGCTCGCTTTC
TGCAGTGCCGCTTCCTCTTTGCGGGGCCCTGGTTACTCTTCAGCGAAATCTCCTTCATCTCTGATGTGGT
GAACAATTCCTCTCCGGCACTGGGAGGCACCTTCCCGCCAGCCCCCTGGTGGCCGCCTGGCCCACCTCCC
ACCAACTTCAGCAGCTTGGAGCTGGAGCCCAGAGGCCAGCAGCCCGTGGCCAAGGCCGAGGGGAGCCCGA
CCGCCATCCTCATCGGCTGCCTGGTGGCCATCATCCTGCTCCTGCTGCTCATCATTGCCCTCATGCTCTG
GCGGCTGCACTGGCGCAGGCTCCTCAGCAAGGCTGAACGGAGGGTGTTGGAAGAGGAGCTGACGGTTCAC
CTCTCTGTCCCTGGGGACACTATCCTCATCAACAACCGCCCAGGTCCTAGAGAGCCACCCCCGTACCAGG
AGCCCCGGCCTCGTGGGAATCCGCCCCACTCCGCTCCCTGTGTCCCCAATGGCTCTGCCTACAGTGGGGA
CTATATGGAGCCTGAGAAGCCAGGCGCCCCGCTTCTGCCCCCACCTCCCCAGAACAGCGTCCCCCATTAT
GCCGAGGCTGACATTGTTACCCTGCAGGGCGTCACCGGGGGCAACACCTATGCTGTGCCTGCACTGCCCC
CAGGGGCAGTCGGGGATGGGCCCCCCAGAGTGGATTTCCCTCGATCTCGACTCCGCTTCAAGGAGAAGCT
TGGCGAGGGCCAGTTTGGGGAGGTGCACCTGTGTGAGGTCGACAGCCCTCAAGATCTGGTTAGTCTTGAT
TTCCCCCTTAATGTGCGTAAGGGACACCCTTTGCTGGTAGCTGTCAAGATCTTACGGCCAGATGCCACCA
AGAATGCCAGGAATGATTTCCTGAAAGAGGTGAAGATCATGTCGAGGCTCAAGGACCCAAACATCATTCG
TGTCTGTGGGCCAGGATGAGCTCGTCTCCGGTGGTTTCCCATGACATTCTGGAGGAGCTGCAGCTCTACA
CCGCTCAGAACCTGGAGAAGCTGGAGGTCAATAAATACTATGAGGTGATCCGGGAGCT
genometools-1.5.1/testdata/matchtool_blastp.db000066400000000000000000000035361211610345200215320ustar00rootroot00000000000000>gi|281364575|ref|NP_001162903.1| r2d2, isoform B [Drosophila melanogaster]
MDNKSAVSALQEFCARTQINLPTYSFIPGEDGGYVCKVELLEIEALGNGRSKRDAKHLAASNILRKIQLL
PGIHGLMKDSTVGDLDEELTNLNRDMVKELRDYCVRREMPLPCIEVVQQSGTPSAPEFVACCSVASIVRY
GKSDKKKDARQRAAIEMLALISSNSDNLRPDQMQVASTSKLKVVDMEESMEELEALRRKKFTTYWELKEA
GSVDHTGMRLCDRHNYFKNFYPTLKKEAIEAINSDEYESSKDKAMDVMSSLKITPKISEVESSSLVPLLS
VELNCAFDVVLMAKETDIYDHIIDYFRTMLI

>gi|166317|gb|AAA32629.1| actinidin [Actinidia deliciosa]
MGLPKSFVSMSLLFFSTLLILSLAFNAKNLTQRTNDEVKAMYESWLIKYGKSYNSLGEWERRFEIFKETL
RFIDEHNADTNRSYKVGLNQFADLTDEEFRSTYLGFTSGSNKTKVSNRYEPRVGQVLPSYVDWRSAGAVV
DIKSQGECGGCWAFSAIATVEGINKIVTGVLISLSEQELIDCGRTQNTRGCNGGYITDGFQFIINNGGIN
TEENYPYTAQDGECNVELQNEKYVTIDTYENVPYNNEWALQTAVTYQPVSVALDAAGDAFKQYSSGIFTG
PCGTAIDHAVTIVGYGTEGGIDYWIVKNSWDTTWGEEGYMRILRNVGGAGTCGIATMPSYPVKYNNQNYP
EPYSSLINPPAFSMSKDGPVGVEDGQRYSA

>gi|160797|gb|AAA29796.1| hemoglobin [Pseudoterranova decipiens]
MHSSIVLATVLFVAIASASKTRELCMKSLEHAKVGTSKEAKQDGIDLYKHMFEHYPAMKKYFKHRENYTP
ADVQKDPFFIKQGQNILLACHVLCATYDDRETFDAYVGELMARHERDHVKVPNDVWNHFWEHFIEFLGSK
TTLDEPTKHAWQEIGKEFSHEISHHGRHSVRDHCMNSLEYIAIGDKEHQKQNGIDLYKHMFEHYPHMRKA
FKGRENFTKEDVQKDAFFVNKDTRFCWPFVCCDSSYDDEPTFDYFVDALMDRHIKDDIHLPQEQWHEFWK
LFAEYLNEKSHQHLTEAEKHAWSTIGEDFAHEADKHAKAEKDHHEGEHKEEHH

>gi|157386153|gb|ABV52468.1| ATP; phosphoenolpyruvate carboxykinase [Campylobacter jejuni subsp. jejuni 81116]
MKKFDNLGLDNIKEIFHNLSYDELNAHEKANNEGLSTDNDTFCVDTGIFTGRSPKDKYFVKQDPSSKYIA
WGKINQPITKELFDKLLTKAKQELSGKKIYVQDAFCGASLQSRKAVRFVTEIAWQAHFVKNMFIRPSQEE
LENFKADFIVYNACKCINEDYKQDGLNSEVFVIFNVEENIAVIGGTWYGGEMKKGIFSMMNYWLPLENKL
SMHCSANVGEKDDVALFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDEGVFNFEGGCYAKTINLDPEHEPE
IYGAIKRNALLENVVLRADKSVDYADASKTENTRVSYPIEHIENHEPSLKAGHPKNIIFLSADAFGILPP
VSKLSKEQAMYYFLSGYTAKVAGTERGITEPQATFSACFGEPFMPLHPTVYARLLGEKIEKHEVNVYLVN
TGWSGGSYGVGKRMSIKATRACINAILDGSIAKCEFENFEVFNLAIPKALEGVESTLLNPINTWLDKNAY
TETRDKLAHMFVQNFKRYEDVKEGIEFSKFGPKI

genometools-1.5.1/testdata/matchtool_blastp.out000066400000000000000000000010711211610345200217440ustar00rootroot00000000000000query	dbname2	q.startpos	d.startpos	q.endpos	d.endpos	bit score	evalue	ali length
gi|159663|gb|AAA29374.1|	gi|160797|gb|AAA29796.1|	1	1	316	318	416.000	2e-120	318
gi|159663|gb|AAA29374.1|	gi|160797|gb|AAA29796.1|	170	21	321	206	182.000	4e-50	186
gi|159663|gb|AAA29374.1|	gi|157386153|gb|ABV52468.1|	274	397	313	440	17.300	2.7	44
gi|159663|gb|AAA29374.1|	gi|157386153|gb|ABV52468.1|	71	509	86	524	16.200	5.2	16
gi|159663|gb|AAA29374.1|	gi|157386153|gb|ABV52468.1|	150	70	162	82	16.200	5.5	13
gi|159663|gb|AAA29374.1|	gi|157386153|gb|ABV52468.1|	44	8	83	47	16.200	5.8	42
genometools-1.5.1/testdata/matchtool_blastp.query000066400000000000000000000006151211610345200223050ustar00rootroot00000000000000>gi|159663|gb|AAA29374.1| hemoglobin [Ascaris suum]
MRSLLLLSIVFFVVTVSANKTRELCMKSLEHAKVDTSNEARQDGIDLYKHMFENYPPLRKYFKNREEYTA
EDVQNDPFFAKQGQKILLACHVLCATYDDRETFNAYTRELLDRHARDHVHMPPEVWTDFWKLFEEYLGKK
TTLDEPTKQAWHEIGREFAKEINKHGRHAVRHQCMRSLQHIDIGHSETAKQNGIDLYKHMFENYPSMREA
FKDRENYTAEDVQKDPFFVKQGQRILLACHLLCASYDDEETFHMYVHELMERHERLGVQLPDQHWTDFWK
LFEEFLEKKSHLCEHTKHAWAVIGKEFAYEATRHGKEHHEHKEEHKEEHKEEHKEEQH
 
genometools-1.5.1/testdata/matchtool_open.match000066400000000000000000035156401211610345200217240ustar00rootroot00000000000000# args=-l 100
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
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 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
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 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
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  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
 360    101    273   D   360    149      0   0   2.43e-207    720   100.00
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  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
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  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
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2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
101	149	273	0	632	359	720
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
101	149	273	0	632	359	720
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
101	149	273	0	632	359	720
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
101	149	273	0	632	359	720
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	511	613	776	878	532
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
101	149	273	0	632	359	720
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
101	149	273	0	632	359	720
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
101	149	273	0	632	359	720
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	511	613	776	878	532
46	47	0	0	1289	1289	2580
26	27	254	0	359	105	212
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
2	100	90	192	509	611	840
2	100	511	613	776	878	532
4	102	0	0	527	527	1056
141	141	1206	1533	1415	1742	420
2	100	90	192	509	611	840
2	100	511	613	776	878	532
genometools-1.5.1/testdata/matchtool_open_corrupt.match000066400000000000000000000013211211610345200234610ustar00rootroot00000000000000# args=-l 100
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
this is a broken file!
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141    123   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
genometools-1.5.1/testdata/matchtool_open_empty.match000066400000000000000000000000001211610345200231120ustar00rootroot00000000000000genometools-1.5.1/testdata/matchtool_open_empty.out000066400000000000000000000000711211610345200226350ustar00rootroot00000000000000seqid1	seqid2	startpos1	startpos2	endpos1	endpos2	weight
genometools-1.5.1/testdata/matchtool_open_neg.match000066400000000000000000000012721211610345200225410ustar00rootroot00000000000000# args=-l 100
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
 -360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141   1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
genometools-1.5.1/testdata/matchtool_open_too_few.match000066400000000000000000000012231211610345200234260ustar00rootroot00000000000000# args=-l 100
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210      4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
genometools-1.5.1/testdata/matchtool_open_too_many.match000066400000000000000000000012771211610345200236220ustar00rootroot00000000000000# args=-l 100
  633      3      0   D   633    101      0   0    0.00e+00   1266   100.00
  360      3    273   D   360    149      0   0   2.43e-207    720   100.00
  360    101    273   D   360    149      0   0   2.43e-207    720   100.00
 1290     46      0   D  1290     47      0   0    0.00e+00   2580   100.00
  106     26    254   D   106     27      0   0    2.04e-54    212   100.00
  528      4      0   D   528    102      0   0    0.00e+00   1056   100.00
  210    141   1206   D   210    141    123 1533   0   4.96e-117    420   100.00
  420      2     90   D   420    100    192   0   1.83e-243    840   100.00
  266      2    511   D   266    100    613   0   9.55e-151    532   100.00
genometools-1.5.1/testdata/md5_seqid_missing_seqid.gff3000066400000000000000000000003401211610345200232110ustar00rootroot00000000000000##gff-version   3
##sequence-region   md5:063b1024d68e26716b7f38caf958316f:1877523 1 106973
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	1074	1540	1	+	.	ID=gene1;Target=md5:14c0ff5e76ef8ac009fdcc923f701356: 1 303 +
genometools-1.5.1/testdata/md5_seqid_too_short.gff3000066400000000000000000000003361211610345200224000ustar00rootroot00000000000000##gff-version   3
##sequence-region   md5:063b1024d68e26716b7f38caf958316 1 106973
md5:063b1024d68e26716b7f38caf958316f:1877523	gth	gene	1074	1540	1	+	.	ID=gene1;Target=md5:14c0ff5e76ef8ac009fdcc923f701356:8721428 1 303 +
genometools-1.5.1/testdata/md5_seqid_wrong_separator.gff3000066400000000000000000000003471211610345200235760ustar00rootroot00000000000000##gff-version   3
##sequence-region   md5:063b1024d68e26716b7f38caf958316f:1877523 1 106973
md5:063b1024d68e26716b7f38caf958316fx1877523	gth	gene	1074	1540	1	+	.	ID=gene1;Target=md5:14c0ff5e76ef8ac009fdcc923f701356:8721428 1 303 +
genometools-1.5.1/testdata/mergefeat.gff3000066400000000000000000000002511211610345200203610ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
seq1	.	gene	1000	10000	.	+	.	ID=gene
seq1	.	exon	1000	5000	.	+	.	Parent=gene
seq1	.	exon	5001	10000	.	+	.	Parent=gene
genometools-1.5.1/testdata/mergefeat.out000066400000000000000000000002071211610345200203440ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10000
seq1	.	gene	1000	10000	.	+	.	ID=gene1
seq1	.	exon	1000	10000	.	+	.	Parent=gene1
###
genometools-1.5.1/testdata/mergefeat_no_merge.gff3000066400000000000000000000004421211610345200222360ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
ctg123	.	mRNA	1050	7000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	7000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	7001	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	7001	9000	.	+	.	Parent=mRNA2
###
genometools-1.5.1/testdata/meta_directives.gff3000066400000000000000000000003601211610345200215720ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
##feature-ontology URI
##attribute-ontology URI
##source-ontology URI
##species NCBI_Taxonomy_URI
##genome-build source buildName
##genome-build NCBI B36
##genome-build WormBase ws110 (worm)
genometools-1.5.1/testdata/minimal_fasta.gff3000066400000000000000000000011451211610345200212310ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	.
##FASTA
>ctg123
cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg
tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta
tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa
aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat
aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat
cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc
gtatttgatttgggtttactatcgaataatgagaattttcaggcttaggc
ttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt
aggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttag
aatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattc
genometools-1.5.1/testdata/minimal_fasta_without_directive.gff3000066400000000000000000000011351211610345200250510ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	.
>ctg123
cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg
tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta
tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa
aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat
aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat
cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc
gtatttgatttgggtttactatcgaataatgagaattttcaggcttaggc
ttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt
aggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttag
aatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattc
genometools-1.5.1/testdata/missing_gff3_header.gff3000066400000000000000000000013751211610345200223200ustar00rootroot00000000000000##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/multi_feature_different_sequence_id.gff3000066400000000000000000000002151211610345200256610ustar00rootroot00000000000000##gff-version	3
11	ucb	MIR	26423868	26423948	.	+	.	ID=osa-MIR531;rfam=MI0003204
8	ucb	MIR	1214013	1214093	.	-	.	ID=osa-MIR531;rfam=MI0003204
genometools-1.5.1/testdata/multi_feature_multi.gff3000066400000000000000000000011021211610345200224750ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1
ctg123	.	CDS	1201	1500	.	+	0	ID=CDS1;Parent=gene1
ctg123	.	CDS	3000	3902	.	+	0	ID=CDS1;Parent=gene1
###
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1.1
ctg123	.	CDS	1201	1500	.	+	0	ID=CDS1.1;Parent=gene1.1
ctg123	.	CDS	3000	3902	.	+	0	ID=CDS1.1;Parent=gene1.1
###
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1.2
ctg123	.	CDS	1201	1500	.	+	0	ID=CDS1.2;Parent=gene1.2
ctg123	.	CDS	3000	3902	.	+	0	ID=CDS1.2;Parent=gene1.2
###
genometools-1.5.1/testdata/multi_feature_simple.gff3000066400000000000000000000003061211610345200226410ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1
ctg123	.	CDS	1201	1500	.	+	0	ID=CDS1;Parent=gene1
ctg123	.	CDS	3000	3902	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/multi_feature_simple_reverted.gff3000066400000000000000000000003061211610345200245410ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1
ctg123	.	CDS	3000	3902	.	+	0	ID=CDS1;Parent=gene1
ctg123	.	CDS	1201	1500	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/multi_feature_undefined_parent.gff3000066400000000000000000000002371211610345200246650ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	CDS	1201	1500	.	+	0	ID=CDS1;Parent=gene1
ctg123	.	CDS	3000	3902	.	+	0	ID=CDS1;Parent=gene1
###
genometools-1.5.1/testdata/multi_feature_with_different_parent_1.gff3000066400000000000000000000006671211610345200261540ustar00rootroot00000000000000##gff-version 3
# region I:2000001..3000000
I	Coding_transcript	gene	2929785	2931362	.	+	.	Alias=Y71F9AM.5;Dbxref=CGC:nxt-1;ID=Gene:WBGene00003836;Name=WBGene00003836
I	Coding_transcript	exon	2929947	2930089	.	+	.	ID=45166;Parent=Gene:WBGene00003836
I	Coding_transcript	gene	2928394	2931254	.	+	.	Alias=Y71F9AM.6;ID=Gene:WBGene00022122;Name=WBGene00022122
I	Coding_transcript	exon	2929947	2930089	.	+	.	ID=45166;Parent=Gene:WBGene00022122
genometools-1.5.1/testdata/multi_feature_with_different_parent_1_tidy.gff3000066400000000000000000000006351211610345200272000ustar00rootroot00000000000000##gff-version   3
# region I:2000001..3000000
##sequence-region   I 2928394 2931362
I	Coding_transcript	gene	2929785	2931362	.	+	.	ID=gene1;Alias=Y71F9AM.5;Dbxref=CGC:nxt-1;Name=WBGene00003836
I	Coding_transcript	exon	2929947	2930089	.	+	.	Parent=gene1
###
I	Coding_transcript	gene	2928394	2931254	.	+	.	ID=gene2;Alias=Y71F9AM.6;Name=WBGene00022122
I	Coding_transcript	exon	2929947	2930089	.	+	.	Parent=gene2
###
genometools-1.5.1/testdata/multi_feature_with_different_parent_2.gff3000066400000000000000000000003631211610345200261460ustar00rootroot00000000000000##gff-version 3
I	.	gene	2929785	2931362	.	+	.	ID=Gene1
I	.	exon	2929947	2930089	.	+	.	ID=1;Parent=Gene1
I	.	exon	2921000	2931362	.	+	.	ID=1;Parent=Gene1
I	.	gene	2928394	2931254	.	+	.	ID=Gene2
I	.	exon	2929947	2930089	.	+	.	ID=1;Parent=Gene2
genometools-1.5.1/testdata/multi_feature_with_different_parent_2_tidy.gff3000066400000000000000000000004461211610345200272010ustar00rootroot00000000000000##gff-version   3
##sequence-region   I 2921000 2931362
I	.	gene	2929785	2931362	.	+	.	ID=gene1
I	.	exon	2921000	2931362	.	+	.	ID=exon1;Parent=gene1
I	.	exon	2929947	2930089	.	+	.	ID=exon1;Parent=gene1
###
I	.	gene	2928394	2931254	.	+	.	ID=gene2
I	.	exon	2929947	2930089	.	+	.	Parent=gene2
###
genometools-1.5.1/testdata/multiple_header_lines.gff3000066400000000000000000000014411211610345200227610ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
##gff-version   3
genometools-1.5.1/testdata/multiple_top_level_parents.gff3000066400000000000000000000006531211610345200240700ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1,mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1,mRNA2,mRNA3
###
genometools-1.5.1/testdata/nGASP/000077500000000000000000000000001211610345200165655ustar00rootroot00000000000000genometools-1.5.1/testdata/nGASP/III.fas000066400000000000000000036411271211610345200177100ustar00rootroot00000000000000>III:1000001..2000000
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
genometools-1.5.1/testdata/nGASP/protein_10.fas000066400000000000000000000204431211610345200212430ustar00rootroot00000000000000>BP:CBP00004
GSHQIAKNFVNSSTPDLRPTFVVNFDTSTVICQHSSDPTDLHIHNMSSLCDGKQDCFVNPAMHDEVFPYCEHKCESTCSGKGACLYDGSKPQCYCDSGFSGAACELQDKNECLEHPCHMMAQCQNTLGSYECRCLPGYQGNGHECSDIDECADNIATRCPEHSQCINLPGTYYCNCTQGFSPKGNQGSGLDKCADINECETGAHNCETNEICENTIGSFKCVTKCSPGYSLIDGKCEDVNECDSEKLHKCDVRAECINTVGGYECECEEGFDGDGKNCQRGNPMSLSIAKSSCRKNSAICDRHASCNIFLDICDCKTGYTGDGITCHDVNECDAKETPCSEGGRCLNLDGGYVCCKDGQDDAACIKDQRAFCSGGCCDNAICSNATCACIDGFRGDPHKKCVDINECVENDSVCGGVGDRCVNLFGGYKCCQHGSQEVECTDQAFSSDSSTVSSHGADFTTTGEQVIEGSGSIQTSSGGSITVTRGLIPKEVELTTSGRLACTSYCPPNSECVGGFCECVKGYGGNALVGCEDVDECITETCNVEANEWCVNLIGGFVCCNPTNATHDDCIVLSLGSNVPFSDFLTVPGLEITKEKGLHVIGPNEEDTVVATRSNHSVTSDQLITEVVQQSKNFSSGQIILTRKSVTGGEAVTQTTDGDGEFGLEISAKDFGITLPATLEPRVEGSGKSPVAGVWTEEEDGGEDDDLMEASGSHGSWSTTINGTGFTGSPRSEGTIRVRITTLGEDGETETATKPGITVPGKDGKLAIEKEGHESVSSGSSATSSSGSTGSGASGSTATGKSGSSATSSSGSSSSGSTESGSSGSSATSSSGSTSSGESGSTATEESGKSEPSGATGTESSGKSESGASGESGPAGSSTTSSSGSTESGASGSNATSSSGSSATGESGSSSSGSTESGASGSNATGGSGATGNESSESAGTTASPESVTASRESVEGSGTTPSESTSSLPEGSGEWIETGSKGHFERGNKVSVSHGNGKPEGSGPKESGKPEVPGSQGSGAKESGAGKPGSGSRGPEITTDGEESESTSSGSGKPKNPKITTDGEGSKSTPIGDGKHPEDVEGSGILTTSSGGKNSTLEHGTKLVEVKPEGSDKNPGVGLEISAGKVTSAPEDKEKSNEVGLEIVWESTTPEPTTPDTDNVGLEISGRDLITKRPHQIEGSGTGDEEITATTRDVSKSTKKPRLEIDGGDNGETSGVDGKASTPSPTSPGAPESTTPSAPTTAPEDVTPETGSGEPGIPDGSGESSTAAPEGVSPTSSAPAPEVPTTPEGSEESTKTPEEATTATSPEEETTTQEPLILTAAPSKAPESSTKPSEAPEASSESTAAPPTAQPATVIPPQNREEKPEPTKETFALPTTTEKPVNETIENTKCMSSDECGLDALCERRTGVCRCEPGFEGAPPKKACVDVDECATGDHKCHDSARCQNFIGGYACFCPTGFRKTDDGSCEDIDECKEHNSTCCGANAHCVNKPGTYSCECENGFLGDGYHCVPSTKKPCDKEQSTKSHCAESNMSCEVDTTDGSVECKECMSGYKKSGTTCEDINECDEQSPCSPSASCVNLNGTFSCSCKPGFRGDGFMCTDINECDEKHPCHPHAECTNLEGSFKCECHSGFEGDGIKKCTNPLERSCEDVEKFCGRVDHVSCLSVRIYNGSLSSVCECEPGFRFEKESNSCVDIDECEENRNNCDPASAVCVNTEGSFKCECAEGYEGEGGVCTDIDECDRGMAGCDSMAMCINRMGSCGCKCMAGYTGDGAHCTKIEEPKEASKTACTEEWSRLCELEKKQCAVDEEEVPQCGACLPGHHPINGTCQSLQISGLCAQKNDCNKHAECIDILPDSHFCSCPDGFIGDGMMCDDVDECNNAGMCDDENSKCENTIGSFNCVCLEGFKKSDDDKCVLKTPNREKIEINEENSSSTPSESQKPESTTQGTVTTSVLSSEPTSEAPTSSTSPVTSSEKASESTTSSESPVTPSETSVTTTSLCSTVTCHSLATCEPSTGVCICRDGFIGDGTSSCSKKSTADCISLPSLCAENAKCDNSARSCECDAGYIGDGYVCSPHPQDCVLRDNLCSPEAICQNRRCQCLPGFTGDGVKCVSIHERASNCSQCDANAHCVGGTTCKCNPGYFGNGLCCVPDPLDCVHFTGICHPNAVCNPDTRQCQCSSGFSGNGVSCFPQKSCRTDKSVCAKNAICLPTGSCICRHGFKGDPFYKCTSLVAKEPSNAQDLSDVSSCVTPCDASSQLCISGECICKPGFRQNPGSKTCADIDECAEKTHRCNRIATCRNTFGSHVCSCPEGHVGDGVTCVPHVNQGKLSVYCEADGMTLVLGNETSDFEGKIFVKGQAENPYCSKSFSALLNSHKPYVFKVAFQHCDVQLLDNHTMASTVVVQKHAMFLTNKADSYDLRCQYPIGSRAVQSHVNVSELATTSTLTDKNSTLAPICRLSVSNDQHSSISSAMVGDTLKLALEVTPSENFGILPRNCFAVNIESGERYTLTDEQGCAIDESLFPQWSVTNSAK
>BP:CBP00012
MAPKDDPDNRGFDDQRRPSQRSTVLAIPALAVNDPKADPKIASDLPANYVDDDDDAPKLYTPSLFEKILNYLLCRGDIANQQLEAQPVSIPGLFRYGKRFDYLLLFIGTICAIISGVSQPIMALVSGRVTNALLVYPPTSKQFRNKANENVYIFLGIGIFISITNWIQYMCFQHCCSRVMAQMRHRFVYSVLRQNAGWFDKNHSGTITTKLNDSMERIREGIGDKLGVLLRGFAMLIAAIVVAYIYEWRLASMMLGVAPVCCICMSLLARQMTSTTIKELIGVGKAGSIAEESLMGVRTVQAFNGQEEMVGRYQTELEKGRRFAVWKGFWSGFFGGLFFLCLFSFLGTGMLYGAYLLKVGIIGSPGDVFIVVMSMLLGAYFLGLISPHMMVLLNARVSAATIYQTIDRVPKIDPYSKAGKRLPNVVGRVKFENVHFRYPSRKEAKILNGLNLTVEPGTSVALVGHSGCGKSTSVGLLTRLYEPEAGNVTIDGTDVRELNIDWLRNVVGIVQQEPILFNDTIHNNLLIGNPGATREKMIEVCKMANAHDFIEKMPKGYDTLIGDGGVQLSGGQKQRVAIARTLIRDPKILLLDEATSALDAQSESVVQSALNNAAKGRTTIMIAHRLSTIREADKIVFFEKGVIVEAGNHEELVHLGGRYFDLVKAQQFKADPEATEEFEEEEIDLDDNSRSSRRSSMTSARSGSEAFQRGNSLNDSFSGSRRSARADAENDAFAAHEAEVMAQDGQITAGYLDIFKNAKGNYIYMFLGTVFALIRGLELPALALIFGWVFEGFTFVPYGGRMMHRMAMAVIAFASVGVGVWISQVASSVLFAIVSENLSLRFRVQSFRNLLYQDASYFDNPAHAPGKLITRLASDAPNIKAVVDARMLQVIYALAAIIANIVIAFIYCWQVAILGTSLILLLAFVMIGLAYKISLMNIEQIKNDEAGRTAIEIIENVKTIQLLTRCELFFDHYQTSSKQQKRSELKKGMIEAINYSITQSFMYFMMCFTYAVGIRVIYDGDKSSDVTFKGIISMMLGAVAVMNSAQYFPEFVKAKTAAGLLFNIIYRKPRTGDLMEGDRPEIRGNILFENVKFSYPQRPLQPIMKGLQWTALRGQTVALVGPSGSGKSTNIGMLERFYDVTGGVLRIDGQDIRNLSLYHLRTQMALVGQEPRLFAGSIRENVCLGLKDVPLEKINKALELANANRFLANLPAGIDTDVGEKGGQLSGGQKQRIAIARALVRDPKILLLDEATSALDSESERAVQEALDRAREGRTCITIAHRLSSIQNSDLIVYIDKGKVQEAGNHAQLMQKKGRYYKLIKKQDLAV
>BP:CBP00016
MSVEWKSALRLQIEALAKRNDLHRKSSEEEIKKRIVDMDRRIVKLRELVSTSANDAAIFYLECVCHADETERLLNRESSVEKEKKWRKMKRKPSSQIGPTESRTVSSLPSVSPPDVIQTINVSTLEAQDQMPQRPHWWDQFQIYRRTDLLRFSKQNDRRELWRTQKDFFLTCLGFMVGVGHTMRFPAKVYQHGGGVFFIPFFSLVFFGLPLVFLHLSLGQYTGQAANTAFSKLMPIGSGVGWALVVIAIPVAVYYNIIVAWAIHYFFQSAKGLLLGDELPWETCRDEWQLDNRCCNLHNLHSCFNSSNSITAPEAFFHSEVLSLSTFGDFALGPLQSHLVLSLAAAWLLVFFGVFKGLGSIAQTMNVTATVPYLLLSILLLRGISLPGANKGLSFFFTVDSTKLWKWQIWKSAAEQVFYELGIDAGPLISMAAFSRYRNNVYRDSVLLVIMDALTSILSGMVIFSFVGFIASESNSNVNDVLKHDPLYLSFTVYPGVTSFMYWGGLWATMFFGMLVMAALDAEFAWLEMIASAFMNHFSTKNKAVENRLLAFLCLVGFFFGLPLCAQGGIFVFHAIENLNANWNSFSLALLSVAIVCYVYGIDNYLTDISGMLRVPRIPISKAIRFRDKIVSILGPGGIYIKFSLCFICPVILTVLLVASVLGYQRISFAGRPIPIDYEIVAWVVMIGPLLVVPLVAFLQVRQIRNEGKLLKSLFDTSEWRENPDDLLEPKDAYMKQDSKYESPPNRRRTPTIFTHRENTYMYIDSRGPTVRSRVFPMGAPLDPYGWKLGRLRDHQQHIEEVESNYSEEGSTTNNSFMASTVKHNDDVELTLFGSPPAIMGDEDKNMVTKFSESMPVNYKCRNEQAAPVQSRREPRLGRMARKTRRKRSSPSASDPPVPTSPLPPPPRLYHCKSEPPMMRSEEEHGTPKIITPDGSCSISDSSDDSSDDNIRRATVIRRKTSDDDAFTQISTAESISITPLDFPRQRSLSSVAIYDQEQKNGRSKVLSQLKRPTPIVMPPK
>BP:CBP00018
KMSNSTSPNAAATVGNIAYCYVLPCICVIGIVGNITNLVVLASRRLRAVSYMYLRALAVADLLCMLFVLVFVSTEYMAKNGSTINQYKIYQIYQCHLMLTLINWALGAGVYVVVALSLERYISIVFPMHFRTWNSPQRATRAIIIAFLIPAIFYIPYAVTRYKGKQRWDPIQNVTIYSMDDHPIYTTFYWQIYKWTREALLRFLPIIILTVLNLQIMFAFRKRQKMFQQLTKRKEQGTQKDDTLMYMLGGTVLMSLVCNIPAAINLLLIDETLKKRLDYQIFRAVANLLEITNHASQFYVFCACSTDYRTTFLQKFPCFKTDYANRDRLRSFVRRTQSVIQKQGSVEHTTNSKVWIMFKSKFQRDSLSHHSRKFSRHMPIEQDTVDIQLASGEQSTSGETCEADTLIKYGGSIQLCNDENNTTFL
>BP:CBP00022
CVICGQSTSLYNYGTISCSACSSFFRRTVLAKVPIQQCPHQDACYTPENRATHSECKYCRFHKCVDVGMINTQKYTNLTKLINQLSVLDKKRSYTCANMMLPPDFRLSSIFDYEHIKLIKKTPEVRFISHDWGCVHQLASMEFIKTFQFVKFLSLQDLQVFMKTAHFNHVIFASAMRSFGIRQGYLSFPDGSDVFPECIKRITCYNPEFLNRIRCKLMGRIIELNINPEEYLLLSAIILCNPAAVNLSVKGRTLISSYQKVYGSLLFQYCCQVNKKNGPLRFSELLTIFHAISQTHHDIGQFFLLFQMYQPNAQPIQLYQEVIDYM
>BP:CBP00024
FQSVHHHLNEEELKQVFGVSNKHEVPEYSLIETTRHPLKNGGLKMKFVAWNDTYHLNLRKNSRIVSPHIISVIRHGDDAVTTYDGLRDYNQCHYQGEVKSHGNMKAAISDCGALMGSLVMEDHFLVLQTLPKRVHHLQKERHLVYKRSAGLLTDTENKIREEITRLQEEQESFCDTSEQLDDPAMTIPAHLHFNYTIPTSAQLDSPFIFPNMDPITLEIGLFLDSKLFEHFEREYIQDAEQHLLEFSLALINNVHVLYQQDTLTPNLDIVIVRYEMWKTQPSSLSTGVHKNGQAQSLLDAFCRYQAHMNPGTDLTDMNHWDHGVLLTGYDIYHTTTSVAGVAPVARMCDPLFACSLVEGLHLGRSFVLAHEMGHNMGMVHDGVQNQCNKGCCLMSAVNGAGKTTWSDCSVREFNAFLLQLDESGRGNCLRDASPGLISTNHLSDTRLPGQRFTADQQCSYFWGRDYRVEIPNGKAMDDICRILWCGNSGSTISTAHPALEGSWCGHNKWCHKGHCTSWNFDLPPVPIDGQWSEWGGAEKGCPIQQCAVSGSITIQAQHRDCVNPAPNNGGRTCEGANIRGIVCGATSSNCLGFTREEFGNKICSSIKFDPHKPDQQLTGEGFEHSTQPCRVWCHLIGSELIRNKGQFPDGTPCGFDAYCVGGQCLALSCDNKALVEQQEDCPRLEGRSIHQWEDWSSWSECSVSCGPGGRQVRERKCSSGRKCQGVSEESRACEGVLRDCEEFGEWKDWGPCSEKCALGIQKRFRPCLTDQCASEHLQEKRPCDNEGCWTNWDEWSSCSQTCGGGRRYRLRKCLDFKCEGDDLEKESCNTQKCISQTWGDWLPCSVSCGIGFQIRERLCDGELCATANKQARTCNQQQCPSTFSLAVWSEWGEWTTCSATCGEGLQSRERSCRRGSCQESDAAQTRRCVNGPCDHTFLPWSEWTPCETCSSFDSRKRIAKCDGTTDNCQDKIDEETCDNACLREQHSFGPISPKRPKLITSNELRKAFGRPLLPIESITSSKWSEWGPCSVTCGSGRRVRTRDCQEENCPEQNIQHEECSLNSCLDLFIWSDWSSCSKSCGHDATQTRQKLCLFNNAECSSYAESRRCKNLPTCTSISSGNTISENSFDAPQWSEWSSWSACSCFSLTSTRRRFCQVADPTVQGFCAGSILEQIPCAPGNCSPSAGGWSSWSEWSSCSKDCGDTGHQIRNRMCSEPIPSNRGAYCSGYSFDQRPCVMDNVCGEEKVNGGWTDWTSWSECTDYCRNGHRSRTRFCANPKPSQGGAQCSGSDFELNPCFDPARCHLRDGGWSIWSDWSPCSASCGFGVQTRDRTCSSPEPRGGQLCTGLAHQTSLCDLPACDHESDGEWSAWNEWSGCMGNCGFGTRTRVRACVSPPASHGGQPCFGRSSEITECRQSESTCSSFITSSLLADGYFIETDQQQ
>BP:CBP00025
MLAFESPIAESSYSRQKAKDLAKKFTPGELCTVCGDVASGIHYSVAACNGCKTFFRRVVLENRTYSCKNNGDCIIDKSMRCSCRHCRYKKCIIAGMDRAELSMERRRKRKKLNGIEGLEERYETTNPLINLLLHKEKLYQKLLHSSAMTIHTSLREALDMSQIAFNDTNNKYDDRMDPKYPTNFSYWRAKILTVLVEWAKSFEASFSHLQPEDQKRLFIHTAFSNLVLAEAFHTPEKYNDRIVFPDGLCGFRNVAQTVSSDGVSTKTYGLTPTVVAVINDVLVPIRRMRLTKVEYVLLQAIIFFDPDCLSLTKHGSQLIAAKRRRLLHALQDWLQQQNKHEAAGRFAEILLRICNVQKVAAFKRETLCTIETFELMQPHPFTMEISKSYPDFSYF
>BP:CBP00027
MVDLKQQLQWIDYLGVVAVWLCFFGTVLVISVTCILWCCVGKEDDPTVFAKYGFGPQPRVPSQRSKLEVEKDF
>BP:CBP00029
MTRLLNGIKVVELAGLAPVPHCGMMLADFGADVTVIDKKHPVVEQRMNRGKTMKEFDLRKPEDVKKVRELCKTSDVLLDPYRPGTLEKMGLDPLSLWNDNKGLIICRISGYGQTGRMKDEAGHDINYVAMSGMMPTFAGTEASRPWPPVNMLADFAGGGLSAAFGIVSAIHARHHNGGKGCVLDCSMTEGTAYLASFVQHYYDQTHLFTDKYAAFTGECPIYRTYKTKDGKFMAVGPLEPKFHQNMFEVLGIDGDDLFSDPDRITKELEATFLQKTRDEWSKIFEGKDCCVTPVLDIHEVGTYGQHVDRQNFSKSDKFGGTWIAKPSPRVQTIEELTAAATR
>BP:CBP00030
MAIVAAGVSKVLTTFQKTFKGLLPLIILVIYTLLGAWIFWMIEGENEREMLIEQQKERDDLIRRTVYKINQLQIKRQRRLMTAEEEYNRTAKVLTTFQETLGILPADMDKDIHWTFLGSIFYCMTVYTTIGYGNIVPGTGWGRFATIVYAFLGIPLTVLSLYCLGSLFAKGCKILWKFFLRSTRVVSKDLSEKISEAADNIEEGTTAVAPASKEENDDDDLLSFPISGLLLITVIWVIFCAVLFTFLEEWDFGTSLYFTLISFTTIGFGDILPSDYDFMPIVGVLLLIGLSLVSTVMTLIQQQIEALASGMKDNIDQEYARALNEAREDGEVDEHVDPEEDPETNKKSLNAVVSRMPLSKRALYYFLPASQKKQLEQQSEKKMGRKSIKVQTDSELLETLIREEILKAELNNEMHKFNGPRSSQQPRLIHSEIREKEVPIEVVRVEQYNHGGHDDYLEHDI
genometools-1.5.1/testdata/nGASP/protein_100.fas000066400000000000000000001462271211610345200213340ustar00rootroot00000000000000>BP:CBP00004
GSHQIAKNFVNSSTPDLRPTFVVNFDTSTVICQHSSDPTDLHIHNMSSLCDGKQDCFVNPAMHDEVFPYCEHKCESTCSGKGACLYDGSKPQCYCDSGFSGAACELQDKNECLEHPCHMMAQCQNTLGSYECRCLPGYQGNGHECSDIDECADNIATRCPEHSQCINLPGTYYCNCTQGFSPKGNQGSGLDKCADINECETGAHNCETNEICENTIGSFKCVTKCSPGYSLIDGKCEDVNECDSEKLHKCDVRAECINTVGGYECECEEGFDGDGKNCQRGNPMSLSIAKSSCRKNSAICDRHASCNIFLDICDCKTGYTGDGITCHDVNECDAKETPCSEGGRCLNLDGGYVCCKDGQDDAACIKDQRAFCSGGCCDNAICSNATCACIDGFRGDPHKKCVDINECVENDSVCGGVGDRCVNLFGGYKCCQHGSQEVECTDQAFSSDSSTVSSHGADFTTTGEQVIEGSGSIQTSSGGSITVTRGLIPKEVELTTSGRLACTSYCPPNSECVGGFCECVKGYGGNALVGCEDVDECITETCNVEANEWCVNLIGGFVCCNPTNATHDDCIVLSLGSNVPFSDFLTVPGLEITKEKGLHVIGPNEEDTVVATRSNHSVTSDQLITEVVQQSKNFSSGQIILTRKSVTGGEAVTQTTDGDGEFGLEISAKDFGITLPATLEPRVEGSGKSPVAGVWTEEEDGGEDDDLMEASGSHGSWSTTINGTGFTGSPRSEGTIRVRITTLGEDGETETATKPGITVPGKDGKLAIEKEGHESVSSGSSATSSSGSTGSGASGSTATGKSGSSATSSSGSSSSGSTESGSSGSSATSSSGSTSSGESGSTATEESGKSEPSGATGTESSGKSESGASGESGPAGSSTTSSSGSTESGASGSNATSSSGSSATGESGSSSSGSTESGASGSNATGGSGATGNESSESAGTTASPESVTASRESVEGSGTTPSESTSSLPEGSGEWIETGSKGHFERGNKVSVSHGNGKPEGSGPKESGKPEVPGSQGSGAKESGAGKPGSGSRGPEITTDGEESESTSSGSGKPKNPKITTDGEGSKSTPIGDGKHPEDVEGSGILTTSSGGKNSTLEHGTKLVEVKPEGSDKNPGVGLEISAGKVTSAPEDKEKSNEVGLEIVWESTTPEPTTPDTDNVGLEISGRDLITKRPHQIEGSGTGDEEITATTRDVSKSTKKPRLEIDGGDNGETSGVDGKASTPSPTSPGAPESTTPSAPTTAPEDVTPETGSGEPGIPDGSGESSTAAPEGVSPTSSAPAPEVPTTPEGSEESTKTPEEATTATSPEEETTTQEPLILTAAPSKAPESSTKPSEAPEASSESTAAPPTAQPATVIPPQNREEKPEPTKETFALPTTTEKPVNETIENTKCMSSDECGLDALCERRTGVCRCEPGFEGAPPKKACVDVDECATGDHKCHDSARCQNFIGGYACFCPTGFRKTDDGSCEDIDECKEHNSTCCGANAHCVNKPGTYSCECENGFLGDGYHCVPSTKKPCDKEQSTKSHCAESNMSCEVDTTDGSVECKECMSGYKKSGTTCEDINECDEQSPCSPSASCVNLNGTFSCSCKPGFRGDGFMCTDINECDEKHPCHPHAECTNLEGSFKCECHSGFEGDGIKKCTNPLERSCEDVEKFCGRVDHVSCLSVRIYNGSLSSVCECEPGFRFEKESNSCVDIDECEENRNNCDPASAVCVNTEGSFKCECAEGYEGEGGVCTDIDECDRGMAGCDSMAMCINRMGSCGCKCMAGYTGDGAHCTKIEEPKEASKTACTEEWSRLCELEKKQCAVDEEEVPQCGACLPGHHPINGTCQSLQISGLCAQKNDCNKHAECIDILPDSHFCSCPDGFIGDGMMCDDVDECNNAGMCDDENSKCENTIGSFNCVCLEGFKKSDDDKCVLKTPNREKIEINEENSSSTPSESQKPESTTQGTVTTSVLSSEPTSEAPTSSTSPVTSSEKASESTTSSESPVTPSETSVTTTSLCSTVTCHSLATCEPSTGVCICRDGFIGDGTSSCSKKSTADCISLPSLCAENAKCDNSARSCECDAGYIGDGYVCSPHPQDCVLRDNLCSPEAICQNRRCQCLPGFTGDGVKCVSIHERASNCSQCDANAHCVGGTTCKCNPGYFGNGLCCVPDPLDCVHFTGICHPNAVCNPDTRQCQCSSGFSGNGVSCFPQKSCRTDKSVCAKNAICLPTGSCICRHGFKGDPFYKCTSLVAKEPSNAQDLSDVSSCVTPCDASSQLCISGECICKPGFRQNPGSKTCADIDECAEKTHRCNRIATCRNTFGSHVCSCPEGHVGDGVTCVPHVNQGKLSVYCEADGMTLVLGNETSDFEGKIFVKGQAENPYCSKSFSALLNSHKPYVFKVAFQHCDVQLLDNHTMASTVVVQKHAMFLTNKADSYDLRCQYPIGSRAVQSHVNVSELATTSTLTDKNSTLAPICRLSVSNDQHSSISSAMVGDTLKLALEVTPSENFGILPRNCFAVNIESGERYTLTDEQGCAIDESLFPQWSVTNSAK
>BP:CBP00012
MAPKDDPDNRGFDDQRRPSQRSTVLAIPALAVNDPKADPKIASDLPANYVDDDDDAPKLYTPSLFEKILNYLLCRGDIANQQLEAQPVSIPGLFRYGKRFDYLLLFIGTICAIISGVSQPIMALVSGRVTNALLVYPPTSKQFRNKANENVYIFLGIGIFISITNWIQYMCFQHCCSRVMAQMRHRFVYSVLRQNAGWFDKNHSGTITTKLNDSMERIREGIGDKLGVLLRGFAMLIAAIVVAYIYEWRLASMMLGVAPVCCICMSLLARQMTSTTIKELIGVGKAGSIAEESLMGVRTVQAFNGQEEMVGRYQTELEKGRRFAVWKGFWSGFFGGLFFLCLFSFLGTGMLYGAYLLKVGIIGSPGDVFIVVMSMLLGAYFLGLISPHMMVLLNARVSAATIYQTIDRVPKIDPYSKAGKRLPNVVGRVKFENVHFRYPSRKEAKILNGLNLTVEPGTSVALVGHSGCGKSTSVGLLTRLYEPEAGNVTIDGTDVRELNIDWLRNVVGIVQQEPILFNDTIHNNLLIGNPGATREKMIEVCKMANAHDFIEKMPKGYDTLIGDGGVQLSGGQKQRVAIARTLIRDPKILLLDEATSALDAQSESVVQSALNNAAKGRTTIMIAHRLSTIREADKIVFFEKGVIVEAGNHEELVHLGGRYFDLVKAQQFKADPEATEEFEEEEIDLDDNSRSSRRSSMTSARSGSEAFQRGNSLNDSFSGSRRSARADAENDAFAAHEAEVMAQDGQITAGYLDIFKNAKGNYIYMFLGTVFALIRGLELPALALIFGWVFEGFTFVPYGGRMMHRMAMAVIAFASVGVGVWISQVASSVLFAIVSENLSLRFRVQSFRNLLYQDASYFDNPAHAPGKLITRLASDAPNIKAVVDARMLQVIYALAAIIANIVIAFIYCWQVAILGTSLILLLAFVMIGLAYKISLMNIEQIKNDEAGRTAIEIIENVKTIQLLTRCELFFDHYQTSSKQQKRSELKKGMIEAINYSITQSFMYFMMCFTYAVGIRVIYDGDKSSDVTFKGIISMMLGAVAVMNSAQYFPEFVKAKTAAGLLFNIIYRKPRTGDLMEGDRPEIRGNILFENVKFSYPQRPLQPIMKGLQWTALRGQTVALVGPSGSGKSTNIGMLERFYDVTGGVLRIDGQDIRNLSLYHLRTQMALVGQEPRLFAGSIRENVCLGLKDVPLEKINKALELANANRFLANLPAGIDTDVGEKGGQLSGGQKQRIAIARALVRDPKILLLDEATSALDSESERAVQEALDRAREGRTCITIAHRLSSIQNSDLIVYIDKGKVQEAGNHAQLMQKKGRYYKLIKKQDLAV
>BP:CBP00016
MSVEWKSALRLQIEALAKRNDLHRKSSEEEIKKRIVDMDRRIVKLRELVSTSANDAAIFYLECVCHADETERLLNRESSVEKEKKWRKMKRKPSSQIGPTESRTVSSLPSVSPPDVIQTINVSTLEAQDQMPQRPHWWDQFQIYRRTDLLRFSKQNDRRELWRTQKDFFLTCLGFMVGVGHTMRFPAKVYQHGGGVFFIPFFSLVFFGLPLVFLHLSLGQYTGQAANTAFSKLMPIGSGVGWALVVIAIPVAVYYNIIVAWAIHYFFQSAKGLLLGDELPWETCRDEWQLDNRCCNLHNLHSCFNSSNSITAPEAFFHSEVLSLSTFGDFALGPLQSHLVLSLAAAWLLVFFGVFKGLGSIAQTMNVTATVPYLLLSILLLRGISLPGANKGLSFFFTVDSTKLWKWQIWKSAAEQVFYELGIDAGPLISMAAFSRYRNNVYRDSVLLVIMDALTSILSGMVIFSFVGFIASESNSNVNDVLKHDPLYLSFTVYPGVTSFMYWGGLWATMFFGMLVMAALDAEFAWLEMIASAFMNHFSTKNKAVENRLLAFLCLVGFFFGLPLCAQGGIFVFHAIENLNANWNSFSLALLSVAIVCYVYGIDNYLTDISGMLRVPRIPISKAIRFRDKIVSILGPGGIYIKFSLCFICPVILTVLLVASVLGYQRISFAGRPIPIDYEIVAWVVMIGPLLVVPLVAFLQVRQIRNEGKLLKSLFDTSEWRENPDDLLEPKDAYMKQDSKYESPPNRRRTPTIFTHRENTYMYIDSRGPTVRSRVFPMGAPLDPYGWKLGRLRDHQQHIEEVESNYSEEGSTTNNSFMASTVKHNDDVELTLFGSPPAIMGDEDKNMVTKFSESMPVNYKCRNEQAAPVQSRREPRLGRMARKTRRKRSSPSASDPPVPTSPLPPPPRLYHCKSEPPMMRSEEEHGTPKIITPDGSCSISDSSDDSSDDNIRRATVIRRKTSDDDAFTQISTAESISITPLDFPRQRSLSSVAIYDQEQKNGRSKVLSQLKRPTPIVMPPK
>BP:CBP00018
KMSNSTSPNAAATVGNIAYCYVLPCICVIGIVGNITNLVVLASRRLRAVSYMYLRALAVADLLCMLFVLVFVSTEYMAKNGSTINQYKIYQIYQCHLMLTLINWALGAGVYVVVALSLERYISIVFPMHFRTWNSPQRATRAIIIAFLIPAIFYIPYAVTRYKGKQRWDPIQNVTIYSMDDHPIYTTFYWQIYKWTREALLRFLPIIILTVLNLQIMFAFRKRQKMFQQLTKRKEQGTQKDDTLMYMLGGTVLMSLVCNIPAAINLLLIDETLKKRLDYQIFRAVANLLEITNHASQFYVFCACSTDYRTTFLQKFPCFKTDYANRDRLRSFVRRTQSVIQKQGSVEHTTNSKVWIMFKSKFQRDSLSHHSRKFSRHMPIEQDTVDIQLASGEQSTSGETCEADTLIKYGGSIQLCNDENNTTFL
>BP:CBP00022
CVICGQSTSLYNYGTISCSACSSFFRRTVLAKVPIQQCPHQDACYTPENRATHSECKYCRFHKCVDVGMINTQKYTNLTKLINQLSVLDKKRSYTCANMMLPPDFRLSSIFDYEHIKLIKKTPEVRFISHDWGCVHQLASMEFIKTFQFVKFLSLQDLQVFMKTAHFNHVIFASAMRSFGIRQGYLSFPDGSDVFPECIKRITCYNPEFLNRIRCKLMGRIIELNINPEEYLLLSAIILCNPAAVNLSVKGRTLISSYQKVYGSLLFQYCCQVNKKNGPLRFSELLTIFHAISQTHHDIGQFFLLFQMYQPNAQPIQLYQEVIDYM
>BP:CBP00024
FQSVHHHLNEEELKQVFGVSNKHEVPEYSLIETTRHPLKNGGLKMKFVAWNDTYHLNLRKNSRIVSPHIISVIRHGDDAVTTYDGLRDYNQCHYQGEVKSHGNMKAAISDCGALMGSLVMEDHFLVLQTLPKRVHHLQKERHLVYKRSAGLLTDTENKIREEITRLQEEQESFCDTSEQLDDPAMTIPAHLHFNYTIPTSAQLDSPFIFPNMDPITLEIGLFLDSKLFEHFEREYIQDAEQHLLEFSLALINNVHVLYQQDTLTPNLDIVIVRYEMWKTQPSSLSTGVHKNGQAQSLLDAFCRYQAHMNPGTDLTDMNHWDHGVLLTGYDIYHTTTSVAGVAPVARMCDPLFACSLVEGLHLGRSFVLAHEMGHNMGMVHDGVQNQCNKGCCLMSAVNGAGKTTWSDCSVREFNAFLLQLDESGRGNCLRDASPGLISTNHLSDTRLPGQRFTADQQCSYFWGRDYRVEIPNGKAMDDICRILWCGNSGSTISTAHPALEGSWCGHNKWCHKGHCTSWNFDLPPVPIDGQWSEWGGAEKGCPIQQCAVSGSITIQAQHRDCVNPAPNNGGRTCEGANIRGIVCGATSSNCLGFTREEFGNKICSSIKFDPHKPDQQLTGEGFEHSTQPCRVWCHLIGSELIRNKGQFPDGTPCGFDAYCVGGQCLALSCDNKALVEQQEDCPRLEGRSIHQWEDWSSWSECSVSCGPGGRQVRERKCSSGRKCQGVSEESRACEGVLRDCEEFGEWKDWGPCSEKCALGIQKRFRPCLTDQCASEHLQEKRPCDNEGCWTNWDEWSSCSQTCGGGRRYRLRKCLDFKCEGDDLEKESCNTQKCISQTWGDWLPCSVSCGIGFQIRERLCDGELCATANKQARTCNQQQCPSTFSLAVWSEWGEWTTCSATCGEGLQSRERSCRRGSCQESDAAQTRRCVNGPCDHTFLPWSEWTPCETCSSFDSRKRIAKCDGTTDNCQDKIDEETCDNACLREQHSFGPISPKRPKLITSNELRKAFGRPLLPIESITSSKWSEWGPCSVTCGSGRRVRTRDCQEENCPEQNIQHEECSLNSCLDLFIWSDWSSCSKSCGHDATQTRQKLCLFNNAECSSYAESRRCKNLPTCTSISSGNTISENSFDAPQWSEWSSWSACSCFSLTSTRRRFCQVADPTVQGFCAGSILEQIPCAPGNCSPSAGGWSSWSEWSSCSKDCGDTGHQIRNRMCSEPIPSNRGAYCSGYSFDQRPCVMDNVCGEEKVNGGWTDWTSWSECTDYCRNGHRSRTRFCANPKPSQGGAQCSGSDFELNPCFDPARCHLRDGGWSIWSDWSPCSASCGFGVQTRDRTCSSPEPRGGQLCTGLAHQTSLCDLPACDHESDGEWSAWNEWSGCMGNCGFGTRTRVRACVSPPASHGGQPCFGRSSEITECRQSESTCSSFITSSLLADGYFIETDQQQ
>BP:CBP00025
MLAFESPIAESSYSRQKAKDLAKKFTPGELCTVCGDVASGIHYSVAACNGCKTFFRRVVLENRTYSCKNNGDCIIDKSMRCSCRHCRYKKCIIAGMDRAELSMERRRKRKKLNGIEGLEERYETTNPLINLLLHKEKLYQKLLHSSAMTIHTSLREALDMSQIAFNDTNNKYDDRMDPKYPTNFSYWRAKILTVLVEWAKSFEASFSHLQPEDQKRLFIHTAFSNLVLAEAFHTPEKYNDRIVFPDGLCGFRNVAQTVSSDGVSTKTYGLTPTVVAVINDVLVPIRRMRLTKVEYVLLQAIIFFDPDCLSLTKHGSQLIAAKRRRLLHALQDWLQQQNKHEAAGRFAEILLRICNVQKVAAFKRETLCTIETFELMQPHPFTMEISKSYPDFSYF
>BP:CBP00027
MVDLKQQLQWIDYLGVVAVWLCFFGTVLVISVTCILWCCVGKEDDPTVFAKYGFGPQPRVPSQRSKLEVEKDF
>BP:CBP00029
MTRLLNGIKVVELAGLAPVPHCGMMLADFGADVTVIDKKHPVVEQRMNRGKTMKEFDLRKPEDVKKVRELCKTSDVLLDPYRPGTLEKMGLDPLSLWNDNKGLIICRISGYGQTGRMKDEAGHDINYVAMSGMMPTFAGTEASRPWPPVNMLADFAGGGLSAAFGIVSAIHARHHNGGKGCVLDCSMTEGTAYLASFVQHYYDQTHLFTDKYAAFTGECPIYRTYKTKDGKFMAVGPLEPKFHQNMFEVLGIDGDDLFSDPDRITKELEATFLQKTRDEWSKIFEGKDCCVTPVLDIHEVGTYGQHVDRQNFSKSDKFGGTWIAKPSPRVQTIEELTAAATR
>BP:CBP00030
MAIVAAGVSKVLTTFQKTFKGLLPLIILVIYTLLGAWIFWMIEGENEREMLIEQQKERDDLIRRTVYKINQLQIKRQRRLMTAEEEYNRTAKVLTTFQETLGILPADMDKDIHWTFLGSIFYCMTVYTTIGYGNIVPGTGWGRFATIVYAFLGIPLTVLSLYCLGSLFAKGCKILWKFFLRSTRVVSKDLSEKISEAADNIEEGTTAVAPASKEENDDDDLLSFPISGLLLITVIWVIFCAVLFTFLEEWDFGTSLYFTLISFTTIGFGDILPSDYDFMPIVGVLLLIGLSLVSTVMTLIQQQIEALASGMKDNIDQEYARALNEAREDGEVDEHVDPEEDPETNKKSLNAVVSRMPLSKRALYYFLPASQKKQLEQQSEKKMGRKSIKVQTDSELLETLIREEILKAELNNEMHKFNGPRSSQQPRLIHSEIREKEVPIEVVRVEQYNHGGHDDYLEHDI
>BP:CBP00032
MLKVCMNVTDQCDCLAIECPIAYSNSVEEKEACYMEHCFISKRALDDVTLYKVTALYLVIFIIGVFGNTATCLVMRKHPMMKTHTSMYLINLAVSDLVTLCVGLPFEMMMNWHQYPWPFPDVICNLKALIAETTSSVSILTILVFAIERYVAVCHPLYLVKNQFFKRNMKSIIGLSWIVSILCATPFGIYHRADYLMRSWPGTDDKIPVISSKMCMVAVMFEPKLEPTFKVLFHFSAIAFFVVPLLTILVLYARIACKVSNNRTIQAGELDITEELQLKINAILCAIVSAFFICYLPFQFQRLLFFYLDNEVILVWINQYVYFISGFLFYLATIINPIAYNVASSRFRRAFKDILFYYCFGRKSNGYPRSSFSKYSL
>BP:CBP00039
FREMADSPKFALVTFAVYAVILYNVNSFFWKFVFIGYVVFRLLRTDFGRRAMATIPRDFAGLKLLISVKSTINALFKKDRPIHEIFLDQVRQHPNKIAVVEIESGRKLTYKELNELSNQYANLYVNEGYKIGDVVALFMENSIDFFAIWLGLSKIGVVSAFINSNLKLEPLAHSINVSKCKSCITNNSLLPMYKAALEKGLISKDIHVFLAGTEVDGRHRSLQQDLQLFSTEEPAPVDGLNFRSVLCYIYTSGTTGNPKPAVIKHFRYYWIAMGAGKAFGMTKPDVVYITMPMYHSAAGIMGVGSLIAFGTTCVIRKKFSASNFWKDCVKYNVTATQYIGEICRYLLAAKPCPEEKEHKVRLMWGNGLRGQIWKEFVGRFGIKKIGELYGSTEGNSNIVNLDNHVGSCGFMPIYPHIGAFYPVRLIKVDRATGELERDKNGLCVPCVPGETGEMVGVIKEKDALLKFEGYVSEGDTAKKIYRDVFKHGDKVFASGDILHWDELGYLYFVDRCGDTFRWKGENVSTTEVEGILQPVMDVEDATVYGVTIGKMEGRAGMAGVVVKDGIDIDKFLADITSRLTENLASYAIPVFIRLCKEVDRTGTFKLKKTDLQKQGYDLAACKGDKIYYWVGSEKSYKPLTEKMQQDIDAGIYDRF
>BP:CBP00040
MLHPIVLLLVASSAVYAARPRRALDGLDGSGFGFDKRALNSLDGAGFGFEKRALNSLDGQGFGFEKRALDGLDGMGFGFDKRALNSLDGAGFGFEKRALDGLDGAGFGFDKRALNSLDGQGFGFEKRALNSLDGAGFGFEKRALDGLDGAGFGFDKRALNSLDGAGFGFEKRALDGLDGAGFGFDKRALNSLDGQGFGFDKRSSFKHQSSKLRSVFRNLRGFNKQH
>BP:CBP00046
MSSLRCHVVVSALLFISIVPISQQVLNEHNQKLEWIVGKWRSEFSGKIFWPTVPTMTFGEELVINEAPIAKSANVQFLNFSARAWSHSTKDHFHDEWGFLTVDPVGNATLMTTGNNGFTTYETGTVSPNKLVLTLKDIGRISFSRDLPVEDLRRTFIRHDDRYMEQVIEMRTATHPKVGYLEHTRVVYTKLK
>BP:CBP00048
EGRGNKRTFFDITINGEPAGRIVFALYNHSCPSTAENFRALCTGELGQLYGHNASYQGSIFHRCIKGFMIQGGDLTHKNGQGGFSIYGRTFDDENLSLPHNKPFLLSMANRGPDTNGSQFFITTEKVPHLDGKHVVFGEVVKGFDVVKRIEKVETEEEDMPVQRVTIAHCGEMVRKSDVMASDKKKKQDEQEPVGCKMDDEPKTVNWLMRRSRSRTPEDSKKSKKDRERGGNRGDRRRHDRQRDRYGRERRSRSRSGSRDRHRDRERNRVPDERRSGKRPVSIPISKADCEVNKYERELGDCQEILVITNKDGIKVRGRGKLTFMGSRDRSTTPPHWKREESKKLTLEEHQKRQEEMEERKRLRAEREKEDVERKEREEKEAMERAAQRELERQEEEEARKRSRSNSPQSPRVKQELMSQRQESKAESNSSRSSSSSSGSSSSSDSDS
>BP:CBP00060
MEQIVESLQYFGFLGSLVLNSFLLFLLHTRAHRNFGKYRILMIVFCLFAIVYSLVEVLTLPVMFVKGRSLCVCSNGPLRLYRPIGVPLTSIYCGSFGMCISLLTLHFFYRYVAVCKPDKMRYFNGKHIFLTFSPSLFIFVTWSMTTYWPMAPDEMREIHYHDVLMKTFQTNSFEASFVAMISIFLQDPQTSTWLPSQLLSCAYMSFLMSVCFSVIVFCGYQALKQMRSHASHMSSKTKELNKQLFMTLGIQTLLPVFTMYIPVGCLMILPMFGIELGAAANNAAAFLGLYPALDPLVAILLIKDFRNFVFCKSVTSTYASAVSNTAPPSKILQ
>BP:CBP00061
MDADKLIEYIQYGGFVSSQLINALLLYLLCFQASNNFGRYRILMIVFSIFAMIYSLIEVVTFPVMMCKGRSLCVCSNGPFTLYRSIGVPLLSIYCGSFGMCISLLALHFFYRYIAICKPEKLYYFEGKQIISTLSPCFIIFVIWSLLVYFFMDVTEEKERIYHDVLFRSYNVDSHKVSFISMLYKSPATETSPEHWNFDQLVPFFGCCFIMDSCFFAIIYYGSKAFLQMKSCGTEMSKKTKELNRQLFLTLGIQTLLPLITMYVPVGCFIILPIFGVELGVEANKTGAFLGIYPALDPLIAILLIKDFRNYVFCQKRTLAKVSTTSGIASKITSTFQA
>BP:CBP00071
MGDEGYRGWIKLEIPCFEPERHMNNIIRCHTTKLEPALNSYNMRIHTKGQVQAVEEQDCEPFYESNYEIVSSHFSHHLIIAIQNYLKSLSMDRLMPFQLGNLVLHSSDFWSSELTCHLADIPLSAFFFGNIQGGTFINHWEVSFWEDTHRRNRLRQKNMQPTASDRQGLNQIRVEFEFDKVDFMTVHFKHKEGDFEVISKDFRKTRETVTMYYQITVRRTSIRRVIVDPVVNDTNGGDRIRIHFELNCPVLIRRAYKTEKQEAEAKHQVPHYRRFLVINRGRSANMYPTPKAITDSPVFTIEFDTSVSLEEVYRLISRLRIRTGVSIEFATIPSVDCLIWRENPYHRWTFHGSSHLSPTHFSAPIYRDFITTAFPRKHEVCGSREVDTNRERKFAITYLLECLISRGAVVKDQILLDDTIWHRFLEVILHYYTKDDKLCEAGLEDLVHMIDGRKRIGSLIKCFDRICQTRQKNSLVNGLTTEEMREGYQRVRKIIFTPTRVIYVAPETLMGNRVLRRYDHDGTRVLRITFRDDDNQKMRTNKTSTLLEKTVNTYLMNGITVAGRNFGYLGSSNSQMRDNGAYFMEKYSSSQCREYEKMCRMAPPITFNPKIQAARKNLGRFETIDNIPKMMARLGQCFTQSRLSGVNLDRCTYVTMYDLTGGKNIKGDEYTFSDGVGMMSMNFAQMVSQVMDFGKGVPSCFQFRFRGMKGVIAVEPFLDDLRQWSIENDIQEVSEDTAWGLNCVFRPSQIKFISKRHPRDQVEIVKYSSPVPVSLNKPFINILDQVSEMQSLECHRRVTNRIEELLDRQMLSFAQQMIDETFCRNRLKELPRRIDIDYLRTTWGFTLSSEPFFRSLIKASIKFSITKQLRKEQIPIPADLGRSMLGVVDETGRLQYGQIFVQYTRNLALKLPPKSASRSVLTGTVLLTKNPCIVAGDVRIFEAVDIPELHHMCDVVVFPQHGPRPHPDEMAGSDLDGDEYSIIWDQQLLLDRNEDPFDFTSEKQKSSFKEEEIDDLMREFYVKYLKLDSVGTISNSHLHNSDQYGLNARVCMDLAKKNCQAVDFTKSGQPPEELERKWRKDEVTGEMIPPERAERVPDYHMGNDHTPMYVSPRLCGKLFREFKAIDDVLKISEERDEQVEITIDETIMVDGYKEYMHSAREDLARYNAQLRSMMENYGIKTEGEVFSGCIVDMRNRISDKDQDDMSFYNTNQMIETKVTNLYKKYREHFFEEFEGAWEANTEGTSRGESDTNILQRHCRAPTQNMMKKAVAWYRACYEEARVTRENKKLSFAWLMYDVLAMVKQTKSLTSDDIRMGGSNPLYTMLDAHRSQYLLDNRSVFEDYIRFAPSKNQGEQVARALEIIRMYVETNPGLEEVMFVINEWARASKLFENQPIRNYHLSLLFILFATRQFSSVDGNAAAFFPKIDERGWREEKANGEFKQGLEFMEMKKSQMIVKFLEFLASRKFRKLPNVSFRTLRFSSIFMRGEWQIFHVAALKTYYNLLFNLRFEELPVSTDPTMTVRSIIRENEPFVVELPADADRTLVHRKLIEHTGVEEIYMRNMEKSVRGVDEQQKANTRYLVSTRGTLESMYKLRQLVAVKVPIKTYVTGQEISTQMARLCYEKIVKGHIS
>BP:CBP00076
MSKHNAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFDDPAVQSDMKHWPFKVISAEGAKPKVQVEYKGETKIFTPEEISSMVLLKMKETAEAFLGSTVKDAVITVPAYFNDSQRQATKDAGAISGLNVLRIINEPTAAAIAYGLDKKGAGERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFVAEFKRKHKKDLASNPRALRRLRTACERAKRTLSSSSQASIEIDSLFEGIDFYTNITRARFEELCADLFRSTMDPVEKSLRDAKMDKSQVHDIVLVGGSTRIPKVQKLLSDLFSGKELNKSINPDEAVAYGAAVQAAILSGDKSEAVQDLLLLDVAPLSLGIETAGGVMTALIKRNTTIPTKTAQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELSGIPPAPRGVPQIEVTFDIDANGILNVSATDKSTGKQNKITITNDKGRLSKDDIERMVNEAEKYKADDEAQKERIGAKNGLESYAFNLKQTIEDEKLKDKISPEDKKKVEDKCDEILKWLDSNQTAEKEEFEHQQKDLEQLANPIISKLYQSAGGAPPGAAPGAAGGAGGPTIEEVD
>BP:CBP00078
MLRAVVRLSKTGAKAQRRFLNLQEFQSKEILEKHGCSVQKFVVAANRKEAEEKWMSFGNHEYVVKAQILAGGRGKGKFIDGTKGIGGVYITKEKKEALDAIDEMIGKRLVTKQTTEDGVRVDKVMIAEGVDIKRETYLAVLMDRESNGPVVVASPDGGMDIEAVAEKTPDRIFKTPIDIQMGMTEAQSLKIAKELQFEGKLLGAAATEIKRLYDLFIAVDATQVEINPLVETADGRVFCVDAKMNFDDSASYRQKDIFAYETFEEHDPREVDAHQFNLNYIGMDGNIACLVNGAGLAMATMDLIKLHGGEPANFLDVGGAVTEDAVFNAVRIITSDPRVKCVLINIFGGIVNCATIANGVVNAVNKIGLKVPMVVRLEGTNVDAAKQIMKKSGLKILTANNLDEAAAKAVESLPK
>BP:CBP00081
MLTDGVVDYTKEGSILTAEQRQFYEKNGYLLIRNCVPQYELNRFRQRFQDICEKKVKAPDNMTVMKDISIAKSEFKDGEKAITKIQDFADDPVLFEYCKYPGVVDVVKDLIGNPKSTVMAMHTMLINKPPDNGKLTSRHPMHQDLQYFPFRPADFICCAWTAMEKINRANGCLVVVPGTHKGVLLPHEYPKWEGGVNKAYHGIQDYDPSNPRIHVEMEAGDTVFFHPILIHGSGANRTEGFRKAISCHYANDDICRYVNVEGTTQENLAEEIIEIAKKRLTKYGLDPNTVTLDFADIWRVRAREVNGTRSNL
>BP:CBP00086
MTATMDVDNLMSRLLNVGMSGGRLTTSVNEQELMTCCDITKSVFASQASLLEVEPPIIVCGDIHGQYSDLLRIFDKNGFPPDVNFLFLGDYVDRGRQNIETICLMFSFKIKYPENFFMLRGNHEPAINRVYGFYEECNRRYKSTRLWSTFQDTFNWMPLCGLIGSRILCMHGGLSPHLQSLDQLRQLPRPQDPPNPSIGIDLLWADPDQWVKGWQANTRGVSYVFGQDVVNDLCAKLELDLVARAHQVVQDGYEFFASKRMVTIFSAPHYCGQFDNSAATMKVDENMVCTFVMYKPTPKALRRG
>BP:CBP00091
MDASTEAGVYKKELYSRLMASINATMCHEQPDGILYCPNHTGGPVWVRNVYPPIQELQPKVLIVVVVFVLCFIVGVCGNSSIITIIRGVVEDRRKRMKRHGDNAILYIGALCVCDFVMSLSLPPAILDSVIGFWIFGTTMCKVHHVFGSVGRIASTFLITAMSFDRYVAVCYPHQHRLRSRTFVVSTIVCLSAIAFVLLLPMLTYASAKEMVLHELKAHESANITRVRVFKCSDMMPGPIFYWFTSTTFILGYVVPLILIVYFNLKLINKLYAHKRVLPRSAIPVRRVVVYTVLIAAVYFVCWTPYWFSVLYAIIMSLLGKPTTNSEWVLFAIYCVHLLPYFGSSSNWILYGLLNTQLQMKNDIGDDGQSIMTTNGVPDLPRRSTSRGICDGASTSRSLPAASNPQWQVDPMLTRGNSDTSMVFYQDTEQTHL
>BP:CBP00094
FRIGHLEYENSNETKILEICMKTAGTRKQHTLISLPSCHNFNGLENAANLNYQYAVDLLIGAACDEETQTVSRLALRWHKLYLSSAPLSTKEKEGTTIALKPHSLAGTAEVILAVCKSMKWKEIGLIYSDETKYTAHAIYDMLAEKEEEDIKINVFLQTDGTMNTYTILHSARVLISFLSTSDLSRFVKTLKDKAFRPLEFSIIHVDCYKSETTEFYTHLDQKASEETNPISAARLRKLHRHVALLRNSHDDKGNMEEFATKHGMIVIFFVFPFPTLCFQPSHTLYKALILCDGLQLLSDYKPLSDNLTIVQQQPTLWEHVTNTEIHGYSGPMFIGSDGVRLPYYEMFMWRDGKTQHVASVRPRESEFCEKEKMSNESKNCYEITRTIPFGQLLDDLPPYSSDCGYDNNLCSDFHVFMIAAIVFSILLIPMAIAFYLQRKEHLIQQMPWRVPLDTINFDDSRNGRLLSVSRRVSTVSTARASYSSIFSANVSEHAHVNKQKVSIKRYVQRRPITFTRQEMEMLNQLKYMSHTNINPFTGICFNQGSELIVMWQFTARYSLEDLIFGKEQKFGRNFQSTFIKHIMHGINFIHNSSIKVHGTLYLSNCVVDSYWVVKLTDFGIKNILKERMHHKELAPNSSFDIDAIHYKYLQLAPEHLSSLLEKHEEPMGTVEGDIYQLAMVIYQILFYMKPFAERQEDIKAVKKLFFLELATLLSNQSTAPLHPKVPEGNSFTMRLLSIIQQCWLYKPAARPTLIKITDAVNREFGQDVKGTLIDQMIEMIDEYSANLEHIVAERTRELEQDMATTENLLYQLLPKSIADSIRSGKSVVPEQHSSVSLLVVDVCQFTKFCEAFIPVHILETLQELYSSFDYIVQKNKAFKVENVGDAYLICSGIPEMTACRHLREVSKISLKLQEFMKTFTVRHRPSHILQIKMGITSGAVAAGILGSIAPRIITGICKNLAYKILNNIQPGTIQLSELTANTMMEKFPSFIIEERGMIDVKGKGTCLTFWLTGEKDQMRRQSSRSSCISHSQIKFEIEEANKTNNQFL
>BP:CBP00095
QLSVPQYKEFLEVQSNLTKNLFTDYDPTISPVYTWIDVDQPIGYDSQAPKRWNYTVFLYYLKLVEVQEPEEKVSVVMELMEYWYDARLSWNTSLYQNTTSFYARQDNVWSPTLTVFGVNDIMDFRDQDNRMVAIDNFGFLWDYISVRISANCQMDVSRFPFDTQTCQIRFCLPIFYRVQVEILNEIYEGIMDENIFKTMGNSEWKLINLTNRVEVLKYNDNMGNMDLAIFEITIRRNPLYYIYMIVFPSFVINFVSIVGVFLNGADKMSRLNVGLTNIMTMTFILGVMADKIPRTGNIPLLGIYIIINLVIITQLEIFLGPPLEYTSAIILELMTCANFLVMVGFWFDDGS
>BP:CBP00102
MTSFVDNQSLTNYLIIDYDTDNEEDDDDDYDVFPTANEFISNVPKKNRKRARKCVKKGFICCFKTIKYTFLCCRCVIVWRCLWLFVILLIGLFLFTCFYYDDARKIFQFVYIVIETSIHFLKPTKPCRSINRPSSVLHFLQNYSFHPQAFFIYKKGCVRSVKGVLYRLQMKLLLISTVVLIASVSAIGNLYSGGGKQCTECPPGYDYYSRQHDRGWCMKFFPGNVTFFEAEKVCRCQGGATLSGIENTKELKKLSRKINEYFDENGIKSGGIWVGAYRRKDCRVPKSEKKAECTKEFQYQWTDRSTFGRDMWISHWTEGAPHNNVVGNHSEFCVQLQVTDPTKTALNEHFDNRICVHRDGSSAFETEGFICGRPPKCKGGYNGGYSGGDGVIVIGAARPTQKP
>BP:CBP00103
MDLFSIVKSVSFWFVSTVDCLDSQWQYSEYISSTDMVQSFSERFLPGNWVYMLFAIPLWYGTWWAVLCYIYFYYTDITDAYMKETIEYHYGIPIKDSSYIIVYFQPTGADGKPHPDPKIFFAIGCMWYMIISSMFSVFYFGIRCYWQIRKTINQSAAVSATTKNLQTQLFHALVVQTFIPLVLMYIPIGILFFFPMVIWELPFTTEFVGYTIALYPAIDPLPNMIIIKCYRHAIQGFFMKIFGRGKRGETQHSLNTDAQSGS
>BP:CBP00104
LQHIYQSLCTMISLILNSVLIYLILYKSPKKLGDYKWLMIYTAVFEQIYTVVDLLTEPTAYSYGYSFVVFRRYNATWTDSNKSQVLIVTWCGLFGSSMAVFGVHFVYRFASVHPKNITKTLYNLNIEDISYISAVFYVDDPNNGSIHLSWGSWIALVQFSTMVGSSMFCVSFLGYLCYSELSSQLSMTSSQSQVANSLKKQLYFALVGQTVIPITFMYLPVCVFVFGPVFMVEIGVISTYLTHAVTLYPVLNPLPNMFIIKSYRNTI
>BP:CBP00116
MTSWADIQKLASDLQRVQLTQSSKKLSEVNCIEVLQKLIASQQIDVVYTRDGHTYVTKKHLETEIKNECVAAGGRAPLTDIAVALNIDFDHIERTARLIVSSDDEFTLSNAELFATEYVHSLRNELRSLLDEQGHQTTAALCKHNLSPELLQSLLIEKLSSTDFEGVVDGDTIYTSSFLDARQLVLRAVLVALTKVTPISTIQKRVGLTPKRFWIAFENLQALGEVPGTLIGSRTSPACSYRPKMYDYLVKTCVTNQYRQNEFLQMSTLKTLGLDSKTALEEVLGASEVKKLVNLNSIYMSKELMEQCVQTVQDDIQNSGIAEIRMSLQTLNLPLDTADEDLIGEKIASTEKDTNFSDGFVYNNSILTEALKSINTQIEAKAHQEVEKIDVEKKKQCGSKAPAKVQEDTDDWGDNKKGGKGGKKGGKGGKNGGGGGKGATSSVPTGSGTVQVNSEELEEWLRESQTVPEEILTVVVETLHQDATSALRKQVQEIQALQLVVNAANSKKSLSAIGDKCRQLYDSFNTFEAGTTSFADPLGTDLRQYLLKTVGVDLACAILSYAIGIDNVHQLKEKQRDETIESLPEMVREPIRALFASLKSTDEDAVEKFHDAVYDCSVPSATSLSLRKIDKKGRAEVGVKVSADLCDQLASQSDPATTLLLSVLYLFSQAGRPTTASGKFVAQLIAQMKDFCPTNTFELLQSCQKGVVTCIKNQDDDVAKEILSEDIEKLKSAVL
>BP:CBP00121
MDTAFSPNEVKIMEKAFDSYRRNTCIRFEKREGQTDYLNIVKGYGCYSQVGRTGGKQEISLGRGCFFHEIIVHELMHSVGFWHEHSRADRDDHIKILWDNILPGMKSQFDKISAVLQDLQGENYDYKSIMHYDSTAFSRNGRNTIETVEDGFTQVIGTNQDLSELDIINKLYSCKAKKKEKMRVTTEEPRRLIPQVGEKKPVDSGEKCVDHFADCPHFAQYCTRASFFFVMKSYCPFTCKHCPGDRKIKKSG
>BP:CBP00122
MESATNSSSEESIFHEQTRKLFRLCDAQNIGLIGKADLDVLVDLIPPDDLQKISRFIGEQKVNEPAFCRILKAIVSQALQQEMAKIEAQIPAFDKNQYLQESSLEDEMRAIEQNRSYLDDPLTKILKKELEEIQRYENSQIQNEHAINNTMIKKPLYRPIQPEPTIPKVSSLAEELNAIDKKVPQRKEEEELTQPDRIFKVVFVGDSAVGKTCFLHRFCHNRFKPLFNATIGVDFTVKTMKIAPNRAIAMQLWDTAGQERFRSITKQYFRKADGVVLMFDVTSEQSFLNVRNWIDSVRAGVDEATVMCLVGNKVDLFGSDIARSGVYRAAEKLALEFKIPFYETSAYTGYGIENCMRQMAESLQRREDNHLEEALKLDINSNYKKRSWCCI
>BP:CBP00124
MGITTLPPSQLRPELEWLFPKEVTTTSSAVLQRNSAAEIPLNFLAEHSLALIAALFLIVLTVALLAVLVQYHCQKGSSSGSAGAISPKSFSTSPSQWTTCSTVSSTYSTQSLLQLIGSGLRQSLQGLLLPSEAVVLETIVGKGYFGNVYRGRMRDPAGRLIPVAVKTLKGERARDIAHIEKFLREGVVMKHLDHPHVLSLLGISISPAGNPWVVLPFMEGGDLKTYIADPNRALCVLELLDFAHQVAQGMSYLAAQHFVHRDLAARNCMISAERIVKVADFGLAVDLLDKESYIDESETGPARLPLKWLAPESLRDRRVFSSATDVWSFGVLMWELLTRAASPYGEVSNAKVRHYLETGMRLPQPTHCPDIIYDLMQCCWRATPEDRPDFVFLSHRLRALLQENSPDPFTRRFRPNAEQFLLPVLPGRLFTNYFAAQMHA
>BP:CBP00131
RIPIGKLLSRRIHHQTNGLIIPSKNVLPRQQKRQILFKMGNETPARVVGYYVVFPVIPEETVENNCFMCNIAKSEDWPKLATAEPREMYEGTVRMLMDYGATVMEHMEHLATLPAEDRKFENVVDPLLTEEYDVNFAFQTLVLKMLTDWPDCNRKLFDADLHHIKIMCARDQMEKLTNKDFQDAIKQLYESKENGLSEWQSRLLEWYLLEIKASGLDKHDDKTRKVLGSWSKFIDEYRSKYITGVMSTNDQQTFVVNDKKIIKDAPPHILQKLAVDEQSWESGPWRGRMTPHTIYPFMQYCGDRQLRATAWEKWTSKAGFDHDFYNNSINIEELRHNNEGLAKTLGYASVAEHRLANKMAASPDTVRGFINALTRRIRPVVIDRMESWSAWASRCELITGELQAYDMPYVCRKEAEHHYDVNPLDLMNHFPFWPTFQNIVGVVGHIFNLEFKDITDKGYEKAHADARIYSVGDKFSGQHYGRLYIDPYDRQNKRGGWNVMLARPESKERGLDKIVYFIGSAVAPTANGPSLLHHQQLQQLLFHVRRGSRNPTVGDSKLNSNFSYFQFGRSVQLLLSQSPYRDIAIPWSPFYASDWDAADMFPTFLQMFVTKPNLLATISSPHIITNQPLTEEHANSVALTISRASLWETYRTLFWSDFDLSIYEMEDRKQKFWLDMYKQMYEEYFPFKRNKNDYQPCSFTPIFALQPHMSMYYRKLWAEMLALDIHETFDEEDNEVQTGERLKTTVLNRGSGDVAKELFKRFQGRNPSVGAICDHYAPPLTLQEGMK
>BP:CBP00137
MSETSGRSNSKLSDSSSVSEQQTADLSIFSGSFDGGVFSSNIPMFNFAGQGSQSALYSPHPFVKSNDPCRLTALTQSTPKEPMNLTPADFGLADFSVGSESFADFSANNSSFVGNFQSNVRSTRLLPAWAVDASGNIRDDLTLADVVLNGSLIDFAMDRTGVKFLERHFPAENDDEMHRILFDKLTEHSAVFTSLCRSAAGNFIIQKFVEHASLEEQYRLVETMSENGLIELCLDKFACRVVQLSIQKFDESNAMKLVEKISNLDFLPLCTDQCAIHVLQKVVKILPVSAWSFFVKFLCRDDNLMTVCQDKYGCRLVQQTIDKLSDNPKSPCFNTRLQLLHGLMTSVARNCFRLSSNEFANYVVQYVIKSSGVMEMYRDTIIEKCLLRNILSMSQDKYASHVIEGAFLFAPPHLLSEMMEEIFDGYVKDQETNRDALDILLFHQYGNYVIQQMISICISALLGKEERKMLPTEMRLYAKWFDRIKNRVNRHSSRLERFSSGKKIIESLQKLSVPMTMTNEPMPLWAVPTPLMDITAQFLNRQNFQKQHSVFDD
>BP:CBP00139
ICRMLIPQSSQSMLVASTIISTFAFLATITILPIFFMKVQRINSQMLTDLRNCHQDSSDIWKQLSHKSVREKRSYGGQNSIPSGKCCSCQQGKPGAMGPKGSDGAPGSPGIIGLNGRNGRNGKYVASEAHNEPACQKCPVAPPGPPGHPGRKGLRGQSGNAGTAGKNGIPGRMGPPGPPGVRGPPGELGMQGPQGDPGKVLNGAPQGQPGRPGKVGPRGKGGHTGRDGRPGLEGIAGARGVQGERGSRGARGPPGPPGPSGTDGRKGSCSHCQSDDKPHRGAPQEEPNPEGEYSEQQPVESIEPVPQRRPAPVPTTTTTEAAPVYTDPVTQEPVRHRAYPAAAPPSSYNTGNSEVVPKTINYPDTINQPNYKHDGDVSGAAGTSDDSEDVNVIPAGQYSSRQYASKTNKIGKAIHFGYSNDQLSAFKPMGGGADEEEEIEGYGQPRAFQTNKGYNVQIMGSSPTNNNPTYQAAPVGTAWKQPENHKNRHYTPQYLPPPAY
>BP:CBP00144
VICLLYFSLSAVAIAQQPQFTCPNNANPLVANSGTNLFCTSAGSNTDCPTGSICTTAANAAGILICCSQSTNVNPVCPNSAISQPSNIGYVECQFNNPTNCISGYQCVQSANLANTFICCSTSASVGSCPSDFTPAVGTNGGTISCNPSASTCPSGSSCMQSTLNTAFICCRSANSQRICANNQNALITNGALELCTTPGTQCSSTGYTCQLSVLLATYVCCGQGSTGSSIGCADGRPVYQQRVGETYTCDITSSLNSCPSGYDCALSDDSFVNVCCLTGSTPIPENLSCPTGWNPFRNEVDNAVRTCTAVLDTSCPIGFSCAPSNQVSQFLCCRLASSLVCINGKTLLVNGAPKLCTPTTYSQCPYNYSCQQSVNPTVTVCCSNT
>BP:CBP00162
MASYILNALTLRHDHDAAERTLHHFWDTVCFNISLRMLDDWIIDTDNKDLLDTGLFEEHITSQPLLAASLFSLIACSIGLIVFAIIFLICRFRGQCGSQKYQEYPSNATNYAIYLMLFFISWLIVTSASAYFVLAGIGFWSEKLDARKPFTNASLRLSRSTIGDLYASYDYHGDFENVSEAPRKSLKRIHIHRKPLLHTFRKRIEIPIRPLAEVTFTGTSDKFITKNRPILDLNSNQNDGSEEDKIDEFESFKRLQNLPEPSLPTEEEIKNQVQEHSGIPGIAEIFGNSEDPEDVADNSEEAETSENQSLVVTGGTMTIEEEDSEDVESEESTTTTTTITMTTTTTVPITTVPTTTASTTKSTTTVAPTMETTKTTTTTTKTTTTASPSTISAIFPEVTWTQIEETNSDDVLDQLLTHAETHPDVPADNSLSYNPNLTYFSLHSRFLVFVCRLTFCFVALALLFVILPTFFLVVAGTGCYIYSDHPMNRSSVSNKIGQVVSINASILLFMSPCMLIFSSFTLFYTHCHELLCATIQLQNQQARGIIDTNHQSLIENYSINTNQCARSLAPVQSLLLSSLLLCISLLPCVFAMFKLVKYYFRMSSEFYWNAADNFAGRQFSKQQDFPRYQSTVIYPDDDMTAGYAVYGQI
>BP:CBP00169
LKFENAPFPSITICNLNPYKKSAIQSNPNTKAMMEAYSRRIGSGDKSEGIAAALSASGALHAKVRRAKRKAKGKPRLRDRRYHQAFAQCLCDIEPLTGDRKGSCFAAFKGKIEIDTNSTAGFMNLHTSRCLCQLDTISKTLWPCFPYSSWKEKLCSECVDNTGHCPMRFYKGNELYENIKEQVDLCLCHKEYNHCVSTRDDGVIIEIDPNDELGNLDIGKKVASQLSLREEKLAETTTTEAPAVTQALGFEELTDDIAITSQAQENLMFAVGEMPQSAKEGMSYELDELILKCSFNQKDCQMERDFILHYDNTFGNCYTFNHNRTAEVASHRAGANYGLRVLLYANVSEYLPTTDAVGFRITVHDKHIVPFPDAFGYSAPTGFMSSFGVRMKQFIRLEPPYGHCRHGGEDSPTYAYDGFHYSVEACHRSCAQKVIVDTCGCADPMYPIAEMFGNDTKPCQAVNMEQRECLRNTTLYLGELYSKGKESVIPDCYCHQPCQETNYEVTYSSARWPSGSAKVMECLPGDFMCLEKYRKNAAMVQIFYEELNYETMKETPAYTLTSVLADLGGLTGLWIGASVVSMLEIVSLICMAANGYYKDKTEERKSSLSAQSHHSIPVQRASRGSLNTLHKSSTTQSVKLSVIDIRSLHSNHSSKSKQSIFIEDLPPAIQEQSDDEETSESSRTNGSCRYLAPGEDLPCLCKYHSDGTIKVMKALCPVHGYMVRRNYDYSVSNSEEEDVEDEVHLEPEPFYTAPYEHRKK
>BP:CBP00170
MDTEHRVILNVGGIRHETYSHVLKKIPATRLSRLTPNTANYDPVLNEYFFDRHPGVFSMIMNYYRTGKLHYPTNVCGPLFEEELEFWGLDANQVEPCCWMTYTQHRDTQETLAVIESLDLDGDPPSQEEIAKKFGWEDDFHSGSLSQWQRLKPRVWSLFDEPYSSKYARAISCISVAFILVSTCSFILKTDPSFQIPDIDVFYSLRVVDENGFKNYHKTIGTDKPVTSPHPNFFYVDLICNIWFTFELFIRSIFCPSFHKFVRSPLTIIDVVSTGAFFFESLLHAILIQTGSLVTLDFLSMICVLRLFKLTQHFSGLKILIQTFKASAQELSLLVFFVVLAIVIFAALVYYAERSQLNKDNQFTSIPLGLWWSLVTISTVGFGDMVPKTYLGMLVGSLCALMGVLTIALPVPVIVSNFSNLYSHSQARGKLPKKRRRVLVSLVNIIFVIISIVCFCLKTHPNYRIPDIDISTHMGNLSIGNGPSKIQLNTIYVGKMATRAHPAFFYVELFCNIWFSAEFLVRMVFCPNLGRFLKTPVNIIDFIATVSFYIDWALDRALSGSNRDSVEFFSIIRILRLFKLTQHSTGLKILIQTFKASAQELFLLVFFVLLGIVIFAALVYYAERVERNENNQFSSIPVPQTSLGRVVGSVCALMGVLTIALPVPVIVSNFAMFYSHAQARSKLPKKRRRVLQANEAKVGRGTAAVMINAFTPRGPVGGGGSNPSDGNPLSAFSKTPLLVCTPDGTDKPRRLSQNKNGGNVPPVTQNNNCKANKLI
>BP:CBP00175
MSLRFLFAFYVFYDVRASVDEYRLLQYLKENYDSFERPVENSSAPLDVQVRFLLNQILDIDEKNQVMSILAYMDYHWNDYKLKWDPKMFGGIRDVRFSGDDDASFKLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFICQIDVTYYPFDRQTCFLKLGSWTYNGQYINLDFLLREIIGLHGKPIIVEPERSSTNSASYFVNESIDLQVYLQNGEWDLEGTPGKRVVQKFGTDEYHELYFYIHIRRRTLAYGINLIIPSLVISMMTILGFTLPPDACEKITLETTVLLSVIFFLQMVSNTSPPQSQSVPILAAFFSCCLMLVACSCVFTVLTLSLHHRKPETHEMSPTMRKIFIDWLPYILCMCKPDHPKTPKPKVLGKSIAPIHRLSTIPMLNLPRVSQTQFPDRSVFVYHEVPAIIKNTSRICSELLIIEKDIEKMVNKIEEDSKEEMLRSEWRFAAMAVDRLCLYVFSAFITVITCGLIVPHIIANL
>BP:CBP00176
MSNWDYIDEVDIIPKLPPNFDELRESKKWQERKEALEALLKVLTDSERLSTKVSYAELIGNVQTVLAKDANINCQALAAKCIAKFATGLRTKFSAFATPLLPVIFDKMKEKKPTLREPLVECAMEVGRTMPSLEAGQEDILAALAKPNPQIKQQTALFVAKQLDLVVPAKQPKGFIKAAVPVFGKLTGDADQDVREASLQALGAVQRIIGDKNVKSLLGDLSSDEGKMKKIGEYADKSAASYAEEQAKNAPPPSSSASAPSAAAASGSSGNVTSAAVTTAEPAAEADPWDFLDAFDVLSKMPEGFDTNIESKKWQERKEALEGLQQLLTANPKLDPKANYGALVERLQKVLEKDANINVAALAANCITGIANGLRTKFQAFAISVAPIVFEKFKEKKPTLRDPLVACIDAVVATSNLEALGEIVLTALGKPNPSIKTQTDLFLQRTFMKLNSQTMPKKTLKTLVPLLIKHSGDSDAEVRDASYAAMGAMMRAIGEKPSLQLLADIVTDNLKMGKIKEYHQKALAEAGPAEIAAMVQSMHKADAPPAAAAPPKKAAPPPKRQESEEEQVEEEEEPLKLPAEEKKKAAPTKENAENEPPVAPKTELLLNDNGEKAQRIKEEKQLKLVKWNFQTPTDEHIAQLQTLLGNQAKVSLMSQLFHKDFKQHLAALDTLIRLADTAPRSLLANSDLLLKWCTLRFFETNPAALIKVLELCRVLVELTRDTETPMSQEELTAFVPYLLLKTGEAKENMRTAVRDIINVLSDIVGPLKMTPMLLDALKSKNARQRSECLLVIESYISSSGISPLKSLTVEKIVAPFVGDKDVNVRNAAINVLVACFKFEGDQMWKAAGRMADKDKSLVEERIKRSGVKAGSGVATSPPNGGPKIVVPQQQQSVVRRPASRSRTREPEPEDDYQDQRAIANSTFTKGNSSSRYALRDDVFATAINRLADSTYVVTPPQPPSAWANNTFQMKRTNSSSSISSIDTSDQIQRSINNISSSLADVAQDAMYQVTYVLNQPEQRHLVDRKADMVFRASAAQLDMIIDEFKAGKDVTGTMDACSQMLFILMGGVEAEHGLEPLNASPETVKAIISSVLRCITQIGSTDAGYTMARSLNRLAMRLVYRVELSNLLCGLILAMIESIQLNSGITDLVSKLSSKWCDELEKRRAQLRASDIVDVFNQFYICTLTEQKMDITHIHIQVVDNYLERVILQQGDVVLDAARRLSSPHIHLTRMINKILQMMKEQNIDPIMPGTLDARAPDEEEAVVVRTGVQVCVNNILRDLKNVSTYNEQLNKLVQSSDKCRNEYSELVKNHALGEAVEELVSEQTIHGAPNFNKPDVVNAMTMTWKALDLLGPTRAETPTTPPQNLSRMDTTIVGTPLSRAEGAGTITRARGNIMRPKQRPTMSREQHEELRNRLQQAK
>BP:CBP00179
KSKKLEQKPDWDTLDGIGFEFEENKPIVMDPRFYDMLKLPQCDLTKDKVPSKINIKEAMNQFQQCVRPIVERWRGDIKSMNTKFSETRLCEAAFKDMDVIPMTNLHETKWAILPHCVRENPVEQTCIFTFIERGEYHDWGIGLHCDMLVFAGTLGYSSSYKHHQVKLRTKICTNAPEHKFFGADPIIEPNRQLYTAFGKYFPFAIGKKPGFTKFRVLPNQNQKTRKYEFQDVTTIPFTYFLWDILGLKQIDIAWIDIEGGEFEFLDQFYRGGPMDEKGIVICQFNLEVHSKFNPPGAQVFHDFVFRILDDKRYIFTKVLNTDVGIHRMFFVNVEDEKCVRKFLQ
>BP:CBP00188
MSFAQSFYADQKKVEQQPRQQENASPLTTAAIPAHTPIAEDPLTPAQIREAIRIYRSVLSTNSAPASPVRAPAAPPIAERPEVHSNYYGGGPTDIPQSYLLNYATSSPQQPASAPATQAPEPLFTEQQLIAQLQALQVQQQQVAEPVCEVPVVQQQQQPKAAPNKAPVLQKMYDDEESGYCFNRKGRDEDGPEEIPEAHVATPTSAPAANYSIPAPQQQVNYSPAPVANNYSKVVCGPSEYIGMANDNKFIYDAQKALPVSYAQNNSYTLVNPTAQAPIAQPRFEETDDQGVTTTEDVTQVPASPAVTSRFRGMIRNAQTPVQAPPAPIVVERVAEPVNTTPSHNYNNYGAFMPVNQMSMESEYQLPVLNDLASCIEHY
>BP:CBP00192
SKFWKIKQLFIFILVALAANFNYGFSTTYINTSVDQFKNFLNTSLSHRHVVMTETKYDIIWNLFLNCWFVGYFVGVWFSPIFIGFLIGNSTAFLASILQCLAILWYCPELLIVSRFITSICMAVTYQSCILFLQLVTRTSGKHKPTFFECSPTHLRGSFSFLSEVSYSSMTMVGSFLGQDYILGSHLFWLCFFVVPFCLFFTLALFLLPETPKFLLISKDSEEQATESVKYYHGVDSDAKQVLEEIRKEAECENDPLEDSTTFRKMKELFTEPHLRMALILSVSALTNTVGLWALLLSSTFFLENANVESEVAEWSTTAMSLAYVSGTVTGGIIIEKVGRRTLLLLFTFLNNLALLAFVFFAKIRILIDPMKYGCLGALIIYGYTYGTGVGPISWFISSELVPQKHRSIAQSVAYAINTLMVVISTFTVLPLYSVIGSYAFVILYSIPSFISMLILFRYLPETKRREIHDIVNELKNK
>BP:CBP00210
MANIPSFIDRLLSVNDTANPSLTHCIKEAEIDDVIQMCTQIILEQATMVEVQAPIAVCGDIHGQYVDLLRIFNRCNFPPDQNYLFLGDYVDRGRQQLEVICLLMAYKIRYRNTFFILRGNHECASINRTYGFYDECKRRYSLSLYNAFQDLFNGLPLCAMISGRIFCMHGGLSPQLESWKQLAAIKRPFDPPNKSIAMDLLWADPENNMNGWAKNSRGVSYIFGADVVKDFTDKMNIDLIARGHQVVQDGYEFFAGKRLVTIFSAPKYCGEFDNNAGVMIVDERLIISFDILKPAIREVTIRARGTSKNASTRSMLVSSRGPKSKMG
>BP:CBP00211
LEHPVFLKDILHTITYFAIPIHIFGTYCILFKTPKTMGSVKWIMLNFHVWCMCLDYGLTVLTVPIVIFPALGGYPFGILTEWGVSAEFQTYLIVTLIPVVSAAVITIFENRYFLVFGHNSKWRRFRVLLSIFNYLYAATWCLPSFMIIPEQNMARKVALEMLGPNVSDYIRHFPIFMMSLEITYLTLPCLLIVLTFATEVILFVAIIKKGMTELAKTARFSKNTLKMQKNFLKAVYIQVSMYMTSIQLPLAYFFVSIFFKIYNQSANNFCFVVFSLNGLSSTILMLWVHTPYRDFCYKLLRIEKWRKKIGQANSQDNVVSVAPTA
>BP:CBP00214
SKEKVPEEDLNLPYFHGALMNQDADQLLVNDGDFMVTMKLQIDINKLVVYLAVRLKKGIRRYEIKRLPGSAKLGSRSKETIDKLINSLKTDVLEIKGEKIVLKRAIAKGKFQLMHKDVIFKKKIGAGAYGTVYRGRLVKTNEVIAVKKLDPESADEDGLAEMMKEARVMQLYDHPNIVKFHGFILDDLPYLLVLEFCNGGSVEDRLRDKGSRLTVPTRVHYTYMAACGMDYLHKKGCIHRDIASRNCLIHRGIVKMADFGMCRATTVYKMDMSKPCNVRWLAPEVWDNGETRFNTDVYAFGIMMWEFFEIPYATPYAEMKAGQVKRKTRTGYRLPPPAAMPKEVGDIMKECCQPAADKRPNAEKLKEMLEEVYKKQNPTETTHNSS
>BP:CBP00223
SRAAEMAGGNSEEGKGMLLRNGDDKVRHPSPQRGTPDSSSTQGHQFIDQIVTINVSGMRFQTFESTLARYPHSLLGDPTKRQHYFVPDTNEYFFDRHRTTFESILYIYQSGGRVKRPEIVPIDIFLREMRFYEMGDELLEEFWIAEGYEKPKEVMMPTNKTQRKIWELMEYPDSSLSARIIAFISIFVIALSIISFCWETVPSDNDDKVINMTTGELIDELDEKHYSPFFWIELMCILWFTIELILRFISCPCKVTFVTSILNIIDFVAIAPFFVNFFLADTNKSNSSMSFAVLRVLRLVRVFRVFKLSRHSVGLQILGKTFRSSVQEFCLLIFFMAIALVLFASGMYFAEQGEPNSKFTSIPASFWFVLVTMTTVGYGDLVPLSPFGKVVGSMCALIGVLTLALPVPIIVANFKHFYRQENRLASMKSTTKGDHEDDDVA
>BP:CBP00226
MHPRGKFLAGHLSAFYIAPATTAALISRNHNDWAHLQLLRRTPSSDAGTMNQVHFGRTSARRRNAMILENNSGDGDDEDRPKEEIFRKIESYQFSRFQTSVINSAKLWASRNRSLKLINNFLPGFLANLRLALFHLVLIFATVAYIIAGAYLFTKIEHQAELDRYQSYHSIYKNFVQNLIYDSSGNRSVSEVENMIDAFTSINFRAFKDGLKPTDFLVPQETSRWSMISAIFFTTTVLTSIGYGNLIPISTGGKIFCVGYAIIPLTLVTIADLAKFVADMLIMDPTEDPKTGRQLLVLVFLLGYMTISACVYTILEPMWSFLDSFYFCLVSLLTVGFGDLYPSGTVEYMLCSIVFIFIGLILTTLAVDVSGSVGIAKMHSIGRGFDAMKMLNVLR
>BP:CBP00231
NAMLIYLILKRTPLLMKSYSVYLMNFAFFDFATCIISFFSCQKVIFSGWSLIYIFHGPCKHVSSWFCYFCHCFECHTLAHSQWILLGSFMYRYDVLKGSTPTVQKMWRNSGAFYSMSLCFLVVYLFDISDSEELLRIMTDLHPEYHYDDGTGNISMFAPITFISIMYMTTPCVPIYCAILYFRHHTLKILNNPSINLSPAAKISHQKLVRALTVQAGIPIFWLVASGIYSLAQFGFISGPIPENITFRLMDCIPMVSPIVTIAFIQPYRDGLLHLFHKGSSIFIPNTIGSSVVDVS
>BP:CBP00234
MGMSTNKCGARWTSWLTKNMLLLMTMAGIVMGVIIGGVLRNLEPSQEIVKYVGFPGELFMNMLKAMVLPLIAASIVSGLSQLDGKTSGRLGSRAVMYYVITTTHAVILGIIVVSIIHPGDPTIKQKMGIEEGATANESAAQKFLDLFRNAFPENIMRATFSQYQTHYVNVTNSNGIQKTELKTGYVDGMNVLGIIVFCIVMGLVISKIGEEAKPLANLFHALDVVITRMVMIIMWLGPIGIPSLIAQKMLEVSDLWQTARVLGLFVFTVILGLGIQAFITLPLIYVIGTRHNPYKFLSGLGQAIMTALGTSSSAASLPVTFRCLNKLGIDPRVTKFVLPVGAMVNMDGTALYEATASIFIAQMNGLDLSAGQIITVSITATLASIGAASIPSAGLVTMLIVLTALGLPANDISLILAVDWVLDRLRTSVNVIGDALGCGFVHHICADHLNADVAEAEKAHAFVEAHGVNFDELEKEIEQENNNHKTIQHV
>BP:CBP00238
MLKPLFGKADKTPADVVKNLRDALLVIDRQSATQNERKVEKAIEETAKMLALAKTFIYGSDANEPNNEQVTQLAQEVYNANILPMLIKHLHKFEFECKKDVASVFNNLLRRQIGTRSPTVEYLAARPEILITLLLGYEQPDIALTCGSMLREAVRHEHLARIVLYSEYFQRFFVFVQSDVFDIATDAFSTFKDLMTKHKNMCAEYLDNNYDRFFTAYAALTNSENYVTRRQSLKLLGELLLDRHNFSTMNKYITSPENLKTVMELLRDKRRNIQYEAFHVFKIFVANPNKPRPITDILNRNRDKLVEFLTAFHNDRTNDEQFNDEKAYLIKQIQELRV
>BP:CBP00251
MTSEYGCNVCNEEYSVQDPLKCPRVLTGCGHTICHSCAMIIAGRNISIFCPFDRTSTNLPGGDLNNLKKNFALLELLEKIADTGGISEIGEGVQKHDRYAKDRLLNVKCDEDSEHVAVFYCTVCDSNLCDRCSEFTHSTNVLSKHRRVPLTEKPVPKVCCRLHSSYVVEFVCKEVSCDNESPLMCLMCRDYGRHKGHCHVLIEKEVDDLREKLREHLGELTRQSEIVERSLNSINSTIHELTPETDDGSLEETKQEASIRNHFYRLHSTLDQDEIHALETLDRYARNRLESLQAQKDRLEAVSTKIGSTCITLQKALVLEKDNILDRKDDLLALAESTNAEPTEVPDRSQLRTRIAFSFSNDRKLHIGDFIEARVVLLGLDGSGKTSIVRRLKKVRIDAVMAPHPTSGFNIETIHYKNYRLNVWDVGGLPKLRNLWKHYYSNAQAIFYVIDGHAVERFNEAIKELNKVMSDPLLISCPVIVAINRKGGASSLNGHMDVLMSQLEALPFQHELHFCDAAQGSGIDQILDQITVCLSRLNGTCPV
>BP:CBP00252
MTSFLKLVVVGMILVGVAHGASVATADAKGTNCTLTDGFQALSCIMRLSDFAEKIDELDMDDKNEVKEFKKSCDSLEKCFSMLTCGKQQDAETKQAVSSIRNYCDAVVYMAADFGECSEKLEKNKSECFENWDPFPDAIDEEKDEKKKEELKKNACKNYFGKDQCLKKLITETCSEKEWQGFRDHFISISSVLLTCDFKDV
>BP:CBP00254
SILNWTIFYAINKLQSFNLAFGYLSANQALADALHSTTFLLYFCPMVLLDQPLMKEFSHYCGFILLFCYELSVKIHLAISINRFCAVWAPYKYKHIFSDRNTKIYIFGIWVFTGSVAVLFYEKFCHFFYDDQIHFLTFTNNSFCGYIGWYGDFLKNAAIVAAVVSIDIFTILKVRQMSKKVVSNISNQSQNNLSHREVRFLKQTVTQGAVFMLELLTYFFVPLYFENKWIVFFGTSFAWVAVHAVDGMVVVLLNSEVRSFLIGQRSKSHGPSTNRATA
>BP:CBP00262
CVASSQYLGDPEVYKLVFHILTCIEIPIHIYGAWCIIFKTSALMRSVKYLLLWSHFLSAQLDLLFSFISIPYMLLLSFSGYALGIFDQPRWEVYICLIVTAFVVTSILGIYENRFFVLYGYRENPSWCRIRKPFIAFNYFLAVIFIAPMYFLDPDQEIGFQNLATVLPCSPESAIGDRRIYVAFTDSLLPYIGLSLEALLLACEIVVFLVITISKLKSRDGQNCSQLSVKTKKLQKNFIKALFAKSSIPITFLLTPVLYVLVTMQLTYRNQNLSNVCVMLASSHGLFSTIVMVLVHQPYREATWNNLYFCFRCKR
>BP:CBP00263
PDSESWLDSPETVLIFSHIMALLVTPLHLFGAYCILKKTPSTMHSVKLTLLNFHFWNVLVDLMLNVFAIPFPLFPSASGFLLGLFSYWGIRQTVQLWILITSLCFICVSTTMIFENRFRLLNHKNKHWKKFQPFWVVGNILFVFIFLIPTMLQVPDQDQARQMVFSKLPCTPEHSIDDRRIFVGAIDLNFTFFSLTIEAILLFIEIATFFFIVFFKLVHRNKRKMSLMSNRTHGLQTKFVIALCLQTISPCLLISIPVEYLALATYLNYYNTSLNRFSMILFGLHGVCSTLTMIFVHQPYREATVDNFYWLMMCRQNSKKISV
>BP:CBP00264
MATPSPSTSNDSSDFEKICTICGRPAFVRYYGAVACGPCKMFFRRMVIEKLTYKCKKIKICYITEPKPLKCKSCRFKRCVEVGMKLPPTNCTVLELKNREDDELVRLFGFLKIRDDQRMETYMNFYTTQNPSLEDILDGVKPVKMDVERSMITPVEWSFTAILSVINHFRSFDFEQLESRDKKLIFQFNTFKSNILCGAVRACKEHREKMVTPSGHDIFPDILVTKFNASAELLNRICCQVVARLMELKVTDEEFVLLNIIFFCNSADAHSDKAKSILAARQRFYVSALFKYCQLTYQNNAPSRLNELLSVYHIVQKNASEMQYIGIMIHGFIPNFPIRKLVSDTYML
>BP:CBP00268
RNYIFPLCIGSLVLGTYLYSFIFKEARYTVILDGKEVNFTGVEDFIQPYVNIVSDFFVASNYKMMSCGIRKSMSQLTVNTMCLLHDEERFLQENHSLNETWVTIRSCQNNQAFRKPSEDLLNNPETIRFAFIRDPIERFVSLYLDKCVKEQNCWACKNDMRCVVKEIYEALKNLQNHRDWKPIPTYMDWHAAPLSWNCNFDKDLSKWTLLMMGADAEERKSSILQLGNIMKRRGVSENVVQMVQEQSLAGETAHSTHKSTRRLEAERQVREDPVVRDYLHKIYFFDYLVFPFNRERLDAKYQTDFWKVPE
>BP:CBP00282
AAAETNQTGSVGWSVCGGAVPLAIERLRQFGFVENFDFEYIVEYTECDLGSVVRAGMKFIKEDKVDVIIGPPCAQALRTMSILASNSRKPVLGYGFVSDSDLSDVIRFPYLTTVLPNSQMLGFAVAKVLQQYHWSRVAMLYYQSDIQYCSSVMTDVESTLSDPEADFDVNIVIKAEIYLNDNQTTDIVLQSVKSRARIILWCSQTAFEKRDYLLKMSGHDMISDEYVHIMLSMRNIAFGVQSSLGKSVFSQSGLTPIWESFSEGTDGFESIAKQAAQRMLVLDVNSEVTDKAYLHYMQNNIIRAVREAPMNCSTMACMSANNTVMGAYARHLFDVVYLYGVALTHTNSTDPEVYSNVDVIVPQFITSFQGMTGEVKISTNLTRMSIFQLYGLNEHYDQVAYINFTFLNEKMNVSLFYKDEGPTVWHFYSNHRPLDIPICGFLGKSCPVSFFQQYQLLIIVALVVIILMLITLIIGCCFIMSSRRAEQLRINSEWQIPFLSLMEPENRKNAHHTSKRSLQSAQTGESKTTAVSDFCENYTIMIYEKDMVLTMKYQYMNLTKSDMEKFVKLRKLEHENLNKFIGLSIDGSQFISVTKLCSRGSLQDILSRGNFSMDYFFMFCIIKDVAEGLNYLHKSFLRLHGNLRSATCLVNDSWQVKLAEFGIENLVENEIPPKKRLLWVAPEVLRGSLTVSQMDPSADVYSFAIVASEILTKKEAWDFLDRKEDSEEIVYMVKKGGVFPIRPELITDIPDVNPDLTERLKAGQTVEPEGFDSVTVFFSDVVKFTQLSQKCSPFQVVNLLNDLYSNFDTIIEEHGVYKVESIGDGYLCSLQYSRQVAERLKAGQTVEPEGFDSVTVFFSDVVKFTQLSQKCSPFQVVNLLNDLYSNFDTIIEEHGVYKVESIGDGYLCVSGLPTRNGYAHIKQIVDMSLQFMEYCRKFKIPHLPREQVELRIGVNSG
>BP:CBP00283
MECNDTRLFDTSNNVTYFIIEQFYRFRYLYSNVHPYLSFVLCILGLAANLIHICVLTRPRMRHSSVHTVLVCIAFSDMGTMSSYLLYISRFEFLPEKEGYPYIWALFLKCHAMVSIALHAITLYLVVLMAFIRLSAMKLTTSRWLDHTRALTSAIFIALFVFIMCVPTLLAHQIDETTRGVTLTGMYYRYSVGFSTLMLQNGCFLMKGNLWLTGIFLKALPCLLLLTFTIALIHRLRENNEKRKILIKEERAKKRGDFTTYMLLLMVTVFLFTELPQGIMAIMNALFTTQFHQMVYLNLADVLDLLSLINCYVAFLVYSFTSSRYRQTLFSLLPLTRISYSGISTRQGTLRSHPNQPAAPKTLVQRANSVEVASVRSPLVDKSAATTRPNSAQPTEF
>BP:CBP00296
LHALETEKNVFSQFYAKKWPRQLRKPKNREISNFKHSEGAEFAAKSYFWDNNWDFDLPELPKPEQMIMPLPTSTPDVYDDFAFYRVLMEKEDKYILVACHANVHGFHRGDLRFLEINSRSRLNRLEGQSVIGSLFLGDIVAVTELARNSEAISPVRDVDVSLVTPDTSCYWIVSKMILYPRNVDKKSPVLFSIVNRMAAIKGENEPMNLNVDNWDMMHADSIYTGLTFRPETLEYHFSKDYQKKKINELVVSARTIRSYPGIYGTIFKFKEGDHREEFKKEMHLNTYTDESKELKRLAELEHEKNVFSQYYQKKSGNRRENHRGRKKPSSCKHHEAIEFAAKSNLWDNNWDKDLPMLPRSQEIIMPLPASAPAQTEVCGLYRVLMEKNDKYILIACHVNVHGYHRGDLRFLEVNSRSRLKGLSEQSVIGSLFLGDIVAVTELARNSNAQSSVRDVKVSSVTQETRCYWIVSNMILYPRILKPDVTFSFLKNRMAVVKGEDEPMRVNCDDWKTVAPDLIYTGMAFSPIKLDDNFSDDFQRKSKNLLISNVLKISSYPNAFGIIYSYEECSEQNEEFKIGTKAYSDTLEIHKYKRERIVETCSLMGFSAANTIFNGRFDCRAFHMYDVSKEGPTVRFRIENPRNRPTLGLWNNGNKILIGGPTGDTNGTIETVMCNSSHMGWLKIAARLTRECPKDFRFNGDLFVSQREPKDHYYLYDGYFQDMAPESNGRKIIETLYGGKPLELRTGDVGGEYFFPSTPEPIRLNVFQKEYVQMLLDGNPLVIGSSPFGCGKSMTIITAALEIYKRNAERNLVGKTHQLLITQSNFASVNLIEIARKTCNSGDEKLRNMKFMRFITDKNWNEQPDHGRTKFDMPFLMNKVFKQWAIGELDGNELMTHHTKSMIAHIIRNGTVTVDELCSAARRVFDKYGDCKIPFSGHLTEAFFILYEPDLIMTTADSSKSVCTLLDKKYETNKNECTTVQIDEASQLPEYTLLGLLKTYNKANFGLIGDIHQLPPFCMEELEGRLKEFGIGNTMERAIQNKLFPISNLRYVYRCHPQTTALLSELFYDGKLISGVTESQRNEFMIKRKDFWPNPSYPVMIINHMGTCQRMGTSAQNHSEKDLVSYMVQNLLDQRKYTLKPQDIGVISFYAAQTSLLTEQLRRSGVKCGTVDAFQGSEKEVIILCCTNEHATEFMQCKFRLNVALSRAKQATVIVGNLGYLRKAKYWNAIVKRVEAYGNL
>BP:CBP00300
MIFHGEKLEHHDTPVHDFLMDRFERHEKNDPNCLAFTTAENEQDSISYKNLKKKIIQISEWFLENGYKKGDVVLLAAHNNWRCFAFCMGAWRAGLVVSAASSQFTAYEMNYQIEDSHSQLILADAQTLPVVLEASKNLKFVKNVVSIAPNSPKPVIEFEVLTSRLIRNLKMPKIDPMNDLVLLPYSSGTTGKPKGVMITHLNVSMMMVSCIQFHDAIAKSYGLPPDFIFPHELHFLPLYHVMGLFRALLTSYRGSNQILFTKFDMELMLKSVEKYSIAILAAVPAIIVRMVNFPLLKNYDLSSLGTISVGSAPLPDGALQKLKKLIPDLRIVQGYGMTEFSFATHMQSPDCADGSVGRPVPGTSMKVKKEDGTLCGPHEVGELWIKGPQMMKGYWKKEAATQELKDEDGFMRTGDIVYFNENGDTFICDRIKELIKVNAKQVAPAELESVILEHDDVADVCVFGVDDKDSGERPVACVVSKQGKRDLETMKAIMRHINQKLARYKHIKEIEFVGEILRTGTGKILRRTMKKAFLDAKKSRL
>BP:CBP00304
TLYYVITHKFDLWPDAYECSGNYTVPTARWPKFGIYLWTSGSIFLTLYILCFIAICKIKSSAPVYQLMFFIAIFDIIAIIVGSLILGYLTFHGIFFCQCPLFFFIIGSLAMFTWLFNCVSCIILAIERCSEVNPKFFLSFLFGKKVFRVVKTLVFIYGINGLMFSKPVIFSPEYTSFIYDPMIGKDIILQGVVMCFFHSAAACIYEYMAYFTPTLYVIVAGEVVYQLACSCLSVVYLTLNRTIRNTVVKMVIPKSIRAKYGWHIGVEEHLAVEQAAESNGIALVNASGMPVKFDNFFVN
>BP:CBP00305
MTMNLIPRPIIGSYFMISGIALIIIYLPCFVVMIKSKCRAPSYQLMMLLAIFDLTSLMVNSVTTGILGIMGASFCHYPLFVFTAGSIGLGSWMGGCVVCILLAVDRCVEINSNFPLAIIFHKQVFRLVMLVICIYWVYASFFTNPLLFTAQYSSWFFDPFIGKEGDLYHNIPHTINNLLVSASSTPLYIYLCYHLIFKFGYSTSMWLYRSKQQIIIQAVILCFFHATAACIYVYMQFFPTPSWLIIIGQLAWQYSNGCVCLAYWTLNRTIRNAAIRMMLSKRIRKRFKLHMGIDEQIAAERDGEVASVSNVMNLMSGTAKVAPFLCE
>BP:CBP00306
ALQMSLYHVFTNSFTLWDEAYDCPQNLTNLKFERPVLGSFFLFFGVMFIVINSVCTGIFDILGISFCHSPLIIFCLGAIAGGSWMAGCLACVMLAIERCVEINPQFPLEFLFRKSVFPFVRILMGMYTLYAYLFVKGLTFSSQFSCWFFDPLIGKDPLLYHSYPHTINNFAVGIATTALYIYISYRLICKFGYTTSMWLYKTKRQILFQAITLCIFHTAAAFIYEYMQFIEVTPVIIIASQFIWQWSNGAVCLAYLIFNRTIRNLVVKIMVPKSVRKRFGWYIGADEHIALEEAGGPTLSAGLGTVNAIGGVIKFDNFM
>BP:CBP00307
MSDLQMSMAYMLTHSFTLYPEIYKCPGNTSAMRTKRPILGTYFLASGLIFILLYTPCFIVMVRSKCRVPAFQVMLILAVFDLLSLSVNSVITGLLDIMGFSFSHFPVFIFCAGAIGKGSWMGGCVACILLAVDRCVEVNAKFRLGFLFKKKVFRVVMGLMVLYWVYSCGFTKPLLFKAEYSSWFFDPKIGKEPYLYHSIDHTINNLVVSLATTSLYIYLCYHLIYKIGYSTSMWLYRSKQQIIIQAVILCSFHAIAAYIYVYMQFFYSPPWLIIIGQLAWQWSNGCFCVAYLTLNQAIRNAVVRMLVPKKLRERFDLHIGIDEHLTSVKQITQINTVSI
>BP:CBP00308
IDMSLFRLLSDFFDLPAEYQCPDCLQNDYFVRLRLGIYFLLSGILLILLYIPCFIVMLKSKSRNPSFRVMIILAVFDIINLAVNSVSTGIFSILGASFCQYPRLIFIVGAIGNGTWMAGCAMCILLAMDRCVEIHSKFFLAFLFHKKAFRVVLGVVGMYWMYSVWFTKPLLFSARYSSWFFDPKINRDPNIYRNVPHTINNLVVSASTTGLYIYMCIFLLYKKGKSTNSMWMSRNKNQVILQAIIICSFHALAAYIYVYMQLFYSPPLLIILGQLTWQWSNGCFCVVYLTINKSIRSSVKKMLL
>BP:CBP00309
FQMSTFYLFTNDFALWDEAYGCPKNLTTIRFERPVLGGFFAFSGVLFIILYILCLIAMLKRDLIRHPAYKIMVCLAMFDIPSLFIACIFTGYFGYFGIYFCDYPRLIFVLGSFAFGLWMGCTFSCSALALCRISGVNHNLEIGYIFKSHCIYYLIVIIFALPSYGIFFTEPLIFRTEYMSWFFDPGTGLFDSSNYHNISQVINNAAESVITTILYAYLVFYIIRNLTNVILSAHDVRVQRQVILQATIICFFHSLASSVYVYMQFFYSPAWLVIFAQISWHICTG
>BP:CBP00311
LSSPEFLKITFHVITIIAIPIHTFGFYCIIRKTPKHMDSVKMLLFNLHCWCVLLDIAITVFGIPYIFLPALAGYQLGFVDAPALVFYLVVTFLTGVSTSIFVIYENRYHILFGRNCSWRFFRKYCIVLSYCLVPLYFVAPIFSVPEQETARKIVWESLSCAPEIPEGHFDFFVISLNIRLMAITIAIAEGVPFFQILIFFSLNFYNLILARQPSGLSRKTTQMQNRLVLALFVQSSVTLVLFVVPVNSIILSVYTGYQNQILNNFIFLAFASHGIASTVIMVVVHNPYRRFLRSLSLQSSRKFTIMVINSEIRF
>BP:CBP00312
IKMIQCPTDDTYLASPEFLSFALHTLTCISLPLHVLGFYCILEKTPKTMGSVKLLLLNIHTCGFFLDILITILGVPYGIFPAMAGYGLGFVDLPGLCLYLIVMTINAISVGIFLIFENRFFILFAENSWWRHFRKPVFVASYAVSVIYFLPAQFLIPEQEGARKFVWEMLPELPQEIYDAPVFVLAIDFHYVVIPVFIMSNLLIAESGCFIILIYGNMNERTKKLSLSRHTIKMQRKFLRALNIQTAIPLLYLMLPMGYLVTSRIFNLYFQSANNLCFIIIGLHGLFSTIIMLYIHAPYREVCKKVFHCK
>BP:CBP00315
MDNLLRRDYLDGVDSLAEFLQYNFTVPCNGVKGKNQIDCSFSDLCSGQCNDNQVIPLFNLIYRNASSRLHPNFRLTYPTMHLYNDEYYVGEHFAGVKIDPKTNVISRVKVVVLYFRTDRQTPQISSVINEWERSLFDYVAHFNHPTLNMTLNSDAMIAREVRTNGLSCVPYFGASVIAVVLFIFATNQREHFVMSHNIVMAILGIAGPLMAVGTTFGFLFLFGFPFNSITLVMPFLIIGVGCDDVFIIIHAMRKTDKRESLENQIAETMEEAGPSITVTSATNILSFAIGIATPTPAISLFCLYTCIAVAVDFVYQLTFFVAVLVFEEKRLEAMRLSKKQEKVEEALGAPKQVLSIQNSIRSTAGAHPLPANPDGIVSRYCRFLKDWRTRVALLLILSGYWTASYYGCKTMEIKMDTTNLIMKDSPLNNIAWIYERFLWSEGQLVLVFVNNPPDLANEHNQHEVLELVRRFETLPYSMGRNSTSIWLRSFLYQSSLYHNTKGFNGLLQEWLDDSEGGGARWNDMLRLKKAENGTILGVDKFMFATACAMGDDANWATREKLQKQWRGVAHEYAHFNVTVFQSYSFYIDQLDSIGGTTMSTVIWAAITMDLACLLMIPGINSILTSTIAMMSINVGVFGLLSVWNVNLDPITMCTTLMSIGFSVDFTAHISYHYYRNPTSWTTDERLADALKSIGWPMIQAATSTVLCIVPLMFNSSYMVWVFVKTILLVTVLGILHGIIFLPALLLTSGDLSRLFGGSSDSKIQPEKKEKLGEISQASSFSSTNSETVLVKKDDSTELKTIPQERGS
>BP:CBP00316
MYINWVHHYVPKISFVLSLIANPLFIYLVITCKKTLFGSYRYLLSFFATFNLLASFSDLATPVCVFNYRYVFVTFVADGPFSWKSKYGEQLLYYRCGIVSGTYGILNVHFVFRYLTLKRNAFVNKHFMPYGLILAIMYVAAHIAIWAAVTGLCLHSAQEMRDYIREPFKALHNESFDDITFVAGLFSETTAEIAERSWTGIVLLTVIASYSIVLYIVLGYKIVTGINTKSSTMSKQTAQMQKQLFKALTIQTIIPICVSFMPCSLSFYGAALRIDFVNWVYWGAAVAVSFFPFLDPVAVTLFLPTLRKRL
>BP:CBP00325
MWRLAVFLSLAAFFVHDVLGKGDPELKMTTPQIIERWGYPAMIYSVTTDDGYILEMHRIPFGKTNVTWPNGKRPVIFLQHGLLCASSDWVLNLPDQSAGFIFADAGFDVWMGNMRGNTYSMKHKNLKPSHSAFWDWSWDEMATYDLNAMINHVLEVTGQESVYYMGHSQGTLTMFSHLSKDDGSFAKKIKKFFALAPIGSVKHIKGFLAFFANYFSLEFDGWFDIFGAGEFLPNNWAMKLAAKDICGGLQIESDLCDNVLFLIAGPESDQWNQTRVPVYATHDPAGTSTQNIVHWMQMVHHGGVPAYDWGTKENKKKYGQANPPEYDFTAIKGTQIYLYWSDADWLGDKVDITDYLLTHLDPAVIAQNNHLPDYNHLDFTWGLRAPQDIYHPAVELCTNDYLGK
>BP:CBP00327
MGALSQLRLLLWKNWLQQLRSPWFALFELVVPLILIGASFGLLIGFSDQFETTYDERRYAAWPVSGSAYDLIMPTNPNDSIKSAIVEPYFLFNSQLTCQFLNTYSTGANSYRMDIILAYAPMSAATTDKIMSIIQSRYSLTDLLSPVAPFIHNLYNITTIPTLNTNMSLKGFNTEGDMVSWMQGQFQSECDNPLLAGIVFDDSITKDLFNDNKRDFTYKIRLSNTHRRSRNAFGDDSYPWDTSVSFAIQYVSGPINPDDNDGGSPGYWQEGFMTVQRAVDVAITELITGSGPPISPLLDSYQVSRFPFPGYSTKIIEVGAYFMPVIVIFSFMTSVIYIVRAVVVEKEDRLKEYMRVMGLSQFINWIAHFLINYAKLTFAVIILTILLHFVALKSDMTLMFVFLMVYAFDVVYFAFLISSFMNSATSATLISVVFWMLLYFWYAFFSSIDQTNPYALGVRLINCLNPDIALNYGLQLLAAYETQAAGLKWNEMFNPPSPDNNLTFGHALAALVIDGIILVILTWYIEAVVPGGDGVPQKPWFFILPSYWFPYSGSKTVNSSDQYEHVEYASHVKLEQEPTDLTPTINVVNLTKTYGTSFFKKLFDCKFGKAGEKRAVSKLNLKMYPGQCTVLLGHNGAGKSTTFSMLTGVASPSSGSAYINNYDIRSSLPKIRRETGLCPQYNTLFGFMTVMEHLEFFAKLKERKWDPEEAREILARLRIDFKADFMAGALSGGQKRKLSLAIALIGGSEVVMLDEPTSGMDPGARHETWTLIQREKERRTILLTTHFMEEADLLGDRIAIMAHGQLECCGSPMYLKQQYGDGYHLTVVYSSTETPDVPKTTEIIREYILEANVFSYIGQEATYLLNAKHRPIFPKLFRELENHQRQCGITSFGVSITTMEEVFLKVGHLAEERYNYEHGIEDESSELIEKDDPMLQNLKAPVRLTGFALQMQHAKAMFFKRGIFFFRKWTQFLPQLAFPVAYLMLMVFTSQVIPSVKEQDPQTISLAPFSTKDKPGHVVSDSGNYVTMNGASTKLSNMVQNTVAALGVNQTVVDISSSVESFIMNQTNALGSRNFGLKYALGFVPSSIGIPGLPIPDLKTIRTYFNNFGLFTPALAITFTDSMLLSQAKNKQYTFTAINHPLPPSTQDTLKNTNRSDGAAFLIAYGLIVAFAVCVAGYSQFLITERKKKSKHMQLLSGIRPWMFWFTAFIWDAVWFVIRIICFDAIFYMFDITAYTHDFGIILILTLSFLLYGWTAIPFTYWFQFFFESAPKGFMMVTMYHILTGMIGSIAVPIIQQTSSMDAGYLWSIIFAWFFPTYNISQIATVTFQNENVRMACQKLDCNVPMFKSVVACCGTASQKLYVDNVLFVGNRKGILVYVIFLAVQGFIYWIMVFMRENDQFGKIFNLIKCWKKKDDHIWDITEGDKEEQRDVEDSDVIAEKSVVQRLANSNETALVSNNLVKWYGNFNAVKGVNFHVNSKDCFGLLGVNGAGKTSTFQMLTGENSISSGDAFVNGWSVKNNWREAGANVGYCPQYDAIIKEMSGEETLYMFARIRGIPEKEIPVKVQAVIHAIGIGMYAKRQIKTYSGGNKRRLSLGIAIVGLPDVLLLDEPTSGVDPKARRIIWNILNRLRDLGTALVLTSHSMDECEALCTELAIMVYGKFRCYGSCQHIKSRYGSGYTLLIRLKNRGDAEKTKSTIQQTFRGSKLKEEHILQHNYDIPREGDSWSRLFEKLETLSTSLNWDDYSLSQTTLEQVFIEFSRDAGQLDVDPYGDVPSLTGSGNKQNGYANRAMSVESITEMGTYF
>BP:CBP00329
IPGSIISRGEQPTPSPSDSSQSTLIPNFPWMENIPKIEFTTSKPKKPNAIREGLIEQVRSGKIPRELAPFVNLTKIDEMKKDHNETLDFIIRDEDVADVPDDDVEHRKVNTISHDGNKTIVTISDEARDDLYKHWMDQSLAGLMGAVVTNVINKRKMTKNEKKEHYVCIHESKNVTAHAKCVVTVLDQLKKRNEKLKMYSTLTTRLNSHRKNNRMDNEAFKTTLGHYEKYVKSGAEEFRVKRASGFSIFDELESKRQAAIRGNVQTRKSYTIRENKSLSPLALIARKLTELVRAGKNKKEQPKRWQQVIQDIKEESTRIKSKKRNKDRMKRKFSKFVSTMKEAGINPRKALNTMGMEDLFEDDPILSEKEMELKDRKEMMERMSPDDKILHEPIKLIREAIKIGMTMAGKNASEIGDKKIAFLSPQFMSILPDEVANDTVSLLSPSILALHGEGSTMDRQLSLTKALKLMEDTGQEEWMNFVLEASGVTETVDKMRELEKKEENDEMRKDFIDKDGKPIFFTKENATEIYGEYEAMKLDIIQGVYKNMSQEQMDAMNATGYSILDDRQMEMIYGAGSPYNDSEVLDKFRGIPKESMPSKIEENIRMIAKEELKFELSRK
>BP:CBP00332
SSSFTRIPKRDRTSPEKGEPSSKRSAPFTTPSSTTKIGRDSFAVMDTMEVQMNMFQLDITKMPPVIQRLHVDTLIITSKGKEINLNLGTVSTGGDVNSHNRRLAQHEIMRKFFEKKRSLFSSSSYHSLAYDTAACLYIPEGQYRGGEYEEVCLSQQDFAPEEWDIVSKISRRKDDSFIVRIKPAGAVYTQGDELFEPSNRYELTRIVEIVTSQKLNTTDFYQFGNATFPLRAHPNSEPDASSEIRSGFAKVARLTEGREGKHEMLMTVDTKLSPFYKPTSVIRCVLTKIQESRGGGGGGGGYGGRNDSRDSRGSFGGRSDSRDPRGYGGGYDRRSDSRDSRGGRDSYDSRRGGGDSEDFSSHEIDEIARACMESDKFLYSLESALKGLFAEAIHLKGSACTIRITGIKQCTANNTKFTKKDDKGEREISVSDYFYEEYNIKLKYPNLPLIVSKKMKYECFFPMEVLRIIPGQRIKVNKMSATVQSAMTGRNATMPRQHVDLVQRILQDSLKLERNKYMDAFGIELKSTRPVQLKAKILPPAEIRFKNLTYMPEIKRPGFKNPGKFVEPAHIYRVAVVSFDNAIDMRQAEDFCDRLFDYCRDQGIKCDRESKDWSIRELSSSDNVGIKEAMENWMKKKVDIFVGIARDKKPDVHDIMKYYEESVGMQTIQLCKQTVDKMMNPQGGRQTIDNVMRKFNLKCGGTNFYVDIPSNIRGRSICSNTETLHKKLLEKVQFIGFEISHGAARTLYDRSRNQMDGEPSIVGVSYSLKQSTQLGGFSYMQTQREYKIQKLDDAFPKCVKAYAEDAKTLPTRIVIYRVGAGEGDFKRIKEEIQEIRGTFEKIEKGYNPALVFIVAQKGSHTRIFPSRIDGNKAFEQNVPSGTCIDNVVTSFGYDEFILSSQTPLIGTVRPCKYTIIANDPAWSKNELIHLTYFRAFGHQVSYQPPSVPDVLYAAENLAKRGKNNYRVHQRYVSMQAIERRIISENADFVNENMQEQLASAIIDEMSDAMNGMTIPKRNFWA
>BP:CBP00334
MTDIEKQTEIREKKGRNVMRELKIQKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRTFGIRRNEKIAVHCTVRGPKAEEILEKGLKVKEYELYKENFSDTGNFGFGVQEHIDLGIKYDPGIGIYGMDFYVVLNRNGVRVSKRRRAPGRIGPSHRVDKEETIKWFQQKYDGIILPPKPKTKKNVYRRR
>BP:CBP00335
MFFVLIVFTFLTWLVVRQYQKVSRLPPGPVSLPLIGNLPQIVYYLYTTGGVVSTLDFFRKRYGNIFTLWVGPIPHVSIADYETSHEVFVKNANKYADKFHSPIFREMRKDIGILTANGDHWQEMRRFALFTFRNMGVGKDLMETRIMEELNASFSENMGLISANGESWAEMRRFALLAFRTMGVGRDLMEERILAELDARCAEIDAEAVNGKTIVHTSEFFDLTVGSVINSVLIGKRFDSHNKDEFLKLKGLLDSADELFTMFELTVPVWLLKKCFPERYARIVEVQEEIINFVSREANERYEKVKSGEYTINADDPQDFVEAYLAKIEEEKEKGTTNFYTMQCLKHVIG
>BP:CBP00336
MDGTFFQKDLAPFVKYSLNKKRRWETKGDLNSLKNLQSSYRDMNVVVSDRVWLDMDPYWCFISHINYYHNYFLQFPIRHTYQLDTDNNYRCLSSDSVYGQPLKSLLPENRSPKKSDTLQSATFDMPKVAYHILTPPENYEKLRNEDFCPGSSDRFLKHRSIKHWRRCKKMTEALLAIRYEDFDYLNDPIYFIDNEWDIDFGTPSKL
>BP:CBP00337
DSLLSSPEFVSRTFHFLTFITVPVNMLGAYCILFKTPKSMSSVKLVILNLHLCSMTLDIVFSVLIQPVVFFPAVAAYSNGVLKVFGKCAGIELYFAGTMFAGTVVTDHCTPSRKKPACTPEKPGLLFQKSITVVSMSIVSVMENRFYLLFVINTLWRKIRPFVLFFNYFVACTFLIPLLLQAPNQIIAFEIIQKKFPDIPFSSYSDSLFIFSVDSSYVFLSVFLTGALTVSQINLYCFLIILNMRKLSSNGKMSQRTYHLQRRFLIAIGIQIFTPLIVLFVPATYLDFCFIFEYYNQAVNNICMILISFHGWVSAIVMMFIHEPYRKFCL
>BP:CBP00341
MHRSLQILCILAVFTSLAYSQGSRDENQSAKRNDFSRDIMSFGKRSADAADMYDRRIMAFGKRQPNFDRDIMSFGKRSAPSDFYRDIMSFGKRSASMYDRDIMSFGKRSAAMEYDRPIMAFGKRAEDYERQIMSFGRRK
>BP:CBP00342
MDQFFTKLVALLLILLQIGAILATPIPEAAPEDVETRRELEKRGGARAFYGFYNAGNSKRDQVALPYYLYEKRGGGRAFNHNANLFRYEKRGGGRAFAGSWSPYLERLCDYERSGYPIYFSDNSYY
>BP:CBP00343
VSKPIADAVLRYGKDHPVFRNKLLIPIGRGLVRFTSRMRMKRLGLGEPITHAPVSEAAALEQASDFVQQLVLFSYSVGVFASYYFYTKLTTPESLKIEEYNDFKEQQERAIKELRLQIESLEQRLAAQQKRNFFSQLGFSKDEAPNGPSESSKEASGASESSKPSKPSESLKERFQRISSLPIDAAASLILDDEEYLIVRRDTSVGIELSVNFAARGERLRYRIPSSKLRESLAQLALKEAACHVIGS
>BP:CBP00344
MWELVSAELFSASNLFLLGFMISALAVSSVFTLSHITPWVRRTRDEYLTPEIVYRSSPEKEFSKLLESERDAPKRYTPSRCYLSVVIPAMNESERIEIMLEDCCDYLEKRSKKDLEFSYEIIVVDDGSTDDTADVVVGISQRRQNIRVLKLKANRGKGGAVKMGVLHSSGKLILFADADGATKFEDFEVLEKEMLRAAGGEPFDESFPAVVVGSRAHLEAASVAERSFFRTVLMHGFHALVWLFAVRTVRDTQCGFKLFSRSIAARIFPVLHVERWAFDAELIFLCEKWTVPVSEVSVRWKEIEGSKITPIWSWLQMGRDLVLIWFRYNIGIWTDSQP
>BP:CBP00345
TAISSSPEAPQTMSEVQKVVDDDEDDEWGDFGEAVVAAAPIQNTNPPPTVPPLQMASNDEDDDDWGAFDQARPSTDRSDGPSQLAHQQSLEDWGAFEETQKTSTTNDDNEDDEWQAEFSSASTASTVIPAENLKTLEEMLEDDAFWDDGYCEAMELEEISENDSSSSSPLDIPALFDTEELKELTNEFEDLEKAKYSKLWLSLRVIEEAISQEQKTSTSPAVDSPSVPAVDFDWDTSGLTNPMNRASKQLHEMSQKCRRFVCRATTDCINLLKCNLLLASFNPYNTKTMQIRSVVNALTHRFPNLWKPFSRNFGYKEAYQCSAIIDVDFLGSNGVATAYTSTLQQDLEQFGLTNGSTKSNSNGSSILENLMSRANDSSSTTGRYRTPEVLSLDARQLLERLPDLQYLQSEVLMFPVGTNLPH
>BP:CBP00346
YFLLFLAFFIFKINGGSNECYSCSGVCHNEPCNCQMGSCESGQCFIEKKPTEIPGSMKITKGCLRRTSRIHHGCEYDHFSDHILCVCQGHYCNDKVVMNTTRQKYTRTVTCRECSEKQPDCGSTCEGHWCHEDMSTGASGCGYGPPALPFYYRGPELFYYRSKVCITLSRGAGKPRRHCVCSTKMCNTVYNYQFNQYNIKDREKEGSTRARSLTLSATDYTLPLQTCYNCETNTQDATSMSHTTNCRSNRCLGHYCTYAAQRHTSKSSMGRSNMVHAVSELQGCMNVSDKSHIQLGCSRKWISDEYEEIHCACKGSLCNSDSLTATA
>BP:CBP00347
MDGVYRLFCGCCGLAGGDPEPPYSQLRHDSVTPIRDPPLQYLNQQQQHQQYPPYALQEQGFVNPVHEFSNFDPRPSFRTRDEADGPNYQHSDSGTPRSGLEDEVEDENREREQLDNIVESTQHSIIAVGQTDVDGVIMMDTQYREKAYKQKVQKMATASSTTQLYEPVHEFQFEPTQTPIQVPLRYDEMSATIDKSPIERMPFACPDFQQMRLARTMGVKNAQFLVEHPDPRHAGKSPAMSSSAKHKITAVLDQVHEGVVGIEVEPRDLIVSMDF
>BP:CBP00349
FTWFDGWEYPAYVSHSISLVLIPLNIFGGYCILFQIPKKMEASKWVMINVHFWSSFLDLLVSFLLTPYIFFPAMCGITNGLLSWLHVPIIVQVFLAQWKCILGVGVSLVIIFESRHNVDRFVITRKSSRILFYALNCVYGIFFMTPTYFSLPDQEKAKLELLKIVPCPTPVYFEPNVFVLMDHQGRWFIQLQCTTFFCVLIAQGAFSVSRTVYFLTAYNSKMSEMIQVAIPVFIVILPILYCGCAIEWYWYYQSFSNTAIICVSFHGMSSTIAIF
>BP:CBP00354
SSKLQSLQGLRGISILLVLIFHFFPKNFVNGFVGVDMFFVLSGYLMTRILSKEFTVLSVVDFYKKRFSRIVPLYYFTIFFTLLGVLSLVLKSERTEFILDVKWCLALISNYQPIFEHHSYWDQVSTIRFLTHLWSLATELQYYLIVPIVHLVASNLPFVNRITGYLIAIIILFFFQLLTPFELSYCFLAARVWQFLLGSVAFEMSQRNDLVLDFHTEKKNEKTDFNVFDGIPHIFLVVLLTVLMLPWIFQEHSARLVMSLSAAMLCYSCEKLEQSFLTLQPLVFIGDISYVTYLIHWPVINFVRYIQQKDNSSIDVYEALIAVTIIFVLSLLAHYKLERKLLELEFSVNFTITVFVIGICVALIPCLIRMECLAMKTLSKDLQEKAKFNLIEENVLKPVFELECDYNETTIDLPIDKFGIEYCAHVSNGTGKIMIVGNSLSIRAFPTIYKLVDGQYEEIRLFAKHGGAPLLDIFPYYNYVVMDMAQEMKPDLIWIIQGMNEILFGSDNNGNFSSPVMDRNVPRVLGEFEKLAKMVYLDLPYYITKDMPSKLIARSLIYRKSLERLSVSLEDAEKQVEEQTDRLMNVNCSNCYYNDVQKALINDQDKLYLYEKETYKALTYDGSHLALTGYKYIEPLYQRRINQFYEM
>BP:CBP00365
MCGIWAIIGEQVTPQQQDAFMKIVGRGPDLTVLDEVQPNVHLGFHRLAIVMPGDTPSAQPIVGGGLSVVCNGEIYNHQSLKIDCPYTLKNGGSDCAAIITSFIKHNEDLKETCASLDGVFAFIMADSKNVYIGRDPIGVRPLFYGYNLNGSLLIGSEVKCIEELCERVEYFPPGCCATISLAAPSRPIQPQQYYSVPSIADRFLSIECTQTLVRDILVKSVEKRLMGNRNFGFMLSGGLDSSLIASIATRFLKQKPVAFSVGFEDSPDLEAARKVADYLKIPHEVLVITPQQCVDIIPEVVFALETFDPLIIRCGIAHYLLCQHISKSSDVKVLLSGEGADELFGSYAYMQRAPNALHLHKEILRRMQHLHQYDVLRCDRSTSCHGLEIRVPFLDKRFIDLVSRLPPTYKLMPMKLEKHLLRSAFEGWLPDEVLWRSKEGFAEALGKTDLGDILASHCDKLISKELYEQRAERFPDRTPETTEEYWYRQIFEETFVYDKMGHLVHTKVYRTAAWHRPDEKENIINSPDSENILDVKSDDLLRLRRRSTGSLGVA
>BP:CBP00366
MVVLTKKSVKISYDDVAKSPDQLLRSMSSVHPISDGIPSQQRPLTYRWFPSWRFMTSIMLCFCFGCVHLMNSNMGMAIVCMVNSSVTYDNETYPENAAPLLDWSSDEQGYIFSAFNAGLLVMLFTGGMADKFNAKYMILVSVAIASLANLTLPFMAPISVYWAIFSRFLVGFADALLQPAMNSLITRWFPTSERSYALGLATGGRQIGTLIIIPAAGALCSQTEIFGGWPSIFYLSGFIGIIFIFSYIFLGADKPSKQTCITDNELKFITISNQSEDVGKKRTERKVPWKNILTSGAVWASVISLVCHEFPLMTLIMFLPSYLHDVHHYHSTENGILSALPTVSLWFAKIGSSYLNTWLQKNTSWKKDTICKVLNSIGSIGLGVFLLAATFLDKSHAWMAVLFLCLSMASAGLHTPGCQLALVSVAPAYSGAVTGFTFFFVAVSGIIHPIITKMIVKDRTAAEWNLVFYISTVIAIFPIVIFNVWGSTEVQWWAKSKASMQQDPNNKKMSKSSKAPSTPSIDSIDMA
>BP:CBP00368
LLIFVILVSTTFSDFETDLQRIKEEYTCYPNCTFNYTEINSETAKLFPSSCYSICGLITINENTDVSFATLEKLFHRMYTLKGGLRIENTTLRSFSFLQLHGFLSFFCFPFGTRIVNNTELVDAEALENIVHVSNTSHECKMEILDNSKLDASRLCESQFHNSVQNIEVLDNGKDCGCSSGKITPRNLPDFKNCIVLFDGLVLTNMSYNSNLKSLSKIANIRGNVEIAYTNFKDLSFLKSLSKIRGNTFENLETVILDIHDNPKMKRLGLDSVSVSEPTQYVDTLEQDWVPTMNLENLHPDFCITYQEAVSLSYVRFKNLEAKFCETEWKTDMKSCKFKSLRELESDCIIIYGNVLISSGDEEYVEKLEDTVYIFGSLTIQNSELENIRFLKML
>BP:CBP00383
MWPDTLYWIFIGIIDILAIILNAILIYFALYRTPKMVRVYTTLIINLAFTDCCSAFLNFFVQQRMIPSGFTIGYISNGWCKLIGYRFCFLSHNLMAHFIVHSNYSLVLSFAYRYYILRKPEPRRKTLLIVLFFTYLPSFLQLVLYQFAESDPSEIVRLLQPYHPTYNFTGLTVSGVADIRSVYALYKILQMTVMTVPIFSTILFLRNKIINRLLYRGINISINTKSLHSQLLMALTYQALLPTLYSINVLMYVLEQFGVYSTAFFENFLMSGLVLIPFFSPFTSFFFFTPYKRILLGMVLKKIDKRPAATSETGPGSFPI
>BP:CBP00387
GEDEANRKKFPCEICGKQFNAHYNLTRHMPVHTGERPFVCKVCGKAFRQASTLCRHKIIHTDSKPHKCKTCGKCFNRSSTLNTHVRIHQGFKPFVCEVCGKGFHQNGNYKNHRLTHEETKKYSCTICKRAFHQSYNLAFHMFTHEEHKPFTCHVCSKGFCRNFDLKKHLRKMH
>BP:CBP00391
MTINYHKEIMTSHPWTFFLLLFKWKGSIWKAVYMETIIFLIFYGIISVIYKTALGESSQRTFEAVVRYFDKRLSYIPLEFVLGFFVTTVVNRWTKLYQTIGFIDNVGLMANCYIRGATEKARIYRRNIMRYCELVQVLVFRDMSMRTRRRFPTMETIVAAGFMNKHELELYNSYDTKYNSKLGTKYWIPANWALCMTNKARKDGYIESDYFKAQMEAEIRTWRTNIEWVCNYDWVPLPLMYPQLVCLAVNLYFLVSIVARQLVVEKHKIVDEVDVYFPVMTFLQFIFYMGWLKVIDVMLNPFGEDDDDFETNALIDRNITMGLMIADNPMTTPDLRKDPFYDEVDVPLLYSEESSHVPNHHYHGSASEVRLEHRGSGPVTMMPHSQSAANLKRIMSFKSSEDDEEKTNPFSMSHDDARMRNWREVSLDSSFLSDLNENKEWKLPTSQQKF
>BP:CBP00394
MDSDDGFDYLFKIVLVGDMGVGKTCVVQRFRSGNFVDRQGTTIGVDFTMKTLNVDGKRVKLQIWDTGGQERFRTITQSYYRSANGIVLCYDITCKQSFGSLQRWIDDVSKFAAPNVAKLLIGTKCDLEDQRAIETEEAELLQRANGMFEMLETSAKNDINVDNAFLELATILKRQYDQGVVEQGASGTFQLGSGGTTSINSPWQRCCQY
>BP:CBP00396
RSRTKFRRDSRSRRQTPTSEMRSFVLLILLTSHLSAGSIDWSSLETPPQFTHGKNAETVFFKVEKSGMSDESAKNIPGNLLEQTIHCQAIGNPRPTYRWKKDGKTFLPSMFPEKVVQKPGEGSLVFSRLDETDAGLYQCEAENSNGTAVDRPVRVQETWIRHFKAAEPEVVVVEVGDPYQRNCSPPASNPNARVYWILMGKEPGHFETISSSHISSNEQGTLFFHYVNETDLKSDRYYTCTAENIELKDYKFGNQFSLQITNYKRRSSAPYWPNGPPPNTNTSEGENVSFDCTTYGKPTPKVTFYKNGVELGSQKDDRYMIEGTRLTIYDVKKGTYGKGDNAVYQCKSENKHGWLWTNFYLNLLAFKPQLLIDPGKEEVEAVIGKKVTLECKFFASPNAAVKWEAPMISGSKGNQIPADPHGVGRLVFSEVSASEEGEYECIGTNKYGQASGVITLKVRKPTTVKPFDRAEDVRMAGEEMRLPCDATSDSQLEVKHEWLVDGIPLPEERVNSGHYRIADDHSLIVANPTQDDSAKYKCVVSTKLDKVEKEIKIQFKDVPVAVHSAYVSNCDKNSLTAFIKFDHIESIHTIAPVKEFWVQYQMDSETEGSQWRTHPSPSAAHPNDQVTDQLRTTSGSATVSLQPFGKYVFRVLARNSVGDSATTTVKGICETPAKQPDKNPGEVAAKGTSPENLIVQWKPMAREEWNGAKFHYVVKYRPVDEDQRDGDWKEVAVEDPFADRVTINLDDDKDVKPFQPYEVQVQAVNSEGRTNVVPETVEGRTGEGVPSSIPSGLRVLEKSGTTVTLAWNGVDPATANGNFTGYKITYWVDEADQDVEEPEDDEEEKRKFRWKRSIRAKRQSGVRKTIVFGPSATQGTITDLKPATLNHAYIQVTNGAHEGPSSDTIDFQTDEGVPSPVRSLRAYPMNSKESDEKGVVVLVWKKPRQTNGKLARYEVEYCKTQNGKQVEKTCPRQQIDADAKEIRITGLENETPYRFILRAHTSAGEGDPNSSDATTLPETTAAGVDPGVPSLVENAIGDKYFNVSFRPAKYDDETRAPVGNTYEVQYKPQNGDEWETVKPSDDGLTVHVDGLSPGTKYDVRVAALQVDSDGGETTKTFSGISKITTTGTSPGERNLYFIILILLILLLLLIIICICCVVCRHRGQNYPVSQREREQGREPILGKPDYKTDDDEKRSLTGSKAESETDSMAQYGDTDPGVFTEDGSFIGQYVPQKSLMPAERPEKGSTSTFV
>BP:CBP00406
MGSSESVPIPGGGTEGYHVLRVQENSPGAVAGLEPFFDFIVSIGNIRLDKDNDTMKEVLKQHIDRPLEITVYNSKSQSVRQTSIIPSQNWGGQGLLGVSIRFCSFDGASQHVWHIISVQPNSPASLAGLIADTDYILGAESVLHQADDLIALVQANEGKPLKLYVYNVDTDVVREVSLTPNSAWGGEGCLGCDIGYGYLHRIPVSVDRSKNLPQVPQQARVPVGNPLVDKIVTKPPAATNFPDPSQFSSSVPLPPAPAPATLIQNLPPPPQPVFLPQPPTSYAQSPVDQQPPHTELNNHGHSHSDGGGHGHSHESGNHGHSHDNGHGHSQEHSPSPAAAPVPVSAPTPVTSYPQQYVEQAKPATDYYQQQQPPQQQTYQPPVNPLTSYQAYQSPASSPYYPPSASTAPNASGYQAPYYAPQSFPPQQNTYDYKAPEIPSAVPPMFSANAAPSPPTSYVNPIPPPAPLNFPMPSLSSIGITQLAAPPAPPTSTGFTSFQPPPFPQYGAYPSPPPQ
>BP:CBP00414
SSSSTSSTLPISHVRRHEDVPTPSAPPSKRSNIQPQESYEPKTWLQQQMEQEQQRKLAEEKKKQSTSTTGDDEEDMLQDVLSQPRGPHKRRFNFVMVSNITFAIPEGYDVDSIEYLGGGSFGNVIKTSAVCRDGHRRWVTIKKMREPFFDPHHARRIFREIKLLQLMRHDNIICALDIYTPDEENDFRDVYVVTEFAGRSLYRILKQQRDYGRRVLTEEHVKFIIYQIIRALKYIHSANIIHRDLKPGNLALTDDSDLMILDFGLARSLEKKDTSLTQYVQTRWYRSPEVIYWKIDSYTNLADMWSVGCIAAELLTGDPLFPGDDVNAQYQRITQLCGSPDEELLAKIENDNSSAMKAVIQSYKVYKRRNFREVFAAYSPSADFIDLIEKLLVLDPEKRITVEEAIQHPYLAEFSLPADEPRADHIFDLDDTQARTRFQWRDAVWTEIMNYQRIMQSPIIPGETDR
genometools-1.5.1/testdata/nGASP/protein_100_with_stop.fas000066400000000000000000001463731211610345200234360ustar00rootroot00000000000000>BP:CBP00004
GSHQIAKNFVNSSTPDLRPTFVVNFDTSTVICQHSSDPTDLHIHNMSSLCDGKQDCFVNPAMHDEVFPYCEHKCESTCSGKGACLYDGSKPQCYCDSGFSGAACELQDKNECLEHPCHMMAQCQNTLGSYECRCLPGYQGNGHECSDIDECADNIATRCPEHSQCINLPGTYYCNCTQGFSPKGNQGSGLDKCADINECETGAHNCETNEICENTIGSFKCVTKCSPGYSLIDGKCEDVNECDSEKLHKCDVRAECINTVGGYECECEEGFDGDGKNCQRGNPMSLSIAKSSCRKNSAICDRHASCNIFLDICDCKTGYTGDGITCHDVNECDAKETPCSEGGRCLNLDGGYVCCKDGQDDAACIKDQRAFCSGGCCDNAICSNATCACIDGFRGDPHKKCVDINECVENDSVCGGVGDRCVNLFGGYKCCQHGSQEVECTDQAFSSDSSTVSSHGADFTTTGEQVIEGSGSIQTSSGGSITVTRGLIPKEVELTTSGRLACTSYCPPNSECVGGFCECVKGYGGNALVGCEDVDECITETCNVEANEWCVNLIGGFVCCNPTNATHDDCIVLSLGSNVPFSDFLTVPGLEITKEKGLHVIGPNEEDTVVATRSNHSVTSDQLITEVVQQSKNFSSGQIILTRKSVTGGEAVTQTTDGDGEFGLEISAKDFGITLPATLEPRVEGSGKSPVAGVWTEEEDGGEDDDLMEASGSHGSWSTTINGTGFTGSPRSEGTIRVRITTLGEDGETETATKPGITVPGKDGKLAIEKEGHESVSSGSSATSSSGSTGSGASGSTATGKSGSSATSSSGSSSSGSTESGSSGSSATSSSGSTSSGESGSTATEESGKSEPSGATGTESSGKSESGASGESGPAGSSTTSSSGSTESGASGSNATSSSGSSATGESGSSSSGSTESGASGSNATGGSGATGNESSESAGTTASPESVTASRESVEGSGTTPSESTSSLPEGSGEWIETGSKGHFERGNKVSVSHGNGKPEGSGPKESGKPEVPGSQGSGAKESGAGKPGSGSRGPEITTDGEESESTSSGSGKPKNPKITTDGEGSKSTPIGDGKHPEDVEGSGILTTSSGGKNSTLEHGTKLVEVKPEGSDKNPGVGLEISAGKVTSAPEDKEKSNEVGLEIVWESTTPEPTTPDTDNVGLEISGRDLITKRPHQIEGSGTGDEEITATTRDVSKSTKKPRLEIDGGDNGETSGVDGKASTPSPTSPGAPESTTPSAPTTAPEDVTPETGSGEPGIPDGSGESSTAAPEGVSPTSSAPAPEVPTTPEGSEESTKTPEEATTATSPEEETTTQEPLILTAAPSKAPESSTKPSEAPEASSESTAAPPTAQPATVIPPQNREEKPEPTKETFALPTTTEKPVNETIENTKCMSSDECGLDALCERRTGVCRCEPGFEGAPPKKACVDVDECATGDHKCHDSARCQNFIGGYACFCPTGFRKTDDGSCEDIDECKEHNSTCCGANAHCVNKPGTYSCECENGFLGDGYHCVPSTKKPCDKEQSTKSHCAESNMSCEVDTTDGSVECKECMSGYKKSGTTCEDINECDEQSPCSPSASCVNLNGTFSCSCKPGFRGDGFMCTDINECDEKHPCHPHAECTNLEGSFKCECHSGFEGDGIKKCTNPLERSCEDVEKFCGRVDHVSCLSVRIYNGSLSSVCECEPGFRFEKESNSCVDIDECEENRNNCDPASAVCVNTEGSFKCECAEGYEGEGGVCTDIDECDRGMAGCDSMAMCINRMGSCGCKCMAGYTGDGAHCTKIEEPKEASKTACTEEWSRLCELEKKQCAVDEEEVPQCGACLPGHHPINGTCQSLQISGLCAQKNDCNKHAECIDILPDSHFCSCPDGFIGDGMMCDDVDECNNAGMCDDENSKCENTIGSFNCVCLEGFKKSDDDKCVLKTPNREKIEINEENSSSTPSESQKPESTTQGTVTTSVLSSEPTSEAPTSSTSPVTSSEKASESTTSSESPVTPSETSVTTTSLCSTVTCHSLATCEPSTGVCICRDGFIGDGTSSCSKKSTADCISLPSLCAENAKCDNSARSCECDAGYIGDGYVCSPHPQDCVLRDNLCSPEAICQNRRCQCLPGFTGDGVKCVSIHERASNCSQCDANAHCVGGTTCKCNPGYFGNGLCCVPDPLDCVHFTGICHPNAVCNPDTRQCQCSSGFSGNGVSCFPQKSCRTDKSVCAKNAICLPTGSCICRHGFKGDPFYKCTSLVAKEPSNAQDLSDVSSCVTPCDASSQLCISGECICKPGFRQNPGSKTCADIDECAEKTHRCNRIATCRNTFGSHVCSCPEGHVGDGVTCVPHVNQGKLSVYCEADGMTLVLGNETSDFEGKIFVKGQAENPYCSKSFSALLNSHKPYVFKVAFQHCDVQLLDNHTMASTVVVQKHAMFLTNKADSYDLRCQYPIGSRAVQSHVNVSELATTSTLTDKNSTLAPICRLSVSNDQHSSISSAMVGDTLKLALEVTPSENFGILPRNCFAVNIESGERYTLTDEQGCAIDESLFPQWSVTNSAK*
>BP:CBP00012
MAPKDDPDNRGFDDQRRPSQRSTVLAIPALAVNDPKADPKIASDLPANYVDDDDDAPKLYTPSLFEKILNYLLCRGDIANQQLEAQPVSIPGLFRYGKRFDYLLLFIGTICAIISGVSQPIMALVSGRVTNALLVYPPTSKQFRNKANENVYIFLGIGIFISITNWIQYMCFQHCCSRVMAQMRHRFVYSVLRQNAGWFDKNHSGTITTKLNDSMERIREGIGDKLGVLLRGFAMLIAAIVVAYIYEWRLASMMLGVAPVCCICMSLLARQMTSTTIKELIGVGKAGSIAEESLMGVRTVQAFNGQEEMVGRYQTELEKGRRFAVWKGFWSGFFGGLFFLCLFSFLGTGMLYGAYLLKVGIIGSPGDVFIVVMSMLLGAYFLGLISPHMMVLLNARVSAATIYQTIDRVPKIDPYSKAGKRLPNVVGRVKFENVHFRYPSRKEAKILNGLNLTVEPGTSVALVGHSGCGKSTSVGLLTRLYEPEAGNVTIDGTDVRELNIDWLRNVVGIVQQEPILFNDTIHNNLLIGNPGATREKMIEVCKMANAHDFIEKMPKGYDTLIGDGGVQLSGGQKQRVAIARTLIRDPKILLLDEATSALDAQSESVVQSALNNAAKGRTTIMIAHRLSTIREADKIVFFEKGVIVEAGNHEELVHLGGRYFDLVKAQQFKADPEATEEFEEEEIDLDDNSRSSRRSSMTSARSGSEAFQRGNSLNDSFSGSRRSARADAENDAFAAHEAEVMAQDGQITAGYLDIFKNAKGNYIYMFLGTVFALIRGLELPALALIFGWVFEGFTFVPYGGRMMHRMAMAVIAFASVGVGVWISQVASSVLFAIVSENLSLRFRVQSFRNLLYQDASYFDNPAHAPGKLITRLASDAPNIKAVVDARMLQVIYALAAIIANIVIAFIYCWQVAILGTSLILLLAFVMIGLAYKISLMNIEQIKNDEAGRTAIEIIENVKTIQLLTRCELFFDHYQTSSKQQKRSELKKGMIEAINYSITQSFMYFMMCFTYAVGIRVIYDGDKSSDVTFKGIISMMLGAVAVMNSAQYFPEFVKAKTAAGLLFNIIYRKPRTGDLMEGDRPEIRGNILFENVKFSYPQRPLQPIMKGLQWTALRGQTVALVGPSGSGKSTNIGMLERFYDVTGGVLRIDGQDIRNLSLYHLRTQMALVGQEPRLFAGSIRENVCLGLKDVPLEKINKALELANANRFLANLPAGIDTDVGEKGGQLSGGQKQRIAIARALVRDPKILLLDEATSALDSESERAVQEALDRAREGRTCITIAHRLSSIQNSDLIVYIDKGKVQEAGNHAQLMQKKGRYYKLIKKQDLAV*
>BP:CBP00016
MSVEWKSALRLQIEALAKRNDLHRKSSEEEIKKRIVDMDRRIVKLRELVSTSANDAAIFYLECVCHADETERLLNRESSVEKEKKWRKMKRKPSSQIGPTESRTVSSLPSVSPPDVIQTINVSTLEAQDQMPQRPHWWDQFQIYRRTDLLRFSKQNDRRELWRTQKDFFLTCLGFMVGVGHTMRFPAKVYQHGGGVFFIPFFSLVFFGLPLVFLHLSLGQYTGQAANTAFSKLMPIGSGVGWALVVIAIPVAVYYNIIVAWAIHYFFQSAKGLLLGDELPWETCRDEWQLDNRCCNLHNLHSCFNSSNSITAPEAFFHSEVLSLSTFGDFALGPLQSHLVLSLAAAWLLVFFGVFKGLGSIAQTMNVTATVPYLLLSILLLRGISLPGANKGLSFFFTVDSTKLWKWQIWKSAAEQVFYELGIDAGPLISMAAFSRYRNNVYRDSVLLVIMDALTSILSGMVIFSFVGFIASESNSNVNDVLKHDPLYLSFTVYPGVTSFMYWGGLWATMFFGMLVMAALDAEFAWLEMIASAFMNHFSTKNKAVENRLLAFLCLVGFFFGLPLCAQGGIFVFHAIENLNANWNSFSLALLSVAIVCYVYGIDNYLTDISGMLRVPRIPISKAIRFRDKIVSILGPGGIYIKFSLCFICPVILTVLLVASVLGYQRISFAGRPIPIDYEIVAWVVMIGPLLVVPLVAFLQVRQIRNEGKLLKSLFDTSEWRENPDDLLEPKDAYMKQDSKYESPPNRRRTPTIFTHRENTYMYIDSRGPTVRSRVFPMGAPLDPYGWKLGRLRDHQQHIEEVESNYSEEGSTTNNSFMASTVKHNDDVELTLFGSPPAIMGDEDKNMVTKFSESMPVNYKCRNEQAAPVQSRREPRLGRMARKTRRKRSSPSASDPPVPTSPLPPPPRLYHCKSEPPMMRSEEEHGTPKIITPDGSCSISDSSDDSSDDNIRRATVIRRKTSDDDAFTQISTAESISITPLDFPRQRSLSSVAIYDQEQKNGRSKVLSQLKRPTPIVMPPK*
>BP:CBP00018
KMSNSTSPNAAATVGNIAYCYVLPCICVIGIVGNITNLVVLASRRLRAVSYMYLRALAVADLLCMLFVLVFVSTEYMAKNGSTINQYKIYQIYQCHLMLTLINWALGAGVYVVVALSLERYISIVFPMHFRTWNSPQRATRAIIIAFLIPAIFYIPYAVTRYKGKQRWDPIQNVTIYSMDDHPIYTTFYWQIYKWTREALLRFLPIIILTVLNLQIMFAFRKRQKMFQQLTKRKEQGTQKDDTLMYMLGGTVLMSLVCNIPAAINLLLIDETLKKRLDYQIFRAVANLLEITNHASQFYVFCACSTDYRTTFLQKFPCFKTDYANRDRLRSFVRRTQSVIQKQGSVEHTTNSKVWIMFKSKFQRDSLSHHSRKFSRHMPIEQDTVDIQLASGEQSTSGETCEADTLIKYGGSIQLCNDENNTTFL*
>BP:CBP00022
CVICGQSTSLYNYGTISCSACSSFFRRTVLAKVPIQQCPHQDACYTPENRATHSECKYCRFHKCVDVGMINTQKYTNLTKLINQLSVLDKKRSYTCANMMLPPDFRLSSIFDYEHIKLIKKTPEVRFISHDWGCVHQLASMEFIKTFQFVKFLSLQDLQVFMKTAHFNHVIFASAMRSFGIRQGYLSFPDGSDVFPECIKRITCYNPEFLNRIRCKLMGRIIELNINPEEYLLLSAIILCNPAAVNLSVKGRTLISSYQKVYGSLLFQYCCQVNKKNGPLRFSELLTIFHAISQTHHDIGQFFLLFQMYQPNAQPIQLYQEVIDYM*
>BP:CBP00024
FQSVHHHLNEEELKQVFGVSNKHEVPEYSLIETTRHPLKNGGLKMKFVAWNDTYHLNLRKNSRIVSPHIISVIRHGDDAVTTYDGLRDYNQCHYQGEVKSHGNMKAAISDCGALMGSLVMEDHFLVLQTLPKRVHHLQKERHLVYKRSAGLLTDTENKIREEITRLQEEQESFCDTSEQLDDPAMTIPAHLHFNYTIPTSAQLDSPFIFPNMDPITLEIGLFLDSKLFEHFEREYIQDAEQHLLEFSLALINNVHVLYQQDTLTPNLDIVIVRYEMWKTQPSSLSTGVHKNGQAQSLLDAFCRYQAHMNPGTDLTDMNHWDHGVLLTGYDIYHTTTSVAGVAPVARMCDPLFACSLVEGLHLGRSFVLAHEMGHNMGMVHDGVQNQCNKGCCLMSAVNGAGKTTWSDCSVREFNAFLLQLDESGRGNCLRDASPGLISTNHLSDTRLPGQRFTADQQCSYFWGRDYRVEIPNGKAMDDICRILWCGNSGSTISTAHPALEGSWCGHNKWCHKGHCTSWNFDLPPVPIDGQWSEWGGAEKGCPIQQCAVSGSITIQAQHRDCVNPAPNNGGRTCEGANIRGIVCGATSSNCLGFTREEFGNKICSSIKFDPHKPDQQLTGEGFEHSTQPCRVWCHLIGSELIRNKGQFPDGTPCGFDAYCVGGQCLALSCDNKALVEQQEDCPRLEGRSIHQWEDWSSWSECSVSCGPGGRQVRERKCSSGRKCQGVSEESRACEGVLRDCEEFGEWKDWGPCSEKCALGIQKRFRPCLTDQCASEHLQEKRPCDNEGCWTNWDEWSSCSQTCGGGRRYRLRKCLDFKCEGDDLEKESCNTQKCISQTWGDWLPCSVSCGIGFQIRERLCDGELCATANKQARTCNQQQCPSTFSLAVWSEWGEWTTCSATCGEGLQSRERSCRRGSCQESDAAQTRRCVNGPCDHTFLPWSEWTPCETCSSFDSRKRIAKCDGTTDNCQDKIDEETCDNACLREQHSFGPISPKRPKLITSNELRKAFGRPLLPIESITSSKWSEWGPCSVTCGSGRRVRTRDCQEENCPEQNIQHEECSLNSCLDLFIWSDWSSCSKSCGHDATQTRQKLCLFNNAECSSYAESRRCKNLPTCTSISSGNTISENSFDAPQWSEWSSWSACSCFSLTSTRRRFCQVADPTVQGFCAGSILEQIPCAPGNCSPSAGGWSSWSEWSSCSKDCGDTGHQIRNRMCSEPIPSNRGAYCSGYSFDQRPCVMDNVCGEEKVNGGWTDWTSWSECTDYCRNGHRSRTRFCANPKPSQGGAQCSGSDFELNPCFDPARCHLRDGGWSIWSDWSPCSASCGFGVQTRDRTCSSPEPRGGQLCTGLAHQTSLCDLPACDHESDGEWSAWNEWSGCMGNCGFGTRTRVRACVSPPASHGGQPCFGRSSEITECRQSESTCSSFITSSLLADGYFIETDQQQ*
>BP:CBP00025
MLAFESPIAESSYSRQKAKDLAKKFTPGELCTVCGDVASGIHYSVAACNGCKTFFRRVVLENRTYSCKNNGDCIIDKSMRCSCRHCRYKKCIIAGMDRAELSMERRRKRKKLNGIEGLEERYETTNPLINLLLHKEKLYQKLLHSSAMTIHTSLREALDMSQIAFNDTNNKYDDRMDPKYPTNFSYWRAKILTVLVEWAKSFEASFSHLQPEDQKRLFIHTAFSNLVLAEAFHTPEKYNDRIVFPDGLCGFRNVAQTVSSDGVSTKTYGLTPTVVAVINDVLVPIRRMRLTKVEYVLLQAIIFFDPDCLSLTKHGSQLIAAKRRRLLHALQDWLQQQNKHEAAGRFAEILLRICNVQKVAAFKRETLCTIETFELMQPHPFTMEISKSYPDFSYF*
>BP:CBP00027
MVDLKQQLQWIDYLGVVAVWLCFFGTVLVISVTCILWCCVGKEDDPTVFAKYGFGPQPRVPSQRSKLEVEKDF*
>BP:CBP00029
MTRLLNGIKVVELAGLAPVPHCGMMLADFGADVTVIDKKHPVVEQRMNRGKTMKEFDLRKPEDVKKVRELCKTSDVLLDPYRPGTLEKMGLDPLSLWNDNKGLIICRISGYGQTGRMKDEAGHDINYVAMSGMMPTFAGTEASRPWPPVNMLADFAGGGLSAAFGIVSAIHARHHNGGKGCVLDCSMTEGTAYLASFVQHYYDQTHLFTDKYAAFTGECPIYRTYKTKDGKFMAVGPLEPKFHQNMFEVLGIDGDDLFSDPDRITKELEATFLQKTRDEWSKIFEGKDCCVTPVLDIHEVGTYGQHVDRQNFSKSDKFGGTWIAKPSPRVQTIEELTAAATR*
>BP:CBP00030
MAIVAAGVSKVLTTFQKTFKGLLPLIILVIYTLLGAWIFWMIEGENEREMLIEQQKERDDLIRRTVYKINQLQIKRQRRLMTAEEEYNRTAKVLTTFQETLGILPADMDKDIHWTFLGSIFYCMTVYTTIGYGNIVPGTGWGRFATIVYAFLGIPLTVLSLYCLGSLFAKGCKILWKFFLRSTRVVSKDLSEKISEAADNIEEGTTAVAPASKEENDDDDLLSFPISGLLLITVIWVIFCAVLFTFLEEWDFGTSLYFTLISFTTIGFGDILPSDYDFMPIVGVLLLIGLSLVSTVMTLIQQQIEALASGMKDNIDQEYARALNEAREDGEVDEHVDPEEDPETNKKSLNAVVSRMPLSKRALYYFLPASQKKQLEQQSEKKMGRKSIKVQTDSELLETLIREEILKAELNNEMHKFNGPRSSQQPRLIHSEIREKEVPIEVVRVEQYNHGGHDDYLEHDI*
>BP:CBP00032
MLKVCMNVTDQCDCLAIECPIAYSNSVEEKEACYMEHCFISKRALDDVTLYKVTALYLVIFIIGVFGNTATCLVMRKHPMMKTHTSMYLINLAVSDLVTLCVGLPFEMMMNWHQYPWPFPDVICNLKALIAETTSSVSILTILVFAIERYVAVCHPLYLVKNQFFKRNMKSIIGLSWIVSILCATPFGIYHRADYLMRSWPGTDDKIPVISSKMCMVAVMFEPKLEPTFKVLFHFSAIAFFVVPLLTILVLYARIACKVSNNRTIQAGELDITEELQLKINAILCAIVSAFFICYLPFQFQRLLFFYLDNEVILVWINQYVYFISGFLFYLATIINPIAYNVASSRFRRAFKDILFYYCFGRKSNGYPRSSFSKYSL*
>BP:CBP00039
FREMADSPKFALVTFAVYAVILYNVNSFFWKFVFIGYVVFRLLRTDFGRRAMATIPRDFAGLKLLISVKSTINALFKKDRPIHEIFLDQVRQHPNKIAVVEIESGRKLTYKELNELSNQYANLYVNEGYKIGDVVALFMENSIDFFAIWLGLSKIGVVSAFINSNLKLEPLAHSINVSKCKSCITNNSLLPMYKAALEKGLISKDIHVFLAGTEVDGRHRSLQQDLQLFSTEEPAPVDGLNFRSVLCYIYTSGTTGNPKPAVIKHFRYYWIAMGAGKAFGMTKPDVVYITMPMYHSAAGIMGVGSLIAFGTTCVIRKKFSASNFWKDCVKYNVTATQYIGEICRYLLAAKPCPEEKEHKVRLMWGNGLRGQIWKEFVGRFGIKKIGELYGSTEGNSNIVNLDNHVGSCGFMPIYPHIGAFYPVRLIKVDRATGELERDKNGLCVPCVPGETGEMVGVIKEKDALLKFEGYVSEGDTAKKIYRDVFKHGDKVFASGDILHWDELGYLYFVDRCGDTFRWKGENVSTTEVEGILQPVMDVEDATVYGVTIGKMEGRAGMAGVVVKDGIDIDKFLADITSRLTENLASYAIPVFIRLCKEVDRTGTFKLKKTDLQKQGYDLAACKGDKIYYWVGSEKSYKPLTEKMQQDIDAGIYDRF*
>BP:CBP00040
MLHPIVLLLVASSAVYAARPRRALDGLDGSGFGFDKRALNSLDGAGFGFEKRALNSLDGQGFGFEKRALDGLDGMGFGFDKRALNSLDGAGFGFEKRALDGLDGAGFGFDKRALNSLDGQGFGFEKRALNSLDGAGFGFEKRALDGLDGAGFGFDKRALNSLDGAGFGFEKRALDGLDGAGFGFDKRALNSLDGQGFGFDKRSSFKHQSSKLRSVFRNLRGFNKQH*
>BP:CBP00046
MSSLRCHVVVSALLFISIVPISQQVLNEHNQKLEWIVGKWRSEFSGKIFWPTVPTMTFGEELVINEAPIAKSANVQFLNFSARAWSHSTKDHFHDEWGFLTVDPVGNATLMTTGNNGFTTYETGTVSPNKLVLTLKDIGRISFSRDLPVEDLRRTFIRHDDRYMEQVIEMRTATHPKVGYLEHTRVVYTKLK*
>BP:CBP00048
EGRGNKRTFFDITINGEPAGRIVFALYNHSCPSTAENFRALCTGELGQLYGHNASYQGSIFHRCIKGFMIQGGDLTHKNGQGGFSIYGRTFDDENLSLPHNKPFLLSMANRGPDTNGSQFFITTEKVPHLDGKHVVFGEVVKGFDVVKRIEKVETEEEDMPVQRVTIAHCGEMVRKSDVMASDKKKKQDEQEPVGCKMDDEPKTVNWLMRRSRSRTPEDSKKSKKDRERGGNRGDRRRHDRQRDRYGRERRSRSRSGSRDRHRDRERNRVPDERRSGKRPVSIPISKADCEVNKYERELGDCQEILVITNKDGIKVRGRGKLTFMGSRDRSTTPPHWKREESKKLTLEEHQKRQEEMEERKRLRAEREKEDVERKEREEKEAMERAAQRELERQEEEEARKRSRSNSPQSPRVKQELMSQRQESKAESNSSRSSSSSSGSSSSSDSDS*
>BP:CBP00060
MEQIVESLQYFGFLGSLVLNSFLLFLLHTRAHRNFGKYRILMIVFCLFAIVYSLVEVLTLPVMFVKGRSLCVCSNGPLRLYRPIGVPLTSIYCGSFGMCISLLTLHFFYRYVAVCKPDKMRYFNGKHIFLTFSPSLFIFVTWSMTTYWPMAPDEMREIHYHDVLMKTFQTNSFEASFVAMISIFLQDPQTSTWLPSQLLSCAYMSFLMSVCFSVIVFCGYQALKQMRSHASHMSSKTKELNKQLFMTLGIQTLLPVFTMYIPVGCLMILPMFGIELGAAANNAAAFLGLYPALDPLVAILLIKDFRNFVFCKSVTSTYASAVSNTAPPSKILQ*
>BP:CBP00061
MDADKLIEYIQYGGFVSSQLINALLLYLLCFQASNNFGRYRILMIVFSIFAMIYSLIEVVTFPVMMCKGRSLCVCSNGPFTLYRSIGVPLLSIYCGSFGMCISLLALHFFYRYIAICKPEKLYYFEGKQIISTLSPCFIIFVIWSLLVYFFMDVTEEKERIYHDVLFRSYNVDSHKVSFISMLYKSPATETSPEHWNFDQLVPFFGCCFIMDSCFFAIIYYGSKAFLQMKSCGTEMSKKTKELNRQLFLTLGIQTLLPLITMYVPVGCFIILPIFGVELGVEANKTGAFLGIYPALDPLIAILLIKDFRNYVFCQKRTLAKVSTTSGIASKITSTFQA*
>BP:CBP00071
MGDEGYRGWIKLEIPCFEPERHMNNIIRCHTTKLEPALNSYNMRIHTKGQVQAVEEQDCEPFYESNYEIVSSHFSHHLIIAIQNYLKSLSMDRLMPFQLGNLVLHSSDFWSSELTCHLADIPLSAFFFGNIQGGTFINHWEVSFWEDTHRRNRLRQKNMQPTASDRQGLNQIRVEFEFDKVDFMTVHFKHKEGDFEVISKDFRKTRETVTMYYQITVRRTSIRRVIVDPVVNDTNGGDRIRIHFELNCPVLIRRAYKTEKQEAEAKHQVPHYRRFLVINRGRSANMYPTPKAITDSPVFTIEFDTSVSLEEVYRLISRLRIRTGVSIEFATIPSVDCLIWRENPYHRWTFHGSSHLSPTHFSAPIYRDFITTAFPRKHEVCGSREVDTNRERKFAITYLLECLISRGAVVKDQILLDDTIWHRFLEVILHYYTKDDKLCEAGLEDLVHMIDGRKRIGSLIKCFDRICQTRQKNSLVNGLTTEEMREGYQRVRKIIFTPTRVIYVAPETLMGNRVLRRYDHDGTRVLRITFRDDDNQKMRTNKTSTLLEKTVNTYLMNGITVAGRNFGYLGSSNSQMRDNGAYFMEKYSSSQCREYEKMCRMAPPITFNPKIQAARKNLGRFETIDNIPKMMARLGQCFTQSRLSGVNLDRCTYVTMYDLTGGKNIKGDEYTFSDGVGMMSMNFAQMVSQVMDFGKGVPSCFQFRFRGMKGVIAVEPFLDDLRQWSIENDIQEVSEDTAWGLNCVFRPSQIKFISKRHPRDQVEIVKYSSPVPVSLNKPFINILDQVSEMQSLECHRRVTNRIEELLDRQMLSFAQQMIDETFCRNRLKELPRRIDIDYLRTTWGFTLSSEPFFRSLIKASIKFSITKQLRKEQIPIPADLGRSMLGVVDETGRLQYGQIFVQYTRNLALKLPPKSASRSVLTGTVLLTKNPCIVAGDVRIFEAVDIPELHHMCDVVVFPQHGPRPHPDEMAGSDLDGDEYSIIWDQQLLLDRNEDPFDFTSEKQKSSFKEEEIDDLMREFYVKYLKLDSVGTISNSHLHNSDQYGLNARVCMDLAKKNCQAVDFTKSGQPPEELERKWRKDEVTGEMIPPERAERVPDYHMGNDHTPMYVSPRLCGKLFREFKAIDDVLKISEERDEQVEITIDETIMVDGYKEYMHSAREDLARYNAQLRSMMENYGIKTEGEVFSGCIVDMRNRISDKDQDDMSFYNTNQMIETKVTNLYKKYREHFFEEFEGAWEANTEGTSRGESDTNILQRHCRAPTQNMMKKAVAWYRACYEEARVTRENKKLSFAWLMYDVLAMVKQTKSLTSDDIRMGGSNPLYTMLDAHRSQYLLDNRSVFEDYIRFAPSKNQGEQVARALEIIRMYVETNPGLEEVMFVINEWARASKLFENQPIRNYHLSLLFILFATRQFSSVDGNAAAFFPKIDERGWREEKANGEFKQGLEFMEMKKSQMIVKFLEFLASRKFRKLPNVSFRTLRFSSIFMRGEWQIFHVAALKTYYNLLFNLRFEELPVSTDPTMTVRSIIRENEPFVVELPADADRTLVHRKLIEHTGVEEIYMRNMEKSVRGVDEQQKANTRYLVSTRGTLESMYKLRQLVAVKVPIKTYVTGQEISTQMARLCYEKIVKGHIS*
>BP:CBP00076
MSKHNAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDSERLIGDAAKNQVAMNPHNTVFDAKRLIGRKFDDPAVQSDMKHWPFKVISAEGAKPKVQVEYKGETKIFTPEEISSMVLLKMKETAEAFLGSTVKDAVITVPAYFNDSQRQATKDAGAISGLNVLRIINEPTAAAIAYGLDKKGAGERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFVAEFKRKHKKDLASNPRALRRLRTACERAKRTLSSSSQASIEIDSLFEGIDFYTNITRARFEELCADLFRSTMDPVEKSLRDAKMDKSQVHDIVLVGGSTRIPKVQKLLSDLFSGKELNKSINPDEAVAYGAAVQAAILSGDKSEAVQDLLLLDVAPLSLGIETAGGVMTALIKRNTTIPTKTAQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELSGIPPAPRGVPQIEVTFDIDANGILNVSATDKSTGKQNKITITNDKGRLSKDDIERMVNEAEKYKADDEAQKERIGAKNGLESYAFNLKQTIEDEKLKDKISPEDKKKVEDKCDEILKWLDSNQTAEKEEFEHQQKDLEQLANPIISKLYQSAGGAPPGAAPGAAGGAGGPTIEEVD*
>BP:CBP00078
MLRAVVRLSKTGAKAQRRFLNLQEFQSKEILEKHGCSVQKFVVAANRKEAEEKWMSFGNHEYVVKAQILAGGRGKGKFIDGTKGIGGVYITKEKKEALDAIDEMIGKRLVTKQTTEDGVRVDKVMIAEGVDIKRETYLAVLMDRESNGPVVVASPDGGMDIEAVAEKTPDRIFKTPIDIQMGMTEAQSLKIAKELQFEGKLLGAAATEIKRLYDLFIAVDATQVEINPLVETADGRVFCVDAKMNFDDSASYRQKDIFAYETFEEHDPREVDAHQFNLNYIGMDGNIACLVNGAGLAMATMDLIKLHGGEPANFLDVGGAVTEDAVFNAVRIITSDPRVKCVLINIFGGIVNCATIANGVVNAVNKIGLKVPMVVRLEGTNVDAAKQIMKKSGLKILTANNLDEAAAKAVESLPK*
>BP:CBP00081
MLTDGVVDYTKEGSILTAEQRQFYEKNGYLLIRNCVPQYELNRFRQRFQDICEKKVKAPDNMTVMKDISIAKSEFKDGEKAITKIQDFADDPVLFEYCKYPGVVDVVKDLIGNPKSTVMAMHTMLINKPPDNGKLTSRHPMHQDLQYFPFRPADFICCAWTAMEKINRANGCLVVVPGTHKGVLLPHEYPKWEGGVNKAYHGIQDYDPSNPRIHVEMEAGDTVFFHPILIHGSGANRTEGFRKAISCHYANDDICRYVNVEGTTQENLAEEIIEIAKKRLTKYGLDPNTVTLDFADIWRVRAREVNGTRSNL*
>BP:CBP00086
MTATMDVDNLMSRLLNVGMSGGRLTTSVNEQELMTCCDITKSVFASQASLLEVEPPIIVCGDIHGQYSDLLRIFDKNGFPPDVNFLFLGDYVDRGRQNIETICLMFSFKIKYPENFFMLRGNHEPAINRVYGFYEECNRRYKSTRLWSTFQDTFNWMPLCGLIGSRILCMHGGLSPHLQSLDQLRQLPRPQDPPNPSIGIDLLWADPDQWVKGWQANTRGVSYVFGQDVVNDLCAKLELDLVARAHQVVQDGYEFFASKRMVTIFSAPHYCGQFDNSAATMKVDENMVCTFVMYKPTPKALRRG*
>BP:CBP00091
MDASTEAGVYKKELYSRLMASINATMCHEQPDGILYCPNHTGGPVWVRNVYPPIQELQPKVLIVVVVFVLCFIVGVCGNSSIITIIRGVVEDRRKRMKRHGDNAILYIGALCVCDFVMSLSLPPAILDSVIGFWIFGTTMCKVHHVFGSVGRIASTFLITAMSFDRYVAVCYPHQHRLRSRTFVVSTIVCLSAIAFVLLLPMLTYASAKEMVLHELKAHESANITRVRVFKCSDMMPGPIFYWFTSTTFILGYVVPLILIVYFNLKLINKLYAHKRVLPRSAIPVRRVVVYTVLIAAVYFVCWTPYWFSVLYAIIMSLLGKPTTNSEWVLFAIYCVHLLPYFGSSSNWILYGLLNTQLQMKNDIGDDGQSIMTTNGVPDLPRRSTSRGICDGASTSRSLPAASNPQWQVDPMLTRGNSDTSMVFYQDTEQTHL*
>BP:CBP00094
FRIGHLEYENSNETKILEICMKTAGTRKQHTLISLPSCHNFNGLENAANLNYQYAVDLLIGAACDEETQTVSRLALRWHKLYLSSAPLSTKEKEGTTIALKPHSLAGTAEVILAVCKSMKWKEIGLIYSDETKYTAHAIYDMLAEKEEEDIKINVFLQTDGTMNTYTILHSARVLISFLSTSDLSRFVKTLKDKAFRPLEFSIIHVDCYKSETTEFYTHLDQKASEETNPISAARLRKLHRHVALLRNSHDDKGNMEEFATKHGMIVIFFVFPFPTLCFQPSHTLYKALILCDGLQLLSDYKPLSDNLTIVQQQPTLWEHVTNTEIHGYSGPMFIGSDGVRLPYYEMFMWRDGKTQHVASVRPRESEFCEKEKMSNESKNCYEITRTIPFGQLLDDLPPYSSDCGYDNNLCSDFHVFMIAAIVFSILLIPMAIAFYLQRKEHLIQQMPWRVPLDTINFDDSRNGRLLSVSRRVSTVSTARASYSSIFSANVSEHAHVNKQKVSIKRYVQRRPITFTRQEMEMLNQLKYMSHTNINPFTGICFNQGSELIVMWQFTARYSLEDLIFGKEQKFGRNFQSTFIKHIMHGINFIHNSSIKVHGTLYLSNCVVDSYWVVKLTDFGIKNILKERMHHKELAPNSSFDIDAIHYKYLQLAPEHLSSLLEKHEEPMGTVEGDIYQLAMVIYQILFYMKPFAERQEDIKAVKKLFFLELATLLSNQSTAPLHPKVPEGNSFTMRLLSIIQQCWLYKPAARPTLIKITDAVNREFGQDVKGTLIDQMIEMIDEYSANLEHIVAERTRELEQDMATTENLLYQLLPKSIADSIRSGKSVVPEQHSSVSLLVVDVCQFTKFCEAFIPVHILETLQELYSSFDYIVQKNKAFKVENVGDAYLICSGIPEMTACRHLREVSKISLKLQEFMKTFTVRHRPSHILQIKMGITSGAVAAGILGSIAPRIITGICKNLAYKILNNIQPGTIQLSELTANTMMEKFPSFIIEERGMIDVKGKGTCLTFWLTGEKDQMRRQSSRSSCISHSQIKFEIEEANKTNNQFL*
>BP:CBP00095
QLSVPQYKEFLEVQSNLTKNLFTDYDPTISPVYTWIDVDQPIGYDSQAPKRWNYTVFLYYLKLVEVQEPEEKVSVVMELMEYWYDARLSWNTSLYQNTTSFYARQDNVWSPTLTVFGVNDIMDFRDQDNRMVAIDNFGFLWDYISVRISANCQMDVSRFPFDTQTCQIRFCLPIFYRVQVEILNEIYEGIMDENIFKTMGNSEWKLINLTNRVEVLKYNDNMGNMDLAIFEITIRRNPLYYIYMIVFPSFVINFVSIVGVFLNGADKMSRLNVGLTNIMTMTFILGVMADKIPRTGNIPLLGIYIIINLVIITQLEIFLGPPLEYTSAIILELMTCANFLVMVGFWFDDGS*
>BP:CBP00102
MTSFVDNQSLTNYLIIDYDTDNEEDDDDDYDVFPTANEFISNVPKKNRKRARKCVKKGFICCFKTIKYTFLCCRCVIVWRCLWLFVILLIGLFLFTCFYYDDARKIFQFVYIVIETSIHFLKPTKPCRSINRPSSVLHFLQNYSFHPQAFFIYKKGCVRSVKGVLYRLQMKLLLISTVVLIASVSAIGNLYSGGGKQCTECPPGYDYYSRQHDRGWCMKFFPGNVTFFEAEKVCRCQGGATLSGIENTKELKKLSRKINEYFDENGIKSGGIWVGAYRRKDCRVPKSEKKAECTKEFQYQWTDRSTFGRDMWISHWTEGAPHNNVVGNHSEFCVQLQVTDPTKTALNEHFDNRICVHRDGSSAFETEGFICGRPPKCKGGYNGGYSGGDGVIVIGAARPTQKP*
>BP:CBP00103
MDLFSIVKSVSFWFVSTVDCLDSQWQYSEYISSTDMVQSFSERFLPGNWVYMLFAIPLWYGTWWAVLCYIYFYYTDITDAYMKETIEYHYGIPIKDSSYIIVYFQPTGADGKPHPDPKIFFAIGCMWYMIISSMFSVFYFGIRCYWQIRKTINQSAAVSATTKNLQTQLFHALVVQTFIPLVLMYIPIGILFFFPMVIWELPFTTEFVGYTIALYPAIDPLPNMIIIKCYRHAIQGFFMKIFGRGKRGETQHSLNTDAQSGS*
>BP:CBP00104
LQHIYQSLCTMISLILNSVLIYLILYKSPKKLGDYKWLMIYTAVFEQIYTVVDLLTEPTAYSYGYSFVVFRRYNATWTDSNKSQVLIVTWCGLFGSSMAVFGVHFVYRFASVHPKNITKTLYNLNIEDISYISAVFYVDDPNNGSIHLSWGSWIALVQFSTMVGSSMFCVSFLGYLCYSELSSQLSMTSSQSQVANSLKKQLYFALVGQTVIPITFMYLPVCVFVFGPVFMVEIGVISTYLTHAVTLYPVLNPLPNMFIIKSYRNTI*
>BP:CBP00116
MTSWADIQKLASDLQRVQLTQSSKKLSEVNCIEVLQKLIASQQIDVVYTRDGHTYVTKKHLETEIKNECVAAGGRAPLTDIAVALNIDFDHIERTARLIVSSDDEFTLSNAELFATEYVHSLRNELRSLLDEQGHQTTAALCKHNLSPELLQSLLIEKLSSTDFEGVVDGDTIYTSSFLDARQLVLRAVLVALTKVTPISTIQKRVGLTPKRFWIAFENLQALGEVPGTLIGSRTSPACSYRPKMYDYLVKTCVTNQYRQNEFLQMSTLKTLGLDSKTALEEVLGASEVKKLVNLNSIYMSKELMEQCVQTVQDDIQNSGIAEIRMSLQTLNLPLDTADEDLIGEKIASTEKDTNFSDGFVYNNSILTEALKSINTQIEAKAHQEVEKIDVEKKKQCGSKAPAKVQEDTDDWGDNKKGGKGGKKGGKGGKNGGGGGKGATSSVPTGSGTVQVNSEELEEWLRESQTVPEEILTVVVETLHQDATSALRKQVQEIQALQLVVNAANSKKSLSAIGDKCRQLYDSFNTFEAGTTSFADPLGTDLRQYLLKTVGVDLACAILSYAIGIDNVHQLKEKQRDETIESLPEMVREPIRALFASLKSTDEDAVEKFHDAVYDCSVPSATSLSLRKIDKKGRAEVGVKVSADLCDQLASQSDPATTLLLSVLYLFSQAGRPTTASGKFVAQLIAQMKDFCPTNTFELLQSCQKGVVTCIKNQDDDVAKEILSEDIEKLKSAVL*
>BP:CBP00121
MDTAFSPNEVKIMEKAFDSYRRNTCIRFEKREGQTDYLNIVKGYGCYSQVGRTGGKQEISLGRGCFFHEIIVHELMHSVGFWHEHSRADRDDHIKILWDNILPGMKSQFDKISAVLQDLQGENYDYKSIMHYDSTAFSRNGRNTIETVEDGFTQVIGTNQDLSELDIINKLYSCKAKKKEKMRVTTEEPRRLIPQVGEKKPVDSGEKCVDHFADCPHFAQYCTRASFFFVMKSYCPFTCKHCPGDRKIKKSG*
>BP:CBP00122
MESATNSSSEESIFHEQTRKLFRLCDAQNIGLIGKADLDVLVDLIPPDDLQKISRFIGEQKVNEPAFCRILKAIVSQALQQEMAKIEAQIPAFDKNQYLQESSLEDEMRAIEQNRSYLDDPLTKILKKELEEIQRYENSQIQNEHAINNTMIKKPLYRPIQPEPTIPKVSSLAEELNAIDKKVPQRKEEEELTQPDRIFKVVFVGDSAVGKTCFLHRFCHNRFKPLFNATIGVDFTVKTMKIAPNRAIAMQLWDTAGQERFRSITKQYFRKADGVVLMFDVTSEQSFLNVRNWIDSVRAGVDEATVMCLVGNKVDLFGSDIARSGVYRAAEKLALEFKIPFYETSAYTGYGIENCMRQMAESLQRREDNHLEEALKLDINSNYKKRSWCCI*
>BP:CBP00124
MGITTLPPSQLRPELEWLFPKEVTTTSSAVLQRNSAAEIPLNFLAEHSLALIAALFLIVLTVALLAVLVQYHCQKGSSSGSAGAISPKSFSTSPSQWTTCSTVSSTYSTQSLLQLIGSGLRQSLQGLLLPSEAVVLETIVGKGYFGNVYRGRMRDPAGRLIPVAVKTLKGERARDIAHIEKFLREGVVMKHLDHPHVLSLLGISISPAGNPWVVLPFMEGGDLKTYIADPNRALCVLELLDFAHQVAQGMSYLAAQHFVHRDLAARNCMISAERIVKVADFGLAVDLLDKESYIDESETGPARLPLKWLAPESLRDRRVFSSATDVWSFGVLMWELLTRAASPYGEVSNAKVRHYLETGMRLPQPTHCPDIIYDLMQCCWRATPEDRPDFVFLSHRLRALLQENSPDPFTRRFRPNAEQFLLPVLPGRLFTNYFAAQMHA*
>BP:CBP00131
RIPIGKLLSRRIHHQTNGLIIPSKNVLPRQQKRQILFKMGNETPARVVGYYVVFPVIPEETVENNCFMCNIAKSEDWPKLATAEPREMYEGTVRMLMDYGATVMEHMEHLATLPAEDRKFENVVDPLLTEEYDVNFAFQTLVLKMLTDWPDCNRKLFDADLHHIKIMCARDQMEKLTNKDFQDAIKQLYESKENGLSEWQSRLLEWYLLEIKASGLDKHDDKTRKVLGSWSKFIDEYRSKYITGVMSTNDQQTFVVNDKKIIKDAPPHILQKLAVDEQSWESGPWRGRMTPHTIYPFMQYCGDRQLRATAWEKWTSKAGFDHDFYNNSINIEELRHNNEGLAKTLGYASVAEHRLANKMAASPDTVRGFINALTRRIRPVVIDRMESWSAWASRCELITGELQAYDMPYVCRKEAEHHYDVNPLDLMNHFPFWPTFQNIVGVVGHIFNLEFKDITDKGYEKAHADARIYSVGDKFSGQHYGRLYIDPYDRQNKRGGWNVMLARPESKERGLDKIVYFIGSAVAPTANGPSLLHHQQLQQLLFHVRRGSRNPTVGDSKLNSNFSYFQFGRSVQLLLSQSPYRDIAIPWSPFYASDWDAADMFPTFLQMFVTKPNLLATISSPHIITNQPLTEEHANSVALTISRASLWETYRTLFWSDFDLSIYEMEDRKQKFWLDMYKQMYEEYFPFKRNKNDYQPCSFTPIFALQPHMSMYYRKLWAEMLALDIHETFDEEDNEVQTGERLKTTVLNRGSGDVAKELFKRFQGRNPSVGAICDHYAPPLTLQEGMK*
>BP:CBP00137
MSETSGRSNSKLSDSSSVSEQQTADLSIFSGSFDGGVFSSNIPMFNFAGQGSQSALYSPHPFVKSNDPCRLTALTQSTPKEPMNLTPADFGLADFSVGSESFADFSANNSSFVGNFQSNVRSTRLLPAWAVDASGNIRDDLTLADVVLNGSLIDFAMDRTGVKFLERHFPAENDDEMHRILFDKLTEHSAVFTSLCRSAAGNFIIQKFVEHASLEEQYRLVETMSENGLIELCLDKFACRVVQLSIQKFDESNAMKLVEKISNLDFLPLCTDQCAIHVLQKVVKILPVSAWSFFVKFLCRDDNLMTVCQDKYGCRLVQQTIDKLSDNPKSPCFNTRLQLLHGLMTSVARNCFRLSSNEFANYVVQYVIKSSGVMEMYRDTIIEKCLLRNILSMSQDKYASHVIEGAFLFAPPHLLSEMMEEIFDGYVKDQETNRDALDILLFHQYGNYVIQQMISICISALLGKEERKMLPTEMRLYAKWFDRIKNRVNRHSSRLERFSSGKKIIESLQKLSVPMTMTNEPMPLWAVPTPLMDITAQFLNRQNFQKQHSVFDD*
>BP:CBP00139
ICRMLIPQSSQSMLVASTIISTFAFLATITILPIFFMKVQRINSQMLTDLRNCHQDSSDIWKQLSHKSVREKRSYGGQNSIPSGKCCSCQQGKPGAMGPKGSDGAPGSPGIIGLNGRNGRNGKYVASEAHNEPACQKCPVAPPGPPGHPGRKGLRGQSGNAGTAGKNGIPGRMGPPGPPGVRGPPGELGMQGPQGDPGKVLNGAPQGQPGRPGKVGPRGKGGHTGRDGRPGLEGIAGARGVQGERGSRGARGPPGPPGPSGTDGRKGSCSHCQSDDKPHRGAPQEEPNPEGEYSEQQPVESIEPVPQRRPAPVPTTTTTEAAPVYTDPVTQEPVRHRAYPAAAPPSSYNTGNSEVVPKTINYPDTINQPNYKHDGDVSGAAGTSDDSEDVNVIPAGQYSSRQYASKTNKIGKAIHFGYSNDQLSAFKPMGGGADEEEEIEGYGQPRAFQTNKGYNVQIMGSSPTNNNPTYQAAPVGTAWKQPENHKNRHYTPQYLPPPAY*
>BP:CBP00144
VICLLYFSLSAVAIAQQPQFTCPNNANPLVANSGTNLFCTSAGSNTDCPTGSICTTAANAAGILICCSQSTNVNPVCPNSAISQPSNIGYVECQFNNPTNCISGYQCVQSANLANTFICCSTSASVGSCPSDFTPAVGTNGGTISCNPSASTCPSGSSCMQSTLNTAFICCRSANSQRICANNQNALITNGALELCTTPGTQCSSTGYTCQLSVLLATYVCCGQGSTGSSIGCADGRPVYQQRVGETYTCDITSSLNSCPSGYDCALSDDSFVNVCCLTGSTPIPENLSCPTGWNPFRNEVDNAVRTCTAVLDTSCPIGFSCAPSNQVSQFLCCRLASSLVCINGKTLLVNGAPKLCTPTTYSQCPYNYSCQQSVNPTVTVCCSNT*
>BP:CBP00162
MASYILNALTLRHDHDAAERTLHHFWDTVCFNISLRMLDDWIIDTDNKDLLDTGLFEEHITSQPLLAASLFSLIACSIGLIVFAIIFLICRFRGQCGSQKYQEYPSNATNYAIYLMLFFISWLIVTSASAYFVLAGIGFWSEKLDARKPFTNASLRLSRSTIGDLYASYDYHGDFENVSEAPRKSLKRIHIHRKPLLHTFRKRIEIPIRPLAEVTFTGTSDKFITKNRPILDLNSNQNDGSEEDKIDEFESFKRLQNLPEPSLPTEEEIKNQVQEHSGIPGIAEIFGNSEDPEDVADNSEEAETSENQSLVVTGGTMTIEEEDSEDVESEESTTTTTTITMTTTTTVPITTVPTTTASTTKSTTTVAPTMETTKTTTTTTKTTTTASPSTISAIFPEVTWTQIEETNSDDVLDQLLTHAETHPDVPADNSLSYNPNLTYFSLHSRFLVFVCRLTFCFVALALLFVILPTFFLVVAGTGCYIYSDHPMNRSSVSNKIGQVVSINASILLFMSPCMLIFSSFTLFYTHCHELLCATIQLQNQQARGIIDTNHQSLIENYSINTNQCARSLAPVQSLLLSSLLLCISLLPCVFAMFKLVKYYFRMSSEFYWNAADNFAGRQFSKQQDFPRYQSTVIYPDDDMTAGYAVYGQI*
>BP:CBP00169
LKFENAPFPSITICNLNPYKKSAIQSNPNTKAMMEAYSRRIGSGDKSEGIAAALSASGALHAKVRRAKRKAKGKPRLRDRRYHQAFAQCLCDIEPLTGDRKGSCFAAFKGKIEIDTNSTAGFMNLHTSRCLCQLDTISKTLWPCFPYSSWKEKLCSECVDNTGHCPMRFYKGNELYENIKEQVDLCLCHKEYNHCVSTRDDGVIIEIDPNDELGNLDIGKKVASQLSLREEKLAETTTTEAPAVTQALGFEELTDDIAITSQAQENLMFAVGEMPQSAKEGMSYELDELILKCSFNQKDCQMERDFILHYDNTFGNCYTFNHNRTAEVASHRAGANYGLRVLLYANVSEYLPTTDAVGFRITVHDKHIVPFPDAFGYSAPTGFMSSFGVRMKQFIRLEPPYGHCRHGGEDSPTYAYDGFHYSVEACHRSCAQKVIVDTCGCADPMYPIAEMFGNDTKPCQAVNMEQRECLRNTTLYLGELYSKGKESVIPDCYCHQPCQETNYEVTYSSARWPSGSAKVMECLPGDFMCLEKYRKNAAMVQIFYEELNYETMKETPAYTLTSVLADLGGLTGLWIGASVVSMLEIVSLICMAANGYYKDKTEERKSSLSAQSHHSIPVQRASRGSLNTLHKSSTTQSVKLSVIDIRSLHSNHSSKSKQSIFIEDLPPAIQEQSDDEETSESSRTNGSCRYLAPGEDLPCLCKYHSDGTIKVMKALCPVHGYMVRRNYDYSVSNSEEEDVEDEVHLEPEPFYTAPYEHRKK*
>BP:CBP00170
MDTEHRVILNVGGIRHETYSHVLKKIPATRLSRLTPNTANYDPVLNEYFFDRHPGVFSMIMNYYRTGKLHYPTNVCGPLFEEELEFWGLDANQVEPCCWMTYTQHRDTQETLAVIESLDLDGDPPSQEEIAKKFGWEDDFHSGSLSQWQRLKPRVWSLFDEPYSSKYARAISCISVAFILVSTCSFILKTDPSFQIPDIDVFYSLRVVDENGFKNYHKTIGTDKPVTSPHPNFFYVDLICNIWFTFELFIRSIFCPSFHKFVRSPLTIIDVVSTGAFFFESLLHAILIQTGSLVTLDFLSMICVLRLFKLTQHFSGLKILIQTFKASAQELSLLVFFVVLAIVIFAALVYYAERSQLNKDNQFTSIPLGLWWSLVTISTVGFGDMVPKTYLGMLVGSLCALMGVLTIALPVPVIVSNFSNLYSHSQARGKLPKKRRRVLVSLVNIIFVIISIVCFCLKTHPNYRIPDIDISTHMGNLSIGNGPSKIQLNTIYVGKMATRAHPAFFYVELFCNIWFSAEFLVRMVFCPNLGRFLKTPVNIIDFIATVSFYIDWALDRALSGSNRDSVEFFSIIRILRLFKLTQHSTGLKILIQTFKASAQELFLLVFFVLLGIVIFAALVYYAERVERNENNQFSSIPVPQTSLGRVVGSVCALMGVLTIALPVPVIVSNFAMFYSHAQARSKLPKKRRRVLQANEAKVGRGTAAVMINAFTPRGPVGGGGSNPSDGNPLSAFSKTPLLVCTPDGTDKPRRLSQNKNGGNVPPVTQNNNCKANKLI*
>BP:CBP00175
MSLRFLFAFYVFYDVRASVDEYRLLQYLKENYDSFERPVENSSAPLDVQVRFLLNQILDIDEKNQVMSILAYMDYHWNDYKLKWDPKMFGGIRDVRFSGDDDASFKLWRPDVLLFNSVSESFDSTYSSRFIVSSNGDVQQNPPGIFRFICQIDVTYYPFDRQTCFLKLGSWTYNGQYINLDFLLREIIGLHGKPIIVEPERSSTNSASYFVNESIDLQVYLQNGEWDLEGTPGKRVVQKFGTDEYHELYFYIHIRRRTLAYGINLIIPSLVISMMTILGFTLPPDACEKITLETTVLLSVIFFLQMVSNTSPPQSQSVPILAAFFSCCLMLVACSCVFTVLTLSLHHRKPETHEMSPTMRKIFIDWLPYILCMCKPDHPKTPKPKVLGKSIAPIHRLSTIPMLNLPRVSQTQFPDRSVFVYHEVPAIIKNTSRICSELLIIEKDIEKMVNKIEEDSKEEMLRSEWRFAAMAVDRLCLYVFSAFITVITCGLIVPHIIANL*
>BP:CBP00176
MSNWDYIDEVDIIPKLPPNFDELRESKKWQERKEALEALLKVLTDSERLSTKVSYAELIGNVQTVLAKDANINCQALAAKCIAKFATGLRTKFSAFATPLLPVIFDKMKEKKPTLREPLVECAMEVGRTMPSLEAGQEDILAALAKPNPQIKQQTALFVAKQLDLVVPAKQPKGFIKAAVPVFGKLTGDADQDVREASLQALGAVQRIIGDKNVKSLLGDLSSDEGKMKKIGEYADKSAASYAEEQAKNAPPPSSSASAPSAAAASGSSGNVTSAAVTTAEPAAEADPWDFLDAFDVLSKMPEGFDTNIESKKWQERKEALEGLQQLLTANPKLDPKANYGALVERLQKVLEKDANINVAALAANCITGIANGLRTKFQAFAISVAPIVFEKFKEKKPTLRDPLVACIDAVVATSNLEALGEIVLTALGKPNPSIKTQTDLFLQRTFMKLNSQTMPKKTLKTLVPLLIKHSGDSDAEVRDASYAAMGAMMRAIGEKPSLQLLADIVTDNLKMGKIKEYHQKALAEAGPAEIAAMVQSMHKADAPPAAAAPPKKAAPPPKRQESEEEQVEEEEEPLKLPAEEKKKAAPTKENAENEPPVAPKTELLLNDNGEKAQRIKEEKQLKLVKWNFQTPTDEHIAQLQTLLGNQAKVSLMSQLFHKDFKQHLAALDTLIRLADTAPRSLLANSDLLLKWCTLRFFETNPAALIKVLELCRVLVELTRDTETPMSQEELTAFVPYLLLKTGEAKENMRTAVRDIINVLSDIVGPLKMTPMLLDALKSKNARQRSECLLVIESYISSSGISPLKSLTVEKIVAPFVGDKDVNVRNAAINVLVACFKFEGDQMWKAAGRMADKDKSLVEERIKRSGVKAGSGVATSPPNGGPKIVVPQQQQSVVRRPASRSRTREPEPEDDYQDQRAIANSTFTKGNSSSRYALRDDVFATAINRLADSTYVVTPPQPPSAWANNTFQMKRTNSSSSISSIDTSDQIQRSINNISSSLADVAQDAMYQVTYVLNQPEQRHLVDRKADMVFRASAAQLDMIIDEFKAGKDVTGTMDACSQMLFILMGGVEAEHGLEPLNASPETVKAIISSVLRCITQIGSTDAGYTMARSLNRLAMRLVYRVELSNLLCGLILAMIESIQLNSGITDLVSKLSSKWCDELEKRRAQLRASDIVDVFNQFYICTLTEQKMDITHIHIQVVDNYLERVILQQGDVVLDAARRLSSPHIHLTRMINKILQMMKEQNIDPIMPGTLDARAPDEEEAVVVRTGVQVCVNNILRDLKNVSTYNEQLNKLVQSSDKCRNEYSELVKNHALGEAVEELVSEQTIHGAPNFNKPDVVNAMTMTWKALDLLGPTRAETPTTPPQNLSRMDTTIVGTPLSRAEGAGTITRARGNIMRPKQRPTMSREQHEELRNRLQQAK*
>BP:CBP00179
KSKKLEQKPDWDTLDGIGFEFEENKPIVMDPRFYDMLKLPQCDLTKDKVPSKINIKEAMNQFQQCVRPIVERWRGDIKSMNTKFSETRLCEAAFKDMDVIPMTNLHETKWAILPHCVRENPVEQTCIFTFIERGEYHDWGIGLHCDMLVFAGTLGYSSSYKHHQVKLRTKICTNAPEHKFFGADPIIEPNRQLYTAFGKYFPFAIGKKPGFTKFRVLPNQNQKTRKYEFQDVTTIPFTYFLWDILGLKQIDIAWIDIEGGEFEFLDQFYRGGPMDEKGIVICQFNLEVHSKFNPPGAQVFHDFVFRILDDKRYIFTKVLNTDVGIHRMFFVNVEDEKCVRKFLQ*
>BP:CBP00188
MSFAQSFYADQKKVEQQPRQQENASPLTTAAIPAHTPIAEDPLTPAQIREAIRIYRSVLSTNSAPASPVRAPAAPPIAERPEVHSNYYGGGPTDIPQSYLLNYATSSPQQPASAPATQAPEPLFTEQQLIAQLQALQVQQQQVAEPVCEVPVVQQQQQPKAAPNKAPVLQKMYDDEESGYCFNRKGRDEDGPEEIPEAHVATPTSAPAANYSIPAPQQQVNYSPAPVANNYSKVVCGPSEYIGMANDNKFIYDAQKALPVSYAQNNSYTLVNPTAQAPIAQPRFEETDDQGVTTTEDVTQVPASPAVTSRFRGMIRNAQTPVQAPPAPIVVERVAEPVNTTPSHNYNNYGAFMPVNQMSMESEYQLPVLNDLASCIEHY*
>BP:CBP00192
SKFWKIKQLFIFILVALAANFNYGFSTTYINTSVDQFKNFLNTSLSHRHVVMTETKYDIIWNLFLNCWFVGYFVGVWFSPIFIGFLIGNSTAFLASILQCLAILWYCPELLIVSRFITSICMAVTYQSCILFLQLVTRTSGKHKPTFFECSPTHLRGSFSFLSEVSYSSMTMVGSFLGQDYILGSHLFWLCFFVVPFCLFFTLALFLLPETPKFLLISKDSEEQATESVKYYHGVDSDAKQVLEEIRKEAECENDPLEDSTTFRKMKELFTEPHLRMALILSVSALTNTVGLWALLLSSTFFLENANVESEVAEWSTTAMSLAYVSGTVTGGIIIEKVGRRTLLLLFTFLNNLALLAFVFFAKIRILIDPMKYGCLGALIIYGYTYGTGVGPISWFISSELVPQKHRSIAQSVAYAINTLMVVISTFTVLPLYSVIGSYAFVILYSIPSFISMLILFRYLPETKRREIHDIVNELKNK*
>BP:CBP00210
MANIPSFIDRLLSVNDTANPSLTHCIKEAEIDDVIQMCTQIILEQATMVEVQAPIAVCGDIHGQYVDLLRIFNRCNFPPDQNYLFLGDYVDRGRQQLEVICLLMAYKIRYRNTFFILRGNHECASINRTYGFYDECKRRYSLSLYNAFQDLFNGLPLCAMISGRIFCMHGGLSPQLESWKQLAAIKRPFDPPNKSIAMDLLWADPENNMNGWAKNSRGVSYIFGADVVKDFTDKMNIDLIARGHQVVQDGYEFFAGKRLVTIFSAPKYCGEFDNNAGVMIVDERLIISFDILKPAIREVTIRARGTSKNASTRSMLVSSRGPKSKMG*
>BP:CBP00211
LEHPVFLKDILHTITYFAIPIHIFGTYCILFKTPKTMGSVKWIMLNFHVWCMCLDYGLTVLTVPIVIFPALGGYPFGILTEWGVSAEFQTYLIVTLIPVVSAAVITIFENRYFLVFGHNSKWRRFRVLLSIFNYLYAATWCLPSFMIIPEQNMARKVALEMLGPNVSDYIRHFPIFMMSLEITYLTLPCLLIVLTFATEVILFVAIIKKGMTELAKTARFSKNTLKMQKNFLKAVYIQVSMYMTSIQLPLAYFFVSIFFKIYNQSANNFCFVVFSLNGLSSTILMLWVHTPYRDFCYKLLRIEKWRKKIGQANSQDNVVSVAPTA*
>BP:CBP00214
SKEKVPEEDLNLPYFHGALMNQDADQLLVNDGDFMVTMKLQIDINKLVVYLAVRLKKGIRRYEIKRLPGSAKLGSRSKETIDKLINSLKTDVLEIKGEKIVLKRAIAKGKFQLMHKDVIFKKKIGAGAYGTVYRGRLVKTNEVIAVKKLDPESADEDGLAEMMKEARVMQLYDHPNIVKFHGFILDDLPYLLVLEFCNGGSVEDRLRDKGSRLTVPTRVHYTYMAACGMDYLHKKGCIHRDIASRNCLIHRGIVKMADFGMCRATTVYKMDMSKPCNVRWLAPEVWDNGETRFNTDVYAFGIMMWEFFEIPYATPYAEMKAGQVKRKTRTGYRLPPPAAMPKEVGDIMKECCQPAADKRPNAEKLKEMLEEVYKKQNPTETTHNSS*
>BP:CBP00223
SRAAEMAGGNSEEGKGMLLRNGDDKVRHPSPQRGTPDSSSTQGHQFIDQIVTINVSGMRFQTFESTLARYPHSLLGDPTKRQHYFVPDTNEYFFDRHRTTFESILYIYQSGGRVKRPEIVPIDIFLREMRFYEMGDELLEEFWIAEGYEKPKEVMMPTNKTQRKIWELMEYPDSSLSARIIAFISIFVIALSIISFCWETVPSDNDDKVINMTTGELIDELDEKHYSPFFWIELMCILWFTIELILRFISCPCKVTFVTSILNIIDFVAIAPFFVNFFLADTNKSNSSMSFAVLRVLRLVRVFRVFKLSRHSVGLQILGKTFRSSVQEFCLLIFFMAIALVLFASGMYFAEQGEPNSKFTSIPASFWFVLVTMTTVGYGDLVPLSPFGKVVGSMCALIGVLTLALPVPIIVANFKHFYRQENRLASMKSTTKGDHEDDDVA*
>BP:CBP00226
MHPRGKFLAGHLSAFYIAPATTAALISRNHNDWAHLQLLRRTPSSDAGTMNQVHFGRTSARRRNAMILENNSGDGDDEDRPKEEIFRKIESYQFSRFQTSVINSAKLWASRNRSLKLINNFLPGFLANLRLALFHLVLIFATVAYIIAGAYLFTKIEHQAELDRYQSYHSIYKNFVQNLIYDSSGNRSVSEVENMIDAFTSINFRAFKDGLKPTDFLVPQETSRWSMISAIFFTTTVLTSIGYGNLIPISTGGKIFCVGYAIIPLTLVTIADLAKFVADMLIMDPTEDPKTGRQLLVLVFLLGYMTISACVYTILEPMWSFLDSFYFCLVSLLTVGFGDLYPSGTVEYMLCSIVFIFIGLILTTLAVDVSGSVGIAKMHSIGRGFDAMKMLNVLR*
>BP:CBP00231
NAMLIYLILKRTPLLMKSYSVYLMNFAFFDFATCIISFFSCQKVIFSGWSLIYIFHGPCKHVSSWFCYFCHCFECHTLAHSQWILLGSFMYRYDVLKGSTPTVQKMWRNSGAFYSMSLCFLVVYLFDISDSEELLRIMTDLHPEYHYDDGTGNISMFAPITFISIMYMTTPCVPIYCAILYFRHHTLKILNNPSINLSPAAKISHQKLVRALTVQAGIPIFWLVASGIYSLAQFGFISGPIPENITFRLMDCIPMVSPIVTIAFIQPYRDGLLHLFHKGSSIFIPNTIGSSVVDVS*
>BP:CBP00234
MGMSTNKCGARWTSWLTKNMLLLMTMAGIVMGVIIGGVLRNLEPSQEIVKYVGFPGELFMNMLKAMVLPLIAASIVSGLSQLDGKTSGRLGSRAVMYYVITTTHAVILGIIVVSIIHPGDPTIKQKMGIEEGATANESAAQKFLDLFRNAFPENIMRATFSQYQTHYVNVTNSNGIQKTELKTGYVDGMNVLGIIVFCIVMGLVISKIGEEAKPLANLFHALDVVITRMVMIIMWLGPIGIPSLIAQKMLEVSDLWQTARVLGLFVFTVILGLGIQAFITLPLIYVIGTRHNPYKFLSGLGQAIMTALGTSSSAASLPVTFRCLNKLGIDPRVTKFVLPVGAMVNMDGTALYEATASIFIAQMNGLDLSAGQIITVSITATLASIGAASIPSAGLVTMLIVLTALGLPANDISLILAVDWVLDRLRTSVNVIGDALGCGFVHHICADHLNADVAEAEKAHAFVEAHGVNFDELEKEIEQENNNHKTIQHV*
>BP:CBP00238
MLKPLFGKADKTPADVVKNLRDALLVIDRQSATQNERKVEKAIEETAKMLALAKTFIYGSDANEPNNEQVTQLAQEVYNANILPMLIKHLHKFEFECKKDVASVFNNLLRRQIGTRSPTVEYLAARPEILITLLLGYEQPDIALTCGSMLREAVRHEHLARIVLYSEYFQRFFVFVQSDVFDIATDAFSTFKDLMTKHKNMCAEYLDNNYDRFFTAYAALTNSENYVTRRQSLKLLGELLLDRHNFSTMNKYITSPENLKTVMELLRDKRRNIQYEAFHVFKIFVANPNKPRPITDILNRNRDKLVEFLTAFHNDRTNDEQFNDEKAYLIKQIQELRV*
>BP:CBP00251
MTSEYGCNVCNEEYSVQDPLKCPRVLTGCGHTICHSCAMIIAGRNISIFCPFDRTSTNLPGGDLNNLKKNFALLELLEKIADTGGISEIGEGVQKHDRYAKDRLLNVKCDEDSEHVAVFYCTVCDSNLCDRCSEFTHSTNVLSKHRRVPLTEKPVPKVCCRLHSSYVVEFVCKEVSCDNESPLMCLMCRDYGRHKGHCHVLIEKEVDDLREKLREHLGELTRQSEIVERSLNSINSTIHELTPETDDGSLEETKQEASIRNHFYRLHSTLDQDEIHALETLDRYARNRLESLQAQKDRLEAVSTKIGSTCITLQKALVLEKDNILDRKDDLLALAESTNAEPTEVPDRSQLRTRIAFSFSNDRKLHIGDFIEARVVLLGLDGSGKTSIVRRLKKVRIDAVMAPHPTSGFNIETIHYKNYRLNVWDVGGLPKLRNLWKHYYSNAQAIFYVIDGHAVERFNEAIKELNKVMSDPLLISCPVIVAINRKGGASSLNGHMDVLMSQLEALPFQHELHFCDAAQGSGIDQILDQITVCLSRLNGTCPV*
>BP:CBP00252
MTSFLKLVVVGMILVGVAHGASVATADAKGTNCTLTDGFQALSCIMRLSDFAEKIDELDMDDKNEVKEFKKSCDSLEKCFSMLTCGKQQDAETKQAVSSIRNYCDAVVYMAADFGECSEKLEKNKSECFENWDPFPDAIDEEKDEKKKEELKKNACKNYFGKDQCLKKLITETCSEKEWQGFRDHFISISSVLLTCDFKDV*
>BP:CBP00254
SILNWTIFYAINKLQSFNLAFGYLSANQALADALHSTTFLLYFCPMVLLDQPLMKEFSHYCGFILLFCYELSVKIHLAISINRFCAVWAPYKYKHIFSDRNTKIYIFGIWVFTGSVAVLFYEKFCHFFYDDQIHFLTFTNNSFCGYIGWYGDFLKNAAIVAAVVSIDIFTILKVRQMSKKVVSNISNQSQNNLSHREVRFLKQTVTQGAVFMLELLTYFFVPLYFENKWIVFFGTSFAWVAVHAVDGMVVVLLNSEVRSFLIGQRSKSHGPSTNRATA*
>BP:CBP00262
CVASSQYLGDPEVYKLVFHILTCIEIPIHIYGAWCIIFKTSALMRSVKYLLLWSHFLSAQLDLLFSFISIPYMLLLSFSGYALGIFDQPRWEVYICLIVTAFVVTSILGIYENRFFVLYGYRENPSWCRIRKPFIAFNYFLAVIFIAPMYFLDPDQEIGFQNLATVLPCSPESAIGDRRIYVAFTDSLLPYIGLSLEALLLACEIVVFLVITISKLKSRDGQNCSQLSVKTKKLQKNFIKALFAKSSIPITFLLTPVLYVLVTMQLTYRNQNLSNVCVMLASSHGLFSTIVMVLVHQPYREATWNNLYFCFRCKR*
>BP:CBP00263
PDSESWLDSPETVLIFSHIMALLVTPLHLFGAYCILKKTPSTMHSVKLTLLNFHFWNVLVDLMLNVFAIPFPLFPSASGFLLGLFSYWGIRQTVQLWILITSLCFICVSTTMIFENRFRLLNHKNKHWKKFQPFWVVGNILFVFIFLIPTMLQVPDQDQARQMVFSKLPCTPEHSIDDRRIFVGAIDLNFTFFSLTIEAILLFIEIATFFFIVFFKLVHRNKRKMSLMSNRTHGLQTKFVIALCLQTISPCLLISIPVEYLALATYLNYYNTSLNRFSMILFGLHGVCSTLTMIFVHQPYREATVDNFYWLMMCRQNSKKISV*
>BP:CBP00264
MATPSPSTSNDSSDFEKICTICGRPAFVRYYGAVACGPCKMFFRRMVIEKLTYKCKKIKICYITEPKPLKCKSCRFKRCVEVGMKLPPTNCTVLELKNREDDELVRLFGFLKIRDDQRMETYMNFYTTQNPSLEDILDGVKPVKMDVERSMITPVEWSFTAILSVINHFRSFDFEQLESRDKKLIFQFNTFKSNILCGAVRACKEHREKMVTPSGHDIFPDILVTKFNASAELLNRICCQVVARLMELKVTDEEFVLLNIIFFCNSADAHSDKAKSILAARQRFYVSALFKYCQLTYQNNAPSRLNELLSVYHIVQKNASEMQYIGIMIHGFIPNFPIRKLVSDTYML*
>BP:CBP00268
RNYIFPLCIGSLVLGTYLYSFIFKEARYTVILDGKEVNFTGVEDFIQPYVNIVSDFFVASNYKMMSCGIRKSMSQLTVNTMCLLHDEERFLQENHSLNETWVTIRSCQNNQAFRKPSEDLLNNPETIRFAFIRDPIERFVSLYLDKCVKEQNCWACKNDMRCVVKEIYEALKNLQNHRDWKPIPTYMDWHAAPLSWNCNFDKDLSKWTLLMMGADAEERKSSILQLGNIMKRRGVSENVVQMVQEQSLAGETAHSTHKSTRRLEAERQVREDPVVRDYLHKIYFFDYLVFPFNRERLDAKYQTDFWKVPE*
>BP:CBP00282
AAAETNQTGSVGWSVCGGAVPLAIERLRQFGFVENFDFEYIVEYTECDLGSVVRAGMKFIKEDKVDVIIGPPCAQALRTMSILASNSRKPVLGYGFVSDSDLSDVIRFPYLTTVLPNSQMLGFAVAKVLQQYHWSRVAMLYYQSDIQYCSSVMTDVESTLSDPEADFDVNIVIKAEIYLNDNQTTDIVLQSVKSRARIILWCSQTAFEKRDYLLKMSGHDMISDEYVHIMLSMRNIAFGVQSSLGKSVFSQSGLTPIWESFSEGTDGFESIAKQAAQRMLVLDVNSEVTDKAYLHYMQNNIIRAVREAPMNCSTMACMSANNTVMGAYARHLFDVVYLYGVALTHTNSTDPEVYSNVDVIVPQFITSFQGMTGEVKISTNLTRMSIFQLYGLNEHYDQVAYINFTFLNEKMNVSLFYKDEGPTVWHFYSNHRPLDIPICGFLGKSCPVSFFQQYQLLIIVALVVIILMLITLIIGCCFIMSSRRAEQLRINSEWQIPFLSLMEPENRKNAHHTSKRSLQSAQTGESKTTAVSDFCENYTIMIYEKDMVLTMKYQYMNLTKSDMEKFVKLRKLEHENLNKFIGLSIDGSQFISVTKLCSRGSLQDILSRGNFSMDYFFMFCIIKDVAEGLNYLHKSFLRLHGNLRSATCLVNDSWQVKLAEFGIENLVENEIPPKKRLLWVAPEVLRGSLTVSQMDPSADVYSFAIVASEILTKKEAWDFLDRKEDSEEIVYMVKKGGVFPIRPELITDIPDVNPDLTERLKAGQTVEPEGFDSVTVFFSDVVKFTQLSQKCSPFQVVNLLNDLYSNFDTIIEEHGVYKVESIGDGYLCSLQYSRQVAERLKAGQTVEPEGFDSVTVFFSDVVKFTQLSQKCSPFQVVNLLNDLYSNFDTIIEEHGVYKVESIGDGYLCVSGLPTRNGYAHIKQIVDMSLQFMEYCRKFKIPHLPREQVELRIGVNSG*
>BP:CBP00283
MECNDTRLFDTSNNVTYFIIEQFYRFRYLYSNVHPYLSFVLCILGLAANLIHICVLTRPRMRHSSVHTVLVCIAFSDMGTMSSYLLYISRFEFLPEKEGYPYIWALFLKCHAMVSIALHAITLYLVVLMAFIRLSAMKLTTSRWLDHTRALTSAIFIALFVFIMCVPTLLAHQIDETTRGVTLTGMYYRYSVGFSTLMLQNGCFLMKGNLWLTGIFLKALPCLLLLTFTIALIHRLRENNEKRKILIKEERAKKRGDFTTYMLLLMVTVFLFTELPQGIMAIMNALFTTQFHQMVYLNLADVLDLLSLINCYVAFLVYSFTSSRYRQTLFSLLPLTRISYSGISTRQGTLRSHPNQPAAPKTLVQRANSVEVASVRSPLVDKSAATTRPNSAQPTEF*
>BP:CBP00296
LHALETEKNVFSQFYAKKWPRQLRKPKNREISNFKHSEGAEFAAKSYFWDNNWDFDLPELPKPEQMIMPLPTSTPDVYDDFAFYRVLMEKEDKYILVACHANVHGFHRGDLRFLEINSRSRLNRLEGQSVIGSLFLGDIVAVTELARNSEAISPVRDVDVSLVTPDTSCYWIVSKMILYPRNVDKKSPVLFSIVNRMAAIKGENEPMNLNVDNWDMMHADSIYTGLTFRPETLEYHFSKDYQKKKINELVVSARTIRSYPGIYGTIFKFKEGDHREEFKKEMHLNTYTDESKELKRLAELEHEKNVFSQYYQKKSGNRRENHRGRKKPSSCKHHEAIEFAAKSNLWDNNWDKDLPMLPRSQEIIMPLPASAPAQTEVCGLYRVLMEKNDKYILIACHVNVHGYHRGDLRFLEVNSRSRLKGLSEQSVIGSLFLGDIVAVTELARNSNAQSSVRDVKVSSVTQETRCYWIVSNMILYPRILKPDVTFSFLKNRMAVVKGEDEPMRVNCDDWKTVAPDLIYTGMAFSPIKLDDNFSDDFQRKSKNLLISNVLKISSYPNAFGIIYSYEECSEQNEEFKIGTKAYSDTLEIHKYKRERIVETCSLMGFSAANTIFNGRFDCRAFHMYDVSKEGPTVRFRIENPRNRPTLGLWNNGNKILIGGPTGDTNGTIETVMCNSSHMGWLKIAARLTRECPKDFRFNGDLFVSQREPKDHYYLYDGYFQDMAPESNGRKIIETLYGGKPLELRTGDVGGEYFFPSTPEPIRLNVFQKEYVQMLLDGNPLVIGSSPFGCGKSMTIITAALEIYKRNAERNLVGKTHQLLITQSNFASVNLIEIARKTCNSGDEKLRNMKFMRFITDKNWNEQPDHGRTKFDMPFLMNKVFKQWAIGELDGNELMTHHTKSMIAHIIRNGTVTVDELCSAARRVFDKYGDCKIPFSGHLTEAFFILYEPDLIMTTADSSKSVCTLLDKKYETNKNECTTVQIDEASQLPEYTLLGLLKTYNKANFGLIGDIHQLPPFCMEELEGRLKEFGIGNTMERAIQNKLFPISNLRYVYRCHPQTTALLSELFYDGKLISGVTESQRNEFMIKRKDFWPNPSYPVMIINHMGTCQRMGTSAQNHSEKDLVSYMVQNLLDQRKYTLKPQDIGVISFYAAQTSLLTEQLRRSGVKCGTVDAFQGSEKEVIILCCTNEHATEFMQCKFRLNVALSRAKQATVIVGNLGYLRKAKYWNAIVKRVEAYGNL*
>BP:CBP00300
MIFHGEKLEHHDTPVHDFLMDRFERHEKNDPNCLAFTTAENEQDSISYKNLKKKIIQISEWFLENGYKKGDVVLLAAHNNWRCFAFCMGAWRAGLVVSAASSQFTAYEMNYQIEDSHSQLILADAQTLPVVLEASKNLKFVKNVVSIAPNSPKPVIEFEVLTSRLIRNLKMPKIDPMNDLVLLPYSSGTTGKPKGVMITHLNVSMMMVSCIQFHDAIAKSYGLPPDFIFPHELHFLPLYHVMGLFRALLTSYRGSNQILFTKFDMELMLKSVEKYSIAILAAVPAIIVRMVNFPLLKNYDLSSLGTISVGSAPLPDGALQKLKKLIPDLRIVQGYGMTEFSFATHMQSPDCADGSVGRPVPGTSMKVKKEDGTLCGPHEVGELWIKGPQMMKGYWKKEAATQELKDEDGFMRTGDIVYFNENGDTFICDRIKELIKVNAKQVAPAELESVILEHDDVADVCVFGVDDKDSGERPVACVVSKQGKRDLETMKAIMRHINQKLARYKHIKEIEFVGEILRTGTGKILRRTMKKAFLDAKKSRL*
>BP:CBP00304
TLYYVITHKFDLWPDAYECSGNYTVPTARWPKFGIYLWTSGSIFLTLYILCFIAICKIKSSAPVYQLMFFIAIFDIIAIIVGSLILGYLTFHGIFFCQCPLFFFIIGSLAMFTWLFNCVSCIILAIERCSEVNPKFFLSFLFGKKVFRVVKTLVFIYGINGLMFSKPVIFSPEYTSFIYDPMIGKDIILQGVVMCFFHSAAACIYEYMAYFTPTLYVIVAGEVVYQLACSCLSVVYLTLNRTIRNTVVKMVIPKSIRAKYGWHIGVEEHLAVEQAAESNGIALVNASGMPVKFDNFFVN*
>BP:CBP00305
MTMNLIPRPIIGSYFMISGIALIIIYLPCFVVMIKSKCRAPSYQLMMLLAIFDLTSLMVNSVTTGILGIMGASFCHYPLFVFTAGSIGLGSWMGGCVVCILLAVDRCVEINSNFPLAIIFHKQVFRLVMLVICIYWVYASFFTNPLLFTAQYSSWFFDPFIGKEGDLYHNIPHTINNLLVSASSTPLYIYLCYHLIFKFGYSTSMWLYRSKQQIIIQAVILCFFHATAACIYVYMQFFPTPSWLIIIGQLAWQYSNGCVCLAYWTLNRTIRNAAIRMMLSKRIRKRFKLHMGIDEQIAAERDGEVASVSNVMNLMSGTAKVAPFLCE*
>BP:CBP00306
ALQMSLYHVFTNSFTLWDEAYDCPQNLTNLKFERPVLGSFFLFFGVMFIVINSVCTGIFDILGISFCHSPLIIFCLGAIAGGSWMAGCLACVMLAIERCVEINPQFPLEFLFRKSVFPFVRILMGMYTLYAYLFVKGLTFSSQFSCWFFDPLIGKDPLLYHSYPHTINNFAVGIATTALYIYISYRLICKFGYTTSMWLYKTKRQILFQAITLCIFHTAAAFIYEYMQFIEVTPVIIIASQFIWQWSNGAVCLAYLIFNRTIRNLVVKIMVPKSVRKRFGWYIGADEHIALEEAGGPTLSAGLGTVNAIGGVIKFDNFM*
>BP:CBP00307
MSDLQMSMAYMLTHSFTLYPEIYKCPGNTSAMRTKRPILGTYFLASGLIFILLYTPCFIVMVRSKCRVPAFQVMLILAVFDLLSLSVNSVITGLLDIMGFSFSHFPVFIFCAGAIGKGSWMGGCVACILLAVDRCVEVNAKFRLGFLFKKKVFRVVMGLMVLYWVYSCGFTKPLLFKAEYSSWFFDPKIGKEPYLYHSIDHTINNLVVSLATTSLYIYLCYHLIYKIGYSTSMWLYRSKQQIIIQAVILCSFHAIAAYIYVYMQFFYSPPWLIIIGQLAWQWSNGCFCVAYLTLNQAIRNAVVRMLVPKKLRERFDLHIGIDEHLTSVKQITQINTVSI*
>BP:CBP00308
IDMSLFRLLSDFFDLPAEYQCPDCLQNDYFVRLRLGIYFLLSGILLILLYIPCFIVMLKSKSRNPSFRVMIILAVFDIINLAVNSVSTGIFSILGASFCQYPRLIFIVGAIGNGTWMAGCAMCILLAMDRCVEIHSKFFLAFLFHKKAFRVVLGVVGMYWMYSVWFTKPLLFSARYSSWFFDPKINRDPNIYRNVPHTINNLVVSASTTGLYIYMCIFLLYKKGKSTNSMWMSRNKNQVILQAIIICSFHALAAYIYVYMQLFYSPPLLIILGQLTWQWSNGCFCVVYLTINKSIRSSVKKMLL*
>BP:CBP00309
FQMSTFYLFTNDFALWDEAYGCPKNLTTIRFERPVLGGFFAFSGVLFIILYILCLIAMLKRDLIRHPAYKIMVCLAMFDIPSLFIACIFTGYFGYFGIYFCDYPRLIFVLGSFAFGLWMGCTFSCSALALCRISGVNHNLEIGYIFKSHCIYYLIVIIFALPSYGIFFTEPLIFRTEYMSWFFDPGTGLFDSSNYHNISQVINNAAESVITTILYAYLVFYIIRNLTNVILSAHDVRVQRQVILQATIICFFHSLASSVYVYMQFFYSPAWLVIFAQISWHICTG*
>BP:CBP00311
LSSPEFLKITFHVITIIAIPIHTFGFYCIIRKTPKHMDSVKMLLFNLHCWCVLLDIAITVFGIPYIFLPALAGYQLGFVDAPALVFYLVVTFLTGVSTSIFVIYENRYHILFGRNCSWRFFRKYCIVLSYCLVPLYFVAPIFSVPEQETARKIVWESLSCAPEIPEGHFDFFVISLNIRLMAITIAIAEGVPFFQILIFFSLNFYNLILARQPSGLSRKTTQMQNRLVLALFVQSSVTLVLFVVPVNSIILSVYTGYQNQILNNFIFLAFASHGIASTVIMVVVHNPYRRFLRSLSLQSSRKFTIMVINSEIRF*
>BP:CBP00312
IKMIQCPTDDTYLASPEFLSFALHTLTCISLPLHVLGFYCILEKTPKTMGSVKLLLLNIHTCGFFLDILITILGVPYGIFPAMAGYGLGFVDLPGLCLYLIVMTINAISVGIFLIFENRFFILFAENSWWRHFRKPVFVASYAVSVIYFLPAQFLIPEQEGARKFVWEMLPELPQEIYDAPVFVLAIDFHYVVIPVFIMSNLLIAESGCFIILIYGNMNERTKKLSLSRHTIKMQRKFLRALNIQTAIPLLYLMLPMGYLVTSRIFNLYFQSANNLCFIIIGLHGLFSTIIMLYIHAPYREVCKKVFHCK*
>BP:CBP00315
MDNLLRRDYLDGVDSLAEFLQYNFTVPCNGVKGKNQIDCSFSDLCSGQCNDNQVIPLFNLIYRNASSRLHPNFRLTYPTMHLYNDEYYVGEHFAGVKIDPKTNVISRVKVVVLYFRTDRQTPQISSVINEWERSLFDYVAHFNHPTLNMTLNSDAMIAREVRTNGLSCVPYFGASVIAVVLFIFATNQREHFVMSHNIVMAILGIAGPLMAVGTTFGFLFLFGFPFNSITLVMPFLIIGVGCDDVFIIIHAMRKTDKRESLENQIAETMEEAGPSITVTSATNILSFAIGIATPTPAISLFCLYTCIAVAVDFVYQLTFFVAVLVFEEKRLEAMRLSKKQEKVEEALGAPKQVLSIQNSIRSTAGAHPLPANPDGIVSRYCRFLKDWRTRVALLLILSGYWTASYYGCKTMEIKMDTTNLIMKDSPLNNIAWIYERFLWSEGQLVLVFVNNPPDLANEHNQHEVLELVRRFETLPYSMGRNSTSIWLRSFLYQSSLYHNTKGFNGLLQEWLDDSEGGGARWNDMLRLKKAENGTILGVDKFMFATACAMGDDANWATREKLQKQWRGVAHEYAHFNVTVFQSYSFYIDQLDSIGGTTMSTVIWAAITMDLACLLMIPGINSILTSTIAMMSINVGVFGLLSVWNVNLDPITMCTTLMSIGFSVDFTAHISYHYYRNPTSWTTDERLADALKSIGWPMIQAATSTVLCIVPLMFNSSYMVWVFVKTILLVTVLGILHGIIFLPALLLTSGDLSRLFGGSSDSKIQPEKKEKLGEISQASSFSSTNSETVLVKKDDSTELKTIPQERGS*
>BP:CBP00316
MYINWVHHYVPKISFVLSLIANPLFIYLVITCKKTLFGSYRYLLSFFATFNLLASFSDLATPVCVFNYRYVFVTFVADGPFSWKSKYGEQLLYYRCGIVSGTYGILNVHFVFRYLTLKRNAFVNKHFMPYGLILAIMYVAAHIAIWAAVTGLCLHSAQEMRDYIREPFKALHNESFDDITFVAGLFSETTAEIAERSWTGIVLLTVIASYSIVLYIVLGYKIVTGINTKSSTMSKQTAQMQKQLFKALTIQTIIPICVSFMPCSLSFYGAALRIDFVNWVYWGAAVAVSFFPFLDPVAVTLFLPTLRKRL*
>BP:CBP00325
MWRLAVFLSLAAFFVHDVLGKGDPELKMTTPQIIERWGYPAMIYSVTTDDGYILEMHRIPFGKTNVTWPNGKRPVIFLQHGLLCASSDWVLNLPDQSAGFIFADAGFDVWMGNMRGNTYSMKHKNLKPSHSAFWDWSWDEMATYDLNAMINHVLEVTGQESVYYMGHSQGTLTMFSHLSKDDGSFAKKIKKFFALAPIGSVKHIKGFLAFFANYFSLEFDGWFDIFGAGEFLPNNWAMKLAAKDICGGLQIESDLCDNVLFLIAGPESDQWNQTRVPVYATHDPAGTSTQNIVHWMQMVHHGGVPAYDWGTKENKKKYGQANPPEYDFTAIKGTQIYLYWSDADWLGDKVDITDYLLTHLDPAVIAQNNHLPDYNHLDFTWGLRAPQDIYHPAVELCTNDYLGK*
>BP:CBP00327
MGALSQLRLLLWKNWLQQLRSPWFALFELVVPLILIGASFGLLIGFSDQFETTYDERRYAAWPVSGSAYDLIMPTNPNDSIKSAIVEPYFLFNSQLTCQFLNTYSTGANSYRMDIILAYAPMSAATTDKIMSIIQSRYSLTDLLSPVAPFIHNLYNITTIPTLNTNMSLKGFNTEGDMVSWMQGQFQSECDNPLLAGIVFDDSITKDLFNDNKRDFTYKIRLSNTHRRSRNAFGDDSYPWDTSVSFAIQYVSGPINPDDNDGGSPGYWQEGFMTVQRAVDVAITELITGSGPPISPLLDSYQVSRFPFPGYSTKIIEVGAYFMPVIVIFSFMTSVIYIVRAVVVEKEDRLKEYMRVMGLSQFINWIAHFLINYAKLTFAVIILTILLHFVALKSDMTLMFVFLMVYAFDVVYFAFLISSFMNSATSATLISVVFWMLLYFWYAFFSSIDQTNPYALGVRLINCLNPDIALNYGLQLLAAYETQAAGLKWNEMFNPPSPDNNLTFGHALAALVIDGIILVILTWYIEAVVPGGDGVPQKPWFFILPSYWFPYSGSKTVNSSDQYEHVEYASHVKLEQEPTDLTPTINVVNLTKTYGTSFFKKLFDCKFGKAGEKRAVSKLNLKMYPGQCTVLLGHNGAGKSTTFSMLTGVASPSSGSAYINNYDIRSSLPKIRRETGLCPQYNTLFGFMTVMEHLEFFAKLKERKWDPEEAREILARLRIDFKADFMAGALSGGQKRKLSLAIALIGGSEVVMLDEPTSGMDPGARHETWTLIQREKERRTILLTTHFMEEADLLGDRIAIMAHGQLECCGSPMYLKQQYGDGYHLTVVYSSTETPDVPKTTEIIREYILEANVFSYIGQEATYLLNAKHRPIFPKLFRELENHQRQCGITSFGVSITTMEEVFLKVGHLAEERYNYEHGIEDESSELIEKDDPMLQNLKAPVRLTGFALQMQHAKAMFFKRGIFFFRKWTQFLPQLAFPVAYLMLMVFTSQVIPSVKEQDPQTISLAPFSTKDKPGHVVSDSGNYVTMNGASTKLSNMVQNTVAALGVNQTVVDISSSVESFIMNQTNALGSRNFGLKYALGFVPSSIGIPGLPIPDLKTIRTYFNNFGLFTPALAITFTDSMLLSQAKNKQYTFTAINHPLPPSTQDTLKNTNRSDGAAFLIAYGLIVAFAVCVAGYSQFLITERKKKSKHMQLLSGIRPWMFWFTAFIWDAVWFVIRIICFDAIFYMFDITAYTHDFGIILILTLSFLLYGWTAIPFTYWFQFFFESAPKGFMMVTMYHILTGMIGSIAVPIIQQTSSMDAGYLWSIIFAWFFPTYNISQIATVTFQNENVRMACQKLDCNVPMFKSVVACCGTASQKLYVDNVLFVGNRKGILVYVIFLAVQGFIYWIMVFMRENDQFGKIFNLIKCWKKKDDHIWDITEGDKEEQRDVEDSDVIAEKSVVQRLANSNETALVSNNLVKWYGNFNAVKGVNFHVNSKDCFGLLGVNGAGKTSTFQMLTGENSISSGDAFVNGWSVKNNWREAGANVGYCPQYDAIIKEMSGEETLYMFARIRGIPEKEIPVKVQAVIHAIGIGMYAKRQIKTYSGGNKRRLSLGIAIVGLPDVLLLDEPTSGVDPKARRIIWNILNRLRDLGTALVLTSHSMDECEALCTELAIMVYGKFRCYGSCQHIKSRYGSGYTLLIRLKNRGDAEKTKSTIQQTFRGSKLKEEHILQHNYDIPREGDSWSRLFEKLETLSTSLNWDDYSLSQTTLEQVFIEFSRDAGQLDVDPYGDVPSLTGSGNKQNGYANRAMSVESITEMGTYF*
>BP:CBP00329
IPGSIISRGEQPTPSPSDSSQSTLIPNFPWMENIPKIEFTTSKPKKPNAIREGLIEQVRSGKIPRELAPFVNLTKIDEMKKDHNETLDFIIRDEDVADVPDDDVEHRKVNTISHDGNKTIVTISDEARDDLYKHWMDQSLAGLMGAVVTNVINKRKMTKNEKKEHYVCIHESKNVTAHAKCVVTVLDQLKKRNEKLKMYSTLTTRLNSHRKNNRMDNEAFKTTLGHYEKYVKSGAEEFRVKRASGFSIFDELESKRQAAIRGNVQTRKSYTIRENKSLSPLALIARKLTELVRAGKNKKEQPKRWQQVIQDIKEESTRIKSKKRNKDRMKRKFSKFVSTMKEAGINPRKALNTMGMEDLFEDDPILSEKEMELKDRKEMMERMSPDDKILHEPIKLIREAIKIGMTMAGKNASEIGDKKIAFLSPQFMSILPDEVANDTVSLLSPSILALHGEGSTMDRQLSLTKALKLMEDTGQEEWMNFVLEASGVTETVDKMRELEKKEENDEMRKDFIDKDGKPIFFTKENATEIYGEYEAMKLDIIQGVYKNMSQEQMDAMNATGYSILDDRQMEMIYGAGSPYNDSEVLDKFRGIPKESMPSKIEENIRMIAKEELKFELSRK*
>BP:CBP00332
SSSFTRIPKRDRTSPEKGEPSSKRSAPFTTPSSTTKIGRDSFAVMDTMEVQMNMFQLDITKMPPVIQRLHVDTLIITSKGKEINLNLGTVSTGGDVNSHNRRLAQHEIMRKFFEKKRSLFSSSSYHSLAYDTAACLYIPEGQYRGGEYEEVCLSQQDFAPEEWDIVSKISRRKDDSFIVRIKPAGAVYTQGDELFEPSNRYELTRIVEIVTSQKLNTTDFYQFGNATFPLRAHPNSEPDASSEIRSGFAKVARLTEGREGKHEMLMTVDTKLSPFYKPTSVIRCVLTKIQESRGGGGGGGGYGGRNDSRDSRGSFGGRSDSRDPRGYGGGYDRRSDSRDSRGGRDSYDSRRGGGDSEDFSSHEIDEIARACMESDKFLYSLESALKGLFAEAIHLKGSACTIRITGIKQCTANNTKFTKKDDKGEREISVSDYFYEEYNIKLKYPNLPLIVSKKMKYECFFPMEVLRIIPGQRIKVNKMSATVQSAMTGRNATMPRQHVDLVQRILQDSLKLERNKYMDAFGIELKSTRPVQLKAKILPPAEIRFKNLTYMPEIKRPGFKNPGKFVEPAHIYRVAVVSFDNAIDMRQAEDFCDRLFDYCRDQGIKCDRESKDWSIRELSSSDNVGIKEAMENWMKKKVDIFVGIARDKKPDVHDIMKYYEESVGMQTIQLCKQTVDKMMNPQGGRQTIDNVMRKFNLKCGGTNFYVDIPSNIRGRSICSNTETLHKKLLEKVQFIGFEISHGAARTLYDRSRNQMDGEPSIVGVSYSLKQSTQLGGFSYMQTQREYKIQKLDDAFPKCVKAYAEDAKTLPTRIVIYRVGAGEGDFKRIKEEIQEIRGTFEKIEKGYNPALVFIVAQKGSHTRIFPSRIDGNKAFEQNVPSGTCIDNVVTSFGYDEFILSSQTPLIGTVRPCKYTIIANDPAWSKNELIHLTYFRAFGHQVSYQPPSVPDVLYAAENLAKRGKNNYRVHQRYVSMQAIERRIISENADFVNENMQEQLASAIIDEMSDAMNGMTIPKRNFWA*
>BP:CBP00334
MTDIEKQTEIREKKGRNVMRELKIQKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRTFGIRRNEKIAVHCTVRGPKAEEILEKGLKVKEYELYKENFSDTGNFGFGVQEHIDLGIKYDPGIGIYGMDFYVVLNRNGVRVSKRRRAPGRIGPSHRVDKEETIKWFQQKYDGIILPPKPKTKKNVYRRR*
>BP:CBP00335
MFFVLIVFTFLTWLVVRQYQKVSRLPPGPVSLPLIGNLPQIVYYLYTTGGVVSTLDFFRKRYGNIFTLWVGPIPHVSIADYETSHEVFVKNANKYADKFHSPIFREMRKDIGILTANGDHWQEMRRFALFTFRNMGVGKDLMETRIMEELNASFSENMGLISANGESWAEMRRFALLAFRTMGVGRDLMEERILAELDARCAEIDAEAVNGKTIVHTSEFFDLTVGSVINSVLIGKRFDSHNKDEFLKLKGLLDSADELFTMFELTVPVWLLKKCFPERYARIVEVQEEIINFVSREANERYEKVKSGEYTINADDPQDFVEAYLAKIEEEKEKGTTNFYTMQCLKHVIG*
>BP:CBP00336
MDGTFFQKDLAPFVKYSLNKKRRWETKGDLNSLKNLQSSYRDMNVVVSDRVWLDMDPYWCFISHINYYHNYFLQFPIRHTYQLDTDNNYRCLSSDSVYGQPLKSLLPENRSPKKSDTLQSATFDMPKVAYHILTPPENYEKLRNEDFCPGSSDRFLKHRSIKHWRRCKKMTEALLAIRYEDFDYLNDPIYFIDNEWDIDFGTPSKL*
>BP:CBP00337
DSLLSSPEFVSRTFHFLTFITVPVNMLGAYCILFKTPKSMSSVKLVILNLHLCSMTLDIVFSVLIQPVVFFPAVAAYSNGVLKVFGKCAGIELYFAGTMFAGTVVTDHCTPSRKKPACTPEKPGLLFQKSITVVSMSIVSVMENRFYLLFVINTLWRKIRPFVLFFNYFVACTFLIPLLLQAPNQIIAFEIIQKKFPDIPFSSYSDSLFIFSVDSSYVFLSVFLTGALTVSQINLYCFLIILNMRKLSSNGKMSQRTYHLQRRFLIAIGIQIFTPLIVLFVPATYLDFCFIFEYYNQAVNNICMILISFHGWVSAIVMMFIHEPYRKFCL*
>BP:CBP00341
MHRSLQILCILAVFTSLAYSQGSRDENQSAKRNDFSRDIMSFGKRSADAADMYDRRIMAFGKRQPNFDRDIMSFGKRSAPSDFYRDIMSFGKRSASMYDRDIMSFGKRSAAMEYDRPIMAFGKRAEDYERQIMSFGRRK*
>BP:CBP00342
MDQFFTKLVALLLILLQIGAILATPIPEAAPEDVETRRELEKRGGARAFYGFYNAGNSKRDQVALPYYLYEKRGGGRAFNHNANLFRYEKRGGGRAFAGSWSPYLERLCDYERSGYPIYFSDNSYY*
>BP:CBP00343
VSKPIADAVLRYGKDHPVFRNKLLIPIGRGLVRFTSRMRMKRLGLGEPITHAPVSEAAALEQASDFVQQLVLFSYSVGVFASYYFYTKLTTPESLKIEEYNDFKEQQERAIKELRLQIESLEQRLAAQQKRNFFSQLGFSKDEAPNGPSESSKEASGASESSKPSKPSESLKERFQRISSLPIDAAASLILDDEEYLIVRRDTSVGIELSVNFAARGERLRYRIPSSKLRESLAQLALKEAACHVIGS*
>BP:CBP00344
MWELVSAELFSASNLFLLGFMISALAVSSVFTLSHITPWVRRTRDEYLTPEIVYRSSPEKEFSKLLESERDAPKRYTPSRCYLSVVIPAMNESERIEIMLEDCCDYLEKRSKKDLEFSYEIIVVDDGSTDDTADVVVGISQRRQNIRVLKLKANRGKGGAVKMGVLHSSGKLILFADADGATKFEDFEVLEKEMLRAAGGEPFDESFPAVVVGSRAHLEAASVAERSFFRTVLMHGFHALVWLFAVRTVRDTQCGFKLFSRSIAARIFPVLHVERWAFDAELIFLCEKWTVPVSEVSVRWKEIEGSKITPIWSWLQMGRDLVLIWFRYNIGIWTDSQP*
>BP:CBP00345
TAISSSPEAPQTMSEVQKVVDDDEDDEWGDFGEAVVAAAPIQNTNPPPTVPPLQMASNDEDDDDWGAFDQARPSTDRSDGPSQLAHQQSLEDWGAFEETQKTSTTNDDNEDDEWQAEFSSASTASTVIPAENLKTLEEMLEDDAFWDDGYCEAMELEEISENDSSSSSPLDIPALFDTEELKELTNEFEDLEKAKYSKLWLSLRVIEEAISQEQKTSTSPAVDSPSVPAVDFDWDTSGLTNPMNRASKQLHEMSQKCRRFVCRATTDCINLLKCNLLLASFNPYNTKTMQIRSVVNALTHRFPNLWKPFSRNFGYKEAYQCSAIIDVDFLGSNGVATAYTSTLQQDLEQFGLTNGSTKSNSNGSSILENLMSRANDSSSTTGRYRTPEVLSLDARQLLERLPDLQYLQSEVLMFPVGTNLPH*
>BP:CBP00346
YFLLFLAFFIFKINGGSNECYSCSGVCHNEPCNCQMGSCESGQCFIEKKPTEIPGSMKITKGCLRRTSRIHHGCEYDHFSDHILCVCQGHYCNDKVVMNTTRQKYTRTVTCRECSEKQPDCGSTCEGHWCHEDMSTGASGCGYGPPALPFYYRGPELFYYRSKVCITLSRGAGKPRRHCVCSTKMCNTVYNYQFNQYNIKDREKEGSTRARSLTLSATDYTLPLQTCYNCETNTQDATSMSHTTNCRSNRCLGHYCTYAAQRHTSKSSMGRSNMVHAVSELQGCMNVSDKSHIQLGCSRKWISDEYEEIHCACKGSLCNSDSLTATA*
>BP:CBP00347
MDGVYRLFCGCCGLAGGDPEPPYSQLRHDSVTPIRDPPLQYLNQQQQHQQYPPYALQEQGFVNPVHEFSNFDPRPSFRTRDEADGPNYQHSDSGTPRSGLEDEVEDENREREQLDNIVESTQHSIIAVGQTDVDGVIMMDTQYREKAYKQKVQKMATASSTTQLYEPVHEFQFEPTQTPIQVPLRYDEMSATIDKSPIERMPFACPDFQQMRLARTMGVKNAQFLVEHPDPRHAGKSPAMSSSAKHKITAVLDQVHEGVVGIEVEPRDLIVSMDF*
>BP:CBP00349
FTWFDGWEYPAYVSHSISLVLIPLNIFGGYCILFQIPKKMEASKWVMINVHFWSSFLDLLVSFLLTPYIFFPAMCGITNGLLSWLHVPIIVQVFLAQWKCILGVGVSLVIIFESRHNVDRFVITRKSSRILFYALNCVYGIFFMTPTYFSLPDQEKAKLELLKIVPCPTPVYFEPNVFVLMDHQGRWFIQLQCTTFFCVLIAQGAFSVSRTVYFLTAYNSKMSEMIQVAIPVFIVILPILYCGCAIEWYWYYQSFSNTAIICVSFHGMSSTIAIF*
>BP:CBP00354
SSKLQSLQGLRGISILLVLIFHFFPKNFVNGFVGVDMFFVLSGYLMTRILSKEFTVLSVVDFYKKRFSRIVPLYYFTIFFTLLGVLSLVLKSERTEFILDVKWCLALISNYQPIFEHHSYWDQVSTIRFLTHLWSLATELQYYLIVPIVHLVASNLPFVNRITGYLIAIIILFFFQLLTPFELSYCFLAARVWQFLLGSVAFEMSQRNDLVLDFHTEKKNEKTDFNVFDGIPHIFLVVLLTVLMLPWIFQEHSARLVMSLSAAMLCYSCEKLEQSFLTLQPLVFIGDISYVTYLIHWPVINFVRYIQQKDNSSIDVYEALIAVTIIFVLSLLAHYKLERKLLELEFSVNFTITVFVIGICVALIPCLIRMECLAMKTLSKDLQEKAKFNLIEENVLKPVFELECDYNETTIDLPIDKFGIEYCAHVSNGTGKIMIVGNSLSIRAFPTIYKLVDGQYEEIRLFAKHGGAPLLDIFPYYNYVVMDMAQEMKPDLIWIIQGMNEILFGSDNNGNFSSPVMDRNVPRVLGEFEKLAKMVYLDLPYYITKDMPSKLIARSLIYRKSLERLSVSLEDAEKQVEEQTDRLMNVNCSNCYYNDVQKALINDQDKLYLYEKETYKALTYDGSHLALTGYKYIEPLYQRRINQFYEM*
>BP:CBP00365
MCGIWAIIGEQVTPQQQDAFMKIVGRGPDLTVLDEVQPNVHLGFHRLAIVMPGDTPSAQPIVGGGLSVVCNGEIYNHQSLKIDCPYTLKNGGSDCAAIITSFIKHNEDLKETCASLDGVFAFIMADSKNVYIGRDPIGVRPLFYGYNLNGSLLIGSEVKCIEELCERVEYFPPGCCATISLAAPSRPIQPQQYYSVPSIADRFLSIECTQTLVRDILVKSVEKRLMGNRNFGFMLSGGLDSSLIASIATRFLKQKPVAFSVGFEDSPDLEAARKVADYLKIPHEVLVITPQQCVDIIPEVVFALETFDPLIIRCGIAHYLLCQHISKSSDVKVLLSGEGADELFGSYAYMQRAPNALHLHKEILRRMQHLHQYDVLRCDRSTSCHGLEIRVPFLDKRFIDLVSRLPPTYKLMPMKLEKHLLRSAFEGWLPDEVLWRSKEGFAEALGKTDLGDILASHCDKLISKELYEQRAERFPDRTPETTEEYWYRQIFEETFVYDKMGHLVHTKVYRTAAWHRPDEKENIINSPDSENILDVKSDDLLRLRRRSTGSLGVA*
>BP:CBP00366
MVVLTKKSVKISYDDVAKSPDQLLRSMSSVHPISDGIPSQQRPLTYRWFPSWRFMTSIMLCFCFGCVHLMNSNMGMAIVCMVNSSVTYDNETYPENAAPLLDWSSDEQGYIFSAFNAGLLVMLFTGGMADKFNAKYMILVSVAIASLANLTLPFMAPISVYWAIFSRFLVGFADALLQPAMNSLITRWFPTSERSYALGLATGGRQIGTLIIIPAAGALCSQTEIFGGWPSIFYLSGFIGIIFIFSYIFLGADKPSKQTCITDNELKFITISNQSEDVGKKRTERKVPWKNILTSGAVWASVISLVCHEFPLMTLIMFLPSYLHDVHHYHSTENGILSALPTVSLWFAKIGSSYLNTWLQKNTSWKKDTICKVLNSIGSIGLGVFLLAATFLDKSHAWMAVLFLCLSMASAGLHTPGCQLALVSVAPAYSGAVTGFTFFFVAVSGIIHPIITKMIVKDRTAAEWNLVFYISTVIAIFPIVIFNVWGSTEVQWWAKSKASMQQDPNNKKMSKSSKAPSTPSIDSIDMA*
>BP:CBP00368
LLIFVILVSTTFSDFETDLQRIKEEYTCYPNCTFNYTEINSETAKLFPSSCYSICGLITINENTDVSFATLEKLFHRMYTLKGGLRIENTTLRSFSFLQLHGFLSFFCFPFGTRIVNNTELVDAEALENIVHVSNTSHECKMEILDNSKLDASRLCESQFHNSVQNIEVLDNGKDCGCSSGKITPRNLPDFKNCIVLFDGLVLTNMSYNSNLKSLSKIANIRGNVEIAYTNFKDLSFLKSLSKIRGNTFENLETVILDIHDNPKMKRLGLDSVSVSEPTQYVDTLEQDWVPTMNLENLHPDFCITYQEAVSLSYVRFKNLEAKFCETEWKTDMKSCKFKSLRELESDCIIIYGNVLISSGDEEYVEKLEDTVYIFGSLTIQNSELENIRFLKML*
>BP:CBP00383
MWPDTLYWIFIGIIDILAIILNAILIYFALYRTPKMVRVYTTLIINLAFTDCCSAFLNFFVQQRMIPSGFTIGYISNGWCKLIGYRFCFLSHNLMAHFIVHSNYSLVLSFAYRYYILRKPEPRRKTLLIVLFFTYLPSFLQLVLYQFAESDPSEIVRLLQPYHPTYNFTGLTVSGVADIRSVYALYKILQMTVMTVPIFSTILFLRNKIINRLLYRGINISINTKSLHSQLLMALTYQALLPTLYSINVLMYVLEQFGVYSTAFFENFLMSGLVLIPFFSPFTSFFFFTPYKRILLGMVLKKIDKRPAATSETGPGSFPI*
>BP:CBP00387
GEDEANRKKFPCEICGKQFNAHYNLTRHMPVHTGERPFVCKVCGKAFRQASTLCRHKIIHTDSKPHKCKTCGKCFNRSSTLNTHVRIHQGFKPFVCEVCGKGFHQNGNYKNHRLTHEETKKYSCTICKRAFHQSYNLAFHMFTHEEHKPFTCHVCSKGFCRNFDLKKHLRKMH*
>BP:CBP00391
MTINYHKEIMTSHPWTFFLLLFKWKGSIWKAVYMETIIFLIFYGIISVIYKTALGESSQRTFEAVVRYFDKRLSYIPLEFVLGFFVTTVVNRWTKLYQTIGFIDNVGLMANCYIRGATEKARIYRRNIMRYCELVQVLVFRDMSMRTRRRFPTMETIVAAGFMNKHELELYNSYDTKYNSKLGTKYWIPANWALCMTNKARKDGYIESDYFKAQMEAEIRTWRTNIEWVCNYDWVPLPLMYPQLVCLAVNLYFLVSIVARQLVVEKHKIVDEVDVYFPVMTFLQFIFYMGWLKVIDVMLNPFGEDDDDFETNALIDRNITMGLMIADNPMTTPDLRKDPFYDEVDVPLLYSEESSHVPNHHYHGSASEVRLEHRGSGPVTMMPHSQSAANLKRIMSFKSSEDDEEKTNPFSMSHDDARMRNWREVSLDSSFLSDLNENKEWKLPTSQQKF*
>BP:CBP00394
MDSDDGFDYLFKIVLVGDMGVGKTCVVQRFRSGNFVDRQGTTIGVDFTMKTLNVDGKRVKLQIWDTGGQERFRTITQSYYRSANGIVLCYDITCKQSFGSLQRWIDDVSKFAAPNVAKLLIGTKCDLEDQRAIETEEAELLQRANGMFEMLETSAKNDINVDNAFLELATILKRQYDQGVVEQGASGTFQLGSGGTTSINSPWQRCCQY*
>BP:CBP00396
RSRTKFRRDSRSRRQTPTSEMRSFVLLILLTSHLSAGSIDWSSLETPPQFTHGKNAETVFFKVEKSGMSDESAKNIPGNLLEQTIHCQAIGNPRPTYRWKKDGKTFLPSMFPEKVVQKPGEGSLVFSRLDETDAGLYQCEAENSNGTAVDRPVRVQETWIRHFKAAEPEVVVVEVGDPYQRNCSPPASNPNARVYWILMGKEPGHFETISSSHISSNEQGTLFFHYVNETDLKSDRYYTCTAENIELKDYKFGNQFSLQITNYKRRSSAPYWPNGPPPNTNTSEGENVSFDCTTYGKPTPKVTFYKNGVELGSQKDDRYMIEGTRLTIYDVKKGTYGKGDNAVYQCKSENKHGWLWTNFYLNLLAFKPQLLIDPGKEEVEAVIGKKVTLECKFFASPNAAVKWEAPMISGSKGNQIPADPHGVGRLVFSEVSASEEGEYECIGTNKYGQASGVITLKVRKPTTVKPFDRAEDVRMAGEEMRLPCDATSDSQLEVKHEWLVDGIPLPEERVNSGHYRIADDHSLIVANPTQDDSAKYKCVVSTKLDKVEKEIKIQFKDVPVAVHSAYVSNCDKNSLTAFIKFDHIESIHTIAPVKEFWVQYQMDSETEGSQWRTHPSPSAAHPNDQVTDQLRTTSGSATVSLQPFGKYVFRVLARNSVGDSATTTVKGICETPAKQPDKNPGEVAAKGTSPENLIVQWKPMAREEWNGAKFHYVVKYRPVDEDQRDGDWKEVAVEDPFADRVTINLDDDKDVKPFQPYEVQVQAVNSEGRTNVVPETVEGRTGEGVPSSIPSGLRVLEKSGTTVTLAWNGVDPATANGNFTGYKITYWVDEADQDVEEPEDDEEEKRKFRWKRSIRAKRQSGVRKTIVFGPSATQGTITDLKPATLNHAYIQVTNGAHEGPSSDTIDFQTDEGVPSPVRSLRAYPMNSKESDEKGVVVLVWKKPRQTNGKLARYEVEYCKTQNGKQVEKTCPRQQIDADAKEIRITGLENETPYRFILRAHTSAGEGDPNSSDATTLPETTAAGVDPGVPSLVENAIGDKYFNVSFRPAKYDDETRAPVGNTYEVQYKPQNGDEWETVKPSDDGLTVHVDGLSPGTKYDVRVAALQVDSDGGETTKTFSGISKITTTGTSPGERNLYFIILILLILLLLLIIICICCVVCRHRGQNYPVSQREREQGREPILGKPDYKTDDDEKRSLTGSKAESETDSMAQYGDTDPGVFTEDGSFIGQYVPQKSLMPAERPEKGSTSTFV*
>BP:CBP00406
MGSSESVPIPGGGTEGYHVLRVQENSPGAVAGLEPFFDFIVSIGNIRLDKDNDTMKEVLKQHIDRPLEITVYNSKSQSVRQTSIIPSQNWGGQGLLGVSIRFCSFDGASQHVWHIISVQPNSPASLAGLIADTDYILGAESVLHQADDLIALVQANEGKPLKLYVYNVDTDVVREVSLTPNSAWGGEGCLGCDIGYGYLHRIPVSVDRSKNLPQVPQQARVPVGNPLVDKIVTKPPAATNFPDPSQFSSSVPLPPAPAPATLIQNLPPPPQPVFLPQPPTSYAQSPVDQQPPHTELNNHGHSHSDGGGHGHSHESGNHGHSHDNGHGHSQEHSPSPAAAPVPVSAPTPVTSYPQQYVEQAKPATDYYQQQQPPQQQTYQPPVNPLTSYQAYQSPASSPYYPPSASTAPNASGYQAPYYAPQSFPPQQNTYDYKAPEIPSAVPPMFSANAAPSPPTSYVNPIPPPAPLNFPMPSLSSIGITQLAAPPAPPTSTGFTSFQPPPFPQYGAYPSPPPQ*
>BP:CBP00414
SSSSTSSTLPISHVRRHEDVPTPSAPPSKRSNIQPQESYEPKTWLQQQMEQEQQRKLAEEKKKQSTSTTGDDEEDMLQDVLSQPRGPHKRRFNFVMVSNITFAIPEGYDVDSIEYLGGGSFGNVIKTSAVCRDGHRRWVTIKKMREPFFDPHHARRIFREIKLLQLMRHDNIICALDIYTPDEENDFRDVYVVTEFAGRSLYRILKQQRDYGRRVLTEEHVKFIIYQIIRALKYIHSANIIHRDLKPGNLALTDDSDLMILDFGLARSLEKKDTSLTQYVQTRWYRSPEVIYWKIDSYTNLADMWSVGCIAAELLTGDPLFPGDDVNAQYQRITQLCGSPDEELLAKIENDNSSAMKAVIQSYKVYKRRNFREVFAAYSPSADFIDLIEKLLVLDPEKRITVEEAIQHPYLAEFSLPADEPRADHIFDLDDTQARTRFQWRDAVWTEIMNYQRIMQSPIIPGETDR*
genometools-1.5.1/testdata/nGASP/protein_long.fas000066400000000000000000000370211211610345200217620ustar00rootroot00000000000000>BP:CBP00004
GSHQIAKNFVNSSTPDLRPTFVVNFDTSTVICQHSSDPTDLHIHNMSSLCDGKQDCFVNPAMHDEVFPYCEHKCESTCSGKGACLYDGSKPQCYCDSGFSGAACELQDKNECLEHPCHMMAQCQNTLGSYECRCLPGYQGNGHECSDIDECADNIATRCPEHSQCINLPGTYYCNCTQGFSPKGNQGSGLDKCADINECETGAHNCETNEICENTIGSFKCVTKCSPGYSLIDGKCEDVNECDSEKLHKCDVRAECINTVGGYECECEEGFDGDGKNCQRGNPMSLSIAKSSCRKNSAICDRHASCNIFLDICDCKTGYTGDGITCHDVNECDAKETPCSEGGRCLNLDGGYVCCKDGQDDAACIKDQRAFCSGGCCDNAICSNATCACIDGFRGDPHKKCVDINECVENDSVCGGVGDRCVNLFGGYKCCQHGSQEVECTDQAFSSDSSTVSSHGADFTTTGEQVIEGSGSIQTSSGGSITVTRGLIPKEVELTTSGRLACTSYCPPNSECVGGFCECVKGYGGNALVGCEDVDECITETCNVEANEWCVNLIGGFVCCNPTNATHDDCIVLSLGSNVPFSDFLTVPGLEITKEKGLHVIGPNEEDTVVATRSNHSVTSDQLITEVVQQSKNFSSGQIILTRKSVTGGEAVTQTTDGDGEFGLEISAKDFGITLPATLEPRVEGSGKSPVAGVWTEEEDGGEDDDLMEASGSHGSWSTTINGTGFTGSPRSEGTIRVRITTLGEDGETETATKPGITVPGKDGKLAIEKEGHESVSSGSSATSSSGSTGSGASGSTATGKSGSSATSSSGSSSSGSTESGSSGSSATSSSGSTSSGESGSTATEESGKSEPSGATGTESSGKSESGASGESGPAGSSTTSSSGSTESGASGSNATSSSGSSATGESGSSSSGSTESGASGSNATGGSGATGNESSESAGTTASPESVTASRESVEGSGTTPSESTSSLPEGSGEWIETGSKGHFERGNKVSVSHGNGKPEGSGPKESGKPEVPGSQGSGAKESGAGKPGSGSRGPEITTDGEESESTSSGSGKPKNPKITTDGEGSKSTPIGDGKHPEDVEGSGILTTSSGGKNSTLEHGTKLVEVKPEGSDKNPGVGLEISAGKVTSAPEDKEKSNEVGLEIVWESTTPEPTTPDTDNVGLEISGRDLITKRPHQIEGSGTGDEEITATTRDVSKSTKKPRLEIDGGDNGETSGVDGKASTPSPTSPGAPESTTPSAPTTAPEDVTPETGSGEPGIPDGSGESSTAAPEGVSPTSSAPAPEVPTTPEGSEESTKTPEEATTATSPEEETTTQEPLILTAAPSKAPESSTKPSEAPEASSESTAAPPTAQPATVIPPQNREEKPEPTKETFALPTTTEKPVNETIENTKCMSSDECGLDALCERRTGVCRCEPGFEGAPPKKACVDVDECATGDHKCHDSARCQNFIGGYACFCPTGFRKTDDGSCEDIDECKEHNSTCCGANAHCVNKPGTYSCECENGFLGDGYHCVPSTKKPCDKEQSTKSHCAESNMSCEVDTTDGSVECKECMSGYKKSGTTCEDINECDEQSPCSPSASCVNLNGTFSCSCKPGFRGDGFMCTDINECDEKHPCHPHAECTNLEGSFKCECHSGFEGDGIKKCTNPLERSCEDVEKFCGRVDHVSCLSVRIYNGSLSSVCECEPGFRFEKESNSCVDIDECEENRNNCDPASAVCVNTEGSFKCECAEGYEGEGGVCTDIDECDRGMAGCDSMAMCINRMGSCGCKCMAGYTGDGAHCTKIEEPKEASKTACTEEWSRLCELEKKQCAVDEEEVPQCGACLPGHHPINGTCQSLQISGLCAQKNDCNKHAECIDILPDSHFCSCPDGFIGDGMMCDDVDECNNAGMCDDENSKCENTIGSFNCVCLEGFKKSDDDKCVLKTPNREKIEINEENSSSTPSESQKPESTTQGTVTTSVLSSEPTSEAPTSSTSPVTSSEKASESTTSSESPVTPSETSVTTTSLCSTVTCHSLATCEPSTGVCICRDGFIGDGTSSCSKKSTADCISLPSLCAENAKCDNSARSCECDAGYIGDGYVCSPHPQDCVLRDNLCSPEAICQNRRCQCLPGFTGDGVKCVSIHERASNCSQCDANAHCVGGTTCKCNPGYFGNGLCCVPDPLDCVHFTGICHPNAVCNPDTRQCQCSSGFSGNGVSCFPQKSCRTDKSVCAKNAICLPTGSCICRHGFKGDPFYKCTSLVAKEPSNAQDLSDVSSCVTPCDASSQLCISGECICKPGFRQNPGSKTCADIDECAEKTHRCNRIATCRNTFGSHVCSCPEGHVGDGVTCVPHVNQGKLSVYCEADGMTLVLGNETSDFEGKIFVKGQAENPYCSKSFSALLNSHKPYVFKVAFQHCDVQLLDNHTMASTVVVQKHAMFLTNKADSYDLRCQYPIGSRAVQSHVNVSELATTSTLTDKNSTLAPICRLSVSNDQHSSISSAMVGDTLKLALEVTPSENFGILPRNCFAVNIESGERYTLTDEQGCAIDESLFPQWSVTNSAK
>BP:CBP00012
MAPKDDPDNRGFDDQRRPSQRSTVLAIPALAVNDPKADPKIASDLPANYVDDDDDAPKLYTPSLFEKILNYLLCRGDIANQQLEAQPVSIPGLFRYGKRFDYLLLFIGTICAIISGVSQPIMALVSGRVTNALLVYPPTSKQFRNKANENVYIFLGIGIFISITNWIQYMCFQHCCSRVMAQMRHRFVYSVLRQNAGWFDKNHSGTITTKLNDSMERIREGIGDKLGVLLRGFAMLIAAIVVAYIYEWRLASMMLGVAPVCCICMSLLARQMTSTTIKELIGVGKAGSIAEESLMGVRTVQAFNGQEEMVGRYQTELEKGRRFAVWKGFWSGFFGGLFFLCLFSFLGTGMLYGAYLLKVGIIGSPGDVFIVVMSMLLGAYFLGLISPHMMVLLNARVSAATIYQTIDRVPKIDPYSKAGKRLPNVVGRVKFENVHFRYPSRKEAKILNGLNLTVEPGTSVALVGHSGCGKSTSVGLLTRLYEPEAGNVTIDGTDVRELNIDWLRNVVGIVQQEPILFNDTIHNNLLIGNPGATREKMIEVCKMANAHDFIEKMPKGYDTLIGDGGVQLSGGQKQRVAIARTLIRDPKILLLDEATSALDAQSESVVQSALNNAAKGRTTIMIAHRLSTIREADKIVFFEKGVIVEAGNHEELVHLGGRYFDLVKAQQFKADPEATEEFEEEEIDLDDNSRSSRRSSMTSARSGSEAFQRGNSLNDSFSGSRRSARADAENDAFAAHEAEVMAQDGQITAGYLDIFKNAKGNYIYMFLGTVFALIRGLELPALALIFGWVFEGFTFVPYGGRMMHRMAMAVIAFASVGVGVWISQVASSVLFAIVSENLSLRFRVQSFRNLLYQDASYFDNPAHAPGKLITRLASDAPNIKAVVDARMLQVIYALAAIIANIVIAFIYCWQVAILGTSLILLLAFVMIGLAYKISLMNIEQIKNDEAGRTAIEIIENVKTIQLLTRCELFFDHYQTSSKQQKRSELKKGMIEAINYSITQSFMYFMMCFTYAVGIRVIYDGDKSSDVTFKGIISMMLGAVAVMNSAQYFPEFVKAKTAAGLLFNIIYRKPRTGDLMEGDRPEIRGNILFENVKFSYPQRPLQPIMKGLQWTALRGQTVALVGPSGSGKSTNIGMLERFYDVTGGVLRIDGQDIRNLSLYHLRTQMALVGQEPRLFAGSIRENVCLGLKDVPLEKINKALELANANRFLANLPAGIDTDVGEKGGQLSGGQKQRIAIARALVRDPKILLLDEATSALDSESERAVQEALDRAREGRTCITIAHRLSSIQNSDLIVYIDKGKVQEAGNHAQLMQKKGRYYKLIKKQDLAV
>BP:CBP00016
MSVEWKSALRLQIEALAKRNDLHRKSSEEEIKKRIVDMDRRIVKLRELVSTSANDAAIFYLECVCHADETERLLNRESSVEKEKKWRKMKRKPSSQIGPTESRTVSSLPSVSPPDVIQTINVSTLEAQDQMPQRPHWWDQFQIYRRTDLLRFSKQNDRRELWRTQKDFFLTCLGFMVGVGHTMRFPAKVYQHGGGVFFIPFFSLVFFGLPLVFLHLSLGQYTGQAANTAFSKLMPIGSGVGWALVVIAIPVAVYYNIIVAWAIHYFFQSAKGLLLGDELPWETCRDEWQLDNRCCNLHNLHSCFNSSNSITAPEAFFHSEVLSLSTFGDFALGPLQSHLVLSLAAAWLLVFFGVFKGLGSIAQTMNVTATVPYLLLSILLLRGISLPGANKGLSFFFTVDSTKLWKWQIWKSAAEQVFYELGIDAGPLISMAAFSRYRNNVYRDSVLLVIMDALTSILSGMVIFSFVGFIASESNSNVNDVLKHDPLYLSFTVYPGVTSFMYWGGLWATMFFGMLVMAALDAEFAWLEMIASAFMNHFSTKNKAVENRLLAFLCLVGFFFGLPLCAQGGIFVFHAIENLNANWNSFSLALLSVAIVCYVYGIDNYLTDISGMLRVPRIPISKAIRFRDKIVSILGPGGIYIKFSLCFICPVILTVLLVASVLGYQRISFAGRPIPIDYEIVAWVVMIGPLLVVPLVAFLQVRQIRNEGKLLKSLFDTSEWRENPDDLLEPKDAYMKQDSKYESPPNRRRTPTIFTHRENTYMYIDSRGPTVRSRVFPMGAPLDPYGWKLGRLRDHQQHIEEVESNYSEEGSTTNNSFMASTVKHNDDVELTLFGSPPAIMGDEDKNMVTKFSESMPVNYKCRNEQAAPVQSRREPRLGRMARKTRRKRSSPSASDPPVPTSPLPPPPRLYHCKSEPPMMRSEEEHGTPKIITPDGSCSISDSSDDSSDDNIRRATVIRRKTSDDDAFTQISTAESISITPLDFPRQRSLSSVAIYDQEQKNGRSKVLSQLKRPTPIVMPPK
>BP:CBP00024
FQSVHHHLNEEELKQVFGVSNKHEVPEYSLIETTRHPLKNGGLKMKFVAWNDTYHLNLRKNSRIVSPHIISVIRHGDDAVTTYDGLRDYNQCHYQGEVKSHGNMKAAISDCGALMGSLVMEDHFLVLQTLPKRVHHLQKERHLVYKRSAGLLTDTENKIREEITRLQEEQESFCDTSEQLDDPAMTIPAHLHFNYTIPTSAQLDSPFIFPNMDPITLEIGLFLDSKLFEHFEREYIQDAEQHLLEFSLALINNVHVLYQQDTLTPNLDIVIVRYEMWKTQPSSLSTGVHKNGQAQSLLDAFCRYQAHMNPGTDLTDMNHWDHGVLLTGYDIYHTTTSVAGVAPVARMCDPLFACSLVEGLHLGRSFVLAHEMGHNMGMVHDGVQNQCNKGCCLMSAVNGAGKTTWSDCSVREFNAFLLQLDESGRGNCLRDASPGLISTNHLSDTRLPGQRFTADQQCSYFWGRDYRVEIPNGKAMDDICRILWCGNSGSTISTAHPALEGSWCGHNKWCHKGHCTSWNFDLPPVPIDGQWSEWGGAEKGCPIQQCAVSGSITIQAQHRDCVNPAPNNGGRTCEGANIRGIVCGATSSNCLGFTREEFGNKICSSIKFDPHKPDQQLTGEGFEHSTQPCRVWCHLIGSELIRNKGQFPDGTPCGFDAYCVGGQCLALSCDNKALVEQQEDCPRLEGRSIHQWEDWSSWSECSVSCGPGGRQVRERKCSSGRKCQGVSEESRACEGVLRDCEEFGEWKDWGPCSEKCALGIQKRFRPCLTDQCASEHLQEKRPCDNEGCWTNWDEWSSCSQTCGGGRRYRLRKCLDFKCEGDDLEKESCNTQKCISQTWGDWLPCSVSCGIGFQIRERLCDGELCATANKQARTCNQQQCPSTFSLAVWSEWGEWTTCSATCGEGLQSRERSCRRGSCQESDAAQTRRCVNGPCDHTFLPWSEWTPCETCSSFDSRKRIAKCDGTTDNCQDKIDEETCDNACLREQHSFGPISPKRPKLITSNELRKAFGRPLLPIESITSSKWSEWGPCSVTCGSGRRVRTRDCQEENCPEQNIQHEECSLNSCLDLFIWSDWSSCSKSCGHDATQTRQKLCLFNNAECSSYAESRRCKNLPTCTSISSGNTISENSFDAPQWSEWSSWSACSCFSLTSTRRRFCQVADPTVQGFCAGSILEQIPCAPGNCSPSAGGWSSWSEWSSCSKDCGDTGHQIRNRMCSEPIPSNRGAYCSGYSFDQRPCVMDNVCGEEKVNGGWTDWTSWSECTDYCRNGHRSRTRFCANPKPSQGGAQCSGSDFELNPCFDPARCHLRDGGWSIWSDWSPCSASCGFGVQTRDRTCSSPEPRGGQLCTGLAHQTSLCDLPACDHESDGEWSAWNEWSGCMGNCGFGTRTRVRACVSPPASHGGQPCFGRSSEITECRQSESTCSSFITSSLLADGYFIETDQQQ
>BP:CBP00071
MGDEGYRGWIKLEIPCFEPERHMNNIIRCHTTKLEPALNSYNMRIHTKGQVQAVEEQDCEPFYESNYEIVSSHFSHHLIIAIQNYLKSLSMDRLMPFQLGNLVLHSSDFWSSELTCHLADIPLSAFFFGNIQGGTFINHWEVSFWEDTHRRNRLRQKNMQPTASDRQGLNQIRVEFEFDKVDFMTVHFKHKEGDFEVISKDFRKTRETVTMYYQITVRRTSIRRVIVDPVVNDTNGGDRIRIHFELNCPVLIRRAYKTEKQEAEAKHQVPHYRRFLVINRGRSANMYPTPKAITDSPVFTIEFDTSVSLEEVYRLISRLRIRTGVSIEFATIPSVDCLIWRENPYHRWTFHGSSHLSPTHFSAPIYRDFITTAFPRKHEVCGSREVDTNRERKFAITYLLECLISRGAVVKDQILLDDTIWHRFLEVILHYYTKDDKLCEAGLEDLVHMIDGRKRIGSLIKCFDRICQTRQKNSLVNGLTTEEMREGYQRVRKIIFTPTRVIYVAPETLMGNRVLRRYDHDGTRVLRITFRDDDNQKMRTNKTSTLLEKTVNTYLMNGITVAGRNFGYLGSSNSQMRDNGAYFMEKYSSSQCREYEKMCRMAPPITFNPKIQAARKNLGRFETIDNIPKMMARLGQCFTQSRLSGVNLDRCTYVTMYDLTGGKNIKGDEYTFSDGVGMMSMNFAQMVSQVMDFGKGVPSCFQFRFRGMKGVIAVEPFLDDLRQWSIENDIQEVSEDTAWGLNCVFRPSQIKFISKRHPRDQVEIVKYSSPVPVSLNKPFINILDQVSEMQSLECHRRVTNRIEELLDRQMLSFAQQMIDETFCRNRLKELPRRIDIDYLRTTWGFTLSSEPFFRSLIKASIKFSITKQLRKEQIPIPADLGRSMLGVVDETGRLQYGQIFVQYTRNLALKLPPKSASRSVLTGTVLLTKNPCIVAGDVRIFEAVDIPELHHMCDVVVFPQHGPRPHPDEMAGSDLDGDEYSIIWDQQLLLDRNEDPFDFTSEKQKSSFKEEEIDDLMREFYVKYLKLDSVGTISNSHLHNSDQYGLNARVCMDLAKKNCQAVDFTKSGQPPEELERKWRKDEVTGEMIPPERAERVPDYHMGNDHTPMYVSPRLCGKLFREFKAIDDVLKISEERDEQVEITIDETIMVDGYKEYMHSAREDLARYNAQLRSMMENYGIKTEGEVFSGCIVDMRNRISDKDQDDMSFYNTNQMIETKVTNLYKKYREHFFEEFEGAWEANTEGTSRGESDTNILQRHCRAPTQNMMKKAVAWYRACYEEARVTRENKKLSFAWLMYDVLAMVKQTKSLTSDDIRMGGSNPLYTMLDAHRSQYLLDNRSVFEDYIRFAPSKNQGEQVARALEIIRMYVETNPGLEEVMFVINEWARASKLFENQPIRNYHLSLLFILFATRQFSSVDGNAAAFFPKIDERGWREEKANGEFKQGLEFMEMKKSQMIVKFLEFLASRKFRKLPNVSFRTLRFSSIFMRGEWQIFHVAALKTYYNLLFNLRFEELPVSTDPTMTVRSIIRENEPFVVELPADADRTLVHRKLIEHTGVEEIYMRNMEKSVRGVDEQQKANTRYLVSTRGTLESMYKLRQLVAVKVPIKTYVTGQEISTQMARLCYEKIVKGHIS
>BP:CBP00094
FRIGHLEYENSNETKILEICMKTAGTRKQHTLISLPSCHNFNGLENAANLNYQYAVDLLIGAACDEETQTVSRLALRWHKLYLSSAPLSTKEKEGTTIALKPHSLAGTAEVILAVCKSMKWKEIGLIYSDETKYTAHAIYDMLAEKEEEDIKINVFLQTDGTMNTYTILHSARVLISFLSTSDLSRFVKTLKDKAFRPLEFSIIHVDCYKSETTEFYTHLDQKASEETNPISAARLRKLHRHVALLRNSHDDKGNMEEFATKHGMIVIFFVFPFPTLCFQPSHTLYKALILCDGLQLLSDYKPLSDNLTIVQQQPTLWEHVTNTEIHGYSGPMFIGSDGVRLPYYEMFMWRDGKTQHVASVRPRESEFCEKEKMSNESKNCYEITRTIPFGQLLDDLPPYSSDCGYDNNLCSDFHVFMIAAIVFSILLIPMAIAFYLQRKEHLIQQMPWRVPLDTINFDDSRNGRLLSVSRRVSTVSTARASYSSIFSANVSEHAHVNKQKVSIKRYVQRRPITFTRQEMEMLNQLKYMSHTNINPFTGICFNQGSELIVMWQFTARYSLEDLIFGKEQKFGRNFQSTFIKHIMHGINFIHNSSIKVHGTLYLSNCVVDSYWVVKLTDFGIKNILKERMHHKELAPNSSFDIDAIHYKYLQLAPEHLSSLLEKHEEPMGTVEGDIYQLAMVIYQILFYMKPFAERQEDIKAVKKLFFLELATLLSNQSTAPLHPKVPEGNSFTMRLLSIIQQCWLYKPAARPTLIKITDAVNREFGQDVKGTLIDQMIEMIDEYSANLEHIVAERTRELEQDMATTENLLYQLLPKSIADSIRSGKSVVPEQHSSVSLLVVDVCQFTKFCEAFIPVHILETLQELYSSFDYIVQKNKAFKVENVGDAYLICSGIPEMTACRHLREVSKISLKLQEFMKTFTVRHRPSHILQIKMGITSGAVAAGILGSIAPRIITGICKNLAYKILNNIQPGTIQLSELTANTMMEKFPSFIIEERGMIDVKGKGTCLTFWLTGEKDQMRRQSSRSSCISHSQIKFEIEEANKTNNQFL
>BP:CBP00176
MSNWDYIDEVDIIPKLPPNFDELRESKKWQERKEALEALLKVLTDSERLSTKVSYAELIGNVQTVLAKDANINCQALAAKCIAKFATGLRTKFSAFATPLLPVIFDKMKEKKPTLREPLVECAMEVGRTMPSLEAGQEDILAALAKPNPQIKQQTALFVAKQLDLVVPAKQPKGFIKAAVPVFGKLTGDADQDVREASLQALGAVQRIIGDKNVKSLLGDLSSDEGKMKKIGEYADKSAASYAEEQAKNAPPPSSSASAPSAAAASGSSGNVTSAAVTTAEPAAEADPWDFLDAFDVLSKMPEGFDTNIESKKWQERKEALEGLQQLLTANPKLDPKANYGALVERLQKVLEKDANINVAALAANCITGIANGLRTKFQAFAISVAPIVFEKFKEKKPTLRDPLVACIDAVVATSNLEALGEIVLTALGKPNPSIKTQTDLFLQRTFMKLNSQTMPKKTLKTLVPLLIKHSGDSDAEVRDASYAAMGAMMRAIGEKPSLQLLADIVTDNLKMGKIKEYHQKALAEAGPAEIAAMVQSMHKADAPPAAAAPPKKAAPPPKRQESEEEQVEEEEEPLKLPAEEKKKAAPTKENAENEPPVAPKTELLLNDNGEKAQRIKEEKQLKLVKWNFQTPTDEHIAQLQTLLGNQAKVSLMSQLFHKDFKQHLAALDTLIRLADTAPRSLLANSDLLLKWCTLRFFETNPAALIKVLELCRVLVELTRDTETPMSQEELTAFVPYLLLKTGEAKENMRTAVRDIINVLSDIVGPLKMTPMLLDALKSKNARQRSECLLVIESYISSSGISPLKSLTVEKIVAPFVGDKDVNVRNAAINVLVACFKFEGDQMWKAAGRMADKDKSLVEERIKRSGVKAGSGVATSPPNGGPKIVVPQQQQSVVRRPASRSRTREPEPEDDYQDQRAIANSTFTKGNSSSRYALRDDVFATAINRLADSTYVVTPPQPPSAWANNTFQMKRTNSSSSISSIDTSDQIQRSINNISSSLADVAQDAMYQVTYVLNQPEQRHLVDRKADMVFRASAAQLDMIIDEFKAGKDVTGTMDACSQMLFILMGGVEAEHGLEPLNASPETVKAIISSVLRCITQIGSTDAGYTMARSLNRLAMRLVYRVELSNLLCGLILAMIESIQLNSGITDLVSKLSSKWCDELEKRRAQLRASDIVDVFNQFYICTLTEQKMDITHIHIQVVDNYLERVILQQGDVVLDAARRLSSPHIHLTRMINKILQMMKEQNIDPIMPGTLDARAPDEEEAVVVRTGVQVCVNNILRDLKNVSTYNEQLNKLVQSSDKCRNEYSELVKNHALGEAVEELVSEQTIHGAPNFNKPDVVNAMTMTWKALDLLGPTRAETPTTPPQNLSRMDTTIVGTPLSRAEGAGTITRARGNIMRPKQRPTMSREQHEELRNRLQQAK
>BP:CBP00296
LHALETEKNVFSQFYAKKWPRQLRKPKNREISNFKHSEGAEFAAKSYFWDNNWDFDLPELPKPEQMIMPLPTSTPDVYDDFAFYRVLMEKEDKYILVACHANVHGFHRGDLRFLEINSRSRLNRLEGQSVIGSLFLGDIVAVTELARNSEAISPVRDVDVSLVTPDTSCYWIVSKMILYPRNVDKKSPVLFSIVNRMAAIKGENEPMNLNVDNWDMMHADSIYTGLTFRPETLEYHFSKDYQKKKINELVVSARTIRSYPGIYGTIFKFKEGDHREEFKKEMHLNTYTDESKELKRLAELEHEKNVFSQYYQKKSGNRRENHRGRKKPSSCKHHEAIEFAAKSNLWDNNWDKDLPMLPRSQEIIMPLPASAPAQTEVCGLYRVLMEKNDKYILIACHVNVHGYHRGDLRFLEVNSRSRLKGLSEQSVIGSLFLGDIVAVTELARNSNAQSSVRDVKVSSVTQETRCYWIVSNMILYPRILKPDVTFSFLKNRMAVVKGEDEPMRVNCDDWKTVAPDLIYTGMAFSPIKLDDNFSDDFQRKSKNLLISNVLKISSYPNAFGIIYSYEECSEQNEEFKIGTKAYSDTLEIHKYKRERIVETCSLMGFSAANTIFNGRFDCRAFHMYDVSKEGPTVRFRIENPRNRPTLGLWNNGNKILIGGPTGDTNGTIETVMCNSSHMGWLKIAARLTRECPKDFRFNGDLFVSQREPKDHYYLYDGYFQDMAPESNGRKIIETLYGGKPLELRTGDVGGEYFFPSTPEPIRLNVFQKEYVQMLLDGNPLVIGSSPFGCGKSMTIITAALEIYKRNAERNLVGKTHQLLITQSNFASVNLIEIARKTCNSGDEKLRNMKFMRFITDKNWNEQPDHGRTKFDMPFLMNKVFKQWAIGELDGNELMTHHTKSMIAHIIRNGTVTVDELCSAARRVFDKYGDCKIPFSGHLTEAFFILYEPDLIMTTADSSKSVCTLLDKKYETNKNECTTVQIDEASQLPEYTLLGLLKTYNKANFGLIGDIHQLPPFCMEELEGRLKEFGIGNTMERAIQNKLFPISNLRYVYRCHPQTTALLSELFYDGKLISGVTESQRNEFMIKRKDFWPNPSYPVMIINHMGTCQRMGTSAQNHSEKDLVSYMVQNLLDQRKYTLKPQDIGVISFYAAQTSLLTEQLRRSGVKCGTVDAFQGSEKEVIILCCTNEHATEFMQCKFRLNVALSRAKQATVIVGNLGYLRKAKYWNAIVKRVEAYGNL
>BP:CBP00327
MGALSQLRLLLWKNWLQQLRSPWFALFELVVPLILIGASFGLLIGFSDQFETTYDERRYAAWPVSGSAYDLIMPTNPNDSIKSAIVEPYFLFNSQLTCQFLNTYSTGANSYRMDIILAYAPMSAATTDKIMSIIQSRYSLTDLLSPVAPFIHNLYNITTIPTLNTNMSLKGFNTEGDMVSWMQGQFQSECDNPLLAGIVFDDSITKDLFNDNKRDFTYKIRLSNTHRRSRNAFGDDSYPWDTSVSFAIQYVSGPINPDDNDGGSPGYWQEGFMTVQRAVDVAITELITGSGPPISPLLDSYQVSRFPFPGYSTKIIEVGAYFMPVIVIFSFMTSVIYIVRAVVVEKEDRLKEYMRVMGLSQFINWIAHFLINYAKLTFAVIILTILLHFVALKSDMTLMFVFLMVYAFDVVYFAFLISSFMNSATSATLISVVFWMLLYFWYAFFSSIDQTNPYALGVRLINCLNPDIALNYGLQLLAAYETQAAGLKWNEMFNPPSPDNNLTFGHALAALVIDGIILVILTWYIEAVVPGGDGVPQKPWFFILPSYWFPYSGSKTVNSSDQYEHVEYASHVKLEQEPTDLTPTINVVNLTKTYGTSFFKKLFDCKFGKAGEKRAVSKLNLKMYPGQCTVLLGHNGAGKSTTFSMLTGVASPSSGSAYINNYDIRSSLPKIRRETGLCPQYNTLFGFMTVMEHLEFFAKLKERKWDPEEAREILARLRIDFKADFMAGALSGGQKRKLSLAIALIGGSEVVMLDEPTSGMDPGARHETWTLIQREKERRTILLTTHFMEEADLLGDRIAIMAHGQLECCGSPMYLKQQYGDGYHLTVVYSSTETPDVPKTTEIIREYILEANVFSYIGQEATYLLNAKHRPIFPKLFRELENHQRQCGITSFGVSITTMEEVFLKVGHLAEERYNYEHGIEDESSELIEKDDPMLQNLKAPVRLTGFALQMQHAKAMFFKRGIFFFRKWTQFLPQLAFPVAYLMLMVFTSQVIPSVKEQDPQTISLAPFSTKDKPGHVVSDSGNYVTMNGASTKLSNMVQNTVAALGVNQTVVDISSSVESFIMNQTNALGSRNFGLKYALGFVPSSIGIPGLPIPDLKTIRTYFNNFGLFTPALAITFTDSMLLSQAKNKQYTFTAINHPLPPSTQDTLKNTNRSDGAAFLIAYGLIVAFAVCVAGYSQFLITERKKKSKHMQLLSGIRPWMFWFTAFIWDAVWFVIRIICFDAIFYMFDITAYTHDFGIILILTLSFLLYGWTAIPFTYWFQFFFESAPKGFMMVTMYHILTGMIGSIAVPIIQQTSSMDAGYLWSIIFAWFFPTYNISQIATVTFQNENVRMACQKLDCNVPMFKSVVACCGTASQKLYVDNVLFVGNRKGILVYVIFLAVQGFIYWIMVFMRENDQFGKIFNLIKCWKKKDDHIWDITEGDKEEQRDVEDSDVIAEKSVVQRLANSNETALVSNNLVKWYGNFNAVKGVNFHVNSKDCFGLLGVNGAGKTSTFQMLTGENSISSGDAFVNGWSVKNNWREAGANVGYCPQYDAIIKEMSGEETLYMFARIRGIPEKEIPVKVQAVIHAIGIGMYAKRQIKTYSGGNKRRLSLGIAIVGLPDVLLLDEPTSGVDPKARRIIWNILNRLRDLGTALVLTSHSMDECEALCTELAIMVYGKFRCYGSCQHIKSRYGSGYTLLIRLKNRGDAEKTKSTIQQTFRGSKLKEEHILQHNYDIPREGDSWSRLFEKLETLSTSLNWDDYSLSQTTLEQVFIEFSRDAGQLDVDPYGDVPSLTGSGNKQNGYANRAMSVESITEMGTYF
>BP:CBP00332
SSSFTRIPKRDRTSPEKGEPSSKRSAPFTTPSSTTKIGRDSFAVMDTMEVQMNMFQLDITKMPPVIQRLHVDTLIITSKGKEINLNLGTVSTGGDVNSHNRRLAQHEIMRKFFEKKRSLFSSSSYHSLAYDTAACLYIPEGQYRGGEYEEVCLSQQDFAPEEWDIVSKISRRKDDSFIVRIKPAGAVYTQGDELFEPSNRYELTRIVEIVTSQKLNTTDFYQFGNATFPLRAHPNSEPDASSEIRSGFAKVARLTEGREGKHEMLMTVDTKLSPFYKPTSVIRCVLTKIQESRGGGGGGGGYGGRNDSRDSRGSFGGRSDSRDPRGYGGGYDRRSDSRDSRGGRDSYDSRRGGGDSEDFSSHEIDEIARACMESDKFLYSLESALKGLFAEAIHLKGSACTIRITGIKQCTANNTKFTKKDDKGEREISVSDYFYEEYNIKLKYPNLPLIVSKKMKYECFFPMEVLRIIPGQRIKVNKMSATVQSAMTGRNATMPRQHVDLVQRILQDSLKLERNKYMDAFGIELKSTRPVQLKAKILPPAEIRFKNLTYMPEIKRPGFKNPGKFVEPAHIYRVAVVSFDNAIDMRQAEDFCDRLFDYCRDQGIKCDRESKDWSIRELSSSDNVGIKEAMENWMKKKVDIFVGIARDKKPDVHDIMKYYEESVGMQTIQLCKQTVDKMMNPQGGRQTIDNVMRKFNLKCGGTNFYVDIPSNIRGRSICSNTETLHKKLLEKVQFIGFEISHGAARTLYDRSRNQMDGEPSIVGVSYSLKQSTQLGGFSYMQTQREYKIQKLDDAFPKCVKAYAEDAKTLPTRIVIYRVGAGEGDFKRIKEEIQEIRGTFEKIEKGYNPALVFIVAQKGSHTRIFPSRIDGNKAFEQNVPSGTCIDNVVTSFGYDEFILSSQTPLIGTVRPCKYTIIANDPAWSKNELIHLTYFRAFGHQVSYQPPSVPDVLYAAENLAKRGKNNYRVHQRYVSMQAIERRIISENADFVNENMQEQLASAIIDEMSDAMNGMTIPKRNFWA
>BP:CBP00396
RSRTKFRRDSRSRRQTPTSEMRSFVLLILLTSHLSAGSIDWSSLETPPQFTHGKNAETVFFKVEKSGMSDESAKNIPGNLLEQTIHCQAIGNPRPTYRWKKDGKTFLPSMFPEKVVQKPGEGSLVFSRLDETDAGLYQCEAENSNGTAVDRPVRVQETWIRHFKAAEPEVVVVEVGDPYQRNCSPPASNPNARVYWILMGKEPGHFETISSSHISSNEQGTLFFHYVNETDLKSDRYYTCTAENIELKDYKFGNQFSLQITNYKRRSSAPYWPNGPPPNTNTSEGENVSFDCTTYGKPTPKVTFYKNGVELGSQKDDRYMIEGTRLTIYDVKKGTYGKGDNAVYQCKSENKHGWLWTNFYLNLLAFKPQLLIDPGKEEVEAVIGKKVTLECKFFASPNAAVKWEAPMISGSKGNQIPADPHGVGRLVFSEVSASEEGEYECIGTNKYGQASGVITLKVRKPTTVKPFDRAEDVRMAGEEMRLPCDATSDSQLEVKHEWLVDGIPLPEERVNSGHYRIADDHSLIVANPTQDDSAKYKCVVSTKLDKVEKEIKIQFKDVPVAVHSAYVSNCDKNSLTAFIKFDHIESIHTIAPVKEFWVQYQMDSETEGSQWRTHPSPSAAHPNDQVTDQLRTTSGSATVSLQPFGKYVFRVLARNSVGDSATTTVKGICETPAKQPDKNPGEVAAKGTSPENLIVQWKPMAREEWNGAKFHYVVKYRPVDEDQRDGDWKEVAVEDPFADRVTINLDDDKDVKPFQPYEVQVQAVNSEGRTNVVPETVEGRTGEGVPSSIPSGLRVLEKSGTTVTLAWNGVDPATANGNFTGYKITYWVDEADQDVEEPEDDEEEKRKFRWKRSIRAKRQSGVRKTIVFGPSATQGTITDLKPATLNHAYIQVTNGAHEGPSSDTIDFQTDEGVPSPVRSLRAYPMNSKESDEKGVVVLVWKKPRQTNGKLARYEVEYCKTQNGKQVEKTCPRQQIDADAKEIRITGLENETPYRFILRAHTSAGEGDPNSSDATTLPETTAAGVDPGVPSLVENAIGDKYFNVSFRPAKYDDETRAPVGNTYEVQYKPQNGDEWETVKPSDDGLTVHVDGLSPGTKYDVRVAALQVDSDGGETTKTFSGISKITTTGTSPGERNLYFIILILLILLLLLIIICICCVVCRHRGQNYPVSQREREQGREPILGKPDYKTDDDEKRSLTGSKAESETDSMAQYGDTDPGVFTEDGSFIGQYVPQKSLMPAERPEKGSTSTFV
genometools-1.5.1/testdata/nGASP/protein_short.fas000066400000000000000000000566261211610345200221760ustar00rootroot00000000000000>BP:CBP00018
KMSNSTSPNAAATVGNIAYCYVLPCICVIGIVGNITNLVVLASRRLRAVSYMYLRALAVADLLCMLFVLVFVSTEYMAKNGSTINQYKIYQIYQCHLMLTLINWALGAGVYVVVALSLERYISIVFPMHFRTWNSPQRATRAIIIAFLIPAIFYIPYAVTRYKGKQRWDPIQNVTIYSMDDHPIYTTFYWQIYKWTREALLRFLPIIILTVLNLQIMFAFRKRQKMFQQLTKRKEQGTQKDDTLMYMLGGTVLMSLVCNIPAAINLLLIDETLKKRLDYQIFRAVANLLEITNHASQFYVFCACSTDYRTTFLQKFPCFKTDYANRDRLRSFVRRTQSVIQKQGSVEHTTNSKVWIMFKSKFQRDSLSHHSRKFSRHMPIEQDTVDIQLASGEQSTSGETCEADTLIKYGGSIQLCNDENNTTFL
>BP:CBP00022
CVICGQSTSLYNYGTISCSACSSFFRRTVLAKVPIQQCPHQDACYTPENRATHSECKYCRFHKCVDVGMINTQKYTNLTKLINQLSVLDKKRSYTCANMMLPPDFRLSSIFDYEHIKLIKKTPEVRFISHDWGCVHQLASMEFIKTFQFVKFLSLQDLQVFMKTAHFNHVIFASAMRSFGIRQGYLSFPDGSDVFPECIKRITCYNPEFLNRIRCKLMGRIIELNINPEEYLLLSAIILCNPAAVNLSVKGRTLISSYQKVYGSLLFQYCCQVNKKNGPLRFSELLTIFHAISQTHHDIGQFFLLFQMYQPNAQPIQLYQEVIDYM
>BP:CBP00025
MLAFESPIAESSYSRQKAKDLAKKFTPGELCTVCGDVASGIHYSVAACNGCKTFFRRVVLENRTYSCKNNGDCIIDKSMRCSCRHCRYKKCIIAGMDRAELSMERRRKRKKLNGIEGLEERYETTNPLINLLLHKEKLYQKLLHSSAMTIHTSLREALDMSQIAFNDTNNKYDDRMDPKYPTNFSYWRAKILTVLVEWAKSFEASFSHLQPEDQKRLFIHTAFSNLVLAEAFHTPEKYNDRIVFPDGLCGFRNVAQTVSSDGVSTKTYGLTPTVVAVINDVLVPIRRMRLTKVEYVLLQAIIFFDPDCLSLTKHGSQLIAAKRRRLLHALQDWLQQQNKHEAAGRFAEILLRICNVQKVAAFKRETLCTIETFELMQPHPFTMEISKSYPDFSYF
>BP:CBP00027
MVDLKQQLQWIDYLGVVAVWLCFFGTVLVISVTCILWCCVGKEDDPTVFAKYGFGPQPRVPSQRSKLEVEKDF
>BP:CBP00029
MTRLLNGIKVVELAGLAPVPHCGMMLADFGADVTVIDKKHPVVEQRMNRGKTMKEFDLRKPEDVKKVRELCKTSDVLLDPYRPGTLEKMGLDPLSLWNDNKGLIICRISGYGQTGRMKDEAGHDINYVAMSGMMPTFAGTEASRPWPPVNMLADFAGGGLSAAFGIVSAIHARHHNGGKGCVLDCSMTEGTAYLASFVQHYYDQTHLFTDKYAAFTGECPIYRTYKTKDGKFMAVGPLEPKFHQNMFEVLGIDGDDLFSDPDRITKELEATFLQKTRDEWSKIFEGKDCCVTPVLDIHEVGTYGQHVDRQNFSKSDKFGGTWIAKPSPRVQTIEELTAAATR
>BP:CBP00030
MAIVAAGVSKVLTTFQKTFKGLLPLIILVIYTLLGAWIFWMIEGENEREMLIEQQKERDDLIRRTVYKINQLQIKRQRRLMTAEEEYNRTAKVLTTFQETLGILPADMDKDIHWTFLGSIFYCMTVYTTIGYGNIVPGTGWGRFATIVYAFLGIPLTVLSLYCLGSLFAKGCKILWKFFLRSTRVVSKDLSEKISEAADNIEEGTTAVAPASKEENDDDDLLSFPISGLLLITVIWVIFCAVLFTFLEEWDFGTSLYFTLISFTTIGFGDILPSDYDFMPIVGVLLLIGLSLVSTVMTLIQQQIEALASGMKDNIDQEYARALNEAREDGEVDEHVDPEEDPETNKKSLNAVVSRMPLSKRALYYFLPASQKKQLEQQSEKKMGRKSIKVQTDSELLETLIREEILKAELNNEMHKFNGPRSSQQPRLIHSEIREKEVPIEVVRVEQYNHGGHDDYLEHDI
>BP:CBP00032
MLKVCMNVTDQCDCLAIECPIAYSNSVEEKEACYMEHCFISKRALDDVTLYKVTALYLVIFIIGVFGNTATCLVMRKHPMMKTHTSMYLINLAVSDLVTLCVGLPFEMMMNWHQYPWPFPDVICNLKALIAETTSSVSILTILVFAIERYVAVCHPLYLVKNQFFKRNMKSIIGLSWIVSILCATPFGIYHRADYLMRSWPGTDDKIPVISSKMCMVAVMFEPKLEPTFKVLFHFSAIAFFVVPLLTILVLYARIACKVSNNRTIQAGELDITEELQLKINAILCAIVSAFFICYLPFQFQRLLFFYLDNEVILVWINQYVYFISGFLFYLATIINPIAYNVASSRFRRAFKDILFYYCFGRKSNGYPRSSFSKYSL
>BP:CBP00040
MLHPIVLLLVASSAVYAARPRRALDGLDGSGFGFDKRALNSLDGAGFGFEKRALNSLDGQGFGFEKRALDGLDGMGFGFDKRALNSLDGAGFGFEKRALDGLDGAGFGFDKRALNSLDGQGFGFEKRALNSLDGAGFGFEKRALDGLDGAGFGFDKRALNSLDGAGFGFEKRALDGLDGAGFGFDKRALNSLDGQGFGFDKRSSFKHQSSKLRSVFRNLRGFNKQH
>BP:CBP00046
MSSLRCHVVVSALLFISIVPISQQVLNEHNQKLEWIVGKWRSEFSGKIFWPTVPTMTFGEELVINEAPIAKSANVQFLNFSARAWSHSTKDHFHDEWGFLTVDPVGNATLMTTGNNGFTTYETGTVSPNKLVLTLKDIGRISFSRDLPVEDLRRTFIRHDDRYMEQVIEMRTATHPKVGYLEHTRVVYTKLK
>BP:CBP00048
EGRGNKRTFFDITINGEPAGRIVFALYNHSCPSTAENFRALCTGELGQLYGHNASYQGSIFHRCIKGFMIQGGDLTHKNGQGGFSIYGRTFDDENLSLPHNKPFLLSMANRGPDTNGSQFFITTEKVPHLDGKHVVFGEVVKGFDVVKRIEKVETEEEDMPVQRVTIAHCGEMVRKSDVMASDKKKKQDEQEPVGCKMDDEPKTVNWLMRRSRSRTPEDSKKSKKDRERGGNRGDRRRHDRQRDRYGRERRSRSRSGSRDRHRDRERNRVPDERRSGKRPVSIPISKADCEVNKYERELGDCQEILVITNKDGIKVRGRGKLTFMGSRDRSTTPPHWKREESKKLTLEEHQKRQEEMEERKRLRAEREKEDVERKEREEKEAMERAAQRELERQEEEEARKRSRSNSPQSPRVKQELMSQRQESKAESNSSRSSSSSSGSSSSSDSDS
>BP:CBP00060
MEQIVESLQYFGFLGSLVLNSFLLFLLHTRAHRNFGKYRILMIVFCLFAIVYSLVEVLTLPVMFVKGRSLCVCSNGPLRLYRPIGVPLTSIYCGSFGMCISLLTLHFFYRYVAVCKPDKMRYFNGKHIFLTFSPSLFIFVTWSMTTYWPMAPDEMREIHYHDVLMKTFQTNSFEASFVAMISIFLQDPQTSTWLPSQLLSCAYMSFLMSVCFSVIVFCGYQALKQMRSHASHMSSKTKELNKQLFMTLGIQTLLPVFTMYIPVGCLMILPMFGIELGAAANNAAAFLGLYPALDPLVAILLIKDFRNFVFCKSVTSTYASAVSNTAPPSKILQ
>BP:CBP00061
MDADKLIEYIQYGGFVSSQLINALLLYLLCFQASNNFGRYRILMIVFSIFAMIYSLIEVVTFPVMMCKGRSLCVCSNGPFTLYRSIGVPLLSIYCGSFGMCISLLALHFFYRYIAICKPEKLYYFEGKQIISTLSPCFIIFVIWSLLVYFFMDVTEEKERIYHDVLFRSYNVDSHKVSFISMLYKSPATETSPEHWNFDQLVPFFGCCFIMDSCFFAIIYYGSKAFLQMKSCGTEMSKKTKELNRQLFLTLGIQTLLPLITMYVPVGCFIILPIFGVELGVEANKTGAFLGIYPALDPLIAILLIKDFRNYVFCQKRTLAKVSTTSGIASKITSTFQA
>BP:CBP00078
MLRAVVRLSKTGAKAQRRFLNLQEFQSKEILEKHGCSVQKFVVAANRKEAEEKWMSFGNHEYVVKAQILAGGRGKGKFIDGTKGIGGVYITKEKKEALDAIDEMIGKRLVTKQTTEDGVRVDKVMIAEGVDIKRETYLAVLMDRESNGPVVVASPDGGMDIEAVAEKTPDRIFKTPIDIQMGMTEAQSLKIAKELQFEGKLLGAAATEIKRLYDLFIAVDATQVEINPLVETADGRVFCVDAKMNFDDSASYRQKDIFAYETFEEHDPREVDAHQFNLNYIGMDGNIACLVNGAGLAMATMDLIKLHGGEPANFLDVGGAVTEDAVFNAVRIITSDPRVKCVLINIFGGIVNCATIANGVVNAVNKIGLKVPMVVRLEGTNVDAAKQIMKKSGLKILTANNLDEAAAKAVESLPK
>BP:CBP00081
MLTDGVVDYTKEGSILTAEQRQFYEKNGYLLIRNCVPQYELNRFRQRFQDICEKKVKAPDNMTVMKDISIAKSEFKDGEKAITKIQDFADDPVLFEYCKYPGVVDVVKDLIGNPKSTVMAMHTMLINKPPDNGKLTSRHPMHQDLQYFPFRPADFICCAWTAMEKINRANGCLVVVPGTHKGVLLPHEYPKWEGGVNKAYHGIQDYDPSNPRIHVEMEAGDTVFFHPILIHGSGANRTEGFRKAISCHYANDDICRYVNVEGTTQENLAEEIIEIAKKRLTKYGLDPNTVTLDFADIWRVRAREVNGTRSNL
>BP:CBP00086
MTATMDVDNLMSRLLNVGMSGGRLTTSVNEQELMTCCDITKSVFASQASLLEVEPPIIVCGDIHGQYSDLLRIFDKNGFPPDVNFLFLGDYVDRGRQNIETICLMFSFKIKYPENFFMLRGNHEPAINRVYGFYEECNRRYKSTRLWSTFQDTFNWMPLCGLIGSRILCMHGGLSPHLQSLDQLRQLPRPQDPPNPSIGIDLLWADPDQWVKGWQANTRGVSYVFGQDVVNDLCAKLELDLVARAHQVVQDGYEFFASKRMVTIFSAPHYCGQFDNSAATMKVDENMVCTFVMYKPTPKALRRG
>BP:CBP00091
MDASTEAGVYKKELYSRLMASINATMCHEQPDGILYCPNHTGGPVWVRNVYPPIQELQPKVLIVVVVFVLCFIVGVCGNSSIITIIRGVVEDRRKRMKRHGDNAILYIGALCVCDFVMSLSLPPAILDSVIGFWIFGTTMCKVHHVFGSVGRIASTFLITAMSFDRYVAVCYPHQHRLRSRTFVVSTIVCLSAIAFVLLLPMLTYASAKEMVLHELKAHESANITRVRVFKCSDMMPGPIFYWFTSTTFILGYVVPLILIVYFNLKLINKLYAHKRVLPRSAIPVRRVVVYTVLIAAVYFVCWTPYWFSVLYAIIMSLLGKPTTNSEWVLFAIYCVHLLPYFGSSSNWILYGLLNTQLQMKNDIGDDGQSIMTTNGVPDLPRRSTSRGICDGASTSRSLPAASNPQWQVDPMLTRGNSDTSMVFYQDTEQTHL
>BP:CBP00095
QLSVPQYKEFLEVQSNLTKNLFTDYDPTISPVYTWIDVDQPIGYDSQAPKRWNYTVFLYYLKLVEVQEPEEKVSVVMELMEYWYDARLSWNTSLYQNTTSFYARQDNVWSPTLTVFGVNDIMDFRDQDNRMVAIDNFGFLWDYISVRISANCQMDVSRFPFDTQTCQIRFCLPIFYRVQVEILNEIYEGIMDENIFKTMGNSEWKLINLTNRVEVLKYNDNMGNMDLAIFEITIRRNPLYYIYMIVFPSFVINFVSIVGVFLNGADKMSRLNVGLTNIMTMTFILGVMADKIPRTGNIPLLGIYIIINLVIITQLEIFLGPPLEYTSAIILELMTCANFLVMVGFWFDDGS
>BP:CBP00102
MTSFVDNQSLTNYLIIDYDTDNEEDDDDDYDVFPTANEFISNVPKKNRKRARKCVKKGFICCFKTIKYTFLCCRCVIVWRCLWLFVILLIGLFLFTCFYYDDARKIFQFVYIVIETSIHFLKPTKPCRSINRPSSVLHFLQNYSFHPQAFFIYKKGCVRSVKGVLYRLQMKLLLISTVVLIASVSAIGNLYSGGGKQCTECPPGYDYYSRQHDRGWCMKFFPGNVTFFEAEKVCRCQGGATLSGIENTKELKKLSRKINEYFDENGIKSGGIWVGAYRRKDCRVPKSEKKAECTKEFQYQWTDRSTFGRDMWISHWTEGAPHNNVVGNHSEFCVQLQVTDPTKTALNEHFDNRICVHRDGSSAFETEGFICGRPPKCKGGYNGGYSGGDGVIVIGAARPTQKP
>BP:CBP00103
MDLFSIVKSVSFWFVSTVDCLDSQWQYSEYISSTDMVQSFSERFLPGNWVYMLFAIPLWYGTWWAVLCYIYFYYTDITDAYMKETIEYHYGIPIKDSSYIIVYFQPTGADGKPHPDPKIFFAIGCMWYMIISSMFSVFYFGIRCYWQIRKTINQSAAVSATTKNLQTQLFHALVVQTFIPLVLMYIPIGILFFFPMVIWELPFTTEFVGYTIALYPAIDPLPNMIIIKCYRHAIQGFFMKIFGRGKRGETQHSLNTDAQSGS
>BP:CBP00104
LQHIYQSLCTMISLILNSVLIYLILYKSPKKLGDYKWLMIYTAVFEQIYTVVDLLTEPTAYSYGYSFVVFRRYNATWTDSNKSQVLIVTWCGLFGSSMAVFGVHFVYRFASVHPKNITKTLYNLNIEDISYISAVFYVDDPNNGSIHLSWGSWIALVQFSTMVGSSMFCVSFLGYLCYSELSSQLSMTSSQSQVANSLKKQLYFALVGQTVIPITFMYLPVCVFVFGPVFMVEIGVISTYLTHAVTLYPVLNPLPNMFIIKSYRNTI
>BP:CBP00121
MDTAFSPNEVKIMEKAFDSYRRNTCIRFEKREGQTDYLNIVKGYGCYSQVGRTGGKQEISLGRGCFFHEIIVHELMHSVGFWHEHSRADRDDHIKILWDNILPGMKSQFDKISAVLQDLQGENYDYKSIMHYDSTAFSRNGRNTIETVEDGFTQVIGTNQDLSELDIINKLYSCKAKKKEKMRVTTEEPRRLIPQVGEKKPVDSGEKCVDHFADCPHFAQYCTRASFFFVMKSYCPFTCKHCPGDRKIKKSG
>BP:CBP00122
MESATNSSSEESIFHEQTRKLFRLCDAQNIGLIGKADLDVLVDLIPPDDLQKISRFIGEQKVNEPAFCRILKAIVSQALQQEMAKIEAQIPAFDKNQYLQESSLEDEMRAIEQNRSYLDDPLTKILKKELEEIQRYENSQIQNEHAINNTMIKKPLYRPIQPEPTIPKVSSLAEELNAIDKKVPQRKEEEELTQPDRIFKVVFVGDSAVGKTCFLHRFCHNRFKPLFNATIGVDFTVKTMKIAPNRAIAMQLWDTAGQERFRSITKQYFRKADGVVLMFDVTSEQSFLNVRNWIDSVRAGVDEATVMCLVGNKVDLFGSDIARSGVYRAAEKLALEFKIPFYETSAYTGYGIENCMRQMAESLQRREDNHLEEALKLDINSNYKKRSWCCI
>BP:CBP00124
MGITTLPPSQLRPELEWLFPKEVTTTSSAVLQRNSAAEIPLNFLAEHSLALIAALFLIVLTVALLAVLVQYHCQKGSSSGSAGAISPKSFSTSPSQWTTCSTVSSTYSTQSLLQLIGSGLRQSLQGLLLPSEAVVLETIVGKGYFGNVYRGRMRDPAGRLIPVAVKTLKGERARDIAHIEKFLREGVVMKHLDHPHVLSLLGISISPAGNPWVVLPFMEGGDLKTYIADPNRALCVLELLDFAHQVAQGMSYLAAQHFVHRDLAARNCMISAERIVKVADFGLAVDLLDKESYIDESETGPARLPLKWLAPESLRDRRVFSSATDVWSFGVLMWELLTRAASPYGEVSNAKVRHYLETGMRLPQPTHCPDIIYDLMQCCWRATPEDRPDFVFLSHRLRALLQENSPDPFTRRFRPNAEQFLLPVLPGRLFTNYFAAQMHA
>BP:CBP00144
VICLLYFSLSAVAIAQQPQFTCPNNANPLVANSGTNLFCTSAGSNTDCPTGSICTTAANAAGILICCSQSTNVNPVCPNSAISQPSNIGYVECQFNNPTNCISGYQCVQSANLANTFICCSTSASVGSCPSDFTPAVGTNGGTISCNPSASTCPSGSSCMQSTLNTAFICCRSANSQRICANNQNALITNGALELCTTPGTQCSSTGYTCQLSVLLATYVCCGQGSTGSSIGCADGRPVYQQRVGETYTCDITSSLNSCPSGYDCALSDDSFVNVCCLTGSTPIPENLSCPTGWNPFRNEVDNAVRTCTAVLDTSCPIGFSCAPSNQVSQFLCCRLASSLVCINGKTLLVNGAPKLCTPTTYSQCPYNYSCQQSVNPTVTVCCSNT
>BP:CBP00179
KSKKLEQKPDWDTLDGIGFEFEENKPIVMDPRFYDMLKLPQCDLTKDKVPSKINIKEAMNQFQQCVRPIVERWRGDIKSMNTKFSETRLCEAAFKDMDVIPMTNLHETKWAILPHCVRENPVEQTCIFTFIERGEYHDWGIGLHCDMLVFAGTLGYSSSYKHHQVKLRTKICTNAPEHKFFGADPIIEPNRQLYTAFGKYFPFAIGKKPGFTKFRVLPNQNQKTRKYEFQDVTTIPFTYFLWDILGLKQIDIAWIDIEGGEFEFLDQFYRGGPMDEKGIVICQFNLEVHSKFNPPGAQVFHDFVFRILDDKRYIFTKVLNTDVGIHRMFFVNVEDEKCVRKFLQ
>BP:CBP00188
MSFAQSFYADQKKVEQQPRQQENASPLTTAAIPAHTPIAEDPLTPAQIREAIRIYRSVLSTNSAPASPVRAPAAPPIAERPEVHSNYYGGGPTDIPQSYLLNYATSSPQQPASAPATQAPEPLFTEQQLIAQLQALQVQQQQVAEPVCEVPVVQQQQQPKAAPNKAPVLQKMYDDEESGYCFNRKGRDEDGPEEIPEAHVATPTSAPAANYSIPAPQQQVNYSPAPVANNYSKVVCGPSEYIGMANDNKFIYDAQKALPVSYAQNNSYTLVNPTAQAPIAQPRFEETDDQGVTTTEDVTQVPASPAVTSRFRGMIRNAQTPVQAPPAPIVVERVAEPVNTTPSHNYNNYGAFMPVNQMSMESEYQLPVLNDLASCIEHY
>BP:CBP00192
SKFWKIKQLFIFILVALAANFNYGFSTTYINTSVDQFKNFLNTSLSHRHVVMTETKYDIIWNLFLNCWFVGYFVGVWFSPIFIGFLIGNSTAFLASILQCLAILWYCPELLIVSRFITSICMAVTYQSCILFLQLVTRTSGKHKPTFFECSPTHLRGSFSFLSEVSYSSMTMVGSFLGQDYILGSHLFWLCFFVVPFCLFFTLALFLLPETPKFLLISKDSEEQATESVKYYHGVDSDAKQVLEEIRKEAECENDPLEDSTTFRKMKELFTEPHLRMALILSVSALTNTVGLWALLLSSTFFLENANVESEVAEWSTTAMSLAYVSGTVTGGIIIEKVGRRTLLLLFTFLNNLALLAFVFFAKIRILIDPMKYGCLGALIIYGYTYGTGVGPISWFISSELVPQKHRSIAQSVAYAINTLMVVISTFTVLPLYSVIGSYAFVILYSIPSFISMLILFRYLPETKRREIHDIVNELKNK
>BP:CBP00210
MANIPSFIDRLLSVNDTANPSLTHCIKEAEIDDVIQMCTQIILEQATMVEVQAPIAVCGDIHGQYVDLLRIFNRCNFPPDQNYLFLGDYVDRGRQQLEVICLLMAYKIRYRNTFFILRGNHECASINRTYGFYDECKRRYSLSLYNAFQDLFNGLPLCAMISGRIFCMHGGLSPQLESWKQLAAIKRPFDPPNKSIAMDLLWADPENNMNGWAKNSRGVSYIFGADVVKDFTDKMNIDLIARGHQVVQDGYEFFAGKRLVTIFSAPKYCGEFDNNAGVMIVDERLIISFDILKPAIREVTIRARGTSKNASTRSMLVSSRGPKSKMG
>BP:CBP00211
LEHPVFLKDILHTITYFAIPIHIFGTYCILFKTPKTMGSVKWIMLNFHVWCMCLDYGLTVLTVPIVIFPALGGYPFGILTEWGVSAEFQTYLIVTLIPVVSAAVITIFENRYFLVFGHNSKWRRFRVLLSIFNYLYAATWCLPSFMIIPEQNMARKVALEMLGPNVSDYIRHFPIFMMSLEITYLTLPCLLIVLTFATEVILFVAIIKKGMTELAKTARFSKNTLKMQKNFLKAVYIQVSMYMTSIQLPLAYFFVSIFFKIYNQSANNFCFVVFSLNGLSSTILMLWVHTPYRDFCYKLLRIEKWRKKIGQANSQDNVVSVAPTA
>BP:CBP00214
SKEKVPEEDLNLPYFHGALMNQDADQLLVNDGDFMVTMKLQIDINKLVVYLAVRLKKGIRRYEIKRLPGSAKLGSRSKETIDKLINSLKTDVLEIKGEKIVLKRAIAKGKFQLMHKDVIFKKKIGAGAYGTVYRGRLVKTNEVIAVKKLDPESADEDGLAEMMKEARVMQLYDHPNIVKFHGFILDDLPYLLVLEFCNGGSVEDRLRDKGSRLTVPTRVHYTYMAACGMDYLHKKGCIHRDIASRNCLIHRGIVKMADFGMCRATTVYKMDMSKPCNVRWLAPEVWDNGETRFNTDVYAFGIMMWEFFEIPYATPYAEMKAGQVKRKTRTGYRLPPPAAMPKEVGDIMKECCQPAADKRPNAEKLKEMLEEVYKKQNPTETTHNSS
>BP:CBP00223
SRAAEMAGGNSEEGKGMLLRNGDDKVRHPSPQRGTPDSSSTQGHQFIDQIVTINVSGMRFQTFESTLARYPHSLLGDPTKRQHYFVPDTNEYFFDRHRTTFESILYIYQSGGRVKRPEIVPIDIFLREMRFYEMGDELLEEFWIAEGYEKPKEVMMPTNKTQRKIWELMEYPDSSLSARIIAFISIFVIALSIISFCWETVPSDNDDKVINMTTGELIDELDEKHYSPFFWIELMCILWFTIELILRFISCPCKVTFVTSILNIIDFVAIAPFFVNFFLADTNKSNSSMSFAVLRVLRLVRVFRVFKLSRHSVGLQILGKTFRSSVQEFCLLIFFMAIALVLFASGMYFAEQGEPNSKFTSIPASFWFVLVTMTTVGYGDLVPLSPFGKVVGSMCALIGVLTLALPVPIIVANFKHFYRQENRLASMKSTTKGDHEDDDVA
>BP:CBP00226
MHPRGKFLAGHLSAFYIAPATTAALISRNHNDWAHLQLLRRTPSSDAGTMNQVHFGRTSARRRNAMILENNSGDGDDEDRPKEEIFRKIESYQFSRFQTSVINSAKLWASRNRSLKLINNFLPGFLANLRLALFHLVLIFATVAYIIAGAYLFTKIEHQAELDRYQSYHSIYKNFVQNLIYDSSGNRSVSEVENMIDAFTSINFRAFKDGLKPTDFLVPQETSRWSMISAIFFTTTVLTSIGYGNLIPISTGGKIFCVGYAIIPLTLVTIADLAKFVADMLIMDPTEDPKTGRQLLVLVFLLGYMTISACVYTILEPMWSFLDSFYFCLVSLLTVGFGDLYPSGTVEYMLCSIVFIFIGLILTTLAVDVSGSVGIAKMHSIGRGFDAMKMLNVLR
>BP:CBP00231
NAMLIYLILKRTPLLMKSYSVYLMNFAFFDFATCIISFFSCQKVIFSGWSLIYIFHGPCKHVSSWFCYFCHCFECHTLAHSQWILLGSFMYRYDVLKGSTPTVQKMWRNSGAFYSMSLCFLVVYLFDISDSEELLRIMTDLHPEYHYDDGTGNISMFAPITFISIMYMTTPCVPIYCAILYFRHHTLKILNNPSINLSPAAKISHQKLVRALTVQAGIPIFWLVASGIYSLAQFGFISGPIPENITFRLMDCIPMVSPIVTIAFIQPYRDGLLHLFHKGSSIFIPNTIGSSVVDVS
>BP:CBP00234
MGMSTNKCGARWTSWLTKNMLLLMTMAGIVMGVIIGGVLRNLEPSQEIVKYVGFPGELFMNMLKAMVLPLIAASIVSGLSQLDGKTSGRLGSRAVMYYVITTTHAVILGIIVVSIIHPGDPTIKQKMGIEEGATANESAAQKFLDLFRNAFPENIMRATFSQYQTHYVNVTNSNGIQKTELKTGYVDGMNVLGIIVFCIVMGLVISKIGEEAKPLANLFHALDVVITRMVMIIMWLGPIGIPSLIAQKMLEVSDLWQTARVLGLFVFTVILGLGIQAFITLPLIYVIGTRHNPYKFLSGLGQAIMTALGTSSSAASLPVTFRCLNKLGIDPRVTKFVLPVGAMVNMDGTALYEATASIFIAQMNGLDLSAGQIITVSITATLASIGAASIPSAGLVTMLIVLTALGLPANDISLILAVDWVLDRLRTSVNVIGDALGCGFVHHICADHLNADVAEAEKAHAFVEAHGVNFDELEKEIEQENNNHKTIQHV
>BP:CBP00238
MLKPLFGKADKTPADVVKNLRDALLVIDRQSATQNERKVEKAIEETAKMLALAKTFIYGSDANEPNNEQVTQLAQEVYNANILPMLIKHLHKFEFECKKDVASVFNNLLRRQIGTRSPTVEYLAARPEILITLLLGYEQPDIALTCGSMLREAVRHEHLARIVLYSEYFQRFFVFVQSDVFDIATDAFSTFKDLMTKHKNMCAEYLDNNYDRFFTAYAALTNSENYVTRRQSLKLLGELLLDRHNFSTMNKYITSPENLKTVMELLRDKRRNIQYEAFHVFKIFVANPNKPRPITDILNRNRDKLVEFLTAFHNDRTNDEQFNDEKAYLIKQIQELRV
>BP:CBP00252
MTSFLKLVVVGMILVGVAHGASVATADAKGTNCTLTDGFQALSCIMRLSDFAEKIDELDMDDKNEVKEFKKSCDSLEKCFSMLTCGKQQDAETKQAVSSIRNYCDAVVYMAADFGECSEKLEKNKSECFENWDPFPDAIDEEKDEKKKEELKKNACKNYFGKDQCLKKLITETCSEKEWQGFRDHFISISSVLLTCDFKDV
>BP:CBP00254
SILNWTIFYAINKLQSFNLAFGYLSANQALADALHSTTFLLYFCPMVLLDQPLMKEFSHYCGFILLFCYELSVKIHLAISINRFCAVWAPYKYKHIFSDRNTKIYIFGIWVFTGSVAVLFYEKFCHFFYDDQIHFLTFTNNSFCGYIGWYGDFLKNAAIVAAVVSIDIFTILKVRQMSKKVVSNISNQSQNNLSHREVRFLKQTVTQGAVFMLELLTYFFVPLYFENKWIVFFGTSFAWVAVHAVDGMVVVLLNSEVRSFLIGQRSKSHGPSTNRATA
>BP:CBP00262
CVASSQYLGDPEVYKLVFHILTCIEIPIHIYGAWCIIFKTSALMRSVKYLLLWSHFLSAQLDLLFSFISIPYMLLLSFSGYALGIFDQPRWEVYICLIVTAFVVTSILGIYENRFFVLYGYRENPSWCRIRKPFIAFNYFLAVIFIAPMYFLDPDQEIGFQNLATVLPCSPESAIGDRRIYVAFTDSLLPYIGLSLEALLLACEIVVFLVITISKLKSRDGQNCSQLSVKTKKLQKNFIKALFAKSSIPITFLLTPVLYVLVTMQLTYRNQNLSNVCVMLASSHGLFSTIVMVLVHQPYREATWNNLYFCFRCKR
>BP:CBP00263
PDSESWLDSPETVLIFSHIMALLVTPLHLFGAYCILKKTPSTMHSVKLTLLNFHFWNVLVDLMLNVFAIPFPLFPSASGFLLGLFSYWGIRQTVQLWILITSLCFICVSTTMIFENRFRLLNHKNKHWKKFQPFWVVGNILFVFIFLIPTMLQVPDQDQARQMVFSKLPCTPEHSIDDRRIFVGAIDLNFTFFSLTIEAILLFIEIATFFFIVFFKLVHRNKRKMSLMSNRTHGLQTKFVIALCLQTISPCLLISIPVEYLALATYLNYYNTSLNRFSMILFGLHGVCSTLTMIFVHQPYREATVDNFYWLMMCRQNSKKISV
>BP:CBP00264
MATPSPSTSNDSSDFEKICTICGRPAFVRYYGAVACGPCKMFFRRMVIEKLTYKCKKIKICYITEPKPLKCKSCRFKRCVEVGMKLPPTNCTVLELKNREDDELVRLFGFLKIRDDQRMETYMNFYTTQNPSLEDILDGVKPVKMDVERSMITPVEWSFTAILSVINHFRSFDFEQLESRDKKLIFQFNTFKSNILCGAVRACKEHREKMVTPSGHDIFPDILVTKFNASAELLNRICCQVVARLMELKVTDEEFVLLNIIFFCNSADAHSDKAKSILAARQRFYVSALFKYCQLTYQNNAPSRLNELLSVYHIVQKNASEMQYIGIMIHGFIPNFPIRKLVSDTYML
>BP:CBP00268
RNYIFPLCIGSLVLGTYLYSFIFKEARYTVILDGKEVNFTGVEDFIQPYVNIVSDFFVASNYKMMSCGIRKSMSQLTVNTMCLLHDEERFLQENHSLNETWVTIRSCQNNQAFRKPSEDLLNNPETIRFAFIRDPIERFVSLYLDKCVKEQNCWACKNDMRCVVKEIYEALKNLQNHRDWKPIPTYMDWHAAPLSWNCNFDKDLSKWTLLMMGADAEERKSSILQLGNIMKRRGVSENVVQMVQEQSLAGETAHSTHKSTRRLEAERQVREDPVVRDYLHKIYFFDYLVFPFNRERLDAKYQTDFWKVPE
>BP:CBP00283
MECNDTRLFDTSNNVTYFIIEQFYRFRYLYSNVHPYLSFVLCILGLAANLIHICVLTRPRMRHSSVHTVLVCIAFSDMGTMSSYLLYISRFEFLPEKEGYPYIWALFLKCHAMVSIALHAITLYLVVLMAFIRLSAMKLTTSRWLDHTRALTSAIFIALFVFIMCVPTLLAHQIDETTRGVTLTGMYYRYSVGFSTLMLQNGCFLMKGNLWLTGIFLKALPCLLLLTFTIALIHRLRENNEKRKILIKEERAKKRGDFTTYMLLLMVTVFLFTELPQGIMAIMNALFTTQFHQMVYLNLADVLDLLSLINCYVAFLVYSFTSSRYRQTLFSLLPLTRISYSGISTRQGTLRSHPNQPAAPKTLVQRANSVEVASVRSPLVDKSAATTRPNSAQPTEF
>BP:CBP00304
TLYYVITHKFDLWPDAYECSGNYTVPTARWPKFGIYLWTSGSIFLTLYILCFIAICKIKSSAPVYQLMFFIAIFDIIAIIVGSLILGYLTFHGIFFCQCPLFFFIIGSLAMFTWLFNCVSCIILAIERCSEVNPKFFLSFLFGKKVFRVVKTLVFIYGINGLMFSKPVIFSPEYTSFIYDPMIGKDIILQGVVMCFFHSAAACIYEYMAYFTPTLYVIVAGEVVYQLACSCLSVVYLTLNRTIRNTVVKMVIPKSIRAKYGWHIGVEEHLAVEQAAESNGIALVNASGMPVKFDNFFVN
>BP:CBP00305
MTMNLIPRPIIGSYFMISGIALIIIYLPCFVVMIKSKCRAPSYQLMMLLAIFDLTSLMVNSVTTGILGIMGASFCHYPLFVFTAGSIGLGSWMGGCVVCILLAVDRCVEINSNFPLAIIFHKQVFRLVMLVICIYWVYASFFTNPLLFTAQYSSWFFDPFIGKEGDLYHNIPHTINNLLVSASSTPLYIYLCYHLIFKFGYSTSMWLYRSKQQIIIQAVILCFFHATAACIYVYMQFFPTPSWLIIIGQLAWQYSNGCVCLAYWTLNRTIRNAAIRMMLSKRIRKRFKLHMGIDEQIAAERDGEVASVSNVMNLMSGTAKVAPFLCE
>BP:CBP00306
ALQMSLYHVFTNSFTLWDEAYDCPQNLTNLKFERPVLGSFFLFFGVMFIVINSVCTGIFDILGISFCHSPLIIFCLGAIAGGSWMAGCLACVMLAIERCVEINPQFPLEFLFRKSVFPFVRILMGMYTLYAYLFVKGLTFSSQFSCWFFDPLIGKDPLLYHSYPHTINNFAVGIATTALYIYISYRLICKFGYTTSMWLYKTKRQILFQAITLCIFHTAAAFIYEYMQFIEVTPVIIIASQFIWQWSNGAVCLAYLIFNRTIRNLVVKIMVPKSVRKRFGWYIGADEHIALEEAGGPTLSAGLGTVNAIGGVIKFDNFM
>BP:CBP00307
MSDLQMSMAYMLTHSFTLYPEIYKCPGNTSAMRTKRPILGTYFLASGLIFILLYTPCFIVMVRSKCRVPAFQVMLILAVFDLLSLSVNSVITGLLDIMGFSFSHFPVFIFCAGAIGKGSWMGGCVACILLAVDRCVEVNAKFRLGFLFKKKVFRVVMGLMVLYWVYSCGFTKPLLFKAEYSSWFFDPKIGKEPYLYHSIDHTINNLVVSLATTSLYIYLCYHLIYKIGYSTSMWLYRSKQQIIIQAVILCSFHAIAAYIYVYMQFFYSPPWLIIIGQLAWQWSNGCFCVAYLTLNQAIRNAVVRMLVPKKLRERFDLHIGIDEHLTSVKQITQINTVSI
>BP:CBP00308
IDMSLFRLLSDFFDLPAEYQCPDCLQNDYFVRLRLGIYFLLSGILLILLYIPCFIVMLKSKSRNPSFRVMIILAVFDIINLAVNSVSTGIFSILGASFCQYPRLIFIVGAIGNGTWMAGCAMCILLAMDRCVEIHSKFFLAFLFHKKAFRVVLGVVGMYWMYSVWFTKPLLFSARYSSWFFDPKINRDPNIYRNVPHTINNLVVSASTTGLYIYMCIFLLYKKGKSTNSMWMSRNKNQVILQAIIICSFHALAAYIYVYMQLFYSPPLLIILGQLTWQWSNGCFCVVYLTINKSIRSSVKKMLL
>BP:CBP00309
FQMSTFYLFTNDFALWDEAYGCPKNLTTIRFERPVLGGFFAFSGVLFIILYILCLIAMLKRDLIRHPAYKIMVCLAMFDIPSLFIACIFTGYFGYFGIYFCDYPRLIFVLGSFAFGLWMGCTFSCSALALCRISGVNHNLEIGYIFKSHCIYYLIVIIFALPSYGIFFTEPLIFRTEYMSWFFDPGTGLFDSSNYHNISQVINNAAESVITTILYAYLVFYIIRNLTNVILSAHDVRVQRQVILQATIICFFHSLASSVYVYMQFFYSPAWLVIFAQISWHICTG
>BP:CBP00311
LSSPEFLKITFHVITIIAIPIHTFGFYCIIRKTPKHMDSVKMLLFNLHCWCVLLDIAITVFGIPYIFLPALAGYQLGFVDAPALVFYLVVTFLTGVSTSIFVIYENRYHILFGRNCSWRFFRKYCIVLSYCLVPLYFVAPIFSVPEQETARKIVWESLSCAPEIPEGHFDFFVISLNIRLMAITIAIAEGVPFFQILIFFSLNFYNLILARQPSGLSRKTTQMQNRLVLALFVQSSVTLVLFVVPVNSIILSVYTGYQNQILNNFIFLAFASHGIASTVIMVVVHNPYRRFLRSLSLQSSRKFTIMVINSEIRF
>BP:CBP00312
IKMIQCPTDDTYLASPEFLSFALHTLTCISLPLHVLGFYCILEKTPKTMGSVKLLLLNIHTCGFFLDILITILGVPYGIFPAMAGYGLGFVDLPGLCLYLIVMTINAISVGIFLIFENRFFILFAENSWWRHFRKPVFVASYAVSVIYFLPAQFLIPEQEGARKFVWEMLPELPQEIYDAPVFVLAIDFHYVVIPVFIMSNLLIAESGCFIILIYGNMNERTKKLSLSRHTIKMQRKFLRALNIQTAIPLLYLMLPMGYLVTSRIFNLYFQSANNLCFIIIGLHGLFSTIIMLYIHAPYREVCKKVFHCK
>BP:CBP00316
MYINWVHHYVPKISFVLSLIANPLFIYLVITCKKTLFGSYRYLLSFFATFNLLASFSDLATPVCVFNYRYVFVTFVADGPFSWKSKYGEQLLYYRCGIVSGTYGILNVHFVFRYLTLKRNAFVNKHFMPYGLILAIMYVAAHIAIWAAVTGLCLHSAQEMRDYIREPFKALHNESFDDITFVAGLFSETTAEIAERSWTGIVLLTVIASYSIVLYIVLGYKIVTGINTKSSTMSKQTAQMQKQLFKALTIQTIIPICVSFMPCSLSFYGAALRIDFVNWVYWGAAVAVSFFPFLDPVAVTLFLPTLRKRL
>BP:CBP00325
MWRLAVFLSLAAFFVHDVLGKGDPELKMTTPQIIERWGYPAMIYSVTTDDGYILEMHRIPFGKTNVTWPNGKRPVIFLQHGLLCASSDWVLNLPDQSAGFIFADAGFDVWMGNMRGNTYSMKHKNLKPSHSAFWDWSWDEMATYDLNAMINHVLEVTGQESVYYMGHSQGTLTMFSHLSKDDGSFAKKIKKFFALAPIGSVKHIKGFLAFFANYFSLEFDGWFDIFGAGEFLPNNWAMKLAAKDICGGLQIESDLCDNVLFLIAGPESDQWNQTRVPVYATHDPAGTSTQNIVHWMQMVHHGGVPAYDWGTKENKKKYGQANPPEYDFTAIKGTQIYLYWSDADWLGDKVDITDYLLTHLDPAVIAQNNHLPDYNHLDFTWGLRAPQDIYHPAVELCTNDYLGK
>BP:CBP00334
MTDIEKQTEIREKKGRNVMRELKIQKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRTFGIRRNEKIAVHCTVRGPKAEEILEKGLKVKEYELYKENFSDTGNFGFGVQEHIDLGIKYDPGIGIYGMDFYVVLNRNGVRVSKRRRAPGRIGPSHRVDKEETIKWFQQKYDGIILPPKPKTKKNVYRRR
>BP:CBP00335
MFFVLIVFTFLTWLVVRQYQKVSRLPPGPVSLPLIGNLPQIVYYLYTTGGVVSTLDFFRKRYGNIFTLWVGPIPHVSIADYETSHEVFVKNANKYADKFHSPIFREMRKDIGILTANGDHWQEMRRFALFTFRNMGVGKDLMETRIMEELNASFSENMGLISANGESWAEMRRFALLAFRTMGVGRDLMEERILAELDARCAEIDAEAVNGKTIVHTSEFFDLTVGSVINSVLIGKRFDSHNKDEFLKLKGLLDSADELFTMFELTVPVWLLKKCFPERYARIVEVQEEIINFVSREANERYEKVKSGEYTINADDPQDFVEAYLAKIEEEKEKGTTNFYTMQCLKHVIG
>BP:CBP00336
MDGTFFQKDLAPFVKYSLNKKRRWETKGDLNSLKNLQSSYRDMNVVVSDRVWLDMDPYWCFISHINYYHNYFLQFPIRHTYQLDTDNNYRCLSSDSVYGQPLKSLLPENRSPKKSDTLQSATFDMPKVAYHILTPPENYEKLRNEDFCPGSSDRFLKHRSIKHWRRCKKMTEALLAIRYEDFDYLNDPIYFIDNEWDIDFGTPSKL
>BP:CBP00337
DSLLSSPEFVSRTFHFLTFITVPVNMLGAYCILFKTPKSMSSVKLVILNLHLCSMTLDIVFSVLIQPVVFFPAVAAYSNGVLKVFGKCAGIELYFAGTMFAGTVVTDHCTPSRKKPACTPEKPGLLFQKSITVVSMSIVSVMENRFYLLFVINTLWRKIRPFVLFFNYFVACTFLIPLLLQAPNQIIAFEIIQKKFPDIPFSSYSDSLFIFSVDSSYVFLSVFLTGALTVSQINLYCFLIILNMRKLSSNGKMSQRTYHLQRRFLIAIGIQIFTPLIVLFVPATYLDFCFIFEYYNQAVNNICMILISFHGWVSAIVMMFIHEPYRKFCL
>BP:CBP00341
MHRSLQILCILAVFTSLAYSQGSRDENQSAKRNDFSRDIMSFGKRSADAADMYDRRIMAFGKRQPNFDRDIMSFGKRSAPSDFYRDIMSFGKRSASMYDRDIMSFGKRSAAMEYDRPIMAFGKRAEDYERQIMSFGRRK
>BP:CBP00342
MDQFFTKLVALLLILLQIGAILATPIPEAAPEDVETRRELEKRGGARAFYGFYNAGNSKRDQVALPYYLYEKRGGGRAFNHNANLFRYEKRGGGRAFAGSWSPYLERLCDYERSGYPIYFSDNSYY
>BP:CBP00343
VSKPIADAVLRYGKDHPVFRNKLLIPIGRGLVRFTSRMRMKRLGLGEPITHAPVSEAAALEQASDFVQQLVLFSYSVGVFASYYFYTKLTTPESLKIEEYNDFKEQQERAIKELRLQIESLEQRLAAQQKRNFFSQLGFSKDEAPNGPSESSKEASGASESSKPSKPSESLKERFQRISSLPIDAAASLILDDEEYLIVRRDTSVGIELSVNFAARGERLRYRIPSSKLRESLAQLALKEAACHVIGS
>BP:CBP00344
MWELVSAELFSASNLFLLGFMISALAVSSVFTLSHITPWVRRTRDEYLTPEIVYRSSPEKEFSKLLESERDAPKRYTPSRCYLSVVIPAMNESERIEIMLEDCCDYLEKRSKKDLEFSYEIIVVDDGSTDDTADVVVGISQRRQNIRVLKLKANRGKGGAVKMGVLHSSGKLILFADADGATKFEDFEVLEKEMLRAAGGEPFDESFPAVVVGSRAHLEAASVAERSFFRTVLMHGFHALVWLFAVRTVRDTQCGFKLFSRSIAARIFPVLHVERWAFDAELIFLCEKWTVPVSEVSVRWKEIEGSKITPIWSWLQMGRDLVLIWFRYNIGIWTDSQP
>BP:CBP00345
TAISSSPEAPQTMSEVQKVVDDDEDDEWGDFGEAVVAAAPIQNTNPPPTVPPLQMASNDEDDDDWGAFDQARPSTDRSDGPSQLAHQQSLEDWGAFEETQKTSTTNDDNEDDEWQAEFSSASTASTVIPAENLKTLEEMLEDDAFWDDGYCEAMELEEISENDSSSSSPLDIPALFDTEELKELTNEFEDLEKAKYSKLWLSLRVIEEAISQEQKTSTSPAVDSPSVPAVDFDWDTSGLTNPMNRASKQLHEMSQKCRRFVCRATTDCINLLKCNLLLASFNPYNTKTMQIRSVVNALTHRFPNLWKPFSRNFGYKEAYQCSAIIDVDFLGSNGVATAYTSTLQQDLEQFGLTNGSTKSNSNGSSILENLMSRANDSSSTTGRYRTPEVLSLDARQLLERLPDLQYLQSEVLMFPVGTNLPH
>BP:CBP00346
YFLLFLAFFIFKINGGSNECYSCSGVCHNEPCNCQMGSCESGQCFIEKKPTEIPGSMKITKGCLRRTSRIHHGCEYDHFSDHILCVCQGHYCNDKVVMNTTRQKYTRTVTCRECSEKQPDCGSTCEGHWCHEDMSTGASGCGYGPPALPFYYRGPELFYYRSKVCITLSRGAGKPRRHCVCSTKMCNTVYNYQFNQYNIKDREKEGSTRARSLTLSATDYTLPLQTCYNCETNTQDATSMSHTTNCRSNRCLGHYCTYAAQRHTSKSSMGRSNMVHAVSELQGCMNVSDKSHIQLGCSRKWISDEYEEIHCACKGSLCNSDSLTATA
>BP:CBP00347
MDGVYRLFCGCCGLAGGDPEPPYSQLRHDSVTPIRDPPLQYLNQQQQHQQYPPYALQEQGFVNPVHEFSNFDPRPSFRTRDEADGPNYQHSDSGTPRSGLEDEVEDENREREQLDNIVESTQHSIIAVGQTDVDGVIMMDTQYREKAYKQKVQKMATASSTTQLYEPVHEFQFEPTQTPIQVPLRYDEMSATIDKSPIERMPFACPDFQQMRLARTMGVKNAQFLVEHPDPRHAGKSPAMSSSAKHKITAVLDQVHEGVVGIEVEPRDLIVSMDF
>BP:CBP00349
FTWFDGWEYPAYVSHSISLVLIPLNIFGGYCILFQIPKKMEASKWVMINVHFWSSFLDLLVSFLLTPYIFFPAMCGITNGLLSWLHVPIIVQVFLAQWKCILGVGVSLVIIFESRHNVDRFVITRKSSRILFYALNCVYGIFFMTPTYFSLPDQEKAKLELLKIVPCPTPVYFEPNVFVLMDHQGRWFIQLQCTTFFCVLIAQGAFSVSRTVYFLTAYNSKMSEMIQVAIPVFIVILPILYCGCAIEWYWYYQSFSNTAIICVSFHGMSSTIAIF
>BP:CBP00368
LLIFVILVSTTFSDFETDLQRIKEEYTCYPNCTFNYTEINSETAKLFPSSCYSICGLITINENTDVSFATLEKLFHRMYTLKGGLRIENTTLRSFSFLQLHGFLSFFCFPFGTRIVNNTELVDAEALENIVHVSNTSHECKMEILDNSKLDASRLCESQFHNSVQNIEVLDNGKDCGCSSGKITPRNLPDFKNCIVLFDGLVLTNMSYNSNLKSLSKIANIRGNVEIAYTNFKDLSFLKSLSKIRGNTFENLETVILDIHDNPKMKRLGLDSVSVSEPTQYVDTLEQDWVPTMNLENLHPDFCITYQEAVSLSYVRFKNLEAKFCETEWKTDMKSCKFKSLRELESDCIIIYGNVLISSGDEEYVEKLEDTVYIFGSLTIQNSELENIRFLKML
>BP:CBP00383
MWPDTLYWIFIGIIDILAIILNAILIYFALYRTPKMVRVYTTLIINLAFTDCCSAFLNFFVQQRMIPSGFTIGYISNGWCKLIGYRFCFLSHNLMAHFIVHSNYSLVLSFAYRYYILRKPEPRRKTLLIVLFFTYLPSFLQLVLYQFAESDPSEIVRLLQPYHPTYNFTGLTVSGVADIRSVYALYKILQMTVMTVPIFSTILFLRNKIINRLLYRGINISINTKSLHSQLLMALTYQALLPTLYSINVLMYVLEQFGVYSTAFFENFLMSGLVLIPFFSPFTSFFFFTPYKRILLGMVLKKIDKRPAATSETGPGSFPI
>BP:CBP00387
GEDEANRKKFPCEICGKQFNAHYNLTRHMPVHTGERPFVCKVCGKAFRQASTLCRHKIIHTDSKPHKCKTCGKCFNRSSTLNTHVRIHQGFKPFVCEVCGKGFHQNGNYKNHRLTHEETKKYSCTICKRAFHQSYNLAFHMFTHEEHKPFTCHVCSKGFCRNFDLKKHLRKMH
>BP:CBP00391
MTINYHKEIMTSHPWTFFLLLFKWKGSIWKAVYMETIIFLIFYGIISVIYKTALGESSQRTFEAVVRYFDKRLSYIPLEFVLGFFVTTVVNRWTKLYQTIGFIDNVGLMANCYIRGATEKARIYRRNIMRYCELVQVLVFRDMSMRTRRRFPTMETIVAAGFMNKHELELYNSYDTKYNSKLGTKYWIPANWALCMTNKARKDGYIESDYFKAQMEAEIRTWRTNIEWVCNYDWVPLPLMYPQLVCLAVNLYFLVSIVARQLVVEKHKIVDEVDVYFPVMTFLQFIFYMGWLKVIDVMLNPFGEDDDDFETNALIDRNITMGLMIADNPMTTPDLRKDPFYDEVDVPLLYSEESSHVPNHHYHGSASEVRLEHRGSGPVTMMPHSQSAANLKRIMSFKSSEDDEEKTNPFSMSHDDARMRNWREVSLDSSFLSDLNENKEWKLPTSQQKF
>BP:CBP00394
MDSDDGFDYLFKIVLVGDMGVGKTCVVQRFRSGNFVDRQGTTIGVDFTMKTLNVDGKRVKLQIWDTGGQERFRTITQSYYRSANGIVLCYDITCKQSFGSLQRWIDDVSKFAAPNVAKLLIGTKCDLEDQRAIETEEAELLQRANGMFEMLETSAKNDINVDNAFLELATILKRQYDQGVVEQGASGTFQLGSGGTTSINSPWQRCCQY
>BP:CBP00414
SSSSTSSTLPISHVRRHEDVPTPSAPPSKRSNIQPQESYEPKTWLQQQMEQEQQRKLAEEKKKQSTSTTGDDEEDMLQDVLSQPRGPHKRRFNFVMVSNITFAIPEGYDVDSIEYLGGGSFGNVIKTSAVCRDGHRRWVTIKKMREPFFDPHHARRIFREIKLLQLMRHDNIICALDIYTPDEENDFRDVYVVTEFAGRSLYRILKQQRDYGRRVLTEEHVKFIIYQIIRALKYIHSANIIHRDLKPGNLALTDDSDLMILDFGLARSLEKKDTSLTQYVQTRWYRSPEVIYWKIDSYTNLADMWSVGCIAAELLTGDPLFPGDDVNAQYQRITQLCGSPDEELLAKIENDNSSAMKAVIQSYKVYKRRNFREVFAAYSPSADFIDLIEKLLVLDPEKRITVEEAIQHPYLAEFSLPADEPRADHIFDLDDTQARTRFQWRDAVWTEIMNYQRIMQSPIIPGETDR
genometools-1.5.1/testdata/nGASP/resIII.gff3000066400000000000000000004447771211610345200205070ustar00rootroot00000000000000##gff-version   3
##sequence-region   III 1000001 2000000
III	gt csa	gene	1001124	1001929	.	+	.	ID=gene1
III	gt csa	mRNA	1001124	1001415	.	+	.	ID=mRNA1;Parent=gene1;Target=CESAC87R 1 276 +,CEESA72R 1 286 +
III	gt csa	exon	1001124	1001415	0.961	+	.	Parent=mRNA1
III	gt csa	mRNA	1001583	1001929	.	+	.	ID=mRNA2;Parent=gene1;Target=yk1113e09.3 16 235 -,yk1113e09.5 16 273 +
III	gt csa	exon	1001583	1001711	1	+	.	Parent=mRNA2
III	gt csa	exon	1001801	1001929	0.961	+	.	Parent=mRNA2
###
III	gt csa	gene	1002693	1006177	.	+	.	ID=gene2
III	gt csa	mRNA	1002693	1006177	.	+	.	ID=mRNA3;Parent=gene2;Target=yk1191d02.5 1 502 +,yk741d1.5 1 337 +,yk119f11.5 1 360 +,yk263f3.5 1 360 +,yk1191d02.3 1 625 -,yk263f3.3 1 300 -,yk741d1.3 1 300 -,yk735g1.3 1 197 -
III	gt csa	exon	1002693	1002823	0.985	+	.	Parent=mRNA3
III	gt csa	exon	1003572	1003690	1	+	.	Parent=mRNA3
III	gt csa	exon	1003754	1003876	1	+	.	Parent=mRNA3
III	gt csa	exon	1003923	1004051	1	+	.	Parent=mRNA3
III	gt csa	exon	1004874	1004992	1	+	.	Parent=mRNA3
III	gt csa	exon	1005039	1005141	1	+	.	Parent=mRNA3
III	gt csa	exon	1005251	1005368	1	+	.	Parent=mRNA3
III	gt csa	exon	1005890	1006050	1	+	.	Parent=mRNA3
III	gt csa	exon	1006097	1006177	0.975	+	.	Parent=mRNA3
###
III	gt csa	gene	1010540	1011351	.	+	.	ID=gene3
III	gt csa	mRNA	1010540	1011351	.	+	.	ID=mRNA4;Parent=gene3;Target=yk708f5.5 1 316 +,WP 1 199 +,yk708f5.3 1 212 -
III	gt csa	exon	1010540	1010705	0.994	+	.	Parent=mRNA4
III	gt csa	exon	1010749	1010997	1	+	.	Parent=mRNA4
III	gt csa	exon	1011163	1011351	1	+	.	Parent=mRNA4
###
III	gt csa	gene	1020968	1021291	.	+	.	ID=gene4
III	gt csa	mRNA	1020968	1021291	.	+	.	ID=mRNA5;Parent=gene4;Target=WP 1 87 +
III	gt csa	exon	1020968	1021129	1	+	.	Parent=mRNA5
III	gt csa	exon	1021193	1021291	1	+	.	Parent=mRNA5
###
III	gt csa	gene	1023281	1023580	.	+	.	ID=gene5
III	gt csa	mRNA	1023281	1023580	.	+	.	ID=mRNA6;Parent=gene5;Target=yk720d6.3 1 300 +
III	gt csa	exon	1023281	1023580	0.997	+	.	Parent=mRNA6
###
III	gt csa	gene	1023729	1024566	.	-	.	ID=gene6
III	gt csa	mRNA	1023729	1024566	.	-	.	ID=mRNA7;Parent=gene6;Target=yk720d6.5 1 335 +
III	gt csa	exon	1023729	1023771	1	-	.	Parent=mRNA7
III	gt csa	exon	1023816	1023910	0.953	-	.	Parent=mRNA7
III	gt csa	exon	1024370	1024566	0.964	-	.	Parent=mRNA7
###
III	gt csa	gene	1026929	1028347	.	-	.	ID=gene7
III	gt csa	mRNA	1026929	1028347	.	-	.	ID=mRNA8;Parent=gene7;Target=WP 1 192 +,yk1105f03.3 41 639 -,yk1105f03.5 41 543 +
III	gt csa	exon	1026929	1027102	1	-	.	Parent=mRNA8
III	gt csa	exon	1027314	1027467	1	-	.	Parent=mRNA8
III	gt csa	exon	1027515	1027609	1	-	.	Parent=mRNA8
III	gt csa	exon	1028167	1028347	1	-	.	Parent=mRNA8
###
III	gt csa	gene	1028790	1037200	.	-	.	ID=gene8
III	gt csa	mRNA	1028790	1031062	.	-	.	ID=mRNA9;Parent=gene8;Target=WP 1 227 +
III	gt csa	exon	1028790	1028969	1	-	.	Parent=mRNA9
III	gt csa	exon	1029692	1029845	1	-	.	Parent=mRNA9
III	gt csa	exon	1029891	1029985	1	-	.	Parent=mRNA9
III	gt csa	exon	1030811	1031062	0.933	-	.	Parent=mRNA9
III	gt csa	mRNA	1031337	1037200	.	-	.	ID=mRNA10;Parent=gene8;Target=yk1677a04.3 1 666 -,yk1707c12.3 1 704 -,RP 1 422 +,yk1677a04.5 1 607 +,yk1707c12.5 23 589 +,yk623f3.5 1 360 +
III	gt csa	exon	1031337	1031862	0.994	-	.	Parent=mRNA10
III	gt csa	exon	1032740	1032809	1	-	.	Parent=mRNA10
III	gt csa	exon	1033111	1033262	1	-	.	Parent=mRNA10
III	gt csa	exon	1034167	1034457	1	-	.	Parent=mRNA10
III	gt csa	exon	1034874	1035024	0.898	-	.	Parent=mRNA10
III	gt csa	exon	1036294	1036442	1	-	.	Parent=mRNA10
III	gt csa	exon	1036772	1036888	1	-	.	Parent=mRNA10
III	gt csa	exon	1036937	1037082	1	-	.	Parent=mRNA10
III	gt csa	exon	1037168	1037200	1	-	.	Parent=mRNA10
III	gt csa	mRNA	1031337	1037200	.	-	.	ID=mRNA11;Parent=gene8;Target=yk1677a04.3 1 666 -,yk1707c12.3 1 704 -,BP 1 433 +,yk1707c12.5 23 589 +,yk623f3.5 1 360 +
III	gt csa	exon	1031337	1031862	0.994	-	.	Parent=mRNA11
III	gt csa	exon	1032740	1032809	1	-	.	Parent=mRNA11
III	gt csa	exon	1033111	1033262	0.924	-	.	Parent=mRNA11
III	gt csa	exon	1034167	1034457	0.894	-	.	Parent=mRNA11
III	gt csa	exon	1034642	1034679	0.215	-	.	Parent=mRNA11
III	gt csa	exon	1034874	1035024	0.985	-	.	Parent=mRNA11
III	gt csa	exon	1036294	1036442	1	-	.	Parent=mRNA11
III	gt csa	exon	1036772	1036888	1	-	.	Parent=mRNA11
III	gt csa	exon	1036937	1037082	1	-	.	Parent=mRNA11
III	gt csa	exon	1037168	1037200	1	-	.	Parent=mRNA11
###
III	gt csa	gene	1031495	1031674	.	+	.	ID=gene9
III	gt csa	mRNA	1031495	1031674	.	+	.	ID=mRNA12;Parent=gene9;Target=yk623f3.3 1 180 +
III	gt csa	exon	1031495	1031674	1	+	.	Parent=mRNA12
###
III	gt csa	gene	1040341	1043441	.	+	.	ID=gene10
III	gt csa	mRNA	1040341	1041938	.	+	.	ID=mRNA13;Parent=gene10;Target=yk645b4.5 36 382 +
III	gt csa	exon	1040341	1040503	0.939	+	.	Parent=mRNA13
III	gt csa	exon	1041759	1041938	1	+	.	Parent=mRNA13
III	gt csa	mRNA	1042042	1043441	.	+	.	ID=mRNA14;Parent=gene10;Target=yk64a11.5 1 360 +
III	gt csa	exon	1042042	1042093	1	+	.	Parent=mRNA14
III	gt csa	exon	1043134	1043441	0.984	+	.	Parent=mRNA14
###
III	gt csa	gene	1046267	1046555	.	+	.	ID=gene11
III	gt csa	mRNA	1046267	1046555	.	+	.	ID=mRNA15;Parent=gene11;Target=yk1391c06.3 1 287 +
III	gt csa	exon	1046267	1046555	0.955	+	.	Parent=mRNA15
###
III	gt csa	gene	1046557	1059998	.	-	.	ID=gene12
III	gt csa	mRNA	1046557	1059998	.	-	.	ID=mRNA16;Parent=gene12;Target=WP 1 1158 +
III	gt csa	exon	1046557	1046617	1	-	.	Parent=mRNA16
III	gt csa	exon	1046663	1046761	1	-	.	Parent=mRNA16
III	gt csa	exon	1047490	1047637	1	-	.	Parent=mRNA16
III	gt csa	exon	1048507	1048990	1	-	.	Parent=mRNA16
III	gt csa	exon	1049960	1050356	1	-	.	Parent=mRNA16
III	gt csa	exon	1051280	1051470	1	-	.	Parent=mRNA16
III	gt csa	exon	1051832	1052354	1	-	.	Parent=mRNA16
III	gt csa	exon	1052641	1052770	1	-	.	Parent=mRNA16
III	gt csa	exon	1053104	1053230	1	-	.	Parent=mRNA16
III	gt csa	exon	1053750	1053789	1	-	.	Parent=mRNA16
III	gt csa	exon	1054974	1055025	1	-	.	Parent=mRNA16
III	gt csa	exon	1055100	1055216	1	-	.	Parent=mRNA16
III	gt csa	exon	1056330	1056534	1	-	.	Parent=mRNA16
III	gt csa	exon	1057718	1058011	1	-	.	Parent=mRNA16
III	gt csa	exon	1058066	1058194	1	-	.	Parent=mRNA16
III	gt csa	exon	1058517	1058636	1	-	.	Parent=mRNA16
III	gt csa	exon	1058794	1058967	1	-	.	Parent=mRNA16
III	gt csa	exon	1059816	1059998	1	-	.	Parent=mRNA16
III	gt csa	mRNA	1052040	1052771	.	-	.	ID=mRNA17;Parent=gene12;Target=CK580775 1 445 +,CK575409 1 430 +,CK575411 1 416 +,CK583013 1 411 +,CK575408 1 354 +,CK575413 1 347 +,CK583019 1 334 +
III	gt csa	exon	1052040	1052354	0.997	-	.	Parent=mRNA17
III	gt csa	exon	1052641	1052771	1	-	.	Parent=mRNA17
III	gt csa	mRNA	1052047	1053234	.	-	.	ID=mRNA18;Parent=gene12;Target=yk1391c06.5 1 569 +
III	gt csa	exon	1052047	1052354	1	-	.	Parent=mRNA18
III	gt csa	exon	1052641	1052770	0.992	-	.	Parent=mRNA18
III	gt csa	exon	1053104	1053234	1	-	.	Parent=mRNA18
III	gt csa	mRNA	1056259	1059192	.	-	.	ID=mRNA19;Parent=gene12;Target=BP 75 367 +
III	gt csa	exon	1056259	1056534	0.894	-	.	Parent=mRNA19
III	gt csa	exon	1057718	1058011	0.954	-	.	Parent=mRNA19
III	gt csa	exon	1058517	1058636	0.856	-	.	Parent=mRNA19
III	gt csa	exon	1058794	1058967	0.818	-	.	Parent=mRNA19
III	gt csa	exon	1059181	1059192	0.273	-	.	Parent=mRNA19
III	gt csa	mRNA	1056259	1059224	.	-	.	ID=mRNA20;Parent=gene12;Target=RP 72 369 +
III	gt csa	exon	1056259	1056534	0.853	-	.	Parent=mRNA20
III	gt csa	exon	1057718	1058011	0.969	-	.	Parent=mRNA20
III	gt csa	exon	1058517	1058636	0.927	-	.	Parent=mRNA20
III	gt csa	exon	1058794	1058967	0.833	-	.	Parent=mRNA20
III	gt csa	exon	1059198	1059224	0.22	-	.	Parent=mRNA20
###
III	gt csa	gene	1062769	1063139	.	+	.	ID=gene13
III	gt csa	mRNA	1062769	1063139	.	+	.	ID=mRNA21;Parent=gene13;Target=yk681f11.5 1 370 +,CEESV83F 1 359 +,yk117f1.3 1 332 +,yk1170b11.3 1 181 +,yk1376a02.3 1 215 +,yk1704g11.3 1 255 +,yk117c1.3 1 323 +,yk617a4.3 1 300 +,yk621h1.3 1 299 +,yk659c10.3 1 297 +,yk602e8.3 1 297 +,yk652b11.3 1 297 +,yk675h9.3 1 296 +,yk337c2.3 1 295 +,yk658b12.3 1 294 +,yk393b4.3 1 180 +,yk394b5.3 1 295 +,yk363h2.3 1 292 +,yk525g8.3 1 291 +,yk656g8.3 1 291 +,yk255h9.3 1 289 +,yk572f4.3 1 288 +,yk592b8.3 1 286 +
III	gt csa	exon	1062769	1063139	0.978	+	.	Parent=mRNA21
###
III	gt csa	gene	1062771	1076543	.	-	.	ID=gene14
III	gt csa	mRNA	1062771	1076543	.	-	.	ID=mRNA22;Parent=gene14;Target=U79157 1 1736 +,yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,WP 1 497 +,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk117f1.5 1 360 +,CK579359 1 613 +,yk1101a09.5 23 632 +,yk1034a11.5 23 628 +,yk363h2.5 1 360 +,yk1172f12.5 23 612 +,yk1053h12.5 22 598 +,yk1339g04.5 24 597 +,yk1169g11.5 23 596 +,yk1170b11.5 23 594 +,yk1120d08.5 23 590 +,yk1286b11.5 23 589 +,yk1120g02.5 23 587 +,yk1058c11.5 23 586 +,yk1254h08.5 23 584 +,yk1722g08.5 23 543 +,yk804f05.5 23 542 +,yk1096a09.5 23 539 +,yk1516e02.5 23 528 +,yk1652g01.5 23 510 +,yk1401h02.5 23 497 +,yk1061h02.5 23 497 +,yk1369c04.5 23 488 +,yk505f9.5 1 368 +,yk1141g04.5 23 448 +,yk820f07.5 23 446 +,yk1741a10.5 24 446 +,yk1026h07.5 1 370 +,yk656g8.5 1 360 +,yk216b5.5 1 360 +,yk568d7.5 1 360 +,yk659c10.5 1 379 +,yk592b8.5 1 360 +,yk658b12.5 1 360 +,yk269b4.5 1 376 +,yk525g8.5 1 377 +,yk482b6.5 1 360 +,yk569b4.5 1 360 +,yk675h9.5 1 360 +,yk456c8.5 1 377 +,yk393b4.5 1 373 +,yk626a1.5 1 360 +,yk602e8.5 1 360 +,yk617a4.5 1 360 +,yk332b1.5 1 378 +,yk337c2.5 1 374 +,yk61b9.5 1 360 +,yk434f11.5 1 360 +,yk117c1.5 1 360 +,yk621h1.5 1 218 +,yk1376a02.5 23 252 +,yk106d3.5 1 181 +,yk768a10.5 23 200 +
III	gt csa	exon	1062771	1063137	0.858	-	.	Parent=mRNA22
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA22
III	gt csa	exon	1067821	1067940	1	-	.	Parent=mRNA22
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA22
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA22
III	gt csa	exon	1074168	1074463	1	-	.	Parent=mRNA22
III	gt csa	exon	1076314	1076543	1	-	.	Parent=mRNA22
III	gt csa	mRNA	1062781	1068054	.	-	.	ID=mRNA23;Parent=gene14;Target=yk1101a09.3 26 698 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1061h02.3 1 616 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1276g05.3 1 729 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA23
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA23
III	gt csa	exon	1067821	1067837	1	-	.	Parent=mRNA23
III	gt csa	exon	1067912	1067940	1	-	.	Parent=mRNA23
III	gt csa	exon	1068024	1068054	1	-	.	Parent=mRNA23
III	gt csa	mRNA	1062781	1074608	.	-	.	ID=mRNA24;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,BP 66 487 +,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk117f1.5 1 360 +,yk363h2.5 1 360 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA24
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA24
III	gt csa	exon	1067821	1067940	1	-	.	Parent=mRNA24
III	gt csa	exon	1070411	1070643	0.976	-	.	Parent=mRNA24
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA24
III	gt csa	exon	1074168	1074463	0.645	-	.	Parent=mRNA24
III	gt csa	exon	1074601	1074608	0	-	.	Parent=mRNA24
III	gt csa	mRNA	1062781	1074628	.	-	.	ID=mRNA25;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,RP 81 497 +,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk117f1.5 1 360 +,yk363h2.5 1 360 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA25
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA25
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA25
III	gt csa	exon	1070411	1070643	0.968	-	.	Parent=mRNA25
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA25
III	gt csa	exon	1074168	1074463	0.683	-	.	Parent=mRNA25
III	gt csa	exon	1074624	1074628	0	-	.	Parent=mRNA25
III	gt csa	mRNA	1062781	1076543	.	-	.	ID=mRNA26;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk1213f07.5 23 619 +,yk1199c10.5 16 513 +,yk621h1.5 1 218 +,yk1376a02.5 23 252 +,yk106d3.5 1 181 +,yk768a10.5 23 200 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA26
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA26
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA26
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA26
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA26
III	gt csa	exon	1074168	1074350	1	-	.	Parent=mRNA26
III	gt csa	exon	1074426	1074463	1	-	.	Parent=mRNA26
III	gt csa	exon	1076314	1076543	1	-	.	Parent=mRNA26
III	gt csa	mRNA	1062781	1076543	.	-	.	ID=mRNA27;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk899h02.5 21 464 +,yk621h1.5 1 218 +,yk1376a02.5 23 252 +,yk106d3.5 1 181 +,yk768a10.5 23 200 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA27
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA27
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA27
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA27
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA27
III	gt csa	exon	1074168	1074350	0.973	-	.	Parent=mRNA27
III	gt csa	exon	1074432	1074463	1	-	.	Parent=mRNA27
III	gt csa	exon	1076314	1076543	1	-	.	Parent=mRNA27
III	gt csa	mRNA	1062781	1076543	.	-	.	ID=mRNA28;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk778d02.5 21 613 +,yk117f1.5 1 360 +,yk363h2.5 1 360 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA28
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA28
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA28
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA28
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA28
III	gt csa	exon	1074168	1074463	0.993	-	.	Parent=mRNA28
III	gt csa	exon	1076380	1076543	1	-	.	Parent=mRNA28
III	gt csa	mRNA	1062781	1076543	.	-	.	ID=mRNA29;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk1351e07.5 23 549 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA29
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA29
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA29
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA29
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA29
III	gt csa	exon	1074168	1074374	0.995	-	.	Parent=mRNA29
III	gt csa	exon	1076372	1076543	0.994	-	.	Parent=mRNA29
III	gt csa	mRNA	1062794	1064950	.	-	.	ID=mRNA30;Parent=gene14;Target=yk1172f12.3 68 589 -
III	gt csa	exon	1062794	1063137	1	-	.	Parent=mRNA30
III	gt csa	exon	1064630	1064798	0.932	-	.	Parent=mRNA30
III	gt csa	exon	1064945	1064950	0.833	-	.	Parent=mRNA30
III	gt csa	mRNA	1067962	1068321	.	-	.	ID=mRNA31;Parent=gene14;Target=yk394b5.5 1 360 +
III	gt csa	exon	1067962	1068321	1	-	.	Parent=mRNA31
III	gt csa	mRNA	1072370	1076543	.	-	.	ID=mRNA32;Parent=gene14;Target=yk572f4.5 1 360 +,yk117f1.5 1 360 +,CK579359 1 613 +,yk1101a09.5 23 632 +,yk1034a11.5 23 628 +,yk363h2.5 1 360 +,yk1172f12.5 23 612 +,yk1053h12.5 22 598 +,yk1339g04.5 24 597 +,yk1169g11.5 23 596 +,yk1170b11.5 23 594 +,yk1120d08.5 23 590 +,yk1286b11.5 23 589 +,yk1120g02.5 23 587 +,yk1058c11.5 23 586 +,yk1254h08.5 23 584 +,yk1722g08.5 23 543 +,yk804f05.5 23 542 +,yk1096a09.5 23 539 +,yk1516e02.5 23 528 +,yk1652g01.5 23 510 +,yk1401h02.5 23 497 +,yk1061h02.5 23 497 +,yk1369c04.5 23 488 +,yk505f9.5 1 368 +,yk1141g04.5 23 448 +,yk820f07.5 23 446 +,yk1741a10.5 24 446 +,yk1026h07.5 1 370 +,yk656g8.5 1 360 +,yk216b5.5 1 360 +,yk568d7.5 1 360 +,yk659c10.5 1 379 +,yk592b8.5 1 360 +,yk658b12.5 1 360 +,yk269b4.5 1 376 +,yk525g8.5 1 377 +,yk482b6.5 1 360 +,yk569b4.5 1 360 +,yk675h9.5 1 360 +,yk456c8.5 1 377 +,yk393b4.5 1 373 +,yk626a1.5 1 360 +,yk602e8.5 1 360 +,yk617a4.5 1 360 +,yk332b1.5 1 378 +,yk337c2.5 1 374 +,yk61b9.5 1 360 +,yk434f11.5 1 360 +,yk117c1.5 1 360 +,yk621h1.5 1 218 +,yk1376a02.5 23 252 +,yk106d3.5 1 181 +,yk768a10.5 23 200 +
III	gt csa	exon	1072370	1072533	0.976	-	.	Parent=mRNA32
III	gt csa	exon	1074168	1074463	1	-	.	Parent=mRNA32
III	gt csa	exon	1076314	1076543	1	-	.	Parent=mRNA32
###
III	gt csa	gene	1078138	1080469	.	-	.	ID=gene15
III	gt csa	mRNA	1078138	1079228	.	-	.	ID=mRNA33;Parent=gene15;Target=yk1340e12.3 1 864 -,yk616a3.5 1 360 +
III	gt csa	exon	1078138	1078930	0.996	-	.	Parent=mRNA33
III	gt csa	exon	1079155	1079228	0.932	-	.	Parent=mRNA33
III	gt csa	mRNA	1079466	1080469	.	-	.	ID=mRNA34;Parent=gene15;Target=yk1243e09.3 1 706 -,BP 1 203 +,RP 1 203 +,yk1243e09.5 24 582 +,yk1340e12.5 23 491 +,yk493c1.5 1 375 +,yk291g7.5 1 240 +,U23938 1 107 +
III	gt csa	exon	1079466	1079894	1	-	.	Parent=mRNA34
III	gt csa	exon	1079946	1080199	1	-	.	Parent=mRNA34
III	gt csa	exon	1080275	1080330	1	-	.	Parent=mRNA34
III	gt csa	exon	1080393	1080469	1	-	.	Parent=mRNA34
III	gt csa	mRNA	1079821	1080352	.	-	.	ID=mRNA35;Parent=gene15;Target=yk1013b10.5 1 457 +
III	gt csa	exon	1079821	1080199	0.995	-	.	Parent=mRNA35
III	gt csa	exon	1080275	1080352	0.885	-	.	Parent=mRNA35
###
III	gt csa	gene	1078143	1079828	.	+	.	ID=gene16
III	gt csa	mRNA	1078143	1078790	.	+	.	ID=mRNA36;Parent=gene16;Target=yk1013b10.3 1 651 +,yk616a3.3 1 300 +
III	gt csa	exon	1078143	1078790	0.979	+	.	Parent=mRNA36
III	gt csa	mRNA	1079525	1079828	.	+	.	ID=mRNA37;Parent=gene16;Target=yk291g7.3 1 300 +,yk493c1.3 1 300 +
III	gt csa	exon	1079525	1079828	0.992	+	.	Parent=mRNA37
###
III	gt csa	gene	1080895	1095067	.	+	.	ID=gene17
III	gt csa	mRNA	1080895	1081298	.	+	.	ID=mRNA38;Parent=gene17;Target=yk628f9.3 1 285 -,CESAC24R 12 322 +,yk628f9.5 1 320 +
III	gt csa	exon	1080895	1081097	0.97	+	.	Parent=mRNA38
III	gt csa	exon	1081143	1081298	0.936	+	.	Parent=mRNA38
III	gt csa	mRNA	1081386	1095067	.	+	.	ID=mRNA39;Parent=gene17;Target=L26987 1 2172 +,yk96h7.5 1 360 +,yk628a12.5 1 378 +,yk375g6.5 1 240 +
III	gt csa	exon	1081386	1081507	0.984	+	.	Parent=mRNA39
III	gt csa	exon	1081621	1081704	1	+	.	Parent=mRNA39
III	gt csa	exon	1082982	1083119	1	+	.	Parent=mRNA39
III	gt csa	exon	1084050	1084121	1	+	.	Parent=mRNA39
III	gt csa	exon	1084325	1084449	1	+	.	Parent=mRNA39
III	gt csa	exon	1087773	1088553	0.996	+	.	Parent=mRNA39
III	gt csa	exon	1091545	1091685	0.986	+	.	Parent=mRNA39
III	gt csa	exon	1092617	1092679	0.984	+	.	Parent=mRNA39
III	gt csa	exon	1092734	1092865	1	+	.	Parent=mRNA39
III	gt csa	exon	1094216	1094362	0.973	+	.	Parent=mRNA39
III	gt csa	exon	1094697	1095067	0.997	+	.	Parent=mRNA39
III	gt csa	mRNA	1081392	1094789	.	+	.	ID=mRNA40;Parent=gene17;Target=yk325e4.5 1 374 +,WP 1 583 +
III	gt csa	exon	1081392	1081507	1	+	.	Parent=mRNA40
III	gt csa	exon	1081621	1081704	1	+	.	Parent=mRNA40
III	gt csa	exon	1084050	1084121	1	+	.	Parent=mRNA40
III	gt csa	exon	1084325	1084449	1	+	.	Parent=mRNA40
III	gt csa	exon	1087773	1088553	1	+	.	Parent=mRNA40
III	gt csa	exon	1091545	1091685	1	+	.	Parent=mRNA40
III	gt csa	exon	1092617	1092679	1	+	.	Parent=mRNA40
III	gt csa	exon	1092734	1092865	1	+	.	Parent=mRNA40
III	gt csa	exon	1094216	1094362	1	+	.	Parent=mRNA40
III	gt csa	exon	1094697	1094789	1	+	.	Parent=mRNA40
III	gt csa	mRNA	1086135	1086598	.	+	.	ID=mRNA41;Parent=gene17;Target=yk64a7.5 1 360 +,yk774d01.5 23 484 +,yk168e1.5 1 360 +
III	gt csa	exon	1086135	1086598	0.998	+	.	Parent=mRNA41
###
III	gt csa	gene	1086142	1095035	.	-	.	ID=gene18
III	gt csa	mRNA	1086142	1086645	.	-	.	ID=mRNA42;Parent=gene18;Target=yk774d01.3 1 496 +,yk168e1.3 1 300 +,yk64a7.3 1 340 +
III	gt csa	exon	1086142	1086645	0.968	-	.	Parent=mRNA42
III	gt csa	mRNA	1092456	1092592	.	-	.	ID=mRNA43;Parent=gene18;Target=yk623f3.3 45 180 +
III	gt csa	exon	1092456	1092592	0.883	-	.	Parent=mRNA43
III	gt csa	mRNA	1094701	1095035	.	-	.	ID=mRNA44;Parent=gene18;Target=yk628a12.3 1 300 +,yk325e4.3 1 300 +,yk96h7.3 1 317 +
III	gt csa	exon	1094701	1095035	0.97	-	.	Parent=mRNA44
###
III	gt csa	gene	1103215	1104223	.	+	.	ID=gene19
III	gt csa	mRNA	1103215	1104223	.	+	.	ID=mRNA45;Parent=gene19;Target=yk509d9.5 1 240 +
III	gt csa	exon	1103215	1103340	0.917	+	.	Parent=mRNA45
III	gt csa	exon	1104113	1104223	0.973	+	.	Parent=mRNA45
###
III	gt csa	gene	1105166	1108112	.	+	.	ID=gene20
III	gt csa	mRNA	1105166	1108112	.	+	.	ID=mRNA46;Parent=gene20;Target=yk1464f04.5 1 530 +
III	gt csa	exon	1105166	1105213	1	+	.	Parent=mRNA46
III	gt csa	exon	1105382	1105479	1	+	.	Parent=mRNA46
III	gt csa	exon	1106989	1107077	1	+	.	Parent=mRNA46
III	gt csa	exon	1107132	1107310	1	+	.	Parent=mRNA46
III	gt csa	exon	1107997	1108112	1	+	.	Parent=mRNA46
###
III	gt csa	gene	1108452	1111917	.	+	.	ID=gene21
III	gt csa	mRNA	1108452	1110379	.	+	.	ID=mRNA47;Parent=gene21;Target=yk387g5.5 1 374 +,yk73h4.5 1 360 +
III	gt csa	exon	1108452	1108493	0.976	+	.	Parent=mRNA47
III	gt csa	exon	1109102	1109194	1	+	.	Parent=mRNA47
III	gt csa	exon	1109306	1109456	1	+	.	Parent=mRNA47
III	gt csa	exon	1110211	1110379	0.95	+	.	Parent=mRNA47
III	gt csa	mRNA	1110444	1111917	.	+	.	ID=mRNA48;Parent=gene21;Target=yk654h1.5 1 379 +,yk1464f04.3 1 511 -,yk654h1.3 1 300 -,yk73h4.3 1 339 -
III	gt csa	exon	1110444	1110660	1	+	.	Parent=mRNA48
III	gt csa	exon	1111612	1111917	0.997	+	.	Parent=mRNA48
###
III	gt csa	gene	1113142	1113501	.	+	.	ID=gene22
III	gt csa	mRNA	1113142	1113501	.	+	.	ID=mRNA49;Parent=gene22;Target=yk540h4.5 1 360 +
III	gt csa	exon	1113142	1113501	0.962	+	.	Parent=mRNA49
###
III	gt csa	gene	1116479	1145189	.	+	.	ID=gene23
III	gt csa	mRNA	1116479	1142875	.	+	.	ID=mRNA50;Parent=gene23;Target=yk476e8.5 1 375 +,yk413d2.5 1 378 +,yk115h9.5 1 360 +,AB071420 1 1206 +,CEESU89F 1 378 +,yk476e8.3 1 300 -,yk115h9.3 1 316 -
III	gt csa	exon	1116479	1116537	1	+	.	Parent=mRNA50
III	gt csa	exon	1116980	1117047	1	+	.	Parent=mRNA50
III	gt csa	exon	1117143	1117225	1	+	.	Parent=mRNA50
III	gt csa	exon	1117275	1117383	1	+	.	Parent=mRNA50
III	gt csa	exon	1122635	1122766	1	+	.	Parent=mRNA50
III	gt csa	exon	1139058	1139117	1	+	.	Parent=mRNA50
III	gt csa	exon	1139983	1140084	1	+	.	Parent=mRNA50
III	gt csa	exon	1140353	1140439	1	+	.	Parent=mRNA50
III	gt csa	exon	1141806	1142171	1	+	.	Parent=mRNA50
III	gt csa	exon	1142665	1142875	0.981	+	.	Parent=mRNA50
III	gt csa	mRNA	1116738	1142838	.	+	.	ID=mRNA51;Parent=gene23;Target=BP 1 356 +,CEESU89F 1 378 +
III	gt csa	exon	1116738	1116762	0.381	+	.	Parent=mRNA51
III	gt csa	exon	1116980	1117047	0.868	+	.	Parent=mRNA51
III	gt csa	exon	1117143	1117225	1	+	.	Parent=mRNA51
III	gt csa	exon	1117275	1117383	1	+	.	Parent=mRNA51
III	gt csa	exon	1122635	1122766	0.914	+	.	Parent=mRNA51
III	gt csa	exon	1139983	1140084	0.767	+	.	Parent=mRNA51
III	gt csa	exon	1141806	1142171	0.882	+	.	Parent=mRNA51
III	gt csa	exon	1142656	1142838	0.85	+	.	Parent=mRNA51
III	gt csa	mRNA	1125293	1125473	.	+	.	ID=mRNA52;Parent=gene23;Target=yk553h3.3 1 180 +
III	gt csa	exon	1125293	1125473	0.95	+	.	Parent=mRNA52
III	gt csa	mRNA	1133548	1142889	.	+	.	ID=mRNA53;Parent=gene23;Target=yk1661g06.3 1 722 -,yk476e8.3 1 300 -,yk115h9.3 1 316 -
III	gt csa	exon	1133548	1133558	0.727	+	.	Parent=mRNA53
III	gt csa	exon	1135590	1135608	0.737	+	.	Parent=mRNA53
III	gt csa	exon	1139983	1140084	1	+	.	Parent=mRNA53
III	gt csa	exon	1141806	1142171	1	+	.	Parent=mRNA53
III	gt csa	exon	1142665	1142889	0.991	+	.	Parent=mRNA53
III	gt csa	mRNA	1143062	1145189	.	+	.	ID=mRNA54;Parent=gene23;Target=yk343a3.5 1 372 +,yk187d1.5 1 120 +,yk123d7.5 1 360 +,yk438f8.5 1 383 +,yk1158b07.3 1 574 -,yk550b4.5 1 360 +,yk543h10.5 11 360 +
III	gt csa	exon	1143062	1143459	1	+	.	Parent=mRNA54
III	gt csa	exon	1143525	1143621	1	+	.	Parent=mRNA54
III	gt csa	exon	1143690	1143814	1	+	.	Parent=mRNA54
III	gt csa	exon	1144839	1145189	0.997	+	.	Parent=mRNA54
III	gt csa	mRNA	1143154	1145132	.	+	.	ID=mRNA55;Parent=gene23;Target=yk60d1.5 1 360 +,yk142e6.5 1 373 +,yk657a9.5 2 379 +,yk103e11.5 1 330 +,yk604a1.5 1 360 +,yk470d12.5 1 360 +,yk647g1.5 1 360 +,RP 1 235 +,yk187d1.5 1 120 +,yk312d12.5 1 360 +,yk561h2.5 1 360 +,yk473b11.5 1 360 +,yk328f10.5 1 360 +,yk123d7.5 1 360 +,yk438f8.5 1 383 +
III	gt csa	exon	1143154	1143303	0.993	+	.	Parent=mRNA55
III	gt csa	exon	1143382	1143459	1	+	.	Parent=mRNA55
III	gt csa	exon	1143525	1143621	1	+	.	Parent=mRNA55
III	gt csa	exon	1143690	1143814	1	+	.	Parent=mRNA55
III	gt csa	exon	1144839	1145034	0.95	+	.	Parent=mRNA55
III	gt csa	exon	1145050	1145132	0.868	+	.	Parent=mRNA55
III	gt csa	mRNA	1143154	1145189	.	+	.	ID=mRNA56;Parent=gene23;Target=yk60d1.5 1 360 +,yk142e6.5 1 373 +,yk657a9.5 2 379 +,yk103e11.5 1 330 +,yk604a1.5 1 360 +,yk470d12.5 1 360 +,yk647g1.5 1 360 +,BP 1 234 +,yk187d1.5 1 120 +,yk312d12.5 1 360 +,yk561h2.5 1 360 +,yk473b11.5 1 360 +,yk328f10.5 1 360 +,yk123d7.5 1 360 +,yk438f8.5 1 383 +,yk1158b07.3 1 574 -,yk550b4.5 1 360 +,yk543h10.5 11 360 +
III	gt csa	exon	1143154	1143303	0.993	+	.	Parent=mRNA56
III	gt csa	exon	1143382	1143459	1	+	.	Parent=mRNA56
III	gt csa	exon	1143525	1143621	1	+	.	Parent=mRNA56
III	gt csa	exon	1143690	1143814	1	+	.	Parent=mRNA56
III	gt csa	exon	1144839	1145189	0.997	+	.	Parent=mRNA56
###
III	gt csa	gene	1125231	1145193	.	-	.	ID=gene24
III	gt csa	mRNA	1125231	1135544	.	-	.	ID=mRNA57;Parent=gene24;Target=yk1034b01.3 1 771 -,yk1181b08.3 1 560 -,yk863a05.3 1 746 -,BP 1 507 +,RP 1 507 +,WP 1 509 +,yk553h3.5 1 360 +
III	gt csa	exon	1125231	1125670	0.981	-	.	Parent=mRNA57
III	gt csa	exon	1125798	1125884	1	-	.	Parent=mRNA57
III	gt csa	exon	1126918	1127243	1	-	.	Parent=mRNA57
III	gt csa	exon	1127709	1127839	1	-	.	Parent=mRNA57
III	gt csa	exon	1128867	1128978	1	-	.	Parent=mRNA57
III	gt csa	exon	1129237	1129354	1	-	.	Parent=mRNA57
III	gt csa	exon	1129814	1129916	1	-	.	Parent=mRNA57
III	gt csa	exon	1134086	1134290	1	-	.	Parent=mRNA57
III	gt csa	exon	1134380	1134448	1	-	.	Parent=mRNA57
III	gt csa	exon	1135196	1135288	1	-	.	Parent=mRNA57
III	gt csa	exon	1135380	1135544	0.687	-	.	Parent=mRNA57
III	gt csa	mRNA	1129245	1136013	.	-	.	ID=mRNA58;Parent=gene24;Target=yk553h3.5 1 360 +,yk1034b01.5 24 613 +,yk863a05.5 17 604 +
III	gt csa	exon	1129245	1129354	0.991	-	.	Parent=mRNA58
III	gt csa	exon	1129814	1129916	1	-	.	Parent=mRNA58
III	gt csa	exon	1134086	1134290	1	-	.	Parent=mRNA58
III	gt csa	exon	1134380	1134448	1	-	.	Parent=mRNA58
III	gt csa	exon	1135196	1135288	1	-	.	Parent=mRNA58
III	gt csa	exon	1135380	1135488	1	-	.	Parent=mRNA58
III	gt csa	exon	1135900	1136013	1	-	.	Parent=mRNA58
III	gt csa	mRNA	1144830	1145193	.	-	.	ID=mRNA59;Parent=gene24;Target=yk470d12.3 1 300 +,yk604a1.3 1 300 +,yk473b11.3 1 300 +,yk312d12.3 1 300 +,yk343a3.3 1 300 +,yk530f6.3 1 300 +,yk438f8.3 1 285 +,yk561h2.3 1 292 +,yk543h10.3 1 300 +,yk647g1.3 1 300 +,yk142e6.3 1 300 +,yk60d1.3 1 343 +,yk103e11.3 1 334 +,yk123d7.3 1 180 +
III	gt csa	exon	1144830	1145193	0.971	-	.	Parent=mRNA59
###
III	gt csa	gene	1172435	1172612	.	+	.	ID=gene25
III	gt csa	mRNA	1172435	1172612	.	+	.	ID=mRNA60;Parent=gene25;Target=yk511h7.5 1 180 +
III	gt csa	exon	1172435	1172612	0.933	+	.	Parent=mRNA60
###
III	gt csa	gene	1180689	1181054	.	+	.	ID=gene26
III	gt csa	mRNA	1180689	1181054	.	+	.	ID=mRNA61;Parent=gene26;Target=yk511h7.3 1 300 -
III	gt csa	exon	1180689	1180787	0.929	+	.	Parent=mRNA61
III	gt csa	exon	1180855	1181054	0.942	+	.	Parent=mRNA61
###
III	gt csa	gene	1182067	1184916	.	+	.	ID=gene27
III	gt csa	mRNA	1182067	1184916	.	+	.	ID=mRNA62;Parent=gene27;Target=yk94h5.5 1 248 +,yk101e7.5 1 360 +,yk409f1.5 1 377 +,yk362f12.5 1 380 +,yk308d11.5 1 360 +,yk191a10.5 1 360 +,yk409a1.5 1 360 +,yk263d8.5 1 360 +,yk440h2.5 1 360 +,yk440h2.3 1 300 -,yk545f3.5 1 360 -,yk191a10.3 1 300 -,yk362f12.3 1 300 -,yk190e9.3 1 300 -,yk409f1.3 1 300 -,yk308d11.3 1 300 -,yk409a1.3 1 300 -
III	gt csa	exon	1182067	1182083	1	+	.	Parent=mRNA62
III	gt csa	exon	1182151	1182302	1	+	.	Parent=mRNA62
III	gt csa	exon	1183141	1183324	1	+	.	Parent=mRNA62
III	gt csa	exon	1183376	1183473	0.974	+	.	Parent=mRNA62
III	gt csa	exon	1184629	1184916	0.993	+	.	Parent=mRNA62
###
III	gt csa	gene	1184691	1184913	.	-	.	ID=gene28
III	gt csa	mRNA	1184691	1184913	.	-	.	ID=mRNA63;Parent=gene28;Target=yk388g7.3 1 176 +,yk94h5.3 1 180 +
III	gt csa	exon	1184691	1184913	0.944	-	.	Parent=mRNA63
###
III	gt csa	gene	1185272	1189478	.	-	.	ID=gene29
III	gt csa	mRNA	1185272	1189478	.	-	.	ID=mRNA64;Parent=gene29;Target=yk1481a08.3 1 678 -,yk1392d03.3 1 601 -
III	gt csa	exon	1185272	1185683	0.998	-	.	Parent=mRNA64
III	gt csa	exon	1187296	1187356	0.984	-	.	Parent=mRNA64
III	gt csa	exon	1187434	1187550	0.991	-	.	Parent=mRNA64
III	gt csa	exon	1187601	1187741	0.992	-	.	Parent=mRNA64
III	gt csa	exon	1189002	1189478	1	-	.	Parent=mRNA64
###
III	gt csa	gene	1191338	1193802	.	-	.	ID=gene30
III	gt csa	mRNA	1191338	1193802	.	-	.	ID=mRNA65;Parent=gene30;Target=yk1392d03.5 23 588 +,yk1481a08.5 23 461 +
III	gt csa	exon	1191338	1191568	0.996	-	.	Parent=mRNA65
III	gt csa	exon	1191631	1191720	1	-	.	Parent=mRNA65
III	gt csa	exon	1193558	1193802	1	-	.	Parent=mRNA65
###
III	gt csa	gene	1194399	1196282	.	-	.	ID=gene31
III	gt csa	mRNA	1194399	1196282	.	-	.	ID=mRNA66;Parent=gene31;Target=CB103439 99 622 +,CB103483 90 610 +,CB103504 61 572 +,yk1752b03.3 242 747 -,CB103472 81 584 +,yk1160g10.3 24 520 -,yk1160g10.5 24 516 +,CB103430 73 559 +,CK583320 1 435 +,yk368b4.5 1 374 +,CB103451 106 494 +,yk115f10.5 12 360 +
III	gt csa	exon	1194399	1194795	1	-	.	Parent=mRNA66
III	gt csa	exon	1196156	1196282	1	-	.	Parent=mRNA66
###
III	gt csa	gene	1194424	1194755	.	+	.	ID=gene32
III	gt csa	mRNA	1194424	1194755	.	+	.	ID=mRNA67;Parent=gene32;Target=yk115f10.3 1 332 +
III	gt csa	exon	1194424	1194755	0.997	+	.	Parent=mRNA67
###
III	gt csa	gene	1200240	1201998	.	-	.	ID=gene33
III	gt csa	mRNA	1200240	1201998	.	-	.	ID=mRNA68;Parent=gene33;Target=yk1488e08.5 23 608 +
III	gt csa	exon	1200240	1200461	0.995	-	.	Parent=mRNA68
III	gt csa	exon	1201465	1201639	1	-	.	Parent=mRNA68
III	gt csa	exon	1201810	1201998	0.995	-	.	Parent=mRNA68
###
III	gt csa	gene	1202535	1207288	.	+	.	ID=gene34
III	gt csa	mRNA	1202535	1207255	.	+	.	ID=mRNA69;Parent=gene34;Target=yk531a4.5 1 376 +,yk1387f11.5 23 512 +,WP 1 337 +,yk172c10.5 1 377 +,yk342c4.5 1 373 +,yk550b8.5 1 360 +,yk409b7.5 1 376 +,yk342c4.3 1 300 -,yk409b7.3 1 300 -,yk172c10.3 1 300 -
III	gt csa	exon	1202535	1202609	0.987	+	.	Parent=mRNA69
III	gt csa	exon	1202655	1202765	1	+	.	Parent=mRNA69
III	gt csa	exon	1202829	1203135	1	+	.	Parent=mRNA69
III	gt csa	exon	1203589	1203699	1	+	.	Parent=mRNA69
III	gt csa	exon	1205327	1205739	1	+	.	Parent=mRNA69
III	gt csa	exon	1206843	1206957	1	+	.	Parent=mRNA69
III	gt csa	exon	1207184	1207255	0.972	+	.	Parent=mRNA69
III	gt csa	mRNA	1202535	1207260	.	+	.	ID=mRNA70;Parent=gene34;Target=yk531a4.5 1 376 +,yk1387f11.5 23 512 +,WP 1 337 +,yk172c10.5 1 377 +,yk342c4.5 1 373 +,yk550b8.5 1 360 +,yk550b8.3 1 300 -
III	gt csa	exon	1202535	1202609	0.987	+	.	Parent=mRNA70
III	gt csa	exon	1202655	1202765	1	+	.	Parent=mRNA70
III	gt csa	exon	1202829	1203135	1	+	.	Parent=mRNA70
III	gt csa	exon	1203589	1203699	1	+	.	Parent=mRNA70
III	gt csa	exon	1205327	1205739	1	+	.	Parent=mRNA70
III	gt csa	exon	1206843	1206932	0.878	+	.	Parent=mRNA70
III	gt csa	exon	1207184	1207260	0.961	+	.	Parent=mRNA70
III	gt csa	mRNA	1202535	1207288	.	+	.	ID=mRNA71;Parent=gene34;Target=yk531a4.5 1 376 +,yk1387f11.5 23 512 +,WP 1 337 +,yk172c10.5 1 377 +,yk342c4.5 1 373 +,yk550b8.5 1 360 +,yk409b7.5 1 376 +,yk1387f11.3 1 649 -
III	gt csa	exon	1202535	1202609	0.987	+	.	Parent=mRNA71
III	gt csa	exon	1202655	1202765	1	+	.	Parent=mRNA71
III	gt csa	exon	1202829	1203135	1	+	.	Parent=mRNA71
III	gt csa	exon	1203589	1203699	1	+	.	Parent=mRNA71
III	gt csa	exon	1205327	1205739	1	+	.	Parent=mRNA71
III	gt csa	exon	1206843	1207288	1	+	.	Parent=mRNA71
III	gt csa	mRNA	1203589	1207248	.	+	.	ID=mRNA72;Parent=gene34;Target=yk531a4.3 10 300 -
III	gt csa	exon	1203589	1203699	1	+	.	Parent=mRNA72
III	gt csa	exon	1206843	1206957	0.983	+	.	Parent=mRNA72
III	gt csa	exon	1207184	1207248	0.969	+	.	Parent=mRNA72
###
III	gt csa	gene	1208120	1209321	.	+	.	ID=gene35
III	gt csa	mRNA	1208120	1209321	.	+	.	ID=mRNA73;Parent=gene35;Target=yk681h11.5 1 360 +,yk1103g05.5 41 657 +,cm13d11.5 1 287 +,yk660b11.5 1 378 +,yk669g11.5 1 360 +,yk210b6.5 1 376 +,yk608g3.5 1 360 +,yk506a7.5 1 360 +
III	gt csa	exon	1208120	1208251	1	+	.	Parent=mRNA73
III	gt csa	exon	1208372	1208714	0.997	+	.	Parent=mRNA73
III	gt csa	exon	1209177	1209321	1	+	.	Parent=mRNA73
###
III	gt csa	gene	1211225	1213642	.	+	.	ID=gene36
III	gt csa	mRNA	1211225	1213642	.	+	.	ID=mRNA74;Parent=gene36;Target=yk93h2.5 1 265 +,yk1535b11.3 1 614 -,CEEST24F 1 422 -,yk669g11.3 1 300 -,yk506a7.3 1 300 -,yk210b6.3 1 300 -,yk660b11.3 1 300 -,yk681h11.3 1 300 -,yk1624b11.3 1 340 -,yk93h2.3 1 331 -,CEESE53F 1 342 -
III	gt csa	exon	1211225	1211488	0.964	+	.	Parent=mRNA74
III	gt csa	exon	1212576	1212824	0.992	+	.	Parent=mRNA74
III	gt csa	exon	1213437	1213642	0.981	+	.	Parent=mRNA74
###
III	gt csa	gene	1214935	1215287	.	+	.	ID=gene37
III	gt csa	mRNA	1214935	1215287	.	+	.	ID=mRNA75;Parent=gene37;Target=yk726c5.5 1 340 +,yk843g10.5 1 341 +,yk726h9.5 1 330 +,yk1454b03.5 1 335 +,yk1693g03.5 1 335 +,yk1613b06.5 1 335 +,yk1376c06.5 1 345 +,yk1619d03.5 1 345 +,yk1657e01.5 1 343 +,yk151f9.5 1 240 +,yk70e6.5 1 317 +,yk309g3.5 1 308 +,yk367e7.5 1 311 +,yk275e11.5 1 298 +,yk383a12.5 1 290 +,yk1313b02.5 1 156 +
III	gt csa	exon	1214935	1215287	0.977	+	.	Parent=mRNA75
###
III	gt csa	gene	1214942	1215266	.	-	.	ID=gene38
III	gt csa	mRNA	1214942	1215266	.	-	.	ID=mRNA76;Parent=gene38;Target=yk726c5.3 1 267 +,yk726h9.3 1 270 +,yk734c7.3 1 275 +,yk1613b06.3 1 309 +,yk1641g01.3 1 312 +,yk1693g03.3 1 323 +,yk275e11.3 1 278 +,yk367e7.3 1 249 +,yk383a12.3 1 248 +,yk151f9.3 1 240 +,yk70e6.3 1 299 +,yk309g3.3 1 245 +
III	gt csa	exon	1214942	1215266	0.957	-	.	Parent=mRNA76
###
III	gt csa	gene	1216021	1216795	.	+	.	ID=gene39
III	gt csa	mRNA	1216021	1216795	.	+	.	ID=mRNA77;Parent=gene39;Target=yk808h01.3 1 641 +,yk831f01.3 1 241 +,yk1315b01.3 1 501 +,yk754f09.3 1 350 +,yk781a01.3 1 267 +,yk1358a10.3 1 302 +,yk413h8.5 1 120 +
III	gt csa	exon	1216021	1216795	0.881	+	.	Parent=mRNA77
###
III	gt csa	gene	1216578	1216806	.	-	.	ID=gene40
III	gt csa	mRNA	1216578	1216806	.	-	.	ID=mRNA78;Parent=gene40;Target=yk264h7.5 12 240 +
III	gt csa	exon	1216578	1216806	0.983	-	.	Parent=mRNA78
###
III	gt csa	gene	1220307	1222062	.	-	.	ID=gene41
III	gt csa	mRNA	1220307	1222062	.	-	.	ID=mRNA79;Parent=gene41;Target=yk1221d02.5 22 628 +,yk754f09.5 23 562 +,yk1358a10.5 23 547 +,yk808h01.5 26 550 +,yk781a01.5 23 546 +,yk236b4.5 1 360 +,yk629h11.5 1 356 +,yk831f01.5 23 175 +
III	gt csa	exon	1220307	1220373	1	-	.	Parent=mRNA79
III	gt csa	exon	1221160	1221571	1	-	.	Parent=mRNA79
III	gt csa	exon	1221935	1222062	1	-	.	Parent=mRNA79
###
III	gt csa	gene	1225449	1225807	.	+	.	ID=gene42
III	gt csa	mRNA	1225449	1225807	.	+	.	ID=mRNA80;Parent=gene42;Target=yk549c5.5 1 360 +
III	gt csa	exon	1225449	1225807	0.976	+	.	Parent=mRNA80
###
III	gt csa	gene	1225754	1226053	.	-	.	ID=gene43
III	gt csa	mRNA	1225754	1226053	.	-	.	ID=mRNA81;Parent=gene43;Target=yk549c5.3 1 300 +
III	gt csa	exon	1225754	1226053	1	-	.	Parent=mRNA81
###
III	gt csa	gene	1236005	1237038	.	+	.	ID=gene44
III	gt csa	mRNA	1236005	1237038	.	+	.	ID=mRNA82;Parent=gene44;Target=WP 1 254 +
III	gt csa	exon	1236005	1236093	1	+	.	Parent=mRNA82
III	gt csa	exon	1236319	1236772	1	+	.	Parent=mRNA82
III	gt csa	exon	1236820	1237038	1	+	.	Parent=mRNA82
###
III	gt csa	gene	1239313	1242728	.	+	.	ID=gene45
III	gt csa	mRNA	1239313	1242728	.	+	.	ID=mRNA83;Parent=gene45;Target=WP 1 307 +
III	gt csa	exon	1239313	1239401	1	+	.	Parent=mRNA83
III	gt csa	exon	1241115	1241739	1	+	.	Parent=mRNA83
III	gt csa	exon	1242522	1242728	1	+	.	Parent=mRNA83
###
III	gt csa	gene	1243521	1245273	.	+	.	ID=gene46
III	gt csa	mRNA	1243521	1245273	.	+	.	ID=mRNA84;Parent=gene46;Target=WP 1 306 +
III	gt csa	exon	1243521	1243636	1	+	.	Parent=mRNA84
III	gt csa	exon	1244420	1245014	1	+	.	Parent=mRNA84
III	gt csa	exon	1245067	1245273	1	+	.	Parent=mRNA84
###
III	gt csa	gene	1247626	1249143	.	-	.	ID=gene47
III	gt csa	mRNA	1247626	1249143	.	-	.	ID=mRNA85;Parent=gene47;Target=WP 1 270 +
III	gt csa	exon	1247626	1247808	1	-	.	Parent=mRNA85
III	gt csa	exon	1247862	1248417	1	-	.	Parent=mRNA85
III	gt csa	exon	1249073	1249143	1	-	.	Parent=mRNA85
###
III	gt csa	gene	1249509	1251814	.	+	.	ID=gene48
III	gt csa	mRNA	1249509	1251814	.	+	.	ID=mRNA86;Parent=gene48;Target=WP 1 265 +,yk252g1.5 1 376 +
III	gt csa	exon	1249509	1249579	1	+	.	Parent=mRNA86
III	gt csa	exon	1250603	1251143	1	+	.	Parent=mRNA86
III	gt csa	exon	1251632	1251814	1	+	.	Parent=mRNA86
###
III	gt csa	gene	1253374	1254391	.	-	.	ID=gene49
III	gt csa	mRNA	1253374	1254391	.	-	.	ID=mRNA87;Parent=gene49;Target=WP 1 252 +
III	gt csa	exon	1253374	1253548	1	-	.	Parent=mRNA87
III	gt csa	exon	1253764	1254273	1	-	.	Parent=mRNA87
III	gt csa	exon	1254321	1254391	1	-	.	Parent=mRNA87
###
III	gt csa	gene	1255541	1256919	.	+	.	ID=gene50
III	gt csa	mRNA	1255541	1256919	.	+	.	ID=mRNA88;Parent=gene50;Target=WP 1 282 +
III	gt csa	exon	1255541	1256020	1	+	.	Parent=mRNA88
III	gt csa	exon	1256067	1256195	1	+	.	Parent=mRNA88
III	gt csa	exon	1256630	1256677	1	+	.	Parent=mRNA88
III	gt csa	exon	1256731	1256919	1	+	.	Parent=mRNA88
###
III	gt csa	gene	1257203	1258404	.	-	.	ID=gene51
III	gt csa	mRNA	1257203	1258404	.	-	.	ID=mRNA89;Parent=gene51;Target=yk1419f09.3 1 775 -,WP 1 278 +
III	gt csa	exon	1257203	1257419	0.995	-	.	Parent=mRNA89
III	gt csa	exon	1257724	1258291	1	-	.	Parent=mRNA89
III	gt csa	exon	1258337	1258404	1	-	.	Parent=mRNA89
###
III	gt csa	gene	1259414	1260174	.	+	.	ID=gene52
III	gt csa	mRNA	1259414	1260174	.	+	.	ID=mRNA90;Parent=gene52;Target=WP 1 91 +
III	gt csa	exon	1259414	1259503	1	+	.	Parent=mRNA90
III	gt csa	exon	1259992	1260174	1	+	.	Parent=mRNA90
###
III	gt csa	gene	1261815	1262832	.	-	.	ID=gene53
III	gt csa	mRNA	1261815	1262832	.	-	.	ID=mRNA91;Parent=gene53;Target=WP 1 252 +
III	gt csa	exon	1261815	1261989	1	-	.	Parent=mRNA91
III	gt csa	exon	1262205	1262714	1	-	.	Parent=mRNA91
III	gt csa	exon	1262762	1262832	1	-	.	Parent=mRNA91
###
III	gt csa	gene	1265663	1266845	.	-	.	ID=gene54
III	gt csa	mRNA	1265663	1266845	.	-	.	ID=mRNA92;Parent=gene54;Target=WP 1 278 +
III	gt csa	exon	1265663	1265860	1	-	.	Parent=mRNA92
III	gt csa	exon	1266165	1266732	1	-	.	Parent=mRNA92
III	gt csa	exon	1266778	1266845	1	-	.	Parent=mRNA92
###
III	gt csa	gene	1267393	1269234	.	-	.	ID=gene55
III	gt csa	mRNA	1267393	1269234	.	-	.	ID=mRNA93;Parent=gene55;Target=WP 1 306 +
III	gt csa	exon	1267393	1267608	1	-	.	Parent=mRNA93
III	gt csa	exon	1268344	1268962	1	-	.	Parent=mRNA93
III	gt csa	exon	1269152	1269234	1	-	.	Parent=mRNA93
###
III	gt csa	gene	1269569	1271418	.	-	.	ID=gene56
III	gt csa	mRNA	1269569	1271418	.	-	.	ID=mRNA94;Parent=gene56;Target=yk1217b07.3 1 777 -,WP 1 307 +,yk1217b07.5 23 624 +
III	gt csa	exon	1269569	1269841	0.96	-	.	Parent=mRNA94
III	gt csa	exon	1269904	1270519	1	-	.	Parent=mRNA94
III	gt csa	exon	1271293	1271418	1	-	.	Parent=mRNA94
###
III	gt csa	gene	1272534	1273666	.	-	.	ID=gene57
III	gt csa	mRNA	1272534	1273666	.	-	.	ID=mRNA95;Parent=gene57;Target=WP 1 305 +
III	gt csa	exon	1272534	1272749	1	-	.	Parent=mRNA95
III	gt csa	exon	1272798	1273413	1	-	.	Parent=mRNA95
III	gt csa	exon	1273584	1273666	1	-	.	Parent=mRNA95
###
III	gt csa	gene	1274504	1275578	.	-	.	ID=gene58
III	gt csa	mRNA	1274504	1275578	.	-	.	ID=mRNA96;Parent=gene58;Target=WP 1 306 +
III	gt csa	exon	1274504	1274719	1	-	.	Parent=mRNA96
III	gt csa	exon	1274773	1275391	1	-	.	Parent=mRNA96
III	gt csa	exon	1275496	1275578	1	-	.	Parent=mRNA96
###
III	gt csa	gene	1282418	1282768	.	-	.	ID=gene59
III	gt csa	mRNA	1282418	1282768	.	-	.	ID=mRNA97;Parent=gene59;Target=yk720c2.3 1 300 -
III	gt csa	exon	1282418	1282633	0.991	-	.	Parent=mRNA97
III	gt csa	exon	1282685	1282768	1	-	.	Parent=mRNA97
###
III	gt csa	gene	1283269	1288513	.	-	.	ID=gene60
III	gt csa	mRNA	1283269	1284322	.	-	.	ID=mRNA98;Parent=gene60;Target=yk720c2.5 105 341 +,yk729a8.5 114 340 +
III	gt csa	exon	1283269	1283321	0.981	-	.	Parent=mRNA98
III	gt csa	exon	1284052	1284148	1	-	.	Parent=mRNA98
III	gt csa	exon	1284236	1284322	1	-	.	Parent=mRNA98
III	gt csa	mRNA	1287289	1288513	.	-	.	ID=mRNA99;Parent=gene60;Target=WP 1 312 +
III	gt csa	exon	1287289	1287501	1	-	.	Parent=mRNA99
III	gt csa	exon	1287544	1288153	1	-	.	Parent=mRNA99
III	gt csa	exon	1288401	1288513	1	-	.	Parent=mRNA99
###
III	gt csa	gene	1284398	1287041	.	+	.	ID=gene61
III	gt csa	mRNA	1284398	1284757	.	+	.	ID=mRNA100;Parent=gene61;Target=yk53f10.5 1 360 +
III	gt csa	exon	1284398	1284757	0.989	+	.	Parent=mRNA100
III	gt csa	mRNA	1285006	1287041	.	+	.	ID=mRNA101;Parent=gene61;Target=WP 1 303 +
III	gt csa	exon	1285006	1285088	1	+	.	Parent=mRNA101
III	gt csa	exon	1286162	1286777	1	+	.	Parent=mRNA101
III	gt csa	exon	1286832	1287041	1	+	.	Parent=mRNA101
###
III	gt csa	gene	1292041	1293205	.	-	.	ID=gene62
III	gt csa	mRNA	1292041	1293205	.	-	.	ID=mRNA102;Parent=gene62;Target=WP 1 311 +
III	gt csa	exon	1292041	1292250	1	-	.	Parent=mRNA102
III	gt csa	exon	1292333	1292972	1	-	.	Parent=mRNA102
III	gt csa	exon	1293123	1293205	1	-	.	Parent=mRNA102
###
III	gt csa	gene	1295674	1297059	.	+	.	ID=gene63
III	gt csa	mRNA	1295674	1297059	.	+	.	ID=mRNA103;Parent=gene63;Target=WP 1 311 +,yk720c2.3 1 237 -
III	gt csa	exon	1295674	1295756	1	+	.	Parent=mRNA103
III	gt csa	exon	1296149	1296785	1	+	.	Parent=mRNA103
III	gt csa	exon	1296847	1297059	1	+	.	Parent=mRNA103
###
III	gt csa	gene	1298564	1299474	.	+	.	ID=gene64
III	gt csa	mRNA	1298564	1299474	.	+	.	ID=mRNA104;Parent=gene64;Target=WP 1 292 +
III	gt csa	exon	1298564	1299238	0.952	+	.	Parent=mRNA104
III	gt csa	exon	1299280	1299474	1	+	.	Parent=mRNA104
###
III	gt csa	gene	1303704	1305451	.	+	.	ID=gene65
III	gt csa	mRNA	1303704	1305451	.	+	.	ID=mRNA105;Parent=gene65;Target=WP 1 322 +
III	gt csa	exon	1303704	1303792	1	+	.	Parent=mRNA105
III	gt csa	exon	1303837	1304464	1	+	.	Parent=mRNA105
III	gt csa	exon	1305203	1305451	1	+	.	Parent=mRNA105
###
III	gt csa	gene	1305794	1308239	.	-	.	ID=gene66
III	gt csa	mRNA	1305794	1308239	.	-	.	ID=mRNA106;Parent=gene66;Target=WP 1 301 +
III	gt csa	exon	1305794	1305988	1	-	.	Parent=mRNA106
III	gt csa	exon	1306824	1307478	1	-	.	Parent=mRNA106
III	gt csa	exon	1308187	1308239	1	-	.	Parent=mRNA106
###
III	gt csa	gene	1309177	1311200	.	+	.	ID=gene67
III	gt csa	mRNA	1309177	1311200	.	+	.	ID=mRNA107;Parent=gene67;Target=WP 1 337 +
III	gt csa	exon	1309177	1309335	1	+	.	Parent=mRNA107
III	gt csa	exon	1309577	1309744	1	+	.	Parent=mRNA107
III	gt csa	exon	1309838	1309936	1	+	.	Parent=mRNA107
III	gt csa	exon	1310015	1310083	1	+	.	Parent=mRNA107
III	gt csa	exon	1310130	1310283	1	+	.	Parent=mRNA107
III	gt csa	exon	1310329	1310399	1	+	.	Parent=mRNA107
III	gt csa	exon	1310910	1311200	1	+	.	Parent=mRNA107
###
III	gt csa	gene	1311218	1312383	.	-	.	ID=gene68
III	gt csa	mRNA	1311218	1312383	.	-	.	ID=mRNA108;Parent=gene68;Target=WP 1 241 +
III	gt csa	exon	1311218	1311421	1	-	.	Parent=mRNA108
III	gt csa	exon	1311716	1312111	1	-	.	Parent=mRNA108
III	gt csa	exon	1312266	1312383	0.463	-	.	Parent=mRNA108
###
III	gt csa	gene	1313348	1315208	.	-	.	ID=gene69
III	gt csa	mRNA	1313348	1315208	.	-	.	ID=mRNA109;Parent=gene69;Target=yk1237h07.3 1 660 -,WP 1 302 +,yk1237h07.5 1 139 +
III	gt csa	exon	1313348	1313559	0.995	-	.	Parent=mRNA109
III	gt csa	exon	1314031	1314655	1	-	.	Parent=mRNA109
III	gt csa	exon	1315090	1315208	0.992	-	.	Parent=mRNA109
###
III	gt csa	gene	1315254	1316655	.	+	.	ID=gene70
III	gt csa	mRNA	1315254	1316655	.	+	.	ID=mRNA110;Parent=gene70;Target=WP 1 274 +
III	gt csa	exon	1315254	1315357	1	+	.	Parent=mRNA110
III	gt csa	exon	1315402	1315494	1	+	.	Parent=mRNA110
III	gt csa	exon	1316031	1316655	1	+	.	Parent=mRNA110
###
III	gt csa	gene	1319006	1321651	.	-	.	ID=gene71
III	gt csa	mRNA	1319006	1321651	.	-	.	ID=mRNA111;Parent=gene71;Target=WP 1 302 +
III	gt csa	exon	1319006	1319215	1	-	.	Parent=mRNA111
III	gt csa	exon	1319264	1319888	1	-	.	Parent=mRNA111
III	gt csa	exon	1321581	1321651	1	-	.	Parent=mRNA111
###
III	gt csa	gene	1322136	1323621	.	-	.	ID=gene72
III	gt csa	mRNA	1322136	1323621	.	-	.	ID=mRNA112;Parent=gene72;Target=yk546f3.5 1 377 -,WP 1 304 +
III	gt csa	exon	1322136	1322353	0.995	-	.	Parent=mRNA112
III	gt csa	exon	1322402	1323026	1	-	.	Parent=mRNA112
III	gt csa	exon	1323551	1323621	1	-	.	Parent=mRNA112
###
III	gt csa	gene	1328634	1333667	.	+	.	ID=gene73
III	gt csa	mRNA	1328634	1333667	.	+	.	ID=mRNA113;Parent=gene73;Target=WP 1 500 +
III	gt csa	exon	1328634	1328704	1	+	.	Parent=mRNA113
III	gt csa	exon	1329933	1330529	1	+	.	Parent=mRNA113
III	gt csa	exon	1331997	1332615	1	+	.	Parent=mRNA113
III	gt csa	exon	1333455	1333667	1	+	.	Parent=mRNA113
###
III	gt csa	gene	1333841	1334165	.	-	.	ID=gene74
III	gt csa	mRNA	1333841	1334165	.	-	.	ID=mRNA114;Parent=gene74;Target=WP 1 92 +
III	gt csa	exon	1333841	1333873	0.825	-	.	Parent=mRNA114
III	gt csa	exon	1333923	1334165	0.915	-	.	Parent=mRNA114
###
III	gt csa	gene	1336697	1342484	.	-	.	ID=gene75
III	gt csa	mRNA	1336697	1340323	.	-	.	ID=mRNA115;Parent=gene75;Target=yk872h02.3 1 703 -,WP 1 327 +
III	gt csa	exon	1336697	1337005	0.997	-	.	Parent=mRNA115
III	gt csa	exon	1338016	1338619	1	-	.	Parent=mRNA115
III	gt csa	exon	1340092	1340175	1	-	.	Parent=mRNA115
III	gt csa	exon	1340235	1340323	1	-	.	Parent=mRNA115
III	gt csa	mRNA	1340606	1342484	.	-	.	ID=mRNA116;Parent=gene75;Target=WP 1 329 +
III	gt csa	exon	1340606	1340800	1	-	.	Parent=mRNA116
III	gt csa	exon	1340854	1341023	1	-	.	Parent=mRNA116
III	gt csa	exon	1341072	1341547	1	-	.	Parent=mRNA116
III	gt csa	exon	1342339	1342484	1	-	.	Parent=mRNA116
###
III	gt csa	gene	1342986	1344682	.	+	.	ID=gene76
III	gt csa	mRNA	1342986	1344682	.	+	.	ID=mRNA117;Parent=gene76;Target=WP 1 325 +
III	gt csa	exon	1342986	1343131	1	+	.	Parent=mRNA117
III	gt csa	exon	1343802	1344423	1	+	.	Parent=mRNA117
III	gt csa	exon	1344476	1344682	1	+	.	Parent=mRNA117
###
III	gt csa	gene	1344968	1345784	.	-	.	ID=gene77
III	gt csa	mRNA	1344968	1345784	.	-	.	ID=mRNA118;Parent=gene77;Target=WP 1 254 +
III	gt csa	exon	1344968	1345417	1	-	.	Parent=mRNA118
III	gt csa	exon	1345473	1345784	1	-	.	Parent=mRNA118
###
III	gt csa	gene	1346305	1347118	.	-	.	ID=gene78
III	gt csa	mRNA	1346305	1347118	.	-	.	ID=mRNA119;Parent=gene78;Target=WP 1 251 +
III	gt csa	exon	1346305	1346754	1	-	.	Parent=mRNA119
III	gt csa	exon	1346816	1347118	1	-	.	Parent=mRNA119
###
III	gt csa	gene	1347777	1349390	.	-	.	ID=gene79
III	gt csa	mRNA	1347777	1349390	.	-	.	ID=mRNA120;Parent=gene79;Target=WP 1 268 +
III	gt csa	exon	1347777	1347980	1	-	.	Parent=mRNA120
III	gt csa	exon	1348040	1348143	1	-	.	Parent=mRNA120
III	gt csa	exon	1348299	1348657	1	-	.	Parent=mRNA120
III	gt csa	exon	1349254	1349390	1	-	.	Parent=mRNA120
###
III	gt csa	gene	1349742	1350826	.	-	.	ID=gene80
III	gt csa	mRNA	1349742	1350826	.	-	.	ID=mRNA121;Parent=gene80;Target=WP 1 253 +
III	gt csa	exon	1349742	1350188	1	-	.	Parent=mRNA121
III	gt csa	exon	1350515	1350826	1	-	.	Parent=mRNA121
###
III	gt csa	gene	1351206	1353035	.	-	.	ID=gene81
III	gt csa	mRNA	1351206	1353035	.	-	.	ID=mRNA122;Parent=gene81;Target=WP 18 236 +
III	gt csa	exon	1351206	1351652	1	-	.	Parent=mRNA122
III	gt csa	exon	1352826	1353035	1	-	.	Parent=mRNA122
###
III	gt csa	gene	1354987	1355410	.	-	.	ID=gene82
III	gt csa	mRNA	1354987	1355410	.	-	.	ID=mRNA123;Parent=gene82;Target=WP 1 125 +
III	gt csa	exon	1354987	1355171	1	-	.	Parent=mRNA123
III	gt csa	exon	1355221	1355410	1	-	.	Parent=mRNA123
###
III	gt csa	gene	1357070	1359759	.	-	.	ID=gene83
III	gt csa	mRNA	1357070	1359125	.	-	.	ID=mRNA124;Parent=gene83;Target=WP 1 391 +
III	gt csa	exon	1357070	1357311	1	-	.	Parent=mRNA124
III	gt csa	exon	1357360	1357471	1	-	.	Parent=mRNA124
III	gt csa	exon	1357509	1357735	0.969	-	.	Parent=mRNA124
III	gt csa	exon	1357835	1357952	1	-	.	Parent=mRNA124
III	gt csa	exon	1357998	1358245	1	-	.	Parent=mRNA124
III	gt csa	exon	1358287	1358398	1	-	.	Parent=mRNA124
III	gt csa	exon	1359006	1359125	1	-	.	Parent=mRNA124
III	gt csa	mRNA	1359244	1359759	.	-	.	ID=mRNA125;Parent=gene83;Target=WP 1 140 +
III	gt csa	exon	1359244	1359488	1	-	.	Parent=mRNA125
III	gt csa	exon	1359538	1359655	1	-	.	Parent=mRNA125
III	gt csa	exon	1359703	1359759	1	-	.	Parent=mRNA125
###
III	gt csa	gene	1360497	1362666	.	+	.	ID=gene84
III	gt csa	mRNA	1360497	1362666	.	+	.	ID=mRNA126;Parent=gene84;Target=WP 1 537 +
III	gt csa	exon	1360497	1360553	1	+	.	Parent=mRNA126
III	gt csa	exon	1360601	1360718	1	+	.	Parent=mRNA126
III	gt csa	exon	1360779	1360948	1	+	.	Parent=mRNA126
III	gt csa	exon	1361034	1361151	1	+	.	Parent=mRNA126
III	gt csa	exon	1361197	1361420	1	+	.	Parent=mRNA126
III	gt csa	exon	1361465	1361576	1	+	.	Parent=mRNA126
III	gt csa	exon	1361749	1361960	1	+	.	Parent=mRNA126
III	gt csa	exon	1362006	1362123	1	+	.	Parent=mRNA126
III	gt csa	exon	1362185	1362666	1	+	.	Parent=mRNA126
###
III	gt csa	gene	1374142	1374515	.	+	.	ID=gene85
III	gt csa	mRNA	1374142	1374515	.	+	.	ID=mRNA127;Parent=gene85;Target=yk604h8.5 1 374 +
III	gt csa	exon	1374142	1374515	1	+	.	Parent=mRNA127
###
III	gt csa	gene	1374575	1374874	.	-	.	ID=gene86
III	gt csa	mRNA	1374575	1374874	.	-	.	ID=mRNA128;Parent=gene86;Target=yk604h8.3 1 300 +
III	gt csa	exon	1374575	1374874	0.993	-	.	Parent=mRNA128
###
III	gt csa	gene	1376935	1377993	.	-	.	ID=gene87
III	gt csa	mRNA	1376935	1377993	.	-	.	ID=mRNA129;Parent=gene87;Target=WP 1 215 +
III	gt csa	exon	1376935	1377144	1	-	.	Parent=mRNA129
III	gt csa	exon	1377379	1377681	1	-	.	Parent=mRNA129
III	gt csa	exon	1377862	1377993	1	-	.	Parent=mRNA129
###
III	gt csa	gene	1379130	1383572	.	-	.	ID=gene88
III	gt csa	mRNA	1379130	1383572	.	-	.	ID=mRNA130;Parent=gene88;Target=WP 1 439 +
III	gt csa	exon	1379130	1379360	1	-	.	Parent=mRNA130
III	gt csa	exon	1379412	1379579	1	-	.	Parent=mRNA130
III	gt csa	exon	1380424	1380553	1	-	.	Parent=mRNA130
III	gt csa	exon	1380609	1380685	0.902	-	.	Parent=mRNA130
III	gt csa	exon	1382653	1382989	1	-	.	Parent=mRNA130
III	gt csa	exon	1383057	1383140	1	-	.	Parent=mRNA130
III	gt csa	exon	1383283	1383572	1	-	.	Parent=mRNA130
###
III	gt csa	gene	1387471	1388069	.	+	.	ID=gene89
III	gt csa	mRNA	1387471	1388069	.	+	.	ID=mRNA131;Parent=gene89;Target=yk539a12.5 1 360 +
III	gt csa	exon	1387471	1387545	0.967	+	.	Parent=mRNA131
III	gt csa	exon	1387786	1388069	1	+	.	Parent=mRNA131
###
III	gt csa	gene	1387828	1388127	.	-	.	ID=gene90
III	gt csa	mRNA	1387828	1388127	.	-	.	ID=mRNA132;Parent=gene90;Target=yk539a12.3 1 300 +
III	gt csa	exon	1387828	1388127	0.987	-	.	Parent=mRNA132
###
III	gt csa	gene	1390536	1391840	.	-	.	ID=gene91
III	gt csa	mRNA	1390536	1391840	.	-	.	ID=mRNA133;Parent=gene91;Target=WP 1 252 +,CK579587 1 622 +,CB102366 100 678 +,CB102201 91 657 +,CK579588 1 556 +,CK583482 1 503 +,CB102373 95 478 +,CK583393 1 222 +
III	gt csa	exon	1390536	1390718	1	-	.	Parent=mRNA133
III	gt csa	exon	1390764	1391067	1	-	.	Parent=mRNA133
III	gt csa	exon	1391411	1391499	1	-	.	Parent=mRNA133
III	gt csa	exon	1391551	1391638	1	-	.	Parent=mRNA133
III	gt csa	exon	1391688	1391736	1	-	.	Parent=mRNA133
III	gt csa	exon	1391782	1391840	1	-	.	Parent=mRNA133
###
III	gt csa	gene	1399366	1401295	.	+	.	ID=gene92
III	gt csa	mRNA	1399366	1401295	.	+	.	ID=mRNA134;Parent=gene92;Target=WP 1 357 +
III	gt csa	exon	1399366	1399462	1	+	.	Parent=mRNA134
III	gt csa	exon	1399964	1400070	1	+	.	Parent=mRNA134
III	gt csa	exon	1400121	1400270	1	+	.	Parent=mRNA134
III	gt csa	exon	1400319	1400648	1	+	.	Parent=mRNA134
III	gt csa	exon	1400696	1400854	1	+	.	Parent=mRNA134
III	gt csa	exon	1401068	1401295	1	+	.	Parent=mRNA134
###
III	gt csa	gene	1401956	1403309	.	+	.	ID=gene93
III	gt csa	mRNA	1401956	1403309	.	+	.	ID=mRNA135;Parent=gene93;Target=WP 1 258 +
III	gt csa	exon	1401956	1402065	1	+	.	Parent=mRNA135
III	gt csa	exon	1402385	1402463	1	+	.	Parent=mRNA135
III	gt csa	exon	1402510	1402610	1	+	.	Parent=mRNA135
III	gt csa	exon	1402777	1403077	1	+	.	Parent=mRNA135
III	gt csa	exon	1403127	1403309	1	+	.	Parent=mRNA135
###
III	gt csa	gene	1404782	1406220	.	+	.	ID=gene94
III	gt csa	mRNA	1404782	1406220	.	+	.	ID=mRNA136;Parent=gene94;Target=yk1098g06.5 11 546 +,WP 1 257 +,yk1098g06.3 1 708 -
III	gt csa	exon	1404782	1404928	0.993	+	.	Parent=mRNA136
III	gt csa	exon	1404984	1405322	1	+	.	Parent=mRNA136
III	gt csa	exon	1405369	1405527	1	+	.	Parent=mRNA136
III	gt csa	exon	1405927	1406220	0.997	+	.	Parent=mRNA136
###
III	gt csa	gene	1409301	1414108	.	-	.	ID=gene95
III	gt csa	mRNA	1409301	1412855	.	-	.	ID=mRNA137;Parent=gene95;Target=yk802c04.3 1 671 -,yk1740f01.3 1 653 -,yk1067h09.3 1 728 -,yk482a5.3 1 300 -,WP 1 305 +
III	gt csa	exon	1409301	1409698	0.997	-	.	Parent=mRNA137
III	gt csa	exon	1410797	1410956	1	-	.	Parent=mRNA137
III	gt csa	exon	1412055	1412310	1	-	.	Parent=mRNA137
III	gt csa	exon	1412537	1412855	1	-	.	Parent=mRNA137
III	gt csa	mRNA	1409301	1414108	.	-	.	ID=mRNA138;Parent=gene95;Target=yk802c04.3 1 671 -,yk1740f01.3 1 653 -,yk1403f06.3 1 732 -,yk482a5.3 1 300 -,RP 1 229 +,BP 1 231 +,yk1403f06.5 23 637 +,yk1740f01.5 23 593 +,yk802c04.5 23 538 +,yk71h4.5 1 360 +,yk336a10.5 1 377 +,yk647g12.5 1 380 +,yk625f5.5 1 383 +,yk498e8.5 1 360 +,yk236b3.5 1 360 +,yk624b7.5 1 360 +,yk614c9.5 1 360 +,yk376c11.5 1 373 +,yk596b12.5 1 377 +,yk482a5.5 1 342 +,yk424h6.5 1 348 +,yk91b11.5 1 348 +,yk743g6.5 23 194 +
III	gt csa	exon	1409301	1409698	0.997	-	.	Parent=mRNA138
III	gt csa	exon	1410797	1410956	1	-	.	Parent=mRNA138
III	gt csa	exon	1412055	1412238	1	-	.	Parent=mRNA138
III	gt csa	exon	1413935	1414108	0.986	-	.	Parent=mRNA138
III	gt csa	mRNA	1412867	1413610	.	-	.	ID=mRNA139;Parent=gene95;Target=yk1067h09.5 1 744 +
III	gt csa	exon	1412867	1413610	0.995	-	.	Parent=mRNA139
###
III	gt csa	gene	1409354	1409706	.	+	.	ID=gene96
III	gt csa	mRNA	1409354	1409706	.	+	.	ID=mRNA140;Parent=gene96;Target=yk91b11.3 1 335 +,yk71h4.3 1 335 +,yk596b12.3 1 300 +,yk236b3.3 16 300 +,yk743g6.3 1 300 +,yk647g12.3 1 300 +,yk614c9.3 1 300 +,yk376c11.3 1 300 +,yk424h6.3 1 283 +,yk336a10.3 1 283 +,yk498e8.3 1 282 +
III	gt csa	exon	1409354	1409706	0.983	+	.	Parent=mRNA140
###
III	gt csa	gene	1415536	1417177	.	-	.	ID=gene97
III	gt csa	mRNA	1415536	1417177	.	-	.	ID=mRNA141;Parent=gene97;Target=CK583137 1 508 +,BP 1 124 +
III	gt csa	exon	1415536	1415865	1	-	.	Parent=mRNA141
III	gt csa	exon	1417000	1417177	1	-	.	Parent=mRNA141
###
III	gt csa	gene	1418971	1420424	.	+	.	ID=gene98
III	gt csa	mRNA	1418971	1420424	.	+	.	ID=mRNA142;Parent=gene98;Target=yk427c9.5 1 375 +,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1310e07.5 23 555 +,yk1089d01.5 23 572 +,yk1527c07.5 23 589 +,yk1344e01.3 19 587 -,yk761f11.5 17 614 +,yk809d12.3 23 628 -,yk1310e07.3 23 628 -,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1299c02.5 1 380 +,yk361d12.5 1 375 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +,CEESB14F 1 300 +,CEESY61FB 1 319 +,yk1382d08.3 1 222 +,yk621b1.3 1 300 +,yk739c4.3 1 300 +,yk597g10.3 1 300 +,yk421a11.3 1 292 +,yk447b3.3 1 300 +,yk599b8.3 1 300 +,yk639a10.3 1 300 +,yk555f9.3 1 300 +,yk615c7.3 1 240 +,yk525g4.3 1 240 +,yk556a10.5 1 365 +,yk1475h10.3 1 136 +
III	gt csa	exon	1418971	1418973	0.667	+	.	Parent=mRNA142
III	gt csa	exon	1419186	1419251	1	+	.	Parent=mRNA142
III	gt csa	exon	1419321	1420424	0.99	+	.	Parent=mRNA142
III	gt csa	mRNA	1419094	1420424	.	+	.	ID=mRNA143;Parent=gene98;Target=yk1587h06.3 135 661 -,yk1212c10.5 1 546 +,yk64h2.5 1 341 +,yk371c5.5 1 370 +,yk596e1.5 1 374 +,yk654c2.5 1 376 +,yk474d11.5 1 377 +,yk1005d11.3 1 502 -,yk1221a01.3 1 512 -,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1310e07.5 23 555 +,yk1089d01.5 23 572 +,yk1527c07.5 23 589 +,yk1344e01.3 19 587 -,yk761f11.5 17 614 +,yk809d12.3 23 628 -,yk1310e07.3 23 628 -,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1299c02.5 1 380 +,yk361d12.5 1 375 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +,CEESB14F 1 300 +,CEESY61FB 1 319 +,yk1382d08.3 1 222 +,yk621b1.3 1 300 +,yk739c4.3 1 300 +,yk597g10.3 1 300 +,yk421a11.3 1 292 +,yk447b3.3 1 300 +,yk599b8.3 1 300 +,yk639a10.3 1 300 +,yk555f9.3 1 300 +,yk615c7.3 1 240 +,yk525g4.3 1 240 +,yk556a10.5 1 365 +,yk1475h10.3 1 136 +
III	gt csa	exon	1419094	1419103	1	+	.	Parent=mRNA143
III	gt csa	exon	1419166	1419251	0.919	+	.	Parent=mRNA143
III	gt csa	exon	1419321	1420424	0.99	+	.	Parent=mRNA143
III	gt csa	mRNA	1419138	1420087	.	+	.	ID=mRNA144;Parent=gene98;Target=yk844c03.3 152 710 -,yk1072g09.3 120 674 -,yk1344a02.3 179 720 -,yk1398d04.3 114 643 -,yk1119f04.3 190 729 -,yk1396f08.3 94 712 -,yk865b04.3 146 680 -,yk1339f10.3 103 734 -,yk1212c10.5 1 546 +,yk64h2.5 1 341 +,yk371c5.5 1 370 +,yk596e1.5 1 374 +,yk654c2.5 1 376 +,yk474d11.5 1 377 +,yk1005d11.3 1 502 -,yk1221a01.3 1 512 -,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1310e07.5 23 555 +,yk1089d01.5 23 572 +,yk1527c07.5 23 589 +,yk1344e01.3 19 587 -,yk761f11.5 17 614 +,yk809d12.3 23 628 -,yk1310e07.3 23 628 -,yk757f11.5 17 635 +,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1299c02.5 1 380 +,yk361d12.5 1 375 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +
III	gt csa	exon	1419138	1419251	0.842	+	.	Parent=mRNA144
III	gt csa	exon	1419321	1419863	0.995	+	.	Parent=mRNA144
III	gt csa	exon	1420079	1420087	0.667	+	.	Parent=mRNA144
III	gt csa	mRNA	1419138	1420087	.	+	.	ID=mRNA145;Parent=gene98;Target=yk844c03.3 152 710 -,yk1072g09.3 120 674 -,yk1344a02.3 179 720 -,yk1398d04.3 114 643 -,yk1119f04.3 190 729 -,yk865b04.3 146 680 -,yk1212c10.5 1 546 +,yk64h2.5 1 341 +,yk371c5.5 1 370 +,yk596e1.5 1 374 +,yk654c2.5 1 376 +,yk474d11.5 1 377 +,yk1005d11.3 1 502 -,yk1221a01.3 1 512 -,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1258a02.5 23 558 +,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1195a11.5 1 417 +,yk1299c02.5 1 380 +,yk1133g01.5 1 368 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +
III	gt csa	exon	1419138	1419251	0.842	+	.	Parent=mRNA145
III	gt csa	exon	1419321	1419783	1	+	.	Parent=mRNA145
III	gt csa	exon	1420079	1420087	0.778	+	.	Parent=mRNA145
III	gt csa	mRNA	1419138	1420424	.	+	.	ID=mRNA146;Parent=gene98;Target=yk844c03.3 152 710 -,yk1072g09.3 120 674 -,yk1344a02.3 179 720 -,yk1398d04.3 114 643 -,yk1119f04.3 190 729 -,yk1396f08.3 94 712 -,yk865b04.3 146 680 -,yk1339f10.3 103 734 -,yk1212c10.5 1 546 +,yk64h2.5 1 341 +,yk371c5.5 1 370 +,yk596e1.5 1 374 +,yk654c2.5 1 376 +,yk474d11.5 1 377 +,yk1005d11.3 1 502 -,yk1221a01.3 1 512 -,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1310e07.5 23 555 +,yk1089d01.5 23 572 +,yk1527c07.5 23 589 +,yk1344e01.3 19 587 -,yk761f11.5 17 614 +,yk809d12.3 23 628 -,yk1310e07.3 23 628 -,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1299c02.5 1 380 +,yk361d12.5 1 375 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +,CEESB14F 1 300 +,CEESY61FB 1 319 +,yk1382d08.3 1 222 +,yk621b1.3 1 300 +,yk739c4.3 1 300 +,yk597g10.3 1 300 +,yk421a11.3 1 292 +,yk447b3.3 1 300 +,yk599b8.3 1 300 +,yk639a10.3 1 300 +,yk555f9.3 1 300 +,yk615c7.3 1 240 +,yk525g4.3 1 240 +,yk556a10.5 1 365 +,yk1475h10.3 1 136 +
III	gt csa	exon	1419138	1419251	0.842	+	.	Parent=mRNA146
III	gt csa	exon	1419321	1420424	0.99	+	.	Parent=mRNA146
###
III	gt csa	gene	1419326	1427216	.	-	.	ID=gene99
III	gt csa	mRNA	1419326	1419839	.	-	.	ID=mRNA147;Parent=gene99;Target=yk1230h08.3 1 312 +,yk1527c07.3 1 508 +,yk1032a02.3 1 376 +,yk602g4.3 1 300 +,yk1195a11.3 1 378 +,yk639e2.3 1 300 +,yk763c11.3 1 356 +,CEESU49F 1 379 +,yk667h3.3 1 300 +,yk1526d06.3 1 360 +,CEESM53F 1 381 +,yk596e1.3 1 300 +,yk654e2.3 1 180 +,yk586d10.3 1 240 +,yk281f9.3 1 300 +,yk255e5.3 1 300 +,yk654e1.3 1 180 +,yk591h11.3 1 240 +,yk634d3.3 1 300 +,yk654c2.3 1 300 +,yk487f9.3 1 300 +,yk515d3.3 1 300 +,yk654d2.3 1 300 +,yk672d12.3 1 300 +,yk631d3.3 1 300 +,yk612a2.3 1 300 +,yk654g12.3 1 180 +,yk281a2.3 1 300 +,yk609a6.3 1 300 +,yk612e4.3 1 300 +,yk371c5.3 1 300 +,yk648e7.3 1 300 +,yk1133g01.3 1 342 +,yk579f1.3 1 300 +,yk289b9.3 1 300 +,yk110a8.3 1 342 +,CEESH76F 1 352 +,yk114f3.3 1 326 +,yk67e2.3 1 332 +,yk64h2.3 1 337 +,yk1382h02.3 1 106 +,CEESV10F 1 307 +,yk92d5.3 1 292 +,CEESN05F 1 295 +,yk677a10.3 1 300 +,yk847c05.3 1 253 +,yk833b04.3 1 252 +,yk78a9.3 1 300 +,CEESX12F 1 238 +,yk62e4.3 1 180 +,yk92c4.3 1 152 +,yk1692c10.3 1 127 +,yk1637f01.3 1 136 +
III	gt csa	exon	1419326	1419839	0.96	-	.	Parent=mRNA147
III	gt csa	mRNA	1419858	1427216	.	-	.	ID=mRNA148;Parent=gene99;Target=yk1572a07.3 1 708 -,yk1483e05.3 1 710 -,yk845a11.3 1 671 -,yk1091h10.3 1 703 -,yk777g07.3 1 702 -,yk843d03.3 1 655 -,yk1037c05.3 1 702 -,yk1339b07.3 1 706 -,yk1156e02.3 1 713 -,yk1221d11.3 1 718 -,yk1271e02.3 1 702 -,yk1175h04.3 1 701 -,yk1068f01.3 1 777 -,yk1534a04.3 1 671 -,yk1397e11.3 1 735 -,yk1467c02.3 1 668 -,yk1447g10.3 1 689 -,yk1588c10.3 1 694 -,yk1616c04.3 1 745 -,yk1449e07.3 1 743 -,yk1422c01.3 1 711 -,yk1433e11.3 1 713 -,yk1359d11.3 1 739 -,yk1741b07.3 1 645 -,yk1382d05.3 1 724 -,yk1491e06.3 1 722 -,yk1111g04.3 1 667 -,yk1677f12.3 1 683 -,RP 1 549 +,BP 1 546 +,yk421a11.5 1 360 +,yk384h6.5 1 375 +,yk639a10.5 1 360 +,yk1021a01.5 20 655 +,yk1483e05.5 17 650 +,yk1359d11.5 23 655 +,yk1382d05.5 23 654 +,yk1433e11.5 22 650 +,yk1422c01.5 23 628 +,yk1397e11.5 22 625 +,yk1091h10.5 23 616 +,yk1221d11.5 23 614 +,yk845a11.5 23 613 +,yk1339b07.5 23 612 +,yk1068f01.5 23 611 +,yk1677f12.5 24 611 +,yk1382d08.5 23 610 +,yk1680g05.5 23 610 +,yk1439g04.5 23 609 +,yk1741b07.5 22 608 +,yk1037c05.5 23 606 +,yk1491e06.5 23 606 +,yk1588c10.5 23 604 +,yk1175h04.5 23 603 +,yk777g07.5 20 534 +,yk843d03.5 23 534 +,yk1111g04.5 23 512 +,yk1467c02.5 22 500 +,yk1449c10.5 23 463 +,yk1572a07.5 23 461 +,yk1447g10.5 23 460 +,yk1449e07.5 23 460 +,yk525g4.5 1 375 +,cm20f7.5 11 407 +,yk275h6.5 1 351 +,yk597g10.5 1 354 +,yk447b3.5 1 355 +,yk599b8.5 1 359 +,yk615c7.5 1 370 +,yk1534a04.5 27 403 +,yk739c4.5 23 340 +
III	gt csa	exon	1419858	1420431	0.998	-	.	Parent=mRNA148
III	gt csa	exon	1421391	1421771	0.897	-	.	Parent=mRNA148
III	gt csa	exon	1424258	1424349	0.948	-	.	Parent=mRNA148
III	gt csa	exon	1425095	1425427	0.96	-	.	Parent=mRNA148
III	gt csa	exon	1425902	1425994	1	-	.	Parent=mRNA148
III	gt csa	exon	1426159	1426285	1	-	.	Parent=mRNA148
III	gt csa	exon	1427060	1427216	1	-	.	Parent=mRNA148
III	gt csa	mRNA	1420034	1420559	.	-	.	ID=mRNA149;Parent=gene99;Target=yk421a11.5 1 360 +,yk555f9.5 1 360 +
III	gt csa	exon	1420034	1420559	0.993	-	.	Parent=mRNA149
III	gt csa	mRNA	1421684	1424322	.	-	.	ID=mRNA150;Parent=gene99;Target=yk621b1.5 1 240 +
III	gt csa	exon	1421684	1421858	0.943	-	.	Parent=mRNA150
III	gt csa	exon	1424258	1424322	1	-	.	Parent=mRNA150
###
III	gt csa	gene	1439086	1443180	.	+	.	ID=gene100
III	gt csa	mRNA	1439086	1443180	.	+	.	ID=mRNA151;Parent=gene100;Target=WP 1 531 +
III	gt csa	exon	1439086	1439148	1	+	.	Parent=mRNA151
III	gt csa	exon	1439194	1439289	1	+	.	Parent=mRNA151
III	gt csa	exon	1439346	1439507	1	+	.	Parent=mRNA151
III	gt csa	exon	1439552	1439628	1	+	.	Parent=mRNA151
III	gt csa	exon	1439705	1439927	1	+	.	Parent=mRNA151
III	gt csa	exon	1440041	1440100	1	+	.	Parent=mRNA151
III	gt csa	exon	1440409	1440543	1	+	.	Parent=mRNA151
III	gt csa	exon	1440839	1440928	1	+	.	Parent=mRNA151
III	gt csa	exon	1441573	1441826	1	+	.	Parent=mRNA151
III	gt csa	exon	1441882	1442030	1	+	.	Parent=mRNA151
III	gt csa	exon	1442396	1442547	1	+	.	Parent=mRNA151
III	gt csa	exon	1443049	1443180	1	+	.	Parent=mRNA151
###
III	gt csa	gene	1443038	1443263	.	-	.	ID=gene101
III	gt csa	mRNA	1443038	1443263	.	-	.	ID=mRNA152;Parent=gene101;Target=yk525g8.3 80 300 +,yk656g8.3 80 300 +,yk658b12.3 83 300 +,yk337c2.3 84 300 +,yk675h9.3 85 300 +,yk602e8.3 86 300 +,yk652b11.3 86 300 +,yk659c10.3 86 300 +,yk621h1.3 88 300 +,yk572f4.3 77 288 +,yk592b8.3 75 286 +,yk617a4.3 81 300 +
III	gt csa	exon	1443038	1443263	0.866	-	.	Parent=mRNA152
###
III	gt csa	gene	1447545	1455750	.	-	.	ID=gene102
III	gt csa	mRNA	1447545	1455750	.	-	.	ID=mRNA153;Parent=gene102;Target=yk674c5.3 1 300 -,yk513e12.3 1 300 -,WP 1 482 +,yk674c5.5 1 360 +
III	gt csa	exon	1447545	1447665	1	-	.	Parent=mRNA153
III	gt csa	exon	1449965	1450063	1	-	.	Parent=mRNA153
III	gt csa	exon	1450108	1450340	1	-	.	Parent=mRNA153
III	gt csa	exon	1450555	1450692	1	-	.	Parent=mRNA153
III	gt csa	exon	1450743	1450802	1	-	.	Parent=mRNA153
III	gt csa	exon	1450847	1450919	1	-	.	Parent=mRNA153
III	gt csa	exon	1451910	1452038	1	-	.	Parent=mRNA153
III	gt csa	exon	1452084	1452139	1	-	.	Parent=mRNA153
III	gt csa	exon	1452429	1452468	1	-	.	Parent=mRNA153
III	gt csa	exon	1453036	1453163	1	-	.	Parent=mRNA153
III	gt csa	exon	1454216	1454391	1	-	.	Parent=mRNA153
III	gt csa	exon	1454479	1454572	1	-	.	Parent=mRNA153
III	gt csa	exon	1454621	1454698	1	-	.	Parent=mRNA153
III	gt csa	exon	1455676	1455750	1	-	.	Parent=mRNA153
III	gt csa	mRNA	1448290	1449007	.	-	.	ID=mRNA154;Parent=gene102;Target=yk1044a02.5 1 718 +
III	gt csa	exon	1448290	1449007	0.997	-	.	Parent=mRNA154
III	gt csa	mRNA	1452028	1452748	.	-	.	ID=mRNA155;Parent=gene102;Target=yk513e12.5 1 386 +
III	gt csa	exon	1452028	1452038	1	-	.	Parent=mRNA155
III	gt csa	exon	1452084	1452139	0.982	-	.	Parent=mRNA155
III	gt csa	exon	1452429	1452748	1	-	.	Parent=mRNA155
###
III	gt csa	gene	1449026	1449551	.	+	.	ID=gene103
III	gt csa	mRNA	1449026	1449551	.	+	.	ID=mRNA156;Parent=gene103;Target=yk1044a02.3 208 712 +
III	gt csa	exon	1449026	1449522	0.991	+	.	Parent=mRNA156
III	gt csa	exon	1449545	1449551	0.571	+	.	Parent=mRNA156
###
III	gt csa	gene	1458223	1466441	.	+	.	ID=gene104
III	gt csa	mRNA	1458223	1466441	.	+	.	ID=mRNA157;Parent=gene104;Target=WP 1 503 +
III	gt csa	exon	1458223	1458465	1	+	.	Parent=mRNA157
III	gt csa	exon	1458508	1458597	1	+	.	Parent=mRNA157
III	gt csa	exon	1458884	1458935	1	+	.	Parent=mRNA157
III	gt csa	exon	1459883	1460049	1	+	.	Parent=mRNA157
III	gt csa	exon	1461819	1461874	1	+	.	Parent=mRNA157
III	gt csa	exon	1461919	1462047	1	+	.	Parent=mRNA157
III	gt csa	exon	1463286	1463358	1	+	.	Parent=mRNA157
III	gt csa	exon	1463515	1463584	1	+	.	Parent=mRNA157
III	gt csa	exon	1465126	1465193	1	+	.	Parent=mRNA157
III	gt csa	exon	1465240	1465469	1	+	.	Parent=mRNA157
III	gt csa	exon	1465516	1465614	1	+	.	Parent=mRNA157
III	gt csa	exon	1465770	1465832	1	+	.	Parent=mRNA157
III	gt csa	exon	1465923	1466021	1	+	.	Parent=mRNA157
III	gt csa	exon	1466372	1466441	1	+	.	Parent=mRNA157
###
III	gt csa	gene	1466377	1466722	.	-	.	ID=gene105
III	gt csa	mRNA	1466377	1466722	.	-	.	ID=mRNA158;Parent=gene105;Target=CEESB41F 1 346 +
III	gt csa	exon	1466377	1466722	0.965	-	.	Parent=mRNA158
###
III	gt csa	gene	1467863	1483497	.	-	.	ID=gene106
III	gt csa	mRNA	1467863	1483497	.	-	.	ID=mRNA159;Parent=gene106;Target=yk1170a01.3 1 765 -,yk1128d05.3 1 726 -,yk405c3.3 1 300 -,yk500f5.3 1 300 -,yk288a6.3 1 300 -,WP 1 922 +,yk135h2.5 1 373 +,yk288a6.5 1 360 +,yk1170a01.5 22 593 +,yk1128d05.5 23 588 +
III	gt csa	exon	1467863	1468170	0.981	-	.	Parent=mRNA159
III	gt csa	exon	1469171	1469260	1	-	.	Parent=mRNA159
III	gt csa	exon	1470517	1471342	1	-	.	Parent=mRNA159
III	gt csa	exon	1472209	1472382	1	-	.	Parent=mRNA159
III	gt csa	exon	1473915	1474201	1	-	.	Parent=mRNA159
III	gt csa	exon	1474848	1475099	1	-	.	Parent=mRNA159
III	gt csa	exon	1476256	1476485	1	-	.	Parent=mRNA159
III	gt csa	exon	1477039	1477574	1	-	.	Parent=mRNA159
III	gt csa	exon	1478937	1479126	1	-	.	Parent=mRNA159
III	gt csa	exon	1483404	1483497	1	-	.	Parent=mRNA159
III	gt csa	mRNA	1474973	1476685	.	-	.	ID=mRNA160;Parent=gene106;Target=yk500f5.5 1 360 +
III	gt csa	exon	1474973	1475099	1	-	.	Parent=mRNA160
III	gt csa	exon	1476256	1476485	0.989	-	.	Parent=mRNA160
III	gt csa	exon	1476684	1476685	1	-	.	Parent=mRNA160
###
III	gt csa	gene	1467866	1468169	.	+	.	ID=gene107
III	gt csa	mRNA	1467866	1468169	.	+	.	ID=mRNA161;Parent=gene107;Target=CEESH11F 1 304 +
III	gt csa	exon	1467866	1468169	0.984	+	.	Parent=mRNA161
###
III	gt csa	gene	1484961	1495320	.	-	.	ID=gene108
III	gt csa	mRNA	1484961	1495320	.	-	.	ID=mRNA162;Parent=gene108;Target=WP 1 418 +
III	gt csa	exon	1484961	1485116	1	-	.	Parent=mRNA162
III	gt csa	exon	1487387	1487633	1	-	.	Parent=mRNA162
III	gt csa	exon	1487730	1487831	1	-	.	Parent=mRNA162
III	gt csa	exon	1490092	1490294	1	-	.	Parent=mRNA162
III	gt csa	exon	1491404	1491494	1	-	.	Parent=mRNA162
III	gt csa	exon	1491548	1491666	1	-	.	Parent=mRNA162
III	gt csa	exon	1493719	1493970	1	-	.	Parent=mRNA162
III	gt csa	exon	1495237	1495320	1	-	.	Parent=mRNA162
###
III	gt csa	gene	1509455	1510895	.	+	.	ID=gene109
III	gt csa	mRNA	1509455	1510895	.	+	.	ID=mRNA163;Parent=gene109;Target=yk1187f01.3 1 381 +
III	gt csa	exon	1509455	1509613	0.855	+	.	Parent=mRNA163
III	gt csa	exon	1510265	1510335	0.817	+	.	Parent=mRNA163
III	gt csa	exon	1510742	1510895	0.916	+	.	Parent=mRNA163
###
III	gt csa	gene	1509574	1517983	.	-	.	ID=gene110
III	gt csa	mRNA	1509574	1512913	.	-	.	ID=mRNA164;Parent=gene110;Target=yk275e6.5 1 360 +,yk1146d12.3 1 312 -
III	gt csa	exon	1509574	1509618	0.978	-	.	Parent=mRNA164
III	gt csa	exon	1510270	1510341	0.986	-	.	Parent=mRNA164
III	gt csa	exon	1510751	1510948	0.987	-	.	Parent=mRNA164
III	gt csa	exon	1512871	1512913	0.872	-	.	Parent=mRNA164
III	gt csa	mRNA	1512956	1517983	.	-	.	ID=mRNA165;Parent=gene110;Target=yk1146d12.5 35 612 +,yk774d03.5 23 597 +,yk479a10.5 1 378 +,yk237e8.5 1 360 +,yk714f9.5 23 365 +
III	gt csa	exon	1512956	1513125	1	-	.	Parent=mRNA165
III	gt csa	exon	1515550	1515605	1	-	.	Parent=mRNA165
III	gt csa	exon	1515725	1515894	1	-	.	Parent=mRNA165
III	gt csa	exon	1517731	1517849	1	-	.	Parent=mRNA165
III	gt csa	exon	1517921	1517983	1	-	.	Parent=mRNA165
###
III	gt csa	gene	1520214	1532758	.	-	.	ID=gene111
III	gt csa	mRNA	1520214	1532758	.	-	.	ID=mRNA166;Parent=gene111;Target=AY661556 1 2145 +
III	gt csa	exon	1520214	1520363	1	-	.	Parent=mRNA166
III	gt csa	exon	1521573	1521926	1	-	.	Parent=mRNA166
III	gt csa	exon	1523142	1523685	1	-	.	Parent=mRNA166
III	gt csa	exon	1525164	1525402	1	-	.	Parent=mRNA166
III	gt csa	exon	1526403	1526535	1	-	.	Parent=mRNA166
III	gt csa	exon	1528084	1528234	1	-	.	Parent=mRNA166
III	gt csa	exon	1528291	1528435	1	-	.	Parent=mRNA166
III	gt csa	exon	1529809	1529984	1	-	.	Parent=mRNA166
III	gt csa	exon	1531762	1531821	1	-	.	Parent=mRNA166
III	gt csa	exon	1532182	1532275	1	-	.	Parent=mRNA166
III	gt csa	exon	1532660	1532758	1	-	.	Parent=mRNA166
III	gt csa	mRNA	1521343	1529982	.	-	.	ID=mRNA167;Parent=gene111;Target=BP 1 525 +
III	gt csa	exon	1521343	1521363	0.189	-	.	Parent=mRNA167
III	gt csa	exon	1521573	1521926	0.879	-	.	Parent=mRNA167
III	gt csa	exon	1523142	1523685	0.95	-	.	Parent=mRNA167
III	gt csa	exon	1525164	1525402	0.893	-	.	Parent=mRNA167
III	gt csa	exon	1526403	1526535	0.988	-	.	Parent=mRNA167
III	gt csa	exon	1528323	1528435	1	-	.	Parent=mRNA167
III	gt csa	exon	1529809	1529982	0.921	-	.	Parent=mRNA167
III	gt csa	mRNA	1521569	1531828	.	-	.	ID=mRNA168;Parent=gene111;Target=RP 1 544 +
III	gt csa	exon	1521569	1521926	0.88	-	.	Parent=mRNA168
III	gt csa	exon	1523142	1523685	0.947	-	.	Parent=mRNA168
III	gt csa	exon	1525164	1525402	0.895	-	.	Parent=mRNA168
III	gt csa	exon	1526403	1526535	0.969	-	.	Parent=mRNA168
III	gt csa	exon	1528323	1528435	1	-	.	Parent=mRNA168
III	gt csa	exon	1529809	1529984	0.923	-	.	Parent=mRNA168
III	gt csa	exon	1531762	1531828	0.969	-	.	Parent=mRNA168
###
III	gt csa	gene	1537499	1538168	.	-	.	ID=gene112
III	gt csa	mRNA	1537499	1538168	.	-	.	ID=mRNA169;Parent=gene112;Target=yk1272b06.3 1 670 +
III	gt csa	exon	1537499	1538168	0.997	-	.	Parent=mRNA169
###
III	gt csa	gene	1540487	1543445	.	+	.	ID=gene113
III	gt csa	mRNA	1540487	1543445	.	+	.	ID=mRNA170;Parent=gene113;Target=yk427d4.5 1 361 +,yk630d2.5 1 376 +,RP 1 157 +,yk308b12.5 1 360 +,yk1375b08.3 1 496 -,yk1375b08.5 1 531 +,yk308b12.3 1 300 -,yk427d4.3 1 300 -
III	gt csa	exon	1540487	1540540	0.954	+	.	Parent=mRNA170
III	gt csa	exon	1540708	1540869	1	+	.	Parent=mRNA170
III	gt csa	exon	1541916	1542059	1	+	.	Parent=mRNA170
III	gt csa	exon	1543175	1543445	0.985	+	.	Parent=mRNA170
###
III	gt csa	gene	1544928	1554435	.	-	.	ID=gene114
III	gt csa	mRNA	1544928	1554435	.	-	.	ID=mRNA171;Parent=gene114;Target=CESAC53F 1 323 -,yk236c12.3 1 300 -,yk670g3.3 1 300 -,RP 1 723 +,BP 1 717 +,yk166a9.5 1 380 +,yk670g3.5 1 360 +,yk341h12.5 1 364 +
III	gt csa	exon	1544928	1545199	0.982	-	.	Parent=mRNA171
III	gt csa	exon	1546519	1546675	0.932	-	.	Parent=mRNA171
III	gt csa	exon	1547363	1547757	0.918	-	.	Parent=mRNA171
III	gt csa	exon	1548432	1548499	0.924	-	.	Parent=mRNA171
III	gt csa	exon	1549231	1549616	0.9	-	.	Parent=mRNA171
III	gt csa	exon	1550539	1550735	0.873	-	.	Parent=mRNA171
III	gt csa	exon	1551380	1551622	0.988	-	.	Parent=mRNA171
III	gt csa	exon	1552597	1552760	1	-	.	Parent=mRNA171
III	gt csa	exon	1552826	1552996	0.95	-	.	Parent=mRNA171
III	gt csa	exon	1554189	1554435	0.945	-	.	Parent=mRNA171
###
III	gt csa	gene	1555385	1560461	.	+	.	ID=gene115
III	gt csa	mRNA	1555385	1556102	.	+	.	ID=mRNA172;Parent=gene115;Target=yk1111d10.3 1 616 +,yk475g1.3 1 300 +,yk415h12.3 1 300 +,yk491d7.3 1 300 +,yk589g10.3 1 300 +,yk607b8.3 1 300 +,yk157b1.3 1 300 +
III	gt csa	exon	1555385	1556102	0.978	+	.	Parent=mRNA172
III	gt csa	mRNA	1558790	1560461	.	+	.	ID=mRNA173;Parent=gene115;Target=yk1371c11.5 23 357 +,yk1030d09.5 23 357 +,yk1508a02.5 23 521 +,yk1540b10.5 23 524 +,yk1532h03.5 23 561 +,yk1371c12.5 23 602 +,yk1364c12.5 23 604 +,yk1395h09.5 22 605 +,yk1377c09.5 23 614 +,yk498e1.5 1 360 +
III	gt csa	exon	1558790	1558898	1	+	.	Parent=mRNA173
III	gt csa	exon	1558949	1559033	1	+	.	Parent=mRNA173
III	gt csa	exon	1559100	1559240	1	+	.	Parent=mRNA173
III	gt csa	exon	1560205	1560461	1	+	.	Parent=mRNA173
###
III	gt csa	gene	1555397	1558519	.	-	.	ID=gene116
III	gt csa	mRNA	1555397	1558519	.	-	.	ID=mRNA174;Parent=gene116;Target=yk1111d10.5 1 607 +,yk607b8.5 1 377 +,yk1518a06.3 1 610 -,yk475g1.5 1 360 +,yk415h12.5 1 360 +,yk1518a06.5 23 582 +,CK580339 1 480 +,yk491d7.5 1 360 +,yk236h2.5 1 360 +,yk157b1.5 16 384 +,yk589g10.5 1 360 +
III	gt csa	exon	1555397	1556159	1	-	.	Parent=mRNA174
III	gt csa	exon	1557562	1557862	1	-	.	Parent=mRNA174
III	gt csa	exon	1558159	1558268	1	-	.	Parent=mRNA174
III	gt csa	exon	1558323	1558397	1	-	.	Parent=mRNA174
III	gt csa	exon	1558446	1558519	1	-	.	Parent=mRNA174
###
III	gt csa	gene	1563434	1577849	.	+	.	ID=gene117
III	gt csa	mRNA	1563434	1570107	.	+	.	ID=mRNA175;Parent=gene117;Target=yk1532h03.3 1 751 -,yk1364c12.3 1 710 -,yk1377c09.3 1 708 -,yk1030d09.3 1 689 -,yk1508a02.3 1 658 -,yk1540b10.3 1 642 -,yk1371c11.3 1 611 -,yk1371c12.3 1 550 -,yk1395h09.3 1 549 -
III	gt csa	exon	1563434	1563617	0.97	+	.	Parent=mRNA175
III	gt csa	exon	1564968	1565122	0.994	+	.	Parent=mRNA175
III	gt csa	exon	1565383	1565545	0.994	+	.	Parent=mRNA175
III	gt csa	exon	1569746	1570107	0.983	+	.	Parent=mRNA175
III	gt csa	mRNA	1570296	1573761	.	+	.	ID=mRNA176;Parent=gene117;Target=yk267a5.5 1 376 +,yk832e07.5 23 479 +,yk1755e04.5 22 536 +,yk1344g03.5 24 566 +,yk1736b09.5 24 568 +,yk1654g06.5 25 578 +,yk1672c02.5 24 581 +,yk1648c12.5 24 586 +,yk1743a02.5 23 609 +,yk1365e09.5 23 634 +,yk1618f02.5 15 652 +,yk1612a04.5 1 398 +,yk548h9.5 1 372 +
III	gt csa	exon	1570296	1570429	1	+	.	Parent=mRNA176
III	gt csa	exon	1571414	1571483	1	+	.	Parent=mRNA176
III	gt csa	exon	1571534	1571764	1	+	.	Parent=mRNA176
III	gt csa	exon	1572543	1572694	1	+	.	Parent=mRNA176
III	gt csa	exon	1572790	1572997	1	+	.	Parent=mRNA176
III	gt csa	exon	1573737	1573761	1	+	.	Parent=mRNA176
III	gt csa	mRNA	1573827	1576628	.	+	.	ID=mRNA177;Parent=gene117;Target=yk1618f02.3 1 742 -,yk1755e04.3 1 743 -,yk1344g03.3 1 711 -,yk1736b09.3 1 649 -,yk1365e09.3 1 704 -,yk1654g06.3 1 694 -,yk1672c02.3 21 686 -,yk1612a04.3 1 663 -,yk1743a02.3 1 617 -,yk1648c12.3 1 629 -,yk832e07.3 1 524 -,yk1235d02.3 1 465 -,yk605e4.3 1 300 -
III	gt csa	exon	1573827	1573915	0.989	+	.	Parent=mRNA177
III	gt csa	exon	1574217	1574376	1	+	.	Parent=mRNA177
III	gt csa	exon	1574938	1575034	1	+	.	Parent=mRNA177
III	gt csa	exon	1575084	1575161	1	+	.	Parent=mRNA177
III	gt csa	exon	1576071	1576198	1	+	.	Parent=mRNA177
III	gt csa	exon	1576416	1576628	0.995	+	.	Parent=mRNA177
III	gt csa	mRNA	1573884	1576610	.	+	.	ID=mRNA178;Parent=gene117;Target=yk1154b02.3 1 687 -,yk446d1.5 1 234 +,yk1235d02.3 1 465 -,yk605e4.3 1 300 -
III	gt csa	exon	1573884	1573915	1	+	.	Parent=mRNA178
III	gt csa	exon	1574217	1574257	1	+	.	Parent=mRNA178
III	gt csa	exon	1574822	1575034	0.995	+	.	Parent=mRNA178
III	gt csa	exon	1575084	1575161	1	+	.	Parent=mRNA178
III	gt csa	exon	1576071	1576198	1	+	.	Parent=mRNA178
III	gt csa	exon	1576416	1576610	1	+	.	Parent=mRNA178
III	gt csa	mRNA	1576754	1577849	.	+	.	ID=mRNA179;Parent=gene117;Target=yk423d1.5 1 360 +
III	gt csa	exon	1576754	1576868	0.974	+	.	Parent=mRNA179
III	gt csa	exon	1577605	1577849	1	+	.	Parent=mRNA179
###
III	gt csa	gene	1569814	1570053	.	-	.	ID=gene118
III	gt csa	mRNA	1569814	1570053	.	-	.	ID=mRNA180;Parent=gene118;Target=yk252b6.3 1 240 +
III	gt csa	exon	1569814	1570053	0.938	-	.	Parent=mRNA180
###
III	gt csa	gene	1579272	1580784	.	+	.	ID=gene119
III	gt csa	mRNA	1579272	1580784	.	+	.	ID=mRNA181;Parent=gene119;Target=yk672c6.3 1 300 -,yk423d1.3 1 300 -
III	gt csa	exon	1579272	1579319	1	+	.	Parent=mRNA181
III	gt csa	exon	1580527	1580784	1	+	.	Parent=mRNA181
###
III	gt csa	gene	1583146	1584881	.	-	.	ID=gene120
III	gt csa	mRNA	1583146	1584881	.	-	.	ID=mRNA182;Parent=gene120;Target=yk1513e11.5 1 611 +,yk1513e11.3 1 577 -,yk378b9.5 1 376 +,yk102a5.5 1 360 +
III	gt csa	exon	1583146	1583491	1	-	.	Parent=mRNA182
III	gt csa	exon	1584617	1584881	0.992	-	.	Parent=mRNA182
###
III	gt csa	gene	1583159	1583488	.	+	.	ID=gene121
III	gt csa	mRNA	1583159	1583488	.	+	.	ID=mRNA183;Parent=gene121;Target=yk102a5.3 1 315 +,yk378b9.3 1 279 +
III	gt csa	exon	1583159	1583488	0.957	+	.	Parent=mRNA183
###
III	gt csa	gene	1605742	1606803	.	+	.	ID=gene122
III	gt csa	mRNA	1605742	1606803	.	+	.	ID=mRNA184;Parent=gene122;Target=BP 1 152 +
III	gt csa	exon	1605742	1605953	0.982	+	.	Parent=mRNA184
III	gt csa	exon	1606445	1606556	0.751	+	.	Parent=mRNA184
III	gt csa	exon	1606672	1606803	1	+	.	Parent=mRNA184
III	gt csa	mRNA	1605745	1606803	.	+	.	ID=mRNA185;Parent=gene122;Target=RP 1 142 +
III	gt csa	exon	1605745	1605953	0.983	+	.	Parent=mRNA185
III	gt csa	exon	1606472	1606556	0.972	+	.	Parent=mRNA185
III	gt csa	exon	1606672	1606803	1	+	.	Parent=mRNA185
###
III	gt csa	gene	1606834	1610636	.	-	.	ID=gene123
III	gt csa	mRNA	1606834	1609423	.	-	.	ID=mRNA186;Parent=gene123;Target=yk1416d09.3 1 705 -,yk1362f07.3 1 706 -,yk1547d11.3 1 703 -,yk517d4.3 1 300 -,yk539b10.3 1 300 -,yk579b9.3 1 172 -
III	gt csa	exon	1606834	1606880	0.979	-	.	Parent=mRNA186
III	gt csa	exon	1606929	1607019	1	-	.	Parent=mRNA186
III	gt csa	exon	1607623	1607756	1	-	.	Parent=mRNA186
III	gt csa	exon	1607809	1608154	1	-	.	Parent=mRNA186
III	gt csa	exon	1609334	1609423	1	-	.	Parent=mRNA186
III	gt csa	mRNA	1609706	1610636	.	-	.	ID=mRNA187;Parent=gene123;Target=yk539b10.5 1 360 +
III	gt csa	exon	1609706	1609870	0.994	-	.	Parent=mRNA187
III	gt csa	exon	1610442	1610636	1	-	.	Parent=mRNA187
###
III	gt csa	gene	1611351	1614022	.	-	.	ID=gene124
III	gt csa	mRNA	1611351	1614022	.	-	.	ID=mRNA188;Parent=gene124;Target=yk1547d11.5 1 438 +,yk1416d09.5 23 573 +,yk1362f07.5 23 549 +,yk517d4.5 1 360 +
III	gt csa	exon	1611351	1611537	1	-	.	Parent=mRNA188
III	gt csa	exon	1612158	1612264	1	-	.	Parent=mRNA188
III	gt csa	exon	1612870	1613031	1	-	.	Parent=mRNA188
III	gt csa	exon	1613520	1614022	1	-	.	Parent=mRNA188
###
III	gt csa	gene	1617126	1618924	.	-	.	ID=gene125
III	gt csa	mRNA	1617126	1618924	.	-	.	ID=mRNA189;Parent=gene125;Target=CK589550 1 323 +,BP 1 109 +,RP 1 109 +,yk81b11.5 1 330 +,yk175h6.5 1 222 +
III	gt csa	exon	1617126	1617142	0.647	-	.	Parent=mRNA189
III	gt csa	exon	1617362	1617429	0.956	-	.	Parent=mRNA189
III	gt csa	exon	1618260	1618379	1	-	.	Parent=mRNA189
III	gt csa	exon	1618719	1618832	0.991	-	.	Parent=mRNA189
III	gt csa	exon	1618885	1618924	0.975	-	.	Parent=mRNA189
III	gt csa	mRNA	1617142	1618924	.	-	.	ID=mRNA190;Parent=gene125;Target=yk1213c04.5 23 578 +,yk762h06.5 23 577 +,yk62a4.3 1 298 -,yk1597b03.3 164 675 -,yk1378f10.3 23 532 -,yk1213c04.3 23 531 -,yk341e7.3 1 300 -,yk762h06.3 1 322 -,yk333g8.3 1 300 -,yk289b11.3 1 300 -,yk1491d07.5 9 502 +,yk603g6.3 1 300 -,yk140f8.3 1 300 -,yk383e5.3 1 300 -,yk642a2.3 1 300 -,yk607b2.3 1 300 -,yk1410e10.5 9 492 +,yk1410e10.3 9 482 -,yk1491d07.3 9 481 -,yk342g4.3 1 300 -,yk383e5.5 1 386 +,yk140f8.5 1 381 +,yk599a12.5 1 360 +,yk494f1.5 1 360 +,yk342g4.5 1 377 +,yk333g8.5 1 360 +,yk452a10.5 1 360 +,yk642a2.5 1 376 +,yk603g6.5 1 360 +,yk607b2.5 1 376 +,yk341e7.5 1 372 +,yk289b11.5 13 375 +,BP 1 109 +,RP 1 109 +,yk81b11.5 1 330 +,yk175h6.5 1 222 +
III	gt csa	exon	1617142	1617429	1	-	.	Parent=mRNA190
III	gt csa	exon	1618260	1618379	1	-	.	Parent=mRNA190
III	gt csa	exon	1618719	1618832	1	-	.	Parent=mRNA190
III	gt csa	exon	1618885	1618924	0.975	-	.	Parent=mRNA190
III	gt csa	mRNA	1617181	1618918	.	-	.	ID=mRNA191;Parent=gene125;Target=yk1405h09.3 1 391 -,yk1405h09.5 23 302 +
III	gt csa	exon	1617181	1617429	0.972	-	.	Parent=mRNA191
III	gt csa	exon	1618260	1618267	1	-	.	Parent=mRNA191
III	gt csa	exon	1618731	1618832	1	-	.	Parent=mRNA191
III	gt csa	exon	1618885	1618918	1	-	.	Parent=mRNA191
###
III	gt csa	gene	1617159	1617431	.	+	.	ID=gene126
III	gt csa	mRNA	1617159	1617431	.	+	.	ID=mRNA192;Parent=gene126;Target=yk81b11.3 1 120 +,yk599a12.3 1 229 +
III	gt csa	exon	1617159	1617431	0.987	+	.	Parent=mRNA192
###
III	gt csa	gene	1619718	1625773	.	+	.	ID=gene127
III	gt csa	mRNA	1619718	1623324	.	+	.	ID=mRNA193;Parent=gene127;Target=yk515d7.5 1 369 +,yk1371g11.5 1 457 +,yk1502h06.5 23 475 +,yk1315f04.5 23 476 +,yk769d02.5 23 487 +,yk1620h12.5 23 600 +,yk566g5.5 1 360 +,yk434a10.5 1 374 +,yk416a11.5 1 240 +,yk413g4.5 1 360 +,yk458a7.5 1 360 +,yk498g8.5 1 360 +,yk344h2.5 1 360 +,yk416f6.5 1 360 +,yk432a10.5 1 360 +,yk638c1.5 1 360 +,yk631h7.5 1 360 +,yk538g9.5 1 360 +,yk499e12.5 1 360 +,yk678h2.5 1 360 +,yk534c9.5 1 360 +,yk591c9.5 1 360 +,yk629b10.5 1 360 +,yk460e6.5 1 360 +,yk668e7.5 1 240 +,yk586g3.5 1 360 +,yk394h5.5 1 360 +,yk542c5.5 1 360 +
III	gt csa	exon	1619718	1619894	0.972	+	.	Parent=mRNA193
III	gt csa	exon	1620044	1620352	1	+	.	Parent=mRNA193
III	gt csa	exon	1623213	1623324	1	+	.	Parent=mRNA193
III	gt csa	mRNA	1619718	1625773	.	+	.	ID=mRNA194;Parent=gene127;Target=yk515d7.5 1 369 +,L36035 1 1781 +,yk1614a02.5 1 633 +,yk1371g11.5 1 457 +,yk761g06.5 1 588 +,yk1502h06.5 23 475 +,yk1315f04.5 23 476 +,yk769d02.5 23 487 +,yk1545g12.5 23 531 +,yk1421h01.5 23 532 +,yk1399b07.5 23 533 +,yk1651f03.5 23 569 +,yk1664c02.5 22 568 +,yk1696f05.5 23 570 +,yk1528f03.5 23 570 +,yk1741c08.5 23 571 +,yk1444d01.5 23 571 +,yk1500h01.5 23 571 +,yk1645f10.5 23 572 +,yk1695g01.5 23 572 +,yk1592g09.5 23 572 +,yk1526g10.5 22 573 +,yk1522d12.5 21 573 +,yk1387h03.5 22 574 +,yk1526h01.5 23 575 +,yk1493d05.5 23 577 +,yk1363e02.5 23 577 +,yk1657c03.5 23 578 +,yk816g12.5 23 581 +,yk566g5.5 1 360 +,yk434a10.5 1 374 +,yk416a11.5 1 240 +,yk413g4.5 1 360 +,yk458a7.5 1 360 +,yk498g8.5 1 360 +,RP 1 568 +,BP 1 568 +,yk344h2.5 1 360 +,yk416f6.5 1 360 +,yk432a10.5 1 360 +,yk638c1.5 1 360 +,yk631h7.5 1 360 +,yk538g9.5 1 360 +,yk499e12.5 1 360 +,yk678h2.5 1 360 +,yk534c9.5 1 360 +,yk591c9.5 1 360 +,yk629b10.5 1 360 +,yk460e6.5 1 360 +,yk668e7.5 1 240 +,yk586g3.5 1 360 +,yk394h5.5 1 360 +,yk755a01.5 1 538 +,yk542c5.5 1 360 +,yk1004c09.5 1 603 +,AJ270981 1 670 +,yk455e6.5 1 360 +,yk405a9.5 1 360 +,yk343g7.5 1 360 +,CB104502 83 407 +,yk257b9.5 1 375 +,yk545c7.5 1 360 +,yk7b1.5 1 359 +,cm9c7.5 1 402 +,CEMSF82F 1 211 -,yk1315f04.3 1 607 -,yk1645f10.3 1 675 -,yk1528f03.3 1 674 -,yk1500h01.3 1 644 -,yk20e11.5 1 300 +,yk272b10.5 1 360 +,yk221g12.5 1 240 +
III	gt csa	exon	1619718	1619894	0.972	+	.	Parent=mRNA194
III	gt csa	exon	1620044	1620352	1	+	.	Parent=mRNA194
III	gt csa	exon	1621416	1621808	0.997	+	.	Parent=mRNA194
III	gt csa	exon	1623048	1623425	1	+	.	Parent=mRNA194
III	gt csa	exon	1624423	1624740	1	+	.	Parent=mRNA194
III	gt csa	exon	1625234	1625773	0.959	+	.	Parent=mRNA194
III	gt csa	mRNA	1619718	1625773	.	+	.	ID=mRNA195;Parent=gene127;Target=yk515d7.5 1 369 +,yk1614a02.5 1 633 +,yk1371g11.5 1 457 +,yk761g06.5 1 588 +,yk1502h06.5 23 475 +,yk1315f04.5 23 476 +,yk769d02.5 23 487 +,yk1545g12.5 23 531 +,yk1421h01.5 23 532 +,yk1399b07.5 23 533 +,yk1651f03.5 23 569 +,yk1664c02.5 22 568 +,yk1696f05.5 23 570 +,yk1528f03.5 23 570 +,yk1741c08.5 23 571 +,yk1444d01.5 23 571 +,yk1500h01.5 23 571 +,yk1645f10.5 23 572 +,yk1695g01.5 23 572 +,yk1592g09.5 23 572 +,yk1526g10.5 22 573 +,yk1522d12.5 21 573 +,yk1387h03.5 22 574 +,yk1526h01.5 23 575 +,yk1493d05.5 23 577 +,yk1363e02.5 23 577 +,yk1657c03.5 23 578 +,yk816g12.5 23 581 +,yk566g5.5 1 360 +,yk434a10.5 1 374 +,yk416a11.5 1 240 +,yk413g4.5 1 360 +,yk458a7.5 1 360 +,yk498g8.5 1 360 +,yk344h2.5 1 360 +,yk416f6.5 1 360 +,yk432a10.5 1 360 +,yk638c1.5 1 360 +,yk631h7.5 1 360 +,yk538g9.5 1 360 +,yk499e12.5 1 360 +,yk678h2.5 1 360 +,yk534c9.5 1 360 +,yk591c9.5 1 360 +,yk629b10.5 1 360 +,yk460e6.5 1 360 +,yk668e7.5 1 240 +,yk586g3.5 1 360 +,yk394h5.5 1 360 +,yk755a01.5 1 538 +,yk542c5.5 1 360 +,yk777d06.5 1 646 +,cm9c7.5 1 402 +,CEMSF82F 1 211 -,yk1315f04.3 1 607 -,yk1645f10.3 1 675 -,yk1528f03.3 1 674 -,yk1500h01.3 1 644 -,yk20e11.5 1 300 +,yk272b10.5 1 360 +,yk221g12.5 1 240 +
III	gt csa	exon	1619718	1619894	0.972	+	.	Parent=mRNA195
III	gt csa	exon	1620044	1620352	1	+	.	Parent=mRNA195
III	gt csa	exon	1621416	1621679	1	+	.	Parent=mRNA195
III	gt csa	exon	1623279	1623425	1	+	.	Parent=mRNA195
III	gt csa	exon	1624423	1624740	0.958	+	.	Parent=mRNA195
III	gt csa	exon	1625234	1625773	0.959	+	.	Parent=mRNA195
###
III	gt csa	gene	1623119	1625784	.	-	.	ID=gene128
III	gt csa	mRNA	1623119	1623227	.	-	.	ID=mRNA196;Parent=gene128;Target=yk125c12.5 1 111 +
III	gt csa	exon	1623119	1623227	0.872	-	.	Parent=mRNA196
III	gt csa	mRNA	1625267	1625784	.	-	.	ID=mRNA197;Parent=gene128;Target=yk755a01.3 1 509 +,yk1371g11.3 1 500 +,yk1741c08.3 1 502 +,yk1620h12.3 1 499 +,yk1522d12.3 1 505 +,yk1592g09.3 1 484 +,yk1502h06.3 1 491 +,yk1651f03.3 1 490 +,yk1545g12.3 1 481 +,yk1526h01.3 1 487 +,yk1664c02.3 1 489 +,yk1614a02.3 1 489 +,yk1657c03.3 1 488 +,yk1696f05.3 1 489 +,yk1493d05.3 1 490 +,yk777d06.3 1 470 +,yk769d02.3 1 474 +,yk816g12.3 1 487 +,yk1004c09.3 1 455 +,yk1399b07.3 1 434 +,yk1363e02.3 1 430 +,yk1695g01.3 1 430 +,yk1387h03.3 1 430 +
III	gt csa	exon	1625267	1625784	0.904	-	.	Parent=mRNA197
###
III	gt csa	gene	1626655	1629966	.	+	.	ID=gene129
III	gt csa	mRNA	1626655	1629966	.	+	.	ID=mRNA198;Parent=gene129;Target=yk473d1.5 1 360 +
III	gt csa	exon	1626655	1626760	0.976	+	.	Parent=mRNA198
III	gt csa	exon	1629399	1629553	0.994	+	.	Parent=mRNA198
III	gt csa	exon	1629869	1629966	0.99	+	.	Parent=mRNA198
###
III	gt csa	gene	1630786	1634440	.	-	.	ID=gene130
III	gt csa	mRNA	1630786	1634440	.	-	.	ID=mRNA199;Parent=gene130;Target=yk1400h01.3 1 669 -,yk1673f09.3 1 729 -,WP 1 505 +,yk1400h01.5 1 601 +
III	gt csa	exon	1630786	1630944	1	-	.	Parent=mRNA199
III	gt csa	exon	1630996	1631105	1	-	.	Parent=mRNA199
III	gt csa	exon	1631542	1631671	1	-	.	Parent=mRNA199
III	gt csa	exon	1632010	1632261	1	-	.	Parent=mRNA199
III	gt csa	exon	1632410	1632578	1	-	.	Parent=mRNA199
III	gt csa	exon	1632625	1632755	1	-	.	Parent=mRNA199
III	gt csa	exon	1632894	1633031	1	-	.	Parent=mRNA199
III	gt csa	exon	1633206	1633356	1	-	.	Parent=mRNA199
III	gt csa	exon	1633716	1633864	1	-	.	Parent=mRNA199
III	gt csa	exon	1634294	1634440	1	-	.	Parent=mRNA199
###
III	gt csa	gene	1636110	1637235	.	+	.	ID=gene131
III	gt csa	mRNA	1636110	1637235	.	+	.	ID=mRNA200;Parent=gene131;Target=yk473d1.3 1 300 -
III	gt csa	exon	1636110	1636349	0.95	+	.	Parent=mRNA200
III	gt csa	exon	1637174	1637235	0.984	+	.	Parent=mRNA200
###
III	gt csa	gene	1638270	1638592	.	-	.	ID=gene132
III	gt csa	mRNA	1638270	1638592	.	-	.	ID=mRNA201;Parent=gene132;Target=yk384f7.5 1 324 +
III	gt csa	exon	1638270	1638592	0.98	-	.	Parent=mRNA201
###
III	gt csa	gene	1641900	1642133	.	+	.	ID=gene133
III	gt csa	mRNA	1641900	1642133	.	+	.	ID=mRNA202;Parent=gene133;Target=yk296c8.3 1 221 +
III	gt csa	exon	1641900	1641940	0.878	+	.	Parent=mRNA202
III	gt csa	exon	1641952	1642133	0.846	+	.	Parent=mRNA202
###
III	gt csa	gene	1658190	1659850	.	-	.	ID=gene134
III	gt csa	mRNA	1658190	1659850	.	-	.	ID=mRNA203;Parent=gene134;Target=yk1658h08.5 1 538 +,yk1178b07.5 23 565 +,yk869h10.3 179 673 -,yk1658h08.3 1 488 -,yk1178b07.3 23 514 -,yk1004a04.3 102 584 -,yk1016a02.3 128 579 -
III	gt csa	exon	1658190	1658447	0.965	-	.	Parent=mRNA203
III	gt csa	exon	1659566	1659850	1	-	.	Parent=mRNA203
###
III	gt csa	gene	1667817	1668608	.	-	.	ID=gene135
III	gt csa	mRNA	1667817	1668608	.	-	.	ID=mRNA204;Parent=gene135;Target=WP 1 89 +,BP 1 75 +
III	gt csa	exon	1667817	1667916	1	-	.	Parent=mRNA204
III	gt csa	exon	1667967	1668062	1	-	.	Parent=mRNA204
III	gt csa	exon	1668538	1668608	1	-	.	Parent=mRNA204
###
III	gt csa	gene	1672506	1672805	.	+	.	ID=gene136
III	gt csa	mRNA	1672506	1672805	.	+	.	ID=mRNA205;Parent=gene136;Target=yk204f5.3 1 300 +
III	gt csa	exon	1672506	1672805	0.97	+	.	Parent=mRNA205
###
III	gt csa	gene	1672790	1676716	.	-	.	ID=gene137
III	gt csa	mRNA	1672790	1676716	.	-	.	ID=mRNA206;Parent=gene137;Target=RP 1 300 +,yk204f5.5 1 360 +
III	gt csa	exon	1672790	1672941	0.778	-	.	Parent=mRNA206
III	gt csa	exon	1673902	1674102	0.662	-	.	Parent=mRNA206
III	gt csa	exon	1674163	1674368	0.916	-	.	Parent=mRNA206
III	gt csa	exon	1675422	1675681	0.939	-	.	Parent=mRNA206
III	gt csa	exon	1676386	1676474	1	-	.	Parent=mRNA206
III	gt csa	exon	1676687	1676716	0.8	-	.	Parent=mRNA206
###
III	gt csa	gene	1683619	1688088	.	-	.	ID=gene138
III	gt csa	mRNA	1683619	1688088	.	-	.	ID=mRNA207;Parent=gene138;Target=WP 1 768 +
III	gt csa	exon	1683619	1683804	1	-	.	Parent=mRNA207
III	gt csa	exon	1684468	1684619	1	-	.	Parent=mRNA207
III	gt csa	exon	1684685	1684830	1	-	.	Parent=mRNA207
III	gt csa	exon	1684885	1685265	1	-	.	Parent=mRNA207
III	gt csa	exon	1686234	1686438	1	-	.	Parent=mRNA207
III	gt csa	exon	1686481	1686665	1	-	.	Parent=mRNA207
III	gt csa	exon	1687040	1688088	1	-	.	Parent=mRNA207
###
III	gt csa	gene	1692070	1695095	.	-	.	ID=gene139
III	gt csa	mRNA	1692070	1695095	.	-	.	ID=mRNA208;Parent=gene139;Target=yk1146g09.3 1 616 -,WP 1 320 +
III	gt csa	exon	1692070	1692299	0.983	-	.	Parent=mRNA208
III	gt csa	exon	1692347	1692704	1	-	.	Parent=mRNA208
III	gt csa	exon	1692749	1692889	1	-	.	Parent=mRNA208
III	gt csa	exon	1694480	1694576	1	-	.	Parent=mRNA208
III	gt csa	exon	1694902	1695095	1	-	.	Parent=mRNA208
###
III	gt csa	gene	1697210	1697895	.	+	.	ID=gene140
III	gt csa	mRNA	1697210	1697895	.	+	.	ID=mRNA209;Parent=gene140;Target=yk1108h12.3 1 685 +
III	gt csa	exon	1697210	1697895	0.997	+	.	Parent=mRNA209
###
III	gt csa	gene	1697728	1698972	.	-	.	ID=gene141
III	gt csa	mRNA	1697728	1698972	.	-	.	ID=mRNA210;Parent=gene141;Target=WP 1 305 +,yk1146g09.5 1 585 +
III	gt csa	exon	1697728	1697934	1	-	.	Parent=mRNA210
III	gt csa	exon	1697997	1698621	1	-	.	Parent=mRNA210
III	gt csa	exon	1698827	1698972	1	-	.	Parent=mRNA210
###
III	gt csa	gene	1701749	1702396	.	-	.	ID=gene142
III	gt csa	mRNA	1701749	1702396	.	-	.	ID=mRNA211;Parent=gene142;Target=yk280d6.5 1 211 +
III	gt csa	exon	1701749	1701916	1	-	.	Parent=mRNA211
III	gt csa	exon	1702354	1702396	1	-	.	Parent=mRNA211
###
III	gt csa	gene	1703536	1705475	.	-	.	ID=gene143
III	gt csa	mRNA	1703536	1705475	.	-	.	ID=mRNA212;Parent=gene143;Target=WP 1 286 +
III	gt csa	exon	1703536	1703760	1	-	.	Parent=mRNA212
III	gt csa	exon	1704360	1704909	1	-	.	Parent=mRNA212
III	gt csa	exon	1705393	1705475	1	-	.	Parent=mRNA212
###
III	gt csa	gene	1706545	1714620	.	+	.	ID=gene144
III	gt csa	mRNA	1706545	1713333	.	+	.	ID=mRNA213;Parent=gene144;Target=WP 1 1141 +
III	gt csa	exon	1706545	1707024	1	+	.	Parent=mRNA213
III	gt csa	exon	1708672	1708784	1	+	.	Parent=mRNA213
III	gt csa	exon	1710053	1710138	1	+	.	Parent=mRNA213
III	gt csa	exon	1710199	1711458	1	+	.	Parent=mRNA213
III	gt csa	exon	1711552	1712548	1	+	.	Parent=mRNA213
III	gt csa	exon	1712599	1712789	1	+	.	Parent=mRNA213
III	gt csa	exon	1712852	1712921	1	+	.	Parent=mRNA213
III	gt csa	exon	1713108	1713333	1	+	.	Parent=mRNA213
III	gt csa	mRNA	1713421	1714620	.	+	.	ID=mRNA214;Parent=gene144;Target=WP 1 351 +
III	gt csa	exon	1713421	1713545	1	+	.	Parent=mRNA214
III	gt csa	exon	1713600	1713772	1	+	.	Parent=mRNA214
III	gt csa	exon	1713817	1713953	1	+	.	Parent=mRNA214
III	gt csa	exon	1714003	1714620	1	+	.	Parent=mRNA214
###
III	gt csa	gene	1716518	1721899	.	-	.	ID=gene145
III	gt csa	mRNA	1716518	1721899	.	-	.	ID=mRNA215;Parent=gene145;Target=WP 1 1138 +
III	gt csa	exon	1716518	1716778	1	-	.	Parent=mRNA215
III	gt csa	exon	1717664	1717815	1	-	.	Parent=mRNA215
III	gt csa	exon	1717868	1718037	1	-	.	Parent=mRNA215
III	gt csa	exon	1718081	1718509	1	-	.	Parent=mRNA215
III	gt csa	exon	1718571	1718778	1	-	.	Parent=mRNA215
III	gt csa	exon	1719192	1719264	0.909	-	.	Parent=mRNA215
III	gt csa	exon	1719730	1719854	1	-	.	Parent=mRNA215
III	gt csa	exon	1719904	1721899	1	-	.	Parent=mRNA215
###
III	gt csa	gene	1723183	1733090	.	-	.	ID=gene146
III	gt csa	mRNA	1723183	1724814	.	-	.	ID=mRNA216;Parent=gene146;Target=CEESX92F 1 375 -,yk405f8.3 1 300 -,yk405f8.5 1 375 +
III	gt csa	exon	1723183	1723463	0.996	-	.	Parent=mRNA216
III	gt csa	exon	1723517	1723621	1	-	.	Parent=mRNA216
III	gt csa	exon	1724588	1724814	0.969	-	.	Parent=mRNA216
III	gt csa	mRNA	1723183	1733090	.	-	.	ID=mRNA217;Parent=gene146;Target=CEESX92F 1 375 -,U15167 13 1528 +,yk793h08.3 1 731 -,yk1219f04.3 1 767 -,yk1236d10.3 1 706 -,yk405f8.3 1 300 -,BP 1 447 +,WP 1 446 +,yk793h08.5 23 628 +,yk1236d10.5 28 615 +
III	gt csa	exon	1723183	1723463	0.996	-	.	Parent=mRNA217
III	gt csa	exon	1723517	1723621	1	-	.	Parent=mRNA217
III	gt csa	exon	1724588	1724810	1	-	.	Parent=mRNA217
III	gt csa	exon	1725626	1725883	1	-	.	Parent=mRNA217
III	gt csa	exon	1728036	1728084	1	-	.	Parent=mRNA217
III	gt csa	exon	1729126	1729418	1	-	.	Parent=mRNA217
III	gt csa	exon	1732543	1732692	1	-	.	Parent=mRNA217
III	gt csa	exon	1732928	1733090	1	-	.	Parent=mRNA217
III	gt csa	mRNA	1723354	1733090	.	-	.	ID=mRNA218;Parent=gene146;Target=RP 1 309 +,yk793h08.5 23 628 +,yk1236d10.5 28 615 +
III	gt csa	exon	1723354	1723463	1	-	.	Parent=mRNA218
III	gt csa	exon	1724588	1724810	0.796	-	.	Parent=mRNA218
III	gt csa	exon	1725626	1725883	0.905	-	.	Parent=mRNA218
III	gt csa	exon	1728036	1728084	1	-	.	Parent=mRNA218
III	gt csa	exon	1729126	1729418	1	-	.	Parent=mRNA218
III	gt csa	exon	1732543	1732692	1	-	.	Parent=mRNA218
III	gt csa	exon	1732928	1733090	1	-	.	Parent=mRNA218
###
III	gt csa	gene	1752185	1754928	.	-	.	ID=gene147
III	gt csa	mRNA	1752185	1752773	.	-	.	ID=mRNA219;Parent=gene147;Target=yk662d4.3 1 300 -
III	gt csa	exon	1752185	1752363	1	-	.	Parent=mRNA219
III	gt csa	exon	1752588	1752653	1	-	.	Parent=mRNA219
III	gt csa	exon	1752719	1752773	1	-	.	Parent=mRNA219
III	gt csa	mRNA	1752791	1754928	.	-	.	ID=mRNA220;Parent=gene147;Target=yk662d4.5 1 379 +
III	gt csa	exon	1752791	1752886	0.865	-	.	Parent=mRNA220
III	gt csa	exon	1753877	1754092	0.995	-	.	Parent=mRNA220
III	gt csa	exon	1754866	1754928	1	-	.	Parent=mRNA220
###
III	gt csa	gene	1763529	1764816	.	+	.	ID=gene148
III	gt csa	mRNA	1763529	1764816	.	+	.	ID=mRNA221;Parent=gene148;Target=yk58h5.5 1 239 +,yk411g7.5 1 360 +,yk261e7.5 1 180 +
III	gt csa	exon	1763529	1763655	0.984	+	.	Parent=mRNA221
III	gt csa	exon	1764575	1764816	0.996	+	.	Parent=mRNA221
###
III	gt csa	gene	1763606	1764825	.	-	.	ID=gene149
III	gt csa	mRNA	1763606	1764825	.	-	.	ID=mRNA222;Parent=gene149;Target=yk261e7.3 1 300 +,yk411g7.3 1 300 +
III	gt csa	exon	1763606	1763648	1	-	.	Parent=mRNA222
III	gt csa	exon	1764567	1764825	0.95	-	.	Parent=mRNA222
###
III	gt csa	gene	1771090	1771264	.	-	.	ID=gene150
III	gt csa	mRNA	1771090	1771264	.	-	.	ID=mRNA223;Parent=gene150;Target=yk581g6.5 186 360 +
III	gt csa	exon	1771090	1771264	0.954	-	.	Parent=mRNA223
###
III	gt csa	gene	1772556	1774226	.	-	.	ID=gene151
III	gt csa	mRNA	1772556	1774226	.	-	.	ID=mRNA224;Parent=gene151;Target=yk1484e10.3 1 505 -,yk655d4.3 1 300 -,yk541b2.3 1 300 -,yk550e12.3 1 300 -
III	gt csa	exon	1772556	1772820	0.943	-	.	Parent=mRNA224
III	gt csa	exon	1773987	1774226	0.946	-	.	Parent=mRNA224
###
III	gt csa	gene	1775021	1777597	.	-	.	ID=gene152
III	gt csa	mRNA	1775021	1777406	.	-	.	ID=mRNA225;Parent=gene152;Target=yk543e1.5 1 360 +,yk541b2.5 7 360 +
III	gt csa	exon	1775021	1775112	1	-	.	Parent=mRNA225
III	gt csa	exon	1775494	1775616	0.992	-	.	Parent=mRNA225
III	gt csa	exon	1775887	1775990	1	-	.	Parent=mRNA225
III	gt csa	exon	1777076	1777202	1	-	.	Parent=mRNA225
III	gt csa	exon	1777260	1777406	0.966	-	.	Parent=mRNA225
III	gt csa	mRNA	1775021	1777597	.	-	.	ID=mRNA226;Parent=gene152;Target=yk543e1.5 1 360 +,yk1484e10.5 1 544 +,yk550e12.5 1 380 +,yk618c5.5 1 360 +,yk276b6.5 1 360 +,yk549f11.5 1 359 +,yk655d4.5 1 359 +,yk444c12.5 1 360 +,yk411g1.5 14 360 +
III	gt csa	exon	1775021	1775112	1	-	.	Parent=mRNA226
III	gt csa	exon	1775494	1775616	0.992	-	.	Parent=mRNA226
III	gt csa	exon	1775887	1775990	1	-	.	Parent=mRNA226
III	gt csa	exon	1777076	1777214	1	-	.	Parent=mRNA226
III	gt csa	exon	1777260	1777406	0.993	-	.	Parent=mRNA226
III	gt csa	exon	1777492	1777597	1	-	.	Parent=mRNA226
###
III	gt csa	gene	1777799	1778203	.	+	.	ID=gene153
III	gt csa	mRNA	1777799	1778203	.	+	.	ID=mRNA227;Parent=gene153;Target=RP 1 41 +,BP 1 41 +
III	gt csa	exon	1777799	1777904	1	+	.	Parent=mRNA227
III	gt csa	exon	1778187	1778203	1	+	.	Parent=mRNA227
###
III	gt csa	gene	1785208	1785635	.	-	.	ID=gene154
III	gt csa	mRNA	1785208	1785635	.	-	.	ID=mRNA228;Parent=gene154;Target=yk1303c12.3 24 419 +
III	gt csa	exon	1785208	1785302	0.989	-	.	Parent=mRNA228
III	gt csa	exon	1785317	1785531	0.919	-	.	Parent=mRNA228
III	gt csa	exon	1785550	1785635	0.988	-	.	Parent=mRNA228
###
III	gt csa	gene	1807719	1818322	.	-	.	ID=gene155
III	gt csa	mRNA	1807719	1809245	.	-	.	ID=mRNA229;Parent=gene155;Target=yk750h11.5 1 183 +,yk1048a06.3 1 538 -,yk872f09.3 1 534 -,yk1102f12.3 1 536 -,yk1354g01.3 1 700 -,yk1490a04.3 1 496 -,yk530e1.3 1 300 -,yk264d2.3 1 300 -,yk501h12.3 1 300 -,yk407d6.3 1 300 -
III	gt csa	exon	1807719	1807889	0.959	-	.	Parent=mRNA229
III	gt csa	exon	1807944	1808358	1	-	.	Parent=mRNA229
III	gt csa	exon	1809107	1809245	0.953	-	.	Parent=mRNA229
III	gt csa	mRNA	1807719	1815816	.	-	.	ID=mRNA230;Parent=gene155;Target=yk750h11.5 1 183 +,yk871f07.3 1 702 -,yk1048a06.3 1 538 -,yk872f09.3 1 534 -,yk1102f12.3 1 536 -,yk1314a11.3 1 729 -,yk1091a04.3 1 689 -,yk1012a09.3 1 682 -,yk1297g02.3 1 682 -,yk1166d10.3 1 717 -,yk1036a09.3 1 696 -,yk1490a04.3 1 496 -,yk530e1.3 1 300 -,yk264d2.3 1 300 -,yk501h12.3 1 300 -,yk407d6.3 1 300 -,yk1755a05.3 1 696 -,WP 1 717 +,yk1048a06.5 1 607 +,yk264d2.5 1 240 +,yk501h12.5 1 375 +,yk407d6.5 1 360 +,yk1091a04.5 1 262 +,yk1755a05.5 1 598 +,yk1036a09.5 11 576 +,yk872f09.5 14 372 +,yk530e1.5 44 360 +
III	gt csa	exon	1807719	1807889	0.959	-	.	Parent=mRNA230
III	gt csa	exon	1807944	1808363	1	-	.	Parent=mRNA230
III	gt csa	exon	1809107	1809381	1	-	.	Parent=mRNA230
III	gt csa	exon	1809679	1809822	1	-	.	Parent=mRNA230
III	gt csa	exon	1811041	1811363	1	-	.	Parent=mRNA230
III	gt csa	exon	1812744	1813091	1	-	.	Parent=mRNA230
III	gt csa	exon	1814386	1814835	1	-	.	Parent=mRNA230
III	gt csa	exon	1815432	1815557	1	-	.	Parent=mRNA230
III	gt csa	exon	1815760	1815816	0.269	-	.	Parent=mRNA230
III	gt csa	mRNA	1809707	1818322	.	-	.	ID=mRNA231;Parent=gene155;Target=yk1048a06.5 1 607 +,yk264d2.5 1 240 +,yk501h12.5 1 375 +,yk407d6.5 1 360 +,yk1091a04.5 1 262 +,yk1755a05.5 1 598 +,yk1036a09.5 11 576 +,yk1166d10.5 1 559 +,yk1102f12.5 23 595 +,yk1314a11.5 1 585 +,yk1012a09.5 22 578 +,yk1297g02.5 23 533 +,yk1490a04.5 23 510 +,yk872f09.5 14 372 +,yk530e1.5 44 360 +
III	gt csa	exon	1809707	1809822	0.983	-	.	Parent=mRNA231
III	gt csa	exon	1811041	1811363	1	-	.	Parent=mRNA231
III	gt csa	exon	1812744	1813091	1	-	.	Parent=mRNA231
III	gt csa	exon	1814386	1814835	0.998	-	.	Parent=mRNA231
III	gt csa	exon	1815432	1815557	1	-	.	Parent=mRNA231
III	gt csa	exon	1818254	1818322	0.906	-	.	Parent=mRNA231
###
III	gt csa	gene	1807745	1807902	.	+	.	ID=gene156
III	gt csa	mRNA	1807745	1807902	.	+	.	ID=mRNA232;Parent=gene156;Target=yk750h11.3 1 157 +
III	gt csa	exon	1807745	1807902	0.968	+	.	Parent=mRNA232
###
III	gt csa	gene	1821203	1824103	.	-	.	ID=gene157
III	gt csa	mRNA	1821203	1822732	.	-	.	ID=mRNA233;Parent=gene157;Target=yk305g9.3 1 300 -,yk383c1.3 1 300 -,yk412f9.3 1 300 -,yk665f3.3 1 300 -,yk383c1.5 1 360 +
III	gt csa	exon	1821203	1821412	1	-	.	Parent=mRNA233
III	gt csa	exon	1821473	1821557	1	-	.	Parent=mRNA233
III	gt csa	exon	1821604	1821711	1	-	.	Parent=mRNA233
III	gt csa	exon	1822654	1822732	1	-	.	Parent=mRNA233
III	gt csa	mRNA	1822859	1824103	.	-	.	ID=mRNA234;Parent=gene157;Target=yk665f3.5 1 377 +,yk305g9.5 1 376 +
III	gt csa	exon	1822859	1823006	1	-	.	Parent=mRNA234
III	gt csa	exon	1823643	1823760	1	-	.	Parent=mRNA234
III	gt csa	exon	1823964	1824103	1	-	.	Parent=mRNA234
###
III	gt csa	gene	1824908	1831849	.	+	.	ID=gene158
III	gt csa	mRNA	1824908	1831849	.	+	.	ID=mRNA235;Parent=gene158;Target=yk1471g06.5 23 598 +
III	gt csa	exon	1824908	1824965	1	+	.	Parent=mRNA235
III	gt csa	exon	1825145	1825214	1	+	.	Parent=mRNA235
III	gt csa	exon	1827228	1827355	1	+	.	Parent=mRNA235
III	gt csa	exon	1830455	1830596	1	+	.	Parent=mRNA235
III	gt csa	exon	1830776	1830907	1	+	.	Parent=mRNA235
III	gt csa	exon	1831804	1831849	1	+	.	Parent=mRNA235
III	gt csa	mRNA	1824936	1827299	.	+	.	ID=mRNA236;Parent=gene158;Target=yk428b11.5 1 360 +
III	gt csa	exon	1824936	1824965	0.85	+	.	Parent=mRNA236
III	gt csa	exon	1825145	1825400	0.963	+	.	Parent=mRNA236
III	gt csa	exon	1827228	1827299	0.986	+	.	Parent=mRNA236
###
III	gt csa	gene	1833860	1834336	.	-	.	ID=gene159
III	gt csa	mRNA	1833860	1834336	.	-	.	ID=mRNA237;Parent=gene159;Target=yk1471g06.3 1 477 +,yk428b11.3 1 180 +
III	gt csa	exon	1833860	1834336	0.918	-	.	Parent=mRNA237
###
III	gt csa	gene	1834502	1842946	.	+	.	ID=gene160
III	gt csa	mRNA	1834502	1842946	.	+	.	ID=mRNA238;Parent=gene160;Target=yk1579g04.5 24 347 +,yk392a4.5 7 371 +,yk1171d07.5 23 574 +,yk1521f03.5 23 574 +,yk1520e11.5 23 587 +,yk1537h08.5 23 589 +,yk614f12.5 1 360 +,yk273b4.5 1 360 +,yk1094h04.5 1 598 +,yk93h5.5 1 292 +,yk1521e10.5 1 446 +,yk460h8.5 1 360 +,yk240e10.5 1 374 +,yk163b1.5 2 360 +,yk14g9.5 1 360 +
III	gt csa	exon	1834502	1834595	1	+	.	Parent=mRNA238
III	gt csa	exon	1836122	1836195	1	+	.	Parent=mRNA238
III	gt csa	exon	1836253	1836355	1	+	.	Parent=mRNA238
III	gt csa	exon	1837108	1837249	1	+	.	Parent=mRNA238
III	gt csa	exon	1838335	1838703	1	+	.	Parent=mRNA238
III	gt csa	exon	1838765	1838877	1	+	.	Parent=mRNA238
III	gt csa	exon	1840158	1840486	0.988	+	.	Parent=mRNA238
III	gt csa	exon	1841743	1841899	0.987	+	.	Parent=mRNA238
III	gt csa	exon	1842859	1842946	0.966	+	.	Parent=mRNA238
###
III	gt csa	gene	1844378	1846728	.	+	.	ID=gene161
III	gt csa	mRNA	1844378	1846728	.	+	.	ID=mRNA239;Parent=gene161;Target=yk1520e11.3 1 527 -,yk1521e10.3 1 432 -,yk1171d07.3 1 410 -
III	gt csa	exon	1844378	1844512	0.904	+	.	Parent=mRNA239
III	gt csa	exon	1846336	1846728	0.919	+	.	Parent=mRNA239
###
III	gt csa	gene	1846366	1846740	.	-	.	ID=gene162
III	gt csa	mRNA	1846366	1846740	.	-	.	ID=mRNA240;Parent=gene162;Target=yk1094h04.3 1 361 +,yk14g9.3 1 373 +,yk1537h08.3 1 247 +,yk1521f03.3 1 204 +,yk1579g04.3 1 199 +,yk93h5.3 1 120 +
III	gt csa	exon	1846366	1846740	0.965	-	.	Parent=mRNA240
###
III	gt csa	gene	1849052	1852447	.	+	.	ID=gene163
III	gt csa	mRNA	1849052	1850827	.	+	.	ID=mRNA241;Parent=gene163;Target=yk532h6.5 1 381 +,yk332d10.5 1 360 +,yk506e3.5 1 383 +,yk174g9.5 1 360 +,yk521e8.5 1 360 +
III	gt csa	exon	1849052	1849121	0.964	+	.	Parent=mRNA241
III	gt csa	exon	1849263	1849349	1	+	.	Parent=mRNA241
III	gt csa	exon	1849404	1849502	1	+	.	Parent=mRNA241
III	gt csa	exon	1850353	1850445	1	+	.	Parent=mRNA241
III	gt csa	exon	1850707	1850827	1	+	.	Parent=mRNA241
III	gt csa	mRNA	1849294	1850837	.	+	.	ID=mRNA242;Parent=gene163;Target=yk487d2.5 1 381 +
III	gt csa	exon	1849294	1849350	0.939	+	.	Parent=mRNA242
III	gt csa	exon	1849404	1849502	1	+	.	Parent=mRNA242
III	gt csa	exon	1850353	1850445	1	+	.	Parent=mRNA242
III	gt csa	exon	1850707	1850837	0.992	+	.	Parent=mRNA242
III	gt csa	mRNA	1851033	1852447	.	+	.	ID=mRNA243;Parent=gene163;Target=yk66f12.5 1 360 +
III	gt csa	exon	1851033	1851113	1	+	.	Parent=mRNA243
III	gt csa	exon	1852169	1852447	0.993	+	.	Parent=mRNA243
###
III	gt csa	gene	1852263	1852877	.	-	.	ID=gene164
III	gt csa	mRNA	1852263	1852562	.	-	.	ID=mRNA244;Parent=gene164;Target=yk334d11.3 1 300 +
III	gt csa	exon	1852263	1852562	0.997	-	.	Parent=mRNA244
III	gt csa	mRNA	1852697	1852877	.	-	.	ID=mRNA245;Parent=gene164;Target=yk66f12.3 1 180 +
III	gt csa	exon	1852697	1852877	0.925	-	.	Parent=mRNA245
###
III	gt csa	gene	1859880	1864478	.	+	.	ID=gene165
III	gt csa	mRNA	1859880	1860325	.	+	.	ID=mRNA246;Parent=gene165;Target=yk521e3.3 1 281 -,AF150086 1 252 +,RP 1 84 +,BP 1 84 +,yk521e3.5 1 337 +
III	gt csa	exon	1859880	1860055	0.983	+	.	Parent=mRNA246
III	gt csa	exon	1860146	1860325	0.961	+	.	Parent=mRNA246
III	gt csa	mRNA	1860418	1864478	.	+	.	ID=mRNA247;Parent=gene165;Target=yk1220d04.5 23 647 +,yk772h10.5 21 646 +
III	gt csa	exon	1860418	1860607	1	+	.	Parent=mRNA247
III	gt csa	exon	1861659	1861816	1	+	.	Parent=mRNA247
III	gt csa	exon	1864021	1864120	1	+	.	Parent=mRNA247
III	gt csa	exon	1864301	1864478	1	+	.	Parent=mRNA247
###
III	gt csa	gene	1872178	1874286	.	+	.	ID=gene166
III	gt csa	mRNA	1872178	1874286	.	+	.	ID=mRNA248;Parent=gene166;Target=yk1220d04.3 1 668 -
III	gt csa	exon	1872178	1872266	1	+	.	Parent=mRNA248
III	gt csa	exon	1873707	1874286	0.988	+	.	Parent=mRNA248
###
III	gt csa	gene	1874643	1877104	.	+	.	ID=gene167
III	gt csa	mRNA	1874643	1877104	.	+	.	ID=mRNA249;Parent=gene167;Target=yk772h10.3 1 592 -
III	gt csa	exon	1874643	1874750	1	+	.	Parent=mRNA249
III	gt csa	exon	1875972	1876159	0.995	+	.	Parent=mRNA249
III	gt csa	exon	1876806	1877104	0.983	+	.	Parent=mRNA249
###
III	gt csa	gene	1878354	1880837	.	+	.	ID=gene168
III	gt csa	mRNA	1878354	1880828	.	+	.	ID=mRNA250;Parent=gene168;Target=yk1169f09.5 20 395 +,yk1473c02.3 1 783 -,yk1169f09.3 1 705 -
III	gt csa	exon	1878354	1878595	0.996	+	.	Parent=mRNA250
III	gt csa	exon	1879233	1879361	1	+	.	Parent=mRNA250
III	gt csa	exon	1879426	1879560	1	+	.	Parent=mRNA250
III	gt csa	exon	1880174	1880328	1	+	.	Parent=mRNA250
III	gt csa	exon	1880625	1880828	1	+	.	Parent=mRNA250
III	gt csa	mRNA	1878558	1878800	.	+	.	ID=mRNA251;Parent=gene168;Target=yk1251d11.5 1 243 +
III	gt csa	exon	1878558	1878800	0.988	+	.	Parent=mRNA251
III	gt csa	mRNA	1879975	1880837	.	+	.	ID=mRNA252;Parent=gene168;Target=yk1512g12.3 1 565 -
III	gt csa	exon	1879975	1880328	1	+	.	Parent=mRNA252
III	gt csa	exon	1880625	1880837	0.991	+	.	Parent=mRNA252
###
III	gt csa	gene	1880375	1880798	.	-	.	ID=gene169
III	gt csa	mRNA	1880375	1880798	.	-	.	ID=mRNA253;Parent=gene169;Target=yk1251d11.3 1 424 +
III	gt csa	exon	1880375	1880798	0.979	-	.	Parent=mRNA253
###
III	gt csa	gene	1883596	1886207	.	-	.	ID=gene170
III	gt csa	mRNA	1883596	1886207	.	-	.	ID=mRNA254;Parent=gene170;Target=WP 1 773 +
III	gt csa	exon	1883596	1884789	1	-	.	Parent=mRNA254
III	gt csa	exon	1884882	1885107	1	-	.	Parent=mRNA254
III	gt csa	exon	1885194	1885938	1	-	.	Parent=mRNA254
III	gt csa	exon	1885987	1886117	1	-	.	Parent=mRNA254
III	gt csa	exon	1886185	1886207	1	-	.	Parent=mRNA254
###
III	gt csa	gene	1891444	1893894	.	-	.	ID=gene171
III	gt csa	mRNA	1891444	1893894	.	-	.	ID=mRNA255;Parent=gene171;Target=yk233a7.3 1 300 -,yk233a7.5 1 345 +
III	gt csa	exon	1891444	1891508	1	-	.	Parent=mRNA255
III	gt csa	exon	1891927	1892079	0.993	-	.	Parent=mRNA255
III	gt csa	exon	1893273	1893544	0.969	-	.	Parent=mRNA255
III	gt csa	exon	1893825	1893894	0.929	-	.	Parent=mRNA255
###
III	gt csa	gene	1906128	1906538	.	+	.	ID=gene172
III	gt csa	mRNA	1906128	1906538	.	+	.	ID=mRNA256;Parent=gene172;Target=yk1723c04.5 1 340 +
III	gt csa	exon	1906128	1906256	0.953	+	.	Parent=mRNA256
III	gt csa	exon	1906330	1906538	0.967	+	.	Parent=mRNA256
###
III	gt csa	gene	1907887	1910519	.	+	.	ID=gene173
III	gt csa	mRNA	1907887	1910519	.	+	.	ID=mRNA257;Parent=gene173;Target=yk1723c04.3 1 651 -
III	gt csa	exon	1907887	1907987	0.901	+	.	Parent=mRNA257
III	gt csa	exon	1908176	1908310	1	+	.	Parent=mRNA257
III	gt csa	exon	1909274	1909432	1	+	.	Parent=mRNA257
III	gt csa	exon	1910268	1910519	1	+	.	Parent=mRNA257
###
III	gt csa	gene	1927666	1929298	.	+	.	ID=gene174
III	gt csa	mRNA	1927666	1929298	.	+	.	ID=mRNA258;Parent=gene174;Target=yk1053g10.5 17 224 +,yk1716g06.5 1 386 +
III	gt csa	exon	1927666	1927938	1	+	.	Parent=mRNA258
III	gt csa	exon	1929095	1929298	0.995	+	.	Parent=mRNA258
###
III	gt csa	gene	1930845	1931242	.	+	.	ID=gene175
III	gt csa	mRNA	1930845	1931242	.	+	.	ID=mRNA259;Parent=gene175;Target=yk1564h09.5 1 398 +
III	gt csa	exon	1930845	1931242	0.985	+	.	Parent=mRNA259
###
III	gt csa	gene	1932215	1939546	.	+	.	ID=gene176
III	gt csa	mRNA	1932215	1939375	.	+	.	ID=mRNA260;Parent=gene176;Target=yk1222g11.5 1 557 +,yk652e1.5 1 383 +,yk205e6.5 1 373 +,yk677h7.5 1 354 +,yk638h1.5 1 360 +,yk205h4.5 1 360 +,yk252c12.3 1 300 +
III	gt csa	exon	1932215	1932363	1	+	.	Parent=mRNA260
III	gt csa	exon	1934173	1934512	1	+	.	Parent=mRNA260
III	gt csa	exon	1936356	1936529	1	+	.	Parent=mRNA260
III	gt csa	exon	1937670	1938089	1	+	.	Parent=mRNA260
III	gt csa	exon	1939008	1939375	0.983	+	.	Parent=mRNA260
III	gt csa	mRNA	1934173	1939534	.	+	.	ID=mRNA261;Parent=gene176;Target=yk1716g06.3 35 413 -
III	gt csa	exon	1934173	1934226	0.87	+	.	Parent=mRNA261
III	gt csa	exon	1939167	1939225	0.814	+	.	Parent=mRNA261
III	gt csa	exon	1939269	1939534	0.94	+	.	Parent=mRNA261
III	gt csa	mRNA	1938000	1939546	.	+	.	ID=mRNA262;Parent=gene176;Target=yk1596d03.3 1 585 -,yk252c12.3 1 300 +
III	gt csa	exon	1938000	1938047	0.833	+	.	Parent=mRNA262
III	gt csa	exon	1939008	1939546	0.954	+	.	Parent=mRNA262
III	gt csa	mRNA	1938966	1939375	.	+	.	ID=mRNA263;Parent=gene176;Target=yk440d6.5 1 360 +,yk252c12.3 1 300 +
III	gt csa	exon	1938966	1939375	0.983	+	.	Parent=mRNA263
###
III	gt csa	gene	1939092	1943594	.	-	.	ID=gene177
III	gt csa	mRNA	1939092	1939557	.	-	.	ID=mRNA264;Parent=gene177;Target=yk864f11.3 1 360 +,CEESA81F 1 359 +,yk1618b12.3 1 264 +,yk1222g11.3 1 206 +
III	gt csa	exon	1939092	1939557	0.969	-	.	Parent=mRNA264
III	gt csa	mRNA	1939558	1943594	.	-	.	ID=mRNA265;Parent=gene177;Target=yk95d7.3 1 326 -,yk410b4.3 1 300 -,yk410b4.5 1 360 +,yk95d7.5 1 309 +,yk56h1.5 1 292 +
III	gt csa	exon	1939558	1939643	1	-	.	Parent=mRNA265
III	gt csa	exon	1940648	1940818	1	-	.	Parent=mRNA265
III	gt csa	exon	1941527	1941644	1	-	.	Parent=mRNA265
III	gt csa	exon	1941693	1941742	1	-	.	Parent=mRNA265
III	gt csa	exon	1943454	1943594	1	-	.	Parent=mRNA265
###
III	gt csa	gene	1945109	1961934	.	-	.	ID=gene178
III	gt csa	mRNA	1945109	1950246	.	-	.	ID=mRNA266;Parent=gene178;Target=AB244413 1 1755 +,yk604a10.3 1 300 -,yk411e9.3 1 300 -,cm12f1.5 1 418 +,yk411e9.5 1 360 +,yk604a10.5 1 360 +
III	gt csa	exon	1945109	1945261	1	-	.	Parent=mRNA266
III	gt csa	exon	1946058	1946234	1	-	.	Parent=mRNA266
III	gt csa	exon	1946292	1946488	1	-	.	Parent=mRNA266
III	gt csa	exon	1947633	1948044	1	-	.	Parent=mRNA266
III	gt csa	exon	1948959	1949134	1	-	.	Parent=mRNA266
III	gt csa	exon	1949218	1949422	1	-	.	Parent=mRNA266
III	gt csa	exon	1949713	1949872	1	-	.	Parent=mRNA266
III	gt csa	exon	1949921	1950067	1	-	.	Parent=mRNA266
III	gt csa	exon	1950119	1950246	1	-	.	Parent=mRNA266
III	gt csa	mRNA	1951049	1951408	.	-	.	ID=mRNA267;Parent=gene178;Target=yk492f11.3 1 300 +,yk453a11.3 1 300 +,yk199f2.3 1 300 +,yk558h2.3 1 300 +,yk281d11.3 1 300 +,yk278c2.3 1 300 +,yk229f4.3 1 300 +,yk483c3.3 1 300 +,yk615h4.3 1 300 +,yk647d12.3 1 300 +,yk448f2.3 1 283 +,yk551b11.3 1 284 +,yk448c12.3 1 289 +,yk457d7.3 1 293 +,yk446a5.3 1 300 +,yk664b3.3 1 300 +,yk602c4.3 1 285 +,yk253d3.3 1 287 +,yk516c9.3 1 288 +,yk645g1.3 1 288 +,yk646a8.3 1 288 +,yk140h11.3 1 289 +,yk116e3.3 1 338 +,yk60a11.3 1 336 +,yk497d11.3 1 269 +,yk330h9.3 1 270 +,yk800a07.3 1 300 +,yk494c8.3 1 240 +,yk373f11.3 1 240 +,yk222d9.3 1 227 +
III	gt csa	exon	1951049	1951408	0.991	-	.	Parent=mRNA267
III	gt csa	mRNA	1952007	1961934	.	-	.	ID=mRNA268;Parent=gene178;Target=yk1042c08.3 1 509 -,yk1611f05.3 1 724 -,yk1039c09.3 1 700 -,yk1339d07.3 1 770 -,yk1391f02.3 1 685 -,yk1444h05.3 1 727 -,yk1720g01.3 1 727 -,yk1372c05.3 1 768 -,yk1372c06.3 1 792 -,yk837g07.3 1 699 -,yk1474e07.3 1 717 -,yk63f12.3 1 325 -,yk1618b03.3 1 688 -,yk1672e09.3 1 756 -,yk1483a12.3 1 757 -,yk1556a02.3 1 756 -,yk1592b08.3 1 737 -,yk1755g08.3 1 759 -,yk376f5.3 1 300 -,yk312g4.3 1 300 -,yk474e3.3 1 300 -,yk603e10.3 1 300 -,yk470a7.3 1 300 -,yk453c10.3 1 300 -,yk645b1.3 1 300 -,yk577a10.3 1 300 -,yk163e8.3 1 300 -,yk142b8.3 1 300 -,yk187h9.3 1 300 -,yk740a4.3 1 300 -,yk520b2.5 1 358 +,yk577a10.5 1 360 +,yk1703a04.5 1 564 +,yk163e8.5 1 360 +,yk474e3.5 1 360 +,yk1672e09.5 15 652 +,yk1556a02.5 17 620 +,yk470a7.5 1 360 +,yk1339d07.5 23 658 +,yk1042c08.5 23 622 +,yk1660c12.5 23 621 +,yk1474e07.5 24 621 +,yk1618b03.5 23 619 +,yk1720g01.5 22 616 +,yk1611f05.5 23 616 +,yk1755g08.5 23 611 +,yk1444h05.5 23 606 +,yk1039c09.5 23 597 +,yk1592b08.5 23 595 +,yk1654a06.5 23 578 +,yk773f01.5 23 532 +,yk1483a12.5 23 518 +,yk645b1.5 1 383 +,yk603e10.5 1 382 +,yk228a2.5 1 360 +,yk312g4.5 1 372 +,yk837g07.5 1 376 +,yk376f5.5 1 360 +,yk453c10.5 1 360 +,yk142b8.5 1 372 +,yk63f12.5 1 320 +,yk740a4.5 23 340 +,yk187h9.5 1 240 +,yk1391f02.5 23 218 +
III	gt csa	exon	1952007	1952267	0.99	-	.	Parent=mRNA268
III	gt csa	exon	1953525	1953831	1	-	.	Parent=mRNA268
III	gt csa	exon	1954624	1954728	1	-	.	Parent=mRNA268
III	gt csa	exon	1956031	1956288	0.971	-	.	Parent=mRNA268
III	gt csa	exon	1957574	1957668	1	-	.	Parent=mRNA268
III	gt csa	exon	1957716	1957848	1	-	.	Parent=mRNA268
III	gt csa	exon	1959816	1960116	1	-	.	Parent=mRNA268
III	gt csa	exon	1961827	1961934	1	-	.	Parent=mRNA268
III	gt csa	mRNA	1952007	1961934	.	-	.	ID=mRNA269;Parent=gene178;Target=yk1042c08.3 1 509 -,yk63f12.3 1 325 -,yk376f5.3 1 300 -,yk312g4.3 1 300 -,yk474e3.3 1 300 -,yk603e10.3 1 300 -,yk470a7.3 1 300 -,yk453c10.3 1 300 -,yk645b1.3 1 300 -,yk577a10.3 1 300 -,yk163e8.3 1 300 -,yk142b8.3 1 300 -,yk187h9.3 1 300 -,yk740a4.3 1 300 -,BP 1 492 +,yk520b2.5 1 358 +,yk577a10.5 1 360 +,yk163e8.5 1 360 +,yk474e3.5 1 360 +,yk1672e09.5 15 652 +,yk1556a02.5 17 620 +,yk470a7.5 1 360 +,yk1339d07.5 23 658 +,yk1042c08.5 23 622 +,yk1660c12.5 23 621 +,yk1474e07.5 24 621 +,yk1618b03.5 23 619 +,yk1720g01.5 22 616 +,yk1611f05.5 23 616 +,yk1755g08.5 23 611 +,yk1444h05.5 23 606 +,yk1039c09.5 23 597 +,yk1592b08.5 23 595 +,yk1654a06.5 23 578 +,yk773f01.5 23 532 +,yk1483a12.5 23 518 +,yk645b1.5 1 383 +,yk603e10.5 1 382 +,yk228a2.5 1 360 +,yk312g4.5 1 372 +,yk837g07.5 1 376 +,yk376f5.5 1 360 +,yk453c10.5 1 360 +,yk142b8.5 1 372 +,yk63f12.5 1 320 +,yk740a4.5 23 340 +,yk187h9.5 1 240 +,yk1391f02.5 23 218 +
III	gt csa	exon	1952007	1952267	0.99	-	.	Parent=mRNA269
III	gt csa	exon	1953525	1953878	0.832	-	.	Parent=mRNA269
III	gt csa	exon	1954624	1954728	0.987	-	.	Parent=mRNA269
III	gt csa	exon	1956031	1956288	0.913	-	.	Parent=mRNA269
III	gt csa	exon	1957574	1957668	1	-	.	Parent=mRNA269
III	gt csa	exon	1957716	1957848	1	-	.	Parent=mRNA269
III	gt csa	exon	1959816	1960116	1	-	.	Parent=mRNA269
III	gt csa	exon	1961827	1961934	1	-	.	Parent=mRNA269
III	gt csa	mRNA	1952017	1961934	.	-	.	ID=mRNA270;Parent=gene178;Target=yk1660c12.3 1 703 -,yk63f12.3 1 325 -,yk376f5.3 1 300 -,yk312g4.3 1 300 -,yk474e3.3 1 300 -,yk603e10.3 1 300 -,yk470a7.3 1 300 -,yk453c10.3 1 300 -,yk645b1.3 1 300 -,yk577a10.3 1 300 -,yk163e8.3 1 300 -,yk142b8.3 1 300 -,yk187h9.3 1 300 -,yk740a4.3 1 300 -,yk520b2.5 1 358 +,yk163e8.5 1 360 +,yk474e3.5 1 360 +,yk1672e09.5 15 652 +,yk1556a02.5 17 620 +,yk470a7.5 1 360 +,yk1339d07.5 23 658 +,yk1042c08.5 23 622 +,yk1660c12.5 23 621 +,yk1474e07.5 24 621 +,yk1618b03.5 23 619 +,yk1720g01.5 22 616 +,yk1611f05.5 23 616 +,yk1755g08.5 23 611 +,yk1444h05.5 23 606 +,yk1039c09.5 23 597 +,yk1592b08.5 23 595 +,yk1654a06.5 23 578 +,yk773f01.5 23 532 +,yk1483a12.5 23 518 +,yk645b1.5 1 383 +,yk603e10.5 1 382 +,yk228a2.5 1 360 +,yk312g4.5 1 372 +,yk837g07.5 1 376 +,yk376f5.5 1 360 +,yk453c10.5 1 360 +,yk142b8.5 1 372 +,yk63f12.5 1 320 +,yk740a4.5 23 340 +,yk187h9.5 1 240 +,yk1391f02.5 23 218 +
III	gt csa	exon	1952017	1952267	0.996	-	.	Parent=mRNA270
III	gt csa	exon	1953525	1953758	1	-	.	Parent=mRNA270
III	gt csa	exon	1954640	1954728	1	-	.	Parent=mRNA270
III	gt csa	exon	1956031	1956288	0.971	-	.	Parent=mRNA270
III	gt csa	exon	1957574	1957668	1	-	.	Parent=mRNA270
III	gt csa	exon	1957716	1957848	1	-	.	Parent=mRNA270
III	gt csa	exon	1959816	1960116	1	-	.	Parent=mRNA270
III	gt csa	exon	1961827	1961934	1	-	.	Parent=mRNA270
III	gt csa	mRNA	1953222	1956293	.	-	.	ID=mRNA271;Parent=gene178;Target=RP 1 244 +,yk1703a04.5 1 564 +
III	gt csa	exon	1953222	1953278	0.12	-	.	Parent=mRNA271
III	gt csa	exon	1953525	1953831	0.944	-	.	Parent=mRNA271
III	gt csa	exon	1954624	1954728	1	-	.	Parent=mRNA271
III	gt csa	exon	1956031	1956293	0.883	-	.	Parent=mRNA271
III	gt csa	mRNA	1959320	1959824	.	-	.	ID=mRNA272;Parent=gene178;Target=yk1245c12.5 1 503 +
III	gt csa	exon	1959320	1959824	0.994	-	.	Parent=mRNA272
###
III	gt csa	gene	1950524	1952513	.	+	.	ID=gene179
III	gt csa	mRNA	1950524	1951426	.	+	.	ID=mRNA273;Parent=gene179;Target=yk1454g11.3 198 646 -,yk1066a07.3 236 686 -,yk1507e02.3 254 710 -,yk1678d01.3 237 693 -,yk1370c12.3 200 660 -,yk1370d03.3 236 711 -,yk1479a03.3 200 674 -,yk1537d05.3 202 677 -,yk1327d02.3 262 742 -,yk457d7.5 1 376 +,yk602c4.5 1 372 +,yk664b3.5 1 376 +,yk647d12.5 1 383 +,yk229f4.5 1 374 +,yk1020a05.3 1 468 -,yk1020a05.5 1 481 +,yk1016a08.3 23 271 -,yk116e3.5 1 360 +,yk1064e06.3 23 443 -,yk1151e09.3 23 447 -,yk1580b09.3 23 449 -,yk1587h09.3 35 461 -,yk1594g06.3 23 449 -,yk1362f01.3 23 459 -,yk1393f05.3 23 459 -,yk1521b10.5 23 466 +,yk1521b10.3 23 467 -,yk892h07.5 23 471 +,yk1176h06.3 24 475 -,yk1155e04.3 23 473 -,yk1291e10.3 23 473 -,yk892h07.3 23 473 -,yk1159h09.3 23 473 -,yk1130b02.3 23 485 -,yk1125f08.3 23 485 -,yk1693h02.5 23 487 +,yk1025d03.5 23 490 +,yk1064e06.5 23 495 +,yk1155e04.5 23 496 +,yk1291e10.5 23 496 +,yk1176h06.5 23 496 +,yk1362f01.5 23 496 +,yk1580b09.5 23 496 +,yk1130b02.5 23 498 +,yk1151e09.5 23 498 +,yk1016a08.5 23 498 +,yk1159h09.5 23 498 +,yk1587h09.5 23 498 +,yk1594g06.5 23 498 +,yk1125f08.5 23 499 +,yk1393f05.5 23 499 +,yk199f2.5 1 377 +,yk497d11.5 1 380 +,yk645g1.5 1 375 +,yk483c3.5 1 378 +,yk253d3.5 1 379 +,yk615h4.5 1 376 +,yk281d11.5 1 360 +,yk330h9.5 1 360 +,yk446a5.5 1 377 +,yk498f9.5 1 360 +,yk453a11.5 1 360 +,yk326h8.5 1 360 +,yk140h11.5 1 360 +,yk627c5.5 1 360 +,FLYBASE 1 131 +,BP 1 131 +,RP 1 131 +,yk448c12.5 1 360 +,yk373f11.5 1 360 +,yk60a11.5 1 360 +,SW 1 130 +,yk476f7.5 1 360 +,yk516c9.5 1 360 +,yk448f2.5 1 360 +,yk558h2.5 1 360 +,yk494c8.5 1 360 +,yk492f11.5 1 360 +,yk551b11.5 1 360 +,yk646a8.5 1 360 +,yk278c2.5 1 374 +,yk471g11.5 1 360 -,yk222d9.5 1 302 +,yk814a07.5 1 104 +
III	gt csa	exon	1950524	1950539	0.938	+	.	Parent=mRNA273
III	gt csa	exon	1950634	1950760	0.969	+	.	Parent=mRNA273
III	gt csa	exon	1951062	1951426	0.975	+	.	Parent=mRNA273
III	gt csa	mRNA	1950628	1951426	.	+	.	ID=mRNA274;Parent=gene179;Target=yk778a10.5 1 197 +,yk779g10.3 1 447 -,yk1617c03.3 1 461 -,yk1369h11.3 1 472 -,yk1369h11.5 1 479 +,yk1617c03.5 1 493 +,yk890g04.3 1 447 -,yk1010f03.3 1 462 -,yk890g04.5 1 477 +,yk1010f03.5 1 494 +,yk779g10.5 1 495 +,yk1160b11.5 84 440 +,yk1660d01.3 144 579 -,yk1450d10.3 220 663 -,yk1470f08.3 228 671 -,yk1691a10.3 178 621 -,yk1711g11.3 170 613 -,yk1319b02.3 270 730 -,yk1160b11.3 84 545 -,yk457d7.5 1 376 +,yk602c4.5 1 372 +,yk664b3.5 1 376 +,yk647d12.5 1 383 +,yk229f4.5 1 374 +,yk1020a05.3 1 468 -,yk1020a05.5 1 481 +,yk1016a08.3 23 271 -,yk116e3.5 1 360 +,yk1064e06.3 23 443 -,yk1151e09.3 23 447 -,yk1580b09.3 23 449 -,yk1587h09.3 35 461 -,yk1594g06.3 23 449 -,yk1362f01.3 23 459 -,yk1393f05.3 23 459 -,yk1521b10.5 23 466 +,yk1521b10.3 23 467 -,yk892h07.5 23 471 +,yk1176h06.3 24 475 -,yk1155e04.3 23 473 -,yk1291e10.3 23 473 -,yk892h07.3 23 473 -,yk1159h09.3 23 473 -,yk1130b02.3 23 485 -,yk1125f08.3 23 485 -,yk1693h02.5 23 487 +,yk1025d03.5 23 490 +,yk1064e06.5 23 495 +,yk1155e04.5 23 496 +,yk1291e10.5 23 496 +,yk1176h06.5 23 496 +,yk1362f01.5 23 496 +,yk1580b09.5 23 496 +,yk1130b02.5 23 498 +,yk1151e09.5 23 498 +,yk1016a08.5 23 498 +,yk1159h09.5 23 498 +,yk1587h09.5 23 498 +,yk1594g06.5 23 498 +,yk1125f08.5 23 499 +,yk1393f05.5 23 499 +,yk199f2.5 1 377 +,yk497d11.5 1 380 +,yk645g1.5 1 375 +,yk483c3.5 1 378 +,yk253d3.5 1 379 +,yk615h4.5 1 376 +,yk281d11.5 1 360 +,yk330h9.5 1 360 +,yk446a5.5 1 377 +,yk498f9.5 1 360 +,yk453a11.5 1 360 +,yk326h8.5 1 360 +,yk140h11.5 1 360 +,yk627c5.5 1 360 +,FLYBASE 1 131 +,BP 1 131 +,RP 1 131 +,yk448c12.5 1 360 +,yk373f11.5 1 360 +,yk60a11.5 1 360 +,SW 1 130 +,yk476f7.5 1 360 +,yk516c9.5 1 360 +,yk448f2.5 1 360 +,yk558h2.5 1 360 +,yk494c8.5 1 360 +,yk492f11.5 1 360 +,yk551b11.5 1 360 +,yk646a8.5 1 360 +,yk278c2.5 1 374 +,yk471g11.5 1 360 -,yk222d9.5 1 302 +,yk814a07.5 1 104 +
III	gt csa	exon	1950628	1950760	0.947	+	.	Parent=mRNA274
III	gt csa	exon	1951062	1951426	0.975	+	.	Parent=mRNA274
III	gt csa	mRNA	1950628	1951721	.	+	.	ID=mRNA275;Parent=gene179;Target=yk778a10.5 1 197 +,yk779g10.3 1 447 -,yk1617c03.3 1 461 -,yk1369h11.3 1 472 -,yk1369h11.5 1 479 +,yk890g04.3 1 447 -,yk1010f03.3 1 462 -,yk890g04.5 1 477 +,yk1160b11.5 84 440 +,yk1660d01.3 144 579 -,yk1450d10.3 220 663 -,yk1470f08.3 228 671 -,yk1691a10.3 178 621 -,yk1711g11.3 170 613 -,yk1319b02.3 270 730 -,yk1160b11.3 84 545 -,yk457d7.5 1 376 +,yk602c4.5 1 372 +,yk664b3.5 1 376 +,yk647d12.5 1 383 +,yk229f4.5 1 374 +,yk1016a08.3 23 271 -,yk116e3.5 1 360 +,yk1064e06.3 23 443 -,yk1151e09.3 23 447 -,yk1580b09.3 23 449 -,yk1587h09.3 35 461 -,yk1594g06.3 23 449 -,yk1362f01.3 23 459 -,yk1393f05.3 23 459 -,yk1521b10.5 23 466 +,yk1521b10.3 23 467 -,yk892h07.5 23 471 +,yk1176h06.3 24 475 -,yk1155e04.3 23 473 -,yk1291e10.3 23 473 -,yk892h07.3 23 473 -,yk1159h09.3 23 473 -,yk199f2.5 1 377 +,yk497d11.5 1 380 +,yk645g1.5 1 375 +,yk483c3.5 1 378 +,yk253d3.5 1 379 +,yk615h4.5 1 376 +,yk281d11.5 1 360 +,yk330h9.5 1 360 +,yk446a5.5 1 377 +,yk498f9.5 1 360 +,yk453a11.5 1 360 +,yk326h8.5 1 360 +,yk140h11.5 1 360 +,yk627c5.5 1 360 +,FLYBASE 1 131 +,BP 1 131 +,RP 1 131 +,yk448c12.5 1 360 +,yk373f11.5 1 360 +,yk60a11.5 1 360 +,SW 1 130 +,yk476f7.5 1 360 +,yk516c9.5 1 360 +,yk448f2.5 1 360 +,yk558h2.5 1 360 +,yk494c8.5 1 360 +,yk492f11.5 1 360 +,yk551b11.5 1 360 +,yk646a8.5 1 360 +,yk278c2.5 1 374 +,yk471g11.5 1 360 -,CK580762 1 219 +
III	gt csa	exon	1950628	1950760	0.947	+	.	Parent=mRNA275
III	gt csa	exon	1951062	1951411	0.995	+	.	Parent=mRNA275
III	gt csa	exon	1951713	1951721	0.556	+	.	Parent=mRNA275
III	gt csa	mRNA	1951519	1952513	.	+	.	ID=mRNA276;Parent=gene179;Target=yk372d12.5 1 375 +,yk372d12.3 1 300 -,yk1703a04.3 1 500 +
III	gt csa	exon	1951519	1951659	0.982	+	.	Parent=mRNA276
III	gt csa	exon	1951713	1951829	1	+	.	Parent=mRNA276
III	gt csa	exon	1951902	1952513	0.991	+	.	Parent=mRNA276
###
III	gt csa	gene	1963554	1970446	.	-	.	ID=gene180
III	gt csa	mRNA	1963554	1970446	.	-	.	ID=mRNA277;Parent=gene180;Target=yk23e3.3 1 390 -,WP 1 1309 +,yk23e3.5 1 360 +
III	gt csa	exon	1963554	1963898	0.975	-	.	Parent=mRNA277
III	gt csa	exon	1963953	1964107	1	-	.	Parent=mRNA277
III	gt csa	exon	1964993	1965165	1	-	.	Parent=mRNA277
III	gt csa	exon	1966002	1966439	1	-	.	Parent=mRNA277
III	gt csa	exon	1966813	1967020	0.987	-	.	Parent=mRNA277
III	gt csa	exon	1967077	1967198	0.91	-	.	Parent=mRNA277
III	gt csa	exon	1967254	1969663	1	-	.	Parent=mRNA277
III	gt csa	exon	1970232	1970363	1	-	.	Parent=mRNA277
III	gt csa	exon	1970410	1970446	1	-	.	Parent=mRNA277
###
III	gt csa	gene	1971220	1975502	.	-	.	ID=gene181
III	gt csa	mRNA	1971220	1975502	.	-	.	ID=mRNA278;Parent=gene181;Target=WP 1 1166 +
III	gt csa	exon	1971220	1971570	1	-	.	Parent=mRNA278
III	gt csa	exon	1971619	1971773	1	-	.	Parent=mRNA278
III	gt csa	exon	1971899	1972068	1	-	.	Parent=mRNA278
III	gt csa	exon	1972118	1972501	1	-	.	Parent=mRNA278
III	gt csa	exon	1972550	1972766	1	-	.	Parent=mRNA278
III	gt csa	exon	1973235	1973470	1	-	.	Parent=mRNA278
III	gt csa	exon	1973518	1975502	1	-	.	Parent=mRNA278
###
III	gt csa	gene	1977303	1980450	.	+	.	ID=gene182
III	gt csa	mRNA	1977303	1980450	.	+	.	ID=mRNA279;Parent=gene182;Target=WP 1 874 +
III	gt csa	exon	1977303	1977441	1	+	.	Parent=mRNA279
III	gt csa	exon	1977492	1977554	1	+	.	Parent=mRNA279
III	gt csa	exon	1977881	1978741	1	+	.	Parent=mRNA279
III	gt csa	exon	1978792	1979883	1	+	.	Parent=mRNA279
III	gt csa	exon	1979937	1980162	1	+	.	Parent=mRNA279
III	gt csa	exon	1980210	1980450	1	+	.	Parent=mRNA279
###
III	gt csa	gene	1980811	1982635	.	-	.	ID=gene183
III	gt csa	mRNA	1980811	1982635	.	-	.	ID=mRNA280;Parent=gene183;Target=WP 1 324 +
III	gt csa	exon	1980811	1980995	1	-	.	Parent=mRNA280
III	gt csa	exon	1981163	1981517	1	-	.	Parent=mRNA280
III	gt csa	exon	1981877	1982017	1	-	.	Parent=mRNA280
III	gt csa	exon	1982226	1982322	1	-	.	Parent=mRNA280
III	gt csa	exon	1982442	1982635	1	-	.	Parent=mRNA280
###
genometools-1.5.1/testdata/nGASP/resIIIcds.gff3000066400000000000000000006200541211610345200211610ustar00rootroot00000000000000##gff-version   3
##sequence-region   III 1000001 2000000
III	gt csa	gene	1001124	1001929	.	+	.	ID=gene1
III	gt csa	mRNA	1001124	1001415	.	+	.	ID=mRNA1;Parent=gene1;Target=CESAC87R 1 276 +,CEESA72R 1 286 +
III	gt csa	exon	1001124	1001415	0.961	+	.	Parent=mRNA1
III	gt csa	mRNA	1001583	1001929	.	+	.	ID=mRNA2;Parent=gene1;Target=yk1113e09.3 16 235 -,yk1113e09.5 16 273 +
III	gt csa	exon	1001583	1001711	1	+	.	Parent=mRNA2
III	gt cds	CDS	1001596	1001711	.	+	0	ID=CDS1;Parent=mRNA2
III	gt cds	CDS	1001801	1001882	.	+	1	ID=CDS1;Parent=mRNA2
III	gt csa	exon	1001801	1001929	0.961	+	.	Parent=mRNA2
###
III	gt csa	gene	1002693	1006177	.	+	.	ID=gene2
III	gt csa	mRNA	1002693	1006177	.	+	.	ID=mRNA3;Parent=gene2;Target=yk1191d02.5 1 502 +,yk741d1.5 1 337 +,yk119f11.5 1 360 +,yk263f3.5 1 360 +,yk1191d02.3 1 625 -,yk263f3.3 1 300 -,yk741d1.3 1 300 -,yk735g1.3 1 197 -
III	gt csa	exon	1002693	1002823	0.985	+	.	Parent=mRNA3
III	gt cds	CDS	1002714	1002823	.	+	0	ID=CDS2;Parent=mRNA3
III	gt csa	exon	1003572	1003690	1	+	.	Parent=mRNA3
III	gt cds	CDS	1003572	1003690	.	+	1	ID=CDS2;Parent=mRNA3
III	gt csa	exon	1003754	1003876	1	+	.	Parent=mRNA3
III	gt cds	CDS	1003754	1003876	.	+	2	ID=CDS2;Parent=mRNA3
III	gt csa	exon	1003923	1004051	1	+	.	Parent=mRNA3
III	gt cds	CDS	1003923	1004051	.	+	2	ID=CDS2;Parent=mRNA3
III	gt csa	exon	1004874	1004992	1	+	.	Parent=mRNA3
III	gt cds	CDS	1004874	1004992	.	+	2	ID=CDS2;Parent=mRNA3
III	gt csa	exon	1005039	1005141	1	+	.	Parent=mRNA3
III	gt cds	CDS	1005039	1005141	.	+	0	ID=CDS2;Parent=mRNA3
III	gt csa	exon	1005251	1005368	1	+	.	Parent=mRNA3
III	gt cds	CDS	1005251	1005368	.	+	2	ID=CDS2;Parent=mRNA3
III	gt csa	exon	1005890	1006050	1	+	.	Parent=mRNA3
III	gt cds	CDS	1005890	1006050	.	+	1	ID=CDS2;Parent=mRNA3
III	gt cds	CDS	1006097	1006176	.	+	2	ID=CDS2;Parent=mRNA3
III	gt csa	exon	1006097	1006177	0.975	+	.	Parent=mRNA3
###
III	gt csa	gene	1010540	1011351	.	+	.	ID=gene3
III	gt csa	mRNA	1010540	1011351	.	+	.	ID=mRNA4;Parent=gene3;Target=yk708f5.5 1 316 +,WP 1 199 +,yk708f5.3 1 212 -
III	gt csa	exon	1010540	1010705	0.994	+	.	Parent=mRNA4
III	gt cds	CDS	1010547	1010705	.	+	0	ID=CDS3;Parent=mRNA4
III	gt csa	exon	1010749	1010997	1	+	.	Parent=mRNA4
III	gt cds	CDS	1010749	1010997	.	+	0	ID=CDS3;Parent=mRNA4
III	gt csa	exon	1011163	1011351	1	+	.	Parent=mRNA4
III	gt cds	CDS	1011163	1011351	.	+	0	ID=CDS3;Parent=mRNA4
###
III	gt csa	gene	1020968	1021291	.	+	.	ID=gene4
III	gt csa	mRNA	1020968	1021291	.	+	.	ID=mRNA5;Parent=gene4;Target=WP 1 87 +
III	gt csa	exon	1020968	1021129	1	+	.	Parent=mRNA5
III	gt cds	CDS	1020968	1021129	.	+	0	ID=CDS4;Parent=mRNA5
III	gt csa	exon	1021193	1021291	1	+	.	Parent=mRNA5
III	gt cds	CDS	1021193	1021291	.	+	0	ID=CDS4;Parent=mRNA5
###
III	gt csa	gene	1023281	1023580	.	+	.	ID=gene5
III	gt csa	mRNA	1023281	1023580	.	+	.	ID=mRNA6;Parent=gene5;Target=yk720d6.3 1 300 +
III	gt csa	exon	1023281	1023580	0.997	+	.	Parent=mRNA6
###
III	gt csa	gene	1023729	1024566	.	-	.	ID=gene6
III	gt csa	mRNA	1023729	1024566	.	-	.	ID=mRNA7;Parent=gene6;Target=yk720d6.5 1 335 +
III	gt csa	exon	1023729	1023771	1	-	.	Parent=mRNA7
III	gt cds	CDS	1023729	1023771	.	-	1	ID=CDS5;Parent=mRNA7
III	gt csa	exon	1023816	1023910	0.953	-	.	Parent=mRNA7
III	gt cds	CDS	1023816	1023910	.	-	0	ID=CDS5;Parent=mRNA7
III	gt cds	CDS	1024370	1024531	.	-	0	ID=CDS5;Parent=mRNA7
III	gt csa	exon	1024370	1024566	0.964	-	.	Parent=mRNA7
###
III	gt csa	gene	1026929	1028347	.	-	.	ID=gene7
III	gt csa	mRNA	1026929	1028347	.	-	.	ID=mRNA8;Parent=gene7;Target=WP 1 192 +,yk1105f03.3 41 639 -,yk1105f03.5 41 543 +
III	gt csa	exon	1026929	1027102	1	-	.	Parent=mRNA8
III	gt cds	CDS	1026929	1027102	.	-	0	ID=CDS6;Parent=mRNA8
III	gt csa	exon	1027314	1027467	1	-	.	Parent=mRNA8
III	gt cds	CDS	1027314	1027467	.	-	1	ID=CDS6;Parent=mRNA8
III	gt csa	exon	1027515	1027609	1	-	.	Parent=mRNA8
III	gt cds	CDS	1027515	1027609	.	-	0	ID=CDS6;Parent=mRNA8
III	gt cds	CDS	1028167	1028319	.	-	0	ID=CDS6;Parent=mRNA8
III	gt csa	exon	1028167	1028347	1	-	.	Parent=mRNA8
###
III	gt csa	gene	1028790	1037200	.	-	.	ID=gene8
III	gt csa	mRNA	1028790	1031062	.	-	.	ID=mRNA9;Parent=gene8;Target=WP 1 227 +
III	gt csa	exon	1028790	1028969	1	-	.	Parent=mRNA9
III	gt cds	CDS	1028790	1028969	.	-	0	ID=CDS7;Parent=mRNA9
III	gt csa	exon	1029692	1029845	1	-	.	Parent=mRNA9
III	gt cds	CDS	1029692	1029845	.	-	1	ID=CDS7;Parent=mRNA9
III	gt csa	exon	1029891	1029985	1	-	.	Parent=mRNA9
III	gt cds	CDS	1029891	1029985	.	-	0	ID=CDS7;Parent=mRNA9
III	gt cds	CDS	1030811	1031014	.	-	0	ID=CDS7;Parent=mRNA9
III	gt csa	exon	1030811	1031062	0.933	-	.	Parent=mRNA9
III	gt csa	mRNA	1031337	1037200	.	-	.	ID=mRNA10;Parent=gene8;Target=yk1677a04.3 1 666 -,yk1707c12.3 1 704 -,RP 1 422 +,yk1677a04.5 1 607 +,yk1707c12.5 23 589 +,yk623f3.5 1 360 +
III	gt csa	exon	1031337	1031862	0.994	-	.	Parent=mRNA10
III	gt cds	CDS	1031704	1031862	.	-	0	ID=CDS8;Parent=mRNA10
III	gt csa	exon	1032740	1032809	1	-	.	Parent=mRNA10
III	gt cds	CDS	1032740	1032809	.	-	1	ID=CDS8;Parent=mRNA10
III	gt csa	exon	1033111	1033262	1	-	.	Parent=mRNA10
III	gt cds	CDS	1033111	1033262	.	-	0	ID=CDS8;Parent=mRNA10
III	gt csa	exon	1034167	1034457	1	-	.	Parent=mRNA10
III	gt cds	CDS	1034167	1034457	.	-	0	ID=CDS8;Parent=mRNA10
III	gt csa	exon	1034874	1035024	0.898	-	.	Parent=mRNA10
III	gt cds	CDS	1034874	1035024	.	-	1	ID=CDS8;Parent=mRNA10
III	gt csa	exon	1036294	1036442	1	-	.	Parent=mRNA10
III	gt cds	CDS	1036294	1036442	.	-	0	ID=CDS8;Parent=mRNA10
III	gt csa	exon	1036772	1036888	1	-	.	Parent=mRNA10
III	gt cds	CDS	1036772	1036888	.	-	0	ID=CDS8;Parent=mRNA10
III	gt csa	exon	1036937	1037082	1	-	.	Parent=mRNA10
III	gt cds	CDS	1036937	1037082	.	-	2	ID=CDS8;Parent=mRNA10
III	gt cds	CDS	1037168	1037198	.	-	0	ID=CDS8;Parent=mRNA10
III	gt csa	exon	1037168	1037200	1	-	.	Parent=mRNA10
III	gt csa	mRNA	1031337	1037200	.	-	.	ID=mRNA11;Parent=gene8;Target=yk1677a04.3 1 666 -,yk1707c12.3 1 704 -,BP 1 433 +,yk1707c12.5 23 589 +,yk623f3.5 1 360 +
III	gt csa	exon	1031337	1031862	0.994	-	.	Parent=mRNA11
III	gt csa	exon	1032740	1032809	1	-	.	Parent=mRNA11
III	gt csa	exon	1033111	1033262	0.924	-	.	Parent=mRNA11
III	gt csa	exon	1034167	1034457	0.894	-	.	Parent=mRNA11
III	gt cds	CDS	1034367	1034457	.	-	1	ID=CDS9;Parent=mRNA11
III	gt csa	exon	1034642	1034679	0.215	-	.	Parent=mRNA11
III	gt cds	CDS	1034642	1034679	.	-	0	ID=CDS9;Parent=mRNA11
III	gt csa	exon	1034874	1035024	0.985	-	.	Parent=mRNA11
III	gt cds	CDS	1034874	1035024	.	-	1	ID=CDS9;Parent=mRNA11
III	gt csa	exon	1036294	1036442	1	-	.	Parent=mRNA11
III	gt cds	CDS	1036294	1036442	.	-	0	ID=CDS9;Parent=mRNA11
III	gt csa	exon	1036772	1036888	1	-	.	Parent=mRNA11
III	gt cds	CDS	1036772	1036888	.	-	0	ID=CDS9;Parent=mRNA11
III	gt csa	exon	1036937	1037082	1	-	.	Parent=mRNA11
III	gt cds	CDS	1036937	1037082	.	-	2	ID=CDS9;Parent=mRNA11
III	gt cds	CDS	1037168	1037198	.	-	0	ID=CDS9;Parent=mRNA11
III	gt csa	exon	1037168	1037200	1	-	.	Parent=mRNA11
###
III	gt csa	gene	1031495	1031674	.	+	.	ID=gene9
III	gt csa	mRNA	1031495	1031674	.	+	.	ID=mRNA12;Parent=gene9;Target=yk623f3.3 1 180 +
III	gt csa	exon	1031495	1031674	1	+	.	Parent=mRNA12
###
III	gt csa	gene	1040341	1043441	.	+	.	ID=gene10
III	gt csa	mRNA	1040341	1041938	.	+	.	ID=mRNA13;Parent=gene10;Target=yk645b4.5 36 382 +
III	gt csa	exon	1040341	1040503	0.939	+	.	Parent=mRNA13
III	gt cds	CDS	1040432	1040503	.	+	0	ID=CDS10;Parent=mRNA13
III	gt csa	exon	1041759	1041938	1	+	.	Parent=mRNA13
III	gt cds	CDS	1041759	1041938	.	+	0	ID=CDS10;Parent=mRNA13
III	gt csa	mRNA	1042042	1043441	.	+	.	ID=mRNA14;Parent=gene10;Target=yk64a11.5 1 360 +
III	gt csa	exon	1042042	1042093	1	+	.	Parent=mRNA14
III	gt cds	CDS	1042049	1042093	.	+	0	ID=CDS11;Parent=mRNA14
III	gt cds	CDS	1043134	1043439	.	+	0	ID=CDS11;Parent=mRNA14
III	gt csa	exon	1043134	1043441	0.984	+	.	Parent=mRNA14
###
III	gt csa	gene	1046267	1046555	.	+	.	ID=gene11
III	gt csa	mRNA	1046267	1046555	.	+	.	ID=mRNA15;Parent=gene11;Target=yk1391c06.3 1 287 +
III	gt csa	exon	1046267	1046555	0.955	+	.	Parent=mRNA15
###
III	gt csa	gene	1046557	1059998	.	-	.	ID=gene12
III	gt csa	mRNA	1046557	1059998	.	-	.	ID=mRNA16;Parent=gene12;Target=WP 1 1158 +
III	gt csa	exon	1046557	1046617	1	-	.	Parent=mRNA16
III	gt cds	CDS	1046557	1046617	.	-	1	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1046663	1046761	1	-	.	Parent=mRNA16
III	gt cds	CDS	1046663	1046761	.	-	1	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1047490	1047637	1	-	.	Parent=mRNA16
III	gt cds	CDS	1047490	1047637	.	-	2	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1048507	1048990	1	-	.	Parent=mRNA16
III	gt cds	CDS	1048507	1048990	.	-	0	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1049960	1050356	1	-	.	Parent=mRNA16
III	gt cds	CDS	1049960	1050356	.	-	1	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1051280	1051470	1	-	.	Parent=mRNA16
III	gt cds	CDS	1051280	1051470	.	-	0	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1051832	1052354	1	-	.	Parent=mRNA16
III	gt cds	CDS	1051832	1052354	.	-	1	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1052641	1052770	1	-	.	Parent=mRNA16
III	gt cds	CDS	1052641	1052770	.	-	2	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1053104	1053230	1	-	.	Parent=mRNA16
III	gt cds	CDS	1053104	1053230	.	-	0	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1053750	1053789	1	-	.	Parent=mRNA16
III	gt cds	CDS	1053750	1053789	.	-	1	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1054974	1055025	1	-	.	Parent=mRNA16
III	gt cds	CDS	1054974	1055025	.	-	2	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1055100	1055216	1	-	.	Parent=mRNA16
III	gt cds	CDS	1055100	1055216	.	-	2	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1056330	1056534	1	-	.	Parent=mRNA16
III	gt cds	CDS	1056330	1056534	.	-	0	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1057718	1058011	1	-	.	Parent=mRNA16
III	gt cds	CDS	1057718	1058011	.	-	0	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1058066	1058194	1	-	.	Parent=mRNA16
III	gt cds	CDS	1058066	1058194	.	-	0	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1058517	1058636	1	-	.	Parent=mRNA16
III	gt cds	CDS	1058517	1058636	.	-	0	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1058794	1058967	1	-	.	Parent=mRNA16
III	gt cds	CDS	1058794	1058967	.	-	0	ID=CDS12;Parent=mRNA16
III	gt csa	exon	1059816	1059998	1	-	.	Parent=mRNA16
III	gt cds	CDS	1059816	1059998	.	-	0	ID=CDS12;Parent=mRNA16
III	gt csa	mRNA	1052040	1052771	.	-	.	ID=mRNA17;Parent=gene12;Target=CK580775 1 445 +,CK575409 1 430 +,CK575411 1 416 +,CK583013 1 411 +,CK575408 1 354 +,CK575413 1 347 +,CK583019 1 334 +
III	gt csa	exon	1052040	1052354	0.997	-	.	Parent=mRNA17
III	gt cds	CDS	1052042	1052354	.	-	1	ID=CDS13;Parent=mRNA17
III	gt cds	CDS	1052641	1052711	.	-	0	ID=CDS13;Parent=mRNA17
III	gt csa	exon	1052641	1052771	1	-	.	Parent=mRNA17
III	gt csa	mRNA	1052047	1053234	.	-	.	ID=mRNA18;Parent=gene12;Target=yk1391c06.5 1 569 +
III	gt csa	exon	1052047	1052354	1	-	.	Parent=mRNA18
III	gt cds	CDS	1052048	1052354	.	-	1	ID=CDS14;Parent=mRNA18
III	gt csa	exon	1052641	1052770	0.992	-	.	Parent=mRNA18
III	gt cds	CDS	1052641	1052770	.	-	2	ID=CDS14;Parent=mRNA18
III	gt cds	CDS	1053104	1053230	.	-	0	ID=CDS14;Parent=mRNA18
III	gt csa	exon	1053104	1053234	1	-	.	Parent=mRNA18
III	gt csa	mRNA	1056259	1059192	.	-	.	ID=mRNA19;Parent=gene12;Target=BP 75 367 +
III	gt csa	exon	1056259	1056534	0.894	-	.	Parent=mRNA19
III	gt cds	CDS	1056259	1056534	.	-	0	ID=CDS15;Parent=mRNA19
III	gt csa	exon	1057718	1058011	0.954	-	.	Parent=mRNA19
III	gt cds	CDS	1057718	1058011	.	-	0	ID=CDS15;Parent=mRNA19
III	gt csa	exon	1058517	1058636	0.856	-	.	Parent=mRNA19
III	gt cds	CDS	1058517	1058636	.	-	0	ID=CDS15;Parent=mRNA19
III	gt cds	CDS	1058794	1058868	.	-	0	ID=CDS15;Parent=mRNA19
III	gt csa	exon	1058794	1058967	0.818	-	.	Parent=mRNA19
III	gt csa	exon	1059181	1059192	0.273	-	.	Parent=mRNA19
III	gt csa	mRNA	1056259	1059224	.	-	.	ID=mRNA20;Parent=gene12;Target=RP 72 369 +
III	gt csa	exon	1056259	1056534	0.853	-	.	Parent=mRNA20
III	gt cds	CDS	1056259	1056534	.	-	0	ID=CDS16;Parent=mRNA20
III	gt csa	exon	1057718	1058011	0.969	-	.	Parent=mRNA20
III	gt cds	CDS	1057718	1058011	.	-	0	ID=CDS16;Parent=mRNA20
III	gt csa	exon	1058517	1058636	0.927	-	.	Parent=mRNA20
III	gt cds	CDS	1058517	1058636	.	-	0	ID=CDS16;Parent=mRNA20
III	gt csa	exon	1058794	1058967	0.833	-	.	Parent=mRNA20
III	gt cds	CDS	1058794	1058967	.	-	0	ID=CDS16;Parent=mRNA20
III	gt cds	CDS	1059198	1059215	.	-	0	ID=CDS16;Parent=mRNA20
III	gt csa	exon	1059198	1059224	0.22	-	.	Parent=mRNA20
###
III	gt csa	gene	1062769	1063139	.	+	.	ID=gene13
III	gt csa	mRNA	1062769	1063139	.	+	.	ID=mRNA21;Parent=gene13;Target=yk681f11.5 1 370 +,CEESV83F 1 359 +,yk117f1.3 1 332 +,yk1170b11.3 1 181 +,yk1376a02.3 1 215 +,yk1704g11.3 1 255 +,yk117c1.3 1 323 +,yk617a4.3 1 300 +,yk621h1.3 1 299 +,yk659c10.3 1 297 +,yk602e8.3 1 297 +,yk652b11.3 1 297 +,yk675h9.3 1 296 +,yk337c2.3 1 295 +,yk658b12.3 1 294 +,yk393b4.3 1 180 +,yk394b5.3 1 295 +,yk363h2.3 1 292 +,yk525g8.3 1 291 +,yk656g8.3 1 291 +,yk255h9.3 1 289 +,yk572f4.3 1 288 +,yk592b8.3 1 286 +
III	gt csa	exon	1062769	1063139	0.978	+	.	Parent=mRNA21
###
III	gt csa	gene	1062771	1076543	.	-	.	ID=gene14
III	gt csa	mRNA	1062771	1076543	.	-	.	ID=mRNA22;Parent=gene14;Target=U79157 1 1736 +,yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,WP 1 497 +,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk117f1.5 1 360 +,CK579359 1 613 +,yk1101a09.5 23 632 +,yk1034a11.5 23 628 +,yk363h2.5 1 360 +,yk1172f12.5 23 612 +,yk1053h12.5 22 598 +,yk1339g04.5 24 597 +,yk1169g11.5 23 596 +,yk1170b11.5 23 594 +,yk1120d08.5 23 590 +,yk1286b11.5 23 589 +,yk1120g02.5 23 587 +,yk1058c11.5 23 586 +,yk1254h08.5 23 584 +,yk1722g08.5 23 543 +,yk804f05.5 23 542 +,yk1096a09.5 23 539 +,yk1516e02.5 23 528 +,yk1652g01.5 23 510 +,yk1401h02.5 23 497 +,yk1061h02.5 23 497 +,yk1369c04.5 23 488 +,yk505f9.5 1 368 +,yk1141g04.5 23 448 +,yk820f07.5 23 446 +,yk1741a10.5 24 446 +,yk1026h07.5 1 370 +,yk656g8.5 1 360 +,yk216b5.5 1 360 +,yk568d7.5 1 360 +,yk659c10.5 1 379 +,yk592b8.5 1 360 +,yk658b12.5 1 360 +,yk269b4.5 1 376 +,yk525g8.5 1 377 +,yk482b6.5 1 360 +,yk569b4.5 1 360 +,yk675h9.5 1 360 +,yk456c8.5 1 377 +,yk393b4.5 1 373 +,yk626a1.5 1 360 +,yk602e8.5 1 360 +,yk617a4.5 1 360 +,yk332b1.5 1 378 +,yk337c2.5 1 374 +,yk61b9.5 1 360 +,yk434f11.5 1 360 +,yk117c1.5 1 360 +,yk621h1.5 1 218 +,yk1376a02.5 23 252 +,yk106d3.5 1 181 +,yk768a10.5 23 200 +
III	gt csa	exon	1062771	1063137	0.858	-	.	Parent=mRNA22
III	gt cds	CDS	1063006	1063137	.	-	0	ID=CDS17;Parent=mRNA22
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA22
III	gt cds	CDS	1064630	1064950	.	-	0	ID=CDS17;Parent=mRNA22
III	gt csa	exon	1067821	1067940	1	-	.	Parent=mRNA22
III	gt cds	CDS	1067821	1067940	.	-	0	ID=CDS17;Parent=mRNA22
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA22
III	gt cds	CDS	1070411	1070643	.	-	2	ID=CDS17;Parent=mRNA22
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA22
III	gt cds	CDS	1072375	1072533	.	-	2	ID=CDS17;Parent=mRNA22
III	gt csa	exon	1074168	1074463	1	-	.	Parent=mRNA22
III	gt cds	CDS	1074168	1074463	.	-	1	ID=CDS17;Parent=mRNA22
III	gt csa	exon	1076314	1076543	1	-	.	Parent=mRNA22
III	gt cds	CDS	1076314	1076543	.	-	0	ID=CDS17;Parent=mRNA22
III	gt csa	mRNA	1062781	1068054	.	-	.	ID=mRNA23;Parent=gene14;Target=yk1101a09.3 26 698 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1061h02.3 1 616 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1276g05.3 1 729 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA23
III	gt cds	CDS	1063006	1063137	.	-	0	ID=CDS18;Parent=mRNA23
III	gt cds	CDS	1064630	1064929	.	-	0	ID=CDS18;Parent=mRNA23
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA23
III	gt csa	exon	1067821	1067837	1	-	.	Parent=mRNA23
III	gt csa	exon	1067912	1067940	1	-	.	Parent=mRNA23
III	gt csa	exon	1068024	1068054	1	-	.	Parent=mRNA23
III	gt csa	mRNA	1062781	1074608	.	-	.	ID=mRNA24;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,BP 66 487 +,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk117f1.5 1 360 +,yk363h2.5 1 360 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA24
III	gt cds	CDS	1063006	1063137	.	-	0	ID=CDS19;Parent=mRNA24
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA24
III	gt cds	CDS	1064630	1064950	.	-	0	ID=CDS19;Parent=mRNA24
III	gt csa	exon	1067821	1067940	1	-	.	Parent=mRNA24
III	gt cds	CDS	1067821	1067940	.	-	0	ID=CDS19;Parent=mRNA24
III	gt csa	exon	1070411	1070643	0.976	-	.	Parent=mRNA24
III	gt cds	CDS	1070411	1070643	.	-	2	ID=CDS19;Parent=mRNA24
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA24
III	gt cds	CDS	1072375	1072533	.	-	2	ID=CDS19;Parent=mRNA24
III	gt cds	CDS	1074168	1074240	.	-	0	ID=CDS19;Parent=mRNA24
III	gt csa	exon	1074168	1074463	0.645	-	.	Parent=mRNA24
III	gt csa	exon	1074601	1074608	0	-	.	Parent=mRNA24
III	gt csa	mRNA	1062781	1074628	.	-	.	ID=mRNA25;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,RP 81 497 +,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk117f1.5 1 360 +,yk363h2.5 1 360 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA25
III	gt cds	CDS	1063006	1063137	.	-	0	ID=CDS20;Parent=mRNA25
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA25
III	gt cds	CDS	1064630	1064950	.	-	0	ID=CDS20;Parent=mRNA25
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA25
III	gt cds	CDS	1067821	1067940	.	-	0	ID=CDS20;Parent=mRNA25
III	gt csa	exon	1070411	1070643	0.968	-	.	Parent=mRNA25
III	gt cds	CDS	1070411	1070643	.	-	2	ID=CDS20;Parent=mRNA25
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA25
III	gt cds	CDS	1072375	1072533	.	-	2	ID=CDS20;Parent=mRNA25
III	gt cds	CDS	1074168	1074240	.	-	0	ID=CDS20;Parent=mRNA25
III	gt csa	exon	1074168	1074463	0.683	-	.	Parent=mRNA25
III	gt csa	exon	1074624	1074628	0	-	.	Parent=mRNA25
III	gt csa	mRNA	1062781	1076543	.	-	.	ID=mRNA26;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk1213f07.5 23 619 +,yk1199c10.5 16 513 +,yk621h1.5 1 218 +,yk1376a02.5 23 252 +,yk106d3.5 1 181 +,yk768a10.5 23 200 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA26
III	gt cds	CDS	1063006	1063137	.	-	0	ID=CDS21;Parent=mRNA26
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA26
III	gt cds	CDS	1064630	1064950	.	-	0	ID=CDS21;Parent=mRNA26
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA26
III	gt cds	CDS	1067821	1067940	.	-	0	ID=CDS21;Parent=mRNA26
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA26
III	gt cds	CDS	1070411	1070643	.	-	2	ID=CDS21;Parent=mRNA26
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA26
III	gt cds	CDS	1072375	1072533	.	-	2	ID=CDS21;Parent=mRNA26
III	gt csa	exon	1074168	1074350	1	-	.	Parent=mRNA26
III	gt cds	CDS	1074168	1074350	.	-	2	ID=CDS21;Parent=mRNA26
III	gt csa	exon	1074426	1074463	1	-	.	Parent=mRNA26
III	gt cds	CDS	1074426	1074463	.	-	1	ID=CDS21;Parent=mRNA26
III	gt csa	exon	1076314	1076543	1	-	.	Parent=mRNA26
III	gt cds	CDS	1076314	1076543	.	-	0	ID=CDS21;Parent=mRNA26
III	gt csa	mRNA	1062781	1076543	.	-	.	ID=mRNA27;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk899h02.5 21 464 +,yk621h1.5 1 218 +,yk1376a02.5 23 252 +,yk106d3.5 1 181 +,yk768a10.5 23 200 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA27
III	gt cds	CDS	1063006	1063137	.	-	0	ID=CDS22;Parent=mRNA27
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA27
III	gt cds	CDS	1064630	1064950	.	-	0	ID=CDS22;Parent=mRNA27
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA27
III	gt cds	CDS	1067821	1067940	.	-	0	ID=CDS22;Parent=mRNA27
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA27
III	gt cds	CDS	1070411	1070643	.	-	2	ID=CDS22;Parent=mRNA27
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA27
III	gt cds	CDS	1072375	1072533	.	-	2	ID=CDS22;Parent=mRNA27
III	gt csa	exon	1074168	1074350	0.973	-	.	Parent=mRNA27
III	gt cds	CDS	1074168	1074350	.	-	2	ID=CDS22;Parent=mRNA27
III	gt csa	exon	1074432	1074463	1	-	.	Parent=mRNA27
III	gt cds	CDS	1074432	1074463	.	-	1	ID=CDS22;Parent=mRNA27
III	gt csa	exon	1076314	1076543	1	-	.	Parent=mRNA27
III	gt cds	CDS	1076314	1076543	.	-	0	ID=CDS22;Parent=mRNA27
III	gt csa	mRNA	1062781	1076543	.	-	.	ID=mRNA28;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk778d02.5 21 613 +,yk117f1.5 1 360 +,yk363h2.5 1 360 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA28
III	gt cds	CDS	1063006	1063137	.	-	0	ID=CDS23;Parent=mRNA28
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA28
III	gt cds	CDS	1064630	1064950	.	-	0	ID=CDS23;Parent=mRNA28
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA28
III	gt cds	CDS	1067821	1067940	.	-	0	ID=CDS23;Parent=mRNA28
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA28
III	gt cds	CDS	1070411	1070643	.	-	2	ID=CDS23;Parent=mRNA28
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA28
III	gt cds	CDS	1072375	1072533	.	-	2	ID=CDS23;Parent=mRNA28
III	gt csa	exon	1074168	1074463	0.993	-	.	Parent=mRNA28
III	gt cds	CDS	1074168	1074463	.	-	1	ID=CDS23;Parent=mRNA28
III	gt csa	exon	1076380	1076543	1	-	.	Parent=mRNA28
III	gt cds	CDS	1076380	1076543	.	-	0	ID=CDS23;Parent=mRNA28
III	gt csa	mRNA	1062781	1076543	.	-	.	ID=mRNA29;Parent=gene14;Target=yk1101a09.3 26 698 -,yk1169g11.3 1 752 -,yk1339g04.3 1 746 -,yk804f05.3 1 665 -,yk899h02.3 1 614 -,yk1120g02.3 24 690 -,yk1213f07.3 9 673 -,yk1120d08.3 1 686 -,yk1061h02.3 1 616 -,yk1053h12.3 1 685 -,yk1058c11.3 1 734 -,yk1401h02.3 28 684 -,yk1369c04.3 1 639 -,yk1652g01.3 23 678 -,yk1741a10.3 10 665 -,yk1722g08.3 1 733 -,yk1516e02.3 1 732 -,yk1141g04.3 1 677 -,yk1286b11.3 1 677 -,yk1199c10.3 1 546 -,yk820f07.3 1 586 -,yk778d02.3 1 652 -,yk1096a09.3 11 661 -,yk1254h08.3 1 704 -,yk1351e07.3 1 623 -,yk1093g01.3 1 570 -,yk1034a11.3 1 259 -,yk65a10.5 1 360 +,yk255h9.5 5 379 +,yk652b11.5 1 360 +,yk1351e07.5 23 549 +
III	gt csa	exon	1062781	1063137	0.983	-	.	Parent=mRNA29
III	gt cds	CDS	1063006	1063137	.	-	0	ID=CDS24;Parent=mRNA29
III	gt csa	exon	1064630	1064950	1	-	.	Parent=mRNA29
III	gt cds	CDS	1064630	1064950	.	-	0	ID=CDS24;Parent=mRNA29
III	gt csa	exon	1067821	1067940	0.983	-	.	Parent=mRNA29
III	gt cds	CDS	1067821	1067940	.	-	0	ID=CDS24;Parent=mRNA29
III	gt csa	exon	1070411	1070643	1	-	.	Parent=mRNA29
III	gt cds	CDS	1070411	1070643	.	-	2	ID=CDS24;Parent=mRNA29
III	gt csa	exon	1072375	1072533	1	-	.	Parent=mRNA29
III	gt cds	CDS	1072375	1072533	.	-	2	ID=CDS24;Parent=mRNA29
III	gt csa	exon	1074168	1074374	0.995	-	.	Parent=mRNA29
III	gt cds	CDS	1074168	1074374	.	-	2	ID=CDS24;Parent=mRNA29
III	gt csa	exon	1076372	1076543	0.994	-	.	Parent=mRNA29
III	gt cds	CDS	1076372	1076543	.	-	0	ID=CDS24;Parent=mRNA29
III	gt csa	mRNA	1062794	1064950	.	-	.	ID=mRNA30;Parent=gene14;Target=yk1172f12.3 68 589 -
III	gt csa	exon	1062794	1063137	1	-	.	Parent=mRNA30
III	gt cds	CDS	1063006	1063137	.	-	0	ID=CDS25;Parent=mRNA30
III	gt cds	CDS	1064630	1064782	.	-	0	ID=CDS25;Parent=mRNA30
III	gt csa	exon	1064630	1064798	0.932	-	.	Parent=mRNA30
III	gt csa	exon	1064945	1064950	0.833	-	.	Parent=mRNA30
III	gt csa	mRNA	1067962	1068321	.	-	.	ID=mRNA31;Parent=gene14;Target=yk394b5.5 1 360 +
III	gt csa	exon	1067962	1068321	1	-	.	Parent=mRNA31
III	gt csa	mRNA	1072370	1076543	.	-	.	ID=mRNA32;Parent=gene14;Target=yk572f4.5 1 360 +,yk117f1.5 1 360 +,CK579359 1 613 +,yk1101a09.5 23 632 +,yk1034a11.5 23 628 +,yk363h2.5 1 360 +,yk1172f12.5 23 612 +,yk1053h12.5 22 598 +,yk1339g04.5 24 597 +,yk1169g11.5 23 596 +,yk1170b11.5 23 594 +,yk1120d08.5 23 590 +,yk1286b11.5 23 589 +,yk1120g02.5 23 587 +,yk1058c11.5 23 586 +,yk1254h08.5 23 584 +,yk1722g08.5 23 543 +,yk804f05.5 23 542 +,yk1096a09.5 23 539 +,yk1516e02.5 23 528 +,yk1652g01.5 23 510 +,yk1401h02.5 23 497 +,yk1061h02.5 23 497 +,yk1369c04.5 23 488 +,yk505f9.5 1 368 +,yk1141g04.5 23 448 +,yk820f07.5 23 446 +,yk1741a10.5 24 446 +,yk1026h07.5 1 370 +,yk656g8.5 1 360 +,yk216b5.5 1 360 +,yk568d7.5 1 360 +,yk659c10.5 1 379 +,yk592b8.5 1 360 +,yk658b12.5 1 360 +,yk269b4.5 1 376 +,yk525g8.5 1 377 +,yk482b6.5 1 360 +,yk569b4.5 1 360 +,yk675h9.5 1 360 +,yk456c8.5 1 377 +,yk393b4.5 1 373 +,yk626a1.5 1 360 +,yk602e8.5 1 360 +,yk617a4.5 1 360 +,yk332b1.5 1 378 +,yk337c2.5 1 374 +,yk61b9.5 1 360 +,yk434f11.5 1 360 +,yk117c1.5 1 360 +,yk621h1.5 1 218 +,yk1376a02.5 23 252 +,yk106d3.5 1 181 +,yk768a10.5 23 200 +
III	gt csa	exon	1072370	1072533	0.976	-	.	Parent=mRNA32
III	gt cds	CDS	1072370	1072533	.	-	2	ID=CDS26;Parent=mRNA32
III	gt csa	exon	1074168	1074463	1	-	.	Parent=mRNA32
III	gt cds	CDS	1074168	1074463	.	-	1	ID=CDS26;Parent=mRNA32
III	gt csa	exon	1076314	1076543	1	-	.	Parent=mRNA32
III	gt cds	CDS	1076314	1076543	.	-	0	ID=CDS26;Parent=mRNA32
###
III	gt csa	gene	1078138	1080469	.	-	.	ID=gene15
III	gt csa	mRNA	1078138	1079228	.	-	.	ID=mRNA33;Parent=gene15;Target=yk1340e12.3 1 864 -,yk616a3.5 1 360 +
III	gt csa	exon	1078138	1078930	0.996	-	.	Parent=mRNA33
III	gt csa	exon	1079155	1079228	0.932	-	.	Parent=mRNA33
III	gt csa	mRNA	1079466	1080469	.	-	.	ID=mRNA34;Parent=gene15;Target=yk1243e09.3 1 706 -,BP 1 203 +,RP 1 203 +,yk1243e09.5 24 582 +,yk1340e12.5 23 491 +,yk493c1.5 1 375 +,yk291g7.5 1 240 +,U23938 1 107 +
III	gt csa	exon	1079466	1079894	1	-	.	Parent=mRNA34
III	gt cds	CDS	1079670	1079894	.	-	0	ID=CDS27;Parent=mRNA34
III	gt csa	exon	1079946	1080199	1	-	.	Parent=mRNA34
III	gt cds	CDS	1079946	1080199	.	-	2	ID=CDS27;Parent=mRNA34
III	gt csa	exon	1080275	1080330	1	-	.	Parent=mRNA34
III	gt cds	CDS	1080275	1080330	.	-	1	ID=CDS27;Parent=mRNA34
III	gt csa	exon	1080393	1080469	1	-	.	Parent=mRNA34
III	gt cds	CDS	1080393	1080469	.	-	0	ID=CDS27;Parent=mRNA34
III	gt csa	mRNA	1079821	1080352	.	-	.	ID=mRNA35;Parent=gene15;Target=yk1013b10.5 1 457 +
III	gt csa	exon	1079821	1080199	0.995	-	.	Parent=mRNA35
III	gt cds	CDS	1079823	1080199	.	-	2	ID=CDS28;Parent=mRNA35
III	gt cds	CDS	1080275	1080326	.	-	0	ID=CDS28;Parent=mRNA35
III	gt csa	exon	1080275	1080352	0.885	-	.	Parent=mRNA35
###
III	gt csa	gene	1078143	1079828	.	+	.	ID=gene16
III	gt csa	mRNA	1078143	1078790	.	+	.	ID=mRNA36;Parent=gene16;Target=yk1013b10.3 1 651 +,yk616a3.3 1 300 +
III	gt csa	exon	1078143	1078790	0.979	+	.	Parent=mRNA36
III	gt csa	mRNA	1079525	1079828	.	+	.	ID=mRNA37;Parent=gene16;Target=yk291g7.3 1 300 +,yk493c1.3 1 300 +
III	gt csa	exon	1079525	1079828	0.992	+	.	Parent=mRNA37
###
III	gt csa	gene	1080895	1095067	.	+	.	ID=gene17
III	gt csa	mRNA	1080895	1081298	.	+	.	ID=mRNA38;Parent=gene17;Target=yk628f9.3 1 285 -,CESAC24R 12 322 +,yk628f9.5 1 320 +
III	gt csa	exon	1080895	1081097	0.97	+	.	Parent=mRNA38
III	gt cds	CDS	1080908	1081097	.	+	0	ID=CDS29;Parent=mRNA38
III	gt cds	CDS	1081143	1081246	.	+	2	ID=CDS29;Parent=mRNA38
III	gt csa	exon	1081143	1081298	0.936	+	.	Parent=mRNA38
III	gt csa	mRNA	1081386	1095067	.	+	.	ID=mRNA39;Parent=gene17;Target=L26987 1 2172 +,yk96h7.5 1 360 +,yk628a12.5 1 378 +,yk375g6.5 1 240 +
III	gt csa	exon	1081386	1081507	0.984	+	.	Parent=mRNA39
III	gt cds	CDS	1081397	1081507	.	+	0	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1081621	1081704	1	+	.	Parent=mRNA39
III	gt cds	CDS	1081621	1081704	.	+	0	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1082982	1083119	1	+	.	Parent=mRNA39
III	gt cds	CDS	1082982	1083119	.	+	0	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1084050	1084121	1	+	.	Parent=mRNA39
III	gt cds	CDS	1084050	1084121	.	+	0	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1084325	1084449	1	+	.	Parent=mRNA39
III	gt cds	CDS	1084325	1084449	.	+	0	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1087773	1088553	0.996	+	.	Parent=mRNA39
III	gt cds	CDS	1087773	1088553	.	+	1	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1091545	1091685	0.986	+	.	Parent=mRNA39
III	gt cds	CDS	1091545	1091685	.	+	0	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1092617	1092679	0.984	+	.	Parent=mRNA39
III	gt cds	CDS	1092617	1092679	.	+	0	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1092734	1092865	1	+	.	Parent=mRNA39
III	gt cds	CDS	1092734	1092865	.	+	0	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1094216	1094362	0.973	+	.	Parent=mRNA39
III	gt cds	CDS	1094216	1094362	.	+	0	ID=CDS30;Parent=mRNA39
III	gt cds	CDS	1094697	1094789	.	+	0	ID=CDS30;Parent=mRNA39
III	gt csa	exon	1094697	1095067	0.997	+	.	Parent=mRNA39
III	gt csa	mRNA	1081392	1094789	.	+	.	ID=mRNA40;Parent=gene17;Target=yk325e4.5 1 374 +,WP 1 583 +
III	gt csa	exon	1081392	1081507	1	+	.	Parent=mRNA40
III	gt cds	CDS	1081397	1081507	.	+	0	ID=CDS31;Parent=mRNA40
III	gt csa	exon	1081621	1081704	1	+	.	Parent=mRNA40
III	gt cds	CDS	1081621	1081704	.	+	0	ID=CDS31;Parent=mRNA40
III	gt csa	exon	1084050	1084121	1	+	.	Parent=mRNA40
III	gt cds	CDS	1084050	1084121	.	+	0	ID=CDS31;Parent=mRNA40
III	gt csa	exon	1084325	1084449	1	+	.	Parent=mRNA40
III	gt cds	CDS	1084325	1084449	.	+	0	ID=CDS31;Parent=mRNA40
III	gt csa	exon	1087773	1088553	1	+	.	Parent=mRNA40
III	gt cds	CDS	1087773	1088553	.	+	1	ID=CDS31;Parent=mRNA40
III	gt csa	exon	1091545	1091685	1	+	.	Parent=mRNA40
III	gt cds	CDS	1091545	1091685	.	+	0	ID=CDS31;Parent=mRNA40
III	gt csa	exon	1092617	1092679	1	+	.	Parent=mRNA40
III	gt cds	CDS	1092617	1092679	.	+	0	ID=CDS31;Parent=mRNA40
III	gt csa	exon	1092734	1092865	1	+	.	Parent=mRNA40
III	gt cds	CDS	1092734	1092865	.	+	0	ID=CDS31;Parent=mRNA40
III	gt csa	exon	1094216	1094362	1	+	.	Parent=mRNA40
III	gt cds	CDS	1094216	1094362	.	+	0	ID=CDS31;Parent=mRNA40
III	gt csa	exon	1094697	1094789	1	+	.	Parent=mRNA40
III	gt cds	CDS	1094697	1094789	.	+	0	ID=CDS31;Parent=mRNA40
III	gt csa	mRNA	1086135	1086598	.	+	.	ID=mRNA41;Parent=gene17;Target=yk64a7.5 1 360 +,yk774d01.5 23 484 +,yk168e1.5 1 360 +
III	gt csa	exon	1086135	1086598	0.998	+	.	Parent=mRNA41
III	gt cds	CDS	1086147	1086596	.	+	0	ID=CDS32;Parent=mRNA41
###
III	gt csa	gene	1086142	1095035	.	-	.	ID=gene18
III	gt csa	mRNA	1086142	1086645	.	-	.	ID=mRNA42;Parent=gene18;Target=yk774d01.3 1 496 +,yk168e1.3 1 300 +,yk64a7.3 1 340 +
III	gt csa	exon	1086142	1086645	0.968	-	.	Parent=mRNA42
III	gt cds	CDS	1086144	1086575	.	-	0	ID=CDS33;Parent=mRNA42
III	gt csa	mRNA	1092456	1092592	.	-	.	ID=mRNA43;Parent=gene18;Target=yk623f3.3 45 180 +
III	gt csa	exon	1092456	1092592	0.883	-	.	Parent=mRNA43
III	gt csa	mRNA	1094701	1095035	.	-	.	ID=mRNA44;Parent=gene18;Target=yk628a12.3 1 300 +,yk325e4.3 1 300 +,yk96h7.3 1 317 +
III	gt csa	exon	1094701	1095035	0.97	-	.	Parent=mRNA44
###
III	gt csa	gene	1103215	1104223	.	+	.	ID=gene19
III	gt csa	mRNA	1103215	1104223	.	+	.	ID=mRNA45;Parent=gene19;Target=yk509d9.5 1 240 +
III	gt csa	exon	1103215	1103340	0.917	+	.	Parent=mRNA45
III	gt csa	exon	1104113	1104223	0.973	+	.	Parent=mRNA45
###
III	gt csa	gene	1105166	1108112	.	+	.	ID=gene20
III	gt csa	mRNA	1105166	1108112	.	+	.	ID=mRNA46;Parent=gene20;Target=yk1464f04.5 1 530 +
III	gt csa	exon	1105166	1105213	1	+	.	Parent=mRNA46
III	gt cds	CDS	1105193	1105213	.	+	0	ID=CDS34;Parent=mRNA46
III	gt csa	exon	1105382	1105479	1	+	.	Parent=mRNA46
III	gt cds	CDS	1105382	1105479	.	+	0	ID=CDS34;Parent=mRNA46
III	gt csa	exon	1106989	1107077	1	+	.	Parent=mRNA46
III	gt cds	CDS	1106989	1107077	.	+	1	ID=CDS34;Parent=mRNA46
III	gt csa	exon	1107132	1107310	1	+	.	Parent=mRNA46
III	gt cds	CDS	1107132	1107310	.	+	2	ID=CDS34;Parent=mRNA46
III	gt cds	CDS	1107997	1108110	.	+	0	ID=CDS34;Parent=mRNA46
III	gt csa	exon	1107997	1108112	1	+	.	Parent=mRNA46
###
III	gt csa	gene	1108452	1111917	.	+	.	ID=gene21
III	gt csa	mRNA	1108452	1110379	.	+	.	ID=mRNA47;Parent=gene21;Target=yk387g5.5 1 374 +,yk73h4.5 1 360 +
III	gt csa	exon	1108452	1108493	0.976	+	.	Parent=mRNA47
III	gt csa	exon	1109102	1109194	1	+	.	Parent=mRNA47
III	gt cds	CDS	1109133	1109194	.	+	0	ID=CDS35;Parent=mRNA47
III	gt csa	exon	1109306	1109456	1	+	.	Parent=mRNA47
III	gt cds	CDS	1109306	1109456	.	+	1	ID=CDS35;Parent=mRNA47
III	gt cds	CDS	1110211	1110378	.	+	0	ID=CDS35;Parent=mRNA47
III	gt csa	exon	1110211	1110379	0.95	+	.	Parent=mRNA47
III	gt csa	mRNA	1110444	1111917	.	+	.	ID=mRNA48;Parent=gene21;Target=yk654h1.5 1 379 +,yk1464f04.3 1 511 -,yk654h1.3 1 300 -,yk73h4.3 1 339 -
III	gt csa	exon	1110444	1110660	1	+	.	Parent=mRNA48
III	gt cds	CDS	1110607	1110660	.	+	0	ID=CDS36;Parent=mRNA48
III	gt cds	CDS	1111612	1111830	.	+	0	ID=CDS36;Parent=mRNA48
III	gt csa	exon	1111612	1111917	0.997	+	.	Parent=mRNA48
###
III	gt csa	gene	1113142	1113501	.	+	.	ID=gene22
III	gt csa	mRNA	1113142	1113501	.	+	.	ID=mRNA49;Parent=gene22;Target=yk540h4.5 1 360 +
III	gt cds	CDS	1113142	1113336	.	+	0	ID=CDS37;Parent=mRNA49
III	gt csa	exon	1113142	1113501	0.962	+	.	Parent=mRNA49
###
III	gt csa	gene	1116479	1145189	.	+	.	ID=gene23
III	gt csa	mRNA	1116479	1142875	.	+	.	ID=mRNA50;Parent=gene23;Target=yk476e8.5 1 375 +,yk413d2.5 1 378 +,yk115h9.5 1 360 +,AB071420 1 1206 +,CEESU89F 1 378 +,yk476e8.3 1 300 -,yk115h9.3 1 316 -
III	gt csa	exon	1116479	1116537	1	+	.	Parent=mRNA50
III	gt cds	CDS	1116513	1116537	.	+	0	ID=CDS38;Parent=mRNA50
III	gt csa	exon	1116980	1117047	1	+	.	Parent=mRNA50
III	gt cds	CDS	1116980	1117047	.	+	2	ID=CDS38;Parent=mRNA50
III	gt csa	exon	1117143	1117225	1	+	.	Parent=mRNA50
III	gt cds	CDS	1117143	1117225	.	+	0	ID=CDS38;Parent=mRNA50
III	gt csa	exon	1117275	1117383	1	+	.	Parent=mRNA50
III	gt cds	CDS	1117275	1117383	.	+	1	ID=CDS38;Parent=mRNA50
III	gt csa	exon	1122635	1122766	1	+	.	Parent=mRNA50
III	gt cds	CDS	1122635	1122766	.	+	0	ID=CDS38;Parent=mRNA50
III	gt csa	exon	1139058	1139117	1	+	.	Parent=mRNA50
III	gt cds	CDS	1139058	1139117	.	+	0	ID=CDS38;Parent=mRNA50
III	gt csa	exon	1139983	1140084	1	+	.	Parent=mRNA50
III	gt cds	CDS	1139983	1140084	.	+	0	ID=CDS38;Parent=mRNA50
III	gt csa	exon	1140353	1140439	1	+	.	Parent=mRNA50
III	gt cds	CDS	1140353	1140439	.	+	0	ID=CDS38;Parent=mRNA50
III	gt csa	exon	1141806	1142171	1	+	.	Parent=mRNA50
III	gt cds	CDS	1141806	1142171	.	+	0	ID=CDS38;Parent=mRNA50
III	gt cds	CDS	1142665	1142838	.	+	0	ID=CDS38;Parent=mRNA50
III	gt csa	exon	1142665	1142875	0.981	+	.	Parent=mRNA50
III	gt csa	mRNA	1116738	1142838	.	+	.	ID=mRNA51;Parent=gene23;Target=BP 1 356 +,CEESU89F 1 378 +
III	gt csa	exon	1116738	1116762	0.381	+	.	Parent=mRNA51
III	gt csa	exon	1116980	1117047	0.868	+	.	Parent=mRNA51
III	gt csa	exon	1117143	1117225	1	+	.	Parent=mRNA51
III	gt cds	CDS	1117200	1117225	.	+	0	ID=CDS39;Parent=mRNA51
III	gt csa	exon	1117275	1117383	1	+	.	Parent=mRNA51
III	gt cds	CDS	1117275	1117383	.	+	1	ID=CDS39;Parent=mRNA51
III	gt csa	exon	1122635	1122766	0.914	+	.	Parent=mRNA51
III	gt cds	CDS	1122635	1122766	.	+	0	ID=CDS39;Parent=mRNA51
III	gt csa	exon	1139983	1140084	0.767	+	.	Parent=mRNA51
III	gt cds	CDS	1139983	1140084	.	+	0	ID=CDS39;Parent=mRNA51
III	gt csa	exon	1141806	1142171	0.882	+	.	Parent=mRNA51
III	gt cds	CDS	1141806	1142171	.	+	0	ID=CDS39;Parent=mRNA51
III	gt csa	exon	1142656	1142838	0.85	+	.	Parent=mRNA51
III	gt cds	CDS	1142656	1142838	.	+	0	ID=CDS39;Parent=mRNA51
III	gt csa	mRNA	1125293	1125473	.	+	.	ID=mRNA52;Parent=gene23;Target=yk553h3.3 1 180 +
III	gt csa	exon	1125293	1125473	0.95	+	.	Parent=mRNA52
III	gt csa	mRNA	1133548	1142889	.	+	.	ID=mRNA53;Parent=gene23;Target=yk1661g06.3 1 722 -,yk476e8.3 1 300 -,yk115h9.3 1 316 -
III	gt csa	exon	1133548	1133558	0.727	+	.	Parent=mRNA53
III	gt csa	exon	1135590	1135608	0.737	+	.	Parent=mRNA53
III	gt csa	exon	1139983	1140084	1	+	.	Parent=mRNA53
III	gt cds	CDS	1140004	1140084	.	+	0	ID=CDS40;Parent=mRNA53
III	gt csa	exon	1141806	1142171	1	+	.	Parent=mRNA53
III	gt cds	CDS	1141806	1142171	.	+	0	ID=CDS40;Parent=mRNA53
III	gt cds	CDS	1142665	1142838	.	+	0	ID=CDS40;Parent=mRNA53
III	gt csa	exon	1142665	1142889	0.991	+	.	Parent=mRNA53
III	gt csa	mRNA	1143062	1145189	.	+	.	ID=mRNA54;Parent=gene23;Target=yk343a3.5 1 372 +,yk187d1.5 1 120 +,yk123d7.5 1 360 +,yk438f8.5 1 383 +,yk1158b07.3 1 574 -,yk550b4.5 1 360 +,yk543h10.5 11 360 +
III	gt csa	exon	1143062	1143459	1	+	.	Parent=mRNA54
III	gt csa	exon	1143525	1143621	1	+	.	Parent=mRNA54
III	gt csa	exon	1143690	1143814	1	+	.	Parent=mRNA54
III	gt csa	exon	1144839	1145189	0.997	+	.	Parent=mRNA54
III	gt cds	CDS	1144841	1145098	.	+	0	ID=CDS41;Parent=mRNA54
III	gt csa	mRNA	1143154	1145132	.	+	.	ID=mRNA55;Parent=gene23;Target=yk60d1.5 1 360 +,yk142e6.5 1 373 +,yk657a9.5 2 379 +,yk103e11.5 1 330 +,yk604a1.5 1 360 +,yk470d12.5 1 360 +,yk647g1.5 1 360 +,RP 1 235 +,yk187d1.5 1 120 +,yk312d12.5 1 360 +,yk561h2.5 1 360 +,yk473b11.5 1 360 +,yk328f10.5 1 360 +,yk123d7.5 1 360 +,yk438f8.5 1 383 +
III	gt csa	exon	1143154	1143303	0.993	+	.	Parent=mRNA55
III	gt cds	CDS	1143178	1143303	.	+	0	ID=CDS42;Parent=mRNA55
III	gt csa	exon	1143382	1143459	1	+	.	Parent=mRNA55
III	gt cds	CDS	1143382	1143459	.	+	0	ID=CDS42;Parent=mRNA55
III	gt csa	exon	1143525	1143621	1	+	.	Parent=mRNA55
III	gt cds	CDS	1143525	1143621	.	+	0	ID=CDS42;Parent=mRNA55
III	gt csa	exon	1143690	1143814	1	+	.	Parent=mRNA55
III	gt cds	CDS	1143690	1143814	.	+	2	ID=CDS42;Parent=mRNA55
III	gt csa	exon	1144839	1145034	0.95	+	.	Parent=mRNA55
III	gt cds	CDS	1144839	1145034	.	+	0	ID=CDS42;Parent=mRNA55
III	gt csa	exon	1145050	1145132	0.868	+	.	Parent=mRNA55
III	gt cds	CDS	1145050	1145132	.	+	2	ID=CDS42;Parent=mRNA55
III	gt csa	mRNA	1143154	1145189	.	+	.	ID=mRNA56;Parent=gene23;Target=yk60d1.5 1 360 +,yk142e6.5 1 373 +,yk657a9.5 2 379 +,yk103e11.5 1 330 +,yk604a1.5 1 360 +,yk470d12.5 1 360 +,yk647g1.5 1 360 +,BP 1 234 +,yk187d1.5 1 120 +,yk312d12.5 1 360 +,yk561h2.5 1 360 +,yk473b11.5 1 360 +,yk328f10.5 1 360 +,yk123d7.5 1 360 +,yk438f8.5 1 383 +,yk1158b07.3 1 574 -,yk550b4.5 1 360 +,yk543h10.5 11 360 +
III	gt csa	exon	1143154	1143303	0.993	+	.	Parent=mRNA56
III	gt cds	CDS	1143178	1143303	.	+	0	ID=CDS43;Parent=mRNA56
III	gt csa	exon	1143382	1143459	1	+	.	Parent=mRNA56
III	gt cds	CDS	1143382	1143459	.	+	0	ID=CDS43;Parent=mRNA56
III	gt csa	exon	1143525	1143621	1	+	.	Parent=mRNA56
III	gt cds	CDS	1143525	1143621	.	+	0	ID=CDS43;Parent=mRNA56
III	gt csa	exon	1143690	1143814	1	+	.	Parent=mRNA56
III	gt cds	CDS	1143690	1143814	.	+	2	ID=CDS43;Parent=mRNA56
III	gt cds	CDS	1144839	1145132	.	+	0	ID=CDS43;Parent=mRNA56
III	gt csa	exon	1144839	1145189	0.997	+	.	Parent=mRNA56
###
III	gt csa	gene	1125231	1145193	.	-	.	ID=gene24
III	gt csa	mRNA	1125231	1135544	.	-	.	ID=mRNA57;Parent=gene24;Target=yk1034b01.3 1 771 -,yk1181b08.3 1 560 -,yk863a05.3 1 746 -,BP 1 507 +,RP 1 507 +,WP 1 509 +,yk553h3.5 1 360 +
III	gt csa	exon	1125231	1125670	0.981	-	.	Parent=mRNA57
III	gt cds	CDS	1125553	1125670	.	-	1	ID=CDS44;Parent=mRNA57
III	gt csa	exon	1125798	1125884	1	-	.	Parent=mRNA57
III	gt cds	CDS	1125798	1125884	.	-	1	ID=CDS44;Parent=mRNA57
III	gt csa	exon	1126918	1127243	1	-	.	Parent=mRNA57
III	gt cds	CDS	1126918	1127243	.	-	0	ID=CDS44;Parent=mRNA57
III	gt csa	exon	1127709	1127839	1	-	.	Parent=mRNA57
III	gt cds	CDS	1127709	1127839	.	-	2	ID=CDS44;Parent=mRNA57
III	gt csa	exon	1128867	1128978	1	-	.	Parent=mRNA57
III	gt cds	CDS	1128867	1128978	.	-	0	ID=CDS44;Parent=mRNA57
III	gt csa	exon	1129237	1129354	1	-	.	Parent=mRNA57
III	gt cds	CDS	1129237	1129354	.	-	1	ID=CDS44;Parent=mRNA57
III	gt csa	exon	1129814	1129916	1	-	.	Parent=mRNA57
III	gt cds	CDS	1129814	1129916	.	-	2	ID=CDS44;Parent=mRNA57
III	gt csa	exon	1134086	1134290	1	-	.	Parent=mRNA57
III	gt cds	CDS	1134086	1134290	.	-	0	ID=CDS44;Parent=mRNA57
III	gt csa	exon	1134380	1134448	1	-	.	Parent=mRNA57
III	gt cds	CDS	1134380	1134448	.	-	0	ID=CDS44;Parent=mRNA57
III	gt cds	CDS	1135196	1135234	.	-	0	ID=CDS44;Parent=mRNA57
III	gt csa	exon	1135196	1135288	1	-	.	Parent=mRNA57
III	gt csa	exon	1135380	1135544	0.687	-	.	Parent=mRNA57
III	gt csa	mRNA	1129245	1136013	.	-	.	ID=mRNA58;Parent=gene24;Target=yk553h3.5 1 360 +,yk1034b01.5 24 613 +,yk863a05.5 17 604 +
III	gt csa	exon	1129245	1129354	0.991	-	.	Parent=mRNA58
III	gt cds	CDS	1129246	1129354	.	-	1	ID=CDS45;Parent=mRNA58
III	gt csa	exon	1129814	1129916	1	-	.	Parent=mRNA58
III	gt cds	CDS	1129814	1129916	.	-	2	ID=CDS45;Parent=mRNA58
III	gt csa	exon	1134086	1134290	1	-	.	Parent=mRNA58
III	gt cds	CDS	1134086	1134290	.	-	0	ID=CDS45;Parent=mRNA58
III	gt csa	exon	1134380	1134448	1	-	.	Parent=mRNA58
III	gt cds	CDS	1134380	1134448	.	-	0	ID=CDS45;Parent=mRNA58
III	gt csa	exon	1135196	1135288	1	-	.	Parent=mRNA58
III	gt cds	CDS	1135196	1135288	.	-	0	ID=CDS45;Parent=mRNA58
III	gt csa	exon	1135380	1135488	1	-	.	Parent=mRNA58
III	gt cds	CDS	1135380	1135488	.	-	1	ID=CDS45;Parent=mRNA58
III	gt cds	CDS	1135900	1135955	.	-	0	ID=CDS45;Parent=mRNA58
III	gt csa	exon	1135900	1136013	1	-	.	Parent=mRNA58
III	gt csa	mRNA	1144830	1145193	.	-	.	ID=mRNA59;Parent=gene24;Target=yk470d12.3 1 300 +,yk604a1.3 1 300 +,yk473b11.3 1 300 +,yk312d12.3 1 300 +,yk343a3.3 1 300 +,yk530f6.3 1 300 +,yk438f8.3 1 285 +,yk561h2.3 1 292 +,yk543h10.3 1 300 +,yk647g1.3 1 300 +,yk142e6.3 1 300 +,yk60d1.3 1 343 +,yk103e11.3 1 334 +,yk123d7.3 1 180 +
III	gt csa	exon	1144830	1145193	0.971	-	.	Parent=mRNA59
###
III	gt csa	gene	1172435	1172612	.	+	.	ID=gene25
III	gt csa	mRNA	1172435	1172612	.	+	.	ID=mRNA60;Parent=gene25;Target=yk511h7.5 1 180 +
III	gt csa	exon	1172435	1172612	0.933	+	.	Parent=mRNA60
###
III	gt csa	gene	1180689	1181054	.	+	.	ID=gene26
III	gt csa	mRNA	1180689	1181054	.	+	.	ID=mRNA61;Parent=gene26;Target=yk511h7.3 1 300 -
III	gt csa	exon	1180689	1180787	0.929	+	.	Parent=mRNA61
III	gt csa	exon	1180855	1181054	0.942	+	.	Parent=mRNA61
###
III	gt csa	gene	1182067	1184916	.	+	.	ID=gene27
III	gt csa	mRNA	1182067	1184916	.	+	.	ID=mRNA62;Parent=gene27;Target=yk94h5.5 1 248 +,yk101e7.5 1 360 +,yk409f1.5 1 377 +,yk362f12.5 1 380 +,yk308d11.5 1 360 +,yk191a10.5 1 360 +,yk409a1.5 1 360 +,yk263d8.5 1 360 +,yk440h2.5 1 360 +,yk440h2.3 1 300 -,yk545f3.5 1 360 -,yk191a10.3 1 300 -,yk362f12.3 1 300 -,yk190e9.3 1 300 -,yk409f1.3 1 300 -,yk308d11.3 1 300 -,yk409a1.3 1 300 -
III	gt csa	exon	1182067	1182083	1	+	.	Parent=mRNA62
III	gt csa	exon	1182151	1182302	1	+	.	Parent=mRNA62
III	gt csa	exon	1183141	1183324	1	+	.	Parent=mRNA62
III	gt cds	CDS	1183219	1183324	.	+	0	ID=CDS46;Parent=mRNA62
III	gt csa	exon	1183376	1183473	0.974	+	.	Parent=mRNA62
III	gt cds	CDS	1183376	1183473	.	+	2	ID=CDS46;Parent=mRNA62
III	gt cds	CDS	1184629	1184883	.	+	0	ID=CDS46;Parent=mRNA62
III	gt csa	exon	1184629	1184916	0.993	+	.	Parent=mRNA62
###
III	gt csa	gene	1184691	1184913	.	-	.	ID=gene28
III	gt csa	mRNA	1184691	1184913	.	-	.	ID=mRNA63;Parent=gene28;Target=yk388g7.3 1 176 +,yk94h5.3 1 180 +
III	gt csa	exon	1184691	1184913	0.944	-	.	Parent=mRNA63
###
III	gt csa	gene	1185272	1189478	.	-	.	ID=gene29
III	gt csa	mRNA	1185272	1189478	.	-	.	ID=mRNA64;Parent=gene29;Target=yk1481a08.3 1 678 -,yk1392d03.3 1 601 -
III	gt csa	exon	1185272	1185683	0.998	-	.	Parent=mRNA64
III	gt cds	CDS	1185331	1185683	.	-	2	ID=CDS47;Parent=mRNA64
III	gt csa	exon	1187296	1187356	0.984	-	.	Parent=mRNA64
III	gt cds	CDS	1187296	1187356	.	-	0	ID=CDS47;Parent=mRNA64
III	gt csa	exon	1187434	1187550	0.991	-	.	Parent=mRNA64
III	gt cds	CDS	1187434	1187550	.	-	0	ID=CDS47;Parent=mRNA64
III	gt csa	exon	1187601	1187741	0.992	-	.	Parent=mRNA64
III	gt cds	CDS	1187601	1187741	.	-	0	ID=CDS47;Parent=mRNA64
III	gt cds	CDS	1189002	1189469	.	-	0	ID=CDS47;Parent=mRNA64
III	gt csa	exon	1189002	1189478	1	-	.	Parent=mRNA64
###
III	gt csa	gene	1191338	1193802	.	-	.	ID=gene30
III	gt csa	mRNA	1191338	1193802	.	-	.	ID=mRNA65;Parent=gene30;Target=yk1392d03.5 23 588 +,yk1481a08.5 23 461 +
III	gt csa	exon	1191338	1191568	0.996	-	.	Parent=mRNA65
III	gt cds	CDS	1191339	1191568	.	-	2	ID=CDS48;Parent=mRNA65
III	gt csa	exon	1191631	1191720	1	-	.	Parent=mRNA65
III	gt cds	CDS	1191631	1191720	.	-	2	ID=CDS48;Parent=mRNA65
III	gt cds	CDS	1193558	1193780	.	-	0	ID=CDS48;Parent=mRNA65
III	gt csa	exon	1193558	1193802	1	-	.	Parent=mRNA65
###
III	gt csa	gene	1194399	1196282	.	-	.	ID=gene31
III	gt csa	mRNA	1194399	1196282	.	-	.	ID=mRNA66;Parent=gene31;Target=CB103439 99 622 +,CB103483 90 610 +,CB103504 61 572 +,yk1752b03.3 242 747 -,CB103472 81 584 +,yk1160g10.3 24 520 -,yk1160g10.5 24 516 +,CB103430 73 559 +,CK583320 1 435 +,yk368b4.5 1 374 +,CB103451 106 494 +,yk115f10.5 12 360 +
III	gt csa	exon	1194399	1194795	1	-	.	Parent=mRNA66
III	gt cds	CDS	1194658	1194795	.	-	0	ID=CDS49;Parent=mRNA66
III	gt cds	CDS	1196156	1196266	.	-	0	ID=CDS49;Parent=mRNA66
III	gt csa	exon	1196156	1196282	1	-	.	Parent=mRNA66
###
III	gt csa	gene	1194424	1194755	.	+	.	ID=gene32
III	gt csa	mRNA	1194424	1194755	.	+	.	ID=mRNA67;Parent=gene32;Target=yk115f10.3 1 332 +
III	gt csa	exon	1194424	1194755	0.997	+	.	Parent=mRNA67
III	gt cds	CDS	1194550	1194753	.	+	0	ID=CDS50;Parent=mRNA67
###
III	gt csa	gene	1200240	1201998	.	-	.	ID=gene33
III	gt csa	mRNA	1200240	1201998	.	-	.	ID=mRNA68;Parent=gene33;Target=yk1488e08.5 23 608 +
III	gt csa	exon	1200240	1200461	0.995	-	.	Parent=mRNA68
III	gt cds	CDS	1200241	1200461	.	-	2	ID=CDS51;Parent=mRNA68
III	gt csa	exon	1201465	1201639	1	-	.	Parent=mRNA68
III	gt cds	CDS	1201465	1201639	.	-	0	ID=CDS51;Parent=mRNA68
III	gt cds	CDS	1201810	1201989	.	-	0	ID=CDS51;Parent=mRNA68
III	gt csa	exon	1201810	1201998	0.995	-	.	Parent=mRNA68
###
III	gt csa	gene	1202535	1207288	.	+	.	ID=gene34
III	gt csa	mRNA	1202535	1207255	.	+	.	ID=mRNA69;Parent=gene34;Target=yk531a4.5 1 376 +,yk1387f11.5 23 512 +,WP 1 337 +,yk172c10.5 1 377 +,yk342c4.5 1 373 +,yk550b8.5 1 360 +,yk409b7.5 1 376 +,yk342c4.3 1 300 -,yk409b7.3 1 300 -,yk172c10.3 1 300 -
III	gt csa	exon	1202535	1202609	0.987	+	.	Parent=mRNA69
III	gt cds	CDS	1202541	1202609	.	+	0	ID=CDS52;Parent=mRNA69
III	gt csa	exon	1202655	1202765	1	+	.	Parent=mRNA69
III	gt cds	CDS	1202655	1202765	.	+	0	ID=CDS52;Parent=mRNA69
III	gt csa	exon	1202829	1203135	1	+	.	Parent=mRNA69
III	gt cds	CDS	1202829	1203135	.	+	0	ID=CDS52;Parent=mRNA69
III	gt csa	exon	1203589	1203699	1	+	.	Parent=mRNA69
III	gt cds	CDS	1203589	1203699	.	+	2	ID=CDS52;Parent=mRNA69
III	gt csa	exon	1205327	1205739	1	+	.	Parent=mRNA69
III	gt cds	CDS	1205327	1205739	.	+	2	ID=CDS52;Parent=mRNA69
III	gt cds	CDS	1206843	1206851	.	+	0	ID=CDS52;Parent=mRNA69
III	gt csa	exon	1206843	1206957	1	+	.	Parent=mRNA69
III	gt csa	exon	1207184	1207255	0.972	+	.	Parent=mRNA69
III	gt csa	mRNA	1202535	1207260	.	+	.	ID=mRNA70;Parent=gene34;Target=yk531a4.5 1 376 +,yk1387f11.5 23 512 +,WP 1 337 +,yk172c10.5 1 377 +,yk342c4.5 1 373 +,yk550b8.5 1 360 +,yk550b8.3 1 300 -
III	gt csa	exon	1202535	1202609	0.987	+	.	Parent=mRNA70
III	gt cds	CDS	1202541	1202609	.	+	0	ID=CDS53;Parent=mRNA70
III	gt csa	exon	1202655	1202765	1	+	.	Parent=mRNA70
III	gt cds	CDS	1202655	1202765	.	+	0	ID=CDS53;Parent=mRNA70
III	gt csa	exon	1202829	1203135	1	+	.	Parent=mRNA70
III	gt cds	CDS	1202829	1203135	.	+	0	ID=CDS53;Parent=mRNA70
III	gt csa	exon	1203589	1203699	1	+	.	Parent=mRNA70
III	gt cds	CDS	1203589	1203699	.	+	2	ID=CDS53;Parent=mRNA70
III	gt csa	exon	1205327	1205739	1	+	.	Parent=mRNA70
III	gt cds	CDS	1205327	1205739	.	+	2	ID=CDS53;Parent=mRNA70
III	gt cds	CDS	1206843	1206851	.	+	0	ID=CDS53;Parent=mRNA70
III	gt csa	exon	1206843	1206932	0.878	+	.	Parent=mRNA70
III	gt csa	exon	1207184	1207260	0.961	+	.	Parent=mRNA70
III	gt csa	mRNA	1202535	1207288	.	+	.	ID=mRNA71;Parent=gene34;Target=yk531a4.5 1 376 +,yk1387f11.5 23 512 +,WP 1 337 +,yk172c10.5 1 377 +,yk342c4.5 1 373 +,yk550b8.5 1 360 +,yk409b7.5 1 376 +,yk1387f11.3 1 649 -
III	gt csa	exon	1202535	1202609	0.987	+	.	Parent=mRNA71
III	gt cds	CDS	1202541	1202609	.	+	0	ID=CDS54;Parent=mRNA71
III	gt csa	exon	1202655	1202765	1	+	.	Parent=mRNA71
III	gt cds	CDS	1202655	1202765	.	+	0	ID=CDS54;Parent=mRNA71
III	gt csa	exon	1202829	1203135	1	+	.	Parent=mRNA71
III	gt cds	CDS	1202829	1203135	.	+	0	ID=CDS54;Parent=mRNA71
III	gt csa	exon	1203589	1203699	1	+	.	Parent=mRNA71
III	gt cds	CDS	1203589	1203699	.	+	2	ID=CDS54;Parent=mRNA71
III	gt csa	exon	1205327	1205739	1	+	.	Parent=mRNA71
III	gt cds	CDS	1205327	1205739	.	+	2	ID=CDS54;Parent=mRNA71
III	gt cds	CDS	1206843	1206851	.	+	0	ID=CDS54;Parent=mRNA71
III	gt csa	exon	1206843	1207288	1	+	.	Parent=mRNA71
III	gt csa	mRNA	1203589	1207248	.	+	.	ID=mRNA72;Parent=gene34;Target=yk531a4.3 10 300 -
III	gt csa	exon	1203589	1203699	1	+	.	Parent=mRNA72
III	gt csa	exon	1206843	1206957	0.983	+	.	Parent=mRNA72
III	gt csa	exon	1207184	1207248	0.969	+	.	Parent=mRNA72
###
III	gt csa	gene	1208120	1209321	.	+	.	ID=gene35
III	gt csa	mRNA	1208120	1209321	.	+	.	ID=mRNA73;Parent=gene35;Target=yk681h11.5 1 360 +,yk1103g05.5 41 657 +,cm13d11.5 1 287 +,yk660b11.5 1 378 +,yk669g11.5 1 360 +,yk210b6.5 1 376 +,yk608g3.5 1 360 +,yk506a7.5 1 360 +
III	gt csa	exon	1208120	1208251	1	+	.	Parent=mRNA73
III	gt cds	CDS	1208130	1208251	.	+	0	ID=CDS55;Parent=mRNA73
III	gt csa	exon	1208372	1208714	0.997	+	.	Parent=mRNA73
III	gt cds	CDS	1208372	1208714	.	+	1	ID=CDS55;Parent=mRNA73
III	gt cds	CDS	1209177	1209320	.	+	0	ID=CDS55;Parent=mRNA73
III	gt csa	exon	1209177	1209321	1	+	.	Parent=mRNA73
###
III	gt csa	gene	1211225	1213642	.	+	.	ID=gene36
III	gt csa	mRNA	1211225	1213642	.	+	.	ID=mRNA74;Parent=gene36;Target=yk93h2.5 1 265 +,yk1535b11.3 1 614 -,CEEST24F 1 422 -,yk669g11.3 1 300 -,yk506a7.3 1 300 -,yk210b6.3 1 300 -,yk660b11.3 1 300 -,yk681h11.3 1 300 -,yk1624b11.3 1 340 -,yk93h2.3 1 331 -,CEESE53F 1 342 -
III	gt csa	exon	1211225	1211488	0.964	+	.	Parent=mRNA74
III	gt cds	CDS	1211387	1211488	.	+	0	ID=CDS56;Parent=mRNA74
III	gt csa	exon	1212576	1212824	0.992	+	.	Parent=mRNA74
III	gt cds	CDS	1212576	1212824	.	+	0	ID=CDS56;Parent=mRNA74
III	gt cds	CDS	1213437	1213589	.	+	0	ID=CDS56;Parent=mRNA74
III	gt csa	exon	1213437	1213642	0.981	+	.	Parent=mRNA74
###
III	gt csa	gene	1214935	1215287	.	+	.	ID=gene37
III	gt csa	mRNA	1214935	1215287	.	+	.	ID=mRNA75;Parent=gene37;Target=yk726c5.5 1 340 +,yk843g10.5 1 341 +,yk726h9.5 1 330 +,yk1454b03.5 1 335 +,yk1693g03.5 1 335 +,yk1613b06.5 1 335 +,yk1376c06.5 1 345 +,yk1619d03.5 1 345 +,yk1657e01.5 1 343 +,yk151f9.5 1 240 +,yk70e6.5 1 317 +,yk309g3.5 1 308 +,yk367e7.5 1 311 +,yk275e11.5 1 298 +,yk383a12.5 1 290 +,yk1313b02.5 1 156 +
III	gt csa	exon	1214935	1215287	0.977	+	.	Parent=mRNA75
III	gt cds	CDS	1214990	1215190	.	+	0	ID=CDS57;Parent=mRNA75
###
III	gt csa	gene	1214942	1215266	.	-	.	ID=gene38
III	gt csa	mRNA	1214942	1215266	.	-	.	ID=mRNA76;Parent=gene38;Target=yk726c5.3 1 267 +,yk726h9.3 1 270 +,yk734c7.3 1 275 +,yk1613b06.3 1 309 +,yk1641g01.3 1 312 +,yk1693g03.3 1 323 +,yk275e11.3 1 278 +,yk367e7.3 1 249 +,yk383a12.3 1 248 +,yk151f9.3 1 240 +,yk70e6.3 1 299 +,yk309g3.3 1 245 +
III	gt csa	exon	1214942	1215266	0.957	-	.	Parent=mRNA76
###
III	gt csa	gene	1216021	1216795	.	+	.	ID=gene39
III	gt csa	mRNA	1216021	1216795	.	+	.	ID=mRNA77;Parent=gene39;Target=yk808h01.3 1 641 +,yk831f01.3 1 241 +,yk1315b01.3 1 501 +,yk754f09.3 1 350 +,yk781a01.3 1 267 +,yk1358a10.3 1 302 +,yk413h8.5 1 120 +
III	gt csa	exon	1216021	1216795	0.881	+	.	Parent=mRNA77
###
III	gt csa	gene	1216578	1216806	.	-	.	ID=gene40
III	gt csa	mRNA	1216578	1216806	.	-	.	ID=mRNA78;Parent=gene40;Target=yk264h7.5 12 240 +
III	gt csa	exon	1216578	1216806	0.983	-	.	Parent=mRNA78
###
III	gt csa	gene	1220307	1222062	.	-	.	ID=gene41
III	gt csa	mRNA	1220307	1222062	.	-	.	ID=mRNA79;Parent=gene41;Target=yk1221d02.5 22 628 +,yk754f09.5 23 562 +,yk1358a10.5 23 547 +,yk808h01.5 26 550 +,yk781a01.5 23 546 +,yk236b4.5 1 360 +,yk629h11.5 1 356 +,yk831f01.5 23 175 +
III	gt csa	exon	1220307	1220373	1	-	.	Parent=mRNA79
III	gt cds	CDS	1220308	1220373	.	-	0	ID=CDS58;Parent=mRNA79
III	gt csa	exon	1221160	1221571	1	-	.	Parent=mRNA79
III	gt cds	CDS	1221160	1221571	.	-	1	ID=CDS58;Parent=mRNA79
III	gt csa	exon	1221935	1222062	1	-	.	Parent=mRNA79
III	gt cds	CDS	1221935	1222062	.	-	0	ID=CDS58;Parent=mRNA79
###
III	gt csa	gene	1225449	1225807	.	+	.	ID=gene42
III	gt csa	mRNA	1225449	1225807	.	+	.	ID=mRNA80;Parent=gene42;Target=yk549c5.5 1 360 +
III	gt csa	exon	1225449	1225807	0.976	+	.	Parent=mRNA80
###
III	gt csa	gene	1225754	1226053	.	-	.	ID=gene43
III	gt csa	mRNA	1225754	1226053	.	-	.	ID=mRNA81;Parent=gene43;Target=yk549c5.3 1 300 +
III	gt csa	exon	1225754	1226053	1	-	.	Parent=mRNA81
###
III	gt csa	gene	1236005	1237038	.	+	.	ID=gene44
III	gt csa	mRNA	1236005	1237038	.	+	.	ID=mRNA82;Parent=gene44;Target=WP 1 254 +
III	gt csa	exon	1236005	1236093	1	+	.	Parent=mRNA82
III	gt cds	CDS	1236005	1236093	.	+	0	ID=CDS59;Parent=mRNA82
III	gt csa	exon	1236319	1236772	1	+	.	Parent=mRNA82
III	gt cds	CDS	1236319	1236772	.	+	1	ID=CDS59;Parent=mRNA82
III	gt csa	exon	1236820	1237038	1	+	.	Parent=mRNA82
III	gt cds	CDS	1236820	1237038	.	+	0	ID=CDS59;Parent=mRNA82
###
III	gt csa	gene	1239313	1242728	.	+	.	ID=gene45
III	gt csa	mRNA	1239313	1242728	.	+	.	ID=mRNA83;Parent=gene45;Target=WP 1 307 +
III	gt csa	exon	1239313	1239401	1	+	.	Parent=mRNA83
III	gt cds	CDS	1239313	1239401	.	+	0	ID=CDS60;Parent=mRNA83
III	gt csa	exon	1241115	1241739	1	+	.	Parent=mRNA83
III	gt cds	CDS	1241115	1241739	.	+	1	ID=CDS60;Parent=mRNA83
III	gt csa	exon	1242522	1242728	1	+	.	Parent=mRNA83
III	gt cds	CDS	1242522	1242728	.	+	0	ID=CDS60;Parent=mRNA83
###
III	gt csa	gene	1243521	1245273	.	+	.	ID=gene46
III	gt csa	mRNA	1243521	1245273	.	+	.	ID=mRNA84;Parent=gene46;Target=WP 1 306 +
III	gt csa	exon	1243521	1243636	1	+	.	Parent=mRNA84
III	gt cds	CDS	1243521	1243636	.	+	0	ID=CDS61;Parent=mRNA84
III	gt csa	exon	1244420	1245014	1	+	.	Parent=mRNA84
III	gt cds	CDS	1244420	1245014	.	+	1	ID=CDS61;Parent=mRNA84
III	gt csa	exon	1245067	1245273	1	+	.	Parent=mRNA84
III	gt cds	CDS	1245067	1245273	.	+	0	ID=CDS61;Parent=mRNA84
###
III	gt csa	gene	1247626	1249143	.	-	.	ID=gene47
III	gt csa	mRNA	1247626	1249143	.	-	.	ID=mRNA85;Parent=gene47;Target=WP 1 270 +
III	gt csa	exon	1247626	1247808	1	-	.	Parent=mRNA85
III	gt cds	CDS	1247626	1247808	.	-	0	ID=CDS62;Parent=mRNA85
III	gt csa	exon	1247862	1248417	1	-	.	Parent=mRNA85
III	gt cds	CDS	1247862	1248417	.	-	1	ID=CDS62;Parent=mRNA85
III	gt csa	exon	1249073	1249143	1	-	.	Parent=mRNA85
III	gt cds	CDS	1249073	1249143	.	-	0	ID=CDS62;Parent=mRNA85
###
III	gt csa	gene	1249509	1251814	.	+	.	ID=gene48
III	gt csa	mRNA	1249509	1251814	.	+	.	ID=mRNA86;Parent=gene48;Target=WP 1 265 +,yk252g1.5 1 376 +
III	gt csa	exon	1249509	1249579	1	+	.	Parent=mRNA86
III	gt cds	CDS	1249509	1249579	.	+	0	ID=CDS63;Parent=mRNA86
III	gt csa	exon	1250603	1251143	1	+	.	Parent=mRNA86
III	gt cds	CDS	1250603	1251143	.	+	1	ID=CDS63;Parent=mRNA86
III	gt csa	exon	1251632	1251814	1	+	.	Parent=mRNA86
III	gt cds	CDS	1251632	1251814	.	+	0	ID=CDS63;Parent=mRNA86
###
III	gt csa	gene	1253374	1254391	.	-	.	ID=gene49
III	gt csa	mRNA	1253374	1254391	.	-	.	ID=mRNA87;Parent=gene49;Target=WP 1 252 +
III	gt csa	exon	1253374	1253548	1	-	.	Parent=mRNA87
III	gt cds	CDS	1253374	1253548	.	-	1	ID=CDS64;Parent=mRNA87
III	gt csa	exon	1253764	1254273	1	-	.	Parent=mRNA87
III	gt cds	CDS	1253764	1254273	.	-	1	ID=CDS64;Parent=mRNA87
III	gt csa	exon	1254321	1254391	1	-	.	Parent=mRNA87
III	gt cds	CDS	1254321	1254391	.	-	0	ID=CDS64;Parent=mRNA87
###
III	gt csa	gene	1255541	1256919	.	+	.	ID=gene50
III	gt csa	mRNA	1255541	1256919	.	+	.	ID=mRNA88;Parent=gene50;Target=WP 1 282 +
III	gt csa	exon	1255541	1256020	1	+	.	Parent=mRNA88
III	gt cds	CDS	1255541	1256020	.	+	0	ID=CDS65;Parent=mRNA88
III	gt csa	exon	1256067	1256195	1	+	.	Parent=mRNA88
III	gt cds	CDS	1256067	1256195	.	+	0	ID=CDS65;Parent=mRNA88
III	gt csa	exon	1256630	1256677	1	+	.	Parent=mRNA88
III	gt cds	CDS	1256630	1256677	.	+	0	ID=CDS65;Parent=mRNA88
III	gt csa	exon	1256731	1256919	1	+	.	Parent=mRNA88
III	gt cds	CDS	1256731	1256919	.	+	0	ID=CDS65;Parent=mRNA88
###
III	gt csa	gene	1257203	1258404	.	-	.	ID=gene51
III	gt csa	mRNA	1257203	1258404	.	-	.	ID=mRNA89;Parent=gene51;Target=yk1419f09.3 1 775 -,WP 1 278 +
III	gt csa	exon	1257203	1257419	0.995	-	.	Parent=mRNA89
III	gt cds	CDS	1257222	1257419	.	-	0	ID=CDS66;Parent=mRNA89
III	gt csa	exon	1257724	1258291	1	-	.	Parent=mRNA89
III	gt cds	CDS	1257724	1258291	.	-	1	ID=CDS66;Parent=mRNA89
III	gt csa	exon	1258337	1258404	1	-	.	Parent=mRNA89
III	gt cds	CDS	1258337	1258404	.	-	0	ID=CDS66;Parent=mRNA89
###
III	gt csa	gene	1259414	1260174	.	+	.	ID=gene52
III	gt csa	mRNA	1259414	1260174	.	+	.	ID=mRNA90;Parent=gene52;Target=WP 1 91 +
III	gt csa	exon	1259414	1259503	1	+	.	Parent=mRNA90
III	gt cds	CDS	1259414	1259503	.	+	0	ID=CDS67;Parent=mRNA90
III	gt csa	exon	1259992	1260174	1	+	.	Parent=mRNA90
III	gt cds	CDS	1259992	1260174	.	+	0	ID=CDS67;Parent=mRNA90
###
III	gt csa	gene	1261815	1262832	.	-	.	ID=gene53
III	gt csa	mRNA	1261815	1262832	.	-	.	ID=mRNA91;Parent=gene53;Target=WP 1 252 +
III	gt csa	exon	1261815	1261989	1	-	.	Parent=mRNA91
III	gt cds	CDS	1261815	1261989	.	-	1	ID=CDS68;Parent=mRNA91
III	gt csa	exon	1262205	1262714	1	-	.	Parent=mRNA91
III	gt cds	CDS	1262205	1262714	.	-	1	ID=CDS68;Parent=mRNA91
III	gt csa	exon	1262762	1262832	1	-	.	Parent=mRNA91
III	gt cds	CDS	1262762	1262832	.	-	0	ID=CDS68;Parent=mRNA91
###
III	gt csa	gene	1265663	1266845	.	-	.	ID=gene54
III	gt csa	mRNA	1265663	1266845	.	-	.	ID=mRNA92;Parent=gene54;Target=WP 1 278 +
III	gt csa	exon	1265663	1265860	1	-	.	Parent=mRNA92
III	gt cds	CDS	1265663	1265860	.	-	0	ID=CDS69;Parent=mRNA92
III	gt csa	exon	1266165	1266732	1	-	.	Parent=mRNA92
III	gt cds	CDS	1266165	1266732	.	-	1	ID=CDS69;Parent=mRNA92
III	gt csa	exon	1266778	1266845	1	-	.	Parent=mRNA92
III	gt cds	CDS	1266778	1266845	.	-	0	ID=CDS69;Parent=mRNA92
###
III	gt csa	gene	1267393	1269234	.	-	.	ID=gene55
III	gt csa	mRNA	1267393	1269234	.	-	.	ID=mRNA93;Parent=gene55;Target=WP 1 306 +
III	gt csa	exon	1267393	1267608	1	-	.	Parent=mRNA93
III	gt cds	CDS	1267393	1267608	.	-	0	ID=CDS70;Parent=mRNA93
III	gt csa	exon	1268344	1268962	1	-	.	Parent=mRNA93
III	gt cds	CDS	1268344	1268962	.	-	1	ID=CDS70;Parent=mRNA93
III	gt csa	exon	1269152	1269234	1	-	.	Parent=mRNA93
III	gt cds	CDS	1269152	1269234	.	-	0	ID=CDS70;Parent=mRNA93
###
III	gt csa	gene	1269569	1271418	.	-	.	ID=gene56
III	gt csa	mRNA	1269569	1271418	.	-	.	ID=mRNA94;Parent=gene56;Target=yk1217b07.3 1 777 -,WP 1 307 +,yk1217b07.5 23 624 +
III	gt csa	exon	1269569	1269841	0.96	-	.	Parent=mRNA94
III	gt cds	CDS	1269620	1269841	.	-	0	ID=CDS71;Parent=mRNA94
III	gt csa	exon	1269904	1270519	1	-	.	Parent=mRNA94
III	gt cds	CDS	1269904	1270519	.	-	1	ID=CDS71;Parent=mRNA94
III	gt cds	CDS	1271293	1271375	.	-	0	ID=CDS71;Parent=mRNA94
III	gt csa	exon	1271293	1271418	1	-	.	Parent=mRNA94
###
III	gt csa	gene	1272534	1273666	.	-	.	ID=gene57
III	gt csa	mRNA	1272534	1273666	.	-	.	ID=mRNA95;Parent=gene57;Target=WP 1 305 +
III	gt csa	exon	1272534	1272749	1	-	.	Parent=mRNA95
III	gt cds	CDS	1272534	1272749	.	-	0	ID=CDS72;Parent=mRNA95
III	gt csa	exon	1272798	1273413	1	-	.	Parent=mRNA95
III	gt cds	CDS	1272798	1273413	.	-	1	ID=CDS72;Parent=mRNA95
III	gt csa	exon	1273584	1273666	1	-	.	Parent=mRNA95
III	gt cds	CDS	1273584	1273666	.	-	0	ID=CDS72;Parent=mRNA95
###
III	gt csa	gene	1274504	1275578	.	-	.	ID=gene58
III	gt csa	mRNA	1274504	1275578	.	-	.	ID=mRNA96;Parent=gene58;Target=WP 1 306 +
III	gt csa	exon	1274504	1274719	1	-	.	Parent=mRNA96
III	gt cds	CDS	1274504	1274719	.	-	0	ID=CDS73;Parent=mRNA96
III	gt csa	exon	1274773	1275391	1	-	.	Parent=mRNA96
III	gt cds	CDS	1274773	1275391	.	-	1	ID=CDS73;Parent=mRNA96
III	gt csa	exon	1275496	1275578	1	-	.	Parent=mRNA96
III	gt cds	CDS	1275496	1275578	.	-	0	ID=CDS73;Parent=mRNA96
###
III	gt csa	gene	1282418	1282768	.	-	.	ID=gene59
III	gt csa	mRNA	1282418	1282768	.	-	.	ID=mRNA97;Parent=gene59;Target=yk720c2.3 1 300 -
III	gt csa	exon	1282418	1282633	0.991	-	.	Parent=mRNA97
III	gt csa	exon	1282685	1282768	1	-	.	Parent=mRNA97
###
III	gt csa	gene	1283269	1288513	.	-	.	ID=gene60
III	gt csa	mRNA	1283269	1284322	.	-	.	ID=mRNA98;Parent=gene60;Target=yk720c2.5 105 341 +,yk729a8.5 114 340 +
III	gt csa	exon	1283269	1283321	0.981	-	.	Parent=mRNA98
III	gt csa	exon	1284052	1284148	1	-	.	Parent=mRNA98
III	gt csa	exon	1284236	1284322	1	-	.	Parent=mRNA98
III	gt csa	mRNA	1287289	1288513	.	-	.	ID=mRNA99;Parent=gene60;Target=WP 1 312 +
III	gt csa	exon	1287289	1287501	1	-	.	Parent=mRNA99
III	gt cds	CDS	1287289	1287501	.	-	0	ID=CDS74;Parent=mRNA99
III	gt csa	exon	1287544	1288153	1	-	.	Parent=mRNA99
III	gt cds	CDS	1287544	1288153	.	-	1	ID=CDS74;Parent=mRNA99
III	gt csa	exon	1288401	1288513	1	-	.	Parent=mRNA99
III	gt cds	CDS	1288401	1288513	.	-	0	ID=CDS74;Parent=mRNA99
###
III	gt csa	gene	1284398	1287041	.	+	.	ID=gene61
III	gt csa	mRNA	1284398	1284757	.	+	.	ID=mRNA100;Parent=gene61;Target=yk53f10.5 1 360 +
III	gt csa	exon	1284398	1284757	0.989	+	.	Parent=mRNA100
III	gt csa	mRNA	1285006	1287041	.	+	.	ID=mRNA101;Parent=gene61;Target=WP 1 303 +
III	gt csa	exon	1285006	1285088	1	+	.	Parent=mRNA101
III	gt cds	CDS	1285006	1285088	.	+	0	ID=CDS75;Parent=mRNA101
III	gt csa	exon	1286162	1286777	1	+	.	Parent=mRNA101
III	gt cds	CDS	1286162	1286777	.	+	1	ID=CDS75;Parent=mRNA101
III	gt csa	exon	1286832	1287041	1	+	.	Parent=mRNA101
III	gt cds	CDS	1286832	1287041	.	+	0	ID=CDS75;Parent=mRNA101
###
III	gt csa	gene	1292041	1293205	.	-	.	ID=gene62
III	gt csa	mRNA	1292041	1293205	.	-	.	ID=mRNA102;Parent=gene62;Target=WP 1 311 +
III	gt csa	exon	1292041	1292250	1	-	.	Parent=mRNA102
III	gt cds	CDS	1292041	1292250	.	-	0	ID=CDS76;Parent=mRNA102
III	gt csa	exon	1292333	1292972	1	-	.	Parent=mRNA102
III	gt cds	CDS	1292333	1292972	.	-	1	ID=CDS76;Parent=mRNA102
III	gt csa	exon	1293123	1293205	1	-	.	Parent=mRNA102
III	gt cds	CDS	1293123	1293205	.	-	0	ID=CDS76;Parent=mRNA102
###
III	gt csa	gene	1295674	1297059	.	+	.	ID=gene63
III	gt csa	mRNA	1295674	1297059	.	+	.	ID=mRNA103;Parent=gene63;Target=WP 1 311 +,yk720c2.3 1 237 -
III	gt csa	exon	1295674	1295756	1	+	.	Parent=mRNA103
III	gt cds	CDS	1295674	1295756	.	+	0	ID=CDS77;Parent=mRNA103
III	gt csa	exon	1296149	1296785	1	+	.	Parent=mRNA103
III	gt cds	CDS	1296149	1296785	.	+	1	ID=CDS77;Parent=mRNA103
III	gt csa	exon	1296847	1297059	1	+	.	Parent=mRNA103
III	gt cds	CDS	1296847	1297059	.	+	0	ID=CDS77;Parent=mRNA103
###
III	gt csa	gene	1298564	1299474	.	+	.	ID=gene64
III	gt csa	mRNA	1298564	1299474	.	+	.	ID=mRNA104;Parent=gene64;Target=WP 1 292 +
III	gt csa	exon	1298564	1299238	0.952	+	.	Parent=mRNA104
III	gt cds	CDS	1298906	1299238	.	+	0	ID=CDS78;Parent=mRNA104
III	gt csa	exon	1299280	1299474	1	+	.	Parent=mRNA104
III	gt cds	CDS	1299280	1299474	.	+	0	ID=CDS78;Parent=mRNA104
###
III	gt csa	gene	1303704	1305451	.	+	.	ID=gene65
III	gt csa	mRNA	1303704	1305451	.	+	.	ID=mRNA105;Parent=gene65;Target=WP 1 322 +
III	gt csa	exon	1303704	1303792	1	+	.	Parent=mRNA105
III	gt cds	CDS	1303704	1303792	.	+	0	ID=CDS79;Parent=mRNA105
III	gt csa	exon	1303837	1304464	1	+	.	Parent=mRNA105
III	gt cds	CDS	1303837	1304464	.	+	1	ID=CDS79;Parent=mRNA105
III	gt csa	exon	1305203	1305451	1	+	.	Parent=mRNA105
III	gt cds	CDS	1305203	1305451	.	+	0	ID=CDS79;Parent=mRNA105
###
III	gt csa	gene	1305794	1308239	.	-	.	ID=gene66
III	gt csa	mRNA	1305794	1308239	.	-	.	ID=mRNA106;Parent=gene66;Target=WP 1 301 +
III	gt csa	exon	1305794	1305988	1	-	.	Parent=mRNA106
III	gt cds	CDS	1305794	1305988	.	-	0	ID=CDS80;Parent=mRNA106
III	gt csa	exon	1306824	1307478	1	-	.	Parent=mRNA106
III	gt cds	CDS	1306824	1307478	.	-	1	ID=CDS80;Parent=mRNA106
III	gt csa	exon	1308187	1308239	1	-	.	Parent=mRNA106
III	gt cds	CDS	1308187	1308239	.	-	0	ID=CDS80;Parent=mRNA106
###
III	gt csa	gene	1309177	1311200	.	+	.	ID=gene67
III	gt csa	mRNA	1309177	1311200	.	+	.	ID=mRNA107;Parent=gene67;Target=WP 1 337 +
III	gt csa	exon	1309177	1309335	1	+	.	Parent=mRNA107
III	gt cds	CDS	1309177	1309335	.	+	0	ID=CDS81;Parent=mRNA107
III	gt csa	exon	1309577	1309744	1	+	.	Parent=mRNA107
III	gt cds	CDS	1309577	1309744	.	+	0	ID=CDS81;Parent=mRNA107
III	gt csa	exon	1309838	1309936	1	+	.	Parent=mRNA107
III	gt cds	CDS	1309838	1309936	.	+	0	ID=CDS81;Parent=mRNA107
III	gt csa	exon	1310015	1310083	1	+	.	Parent=mRNA107
III	gt cds	CDS	1310015	1310083	.	+	0	ID=CDS81;Parent=mRNA107
III	gt csa	exon	1310130	1310283	1	+	.	Parent=mRNA107
III	gt cds	CDS	1310130	1310283	.	+	0	ID=CDS81;Parent=mRNA107
III	gt csa	exon	1310329	1310399	1	+	.	Parent=mRNA107
III	gt cds	CDS	1310329	1310399	.	+	2	ID=CDS81;Parent=mRNA107
III	gt csa	exon	1310910	1311200	1	+	.	Parent=mRNA107
III	gt cds	CDS	1310910	1311200	.	+	0	ID=CDS81;Parent=mRNA107
###
III	gt csa	gene	1311218	1312383	.	-	.	ID=gene68
III	gt csa	mRNA	1311218	1312383	.	-	.	ID=mRNA108;Parent=gene68;Target=WP 1 241 +
III	gt csa	exon	1311218	1311421	1	-	.	Parent=mRNA108
III	gt cds	CDS	1311218	1311421	.	-	0	ID=CDS82;Parent=mRNA108
III	gt cds	CDS	1311716	1312039	.	-	0	ID=CDS82;Parent=mRNA108
III	gt csa	exon	1311716	1312111	1	-	.	Parent=mRNA108
III	gt csa	exon	1312266	1312383	0.463	-	.	Parent=mRNA108
###
III	gt csa	gene	1313348	1315208	.	-	.	ID=gene69
III	gt csa	mRNA	1313348	1315208	.	-	.	ID=mRNA109;Parent=gene69;Target=yk1237h07.3 1 660 -,WP 1 302 +,yk1237h07.5 1 139 +
III	gt csa	exon	1313348	1313559	0.995	-	.	Parent=mRNA109
III	gt cds	CDS	1313362	1313559	.	-	0	ID=CDS83;Parent=mRNA109
III	gt csa	exon	1314031	1314655	1	-	.	Parent=mRNA109
III	gt cds	CDS	1314031	1314655	.	-	1	ID=CDS83;Parent=mRNA109
III	gt cds	CDS	1315090	1315172	.	-	0	ID=CDS83;Parent=mRNA109
III	gt csa	exon	1315090	1315208	0.992	-	.	Parent=mRNA109
###
III	gt csa	gene	1315254	1316655	.	+	.	ID=gene70
III	gt csa	mRNA	1315254	1316655	.	+	.	ID=mRNA110;Parent=gene70;Target=WP 1 274 +
III	gt csa	exon	1315254	1315357	1	+	.	Parent=mRNA110
III	gt cds	CDS	1315254	1315357	.	+	0	ID=CDS84;Parent=mRNA110
III	gt csa	exon	1315402	1315494	1	+	.	Parent=mRNA110
III	gt cds	CDS	1315402	1315494	.	+	1	ID=CDS84;Parent=mRNA110
III	gt csa	exon	1316031	1316655	1	+	.	Parent=mRNA110
III	gt cds	CDS	1316031	1316655	.	+	1	ID=CDS84;Parent=mRNA110
###
III	gt csa	gene	1319006	1321651	.	-	.	ID=gene71
III	gt csa	mRNA	1319006	1321651	.	-	.	ID=mRNA111;Parent=gene71;Target=WP 1 302 +
III	gt csa	exon	1319006	1319215	1	-	.	Parent=mRNA111
III	gt cds	CDS	1319006	1319215	.	-	0	ID=CDS85;Parent=mRNA111
III	gt csa	exon	1319264	1319888	1	-	.	Parent=mRNA111
III	gt cds	CDS	1319264	1319888	.	-	1	ID=CDS85;Parent=mRNA111
III	gt csa	exon	1321581	1321651	1	-	.	Parent=mRNA111
III	gt cds	CDS	1321581	1321651	.	-	0	ID=CDS85;Parent=mRNA111
###
III	gt csa	gene	1322136	1323621	.	-	.	ID=gene72
III	gt csa	mRNA	1322136	1323621	.	-	.	ID=mRNA112;Parent=gene72;Target=yk546f3.5 1 377 -,WP 1 304 +
III	gt csa	exon	1322136	1322353	0.995	-	.	Parent=mRNA112
III	gt cds	CDS	1322138	1322353	.	-	0	ID=CDS86;Parent=mRNA112
III	gt csa	exon	1322402	1323026	1	-	.	Parent=mRNA112
III	gt cds	CDS	1322402	1323026	.	-	1	ID=CDS86;Parent=mRNA112
III	gt csa	exon	1323551	1323621	1	-	.	Parent=mRNA112
III	gt cds	CDS	1323551	1323621	.	-	0	ID=CDS86;Parent=mRNA112
###
III	gt csa	gene	1328634	1333667	.	+	.	ID=gene73
III	gt csa	mRNA	1328634	1333667	.	+	.	ID=mRNA113;Parent=gene73;Target=WP 1 500 +
III	gt csa	exon	1328634	1328704	1	+	.	Parent=mRNA113
III	gt cds	CDS	1328634	1328704	.	+	0	ID=CDS87;Parent=mRNA113
III	gt csa	exon	1329933	1330529	1	+	.	Parent=mRNA113
III	gt cds	CDS	1329933	1330529	.	+	1	ID=CDS87;Parent=mRNA113
III	gt csa	exon	1331997	1332615	1	+	.	Parent=mRNA113
III	gt cds	CDS	1331997	1332615	.	+	1	ID=CDS87;Parent=mRNA113
III	gt csa	exon	1333455	1333667	1	+	.	Parent=mRNA113
III	gt cds	CDS	1333455	1333667	.	+	0	ID=CDS87;Parent=mRNA113
###
III	gt csa	gene	1333841	1334165	.	-	.	ID=gene74
III	gt csa	mRNA	1333841	1334165	.	-	.	ID=mRNA114;Parent=gene74;Target=WP 1 92 +
III	gt csa	exon	1333841	1333873	0.825	-	.	Parent=mRNA114
III	gt cds	CDS	1333841	1333873	.	-	0	ID=CDS88;Parent=mRNA114
III	gt cds	CDS	1333923	1334126	.	-	0	ID=CDS88;Parent=mRNA114
III	gt csa	exon	1333923	1334165	0.915	-	.	Parent=mRNA114
###
III	gt csa	gene	1336697	1342484	.	-	.	ID=gene75
III	gt csa	mRNA	1336697	1340323	.	-	.	ID=mRNA115;Parent=gene75;Target=yk872h02.3 1 703 -,WP 1 327 +
III	gt csa	exon	1336697	1337005	0.997	-	.	Parent=mRNA115
III	gt cds	CDS	1336802	1337005	.	-	0	ID=CDS89;Parent=mRNA115
III	gt csa	exon	1338016	1338619	1	-	.	Parent=mRNA115
III	gt cds	CDS	1338016	1338619	.	-	1	ID=CDS89;Parent=mRNA115
III	gt csa	exon	1340092	1340175	1	-	.	Parent=mRNA115
III	gt cds	CDS	1340092	1340175	.	-	1	ID=CDS89;Parent=mRNA115
III	gt csa	exon	1340235	1340323	1	-	.	Parent=mRNA115
III	gt cds	CDS	1340235	1340323	.	-	0	ID=CDS89;Parent=mRNA115
III	gt csa	mRNA	1340606	1342484	.	-	.	ID=mRNA116;Parent=gene75;Target=WP 1 329 +
III	gt csa	exon	1340606	1340800	1	-	.	Parent=mRNA116
III	gt cds	CDS	1340606	1340800	.	-	0	ID=CDS90;Parent=mRNA116
III	gt csa	exon	1340854	1341023	1	-	.	Parent=mRNA116
III	gt cds	CDS	1340854	1341023	.	-	2	ID=CDS90;Parent=mRNA116
III	gt csa	exon	1341072	1341547	1	-	.	Parent=mRNA116
III	gt cds	CDS	1341072	1341547	.	-	1	ID=CDS90;Parent=mRNA116
III	gt csa	exon	1342339	1342484	1	-	.	Parent=mRNA116
III	gt cds	CDS	1342339	1342484	.	-	0	ID=CDS90;Parent=mRNA116
###
III	gt csa	gene	1342986	1344682	.	+	.	ID=gene76
III	gt csa	mRNA	1342986	1344682	.	+	.	ID=mRNA117;Parent=gene76;Target=WP 1 325 +
III	gt csa	exon	1342986	1343131	1	+	.	Parent=mRNA117
III	gt cds	CDS	1342986	1343131	.	+	0	ID=CDS91;Parent=mRNA117
III	gt csa	exon	1343802	1344423	1	+	.	Parent=mRNA117
III	gt cds	CDS	1343802	1344423	.	+	1	ID=CDS91;Parent=mRNA117
III	gt csa	exon	1344476	1344682	1	+	.	Parent=mRNA117
III	gt cds	CDS	1344476	1344682	.	+	0	ID=CDS91;Parent=mRNA117
###
III	gt csa	gene	1344968	1345784	.	-	.	ID=gene77
III	gt csa	mRNA	1344968	1345784	.	-	.	ID=mRNA118;Parent=gene77;Target=WP 1 254 +
III	gt csa	exon	1344968	1345417	1	-	.	Parent=mRNA118
III	gt cds	CDS	1344968	1345417	.	-	0	ID=CDS92;Parent=mRNA118
III	gt csa	exon	1345473	1345784	1	-	.	Parent=mRNA118
III	gt cds	CDS	1345473	1345784	.	-	0	ID=CDS92;Parent=mRNA118
###
III	gt csa	gene	1346305	1347118	.	-	.	ID=gene78
III	gt csa	mRNA	1346305	1347118	.	-	.	ID=mRNA119;Parent=gene78;Target=WP 1 251 +
III	gt csa	exon	1346305	1346754	1	-	.	Parent=mRNA119
III	gt cds	CDS	1346305	1346754	.	-	0	ID=CDS93;Parent=mRNA119
III	gt csa	exon	1346816	1347118	1	-	.	Parent=mRNA119
III	gt cds	CDS	1346816	1347118	.	-	0	ID=CDS93;Parent=mRNA119
###
III	gt csa	gene	1347777	1349390	.	-	.	ID=gene79
III	gt csa	mRNA	1347777	1349390	.	-	.	ID=mRNA120;Parent=gene79;Target=WP 1 268 +
III	gt csa	exon	1347777	1347980	1	-	.	Parent=mRNA120
III	gt cds	CDS	1347777	1347980	.	-	0	ID=CDS94;Parent=mRNA120
III	gt csa	exon	1348040	1348143	1	-	.	Parent=mRNA120
III	gt cds	CDS	1348040	1348143	.	-	2	ID=CDS94;Parent=mRNA120
III	gt csa	exon	1348299	1348657	1	-	.	Parent=mRNA120
III	gt cds	CDS	1348299	1348657	.	-	1	ID=CDS94;Parent=mRNA120
III	gt csa	exon	1349254	1349390	1	-	.	Parent=mRNA120
III	gt cds	CDS	1349254	1349390	.	-	0	ID=CDS94;Parent=mRNA120
###
III	gt csa	gene	1349742	1350826	.	-	.	ID=gene80
III	gt csa	mRNA	1349742	1350826	.	-	.	ID=mRNA121;Parent=gene80;Target=WP 1 253 +
III	gt csa	exon	1349742	1350188	1	-	.	Parent=mRNA121
III	gt cds	CDS	1349742	1350188	.	-	0	ID=CDS95;Parent=mRNA121
III	gt csa	exon	1350515	1350826	1	-	.	Parent=mRNA121
III	gt cds	CDS	1350515	1350826	.	-	0	ID=CDS95;Parent=mRNA121
###
III	gt csa	gene	1351206	1353035	.	-	.	ID=gene81
III	gt csa	mRNA	1351206	1353035	.	-	.	ID=mRNA122;Parent=gene81;Target=WP 18 236 +
III	gt csa	exon	1351206	1351652	1	-	.	Parent=mRNA122
III	gt cds	CDS	1351206	1351652	.	-	0	ID=CDS96;Parent=mRNA122
III	gt cds	CDS	1352826	1352909	.	-	0	ID=CDS96;Parent=mRNA122
III	gt csa	exon	1352826	1353035	1	-	.	Parent=mRNA122
###
III	gt csa	gene	1354987	1355410	.	-	.	ID=gene82
III	gt csa	mRNA	1354987	1355410	.	-	.	ID=mRNA123;Parent=gene82;Target=WP 1 125 +
III	gt csa	exon	1354987	1355171	1	-	.	Parent=mRNA123
III	gt cds	CDS	1354987	1355171	.	-	2	ID=CDS97;Parent=mRNA123
III	gt csa	exon	1355221	1355410	1	-	.	Parent=mRNA123
III	gt cds	CDS	1355221	1355410	.	-	0	ID=CDS97;Parent=mRNA123
###
III	gt csa	gene	1357070	1359759	.	-	.	ID=gene83
III	gt csa	mRNA	1357070	1359125	.	-	.	ID=mRNA124;Parent=gene83;Target=WP 1 391 +
III	gt csa	exon	1357070	1357311	1	-	.	Parent=mRNA124
III	gt cds	CDS	1357070	1357311	.	-	2	ID=CDS98;Parent=mRNA124
III	gt csa	exon	1357360	1357471	1	-	.	Parent=mRNA124
III	gt cds	CDS	1357360	1357471	.	-	0	ID=CDS98;Parent=mRNA124
III	gt csa	exon	1357509	1357735	0.969	-	.	Parent=mRNA124
III	gt cds	CDS	1357509	1357735	.	-	2	ID=CDS98;Parent=mRNA124
III	gt csa	exon	1357835	1357952	1	-	.	Parent=mRNA124
III	gt cds	CDS	1357835	1357952	.	-	0	ID=CDS98;Parent=mRNA124
III	gt csa	exon	1357998	1358245	1	-	.	Parent=mRNA124
III	gt cds	CDS	1357998	1358245	.	-	2	ID=CDS98;Parent=mRNA124
III	gt csa	exon	1358287	1358398	1	-	.	Parent=mRNA124
III	gt cds	CDS	1358287	1358398	.	-	0	ID=CDS98;Parent=mRNA124
III	gt csa	exon	1359006	1359125	1	-	.	Parent=mRNA124
III	gt cds	CDS	1359006	1359125	.	-	0	ID=CDS98;Parent=mRNA124
III	gt csa	mRNA	1359244	1359759	.	-	.	ID=mRNA125;Parent=gene83;Target=WP 1 140 +
III	gt csa	exon	1359244	1359488	1	-	.	Parent=mRNA125
III	gt cds	CDS	1359244	1359488	.	-	2	ID=CDS99;Parent=mRNA125
III	gt csa	exon	1359538	1359655	1	-	.	Parent=mRNA125
III	gt cds	CDS	1359538	1359655	.	-	0	ID=CDS99;Parent=mRNA125
III	gt csa	exon	1359703	1359759	1	-	.	Parent=mRNA125
III	gt cds	CDS	1359703	1359759	.	-	0	ID=CDS99;Parent=mRNA125
###
III	gt csa	gene	1360497	1362666	.	+	.	ID=gene84
III	gt csa	mRNA	1360497	1362666	.	+	.	ID=mRNA126;Parent=gene84;Target=WP 1 537 +
III	gt csa	exon	1360497	1360553	1	+	.	Parent=mRNA126
III	gt cds	CDS	1360497	1360553	.	+	0	ID=CDS100;Parent=mRNA126
III	gt csa	exon	1360601	1360718	1	+	.	Parent=mRNA126
III	gt cds	CDS	1360601	1360718	.	+	0	ID=CDS100;Parent=mRNA126
III	gt csa	exon	1360779	1360948	1	+	.	Parent=mRNA126
III	gt cds	CDS	1360779	1360948	.	+	2	ID=CDS100;Parent=mRNA126
III	gt csa	exon	1361034	1361151	1	+	.	Parent=mRNA126
III	gt cds	CDS	1361034	1361151	.	+	0	ID=CDS100;Parent=mRNA126
III	gt csa	exon	1361197	1361420	1	+	.	Parent=mRNA126
III	gt cds	CDS	1361197	1361420	.	+	2	ID=CDS100;Parent=mRNA126
III	gt csa	exon	1361465	1361576	1	+	.	Parent=mRNA126
III	gt cds	CDS	1361465	1361576	.	+	0	ID=CDS100;Parent=mRNA126
III	gt csa	exon	1361749	1361960	1	+	.	Parent=mRNA126
III	gt cds	CDS	1361749	1361960	.	+	2	ID=CDS100;Parent=mRNA126
III	gt csa	exon	1362006	1362123	1	+	.	Parent=mRNA126
III	gt cds	CDS	1362006	1362123	.	+	0	ID=CDS100;Parent=mRNA126
III	gt csa	exon	1362185	1362666	1	+	.	Parent=mRNA126
III	gt cds	CDS	1362185	1362666	.	+	2	ID=CDS100;Parent=mRNA126
###
III	gt csa	gene	1374142	1374515	.	+	.	ID=gene85
III	gt csa	mRNA	1374142	1374515	.	+	.	ID=mRNA127;Parent=gene85;Target=yk604h8.5 1 374 +
III	gt csa	exon	1374142	1374515	1	+	.	Parent=mRNA127
###
III	gt csa	gene	1374575	1374874	.	-	.	ID=gene86
III	gt csa	mRNA	1374575	1374874	.	-	.	ID=mRNA128;Parent=gene86;Target=yk604h8.3 1 300 +
III	gt csa	exon	1374575	1374874	0.993	-	.	Parent=mRNA128
###
III	gt csa	gene	1376935	1377993	.	-	.	ID=gene87
III	gt csa	mRNA	1376935	1377993	.	-	.	ID=mRNA129;Parent=gene87;Target=WP 1 215 +
III	gt csa	exon	1376935	1377144	1	-	.	Parent=mRNA129
III	gt cds	CDS	1376935	1377144	.	-	0	ID=CDS101;Parent=mRNA129
III	gt csa	exon	1377379	1377681	1	-	.	Parent=mRNA129
III	gt cds	CDS	1377379	1377681	.	-	0	ID=CDS101;Parent=mRNA129
III	gt csa	exon	1377862	1377993	1	-	.	Parent=mRNA129
III	gt cds	CDS	1377862	1377993	.	-	0	ID=CDS101;Parent=mRNA129
###
III	gt csa	gene	1379130	1383572	.	-	.	ID=gene88
III	gt csa	mRNA	1379130	1383572	.	-	.	ID=mRNA130;Parent=gene88;Target=WP 1 439 +
III	gt csa	exon	1379130	1379360	1	-	.	Parent=mRNA130
III	gt cds	CDS	1379130	1379360	.	-	0	ID=CDS102;Parent=mRNA130
III	gt csa	exon	1379412	1379579	1	-	.	Parent=mRNA130
III	gt cds	CDS	1379412	1379579	.	-	0	ID=CDS102;Parent=mRNA130
III	gt csa	exon	1380424	1380553	1	-	.	Parent=mRNA130
III	gt cds	CDS	1380424	1380553	.	-	1	ID=CDS102;Parent=mRNA130
III	gt csa	exon	1380609	1380685	0.902	-	.	Parent=mRNA130
III	gt cds	CDS	1380609	1380685	.	-	0	ID=CDS102;Parent=mRNA130
III	gt csa	exon	1382653	1382989	1	-	.	Parent=mRNA130
III	gt cds	CDS	1382653	1382989	.	-	1	ID=CDS102;Parent=mRNA130
III	gt csa	exon	1383057	1383140	1	-	.	Parent=mRNA130
III	gt cds	CDS	1383057	1383140	.	-	1	ID=CDS102;Parent=mRNA130
III	gt csa	exon	1383283	1383572	1	-	.	Parent=mRNA130
III	gt cds	CDS	1383283	1383572	.	-	0	ID=CDS102;Parent=mRNA130
###
III	gt csa	gene	1387471	1388069	.	+	.	ID=gene89
III	gt csa	mRNA	1387471	1388069	.	+	.	ID=mRNA131;Parent=gene89;Target=yk539a12.5 1 360 +
III	gt csa	exon	1387471	1387545	0.967	+	.	Parent=mRNA131
III	gt csa	exon	1387786	1388069	1	+	.	Parent=mRNA131
###
III	gt csa	gene	1387828	1388127	.	-	.	ID=gene90
III	gt csa	mRNA	1387828	1388127	.	-	.	ID=mRNA132;Parent=gene90;Target=yk539a12.3 1 300 +
III	gt cds	CDS	1387828	1388031	.	-	0	ID=CDS103;Parent=mRNA132
III	gt csa	exon	1387828	1388127	0.987	-	.	Parent=mRNA132
###
III	gt csa	gene	1390536	1391840	.	-	.	ID=gene91
III	gt csa	mRNA	1390536	1391840	.	-	.	ID=mRNA133;Parent=gene91;Target=WP 1 252 +,CK579587 1 622 +,CB102366 100 678 +,CB102201 91 657 +,CK579588 1 556 +,CK583482 1 503 +,CB102373 95 478 +,CK583393 1 222 +
III	gt csa	exon	1390536	1390718	1	-	.	Parent=mRNA133
III	gt cds	CDS	1390536	1390718	.	-	0	ID=CDS104;Parent=mRNA133
III	gt csa	exon	1390764	1391067	1	-	.	Parent=mRNA133
III	gt cds	CDS	1390764	1391067	.	-	1	ID=CDS104;Parent=mRNA133
III	gt csa	exon	1391411	1391499	1	-	.	Parent=mRNA133
III	gt cds	CDS	1391411	1391499	.	-	0	ID=CDS104;Parent=mRNA133
III	gt csa	exon	1391551	1391638	1	-	.	Parent=mRNA133
III	gt cds	CDS	1391551	1391638	.	-	1	ID=CDS104;Parent=mRNA133
III	gt csa	exon	1391688	1391736	1	-	.	Parent=mRNA133
III	gt cds	CDS	1391688	1391736	.	-	2	ID=CDS104;Parent=mRNA133
III	gt cds	CDS	1391782	1391824	.	-	0	ID=CDS104;Parent=mRNA133
III	gt csa	exon	1391782	1391840	1	-	.	Parent=mRNA133
###
III	gt csa	gene	1399366	1401295	.	+	.	ID=gene92
III	gt csa	mRNA	1399366	1401295	.	+	.	ID=mRNA134;Parent=gene92;Target=WP 1 357 +
III	gt csa	exon	1399366	1399462	1	+	.	Parent=mRNA134
III	gt cds	CDS	1399366	1399462	.	+	0	ID=CDS105;Parent=mRNA134
III	gt csa	exon	1399964	1400070	1	+	.	Parent=mRNA134
III	gt cds	CDS	1399964	1400070	.	+	2	ID=CDS105;Parent=mRNA134
III	gt csa	exon	1400121	1400270	1	+	.	Parent=mRNA134
III	gt cds	CDS	1400121	1400270	.	+	0	ID=CDS105;Parent=mRNA134
III	gt csa	exon	1400319	1400648	1	+	.	Parent=mRNA134
III	gt cds	CDS	1400319	1400648	.	+	0	ID=CDS105;Parent=mRNA134
III	gt csa	exon	1400696	1400854	1	+	.	Parent=mRNA134
III	gt cds	CDS	1400696	1400854	.	+	0	ID=CDS105;Parent=mRNA134
III	gt csa	exon	1401068	1401295	1	+	.	Parent=mRNA134
III	gt cds	CDS	1401068	1401295	.	+	0	ID=CDS105;Parent=mRNA134
###
III	gt csa	gene	1401956	1403309	.	+	.	ID=gene93
III	gt csa	mRNA	1401956	1403309	.	+	.	ID=mRNA135;Parent=gene93;Target=WP 1 258 +
III	gt csa	exon	1401956	1402065	1	+	.	Parent=mRNA135
III	gt cds	CDS	1401956	1402065	.	+	0	ID=CDS106;Parent=mRNA135
III	gt csa	exon	1402385	1402463	1	+	.	Parent=mRNA135
III	gt cds	CDS	1402385	1402463	.	+	1	ID=CDS106;Parent=mRNA135
III	gt csa	exon	1402510	1402610	1	+	.	Parent=mRNA135
III	gt cds	CDS	1402510	1402610	.	+	0	ID=CDS106;Parent=mRNA135
III	gt csa	exon	1402777	1403077	1	+	.	Parent=mRNA135
III	gt cds	CDS	1402777	1403077	.	+	1	ID=CDS106;Parent=mRNA135
III	gt csa	exon	1403127	1403309	1	+	.	Parent=mRNA135
III	gt cds	CDS	1403127	1403309	.	+	0	ID=CDS106;Parent=mRNA135
###
III	gt csa	gene	1404782	1406220	.	+	.	ID=gene94
III	gt csa	mRNA	1404782	1406220	.	+	.	ID=mRNA136;Parent=gene94;Target=yk1098g06.5 11 546 +,WP 1 257 +,yk1098g06.3 1 708 -
III	gt csa	exon	1404782	1404928	0.993	+	.	Parent=mRNA136
III	gt cds	CDS	1404893	1404928	.	+	0	ID=CDS107;Parent=mRNA136
III	gt csa	exon	1404984	1405322	1	+	.	Parent=mRNA136
III	gt cds	CDS	1404984	1405322	.	+	0	ID=CDS107;Parent=mRNA136
III	gt csa	exon	1405369	1405527	1	+	.	Parent=mRNA136
III	gt cds	CDS	1405369	1405527	.	+	0	ID=CDS107;Parent=mRNA136
III	gt cds	CDS	1405927	1406163	.	+	0	ID=CDS107;Parent=mRNA136
III	gt csa	exon	1405927	1406220	0.997	+	.	Parent=mRNA136
###
III	gt csa	gene	1409301	1414108	.	-	.	ID=gene95
III	gt csa	mRNA	1409301	1412855	.	-	.	ID=mRNA137;Parent=gene95;Target=yk802c04.3 1 671 -,yk1740f01.3 1 653 -,yk1067h09.3 1 728 -,yk482a5.3 1 300 -,WP 1 305 +
III	gt csa	exon	1409301	1409698	0.997	-	.	Parent=mRNA137
III	gt cds	CDS	1409519	1409698	.	-	0	ID=CDS108;Parent=mRNA137
III	gt csa	exon	1410797	1410956	1	-	.	Parent=mRNA137
III	gt cds	CDS	1410797	1410956	.	-	1	ID=CDS108;Parent=mRNA137
III	gt csa	exon	1412055	1412310	1	-	.	Parent=mRNA137
III	gt cds	CDS	1412055	1412310	.	-	2	ID=CDS108;Parent=mRNA137
III	gt csa	exon	1412537	1412855	1	-	.	Parent=mRNA137
III	gt cds	CDS	1412537	1412855	.	-	0	ID=CDS108;Parent=mRNA137
III	gt csa	mRNA	1409301	1414108	.	-	.	ID=mRNA138;Parent=gene95;Target=yk802c04.3 1 671 -,yk1740f01.3 1 653 -,yk1403f06.3 1 732 -,yk482a5.3 1 300 -,RP 1 229 +,BP 1 231 +,yk1403f06.5 23 637 +,yk1740f01.5 23 593 +,yk802c04.5 23 538 +,yk71h4.5 1 360 +,yk336a10.5 1 377 +,yk647g12.5 1 380 +,yk625f5.5 1 383 +,yk498e8.5 1 360 +,yk236b3.5 1 360 +,yk624b7.5 1 360 +,yk614c9.5 1 360 +,yk376c11.5 1 373 +,yk596b12.5 1 377 +,yk482a5.5 1 342 +,yk424h6.5 1 348 +,yk91b11.5 1 348 +,yk743g6.5 23 194 +
III	gt csa	exon	1409301	1409698	0.997	-	.	Parent=mRNA138
III	gt cds	CDS	1409519	1409698	.	-	0	ID=CDS109;Parent=mRNA138
III	gt csa	exon	1410797	1410956	1	-	.	Parent=mRNA138
III	gt cds	CDS	1410797	1410956	.	-	1	ID=CDS109;Parent=mRNA138
III	gt csa	exon	1412055	1412238	1	-	.	Parent=mRNA138
III	gt cds	CDS	1412055	1412238	.	-	2	ID=CDS109;Parent=mRNA138
III	gt cds	CDS	1413935	1414106	.	-	0	ID=CDS109;Parent=mRNA138
III	gt csa	exon	1413935	1414108	0.986	-	.	Parent=mRNA138
III	gt csa	mRNA	1412867	1413610	.	-	.	ID=mRNA139;Parent=gene95;Target=yk1067h09.5 1 744 +
III	gt csa	exon	1412867	1413610	0.995	-	.	Parent=mRNA139
###
III	gt csa	gene	1409354	1409706	.	+	.	ID=gene96
III	gt csa	mRNA	1409354	1409706	.	+	.	ID=mRNA140;Parent=gene96;Target=yk91b11.3 1 335 +,yk71h4.3 1 335 +,yk596b12.3 1 300 +,yk236b3.3 16 300 +,yk743g6.3 1 300 +,yk647g12.3 1 300 +,yk614c9.3 1 300 +,yk376c11.3 1 300 +,yk424h6.3 1 283 +,yk336a10.3 1 283 +,yk498e8.3 1 282 +
III	gt csa	exon	1409354	1409706	0.983	+	.	Parent=mRNA140
###
III	gt csa	gene	1415536	1417177	.	-	.	ID=gene97
III	gt csa	mRNA	1415536	1417177	.	-	.	ID=mRNA141;Parent=gene97;Target=CK583137 1 508 +,BP 1 124 +
III	gt csa	exon	1415536	1415865	1	-	.	Parent=mRNA141
III	gt cds	CDS	1415669	1415865	.	-	2	ID=CDS110;Parent=mRNA141
III	gt csa	exon	1417000	1417177	1	-	.	Parent=mRNA141
III	gt cds	CDS	1417000	1417177	.	-	0	ID=CDS110;Parent=mRNA141
###
III	gt csa	gene	1418971	1420424	.	+	.	ID=gene98
III	gt csa	mRNA	1418971	1420424	.	+	.	ID=mRNA142;Parent=gene98;Target=yk427c9.5 1 375 +,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1310e07.5 23 555 +,yk1089d01.5 23 572 +,yk1527c07.5 23 589 +,yk1344e01.3 19 587 -,yk761f11.5 17 614 +,yk809d12.3 23 628 -,yk1310e07.3 23 628 -,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1299c02.5 1 380 +,yk361d12.5 1 375 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +,CEESB14F 1 300 +,CEESY61FB 1 319 +,yk1382d08.3 1 222 +,yk621b1.3 1 300 +,yk739c4.3 1 300 +,yk597g10.3 1 300 +,yk421a11.3 1 292 +,yk447b3.3 1 300 +,yk599b8.3 1 300 +,yk639a10.3 1 300 +,yk555f9.3 1 300 +,yk615c7.3 1 240 +,yk525g4.3 1 240 +,yk556a10.5 1 365 +,yk1475h10.3 1 136 +
III	gt csa	exon	1418971	1418973	0.667	+	.	Parent=mRNA142
III	gt csa	exon	1419186	1419251	1	+	.	Parent=mRNA142
III	gt csa	exon	1419321	1420424	0.99	+	.	Parent=mRNA142
III	gt cds	CDS	1420005	1420424	.	+	0	ID=CDS111;Parent=mRNA142
III	gt csa	mRNA	1419094	1420424	.	+	.	ID=mRNA143;Parent=gene98;Target=yk1587h06.3 135 661 -,yk1212c10.5 1 546 +,yk64h2.5 1 341 +,yk371c5.5 1 370 +,yk596e1.5 1 374 +,yk654c2.5 1 376 +,yk474d11.5 1 377 +,yk1005d11.3 1 502 -,yk1221a01.3 1 512 -,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1310e07.5 23 555 +,yk1089d01.5 23 572 +,yk1527c07.5 23 589 +,yk1344e01.3 19 587 -,yk761f11.5 17 614 +,yk809d12.3 23 628 -,yk1310e07.3 23 628 -,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1299c02.5 1 380 +,yk361d12.5 1 375 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +,CEESB14F 1 300 +,CEESY61FB 1 319 +,yk1382d08.3 1 222 +,yk621b1.3 1 300 +,yk739c4.3 1 300 +,yk597g10.3 1 300 +,yk421a11.3 1 292 +,yk447b3.3 1 300 +,yk599b8.3 1 300 +,yk639a10.3 1 300 +,yk555f9.3 1 300 +,yk615c7.3 1 240 +,yk525g4.3 1 240 +,yk556a10.5 1 365 +,yk1475h10.3 1 136 +
III	gt csa	exon	1419094	1419103	1	+	.	Parent=mRNA143
III	gt csa	exon	1419166	1419251	0.919	+	.	Parent=mRNA143
III	gt csa	exon	1419321	1420424	0.99	+	.	Parent=mRNA143
III	gt cds	CDS	1420005	1420424	.	+	0	ID=CDS112;Parent=mRNA143
III	gt csa	mRNA	1419138	1420087	.	+	.	ID=mRNA144;Parent=gene98;Target=yk844c03.3 152 710 -,yk1072g09.3 120 674 -,yk1344a02.3 179 720 -,yk1398d04.3 114 643 -,yk1119f04.3 190 729 -,yk1396f08.3 94 712 -,yk865b04.3 146 680 -,yk1339f10.3 103 734 -,yk1212c10.5 1 546 +,yk64h2.5 1 341 +,yk371c5.5 1 370 +,yk596e1.5 1 374 +,yk654c2.5 1 376 +,yk474d11.5 1 377 +,yk1005d11.3 1 502 -,yk1221a01.3 1 512 -,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1310e07.5 23 555 +,yk1089d01.5 23 572 +,yk1527c07.5 23 589 +,yk1344e01.3 19 587 -,yk761f11.5 17 614 +,yk809d12.3 23 628 -,yk1310e07.3 23 628 -,yk757f11.5 17 635 +,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1299c02.5 1 380 +,yk361d12.5 1 375 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +
III	gt csa	exon	1419138	1419251	0.842	+	.	Parent=mRNA144
III	gt cds	CDS	1419207	1419251	.	+	0	ID=CDS113;Parent=mRNA144
III	gt cds	CDS	1419321	1419626	.	+	0	ID=CDS113;Parent=mRNA144
III	gt csa	exon	1419321	1419863	0.995	+	.	Parent=mRNA144
III	gt csa	exon	1420079	1420087	0.667	+	.	Parent=mRNA144
III	gt csa	mRNA	1419138	1420087	.	+	.	ID=mRNA145;Parent=gene98;Target=yk844c03.3 152 710 -,yk1072g09.3 120 674 -,yk1344a02.3 179 720 -,yk1398d04.3 114 643 -,yk1119f04.3 190 729 -,yk865b04.3 146 680 -,yk1212c10.5 1 546 +,yk64h2.5 1 341 +,yk371c5.5 1 370 +,yk596e1.5 1 374 +,yk654c2.5 1 376 +,yk474d11.5 1 377 +,yk1005d11.3 1 502 -,yk1221a01.3 1 512 -,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1258a02.5 23 558 +,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1195a11.5 1 417 +,yk1299c02.5 1 380 +,yk1133g01.5 1 368 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +
III	gt csa	exon	1419138	1419251	0.842	+	.	Parent=mRNA145
III	gt cds	CDS	1419207	1419251	.	+	0	ID=CDS114;Parent=mRNA145
III	gt cds	CDS	1419321	1419626	.	+	0	ID=CDS114;Parent=mRNA145
III	gt csa	exon	1419321	1419783	1	+	.	Parent=mRNA145
III	gt csa	exon	1420079	1420087	0.778	+	.	Parent=mRNA145
III	gt csa	mRNA	1419138	1420424	.	+	.	ID=mRNA146;Parent=gene98;Target=yk844c03.3 152 710 -,yk1072g09.3 120 674 -,yk1344a02.3 179 720 -,yk1398d04.3 114 643 -,yk1119f04.3 190 729 -,yk1396f08.3 94 712 -,yk865b04.3 146 680 -,yk1339f10.3 103 734 -,yk1212c10.5 1 546 +,yk64h2.5 1 341 +,yk371c5.5 1 370 +,yk596e1.5 1 374 +,yk654c2.5 1 376 +,yk474d11.5 1 377 +,yk1005d11.3 1 502 -,yk1221a01.3 1 512 -,yk1446h08.3 23 168 -,CEESI82R 12 304 +,yk1423c01.3 23 334 -,yk827b03.5 22 336 +,yk1457b06.5 23 366 +,yk573e8.5 11 360 +,yk289b9.5 11 373 +,yk1446h08.5 23 392 +,yk497f5.5 1 377 +,yk1299h01.3 192 594 -,yk1637f01.5 22 432 +,yk1156a09.5 23 434 +,yk1498f01.5 23 435 +,yk1370f10.5 23 435 +,yk1692c10.5 22 434 +,yk1050c09.3 23 436 -,yk1099h06.5 23 435 +,yk1438b02.5 23 436 +,yk1490c07.5 23 435 +,yk1667g11.5 23 436 +,yk1500g09.5 23 436 +,yk1743g04.5 23 436 +,yk1662h02.5 23 437 +,yk1699g12.5 23 438 +,yk809d12.5 23 437 +,yk891h02.5 23 438 +,yk1324a12.5 23 439 +,yk1581b07.5 23 439 +,yk1597e02.5 22 438 +,yk1005d11.5 23 439 +,yk1015e03.3 23 440 -,yk1258f10.5 24 442 +,yk1134e12.5 23 441 +,yk1329c12.5 24 442 +,yk1348g09.5 23 442 +,yk1281b11.5 23 442 +,yk1347e08.5 23 443 +,yk819c03.5 23 443 +,yk1370f08.5 23 447 +,yk1505b08.3 37 462 -,yk1307b12.3 182 609 -,yk1076e08.5 23 454 +,yk1299h06.3 291 730 -,yk1304f10.3 27 468 -,yk1304f10.5 27 484 +,yk763c11.5 23 480 +,yk776c05.5 23 484 +,yk1167g12.5 22 484 +,yk1340a03.5 22 484 +,yk1261h11.3 195 659 -,yk1033d09.5 18 482 +,yk1041d01.5 23 487 +,yk1307e07.3 224 690 -,yk776b07.5 18 504 +,yk1717f07.5 22 512 +,yk1099h06.3 23 517 -,yk1122e01.3 23 519 -,yk1151e05.3 24 518 -,yk1033d09.3 18 513 -,yk1200b10.3 22 517 -,yk1445a08.3 218 714 -,yk1499d03.3 226 722 -,yk1508b06.3 222 718 -,yk1523g04.3 78 575 -,yk1701c04.3 85 583 -,yk1276a07.3 229 729 -,yk1566c03.3 23 522 -,yk1534b01.3 227 726 -,yk1559d06.3 140 640 -,yk1597e02.3 22 523 -,yk1420g05.3 23 524 -,yk1476g05.3 224 725 -,yk1502f07.3 203 704 -,yk1526c08.3 102 605 -,yk1564e02.3 186 690 -,yk1581b07.3 23 525 -,yk1411e02.3 22 524 -,yk1460g06.3 191 693 -,yk1490c07.3 23 524 -,yk1459c06.3 212 714 -,yk1468c03.3 123 625 -,yk1662h02.3 23 525 -,yk1706f01.3 23 525 -,yk1730a09.3 23 525 -,yk1751g08.3 222 724 -,yk1450f03.3 220 723 -,yk1498f01.3 23 526 -,yk1347e08.3 23 526 -,yk1281f04.3 23 528 -,yk1026f10.3 25 529 -,yk1326f10.3 145 649 -,yk776b07.3 18 522 -,yk819c03.3 23 527 -,yk1363d08.3 23 528 -,yk1141a10.3 23 531 -,yk891h02.3 23 531 -,yk1079e02.3 23 530 -,yk1142c02.3 192 699 -,yk827b03.3 22 529 -,yk1041d01.3 23 532 -,yk1022f05.3 188 696 -,yk1161d09.3 23 531 -,yk1175b05.3 23 531 -,yk1229f01.3 223 731 -,yk776c05.3 23 531 -,yk1258a02.3 23 533 -,yk1258f10.3 24 533 -,yk1213d11.3 257 767 -,yk1021b10.3 23 532 -,yk1212f06.3 183 692 -,yk1338c06.3 23 532 -,yk1041a09.3 233 742 -,yk1076e08.3 23 532 -,yk1134e12.3 23 532 -,yk1156a09.3 23 532 -,yk1167g12.3 22 531 -,yk1217d06.3 183 692 -,yk1238d11.3 23 532 -,yk1239g07.3 223 732 -,yk1261c01.3 218 727 -,yk1266c12.3 23 532 -,yk1266e05.3 23 532 -,yk1281b07.3 23 532 -,yk1289h06.3 101 610 -,yk1309b05.3 224 733 -,yk1382h02.5 23 532 +,yk1329c12.3 24 537 -,yk1063g09.3 154 665 -,yk1089d01.3 23 533 -,yk1667g11.3 23 534 -,yk1500g09.3 23 534 -,yk1653c08.3 23 534 -,yk1370f08.3 23 535 -,yk1370f10.3 23 535 -,yk1629g01.3 23 535 -,yk1743g04.3 23 536 -,yk1239f04.3 23 538 -,yk1717f07.3 22 538 -,yk1274f02.3 23 540 -,yk1223a01.3 150 668 -,yk812e07.5 23 541 +,yk812e07.3 23 540 -,yk1340a03.3 22 541 -,yk1021b10.5 23 543 +,yk1514e03.3 184 709 -,yk1338c06.5 23 553 +,yk1238d11.5 23 553 +,yk1026f10.5 25 554 +,yk1363d08.5 23 552 +,yk1274f02.5 23 552 +,yk1420g05.5 23 552 +,yk1566c03.5 23 552 +,yk1629g01.5 23 552 +,yk1706f01.5 23 552 +,yk1730a09.5 23 552 +,yk1122e01.5 23 552 +,yk1141a10.5 23 552 +,yk1151e05.5 24 553 +,yk1161d09.5 23 552 +,yk1175b05.5 23 552 +,yk1281f04.5 23 552 +,yk1079e02.5 23 551 +,yk1310e07.5 23 555 +,yk1089d01.5 23 572 +,yk1527c07.5 23 589 +,yk1344e01.3 19 587 -,yk761f11.5 17 614 +,yk809d12.3 23 628 -,yk1310e07.3 23 628 -,yk470d10.5 1 376 +,yk1015e03.5 1 388 +,yk110a8.5 1 360 +,yk114f3.5 1 360 +,yk78a9.5 1 383 +,yk60a2.5 1 330 +,yk677a10.5 1 373 +,yk634d3.5 1 374 +,yk389a2.5 1 376 +,yk591g5.5 1 375 +,yk247h2.5 1 244 +,yk92d5.5 1 322 +,yk62e4.5 1 330 +,yk82d9.5 1 352 +,yk484e3.5 1 367 +,yk342c11.5 1 371 +,yk210g1.5 1 371 +,yk199b1.5 1 372 +,yk609a6.5 1 372 +,yk602g4.5 1 374 +,yk472b4.5 1 376 +,yk532b2.5 1 376 +,yk628h8.5 1 384 +,yk470d10.3 1 300 -,yk67e2.5 1 360 +,yk495b4.5 1 360 +,yk515d3.5 1 367 +,yk586d10.5 1 377 +,yk631d3.5 1 383 +,yk77e2.5 1 385 +,yk573e6.5 1 360 +,yk561d9.5 1 376 +,yk487f9.5 1 360 +,yk491d2.5 1 360 +,yk418d7.5 1 373 +,yk391d4.5 1 377 +,yk281f9.5 1 376 +,yk612a2.5 1 360 +,yk667h3.5 1 378 +,yk103f11.5 1 330 +,yk82d4.5 1 330 +,yk502f2.5 1 370 +,yk399b1.5 1 377 +,yk1388g06.3 1 499 -,yk1388g06.5 1 513 +,yk255e5.5 1 360 +,yk1230h08.5 1 172 +,yk1281b07.5 1 174 +,CK576705 1 199 +,BP 1 117 +,RP 1 117 +,yk393a4.5 1 360 +,CK575334 1 379 +,CK579527 1 498 +,yk1411e02.5 1 103 +,yk568f5.5 1 374 +,yk612e4.5 1 360 +,yk1239f04.5 1 492 +,yk1050c09.5 1 505 +,yk591h11.5 1 360 +,yk635a9.5 1 360 +,yk639e2.5 1 360 +,yk654d2.5 1 382 +,yk648e7.5 1 360 +,yk486b11.5 1 360 +,yk650f12.5 1 360 +,yk1012b08.3 1 317 -,yk1123h12.3 1 463 -,yk579f1.5 1 360 +,yk752f11.5 1 326 +,CEESE35F 1 285 +,CEESP60F 1 283 +,yk1032a02.5 53 422 +,yk633a4.5 1 382 +,yk1299c02.5 1 380 +,yk361d12.5 1 375 +,yk594f10.5 1 356 +,yk847c05.5 1 353 +,CEESB14F 1 300 +,CEESY61FB 1 319 +,yk1382d08.3 1 222 +,yk621b1.3 1 300 +,yk739c4.3 1 300 +,yk597g10.3 1 300 +,yk421a11.3 1 292 +,yk447b3.3 1 300 +,yk599b8.3 1 300 +,yk639a10.3 1 300 +,yk555f9.3 1 300 +,yk615c7.3 1 240 +,yk525g4.3 1 240 +,yk556a10.5 1 365 +,yk1475h10.3 1 136 +
III	gt csa	exon	1419138	1419251	0.842	+	.	Parent=mRNA146
III	gt csa	exon	1419321	1420424	0.99	+	.	Parent=mRNA146
III	gt cds	CDS	1420005	1420424	.	+	0	ID=CDS115;Parent=mRNA146
###
III	gt csa	gene	1419326	1427216	.	-	.	ID=gene99
III	gt csa	mRNA	1419326	1419839	.	-	.	ID=mRNA147;Parent=gene99;Target=yk1230h08.3 1 312 +,yk1527c07.3 1 508 +,yk1032a02.3 1 376 +,yk602g4.3 1 300 +,yk1195a11.3 1 378 +,yk639e2.3 1 300 +,yk763c11.3 1 356 +,CEESU49F 1 379 +,yk667h3.3 1 300 +,yk1526d06.3 1 360 +,CEESM53F 1 381 +,yk596e1.3 1 300 +,yk654e2.3 1 180 +,yk586d10.3 1 240 +,yk281f9.3 1 300 +,yk255e5.3 1 300 +,yk654e1.3 1 180 +,yk591h11.3 1 240 +,yk634d3.3 1 300 +,yk654c2.3 1 300 +,yk487f9.3 1 300 +,yk515d3.3 1 300 +,yk654d2.3 1 300 +,yk672d12.3 1 300 +,yk631d3.3 1 300 +,yk612a2.3 1 300 +,yk654g12.3 1 180 +,yk281a2.3 1 300 +,yk609a6.3 1 300 +,yk612e4.3 1 300 +,yk371c5.3 1 300 +,yk648e7.3 1 300 +,yk1133g01.3 1 342 +,yk579f1.3 1 300 +,yk289b9.3 1 300 +,yk110a8.3 1 342 +,CEESH76F 1 352 +,yk114f3.3 1 326 +,yk67e2.3 1 332 +,yk64h2.3 1 337 +,yk1382h02.3 1 106 +,CEESV10F 1 307 +,yk92d5.3 1 292 +,CEESN05F 1 295 +,yk677a10.3 1 300 +,yk847c05.3 1 253 +,yk833b04.3 1 252 +,yk78a9.3 1 300 +,CEESX12F 1 238 +,yk62e4.3 1 180 +,yk92c4.3 1 152 +,yk1692c10.3 1 127 +,yk1637f01.3 1 136 +
III	gt cds	CDS	1419326	1419607	.	-	0	ID=CDS116;Parent=mRNA147
III	gt csa	exon	1419326	1419839	0.96	-	.	Parent=mRNA147
III	gt csa	mRNA	1419858	1427216	.	-	.	ID=mRNA148;Parent=gene99;Target=yk1572a07.3 1 708 -,yk1483e05.3 1 710 -,yk845a11.3 1 671 -,yk1091h10.3 1 703 -,yk777g07.3 1 702 -,yk843d03.3 1 655 -,yk1037c05.3 1 702 -,yk1339b07.3 1 706 -,yk1156e02.3 1 713 -,yk1221d11.3 1 718 -,yk1271e02.3 1 702 -,yk1175h04.3 1 701 -,yk1068f01.3 1 777 -,yk1534a04.3 1 671 -,yk1397e11.3 1 735 -,yk1467c02.3 1 668 -,yk1447g10.3 1 689 -,yk1588c10.3 1 694 -,yk1616c04.3 1 745 -,yk1449e07.3 1 743 -,yk1422c01.3 1 711 -,yk1433e11.3 1 713 -,yk1359d11.3 1 739 -,yk1741b07.3 1 645 -,yk1382d05.3 1 724 -,yk1491e06.3 1 722 -,yk1111g04.3 1 667 -,yk1677f12.3 1 683 -,RP 1 549 +,BP 1 546 +,yk421a11.5 1 360 +,yk384h6.5 1 375 +,yk639a10.5 1 360 +,yk1021a01.5 20 655 +,yk1483e05.5 17 650 +,yk1359d11.5 23 655 +,yk1382d05.5 23 654 +,yk1433e11.5 22 650 +,yk1422c01.5 23 628 +,yk1397e11.5 22 625 +,yk1091h10.5 23 616 +,yk1221d11.5 23 614 +,yk845a11.5 23 613 +,yk1339b07.5 23 612 +,yk1068f01.5 23 611 +,yk1677f12.5 24 611 +,yk1382d08.5 23 610 +,yk1680g05.5 23 610 +,yk1439g04.5 23 609 +,yk1741b07.5 22 608 +,yk1037c05.5 23 606 +,yk1491e06.5 23 606 +,yk1588c10.5 23 604 +,yk1175h04.5 23 603 +,yk777g07.5 20 534 +,yk843d03.5 23 534 +,yk1111g04.5 23 512 +,yk1467c02.5 22 500 +,yk1449c10.5 23 463 +,yk1572a07.5 23 461 +,yk1447g10.5 23 460 +,yk1449e07.5 23 460 +,yk525g4.5 1 375 +,cm20f7.5 11 407 +,yk275h6.5 1 351 +,yk597g10.5 1 354 +,yk447b3.5 1 355 +,yk599b8.5 1 359 +,yk615c7.5 1 370 +,yk1534a04.5 27 403 +,yk739c4.5 23 340 +
III	gt csa	exon	1419858	1420431	0.998	-	.	Parent=mRNA148
III	gt cds	CDS	1419963	1420431	.	-	1	ID=CDS117;Parent=mRNA148
III	gt csa	exon	1421391	1421771	0.897	-	.	Parent=mRNA148
III	gt cds	CDS	1421391	1421771	.	-	1	ID=CDS117;Parent=mRNA148
III	gt csa	exon	1424258	1424349	0.948	-	.	Parent=mRNA148
III	gt cds	CDS	1424258	1424349	.	-	0	ID=CDS117;Parent=mRNA148
III	gt csa	exon	1425095	1425427	0.96	-	.	Parent=mRNA148
III	gt cds	CDS	1425095	1425427	.	-	0	ID=CDS117;Parent=mRNA148
III	gt csa	exon	1425902	1425994	1	-	.	Parent=mRNA148
III	gt cds	CDS	1425902	1425994	.	-	0	ID=CDS117;Parent=mRNA148
III	gt csa	exon	1426159	1426285	1	-	.	Parent=mRNA148
III	gt cds	CDS	1426159	1426285	.	-	1	ID=CDS117;Parent=mRNA148
III	gt cds	CDS	1427060	1427205	.	-	0	ID=CDS117;Parent=mRNA148
III	gt csa	exon	1427060	1427216	1	-	.	Parent=mRNA148
III	gt csa	mRNA	1420034	1420559	.	-	.	ID=mRNA149;Parent=gene99;Target=yk421a11.5 1 360 +,yk555f9.5 1 360 +
III	gt csa	exon	1420034	1420559	0.993	-	.	Parent=mRNA149
III	gt cds	CDS	1420035	1420361	.	-	0	ID=CDS118;Parent=mRNA149
III	gt csa	mRNA	1421684	1424322	.	-	.	ID=mRNA150;Parent=gene99;Target=yk621b1.5 1 240 +
III	gt csa	exon	1421684	1421858	0.943	-	.	Parent=mRNA150
III	gt csa	exon	1424258	1424322	1	-	.	Parent=mRNA150
###
III	gt csa	gene	1439086	1443180	.	+	.	ID=gene100
III	gt csa	mRNA	1439086	1443180	.	+	.	ID=mRNA151;Parent=gene100;Target=WP 1 531 +
III	gt csa	exon	1439086	1439148	1	+	.	Parent=mRNA151
III	gt cds	CDS	1439086	1439148	.	+	0	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1439194	1439289	1	+	.	Parent=mRNA151
III	gt cds	CDS	1439194	1439289	.	+	0	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1439346	1439507	1	+	.	Parent=mRNA151
III	gt cds	CDS	1439346	1439507	.	+	0	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1439552	1439628	1	+	.	Parent=mRNA151
III	gt cds	CDS	1439552	1439628	.	+	0	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1439705	1439927	1	+	.	Parent=mRNA151
III	gt cds	CDS	1439705	1439927	.	+	1	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1440041	1440100	1	+	.	Parent=mRNA151
III	gt cds	CDS	1440041	1440100	.	+	0	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1440409	1440543	1	+	.	Parent=mRNA151
III	gt cds	CDS	1440409	1440543	.	+	0	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1440839	1440928	1	+	.	Parent=mRNA151
III	gt cds	CDS	1440839	1440928	.	+	0	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1441573	1441826	1	+	.	Parent=mRNA151
III	gt cds	CDS	1441573	1441826	.	+	0	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1441882	1442030	1	+	.	Parent=mRNA151
III	gt cds	CDS	1441882	1442030	.	+	1	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1442396	1442547	1	+	.	Parent=mRNA151
III	gt cds	CDS	1442396	1442547	.	+	2	ID=CDS119;Parent=mRNA151
III	gt csa	exon	1443049	1443180	1	+	.	Parent=mRNA151
III	gt cds	CDS	1443049	1443180	.	+	0	ID=CDS119;Parent=mRNA151
###
III	gt csa	gene	1443038	1443263	.	-	.	ID=gene101
III	gt csa	mRNA	1443038	1443263	.	-	.	ID=mRNA152;Parent=gene101;Target=yk525g8.3 80 300 +,yk656g8.3 80 300 +,yk658b12.3 83 300 +,yk337c2.3 84 300 +,yk675h9.3 85 300 +,yk602e8.3 86 300 +,yk652b11.3 86 300 +,yk659c10.3 86 300 +,yk621h1.3 88 300 +,yk572f4.3 77 288 +,yk592b8.3 75 286 +,yk617a4.3 81 300 +
III	gt csa	exon	1443038	1443263	0.866	-	.	Parent=mRNA152
###
III	gt csa	gene	1447545	1455750	.	-	.	ID=gene102
III	gt csa	mRNA	1447545	1455750	.	-	.	ID=mRNA153;Parent=gene102;Target=yk674c5.3 1 300 -,yk513e12.3 1 300 -,WP 1 482 +,yk674c5.5 1 360 +
III	gt csa	exon	1447545	1447665	1	-	.	Parent=mRNA153
III	gt cds	CDS	1447596	1447665	.	-	1	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1449965	1450063	1	-	.	Parent=mRNA153
III	gt cds	CDS	1449965	1450063	.	-	1	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1450108	1450340	1	-	.	Parent=mRNA153
III	gt cds	CDS	1450108	1450340	.	-	0	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1450555	1450692	1	-	.	Parent=mRNA153
III	gt cds	CDS	1450555	1450692	.	-	0	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1450743	1450802	1	-	.	Parent=mRNA153
III	gt cds	CDS	1450743	1450802	.	-	0	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1450847	1450919	1	-	.	Parent=mRNA153
III	gt cds	CDS	1450847	1450919	.	-	1	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1451910	1452038	1	-	.	Parent=mRNA153
III	gt cds	CDS	1451910	1452038	.	-	1	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1452084	1452139	1	-	.	Parent=mRNA153
III	gt cds	CDS	1452084	1452139	.	-	0	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1452429	1452468	1	-	.	Parent=mRNA153
III	gt cds	CDS	1452429	1452468	.	-	1	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1453036	1453163	1	-	.	Parent=mRNA153
III	gt cds	CDS	1453036	1453163	.	-	0	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1454216	1454391	1	-	.	Parent=mRNA153
III	gt cds	CDS	1454216	1454391	.	-	2	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1454479	1454572	1	-	.	Parent=mRNA153
III	gt cds	CDS	1454479	1454572	.	-	0	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1454621	1454698	1	-	.	Parent=mRNA153
III	gt cds	CDS	1454621	1454698	.	-	0	ID=CDS120;Parent=mRNA153
III	gt cds	CDS	1455676	1455747	.	-	0	ID=CDS120;Parent=mRNA153
III	gt csa	exon	1455676	1455750	1	-	.	Parent=mRNA153
III	gt csa	mRNA	1448290	1449007	.	-	.	ID=mRNA154;Parent=gene102;Target=yk1044a02.5 1 718 +
III	gt csa	exon	1448290	1449007	0.997	-	.	Parent=mRNA154
III	gt csa	mRNA	1452028	1452748	.	-	.	ID=mRNA155;Parent=gene102;Target=yk513e12.5 1 386 +
III	gt csa	exon	1452028	1452038	1	-	.	Parent=mRNA155
III	gt csa	exon	1452084	1452139	0.982	-	.	Parent=mRNA155
III	gt csa	exon	1452429	1452748	1	-	.	Parent=mRNA155
###
III	gt csa	gene	1449026	1449551	.	+	.	ID=gene103
III	gt csa	mRNA	1449026	1449551	.	+	.	ID=mRNA156;Parent=gene103;Target=yk1044a02.3 208 712 +
III	gt csa	exon	1449026	1449522	0.991	+	.	Parent=mRNA156
III	gt csa	exon	1449545	1449551	0.571	+	.	Parent=mRNA156
###
III	gt csa	gene	1458223	1466441	.	+	.	ID=gene104
III	gt csa	mRNA	1458223	1466441	.	+	.	ID=mRNA157;Parent=gene104;Target=WP 1 503 +
III	gt csa	exon	1458223	1458465	1	+	.	Parent=mRNA157
III	gt cds	CDS	1458223	1458465	.	+	0	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1458508	1458597	1	+	.	Parent=mRNA157
III	gt cds	CDS	1458508	1458597	.	+	0	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1458884	1458935	1	+	.	Parent=mRNA157
III	gt cds	CDS	1458884	1458935	.	+	0	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1459883	1460049	1	+	.	Parent=mRNA157
III	gt cds	CDS	1459883	1460049	.	+	2	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1461819	1461874	1	+	.	Parent=mRNA157
III	gt cds	CDS	1461819	1461874	.	+	0	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1461919	1462047	1	+	.	Parent=mRNA157
III	gt cds	CDS	1461919	1462047	.	+	1	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1463286	1463358	1	+	.	Parent=mRNA157
III	gt cds	CDS	1463286	1463358	.	+	1	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1463515	1463584	1	+	.	Parent=mRNA157
III	gt cds	CDS	1463515	1463584	.	+	0	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1465126	1465193	1	+	.	Parent=mRNA157
III	gt cds	CDS	1465126	1465193	.	+	2	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1465240	1465469	1	+	.	Parent=mRNA157
III	gt cds	CDS	1465240	1465469	.	+	0	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1465516	1465614	1	+	.	Parent=mRNA157
III	gt cds	CDS	1465516	1465614	.	+	1	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1465770	1465832	1	+	.	Parent=mRNA157
III	gt cds	CDS	1465770	1465832	.	+	1	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1465923	1466021	1	+	.	Parent=mRNA157
III	gt cds	CDS	1465923	1466021	.	+	1	ID=CDS121;Parent=mRNA157
III	gt csa	exon	1466372	1466441	1	+	.	Parent=mRNA157
III	gt cds	CDS	1466372	1466441	.	+	1	ID=CDS121;Parent=mRNA157
###
III	gt csa	gene	1466377	1466722	.	-	.	ID=gene105
III	gt csa	mRNA	1466377	1466722	.	-	.	ID=mRNA158;Parent=gene105;Target=CEESB41F 1 346 +
III	gt csa	exon	1466377	1466722	0.965	-	.	Parent=mRNA158
###
III	gt csa	gene	1467863	1483497	.	-	.	ID=gene106
III	gt csa	mRNA	1467863	1483497	.	-	.	ID=mRNA159;Parent=gene106;Target=yk1170a01.3 1 765 -,yk1128d05.3 1 726 -,yk405c3.3 1 300 -,yk500f5.3 1 300 -,yk288a6.3 1 300 -,WP 1 922 +,yk135h2.5 1 373 +,yk288a6.5 1 360 +,yk1170a01.5 22 593 +,yk1128d05.5 23 588 +
III	gt csa	exon	1467863	1468170	0.981	-	.	Parent=mRNA159
III	gt cds	CDS	1468054	1468170	.	-	0	ID=CDS122;Parent=mRNA159
III	gt csa	exon	1469171	1469260	1	-	.	Parent=mRNA159
III	gt cds	CDS	1469171	1469260	.	-	0	ID=CDS122;Parent=mRNA159
III	gt csa	exon	1470517	1471342	1	-	.	Parent=mRNA159
III	gt cds	CDS	1470517	1471342	.	-	1	ID=CDS122;Parent=mRNA159
III	gt csa	exon	1472209	1472382	1	-	.	Parent=mRNA159
III	gt cds	CDS	1472209	1472382	.	-	1	ID=CDS122;Parent=mRNA159
III	gt csa	exon	1473915	1474201	1	-	.	Parent=mRNA159
III	gt cds	CDS	1473915	1474201	.	-	0	ID=CDS122;Parent=mRNA159
III	gt csa	exon	1474848	1475099	1	-	.	Parent=mRNA159
III	gt cds	CDS	1474848	1475099	.	-	0	ID=CDS122;Parent=mRNA159
III	gt csa	exon	1476256	1476485	1	-	.	Parent=mRNA159
III	gt cds	CDS	1476256	1476485	.	-	2	ID=CDS122;Parent=mRNA159
III	gt csa	exon	1477039	1477574	1	-	.	Parent=mRNA159
III	gt cds	CDS	1477039	1477574	.	-	1	ID=CDS122;Parent=mRNA159
III	gt csa	exon	1478937	1479126	1	-	.	Parent=mRNA159
III	gt cds	CDS	1478937	1479126	.	-	2	ID=CDS122;Parent=mRNA159
III	gt cds	CDS	1483404	1483467	.	-	0	ID=CDS122;Parent=mRNA159
III	gt csa	exon	1483404	1483497	1	-	.	Parent=mRNA159
III	gt csa	mRNA	1474973	1476685	.	-	.	ID=mRNA160;Parent=gene106;Target=yk500f5.5 1 360 +
III	gt csa	exon	1474973	1475099	1	-	.	Parent=mRNA160
III	gt cds	CDS	1474974	1475099	.	-	0	ID=CDS123;Parent=mRNA160
III	gt cds	CDS	1476256	1476435	.	-	0	ID=CDS123;Parent=mRNA160
III	gt csa	exon	1476256	1476485	0.989	-	.	Parent=mRNA160
III	gt csa	exon	1476684	1476685	1	-	.	Parent=mRNA160
###
III	gt csa	gene	1467866	1468169	.	+	.	ID=gene107
III	gt csa	mRNA	1467866	1468169	.	+	.	ID=mRNA161;Parent=gene107;Target=CEESH11F 1 304 +
III	gt csa	exon	1467866	1468169	0.984	+	.	Parent=mRNA161
###
III	gt csa	gene	1484961	1495320	.	-	.	ID=gene108
III	gt csa	mRNA	1484961	1495320	.	-	.	ID=mRNA162;Parent=gene108;Target=WP 1 418 +
III	gt csa	exon	1484961	1485116	1	-	.	Parent=mRNA162
III	gt cds	CDS	1484961	1485116	.	-	0	ID=CDS124;Parent=mRNA162
III	gt csa	exon	1487387	1487633	1	-	.	Parent=mRNA162
III	gt cds	CDS	1487387	1487633	.	-	1	ID=CDS124;Parent=mRNA162
III	gt csa	exon	1487730	1487831	1	-	.	Parent=mRNA162
III	gt cds	CDS	1487730	1487831	.	-	1	ID=CDS124;Parent=mRNA162
III	gt csa	exon	1490092	1490294	1	-	.	Parent=mRNA162
III	gt cds	CDS	1490092	1490294	.	-	0	ID=CDS124;Parent=mRNA162
III	gt csa	exon	1491404	1491494	1	-	.	Parent=mRNA162
III	gt cds	CDS	1491404	1491494	.	-	1	ID=CDS124;Parent=mRNA162
III	gt csa	exon	1491548	1491666	1	-	.	Parent=mRNA162
III	gt cds	CDS	1491548	1491666	.	-	0	ID=CDS124;Parent=mRNA162
III	gt csa	exon	1493719	1493970	1	-	.	Parent=mRNA162
III	gt cds	CDS	1493719	1493970	.	-	0	ID=CDS124;Parent=mRNA162
III	gt csa	exon	1495237	1495320	1	-	.	Parent=mRNA162
III	gt cds	CDS	1495237	1495320	.	-	0	ID=CDS124;Parent=mRNA162
###
III	gt csa	gene	1509455	1510895	.	+	.	ID=gene109
III	gt csa	mRNA	1509455	1510895	.	+	.	ID=mRNA163;Parent=gene109;Target=yk1187f01.3 1 381 +
III	gt csa	exon	1509455	1509613	0.855	+	.	Parent=mRNA163
III	gt csa	exon	1510265	1510335	0.817	+	.	Parent=mRNA163
III	gt csa	exon	1510742	1510895	0.916	+	.	Parent=mRNA163
###
III	gt csa	gene	1509574	1517983	.	-	.	ID=gene110
III	gt csa	mRNA	1509574	1512913	.	-	.	ID=mRNA164;Parent=gene110;Target=yk275e6.5 1 360 +,yk1146d12.3 1 312 -
III	gt csa	exon	1509574	1509618	0.978	-	.	Parent=mRNA164
III	gt cds	CDS	1509574	1509618	.	-	0	ID=CDS125;Parent=mRNA164
III	gt csa	exon	1510270	1510341	0.986	-	.	Parent=mRNA164
III	gt cds	CDS	1510270	1510341	.	-	0	ID=CDS125;Parent=mRNA164
III	gt cds	CDS	1510751	1510831	.	-	0	ID=CDS125;Parent=mRNA164
III	gt csa	exon	1510751	1510948	0.987	-	.	Parent=mRNA164
III	gt csa	exon	1512871	1512913	0.872	-	.	Parent=mRNA164
III	gt csa	mRNA	1512956	1517983	.	-	.	ID=mRNA165;Parent=gene110;Target=yk1146d12.5 35 612 +,yk774d03.5 23 597 +,yk479a10.5 1 378 +,yk237e8.5 1 360 +,yk714f9.5 23 365 +
III	gt csa	exon	1512956	1513125	1	-	.	Parent=mRNA165
III	gt cds	CDS	1512958	1513125	.	-	0	ID=CDS126;Parent=mRNA165
III	gt csa	exon	1515550	1515605	1	-	.	Parent=mRNA165
III	gt cds	CDS	1515550	1515605	.	-	2	ID=CDS126;Parent=mRNA165
III	gt csa	exon	1515725	1515894	1	-	.	Parent=mRNA165
III	gt cds	CDS	1515725	1515894	.	-	1	ID=CDS126;Parent=mRNA165
III	gt csa	exon	1517731	1517849	1	-	.	Parent=mRNA165
III	gt cds	CDS	1517731	1517849	.	-	0	ID=CDS126;Parent=mRNA165
III	gt csa	exon	1517921	1517983	1	-	.	Parent=mRNA165
III	gt cds	CDS	1517921	1517983	.	-	0	ID=CDS126;Parent=mRNA165
###
III	gt csa	gene	1520214	1532758	.	-	.	ID=gene111
III	gt csa	mRNA	1520214	1532758	.	-	.	ID=mRNA166;Parent=gene111;Target=AY661556 1 2145 +
III	gt csa	exon	1520214	1520363	1	-	.	Parent=mRNA166
III	gt cds	CDS	1520214	1520363	.	-	0	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1521573	1521926	1	-	.	Parent=mRNA166
III	gt cds	CDS	1521573	1521926	.	-	0	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1523142	1523685	1	-	.	Parent=mRNA166
III	gt cds	CDS	1523142	1523685	.	-	1	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1525164	1525402	1	-	.	Parent=mRNA166
III	gt cds	CDS	1525164	1525402	.	-	0	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1526403	1526535	1	-	.	Parent=mRNA166
III	gt cds	CDS	1526403	1526535	.	-	1	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1528084	1528234	1	-	.	Parent=mRNA166
III	gt cds	CDS	1528084	1528234	.	-	2	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1528291	1528435	1	-	.	Parent=mRNA166
III	gt cds	CDS	1528291	1528435	.	-	0	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1529809	1529984	1	-	.	Parent=mRNA166
III	gt cds	CDS	1529809	1529984	.	-	2	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1531762	1531821	1	-	.	Parent=mRNA166
III	gt cds	CDS	1531762	1531821	.	-	2	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1532182	1532275	1	-	.	Parent=mRNA166
III	gt cds	CDS	1532182	1532275	.	-	0	ID=CDS127;Parent=mRNA166
III	gt csa	exon	1532660	1532758	1	-	.	Parent=mRNA166
III	gt cds	CDS	1532660	1532758	.	-	0	ID=CDS127;Parent=mRNA166
III	gt csa	mRNA	1521343	1529982	.	-	.	ID=mRNA167;Parent=gene111;Target=BP 1 525 +
III	gt csa	exon	1521343	1521363	0.189	-	.	Parent=mRNA167
III	gt cds	CDS	1521352	1521363	.	-	0	ID=CDS128;Parent=mRNA167
III	gt csa	exon	1521573	1521926	0.879	-	.	Parent=mRNA167
III	gt cds	CDS	1521573	1521926	.	-	0	ID=CDS128;Parent=mRNA167
III	gt csa	exon	1523142	1523685	0.95	-	.	Parent=mRNA167
III	gt cds	CDS	1523142	1523685	.	-	1	ID=CDS128;Parent=mRNA167
III	gt csa	exon	1525164	1525402	0.893	-	.	Parent=mRNA167
III	gt cds	CDS	1525164	1525402	.	-	0	ID=CDS128;Parent=mRNA167
III	gt csa	exon	1526403	1526535	0.988	-	.	Parent=mRNA167
III	gt cds	CDS	1526403	1526535	.	-	1	ID=CDS128;Parent=mRNA167
III	gt csa	exon	1528323	1528435	1	-	.	Parent=mRNA167
III	gt cds	CDS	1528323	1528435	.	-	0	ID=CDS128;Parent=mRNA167
III	gt cds	CDS	1529809	1529913	.	-	0	ID=CDS128;Parent=mRNA167
III	gt csa	exon	1529809	1529982	0.921	-	.	Parent=mRNA167
III	gt csa	mRNA	1521569	1531828	.	-	.	ID=mRNA168;Parent=gene111;Target=RP 1 544 +
III	gt csa	exon	1521569	1521926	0.88	-	.	Parent=mRNA168
III	gt cds	CDS	1521570	1521926	.	-	0	ID=CDS129;Parent=mRNA168
III	gt csa	exon	1523142	1523685	0.947	-	.	Parent=mRNA168
III	gt cds	CDS	1523142	1523685	.	-	1	ID=CDS129;Parent=mRNA168
III	gt csa	exon	1525164	1525402	0.895	-	.	Parent=mRNA168
III	gt cds	CDS	1525164	1525402	.	-	0	ID=CDS129;Parent=mRNA168
III	gt csa	exon	1526403	1526535	0.969	-	.	Parent=mRNA168
III	gt cds	CDS	1526403	1526535	.	-	1	ID=CDS129;Parent=mRNA168
III	gt csa	exon	1528323	1528435	1	-	.	Parent=mRNA168
III	gt cds	CDS	1528323	1528435	.	-	0	ID=CDS129;Parent=mRNA168
III	gt cds	CDS	1529809	1529913	.	-	0	ID=CDS129;Parent=mRNA168
III	gt csa	exon	1529809	1529984	0.923	-	.	Parent=mRNA168
III	gt csa	exon	1531762	1531828	0.969	-	.	Parent=mRNA168
###
III	gt csa	gene	1537499	1538168	.	-	.	ID=gene112
III	gt csa	mRNA	1537499	1538168	.	-	.	ID=mRNA169;Parent=gene112;Target=yk1272b06.3 1 670 +
III	gt csa	exon	1537499	1538168	0.997	-	.	Parent=mRNA169
###
III	gt csa	gene	1540487	1543445	.	+	.	ID=gene113
III	gt csa	mRNA	1540487	1543445	.	+	.	ID=mRNA170;Parent=gene113;Target=yk427d4.5 1 361 +,yk630d2.5 1 376 +,RP 1 157 +,yk308b12.5 1 360 +,yk1375b08.3 1 496 -,yk1375b08.5 1 531 +,yk308b12.3 1 300 -,yk427d4.3 1 300 -
III	gt csa	exon	1540487	1540540	0.954	+	.	Parent=mRNA170
III	gt cds	CDS	1540496	1540540	.	+	0	ID=CDS130;Parent=mRNA170
III	gt csa	exon	1540708	1540869	1	+	.	Parent=mRNA170
III	gt cds	CDS	1540708	1540869	.	+	0	ID=CDS130;Parent=mRNA170
III	gt csa	exon	1541916	1542059	1	+	.	Parent=mRNA170
III	gt cds	CDS	1541916	1542059	.	+	0	ID=CDS130;Parent=mRNA170
III	gt cds	CDS	1543175	1543294	.	+	0	ID=CDS130;Parent=mRNA170
III	gt csa	exon	1543175	1543445	0.985	+	.	Parent=mRNA170
###
III	gt csa	gene	1544928	1554435	.	-	.	ID=gene114
III	gt csa	mRNA	1544928	1554435	.	-	.	ID=mRNA171;Parent=gene114;Target=CESAC53F 1 323 -,yk236c12.3 1 300 -,yk670g3.3 1 300 -,RP 1 723 +,BP 1 717 +,yk166a9.5 1 380 +,yk670g3.5 1 360 +,yk341h12.5 1 364 +
III	gt csa	exon	1544928	1545199	0.982	-	.	Parent=mRNA171
III	gt cds	CDS	1545025	1545199	.	-	1	ID=CDS131;Parent=mRNA171
III	gt csa	exon	1546519	1546675	0.932	-	.	Parent=mRNA171
III	gt cds	CDS	1546519	1546675	.	-	2	ID=CDS131;Parent=mRNA171
III	gt csa	exon	1547363	1547757	0.918	-	.	Parent=mRNA171
III	gt cds	CDS	1547363	1547757	.	-	1	ID=CDS131;Parent=mRNA171
III	gt csa	exon	1548432	1548499	0.924	-	.	Parent=mRNA171
III	gt cds	CDS	1548432	1548499	.	-	0	ID=CDS131;Parent=mRNA171
III	gt csa	exon	1549231	1549616	0.9	-	.	Parent=mRNA171
III	gt cds	CDS	1549231	1549616	.	-	2	ID=CDS131;Parent=mRNA171
III	gt csa	exon	1550539	1550735	0.873	-	.	Parent=mRNA171
III	gt cds	CDS	1550539	1550735	.	-	1	ID=CDS131;Parent=mRNA171
III	gt csa	exon	1551380	1551622	0.988	-	.	Parent=mRNA171
III	gt cds	CDS	1551380	1551622	.	-	1	ID=CDS131;Parent=mRNA171
III	gt csa	exon	1552597	1552760	1	-	.	Parent=mRNA171
III	gt cds	CDS	1552597	1552760	.	-	0	ID=CDS131;Parent=mRNA171
III	gt csa	exon	1552826	1552996	0.95	-	.	Parent=mRNA171
III	gt cds	CDS	1552826	1552996	.	-	0	ID=CDS131;Parent=mRNA171
III	gt cds	CDS	1554189	1554431	.	-	0	ID=CDS131;Parent=mRNA171
III	gt csa	exon	1554189	1554435	0.945	-	.	Parent=mRNA171
###
III	gt csa	gene	1555385	1560461	.	+	.	ID=gene115
III	gt csa	mRNA	1555385	1556102	.	+	.	ID=mRNA172;Parent=gene115;Target=yk1111d10.3 1 616 +,yk475g1.3 1 300 +,yk415h12.3 1 300 +,yk491d7.3 1 300 +,yk589g10.3 1 300 +,yk607b8.3 1 300 +,yk157b1.3 1 300 +
III	gt csa	exon	1555385	1556102	0.978	+	.	Parent=mRNA172
III	gt csa	mRNA	1558790	1560461	.	+	.	ID=mRNA173;Parent=gene115;Target=yk1371c11.5 23 357 +,yk1030d09.5 23 357 +,yk1508a02.5 23 521 +,yk1540b10.5 23 524 +,yk1532h03.5 23 561 +,yk1371c12.5 23 602 +,yk1364c12.5 23 604 +,yk1395h09.5 22 605 +,yk1377c09.5 23 614 +,yk498e1.5 1 360 +
III	gt csa	exon	1558790	1558898	1	+	.	Parent=mRNA173
III	gt cds	CDS	1558872	1558898	.	+	0	ID=CDS132;Parent=mRNA173
III	gt csa	exon	1558949	1559033	1	+	.	Parent=mRNA173
III	gt cds	CDS	1558949	1559033	.	+	0	ID=CDS132;Parent=mRNA173
III	gt csa	exon	1559100	1559240	1	+	.	Parent=mRNA173
III	gt cds	CDS	1559100	1559240	.	+	2	ID=CDS132;Parent=mRNA173
III	gt csa	exon	1560205	1560461	1	+	.	Parent=mRNA173
III	gt cds	CDS	1560205	1560461	.	+	2	ID=CDS132;Parent=mRNA173
###
III	gt csa	gene	1555397	1558519	.	-	.	ID=gene116
III	gt csa	mRNA	1555397	1558519	.	-	.	ID=mRNA174;Parent=gene116;Target=yk1111d10.5 1 607 +,yk607b8.5 1 377 +,yk1518a06.3 1 610 -,yk475g1.5 1 360 +,yk415h12.5 1 360 +,yk1518a06.5 23 582 +,CK580339 1 480 +,yk491d7.5 1 360 +,yk236h2.5 1 360 +,yk157b1.5 16 384 +,yk589g10.5 1 360 +
III	gt csa	exon	1555397	1556159	1	-	.	Parent=mRNA174
III	gt cds	CDS	1555819	1556159	.	-	2	ID=CDS133;Parent=mRNA174
III	gt csa	exon	1557562	1557862	1	-	.	Parent=mRNA174
III	gt cds	CDS	1557562	1557862	.	-	0	ID=CDS133;Parent=mRNA174
III	gt csa	exon	1558159	1558268	1	-	.	Parent=mRNA174
III	gt cds	CDS	1558159	1558268	.	-	2	ID=CDS133;Parent=mRNA174
III	gt csa	exon	1558323	1558397	1	-	.	Parent=mRNA174
III	gt cds	CDS	1558323	1558397	.	-	2	ID=CDS133;Parent=mRNA174
III	gt cds	CDS	1558446	1558512	.	-	0	ID=CDS133;Parent=mRNA174
III	gt csa	exon	1558446	1558519	1	-	.	Parent=mRNA174
###
III	gt csa	gene	1563434	1577849	.	+	.	ID=gene117
III	gt csa	mRNA	1563434	1570107	.	+	.	ID=mRNA175;Parent=gene117;Target=yk1532h03.3 1 751 -,yk1364c12.3 1 710 -,yk1377c09.3 1 708 -,yk1030d09.3 1 689 -,yk1508a02.3 1 658 -,yk1540b10.3 1 642 -,yk1371c11.3 1 611 -,yk1371c12.3 1 550 -,yk1395h09.3 1 549 -
III	gt csa	exon	1563434	1563617	0.97	+	.	Parent=mRNA175
III	gt cds	CDS	1563492	1563617	.	+	0	ID=CDS134;Parent=mRNA175
III	gt csa	exon	1564968	1565122	0.994	+	.	Parent=mRNA175
III	gt cds	CDS	1564968	1565122	.	+	0	ID=CDS134;Parent=mRNA175
III	gt csa	exon	1565383	1565545	0.994	+	.	Parent=mRNA175
III	gt cds	CDS	1565383	1565545	.	+	1	ID=CDS134;Parent=mRNA175
III	gt cds	CDS	1569746	1569841	.	+	0	ID=CDS134;Parent=mRNA175
III	gt csa	exon	1569746	1570107	0.983	+	.	Parent=mRNA175
III	gt csa	mRNA	1570296	1573761	.	+	.	ID=mRNA176;Parent=gene117;Target=yk267a5.5 1 376 +,yk832e07.5 23 479 +,yk1755e04.5 22 536 +,yk1344g03.5 24 566 +,yk1736b09.5 24 568 +,yk1654g06.5 25 578 +,yk1672c02.5 24 581 +,yk1648c12.5 24 586 +,yk1743a02.5 23 609 +,yk1365e09.5 23 634 +,yk1618f02.5 15 652 +,yk1612a04.5 1 398 +,yk548h9.5 1 372 +
III	gt csa	exon	1570296	1570429	1	+	.	Parent=mRNA176
III	gt cds	CDS	1570314	1570429	.	+	0	ID=CDS135;Parent=mRNA176
III	gt csa	exon	1571414	1571483	1	+	.	Parent=mRNA176
III	gt cds	CDS	1571414	1571483	.	+	1	ID=CDS135;Parent=mRNA176
III	gt csa	exon	1571534	1571764	1	+	.	Parent=mRNA176
III	gt cds	CDS	1571534	1571764	.	+	0	ID=CDS135;Parent=mRNA176
III	gt csa	exon	1572543	1572694	1	+	.	Parent=mRNA176
III	gt cds	CDS	1572543	1572694	.	+	0	ID=CDS135;Parent=mRNA176
III	gt csa	exon	1572790	1572997	1	+	.	Parent=mRNA176
III	gt cds	CDS	1572790	1572997	.	+	1	ID=CDS135;Parent=mRNA176
III	gt cds	CDS	1573737	1573760	.	+	0	ID=CDS135;Parent=mRNA176
III	gt csa	exon	1573737	1573761	1	+	.	Parent=mRNA176
III	gt csa	mRNA	1573827	1576628	.	+	.	ID=mRNA177;Parent=gene117;Target=yk1618f02.3 1 742 -,yk1755e04.3 1 743 -,yk1344g03.3 1 711 -,yk1736b09.3 1 649 -,yk1365e09.3 1 704 -,yk1654g06.3 1 694 -,yk1672c02.3 21 686 -,yk1612a04.3 1 663 -,yk1743a02.3 1 617 -,yk1648c12.3 1 629 -,yk832e07.3 1 524 -,yk1235d02.3 1 465 -,yk605e4.3 1 300 -
III	gt csa	exon	1573827	1573915	0.989	+	.	Parent=mRNA177
III	gt csa	exon	1574217	1574376	1	+	.	Parent=mRNA177
III	gt cds	CDS	1574269	1574376	.	+	0	ID=CDS136;Parent=mRNA177
III	gt csa	exon	1574938	1575034	1	+	.	Parent=mRNA177
III	gt cds	CDS	1574938	1575034	.	+	0	ID=CDS136;Parent=mRNA177
III	gt csa	exon	1575084	1575161	1	+	.	Parent=mRNA177
III	gt cds	CDS	1575084	1575161	.	+	2	ID=CDS136;Parent=mRNA177
III	gt csa	exon	1576071	1576198	1	+	.	Parent=mRNA177
III	gt cds	CDS	1576071	1576198	.	+	2	ID=CDS136;Parent=mRNA177
III	gt cds	CDS	1576416	1576529	.	+	0	ID=CDS136;Parent=mRNA177
III	gt csa	exon	1576416	1576628	0.995	+	.	Parent=mRNA177
III	gt csa	mRNA	1573884	1576610	.	+	.	ID=mRNA178;Parent=gene117;Target=yk1154b02.3 1 687 -,yk446d1.5 1 234 +,yk1235d02.3 1 465 -,yk605e4.3 1 300 -
III	gt csa	exon	1573884	1573915	1	+	.	Parent=mRNA178
III	gt csa	exon	1574217	1574257	1	+	.	Parent=mRNA178
III	gt csa	exon	1574822	1575034	0.995	+	.	Parent=mRNA178
III	gt csa	exon	1575084	1575161	1	+	.	Parent=mRNA178
III	gt csa	exon	1576071	1576198	1	+	.	Parent=mRNA178
III	gt cds	CDS	1576091	1576198	.	+	0	ID=CDS137;Parent=mRNA178
III	gt cds	CDS	1576416	1576529	.	+	0	ID=CDS137;Parent=mRNA178
III	gt csa	exon	1576416	1576610	1	+	.	Parent=mRNA178
III	gt csa	mRNA	1576754	1577849	.	+	.	ID=mRNA179;Parent=gene117;Target=yk423d1.5 1 360 +
III	gt csa	exon	1576754	1576868	0.974	+	.	Parent=mRNA179
III	gt cds	CDS	1576826	1576868	.	+	0	ID=CDS138;Parent=mRNA179
III	gt csa	exon	1577605	1577849	1	+	.	Parent=mRNA179
III	gt cds	CDS	1577605	1577849	.	+	2	ID=CDS138;Parent=mRNA179
###
III	gt csa	gene	1569814	1570053	.	-	.	ID=gene118
III	gt csa	mRNA	1569814	1570053	.	-	.	ID=mRNA180;Parent=gene118;Target=yk252b6.3 1 240 +
III	gt csa	exon	1569814	1570053	0.938	-	.	Parent=mRNA180
###
III	gt csa	gene	1579272	1580784	.	+	.	ID=gene119
III	gt csa	mRNA	1579272	1580784	.	+	.	ID=mRNA181;Parent=gene119;Target=yk672c6.3 1 300 -,yk423d1.3 1 300 -
III	gt csa	exon	1579272	1579319	1	+	.	Parent=mRNA181
III	gt cds	CDS	1579299	1579319	.	+	0	ID=CDS139;Parent=mRNA181
III	gt cds	CDS	1580527	1580757	.	+	0	ID=CDS139;Parent=mRNA181
III	gt csa	exon	1580527	1580784	1	+	.	Parent=mRNA181
###
III	gt csa	gene	1583146	1584881	.	-	.	ID=gene120
III	gt csa	mRNA	1583146	1584881	.	-	.	ID=mRNA182;Parent=gene120;Target=yk1513e11.5 1 611 +,yk1513e11.3 1 577 -,yk378b9.5 1 376 +,yk102a5.5 1 360 +
III	gt csa	exon	1583146	1583491	1	-	.	Parent=mRNA182
III	gt cds	CDS	1583459	1583491	.	-	0	ID=CDS140;Parent=mRNA182
III	gt cds	CDS	1584617	1584877	.	-	0	ID=CDS140;Parent=mRNA182
III	gt csa	exon	1584617	1584881	0.992	-	.	Parent=mRNA182
###
III	gt csa	gene	1583159	1583488	.	+	.	ID=gene121
III	gt csa	mRNA	1583159	1583488	.	+	.	ID=mRNA183;Parent=gene121;Target=yk102a5.3 1 315 +,yk378b9.3 1 279 +
III	gt csa	exon	1583159	1583488	0.957	+	.	Parent=mRNA183
###
III	gt csa	gene	1605742	1606803	.	+	.	ID=gene122
III	gt csa	mRNA	1605742	1606803	.	+	.	ID=mRNA184;Parent=gene122;Target=BP 1 152 +
III	gt csa	exon	1605742	1605953	0.982	+	.	Parent=mRNA184
III	gt cds	CDS	1605847	1605953	.	+	0	ID=CDS141;Parent=mRNA184
III	gt csa	exon	1606445	1606556	0.751	+	.	Parent=mRNA184
III	gt cds	CDS	1606445	1606556	.	+	1	ID=CDS141;Parent=mRNA184
III	gt csa	exon	1606672	1606803	1	+	.	Parent=mRNA184
III	gt cds	CDS	1606672	1606803	.	+	0	ID=CDS141;Parent=mRNA184
III	gt csa	mRNA	1605745	1606803	.	+	.	ID=mRNA185;Parent=gene122;Target=RP 1 142 +
III	gt csa	exon	1605745	1605953	0.983	+	.	Parent=mRNA185
III	gt cds	CDS	1605847	1605953	.	+	0	ID=CDS142;Parent=mRNA185
III	gt csa	exon	1606472	1606556	0.972	+	.	Parent=mRNA185
III	gt cds	CDS	1606472	1606556	.	+	1	ID=CDS142;Parent=mRNA185
III	gt csa	exon	1606672	1606803	1	+	.	Parent=mRNA185
III	gt cds	CDS	1606672	1606803	.	+	0	ID=CDS142;Parent=mRNA185
###
III	gt csa	gene	1606834	1610636	.	-	.	ID=gene123
III	gt csa	mRNA	1606834	1609423	.	-	.	ID=mRNA186;Parent=gene123;Target=yk1416d09.3 1 705 -,yk1362f07.3 1 706 -,yk1547d11.3 1 703 -,yk517d4.3 1 300 -,yk539b10.3 1 300 -,yk579b9.3 1 172 -
III	gt csa	exon	1606834	1606880	0.979	-	.	Parent=mRNA186
III	gt csa	exon	1606929	1607019	1	-	.	Parent=mRNA186
III	gt cds	CDS	1606983	1607019	.	-	1	ID=CDS143;Parent=mRNA186
III	gt csa	exon	1607623	1607756	1	-	.	Parent=mRNA186
III	gt cds	CDS	1607623	1607756	.	-	0	ID=CDS143;Parent=mRNA186
III	gt csa	exon	1607809	1608154	1	-	.	Parent=mRNA186
III	gt cds	CDS	1607809	1608154	.	-	1	ID=CDS143;Parent=mRNA186
III	gt cds	CDS	1609334	1609368	.	-	0	ID=CDS143;Parent=mRNA186
III	gt csa	exon	1609334	1609423	1	-	.	Parent=mRNA186
III	gt csa	mRNA	1609706	1610636	.	-	.	ID=mRNA187;Parent=gene123;Target=yk539b10.5 1 360 +
III	gt csa	exon	1609706	1609870	0.994	-	.	Parent=mRNA187
III	gt cds	CDS	1609708	1609870	.	-	1	ID=CDS144;Parent=mRNA187
III	gt cds	CDS	1610442	1610491	.	-	0	ID=CDS144;Parent=mRNA187
III	gt csa	exon	1610442	1610636	1	-	.	Parent=mRNA187
###
III	gt csa	gene	1611351	1614022	.	-	.	ID=gene124
III	gt csa	mRNA	1611351	1614022	.	-	.	ID=mRNA188;Parent=gene124;Target=yk1547d11.5 1 438 +,yk1416d09.5 23 573 +,yk1362f07.5 23 549 +,yk517d4.5 1 360 +
III	gt csa	exon	1611351	1611537	1	-	.	Parent=mRNA188
III	gt cds	CDS	1611352	1611537	.	-	0	ID=CDS145;Parent=mRNA188
III	gt csa	exon	1612158	1612264	1	-	.	Parent=mRNA188
III	gt cds	CDS	1612158	1612264	.	-	2	ID=CDS145;Parent=mRNA188
III	gt csa	exon	1612870	1613031	1	-	.	Parent=mRNA188
III	gt cds	CDS	1612870	1613031	.	-	2	ID=CDS145;Parent=mRNA188
III	gt cds	CDS	1613520	1614015	.	-	0	ID=CDS145;Parent=mRNA188
III	gt csa	exon	1613520	1614022	1	-	.	Parent=mRNA188
###
III	gt csa	gene	1617126	1618924	.	-	.	ID=gene125
III	gt csa	mRNA	1617126	1618924	.	-	.	ID=mRNA189;Parent=gene125;Target=CK589550 1 323 +,BP 1 109 +,RP 1 109 +,yk81b11.5 1 330 +,yk175h6.5 1 222 +
III	gt csa	exon	1617126	1617142	0.647	-	.	Parent=mRNA189
III	gt csa	exon	1617362	1617429	0.956	-	.	Parent=mRNA189
III	gt cds	CDS	1617364	1617429	.	-	0	ID=CDS146;Parent=mRNA189
III	gt csa	exon	1618260	1618379	1	-	.	Parent=mRNA189
III	gt cds	CDS	1618260	1618379	.	-	0	ID=CDS146;Parent=mRNA189
III	gt csa	exon	1618719	1618832	0.991	-	.	Parent=mRNA189
III	gt cds	CDS	1618719	1618832	.	-	0	ID=CDS146;Parent=mRNA189
III	gt cds	CDS	1618885	1618911	.	-	0	ID=CDS146;Parent=mRNA189
III	gt csa	exon	1618885	1618924	0.975	-	.	Parent=mRNA189
III	gt csa	mRNA	1617142	1618924	.	-	.	ID=mRNA190;Parent=gene125;Target=yk1213c04.5 23 578 +,yk762h06.5 23 577 +,yk62a4.3 1 298 -,yk1597b03.3 164 675 -,yk1378f10.3 23 532 -,yk1213c04.3 23 531 -,yk341e7.3 1 300 -,yk762h06.3 1 322 -,yk333g8.3 1 300 -,yk289b11.3 1 300 -,yk1491d07.5 9 502 +,yk603g6.3 1 300 -,yk140f8.3 1 300 -,yk383e5.3 1 300 -,yk642a2.3 1 300 -,yk607b2.3 1 300 -,yk1410e10.5 9 492 +,yk1410e10.3 9 482 -,yk1491d07.3 9 481 -,yk342g4.3 1 300 -,yk383e5.5 1 386 +,yk140f8.5 1 381 +,yk599a12.5 1 360 +,yk494f1.5 1 360 +,yk342g4.5 1 377 +,yk333g8.5 1 360 +,yk452a10.5 1 360 +,yk642a2.5 1 376 +,yk603g6.5 1 360 +,yk607b2.5 1 376 +,yk341e7.5 1 372 +,yk289b11.5 13 375 +,BP 1 109 +,RP 1 109 +,yk81b11.5 1 330 +,yk175h6.5 1 222 +
III	gt csa	exon	1617142	1617429	1	-	.	Parent=mRNA190
III	gt cds	CDS	1617364	1617429	.	-	0	ID=CDS147;Parent=mRNA190
III	gt csa	exon	1618260	1618379	1	-	.	Parent=mRNA190
III	gt cds	CDS	1618260	1618379	.	-	0	ID=CDS147;Parent=mRNA190
III	gt csa	exon	1618719	1618832	1	-	.	Parent=mRNA190
III	gt cds	CDS	1618719	1618832	.	-	0	ID=CDS147;Parent=mRNA190
III	gt cds	CDS	1618885	1618911	.	-	0	ID=CDS147;Parent=mRNA190
III	gt csa	exon	1618885	1618924	0.975	-	.	Parent=mRNA190
III	gt csa	mRNA	1617181	1618918	.	-	.	ID=mRNA191;Parent=gene125;Target=yk1405h09.3 1 391 -,yk1405h09.5 23 302 +
III	gt csa	exon	1617181	1617429	0.972	-	.	Parent=mRNA191
III	gt cds	CDS	1617279	1617429	.	-	1	ID=CDS148;Parent=mRNA191
III	gt csa	exon	1618260	1618267	1	-	.	Parent=mRNA191
III	gt cds	CDS	1618260	1618267	.	-	0	ID=CDS148;Parent=mRNA191
III	gt csa	exon	1618731	1618832	1	-	.	Parent=mRNA191
III	gt cds	CDS	1618731	1618832	.	-	0	ID=CDS148;Parent=mRNA191
III	gt cds	CDS	1618885	1618911	.	-	0	ID=CDS148;Parent=mRNA191
III	gt csa	exon	1618885	1618918	1	-	.	Parent=mRNA191
###
III	gt csa	gene	1617159	1617431	.	+	.	ID=gene126
III	gt csa	mRNA	1617159	1617431	.	+	.	ID=mRNA192;Parent=gene126;Target=yk81b11.3 1 120 +,yk599a12.3 1 229 +
III	gt csa	exon	1617159	1617431	0.987	+	.	Parent=mRNA192
###
III	gt csa	gene	1619718	1625773	.	+	.	ID=gene127
III	gt csa	mRNA	1619718	1623324	.	+	.	ID=mRNA193;Parent=gene127;Target=yk515d7.5 1 369 +,yk1371g11.5 1 457 +,yk1502h06.5 23 475 +,yk1315f04.5 23 476 +,yk769d02.5 23 487 +,yk1620h12.5 23 600 +,yk566g5.5 1 360 +,yk434a10.5 1 374 +,yk416a11.5 1 240 +,yk413g4.5 1 360 +,yk458a7.5 1 360 +,yk498g8.5 1 360 +,yk344h2.5 1 360 +,yk416f6.5 1 360 +,yk432a10.5 1 360 +,yk638c1.5 1 360 +,yk631h7.5 1 360 +,yk538g9.5 1 360 +,yk499e12.5 1 360 +,yk678h2.5 1 360 +,yk534c9.5 1 360 +,yk591c9.5 1 360 +,yk629b10.5 1 360 +,yk460e6.5 1 360 +,yk668e7.5 1 240 +,yk586g3.5 1 360 +,yk394h5.5 1 360 +,yk542c5.5 1 360 +
III	gt csa	exon	1619718	1619894	0.972	+	.	Parent=mRNA193
III	gt cds	CDS	1619748	1619894	.	+	0	ID=CDS149;Parent=mRNA193
III	gt csa	exon	1620044	1620352	1	+	.	Parent=mRNA193
III	gt cds	CDS	1620044	1620352	.	+	0	ID=CDS149;Parent=mRNA193
III	gt cds	CDS	1623213	1623323	.	+	0	ID=CDS149;Parent=mRNA193
III	gt csa	exon	1623213	1623324	1	+	.	Parent=mRNA193
III	gt csa	mRNA	1619718	1625773	.	+	.	ID=mRNA194;Parent=gene127;Target=yk515d7.5 1 369 +,L36035 1 1781 +,yk1614a02.5 1 633 +,yk1371g11.5 1 457 +,yk761g06.5 1 588 +,yk1502h06.5 23 475 +,yk1315f04.5 23 476 +,yk769d02.5 23 487 +,yk1545g12.5 23 531 +,yk1421h01.5 23 532 +,yk1399b07.5 23 533 +,yk1651f03.5 23 569 +,yk1664c02.5 22 568 +,yk1696f05.5 23 570 +,yk1528f03.5 23 570 +,yk1741c08.5 23 571 +,yk1444d01.5 23 571 +,yk1500h01.5 23 571 +,yk1645f10.5 23 572 +,yk1695g01.5 23 572 +,yk1592g09.5 23 572 +,yk1526g10.5 22 573 +,yk1522d12.5 21 573 +,yk1387h03.5 22 574 +,yk1526h01.5 23 575 +,yk1493d05.5 23 577 +,yk1363e02.5 23 577 +,yk1657c03.5 23 578 +,yk816g12.5 23 581 +,yk566g5.5 1 360 +,yk434a10.5 1 374 +,yk416a11.5 1 240 +,yk413g4.5 1 360 +,yk458a7.5 1 360 +,yk498g8.5 1 360 +,RP 1 568 +,BP 1 568 +,yk344h2.5 1 360 +,yk416f6.5 1 360 +,yk432a10.5 1 360 +,yk638c1.5 1 360 +,yk631h7.5 1 360 +,yk538g9.5 1 360 +,yk499e12.5 1 360 +,yk678h2.5 1 360 +,yk534c9.5 1 360 +,yk591c9.5 1 360 +,yk629b10.5 1 360 +,yk460e6.5 1 360 +,yk668e7.5 1 240 +,yk586g3.5 1 360 +,yk394h5.5 1 360 +,yk755a01.5 1 538 +,yk542c5.5 1 360 +,yk1004c09.5 1 603 +,AJ270981 1 670 +,yk455e6.5 1 360 +,yk405a9.5 1 360 +,yk343g7.5 1 360 +,CB104502 83 407 +,yk257b9.5 1 375 +,yk545c7.5 1 360 +,yk7b1.5 1 359 +,cm9c7.5 1 402 +,CEMSF82F 1 211 -,yk1315f04.3 1 607 -,yk1645f10.3 1 675 -,yk1528f03.3 1 674 -,yk1500h01.3 1 644 -,yk20e11.5 1 300 +,yk272b10.5 1 360 +,yk221g12.5 1 240 +
III	gt csa	exon	1619718	1619894	0.972	+	.	Parent=mRNA194
III	gt cds	CDS	1619748	1619894	.	+	0	ID=CDS150;Parent=mRNA194
III	gt csa	exon	1620044	1620352	1	+	.	Parent=mRNA194
III	gt cds	CDS	1620044	1620352	.	+	0	ID=CDS150;Parent=mRNA194
III	gt csa	exon	1621416	1621808	0.997	+	.	Parent=mRNA194
III	gt cds	CDS	1621416	1621808	.	+	0	ID=CDS150;Parent=mRNA194
III	gt csa	exon	1623048	1623425	1	+	.	Parent=mRNA194
III	gt cds	CDS	1623048	1623425	.	+	0	ID=CDS150;Parent=mRNA194
III	gt csa	exon	1624423	1624740	1	+	.	Parent=mRNA194
III	gt cds	CDS	1624423	1624740	.	+	0	ID=CDS150;Parent=mRNA194
III	gt cds	CDS	1625234	1625395	.	+	0	ID=CDS150;Parent=mRNA194
III	gt csa	exon	1625234	1625773	0.959	+	.	Parent=mRNA194
III	gt csa	mRNA	1619718	1625773	.	+	.	ID=mRNA195;Parent=gene127;Target=yk515d7.5 1 369 +,yk1614a02.5 1 633 +,yk1371g11.5 1 457 +,yk761g06.5 1 588 +,yk1502h06.5 23 475 +,yk1315f04.5 23 476 +,yk769d02.5 23 487 +,yk1545g12.5 23 531 +,yk1421h01.5 23 532 +,yk1399b07.5 23 533 +,yk1651f03.5 23 569 +,yk1664c02.5 22 568 +,yk1696f05.5 23 570 +,yk1528f03.5 23 570 +,yk1741c08.5 23 571 +,yk1444d01.5 23 571 +,yk1500h01.5 23 571 +,yk1645f10.5 23 572 +,yk1695g01.5 23 572 +,yk1592g09.5 23 572 +,yk1526g10.5 22 573 +,yk1522d12.5 21 573 +,yk1387h03.5 22 574 +,yk1526h01.5 23 575 +,yk1493d05.5 23 577 +,yk1363e02.5 23 577 +,yk1657c03.5 23 578 +,yk816g12.5 23 581 +,yk566g5.5 1 360 +,yk434a10.5 1 374 +,yk416a11.5 1 240 +,yk413g4.5 1 360 +,yk458a7.5 1 360 +,yk498g8.5 1 360 +,yk344h2.5 1 360 +,yk416f6.5 1 360 +,yk432a10.5 1 360 +,yk638c1.5 1 360 +,yk631h7.5 1 360 +,yk538g9.5 1 360 +,yk499e12.5 1 360 +,yk678h2.5 1 360 +,yk534c9.5 1 360 +,yk591c9.5 1 360 +,yk629b10.5 1 360 +,yk460e6.5 1 360 +,yk668e7.5 1 240 +,yk586g3.5 1 360 +,yk394h5.5 1 360 +,yk755a01.5 1 538 +,yk542c5.5 1 360 +,yk777d06.5 1 646 +,cm9c7.5 1 402 +,CEMSF82F 1 211 -,yk1315f04.3 1 607 -,yk1645f10.3 1 675 -,yk1528f03.3 1 674 -,yk1500h01.3 1 644 -,yk20e11.5 1 300 +,yk272b10.5 1 360 +,yk221g12.5 1 240 +
III	gt csa	exon	1619718	1619894	0.972	+	.	Parent=mRNA195
III	gt cds	CDS	1619748	1619894	.	+	0	ID=CDS151;Parent=mRNA195
III	gt csa	exon	1620044	1620352	1	+	.	Parent=mRNA195
III	gt cds	CDS	1620044	1620352	.	+	0	ID=CDS151;Parent=mRNA195
III	gt csa	exon	1621416	1621679	1	+	.	Parent=mRNA195
III	gt cds	CDS	1621416	1621679	.	+	0	ID=CDS151;Parent=mRNA195
III	gt csa	exon	1623279	1623425	1	+	.	Parent=mRNA195
III	gt cds	CDS	1623279	1623425	.	+	0	ID=CDS151;Parent=mRNA195
III	gt csa	exon	1624423	1624740	0.958	+	.	Parent=mRNA195
III	gt cds	CDS	1624423	1624740	.	+	0	ID=CDS151;Parent=mRNA195
III	gt cds	CDS	1625234	1625395	.	+	0	ID=CDS151;Parent=mRNA195
III	gt csa	exon	1625234	1625773	0.959	+	.	Parent=mRNA195
###
III	gt csa	gene	1623119	1625784	.	-	.	ID=gene128
III	gt csa	mRNA	1623119	1623227	.	-	.	ID=mRNA196;Parent=gene128;Target=yk125c12.5 1 111 +
III	gt csa	exon	1623119	1623227	0.872	-	.	Parent=mRNA196
III	gt csa	mRNA	1625267	1625784	.	-	.	ID=mRNA197;Parent=gene128;Target=yk755a01.3 1 509 +,yk1371g11.3 1 500 +,yk1741c08.3 1 502 +,yk1620h12.3 1 499 +,yk1522d12.3 1 505 +,yk1592g09.3 1 484 +,yk1502h06.3 1 491 +,yk1651f03.3 1 490 +,yk1545g12.3 1 481 +,yk1526h01.3 1 487 +,yk1664c02.3 1 489 +,yk1614a02.3 1 489 +,yk1657c03.3 1 488 +,yk1696f05.3 1 489 +,yk1493d05.3 1 490 +,yk777d06.3 1 470 +,yk769d02.3 1 474 +,yk816g12.3 1 487 +,yk1004c09.3 1 455 +,yk1399b07.3 1 434 +,yk1363e02.3 1 430 +,yk1695g01.3 1 430 +,yk1387h03.3 1 430 +
III	gt csa	exon	1625267	1625784	0.904	-	.	Parent=mRNA197
###
III	gt csa	gene	1626655	1629966	.	+	.	ID=gene129
III	gt csa	mRNA	1626655	1629966	.	+	.	ID=mRNA198;Parent=gene129;Target=yk473d1.5 1 360 +
III	gt csa	exon	1626655	1626760	0.976	+	.	Parent=mRNA198
III	gt cds	CDS	1626661	1626760	.	+	0	ID=CDS152;Parent=mRNA198
III	gt csa	exon	1629399	1629553	0.994	+	.	Parent=mRNA198
III	gt cds	CDS	1629399	1629553	.	+	2	ID=CDS152;Parent=mRNA198
III	gt cds	CDS	1629869	1629964	.	+	0	ID=CDS152;Parent=mRNA198
III	gt csa	exon	1629869	1629966	0.99	+	.	Parent=mRNA198
###
III	gt csa	gene	1630786	1634440	.	-	.	ID=gene130
III	gt csa	mRNA	1630786	1634440	.	-	.	ID=mRNA199;Parent=gene130;Target=yk1400h01.3 1 669 -,yk1673f09.3 1 729 -,WP 1 505 +,yk1400h01.5 1 601 +
III	gt csa	exon	1630786	1630944	1	-	.	Parent=mRNA199
III	gt cds	CDS	1630807	1630944	.	-	0	ID=CDS153;Parent=mRNA199
III	gt csa	exon	1630996	1631105	1	-	.	Parent=mRNA199
III	gt cds	CDS	1630996	1631105	.	-	2	ID=CDS153;Parent=mRNA199
III	gt csa	exon	1631542	1631671	1	-	.	Parent=mRNA199
III	gt cds	CDS	1631542	1631671	.	-	0	ID=CDS153;Parent=mRNA199
III	gt csa	exon	1632010	1632261	1	-	.	Parent=mRNA199
III	gt cds	CDS	1632010	1632261	.	-	0	ID=CDS153;Parent=mRNA199
III	gt csa	exon	1632410	1632578	1	-	.	Parent=mRNA199
III	gt cds	CDS	1632410	1632578	.	-	1	ID=CDS153;Parent=mRNA199
III	gt csa	exon	1632625	1632755	1	-	.	Parent=mRNA199
III	gt cds	CDS	1632625	1632755	.	-	0	ID=CDS153;Parent=mRNA199
III	gt csa	exon	1632894	1633031	1	-	.	Parent=mRNA199
III	gt cds	CDS	1632894	1633031	.	-	0	ID=CDS153;Parent=mRNA199
III	gt csa	exon	1633206	1633356	1	-	.	Parent=mRNA199
III	gt cds	CDS	1633206	1633356	.	-	1	ID=CDS153;Parent=mRNA199
III	gt csa	exon	1633716	1633864	1	-	.	Parent=mRNA199
III	gt cds	CDS	1633716	1633864	.	-	0	ID=CDS153;Parent=mRNA199
III	gt csa	exon	1634294	1634440	1	-	.	Parent=mRNA199
III	gt cds	CDS	1634294	1634440	.	-	0	ID=CDS153;Parent=mRNA199
###
III	gt csa	gene	1636110	1637235	.	+	.	ID=gene131
III	gt csa	mRNA	1636110	1637235	.	+	.	ID=mRNA200;Parent=gene131;Target=yk473d1.3 1 300 -
III	gt csa	exon	1636110	1636349	0.95	+	.	Parent=mRNA200
III	gt cds	CDS	1636126	1636349	.	+	0	ID=CDS154;Parent=mRNA200
III	gt cds	CDS	1637174	1637234	.	+	1	ID=CDS154;Parent=mRNA200
III	gt csa	exon	1637174	1637235	0.984	+	.	Parent=mRNA200
###
III	gt csa	gene	1638270	1638592	.	-	.	ID=gene132
III	gt csa	mRNA	1638270	1638592	.	-	.	ID=mRNA201;Parent=gene132;Target=yk384f7.5 1 324 +
III	gt csa	exon	1638270	1638592	0.98	-	.	Parent=mRNA201
###
III	gt csa	gene	1641900	1642133	.	+	.	ID=gene133
III	gt csa	mRNA	1641900	1642133	.	+	.	ID=mRNA202;Parent=gene133;Target=yk296c8.3 1 221 +
III	gt csa	exon	1641900	1641940	0.878	+	.	Parent=mRNA202
III	gt csa	exon	1641952	1642133	0.846	+	.	Parent=mRNA202
###
III	gt csa	gene	1658190	1659850	.	-	.	ID=gene134
III	gt csa	mRNA	1658190	1659850	.	-	.	ID=mRNA203;Parent=gene134;Target=yk1658h08.5 1 538 +,yk1178b07.5 23 565 +,yk869h10.3 179 673 -,yk1658h08.3 1 488 -,yk1178b07.3 23 514 -,yk1004a04.3 102 584 -,yk1016a02.3 128 579 -
III	gt csa	exon	1658190	1658447	0.965	-	.	Parent=mRNA203
III	gt cds	CDS	1658265	1658447	.	-	0	ID=CDS155;Parent=mRNA203
III	gt cds	CDS	1659566	1659841	.	-	0	ID=CDS155;Parent=mRNA203
III	gt csa	exon	1659566	1659850	1	-	.	Parent=mRNA203
###
III	gt csa	gene	1667817	1668608	.	-	.	ID=gene135
III	gt csa	mRNA	1667817	1668608	.	-	.	ID=mRNA204;Parent=gene135;Target=WP 1 89 +,BP 1 75 +
III	gt csa	exon	1667817	1667916	1	-	.	Parent=mRNA204
III	gt cds	CDS	1667817	1667916	.	-	1	ID=CDS156;Parent=mRNA204
III	gt csa	exon	1667967	1668062	1	-	.	Parent=mRNA204
III	gt cds	CDS	1667967	1668062	.	-	1	ID=CDS156;Parent=mRNA204
III	gt csa	exon	1668538	1668608	1	-	.	Parent=mRNA204
III	gt cds	CDS	1668538	1668608	.	-	0	ID=CDS156;Parent=mRNA204
###
III	gt csa	gene	1672506	1672805	.	+	.	ID=gene136
III	gt csa	mRNA	1672506	1672805	.	+	.	ID=mRNA205;Parent=gene136;Target=yk204f5.3 1 300 +
III	gt csa	exon	1672506	1672805	0.97	+	.	Parent=mRNA205
###
III	gt csa	gene	1672790	1676716	.	-	.	ID=gene137
III	gt csa	mRNA	1672790	1676716	.	-	.	ID=mRNA206;Parent=gene137;Target=RP 1 300 +,yk204f5.5 1 360 +
III	gt csa	exon	1672790	1672941	0.778	-	.	Parent=mRNA206
III	gt cds	CDS	1672790	1672941	.	-	2	ID=CDS157;Parent=mRNA206
III	gt csa	exon	1673902	1674102	0.662	-	.	Parent=mRNA206
III	gt cds	CDS	1673902	1674102	.	-	2	ID=CDS157;Parent=mRNA206
III	gt csa	exon	1674163	1674368	0.916	-	.	Parent=mRNA206
III	gt cds	CDS	1674163	1674368	.	-	1	ID=CDS157;Parent=mRNA206
III	gt csa	exon	1675422	1675681	0.939	-	.	Parent=mRNA206
III	gt cds	CDS	1675422	1675681	.	-	0	ID=CDS157;Parent=mRNA206
III	gt cds	CDS	1676386	1676469	.	-	0	ID=CDS157;Parent=mRNA206
III	gt csa	exon	1676386	1676474	1	-	.	Parent=mRNA206
III	gt csa	exon	1676687	1676716	0.8	-	.	Parent=mRNA206
###
III	gt csa	gene	1683619	1688088	.	-	.	ID=gene138
III	gt csa	mRNA	1683619	1688088	.	-	.	ID=mRNA207;Parent=gene138;Target=WP 1 768 +
III	gt csa	exon	1683619	1683804	1	-	.	Parent=mRNA207
III	gt cds	CDS	1683619	1683804	.	-	0	ID=CDS158;Parent=mRNA207
III	gt csa	exon	1684468	1684619	1	-	.	Parent=mRNA207
III	gt cds	CDS	1684468	1684619	.	-	2	ID=CDS158;Parent=mRNA207
III	gt csa	exon	1684685	1684830	1	-	.	Parent=mRNA207
III	gt cds	CDS	1684685	1684830	.	-	1	ID=CDS158;Parent=mRNA207
III	gt csa	exon	1684885	1685265	1	-	.	Parent=mRNA207
III	gt cds	CDS	1684885	1685265	.	-	1	ID=CDS158;Parent=mRNA207
III	gt csa	exon	1686234	1686438	1	-	.	Parent=mRNA207
III	gt cds	CDS	1686234	1686438	.	-	2	ID=CDS158;Parent=mRNA207
III	gt csa	exon	1686481	1686665	1	-	.	Parent=mRNA207
III	gt cds	CDS	1686481	1686665	.	-	1	ID=CDS158;Parent=mRNA207
III	gt csa	exon	1687040	1688088	1	-	.	Parent=mRNA207
III	gt cds	CDS	1687040	1688088	.	-	0	ID=CDS158;Parent=mRNA207
###
III	gt csa	gene	1692070	1695095	.	-	.	ID=gene139
III	gt csa	mRNA	1692070	1695095	.	-	.	ID=mRNA208;Parent=gene139;Target=yk1146g09.3 1 616 -,WP 1 320 +
III	gt csa	exon	1692070	1692299	0.983	-	.	Parent=mRNA208
III	gt cds	CDS	1692130	1692299	.	-	2	ID=CDS159;Parent=mRNA208
III	gt csa	exon	1692347	1692704	1	-	.	Parent=mRNA208
III	gt cds	CDS	1692347	1692704	.	-	0	ID=CDS159;Parent=mRNA208
III	gt csa	exon	1692749	1692889	1	-	.	Parent=mRNA208
III	gt cds	CDS	1692749	1692889	.	-	0	ID=CDS159;Parent=mRNA208
III	gt csa	exon	1694480	1694576	1	-	.	Parent=mRNA208
III	gt cds	CDS	1694480	1694576	.	-	1	ID=CDS159;Parent=mRNA208
III	gt csa	exon	1694902	1695095	1	-	.	Parent=mRNA208
III	gt cds	CDS	1694902	1695095	.	-	0	ID=CDS159;Parent=mRNA208
###
III	gt csa	gene	1697210	1697895	.	+	.	ID=gene140
III	gt csa	mRNA	1697210	1697895	.	+	.	ID=mRNA209;Parent=gene140;Target=yk1108h12.3 1 685 +
III	gt csa	exon	1697210	1697895	0.997	+	.	Parent=mRNA209
###
III	gt csa	gene	1697728	1698972	.	-	.	ID=gene141
III	gt csa	mRNA	1697728	1698972	.	-	.	ID=mRNA210;Parent=gene141;Target=WP 1 305 +,yk1146g09.5 1 585 +
III	gt csa	exon	1697728	1697934	1	-	.	Parent=mRNA210
III	gt cds	CDS	1697728	1697934	.	-	0	ID=CDS160;Parent=mRNA210
III	gt csa	exon	1697997	1698621	1	-	.	Parent=mRNA210
III	gt cds	CDS	1697997	1698621	.	-	1	ID=CDS160;Parent=mRNA210
III	gt cds	CDS	1698827	1698909	.	-	0	ID=CDS160;Parent=mRNA210
III	gt csa	exon	1698827	1698972	1	-	.	Parent=mRNA210
###
III	gt csa	gene	1701749	1702396	.	-	.	ID=gene142
III	gt csa	mRNA	1701749	1702396	.	-	.	ID=mRNA211;Parent=gene142;Target=yk280d6.5 1 211 +
III	gt csa	exon	1701749	1701916	1	-	.	Parent=mRNA211
III	gt csa	exon	1702354	1702396	1	-	.	Parent=mRNA211
###
III	gt csa	gene	1703536	1705475	.	-	.	ID=gene143
III	gt csa	mRNA	1703536	1705475	.	-	.	ID=mRNA212;Parent=gene143;Target=WP 1 286 +
III	gt csa	exon	1703536	1703760	1	-	.	Parent=mRNA212
III	gt cds	CDS	1703536	1703760	.	-	0	ID=CDS161;Parent=mRNA212
III	gt csa	exon	1704360	1704909	1	-	.	Parent=mRNA212
III	gt cds	CDS	1704360	1704909	.	-	1	ID=CDS161;Parent=mRNA212
III	gt csa	exon	1705393	1705475	1	-	.	Parent=mRNA212
III	gt cds	CDS	1705393	1705475	.	-	0	ID=CDS161;Parent=mRNA212
###
III	gt csa	gene	1706545	1714620	.	+	.	ID=gene144
III	gt csa	mRNA	1706545	1713333	.	+	.	ID=mRNA213;Parent=gene144;Target=WP 1 1141 +
III	gt csa	exon	1706545	1707024	1	+	.	Parent=mRNA213
III	gt cds	CDS	1706545	1707024	.	+	0	ID=CDS162;Parent=mRNA213
III	gt csa	exon	1708672	1708784	1	+	.	Parent=mRNA213
III	gt cds	CDS	1708672	1708784	.	+	0	ID=CDS162;Parent=mRNA213
III	gt csa	exon	1710053	1710138	1	+	.	Parent=mRNA213
III	gt cds	CDS	1710053	1710138	.	+	1	ID=CDS162;Parent=mRNA213
III	gt csa	exon	1710199	1711458	1	+	.	Parent=mRNA213
III	gt cds	CDS	1710199	1711458	.	+	2	ID=CDS162;Parent=mRNA213
III	gt csa	exon	1711552	1712548	1	+	.	Parent=mRNA213
III	gt cds	CDS	1711552	1712548	.	+	2	ID=CDS162;Parent=mRNA213
III	gt csa	exon	1712599	1712789	1	+	.	Parent=mRNA213
III	gt cds	CDS	1712599	1712789	.	+	1	ID=CDS162;Parent=mRNA213
III	gt csa	exon	1712852	1712921	1	+	.	Parent=mRNA213
III	gt cds	CDS	1712852	1712921	.	+	2	ID=CDS162;Parent=mRNA213
III	gt csa	exon	1713108	1713333	1	+	.	Parent=mRNA213
III	gt cds	CDS	1713108	1713333	.	+	1	ID=CDS162;Parent=mRNA213
III	gt csa	mRNA	1713421	1714620	.	+	.	ID=mRNA214;Parent=gene144;Target=WP 1 351 +
III	gt csa	exon	1713421	1713545	1	+	.	Parent=mRNA214
III	gt cds	CDS	1713421	1713545	.	+	0	ID=CDS163;Parent=mRNA214
III	gt csa	exon	1713600	1713772	1	+	.	Parent=mRNA214
III	gt cds	CDS	1713600	1713772	.	+	1	ID=CDS163;Parent=mRNA214
III	gt csa	exon	1713817	1713953	1	+	.	Parent=mRNA214
III	gt cds	CDS	1713817	1713953	.	+	2	ID=CDS163;Parent=mRNA214
III	gt csa	exon	1714003	1714620	1	+	.	Parent=mRNA214
III	gt cds	CDS	1714003	1714620	.	+	0	ID=CDS163;Parent=mRNA214
###
III	gt csa	gene	1716518	1721899	.	-	.	ID=gene145
III	gt csa	mRNA	1716518	1721899	.	-	.	ID=mRNA215;Parent=gene145;Target=WP 1 1138 +
III	gt csa	exon	1716518	1716778	1	-	.	Parent=mRNA215
III	gt cds	CDS	1716518	1716778	.	-	0	ID=CDS164;Parent=mRNA215
III	gt csa	exon	1717664	1717815	1	-	.	Parent=mRNA215
III	gt cds	CDS	1717664	1717815	.	-	2	ID=CDS164;Parent=mRNA215
III	gt csa	exon	1717868	1718037	1	-	.	Parent=mRNA215
III	gt cds	CDS	1717868	1718037	.	-	1	ID=CDS164;Parent=mRNA215
III	gt csa	exon	1718081	1718509	1	-	.	Parent=mRNA215
III	gt cds	CDS	1718081	1718509	.	-	1	ID=CDS164;Parent=mRNA215
III	gt csa	exon	1718571	1718778	1	-	.	Parent=mRNA215
III	gt cds	CDS	1718571	1718778	.	-	2	ID=CDS164;Parent=mRNA215
III	gt csa	exon	1719192	1719264	0.909	-	.	Parent=mRNA215
III	gt cds	CDS	1719192	1719264	.	-	0	ID=CDS164;Parent=mRNA215
III	gt csa	exon	1719730	1719854	1	-	.	Parent=mRNA215
III	gt cds	CDS	1719730	1719854	.	-	2	ID=CDS164;Parent=mRNA215
III	gt csa	exon	1719904	1721899	1	-	.	Parent=mRNA215
III	gt cds	CDS	1719904	1721899	.	-	0	ID=CDS164;Parent=mRNA215
###
III	gt csa	gene	1723183	1733090	.	-	.	ID=gene146
III	gt csa	mRNA	1723183	1724814	.	-	.	ID=mRNA216;Parent=gene146;Target=CEESX92F 1 375 -,yk405f8.3 1 300 -,yk405f8.5 1 375 +
III	gt csa	exon	1723183	1723463	0.996	-	.	Parent=mRNA216
III	gt cds	CDS	1723354	1723463	.	-	2	ID=CDS165;Parent=mRNA216
III	gt csa	exon	1723517	1723621	1	-	.	Parent=mRNA216
III	gt cds	CDS	1723517	1723621	.	-	2	ID=CDS165;Parent=mRNA216
III	gt cds	CDS	1724588	1724756	.	-	0	ID=CDS165;Parent=mRNA216
III	gt csa	exon	1724588	1724814	0.969	-	.	Parent=mRNA216
III	gt csa	mRNA	1723183	1733090	.	-	.	ID=mRNA217;Parent=gene146;Target=CEESX92F 1 375 -,U15167 13 1528 +,yk793h08.3 1 731 -,yk1219f04.3 1 767 -,yk1236d10.3 1 706 -,yk405f8.3 1 300 -,BP 1 447 +,WP 1 446 +,yk793h08.5 23 628 +,yk1236d10.5 28 615 +
III	gt csa	exon	1723183	1723463	0.996	-	.	Parent=mRNA217
III	gt cds	CDS	1723354	1723463	.	-	2	ID=CDS166;Parent=mRNA217
III	gt csa	exon	1723517	1723621	1	-	.	Parent=mRNA217
III	gt cds	CDS	1723517	1723621	.	-	2	ID=CDS166;Parent=mRNA217
III	gt csa	exon	1724588	1724810	1	-	.	Parent=mRNA217
III	gt cds	CDS	1724588	1724810	.	-	0	ID=CDS166;Parent=mRNA217
III	gt csa	exon	1725626	1725883	1	-	.	Parent=mRNA217
III	gt cds	CDS	1725626	1725883	.	-	0	ID=CDS166;Parent=mRNA217
III	gt csa	exon	1728036	1728084	1	-	.	Parent=mRNA217
III	gt cds	CDS	1728036	1728084	.	-	1	ID=CDS166;Parent=mRNA217
III	gt csa	exon	1729126	1729418	1	-	.	Parent=mRNA217
III	gt cds	CDS	1729126	1729418	.	-	0	ID=CDS166;Parent=mRNA217
III	gt csa	exon	1732543	1732692	1	-	.	Parent=mRNA217
III	gt cds	CDS	1732543	1732692	.	-	0	ID=CDS166;Parent=mRNA217
III	gt cds	CDS	1732928	1733077	.	-	0	ID=CDS166;Parent=mRNA217
III	gt csa	exon	1732928	1733090	1	-	.	Parent=mRNA217
III	gt csa	mRNA	1723354	1733090	.	-	.	ID=mRNA218;Parent=gene146;Target=RP 1 309 +,yk793h08.5 23 628 +,yk1236d10.5 28 615 +
III	gt csa	exon	1723354	1723463	1	-	.	Parent=mRNA218
III	gt cds	CDS	1723354	1723463	.	-	2	ID=CDS167;Parent=mRNA218
III	gt csa	exon	1724588	1724810	0.796	-	.	Parent=mRNA218
III	gt cds	CDS	1724588	1724810	.	-	0	ID=CDS167;Parent=mRNA218
III	gt csa	exon	1725626	1725883	0.905	-	.	Parent=mRNA218
III	gt cds	CDS	1725626	1725883	.	-	0	ID=CDS167;Parent=mRNA218
III	gt csa	exon	1728036	1728084	1	-	.	Parent=mRNA218
III	gt cds	CDS	1728036	1728084	.	-	1	ID=CDS167;Parent=mRNA218
III	gt csa	exon	1729126	1729418	1	-	.	Parent=mRNA218
III	gt cds	CDS	1729126	1729418	.	-	0	ID=CDS167;Parent=mRNA218
III	gt csa	exon	1732543	1732692	1	-	.	Parent=mRNA218
III	gt cds	CDS	1732543	1732692	.	-	0	ID=CDS167;Parent=mRNA218
III	gt cds	CDS	1732928	1733077	.	-	0	ID=CDS167;Parent=mRNA218
III	gt csa	exon	1732928	1733090	1	-	.	Parent=mRNA218
###
III	gt csa	gene	1752185	1754928	.	-	.	ID=gene147
III	gt csa	mRNA	1752185	1752773	.	-	.	ID=mRNA219;Parent=gene147;Target=yk662d4.3 1 300 -
III	gt csa	exon	1752185	1752363	1	-	.	Parent=mRNA219
III	gt csa	exon	1752588	1752653	1	-	.	Parent=mRNA219
III	gt csa	exon	1752719	1752773	1	-	.	Parent=mRNA219
III	gt csa	mRNA	1752791	1754928	.	-	.	ID=mRNA220;Parent=gene147;Target=yk662d4.5 1 379 +
III	gt csa	exon	1752791	1752886	0.865	-	.	Parent=mRNA220
III	gt cds	CDS	1752791	1752886	.	-	0	ID=CDS168;Parent=mRNA220
III	gt csa	exon	1753877	1754092	0.995	-	.	Parent=mRNA220
III	gt cds	CDS	1753877	1754092	.	-	0	ID=CDS168;Parent=mRNA220
III	gt cds	CDS	1754866	1754901	.	-	0	ID=CDS168;Parent=mRNA220
III	gt csa	exon	1754866	1754928	1	-	.	Parent=mRNA220
###
III	gt csa	gene	1763529	1764816	.	+	.	ID=gene148
III	gt csa	mRNA	1763529	1764816	.	+	.	ID=mRNA221;Parent=gene148;Target=yk58h5.5 1 239 +,yk411g7.5 1 360 +,yk261e7.5 1 180 +
III	gt csa	exon	1763529	1763655	0.984	+	.	Parent=mRNA221
III	gt cds	CDS	1763643	1763655	.	+	0	ID=CDS169;Parent=mRNA221
III	gt cds	CDS	1764575	1764795	.	+	2	ID=CDS169;Parent=mRNA221
III	gt csa	exon	1764575	1764816	0.996	+	.	Parent=mRNA221
###
III	gt csa	gene	1763606	1764825	.	-	.	ID=gene149
III	gt csa	mRNA	1763606	1764825	.	-	.	ID=mRNA222;Parent=gene149;Target=yk261e7.3 1 300 +,yk411g7.3 1 300 +
III	gt csa	exon	1763606	1763648	1	-	.	Parent=mRNA222
III	gt csa	exon	1764567	1764825	0.95	-	.	Parent=mRNA222
###
III	gt csa	gene	1771090	1771264	.	-	.	ID=gene150
III	gt csa	mRNA	1771090	1771264	.	-	.	ID=mRNA223;Parent=gene150;Target=yk581g6.5 186 360 +
III	gt csa	exon	1771090	1771264	0.954	-	.	Parent=mRNA223
###
III	gt csa	gene	1772556	1774226	.	-	.	ID=gene151
III	gt csa	mRNA	1772556	1774226	.	-	.	ID=mRNA224;Parent=gene151;Target=yk1484e10.3 1 505 -,yk655d4.3 1 300 -,yk541b2.3 1 300 -,yk550e12.3 1 300 -
III	gt csa	exon	1772556	1772820	0.943	-	.	Parent=mRNA224
III	gt csa	exon	1773987	1774226	0.946	-	.	Parent=mRNA224
###
III	gt csa	gene	1775021	1777597	.	-	.	ID=gene152
III	gt csa	mRNA	1775021	1777406	.	-	.	ID=mRNA225;Parent=gene152;Target=yk543e1.5 1 360 +,yk541b2.5 7 360 +
III	gt csa	exon	1775021	1775112	1	-	.	Parent=mRNA225
III	gt cds	CDS	1775023	1775112	.	-	0	ID=CDS170;Parent=mRNA225
III	gt csa	exon	1775494	1775616	0.992	-	.	Parent=mRNA225
III	gt cds	CDS	1775494	1775616	.	-	0	ID=CDS170;Parent=mRNA225
III	gt csa	exon	1775887	1775990	1	-	.	Parent=mRNA225
III	gt cds	CDS	1775887	1775990	.	-	2	ID=CDS170;Parent=mRNA225
III	gt csa	exon	1777076	1777202	1	-	.	Parent=mRNA225
III	gt cds	CDS	1777076	1777202	.	-	0	ID=CDS170;Parent=mRNA225
III	gt csa	exon	1777260	1777406	0.966	-	.	Parent=mRNA225
III	gt cds	CDS	1777260	1777406	.	-	0	ID=CDS170;Parent=mRNA225
III	gt csa	mRNA	1775021	1777597	.	-	.	ID=mRNA226;Parent=gene152;Target=yk543e1.5 1 360 +,yk1484e10.5 1 544 +,yk550e12.5 1 380 +,yk618c5.5 1 360 +,yk276b6.5 1 360 +,yk549f11.5 1 359 +,yk655d4.5 1 359 +,yk444c12.5 1 360 +,yk411g1.5 14 360 +
III	gt csa	exon	1775021	1775112	1	-	.	Parent=mRNA226
III	gt cds	CDS	1775023	1775112	.	-	0	ID=CDS171;Parent=mRNA226
III	gt csa	exon	1775494	1775616	0.992	-	.	Parent=mRNA226
III	gt cds	CDS	1775494	1775616	.	-	0	ID=CDS171;Parent=mRNA226
III	gt csa	exon	1775887	1775990	1	-	.	Parent=mRNA226
III	gt cds	CDS	1775887	1775990	.	-	2	ID=CDS171;Parent=mRNA226
III	gt csa	exon	1777076	1777214	1	-	.	Parent=mRNA226
III	gt cds	CDS	1777076	1777214	.	-	0	ID=CDS171;Parent=mRNA226
III	gt csa	exon	1777260	1777406	0.993	-	.	Parent=mRNA226
III	gt cds	CDS	1777260	1777406	.	-	0	ID=CDS171;Parent=mRNA226
III	gt cds	CDS	1777492	1777512	.	-	0	ID=CDS171;Parent=mRNA226
III	gt csa	exon	1777492	1777597	1	-	.	Parent=mRNA226
###
III	gt csa	gene	1777799	1778203	.	+	.	ID=gene153
III	gt csa	mRNA	1777799	1778203	.	+	.	ID=mRNA227;Parent=gene153;Target=RP 1 41 +,BP 1 41 +
III	gt csa	exon	1777799	1777904	1	+	.	Parent=mRNA227
III	gt csa	exon	1778187	1778203	1	+	.	Parent=mRNA227
###
III	gt csa	gene	1785208	1785635	.	-	.	ID=gene154
III	gt csa	mRNA	1785208	1785635	.	-	.	ID=mRNA228;Parent=gene154;Target=yk1303c12.3 24 419 +
III	gt csa	exon	1785208	1785302	0.989	-	.	Parent=mRNA228
III	gt csa	exon	1785317	1785531	0.919	-	.	Parent=mRNA228
III	gt csa	exon	1785550	1785635	0.988	-	.	Parent=mRNA228
###
III	gt csa	gene	1807719	1818322	.	-	.	ID=gene155
III	gt csa	mRNA	1807719	1809245	.	-	.	ID=mRNA229;Parent=gene155;Target=yk750h11.5 1 183 +,yk1048a06.3 1 538 -,yk872f09.3 1 534 -,yk1102f12.3 1 536 -,yk1354g01.3 1 700 -,yk1490a04.3 1 496 -,yk530e1.3 1 300 -,yk264d2.3 1 300 -,yk501h12.3 1 300 -,yk407d6.3 1 300 -
III	gt csa	exon	1807719	1807889	0.959	-	.	Parent=mRNA229
III	gt cds	CDS	1807880	1807889	.	-	1	ID=CDS172;Parent=mRNA229
III	gt csa	exon	1807944	1808358	1	-	.	Parent=mRNA229
III	gt cds	CDS	1807944	1808358	.	-	2	ID=CDS172;Parent=mRNA229
III	gt cds	CDS	1809107	1809140	.	-	0	ID=CDS172;Parent=mRNA229
III	gt csa	exon	1809107	1809245	0.953	-	.	Parent=mRNA229
III	gt csa	mRNA	1807719	1815816	.	-	.	ID=mRNA230;Parent=gene155;Target=yk750h11.5 1 183 +,yk871f07.3 1 702 -,yk1048a06.3 1 538 -,yk872f09.3 1 534 -,yk1102f12.3 1 536 -,yk1314a11.3 1 729 -,yk1091a04.3 1 689 -,yk1012a09.3 1 682 -,yk1297g02.3 1 682 -,yk1166d10.3 1 717 -,yk1036a09.3 1 696 -,yk1490a04.3 1 496 -,yk530e1.3 1 300 -,yk264d2.3 1 300 -,yk501h12.3 1 300 -,yk407d6.3 1 300 -,yk1755a05.3 1 696 -,WP 1 717 +,yk1048a06.5 1 607 +,yk264d2.5 1 240 +,yk501h12.5 1 375 +,yk407d6.5 1 360 +,yk1091a04.5 1 262 +,yk1755a05.5 1 598 +,yk1036a09.5 11 576 +,yk872f09.5 14 372 +,yk530e1.5 44 360 +
III	gt csa	exon	1807719	1807889	0.959	-	.	Parent=mRNA230
III	gt cds	CDS	1807880	1807889	.	-	1	ID=CDS173;Parent=mRNA230
III	gt csa	exon	1807944	1808363	1	-	.	Parent=mRNA230
III	gt cds	CDS	1807944	1808363	.	-	1	ID=CDS173;Parent=mRNA230
III	gt csa	exon	1809107	1809381	1	-	.	Parent=mRNA230
III	gt cds	CDS	1809107	1809381	.	-	0	ID=CDS173;Parent=mRNA230
III	gt csa	exon	1809679	1809822	1	-	.	Parent=mRNA230
III	gt cds	CDS	1809679	1809822	.	-	0	ID=CDS173;Parent=mRNA230
III	gt csa	exon	1811041	1811363	1	-	.	Parent=mRNA230
III	gt cds	CDS	1811041	1811363	.	-	2	ID=CDS173;Parent=mRNA230
III	gt csa	exon	1812744	1813091	1	-	.	Parent=mRNA230
III	gt cds	CDS	1812744	1813091	.	-	2	ID=CDS173;Parent=mRNA230
III	gt csa	exon	1814386	1814835	1	-	.	Parent=mRNA230
III	gt cds	CDS	1814386	1814835	.	-	2	ID=CDS173;Parent=mRNA230
III	gt cds	CDS	1815432	1815438	.	-	0	ID=CDS173;Parent=mRNA230
III	gt csa	exon	1815432	1815557	1	-	.	Parent=mRNA230
III	gt csa	exon	1815760	1815816	0.269	-	.	Parent=mRNA230
III	gt csa	mRNA	1809707	1818322	.	-	.	ID=mRNA231;Parent=gene155;Target=yk1048a06.5 1 607 +,yk264d2.5 1 240 +,yk501h12.5 1 375 +,yk407d6.5 1 360 +,yk1091a04.5 1 262 +,yk1755a05.5 1 598 +,yk1036a09.5 11 576 +,yk1166d10.5 1 559 +,yk1102f12.5 23 595 +,yk1314a11.5 1 585 +,yk1012a09.5 22 578 +,yk1297g02.5 23 533 +,yk1490a04.5 23 510 +,yk872f09.5 14 372 +,yk530e1.5 44 360 +
III	gt csa	exon	1809707	1809822	0.983	-	.	Parent=mRNA231
III	gt cds	CDS	1809709	1809822	.	-	0	ID=CDS174;Parent=mRNA231
III	gt csa	exon	1811041	1811363	1	-	.	Parent=mRNA231
III	gt cds	CDS	1811041	1811363	.	-	2	ID=CDS174;Parent=mRNA231
III	gt csa	exon	1812744	1813091	1	-	.	Parent=mRNA231
III	gt cds	CDS	1812744	1813091	.	-	2	ID=CDS174;Parent=mRNA231
III	gt csa	exon	1814386	1814835	0.998	-	.	Parent=mRNA231
III	gt cds	CDS	1814386	1814835	.	-	2	ID=CDS174;Parent=mRNA231
III	gt csa	exon	1815432	1815557	1	-	.	Parent=mRNA231
III	gt cds	CDS	1815432	1815557	.	-	2	ID=CDS174;Parent=mRNA231
III	gt cds	CDS	1818254	1818308	.	-	0	ID=CDS174;Parent=mRNA231
III	gt csa	exon	1818254	1818322	0.906	-	.	Parent=mRNA231
###
III	gt csa	gene	1807745	1807902	.	+	.	ID=gene156
III	gt csa	mRNA	1807745	1807902	.	+	.	ID=mRNA232;Parent=gene156;Target=yk750h11.3 1 157 +
III	gt csa	exon	1807745	1807902	0.968	+	.	Parent=mRNA232
###
III	gt csa	gene	1821203	1824103	.	-	.	ID=gene157
III	gt csa	mRNA	1821203	1822732	.	-	.	ID=mRNA233;Parent=gene157;Target=yk305g9.3 1 300 -,yk383c1.3 1 300 -,yk412f9.3 1 300 -,yk665f3.3 1 300 -,yk383c1.5 1 360 +
III	gt csa	exon	1821203	1821412	1	-	.	Parent=mRNA233
III	gt cds	CDS	1821204	1821412	.	-	2	ID=CDS175;Parent=mRNA233
III	gt csa	exon	1821473	1821557	1	-	.	Parent=mRNA233
III	gt cds	CDS	1821473	1821557	.	-	0	ID=CDS175;Parent=mRNA233
III	gt cds	CDS	1821604	1821675	.	-	0	ID=CDS175;Parent=mRNA233
III	gt csa	exon	1821604	1821711	1	-	.	Parent=mRNA233
III	gt csa	exon	1822654	1822732	1	-	.	Parent=mRNA233
III	gt csa	mRNA	1822859	1824103	.	-	.	ID=mRNA234;Parent=gene157;Target=yk665f3.5 1 377 +,yk305g9.5 1 376 +
III	gt csa	exon	1822859	1823006	1	-	.	Parent=mRNA234
III	gt cds	CDS	1822861	1823006	.	-	2	ID=CDS176;Parent=mRNA234
III	gt csa	exon	1823643	1823760	1	-	.	Parent=mRNA234
III	gt cds	CDS	1823643	1823760	.	-	0	ID=CDS176;Parent=mRNA234
III	gt cds	CDS	1823964	1824047	.	-	0	ID=CDS176;Parent=mRNA234
III	gt csa	exon	1823964	1824103	1	-	.	Parent=mRNA234
###
III	gt csa	gene	1824908	1831849	.	+	.	ID=gene158
III	gt csa	mRNA	1824908	1831849	.	+	.	ID=mRNA235;Parent=gene158;Target=yk1471g06.5 23 598 +
III	gt csa	exon	1824908	1824965	1	+	.	Parent=mRNA235
III	gt cds	CDS	1824915	1824965	.	+	0	ID=CDS177;Parent=mRNA235
III	gt csa	exon	1825145	1825214	1	+	.	Parent=mRNA235
III	gt cds	CDS	1825145	1825214	.	+	0	ID=CDS177;Parent=mRNA235
III	gt csa	exon	1827228	1827355	1	+	.	Parent=mRNA235
III	gt cds	CDS	1827228	1827355	.	+	2	ID=CDS177;Parent=mRNA235
III	gt csa	exon	1830455	1830596	1	+	.	Parent=mRNA235
III	gt cds	CDS	1830455	1830596	.	+	0	ID=CDS177;Parent=mRNA235
III	gt csa	exon	1830776	1830907	1	+	.	Parent=mRNA235
III	gt cds	CDS	1830776	1830907	.	+	2	ID=CDS177;Parent=mRNA235
III	gt cds	CDS	1831804	1831847	.	+	2	ID=CDS177;Parent=mRNA235
III	gt csa	exon	1831804	1831849	1	+	.	Parent=mRNA235
III	gt csa	mRNA	1824936	1827299	.	+	.	ID=mRNA236;Parent=gene158;Target=yk428b11.5 1 360 +
III	gt csa	exon	1824936	1824965	0.85	+	.	Parent=mRNA236
III	gt csa	exon	1825145	1825400	0.963	+	.	Parent=mRNA236
III	gt csa	exon	1827228	1827299	0.986	+	.	Parent=mRNA236
###
III	gt csa	gene	1833860	1834336	.	-	.	ID=gene159
III	gt csa	mRNA	1833860	1834336	.	-	.	ID=mRNA237;Parent=gene159;Target=yk1471g06.3 1 477 +,yk428b11.3 1 180 +
III	gt csa	exon	1833860	1834336	0.918	-	.	Parent=mRNA237
###
III	gt csa	gene	1834502	1842946	.	+	.	ID=gene160
III	gt csa	mRNA	1834502	1842946	.	+	.	ID=mRNA238;Parent=gene160;Target=yk1579g04.5 24 347 +,yk392a4.5 7 371 +,yk1171d07.5 23 574 +,yk1521f03.5 23 574 +,yk1520e11.5 23 587 +,yk1537h08.5 23 589 +,yk614f12.5 1 360 +,yk273b4.5 1 360 +,yk1094h04.5 1 598 +,yk93h5.5 1 292 +,yk1521e10.5 1 446 +,yk460h8.5 1 360 +,yk240e10.5 1 374 +,yk163b1.5 2 360 +,yk14g9.5 1 360 +
III	gt csa	exon	1834502	1834595	1	+	.	Parent=mRNA238
III	gt cds	CDS	1834509	1834595	.	+	0	ID=CDS178;Parent=mRNA238
III	gt csa	exon	1836122	1836195	1	+	.	Parent=mRNA238
III	gt cds	CDS	1836122	1836195	.	+	0	ID=CDS178;Parent=mRNA238
III	gt csa	exon	1836253	1836355	1	+	.	Parent=mRNA238
III	gt cds	CDS	1836253	1836355	.	+	1	ID=CDS178;Parent=mRNA238
III	gt csa	exon	1837108	1837249	1	+	.	Parent=mRNA238
III	gt cds	CDS	1837108	1837249	.	+	0	ID=CDS178;Parent=mRNA238
III	gt csa	exon	1838335	1838703	1	+	.	Parent=mRNA238
III	gt cds	CDS	1838335	1838703	.	+	2	ID=CDS178;Parent=mRNA238
III	gt csa	exon	1838765	1838877	1	+	.	Parent=mRNA238
III	gt cds	CDS	1838765	1838877	.	+	2	ID=CDS178;Parent=mRNA238
III	gt csa	exon	1840158	1840486	0.988	+	.	Parent=mRNA238
III	gt cds	CDS	1840158	1840486	.	+	0	ID=CDS178;Parent=mRNA238
III	gt csa	exon	1841743	1841899	0.987	+	.	Parent=mRNA238
III	gt cds	CDS	1841743	1841899	.	+	1	ID=CDS178;Parent=mRNA238
III	gt cds	CDS	1842859	1842945	.	+	0	ID=CDS178;Parent=mRNA238
III	gt csa	exon	1842859	1842946	0.966	+	.	Parent=mRNA238
###
III	gt csa	gene	1844378	1846728	.	+	.	ID=gene161
III	gt csa	mRNA	1844378	1846728	.	+	.	ID=mRNA239;Parent=gene161;Target=yk1520e11.3 1 527 -,yk1521e10.3 1 432 -,yk1171d07.3 1 410 -
III	gt csa	exon	1844378	1844512	0.904	+	.	Parent=mRNA239
III	gt csa	exon	1846336	1846728	0.919	+	.	Parent=mRNA239
III	gt cds	CDS	1846377	1846622	.	+	0	ID=CDS179;Parent=mRNA239
###
III	gt csa	gene	1846366	1846740	.	-	.	ID=gene162
III	gt csa	mRNA	1846366	1846740	.	-	.	ID=mRNA240;Parent=gene162;Target=yk1094h04.3 1 361 +,yk14g9.3 1 373 +,yk1537h08.3 1 247 +,yk1521f03.3 1 204 +,yk1579g04.3 1 199 +,yk93h5.3 1 120 +
III	gt csa	exon	1846366	1846740	0.965	-	.	Parent=mRNA240
###
III	gt csa	gene	1849052	1852447	.	+	.	ID=gene163
III	gt csa	mRNA	1849052	1850827	.	+	.	ID=mRNA241;Parent=gene163;Target=yk532h6.5 1 381 +,yk332d10.5 1 360 +,yk506e3.5 1 383 +,yk174g9.5 1 360 +,yk521e8.5 1 360 +
III	gt csa	exon	1849052	1849121	0.964	+	.	Parent=mRNA241
III	gt cds	CDS	1849071	1849121	.	+	0	ID=CDS180;Parent=mRNA241
III	gt csa	exon	1849263	1849349	1	+	.	Parent=mRNA241
III	gt cds	CDS	1849263	1849349	.	+	0	ID=CDS180;Parent=mRNA241
III	gt csa	exon	1849404	1849502	1	+	.	Parent=mRNA241
III	gt cds	CDS	1849404	1849502	.	+	0	ID=CDS180;Parent=mRNA241
III	gt csa	exon	1850353	1850445	1	+	.	Parent=mRNA241
III	gt cds	CDS	1850353	1850445	.	+	0	ID=CDS180;Parent=mRNA241
III	gt cds	CDS	1850707	1850826	.	+	0	ID=CDS180;Parent=mRNA241
III	gt csa	exon	1850707	1850827	1	+	.	Parent=mRNA241
III	gt csa	mRNA	1849294	1850837	.	+	.	ID=mRNA242;Parent=gene163;Target=yk487d2.5 1 381 +
III	gt csa	exon	1849294	1849350	0.939	+	.	Parent=mRNA242
III	gt csa	exon	1849404	1849502	1	+	.	Parent=mRNA242
III	gt cds	CDS	1849425	1849502	.	+	0	ID=CDS181;Parent=mRNA242
III	gt csa	exon	1850353	1850445	1	+	.	Parent=mRNA242
III	gt cds	CDS	1850353	1850445	.	+	0	ID=CDS181;Parent=mRNA242
III	gt cds	CDS	1850707	1850835	.	+	0	ID=CDS181;Parent=mRNA242
III	gt csa	exon	1850707	1850837	0.992	+	.	Parent=mRNA242
III	gt csa	mRNA	1851033	1852447	.	+	.	ID=mRNA243;Parent=gene163;Target=yk66f12.5 1 360 +
III	gt csa	exon	1851033	1851113	1	+	.	Parent=mRNA243
III	gt cds	CDS	1851052	1851113	.	+	0	ID=CDS182;Parent=mRNA243
III	gt cds	CDS	1852169	1852445	.	+	1	ID=CDS182;Parent=mRNA243
III	gt csa	exon	1852169	1852447	0.993	+	.	Parent=mRNA243
###
III	gt csa	gene	1852263	1852877	.	-	.	ID=gene164
III	gt csa	mRNA	1852263	1852562	.	-	.	ID=mRNA244;Parent=gene164;Target=yk334d11.3 1 300 +
III	gt csa	exon	1852263	1852562	0.997	-	.	Parent=mRNA244
III	gt csa	mRNA	1852697	1852877	.	-	.	ID=mRNA245;Parent=gene164;Target=yk66f12.3 1 180 +
III	gt csa	exon	1852697	1852877	0.925	-	.	Parent=mRNA245
###
III	gt csa	gene	1859880	1864478	.	+	.	ID=gene165
III	gt csa	mRNA	1859880	1860325	.	+	.	ID=mRNA246;Parent=gene165;Target=yk521e3.3 1 281 -,AF150086 1 252 +,RP 1 84 +,BP 1 84 +,yk521e3.5 1 337 +
III	gt csa	exon	1859880	1860055	0.983	+	.	Parent=mRNA246
III	gt cds	CDS	1859882	1860055	.	+	0	ID=CDS183;Parent=mRNA246
III	gt cds	CDS	1860146	1860223	.	+	0	ID=CDS183;Parent=mRNA246
III	gt csa	exon	1860146	1860325	0.961	+	.	Parent=mRNA246
III	gt csa	mRNA	1860418	1864478	.	+	.	ID=mRNA247;Parent=gene165;Target=yk1220d04.5 23 647 +,yk772h10.5 21 646 +
III	gt csa	exon	1860418	1860607	1	+	.	Parent=mRNA247
III	gt cds	CDS	1860427	1860607	.	+	0	ID=CDS184;Parent=mRNA247
III	gt csa	exon	1861659	1861816	1	+	.	Parent=mRNA247
III	gt cds	CDS	1861659	1861816	.	+	2	ID=CDS184;Parent=mRNA247
III	gt csa	exon	1864021	1864120	1	+	.	Parent=mRNA247
III	gt cds	CDS	1864021	1864120	.	+	0	ID=CDS184;Parent=mRNA247
III	gt cds	CDS	1864301	1864476	.	+	2	ID=CDS184;Parent=mRNA247
III	gt csa	exon	1864301	1864478	1	+	.	Parent=mRNA247
###
III	gt csa	gene	1872178	1874286	.	+	.	ID=gene166
III	gt csa	mRNA	1872178	1874286	.	+	.	ID=mRNA248;Parent=gene166;Target=yk1220d04.3 1 668 -
III	gt csa	exon	1872178	1872266	1	+	.	Parent=mRNA248
III	gt cds	CDS	1872221	1872266	.	+	0	ID=CDS185;Parent=mRNA248
III	gt cds	CDS	1873707	1874068	.	+	2	ID=CDS185;Parent=mRNA248
III	gt csa	exon	1873707	1874286	0.988	+	.	Parent=mRNA248
###
III	gt csa	gene	1874643	1877104	.	+	.	ID=gene167
III	gt csa	mRNA	1874643	1877104	.	+	.	ID=mRNA249;Parent=gene167;Target=yk772h10.3 1 592 -
III	gt csa	exon	1874643	1874750	1	+	.	Parent=mRNA249
III	gt cds	CDS	1874715	1874750	.	+	0	ID=CDS186;Parent=mRNA249
III	gt csa	exon	1875972	1876159	0.995	+	.	Parent=mRNA249
III	gt cds	CDS	1875972	1876159	.	+	0	ID=CDS186;Parent=mRNA249
III	gt cds	CDS	1876806	1876989	.	+	1	ID=CDS186;Parent=mRNA249
III	gt csa	exon	1876806	1877104	0.983	+	.	Parent=mRNA249
###
III	gt csa	gene	1878354	1880837	.	+	.	ID=gene168
III	gt csa	mRNA	1878354	1880828	.	+	.	ID=mRNA250;Parent=gene168;Target=yk1169f09.5 20 395 +,yk1473c02.3 1 783 -,yk1169f09.3 1 705 -
III	gt csa	exon	1878354	1878595	0.996	+	.	Parent=mRNA250
III	gt cds	CDS	1878362	1878595	.	+	0	ID=CDS187;Parent=mRNA250
III	gt csa	exon	1879233	1879361	1	+	.	Parent=mRNA250
III	gt cds	CDS	1879233	1879361	.	+	0	ID=CDS187;Parent=mRNA250
III	gt csa	exon	1879426	1879560	1	+	.	Parent=mRNA250
III	gt cds	CDS	1879426	1879560	.	+	0	ID=CDS187;Parent=mRNA250
III	gt csa	exon	1880174	1880328	1	+	.	Parent=mRNA250
III	gt cds	CDS	1880174	1880328	.	+	0	ID=CDS187;Parent=mRNA250
III	gt cds	CDS	1880625	1880736	.	+	1	ID=CDS187;Parent=mRNA250
III	gt csa	exon	1880625	1880828	1	+	.	Parent=mRNA250
III	gt csa	mRNA	1878558	1878800	.	+	.	ID=mRNA251;Parent=gene168;Target=yk1251d11.5 1 243 +
III	gt csa	exon	1878558	1878800	0.988	+	.	Parent=mRNA251
III	gt csa	mRNA	1879975	1880837	.	+	.	ID=mRNA252;Parent=gene168;Target=yk1512g12.3 1 565 -
III	gt csa	exon	1879975	1880328	1	+	.	Parent=mRNA252
III	gt csa	exon	1880625	1880837	0.991	+	.	Parent=mRNA252
###
III	gt csa	gene	1880375	1880798	.	-	.	ID=gene169
III	gt csa	mRNA	1880375	1880798	.	-	.	ID=mRNA253;Parent=gene169;Target=yk1251d11.3 1 424 +
III	gt csa	exon	1880375	1880798	0.979	-	.	Parent=mRNA253
###
III	gt csa	gene	1883596	1886207	.	-	.	ID=gene170
III	gt csa	mRNA	1883596	1886207	.	-	.	ID=mRNA254;Parent=gene170;Target=WP 1 773 +
III	gt csa	exon	1883596	1884789	1	-	.	Parent=mRNA254
III	gt cds	CDS	1883596	1884789	.	-	0	ID=CDS188;Parent=mRNA254
III	gt csa	exon	1884882	1885107	1	-	.	Parent=mRNA254
III	gt cds	CDS	1884882	1885107	.	-	1	ID=CDS188;Parent=mRNA254
III	gt csa	exon	1885194	1885938	1	-	.	Parent=mRNA254
III	gt cds	CDS	1885194	1885938	.	-	2	ID=CDS188;Parent=mRNA254
III	gt csa	exon	1885987	1886117	1	-	.	Parent=mRNA254
III	gt cds	CDS	1885987	1886117	.	-	1	ID=CDS188;Parent=mRNA254
III	gt csa	exon	1886185	1886207	1	-	.	Parent=mRNA254
III	gt cds	CDS	1886185	1886207	.	-	0	ID=CDS188;Parent=mRNA254
###
III	gt csa	gene	1891444	1893894	.	-	.	ID=gene171
III	gt csa	mRNA	1891444	1893894	.	-	.	ID=mRNA255;Parent=gene171;Target=yk233a7.3 1 300 -,yk233a7.5 1 345 +
III	gt csa	exon	1891444	1891508	1	-	.	Parent=mRNA255
III	gt cds	CDS	1891446	1891508	.	-	0	ID=CDS189;Parent=mRNA255
III	gt csa	exon	1891927	1892079	0.993	-	.	Parent=mRNA255
III	gt cds	CDS	1891927	1892079	.	-	0	ID=CDS189;Parent=mRNA255
III	gt csa	exon	1893273	1893544	0.969	-	.	Parent=mRNA255
III	gt cds	CDS	1893273	1893544	.	-	2	ID=CDS189;Parent=mRNA255
III	gt cds	CDS	1893825	1893831	.	-	0	ID=CDS189;Parent=mRNA255
III	gt csa	exon	1893825	1893894	0.929	-	.	Parent=mRNA255
###
III	gt csa	gene	1906128	1906538	.	+	.	ID=gene172
III	gt csa	mRNA	1906128	1906538	.	+	.	ID=mRNA256;Parent=gene172;Target=yk1723c04.5 1 340 +
III	gt csa	exon	1906128	1906256	0.953	+	.	Parent=mRNA256
III	gt csa	exon	1906330	1906538	0.967	+	.	Parent=mRNA256
###
III	gt csa	gene	1907887	1910519	.	+	.	ID=gene173
III	gt csa	mRNA	1907887	1910519	.	+	.	ID=mRNA257;Parent=gene173;Target=yk1723c04.3 1 651 -
III	gt csa	exon	1907887	1907987	0.901	+	.	Parent=mRNA257
III	gt cds	CDS	1907889	1907987	.	+	0	ID=CDS190;Parent=mRNA257
III	gt csa	exon	1908176	1908310	1	+	.	Parent=mRNA257
III	gt cds	CDS	1908176	1908310	.	+	0	ID=CDS190;Parent=mRNA257
III	gt csa	exon	1909274	1909432	1	+	.	Parent=mRNA257
III	gt cds	CDS	1909274	1909432	.	+	0	ID=CDS190;Parent=mRNA257
III	gt csa	exon	1910268	1910519	1	+	.	Parent=mRNA257
III	gt cds	CDS	1910268	1910519	.	+	0	ID=CDS190;Parent=mRNA257
###
III	gt csa	gene	1927666	1929298	.	+	.	ID=gene174
III	gt csa	mRNA	1927666	1929298	.	+	.	ID=mRNA258;Parent=gene174;Target=yk1053g10.5 17 224 +,yk1716g06.5 1 386 +
III	gt csa	exon	1927666	1927938	1	+	.	Parent=mRNA258
III	gt csa	exon	1929095	1929298	0.995	+	.	Parent=mRNA258
###
III	gt csa	gene	1930845	1931242	.	+	.	ID=gene175
III	gt csa	mRNA	1930845	1931242	.	+	.	ID=mRNA259;Parent=gene175;Target=yk1564h09.5 1 398 +
III	gt csa	exon	1930845	1931242	0.985	+	.	Parent=mRNA259
###
III	gt csa	gene	1932215	1939546	.	+	.	ID=gene176
III	gt csa	mRNA	1932215	1939375	.	+	.	ID=mRNA260;Parent=gene176;Target=yk1222g11.5 1 557 +,yk652e1.5 1 383 +,yk205e6.5 1 373 +,yk677h7.5 1 354 +,yk638h1.5 1 360 +,yk205h4.5 1 360 +,yk252c12.3 1 300 +
III	gt csa	exon	1932215	1932363	1	+	.	Parent=mRNA260
III	gt csa	exon	1934173	1934512	1	+	.	Parent=mRNA260
III	gt cds	CDS	1934393	1934512	.	+	0	ID=CDS191;Parent=mRNA260
III	gt csa	exon	1936356	1936529	1	+	.	Parent=mRNA260
III	gt cds	CDS	1936356	1936529	.	+	0	ID=CDS191;Parent=mRNA260
III	gt csa	exon	1937670	1938089	1	+	.	Parent=mRNA260
III	gt cds	CDS	1937670	1938089	.	+	0	ID=CDS191;Parent=mRNA260
III	gt cds	CDS	1939008	1939319	.	+	0	ID=CDS191;Parent=mRNA260
III	gt csa	exon	1939008	1939375	0.983	+	.	Parent=mRNA260
III	gt csa	mRNA	1934173	1939534	.	+	.	ID=mRNA261;Parent=gene176;Target=yk1716g06.3 35 413 -
III	gt csa	exon	1934173	1934226	0.87	+	.	Parent=mRNA261
III	gt csa	exon	1939167	1939225	0.814	+	.	Parent=mRNA261
III	gt csa	exon	1939269	1939534	0.94	+	.	Parent=mRNA261
III	gt csa	mRNA	1938000	1939546	.	+	.	ID=mRNA262;Parent=gene176;Target=yk1596d03.3 1 585 -,yk252c12.3 1 300 +
III	gt csa	exon	1938000	1938047	0.833	+	.	Parent=mRNA262
III	gt csa	exon	1939008	1939546	0.954	+	.	Parent=mRNA262
III	gt csa	mRNA	1938966	1939375	.	+	.	ID=mRNA263;Parent=gene176;Target=yk440d6.5 1 360 +,yk252c12.3 1 300 +
III	gt csa	exon	1938966	1939375	0.983	+	.	Parent=mRNA263
###
III	gt csa	gene	1939092	1943594	.	-	.	ID=gene177
III	gt csa	mRNA	1939092	1939557	.	-	.	ID=mRNA264;Parent=gene177;Target=yk864f11.3 1 360 +,CEESA81F 1 359 +,yk1618b12.3 1 264 +,yk1222g11.3 1 206 +
III	gt csa	exon	1939092	1939557	0.969	-	.	Parent=mRNA264
III	gt csa	mRNA	1939558	1943594	.	-	.	ID=mRNA265;Parent=gene177;Target=yk95d7.3 1 326 -,yk410b4.3 1 300 -,yk410b4.5 1 360 +,yk95d7.5 1 309 +,yk56h1.5 1 292 +
III	gt csa	exon	1939558	1939643	1	-	.	Parent=mRNA265
III	gt cds	CDS	1939572	1939643	.	-	0	ID=CDS192;Parent=mRNA265
III	gt csa	exon	1940648	1940818	1	-	.	Parent=mRNA265
III	gt cds	CDS	1940648	1940818	.	-	0	ID=CDS192;Parent=mRNA265
III	gt csa	exon	1941527	1941644	1	-	.	Parent=mRNA265
III	gt cds	CDS	1941527	1941644	.	-	1	ID=CDS192;Parent=mRNA265
III	gt csa	exon	1941693	1941742	1	-	.	Parent=mRNA265
III	gt cds	CDS	1941693	1941742	.	-	0	ID=CDS192;Parent=mRNA265
III	gt cds	CDS	1943454	1943513	.	-	0	ID=CDS192;Parent=mRNA265
III	gt csa	exon	1943454	1943594	1	-	.	Parent=mRNA265
###
III	gt csa	gene	1945109	1961934	.	-	.	ID=gene178
III	gt csa	mRNA	1945109	1950246	.	-	.	ID=mRNA266;Parent=gene178;Target=AB244413 1 1755 +,yk604a10.3 1 300 -,yk411e9.3 1 300 -,cm12f1.5 1 418 +,yk411e9.5 1 360 +,yk604a10.5 1 360 +
III	gt csa	exon	1945109	1945261	1	-	.	Parent=mRNA266
III	gt cds	CDS	1945109	1945261	.	-	0	ID=CDS193;Parent=mRNA266
III	gt csa	exon	1946058	1946234	1	-	.	Parent=mRNA266
III	gt cds	CDS	1946058	1946234	.	-	0	ID=CDS193;Parent=mRNA266
III	gt csa	exon	1946292	1946488	1	-	.	Parent=mRNA266
III	gt cds	CDS	1946292	1946488	.	-	2	ID=CDS193;Parent=mRNA266
III	gt csa	exon	1947633	1948044	1	-	.	Parent=mRNA266
III	gt cds	CDS	1947633	1948044	.	-	0	ID=CDS193;Parent=mRNA266
III	gt csa	exon	1948959	1949134	1	-	.	Parent=mRNA266
III	gt cds	CDS	1948959	1949134	.	-	2	ID=CDS193;Parent=mRNA266
III	gt csa	exon	1949218	1949422	1	-	.	Parent=mRNA266
III	gt cds	CDS	1949218	1949422	.	-	0	ID=CDS193;Parent=mRNA266
III	gt csa	exon	1949713	1949872	1	-	.	Parent=mRNA266
III	gt cds	CDS	1949713	1949872	.	-	1	ID=CDS193;Parent=mRNA266
III	gt csa	exon	1949921	1950067	1	-	.	Parent=mRNA266
III	gt cds	CDS	1949921	1950067	.	-	1	ID=CDS193;Parent=mRNA266
III	gt csa	exon	1950119	1950246	1	-	.	Parent=mRNA266
III	gt cds	CDS	1950119	1950246	.	-	0	ID=CDS193;Parent=mRNA266
III	gt csa	mRNA	1951049	1951408	.	-	.	ID=mRNA267;Parent=gene178;Target=yk492f11.3 1 300 +,yk453a11.3 1 300 +,yk199f2.3 1 300 +,yk558h2.3 1 300 +,yk281d11.3 1 300 +,yk278c2.3 1 300 +,yk229f4.3 1 300 +,yk483c3.3 1 300 +,yk615h4.3 1 300 +,yk647d12.3 1 300 +,yk448f2.3 1 283 +,yk551b11.3 1 284 +,yk448c12.3 1 289 +,yk457d7.3 1 293 +,yk446a5.3 1 300 +,yk664b3.3 1 300 +,yk602c4.3 1 285 +,yk253d3.3 1 287 +,yk516c9.3 1 288 +,yk645g1.3 1 288 +,yk646a8.3 1 288 +,yk140h11.3 1 289 +,yk116e3.3 1 338 +,yk60a11.3 1 336 +,yk497d11.3 1 269 +,yk330h9.3 1 270 +,yk800a07.3 1 300 +,yk494c8.3 1 240 +,yk373f11.3 1 240 +,yk222d9.3 1 227 +
III	gt csa	exon	1951049	1951408	0.991	-	.	Parent=mRNA267
III	gt csa	mRNA	1952007	1961934	.	-	.	ID=mRNA268;Parent=gene178;Target=yk1042c08.3 1 509 -,yk1611f05.3 1 724 -,yk1039c09.3 1 700 -,yk1339d07.3 1 770 -,yk1391f02.3 1 685 -,yk1444h05.3 1 727 -,yk1720g01.3 1 727 -,yk1372c05.3 1 768 -,yk1372c06.3 1 792 -,yk837g07.3 1 699 -,yk1474e07.3 1 717 -,yk63f12.3 1 325 -,yk1618b03.3 1 688 -,yk1672e09.3 1 756 -,yk1483a12.3 1 757 -,yk1556a02.3 1 756 -,yk1592b08.3 1 737 -,yk1755g08.3 1 759 -,yk376f5.3 1 300 -,yk312g4.3 1 300 -,yk474e3.3 1 300 -,yk603e10.3 1 300 -,yk470a7.3 1 300 -,yk453c10.3 1 300 -,yk645b1.3 1 300 -,yk577a10.3 1 300 -,yk163e8.3 1 300 -,yk142b8.3 1 300 -,yk187h9.3 1 300 -,yk740a4.3 1 300 -,yk520b2.5 1 358 +,yk577a10.5 1 360 +,yk1703a04.5 1 564 +,yk163e8.5 1 360 +,yk474e3.5 1 360 +,yk1672e09.5 15 652 +,yk1556a02.5 17 620 +,yk470a7.5 1 360 +,yk1339d07.5 23 658 +,yk1042c08.5 23 622 +,yk1660c12.5 23 621 +,yk1474e07.5 24 621 +,yk1618b03.5 23 619 +,yk1720g01.5 22 616 +,yk1611f05.5 23 616 +,yk1755g08.5 23 611 +,yk1444h05.5 23 606 +,yk1039c09.5 23 597 +,yk1592b08.5 23 595 +,yk1654a06.5 23 578 +,yk773f01.5 23 532 +,yk1483a12.5 23 518 +,yk645b1.5 1 383 +,yk603e10.5 1 382 +,yk228a2.5 1 360 +,yk312g4.5 1 372 +,yk837g07.5 1 376 +,yk376f5.5 1 360 +,yk453c10.5 1 360 +,yk142b8.5 1 372 +,yk63f12.5 1 320 +,yk740a4.5 23 340 +,yk187h9.5 1 240 +,yk1391f02.5 23 218 +
III	gt csa	exon	1952007	1952267	0.99	-	.	Parent=mRNA268
III	gt cds	CDS	1952124	1952267	.	-	0	ID=CDS194;Parent=mRNA268
III	gt csa	exon	1953525	1953831	1	-	.	Parent=mRNA268
III	gt cds	CDS	1953525	1953831	.	-	1	ID=CDS194;Parent=mRNA268
III	gt csa	exon	1954624	1954728	1	-	.	Parent=mRNA268
III	gt cds	CDS	1954624	1954728	.	-	1	ID=CDS194;Parent=mRNA268
III	gt csa	exon	1956031	1956288	0.971	-	.	Parent=mRNA268
III	gt cds	CDS	1956031	1956288	.	-	1	ID=CDS194;Parent=mRNA268
III	gt csa	exon	1957574	1957668	1	-	.	Parent=mRNA268
III	gt cds	CDS	1957574	1957668	.	-	0	ID=CDS194;Parent=mRNA268
III	gt csa	exon	1957716	1957848	1	-	.	Parent=mRNA268
III	gt cds	CDS	1957716	1957848	.	-	1	ID=CDS194;Parent=mRNA268
III	gt csa	exon	1959816	1960116	1	-	.	Parent=mRNA268
III	gt cds	CDS	1959816	1960116	.	-	2	ID=CDS194;Parent=mRNA268
III	gt cds	CDS	1961827	1961905	.	-	0	ID=CDS194;Parent=mRNA268
III	gt csa	exon	1961827	1961934	1	-	.	Parent=mRNA268
III	gt csa	mRNA	1952007	1961934	.	-	.	ID=mRNA269;Parent=gene178;Target=yk1042c08.3 1 509 -,yk63f12.3 1 325 -,yk376f5.3 1 300 -,yk312g4.3 1 300 -,yk474e3.3 1 300 -,yk603e10.3 1 300 -,yk470a7.3 1 300 -,yk453c10.3 1 300 -,yk645b1.3 1 300 -,yk577a10.3 1 300 -,yk163e8.3 1 300 -,yk142b8.3 1 300 -,yk187h9.3 1 300 -,yk740a4.3 1 300 -,BP 1 492 +,yk520b2.5 1 358 +,yk577a10.5 1 360 +,yk163e8.5 1 360 +,yk474e3.5 1 360 +,yk1672e09.5 15 652 +,yk1556a02.5 17 620 +,yk470a7.5 1 360 +,yk1339d07.5 23 658 +,yk1042c08.5 23 622 +,yk1660c12.5 23 621 +,yk1474e07.5 24 621 +,yk1618b03.5 23 619 +,yk1720g01.5 22 616 +,yk1611f05.5 23 616 +,yk1755g08.5 23 611 +,yk1444h05.5 23 606 +,yk1039c09.5 23 597 +,yk1592b08.5 23 595 +,yk1654a06.5 23 578 +,yk773f01.5 23 532 +,yk1483a12.5 23 518 +,yk645b1.5 1 383 +,yk603e10.5 1 382 +,yk228a2.5 1 360 +,yk312g4.5 1 372 +,yk837g07.5 1 376 +,yk376f5.5 1 360 +,yk453c10.5 1 360 +,yk142b8.5 1 372 +,yk63f12.5 1 320 +,yk740a4.5 23 340 +,yk187h9.5 1 240 +,yk1391f02.5 23 218 +
III	gt csa	exon	1952007	1952267	0.99	-	.	Parent=mRNA269
III	gt csa	exon	1953525	1953878	0.832	-	.	Parent=mRNA269
III	gt cds	CDS	1953779	1953878	.	-	1	ID=CDS195;Parent=mRNA269
III	gt csa	exon	1954624	1954728	0.987	-	.	Parent=mRNA269
III	gt cds	CDS	1954624	1954728	.	-	1	ID=CDS195;Parent=mRNA269
III	gt csa	exon	1956031	1956288	0.913	-	.	Parent=mRNA269
III	gt cds	CDS	1956031	1956288	.	-	1	ID=CDS195;Parent=mRNA269
III	gt csa	exon	1957574	1957668	1	-	.	Parent=mRNA269
III	gt cds	CDS	1957574	1957668	.	-	0	ID=CDS195;Parent=mRNA269
III	gt csa	exon	1957716	1957848	1	-	.	Parent=mRNA269
III	gt cds	CDS	1957716	1957848	.	-	1	ID=CDS195;Parent=mRNA269
III	gt csa	exon	1959816	1960116	1	-	.	Parent=mRNA269
III	gt cds	CDS	1959816	1960116	.	-	2	ID=CDS195;Parent=mRNA269
III	gt cds	CDS	1961827	1961905	.	-	0	ID=CDS195;Parent=mRNA269
III	gt csa	exon	1961827	1961934	1	-	.	Parent=mRNA269
III	gt csa	mRNA	1952017	1961934	.	-	.	ID=mRNA270;Parent=gene178;Target=yk1660c12.3 1 703 -,yk63f12.3 1 325 -,yk376f5.3 1 300 -,yk312g4.3 1 300 -,yk474e3.3 1 300 -,yk603e10.3 1 300 -,yk470a7.3 1 300 -,yk453c10.3 1 300 -,yk645b1.3 1 300 -,yk577a10.3 1 300 -,yk163e8.3 1 300 -,yk142b8.3 1 300 -,yk187h9.3 1 300 -,yk740a4.3 1 300 -,yk520b2.5 1 358 +,yk163e8.5 1 360 +,yk474e3.5 1 360 +,yk1672e09.5 15 652 +,yk1556a02.5 17 620 +,yk470a7.5 1 360 +,yk1339d07.5 23 658 +,yk1042c08.5 23 622 +,yk1660c12.5 23 621 +,yk1474e07.5 24 621 +,yk1618b03.5 23 619 +,yk1720g01.5 22 616 +,yk1611f05.5 23 616 +,yk1755g08.5 23 611 +,yk1444h05.5 23 606 +,yk1039c09.5 23 597 +,yk1592b08.5 23 595 +,yk1654a06.5 23 578 +,yk773f01.5 23 532 +,yk1483a12.5 23 518 +,yk645b1.5 1 383 +,yk603e10.5 1 382 +,yk228a2.5 1 360 +,yk312g4.5 1 372 +,yk837g07.5 1 376 +,yk376f5.5 1 360 +,yk453c10.5 1 360 +,yk142b8.5 1 372 +,yk63f12.5 1 320 +,yk740a4.5 23 340 +,yk187h9.5 1 240 +,yk1391f02.5 23 218 +
III	gt csa	exon	1952017	1952267	0.996	-	.	Parent=mRNA270
III	gt csa	exon	1953525	1953758	1	-	.	Parent=mRNA270
III	gt cds	CDS	1953712	1953758	.	-	2	ID=CDS196;Parent=mRNA270
III	gt csa	exon	1954640	1954728	1	-	.	Parent=mRNA270
III	gt cds	CDS	1954640	1954728	.	-	1	ID=CDS196;Parent=mRNA270
III	gt csa	exon	1956031	1956288	0.971	-	.	Parent=mRNA270
III	gt cds	CDS	1956031	1956288	.	-	1	ID=CDS196;Parent=mRNA270
III	gt csa	exon	1957574	1957668	1	-	.	Parent=mRNA270
III	gt cds	CDS	1957574	1957668	.	-	0	ID=CDS196;Parent=mRNA270
III	gt csa	exon	1957716	1957848	1	-	.	Parent=mRNA270
III	gt cds	CDS	1957716	1957848	.	-	1	ID=CDS196;Parent=mRNA270
III	gt csa	exon	1959816	1960116	1	-	.	Parent=mRNA270
III	gt cds	CDS	1959816	1960116	.	-	2	ID=CDS196;Parent=mRNA270
III	gt cds	CDS	1961827	1961905	.	-	0	ID=CDS196;Parent=mRNA270
III	gt csa	exon	1961827	1961934	1	-	.	Parent=mRNA270
III	gt csa	mRNA	1953222	1956293	.	-	.	ID=mRNA271;Parent=gene178;Target=RP 1 244 +,yk1703a04.5 1 564 +
III	gt csa	exon	1953222	1953278	0.12	-	.	Parent=mRNA271
III	gt cds	CDS	1953273	1953278	.	-	0	ID=CDS197;Parent=mRNA271
III	gt csa	exon	1953525	1953831	0.944	-	.	Parent=mRNA271
III	gt cds	CDS	1953525	1953831	.	-	1	ID=CDS197;Parent=mRNA271
III	gt csa	exon	1954624	1954728	1	-	.	Parent=mRNA271
III	gt cds	CDS	1954624	1954728	.	-	1	ID=CDS197;Parent=mRNA271
III	gt cds	CDS	1956031	1956245	.	-	0	ID=CDS197;Parent=mRNA271
III	gt csa	exon	1956031	1956293	0.883	-	.	Parent=mRNA271
III	gt csa	mRNA	1959320	1959824	.	-	.	ID=mRNA272;Parent=gene178;Target=yk1245c12.5 1 503 +
III	gt csa	exon	1959320	1959824	0.994	-	.	Parent=mRNA272
###
III	gt csa	gene	1950524	1952513	.	+	.	ID=gene179
III	gt csa	mRNA	1950524	1951426	.	+	.	ID=mRNA273;Parent=gene179;Target=yk1454g11.3 198 646 -,yk1066a07.3 236 686 -,yk1507e02.3 254 710 -,yk1678d01.3 237 693 -,yk1370c12.3 200 660 -,yk1370d03.3 236 711 -,yk1479a03.3 200 674 -,yk1537d05.3 202 677 -,yk1327d02.3 262 742 -,yk457d7.5 1 376 +,yk602c4.5 1 372 +,yk664b3.5 1 376 +,yk647d12.5 1 383 +,yk229f4.5 1 374 +,yk1020a05.3 1 468 -,yk1020a05.5 1 481 +,yk1016a08.3 23 271 -,yk116e3.5 1 360 +,yk1064e06.3 23 443 -,yk1151e09.3 23 447 -,yk1580b09.3 23 449 -,yk1587h09.3 35 461 -,yk1594g06.3 23 449 -,yk1362f01.3 23 459 -,yk1393f05.3 23 459 -,yk1521b10.5 23 466 +,yk1521b10.3 23 467 -,yk892h07.5 23 471 +,yk1176h06.3 24 475 -,yk1155e04.3 23 473 -,yk1291e10.3 23 473 -,yk892h07.3 23 473 -,yk1159h09.3 23 473 -,yk1130b02.3 23 485 -,yk1125f08.3 23 485 -,yk1693h02.5 23 487 +,yk1025d03.5 23 490 +,yk1064e06.5 23 495 +,yk1155e04.5 23 496 +,yk1291e10.5 23 496 +,yk1176h06.5 23 496 +,yk1362f01.5 23 496 +,yk1580b09.5 23 496 +,yk1130b02.5 23 498 +,yk1151e09.5 23 498 +,yk1016a08.5 23 498 +,yk1159h09.5 23 498 +,yk1587h09.5 23 498 +,yk1594g06.5 23 498 +,yk1125f08.5 23 499 +,yk1393f05.5 23 499 +,yk199f2.5 1 377 +,yk497d11.5 1 380 +,yk645g1.5 1 375 +,yk483c3.5 1 378 +,yk253d3.5 1 379 +,yk615h4.5 1 376 +,yk281d11.5 1 360 +,yk330h9.5 1 360 +,yk446a5.5 1 377 +,yk498f9.5 1 360 +,yk453a11.5 1 360 +,yk326h8.5 1 360 +,yk140h11.5 1 360 +,yk627c5.5 1 360 +,FLYBASE 1 131 +,BP 1 131 +,RP 1 131 +,yk448c12.5 1 360 +,yk373f11.5 1 360 +,yk60a11.5 1 360 +,SW 1 130 +,yk476f7.5 1 360 +,yk516c9.5 1 360 +,yk448f2.5 1 360 +,yk558h2.5 1 360 +,yk494c8.5 1 360 +,yk492f11.5 1 360 +,yk551b11.5 1 360 +,yk646a8.5 1 360 +,yk278c2.5 1 374 +,yk471g11.5 1 360 -,yk222d9.5 1 302 +,yk814a07.5 1 104 +
III	gt csa	exon	1950524	1950539	0.938	+	.	Parent=mRNA273
III	gt csa	exon	1950634	1950760	0.969	+	.	Parent=mRNA273
III	gt cds	CDS	1950665	1950760	.	+	0	ID=CDS198;Parent=mRNA273
III	gt cds	CDS	1951062	1951358	.	+	0	ID=CDS198;Parent=mRNA273
III	gt csa	exon	1951062	1951426	0.975	+	.	Parent=mRNA273
III	gt csa	mRNA	1950628	1951426	.	+	.	ID=mRNA274;Parent=gene179;Target=yk778a10.5 1 197 +,yk779g10.3 1 447 -,yk1617c03.3 1 461 -,yk1369h11.3 1 472 -,yk1369h11.5 1 479 +,yk1617c03.5 1 493 +,yk890g04.3 1 447 -,yk1010f03.3 1 462 -,yk890g04.5 1 477 +,yk1010f03.5 1 494 +,yk779g10.5 1 495 +,yk1160b11.5 84 440 +,yk1660d01.3 144 579 -,yk1450d10.3 220 663 -,yk1470f08.3 228 671 -,yk1691a10.3 178 621 -,yk1711g11.3 170 613 -,yk1319b02.3 270 730 -,yk1160b11.3 84 545 -,yk457d7.5 1 376 +,yk602c4.5 1 372 +,yk664b3.5 1 376 +,yk647d12.5 1 383 +,yk229f4.5 1 374 +,yk1020a05.3 1 468 -,yk1020a05.5 1 481 +,yk1016a08.3 23 271 -,yk116e3.5 1 360 +,yk1064e06.3 23 443 -,yk1151e09.3 23 447 -,yk1580b09.3 23 449 -,yk1587h09.3 35 461 -,yk1594g06.3 23 449 -,yk1362f01.3 23 459 -,yk1393f05.3 23 459 -,yk1521b10.5 23 466 +,yk1521b10.3 23 467 -,yk892h07.5 23 471 +,yk1176h06.3 24 475 -,yk1155e04.3 23 473 -,yk1291e10.3 23 473 -,yk892h07.3 23 473 -,yk1159h09.3 23 473 -,yk1130b02.3 23 485 -,yk1125f08.3 23 485 -,yk1693h02.5 23 487 +,yk1025d03.5 23 490 +,yk1064e06.5 23 495 +,yk1155e04.5 23 496 +,yk1291e10.5 23 496 +,yk1176h06.5 23 496 +,yk1362f01.5 23 496 +,yk1580b09.5 23 496 +,yk1130b02.5 23 498 +,yk1151e09.5 23 498 +,yk1016a08.5 23 498 +,yk1159h09.5 23 498 +,yk1587h09.5 23 498 +,yk1594g06.5 23 498 +,yk1125f08.5 23 499 +,yk1393f05.5 23 499 +,yk199f2.5 1 377 +,yk497d11.5 1 380 +,yk645g1.5 1 375 +,yk483c3.5 1 378 +,yk253d3.5 1 379 +,yk615h4.5 1 376 +,yk281d11.5 1 360 +,yk330h9.5 1 360 +,yk446a5.5 1 377 +,yk498f9.5 1 360 +,yk453a11.5 1 360 +,yk326h8.5 1 360 +,yk140h11.5 1 360 +,yk627c5.5 1 360 +,FLYBASE 1 131 +,BP 1 131 +,RP 1 131 +,yk448c12.5 1 360 +,yk373f11.5 1 360 +,yk60a11.5 1 360 +,SW 1 130 +,yk476f7.5 1 360 +,yk516c9.5 1 360 +,yk448f2.5 1 360 +,yk558h2.5 1 360 +,yk494c8.5 1 360 +,yk492f11.5 1 360 +,yk551b11.5 1 360 +,yk646a8.5 1 360 +,yk278c2.5 1 374 +,yk471g11.5 1 360 -,yk222d9.5 1 302 +,yk814a07.5 1 104 +
III	gt csa	exon	1950628	1950760	0.947	+	.	Parent=mRNA274
III	gt cds	CDS	1950665	1950760	.	+	0	ID=CDS199;Parent=mRNA274
III	gt cds	CDS	1951062	1951358	.	+	0	ID=CDS199;Parent=mRNA274
III	gt csa	exon	1951062	1951426	0.975	+	.	Parent=mRNA274
III	gt csa	mRNA	1950628	1951721	.	+	.	ID=mRNA275;Parent=gene179;Target=yk778a10.5 1 197 +,yk779g10.3 1 447 -,yk1617c03.3 1 461 -,yk1369h11.3 1 472 -,yk1369h11.5 1 479 +,yk890g04.3 1 447 -,yk1010f03.3 1 462 -,yk890g04.5 1 477 +,yk1160b11.5 84 440 +,yk1660d01.3 144 579 -,yk1450d10.3 220 663 -,yk1470f08.3 228 671 -,yk1691a10.3 178 621 -,yk1711g11.3 170 613 -,yk1319b02.3 270 730 -,yk1160b11.3 84 545 -,yk457d7.5 1 376 +,yk602c4.5 1 372 +,yk664b3.5 1 376 +,yk647d12.5 1 383 +,yk229f4.5 1 374 +,yk1016a08.3 23 271 -,yk116e3.5 1 360 +,yk1064e06.3 23 443 -,yk1151e09.3 23 447 -,yk1580b09.3 23 449 -,yk1587h09.3 35 461 -,yk1594g06.3 23 449 -,yk1362f01.3 23 459 -,yk1393f05.3 23 459 -,yk1521b10.5 23 466 +,yk1521b10.3 23 467 -,yk892h07.5 23 471 +,yk1176h06.3 24 475 -,yk1155e04.3 23 473 -,yk1291e10.3 23 473 -,yk892h07.3 23 473 -,yk1159h09.3 23 473 -,yk199f2.5 1 377 +,yk497d11.5 1 380 +,yk645g1.5 1 375 +,yk483c3.5 1 378 +,yk253d3.5 1 379 +,yk615h4.5 1 376 +,yk281d11.5 1 360 +,yk330h9.5 1 360 +,yk446a5.5 1 377 +,yk498f9.5 1 360 +,yk453a11.5 1 360 +,yk326h8.5 1 360 +,yk140h11.5 1 360 +,yk627c5.5 1 360 +,FLYBASE 1 131 +,BP 1 131 +,RP 1 131 +,yk448c12.5 1 360 +,yk373f11.5 1 360 +,yk60a11.5 1 360 +,SW 1 130 +,yk476f7.5 1 360 +,yk516c9.5 1 360 +,yk448f2.5 1 360 +,yk558h2.5 1 360 +,yk494c8.5 1 360 +,yk492f11.5 1 360 +,yk551b11.5 1 360 +,yk646a8.5 1 360 +,yk278c2.5 1 374 +,yk471g11.5 1 360 -,CK580762 1 219 +
III	gt csa	exon	1950628	1950760	0.947	+	.	Parent=mRNA275
III	gt cds	CDS	1950665	1950760	.	+	0	ID=CDS200;Parent=mRNA275
III	gt cds	CDS	1951062	1951358	.	+	0	ID=CDS200;Parent=mRNA275
III	gt csa	exon	1951062	1951411	0.995	+	.	Parent=mRNA275
III	gt csa	exon	1951713	1951721	0.556	+	.	Parent=mRNA275
III	gt csa	mRNA	1951519	1952513	.	+	.	ID=mRNA276;Parent=gene179;Target=yk372d12.5 1 375 +,yk372d12.3 1 300 -,yk1703a04.3 1 500 +
III	gt csa	exon	1951519	1951659	0.982	+	.	Parent=mRNA276
III	gt csa	exon	1951713	1951829	1	+	.	Parent=mRNA276
III	gt csa	exon	1951902	1952513	0.991	+	.	Parent=mRNA276
###
III	gt csa	gene	1963554	1970446	.	-	.	ID=gene180
III	gt csa	mRNA	1963554	1970446	.	-	.	ID=mRNA277;Parent=gene180;Target=yk23e3.3 1 390 -,WP 1 1309 +,yk23e3.5 1 360 +
III	gt csa	exon	1963554	1963898	0.975	-	.	Parent=mRNA277
III	gt cds	CDS	1963647	1963898	.	-	0	ID=CDS201;Parent=mRNA277
III	gt csa	exon	1963953	1964107	1	-	.	Parent=mRNA277
III	gt cds	CDS	1963953	1964107	.	-	2	ID=CDS201;Parent=mRNA277
III	gt csa	exon	1964993	1965165	1	-	.	Parent=mRNA277
III	gt cds	CDS	1964993	1965165	.	-	1	ID=CDS201;Parent=mRNA277
III	gt csa	exon	1966002	1966439	1	-	.	Parent=mRNA277
III	gt cds	CDS	1966002	1966439	.	-	1	ID=CDS201;Parent=mRNA277
III	gt csa	exon	1966813	1967020	0.987	-	.	Parent=mRNA277
III	gt cds	CDS	1966813	1967020	.	-	2	ID=CDS201;Parent=mRNA277
III	gt csa	exon	1967077	1967198	0.91	-	.	Parent=mRNA277
III	gt cds	CDS	1967077	1967198	.	-	1	ID=CDS201;Parent=mRNA277
III	gt csa	exon	1967254	1969663	1	-	.	Parent=mRNA277
III	gt cds	CDS	1967254	1969663	.	-	2	ID=CDS201;Parent=mRNA277
III	gt csa	exon	1970232	1970363	1	-	.	Parent=mRNA277
III	gt cds	CDS	1970232	1970363	.	-	2	ID=CDS201;Parent=mRNA277
III	gt csa	exon	1970410	1970446	1	-	.	Parent=mRNA277
III	gt cds	CDS	1970410	1970446	.	-	0	ID=CDS201;Parent=mRNA277
###
III	gt csa	gene	1971220	1975502	.	-	.	ID=gene181
III	gt csa	mRNA	1971220	1975502	.	-	.	ID=mRNA278;Parent=gene181;Target=WP 1 1166 +
III	gt csa	exon	1971220	1971570	1	-	.	Parent=mRNA278
III	gt cds	CDS	1971220	1971570	.	-	0	ID=CDS202;Parent=mRNA278
III	gt csa	exon	1971619	1971773	1	-	.	Parent=mRNA278
III	gt cds	CDS	1971619	1971773	.	-	2	ID=CDS202;Parent=mRNA278
III	gt csa	exon	1971899	1972068	1	-	.	Parent=mRNA278
III	gt cds	CDS	1971899	1972068	.	-	1	ID=CDS202;Parent=mRNA278
III	gt csa	exon	1972118	1972501	1	-	.	Parent=mRNA278
III	gt cds	CDS	1972118	1972501	.	-	1	ID=CDS202;Parent=mRNA278
III	gt csa	exon	1972550	1972766	1	-	.	Parent=mRNA278
III	gt cds	CDS	1972550	1972766	.	-	2	ID=CDS202;Parent=mRNA278
III	gt csa	exon	1973235	1973470	1	-	.	Parent=mRNA278
III	gt cds	CDS	1973235	1973470	.	-	1	ID=CDS202;Parent=mRNA278
III	gt csa	exon	1973518	1975502	1	-	.	Parent=mRNA278
III	gt cds	CDS	1973518	1975502	.	-	0	ID=CDS202;Parent=mRNA278
###
III	gt csa	gene	1977303	1980450	.	+	.	ID=gene182
III	gt csa	mRNA	1977303	1980450	.	+	.	ID=mRNA279;Parent=gene182;Target=WP 1 874 +
III	gt csa	exon	1977303	1977441	1	+	.	Parent=mRNA279
III	gt cds	CDS	1977303	1977441	.	+	0	ID=CDS203;Parent=mRNA279
III	gt csa	exon	1977492	1977554	1	+	.	Parent=mRNA279
III	gt cds	CDS	1977492	1977554	.	+	2	ID=CDS203;Parent=mRNA279
III	gt csa	exon	1977881	1978741	1	+	.	Parent=mRNA279
III	gt cds	CDS	1977881	1978741	.	+	2	ID=CDS203;Parent=mRNA279
III	gt csa	exon	1978792	1979883	1	+	.	Parent=mRNA279
III	gt cds	CDS	1978792	1979883	.	+	2	ID=CDS203;Parent=mRNA279
III	gt csa	exon	1979937	1980162	1	+	.	Parent=mRNA279
III	gt cds	CDS	1979937	1980162	.	+	2	ID=CDS203;Parent=mRNA279
III	gt csa	exon	1980210	1980450	1	+	.	Parent=mRNA279
III	gt cds	CDS	1980210	1980450	.	+	1	ID=CDS203;Parent=mRNA279
###
III	gt csa	gene	1980811	1982635	.	-	.	ID=gene183
III	gt csa	mRNA	1980811	1982635	.	-	.	ID=mRNA280;Parent=gene183;Target=WP 1 324 +
III	gt csa	exon	1980811	1980995	1	-	.	Parent=mRNA280
III	gt cds	CDS	1980811	1980995	.	-	2	ID=CDS204;Parent=mRNA280
III	gt csa	exon	1981163	1981517	1	-	.	Parent=mRNA280
III	gt cds	CDS	1981163	1981517	.	-	0	ID=CDS204;Parent=mRNA280
III	gt csa	exon	1981877	1982017	1	-	.	Parent=mRNA280
III	gt cds	CDS	1981877	1982017	.	-	0	ID=CDS204;Parent=mRNA280
III	gt csa	exon	1982226	1982322	1	-	.	Parent=mRNA280
III	gt cds	CDS	1982226	1982322	.	-	1	ID=CDS204;Parent=mRNA280
III	gt csa	exon	1982442	1982635	1	-	.	Parent=mRNA280
III	gt cds	CDS	1982442	1982635	.	-	0	ID=CDS204;Parent=mRNA280
###
genometools-1.5.1/testdata/nGASP/test.fas000066400000000000000000000370211211610345200202420ustar00rootroot00000000000000>BP:CBP00004
GSHQIAKNFVNSSTPDLRPTFVVNFDTSTVICQHSSDPTDLHIHNMSSLCDGKQDCFVNPAMHDEVFPYCEHKCESTCSGKGACLYDGSKPQCYCDSGFSGAACELQDKNECLEHPCHMMAQCQNTLGSYECRCLPGYQGNGHECSDIDECADNIATRCPEHSQCINLPGTYYCNCTQGFSPKGNQGSGLDKCADINECETGAHNCETNEICENTIGSFKCVTKCSPGYSLIDGKCEDVNECDSEKLHKCDVRAECINTVGGYECECEEGFDGDGKNCQRGNPMSLSIAKSSCRKNSAICDRHASCNIFLDICDCKTGYTGDGITCHDVNECDAKETPCSEGGRCLNLDGGYVCCKDGQDDAACIKDQRAFCSGGCCDNAICSNATCACIDGFRGDPHKKCVDINECVENDSVCGGVGDRCVNLFGGYKCCQHGSQEVECTDQAFSSDSSTVSSHGADFTTTGEQVIEGSGSIQTSSGGSITVTRGLIPKEVELTTSGRLACTSYCPPNSECVGGFCECVKGYGGNALVGCEDVDECITETCNVEANEWCVNLIGGFVCCNPTNATHDDCIVLSLGSNVPFSDFLTVPGLEITKEKGLHVIGPNEEDTVVATRSNHSVTSDQLITEVVQQSKNFSSGQIILTRKSVTGGEAVTQTTDGDGEFGLEISAKDFGITLPATLEPRVEGSGKSPVAGVWTEEEDGGEDDDLMEASGSHGSWSTTINGTGFTGSPRSEGTIRVRITTLGEDGETETATKPGITVPGKDGKLAIEKEGHESVSSGSSATSSSGSTGSGASGSTATGKSGSSATSSSGSSSSGSTESGSSGSSATSSSGSTSSGESGSTATEESGKSEPSGATGTESSGKSESGASGESGPAGSSTTSSSGSTESGASGSNATSSSGSSATGESGSSSSGSTESGASGSNATGGSGATGNESSESAGTTASPESVTASRESVEGSGTTPSESTSSLPEGSGEWIETGSKGHFERGNKVSVSHGNGKPEGSGPKESGKPEVPGSQGSGAKESGAGKPGSGSRGPEITTDGEESESTSSGSGKPKNPKITTDGEGSKSTPIGDGKHPEDVEGSGILTTSSGGKNSTLEHGTKLVEVKPEGSDKNPGVGLEISAGKVTSAPEDKEKSNEVGLEIVWESTTPEPTTPDTDNVGLEISGRDLITKRPHQIEGSGTGDEEITATTRDVSKSTKKPRLEIDGGDNGETSGVDGKASTPSPTSPGAPESTTPSAPTTAPEDVTPETGSGEPGIPDGSGESSTAAPEGVSPTSSAPAPEVPTTPEGSEESTKTPEEATTATSPEEETTTQEPLILTAAPSKAPESSTKPSEAPEASSESTAAPPTAQPATVIPPQNREEKPEPTKETFALPTTTEKPVNETIENTKCMSSDECGLDALCERRTGVCRCEPGFEGAPPKKACVDVDECATGDHKCHDSARCQNFIGGYACFCPTGFRKTDDGSCEDIDECKEHNSTCCGANAHCVNKPGTYSCECENGFLGDGYHCVPSTKKPCDKEQSTKSHCAESNMSCEVDTTDGSVECKECMSGYKKSGTTCEDINECDEQSPCSPSASCVNLNGTFSCSCKPGFRGDGFMCTDINECDEKHPCHPHAECTNLEGSFKCECHSGFEGDGIKKCTNPLERSCEDVEKFCGRVDHVSCLSVRIYNGSLSSVCECEPGFRFEKESNSCVDIDECEENRNNCDPASAVCVNTEGSFKCECAEGYEGEGGVCTDIDECDRGMAGCDSMAMCINRMGSCGCKCMAGYTGDGAHCTKIEEPKEASKTACTEEWSRLCELEKKQCAVDEEEVPQCGACLPGHHPINGTCQSLQISGLCAQKNDCNKHAECIDILPDSHFCSCPDGFIGDGMMCDDVDECNNAGMCDDENSKCENTIGSFNCVCLEGFKKSDDDKCVLKTPNREKIEINEENSSSTPSESQKPESTTQGTVTTSVLSSEPTSEAPTSSTSPVTSSEKASESTTSSESPVTPSETSVTTTSLCSTVTCHSLATCEPSTGVCICRDGFIGDGTSSCSKKSTADCISLPSLCAENAKCDNSARSCECDAGYIGDGYVCSPHPQDCVLRDNLCSPEAICQNRRCQCLPGFTGDGVKCVSIHERASNCSQCDANAHCVGGTTCKCNPGYFGNGLCCVPDPLDCVHFTGICHPNAVCNPDTRQCQCSSGFSGNGVSCFPQKSCRTDKSVCAKNAICLPTGSCICRHGFKGDPFYKCTSLVAKEPSNAQDLSDVSSCVTPCDASSQLCISGECICKPGFRQNPGSKTCADIDECAEKTHRCNRIATCRNTFGSHVCSCPEGHVGDGVTCVPHVNQGKLSVYCEADGMTLVLGNETSDFEGKIFVKGQAENPYCSKSFSALLNSHKPYVFKVAFQHCDVQLLDNHTMASTVVVQKHAMFLTNKADSYDLRCQYPIGSRAVQSHVNVSELATTSTLTDKNSTLAPICRLSVSNDQHSSISSAMVGDTLKLALEVTPSENFGILPRNCFAVNIESGERYTLTDEQGCAIDESLFPQWSVTNSAK
>BP:CBP00012
MAPKDDPDNRGFDDQRRPSQRSTVLAIPALAVNDPKADPKIASDLPANYVDDDDDAPKLYTPSLFEKILNYLLCRGDIANQQLEAQPVSIPGLFRYGKRFDYLLLFIGTICAIISGVSQPIMALVSGRVTNALLVYPPTSKQFRNKANENVYIFLGIGIFISITNWIQYMCFQHCCSRVMAQMRHRFVYSVLRQNAGWFDKNHSGTITTKLNDSMERIREGIGDKLGVLLRGFAMLIAAIVVAYIYEWRLASMMLGVAPVCCICMSLLARQMTSTTIKELIGVGKAGSIAEESLMGVRTVQAFNGQEEMVGRYQTELEKGRRFAVWKGFWSGFFGGLFFLCLFSFLGTGMLYGAYLLKVGIIGSPGDVFIVVMSMLLGAYFLGLISPHMMVLLNARVSAATIYQTIDRVPKIDPYSKAGKRLPNVVGRVKFENVHFRYPSRKEAKILNGLNLTVEPGTSVALVGHSGCGKSTSVGLLTRLYEPEAGNVTIDGTDVRELNIDWLRNVVGIVQQEPILFNDTIHNNLLIGNPGATREKMIEVCKMANAHDFIEKMPKGYDTLIGDGGVQLSGGQKQRVAIARTLIRDPKILLLDEATSALDAQSESVVQSALNNAAKGRTTIMIAHRLSTIREADKIVFFEKGVIVEAGNHEELVHLGGRYFDLVKAQQFKADPEATEEFEEEEIDLDDNSRSSRRSSMTSARSGSEAFQRGNSLNDSFSGSRRSARADAENDAFAAHEAEVMAQDGQITAGYLDIFKNAKGNYIYMFLGTVFALIRGLELPALALIFGWVFEGFTFVPYGGRMMHRMAMAVIAFASVGVGVWISQVASSVLFAIVSENLSLRFRVQSFRNLLYQDASYFDNPAHAPGKLITRLASDAPNIKAVVDARMLQVIYALAAIIANIVIAFIYCWQVAILGTSLILLLAFVMIGLAYKISLMNIEQIKNDEAGRTAIEIIENVKTIQLLTRCELFFDHYQTSSKQQKRSELKKGMIEAINYSITQSFMYFMMCFTYAVGIRVIYDGDKSSDVTFKGIISMMLGAVAVMNSAQYFPEFVKAKTAAGLLFNIIYRKPRTGDLMEGDRPEIRGNILFENVKFSYPQRPLQPIMKGLQWTALRGQTVALVGPSGSGKSTNIGMLERFYDVTGGVLRIDGQDIRNLSLYHLRTQMALVGQEPRLFAGSIRENVCLGLKDVPLEKINKALELANANRFLANLPAGIDTDVGEKGGQLSGGQKQRIAIARALVRDPKILLLDEATSALDSESERAVQEALDRAREGRTCITIAHRLSSIQNSDLIVYIDKGKVQEAGNHAQLMQKKGRYYKLIKKQDLAV
>BP:CBP00016
MSVEWKSALRLQIEALAKRNDLHRKSSEEEIKKRIVDMDRRIVKLRELVSTSANDAAIFYLECVCHADETERLLNRESSVEKEKKWRKMKRKPSSQIGPTESRTVSSLPSVSPPDVIQTINVSTLEAQDQMPQRPHWWDQFQIYRRTDLLRFSKQNDRRELWRTQKDFFLTCLGFMVGVGHTMRFPAKVYQHGGGVFFIPFFSLVFFGLPLVFLHLSLGQYTGQAANTAFSKLMPIGSGVGWALVVIAIPVAVYYNIIVAWAIHYFFQSAKGLLLGDELPWETCRDEWQLDNRCCNLHNLHSCFNSSNSITAPEAFFHSEVLSLSTFGDFALGPLQSHLVLSLAAAWLLVFFGVFKGLGSIAQTMNVTATVPYLLLSILLLRGISLPGANKGLSFFFTVDSTKLWKWQIWKSAAEQVFYELGIDAGPLISMAAFSRYRNNVYRDSVLLVIMDALTSILSGMVIFSFVGFIASESNSNVNDVLKHDPLYLSFTVYPGVTSFMYWGGLWATMFFGMLVMAALDAEFAWLEMIASAFMNHFSTKNKAVENRLLAFLCLVGFFFGLPLCAQGGIFVFHAIENLNANWNSFSLALLSVAIVCYVYGIDNYLTDISGMLRVPRIPISKAIRFRDKIVSILGPGGIYIKFSLCFICPVILTVLLVASVLGYQRISFAGRPIPIDYEIVAWVVMIGPLLVVPLVAFLQVRQIRNEGKLLKSLFDTSEWRENPDDLLEPKDAYMKQDSKYESPPNRRRTPTIFTHRENTYMYIDSRGPTVRSRVFPMGAPLDPYGWKLGRLRDHQQHIEEVESNYSEEGSTTNNSFMASTVKHNDDVELTLFGSPPAIMGDEDKNMVTKFSESMPVNYKCRNEQAAPVQSRREPRLGRMARKTRRKRSSPSASDPPVPTSPLPPPPRLYHCKSEPPMMRSEEEHGTPKIITPDGSCSISDSSDDSSDDNIRRATVIRRKTSDDDAFTQISTAESISITPLDFPRQRSLSSVAIYDQEQKNGRSKVLSQLKRPTPIVMPPK
>BP:CBP00024
FQSVHHHLNEEELKQVFGVSNKHEVPEYSLIETTRHPLKNGGLKMKFVAWNDTYHLNLRKNSRIVSPHIISVIRHGDDAVTTYDGLRDYNQCHYQGEVKSHGNMKAAISDCGALMGSLVMEDHFLVLQTLPKRVHHLQKERHLVYKRSAGLLTDTENKIREEITRLQEEQESFCDTSEQLDDPAMTIPAHLHFNYTIPTSAQLDSPFIFPNMDPITLEIGLFLDSKLFEHFEREYIQDAEQHLLEFSLALINNVHVLYQQDTLTPNLDIVIVRYEMWKTQPSSLSTGVHKNGQAQSLLDAFCRYQAHMNPGTDLTDMNHWDHGVLLTGYDIYHTTTSVAGVAPVARMCDPLFACSLVEGLHLGRSFVLAHEMGHNMGMVHDGVQNQCNKGCCLMSAVNGAGKTTWSDCSVREFNAFLLQLDESGRGNCLRDASPGLISTNHLSDTRLPGQRFTADQQCSYFWGRDYRVEIPNGKAMDDICRILWCGNSGSTISTAHPALEGSWCGHNKWCHKGHCTSWNFDLPPVPIDGQWSEWGGAEKGCPIQQCAVSGSITIQAQHRDCVNPAPNNGGRTCEGANIRGIVCGATSSNCLGFTREEFGNKICSSIKFDPHKPDQQLTGEGFEHSTQPCRVWCHLIGSELIRNKGQFPDGTPCGFDAYCVGGQCLALSCDNKALVEQQEDCPRLEGRSIHQWEDWSSWSECSVSCGPGGRQVRERKCSSGRKCQGVSEESRACEGVLRDCEEFGEWKDWGPCSEKCALGIQKRFRPCLTDQCASEHLQEKRPCDNEGCWTNWDEWSSCSQTCGGGRRYRLRKCLDFKCEGDDLEKESCNTQKCISQTWGDWLPCSVSCGIGFQIRERLCDGELCATANKQARTCNQQQCPSTFSLAVWSEWGEWTTCSATCGEGLQSRERSCRRGSCQESDAAQTRRCVNGPCDHTFLPWSEWTPCETCSSFDSRKRIAKCDGTTDNCQDKIDEETCDNACLREQHSFGPISPKRPKLITSNELRKAFGRPLLPIESITSSKWSEWGPCSVTCGSGRRVRTRDCQEENCPEQNIQHEECSLNSCLDLFIWSDWSSCSKSCGHDATQTRQKLCLFNNAECSSYAESRRCKNLPTCTSISSGNTISENSFDAPQWSEWSSWSACSCFSLTSTRRRFCQVADPTVQGFCAGSILEQIPCAPGNCSPSAGGWSSWSEWSSCSKDCGDTGHQIRNRMCSEPIPSNRGAYCSGYSFDQRPCVMDNVCGEEKVNGGWTDWTSWSECTDYCRNGHRSRTRFCANPKPSQGGAQCSGSDFELNPCFDPARCHLRDGGWSIWSDWSPCSASCGFGVQTRDRTCSSPEPRGGQLCTGLAHQTSLCDLPACDHESDGEWSAWNEWSGCMGNCGFGTRTRVRACVSPPASHGGQPCFGRSSEITECRQSESTCSSFITSSLLADGYFIETDQQQ
>BP:CBP00071
MGDEGYRGWIKLEIPCFEPERHMNNIIRCHTTKLEPALNSYNMRIHTKGQVQAVEEQDCEPFYESNYEIVSSHFSHHLIIAIQNYLKSLSMDRLMPFQLGNLVLHSSDFWSSELTCHLADIPLSAFFFGNIQGGTFINHWEVSFWEDTHRRNRLRQKNMQPTASDRQGLNQIRVEFEFDKVDFMTVHFKHKEGDFEVISKDFRKTRETVTMYYQITVRRTSIRRVIVDPVVNDTNGGDRIRIHFELNCPVLIRRAYKTEKQEAEAKHQVPHYRRFLVINRGRSANMYPTPKAITDSPVFTIEFDTSVSLEEVYRLISRLRIRTGVSIEFATIPSVDCLIWRENPYHRWTFHGSSHLSPTHFSAPIYRDFITTAFPRKHEVCGSREVDTNRERKFAITYLLECLISRGAVVKDQILLDDTIWHRFLEVILHYYTKDDKLCEAGLEDLVHMIDGRKRIGSLIKCFDRICQTRQKNSLVNGLTTEEMREGYQRVRKIIFTPTRVIYVAPETLMGNRVLRRYDHDGTRVLRITFRDDDNQKMRTNKTSTLLEKTVNTYLMNGITVAGRNFGYLGSSNSQMRDNGAYFMEKYSSSQCREYEKMCRMAPPITFNPKIQAARKNLGRFETIDNIPKMMARLGQCFTQSRLSGVNLDRCTYVTMYDLTGGKNIKGDEYTFSDGVGMMSMNFAQMVSQVMDFGKGVPSCFQFRFRGMKGVIAVEPFLDDLRQWSIENDIQEVSEDTAWGLNCVFRPSQIKFISKRHPRDQVEIVKYSSPVPVSLNKPFINILDQVSEMQSLECHRRVTNRIEELLDRQMLSFAQQMIDETFCRNRLKELPRRIDIDYLRTTWGFTLSSEPFFRSLIKASIKFSITKQLRKEQIPIPADLGRSMLGVVDETGRLQYGQIFVQYTRNLALKLPPKSASRSVLTGTVLLTKNPCIVAGDVRIFEAVDIPELHHMCDVVVFPQHGPRPHPDEMAGSDLDGDEYSIIWDQQLLLDRNEDPFDFTSEKQKSSFKEEEIDDLMREFYVKYLKLDSVGTISNSHLHNSDQYGLNARVCMDLAKKNCQAVDFTKSGQPPEELERKWRKDEVTGEMIPPERAERVPDYHMGNDHTPMYVSPRLCGKLFREFKAIDDVLKISEERDEQVEITIDETIMVDGYKEYMHSAREDLARYNAQLRSMMENYGIKTEGEVFSGCIVDMRNRISDKDQDDMSFYNTNQMIETKVTNLYKKYREHFFEEFEGAWEANTEGTSRGESDTNILQRHCRAPTQNMMKKAVAWYRACYEEARVTRENKKLSFAWLMYDVLAMVKQTKSLTSDDIRMGGSNPLYTMLDAHRSQYLLDNRSVFEDYIRFAPSKNQGEQVARALEIIRMYVETNPGLEEVMFVINEWARASKLFENQPIRNYHLSLLFILFATRQFSSVDGNAAAFFPKIDERGWREEKANGEFKQGLEFMEMKKSQMIVKFLEFLASRKFRKLPNVSFRTLRFSSIFMRGEWQIFHVAALKTYYNLLFNLRFEELPVSTDPTMTVRSIIRENEPFVVELPADADRTLVHRKLIEHTGVEEIYMRNMEKSVRGVDEQQKANTRYLVSTRGTLESMYKLRQLVAVKVPIKTYVTGQEISTQMARLCYEKIVKGHIS
>BP:CBP00094
FRIGHLEYENSNETKILEICMKTAGTRKQHTLISLPSCHNFNGLENAANLNYQYAVDLLIGAACDEETQTVSRLALRWHKLYLSSAPLSTKEKEGTTIALKPHSLAGTAEVILAVCKSMKWKEIGLIYSDETKYTAHAIYDMLAEKEEEDIKINVFLQTDGTMNTYTILHSARVLISFLSTSDLSRFVKTLKDKAFRPLEFSIIHVDCYKSETTEFYTHLDQKASEETNPISAARLRKLHRHVALLRNSHDDKGNMEEFATKHGMIVIFFVFPFPTLCFQPSHTLYKALILCDGLQLLSDYKPLSDNLTIVQQQPTLWEHVTNTEIHGYSGPMFIGSDGVRLPYYEMFMWRDGKTQHVASVRPRESEFCEKEKMSNESKNCYEITRTIPFGQLLDDLPPYSSDCGYDNNLCSDFHVFMIAAIVFSILLIPMAIAFYLQRKEHLIQQMPWRVPLDTINFDDSRNGRLLSVSRRVSTVSTARASYSSIFSANVSEHAHVNKQKVSIKRYVQRRPITFTRQEMEMLNQLKYMSHTNINPFTGICFNQGSELIVMWQFTARYSLEDLIFGKEQKFGRNFQSTFIKHIMHGINFIHNSSIKVHGTLYLSNCVVDSYWVVKLTDFGIKNILKERMHHKELAPNSSFDIDAIHYKYLQLAPEHLSSLLEKHEEPMGTVEGDIYQLAMVIYQILFYMKPFAERQEDIKAVKKLFFLELATLLSNQSTAPLHPKVPEGNSFTMRLLSIIQQCWLYKPAARPTLIKITDAVNREFGQDVKGTLIDQMIEMIDEYSANLEHIVAERTRELEQDMATTENLLYQLLPKSIADSIRSGKSVVPEQHSSVSLLVVDVCQFTKFCEAFIPVHILETLQELYSSFDYIVQKNKAFKVENVGDAYLICSGIPEMTACRHLREVSKISLKLQEFMKTFTVRHRPSHILQIKMGITSGAVAAGILGSIAPRIITGICKNLAYKILNNIQPGTIQLSELTANTMMEKFPSFIIEERGMIDVKGKGTCLTFWLTGEKDQMRRQSSRSSCISHSQIKFEIEEANKTNNQFL
>BP:CBP00176
MSNWDYIDEVDIIPKLPPNFDELRESKKWQERKEALEALLKVLTDSERLSTKVSYAELIGNVQTVLAKDANINCQALAAKCIAKFATGLRTKFSAFATPLLPVIFDKMKEKKPTLREPLVECAMEVGRTMPSLEAGQEDILAALAKPNPQIKQQTALFVAKQLDLVVPAKQPKGFIKAAVPVFGKLTGDADQDVREASLQALGAVQRIIGDKNVKSLLGDLSSDEGKMKKIGEYADKSAASYAEEQAKNAPPPSSSASAPSAAAASGSSGNVTSAAVTTAEPAAEADPWDFLDAFDVLSKMPEGFDTNIESKKWQERKEALEGLQQLLTANPKLDPKANYGALVERLQKVLEKDANINVAALAANCITGIANGLRTKFQAFAISVAPIVFEKFKEKKPTLRDPLVACIDAVVATSNLEALGEIVLTALGKPNPSIKTQTDLFLQRTFMKLNSQTMPKKTLKTLVPLLIKHSGDSDAEVRDASYAAMGAMMRAIGEKPSLQLLADIVTDNLKMGKIKEYHQKALAEAGPAEIAAMVQSMHKADAPPAAAAPPKKAAPPPKRQESEEEQVEEEEEPLKLPAEEKKKAAPTKENAENEPPVAPKTELLLNDNGEKAQRIKEEKQLKLVKWNFQTPTDEHIAQLQTLLGNQAKVSLMSQLFHKDFKQHLAALDTLIRLADTAPRSLLANSDLLLKWCTLRFFETNPAALIKVLELCRVLVELTRDTETPMSQEELTAFVPYLLLKTGEAKENMRTAVRDIINVLSDIVGPLKMTPMLLDALKSKNARQRSECLLVIESYISSSGISPLKSLTVEKIVAPFVGDKDVNVRNAAINVLVACFKFEGDQMWKAAGRMADKDKSLVEERIKRSGVKAGSGVATSPPNGGPKIVVPQQQQSVVRRPASRSRTREPEPEDDYQDQRAIANSTFTKGNSSSRYALRDDVFATAINRLADSTYVVTPPQPPSAWANNTFQMKRTNSSSSISSIDTSDQIQRSINNISSSLADVAQDAMYQVTYVLNQPEQRHLVDRKADMVFRASAAQLDMIIDEFKAGKDVTGTMDACSQMLFILMGGVEAEHGLEPLNASPETVKAIISSVLRCITQIGSTDAGYTMARSLNRLAMRLVYRVELSNLLCGLILAMIESIQLNSGITDLVSKLSSKWCDELEKRRAQLRASDIVDVFNQFYICTLTEQKMDITHIHIQVVDNYLERVILQQGDVVLDAARRLSSPHIHLTRMINKILQMMKEQNIDPIMPGTLDARAPDEEEAVVVRTGVQVCVNNILRDLKNVSTYNEQLNKLVQSSDKCRNEYSELVKNHALGEAVEELVSEQTIHGAPNFNKPDVVNAMTMTWKALDLLGPTRAETPTTPPQNLSRMDTTIVGTPLSRAEGAGTITRARGNIMRPKQRPTMSREQHEELRNRLQQAK
>BP:CBP00296
LHALETEKNVFSQFYAKKWPRQLRKPKNREISNFKHSEGAEFAAKSYFWDNNWDFDLPELPKPEQMIMPLPTSTPDVYDDFAFYRVLMEKEDKYILVACHANVHGFHRGDLRFLEINSRSRLNRLEGQSVIGSLFLGDIVAVTELARNSEAISPVRDVDVSLVTPDTSCYWIVSKMILYPRNVDKKSPVLFSIVNRMAAIKGENEPMNLNVDNWDMMHADSIYTGLTFRPETLEYHFSKDYQKKKINELVVSARTIRSYPGIYGTIFKFKEGDHREEFKKEMHLNTYTDESKELKRLAELEHEKNVFSQYYQKKSGNRRENHRGRKKPSSCKHHEAIEFAAKSNLWDNNWDKDLPMLPRSQEIIMPLPASAPAQTEVCGLYRVLMEKNDKYILIACHVNVHGYHRGDLRFLEVNSRSRLKGLSEQSVIGSLFLGDIVAVTELARNSNAQSSVRDVKVSSVTQETRCYWIVSNMILYPRILKPDVTFSFLKNRMAVVKGEDEPMRVNCDDWKTVAPDLIYTGMAFSPIKLDDNFSDDFQRKSKNLLISNVLKISSYPNAFGIIYSYEECSEQNEEFKIGTKAYSDTLEIHKYKRERIVETCSLMGFSAANTIFNGRFDCRAFHMYDVSKEGPTVRFRIENPRNRPTLGLWNNGNKILIGGPTGDTNGTIETVMCNSSHMGWLKIAARLTRECPKDFRFNGDLFVSQREPKDHYYLYDGYFQDMAPESNGRKIIETLYGGKPLELRTGDVGGEYFFPSTPEPIRLNVFQKEYVQMLLDGNPLVIGSSPFGCGKSMTIITAALEIYKRNAERNLVGKTHQLLITQSNFASVNLIEIARKTCNSGDEKLRNMKFMRFITDKNWNEQPDHGRTKFDMPFLMNKVFKQWAIGELDGNELMTHHTKSMIAHIIRNGTVTVDELCSAARRVFDKYGDCKIPFSGHLTEAFFILYEPDLIMTTADSSKSVCTLLDKKYETNKNECTTVQIDEASQLPEYTLLGLLKTYNKANFGLIGDIHQLPPFCMEELEGRLKEFGIGNTMERAIQNKLFPISNLRYVYRCHPQTTALLSELFYDGKLISGVTESQRNEFMIKRKDFWPNPSYPVMIINHMGTCQRMGTSAQNHSEKDLVSYMVQNLLDQRKYTLKPQDIGVISFYAAQTSLLTEQLRRSGVKCGTVDAFQGSEKEVIILCCTNEHATEFMQCKFRLNVALSRAKQATVIVGNLGYLRKAKYWNAIVKRVEAYGNL
>BP:CBP00327
MGALSQLRLLLWKNWLQQLRSPWFALFELVVPLILIGASFGLLIGFSDQFETTYDERRYAAWPVSGSAYDLIMPTNPNDSIKSAIVEPYFLFNSQLTCQFLNTYSTGANSYRMDIILAYAPMSAATTDKIMSIIQSRYSLTDLLSPVAPFIHNLYNITTIPTLNTNMSLKGFNTEGDMVSWMQGQFQSECDNPLLAGIVFDDSITKDLFNDNKRDFTYKIRLSNTHRRSRNAFGDDSYPWDTSVSFAIQYVSGPINPDDNDGGSPGYWQEGFMTVQRAVDVAITELITGSGPPISPLLDSYQVSRFPFPGYSTKIIEVGAYFMPVIVIFSFMTSVIYIVRAVVVEKEDRLKEYMRVMGLSQFINWIAHFLINYAKLTFAVIILTILLHFVALKSDMTLMFVFLMVYAFDVVYFAFLISSFMNSATSATLISVVFWMLLYFWYAFFSSIDQTNPYALGVRLINCLNPDIALNYGLQLLAAYETQAAGLKWNEMFNPPSPDNNLTFGHALAALVIDGIILVILTWYIEAVVPGGDGVPQKPWFFILPSYWFPYSGSKTVNSSDQYEHVEYASHVKLEQEPTDLTPTINVVNLTKTYGTSFFKKLFDCKFGKAGEKRAVSKLNLKMYPGQCTVLLGHNGAGKSTTFSMLTGVASPSSGSAYINNYDIRSSLPKIRRETGLCPQYNTLFGFMTVMEHLEFFAKLKERKWDPEEAREILARLRIDFKADFMAGALSGGQKRKLSLAIALIGGSEVVMLDEPTSGMDPGARHETWTLIQREKERRTILLTTHFMEEADLLGDRIAIMAHGQLECCGSPMYLKQQYGDGYHLTVVYSSTETPDVPKTTEIIREYILEANVFSYIGQEATYLLNAKHRPIFPKLFRELENHQRQCGITSFGVSITTMEEVFLKVGHLAEERYNYEHGIEDESSELIEKDDPMLQNLKAPVRLTGFALQMQHAKAMFFKRGIFFFRKWTQFLPQLAFPVAYLMLMVFTSQVIPSVKEQDPQTISLAPFSTKDKPGHVVSDSGNYVTMNGASTKLSNMVQNTVAALGVNQTVVDISSSVESFIMNQTNALGSRNFGLKYALGFVPSSIGIPGLPIPDLKTIRTYFNNFGLFTPALAITFTDSMLLSQAKNKQYTFTAINHPLPPSTQDTLKNTNRSDGAAFLIAYGLIVAFAVCVAGYSQFLITERKKKSKHMQLLSGIRPWMFWFTAFIWDAVWFVIRIICFDAIFYMFDITAYTHDFGIILILTLSFLLYGWTAIPFTYWFQFFFESAPKGFMMVTMYHILTGMIGSIAVPIIQQTSSMDAGYLWSIIFAWFFPTYNISQIATVTFQNENVRMACQKLDCNVPMFKSVVACCGTASQKLYVDNVLFVGNRKGILVYVIFLAVQGFIYWIMVFMRENDQFGKIFNLIKCWKKKDDHIWDITEGDKEEQRDVEDSDVIAEKSVVQRLANSNETALVSNNLVKWYGNFNAVKGVNFHVNSKDCFGLLGVNGAGKTSTFQMLTGENSISSGDAFVNGWSVKNNWREAGANVGYCPQYDAIIKEMSGEETLYMFARIRGIPEKEIPVKVQAVIHAIGIGMYAKRQIKTYSGGNKRRLSLGIAIVGLPDVLLLDEPTSGVDPKARRIIWNILNRLRDLGTALVLTSHSMDECEALCTELAIMVYGKFRCYGSCQHIKSRYGSGYTLLIRLKNRGDAEKTKSTIQQTFRGSKLKEEHILQHNYDIPREGDSWSRLFEKLETLSTSLNWDDYSLSQTTLEQVFIEFSRDAGQLDVDPYGDVPSLTGSGNKQNGYANRAMSVESITEMGTYF
>BP:CBP00332
SSSFTRIPKRDRTSPEKGEPSSKRSAPFTTPSSTTKIGRDSFAVMDTMEVQMNMFQLDITKMPPVIQRLHVDTLIITSKGKEINLNLGTVSTGGDVNSHNRRLAQHEIMRKFFEKKRSLFSSSSYHSLAYDTAACLYIPEGQYRGGEYEEVCLSQQDFAPEEWDIVSKISRRKDDSFIVRIKPAGAVYTQGDELFEPSNRYELTRIVEIVTSQKLNTTDFYQFGNATFPLRAHPNSEPDASSEIRSGFAKVARLTEGREGKHEMLMTVDTKLSPFYKPTSVIRCVLTKIQESRGGGGGGGGYGGRNDSRDSRGSFGGRSDSRDPRGYGGGYDRRSDSRDSRGGRDSYDSRRGGGDSEDFSSHEIDEIARACMESDKFLYSLESALKGLFAEAIHLKGSACTIRITGIKQCTANNTKFTKKDDKGEREISVSDYFYEEYNIKLKYPNLPLIVSKKMKYECFFPMEVLRIIPGQRIKVNKMSATVQSAMTGRNATMPRQHVDLVQRILQDSLKLERNKYMDAFGIELKSTRPVQLKAKILPPAEIRFKNLTYMPEIKRPGFKNPGKFVEPAHIYRVAVVSFDNAIDMRQAEDFCDRLFDYCRDQGIKCDRESKDWSIRELSSSDNVGIKEAMENWMKKKVDIFVGIARDKKPDVHDIMKYYEESVGMQTIQLCKQTVDKMMNPQGGRQTIDNVMRKFNLKCGGTNFYVDIPSNIRGRSICSNTETLHKKLLEKVQFIGFEISHGAARTLYDRSRNQMDGEPSIVGVSYSLKQSTQLGGFSYMQTQREYKIQKLDDAFPKCVKAYAEDAKTLPTRIVIYRVGAGEGDFKRIKEEIQEIRGTFEKIEKGYNPALVFIVAQKGSHTRIFPSRIDGNKAFEQNVPSGTCIDNVVTSFGYDEFILSSQTPLIGTVRPCKYTIIANDPAWSKNELIHLTYFRAFGHQVSYQPPSVPDVLYAAENLAKRGKNNYRVHQRYVSMQAIERRIISENADFVNENMQEQLASAIIDEMSDAMNGMTIPKRNFWA
>BP:CBP00396
RSRTKFRRDSRSRRQTPTSEMRSFVLLILLTSHLSAGSIDWSSLETPPQFTHGKNAETVFFKVEKSGMSDESAKNIPGNLLEQTIHCQAIGNPRPTYRWKKDGKTFLPSMFPEKVVQKPGEGSLVFSRLDETDAGLYQCEAENSNGTAVDRPVRVQETWIRHFKAAEPEVVVVEVGDPYQRNCSPPASNPNARVYWILMGKEPGHFETISSSHISSNEQGTLFFHYVNETDLKSDRYYTCTAENIELKDYKFGNQFSLQITNYKRRSSAPYWPNGPPPNTNTSEGENVSFDCTTYGKPTPKVTFYKNGVELGSQKDDRYMIEGTRLTIYDVKKGTYGKGDNAVYQCKSENKHGWLWTNFYLNLLAFKPQLLIDPGKEEVEAVIGKKVTLECKFFASPNAAVKWEAPMISGSKGNQIPADPHGVGRLVFSEVSASEEGEYECIGTNKYGQASGVITLKVRKPTTVKPFDRAEDVRMAGEEMRLPCDATSDSQLEVKHEWLVDGIPLPEERVNSGHYRIADDHSLIVANPTQDDSAKYKCVVSTKLDKVEKEIKIQFKDVPVAVHSAYVSNCDKNSLTAFIKFDHIESIHTIAPVKEFWVQYQMDSETEGSQWRTHPSPSAAHPNDQVTDQLRTTSGSATVSLQPFGKYVFRVLARNSVGDSATTTVKGICETPAKQPDKNPGEVAAKGTSPENLIVQWKPMAREEWNGAKFHYVVKYRPVDEDQRDGDWKEVAVEDPFADRVTINLDDDKDVKPFQPYEVQVQAVNSEGRTNVVPETVEGRTGEGVPSSIPSGLRVLEKSGTTVTLAWNGVDPATANGNFTGYKITYWVDEADQDVEEPEDDEEEKRKFRWKRSIRAKRQSGVRKTIVFGPSATQGTITDLKPATLNHAYIQVTNGAHEGPSSDTIDFQTDEGVPSPVRSLRAYPMNSKESDEKGVVVLVWKKPRQTNGKLARYEVEYCKTQNGKQVEKTCPRQQIDADAKEIRITGLENETPYRFILRAHTSAGEGDPNSSDATTLPETTAAGVDPGVPSLVENAIGDKYFNVSFRPAKYDDETRAPVGNTYEVQYKPQNGDEWETVKPSDDGLTVHVDGLSPGTKYDVRVAALQVDSDGGETTKTFSGISKITTTGTSPGERNLYFIILILLILLLLLIIICICCVVCRHRGQNYPVSQREREQGREPILGKPDYKTDDDEKRSLTGSKAESETDSMAQYGDTDPGVFTEDGSFIGQYVPQKSLMPAERPEKGSTSTFV
genometools-1.5.1/testdata/not_sorted.gff3000066400000000000000000000026371211610345200206140ustar00rootroot00000000000000##gff-version 3
#date 2012-06-06
#source-version exonerate:est2genome 2.2.0
contig_43704	exonerate:est2genome	mRNA	332	6404	10204	-	.	ID=gi1051257
contig_43704	exonerate:est2genome	exon	332	790	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	900	988	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	2295	2373	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	2460	2557	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	2889	2993	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	3084	3170	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	3268	3462	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	3922	4028	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	4574	4769	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	4884	4985	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	5147	5218	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	5299	5355	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	5437	5538	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	5674	5711	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	5822	5933	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	6022	6078	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	6169	6224	.	-	.	Parent=gi1051257
contig_43704	exonerate:est2genome	exon	6328	6404	.	-	.	Parent=gi1051257
genometools-1.5.1/testdata/nowildcardatend.fna000066400000000000000000000000311211610345200214770ustar00rootroot00000000000000>seq1
AAA
>seq2
AANNAAAA
genometools-1.5.1/testdata/nowildcardatend_rev.fna000066400000000000000000000000631211610345200223600ustar00rootroot00000000000000>seq1
AAA
>seq2
AANNAAAA
>seq2
TTTTNNTT
>seq1
TTT

genometools-1.5.1/testdata/obo_files/000077500000000000000000000000001211610345200176165ustar00rootroot00000000000000genometools-1.5.1/testdata/obo_files/blank_comment_line.obo000066400000000000000000000000271211610345200241360ustar00rootroot00000000000000   ! this is a comment
genometools-1.5.1/testdata/obo_files/blank_line.obo000066400000000000000000000000031211610345200224060ustar00rootroot00000000000000  
genometools-1.5.1/testdata/obo_files/comment_in_stanza.obo000066400000000000000000000000711211610345200240250ustar00rootroot00000000000000format-version: 1.2

[stanza]
id: id
!comment
name: name
genometools-1.5.1/testdata/obo_files/comment_line.obo000066400000000000000000000000231211610345200227630ustar00rootroot00000000000000!this is a comment
genometools-1.5.1/testdata/obo_files/corrupt_header.obo000066400000000000000000000000241211610345200233210ustar00rootroot00000000000000format-VERSION: 1.2
genometools-1.5.1/testdata/obo_files/corrupt_instance_stanza.obo000066400000000000000000000000721211610345200252600ustar00rootroot00000000000000format-version: 1.2

[Instance]
id: 1
name: instance_name
genometools-1.5.1/testdata/obo_files/corrupt_term_stanza.obo000066400000000000000000000000421211610345200244200ustar00rootroot00000000000000format-version: 1.2

[Term]
id: 1
genometools-1.5.1/testdata/obo_files/corrupt_typedef_stanza.obo000066400000000000000000000000451211610345200251140ustar00rootroot00000000000000format-version: 1.2

[Typedef]
id: 1
genometools-1.5.1/testdata/obo_files/minimal_header.obo000066400000000000000000000000241211610345200232510ustar00rootroot00000000000000format-version: 1.2
genometools-1.5.1/testdata/obo_files/minimal_stanza.obo000066400000000000000000000000361211610345200233240ustar00rootroot00000000000000format-version: 1.2

[stanza]
genometools-1.5.1/testdata/obo_files/missing_value.obo000066400000000000000000000000201211610345200231540ustar00rootroot00000000000000format-version:
genometools-1.5.1/testdata/obo_files/tag_only.obo000066400000000000000000000000171211610345200221310ustar00rootroot00000000000000format-version
genometools-1.5.1/testdata/obo_files/windows_newline.obo000066400000000000000000000003361211610345200235340ustar00rootroot00000000000000format-version: 1.0
date: 03:10:2007 16:20
auto-generated-by: OBO-Edit 1.002
remark: version: 1.62

[Term]
id: IEV:0000000
name: Event

[Term]
id: IEV:0000001
name: Pathway
is_a: IEV:0000071 ! Molecular event
genometools-1.5.1/testdata/order_sketch_out.txt000066400000000000000000000000521211610345200217560ustar00rootroot00000000000000string: foooo
string: foooo
string: foooo
genometools-1.5.1/testdata/orphaned_parent.gff3000066400000000000000000000005101211610345200215710ustar00rootroot00000000000000##gff-version 3
##sequence-region ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001;Name=EDEN
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001,exon00001;Name=EDEN.1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00002;Parent=gene00001;Name=EDEN.2
ctg123	.	exon	1050	1500	.	+	.	ID=exon00002;Parent=mRNA00001,mRNA00002
genometools-1.5.1/testdata/png_devel_1.gff3000066400000000000000000000000651211610345200206100ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 10000
genometools-1.5.1/testdata/png_devel_10.gff3000066400000000000000000000014051211610345200206670ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 4294967295
NC_003070	gth	gene	197812	198446	.	+	.	ID=gene20
NC_003070	gth	mRNA	197812	198446	.	+	.	ID=mRNA20;Parent=gene20
NC_003070	gth	exon	197812	197904	0.946237	+	.	Parent=mRNA20
NC_003070	gth	exon	197974	198183	0.985714	+	.	Parent=mRNA20
NC_003070	gth	exon	198267	198446	0.872222	+	.	Parent=mRNA20
###
NC_003070	gth	gene	197884	198811	.	-	.	ID=gene21
NC_003070	gth	mRNA	197884	198811	.	-	.	ID=mRNA21;Parent=gene21
NC_003070	gth	exon	197884	198005	1.000000	-	.	Parent=mRNA21
NC_003070	gth	exon	198078	198185	1.000000	-	.	Parent=mRNA21
NC_003070	gth	exon	198283	198414	1.000000	-	.	Parent=mRNA21
NC_003070	gth	exon	198523	198579	1.000000	-	.	Parent=mRNA21
NC_003070	gth	exon	198724	198811	1.000000	-	.	Parent=mRNA21
###
genometools-1.5.1/testdata/png_devel_11.gff3000066400000000000000000000020551211610345200206720ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 4294967295
NC_003070	gth	gene	191610	192404	.	-	.	ID=gene19
NC_003070	gth	mRNA	191610	192404	.	-	.	ID=mRNA19;Parent=gene19
NC_003070	gth	exon	191610	191650	1.000000	-	.	Parent=mRNA19
NC_003070	gth	exon	191730	191816	1.000000	-	.	Parent=mRNA19
NC_003070	gth	exon	191944	192404	1.000000	-	.	Parent=mRNA19
###
NC_003070	gth	gene	197812	198446	.	+	.	ID=gene20
NC_003070	gth	mRNA	197812	198446	.	+	.	ID=mRNA20;Parent=gene20
NC_003070	gth	exon	197812	197904	0.946237	+	.	Parent=mRNA20
NC_003070	gth	exon	197974	198183	0.985714	+	.	Parent=mRNA20
NC_003070	gth	exon	198267	198446	0.872222	+	.	Parent=mRNA20
###
NC_003070	gth	gene	197884	198811	.	-	.	ID=gene21
NC_003070	gth	mRNA	197884	198811	.	-	.	ID=mRNA21;Parent=gene21
NC_003070	gth	exon	197884	198005	1.000000	-	.	Parent=mRNA21
NC_003070	gth	exon	198078	198185	1.000000	-	.	Parent=mRNA21
NC_003070	gth	exon	198283	198414	1.000000	-	.	Parent=mRNA21
NC_003070	gth	exon	198523	198579	1.000000	-	.	Parent=mRNA21
NC_003070	gth	exon	198724	198811	1.000000	-	.	Parent=mRNA21
###
genometools-1.5.1/testdata/png_devel_12.gff3000066400000000000000000000003451211610345200206730ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 4294967295
NC_003070	gth	gene	5867996	5869531	.	-	.	ID=gene486
###
NC_003070	gth	gene	5868674	5869264	.	+	.	ID=gene487
###
NC_003070	gth	gene	5869883	5872798	.	+	.	ID=gene488
###
genometools-1.5.1/testdata/png_devel_2.gff3000066400000000000000000000001401211610345200206030ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 10000
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001
genometools-1.5.1/testdata/png_devel_3.gff3000066400000000000000000000002341211610345200206100ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 10000
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001
genometools-1.5.1/testdata/png_devel_4.gff3000066400000000000000000000005301211610345200206100ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 10000
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA00001
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA00001
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA00001
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA00001
genometools-1.5.1/testdata/png_devel_5.gff3000066400000000000000000000003301211610345200206070ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 10000
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00002;Parent=gene00001
genometools-1.5.1/testdata/png_devel_6.gff3000066400000000000000000000006621211610345200206200ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 10000
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00002;Parent=gene00001
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA00001,mRNA00002
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA00001
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA00001,mRNA00002
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA00001,mRNA00002
genometools-1.5.1/testdata/png_devel_7.gff3000066400000000000000000000011651211610345200206200ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 10000
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00002;Parent=gene00001
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA00003;Parent=gene00001
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA00003
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA00001,mRNA00002
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA00001,mRNA00003
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA00001,mRNA00002,mRNA00003
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA00001,mRNA00002,mRNA00003
genometools-1.5.1/testdata/png_devel_8.gff3000066400000000000000000000005451211610345200206220ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 4294967295
NC_003070	gth	gene	191610	192404	.	-	.	ID=gene19
NC_003070	gth	mRNA	191610	192404	.	-	.	ID=mRNA19;Parent=gene19
NC_003070	gth	exon	191610	191650	1.000000	-	.	Parent=mRNA19
NC_003070	gth	exon	191730	191816	1.000000	-	.	Parent=mRNA19
NC_003070	gth	exon	191944	192404	1.000000	-	.	Parent=mRNA19
###
genometools-1.5.1/testdata/png_devel_9.gff3000066400000000000000000000012151211610345200206160ustar00rootroot00000000000000##gff-version   3
##sequence-region   NC_003070 1 4294967295
NC_003070	gth	gene	191610	192404	.	-	.	ID=gene19
NC_003070	gth	mRNA	191610	192404	.	-	.	ID=mRNA19;Parent=gene19
NC_003070	gth	exon	191610	191650	1.000000	-	.	Parent=mRNA19
NC_003070	gth	exon	191730	191816	1.000000	-	.	Parent=mRNA19
NC_003070	gth	exon	191944	192404	1.000000	-	.	Parent=mRNA19
###
NC_003070	gth	gene	197812	198446	.	+	.	ID=gene20
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###
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###
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###
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###
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prefixlength=0
largelcpvalues=0
maxbranchdepth=0
integersize=32
littleendian=1
readmode=0
genometools-1.5.1/testdata/prj-files/tis-lcp-suf-bwt-tis-suf-lcp-dbat100K1.prj000066400000000000000000000005161211610345200267200ustar00rootroot00000000000000dbfile=/Users/stefan/gttestdata/Iowa/at100K1 76198 74997
totallength=74997
specialcharacters=1083
specialranges=962
realspecialranges=962
lengthofspecialprefix=0
lengthofspecialsuffix=0
numofsequences=1
numofdbsequences=1
numofquerysequences=0
prefixlength=0
largelcpvalues=0
maxbranchdepth=0
integersize=32
littleendian=1
readmode=0
genometools-1.5.1/testdata/problematic.fas000066400000000000000000000005451211610345200206550ustar00rootroot00000000000000>gb|U00096|U00096 Escherichia coli K-12 MG1655 complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
>
NTTTTNC
genometools-1.5.1/testdata/pseudo_feature_minimal.gff3000066400000000000000000000004561211610345200231510ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	cDNA_match	1050	1500	5.8e-42	+	.	ID=cDNA_match1;Target=cdna0123 12 462
ctg123	.	cDNA_match	5000	5500	8.1e-43	+	.	ID=cDNA_match1;Target=cdna0123 463 963
ctg123	.	cDNA_match	7000	9000	1.4e-40	+	.	ID=cDNA_match1;Target=cdna0123 964 2964
###
genometools-1.5.1/testdata/rcr_testreads.fq000066400000000000000000000005001211610345200210440ustar00rootroot00000000000000@read:1
AGAAACCCC
+
(((((((((
@read:2
AACCCCCGG
+
&7097&%&&
@read:3 this is info-text
CCCCGGGG
+
<=<9<(<)
@read:4
CCGGGTT
+
&7097&%
@read:5
GGGGTTTT
+
<=<=<=<=
@read:6
GGTTAACC
+
(())9999
@read:7
TTAACCGG
+
<<<<<<<<
@read:8 this is other text
AACCGGTT
+
9999(())
@read:9
CCGGTTAA
+
99==99==
@read:10
GGTTAACC
+
;<=9;<=9
genometools-1.5.1/testdata/rcr_testreads_on_seq.bam000066400000000000000000000010371211610345200225470ustar00rootroot00000000000000BCcsreta``p*N-424BD9=]9Tn	V  9aqjBCO@Ňvlm!D8b֖z&6M8xjأ”BKC&r7oEi0S:?TSMDZo(+1ǖ5E Fo^zgC7CˇA6Xfʭ$VGtaZJgcRWsAl[q9UUfPI_A-gЇwįsxAc7}Nyt
Rܓbt,۔_Exu x-fM:[TK+1w6̷]׳^w7	¶MS6yWmO4~of BCgenometools-1.5.1/testdata/rcr_testreads_on_seq.bam.bai000066400000000000000000000002601211610345200232760ustar00rootroot00000000000000BAIIddJdddIdJddgenometools-1.5.1/testdata/rcr_testreads_on_seq.sam000066400000000000000000000023061211610345200225700ustar00rootroot00000000000000@SQ	SN:seq1	LN:16
@SQ	SN:seq2	LN:16
@PG	ID:bwa	PN:bwa	VN:0.6.1-r104
read:5	16	seq1	1	0	8M	*	0	0	AAAACCCC	=<=<=<=<	XT:A:R	NM:i:0	X0:i:2	X1:i:2	XM:i:0	XO:i:0	XG:i:0	MD:Z:8	XA:Z:seq1,+9,8M,0;seq1,+9,7M1S,1;seq1,-2,1S7M,1;
read:3	0	seq1	5	0	8M	*	0	0	CCCCGGGG	<=<9<(<)	XT:A:R	NM:i:0	X0:i:2	X1:i:2	XM:i:0	XO:i:0	XG:i:0	MD:Z:8	XA:Z:seq1,+5,7M1S,1;seq1,-6,1S7M,1;
read:2	16	seq1	6	0	9M	*	0	0	CCGGGGGTT	&&%&7907&	XT:A:R	NM:i:1	X0:i:6	X1:i:4	XM:i:1	XO:i:0	XG:i:0	MD:Z:2C6
read:1	16	seq1	9	0	7M1I1M	*	0	0	GGGGTTTCT	(((((((((	XT:A:R	NM:i:1	X0:i:2	X1:i:1	XM:i:0	XO:i:1	XG:i:1	MD:Z:8	XA:Z:seq1,+1,1M1I7M,1;
read:8	0	seq2	1	0	8M	*	0	0	AACCGGTT	9999(())	XT:A:R	NM:i:0	X0:i:4	X1:i:4	XM:i:0	XO:i:0	XG:i:0	MD:Z:8
read:4	0	seq2	3	0	2M1I4M	*	0	0	CCGGGTT	&7097&%	XT:A:R	NM:i:1	X0:i:10	X1:i:16	XM:i:0	XO:i:1	XG:i:1	MD:Z:6
read:10	0	seq2	5	0	8M	*	0	0	GGTTAACC	;<=9;<=9	XT:A:R	NM:i:0	X0:i:3	X1:i:3	XM:i:0	XO:i:0	XG:i:0	MD:Z:8
read:7	20	seq2	11	0	8M	*	0	0	CCGGTTAA	<<<<<<<<	XT:A:R	NM:i:0	X0:i:4	X1:i:8	XM:i:0	XO:i:0	XG:i:0	MD:Z:8
read:6	20	seq2	13	0	8M	*	0	0	GGTTAACC	9999))((	XT:A:R	NM:i:2	X0:i:3	X1:i:3	XM:i:0	XO:i:0	XG:i:0	MD:Z:6A0A0
read:9	20	seq2	15	0	8M	*	0	0	TTAACCGG	==99==99	XT:A:R	NM:i:4	X0:i:4	X1:i:5	XM:i:0	XO:i:0	XG:i:0	MD:Z:4A0A0A0A0
genometools-1.5.1/testdata/rcr_testseq.fa000066400000000000000000000000561211610345200205240ustar00rootroot00000000000000>seq1
AAAACCCCGGGGTTTT
>seq2
AACCGGTTAACCGGTT
genometools-1.5.1/testdata/rcr_testseq.fa.fai000066400000000000000000000000411211610345200212540ustar00rootroot00000000000000seq1	16	6	16	17
seq2	16	29	16	17
genometools-1.5.1/testdata/readjoiner/000077500000000000000000000000001211610345200177775ustar00rootroot00000000000000genometools-1.5.1/testdata/readjoiner/2x3nt_1.fas000066400000000000000000000000161211610345200216650ustar00rootroot00000000000000>0
acc
>1
ccg
genometools-1.5.1/testdata/readjoiner/2x3nt_2.fas000066400000000000000000000000161211610345200216660ustar00rootroot00000000000000>2
tgt
>3
cga
genometools-1.5.1/testdata/readjoiner/2x3nt_3.fas000066400000000000000000000000161211610345200216670ustar00rootroot00000000000000>2
tta
>3
cca
genometools-1.5.1/testdata/readjoiner/30x_800nt.fas000066400000000000000000000571141211610345200220450ustar00rootroot00000000000000>0
GAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCG
>1
TCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGA
>2
TAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAACGCGAATTTTAACAAAATATTAACGCTTACAATTTCCATTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAGCGCGCGTAATACGACTCACTATAGGGCGAATTGGAGCTCCACCGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGACTGTGTGTCAGATCTGACTAAGGGTCGGAATTCGATATCAAGCTTATCGATACCGTCGACCTCGAGGGGGGGCCCGGTACCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTGCGCGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAAC
>3
TTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTT
>4
TCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCA
>5
TGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTA
>6
GAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAA
>7
TGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTAACCAATAGGCCGAAATCGGCAAAATCCCTTATAAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCACTATTAAAGAACGTGGACTCCAACGTCAAAGGGCGAAAAACCGTCTATCAGGGCGATGGCCCACTACGTGAACCATCACCCTAATCAAGTTTTTTGGGGTCGAGGTGCCG
>8
GGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACC
>9
GAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTAACCAATAGGCCGAAATCGGCAAAATCCCTTATAAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCACTATTAAAGAACGTGGACTC
>10
GAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAA
>11
AGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGC
>12
GGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTA
>13
GGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTG
>14
GGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGC
>15
CGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGA
>16
ATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAA
>17
ATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGAT
>18
TTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGC
>19
TGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGT
>20
ACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATC
>21
ACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAACGCGAATTTTAACAAAATATTAACGCTTACAATTTCCATTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAGCGCGCGTAATACGACTCACTATAGGGCGAATTGGAGCTCCACCGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGACTGTGTGTCAGATCTGACTAAGGGTCGGAATTCGATATCAAGCTTATCGATACCGTCGACCTCGAGGGGGGGCCCGGTACCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTGCGCGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCAC
>22
TTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCAT
>23
ACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTG
>24
TTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCG
>25
TGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTT
>26
CATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCT
>27
GCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACC
>28
AGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGAT
>29
TCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCA
genometools-1.5.1/testdata/readjoiner/30x_long_varlen.fas000066400000000000000000000553341211610345200235040ustar00rootroot00000000000000>0
AGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCG
>1
TCAGACCCCGTAGAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGA
>2
TAGTGGGCCATCGCATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAACGCGAATTTTAACAAAATATTAACGCTTACAATTTCCATTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAGCGCGCGTAATACGACTCACTATAGGGCGAATTGGAGCTCCACCGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGACTGTGTGTCAGATCTGACTAAGGGTCGGAATTCGATATCAAGCTTATCGATACCGTCGACCTCGAGGGGGGGCCCGGTACCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTGCGCGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAAC
>3
TTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTAAA
>4
TCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGGCCA
>5
TGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTGGTA
>6
GAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAA
>7
TGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTAACCAATAGGCCGAAATCGGCAAAATCCCTTATAAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCACTATTAAAGAACGTGGACTCCAACGTCAAAGGGCGAAAAACCGTCTATCAGGGCGATGGCCCACTACGTGAACCATCACCCTAATCAAGTTTTTTGGGGTCGAGTGCCG
>8
GGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTAACACC
>9
GAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTAACCAATAGGCCGAAATCGGCAAAATCCCTTATAAATCAAAAGAATAGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCACTATTAAAGAACGCTC
>10
GAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAA
>11
AGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAACGC
>12
GGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAAGGGTTA
>13
GGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCGACCCTTAGTCAGATCTGACACACAGTCCGAATTCCTGCAGCCCGGGGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAATTCGCCCTATAGTGAGTCGTATTACGCGCGCTCACTG
>14
CAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGC
>15
CGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAAAGACAGA
>16
ATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAGGACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAA
>17
ATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGAT
>18
TTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATACAGTAAGAGAATTGATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGC
>19
TGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGT
>20
ACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATC
>21
ACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGTCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAACGCGAATTTTAACAAAATATTAACGCTTACAATTTCCATTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACCAGTGAGCGCGCGTAATACGACTCACTATAGGGCGAATTGGAGCTCCACCGCGGTGGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGAATTCGGACTGTGTGTCAGATCTGACTAAGGGTCGGAATTCGATATCAAGCTTATCGATACCGTCGACCTCGAGGGGGGGCCCGGTACCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTGCGCGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCAC
>22
TTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCAT
>23
ACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTG
>24
TTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCAAAATCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCG
>25
TGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAACTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTT
>26
CATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACACAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACAAAGGGGAAAAAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCT
>27
GCTCACTGCCCGCTTTCCAGTCG
>28
AGTTACCGGATAAGGCGCAGCGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGAAGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGAT
>29
TCAGCCCGACCGCTGCGCCTTATATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTAAATCCCCAAAGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCAAAAAAAAAAAAAAAAAAAAAAAA
genometools-1.5.1/testdata/readjoiner/70x_100nt.fas000066400000000000000000000162541211610345200220420ustar00rootroot00000000000000>0
cttgttcctgacctgggatcccgcaggatggaatttaggccccaccctgtggccctggaggaggtagtgccatgccctccttgggcatgaagctgacttt
>1
gggatggcagaggccatgtttgccactgtcctaaagcctaaagcagcctgtggaatgtgggtggggtgaactggctgagtggctgtatcatagggcctgt
>2
ggtcaggagactgagaccatcctagctaagacagtgaaaacccgtctctactaaaaatacaaaaaattagccaggcatggtggcaggtgcctgtagtccc
>3
ttttgctgctcacaggctggtgggaagagaccattactgttccccgcaggagcccagtagcaaagtgccaggaccctggacctgtgtggggccctgggac
>4
gtgatcagtggcccatcgcctgccctcgtggtgggtgcagttcacaggtgctgccccaggcctggcacagtggccttttcagcctgtcccaggatagggg
>5
tggtgccacctgggacctgctgggctgtagccacaataggctgagcaaaaggtgagtgcctcccacaaggacgaccaaggggatgtggacaccacagagt
>6
gagggcaggcctgcctttgaggctgtgaggcagggctgcggcaggcagtggccagtggagggaacggggtgggtgccgaggggctacatggccatctccc
>7
ctttctttctttctttctttctttttgttttctttcatctttccttcttcttttttgatggagtctcactctgttgcctgggctggagtgcagtaagtgg
>8
aatttggctaagcaattgtacttctagattatttatttatttatttatttatttatttatttattattgggacagagtctcactctgtcccccagactgg
>9
ccaaatggtgctgggattacaggtttgagccaccgcacctggccagtttataatgttcataatggcttttggagcaggaaccagtgggtgctgcttcttg
>10
atgaaggtggcattgagggctgaagtctccctcaccatgaagggatgatgtatagtgggtggggcctcaggaggaagagggccaccaaccctacctggcc
>11
cagataccaaacacccagaaattccatcttgtcatttatttccacaagaaaaaacaagagacctgtattaaaatatccacttctattgaaaataatcaca
>12
gaaaggtcagctccatgggtctcagctggctgggcccatttgggagttctatctttggggaaggatgctttcctaggctctgttgcacgctggccctagg
>13
aagcttctccaagcaggcttggaaagaaatttccgcatatcacttacgtcactcttgccactagaaggacaatttttacggtggagtggaagaaaatgaa
>14
aaggatgccatttttaatctgggctcgtacaaagtcaatcattctttggtgcctggcaatggtggccactgcagacactttaatcttgggctaggaattg
>15
gagactccatctcagaataaataagtaaataaattaattaatttttaaaatcccactacacaggaaaccattctttcatcctggacctctaggtctctgc
>16
ttgagaagggatgattgtattttgcaatgtgagaaggacatgagatttgaagggccagggatggaatgaaatagtttggatgttgtaccctttaagtcgc
>17
aaagggctccagatgagctcaggccatggcctcagagggtgcaaactataagccttggtggcttccatgtggtgttaagcctgcaggtgagcaaagtgca
>18
caagctctccaggctgagggaacaggagcaggggttatgttgggtgaaagtggaagtgagggacctcccaggaggtgtagaatattccactagggacacc
>19
caagtagaatatattatgcttgaatgaaattatgagttgagagtaggaaatctatggttaaccaaacaaattaaataatgtttatgaggaaattatactg
>20
gctgggatgagctgctgcaaagatttctgaaatgccttcaagacctttttttaattgtcttggctatcagcacctagctttttttcagttatgcaaatgt
>21
aaaacctgaaatcactagaaaggaatgtctagtgacttgtgggggccaaggcccttgttatggggatgaaggctcttaggtggtagccctccaagagaat
>22
ctatactcagatccaggagcaaagaaatgacttaaagctggaatttatgtttaaacaggaagcagaccagaaaaatttggaaaatttgcagtctggccat
>23
aagggtcctcagggaggttttacacatggcagaaggtgaagcaaaagaaggtatgtcacatggccagagcaggagcaagcagggagaggtgccacacact
>24
gtgaatttttcttaatatgctctggcaggatcagaaaactaattatttacactagagtcacttaacctttcctcttggtcatttgcatgtaaattatttt
>25
tcaggaggtcctgacagcatgtgcccaaggtggtcaggatacagcttgcttctatatattttagggagaaaatacatcagcctgtaaacaaaaaattaaa
>26
gcccctggtgtttctccctcaccagggagcagcaccttttgccagtgactcatctggcaggtatctcaagtcagcccttgcctggcctggcaccttgctg
>27
agagacaggattcatgccaagcctgcctacccagcacatctctcctcatggacatgagagaaaaccctccagcttggccctcacatctgtgaaacccaca
>28
ttgtcatatacagatgctcacattgttttgtttatatgaaaatgtttgtaactactacgcgcatttttgctacttaagccttttggtcttgctgccatag
>29
tgagacggagtctcactgttgcccaggctggagtgcagtggcatgatttcagctcactgtcgtctctgcctccctgactcaagtgattctcctgcctcag
>30
ttatatacatatatatctgtctaatatatatacacatatacatatatatgtatatgtgtatatatacatatacatatataatatatgtatatgtgtatat
>31
gaacatagggttagcccagaaagtccatcattccctcacttccagagctcctctctacagccagcctctgctggctccctggggagggtggactcctggg
>32
gagagcacaatgagaaagggaaagagggacatctggacataagggccaactggagggcagggaaggtaattttccttacattttaaactcagaccacata
>33
acagtgcccagttcccccaggaggacctggctcaccccaagcccacaggaagcacagggaagtttctgcatgccacagaaaccaggctctccccaagagg
>34
agagacaaacatctgaaattaaaatgttttatttgagatacaagtattacaatttgacacatacatgcagaatgggtgtctttagtatgtccgaaacata
>35
gccaaggtatgtttctctcctgggattactggtcagttttatttttttcctcggatagatgttttaagccataaatcttgacatagacctgatgtagacc
>36
accagaccccaactccaacactgggaattacaattcaacatgcgacttaaagggtacaacatccaaactatttcattccatccctggcccttcaaatctc
>37
aaggttaagtgactctagtgtaaataattagttttctgatcctgccagagcatattaagaaaaattcactttggcagaattatatggatttgaagaagta
>38
gaggactttgggttcaacctaagcactttatatcctttattttcaattgggtaggagataaaataattcagcagcaataaaagtcacacttcttaaagtt
>39
cctgcagcttttctgagtgtctttcctctttccccatctctcagccacttttgtgccagctctaagcacataagtgctttcttgggagaaacagactgct
>40
cgagaatatgttaagataccacaaaaacaaaaaatatacatagttaagagctttcatgagtaagcaaattttatacatataaaaataatttacatgcaaa
>41
ttcgaatttgccaaggtatgtttctctcctgggattactggtcagttttatttttttcctcggatagatgttttaagccataaatcttgacatagacctg
>42
tcatcataaattgtaggatagatctgatccagttggcttttcagattgaaccctaggccttactccctctcaccacttaaacaattggctattaaatcag
>43
ggctggtacagaggggctgagttgcagcagaagacccagcccctgagctgcagcacagagtggaggtagtggggagctgtcacctgggtatgccaccctt
>44
ggaatacacagtgtcagaaggaggacctgtgtccagcccctgtgttccccactcctgggcagatgcgtacccagtgcagcgagaatgtctgcgaggggga
>45
ttttacatttacccctttccatcaagatctttctcttaaagcatcaaccatgtttatagttgtacaacgactacaagttaggcttaatcatcccttagtg
>46
gggaaatattcactcctgttttcttctctccccaatctcagcctttcggtgactgtttgggcaaagcctcccttgtggtaaaagatgcctcacttctggg
>47
ggagggaggctgaggtgggaggattgcttgagcctaggcgttggagactacaacgatctaggattacaccactgcactccagtctcagcaacagtaagac
>48
tacttttaaaaatcaagaaaatagattggtcaagagaattctgcttgttttgattttgttatcactcgattagattaactgtgttagtataaatgtcagt
>49
gaggtcctctttgagggctccagccgggcataggcttctccctgggcatccagcctttctcatacatcctctgaaatttaggcagagaatgacaagcctc
>50
tacctatgacctggaagcccccactttgcaccctgagatcaaaccagtgcaaatcttatatgtattgatttgtcaatgaaaacagtcaaagccagtcagg
>51
tgtcaatagacttttgaagtttatgatcaatcttatttgaggattgtaggaccaacaccaaatcagagtgcagtaaacttaatttctcttctggccaact
>52
acagggtggggcctaaattccatcctgcgggatcccaggtcaggaacaaggcccagggatgctgcttctgggtctgaaccccaggtatgggtcaagaggg
>53
gagactaaagttttattatgcagatgaagcctccaggtagcagggttcagagagaatagatcggaaagaaacctaagatctgaaaatctgtgttgatgtt
>54
gggagcagctgggagtgtggccagctgggaggtaggaggactcttggggaagtgacagtcacctgcatgaactcagggctagagagctgtggctctggga
>55
tattctagggtaattattaaaacattaagaaatactctttaatcatatatgtttaaacttgtagaaaatcaataacatacaagtaaagaagatcaagaag
>56
acttttaaacaaatagatcttgcaagaattcactcaccatcacaaggacagcaccagggagatgatgctagaccattcctgagaaatccatccccatgat
>57
aacaaacaaacaaactgtcaaaatctgtacagtatgtgaagagatttgttctgaaccaaatatgaatgaccatggtccatgacacagccctcagaagacc
>58
tgagtttaaaagcttcctttggagatgcccctggccccctccacctgtcaagaagaggccatcctatctgcctgtcaagaagaggccatcctgggcagca
>59
gtcacaatgcagacattcctttctattgacaactctttcaaccaattgtcaatcagaaaaattttaaatctacttataacctggaaacccctgctttgag
>60
gtagtagttacaaacattttcatataaacaaaacaatgtgagcatctgtatatgacaataactcatgcaaaaaatattttttaactgagacagaaatcat
>61
tattaaataagaatgaccaggagagccatgggtaagctccctcctcagtcatcaggaccgcaacagagagttttcccctgtgtggacagggttctgaatt
>62
gctcttaagactgtgtaaccctaggccatggtcactcatattggcttagaataaagctatctaaatactttggcagaatttggttttttcatcaccacaa
>63
ggcatgtgccaccaccctcggctaattgtgtatttttagtagagacggggtttcaccatgttggtcaggctggtctcgaactcctgacctcaagtgatcc
>64
atattattaaaagataacggaatacctaactaaaaaaaatgcgaggaggcattgatgggcccatgtttactgagcacatcctgactccagaattagaaat
>65
ctcgggaggctgaggtagggcaattgcctgaacccacgaggcggaggttgcagtgagctgagatcatgtcactggactccagtctgggggacagagtgag
>66
aaccatctgaatgggctttcttctaggccagggcactctaaaattgaagaacctgaacattcctttctattgataatactttcagccagttgagcccatt
>67
agacaggatttttggcaagagaataaaaggtcagagttgaggcctcagtccccactattggccaaagatcattttatggaatgtatgtgaaggccaacaa
>68
agacacaagtaattccaggaaaactggaatttaagttcaatatgttacactaagtacatttgaaagtgcatgcatttttattttaatttaaaaaataaat
>69
atcccatgtcccccagccggaccccatgtccgggagatggccatgtagcccctcggcacccaccccgttccctccactggccactgcctgccgcagccct
genometools-1.5.1/testdata/readjoiner/70x_100nt.fastq000066400000000000000000000343261211610345200224070ustar00rootroot00000000000000@0
cttgttcctgacctgggatcccgcaggatggaatttaggccccaccctgtggccctggaggaggtagtgccatgccctccttgggcatgaagctgacttt
+
9=B.C==/9;;EI7I-+E,-=0+E@H8F46A/4<5EI2E/395206E>3=>3:
@1
gggatggcagaggccatgtttgccactgtcctaaagcctaaagcagcctgtggaatgtgggtggggtgaactggctgagtggctgtatcatagggcctgt
+
+E0AHCG5/./D:81.B2=A/3414CB?88H>/>@+:9.>A@C76D2;
@3
ttttgctgctcacaggctggtgggaagagaccattactgttccccgcaggagcccagtagcaaagtgccaggaccctggacctgtgtggggccctgggac
+
.-6F3:@@;=6?6@7I,>->6E6IIBFED7=:=4I9-003H2/+G/HF-3+A/-I,;H>BE<@+67BF1+9E8A3D+?AH31EF@D+3BG;H+3?440;,FH,
@5
tggtgccacctgggacctgctgggctgtagccacaataggctgagcaaaaggtgagtgcctcccacaaggacgaccaaggggatgtggacaccacagagt
+
5+EC>IH=>4+H3;;E3;9>8/D.,5<,B4FE:F>D74HEE,?5=+:?2?2I:>111;5DH?798HI762?;-G.1.968H?1H3D99>24=++3.-:-:
@6
gagggcaggcctgcctttgaggctgtgaggcagggctgcggcaggcagtggccagtggagggaacggggtgggtgccgaggggctacatggccatctccc
+
860-8H<+4/<1,I.,GH>E?88/A:7+E;1>,72B/>6@>I2@5@=G;C1B4,;=2IHG0>D64@IIII73/,.D0A.3>>-1I@BB;4F3HID3-H->IE98>.H2E:6I<99946,:21F:EB.=
@8
aatttggctaagcaattgtacttctagattatttatttatttatttatttatttatttatttattattgggacagagtctcactctgtcccccagactgg
+
5/18/,A8D4@C/-1<<3.353.DGF>C221I,9A+-:815>EI1;BIB@32E:5F@2G559D,,=?53.1
@9
ccaaatggtgctgggattacaggtttgagccaccgcacctggccagtttataatgttcataatggcttttggagcaggaaccagtgggtgctgcttcttg
+
A.E@E-/@H7,IA34F<-9C/+I;4@C569I@F-.,B72E59106:D9CGI-@/@86?A7B4:8D.FB1DCEA3<75,GH>>HI,;+4+@0/I093,BA8
@10
atgaaggtggcattgagggctgaagtctccctcaccatgaagggatgatgtatagtgggtggggcctcaggaggaagagggccaccaaccctacctggcc
+
=2?46E:-?G5I5C>+:>64.6B787B10@<37:64+305A=9950>439A
@11
cagataccaaacacccagaaattccatcttgtcatttatttccacaagaaaaaacaagagacctgtattaaaatatccacttctattgaaaataatcaca
+
BC+55I;I55-;5?;E=@63103006/@A6?H9?:1:F85,.1/:EA1C34:0E04G162=5@3@-F;CII60-HD4H;D+FEB,.2H:=EID:84A177
@12
gaaaggtcagctccatgggtctcagctggctgggcccatttgggagttctatctttggggaaggatgctttcctaggctctgttgcacgctggccctagg
+
8E39H;45@I-C0EC@7;=@0@8H5AAH620;2H1F,38.C=<11-@43D2G-BH2;0:IH-=71:BFA=E4H--I==D87FE4>E+018=7+.;G;F6?=9.D<9=<1/92.7CIC;+C15-B@6EE06HDH@4E7,247/5/IA6CA3::C+?=91EAG24ID74?<9A2602/B378FC7//;-?8G9B3,?.2943B5G3?G/
@16
ttgagaagggatgattgtattttgcaatgtgagaaggacatgagatttgaagggccagggatggaatgaaatagtttggatgttgtaccctttaagtcgc
+
7?+ED-IH7:9<86;I3;+EF6.96E1;+++?;4B3C=7=<2-A-:83?>G/-BG;.CB.;7?.3DD/9;C-3D:7@/-G?C26GE>83B0525?,+777
@17
aaagggctccagatgagctcaggccatggcctcagagggtgcaaactataagccttggtggcttccatgtggtgttaagcctgcaggtgagcaaagtgca
+
33;;BGDC@:G72+F4IA
    A6;C0.:C9F,I30A=F3;@C:58BF1-322C28H>A<9E04.IF673/3//-HI9@341=H5@D-/<-<3I;14II6:-D=D??D8I<:@.I,42.+->,=6>+0B+4;/I7-10>4-/1=8>A;83<>F0?30;<;--6BH2+8DE5E.D.G;?07,G:@??C/<02?2H:<4A>B/9;
@20
gctgggatgagctgctgcaaagatttctgaaatgccttcaagacctttttttaattgtcttggctatcagcacctagctttttttcagttatgcaaatgt
+
C:F.F+@3;4.F50@=C1E:.9G97@>,H-25FD2C0,4E+=A.G,>H6,2GC?DB5H,+46I/81/B8/,>@>C=4H;D0G>;8@@6F2?>I9,307DI
@21
aaaacctgaaatcactagaaaggaatgtctagtgacttgtgggggccaaggcccttgttatggggatgaaggctcttaggtggtagccctccaagagaat
+
4@2+AB.-GF05+>4>.,DH5I65<5AB5D+1A+78739BE5;,@-62;/A-=164>E7C5B4@.>=,6G,G32C4;.2HE=?->;?<3=5>006?@39G75IA5GE9GIEA0:.7@/C7+@5D><1?E@G4/-I00D88E341?
@23
aagggtcctcagggaggttttacacatggcagaaggtgaagcaaaagaaggtatgtcacatggccagagcaggagcaagcagggagaggtgccacacact
+
2F2-//<248+GHF74?=89AGCH092E4@<=IIDFF:?B+?AC@7H2BH1>E@@@+D1+.@..A>EI<<=6;9AH6II+9+6
@24
gtgaatttttcttaatatgctctggcaggatcagaaaactaattatttacactagagtcacttaacctttcctcttggtcatttgcatgtaaattatttt
+
1HA,=;=9G2@G1/=C,4;1B8180BB35+2C/?1FA/B:FBB5@H39F8/A@>2.H>614:>31HHE5>,CH9-EAF469/C?1-I?7;EECFA,128H
@25
tcaggaggtcctgacagcatgtgcccaaggtggtcaggatacagcttgcttctatatattttagggagaaaatacatcagcctgtaaacaaaaaattaaa
+
2C>CB96-3-69E,A,=8/4@41B.:3<./73IG6/33-4F<85G@-EF6,4B-;B-=?EF?94A.79=3DD946?3+E5A0BFD6F>-/:-;A,-67D>>@6H2?1I;/7/:6DH;8@:/?ICD196B@75BF?@1FF1:/HC9B;E6,07-E9>-,23=?3G37<7@@4;3D64CE--BC:>
@27
agagacaggattcatgccaagcctgcctacccagcacatctctcctcatggacatgagagaaaaccctccagcttggccctcacatctgtgaaacccaca
+
;B..;B.<<<-5HE6=9@,625BBA:=1?6-FCE?3@.-G=,8:+9H.,44G>F=5798/;>@4;?9056@4E//9+I,,.IA746D7+D41F/I.DIGE
@28
ttgtcatatacagatgctcacattgttttgtttatatgaaaatgtttgtaactactacgcgcatttttgctacttaagccttttggtcttgctgccatag
+
-B--7B90C057::1>:67+/0G0F6965<48+95D@59HD/3I6?H7+HA>>H01BIG@F6>>/56,9F/EH-?-/ECC;/AEB7,I/:I83?48>4@=
@29
tgagacggagtctcactgttgcccaggctggagtgcagtggcatgatttcagctcactgtcgtctctgcctccctgactcaagtgattctcctgcctcag
+
F6F6;34A=?@H9-@8:8+H0+H7G-:3:++2F7IDF8->>--3I911F2=0E:G0@;102I=B1>HC3,DD>4=D,33/5AEB<39DG4D3-:I48>F+
@30
ttatatacatatatatctgtctaatatatatacacatatacatatatatgtatatgtgtatatatacatatacatatataatatatgtatatgtgtatat
+
/;9+2FB01=@;4=4;EE67/I5C=:==D=.1/D/I++76FC8B0A@F4F9B9@7FD4813EB6E6E:43EE/,;,6
@31
gaacatagggttagcccagaaagtccatcattccctcacttccagagctcctctctacagccagcctctgctggctccctggggagggtggactcctggg
+
B:BB5DG;?0>;.:,D3?:4293G5=+2619CC3;?+1G,7=.+C+:H/GH<-,ED5:E:H=A;311G4D4D9I=9FI63@-B,;@+6A400=6+2G85.
@32
gagagcacaatgagaaagggaaagagggacatctggacataagggccaactggagggcagggaaggtaattttccttacattttaaactcagaccacata
+
A9=0/5=,EG@7@5-6;+8=+05/B9F8?+=@>6?E=4FC=E-.=C+;I24BBAD1@@@H>.1.844,GAI=
@33
acagtgcccagttcccccaggaggacctggctcaccccaagcccacaggaagcacagggaagtttctgcatgccacagaaaccaggctctccccaagagg
+
9=HE=+4CF/>?D840DF>A8AC95D0C;2D-E1+?A/DC-F,B2HCIF>F:8978.IE=324IGA8B0.2I-+?HIG;@=0@F-63=I@,F??I-;3BF;A41C48.8+C=?I-ACFE;I>8I;=
@35
gccaaggtatgtttctctcctgggattactggtcagttttatttttttcctcggatagatgttttaagccataaatcttgacatagacctgatgtagacc
+
5820,B4HF82;+/E5>5EB+0G6EH38I,F@=04<57+1.:-G?F<;8//1F@0FA9882H5FD1D?<.I+>+F,D>.1,1.:+9<;C7@2>730@4F+
@36
accagaccccaactccaacactgggaattacaattcaacatgcgacttaaagggtacaacatccaaactatttcattccatccctggcccttcaaatctc
+
=38=;>,..ID>BBEI;+D6.772448DF,0FC0:-6EA4A8D.E76-<-6E5IGE956?E>:/=13B/@;1;8?881=I?D.B39A+F=.,C0EI2CF=
@37
aaggttaagtgactctagtgtaaataattagttttctgatcctgccagagcatattaagaaaaattcactttggcagaattatatggatttgaagaagta
+
80H7A6<4+1B49.-9A,153C89BA5G0ED9>6195?I72F?>1I3BB=0,I1<?DC2G+5;:H:,HD,AB:C@E8;>HI>3+2-GH:B16D0,EF95+H:C:E87712FEG9FD?3,31+BI+8B5/31>7@?+94C2I0E:IDI5;<=,E;1=.D+D0C=4BH=749HI6I;.>09.3EE;;H38-<,9+/B<<00+-30+3C+/A36/4C/F2>:2B-1C<847016
@40
cgagaatatgttaagataccacaaaaacaaaaaatatacatagttaagagctttcatgagtaagcaaattttatacatataaaaataatttacatgcaaa
+
>9H4@16C>HAFIF+=DAG?5765?/?5+219?2@136>E=B7@B00G,5:00,-H1.
@41
ttcgaatttgccaaggtatgtttctctcctgggattactggtcagttttatttttttcctcggatagatgttttaagccataaatcttgacatagacctg
+
4H2G:C@3.;G0+=85CDH7307H=76A+G>4I?H;1D+-I217:47,1A,;G>87;B/C<6F6@465354B=H8:337DC>0CD5C+->01-I751
@42
tcatcataaattgtaggatagatctgatccagttggcttttcagattgaaccctaggccttactccctctcaccacttaaacaattggctattaaatcag
+
C5B6>3GD105C:56->;BC+5I7+C5=36AB2?:D:7;B-;EDA/F36437.>3=;:;9AA7B3A<+8:699I1++,D;732770D856<3DE..G<+7+G,4A=/:?1@H-BB4>1/64>.,?B:I75-H?=C.0C,-I
@44
ggaatacacagtgtcagaaggaggacctgtgtccagcccctgtgttccccactcctgggcagatgcgtacccagtgcagcgagaatgtctgcgaggggga
+
;7=;3.7G=4EF6=H4HD=F+G5-7800.+C2.@?,3.I92II5F1=0+GDG;HD>=8I8?6>?4F>.4:8?<273.G37;22D=7/9+F815.<6:2E833D8?B?+4H0H?96A.673+=>;-+3==F=E?@+D-010=HD/G;:=;E
@46
gggaaatattcactcctgttttcttctctccccaatctcagcctttcggtgactgtttgggcaaagcctcccttgtggtaaaagatgcctcacttctggg
+
29C3D85=G5,1;I=;5H:B4;37:4.1AA=91515B:5?>I?G08EIC=,017,-/0@A3D;E5I4;F4>//E>4.BC:;B@-10./17-284C?GDDE
@47
ggagggaggctgaggtgggaggattgcttgagcctaggcgttggagactacaacgatctaggattacaccactgcactccagtctcagcaacagtaagac
+
>>5GF6A>HF+4A<.8E>=0476EC=D@1HI;6+6<.;E3B,?.4:>E3,4.8C.<73?G-?<>F72H31.82CCBGD-//.-6<.7II1
@48
tacttttaaaaatcaagaaaatagattggtcaagagaattctgcttgttttgattttgttatcactcgattagattaactgtgttagtataaatgtcagt
+
7C/2F<0C5>6A>=G4I<=D88;,B>63,<<>9A5I.A2E:D@4=9E6>-+I+H1C05=D<+5<,@D+FA61.4A329<3>F5DD6=/?-F2EGAC
@49
gaggtcctctttgagggctccagccgggcataggcttctccctgggcatccagcctttctcatacatcctctgaaatttaggcagagaatgacaagcctc
+
+9IIC,;63EAFG:3097:.=/CCDCB?6B185601-1F96.>;<0F:31=:71I1.5591D+;@>-3-38?<
@50
tacctatgacctggaagcccccactttgcaccctgagatcaaaccagtgcaaatcttatatgtattgatttgtcaatgaaaacagtcaaagccagtcagg
+
8>6;;G:85.==>AF7@4/6.IB>8<45IC6<:6,F<88E?6C1?4=B3D1+B7I+?E:=A+=>3,B9D9D/95@53?1
@53
gagactaaagttttattatgcagatgaagcctccaggtagcagggttcagagagaatagatcggaaagaaacctaagatctgaaaatctgtgttgatgtt
+
BH7A>HAI2:?67B96+5E>3?9,FCDE3E5./.39,.9D,/<3I:DI6?-C;@-618F-C/C<9B1+42+?:I3F/=3:42D>=EF:A3H3@05C:9/9
@54
gggagcagctgggagtgtggccagctgggaggtaggaggactcttggggaagtgacagtcacctgcatgaactcagggctagagagctgtggctctggga
+
51HF=.BF>5+3;G>F73<:H=A5H;E7.
@55
tattctagggtaattattaaaacattaagaaatactctttaatcatatatgtttaaacttgtagaaaatcaataacatacaagtaaagaagatcaagaag
+
<=C<;1+/>;:8>I7I9@4?@H/;7?15.GI===FIA:E;1?F>4@28HFHH.=BH5E;B?2HIEI>H==81?,D,9,
@56
acttttaaacaaatagatcttgcaagaattcactcaccatcacaaggacagcaccagggagatgatgctagaccattcctgagaaatccatccccatgat
+
.<7/C7.:+E:0.875@9:+F@45:-?1:7I-46F9GC-2/5=2I1,<-0>9;/23B--A->I/6?;94DG660>4<,=I,=3>9AC:6,EIF60-;>,8:?5:?544>A88:.B++.86/C9H84CG34258C,-?6G0CD8?D88H>1FE/G4D?=92,I8@:.5?7@57;;AF3-4H@691+2,
@59
gtcacaatgcagacattcctttctattgacaactctttcaaccaattgtcaatcagaaaaattttaaatctacttataacctggaaacccctgctttgag
+
>B77?>--E=DA0=D2;898DG0482=@,=IG><@GC6,+HFI-7FBB>6/I+>?@,64/B2;BBC1221@A4
@61
tattaaataagaatgaccaggagagccatgggtaagctccctcctcagtcatcaggaccgcaacagagagttttcccctgtgtggacagggttctgaatt
+
00D582C2F611>,0I84D-I<9>0CD.<5?259?C;3I2A?;.328:2?AB7/IC3,,B8?B895G;;@=C9=1D@93//A-3+H@99B:6:,6+=7I3
@62
gctcttaagactgtgtaaccctaggccatggtcactcatattggcttagaataaagctatctaaatactttggcagaatttggttttttcatcaccacaa
+
E.E0F1@>8+<<.:8CF3IG.8G:5B4+GH5HH;ECEC;I95C?-17-6B-/1C,;956I258I2449;8,DI.FED31-/3B.6=?634ED-G9:A41D=C06F6,590./=.1AD6+57
@65
ctcgggaggctgaggtagggcaattgcctgaacccacgaggcggaggttgcagtgagctgagatcatgtcactggactccagtctgggggacagagtgag
+
,@3:D56+38,77C1C;.;38-:,3I,E4:9H0BB/HH9A;6BEI9>=0F3D?C@I=81./3=G17<=3/?57B4>6B6A=/1=<63?C1I32B=<=->/GI;GGA/0>,C>8<2E6F5.,12A:2IF<:3-B,?:3.HIDI/:A@@D644GH0=:1?F9@I5F;@<+D=AA<
@67
agacaggatttttggcaagagaataaaaggtcagagttgaggcctcagtccccactattggccaaagatcattttatggaatgtatgtgaaggccaacaa
+
94G+51-0G6;4451B5A3GCIG+I+5F807+B
@68
agacacaagtaattccaggaaaactggaatttaagttcaatatgttacactaagtacatttgaaagtgcatgcatttttattttaatttaaaaaataaat
+
1.IDH.A@-;-3G<,B.F8G0033<7.E>83C4,CCF8846-/I1B=5FFBB;=5DCB7:-CC=2+8B5H50H124F9E.6.:64E36;I.1G;<>=93=
@69
atcccatgtcccccagccggaccccatgtccgggagatggccatgtagcccctcggcacccaccccgttccctccactggccactgcctgccgcagccct
+
1B+;<+4D3<.+DHD@<+@4I5=17+?@95+F498GD6@F6=;GC//E+G8.<85G7.-+0-I.9,D:0read_0
ataaattatctactatatttttattatttgtgtatctacccatgttttttacatacatac
ttacatttctgttgtacaaacaagtataacattaatcaatatctctattctcttctaaga
caaaaaaattagtaataacgtccgtccaaactttctacact
>read_1
aggagaatcgcttgaacccaggaggtggaggttgcagtgagccgagatggcaccactgca
ctccagcctgggcaacagaacgagactctgtctcaaaaaaaaaaaaaaaaatgagacaca
gacaagatcccacagctatcacgtttacagcaggtctgttc
>read_2
ttctttttgaatagaacaaggaaaaagaactcttcaaaaagagtggaaaagatagctaat
cctctgtggttttatgtgctaaaacagtcctgagatacacaagttaaacttggcatactt
tggatctgggccaaaaattgtttttattggctgtagaaaat
>read_3
actctgctccaacctgccctttcgaccttacttcctgctccggtgcaggaacctggctcc
aggtcagcagatctatatacttcctcatgcctacatcttggcctagccagtgtggttgct
ttggctttcccacctagtaaaggacaaacatatgcttatgc
>read_4
atgaaaagcttttttttttttcaccatggaagggcattgaatgttgttaaatactttttc
ttcaccaatggagatgactgtttatttccattattctgttaatgtggtatattacattga
ttgctttttgtatgttgaacaatcttttcatactaataata
>read_5
aacctttccagttggggagagattgcccctccctggaccagccaattcttagatacagca
aagtgctcggcctagagtatgcctctgatagacaaattaaccaattcagagccagacccc
ttctatctggcccttgtatcccaggaggcaatattctctgc
>read_6
ggccttcgtgcctatacaggtccttgggagggagggaggactccttaacctctgtagtgc
aggggtcagcaaactgttttctctaaagggcaaataaagacagcaaattttacagacttt
cccataaggtcccaaatgcagctactccagtctgtggtgag
>read_7
taagttgataacatgttaaacaaaatggatttacattttggcagtttacatggaaccaag
aataacgtttttgaaacaggctttacacccatttaaatggctgaagctattcttttaaac
tagaatgtatcttcagattctggaaaaaaggatgccttaga
>read_8
tcctgtatactaactggctatactggaggtcagtgtgcattaaaccaaactgctgtatgg
ttctccttctcctatgttcatcatctattttgctggatatgtaagtggatgcagcctgat
ttctcaggagtgtctgagcattttcctctcacacagttaac
>read_9
acttttcctgtaaaataatttcaaacgcaatcggaaatctgcacttctaaatttcaaaaa
gaaaaattttagagttcagaaatctgctaagtacatatgggcacaaacaaagtatgtgtg
tggatggcaggagtgctttctagaagaggctggaggggagg
>read_10
tgtctgcaaacagggacaatttgacttcctcttttcctaattgaataccctttatttcct
tctcctgcctaattgccctggccagaatttccaacactatgttgaataggagtggtgaga
gagggcgtctctgtcttgtgccagttttcaaagggaatgct
>read_11
attctagaacatacagttctagtgacaggaagcagaataatggtttcctaggaatgtaaa
tagggttagaaaaagagttataagagaggaattatgaaaacgcatgaggaaattttgtgg
gctgatgaattggaataatgaacatatccatccatcacccc
>read_12
ataatatttaaactttatcctgtaacaagtattcttacattccctcttagcttaccttgc
ctatcttctcacaaatacttacatttgtgttagcattcaagaaattggtccttaaccaca
cattccattttcatagcagaaggattaaggaaaagccagaa
>read_13
tttttcttttctaaatgcttctcctaaggcagcccactgttgtgcttgtcgtgtcacttg
ggtgcctctagacatctgtacgcttctccagctgcatgggagacacacttcaccttgtgg
ctcctcctttcaaaggttgcctgtgctgcatggaagaacag
>read_14
agctttgagaagaaaaaaaaaaaccctatacttagtgaatgcctgtaagtatcaaagagt
tgttctattgaaaggaattaacaattttttttttttttgagacagagtttcgctcttgtt
gcccaggctggagtgcaatggcgcaatctcagctcactgca
>read_15
ccagagcaggcggggaactccgggacgctctgctgctgctgttgtggtggtggtgttgtg
ttgtgtagtgttgtgttgttgtgttattgtttttctgttgtgcagttgtgttgttgtgat
tttgtgtggtggtgtggttctgtgattgtgttttgttctgt
>read_16
tgtgttctcttatggaaagagaagactgtcagatttaagggcccaagcaaacaagaaaca
gggcatgttaattgaaagaattattgtaattgaagtttgagtgcaaaattacacccttca
taattttacacttaagtgcatttctgtccatgcttggaaag
>read_17
cataaatgatttgtttttatcctgcctgccccaatcccttttccaagagactaaaagagt
atctagtgcaaagtagatactcaaatattttttaataaacagtgatcccagccgcccagt
gcatgttgccaaatgccaaccccataaatgatcaaacacat
>read_18
gtaaataatttttagcataagtatgactcatgtaatatttgagacgtacttattctagaa
aaattatttgtttatctgaaattcagttttatcctggtatcctgtattttatctgacaac
cctcttccatacacaaccctaaattctcagtgttaaaaaat
>read_19
cacctgaggtcaggctttcaagaccagcctggccaacagggtgaaaccctgtctctacta
aaaatacaaaaattaccttgacgtggcatcctgtctgtaatcccagctacttgggaggct
gaagcagaatcgcttgaacctgggaggcagaggttgcagtg
>read_20
atcactgtgcagctcctctccagctattatctattaagcctctctcttactcactgaata
tttcatacgtgaagtaatggaatgctgagctgtgggctgtgtactatccttttggtttcc
atttaaatttacagcttgccagtatgaaaagagtcccgggg
>read_21
attttattaccatgtcatcaaaaatgtctttacttaggaacctaagaggttttcttttaa
tactaatacagcaactgaaaagagtaaaaccttgacatgcatctgttaaagtcccatcta
tagtcatcattatcatcattgttacctttattatttaagta
>read_22
aaatatatactttttttccccacgcatccatttaacatttagcaatttagaacatatctt
gggacataaaaaatattaaagtattgacataatacagaatgtatcttgttatcatatgga
attaaactagaaacaaaaacagaaagataatacaaaaaaac
>read_23
aatatgtgtcatatactcatttagggctttataaaccttgagagatagtttgactatatt
acactattccatcctcagtatatctttgagtggtaggcaaatattatcctagtaaacgag
atgtatttaacgcaaatttattcccccaaagacaatataat
>read_24
aaagaatgtgacatttggccgggtgtggtggctcacatctgtaattccagcactttggga
ggccgaggcaggcggatcatctaaggtcaggagttcaagaccagcctgaccaacatggtg
aaaccctgtctctactaaaaatacaaaaattagctgggcgt
>read_25
tgcccaggctggagtgcagcggtgcaatcttggctcactgcaacctctacctcacaggtt
caagcaattctcgtgcctcagcctcccgagtagctgggactacagggcgtgcgccaccac
ccccagctaattttgtttgtatttttagtagagacagggtt
>read_26
aggaaatcccccaaattactgaggtttgatggtgttagtgatgaattcattcaaacttct
aagaaataagtaattctcacatcacaaattatttctggctcggtgcagtggctcatgcct
gtaatcccagcactttgggaggccgaggcgggtggatcact
>read_27
tgcgtgtccaacagtaatcccatacgattataatggctatactcaatagcctaggtgtat
agtaggctataccatctgggcttgtataagtacactctatgatgttcacacaacaccaaa
atcacctaacaatgcatttctcagagcgtatcctcgttgtt
>read_28
ctttgtatctcattcagccttgaagtcaaagcaatgggatcctacataaatgaaatttgt
tgatctagtgcaagctaatacagaaatcaatttcaatttcctttggatgtactattagtg
tttatctgatggtggatttgtgttgttttaagtgatagcta
>read_29
atgggctctgaaaatcccttcaataatgtcctttcaattatttaaacaactttcactatg
actcagcaacatggaacaagtacccacaaaaagatcatgagcctaagaagcaaatactct
atgagggtcttgattaaagcttataaataataatagacata
>read_30
aagtaccatgctgttttggttactatagccttgtagtatactttgaagtcaggtagtgtg
atgcctccagctttgttcttttggcttaggattgacttggcgatgcgggctcttttttgg
ttccatatgaactttaaagtagttttttccaattctgtgaa
>read_31
aatctgcaattgcctttccctgttgttatcattagccactctttcaacctcaattcccca
gaaatcagagcttgagattatggcctagttctgattgttgatggagcatatgatttccag
aggtagaaataagagatgagaagtgatgcaagcatgggggg
>read_32
ataaaccaattccccctcattaaatctttccctagtaagattgcatttcttctcacagtc
ctcttcttctgctgctgctttctctctcttctccttttactttatttttgtccctcttgt
cctttctctgctccctttcactatttccgttttaacctccc
>read_33
ctagctcacctgattcccaccctcatgccgacatgccaagaacctgaccttttgatcttt
actcgtctgataaagaatggtatctccagtttgggttgaaaactacatttctcttactgt
gagtgtggtttaacatcttttcagatatacttgtatatttc
>read_34
cacatctttgagtagttcctttgcaaacatggactattcagtactcagctgaagaatcaa
ggggagccctttgcagtcttcttcctggtactctgccccgtaaattctgaccaaactctc
aactctgcctcttcaactctgagagaatgccaggctctatt
>read_35
gggtacatgagatgttgtgatacaggcctgcaatgagtaataatcacatcatggaaaacg
gggtatccatcccttcaagtatttattctttgtattacaaacaatccaattatacttttt
aagttatttttaaatgtacaattaaattattattggctata
>read_36
ggagatatttcctatgaaagcaaaaatgaaacctctactgcaagattccccttttcctga
agccccgtcttcttcctgggtgtctggctcactcactctctgccctgcacagccgatccc
tgtcccgatttgccctctgaaacctgcccatcactcccggc
>read_37
gccctgtctctgcccttgctttttaaagggatgtttagtacacagtccttctgattgggt
aacctaactggagttgttagttaagtcatgagaaaagaaaatgaggtcaagattcttaaa
gaccatttacttgctgatccagaagatcagagttaaagggg
>read_38
tcattcctgttgctcaggctggagtgcaatgacatggtctcagctcactgcaactctccc
tcctgggttcaagtgattctcctgcctcagcctcctcagtagctgggattacaggcatcc
accaccacacccggctaatttttgtatttttagtagagaca
>read_39
aggctgatcagtggcttgtccatctcttctggcattttggtggctgcaagagaagtcagg
aacctggtcagtggagggctcctggactgccccttctgccacctccctcctcttatacat
cgtaactacacggcagtcagacattcacccagcaggtgttc
>read_40
ggttatttttttctaaaaaatgatgccctaagactaccagggtgagaatcatcaatatca
gaatcagatgcttgttaaaaatgaagattctcagacctgctaaatagtacttccggcatt
gagctgcagaagccctatttttcacagccccaaccagaatg
>read_41
ggtggatcacttgaggtcaggagctcgagagcagcctggccaacatggtgaaaccttatc
tctactaaaaatacaaaagttagtgggcgcctgtagtcccagctacttgggagggtgacg
cacgaaaatcacttgaacctggaaggcgaagtttgcagtga
>read_42
gaaaagaaaagaaaaaggaaagaaagaaaaaggaaaaaaaaaagaaattgtataaaaata
tctgtttcaatgaaaggaagaagagatacaaataagaccacaaaaaaaccattaacccca
agattatatatgtataactcaacccctccaccaaagtattc
>read_43
tcccatgtgtccaacacagaactcacaagactcttggctggatgtcctcttttcaggaaa
gaaggttcatttttagagataattacacactgtgtaagcatagaagtctcccttttattc
tgaatggtttcctgaaaacgctgtaactactgcatttagtt
>read_44
taacagaacagaacagcagtgggcgtctgtgctacagatgatattcttagggtatttgct
gccatccactctcctttctaaatttggtgttacagattcaacttctgtttttaaaaggga
agttgcagatagatcattcacactattattttctccttaaa
>read_45
ttattttcaagagaaaactgaagctaaataaaatcattctttagggctagcacacgttgt
ctcgaaatagactgaattcatttgttatctatataacatttttatatgcttcacattact
cactttatgccattaggaaagcactgaatctttaaagagaa
>read_46
taccattattgacagagtaaaaagtcaaccaacagaatgagagaaaatacatggaaatca
tttatttgataaaggtttaatattcaaattataaagaattactataactaaaaagcaaaa
agataaaccacccaattaaaaataggcaaagggtttgaata
>read_47
ttagaagtgcatgactgagacttctgttttttacttctggtaatattagactagacaatc
aaagtctgctctttaaattaggataactgggaaacctgaactatgtatctatgtgcttga
gggaatcatagagctaagaacataatgaatatttatgagaa
>read_48
ttttttcccttaccttttaatatagtaaaatcctaagttgaaacatcttttggctcattt
attatttcagccacgcttaatcaaaatatcttattattttagcaaacatctgtattttac
ttggtaacatttaacttaggattcttatataaatattcata
>read_49
tgttctttttttttaatagaagatgaacctgaaacttaataaataacactaaacatctga
taaaagaatatcattgatgtttaatgagctgttctaaagtagccaaatagggaaggaacc
tcctaagaagaggagctctctttaatcatttccagtattat
>read_50
tagtcctggctaattttttttttttttttttttagtagagagggggtgtggctcacacct
gtaacaccagcattttgggaggctgaggcaggcagatcacttgagtacaggaggtccaga
tcagcctgggcagcacggtgaaatcctctctctactaaaaa
>read_51
ttaagaatttcctgataaatgtcaatttgagaacattaaatatttttatagaaaaacata
tgaaactaatttacttaaattgaaaaacaaggaaaaatagaatataactagttagaaaaa
agtcactgttttaaatatgatttattataggactttgatag
>read_52
gggcattcagttcccactcgatctgttggtggtcacgcctctcaacatctgtcttcaata
gcagcagaaagtaatcaccataagatcactatgctttctcagtcggctgtatcaaatatc
tataattgctctttagttagataaaagttaccgagaacaaa
>read_53
cactccagccagggcaacaagagcgaaactccgtctcaaaaaaaaaaaaaaaagaaaaga
aaagaaaaagaaagaaagcaagcatttttgaagccactcactgacttcactgataggatg
cacagaataagtcagaaaggcaaagctcccgagtctgcttc
>read_54
tgtagaccacttggaaatttcatacattgctggtgagaatgccaaatggtatagccacct
agaaatcagtttgatagcttcctacaaagttaaatacacttactatatgacccatacatt
ttactcctacatatttcaaatgaaattaaaattcatgtttg
>read_55
aatcccattactggatatataccccccaaaatatacatttttctatgataaagatacatg
catgtgtatgttcattgcagcactattcacaacagcaaagacgtggaatcagcctaaatg
cccatgaatgacagactggataaagaaaatgtggtacatat
>read_56
ctagtgggaggtgtttgggtcacgaatggcttcgtgccatccttgcggtaatggatgagc
tcttgctctattagttcacaggagagagctggttgttaaaaagaacctgacacctcctct
ctctctgtctctctctctgtctcttggtccctcttaccatg
>read_57
gctataaagacacatgcacatgtatgtttattgtggcactattcccaatagcaaaacctt
ggaaccaacccaaatggattaagaaaatgtggcacatatacaccatggaatattatgcaa
ccataaatatgaatgagttcatgtcctttgcagggacaggg
>read_58
ttccttcttcccttcctgctcaccagccggccgccggcagcggctccaggaaggagcacc
aacccgcgctgggggcggaggttcaggcggcaggaatggagaggctgatcctcctctagc
cccggcgcattcacttaggtgcgggagccctgaggttcagc
>read_59
aggtcatgaggtcttgggattaatggctgcaaaatagccccaagggacttgtttgttttt
ctaccacgtgaggaaggaggaagacacagggagaactgtgaggtctaaaacctggaaggg
agccctcacccgaacccgatcgtcctggcactctgatctca
>read_60
ggatttgtgtggtggttcacagctaagactgcctggattcaaatcccaaatctgccaagg
caattatggggactgagcccccaacctgtgggatctgacactgtctccagataaatagcg
tcagaattgagttggaggacacctagctggtgtccactgcg
>read_61
tagtcctaatgatctttcccacctagttttttacatgtacttggattccccatcttcgca
gccaccatttcccaatattcttctgacctgtccattccccaagactctatcctcccagaa
gaaaggttacattgtagaatgattgctgaggtttatacttg
>read_62
tggaagagctctcttgggattattttataagagtactagtcccatgcacctcccaatcac
cttgaggaggtcccacctcttagtaccatcacctcgaaggtcaggatcccaacataagaa
ttttaagggggcacaaacgttcagaccataacaccaggttc
>read_63
acaggacagaaaaggttctagtactgattattacatgtggtttaggacatttaaaaatgt
atgctgacatgctgacagcaaaagtatactcactgtgtacaagaaaacaaaaatctttcc
acatcagcagcagagtgagttttgtaaagccttctgcatca
>read_64
gccacaccagctttctttcaattcctccaatgttctcccatgctccctccatctgcagaa
catcattgtttacttcaaggttcaagtaatatcaatgaaaatacaggcaaggcttctgtt
ctgaatggtgcttacttctagtggagcaggagaagacatac
>read_65
aaattcagggagtaaccacttctgcccgttttcttgccccacattttcacttctgattat
attttcctcataggtaggagttagttatccatatttgttccttttttttttttttttttt
ttgctaagaaaggtttttcttttctttcctttttttttttt
>read_66
aaaagagactgacagagagagagaggaagagagagatacacacattgtactcaaagacag
agagacggtacaggatcacatgaataagtctttagagtatgcatattatactctaggcca
tatggcataacctgagattaaaatggtcctttcaaactaac
>read_67
agataaaactaaaaaattcttgcagcaaaatttcaaaagtgcattatcatagcatcataa
atatatgattgatacatatatgattggttggataattggataatagtacaatttcttata
atgttcaaaactatacattattttaaactagaaaaggacat
>read_68
agctcaagcaattcccccagccttgacctcccaaaatgctgggattacaggcatgagcca
ccgcacccagcccacagctttgttttttgcagtaatcacctccctctcacatggggaaat
atgccacaaaatatacctgaaggaggatatttaattctcca
>read_69
tctgcgatgcagtcagactgcgttgatgccagtgttctcttggttcctgcaagactttct
tgaggtttcttgtttccgcaagctctgaactgggctctggctttgcctcagaagcacaga
gctggagcatctgtgggagaaagtggaaatggagcaataat
genometools-1.5.1/testdata/readjoiner/70x_161nt_phred64.fastq000066400000000000000000000556201211610345200237520ustar00rootroot00000000000000@read_0
ataaattatctactatatttttattatttgtgtatctacccatgttttttacatacatacttacatttctgttgtacaaacaagtataacattaatcaatatctctattctcttctaagacaaaaaaattagtaataacgtccgtccaaactttctacact
+
VMN]]D\DVJDIeZUM]lXickYaXieIJLlf_MOGEbglJN\IEbXk\T[]jIcdI_PiHPlbedTUU[XRNGfI\ZFJSQ`_diDZU_Sd]LO[_RWiagkL]QKih[XPRNlh_KMdhJV[\\DcceSa^HQV\hiagNi]P^eHbRUcVSGL`]^XK
@read_1
aggagaatcgcttgaacccaggaggtggaggttgcagtgagccgagatggcaccactgcactccagcctgggcaacagaacgagactctgtctcaaaaaaaaaaaaaaaaatgagacacagacaagatcccacagctatcacgtttacagcaggtctgttc
+
PWg]JFfIVFOa^LLhN]LHJSkjWOTPPORQ\WZNgaLTSQbORXNfEhZ`JGX`^SEih[j_MkXWjY]KjbeGU`JjNbDDkiXOEM]E^E]^L[YgDQlK`[OWH`[WLZHLNWF\EdYZLi_gHYRSkaNiTJKkVdFVeOabPcahcbJWjDbLR
@read_2
ttctttttgaatagaacaaggaaaaagaactcttcaaaaagagtggaaaagatagctaatcctctgtggttttatgtgctaaaacagtcctgagatacacaagttaaacttggcatactttggatctgggccaaaaattgtttttattggctgtagaaaat
+
SVMHNMVKadIKPMDOkXYbM^[fjUcJHKLWMGWf\EW^JUWUEYUbDGH^N`f_LWKVPkTJGkIIJEaWQkMO\Kg]`ic^Q\EV[a``IcOTEKXHejT[SkbMSWJHIPL]FjW[cfikLEJcKaWNM^ElYcjOiN]E`TZFEGaYUkPeJeGUW
@read_3
actctgctccaacctgccctttcgaccttacttcctgctccggtgcaggaacctggctccaggtcagcagatctatatacttcctcatgcctacatcttggcctagccagtgtggttgctttggctttcccacctagtaaaggacaaacatatgcttatgc
+
bZlgcWV\\[aUOPSShH]EaIJeRGJQ[UX\_VJXXhWbUbgTfQ`i^HfLbJhLQje`ki`KFeblW\]iT]TERJTVbiEMaFNTQjgNEdLGOQSaMSZONK_O[\\eOgXJJ_hEKEkl]VDFb`fHVQ^`a[eRMGigkHfOiJO`TlHXeeiSI
@read_4
atgaaaagcttttttttttttcaccatggaagggcattgaatgttgttaaatactttttcttcaccaatggagatgactgtttatttccattattctgttaatgtggtatattacattgattgctttttgtatgttgaacaatcttttcatactaataata
+
cEINLMjeNPTQPHPM[KOSfW]hX_NggSRZ_JfeFPFIeO^PVLKG\iaPUGeMYYQ]JNEQLM\bjb[_QZVc[DfdXlXl\RJQ\lRW`dQYPGaQbWMWMUlKX`FZegWl[eUjP`kcJeJ`GXRRGMgUSeO]kGOe\UUhfgNUSRWDTWDVV
@read_5
aacctttccagttggggagagattgcccctccctggaccagccaattcttagatacagcaaagtgctcggcctagagtatgcctctgatagacaaattaaccaattcagagccagaccccttctatctggcccttgtatcccaggaggcaatattctctgc
+
DcDGjfaY_KLlRkalJlfbQXiD[cdX]TaIggkUQlZPHLdGQFQRhWfUZRSdLFjPkFReFc`KLES_ebO`MaUgTIFM]jI`KkQ__dDMON]dTYeZ\HZbWUS`HUiWjP`MJINKlM\JG]]F\kRdhZiQ^ETT`kii\ZNWLXWTIdIMX
@read_6
ggccttcgtgcctatacaggtccttgggagggagggaggactccttaacctctgtagtgcaggggtcagcaaactgttttctctaaagggcaaataaagacagcaaattttacagactttcccataaggtcccaaatgcagctactccagtctgtggtgag
+
k^^KQZjPGlWPOk^RVaj[kWfXSVkF^bVPD_calN[]ajWDX]fUgX__kG\gVKHNJUlMi]YRYhKIR\UY[_[XZUWhUWfKJLjhgeHW[QVf[JkI_JYVYUfjceO^bSSW^_MR[YNc]RKl^W_O]_ahQhLQGgYHIj[bMkOePjfTT
@read_7
taagttgataacatgttaaacaaaatggatttacattttggcagtttacatggaaccaagaataacgtttttgaaacaggctttacacccatttaaatggctgaagctattcttttaaactagaatgtatcttcagattctggaaaaaaggatgccttaga
+
cfjIZhldUQLcXM^P[YbbIbUlLSYfPWNPahDXaVMGGGDFWZjjEe_JVJhMhFGcN]HliLGOL_`_c\aPZ\e]PJYlOWJeH[clOJ`IK^RLEjGMU\Dde`RlR^hHERbNQbOD`SffV`MgfMELSFMjQjUGLSS\lHGDF\VVcc[MY
@read_8
tcctgtatactaactggctatactggaggtcagtgtgcattaaaccaaactgctgtatggttctccttctcctatgttcatcatctattttgctggatatgtaagtggatgcagcctgatttctcaggagtgtctgagcattttcctctcacacagttaac
+
WZWNSXdGESYOJKMKK_geML]HHY`\cVYRJXNUDhXDjhXkDOdiY^aUaDXEbJjXRlQPYjl_MWgDa\KOagiQeUEMbjHjb^HGMIWalkYEJhRYjQhi\U`GbD]G[XWNMFXG_FZeXHcD^IVTkgU_T_GIdFc\TH]O[kGhZIaaZ
@read_9
acttttcctgtaaaataatttcaaacgcaatcggaaatctgcacttctaaatttcaaaaagaaaaattttagagttcagaaatctgctaagtacatatgggcacaaacaaagtatgtgtgtggatggcaggagtgctttctagaagaggctggaggggagg
+
HPV_leGYfRIZFNkeLglGc^KQl]ZI]Y[iULU^cXHXJ`VhWP]NE_NlMN`J]aS[NffMPk_Zb^_`cYEaVYdjdHUK[TZKjTLhHe\V^MTdVa^JQkaPkga_TeTYZebQFGdFT[`kagLbcKINPEJieYJG\PIN_RGWEjMlH]Vej
@read_10
tgtctgcaaacagggacaatttgacttcctcttttcctaattgaataccctttatttccttctcctgcctaattgccctggccagaatttccaacactatgttgaataggagtggtgagagagggcgtctctgtcttgtgccagttttcaaagggaatgct
+
gk\Sh[diQbGe_GhkIXW`fij\`ecEDNG`kHRcXcaG\EiXP]^H`EZge`UOKddLhY]TRikSFbWjTIUfQLaQ]jQSRkkTSeMVLlNdIFkTcN`bb^DO`KDX^LR^]UJG[_M[\eh`\VSWVFTh]FGcKDEGW^G]HhSREUTQFSHfg
@read_11
attctagaacatacagttctagtgacaggaagcagaataatggtttcctaggaatgtaaatagggttagaaaaagagttataagagaggaattatgaaaacgcatgaggaaattttgtgggctgatgaattggaataatgaacatatccatccatcacccc
+
ghZNK`P^DGXPPlk^HIhH^[S\IUei_iJNRlRSSHLLMDgikhjc[dZOOM`bRhVUTaa^JjfRIMXJc`]KiQ[biTccdaGbJjKaljIWgSF\V\JI^ckcEiSTIQdhFQckfaUW`QYgKf`[gWSdKiW^ZikJV`XeZNPOD`h]J^bUY
@read_12
ataatatttaaactttatcctgtaacaagtattcttacattccctcttagcttaccttgcctatcttctcacaaatacttacatttgtgttagcattcaagaaattggtccttaaccacacattccattttcatagcagaaggattaaggaaaagccagaa
+
VaUhbL\WgiHXGeMlbQga[RIZkSTILjOUX]^S\ISWIIDH]L`SDW]XDGcDb_MLlQVihGNQLJMiDf`^EkVU_c[W\VOJDc_eOSNhXPZPdeXgbNfcHQH^c_bkFlZHkc]ebf]TGUDhld[fOdPbM`gbb]KNFSe[jIcZS\i]_
@read_13
tttttcttttctaaatgcttctcctaaggcagcccactgttgtgcttgtcgtgtcacttgggtgcctctagacatctgtacgcttctccagctgcatgggagacacacttcaccttgtggctcctcctttcaaaggttgcctgtgctgcatggaagaacag
+
FOcjV_RTMe]OSOES`DXGh_TO^cKiGPMJaYRSbPkdiXfiWFabP`E`ZLNdVbjS_aDIHH_IFLjjR_VYgF`lfFDlJF^eYIEY_\d^KZebHKbaHZb^^I^RRHGYJOGi`ZG`Yd\_`V^^FbhFaUTacPUgFgPKZMdLhhh\Pg`jN
@read_14
agctttgagaagaaaaaaaaaaaccctatacttagtgaatgcctgtaagtatcaaagagttgttctattgaaaggaattaacaattttttttttttttgagacagagtttcgctcttgttgcccaggctggagtgcaatggcgcaatctcagctcactgca
+
S\aQYlDhLcO_KJUjjPeJlfaNQMOd^IIdVebQI[]\VbYSdS]FGHVFKOUehHg^RFcc[SSgcWKFc]UdLGflViVeX\USbVXaFgDPO\cIOUblM]idSIZELeIWZFh]^d^KRQDee[_gaZRShijZ_FlNgkibSO\OWjRQJGFZU
@read_15
ccagagcaggcggggaactccgggacgctctgctgctgctgttgtggtggtggtgttgtgttgtgtagtgttgtgttgttgtgttattgtttttctgttgtgcagttgtgttgttgtgattttgtgtggtggtgtggttctgtgattgtgttttgttctgt
+
fJhacXgXFd^g_FE[\SF^iKbDYKilGXS\R\TkhNMUNXPfb\ZlkFOdli[IGYPXlJlHOh[Qbh`MOVkc\TOgXE^cP_\feaNb^cWedHbLXT\fIUMaSRRMHXfb^`ejZ\QLEb[^]EN\iSbRW[dOR\fKVIPlaKY`bFISEP_TQ
@read_16
tgtgttctcttatggaaagagaagactgtcagatttaagggcccaagcaaacaagaaacagggcatgttaattgaaagaattattgtaattgaagtttgagtgcaaaattacacccttcataattttacacttaagtgcatttctgtccatgcttggaaag
+
L[c\MSeJ`jeSMPQkVhc`Fd]UYKOIbQ[i\MTRM_EJ[SO]SPkDY\gcffXFJRUMkYGRd^LRJFI^TkPOHkK^lEMOjfFY[[`hQJOgPEgZDRUgURJ_hiLJfEXRQJGc`iZKcaiXMO\^hUaj\TTc[YNQTeK]EalZYPHhWE]kP
@read_17
cataaatgatttgtttttatcctgcctgccccaatcccttttccaagagactaaaagagtatctagtgcaaagtagatactcaaatattttttaataaacagtgatcccagccgcccagtgcatgttgccaaatgccaaccccataaatgatcaaacacat
+
fWkD[lZ]ldOHiaOQcIiaFIMRcQF`g\aTHIDicEklIScWbPPlP`NVQMKRbSLH]JcTKg]_leEfNkTObJg_SiD[jIScdaO[N^kk[RLeOaZbGb^KDHRfGhg\Ef^RRKEglkSJRebIfUYf]W[dO_YTXLDPiVWPZic_GTFYH
@read_18
gtaaataatttttagcataagtatgactcatgtaatatttgagacgtacttattctagaaaaattatttgtttatctgaaattcagttttatcctggtatcctgtattttatctgacaaccctcttccatacacaaccctaaattctcagtgttaaaaaat
+
`l]TFTWaE]EbKgDRi]agKXFEHgWbbXUZa_KTdebXWLjgIYFRFcVjh^[[PXDVDVbV`VPPS]QDD[XQlkVWhFOLlaTXHdUfEVHf_]TdSGbK^eg[^GRdEgdIVYMQdUWJJEGFGTX^h[QSeRD[j^OdPOUIgIcHSN__FG\^b
@read_19
cacctgaggtcaggctttcaagaccagcctggccaacagggtgaaaccctgtctctactaaaaatacaaaaattaccttgacgtggcatcctgtctgtaatcccagctacttgggaggctgaagcagaatcgcttgaacctgggaggcagaggttgcagtg
+
QKWTJYhZT\LgJEWdX^FJa[ckLJNbb`XQiLebhPRPjGfOYU[lOjhWMQVF^KXLe_NE\jc^VkOjUb[fdMiIdUREN_bYfeFF[Ufc[]REghbM_iFFLMRcYFfW\R_KM_SW\H[iKkZbcPfOFONP^UiXU_S\iMkDDdY[NWe\Y
@read_20
atcactgtgcagctcctctccagctattatctattaagcctctctcttactcactgaatatttcatacgtgaagtaatggaatgctgagctgtgggctgtgtactatccttttggtttccatttaaatttacagcttgccagtatgaaaagagtcccgggg
+
VegdMNEJIl\XbdV`WN]JM^aa_PdiHVYQRLThS[SOVIlLIeL_HYQhKf^iaJ\EDXdUEf^li]gFUUVEHNkfKQI\ajL_PfFPbkGgMF^HhIkMNDeSM\R`YWZTjacbPf\RWYZl`fGbjJQTLaNfJNEDIYVj[ELb[h^IcK_Kl
@read_21
attttattaccatgtcatcaaaaatgtctttacttaggaacctaagaggttttcttttaatactaatacagcaactgaaaagagtaaaaccttgacatgcatctgttaaagtcccatctatagtcatcattatcatcattgttacctttattatttaagta
+
jVe[bH[`b\ea\MIGegKhLkIdYXiOKRgkEQLWd\gZ^_\JEOVM`^jEFh[`gigaVTOgdjNkhLZ^hH]QRQWHliX]el`aahRcFZFZWYWDFEgFZaLDZIO\ThSdK[PO\WaTDWJX]OUhD]jRTcEkUW^TelQUMUgXFUTQVKjia
@read_22
aaatatatactttttttccccacgcatccatttaacatttagcaatttagaacatatcttgggacataaaaaatattaaagtattgacataatacagaatgtatcttgttatcatatggaattaaactagaaacaaaaacagaaagataatacaaaaaaac
+
^Llc[diD`hYIGceYTZde]c]_XODJdd`MDlM_GW^eSDee[Hk]Tbk`MMLcEfFYTRXUEaRIifQOgTRK_PZ]UNdhlhPidIHlWdaY[GHELDOQHXd`KY]QNNOFYElEjLHiaOE`LQV_KebLcDKDJO`NbYbXljeZTPO]fhQhM
@read_23
aatatgtgtcatatactcatttagggctttataaaccttgagagatagtttgactatattacactattccatcctcagtatatctttgagtggtaggcaaatattatcctagtaaacgagatgtatttaacgcaaatttattcccccaaagacaatataat
+
OL_k_fbGk`YK^IgeGifYZXPNKKhGHP_iSOEjjbeHS`Zd`U\aa`DfQbFWeX^iQacVd^f^WNdEiTdgJahd\SWGiKQaHjScMXVEiRFZWMa[\e`jbH]HSEEJab[HFPHbZTjikTj]`RQSOMiJ\DUjD_jGdZbfHE\U`XhgR
@read_24
aaagaatgtgacatttggccgggtgtggtggctcacatctgtaattccagcactttgggaggccgaggcaggcggatcatctaaggtcaggagttcaagaccagcctgaccaacatggtgaaaccctgtctctactaaaaatacaaaaattagctgggcgt
+
iHGFUlfa_YJ]XDKhgPJfbGOX]VIaKhN]XQNRjcUVNZ_jUSFSaXkFZZMleWbHiEDk^PjhblfUYXYgQFcZEHV`lcHQFY_k\OW\a`eINOk\kFbK]hSdEVWWidbGhOdHPN_k_HRYfeVVW`IbWV^QHDL_bGaY^JUg`UjSN
@read_25
tgcccaggctggagtgcagcggtgcaatcttggctcactgcaacctctacctcacaggttcaagcaattctcgtgcctcagcctcccgagtagctgggactacagggcgtgcgccaccacccccagctaattttgtttgtatttttagtagagacagggtt
+
HaRS_VZhDhjY`]Qh\chb`kDeiUj_fdPPHOLX`fkVMSQRlelcgZG`^DlIQQZ^\MbKSLDJPFTgHgdR[aI\jQceiJ`KfcebYGaiW[EcPIiRbjDOgEhgJWLPaONU\LhjafbKJbZZhlX[KUYNQY]_kYYRS`lTHe`VaKUha
@read_26
aggaaatcccccaaattactgaggtttgatggtgttagtgatgaattcattcaaacttctaagaaataagtaattctcacatcacaaattatttctggctcggtgcagtggctcatgcctgtaatcccagcactttgggaggccgaggcgggtggatcact
+
YRVDkdbhNlSJHXZedXgYccPDchN]Wc]FgXI_XVFX^[TfJbYLV_jGeRIXIcdZKJbYai\_eS_JeMTFXQ_cUGIk\N\[KMkeRJPGPHOFWkcHDKL^IWjS\MfkU\UGhH]PKUjXMaQkIiUNTlVjQLdMSEOWPRDRhFlEQZZTf
@read_27
tgcgtgtccaacagtaatcccatacgattataatggctatactcaatagcctaggtgtatagtaggctataccatctgggcttgtataagtacactctatgatgttcacacaacaccaaaatcacctaacaatgcatttctcagagcgtatcctcgttgtt
+
]RiK[\jXbf]UjaabgPX_VXMcjXHEGN\LlPaFZe\US]]NiFE[]\GiV[iT\PXkW]FYhfD[llDlhYDdSQGdK[h_aLac`OlWhcMHRGehPW`i]akfeZlVlNTVk]eNGEfFJ\Ok\diSlXkDd[gjRd_WYdZ^QJGPOZUgJkWFj
@read_28
ctttgtatctcattcagccttgaagtcaaagcaatgggatcctacataaatgaaatttgttgatctagtgcaagctaatacagaaatcaatttcaatttcctttggatgtactattagtgtttatctgatggtggatttgtgttgttttaagtgatagcta
+
SighiehXWQjKkd]]UcHYHbPFiIdJk_liGXOF`aXUgfcfiFEiVFgQ_aHaN^GFbMTddT[_YX_kIUQQ[`k`F_WIEDGJNDPdb`WjQMURJUGb\VLcYShZWRV_^XPUaJQWMKPDigDfSbfOL^ILSFLhQif``QjT]Mhhd]lRT
@read_29
atgggctctgaaaatcccttcaataatgtcctttcaattatttaaacaactttcactatgactcagcaacatggaacaagtacccacaaaaagatcatgagcctaagaagcaaatactctatgagggtcttgattaaagcttataaataataatagacata
+
ILh_g_EYQVIEgFJ^]XL^g\ZYh`ODblSab[Wd^\TGDfIDTjeSUPkF_Veh`k[OU\fXla_]`EEgfTkRRRDKGQ_LNg`YSQOcGh^a]MVEYQMLakEcXJkYbLceDiRRKfJlNE\gKEJFlUWlgU`f[U^iJU^P\de]leXEP`\fd
@read_30
aagtaccatgctgttttggttactatagccttgtagtatactttgaagtcaggtagtgtgatgcctccagctttgttcttttggcttaggattgacttggcgatgcgggctcttttttggttccatatgaactttaaagtagttttttccaattctgtgaa
+
d`lLcdfXWIiU]TNEgWYTd[SUNI\d]RFh_eDER\W\QS^aicihePOagSlS^]UGecWUEXUYjRNN[MGdVlOl_MlEHHfcUWX^bbKjIcFIQjTfTiQdQfPcTkdcXh]QXF_F_aWdEUe]^fN`dfHOj\gFdOMDE\klXJLadgF[[
@read_31
aatctgcaattgcctttccctgttgttatcattagccactctttcaacctcaattccccagaaatcagagcttgagattatggcctagttctgattgttgatggagcatatgatttccagaggtagaaataagagatgagaagtgatgcaagcatgggggg
+
DWekaGjhZIaSQaIMEZG[OcHVJd_SPd]KakNaFdKf[[Hb`P_fUHeVeIfE^\XKaeGU_IcRRZPIO[Eb]]cNJbZgZTjM^FHJV]VRK\b]_]]GWF^_ZiVaDZZk_GlTZIebiVeS^X]ga[gVdNNi]QYlKS[QFbYSZQiHgcfKL
@read_32
ataaaccaattccccctcattaaatctttccctagtaagattgcatttcttctcacagtcctcttcttctgctgctgctttctctctcttctccttttactttatttttgtccctcttgtcctttctctgctccctttcactatttccgttttaacctccc
+
GX^X]`hOVNij][EXaOjkhhcljcZM\aMebjbH\fT\jUfk]`c[EbTf^]aO^\MJR`SNGVNIa`I\TfX`M`kHGQFRG`J]fccVcDSb[fL^dI]TPQFgIb\a\SeYXc\kINHgZUkPLdZZcGIacifWfWkhKec_HDidjUEG\Ul[M
@read_33
ctagctcacctgattcccaccctcatgccgacatgccaagaacctgaccttttgatctttactcgtctgataaagaatggtatctccagtttgggttgaaaactacatttctcttactgtgagtgtggtttaacatcttttcagatatacttgtatatttc
+
`OHlJTDc[e_SDIE`Df[lPOEN_[XWeGE]lD_VWhH^YckSkIYRgiIj^ULZXDdNghgQUTQJ\dKJXWaGEN^faXiPM^fjVLD]eOOLLZ_`MRb\ZINZcbQhfOMOTQYjKT`kDjXUYbaMHZkYVVGJeN\H\QLGXRfdVDMGegSZQ
@read_34
cacatctttgagtagttcctttgcaaacatggactattcagtactcagctgaagaatcaaggggagccctttgcagtcttcttcctggtactctgccccgtaaattctgaccaaactctcaactctgcctcttcaactctgagagaatgccaggctctatt
+
c^QVFVlGQLRTZHKD^WGZbK\_eGNVIa[gU`PPUV`O]PSbKT\F[HacGHYgRYVPLE[QXMYgPgVi`QUPDHa]XkH`[SkkTNMYIIc^ZXaQYTWNEcaU]PSFlcS^`Mh]\GGgVT^\eRKUTdQSaGaPWcXR]jRZXEeSM_cFi[TRY
@read_35
gggtacatgagatgttgtgatacaggcctgcaatgagtaataatcacatcatggaaaacggggtatccatcccttcaagtatttattctttgtattacaaacaatccaattatactttttaagttatttttaaatgtacaattaaattattattggctata
+
L[IX[kEcYd_hJkDWkiieJd`IfYf]f]VZY[cIjSLf]NYbdh]YSEPjOiOfY[kEFSf[FhSVa\TGkV[X`FbcVO]LSSckgH^ljQf_`NN_HGiUPN`LKIZRUii_VYYOQOkMG[^NgZMF`EjXLaRbUGYRXHJVcVUfVhPZF[YH^
@read_36
ggagatatttcctatgaaagcaaaaatgaaacctctactgcaagattccccttttcctgaagccccgtcttcttcctgggtgtctggctcactcactctctgccctgcacagccgatccctgtcccgatttgccctctgaaacctgcccatcactcccggc
+
^ZRI`OERhNkVMW]jcSMMWebjUj]\HKQOgJWQUDEfTW]FhSWEH_XiSXb[^X[\WUUjRENZhcTSV[UPjMKjZgZlgljIEeUUd[HJINVFJdKS^VE\^gYIXjGWe``ecEL^fec]k_ObK^FhlL_`OG_bWOkhOhkQajdeFjSOe
@read_37
gccctgtctctgcccttgctttttaaagggatgtttagtacacagtccttctgattgggtaacctaactggagttgttagttaagtcatgagaaaagaaaatgaggtcaagattcttaaagaccatttacttgctgatccagaagatcagagttaaagggg
+
S^Pb_k^GI``FEdGRGYH_]jXDhKcMRbWM[HaQOWVQP^R]ihMNXYZ`JNV^hPSdKdKEfFDWSGk^ZRi`gRgaJVPkEQMQKKF__\YdKV`Y_IfNJVlRiFYEDEdXRkGTlVcRgeOWhOhNMQUV`^[\DLhlD]JNIILFlShjFdjZi
@read_38
tcattcctgttgctcaggctggagtgcaatgacatggtctcagctcactgcaactctccctcctgggttcaagtgattctcctgcctcagcctcctcagtagctgggattacaggcatccaccaccacacccggctaatttttgtatttttagtagagaca
+
PJZaL^_fMEO_\`bkFGIRJPVjWKTNlMDQODDUHIYVF[\HOaLQQWWf]E^JKekbfIRaM\K^UhjPfbR\cVEDNFSkFVGXl]OOZTlTgN_FHh`SI[KMeifFShRY\M\hg^fVN`Pe]YSggiNSgWPVFTjfEjHecbDjEO\^XSjSX
@read_39
aggctgatcagtggcttgtccatctcttctggcattttggtggctgcaagagaagtcaggaacctggtcagtggagggctcctggactgccccttctgccacctccctcctcttatacatcgtaactacacggcagtcagacattcacccagcaggtgttc
+
SX_XcR]gcFjGfLUcEDPldaFecITOUWe\jWfQkYGYeQjWlg]ISakEQQc_TEhHFLNlVOa[SOcecTKalgObePH\beMFd\SI]eRUEJ[F`iGTXPcT]QNGLQ`agINTD_M]IRRJRVh[iXHaYLiSTbaY`MFHY[fbdaaDl]hSM
@read_40
ggttatttttttctaaaaaatgatgccctaagactaccagggtgagaatcatcaatatcagaatcagatgcttgttaaaaatgaagattctcagacctgctaaatagtacttccggcattgagctgcagaagccctatttttcacagccccaaccagaatg
+
PZhYXPHHfMRWN`\MgXHS[He[K\DKeXehX_dUbNQU\USeKEPlKYHY`bg`PdKWbe[jGe\idFHWh[N\gYhhG[_VOcOdbW^P[ZWaFUK_X`W_KQILXZUjSIRPLdGE_]Y_IiceZeVSSVhk_OIdTSdW]kkUXZc^bj^`_`UEY
@read_41
ggtggatcacttgaggtcaggagctcgagagcagcctggccaacatggtgaaaccttatctctactaaaaatacaaaagttagtgggcgcctgtagtcccagctacttgggagggtgacgcacgaaaatcacttgaacctggaaggcgaagtttgcagtga
+
cG_D^EkdjdKTJQPbHXfXYRHIS_YRD[QjGJ^DTjdhPKYHUOZ\SJkk\VTcUgLZDiaWfigk^e^c_VPWciQSVRlXaK\djjlagg]UN\bdTL\J`QgJTgbVOOccMSFfY[VH[MI`fk[HgbQEfa^dkZ^bhVkVldgL_gbD]]VMN
@read_42
gaaaagaaaagaaaaaggaaagaaagaaaaaggaaaaaaaaaagaaattgtataaaaatatctgtttcaatgaaaggaagaagagatacaaataagaccacaaaaaaaccattaaccccaagattatatatgtataactcaacccctccaccaaagtattc
+
ZTVThOYT_]eiIlPKWSLbFGVJTMbZ]jRdOLKhPaKW[fQ]O^[kPSj\\USbLX_DS`PlWDjO^VH`[JRUgZ`MS`RV_]ILGH\eSJ^bUUUhRRQGcN[VVgWjiUQIeddTQTOTPWPQENcOTTGbc\adWiS_k^kSOKSDSK^jS]bGk
@read_43
tcccatgtgtccaacacagaactcacaagactcttggctggatgtcctcttttcaggaaagaaggttcatttttagagataattacacactgtgtaagcatagaagtctcccttttattctgaatggtttcctgaaaacgctgtaactactgcatttagtt
+
fjIWldQZkE_Xe^WQOhNIgNlGedFLWUlkHRjZPRWiWlkWe]cegTJiTj^KPGfiMXciLQlccPXWSQkLElUS[UFFMWYeg\LH[hRbEW\il`kOUkIYGjPhZRSGiDXFdjP`\`YOdeiFiX]ldgg[UZcdhD[`V^FD_ig`PLhUe
@read_44
taacagaacagaacagcagtgggcgtctgtgctacagatgatattcttagggtatttgctgccatccactctcctttctaaatttggtgttacagattcaacttctgtttttaaaagggaagttgcagatagatcattcacactattattttctccttaaa
+
IPkXU[kLQFkejgjidJaYIkiYQZL]iQHNYKOJaFQfclUdQk`Y[YZdPGdbGeWVEIi^_RDUgDTMfJjc^QODK_HdKOQVRFLVL[dJPEaOHjLjRITRkJ[YTRRfePHRN]hYW]lGf^lMa`XRl]dThPNTdVLJLiXZFOU`jOL\b
@read_45
ttattttcaagagaaaactgaagctaaataaaatcattctttagggctagcacacgttgtctcgaaatagactgaattcatttgttatctatataacatttttatatgcttcacattactcactttatgccattaggaaagcactgaatctttaaagagaa
+
H^d_jYY__iTiL[MPhdMbGIZGIfkWYNkcPYkDOdjcjEQ`X[kM\PjHNOLOhED^lj]KJF`eEbNQPDjaLaX_\gTIWchIjlbZckUHRjbag[DdPS[hWl[jhDQWkidJgaHE`MXgfMYHP\DDcQZGJl]dbiJl]cP_VcSQWU`Yj
@read_46
taccattattgacagagtaaaaagtcaaccaacagaatgagagaaaatacatggaaatcatttatttgataaaggtttaatattcaaattataaagaattactataactaaaaagcaaaaagataaaccacccaattaaaaataggcaaagggtttgaata
+
_JTUdFgGiGgb]HMGTFYRhGIZXDKH^Kdl^_\IkaR`b`heEcjEg`JVDG[IWldhfPh]KNSZ^UDhcjGLfGOlNIlQ^MYRX_eWKJSDDcX_lg^J`XG[eE`JSgGH_lNObkk[El`^YDLgLccQVXlEQTcQ\IPj`LJ_aWk_UQ[T]
@read_47
ttagaagtgcatgactgagacttctgttttttacttctggtaatattagactagacaatcaaagtctgctctttaaattaggataactgggaaacctgaactatgtatctatgtgcttgagggaatcatagagctaagaacataatgaatatttatgagaa
+
iHWT`DFZD]dRhY`MfILlKUVKSaVDDjkifIFVO`FeZh`IJdLSdYVEdKUiVcJMLg^iTMZMbPYUjgl`hIghbZkMDi]N_HGeNbJL]UJfKTJONIDOWLXOfRUjPYFg`^VE[UERE\Kb^JbaghXgQGN]OGOLdkI`IJSeVU_NE
@read_48
ttttttcccttaccttttaatatagtaaaatcctaagttgaaacatcttttggctcatttattatttcagccacgcttaatcaaaatatcttattattttagcaaacatctgtattttacttggtaacatttaacttaggattcttatataaatattcata
+
fMWI\IW[iGFgjUDPJPEfcTKeYhik^ai^UkLWhNRKeGjJGfkHVgWkQ^ShTYdd]Lg\EjOIUMVhPFhbHhfVfU`Mdk`S[]TRi\HPMgGabRSVNhEDVdVUJWL\^eGIfNHgMeIXVIZEV`RYeEjIEP\QMd[d`chT_PRk\E^Lj
@read_49
tgttctttttttttaatagaagatgaacctgaaacttaataaataacactaaacatctgataaaagaatatcattgatgtttaatgagctgttctaaagtagccaaatagggaaggaacctcctaagaagaggagctctctttaatcatttccagtattat
+
RQihKSNDJGaUi`TNZEbIVJjML`_W^LJlXTdfgTUY\UlHPQOikXPRPNUT_[P_UEHJOJ]JWMk[J^G[\h]H\USjgHVbUWUjFRHbd`XHl\UgRWfQKfdkNY_eKRYgkaeIVXWJQ]aQeJLkjMdcdb[WNkRL]eiV`gSTFclQb
@read_50
tagtcctggctaattttttttttttttttttttagtagagagggggtgtggctcacacctgtaacaccagcattttgggaggctgaggcaggcagatcacttgagtacaggaggtccagatcagcctgggcagcacggtgaaatcctctctctactaaaaa
+
RNDkc_OW[dEXO_SFQHjWfgHkZ\IGP[NQV^QjTLX]UjcWZV`iTSM^PeFIaQDOXjYPcThFVkNQHLHQSHf_M]UVJPOLL][RYbS\SfH[JWF_dcWgkRPbFGZO[H^ZKg`bcYHGiSUXMRlZ[_MOEdNJdZaci]ROYhDGNIIda
@read_51
ttaagaatttcctgataaatgtcaatttgagaacattaaatatttttatagaaaaacatatgaaactaatttacttaaattgaaaaacaaggaaaaatagaatataactagttagaaaaaagtcactgttttaaatatgatttattataggactttgatag
+
SEb`FgXdPhUWfKiNfRKJGheOFfJ`SKikDfZOWclaVGHhlh\X[GMXDTHdYcXLZYF\VKdT\\NGfe^FOJVPkWQPXbb`GESObhKDiYWNXDUiQO\OXQRkkTQa_NFWUVPUQFkGDPgHWM^`WJZWYZFI`TKVgbGXih`gHIabd
@read_52
gggcattcagttcccactcgatctgttggtggtcacgcctctcaacatctgtcttcaatagcagcagaaagtaatcaccataagatcactatgctttctcagtcggctgtatcaaatatctataattgctctttagttagataaaagttaccgagaacaaa
+
]EeJkMh[NgfK]NH`dMLYMULWNgZOQEh\dhZGF[FadQ\kNh^RiYFRl]S^^dVEQh[WekHFEHLTKcVPHKMlIif^DJQcLLFGRiU[FfkN]GZT_eiaFFTKlSfaOXleShbGNfNQUYafdTPX_dX`FfUegLOMYUf]Z[STikJVc
@read_53
cactccagccagggcaacaagagcgaaactccgtctcaaaaaaaaaaaaaaaagaaaagaaaagaaaaagaaagaaagcaagcatttttgaagccactcactgacttcactgataggatgcacagaataagtcagaaaggcaaagctcccgagtctgcttc
+
\KQl^DjYej]QjPZZEN]\MQLhWY\XEcQVFkkSLh_cOMgIW[WQRaGFNUE_XJYlObIK_HH\XGK[LIPNbc^RcHIKN_\R`]SSM^EkSkPDRVXUTaeXkXUM^hUSMPPRSDgUbV`]PRZjP[cJd^FSHKgbXj`PJkP\HMiFMeaQ]
@read_54
tgtagaccacttggaaatttcatacattgctggtgagaatgccaaatggtatagccacctagaaatcagtttgatagcttcctacaaagttaaatacacttactatatgacccatacattttactcctacatatttcaaatgaaattaaaattcatgtttg
+
WHijPWe`iRSdPG`HFVVTZZ\U\e`HEYFH_LQcaM\jTjLg]]l_NZ^LEjKdMYOhbYl^SQb`RKVaFKOLJjTRbgPLgPZJh^NNhFPf_VbHkRGRJj_GiXkKgeVQl^RelQVSElIfYRYbF[T[OIMN\eK]gljhl]djjTjMVkLic
@read_55
aatcccattactggatatataccccccaaaatatacatttttctatgataaagatacatgcatgtgtatgttcattgcagcactattcacaacagcaaagacgtggaatcagcctaaatgcccatgaatgacagactggataaagaaaatgtggtacatat
+
PLkKZSIKOeQ]k`E[Gke^VSFKWEJ[QIHfNIcUl\ah[VJjGdHFlhXGUM`VWTDiNTfQcbPdch]`YgagIjKcWOYW[RdkcY`GVYbkfldS\P]GikPbMlZ_FVIUfdjka]SZcXdNPhUESebWHeeE]KRfaaiJ]hHShIMhgDNhe
@read_56
ctagtgggaggtgtttgggtcacgaatggcttcgtgccatccttgcggtaatggatgagctcttgctctattagttcacaggagagagctggttgttaaaaagaacctgacacctcctctctctctgtctctctctctgtctcttggtccctcttaccatg
+
FXKG^EPINeSEHhciPTFeaaTilUK\W[M_e\eVQ\cb\]FRNGjgOePILXaf]F\SlY]LSgDV\FGRORYaOSWZaUIZDQIijJYOfLZQ[HSHhiII`KdSWETK^TiDiXK`]HlWXdT]EPKY^k_U_lHjIHHEJ`JHHklLHV_ciEc_U
@read_57
gctataaagacacatgcacatgtatgtttattgtggcactattcccaatagcaaaaccttggaaccaacccaaatggattaagaaaatgtggcacatatacaccatggaatattatgcaaccataaatatgaatgagttcatgtcctttgcagggacaggg
+
]DJZSeXGj`Pe\ijNM\aD`M[UeDX^ZgkPibVk[Qi^Tl\iDNQ]_lTDHI`kcLlUZcdcWIZJaNfFPVXLW]hJWkZHRP^dk`aL_PbSSfKRUPE_DdZaTX]OLhFQLgcHiHTYkXellNhJH]WKfhTa^XZgb\a``PbD^PjNJQQYH
@read_58
ttccttcttcccttcctgctcaccagccggccgccggcagcggctccaggaaggagcaccaacccgcgctgggggcggaggttcaggcggcaggaatggagaggctgatcctcctctagccccggcgcattcacttaggtgcgggagccctgaggttcagc
+
hO^FkJXF_\KdfUQRMDQeaJRJJEYLRDbcOiEJ_WcfcjOQcXDEWbU[I]QPIcYkQiRMXKJMNQNZX^UiaGhU\QKITQUKNIi]KS[cjk_iQE^QQejfL_Q`cl^SXQK\bf^EbMWOg[`kRVVMRPe]LhecJF_fK^_GJPiDL`\]d
@read_59
aggtcatgaggtcttgggattaatggctgcaaaatagccccaagggacttgtttgtttttctaccacgtgaggaaggaggaagacacagggagaactgtgaggtctaaaacctggaagggagccctcacccgaacccgatcgtcctggcactctgatctca
+
j^ZOa[dEHlPPMZbbKkGiZPfTcQNYRl]LYcaDgHdOL^N^k^b_FabHR_ZZffaidKg^e`SiNflNZIcK[\YKe]NYIcPVOKZPgbOiMl\aX_fHcYGOlLiITMJckVgjIPkiLlLXkSi^h[hbNZUd_Ri\bJ`EQ_hGdKe_X\LWG
@read_60
ggatttgtgtggtggttcacagctaagactgcctggattcaaatcccaaatctgccaaggcaattatggggactgagcccccaacctgtgggatctgacactgtctccagataaatagcgtcagaattgagttggaggacacctagctggtgtccactgcg
+
`clZQQhDjiYRX[I\kUh_X[iJcF_WXTkVMFchXiKGaV[kDUJPPOclb[IXgSc[dQ[D]QidagUOi[fi^ERfJFUD_c\XgLSb]kgeIYiiD]cTPeU`e_gcVadDY\g`\]aNX^khYYbSD`Mdh_dhUeS\Fk_aNJeWXJbQdX`QO
@read_61
tagtcctaatgatctttcccacctagttttttacatgtacttggattccccatcttcgcagccaccatttcccaatattcttctgacctgtccattccccaagactctatcctcccagaagaaaggttacattgtagaatgattgctgaggtttatacttg
+
XMKXeYEXGLWKFLE\QkWclM]PTNXGlc^^FfVdbh[fYX`O]hXaHF]I\SJ]DTbk__WgKJ[jdcUlKgPENUcTbFUdL]RX[fEVSD[l]QYii`d^h_PXe]NiKeKFNRMUIYJS^PQUVX\jDYkglSjR^d_\UaFY\`ORYheT\Vba[
@read_62
tggaagagctctcttgggattattttataagagtactagtcccatgcacctcccaatcaccttgaggaggtcccacctcttagtaccatcacctcgaaggtcaggatcccaacataagaattttaagggggcacaaacgttcagaccataacaccaggttc
+
SdOaU[VGWO]^[dVIcMTLYdc`[FkdgUc[Gl]SfEIge]LG]lcVMSDbKHbDjRDH]PdG\YR^ckNTFkPhIZjIbgSHKcHbT]NIIi]XXNMDMT]_YV_cRbdDjLGK[N_\ljWakeKMjJLaeRGjZQdN\[Q`[HFief`_fYZNJL_TS
@read_63
acaggacagaaaaggttctagtactgattattacatgtggtttaggacatttaaaaatgtatgctgacatgctgacagcaaaagtatactcactgtgtacaagaaaacaaaaatctttccacatcagcagcagagtgagttttgtaaagccttctgcatca
+
N[dZQfINaQGKIUXLZDfLRWlQ[GHJeTDdLE[]k^Wjkbc\O^ObKg\TgiPaMRkDfkN\Ucdb^Ufbe`POUI^SZWLU\hQUSKbRae_GMjiLNfc_]bbKf^ilReT_QORi\GlfVjZYfUEIMFdliGcF_baZORJVPcfQdeQiELGLX
@read_64
gccacaccagctttctttcaattcctccaatgttctcccatgctccctccatctgcagaacatcattgtttacttcaaggttcaagtaatatcaatgaaaatacaggcaaggcttctgttctgaatggtgcttacttctagtggagcaggagaagacatac
+
^GdUPieNKQQc_R\IFbgjIGS[ROEDcD^\`SNdbl]hJfPTaSTXEFKiDRFf\Uh]IdGi]`O[^KdGDhRTF_SUhdKJYMcIfSQFGiY_[idVhIbJ]cUc`YS_gk_Q\VJhQXKdbdeSIPXWWbRehWRli_f]agK^d]KeEM\lWhXJH
@read_65
aaattcagggagtaaccacttctgcccgttttcttgccccacattttcacttctgattatattttcctcataggtaggagttagttatccatatttgttcctttttttttttttttttttttgctaagaaaggtttttcttttctttcctttttttttttt
+
Eaa^YiEiMHkN`^TkYKiah[cXcLHEDiYhXZcFRFcWiE]HK[Mjg\ISLUJfeIiEIdEihIDTTNg\``IWJ`IKkNdOW\G[YJh[IX\Dl_LaI^Hgh_Kjefk^UXjY]WcTdRXSPS`cWebE[K_E\UJeJLVRgQMaLlH`ZjFcldKLS
@read_66
aaaagagactgacagagagagagaggaagagagagatacacacattgtactcaaagacagagagacggtacaggatcacatgaataagtctttagagtatgcatattatactctaggccatatggcataacctgagattaaaatggtcctttcaaactaac
+
V\JEG`]j]VlQcWN`LEeKaDRIXaIUhJD_EV[J]YUNJ\WW_McGIRJhhFS^K[Pg\K`jMlc`h]gOdO\Ya^eYETjR\lRMbMiXaPg[WOUKdGQggXSlPUIc\^eSXHdTLDSP[IGUfFRWX[W^ikbDeSkH[gDPMdNML`ZULihNb
@read_67
agataaaactaaaaaattcttgcagcaaaatttcaaaagtgcattatcatagcatcataaatatatgattgatacatatatgattggttggataattggataatagtacaatttcttataatgttcaaaactatacattattttaaactagaaaaggacat
+
SfFRJgPGWDDVdhebDeQOZ]fXe__LhVRFV`]FUSEEa[ihGgQbS_gUFEPLOMMeSERXX_diN`OiZHQkMLMiDiZJO`LO[K^^XhfJjDJ[YhMZ\WdkLceRcTHElI]SGOGhGdZS\_]lHgULVKTXeY]ikUWNcYSUNHXHQIZIb
@read_68
agctcaagcaattcccccagccttgacctcccaaaatgctgggattacaggcatgagccaccgcacccagcccacagctttgttttttgcagtaatcacctccctctcacatggggaaatatgccacaaaatatacctgaaggaggatatttaattctcca
+
KNkQlHDhFe^PibjMhWa\^UMZD^OTLGXKaQePMhgNeHVbMhkhNFYVhZMVTFkZZVNW[`kXLkGSYj[iS`[[NYPQ[bHl[YN[Gad\PNJhFJJ[UQ[fGc^`KMhDLSYYcPPNMKiD]VDUTkcNYZZhH]TdbPe`dN[_PJcFlXcXR
@read_69
tctgcgatgcagtcagactgcgttgatgccagtgttctcttggttcctgcaagactttcttgaggtttcttgtttccgcaagctctgaactgggctctggctttgcctcagaagcacagagctggagcatctgtgggagaaagtggaaatggagcaataat
+
lHcgOGdHEkUSjUVWVLPccOSdegaL]R_LMiYLlGHPVJgdcUihbUchjcIDiXKGP]eX[^iZQhQglO]GHKkUMSUOJc\DhdGYIcl[Y[]jNOdSILJFhkgeeQbKlUSD\YPVebX`cfbLhMKZ\T]U\IkVPOGebe\\MX[lkOUj^
genometools-1.5.1/testdata/readjoiner/contained_eqlen.cnt000066400000000000000000000000171211610345200236330ustar00rootroot00000000000000[n: 6]
1
2
3
4
genometools-1.5.1/testdata/readjoiner/contained_eqlen.fas000066400000000000000000000007751211610345200236330ustar00rootroot00000000000000>0 read
gctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
>1 copy
gctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
>2 another_copy
gctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
>3 yet_another_copy
gctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
>4 revcompl
aatcgctcgatgccatgatcgaatgactctcctctcctcgccgcatcgatcgaaaaaaaaaactgactagc
>5 different
gctagtcagtttttattttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
genometools-1.5.1/testdata/readjoiner/contained_eqlen_ss.cnt000066400000000000000000000000151211610345200243360ustar00rootroot00000000000000[n: 6]
1
2
3
genometools-1.5.1/testdata/readjoiner/contained_varlen.cnt000066400000000000000000000000401211610345200240120ustar00rootroot00000000000000[n: 13]
1
2
3
4
5
6
7
8
9
10
11
genometools-1.5.1/testdata/readjoiner/contained_varlen.fas000066400000000000000000000021461211610345200240100ustar00rootroot00000000000000>0 read
gctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
>1 copy
gctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
>2 another_copy
gctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
>3 yet_another_copy
gctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
>4 prefix
gctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgat
>5 suffix
ctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
>6 internal
ctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgat
>7 copy_of_internal
ctagtcagttttttttttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgat
>8 revcompl
aatcgctcgatgccatgatcgaatgactctcctctcctcgccgcatcgatcgaaaaaaaaaactgactagc
>9 revcompl_of_prefix
atcgctcgatgccatgatcgaatgactctcctctcctcgccgcatcgatcgaaaaaaaaaactgactagc
>10 revcompl_of_suffix
aatcgctcgatgccatgatcgaatgactctcctctcctcgccgcatcgatcgaaaaaaaaaactgactag
>11 revcompl_of_internal
atcgctcgatgccatgatcgaatgactctcctctcctcgccgcatcgatcgaaaaaaaaaactgactag
>12 different
gctagtcagtttttattttcgatcgatgcggcgaggagaggagagtcattcgatcatggcatcgagcgatt
genometools-1.5.1/testdata/readjoiner/contained_varlen_ss.cnt000066400000000000000000000000361211610345200245240ustar00rootroot00000000000000[n: 13]
1
2
3
4
5
6
7
9
10
11
genometools-1.5.1/testdata/readjoiner/errors_1.corrected.fas000066400000000000000000000004061211610345200241770ustar00rootroot00000000000000>0
cgatcgatcgtagctagctggcggcggcgtagct
>1 (encseq pos 62 should be g, is a)
gatcgatcgtagctagctggcggcggcgtagctt
>2
atcgatcgtagctagctggcggcggcgtagcttg
>3
tcgatcgtagctagctggcggcggcgtagcttgc
>4
cgtagctagctggcggcggcgtagcttgccgtgc
>5
cgattggcgggatcggcgtcgtatacggctagca
genometools-1.5.1/testdata/readjoiner/errors_1.fas000066400000000000000000000004061211610345200222260ustar00rootroot00000000000000>0
cgatcgatcgtagctagctggcggcggcgtagct
>1 (encseq pos 62 should be g, is a)
gatcgatcgtagctagctggcggcggcatagctt
>2
atcgatcgtagctagctggcggcggcgtagcttg
>3
tcgatcgtagctagctggcggcggcgtagcttgc
>4
cgtagctagctggcggcggcgtagcttgccgtgc
>5
cgattggcgggatcggcgtcgtatacggctagca
genometools-1.5.1/testdata/readjoiner/large_count.fas000066400000000000000000000063141211610345200230000ustar00rootroot00000000000000>
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genometools-1.5.1/testdata/readjoiner/pw-ex.spm000066400000000000000000000001321211610345200215540ustar00rootroot000000000000001 + 0 + 4
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genometools-1.5.1/testdata/readjoiner/self_spm.fas000066400000000000000000000001061211610345200222770ustar00rootroot00000000000000>0 self-SPM 8 nt
gatgcgatcttacgatgcgat
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genometools-1.5.1/testdata/readjoiner/test_1.fas000066400000000000000000000006401211610345200216710ustar00rootroot00000000000000>0
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>read_39273
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>read_51792
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genometools-1.5.1/testdata/readjoiner/tiny.fas000066400000000000000000000000501211610345200214500ustar00rootroot00000000000000>0
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acagcatgcggcagtg
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genometools-1.5.1/testdata/readjoiner/tiny_mirrored.spm000066400000000000000000000000241211610345200234020ustar00rootroot000000000000000 + 1 + 5
1 + 1 - 4
genometools-1.5.1/testdata/readjoiner/tiny_singlestrand.spm000066400000000000000000000000121211610345200242510ustar00rootroot000000000000000 + 1 + 5
genometools-1.5.1/testdata/readjoiner/trans_and_submax_ovl.fas000066400000000000000000000005071211610345200247040ustar00rootroot00000000000000>read_0
tgataagtcccaggacttcagaagagctgtgagaccttggccaagtcacttcctccgtgggcctaagtgcctcctctcgggacttcagaagagctgtgag
>read_1
ccaggacttcagaagagctgtgagaccttggccaagtcacttcctccgtgggcctaagtgcctcctctcgggacttcagaagagctgtgagggtatgggg
>read_2
gacttcagaagagctgtgagaccttggccaagtcacttcctccgtgggcctaagtgcctcctctcgggacttcagaagagctgtgagggtatggggacgg
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genometools-1.5.1/testdata/readjoiner/transred_1_targetseq.fas000066400000000000000000000000711211610345200246110ustar00rootroot00000000000000catcgatcgatcttcgagcattgctgattaatcgtgattcttgctagcgatgcggt
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genometools-1.5.1/testdata/readjoiner/transred_3.dot000066400000000000000000000017121211610345200225540ustar00rootroot00000000000000graph StringGraph {
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genometools-1.5.1/testdata/readjoiner/transred_3.fas000066400000000000000000000012221211610345200225330ustar00rootroot00000000000000>0
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genometools-1.5.1/testdata/readjoiner/transred_3.r.dot000066400000000000000000000007041211610345200230140ustar00rootroot00000000000000graph StringGraph {
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}
genometools-1.5.1/testdata/readjoiner/transred_3_targetseq.fas000066400000000000000000000002611211610345200246140ustar00rootroot00000000000000>contig_0 length=130 depth=11 0E-->...-->3E
cgatcgatgtgcatggcatggcgctatgctagctgtagtcgtagctagggcgtactgtcg
atttttagcgggcttaggctagcgggcccttattcgatgctagcattgcgacgatcggct
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gctagctagctagctagctaggcggctagctcgtagcgatcgtagcatgtcgatcgtagctagtcgatgctagtcgatgctgt
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gcatgtcgatcgtagctagtcgatgctagtcgatgctgtccccatcgtaccgtagtgctagtcgatcgtagct
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>two_wildcards
acngatcgatcccagcagctagtngatcgatacggctagctgaggcagtcagcggcgcggcatgcatgcgcgagcgttta
>consecutive_wildcards
acnnnncgatcccagcagctagtcgatcgatacggctagctgaggcagtcagcggcgcggcatgcatgcgcgagcgttta
>only_wildcards
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
genometools-1.5.1/testdata/readjoiner/wildcards.fastq000066400000000000000000000026461211610345200230230ustar00rootroot00000000000000@read
gctagctagctagtcgatcgatcgtagctggctacaccgatcgatcccagcagctagtcgatcgatacggctagctgagg
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250=G=BC?;=;*<;>'%G(BA+4.6)-(%I*83<->*B05?/A-3F7024;C<7*:/="IID*'867@*>+0+)6C<<6
@no_wildcards
accgatcgatcccagcagctagtcgatcgatacggctagctgaggcagtcagcggcgcggcatgcatgcgcgagcgttta
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E'::2I/>G+I"@.%D">>@;I42GHF'">34D?2A8#C757(.6H?250&IF00;A&H
@first_char_wildcard
Nccgatcgatcccagcagctagtcgatcgatacggctagctgaggcagtcagcggcgcggcatgcatgcgcgagcgttta
+
!>F$7.8BFH'.$(#=-58=<.3-:3$E@/>E<*?FA@95;@C48?6D.-$5EGI?C(,/:I64)&8(E#21?5#I$E*7
@last_char_wildcard
accgatcgatcccagcagctagtcgatcgatacggctagctgaggcagtcagcggcgcggcatgcatgcgcgagcgtttN
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/=6D;4A&E2&?FB:&H*;-EC64I&>+2-D9:&+E-2H)93*?9:&+1,6I$097-:$H(%5&@9@GAD-0)>22731!
@internal_wildcard
acNgatcgatcccagcagctagtcgatcgatacggctagctgaggcagtcagcggcgcggcatgcatgcgcgagcgttta
+
1>!>2'8>0GA&D.4E??9-.D<-F49/$5%)@-?G$'=3#.549*8&6<@:4>+/I>9="0(""(HE:1+1@(8H66@5
@two_wildcards
acNgatcgatcccagcagctagtNgatcgatacggctagctgaggcagtcagcggcgcggcatgcatgcgcgagcgttta
+
EB!7>;4313A07&"E5=#D@$95G32=C=-4@4;62(F-9G233>-8#;-101
@consecutive_wildcards
acNNNNcgatcccagcagctagtcgatcgatacggctagctgaggcagtcagcggcgcggcatgcatgcgcgagcgttta
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F0!!!!6?,15CH=%/<$&F3(?<2#$D$(IH/2+$:F94>/3;8-,&I"A+.3F55=3%9%DC"2.-0;A/&>706&7&
@only_wildcards
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
genometools-1.5.1/testdata/readjoiner/with_rc.fas000066400000000000000000000000721211610345200221300ustar00rootroot00000000000000>dummy
cgagtctagtcatgctagcgttt
>1
acctagctagctgatattcgaat
genometools-1.5.1/testdata/regionmapping_1.lua000066400000000000000000000000421211610345200214330ustar00rootroot00000000000000mapping = "wrong type of mapping"
genometools-1.5.1/testdata/regionmapping_2.lua000066400000000000000000000000541211610345200214370ustar00rootroot00000000000000mapping = { bar = "wrong type of mapping" }
genometools-1.5.1/testdata/regionmapping_3.lua000066400000000000000000000000441211610345200214370ustar00rootroot00000000000000mapping = { foo = { bar = "baz" } }
genometools-1.5.1/testdata/regionmapping_4.lua000066400000000000000000000001141211610345200214360ustar00rootroot00000000000000mapping = { foo = os.getenv("GT_TESTDATA") .. "gt_extractfeat_succ_1.fas" }
genometools-1.5.1/testdata/regionmapping_5.lua000066400000000000000000000000441211610345200214410ustar00rootroot00000000000000function mapping()
  return nil
end
genometools-1.5.1/testdata/regionmapping_6.lua000066400000000000000000000001361211610345200214440ustar00rootroot00000000000000function mapping(string)
  return os.getenv("GT_TESTDATA") .. "gt_extractfeat_succ_1.fas"
end
genometools-1.5.1/testdata/repfind-20-extend.txt000066400000000000000000005076151211610345200215670ustar00rootroot00000000000000263 1646 2 F 263 1862 3 486 10 96.20
174 497 268 F 173 1549 163 295 10 94.22
174 1544 186 F 173 1549 163 287 12 93.06
86 1549 163 F 87 1551 171 125 9 89.53
192 1 378 F 187 2 0 343 9 95.19
276 1 294 F 271 16 0 515 8 97.05
334 5 0 F 334 39 34 632 9 97.31
213 7 0 F 213 39 34 406 5 97.65
610 3 0 F 607 39 72 1145 18 97.03
168 719 268 F 168 1199 159 320 4 97.62
221 59 231 F 224 651 48 309 34 84.62
403 1764 7 F 417 1896 0 660 40 90.07
433 1745 0 F 427 1764 1 748 28 93.44
427 1764 1 F 432 1767 0 775 21 95.08
404 1764 10 F 403 1882 0 755 13 96.77
296 960 29 F 303 970 135 543 14 95.27
123 470 352 F 126 991 113 233 4 96.75
53 186 88 F 52 186 121 65 10 80.77
80 35 204 F 80 73 144 152 2 97.50
80 72 215 F 80 73 144 152 2 97.50
22 1932 125 F 22 1932 230 44 0 100.00
274 1039 0 F 274 1435 147 524 6 97.81
384 738 115 F 391 1384 0 671 26 93.23
377 739 2 F 383 1384 8 592 42 88.86
391 470 80 F 395 1013 0 690 24 93.86
119 991 114 F 117 1013 277 224 3 97.44
382 1121 56 F 384 1512 11 674 23 93.98
103 24 164 F 103 43 1 206 0 100.00
399 1882 0 F 414 1896 3 669 36 90.98
405 1745 6 F 413 1896 0 662 39 90.37
405 1767 6 F 413 1896 0 674 36 91.11
449 1745 9 F 440 1882 0 773 27 93.86
446 1767 9 F 440 1882 0 806 20 95.45
191 1734 134 F 194 1814 141 269 29 84.82
163 1578 0 F 163 1682 12 290 9 94.48
423 449 0 F 421 868 143 788 14 96.67
383 318 13 F 387 905 59 678 23 93.99
495 79 129 F 498 1495 70 917 19 96.16
323 915 121 F 325 1070 53 600 12 96.28
278 1288 43 F 275 1374 150 477 19 93.09
378 242 0 F 379 294 0 729 7 98.15
602 5 96 F 601 16 214 1099 26 95.67
228 1132 161 F 230 1140 69 434 6 97.37
455 3 155 F 453 6 156 844 16 96.47
610 3 0 F 607 39 72 1145 18 97.03
411 1696 0 F 412 1781 23 691 33 91.97
432 798 1 F 428 1120 16 716 36 91.59
453 474 87 F 444 1120 0 765 33 92.57
376 543 104 F 376 1120 68 696 14 96.28
444 658 158 F 444 1120 0 752 34 92.34
416 713 24 F 420 1120 24 744 23 94.47
444 1120 0 F 439 1297 36 735 37 91.57
445 912 38 F 439 1120 0 760 31 92.94
395 1120 24 F 396 1327 40 659 33 91.65
353 985 0 F 353 1426 64 654 13 96.32
391 470 80 F 395 1013 0 690 24 93.86
348 1064 63 F 351 1669 2 603 24 93.10
376 634 4 F 377 976 13 689 16 95.74
268 248 0 F 269 292 0 477 15 94.40
404 549 32 F 412 661 104 712 26 93.56
384 738 115 F 391 1384 0 671 26 93.23
267 227 189 F 267 968 0 342 48 82.02
270 313 34 F 265 1782 2 451 21 92.08
223 313 78 F 220 1827 5 383 15 93.18
455 3 155 F 453 6 156 844 16 96.47
610 3 0 F 607 39 72 1145 18 97.03
641 6 156 F 647 39 227 1216 18 97.19
238 2 130 F 238 3 58 408 17 92.86
238 3 58 F 238 16 214 404 18 92.44
141 2 227 F 141 6 156 254 7 95.04
141 6 156 F 141 16 311 250 8 94.33
290 902 26 F 289 988 50 483 24 91.70
289 988 50 F 290 1151 59 491 22 92.39
288 451 41 F 285 988 54 485 22 92.28
337 736 68 F 339 988 0 540 34 89.91
288 846 223 F 290 988 49 490 22 92.36
286 380 10 F 289 988 50 479 24 91.61
290 988 49 F 292 1230 114 478 26 91.03
451 658 126 F 462 826 19 829 21 95.34
237 994 160 F 242 1190 41 423 14 94.09
151 473 90 F 156 1190 41 243 16 89.40
151 766 127 F 156 1190 41 247 15 90.07
319 131 0 F 319 158 0 630 2 99.37
309 1681 0 F 308 1808 0 541 19 93.83
350 867 233 F 355 1602 0 633 18 94.86
326 676 49 F 324 1165 1 538 28 91.36
194 216 0 F 194 277 0 380 2 98.97
391 1787 9 F 389 1810 2 680 25 93.57
299 1871 0 F 296 1892 0 515 20 93.24
278 1288 43 F 275 1374 150 477 19 93.09
404 549 32 F 412 661 104 712 26 93.56
268 248 0 F 269 292 0 477 15 94.40
270 313 34 F 265 1782 2 451 21 92.08
223 313 78 F 220 1827 5 383 15 93.18
174 1564 0 F 174 1847 123 312 9 94.83
309 1649 13 F 309 1931 0 546 18 94.17
309 1708 8 F 305 1931 0 490 30 90.16
20 249 209 F 20 817 234 40 0 100.00
369 724 42 F 407 1826 28 520 62 83.20
369 1475 72 F 376 1594 0 577 42 88.62
224 1196 0 F 222 1456 43 354 23 89.64
359 11 153 F 356 29 155 639 19 94.66
93 1668 56 F 93 1668 101 154 8 91.40
35 1668 56 F 35 1668 146 62 2 94.29
228 473 13 F 226 994 85 382 18 92.04
446 1620 20 F 439 1937 0 721 41 90.66
456 1796 26 F 446 1937 0 718 46 89.69
93 1668 56 F 93 1668 101 154 8 91.40
389 848 138 F 404 1658 0 637 39 89.97
367 881 0 F 364 1248 100 699 8 97.80
300 1910 0 F 299 1926 25 543 14 95.32
188 579 3 F 192 1456 73 300 20 89.36
208 1138 64 F 200 1215 247 280 32 84.00
324 641 0 F 325 1365 50 581 17 94.75
325 630 91 F 324 641 0 569 20 93.83
324 380 79 F 324 641 0 600 12 96.30
324 641 0 F 324 846 294 596 13 95.99
324 641 0 F 324 902 99 604 11 96.60
324 641 0 F 324 1151 132 604 11 96.60
324 641 0 F 327 1230 186 599 13 95.99
322 451 112 F 322 641 0 600 11 96.58
322 641 0 F 322 736 188 600 11 96.58
324 641 0 F 324 1100 119 584 16 95.06
289 481 15 F 282 641 42 503 17 93.97
320 641 0 F 320 1360 95 556 21 93.44
306 483 74 F 304 641 0 558 13 95.72
213 474 180 F 212 641 0 361 16 92.45
212 543 121 F 212 641 0 360 16 92.45
212 641 0 F 210 658 245 354 17 91.90
212 641 0 F 211 713 82 343 20 90.52
212 641 0 F 210 1297 118 346 19 90.95
212 641 0 F 213 912 128 365 15 92.92
212 641 0 F 212 1327 102 344 20 90.57
212 641 0 F 213 761 4 357 17 91.98
212 641 0 F 212 826 147 360 16 92.45
212 641 0 F 213 798 73 353 18 91.51
326 605 57 F 324 641 0 574 19 94.14
324 641 0 F 326 1143 83 582 17 94.75
349 483 31 F 345 902 58 670 6 98.26
349 483 31 F 345 1151 91 670 6 98.26
375 451 41 F 380 483 0 695 15 96.00
349 483 31 F 345 736 147 670 6 98.26
261 483 31 F 258 1049 91 455 16 93.80
256 483 31 F 253 543 80 437 18 92.89
215 483 72 F 215 761 2 390 10 95.35
256 483 31 F 253 826 106 449 15 94.07
349 483 31 F 345 846 253 662 8 97.68
234 483 53 F 231 1327 83 393 18 92.21
344 380 39 F 349 483 31 661 8 97.67
292 483 0 F 285 988 54 469 27 90.53
234 483 53 F 229 1297 99 399 16 93.01
218 483 74 F 221 506 0 355 21 90.37
221 506 0 F 218 630 91 331 27 87.61
217 380 79 F 221 506 0 354 21 90.32
221 506 0 F 217 902 99 358 20 90.78
221 506 0 F 217 1151 132 358 20 90.78
221 506 0 F 220 1230 186 357 21 90.45
217 451 112 F 221 506 0 358 20 90.78
221 506 0 F 217 736 188 358 20 90.78
221 506 0 F 217 1100 119 346 23 89.40
221 506 0 F 219 1143 83 344 24 89.04
342 506 0 F 337 1049 133 635 11 96.74
162 506 0 F 158 1189 14 256 16 89.87
221 506 0 F 219 605 57 336 26 88.13
308 506 0 F 303 988 123 547 16 94.72
221 506 0 F 217 641 0 330 27 87.56
284 474 180 F 289 506 0 441 33 88.38
289 506 0 F 283 543 121 436 34 87.99
273 506 16 F 268 1297 131 413 32 88.06
289 506 0 F 284 912 128 437 34 88.03
279 506 0 F 275 761 4 434 30 89.09
279 506 0 F 274 826 147 433 30 89.05
289 506 0 F 284 798 73 425 37 86.97
289 506 0 F 281 658 245 430 35 87.54
253 506 36 F 251 713 113 392 28 88.84
288 506 0 F 281 1120 87 413 39 86.12
221 506 0 F 217 846 294 350 22 89.86
221 506 0 F 218 1365 50 351 22 89.91
159 35 0 F 159 54 46 298 5 96.86
159 42 0 F 159 54 46 298 5 96.86
350 867 233 F 355 1602 0 633 18 94.86
228 18 192 F 228 40 156 368 22 90.35
251 18 169 F 250 747 47 377 31 87.60
409 1097 23 F 417 1806 1 686 35 91.44
284 386 212 F 293 1201 56 501 19 93.31
203 579 15 F 205 1076 32 312 24 88.18
211 579 7 F 210 1120 87 333 22 89.52
268 579 4 F 276 1196 30 444 25 90.67
220 474 173 F 218 579 0 326 28 87.16
219 543 114 F 218 579 0 329 27 87.61
218 579 0 F 217 658 238 319 29 86.64
211 579 7 F 211 713 82 326 24 88.63
211 579 7 F 210 1297 118 317 26 87.62
218 579 0 F 220 912 121 330 27 87.61
218 579 0 F 219 1327 95 317 30 86.24
211 579 7 F 213 761 4 324 25 88.15
218 579 0 F 219 826 140 329 27 87.61
218 579 0 F 220 798 66 318 30 86.24
313 483 67 F 310 579 0 539 21 93.23
347 579 1 F 350 1365 43 605 23 93.37
348 579 0 F 350 630 84 598 25 92.82
331 380 72 F 330 579 0 581 20 93.94
330 579 0 F 331 846 287 577 21 93.64
330 579 0 F 331 902 92 585 19 94.24
330 579 0 F 331 1151 125 585 19 94.24
330 579 0 F 334 1230 179 588 19 94.24
329 451 105 F 328 579 0 581 19 94.21
328 579 0 F 329 736 181 581 19 94.21
330 579 0 F 331 1100 112 581 20 93.94
348 579 0 F 352 1143 75 608 23 93.39
258 579 37 F 257 642 0 427 22 91.44
208 579 0 F 206 849 54 282 33 83.98
214 506 7 F 211 579 12 297 32 84.83
223 579 0 F 223 1049 126 334 28 87.44
219 579 4 F 221 1328 70 308 33 84.93
192 579 26 F 202 935 48 246 37 80.73
188 579 3 F 192 1456 73 300 20 89.36
304 481 0 F 296 579 34 520 20 93.24
164 579 0 F 166 1189 6 242 22 86.59
248 1868 37 F 248 1948 21 400 24 90.32
343 568 69 F 345 1793 63 652 9 97.38
375 37 0 F 383 1823 0 670 22 94.13
370 483 10 F 363 605 0 637 24 93.39
383 605 0 F 384 902 39 695 18 95.30
383 605 0 F 383 1151 73 702 16 95.82
383 605 0 F 385 1230 128 688 20 94.78
383 451 51 F 381 605 0 692 18 95.28
381 605 0 F 380 736 130 697 16 95.79
383 605 0 F 386 1100 57 649 29 92.43
383 605 0 F 387 1143 22 650 30 92.17
276 605 0 F 275 1049 74 443 27 90.18
107 605 109 F 107 1189 65 202 3 97.20
306 483 74 F 304 641 0 558 13 95.72
324 641 0 F 324 902 99 604 11 96.60
324 641 0 F 324 1151 132 604 11 96.60
324 641 0 F 327 1230 186 599 13 95.99
322 451 112 F 322 641 0 600 11 96.58
322 641 0 F 322 736 188 600 11 96.58
324 641 0 F 324 1100 119 584 16 95.06
324 641 0 F 326 1143 83 582 17 94.75
217 641 0 F 216 1049 133 365 17 92.13
157 641 0 F 158 1189 14 271 11 92.99
326 605 57 F 324 641 0 574 19 94.14
213 474 180 F 212 641 0 361 16 92.45
212 543 121 F 212 641 0 360 16 92.45
212 641 0 F 210 1297 118 346 19 90.95
212 641 0 F 213 912 128 365 15 92.92
212 641 0 F 213 761 4 357 17 91.98
212 641 0 F 212 826 147 360 16 92.45
212 641 0 F 213 798 73 353 18 91.51
272 474 121 F 271 605 0 443 25 90.77
270 543 63 F 271 605 0 421 30 88.89
162 605 109 F 162 1297 166 284 10 93.83
271 605 0 F 270 912 71 437 26 90.37
216 605 55 F 215 761 2 363 17 92.09
271 605 0 F 270 826 89 437 26 90.37
271 605 0 F 270 798 16 401 35 87.04
212 641 0 F 210 658 245 354 17 91.90
271 605 0 F 267 658 188 438 25 90.64
212 641 0 F 211 713 82 343 20 90.52
271 605 0 F 263 713 30 386 37 85.93
212 641 0 F 210 1120 87 338 21 90.00
267 605 4 F 263 1120 34 386 36 86.31
324 641 0 F 324 846 294 596 13 95.99
383 605 0 F 382 846 236 693 18 95.29
324 641 0 F 325 1365 50 581 17 94.75
370 605 13 F 373 1365 2 639 26 92.97
164 641 38 F 165 849 95 261 17 89.63
167 605 94 F 165 849 95 268 16 90.30
185 641 0 F 188 1456 77 293 20 89.19
240 605 4 F 243 1456 22 339 36 85.00
39 99 0 F 39 461 4 74 1 97.44
39 99 0 F 39 1850 264 74 1 97.44
39 99 0 F 38 950 65 65 3 92.11
35 540 250 F 35 540 274 50 5 85.71
47 375 297 F 47 375 343 86 2 95.74
245 885 68 F 247 1021 3 440 13 94.69
250 1021 0 F 250 1051 242 468 8 96.80
299 1548 0 F 300 1554 49 591 2 99.33
287 1170 0 F 283 1347 84 466 26 90.81
389 848 138 F 404 1658 0 637 39 89.97
309 1681 0 F 308 1808 0 541 19 93.83
115 1649 38 F 115 1871 4 154 19 83.48
339 1649 38 F 335 1892 4 478 49 85.37
115 1708 33 F 115 1871 4 154 19 83.48
230 1708 33 F 230 1892 4 332 32 86.09
115 1736 18 F 115 1871 4 146 21 81.74
204 1736 18 F 205 1892 4 269 35 82.84
310 654 103 F 306 807 164 580 9 97.06
461 654 0 F 461 1212 120 758 41 91.11
257 902 54 F 252 1297 76 429 20 92.06
305 1151 39 F 295 1297 33 456 36 87.80
246 451 78 F 241 1297 87 415 18 92.53
304 736 96 F 295 1297 33 459 35 88.14
402 1049 15 F 383 1297 16 553 58 84.86
480 543 0 F 468 1297 7 824 31 93.38
341 761 0 F 338 1297 114 651 7 97.93
414 826 67 F 407 1297 43 733 22 94.59
284 846 222 F 277 1297 51 445 29 89.53
282 380 9 F 277 1297 51 455 26 90.61
304 988 70 F 299 1297 69 467 34 88.63
252 1297 76 F 261 1365 2 413 25 90.08
259 1297 69 F 265 1360 42 400 31 88.03
83 779 294 F 84 783 289 119 12 85.54
83 849 0 F 90 1892 297 93 19 77.11
93 849 0 F 94 912 68 131 14 84.95
352 422 168 F 367 1126 0 611 27 92.33
386 376 0 F 401 1694 81 607 45 88.34
330 1277 1 F 326 1694 81 580 19 94.17
254 1402 3 F 257 1694 225 359 38 85.04
53 1230 71 F 56 1871 243 69 10 81.13
409 1097 23 F 417 1806 1 686 35 91.44
424 454 70 F 432 1837 0 772 21 95.05
352 422 168 F 367 1126 0 611 27 92.33
184 175 74 F 183 1821 0 303 16 91.26
360 544 0 F 358 1343 70 658 15 95.81
367 530 53 F 365 1343 63 688 11 96.99
360 1664 0 F 362 1892 3 622 25 93.06
228 1132 161 F 230 1140 69 434 6 97.37
348 1064 63 F 351 1669 2 603 24 93.10
420 61 134 F 424 65 137 752 22 94.76
381 61 134 F 380 64 137 701 15 96.05
503 2 130 F 522 5 96 845 45 91.05
602 5 96 F 601 16 214 1099 26 95.67
296 3 0 F 296 5 38 572 5 98.31
141 5 193 F 141 6 156 254 7 95.04
334 5 0 F 334 39 34 632 9 97.31
293 22 368 F 282 29 0 471 26 90.78
178 474 215 F 177 642 3 279 18 89.83
181 543 152 F 180 642 0 281 19 89.44
180 642 0 F 180 658 275 276 20 88.89
177 642 3 F 178 713 115 275 19 89.27
180 642 0 F 180 1297 148 276 20 88.89
180 642 0 F 181 912 160 281 19 89.44
180 642 0 F 181 1327 133 273 21 88.33
180 642 0 F 181 761 36 281 19 89.44
180 642 0 F 181 826 178 281 19 89.44
180 642 0 F 182 798 104 278 20 88.89
259 483 106 F 257 642 0 460 14 94.55
254 642 0 F 256 1365 81 462 12 95.28
258 630 123 F 257 642 0 455 15 94.16
258 380 110 F 257 642 0 463 13 94.94
257 642 0 F 258 846 325 455 15 94.16
257 642 0 F 258 902 130 463 13 94.94
257 642 0 F 258 1151 163 463 13 94.94
257 642 0 F 258 1230 220 463 13 94.94
258 451 143 F 257 642 0 463 13 94.94
257 642 0 F 258 736 219 463 13 94.94
257 642 0 F 258 1100 150 459 14 94.55
257 642 0 F 258 1143 116 455 15 94.16
228 642 6 F 231 1196 75 395 16 92.98
187 506 34 F 185 642 0 276 24 87.03
185 642 0 F 185 1049 164 290 20 89.19
185 642 0 F 185 1328 106 282 22 88.11
161 642 0 F 171 935 60 228 26 83.85
177 642 3 F 178 1076 59 255 24 86.44
180 642 0 F 180 1120 117 272 21 88.33
153 642 0 F 155 1456 110 240 17 88.89
258 481 11 F 251 642 6 429 20 92.03
125 642 0 F 126 1189 46 203 12 90.40
195 610 53 F 196 642 61 359 8 95.90
256 641 33 F 257 642 0 441 18 92.97
206 642 51 F 206 1289 3 376 9 95.63
257 642 0 F 258 1360 126 451 16 93.77
239 605 109 F 239 642 18 430 12 94.98
309 244 0 F 309 272 0 590 7 97.73
274 1039 0 F 274 1435 147 524 6 97.81
349 935 48 F 340 1076 44 569 30 91.18
322 849 95 F 323 1076 61 577 17 94.72
329 761 12 F 330 1076 31 599 15 95.44
326 826 155 F 328 1076 31 590 16 95.09
330 1939 0 F 330 1940 10 568 23 93.03
238 2 130 F 238 39 130 412 16 93.28
238 16 214 F 238 39 130 408 17 92.86
503 2 130 F 522 5 96 845 45 91.05
602 5 96 F 601 16 214 1099 26 95.67
238 2 130 F 238 3 58 408 17 92.86
238 3 58 F 238 16 214 404 18 92.44
39 1206 299 F 37 1304 281 56 5 86.49
168 65 149 F 168 65 191 324 3 98.21
168 64 191 F 168 65 149 324 3 98.21
168 61 188 F 168 65 149 324 3 98.21
168 64 149 F 168 65 191 324 3 98.21
168 64 149 F 168 64 191 324 3 98.21
168 61 188 F 168 64 149 324 3 98.21
164 61 150 F 165 65 194 309 5 96.95
164 61 150 F 165 64 194 309 5 96.95
164 61 150 F 165 61 191 309 5 96.95
126 65 149 F 126 65 233 240 3 97.62
126 64 233 F 126 65 149 240 3 97.62
126 61 230 F 126 65 149 240 3 97.62
126 64 149 F 126 65 233 240 3 97.62
126 64 149 F 126 64 233 240 3 97.62
126 61 230 F 126 64 149 240 3 97.62
122 61 150 F 123 65 236 225 5 95.90
122 61 150 F 123 64 236 225 5 95.90
122 61 150 F 123 61 233 225 5 95.90
46 65 149 F 48 65 317 82 3 93.48
46 64 149 F 48 65 317 82 3 93.48
42 61 150 F 45 65 320 67 5 88.10
88 65 149 F 90 65 275 158 5 94.32
88 64 149 F 90 65 275 158 5 94.32
84 61 150 F 87 65 278 143 7 91.67
48 64 317 F 46 65 149 82 3 93.48
46 64 149 F 48 64 317 82 3 93.48
42 61 150 F 45 64 320 67 5 88.10
90 64 275 F 88 65 149 158 5 94.32
88 64 149 F 90 64 275 158 5 94.32
84 61 150 F 87 64 278 143 7 91.67
42 61 314 F 42 65 149 80 1 97.62
42 61 314 F 42 64 149 80 1 97.62
38 61 150 F 39 61 317 65 3 92.11
84 61 272 F 84 65 149 156 3 96.43
84 61 272 F 84 64 149 156 3 96.43
80 61 150 F 81 61 275 141 5 93.75
351 474 189 F 360 935 37 607 26 92.59
350 543 130 F 360 935 37 606 26 92.57
360 935 37 F 348 1297 127 600 27 92.24
346 912 137 F 355 935 37 597 26 92.49
324 935 48 F 314 1327 122 534 26 91.72
336 761 5 F 346 935 28 562 30 91.07
333 826 148 F 344 935 28 561 29 91.29
350 798 83 F 359 935 38 589 30 91.43
321 1941 0 F 323 1942 31 524 30 90.65
415 1663 0 F 414 1893 27 657 43 89.61
339 1802 3 F 340 1877 0 667 3 99.12
391 1787 9 F 389 1810 2 680 25 93.57
389 848 138 F 404 1658 0 637 39 89.97
321 1941 0 F 323 1942 31 524 30 90.65
363 477 0 F 360 1052 64 659 16 95.56
400 542 30 F 413 1056 0 713 25 93.75
348 406 94 F 355 1056 58 615 22 93.68
295 376 132 F 295 1402 3 534 14 95.25
184 1277 151 F 184 1402 3 312 14 92.39
254 1402 3 F 257 1694 225 359 38 85.04
253 461 0 F 259 1850 260 472 10 96.05
365 422 1 F 375 1794 64 576 41 88.77
39 99 0 F 38 1041 55 65 3 92.11
153 461 0 F 151 1041 51 184 30 80.13
151 1041 51 F 153 1850 260 180 31 79.47
365 950 12 F 366 1041 0 639 23 93.70
253 461 0 F 259 1850 260 472 10 96.05
299 808 0 F 305 968 26 308 74 75.25
403 1627 8 F 408 1747 0 735 19 95.29
112 1282 208 F 112 1349 201 160 16 85.71
112 306 77 F 112 1282 208 152 18 83.93
434 426 27 F 429 795 0 675 47 89.04
250 579 80 F 252 1198 76 434 17 93.20
316 630 100 F 326 1198 2 538 26 91.77
315 380 88 F 326 1198 2 545 24 92.38
315 605 68 F 323 1198 5 522 29 90.79
315 846 303 F 326 1198 2 541 25 92.06
315 902 108 F 326 1198 2 549 23 92.70
315 1151 141 F 326 1198 2 549 23 92.70
326 1198 2 F 317 1230 196 551 23 92.74
313 451 121 F 324 1198 2 545 23 92.65
313 736 197 F 324 1198 2 545 23 92.65
316 1143 93 F 326 1198 2 538 26 91.77
315 1100 128 F 326 1198 2 537 26 91.75
242 1198 84 F 239 1289 3 413 17 92.89
294 481 10 F 293 1198 35 499 22 92.49
297 483 83 F 306 1198 2 515 22 92.59
54 1196 311 F 54 1198 274 92 4 92.59
168 610 115 F 171 1198 157 307 8 95.24
282 641 42 F 288 1198 40 490 20 92.91
641 6 156 F 647 39 227 1216 18 97.19
610 3 0 F 607 39 72 1145 18 97.03
200 3 299 F 199 5 337 343 14 92.96
200 3 299 F 199 16 455 335 16 91.96
153 2 371 F 156 3 299 253 14 90.85
309 5 337 F 310 6 300 503 29 90.61
310 6 300 F 309 16 455 495 31 89.97
197 2 371 F 202 6 300 295 26 86.80
334 5 0 F 334 39 34 632 9 97.31
238 16 214 F 238 39 130 408 17 92.86
238 2 130 F 238 39 130 412 16 93.28
365 950 12 F 366 1041 0 639 23 93.70
169 1125 193 F 172 1507 250 313 7 95.86
416 1620 0 F 415 1796 6 743 22 94.70
169 1125 193 F 172 1507 250 313 7 95.86
311 1403 0 F 311 1403 0 582 6 98.07
32 1403 187 F 31 1403 191 55 2 93.55
223 1649 20 F 222 1736 0 409 9 95.95
223 1708 15 F 222 1736 0 401 11 95.05
380 78 86 F 375 80 149 635 30 92.00
277 1649 5 F 278 1708 0 511 11 96.03
145 736 139 F 145 1837 0 246 11 92.41
145 846 245 F 145 1837 0 242 12 91.72
142 658 197 F 144 1837 0 242 11 92.25
293 22 368 F 282 29 0 471 26 90.78
200 204 13 F 200 273 0 400 0 100.00
221 59 231 F 224 651 48 309 34 84.62
263 1646 2 F 263 1862 3 486 10 96.20
248 1868 37 F 248 1948 21 400 24 90.32
78 476 76 F 77 850 181 115 10 87.01
297 483 83 F 306 1198 2 515 22 92.59
326 1198 2 F 316 1365 59 542 25 92.09
316 630 100 F 326 1198 2 538 26 91.77
315 380 88 F 326 1198 2 545 24 92.38
315 846 303 F 326 1198 2 541 25 92.06
315 902 108 F 326 1198 2 549 23 92.70
315 1151 141 F 326 1198 2 549 23 92.70
326 1198 2 F 317 1230 196 551 23 92.74
313 451 121 F 324 1198 2 545 23 92.65
313 736 197 F 324 1198 2 545 23 92.65
315 1100 128 F 326 1198 2 537 26 91.75
294 481 10 F 293 1198 35 499 22 92.49
322 1198 2 F 311 1360 104 513 30 90.35
282 641 42 F 288 1198 40 490 20 92.91
256 483 31 F 250 658 205 442 16 93.60
299 658 156 F 308 902 3 507 25 91.64
334 658 121 F 344 1151 0 558 30 91.02
275 451 49 F 269 658 186 484 15 94.42
375 658 80 F 382 736 18 613 36 90.40
395 658 131 F 405 1049 12 636 41 89.62
477 543 3 F 476 658 126 869 21 95.59
338 658 241 F 341 761 0 659 5 98.52
451 658 126 F 462 826 19 829 21 95.34
402 658 53 F 421 846 85 647 44 89.05
364 658 213 F 365 1327 71 677 13 96.43
290 380 1 F 289 658 166 495 21 92.73
318 658 177 F 324 988 50 534 27 91.51
426 658 176 F 424 1297 51 774 19 95.52
309 244 0 F 309 272 0 590 7 97.73
391 825 86 F 390 1874 2 705 19 95.13
392 432 23 F 392 1874 0 716 17 95.66
336 652 71 F 336 1874 56 600 18 94.64
376 492 0 F 377 1874 14 697 14 96.28
372 862 0 F 385 1874 2 613 36 90.32
377 1469 77 F 372 1874 0 661 22 94.09
333 742 0 F 334 1874 34 567 25 92.49
237 994 160 F 242 1190 41 423 14 94.09
151 473 90 F 156 1190 41 243 16 89.40
151 766 127 F 156 1190 41 247 15 90.07
379 379 0 F 398 1785 85 581 48 87.34
255 1382 47 F 266 1933 214 393 32 87.45
248 1868 37 F 248 1948 21 400 24 90.32
347 474 46 F 344 1151 0 603 22 93.60
369 1475 72 F 376 1594 0 577 42 88.62
95 1260 272 F 98 1615 135 165 7 92.63
389 848 138 F 404 1658 0 637 39 89.97
223 247 130 F 226 880 2 361 22 90.13
291 1294 30 F 299 1786 23 498 23 92.10
327 825 146 F 320 862 53 587 15 95.31
373 492 0 F 361 862 12 638 24 93.35
337 862 22 F 349 1469 105 590 24 92.88
372 862 0 F 385 1874 2 613 36 90.32
375 37 0 F 383 1823 0 670 22 94.13
284 386 212 F 293 1201 56 501 19 93.31
307 624 179 F 327 1619 0 470 41 86.64
391 1787 9 F 389 1810 2 680 25 93.57
341 319 2 F 336 626 202 581 24 92.86
309 1548 7 F 314 1552 0 559 16 94.82
297 1552 0 F 293 1554 56 526 16 94.54
299 1548 0 F 300 1554 49 591 2 99.33
280 871 111 F 279 1401 50 475 21 92.47
282 647 2 F 279 1388 62 493 17 93.91
351 474 189 F 360 935 37 607 26 92.59
350 543 130 F 360 935 37 606 26 92.57
348 658 254 F 360 935 37 596 28 91.95
327 713 113 F 335 935 62 574 22 93.27
323 474 217 F 322 849 95 605 10 96.89
323 543 157 F 322 849 95 605 10 96.89
322 658 280 F 322 849 95 600 11 96.58
323 713 117 F 322 849 95 605 10 96.89
352 474 188 F 353 1076 31 633 18 94.89
351 543 129 F 353 1076 31 636 17 95.16
349 658 253 F 353 1076 31 626 19 94.56
350 713 90 F 353 1076 31 631 18 94.86
360 935 37 F 348 1297 127 600 27 92.24
322 849 95 F 322 1297 153 596 12 96.27
344 1076 40 F 342 1297 133 622 16 95.32
346 912 137 F 355 935 37 597 26 92.49
317 849 95 F 318 912 165 595 10 96.85
347 912 136 F 348 1076 31 631 16 95.39
350 798 83 F 359 935 38 589 30 91.43
324 798 109 F 322 849 95 594 13 95.96
349 798 84 F 349 1076 35 618 20 94.27
341 761 0 F 341 798 69 654 7 97.95
341 474 176 F 341 761 0 666 4 98.83
340 543 117 F 341 761 0 665 4 98.82
338 658 241 F 341 761 0 659 5 98.52
338 713 79 F 340 761 1 650 7 97.93
321 761 20 F 320 1297 132 629 3 99.06
341 761 0 F 341 912 124 666 4 98.83
408 798 0 F 407 826 74 735 20 95.09
480 474 35 F 479 826 2 899 15 96.87
455 543 0 F 466 826 15 829 23 94.95
451 658 126 F 462 826 19 829 21 95.34
405 713 10 F 413 826 68 690 32 92.10
414 826 67 F 407 1297 43 733 22 94.59
467 826 14 F 463 912 0 854 19 95.90
340 935 57 F 330 1120 114 566 26 92.12
322 849 95 F 322 1120 122 588 14 95.65
352 1076 32 F 348 1120 96 624 19 94.54
339 761 0 F 336 1120 83 631 11 96.73
426 826 55 F 419 1120 0 709 34 91.89
324 935 48 F 314 1327 122 534 26 91.72
297 849 95 F 298 1327 138 547 12 95.96
328 1076 31 F 326 1327 110 578 19 94.17
338 761 1 F 337 1327 99 643 8 97.63
367 826 114 F 365 1327 71 676 14 96.16
317 1381 25 F 332 1661 121 421 56 82.33
396 584 79 F 407 1661 35 627 43 89.14
348 1064 63 F 351 1669 2 603 24 93.10
449 1745 9 F 440 1882 0 773 27 93.86
458 1745 0 F 455 1767 0 801 28 93.85
433 1745 0 F 427 1764 1 748 28 93.44
384 738 115 F 391 1384 0 671 26 93.23
377 739 2 F 383 1384 8 592 42 88.86
289 1514 0 F 293 1627 121 494 22 92.39
313 560 59 F 311 1069 28 572 13 95.82
540 4 16 F 523 47 0 935 32 93.88
323 915 121 F 325 1070 53 600 12 96.28
399 815 46 F 415 1699 47 678 33 91.73
328 539 94 F 328 1080 0 584 18 94.51
21 859 210 F 21 1524 237 42 0 100.00
215 1214 205 F 213 1214 207 412 4 98.12
42 1214 205 F 41 1214 209 67 4 90.24
40 1214 205 F 39 1214 211 63 4 89.74
28 1214 205 F 28 1214 213 56 0 100.00
36 1214 205 F 37 1214 215 53 5 86.11
35 1214 205 F 36 1214 217 51 5 85.71
23 859 208 F 23 1214 207 46 0 100.00
37 859 208 F 37 1214 209 50 6 83.78
23 859 208 F 23 1214 211 46 0 100.00
23 859 208 F 23 1214 213 46 0 100.00
23 859 208 F 23 1214 215 46 0 100.00
23 859 208 F 23 1214 217 46 0 100.00
22 859 208 F 22 1214 219 44 0 100.00
35 1214 205 F 34 1214 219 49 5 85.29
21 859 208 F 21 1524 237 42 0 100.00
40 1214 205 F 38 1524 237 58 5 86.84
38 1214 207 F 38 1524 237 60 4 89.47
36 1214 209 F 38 1524 237 58 4 88.89
37 1214 211 F 39 1524 237 52 6 83.78
28 1214 213 F 29 1524 237 45 3 89.29
21 1214 215 F 21 1524 237 42 0 100.00
21 1214 217 F 21 1524 237 42 0 100.00
34 1214 219 F 32 1524 237 54 3 90.62
43 859 208 F 41 859 210 76 2 95.12
21 859 210 F 21 1214 205 42 0 100.00
20 859 208 F 20 1214 221 40 0 100.00
33 1214 205 F 32 1214 221 45 5 84.38
32 1214 221 F 32 1524 237 52 3 90.62
323 1231 2 F 322 1318 24 617 7 97.83
121 354 197 F 121 1077 212 234 2 98.35
159 35 0 F 159 54 46 298 5 96.86
159 42 0 F 159 54 46 298 5 96.86
132 54 44 F 132 146 259 248 4 96.97
409 1097 23 F 417 1806 1 686 35 91.44
200 545 122 F 202 1453 254 358 11 94.50
270 313 34 F 265 1782 2 451 21 92.08
223 313 78 F 220 1827 5 383 15 93.18
192 1 378 F 187 2 0 343 9 95.19
276 1 294 F 271 16 0 515 8 97.05
390 884 31 F 392 890 43 726 14 96.41
339 1820 0 F 340 1909 0 599 20 94.10
324 782 52 F 327 1270 4 579 18 94.44
25 561 420 F 24 840 278 45 1 95.83
128 561 402 F 125 561 405 213 3 97.60
34 561 410 F 34 840 270 48 5 85.29
29 561 412 F 30 840 275 51 2 93.10
38 561 400 F 39 561 406 53 6 84.21
26 840 278 F 26 1231 160 44 2 92.31
26 840 278 F 26 1318 181 44 2 92.31
36 561 411 F 36 1231 158 52 5 86.11
36 561 411 F 36 1318 179 52 5 86.11
274 1415 148 F 273 1724 0 483 16 94.14
456 1796 26 F 446 1937 0 718 46 89.69
416 1620 0 F 415 1796 6 743 22 94.70
379 1784 7 F 381 1799 0 656 26 93.14
330 1939 0 F 330 1940 10 568 23 93.03
291 358 77 F 292 1678 0 523 15 94.85
268 248 0 F 269 292 0 477 15 94.40
367 881 0 F 364 1248 100 699 8 97.80
300 1910 0 F 299 1926 25 543 14 95.32
386 376 0 F 401 1694 81 607 45 88.34
330 1277 1 F 326 1694 81 580 19 94.17
267 1851 45 F 267 1879 0 466 17 93.63
331 18 0 F 337 46 194 536 33 90.03
179 382 45 F 177 918 49 260 24 86.44
355 35 184 F 351 72 196 678 7 98.01
45 42 184 F 45 72 196 50 10 77.78
51 72 196 F 48 73 109 47 13 72.92
345 584 135 F 339 1381 0 544 35 89.68
317 1381 25 F 332 1661 121 421 56 82.33
641 6 156 F 647 39 227 1216 18 97.19
149 413 221 F 148 1250 267 265 8 94.59
332 1536 0 F 332 1630 0 652 3 99.10
391 470 80 F 395 1013 0 690 24 93.86
267 227 189 F 267 968 0 342 48 82.02
78 859 0 F 81 1265 168 119 10 87.18
329 1592 0 F 322 1595 8 583 17 94.72
380 78 86 F 375 80 149 635 30 92.00
352 474 188 F 353 1076 31 633 18 94.89
351 543 129 F 353 1076 31 636 17 95.16
344 1076 40 F 342 1297 133 622 16 95.32
347 912 136 F 348 1076 31 631 16 95.39
329 761 12 F 330 1076 31 599 15 95.44
326 826 155 F 328 1076 31 590 16 95.09
349 798 84 F 349 1076 35 618 20 94.27
352 1828 6 F 353 1947 0 625 20 94.32
111 474 166 F 110 1722 43 185 9 91.82
110 902 85 F 110 1722 43 184 9 91.82
110 1151 118 F 110 1722 43 184 9 91.82
110 451 98 F 110 1722 43 184 9 91.82
110 736 174 F 110 1722 43 184 9 91.82
111 1049 118 F 110 1722 43 181 10 90.91
110 846 280 F 110 1722 43 180 10 90.91
110 380 65 F 110 1722 43 184 9 91.82
110 988 109 F 110 1722 43 180 10 90.91
111 912 114 F 110 1722 43 185 9 91.82
265 454 62 F 264 1722 0 473 14 94.70
256 1722 8 F 256 1837 0 464 12 95.31
111 483 60 F 110 1722 43 181 10 90.91
108 658 231 F 109 1722 43 181 9 91.67
163 1578 0 F 163 1682 12 290 9 94.48
203 1851 33 F 203 1950 58 330 19 90.64
319 131 0 F 319 158 0 630 2 99.37
375 37 0 F 383 1823 0 670 22 94.13
307 877 174 F 311 1627 103 566 13 95.77
416 1620 0 F 415 1796 6 743 22 94.70
391 470 80 F 395 1013 0 690 24 93.86
349 1554 0 F 347 1555 52 632 16 95.39
319 1548 0 F 318 1555 101 605 8 97.48
77 126 94 F 77 1238 156 98 14 81.82
95 530 145 F 95 1238 162 118 18 81.05
95 1238 162 F 95 1343 153 118 18 81.05
222 1206 107 F 222 1238 83 276 42 81.08
306 877 193 F 305 1514 2 547 16 94.75
291 1268 211 F 290 1514 0 517 16 94.48
274 1415 148 F 273 1724 0 483 16 94.14
267 1851 45 F 267 1879 0 466 17 93.63
339 1802 3 F 340 1877 0 667 3 99.12
343 568 69 F 345 1793 63 652 9 97.38
236 1153 0 F 228 1161 110 348 29 87.28
151 42 147 F 146 49 398 261 9 93.84
43 36 332 F 41 49 453 68 4 90.24
40 31 243 F 38 49 453 66 3 92.11
268 62 300 F 271 555 0 407 33 87.69
362 662 80 F 367 1193 8 569 40 88.95
91 658 186 F 92 849 1 147 9 90.11
94 658 138 F 101 1892 244 147 12 87.23
441 658 156 F 447 912 36 844 11 97.51
415 1663 0 F 414 1893 27 657 43 89.61
359 492 0 F 362 1469 92 661 15 95.82
377 1469 77 F 372 1874 0 661 22 94.09
321 738 178 F 321 739 58 602 10 96.88
377 739 2 F 383 1384 8 592 42 88.86
95 7 276 F 96 33 1 183 2 97.89
100 7 259 F 99 264 519 155 11 88.89
60 7 269 F 62 300 280 90 8 86.67
108 237 217 F 108 468 0 164 13 87.96
339 1649 38 F 335 1892 4 478 49 85.37
284 1892 4 F 284 1931 25 372 49 82.75
230 1649 38 F 230 1664 1 308 38 83.48
230 1664 1 F 230 1931 25 272 47 79.57
52 1649 278 F 55 1871 244 75 8 84.62
170 1230 7 F 178 1649 213 180 41 75.88
250 1021 0 F 250 1051 242 468 8 96.80
308 506 0 F 303 988 123 547 16 94.72
377 988 49 F 376 1049 60 693 15 96.01
377 988 49 F 377 1328 1 622 33 91.25
376 634 4 F 377 976 13 689 16 95.74
100 33 0 F 101 73 0 189 3 97.00
95 7 276 F 97 73 1 172 5 94.74
348 579 0 F 352 1143 75 608 23 93.39
74 1143 353 F 74 1196 309 132 4 94.59
425 630 9 F 426 1143 1 683 41 90.35
347 579 1 F 350 1365 43 605 23 93.37
74 1196 309 F 74 1365 319 120 7 90.54
370 630 64 F 372 1365 21 658 21 94.32
392 1143 35 F 391 1365 2 691 23 94.12
242 610 53 F 243 1143 178 449 9 96.28
242 610 53 F 243 1365 144 449 9 96.28
326 1198 2 F 316 1365 59 542 25 92.09
250 579 80 F 252 1198 76 434 17 93.20
316 630 100 F 326 1198 2 538 26 91.77
315 380 88 F 326 1198 2 545 24 92.38
315 605 68 F 323 1198 5 522 29 90.79
315 846 303 F 326 1198 2 541 25 92.06
315 902 108 F 326 1198 2 549 23 92.70
315 1151 141 F 326 1198 2 549 23 92.70
326 1198 2 F 317 1230 196 551 23 92.74
313 451 121 F 324 1198 2 545 23 92.65
313 736 197 F 324 1198 2 545 23 92.65
316 1143 93 F 326 1198 2 538 26 91.77
315 1100 128 F 326 1198 2 537 26 91.75
242 1198 84 F 239 1289 3 413 17 92.89
294 481 10 F 293 1198 35 499 22 92.49
297 483 83 F 306 1198 2 515 22 92.59
168 610 115 F 171 1198 157 307 8 95.24
227 642 30 F 231 1198 62 390 17 92.51
322 1198 2 F 311 1360 104 513 30 90.35
263 1196 43 F 267 1198 2 422 27 89.73
282 641 42 F 288 1198 40 490 20 92.91
411 1696 0 F 412 1781 23 691 33 91.97
284 386 212 F 293 1201 56 501 19 93.31
291 358 77 F 292 1678 0 523 15 94.85
230 35 0 F 229 42 0 423 9 96.07
130 35 0 F 130 146 261 260 0 100.00
130 42 0 F 130 146 261 260 0 100.00
159 35 0 F 159 54 46 298 5 96.86
159 42 0 F 159 54 46 298 5 96.86
341 319 2 F 336 626 202 581 24 92.86
411 1696 0 F 412 1781 23 691 33 91.97
424 454 70 F 432 1837 0 772 21 95.05
366 197 112 F 359 385 0 641 21 94.15
335 197 126 F 336 665 0 567 26 92.24
231 779 30 F 227 783 30 322 34 85.02
641 6 156 F 647 39 227 1216 18 97.19
341 319 2 F 336 626 202 581 24 92.86
282 591 0 F 283 1758 7 461 26 90.78
324 428 0 F 320 1441 29 564 20 93.75
317 428 7 F 312 1513 64 573 14 95.51
376 492 0 F 378 825 98 726 7 98.14
418 432 4 F 419 825 65 773 16 96.17
295 538 0 F 288 667 102 499 21 92.71
409 1097 23 F 417 1806 1 686 35 91.44
295 538 0 F 288 667 102 499 21 92.71
365 422 1 F 375 1794 64 576 41 88.77
435 474 105 F 433 798 0 792 19 95.61
429 543 51 F 430 798 3 771 22 94.87
428 658 174 F 433 798 0 773 22 94.86
423 713 17 F 432 798 1 719 34 91.96
411 798 22 F 406 1297 69 729 22 94.58
428 798 0 F 428 912 55 776 20 95.33
368 798 40 F 365 1327 71 661 18 95.07
324 798 109 F 322 849 95 594 13 95.96
341 761 0 F 341 798 69 654 7 97.95
408 798 0 F 407 826 74 735 20 95.09
349 798 84 F 349 1076 35 618 20 94.27
432 798 1 F 428 1120 16 716 36 91.59
350 798 83 F 359 935 38 589 30 91.43
200 545 122 F 202 1453 254 358 11 94.50
396 584 79 F 407 1661 35 627 43 89.14
321 1941 0 F 323 1942 31 524 30 90.65
104 112 28 F 104 120 53 192 4 96.15
238 2 130 F 238 39 130 412 16 93.28
238 16 214 F 238 39 130 408 17 92.86
61 1 509 F 57 39 130 82 9 84.21
503 2 130 F 522 5 96 845 45 91.05
602 5 96 F 601 16 214 1099 26 95.67
61 1 509 F 57 5 96 82 9 84.21
117 2 130 F 117 7 96 182 13 88.89
117 7 96 F 117 16 214 182 13 88.89
61 1 509 F 57 7 96 82 9 84.21
238 2 130 F 238 3 58 408 17 92.86
238 3 58 F 238 16 214 404 18 92.44
61 1 509 F 57 3 58 78 10 82.46
43 2 130 F 44 4 518 71 4 90.70
44 4 518 F 43 16 214 71 4 90.70
45 1 509 F 44 4 518 69 5 88.64
194 253 2 F 194 276 2 308 20 89.69
344 691 71 F 347 814 135 643 12 96.51
211 899 96 F 212 1798 206 255 42 80.09
365 422 1 F 375 1794 64 576 41 88.77
361 1226 87 F 356 1296 91 649 17 95.22
328 720 0 F 330 1398 19 534 31 90.55
360 369 21 F 360 1409 0 640 20 94.44
304 481 0 F 296 630 120 536 16 94.59
296 380 107 F 304 481 0 544 14 95.27
304 481 0 F 296 846 322 540 15 94.93
304 481 0 F 296 902 127 548 13 95.61
304 481 0 F 296 1151 160 548 13 95.61
304 481 0 F 296 1230 217 548 13 95.61
294 451 140 F 302 481 0 544 13 95.58
302 481 0 F 294 736 216 544 13 95.58
304 481 0 F 296 1100 147 540 15 94.93
304 481 0 F 297 1365 78 533 17 94.28
300 481 0 F 292 1360 123 512 20 93.15
284 481 0 F 277 483 103 509 13 95.31
185 474 208 F 192 481 0 301 19 89.73
192 481 0 F 184 543 149 300 19 89.67
192 481 0 F 183 658 272 295 20 89.07
192 481 0 F 183 713 110 291 21 88.52
192 481 0 F 183 1297 145 291 21 88.52
192 481 0 F 184 912 157 300 19 89.67
192 481 0 F 184 1327 130 292 21 88.59
192 481 0 F 184 761 33 300 19 89.67
192 481 0 F 184 826 175 300 19 89.67
192 481 0 F 185 798 101 293 21 88.65
304 481 0 F 298 605 85 538 16 94.63
304 481 0 F 296 1143 113 536 16 94.59
258 481 11 F 251 642 6 429 20 92.03
173 481 9 F 165 849 95 258 20 87.88
246 481 0 F 243 1196 63 417 18 92.59
375 37 0 F 383 1823 0 670 22 94.13
280 322 70 F 285 793 68 421 35 87.50
309 877 174 F 310 1268 193 599 5 98.38
307 877 174 F 311 1627 103 566 13 95.77
302 877 174 F 310 1747 95 532 20 93.38
223 247 130 F 226 880 2 361 22 90.13
327 33 99 F 327 38 665 614 10 96.94
160 1299 0 F 158 1776 112 242 19 87.97
397 356 33 F 390 496 1 699 22 94.36
376 558 0 F 368 1254 134 668 19 94.84
147 249 222 F 144 968 0 211 20 86.11
350 412 163 F 348 1525 88 646 13 96.26
339 761 0 F 338 826 143 673 1 99.70
340 543 117 F 341 761 0 665 4 98.82
215 761 2 F 214 902 97 393 9 95.79
215 761 2 F 214 1151 130 393 9 95.79
214 451 110 F 215 761 2 393 9 95.79
214 736 186 F 215 761 2 393 9 95.79
277 761 2 F 276 1049 131 473 20 92.75
215 761 2 F 214 846 292 385 11 94.86
214 380 77 F 215 761 2 389 10 95.33
255 761 2 F 253 988 121 428 20 92.09
215 761 2 F 215 1365 48 382 12 94.42
215 761 2 F 214 1360 93 369 15 92.99
341 474 176 F 341 761 0 666 4 98.83
316 442 114 F 317 1510 66 581 13 95.89
540 4 16 F 523 47 0 935 32 93.88
224 1782 39 F 224 1827 0 404 11 95.09
276 4 388 F 272 39 0 428 30 88.97
242 4 422 F 238 5 0 384 24 89.92
215 4 422 F 213 7 0 360 17 92.02
200 3 0 F 204 4 460 312 23 88.50
446 1620 20 F 439 1937 0 721 41 90.66
456 1796 26 F 446 1937 0 718 46 89.69
330 1939 0 F 330 1940 10 568 23 93.03
102 859 84 F 102 1265 231 200 1 99.02
184 175 74 F 183 1821 0 303 16 91.26
268 497 0 F 264 1550 75 444 22 91.67
186 1544 0 F 186 1550 153 352 5 97.31
171 1550 168 F 171 1551 0 318 6 96.49
336 1546 28 F 338 1550 1 630 11 96.73
336 1547 12 F 338 1550 1 622 13 96.13
72 1199 59 F 71 1650 0 115 7 90.14
71 719 170 F 71 1650 0 118 6 91.55
130 1260 138 F 129 1615 1 235 6 95.35
361 1226 87 F 356 1296 91 649 17 95.22
185 1198 2 F 178 1456 87 259 26 85.39
263 1196 43 F 267 1198 2 422 27 89.73
204 474 189 F 212 1198 2 312 26 87.25
203 543 130 F 212 1198 2 315 25 87.68
201 658 254 F 212 1198 2 305 27 86.57
202 713 91 F 212 1198 2 302 28 86.14
212 1198 2 F 201 1297 127 301 28 86.07
204 912 137 F 212 1198 2 316 25 87.75
199 1198 15 F 193 1327 121 296 24 87.56
207 761 10 F 214 1198 0 313 27 86.96
206 826 153 F 214 1198 0 316 26 87.38
202 798 84 F 209 1198 5 307 26 87.13
297 483 83 F 306 1198 2 515 22 92.59
326 1198 2 F 316 1365 59 542 25 92.09
316 630 100 F 326 1198 2 538 26 91.77
315 380 88 F 326 1198 2 545 24 92.38
315 846 303 F 326 1198 2 541 25 92.06
315 902 108 F 326 1198 2 549 23 92.70
315 1151 141 F 326 1198 2 549 23 92.70
326 1198 2 F 317 1230 196 551 23 92.74
313 451 121 F 324 1198 2 545 23 92.65
313 736 197 F 324 1198 2 545 23 92.65
315 1100 128 F 326 1198 2 537 26 91.75
316 1143 93 F 326 1198 2 538 26 91.77
227 642 30 F 231 1198 62 390 17 92.51
211 506 10 F 217 1198 2 300 32 84.83
207 1049 142 F 217 1198 2 316 27 86.96
217 1198 2 F 209 1328 82 294 33 84.21
202 935 48 F 198 1198 16 252 37 81.31
137 1076 100 F 138 1198 76 211 16 88.32
201 1120 96 F 212 1198 2 301 28 86.07
294 481 10 F 293 1198 35 499 22 92.49
145 1189 23 F 152 1198 2 229 17 88.28
59 610 53 F 60 1198 94 99 5 91.53
282 641 42 F 288 1198 40 490 20 92.91
242 1198 84 F 239 1289 3 413 17 92.89
322 1198 2 F 311 1360 104 513 30 90.35
315 605 68 F 323 1198 5 522 29 90.79
438 905 0 F 451 1693 83 677 53 87.90
246 483 14 F 243 1456 22 361 32 86.83
247 902 37 F 249 1456 16 368 32 87.04
247 1151 70 F 250 1456 15 365 33 86.64
249 1230 125 F 250 1456 15 375 31 87.55
249 451 48 F 250 1456 15 367 33 86.75
246 736 127 F 250 1456 15 360 34 86.18
260 1100 44 F 259 1456 6 379 35 86.49
251 1143 19 F 249 1456 16 380 30 87.95
245 1049 71 F 248 1456 15 357 34 86.12
266 474 100 F 265 1456 0 359 42 84.15
238 543 68 F 241 1456 24 367 28 88.24
257 912 57 F 260 1456 5 365 38 85.21
186 761 4 F 188 1456 77 326 12 93.55
263 826 69 F 265 1456 0 356 43 83.65
241 798 18 F 243 1456 22 340 36 85.06
235 658 193 F 241 1456 24 348 32 86.38
239 713 27 F 249 1456 16 380 27 88.70
259 1120 11 F 265 1456 0 388 34 86.87
257 846 222 F 260 1456 5 357 40 84.44
234 1365 2 F 233 1456 32 343 31 86.70
206 849 38 F 211 1456 54 289 32 84.47
176 454 40 F 178 1456 0 166 46 73.86
244 1327 43 F 249 1456 16 333 40 83.61
181 1328 77 F 181 1456 82 298 16 91.16
56 454 160 F 59 1196 77 99 4 92.86
293 483 49 F 297 1196 9 514 19 93.52
299 902 66 F 305 1196 1 516 22 92.64
299 1151 99 F 305 1196 1 516 22 92.64
306 1196 0 F 303 1230 152 525 21 93.07
301 451 77 F 306 1196 0 519 22 92.69
299 736 155 F 305 1196 1 516 22 92.64
301 1100 84 F 306 1196 0 511 24 92.03
304 1143 47 F 306 1196 0 510 25 91.78
240 1049 109 F 246 1196 11 374 28 88.33
215 474 178 F 220 1196 32 359 19 91.16
214 543 119 F 220 1196 32 362 18 91.59
215 912 126 F 220 1196 32 363 18 91.63
215 761 2 F 220 1196 32 359 19 91.16
214 826 145 F 220 1196 32 358 19 91.12
215 798 71 F 220 1196 32 351 21 90.23
188 658 267 F 194 1196 58 326 14 92.55
211 713 82 F 218 1196 34 349 20 90.52
210 1120 87 F 218 1196 34 348 20 90.48
299 846 261 F 305 1196 1 508 24 91.97
274 1196 32 F 269 1365 48 491 13 95.17
157 849 91 F 158 1196 70 263 13 91.72
220 1196 32 F 214 1327 100 350 21 90.19
248 1196 9 F 241 1328 50 353 34 85.89
318 574 96 F 320 1369 78 602 9 97.17
517 64 0 F 517 65 0 1034 0 100.00
434 426 27 F 429 795 0 675 47 89.04
393 451 41 F 391 902 30 744 10 97.44
393 451 41 F 391 1151 63 760 6 98.47
393 451 41 F 389 736 121 762 5 98.71
393 451 41 F 389 846 227 754 7 98.20
387 380 14 F 393 451 41 744 9 97.67
283 451 41 F 279 826 80 494 17 93.91
418 229 0 F 419 270 0 825 3 99.28
452 736 58 F 454 1151 0 866 10 97.79
454 846 164 F 456 1151 0 842 17 96.26
334 658 121 F 344 1151 0 558 30 91.02
146 1151 82 F 145 1837 0 243 12 91.72
299 40 156 F 299 747 69 578 5 98.33
257 1640 92 F 254 1840 0 455 14 94.49
349 483 31 F 345 902 58 670 6 98.26
349 483 31 F 345 1151 91 670 6 98.26
375 451 41 F 380 483 0 695 15 96.00
349 483 31 F 345 736 147 670 6 98.26
349 483 31 F 345 846 253 662 8 97.68
344 380 39 F 349 483 31 661 8 97.67
292 483 0 F 285 988 54 469 27 90.53
349 483 31 F 348 1230 145 657 10 97.13
505 474 35 F 492 658 110 909 22 95.53
480 474 35 F 479 826 2 899 15 96.87
63 541 246 F 63 1006 332 126 0 100.00
255 455 0 F 254 1260 213 481 7 97.24
97 455 58 F 98 1615 135 155 10 89.69
350 372 1 F 348 1348 62 654 11 96.84
376 634 4 F 377 976 13 689 16 95.74
434 426 27 F 429 795 0 675 47 89.04
393 536 87 F 398 567 0 691 25 93.64
396 567 2 F 387 1082 39 679 26 93.28
151 1 149 F 151 4 159 254 12 92.05
151 1 149 F 151 47 143 250 13 91.39
415 223 2 F 414 271 2 793 9 97.83
265 1705 0 F 264 1709 0 481 12 95.45
404 549 32 F 412 661 104 712 26 93.56
163 1578 0 F 163 1682 12 290 9 94.48
453 460 27 F 452 1351 0 793 28 93.81
374 1351 67 F 376 1936 2 678 18 95.19
188 160 117 F 189 160 297 365 3 98.40
272 474 121 F 271 605 0 443 25 90.77
270 543 63 F 271 605 0 421 30 88.89
271 605 0 F 267 658 188 438 25 90.64
271 605 0 F 263 713 30 386 37 85.93
162 605 109 F 162 1297 166 284 10 93.83
271 605 0 F 270 912 71 437 26 90.37
246 605 25 F 243 1327 71 381 27 88.89
216 605 55 F 215 761 2 363 17 92.09
271 605 0 F 270 826 89 437 26 90.37
271 605 0 F 270 798 16 401 35 87.04
370 483 10 F 363 605 0 637 24 93.39
370 605 13 F 373 1365 2 639 26 92.97
274 605 109 F 274 630 142 532 4 98.54
381 380 22 F 383 605 0 688 19 95.01
383 605 0 F 382 846 236 693 18 95.29
383 605 0 F 384 902 39 695 18 95.30
383 605 0 F 383 1151 73 702 16 95.82
383 605 0 F 385 1230 128 688 20 94.78
383 451 51 F 381 605 0 692 18 95.28
381 605 0 F 380 736 130 697 16 95.79
383 605 0 F 386 1100 57 649 29 92.43
383 605 0 F 387 1143 22 650 30 92.17
239 605 109 F 239 642 18 430 12 94.98
167 605 94 F 165 849 95 268 16 90.30
290 605 35 F 295 1196 11 485 25 91.38
221 506 0 F 219 605 57 336 26 88.13
276 605 0 F 275 1049 74 443 27 90.18
274 605 2 F 274 1328 17 392 39 85.77
276 605 0 F 276 988 63 428 31 88.77
204 605 67 F 212 935 38 288 32 84.31
203 605 68 F 202 1076 35 301 26 87.13
267 605 4 F 263 1120 34 386 36 86.31
330 579 0 F 333 605 50 559 26 92.12
240 605 4 F 243 1456 22 339 36 85.00
85 454 220 F 85 605 159 158 3 96.47
140 1205 108 F 141 1942 214 225 14 90.00
360 369 21 F 360 1409 0 640 20 94.44
399 815 46 F 415 1699 47 678 33 91.73
24 859 207 F 24 1214 204 48 0 100.00
157 322 70 F 158 793 68 247 16 89.81
271 679 62 F 273 759 0 488 14 94.83
295 376 132 F 295 1402 3 534 14 95.25
356 989 50 F 347 1350 1 591 28 91.93
43 561 402 F 44 1231 143 51 9 79.07
43 561 402 F 44 1318 164 51 9 79.07
43 561 402 F 44 1231 143 51 9 79.07
43 561 402 F 44 1318 164 51 9 79.07
474 1788 0 F 474 1850 9 836 28 94.09
271 679 62 F 273 759 0 488 14 94.83
359 695 121 F 363 938 64 686 9 97.49
98 1869 183 F 98 1943 2 144 13 86.73
297 1024 75 F 298 1744 100 343 63 78.79
102 1289 3 F 100 1456 165 174 7 93.00
183 1196 123 F 183 1289 3 330 9 95.08
129 474 264 F 129 1289 3 206 13 89.92
129 543 204 F 129 1289 3 206 13 89.92
128 658 327 F 129 1289 3 201 14 89.06
129 713 164 F 129 1289 3 202 14 89.15
129 1289 3 F 129 1297 199 206 13 89.92
129 912 212 F 129 1289 3 206 13 89.92
129 1289 3 F 129 1327 185 206 13 89.92
129 761 88 F 129 1289 3 206 13 89.92
129 826 230 F 129 1289 3 206 13 89.92
222 483 158 F 221 1289 3 415 7 96.83
239 1289 3 F 239 1365 134 438 10 95.82
239 630 175 F 239 1289 3 446 8 96.65
239 380 162 F 239 1289 3 446 8 96.65
239 846 377 F 239 1289 3 442 9 96.23
239 902 182 F 239 1289 3 446 8 96.65
239 1151 215 F 239 1289 3 446 8 96.65
239 1230 272 F 239 1289 3 446 8 96.65
239 451 195 F 239 1289 3 446 8 96.65
239 736 271 F 239 1289 3 446 8 96.65
239 1100 202 F 239 1289 3 442 9 96.23
239 1143 168 F 239 1289 3 438 10 95.82
133 506 88 F 134 1289 3 207 15 88.72
133 1049 216 F 134 1289 3 207 15 88.72
128 1120 169 F 129 1289 3 205 13 89.84
243 481 59 F 241 1289 1 436 12 95.02
74 1189 98 F 75 1289 3 129 5 93.24
239 641 83 F 239 1289 3 422 14 94.14
239 605 142 F 239 1289 3 438 10 95.82
85 454 220 F 85 1289 20 150 5 94.12
133 988 206 F 134 1289 3 203 16 87.97
85 1289 20 F 85 1722 157 142 7 91.76
237 579 91 F 238 1289 4 439 9 96.20
206 642 51 F 206 1289 3 376 9 95.63
172 610 53 F 173 1196 133 317 7 95.93
168 474 225 F 171 610 0 227 28 83.33
168 543 165 F 171 610 0 227 28 83.33
118 610 53 F 118 658 337 188 12 89.83
120 610 51 F 121 713 172 193 12 90.00
171 610 0 F 167 1297 161 222 29 82.63
171 610 0 F 168 912 173 227 28 83.33
171 610 0 F 168 1327 146 227 28 83.33
171 610 0 F 168 761 49 227 28 83.33
171 610 0 F 168 826 191 227 28 83.33
171 610 0 F 169 798 117 224 29 82.84
212 483 168 F 210 610 53 394 7 96.67
242 610 53 F 243 1365 144 449 9 96.28
242 610 53 F 243 630 185 461 6 97.52
231 380 172 F 230 610 53 437 6 97.39
230 610 53 F 231 846 387 433 7 96.96
230 610 53 F 231 902 192 437 6 97.39
230 610 53 F 231 1151 225 437 6 97.39
230 610 53 F 231 1230 282 437 6 97.39
229 451 205 F 228 610 53 433 6 97.37
228 610 53 F 229 736 281 433 6 97.37
230 610 53 F 231 1100 212 429 8 96.52
226 610 53 F 227 1360 188 413 10 95.58
231 605 152 F 230 610 53 429 8 96.52
242 610 53 F 243 1143 178 449 9 96.28
195 610 53 F 196 642 61 359 8 95.90
161 610 0 F 157 849 103 198 30 80.89
123 506 98 F 123 610 53 190 14 88.62
123 610 53 F 123 1049 226 190 14 88.62
123 610 53 F 123 1328 168 190 14 88.62
123 610 53 F 123 988 216 186 15 87.80
119 610 52 F 120 935 130 171 17 85.71
171 610 0 F 167 1076 70 210 32 80.84
171 610 0 F 167 1120 130 222 29 82.63
244 579 98 F 244 610 51 456 8 96.72
231 610 50 F 232 1289 10 415 12 94.81
91 610 53 F 90 1456 175 157 6 93.33
393 536 87 F 388 1082 38 717 16 95.88
434 426 27 F 429 795 0 675 47 89.04
328 593 0 F 323 607 58 603 12 96.28
152 506 168 F 153 1189 178 269 8 94.74
152 1049 296 F 153 1189 178 269 8 94.74
139 988 286 F 140 1189 178 239 9 93.53
343 568 69 F 345 1793 63 652 9 97.38
323 915 121 F 325 1070 53 600 12 96.28
320 409 143 F 318 456 0 630 2 99.37
399 815 46 F 415 1699 47 678 33 91.73
282 647 2 F 279 1388 62 493 17 93.91
383 318 13 F 387 905 59 678 23 93.99
343 1302 67 F 343 1433 4 606 20 94.17
367 530 53 F 365 1343 63 688 11 96.99
360 544 0 F 358 1343 70 658 15 95.81
377 432 37 F 376 492 0 733 5 98.67
376 492 0 F 377 1874 14 697 14 96.28
58 950 2 F 58 1850 210 108 2 96.55
58 950 2 F 58 1788 201 108 2 96.55
159 807 2 F 167 1212 57 198 32 79.87
313 560 59 F 311 1069 28 572 13 95.82
355 35 184 F 351 72 196 678 7 98.01
296 960 29 F 303 970 135 543 14 95.27
200 545 122 F 202 1453 254 358 11 94.50
260 664 16 F 270 1183 3 430 25 90.38
317 428 7 F 312 1513 64 573 14 95.51
356 1441 10 F 356 1513 37 648 16 95.51
47 102 224 F 47 102 257 62 8 82.98
422 819 43 F 431 975 41 761 23 94.55
369 1475 72 F 376 1594 0 577 42 88.62
196 459 64 F 192 587 5 256 33 82.81
341 306 0 F 341 1349 124 618 16 95.31
461 654 0 F 461 1212 120 758 41 91.11
310 654 103 F 306 807 164 580 9 97.06
378 473 13 F 377 766 51 719 9 97.61
345 584 135 F 339 1381 0 544 35 89.68
130 1734 1 F 131 1814 8 189 18 86.15
361 1226 87 F 356 1296 91 649 17 95.22
453 460 27 F 452 1351 0 793 28 93.81
231 460 238 F 231 1859 0 450 3 98.70
231 1351 210 F 231 1859 0 450 3 98.70
374 1351 67 F 376 1936 2 678 18 95.19
231 1859 0 F 231 1936 147 442 5 97.84
378 473 13 F 377 766 51 719 9 97.61
248 1868 37 F 248 1948 21 400 24 90.32
128 1777 94 F 128 1948 90 188 17 86.72
191 735 195 F 194 1479 14 293 23 87.96
306 807 164 F 306 1212 227 592 5 98.37
332 977 26 F 332 1605 73 556 27 91.87
339 440 2 F 335 765 95 606 17 94.93
85 33 0 F 84 264 534 161 2 97.62
30 42 218 F 31 264 528 53 2 93.33
25 33 0 F 25 42 223 50 0 100.00
27 36 348 F 28 264 528 47 2 92.59
22 33 0 F 22 36 353 44 0 100.00
411 1696 0 F 412 1781 23 691 33 91.97
378 473 13 F 377 766 51 719 9 97.61
420 902 3 F 422 1230 91 766 19 95.48
438 1151 18 F 443 1230 70 809 18 95.89
393 451 41 F 392 1230 119 745 10 97.45
485 736 25 F 500 1230 11 869 29 94.02
349 483 31 F 348 1230 145 657 10 97.13
349 483 31 F 350 1143 39 619 20 94.27
378 902 45 F 383 1143 26 677 21 94.44
409 1143 0 F 409 1151 47 706 28 93.15
387 451 47 F 389 1143 18 688 22 94.32
406 736 104 F 407 1143 0 697 29 92.86
349 1049 0 F 356 1230 50 569 34 90.26
300 1049 49 F 302 1143 0 454 37 87.67
475 543 0 F 482 912 1 877 20 95.79
341 761 0 F 341 912 124 666 4 98.83
467 826 14 F 463 912 0 854 19 95.90
320 543 13 F 331 1230 70 515 34 89.38
215 761 2 F 217 1230 184 384 12 94.42
328 826 31 F 331 1230 70 555 26 92.07
289 543 44 F 293 1143 4 454 32 88.93
215 761 2 F 216 1143 81 379 13 93.95
295 826 64 F 297 1143 0 452 35 88.14
256 483 31 F 253 912 88 441 17 93.28
298 902 13 F 297 912 44 511 21 92.93
341 912 0 F 343 1151 1 580 26 92.38
283 451 41 F 279 912 62 486 19 93.19
341 736 59 F 341 912 0 582 25 92.67
411 912 1 F 414 1049 3 653 43 89.54
317 658 138 F 329 1230 72 530 29 90.85
286 658 169 F 293 1143 4 435 36 87.41
441 658 156 F 447 912 36 844 11 97.51
290 1120 7 F 296 1230 105 442 36 87.59
183 1120 114 F 184 1143 113 327 10 94.54
445 912 38 F 439 1120 0 760 31 92.94
493 846 125 F 503 1230 10 832 41 91.68
396 846 222 F 400 1143 9 692 26 93.43
341 846 165 F 341 912 0 566 29 91.50
327 1230 74 F 314 1327 0 469 43 86.31
250 1143 47 F 244 1327 70 382 28 88.52
367 912 96 F 365 1327 71 680 13 96.44
403 380 0 F 409 1230 104 760 13 96.77
401 380 2 F 407 1143 2 692 29 92.77
291 380 0 F 294 912 47 501 21 92.78
290 988 49 F 292 1230 114 478 26 91.03
295 988 44 F 297 1143 5 428 41 86.10
323 912 58 F 324 988 50 531 29 91.02
286 1230 115 F 276 1297 52 446 29 89.49
293 1143 4 F 282 1297 46 403 42 85.11
426 912 57 F 419 1297 51 773 18 95.70
171 483 61 F 172 1189 0 311 8 95.32
170 902 86 F 172 1189 0 314 7 95.88
170 1151 119 F 172 1189 0 314 7 95.88
170 451 99 F 172 1189 0 314 7 95.88
170 736 175 F 172 1189 0 314 7 95.88
171 1049 119 F 172 1189 0 311 8 95.32
169 543 109 F 172 1189 0 301 10 94.08
160 761 2 F 161 1189 11 285 9 94.38
170 826 134 F 172 1189 0 302 10 94.12
168 658 232 F 172 1189 0 296 11 93.45
129 1120 114 F 129 1189 43 242 4 96.90
170 846 281 F 172 1189 0 306 9 94.71
172 1189 0 F 170 1327 89 278 16 90.59
170 380 66 F 172 1189 0 310 8 95.29
170 988 110 F 172 1189 0 302 10 94.12
172 1189 0 F 167 1297 106 291 12 92.81
362 662 80 F 367 1193 8 569 40 88.95
316 442 114 F 317 1510 66 581 13 95.89
415 452 0 F 413 882 3 724 26 93.70
409 1097 23 F 417 1806 1 686 35 91.44
222 600 54 F 218 1251 0 332 27 87.61
376 634 4 F 377 976 13 689 16 95.74
360 530 60 F 360 544 0 672 12 96.67
339 1802 3 F 340 1877 0 667 3 99.12
405 336 36 F 419 1703 0 704 30 92.59
302 317 66 F 297 1128 0 515 21 92.93
108 848 34 F 97 1268 3 117 22 77.32
415 1663 0 F 414 1893 27 657 43 89.61
308 335 0 F 309 1059 206 613 1 99.68
392 671 7 F 402 1334 0 666 32 91.84
348 1064 63 F 351 1669 2 603 24 93.10
171 1550 168 F 171 1551 0 318 6 96.49
258 1544 15 F 258 1551 0 496 5 98.06
171 1546 193 F 171 1551 0 338 1 99.42
171 1547 177 F 171 1551 0 334 2 98.83
268 62 300 F 271 555 0 407 33 87.69
610 3 0 F 607 39 72 1145 18 97.03
455 3 155 F 453 6 156 844 16 96.47
196 454 20 F 193 912 32 321 17 91.19
145 912 80 F 145 1837 0 242 12 91.72
211 454 5 F 213 474 64 360 16 92.42
147 474 130 F 145 1837 0 236 14 90.34
208 454 7 F 201 658 138 325 21 89.55
142 658 197 F 144 1837 0 242 11 92.25
211 454 5 F 212 826 31 335 22 89.57
145 826 98 F 145 1837 0 238 13 91.03
313 483 67 F 310 579 0 539 21 93.23
347 579 1 F 350 1365 43 605 23 93.37
348 579 0 F 350 630 84 598 25 92.82
331 380 72 F 330 579 0 581 20 93.94
330 579 0 F 331 902 92 585 19 94.24
330 579 0 F 331 1151 125 585 19 94.24
330 579 0 F 334 1230 179 588 19 94.24
329 451 105 F 328 579 0 581 19 94.21
328 579 0 F 329 736 181 581 19 94.21
330 579 0 F 331 1100 112 581 20 93.94
348 579 0 F 352 1143 75 608 23 93.39
214 506 7 F 211 579 12 297 32 84.83
223 579 0 F 223 1049 126 334 28 87.44
304 481 0 F 296 579 34 520 20 93.24
164 579 0 F 166 1189 6 242 22 86.59
330 579 0 F 333 605 50 559 26 92.12
223 579 0 F 223 988 116 322 31 86.10
258 579 37 F 257 642 0 427 22 91.44
250 579 80 F 252 1198 76 434 17 93.20
353 985 0 F 353 1426 64 654 13 96.32
323 474 217 F 322 849 95 605 10 96.89
323 543 157 F 322 849 95 605 10 96.89
322 658 280 F 322 849 95 600 11 96.58
323 713 117 F 322 849 95 605 10 96.89
322 849 95 F 322 1297 153 596 12 96.27
317 849 95 F 318 912 165 595 10 96.85
297 849 95 F 298 1327 138 547 12 95.96
300 761 41 F 299 849 95 563 9 96.99
298 826 183 F 297 849 95 559 9 96.97
324 798 109 F 322 849 95 594 13 95.96
166 483 111 F 165 849 95 283 12 92.73
165 849 95 F 166 1365 87 283 12 92.73
166 630 128 F 165 849 95 271 15 90.91
166 380 115 F 165 849 95 279 13 92.12
166 846 330 F 165 849 95 275 14 91.52
165 849 95 F 166 902 135 283 12 92.73
165 849 95 F 166 1151 168 283 12 92.73
165 849 95 F 166 1230 225 283 12 92.73
166 451 148 F 165 849 95 283 12 92.73
166 736 224 F 165 849 95 283 12 92.73
222 849 38 F 227 1100 94 349 25 88.74
165 849 95 F 166 1143 121 283 12 92.73
154 642 6 F 154 849 97 248 15 90.26
157 849 91 F 158 1196 70 263 13 91.72
157 506 40 F 156 849 95 261 13 91.67
156 849 95 F 156 1049 169 272 10 93.59
156 849 95 F 156 1328 111 268 11 92.95
322 849 95 F 331 935 66 537 29 90.99
322 849 95 F 323 1076 61 577 17 94.72
322 849 95 F 322 1120 122 588 14 95.65
206 849 38 F 211 1456 54 289 32 84.47
173 481 9 F 165 849 95 258 20 87.88
121 849 95 F 121 1189 51 202 10 91.74
161 610 0 F 157 849 103 198 30 80.89
164 641 38 F 165 849 95 261 17 89.63
169 849 91 F 174 1198 30 251 23 86.39
118 849 142 F 119 1289 3 173 16 86.44
165 849 95 F 166 1360 131 271 15 90.91
49 650 3 F 50 1268 56 71 7 85.71
295 538 0 F 288 667 102 499 21 92.71
228 1624 108 F 228 1624 138 344 28 87.72
136 120 196 F 136 1624 138 232 10 92.65
106 120 226 F 106 1624 108 192 5 95.28
106 120 196 F 106 120 226 192 5 95.28
323 447 43 F 320 746 51 543 25 92.19
350 412 163 F 348 1525 88 646 13 96.26
160 1299 0 F 158 1776 112 242 19 87.97
130 1260 138 F 129 1615 1 235 6 95.35
326 676 49 F 324 1165 1 538 28 91.36
450 474 90 F 438 713 2 752 34 92.24
448 543 32 F 440 713 0 772 29 93.41
342 713 98 F 343 1297 132 665 5 98.54
435 713 0 F 446 912 37 749 33 92.41
414 713 1 F 420 1327 16 686 37 91.06
338 713 79 F 340 761 1 650 7 97.93
405 713 10 F 413 826 68 690 32 92.10
453 474 87 F 444 1120 0 765 33 92.57
376 543 104 F 376 1120 68 696 14 96.28
444 1120 0 F 439 1297 36 735 37 91.57
445 912 38 F 439 1120 0 760 31 92.94
395 1120 24 F 396 1327 40 659 33 91.65
339 761 0 F 336 1120 83 631 11 96.73
426 826 55 F 419 1120 0 709 34 91.89
416 713 24 F 420 1120 24 744 23 94.47
423 713 17 F 432 798 1 719 34 91.96
432 798 1 F 428 1120 16 716 36 91.59
327 713 113 F 335 935 62 574 22 93.27
340 935 57 F 330 1120 114 566 26 92.12
329 1055 0 F 328 1542 146 605 13 96.04
350 412 163 F 348 1525 88 646 13 96.26
360 369 21 F 360 1409 0 640 20 94.44
244 579 98 F 244 610 51 456 8 96.72
242 610 53 F 243 630 185 461 6 97.52
231 380 172 F 230 610 53 437 6 97.39
230 610 53 F 231 846 387 433 7 96.96
230 610 53 F 231 902 192 437 6 97.39
230 610 53 F 231 1151 225 437 6 97.39
230 610 53 F 231 1230 282 437 6 97.39
229 451 205 F 228 610 53 433 6 97.37
228 610 53 F 229 736 281 433 6 97.37
230 610 53 F 231 1100 212 429 8 96.52
231 610 50 F 232 1289 10 415 12 94.81
231 481 73 F 230 610 53 429 8 96.52
242 610 53 F 243 1365 144 449 9 96.28
226 610 53 F 227 1360 188 413 10 95.58
230 610 53 F 231 641 93 413 12 94.78
168 610 115 F 171 1198 157 307 8 95.24
212 483 168 F 210 610 53 394 7 96.67
184 175 74 F 183 1821 0 303 16 91.26
397 356 33 F 390 496 1 699 22 94.36
329 1592 0 F 322 1595 8 583 17 94.72
397 356 33 F 390 496 1 699 22 94.36
211 454 5 F 213 474 64 360 16 92.42
151 912 17 F 163 1892 244 214 25 83.44
223 1649 20 F 222 1736 0 409 9 95.95
222 1736 0 F 223 1931 7 377 17 92.34
140 1205 108 F 141 1942 214 225 14 90.00
259 461 0 F 259 1788 251 386 33 87.26
474 1788 0 F 474 1850 9 836 28 94.09
39 99 0 F 39 1788 255 70 2 94.87
104 1041 51 F 104 1788 251 152 14 86.54
246 481 0 F 243 1196 63 417 18 92.59
233 974 48 F 232 1310 195 425 10 95.69
404 549 32 F 412 661 104 712 26 93.56
256 310 69 F 255 1363 75 483 7 97.25
361 497 81 F 358 1544 2 699 5 98.60
268 497 0 F 264 1546 100 468 16 93.94
337 497 105 F 336 1549 0 593 17 94.94
344 691 71 F 347 814 135 643 12 96.51
222 849 38 F 227 1100 94 349 25 88.74
182 454 34 F 182 902 13 296 17 90.66
271 679 62 F 273 759 0 488 14 94.83
191 406 80 F 193 1653 152 292 23 87.96
128 406 80 F 132 1947 221 168 23 82.03
188 406 98 F 198 1828 243 290 24 87.23
418 406 24 F 415 542 15 733 25 93.98
320 409 143 F 318 456 0 630 2 99.37
203 579 15 F 205 1076 32 312 24 88.18
344 691 71 F 347 814 135 643 12 96.51
390 546 59 F 385 890 2 699 19 95.06
390 884 31 F 392 890 43 726 14 96.41
370 355 111 F 371 499 1 709 8 97.84
425 404 215 F 423 819 78 748 25 94.09
422 819 43 F 431 975 41 761 23 94.55
335 197 126 F 336 665 0 567 26 92.24
237 994 160 F 242 1190 41 423 14 94.09
440 654 1 F 432 866 142 668 51 88.19
310 826 49 F 311 902 0 541 20 93.55
346 826 13 F 344 1151 0 602 22 93.60
304 736 96 F 304 826 55 552 14 95.39
359 826 0 F 356 846 150 583 33 90.73
323 915 121 F 325 1070 53 600 12 96.28
251 1624 108 F 248 1624 168 327 43 82.66
136 120 196 F 136 1624 168 220 13 90.44
392 432 23 F 392 1874 0 716 17 95.66
176 1209 42 F 172 1349 164 200 37 78.49
302 317 66 F 297 1128 0 515 21 92.93
244 120 88 F 244 1624 0 472 4 98.36
69 112 63 F 69 1624 0 122 4 94.20
259 542 0 F 269 1653 76 412 29 88.80
196 542 0 F 209 1947 144 281 31 84.18
74 542 30 F 80 1056 0 110 11 85.14
242 1056 0 F 238 1653 107 336 36 84.87
179 1056 0 F 177 1947 176 208 37 79.10
228 1624 108 F 228 1624 138 344 28 87.72
106 120 226 F 106 1624 108 192 5 95.28
136 120 196 F 136 1624 138 232 10 92.65
106 120 196 F 106 120 226 192 5 95.28
251 1624 108 F 248 1624 168 327 43 82.66
75 120 256 F 75 1624 108 130 5 93.33
136 120 196 F 136 1624 168 220 13 90.44
75 120 196 F 75 120 256 130 5 93.33
344 691 71 F 347 814 135 643 12 96.51
290 1147 13 F 293 1331 123 503 20 93.10
341 306 0 F 341 1349 124 618 16 95.31
297 1552 0 F 293 1554 56 526 16 94.54
309 1548 7 F 314 1552 0 559 16 94.82
466 819 53 F 474 1500 28 844 24 94.85
256 310 69 F 255 1363 75 483 7 97.25
505 474 35 F 492 658 110 909 22 95.53
477 543 3 F 476 658 126 869 21 95.59
441 658 161 F 438 713 2 743 34 92.24
426 658 176 F 424 1297 51 774 19 95.52
441 658 156 F 447 912 36 844 11 97.51
364 658 213 F 365 1327 71 677 13 96.43
338 658 241 F 341 761 0 659 5 98.52
451 658 126 F 462 826 19 829 21 95.34
444 658 158 F 444 1120 0 752 34 92.34
428 658 174 F 433 798 0 773 22 94.86
348 658 254 F 360 935 37 596 28 91.95
332 977 26 F 332 1605 73 556 27 91.87
304 1068 0 F 303 1517 96 543 16 94.72
324 782 52 F 327 1270 4 579 18 94.44
185 641 0 F 188 1456 77 293 20 89.19
266 641 0 F 272 1196 34 454 21 92.11
213 474 180 F 212 641 0 361 16 92.45
212 543 121 F 212 641 0 360 16 92.45
212 641 0 F 210 658 245 354 17 91.90
212 641 0 F 211 713 82 343 20 90.52
212 641 0 F 210 1297 118 346 19 90.95
212 641 0 F 213 912 128 365 15 92.92
212 641 0 F 212 1327 102 344 20 90.57
212 641 0 F 213 761 4 357 17 91.98
212 641 0 F 212 826 147 360 16 92.45
306 483 74 F 304 641 0 558 13 95.72
324 641 0 F 325 1365 50 581 17 94.75
325 630 91 F 324 641 0 569 20 93.83
324 380 79 F 324 641 0 600 12 96.30
324 641 0 F 324 902 99 604 11 96.60
324 641 0 F 324 1151 132 604 11 96.60
324 641 0 F 327 1230 186 599 13 95.99
322 451 112 F 322 641 0 600 11 96.58
322 641 0 F 322 736 188 600 11 96.58
324 641 0 F 324 1100 119 584 16 95.06
324 641 0 F 326 1143 83 582 17 94.75
221 506 0 F 217 641 0 330 27 87.56
217 641 0 F 216 1049 133 365 17 92.13
212 641 0 F 210 1120 87 338 21 90.00
289 481 15 F 282 641 42 503 17 93.97
157 641 0 F 158 1189 14 271 11 92.99
326 605 57 F 324 641 0 574 19 94.14
84 454 221 F 84 641 101 152 4 95.24
217 641 0 F 216 988 123 353 20 90.74
323 579 7 F 324 641 0 535 28 91.33
256 641 33 F 257 642 0 441 18 92.97
212 641 0 F 213 798 73 353 18 91.51
282 641 42 F 288 1198 40 490 20 92.91
341 306 0 F 341 1349 124 618 16 95.31
67 406 29 F 68 1653 96 123 3 95.52
94 406 2 F 95 1828 144 153 9 90.43
306 807 164 F 306 1212 227 592 5 98.37
409 1097 23 F 417 1806 1 686 35 91.44
360 530 60 F 360 544 0 672 12 96.67
360 544 0 F 358 1343 70 658 15 95.81
367 530 53 F 365 1343 63 688 11 96.99
156 474 64 F 165 1892 242 225 24 84.62
488 474 47 F 483 912 0 919 13 97.31
97 474 65 F 98 1664 240 139 14 85.57
159 454 0 F 170 1892 236 237 23 85.53
196 454 20 F 193 912 32 321 17 91.19
123 454 0 F 128 1664 233 167 21 82.93
480 474 35 F 479 826 2 899 15 96.87
211 454 5 F 212 826 31 335 22 89.57
161 1230 67 F 168 1892 239 209 30 81.37
324 912 17 F 329 1230 72 537 29 91.05
98 1230 71 F 98 1664 240 120 19 80.61
328 826 31 F 331 1230 70 555 26 92.07
290 1147 13 F 293 1331 123 503 20 93.10
379 379 0 F 398 1785 85 581 48 87.34
328 593 0 F 323 607 58 603 12 96.28
268 248 0 F 269 292 0 477 15 94.40
323 447 43 F 320 746 51 543 25 92.19
75 264 513 F 77 300 265 132 5 93.33
55 33 0 F 56 300 286 99 3 94.55
344 691 71 F 347 814 135 643 12 96.51
367 881 0 F 364 1248 100 699 8 97.80
311 833 111 F 315 1146 29 526 25 91.96
324 428 0 F 320 1441 29 564 20 93.75
317 428 7 F 312 1513 64 573 14 95.51
418 406 24 F 415 542 15 733 25 93.98
191 406 80 F 193 1653 152 292 23 87.96
332 1536 0 F 332 1630 0 652 3 99.10
129 626 211 F 134 1023 48 143 30 76.74
130 65 149 F 132 65 233 242 5 96.15
130 64 149 F 132 65 233 242 5 96.15
126 61 150 F 129 65 236 227 7 94.44
132 64 233 F 130 65 149 242 5 96.15
130 64 149 F 132 64 233 242 5 96.15
126 61 150 F 129 64 236 227 7 94.44
126 61 230 F 126 65 149 240 3 97.62
126 61 230 F 126 64 149 240 3 97.62
122 61 150 F 123 61 233 225 5 95.90
168 65 149 F 168 65 191 324 3 98.21
168 64 149 F 168 65 191 324 3 98.21
164 61 150 F 165 65 194 309 5 96.95
168 64 191 F 168 65 149 324 3 98.21
168 64 149 F 168 64 191 324 3 98.21
164 61 150 F 165 64 194 309 5 96.95
168 61 188 F 168 65 149 324 3 98.21
168 61 188 F 168 64 149 324 3 98.21
164 61 150 F 165 61 191 309 5 96.95
84 65 149 F 84 65 275 156 3 96.43
84 64 275 F 84 65 149 156 3 96.43
84 61 272 F 84 65 149 156 3 96.43
84 64 149 F 84 65 275 156 3 96.43
84 64 149 F 84 64 275 156 3 96.43
84 61 272 F 84 64 149 156 3 96.43
80 61 150 F 81 65 278 141 5 93.75
80 61 150 F 81 64 278 141 5 93.75
80 61 150 F 81 61 275 141 5 93.75
172 65 149 F 174 65 191 326 5 97.09
172 64 149 F 174 65 191 326 5 97.09
168 61 150 F 171 65 194 311 7 95.83
174 64 191 F 172 65 149 326 5 97.09
172 64 149 F 174 64 191 326 5 97.09
168 61 150 F 171 64 194 311 7 95.83
168 61 188 F 168 65 149 324 3 98.21
168 61 188 F 168 64 149 324 3 98.21
164 61 150 F 165 61 191 309 5 96.95
418 406 24 F 415 542 15 733 25 93.98
191 406 80 F 193 1653 152 292 23 87.96
188 406 98 F 198 1828 243 290 24 87.23
376 492 0 F 377 1874 14 697 14 96.28
392 432 23 F 392 1874 0 716 17 95.66
362 1912 0 F 358 1913 0 624 24 93.30
132 54 44 F 132 146 259 248 4 96.97
376 634 4 F 377 976 13 689 16 95.74
284 580 73 F 284 762 131 560 2 99.30
341 306 0 F 341 1349 124 618 16 95.31
309 1681 0 F 308 1808 0 541 19 93.83
327 33 99 F 327 38 665 614 10 96.94
420 902 3 F 422 1230 91 766 19 95.48
438 1151 18 F 443 1230 70 809 18 95.89
393 451 41 F 392 1230 119 745 10 97.45
485 736 25 F 500 1230 11 869 29 94.02
493 846 125 F 503 1230 10 832 41 91.68
403 380 0 F 409 1230 104 760 13 96.77
328 826 31 F 331 1230 70 555 26 92.07
403 1764 7 F 417 1896 0 660 40 90.07
189 103 0 F 189 107 0 366 3 98.41
397 902 26 F 399 1100 44 704 23 94.21
399 1100 44 F 397 1151 59 716 20 94.96
440 1100 3 F 442 1230 71 762 30 93.18
393 451 41 F 393 1100 48 710 19 95.17
435 736 75 F 437 1100 4 752 30 93.10
380 483 0 F 375 1100 48 671 21 94.40
399 1100 44 F 399 1143 10 690 27 93.23
329 1049 20 F 332 1100 4 505 39 88.15
328 474 65 F 328 1100 3 508 37 88.72
282 543 51 F 287 1100 44 457 28 90.07
283 912 58 F 287 1100 44 454 29 89.75
215 761 2 F 214 1100 117 381 12 94.39
283 826 76 F 287 1100 44 462 27 90.46
253 798 33 F 255 1100 76 400 27 89.33
278 658 177 F 286 1100 45 456 27 90.29
243 713 50 F 247 1100 84 390 25 89.71
251 1100 80 F 248 1120 49 379 28 88.71
395 846 223 F 399 1100 44 714 20 94.94
349 1100 94 F 351 1365 24 648 13 96.28
166 483 111 F 165 849 95 283 12 92.73
165 849 95 F 166 902 135 283 12 92.73
165 849 95 F 166 1151 168 283 12 92.73
165 849 95 F 166 1230 225 283 12 92.73
166 451 148 F 165 849 95 283 12 92.73
166 736 224 F 165 849 95 283 12 92.73
165 849 95 F 166 1143 121 283 12 92.73
156 849 95 F 156 1049 169 272 10 93.59
323 474 217 F 322 849 95 605 10 96.89
323 543 157 F 322 849 95 605 10 96.89
317 849 95 F 318 912 165 595 10 96.85
300 761 41 F 299 849 95 563 9 96.99
298 826 183 F 297 849 95 559 9 96.97
324 798 109 F 322 849 95 594 13 95.96
322 658 280 F 322 849 95 600 11 96.58
323 713 117 F 322 849 95 605 10 96.89
322 849 95 F 322 1120 122 588 14 95.65
166 846 330 F 165 849 95 275 14 91.52
165 849 95 F 166 1365 87 283 12 92.73
237 1100 94 F 234 1327 80 387 21 91.03
297 849 95 F 298 1327 138 547 12 95.96
293 1100 43 F 290 1328 1 419 41 85.86
156 849 95 F 156 1328 111 268 11 92.95
393 380 10 F 399 1100 44 712 20 94.91
166 380 115 F 165 849 95 279 13 92.12
413 1100 26 F 414 1360 1 663 41 90.07
165 849 95 F 166 1360 131 271 15 90.91
349 483 31 F 346 1360 53 631 16 95.38
404 902 15 F 407 1360 8 711 25 93.81
412 1151 40 F 414 1360 1 714 28 93.20
414 1230 95 F 414 1360 1 704 31 92.51
384 451 48 F 383 1360 32 679 22 94.26
411 736 97 F 414 1360 1 721 26 93.67
405 1143 0 F 405 1360 10 638 43 89.38
307 1049 42 F 311 1360 1 490 32 89.58
305 474 88 F 306 1360 1 487 31 89.84
299 543 34 F 306 1360 1 453 38 87.29
302 912 39 F 306 1360 1 480 32 89.40
215 761 2 F 214 1360 93 369 15 92.99
303 826 56 F 307 1360 0 482 32 89.44
268 798 18 F 268 1360 39 420 29 89.18
296 658 159 F 306 1360 1 462 35 88.18
269 713 24 F 278 1360 29 371 44 83.64
290 1120 7 F 297 1360 10 399 47 83.79
410 846 204 F 414 1360 1 700 31 92.44
334 1360 47 F 337 1365 0 599 18 94.61
243 1327 71 F 246 1360 61 377 28 88.48
291 1328 0 F 293 1360 19 416 42 85.57
399 380 0 F 406 1360 9 705 25 93.73
68 1613 4 F 68 1826 1 124 3 95.59
509 78 256 F 508 1488 40 945 18 96.46
423 902 0 F 422 1151 34 809 9 97.87
414 736 96 F 416 902 5 790 10 97.58
419 846 199 F 422 902 1 777 16 96.18
299 658 156 F 308 902 3 507 25 91.64
349 1049 0 F 349 1151 0 590 27 92.26
347 736 58 F 349 1049 0 596 25 92.80
348 846 163 F 349 1049 0 569 32 90.80
395 658 131 F 405 1049 12 636 41 89.62
316 902 0 F 313 1049 36 533 24 92.33
424 454 70 F 432 1837 0 772 21 95.05
213 454 3 F 212 1151 16 345 20 90.57
212 454 4 F 211 736 73 343 20 90.52
212 454 4 F 210 846 180 322 25 88.10
208 454 7 F 201 658 138 325 21 89.55
146 902 49 F 145 1837 0 239 13 91.03
146 1049 83 F 145 1837 0 235 14 90.34
212 454 4 F 211 1049 18 339 21 90.05
310 826 49 F 311 902 0 541 20 93.55
278 1653 0 F 285 1947 68 491 18 93.53
352 1828 6 F 353 1947 0 625 20 94.32
94 406 2 F 95 1947 138 149 10 89.36
330 1277 1 F 326 1694 81 580 19 94.17
265 376 51 F 270 1277 65 507 7 97.36
330 588 0 F 330 775 103 580 20 93.94
329 1653 0 F 334 1828 74 587 19 94.22
278 1653 0 F 285 1947 68 491 18 93.53
446 1767 9 F 440 1882 0 806 20 95.45
449 1745 9 F 440 1882 0 773 27 93.86
458 1745 0 F 455 1767 0 801 28 93.85
433 1745 0 F 427 1764 1 748 28 93.44
404 1764 10 F 403 1882 0 755 13 96.77
427 1764 1 F 432 1767 0 775 21 95.08
405 1745 6 F 413 1896 0 662 39 90.37
399 1882 0 F 414 1896 3 669 36 90.98
405 1767 6 F 413 1896 0 674 36 91.11
403 1764 7 F 417 1896 0 660 40 90.07
377 1469 77 F 372 1874 0 661 22 94.09
153 885 66 F 152 1051 243 265 10 93.42
250 1021 0 F 250 1051 242 468 8 96.80
151 885 68 F 150 1021 3 257 11 92.67
304 543 29 F 311 902 0 499 29 90.46
333 543 0 F 342 1151 2 555 30 90.99
275 451 49 F 272 543 61 471 19 93.01
333 543 0 F 340 736 60 557 29 91.29
404 543 0 F 414 1049 3 630 47 88.37
333 543 0 F 340 846 166 541 33 90.09
290 380 1 F 292 543 41 494 22 92.41
322 543 51 F 324 988 50 514 33 89.75
369 902 54 F 373 1365 2 690 13 96.48
371 1151 85 F 375 1365 0 694 13 96.50
372 451 62 F 373 1365 0 685 15 95.97
369 736 141 F 373 1365 0 690 13 96.48
262 1049 87 F 266 1365 2 452 19 92.75
371 846 247 F 375 1365 0 686 15 95.96
368 380 35 F 373 1365 2 677 16 95.65
264 988 75 F 268 1365 0 436 24 90.91
257 543 76 F 261 1365 2 446 18 93.00
261 474 132 F 263 1365 0 448 19 92.72
492 474 48 F 480 543 0 880 23 95.21
259 912 82 F 263 1365 0 438 21 91.89
115 454 101 F 116 1365 31 179 13 88.70
116 1365 31 F 115 1837 30 171 15 86.96
475 543 0 F 482 912 1 877 20 95.79
115 454 101 F 113 543 104 192 9 92.04
113 543 104 F 115 1837 30 188 10 91.15
116 1365 31 F 115 1722 38 163 17 85.22
113 543 104 F 115 1722 38 180 12 89.38
349 483 31 F 349 1365 6 634 16 95.42
256 483 31 F 253 543 80 437 18 92.89
343 1302 67 F 343 1433 4 606 20 94.17
259 542 0 F 269 1653 76 412 29 88.80
418 406 24 F 415 542 15 733 25 93.98
196 542 0 F 209 1947 144 281 31 84.18
602 5 96 F 601 16 214 1099 26 95.67
350 412 163 F 348 1525 88 646 13 96.26
380 78 86 F 375 80 149 635 30 92.00
405 336 36 F 419 1703 0 704 30 92.59
108 237 217 F 108 468 0 164 13 87.96
306 877 193 F 305 1514 2 547 16 94.75
291 1268 211 F 290 1514 0 517 16 94.48
307 877 174 F 311 1627 103 566 13 95.77
404 1268 97 F 411 1627 3 723 23 94.31
284 1514 0 F 292 1747 113 452 31 89.08
403 1627 8 F 408 1747 0 735 19 95.29
52 362 208 F 51 362 251 79 6 88.24
354 1301 9 F 352 1500 137 650 14 96.02
351 819 155 F 354 1301 9 653 13 96.30
297 1301 54 F 299 1362 147 548 12 95.96
310 975 162 F 313 1301 9 575 12 96.13
345 404 295 F 349 1301 9 614 20 94.20
295 376 132 F 295 1402 3 534 14 95.25
184 1277 151 F 184 1402 3 312 14 92.39
475 404 165 F 476 1500 8 779 43 90.95
425 404 215 F 423 819 78 748 25 94.09
296 404 337 F 299 1362 147 543 13 95.61
345 404 295 F 349 1301 9 614 20 94.20
389 404 215 F 392 975 80 717 16 95.89
391 318 13 F 406 1693 142 537 65 83.38
438 905 0 F 451 1693 83 677 53 87.90
453 460 27 F 452 1351 0 793 28 93.81
405 336 36 F 419 1703 0 704 30 92.59
139 545 1 F 138 1453 139 241 9 93.48
310 654 103 F 306 807 164 580 9 97.06
461 654 0 F 461 1212 120 758 41 91.11
366 197 112 F 359 385 0 641 21 94.15
335 197 126 F 336 665 0 567 26 92.24
263 1646 2 F 263 1862 3 486 10 96.20
339 1820 0 F 340 1909 0 599 20 94.10
341 319 2 F 336 626 202 581 24 92.86
250 1021 0 F 250 1051 242 468 8 96.80
309 1649 13 F 309 1931 0 546 18 94.17
309 1708 8 F 305 1931 0 490 30 90.16
222 1736 0 F 223 1931 7 377 17 92.34
369 536 109 F 368 965 0 685 13 96.47
222 600 54 F 218 1251 0 332 27 87.61
309 1681 0 F 308 1808 0 541 19 93.83
458 1745 0 F 455 1767 0 801 28 93.85
433 1745 0 F 427 1764 1 748 28 93.44
427 1764 1 F 432 1767 0 775 21 95.08
403 1764 7 F 417 1896 0 660 40 90.07
405 1745 6 F 413 1896 0 662 39 90.37
405 1767 6 F 413 1896 0 674 36 91.11
415 223 2 F 414 271 2 793 9 97.83
361 497 81 F 358 1544 2 699 5 98.60
258 1544 15 F 258 1551 0 496 5 98.06
224 1782 39 F 224 1827 0 404 11 95.09
231 779 30 F 227 783 30 322 34 85.02
255 455 0 F 254 1260 213 481 7 97.24
376 460 93 F 376 1936 2 728 6 98.40
488 474 47 F 483 912 0 919 13 97.31
441 658 156 F 447 912 36 844 11 97.51
467 826 14 F 463 912 0 854 19 95.90
233 974 48 F 232 1310 195 425 10 95.69
104 454 113 F 103 579 0 115 23 77.67
188 579 3 F 192 1456 73 300 20 89.36
313 483 67 F 310 579 0 539 21 93.23
330 579 0 F 331 902 92 585 19 94.24
330 579 0 F 331 1151 125 585 19 94.24
330 579 0 F 334 1230 179 588 19 94.24
329 451 105 F 328 579 0 581 19 94.21
328 579 0 F 329 736 181 581 19 94.21
330 579 0 F 331 1100 112 581 20 93.94
348 579 0 F 352 1143 75 608 23 93.39
223 579 0 F 223 1049 126 334 28 87.44
220 474 173 F 218 579 0 326 28 87.16
219 543 114 F 218 579 0 329 27 87.61
218 579 0 F 220 912 121 330 27 87.61
211 579 7 F 213 761 4 324 25 88.15
218 579 0 F 219 826 140 329 27 87.61
218 579 0 F 220 798 66 318 30 86.24
218 579 0 F 217 658 238 319 29 86.64
211 579 7 F 211 713 82 326 24 88.63
211 579 7 F 210 1120 87 333 22 89.52
330 579 0 F 331 846 287 577 21 93.64
347 579 1 F 350 1365 43 605 23 93.37
208 579 0 F 206 849 54 282 33 83.98
218 579 0 F 219 1327 95 317 30 86.24
324 782 52 F 327 1270 4 579 18 94.44
366 197 112 F 359 385 0 641 21 94.15
360 369 21 F 360 1409 0 640 20 94.44
356 989 50 F 347 1350 1 591 28 91.93
378 242 0 F 379 294 0 729 7 98.15
300 1910 0 F 299 1926 25 543 14 95.32
132 1 0 F 132 4 7 196 17 87.12
123 1 9 F 123 47 0 190 14 88.62
287 1170 0 F 283 1347 84 466 26 90.81
31 125 26 F 30 632 168 49 3 90.00
409 1097 23 F 417 1806 1 686 35 91.44
268 497 0 F 264 1550 75 444 22 91.67
186 1544 0 F 186 1550 153 352 5 97.31
171 1550 168 F 171 1551 0 318 6 96.49
336 1546 28 F 338 1550 1 630 11 96.73
159 1549 0 F 159 1550 177 290 7 95.60
336 1547 12 F 338 1550 1 622 13 96.13
455 3 155 F 453 6 156 844 16 96.47
610 3 0 F 607 39 72 1145 18 97.03
112 3 510 F 110 5 546 158 16 85.45
112 3 510 F 110 16 664 154 17 84.55
309 1681 0 F 308 1808 0 541 19 93.83
458 1745 0 F 455 1767 0 801 28 93.85
449 1745 9 F 440 1882 0 773 27 93.86
446 1767 9 F 440 1882 0 806 20 95.45
433 1745 0 F 427 1764 1 748 28 93.44
427 1764 1 F 432 1767 0 775 21 95.08
404 1764 10 F 403 1882 0 755 13 96.77
405 1745 6 F 413 1896 0 662 39 90.37
405 1767 6 F 413 1896 0 674 36 91.11
399 1882 0 F 414 1896 3 669 36 90.98
361 497 81 F 358 1544 2 699 5 98.60
110 1544 250 F 110 1549 226 208 3 97.27
376 460 93 F 376 1936 2 728 6 98.40
374 1351 67 F 376 1936 2 678 18 95.19
231 1859 0 F 231 1936 147 442 5 97.84
321 738 178 F 321 739 58 602 10 96.88
377 739 2 F 383 1384 8 592 42 88.86
328 385 14 F 335 665 1 567 24 92.68
335 197 126 F 336 665 0 567 26 92.24
299 40 156 F 299 747 69 578 5 98.33
332 1536 0 F 332 1630 0 652 3 99.10
174 1564 0 F 174 1847 123 312 9 94.83
282 591 0 F 283 1758 7 461 26 90.78
382 1121 56 F 384 1512 11 674 23 93.98
389 848 138 F 404 1658 0 637 39 89.97
355 35 184 F 351 72 196 678 7 98.01
339 652 71 F 339 825 141 638 10 97.05
338 432 80 F 339 652 71 645 8 97.63
333 492 43 F 335 652 71 636 8 97.60
318 652 71 F 315 1469 139 593 10 96.83
336 652 71 F 336 1874 56 600 18 94.64
378 473 13 F 377 766 51 719 9 97.61
228 473 13 F 226 994 85 382 18 92.04
466 819 53 F 474 1500 28 844 24 94.85
260 497 95 F 258 1551 0 494 6 97.67
211 936 0 F 215 937 160 370 14 93.36
260 497 95 F 258 1551 0 494 6 97.67
258 1544 15 F 258 1551 0 496 5 98.06
379 379 0 F 398 1785 85 581 48 87.34
302 317 66 F 297 1128 0 515 21 92.93
334 5 0 F 334 39 34 632 9 97.31
213 7 0 F 213 39 34 406 5 97.65
276 4 388 F 272 39 0 428 30 88.97
425 489 0 F 429 1339 12 790 16 96.24
327 33 99 F 327 38 665 614 10 96.94
168 719 268 F 168 1199 159 320 4 97.62
376 460 93 F 376 1936 2 728 6 98.40
362 662 80 F 367 1193 8 569 40 88.95
376 492 0 F 378 825 98 726 7 98.14
422 825 37 F 429 1469 25 719 33 92.18
391 825 86 F 390 1874 2 705 19 95.13
348 1325 136 F 350 1621 0 666 8 97.70
360 369 21 F 360 1409 0 640 20 94.44
393 474 0 F 382 736 18 639 34 91.10
452 736 58 F 454 1151 0 866 10 97.79
189 103 0 F 189 107 0 366 3 98.41
409 1097 23 F 417 1806 1 686 35 91.44
309 1649 13 F 309 1931 0 546 18 94.17
309 1708 8 F 305 1931 0 490 30 90.16
222 1736 0 F 223 1931 7 377 17 92.34
409 1097 23 F 417 1806 1 686 35 91.44
310 654 103 F 306 807 164 580 9 97.06
268 497 0 F 264 1550 75 444 22 91.67
186 1544 0 F 186 1550 153 352 5 97.31
171 1550 168 F 171 1551 0 318 6 96.49
336 1546 28 F 338 1550 1 630 11 96.73
336 1547 12 F 338 1550 1 622 13 96.13
159 1549 0 F 159 1550 177 290 7 95.60
217 1869 0 F 216 1943 47 245 47 78.24
151 42 147 F 146 49 398 261 9 93.84
268 497 0 F 264 1547 84 460 18 93.18
186 1544 0 F 186 1547 162 364 2 98.92
171 1547 177 F 171 1551 0 334 2 98.83
349 1546 15 F 348 1547 0 673 6 98.28
160 1547 186 F 160 1549 0 300 5 96.88
336 1547 12 F 338 1550 1 622 13 96.13
90 1608 30 F 89 1802 15 131 12 86.52
90 1608 30 F 89 1877 12 131 12 86.52
75 264 513 F 77 300 265 132 5 93.33
23 1372 333 F 23 1372 341 46 0 100.00
23 597 198 F 23 1372 341 46 0 100.00
23 597 206 F 23 1372 333 46 0 100.00
23 597 198 F 23 597 206 46 0 100.00
291 1294 30 F 299 1786 23 498 23 92.10
224 1782 39 F 224 1827 0 404 11 95.09
381 309 0 F 374 804 82 691 16 95.72
265 1705 0 F 264 1709 0 481 12 95.45
258 895 170 F 263 1405 10 449 18 93.02
474 1788 0 F 474 1850 9 836 28 94.09
321 738 178 F 321 739 58 602 10 96.88
223 1649 20 F 222 1736 0 409 9 95.95
223 1708 15 F 222 1736 0 401 11 95.05
222 1736 0 F 223 1931 7 377 17 92.34
192 354 0 F 173 1077 34 217 37 78.61
331 18 0 F 337 46 194 536 33 90.03
384 738 115 F 391 1384 0 671 26 93.23
299 1871 0 F 296 1892 0 515 20 93.24
319 131 0 F 319 158 0 630 2 99.37
186 1544 0 F 186 1546 178 372 0 100.00
186 1544 0 F 186 1550 153 352 5 97.31
186 1544 0 F 186 1547 162 364 2 98.92
423 449 0 F 421 868 143 788 14 96.67
411 1696 0 F 412 1781 23 691 33 91.97
293 483 49 F 297 1196 9 514 19 93.52
281 630 77 F 287 1196 19 488 20 92.88
299 380 46 F 306 1196 0 513 23 92.31
299 902 66 F 305 1196 1 516 22 92.64
299 1151 99 F 305 1196 1 516 22 92.64
306 1196 0 F 303 1230 152 525 21 93.07
301 451 77 F 306 1196 0 519 22 92.69
299 736 155 F 305 1196 1 516 22 92.64
301 1100 84 F 306 1196 0 511 24 92.03
304 1143 47 F 306 1196 0 510 25 91.78
240 1049 109 F 246 1196 11 374 28 88.33
172 1189 0 F 176 1196 20 272 19 88.95
290 605 35 F 295 1196 11 485 25 91.38
238 988 101 F 246 1196 11 368 29 87.82
248 1196 9 F 241 1328 50 353 34 85.89
266 641 0 F 272 1196 34 454 21 92.11
215 474 178 F 220 1196 32 359 19 91.16
214 543 119 F 220 1196 32 362 18 91.59
220 1196 32 F 212 1297 116 352 20 90.57
215 912 126 F 220 1196 32 363 18 91.63
215 761 2 F 220 1196 32 359 19 91.16
214 826 145 F 220 1196 32 358 19 91.12
215 798 71 F 220 1196 32 351 21 90.23
188 658 267 F 194 1196 58 326 14 92.55
348 1325 136 F 350 1621 0 666 8 97.70
231 460 238 F 231 1859 0 450 3 98.70
231 1351 210 F 231 1859 0 450 3 98.70
249 541 0 F 252 1006 81 429 18 92.77
274 1415 148 F 273 1724 0 483 16 94.14
379 1784 7 F 381 1799 0 656 26 93.14
292 483 0 F 285 1328 6 437 35 87.72
290 630 19 F 291 1328 0 405 44 84.83
286 380 10 F 289 1328 2 447 32 88.81
290 902 26 F 289 1328 2 451 32 88.93
290 1151 59 F 289 1328 2 455 31 89.27
293 1230 113 F 291 1328 0 464 30 89.69
282 451 47 F 280 1328 11 442 30 89.29
290 736 115 F 291 1328 0 457 31 89.31
293 1100 43 F 290 1328 1 419 41 85.86
222 1143 80 F 221 1328 70 355 22 90.05
389 1049 59 F 390 1328 0 679 25 93.57
172 1189 0 F 171 1328 61 283 15 91.23
274 605 2 F 274 1328 17 392 39 85.77
377 988 49 F 377 1328 1 622 33 91.25
215 641 2 F 216 1328 75 339 23 89.30
358 474 106 F 359 1328 0 529 47 86.87
353 543 51 F 357 1328 2 510 50 85.84
263 1297 136 F 266 1328 93 413 29 88.97
354 912 58 F 357 1328 2 527 46 87.01
277 761 2 F 278 1328 71 443 28 89.89
345 826 76 F 347 1328 2 528 41 88.12
356 798 1 F 359 1328 0 499 54 84.83
349 658 177 F 357 1328 2 514 48 86.25
347 713 17 F 359 1328 0 462 61 82.42
352 1120 16 F 358 1328 0 462 62 82.39
289 846 222 F 291 1328 0 448 33 88.58
318 506 2 F 315 1328 75 561 18 94.29
223 1328 68 F 223 1365 45 362 21 90.58
393 451 41 F 389 736 121 762 5 98.71
393 451 41 F 389 846 227 754 7 98.20
161 1230 67 F 168 1892 239 209 30 81.37
202 935 48 F 198 1196 54 280 30 84.85
351 474 189 F 360 935 37 607 26 92.59
350 543 130 F 360 935 37 606 26 92.57
348 658 254 F 360 935 37 596 28 91.95
327 713 113 F 335 935 62 574 22 93.27
360 935 37 F 348 1297 127 600 27 92.24
346 912 137 F 355 935 37 597 26 92.49
324 935 48 F 314 1327 122 534 26 91.72
336 761 5 F 346 935 28 562 30 91.07
333 826 148 F 344 935 28 561 29 91.29
350 798 83 F 359 935 38 589 30 91.43
204 483 83 F 213 935 37 301 29 85.78
213 935 37 F 204 1365 59 297 30 85.29
192 630 112 F 202 935 48 278 29 84.90
203 380 88 F 213 935 37 300 29 85.71
203 846 303 F 213 935 37 296 30 85.22
203 902 108 F 213 935 37 304 28 86.21
213 935 37 F 203 1151 141 304 28 86.21
213 935 37 F 205 1230 196 302 29 85.85
203 451 121 F 213 935 37 304 28 86.21
203 736 197 F 213 935 37 304 28 86.21
213 935 37 F 203 1100 128 296 30 85.22
213 935 37 F 204 1143 93 297 30 85.29
171 506 58 F 174 935 88 261 21 87.72
225 935 37 F 215 1049 142 320 30 86.05
214 935 48 F 205 1328 94 291 32 84.39
349 935 48 F 340 1076 44 569 30 91.18
340 935 57 F 330 1120 114 566 26 92.12
186 935 37 F 178 1456 87 260 26 85.39
192 481 0 F 193 935 57 257 32 83.33
158 935 37 F 149 1189 23 227 20 86.58
119 610 52 F 120 935 130 171 17 85.71
202 641 10 F 213 935 37 275 35 82.67
121 935 129 F 120 1289 12 185 14 88.33
213 935 37 F 203 1360 104 280 34 83.25
204 605 67 F 212 935 38 288 32 84.31
85 454 220 F 86 935 137 147 6 92.94
174 935 88 F 170 988 177 260 21 87.65
86 935 137 F 85 1722 157 139 8 90.59
86 935 137 F 85 1837 149 139 8 90.59
379 1784 7 F 381 1799 0 656 26 93.14
359 11 153 F 356 29 155 639 19 94.66
344 691 71 F 347 814 135 643 12 96.51
265 1705 0 F 264 1709 0 481 12 95.45
65 733 238 F 65 1678 28 110 5 92.31
211 227 96 F 216 249 126 267 40 81.04
352 1828 6 F 353 1947 0 625 20 94.32
274 1415 148 F 273 1724 0 483 16 94.14
328 539 94 F 328 1080 0 584 18 94.51
110 1851 126 F 110 1950 151 196 6 94.55
108 1879 81 F 108 1950 151 196 5 95.37
307 624 179 F 327 1619 0 470 41 86.64
375 658 80 F 382 736 18 613 36 90.40
402 658 53 F 421 846 85 647 44 89.05
110 451 41 F 116 1892 291 150 19 82.73
355 35 184 F 351 72 196 678 7 98.01
329 1055 0 F 328 1542 146 605 13 96.04
432 701 5 F 422 715 7 690 41 90.28
271 679 62 F 273 759 0 488 14 94.83
30 1480 293 F 30 1480 328 44 4 86.67
365 950 12 F 366 1041 0 639 23 93.70
228 18 192 F 228 40 156 368 22 90.35
251 18 169 F 250 747 47 377 31 87.60
397 221 0 F 397 266 0 786 2 99.50
323 915 121 F 325 1070 53 600 12 96.28
168 719 268 F 168 1199 159 320 4 97.62
168 65 149 F 168 65 191 324 3 98.21
168 64 191 F 168 65 149 324 3 98.21
168 61 188 F 168 65 149 324 3 98.21
168 64 149 F 168 65 191 324 3 98.21
168 64 149 F 168 64 191 324 3 98.21
168 61 188 F 168 64 149 324 3 98.21
359 11 153 F 356 29 155 639 19 94.66
44 42 179 F 44 73 104 80 2 95.45
57 35 179 F 53 73 104 58 13 75.47
43 49 430 F 44 73 104 71 4 90.70
420 61 134 F 424 65 137 752 22 94.76
381 61 134 F 380 64 137 701 15 96.05
228 18 192 F 228 40 156 368 22 90.35
251 18 169 F 250 747 47 377 31 87.60
296 3 0 F 296 5 38 572 5 98.31
141 5 193 F 141 6 156 254 7 95.04
238 2 130 F 238 3 58 408 17 92.86
141 2 227 F 141 6 156 254 7 95.04
249 726 157 F 252 1393 2 457 11 95.58
185 886 89 F 185 1483 100 262 27 85.41
365 950 12 F 366 1041 0 639 23 93.70
311 474 82 F 311 902 0 538 21 93.25
347 474 46 F 344 1151 0 603 22 93.60
283 451 41 F 281 474 112 492 18 93.59
393 474 0 F 382 736 18 639 34 91.10
419 474 45 F 417 1049 0 684 38 90.89
393 474 0 F 392 846 114 625 40 89.80
291 380 0 F 296 474 97 507 20 93.13
376 474 57 F 374 988 0 586 41 89.04
298 902 13 F 297 912 44 511 21 92.93
182 454 34 F 182 902 13 296 17 90.66
146 902 49 F 145 1837 0 239 13 91.03
341 912 0 F 343 1151 1 580 26 92.38
213 454 3 F 212 1151 16 345 20 90.57
146 1151 82 F 145 1837 0 243 12 91.72
283 451 41 F 279 912 62 486 19 93.19
167 451 41 F 164 454 52 259 18 89.02
148 451 60 F 145 1837 0 237 14 90.34
341 736 59 F 341 912 0 582 25 92.67
212 454 4 F 211 736 73 343 20 90.52
145 736 139 F 145 1837 0 246 11 92.41
411 912 1 F 414 1049 3 653 43 89.54
115 454 101 F 114 1049 115 193 9 92.11
114 1049 115 F 115 1837 30 189 10 91.23
341 846 165 F 341 912 0 566 29 91.50
212 454 4 F 210 846 180 322 25 88.10
145 846 245 F 145 1837 0 242 12 91.72
291 380 0 F 294 912 47 501 21 92.78
175 380 0 F 179 454 37 278 19 89.14
144 380 31 F 145 1837 0 233 14 90.28
323 912 58 F 324 988 50 531 29 91.02
212 454 4 F 214 988 5 294 33 84.43
146 988 73 F 145 1837 0 235 14 90.34
254 474 139 F 256 483 31 450 15 94.09
256 483 31 F 253 912 88 441 17 93.28
137 454 79 F 140 483 31 217 15 89.05
140 483 31 F 137 1837 8 213 16 88.32
256 483 31 F 250 658 205 442 16 93.60
299 658 156 F 308 902 3 507 25 91.64
334 658 121 F 344 1151 0 558 30 91.02
275 451 49 F 269 658 186 484 15 94.42
375 658 80 F 382 736 18 613 36 90.40
395 658 131 F 405 1049 12 636 41 89.62
402 658 53 F 421 846 85 647 44 89.05
290 380 1 F 289 658 166 495 21 92.73
318 658 177 F 324 988 50 534 27 91.51
35 310 332 F 35 1363 337 70 0 100.00
343 1302 67 F 343 1433 4 606 20 94.17
331 18 0 F 337 46 194 536 33 90.03
438 905 0 F 451 1693 83 677 53 87.90
194 253 2 F 194 276 2 308 20 89.69
255 597 0 F 253 1372 137 440 17 93.28
149 413 221 F 148 1250 267 265 8 94.59
189 103 0 F 189 107 0 366 3 98.41
351 474 189 F 360 935 37 607 26 92.59
350 543 130 F 360 935 37 606 26 92.57
348 658 254 F 360 935 37 596 28 91.95
327 713 113 F 335 935 62 574 22 93.27
360 935 37 F 348 1297 127 600 27 92.24
346 912 137 F 355 935 37 597 26 92.49
324 935 48 F 314 1327 122 534 26 91.72
322 849 95 F 331 935 66 537 29 90.99
336 761 5 F 346 935 28 562 30 91.07
333 826 148 F 344 935 28 561 29 91.29
349 935 48 F 340 1076 44 569 30 91.18
340 935 57 F 330 1120 114 566 26 92.12
346 826 13 F 344 1151 0 602 22 93.60
423 902 0 F 422 1151 34 809 9 97.87
360 1664 0 F 362 1892 3 622 25 93.06
94 912 17 F 97 1664 241 135 14 85.11
277 1649 5 F 278 1708 0 511 11 96.03
50 1069 68 F 50 1083 145 84 4 92.00
274 1039 0 F 274 1435 147 524 6 97.81
360 1664 0 F 362 1892 3 622 25 93.06
354 1301 9 F 352 1500 137 650 14 96.02
351 819 155 F 354 1301 9 653 13 96.30
310 975 162 F 313 1301 9 575 12 96.13
345 404 295 F 349 1301 9 614 20 94.20
305 1066 1 F 311 1600 69 444 43 85.90
323 915 121 F 325 1070 53 600 12 96.28
602 5 96 F 601 16 214 1099 26 95.67
503 2 130 F 522 5 96 845 45 91.05
216 522 234 F 216 1134 194 424 2 99.07
131 1777 92 F 131 1868 104 210 13 90.08
359 11 153 F 356 29 155 639 19 94.66
330 1939 0 F 330 1940 10 568 23 93.03
291 1294 30 F 299 1786 23 498 23 92.10
83 454 220 F 83 988 223 162 1 98.80
85 454 220 F 84 1456 181 157 3 96.43
85 454 220 F 85 1196 139 162 2 97.65
85 454 220 F 85 474 281 162 2 97.65
85 454 220 F 85 543 221 162 2 97.65
85 454 220 F 85 658 343 162 2 97.65
85 454 220 F 85 713 181 162 2 97.65
85 454 220 F 85 1297 216 162 2 97.65
85 454 220 F 85 912 229 162 2 97.65
85 454 220 F 85 1327 202 162 2 97.65
85 454 220 F 85 761 105 162 2 97.65
85 454 220 F 85 826 247 162 2 97.65
85 454 220 F 85 483 175 162 2 97.65
85 454 220 F 85 1365 151 162 2 97.65
85 454 220 F 85 630 192 162 2 97.65
85 380 179 F 85 454 220 162 2 97.65
85 454 220 F 85 902 199 162 2 97.65
85 454 220 F 85 1151 232 162 2 97.65
85 454 220 F 85 1230 289 162 2 97.65
85 451 212 F 85 454 220 162 2 97.65
85 454 220 F 85 736 288 162 2 97.65
85 454 220 F 85 1100 219 162 2 97.65
85 454 220 F 85 1143 185 162 2 97.65
83 454 220 F 83 506 105 158 2 97.59
83 454 220 F 83 1049 233 158 2 97.59
85 454 220 F 84 1120 186 157 3 96.43
85 454 220 F 85 481 80 158 3 96.47
57 454 220 F 57 1189 115 110 1 98.25
85 454 220 F 85 605 159 158 3 96.47
85 454 220 F 84 579 107 153 4 95.24
85 454 220 F 85 642 68 158 3 96.47
85 454 220 F 86 798 173 159 3 96.47
85 454 220 F 86 1198 101 143 7 91.76
369 724 42 F 407 1826 28 520 62 83.20
474 1788 0 F 474 1850 9 836 28 94.09
249 541 0 F 252 1006 81 429 18 92.77
306 877 193 F 305 1514 2 547 16 94.75
291 1268 211 F 290 1514 0 517 16 94.48
284 1514 0 F 292 1747 113 452 31 89.08
300 1910 0 F 299 1926 25 543 14 95.32
295 376 132 F 295 1402 3 534 14 95.25
184 1277 151 F 184 1402 3 312 14 92.39
337 674 12 F 339 1281 47 600 19 94.36
72 126 102 F 72 530 148 140 1 98.61
72 126 102 F 72 1343 156 140 1 98.61
68 126 102 F 68 1431 261 92 11 83.82
76 126 97 F 76 1304 165 108 11 85.53
367 530 53 F 365 1343 63 688 11 96.99
360 544 0 F 358 1343 70 658 15 95.81
363 477 0 F 360 1052 64 659 16 95.56
290 1147 13 F 293 1331 123 503 20 93.10
194 253 2 F 194 276 2 308 20 89.69
404 549 32 F 412 661 104 712 26 93.56
297 1024 75 F 298 1744 100 343 63 78.79
189 413 38 F 189 1250 74 286 23 87.83
324 428 0 F 320 1441 29 564 20 93.75
198 78 563 F 199 80 592 305 23 88.38
199 80 592 F 198 1488 346 305 23 88.38
404 1764 10 F 403 1882 0 755 13 96.77
427 1764 1 F 432 1767 0 775 21 95.08
433 1745 0 F 427 1764 1 748 28 93.44
399 1882 0 F 414 1896 3 669 36 90.98
405 1767 6 F 413 1896 0 674 36 91.11
405 1745 6 F 413 1896 0 662 39 90.37
403 1764 7 F 417 1896 0 660 40 90.07
256 310 69 F 255 1363 75 483 7 97.25
84 310 149 F 84 1363 114 152 4 95.24
84 1363 114 F 84 1363 154 140 7 91.67
384 738 115 F 391 1384 0 671 26 93.23
80 470 274 F 80 991 38 136 6 92.50
195 991 38 F 196 1013 198 343 11 94.36
380 78 86 F 375 80 149 635 30 92.00
268 62 300 F 271 555 0 407 33 87.69
222 600 54 F 218 1251 0 332 27 87.61
399 815 46 F 415 1699 47 678 33 91.73
213 5 0 F 213 7 0 426 0 100.00
300 761 41 F 299 849 95 563 9 96.99
298 826 183 F 297 849 95 559 9 96.97
323 474 217 F 322 849 95 605 10 96.89
323 543 157 F 322 849 95 605 10 96.89
322 658 280 F 322 849 95 600 11 96.58
323 713 117 F 322 849 95 605 10 96.89
322 849 95 F 322 1297 153 596 12 96.27
317 849 95 F 318 912 165 595 10 96.85
297 849 95 F 298 1327 138 547 12 95.96
322 849 95 F 323 1076 61 577 17 94.72
324 798 109 F 322 849 95 594 13 95.96
322 849 95 F 322 1120 122 588 14 95.65
322 849 95 F 331 935 66 537 29 90.99
311 755 0 F 312 1412 113 535 22 92.93
255 597 0 F 253 1372 137 440 17 93.28
86 17 1 F 86 55 0 172 0 100.00
363 477 0 F 360 1052 64 659 16 95.56
391 470 80 F 395 1013 0 690 24 93.86
369 536 109 F 368 965 0 685 13 96.47
368 965 0 F 366 1082 58 662 18 95.08
360 530 60 F 360 544 0 672 12 96.67
309 5 337 F 309 39 371 510 27 91.26
309 16 455 F 309 39 371 498 30 90.29
197 2 371 F 202 39 371 299 25 87.31
59 35 147 F 59 49 398 118 0 100.00
151 42 147 F 146 49 398 261 9 93.84
336 1544 24 F 336 1549 0 588 18 94.64
160 1546 202 F 160 1549 0 308 3 98.12
159 1549 0 F 159 1550 177 290 7 95.60
249 1549 0 F 249 1551 9 422 16 93.57
160 1547 186 F 160 1549 0 300 5 96.88
236 1153 0 F 228 1161 110 348 29 87.28
379 1784 7 F 381 1799 0 656 26 93.14
316 902 0 F 313 1049 36 533 24 92.33
349 1049 0 F 349 1151 0 590 27 92.26
288 451 41 F 284 1049 65 496 19 93.31
347 736 58 F 349 1049 0 596 25 92.80
348 846 163 F 349 1049 0 569 32 90.80
296 380 0 F 298 1049 51 514 20 93.24
377 988 49 F 376 1049 60 693 15 96.01
261 483 31 F 258 1049 91 455 16 93.80
318 506 2 F 315 1328 75 561 18 94.29
389 1049 59 F 390 1328 0 679 25 93.57
248 1196 9 F 241 1328 50 353 34 85.89
358 474 106 F 359 1328 0 529 47 86.87
353 543 51 F 357 1328 2 510 50 85.84
349 658 177 F 357 1328 2 514 48 86.25
347 713 17 F 359 1328 0 462 61 82.42
263 1297 136 F 266 1328 93 413 29 88.97
354 912 58 F 357 1328 2 527 46 87.01
314 1327 71 F 318 1328 41 460 43 86.31
277 761 2 F 278 1328 71 443 28 89.89
345 826 76 F 347 1328 2 528 41 88.12
292 483 0 F 285 1328 6 437 35 87.72
223 1328 68 F 223 1365 45 362 21 90.58
290 630 19 F 291 1328 0 405 44 84.83
286 380 10 F 289 1328 2 447 32 88.81
289 846 222 F 291 1328 0 448 33 88.58
290 902 26 F 289 1328 2 451 32 88.93
290 1151 59 F 289 1328 2 455 31 89.27
293 1230 113 F 291 1328 0 464 30 89.69
282 451 47 F 280 1328 11 442 30 89.29
290 736 115 F 291 1328 0 457 31 89.31
293 1100 43 F 290 1328 1 419 41 85.86
222 1143 80 F 221 1328 70 355 22 90.05
352 1076 32 F 348 1120 96 624 19 94.54
206 1076 31 F 210 1196 42 316 25 87.86
352 474 188 F 353 1076 31 633 18 94.89
351 543 129 F 353 1076 31 636 17 95.16
349 658 253 F 353 1076 31 626 19 94.56
350 713 90 F 353 1076 31 631 18 94.86
344 1076 40 F 342 1297 133 622 16 95.32
347 912 136 F 348 1076 31 631 16 95.39
328 1076 31 F 326 1327 110 578 19 94.17
329 761 12 F 330 1076 31 599 15 95.44
326 826 155 F 328 1076 31 590 16 95.09
205 483 82 F 206 1076 31 319 23 88.78
206 1076 31 F 205 1365 58 315 24 88.29
205 630 99 F 206 1076 31 315 24 88.29
204 380 87 F 206 1076 31 318 23 88.73
204 846 302 F 206 1076 31 314 24 88.24
204 902 107 F 206 1076 31 322 22 89.22
206 1076 31 F 204 1151 140 322 22 89.22
206 1076 31 F 206 1230 195 328 21 89.81
204 451 120 F 206 1076 31 322 22 89.22
204 736 196 F 206 1076 31 322 22 89.22
206 1076 31 F 204 1100 127 314 24 88.24
206 1076 31 F 205 1143 92 327 21 89.76
231 506 48 F 229 1076 70 352 27 88.21
266 1049 141 F 268 1076 31 402 33 87.59
352 1120 16 F 358 1328 0 462 62 82.39
268 1076 31 F 268 1328 81 396 35 86.94
181 1328 77 F 181 1456 82 298 16 91.16
179 1076 31 F 179 1456 86 286 18 89.94
197 481 0 F 188 1328 103 289 24 87.23
192 481 0 F 184 1076 53 272 26 85.87
172 1189 0 F 171 1328 61 283 15 91.23
151 1076 32 F 149 1189 23 236 16 89.26
91 610 53 F 90 1456 175 157 6 93.33
172 610 53 F 173 1196 133 317 7 95.93
168 474 225 F 171 610 0 227 28 83.33
168 543 165 F 171 610 0 227 28 83.33
118 610 53 F 118 658 337 188 12 89.83
120 610 51 F 121 713 172 193 12 90.00
171 610 0 F 167 1297 161 222 29 82.63
171 610 0 F 168 912 173 227 28 83.33
171 610 0 F 168 1327 146 227 28 83.33
171 610 0 F 168 761 49 227 28 83.33
171 610 0 F 168 826 191 227 28 83.33
212 483 168 F 210 610 53 394 7 96.67
242 610 53 F 243 1365 144 449 9 96.28
242 610 53 F 243 630 185 461 6 97.52
231 380 172 F 230 610 53 437 6 97.39
230 610 53 F 231 846 387 433 7 96.96
230 610 53 F 231 902 192 437 6 97.39
230 610 53 F 231 1151 225 437 6 97.39
230 610 53 F 231 1230 282 437 6 97.39
229 451 205 F 228 610 53 433 6 97.37
228 610 53 F 229 736 281 433 6 97.37
230 610 53 F 231 1100 212 429 8 96.52
242 610 53 F 243 1143 178 449 9 96.28
123 506 98 F 123 610 53 190 14 88.62
123 610 53 F 123 1049 226 190 14 88.62
171 610 0 F 167 1120 130 222 29 82.63
231 481 73 F 230 610 53 429 8 96.52
61 610 53 F 62 1189 108 111 3 95.08
123 610 53 F 123 1328 168 190 14 88.62
171 610 0 F 167 1076 70 210 32 80.84
215 641 2 F 216 1328 75 339 23 89.30
203 641 9 F 206 1076 31 301 27 86.70
230 610 53 F 231 641 93 413 12 94.78
134 1289 3 F 133 1328 158 203 16 87.97
128 1076 109 F 129 1289 3 205 13 89.84
231 610 50 F 232 1289 10 415 12 94.81
248 1360 32 F 249 1456 16 337 40 83.87
305 1196 1 F 300 1360 61 485 30 90.00
305 474 88 F 306 1360 1 487 31 89.84
299 543 34 F 306 1360 1 453 38 87.29
296 658 159 F 306 1360 1 462 35 88.18
269 713 24 F 278 1360 29 371 44 83.64
259 1297 69 F 265 1360 42 400 31 88.03
302 912 39 F 306 1360 1 480 32 89.40
243 1327 71 F 246 1360 61 377 28 88.48
215 761 2 F 214 1360 93 369 15 92.99
303 826 56 F 307 1360 0 482 32 89.44
349 483 31 F 346 1360 53 631 16 95.38
334 1360 47 F 337 1365 0 599 18 94.61
374 630 38 F 375 1360 40 621 32 91.44
399 380 0 F 406 1360 9 705 25 93.73
410 846 204 F 414 1360 1 700 31 92.44
404 902 15 F 407 1360 8 711 25 93.81
412 1151 40 F 414 1360 1 714 28 93.20
414 1230 95 F 414 1360 1 704 31 92.51
384 451 48 F 383 1360 32 679 22 94.26
411 736 97 F 414 1360 1 721 26 93.67
413 1100 26 F 414 1360 1 663 41 90.07
405 1143 0 F 405 1360 10 638 43 89.38
221 506 0 F 217 1360 95 334 26 88.02
307 1049 42 F 311 1360 1 490 32 89.58
290 1120 7 F 297 1360 10 399 47 83.79
300 481 0 F 292 1360 123 512 20 93.15
172 1189 0 F 171 1360 81 283 15 91.23
320 641 0 F 320 1360 95 556 21 93.44
237 1289 3 F 237 1360 178 434 10 95.78
291 1328 0 F 293 1360 19 416 42 85.57
206 1076 31 F 204 1360 103 302 27 86.76
226 610 53 F 227 1360 188 413 10 95.58
274 605 2 F 274 1328 17 392 39 85.77
203 605 68 F 202 1076 35 301 26 87.13
231 605 152 F 230 610 53 429 8 96.52
379 605 0 F 381 1360 34 632 32 91.56
83 454 220 F 83 1328 175 154 3 96.39
377 988 49 F 377 1328 1 622 33 91.25
83 1328 175 F 83 1722 157 146 5 93.98
85 454 220 F 84 1076 126 153 4 95.24
243 988 131 F 246 1076 31 357 33 86.42
84 1076 126 F 85 1722 157 145 6 92.86
85 454 220 F 84 610 60 145 6 92.86
123 610 53 F 123 988 216 186 15 87.80
84 610 60 F 85 1722 157 137 8 90.48
85 454 220 F 85 1360 195 154 4 95.29
276 988 63 F 278 1360 34 450 26 90.58
85 1360 195 F 85 1722 157 146 6 92.94
219 579 4 F 221 1328 70 308 33 84.93
203 579 15 F 205 1076 32 312 24 88.18
244 579 98 F 244 610 51 456 8 96.72
326 579 0 F 327 1360 88 549 26 92.02
324 428 0 F 320 1441 29 564 20 93.75
317 428 7 F 312 1513 64 573 14 95.51
224 1196 0 F 222 1456 43 354 23 89.64
418 406 24 F 415 542 15 733 25 93.98
348 406 94 F 355 1056 58 615 22 93.68
367 530 53 F 365 1343 63 688 11 96.99
360 544 0 F 358 1343 70 658 15 95.81
296 960 29 F 303 970 135 543 14 95.27
391 1787 9 F 389 1810 2 680 25 93.57
254 474 139 F 256 483 31 450 15 94.09
261 474 132 F 263 1365 0 448 19 92.72
307 474 86 F 303 630 1 446 41 86.47
291 380 0 F 296 474 97 507 20 93.13
311 474 82 F 311 902 0 538 21 93.25
347 474 46 F 344 1151 0 603 22 93.60
392 474 1 F 399 1230 2 615 44 88.78
283 451 41 F 281 474 112 492 18 93.59
393 474 0 F 382 736 18 639 34 91.10
328 474 65 F 328 1100 3 508 37 88.72
256 483 31 F 253 543 80 437 18 92.89
257 543 76 F 261 1365 2 446 18 93.00
301 543 32 F 303 630 1 444 40 86.71
290 380 1 F 292 543 41 494 22 92.41
304 543 29 F 311 902 0 499 29 90.46
333 543 0 F 342 1151 2 555 30 90.99
320 543 13 F 331 1230 70 515 34 89.38
275 451 49 F 272 543 61 471 19 93.01
333 543 0 F 340 736 60 557 29 91.29
282 543 51 F 287 1100 44 457 28 90.07
189 483 98 F 188 658 267 345 8 95.74
256 658 199 F 263 1365 0 439 20 92.19
303 630 1 F 298 658 157 433 42 85.91
290 380 1 F 289 658 166 495 21 92.73
299 658 156 F 308 902 3 507 25 91.64
334 658 121 F 344 1151 0 558 30 91.02
317 658 138 F 329 1230 72 530 29 90.85
275 451 49 F 269 658 186 484 15 94.42
375 658 80 F 382 736 18 613 36 90.40
278 658 177 F 286 1100 45 456 27 90.29
256 483 31 F 249 713 44 389 29 88.35
230 713 63 F 232 1365 31 374 22 90.43
227 630 77 F 224 713 69 359 23 89.73
289 380 2 F 283 713 10 416 39 86.22
256 713 37 F 261 902 50 401 29 88.67
291 713 2 F 302 1151 42 429 41 85.91
284 713 9 F 295 1230 106 423 39 86.27
276 451 48 F 266 713 27 410 33 87.59
269 713 24 F 276 736 124 409 34 87.36
243 713 50 F 247 1100 84 390 25 89.71
234 483 53 F 229 1297 99 399 16 93.01
252 1297 76 F 261 1365 2 413 25 90.08
193 630 111 F 192 1297 136 333 13 93.23
282 380 9 F 277 1297 51 455 26 90.61
257 902 54 F 252 1297 76 429 20 92.06
305 1151 39 F 295 1297 33 456 36 87.80
286 1230 115 F 276 1297 52 446 29 89.49
246 451 78 F 241 1297 87 415 18 92.53
304 736 96 F 295 1297 33 459 35 88.14
237 1100 94 F 232 1297 96 397 18 92.24
256 483 31 F 253 912 88 441 17 93.28
259 912 82 F 263 1365 0 438 21 91.89
303 630 1 F 304 912 37 451 39 87.13
291 380 0 F 294 912 47 501 21 92.78
298 902 13 F 297 912 44 511 21 92.93
341 912 0 F 343 1151 1 580 26 92.38
324 912 17 F 329 1230 72 537 29 91.05
283 451 41 F 279 912 62 486 19 93.19
341 736 59 F 341 912 0 582 25 92.67
283 912 58 F 287 1100 44 454 29 89.75
234 483 53 F 231 1327 83 393 18 92.21
230 1327 84 F 232 1365 31 374 22 90.43
240 630 64 F 237 1327 77 373 26 89.03
285 380 6 F 284 1327 30 429 35 87.68
245 902 66 F 243 1327 71 408 20 91.77
245 1151 99 F 243 1327 71 408 20 91.77
327 1230 74 F 314 1327 0 469 43 86.31
247 451 77 F 244 1327 70 407 21 91.39
245 736 155 F 243 1327 71 408 20 91.77
237 1100 94 F 234 1327 80 387 21 91.03
215 483 72 F 215 761 2 390 10 95.35
215 761 2 F 215 1365 48 382 12 94.42
215 630 89 F 215 761 2 362 17 92.09
214 380 77 F 215 761 2 389 10 95.33
215 761 2 F 214 902 97 393 9 95.79
215 761 2 F 214 1151 130 393 9 95.79
215 761 2 F 217 1230 184 384 12 94.42
214 451 110 F 215 761 2 393 9 95.79
214 736 186 F 215 761 2 393 9 95.79
215 761 2 F 214 1100 117 381 12 94.39
256 483 31 F 253 826 106 449 15 94.07
257 826 102 F 261 1365 2 438 20 92.22
304 630 0 F 306 826 53 442 42 86.18
291 380 0 F 293 826 66 520 16 94.50
310 826 49 F 311 902 0 541 20 93.55
346 826 13 F 344 1151 0 602 22 93.60
328 826 31 F 331 1230 70 555 26 92.07
283 451 41 F 279 826 80 494 17 93.91
304 736 96 F 304 826 55 552 14 95.39
283 826 76 F 287 1100 44 462 27 90.46
298 474 95 F 297 1143 0 459 34 88.55
289 543 44 F 293 1143 4 454 32 88.93
286 658 169 F 293 1143 4 435 36 87.41
183 713 110 F 184 1143 113 327 10 94.54
293 1143 4 F 282 1297 46 403 42 85.11
296 912 45 F 297 1143 0 453 35 88.18
250 1143 47 F 244 1327 70 382 28 88.52
215 761 2 F 216 1143 81 379 13 93.95
295 826 64 F 297 1143 0 452 35 88.14
293 483 49 F 297 1196 9 514 19 93.52
274 1196 32 F 269 1365 48 491 13 95.17
281 630 77 F 287 1196 19 488 20 92.88
299 380 46 F 306 1196 0 513 23 92.31
299 902 66 F 305 1196 1 516 22 92.64
299 1151 99 F 305 1196 1 516 22 92.64
306 1196 0 F 303 1230 152 525 21 93.07
301 451 77 F 306 1196 0 519 22 92.69
299 736 155 F 305 1196 1 516 22 92.64
301 1100 84 F 306 1196 0 511 24 92.03
304 1143 47 F 306 1196 0 510 25 91.78
215 474 178 F 220 1196 32 359 19 91.16
214 543 119 F 220 1196 32 362 18 91.59
188 658 267 F 194 1196 58 326 14 92.55
211 713 82 F 218 1196 34 349 20 90.52
220 1196 32 F 212 1297 116 352 20 90.57
215 912 126 F 220 1196 32 363 18 91.63
220 1196 32 F 214 1327 100 350 21 90.19
215 761 2 F 220 1196 32 359 19 91.16
214 826 145 F 220 1196 32 358 19 91.12
221 506 0 F 223 1196 34 324 30 86.43
240 1049 109 F 246 1196 11 374 28 88.33
284 474 180 F 289 506 0 441 33 88.38
419 474 45 F 417 1049 0 684 38 90.89
289 506 0 F 283 543 121 436 34 87.99
404 543 0 F 414 1049 3 630 47 88.37
289 506 0 F 281 658 245 430 35 87.54
395 658 131 F 405 1049 12 636 41 89.62
253 506 36 F 251 713 113 392 28 88.84
362 713 2 F 373 1049 44 503 58 83.98
273 506 16 F 268 1297 131 413 32 88.06
402 1049 15 F 383 1297 16 553 58 84.86
289 506 0 F 284 912 128 437 34 88.03
411 912 1 F 414 1049 3 653 43 89.54
267 506 22 F 264 1327 121 407 31 88.26
318 1049 99 F 314 1327 71 488 36 88.54
279 506 0 F 275 761 4 434 30 89.09
277 761 2 F 276 1049 131 473 20 92.75
279 506 0 F 274 826 147 433 30 89.05
409 826 12 F 407 1049 0 664 38 90.66
210 1120 87 F 218 1196 34 348 20 90.48
238 483 49 F 233 1120 64 387 21 90.99
229 1120 68 F 232 1365 31 377 21 90.83
227 630 77 F 224 1120 73 359 23 89.73
291 380 0 F 288 1120 9 427 38 86.81
258 902 53 F 255 1120 42 409 26 89.80
297 1120 0 F 305 1151 39 446 39 86.87
290 1120 7 F 296 1230 105 442 36 87.59
277 451 47 F 271 1120 26 416 33 87.82
304 736 96 F 297 1120 0 445 39 86.87
251 1100 80 F 248 1120 49 379 28 88.71
183 1120 114 F 184 1143 113 327 10 94.54
288 506 0 F 281 1120 87 413 39 86.12
375 1049 41 F 368 1120 0 523 55 85.05
246 483 14 F 243 1456 22 361 32 86.83
234 1365 2 F 233 1456 32 343 31 86.70
239 630 38 F 242 1456 23 345 34 85.77
209 380 55 F 211 1456 54 344 19 90.91
247 902 37 F 249 1456 16 368 32 87.04
247 1151 70 F 250 1456 15 365 33 86.64
249 1230 125 F 250 1456 15 375 31 87.55
249 451 48 F 250 1456 15 367 33 86.75
246 736 127 F 250 1456 15 360 34 86.18
260 1100 44 F 259 1456 6 379 35 86.49
251 1143 19 F 249 1456 16 380 30 87.95
188 506 0 F 186 1456 77 294 20 89.25
245 1049 71 F 248 1456 15 357 34 86.12
266 474 100 F 265 1456 0 359 42 84.15
238 543 68 F 241 1456 24 367 28 88.24
235 658 193 F 241 1456 24 348 32 86.38
239 713 27 F 249 1456 16 380 27 88.70
169 1297 132 F 171 1456 94 300 10 94.08
257 912 57 F 260 1456 5 365 38 85.21
244 1327 43 F 249 1456 16 333 40 83.61
186 761 4 F 188 1456 77 326 12 93.55
263 826 69 F 265 1456 0 356 43 83.65
259 1120 11 F 265 1456 0 388 34 86.87
165 481 0 F 158 1456 107 259 16 89.87
246 481 0 F 243 1196 63 417 18 92.59
185 474 208 F 192 481 0 301 19 89.73
192 481 0 F 184 543 149 300 19 89.67
192 481 0 F 183 658 272 295 20 89.07
192 481 0 F 183 713 110 291 21 88.52
192 481 0 F 183 1297 145 291 21 88.52
192 481 0 F 184 912 157 300 19 89.67
192 481 0 F 184 1327 130 292 21 88.59
192 481 0 F 184 761 33 300 19 89.67
192 481 0 F 184 826 175 300 19 89.67
192 481 0 F 183 1120 114 291 21 88.52
172 1189 0 F 173 1456 65 265 20 88.37
172 1189 0 F 176 1196 20 272 19 88.95
171 474 167 F 172 1189 0 303 10 94.15
169 543 109 F 172 1189 0 301 10 94.08
168 658 232 F 172 1189 0 296 11 93.45
128 713 110 F 129 1189 43 237 5 96.09
172 1189 0 F 167 1297 106 291 12 92.81
171 912 115 F 172 1189 0 311 8 95.32
172 1189 0 F 170 1327 89 278 16 90.59
160 761 2 F 161 1189 11 285 9 94.38
170 826 134 F 172 1189 0 302 10 94.12
129 1120 114 F 129 1189 43 242 4 96.90
240 605 4 F 243 1456 22 339 36 85.00
290 605 35 F 295 1196 11 485 25 91.38
272 474 121 F 271 605 0 443 25 90.77
270 543 63 F 271 605 0 421 30 88.89
271 605 0 F 267 658 188 438 25 90.64
271 605 0 F 263 713 30 386 37 85.93
162 605 109 F 162 1297 166 284 10 93.83
271 605 0 F 270 912 71 437 26 90.37
246 605 25 F 243 1327 71 381 27 88.89
216 605 55 F 215 761 2 363 17 92.09
271 605 0 F 270 826 89 437 26 90.37
267 605 4 F 263 1120 34 386 36 86.31
239 988 67 F 241 1456 22 344 34 85.77
238 988 101 F 246 1196 11 368 29 87.82
376 474 57 F 374 988 0 586 41 89.04
322 543 51 F 324 988 50 514 33 89.75
318 658 177 F 324 988 50 534 27 91.51
304 713 29 F 312 988 62 436 45 85.20
304 988 70 F 299 1297 69 467 34 88.63
323 912 58 F 324 988 50 531 29 91.02
283 988 91 F 283 1327 71 446 30 89.40
255 761 2 F 253 988 121 428 20 92.09
323 826 76 F 324 988 50 531 29 91.02
346 988 28 F 337 1120 0 467 54 83.98
188 579 3 F 192 1456 73 300 20 89.36
268 579 4 F 276 1196 30 444 25 90.67
220 474 173 F 218 579 0 326 28 87.16
219 543 114 F 218 579 0 329 27 87.61
218 579 0 F 217 658 238 319 29 86.64
211 579 7 F 211 713 82 326 24 88.63
211 579 7 F 210 1297 118 317 26 87.62
218 579 0 F 220 912 121 330 27 87.61
218 579 0 F 219 1327 95 317 30 86.24
211 579 7 F 213 761 4 324 25 88.15
218 579 0 F 219 826 140 329 27 87.61
211 579 7 F 210 1120 87 333 22 89.52
153 642 0 F 155 1456 110 240 17 88.89
228 642 6 F 231 1196 75 395 16 92.98
178 474 215 F 177 642 3 279 18 89.83
181 543 152 F 180 642 0 281 19 89.44
180 642 0 F 180 658 275 276 20 88.89
177 642 3 F 178 713 115 275 19 89.27
180 642 0 F 180 1297 148 276 20 88.89
180 642 0 F 181 912 160 281 19 89.44
180 642 0 F 181 1327 133 273 21 88.33
180 642 0 F 181 761 36 281 19 89.44
180 642 0 F 181 826 178 281 19 89.44
180 642 0 F 180 1120 117 272 21 88.33
241 798 18 F 243 1456 22 340 36 85.06
215 798 71 F 220 1196 32 351 21 90.23
255 483 32 F 253 798 33 428 20 92.09
259 798 27 F 263 1365 0 422 25 90.35
284 630 20 F 283 798 3 399 42 85.16
283 380 8 F 286 798 0 453 29 89.75
286 798 0 F 287 902 24 461 28 90.21
286 798 0 F 287 1151 57 469 26 90.91
285 798 1 F 288 1230 113 453 30 89.47
254 451 70 F 253 798 33 435 18 92.89
286 736 114 F 286 798 0 472 25 91.26
253 798 33 F 255 1100 76 400 27 89.33
232 798 54 F 232 1143 65 376 22 90.52
289 506 0 F 284 798 73 425 37 86.97
357 798 0 F 359 1049 58 544 43 87.96
192 481 0 F 185 798 101 293 21 88.65
171 798 60 F 172 1189 0 291 13 92.40
271 605 0 F 270 798 16 401 35 87.04
292 798 33 F 289 988 84 473 27 90.66
218 579 0 F 220 798 66 318 30 86.24
180 642 0 F 182 798 104 278 20 88.89
185 1198 2 F 178 1456 87 259 26 85.39
263 1196 43 F 267 1198 2 422 27 89.73
204 474 189 F 212 1198 2 312 26 87.25
203 543 130 F 212 1198 2 315 25 87.68
201 658 254 F 212 1198 2 305 27 86.57
202 713 91 F 212 1198 2 302 28 86.14
212 1198 2 F 201 1297 127 301 28 86.07
204 912 137 F 212 1198 2 316 25 87.75
199 1198 15 F 193 1327 121 296 24 87.56
207 761 10 F 214 1198 0 313 27 86.96
206 826 153 F 214 1198 0 316 26 87.38
201 1120 96 F 212 1198 2 301 28 86.07
202 798 84 F 209 1198 5 307 26 87.13
186 935 37 F 178 1456 87 260 26 85.39
202 935 48 F 198 1196 54 280 30 84.85
202 935 48 F 198 1198 16 252 37 81.31
204 483 83 F 213 935 37 301 29 85.78
213 935 37 F 204 1365 59 297 30 85.29
192 630 112 F 202 935 48 278 29 84.90
203 380 88 F 213 935 37 300 29 85.71
203 902 108 F 213 935 37 304 28 86.21
213 935 37 F 203 1151 141 304 28 86.21
213 935 37 F 205 1230 196 302 29 85.85
203 451 121 F 213 935 37 304 28 86.21
203 736 197 F 213 935 37 304 28 86.21
213 935 37 F 203 1100 128 296 30 85.22
213 935 37 F 204 1143 93 297 30 85.29
171 506 58 F 174 935 88 261 21 87.72
225 935 37 F 215 1049 142 320 30 86.05
192 481 0 F 193 935 57 257 32 83.33
158 935 37 F 149 1189 23 227 20 86.58
204 605 67 F 212 935 38 288 32 84.31
174 935 88 F 170 988 177 260 21 87.65
192 579 26 F 202 935 48 246 37 80.73
161 642 0 F 171 935 60 228 26 83.85
399 815 46 F 415 1699 47 678 33 91.73
74 78 25 F 74 80 74 112 9 87.84
52 376 311 F 53 1694 343 65 10 80.77
46 1402 188 F 45 1694 351 63 7 84.44
44 376 258 F 46 376 317 62 7 84.09
44 376 258 F 46 1402 188 62 7 84.09
46 376 317 F 44 1277 277 62 7 84.09
44 1277 277 F 46 1402 188 62 7 84.09
46 376 317 F 44 1402 129 62 7 84.09
44 1402 129 F 46 1402 188 62 7 84.09
296 960 29 F 303 970 135 543 14 95.27
335 546 114 F 332 884 41 639 7 97.89
390 546 59 F 385 890 2 699 19 95.06
282 591 0 F 283 1758 7 461 26 90.78
354 1301 9 F 352 1500 137 650 14 96.02
351 819 155 F 354 1301 9 653 13 96.30
244 707 1 F 255 1623 143 359 35 85.66
253 461 0 F 259 1850 260 472 10 96.05
137 950 50 F 135 1850 252 168 26 80.74
127 461 0 F 126 950 61 169 21 83.33
309 1649 13 F 309 1931 0 546 18 94.17
309 1708 8 F 305 1931 0 490 30 90.16
152 719 114 F 156 1199 0 268 10 93.42
291 358 77 F 292 1678 0 523 15 94.85
446 1767 9 F 440 1882 0 806 20 95.45
427 1764 1 F 432 1767 0 775 21 95.08
461 654 0 F 461 1212 120 758 41 91.11
479 866 95 F 488 1212 73 759 52 89.14
306 807 164 F 306 1212 227 592 5 98.37
352 422 168 F 367 1126 0 611 27 92.33
276 1 294 F 271 16 0 515 8 97.05
71 719 170 F 71 1650 0 118 6 91.55
348 1325 136 F 350 1621 0 666 8 97.70
349 1554 0 F 347 1555 52 632 16 95.39
319 1548 0 F 318 1555 101 605 8 97.48
311 833 111 F 315 1146 29 526 25 91.96
249 541 0 F 252 1006 81 429 18 92.77
540 4 16 F 523 47 0 935 32 93.88
108 1879 81 F 108 1950 151 196 5 95.37
376 558 0 F 368 1254 134 668 19 94.84
176 1209 42 F 172 1349 164 200 37 78.49
171 306 41 F 176 1209 42 199 37 78.36
318 506 2 F 315 1328 75 561 18 94.29
389 1049 59 F 390 1328 0 679 25 93.57
318 574 96 F 320 1369 78 602 9 97.17
297 1552 0 F 293 1554 56 526 16 94.54
309 1548 7 F 314 1552 0 559 16 94.82
314 1552 0 F 308 1555 108 534 22 92.86
309 1548 7 F 314 1552 0 559 16 94.82
314 1552 0 F 308 1555 108 534 22 92.86
297 1552 0 F 293 1554 56 526 16 94.54
71 1543 267 F 71 1543 350 126 4 94.37
390 1449 38 F 392 1451 4 670 28 92.82
370 630 64 F 372 1365 21 658 21 94.32
368 380 35 F 373 1365 2 677 16 95.65
369 902 54 F 373 1365 2 690 13 96.48
371 1151 85 F 375 1365 0 694 13 96.50
372 1230 141 F 373 1365 2 677 17 95.43
372 451 62 F 373 1365 0 685 15 95.97
369 736 141 F 373 1365 0 690 13 96.48
349 1100 94 F 351 1365 24 648 13 96.28
349 483 31 F 349 1365 6 634 16 95.42
392 1143 35 F 391 1365 2 691 23 94.12
342 506 0 F 337 1049 133 635 11 96.74
218 483 74 F 221 506 0 355 21 90.37
221 506 0 F 218 630 91 331 27 87.61
217 380 79 F 221 506 0 354 21 90.32
221 506 0 F 217 902 99 358 20 90.78
221 506 0 F 217 1151 132 358 20 90.78
221 506 0 F 220 1230 186 357 21 90.45
217 451 112 F 221 506 0 358 20 90.78
221 506 0 F 217 736 188 358 20 90.78
221 506 0 F 217 1100 119 346 23 89.40
221 506 0 F 219 1143 83 344 24 89.04
262 1049 87 F 266 1365 2 452 19 92.75
221 506 0 F 218 1365 50 351 22 89.91
284 481 0 F 277 483 103 509 13 95.31
304 481 0 F 296 630 120 536 16 94.59
296 380 107 F 304 481 0 544 14 95.27
304 481 0 F 296 902 127 548 13 95.61
304 481 0 F 296 1151 160 548 13 95.61
304 481 0 F 296 1230 217 548 13 95.61
294 451 140 F 302 481 0 544 13 95.58
302 481 0 F 294 736 216 544 13 95.58
304 481 0 F 296 1100 147 540 15 94.93
304 481 0 F 296 1143 113 536 16 94.59
197 481 0 F 188 1049 161 301 21 88.83
304 481 0 F 297 1365 78 533 17 94.28
197 481 0 F 190 506 31 291 24 87.37
172 1189 0 F 172 1365 36 296 12 93.02
162 506 0 F 158 1189 14 256 16 89.87
137 481 0 F 129 1189 43 214 13 89.92
370 605 13 F 373 1365 2 639 26 92.97
221 506 0 F 219 605 57 336 26 88.13
304 481 0 F 298 605 85 538 16 94.63
264 988 75 F 268 1365 0 436 24 90.91
308 506 0 F 303 988 123 547 16 94.72
197 481 0 F 188 988 151 289 24 87.23
259 483 106 F 257 642 0 460 14 94.55
258 630 123 F 257 642 0 455 15 94.16
258 380 110 F 257 642 0 463 13 94.94
257 642 0 F 258 902 130 463 13 94.94
257 642 0 F 258 1151 163 463 13 94.94
257 642 0 F 258 1230 220 463 13 94.94
258 451 143 F 257 642 0 463 13 94.94
257 642 0 F 258 736 219 463 13 94.94
257 642 0 F 258 1100 150 459 14 94.55
257 642 0 F 258 1143 116 455 15 94.16
185 642 0 F 185 1049 164 290 20 89.19
125 642 0 F 126 1189 46 203 12 90.40
239 605 109 F 239 642 18 430 12 94.98
185 642 0 F 185 988 154 282 22 88.11
254 642 0 F 256 1365 81 462 12 95.28
187 506 34 F 185 642 0 276 24 87.03
258 481 11 F 251 642 6 429 20 92.03
297 483 83 F 306 1198 2 515 22 92.59
316 630 100 F 326 1198 2 538 26 91.77
315 380 88 F 326 1198 2 545 24 92.38
315 902 108 F 326 1198 2 549 23 92.70
315 1151 141 F 326 1198 2 549 23 92.70
326 1198 2 F 317 1230 196 551 23 92.74
313 451 121 F 324 1198 2 545 23 92.65
313 736 197 F 324 1198 2 545 23 92.65
315 1100 128 F 326 1198 2 537 26 91.75
316 1143 93 F 326 1198 2 538 26 91.77
207 1049 142 F 217 1198 2 316 27 86.96
145 1189 23 F 152 1198 2 229 17 88.28
315 605 68 F 323 1198 5 522 29 90.79
207 988 132 F 217 1198 2 304 30 85.51
326 1198 2 F 316 1365 59 542 25 92.09
211 506 10 F 217 1198 2 300 32 84.83
294 481 10 F 293 1198 35 499 22 92.49
227 642 30 F 231 1198 62 390 17 92.51
139 545 1 F 138 1453 139 241 9 93.48
362 662 80 F 367 1193 8 569 40 88.95
347 579 1 F 350 1365 43 605 23 93.37
370 630 64 F 372 1365 21 658 21 94.32
368 380 35 F 373 1365 2 677 16 95.65
370 605 13 F 373 1365 2 639 26 92.97
371 846 247 F 375 1365 0 686 15 95.96
369 902 54 F 373 1365 2 690 13 96.48
371 1151 85 F 375 1365 0 694 13 96.50
372 1230 141 F 373 1365 2 677 17 95.43
372 451 62 F 373 1365 0 685 15 95.97
369 736 141 F 373 1365 0 690 13 96.48
392 1143 35 F 391 1365 2 691 23 94.12
326 1198 2 F 316 1365 59 542 25 92.09
349 1100 94 F 351 1365 24 648 13 96.28
329 1653 0 F 334 1828 74 587 19 94.22
278 1653 0 F 285 1947 68 491 18 93.53
244 707 1 F 255 1623 143 359 35 85.66
168 719 268 F 168 1199 159 320 4 97.62
400 542 30 F 413 1056 0 713 25 93.75
242 1056 0 F 238 1653 107 336 36 84.87
348 406 94 F 355 1056 58 615 22 93.68
411 1696 0 F 412 1781 23 691 33 91.97
328 539 94 F 328 1080 0 584 18 94.51
274 542 0 F 291 1828 150 413 38 86.13
329 1653 0 F 334 1828 74 587 19 94.22
188 406 98 F 198 1828 243 290 24 87.23
382 1121 56 F 384 1512 11 674 23 93.98
381 309 0 F 374 804 82 691 16 95.72
397 221 0 F 397 266 0 786 2 99.50
296 3 0 F 296 5 38 572 5 98.31
175 3 0 F 175 7 38 346 1 99.43
200 3 0 F 204 4 460 312 23 88.50
610 3 0 F 607 39 72 1145 18 97.03
68 16 84 F 68 39 0 136 0 100.00
68 1 378 F 68 39 0 136 0 100.00
196 39 0 F 171 47 372 211 39 77.19
276 4 388 F 272 39 0 428 30 88.97
350 372 1 F 348 1348 62 654 11 96.84
261 474 132 F 263 1365 0 448 19 92.72
306 877 193 F 305 1514 2 547 16 94.75
291 1268 211 F 290 1514 0 517 16 94.48
289 1514 0 F 293 1627 121 494 22 92.39
284 1514 0 F 292 1747 113 452 31 89.08
396 584 79 F 407 1661 35 627 43 89.14
382 1121 56 F 384 1512 11 674 23 93.98
215 361 85 F 220 362 16 315 30 86.05
249 541 0 F 252 1006 81 429 18 92.77
58 950 2 F 58 1850 210 108 2 96.55
58 950 2 F 58 1788 201 108 2 96.55
331 18 0 F 337 46 194 536 33 90.03
329 1055 0 F 328 1542 146 605 13 96.04
419 975 53 F 419 1500 29 762 19 95.47
422 819 43 F 431 975 41 761 23 94.55
20 215 210 F 20 1373 404 40 0 100.00
20 215 207 F 20 1373 404 40 0 100.00
376 474 57 F 374 988 0 586 41 89.04
505 474 35 F 492 658 110 909 22 95.53
200 545 122 F 202 1453 254 358 11 94.50
309 877 174 F 310 1268 193 599 5 98.38
348 1064 63 F 351 1669 2 603 24 93.10
250 1021 0 F 250 1051 242 468 8 96.80
247 885 66 F 249 1051 243 456 10 95.95
245 885 68 F 247 1021 3 440 13 94.69
354 965 14 F 360 1034 0 646 17 95.20
373 567 23 F 368 965 0 621 30 91.85
369 536 109 F 368 965 0 685 13 96.47
368 965 0 F 366 1082 58 662 18 95.08
208 1138 64 F 200 1215 247 280 32 84.00
378 242 0 F 379 294 0 729 7 98.15
130 779 247 F 133 783 240 179 19 85.38
349 935 48 F 340 1076 44 569 30 91.18
340 935 57 F 330 1120 114 566 26 92.12
492 474 48 F 480 543 0 880 23 95.21
488 474 47 F 483 912 0 919 13 97.31
341 474 176 F 341 761 0 666 4 98.83
480 474 35 F 479 826 2 899 15 96.87
435 474 105 F 433 798 0 792 19 95.61
254 474 139 F 256 483 31 450 15 94.09
311 474 82 F 311 902 0 538 21 93.25
347 474 46 F 344 1151 0 603 22 93.60
392 474 1 F 399 1230 2 615 44 88.78
283 451 41 F 281 474 112 492 18 93.59
393 474 0 F 382 736 18 639 34 91.10
298 474 95 F 297 1143 0 459 34 88.55
419 474 45 F 417 1049 0 684 38 90.89
505 474 35 F 492 658 110 909 22 95.53
450 474 90 F 438 713 2 752 34 92.24
453 474 87 F 444 1120 0 765 33 92.57
393 474 0 F 392 846 114 625 40 89.80
368 474 147 F 365 1327 71 681 13 96.44
358 474 106 F 359 1328 0 529 47 86.87
291 380 0 F 296 474 97 507 20 93.13
215 361 85 F 220 362 16 315 30 86.05
176 1205 108 F 175 1941 183 283 17 90.29
334 1360 47 F 337 1365 0 599 18 94.61
374 630 38 F 375 1360 40 621 32 91.44
399 380 0 F 406 1360 9 705 25 93.73
410 846 204 F 414 1360 1 700 31 92.44
404 902 15 F 407 1360 8 711 25 93.81
412 1151 40 F 414 1360 1 714 28 93.20
414 1230 95 F 414 1360 1 704 31 92.51
384 451 48 F 383 1360 32 679 22 94.26
411 736 97 F 414 1360 1 721 26 93.67
413 1100 26 F 414 1360 1 663 41 90.07
349 483 31 F 346 1360 53 631 16 95.38
305 474 88 F 306 1360 1 487 31 89.84
299 543 34 F 306 1360 1 453 38 87.29
296 658 159 F 306 1360 1 462 35 88.18
269 713 24 F 278 1360 29 371 44 83.64
259 1297 69 F 265 1360 42 400 31 88.03
302 912 39 F 306 1360 1 480 32 89.40
243 1327 71 F 246 1360 61 377 28 88.48
215 761 2 F 214 1360 93 369 15 92.99
303 826 56 F 307 1360 0 482 32 89.44
268 798 18 F 268 1360 39 420 29 89.18
379 605 0 F 381 1360 34 632 32 91.56
405 1143 0 F 405 1360 10 638 43 89.38
257 642 0 F 258 1360 126 451 16 93.77
165 849 95 F 166 1360 131 271 15 90.91
305 1196 1 F 300 1360 61 485 30 90.00
221 506 0 F 217 1360 95 334 26 88.02
307 1049 42 F 311 1360 1 490 32 89.58
291 1328 0 F 293 1360 19 416 42 85.57
276 988 63 F 278 1360 34 450 26 90.58
213 935 37 F 203 1360 104 280 34 83.25
237 579 91 F 238 1289 4 439 9 96.20
128 1076 109 F 129 1289 3 205 13 89.84
128 1120 169 F 129 1289 3 205 13 89.84
183 1196 123 F 183 1289 3 330 9 95.08
129 474 264 F 129 1289 3 206 13 89.92
129 543 204 F 129 1289 3 206 13 89.92
128 658 327 F 129 1289 3 201 14 89.06
129 713 164 F 129 1289 3 202 14 89.15
129 1289 3 F 129 1297 199 206 13 89.92
129 912 212 F 129 1289 3 206 13 89.92
129 1289 3 F 129 1327 185 206 13 89.92
129 761 88 F 129 1289 3 206 13 89.92
129 826 230 F 129 1289 3 206 13 89.92
130 798 156 F 129 1289 3 203 14 89.15
222 483 158 F 221 1289 3 415 7 96.83
239 1289 3 F 239 1365 134 438 10 95.82
239 630 175 F 239 1289 3 446 8 96.65
239 380 162 F 239 1289 3 446 8 96.65
239 846 377 F 239 1289 3 442 9 96.23
239 902 182 F 239 1289 3 446 8 96.65
239 1151 215 F 239 1289 3 446 8 96.65
239 1230 272 F 239 1289 3 446 8 96.65
239 451 195 F 239 1289 3 446 8 96.65
239 736 271 F 239 1289 3 446 8 96.65
239 1100 202 F 239 1289 3 442 9 96.23
239 605 142 F 239 1289 3 438 10 95.82
239 1143 168 F 239 1289 3 438 10 95.82
206 642 51 F 206 1289 3 376 9 95.63
118 849 142 F 119 1289 3 173 16 86.44
133 506 88 F 134 1289 3 207 15 88.72
133 1049 216 F 134 1289 3 207 15 88.72
134 1289 3 F 133 1328 158 203 16 87.97
133 988 206 F 134 1289 3 203 16 87.97
121 935 129 F 120 1289 12 185 14 88.33
206 1076 31 F 204 1360 103 302 27 86.76
290 1120 7 F 297 1360 10 399 47 83.79
326 579 0 F 327 1360 88 549 26 92.02
237 1289 3 F 237 1360 178 434 10 95.78
248 1360 32 F 249 1456 16 337 40 83.87
102 1289 3 F 100 1456 165 174 7 93.00
337 674 12 F 339 1281 47 600 19 94.36
382 1121 56 F 384 1512 11 674 23 93.98
445 34 170 F 432 1317 10 749 32 92.59
332 977 26 F 332 1605 73 556 27 91.87
318 574 96 F 320 1369 78 602 9 97.17
309 244 0 F 309 272 0 590 7 97.73
343 1302 67 F 343 1433 4 606 20 94.17
356 989 50 F 347 1350 1 591 28 91.93
149 413 221 F 148 1250 267 265 8 94.59
339 440 2 F 335 765 95 606 17 94.93
339 1820 0 F 340 1909 0 599 20 94.10
299 1871 0 F 296 1892 0 515 20 93.24
293 1664 0 F 296 1871 3 469 30 89.76
328 720 0 F 330 1398 19 534 31 90.55
344 691 71 F 347 814 135 643 12 96.51
309 244 0 F 309 272 0 590 7 97.73
389 848 138 F 404 1658 0 637 39 89.97
179 40 323 F 179 66 137 334 6 96.65
132 66 137 F 132 747 236 240 6 95.45
340 935 57 F 330 1120 114 566 26 92.12
453 474 87 F 444 1120 0 765 33 92.57
376 543 104 F 376 1120 68 696 14 96.28
444 658 158 F 444 1120 0 752 34 92.34
416 713 24 F 420 1120 24 744 23 94.47
322 849 95 F 322 1120 122 588 14 95.65
352 1076 32 F 348 1120 96 624 19 94.54
444 1120 0 F 439 1297 36 735 37 91.57
274 1196 32 F 269 1365 48 491 13 95.17
268 579 4 F 276 1196 30 444 25 90.67
281 630 77 F 287 1196 19 488 20 92.88
299 380 46 F 306 1196 0 513 23 92.31
299 846 261 F 305 1196 1 508 24 91.97
299 902 66 F 305 1196 1 516 22 92.64
299 1151 99 F 305 1196 1 516 22 92.64
306 1196 0 F 303 1230 152 525 21 93.07
301 451 77 F 306 1196 0 519 22 92.69
299 736 155 F 305 1196 1 516 22 92.64
301 1100 84 F 306 1196 0 511 24 92.03
183 1196 123 F 183 1289 3 330 9 95.08
246 481 0 F 243 1196 63 417 18 92.59
172 610 53 F 173 1196 133 317 7 95.93
305 1196 1 F 300 1360 61 485 30 90.00
266 641 0 F 272 1196 34 454 21 92.11
263 1196 43 F 267 1198 2 422 27 89.73
293 483 49 F 297 1196 9 514 19 93.52
200 3 299 F 199 16 455 335 16 91.96
200 3 299 F 199 5 337 343 14 92.96
309 16 455 F 309 39 371 498 30 90.29
309 5 337 F 309 39 371 510 27 91.26
310 6 300 F 309 16 455 495 31 89.97
309 5 337 F 310 6 300 503 29 90.61
153 2 371 F 156 3 299 253 14 90.85
197 2 371 F 202 39 371 299 25 87.31
197 2 371 F 202 6 300 295 26 86.80
231 779 30 F 227 783 30 322 34 85.02
157 322 70 F 158 793 68 247 16 89.81
265 376 51 F 270 1277 65 507 7 97.36
386 376 0 F 401 1694 81 607 45 88.34
100 33 0 F 101 73 0 189 3 97.00
95 7 276 F 97 73 1 172 5 94.74
368 474 147 F 365 1327 71 681 13 96.44
439 543 16 F 436 1327 0 751 31 92.89
363 1297 87 F 365 1327 71 672 14 96.14
367 912 96 F 365 1327 71 680 13 96.44
338 761 1 F 337 1327 99 643 8 97.63
367 826 114 F 365 1327 71 676 14 96.16
368 798 40 F 365 1327 71 661 18 95.07
306 807 164 F 304 866 242 546 16 94.74
479 866 95 F 488 1212 73 759 52 89.14
440 654 1 F 432 866 142 668 51 88.19
349 1100 94 F 351 1365 24 648 13 96.28
359 695 121 F 363 938 64 686 9 97.49
349 1554 0 F 347 1555 52 632 16 95.39
314 1552 0 F 308 1555 108 534 22 92.86
319 1548 0 F 318 1555 101 605 8 97.48
256 310 69 F 255 1363 75 483 7 97.25
84 310 109 F 84 1363 154 148 5 94.05
455 543 0 F 466 826 15 829 23 94.95
310 826 49 F 311 902 0 541 20 93.55
346 826 13 F 344 1151 0 602 22 93.60
283 451 41 F 279 826 80 494 17 93.91
304 736 96 F 304 826 55 552 14 95.39
409 826 12 F 407 1049 0 664 38 90.66
359 826 0 F 356 846 150 583 33 90.73
291 380 0 F 293 826 66 520 16 94.50
323 826 76 F 324 988 50 531 29 91.02
257 826 102 F 261 1365 2 438 20 92.22
303 826 56 F 307 1360 0 482 32 89.44
404 902 15 F 407 1360 8 711 25 93.81
412 1151 40 F 414 1360 1 714 28 93.20
384 451 48 F 383 1360 32 679 22 94.26
411 736 97 F 414 1360 1 721 26 93.67
307 1049 42 F 311 1360 1 490 32 89.58
299 543 34 F 306 1360 1 453 38 87.29
410 846 204 F 414 1360 1 700 31 92.44
399 380 0 F 406 1360 9 705 25 93.73
276 988 63 F 278 1360 34 450 26 90.58
334 1360 47 F 337 1365 0 599 18 94.61
480 474 35 F 479 826 2 899 15 96.87
305 474 88 F 306 1360 1 487 31 89.84
467 826 14 F 463 912 0 854 19 95.90
211 454 5 F 212 826 31 335 22 89.57
145 826 98 F 145 1837 0 238 13 91.03
302 912 39 F 306 1360 1 480 32 89.40
188 454 28 F 191 1360 0 263 29 84.57
145 1360 46 F 144 1837 1 225 16 88.89
110 826 133 F 110 1722 43 184 9 91.82
154 1360 37 F 152 1722 1 222 21 86.18
338 713 79 F 340 761 1 650 7 97.93
110 497 332 F 110 1549 226 212 2 98.18
110 1544 250 F 110 1549 226 208 3 97.27
376 460 93 F 376 1936 2 728 6 98.40
445 34 170 F 432 1317 10 749 32 92.59
349 1546 15 F 348 1547 0 673 6 98.28
211 936 0 F 215 937 160 370 14 93.36
379 1784 7 F 381 1799 0 656 26 93.14
258 895 170 F 263 1405 10 449 18 93.02
610 3 0 F 607 39 72 1145 18 97.03
641 6 156 F 647 39 227 1216 18 97.19
328 720 0 F 330 1398 19 534 31 90.55
237 994 160 F 242 1190 41 423 14 94.09
380 78 86 F 375 80 149 635 30 92.00
332 977 26 F 332 1605 73 556 27 91.87
367 881 0 F 364 1248 100 699 8 97.80
337 674 12 F 339 1281 47 600 19 94.36
148 538 147 F 148 667 242 292 1 99.32
309 16 455 F 309 39 371 498 30 90.29
309 5 337 F 309 39 371 510 27 91.26
310 6 300 F 309 16 455 495 31 89.97
309 5 337 F 310 6 300 503 29 90.61
200 3 299 F 199 16 455 335 16 91.96
200 3 299 F 199 5 337 343 14 92.96
243 782 133 F 240 1279 0 391 23 90.42
243 1270 88 F 240 1279 0 395 22 90.83
354 1301 9 F 352 1500 137 650 14 96.02
351 819 155 F 354 1301 9 653 13 96.30
310 975 162 F 313 1301 9 575 12 96.13
300 1910 0 F 299 1926 25 543 14 95.32
337 497 105 F 336 1549 0 593 17 94.94
336 1544 24 F 336 1549 0 588 18 94.64
249 1549 0 F 249 1551 9 422 16 93.57
160 1546 202 F 160 1549 0 308 3 98.12
160 1547 186 F 160 1549 0 300 5 96.88
159 1549 0 F 159 1550 177 290 7 95.60
216 522 234 F 216 1134 194 424 2 99.07
157 735 388 F 157 1479 204 266 12 92.36
333 742 0 F 336 825 119 585 21 93.69
335 432 58 F 333 742 0 588 20 93.99
308 652 77 F 306 742 27 542 18 94.12
334 492 21 F 333 742 0 587 20 93.99
333 742 0 F 336 1469 114 573 24 92.79
333 742 0 F 334 1874 34 567 25 92.49
290 1147 13 F 293 1331 123 503 20 93.10
330 1939 0 F 330 1940 10 568 23 93.03
135 530 106 F 135 1431 219 166 26 80.74
135 1343 114 F 135 1431 219 162 27 80.00
137 544 45 F 135 1431 219 164 27 80.00
32 463 158 F 32 1304 145 60 1 96.88
223 247 130 F 226 880 2 361 22 90.13
171 483 61 F 172 1189 0 311 8 95.32
170 902 86 F 172 1189 0 314 7 95.88
170 1151 119 F 172 1189 0 314 7 95.88
172 1189 0 F 173 1230 173 313 8 95.35
170 451 99 F 172 1189 0 314 7 95.88
170 736 175 F 172 1189 0 314 7 95.88
170 1100 106 F 172 1189 0 302 10 94.12
173 1143 69 F 172 1189 0 301 11 93.60
171 1049 119 F 172 1189 0 311 8 95.32
453 474 87 F 442 1297 33 779 29 93.44
480 543 0 F 468 1297 7 824 31 93.38
426 912 57 F 419 1297 51 773 18 95.70
321 761 20 F 320 1297 132 629 3 99.06
414 826 67 F 407 1297 43 733 22 94.59
411 798 22 F 406 1297 69 729 22 94.58
234 483 53 F 229 1297 99 399 16 93.01
257 902 54 F 252 1297 76 429 20 92.06
305 1151 39 F 295 1297 33 456 36 87.80
286 1230 115 F 276 1297 52 446 29 89.49
246 451 78 F 241 1297 87 415 18 92.53
304 736 96 F 295 1297 33 459 35 88.14
237 1100 94 F 232 1297 96 397 18 92.24
293 1143 4 F 282 1297 46 403 42 85.11
402 1049 15 F 383 1297 16 553 58 84.86
171 474 167 F 172 1189 0 303 10 94.15
169 543 109 F 172 1189 0 301 10 94.08
171 912 115 F 172 1189 0 311 8 95.32
160 761 2 F 161 1189 11 285 9 94.38
170 826 134 F 172 1189 0 302 10 94.12
171 798 60 F 172 1189 0 291 13 92.40
172 1189 0 F 167 1297 106 291 12 92.81
168 658 232 F 172 1189 0 296 11 93.45
426 658 176 F 424 1297 51 774 19 95.52
128 713 110 F 129 1189 43 237 5 96.09
342 713 98 F 343 1297 132 665 5 98.54
129 1120 114 F 129 1189 43 242 4 96.90
444 1120 0 F 439 1297 36 735 37 91.57
170 846 281 F 172 1189 0 306 9 94.71
284 846 222 F 277 1297 51 445 29 89.53
172 1189 0 F 172 1365 36 296 12 93.02
252 1297 76 F 261 1365 2 413 25 90.08
121 849 95 F 121 1189 51 202 10 91.74
322 849 95 F 322 1297 153 596 12 96.27
172 1189 0 F 173 1456 65 265 20 88.37
169 1297 132 F 171 1456 94 300 10 94.08
260 664 16 F 270 1183 3 430 25 90.38
338 601 17 F 340 609 84 606 18 94.67
80 35 204 F 80 73 144 152 2 97.50
80 72 215 F 80 73 144 152 2 97.50
32 5 228 F 32 7 228 64 0 100.00
32 2 262 F 32 7 228 64 0 100.00
32 7 228 F 32 16 346 64 0 100.00
32 3 190 F 32 7 228 64 0 100.00
32 6 191 F 32 7 228 64 0 100.00
32 7 228 F 32 39 262 64 0 100.00
354 965 14 F 360 1034 0 646 17 95.20
393 536 87 F 388 1082 38 717 16 95.88
309 1649 13 F 309 1931 0 546 18 94.17
309 1708 8 F 305 1931 0 490 30 90.16
228 1132 161 F 230 1140 69 434 6 97.37
377 505 0 F 380 633 21 717 10 97.35
216 522 234 F 216 1134 194 424 2 99.07
329 1592 0 F 322 1595 8 583 17 94.72
445 34 170 F 432 1317 10 749 32 92.59
328 539 94 F 328 1080 0 584 18 94.51
85 33 0 F 84 264 534 161 2 97.62
100 7 259 F 99 264 519 155 11 88.89
328 539 94 F 328 1080 0 584 18 94.51
424 454 70 F 432 1837 0 772 21 95.05
83 988 223 F 83 1837 149 154 3 96.39
256 1722 8 F 256 1837 0 464 12 95.31
84 1456 181 F 85 1837 149 149 5 94.05
85 1196 139 F 85 1837 149 154 4 95.29
85 474 281 F 85 1837 149 154 4 95.29
85 543 221 F 85 1837 149 154 4 95.29
85 658 343 F 85 1837 149 154 4 95.29
85 713 181 F 85 1837 149 154 4 95.29
85 1297 216 F 85 1837 149 154 4 95.29
85 912 229 F 85 1837 149 154 4 95.29
85 1327 202 F 85 1837 149 154 4 95.29
85 761 105 F 85 1837 149 154 4 95.29
85 826 247 F 85 1837 149 154 4 95.29
85 483 175 F 85 1837 149 154 4 95.29
85 1365 151 F 85 1837 149 154 4 95.29
85 630 192 F 85 1837 149 154 4 95.29
85 380 179 F 85 1837 149 154 4 95.29
85 846 394 F 85 1837 149 150 5 94.12
85 902 199 F 85 1837 149 154 4 95.29
85 1151 232 F 85 1837 149 154 4 95.29
85 1230 289 F 85 1837 149 154 4 95.29
85 451 212 F 85 1837 149 154 4 95.29
85 736 288 F 85 1837 149 154 4 95.29
85 1100 219 F 85 1837 149 154 4 95.29
85 1143 185 F 85 1837 149 154 4 95.29
83 506 105 F 83 1837 149 150 4 95.18
83 1049 233 F 83 1837 149 150 4 95.18
83 1328 175 F 83 1837 149 146 5 93.98
84 1076 126 F 85 1837 149 145 6 92.86
84 1120 186 F 85 1837 149 149 5 94.05
85 481 80 F 85 1837 149 150 5 94.12
57 1189 115 F 57 1837 149 102 3 94.74
84 610 60 F 85 1837 149 137 8 90.48
84 641 101 F 84 1837 150 144 6 92.86
85 1289 20 F 85 1837 149 142 7 91.76
85 1360 195 F 85 1837 149 146 6 92.94
85 605 159 F 85 1837 149 150 5 94.12
84 579 107 F 85 1837 149 145 6 92.86
304 1068 0 F 303 1517 96 543 16 94.72
185 1198 2 F 178 1456 87 259 26 85.39
263 1196 43 F 267 1198 2 422 27 89.73
204 474 189 F 212 1198 2 312 26 87.25
203 543 130 F 212 1198 2 315 25 87.68
201 658 254 F 212 1198 2 305 27 86.57
202 713 91 F 212 1198 2 302 28 86.14
212 1198 2 F 201 1297 127 301 28 86.07
204 912 137 F 212 1198 2 316 25 87.75
199 1198 15 F 193 1327 121 296 24 87.56
207 761 10 F 214 1198 0 313 27 86.96
206 826 153 F 214 1198 0 316 26 87.38
202 798 84 F 209 1198 5 307 26 87.13
297 483 83 F 306 1198 2 515 22 92.59
326 1198 2 F 316 1365 59 542 25 92.09
316 630 100 F 326 1198 2 538 26 91.77
315 380 88 F 326 1198 2 545 24 92.38
315 846 303 F 326 1198 2 541 25 92.06
315 902 108 F 326 1198 2 549 23 92.70
315 1151 141 F 326 1198 2 549 23 92.70
326 1198 2 F 317 1230 196 551 23 92.74
313 451 121 F 324 1198 2 545 23 92.65
313 736 197 F 324 1198 2 545 23 92.65
315 1100 128 F 326 1198 2 537 26 91.75
322 1198 2 F 311 1360 104 513 30 90.35
315 605 68 F 323 1198 5 522 29 90.79
316 1143 93 F 326 1198 2 538 26 91.77
227 642 30 F 231 1198 62 390 17 92.51
169 849 91 F 174 1198 30 251 23 86.39
211 506 10 F 217 1198 2 300 32 84.83
207 1049 142 F 217 1198 2 316 27 86.96
217 1198 2 F 209 1328 82 294 33 84.21
207 988 132 F 217 1198 2 304 30 85.51
202 935 48 F 198 1198 16 252 37 81.31
137 1076 100 F 138 1198 76 211 16 88.32
201 1120 96 F 212 1198 2 301 28 86.07
250 579 80 F 252 1198 76 434 17 93.20
242 1198 84 F 239 1289 3 413 17 92.89
313 483 67 F 310 579 0 539 21 93.23
364 483 16 F 358 630 38 630 23 93.58
344 380 39 F 349 483 31 661 8 97.67
370 483 10 F 363 605 0 637 24 93.39
349 483 31 F 345 846 253 662 8 97.68
349 483 31 F 345 902 58 670 6 98.26
349 483 31 F 345 1151 91 670 6 98.26
349 483 31 F 348 1230 145 657 10 97.13
375 451 41 F 380 483 0 695 15 96.00
349 483 31 F 345 736 147 670 6 98.26
349 483 31 F 350 1143 39 619 20 94.27
380 483 0 F 375 1100 48 671 21 94.40
222 483 158 F 221 1289 3 415 7 96.83
284 481 0 F 277 483 103 509 13 95.31
212 483 168 F 210 610 53 394 7 96.67
349 483 31 F 349 1365 6 634 16 95.42
259 483 106 F 257 642 0 460 14 94.55
349 483 31 F 346 1360 53 631 16 95.38
293 483 49 F 297 1196 9 514 19 93.52
306 483 74 F 304 641 0 558 13 95.72
258 871 99 F 264 1710 140 426 24 90.70
300 1401 1 F 301 1710 106 465 34 88.67
420 61 134 F 424 65 137 752 22 94.76
381 61 134 F 380 64 137 701 15 96.05
164 61 150 F 165 65 194 309 5 96.95
164 61 150 F 165 64 194 309 5 96.95
164 61 150 F 165 61 191 309 5 96.95
223 313 78 F 220 1827 5 383 15 93.18
224 1782 39 F 224 1827 0 404 11 95.09
324 428 0 F 320 1441 29 564 20 93.75
317 428 7 F 312 1513 64 573 14 95.51
308 335 0 F 309 1059 206 613 1 99.68
258 895 170 F 263 1405 10 449 18 93.02
321 1941 0 F 323 1942 31 524 30 90.65
223 1649 20 F 222 1736 0 409 9 95.95
223 1708 15 F 222 1736 0 401 11 95.05
238 483 49 F 233 1120 64 387 21 90.99
258 902 53 F 255 1120 42 409 26 89.80
297 1120 0 F 305 1151 39 446 39 86.87
277 451 47 F 271 1120 26 416 33 87.82
304 736 96 F 297 1120 0 445 39 86.87
375 1049 41 F 368 1120 0 523 55 85.05
376 543 104 F 376 1120 68 696 14 96.28
339 761 0 F 336 1120 83 631 11 96.73
426 826 55 F 419 1120 0 709 34 91.89
444 658 158 F 444 1120 0 752 34 92.34
303 846 203 F 297 1120 0 440 40 86.53
395 1120 24 F 396 1327 40 659 33 91.65
291 380 0 F 288 1120 9 427 38 86.81
346 988 28 F 337 1120 0 467 54 83.98
444 1120 0 F 439 1297 36 735 37 91.57
336 1546 28 F 338 1550 1 630 11 96.73
336 1547 12 F 338 1550 1 622 13 96.13
336 1546 28 F 338 1550 1 630 11 96.73
336 1547 12 F 338 1550 1 622 13 96.13
360 369 21 F 360 1409 0 640 20 94.44
318 574 96 F 320 1369 78 602 9 97.17
291 358 77 F 292 1678 0 523 15 94.85
128 358 41 F 129 733 174 165 23 82.03
243 782 133 F 240 1279 0 391 23 90.42
243 1270 88 F 240 1279 0 395 22 90.83
392 474 1 F 399 1230 2 615 44 88.78
214 454 2 F 218 1230 67 320 28 86.92
77 1868 158 F 77 1897 157 122 8 89.61
284 386 212 F 293 1201 56 501 19 93.31
280 871 111 F 279 1401 50 475 21 92.47
300 1401 1 F 301 1710 106 465 34 88.67
329 1653 0 F 334 1828 74 587 19 94.22
352 1828 6 F 353 1947 0 625 20 94.32
274 542 0 F 291 1828 150 413 38 86.13
393 1268 103 F 405 1747 0 686 28 92.88
179 382 45 F 177 918 49 260 24 86.44
155 826 31 F 165 1892 242 216 26 83.23
467 826 14 F 463 912 0 854 19 95.90
98 826 32 F 98 1664 240 132 16 83.67
416 1620 0 F 415 1796 6 743 22 94.70
354 965 14 F 360 1034 0 646 17 95.20
373 567 23 F 368 965 0 621 30 91.85
369 536 109 F 368 965 0 685 13 96.47
368 965 0 F 366 1082 58 662 18 95.08
313 560 59 F 311 1069 28 572 13 95.82
384 355 97 F 380 589 0 712 13 96.58
371 499 1 F 368 589 12 679 15 95.92
201 238 0 F 202 274 0 399 1 99.50
390 884 31 F 392 890 43 726 14 96.41
335 546 114 F 332 884 41 639 7 97.89
352 1828 6 F 353 1947 0 625 20 94.32
404 549 32 F 412 661 104 712 26 93.56
453 460 27 F 452 1351 0 793 28 93.81
374 1351 67 F 376 1936 2 678 18 95.19
235 8 263 F 249 70 266 324 40 82.98
380 78 86 F 375 80 149 635 30 92.00
305 1066 1 F 311 1600 69 444 43 85.90
402 1210 84 F 400 1516 32 730 18 95.50
313 560 59 F 311 1069 28 572 13 95.82
87 871 362 F 87 1401 288 150 6 93.10
313 560 59 F 311 1069 28 572 13 95.82
304 1068 0 F 303 1517 96 543 16 94.72
336 1546 28 F 338 1550 1 630 11 96.73
336 1547 12 F 338 1550 1 622 13 96.13
392 671 7 F 402 1334 0 666 32 91.84
252 766 26 F 252 994 59 408 24 90.48
296 960 29 F 303 970 135 543 14 95.27
299 1871 0 F 296 1892 0 515 20 93.24
293 1664 0 F 296 1871 3 469 30 89.76
360 1664 0 F 362 1892 3 622 25 93.06
185 522 41 F 186 1134 0 275 24 87.03
382 1121 56 F 384 1512 11 674 23 93.98
397 221 0 F 397 266 0 786 2 99.50
418 406 24 F 415 542 15 733 25 93.98
348 406 94 F 355 1056 58 615 22 93.68
81 355 400 F 78 1257 57 103 14 82.05
81 499 291 F 78 1257 57 103 14 82.05
81 589 299 F 78 1257 57 103 14 82.05
350 412 163 F 348 1525 88 646 13 96.26
343 568 69 F 345 1793 63 652 9 97.38
323 579 7 F 324 641 0 535 28 91.33
325 630 91 F 324 641 0 569 20 93.83
324 380 79 F 324 641 0 600 12 96.30
326 605 57 F 324 641 0 574 19 94.14
324 641 0 F 324 846 294 596 13 95.99
324 641 0 F 324 902 99 604 11 96.60
324 641 0 F 324 1151 132 604 11 96.60
324 641 0 F 327 1230 186 599 13 95.99
322 451 112 F 322 641 0 600 11 96.58
322 641 0 F 322 736 188 600 11 96.58
324 641 0 F 326 1143 83 582 17 94.75
324 641 0 F 324 1100 119 584 16 95.06
239 641 83 F 239 1289 3 422 14 94.14
289 481 15 F 282 641 42 503 17 93.97
306 483 74 F 304 641 0 558 13 95.72
230 610 53 F 231 641 93 413 12 94.78
324 641 0 F 325 1365 50 581 17 94.75
256 641 33 F 257 642 0 441 18 92.97
320 641 0 F 320 1360 95 556 21 93.44
339 652 71 F 339 825 141 638 10 97.05
338 432 80 F 339 652 71 645 8 97.63
333 492 43 F 335 652 71 636 8 97.60
318 652 71 F 315 1469 139 593 10 96.83
244 579 98 F 244 610 51 456 8 96.72
242 610 53 F 243 630 185 461 6 97.52
231 380 172 F 230 610 53 437 6 97.39
231 605 152 F 230 610 53 429 8 96.52
230 610 53 F 231 846 387 433 7 96.96
230 610 53 F 231 902 192 437 6 97.39
230 610 53 F 231 1151 225 437 6 97.39
230 610 53 F 231 1230 282 437 6 97.39
229 451 205 F 228 610 53 433 6 97.37
228 610 53 F 229 736 281 433 6 97.37
291 358 77 F 292 1678 0 523 15 94.85
360 1664 0 F 362 1892 3 622 25 93.06
349 1554 0 F 347 1555 52 632 16 95.39
319 1548 0 F 318 1555 101 605 8 97.48
353 985 0 F 353 1426 64 654 13 96.32
364 567 38 F 366 1034 0 634 24 93.41
356 536 124 F 362 1034 0 650 17 95.22
362 1034 0 F 355 1082 71 641 19 94.65
373 567 23 F 368 965 0 621 30 91.85
369 536 109 F 368 965 0 685 13 96.47
368 965 0 F 366 1082 58 662 18 95.08
348 579 0 F 352 1143 75 608 23 93.39
425 630 9 F 426 1143 1 683 41 90.35
401 380 2 F 407 1143 2 692 29 92.77
383 605 0 F 387 1143 22 650 30 92.17
396 846 222 F 400 1143 9 692 26 93.43
378 902 45 F 383 1143 26 677 21 94.44
409 1143 0 F 409 1151 47 706 28 93.15
407 1143 2 F 407 1230 106 718 24 94.10
387 451 47 F 389 1143 18 688 22 94.32
406 736 104 F 407 1143 0 697 29 92.86
399 1100 44 F 399 1143 10 690 27 93.23
239 1143 168 F 239 1289 3 438 10 95.82
304 481 0 F 296 1143 113 536 16 94.59
242 610 53 F 243 1143 178 449 9 96.28
392 1143 35 F 391 1365 2 691 23 94.12
257 642 0 F 258 1143 116 455 15 94.16
405 1143 0 F 405 1360 10 638 43 89.38
304 1143 47 F 306 1196 0 510 25 91.78
324 641 0 F 326 1143 83 582 17 94.75
237 994 160 F 242 1190 41 423 14 94.09
364 567 38 F 366 1034 0 634 24 93.41
356 536 124 F 362 1034 0 650 17 95.22
362 1034 0 F 355 1082 71 641 19 94.65
255 1382 47 F 266 1933 214 393 32 87.45
291 678 95 F 292 1204 14 531 13 95.53
25 31 11 F 25 125 27 46 1 96.00
21 31 11 F 21 632 169 42 0 100.00
260 497 95 F 258 1551 0 494 6 97.67
258 1544 15 F 258 1551 0 496 5 98.06
171 1546 193 F 171 1551 0 338 1 99.42
268 497 0 F 264 1547 84 460 18 93.18
186 1544 0 F 186 1547 162 364 2 98.92
349 1546 15 F 348 1547 0 673 6 98.28
171 1547 177 F 171 1551 0 334 2 98.83
249 1549 0 F 249 1551 9 422 16 93.57
160 1547 186 F 160 1549 0 300 5 96.88
185 522 41 F 186 1134 0 275 24 87.03
409 480 46 F 398 926 0 723 21 94.72
328 539 94 F 328 1080 0 584 18 94.51
211 936 0 F 215 937 160 370 14 93.36
274 1039 0 F 274 1435 147 524 6 97.81
287 1170 0 F 283 1347 84 466 26 90.81
309 1681 0 F 308 1808 0 541 19 93.83
350 412 163 F 348 1525 88 646 13 96.26
330 579 0 F 333 605 50 559 26 92.12
274 605 109 F 274 630 142 532 4 98.54
381 380 22 F 383 605 0 688 19 95.01
383 605 0 F 382 846 236 693 18 95.29
383 605 0 F 384 902 39 695 18 95.30
383 605 0 F 383 1151 73 702 16 95.82
383 605 0 F 385 1230 128 688 20 94.78
383 451 51 F 381 605 0 692 18 95.28
381 605 0 F 380 736 130 697 16 95.79
383 605 0 F 386 1100 57 649 29 92.43
239 605 142 F 239 1289 3 438 10 95.82
304 481 0 F 298 605 85 538 16 94.63
231 605 152 F 230 610 53 429 8 96.52
370 605 13 F 373 1365 2 639 26 92.97
239 605 109 F 239 642 18 430 12 94.98
379 605 0 F 381 1360 34 632 32 91.56
290 605 35 F 295 1196 11 485 25 91.38
326 605 57 F 324 641 0 574 19 94.14
315 605 68 F 323 1198 5 522 29 90.79
370 483 10 F 363 605 0 637 24 93.39
336 1546 28 F 338 1550 1 630 11 96.73
336 1547 12 F 338 1550 1 622 13 96.13
354 965 14 F 360 1034 0 646 17 95.20
474 1788 0 F 474 1850 9 836 28 94.09
328 720 0 F 330 1398 19 534 31 90.55
319 1548 0 F 318 1555 101 605 8 97.48
314 1552 0 F 308 1555 108 534 22 92.86
349 1554 0 F 347 1555 52 632 16 95.39
356 989 50 F 347 1350 1 591 28 91.93
323 1231 2 F 322 1318 24 617 7 97.83
96 579 274 F 96 1196 309 180 3 96.88
74 630 360 F 74 1196 309 136 3 95.95
68 610 227 F 68 1196 309 120 4 94.12
71 1543 267 F 71 1543 350 126 4 94.37
66 1132 92 F 66 1140 0 116 4 93.94
391 825 86 F 390 1874 2 705 19 95.13
392 432 23 F 392 1874 0 716 17 95.66
336 652 71 F 336 1874 56 600 18 94.64
376 492 0 F 377 1874 14 697 14 96.28
377 1469 77 F 372 1874 0 661 22 94.09
364 567 38 F 366 1034 0 634 24 93.41
356 536 124 F 362 1034 0 650 17 95.22
362 1034 0 F 355 1082 71 641 19 94.65
373 567 23 F 368 965 0 621 30 91.85
369 536 109 F 368 965 0 685 13 96.47
368 965 0 F 366 1082 58 662 18 95.08
96 579 274 F 96 1196 309 180 3 96.88
74 630 360 F 74 1196 309 136 3 95.95
56 380 347 F 56 1196 309 100 3 94.64
56 605 327 F 56 1196 309 100 3 94.64
56 846 562 F 56 1196 309 100 3 94.64
56 902 367 F 56 1196 309 100 3 94.64
56 1151 400 F 56 1196 309 100 3 94.64
56 1196 309 F 56 1230 457 100 3 94.64
54 451 380 F 54 1196 309 96 3 94.44
54 736 456 F 54 1196 309 96 3 94.44
74 1143 353 F 74 1196 309 132 4 94.59
56 1100 387 F 56 1196 309 92 5 91.07
54 1196 309 F 54 1289 188 88 5 90.74
56 481 248 F 56 1196 309 100 3 94.64
36 483 344 F 36 1196 309 68 1 97.22
68 610 227 F 68 1196 309 120 4 94.12
56 641 268 F 56 1196 309 92 5 91.07
128 846 78 F 139 1649 164 203 16 87.50
127 846 97 F 135 1931 174 170 23 81.89
291 678 95 F 292 1204 14 531 13 95.53
403 380 0 F 407 902 16 774 9 97.77
403 380 0 F 407 1151 49 778 8 98.01
401 380 0 F 404 736 106 777 7 98.25
400 380 3 F 403 846 215 763 10 97.50
291 380 0 F 293 826 66 520 16 94.50
286 380 10 F 289 1328 2 447 32 88.81
290 902 26 F 289 1328 2 451 32 88.93
290 1151 59 F 289 1328 2 455 31 89.27
290 736 115 F 291 1328 0 457 31 89.31
289 846 222 F 291 1328 0 448 33 88.58
345 826 76 F 347 1328 2 528 41 88.12
194 216 0 F 194 277 0 380 2 98.97
339 440 2 F 335 765 95 606 17 94.93
87 871 362 F 87 1401 288 150 6 93.10
89 871 346 F 88 871 349 77 5 94.32
377 505 0 F 380 633 21 717 10 97.35
44 1133 186 F 44 1133 224 88 0 100.00
323 579 7 F 324 641 0 535 28 91.33
325 630 91 F 324 641 0 569 20 93.83
230 610 53 F 231 641 93 413 12 94.78
324 380 79 F 324 641 0 600 12 96.30
326 605 57 F 324 641 0 574 19 94.14
324 641 0 F 324 846 294 596 13 95.99
324 641 0 F 324 902 99 604 11 96.60
324 641 0 F 324 1151 132 604 11 96.60
324 641 0 F 327 1230 186 599 13 95.99
322 451 112 F 322 641 0 600 11 96.58
322 641 0 F 322 736 188 600 11 96.58
130 1260 138 F 129 1615 1 235 6 95.35
137 454 79 F 140 483 31 217 15 89.05
182 454 34 F 182 902 13 296 17 90.66
213 454 3 F 212 1151 16 345 20 90.57
214 454 2 F 218 1230 67 320 28 86.92
167 451 41 F 164 454 52 259 18 89.02
212 454 4 F 211 736 73 343 20 90.52
115 454 101 F 114 1100 101 181 12 89.47
181 454 35 F 181 1143 0 238 31 82.87
115 454 101 F 114 1049 115 193 9 92.11
211 454 5 F 213 474 64 360 16 92.42
115 454 101 F 113 543 104 192 9 92.04
196 454 20 F 193 912 32 321 17 91.19
100 454 116 F 101 761 0 169 8 92.00
211 454 5 F 212 826 31 335 22 89.57
171 454 45 F 169 798 0 252 22 86.98
208 454 7 F 201 658 138 325 21 89.55
185 454 32 F 173 713 4 206 38 78.03
187 454 29 F 181 1120 1 236 33 81.77
212 454 4 F 210 846 180 322 25 88.10
115 454 101 F 116 1365 31 179 13 88.70
56 454 160 F 56 849 99 92 5 91.07
129 454 87 F 127 1327 71 176 20 84.25
170 454 46 F 171 1328 0 229 28 83.53
175 380 0 F 179 454 37 278 19 89.14
188 454 28 F 191 1360 0 263 29 84.57
255 1382 47 F 266 1933 214 393 32 87.45
328 720 0 F 330 1398 19 534 31 90.55
308 506 0 F 303 988 123 547 16 94.72
377 988 49 F 376 1049 60 693 15 96.01
377 988 49 F 377 1328 1 622 33 91.25
238 988 101 F 246 1196 11 368 29 87.82
376 474 57 F 374 988 0 586 41 89.04
322 543 51 F 324 988 50 514 33 89.75
318 658 177 F 324 988 50 534 27 91.51
304 713 29 F 312 988 62 436 45 85.20
304 988 70 F 299 1297 69 467 34 88.63
323 912 58 F 324 988 50 531 29 91.02
283 988 91 F 283 1327 71 446 30 89.40
255 761 2 F 253 988 121 428 20 92.09
323 826 76 F 324 988 50 531 29 91.02
292 798 33 F 289 988 84 473 27 90.66
292 483 0 F 285 988 54 469 27 90.53
264 988 75 F 268 1365 0 436 24 90.91
289 630 20 F 290 988 49 411 42 85.47
286 380 10 F 289 988 50 479 24 91.61
288 846 223 F 290 988 49 490 22 92.36
290 902 26 F 289 988 50 483 24 91.70
289 988 50 F 290 1151 59 491 22 92.39
290 988 49 F 292 1230 114 478 26 91.03
288 451 41 F 285 988 54 485 22 92.28
337 736 68 F 339 988 0 540 34 89.91
332 988 7 F 333 1100 3 489 44 86.75
295 988 44 F 297 1143 5 428 41 86.10
185 642 0 F 185 988 154 282 22 88.11
156 849 95 F 156 988 159 260 13 91.67
174 935 88 F 170 988 177 260 21 87.65
243 988 131 F 246 1076 31 357 33 86.42
346 988 28 F 337 1120 0 467 54 83.98
223 579 0 F 223 988 116 322 31 86.10
239 988 67 F 241 1456 22 344 34 85.77
85 454 220 F 84 1456 181 157 3 96.43
85 454 220 F 85 1196 139 162 2 97.65
85 454 220 F 85 474 281 162 2 97.65
85 454 220 F 85 543 221 162 2 97.65
85 454 220 F 85 658 343 162 2 97.65
85 454 220 F 85 713 181 162 2 97.65
85 454 220 F 85 1297 216 162 2 97.65
85 454 220 F 85 912 229 162 2 97.65
85 454 220 F 85 1327 202 162 2 97.65
85 454 220 F 85 761 105 162 2 97.65
85 454 220 F 85 826 247 162 2 97.65
85 454 220 F 86 798 173 159 3 96.47
85 454 220 F 85 483 175 162 2 97.65
85 454 220 F 85 1365 151 162 2 97.65
85 454 220 F 85 630 192 162 2 97.65
85 380 179 F 85 454 220 162 2 97.65
85 454 220 F 85 846 394 158 3 96.47
85 454 220 F 85 902 199 162 2 97.65
85 454 220 F 85 1151 232 162 2 97.65
85 454 220 F 85 1230 289 162 2 97.65
85 451 212 F 85 454 220 162 2 97.65
85 454 220 F 85 736 288 162 2 97.65
85 454 220 F 85 1100 219 162 2 97.65
85 454 220 F 85 1143 185 162 2 97.65
85 454 220 F 85 642 68 158 3 96.47
85 454 220 F 85 849 159 146 6 92.94
83 454 220 F 83 506 105 158 2 97.59
83 454 220 F 83 1049 233 158 2 97.59
83 454 220 F 83 1328 175 154 3 96.39
85 454 220 F 86 935 137 147 6 92.94
85 454 220 F 84 1076 126 153 4 95.24
85 454 220 F 84 1120 186 157 3 96.43
85 454 220 F 84 579 107 153 4 95.24
284 580 73 F 284 762 131 560 2 99.30
189 413 38 F 189 1250 74 286 23 87.83
339 1802 3 F 340 1877 0 667 3 99.12
200 3 299 F 199 5 337 343 14 92.96
309 5 337 F 309 39 371 510 27 91.26
309 5 337 F 310 6 300 503 29 90.61
200 3 299 F 199 16 455 335 16 91.96
153 2 371 F 156 3 299 253 14 90.85
309 16 455 F 309 39 371 498 30 90.29
197 2 371 F 202 39 371 299 25 87.31
310 6 300 F 309 16 455 495 31 89.97
197 2 371 F 202 6 300 295 26 86.80
362 662 80 F 367 1193 8 569 40 88.95
189 413 38 F 189 1250 74 286 23 87.83
165 1035 43 F 169 1768 256 226 27 83.64
208 1138 64 F 200 1215 247 280 32 84.00
174 1564 0 F 174 1847 123 312 9 94.83
368 965 0 F 366 1082 58 662 18 95.08
245 902 66 F 243 1327 71 408 20 91.77
245 1151 99 F 243 1327 71 408 20 91.77
247 451 77 F 244 1327 70 407 21 91.39
245 736 155 F 243 1327 71 408 20 91.77
318 1049 99 F 314 1327 71 488 36 88.54
439 543 16 F 436 1327 0 751 31 92.89
338 761 1 F 337 1327 99 643 8 97.63
367 826 114 F 365 1327 71 676 14 96.16
245 846 261 F 243 1327 71 404 21 91.36
285 380 6 F 284 1327 30 429 35 87.68
283 988 91 F 283 1327 71 446 30 89.40
363 1297 87 F 365 1327 71 672 14 96.14
152 506 168 F 153 1189 178 273 8 94.74
152 1049 296 F 153 1189 178 273 8 94.74
153 1189 178 F 152 1328 238 269 9 94.08
139 988 286 F 140 1189 178 243 9 93.53
351 474 189 F 360 935 37 607 26 92.59
350 543 130 F 360 935 37 606 26 92.57
348 658 254 F 360 935 37 596 28 91.95
327 713 113 F 335 935 62 574 22 93.27
360 935 37 F 348 1297 127 600 27 92.24
346 912 137 F 355 935 37 597 26 92.49
324 935 48 F 314 1327 122 534 26 91.72
336 761 5 F 346 935 28 562 30 91.07
333 826 148 F 344 935 28 561 29 91.29
349 935 48 F 340 1076 44 569 30 91.18
350 798 83 F 359 935 38 589 30 91.43
340 935 57 F 330 1120 114 566 26 92.12
435 474 105 F 433 798 0 792 19 95.61
286 798 0 F 287 902 24 461 28 90.21
286 798 0 F 287 1151 57 469 26 90.91
254 451 70 F 253 798 33 435 18 92.89
286 736 114 F 286 798 0 472 25 91.26
357 798 0 F 359 1049 58 544 43 87.96
429 543 51 F 430 798 3 771 22 94.87
408 798 0 F 407 826 74 735 20 95.09
285 798 1 F 284 846 222 461 27 90.49
283 380 8 F 286 798 0 453 29 89.75
292 798 33 F 289 988 84 473 27 90.66
259 798 27 F 263 1365 0 422 25 90.35
268 798 18 F 268 1360 39 420 29 89.18
428 798 0 F 428 912 55 776 20 95.33
171 454 45 F 169 798 0 252 22 86.98
142 798 27 F 143 1837 2 221 16 88.73
110 798 59 F 110 1722 43 176 11 90.00
424 892 0 F 420 1300 64 748 24 94.29
381 309 0 F 374 804 82 691 16 95.72
369 724 42 F 407 1826 28 520 62 83.20
68 643 127 F 69 770 105 101 9 86.76
337 497 105 F 336 1549 0 593 17 94.94
336 1544 24 F 336 1549 0 588 18 94.64
249 1549 0 F 249 1551 9 422 16 93.57
160 1546 202 F 160 1549 0 308 3 98.12
160 1547 186 F 160 1549 0 300 5 96.88
309 1649 13 F 309 1931 0 546 18 94.17
309 1708 8 F 305 1931 0 490 30 90.16
248 1868 37 F 248 1948 21 400 24 90.32
299 1871 0 F 296 1892 0 515 20 93.24
293 1664 0 F 296 1871 3 469 30 89.76
369 1475 72 F 376 1594 0 577 42 88.62
329 1592 0 F 322 1595 8 583 17 94.72
115 809 79 F 115 1427 155 154 19 83.48
415 452 0 F 413 882 3 724 26 93.70
330 588 0 F 330 775 103 580 20 93.94
375 37 0 F 383 1823 0 670 22 94.13
144 16 8 F 141 47 297 185 25 82.27
144 1 302 F 141 47 297 185 25 82.27
143 4 313 F 144 16 8 203 21 85.31
144 1 302 F 143 4 313 203 21 85.31
255 597 0 F 253 1372 137 440 17 93.28
258 871 99 F 264 1710 140 426 24 90.70
343 1302 67 F 343 1433 4 606 20 94.17
309 5 337 F 310 6 300 503 29 90.61
309 5 337 F 309 39 371 510 27 91.26
310 6 300 F 309 16 455 495 31 89.97
309 16 455 F 309 39 371 498 30 90.29
112 3 510 F 110 5 546 158 16 85.45
112 3 510 F 110 16 664 154 17 84.55
404 1268 97 F 411 1627 3 723 23 94.31
403 1627 8 F 408 1747 0 735 19 95.29
270 313 34 F 265 1782 2 451 21 92.08
223 313 78 F 220 1827 5 383 15 93.18
224 1782 39 F 224 1827 0 404 11 95.09
22 215 205 F 22 215 208 44 0 100.00
449 1745 9 F 440 1882 0 773 27 93.86
433 1745 0 F 427 1764 1 748 28 93.44
211 936 0 F 215 937 160 370 14 93.36
366 197 112 F 359 385 0 641 21 94.15
265 454 62 F 264 1722 0 473 14 94.70
256 1722 8 F 256 1837 0 464 12 95.31
247 885 66 F 249 1051 243 456 10 95.95
245 885 68 F 247 1021 3 440 13 94.69
110 497 332 F 110 1549 226 212 2 98.18
110 1544 250 F 110 1549 226 208 3 97.27
23 1549 226 F 23 1551 235 46 0 100.00
51 36 324 F 52 42 193 87 4 92.16
40 31 243 F 40 42 202 80 0 100.00
40 31 243 F 40 36 332 80 0 100.00
20 7 258 F 20 31 243 40 0 100.00
20 7 258 F 20 42 202 40 0 100.00
335 546 114 F 332 884 41 639 7 97.89
446 1620 20 F 439 1937 0 721 41 90.66
349 1546 15 F 348 1547 0 673 6 98.28
80 35 204 F 80 73 144 152 2 97.50
80 72 215 F 80 73 144 152 2 97.50
155 13 260 F 152 35 147 223 21 86.18
114 13 301 F 111 72 199 157 17 84.68
82 13 317 F 80 73 144 122 10 87.50
324 912 17 F 329 1230 72 537 29 91.05
510 736 0 F 522 846 94 872 40 92.16
256 483 31 F 249 713 44 389 29 88.35
256 713 37 F 261 902 50 401 29 88.67
291 713 2 F 302 1151 42 429 41 85.91
284 713 9 F 295 1230 106 423 39 86.27
276 451 48 F 266 713 27 410 33 87.59
269 713 24 F 276 736 124 409 34 87.36
183 713 110 F 184 1143 113 327 10 94.54
362 713 2 F 373 1049 44 503 58 83.98
448 543 32 F 440 713 0 772 29 93.41
435 713 0 F 446 912 37 749 33 92.41
338 713 79 F 340 761 1 650 7 97.93
405 713 10 F 413 826 68 690 32 92.10
423 713 17 F 432 798 1 719 34 91.96
441 658 161 F 438 713 2 743 34 92.24
416 713 24 F 420 1120 24 744 23 94.47
282 713 11 F 291 846 215 409 41 85.46
414 713 1 F 420 1327 16 686 37 91.06
347 713 17 F 359 1328 0 462 61 82.42
289 380 2 F 283 713 10 416 39 86.22
407 630 9 F 408 902 15 695 30 92.63
415 630 1 F 418 1151 38 705 32 92.29
407 630 9 F 407 1230 106 694 30 92.63
348 451 86 F 349 630 65 649 12 96.55
412 630 2 F 414 736 96 698 32 92.23
390 630 26 F 393 1100 50 659 30 92.31
364 483 16 F 358 630 38 630 23 93.58
425 630 9 F 426 1143 1 683 41 90.35
308 630 1 F 309 1049 40 445 43 86.04
171 630 78 F 172 1189 0 283 15 91.23
274 605 109 F 274 630 142 532 4 98.54
325 630 91 F 324 641 0 569 20 93.83
307 474 86 F 303 630 1 446 41 86.47
301 543 32 F 303 630 1 444 40 86.71
193 630 111 F 192 1297 136 333 13 93.23
303 630 1 F 304 912 37 451 39 87.13
215 630 89 F 215 761 2 362 17 92.09
304 630 0 F 306 826 53 442 42 86.18
284 630 20 F 283 798 3 399 42 85.16
303 630 1 F 298 658 157 433 42 85.91
227 630 77 F 224 713 69 359 23 89.73
227 630 77 F 224 1120 73 359 23 89.73
415 630 1 F 416 846 202 695 34 91.81
370 630 64 F 372 1365 21 658 21 94.32
166 630 128 F 165 849 95 271 15 90.91
633 2 0 F 652 16 84 1165 30 95.26
192 1 378 F 187 2 0 343 9 95.19
68 2 0 F 68 39 0 132 1 98.53
68 2 0 F 66 47 372 94 10 84.85
68 2 0 F 68 4 388 104 8 88.24
267 1851 45 F 267 1879 0 466 17 93.63
43 1225 317 F 44 1225 347 75 3 93.02
231 1859 0 F 231 1936 147 442 5 97.84
231 460 238 F 231 1859 0 450 3 98.70
231 1351 210 F 231 1859 0 450 3 98.70
352 422 168 F 367 1126 0 611 27 92.33
242 4 422 F 238 5 0 384 24 89.92
215 4 422 F 213 7 0 360 17 92.02
256 310 69 F 255 1363 75 483 7 97.25
432 701 5 F 422 715 7 690 41 90.28
359 11 153 F 356 29 155 639 19 94.66
322 849 95 F 331 935 66 537 29 90.99
336 761 5 F 346 935 28 562 30 91.07
333 826 148 F 344 935 28 561 29 91.29
350 867 233 F 355 1602 0 633 18 94.86
365 950 12 F 366 1041 0 639 23 93.70
390 1449 38 F 392 1451 4 670 28 92.82
445 1362 1 F 425 1500 52 686 46 89.18
393 819 101 F 413 1362 33 674 33 91.60
396 975 76 F 417 1362 0 645 42 89.39
296 404 337 F 299 1362 147 543 13 95.61
297 1301 54 F 299 1362 147 548 12 95.96
415 223 2 F 414 271 2 793 9 97.83
376 558 0 F 368 1254 134 668 19 94.84
278 1288 43 F 275 1374 150 477 19 93.09
312 1125 50 F 312 1507 110 460 37 88.14
344 322 70 F 346 793 68 514 42 87.79
157 735 388 F 157 1479 204 266 12 92.36
200 3 299 F 199 5 337 343 14 92.96
200 3 299 F 199 16 455 335 16 91.96
309 5 337 F 309 39 371 510 27 91.26
309 16 455 F 309 39 371 498 30 90.29
309 5 337 F 310 6 300 503 29 90.61
310 6 300 F 309 16 455 495 31 89.97
290 1147 13 F 293 1331 123 503 20 93.10
404 1764 10 F 403 1882 0 755 13 96.77
255 1382 47 F 266 1933 214 393 32 87.45
327 825 146 F 320 862 53 587 15 95.31
386 432 25 F 373 862 0 647 28 92.49
332 652 71 F 323 862 50 575 20 93.81
373 492 0 F 361 862 12 638 24 93.35
337 862 22 F 349 1469 105 590 24 92.88
307 742 26 F 302 862 53 517 23 92.38
372 862 0 F 385 1874 2 613 36 90.32
258 695 127 F 257 1324 95 331 46 82.10
237 938 95 F 232 1324 120 301 42 81.90
317 1381 25 F 332 1661 121 421 56 82.33
396 584 79 F 407 1661 35 627 43 89.14
352 474 188 F 353 1076 31 633 18 94.89
351 543 129 F 353 1076 31 636 17 95.16
349 658 253 F 353 1076 31 626 19 94.56
350 713 90 F 353 1076 31 631 18 94.86
344 1076 40 F 342 1297 133 622 16 95.32
347 912 136 F 348 1076 31 631 16 95.39
328 1076 31 F 326 1327 110 578 19 94.17
329 761 12 F 330 1076 31 599 15 95.44
326 826 155 F 328 1076 31 590 16 95.09
349 798 84 F 349 1076 35 618 20 94.27
453 474 87 F 444 1120 0 765 33 92.57
376 543 104 F 376 1120 68 696 14 96.28
444 658 158 F 444 1120 0 752 34 92.34
416 713 24 F 420 1120 24 744 23 94.47
444 1120 0 F 439 1297 36 735 37 91.57
445 912 38 F 439 1120 0 760 31 92.94
395 1120 24 F 396 1327 40 659 33 91.65
339 761 0 F 336 1120 83 631 11 96.73
426 826 55 F 419 1120 0 709 34 91.89
432 798 1 F 428 1120 16 716 36 91.59
351 474 189 F 360 935 37 607 26 92.59
350 543 130 F 360 935 37 606 26 92.57
348 658 254 F 360 935 37 596 28 91.95
327 713 113 F 335 935 62 574 22 93.27
360 935 37 F 348 1297 127 600 27 92.24
346 912 137 F 355 935 37 597 26 92.49
324 935 48 F 314 1327 122 534 26 91.72
336 761 5 F 346 935 28 562 30 91.07
333 826 148 F 344 935 28 561 29 91.29
350 798 83 F 359 935 38 589 30 91.43
348 579 0 F 350 630 84 598 25 92.82
331 380 72 F 330 579 0 581 20 93.94
330 579 0 F 331 846 287 577 21 93.64
330 579 0 F 331 902 92 585 19 94.24
330 579 0 F 331 1151 125 585 19 94.24
330 579 0 F 334 1230 179 588 19 94.24
329 451 105 F 328 579 0 581 19 94.21
328 579 0 F 329 736 181 581 19 94.21
330 579 0 F 331 1100 112 581 20 93.94
239 630 175 F 239 1289 3 446 8 96.65
239 380 162 F 239 1289 3 446 8 96.65
239 846 377 F 239 1289 3 442 9 96.23
239 902 182 F 239 1289 3 446 8 96.65
239 1151 215 F 239 1289 3 446 8 96.65
239 1230 272 F 239 1289 3 446 8 96.65
239 451 195 F 239 1289 3 446 8 96.65
239 736 271 F 239 1289 3 446 8 96.65
239 1100 202 F 239 1289 3 442 9 96.23
304 481 0 F 296 579 34 520 20 93.24
243 481 59 F 241 1289 1 436 12 95.02
347 579 1 F 350 1365 43 605 23 93.37
239 1289 3 F 239 1365 134 438 10 95.82
326 579 0 F 327 1360 88 549 26 92.02
237 1289 3 F 237 1360 178 434 10 95.78
323 579 7 F 324 641 0 535 28 91.33
239 641 83 F 239 1289 3 422 14 94.14
250 579 80 F 252 1198 76 434 17 93.20
242 1198 84 F 239 1289 3 413 17 92.89
313 483 67 F 310 579 0 539 21 93.23
222 483 158 F 221 1289 3 415 7 96.83
321 1941 0 F 323 1942 31 524 30 90.65
475 404 165 F 476 1500 8 779 43 90.95
425 404 215 F 423 819 78 748 25 94.09
389 404 215 F 392 975 80 717 16 95.89
415 630 1 F 416 846 202 695 34 91.81
400 380 3 F 403 846 215 763 10 97.50
419 846 199 F 422 902 1 777 16 96.18
454 846 164 F 456 1151 0 842 17 96.26
493 846 125 F 503 1230 10 832 41 91.68
393 451 41 F 389 846 227 754 7 98.20
510 736 0 F 522 846 94 872 40 92.16
395 846 223 F 399 1100 44 714 20 94.94
371 846 247 F 375 1365 0 686 15 95.96
349 483 31 F 345 846 253 662 8 97.68
393 474 0 F 392 846 114 625 40 89.80
333 543 0 F 340 846 166 541 33 90.09
402 658 53 F 421 846 85 647 44 89.05
282 713 11 F 291 846 215 409 41 85.46
284 846 222 F 277 1297 51 445 29 89.53
341 846 165 F 341 912 0 566 29 91.50
245 846 261 F 243 1327 71 404 21 91.36
215 761 2 F 214 846 292 385 11 94.86
359 826 0 F 356 846 150 583 33 90.73
396 846 222 F 400 1143 9 692 26 93.43
299 846 261 F 305 1196 1 508 24 91.97
221 506 0 F 217 846 294 350 22 89.86
348 846 163 F 349 1049 0 569 32 90.80
303 846 203 F 297 1120 0 440 40 86.53
257 846 222 F 260 1456 5 357 40 84.44
304 481 0 F 296 846 322 540 15 94.93
170 846 281 F 172 1189 0 306 9 94.71
324 641 0 F 324 846 294 596 13 95.99
383 605 0 F 382 846 236 693 18 95.29
265 454 62 F 264 1722 0 473 14 94.70
83 988 223 F 83 1722 157 154 3 96.39
84 1456 181 F 85 1722 157 149 5 94.05
85 1196 139 F 85 1722 157 154 4 95.29
85 474 281 F 85 1722 157 154 4 95.29
85 543 221 F 85 1722 157 154 4 95.29
85 658 343 F 85 1722 157 154 4 95.29
85 713 181 F 85 1722 157 154 4 95.29
85 1297 216 F 85 1722 157 154 4 95.29
85 912 229 F 85 1722 157 154 4 95.29
85 1327 202 F 85 1722 157 154 4 95.29
85 761 105 F 85 1722 157 154 4 95.29
85 826 247 F 85 1722 157 154 4 95.29
85 483 175 F 85 1722 157 154 4 95.29
85 1365 151 F 85 1722 157 154 4 95.29
85 630 192 F 85 1722 157 154 4 95.29
85 380 179 F 85 1722 157 154 4 95.29
85 902 199 F 85 1722 157 154 4 95.29
85 1151 232 F 85 1722 157 154 4 95.29
85 1230 289 F 85 1722 157 154 4 95.29
85 451 212 F 85 1722 157 154 4 95.29
85 736 288 F 85 1722 157 154 4 95.29
85 1100 219 F 85 1722 157 154 4 95.29
85 1143 185 F 85 1722 157 154 4 95.29
83 506 105 F 83 1722 157 150 4 95.18
83 1049 233 F 83 1722 157 150 4 95.18
84 1120 186 F 85 1722 157 149 5 94.05
85 481 80 F 85 1722 157 150 5 94.12
57 1189 115 F 57 1722 157 102 3 94.74
82 641 103 F 82 1722 160 144 5 93.90
85 605 159 F 85 1722 157 150 5 94.12
85 454 220 F 85 846 394 158 3 96.47
288 846 223 F 290 988 49 490 22 92.36
85 846 394 F 85 1722 157 154 4 95.29
330 579 0 F 331 846 287 577 21 93.64
84 579 107 F 85 1722 157 145 6 92.86
257 642 0 F 258 846 325 455 15 94.16
85 642 68 F 85 1722 157 150 5 94.12
285 798 1 F 284 846 222 461 27 90.49
86 798 173 F 85 1722 157 151 5 94.12
157 626 157 F 166 1513 18 187 34 78.34
305 1066 1 F 311 1600 69 444 43 85.90
407 1143 2 F 407 1230 106 718 24 94.10
296 912 45 F 297 1143 0 453 35 88.18
172 1189 0 F 173 1230 173 313 8 95.35
171 912 115 F 172 1189 0 311 8 95.32
173 1143 69 F 172 1189 0 301 11 93.60
257 1640 92 F 254 1840 0 455 14 94.49
282 647 2 F 279 1388 62 493 17 93.91
189 413 38 F 189 1250 74 286 23 87.83
384 738 115 F 391 1384 0 671 26 93.23
377 739 2 F 383 1384 8 592 42 88.86
389 848 138 F 404 1658 0 637 39 89.97
343 1302 67 F 343 1433 4 606 20 94.17
435 474 105 F 433 798 0 792 19 95.61
429 543 51 F 430 798 3 771 22 94.87
428 658 174 F 433 798 0 773 22 94.86
423 713 17 F 432 798 1 719 34 91.96
411 798 22 F 406 1297 69 729 22 94.58
428 798 0 F 428 912 55 776 20 95.33
368 798 40 F 365 1327 71 661 18 95.07
341 761 0 F 341 798 69 654 7 97.95
408 798 0 F 407 826 74 735 20 95.09
255 483 32 F 253 798 33 428 20 92.09
259 798 27 F 263 1365 0 422 25 90.35
284 630 20 F 283 798 3 399 42 85.16
283 380 8 F 286 798 0 453 29 89.75
285 798 1 F 284 846 222 461 27 90.49
286 798 0 F 287 902 24 461 28 90.21
286 798 0 F 287 1151 57 469 26 90.91
285 798 1 F 288 1230 113 453 30 89.47
254 451 70 F 253 798 33 435 18 92.89
286 736 114 F 286 798 0 472 25 91.26
253 798 33 F 255 1100 76 400 27 89.33
232 798 54 F 232 1143 65 376 22 90.52
215 798 71 F 220 1196 32 351 21 90.23
289 506 0 F 284 798 73 425 37 86.97
357 798 0 F 359 1049 58 544 43 87.96
356 798 1 F 359 1328 0 499 54 84.83
349 798 84 F 349 1076 35 618 20 94.27
432 798 1 F 428 1120 16 716 36 91.59
241 798 18 F 243 1456 22 340 36 85.06
192 481 0 F 185 798 101 293 21 88.65
171 798 60 F 172 1189 0 291 13 92.40
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212 641 0 F 213 798 73 353 18 91.51
130 798 156 F 129 1289 3 203 14 89.15
268 798 18 F 268 1360 39 420 29 89.18
271 605 0 F 270 798 16 401 35 87.04
85 454 220 F 86 798 173 159 3 96.47
292 798 33 F 289 988 84 473 27 90.66
86 798 173 F 85 1722 157 151 5 94.12
86 798 173 F 85 1837 149 151 5 94.12
362 1912 0 F 358 1913 0 624 24 93.30
446 1620 20 F 439 1937 0 721 41 90.66
456 1796 26 F 446 1937 0 718 46 89.69
349 483 31 F 349 1365 6 634 16 95.42
369 902 54 F 373 1365 2 690 13 96.48
371 1151 85 F 375 1365 0 694 13 96.50
372 1230 141 F 373 1365 2 677 17 95.43
372 451 62 F 373 1365 0 685 15 95.97
369 736 141 F 373 1365 0 690 13 96.48
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261 474 132 F 263 1365 0 448 19 92.72
257 543 76 F 261 1365 2 446 18 93.00
259 912 82 F 263 1365 0 438 21 91.89
215 761 2 F 215 1365 48 382 12 94.42
257 826 102 F 261 1365 2 438 20 92.22
259 798 27 F 263 1365 0 422 25 90.35
256 658 199 F 263 1365 0 439 20 92.19
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356 1441 10 F 356 1513 37 648 16 95.51
633 2 0 F 652 16 84 1165 30 95.26
602 5 96 F 601 16 214 1099 26 95.67
238 3 58 F 238 16 214 404 18 92.44
141 6 156 F 141 16 311 250 8 94.33
96 59 356 F 97 651 175 145 12 87.50
416 1620 0 F 415 1796 6 743 22 94.70
438 905 0 F 451 1693 83 677 53 87.90
27 31 3 F 26 632 165 49 1 96.15
420 61 134 F 424 65 137 752 22 94.76
381 61 134 F 380 64 137 701 15 96.05
254 642 0 F 256 1365 81 462 12 95.28
258 579 37 F 257 642 0 427 22 91.44
258 630 123 F 257 642 0 455 15 94.16
258 380 110 F 257 642 0 463 13 94.94
257 642 0 F 258 846 325 455 15 94.16
257 642 0 F 258 902 130 463 13 94.94
257 642 0 F 258 1151 163 463 13 94.94
257 642 0 F 258 1230 220 463 13 94.94
258 451 143 F 257 642 0 463 13 94.94
257 642 0 F 258 736 219 463 13 94.94
257 642 0 F 258 1100 150 459 14 94.55
206 642 51 F 206 1289 3 376 9 95.63
258 481 11 F 251 642 6 429 20 92.03
195 610 53 F 196 642 61 359 8 95.90
257 642 0 F 258 1360 126 451 16 93.77
228 642 6 F 231 1196 75 395 16 92.98
256 641 33 F 257 642 0 441 18 92.97
227 642 30 F 231 1198 62 390 17 92.51
259 483 106 F 257 642 0 460 14 94.55
238 2 130 F 238 39 130 412 16 93.28
238 16 214 F 238 39 130 408 17 92.86
503 2 130 F 522 5 96 845 45 91.05
602 5 96 F 601 16 214 1099 26 95.67
238 2 130 F 238 3 58 408 17 92.86
238 3 58 F 238 16 214 404 18 92.44
117 2 130 F 117 7 96 182 13 88.89
117 7 96 F 117 16 214 182 13 88.89
329 1653 0 F 334 1828 74 587 19 94.22
278 1653 0 F 285 1947 68 491 18 93.53
350 372 1 F 348 1348 62 654 11 96.84
424 454 70 F 432 1837 0 772 21 95.05
265 454 62 F 264 1722 0 473 14 94.70
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403 380 0 F 407 902 16 774 9 97.77
403 380 0 F 407 1151 49 778 8 98.01
403 380 0 F 409 1230 104 760 13 96.77
387 380 14 F 393 451 41 744 9 97.67
401 380 0 F 404 736 106 777 7 98.25
393 380 10 F 399 1100 44 712 20 94.91
344 380 39 F 349 483 31 661 8 97.67
401 380 2 F 407 1143 2 692 29 92.77
296 380 0 F 298 1049 51 514 20 93.24
170 380 66 F 172 1189 0 310 8 95.29
381 380 22 F 383 605 0 688 19 95.01
292 483 0 F 285 988 54 469 27 90.53
289 630 20 F 290 988 49 411 42 85.47
290 902 26 F 289 988 50 483 24 91.70
289 988 50 F 290 1151 59 491 22 92.39
290 988 49 F 292 1230 114 478 26 91.03
288 451 41 F 285 988 54 485 22 92.28
337 736 68 F 339 988 0 540 34 89.91
332 988 7 F 333 1100 3 489 44 86.75
295 988 44 F 297 1143 5 428 41 86.10
377 988 49 F 376 1049 60 693 15 96.01
170 988 110 F 172 1189 0 302 10 94.12
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217 641 0 F 216 988 123 353 20 90.74
324 380 79 F 324 641 0 600 12 96.30
376 474 57 F 374 988 0 586 41 89.04
322 543 51 F 324 988 50 514 33 89.75
304 988 70 F 299 1297 69 467 34 88.63
323 912 58 F 324 988 50 531 29 91.02
255 761 2 F 253 988 121 428 20 92.09
323 826 76 F 324 988 50 531 29 91.02
292 798 33 F 289 988 84 473 27 90.66
291 380 0 F 296 474 97 507 20 93.13
290 380 1 F 292 543 41 494 22 92.41
282 380 9 F 277 1297 51 455 26 90.61
291 380 0 F 294 912 47 501 21 92.78
214 380 77 F 215 761 2 389 10 95.33
291 380 0 F 293 826 66 520 16 94.50
283 380 8 F 286 798 0 453 29 89.75
318 658 177 F 324 988 50 534 27 91.51
290 380 1 F 289 658 166 495 21 92.73
304 713 29 F 312 988 62 436 45 85.20
289 380 2 F 283 713 10 416 39 86.22
346 988 28 F 337 1120 0 467 54 83.98
291 380 0 F 288 1120 9 427 38 86.81
288 846 223 F 290 988 49 490 22 92.36
400 380 3 F 403 846 215 763 10 97.50
264 988 75 F 268 1365 0 436 24 90.91
368 380 35 F 373 1365 2 677 16 95.65
156 849 95 F 156 988 159 260 13 91.67
166 380 115 F 165 849 95 279 13 92.12
195 530 95 F 197 1304 115 296 24 87.69
282 591 0 F 283 1758 7 461 26 90.78
270 313 34 F 265 1782 2 451 21 92.08
257 1640 92 F 254 1840 0 455 14 94.49
440 654 1 F 432 866 142 668 51 88.19
306 807 164 F 304 866 242 546 16 94.74
64 390 291 F 68 390 344 88 11 82.81
84 310 109 F 84 310 149 160 2 97.62
84 310 149 F 84 1363 114 152 4 95.24
84 310 109 F 84 1363 154 148 5 94.05
84 1363 114 F 84 1363 154 140 7 91.67
302 877 174 F 310 1747 95 532 20 93.38
393 1268 103 F 405 1747 0 686 28 92.88
307 877 174 F 311 1627 103 566 13 95.77
404 1268 97 F 411 1627 3 723 23 94.31
403 1627 8 F 408 1747 0 735 19 95.29
343 568 69 F 345 1793 63 652 9 97.38
258 871 99 F 264 1710 140 426 24 90.70
125 515 132 F 126 1905 154 191 15 88.00
352 422 168 F 367 1126 0 611 27 92.33
324 428 0 F 320 1441 29 564 20 93.75
317 428 7 F 312 1513 64 573 14 95.51
415 223 2 F 414 271 2 793 9 97.83
191 735 195 F 194 1479 14 293 23 87.96
415 223 2 F 414 271 2 793 9 97.83
68 659 210 F 70 1509 181 98 10 85.29
379 1784 7 F 381 1799 0 656 26 93.14
195 530 95 F 197 1304 115 296 24 87.69
196 1304 116 F 193 1343 105 277 28 85.49
115 1304 124 F 113 1431 217 148 20 82.30
196 544 35 F 196 1304 116 296 24 87.76
362 1912 0 F 358 1913 0 624 24 93.30
152 719 114 F 156 1199 0 268 10 93.42
299 1548 0 F 300 1554 49 591 2 99.33
349 1554 0 F 347 1555 52 632 16 95.39
326 579 0 F 327 1360 88 549 26 92.02
374 630 38 F 375 1360 40 621 32 91.44
399 380 0 F 406 1360 9 705 25 93.73
379 605 0 F 381 1360 34 632 32 91.56
410 846 204 F 414 1360 1 700 31 92.44
404 902 15 F 407 1360 8 711 25 93.81
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384 451 48 F 383 1360 32 679 22 94.26
411 736 97 F 414 1360 1 721 26 93.67
405 1143 0 F 405 1360 10 638 43 89.38
322 1198 2 F 311 1360 104 513 30 90.35
413 1100 26 F 414 1360 1 663 41 90.07
237 1289 3 F 237 1360 178 434 10 95.78
21 7 257 F 21 36 331 42 0 100.00
610 3 0 F 607 39 72 1145 18 97.03
296 3 0 F 296 5 38 572 5 98.31
175 3 0 F 175 7 38 346 1 99.43
318 658 177 F 324 988 50 534 27 91.51
290 902 26 F 289 988 50 483 24 91.70
289 988 50 F 290 1151 59 491 22 92.39
337 736 68 F 339 988 0 540 34 89.91
288 846 223 F 290 988 49 490 22 92.36
377 988 49 F 376 1049 60 693 15 96.01
485 736 25 F 500 1230 11 869 29 94.02
429 543 51 F 430 798 3 771 22 94.87
428 798 0 F 428 912 55 776 20 95.33
341 761 0 F 341 798 69 654 7 97.95
408 798 0 F 407 826 74 735 20 95.09
255 483 32 F 253 798 33 428 20 92.09
286 798 0 F 287 902 24 461 28 90.21
286 798 0 F 287 1151 57 469 26 90.91
285 798 1 F 288 1230 113 453 30 89.47
254 451 70 F 253 798 33 435 18 92.89
286 736 114 F 286 798 0 472 25 91.26
232 798 54 F 232 1143 65 376 22 90.52
357 798 0 F 359 1049 58 544 43 87.96
428 658 174 F 433 798 0 773 22 94.86
432 798 1 F 428 1120 16 716 36 91.59
285 798 1 F 284 846 222 461 27 90.49
368 798 40 F 365 1327 71 661 18 95.07
292 483 0 F 285 1328 6 437 35 87.72
290 902 26 F 289 1328 2 451 32 88.93
290 1151 59 F 289 1328 2 455 31 89.27
293 1230 113 F 291 1328 0 464 30 89.69
282 451 47 F 280 1328 11 442 30 89.29
290 736 115 F 291 1328 0 457 31 89.31
222 1143 80 F 221 1328 70 355 22 90.05
389 1049 59 F 390 1328 0 679 25 93.57
353 543 51 F 357 1328 2 510 50 85.84
354 912 58 F 357 1328 2 527 46 87.01
277 761 2 F 278 1328 71 443 28 89.89
345 826 76 F 347 1328 2 528 41 88.12
349 658 177 F 357 1328 2 514 48 86.25
352 1120 16 F 358 1328 0 462 62 82.39
289 846 222 F 291 1328 0 448 33 88.58
314 1327 71 F 318 1328 41 460 43 86.31
356 798 1 F 359 1328 0 499 54 84.83
283 380 8 F 286 798 0 453 29 89.75
286 380 10 F 289 1328 2 447 32 88.81
292 798 33 F 289 988 84 473 27 90.66
377 988 49 F 377 1328 1 622 33 91.25
386 376 0 F 401 1694 81 607 45 88.34
316 442 114 F 317 1510 66 581 13 95.89
424 454 70 F 432 1837 0 772 21 95.05
265 454 62 F 264 1722 0 473 14 94.70
256 1722 8 F 256 1837 0 464 12 95.31
389 404 215 F 392 975 80 717 16 95.89
445 34 170 F 432 1317 10 749 32 92.59
313 560 59 F 311 1069 28 572 13 95.82
453 474 87 F 444 1120 0 765 33 92.57
376 543 104 F 376 1120 68 696 14 96.28
444 658 158 F 444 1120 0 752 34 92.34
416 713 24 F 420 1120 24 744 23 94.47
444 1120 0 F 439 1297 36 735 37 91.57
445 912 38 F 439 1120 0 760 31 92.94
395 1120 24 F 396 1327 40 659 33 91.65
322 849 95 F 322 1120 122 588 14 95.65
339 761 0 F 336 1120 83 631 11 96.73
426 826 55 F 419 1120 0 709 34 91.89
352 1076 32 F 348 1120 96 624 19 94.54
307 624 179 F 327 1619 0 470 41 86.64
425 489 0 F 429 1339 12 790 16 96.24
327 825 146 F 320 862 53 587 15 95.31
386 432 25 F 373 862 0 647 28 92.49
373 492 0 F 361 862 12 638 24 93.35
337 862 22 F 349 1469 105 590 24 92.88
332 652 71 F 323 862 50 575 20 93.81
247 885 66 F 249 1051 243 456 10 95.95
245 885 68 F 247 1021 3 440 13 94.69
415 223 2 F 414 271 2 793 9 97.83
72 126 102 F 73 544 88 141 1 98.61
360 530 60 F 360 544 0 672 12 96.67
360 544 0 F 358 1343 70 658 15 95.81
475 404 165 F 476 1500 8 779 43 90.95
425 404 215 F 423 819 78 748 25 94.09
296 404 337 F 299 1362 147 543 13 95.61
345 404 295 F 349 1301 9 614 20 94.20
389 404 215 F 392 975 80 717 16 95.89
152 506 168 F 153 1189 178 269 8 94.74
152 1049 296 F 153 1189 178 269 8 94.74
153 1189 178 F 152 1328 238 265 9 94.08
386 376 0 F 401 1694 81 607 45 88.34
330 1277 1 F 326 1694 81 580 19 94.17
254 1402 3 F 257 1694 225 359 38 85.04
418 432 4 F 419 825 65 773 16 96.17
377 432 37 F 376 492 0 733 5 98.67
397 432 0 F 403 1469 51 700 24 93.95
392 432 23 F 392 1874 0 716 17 95.66
293 22 368 F 282 29 0 471 26 90.78
404 549 32 F 412 661 104 712 26 93.56
78 859 0 F 81 1265 168 119 10 87.18
352 422 168 F 367 1126 0 611 27 92.33
236 1153 0 F 228 1161 110 348 29 87.28
123 470 352 F 126 991 113 233 4 96.75
119 991 114 F 117 1013 277 224 3 97.44
540 4 16 F 523 47 0 935 32 93.88
311 755 0 F 312 1412 113 535 22 92.93
123 470 352 F 126 991 113 233 4 96.75
119 991 114 F 117 1013 277 224 3 97.44
360 530 60 F 360 544 0 672 12 96.67
360 544 0 F 358 1343 70 658 15 95.81
287 1170 0 F 283 1347 84 466 26 90.81
genometools-1.5.1/testdata/repfind-20-query-extend.txt000066400000000000000000000051571211610345200227240ustar00rootroot0000000000000031 125 26 F 30 0 5965 45 4 86.67
23 632 166 F 24 0 5962 43 1 95.65
20 31 11 F 20 0 5966 40 0 100.00
23 859 207 F 23 0 17268 46 0 100.00
23 1214 204 F 23 0 17268 46 0 100.00
23 859 208 F 24 0 17266 43 1 95.65
34 1524 237 F 34 0 17269 44 6 82.35
47 1214 182 F 49 0 17242 52 11 76.60
30 1214 201 F 31 0 17260 49 3 90.00
25 1214 208 F 26 0 17265 47 1 96.00
25 1214 210 F 26 0 17265 47 1 96.00
25 1214 212 F 26 0 17265 47 1 96.00
25 1214 214 F 26 0 17265 47 1 96.00
32 1214 216 F 32 0 17265 52 3 90.62
42 1214 206 F 41 0 17256 51 8 80.49
33 1524 237 F 35 0 17271 48 5 84.85
20 859 208 F 20 0 17271 40 0 100.00
20 1214 205 F 20 0 17271 40 0 100.00
29 561 415 F 28 0 71278 49 2 92.86
29 561 415 F 29 0 71281 54 1 96.55
21 1231 159 F 21 0 71282 42 0 100.00
21 1318 180 F 21 0 71282 42 0 100.00
35 840 275 F 33 0 71280 52 4 87.88
33 561 411 F 33 0 71279 54 3 90.91
24 1231 156 F 23 0 71283 43 1 95.65
24 1318 177 F 23 0 71283 43 1 95.65
47 840 261 F 44 0 71270 59 8 81.82
37 561 404 F 34 0 71277 51 5 85.29
243 1265 90 F 243 0 72510 478 2 99.18
78 859 0 F 81 0 72588 119 10 87.18
78 859 0 F 81 0 72588 119 10 87.18
135 859 84 F 135 0 72651 254 4 97.04
40 859 211 F 39 0 72767 63 4 89.74
23 859 208 F 24 0 77812 43 1 95.65
36 1524 237 F 38 0 77815 54 5 86.11
23 859 208 F 23 0 77815 46 0 100.00
38 1214 205 F 38 0 77815 76 0 100.00
36 1214 205 F 37 0 77812 69 1 97.22
36 1214 205 F 35 0 77812 67 1 97.14
34 1214 207 F 33 0 77812 63 1 96.97
46 1214 209 F 44 0 77812 62 7 84.09
49 1214 206 F 48 0 77808 61 9 81.25
44 1214 208 F 43 0 77808 55 8 81.40
43 1214 210 F 42 0 77808 53 8 80.95
48 1214 205 F 46 0 77802 50 11 76.09
36 1524 237 F 36 0 77817 56 4 88.89
43 859 208 F 43 0 77817 50 8 81.40
34 1214 205 F 34 0 77817 68 0 100.00
36 1524 237 F 34 0 77819 54 4 88.24
43 859 208 F 41 0 77819 56 7 82.93
35 1214 205 F 35 0 77819 66 1 97.14
31 1524 237 F 30 0 77821 49 3 90.00
23 859 208 F 23 0 77821 46 0 100.00
33 1214 205 F 33 0 77821 62 1 96.97
32 1524 237 F 31 0 77823 47 4 87.10
23 859 208 F 23 0 77823 46 0 100.00
31 1214 205 F 31 0 77823 58 1 96.77
30 1524 237 F 29 0 77825 43 4 86.21
23 859 208 F 23 0 77825 46 0 100.00
35 1214 205 F 36 0 77825 55 4 88.57
28 1524 237 F 27 0 77827 43 3 88.89
23 859 208 F 23 0 77827 46 0 100.00
33 1214 205 F 34 0 77827 51 4 87.88
23 1524 237 F 24 0 77829 43 1 95.65
30 859 208 F 30 0 77829 48 3 90.00
31 1214 205 F 32 0 77829 47 4 87.10
23 1524 237 F 22 0 77831 41 1 95.45
23 859 208 F 23 0 77831 42 1 95.65
29 1214 205 F 30 0 77831 43 4 86.21
110 1361 1 F 103 0 105325 137 19 81.55
222 1361 148 F 222 0 105629 432 3 98.65
222 1361 148 F 222 0 105629 432 3 98.65
222 1361 148 F 222 0 105629 432 3 98.65
222 1361 148 F 222 0 105629 432 3 98.65
genometools-1.5.1/testdata/repfind-8-Atinsert.txt000066400000000000000000000414301211610345200220030ustar00rootroot00000000000000  16     0   258   F   16     0   259
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  17     1   319   F   17    16    25
  10     1   319   F   10     4   329
  10     4   329   F   10    16    25
   8     3   490   F    8     4   329
   8     1   319   F    8     3   490
   8     3   490   F    8    16    25
   9     4    82   F    9    17    97
  14     1   388   F   14     2    10
  14     1   388   F   14     4   398
  14     2    10   F   14     4   398
  14     1   388   F   14    16    94
  14     2    10   F   14    16    94
  14     4   398   F   14    16    94
   9     3   120   F    9     5   158
   9     3   120   F    9     7   158
   9     5   158   F    9     7   158
   8     3   120   F    8     6   120
   8     5   158   F    8     6   120
   8     6   120   F    8     7   158
   9     2   192   F    9    16   276
   8     8    48   F    8    10   227
   8     8   557   F    8    19   592
   8     3   548   F    8    19   496
   8     5   584   F    8    19   496
   8     6   548   F    8    19   496
   8    16   702   F    8    19   496
  12     3    35   F   12     5    73
  12     3    35   F   12     7    73
  12     5    73   F   12     7    73
   8     5   543   F    8    16   661
   9     2   353   F    9     3   281
   9     2   353   F    9     5   319
   9     3   281   F    9     5   319
   9     2   353   F    9     6   282
   9     3   281   F    9     6   282
   9     5   319   F    9     6   282
   9     2   353   F    9    16   437
   9     3   281   F    9    16   437
   9     5   319   F    9    16   437
   9     6   282   F    9    16   437
   8     0   148   F    8     5   769
   8     3   723   F    8    17   254
  24     3    48   F   24     4   508
  24     3    48   F   24     5    86
  24     4   508   F   24     5    86
  24     3    48   F   24     7    86
  24     4   508   F   24     7    86
  24     5    86   F   24     7    86
   8     2   319   F    8     3   247
   8     2   319   F    8     5   285
   8     3   247   F    8     5   285
   8     2   319   F    8     6   248
   8     3   247   F    8     6   248
   8     5   285   F    8     6   248
   8     3    19   F    8     4   479
   8     3    19   F    8     5    57
   8     4   479   F    8     5    57
   8     3    19   F    8     7    57
   8     4   479   F    8     7    57
   8     5    57   F    8     7    57
   8     0    95   F    8    20   222
   8     2   250   F    8     3   425
   8     2   250   F    8     6   426
   8     3   425   F    8    16   334
   8     6   426   F    8    16   334
   8     6   585   F    8     8   268
   8     1   352   F    8     1   392
   8     1   352   F    8     2    14
   8     1   352   F    8     4   402
   8     1   352   F    8    16    98
   8     1   392   F    8    16    58
   8     2    14   F    8    16    58
   8     4   402   F    8    16    58
   8    16    58   F    8    16    98
  14     1   509   F   14     3    58
  14     2   130   F   14     3    58
  14     1   509   F   14     4   518
  14     2   130   F   14     4   518
  14     1   509   F   14     5    96
  14     2   130   F   14     5    96
  14     1   509   F   14     7    96
  14     2   130   F   14     7    96
  14     3    58   F   14    16   214
  14     4   518   F   14    16   214
  14     5    96   F   14    16   214
  14     7    96   F   14    16   214
   8     5   670   F    8     6   629
   8     4   123   F    8    14   193
   8     8    46   F    8     8   497
  20     3   319   F   20     6   320
  20     2   391   F   20     5   357
  20     2   391   F   20    16   475
  20     5   357   F   20    16   475
  18     2   391   F   18     3   319
  18     3   319   F   18     5   357
  18     3   319   F   18    16   475
  18     2   391   F   18     6   320
  18     5   357   F   18     6   320
  18     6   320   F   18    16   475
   8     2   577   F    8     6   518
   8     6   518   F    8    16   673
   8     2   577   F    8    16   673
   8     4   251   F    8     8    74
  10     2   232   F   10     6   161
  10     6   161   F   10    16   316
  10     5   198   F   10     6   161
  10     3   160   F   10     6   161
  10     6   161   F   10     7   198
   9     3   324   F    9     7   352
   9     6   325   F    9     7   352
   9     2   396   F    9     7   352
   9     5   362   F    9     7   352
   9     7   352   F    9    16   480
   8    15   356   F    8    18    94
  11     3   546   F   11     5   582
  11     3   546   F   11     6   546
  11     5   582   F   11     6   546
  11     3   546   F   11    16   700
  11     5   582   F   11    16   700
  11     6   546   F   11    16   700
   8     8   364   F    8    17    92
   8     1   738   F    8    17   610
   8    11   594   F    8    17   610
   8     0   182   F    8    17   613
   9     2   490   F    9     5   456
   9     2   490   F    9    16   574
  12     2   439   F   12     5   405
  12     2   439   F   12    16   523
  12     5   405   F   12    16   523
  14     1   417   F   14     2    39
  14     1   417   F   14    16   123
  14     2    39   F   14    16   123
  11     2   211   F   11    16   295
  25     3   416   F   25     6   417
  20     1    45   F   20     4    52
   9     3    52   F    9     4   368
   9     4   368   F    9     4   512
   9     4   368   F    9     5    90
   9     4   368   F    9     7    90
   8     1   358   F    8     4   368
   8     4   368   F    8    16    64
   8    18   389   F    8    20   159
  11     5   636   F   11    16   754
   9     3   601   F    9     5   636
   9     3   601   F    9    16   754
   8     4   564   F    8    17   575
  10     6   614   F   10    15   376
   8     3   103   F    8     6   614
   8     3   103   F    8    15   376
   8     5   141   F    8     6   614
   8     5   141   F    8    15   376
   8     3   103   F    8     5   141
   8     6   614   F    8     7   141
   8     7   141   F    8    15   376
   8     3   103   F    8     7   141
   8     5   141   F    8     7   141
   8     4    47   F    8    14   450
   9     3   728   F    9     6   735
   9     0   257   F    9    20   161
   8    16   800   F    8    20   161
   8     2   491   F    8    13   179
   8     5   457   F    8    13   179
   8    13   179   F    8    16   575
  10     1   296   F   10    16     2
   8     1   296   F    8     8   255
   8     8   255   F    8    16     2
  11     2   440   F   11     3   368
  11     3   368   F   11     5   406
  11     2   440   F   11     6   369
  11     5   406   F   11     6   369
  11     3   368   F   11    16   524
  11     6   369   F   11    16   524
  10     9    35   F   10    17   183
  11     5   454   F   11    16   572
   8     6   489   F    8    18   466
   8     6   489   F    8    20   194
   8     3   433   F    8     5   471
   8     5   471   F    8     6   434
   8     3   433   F    8    16   589
   8     6   434   F    8    16   589
   8     3   550   F    8    19   513
   8     2   240   F    8     4   630
   8     4   630   F    8    16   324
   8     4   630   F    8     5   206
   8     3   168   F    8     4   630
  10     2   212   F   10     6   622
  10     6   622   F   10    16   296
   8    14   286   F    8    19   452
   8     4    35   F    8    14   292
  22     3   157   F   22     5   195
  18     5   195   F   18     7   195
  18     3   157   F   18     7   195
  13     3   613   F   13     6   608
   8     1    73   F    8     4    80
   8     1   403   F    8     2    25
   8     1   403   F    8    16   109
   8     2    25   F    8    16   109
   9     0   243   F    9     8   327
   8     1   836   F    8     8    94
   8     2   489   F    8    13   211
  17     5   612   F   17    16   730
   9     1   357   F    9     3    51
   9     3    51   F    9    16    63
   9     1   357   F    9     4   511
   9     4   511   F    9    16    63
   9     1   357   F    9     5    89
   9     5    89   F    9    16    63
   9     1   357   F    9     7    89
   9     7    89   F    9    16    63
   8     1    46   F    8     3   121
   8     3   121   F    8     4    53
   8     1    46   F    8     5   159
   8     4    53   F    8     5   159
   8     1    46   F    8     7   159
   8     4    53   F    8     7   159
   9     5   637   F    9     6   601
   9     6   601   F    9    16   755
   8     3   602   F    8     6   601
  12     3   367   F   12     6   368
   8     1   263   F    8     4   273
  29     2   229   F   29    16   313
   9    18   465   F    9    20   193
   8     0   138   F    8    14   285
   8     0   150   F    8     7   269
   8     1    27   F    8     2   234
   8     1    27   F    8    16   318
   8     1    27   F    8     5   200
   8     1    27   F    8     3   162
   8     1    27   F    8     7   200
   8     1    27   F    8     6   163
   8     1   829   F    8    11   549
  10     1   736   F   10    11   592
  10     1    56   F   10     4    49
   9     4    49   F    9     4    63
   8     1   557   F    8     3   725
   8     3   725   F    8    17   576
   8     1   557   F    8    17   576
   8     2   282   F    8    17   246
   8     3   210   F    8    17   246
   8     5   248   F    8    17   246
   8     6   211   F    8    17   246
   8     7   248   F    8    17   246
   8    16   366   F    8    17   246
   8     6   615   F    8    19   652
   8    15   377   F    8    19   652
   8     1   779   F    8     2   354
   8     1   779   F    8     3   282
   8     1   779   F    8     5   320
   8     1   779   F    8     6   283
   8     1   779   F    8    16   438
   8     3   662   F    8     6   660
   8     3   662   F    8    16   809
   8     6   660   F    8    16   809
   8     6   731   F    8    20    84
   8     2   260   F    8     4   335
   8     3   188   F    8     4   335
   8     4   335   F    8     5   226
   8     4   335   F    8     6   189
   8     4   335   F    8    16   344
   8     4   335   F    8    19   463
   9     1   325   F    9     4   651
   9     4   651   F    9    16    31
   8     1   325   F    8     1   660
   8     1   660   F    8    16    31
   8     0   171   F    8     4    48
  12     2   281   F   12     3   209
  12     2   281   F   12     5   247
  12     3   209   F   12     5   247
  12     2   281   F   12     6   210
  12     3   209   F   12     6   210
  12     5   247   F   12     6   210
  12     2   281   F   12     7   247
  12     3   209   F   12     7   247
  12     5   247   F   12     7   247
  12     6   210   F   12     7   247
  12     2   281   F   12    16   365
  12     3   209   F   12    16   365
  12     5   247   F   12    16   365
  12     6   210   F   12    16   365
  12     7   247   F   12    16   365
   9     1    42   F    9     3    49
   9     1    42   F    9     4   509
   9     1    42   F    9     5    87
   9     1    42   F    9     7    87
   8    14   547   F    8    19   629
   8    16   808   F    8    19   518
   9     2   259   F    9     3   187
   9     2   259   F    9     5   225
   9     3   187   F    9     5   225
   9     2   259   F    9     6   188
   9     3   187   F    9     6   188
   9     5   225   F    9     6   188
   9     2   259   F    9    16   343
   9     3   187   F    9    16   343
   9     5   225   F    9    16   343
   9     6   188   F    9    16   343
   9     2   259   F    9    19   462
   9     3   187   F    9    19   462
   9     5   225   F    9    19   462
   9     6   188   F    9    19   462
   9    16   343   F    9    19   462
   9     1   734   F    9    17   615
  10     1   658   F   10     4   649
   8     0   169   F    8     3   732
   8     5   763   F    8    10   146
   8     1   657   F    8     3   731
   9     3   729   F    9     6   737
   9     6   736   F    9    19   568
   8     3   729   F    8    19   568
   8     6   736   F    8     6   737
   8     6   737   F    8    19   568
   8     3   729   F    8    12    83
   8     6   736   F    8    12    83
   8     6   737   F    8    12    83
   8    12    83   F    8    19   568
   8     3   729   F    8    19   569
   8     6   736   F    8    19   569
   8    19   568   F    8    19   569
   8    12    83   F    8    19   569
genometools-1.5.1/testdata/retain_1.gff3000066400000000000000000000001141211610345200201220ustar00rootroot00000000000000##gff-version 3
1	ucb	gene	2	2	.	-	.	ID=geneA
1	ucb	gene	2	2	.	+	.	ID=geneB
genometools-1.5.1/testdata/retain_2.gff3000066400000000000000000000000561211610345200201300ustar00rootroot00000000000000##gff-version 3
1	ucb	gene	4	4	.	-	.	ID=geneA
genometools-1.5.1/testdata/retain_both.gff3000066400000000000000000000002561211610345200207250ustar00rootroot00000000000000##gff-version   3
##sequence-region   1 2 2
1	ucb	gene	2	2	.	-	.	ID=geneA
###
1	ucb	gene	2	2	.	+	.	ID=geneB
###
##sequence-region   1 4 4
1	ucb	gene	4	4	.	-	.	ID=geneA.1
###
genometools-1.5.1/testdata/retainids.gff3000066400000000000000000000011711211610345200204060ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 10000
ctg123	.	gene	1000	9000	.	.	.	ID=gene00001
ctg123	.	TF_binding_site	1000	1012	.	.	.	Parent=gene00001
ctg123	.	mRNA	1050	9000	.	.	.	ID=mRNA00001;Parent=gene00001
ctg123	.	mRNA	1050	9000	.	.	.	ID=mRNA00002;Parent=gene00001
ctg123	.	exon	1050	1500	.	.	.	Parent=mRNA00001,mRNA00002
ctg123	.	mRNA	1300	9000	.	.	.	ID=mRNA00003;Parent=gene00001
ctg123	.	exon	1300	1500	.	.	.	Parent=mRNA00003
ctg123	.	exon	3000	3902	.	.	.	Parent=mRNA00001,mRNA00003
ctg123	.	exon	5000	5500	.	.	.	Parent=mRNA00001,mRNA00002,mRNA00003
ctg123	.	exon	7000	9000	.	.	.	Parent=mRNA00001,mRNA00002,mRNA00003
###
genometools-1.5.1/testdata/reverse_feature_order.gff3000066400000000000000000000002131211610345200230010ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	mRNA	1050	9000	.	+	.	Parent=gene1
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
genometools-1.5.1/testdata/reverse_feature_order.out000066400000000000000000000002171211610345200227670ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
ctg123	.	mRNA	1050	9000	.	+	.	Parent=gene1
###
genometools-1.5.1/testdata/reverse_feature_order_multiple_parents.gff3000066400000000000000000000002721211610345200264550ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2
###
genometools-1.5.1/testdata/reverse_feature_order_multiple_parents.out000066400000000000000000000002721211610345200264370ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1,mRNA2
###
genometools-1.5.1/testdata/reverse_standard_gene_as_tree.gff3000066400000000000000000000014171211610345200244620ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
###
genometools-1.5.1/testdata/sain.fna000066400000000000000000000001051211610345200172710ustar00rootroot00000000000000>Sequence from almost purely induced suffix sorting
ccaattaattaaggaa
genometools-1.5.1/testdata/script_example.out000066400000000000000000000004631211610345200214300ustar00rootroot00000000000000fold the following RNA sequence with Nussinov Algorithm:
gggaaatcc
length of RNA sequence = 9
using the following parameters:
l_min =  1
alpha(G,C) = alpha(C,G) = -1
alpha(A,U) = alpha(U,A) = -1
alpha(G,U) = alpha(U,G) = -1
all other alpha values have been set to infinity
score: -3
result:
(2,9)(3,8)(5,7)
genometools-1.5.1/testdata/script_filter_output.txt000066400000000000000000000001421211610345200227040ustar00rootroot00000000000000filter name:	name
version:	1.0
author:		author
email:		email@example.com
description:	description
genometools-1.5.1/testdata/self_referential.gff3000066400000000000000000000001551211610345200217360ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1;Parent=gene1
genometools-1.5.1/testdata/sequence_region_1.gff3000066400000000000000000000015221211610345200220170ustar00rootroot00000000000000##gff-version   3
##sequence-region   I 2064302 12995457
I	Coding_transcript	gene	2064302	2064690	.	+	.	ID=gene1;Alias=Y37E3.3;Name=WBGene00021347
I	Coding_transcript	exon	2064302	2064400	.	+	.	Parent=gene1
I	Coding_transcript	mRNA	2064302	2064690	.	+	.	ID=mRNA1;Parent=gene1;Alias=WBGene00021347;prediction_status=Confirmed;Note=Y37E3.3;Dbxref=CDS:Y37E3.3,WormPep:WP:CE26662;Name=Y37E3.3
I	Coding_transcript	five_prime_UTR	2064302	2064306	.	+	.	Parent=mRNA1;Name=Y37E3.3
I	Coding_transcript	CDS	2064307	2064400	.	+	0	Parent=mRNA1;Name=Y37E3.3
I	Coding_transcript	CDS	2064452	2064561	.	+	2	Parent=mRNA1;Name=Y37E3.3
I	Coding_transcript	three_prime_UTR	2064562	2064690	.	+	.	Parent=mRNA1;Name=Y37E3.3
I	Coding_transcript	intron	2064401	2064451	.	+	.	Parent=gene1;confirmed_est=yk498f7.3
I	Coding_transcript	exon	2064452	2064690	.	+	.	Parent=gene1
###
genometools-1.5.1/testdata/sequence_region_2.gff3000066400000000000000000000026331211610345200220240ustar00rootroot00000000000000##gff-version   3
##sequence-region   I 2006120 12983734
I	Coding_transcript	gene	2006120	2010481	.	-	.	ID=gene1;Alias=Y20F4.3;Name=WBGene00021238
I	Coding_transcript	exon	2006120	2006306	.	-	.	Parent=gene1
I	Coding_transcript	mRNA	2006120	2010481	.	-	.	ID=mRNA1;Parent=gene1;Alias=WBGene00021238;prediction_status=Predicted;Note=Y20F4.3;Dbxref=CDS:Y20F4.3,WormPep:WP:CE40152;Name=Y20F4.3
I	Coding_transcript	CDS	2006120	2006306	.	-	1	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2007324	2007568	.	-	0	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2008590	2008772	.	-	0	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2009865	2009961	.	-	1	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2010006	2010259	.	-	0	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2010407	2010481	.	-	0	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	intron	2006307	2007323	.	-	.	Parent=gene1
I	Coding_transcript	exon	2007324	2007568	.	-	.	Parent=gene1
I	Coding_transcript	intron	2007569	2008589	.	-	.	Parent=gene1
I	Coding_transcript	exon	2008590	2008772	.	-	.	Parent=gene1
I	Coding_transcript	intron	2008773	2009864	.	-	.	Parent=gene1
I	Coding_transcript	exon	2009865	2009961	.	-	.	Parent=gene1
I	Coding_transcript	intron	2009962	2010005	.	-	.	Parent=gene1
I	Coding_transcript	exon	2010006	2010259	.	-	.	Parent=gene1
I	Coding_transcript	intron	2010260	2010406	.	-	.	Parent=gene1
I	Coding_transcript	exon	2010407	2010481	.	-	.	Parent=gene1
###
genometools-1.5.1/testdata/sequence_region_joined.gff3000066400000000000000000000042641211610345200231350ustar00rootroot00000000000000##gff-version   3
##sequence-region   I 2006120 12995457
I	Coding_transcript	gene	2006120	2010481	.	-	.	ID=gene1;Alias=Y20F4.3;Name=WBGene00021238
I	Coding_transcript	exon	2006120	2006306	.	-	.	Parent=gene1
I	Coding_transcript	mRNA	2006120	2010481	.	-	.	ID=mRNA1;Parent=gene1;Alias=WBGene00021238;prediction_status=Predicted;Note=Y20F4.3;Dbxref=CDS:Y20F4.3,WormPep:WP:CE40152;Name=Y20F4.3
I	Coding_transcript	CDS	2006120	2006306	.	-	1	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2007324	2007568	.	-	0	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2008590	2008772	.	-	0	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2009865	2009961	.	-	1	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2010006	2010259	.	-	0	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	CDS	2010407	2010481	.	-	0	Parent=mRNA1;Name=Y20F4.3
I	Coding_transcript	intron	2006307	2007323	.	-	.	Parent=gene1
I	Coding_transcript	exon	2007324	2007568	.	-	.	Parent=gene1
I	Coding_transcript	intron	2007569	2008589	.	-	.	Parent=gene1
I	Coding_transcript	exon	2008590	2008772	.	-	.	Parent=gene1
I	Coding_transcript	intron	2008773	2009864	.	-	.	Parent=gene1
I	Coding_transcript	exon	2009865	2009961	.	-	.	Parent=gene1
I	Coding_transcript	intron	2009962	2010005	.	-	.	Parent=gene1
I	Coding_transcript	exon	2010006	2010259	.	-	.	Parent=gene1
I	Coding_transcript	intron	2010260	2010406	.	-	.	Parent=gene1
I	Coding_transcript	exon	2010407	2010481	.	-	.	Parent=gene1
###
I	Coding_transcript	gene	2064302	2064690	.	+	.	ID=gene2;Alias=Y37E3.3;Name=WBGene00021347
I	Coding_transcript	exon	2064302	2064400	.	+	.	Parent=gene2
I	Coding_transcript	mRNA	2064302	2064690	.	+	.	ID=mRNA2;Parent=gene2;Alias=WBGene00021347;prediction_status=Confirmed;Note=Y37E3.3;Dbxref=CDS:Y37E3.3,WormPep:WP:CE26662;Name=Y37E3.3
I	Coding_transcript	five_prime_UTR	2064302	2064306	.	+	.	Parent=mRNA2;Name=Y37E3.3
I	Coding_transcript	CDS	2064307	2064400	.	+	0	Parent=mRNA2;Name=Y37E3.3
I	Coding_transcript	CDS	2064452	2064561	.	+	2	Parent=mRNA2;Name=Y37E3.3
I	Coding_transcript	three_prime_UTR	2064562	2064690	.	+	.	Parent=mRNA2;Name=Y37E3.3
I	Coding_transcript	intron	2064401	2064451	.	+	.	Parent=gene2;confirmed_est=yk498f7.3
I	Coding_transcript	exon	2064452	2064690	.	+	.	Parent=gene2
###
genometools-1.5.1/testdata/sequence_region_negative_end.gff3000066400000000000000000000000701211610345200243040ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 -1497228
genometools-1.5.1/testdata/sequence_region_negative_start.gff3000066400000000000000000000000701211610345200246730ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 -1 1497228
genometools-1.5.1/testdata/simple_orphan.gff3000066400000000000000000000001621211610345200212630ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	CDS	3000	3902	.	+	0	ID=cds000001;Parent=mRNA00001
genometools-1.5.1/testdata/solid_color_reads.fastq000066400000000000000000000020541211610345200224040ustar00rootroot00000000000000@SRR014961.1 VAB_JOAN_20080715_1_1000g_5_1_6_35/2
G3300300010002003003002033
+
!%$$(&)$#$$$%###$#$###$$%%
@SRR014961.2 VAB_JOAN_20080715_1_1000g_5_1_6_47/2
G3220012230032000000121320
+
!&*&%'''%%.&%%%#$&$%$&&*&#
@SRR014961.3 VAB_JOAN_20080715_1_1000g_5_1_6_62/2
G3112033201002121110023230
+
!'&&&++&,*'1($,)&'#-&('(+2
@SRR014961.4 VAB_JOAN_20080715_1_1000g_5_1_6_165/2
G2020222102113212302010001
+
!#+)**'*#0/&,%'+*%('0',8%4
@SRR014961.5 VAB_JOAN_20080715_1_1000g_5_1_6_203/2
G0313322300333000003003032
+
!,'1,*)+/..%$$$+$#&#%#$#%'
@SRR014961.6 VAB_JOAN_20080715_1_1000g_5_1_6_211/2
G0010020120123331103223031
+
!)+(+1'.(*300$(&--$&-))-$'
@SRR014961.7 VAB_JOAN_20080715_1_1000g_5_1_6_220/2
G1000000302222312200222120
+
!,,.+'(+.5(&.''#''5#%+.2$#
@SRR014961.8 VAB_JOAN_20080715_1_1000g_5_1_6_278/2
G2202120322301133030100300
+
!$)/%&'(0*(%-.$%$4*&$%0%*'
@SRR014961.9 VAB_JOAN_20080715_1_1000g_5_1_6_284/2
G1131131002203211000110101
+
!+*(%.&.$$.$%%%()%##)###$)
@SRR014961.10 VAB_JOAN_20080715_1_1000g_5_1_6_310/2
G2303330213030210202021213
+
!2$.'$&)'***&%2*+*''(+*()&
genometools-1.5.1/testdata/splice_site_prob.gff3000066400000000000000000000013121211610345200217460ustar00rootroot00000000000000##gff-version   3
##sequence-region   region.fas|1 1 2000701
region.fas|1	gth	gene	609666	620119	.	-	.	ID=gene1
region.fas|1	gth	mRNA	609666	620119	.	-	.	ID=mRNA1;Parent=gene1
region.fas|1	gth	exon	609666	613203	0.98	-	.	Parent=mRNA1
region.fas|1	region.fas|1	three_prime_cis_splice_site	613205	613205	0.543	-	.	Parent=mRNA1
region.fas|1	region.fas|1	five_prime_cis_splice_site	613276	613277	0.504	-	.	Parent=mRNA1
region.fas|1	gth	exon	613278	613446	0.967	-	.	Parent=mRNA1
region.fas|1	region.fas|1	three_prime_cis_splice_site	613447	613448	0	-	.	Parent=mRNA1
region.fas|1	region.fas|1	five_prime_cis_splice_site	620084	620085	0.472	-	.	Parent=mRNA1
region.fas|1	gth	exon	620086	620119	0.971	-	.	Parent=mRNA1
###
genometools-1.5.1/testdata/splice_site_prob.out000066400000000000000000000000751211610345200217350ustar00rootroot00000000000000##gff-version   3
##sequence-region   region.fas|1 1 2000701
genometools-1.5.1/testdata/standard_fasta_example.gff3000066400000000000000000000030531211610345200231160ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001;Name=EDEN
ctg123	.	TF_binding_site	1000	1012	.	+	.	ID=tfbs00001;Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001;Name=EDEN.1
ctg123	.	five_prime_UTR	1050	1200	.	+	.	Parent=mRNA00001
ctg123	.	CDS	1201	1500	.	+	0	Parent=mRNA00001
ctg123	.	CDS	3000	3902	.	+	0	Parent=mRNA00001
ctg123	.	CDS	5000	5500	.	+	0	Parent=mRNA00001
ctg123	.	CDS	7000	7600	.	+	0	Parent=mRNA00001
ctg123	.	five_prime_UTR	7601	9000	.	+	.	Parent=mRNA00001
ctg123	.	cDNA_match	1050	1500	5.8e-42	+	.	Target=cdna0123 12 462
ctg123	.	cDNA_match	5000	5500	8.1e-43	+	.	Target=cdna0123 463 963
ctg123	.	cDNA_match	7000	9000	1.4e-40	+	.	Target=cdna0123 964 2964
##FASTA
>ctg123
cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg
tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta
tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa
aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat
aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat
cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc
gtatttgatttgggtttactatcgaataatgagaattttcaggcttaggc
ttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt
aggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttag
aatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattc
>cnda0123
ttcaagtgctcagtcaatgtgattcacagtatgtcaccaaatattttggc
agctttctcaagggatcaaaattatggatcattatggaatacctcggtgg
aggctcagcgctcgatttaactaaaagtggaaagctggacgaaagtcata
tcgctgtgattcttcgcgaaattttgaaaggtctcgagtatctgcatagt
gaaagaaaaatccacagagatattaaaggagccaacgttttgttggaccg
tcaaacagcggctgtaaaaatttgtgattatggttaaagg
genometools-1.5.1/testdata/standard_fasta_example_with_id.gff3000066400000000000000000000031261211610345200246260ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001;Name=EDEN
ctg123	.	TF_binding_site	1000	1012	.	+	.	ID=tfbs00001;Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001;Name=EDEN.1
ctg123	.	five_prime_UTR	1050	1200	.	+	.	Parent=mRNA00001
ctg123	.	CDS	1201	1500	.	+	0	Parent=mRNA00001
ctg123	.	CDS	3000	3902	.	+	0	Parent=mRNA00001
ctg123	.	CDS	5000	5500	.	+	0	Parent=mRNA00001
ctg123	.	CDS	7000	7600	.	+	0	Parent=mRNA00001
ctg123	.	three_prime_UTR	7601	9000	.	+	.	Parent=mRNA00001
ctg123	.	cDNA_match	1050	1500	5.8e-42	+	.	ID=match00001;Target=cdna0123 12 462
ctg123	.	cDNA_match	5000	5500	8.1e-43	+	.	ID=match00001;Target=cdna0123 463 963
ctg123	.	cDNA_match	7000	9000	1.4e-40	+	.	ID=match00001;Target=cdna0123 964 2964
##FASTA
>ctg123
cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg
tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta
tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa
aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat
aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat
cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc
gtatttgatttgggtttactatcgaataatgagaattttcaggcttaggc
ttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt
aggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttag
aatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattc
>cnda0123
ttcaagtgctcagtcaatgtgattcacagtatgtcaccaaatattttggc
agctttctcaagggatcaaaattatggatcattatggaatacctcggtgg
aggctcagcgctcgatttaactaaaagtggaaagctggacgaaagtcata
tcgctgtgattcttcgcgaaattttgaaaggtctcgagtatctgcatagt
gaaagaaaaatccacagagatattaaaggagccaacgttttgttggaccg
tcaaacagcggctgtaaaaatttgtgattatggttaaagg
genometools-1.5.1/testdata/standard_fasta_example_with_id.out000066400000000000000000000030541211610345200246100ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1;Name=EDEN
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1;Name=EDEN.1
ctg123	.	five_prime_UTR	1050	1200	.	+	.	Parent=mRNA1
ctg123	.	CDS	1201	1500	.	+	0	Parent=mRNA1
ctg123	.	CDS	3000	3902	.	+	0	Parent=mRNA1
ctg123	.	CDS	5000	5500	.	+	0	Parent=mRNA1
ctg123	.	CDS	7000	7600	.	+	0	Parent=mRNA1
ctg123	.	three_prime_UTR	7601	9000	.	+	.	Parent=mRNA1
###
ctg123	.	cDNA_match	1050	1500	5.8e-42	+	.	ID=cDNA_match1;Target=cdna0123 12 462
ctg123	.	cDNA_match	5000	5500	8.1e-43	+	.	ID=cDNA_match1;Target=cdna0123 463 963
ctg123	.	cDNA_match	7000	9000	1.4e-40	+	.	ID=cDNA_match1;Target=cdna0123 964 2964
###
##FASTA
>ctg123
cttctgggcgtacccgattctcggagaacttgccgcaccattccgccttg
tgttcattgctgcctgcatgttcattgtctacctcggctacgtgtggcta
tctttcctcggtgccctcgtgcacggagtcgagaaaccaaagaacaaaaa
aagaaattaaaatatttattttgctgtggtttttgatgtgtgttttttat
aatgatttttgatgtgaccaattgtacttttcctttaaatgaaatgtaat
cttaaatgtatttccgacgaattcgaggcctgaaaagtgtgacgccattc
gtatttgatttgggtttactatcgaataatgagaattttcaggcttaggc
ttaggcttaggcttaggcttaggcttaggcttaggcttaggcttaggctt
aggcttaggcttaggcttaggcttaggcttaggcttaggcttaggcttag
aatctagctagctatccgaaattcgaggcctgaaaagtgtgacgccattc
>cnda0123
ttcaagtgctcagtcaatgtgattcacagtatgtcaccaaatattttggc
agctttctcaagggatcaaaattatggatcattatggaatacctcggtgg
aggctcagcgctcgatttaactaaaagtggaaagctggacgaaagtcata
tcgctgtgattcttcgcgaaattttgaaaggtctcgagtatctgcatagt
gaaagaaaaatccacagagatattaaaggagccaacgttttgttggaccg
tcaaacagcggctgtaaaaatttgtgattatggttaaagg
genometools-1.5.1/testdata/standard_gene_as_dag.gff3000066400000000000000000000033301211610345200225170ustar00rootroot00000000000000##gff-version 3
##sequence-region ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene00001;Name=EDEN
ctg123	.	TF_binding_site	1000	1012	.	+	.	ID=tfbs00001;Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001;Name=EDEN.1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00002;Parent=gene00001;Name=EDEN.2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA00003;Parent=gene00001;Name=EDEN.3
ctg123	.	exon	1300	1500	.	+	.	ID=exon00001;Parent=mRNA00003
ctg123	.	exon	1050	1500	.	+	.	ID=exon00002;Parent=mRNA00001,mRNA00002
ctg123	.	exon	3000	3902	.	+	.	ID=exon00003;Parent=mRNA00001,mRNA00003
ctg123	.	exon	5000	5500	.	+	.	ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA00003
ctg123	.	exon	7000	9000	.	+	.	ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA00003
ctg123	.	CDS	1201	1500	.	+	0	ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
ctg123	.	CDS	3000	3902	.	+	0	ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
ctg123	.	CDS	5000	5500	.	+	0	ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
ctg123	.	CDS	7000	7600	.	+	0	ID=cds00001;Parent=mRNA00001;Name=edenprotein.1
ctg123	.	CDS	1201	1500	.	+	0	ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
ctg123	.	CDS	5000	5500	.	+	0	ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
ctg123	.	CDS	7000	7600	.	+	0	ID=cds00002;Parent=mRNA00002;Name=edenprotein.2
ctg123	.	CDS	3301	3902	.	+	0	ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
ctg123	.	CDS	5000	5500	.	+	1	ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
ctg123	.	CDS	7000	7600	.	+	1	ID=cds00003;Parent=mRNA00003;Name=edenprotein.3
ctg123	.	CDS	3391	3902	.	+	0	ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
ctg123	.	CDS	5000	5500	.	+	1	ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
ctg123	.	CDS	7000	7600	.	+	1	ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
genometools-1.5.1/testdata/standard_gene_as_dag_sorted.gff3000066400000000000000000000027361211610345200241100ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	.	+	.	ID=gene1;Name=EDEN
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1;Name=EDEN.1
ctg123	.	CDS	1201	1500	.	+	0	ID=CDS1;Parent=mRNA1;Name=edenprotein.1
ctg123	.	CDS	3000	3902	.	+	0	ID=CDS1;Parent=mRNA1;Name=edenprotein.1
ctg123	.	CDS	5000	5500	.	+	0	ID=CDS1;Parent=mRNA1;Name=edenprotein.1
ctg123	.	CDS	7000	7600	.	+	0	ID=CDS1;Parent=mRNA1;Name=edenprotein.1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1;Name=EDEN.2
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1,mRNA2
ctg123	.	CDS	1201	1500	.	+	0	ID=CDS2;Parent=mRNA2;Name=edenprotein.2
ctg123	.	CDS	5000	5500	.	+	0	ID=CDS2;Parent=mRNA2;Name=edenprotein.2
ctg123	.	CDS	7000	7600	.	+	0	ID=CDS2;Parent=mRNA2;Name=edenprotein.2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1;Name=EDEN.3
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1,mRNA3
ctg123	.	CDS	3301	3902	.	+	0	ID=CDS3;Parent=mRNA3;Name=edenprotein.3
ctg123	.	CDS	3391	3902	.	+	0	ID=CDS4;Parent=mRNA3;Name=edenprotein.4
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1,mRNA2,mRNA3
ctg123	.	CDS	5000	5500	.	+	1	ID=CDS3;Parent=mRNA3;Name=edenprotein.3
ctg123	.	CDS	5000	5500	.	+	1	ID=CDS4;Parent=mRNA3;Name=edenprotein.4
ctg123	.	CDS	7000	7600	.	+	1	ID=CDS3;Parent=mRNA3;Name=edenprotein.3
ctg123	.	CDS	7000	7600	.	+	1	ID=CDS4;Parent=mRNA3;Name=edenprotein.4
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1,mRNA2,mRNA3
###
genometools-1.5.1/testdata/standard_gene_as_tree.blocks000066400000000000000000000003131211610345200233510ustar00rootroot00000000000000TF_binding_site + (1000L, 9000L) 1
exon + (1050L, 9000L) 3
exon + (1050L, 9000L) 4
exon + (1300L, 9000L) 4
gene + (1000L, 9000L) 1
mRNA + (1050L, 9000L) 1
mRNA + (1050L, 9000L) 1
mRNA + (1300L, 9000L) 1
genometools-1.5.1/testdata/standard_gene_as_tree.gff3000066400000000000000000000014171211610345200227270ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/standard_gene_as_tree.header000066400000000000000000000000671211610345200233320ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
genometools-1.5.1/testdata/standard_gene_as_tree.hotspots000066400000000000000000000013161211610345200237630ustar00rootroot00000000000000x1=30, y1=90, x2=31, y2=106, gn.type=TF_binding_site
x1=57, y1=243, x2=76, y2=259, gn.type=exon
x1=34, y1=161, x2=76, y2=177, gn.type=exon
x1=34, y1=202, x2=76, y2=218, gn.type=exon
x1=399, y1=161, x2=446, y2=177, gn.type=exon
x1=399, y1=202, x2=446, y2=218, gn.type=exon
x1=399, y1=243, x2=446, y2=259, gn.type=exon
x1=214, y1=161, x2=298, y2=177, gn.type=exon
x1=214, y1=243, x2=298, y2=259, gn.type=exon
x1=584, y1=161, x2=770, y2=177, gn.type=exon
x1=584, y1=202, x2=770, y2=218, gn.type=exon
x1=584, y1=243, x2=770, y2=259, gn.type=exon
x1=57, y1=467, x2=770, y2=483, gn.type=mRNA
x1=34, y1=385, x2=770, y2=401, gn.type=mRNA
x1=34, y1=426, x2=770, y2=442, gn.type=mRNA
x1=30, y1=314, x2=770, y2=330, gn.type=gene
genometools-1.5.1/testdata/standard_gene_as_tree.recmaps000066400000000000000000000005361211610345200235350ustar00rootroot0000000000000030,90,31,106, TF_binding_site
30,162,770,178, gene
35,232,770,248, mRNA
35,232,76,248, exon
215,232,298,248, exon
400,232,446,248, exon
585,232,770,248, exon
35,274,770,290, mRNA
35,274,76,290, exon
400,274,446,290, exon
585,274,770,290, exon
58,314,770,330, mRNA
58,314,76,330, exon
215,314,298,330, exon
400,314,446,330, exon
585,314,770,330, exon
genometools-1.5.1/testdata/standard_gene_as_tree.types000066400000000000000000000000371211610345200232430ustar00rootroot00000000000000TF_binding_site
exon
gene
mRNA
genometools-1.5.1/testdata/standard_gene_simple.gff3000066400000000000000000000013501211610345200225720ustar00rootroot00000000000000##gff-version   3
ctg123	.	gene	1000	9000	.	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/standard_gene_with_introns_as_tree.gff3000066400000000000000000000021741211610345200255370ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.500000	+	.	ID=gene1
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1
ctg123	.	intron	1501	2999	.	+	.	Parent=mRNA1
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA1
ctg123	.	intron	3903	4999	.	+	.	Parent=mRNA1
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA1
ctg123	.	intron	5501	6999	.	+	.	Parent=mRNA1
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA1
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA2;Parent=gene1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA2
ctg123	.	intron	1501	4999	.	+	.	Parent=mRNA2
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA2
ctg123	.	intron	5501	6999	.	+	.	Parent=mRNA2
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA2
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA3;Parent=gene1
ctg123	.	exon	1300	1500	.	+	.	Parent=mRNA3
ctg123	.	intron	1501	2999	.	+	.	Parent=mRNA3
ctg123	.	exon	3000	3902	.	+	.	Parent=mRNA3
ctg123	.	intron	3903	4999	.	+	.	Parent=mRNA3
ctg123	.	exon	5000	5500	.	+	.	Parent=mRNA3
ctg123	.	intron	5501	6999	.	+	.	Parent=mRNA3
ctg123	.	exon	7000	9000	.	+	.	Parent=mRNA3
###
genometools-1.5.1/testdata/sw100K1.fsa000066400000000000000000000133101211610345200174140ustar00rootroot00000000000000>sp|100K_RAT|100 KD PROTEIN (EC 
MMSARGDFLNYALSLMRSHNDEHSDVLPVLDVCSLKHVAYVFQALIYWIKAMNQQTTLDTPQLE
RKRTRELLELGIDNEDSEHENDDDTSQSATLNDKDDESLPAETGQNHPFFRRSDSMTFLGCIPP
NPFEVPLAEAIPLADQPHLLQPNARKEDLFGRPSQGLYSSSAGSGKCLVEVTMDRNCLEVLPTK
MSYAANLKNVMNMQNRQKKAGEDQSMLAEEADSSKPGPSAHDVAAQLKSSLLAEIGLTESEGPP
LTSFRPQCSFMGMVISHDMLLGRWRLSLELFGRVFMEDVGAEPGSILTELGGFEVKESKFRREM
EKLRNQQSRDLSLEVDRDRDLLIQQTMRQLNNHFGRRCATTPMAVHRVKVTFKDEPGEGSGVAR
SFYTAIAQAFLSNEKLPNLDCIQNANKGTHTSLMQRLRNRGERDREREREREMRRSSGLRAGSR
RDRDRDFRRQLSIDTRPFRPASEGNPSDDPDPLPAHRQALGERLYPRVQAMQPAFASKITGMLL
ELSPAQLLLLLASEDSLRARVEEAMELIVAHGRENGADSILDLGLLDSSEKVQENRKRHGSSRS
VVDMDLDDTDDGDDNAPLFYQPGKRGFYTPRPGKNTEARLNCFRNIGRILGLCLLQNELCPITL
NRHVIKVLLGRKVNWHDFAFFDPVMYESLRQLILASQSSDADAVFSAMDLAFAVDLCKEEGGGQ
VELIPNGVNIPVTPQNVYEYVRKYAEHRMLVVAEQPLHAMRKGLLDVLPKNSLEDLTAEDFRLL
VNGCGEVNVQMLISFTSFNDESGENAEKLLQFKRWFWSIVERMSMTERQDLVYFWTSSPSLPAS
EEGFQPMPSITIRPPDDQHLPTANTCISRLYVPLYSSKQILKQKLLLAIKTKNFGFV
>sp|104K_THEPA|104 KD MICRONEME-RHOPTRY ANTIGE
MKFLILLFNILCLFPVLAADNHGVGPQGASGVDPITFDINSNQTGPAFLTAVEMAGVKYLQVQH
GSNVNIHRLVEGNVVIWENASTPLYTGAIVTNNDGPYMAYVEVLGDPNLQFFIKSGDAWVTLSE
HEYLAKLQEIRQAVHIESVFSLNMAFQLENNKYEVETHAKNGANMVTFIPRNGHICKMVYHKNV
RIYKATGNDTVTSVVGFFRGLRLLLINVFSIDDNGMMSNRYFQHVDDKYVPISQKNYETGIVKL
KDYKHAYHPVDLDIKDIDYTMFHLADATYHEPCFKIIPNTGFCITKLFDGDQVLYESFNPLIHC
INEVHIYDRNNGSIICLHLNYSPPSYKAYLVLKDTGWEATTHPLLEEKIEELQDQRACELDVNF
ISDKDLYVAALTNADLNYTMVTPRPHRDVIRVSDGSEVLWYYEGLDNFLVCAWIYVSDGVASLV
HLRIKDRIPANNDIYVLKGDLYWTRITKIQFTQEIKRLVKKSKKKLAPITEEDSDKHDEPPEGP
GASGLPPKAPGDKEGSEGHKGPSKGSDSSKEGKKPGSGKKPGPAREHKPSKIPTLSKKPSGPKD
PKHPRDPKEPRKSKSPRTASPTRRPSPKLPQLSKLPKSTSPRSPPPPTRPSSPERPEGTKIIKT
SKPPSPKPPFDPSFKEKFYDDYSKAASRSKETKTTVVLDESFESILKETLPETPGTPFTTPRPV
PPKRPRTPESPFEPPKDPDSPSTSPSEFFTPPESKRTRFHETPADTPLPDVTAELFKEPDVTAE
TKSPDEAMKRPRSPSEYEDTSPGDYPSLPMKRHRLERLRLTTTEMETDPGRMAKDASGKPVKLK
RSKSFDDLTTVELAPEPKASRIVVDDEGTEADDEETHPPEERQKTEVRRRRPPKKPSKSPRPSK
PKKPKKPDSAYIPSILAILVVSLIVGIL
>sp|108_LYCES|PROTEIN 108 PRECURSO
MASVKSSSSSSSSSFISLLLLILLVIVLQSQVIECQPQQSCTASLTGLNVCAPFLVPGSPTAST
ECCNAVQSINHDCMCNTMRIAAQIPAQCNLPPLSCSAN
>sp|10KD_VIGUN|10 KD PROTEIN PRECURSOR (CLONE PSAS10
MEKKSIAGLCFLFLVLFVAQEVVVQSEAKTCENLVDTYRGPCFTTGSCDDHCKNKEHLLSGRCR
DDVRCWCTRNC
>sp|110K_PLAKN|110 KD ANTIGEN (PK110) (FRAGMENT
FNSNMLRGSVCEEDVSLMTSIDNMIEEIDFYEKEIYKGSHSGGVIKGMDYDLEDDENDEDEMTE
QMVEEVADHITQDMIDEVAHHVLDNITHDMAHMEEIVHGLSGDVTQIKEIVQKVNVAVEKVKHI
VETEETQKTVEPEQIEETQNTVEPEQTEETQKTVEPEQTEETQNTVEPEQIEETQKTVEPEQTE
EAQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQK
TVEPEQTEETQKTVEPEQTEETQNTVEPEPTQETQNTVEP
>sp|11S3_HELAN|11S GLOBULIN SEED STORAGE PROTEIN G3 PR
MASKATLLLAFTLLFATCIARHQQRQQQQNQCQLQNIEALEPIEVIQAEAGVTEIWDAYDQQFQ
CAWSILFDTGFNLVAFSCLPTSTPLFWPSSREGVILPGCRRTYEYSQEQQFSGEGGRRGGGEGT
FRTVIRKLENLKEGDVVAIPTGTAHWLHNDGNTELVVVFLDTQNHENQLDENQRRFFLAGNPQA
QAQSQQQQQRQPRQQSPQRQRQRQRQGQGQNAGNIFNGFTPELIAQSFNVDQETAQKLQGQNDQ
RGHIVNVGQDLQIVRPPQDRRSPRQQQEQATSPRQQQEQQQGRRGGWSNGVEETICSMKFKVNI
DNPSQADFVNPQAGSIANLNSFKFPILEHLRLSVERGELRPNAIQSPHWTINAHNLLYVTEGAL
RVQIVDNQGNSVFDNELREGQVVVIPQNFAVIKRANEQGSRWVSFKTNDNAMIANLAGRVSASA
ASPLTLWANRYQLSREEAQQLKFSQRETVLFAPSFSRGQGIRASR
>sp|11SB_CUCMA|11S GLOBULIN BETA SUBUNIT PRECURSO
MARSSLFTFLCLAVFINGCLSQIEQQSPWEFQGSEVWQQHRYQSPRACRLENLRAQDPVRRAEA
EAIFTEVWDQDNDEFQCAGVNMIRHTIRPKGLLLPGFSNAPKLIFVAQGFGIRGIAIPGCAETY
QTDLRRSQSAGSAFKDQHQKIRPFREGDLLVVPAGVSHWMYNRGQSDLVLIVFADTRNVANQID
PYLRKFYLAGRPEQVERGVEEWERSSRKGSSGEKSGNIFSGFADEFLEEAFQIDGGLVRKLKGE
DDERDRIVQVDEDFEVLLPEKDEEERSRGRYIESESESENGLEETICTLRLKQNIGRSVRADVF
NPRGGRISTANYHTLPILRQVRLSAERGVLYSNAMVAPHYTVNSHSVMYATRGNARVQVVDNFG
QSVFDGEVREGQVLMIPQNFVVIKRASDRGFEWIAFKTNDNAITNLLAGRVSQMRMLPLGVLSN
MYRISREEAQRLKYGQQEMRVLSPGRSQGRRE
>sp|120K_RICRI|120 KD SURFACE-EXPOSED PROTEI
MVIQSANATGQVNFRHIVDVGADGTTAFKTAASKVTITQDSNFGNTDFGNLAAQIKVPNAITLT
GNFTGDASNPGNTAGVITFDANGTLESASADANVAVTNNITAIEASGAGVVQLSGTHAAELRLG
NAGSIFKLADGTVINGKVNQTALVGGALAAGTITLDGSATITGDIGNAGGAAALQRITLANDAK
KTLTLGGANIIGAGGGTIDLQANGGTIKLTSTQNNIVVDFDLAIATDQTGVVDASSLTNAQTLT
INGKIGTIGANNKTLGQFNIGSSKTVLSNGNVAINELVIGNDGAVQFAHDTYLITRTTNAAGQG
KIIFNPVVNNGTTLAAGTNLGSATNPLAEINFGSKGVNVDTVLNVGEGVNLYATNITTTDANVG
SFVFNAGGTNIVSGTVGGQQGNKFNTVALENGTTVKFLGNATFNGNTTIAANSTLQIGGNYTAD
CVASADGTGIVEFVNTGPITVTLNKQAAPVNALKQITVSGPGNVVINEIGNAGNHHGAVTDTIA
FENSSLGAVVFLPRGIPFNDAGNTMPLTIKSTVGNKTAKGFDVPSVVVLGVDSVIADGQVIGDQ
NNIVGLGLGSDNGIIVNATTLYAGISTLNNNQGTVTLSGGVPNTPGTVYGLGTGIGASKFKQVT
FTTDYNNLGNIIATNATINDGVTVTTGGIAGIGFDGKITLGSVNGNGNVRFADGILSNSTSMIG
TTKANNGTVTYLGNAFVGNIGDSDTPVASVRFTGSDSGAGLQGNIYSQVIDFGTYNLGIVNSNI
ILGGGTTAINGKIDLVTNTLTFASGTSTWGNNTSIETTLTLANGNIGHIVILEGAQVNTTTTGT
TTIKVQDNANANFSGTQTYTLIQGGARFNGTLGSPNFAVTGSNRFVNYSLIRAANQDYVITRTN
NAENVVTNDIANSPFGGAPGVDQNVTTFVNATNTAAYNNLLLAKNSANSANFVGAIVTDTSAAI
TNVQLDLAKDIQAQLGNRLGALRYLGTPETAEMAGPEAGAISAAVAAGDEAIDNVAYGIWAKPF
YTDAHQSKKGGLAGYKAKTTGVVIGLDTLANDNLMIGAAIGITKTDIKHQDYKKGDKTDVNGFS
FSLYGAQQLVKNFFAQGSAIFSLNQVKNKSQRYFFDANGNMSKQIAAGHYDNMTFGGNLTVGYD
YNAMQGVLVTPMAGLSYLKSSDENYKETGTTVANKQVNSKFSDRTDLIVGAKVAGSTMNRTDLA
VYPEVHAFVVHKVTGRLSKTQSVLDGQVTPCINQPDRTTKTSYNLGLSASIRSDAKMEYGIGYD
AQISSKYTAHQGTLKVRVNF
>sp|128U_DROME|GTP-BINDING PROTEIN 128U
MITILEKISAIESEMARTQKNKATSAHLGLLKANVAKLRRELISPKGGGGGTGEAGFEVAKTGD
ARVGFVGFPSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPGCIKYKGAKIQLLDLPGIIEGAKDG
KGRGRQVIAVARTCNLIFMVLDCLKPLGHKKLLEHELEGFGIRLNKKPPNIYYKRKDKGGINLN
SMVPQSELDTDLVKTILSEYKIHNADITLRYDATSDDLIDVIEGNRIYIPCIYLLNKIDQISIE
ELDVIYKIPHCVPISAHHHWNFDDLLELMWEYLRLQRIYTKPKGQLPDYNSPVVLHNERTSIED
FCNKLHRSIAKEFKYALVWGSSVKHQPQKVGIEHVLNDEDVVQIVKKV
>sp|12AH_CLOS4|12-ALPHA-HYDROXYSTEROID DEHYDROGENASE (
MIFDGKVAIITGGGKAKSIGYGIAVAYAK
>sp|12KD_FRAAN|AUXIN-REPRESSED 1
MVLLDKLWDDIVAGPQPERGLGMLRKVPQPLNLKDEGESSKITMPTTPTTPVTPTTPISARKDN
VWRSVFHPGSNLSSKTMGNQVFDSPQPNSPTVYDWMYSGETRSKHHR
>sp|12KD_MYCLE|12 KD PROTEI
MNDIIALKFHISLNATTWIGRIGMVILPLLVYFITYRWCIGLQRSDRAVLEHGIETGIIKRLPH
GAYIELHQPLGPVDDHGHPIPLEYQGTAVPKRMNKLGSAGSPSSGSFLFADPVSEDAALREATH
VAEQRALTALREHQDSIASSPNGERGKH
genometools-1.5.1/testdata/sw100K1.magicmatch000066400000000000000000000016121211610345200207420ustar00rootroot000000000000002f5423769db8f8ac34b12ebe0ce79ba4	sp|100K_RAT|100 KD PROTEIN (EC 
828ea1caefdf0882c2fc7dfe0639d422	sp|104K_THEPA|104 KD MICRONEME-RHOPTRY ANTIGE
45c6e4aaae0c760b5133f6b8f57fb324	sp|108_LYCES|PROTEIN 108 PRECURSO
119dbffe7be45367410b8749c11d46cb	sp|10KD_VIGUN|10 KD PROTEIN PRECURSOR (CLONE PSAS10
5f6bbcf62cb8fa766d6b747b290d845d	sp|110K_PLAKN|110 KD ANTIGEN (PK110) (FRAGMENT
219a6cb625d16d7f5905c87cc84adb0d	sp|11S3_HELAN|11S GLOBULIN SEED STORAGE PROTEIN G3 PR
e959b769c2d6bab3b627627a62f7ef64	sp|11SB_CUCMA|11S GLOBULIN BETA SUBUNIT PRECURSO
882f42d03c8a1fb46ca7df722a747711	sp|120K_RICRI|120 KD SURFACE-EXPOSED PROTEI
4e854ba5f1c7cb8d92f6d8da40d4c0d8	sp|128U_DROME|GTP-BINDING PROTEIN 128U
d26d8fd55622ce5c5a04bf0815bb4767	sp|12AH_CLOS4|12-ALPHA-HYDROXYSTEROID DEHYDROGENASE (
ee73cd9bf7cdd70231c1e16f4d3470ee	sp|12KD_FRAAN|AUXIN-REPRESSED 1
d1641d3d5749375e92bedd28a1daf6c7	sp|12KD_MYCLE|12 KD PROTEI
genometools-1.5.1/testdata/sw100K2.fsa000066400000000000000000000132171211610345200174230ustar00rootroot00000000000000>sp|ALR_LACPL|ALANINE RACEMASE (EC 
MVVIGEHRHTQVTVDLQAIKTNISNEMAQKDELTELWAVVKANGYGHGIIQVAQAAKEAGATGF
CVAILDEALALRAAGFAEPILVLGITEPEYAPLVAEKDISLAVGTQDWLTTAAAILAANQVTTP
LHVHLALDTGMGRIGFQTPEELATAVTTLRQPQSPFDFEGIFTHFATADQADDTYFTHQLNNWK
HLIAVVDELPRYVHVSNSATSLWHQACNGNMVRFGVALYGLNPSGRELSAPYPLQPALSLTARL
TFVKRLARGKSVSYGATYTAAQDEWIGTVPIGYADGYERRLQGFHVLVDGEFCEIVGRVCMDQL
MVRLPHEVPVGAKVTLVGTDGARTISLQDIADYCGTIHYEIACGLAPRVPRVYID
>sp|ALR_MOUSE|AUGMENTER OF LIVER REGENERATIO
MRTQQKRDIKFREDCPQDREELGRHTWAFLHTLAAYYPDRPTPEQQQDMAQFIHIFSKFYPCEE
CAEDIRKRIGRNQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSCD
>sp|ALR_MYCLE|ALANINE RACEMASE (EC 
MAVTPISLRPGVLAEAVVDLGAIDYNVRVLREHAGMAQLMVVLKADAYGHGATQVALAALAAGA
AELGVATVDEALALRADGISAPVLAWLHPPGIDFGPALLADVQIAVSSVRQLDELLDAVRRTGR
TATVTVKADTGLNRNGVVTDQYPAMLTALQRAVVEDAVRLRGLMSHLVYADQPDNPSNDVQGKR
FAALLAQAHEQGLRFEVAHLSNSSATMSRPDLAYDLVRPGIAVYGLSPVPSRGDMGLIPAMTVK
CAVAMVKSIRAGEGVSYGHDWIAQHDTNLALLPVGYADGVFRSLGGRLDVLINGKRRPGVGRIC
MDQFVVDLGPGPIDVAEGDEAILFGPGARGEPTAQDWADLLGTIHYEVVTSLRGRITRTYREAQ
TVDR
>sp|ALR_MYCSM|ALANINE RACEMASE (EC 
MQTTEPMTPPAPLASAQTVIDLGAIDHNVRVLRELAGSADVMAVVKADAYGHGALPVARTALAA
GAAALGVATIPEALALREGGITAPVLAWLHPPGTDFAPAIAADVEVAVSSRRQLEQVTAAAAEV
GRTATVTVKVDTGLSRNGVGAADYPEVLDVLRRAQADGAIRVRGLMSHLVHGDDPENPFNGLQG
QRLADMRVYAREHGVDYEVAHLCNSPAAMTRPDLAFEMVRPGISLYGLSPIPERGDMGLRPAMT
LKCPVALVRSVHAGDGVSYGHRWVADRDTTLGLLPIGYADGVYRALSGRIDVLIKGRRRRAVGR
ICMDQFVVDLGPDADDVAVGDDAILFGPGANGEPTAQDWAELLDTIHYEVVTSPRGRVTRTYLP
AGQQD
>sp|ALR_MYCTU|ALANINE RACEMASE (EC 
MKRFWENVGKPNDTTDGRGTTSLAMTPISQTPGLLAEAMVDLGAIEHNVRVLREHAGHAQLMAV
VKADGYGHGATRVAQTALGAGAAELGVATVDEALALRADGITAPVLAWLHPPGIDFGPALLADV
QVAVSSLRQLDELLHAVRRTGRTATVTVKVDTGLNRNGVGPAQFPAMLTALRQAMAEDAVRLRG
LMSHMVYADKPDDSINDVQAQRFTAFLAQAREQGVRFEVAHLSNSSATMARPDLTFDLVRPGIA
VYGLSPVPALGDMGLVPAMTVKCAVALVKSIRAGEGVSYGHTWIAPRDTNLALLPIGYADGVFR
SLGGRLEVLINGRRCPGVGRICMDQFMVDLGPGPLDVAEGDEAILFGPGIRGEPTAQDWADLVG
TIHYEVVTSPRGRITRTYREAENR
>sp|ALR_PSEFL|ALANINE RACEMASE (EC 
MXPARALIDLQALRHNYQLAAEVIG
>sp|ALR_RAT|AUGMENTER OF LIVER REGENERATIO
MRTQQKRDIKFREDCPQDREELGRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEE
CAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSCD
>sp|ALR_STRPN|ALANINE RACEMASE (EC 
AGACMGYGATYQADSEQVIATVPIGYADGWTRDMQNFSVLVDGQACPIVGRVSMDQITIRLPKL
YPLGTKVTLIGSNGDKEITATQVATYRVTINYEEVCLLSDRIPREYY
>sp|ALR_SYNY3|ALANINE RACEMASE (EC 
MVLSRDVKSSPEQASRVSSTLSGYRLAELIRQRAWVEIDQAALVHNVRQFRQYVGPKTNLMAVV
KADAYGHGAVRVAQTALQAGADWLAIATLGEGIELREAGITAPILLLGGINSPEEIEAIAHWRL
QPTLCSPEQAQLFNDILLKLGKVLPVHLKLDTGMTRLGTPWPQAANFVGLVQSLPQLRLASLYS
HLATADDPNTATMLQQQERFAKAIASLRQARLPIPKLHLANSAATLHGQAWHYDMVRVGLGLYG
LYPAPHLGDCLDLKPVLTVRAKITQIRTIPPGTGVSYGHQFVSEETMPMAVVGIGYADGVPRNL
SNQLEVLLRGQPVRQIGAITMDQMMVDLRGIDDPQVGEVVTLIGQDGDRQITADHWASTLGTIS
WEILCGFKHRLPRILI
>sp|ALS1_CANAL|AGGLUTININ-LIKE PROTEIN 1 PRECURSO
MLQQFTLLFLYLSIASAKTITGVFDSFNSLTWSNAANYAFKGPGYPTWNAVLGWSLDGTSANPG
DTFTLNMPCVFKYTTSQTSVDLTADGVKYATCQFYSGEEFTTFSTLTCTVNDALKSSIKAFGTV
TLPIAFNVGGTGSSTDLEDSKCFTAGTNTVTFNDGDKDISIDVEFEKSTVDPSAYLYASRVMPS
LNKVTTLFVAPQCENGYTSGTMGFSSSNGDVAIDCSNIHIGITKGLNDWNYPVSSESFSYTKTC
TSNGIQIKYQNVPAGYRPFIDAYISATDVNQYTLAYTNDYTCAGSRSQSKPFTLRWTGYKNSDA
GSNGIVIVATTRTVTDSTTAVTTLPFNPSVDKTKTIEILQPIPTTTITTSYVGVTTSYSTKTAP
IGETATVIVDVPYHTTTTVTSEWTGTITTTTTRTNPTDSIDTVVVQVPSPNPTVSTTEYWSQSF
ATTTTVTAPPGGTDTVIIREPPNHTVTTTEYWSQSFATTTTVTAPPGGTDSVIIREPPNPTVTT
TEYWSQSFATTTTVTAPPGGTDSVIIREPPNPTVTTTEYWSQSYATTTTVTAPPGGTDSVIIRE
PPNHTVTTTEYWSQSYATTTTVTAPPGGTDTVIIREPPNHTVTTTEYWSQSFATTTTVTGPPSG
TDTVIIREPPNPTVTTTEYWSQSYATTTTITAPPGETDTVLIREPPNHTVTTTEYWSQSYATTT
TVTAPPGETDTVLIREPPNHTVTTTEYWSQSYATTTTVTAPPGGTDTVIIREPPNPTVTTTEYW
SQSFATTTTVTAPPGGTDTVIIYESMSSSKISTSSNDITSIIPSFSRPHYVNSTTSDLSTFESS
SMNTPTSISSDGMLLSSTTLVTESETTTESICSDGKECSRLSSSSGIVTNPDSNESSIVTSTVP
TASTMSDSLSSTDGISATSSDNVSKSGVSVTTETSVTTIQTTPNPLSSSVTSLTQLSSIPSVSE
SESKVTFTSNGDNQSGTHDSQSTSTEIEIVTTSSTKVLPPVVSSNTDLTSEPTNTREQPTTLST
TSNSITEDITTSQPTGDNGDNTSSTNPVPTVATSTLASASEEDNKSGSHESASTSLKPSMGENS
GLTTSTEIEATTTSPTEAPSPAVSSGTDVTTEPTDTREQPTTLSTTSKTNSESVATTQATNENG
GKSPSTDLTSSLTTGTSASTSANSELVTSGSVTGGAVASASNDQSHSTSVTNSNSIVSNTPQTT
LSQQVTSSSPSTNTFIASTYDGSGSIIQHSTWLYGLITLLSLFI
>sp|ALS2_CANAL|AGGLUTININ-LIKE PROTEIN 2 PRECURSOR (FR
MLLQFLLLSLCVSVATAKVITGVFNSFDSLTWTRAGNYAYKGPNRPTWNAVLGWSLDGTSANPG
DTFTLNMPCVFKFITDQTSVDLTAEGVKYATCQFYSGEEFTTFSSLKCTVSNTLTSSIKALGTV
TLPISFNVGGTGSSVDLESSQCFKAGTNTVTFNDGDKKISIDVDFEKTNEDASGYFIASRLIPS
INKVSITYVAPQCANGYTSGAMGFIVLTGDTTIDCSNVHVGITKGLNDWNFPVSSDSLSYNKTC
SSTGISITYENVPAGYRPFFDVYTSVSGQNRQLRYTNDYACVGSSLQSKPFNLRLRGYNNSEAN
SNGFVIVATTRTVTDSTTAVTTLPFNPSVDKTKTIEILQPIPTTTITTSYVGVTTSYSTKTAPI
GETATVIVDVPYHTTTTVTSEWTGTITTTTTRTNPTDSIDTVVVQVPSPNPTVTTTEYWSQSYA
TTTTVTAPPGGTDSVIIREP
>sp|ALS3_CANAL|AGGLUTININ-LIKE PROTEIN 3 PRECURSO
MLQQYTLLLIYLSVATAKTITGVFNSFNSLTWSNAATYNYKGPGTPTWNAVLGWSLDGTSASPG
DTFTLNMPCVFKFTTSQTSVDLTAHGVKYATCQFQAGEEFMTFSTLTCTVSNTLTPSIKALGTV
TLPLAFNVGGTGSSVDLEDSKCFTAGTNTVTFNDGGKKISINVDFERSNVDPKGYLTDSRVIPS
LNKVSTLFVAPQCANGYTSGTMGFANTYGDVQIDCSNIHVGITKGLNDWNYPVSSESFSYTKTC
SSNGIFITYKNVPAGYRPFVDAYISATDVNSYTLSYANEYTCAGGYWQRAPFTLRWTGYRNSDA
GSNGIVIVATTRTVTDSTTAVTTLPFDPNRDKTKTIEILKPIPTTTITTSYVGVTTSYSTKTAP
IGETATVIVDIPYHTTTTVTSKWTGTITSTTTHTNPTDSIDTVIVQVPSPNPTVTTTEYWSQSF
ATTTTITGPPGNTDTVLIREPPNHTVTTTEYWSESYTTTSTFTAPPGGTDSVIIKEPPNPTVTT
TEYWSESYTTTSTFTAPPGGTDSVIIKEPPNHTVTTTEYWSQSYTTTTTVTAPPGGTDTVLVRE
PPNHTVTTTEYWSQSYTTTTTVIAPPGGTDSVIIREPPNPTVTTTEYWSQSYATTTTITAPPGE
TDTVLIREPPNHTVTTTEYWSQSYATTTTITAPPGETDTVLIREPPNHTVTTTEYWSQSFATTT
TVTAPPGGTDTVIIREPPNHTVTTTEYWSQSYATTTTITAPPGETDTVLIREPPNHTVTTTEYW
SQSYATTTTIIAPPGETDTVLIREPPNPTVTTTEYWSQSYTTATTVTAPPGGTDTVIIYDTMSS
SEISSFSRPHYTNHTTLWSTTWVIETKTITETSCEGDKGCSWVSVSTRIVTIPNNIETPMVTNT
VDSTTTESTSQSPSGIFSESGVSVETESSTVTTAQTNPSVPTTESEVVFTTKGNNENGPYESPS
TNVKSSMDENSEFTTSTAASTSTDIENETIATTGSVEASSPIISSSADETTTVTTTAESTSVIE
QPTNNNGGGKAPSATSSPSTTTTANNDSVITGTTSTNQSQSQSQYNSDTQQTTLSQQMTSSLVS
LHMLTTFDGSGSVIQHSTWLCGLITLLSLFI
genometools-1.5.1/testdata/sw100K2.magicmatch000066400000000000000000000015571211610345200207530ustar00rootroot00000000000000ab29483fe97ad9a018c2048587550b62	sp|ALR_LACPL|ALANINE RACEMASE (EC 
7b4e85c042820e17bff3a081bcf128db	sp|ALR_MOUSE|AUGMENTER OF LIVER REGENERATIO
cde4ef824416aad11121e34d00cb03f6	sp|ALR_MYCLE|ALANINE RACEMASE (EC 
71aec2904e1cf3417ce407ab480ff13c	sp|ALR_MYCSM|ALANINE RACEMASE (EC 
350c5a7adef926d6797d14ebe93c1f37	sp|ALR_MYCTU|ALANINE RACEMASE (EC 
eebe67006e5756cc6f3bb03a4dbe3ad9	sp|ALR_PSEFL|ALANINE RACEMASE (EC 
16f4f8ea56c84c3c43eb6ab83762844e	sp|ALR_RAT|AUGMENTER OF LIVER REGENERATIO
8cd8a8b64a87e1e7e1b16b390b87e127	sp|ALR_STRPN|ALANINE RACEMASE (EC 
667123c3b2557916df4f1c7c1ee5025d	sp|ALR_SYNY3|ALANINE RACEMASE (EC 
a8fc29f1d17c132bc3606d2ffad9c7fc	sp|ALS1_CANAL|AGGLUTININ-LIKE PROTEIN 1 PRECURSO
8faafd8d3867e9bcad779aa8d318b4a2	sp|ALS2_CANAL|AGGLUTININ-LIKE PROTEIN 2 PRECURSOR (FR
1e52c0abdb56f11036d6501235730288	sp|ALS3_CANAL|AGGLUTININ-LIKE PROTEIN 3 PRECURSO
genometools-1.5.1/testdata/tRNA.dos.fas000066400000000000000000000030671211610345200177460ustar00rootroot00000000000000>Homo_sapiens_chr6.trna95-AlaAGC (58249908-58249836)  Ala (AGC) 73 bp  Sc: 42.26
GGGGAATTAGCTCAAGCGGTAGAGCGCTCCCTTAGCATGCGAGAGGTAGCGGGATCGACG
CCCCCATTCTCTA
>Homo_sapiens_chr6.trna25-AlaAGC (26859897-26859969)  Ala (AGC) 73 bp  Sc: 46.89
GGGGGATTAGCTCAAGCGGTAGGGTGCCTGCTTAGCATGCAAGAGGTAGCAGGATCGACG
CCTGCATTCTCCA
>Homo_sapiens_chr1.trna87-AlaAGC (148284076-148284006)  Ala (AGC) 71 bp  Sc: 48.21
GGGGGTGTAGATCAGTGGTAGGGCGCACGCTTAGCATGCATGAGGCCCTGGGTCAATCCC
CAGCACCTCCA
>Homo_sapiens_chr6.trna94-AlaAGC (58250620-58250548)  Ala (AGC) 73 bp  Sc: 54.62
GGGGGATTAGCTCAAGCGGTAGAGCGCCTGCTTAGCATGCAAGAGGTAGCAGGATCGATG
CCTGCATTCTCCA
>Homo_sapiens_chr6.trna160-AlaAGC (26881822-26881750)  Ala (AGC) 73 bp  Sc: 54.69
GGGGAATTGGCTCAAGCGGTAGAGCGCTTGCTTAGCATGCAAGAGGTAGCAGGATCGACG
CCTGCACTCTCCA
>Homo_sapiens_chr6.trna23-AlaAGC (26836235-26836307)  Ala (AGC) 73 bp  Sc: 54.69
GGGGAATTGGCTCAAGCGGTAGAGCGCTTGCTTAGCATGCAAGAGGTAGCAGGATCGACG
CCTGCACTCTCCA
>Homo_sapiens_chr6.trna90-AlaAGC (58295475-58295403)  Ala (AGC) 73 bp  Sc: 54.84
GGGGAATTAGCGCAAGTGGTAGAGTGCTTGCTTAGCATGCAAGAGGTAGTGGGATCGATG
CCCACATTCTCCA
>Homo_sapiens_chr6.trna89-AlaAGC (58304654-58304582)  Ala (AGC) 73 bp  Sc: 57.89
GGGGAATTAGCCCAAGTGGTAGAGCGCTTGCTTAGCATGCAAGAGGTAGTGGGATCGATG
CCCACATTCTCCA
>Homo_sapiens_chr14.trna9-AlaAGC (88515195-88515267)  Ala (AGC) 73 bp  Sc: 59.85
GGGGAATTAGCTCAAGTGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGTGGGATCGATG
CCCGCATTCTCCA
>Homo_sapiens_chr6.trna18-AlaAGC (26781569-26781641)  Ala (AGC) 73 bp  Sc: 60.72
GGGGAATTAGCTCAAGTGGTAGAGCGCTTGCTTAGCATGCAAGAGGTAGTGGGATCAATG
CCCACATTCTCCA
genometools-1.5.1/testdata/target_attribute_swapped_range.gff3000066400000000000000000000007271211610345200247020ustar00rootroot00000000000000##gff-version 3
##sequence-region 2L 1 23011544
2L	blastp_Dmel_proteomic	match	11344	11483	.	-	.	ID=proteomic_PAp00018945_HIT_Dmel_proteomic;Name=proteomic_PAp00018945_HIT;program=blastp;programversion=1.0;sourcename=Dmel_proteomic;Target=proteomic_PAp00018945_hsp_0 2 74 -
2L	blastp_Dmel_proteomic	match_part	11344	11344	0.97	-	.	Name=proteomic_PAp00018945_hsp_0;Parent=proteomic_PAp00018945_HIT_Dmel_proteomic;target_type=match;Target=proteomic_PAp00018945_hsp_0 2 1 -
genometools-1.5.1/testdata/target_attribute_without_strand.gff3000066400000000000000000000001411211610345200251270ustar00rootroot00000000000000##gff-version   3
##sequence-region   chr 1 10000
chr	.	gene	1000	9000	0.5	+	.	Target=est 1 1000
genometools-1.5.1/testdata/terminator_separation.gff3000066400000000000000000000002171211610345200230350ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene1
###
ctg123	.	mRNA	1050	9000	.	+	.	Parent=gene1
genometools-1.5.1/testdata/test1.fasta000066400000000000000000000006371211610345200177430ustar00rootroot00000000000000>HWI-EAS306_9_FC305MP_6_1_773_1590
AAATAGGAAAGCACAGTTGAATGTGCTTTATTT
>HWI-EAS306_9_FC305MP_6_1_1240_1912
ACGTAACTTCTGGGGCTATTCTTACAGTAGTGA
>HWI-EAS306_9_FC305MP_6_1_1331_1843
ACGCAACTATCTTCATTATGTCAAGAAATACCA
>HWI-EAS306_9_FC305MP_6_1_336_1194
AATTGATGTTCACATATCTTGATTAGATGGTTG
>HWI-EAS306_9_FC305MP_6_1_1651_244
AAATTTCTCAATATACAAGGGATCCATGGTCCA
>HWI-EAS306_9_FC305MP_6_1_160_327
ACAACACATCCTGGCTCCTTCCGATGCATTCTC
genometools-1.5.1/testdata/test1.fastq000066400000000000000000000011671211610345200177620ustar00rootroot00000000000000@HWI-EAS306_9_FC305MP_6_1_773_1590
AAATAGGAAAGCACAGTTGAATGTGCTTTATTT
+
IIIIIIIIIGIIIIII1.I+I:):H(II2II52
@HWI-EAS306_9_FC305MP_6_1_1240_1912
ACGTAACTTCTGGGGCTATTCTTACAGTAGTGA
+
III;IFIIIIIIIDIIIIIIDDIFB2:5>?E;6
@HWI-EAS306_9_FC305MP_6_1_1331_1843
ACGCAACTATCTTCATTATGTCAAGAAATACCA
+
IIIIIII3IIII5III6III+GIIIIFIC;ICC
@HWI-EAS306_9_FC305MP_6_1_336_1194
AATTGATGTTCACATATCTTGATTAGATGGTTG
+
IIIIIIIIIIII%IIII/II4II%4$&I%)II$
@HWI-EAS306_9_FC305MP_6_1_1651_244
AAATTTCTCAATATACAAGGGATCCATGGTCCA
+
IIIIIIIIIIIIIIII=IIIIBIIIFII8@II,
@HWI-EAS306_9_FC305MP_6_1_160_327
ACAACACATCCTGGCTCCTTCCGATGCATTCTC
+
IIIIIIIIIIIIIIIII=IICI)II.I>'I>IH
genometools-1.5.1/testdata/test10_multiline.fastq000066400000000000000000000004231211610345200221160ustar00rootroot00000000000000@HWI-EAS306_9_FC305MP_6_1_773_1590
AAATAGGAAAGCACAGTTGAATGTGCTTTATTT
CGTACGTACGGCGCGCGGCCCCGTTATACGG
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIGIIIIII1.I+I:):H(II2II52
@HWI-EAS306_9_FC305MP_6_1_1240_1912
ACGTAACTTCTGGGGCTATTCTTACAGTAGTGA
+
III;IFIIIIIIIDIIIIIIDDIFB2:5>?E;6
genometools-1.5.1/testdata/test2_wrong_begin.fastq000066400000000000000000000011661211610345200223420ustar00rootroot00000000000000HWI-EAS306_9_FC305MP_6_1_773_1590
AAATAGGAAAGCACAGTTGAATGTGCTTTATTT
+
IIIIIIIIIGIIIIII1.I+I:):H(II2II52
@HWI-EAS306_9_FC305MP_6_1_1240_1912
ACGTAACTTCTGGGGCTATTCTTACAGTAGTGA
+
III;IFIIIIIIIDIIIIIIDDIFB2:5>?E;6
@HWI-EAS306_9_FC305MP_6_1_1331_1843
ACGCAACTATCTTCATTATGTCAAGAAATACCA
+
IIIIIII3IIII5III6III+GIIIIFIC;ICC
@HWI-EAS306_9_FC305MP_6_1_336_1194
AATTGATGTTCACATATCTTGATTAGATGGTTG
+
IIIIIIIIIIII%IIII/II4II%4$&I%)II$
@HWI-EAS306_9_FC305MP_6_1_1651_244
AAATTTCTCAATATACAAGGGATCCATGGTCCA
+
IIIIIIIIIIIIIIII=IIIIBIIIFII8@II,
@HWI-EAS306_9_FC305MP_6_1_160_327
ACAACACATCCTGGCTCCTTCCGATGCATTCTC
+
IIIIIIIIIIIIIIIII=IICI)II.I>'I>IH
genometools-1.5.1/testdata/test3_different_seqnames.fastq000066400000000000000000000012241211610345200237000ustar00rootroot00000000000000@HWI-EAS306_9_FC305MP_6_1_773_1590
AAATAGGAAAGCACAGTTGAATGTGCTTTATTT
+
IIIIIIIIIGIIIIII1.I+I:):H(II2II52
@HWI-EAS306_9_FC305MP_6_1_1240_1912
ACGTAACTTCTGGGGCTATTCTTACAGTAGTGA
+
III;IFIIIIIIIDIIIIIIDDIFB2:5>?E;6
@HWI-EAS306_9_FC305MP_6_1_1331_1843
ACGCAACTATCTTCATTATGTCAAGAAATACCA
+HWI-EAS306_9_FC305MP_6_1_1331
IIIIIII3IIII5III6III+GIIIIFIC;ICC
@HWI-EAS306_9_FC305MP_6_1_336_1194
AATTGATGTTCACATATCTTGATTAGATGGTTG
+
IIIIIIIIIIII%IIII/II4II%4$&I%)II$
@HWI-EAS306_9_FC305MP_6_1_1651_244
AAATTTCTCAATATACAAGGGATCCATGGTCCA
+
IIIIIIIIIIIIIIII=IIIIBIIIFII8@II,
@HWI-EAS306_9_FC305MP_6_1_160_327
ACAACACATCCTGGCTCCTTCCGATGCATTCTC
+
IIIIIIIIIIIIIIIII=IICI)II.I>'I>IH
genometools-1.5.1/testdata/test4_different_seqlengths.fastq000066400000000000000000000001441211610345200242420ustar00rootroot00000000000000@HWI-EAS306_9_FC305MP_6_1_773_1590
AAATAGGAAAGCACAGTTGAATGTGCTTTATTT
+
IIIIIIIIIGIIIIII1.I+I:):H(II
genometools-1.5.1/testdata/test5_tricky.fastq000066400000000000000000000007121211610345200213460ustar00rootroot00000000000000@071113_EAS56_0053:1:1:998:236
TTTCTTGCCCCCATAGACTGAGACCTTCCCTAAATA
+071113_EAS56_0053:1:1:998:236
IIIIIIIIIIIIIIIIIIIIIIIIIIIIICII+III
@071113_EAS56_0053:1:1:182:712
ACCCAGCTAATTTTTGTATTTTTGTTAGAGACAGTG
+
@IIIIIIIIIIIIIIICDIIIII<%<6&-*).(*%+
@071113_EAS56_0053:1:1:153:10
TGTTCTGAAGGAAGGTGTGCGTGCGTGTGTGTGTGT
+
IIIIIIIIIIIICIIGIIIII>IAIIIE65I=II:6
@071113_EAS56_0053:1:3:990:501
TGGGAGGTTTTATGTGGA
AAGCAGCAATGTACAAGA
+
IIIIIII.IIIIII1@44
@-7.%<&+/$/%4(++(%
genometools-1.5.1/testdata/test6_premature_end.fastq000066400000000000000000000010671211610345200227000ustar00rootroot00000000000000@HWI-EAS306_9_FC305MP_6_1_773_1590
AAATAGGAAAGCACAGTTGAATGTGCTTTATTT
+
IIIIIIIIIGIIIIII1.I+I:):H(II2II52
@HWI-EAS306_9_FC305MP_6_1_1240_1912
ACGTAACTTCTGGGGCTATTCTTACAGTAGTGA
+
III;IFIIIIIIIDIIIIIIDDIFB2:5>?E;6
@HWI-EAS306_9_FC305MP_6_1_1331_1843
ACGCAACTATCTTCATTATGTCAAGAAATACCA
+
IIIIIII3IIII5III6III+GIIIIFIC;ICC
@HWI-EAS306_9_FC305MP_6_1_336_1194
AATTGATGTTCACATATCTTGATTAGATGGTTG
+
IIIIIIIIIIII%IIII/II4II%4$&I%)II$
@HWI-EAS306_9_FC305MP_6_1_1651_244
AAATTTCTCAATATACAAGGGATCCATGGTCCA
+
IIIIIIIIIIIIIIII=IIIIBIIIFII8@II,
@HWI-EAS306_9_FC305MP_6_1_160_327
ACAAC
genometools-1.5.1/testdata/test7_empty_seq.fastq000066400000000000000000000000471211610345200220520ustar00rootroot00000000000000@HWI-EAS306_9_FC305MP_6_1_773_1590

+

genometools-1.5.1/testdata/test9_uneven_length.fastq000066400000000000000000000011561211610345200227110ustar00rootroot00000000000000@HWI-EAS306_9_FC305MP_6_1_773_1590
AAATAGGAAAGCACAGTTGAATGTGCTTTATTT
+
IIIIIIIIIGIIIIII1.I+I:):H(II2II52
@HWI-EAS306_9_FC305MP_6_1_1240_1912
ACGTAACTTCTGGGGCTATTCTTACAGTAGTGA
+
III;IFIIIIIIIDIIIIIIDDIF
@HWI-EAS306_9_FC305MP_6_1_1331_1843
ACGCAACTATCTTCATTATGTCAAGAAATACCA
+
IIIIIII3IIII5III6III+GIIIIFIC;ICC
@HWI-EAS306_9_FC305MP_6_1_336_1194
AATTGATGTTCACATATCTTGATTAGATGGTTG
+
IIIIIIIIIIII%IIII/II4II%4$&I%)II$
@HWI-EAS306_9_FC305MP_6_1_1651_244
AAATTTCTCAATATACAAGGGATCCATGGTCCA
+
IIIIIIIIIIIIIIII=IIIIBIIIFII8@II,
@HWI-EAS306_9_FC305MP_6_1_160_327
ACAACACATCCTGGCTCCTTCCGATGCATTCTC
+
IIIIIIIIIIIIIIIII=IICI)II.I>'I>IH
genometools-1.5.1/testdata/test_1_multiset.txt000066400000000000000000000000041211610345200215350ustar00rootroot00000000000000aabcgenometools-1.5.1/testdata/test_1_result.txt000066400000000000000000000000021211610345200212030ustar00rootroot000000000000006
genometools-1.5.1/testdata/test_1_text.txt000066400000000000000000000000121211610345200206520ustar00rootroot00000000000000abahgcabahgenometools-1.5.1/testdata/test_2_multiset.txt000066400000000000000000000000021211610345200215340ustar00rootroot00000000000000aagenometools-1.5.1/testdata/test_2_result.txt000066400000000000000000000000021211610345200212040ustar00rootroot000000000000003
genometools-1.5.1/testdata/test_2_text.txt000066400000000000000000000000041211610345200206540ustar00rootroot00000000000000abaagenometools-1.5.1/testdata/test_3_multiset.txt000066400000000000000000000000031211610345200215360ustar00rootroot00000000000000aabgenometools-1.5.1/testdata/test_3_result.txt000066400000000000000000000000041211610345200212070ustar00rootroot000000000000001
7
genometools-1.5.1/testdata/test_3_text.txt000066400000000000000000000000121211610345200206540ustar00rootroot00000000000000abahgcabahgenometools-1.5.1/testdata/trackname1.out000066400000000000000000000016611211610345200204400ustar00rootroot00000000000000eden.gff3|gene: gene 1000-9000
eden.gff3|mRNA: mRNA 1050-9000
eden.gff3|mRNA: exon 1050-1500
eden.gff3|mRNA: exon 3000-3902
eden.gff3|mRNA: exon 5000-5500
eden.gff3|mRNA: exon 7000-9000
eden.gff3|mRNA: mRNA 1050-9000
eden.gff3|mRNA: exon 1050-1500
eden.gff3|mRNA: exon 5000-5500
eden.gff3|mRNA: exon 7000-9000
eden.gff3|mRNA: mRNA 1300-9000
eden.gff3|mRNA: exon 1300-1500
eden.gff3|mRNA: exon 3000-3902
eden.gff3|mRNA: exon 5000-5500
eden.gff3|mRNA: exon 7000-9000
eden2.gff3|gene: gene 1000-9000
eden2.gff3|mRNA: mRNA 1050-9000
eden2.gff3|mRNA: exon 1050-1500
eden2.gff3|mRNA: exon 3000-3902
eden2.gff3|mRNA: exon 5000-5500
eden2.gff3|mRNA: exon 7000-9000
eden2.gff3|mRNA: mRNA 1050-9000
eden2.gff3|mRNA: exon 1050-1500
eden2.gff3|mRNA: exon 5000-5500
eden2.gff3|mRNA: exon 7000-9000
eden2.gff3|mRNA: mRNA 1300-9000
eden2.gff3|mRNA: exon 1300-1500
eden2.gff3|mRNA: exon 3000-3902
eden2.gff3|mRNA: exon 5000-5500
eden2.gff3|mRNA: exon 7000-9000
genometools-1.5.1/testdata/trackname1.style000066400000000000000000000125201211610345200207650ustar00rootroot00000000000000--[[
  This is the GenomeTools annotation viewer config file.
  All options must be set inside the 'style' table.
  All items in this table must be tables, called 'sections'.
  Typically there is one section per feature type.

  Color definitions
  -----------------
  Colors are given as RGB triplets
       {red=,green=,blue=(,alpha=)}
  where  is a decimal value between 0 and 1.
  The alpha value is optional, as a default 0.5 will be used.

  Global format settings
  ----------------------
  Global settings, such as margins, spacers, etc. are found at the end of this
  file, in the "format" section.
]]--

function printvals(gn, bar)
  rng = gn:get_range()
  type = gn:get_type()
  print(string.format("%s: %s %d-%d", bar, type, rng:get_start(), rng:get_end()))
  return {red=1.0, green=1.0, blue=0.0}
end

style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = printvals,
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
  },
--------------------------------------
  mRNA = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = printvals,
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
  },
--------------------------------------
  exon = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = printvals,
    style              = "box",
    -- Collapsing options
    collapse_to_parent = true,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
  },
--------------------------------------
  CDS = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.9, green=0.9, blue=0.2},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = true,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = 0,
  },
--------------------------------------
  TF_binding_site = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.8, green=0.6, blue=0.6},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = 0,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    unit = "bp",       -- basepair unit, e.g. "bp"
    ruler_left_text = "5'",  -- text left of the ruler axis
    ruler_right_text = "3'", -- text right of the ruler axis
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/testdata/trembl-difflenkey.faa000066400000000000000000000012201211610345200217240ustar00rootroot00000000000000>tr|A4GW6|A4GIW6_9CREN Putative ammonia monooxygenase subunit A (Fragment) OS=uncultured crenarchaeote GN =amoA PE=4 SV=1
RCTHYLFIVVVAVNSTLLTINAGDYIFYTDWAWTSFVVFSISQTLMLTVGACYYLTFTGV
PGTATYYALIMTVYTWIAKGAWFALGYPYDFIVTPVWLPSAMLLDLAYWATKKNKHSLIL
FGGVLVGMSLPLFNMVNLITVADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAG
AGAVLACTFAALGCKLTTWT
>tr|A4GIW7|A4GIW7_9CREN Putative ammonia monooxygenase subunit A (Fragment) OS=uncultured crenarchaeote GN =amoA PE=4 SV=1
CTHYLFIVVVAVNSTLLTINSGDYIFYTDWAWTSFVVFSIANTLMTIVGAVYYLTFTGVP
GTATYYGLIMQVYTWVAKVAWFALGYPVDFIVHPMWIPSCMLLDLAYWATKKNKHSLIFF
GGVLVGMSMPLFNMVQLMLIADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAGA
GSVLACTFAALGCKLNTWTYRWM
genometools-1.5.1/testdata/trembl-emptykey.faa000066400000000000000000000012131211610345200214550ustar00rootroot00000000000000>tr||A4GIW6_9CREN Putative ammonia monooxygenase subunit A (Fragment) OS=uncultured crenarchaeote GN =amoA PE=4 SV=1
RCTHYLFIVVVAVNSTLLTINAGDYIFYTDWAWTSFVVFSISQTLMLTVGACYYLTFTGV
PGTATYYALIMTVYTWIAKGAWFALGYPYDFIVTPVWLPSAMLLDLAYWATKKNKHSLIL
FGGVLVGMSLPLFNMVNLITVADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAG
AGAVLACTFAALGCKLTTWT
>tr|A4GIW7|A4GIW7_9CREN Putative ammonia monooxygenase subunit A (Fragment) OS=uncultured crenarchaeote GN =amoA PE=4 SV=1
CTHYLFIVVVAVNSTLLTINSGDYIFYTDWAWTSFVVFSIANTLMTIVGAVYYLTFTGVP
GTATYYGLIMQVYTWVAKVAWFALGYPVDFIVHPMWIPSCMLLDLAYWATKKNKHSLIFF
GGVLVGMSMPLFNMVQLMLIADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAGA
GSVLACTFAALGCKLNTWTYRWM
genometools-1.5.1/testdata/trembl-eqlen.faa000066400000000000000000000012161211610345200207150ustar00rootroot00000000000000>tr|A4GIW6|A4GIW6_9CREN Putative ammonia monooxygenase subunit A (Fragment) OS=uncultured crenarchaeote GN =amoA PE=4 SV=1
RCTHYLFIVVVAVNSTLLTINAGDYIFYTDWAWTSFVVFSISQTLMLTVGACYYLTFTGV
PGTATYYALIMTVYTWIAKGAWFALGYPYDFIVTPVWLPSAMLLDLAYWATKKNKHSLIL
FGGVLVGMSLPLFNMVNLITVADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAG
AGAVLACTFAALGCKLTTWT
>tr|A4GIW7|A4GIW7_9CREN Putative ammonia monooxygenase subunit A (Fragment) OS=uncultured crenarchaeote GN =amoA PE=4 SV=1
CTHYLFIVVVAVNSTLLTINSGDYIFYTDWAWTSFVVFSIANTLMTIVGAVYYLTFTGVP
GTATYYGLIMQVYTWVAKVAWFALGYPVDFIVHPMWIPSCMLLDLAYWATKKNKHSLIFF
GGVLVGMSMPLFNMVQLMLIADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAGA
GSVLACTFAALGCKLNTWTY
genometools-1.5.1/testdata/trembl-keys.txt000066400000000000000000000000161211610345200206510ustar00rootroot00000000000000A4GIW6
A4GIW7
genometools-1.5.1/testdata/trembl-wrongkey.txt000066400000000000000000000000331211610345200215420ustar00rootroot00000000000000A0AQI4
A0QI5
A0AQI7
A0AQI8
genometools-1.5.1/testdata/trembl.faa000066400000000000000000000012211211610345200176070ustar00rootroot00000000000000>tr|A4GIW6|A4GIW6_9CREN Putative ammonia monooxygenase subunit A (Fragment) OS=uncultured crenarchaeote GN =amoA PE=4 SV=1
RCTHYLFIVVVAVNSTLLTINAGDYIFYTDWAWTSFVVFSISQTLMLTVGACYYLTFTGV
PGTATYYALIMTVYTWIAKGAWFALGYPYDFIVTPVWLPSAMLLDLAYWATKKNKHSLIL
FGGVLVGMSLPLFNMVNLITVADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAG
AGAVLACTFAALGCKLTTWT
>tr|A4GIW7|A4GIW7_9CREN Putative ammonia monooxygenase subunit A (Fragment) OS=uncultured crenarchaeote GN =amoA PE=4 SV=1
CTHYLFIVVVAVNSTLLTINSGDYIFYTDWAWTSFVVFSIANTLMTIVGAVYYLTFTGVP
GTATYYGLIMQVYTWVAKVAWFALGYPVDFIVHPMWIPSCMLLDLAYWATKKNKHSLIFF
GGVLVGMSMPLFNMVQLMLIADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVALGAGA
GSVLACTFAALGCKLNTWTYRWM
genometools-1.5.1/testdata/trkeys-result.txt000066400000000000000000000012461211610345200212560ustar00rootroot00000000000000>A0AQI4 1 10 tr|A0AQI4|A0AQI4_9ARCH Putative ammonia monooxygenase (Fragment) OS=uncultured archaeon GN=amoA PE=4 SV=1
VWLRRCTHYL
>A0AQI5 60 62 tr|A0AQI5|A0AQI5_9ARCH Putative ammonia monooxygenase (Fragment) OS=uncultured archaeon GN=amoA PE=4 SV=1
TFT
>A0AQI7 1 20 tr|A0AQI7|A0AQI7_9ARCH Putative ammonia monooxygenase (Fragment) OS=uncultured archaeon GN=amoA PE=4 SV=1
VWLRRCTHYLFIVVVAVNST
>A0AQI8 2 22 tr|A0AQI8|A0AQI8_9ARCH Putative ammonia monooxygenase (Fragment) OS=uncultured archaeon GN=amoA PE=4 SV=1
WLRRCTHYLFIVVVAVNSTLL
>A0FGX9 3 28 tr|A0FGX9|A0FGX9_9ARCH Methyl coenzyme M reductase (Fragment) OS=uncultured archaeon GN=mcrA PE=4 SV=1
TDDILDDNVYYDVDYINDKYNGAATI
genometools-1.5.1/testdata/trkeys.txt000066400000000000000000000000751211610345200177410ustar00rootroot00000000000000A0AQI4 1 10
A0AQI5 60 62
A0AQI7 1 20
A0AQI8 2 22
A0FGX9 3 28
genometools-1.5.1/testdata/trna_glutamine.embl000066400000000000000000000004371211610345200215330ustar00rootroot00000000000000ID   tRNA-glutamine
XX
DE   gi|24371439|ref|NR_000037.1| Homo sapiens tRNA glutamine 1 (TRQ1) on
DE   chromosome 17
XX
SQ
     GGTTCCATGG TGTAATGGTT AGCACTCTGG ACTCTGAATC CAGCGATCCG AGTTCAAATC        60
     TCGGTGGAAC CT                                                            72
//
genometools-1.5.1/testdata/trna_glutamine.fna000066400000000000000000000002361211610345200213550ustar00rootroot00000000000000>gi|24371439|ref|NR_000037.1| Homo sapiens tRNA glutamine 1 (TRQ1) on chromosome 17
GGTTCCATGGTGTAATGGTTAGCACTCTGGACTCTGAATCCAGCGATCCGAGTTCAAATCTCGGTGGAAC
CT
genometools-1.5.1/testdata/trna_glutamine.gbk000066400000000000000000000040101211610345200213460ustar00rootroot00000000000000LOCUS       NR_000037                 72 bp    tRNA    linear   PRI 17-DEC-2003
DEFINITION  Homo sapiens tRNA glutamine 1 (TRQ1) on chromosome 17.
ACCESSION   NR_000037
VERSION     NR_000037.1  GI:24371439
KEYWORDS    .
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 72)
  AUTHORS   Morrison,N., Goddard,J.P., Ledbetter,D.H., Boyd,E., Bourn,D. and
            Connor,J.M.
  TITLE     Chromosomal assignment of a large tRNA gene cluster (tRNA(Leu),
            tRNA(Gln), tRNA(Lys), tRNA(Arg), tRNA(Gly)) to 17p13.1
  JOURNAL   Hum. Genet. 87 (2), 226-230 (1991)
   PUBMED   2066114
REFERENCE   2  (bases 1 to 72)
  AUTHORS   Roy,K.L., Cooke,H. and Buckland,R.
  TITLE     Nucleotide sequence of a segment of human DNA containing the three
            tRNA genes
  JOURNAL   Nucleic Acids Res. 10 (22), 7313-7322 (1982)
   PUBMED   6296772
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from K01797.1.
FEATURES             Location/Qualifiers
     source          1..72
                     /organism="Homo sapiens"
                     /mol_type="tRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17p13.1"
     gene            1..72
                     /gene="TRQ1"
                     /db_xref="GeneID:7228"
                     /db_xref="LocusID:7228"
                     /db_xref="MIM:189919"
     tRNA            1..72
                     /gene="TRQ1"
                     /product="tRNA-Gln"
                     /note="codon recognized: CAG; G00-120-457"
                     /db_xref="GeneID:7228"
                     /db_xref="LocusID:7228"
                     /db_xref="MIM:189919"
ORIGIN      
        1 ggttccatgg tgtaatggtt agcactctgg actctgaatc cagcgatccg agttcaaatc
       61 tcggtggaac ct
//

genometools-1.5.1/testdata/trna_glutamine.out000066400000000000000000000011551211610345200214210ustar00rootroot00000000000000fold the following RNA sequence with Nussinov Algorithm:
ggttccatggtgtaatggttagcactctggactctgaatccagcgatccgagttcaaatctcggtggaacct
length of RNA sequence = 72
using the following parameters:
l_min =  3
alpha(G,C) = alpha(C,G) = -3
alpha(A,U) = alpha(U,A) = -2
alpha(G,U) = alpha(U,G) = -1
all other alpha values have been set to infinity
score: -69
result:
(1,71)(2,70)(3,69)(4,68)(5,67)(6,66)(7,47)(8,46)(9,44)(10,25)(11,24)(12,23)(13,21)(14,20)(15,19)(27,43)(28,42)(29,41)(30,40)(31,39)(32,36)(10,25)(11,24)(12,23)(13,21)(14,20)(15,19)(27,43)(28,42)(29,41)(30,40)(31,39)(32,36)(48,64)(49,63)(50,62)(51,61)(52,60)(54,58)
genometools-1.5.1/testdata/two_fasta_seqs.gff3000066400000000000000000000002521211610345200214450ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq1 1 10
##sequence-region   seq2 1 10
seq1	.	gene	1	10	.	+	.	.
seq2	.	gene	1	10	.	+	.	.
##FASTA
>seq1
cttctgggcg
>seq2
tgttcattgc
genometools-1.5.1/testdata/two_fasta_seqs_without_sequence_regions.gff3000066400000000000000000000001561211610345200266510ustar00rootroot00000000000000##gff-version   3
seq1	.	gene	1	10	.	+	.	.
seq2	.	gene	1	10	.	+	.	.
##FASTA
>seq1
cttctgggcg
>seq2
tgttcattgc
genometools-1.5.1/testdata/undefined_parent.gff3000066400000000000000000000002231211610345200217330ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA1
ctg123	.	exon	1050	1500	.	+	.	Parent=mRNA1,mRNA2
###
genometools-1.5.1/testdata/unknown_meta_directive.gff3000066400000000000000000000000521211610345200231640ustar00rootroot00000000000000##gff-version   3
##unknown-directive XXX
genometools-1.5.1/testdata/unsorted_gff3_file.txt000066400000000000000000000001711211610345200221640ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 1497228
ctg123	.	gene	10000	11000	.	+	.	.
ctg123	.	gene	1000	9000	.	+	.	.
genometools-1.5.1/testdata/uppercase_attributes.gff3000066400000000000000000000003331211610345200226600ustar00rootroot00000000000000##gff-version   3
##sequence-region   seq 1 1000
seq	.	gene	1	1000	.	+	.	ID=gene1;Name=gene_name;Alias=gene_alias;Target=cDNA 1 426 +;Gap=xxx;Derives_from=xxx;Note=note;Dbxref=xxx;Ontology_term=xxx;Is_circular=true
###
genometools-1.5.1/testdata/wildcardatend.fna000066400000000000000000000000311211610345200211420ustar00rootroot00000000000000>seq1
AAA
>seq2
AANNAANN
genometools-1.5.1/testdata/wildcardatend_rev.fna000066400000000000000000000000631211610345200220230ustar00rootroot00000000000000>seq1
AAA
>seq2
AANNAANN
>seq2
NNTTNNTT
>seq1
TTT

genometools-1.5.1/testsuite/000077500000000000000000000000001211610345200160755ustar00rootroot00000000000000genometools-1.5.1/testsuite/gcov_include.rb000066400000000000000000000033321211610345200210640ustar00rootroot00000000000000full_coverage_files = [ "src/core/basename.c",
                        "src/core/bittab.c",
                        "src/core/bsearch.c",
                        "src/core/countingsort.c",
                        "src/core/disc_distri.c",
                        "src/core/dynalloc.c",
                        "src/core/fasta.c",
                        "src/core/queue.c",
                        "src/extended/add_introns_stream.c",
                        "src/extended/consensus_sa.c",
                        "src/extended/gff3_escaping.c",
                        "src/extended/gff3_in_stream.c",
                        "src/extended/gff3_out_stream.c",
                        "src/extended/gff3_output.c",
                        "src/extended/gff3_visitor.c",
                        "src/extended/node_stream.c",
                        "src/extended/node_visitor.c",
                        "src/extended/shredder.c",
                        "src/extended/stat_stream.c",
                        "src/extended/stat_visitor.c",
                        "src/extended/uniq_stream.c",
                        "src/tools/gt_bed_to_gff3.c",
                        "src/tools/gt_chseqids.c",
                        "src/tools/gt_fingerprint.c",
                        "src/tools/gt_gff3.c",
                        "src/tools/gt_shredder.c",
                        "src/tools/gt_splicesiteinfo.c",
                        "src/tools/gt_uniq.c"
                      ]

full_coverage_files.each do |file|
  base = File.basename(file)
  Name "full coverage for #{file}"
  Keywords "gcov"
  Test do
    run "cd #{$cur} && gcov -o obj/#{file} #{file} && cd -"
    run "mv #{$cur}/#{base}.gcov ."
    grep(base+".gcov", "^    #####", true)
  end
end
genometools-1.5.1/testsuite/gt_bed_to_gff3_include.rb000066400000000000000000000014231211610345200227600ustar00rootroot00000000000000def process_bed_files(dir)
  for infile in Dir.entries(dir).grep(/\.bed$/) do
    infile = File.join(dir, infile)
    Name "gt bed_to_gff3 #{File.basename(infile).chomp}"
    Keywords "gt_bed_to_gff3"
    Test do
      run_test("#{$bin}gt bed_to_gff3 #{infile}", :maxtime => 320)
      outfile = infile.gsub(/\.bed$/, ".gff3")
      run "diff #{last_stdout} #{outfile}"
    end
  end
end

process_bed_files("#{$testdata}bed_files")

if $gttestdata then
  process_bed_files("#{$gttestdata}bed")
end

Name "gt bed_to_gff3 (type options)"
Keywords "gt_bed_to_gff3"
Test do
  run_test "#{$bin}gt bed_to_gff3 -featuretype gene -thicktype CDS " +
           "-blocktype exon #{$testdata}bed_files/ct_example3.bed"
  run "diff #{last_stdout} #{$testdata}bed_files/ct_example3.gff3_as_gene"
end
genometools-1.5.1/testsuite/gt_cds_include.rb000066400000000000000000000102341211610345200213700ustar00rootroot000000000000001.upto(14) do |i|
  Name "gt cds test #{i}"
  Keywords "gt_cds"
  Test do
    run_test "#{$bin}gt cds -minorflen 1 -startcodon yes " +
             "-seqfile #{$testdata}gt_cds_test_#{i}.fas " +
             "#{$testdata}gt_cds_test_#{i}.in"
    run "diff #{last_stdout} #{$testdata}gt_cds_test_#{i}.out"
  end
end

Name "gt cds error message"
Keywords "gt_cds"
Test do
  run "#{$bin}gt gff3 -offset 1000 #{$testdata}gt_cds_test_1.in | " +
      "#{$bin}gt cds -seqfile #{$testdata}gt_cds_test_1.fas -", :retval => 1
  grep last_stderr, "Has the sequence-region to sequence mapping been defined correctly"
end

1.upto(14) do |i|
  Name "gt cds test #{i} (-usedesc)"
  Keywords "gt_cds usedesc"
  Test do
    run_test "#{$bin}gt cds -minorflen 1 -startcodon yes -usedesc " +
             "-seqfile #{$testdata}gt_cds_test_#{i}.fas " +
             "#{$testdata}gt_cds_test_#{i}.in"
    run "diff #{last_stdout} #{$testdata}gt_cds_test_#{i}.out"
  end
end

Name "gt cds test (description range)"
Keywords "gt_cds usedesc"
Test do
  run_test "#{$bin}gt cds -minorflen 1 -usedesc -seqfile " +
           "#{$testdata}gt_cds_test_descrange.fas " +
           "#{$testdata}gt_cds_test_descrange.in"
  run "diff #{last_stdout} #{$testdata}gt_cds_test_descrange.out"
end

Name "gt cds test (multi description)"
Keywords "gt_cds usedesc"
Test do
  run_test "#{$bin}gt cds -minorflen 1 -usedesc -seqfile " +
           "#{$testdata}gt_cds_descrange_multi.fas " +
           "#{$testdata}gt_cds_descrange_multi.in"
  run "diff #{last_stdout} #{$testdata}gt_cds_descrange_multi.out"
end

Name "gt cds test (multi description fail 1)"
Keywords "gt_cds usedesc"
Test do
  run_test("#{$bin}gt cds -usedesc -seqfile " +
           "#{$testdata}gt_cds_descrange_multi_fail_1.fas " +
           "#{$testdata}gt_cds_test_descrange.in", :retval => 1)
  grep last_stderr, "does contain multiple sequences with ID"
end

Name "gt cds test (multi description fail 2)"
Keywords "gt_cds usedesc"
Test do
  run_test("#{$bin}gt cds -usedesc -seqfile " +
           "#{$testdata}gt_cds_descrange_multi_fail_2.fas " +
           "#{$testdata}gt_cds_test_descrange.in", :retval => 1)
  grep last_stderr, "does contain multiple sequences with ID"
end

Name "gt cds test (wrong ID)"
Keywords "gt_cds usedesc"
Test do
  run_test("#{$bin}gt cds -usedesc -seqfile " +
           "#{$testdata}gt_cds_descrange_wrong_id.fas " +
           "#{$testdata}gt_cds_test_descrange.in", :retval => 1)
  grep last_stderr, "does not contain a sequence with ID"
end

Name "gt cds test (wrong range)"
Keywords "gt_cds usedesc"
Test do
  run_test("#{$bin}gt cds -usedesc -seqfile " +
           "#{$testdata}gt_cds_descrange_wrong_range.fas " +
           "#{$testdata}gt_cds_test_descrange.in", :retval => 1)
  grep last_stderr, "cannot find sequence ID"
end

Name "gt cds test (-startcodon no -finalstopcodon no)"
Keywords "gt_cds"
Test do
  run_test "#{$bin}gt cds -startcodon no -finalstopcodon no -seqfile " +
           "#{$testdata}U89959_genomic.fas " +
           "#{$testdata}gt_cds_nostartcodon_nofinalstopcodon.in"
  run "diff #{last_stdout} " +
      "#{$testdata}gt_cds_nostartcodon_nofinalstopcodon.out"
end

Name "gt cds test (nGASP)"
Keywords "gt_cds nGASP"
Test do
  run_test "#{$bin}gt cds -startcodon yes -finalstopcodon no -minorflen 64 " +
           "-seqfile #{$testdata}nGASP/III.fas -usedesc " +
           "#{$testdata}nGASP/resIII.gff3"
  run "diff #{last_stdout} #{$testdata}nGASP/resIIIcds.gff3"
end

Name "gt cds test (U89959)"
Keywords "gt_cds"
Test do
  run_test "#{$bin}gt cds -seqfile #{$testdata}U89959_genomic.fas " +
           "#{$testdata}U89959_csas.gff3"
  run      "diff #{last_stdout} #{$testdata}U89959_cds.gff3"
end

Name "gt cds test (not sorted)"
Keywords "gt_cds"
Test do
  run_test "#{$bin}gt cds -seqfile #{$testdata}U89959_genomic.fas " +
           "#{$testdata}not_sorted.gff3", :retval => 1
  grep last_stderr, "is not sorted"
end

if $gttestdata then
  Name "gt cds bug"
  Keywords "gt_cds"
  Test do
    run_test "#{$bin}gt cds -startcodon yes -minorflen 1 " +
             "-seqfile #{$gttestdata}cds/marker_region.fas " +
             "#{$gttestdata}cds/marker_bug.gff3"
    run "diff #{last_stdout} #{$gttestdata}cds/marker_bug.out"
  end
end
genometools-1.5.1/testsuite/gt_chain2dim_include.rb000066400000000000000000000042011211610345200224520ustar00rootroot00000000000000def runchain2dimfailure(args,matchfile='matchfile')
  Name "gt chain2dim failure"
  Keywords "gt_chain2dim"
  Test do
    run_test "#{$bin}gt chain2dim -m #{matchfile} " + args,:retval => 1
  end
end

def runchain2dim(args,matchfile)
  Name "gt chain2dim #{args}"
  Keywords "gt_chain2dim"
  Test do
    run_test "#{$bin}gt chain2dim -m #{matchfile} " + args
    argstring = args.gsub(/[ ]/,"")
    run "cmp -s #{last_stdout} #{$testdata}chaindata/chain#{argstring}"
  end
end

def runchain2dimall(params,matchfile)
  params.each do |args|
    runchain2dim(args,matchfile)
  end
end

Name "gt chain2dim small all"
Keywords "gt_chain2dim all"
Test do
  run_test "#{$bin}gt chain2dim -global all -m #{$testdata}chaindata/matches-nd.txt"
  run "cmp -s #{last_stdout} #{$testdata}chaindata/matches-nd.chains"
end

Name "gt chain2dim ecoli all"
Keywords "gt_chain2dim all"
Test do
  [283,298,304,753].each do |lines|
    run "head -n #{lines} #{$testdata}ecolicmp250.of | sed -e 's/[0-9]*$/1/'"
    run_test "#{$bin}gt chain2dim -global all -m #{last_stdout}"
  end
end

runchain2dimfailure("-maxgap 0")
runchain2dimfailure("-maxgap -1")
runchain2dimfailure("-wf 0.0")
runchain2dimfailure("-wf -1.0")
runchain2dimfailure("-wf 1.0")
runchain2dimfailure("-global xv")
runchain2dimfailure("-global ov h")
runchain2dimfailure("-local 2p h")
runchain2dimfailure("-local -global")
runchain2dimfailure("-global","#{$testdata}ecolicmp-neg.of")
runchain2dimfailure("-global","#{$testdata}ecolicmp-se.of")

# runchain2dimall("#{$testdata}ecolicmp.of")

params = ["-global",
	  "-silent -global",
	  "-local -wf 1.8",
	  "-local -wf 0.5",
	  "-local -maxgap 20",
	  "-local 2b",
	  "-local 55p -silent",
	  "-global gc",
	  "-global ov",
	  "-global gc -wf 1.5",
	  "-global ov -wf 1.8",
	  "-global -maxgap 10",
	  "-global gc -wf 1.5 -maxgap 10",
	  "-global ov -wf 1.8 -maxgap 10",
	  "-local",
	  "-local 2p",
	  "-local 20",
	  "-local 2p -wf 1.8",
	  "-local 2b -wf 1.8",
	  "-local 20 -wf 1.8",
	  "-local -wf 1.8 -maxgap 20",
	  "-local 2p -wf 1.8 -maxgap 10",
	  "-local 2b -wf 1.8 -maxgap 10",
	  "-local 20 -wf 1.8 -maxgap 10"]

runchain2dimall(params,"#{$testdata}ecolicmp250.of")
genometools-1.5.1/testsuite/gt_chseqids_include.rb000066400000000000000000000047211211610345200224260ustar00rootroot00000000000000Name "gt chseqids -help"
Keywords "gt_chseqids"
Test do
  run_test "#{$bin}gt chseqids -help"
  grep last_stdout, "Report bugs to"
end

Name "gt chseqids -noop"
Keywords "gt_chseqids"
Test do
  run_test("#{$bin}gt chseqids -noop", :retval => 1)
  grep last_stderr, "unknown option"
end

Name "gt chseqids empty mapping file"
Keywords "gt_chseqids"
Test do
  run_test("#{$bin}gt chseqids #{$testdata}empty_file", :retval => 1)
  grep last_stderr, "not defined"
end

Name "gt chseqids empty gff3 file"
Keywords "gt_chseqids"
Test do
  run_test "#{$bin}gt chseqids #{$testdata}gt_chseqids_test_1.chseqids #{$testdata}empty_file", :retval => 1
  grep last_stderr, "GFF3 file .* is empty"
end

Name "gt chseqids corrupt.gff3"
Keywords "gt_chseqids"
Test do
  run_test("#{$bin}gt chseqids #{$testdata}gt_chseqids_test_1.chseqids #{$testdata}corrupt.gff3", :retval => 1)
end

Name "gt chseqids test 1"
Keywords "gt_chseqids"
Test do
  run_test "#{$bin}gt chseqids -v -o test.out " +
           "#{$testdata}gt_chseqids_test_1.chseqids " +
           "#{$testdata}gt_chseqids_test_1.gff3"
  run "diff test.out #{$testdata}gt_chseqids_test_1.out"
end

Name "gt chseqids test 2"
Keywords "gt_chseqids"
Test do
  run_test "#{$bin}gt chseqids #{$testdata}gt_chseqids_test_2.chseqids #{$testdata}gt_chseqids_test_2.gff3"
  run "diff #{last_stdout} #{$testdata}gt_chseqids_test_2.out"
end

Name "gt chseqids test 3"
Keywords "gt_chseqids"
Test do
  run_test("#{$bin}gt chseqids #{$testdata}gt_chseqids_test_3.chseqids #{$testdata}gt_chseqids_test_3.gff3", :retval => 1)
end

Name "gt chseqids test 4"
Keywords "gt_chseqids"
Test do
  run_test "#{$bin}gt chseqids #{$testdata}gt_chseqids_test_4.chseqids #{$testdata}gt_chseqids_test_4.gff3"
  run "diff #{last_stdout} #{$testdata}gt_chseqids_test_4.out"
end

Name "gt chseqids test 5"
Keywords "gt_chseqids"
Test do
  run_test "#{$bin}gt chseqids #{$testdata}gt_chseqids_test_5.chseqids #{$testdata}gt_chseqids_test_5.gff3"
  run "diff #{last_stdout} #{$testdata}gt_chseqids_test_5.out"
end

Name "gt chseqids test 5 (-sort)"
Keywords "gt_chseqids"
Test do
  run_test "#{$bin}gt chseqids -sort #{$testdata}gt_chseqids_test_5.chseqids #{$testdata}gt_chseqids_test_5.gff3"
  run "diff #{last_stdout} #{$testdata}gt_chseqids_test_5.sorted_out"
end

Name "gt chseqids test 6"
Keywords "gt_chseqids"
Test do
  run_test "#{$bin}gt chseqids #{$testdata}gt_chseqids_test_6.chseqids #{$testdata}gt_chseqids_test_6.gff3"
  run "diff #{last_stdout} #{$testdata}gt_chseqids_test_6.out"
end
genometools-1.5.1/testsuite/gt_cmpprjfiles_include.rb000066400000000000000000000063351211610345200231440ustar00rootroot00000000000000require 'set'
require 'digest/md5'

testdatafiles = Set.new

testdatafiles.add('at1MB')
testdatafiles.add('at100K1')
testdatafiles.add('Random-Small.fna')
testdatafiles.add('Random.fna')
testdatafiles.add('Atinsert.fna')
testdatafiles.add('TTT-small.fna')

def expandfilename(testdatafiles,filename)
  if testdatafiles.member?(filename)
    return "#{$testdata}#{filename}"
  else
    return "#{$gttestdata}DNA-mix/Grumbach.fna/#{filename}"
  end
end

def fromoptions2indexname(options)
  return options.gsub(/[ ]+/,"").gsub(/^-/,"")
end

def fileargs(testdatafiles,options)
  dbarg=['-db']
  doappend = false
  options.split(/ /).each do |opt|
    if opt == '-db'
      doappend = true
    elsif doappend
      dbarg.push(expandfilename(testdatafiles,opt))
    end
  end
  return dbarg.join(" ")
end

def grepprjfile(filename)
begin
  f = File.new(filename)
rescue => error
  STDERR.puts "#{$0}: cannot open \"#{filename}\": #{error}"
  exit 1
end
  return f.readlines.grep(/prefixlength|readmode|realspecialranges/)
end

outoptions="-tis -lcp -suf -bwt"

callargs =   ["#{outoptions} -db Random-Small.fna",
              "#{outoptions} -db Random.fna",
              "#{outoptions} -db Atinsert.fna Random.fna",
              "#{outoptions} -db TTT-small.fna",
              "#{outoptions} -lcp -db at100K1",
              "#{outoptions} -bwt -db at100K1",
              "#{outoptions} -bwt -lcp -db at100K1",
              "#{outoptions} -suf -db at100K1",
              "#{outoptions} -suf -lcp -db at100K1",
              "#{outoptions} -suf -bwt -db at100K1",
              "#{outoptions} -suf -bwt -lcp -db at100K1",
              "#{outoptions} -tis -db at100K1",
              "#{outoptions} -tis -lcp -db at100K1",
              "#{outoptions} -tis -bwt -db at100K1",
              "#{outoptions} -tis -bwt -lcp -db at100K1",
              "#{outoptions} -tis -suf -db at100K1",
              "#{outoptions} -tis -suf -lcp -db at100K1",
              "#{outoptions} -tis -suf -bwt -db at100K1",
              "#{outoptions} -tis -suf -bwt -lcp -db at100K1"]

if $gttestdata then
  callargs.push("#{outoptions} -db at100K1 at1MB Wildcards.fna chntxx.fna " +
               "hs5hcmvcg.fna humdystrop.fna humghcsa.fna " +
               "humhbb.fna humhdabcd.fna humhprtb.fna " +
               "mipacga.fna mpocpcg.fna mpomtcg.fna " +
               "vaccg.fna ychrIII.fna")
end

Name "gt checking project files"
Keywords "gt_checkprjfiles"
Test do
  callargs.each do |args|
    indexfileprefix=fromoptions2indexname(args)
    # long filenames can cause problems on encrypted file systems
    # this will produce a prefix of exactly 100 chars (resulting in 104 byte
    # filenames)
    if indexfileprefix.length >= 100
            indexfileprefix = indexfileprefix[0..67] + 
              Digest::MD5.hexdigest(indexfileprefix)[0..31]
    end
    indexname="#{indexfileprefix}"
    run_test "#{$bin}gt suffixerator -indexname #{indexname} " +
             "-pl -des #{fileargs(testdatafiles,args)}"
    thislist=grepprjfile("#{indexname}.prj")
    reflist=grepprjfile("#{$testdata}prj-files/#{indexname}.prj")
    if thislist != reflist
      STDERR.puts "files #{indexname}.prj and " +
                  "#{$testdata}prj-files/#{indexname}.prj differ"
      exit 1
    end
  end
end
genometools-1.5.1/testsuite/gt_consensus_sa_include.rb000066400000000000000000000005701211610345200233240ustar00rootroot00000000000000i = 1
for infile in Dir.entries(File.join($testdata, "consensus_sa")).grep(/\.in$/) do
  infile = File.join($testdata, "consensus_sa", infile)
  Name "consensus_sa test #{i}"
  Keywords "gt_dev gt_consensus_sa"
  Test do
    run_test "#{$bin}gt dev consensus_sa #{infile}"
    outfile = infile.gsub(/\.in$/, ".out")
    run "diff #{last_stdout} #{outfile}"
  end
  i += 1
end
genometools-1.5.1/testsuite/gt_csa_include.rb000066400000000000000000000017451211610345200213740ustar00rootroot00000000000000Name "gt csa test"
Keywords "gt_csa"
Test do
  run_test("#{$bin}gt csa #{$testdata}gt_csa_test_1.in", :retval => 1)
  grep last_stderr, "is not sorted"
end

1.upto(6) do |i|
  Name "gt csa prob #{i}"
  Keywords "gt_csa"
  Test do
    run_test "#{$bin}gt csa #{$testdata}gt_csa_prob_#{i}.in"
    run "diff #{last_stdout} #{$testdata}gt_csa_prob_#{i}.out"
  end
end

1.upto(4) do |i|
  Name "gt -debug csa prob #{i}"
  Keywords "gt_csa"
  Test do
    run_test "#{$bin}gt -debug csa #{$testdata}gt_csa_prob_#{i}.in"
    run "tail -n +2 #{last_stderr} | diff - #{$testdata}gt_csa_prob_#{i}.debug"
  end
end

Name "gt csa arabidopsis"
Keywords "gt_csa"
Test do
  run_test "#{$bin}gt csa #{$testdata}U89959_sas.gff3"
  run "diff #{last_stdout} #{$testdata}U89959_csas.gff3"
end

Name "gt csa example"
Keywords "gt_csa"
Test do
  run_test "#{$bin}gt csa #{$testdata}csa_example_spliced_alignments.gff3"
  run "diff #{last_stdout} " +
      "#{$testdata}csa_example_consensus_spliced_alignments.gff3"
end
genometools-1.5.1/testsuite/gt_csr_include.rb000066400000000000000000000107401211610345200214100ustar00rootroot00000000000000require 'fileutils'
require 'tempfile'

hcr_testfiles = [
  "csr_testcase.fastq",
  "description_test.fastq",
  "description_test2.fastq"
]

Name "gt hcr reads"
Keywords "gt_csr hcr_nodesc"
Test do
  hcr_testfiles.each do |file|
    run_test "#$bin/gt compreads compress -files #$testdata/#{file} -name test"
    run_test "#$bin/gt compreads decompress -file test"
    `grep -v @ #$testdata/#{file} > original`
    `grep -v @ test.fastq > test_out`
    run_test "diff test_out original"
  end
end

Name "gt hcr reads allfiles"
Keywords "gt_csr hcr_nodesc"
Test do
  files = hcr_testfiles.collect{|file| "#$testdata/" + file}
  run_test "#$bin/gt compreads compress -files #{files.join(' ')} -name test"
  run_test "#$bin/gt compreads decompress -file test"
  `grep -h -v @ #{files.join(' ')} > original`
  `grep -v @ test.fastq > test_out`
  run_test "diff test_out original"
end

Name "gt hcr reads and description"
Keywords "gt_csr hcr_desc"
Test do
  hcr_testfiles.each do |file|
    run_test "#$bin/gt compreads compress -descs" +
             " -files #$testdata/#{file} -name test"
    run_test "#$bin/gt compreads decompress -file test"
    `grep -v @ #$testdata/#{file} > original`
    `grep -v @ test.fastq > test_out`
    run_test "diff test_out original"
    run_test "#$bin/gt compreads decompress -descs -file test"
    run_test "diff test.fastq #$testdata/#{file}"
  end
end

Name "gt hcr reads and description allfiles"
Keywords "gt_csr hcr_desc"
Test do
  files = hcr_testfiles.collect{|file| "#$testdata/" + file}
  run_test "#$bin/gt compreads compress -descs" +
           " -files #{files.join(' ')} -name test"
  run_test "#$bin/gt compreads decompress -descs -file test"
  `cat #{files.join(' ')} > original`
  run_test "diff test.fastq original"
end

Name "gt hcr decompress benchmark"
Keywords "gt_csr hcr benchmark"
Test do
  hcr_testfiles.each do |file|
    run_test "#$bin/gt compreads compress -descs" +
             " -files #$testdata/#{file} -name test_#{file}"
    run_test "#$bin/gt compreads decompress -descs -benchmark 10000" +
             " -file test_#{file}", :maxtime => 300
  end
end

rcr_testfiles = {
  "rcr_testreads_on_seq.bam" => "rcr_testseq.fa",
  "example_1.sorted.bam" => "example_1.fa"
}

Name "gt rcr reads noqual"
Keywords "gt_csr rcr"
Test do
  rcr_testfiles.keys do |file|
    run_test "#$bin/gt encseq encode -dna" +
             " -indexname ./#{rcr_testfiles[file]}" +
             " #$testdata/#{rcr_testfiles[file]}"
    run_test "#$bin/gt compreads refcompress" +
             " -ref ./#{rcr_testfiles[file]}" +
             " -bam #$testdata/#{file}" +
             " -name #{file}"
    run_test "#$bin/gt compreads refdecompress" +
             " -ref ./#{rcr_testfiles[file]}" +
             " -rcr ./#{file}"
  end
end

Name "gt rcr reads qual"
Keywords "gt_csr rcr"
Test do
  rcr_testfiles.keys do |file|
    run_test "#$bin/gt encseq encode -dna" +
             " -indexname ./#{rcr_testfiles[file]}" +
             " #$testdata/#{rcr_testfiles[file]}"
    run_test "#$bin/gt compreads refcompress" +
             " -ref ./#{rcr_testfiles[file]}" +
             " -bam #$testdata/#{file}" +
             " -mquals -quals" +
             " -name #{file}"
    run_test "#$bin/gt compreads refdecompress" +
             " -ref ./#{rcr_testfiles[file]}" +
             " -rcr ./#{file}"
  end
end

Name "gt rcr reads variant qual"
Keywords "gt_csr rcr"
Test do
  rcr_testfiles.keys do |file|
    run_test "#$bin/gt encseq encode -dna" +
             " -indexname ./#{rcr_testfiles[file]}" +
             " #$testdata/#{rcr_testfiles[file]}"
    run_test "#$bin/gt compreads refcompress" +
             " -ref ./#{rcr_testfiles[file]}" +
             " -bam #$testdata/#{file}" +
             " -mquals -vquals" +
             " -name #{file}"
    run_test "#$bin/gt compreads refdecompress" +
             " -ref ./#{rcr_testfiles[file]}" +
             " -rcr ./#{file}"
  end
end

Name "gt rcr reads variant qual, descriptions"
Keywords "gt_csr rcr"
Test do
  rcr_testfiles.keys do |file|
    run_test "#$bin/gt encseq encode -dna" +
             " -indexname ./#{rcr_testfiles[file]}" +
             " #$testdata/#{rcr_testfiles[file]}"
    run_test "#$bin/gt compreads refcompress" +
             " -ref ./#{rcr_testfiles[file]}" +
             " -bam #$testdata/#{file}" +
             " -mquals -vquals -descs" +
             " -name #{file}"
    run_test "#$bin/gt compreads refdecompress" +
             " -ref ./#{rcr_testfiles[file]}" +
             " -rcr ./#{file}"
             " -qnames"
  end
end
genometools-1.5.1/testsuite/gt_encseq2spm_include.rb000066400000000000000000000041761211610345200227070ustar00rootroot00000000000000def run_encseq2spm(readset)
  run_test "#{$bin}/gt suffixerator -db #{readset} -indexname sfx" 
  [32,35].each do |len|
    opts="-l #{len} -ii sfx -spm count -checksuftab"
    run_test "#{$bin}/gt encseq2spm #{opts}"
    [1,2,5].each do |parts|
      [1,2,3].each do |rparts|
        run_test "#{$bin}/gt encseq2spm -parts #{parts} " +
                 "-radixparts #{rparts} #{opts}"
        run_test "env GT_MEM_BOOKKEEPING=off GT_ENV_OPTIONS= " + 
                 "#{$bin}/gt -j #{rparts} encseq2spm -parts #{parts} #{opts}"
      end
    end
  end
end

if $gttestdata

  Name "gt encseq2spm: developer options"
  Keywords "gt_encseq2spm"
  Test do
    readset="#{$gttestdata}/readjoiner/70000x_100nt_reads"
    run_test "#{$bin}/gt suffixerator -db #{readset} -indexname sfx" 
    run_test "#{$bin}/gt encseq2spm -ii sfx -l 45 -singlescan 0 "
    run_test "#{$bin}/gt encseq2spm -ii sfx -l 45 -onlyaccum"
    run_test "#{$bin}/gt encseq2spm -ii sfx -l 45 -onlyallfirstcodes"
    run_test "#{$bin}/gt encseq2spm -ii sfx -l 45 -radixlarge"
    run_test "env GT_MEM_BOOKKEEPING=on " +
             "#{$bin}/gt encseq2spm -ii sfx -l 45 -memlimit 3MB"
    run_test "env GT_MEM_BOOKKEEPING=on " +
             "#{$bin}/gt encseq2spm -ii sfx -l 45 -memlimit 2MB",:retval => 1
    if not Kernel.system("#{$bin}gt -64bit")
      run_test "#{$bin}/gt suffixerator -db #{readset} " + \
               "#{$testdata}/U89959_genomic.fas -indexname sfx-big" 
      run_test "#{$bin}/gt encseq2spm -ii sfx-big -l 45",:retval => 1
    end
  end

  # compare results with precalculated known results
  [700, 7000].each do |nofreads|
    readset="#{$gttestdata}/readjoiner/#{nofreads}x_100nt_reads"
    if File.exists?(readset)
      Name "gt encseq2spm: #{nofreads}x100"
      Keywords "gt_encseq2spm"
      Test do
        run_encseq2spm(readset)
      end
    end

    [161, 200, 300, 400, 600, 1000].each do |len|
      reads = "#{$gttestdata}/readjoiner/#{nofreads}x_#{len}nt_reads"
      if File.exists?(reads)
        Name "gt encseq2spm: #{nofreads}x#{len}"
        Keywords "gt_encseq2spm"
        Test do
          run_encseq2spm(reads)
        end
      end
    end
  end
end
genometools-1.5.1/testsuite/gt_encseq_include.rb000066400000000000000000000325421211610345200221030ustar00rootroot00000000000000Name "gt encseq encode|decode simple"
Keywords "gt_encseq_encode encseq gt_encseq_decode"
Test do
  run "#{$bin}gt encseq encode #{$testdata}foobar.fas"
  run "#{$bin}gt encseq decode foobar.fas"
  run "diff #{last_stdout} #{$testdata}foobar.fas"
end

Name "gt encseq encode|decode w/ empty seq"
Keywords "gt_encseq_encode encseq gt_encseq_decode empty"
Test do
  run_test "#{$bin}gt encseq encode -indexname foo " + \
           "#{$testdata}empty_seq.fas", \
           :retval => 1
  grep(last_stderr, /sequence must not be empty/)
end

Name "gt encseq encode|decode eqlen w/ empty seq"
Keywords "gt_encseq_encode encseq gt_encseq_decode empty"
Test do
  run "#{$bin}gt encseq encode -indexname foo " + \
      "#{$testdata}gt_encseq_eqlen_last_empty.fas"
  run "#{$bin}gt encseq decode foo"
  run "head -n -1 #{last_stdout} | diff - #{$testdata}gt_encseq_eqlen_last_empty.fas"
end

Name "gt encseq encode multiple files without indexname"
Keywords "encseq gt_encseq_encode"
Test do
  run "#{$bin}gt encseq encode #{$testdata}foobar.fas"
  run_test "#{$bin}gt encseq encode #{$testdata}foobar.fas " + \
           "#{$testdata}foobar.fas", :retval => 1
  grep(last_stderr, /if more than one input file is given/)
end

Name "gt encseq decode lossless without ois"
Keywords "encseq gt_encseq_decode lossless"
Test do
  run "#{$bin}gt encseq encode #{$testdata}foobar.fas"
  run_test "#{$bin}gt encseq decode -lossless foobar.fas", \
           :retval => 1
  grep(last_stderr, /cannot open file.*ois/)
end

STDREADMODES  = ["fwd", "rev"]
DNAREADMODES  = STDREADMODES + ["cpl", "rcl"]
DNATESTSEQS   = ["#{$testdata}foobar.fas",
                 "#{$testdata}gt_bioseq_succ_3.fas",
                 "#{$testdata}at100K1"]
AATESTSEQS    = ["#{$testdata}trembl-eqlen.faa"]
NUMSAMPLES    = 5

def es_revcomp(seq)
  es_comp(seq).reverse
end

def es_comp(seq)
  seq.tr("aAcCgGtTnNrRyYmMkKwWsSbBdDhHvV","tTgGcCaAnNyYrRkKmMwWsSvVhHdDbB")
end

def mapwildcards(seq)
  seq.downcase.tr("rRyYmMkKwWsSbBdDhHvV", "nNnNnNnNnNnNnNnNnNnN")
end

def getseq(filename, mirrored = false, rm = "fwd")
  sequences = []
  rcseqs = []
  File.open(filename) do |file|
    seqs = file.read.split(">")
    seqs.shift
    seqs.each do |seq|
      seqarr = seq.split(/\n/)
      header = seqarr.shift.chomp
      seq = seqarr.collect{|v| v.chomp}.join('')
      sequences.push(seq)
      rcseqs.push(es_revcomp(seq))
    end
  end
  ret =  sequences.join("|")
  if mirrored then
    ret += "|" + rcseqs.reverse.join("|")
  end
  case rm
    when "fwd" then
      #pass
    when "rev" then
      ret = ret.reverse
    when "cpl" then
      ret = es_comp(ret)
    when "rcl" then
      ret = es_revcomp(ret)
    else
      raise "unknown readmode"
  end
  ret
end

def run_encseq_comparison(filename, mirrored, lossless, readmode, singlechars,
                          numsamples = NUMSAMPLES)
  seq = getseq(filename, mirrored, readmode)
  ranges = []
  numsamples.times do
    len = rand((seq.length)/2)
    start = rand(seq.length-1-len);
    stop = start + len
    ranges.push([start, stop])
  end

  ranges.each do |rng|
    line = "#{$bin}gt encseq decode -output concat " + \
           "-range #{rng[0]} #{rng[1]} " + \
           "#{"-lossless" if lossless} " + \
           "-dir #{readmode} #{"-mirrored" if mirrored} " + \
           "#{"-singlechars" if singlechars} #{filename.split('/').last}"
    if mirrored and AATESTSEQS.include?(filename)
      # -mirroring should fail on proteins
      run_test(line, :retval => 1)
    else
      run_test line
      File.open("seqout", "w+") do |f|
        outseq = seq[rng[0]..rng[1]]
        if DNATESTSEQS.include?(filename) and !lossless then
          outseq = mapwildcards(outseq)
        end
        f.write(outseq)
        f.write("\n")
      end
      run "diff seqout #{last_stdout}"
    end
  end
end

def testformirrored(s, readmode)
  Name "gt encseq decode #{s.split('/').last} #{readmode}"
  Keywords "encseq gt_encseq_decode mirroring lossless"
  Test do
    [false, true].each do |lossless|
      run "rm -f #{s}.*"
      run "#{$bin}gt encseq encode " + \
              "#{"-lossless" if lossless} " + \
              "#{s}"
      [false, true].each do |mirrored|
        [false, true].each do |singlechars|
          run_encseq_comparison(s, mirrored, lossless, readmode, singlechars)
          seq = getseq(s, mirrored, readmode)
          line = "#{$bin}gt encseq decode -output concat -dir #{readmode} " + \
                  "#{"-mirrored" if mirrored} " + \
                  "#{"-lossless" if lossless} " + \
                  "#{"-singlechars" if singlechars} ./#{s.split('/').last}"
          if mirrored and AATESTSEQS.include?(s)
            # -mirroring should fail on proteins
            run_test(line, :retval => 1)
          else
            run_test line
            File.open("seqout", "w+") do |f|
              if DNATESTSEQS.include?(s) and !lossless then
                seq = mapwildcards(seq)
              end
              f.write(seq)
              f.write("\n")
            end
            run "diff seqout #{last_stdout}"
          end
        end
      end
    end
  end
end

DNATESTSEQS.each do |s|
  DNAREADMODES.each do |readmode|
    testformirrored(s, readmode)
  end
end

AATESTSEQS.each do |s|
  STDREADMODES.each do |readmode|
    testformirrored(s, readmode)
  end
end


fastafiles = ["Atinsert.fna",
              "Duplicate.fna",
              "Random-Small.fna",
              "Random.fna",
              "Copysorttest.fna",
              "Random159.fna",
              "Random160.fna",
              "RandomN.fna",
              "TTT-small.fna",
              "trna_glutamine.fna",
              "Small.fna",
              "Verysmall.fna",
              "Arabidopsis-C99826.fna"]
genbankfiles = fastafiles.collect{ |f| f.gsub(".fna",".gbk") }
emblfiles = fastafiles.collect{ |f| f.gsub(".fna",".embl") }

[genbankfiles, emblfiles].each do |formatfiles|
  formatfiles.each do |formatfile|
    Name "gt sequence formats (#{formatfile})"
    Keywords "gt_encseq formats"
    Test do
      fasta = formatfile.gsub(/\.[a-z]+$/, ".fna")
      if File.exists?("#{$testdata}#{fasta}") then
        run "cp #{$testdata}#{formatfile} infile"
        run_test "#{$bin}gt encseq encode -v -indexname sfx infile"
        run_test "#{$bin}gt encseq decode -output concat sfx > sfx.seq"
        run_test "#{$bin}gt encseq info sfx > sfx.info"
        run_test "#{$bin}gt encseq check sfx"
        run "cp #{$testdata}#{fasta} infile"
        run_test "#{$bin}gt encseq encode -v -indexname sfx infile"
        run_test "#{$bin}gt encseq decode -output concat sfx > sfx2.seq"
        run_test "#{$bin}gt encseq info sfx > sfx2.info"
        run "diff sfx.seq sfx2.seq"
        run "diff sfx.info sfx2.info"
      end
    end
  end
end

Name "gt encseq mirrored trailing wildcard"
Keywords "encseq gt_encseq_encode wildcards mirror"
Test do
  run "cp #{$testdata}wildcardatend.fna infile"
  run_test "#{$bin}gt encseq encode infile"
  run_test "#{$bin}gt encseq info -mirrored infile | grep range > mirr.info"
  run "cp #{$testdata}wildcardatend_rev.fna infile"
  run_test "#{$bin}gt encseq encode infile"
  run_test "#{$bin}gt encseq info infile | grep range > rev.info"
  run "diff mirr.info rev.info"
end

Name "gt encseq mirrored no trailing wildcard"
Keywords "encseq gt_encseq_encode wildcards mirror"
Test do
  run "cp #{$testdata}nowildcardatend.fna infile"
  run_test "#{$bin}gt encseq encode infile"
  run_test "#{$bin}gt encseq info -mirrored infile | grep range > mirr.info"
  run "cp #{$testdata}nowildcardatend_rev.fna infile"
  run_test "#{$bin}gt encseq encode infile"
  run_test "#{$bin}gt encseq info infile | grep range > rev.info"
  run "diff mirr.info rev.info"
end

Name "gt encseq decode single sequence"
Keywords "encseq gt_encseq_decode single"
Test do
  run "#{$bin}gt encseq encode -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq decode -seq 3 foo"
  run "diff #{last_stdout} #{$testdata}Atinsert_single_3.fna"
end

Name "gt encseq decode single sequence (reverse)"
Keywords "encseq gt_encseq_decode single"
Test do
  run "#{$bin}gt encseq encode -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq decode -dir rev -seq 17 foo"
  run "diff #{last_stdout} #{$testdata}Atinsert_single_3_rev.fna"
end

Name "gt encseq decode single sequence (invalid seqnumber)"
Keywords "encseq gt_encseq_decode single"
Test do
  run "#{$bin}gt encseq encode -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq decode -seq 36 foo", :retval => 1
  grep last_stderr, /exceeds/
end

Name "gt encseq decode single sequence (with -output concat)"
Keywords "encseq gt_encseq_decode single"
Test do
  run "#{$bin}gt encseq encode -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq decode -output concat -seq 36 foo", :retval => 1
  grep last_stderr, /can only be used with the/
end

Name "gt encseq decode sequence range"
Keywords "encseq gt_encseq_decode seqrange"
Test do
  run "#{$bin}gt encseq encode -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq decode -seqrange 3 7 foo"
  run "diff #{last_stdout} #{$testdata}Atinsert_seqrange_3-7.fna"
end

Name "gt encseq decode sequence range (reverse)"
Keywords "encseq gt_encseq_decode seqrange"
Test do
  run "#{$bin}gt encseq encode -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq decode -dir rev -seqrange 13 17 foo"
  run "diff #{last_stdout} #{$testdata}Atinsert_seqrange_13-17_rev.fna"
end

Name "gt encseq decode sequence range (invalid range start)"
Keywords "encseq gt_encseq_decode seqrange"
Test do
  run "#{$bin}gt encseq encode -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq decode -seqrange 37 49 foo", :retval => 1
  grep last_stderr, /exceeding/
end

Name "gt encseq decode sequence range (invalid range end)"
Keywords "encseq gt_encseq_decode seqrange"
Test do
  run "#{$bin}gt encseq encode -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq decode -seqrange 3 49 foo", :retval => 1
  grep last_stderr, /exceeding/
end

Name "gt encseq decode sequence range (with -output concat)"
Keywords "encseq gt_encseq_decode seqrange"
Test do
  run "#{$bin}gt encseq encode -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq decode -output concat -seqrange 3 49 foo", \
           :retval => 1
  grep last_stderr, /can only be used with the/
end

Name "gt encseq Lua bindings"
Keywords "encseq gt_scripts "
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/encseq.lua #{$testdata}"
end

Name "gt encseq 64bit/32bit header (success)"
Keywords "encseq encseq_file_format"
Test do
  is64 = Kernel.system("#{$bin}gt -64bit")
  if is64 then
    bit = "64"
  else
    bit = "32"
  end
  run_test "#{$bin}gt encseq info -noindexname #{$testdata}foo.#{bit}"
  run "diff #{last_stdout} #{$testdata}foo.#{bit}.info_map"
  run_test "#{$bin}gt encseq info -noindexname -nomap #{$testdata}foo.#{bit}"
  run "diff #{last_stdout} #{$testdata}foo.#{bit}.info_nomap"
end

Name "gt encseq 64bit/32bit header (failure)"
Keywords "encseq encseq_file_format"
Test do
  is64 = Kernel.system("#{$bin}gt -64bit")
  if !is64 then
    bit = "64"
  else
    bit = "32"
  end
  run_test "#{$bin}gt encseq info -noindexname #{$testdata}foo.#{bit}", \
           :retval => 1
  grep last_stderr, /please use correct index for this platform/
  run_test "#{$bin}gt encseq info -noindexname -nomap #{$testdata}foo.#{bit}", \
           :retval => 1
  grep last_stderr, /please use correct index for this platform/
end

Name "gt encseq incompatible file format version"
Keywords "encseq encseq_file_format"
Test do
  is64 = Kernel.system("#{$bin}gt -64bit")
  if is64 then
    bit = "64"
  else
    bit = "32"
  end
  run_test "#{$bin}gt encseq info -noindexname #{$testdata}foo.#{bit}.ver0", \
           :retval => 1
  grep last_stderr, /is format version 0/
  run_test "#{$bin}gt encseq info -noindexname -nomap #{$testdata}foo.#{bit}.ver0", \
           :retval => 1
  grep last_stderr, /is format version 0/
end

["yes", "no"].each do |yn|
  Name "gt encseq MD5 from file <-> from seq lossless #{yn}"
  Keywords "gt_encseq encseq md5"
  Test do
    fastafiles.each do |fn|
      run "#{$bin}gt encseq encode -lossless #{yn} -indexname idx #{$testdata}/#{fn}"
      run_test "#{$bin}gt encseq md5 -force -o out1 idx"
      run_test "#{$bin}gt encseq md5 -force -fromindex no -o out2 idx"
      run "diff out1 out2"
    end
  end
end

Name "gt encseq MD5 index w/o MD5 support"
Keywords "encseq gt_encseq md5"
Test do
  run "#{$bin}gt encseq encode -md5 no -indexname foo #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt encseq md5 foo", :retval => 1
  grep last_stderr, /does not have MD5 support/
end

Name "gt encseq colorspace FASTQ failure"
Keywords "encseq gt_encseq colorspace"
Test do
  run_test "#{$bin}gt encseq encode -indexname foo #{$testdata}solid_color_reads.fastq", :retval => 1
  grep last_stderr, /illegal character \'3\'/
end

Name "gt encseq custom alphabet storage"
Keywords "encseq gt_encseq alphabet custom_alphabet"
Test do
  Dir.glob("#{$cur}/gtdata/trans/TransDNA*") do |file|
    run_test "#{$bin}gt encseq encode -smap #{file} -indexname foo #{$testdata}at100K1"
    run "#{$bin}gt encseq info -show_alphabet foo"
    alphainesq = File.open(last_stdout).read.match(/alphabet definition:\n([-1-9_a-zA-Z\n]+)\n\n/)
    if alphainesq.nil? then
      raise "saved alphabet definition is empty for file #{file}"
    elsif alphainesq[1]+"\n" != File.read(file) then
      raise "saved alphabet definition is not properly preserved for file #{file}"
    end
  end
end
genometools-1.5.1/testsuite/gt_env_options_include.rb000066400000000000000000000006041211610345200231620ustar00rootroot00000000000000Name "$GT_ENV_OPTIONS parsing (-help)"
Keywords "gt_env_options"
Test do
  run("env GT_ENV_OPTIONS=-help #{$bin}gt", :retval => 1)
  grep last_stdout, /spacepeak/
end

Name "$GT_ENV_OPTIONS parsing (-spacepeak)"
Keywords "gt_env_options"
Test do
  run "env GT_ENV_OPTIONS=-spacepeak #{$bin}gt gff3 #{$testdata}standard_gene_as_tree.gff3"
  grep last_stdout, /space peak in megabytes/
end
genometools-1.5.1/testsuite/gt_eval_include.rb000066400000000000000000000077751211610345200215660ustar00rootroot00000000000000Name "gt eval test 1"
Keywords "gt_eval"
Test do
  run_test "#{$bin}gt eval #{$testdata}gt_eval_test_1.in #{$testdata}gt_eval_test_1.in"
  run "diff #{last_stdout} #{$testdata}gt_eval_test_1.out"
end

2.upto(8) do |i|
  Name "gt eval test #{i}"
  Keywords "gt_eval"
  Test do
    run_test "#{$bin}gt eval #{$testdata}gt_eval_test_#{i}.reality #{$testdata}gt_eval_test_#{i}.prediction"
    run "diff #{last_stdout} #{$testdata}gt_eval_test_#{i}.nuc"
  end

  Name "gt eval test #{i} -nuc no"
  Keywords "gt_eval"
  Test do
    run_test "#{$bin}gt eval -nuc no #{$testdata}gt_eval_test_#{i}.reality #{$testdata}gt_eval_test_#{i}.prediction"
    run "diff #{last_stdout} #{$testdata}gt_eval_test_#{i}.out"
  end
end

9.upto(10) do |i|
  Name "gt eval test #{i}"
  Keywords "gt_eval"
  Test do
    run_test "#{$bin}gt eval #{$testdata}gt_eval_test_#{i}.in #{$testdata}gt_eval_test_#{i}.in"
    run "diff #{last_stdout} #{$testdata}gt_eval_test_#{i}.out"
  end
end

Name "gt eval prob 1"
Keywords "gt_eval"
Test do
  run_test "#{$bin}gt eval -nuc no #{$testdata}gt_eval_prob_1.reality #{$testdata}gt_eval_prob_1.prediction"
  run "diff #{last_stdout} #{$testdata}gt_eval_prob_1.out"
end

Name "gt eval prob 1 (swapped)"
Keywords "gt_eval"
Test do
  run_test "#{$bin}gt eval -nuc no #{$testdata}gt_eval_prob_1.prediction #{$testdata}gt_eval_prob_1.reality"
  run "diff #{last_stdout} #{$testdata}gt_eval_prob_1.out_swapped"
end

Name "gt eval -ltr test 1"
Keywords "gt_eval"
Test do
  run_test "#{$bin}gt eval -ltr #{$testdata}gt_eval_ltr_test_1.in #{$testdata}gt_eval_ltr_test_1.in"
  run "diff #{last_stdout} #{$testdata}gt_eval_ltr_test_1.out"
end

2.upto(9) do |i|
  Name "gt eval -ltr test #{i}"
  Keywords "gt_eval"
  Test do
    run_test "#{$bin}gt eval -ltr #{$testdata}gt_eval_ltr_test_#{i}.reality #{$testdata}gt_eval_ltr_test_#{i}.prediction"
    run "diff #{last_stdout} #{$testdata}gt_eval_ltr_test_#{i}.out"
  end
end

Name "gt eval -ltr prob 1 (failure)"
Keywords "gt_eval"
Test do
  run_test("#{$bin}gt eval -ltrdelta 30 -ltr #{$testdata}gt_eval_ltr_prob_1.reality #{$testdata}gt_eval_ltr_prob_1.prediction", :retval => 1)
  grep(last_stderr, "is not sorted")
end

Name "gt eval -ltr prob 1 (success)"
Keywords "gt_eval"
Test do
  run_test "#{$bin}gt gff3 -sort #{$testdata}gt_eval_ltr_prob_1.prediction | #{$memcheck} #{$bin}gt eval -ltrdelta 30 -ltr #{$testdata}gt_eval_ltr_prob_1.reality -"
  run "diff #{last_stdout} #{$testdata}gt_eval_ltr_prob_1.out"
end

if $gttestdata then
  Name "gt eval test (gth rate 0)"
  Keywords "gt_eval"
  Test do
    run_test("#{$bin}gt eval -nuc no #{$testdata}encode_known_genes_Mar07.gff3 #{$gttestdata}eval/complete_result_all_rate_0_minscr_0.95.gff3", :maxtime => 120)
    run "diff #{last_stdout} #{$gttestdata}eval/gth_analysis_rate_0_minscr_0.95.txt"
  end

  Name "gt eval test (gth rate 1)"
  Keywords "gt_eval"
  Test do
    run_test("#{$bin}gt eval -nuc no #{$testdata}encode_known_genes_Mar07.gff3 #{$gttestdata}eval/complete_result_all_rate_1_minscr_0.95.gff3", :maxtime => 120)
    run "diff #{last_stdout} #{$gttestdata}eval/gth_analysis_rate_1_minscr_0.95.txt"
  end

  Name "gt eval test (gth rate 3)"
  Keywords "gt_eval"
  Test do
    run_test("#{$bin}gt eval -nuc no #{$testdata}encode_known_genes_Mar07.gff3 #{$gttestdata}eval/complete_result_all_rate_3_minscr_0.90.gff3", :maxtime => 240)
    run "diff #{last_stdout} #{$gttestdata}eval/gth_analysis_rate_3_minscr_0.90.txt"
  end

  Name "gt eval test (gth rate 5)"
  Keywords "gt_eval"
  Test do
    run_test("#{$bin}gt eval -nuc no #{$testdata}encode_known_genes_Mar07.gff3 #{$gttestdata}eval/complete_result_all_rate_5_minscr_0.90.gff3", :maxtime => 120)
    run "diff #{last_stdout} #{$gttestdata}eval/gth_analysis_rate_5_minscr_0.90.txt"
  end

  Name "gt eval test (gth rate 10)"
  Keywords "gt_eval"
  Test do
    run_test("#{$bin}gt eval -nuc no #{$testdata}encode_known_genes_Mar07.gff3 #{$gttestdata}eval/complete_result_all_rate_10_minscr_0.85.gff3", :maxtime => 120)
    run "diff #{last_stdout} #{$gttestdata}eval/gth_analysis_rate_10_minscr_0.85.txt"
  end
end
genometools-1.5.1/testsuite/gt_extractfeat_include.rb000066400000000000000000000164111211610345200231340ustar00rootroot00000000000000Name "gt extractfeat -seqfile test 1"
Keywords "gt_extractfeat"
Test do
  run_test "#{$bin}gt extractfeat -type gene -seqfile #{$testdata}gt_extractfeat_succ_1.fas #{$testdata}gt_extractfeat_succ_1.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_succ_1.out"
end

Name "gt extractfeat -seqfile test 1 (compressed)"
Keywords "gt_extractfeat"
Test do
  run_test "#{$bin}gt extractfeat -type gene -seqfile #{$testdata}gt_extractfeat_succ_1.fas.gz  #{$testdata}gt_extractfeat_succ_1.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_succ_1.out"
end

Name "gt extractfeat -seqfile test 1 (with -o)"
Keywords "gt_extractfeat"
Test do
  run_test "#{$bin}gt extractfeat -o test.fas -type gene -seqfile #{$testdata}gt_extractfeat_succ_1.fas.gz  #{$testdata}gt_extractfeat_succ_1.gff3"
  run "diff test.fas #{$testdata}gt_extractfeat_succ_1.out"
end

Name "gt extractfeat -seqfile test 2"
Keywords "gt_extractfeat"
Test do
  run_test "#{$bin}gt extractfeat -type gene -seqfile #{$testdata}gt_extractfeat_succ_2.fas #{$testdata}gt_extractfeat_succ_2.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_succ_2.out1"
end

Name "gt extractfeat -seqfile test 3"
Keywords "gt_extractfeat"
Test do
  run_test "#{$bin}gt extractfeat -type exon -seqfile #{$testdata}gt_extractfeat_succ_2.fas #{$testdata}gt_extractfeat_succ_2.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_succ_2.out2"
end

Name "gt extractfeat -seqfile test 4"
Keywords "gt_extractfeat"
Test do
  run_test "#{$bin}gt extractfeat -type exon -join -seqfile #{$testdata}gt_extractfeat_succ_2.fas #{$testdata}gt_extractfeat_succ_2.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_succ_2.out3"
end

Name "gt extractfeat -seqfile test 5"
Keywords "gt_extractfeat"
Test do
  run_test "#{$bin}gt extractfeat -type exon -join -seqfile #{$testdata}gt_extractfeat_succ_3.fas #{$testdata}gt_extractfeat_succ_3.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_succ_3.out"
end

Name "gt extractfeat -regionmapping fail 1 (no mapping file)"
Keywords "gt_extractfeat"
Test do
  run_test("#{$bin}gt extractfeat -type exon -regionmapping #{$testdata}nonexistent_file #{$testdata}gt_extractfeat_succ_1.gff3", :retval => 1 )
  grep(last_stderr, "cannot run file");
end

Name "gt extractfeat -regionmapping fail 2 (empty file)"
Keywords "gt_extractfeat"
Test do
  run_test("#{$bin}gt extractfeat -type exon -regionmapping #{$testdata}empty_file #{$testdata}gt_extractfeat_succ_1.gff3", :retval => 1 )
  grep(last_stderr, "'mapping' is not defined ");
end

Name "gt extractfeat -regionmapping fail 3 (wrong type)"
Keywords "gt_extractfeat"
Test do
  run_test("#{$bin}gt extractfeat -type exon -regionmapping #{$testdata}regionmapping_1.lua #{$testdata}gt_extractfeat_succ_1.gff3", :retval => 1 )
  grep(last_stderr, "'mapping' must be either a table or a function ");
end

Name "gt extractfeat -regionmapping fail 3 (nil mapping)"
Keywords "gt_extractfeat"
Test do
  run_test("#{$bin}gt extractfeat -type exon -regionmapping #{$testdata}regionmapping_2.lua #{$testdata}gt_extractfeat_succ_2.gff3", :retval => 1 )
  grep(last_stderr, "is nil");
end

Name "gt extractfeat -regionmapping fail 4 (non string mapping)"
Keywords "gt_extractfeat"
Test do
  run_test("#{$bin}gt extractfeat -type exon -regionmapping #{$testdata}regionmapping_3.lua #{$testdata}gt_extractfeat_succ_2.gff3", :retval => 1 )
  grep(last_stderr, "is not a string");
end

Name "gt extractfeat -regionmapping fail 5 (function returns nil)"
Keywords "gt_extractfeat"
Test do
  run_test("#{$bin}gt extractfeat -type exon -regionmapping #{$testdata}regionmapping_5.lua #{$testdata}gt_extractfeat_succ_2.gff3", :retval => 1 )
  grep(last_stderr, "function 'mapping' must return a string");
end

Name "gt extractfeat -regionmapping test 1 (mapping table)"
Keywords "gt_extractfeat"
Test do
  run "env GT_TESTDATA=#{$testdata} #{$memcheck} #{$bin}gt extractfeat -type gene -regionmapping #{$testdata}regionmapping_4.lua #{$testdata}gt_extractfeat_succ_1.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_succ_1.out"
end

Name "gt extractfeat -regionmapping test 1 (mapping function)"
Keywords "gt_extractfeat"
Test do
  run "env GT_TESTDATA=#{$testdata} #{$memcheck} #{$bin}gt extractfeat -type gene -regionmapping #{$testdata}regionmapping_6.lua #{$testdata}gt_extractfeat_succ_1.gff3"
end

Name "gt extractfeat error message"
Keywords "gt_extractfeat"
Test do
  run "#{$bin}gt gff3 -offset 1000 #{$testdata}gt_extractfeat_succ_1.gff3 | " +
      "#{$bin}gt extractfeat -type gene -seqfile " +
      "#{$testdata}gt_extractfeat_succ_1.fas -", :retval => 1
  grep last_stderr, "Has the sequence-region to sequence mapping been defined correctly"
end

Name "gt extractfeat -translate"
Keywords "gt_extractfeat"
Test do
  run "#{$bin}gt extractfeat -seqfile #{$testdata}U89959_genomic.fas " +
      "-type CDS -join -translate #{$testdata}U89959_cds.gff3"
  run "diff #{last_stdout} #{$testdata}U89959_cds.fas"
end

Name "gt extractfeat -help"
Keywords "gt_extractfeat"
Test do
  run_test "#{$bin}gt extractfeat -help"
  grep(last_stdout, "Lua");
end

Name "gt extractfeat -seqid"
Keywords "gt_extractfeat"
Test do
  run "#{$bin}gt extractfeat -seqfile #{$testdata}U89959_genomic.fas " +
      "-type CDS -join -seqid " +
      "#{$testdata}gt_extractfeat_seqid_target.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_seqid.fas"
end

Name "gt extractfeat -target"
Keywords "gt_extractfeat"
Test do
  run "#{$bin}gt extractfeat -seqfile #{$testdata}U89959_genomic.fas " +
      "-type mRNA -join -target " +
      "#{$testdata}gt_extractfeat_seqid_target.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_target.fas"
end

Name "gt extractfeat -seqid -target"
Keywords "gt_extractfeat"
Test do
  run "#{$bin}gt extractfeat -seqfile #{$testdata}U89959_genomic.fas " +
      "-type CDS -join -seqid -target " +
      "#{$testdata}gt_extractfeat_seqid_target.gff3"
  run "diff #{last_stdout} #{$testdata}gt_extractfeat_seqid_target.fas"
end

Name "gt extractfeat compare query method combinations"
Keywords "gt_extractfeat query_methods"
Test do
  run "#{$bin}gt encseq encode -lossless -indexname ./idx " +
      "#{$testdata}gt_extractfeat_mappings.fas"
  ["", ".md5"].each do |md5|
    ["-usedesc","-matchdesc"].each do |method|
      run "#{$bin}gt extractfeat #{method} " +
          "-seqfile #{$testdata}gt_extractfeat_mappings.fas " +
          "-type gene #{$testdata}gt_extractfeat_mappings#{md5}.gff3 "
      run "diff #{last_stdout} #{$testdata}gt_extractfeat_mappings_ref#{md5}.fas"
      run "#{$bin}gt extractfeat #{method} -seqfiles " +
          "#{$testdata}gt_extractfeat_mappings_sep1.fas " +
          "#{$testdata}gt_extractfeat_mappings_sep2.fas " +
          "-type gene #{$testdata}gt_extractfeat_mappings#{md5}.gff3 "
      run "diff #{last_stdout} #{$testdata}gt_extractfeat_mappings_ref#{md5}.fas"
      run "#{$bin}gt extractfeat #{method} -encseq idx " +
          "-type gene #{$testdata}gt_extractfeat_mappings#{md5}.gff3 "
      run "diff #{last_stdout} #{$testdata}gt_extractfeat_mappings_ref#{md5}.fas"
    end
    run "env GT_TESTDATA=#{$testdata} #{$memcheck} #{$bin}gt extractfeat " +
        "-regionmapping #{$testdata}gt_extractfeat_mappings_seprm.lua " +
        "-type gene #{$testdata}gt_extractfeat_mappings#{md5}.gff3 "
    run "diff #{last_stdout} #{$testdata}gt_extractfeat_mappings_ref#{md5}.fas"
  end
end
genometools-1.5.1/testsuite/gt_extractseq_include.rb000066400000000000000000000157301211610345200230100ustar00rootroot00000000000000Name "gt extractseq -help"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -help"
  grep last_stdout, "Report bugs to"
end

Name "gt extractseq -noop"
Keywords "gt_extractseq"
Test do
  run_test("#{$bin}gt extractseq -noop", :retval => 1)
  grep last_stderr, "unknown option"
end

Name "gt extractseq test stdin"
Keywords "gt_extractseq"
Test do
  run "cat #{$testdata}foo.fas | #{$memcheck} #{$bin}gt extractseq -match foo"
  run "diff #{last_stdout} #{$testdata}foo.fas"
end

Name "gt extractseq test foo"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -match foo #{$testdata}foo.fas"
  run "diff #{last_stdout} #{$testdata}foo.fas"
end

Name "gt extractseq test foo width 4"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -match foo -width 4 #{$testdata}foo.fas"
  run "diff #{last_stdout} #{$testdata}foo_width4.fas"
end

Name "gt extractseq test bar"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -match bar -width 4 #{$testdata}bar.fas"
  run "diff #{last_stdout} #{$testdata}bar.fas"
end

Name "gt extractseq test baz"
Keywords "gt_extractseq"
Test do
  run "cat #{$testdata}foo.fas | #{$memcheck} #{$bin}gt extractseq -match baz - #{$testdata}bar.fas"
  grep(last_stdout, ".", true)
end

Name "gt extractseq test foo|bar"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -match 'foo|bar' #{$testdata}foo.fas #{$testdata}bar.fas"
  run "diff #{last_stdout} #{$testdata}foobar.fas"
end

Name "gt extractseq test '(foo'"
Keywords "gt_extractseq"
Test do
  run_test("#{$bin}gt extractseq -match '(foo' #{$testdata}foo.fas", :retval => 1)
end

Name "gt extractseq test corrupt"
Keywords "gt_extractseq"
Test do
  run_test("#{$bin}gt extractseq -match foo #{$testdata}corrupt.fas", :retval => 1)
  grep last_stderr, "cannot guess"
end

Name "gt extractseq test corrupt (stdin)"
Keywords "gt_extractseq"
Test do
  run("cat #{$testdata}corrupt.fas | #{$memcheck} #{$bin}gt extractseq -match foo",
      :retval => 1)
end

Name "gt extractseq -frompos"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -frompos 5 -topos 12 #{$testdata}foobar.fas"
  run "diff #{last_stdout} #{$testdata}frompos.fas"
end

Name "gt extractseq -frompos (stdin)"
Keywords "gt_extractseq"
Test do
  run "cat  #{$testdata}foobar.fas | #{$memcheck} #{$bin}gt extractseq " +
      "-frompos 5 -topos 12"
  run "diff #{last_stdout} #{$testdata}frompos.fas"
end

Name "gt extractseq -frompos (fail 1)"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -frompos 5 -topos 17 #{$testdata}foobar.fas",
           :retval => 1
  grep last_stderr, "larger than"
end

Name "gt extractseq -frompos (fail 2)"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -frompos 18 -topos 17 #{$testdata}foobar.fas",
           :retval => 1
  grep last_stderr, "must be <= argument"
end

Name "gt extractseq marker.fas"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -frompos 21 -topos 40 #{$testdata}marker.fas"
  run "diff #{last_stdout} #{$testdata}marker.out"
end

Name "gt extractseq -keys from fastafile U89959"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -keys #{$testdata}U89959_ginums.txt " +
           "#{$testdata}U89959_ests.fas"
  run "grep -v '^#' #{last_stdout}"
  run "diff #{last_stdout} #{$testdata}U89959_ginums.out"
end

Name "gt extractseq -keys from fastafile at1MB"
Keywords "gt_extractseq"
Test do
  run "sed  -e '/^[^\\>]/d' -e 's/^>gi\|\\([^\|]*\\).*/\\1/' #{$testdata}at1MB"
  run_test "#{$bin}gt extractseq -keys #{last_stdout} -width 70 " +
           "#{$testdata}at1MB"
  run "grep -v '^#' #{last_stdout}"
  run "cmp #{last_stdout} #{$testdata}at1MB"
end

Name "gt extractseq -keys from fastafile TrEMBL"
Keywords "gt_extractseq"
Test do
  run_test "#{$bin}gt extractseq -keys #{$testdata}trembl-keys.txt -width 60 " +
           "#{$testdata}trembl.faa"
  run "grep -v '^#' #{last_stdout}"
  run "cmp #{last_stdout} #{$testdata}trembl.faa"
end

Name "gt extractseq -keys from fastafile (corrupt)"
Keywords "gt_extractseq"
Test do
  run_test("#{$bin}gt extractseq -keys #{$testdata}U89959_ginums.corrupt " +
           "#{$testdata}U89959_ests.fas", :retval => 1)
end

Name "gt extractseq -keys from fastafile (fail)"
Keywords "gt_extractseq"
Test do
  run_test("#{$bin}gt extractseq -keys #{$testdata}U89959_ginums.txt",
           :retval => 1)
  grep last_stderr, /requires at least one file argument/
end

Name "gt suffixerator -kys with key of length 0"
Keywords "gt_extractseq"
Test do
  run_test("#{$bin}gt suffixerator -protein -ssp -tis -des -sds -kys " +
             "-db #{$testdata}trembl-emptykey.faa",:retval => 1)
end

Name "gt suffixerator -kys with keys of different length"
Keywords "gt_extractseq"
Test do
  run_test("#{$bin}gt suffixerator -protein -ssp -tis -des -sds -kys " +
             "-db #{$testdata}trembl-difflenkey.faa",:retval => 1)
end

if $gttestdata then
  Name "gt extractseq -keys from large fastafile"
  Keywords "gt_extractseq"
  Test do
    run_test "#{$bin}gt extractseq -o gi-extract.fna.gz -gzip " +
             "-keys #{$gttestdata}gi-queries/gi-queries.txt " +
             "#{$testdata}at1MB"
  end
  Name "gt extractseq -keys from fastaindex"
  Keywords "gt_extractseq"
  Test do
    run_test("#{$bin}gt suffixerator -protein -ssp -tis -des -sds -kys " +
             "-db #{$gttestdata}trembl/trembl-section.fsa.gz")
    run("gunzip -c #{$gttestdata}trembl/trembl-section.fsa.gz")
    run("mv #{last_stdout} trembl-section.fsa")
    run("#{$scriptsdir}/tr2deskeys.rb #{$gttestdata}trembl/trembl-section.fsa.gz")
    run("mv #{last_stdout} trembl-section.keylist")
    run("#{$scriptsdir}/randlines.rb trembl-section.keylist 1000")
    run("mv #{last_stdout} trembl-section.random-keylist")
    run_test("#{$bin}gt extractseq -keys trembl-section.keylist -width 60 " +
             "trembl-section.fsa.gz")
    run("cmp -s #{last_stdout} trembl-section.fsa")
    run_test("#{$bin}gt extractseq -keys #{$testdata}trkeys.txt -width 60 " +
             "trembl-section.fsa.gz")
    run("cmp -s #{last_stdout} #{$testdata}trkeys-result.txt")
    run_test("#{$bin}gt extractseq -keys #{last_stdout} " +
             "trembl-section.fsa.gz",:retval => 1)
    run_test("#{$bin}gt extractseq -keys #{$testdata}trembl-wrongkey.txt " +
             "trembl-section.fsa.gz",:retval => 1)
    run_test("#{$bin}gt extractseq -keys trembl-section.random-keylist -width 60 " +
             "trembl-section.fsa.gz")
    run_test("#{$bin}gt suffixerator -protein -ssp -tis -des -sds -kys sort " +
             "-db #{last_stdout}")
    run("mv #{last_stdout} trembl-section-sorted.fna")
    run_test("#{$bin}gt suffixerator -protein -ssp -tis -des -sds -kys " +
             "-db trembl-section-sorted.fna")
    run("#{$scriptsdir}/tr2deskeys.rb trembl-section-sorted.fna")
    run("mv #{last_stdout} trembl-section-sorted.keylist")
    run_test("#{$bin}gt extractseq -keys trembl-section-sorted.keylist " +
             "-width 60 trembl-section-sorted.fna")
    run("cmp -s #{last_stdout} trembl-section-sorted.fna")
  end
end
genometools-1.5.1/testsuite/gt_featureindex_include.rb000066400000000000000000000044461211610345200233120ustar00rootroot00000000000000Name "gt featureindex (empty file)"
Keywords "gt_featureindex"
Test do
  run "#{$bin}gt mkfeatureindex -filename tmp.db #{$testdata}/gt_view_prob_1.gff3"
  run "#{$bin}gt featureindex -filename tmp.db", :retval => 1
  grep(last_stderr, /no sequence regions in index/)
end

Name "gt featureindex (empty region)"
Keywords "gt_featureindex"
Test do
  run "#{$bin}gt mkfeatureindex -filename tmp.db #{$testdata}/gt_view_prob_2.gff3"
  run "#{$bin}gt featureindex -filename tmp.db"
  run "diff #{last_stdout} #{$testdata}/gt_view_prob_2.gff3"
end

Name "gt featureindex (parse error in GFF3)"
Keywords "gt_featureindex"
Test do
  run "#{$bin}gt mkfeatureindex -filename tmp.db #{$testdata}/gt_gff3_fail_1.gff3", :retval => 1
  grep(last_stderr, /has already been defined/)
  run "#{$bin}gt featureindex -filename tmp.db", :retval => 1
  grep(last_stderr, /no sequence regions in index/)
end

Name "gt featureindex (invalid sequence ID)"
Keywords "gt_featureindex"
Test do
  run "#{$bin}gt mkfeatureindex -filename tmp.db #{$testdata}/standard_gene_simple.gff3"
  run "#{$bin}gt featureindex -seqid foo -filename tmp.db", :retval => 1
  grep(last_stderr, /not exist/)
end

Name "gt featureindex (corrupt file)"
Keywords "gt_featureindex"
Test do
  File.open("corrupt.db", "w") do |file|
    file.write("sdfnhsnl")
  end
  run "#{$bin}gt featureindex -filename corrupt.db", :retval => 1
end

FEATUREINDEX_TEST_FILES = ["#{$testdata}/eden.gff3",
                           "#{$testdata}/standard_gene_simple.gff3",
                           "#{$testdata}/standard_gene_as_tree.gff3",
                           "#{$testdata}/standard_gene_with_introns_as_tree.gff3",
                           "#{$testdata}/encode_known_genes_Mar07.gff3"
                           ]

FEATUREINDEX_TEST_FILES.each do |file|
  Name "gt featureindex db vs. parser (#{File.basename(file)})"
  Keywords "gt_featureindex"
  Test do
    run "#{$bin}gt seqids #{file}"
    seqids = File.open(last_stdout).readlines
    run "#{$bin}gt mkfeatureindex -filename tmp.db #{file}", :maxtime => 1200
    seqids.each do |seqid|
      seqid.chomp!
      run "#{$bin}gt featureindex -seqid #{seqid} -retain no -filename tmp.db > out.gff3"
      run "#{$bin}gt gff3 -retainids no #{file} | #{$bin}gt select -seqid #{seqid}"
      run "diff out.gff3 #{last_stdout}"
    end
  end
end
genometools-1.5.1/testsuite/gt_fingerprint_include.rb000066400000000000000000000045511211610345200231530ustar00rootroot00000000000000Name "fingerprint"
Keywords "gt_fingerprint"
Test do
  run_test "#{$bin}gt fingerprint #{$testdata}U89959_ests.fas | sort | uniq"
  run "diff #{last_stdout} #{$testdata}U89959_ests.checklist_uniq"
end

Name "fingerprint (nonexistent file)"
Keywords "gt_fingerprint"
Test do
  run_test("#{$bin}gt fingerprint #{$testdata}nonexistent_file", :retval=> 1)
end

Name "fingerprint -check (success)"
Keywords "gt_fingerprint"
Test do
  run_test "#{$bin}gt fingerprint -check #{$testdata}U89959_ests.checklist " +
           "#{$testdata}U89959_ests.fas"
end

Name "fingerprint -check (stdin)"
Keywords "gt_fingerprint"
Test do
  run "cat #{$testdata}U89959_ests.checklist | #{$memcheck} #{$bin}gt " +
      "fingerprint -check - #{$testdata}U89959_ests.fas"
end

Name "fingerprint -check (failure)"
Keywords "gt_fingerprint"
Test do
  run_test("#{$bin}gt fingerprint -check " +
           "#{$testdata}U89959_ests.checklist_uniq " +
           "#{$testdata}U89959_ests.fas", :retval => 1)
  grep last_stderr, /fingerprint comparison failed/
end

Name "fingerprint -check (failure)"
Keywords "gt_fingerprint"
Test do
  run_test("#{$bin}gt sequniq #{$testdata}U89959_ests.fas | #{$memcheck}" +
           "#{$bin}gt fingerprint -check #{$testdata}U89959_ests.checklist -",
           :retval => 1)
  grep last_stderr, /fingerprint comparison failed/
end

Name "fingerprint -collisions"
Keywords "gt_fingerprint"
Test do
  run_test "#{$bin}gt fingerprint -collisions #{$testdata}U89959_ests.fas"
end

Name "fingerprint -duplicates (found)"
Keywords "gt_fingerprint"
Test do
  run_test("#{$bin}gt fingerprint -duplicates #{$testdata}U89959_ests.fas",
           :retval => 1)
  grep last_stderr, /duplicates found/
end

Name "fingerprint -duplicates (none found)"
Keywords "gt_fingerprint"
Test do
  run_test "#{$bin}gt fingerprint -duplicates #{$testdata}U89959_genomic.fas"
end

Name "fingerprint -extract (found)"
Keywords "gt_fingerprint"
Test do
  run_test "#{$bin}gt fingerprint -extract 6d3b4b9db4531cda588528f2c69c0a57 " +
           "#{$testdata}U89959_ests.fas"
  run "diff #{last_stdout} #{$testdata}gt_fingerprint_extract.out"
end

Name "fingerprint -extract (not found)"
Keywords "gt_fingerprint"
Test do
  run_test "#{$bin}gt fingerprint -extract 7d3b4b9db4531cda588528f2c69c0a57 " +
           "#{$testdata}U89959_ests.fas", :retval => 1
  grep last_stderr, /could not find sequence with fingerprint/
end
genometools-1.5.1/testsuite/gt_genomediff_include.rb000066400000000000000000000225411211610345200227260ustar00rootroot00000000000000require 'fileutils'
require 'tempfile'
require '../scripts/genomediff.rb'

Name "gt genomediff pck  failure"
Keywords "gt_genomediff pck failure"
Test do
  run_test "#{$bin}gt suffixerator -suf -lcp -indexname esa " +
           "-db #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt genomediff -indextype pck esa",:retval=>1
end

Name "gt genomediff esa  failure"
Keywords "gt_genomediff esa failure"
Test do
  run_test "#{$bin}gt packedindex mkindex -indexname pck " +
           "-db #{$testdata}Atinsert.fna"
  run_test "#{$bin}gt genomediff -indextype esa pck",:retval=>1
end

def reverse_and_concat(file)
  tf = Tempfile.new("gt_rev")
  tmpfile = tf.path
  tf.close
  dirname = File.dirname(file)
  `#{$bin}gt                \
   convertseq -o #{tmpfile} \
   -force -r #{file}`
  basename = File.basename(file, ".*")
  newfile = basename + "_plus_rev.fas"
  FileUtils.cp(file, newfile)
  file = newfile
  File.open(file, 'a') {|fp|
    File.open(tmpfile, 'r') {|tf|
      while line = tf.gets
        fp.puts line
      end
    }
  }
  failtest unless File.exist?(newfile)
  return newfile
end

kr_testable_files = []
smallfilecodes = []
bigfilecodes = []

allfiles = ["Duplicate.fna",
            "Random159.fna",
            "Random160.fna",
            "TTT-small.fna",
            "trna_glutamine.fna"]

bigfiles = ["U89959_genomic.fas",
            "Random.fna",
            "Atinsert.fna"]

# do not run the big tests with valgrind
if $gttestdata and not $arguments["memcheck"]
  bigfiles.push "at1MB"
end

fp = File.open("#{$testdata}genomediff/testsuite", 'r')
smallfilecodes = fp.readlines
fp.close

smallfilecodes.collect! do |filecode|
  "#{$testdata}genomediff/#{filecode}".chomp
end

# do not run the big tests with valgrind
if $gttestdata and not $arguments["memcheck"]
  fp = File.open("#{$gttestdata}genomediff/codelist", 'r')
  bigfilecodes = fp.readlines
  fp.close

  bigfilecodes.collect! do |filecode|
    "#{$gttestdata}genomediff/#{filecode}".chomp
  end
end

allfilecodes = smallfilecodes + bigfilecodes
allfilecodes.each do |code|
  if code.match /[^_]_0+1_/
    kr_testable_files << code.chomp
  end
end

def test_pck(files, param, idxparam)
  run_test("#{$bin}gt       " +
           "packedindex mkindex " +
           "-db #{files} " +
           "-dna " +
           "-dir rev " +
           "-ssp " +
           "-dc 64 " +
           "-bsize 8 " +
           "-sprank " +
           "-pl " +
           "#{idxparam} " +
           "-indexname pck")
  run_test(
    "#{$bin}gt genomediff #{param} -indextype pck pck",
    :maxtime => 720)
end

def test_esa(files, param, idxparam)
  run_test "#{$bin}gt suffixerator -db #{files} -indexname esa " +
           "-dna -suf -tis -lcp -ssp #{idxparam}"
  run_test "#{$bin}gt genomediff #{param} -indextype esa esa"
end

def test_esq(files, param)
  run_test "#$bin/gt genomediff #{param} #{files}"
end

def compare_2d_result(matrix1, matrix2)
  0.upto(matrix1.length - 1) do |i_idx|
    1.upto(matrix2.length) do |j_idx|
      if i_idx!=j_idx - 1 and
         matrix1[i_idx][j_idx] != matrix2[i_idx][j_idx]
        return matrix1[i_idx][j_idx], matrix2[i_idx][j_idx]
      end
    end
  end
  return false
end

Name "gt genomediff pck testset"
Keywords "gt_genomediff pck"
Test do
  allfilecodes.each do |code|
      test_pck("#{code}*.fas", "", "")
      test_pck("#{code}*.fas", "", "-mirrored")
  end
end
Name "gt genomediff esa testset"
Keywords "gt_genomediff esa"
Test do
  allfilecodes.each do |code|
    test_esa("#{code}*.fas", "", "")
    test_esa("#{code}*.fas", "", "-mirrored")
  end
end

Name "gt genomediff esq testset"
Keywords "gt_genomediff esq"
Test do
  allfilecodes.each do |code|
    test_esq("#{code}*.fas", "-indexname esq")
    test_esq("#{code}*.fas", "-indexname esq -mirrored")
    test_esq("esq", "")
    test_esq("esq", "-mirrored")
  end
end

code = smallfilecodes[0]

Name "gt genomediff compare kr"
Keywords "gt_genomediff esa pck check_kr simulated_data"
Test do
  kr_testable_files.each do |code|
    pck_out = []
    esa_out = []
    esq_out = []
    kr_out = []
    numoffiles = 0
    files = " "
    Dir.glob("#{code}*.fas").sort.each do |file|
      files += reverse_and_concat(file) + ' '
    end

    test_pck("#{files}", "", "")

    File.open(last_stdout, 'r') do |outfile|
      while line = outfile.gets do
        line.chomp!
        next if line.match /^#/
        if numoffiles == 0
          numoffiles = line.match(/^\d+$/)[0].to_i
        else
          pck_out << line.split
        end
      end
      if numoffiles == nil or
        numoffiles != pck_out.length
        failtest("can't parse output")
      end
    end

    test_esa("#{files}", "", "")

    File.open(last_stdout, 'r') do |outfile|
      while line = outfile.gets do
        line.chomp!
        next if line.match /^#/
        unless line.match(/^\d+$/)
          esa_out << line.split
        end
      end
      if numoffiles == nil or
        numoffiles != pck_out.length
        failtest("can't parse output or wrong line numbers")
      end
    end

    test_esq("#{files}", "-indexname esq")

    File.open(last_stdout, 'r') do |outfile|
      while line = outfile.gets do
        line.chomp!
        next if line.match /^#/
        unless line.match(/^\d+$/)
          esq_out << line.split
        end
      end
      if numoffiles == nil or
        numoffiles != pck_out.length
        failtest("can't parse output or wrong line numbers")
      end
    end
    File.open("#{code}-kr.out", 'r') do |krfile|
      line = krfile.gets
      line.chomp!
      if numoffiles != line.to_i
        failtest("different num of files")
      end
      (numoffiles+1).times do
        krfile.gets
      end
      while line = krfile.gets do
        line.chomp!
        if line.match /^\d+$/
          break
        end
        kr_out << line.split
      end
    end
    if result = compare_2d_result(pck_out,esa_out)
      failtest("different results pck-esa #{result[0]},#{result[1]}")
    end
    if result = compare_2d_result(pck_out,esq_out)
      failtest("different results pck-esa #{result[0]},#{result[1]}")
    end
    0.upto(numoffiles - 1) do |i_idx|
      1.upto(numoffiles) do |j_idx|
        unless i_idx==j_idx-1 or
           pck_out[i_idx][j_idx].to_f > 0.3 or
           kr_out[i_idx][j_idx].to_f > 0.3
          if (pck_out[i_idx][j_idx].to_f -
              kr_out[i_idx][j_idx].to_f).abs > 0.001
            failtest("different results pck-kr #{pck_out[i_idx][j_idx]},"+
                     "#{kr_out[i_idx][j_idx]}\n"+
                     "#{pck_out[i_idx][j_idx]} #{kr_out[i_idx][j_idx]}")
          end
        end
      end
    end
  end
end

def check_shulen_for_list_pairwise(list)
  Name "gt genomediff pairwise test"
  Keywords "gt_genomediff pairwise esa pck check_shulen"
  Test do
    start_idx = 1
    list.each do |file1|
      list[start_idx..-1].each do |file2|
        if file1 != file2
          numoffiles = 0
          pck_out = []
          esa_out = []

          test_pck("#{$testdata}#{file1} #{$testdata}#{file2}", "", "")

          File.open(last_stdout, 'r') do |outfile|
            while line = outfile.gets do
              line.chomp!
              next if line.match /^#/
              if numoffiles == 0
                numoffiles = line.match(/^\d+$/)[0].to_i
              else
                pck_out << line.split
              end
            end
            if numoffiles == nil or
              numoffiles != pck_out.length
              failtest("can't parse output pck #{file1} #{file2}")
            end
          end
          test_esa("#{$testdata}#{file1} #{$testdata}#{file2}",
                    "", "")

          File.open(last_stdout, 'r') do |outfile|
            while line = outfile.gets do
              line.chomp!
              next if line.match /^#/
              unless line.match(/^\d+$/)
                esa_out << line.split
              end
            end
            if numoffiles == NIL or
              numoffiles != pck_out.length
              failtest("can't parse output esa #{file1} #{file2}")
            end
          end
          if result = compare_2d_result(pck_out,esa_out)
            failtest("different results pck-esa #{result[0]},#{result[1]}")
          end
        end
      end
      start_idx += 1
    end
  end
end

check_shulen_for_list_pairwise(allfiles)

check_shulen_for_list_pairwise(bigfiles)

Name "gt genomediff smallfiles all at once"
Keywords "gt_genomediff esa pck small check_shulen"
Test do
  realfiles = ""
  allfiles.each do |file|
    realfiles += "#{$testdata}"+ file + " "
  end
  numoffiles = 0
  pck_out = []
  esa_out =[]

  test_pck(realfiles, "", "")

  File.open(last_stdout, 'r') do |outfile|
    while line = outfile.gets do
      line.chomp!
      next if line.match /^#/
      if numoffiles == 0
        numoffiles = line.match(/^\d+$/)[0].to_i
      else
        pck_out << line.split
      end
    end
    if numoffiles == nil or
      numoffiles != pck_out.length
      failtest("can't parse output")
    end
  end
  test_esa(realfiles, "", "")

  File.open(last_stdout, 'r') do |outfile|
    while line = outfile.gets do
      line.chomp!
      next if line.match /^#/
      unless line.match(/^\d+$/)
        esa_out << line.split
      end
    end
    if numoffiles == NIL or
      numoffiles != pck_out.length
      failtest("can't parse output or wrong line numbers")
    end
  end
  if result = compare_2d_result(pck_out,esa_out)
    failtest("different results pck-esa #{result[0]},#{result[1]}")
  end
end
genometools-1.5.1/testsuite/gt_gff3_include.rb000066400000000000000000001127041211610345200214510ustar00rootroot00000000000000Name "gt gff3 -help"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -help"
  grep last_stdout, "Report bugs to"
end

Name "gt gff3 -noop"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -noop", :retval => 1)
  grep last_stderr, "unknown option"
end

Name "gt gff3 short test (stdin)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 < #{$testdata}gff3_file_1_short.txt"
  run "env LC_ALL=C sort #{last_stdout}"
  run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end

Name "gt gff3 short test (file)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gff3_file_1_short.txt"
  run "env LC_ALL=C sort #{last_stdout}"
  run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end

Name "gt gff3 short test (compressed output)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -o test -gzip #{$testdata}gff3_file_1_short.txt"
  grep last_stderr, "appending it"
end

Name "gt gff3 prob 1"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_prob_1.gff3", :retval => 1)
end

Name "gt gff3 prob 2"
Keywords "gt_gff3"
Test do
  run "env LC_ALL=C #{$bin}gt gff3 -sort #{$testdata}gt_gff3_prob_2.in"
  run "diff #{last_stdout} #{$testdata}gt_gff3_prob_2.out"
end

Name "gt gff3 prob 3"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_prob_3.gff3"
end

Name "gt gff3 prob 5"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -sort #{$testdata}gt_gff3_prob_5.in"
  run "diff #{last_stdout} #{$testdata}gt_gff3_prob_5.out"
end

Name "gt gff3 prob 6"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -sort #{$testdata}gt_gff3_prob_6.in", :retval => 1)
  grep(last_stderr, /does not contain/);
end

Name "gt gff3 prob 7 (unsorted)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_prob_7.in | #{$bin}gt gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_prob_7.unsorted"
end

Name "gt gff3 prob 7 (sorted)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -sort #{$testdata}gt_gff3_prob_7.in | #{$bin}gt gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_prob_7.sorted"
end

Name "gt gff3 prob 8"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_prob_8.in"
  run "diff #{last_stdout} #{$testdata}gt_gff3_prob_8.out"
end

Name "gt gff3 prob 9"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_prob_9.in"
  run "diff #{last_stdout} #{$testdata}gt_gff3_prob_9.out"
end

Name "gt gff3 prob 10"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_prob_10.in"
  run "diff #{last_stdout} #{$testdata}gt_gff3_prob_10.out"
end

Name "gt gff3 prob 11"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_prob_11.in"
  run "diff #{last_stdout} #{$testdata}gt_gff3_prob_11.out"
end

Name "gt gff3 prob 12"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_prob_12.gff3", :retval => 1)
  grep last_stderr, "Parent .* was not defined"
end

Name "gt gff3 prob 12 (-checkids)"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -checkids #{$testdata}gt_gff3_prob_12.gff3", :retval => 1)
  grep last_stderr, "is separated from its counterpart on line 5 by terminator"
end

Name "gt gff3 prob 13 (DAG)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -sort -tidy #{$testdata}gt_gff3_prob_13.gff3"
  run_test "#{$bin}gt gff3 #{last_stdout}"
end

Name "gt gff3 test 1.1"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -o /dev/null -force -v #{$testdata}gt_gff3_test_1.in"
end

Name "gt gff3 test 1.2"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 - - < #{$testdata}gt_gff3_test_1.in", :retval => 1)
end

Name "gt gff3 test 1.3"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_1.in | #{$bin}gt gff3"
end

Name "gt gff3 test 2"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_test_2.gff3", :retval => 1)
end

Name "gt gff3 test 3"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_3.gff3"
end

# make sure the -typecheck-built-in option works (for tests below!)
Name "gt gff3 -typecheck-built-in"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -typecheck-built-in " +
           "#{$testdata}standard_gene_as_tree.gff3")
end

Name "gt gff3 (standard gene as DAG)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}standard_gene_as_dag.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_dag_sorted.gff3"
end

4.upto(14) do |i|
  Name "gt gff3 test #{i}"
  Keywords "gt_gff3"
  Test do
    run_test("#{$bin}gt gff3 -typecheck-built-in " +
             "#{$testdata}gt_gff3_test_#{i}.gff3", :retval => 1)
  end
end

Name "gt gff3 test 15"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_15.gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_test_15.out"
end

Name "gt gff3 test 16"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_16.gff3"
end

Name "gt gff3 test 17"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_17.gff3", :retval => 1
  grep(last_stderr, /unknown meta-directive encountered/);
  grep(last_stderr, /does not have data: ##foo/);
end

Name "gt gff3 test 18"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_18.gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_test_18.gff3"
end

Name "gt gff3 test 19"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_19.gff3"
end

Name "gt gff3 test 20"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_test_20.gff3", :retval => 1);
  grep(last_stderr, /could not parse/);
end

Name "gt gff3 test 21"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_test_21.gff3", :retval => 1);
  grep(last_stderr, /does not equal required version/);
end

Name "gt gff3 test 22"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_22.gff3 | #{$bin}gt gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_test_22.gff3"
end

Name "gt gff3 test 22 (-sort)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -sort #{$testdata}gt_gff3_test_22.gff3 | #{$bin}gt gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_test_22.gff3"
end

Name "gt gff3 test 23"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_23.gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_test_23.gff3"
end

Name "gt gff3 test 24"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_24.gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_test_23.gff3"
end

Name "gt gff3 test 25"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_test_25.gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_test_25.out"
end

Name "gt gff3 test 26"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_test_26.gff3", :retval => 1)
end

Name "gt gff3 test 27"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_test_27.gff3", :retval => 1)
  grep(last_stderr, /before the corresponding/);
end

Name "gt gff3 test additional attribute"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}additional_attribute.gff3"
  run "diff #{last_stdout} #{$testdata}additional_attribute.gff3"
end

Name "gt gff3 fail 1"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_fail_1.gff3", :retval => 1)
end

Name "gt gff3 -addintrons overlapping exons"
Keywords "gt_gff3 addintrons"
Test do
  run_test "#{$bin}gt gff3 -addintrons " + \
           "#{$testdata}gt_gff3_addintrons_overlapping_exons.gff3"
  grep last_stderr, /overlapping boundary .* not placing 'intron' inter-feature/
  run "diff #{last_stdout} #{$testdata}gt_gff3_addintrons_overlapping_exons_with_introns.gff3"
end

Name "gt gff3 test option -addintrons"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -addintrons #{$testdata}addintrons.gff3"
  run "diff #{last_stdout} #{$testdata}addintrons.out"
end

Name "gt gff3 test option -offset 1000"
Keywords "gt_gff3 offset"
Test do
  run_test "#{$bin}gt gff3 -offset 1000 #{$testdata}gt_gff3_offset_test.gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_offset_test.out1000"
end

Name "gt gff3 test option -offset -1"
Keywords "gt_gff3 offset"
Test do
  run_test "#{$bin}gt gff3 -offset -1 #{$testdata}gt_gff3_offset_test.gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_offset_test.out-1"
end

Name "gt gff3 test option -offset -999"
Keywords "gt_gff3 offset"
Test do
  run_test "#{$bin}gt gff3 -offset -999 #{$testdata}gt_gff3_offset_test.gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_offset_test.out-999"
end

Name "gt gff3 test option -offset -1001 (overflow)"
Keywords "gt_gff3 offset"
Test do
  run_test("#{$bin}gt gff3 -offset -1001 #{$testdata}gt_gff3_offset_test.gff3",
           :retval => 1)
end

Name "gt gff3 test option -offsetfile"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -offsetfile #{$testdata}gt_gff3_offsetfile_test.offsetfile #{$testdata}gt_gff3_offsetfile_test.gff3"
  run "diff #{last_stdout} #{$testdata}gt_gff3_offsetfile_test.out"
end

Name "gt gff3 test option -mergefeat"
Keywords "gt_gff3 mergefeat"
Test do
  run_test "#{$bin}gt gff3 -sort -mergefeat #{$testdata}mergefeat.gff3"
  run "diff #{last_stdout} #{$testdata}mergefeat.out"
end

Name "gt gff3 fail option -offsetfile"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -offsetfile #{$testdata}empty_file #{$testdata}gt_gff3_offsetfile_test.gff3", :retval => 1)
end

Name "gt gff3 fail attribute after dot"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}attribute_after_dot.gff3", :retval => 1)
  grep last_stderr, "more than one attribute token defined"
end

Name "gt gff3 fail attribute with multiple equal signs"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}attribute_w_multiple_equals.gff3", :retval => 1)
  grep last_stderr, "does not contain exactly one"
end

Name "gt gff3 fail inconsistent sequence ids"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}inconsistent_sequence_ids.gff3", :retval => 1)
  grep last_stderr, "has different sequence id"
end

Name "gt gff3 fail range check"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_range_check.gff3", :retval => 1)
  grep last_stderr, "is not contained in range"
end

Name "gt gff3 fail illegal region start"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_illegal_region_start.gff3", :retval => 1)
  grep last_stderr, "illegal region start"
end

Name "gt gff3 fail illegal feature start"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}gt_gff3_illegal_feature_start.gff3", :retval => 1)
  grep last_stderr, "illegal feature start"
end

Name "gt gff3 corrupt gff3 header"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}corrupt_gff3_header.txt", :retval => 1)
  grep last_stderr, "could not parse integer"
end

Name "gt gff3 corrupt target attribute"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}corrupt_target_attribute.gff3",
           :retval => 1)
  grep last_stderr, "must have 3 or 4 blank separated entries"
end

Name "gt gff3 target attribute with swapped range"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}target_attribute_swapped_range.gff3",
           :retval => 1)
  grep last_stderr, "start '2' is larger then end '1' on line"
end

Name "gt gff3 empty attribute"
Keywords "gt_gff3 gff3_attribute"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}empty_attribute.gff3", :retval => 1)
  grep last_stderr, "has no tag"
end

Name "gt gff3 fix region boundaries (end)"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -fixregionboundaries #{$testdata}gt_gff3_range_check.gff3")
  grep last_stdout, "sr 1000 2001"
end

Name "gt gff3 fix region boundaries (start)"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -fixregionboundaries #{$testdata}gt_gff3_range_check2.gff3")
  grep last_stdout, "sr 900 2000"
end

Name "gt gff3 fix region boundaries (end)"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -fixregionboundaries #{$testdata}gt_gff3_range_check3.gff3")
  grep last_stdout, "sr 900 2001"
end


Name "gt gff3 empty attribute name"
Keywords "gt_gff3 gff3_attribute"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}empty_attribute_name.gff3", :retval => 1)
  grep last_stderr, "has no tag"
end

Name "gt gff3 empty id attribute"
Keywords "gt_gff3 gff3_attribute"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}empty_id_attribute.gff3", :retval => 1)
  grep last_stderr, "has no value"
end

Name "gt gff3 empty other attribute"
Keywords "gt_gff3 gff3_attribute"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}empty_other_attribute.gff3",
           :retval => 1)
  grep last_stderr, "has no value"
end

Name "gt gff3 empty parent attribute"
Keywords "gt_gff3 gff3_attribute"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}empty_parent_attribute.gff3",
           :retval => 1)
  grep last_stderr, "has no value"
end

# test OBO file parsing
obo_gff3_file="#{$testdata}standard_gene_as_tree.gff3"

Name "gt gff3 -typecheck empty file"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck #{$testdata}empty_file #{obo_gff3_file}",
           :retval => 1)
  grep last_stderr, "unexpected end-of-file"
end

Name "gt gff3 -typecheck blank line"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck #{$testdata}obo_files/blank_line.obo " +
           "#{obo_gff3_file}", :retval => 1)
  grep last_stderr, "unexpected end-of-file"
end

Name "gt gff3 -typecheck comment line"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck #{$testdata}obo_files/comment_line.obo " +
           "#{obo_gff3_file}", :retval => 1)
  grep last_stderr, "unexpected end-of-file"
end

Name "gt gff3 -typecheck blank-comment line"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/blank_comment_line.obo #{obo_gff3_file}",
           :retval => 1)
  grep last_stderr, "unexpected end-of-file"
end

Name "gt gff3 -typecheck tag only"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/tag_only.obo #{obo_gff3_file}",
           :retval => 1)
  grep last_stderr, "expected character ':'"
end

Name "gt gff3 -typecheck missing value"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/missing_value.obo #{obo_gff3_file}",
           :retval => 1)
  grep last_stderr, "unexpected newline"
end

Name "gt gff3 -typecheck minimal header"
Keywords "gt_gff3 typecheck"
Test do
  run_test "#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/minimal_header.obo #{$testdata}header.gff3"
end

Name "gt gff3 -typecheck corrupt header"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/corrupt_header.obo #{obo_gff3_file}",
           :retval => 1)
  grep last_stderr, "does not contain \"format-version\" tag"
end

Name "gt gff3 -typecheck minimal stanza"
Keywords "gt_gff3 typecheck"
Test do
  run_test "#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/minimal_stanza.obo #{$testdata}header.gff3"
end

Name "gt gff3 -typecheck corrupt term stanza"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/corrupt_term_stanza.obo #{obo_gff3_file}",
           :retval => 1)
  grep last_stderr, "lacks required \"name\" tag"
end

Name "gt gff3 -typecheck corrupt typedef stanza"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/corrupt_typedef_stanza.obo #{obo_gff3_file}",
           :retval => 1)
  grep last_stderr, "lacks required \"name\" tag"
end

Name "gt gff3 -typecheck corrupt instance stanza"
Keywords "gt_gff3 typecheck"
Test do
  run_test("#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/corrupt_instance_stanza.obo #{obo_gff3_file}",
           :retval => 1)
  grep last_stderr, "lacks required \"instance_of\" tag"
end

Name "gt gff3 -typecheck windows newline"
Keywords "gt_gff3 typecheck"
Test do
  run_test "#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/windows_newline.obo #{$testdata}header.gff3"
end

Name "gt gff3 -typecheck comment in stanza"
Keywords "gt_gff3 typecheck"
Test do
  run_test "#{$bin}gt gff3 -typecheck " +
           "#{$testdata}obo_files/comment_in_stanza.obo #{$testdata}header.gff3"
end

Name "gt gff3 -typecheck sofa"
Keywords "gt_gff3 typecheck"
Test do
  run_test "#{$bin}gt gff3 -typecheck sofa #{obo_gff3_file}"
end

Name "gt gff3 -typecheck so"
Keywords "gt_gff3 typecheck"
Test do
  run_test "#{$bin}gt gff3 -typecheck so #{obo_gff3_file}"
end

Name "gt gff3 -typecheck so-xp"
Keywords "gt_gff3 typecheck"
Test do
  run_test "#{$bin}gt gff3 -typecheck so-xp #{obo_gff3_file}"
end

Name "gt gff3 blank attributes"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}blank_attributes.gff3"
end

Name "gt gff3 minimal fasta file"
Keywords "gt_gff3 fasta"
Test do
  run_test "#{$bin}gt gff3 -width 50 #{$testdata}minimal_fasta.gff3"
  run "diff #{last_stdout} #{$testdata}minimal_fasta.gff3"
end

Name "gt gff3 minimal fasta file (without directive)"
Keywords "gt_gff3 fasta"
Test do
  run_test "#{$bin}gt gff3 -width 50 " +
           "#{$testdata}minimal_fasta_without_directive.gff3"
  run "diff #{last_stdout} #{$testdata}minimal_fasta.gff3"
end

Name "gt gff3 standard fasta example"
Keywords "gt_gff3 fasta"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}standard_fasta_example.gff3"
end

Name "gt gff3 standard fasta example (stdin)"
Keywords "gt_gff3 fasta"
Test do
  run_test "#{$bin}gt gff3 < #{$testdata}standard_fasta_example.gff3"
end

Name "gt gff3 two fasta sequences"
Keywords "gt_gff3 fasta"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}two_fasta_seqs.gff3"
  run "diff #{last_stdout} #{$testdata}two_fasta_seqs.gff3"
end

Name "gt gff3 two fasta sequences without sequence region"
Keywords "gt_gff3 fasta"
Test do
  run_test "#{$bin}gt gff3 -sort #{$testdata}two_fasta_seqs_without_sequence_regions.gff3"
  run "diff #{last_stdout} #{$testdata}two_fasta_seqs.gff3"
end

Name "gt gff3 (-retainids)"
Keywords "gt_gff3 retainids"
Test do
  run_test "#{$bin}gt gff3 -retainids #{$testdata}retainids.gff3"
  run "diff #{last_stdout} #{$testdata}retainids.gff3"
end

Name "gt gff3 ID not unique (-retainids)"
Keywords "gt_gff3 retainids"
Test do
  run_test "#{$bin}gt gff3 -retainids #{$testdata}retain_1.gff3 " +
           "#{$testdata}retain_2.gff3"
  run "diff #{last_stdout} #{$testdata}retain_both.gff3"
end

Name "gt gff3 multi-feature (-retainids)"
Keywords "gt_gff3 multi-feature retainids"
Test do
  run_test "#{$bin}gt gff3 -retainids #{$testdata}multi_feature_simple.gff3"
  run "diff #{last_stdout} #{$testdata}multi_feature_simple.gff3"
end

Name "gt gff3 multi-feature, ID not unique (-retainids)"
Keywords "gt_gff3 multi-feature retainids"
Test do
  run_test "#{$bin}gt gff3 -retainids #{$testdata}multi_feature_simple.gff3 " +
           "#{$testdata}multi_feature_simple.gff3 " +
           "#{$testdata}multi_feature_simple.gff3"
  run "diff #{last_stdout} #{$testdata}multi_feature_multi.gff3"
end

Name "gt gff3 simple multi-feature (round-trip)"
Keywords "gt_gff3 multi-feature"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}multi_feature_simple.gff3"
  run "diff #{last_stdout} #{$testdata}multi_feature_simple.gff3"
end

Name "gt gff3 simple multi-feature (reverted)"
Keywords "gt_gff3 multi-feature"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}multi_feature_simple_reverted.gff3"
  run "diff #{last_stdout} #{$testdata}multi_feature_simple.gff3"
end

Name "gt gff3 simple multi-feature (undefined parent)"
Keywords "gt_gff3 multi-feature"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}multi_feature_undefined_parent.gff3",
           :retval => 1)
  grep last_stderr, "Parent .* on line 3 .* was not defined"
end

Name "gt gff3 multi-feature (different sequence ID)"
Keywords "gt_gff3 multi-feature"
Test do
  run_test("#{$bin}gt gff3 " +
           "#{$testdata}multi_feature_different_sequence_id.gff3", :retval => 1)
  grep last_stderr, "has a different sequence id than its counterpart on line"
end

Name "gt gff3 multi-feature (with pseudo-feature)"
Keywords "gt_gff3 multi-feature pseudo-feature"
Test do
  run_test "#{$bin}gt gff3 -width 50 " +
           "#{$testdata}standard_fasta_example_with_id.gff3"
  run "diff #{last_stdout} #{$testdata}standard_fasta_example_with_id.out"
end

Name "gt gff3 pseudo-feature minimal"
Keywords "gt_gff3 pseudo-feature"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}pseudo_feature_minimal.gff3"
  run "diff #{last_stdout} #{$testdata}pseudo_feature_minimal.gff3"
end

Name "gt gff3 negative sequence region start"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}sequence_region_negative_start.gff3"
  grep last_stderr, "start '-1' is negative"
end

Name "gt gff3 negative sequence region start (-strict)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -strict #{$testdata}sequence_region_negative_start.gff3",
           :retval => 1
  grep last_stderr, "start '-1' is negative"
end

Name "gt gff3 negative sequence region end"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}sequence_region_negative_end.gff3"
  grep last_stderr, "end '-1497228' is negative"
end

Name "gt gff3 negative sequence region end (-strict)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -strict #{$testdata}sequence_region_negative_end.gff3",
           :retval => 1
  grep last_stderr, "end '-1497228' is negative"
end

Name "gt gff3 negative sequence region end"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}sequence_region_negative_end.gff3"
  grep last_stderr, "end '-1497228' is negative"
end

Name "gt gff3 multiple top-level parents"
Keywords "gt_gff3 pseudo-feature"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}multiple_top_level_parents.gff3"
  run "diff #{last_stdout} #{$testdata}multiple_top_level_parents.gff3"
end

Name "gt gff3 undefined parent (one of two)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}undefined_parent.gff3", :retval => 1
  grep last_stderr, "Parent .* was not defined"
end

Name "gt gff3 missing gff3 header"
Keywords "gt_gff3 missing_gff3_header"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}missing_gff3_header.gff3", :retval => 1)
  grep last_stderr, "does not begin with"
end

Name "gt gff3 missing gff3 header (-tidy)"
Keywords "gt_gff3 missing_gff3_header"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}missing_gff3_header.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt gff3 empty attribute value"
Keywords "gt_gff3 empty_attribute_value"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}empty_attribute_value.gff3",
           :retval => 1)
  grep last_stderr, "has no value"
end

Name "gt gff3 empty attribute value (-tidy)"
Keywords "gt_gff3 empty_attribute_value"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}empty_attribute_value.gff3"
end

Name "gt gff3 duplicate attribute"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}duplicate_attribute.gff3", :retval => 1)
  grep last_stderr, "more than one Dbxref attribute on"
end

Name "gt gff3 duplicate attribute (-tidy)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}duplicate_attribute.gff3"
  run "diff #{last_stdout} #{$testdata}duplicate_attribute_fixed.gff3"
end

Name "gt gff3 multi-feature with different parent 1"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 " +
           "#{$testdata}multi_feature_with_different_parent_1.gff3",
           :retval => 1)
  grep last_stderr, "has a different attribute 'Parent' than its counterpart"
end

Name "gt gff3 multi-feature with different parent 1 (-tidy)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -tidy " +
           "#{$testdata}multi_feature_with_different_parent_1.gff3"
  run "diff #{last_stdout} " +
      "#{$testdata}multi_feature_with_different_parent_1_tidy.gff3"
end

Name "gt gff3 multi-feature with different parent 2"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 " +
           "#{$testdata}multi_feature_with_different_parent_2.gff3",
           :retval => 1)
  grep last_stderr, "has a different attribute 'Parent' than its counterpart"
end

Name "gt gff3 multi-feature with different parent 2 (-tidy)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -tidy " +
           "#{$testdata}multi_feature_with_different_parent_2.gff3"
  run "diff #{last_stdout} " +
      "#{$testdata}multi_feature_with_different_parent_2_tidy.gff3"
end

Name "gt gff3 join sequence regions with same ID (-sort)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -sort #{$testdata}sequence_region_1.gff3 " +
           "#{$testdata}sequence_region_2.gff3 "
  run "diff #{last_stdout} #{$testdata}sequence_region_joined.gff3"
end

Name "gt gff3 print very long attributes"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -o out.gff3 -sort #{$testdata}dynbuf.gff3"
  run_test "#{$bin}gt gff3 out.gff3 | diff #{$testdata}dynbuf.gff3 -"
end

Name "gt gff3 print very long attributes (-gzip)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -gzip -o out.gff3.gz -sort #{$testdata}dynbuf.gff3"
  run_test "#{$bin}gt gff3 out.gff3.gz | diff #{$testdata}dynbuf.gff3 -"
end

Name "gt gff3 print very long attributes (-bzip2)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -bzip2 -o out.gff3.bz2 -sort #{$testdata}dynbuf.gff3"
  run_test "#{$bin}gt gff3 out.gff3.bz2 | diff #{$testdata}dynbuf.gff3 -"
end

Name "custom_stream (C)"
Keywords "gt_gff3 examples"
Test do
  run_test "#{$bin}examples/custom_stream"
  run "diff #{last_stdout} #{$testdata}standard_gene_simple.gff3"
end

1.upto(12) do |i|
  Name "gt gff3 (CDS check succ #{i})"
  Keywords "gt_gff3 cds_check"
  Test do
    run_test "#{$bin}gt gff3 #{$testdata}cds_check_succ_#{i}.gff3"
  end
end

Name "gt gff3 (CDS check fail 1)"
Keywords "gt_gff3 cds_check"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}cds_check_fail_1.gff3", :retval => 1
  grep last_stderr, /has the wrong phase 1 \(should be 0\)/
end

Name "gt gff3 (CDS check fail 1, -tidy)"
Keywords "gt_gff3 cds_check"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}cds_check_fail_1.gff3"
  run "diff #{last_stdout} #{$testdata}cds_check_succ_1.gff3"
end

Name "gt gff3 (CDS check fail 2)"
Keywords "gt_gff3 cds_check"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}cds_check_fail_2.gff3", :retval => 1
  grep last_stderr, /has the wrong phase 2 \(should be 1\)/
end

Name "gt gff3 (CDS check fail 2, -tidy)"
Keywords "gt_gff3 cds_check"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}cds_check_fail_2.gff3"
  run "diff #{last_stdout} #{$testdata}cds_check_succ_5.gff3"
end

Name "gt gff3 (CDS check fail 3)"
Keywords "gt_gff3 cds_check"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}cds_check_fail_3.gff3", :retval => 1
  grep last_stderr, /has the wrong phase 0 \(should be 2\)/
end

Name "gt gff3 (CDS check fail 3, -tidy)"
Keywords "gt_gff3 cds_check"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}cds_check_fail_3.gff3"
  run "diff #{last_stdout} #{$testdata}cds_check_succ_9.gff3"
end

Name "gt gff3 (CDS check fail 4)"
Keywords "gt_gff3 cds_check"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}cds_check_fail_4.gff3", :retval => 1
  grep last_stderr, /has the wrong phase 0 \(should be 1\)/
end

Name "gt gff3 (CDS check fail 4, -tidy)"
Keywords "gt_gff3 cds_check"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}cds_check_fail_4.gff3"
  run "diff #{last_stdout} #{$testdata}cds_check_succ_12.gff3"
end

Name "gt gff3 (-addids no)"
Keywords "gt_gff3 addids"
Test do
  run_test "#{$bin}gt gff3 -addids no #{$testdata}standard_gene_simple.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_simple.gff3"
end

Name "gt gff3 lone node with undefined range"
Keywords "gt_gff3 undefinedrange"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_undefined_range.gff3", \
           :retval => 1
  grep last_stderr, /could not parse number '.'/
end

Name "gt gff3 lone node with undefined range (-tidy)"
Keywords "gt_gff3 undefinedrange"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}gt_gff3_undefined_range.gff3"
  grep last_stderr, /has undefined range, discarding/
  run "diff #{last_stdout} #{$testdata}gt_gff3_undefined_range_tidy.gff3"
end

Name "gt gff3 parent node with undefined range"
Keywords "gt_gff3 undefinedrange"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}gt_gff3_undefined_range_parent.gff3", \
           :retval => 1
  grep last_stderr, /could not parse number '.'/
end

Name "gt gff3 parent node with undefined range (-tidy)"
Keywords "gt_gff3 undefinedrange"
Test do
  run_test "#{$bin}gt gff3 -tidy " + \
           "#{$testdata}gt_gff3_undefined_range_parent.gff3", :retval => 1
  grep last_stderr, /has undefined range, discarding/
  grep last_stderr, "Parent .* on line 4 .* was not defined"
end

Name "gt gff3 self-referential feature node"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}self_referential.gff3", :retval => 1
  grep last_stderr, /self-referential/
end

Name "gt gff3 reverse feature order"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}reverse_feature_order.gff3"
  run "diff #{last_stdout} #{$testdata}reverse_feature_order.out"
end

Name "gt gff3 reverse feature order (-strict)"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -strict #{$testdata}reverse_feature_order.gff3", :retval => 1)
  grep last_stderr, "was not previously defined"
end

Name "gt gff3 reverse feature order, multiple parents"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}reverse_feature_order_multiple_parents.gff3"
  run "diff #{last_stdout} #{$testdata}reverse_feature_order_multiple_parents.out"
end

Name "gt gff3 reverse feature order, multiple parents (-strict)"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -strict #{$testdata}reverse_feature_order_multiple_parents.gff3", :retval => 1)
  grep last_stderr, "was not previously defined"
end

Name "gt gff3 reverse feature order, multi-level orphans"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}reverse_standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt gff3 reverse feature order, multi-level orphans (-strict)"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 -strict #{$testdata}reverse_standard_gene_as_tree.gff3", :retval => 1)
  grep last_stderr, "was not previously defined"
end

Name "gt gff3 simple orphan"
Keywords "gt_gff3"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}simple_orphan.gff3", :retval => 1)
  grep last_stderr, "Parent .* was not defined"
end

Name "gt gff3 terminator separation"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}terminator_separation.gff3", :retval => 1
  grep last_stderr, "Parent .* was not defined"
end

Name "gt gff3 terminator separation (-checkids)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -checkids #{$testdata}terminator_separation.gff3", :retval => 1
  grep last_stderr, "the child with Parent .* is separated from its corresponding Parent"
end

Name "gt gff3 CDS feature with multiple (incompatible) parents"
Keywords "gt_gff3 "
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}cds_feature_with_multiple_parents.gff3"
  grep last_stderr, "has multiple parents which require different phases"
end

Name "gt gff3 empty file"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}empty_file", :retval => 1
  grep last_stderr, "is empty"
end

Name "gt gff3 header file"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}header.gff3"
  run "diff #{last_stdout} #{$testdata}header.gff3"
end

Name "gt gff3 header 3.1.21 file"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}header_3_1_21.gff3"
  run "diff #{last_stdout} #{$testdata}header.gff3"
end

Name "gt gff3 fasta sequence file"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}fasta_seq.gff3"
end

Name "gt gff3 multiple header lines"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}multiple_header_lines.gff3", :retval => 1
  grep last_stderr, "illegal GFF version pragma"
end

Name "gt gff3 multiple header lines (-tidy)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}multiple_header_lines.gff3"
  grep last_stderr, "skipping illegal GFF version pragma"
end

Name "gt gff3 meta directives"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}meta_directives.gff3"
  grep last_stderr, ".*", true
  run "diff #{last_stdout} #{$testdata}meta_directives.gff3"
end

Name "gt gff3 unknown meta directive"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}unknown_meta_directive.gff3"
  grep last_stderr, "unknown meta-directive encountered in line"
  run "diff #{last_stdout} #{$testdata}unknown_meta_directive.gff3"
end

Name "gt gff3 simple cycle"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}cycle_simple.gff3", :retval => 1
  grep last_stderr, "would cause a cycle"
end

Name "gt gff3 simple cycle (-strict)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -strict #{$testdata}cycle_simple.gff3", :retval => 1
  grep last_stderr, "was not previously defined"
end

Name "gt gff3 orphaned parent"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}orphaned_parent.gff3", :retval => 1
  grep last_stderr, "was not defined"
end

Name "gt gff3 uppercase attributes"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}uppercase_attributes.gff3"
end

Name "gt gff3 illegal uppercase attribute"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}illegal_uppercase_attribute.gff3", :retval => 1
  grep last_stderr, "illegal uppercase attribute"
end

Name "gt gff3 illegal uppercase attribute (-tidy)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 -tidy #{$testdata}illegal_uppercase_attribute.gff3"
  grep last_stderr, "illegal uppercase attribute"
end

Name "gt gff3 illegal Is_circular value"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}illegal_is_circular_value.gff3", :retval => 1
  grep last_stderr, " of Is_circular attribute .* does not equal "
end

Name "gt gff3 Is_circular example"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}is_circular_example.gff3"
  run "diff #{last_stdout} #{$testdata}is_circular_example_with_sequence_region.gff3"
end

Name "gt gff3 Is_circular example (with sequence-region)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}is_circular_example_with_sequence_region.gff3"
end

Name "gt gff3 cds_feature_with_multiple_parents.gff3"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}cds_feature_with_multiple_parents_tidied.gff3"
  run_test "#{$bin}gt gff3 -tidy #{$testdata}cds_feature_with_multiple_parents.gff3"
  run "diff #{last_stdout} #{$testdata}cds_feature_with_multiple_parents_tidied.gff3"
end

Name "gt gff3 cds_with_multiple_parents_1.gff3"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}cds_with_multiple_parents_1_tidied.gff3"
  run_test "#{$bin}gt gff3 -tidy #{$testdata}cds_with_multiple_parents_1.gff3"
  run "diff #{last_stdout} #{$testdata}cds_with_multiple_parents_1_tidied.gff3"
end

Name "gt gff3 cds_with_multiple_parents_2.gff3"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}cds_with_multiple_parents_2_tidied.gff3"
  run_test "#{$bin}gt gff3 -tidy #{$testdata}cds_with_multiple_parents_2.gff3"
  run "diff #{last_stdout} #{$testdata}cds_with_multiple_parents_2_tidied.gff3"
end

Name "gt gff3 MD5 seqid (missing seqid)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}md5_seqid_missing_seqid.gff3",
           :retval => 1
  grep last_stderr, "has missing sequence ID after separator"
end

Name "gt gff3 MD5 seqid (too short)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}md5_seqid_too_short.gff3",
           :retval => 1
  grep last_stderr, "too short"
end

Name "gt gff3 MD5 seqid (wrong separator)"
Keywords "gt_gff3"
Test do
  run_test "#{$bin}gt gff3 #{$testdata}md5_seqid_wrong_separator.gff3",
           :retval => 1
  grep last_stderr, "wrong separator"
end

def large_gff3_test(name, file)
  Name "gt gff3 #{name}"
  Keywords "gt_gff3 large_gff3"
  Test do
    run_test("#{$bin}gt gff3 #{$gttestdata}gff3/#{file}", :maxtime => 320)
  end

  Name "gt gff3 #{name} (-sort)"
  Keywords "gt_gff3 large_gff3"
  Test do
    run_test("#{$bin}gt gff3 -sort -width 80 #{$gttestdata}gff3/#{file}",
             :maxtime => 320)
    run      "diff #{last_stdout} #{$gttestdata}gff3/#{file}.sorted"
  end

  Name "gt gff3 #{name} (sorted)"
  Keywords "gt_gff3 large_gff3"
  Test do
    run_test("#{$bin}gt gff3 -width 80 #{$gttestdata}gff3/#{file}.sorted",
             :maxtime => 320)
    run      "diff #{last_stdout} #{$gttestdata}gff3/#{file}.sorted"
  end
end

if $gttestdata then
  large_gff3_test("maker", "maker/maker.gff3")
  large_gff3_test("Saccharomyces cerevisiae", "sgd/saccharomyces_cerevisiae.gff")
  large_gff3_test("Drosophila melanogaster",
                  "Drosophila_melanogaster.BDGP5.4.50.gff3")

  Name "gt gff3 TAIR10"
  Keywords "gt_gff3"
  Test do
    run_test "#{$bin}gt gff3 -tidy -sort " +
             "#{$gttestdata}gff3testruns/TAIR10_GFF3_genes.gff",
             :maxtime => 3600
    run      "diff #{last_stdout} #{$gttestdata}gff3testruns/tair.gff3"
  end

  Name "gt gff3 Fruitfly ESTs"
  Keywords "gt_gff3"
  Test do
    run_test "#{$bin}gt gff3 -sort #{$gttestdata}gff3testruns/EST.gff",
             :maxtime => 3600
    run      "diff #{last_stdout} #{$gttestdata}gff3testruns/fruitfly.gff3"
  end

  Name "gt gff3 Homo sapiens ENSEMBL"
  Keywords "gt_gff3"
  Test do
    run_test "#{$bin}gt gff3 -sort " +
             "#{$gttestdata}gff3testruns/Homo_sapiens_ENSEMBL.gff3",
             :maxtime => 3600
    run      "diff #{last_stdout} #{$gttestdata}gff3testruns/ensembl.gff3"
  end
end
genometools-1.5.1/testsuite/gt_gff3validator_include.rb000066400000000000000000000020311211610345200233460ustar00rootroot00000000000000# test OBO file parsing
obo_gff3_file="#{$testdata}standard_gene_as_tree.gff3"

Name "gt gff3validator valid file"
Keywords "gt_gff3validator"
Test do
  run_test "#{$bin}gt gff3validator #{obo_gff3_file}"
  grep last_stdout, "input is valid GFF3"
end

Name "gt gff3validator -typecheck sofa.obo"
Keywords "gt_gff3validator typecheck"
Test do
  run_test "#{$bin}gt gff3validator -typecheck sofa #{obo_gff3_file}"
  grep last_stdout, "input is valid GFF3"
end

Name "gt gff3validator -typecheck so.obo"
Keywords "gt_gff3validator typecheck"
Test do
  run_test "#{$bin}gt gff3validator -typecheck so #{obo_gff3_file}"
  grep last_stdout, "input is valid GFF3"
end

Name "gt gff3validator -typecheck so-xp.obo"
Keywords "gt_gff3validator typecheck"
Test do
  run_test "#{$bin}gt gff3validator -typecheck so-xp #{obo_gff3_file}"
  grep last_stdout, "input is valid GFF3"
end

Name "gt gff3validator corrupt file"
Keywords "gt_gff3validator"
Test do
  run_test("#{$bin}gt gff3 #{$testdata}corrupt.gff3", :retval => 1)
  grep last_stderr, "strand 'X'"
end
genometools-1.5.1/testsuite/gt_gtf_to_gff3_include.rb000066400000000000000000000017231211610345200230110ustar00rootroot00000000000000Name "gt gtf_to_gff3 test"
Keywords "gt_gtf_to_gff3"
Test do
  run_test "#{$bin}gt gtf_to_gff3 #{$testdata}gt_gtf_to_gff3_test.gtf"
  run "diff #{last_stdout} #{$testdata}gt_gtf_to_gff3_test.gff3"
end

if $gttestdata then
  Name "gt gtf_to_gff3 test"
  Keywords "gt_gtf_to_gff3 large_gtf"
  Test do
  run "#{$bin}gt gff3 -sort #{$gttestdata}gff3/Drosophila_melanogaster.BDGP5.4.50.gff3 " +
      "> ref_sorted.gff3"
  run_test("#{$bin}gt gtf_to_gff3 " +
           "#{$gttestdata}gtf/Drosophila_melanogaster.BDGP5.4.50.gtf " +
           "| #{$bin}gt gff3 -sort ", :maxtime => 3600)
  run "diff #{last_stdout} " +
      "ref_sorted.gff3"
  end

  Name "gt gtf_to_gff3 test (GENCODE)"
  Keywords "gt_gtf_to_gff3 large_gtf"
  Test do
  run_test "#{$bin}gt gtf_to_gff3 " +
           "#{$gttestdata}gtf/gencode.v11.annotation.gtf.gz " +
           "| #{$bin}gt gff3 -sort -tidy", :maxtime => 3600
  run "diff #{last_stdout} #{$gttestdata}gff3/gencode.v11.annotation.gff3"
  end
end
genometools-1.5.1/testsuite/gt_hop_include.rb000066400000000000000000000126251211610345200214130ustar00rootroot00000000000000Name "gt hop: bam == sam"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/genome.fas"
  run_test "#{$bin}gt hop -ref genome.fas "+
           "-map #{$testdata}hop/map.sam -sam -aggressive "+
           "-reads #{$testdata}hop/reads.fastq"
  run "mv hop_reads.fastq using_sam.fastq"
  run_test "#{$bin}gt hop -ref genome.fas "+
           "-map #{$testdata}hop/map.bam -aggressive "+
           "-reads #{$testdata}hop/reads.fastq"
  run "diff using_sam.fastq hop_reads.fastq"
end

Name "gt hop: -aggressive"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/genome.fas"
  run_test "#{$bin}gt hop -ref genome.fas "+
           "-map #{$testdata}hop/map.bam -aggressive "+
           "-reads #{$testdata}hop/reads.fastq"
  run "diff #{$testdata}hop/hop_aggressive.fastq hop_reads.fastq"
end

Name "gt hop: -moderate"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/genome.fas"
  run_test "#{$bin}gt hop -ref genome.fas "+
           "-map #{$testdata}hop/map.bam -moderate "+
           "-reads #{$testdata}hop/reads.fastq"
  run "diff #{$testdata}hop/hop_moderate.fastq hop_reads.fastq"
end

Name "gt hop: -conservative"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/genome.fas"
  run_test "#{$bin}gt hop -ref genome.fas "+
           "-map #{$testdata}hop/map.bam -conservative "+
           "-reads #{$testdata}hop/reads.fastq"
  run "diff #{$testdata}hop/hop_conservative.fastq hop_reads.fastq"
end

Name "gt hop: -expert -hmin 4"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/genome.fas"
  run_test "#{$bin}gt hop -ref genome.fas "+
           "-map #{$testdata}hop/map.bam -expert -hmin 4 "+
           "-reads #{$testdata}hop/reads.fastq"
  run "diff #{$testdata}hop/hop_hmin4.fastq hop_reads.fastq"
end

Name "gt hop: -expert -read-hmin 3"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/genome.fas"
  run_test "#{$bin}gt hop -ref genome.fas "+
           "-map #{$testdata}hop/map.bam -expert -read-hmin 3 "+
           "-reads #{$testdata}hop/reads.fastq"
  run "diff #{$testdata}hop/hop_read-hmin3.fastq hop_reads.fastq"
end

Name "gt hop: -reads with 2 input files"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/genome.fas"
  run_test "#{$bin}gt hop -ref genome.fas "+
           "-map #{$testdata}hop/map2.bam -aggressive "+
           "-reads #{$testdata}hop/10reads.fastq "+
           "#{$testdata}hop/other10reads.fastq"
  run "diff #{$testdata}hop/hop_10reads.fastq hop_10reads.fastq"
  run "diff #{$testdata}hop/hop_other10reads.fastq hop_other10reads.fastq"
end

Name "gt hop: -expert -refmin"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/smallgenome.fas"
  run_test "#{$bin}gt hop -stats -ref smallgenome.fas "+
           "-map #{$testdata}hop/sg_map.bam -v -expert -refmin 0.25 "+
           "-reads #{$testdata}hop/sg_reads.fastq"
  grep(last_stdout, /and not edited:\s+4/)
  grep(last_stdout, /and edited:\s+0/)
  run_test "#{$bin}gt hop -stats -ref smallgenome.fas "+
           "-map #{$testdata}hop/sg_map.bam -v -expert -refmin 0.24 "+
           "-reads #{$testdata}hop/sg_reads.fastq"
  grep(last_stdout, /and not edited:\s+0/)
  grep(last_stdout, /and edited:\s+4/)
end

Name "gt hop: -expert -altmax"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/smallgenome.fas"
  run_test "#{$bin}gt hop -stats -ref smallgenome.fas "+
           "-map #{$testdata}hop/sg_map.bam -v -expert -altmax 0.49 "+
           "-reads #{$testdata}hop/sg_reads.fastq"
  grep(last_stdout, /and not edited:\s+4/)
  grep(last_stdout, /and edited:\s+0/)
  run_test "#{$bin}gt hop -stats -ref smallgenome.fas "+
           "-map #{$testdata}hop/sg_map.bam -v -expert -altmax 0.50 "+
           "-reads #{$testdata}hop/sg_reads.fastq"
  grep(last_stdout, /and not edited:\s+0/)
  grep(last_stdout, /and edited:\s+4/)
end

Name "gt hop: -expert -covmin"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/smallgenome.fas"
  run_test "#{$bin}gt hop -stats -ref smallgenome.fas "+
           "-map #{$testdata}hop/sg_map.bam -v -expert -covmin 6 "+
           "-reads #{$testdata}hop/sg_reads.fastq"
  grep(last_stdout, /and not edited:\s+4/)
  grep(last_stdout, /and edited:\s+0/)
  run_test "#{$bin}gt hop -stats -ref smallgenome.fas "+
           "-map #{$testdata}hop/sg_map.bam -v -expert -covmin 4 "+
           "-reads #{$testdata}hop/sg_reads.fastq"
  grep(last_stdout, /and not edited:\s+0/)
  grep(last_stdout, /and edited:\s+4/)
end

Name "gt hop: -expert -mapqmin"
Keywords "gt_hop"
Test do
  run "#{$bin}gt encseq encode #{$testdata}hop/smallgenome.fas"
  run_test "#{$bin}gt hop -stats -ref smallgenome.fas -sam "+
           "-map #{$testdata}hop/sg_map_q.sam -v -expert -mapqmin 0 "+
           "-reads #{$testdata}hop/sg_reads.fastq"
  grep(last_stdout, /and not edited:\s+0/)
  grep(last_stdout, /and edited:\s+4/)
  run_test "#{$bin}gt hop -stats -ref smallgenome.fas -sam "+
           "-map #{$testdata}hop/sg_map_q.sam -v -expert -mapqmin 10 "+
           "-reads #{$testdata}hop/sg_reads.fastq"
  grep(last_stdout, /and not edited:\s+1/)
  grep(last_stdout, /and edited:\s+3/)
  run_test "#{$bin}gt hop -stats -ref smallgenome.fas -sam "+
           "-map #{$testdata}hop/sg_map_q.sam -v -expert -mapqmin 21 "+
           "-reads #{$testdata}hop/sg_reads.fastq"
  grep(last_stdout, /and not edited:\s+2/)
  grep(last_stdout, /and edited:\s+2/)
end
genometools-1.5.1/testsuite/gt_id_to_md5_include.rb000066400000000000000000000011501211610345200224570ustar00rootroot00000000000000Name "gt id_to_md5 (U89959_sas.gff3)"
Keywords "gt_id_to_md5"
Test do
  run_test "#{$bin}gt id_to_md5 -seqfiles " +
           "#{$testdata}U89959_genomic.fas #{$testdata}U89959_ests.fas " +
           "-matchdesc #{$testdata}U89959_sas.gff3"
  run "diff #{last_stdout} #{$testdata}U89959_sas.gff3md5"
end

Name "gt id_to_md5 (U89959_csas.gff3)"
Keywords "gt_id_to_md5"
Test do
  run_test "#{$bin}gt id_to_md5 -seqfiles " +
           "#{$testdata}U89959_genomic.fas #{$testdata}U89959_ests.fas " +
           "-matchdesc #{$testdata}U89959_csas.gff3"
  run "diff #{last_stdout} #{$testdata}U89959_csas.gff3md5"
end
genometools-1.5.1/testsuite/gt_idxsearch_include.rb000066400000000000000000000222621211610345200225750ustar00rootroot00000000000000allfiles = ["Atinsert.fna",
            "Duplicate.fna",
            "Random-Small.fna",
            "Random.fna",
            "Random159.fna",
            "Random160.fna",
            "RandomN.fna",
            "TTT-small.fna",
            "trna_glutamine.fna"]

repfindtestfiles=["Duplicate.fna",
                  "Wildcards.fna",
                  "hs5hcmvcg.fna",
                  "humhbb.fna",
                  "mpomtcg.fna",
                  "at1MB",
                  "ychrIII.fna"]

def makegreedyfwdmatcall(queryfile,indexarg,ms)
  prog=""
  if ms
    prog="#{$bin}gt matstat -verify"
  else
    prog="#{$bin}gt uniquesub"
  end
  constantargs="-min 1 -max 20 -query #{queryfile} #{indexarg}"
  return "#{prog} -output querypos #{constantargs}"
end

def checkgreedyfwdmat(queryfile,ms)
  run_test(makegreedyfwdmatcall(queryfile,"-fmi fmi",ms), :maxtime => 1200)
  run "mv #{last_stdout} tmp.fmi"
  run_test(makegreedyfwdmatcall(queryfile,"-esa sfx",ms), :maxtime => 1200)
  run "mv #{last_stdout} tmp.esa"
  run "diff tmp.esa tmp.fmi"
  run_test(makegreedyfwdmatcall(queryfile,"-pck pck",ms), :maxtime => 1200)
  run "mv #{last_stdout} tmp.pck"
  run "diff tmp.pck tmp.fmi"
end

def checktagerator(queryfile,ms)
  run "#{$bin}gt shredder -minlength 12 -maxlength 15 #{queryfile} | " +
      "#{$bin}gt seqfilter -minlength 12 - | " +
      "sed -e \'s/^>.*/>/\' > patternfile"
  if File.size("patternfile") > 0
    run_test("#{$bin}gt tagerator -rw -cmp -e 0 -esa sfx -q patternfile",
             :maxtime => 240)
    run_test("#{$bin}gt tagerator -rw -cmp -e 1 -esa sfx -q patternfile " +
             "-withwildcards",:maxtime => 240)
    run_test("#{$bin}gt tagerator -rw -cmp -e 2 -esa sfx -q patternfile " +
             "-withwildcards",:maxtime => 240)
    run_test("#{$bin}gt tagerator -rw -cmp -esa sfx -q patternfile " +
             " -maxocc 10",
             :maxtime => 240)
    run_test "#{$bin}gt prebwt -maxdepth 4 -pck pck", :maxtime => 180
    run_test("#{$bin}gt tagerator -rw -cmp -e 0 -pck pck -q patternfile",
             :maxtime => 240)
    run_test("#{$bin}gt tagerator -rw -cmp -e 1 -pck pck -q patternfile",
             :maxtime => 240)
    run_test("#{$bin}gt tagerator -rw -cmp -e 2 -pck pck -q patternfile",
             :maxtime => 240)
    run_test("#{$bin}gt tagerator -rw -cmp -pck pck -q patternfile " +
             "-maxocc 10",
             :maxtime => 300)
  end
end

def createandcheckgreedyfwdmat(reffile,queryfile)
  run "#{$scriptsdir}/runmkfm.sh #{$bin}gt 0 . fmi #{reffile}",
      :maxtime => 100
  run "#{$bin}gt suffixerator -indexname sfx -tis -suf -ssp -dna -v " +
           "-db #{reffile}"
  run "#{$bin}gt packedindex mkindex -tis -ssp -indexname pck -db #{reffile} " +
      "-sprank -dna -pl -bsize 10 -locfreq 32 -dir rev", :maxtime => 180
  run_test "#{$bin}gt prebwt -maxdepth 4 -pck pck", :maxtime => 180
  checkgreedyfwdmat(queryfile,false)
  checkgreedyfwdmat(queryfile,true)
end

def addfilepath(filename)
  if filename == 'Duplicate.fna' or filename == 'at1MB'
    return "#{$testdata}#{filename}"
  else
    return "#{$gttestdata}DNA-mix/Grumbach.fna/#{filename}"
  end
end

def determineminlength(reffile)
  if reffile == 'at1MB'
    return 22
  else
    return 14
  end
end

def checkrepfind(reffile)
  reffilepath=addfilepath(reffile)
  run_test("#{$bin}gt suffixerator -algbds 3 31 80 -db " +
           "#{reffilepath} -indexname sfxidx -dna -suf -tis -lcp -ssp -pl",
           :maxtime => 320)
  minlength = determineminlength(reffile)
  run_test("#{$bin}gt repfind -l #{minlength} -ii sfxidx", :maxtime => 600)
  resultfile="#{$gttestdata}repfind-result/#{reffile}.result"
  run "cmp -s #{last_stdout} #{resultfile}"
  run_test("#{$bin}gt repfind -l #{minlength} -r -ii sfxidx", :maxtime => 600)
  resultfile="#{$gttestdata}repfind-result/#{reffile}-r.result"
  run "cmp -s #{last_stdout} #{resultfile}"
end

def checkrepfindwithquery(reffile,queryfile)
  reffilepath=addfilepath(reffile)
  queryfilepath=addfilepath(queryfile)
  idxname=reffile + "-idx"
  run_test "#{$bin}gt suffixerator -algbds 3 31 80 -db " +
           "#{reffilepath} -indexname #{idxname} -dna -suf -tis -lcp -ssp -pl"
  run_test("#{$bin}gt repfind -l 15 -ii #{idxname} -q #{queryfilepath}",
           :maxtime => 600)
  # run "sort #{last_stdout}"
  #run "/Users/kurtz/bin-ops/i686-apple-darwin/mkvtree.x -indexname mkv-idx " +
  #    "-allout -v -pl -dna -db #{reffilepath}"
  #run "/Users/kurtz/bin-ops/i686-apple-darwin/vmatch-mini.x 15 mkv-idx " +
  #    "#{queryfilepath}"
  #run "sed -e '/^#/d' #{last_stdout} | sort"
  # run "#{$scriptsdir}repfind-cmp.rb #{last_stdout} #{$gttestdata}repfind-result/#{reffile}-#{queryfile}.result"
  run "cmp -s #{last_stdout} #{$gttestdata}repfind-result/#{reffile}-#{queryfile}.result"
end

Name "gt paircmp"
Keywords "gt_paircmp"
Test do
  run_test "#{$bin}gt dev paircmp -a ac 11" # mv to idx
end

Name "gt patternmatch"
Keywords "gt_patternmatch"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Atinsert.fna " +
           "-indexname sfx -dna -bck -suf -tis -pl"
  run_test "#{$bin}gt dev patternmatch -samples 10000 -minpl 10 -maxpl 15 " +
           " -bck -imm -ii sfx"
  run_test "#{$bin}gt dev patternmatch -samples 10000 -ii sfx"
end

Name "gt repfind small"
Keywords "gt_repfind"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Atinsert.fna " +
           "-indexname sfx -dna -tis -suf -lcp -ssp -pl"
  run_test "#{$bin}gt repfind -l 8 -ii sfx"
  run "grep -v '^#' #{last_stdout}"
  run "diff -w #{last_stdout} #{$testdata}repfind-8-Atinsert.txt"
  run_test "#{$bin}gt repfind -scan -l 8 -ii sfx"
  run "grep -v '^#' #{last_stdout}"
  run "diff -w #{last_stdout} #{$testdata}repfind-8-Atinsert.txt"
  run_test "#{$bin}gt repfind -samples 40 -l 6 -ii sfx",:maxtime => 600
end

if $gttestdata then
  Name "gt repfind extend at1MB"
  Keywords "gt_repfind extend"
  Test do
    run_test "#{$bin}gt suffixerator -db #{$testdata}at1MB " +
             "-indexname sfx -dna -tis -suf -lcp"
    run_test "#{$bin}gt repfind -l 20 -extend -ii sfx"
    run "diff #{last_stdout} #{$testdata}repfind-20-extend.txt"
    run_test "#{$bin}gt repfind -l 20 -extend -ii sfx -q " +
             "#{$testdata}/U89959_genomic.fas"
    run "diff #{last_stdout} #{$testdata}repfind-20-query-extend.txt"
  end
  repfindtestfiles.each do |reffile|
    Name "gt repfind #{reffile}"
    Keywords "gt_repfind gttestdata"
    Test do
      checkrepfind(reffile)
    end
    repfindtestfiles.each do |queryfile|
      if reffile != queryfile
        Name "gt repfind #{reffile} versus #{queryfile}"
        Keywords "gt_repfind gttestdata"
        Test do
          checkrepfindwithquery(reffile,queryfile)
        end
      end
    end
  end
end

allfiles.each do |reffile|
  allfiles.each do |queryfile|
    if queryfile != reffile
      Name "gt greedyfwdmat #{reffile} #{queryfile}"
      Keywords "gt_greedyfwdmat small"
      Test do
        createandcheckgreedyfwdmat("#{$testdata}#{reffile}",
                                   "#{$testdata}#{queryfile}")
        checktagerator("#{$testdata}#{reffile}",
                       "#{$testdata}#{queryfile}")
        run "rm -f sfx.* fmi.* pck.*"
      end
    end
  end
end

allfiles.each do |reffile|
  allfiles.each do |queryfile|
    if queryfile != reffile
      Name "gt idxlocali #{reffile} #{queryfile}"
      Keywords "gt_idxlocali"
      Test do
        run("#{$bin}gt packedindex mkindex -ssp -tis -indexname pck -db " +
            "#{$testdata}#{reffile} -sprank -dna -pl -bsize 10 " +
            "-locfreq 32 -dir rev",
            :maxtime => 180)
        run_test("#{$bin}gt dev idxlocali -s -th 7 -pck pck " +
                 "-q #{$testdata}#{queryfile}",
                 :maxtime => 180)
        run_test("#{$bin}gt dev idxlocali -s -th 7 -pck pck -online " +
                 "-q #{$testdata}#{queryfile}",
                 :maxtime => 180)
        run_test "#{$bin}gt suffixerator -indexname sfx -ssp -tis -suf -dna " +
                 "-v -db #{$testdata}#{reffile}"
        run_test("#{$bin}gt dev idxlocali -s -th 7 -esa sfx " +
                 "-q #{$testdata}#{queryfile}",
                 :maxtime => 180)
        run_test("#{$bin}gt dev idxlocali -s -th 7 -esa sfx -online " +
                 "-q #{$testdata}#{queryfile}",
                 :maxtime => 180)
      end
    end
  end
end

Name "gt uniquesub"
Keywords "gt_uniquesub"
Test do
  run "#{$scriptsdir}runmkfm.sh #{$bin}gt 1 . Combined.fna #{$testdata}at1MB"
  run_test "#{$bin}gt uniquesub -output sequence querypos -min 10 " +
           "-max 20 -fmi Combined.fna -query #{$testdata}U89959_genomic.fas", \
           :maxtime => 600
end

allfiles.each do |reffile|
  Name "gt packedindex #{reffile}"
  Keywords "gt_packedindex small"
  Test do
    run_test("#{$bin}gt packedindex mkindex -tis -ssp -indexname pck " +
             "-sprank -db #{$testdata}#{reffile} -dna -pl -bsize 10 " +
             " -locfreq 32 -dir rev",
             :maxtime => 1200)
  end
end

Name "gt matstat/uniquesub at1MB U8"
Keywords "gt_greedyfwdmat gt_matstat gt_uniquesub gttestdata"
Test do
  createandcheckgreedyfwdmat("#{$testdata}at1MB",
                             "#{$testdata}U89959_genomic.fas")
  run_test "#{$bin}gt tagerator -e 0 -q #{$testdata}corruptpatternfile.fna -pck",
           :retval => 1
  run "rm -f sfx.* fmi.* pck.*"
end
genometools-1.5.1/testsuite/gt_include.rb000066400000000000000000000002361211610345200205400ustar00rootroot00000000000000Name "gt -help"
Keywords "gt"
Test do
  run_test "#{$bin}gt -help"
end

Name "gt -noop"
Keywords "gt"
Test do
  run_test("#{$bin}gt -noop", :retval => 1)
end
genometools-1.5.1/testsuite/gt_interfeat_include.rb000066400000000000000000000002611211610345200225770ustar00rootroot00000000000000Name "gt interfeat test"
Keywords "gt_interfeat"
Test do
  run_test "#{$bin}gt interfeat #{$testdata}addintrons.gff3"
  run "diff #{last_stdout} #{$testdata}addintrons.out"
end
genometools-1.5.1/testsuite/gt_ltrdigest_include.rb000066400000000000000000000520171211610345200226250ustar00rootroot00000000000000# simple reverse complement
def revcomp(seq)
  seq.tr("aAcCgGtTnN","tTgGcCaSAnN").reverse
end

# simple DNA->AA translation
def translate_dna(sequence)
  genetic_code = {
  'ATA'=>'I', 'ATC'=>'I', 'ATT'=>'I', 'ATG'=>'M',
  'ACA'=>'T', 'ACC'=>'T', 'ACG'=>'T', 'ACT'=>'T',
  'AAC'=>'N', 'AAT'=>'N', 'AAA'=>'K', 'AAG'=>'K',
  'AGC'=>'S', 'AGT'=>'S', 'AGA'=>'R', 'AGG'=>'R',
  'CTA'=>'L', 'CTC'=>'L', 'CTG'=>'L', 'CTT'=>'L',
  'CCA'=>'P', 'CCC'=>'P', 'CCG'=>'P', 'CCT'=>'P',
  'CAC'=>'H', 'CAT'=>'H', 'CAA'=>'Q', 'CAG'=>'Q',
  'CGA'=>'R', 'CGC'=>'R', 'CGG'=>'R', 'CGT'=>'R',
  'GTA'=>'V', 'GTC'=>'V', 'GTG'=>'V', 'GTT'=>'V',
  'GCA'=>'A', 'GCC'=>'A', 'GCG'=>'A', 'GCT'=>'A',
  'GAC'=>'D', 'GAT'=>'D', 'GAA'=>'E', 'GAG'=>'E',
  'GGA'=>'G', 'GGC'=>'G', 'GGG'=>'G', 'GGT'=>'G',
  'TCA'=>'S', 'TCC'=>'S', 'TCG'=>'S', 'TCT'=>'S',
  'TTC'=>'F', 'TTT'=>'F', 'TTA'=>'L', 'TTG'=>'L',
  'TAC'=>'Y', 'TAT'=>'Y', 'TAA'=>'X', 'TAG'=>'X',
  'TGC'=>'C', 'TGT'=>'C', 'TGA'=>'X', 'TGG'=>'W',
  }
  proteinseq = ""
  (0..sequence.length).step(3) do |i|
    codon = sequence[i..i+2].upcase
    next if codon.length != 3
    if genetic_code.has_key?(codon) then
      proteinseq += genetic_code[codon]
    else
      raise "unknown codon '#{codon}'"
    end
  end
  proteinseq
end

# returns a hash indexed by element coordinates
# containing an array of DNA sequences (one per hit fragment)
def get_protdom_dna_seqs(gff3filename, chr)
  seqs = Hash.new
  File.open(gff3filename) do |file|
    mainstart, mainstop = 0, 0
    mainstrand = ''
    file.readlines.each do |ln|
      _, _, type, start, stop, _, strand = ln.split("\t")
      if type == "LTR_retrotransposon" then
        mainstart = start.to_i
        mainstop = stop.to_i
        mainstrand = strand
      elsif type == "protein_match" then
        run_test "#{$bin}gt extractseq -frompos " + \
                 "#{start} -topos " + \
                 "#{stop} " + \
                 "#{$gttestdata}ltrdigest/#{chr}_genomic_dmel_" + \
                 "RELEASE3-1.FASTA.gz > tmp.fas"
        outa = File.open("tmp.fas").read.split("\n")
        outa.shift
        if seqs[[mainstart, mainstop]].nil? then
          seqs[[mainstart, mainstop]] = []
        end
        out = outa.collect{|l| l.chomp.downcase}.join
        # we want to provide DNA sequences in reading direction
        if mainstrand == '-' then
          seqs[[mainstart, mainstop]].insert(0,(revcomp(out)))
        else
          seqs[[mainstart, mainstop]].push(out)
        end
      end
    end
  end
  seqs
end

# checks whether the sequences output by the LTRFileOutStream match those
# referenced in the GFF3 file
def check_ppt_pbs(gff3filename, chr)
  coords = {:ppt => {}, :pbs => {}}
  File.open(gff3filename) do |file|
    mainstart, mainstop = 0, 0
    file.readlines.each do |ln|
      _, _, type, start, stop = ln.split("\t")
      if type == "LTR_retrotransposon" then
        mainstart = start.to_i
        mainstop = stop.to_i
      elsif type == "RR_tract" then
        coords[:ppt][[mainstart,mainstop]] = [start.to_i, stop.to_i]
      elsif type == "primer_binding_site" then
        coords[:pbs][[mainstart,mainstop]] = [start.to_i, stop.to_i]
      end
    end
  end
  [:ppt,:pbs].each do |feat|
    File.open("result#{chr}_#{feat}.fas") do |file|
      (farr = file.read.split(">")).each do |fitem|
        seqa = fitem.split("\n")
        fline = seqa.shift
        next if fline.nil?
        if m = /_(\d+)_(\d+)$/.match(fline) then
          start, stop = m[1].to_i, m[2].to_i
          seq = seqa.collect{|l| l.chomp.downcase}.join
          run_test "#{$bin}gt extractseq -frompos " + \
                   "#{coords[feat][[start,stop]][0]} -topos " + \
                   "#{coords[feat][[start,stop]][1]} " + \
                   "#{$gttestdata}ltrdigest/#{chr}_genomic_dmel_" + \
                   "RELEASE3-1.FASTA.gz > tmp.fas"
          outa = File.open("tmp.fas").read.split("\n")
          outa.shift
          out = outa.collect{|l| l.chomp.downcase}.join
          unless out == seq or revcomp(out) == seq
            raise "sequence output and GFF3 coordinates do not match " + \
                  "(#{seq} != #{out}) for the #{feat} with coords " + \
                  "#{coords[feat][[start,stop]][0]}-" + \
                  "#{coords[feat][[start,stop]][1]}, neither does reverse " + \
                  "complement!"
          end
        end
      end
    end
  end
end

def load_seqfile(filename)
  contents = {}
  File.open(filename) do |file|
    (farr = file.read.split(">")).each do |fitem|
      seqa = fitem.split("\n")
      fline = seqa.shift
      next if fline.nil?
      if m = /_(\d+)_(\d+)$/.match(fline) then
        start, stop = m[1].to_i, m[2].to_i
        seq = seqa.collect{|l| l.chomp.downcase}.join
        contents[[start,stop]] = seq
      end
    end
  end
  contents
end

def check_amino_acid_output(gff3file, chr, pdoms)
  pdoms.each do |dom|
    dnaseqfile = load_seqfile("result#{chr}_pdom_#{dom}.fas")
    aaseqfile  = load_seqfile("result#{chr}_pdom_#{dom}_aa.fas")
    seqs = get_protdom_dna_seqs(gff3file, chr)
    if dnaseqfile.keys.length != aaseqfile.keys.length then
      raise "number of DNA and AA sequences is not equal"
    end
    if (dnaseqfile.keys - aaseqfile.keys).length != 0 then
      raise "DNA and AA sequence keys are not identical"
    end
    dnaseqfile.keys.each do |key|
      if seqs[key].nil? or seqs[key].length == 0 then
        raise "no protein domain sequences extracted from GFF3+sequence " + \
              "for element #{key.inspect} of chromosome #{chr}"
      elsif seqs[key].length == 1 then
        # hit was not fragmented, we can check directly
        # first, DNA sequence in the output file must match the GFF coordinates
        unless seqs[key][0] == dnaseqfile[key] then
          raise "DNA sequence from FASTA file \n" + \
                "'#{seqs[key][0]}' does " + \
                "not match the sequence referred to in the GFF3 file \n" + \
                "'#{dnaseqfile[key]}' in element " + \
                "#{key.inspect}"
        end
        # also, translated DNA seq must match the AA sequence from FASTA out
        if translate_dna(seqs[key][0]) != aaseqfile[key].upcase then
          raise "translated sequence \n'#{translate_dna(seqs[key][0])}' " + \
                "is not equal to sequence \n'#{aaseqfile[key].upcase}' in " + \
                "element #{key.inspect}"
        end
      else
        # number of fragments > 1
        # translate each fragment's DNA sequence separately and concatenate
        # into one => this must match the AA sequence output by LTRdigest
        translated_seqs = seqs[key].collect{|s| translate_dna(s)}.join
        if translated_seqs != aaseqfile[key].upcase then
          raise "sequence translated from #{seqs[key].length} frags\n" + \
                "'#{translated_seqs}' " + \
                "is not equal to sequence \n'#{aaseqfile[key].upcase}' in " + \
                "element #{key.inspect}"
        end
      end
    end
  end
end

if $gttestdata then
  Name "gt ltrdigest missing input GFF"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt ltrdigest #{$gttestdata}ltrdigest/2L_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
  end

  Name "gt ltrdigest unsorted input GFF"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt ltrdigest #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    grep(last_stderr, /is not sorted/)
  end

  Name "gt ltrdigest wrong sequence regions in input GFF"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt ltrdigest #{$gttestdata}ltrdigest/dmel_test_Run9_4_wrong_seqid.gff3 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    grep(last_stderr, "Feature 'LTR_retrotransposon1' on line 6 has invalid region identifier,must be 'seqX' with X being a sequence number, but was 'chr4'")
  end

  Name "gt ltrdigest missing input sequence"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt ltrdigest #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted", :retval => 1
    grep(last_stderr, /missing argument/)
  end

  Name "gt ltrdigest missing tRNA library but -trna given"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt ltrdigest -trnas -outfileprefix foo #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    grep(last_stderr, /missing argument to option/)
  end

  Name "gt ltrdigest corrupt tRNA library"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt ltrdigest -trnas #{$gttestdata}ltrdigest/corrupt_trna.fas #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    grep(last_stderr, /cannot guess file type of file/)
  end

  Name "gt ltrdigest tRNA implied options"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt ltrdigest -pbsalilen 10 20 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    grep(last_stderr, /option "-pbsalilen" requires option "-trnas"/)
    run_test "#{$bin}gt ltrdigest -pbsoffset 10 20 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    grep(last_stderr, /option "-pbsoffset" requires option "-trnas"/)
    run_test "#{$bin}gt ltrdigest -pbstrnaoffset 10 20 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    grep(last_stderr, /option "-pbstrnaoffset" requires option "-trnas"/)
    run_test "#{$bin}gt ltrdigest -trnas #{$gttestdata}ltrdigest/Dm-tRNAs-uniq.fa #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 0
    #run "diff #{last_stdout} #{$gttestdata}ltrdigest/4_ref_noHMM.gff3"
  end

  if $arguments["hmmer"] then
    Name "gt ltrdigest corrupt pHMM"
    Keywords "gt_ltrdigest"
    Test do
      run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
      run_test "#{$bin}gt ltrdigest -hmms #{$gttestdata}ltrdigest/corrupt.hmm -- #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
      grep(last_stderr, /Failed to open HMM file/)
    end

    Name "gt ltrdigest HMM list not properly closed (--)"
    Keywords "gt_ltrdigest"
    Test do
      run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
      run_test "#{$bin}gt ltrdigest -hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
      grep(last_stderr, /missing argument/)
    end

    Name "gt ltrdigest pHMM implied options"
    Keywords "gt_ltrdigest"
    Test do
      run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
      run_test "#{$bin}gt ltrdigest -pdomevalcutoff 0.2 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
      grep(last_stderr, /option "-pdomevalcutoff" requires option "-hmms"/)
      run_test "#{$bin}gt ltrdigest -pdomevalcutoff 2.2 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
      grep(last_stderr, /argument to option "-pdomevalcutoff" must be a floating point value <= 1.000000/)
    end

    Name "gt ltrdigest use of deprecated '-threads' switch"
    Keywords "gt_ltrdigest"
    Test do
      run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
      run_test "#{$bin}gt ltrdigest -threads 2 -outfileprefix result4 -trnas #{$gttestdata}ltrdigest/Dm-tRNAs-uniq.fa -hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm --  #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 0, :maxtime => 12000
      grep(last_stderr, /option is deprecated. Please use/)
    end
  end

  Name "gt ltrdigest PPT HMM parameters (background distribution)"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    # probabilities do not add up to 1, sum > 0
    run_test "#{$bin}gt ltrdigest -ppttprob 0.3 -pptaprob 0.3 -pptgprob 0.9 -pptcprob 0.2 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    # probability > 1
    run_test "#{$bin}gt ltrdigest -ppttprob 1.3 -pptaprob 0.3 -pptgprob 0.9 -pptcprob 0.2 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    # negative probability
    run_test "#{$bin}gt ltrdigest -ppttprob -0.3 -pptaprob 0.3 -pptgprob 0.9 -pptcprob 0.2 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    # probabilities do not add up to 1, sum < 0
    run_test "#{$bin}gt ltrdigest -ppttprob 0.1 -pptaprob 0.1 -pptgprob 0.2 -pptcprob 0.2 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    # positive test
    run_test "#{$bin}gt ltrdigest -ppttprob 0.25 -pptaprob 0.25 -pptgprob 0.25 -pptcprob 0.25 -trnas #{$gttestdata}ltrdigest/Dm-tRNAs-uniq.fa #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 0
    #run "diff #{last_stdout} #{$gttestdata}ltrdigest/4_ref_noHMM.gff3"
  end

  Name "gt ltrdigest PPT HMM parameters (U-box U frequency)"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt ltrdigest -pptuprob 1.3 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    run_test "#{$bin}gt ltrdigest -pptuprob 0.0 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 0
    run_test "#{$bin}gt ltrdigest -pptuprob 0.91 -trnas #{$gttestdata}ltrdigest/Dm-tRNAs-uniq.fa #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 0
    #run "diff #{last_stdout} #{$gttestdata}ltrdigest/4_ref_noHMM.gff3"
  end

  Name "gt ltrdigest PPT HMM parameters (PPT R/Y frequencies)"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt ltrdigest -pptrprob 1.3 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    run_test "#{$bin}gt ltrdigest -pptyprob 1.3 #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    run_test "#{$bin}gt ltrdigest -pptrprob 0.97 -pptyprob 0.03 -trnas #{$gttestdata}ltrdigest/Dm-tRNAs-uniq.fa #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 0
    #run "diff #{last_stdout} #{$gttestdata}ltrdigest/4_ref_noHMM.gff3"
    run_test "#{$bin}gt ltrdigest -pptrprob 0.6 -pptyprob 0.4 -trnas #{$gttestdata}ltrdigest/Dm-tRNAs-uniq.fa #{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 0
    #run "diff #{last_stdout} #{$gttestdata}ltrdigest/4_ref_noHMM.gff3", :retval => 1
  end

  Name "gt ltrdigest GFF and sequence do not match"
  Keywords "gt_ltrdigest"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt ltrdigest #{$gttestdata}ltrdigest/dmel_test_Run9_2L.gff3.sorted 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    grep(last_stderr, "exceeds sequence boundaries!")
  end

  # positive test for all D.mel chromosomes -> must match reference
  chromosomes_dmel = ["2L","2R","3L","3R","4","X"]
  chromosomes_dmel.each do |chr|
    if $arguments["hmmer"] then
      Name "gt ltrdigest D. melanogaster chromosome #{chr} basic test w/ RT"
      Keywords "gt_ltrdigest"
      Test do
        run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/#{chr}_genomic_dmel_RELEASE3-1.FASTA.gz", :maxtime => 600
        run_test "#{$bin}gt ltrdigest -outfileprefix result#{chr} -trnas #{$gttestdata}ltrdigest/Dm-tRNAs-uniq.fa -hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm --  #{$gttestdata}ltrdigest/dmel_test_Run9_#{chr}.gff3.sorted #{chr}_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 0, :maxtime => 12000
        check_ppt_pbs(last_stdout, chr)
        #run "diff #{last_stdout} #{$gttestdata}ltrdigest/#{chr}_ref.gff3"
      end
    else
      Name "gt ltrdigest D. mel. chromosome #{chr} basic test, no HMM"
      Keywords "gt_ltrdigest"
      Test do
        run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrdigest/#{chr}_genomic_dmel_RELEASE3-1.FASTA.gz", :maxtime => 600
        run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result#{chr} -trnas #{$gttestdata}ltrdigest/Dm-tRNAs-uniq.fa #{$gttestdata}ltrdigest/dmel_test_Run9_#{chr}.gff3.sorted #{chr}_genomic_dmel_RELEASE3-1.FASTA.gz",\
       :retval => 0, :maxtime => 700
        check_ppt_pbs(last_stdout, chr)
        #run "diff #{last_stdout} #{$gttestdata}ltrdigest/#{chr}_ref_noHMM.gff3"
      end
    end
  end

  chromosomes_dmel.each do |chr|
    if $arguments["hmmer"] then
      Name "gt ltrdigest D. melanogaster chromosome #{chr} AAseq out"
      Keywords "gt_ltrdigest aminoacidout"
      Test do
        run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v " + \
                 "-db #{$gttestdata}ltrdigest/#{chr}_genomic_dmel_RELEASE3-1.FASTA.gz", \
                 :maxtime => 600
        run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result#{chr} " + \
                 "-hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm " + \
                 "-aaout yes " + \
                 " #{$gttestdata}ltrdigest/dmel_test_Run9_#{chr}.gff3.sorted " + \
                 " #{chr}_genomic_dmel_RELEASE3-1.FASTA.gz", \
                 :retval => 0, :maxtime => 12000
        check_amino_acid_output(last_stdout, chr, ["RVT_1"])
      end
    end
  end

  if $arguments["hmmer"] then
    Name "gt ltrdigest -aliout"
    Keywords "gt_ltrdigest aminoacidout aliout"
    Test do
      run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v " + \
               "-db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz", \
               :maxtime => 600
      run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result4 " + \
               "-hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm -- " + \
               "#{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted " + \
               "4_genomic_dmel_RELEASE3-1.FASTA.gz", \
               :retval => 0, :maxtime => 12000
      if File.exists?("result4_pdom_RVT_1.ali") then
        raise TestFailed, "file \"result4_pdom_RVT_1.ali\" should not exist"
      end
      run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result4 " + \
               "-hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm " + \
               "-aliout yes " + \
               "#{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted " + \
               "4_genomic_dmel_RELEASE3-1.FASTA.gz", \
               :retval => 0, :maxtime => 12000
      if !File.exists?("result4_pdom_RVT_1.ali") then
        raise TestFailed, "file \"result4_pdom_RVT_1.ali\" does not exist"
      end
    end

    Name "gt ltrdigest -aaout"
    Keywords "gt_ltrdigest aminoacidout aaout"
    Test do
      run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v " + \
               "-db #{$gttestdata}ltrdigest/4_genomic_dmel_RELEASE3-1.FASTA.gz", \
               :maxtime => 600
      run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result4 " + \
               "-hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm -- " + \
               "#{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted " + \
               "4_genomic_dmel_RELEASE3-1.FASTA.gz", \
               :retval => 0, :maxtime => 12000
      if File.exists?("result4_pdom_RVT_1_aa.fas") then
        raise TestFailed, "file \"result4_pdom_RVT_1_aa.fas\" should not exist"
      end
      run_test "#{$bin}gt -j 2 ltrdigest -outfileprefix result4 " + \
               "-hmms #{$gttestdata}ltrdigest/hmms/RVT_1.hmm " + \
               "-aaout yes " + \
               "#{$gttestdata}ltrdigest/dmel_test_Run9_4.gff3.sorted " + \
               "4_genomic_dmel_RELEASE3-1.FASTA.gz", \
               :retval => 0, :maxtime => 12000
      if !File.exists?("result4_pdom_RVT_1_aa.fas") then
        raise TestFailed, "file \"result4_pdom_RVT_1_aa.fas\" does not exist"
      end
    end
  end
end
genometools-1.5.1/testsuite/gt_ltrharvest_include.rb000066400000000000000000000320021211610345200230120ustar00rootroot00000000000000require 'ltrun'
require 'ltresult'

chromosomes_dmel = ["2L","2R","3L","3R","4","X"]

runs_dmel = {}
runs_dmel["5-1"] = {:seed  => 30,
                  :minlenltr => 100,
                  :maxlenltr => 1000,
                  :mindistltr => 1000,
                  :maxdistltr => 15000,
                  :xdrop => 5,
                  :similar => 85}
runs_dmel["9"] = {:seed  => 76,
                  :minlenltr => 116,
                  :maxlenltr => 800,
                  :mindistltr => 2280,
                  :maxdistltr => 8773,
                  :xdrop => 7,
                  :similar => 91}
runs_dmel["10"] = {:seed  => 30,
                  :minlenltr => 100,
                  :maxlenltr => 200,
                  :mindistltr => 600,
                  :maxdistltr => 15000,
                  :xdrop => 5,
                  :similar => 85}
runs_dmel["11"] = {:seed  => 40,
                  :minlenltr => 1,
                  :maxlenltr => 1000,
                  :mindistltr => 1100,
                  :maxdistltr => 16000,
                  :xdrop => 7,
                  :similar => 80}
runs_dmel["12"] = {:seed  => 20,
                  :minlenltr => 100,
                  :maxlenltr => 1000,
                  :mindistltr => 1000,
                  :maxdistltr => 20000,
                  :xdrop => 7,
                  :similar => 70}

# Test Drosophila melanogaster predictions for the parameter sets as
# described in the LTRharvest paper and compare them with prior runs.
# This is used to ensure result integrity across LTRharvest versions.
if $gttestdata then

  scer_files = {"chr01"  => "chr01.19960731.fsa.gz",
                "chr02"  => "chr02.19970727.fsa.gz",
                "chr03"  => "chr03.19970727.fsa.gz",
                "chr04"  => "chr04.19960731.fsa.gz",
                "chr05"  => "chr05.19960731.fsa.gz",
                "chr06"  => "chr06.19960731.fsa.gz",
                "chr07"  => "chr07.19960731.fsa.gz",
                "chr08"  => "chr08.19960731.fsa.gz",
                "chr09"  => "chr09.19941210.fsa.gz",
                "chr10"  => "chr10.19970727.fsa.gz",
                "chr11"  => "chr11.19960731.fsa.gz",
                "chr12"  => "chr12.19970730.fsa.gz",
                "chr13"  => "chr13.19960731.fsa.gz",
                "chr14"  => "chr14.19970727.fsa.gz",
                "chr15"  => "chr15.19960731.fsa.gz",
                "chr16"  => "chr16.19960731.fsa.gz",
                "chrAll" => "chrAll_before-1997-10-01.fsa.gz"}

  scer_files.sort.each do |k, v|
    Name "gt ltrharvest test #{k} yeast"
    Keywords "gt_ltrharvest"
    Test do
      run_test "#{$bin}gt suffixerator -db #{$gttestdata}ltrharvest/s_cer/#{v}"\
             + " -dna -suf -lcp -tis -des -sds -ssp", :maxtime => 720
      run_test "#{$bin}gt ltrharvest -index #{v} -seed 100 -minlenltr 100"\
             + " -maxlenltr 1000 -mindistltr 1500 -maxdistltr 15000 -similar 80"\
             + " -mintsd 5 -maxtsd 20 -motif tgca -motifmis 0 -vic 60"\
             + " -overlaps best -xdrop 5 -mat 2 -mis -2 -ins -3 -del -3 -v"\
             + " -gff3 #{k}.gff3 -out #{k}.fas -outinner #{k}_inner.fas", \
             :maxtime => 25000
      if k != "chr11" then
        run "diff #{last_stdout} #{$gttestdata}ltrharvest/s_cer/#{k}.out"
        run "#{$bin}gt gff3 -sort #{$gttestdata}ltrharvest/s_cer/#{k}.gff3 > ref.gff3"
        run "#{$bin}gt gff3 -sort #{k}.gff3 > out.gff3"
        run "#{$bin}gt eval -ltr out.gff3 ref.gff3"
        grep(last_stdout, "LTR_retrotransposon sensitivity: 100.00%")
        grep(last_stdout, "LTR_retrotransposon specificity: 100.00%")
      end
      run "diff #{k}.fas #{$gttestdata}ltrharvest/s_cer/#{k}.fas"
      run "diff #{k}_inner.fas #{$gttestdata}ltrharvest/s_cer/#{k}_inner.fas"
    end

    Name "gt ltrharvest test #{k} yeast longoutput"
    Keywords "gt_ltrharvest"
    Test do
      run_test "#{$bin}gt suffixerator -db #{$gttestdata}ltrharvest/s_cer/#{v}"\
             + " -dna -suf -lcp -tis -des -sds -ssp", :maxtime => 540
      run_test "#{$bin}gt ltrharvest -longoutput -index #{v} -seed 100 "\
             + " -minlenltr 100 -maxlenltr 1000 -mindistltr 1500"\
             + " -maxdistltr 15000 -similar 80"\
             + " -mintsd 5 -maxtsd 20 -motif tgca -motifmis 0 -vic 60"\
             + " -overlaps best -xdrop 5 -mat 2 -mis -2 -ins -3 -del -3 -v"\
             + " -gff3 #{k}.gff3 -out #{k}.fas -outinner #{k}_inner.fas", \
             :maxtime => 7200
      if k != "chr11" then
        run "diff #{last_stdout} #{$gttestdata}ltrharvest/s_cer/#{k}_longoutput.out"
        run "#{$bin}gt gff3 -sort #{$gttestdata}ltrharvest/s_cer/#{k}.gff3 > ref.gff3"
        run "#{$bin}gt gff3 -sort #{k}.gff3 > out.gff3"
        run "#{$bin}gt eval -ltr out.gff3 ref.gff3"
        grep(last_stdout, "LTR_retrotransposon sensitivity: 100.00%")
        grep(last_stdout, "LTR_retrotransposon specificity: 100.00%")
      end
      run "diff #{k}.fas #{$gttestdata}ltrharvest/s_cer/#{k}.fas"
      run "diff #{k}_inner.fas #{$gttestdata}ltrharvest/s_cer/#{k}_inner.fas"
    end
  end

  dmel_files = {"chr2L" => "2L_genomic_dmel_RELEASE3-1.FASTA.gz",
                "chr2R" => "2R_genomic_dmel_RELEASE3-1.FASTA.gz",
                "chr3L" => "3L_genomic_dmel_RELEASE3-1.FASTA.gz",
                "chr3R" => "3R_genomic_dmel_RELEASE3-1.FASTA.gz",
                "chr4"  =>  "4_genomic_dmel_RELEASE3-1.FASTA.gz",
                "chrX"  =>  "X_genomic_dmel_RELEASE3-1.FASTA.gz"}

  dmel_files.sort.each do |k, v|
    Name "gt ltrharvest test on #{k} Dmel"
    Keywords "gt_ltrharvest"
    Test do
      run_test "#{$bin}gt suffixerator -db #{$gttestdata}ltrharvest/d_mel/#{v} -dna -suf -sds -lcp -tis -des -ssp", :maxtime => 36000
      run_test "#{$bin}gt ltrharvest -index #{v} -seed 76 -minlenltr 116 -maxlenltr 800 -mindistltr 2280 -maxdistltr 8773 -similar 91 -mintsd 4 -maxtsd 20 -vic 60 -overlaps best -xdrop 7 -mat 2 -mis -2 -ins -3 -del -3 -v -gff3 #{k}.gff3", :maxtime => 3600
      run "diff #{last_stdout} #{$gttestdata}ltrharvest/d_mel/#{k}.out"
      run "#{$bin}gt gff3 -sort #{$gttestdata}ltrharvest/d_mel/#{k}.gff3 > ref.gff3"
      run "#{$bin}gt gff3 -sort #{k}.gff3 > out.gff3"
      run "#{$bin}gt  eval -ltr out.gff3 ref.gff3"
      grep(last_stdout, "LTR_retrotransposon sensitivity: 100.00%")
      grep(last_stdout, "LTR_retrotransposon specificity: 100.00%")
    end
  end
end

Name "gt ltrharvest missing index"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt ltrharvest -index ", :retval => 1
end

Name "gt ltrharvest only index"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna"
end

Name "gt ltrharvest motif and motifmis"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -motif tgca -motifmis 0"
end

Name "gt ltrharvest invalid motif characters"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -motif qgca -motifmis 0", :retval => 1
end

Name "gt ltrharvest motif not palindromic"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -motif agga -motifmis 0", :retval => 1
end

Name "gt ltrharvest maxtsd requires mintsd"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -maxtsd 20", :retval => 1
end

Name "gt ltrharvest mintsd and maxtsd"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -mintsd 4 -maxtsd 20"
end

Name "gt ltrharvest motifmis requires motif"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -motifmis 0", :retval => 1
end

Name "gt ltrharvest longoutput missing args"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -longoutput", :retval => 1
end

Name "gt ltrharvest longoutput motif random"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -longoutput -motif tgca"
end

Name "gt ltrharvest longoutput mintsd random"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -longoutput -mintsd 5"
end

Name "gt ltrharvest overlaps1"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -overlaps no"
end

Name "gt ltrharvest overlaps2"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -overlaps best"
end

Name "gt ltrharvest overlaps3"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -overlaps all"
end

Name "gt ltrharvest FASTA output"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -out out.fna"
end

Name "gt ltrharvest FASTA inner output"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -outinner outinner.fna"
end

Name "gt ltrharvest GFF3 output"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -lcp -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna" +
           " -gff3 out.gff3"
end

Name "gt ltrharvest missing tables (lcp)"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna -suf -sds -tis -des -ssp"
  run_test "#{$bin}gt ltrharvest -index Random.fna", :retval => 1
  grep(last_stderr, "cannot open file 'Random.fna.lcp'")
end

Name "gt ltrharvest missing tables (suf)"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random159.fna -dna -ssp -sds -tis -des -lcp"
  run_test "#{$bin}gt ltrharvest -index Random159.fna", :retval => 1
  grep(last_stderr, "cannot open file descriptor 'Random159.fna.suf'")
end

Name "gt ltrharvest missing tables (des)"
Keywords "gt_ltrharvest"
Test do
  run_test "#{$bin}gt suffixerator -db #{$testdata}Random159.fna -dna -ssp -sds -tis -lcp -suf -des"
  File.unlink("Random159.fna.des")
  run_test "#{$bin}gt ltrharvest -index Random159.fna", :retval => 1
  grep(last_stderr, "cannot open file \"Random159.fna.des\"")
end

# test all combinations of options, test only some of them
outlist = (["-seed 100",
            "-minlenltr 100",# "-maxlenltr 1000",
            "-mindistltr 1500",# "-maxdistltr 15000",
            "-similar 80",
            "-mintsd 5",
            "-range 1000 20000",#"-maxtsd 20",
           #"-motif tgca",#, #"-motifmis 0",
           #"-vic 60",
           #"-overlaps best",
           #"-xdrop 5",
           #"-mat 2","-mis -3","-ins -3","-del -3",
           #"-v",
           #"-out pred.fna",
           #"-outinner pred-inner.fna",
           #"-gff3 pred.gff3"
          ])
numofalphabets = outlist.length
wheelspace = Array.new
alphasizes = Array.new
counter = 0
0.upto(numofalphabets-1) do |z|
  alphasizes[z] = 2
  wheelspace[z] = 0
end
z = numofalphabets-1
thisisnottheend = true
while thisisnottheend
  output = false
  string = ""
  0.upto(numofalphabets-1) do |i|
    if wheelspace[i] == 1
      output = true
      string = string + " #{outlist[i]}"
    end
  end
  if output
    counter = counter + 1
    Name "gt ltrharvest mixed options #{counter}"
    Keywords "gt_ltrharvest"
    Test do
      run_test "#{$bin}gt suffixerator -db #{$testdata}Random.fna -dna " + \
               "-suf -sds -lcp -tis -des -ssp"
      run_test "#{$bin}gt ltrharvest -index " +
               "Random.fna #{string}"
    end
  end
  stop = false
  while not stop
    wheelspace[z] = wheelspace[z]+1
    if wheelspace[z] == alphasizes[z]
      wheelspace[z] = 0
      if z == 0
        thisisnottheend = false
      end
      z = z - 1
    else
      z = numofalphabets-1
      stop = true
    end
  end
end
genometools-1.5.1/testsuite/gt_magicmatch_include.rb000066400000000000000000000006121211610345200227130ustar00rootroot00000000000000for seqfile in ['sw100K1.fsa', 'sw100K2.fsa', 'U89959_ests.fas',
                'U89959_genomic.fas', 'Random.fna', 'RandomN.fna']
  Name "magicmatch #{seqfile}"
  Keywords "gt_magicmatch"
  Test do
    run "cp #{$testdata+seqfile} ./#{seqfile}"
    run_test "#{$bin}gt dev magicmatch -t -f  #{seqfile}"
    run "diff #{last_stdout} #{$testdata+seqfile.sub(/\..+$/, '.magicmatch')}"
  end
end
genometools-1.5.1/testsuite/gt_matchtool_include.rb000066400000000000000000000073301211610345200226140ustar00rootroot00000000000000Name "gt matchtool test (open match format)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -matchfile #{$testdata}matchtool_open.match"
  run "diff #{last_stdout} #{$testdata}matchtool_open.out"
end

Name "gt matchtool test (open match format corrupt)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -matchfile #{$testdata}matchtool_open_corrupt.match",
  :retval => 1
  grep last_stderr, /invalid format/
end

Name "gt matchtool test (open match format empty)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -matchfile #{$testdata}matchtool_open_empty.match"
  run "diff #{last_stdout} #{$testdata}matchtool_open_empty.out"
end

Name "gt matchtool test (open match format neg value)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -matchfile #{$testdata}matchtool_open_neg.match",
  :retval => 1
  grep last_stderr, /non-negative/
end

Name "gt matchtool test (open match format too few columns)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -matchfile #{$testdata}matchtool_open_too_few.match",
  :retval => 1
  grep last_stderr, /invalid format/
end

Name "gt matchtool test (open match format too many columns)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -matchfile #{$testdata}matchtool_open_too_many.match",
  :retval => 1
  grep last_stderr, /invalid format/
end

Name "gt matchtool test (open match format gz)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -matchfile #{$testdata}matchtool_open.match.gz"
  run "diff #{last_stdout} #{$testdata}matchtool_open.out"
end

Name "gt matchtool test (open match format bz2)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -matchfile #{$testdata}matchtool_open.match.bz2"
  run "diff #{last_stdout} #{$testdata}matchtool_open.out"
end

Name "gt matchtool test (blast match format)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -type BLASTOUT -matchfile #{$testdata}matchtool_blast.match"
  run "diff #{last_stdout} #{$testdata}matchtool_blast.out"
end

Name "gt matchtool test (blast match format corrupt)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -type BLASTOUT -matchfile #{$testdata}matchtool_blast_corrupt.match",
  :retval => 1
  grep last_stderr, /invalid format/
end

Name "gt matchtool test (blast match format empty)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -type BLASTOUT -matchfile #{$testdata}matchtool_blast_empty.match"
  run "diff #{last_stdout} #{$testdata}matchtool_blast_empty.out"
end

Name "gt matchtool test (blast match format too few columns)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -type BLASTOUT -matchfile #{$testdata}matchtool_blast_too_few.match",
  :retval => 1
  grep last_stderr, /invalid format/
end

Name "gt matchtool test (blast match format too many columns)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -type BLASTOUT -matchfile #{$testdata}matchtool_blast_too_many.match",
  :retval => 1
  grep last_stderr, /invalid format/
end

Name "gt matchtool test (blast match format neg values)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -type BLASTOUT -matchfile #{$testdata}matchtool_blast_neg.match",
  :retval => 1
  grep last_stderr, /non-negative/
end

Name "gt matchtool test (blast match format gz)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -type BLASTOUT -matchfile #{$testdata}matchtool_blast.match.gz"
  run "diff #{last_stdout} #{$testdata}matchtool_blast.out"
end

Name "gt matchtool test (blast match format bz2)"
Keywords "gt_matchtool"
Test do
  run_test "#{$bin}gt matchtool -type BLASTOUT -matchfile #{$testdata}matchtool_blast.match.bz2"
  run "diff #{last_stdout} #{$testdata}matchtool_blast.out"
end
genometools-1.5.1/testsuite/gt_mathsupport_include.rb000066400000000000000000000005311211610345200232040ustar00rootroot00000000000000Name "mathsupport Lua rand_max"
Keywords "gt_scripts mathsupport"
Test do
  run_test "#{$bin}gt -seed 12345 #{$testdata}/gtscripts/mathsupport.lua"
end

Name "mathsupport Lua rand_max (wrong seed)"
Keywords "gt_scripts mathsupport"
Test do
  run_test "#{$bin}gt -seed 54321 #{$testdata}/gtscripts/mathsupport.lua", \
           :retval => 1
end
genometools-1.5.1/testsuite/gt_md5_to_id_include.rb000066400000000000000000000017611211610345200224670ustar00rootroot00000000000000Name "gt md5_to_id (U89959_sas.gff3, old)"
Keywords "gt_md5_to_id"
Test do
  run_test "#{$bin}gt md5_to_id -seqfiles " +
           "#{$testdata}U89959_genomic.fas #{$testdata}U89959_ests.fas -- " +
           "#{$testdata}U89959_sas.gff3md5old"
  run "diff #{last_stdout} #{$testdata}U89959_sas.gff3"
end

Name "gt md5_to_id (U89959_sas.gff3)"
Keywords "gt_md5_to_id"
Test do
  run_test "#{$bin}gt md5_to_id #{$testdata}U89959_sas.gff3md5"
  run "diff #{last_stdout} #{$testdata}U89959_sas.gff3"
end

Name "gt md5_to_id (U89959_csas.gff3, old)"
Keywords "gt_md5_to_id"
Test do
  run_test "#{$bin}gt md5_to_id -seqfiles " +
           "#{$testdata}U89959_genomic.fas #{$testdata}U89959_ests.fas -- " +
           "#{$testdata}U89959_csas.gff3md5old"
  run "diff #{last_stdout} #{$testdata}U89959_csas.gff3"
end

Name "gt md5_to_id (U89959_csas.gff3)"
Keywords "gt_md5_to_id"
Test do
  run_test "#{$bin}gt md5_to_id #{$testdata}U89959_csas.gff3md5"
  run "diff #{last_stdout} #{$testdata}U89959_csas.gff3"
end
genometools-1.5.1/testsuite/gt_merge_include.rb000066400000000000000000000015021211610345200217140ustar00rootroot00000000000000Name "gt merge test 1"
Keywords "gt_merge"
Test do
  run_test "#{$bin}gt merge #{$testdata}gff3_file_1_short.txt"
end

Name "gt merge test 2"
Keywords "gt_merge"
Test do
  run_test "#{$bin}gt merge #{$testdata}gff3_file_1_short.txt"
end

Name "gt merge test 3"
Keywords "gt_merge"
Test do
  run_test "#{$bin}gt merge #{$testdata}gt_merge_prob_1.in1 #{$testdata}gt_merge_prob_1.in2"
  run "diff #{last_stdout} #{$testdata}gt_merge_prob_1.out"
end

Name "gt merge test 4"
Keywords "gt_merge"
Test do
  run_test "#{$bin}gt merge #{$testdata}gt_merge_prob_2.in1 #{$testdata}gt_merge_prob_2.in2"
  run "diff #{last_stdout} #{$testdata}gt_merge_prob_2.out"
end

Name "gt merge unsorted file"
Keywords "gt_merge"
Test do
  run_test("#{$bin}gt merge #{$testdata}unsorted_gff3_file.txt", :retval => 1)
  grep(last_stderr, "is not sorted")
end
genometools-1.5.1/testsuite/gt_mergeesa_include.rb000066400000000000000000000031621211610345200224110ustar00rootroot00000000000000def runmerge(queryfile,referencefiles)
  sfxopts="-dna -algbds 3 31 80 -suf -lcp -tis -pl"
  run_test "#{$bin}gt suffixerator #{sfxopts} -indexname all " +
           "-db #{referencefiles.join(" ")}"
  num = 0
  indexlist = Array.new()
  referencefiles.each do |filename|
    run_test "#{$bin}gt suffixerator #{sfxopts} -indexname midx#{num} " +
             "-db #{filename}"
    run_test "#{$bin}gt dev sfxmap -tis -suf -lcp -esa midx#{num}"
    indexlist.push("midx#{num}")
    num+=1
  end
  run_test "#{$bin}gt dev mergeesa -indexname midx-all " +
           "-ii #{indexlist.join(" ")}"
  run "cmp -s midx-all.suf all.suf"
  run "cmp -s midx-all.lcp all.lcp"
  run "cmp -s midx-all.llv all.llv"
  run_test "#{$bin}gt mkfmindex -noindexpos -fmout fm-all " + 
           "-ii #{indexlist.join(" ")}"
  run_test "#{$bin}gt suffixerator -indexname fm-all -plain -des no -ssp no" +
           " -sds no -smap fm-all.al1 -tis -db fm-all.bwt"
  run_test "#{$bin}gt uniquesub -fmi fm-all -query #{queryfile} " +
           "-output sequence querypos -min 10 -max 10"
end

def iterrunmerge(numtoselect)
  reference="#{$testdata}at1MB"
  run "#{$scriptsdir}seqselect.rb #{numtoselect} #{reference}"
  run "#{$scriptsdir}splitmultifasta.rb TMP 0 #{last_stdout}"
  referencefiles = Array.new()
  Dir.new('.').each do |filename|
    if filename.match(/^TMP-/)
      referencefiles.push(filename)
    end
  end
  queryfile="#{$testdata}U89959_genomic.fas"
  runmerge(queryfile,referencefiles)
end

2.upto(10) do |numtoselect|
  Name "gt merge #{numtoselect} enhanced suffix arrays"
  Keywords "gt_mergeesa"
  Test do
    iterrunmerge(numtoselect)
  end
end
genometools-1.5.1/testsuite/gt_mergefeat_include.rb000066400000000000000000000006211211610345200225550ustar00rootroot00000000000000Name "gt mergefeat test"
Keywords "gt_mergefeat mergefeat"
Test do
  run_test "#{$bin}gt mergefeat #{$testdata}mergefeat.gff3"
  run "diff #{last_stdout} #{$testdata}mergefeat.out"
end

Name "gt mergefeat test (no merge)"
Keywords "gt_mergefeat mergefeat"
Test do
  run_test "#{$bin}gt mergefeat #{$testdata}mergefeat_no_merge.gff3"
  run "diff #{last_stdout} #{$testdata}mergefeat_no_merge.gff3"
end
genometools-1.5.1/testsuite/gt_mgth_include.rb000066400000000000000000000117501211610345200215620ustar00rootroot00000000000000if $gttestdata then
  Name "gt mgth testdata mixed options 1"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Pyrococcus_NTo1_horikoshii -g yes -r 3 -e 3 -x yes -t yes #{$gttestdata}mgth/Pyrococcus_NTo1_horikoshii.xml.gz #{$gttestdata}mgth/Pyrococcus_horikoshii.txt.gz #{$gttestdata}mgth/Hits_NTo1_Pyrococcus_horikoshii.txt.gz", :maxtime => 200
    run "diff Pyrococcus_NTo1_horikoshii.xml #{$gttestdata}mgth/Pyrococcus_NTo1_horikoshii_ori_1.xml"
  end

  Name "gt mgth testdata mixed options 2"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Pyrococcus_NTo1_horikoshii -s 1.17 -n 3 -b -9.10 -q -3.0 -h -3.98 -l -1.3 -p 368 -f 217.0 -t yes -g yes -m yes -x yes -r 2 -e 3 -d 0.73 #{$gttestdata}mgth/Pyrococcus_NTo1_horikoshii.xml.gz #{$gttestdata}mgth/Pyrococcus_horikoshii.txt.gz #{$gttestdata}mgth/Hits_NTo1_Pyrococcus_horikoshii.txt.gz", :maxtime => 200
    run "diff Pyrococcus_NTo1_horikoshii.html #{$gttestdata}mgth/Pyrococcus_NTo1_horikoshii_ori_2.html"
  end

  Name "gt mgth testdata mixed options 3"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Pyrococcus_NTo1_horikoshii -s 5 -n 3.5 -b -14.23 -q -2.88 -h -5 -l -0.75 -p 295.75 -f 300.20 -t yes -g yes -m no -x no -r 3 -e 2 -a 25 -d 0.2 #{$gttestdata}mgth/Pyrococcus_NTo1_horikoshii.xml.gz #{$gttestdata}mgth/Pyrococcus_horikoshii.txt.gz #{$gttestdata}mgth/Hits_NTo1_Pyrococcus_horikoshii.txt.gz", :maxtime => 200
    run "diff Pyrococcus_NTo1_horikoshii.xml #{$gttestdata}mgth/Pyrococcus_NTo1_horikoshii_ori_3.xml"
  end

  Name "gt mgth testdata mixed options 4"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Pyrococcus_horikoshii -s 3.17 -n 2.32 -b -13.64 -q -3.45 -h -4.77 -l -1.5 -p 325.50 -f 225.25 -t yes -g yes -m no -x yes -r 1 -e 1 -d 0.21  #{$gttestdata}mgth/Pyrococcus_horikoshii.xml.gz #{$gttestdata}mgth/Pyrococcus_horikoshii.txt.gz #{$gttestdata}mgth/Hits_Pyrococcus_horikoshii.txt.gz", :maxtime => 200
    run "diff Pyrococcus_horikoshii.txt #{$gttestdata}mgth/Pyrococcus_horikoshii_ori_4.txt"
  end

  Name "gt mgth testdata mixed options 5"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Pyrococcus_horikoshii -s 2.55 -n 4.77 -b -15 -q -3 -h -3.27 -l -1.2 -p 177.13 -f 123 -t yes -g yes -m no -x yes -r 2 -e 2 -d 0.05 #{$gttestdata}mgth/Pyrococcus_horikoshii.xml.gz #{$gttestdata}mgth/Pyrococcus_horikoshii.txt.gz #{$gttestdata}mgth/Hits_Pyrococcus_horikoshii.txt.gz", :maxtime => 200
    run "diff Pyrococcus_horikoshii.html #{$gttestdata}mgth/Pyrococcus_horikoshii_ori_5.html"
  end


  Name "gt mgth testdata mixed options 6"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Pyrococcus_horikoshii -s 4.12 -n 2.9 -b -10 -q -7.5 -h -2 -l -0.5 -p 300 -f 211 -t yes -g yes -m no -x no -r 1 -e 3 -a 17 -d 0.13 #{$gttestdata}mgth/Pyrococcus_horikoshii.xml.gz #{$gttestdata}mgth/Pyrococcus_horikoshii.txt.gz #{$gttestdata}mgth/Hits_Pyrococcus_horikoshii.txt.gz", :maxtime => 100
    run "diff Pyrococcus_horikoshii.txt #{$gttestdata}mgth/Pyrococcus_horikoshii_ori_6.txt"
  end

  Name "gt mgth testdata mixed options 7"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Metagenome -s 3.17 -n 2.32 -b -13.64 -q -3.45 -h -4.77 -l -1.5 -p 325.50 -f 225.25 -t yes -g yes -m no -x yes -r 1 -e 1 -d 0.01 #{$gttestdata}mgth/Metagenome_NT.xml.gz #{$gttestdata}mgth/Metagenome.txt.gz #{$gttestdata}mgth/Hits_NT_Metagenome.txt.gz", :maxtime => 3200
    run "diff Metagenome.txt #{$gttestdata}mgth/Metagenome_ori_1.txt"
  end

  Name "gt mgth testdata mixed options 8"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Metagenome -s 1.17 -n 3 -b -9.10 -q -3.0 -h -3.98 -l -1.3 -p 368 -f 217.0 -t yes -g yes -m no -x yes -r 2 -e 3 -d 0.05  #{$gttestdata}mgth/Metagenome_NTo1.xml.gz #{$gttestdata}mgth/Metagenome.txt.gz #{$gttestdata}mgth/Hits_NTo1_Metagenome.txt.gz", :maxtime => 3200
    run "diff Metagenome.html #{$gttestdata}mgth/Metagenome_ori_2.html"
  end

  Name "gt mgth testdata mixed options 9"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Metagenome_454 -s 3.17 -n 2.32 -b -13.64 -q -3.45 -h -4.77 -l -1.5 -p 325.50 -f 225.25 -t yes -g yes -m no -x yes -r 1 -e 1 -d 0.01  #{$gttestdata}mgth/Metagenome_NT_454.xml.gz #{$gttestdata}mgth/Metagenome_454.txt.gz #{$gttestdata}mgth/Hits_NT_Metagenome_454.txt.gz", :maxtime => 3200
    run "diff Metagenome_454.txt #{$gttestdata}mgth/Metagenome_454_ori_3.txt"
  end

  Name "gt mgth testdata mixed options 10"
  Keywords "gt_mgth"
  Test do
    run_test "#{$bin}gt mgth -o Metagenome_454 -s 1.17 -n 3 -b -9.10 -q -3.0 -h -3.98 -l -1.3 -p 368 -f 217.0 -t yes -g yes -m no -x yes -r 2 -e 3 -d 0.05  #{$gttestdata}mgth/Metagenome_NTo1_454.xml.gz #{$gttestdata}mgth/Metagenome_454.txt.gz #{$gttestdata}mgth/Hits_NTo1_Metagenome_454.txt.gz", :maxtime => 3200
    run "diff Metagenome_454.html #{$gttestdata}mgth/Metagenome_454_ori_4.html"
    run "rm -f #{$gttestdata}mgth/*.des #{$gttestdata}mgth/*.esq " + \
        "#{$gttestdata}mgth/*.md5 #{$gttestdata}mgth/*.ois " + \
        "#{$gttestdata}mgth/*.sds #{$gttestdata}mgth/*.ssp"
  end
end
genometools-1.5.1/testsuite/gt_mmapandread_include.rb000066400000000000000000000016071211610345200230740ustar00rootroot00000000000000Name "gt mmapandread test 1"
Keywords "gt_mmapandread"
Test do
  run_test("#{$bin}gt mmapandread", :retval => 1)
end

Name "gt mmapandread test 2"
Keywords "gt_mmapandread"
Test do
  run_test "#{$bin}gt mmapandread #{$testdata}gt_mmapandread_test_1.in"
end

Name "gt mmapandread test 3"
Keywords "gt_mmapandread"
Test do
  run_test "#{$bin}gt mmapandread #{$testdata}gt_mmapandread_test_2.in"
end

Name "gt mmapandread test 4"
Keywords "gt_mmapandread"
Test do
  run_test "#{$bin}gt mmapandread #{$testdata}gt_mmapandread_test_3.in"
end

Name "gt mmapandread test 5"
Keywords "gt_mmapandread"
Test do
  run "ln -s /dev/null devnulllink" 
  run_test "#{$bin}gt mmapandread devnulllink"
end

Name "gt mmapandread test 6"
Keywords "gt_mmapandread"
Test do
  run_test "#{$bin}gt mmapandread #{$testdata}gt_mmapandread_test_1.in #{$testdata}gt_mmapandread_test_2.in #{$testdata}gt_mmapandread_test_3.in"
end
genometools-1.5.1/testsuite/gt_orffinder_include.rb000066400000000000000000000114671211610345200226060ustar00rootroot00000000000000if $gttestdata then
  Name "gt orffinder missing input sequence"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt orffinder", :retval => 1, :maxtime => 120
    grep(last_stderr, /missing argument/)
  end

  Name "gt orffinder missing value for -min"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -min 4_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chr4.gff3", :retval => 1
    grep(last_stderr, /error/)
  end

  Name "gt orffinder missing value for -max"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -max #{$gttestdata}orffinder/chr4.gff3 4_genomic_dmel_RELEASE3-1.FASTA.gz", :retval => 1
    grep(last_stderr, /error/)
  end

  Name "gt orffinder value for -min < 30"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -min 1 -o foo 4_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chr4.gff3", :retval => 1
    grep(last_stderr, /error/)
  end

  Name "gt orffinder value for -min > -max"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/4_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -min 130 -max 120  -o foo 4_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chr4.gff3", :retval => 1
    grep(last_stderr, /Value for/)
  end

  Name "gt orffinder -types ltrs is not a node"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/3R_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -types altrs -- 3R_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chr3R.gff3", :maxtime => 120
    run "diff #{last_stdout} #{$gttestdata}orffinder/chr3R_no_node_altrs.gff3"
  end

  Name "gt orffinder find longest orfs for 2R"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/2R_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder 2R_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chr2R.gff3", :maxtime => 120
    run "diff #{last_stdout} #{$gttestdata}orffinder/chr2R_longest_orfs.orffinder"
  end

  Name "gt orffinder find all orfs for 3L"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/3L_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -allorfs 3L_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chr3L.gff3", :maxtime => 120
    run "diff #{last_stdout} #{$gttestdata}orffinder/chr3L_all_orfs.orffinder"
  end

  Name "gt orffinder find all orfs in long_terminal_repeat"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/3R_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -allorfs -types long_terminal_repeat -- 3R_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chr3R.gff3", :maxtime => 200
    run "diff #{last_stdout} #{$gttestdata}orffinder/chr3R_all_orfs_longterminalrepeat.orffinder"
  end

  Name "gt orffinder find longest orfs in long_terminal_repeat"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/3R_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -types long_terminal_repeat -- 3R_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chr3R.gff3", :maxtime => 200
    run "diff #{last_stdout} #{$gttestdata}orffinder/chr3R_longest_orfs_longterminalrepeat.orffinder"
  end

  Name "gt orffinder find all orfs > 300nt for X"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/X_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -allorfs -min 300 X_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chrX.gff3", :maxtime => 120
    run "diff #{last_stdout} #{$gttestdata}orffinder/chrX_all_min300nt.orffinder"
  end

  Name "gt orffinder find longest orfs > 300nt for X"
  Keywords "gt_orffinder"
  Test do
    run_test "#{$bin}gt suffixerator -dna -des -ssp -tis -v -db #{$gttestdata}ltrharvest/d_mel/X_genomic_dmel_RELEASE3-1.FASTA.gz"
    run_test "#{$bin}gt orffinder -min 300 X_genomic_dmel_RELEASE3-1.FASTA.gz #{$gttestdata}orffinder/chrX.gff3", :maxtime => 120
    run "diff #{last_stdout} #{$gttestdata}orffinder/chrX_longest_min300nt.orffinder"
  end
end
genometools-1.5.1/testsuite/gt_packedindex_include.rb000066400000000000000000000156041211610345200231040ustar00rootroot00000000000000def aPrefix(prefix, list)
  return (list.collect {|x| prefix + x})
end

def prependTestdata(filelist)
  return aPrefix("#{$testdata}", filelist)
end

def paramList(paramsHash)
  if paramsHash != nil
    return paramsHash.to_a.flatten.compact
  else
    return []
  end
end

def runAndCheckPackedIndex(indexName,dbFiles, extraParams=Hash.new)
  params = {
    :create => { '-tis' => nil, '-des' => nil },
    :timeOuts => { :bdxcreat => 100, :suffixerator => 100,
      :chkintegrity => 400, :chksearch => 400, :trsuftab => 100,
      :mkctxmap => 100 },
    :bdx => {},
    :chksearch => { '-chksfxarray' => nil, '-nsamples' => '100' },
    :mkctxmap => { '-ctxilog' => -1 }
  }
  extraParams.keys.each do |key|
    params[key].merge!(extraParams[key]) if params.has_key?(key)
  end
  if indexName != nil
    params[:create]['-indexname'] = indexName
  else
    indexName = dbFiles.compact[0].sub(/.*\//,'')
  end
  #  puts('timeout: ', params[:timeOuts][:bdxcreat])
  if !extraParams.has_key?(:useSuftabTranslation) ||
      !extraParams[:useSuftabTranslation]
    run_test((["#{$bin}gt", '-debug', 'packedindex', 'mkindex'] +
              paramList(params[:create]) + paramList(params[:bdx]) +
              ['-db'] + dbFiles).join(' '),
             :maxtime => params[:timeOuts][:bdxcreat])
  end
  run_test((["#{$bin}gt", '-debug', 'suffixerator'] +
            paramList(params[:create]) +
            ['-bwt', '-suf', '-db'] + dbFiles).join(' '),
           :maxtime => params[:timeOuts][:suffixerator])
  if extraParams.has_key?(:useSuftabTranslation) &&
      extraParams[:useSuftabTranslation]
    run_test((["#{$bin}gt", '-debug', 'packedindex', 'trsuftab'] +
              paramList(params[:bdx]) + [indexName]).join(' '),
             :maxtime => params[:timeOuts][:trsuftab])
  end
  if extraParams.has_key?(:mkctxmap) &&
      extraParams[:mkctxmap]
    run_test((["#{$bin}gt", '-debug', 'packedindex', 'mkctxmap'] +
              paramList(params[:mkctxmap]) + [indexName]).join(' '),
             :maxtime => params[:timeOuts][:mkctxmap])    
  end
  run_test(["#{$bin}gt", '-debug', 'packedindex', 'chkintegrity',
            '-ticks', '1000', indexName].join(' '),
           :maxtime => params[:timeOuts][:chkintegrity])
  run_test((["#{$bin}gt", '-debug', 'packedindex', 'chksearch'] +
            paramList(params[:chksearch]) + [indexName]).join(' '),
           :maxtime => params[:timeOuts][:chksearch])
end

myfilelist = ["RandomN.fna","Random.fna","Atinsert.fna",
              "TTT-small.fna","trna_glutamine.fna",
              "Random-Small.fna","Duplicate.fna"]

Name "gt packedindex check tools for simple sequences"
Keywords "gt_packedindex"
Test do
  allfiles = prependTestdata(myfilelist)
  runAndCheckPackedIndex('miniindex', allfiles)
end

Name "gt packedindex check tools for simple sequences w/o locate"
Keywords "gt_packedindex"
Test do
  allfiles = prependTestdata(myfilelist)
  runAndCheckPackedIndex('miniindex', allfiles,
                         :bdx => { '-locfreq' => 0 },
                         :chksearch => { '-chksfxarray' => 'no' })
end

Name "gt packedindex check tools for simple sequences with sprank"
Keywords "gt_packedindex"
Test do
  allfiles = prependTestdata(myfilelist)
  runAndCheckPackedIndex('miniindex', allfiles,
                         :bdx => { '-sprank' => nil },
                         :chksearch => { '-full-lfmap' => nil },
                         :timeOuts => { :chksearch => 800 })
end

Name "gt packedindex check tools for revcom sequence with sprank"
Keywords "gt_packedindex"
Test do
  allfiles = prependTestdata(["Atinsert.fna"])
  runAndCheckPackedIndex('miniindex', allfiles,
                         :create => { '-dir' => 'rev' },
                         :bdx => { '-sprank' => nil },
                         :chksearch => { '-full-lfmap' => nil },
                         :timeOuts => { :chksearch => 800 })
end

#exclude this because it does not run on stefans laptop

Name "gt packedindex check tools for simple sequences with context"
Keywords "gt_packedindex"
Test do
  allfiles = prependTestdata(myfilelist)
  runAndCheckPackedIndex('miniindex', allfiles,
                         :bdx => { '-sprank' => nil, '-ctxilog' => -1 },
                         :chksearch => { '-chkcontext' => nil },
                         :timeOuts => { :chksearch => 800 })
end

Name "gt packedindex check tools for protein sample"
Keywords "gt_packedindex"
Test do
  runAndCheckPackedIndex(nil, prependTestdata(['sw100K2.fsa']),
                         :bdx => { '-bsize' => 1 })
end

#exclude this because it does not run on stefans laptop

Name "gt packedindex check tools for simple sequences, tr-mode"
Keywords "gt_packedindex"
Test do
  allfiles = prependTestdata(myfilelist)
  runAndCheckPackedIndex('miniindex', allfiles,
                         :useSuftabTranslation => true,
                         :bdx => { '-sprank' => nil },
                         :mkctxmap => {})
end

Name "gt packedindex check tools for boundary-case sequences"
Keywords "gt_packedindex"
Test do
  allfiles = prependTestdata(['Random160.fna', 'Random159.fna'])
  allfiles.each do |file|
    runAndCheckPackedIndex(nil, [file], :bdx => { '-blbuck' => 20 })
  end
  runAndCheckPackedIndex(nil, prependTestdata(['Random80.fna']),
                         :bdx => { '-bsize' => 10 })
end

Name "gt packedindex check tools for at1MB"
Keywords "gt_packedindex"
Test do
  runAndCheckPackedIndex('at1MB', ["#{$testdata}at1MB"],
                         :timeOuts => { :bdxcreat => 400,
                         :suffixerator => 400,
                         :chkintegrity => 800, :chksearch => 400 })
end

if $gttestdata then
  Name "gt packedindex check tools for chr01 yeast"
  Keywords "gt_packedindex"
  Test do
    runAndCheckPackedIndex('chr01.19960731',
      ["#{$gttestdata}ltrharvest/s_cer/chr01.19960731.fsa.gz"])
  end

  dmelFiles = aPrefix("#{$gttestdata}ltrharvest/d_mel/",
                      [
                       'X_genomic_dmel_RELEASE3-1.FASTA.gz',
                       '2L_genomic_dmel_RELEASE3-1.FASTA.gz',
                       '2R_genomic_dmel_RELEASE3-1.FASTA.gz',
                       '3L_genomic_dmel_RELEASE3-1.FASTA.gz',
                       '3R_genomic_dmel_RELEASE3-1.FASTA.gz',
                       '4_genomic_dmel_RELEASE3-1.FASTA.gz',
                       ])
  dmelFiles.each do |file|
    shortFileName = file.match('[^/]*$')[0]
    maxDisplay = 12
    if shortFileName.length > maxDisplay
      shortFileName = shortFileName[0,maxDisplay - 4] + '...'
    end
    Name 'gt packedindex check tools for d.melanogaster (' +
      shortFileName + ')'
    Keywords 'gt_packedindex'
    Test do
      runAndCheckPackedIndex('dmel',
                             [file],
                             :timeOuts =>
                             { :trsuftab => 7200, :suffixerator => 57600,
                               :chkintegrity => 3200, :chksearch => 800 },
                             :useSuftabTranslation => true)
    end
  end
end
genometools-1.5.1/testsuite/gt_python_include.rb000066400000000000000000000105761211610345200221510ustar00rootroot00000000000000Name "gtpython: genome_stream bindings (output stream)"
Keywords "gt_python"
Test do
  run_python "#{$testdata}gtpython/gff3.py #{$testdata}gff3_file_1_short.txt"
  run "env LC_ALL=C sort #{last_stdout}"
  run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end

Name "gtpython: genome_visitor bindings (output stream)"
Keywords "gt_python"
Test do
  run_python "#{$testdata}gtpython/genome_visitor.py #{$testdata}gff3_file_1_short.txt"
  run "env LC_ALL=C sort #{last_stdout}"
  run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end

Name "gtpython: feature_index and feature_stream bindings"
Keywords "gt_python"
Test do
  run_python "#{$testdata}gtpython/feature_stuff.py " +
             "#{$testdata}gff3_file_1_short.txt"
  run "env LC_ALL=C sort #{last_stdout}"
  run "grep -v '^##sequence-region' #{$testdata}gff3_file_1_short_sorted.txt | diff #{last_stdout} -"
end

if not $arguments["nocairo"] then
  Name "gtpython: AnnotationSketch bindings (valid gff3 file)"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/sketch.py test.png " +
               "#{$testdata}gff3_file_1_short.txt"
  end

  Name "gtpython: AnnotationSketch bindings (corrupt gff3 file)"
  Keywords "gt_python"
  Test do
    run_python("#{$testdata}gtpython/sketch.py test.png #{$testdata}corrupt.gff3",
               :retval => 1)
    grep last_stderr, "GenomeTools error"
  end

  Name "gtpython: AnnotationSketch bindings (nonexistent gff3 file)"
  Keywords "gt_python"
  Test do
    run_python("#{$testdata}gtpython/sketch.py test.png " +
               "#{$testdata}nonexistent_file", :retval => 1)
    grep last_stderr, "GenomeTools error"
  end

  Name "gtpython: AnnotationSketch bindings (simple sketch)"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/sketch_simple.py test.png " +
               "#{$testdata}gff3_file_1_short.txt"
  end

  Name "gtpython: AnnotationSketch bindings (PNG stream)"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/sketch_stream.py test.png " +
               "#{$testdata}gff3_file_1_short.txt"
  end

  Name "gtpython: AnnotationSketch bindings (TrackSelectorFunc)"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/block_stuff.py " +
             "#{$testdata}gff3_file_1_short.txt"
    run "env LC_ALL=C sort #{last_stdout}"
    run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.blocks"
  end

  Name "gtpython: AnnotationSketch bindings (style)"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/style.py #{$cur}/gtdata/sketch/default.style"
  end

  Name "gtpython: AnnotationSketch bindings (error reporting)"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/sketch-failures.py " +
               "#{$testdata}gff3_file_1_short.txt"
  end

  Name "gtpython: AnnotationSketch bindings (Graphics)"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/graphics_stuff.py " +
             "#{$testdata}graphics_curve_test_coords.txt " +
             "out.svg"
    # will fail e.g. if cairo toy font setup is different from test machine
    # disabled for now
    # run "diff out.svg #{$testdata}graphics_test.out"
  end

  Name "gtpython: AnnotationSketch bindings (FeatureNode(Iterator))"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/feature_node.py"
  end

  Name "gtpython: show_seqids"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/show_seqids.py #{$testdata}encode_known_genes_Mar07.gff3"
    run "diff #{last_stdout} #{$testdata}encode_known_genes_Mar07.seqids"
  end

  Name "gtpython: used_types"
  Keywords "gt_python"
  Test do
    run_python "#{$testdata}gtpython/used_types.py " +
               "#{$testdata}standard_gene_as_tree.gff3"
    run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.types"
  end

  Name "gtpython: show_recmaps"
  Keywords "gt_python showrecmaps"
  Test do
    run_python "#{$testdata}gtpython/show_recmaps.py " +
               "#{$testdata}standard_gene_as_tree.gff3"
    run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.hotspots"
  end

  Name "gtpython: unicode strings"
  Keywords "gt_python"
  Test do
    run_python("#{$testdata}gtpython/unicode_strings.py #{$cur}/gtdata/sketch/default.style test.png")
  end
end


Name "gtpython: unittests"
Keywords "gt_python unittests"
Test do
  run_python "#{$gtpython}/tests/__init__.py "
  grep last_stderr, "OK"
end
genometools-1.5.1/testsuite/gt_readjoiner_include.rb000066400000000000000000001244001211610345200227420ustar00rootroot00000000000000rdjO = "#{$bin}gt readjoiner overlap"
rdjA = "#{$bin}gt readjoiner assembly"
spmtest = "#{$bin}gt readjoiner spmtest"
cnttest = "#{$bin}gt readjoiner cnttest"

def run_correct(input, k, c)
  run "#{$bin}gt suffixerator -mirrored -suf -lcp -ssp"+
      " -indexname reads -db #{input}"
  run "#{$bin}gt readjoiner correct -k #{k} -c #{c} -ii reads"
end

def run_prefilter(input, moreopts="")
  run "#{$bin}gt readjoiner prefilter -readset reads "+
      "-db #{input} #{moreopts}"
end

def run_overlap(minlen, moreopts="")
  run "#{$bin}gt readjoiner overlap -readset reads "+
    "-l #{minlen} #{moreopts}"
end

def run_assembly(moreopts="")
  run "#{$bin}gt readjoiner assembly -readset reads #{moreopts}"
end

def encode_reads(input, moreopts="")
  run "#{$bin}gt encseq encode -des no -sds no -md5 no -indexname reads "+
      "#{moreopts} #{input}"
end

def prepare_esa(indexname, mirrored)
  run "#{$bin}gt suffixerator -ii #{indexname} -suf -lcp -ssp "+
      "#{mirrored ? '-mirrored' : ''}"
end

def compare_encseqs(indexname1, indexname2)
  run "#{$bin}gt encseq decode #{indexname1}"
  decoded1 = last_stdout
  run "#{$bin}gt encseq decode #{indexname2}"
  decoded2 = last_stdout
  run "diff #{decoded1} #{decoded2}"
  run "#{$bin}gt encseq info #{indexname1}"
  run "grep -v 'index name' #{last_stdout}"
  info1 = last_stdout
  run "#{$bin}gt encseq info #{indexname2}"
  run "grep -v 'index name' #{last_stdout}"
  info2 = last_stdout
  run "diff #{info1} #{info2}"
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U -readset reads_prefilter"
  encode_reads("U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U -readset reads_prefilter"
  encode_reads("U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Varlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1v.fas 1v"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1v -readset reads_prefilter"
  encode_reads("1v")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Varlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1v.fastq 1v"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1v -readset reads_prefilter"
  encode_reads("1v")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PEi/Fasta/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas 1_2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1_2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1_2:100'"
  encode_reads("1_2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PEi/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fastq 1_2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1_2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fastq '1_2:100'"
  encode_reads("1_2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PE2/Fasta/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1.fas 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fas 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PE2/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen + PE2/Fasta/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1.fas 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fas 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  encode_reads("U 1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen + PEi/Fasta/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas 1_2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1_2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1_2:100'"
  encode_reads("U 1_2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Eqlen + PE2/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "cp #{$testdata}/readjoiner/paired_reads_1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  encode_reads("U 1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Eqlen + PEi/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fastq 1_2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1_2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1_2:100'"
  encode_reads("U 1_2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen + PE2/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  encode_reads("U 1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Eqlen + PE2/Fasta/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "cp #{$testdata}/readjoiner/paired_reads_1.fas 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fas 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  encode_reads("U 1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PE2/Fasta/Eqlen + SE/Fasta/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1.fas 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fas 2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1:2:100 U -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  encode_reads("1:2:100 U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PE2/FastQ/Eqlen + SE/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1:2:100 U -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  encode_reads("1:2:100 U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: 2xPE2/Fasta/Eqlen + SE/Fasta/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1.fas 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fas 2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1:2:100 1:2:200 U -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:200'"
  encode_reads("1:2:100 1:2:200 U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: 2xPE2/FastQ/Eqlen + SE/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1:2:100 1:2:200 U -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:200'"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  encode_reads("1:2:100 1:2:200 U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PE2/fQ/Eq + SE/fQ/Eq + PEi/fQ/Eq"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fastq '1_2'"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1:2:100 U 1_2:10000,1200 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1_2:10000,1200'"
  encode_reads("1:2:100 U 1_2:10000,1200")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: 2xPE2/Fas/Eq/Wild1 + SE/Fasta/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1N.fas 1N"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fas 2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1N:2:100 1N:2:200 U -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.p.fas '1N:2:100'"
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.p.fas '1N:2:200'"
  encode_reads("1N:2:100 1N:2:200 U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PEi/fQ/Eq/Wild1 + SE/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.fastq 1N_2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1N_2:180,10 U -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.p.fas '1N_2:180,10'"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  encode_reads("1N_2:180,10 U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: 2xPE2/fQ/Eq/Wild1 + SE/FastQ/Eqlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1N.fastq 1N"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1N:2:100 1N:2:200 U -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.p.fas '1N:2:100'"
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.p.fas '1N:2:200'"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  encode_reads("1N:2:100 1N:2:200 U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen + PEi/Fasta/Eq/Wild1b"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1Nb_2.fas 1Nb_2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1Nb_2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1Nb_2.p.fas '1Nb_2:100'"
  encode_reads("U 1Nb_2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen + PE2/Fasta/Eq/Wild1b"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1Nb.fas 1Nb"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fas 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1Nb:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1Nb_2.p.fas '1Nb:2:100'"
  encode_reads("U 1Nb:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Eqlen + PE2/FastQ/Eq/Wild1b"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "cp #{$testdata}/readjoiner/paired_reads_1Nb.fastq 1Nb"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1Nb:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1Nb_2.p.fas '1Nb:2:100'"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  encode_reads("U 1Nb:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen + PE2/Fasta/Eq/Wild2"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1.fas 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2N.fas 2N"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1:2N:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2N.p.fas '1:2N:100'"
  encode_reads("U 1:2N:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Eqlen + PE2/FastQ/Eq/Wild2"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "cp #{$testdata}/readjoiner/paired_reads_1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2N.fastq 2N"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1:2N:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2N.p.fas '1:2N:100'"
  encode_reads("U 1:2N:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen + PE2/Fasta/Eq/Wild2b"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1.fas 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2Nb.fas 2Nb"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1:2Nb:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2Nb.p.fas '1:2Nb:100'"
  encode_reads("U 1:2Nb:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen + PE2/FastQ/Eq/Wild2b"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2Nb.fastq 2Nb"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1:2Nb:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2Nb.p.fas '1:2Nb:100'"
  encode_reads("U 1:2Nb:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eqlen + PE2/Fasta/Varlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1v.fas 1v"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fas 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1v:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1v_2.fas '1v:2:100'"
  encode_reads("U 1v:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Eqlen + PE2/FastQ/Varlen"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "cp #{$testdata}/readjoiner/paired_reads_1v.fastq 1v"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1v:2:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1v_2.fas '1v:2:100'"
  encode_reads("U 1v:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/Fasta/Eq + PE2/Fasta/Var/Wild2b"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1v.fas 1v"
  run "cp #{$testdata}/readjoiner/paired_reads_2Nb.fas 2Nb"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1v:2Nb:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1v_2Nb.p.fas "+
    "'1v:2Nb:100'"
  encode_reads("U 1v:2Nb:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Eq + PEi/FastQ/Var/Wild2b"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "cp #{$testdata}/readjoiner/paired_reads_1v_2Nb.fastq 1v_2Nb"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1v_2Nb:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1v_2Nb.p.fas "+
    "'1v_2Nb:100'"
  encode_reads("U 1v_2Nb:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: SE/FastQ/Eq + PE2/FastQ/Var/Wild2b"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_U.fastq U"
  run "cp #{$testdata}/readjoiner/paired_reads_1v.fastq 1v"
  run "cp #{$testdata}/readjoiner/paired_reads_2Nb.fastq 2Nb"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db U 1v:2Nb:100 -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "cp #{$testdata}/readjoiner/paired_reads_1v_2Nb.p.fas "+
    "'1v:2Nb:100'"
  encode_reads("U 1v:2Nb:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PE2/Fasta/Var/Wild1N + SE/Fasta/Eq"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1Nv.fas 1Nv"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fas 2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1Nv:2:200 U -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1Nv_2.p.fas "+
    "'1Nv:2:200'"
  encode_reads("1Nv:2:200 U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: PE2/FastQ/Var/Wild1N + SE/Fasta/Eq"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1Nv.fastq 1Nv"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  run "#{$bin}gt readjoiner prefilter -encodeonly "+
    "-db 1Nv:2:200 U -readset reads_prefilter"
  run "cp #{$testdata}/readjoiner/paired_reads_1Nv_2.p.fas "+
    "'1Nv:2:200'"
  run "cp #{$testdata}/readjoiner/paired_reads_U.fas U"
  encode_reads("1Nv:2:200 U")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: quality filter (-maxlow, 1L1)"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1L1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -maxlow 3 -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "grep 'number of reads in output readset = 4' #{last_stdout}"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
  run "#{$bin}gt readjoiner prefilter -maxlow 0 -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "grep 'number of reads in output readset = 0' #{last_stdout}"
end

Name "gt readjoiner encoder: quality filter (-maxlow, 1L2)"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1L2.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -maxlow 3 -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "grep 'number of reads in output readset = 4' #{last_stdout}"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
  run "#{$bin}gt readjoiner prefilter -maxlow 1 -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "grep 'number of reads in output readset = 2' #{last_stdout}"
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.p.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: quality filter (-maxlow, 1L4)"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1L4.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -maxlow 3 -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "grep 'number of reads in output readset = 2' #{last_stdout}"
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.p.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: quality filter (-maxlow -lowqual)"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1L1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -maxlow 2 -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "grep 'number of reads in output readset = 4' #{last_stdout}"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
  run "cp #{$testdata}/readjoiner/paired_reads_1L1.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2.fastq 2"
  run "#{$bin}gt readjoiner prefilter -maxlow 2 -lowqual 10 -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "grep 'number of reads in output readset = 2' #{last_stdout}"
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.p.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner encoder: quality filter (-maxlow -phred64)"
Keywords "gt_readjoiner gt_readjoiner_prefilter reads2twobit"
Test do
  run "cp #{$testdata}/readjoiner/paired_reads_1L2_ph64.fastq 1"
  run "cp #{$testdata}/readjoiner/paired_reads_2_ph64.fastq 2"
  run "#{$bin}gt readjoiner prefilter -maxlow 3 -phred64 -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "grep 'number of reads in output readset = 4' #{last_stdout}"
  run "cp #{$testdata}/readjoiner/paired_reads_1_2.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
  run "#{$bin}gt readjoiner prefilter -maxlow 1 -phred64 -encodeonly "+
    "-db 1:2:100 -readset reads_prefilter"
  run "grep 'number of reads in output readset = 2' #{last_stdout}"
  run "cp #{$testdata}/readjoiner/paired_reads_1N_2.p.fas '1:2:100'"
  encode_reads("1:2:100")
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner prefilter: correct encseq output (eqlen)"
Keywords "gt_readjoiner gt_readjoiner_prefilter"
Test do
  # first prepare contfree readset in fasta format
  run_prefilter("#{$testdata}/readjoiner/30x_800nt.fas",
                "-encseq false -fasta true -q true")
  contfree = "reads.pf.fas"
  # prepare encseq using prefilter
  run_prefilter(contfree)
  run "mv reads.esq reads_prefilter.esq"
  # prepare encseq using encseq encode
  encode_reads(contfree)
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner prefilter: multiple input files (eqlen)"
Keywords "gt_readjoiner gt_readjoiner_prefilter"
Test do
  run_prefilter("#{$testdata}/readjoiner/2x3nt_1.fas "+
                "#{$testdata}/readjoiner/2x3nt_2.fas "+
                "#{$testdata}/readjoiner/2x3nt_3.fas")
end

Name "gt readjoiner prefilter: correct encseq output (varlen)"
Keywords "gt_readjoiner gt_readjoiner_prefilter"
Test do
  run_prefilter("#{$testdata}/readjoiner/30x_long_varlen.fas",
                "-encseq false -fasta true -q true")
  contfree = "reads.pf.fas"
  run_prefilter(contfree)
  run "mv reads.esq reads_prefilter.esq"
  run "mv reads.ssp reads_prefilter.ssp"
  encode_reads(contfree)
  compare_encseqs("reads", "reads_prefilter")
end

Name "gt readjoiner: no crash when no spm found"
Keywords "gt_readjoiner"
Test do
   run_prefilter("#$testdata/readjoiner/tiny.fas")
   run_overlap(12)
   run "grep 'number of irreducible suffix-prefix matches = 0' #{last_stdout}"
   run_assembly
   run "grep 'no contigs' #{last_stdout}"
end

Name "gt readjoiner correct"
Keywords "gt_readjoiner gt_readjoiner_correct"
Test do
  run_correct("#{$testdata}/readjoiner/errors_1.fas", 12, 2)
  run "#{$bin}gt encseq decode reads"
  run "diff #{last_stdout} #{$testdata}/readjoiner/errors_1.corrected.fas"
end

Name "gt readjoiner overlap: eqlen; minlen > readlen"
Keywords "gt_readjoiner gt_readjoiner_overlap"
Test do
  run_prefilter("#$testdata/readjoiner/tiny.fas")
  run_test "#{$bin}gt readjoiner overlap -readset reads -l 17"
end

=begin singlestrand
Name "gt readjoiner overlap: singlestrand vs mirrored mode"
Keywords "gt_readjoiner gt_readjoiner_overlap"
Test do
  run_prefilter("#$testdata/readjoiner/tiny.fas")
  run_overlap(4, "-singlestrand")
  run "#{spmtest} -test showlist -readset reads"
  spm = last_stdout
  run_test "diff #{spm} " +
    "#$testdata/readjoiner/tiny_singlestrand.spm", :retval => 0
  run_overlap(4)
  run "#{spmtest} -test showlist -readset reads"
  spm = last_stdout
  run_test "diff #{spm} " +
    "#$testdata/readjoiner/tiny_mirrored.spm", :retval => 0
end
=end

def assert_empty(fn, desc)
  fncontent = IO.read(fn)
  fncontent = fncontent.split("\n")
  # tolerate this ruby warning:
  fncontent.reject! {|line| line =~ /Insecure world writable/}
  failtest(desc + " should be empty") unless fncontent.join == ""
end

def assert_not_empty(fn, desc)
  failtest(desc + " should not be empty") unless IO.read(fn) != ""
end

Name "gt readjoiner: verbosity levels (-q/default/-v)"
Keywords "gt_readjoiner gt_readjoiner_prefilter "+
         "gt_readjoiner_overlap gt_readjoiner_assembly"
Test do
  # -- prefilter -- #

  # default mode
  run_prefilter("#$testdata/readjoiner/tiny.fas")
  assert_not_empty(last_stdout, "stdout")
  assert_empty(last_stderr, "stderr")
  # quiet mode
  run_prefilter("#$testdata/readjoiner/tiny.fas", "-q")
  assert_empty(last_stdout, "stdout")
  assert_empty(last_stderr, "stderr")
  # verbose mode
  run_prefilter("#$testdata/readjoiner/tiny.fas", "-v")
  assert_not_empty(last_stdout, "stdout")
  assert_empty(last_stderr, "stderr")

  # -- overlap -- #

  # default mode
  run_overlap(4)
  assert_not_empty(last_stdout, "stdout")
  assert_empty(last_stderr, "stderr")
  # quiet mode
  run_overlap(4, "-q")
  assert_empty(last_stdout, "stdout")
  assert_empty(last_stderr, "stderr")
  # verbose mode
  run_overlap(4, "-v")
  assert_not_empty(last_stdout, "stdout")
  assert_empty(last_stderr, "stderr")

  # -- assembly -- #

  # default mode
  run_assembly
  assert_not_empty(last_stdout, "stdout")
  assert_empty(last_stderr, "stderr")
  # quiet mode
  run_assembly("-q")
  assert_empty(last_stdout, "stdout")
  assert_empty(last_stderr, "stderr")
  # verbose mode
  run_assembly("-v")
  assert_not_empty(last_stdout, "stdout")
  assert_empty(last_stderr, "stderr")
end

Name "gt readjoiner: wildcards (Fasta)"
Keywords "gt_readjoiner gt_readjoiner_prefilter"
Test do
  run_prefilter("#$testdata/readjoiner/wildcard1.fas")
  grep last_stdout, 'low-quality reads = 1'
  grep last_stdout, 'number of reads in filtered readset = 1'
  run_prefilter("#$testdata/readjoiner/wildcard2.fas")
  grep last_stdout, 'low-quality reads = 1'
  grep last_stdout, 'number of reads in filtered readset = 1'
  run_prefilter("#$testdata/readjoiner/wildcards.fas")
  grep last_stdout, 'low-quality reads = 6'
  grep last_stdout, 'number of reads in filtered readset = 2'
  # wildcard1 / wildcard2 have a 8 chars match between read 0 and read 1;
  # the current version of readjoiner eliminates the wildcard-containing
  # sequences; update the test if this is changed
end

Name "gt readjoiner: wildcards (FastQ)"
Keywords "gt_readjoiner gt_readjoiner_prefilter"
Test do
  run_prefilter("#$testdata/readjoiner/wildcard1.fastq")
  grep last_stdout, 'low-quality reads = 1'
  grep last_stdout, 'number of reads in filtered readset = 1'
  run_prefilter("#$testdata/readjoiner/wildcard2.fastq")
  grep last_stdout, 'low-quality reads = 1'
  grep last_stdout, 'number of reads in filtered readset = 1'
  run_prefilter("#$testdata/readjoiner/wildcards.fastq")
  grep last_stdout, 'low-quality reads = 6'
  grep last_stdout, 'number of reads in filtered readset = 2'
end

Name "gt readjoiner overlap: self-match"
Keywords "gt_readjoiner gt_readjoiner_overlap"
Test do
  # direct
  run_prefilter("#{$testdata}/readjoiner/self_spm.fas")
  run_overlap(8)
  grep last_stdout, 'number of irreducible suffix-prefix matches = 1'
  # with reverse complement of self
  run_prefilter("#{$testdata}/readjoiner/with_rc.fas")
  run_overlap(8)
  grep last_stdout, 'number of irreducible suffix-prefix matches = 1'
end

# the next test compares direct construction with complete graph + trans.red.
Name "gt readjoiner: transitive spm determination test - 1"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/transred_1.fas", "")
  run_overlap(4, "-singlestrand")
  run_assembly("-lengthcutoff 1 -depthcutoff 1")
  run_test "grep -f #{$testdata}/readjoiner/transred_1_targetseq.fas "+
           " reads.contigs.fas"
  run_overlap(4, "-singlestrand -elimtrans false")
  run_assembly("-redtrans -lengthcutoff 1 -depthcutoff 1")
  run_test "grep -f #{$testdata}/readjoiner/transred_1_targetseq.fas "+
           " reads.contigs.fas"
end

Name "gt readjoiner: transitive spm determination test - 2"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/transred_2.fas", "")
  run_overlap(4)
  run_assembly("-lengthcutoff 1 -depthcutoff 1")
  run_test "grep -f #{$testdata}/readjoiner/transred_1_targetseq.fas "+
           " reads.contigs.fas"
  run_overlap(4, "-elimtrans false")
  run_assembly("-redtrans -lengthcutoff 1 -depthcutoff 1")
  run_test "grep -f #{$testdata}/readjoiner/transred_1_targetseq.fas "+
           " reads.contigs.fas"
end

# currently the spm list obtained from transred_3 appears to be incorrect
# (the readset is varlen, currently not completely supported)
# the expected spm list from -l 10 -singlestrand is in transred_3.l10.ss.spm

Name "gt readjoiner: transitive spm determination test - 3"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/test_1.fas")
  run_overlap(39)
  run_assembly
  run "mv reads.contigs.fas contigs"
  run_overlap(39, "-elimtrans false")
  run_assembly("-redtrans")
  run "diff reads.contigs.fas contigs"
end


Name "gt readjoiner: transitive spm determination test - 4"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/test_2.fas")
  run_overlap(20)
  run_assembly
  run "mv reads.contigs.fas contigs"
  run_overlap(20, "-elimtrans false")
  run_assembly("-redtrans")
  run "diff reads.contigs.fas contigs"
end

Name "gt readjoiner: transitive spm determination test - 5"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/test_3.fas")
  run_overlap(20)
  run_assembly
  run "mv reads.contigs.fas contigs"
  run_overlap(20, "-elimtrans false")
  run_assembly("-redtrans")
  run "diff reads.contigs.fas contigs"
end

Name "gt readjoiner: transitive spm determination test - 6"
Keywords "gt_readjoiner"
Test do
  # this describes the next test case:
  #
  # 0 ctgataagtcccaggacttcagaagagctgtgag...ggacttcagaagagctgtgag
  # 2              ggacttcagaagagctgtgag...ggacttcagaagagctgtgagggtatggggacgg
  # 1          cccaggacttcagaagagctgtgag...ggacttcagaagagctgtgagggtatgggg
  #   |---A---|-B-|----------C----------|D|---------C----------|---E----|--F-|
  # 2                                      ggacttcagaagagctgtgagaccttggccaagtc..
  #                                       |---------C----------|-------D------..
  # assembly:
  # read_0:  ABCDC
  # read_1:   BCDCE
  # read_2:    CDCEF
  #
  # alternative assembly:
  # read_0:  ABCDC
  # read_1:   BCDCE
  # +
  # read_0: ABCDC
  # read_2:     CDCEF
  #
  #     ->2
  #    // ^
  #   0   |   only the longest of the two overlaps 0..2 is really transitive
  #    \  |
  #     ->1
  #

  run_prefilter("#{$testdata}/readjoiner/trans_and_submax_ovl.fas")
  run_overlap(20, "-singlestrand")
  run_assembly
  run "mv reads.contigs.fas contigs"
  run_overlap(20, "-singlestrand -elimtrans false")
  run_assembly("-redtrans")
  run "diff reads.contigs.fas contigs"
end

Name "gt readjoiner: transitive spm determination test - 7"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/large_count.fas")
  run_overlap(4)
  run_assembly
  run "mv reads.contigs.fas contigs"
  run_overlap(4, "-elimtrans false")
  run_assembly("-redtrans")
  run "diff reads.contigs.fas contigs"
end

Name "gt readjoiner: transitive spm determination test - 8"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/large_wset.fas")
  run_overlap(4)
  run_assembly
  run "mv reads.contigs.fas contigs"
  run_overlap(4, "-elimtrans false")
  run_assembly("-redtrans")
  run "diff reads.contigs.fas contigs"
end

Name "gt readjoiner: fastq vs fasta, 70x100nt"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/70x_100nt.fas")
  run_overlap(30)
  run_assembly
  run_prefilter("#{$testdata}/readjoiner/70x_100nt.fastq")
  run_overlap(30)
  run_assembly
end

Name "gt readjoiner: fastq phred64, 70x161nt"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/70x_161nt.fas")
  run_overlap(30)
  run_assembly
  run_prefilter("#{$testdata}/readjoiner/70x_161nt_phred64.fastq", "-phred64")
  run_overlap(30)
  run_assembly
end

Name "gt readjoiner: test different read lengths"
Keywords "gt_readjoiner"
Test do
  run_prefilter("#{$testdata}/readjoiner/70x_161nt.fas")
  run_overlap(30)
  run_assembly
end

Name "gt readjoiner spmtest pw"
Keywords "gt_readjoiner gt_readjoiner_spmtest"
Test do
  encode_reads("#$testdata/readjoiner/pw.fas")
  run_test "#{spmtest} -test bruteforce -readset reads -l 3", :retval => 0
  bf = last_stdout
  run_test "#{spmtest} -test kmp -readset reads -l 3", :retval => 0
  kmp = last_stdout
  run "diff #{kmp} #{bf}"
  run "diff #{bf} #$testdata/readjoiner/pw-ex.spm"
end

# spmtest
[true, false].each do |mirrored|
  %w{contained_eqlen contained_varlen 30x_800nt 70x_100nt}.each do |fasta|
    Name "gt readjoiner spmtest#{' singlestrand' if !mirrored}: #{fasta}"
    Keywords "gt_readjoiner gt_readjoiner_spmtest"
    Test do
      spmtest += " -singlestrand" if !mirrored
      encode_reads("#$testdata/readjoiner/#{fasta}.fas")
      run_test "#{spmtest} -test bruteforce -readset reads -l 32", :retval => 0
      bf = last_stdout
      run_test "#{spmtest} -test kmp -readset reads -l 32", :retval => 0
      kmp = last_stdout
      run "diff #{kmp} #{bf}"
      prepare_esa("reads", mirrored)
      if (!%w{70x_100nt}.include?(fasta))
        run_test "#{spmtest} -test gusfield -readset reads -l 32", :retval => 0
        run "sort -u #{last_stdout}"
        gf = last_stdout
        run "sort -u #{kmp}"
        kmp = last_stdout
        run "diff #{gf} #{kmp}"
      end
      if (!%w{contained_eqlen contained_varlen 30x_800nt}.include?(fasta))
        rdjO += " -singlestrand" if !mirrored
        run_test "#{rdjO} -readset reads -l 32 -showspm -elimtrans false -q",
          :retval => 0
        run "sort -u #{last_stdout}"
        our = last_stdout
        run "sort -u #{kmp}"
        kmp = last_stdout
        run "diff #{our} #{kmp}"
      end
    end
  end
end

# cnttest

[true, false].each do |mirrored|
  %w{contained_eqlen contained_varlen}.each do |fasta|
    Name "gt readjoiner cnttest#{' singlestrand' if !mirrored}: #{fasta}"
    Keywords "gt_readjoiner gt_readjoiner_cnttest"
    Test do
      cnttest += " -singlestrand" if !mirrored
      encode_reads("#$testdata/readjoiner/#{fasta}.fas")
      run_test "#{cnttest} -test bruteforce -readset reads", :retval => 0
      bf = last_stdout
      run_test "#{cnttest} -test kmp -readset reads", :retval => 0
      kmp = last_stdout
      run "diff #{kmp} #{bf}"
      prepare_esa("reads", mirrored)
      run_test "#{cnttest} -test esa -readset reads", :retval => 0
      esa = last_stdout
      run "diff #{esa} #{$testdata}readjoiner/#{fasta}#{'_ss' if !mirrored}.cnt"
      run "sort -u #{esa}"
      esas = last_stdout
      run "sort -u #{kmp}"
      kmps = last_stdout
      run "diff #{esas} #{kmps}"
    end
  end
end

def assert_nofspm(irreducible, transitive = nil)
  grep last_stdout,
    "number of irreducible suffix-prefix matches = #{irreducible}"
  if !transitive.nil?
    grep last_stdout,
      "number of transitive suffix-prefix matches = #{transitive}"
  end
end

[1, 2].each do |varlen_test|
  Name "gt encseq2spm: different minlen values - test #{varlen_test}"
  Keywords "gt_readjoiner gt_encseq2spm"
  Test do
    encode_reads("#$testdata/readjoiner/varlen_#{varlen_test}.fas")
    [10, 13, 15, 33, 65, 84].each do |minlen|
      run "#$bin/gt encseq2spm -l #{minlen} -ii reads"
    end
  end
end

Name "gt encseq2spm: different minlen values - test 3"
Keywords "gt_readjoiner gt_encseq2spm"
Test do
  run_prefilter("#$testdata/readjoiner/minlen_test.fas")
  run "#$bin/gt encseq2spm -l 14 -ii reads"
  run "#$bin/gt encseq2spm -l 15 -ii reads"
end

Name "gt readjoiner overlap: different min match lengths"
Keywords "gt_readjoiner gt_readjoiner_overlap"
Test do
  run_prefilter("#$testdata/readjoiner/minlen_test.fas")
  2.upto(40) do |minlen|
    run_overlap(minlen)
    assert_nofspm(40 - minlen)
  end
end

def unpack_array_file(i_filename, o_filename, low_filter, sizeofint, unpackstr)
  i_file = File.open(i_filename)
  o_file = File.open(o_filename, "w")
  loop do
    v = i_file.read(sizeofint)
    break if v.nil?
    value = v.unpack(unpackstr)[0]
    if value >= low_filter
      o_file.puts value
    end
  end
  i_file.close
  o_file.close
end

[true, false].each do |singlestrand|
  %w{70x_100nt 30x_800nt}.each do |dataset|
    Name "gt readjoiner radixsort_str test "+
      "(#{dataset}, #{singlestrand ? 'single strand' : 'mirrored'})"
    Keywords "gt_readjoiner radixsort_str"
    Test do
      db = "#$testdata/readjoiner/#{dataset}.fas"
      run_prefilter(db, "-testrs -encseq no -q"+
		    "#{' -singlestrand' if singlestrand}")
      radixsort_results = last_stdout
      run "#{$bin}gt suffixerator -suf -db #{db}"+
        "#{' -mirrored' unless singlestrand} -indexname i"
      is64bit = Kernel.system("#{$bin}gt -64bit")
      sizeofint = is64bit ? 8 : 4
      unpackstr = is64bit ? "Q" : "L"
      unpack_array_file("i.suf", "i.suf.txt", 0, sizeofint, unpackstr)
      run "diff i.suf.txt #{radixsort_results}"
    end
  end
end

if $gttestdata

  # compare results with precalculated known results
  [700, 7000, 70000].each do |nofreads|
    readset="#{$gttestdata}/readjoiner/#{nofreads}x_100nt_reads"
    if File.exists?(readset)
      Name "gt readjoiner: #{nofreads}x100"
      Keywords "gt_readjoiner"
      Test do
        readset="#{$gttestdata}/readjoiner/#{nofreads}x_100nt_reads"
        run_prefilter(readset, "-cnt")
        run "#{cnttest} -test showlist -readset reads"
        run "diff #{last_stdout} #{readset}.cnt"
        run_overlap(45)
        run "#{spmtest} -test showlist -readset reads.0"
        run "sort #{last_stdout}"
        spm = last_stdout
        run "sort #{readset}.l45.spm"
        ref = last_stdout
        run "diff #{spm} #{ref}"
        run_assembly
        run "diff reads.contigs.fas #{readset}.l45.contigs"
      end
    end

    [161, 200, 300, 400, 600, 800, 1000].each do |len|
      reads = "#{$gttestdata}/readjoiner/#{nofreads}x_#{len}nt_reads"
      if File.exists?(reads)
        Name "gt readjoiner: #{nofreads}x#{len}"
        Keywords "gt_readjoiner"
        Test do
          run_prefilter(reads)
          run_overlap(30)
          run_assembly
        end
      end
    end
  end

  Name "gt readjoiner: multiple input files (eqlen)"
  Keywords "gt_readjoiner"
  Test do
    readset = "#{$gttestdata}/readjoiner/7000x_100nt_reads"
    run "head -n 3000 #{readset}"
    reads1 = last_stdout
    run "head -n 7000 #{readset} | tail -n 4000"
    reads2 = last_stdout
    run "head -n 13000 #{readset} | tail -n 6000"
    reads3 = last_stdout
    run "tail -n 1000 #{readset}"
    reads4 = last_stdout
    run_prefilter("#{reads1} #{reads2} #{reads3} #{reads4}")
    run_overlap(45)
    run "#{spmtest} -test showlist -readset reads.0"
    run "sort #{last_stdout}"
    spm = last_stdout
    run "sort #{readset}.l45.spm"
    ref = last_stdout
    run "diff #{spm} #{ref}"
  end

end
genometools-1.5.1/testsuite/gt_readreads_include.rb000066400000000000000000000046671211610345200225660ustar00rootroot00000000000000Name "gt readreads (success)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads -showseq #{$testdata}test1.fastq"
end

Name "gt readreads colorspace (success)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads -colorspace -showseq "+
    "#{$testdata}solid_color_reads.fastq"
end

Name "gt readreads (non-FASTQ file)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads #{$testdata}eden.gff3", \
           :retval => 1
  grep(last_stderr, /expected/)
end

Name "gt readreads (invalid block start)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads #{$testdata}test2_wrong_begin.fastq", \
           :retval => 1
  grep(last_stderr, /expected/)
end

Name "gt readreads (different seqnames)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads " + \
           "#{$testdata}test3_different_seqnames.fastq", \
           :retval => 1
  grep(last_stderr, "sequence description 'HWI-EAS306_9_FC305MP_6_1_1331" + \
                     "_1843' is not equal to qualities description 'HWI-EAS3" +\
                     "06_9_FC305MP_6_1_1331' in line")
end

Name "gt readreads (different seqlengths 1)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads " + \
           "#{$testdata}test4_different_seqlengths.fastq", \
           :retval => 1
  grep(last_stderr, "lengths of character sequence and qualities sequence " + \
                     "differ")
end

Name "gt readreads (different seqlengths 2)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads " + \
           "#{$testdata}test9_uneven_length.fastq", \
           :retval => 1
  grep(last_stderr, "qualities string of sequence length 33 is not ended " + \
                     "by newline")
end

Name "gt readreads (tricky)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads " + \
           "#{$testdata}test5_tricky.fastq"
end

Name "gt readreads (empty sequence)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads #{$testdata}test7_empty_seq.fastq", \
           :retval => 1
  grep(last_stderr, /empty sequence/)
end

Name "gt readreads (premature end)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads #{$testdata}test6_premature_end.fastq", \
           :retval => 1
  grep(last_stderr, /premature end/)
end

Name "gt readreads (multiline)"
Keywords "gt_readreads"
Test do
  run_test "#{$bin}gt dev readreads #{$testdata}test10_multiline.fastq"
end
genometools-1.5.1/testsuite/gt_regioncov_include.rb000066400000000000000000000007111211610345200226110ustar00rootroot00000000000000Name "gt regioncov test 1 (no options)"
Keywords "gt_regioncov"
Test do
  run "#{$bin}gt dev regioncov #{$testdata}encode_known_genes_Mar07.gff3"
  run "diff #{last_stdout} #{$testdata}gt_regioncov_test_1.out"
end

Name "gt regioncov test 2 (-maxfeaturedist)"
Keywords "gt_regioncov"
Test do
  run "#{$bin}gt dev regioncov -maxfeaturedist 220000 #{$testdata}encode_known_genes_Mar07.gff3"
  run "diff #{last_stdout} #{$testdata}gt_regioncov_test_2.out"
end
genometools-1.5.1/testsuite/gt_ruby_include.rb000066400000000000000000000120321211610345200215760ustar00rootroot00000000000000rv = RUBY_VERSION.match(/^(\d+\.\d+)/)
if (!rv.nil? && rv[1].to_f < 1.9)  then
  Name "gtruby: genome_stream bindings (output stream)"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/gff3.rb #{$testdata}gff3_file_1_short.txt"
    run "env LC_ALL=C sort #{last_stdout}"
    run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
  end

  Name "gtruby: genome_visitor bindings (output stream)"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/genome_visitor.rb #{$testdata}gff3_file_1_short.txt"
    run "env LC_ALL=C sort #{last_stdout}"
    run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
  end

  Name "gtruby: feature_index and feature_stream bindings"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/feature_stuff.rb " +
             "#{$testdata}gff3_file_1_short.txt"
    run "env LC_ALL=C sort #{last_stdout}"
    run "grep -v '^##sequence-region' #{$testdata}gff3_file_1_short_sorted.txt | diff #{last_stdout} -"
  end
  if not $arguments["nocairo"] then
    Name "gtruby: AnnotationSketch bindings (valid gff3 file)"
    Keywords "gt_ruby"
    Test do
      run_ruby "#{$testdata}gtruby/sketch.rb test.png " +
               "#{$testdata}gff3_file_1_short.txt"
    end

    Name "gtruby: AnnotationSketch bindings (corrupt gff3 file)"
    Keywords "gt_ruby"
    Test do
      run_ruby("#{$testdata}gtruby/sketch.rb test.png #{$testdata}corrupt.gff3",
               :retval => 1)
      grep last_stderr, "GenomeTools error"
    end

    Name "gtruby: AnnotationSketch bindings (nonexistent gff3 file)"
    Keywords "gt_ruby"
    Test do
      run_ruby("#{$testdata}gtruby/sketch.rb test.png " +
               "#{$testdata}nonexistent_file", :retval => 1)
      grep last_stderr, "GenomeTools error"
    end

    Name "gtruby: AnnotationSketch bindings (PNG stream)"
    Keywords "gt_ruby"
    Test do
      run_ruby "#{$testdata}gtruby/sketch_stream.rb test.png " +
               "#{$testdata}gff3_file_1_short.txt"
    end

    Name "gtruby: AnnotationSketch bindings (TrackSelectorFunc)"
    Keywords "gt_ruby"
    Test do
      run_ruby "#{$testdata}gtruby/block_stuff.rb " +
               "#{$testdata}gff3_file_1_short.txt"
      run "env LC_ALL=C sort #{last_stdout}"
      run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.blocks"
    end

    Name "gtruby: AnnotationSketch bindings (style)"
    Keywords "gt_ruby"
    Test do
      run_ruby "#{$testdata}gtruby/style.rb #{$cur}/gtdata/sketch/default.style"
    end

    Name "gtruby: AnnotationSketch bindings (error reporting)"
    Keywords "gt_ruby"
    Test do
      run_ruby "#{$testdata}gtruby/sketch-failures.rb " +
               "#{$testdata}gff3_file_1_short.txt"
    end

    Name "gtruby: AnnotationSketch bindings (Graphics)"
    Keywords "gt_ruby"
    Test do
      run_ruby "#{$testdata}gtruby/graphics_stuff.rb " +
               "#{$testdata}graphics_curve_test_coords.txt " +
               "out.svg"
      # will fail e.g. if cairo toy font setup is different from test machine
      # disabled for now
      # run "diff out.svg #{$testdata}graphics_test.out"
    end

    Name "gtruby: AnnotationSketch bindings (FeatureNode(Iterator))"
    Keywords "gt_ruby"
    Test do
      run_ruby "#{$testdata}gtruby/feature_node.rb"
    end

    Name "gtruby: show_recmaps"
    Keywords "gt_ruby showrecmaps"
    Test do
      run_ruby "#{$testdata}gtruby/show_recmaps.rb " +
               "#{$testdata}standard_gene_as_tree.gff3"
      run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.hotspots"
    end
  end

  Name "gtruby: Encseq bindings"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/encseq.rb"
  end

  Name "gtruby: show_seqids"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/show_seqids.rb #{$testdata}encode_known_genes_Mar07.gff3"
    run "diff #{last_stdout} #{$testdata}encode_known_genes_Mar07.seqids"
  end

  Name "gtruby: used_types"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/used_types.rb " +
             "#{$testdata}standard_gene_as_tree.gff3"
    run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.types"
  end

  Name "gtruby: {Comment,Sequence,Region,Meta,EOF}Node classes"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/node_types.rb"
  end

  Name "gtruby: CustomStream/CustomVisitor basic tests"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/custom_stuff.rb #{$testdata}eden.gff3"
    run "diff #{last_stdout} #{$testdata}custom_streams_ref.txt"
  end

  Name "gtruby: CustomStream/CustomVisitor all node types"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/custom_visitor.rb"
  end

  Name "gtruby: Range class"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/range.rb"
  end

  Name "gtruby: TypeChecker class"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/type_checker.rb #{$cur}/gtdata/obo_files/so.obo"
  end

  Name "gtruby: TypeChecker class (failure)"
  Keywords "gt_ruby"
  Test do
    run_ruby "#{$testdata}gtruby/type_checker.rb #{$gtdata}/obo_files/so", :retval => 1
  end
end
genometools-1.5.1/testsuite/gt_sambam_include.rb000066400000000000000000000026441211610345200220650ustar00rootroot00000000000000Name "gt dev sambam read_sam"
Keywords "gt_sambam read_sambam sam"
Test do
  run_test "#{$bin}gt dev sambam -sam " +
           "-idxfile #{$testdata}/example_1.fa.fai " +
           "#{$testdata}/example_1.sam.gz"
  run_test "diff #{$testdata}/example_1.sam.extract " +
           "#{last_stdout}"
end

Name "gt dev sambam read_sam fail without header"
Keywords "gt_sambam read_sambam sam"
Test do
  run_test "#{$bin}gt dev sambam -sam " +
           "#{$testdata}/example_1.sam.gz", :retval => 1
end

Name "gt dev sambam read bam"
Keywords "gt_sambam read_sambam bam"
Test do
  run_test "#{$bin}gt dev sambam " +
           "#{$testdata}/example_1.bam"
  run_test "diff #{$testdata}/example_1.sam.extract " +
           "#{last_stdout}"
end

Name "gt dev sambam read sam lines"
Keywords "gt_sambam read_sambam sam"
Test do
  (50..200).step(50) do |i|
    run_test "#{$bin}gt dev sambam -sam -lines #{i} " +
             "-idxfile #{$testdata}/example_1.fa.fai " +
             "#{$testdata}/example_1.sam.gz"
    run_test "head -n #{i} #{$testdata}/example_1.sam.extract | " +
             "diff #{last_stdout} -"
  end
end

Name "gt dev sambam read bam lines"
Keywords "gt_sambam read_sambam bam"
Test do
  (50..200).step(50) do |i|
    run_test "#{$bin}gt dev sambam -lines #{i} " +
             "#{$testdata}/example_1.bam"
    run_test "head -n #{i} #{$testdata}/example_1.sam.extract | " +
             "diff #{last_stdout} -"
  end
end
genometools-1.5.1/testsuite/gt_script_filter_include.rb000066400000000000000000000016251211610345200234740ustar00rootroot00000000000000SCRIPT_FILTER_FIELDS = ["name", "author", "version", "email", "short_description", "description"]

Name "gt scriptfilter metadata"
Keywords "gt_scriptfilter"
Test do
  run "#{$bin}gt scriptfilter -scriptname false " + \
      " #{$testdata}/gtscripts/filter_metadata_test_all_strings.lua"
  run_test "diff #{$testdata}/script_filter_output.txt #{last_stdout}"
end

["", "-oneline"].each do |par|
  Name "gt scriptfilter metadata as functions #{par}"
  Keywords "gt_scriptfilter"
  Test do
    run "#{$bin}gt scriptfilter -scriptname false #{par} " + \
        " #{$testdata}/gtscripts/filter_metadata_test_all_strings.lua " + \
        " > strings.txt"
    SCRIPT_FILTER_FIELDS.each do |field|
      run_test "#{$bin}gt scriptfilter -scriptname false #{par} " + \
               "#{$testdata}/gtscripts/filter_metadata_test_#{field}_function.lua"
      run_test "diff strings.txt #{last_stdout}"
    end
  end
end
  
genometools-1.5.1/testsuite/gt_scripts_include.rb000066400000000000000000000125261211610345200223140ustar00rootroot00000000000000Name "arg passing test 1"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/arg.lua"
  grep(last_stdout, /^arg\[0\]=.*gt.*arg\.lua/)
end

Name "arg passing test 2"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/arg.lua foo"
  grep(last_stdout, /^arg\[0\]=.*gt.*arg\.lua/)
  grep(last_stdout, /^arg\[1\]=foo$/)
end

Name "bittab bindings"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/bittab.lua"
end

1.upto(4) do |i|
  Name "csa_stream bindings #{i}"
  Keywords "gt_scripts"
  Test do
    run_test "#{$bin}gt  #{$testdata}gtscripts/csa_stream.lua " +
             "#{$testdata}gt_csa_prob_#{i}.in"
    run "diff #{last_stdout} #{$testdata}gt_csa_prob_#{i}.out"
  end
end

1.upto(14) do |i|
  Name "cds_stream bindings #{i}"
  Keywords "gt_scripts"
  Test do
    run_test "#{$bin}gt  #{$testdata}gtscripts/cds_stream.lua " +
             "#{$testdata}gt_cds_test_#{i}.fas " +
             "#{$testdata}gt_cds_test_#{i}.in"
    run "sed 's/gtscript/gt cds/' #{last_stdout}"
    run "diff #{last_stdout} #{$testdata}gt_cds_test_#{i}.out"
  end
end

Name "genome_node bindings"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/genome_node.lua"
end

Name "genome_stream bindings"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/genome_stream.lua #{$testdata}"
end

Name "genome_stream bindings (output stream)"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/gff3.lua #{$testdata}gff3_file_1_short.txt"
  run "env LC_ALL=C sort #{last_stdout}"
  run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end

Name "genome_visitor bindings"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/genome_visitor.lua #{$testdata}gff3_file_1_short.txt"
  run "env LC_ALL=C sort #{last_stdout}"
  run "diff #{last_stdout} #{$testdata}gff3_file_1_short_sorted.txt"
end

Name "range bindings"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/range.lua"
end

Name "memleak.lua"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/memleak.lua #{$testdata}standard_gene_as_tree.gff3"
end

Name "scorematrix2c"
Keywords "gt_scripts scorematrix"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/scorematrix2c.lua #{$testdata}BLOSUM62"
  run "diff #{last_stdout} #{$testdata}blosum62.c"
end

Name "scorematrix2stdout"
Keywords "gt_scripts scorematrix"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/scorematrix2stdout.lua " +
           "#{$testdata}BLOSUM62.gth"
  run "diff #{last_stdout} #{$testdata}BLOSUM62.out"
end

Name "require 'gtlua'"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/require_gtlua.lua"
end

Name "LPeg library"
Keywords "gt_scripts lpeg"
Test do
  run "cp #{$cur}/src/external/lpeg-0.10.2/test.lua ."
  run "cp #{$cur}/src/external/lpeg-0.10.2/re.lua ."
  run_test "#{$bin}gt test.lua"
end

Name "MD5 library"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$cur}/src/external/md5-1.1.2/tests/test.lua"
end

Name "gtdoc"
Keywords "gt_scripts gtdoc"
Test do
  run_test "#{$bin}gt #{$testdata}../gtscripts/gtdoc.lua #{$cur}"
end

Name "gtdoc -v"
Keywords "gt_scripts gtdoc"
Test do
  run_test "#{$bin}gt #{$testdata}../gtscripts/gtdoc.lua -v #{$cur}"
end

Name "gtdoc -html"
Keywords "gt_scripts gtdoc"
Test do
  run_test "#{$bin}gt #{$testdata}../gtscripts/gtdoc.lua -html #{$cur}"
end

Name "gtdoc -html -v"
Keywords "gt_scripts gtdoc"
Test do
  run_test "#{$bin}gt #{$testdata}../gtscripts/gtdoc.lua -html -v #{$cur}"
end

Name "feature_index and feature_stream bindings"
Keywords "gt_scripts"
Test do
  run_test "#{$bin}gt #{$testdata}gtscripts/feature_stuff.lua #{$testdata}"
  run "env LC_ALL=C sort #{last_stdout}"
  run "grep -v '^##sequence-region' #{$testdata}gff3_file_1_short_sorted.txt | diff #{last_stdout} -"
end

if not $arguments["nocairo"] then
  Name "AnnotationSketch (general bindings)"
  Keywords "gt_scripts"
  Test do
    run_test "#{$bin}gt #{$testdata}gtscripts/sketch.lua test.png " +
             "#{$testdata}gff3_file_1_short.txt"
  end

  Name "AnnotationSketch (recmaps)"
  Keywords "gt_scripts"
  Test do
    run_test "#{$bin}gt #{$testdata}gtscripts/recmap.lua #{$testdata}gff3_file_1_short.txt"
    run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.recmaps"
  end

  Name "AnnotationSketch (invalid ImageInfo object)"
  Keywords "gt_scripts"
  Test do
    run_test("#{$bin}gt #{$testdata}gtscripts/ii_fail.lua #{$testdata}gff3_file_1_short.txt", :retval => 1)
  end

  Name "show_seqids"
  Keywords "gt_scripts"
  Test do
    run_test("#{$bin}gt #{$testdata}gtscripts/show_seqids.lua #{$testdata}encode_known_genes_Mar07.gff3", :maxtime => 100)
    run "diff #{last_stdout} #{$testdata}encode_known_genes_Mar07.seqids"
  end

  Name "evalviz.lua test 1"
  Keywords "gt_scripts"
  Test do
    run_test "#{$bin}gt #{$testdata}../gtscripts/evalviz.lua png_files #{$testdata}gt_eval_test_1.in #{$testdata}gt_eval_test_1.in"
    run "grep -v seqid #{last_stdout}"
    run "diff #{last_stdout} #{$testdata}gt_eval_test_1.out"
  end

=begin XXX: takes too long
  Name "evalviz.lua test 2"
  Keywords "gt_scripts"
  Test do
    run_test "#{$bin}gt #{$testdata}../gtscripts/evalviz.lua png_files #{$testdata}gt_evalviz_test.reality #{$testdata}gt_evalviz_test.prediction"
    run "diff #{last_stdout} #{$testdata}gt_evalviz_test.out"
  end
=end
end
genometools-1.5.1/testsuite/gt_select_include.rb000066400000000000000000000300121211610345200220720ustar00rootroot00000000000000Name "gt select test (no filter)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-seqid ctg123)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -seqid ctg123 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-seqid undef)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -seqid undef #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}header.gff3"
end

Name "gt select test (-source .)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -source . #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-source undef)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -source undef #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.header"
end

Name "gt select test (-maxgenelength)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -maxgenelength 8001 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-maxgenelength)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -maxgenelength 8000 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test.out"
end

Name "gt select test (-mingenescore)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -mingenescore .5 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-mingenescore)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -mingenescore .6 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test.out"
end

Name "gt select test (-maxgenescore)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -maxgenescore .5 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-maxgenescore)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -maxgenescore .4 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test.out"
end

Name "gt select test (-maxgenenum)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -maxgenenum 1 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-maxgenenum)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -maxgenenum 0 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test.out"
end
Name "gt select test (-maxgenenum)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -maxgenenum 0 #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test.out"
end

Name "gt select test (-strand)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -strand + #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-strand)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -strand - #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test.out"
end

Name "gt select test (-strand)"
Keywords "gt_select"
Test do
  run_test("#{$bin}gt select -strand foo #{$testdata}standard_gene_as_tree.gff3",
           :retval => 1)
  grep last_stderr, /must be one of/
end

Name "gt select test (-overlap)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -overlap 2000 3000 " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-overlap)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -overlap 9001 10000 " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test.out"
end

Name "gt select test (-minaveragessp)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -minaveragessp 0.5 " +
           "#{$testdata}splice_site_prob.gff3"
  run "diff #{last_stdout} #{$testdata}splice_site_prob.out"
end

Name "gt select test (-minaveragessp)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -minaveragessp 0.35 " +
           "#{$testdata}splice_site_prob.gff3"
  run "diff #{last_stdout} #{$testdata}splice_site_prob.gff3"
end

Name "gt select test (-hascds)"
Keywords "gt_select"
Test do
  run_test("#{$bin}gt select -hascds " +
           "#{$testdata}encode_known_genes_Mar07.gff3 | " +
           "#{$memcheck} #{$bin}gt stat", :maxtime => 120)
  run "diff #{last_stdout} #{$testdata}gt_select_encode.out"
end

Name "gt select test (-contain)"
Keywords "gt_select contain"
Test do
  run_test "#{$bin}gt select -contain 1000 9000 " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test_contain.1000-9000"
end

Name "gt select test (-contain)"
Keywords "gt_select contain"
Test do
  run_test "#{$bin}gt select -contain 1001 9000 " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test_contain.1001-9000"
end

Name "gt select test (-contain)"
Keywords "gt_select contain"
Test do
  run_test "#{$bin}gt select -contain 1000 8999 " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test_contain.1000-8999"
end

Name "gt select test (-contain)"
Keywords "gt_select contain"
Test do
  run_test "#{$bin}gt select -contain 1500000 1600000 " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}header.gff3"
end

Name "gt select test (-targetstrand)"
Keywords "gt_select targetstrand"
Test do
  run_test "#{$bin}gt select -targetstrand - #{$testdata}U89959_sas.gff3"
  run "diff #{last_stdout} #{$testdata}U89959_sas.minus_targets"
end

Name "gt select test (-targetstrand)"
Keywords "gt_select targetstrand"
Test do
  run_test "#{$bin}gt select -targetstrand + " +
            "#{$testdata}target_attribute_without_strand.gff3"
  run "diff #{last_stdout} #{$testdata}target_attribute_without_strand.gff3"
end

Name "gt select test (-targetbest, simple)"
Keywords "gt_select targetbest"
Test do
  run_test "#{$bin}gt select -targetbest " +
           "#{$testdata}filter_targetbest_simple_test.gff3"
  run "diff #{last_stdout} #{$testdata}filter_targetbest_simple_test.out"
end

Name "gt select test (-targetbest, complex)"
Keywords "gt_select targetbest"
Test do
  run_test "#{$bin}gt select -targetbest " +
           "#{$testdata}filter_targetbest_complex_test.gff3"
  run "diff #{last_stdout} #{$testdata}filter_targetbest_complex_test.out"
end

Name "gt select test (-targetbest, corrupt file)"
Keywords "gt_select targetbest"
Test do
  run_test("#{$bin}gt select -targetbest #{$testdata}corrupt_large.gff3",
           :retval => 1)
  grep last_stderr, "not a valid character"
end

Name "gt select test (-targetbest, multiple targets)"
Keywords "gt_select targetbest"
Test do
  run_test "#{$bin}gt select -targetbest " +
           "#{$testdata}filter_targetbest_multiple_test.gff3"
  run      "diff #{last_stdout} " +
           "#{$testdata}filter_targetbest_multiple_test.gff3"
end

Name "gt select test (-rule_files, one file, node type in gff3)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_files " + 
           "#{$testdata}gtscripts/filter_test_nodetype.lua -- " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-rule_files, one file, node type not in gff3)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_files " + 
           "#{$testdata}gtscripts/filter_test_wrong_nodetype.lua -- " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test.out"
end

Name "gt select test (-rule_files, two files, logic = AND)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_files " + 
           "#{$testdata}gtscripts/filter_test_nodetype.lua " +
           "#{$testdata}gtscripts/filter_test_wrong_nodetype.lua -- " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_select_test.out"
end

Name "gt select test (-rule_files, two files, logic = OR)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_logic OR -rule_files " + 
           "#{$testdata}gtscripts/filter_test_nodetype.lua " +
           "#{$testdata}gtscripts/filter_test_wrong_nodetype.lua -- " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.gff3"
end

Name "gt select test (-rule_files, one file, wrong function name)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_files " + 
           "#{$testdata}gtscripts/filter_test_wrong_function_name.lua -- " +
           "#{$testdata}standard_gene_as_tree.gff3", :retval => 1
  grep last_stderr, /error/
end

Name "gt select test (reading_frame_length % 3 != 0)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_files " + 
           "#{$testdata}gtscripts/filter_test_orflength.lua -- " +
           "#{$testdata}filter_luafilter_test.gff3"
  run "diff #{last_stdout} #{$testdata}filter_luafilter_filtered_orfs.gff3"
end
  
Name "gt select test (check for LTR_retrotransposon and LTRs)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_files " + 
           "#{$testdata}gtscripts/filter_test_LTR.lua -- " +
           "#{$testdata}filter_luafilter_test.gff3"
  run "diff #{last_stdout} #{$testdata}filter_luafilter_filtered_LTR.gff3"
end

Name "gt select test (min two orfs on forward strand)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_files " + 
           "#{$testdata}gtscripts/filter_test_orf_pos_strand.lua -- " +
           "#{$testdata}filter_luafilter_test.gff3"
  run "diff #{last_stdout} #{$testdata}filter_luafilter_filtered_orf_pos.gff3"
end

Name "gt select test (orfs without frame attribute)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_files " + 
           "#{$testdata}gtscripts/filter_test_frame_attribute.lua -- " +
           "#{$testdata}filter_luafilter_test_no_frame_attribute.gff3"
  run "diff #{last_stdout} #{$testdata}filter_luafilter_filtered_orf_frame.gff3"
end

Name "gt select test (dropped to file (1))"
 Keywords "gt_select"
 Test do
   run_test "#{$bin}gt select -dropped_file nh_file01.gff3 -rule_files " + 
            "#{$testdata}gtscripts/filter_test_orflength.lua -- " +
            "#{$testdata}filter_luafilter_test.gff3"
   run "diff nh_file01.gff3 #{$testdata}filter_nh_file01.gff3"
end
  
Name "gt select test (dropped to file (2))"
 Keywords "gt_select"
 Test do
   run_test "#{$bin}gt select -dropped_file nh_file02.gff3 -rule_files " + 
            "#{$testdata}gtscripts/filter_test_LTR.lua -- " +
            "#{$testdata}filter_luafilter_test.gff3"
   run "diff nh_file02.gff3 #{$testdata}filter_nh_file02.gff3"
end

Name "gt select test (dropped to file (3))"
 Keywords "gt_select"
 Test do
   run_test "#{$bin}gt select -dropped_file nh_file03.gff3 -rule_files " + 
            "#{$testdata}gtscripts/filter_test_orf_pos_strand.lua -- " +
            "#{$testdata}filter_luafilter_test.gff3"
   run "diff nh_file03.gff3 #{$testdata}filter_nh_file03.gff3"
end

Name "gt select test (dropped to file (4))"
 Keywords "gt_select"
 Test do
   run_test "#{$bin}gt select -dropped_file nh_file04.gff3 -rule_files " + 
            "#{$testdata}gtscripts/filter_test_frame_attribute.lua -- " +
            "#{$testdata}filter_luafilter_test_no_frame_attribute.gff3"
   run "diff nh_file04.gff3 #{$testdata}filter_nh_file04.gff3"
end

Name "gt select test (lua syntax fail)"
Keywords "gt_select"
Test do
  run_test "#{$bin}gt select -rule_files " + 
           "#{$testdata}gtscripts/filter_test_syntax_fail.lua -- " +
           "#{$testdata}filter_luafilter_test_no_frame_attribute.gff3",
           :retval => 1
  grep last_stderr, /error/
end
genometools-1.5.1/testsuite/gt_seq_include.rb000066400000000000000000000122361211610345200214130ustar00rootroot00000000000000Name "gt seq nonexistent file"
Keywords "gt_seq"
Test do
  run_test("#{$bin}gt seq #{$testdata}nonexistent_file", :retval => 1)
end

1.upto(7) do |i|
  Name "gt seq fail #{i}"
  Keywords "gt_seq"
  Test do
    run_test("#{$bin}gt seq -recreate #{$testdata}gt_bioseq_fail_#{i}.fas",
             :retval => 1)
  end
end

1.upto(7) do |i|
  Name "gt seq fail #{i} (stdin)"
  Keywords "gt_seq"
  Test do
    run_test("cat #{$testdata}gt_bioseq_fail_#{i}.fas | #{$bin}gt seq -recreate -", :retval => 1)
  end
end

Name "gt seq (DOS line breaks)"
Keywords "gt_seq"
Test do
  run "#{$scriptsdir}dos2unix #{$testdata}tRNA.dos.fas > ./tRNA.unix.fas"
  run_test "#{$bin}gt seq -showfasta -width 60 #{$testdata}tRNA.dos.fas"
  run "diff #{last_stdout} tRNA.unix.fas"
  run "diff #{last_stdout} #{$testdata}tRNA.dos.fas", :retval => 1
end

Name "gt seq test 1"
Keywords "gt_seq"
Test do
  run "cp  #{$testdata}gt_bioseq_succ_1.fas ./gt_bioseq_succ_1.fas"
  run_test "#{$bin}gt seq -recreate gt_bioseq_succ_1.fas"
  if not File.exists?("gt_bioseq_succ_1.fas.esq") then
    raise TestFailed, "file \"gt_bioseq_succ_1.fas.esq\" does not exist"
  end
  if not File.exists?("gt_bioseq_succ_1.fas.esq") then
    raise TestFailed, "file \"gt_bioseq_succ_1.fas.esq\" does not exist"
  end
  old_esq_mtime = File.mtime("gt_bioseq_succ_1.fas.esq")
  old_des_mtime = File.mtime("gt_bioseq_succ_1.fas.des")
  sleep(1)
  run_test "#{$bin}gt seq gt_bioseq_succ_1.fas"
  new_esq_mtime = File.mtime("gt_bioseq_succ_1.fas.esq")
  new_des_mtime = File.mtime("gt_bioseq_succ_1.fas.des")
  # make sure the index file have not been recreated
  if (old_esq_mtime != new_esq_mtime) or (old_des_mtime != new_des_mtime) then
    raise TestFailed, "index files have been recreated"
  end
end

Name "gt seq test 1 (stdin)"
Keywords "gt_seq"
Test do
  run "cat #{$testdata}gt_bioseq_succ_1.fas | #{$memcheck} #{$bin}gt seq -"
end

Name "gt seq test 2"
Keywords "gt_seq"
Test do
  run "cp  #{$testdata}gt_bioseq_succ_2.fas ./gt_bioseq_succ_2.fas"
  run_test "#{$bin}gt seq -recreate gt_bioseq_succ_2.fas"
  if not File.exists?("gt_bioseq_succ_2.fas.esq") then
    raise TestFailed, "file \"gt_bioseq_succ_2.fas.esq\" does not exist"
  end
  if not File.exists?("gt_bioseq_succ_2.fas.des") then
    raise TestFailed, "file \"gt_bioseq_succ_2.fas.des\" does not exist"
  end
  old_esq_mtime = File.mtime("gt_bioseq_succ_2.fas.esq")
  old_des_mtime = File.mtime("gt_bioseq_succ_2.fas.des")
  sleep(1)
  run_test "#{$bin}gt seq gt_bioseq_succ_2.fas"
  new_esq_mtime = File.mtime("gt_bioseq_succ_2.fas.esq")
  new_des_mtime = File.mtime("gt_bioseq_succ_2.fas.des")
  # make sure the index file have not been recreated
  if (old_esq_mtime != new_esq_mtime) or (old_des_mtime != new_des_mtime) then
    raise TestFailed, "index files have been recreated"
  end
end

Name "gt seq test 2 (stdin)"
Keywords "gt_seq"
Test do
  run "cat #{$testdata}gt_bioseq_succ_2.fas | #{$memcheck} #{$bin}gt seq -"
end

Name "gt seq test 3"
Keywords "gt_seq"
Test do
  run_test "#{$bin}gt seq -recreate -showfasta -width 70 #{$testdata}gt_bioseq_succ_3.fas"
  run "diff #{last_stdout} #{$testdata}gt_bioseq_succ_3.fas"
end

Name "gt seq test 3 (stdin)"
Keywords "gt_seq"
Test do
  run "cat #{$testdata}gt_bioseq_succ_3.fas | #{$memcheck} #{$bin}gt seq -recreate -showfasta -width 70 -"
  run "diff #{last_stdout} #{$testdata}gt_bioseq_succ_3.fas"
end

1.upto(3) do |i|
  Name "gt seq test 3 out #{i}"
  Keywords "gt_seq"
  Test do
    run_test "#{$bin}gt seq -showseqnum #{i} -width 70 #{$testdata}gt_bioseq_succ_3.fas"
    run "diff #{last_stdout} #{$testdata}gt_bioseq_succ_3.out#{i}"
  end
end

1.upto(3) do |i|
  Name "gt seq test 3 out #{i} (stdin)"
  Keywords "gt_seq"
  Test do
    run "cat #{$testdata}gt_bioseq_succ_3.fas | #{$memcheck} #{$bin}gt seq -showseqnum #{i} -width 70 -"
    run "diff #{last_stdout} #{$testdata}gt_bioseq_succ_3.out#{i}"
  end
end

Name "gt seq test 3 out 4 fail"
Keywords "gt_seq"
Test do
  run_test("#{$bin}gt seq -showseqnum 4 #{$testdata}gt_bioseq_succ_3.fas",
           :retval => 1)
end

Name "gt seq test 3 stat"
Keywords "gt_seq"
Test do
  run_test "#{$bin}gt seq -stat #{$testdata}gt_bioseq_succ_3.fas"
end

Name "gt seq test 3 stat (stdin)"
Keywords "gt_seq"
Test do
  run "cat #{$testdata}gt_bioseq_succ_3.fas | #{$memcheck} #{$bin}gt seq -stat -"
end

Name "gt seq test multiple sequence files"
Keywords "gt_seq"
Test do
  run_test "#{$bin}gt seq -recreate #{$testdata}gt_bioseq_succ_1.fas #{$testdata}gt_bioseq_succ_2.fas"
end

Name "gt seq test multiple sequence files (incl. stdin)"
Keywords "gt_seq"
Test do
  run "cat #{$testdata}gt_bioseq_succ_2.fas | #{$memcheck} #{$bin}gt seq -recreate #{$testdata}gt_bioseq_succ_1.fas -"
end

Name "gt seq -gc-content"
Keywords "gt_seq"
Test do
  run "cat #{$testdata}gt_bioseq_succ_3.fas | #{$memcheck} #{$bin}gt seq -gc-content -"
  run "diff #{last_stdout} #{$testdata}gt_bioseq_succ_3.gc"
end

Name "gt seq -seqlengthdistri"
Keywords "gt_seq"
Test do
  run_test "#{$bin}gt seq -seqlengthdistri #{$testdata}sw100K1.fsa"
  run "diff #{last_stdout} #{$testdata}gt_bioseq_seqlengthdistri.out"
end

Name "gt seq -showseqnum 1.5"
Keywords "gt_seq"
Test do
  run_test("#{$bin}gt seq -showseqnum 1.5 #{$testdata}sw100K1.fsa",
           :retval => 1)
end
genometools-1.5.1/testsuite/gt_seqbuffer_include.rb000066400000000000000000000241361211610345200226070ustar00rootroot00000000000000Name "sequence buffer: EMBL 2-character code missing"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}embl_test1.embl", :retval => 1
  grep(last_stderr, "2-character line code not found in line 2")
end

Name "sequence buffer: EMBL file type unguessable"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}embl_test2.embl", :retval => 1
  grep(last_stderr, "cannot guess file type of file")
end

Name "sequence buffer: EMBL missing blanks"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}embl_test3.embl", :retval => 1
  grep(last_stderr, "3 blanks expected between")
end

Name "sequence buffer: EMBL unterminated sequence"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}embl_test4.embl", :retval => 1
  grep(last_stderr, "unterminated sequence")
end

Name "sequence buffer: EMBL multi-line description"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}embl_test5.embl"
  run "diff #{last_stdout} #{$testdata}embl_test5.fas"
end

Name "sequence buffer: EMBL empty sequence"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}embl_test6.embl", :retval => 1
  grep(last_stderr, "sequence 0 is empty")
end

Name "sequence buffer: EMBL files mixed with GenBank"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}Random.embl " + \
           "#{$testdata}Random.gbk", :retval => 1
end

Name "sequence buffer: EMBL files mixed with FASTA"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}Random.embl " + \
           "#{$testdata}Random.fna", :retval => 1
end

allfiles = ["Atinsert",
            "Duplicate",
            "Random-Small",
            "Random",
            "Random159",
            "Random160",
            "RandomN",
            "TTT-small",
            "trna_glutamine"]

allfiles.each do |file|
  Name "sequence buffer: check EMBL <-> FASTA #{file}"
  Keywords "gt_convertseq sequencebuffer"
  Test do
    run_test "#{$bin}gt convertseq #{$testdata}#{file}.fna " + \
             "| grep -v '>'  > #{file}_out1"
    run_test "#{$bin}gt convertseq #{$testdata}#{file}.embl " + \
             "| grep -v '>' > #{file}_out2"
    run "diff -i #{file}_out1 #{file}_out2"
  end

  Name "sequence buffer: check EMBL effectivelength #{file}"
  Keywords "gt_convertseq sequencebuffer filelengthvalues"
  Test do
    run_test "#{$bin}gt convertseq -noseq -showfilelengthvalues " + \
             "#{$testdata}#{file}.embl"
    efflength1 = File.open(last_stderr).read.match(/ \d+\/(\d+)$/)[1].to_i
    run_test "#{$bin}gt convertseq -noseq -showfilelengthvalues " + \
             "#{$testdata}#{file}.fna"
    efflength2 = File.open(last_stderr).read.match(/ \d+\/(\d+)$/)[1].to_i
    raise if efflength1 != efflength2
  end

  Name "sequence buffer: check EMBL rawfilelength #{file}"
  Keywords "gt_convertseq sequencebuffer filelengthvalues"
  Test do
    run_test "#{$bin}gt convertseq -noseq -showfilelengthvalues " + \
             "#{$testdata}#{file}.embl"
    rawlength = File.open(last_stderr).read.match(/ (\d+)\/\d+$/)[1].to_i
    realsize = File.size("#{$testdata}#{file}.embl")
    raise if rawlength != realsize
  end
end

Name "sequence buffer: GenBank empty sequence"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}genbank_test1.gbk", \
           :retval => 1
  grep(last_stderr, "sequence 0 is empty")
end

Name "sequence buffer: GenBank file type unguessable"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}genbank_test3.gbk", \
           :retval => 1
  grep(last_stderr, "cannot guess file type of file")
end

Name "sequence buffer: GenBank unterminated sequence"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}genbank_test4.gbk", \
           :retval => 1
  grep(last_stderr, "only terminators")
end

Name "sequence buffer: GenBank missing sequence offset numbers"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}genbank_test6.gbk", \
           :retval => 1
  grep(last_stderr, "sequence offset")
end

Name "sequence buffer: GenBank blank missing"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}genbank_test5.gbk", \
           :retval => 1
  grep(last_stderr, "blank expected")
end

Name "sequence buffer: GenBank text before LOCUS"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}genbank_test2.gbk"
  run "diff #{last_stdout} #{$testdata}genbank_test2.fas"
end

Name "sequence buffer: GenBank missing DEFINITION line"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}genbank_test2.gbk"
end

Name "sequence buffer: GenBank multiple DEFINITION lines"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}genbank_test8.gbk", \
           :retval => 1
  grep(last_stderr, "encountered another DEFINITION line")
end

Name "sequence buffer: GenBank files mixed with EMBL"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}Random.gbk " + \
           "#{$testdata}Random.embl"
end

Name "sequence buffer: GenBank files mixed with FASTA"
Keywords "gt_convertseq sequencebuffer"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}Random.gbk " + \
           "#{$testdata}Random.fna"
end

gbfiles = ["Atinsert",
           "Duplicate",
           "Random-Small",
           "Random",
           "Random159",
           "Random160",
           "RandomN",
           "TTT-small",
           "trna_glutamine"]

gbfiles.each do |file|
  Name "sequence buffer: check GenBank <-> FASTA #{file}"
  Keywords "gt_convertseq sequencebuffer"
  Test do
    run_test "#{$bin}gt convertseq #{$testdata}#{file}.fna " + \
             "| grep -v '>' > #{file}_out1"
    run_test "#{$bin}gt convertseq #{$testdata}#{file}.gbk " + \
             "| grep -v '>' > #{file}_out2"
    run "diff -i #{file}_out1 #{file}_out2"
  end

  Name "sequence buffer: check GenBank effectivelength #{file}"
  Keywords "gt_convertseq sequencebuffer filelengthvalues"
  Test do
    run_test "#{$bin}gt convertseq -noseq -showfilelengthvalues " + \
             "#{$testdata}#{file}.gbk"
    efflength1 = File.open(last_stderr).read.match(/ \d+\/(\d+)$/)[1].to_i
    run_test "#{$bin}gt convertseq -noseq -showfilelengthvalues " + \
             "#{$testdata}#{file}.fna"
    efflength2 = File.open(last_stderr).read.match(/ \d+\/(\d+)$/)[1].to_i
    raise if efflength1 != efflength2
  end

  Name "sequence buffer: check GenBank rawfilelength #{file}"
  Keywords "gt_convertseq sequencebuffer filelengthvalues"
  Test do
    run_test "#{$bin}gt convertseq -noseq -showfilelengthvalues " + \
             "#{$testdata}#{file}.gbk"
    rawlength = File.open(last_stderr).read.match(/ (\d+)\/\d+$/)[1].to_i
    realsize = File.size("#{$testdata}#{file}.gbk")
    raise if rawlength != realsize
  end
end

Name "sequence buffer: FastQ success"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}test1.fastq"
  run "diff -i #{last_stdout} #{$testdata}test1.fasta"
end

Name "sequence buffer: FastQ success, seq > buffersize"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt dev readreads -fasta #{$testdata}fastq_long.fastq > ref.fasta"
  run_test "#{$bin}gt convertseq #{$testdata}fastq_long.fastq"
  run "diff -i #{last_stdout} ref.fasta"
end

Name "sequence buffer: FastQ non-FASTQ file"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}eden.gff3", \
           :retval => 1
  grep(last_stderr, /unknown file contents/)
end

Name "sequence buffer: FastQ invalid block start"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}test2_wrong_begin.fastq", \
           :retval => 1
  grep(last_stderr, /unknown file contents/)
end

Name "sequence buffer: FastQ different seqnames"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt convertseq " + \
           "#{$testdata}test3_different_seqnames.fastq", \
           :retval => 1
  grep(last_stderr, "sequence description 'HWI-EAS306_9_FC305MP_6_1_1331" + \
                     "_1843' is not equal to qualities description 'HWI-EAS3" +\
                     "06_9_FC305MP_6_1_1331' in line")
end

Name "sequence buffer: FastQ different seqlengths 1"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt convertseq " + \
           "#{$testdata}test4_different_seqlengths.fastq", \
           :retval => 1
  grep(last_stderr, "lengths of character sequence and qualities sequence " + \
                     "differ")
end

Name "sequence buffer: FastQ different seqlengths 2"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt convertseq " + \
           "#{$testdata}test9_uneven_length.fastq", \
           :retval => 1
  grep(last_stderr, "qualities string of sequence length 33 is not ended " + \
                     "by newline")
end

Name "sequence buffer: FastQ tricky"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt dev readreads -fasta " + \
           "#{$testdata}test5_tricky.fastq > ref.fas"
  run_test "#{$bin}gt convertseq " + \
           "#{$testdata}test5_tricky.fastq"
  run "diff -i #{last_stdout} ref.fas"
end

Name "sequence buffer: FastQ empty sequence"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}test7_empty_seq.fastq", \
           :retval => 1
  grep(last_stderr, /empty sequence/)
end

Name "sequence buffer: FastQ premature end"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}test6_premature_end.fastq", \
           :retval => 1
  grep(last_stderr, /premature end/)
end

Name "sequence buffer: FastQ multiline"
Keywords "gt_convertseq sequencebuffer fastq"
Test do
  run_test "#{$bin}gt convertseq #{$testdata}test10_multiline.fastq"
end
genometools-1.5.1/testsuite/gt_seqfilter_include.rb000066400000000000000000000012551211610345200226200ustar00rootroot00000000000000Name "gt seqfilter -minlength"
Keywords "gt_seqfilter"
Test do
  run_test "#{$bin}gt seqfilter -minlength 1000 " +
           "#{$testdata}nGASP/protein_100.fas"
  run "diff #{last_stdout} #{$testdata}nGASP/protein_long.fas"
end

Name "gt seqfilter -maxlength"
Keywords "gt_seqfilter"
Test do
  run_test "#{$bin}gt seqfilter -maxlength 499 " +
           "#{$testdata}nGASP/protein_100.fas"
  run "diff #{last_stdout} #{$testdata}nGASP/protein_short.fas"
end

Name "gt seqfilter -maxseqnum"
Keywords "gt_seqfilter"
Test do
  run_test "#{$bin}gt seqfilter -maxseqnum 10 " +
           "#{$testdata}nGASP/protein_100.fas"
  run "diff #{last_stdout} #{$testdata}nGASP/protein_10.fas"
end
genometools-1.5.1/testsuite/gt_seqids_include.rb000066400000000000000000000010221211610345200221020ustar00rootroot00000000000000Name "gt seqids"
Keywords "gt_seqids"
Test do
  run "#{$bin}gt seqids #{$testdata}/encode_known_genes_Mar07.gff3"
  run "diff #{last_stdout} #{$testdata}/encode_known_genes_Mar07.seqids"
end

Name "gt seqids (empty file)"
Keywords "gt_seqids"
Test do
  run "#{$bin}gt seqids #{$testdata}/gt_view_prob_1.gff3 > out"
  run "touch tmp"
  run "diff out tmp"
end

Name "gt seqids (nonexistant file)"
Keywords "gt_seqids"
Test do
  run "#{$bin}gt seqids #{$testdata}/foo", :retval => 1
  grep(last_stderr, /such file or directory/)
end
genometools-1.5.1/testsuite/gt_seqlensort_include.rb000066400000000000000000000016411211610345200230200ustar00rootroot00000000000000def compare_encseqs3(indexname1, indexname2, cmpinfos)
  run "#{$bin}gt encseq decode #{indexname1}"
  decoded1 = last_stdout
  run "#{$bin}gt encseq decode #{indexname2}"
  decoded2 = last_stdout
  run "diff #{decoded1} #{decoded2}"
  if cmpinfos
    run "#{$bin}gt encseq info #{indexname1}"
    run "grep -v 'index name' #{last_stdout}"
    info1 = last_stdout
    run "#{$bin}gt encseq info #{indexname2}"
    run "grep -v 'index name' #{last_stdout}"
    info2 = last_stdout
    run "diff #{info1} #{info2}"
  end
end

Name "gt seqlensort"
Keywords "gt_seqlensort"
Test do
  run "cp #{$testdata}/gt_seqlensort_test.fas sequences"
  run "#{$bin}gt dev seqlensort -db sequences -indexname seqlensort"
  run "cp #{$testdata}/gt_seqlensort_test_sorted.fas sequences"
  run "#{$bin}gt encseq encode -des no -sds no -md5 no "+
      "-indexname encseq_encode sequences"
  compare_encseqs3("seqlensort", "encseq_encode", true)
end
genometools-1.5.1/testsuite/gt_seqmutate_include.rb000066400000000000000000000012201211610345200226220ustar00rootroot00000000000000Name "gt seqmutate test 1"
Keywords "gt_seqmutate"
Test do
  run_test "#{$bin}gt -seed 1 seqmutate #{$testdata}gt_mutate_test_1.fas"
  run "diff #{last_stdout} #{$testdata}gt_mutate_test_1.out"
end

Name "gt seqmutate test 2"
Keywords "gt_seqmutate"
Test do
  run_test "#{$bin}gt -seed 987654321 seqmutate #{$testdata}gt_mutate_test_2.fas"
  run "diff #{last_stdout} #{$testdata}gt_mutate_test_2.out"
end

Name "gt seqmutate test both"
Keywords "gt_seqmutate"
Test do
  run_test "#{$bin}gt -seed 555555555 mutate -rate 2 #{$testdata}gt_mutate_test_1.fas #{$testdata}gt_mutate_test_2.fas"
  run "diff #{last_stdout} #{$testdata}gt_mutate_test_both.out"
end
genometools-1.5.1/testsuite/gt_seqorder_include.rb000066400000000000000000000031111211610345200224370ustar00rootroot00000000000000Name "gt seqorder -sort test"
Keywords "gt_seqorder"
Test do
  seq = "gt_seqorder_test.fas"
  run "#{$bin}gt encseq encode #$testdata#{seq}"
  run_test "#{$bin}gt seqorder -sort #{seq}"
  run "diff #{last_stdout} #{$testdata}gt_seqorder_test_sort.fas"
end

Name "gt seqorder -revsort test"
Keywords "gt_seqorder"
Test do
  seq = "gt_seqorder_test.fas"
  run "#{$bin}gt encseq encode #$testdata#{seq}"
  run_test "#{$bin}gt seqorder -revsort #{seq}"
  run "diff #{last_stdout} #{$testdata}gt_seqorder_test_revsort.fas"
end

Name "gt seqorder -invert test"
Keywords "gt_seqorder"
Test do
  seq = "gt_seqorder_test.fas"
  run "#{$bin}gt encseq encode #$testdata#{seq}"
  origdesc = []
  IO.read("#$testdata#{seq}").each_line {|l| origdesc << l if l[0] == '>'}
  run_test "#{$bin}gt seqorder -invert #{seq}"
  invertdesc = []
  IO.read("#{last_stdout}").each_line {|l| invertdesc << l if l[0] == '>'}
  if (origdesc != invertdesc.reverse)
    fail("inverted invert differ from original")
  end
end

Name "gt seqorder -shuffle test"
Keywords "gt_seqorder"
Test do
  seq = "gt_seqorder_test.fas"
  run "#{$bin}gt encseq encode #$testdata#{seq}"
  run "sort #$testdata#{seq}"
  sorted_original = last_stdout
  run_test "#{$bin}gt seqorder -shuffle #{seq}"
  run "sort #{last_stdout}"
  run "diff #{last_stdout} #{sorted_original}"
end

Name "gt seqorder without description support"
Keywords "gt_seqorder"
Test do
  seq = "gt_seqorder_test.fas"
  run "#{$bin}gt encseq encode -des no -sds no #$testdata#{seq}"
  run_test "#{$bin}gt seqorder -sort #{seq}"
  grep last_stderr, "warning"
  grep last_stdout, ">\n"
end

genometools-1.5.1/testsuite/gt_seqstat_include.rb000066400000000000000000000054661211610345200223160ustar00rootroot00000000000000Name "gt seqstat (FASTA)"
Keywords "gt_seqstat"
Test do
  run_test "#{$bin}gt seqstat -v -distlen #{$testdata}Atinsert.fna"
  grep(last_stdout, /21 sequences/)
end

Name "gt seqstat (GenBank)"
Keywords "gt_seqstat"
Test do
  run_test "#{$bin}gt seqstat -v -distlen #{$testdata}Atinsert.gbk"
  grep(last_stdout, /21 sequences/)
end

Name "gt seqstat (EMBL)"
Keywords "gt_seqstat"
Test do
  run_test "#{$bin}gt seqstat -v -distlen #{$testdata}Atinsert.embl"
  grep(last_stdout, /21 sequences/)
end

Name "gt seqstat distlen"
Keywords "gt_seqstat"
Test do
  {10 => "860--869 1",
   100 => "800--899 4",
   1000 => "0--999 21"}.each_pair do |bucketsize, expected|
    run_test "#{$bin}gt seqstat -v -distlen"+
                      " -b #{bucketsize} #{$testdata}Atinsert.gbk"
    grep(last_stdout, expected)
  end
end

Name "gt seqstat -contigs"
Keywords "gt_seqstat"
Test do
  run_test "#{$bin}gt seqstat -contigs #{$testdata}at1MB"
  grep(last_stdout, "number.*1952")
  grep(last_stdout, "total.*770425")
  grep(last_stdout, "mean.*394")
  grep(last_stdout, "median.*399")
  grep(last_stdout, "longest.*1102")
  grep(last_stdout, "shortest.*56")
  grep(last_stdout, "contigs > 500.*198")
  grep(last_stdout, "contigs > 1K.*3")
  grep(last_stdout, "contigs > 10K.*0")
  grep(last_stdout, "contigs > 100K.*0")
  grep(last_stdout, "contigs > 1M.*0")
  grep(last_stdout, "N50.*421")
  grep(last_stdout, "L50.*797")
end

Name "gt seqstat -contigs -genome"
Keywords "gt_seqstat"
Test do
  run_test "#{$bin}gt seqstat -genome 770425 -contigs #{$testdata}at1MB"
  grep(last_stdout, "total.*770425")
  grep(last_stdout, "genome.*770425")
  grep(last_stdout, "genome.*100.00 %")
  grep(last_stdout, "N50.*421")
  grep(last_stdout, "NG50.*421")
  grep(last_stdout, "L50.*797")
  grep(last_stdout, "LG50.*797")
  run_test "#{$bin}gt seqstat -genome 100000 -contigs #{$testdata}at1MB"
  grep(last_stdout, "genome.*100000")
  grep(last_stdout, "genome.*770.42 %")
  grep(last_stdout, "N50.*421")
  grep(last_stdout, "NG50.*591")
  grep(last_stdout, "L50.*797")
  grep(last_stdout, "LG50.*74")
  run_test "#{$bin}gt seqstat -genome 1000000 -contigs #{$testdata}at1MB"
  grep(last_stdout, "genome.*1000000")
  grep(last_stdout, "genome.*77.04 %")
  grep(last_stdout, "N50.*421")
  grep(last_stdout, "NG50.*386")
  grep(last_stdout, "L50.*797")
  grep(last_stdout, "LG50.*1086")
  run_test "#{$bin}gt seqstat -genome 1600000 -contigs #{$testdata}at1MB"
  grep(last_stdout, "genome.*1600000")
  grep(last_stdout, "genome.*48.15 %")
  grep(last_stdout, "N50.*421")
  grep(last_stdout, "NG50.*n\.a\.")
  grep(last_stdout, "L50.*797")
  grep(last_stdout, "LG50.*n\.a\.")
end

Name "gt seqstat fail (unknown file type)"
Keywords "gt_seqstat"
Test do
  run_test "#{$bin}gt seqstat -v -distlen #{$testdata}empty_file", \
           :retval => 1
  grep(last_stderr, /cannot guess file type/)
end
genometools-1.5.1/testsuite/gt_seqtransform_include.rb000066400000000000000000000013321211610345200233420ustar00rootroot00000000000000Name "gt seqtransform"
Keywords "gt_seqtransform (invariant)"
Test do
  run_test "#{$bin}gt seqtransform #{$testdata}nGASP/protein_100.fas"
  run "diff #{last_stdout} #{$testdata}nGASP/protein_100.fas"
end

Name "gt seqtransform"
Keywords "gt_seqtransform -addstopaminos"
Test do
  run_test "#{$bin}gt seqtransform -addstopaminos " +
           "#{$testdata}nGASP/protein_100.fas"
  run "diff #{last_stdout} #{$testdata}nGASP/protein_100_with_stop.fas"
end

Name "gt seqtransform"
Keywords "gt_seqtransform -addstopaminos (invariant)"
Test do
  run_test "#{$bin}gt seqtransform -addstopaminos " +
           "#{$testdata}nGASP/protein_100_with_stop.fas"
  run "diff #{last_stdout} #{$testdata}nGASP/protein_100_with_stop.fas"
end
genometools-1.5.1/testsuite/gt_sequniq_include.rb000066400000000000000000000024501211610345200223050ustar00rootroot00000000000000["", " -rev", " -seqit", " -seqit -rev"].each do |opt|
  Name "gt sequniq#{opt} 2xfoo test"
  Keywords "gt_sequniq"
  Test do
    run_test "#{$bin}gt sequniq#{opt} #{$testdata}foofoo.fas"
    run "diff #{last_stdout} #{$testdata}foo.fas"
  end

  Name "gt sequniq#{opt} 3xfoo test "
  Keywords "gt_sequniq"
  Test do
    run_test "#{$bin}gt sequniq#{opt} #{$testdata}foofoofoo.fas"
    run "diff #{last_stdout} #{$testdata}foo.fas"
  end
end

["", " -seqit"].each do |opt|
  Name "gt sequniq#{opt} foo + rc(foo) test "
  Keywords "gt_sequniq"
  Test do
    run_test "#{$bin}gt sequniq#{opt} #{$testdata}foorcfoo.fas"
    run "diff #{last_stdout} #{$testdata}foorcfoo.fas"
  end

  Name "gt sequniq#{opt} -rev foo + rc(foo) test "
  Keywords "gt_sequniq"
  Test do
    run_test "#{$bin}gt sequniq#{opt} -rev #{$testdata}foorcfoo.fas"
    run "diff #{last_stdout} #{$testdata}foo.fas"
  end

  Name "gt sequniq#{opt} 2xfoo + rc(foo) test "
  Keywords "gt_sequniq"
  Test do
    run_test "#{$bin}gt sequniq#{opt} #{$testdata}foorcfoofoo.fas"
    run "diff #{last_stdout} #{$testdata}foorcfoo.fas"
  end

  Name "gt sequniq#{opt} -rev 2xfoo + rc(foo) test "
  Keywords "gt_sequniq"
  Test do
    run_test "#{$bin}gt sequniq#{opt} -rev #{$testdata}foorcfoofoo.fas"
    run "diff #{last_stdout} #{$testdata}foo.fas"
  end
end
genometools-1.5.1/testsuite/gt_shredder_include.rb000066400000000000000000000022241211610345200224170ustar00rootroot00000000000000Name "gt shredder"
Keywords "gt_shredder"
Test do
  run_test "#{$bin}gt shredder #{$testdata}U89959_genomic.fas"
end

Name "gt shredder (-coverage)"
Keywords "gt_shredder"
Test do
  run_test "#{$bin}gt shredder -coverage 5 #{$testdata}U89959_genomic.fas"
end

Name "gt shredder (-overlap)"
Keywords "gt_shredder"
Test do
  run_test "#{$bin}gt shredder -overlap 500 #{$testdata}U89959_genomic.fas"
end

Name "gt shredder (-sample)"
Keywords "gt_shredder"
Test do
  run_test "#{$bin}gt shredder -sample 0.1 #{$testdata}U89959_ests.fas"
end

Name "gt shredder (nonexistent file)"
Keywords "gt_shredder"
Test do
  run_test("#{$bin}gt shredder #{$testdata}nonexistent_file", :retval => 1)
end

Name "gt shredder (wrong argument usage)"
Keywords "gt_shredder"
Test do
  run_test("#{$bin}gt shredder -maxlength 15  #{$testdata}U89959_genomic.fas",
           :retval => 1)
  grep last_stderr, /-minlength must be <= than -maxlength/
end

Name "gt shredder (minlength = maxlength)"
Keywords "gt_shredder"
Test do
  run_test "#{$bin}gt shredder -minlength 30 -maxlength 30 " +
           "#{$testdata}Duplicate.fna"
  run "diff #{last_stdout} #{$testdata}Duplicate.shreddered"
end
genometools-1.5.1/testsuite/gt_simreads_include.rb000066400000000000000000000074471211610345200224420ustar00rootroot00000000000000def total_length(fas)
  run_test %Q(grep -v ">" #{fas} | tr -d "[:space:]" | wc -c)
  return Integer(IO.read(last_stdout))
end

def nof_seq(fas)
  run_test %Q(grep  "^>" #{fas} | wc -l)
  return Integer(IO.read(last_stdout))
end

def expect(label, value, expected)
  if value != expected
    failtest("#{label}: expected value #{expected}, "+
                       "found #{value}")
  end
end

def expect_range(label, value, min, max)
  if value < min or value > max
    failtest("#{label}: expected value in range #{min}-#{max}, "+
                       "found #{value}")
  end
end

Name "gt simreads -num -len test"
Keywords "gt_simreads"
Test do
  fas = "#{$testdata}U89959_genomic.fas"
  run_test "#{$bin}gt encseq encode #{fas}"

  run_test "#{$bin}gt simreads -num 100 -len 100 "+
                   "-force -o reads #{File.basename(fas)}"

  expect("number of reads", nof_seq("reads"), 100)  
  expect("total length", total_length("reads"), 10000)
end


Name "gt simreads test -minlen/-maxlen"
Keywords "gt_simreads"
Test do
  fas = "#{$testdata}U89959_genomic.fas"
  run_test "#{$bin}gt encseq encode #{fas}"

  run_test "#{$bin}gt simreads -num 100 -minlen 10 -maxlen 100 "+
                   "-force -o reads #{File.basename(fas)}"

  expect("number of reads", nof_seq("reads"), 100)  
  expect_range("total length", total_length("reads"), 1000, 10000)
end

Name "gt simreads -coverage test"
Keywords "gt_simreads"
Test do
  fas = "#{$testdata}U89959_genomic.fas"
  run_test "#{$bin}gt encseq encode #{fas}"

  cov = 5
  len = 100
  run_test "#{$bin}gt simreads -coverage #{cov} -len #{len} "+
                   "-force -o reads #{File.basename(fas)}"
  n = total_length(fas)
  exptlen = n * cov
  mod = exptlen % len
  exptlen += (len-mod) if mod > 0
  expnreads = exptlen / len
  expect("total length", total_length("reads"), exptlen)
  expect("number of reads", nof_seq("reads"), expnreads)
end

Name "gt simreads grep test"
Keywords "gt_simreads"
Test do
  fas = "#{$testdata}U89959_genomic.fas"
  run_test "#{$bin}gt encseq encode #{fas}"

  cov = 3
  len = 100
  n = total_length(fas)

  run_test "#{$bin}gt simreads -coverage #{cov} -len #{len} "+
                   "-force -o reads #{File.basename(fas)}"

  # test that reads originate from target sequence
  # or its reverse complement
  run_test "#{$bin}gt convertseq -fastawidth #{n+1} #{fas}"
  run_test "tail -n 1 #{last_stdout}"
  direct = IO.read(last_stdout)
  run_test "#{$bin}gt convertseq -r -fastawidth #{n+1} #{fas}"
  run_test "tail -n 1 #{last_stdout}"
  rc = IO.read(last_stdout)

  run_test "#{$bin}gt convertseq -fastawidth #{len+1} -force -o reads2 reads"
  
  f = File.open("reads2")
  i = 0
  f.each do |line|
    if !(line =~ /^>/)
      pattern = Regexp.new(Regexp.escape(line.chomp!), Regexp::IGNORECASE)
      if !(direct =~ pattern) && !(rc =~ pattern)
        failtest("read #{i} does not match")
      end
    end
    i+=1
  end  
end

def test_distfile_format(filename)
  f = File.open(filename)
  f.each do |line|
    if (line !~ /^#/ && line.chomp !~ /^\d+ \d+$/)
      failtest("distribution output file format error: #{line}")
    end
  end
  f.close
end

Name "gt simreads -ds test"
Keywords "gt_simreads"
Test do
  fas = "#{$testdata}U89959_genomic.fas"
  run_test "#{$bin}gt encseq encode #{fas}"

  cov = 10
  len = 10
  run_test "#{$bin}gt simreads -coverage #{cov} -len #{len} "+
                  "-ds starts -force -o reads #{File.basename(fas)}"
  test_distfile_format("starts")
end

Name "gt simreads -dl test"
Keywords "gt_simreads"
Test do
  fas = "#{$testdata}U89959_genomic.fas"
  run_test "#{$bin}gt encseq encode #{fas}"

  cov = 10
  minlen = 10
  maxlen = 100
  run_test "#{$bin}gt simreads -coverage #{cov} -minlen #{minlen} "+
                  "-maxlen #{maxlen} -dl lengths -force -o reads #{File.basename(fas)}"
  test_distfile_format("lengths")
end
genometools-1.5.1/testsuite/gt_sketch_include.rb000066400000000000000000000272411211610345200221060ustar00rootroot00000000000000Name "gt sketch short test"
Keywords "gt_sketch"
Test do
  run_test "#{$bin}gt sketch out.png #{$testdata}gff3_file_1_short.txt", \
           :maxtime => 600
  run "test -e out.png"
end

Name "gt sketch short test (stdin)"
Keywords "gt_sketch"
Test do
  run_test "#{$bin}gt sketch out.png < #{$testdata}gff3_file_1_short.txt", \
           :maxtime => 600
  run "test -e out.png"
end

Name "gt sketch short test (unknown output format)"
Keywords "gt_sketch"
Test do
  run_test("#{$bin}gt sketch -format unknown out.png " + \
           "#{$testdata}gff3_file_1_short.txt", :retval => 1, :maxtime => 600)
  grep(last_stderr, /must be one of:/)
end

Name "gt sketch short test (unwriteable PNG file)"
Keywords "gt_sketch"
Test do
  run "touch unwriteable.png"
  run "chmod u-w unwriteable.png"
  run_test("#{$bin}gt sketch -force unwriteable.png " + \
           "#{$testdata}gff3_file_1_short.txt", :retval => 1, :maxtime => 600)
  grep(last_stderr, /an I\/O error occurred/)
end

Name "gt sketch short test (unwriteable PDF file)"
Keywords "gt_sketch"
Test do
  run "touch unwriteable.pdf"
  run "chmod u-w unwriteable.pdf"
  run_test("#{$bin}gt sketch -format pdf -force unwriteable.pdf " + \
           "#{$testdata}gff3_file_1_short.txt", :retval => 1, :maxtime => 600)
  grep(last_stderr, /Permission denied/)
end

Name "gt sketch short test (nonexistant style file)"
Keywords "gt_sketch"
Test do
  run_test("#{$bin}gt sketch -style foo.bar out.png " + \
           "#{$testdata}gff3_file_1_short.txt", :retval => 1, :maxtime => 600)
  grep(last_stderr, /style file 'foo.bar' does not exist/)
end

Name "gt sketch short test (invalid style file)"
Keywords "gt_sketch"
Test do
  run "echo thisisnotlua > foo.bar"
  run_test("#{$bin}gt sketch  -style foo.bar out.png " + \
           "#{$testdata}gff3_file_1_short.txt", :retval => 1, :maxtime => 600)
  grep(last_stderr, /cannot run style file/)
end

Name "gt sketch prob 1"
Keywords "gt_sketch"
Test do
  run_test("#{$bin}gt sketch out.png #{$testdata}gt_view_prob_1.gff3", \
           :retval => 1, :maxtime => 600)
end

Name "gt sketch prob 2"
Keywords "gt_sketch"
Test do
  run_test "#{$bin}gt sketch out.png #{$testdata}gt_view_prob_2.gff3", \
           :maxtime => 600
  run "test -e out.png"
end

Name "gt sketch track IDs to style file"
Keywords "gt_sketch"
Test do
  run "cp #{$testdata}eden.gff3 eden2.gff3"
  run_test "#{$bin}gt sketch -force -style " + \
           "#{$testdata}trackname1.style out.png #{$testdata}eden.gff3 " + \
           "eden2.gff3"
  run "diff #{last_stdout} #{$testdata}trackname1.out"
  run "test -e out.png"
end

Name "gt sketch multiline without parent"
Keywords "gt_sketch"
Test do
  run_test "#{$bin}gt sketch out.png #{$testdata}gt_sketch_multiline_without_parent.gff3", :maxtime => 600
  run "test -e out.png"
end

Name "gt sketch pipe"
Keywords "gt_sketch"
Test do
  run "#{$bin}gt gff3 #{$testdata}gff3_file_1_short.txt > in.gff3"
  run_test "#{$bin}gt sketch -pipe out.png in.gff3 > out.gff3", :maxtime => 600
  run "diff in.gff3 out.gff3"
end

Name "gt sketch streams <-> file output"
Keywords "gt_sketch streams annotationsketch"
Test do
  m = `#{$bin}gt sketch -help`.match(/graphics format\s+choose from ([^ ]+)/m)
  raise TestFailedError if m.nil?
  m[1].chomp.split("|").each do |format|
    run_test "#{$bin}gt sketch -format #{format} out.#{format} #{$testdata}eden.gff3"
    run_test "#{$bin}gt sketch -streams -format #{format} streamout.#{format} #{$testdata}eden.gff3"
    # some formats will diff in their creation date, remove it
    run "sed -i '/CreationDate/d' out.#{format} streamout.#{format}"
    run "diff out.#{format} streamout.#{format}"
  end
end

Name "gt sketch -showrecmaps"
Keywords "gt_sketch showrecmaps"
Test do
  run_test "#{$bin}gt sketch -showrecmaps out.png " +
           "#{$testdata}standard_gene_as_tree.gff3", :maxtime => 600
  run "diff #{last_stdout} #{$testdata}standard_gene_as_tree.recmaps"
end

Name "gt sketch -showrecmaps (normal text size)"
Keywords "gt_sketch showrecmaps"
Test do
  run_test "#{$bin}gt sketch -showrecmaps out.png " +
           "#{$testdata}gt_sketch_textwidth.gff3", :maxtime => 600
  run "diff #{last_stdout} #{$testdata}gt_sketch_textwidth_0.recmaps"
end

Name "gt sketch -showrecmaps (narrow image)"
Keywords "gt_sketch showrecmaps"
Test do
  run_test "#{$bin}gt sketch -width 300 -showrecmaps out.png " +
           "#{$testdata}gt_sketch_textwidth.gff3", :maxtime => 600
  run "diff #{last_stdout} #{$testdata}gt_sketch_textwidth_1.recmaps"
end

Name "gt sketch -showrecmaps (large text size)"
Keywords "gt_sketch showrecmaps"
Test do
  run_test "#{$bin}gt sketch -style #{$testdata}bigfonts.style " + \
           "-showrecmaps out.png #{$testdata}gt_sketch_textwidth.gff3", \
           :maxtime => 600
  run "diff #{last_stdout} #{$testdata}gt_sketch_textwidth_2.recmaps"
end

Name "gt sketch runtime Lua failures"
Keywords "gt_sketch lua"
Test do
  Dir.glob("#{$testdata}fail*style") do |file|
    run_test("#{$bin}gt sketch -style #{file} " + \
             "out.png #{$testdata}eden.gff3", \
             :maxtime => 600, :retval => 1)
    grep(last_stderr, 'attempt to call global \'fail\'')
  end
end

Name "sketch_constructed (C)"
Keywords "gt_sketch annotationsketch"
Test do
  run_test "#{$bin}examples/sketch_constructed " + \
           "#{$cur}/gtdata/sketch/default.style sketch_constructed.png", \
           :maxtime => 600
end

Name "sketch_parsed (C)"
Keywords "gt_sketch annotationsketch"
Test do
  run_test "#{$bin}examples/sketch_parsed " + \
           "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
           "#{$testdata}standard_gene_with_introns_as_tree.gff3 ", \
           :maxtime => 600
end

Name "sketch_parsed reverse order (C)"
Keywords "gt_sketch annotationsketch"
Test do
  run_test "#{$bin}examples/sketch_parsed_with_ordering " + \
           "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
           "#{$testdata}eden.gff3 ", \
           :maxtime => 600
  run "diff #{last_stdout} #{$testdata}order_sketch_out.txt"
end

Name "sketch_constructed (Lua)"
Keywords "gt_sketch gt_scripts annotationsketch"
Test do
  run_test "#{$bin}gt #{$cur}/gtscripts/sketch_constructed.lua " + \
           "#{$cur}/gtdata/sketch/default.style sketch_constructed.png", \
           :maxtime => 600
end

Name "sketch_parsed (Lua)"
Keywords "gt_sketch gt_scripts annotationsketch"
Test do
  run_test "#{$bin}gt #{$cur}/gtscripts/sketch_parsed.lua " + \
           "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
           "#{$testdata}standard_gene_with_introns_as_tree.gff3", \
           :maxtime => 600
end

Name "sketch_constructed (Python)"
Keywords "gt_sketch gt_python annotationsketch"
Test do
  run_python "#{$cur}/gtpython/sketch_constructed.py " + \
             "#{$cur}/gtdata/sketch/default.style sketch_constructed.png", \
             :maxtime => 600
end

Name "sketch_parsed (Python)"
Keywords "gt_sketch gt_python annotationsketch"
Test do
  run_python "#{$cur}/gtpython/sketch_parsed.py " + \
             "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
             "#{$testdata}standard_gene_with_introns_as_tree.gff3", \
             :maxtime => 600
end

Name "sketch_parsed reverse order (Python)"
Keywords "gt_sketch gt_python annotationsketch"
Test do
  run_python "#{$testdata}gtpython/sketch_parsed_with_ordering.py " + \
             "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
             "#{$testdata}standard_gene_with_introns_as_tree.gff3", \
             :maxtime => 600
end

Name "sketch_parsed invalid order (Python, string != int)"
Keywords "gt_sketch gt_python annotationsketch"
Test do
  run_python "#{$testdata}gtpython/sketch_parsed_with_invalid_ordering.py " + \
             "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
             "#{$testdata}standard_gene_with_introns_as_tree.gff3", \
             :maxtime => 600
  grep(last_stderr, /Track ordering function must return a number/)
end

Name "sketch_parsed invalid order (Python, None)"
Keywords "gt_sketch gt_python annotationsketch"
Test do
  run_python "#{$testdata}gtpython/sketch_parsed_with_invalid_ordering_2.py " + \
             "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
             "#{$testdata}standard_gene_with_introns_as_tree.gff3", \
             :maxtime => 600
  grep(last_stderr, /Track ordering function must return a number/)
end

Name "Python runtime style failures"
  Keywords "gt_sketch gt_python annotationsketch"
  Test do
  Dir.glob("#{$testdata}fail*style") do |file|
    run_python "#{$cur}/gtpython/sketch_parsed.py " + \
               "#{file} sketch_parsed.png " + \
               "#{$testdata}eden.gff3", \
               :maxtime => 600, :retval => 1
    grep(last_stderr, 'attempt to call global \'fail\'')

    run_python "#{$cur}/gtpython/sketch_constructed.py " + \
               "#{file} sketch_constructed.png", \
               :maxtime => 600, :retval => 1
    grep(last_stderr, 'attempt to call global \'fail\'')

    run_python "#{$testdata}gtpython/style_serialize.py #{file}", :retval => 1
    grep(last_stderr, 'expected boolean, number, or string')
  end
end

rv = RUBY_VERSION.match(/^(\d+\.\d+)/)
if (!rv.nil? && rv[1].to_f < 1.9) and not $arguments["nocairo"] then
  Name "sketch_constructed (Ruby)"
  Keywords "gt_sketch gt_ruby annotationsketch"
  Test do
    run_ruby "#{$cur}/gtruby/sketch_constructed.rb " + \
             "#{$cur}/gtdata/sketch/default.style sketch_constructed.png", \
             :maxtime => 600
  end

  Name "sketch_parsed (Ruby)"
  Keywords "gt_sketch gt_ruby annotationsketch"
  Test do
    run_ruby "#{$cur}/gtruby/sketch_parsed.rb " + \
             "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
             "#{$testdata}standard_gene_with_introns_as_tree.gff3", \
             :maxtime => 600
  end

  Name "sketch_parsed reverse order (Ruby)"
  Keywords "gt_sketch gt_ruby annotationsketch"
  Test do
    run_ruby "#{$testdata}gtruby/sketch_parsed_with_ordering.rb " + \
             "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
             "#{$testdata}standard_gene_with_introns_as_tree.gff3", \
             :maxtime => 600
  end

  Name "sketch_parsed invalid order (Ruby, string != numeric)"
  Keywords "gt_sketch gt_ruby annotationsketch"
  Test do
    run_ruby "#{$testdata}gtruby/sketch_parsed_with_invalid_ordering.rb " + \
             "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
             "#{$testdata}standard_gene_with_introns_as_tree.gff3", \
             :maxtime => 600, :retval => 1
    grep(last_stderr, /Track ordering callback must return a number/)
  end

  Name "sketch_parsed invalid order (Ruby, nil)"
  Keywords "gt_sketch gt_ruby annotationsketch"
  Test do
    run_ruby "#{$testdata}gtruby/sketch_parsed_with_invalid_ordering_2.rb " + \
             "#{$cur}/gtdata/sketch/default.style sketch_parsed.png " + \
             "#{$testdata}standard_gene_with_introns_as_tree.gff3", \
             :maxtime => 600, :retval => 1
    grep(last_stderr, /Track ordering callback must return a number/)
  end

  Name "Ruby runtime style failures"
  Keywords "gt_sketch gt_ruby annotationsketch"
  Test do
    Dir.glob("#{$testdata}fail*style") do |file|
      run_ruby "#{$cur}/gtruby/sketch_parsed.rb " + \
               "#{file} sketch_parsed.png " + \
               "#{$testdata}eden.gff3", \
               :maxtime => 600, :retval => 1
      grep(last_stderr, 'attempt to call global \'fail\'')

      run_ruby "#{$cur}/gtruby/sketch_constructed.rb " + \
               "#{file} sketch_constructed.png", \
               :maxtime => 600, :retval => 1
      grep(last_stderr, 'attempt to call global \'fail\'')

      run_ruby "#{$testdata}gtruby/style_serialize.rb #{file}", :retval => 1
      grep(last_stderr, 'expected boolean, number, or string')
    end
  end
endgenometools-1.5.1/testsuite/gt_sortbench_include.rb000066400000000000000000000012621211610345200226070ustar00rootroot00000000000000methods = ["radixinplace","radixlsb",
           "thomas","system","inlinedptr","inlinedarr","direct"]

lenlist=[10,20,30,1000,2000,4000,1000000,2000000]

methods.each do |met|
  Name "gt sortbench #{met}"
  Keywords "gt_sortbench"
  Test do
    lenlist.each do |len|
      if met.match(/^radixinplace/)
        ["","-j 4"].each do |opt|
          run "#{$bin}gt #{opt} dev sortbench -impl #{met} -size #{len} -maxval 1000"
          run "#{$bin}gt #{opt} dev sortbench -impl #{met} -size #{len}"
        end
      else
        run "#{$bin}gt dev sortbench -impl #{met} -size #{len}"
        run "#{$bin}gt dev sortbench -impl #{met} -size #{len} -maxval 10000"
      end
    end
  end
end
genometools-1.5.1/testsuite/gt_splicesiteinfo_include.rb000066400000000000000000000056271211610345200236510ustar00rootroot00000000000000Name "gt splicesiteinfo -help"
Keywords "gt_splicesiteinfo"
Test do
  run_test "#{$bin}gt splicesiteinfo -help"
  grep last_stdout, "Report bugs to"
end

Name "gt splicesiteinfo -noop"
Keywords "gt_splicesiteinfo"
Test do
  run_test("#{$bin}gt splicesiteinfo -noop", :retval => 1)
  grep last_stderr, "unknown option"
end

Name "gt splicesiteinfo -seqfile nonexistent_file"
Keywords "gt_splicesiteinfo"
Test do
  run_test("#{$bin}gt splicesiteinfo -regionmapping #{$testdata}nonexistent_file",
           :retval => 1)
end

Name "gt splicesiteinfo test 1"
Keywords "gt_splicesiteinfo"
Test do
  run_test "#{$bin}gt splicesiteinfo -seqfile #{$testdata}gt_splicesiteinfo_test_1.fas #{$testdata}gt_splicesiteinfo_test_1.gff3"
  run "diff #{last_stdout} #{$testdata}gt_splicesiteinfo_test_1.out"
end

Name "gt splicesiteinfo test 2"
Keywords "gt_splicesiteinfo"
Test do
  run_test "#{$bin}gt splicesiteinfo -seqfile #{$testdata}gt_splicesiteinfo_test_2.fas #{$testdata}gt_splicesiteinfo_test_2.gff3"
  run "diff #{last_stdout} #{$testdata}gt_splicesiteinfo_test_2.out"
end

Name "gt splicesiteinfo test 3"
Keywords "gt_splicesiteinfo"
Test do
  run_test "#{$bin}gt splicesiteinfo -seqfile #{$testdata}gt_splicesiteinfo_test_1.fas #{$testdata}gt_splicesiteinfo_test_3.gff3"
  grep last_stderr, "unknown orientation"
end

Name "gt splicesiteinfo test 4"
Keywords "gt_splicesiteinfo"
Test do
  run_test "#{$bin}gt splicesiteinfo -seqfile #{$testdata}gt_splicesiteinfo_test_4.fas #{$testdata}gt_splicesiteinfo_test_4.gff3"
  run "diff #{last_stdout} #{$testdata}gt_splicesiteinfo_test_4.out"
end

Name "gt splicesiteinfo test 5 (-addintrons)"
Keywords "gt_splicesiteinfo"
Test do
  run_test "#{$bin}gt splicesiteinfo -addintrons -seqfile #{$testdata}gt_splicesiteinfo_test_5.fas #{$testdata}gt_splicesiteinfo_test_5.gff3"
  run "diff #{last_stdout} #{$testdata}gt_splicesiteinfo_test_5.out"
end

Name "gt splicesiteinfo test 6"
Keywords "gt_splicesiteinfo"
Test do
  run_test("#{$bin}gt splicesiteinfo -regionmapping #{$testdata}gt_splicesiteinfo_test_6.mapping #{$testdata}gt_splicesiteinfo_test_6.gff3", :retval => 1)
  grep last_stderr, "is nil"
end
Name "gt splicesiteinfo test 6"
Keywords "gt_splicesiteinfo"
Test do
  run_test("#{$bin}gt splicesiteinfo -regionmapping #{$testdata}gt_splicesiteinfo_test_6.mapping #{$testdata}gt_splicesiteinfo_test_6.gff3", :retval => 1)
  grep last_stderr, "is nil"
end

Name "gt splicesiteinfo prob 1"
Keywords "gt_splicesiteinfo"
Test do
  run_test "#{$bin}gt splicesiteinfo -seqfile #{$testdata}gt_splicesiteinfo_test_5.fas #{$testdata}gt_splicesiteinfo_prob_1.gff3"
end

Name "gt splicesiteinfo error message"
Keywords "gt_splicesiteinfo"
Test do
  run "#{$bin}gt gff3 -offset 1000 #{$testdata}gt_splicesiteinfo_test_1.gff3 " +
      "| #{$bin}gt splicesiteinfo -seqfile " +
      "#{$testdata}gt_splicesiteinfo_test_1.fas", :retval => 1
  grep last_stderr, "Has the sequence-region to sequence mapping been defined correctly"
end
genometools-1.5.1/testsuite/gt_splitfasta_include.rb000066400000000000000000000122251211610345200227730ustar00rootroot00000000000000Name "gt splitfasta (default)"
Keywords "gt_splitfasta"
Test do
  run "cp #{$testdata}U89959_genomic.fas ."
  run_test "#{$bin}gt splitfasta U89959_genomic.fas"
  if not File.exists?("U89959_genomic.fas.1") then
    raise TestFailed, "file 'U89959_genomic.fas.1' does not exist"
  end
end

Name "gt splitfasta (compressed file)"
Keywords "gt_splitfasta"
Test do
  run "cp #{$testdata}U89959_genomic.fas ."
  run "gzip U89959_genomic.fas"
  run_test "#{$bin}gt splitfasta U89959_genomic.fas.gz"
  if not File.exists?("U89959_genomic.fas.1.gz") then
    raise TestFailed, "file 'U89959_genomic.fas.1.gz' does not exist"
  end
end

Name "gt splitfasta (-numfiles)"
Keywords "gt_splitfasta"
Test do
  run "cp #{$testdata}U89959_ests.fas ."
  run_test "#{$bin}gt splitfasta -numfiles 8 U89959_ests.fas"
  if not File.exists?("U89959_ests.fas.1") then
    raise TestFailed, "file 'U89959_ests.fas.1' does not exist"
  end
  if not File.exists?("U89959_ests.fas.8") then
    raise TestFailed, "file 'U89959_ests.fas.8' does not exist"
  end
  if File.exists?("U89959_ests.fas.9") then
    raise TestFailed, "file 'U89959_ests.fas.9' does exist"
  end
end

Name "gt splitfasta (file exists)"
Keywords "gt_splitfasta"
Test do
  run "cp #{$testdata}U89959_genomic.fas ."
  run "touch U89959_genomic.fas.1"
  run_test("#{$bin}gt splitfasta U89959_genomic.fas", :retval => 1)
  grep last_stderr, /exists already/
end

Name "gt splitfasta (-force)"
Keywords "gt_splitfasta"
Test do
  run "cp #{$testdata}U89959_genomic.fas ."
  run "touch U89959_genomic.fas.1"
  run_test "#{$bin}gt splitfasta -force U89959_genomic.fas"
  if not File.exists?("U89959_genomic.fas.1") then
    raise TestFailed, "file 'U89959_genomic.fas.1' does not exist"
  end
end

Name "gt splitfasta (-targetsize)"
Keywords "gt_splitfasta"
Test do
  run "cp #{$testdata}U89959_genomic.fas ."
  run_test "#{$bin}gt splitfasta -targetsize 1 U89959_genomic.fas"
  if not File.exists?("U89959_genomic.fas.1") then
    raise TestFailed, "file 'U89959_genomic.fas.1' does not exist"
  end
end

Name "gt splitfasta (-splitdesc, nonexistent file)"
Keywords "gt_splitfasta"
Test do
  run_test("#{$bin}gt splitfasta -splitdesc . #{$testdata}nonexistent_file",
           :retval => 1)
  grep last_stderr, /does not exist or is not readable/
end

Name "gt splitfasta (empty file)"
Keywords "gt_splitfasta"
Test do
  run_test("#{$bin}gt splitfasta #{$testdata}empty_file", :retval => 1)
  grep last_stderr, /is empty/
end


Name "gt splitfasta (corrupt file)"
Keywords "gt_splitfasta"
Test do
  run_test("#{$bin}gt splitfasta #{$testdata}gt_bioseq_fail_2.fas",
           :retval => 1)
  grep last_stderr, /file is not in FASTA format/
end

Name "gt splitfasta (-splitdesc)"
Keywords "gt_splitfasta"
Test do
  run_test "#{$bin}gt splitfasta -splitdesc . #{$testdata}foobar.fas"
  if not File.exists?("foo.fas") then
    raise TestFailed, "file 'foo.fas' does not exist"
  end
  if not File.exists?("bar.fas") then
    raise TestFailed, "file 'bar.fas' does not exist"
  end
end

Name "gt splitfasta (-splitdesc, file exists)"
Keywords "gt_splitfasta"
Test do
  run "touch foo.fas"
  run_test("#{$bin}gt splitfasta -splitdesc . #{$testdata}foobar.fas",
           :retval => 1)
  grep last_stderr, /exists already/
end

Name "gt splitfasta (-splitdesc -force)"
Keywords "gt_splitfasta"
Test do
  run "touch foo.fas"
  run_test "#{$bin}gt splitfasta -force -splitdesc . #{$testdata}foobar.fas"
  if not File.exists?("foo.fas") then
    raise TestFailed, "file 'foo.fas' does not exist"
  end
  if not File.exists?("bar.fas") then
    raise TestFailed, "file 'bar.fas' does not exist"
  end
end

Name "gt splitfasta (-splitdesc, compressed file)"
Keywords "gt_splitfasta"
Test do
  run "cp #{$testdata}foobar.fas ."
  run "gzip foobar.fas"
  run_test "#{$bin}gt splitfasta -splitdesc . foobar.fas.gz"
  if not File.exists?("foo.fas.gz") then
    raise TestFailed, "file 'foo.fas.gz' does not exist"
  end
  if not File.exists?("bar.fas.gz") then
    raise TestFailed, "file 'bar.fas.gz' does not exist"
  end
end

if $gttestdata then
  Name "gt splitfasta (large data, compressed)"
  Keywords "gt_splitfasta"
  Test do
    run "cp #{$gttestdata}ltrharvest/s_cer/chrAll_before-1997-10-01.fsa.gz " +
        "test.fas.gz"
    run_test("#{$bin}gt splitfasta -targetsize 2 test.fas.gz", :maxtime => 160)
    # check sample
    if not File.exists?("test.fas.2.gz") then
      raise TestFailed, "file 'test.fas.2.gz' does not exist"
    end
  end

  Name "gt splitfasta (large data, uncompressed)"
  Keywords "gt_splitfasta"
  Test do
    run "cp #{$gttestdata}ltrharvest/s_cer/chrAll_before-1997-10-01.fsa.gz " +
        "test.fas.gz"
    run "gunzip test.fas.gz"
    run_test "#{$bin}gt splitfasta -targetsize 2 test.fas"
    # check sample
    if not File.exists?("test.fas.2") then
      raise TestFailed, "file 'test.fas.2' does not exist"
    end
  end

  Name "gt splitfasta (large data, file exists)"
  Keywords "gt_splitfasta"
  Test do
    run "cp #{$gttestdata}ltrharvest/s_cer/chrAll_before-1997-10-01.fsa.gz " +
        "test.fas.gz"
    run "touch test.fas.2.gz"
    run_test("#{$bin}gt splitfasta -targetsize 1 test.fas.gz",
             :retval => 1, :maxtime => 120)
    grep last_stderr, /exists already/
  end
end
genometools-1.5.1/testsuite/gt_stat_include.rb000066400000000000000000000054261211610345200216010ustar00rootroot00000000000000Name "gt stat -help"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -help"
  grep last_stdout, "Report bugs to"
end

Name "gt stat -noop"
Keywords "gt_stat"
Test do
  run_test("#{$bin}gt stat -noop", :retval => 1)
  grep last_stderr, "unknown option"
end

Name "gt stat (no options)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_stat_test_1.out"
end

Name "gt stat (-genelengthdistri)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -genelengthdistri " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_stat_test_2.out"
end

Name "gt stat (-exonlengthdistri)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -exonlengthdistri " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_stat_test_3.out"
end

Name "gt stat (-intronlengthdistri)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -intronlengthdistri " +
           "#{$testdata}standard_gene_with_introns_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_stat_test_4.out"
end

Name "gt stat (-genescoredistri)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -genescoredistri " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_stat_test_5.out"
end

Name "gt stat (count LTR retrotransposons)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -v #{$testdata}gt_eval_ltr_test_1.in"
  run "grep -v 'processing file' #{last_stdout}"
  run "diff #{last_stdout} #{$testdata}gt_stat_test_6.out"
end

Name "gt stat (-exonnumberdistri standard gene)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -exonnumberdistri " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_stat_exonnumberdistri_standard.out"
end

Name "gt stat (-exonnumberdistri encode)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -exonnumberdistri " +
           "#{$testdata}encode_known_genes_Mar07.gff3", :maxtime => 300
  run "diff #{last_stdout} #{$testdata}gt_stat_exonnumberdistri_encode.out"
end

Name "gt stat (-cdslengthdistri)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -cdslengthdistri " +
           "#{$testdata}standard_fasta_example_with_id.gff3"
  run "diff #{last_stdout} #{$testdata}gt_stat_cdslengthdistri.out"
end

Name "gt stat (-source)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat -source #{$testdata}standard_gene_as_tree.gff3"
  run "diff #{last_stdout} #{$testdata}gt_stat_source.out"
end

Name "gt stat (unsorted)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat #{$testdata}unsorted_gff3_file.txt"
end

Name "gt stat (embedded FASTA sequence)"
Keywords "gt_stat"
Test do
  run_test "#{$bin}gt stat #{$testdata}minimal_fasta.gff3"
end
genometools-1.5.1/testsuite/gt_suffixerator_include.rb000066400000000000000000000505211211610345200233430ustar00rootroot00000000000000def flattenfilelist(filelist)
  s=""
  filelist.each do |f|
    s += "#{$testdata}#{f} "
  end
  return s
end

def outoptionsnobck
  return "-tis -suf -des -sds -ssp -lcp -bwt"
end

def outoptions
  return outoptionsnobck + " -bck"
end

def checksfx(parts,extra,cmp,filelist,alldirs=true)
  filearg=flattenfilelist(filelist)
  if alldirs
    dirlist=["fwd","rev","cpl","rcl"]
  else
    dirlist=["fwd","rev"]
  end
  dirlist.each do |dirarg|
    extra=""
    if cmp
      extra=extra + " -cmpcharbychar"
    end
    run_test "#{$bin}gt suffixerator -v -parts #{parts} -pl " +
             "-algbds 10 31 80 #{extra} #{outoptions} " +
             "-indexname esa -dir " + dirarg + " -db " + filearg
    if dirarg == "cpl" or dirarg == "rcl"
      run_test "#{$bin}gt dev sfxmap #{outoptions} -v " +
               "-esa esa",
               :maxtime => 600
    else
      if dirarg == "fwd"
        dirarg_rev = "rev"
      else
        dirarg_rev = "fwd"
      end
      run_test "#{$bin}gt suffixerator -v -parts #{parts} -pl " +
               "-algbds 10 31 80 #{extra} #{outoptions} " +
               "-indexname esa-#{dirarg_rev} -dir " + dirarg_rev +
               " -db " + filearg
      run_test "#{$bin}gt packedindex mkindex -v -indexname pck -dir " + dirarg +
               " -db " + filearg
      run_test "#{$bin}gt dev sfxmap #{outoptions} -v " +
               "-esa esa -pck pck -cmpsuf",
               :maxtime => 600
      run_test "#{$bin}gt dev sfxmap #{outoptions} -v " +
               "-esa esa-#{dirarg_rev} -pck pck -cmplcp",
               :maxtime => 600
    end
  end
end

def checkdc(filelist)
  filearg=flattenfilelist(filelist)
  run_test "#{$bin}gt suffixerator -v -pl -dc 64 -dccheck " +
           "-lcp -suf -ssp -tis -indexname sfx -db " + flattenfilelist(filelist)
  run_test "#{$bin}gt dev sfxmap -lcp -suf -tis -ssp -v -esa sfx",
           :maxtime => 600
  run_test "#{$bin}gt suffixerator -v -pl -parts 3 -dc 64 " +
           "-lcp -suf -tis -indexname sfx3 -db " + flattenfilelist(filelist)
  run_test "#{$bin}gt dev sfxmap -lcp -suf -ssp -v -esa sfx3",
           :maxtime => 600
  run "diff sfx3.suf sfx.suf"
end

def checkbwt(filelist)
  run_test "#{$bin}gt suffixerator -pl #{outoptions} -indexname sfx -db " +
           flattenfilelist(filelist)
end

Name "gt suffixerator spmopt"
Keywords "gt_suffixerator spmopt"
Test do
  run_test "#{$bin}/gt suffixerator -des -tis -ssp -dna " +
           "-db #{$testdata}/U89959_genomic.fas -indexname genome-idx"
  run "#{$bin}/gt simreads -coverage 5 -len 100 -gzip -force " +
      "-o genome-idx-100-5-reads.fna.gz genome-idx"
  run_test "#{$bin}/gt suffixerator -mirrored -v -spmopt 45 -suf -lcp -dna " +
           "-parts 4 -db genome-idx-100-5-reads.fna.gz"
  run "#{$bin}/gt sequniq -rev genome-idx-100-5-reads.fna.gz"
  run "mv #{last_stdout} tmp.fas"
  sfxopt="-pl 2 -dna -lcp -suf -tis -ssp -db tmp.fas"
  indexname="sfx"
  mirrored=1
  minlen=35
  if mirrored
    sfxopt="#{sfxopt} -mirrored"
    indexname="sfx-m"
  else
    indexname="sfx"
    run "#{$bin}/gt encseq encode -indexname seq #{last_stdout}"
    run "#{$bin}/gt encseq decode -mirrored seq"
    run "mv #{last_stdout} tmp.fas"
  end
  sfxmapopt="-tis -suf -lcp -ssp -wholeleafcheck"
  run_test "#{$bin}/gt suffixerator -indexname #{indexname}-#{minlen} " +
           "-spmopt #{minlen} #{sfxopt}", :maxtime => 1000
  run_test "#{$bin}/gt dev sfxmap #{sfxmapopt} -esa #{indexname}-#{minlen}",
           :maxtime => 1000
  run_test "#{$bin}/gt suffixerator -indexname #{indexname} #{sfxopt}",
           :maxtime => 1000
  run_test "#{$bin}/gt dev sfxmap #{sfxmapopt} -esa #{indexname}",
           :maxtime => 1000
  run_test "#{$bin}/gt repfind -spm -l #{minlen} -ii #{indexname}",
           :maxtime => 1000
  run "mv #{last_stdout} result.repfind"
  run_test "#{$bin}/gt encseq2spm -parts 3 -l #{minlen} -spm show " + \
           "-ii #{indexname}", :maxtime => 1000
  run "mv #{last_stdout} result.firstcodes"
  run "cmp result.repfind result.firstcodes"
end

allfiles = []
all_fastafiles = ["Arabidopsis-C99826.fna",
                  "Atinsert.fna",
                  "Atinsert_seqrange_13-17_rev.fna",
                  "Atinsert_seqrange_3-7.fna",
                  "Atinsert_single_3.fna",
                  "Atinsert_single_3_rev.fna",
                  "Copysorttest.fna",
                  "Duplicate.fna",
                  "Ecoli-section1.fna",
                  "Ecoli-section2.fna",
                  "Random-Small.fna",
                  "Random.fna",
                  "Random159.fna",
                  "Random160.fna",
                  "RandomN.fna",
                  "Reads1.fna",
                  "Reads2.fna",
                  "Reads3.fna",
                  "Repfind-example.fna",
                  "TTTN.fna",
                  "Small.fna",
                  "Smalldup.fna",
                  "TTT-small.fna",
                  "trna_glutamine.fna",
                  "Verysmall.fna"]

allfiles += all_fastafiles

allmultifiles = []
all_multifastafiles = ["Atinsert.fna",
                       "Duplicate.fna",
                       "Small.fna",
                       "Verysmall.fna",
                       "Random159.fna",
                       "Random160.fna"]

allmultifiles += all_multifastafiles

all_fastqfiles = ["fastq_long.fastq",
                  "test10_multiline.fastq",
                  "test1.fastq",
                  "test5_tricky.fastq"]

allmultifiles += all_fastqfiles
allfiles += all_fastqfiles

alldir = ["fwd","cpl","rev","rcl"]

Name "gt suffixerator + sfxmap allfiles"
Keywords "gt_suffixerator tis"
Test do
  run_test "#{$bin}gt suffixerator -tis -ssp -indexname sfx -db " +
     flattenfilelist(all_fastafiles)
  run_test "#{$bin}gt dev sfxmap -ssp -tis -esa sfx"
end


Name "gt suffixerator + sfxmap"
Keywords "gt_suffixerator tis"
Test do
  all_fastafiles.each do |filename|
    run_test "#{$bin}gt suffixerator -tis -ssp -indexname sfx -db " +
             "#{$testdata}#{filename}"
    run_test "#{$bin}gt dev sfxmap -ssp -tis -esa sfx"
  end
end

Name "gt suffixerator all accesstypes"
Keywords "gt_suffixerator tis"
Test do
  all_fastafiles.each do |filename|
    ["direct", "bit", "uchar", "ushort", "uint32"].each do |sat|
      run_test "#{$bin}gt suffixerator -tis -indexname sfx -sat #{sat} " +
               "-db #{$testdata}#{filename}"
    end
  end
end

Name "gt suffixerator file of reads of equal length"
Keywords "gt_suffixerator reads"
Test do
  run_test "#{$bin}/gt suffixerator -des -tis -ssp -dna " +
           "-db #{$testdata}U89959_genomic.fas -indexname u8idx"
  run_test "#{$bin}/gt simreads -coverage 4 -len 100 -force -o u8.reads u8idx"
  run_test "#{$bin}/gt suffixerator -v #{outoptionsnobck} -dna -db u8.reads"
  run "grep -q '# init character encoding (eqlen ' #{last_stdout}"
  run_test "#{$bin}/gt dev sfxmap -bwt -suf -lcp -des -sds -ssp -esa u8.reads",\
           :maxtime => 200
  run_test "#{$bin}/gt suffixerator -v #{outoptionsnobck} -dir rev -dna -db u8.reads"
  run_test "#{$bin}/gt dev sfxmap -suf -lcp -des -sds -ssp -esa u8.reads", \
           :maxtime => 200
  run_test "#{$bin}/gt dev sfxmap -ownencseq2file -esa u8.reads"
  run "cmp u8.reads.esq u8.reads2.esq"
end

Name "gt suffixerator -dc 64 -dccheck -lcp -parts 1+3"
Keywords "gt_suffixerator dc"
Test do
  all_fastafiles.each do |filename|
    checkdc([filename])
  end
end

Name "gt suffixerator -dc 64 -dccheck -lcp -parts 1+3 all files"
Keywords "gt_suffixerator dc"
Test do
  checkdc(all_fastafiles)
end

alldir.each do |dir|
  Name "gt suffixerator single files #{dir}"
  Keywords "gt_suffixerator"
  Test do
    all_fastafiles.each do |filename|
      run_test "#{$bin}gt suffixerator -dir #{dir} -tis -suf -bwt -lcp " +
               "-indexname sfx -pl -db " +
               "#{$testdata}#{filename}"
      run_test "#{$bin}gt suffixerator -storespecialcodes -dir #{dir} -tis " +
               "-suf -lcp -indexname sfx -pl -db " +
               "#{$testdata}#{filename}"
      run_test "#{$bin}gt suffixerator -tis -bwt -lcp -pl -ii sfx"
    end
  end
end

faillist = ["-indexname sfx -db /nothing",
            "-indexname /nothing/sfx -db #{$testdata}TTT-small.fna",
            "-smap /nothing -db #{$testdata}TTT-small.fna",
            "-dna -db #{$testdata}sw100K1.fsa",
            "-protein -dir cpl -db #{$testdata}sw100K1.fsa",
            "-dna -db #{$testdata}Random.fna RandomN.fna",
            "-dna -suf -pl 10 -db #{$testdata}Random.fna",
            "-dna -tis -sat plain -db #{$testdata}TTT-small.fna"]
Name "gt suffixerator failures"
Keywords "gt_suffixerator"
Test do
  faillist.each do |failcommand|
    run_test "#{$bin}gt suffixerator -tis " + failcommand,:retval => 1
  end
end

Name "gt suffixerator sfxmap failures"
Keywords "gt_suffixerator"
Test do
  allmultifiles.each do |filename|
    run_test "#{$bin}gt suffixerator -tis -dna -des no -sds no -ssp no " +
             "-indexname localidx  -sat direct " +
             "-db #{$testdata}#{filename}"
    run_test "#{$bin}gt suffixerator -suf -lcp -pl -dir rev -ii localidx"
    run_test "#{$bin}gt dev sfxmap -tis -des -sds -esa localidx",
             :retval => 1
    # In short read files with equal read lengths, ssptabs need not
    # be built explicitly.
    # Thus these tests only fail for non-equal length files.
    if !all_fastqfiles.include?(filename) then
      run_test "#{$bin}gt dev sfxmap -tis -ssp -esa localidx",
               :retval => 1
      run_test "#{$bin}gt dev sfxmap -ssp -esa localidx",
               :retval => 1
    end
    run_test "#{$bin}gt dev sfxmap -des -esa localidx",
             :retval => 1
    run_test "#{$bin}gt dev sfxmap -tis -bck -esa localidx",
             :retval => 1
  end
end

Name "gt suffixerator bwt"
Keywords "gt_suffixerator"
Test do
  checkbwt(all_fastafiles)
end

1.upto(3) do |parts|
  [0,1,2].each do |withsmap|
    extra=""
    extraname=""
    if withsmap == 1
      extra="-protein"
      extraname="protein"
    elsif withsmap == 2
      extra="-smap TransProt11"
      extraname="TransProt11"
    end
    Name "gt suffixerator+map protein filelist #{extraname} #{parts} parts"
    Keywords "gt_suffixerator"
    Test do
      checksfx(parts,extra,true,["sw100K1.fsa","sw100K2.fsa"],false)
    end
  end
end

0.upto(2) do |cmpval|
  1.upto(2) do |parts|
    [0,1,2].each do |withsmap|
      extra=""
      if withsmap == 1
        extra="-dna"
        extraname=" dna"
      elsif withsmap == 2
        extra="-smap TransDNA"
        extraname=" trans"
      end
      if cmpval == 0
        cmp=false
      elsif cmpval == 1
        cmp=true
      else
        cmp=true
      end
      Name "gt suffixerator+map #{extraname} #{parts} parts"
      Keywords "gt_suffixerator"
      Test do
        all_fastafiles.each do |filename|
          checksfx(parts,extra,cmp,[filename])
        end
      end
      filelist=["RandomN.fna","Random.fna","Atinsert.fna"]
      Name "gt suffixerator+map dna filelist#{extraname} #{parts} parts"
      Keywords "gt_suffixerator"
      Test do
        checksfx(parts,extra,cmp,filelist)
      end
    end
  end
end

def checkmapped(keyword,args)
  Name "gt suffixerator checkmapped #{keyword}"
  Keywords "gt_suffixerator gttestdata"
  Test do
    run_test "#{$bin}gt suffixerator #{outoptions} -algbds 3 31 90 " +
             "-indexname sfxidx #{args}",
             :maxtime => 1200
    run_test "#{$bin}gt dev sfxmap #{outoptions} -v -esa sfxidx",
             :maxtime => 2400
    run_test "#{$bin}gt dev sfxmap #{outoptionsnobck} -stream -v -esa sfxidx",
             :maxtime => 2400
  end
end

def grumbach()
  return "#{$gttestdata}DNA-mix/Grumbach.fna/"
end

if $gttestdata then
  checkmapped("many .fna files","-db " +
              "#{$gttestdata}Iowa/at100K1 " +
              "#{grumbach()}Wildcards.fna " +
              "#{grumbach()}chntxx.fna " +
              "#{grumbach()}hs5hcmvcg.fna " +
              "#{grumbach()}humdystrop.fna " +
              "#{grumbach()}humghcsa.fna " +
              "#{grumbach()}humhdabcd.fna " +
              "#{grumbach()}humhprtb.fna " +
              "#{grumbach()}mipacga.fna " +
              "#{grumbach()}mpocpcg.fna " +
              "#{grumbach()}ychrIII.fna " +
              "-parts 3 -pl")

  checkmapped("swiss with parts=1",
              "-parts 1 -pl -db #{$gttestdata}swissprot/swiss10K " +
              "#{$gttestdata}swissprot/swiss1MB")

  checkmapped("swiss with parts=3",
              "-db #{$gttestdata}swissprot/swiss10K " +
              "#{$gttestdata}swissprot/swiss1MB -parts 3 -pl")

  checkmapped("at100K1",
              "-parts 2 -pl -smap TransDNA -db  #{$gttestdata}Iowa/at100K1")

  checkmapped("swiss with TransProt11",
              "-db #{$gttestdata}swissprot/swiss10K -parts 1 -pl -smap " +
              "TransProt11")
end

SATS = ["direct", "bytecompress", "eqlen", "bit", "uchar", "ushort", "uint32"]

EQLENDNAFILE = {:filename => "#{$testdata}test1.fasta",
                :desc => "equal length DNA",
                :msgs => {
                  "bytecompress" => "cannot use bytecompress on DNA sequences"}}
DNAFILE   = {:filename => "#{$testdata}Atinsert.fna",
             :desc => "non-equal length DNA",
             :msgs => {
                "bytecompress" => "cannot use bytecompress on DNA sequences",
                "eqlen" => "all sequences are of equal length and no " + \
                "sequence contains"}}
EQLENAAFILE = {:filename => "#{$testdata}trembl-eqlen.faa",
                :desc => "equal length AA",
                :msgs => {
                  "eqlen" => "as the sequence is not DNA",
                  "bit" => "as the sequence is not DNA",
                  "uchar" => "as the sequence is not DNA",
                  "ushort" => "as the sequence is not DNA",
                  "uint32" => "as the sequence is not DNA"}}
AAFILE    = {:filename => "#{$testdata}trembl.faa",
                :desc => "non-equal length AA",
                :msgs => {
                  "eqlen" => "as the sequence is not DNA",
                  "bit" => "as the sequence is not DNA",
                  "uchar" => "as the sequence is not DNA",
                  "ushort" => "as the sequence is not DNA",
                  "uint32" => "as the sequence is not DNA"}}

excludefiles = ["RandomN.fna","Small.fna","Verysmall.fna"]

Name "gt sfxmap ownencseq"
Keywords "gt_suffixerator ownencseq"
Test do
  all_fastafiles.each do |filename|
    if not excludefiles.member?(filename)
      run "#{$scriptsdir}rmwildcard.rb #{$testdata}#{filename}"
      run_test "#{$bin}/gt suffixerator -db #{last_stdout} -dna -v -tis -sds no -des no -md5 no -indexname sfx"
      run_test "#{$bin}/gt dev sfxmap -ownencseq2file -esa sfx"
      if File.exists?("sfx.ssp")
        run "cmp -s sfx.ssp sfx2.ssp"
      end
    end
  end
end

SATTESTFILES = [EQLENDNAFILE, DNAFILE, EQLENAAFILE, AAFILE]

SATTESTFILES.each do |file|
  SATS.each do |sat|
    Name "gt suffixerator sat #{sat} -> #{file[:desc]}"
    Keywords "gt_suffixerator sats"
    Test do
      if !file[:msgs][sat].nil? then
        retval = 1
      else
        retval = 0
      end
      run_test "#{$bin}/gt suffixerator -sat #{sat} -v -suf -lcp -des -sds " + \
               "-ssp -tis -db #{file[:filename]} -indexname myidx", \
               :retval => retval
      if !file[:msgs][sat].nil? then
        grep(last_stderr, /#{file[:msgs][sat]}/)
      end
      run_test "#{$bin}/gt dev sfxmap -suf -lcp -des -sds -ssp -esa myidx", \
               :retval => retval
    end
  end
end

[EQLENDNAFILE, DNAFILE].each do |file|
  (SATS-(file[:msgs].keys)).each do |sat|
    Name "gt suffixerator mirror #{sat} #{file[:desc]}"
    Keywords "gt_suffixerator mirror #{sat}"
    Test do
      alldir.each do |dir|
        run_test "#{$bin}/gt suffixerator -mirrored -sat #{sat} -v -suf " + \
                 "-lcp -bwt -dir #{dir} -db #{file[:filename]} -indexname myidx"
        run      "#{$scriptsdir}/add_revcmp.rb #{file[:filename]} > reverse.fna"
        run_test "#{$bin}/gt suffixerator -sat #{sat} -v -suf -lcp " + \
                 "-bwt -dir #{dir} -db reverse.fna -indexname myidx_r"
        run      "diff myidx.suf myidx_r.suf"
        run      "diff myidx.lcp myidx_r.lcp"
        run      "diff myidx.bwt myidx_r.bwt"
        run_test "#{$bin}/gt dev sfxmap -suf -lcp -des -sds -ssp -esa myidx", \
                 :maxtime => 600
        run_test "#{$bin}/gt dev sfxmap -suf -lcp -des -sds -ssp -esa " + \
                 "myidx_r", :maxtime => 600

      end
    end
  end
end

small_fastafiles = ["Duplicate.fna",
                    "Random-Small.fna",
                    "Copysorttest.fna",
                    "Random159.fna",
                    "Random160.fna",
                    "TTT-small.fna",
                    "trna_glutamine.fna",
                    "Small.fna",
                    "Verysmall.fna",
                    "Arabidopsis-C99826.fna"]
Name "differencecover sortmaxdepth"
Keywords "differencecover sortmaxdepth"
Test do
  small_fastafiles.each do |file|
    file = "#{$testdata}/#{file}"
    run "#{$bin}/gt suffixerator -tis -db #{file} -indexname esa"
    [2, 10].each do |maxinsertionsort|
      [10, 30, 100].each do |maxbltriesort|
        [2, 7, 13].each do |maxdepth|
          run_test "#{$bin}/gt dev sfxmap -sortmaxdepth #{maxdepth} -esa " + \
                   "esa -v -algbds #{maxinsertionsort} #{maxbltriesort} 1000"
        end
        run_test "#{$bin}/gt suffixerator -db #{file} -indexname esa2 " + \
                 "-suf -v -algbds #{maxinsertionsort} #{maxbltriesort} 1000"
        run_test "#{$bin}/gt dev sfxmap -suf -esa esa2"
      end
    end
  end
end

# check whether -memlimit is available as an option to enable
# conditional tests
if !`#{$bin}/gt suffixerator -help`.match(/memlimit/).nil? then
  if $gttestdata then
    ["2L", "2R", "3L", "3R"].each do |chr|
      Name "gt suffixerator -memlimit D. mel #{chr}"
      Keywords "gt_suffixerator memlimit"
      Test do
        size = nil
        run "#{$bin}/gt encseq encode -indexname dmel " + \
            "#{$gttestdata}ltrharvest/d_mel/" + \
            "#{chr}_genomic_dmel_RELEASE3-1.FASTA.gz", \
            :maxtime => 600
        out = `env GT_MEM_BOOKKEEPING=on GT_ENV_OPTIONS=-spacepeak #{$bin}/gt suffixerator -v -suf -ii dmel`
        if m = out.match(/space peak in megabytes: ([.0-9]+) /) then
          size = m[1].to_f
        else
            raise "could not get normal space peak"
        end
        [0.25, 0.5, 0.75].each do |frac|
          limit = size * frac
          run_test "env GT_MEM_BOOKKEEPING=on GT_ENV_OPTIONS=-spacepeak " + \
                   "#{$bin}/gt suffixerator " + \
                   "-suf -v " + \
                   "-memlimit #{limit.floor}MB " + \
                   "-ii dmel", :maxtime => 600
          lastout = nil
          File.open(last_stdout) do |f|
            out = f.read
            if m = out.match(/space peak in megabytes: ([.0-9]+) /) then
              mysize = m[1].to_f
            else
              raise "could not get actual space peak!"
            end
            if mysize > limit and mysize - limit > (mysize/10) then
              raise "required size (#{mysize}) was higher than limit (#{limit})"
            end
          end
        end
      end
    end
  end

  Name "gt suffixerator -memlimit excludes -parts"
  Keywords "gt_suffixerator memlimit"
  Test do
    run "#{$bin}/gt suffixerator -db #{$testdata}/at1MB -indexname foo " + \
        "-parts 3 -memlimit 2MB", :retval => 1
    grep(last_stderr, /exclude each other/)
  end

  Name "gt suffixerator -memlimit invalid size"
  Keywords "gt_suffixerator memlimit"
  Test do
    run "#{$bin}/gt suffixerator -db #{$testdata}/at1MB -indexname foo " + \
        "-memlimit 2TB", :retval => 1
    grep(last_stderr, /one of the keywords MB and GB/)
  end

  Name "gt suffixerator -memlimit invalid size"
  Keywords "gt_suffixerator memlimit"
  Test do
    run "#{$bin}/gt suffixerator -db #{$testdata}/at1MB -indexname foo " + \
        "-memlimit 2.2GB", :retval => 1
    grep(last_stderr, /one of the keywords MB and GB/)
  end
end

Name "gt sfxmap spmitv"
Keywords "gt_suffixerator spmitv"
Test do
  run "#{$bin}/gt suffixerator -db #{$testdata}/Reads2.fna -suf -lcp"
  run "#{$bin}/gt dev sfxmap -spmitv -esa Reads2.fna"
  run "diff #{last_stdout} #{$testdata}/Reads2-spmitv.txt"
end

Name "gt sfxmap lcp-interval trees bottomup"
Keywords "gt_suffixerator lcpitv"
Test do
  run "#{$bin}/gt suffixerator -db #{$testdata}/Reads2.fna -suf -lcp " + \
      "-indexname sfx"
  run "#{$bin}/gt dev sfxmap -enumlcpitvtreeBU -esa sfx > withBU.txt"
  run "#{$bin}/gt dev sfxmap -enumlcpitvtree -esa sfx > noBU.txt"
  run "diff withBU.txt noBU.txt"
end
genometools-1.5.1/testsuite/gt_tallymer_include.rb000066400000000000000000000040421211610345200224500ustar00rootroot00000000000000def runtyrmkifail(args)
  inputfile = "#{$testdata}Duplicate.fna"
  Name "gt tallymer mkindex failure"
  Keywords "gt_tallymer mkindex"
  Test do
    run_test "#{$bin}gt suffixerator -db #{inputfile} -tis " +
             "-suf -lcp -pl -dna -indexname sfxidx"
    run_test "#{$bin}gt tallymer mkindex " + args + " sfxidx", :retval => 1
  end
end

def checktallymer(reffile,mersize)
  reffilepath="#{$testdata}#{reffile}"
  if reffile == 'at1MB'
    query="#{$testdata}U89959_genomic.fas"
  else
    query="#{$testdata}at1MB"
  end
  reftestdir="#{$gttestdata}tallymer"
  outoptions="-counts -pl -mersize #{mersize} -minocc 2 -maxocc 30"
  run_test "#{$bin}gt suffixerator -pl -dna -tis -suf -lcp " +
           "-indexname sfxidx -db #{reffilepath}", :maxtime => 360
  run_test("#{$bin}gt tallymer mkindex -test -mersize #{mersize} -esa sfxidx",
           :maxtime => 360)
  suffix="tyrmkiout"
  run "mv #{last_stdout} #{reffile}.gt#{suffix}"
  run "cmp -s #{reffile}.gt#{suffix} #{reftestdir}/#{reffile}.#{suffix}"
  run_test "#{$bin}gt tallymer mkindex #{outoptions} " + 
           "-indexname tyr-index -esa sfxidx", :maxtime => 360
  if not File.zero?("tyr-index.mct")
    suffix="tyrseaout"
    run_test "#{$bin}gt tallymer search -strand fp -output qseqnum qpos " + 
             "counts sequence -test -tyr tyr-index -q #{query}", :maxtime => 360
    run "mv #{last_stdout} #{reffile}.gt#{suffix}"
    run "cmp -s #{reffile}.gt#{suffix} #{reftestdir}/#{reffile}.#{suffix}"
  end
end

tyrfiles = {"Atinsert.fna" => 19,
            "Duplicate.fna" => 12,
            "Random.fna" => 10,
            "Random159.fna" => 6,
            "Random160.fna" => 7,
            "RandomN.fna" => 3,
            "trna_glutamine.fna" => 10,
            "at1MB" => 20}

runtyrmkifail("-mersize 21 -pl")
runtyrmkifail("-mersize 21 -pl -minocc")
runtyrmkifail("-pl -minocc 30 -maxocc 40")

if $gttestdata then
  tyrfiles.each_pair do |reffile,mersize|
    Name "gt tallymer #{reffile}"
    Keywords "gt_tallymer gttestdata"
    Test do
      checktallymer(reffile,mersize)
    end
  end
end
genometools-1.5.1/testsuite/gt_trieins_include.rb000066400000000000000000000003021211610345200222670ustar00rootroot00000000000000Name "gt trieins"
Keywords "gt_trieins"
Test do
  run "#{$bin}gt suffixerator -indexname trieins-idx -pl 1 -tis -db #{$testdata}trna_glutamine.fna"
  run "#{$bin}gt dev trieins trieins-idx"
end
genometools-1.5.1/testsuite/gt_uniq_include.rb000066400000000000000000000017061211610345200215770ustar00rootroot00000000000000Name "gt uniq -help"
Keywords "gt_uniq"
Test do
  run_test "#{$bin}gt uniq -help"
  grep last_stdout, "Report bugs to"
end

Name "gt uniq -noop"
Keywords "gt_uniq"
Test do
  run_test("#{$bin}gt uniq -noop", :retval => 1)
  grep last_stderr, "unknown option"
end

Name "gt uniq nonexistent file"
Keywords "gt_uniq"
Test do
  run_test("#{$bin}gt uniq #{$testdata}nonexistent_file", :retval => 1)
end

Name "gt uniq corrupt file"
Keywords "gt_uniq"
Test do
  run_test("#{$bin}gt uniq #{$testdata}corrupt.gff3", :retval => 1)
end

Name "gt uniq test standard gene"
Keywords "gt_uniq"
Test do
  run_test "#{$bin}gt uniq -v -o test.out " +
           "#{$testdata}standard_gene_as_tree.gff3"
  run "diff test.out #{$testdata}standard_gene_as_tree.gff3"
end

1.upto(6) do |i|
  Name "gt uniq test #{i}"
  Keywords "gt_uniq"
  Test do
    run_test "#{$bin}gt uniq #{$testdata}gt_uniq_test_#{i}.gff3"
    run "diff #{last_stdout} #{$testdata}gt_uniq_test_#{i}.out"
  end
end
genometools-1.5.1/testsuite/ltresult.rb000066400000000000000000000241771211610345200203130ustar00rootroot00000000000000#!/usr/bin/env ruby
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

class LTRAnnotation
  attr_accessor :indexm, :indexs, :data, :file, :commentlines

  def initialize
    @data = []
    @commentlines = []
    @indexm = {}
    @indexs = {}
    @file = ""
  end

  # The 'load_from_*' functions require at least that the first two items on
  # a line represent a LTR retrotransposon start and end. How the rest of each
  # line is read and processed depends on the file type, according to each
  # load function.

  def load_from_ltrharvest(file)
    File.open(file) do |ltr|
    @file = file
      ltr.each_line do |line|
        if line[0].chr != "#" then
          (sltr,eltr,lltr,sleft,eleft,lleft,sright,eright,lright) = \
            line.split(" ").collect{|i| i.strip}
          smiddle = (eleft.to_i+1).to_s
          newitem = {:sltr => sltr.to_i,
                    :eltr => eltr.to_i,
                    :lltr => lltr.to_i,
                    :sleft => sleft.to_i,
                    :eleft => eleft.to_i,
                    :lleft => lleft.to_i,
                    :sright => sright.to_i,
                    :eright => eright.to_i,
                    :lright => lright.to_i}
          @data.push(newitem)
          @indexm[smiddle] = newitem
          @indexs[sltr] = newitem
        else
          @commentlines.push(line.chop)
        end
      end
    end
  end

  def load_from_berkeley(file)
    File.open(file) do |anno|
    @file=file
      anno.each_line do |line|
        if line[0].chr != "#" then
          (sltr, eltr, fbti_id, family_name, fbgn_id, chromosome_arm, release)\
             = line.split(" ").collect{|i| i.strip}
          newitem = {:sltr => sltr.to_i,
                    :eltr => eltr.to_i,
                    :length => eltr.to_i - sltr.to_i + 1,
                    :fbti_id => fbti_id,
                    :family_name => family_name,
                    :fbgn_id => fbgn_id,
                    :chromosome_arm => chromosome_arm,
                    :release => release}
          @data.push(newitem)
          @indexs[sltr] = newitem
        else
          @commentlines.push(line.chop)
        end
      end
    end
  end

  def load_from_custom(file)
    File.open(file) do |anno|
    @file=file
      anno.each_line do |line|
        if line[0].chr != "#" then
          (sltr, eltr, lltr, lname, ltype, lstrand)\
             = line.split(" ").collect{|i| i.strip}
          newitem = {:sltr => sltr.to_i,
                    :eltr => eltr.to_i,
                    :lltr => lltr.to_i,
                    :lname => lname,
                    :ltype => ltype,
                    :lstrand => lstrand}
          @data.push(newitem)
          @indexs[sltr] = newitem
        else
          @commentlines.push(line.chop)
        end
      end
    end
  end

  def print_content
    @data.each do |item|
      puts item.inspect
    end
  end

  def merge_hits(ref_hit, pred_hit)
    return {:s_pred => pred_hit[:sltr],
            :e_pred => pred_hit[:eltr],
            :s_ref => ref_hit[:sltr],
            :e_ref => ref_hit[:eltr],
            :length => ref_hit[:length],
            :fbti_id => ref_hit[:fbti_id],
            :family_name => ref_hit[:family_name],
            :fbgn_id => ref_hit[:fbgn_id],
            :chromosome_arm => ref_hit[:chromosome_arm],
            :release => ref_hit[:release]
            }
  end

  #compare a LTRharvest annotation with a reference annotation
  def compare(refAnno, difference=0, shift=0, without_ltrs=false)
    tp_list           = []
    htp_startpos_list = []
    htp_endpos_list   = []
    fp_list           = []
    fn_list           = []
    foundlist         = []
    nof_fn            = 0
    @data.each do |item|
      found = false
      item[:sltr] += shift
      item[:eltr] += shift
      if without_ltrs then
        item[:sltr] += item[:lleft]
        item[:eltr] -= item[:lright]
      end
      refAnno.data.each do |ref_item|
        p_start = false
        p_end = false
        if (ref_item[:sltr] - difference <= item[:sltr] && \
            item[:sltr] <= ref_item[:sltr] + difference) then
          p_start = true
        end
        if (ref_item[:eltr] - difference <= item[:eltr] && \
            item[:eltr] <= ref_item[:eltr] + difference) then
          p_end = true
        end
        if (p_start and not p_end) then
          htp_startpos_list.push(merge_hits(ref_item, item))
          foundlist.push([ref_item[:sltr],ref_item[:eltr]])
          found = true
        elsif (p_end and not p_start) then
          htp_endpos_list.push(merge_hits(ref_item, item))
          foundlist.push([ref_item[:sltr],ref_item[:eltr]])
          found = true
        elsif (p_start and p_end) then
          tp_list.push(merge_hits(ref_item, item))
          foundlist.push([ref_item[:sltr],ref_item[:eltr]])
          found = true
        end
      end
      if !found then
        fp_list.push(item)
      end
    end
    fn_list = refAnno.data.reject do |ref_item|
      foundlist.include?([ref_item[:sltr],ref_item[:eltr]])
    end
    yield tp_list, htp_startpos_list, htp_endpos_list,\
          fp_list, fn_list, difference
  end

  #output comparison results in old evalscript format
  def compare_output(refAnno, difference)
    compare(refAnno, 20) do |tp_list, htp_startpos_list, htp_endpos_list,\
                           fp_list, fn_list, difference|
      puts "# compared start- and endpositions from \n#  file \"#{@file}\" and\n#"\
           + "  file \"#{refAnno.file}\"\n#"
      puts "# parameters from LTRharvest (comments from\n#   file \"#{@file}\"):"
      @commentlines.each do |line|
        puts line
      end
      puts "#\n# read #{refAnno.data.length} annotations of" +\
         " LTR retrotransposons from\n" +\
         "#   file #{refAnno.file} \n#"
      puts("# results: each row = 1 LTR-pair\n" +\
         "#          startpos = 5'-boundary (of leftLTR)\n" +\
         "#          endpos   = 3'-boundary (of rightLTR)\n#\n" +\
         "# start- and endpositions may vary +/-#{difference}" +\
         "bp.\n#")

      puts "# true  positive(s) (TP) = #{tp_list.length}"
      puts "# half true positive(s) (TP) = #{htp_startpos_list.length\
                                           + htp_endpos_list.length}"
      puts "# false positive(s) (FP) = #{fp_list.length}"
      puts "# false negative(s) (FN) = #{fn_list.length}"
      puts "#"
#      puts "# duplicated TP predictions = "  #?
      puts "#"
      #print TPs
      puts "# #{tp_list.length} true positive(s) (TP)\n" +\
           "# startposition  endposition  " +\
           "+/-startposition_berkeley  +/-endposition_berkeley  " +\
           "length  FBti_id  family_name  FBgn_id  chromosome_arm  release"
      tp_list.sort{|i1, i2| i1[:s_pred] <=> i2[:s_pred]}.each do |tp|
        puts "#{tp[:s_pred]} #{tp[:e_pred]} #{tp[:s_ref]-tp[:s_pred]} "\
             +"#{tp[:e_ref]-tp[:e_pred]} #{tp[:length]} #{tp[:fbti_id]} "\
             +"#{tp[:family_name]} #{tp[:fbgn_id]} #{tp[:chromosome_arm]} "\
             +"#{tp[:release]}"
      end
      #print hTPs
      puts "# #{htp_startpos_list.length} half true positive(s) (only first position correct)\n" +\
           "# startposition  false_endposition  "+\
           "+/-startposition_berkeley  berkeley_endposition  "+\
           "length  FBti_id  family_name  FBgn_id  chromosome_arm  release"
      htp_startpos_list.sort{|i1, i2| i1[:s_pred] <=> i2[:s_pred]}.each do |htp|
        puts "#{htp[:s_pred]} #{htp[:e_pred]} #{htp[:s_ref]-htp[:s_pred]} "\
             +"#{htp[:e_ref]} #{htp[:length]} #{htp[:fbti_id]} "\
             +"#{htp[:family_name]} #{htp[:fbgn_id]} #{htp[:chromosome_arm]} "\
             +"#{htp[:release]}"
      end
      puts "# #{htp_endpos_list.length} half true positive(s) (only second position correct)\n" +\
            "# false_startposition  endposition  "+\
            "berkeley_startposition  +/-endposition_berkeley"+\
            "length  FBti_id  family_name  FBgn_id  chromosome_arm  release"
      htp_endpos_list.sort{|i1, i2| i1[:s_pred] <=> i2[:s_pred]}.each do |htp|
        puts "#{htp[:s_pred]} #{htp[:e_pred]} #{htp[:s_ref]} "\
             +"#{htp[:e_ref]-htp[:e_pred]} #{htp[:length]} #{htp[:fbti_id]} "\
             +"#{htp[:family_name]} #{htp[:fbgn_id]} #{htp[:chromosome_arm]} "\
             +"#{htp[:release]}"
      end
      #print FPs
      puts "# #{fp_list.length} false positive(s) (FP)\n" +\
           "# false_startposition  false_endposition  length  " +\
           "startleftLTR  endleftLTR  lengthleftLTR  " +\
          "startrightLTR  endrightLTR  lengthrightLTR"
      fp_list.sort{|i1, i2| i1[:sltr] <=> i2[:sltr]}.each do |fp|
        puts "#{fp[:sltr]} #{fp[:eltr]} #{fp[:lltr]} "\
             +"#{fp[:sleft]} #{fp[:eleft]} #{fp[:lleft]} "\
             +"#{fp[:sright]} #{fp[:eright]} #{fp[:lright]}"
      end
      #print FNs
      puts "# #{fn_list.length} false negative(s) (FN)\n" +\
           "# not predicted startposition, not predicted endposition"
      fn_list.sort{|i1, i2| i1[:sltr] <=> i2[:sltr]}.each do |fn|
        puts "#{fn[:sltr]} #{fn[:eltr]} #{fn[:length]} #{fn[:fbti_id]} "\
             +"#{fn[:family_name]} #{fn[:fbgn_id]} #{fn[:chromosome_arm]} "\
             +"#{fn[:release]}"
      end
    end
  end
end

#mixin for arbitrary decimal rounding
class Float
  def round_to(x)
    (self * 10**x).round.to_f / 10**x
  end

  def ceil_to(x)
    (self * 10**x).ceil.to_f / 10**x
  end

  def floor_to(x)
    (self * 10**x).floor.to_f / 10**x
  end
end
genometools-1.5.1/testsuite/ltrun.rb000066400000000000000000000107471211610345200175770ustar00rootroot00000000000000#!/usr/bin/env ruby
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

#require 'escape'
require 'tmpdir'

class LTRharvestRun
  attr_accessor :config, :opts

  def initialize(job, config=nil, opts=nil)
    #default options, can be overridden using the 'config' parameter
    @config = {
      :seed =>"40",          #e.g. "40"
      :minlenltr => 100,     #e.g. "100"
      :maxlenltr => 1000,    #e.g. "1000"
      :mindistltr => 1500,   #e.g. "1500"
      :maxdistltr => 15000,  #e.g. "15000"
      :similar => 90,        #e.g. "90.0"
      :mintsd => 4,          #e.g. "4"
      :maxtsd => 20,         #e.g. "20"
      :motif => "",          #e.g. "tgca" ; not set by default
      :motifmis => "",       #e.g. "0" ; requires motif
      :overlaps => "best",   #e.g. "no"|"best"|"all"
      :xdrop => 5,           #e.g. "5"
      :mat =>  2,            #e.g. "2"
      :mis => -2,            #e.g. "-2"
      :ins => -3,            #e.g. "-3"
      :del => -3,            #e.g. "-3"
    }
    #default options, can be overridden using the 'opts' parameter
    #e.g. when files should be written to persistent directories instead of
    #tempdir
    #at least specify a path to the 'gt' executable!
    @opts ={
      :gtpath => nil,
      :outdir => Dir.tmpdir,
      :with_innerfile=>true,
      :with_outfile=>true,
      :with_gff3file=>true,
      :with_fastafile=>true
    }
    #job id, e.g. species
    @job = job
    #override defaults
    @config.merge!(config) unless config.nil?
    @opts.merge!(opts) unless opts.nil?
    @ids = []
    @seqs = {}
  end

  def add_seq(chr, file, config={})
    raise "sequence with id #{chr} duplicate" if @seqs.has_key?(chr)
    raise "file #{file}.prj not accessible" if !File.exist?("#{file}.prj")
    @ids.push(chr)
    @seqs[chr] = {
                   :chr => chr, :file => file, :config => config,
                   :innerfile => "#{@opts[:outdir]}/#{@job}_#{chr}"\
                                +"-innerregion.fsa",
                   :gff3file => "#{@opts[:outdir]}/#{@job}_#{chr}.gff3",
                   :fastafile => "#{@opts[:outdir]}/#{@job}_#{chr}.fsa",
                   :resultfile => "#{@opts[:outdir]}/#{@job}_#{chr}.result"
                 }
  end

  def each_seq
    @ids.each do |id|
      nr = id
      chr = @seqs[id]
      args = []
      if File.exist?("#{chr[:file]}.prj")
        args.push("ltrharvest")
        myconf = @config.merge(chr[:config]).reject{|k,v| (v.nil?||v=="")}
        myconf.each do |k,v|
          args.push("-#{k} #{v.to_s}")
        end
        args.push("-v")
        args.push("-out #{chr[:fastafile]}") unless !@opts[:with_fastafile]
        args.push("-gff3 #{chr[:gff3file]}") unless !@opts[:with_gff3file]
        args.push("-outinner #{chr[:innerfile]}") unless !@opts[:with_innerfile]
        args.push("-index #{chr[:file]}")
        args.push("> #{chr[:resultfile]}") unless !@opts[:with_outfile]
        yield nr, chr, args, myconf
      end
    end
  end

  # set 'test' to true to enable stest return code checking
  def run_seq(test=false)
    if @opts[:gtpath].nil?\
       || !File.exist?(@opts[:gtpath])\
       || !File.executable?(@opts[:gtpath]) then
      raise "gt binary not found or executable: #{@opts[:gtpath]}"
    end
    each_seq do |nr, chr, arglist, chr_cfg|
      if test then
        run "#{@opts[:gtpath]} #{arglist.join(" ")}", :maxtime => 500
      else
        STDERR.puts "Running #{@job}: seq '#{nr}'"
        success = Kernel.system("#{@opts[:gtpath]} #{arglist.join(" ")}")
      end
      if success or test then
        yield nr, chr[:resultfile], chr[:innerfile], \
              chr[:gff3file], chr[:fastafile]
      else
        raise "canceled command: #{@opts[:gtpath]} #{arglist.join(" ")}"
      end
    end
  end
end
genometools-1.5.1/testsuite/multidimarray.rb000066400000000000000000000027651211610345200213170ustar00rootroot00000000000000class MultiDimensionalArray
  def initialize(*dimensions)
    @dimensions = Array.new(dimensions.length)
    @factors = Array.new(dimensions.length)
    product = 1
    i = dimensions.length - 1
    while i>=0
      @dimensions[i] = dimensions[i]
      @factors[i] = product
      product *= @dimensions[i]
      i -= 1
    end
    @data = Array.new(product)
  end
  def getOffset(indices)
    if indices.length != @dimensions.length
      STDERR.puts "#{$0}: getOffset indices.length = #{indices.length} " +
                  "!= #{@dimensions.length} = @dimensions.length"
      exit 1
    end
    offset = 0
    0.upto(@dimensions.length-1) do |i|
      if indices[i] < 0 or indices[i] >= @dimensions[i]
        STDERR.puts "#{$0}: illegal value indices[#{i}]=#{indices[i]}"
        exit 1
      end
      offset += @factors[i] * indices[i]
    end
    return offset
  end

  def [](*indices)
    return @data[self.getOffset(indices)]
  end

  def []=(*indicesAndValue)
    value = indicesAndValue.pop
    @data[self.getOffset(indicesAndValue)] = value
  end

  def enumaccesstubles()
    numofwheels = @dimensions.length
    wheelspace = Array.new(numofwheels)
    idx = numofwheels - 1
    0.upto(numofwheels-1) do |i|
      wheelspace[i] = 0
    end
    loop do
      wheelspace[idx] += 1
      if wheelspace[idx] == @dimensions[idx]
        wheelspace[idx] = 0
        if idx == 0
          break
        end
        idx -= 1
      else
        idx = numofwheels-1
        yield wheelspace
      end
    end
  end
end
genometools-1.5.1/testsuite/scripts_include.rb000066400000000000000000000002531211610345200216140ustar00rootroot00000000000000Name "gmap2gff3"
Keywords "scripts"
Test do
  run "#{$scriptsdir}gmap2gff3 #{$testdata}gmap2gff3_prob.gmap"
  run "diff #{last_stdout} #{$testdata}gmap2gff3_prob.out"
end
genometools-1.5.1/testsuite/stest.rb000077500000000000000000000274441211610345200176020ustar00rootroot00000000000000#!/usr/bin/env ruby

# Patrick Maass, 2006

require 'fileutils'
require 'thread'

class TestFailed < Exception
end
class TestError < Exception
end

class Testsuite
  attr_writer :nof_threads
  attr_reader :outlock

  def initialize
    @tests = []
    @nof_threads = 1
    @outlock = Mutex.new
  end

  def run
    inlock = Mutex.new
    threads = []
    1.upto(@nof_threads) do |n|
      threads << Thread.new(n, @tests, inlock) do |n, tests, inlock|
        while tests.length > 0
          t = nil
          inlock.synchronize do
            t = tests.shift
          end
          if !t.nil?
            t.process
          end
        end
      end
    end
    threads.each do |thread|
      thread.join
    end
  end

  def threaded?
    (@nof_threads > 1)
  end

  def add(t)
    @tests.push(t)
  end
end

$testsuite = Testsuite.new

class Test
  @@id = 1
  @@prefix = "stest"
  @@failed = 0
  @@errors = 0
  @@feature_check = nil
  def self.prefix(str)
    @@prefix = str
  end
  def self.have_features(&bl)
    @@feature_check = bl
  end

  def initialize(str)
    @name = str
    @code = nil
    @id = @@id
    @@id += 1
    @requirements = nil
  end

  def requires(str)
    @requirements = str
  end
  def code(block)
    @code = block
  end
  def keywords(str)
    @keywords ||= nil
    @did_run ||= nil
    raise "keyword reset" if @keywords
    raise "already run" if @did_run
    @keywords = {}
    str.split.each do |kw|
      if kw =~ /--/
        kws = kw.split(/--/)
        while kws.size > 0 do
          k = kws.join("--")
          @keywords[k] = true
          kws.pop
        end
      end
      @keywords[kw] = true
    end
  end

  def setup_dir
    begin
      ds = "#{@@prefix}/test#{@id}"
      if File.exists?(ds)
        FileUtils.rm_r(ds)
      end
      FileUtils.mkdir_p(ds)
      FileUtils.chdir(ds)
    rescue => e
      raise TestError, "could not create test dir '#{ds}'"
    end
  end

  def self.problems
    return @@failed, @@errors
  end

  def process
    if @code != nil
      self.test($arguments["keywords"], $arguments["select"],
                $arguments["name"], &@code)
    end
  end

  def printmsg(msg)
    if $testsuite.threaded?
      $testsuite.outlock.synchronize do
        STDOUT.print msg
      end
    else
      STDOUT.print msg
    end
  end

  def test(keywords, selection, name)
    raise "already run" if @did_run
    if name
      if not @name =~ name
        return
      end
    end
    if keywords
      @keywords ||= {}
      if not keywords.is_selected(@keywords)
        return
      end
    end
    if selection
      if not selection[@id]
        return
      end
    end
    if @requirements
      if @@feature_check
        ok, info = @@feature_check.call(@requirements)
        if not ok
          if info then
            STDOUT.printf "%3d: %-60s: #{info}\n", @id, @name
          end
          return
        end
      end
    end
    msg = ""
    pid = fork do
      msg << "%3d: %-60s: " % [@id, @name]
      if !$testsuite.threaded?
        STDOUT.print msg
        STDOUT.flush
        msg = ""
      end
      e_info = nil
      e_code = 0
      begin
        setup_dir
        yield
      rescue TestFailed => e
        e_info = e
        e_code = 1
      rescue Interrupt => e
        exit 3
      rescue Exception => e
        e_info = e
        e_code = 2
      end
      if e_info
        i = "failed"
        if e_code != 1 then i = "error" end
        msg << i << "\n"
        msg << "     [ problem: #{e_info.message}" << "\n"
        msg << "       in: #{Dir.pwd} ]" << "\n"
        File.open("stest_error", "w") do |f|
          f.puts("Test #{@id} '#{@name}': #{i}:")
          f.puts("#{e_info.message}:")
          f.puts(e_info.backtrace)
        end
        printmsg msg
        exit e_code
      else
        msg << "ok" << "\n"
        printmsg msg
        exit 0
      end
    end
    printmsg msg
    begin
      p, s = Process::waitpid2(pid)
    rescue Interrupt => e
      puts "interrupted"
      exit 1
    end
    if s.exitstatus == 1
      @@failed += 1
    elsif s.exitstatus == 2
      @@errors += 1
    end
    @did_run = true
  end
end

def Test.exec(cmd, env, out_filename, err_filename, cmd_filename, max_t)
  pid = fork do
    env.each do |k,v|
      ENV[k] = v
    end
    begin
      File.open(cmd_filename, "w") do |f|
        env.each do |k, v|
          f.print "#{k}=#{v} "
        end
        # help for debugging failed tests:
        f.print "$CMD_PREFIX "
        f.puts(*cmd)
      end
      f_out = File.new(out_filename, "w")
      f_err = File.new(err_filename, "w")
      $stdout.reopen(f_out)
      $stderr.reopen(f_err)
    rescue Errno::ENOENT => e
      exit 90
    end
    begin
      Kernel.exec(*cmd)
    rescue Errno::ENOENT => e
      # XXX: better solution (signal/kill?)
      exit 91
    end
  end
  time_left = max_t
  sleep_step = 0.1
  s = false
  while time_left > 0
    sleep(sleep_step)
    time_left -= sleep_step
    p, s = Process.waitpid2(pid, Process::WNOHANG)
    break if s
  end
  if not s
    Process.kill("HUP", pid)
    sleep(sleep_step)
    p, s = Process.waitpid2(pid, Process::WNOHANG)
    raise TestError, "'#{cmd}' did not finish on time"
  end
  if not s.exited?
    if s.signaled?
      raise TestError, "'#{cmd}' received signal #{s.termsig}"
    else
      raise TestError, "'#{cmd}' stopped"
    end
  end
  if s.exitstatus == 90
    raise TestError, "cannot create output files for '#{cmd}'"
  end
  if s.exitstatus == 91
    raise TestError, "exec failed for '#{cmd}'"
  end
  if s.exitstatus == 92
    raise TestError, "exec error for '#{cmd}'"
  end
  return s.exitstatus
end

def Test.run(cmd, env, o_fn, r_fn, c_fn, rv, max_t)
  r = Test.exec(cmd, env, o_fn, r_fn, c_fn, max_t)
  if r != rv
    raise TestFailed, "unexpected return code: #{r} != #{rv}"
  end
end

class Keywords
  def initialize(kw_str)
    e, @root = OrNode.parse(kw_str, 0)
    if e != kw_str.size
      raise "extra tokens after '#{kw_str[0, e]}': '#{kw_str[e,kw_str.size]}'"
    end
  end
  def is_selected(valmap)
    return @root.is_selected(valmap)
  end

  class Node
    def self.skip_space(str, i)
      if i.class == NilClass
        raise "hu"
      end
      while str[i] and str[i] == ?\s
        i += 1
      end
      return i
    end
  end
  class VarNode < Node
    def self.parse(str, i)
      j = skip_space(str, i)
      if str[j] == ?(
        j += 1
        j, n = OrNode.parse(str, j)
        j = skip_space(str, j)
        if str[j] != ?)
          raise "missing ')'"
        end
        j += 1
        return j, n
      else
        s = j
        while str[j] and str[j] != ?\s and str[j] != ?( and str[j] != ?)
          j += 1
        end
        vn = str[s, j - s]
        if vn.size < 1 then raise "empty variable" end
        n = VarNode.new(vn)
        return j, n
      end
    end
    def is_selected(valset)
      if valset[@name] then return true end
      return false
    end
    def print
      puts "var: #{@name}"
    end
    private
    def initialize(name)
      @name = name
    end
  end
  class NotNode < Node
    def self.parse(str, i)
      is_neg = false
      j = skip_space(str, i)
      if str[j, 4] =~ /^not[ ()]?$/
        j += 3
        is_neg = true
      end
      j, n1 = VarNode.parse(str, j)
      if is_neg then n = NotNode.new(n1) else n = n1 end
      return j, n
    end
    def is_selected(valset)
      return !@n.is_selected(valset)
    end
    def print
      puts "not:"
      @n.print
    end
    private
    def initialize(n) @n = n end
  end
  class AndNode < Node
    def self.parse(str, i)
      j = skip_space(str, i)
      j, n1 = NotNode.parse(str, j)
      j = skip_space(str, j)
      if str[j, 4] =~ /^and[ ()]?$/
        j += 3
        j, n2 = AndNode.parse(str, j)
        n = self.new(n1, n2)
        return j, n
      end
      return j, n1
    end
    def is_selected(valset)
      return @n1.is_selected(valset) && @n2.is_selected(valset)
    end
    def print
      puts "A["
      @n1.print
      puts "and"
      @n2.print
      puts "]"
    end
    private
    def initialize(n1, n2) @n1 = n1; @n2 = n2 end
  end
  class OrNode < AndNode
    def self.parse(str, i)
      j = skip_space(str, i)
      j, n1 = AndNode.parse(str, j)
      j = skip_space(str, j)
      if str[j, 3] =~ /^or[ ()]?$/
        j += 2
        j, n2 = OrNode.parse(str, j)
        n = self.new(n1, n2)
        return j, n
      else
        return j, n1
      end
    end
    def is_selected(valset)
      return @n1.is_selected(valset) || @n2.is_selected(valset)
    end
    def print
      puts "O["
      @n1.print
      puts "or"
      @n2.print
      puts "]"
    end
  end

end

# Interface to Test class and helpers
# we use global variables for a simple user interface

$arguments = {}
$curr_test = nil
$run_no = 1

def run(str, opts = {})
  rv = 0
  if opts[:retval]
    rv = opts[:retval].to_i
  end
  o_fn = opts[:stdout]
  if not o_fn then o_fn = "stdout_#{$run_no}" end
  r_fn = opts[:stderr]
  if not r_fn then r_fn = "stderr_#{$run_no}" end
  c_fn = "run_#{$run_no}"
  $run_no += 1
  cmd = [ str ]
  if opts[:arguments]
    cmd += opts[:arguments]
  end
  env = opts[:env]
  env ||= {}
  max_t = opts[:maxtime]
  max_t ||= 60
  Test.run(cmd, env, o_fn, r_fn, c_fn, rv, max_t)
  Thread.current[:last_stdout] = o_fn
  Thread.current[:last_stderr] = r_fn
end

def last_stdout
  Thread.current[:last_stdout]
end

def last_stderr
  Thread.current[:last_stderr]
end

def failtest(msg)
  raise TestFailed, msg
end

def grep(f, patt, inverse=false)
  if not patt.respond_to?(:source)
    patt = Regexp.new(patt)
  end
  hit = nil
  if f.respond_to?(:to_str)
    files = [ f ]
  else
    files = f
  end
  files.each do |fn|
    File.open(fn) do |f|
      m = f.grep patt
      hit = m && m.size > 0
    end
    if hit then break end
  end
  p = "missing"
  if inverse then
    hit = !hit
    p = "unexpected"
  end
  if not hit
    raise TestFailed, "#{p} /#{patt.source}/ in #{files.join(" / ")}"
  end
end

def write_file(fn, str)
  File.open(fn, "w") do |f|
    # 1. remove first and last line
    # 2. remove offset
    a = str.split("\n")
    e = a.size - 1
    a[1] =~ /^( *)/
    off = $1.size
    a.each_with_index do |l, i|
      next if i == 0
      next if i == e
      f.puts "#{l[off, l.size]}"
    end
  end
end

def Name(str)
  t = Test.new(str)
  $curr_test = t
end

alias Description Name
alias Descr Name

def Keywords(str)
  t = $curr_test
  t.keywords(str)
end

def Requires(str)
  t = $curr_test
  t.requires(str)
end

def Test(&block)
  t = $curr_test
  t.code(block)
  $testsuite.add(t)
end

def OnError
  f, e = Test.problems
  if f > 0 || e > 0
    yield(f, e)
  end
end

# Set defaults

Test.prefix "stest_#{File.basename($0, ".rb")}"

$runpath = Dir.pwd

# Set arguments from command line

testfile = nil

if ARGV.size > 0
  i = 0
  while i < ARGV.size do
    a = ARGV[i]
    if a[0] == ?- then
      v = ARGV[i + 1]
      k = a[1..a.size]
      $arguments[k] ||= ""
      av = []
      while ARGV[i + 1] and ARGV[i + 1][0] != ?-
        av.push(ARGV[i + 1])
        i += 1
      end
      $arguments[k] = if av.size > 0 then av.join(" ") else "yes" end
    elsif $0 == __FILE__ and not testfile
      testfile = a
      Test.prefix "stest_#{File.basename(testfile, ".rb")}"
    else
      raise "invalid argument '#{a}'"
    end
    i += 1
  end
end

# Handle built-in options

if $arguments["keywords"]
  keywords = $arguments["keywords"]
  $arguments["keywords"] = Keywords.new(keywords)
end
if $arguments["select"]
  sel = $arguments["select"]
  $arguments["select"] = {}
  if sel =~ /(\d+)\.\.(\d+)/
    Range.new(Integer($1), Integer($2)).each do |id|
      $arguments["select"][Integer(id)] = true
    end
  else
    sel.split.each do |id|
      $arguments["select"][Integer(id)] = true
    end
  end
end
if $arguments["name"]
  $arguments["name"] = Regexp.new($arguments["name"])
end

if $0 == __FILE__
  if not testfile
    raise "missing test file argument"
  end
  require testfile
  OnError do exit(1) end
end
genometools-1.5.1/testsuite/stest_tests.rb000077500000000000000000000155731211610345200210240ustar00rootroot00000000000000
# Patrick Maass, 2006

if $0 == __FILE__
  require 'stest'
  at_exit do
    OnError do exit 1 end
  end
end

def run_g(str, opts = {})
  cmd = {}
  prefix = ""
  if $arguments["valgrind"] == "yes"
    prefix = "valgrind --leak-check=yes "
  end
  opts[:stdout] = "std_out"
  opts[:stderr] = "std_err"
  run(prefix + str, opts)
  if $arguments["valgrind"] == "yes"
    run %{grep "ERROR SUMMARY: 0 errors" std_out std_err}
  end
end

def run_stest(fn, str, args = [], opts = {})
  tfn = "#{fn}.rb"
  File.open(tfn, "w") do |f|
    f.print(str)
  end
  run "ruby #{$runpath}/stest.rb #{tfn} #{args.join(" ")}", opts
end

Description "Hello, World"
Keywords "basics--apply--run"
Test do
  run_g "echo huhu"
  run "echo hello"
end

Name "Hello, World 2 and a long ending"
Keywords "basics--retval"
Test do
  run("grep foo barbaz", :retval => 2)
end

Descr "Unavailable executable"
Keywords "basics--no-exec"
Test do
  run_stest "tt", %{
    Name "No such exe"
    Keywords "test--no-exe"
    Test do
      run "no-such-exe foo"
    end
  }, [], :retval => 1
  grep(last_stdout, /problem: exec failed/)
end

Name "Unavailable executables"
Keywords "basics--multi-no-exec"
Test do
  run_stest "tt", %{
    Name "No such exe"
    Keywords "test--no-exe"
    Test do
      run "no-such-exe foo"
      run "no-such-exe-either"
    end
    Name "No such exe2"
    Keywords "test--no-exe2"
    Test do
      run "some-other bar"
    end
  }, [], :retval => 1
  grep(last_stdout, /problem: exec failed/)
  grep(last_stdout, /2:.*: error/)
end

Name "Arguments"
Keywords "basics--run-arguments"
Test do
  run "echo *"
  run "echo ______"
  run("echo", :arguments => [ "*" ])
end

Name "Environment"
Keywords "basics--environment"
Test do
  run("sh -c 'echo LL $TATA'", :env => { "TATA" => "foo" })
end

Name "Test Input Files"
Keywords "basics--write-file"
Test do
  rundir = $runpath
  File.open("tt.rb", "w") do |f|
    f.puts %{
      require 'stest'
      Name "TestTest"
      Test do
        run "echo hello"
      end
    }
  end
  run "ruby -I#{rundir} tt.rb"
end

Name "Test Error Log"
Keywords "basics--error-log"
Test do
  run_stest "tt", %{
    Name "Foo"
    Test do
      failtest "and this is why"
    end
  }, [], :retval => 1
  grep("stest_tt/test1/stest_error", /^and this is why:$/)
end

Name "Numbered output files"
Keywords "basics--output-files"
Test do
  run_stest "tt", %{
    Name "foo"
    Test do
      run "echo hello"
      run "echo huhu"
    end
  }
  run "test -r stest_tt/test1/stdout_1"
  run "test -r stest_tt/test1/stdout_2"
end

Name "Store commands"
Keywords "basics--store-commands"
Test do
  run_stest "tt", %{
    Name "foo"
    Test do
      run "echo hello"
    end
  }
  File.open("stest_tt/test1/run_1") do |f|
    l = f.readlines
    if l[0].chomp != "$CMD_PREFIX echo hello"
      failtest "invalid command stored"
    end
  end
end

Name "Test without keywords"
Keywords "basics--without-keywords"
Test do
  run_stest "tt", %{
    Name "foo"
    Test do
      run "echo"
    end
  }, [ "-keywords", "some" ]
  run "test ! -d stest_tt"
  run_stest "kk", %{
    Name "foo"
    Test do
      run "echo hello"
    end
  }, [ "-keywords", "not foo" ]
  run "test -r stest_kk/test1/run_1"
end

Name "Keyword Tokens"
Keywords "basics--keyword-parser"
Test do
  run_stest "tt", %{
    Name "foo"
    Keywords "x"
    Test do
      run "echo hello"
    end
    Name "bar"
    Keywords "notfoo foo"
    Test do
      run "echo huhu"
    end
  }, [ "-keywords", "notfoo" ]
  run "test ! -d stest_tt/test1"
  run "test -d stest_tt/test2"
end

Name "Test Selection"
Keywords "basics--selection"
Test do
  run_stest "tt", %{
    Name "s1"
    Test do
      run "echo foo"
    end
    Name "s2"
    Test do
      run "echo bar"
    end
    Name "s3"
    Test do
      run "echo baz"
    end
  }, %w{-select 2 3}
  grep("stest_tt/test2/stdout_1", "^bar$")
  grep("stest_tt/test3/stdout_1", "^baz$")
  run "test ! -d stest_tt/test1"
end

Name "Test Selection (name)"
Keywords "basics--name-selection"
Test do
  run_stest "tt", %{
    Name "foo"
    Test do
      run "echo hello"
    end
    Name "bar"
    Test do
      run "echo huhu"
    end
  }, [ "-name", "b.r" ]
  grep("stest_tt/test2/stdout_1", /^huhu$/)
  run "test ! -d stest_tt/test1"
end

Name "Inverse grep"
Keywords "utils--inverse-grep"
Test do
  run_stest "tt", %{
    Name "gt"
    Test do
      run "echo foo"
      grep(last_stdout, /foo/)
      grep(last_stdout, /bar/, true)
    end
  }
end

Name "Grep string"
Keywords "utils--string-grep"
Test do
  run_stest "tt", %{
    Name "sg"
    Test do
      run "echo foo"
      grep(last_stdout, ".")
    end
  }
end

Name "Multi-file grep"
Keywords "utils--multi-grep"
Test do
  run_stest "tt", %{
    Name "foo"
    Test do
      run "echo foo"
      grep([last_stdout, last_stderr], /^foo/)
      run "echo bar", :stdout => "s", :stderr => "e"
      grep(%w{e s}, /^bar/)
    end
  }
  run_stest "ft", %{
    Name "will-fail"
    Test do
      run "echo hello"
      grep([last_stdout, last_stderr], /nowhere/)
    end
  }, [], :retval => 1
  grep(last_stdout, /: failed/)
end

Name "Return Codes"
Keywords "basics--return-codes"
Test do
  run_stest "tt", %{
    Name "sg"
    Test do
      # will fail:
      run "echo foo", :retval => 1
    end
  }, [], :retval => 1
end

Name "Command Line Arguments"
Keywords "basics--command-line"
Test do
  run_stest "tt", %{
    Name "pa"
    Test do
      run "echo #\{$arguments["hello"]\}"
      run "echo #\{$arguments["flag"]\}"
    end
  }, %w{-hello hello world -flag}
  grep("stest_tt/test1/stdout_1", /^hello world$/)
  grep("stest_tt/test1/stdout_2", /^yes$/)
end

Name "Write-File"
Keywords "utils--write-file"
Test do
  run_stest "tt", %{
    Name "wf"
    Test do
      write_file "foo", %{
        from column 0
          indent
        end block
      }
    end
  }
  File.open("stest_tt/test1/foo", "r") do |f|
    l = f.readlines
    failtest "bad offset" if l[0] != "from column 0\n"
    failtest "line 1 != '  indent'" if l[1] != "  indent\n"
    failtest "line 2 != 'end block'" if l[2] != "end block\n"
    failtest "too many lines" if l.size != 3
  end
end

Name "Max Time"
Keywords "basics--max-time"
Test do
  run_stest "tt", %{
    Name "foo"
    Test do
      run "sleep 3", :maxtime => 1
    end
  }, [], :retval => 1
  grep last_stdout, /did not finish on time/
end

Name "Range Selection"
Keywords "selection--ranges"
Test do
  run_stest "tt", %{
    Name "foo"
    Test {}
    Name "bar"
    Test {}
    Name "baz"
    Test {}
  }, %w{-select 2..3}
  grep last_stdout, "bar"
  grep last_stdout, "baz"
  grep last_stdout, "foo", true
end

Name "Require/Provide"
Keywords "basics--require"
Test do
  run_stest "tt", %{
    Test.have_features do |str|
      if str =~ /^x/
        true
      else
        [ false, "skipped" ]
      end
    end
    Name "foo"
    Requires "x y v"
    Test do
      run "echo"
    end
    Name "bar"
    Requires "k y v"
    Test do
      run "echo"
    end
  }
  grep last_stdout, /1:.*: ok/
end

genometools-1.5.1/testsuite/testsuite.rb000077500000000000000000000123131211610345200204560ustar00rootroot00000000000000#!/usr/bin/env ruby
#
# Copyright (c) 2006-2008 Gordon Gremme 
# Copyright (c) 2006-2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

# the GenomeTools test suite (employs ``stest'').
if $0 == __FILE__
  $:<< "."            # favor the local stest version
  require 'stest'
  at_exit do
    OnError do exit 1 end
  end
end

# set some global variables
if $arguments["path"] then
  $path=File.join($arguments["path"], "")
else
  $path=""
end

if $arguments["testdata"] then
  $testdata=File.join($arguments["testdata"], "")
else
  $testdata=File.join(Dir.pwd, "..", "testdata", "")
end

if $arguments["bin"] then
  $bin=File.join($arguments["bin"], "")
else
  $bin=File.join(Dir.pwd, "..", "bin", "")
end

if $arguments["cur"] then
  $cur=$arguments["cur"]
else
  $cur=File.join(Dir.pwd, "..", "")
end

$transdir=File.join(Dir.pwd, "..", "gtdata" , "trans", "")

$scriptsdir=File.join(Dir.pwd, "..", "scripts", "")

if $arguments["gtruby"] then
  $gtruby=File.join($arguments["gtruby"], "")
else
  $gtruby=File.join(Dir.pwd, "..", "gtruby", "")
end

if $arguments["gtpython"] then
  $gtpython=File.join($arguments["gtpython"], "")
else
  $gtpython=File.join(Dir.pwd, "..", "gtpython", "")
end

if $arguments["gttestdata"] then
  $gttestdata=File.join($arguments["gttestdata"], "")
end

$systemname=`uname -s`
$systemname.chomp!

$MEMCHECK_SUPPORTEDPLATFORMS = ["Linux", "Darwin"]

# define helper function
def run_test(str, opts = {})
  if $arguments["memcheck"] then
    if $MEMCHECK_SUPPORTEDPLATFORMS.include?($systemname) then
      $memcheck = "valgrind --tool=memcheck --suppressions="+
                  File.join($testdata, "gt.supp")+
                  " --leak-check=yes --error-exitcode=1 -q"
    elsif $systemname == "OpenBSD" then
      $memcheck = "env MALLOC_OPTIONS='GJ'"
    end
  else
    $memcheck = ""
  end
  run("#{$memcheck} #{$path}#{str}", opts)
end

def run_ruby(str, opts = {})
  run("env LD_LIBRARY_PATH=#{$cur}/lib ruby -I #{$gtruby} #{$path}#{str}", opts)
end

def run_python(str, opts = {})
  run("env PYTHONPATH=#{$gtpython} LD_LIBRARY_PATH=#{$cur}/lib python " + \
      "#{$path}#{str}", opts)
end

# include the actual test modules
require 'gt_bed_to_gff3_include'
require 'gt_cds_include'
require 'gt_chseqids_include'
require 'gt_consensus_sa_include'
require 'gt_csa_include'
require 'gt_csr_include.rb'
require 'gt_encseq_include'
require 'gt_eval_include'
require 'gt_extractfeat_include'
require 'gt_featureindex_include'
require 'gt_fingerprint_include'
require 'gt_genomediff_include'
require 'gt_gff3_include'
require 'gt_gff3validator_include'
require 'gt_gtf_to_gff3_include'
require 'gt_hop_include'
require 'gt_id_to_md5_include'
require 'gt_include'
require 'gt_interfeat_include'
require 'gt_ltrdigest_include'
require 'gt_ltrharvest_include'
require 'gt_magicmatch_include'
require 'gt_matchtool_include'
require 'gt_mathsupport_include'
require 'gt_md5_to_id_include'
require 'gt_merge_include'
require 'gt_mergefeat_include'
require 'gt_mgth_include'
require 'gt_mmapandread_include'
require 'gt_orffinder_include'
require 'gt_python_include'
require 'gt_readjoiner_include'
require 'gt_readreads_include'
require 'gt_regioncov_include'
require 'gt_ruby_include'
require 'gt_sambam_include'
require 'gt_script_filter_include'
require 'gt_scripts_include'
require 'gt_select_include'
require 'gt_seq_include'
require 'gt_seqbuffer_include'
require 'gt_seqfilter_include'
require 'gt_seqids_include'
require 'gt_seqlensort_include'
require 'gt_seqmutate_include'
require 'gt_seqorder_include'
require 'gt_seqstat_include'
require 'gt_seqtransform_include'
require 'gt_sequniq_include'
require 'gt_shredder_include'
require 'gt_simreads_include'
require 'gt_splicesiteinfo_include'
require 'gt_splitfasta_include'
require 'gt_stat_include'
require 'gt_uniq_include'
if not $arguments["nocairo"] then
  require 'gt_sketch_include'
end

#now the test cases for the tools implemented or supervised by SK.

require 'gt_chain2dim_include'
require 'gt_cmpprjfiles_include'
require 'gt_env_options_include'
require 'gt_extractseq_include'
require 'gt_idxsearch_include'
require 'gt_mergeesa_include'
require 'gt_packedindex_include'
require 'gt_sortbench_include'
require 'gt_suffixerator_include'
require 'gt_encseq2spm_include'
require 'gt_tallymer_include'
require 'gt_trieins_include'
require 'scripts_include'

if $arguments["gcov"] then
  require 'gcov_include' # must be last
end

#we now have all tests in $testsuite.

if $arguments["threads"] then
  $testsuite.nof_threads = $arguments["threads"].to_i
end
$testsuite.run
genometools-1.5.1/www/000077500000000000000000000000001211610345200146705ustar00rootroot00000000000000genometools-1.5.1/www/genometools.org/000077500000000000000000000000001211610345200200115ustar00rootroot00000000000000genometools-1.5.1/www/genometools.org/htdocs/000077500000000000000000000000001211610345200212755ustar00rootroot00000000000000genometools-1.5.1/www/genometools.org/htdocs/.gitignore000066400000000000000000000001521211610345200232630ustar00rootroot00000000000000examples.html
docs.html
images/callbacks.png
images/constructed.png
images/parsed.png
libgenometools.html
genometools-1.5.1/www/genometools.org/htdocs/annotationsketch.html000066400000000000000000000447041211610345200255500ustar00rootroot00000000000000



The AnnotationSketch module







    

    The AnnotationSketch annotation drawing library
    


    
The AnnotationSketch
module is a versatile and efficient C-based drawing library for GFF3-compatible genomic annotations. It is included in the GenomeTools distribution. Additionally, bindings to the Lua, Python and Ruby programming languages are provided.

    Contents
    


    

    Overview
    


    
AnnotationSketch consists of several classes (see Fig. 1), which take part in three visualization phases.

    

    
  
    [Dataflow]
    
  
    Figure 1: Schematic of the AnnotationSketch classes involved in image creation. Interfaces are printed in italics. 
    

    



    Phase 1: Feature selection
    

    
The GFF3 input data are parsed into a directed acyclic graph (annotation graph, see Fig. 2 for an example) whose nodes correspond to single features (i.e. lines from the GFF3 file). Consequently, edges in the graph represent the part-of relationships between groups of genomic features according to the Sequence Ontology hierarchy. Note that GFF3 input files must be valid according to the GFF3 specification to ensure that they can be read for AnnotationSketch drawing or any other kind of manipulation using GenomeTools. A validating GFF3 parser is available in GenomeTools (and can be run using gt gff3validator).

    

    
  
    [GFF3 tree]
    
  
    Figure 2: Example sequence region containing two genes in an annotation graph depicting the part-of relationships between their components.
    

    

    
Each top-level node (which is a node without a parent) is then registered into a persistent FeatureIndex object. The FeatureIndex holds a collection of the top-level nodes of all features in each sequence region in an interval tree data structure that can be efficiently queried for features in a genomic region of interest. All child nodes of the top-level node are then available by the use of traversal functions.

    

    
Alternatively, annotation graphs can be built by the user by creating each node explicitly and then connecting the nodes in a way such that the relationships are reflected in the graph structure (see example section for example code).

    

    Phase 2: Layout
    

    
The next step consists of processing the features (given via a FeatureIndex or a simple array of top level nodes) into a structural Diagram object which represents a single view of the annotations of a genomic region. First, semantic units are formed from the annotation subgraphs. This is done by building blocks out of connected features by grouping and overlaying them according to several user-defined collapsing options (see Collapsing). By default, a separate track is then created for each Sequence Ontology feature type. Alternatively, if more granularity in track assignment is desired, track selector functions can be used to create tracks and assign blocks to them based on arbitrary feature characteristics. This is simply done by creating a unique identifier string per track. The Diagram object can also be used to hold one or more custom tracks, which allow users to develop their own graphical representations as plugins.

The Diagram is then prepared for image output by calculating a compact Layout in which the Block objects in a track are distributed into Line objects, each containing non-overlapping blocks (see Fig. 3). The overall layout calculated this way tries to keep lines as compact as possible, minimising the amount of vertical space used. How new Lines are created depends on the chosen implementation of the LineBreaker interface, by default a Block is pushed into a new Line when either the Block or its caption overlaps with another one.

    


    
  
    [Diagram]
    
  
    Figure 3: The components of the Layout class reflect sections of the resulting image.
    

    

    Phase 3: Rendering
    

    
In the final phase, the Layout object is used as a blueprint to create an
image of a given type and size, considering user-defined options.

The rendering process is invoked by calling the sketch() method of a Layout object. All rendering logic is implemented in classes implementing the Canvas interface, whose methods are called during traversal of the Layout members. It encapsulates the state of a drawing and works independently of the chosen rendering back-end. Instead, rendering backend-dependent subclasses of Canvas are closely tied to a specific implementation of the Graphics interface, which provides methods to draw a number of primitives to a drawing surface abstraction. It wraps around the respective low-level graphics engine and allows for its easy extension or replacement.
    
 Currently, there is a Graphics implementation for the Cairo 2D graphics library (GraphicsCairo) and two Canvas subclasses providing access to the image file formats supported by Cairo (CanvasCairoFile) and to arbitrary Cairo contexts (CanvasCairoContext, which directly accesses a cairo_t). This class can be used, for example, to directly draw AnnotationSketch output in any graphical environment which is supported by Cairo (see  list of supported surface types).

    



    Collapsing
    

    
By default, Lines are grouped by the Sequence Ontology type associated with the top-level elements of their Blocks, resulting in one track per type.
To obtain a shorter yet concise output, tracks for parent types in the feature graph can be enabled to contain all the features of their child types. The features with the given type are then drawn on top of their parent features (e.g. all exon and intron features are placed into their parent mRNA or gene track). This process is called collapsing. Collapsing can be enabled by setting the collapse_to_parent option for the respective child type to true, e.g. the following options:

    

    style = {
  exon = {
    ...,
    collapse_to_parent = true,
    ...,
  },
  intron = {
    ...,
    collapse_to_parent = true,
    ...,
  },
  CDS = {
    ...,
    collapse_to_parent = true,
    ...,
  },
}

    
would lead to all features of the exon, intron and CDS types collapsing into the mRNA track (see Fig. 4 and 5).

    

    

    Figure 4: Schematic of the relationships between the gene, mRNA, exon, intron and CDS types and the colors of their representations in a diagram. The arrows illustrate how the relationships influence the collapsing process if collapsing is enabled for the exon, intron and CDS types. In this example, they will be drawn on top of their parent mRNA features.
    

    

    

    [collapsing]
    

    

    

    

    

    [collapsed/uncollapsed views]
    

    Figure 5:(click to enlarge) Example image of the cnn and cbs genes from Drosophila melanogaster (Ensembl release 51, positions 9326816--9341000 on chromosome arm 2R) as drawn by AnnotationSketch. At the bottom, the calculated GC content of the respective sequence is drawn via a custom track attached to the diagram. (a) shows a collapsed view in which all exon, intron and CDS types are collapsed into their parent type's track. In contrast, (b) shows the cbs gene with all collapsing options set to false, resulting in each type being drawn in its own track.
    

    



     Styles
    

    
The Lua scripting language is used to provide
user-defined settings. Settings can be imported from a script that is executed
when loaded, thus eliminating the need for another parser. The Lua configuration
data are made accessible to C via the Style class. Configurable options
include assignment of display styles to each feature type, spacer and margin
sizes, and collapsing parameters.

    

    Instead of giving direct values, callback Lua functions can be used in some options to generate feature-dependent configuration settings at run-time. During layout and/or rendering, the GenomeNode object for the feature to be rendered is passed to the callback function which can then be evaluated and the appropriate type can be returned.
    

    For example, setting the following options in the style file (or via the Lua bindings):
    

    style = {
  ...,
  mRNA = {
    block_caption      = function(gn)
                           rng = gn:get_range()
                           return string.format("%s/%s (%dbp, %d exons)",
                                 gn:get_attribute("Parent"),
                                 gn:get_attribute("ID"),
                                 rng:get_end() - rng:get_start() + 1,
                                 #(gn:get_exons()))
                         end,
    ...
  },

  exon = {
    -- Color definitions
    fill               = function(gn)
                           if gn:get_score() then
                             aval = gn:get_score()*1.0
                           else
                             aval = 0.0
                           end
                           return {red=1.0, green=0.0, blue=0.0, alpha=aval}
                         end,
    ...
  },
  ...
}

    

    will result in a changed rendering (see Fig. 6). The block_caption function overrides the default block naming scheme, allowing to set custom captions to each block depending on feature properties. Color definitions such as the fill setting for a feature's fill color can also be individually styled using callbacks. In this case, the color intensity is shaded by the exon feature's score value (e.g. given in a GFF file).
    

    
  
    [Example rendering with callback functions]
    
  
    Figure 6: Example rendering of a GFF file using callback functions to enable custom block captions and score-dependent shading of exon features.
    

    

    An overview of the keywords used in a style file is available.
    



    Track assignment
    
Tracks are normally created for each annotation source and/or Sequence Ontology type encountered in the annotation graph. More control is possible using track selector functions (read more).



    Custom tracks
    
Even more customisability is possible using custom tracks. Custom tracks are classes which contain custom drawing functionality, making it easy to add user-defined graphical content to any AnnotationSketch drawing (read more).



    The gt sketch tool
    

The GenomeTools gt executable provides a new tool which uses the AnnotationSketch library to create a drawing in PNG, PDF, PostScript or SVG format from GFF3 annotations. The annotations can be given by supplying one or more file names as command line arguments:

    $ gt sketch output.png annotation.gff3
$

    
or by receiving GFF3 data via the standard input, here prepared by the gt gff3 tool:

    $ gt gff3 -sort -addintrons annotation.gff3 | gt sketch output.png
$

    
The region to create a diagram for can be specified in detail by using the -seqid, -start and -end parameters. For example, if the D. melanogaster gene annotation is given as a dmel_annotation.gff3, use

    $ gt sketch -format pdf -seqid 2R -start 9326816 -end 9332879 output.pdf dmel_annotation.gff3
$

    
to plot the gene from the FlyBase default view in PDF format.
The -force switch is used to force overwriting of an already existing output file. The -pipe option additionally allows passing the GFF3 input through the sketch tool via the standard output, allowing the intermediate visualisation of results in a longer pipeline of connected GFF3 tools. More command line options are available; their documentation can be viewed using the -help option.

If an input file is not plotted due to parsing errors, GenomeTools includes a strict GFF3 validator tool to check whether the input file is in valid GFF3 format. Simply run a command like the following:

    $ gt gff3validator input_file.gff3
input is valid GFF3
$

    
This validator also allows one to check the SO types occurring in a GFF3 file against a given OBO ontology file. This checking can be enabled by specifying the file as an argument to the -typecheck option.

    
If the PDF, SVG and/or PostScript output format options are not available in the gt binary, the most likely cause is that PDF, SVG and/or PostScript support is disabled in your local Cairo headers and thus also not available in your local Cairo library. This issue is not directly related to AnnotationSketch and can be resolved by recompiling the Cairo library with the proper backend support enabled.

    


    Code examples
    
Besides the native C programming interface, AnnotationSketch is usable from a variety of programming languages. Code examples for the individual languages can be found here.



    Try AnnotationSketch online!
    
Upload your own annotations to a simple AnnotationSketch-based web application showing how output can look like.



    API Reference
    
A function reference for the AnnotationSketch classes can be found in
the GenomeTools C API reference.





    





genometools-1.5.1/www/genometools.org/htdocs/annotationsketch/000077500000000000000000000000001211610345200246515ustar00rootroot00000000000000genometools-1.5.1/www/genometools.org/htdocs/annotationsketch/callback_examples_with_score.gff3000066400000000000000000000012061211610345200332770ustar00rootroot00000000000000##gff-version   3
##sequence-region   ctg123 1 10000
ctg123	.	gene	1000	9000	0.5	+	.	ID=gene00001
ctg123	.	TF_binding_site	1000	1012	.	+	.	Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00001;Parent=gene00001
ctg123	.	mRNA	1050	9000	.	+	.	ID=mRNA00002;Parent=gene00001
ctg123	.	mRNA	1300	9000	.	+	.	ID=mRNA00003;Parent=gene00001
ctg123	.	exon	1300	1500	0.6	+	.	ID=exon1;Parent=mRNA00003
ctg123	.	exon	1050	1500	0.2	+	.	Parent=mRNA00001,mRNA00002
ctg123	.	exon	3000	3902	1	+	.	Parent=mRNA00001,mRNA00003
ctg123	.	exon	5000	5500	0.3	+	.	Parent=mRNA00001,mRNA00002,mRNA00003
ctg123	.	exon	7000	9000	1	+	.	Parent=mRNA00001,mRNA00002,mRNA00003
genometools-1.5.1/www/genometools.org/htdocs/annotationsketch/callbacks.style000066400000000000000000000250331211610345200276550ustar00rootroot00000000000000-- This is a GenomeTools annotation viewer style file.
-- All options must be set inside the 'style' table.
-- All items in this table must be tables, called 'sections'.

style =
{
  gene = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.9, green=0.9, blue=1.0},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
--    max_num_lines      = 10,
  },
--------------------------------------
  mRNA = {
    block_caption      = function(gn)
                           rng = gn:get_range()
                           return string.format("%s/%s (%dbp, %d exons)",
                                 gn:get_attribute("Parent"),
                                 gn:get_attribute("ID"),
                                 rng:get_end() - rng:get_start() + 1,
                                 #(gn:get_exons()))
                         end,
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.4, green=0.5, blue=0.6},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
--------------------------------------
  exon = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = function(gn)
                           if gn:get_score() then
                             aval = gn:get_score()*1.0
                           else
                             aval = 0.0
                           end
                           return {red=1.0, green=0.0, blue=0.0, alpha=aval}
                         end,
    style              = "box",
    -- Collapsing options
    collapse_to_parent = true,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
--------------------------------------
  CDS = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.9, green=0.9, blue=0.2},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = true,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
--------------------------------------
  TF_binding_site = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.8, green=0.6, blue=0.6},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
--------------------------------------
  intron = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=1.0, green=1.0, blue=1.0},
    style              = "caret",
    -- Collapsing options
    collapse_to_parent = true,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
--------------------------------------
  repeat_region = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.8, green=0.3, blue=0.3},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = false,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
--------------------------------------
  LTR_retrotransposon = {
    -- Color definitions
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.8, green=0.5, blue=0.5},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = true,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
--------------------------------------
  long_terminal_repeat = {
    -- Color definitions
    -- RGB triplets {red=,green=,blue=}
    -- where  is a decimal value between 0 and 1.
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.9, green=0.9, blue=0.4},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = true,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
--------------------------------------
    protein_match = {
    -- Color definitions
    -- RGB triplets {red=,green=,blue=}
    -- where  is a decimal value between 0 and 1.
    stroke             = {red=0.0, green=0.0, blue=0.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.1, green=0.1, blue=0.5},
    style              = "box",
    -- Collapsing options
    collapse_to_parent = true,
    split_lines        = true,
    -- Caption options
    max_capt_show_width= nil,
    -- Display this track only if the viewport is not wider than this
    -- number of nucleotides. Set to 0 to disable type track.
    max_show_width     = nil,
    -- Limit the number of tracks
    max_num_lines      = 10,
  },
--------------------------------------
  five_prime_cis_splice_site = {
    collapse_to_parent = true,
  },
--------------------------------------
  three_prime_cis_splice_site = {
    collapse_to_parent = true,
  },
--------------------------------------
  expressed_sequence_match = {
    fill               = {red=0.2, green=0.2, blue=0.8},
    max_show_width     = 10000,
    max_num_lines      = 10,
    max_capt_show_width= 5000,
  },
--------------------------------------
  binding_site = {
    fill               = {red=0.7, green=0.2, blue=0.8},
    max_show_width     = 10000,
    max_num_lines      = 10,
    max_capt_show_width= 10000,
  },
--------------------------------------
  SNP = {
    fill               = {red=0.1, green=0.8, blue=0.8},
    max_show_width     = 10000,
    max_num_lines      = 10,
    max_capt_show_width= 10000,
  },
--------------------------------------
  deletion = {
    fill               = {red=0.1, green=0.8, blue=0.8},
    max_show_width     = nil,
    max_num_lines      = 10,
    max_capt_show_width= 10000,
  },
--------------------------------------
  chromosome = {
    fill               = {red=0.1, green=0.8, blue=0.8},
    max_show_width     = nil,
    max_num_lines      = 10,
  },
--------------------------------------
  substitution = {
    fill               = {red=1.0, green=0.1, blue=0.05},
    max_show_width     = 10000,
    max_num_lines      = 10,
    max_capt_show_width= 1000,
  },
  -- Defines various format options for drawing.
  format =
  {
    -- Set the following three settings to 'false' to globally disable them.
    split_lines = true, -- generally enable splitting
    show_block_captions = true, -- generally show captions
    show_track_captions = true, -- generally show track captions
    margins = 30,      -- space left and right of diagram, in pixels
    bar_height = 16,   -- height of a feature bar, in pixels
    bar_vspace = 10,   -- space between feature bars, in pixels
    track_vspace = 15, -- space between tracks, in pixels
    ruler_font_size = 10, -- size of scale labels
    ruler_space = 20, -- space between ruler and first track
    block_caption_font_size = 10, -- size of block captions
    block_caption_space = 7, -- space between blocks and their captions
    track_caption_font_size = 10, -- size of track captions
    track_caption_space = 7, -- space between tracks and their captions
    scale_arrow_width = 6,     -- width of scale arrowheads, in pixels
    scale_arrow_height = 10,   -- height of scale arrowheads, in pixels
    arrow_width = 6,   -- width of feature arrowheads, in pixels
    stroke_width = .5, -- width of outlines, in pixels
    stroke_marked_width = 1.5, -- width of outlines for marked elements, in pixels
    show_grid = true, -- shows light vertical lines for orientation
    min_len_block = 20 , -- minimum length of a block in which single elements are shown
    track_title_color     = {red=0.7, green=0.7, blue=0.7, alpha = 1.0},
    default_stroke_color  = {red=0.1, green=0.1, blue=0.1, alpha = 1.0},
    background_color      = {red=1.0, green=1.0, blue=1.0, alpha = 1.0},
  },
}
genometools-1.5.1/www/genometools.org/htdocs/cgi-bin/000077500000000000000000000000001211610345200226055ustar00rootroot00000000000000genometools-1.5.1/www/genometools.org/htdocs/cgi-bin/README000066400000000000000000000455101211610345200234720ustar00rootroot00000000000000GIT web Interface
=================

The one working on:
  http://git.kernel.org/

From the git version 1.4.0 gitweb is bundled with git.


How to configure gitweb for your local system
---------------------------------------------

See also the "Build time configuration" section in the INSTALL
file for gitweb (in gitweb/INSTALL).

You can specify the following configuration variables when building GIT:
 * GIT_BINDIR
   Points where to find the git executable.  You should set it up to
   the place where the git binary was installed (usually /usr/bin) if you
   don't install git from sources together with gitweb.  [Default: $(bindir)]
 * GITWEB_SITENAME
   Shown in the title of all generated pages, defaults to the server name
   (SERVER_NAME CGI environment variable) if not set. [No default]
 * GITWEB_PROJECTROOT
   The root directory for all projects shown by gitweb. Must be set
   correctly for gitweb to find repositories to display.  See also
   "Gitweb repositories" in the INSTALL file for gitweb.  [Default: /pub/git]
 * GITWEB_PROJECT_MAXDEPTH
   The filesystem traversing limit for getting the project list; the number
   is taken as depth relative to the projectroot.  It is used when
   GITWEB_LIST is a directory (or is not set; then project root is used).
   Is is meant to speed up project listing on large work trees by limiting
   search depth.  [Default: 2007]
 * GITWEB_LIST
   Points to a directory to scan for projects (defaults to project root
   if not set / if empty) or to a file with explicit listing of projects
   (together with projects' ownership). See "Generating projects list
   using gitweb" in INSTALL file for gitweb to find out how to generate
   such file from scan of a directory. [No default, which means use root
   directory for projects]
 * GITWEB_EXPORT_OK
   Show repository only if this file exists (in repository).  Only
   effective if this variable evaluates to true.  [No default / Not set]
 * GITWEB_STRICT_EXPORT
   Only allow viewing of repositories also shown on the overview page.
   This for example makes GITWEB_EXPORT_OK to decide if repository is
   available and not only if it is shown.  If GITWEB_LIST points to
   file with list of project, only those repositories listed would be
   available for gitweb.  [No default]
 * GITWEB_HOMETEXT
   Points to an .html file which is included on the gitweb project
   overview page ('projects_list' view), if it exists.  Relative to
   gitweb.cgi script.  [Default: indextext.html]
 * GITWEB_SITE_HEADER
   Filename of html text to include at top of each page.  Relative to
   gitweb.cgi script.  [No default]
 * GITWEB_SITE_FOOTER
   Filename of html text to include at bottom of each page.  Relative to
   gitweb.cgi script.  [No default]
 * GITWEB_HOME_LINK_STR
   String of the home link on top of all pages, leading to $home_link
   (usually main gitweb page, which means projects list).  Used as first
   part of gitweb view "breadcrumb trail":  /  / .
   [Default: projects]
 * GITWEB_SITENAME
   Name of your site or organization to appear in page titles.  Set it
   to something descriptive for clearer bookmarks etc.  If not set
   (if empty) gitweb uses "$SERVER_NAME Git", or "Untitled Git" if
   SERVER_NAME CGI environment variable is not set (e.g. if running
   gitweb as standalone script).  [No default]
 * GITWEB_BASE_URL
   Git base URLs used for URL to where fetch project from, i.e. full
   URL is "$git_base_url/$project".  Shown on projects summary page.
   Repository URL for project can be also configured per repository; this
   takes precedence over URLs composed from base URL and a project name.
   Note that you can setup multiple base URLs (for example one for
   git:// protocol access, another for http:// access) from the gitweb
   config file.  [No default]
 * GITWEB_CSS
   Points to the location where you put gitweb.css on your web server
   (or to be more generic, the URI of gitweb stylesheet).  Relative to the
   base URI of gitweb.  Note that you can setup multiple stylesheets from
   the gitweb config file.  [Default: gitweb.css]
 * GITWEB_LOGO
   Points to the location where you put git-logo.png on your web server
   (or to be more generic URI of logo, 72x27 size, displayed in top right
   corner of each gitweb page, and used as logo for Atom feed).  Relative
   to base URI of gitweb.  [Default: git-logo.png]
 * GITWEB_FAVICON
   Points to the location where you put git-favicon.png on your web server
   (or to be more generic URI of favicon, assumed to be image/png type;
   web browsers that support favicons (website icons) may display them
   in the browser's URL bar and next to site name in bookmarks).  Relative
   to base URI of gitweb.  [Default: git-favicon.png]
 * GITWEB_JS
   Points to the localtion where you put gitweb.js on your web server
   (or to be more generic URI of JavaScript code used by gitweb).
   Relative to base URI of gitweb.  [Default: gitweb.js (or gitweb.min.js
   if JSMIN build variable is defined / JavaScript minifier is used)]
 * GITWEB_CONFIG
   This Perl file will be loaded using 'do' and can be used to override any
   of the options above as well as some other options -- see the "Runtime
   gitweb configuration" section below, and top of 'gitweb.cgi' for their
   full list and description.  If the environment variable GITWEB_CONFIG
   is set when gitweb.cgi is executed, then the file specified in the
   environment variable will be loaded instead of the file specified
   when gitweb.cgi was created.  [Default: gitweb_config.perl]
 * GITWEB_CONFIG_SYSTEM
   This Perl file will be loaded using 'do' as a fallback if GITWEB_CONFIG
   does not exist.  If the environment variable GITWEB_CONFIG_SYSTEM is set
   when gitweb.cgi is executed, then the file specified in the environment
   variable will be loaded instead of the file specified when gitweb.cgi was
   created.  [Default: /etc/gitweb.conf]


Runtime gitweb configuration
----------------------------

You can adjust gitweb behaviour using the file specified in `GITWEB_CONFIG`
(defaults to 'gitweb_config.perl' in the same directory as the CGI), and
as a fallback `GITWEB_CONFIG_SYSTEM` (defaults to /etc/gitweb.conf).
The most notable thing that is not configurable at compile time are the
optional features, stored in the '%features' variable.

Ultimate description on how to reconfigure the default features setting
in your `GITWEB_CONFIG` or per-project in `project.git/config` can be found
as comments inside 'gitweb.cgi'.

See also the "Gitweb config file" (with an example of config file), and
the "Gitweb repositories" sections in INSTALL file for gitweb.


The gitweb config file is a fragment of perl code. You can set variables
using "our $variable = value"; text from "#" character until the end
of a line is ignored. See perlsyn(1) man page for details.

Below is the list of variables which you might want to set in gitweb config.
See the top of 'gitweb.cgi' for the full list of variables and their
descriptions.

Gitweb config file variables
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

You can set, among others, the following variables in gitweb config files
(with the exception of $projectroot and $projects_list this list does
not include variables usually directly set during build):
 * $GIT
   Core git executable to use.  By default set to "$GIT_BINDIR/git", which
   in turn is by default set to "$(bindir)/git".  If you use git from binary
   package, set this to "/usr/bin/git".  This can just be "git" if your
   webserver has a sensible PATH.  If you have multiple git versions
   installed it can be used to choose which one to use.
 * $version
   Gitweb version, set automatically when creating gitweb.cgi from
   gitweb.perl. You might want to modify it if you are running modified
   gitweb.
 * $projectroot
   Absolute filesystem path which will be prepended to project path;
   the path to repository is $projectroot/$project.  Set to
   $GITWEB_PROJECTROOT during installation.  This variable have to be
   set correctly for gitweb to find repositories.
 * $projects_list
   Source of projects list, either directory to scan, or text file
   with list of repositories (in the " SP
   " line format; actually there can be
   any sequence of whitespace in place of space (SP)).  Set to
   $GITWEB_LIST during installation.  If empty, $projectroot is used
   to scan for repositories.
 * $my_url, $my_uri
   Full URL and absolute URL of gitweb script;
   in earlier versions of gitweb you might have need to set those
   variables, now there should be no need to do it.
 * $base_url
   Base URL for relative URLs in pages generated by gitweb,
   (e.g. $logo, $favicon, @stylesheets if they are relative URLs),
   needed and used only for URLs with nonempty PATH_INFO via
     - path to repository GIT_DIR, relative to $projectroot
 *  - displayed as repository owner, preferably full name,
                        or email, or both

You can additionally use $projects_list file to limit which repositories
are visible, and together with $strict_export to limit access to
repositories (see "Gitweb repositories" section in gitweb/INSTALL).


Per-repository gitweb configuration
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

You can also configure individual repositories shown in gitweb by creating
file in the GIT_DIR of git repository, or by setting some repo configuration
variable (in GIT_DIR/config).

You can use the following files in repository:
 * README.html
   A .html file (HTML fragment) which is included on the gitweb project
   summary page inside 
     block element. You can use it for longer
   description of a project, to provide links (for example to project's
   homepage), etc. This is recognized only if XSS prevention is off
   ($prevent_xss is false); a way to include a readme safely when XSS
   prevention is on may be worked out in the future.
 * description (or gitweb.description)
   Short (shortened by default to 25 characters in the projects list page)
   single line description of a project (of a repository). Plain text file;
   HTML will be escaped. By default set to
     Unnamed repository; edit this file to name it for gitweb.
   from the template during repository creation. You can use the
   gitweb.description repo configuration variable, but the file takes
   precedence.
 * cloneurl (or multiple-valued gitweb.url)
   File with repository URL (used for clone and fetch), one per line.
   Displayed in the project summary page. You can use multiple-valued
   gitweb.url repository configuration variable for that, but the file
   takes precedence.
 * gitweb.owner
   You can use the gitweb.owner repository configuration variable to set
   repository's owner. It is displayed in the project list and summary
   page. If it's not set, filesystem directory's owner is used
   (via GECOS field / real name field from getpwiud(3)).
 * various gitweb.* config variables (in config)
   Read description of %feature hash for detailed list, and some
   descriptions.


Webserver configuration
-----------------------

If you want to have one URL for both gitweb and your http://
repositories, you can configure apache like this:


    ServerName git.example.org
    DocumentRoot /pub/git
    SetEnv	GITWEB_CONFIG	/etc/gitweb.conf
    RewriteEngine on
    # make the front page an internal rewrite to the gitweb script
    RewriteRule ^/$  /cgi-bin/gitweb.cgi
    # make access for "dumb clients" work
    RewriteRule ^/(.*\.git/(?!/?(HEAD|info|objects|refs)).*)?$ /cgi-bin/gitweb.cgi%{REQUEST_URI}  [L,PT]


The above configuration expects your public repositories to live under
/pub/git and will serve them as http://git.domain.org/dir-under-pub-git,
both as cloneable GIT URL and as browseable gitweb interface.
If you then start your git-daemon with --base-path=/pub/git --export-all
then you can even use the git:// URL with exactly the same path.

Setting the environment variable GITWEB_CONFIG will tell gitweb to use
the named file (i.e. in this example /etc/gitweb.conf) as a
configuration for gitweb.  Perl variables defined in here will
override the defaults given at the head of the gitweb.perl (or
gitweb.cgi).  Look at the comments in that file for information on
which variables and what they mean.

If you use the rewrite rules from the example you'll likely also need
something like the following in your gitweb.conf (or gitweb_config.perl) file:

  @stylesheets = ("/some/absolute/path/gitweb.css");
  $my_uri = "/";
  $home_link = "/";


PATH_INFO usage
-----------------------
If you enable PATH_INFO usage in gitweb by putting

   $feature{'pathinfo'}{'default'} = [1];

in your gitweb.conf, it is possible to set up your server so that it
consumes and produces URLs in the form

http://git.example.com/project.git/shortlog/sometag

by using a configuration such as the following, that assumes that
/var/www/gitweb is the DocumentRoot of your webserver, and that it
contains the gitweb.cgi script and complementary static files
(stylesheet, favicon):


	ServerAlias git.example.com

	DocumentRoot /var/www/gitweb

	
		Options ExecCGI
		AddHandler cgi-script cgi

		DirectoryIndex gitweb.cgi

		RewriteEngine On
		RewriteCond %{REQUEST_FILENAME} !-f
		RewriteCond %{REQUEST_FILENAME} !-d
		RewriteRule ^.* /gitweb.cgi/$0 [L,PT]
	


The rewrite rule guarantees that existing static files will be properly
served, whereas any other URL will be passed to gitweb as PATH_INFO
parameter.

Notice that in this case you don't need special settings for
@stylesheets, $my_uri and $home_link, but you lose "dumb client" access
to your project .git dirs. A possible workaround for the latter is the
following: in your project root dir (e.g. /pub/git) have the projects
named without a .git extension (e.g. /pub/git/project instead of
/pub/git/project.git) and configure Apache as follows:


	ServerAlias git.example.com

	DocumentRoot /var/www/gitweb

	AliasMatch ^(/.*?)(\.git)(/.*)?$ /pub/git$1$3
	
		Options ExecCGI
		AddHandler cgi-script cgi

		DirectoryIndex gitweb.cgi

		RewriteEngine On
		RewriteCond %{REQUEST_FILENAME} !-f
		RewriteCond %{REQUEST_FILENAME} !-d
		RewriteRule ^.* /gitweb.cgi/$0 [L,PT]
	


The additional AliasMatch makes it so that

http://git.example.com/project.git

will give raw access to the project's git dir (so that the project can
be cloned), while

http://git.example.com/project

will provide human-friendly gitweb access.

This solution is not 100% bulletproof, in the sense that if some project
has a named ref (branch, tag) starting with 'git/', then paths such as

http://git.example.com/project/command/abranch..git/abranch

will fail with a 404 error.



Originally written by:
  Kay Sievers 

Any comment/question/concern to:
  Git mailing list 
genometools-1.5.1/www/genometools.org/htdocs/cgi-bin/annotationsketch_demo.cgi000077500000000000000000000244761211610345200276710ustar00rootroot00000000000000#!/usr/bin/env ruby
#
# Copyright (c) 2008 Sascha Steinbiss 
# Copyright (c) 2008 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

GENOMETOOLS_PATH = "/home/satta/genometools_for_web"
GTRUBY_PATH      = "#{GENOMETOOLS_PATH}/gtruby"
# the LD_LIBRARY_PATH has to be set externally to "#{GENOMETOOLS_PATH}/lib"!
STYLE_FILE       = "#{GENOMETOOLS_PATH}/gtdata/sketch/default.style"
DEFAULT_ANNOTATION_FILE = "#{GENOMETOOLS_PATH}/testdata/standard_gene_as_tree.gff3"
SCRIPT_PATH      = "/var/www/servers/genometools.org/htdocs/cgi-bin"
UPLOAD_PATH      = "/tmp"
IMAGE_DIR        = "imgs"   # relative paths from SCRIPT_PATH please
MAXSIZE          = 2097152

$: << (GTRUBY_PATH)
require "gtruby"
require "cgi"

puts "Content-type: text/html"
puts ""

cgi = CGI.new("html4")

class String
# String#strip_html - Removes HTML tags from a string.
# Author:: Rob Pitt
# Removes HTML tags from a string. Allows you to specify some tags to be kept.
  def strip_html( allowed = [] )
    re = if allowed.any?
      Regexp.new(
        %(<(?!(\\s|\\/)*(#{
          allowed.map {|tag| Regexp.escape( tag )}.join( "|" )
        })( |>|\\/|'|"|<|\\s*\\z))[^>]*(>+|\\s*\\z)),
        Regexp::IGNORECASE | Regexp::MULTILINE, 'u'
      )
    else
      /<[^>]*(>+|\s*\z)/m
    end
    gsub(re,'')
  end
end

HTML_HEADER = <



The AnnotationSketch module






    
  
    AnnotationSketch online demo
    
  
    Use this form to upload a GFF3 annotation file (up to 2MB) which is then
     drawn using an AnnotationSketch-based Ruby script and output to
     your browser. Some basic options, such as displayed sequence region and
     range, or the generated image width, can be set. For more options, the
     stand-alone gt sketch tool can be used.
    
END

HTML_FOOTER = <
Copyright © 2007-2011 Sascha Steinbiss. Last update: 2011-02-11

    

    





END

UPLOAD_FORM = <
    
    "
                    "

    "
                    "Statistic-Section

    
      
    Annotation file:
        
          Example file
    
          Custom file: 
          
            		
      
    
      
    
        Sequence region:
        
      
    
      
    
                   (leave blank to use first sequence region in file)
      
    
      
    
        Range to display:
        bp
         –
        bp
        
    
                     (leave blank to show complete sequence region)
      
    
      
    
        Image width:
         pixels
      
    
      
    
        
      
    
      
    
    
END

HTML_IMAGE = <AnnotationSketch diagram of %s
 
    
  
    AnnotationSketch diagram
    
 
    
END

puts HTML_HEADER

if cgi.params.has_key?('submitted') then
  # CGI parameters behave differently with uploaded file size.
  # StringIO.read does not seem to work right either.
  # account for that by checking for the type of the parameters
  if cgi["example"].kind_of?(StringIO) then
    read_method = :string
  else
    read_method = :read
  end
  begin
    if cgi["example"].nil? or cgi["example"].send(read_method) == "example" then
      e_str = 'checked="checked"'
      d_str1 = ""
      d_str2 = 'disabled="disabled"'
    else
      e_str = ""
      d_str1 = 'checked="checked"'
      d_str2 = ""
    end
    puts UPLOAD_FORM % [e_str, \
                        d_str1, \
                        d_str2, \
                        cgi['seqid'].string.strip_html, \
                        cgi['rangestart'].string.strip_html, \
                        cgi['rangeend'].string.strip_html, \
                        cgi['width'].string.strip_html]

    if cgi["example"].nil? or cgi["example"].send(read_method) == "example" then
      targetfilename = DEFAULT_ANNOTATION_FILE
      originalfilename = File.basename(DEFAULT_ANNOTATION_FILE)
    else
      ufile = cgi.params['file']
      if ufile.first.length == 0 then
        GT::gterror("No file was uploaded!")
      elsif ufile.first.length > MAXSIZE then
        GT::gterror("Your uploaded file was too large! This demo service
                     supports annotation files up to #{(MAXSIZE/1024)}KB. Please
                     upload a smaller file.")
      end
      # mangle file path to avoid directory traversal attacks
      originalfilename = ufile.first.original_filename
      truncated_filename = File.basename(File.expand_path(originalfilename))
      targetfilename = "#{UPLOAD_PATH}/#{truncated_filename}"
      File.open(targetfilename, "w+") do |file|
        file.write(ufile.first.read)
      end
    end
    feature_index = GT::FeatureIndexMemory.new()
    feature_index.add_gff3file(targetfilename)

    if cgi['width'].string != "" then
      width = cgi['width'].send(read_method).to_i
      if width < 70 then
        GT::gterror("Please set a width of more than 70 pixels!")
      end
    else
      width = 800
    end

    if cgi['seqid'].string.to_s != "" then
      seqid = cgi['seqid'].string
      seqids = feature_index.get_seqids
      if !seqids.include?(seqid) then
        if not cgi["example"].send(read_method) == "example" then
          File.unlink(targetfilename)
        end
        GT::gterror("Invalid sequence region '#{seqid}':
                     must be #{"one of" unless seqids.length == 1}
                     #{seqids.collect{|v|""#{v}""}.join(" or ")}!")
      end
    else
      seqid = feature_index.get_first_seqid
    end

    if cgi['rangestart'] and cgi['rangestart'].string != "" \
     and cgi['rangeend'] and  cgi['rangeend'].string != "" then
      range = GT::Range.malloc
      range.start = cgi['rangestart'].string.to_i
      range.end   = cgi['rangeend'].string.to_i
      if range.start >= range.end then
        GT::gterror("Invalid range, must be numeric and
                     start must be < end!")
      end
    else
      range = feature_index.get_range_for_seqid(seqid)
    end

    style = GT::Style.new()
    style.load_file(STYLE_FILE)
    d = GT::Diagram.from_index(feature_index, seqid, range, style)
    l = GT::Layout.new(d, width, style)
    c = GT::CanvasCairoFile.new(style, width, l.get_height())
    l.sketch(c)
    c.to_file("#{SCRIPT_PATH}/#{IMAGE_DIR}/#{originalfilename}.png")
    puts HTML_IMAGE % [originalfilename.strip_html, \
                       "#{IMAGE_DIR}/#{originalfilename}.png"]
    if not cgi["example"].send(read_method) == "example" then
      File.unlink(targetfilename)
    end
  rescue Exception => err:
    puts "
    An error has occurred
    #{err}
    "
  end
else
  puts UPLOAD_FORM % ['checked="checked"', '', 'disabled="disabled"', '', '', \
                      '', 800]
end

print HTML_FOOTER
genometools-1.5.1/www/genometools.org/htdocs/cgi-bin/gff3validator.cgi000066400000000000000000000173031211610345200260300ustar00rootroot00000000000000#!/usr/bin/env ruby
#
# Copyright (c) 2012 Sascha Steinbiss 
# Copyright (c) 2012 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#

GENOMETOOLS_PATH = "/home/satta/genometools_for_web"
GTRUBY_PATH      = "#{GENOMETOOLS_PATH}/gtruby"
# the LD_LIBRARY_PATH has to be set externally to "#{GENOMETOOLS_PATH}/lib"!
SCRIPT_PATH      = "/var/www/servers/genometools.org/htdocs/cgi-bin"
UPLOAD_PATH      = "/tmp"
MAXSIZE          = 52428800

$: << (GTRUBY_PATH)
require "gtruby"
require "cgi"
require 'tempfile'

puts "Content-type: text/html"
puts ""

cgi = CGI.new("html4")

HTML_HEADER = <



GFF3 Online Validator







    
  
    GFF3 online validator
    
  
    Use this form to upload a GFF3 annotation file (up to 50 MB, can be .gz or
.bz2 compressed) which is then validated against the GFF3 specification using the current Sequence Ontology OBO file.
    
END

HTML_FOOTER = <
Copyright © 2012 Sascha Steinbiss. Last update: 2012-04-11
    END UPLOAD_FORM = <
    Annotation file:
    enable "tidy" mode (tries to fix errors)
    also report content of affected GFF lines

    This GFF3 validator is part of the GenomeTools distribution which you can download to your computer. Use the gff3validator tool to validate your own – possibly larger – GFF3 files and the gff3 tool with option -tidy to tidy them up (-help shows further options).

    END puts HTML_HEADER def print_gff3line(line, lineno, red = false) puts "" puts "#{lineno}" puts "#{if red then "→" end}" line.split("\t").each do |v| print "#{v}" end puts puts "" end if cgi.params.has_key?('submitted') then tidy = (cgi.params["tidy"].length > 0) show = (cgi.params["show"].length > 0) begin show_checked = '' tidy_checked = '' if tidy then tidy_checked = 'checked="checked"' end if show then show_checked = 'checked="checked"' end puts UPLOAD_FORM % [tidy_checked, show_checked] ufile = cgi.params['file'] if ufile.first.length == 0 then GT::gterror("No file was uploaded!") elsif ufile.first.length > MAXSIZE then GT::gterror("Your uploaded file was too large! This service supports annotation files up to #{(MAXSIZE/1024)}KB. Please upload a smaller file.") end # mangle file path to avoid directory traversal attacks originalfilename = ufile.first.original_filename truncated_filename = File.basename(File.expand_path(originalfilename)) targetfilename = "#{UPLOAD_PATH}/#{truncated_filename}" File.open(targetfilename, "w+") do |file| file.write(ufile.first.read) end errfile = Tempfile.new('validator') $stderr.reopen(errfile) checker = GT::TypeCheckerOBO.new("#{GENOMETOOLS_PATH}/gtdata/obo_files/so.obo") stream = GT::GFF3InStream.new(targetfilename, false) stream.set_type_checker(checker) if tidy then stream.enable_tidy_mode end gn = stream.next_tree() while (gn) do gn = stream.next_tree() end errfile.flush puts "

    Validation successful!

    " errfile.rewind entries = errfile.readlines if entries.length > 0 then puts "

    #{entries.length} issue#{"s" unless entries.length == 1} remaining:

    " file = File.open(targetfilename).readlines entries.each do |entry| puts "
    " puts "

    #{entry}

    " if show and (m = /line ([0-9]+)/.match(entry)) then linenumber = m[1].to_i puts "

    "
          if linenumber-1 > 0 then
            print_gff3line(file[linenumber-2].chomp,linenumber-1)
          end
          print_gff3line(file[linenumber-1].chomp, linenumber, true)
          if linenumber <= (file.length)-1 then
            print_gff3line(file[linenumber].chomp, linenumber+1)
          end
          puts "

    " end puts "
    " end end errfile.close errfile.unlink rescue Exception => err puts "

    Validation unsuccessful!

    #{err}

    " end else puts UPLOAD_FORM % ['', 'checked="checked"'] end print HTML_FOOTER genometools-1.5.1/www/genometools.org/htdocs/cgi-bin/git-favicon.png000066400000000000000000000001631211610345200255210ustar00rootroot00000000000000PNG  IHDRb PLTE|%IDATcX ؈&[2+ajjdsQ#[ovIENDB`genometools-1.5.1/www/genometools.org/htdocs/cgi-bin/git-logo.png000066400000000000000000000003171211610345200250350ustar00rootroot00000000000000PNG  IHDRH)9,PLTE``] GrIDATx CwKK4tC!EɦI$-4 VNTC0mFB)yV6׊PhS'jjiWqD_H"F'<pG SIENDB`genometools-1.5.1/www/genometools.org/htdocs/cgi-bin/gitweb.cgi000077500000000000000000006127301211610345200245660ustar00rootroot00000000000000#!/usr/bin/perl # gitweb - simple web interface to track changes in git repositories # # (C) 2005-2006, Kay Sievers # (C) 2005, Christian Gierke # # This program is licensed under the GPLv2 use strict; use warnings; use CGI qw(:standard :escapeHTML -nosticky); use CGI::Util qw(unescape); use CGI::Carp qw(fatalsToBrowser); use Encode; use Fcntl ':mode'; use File::Find qw(); use File::Basename qw(basename); binmode STDOUT, ':utf8'; our $t0; if (eval { require Time::HiRes; 1; }) { $t0 = [Time::HiRes::gettimeofday()]; } our $number_of_git_cmds = 0; BEGIN { CGI->compile() if $ENV{'MOD_PERL'}; } our $cgi = new CGI; our $version = "1.6.6.1"; our $my_url = $cgi->url(); our $my_uri = $cgi->url(-absolute => 1); # Base URL for relative URLs in gitweb ($logo, $favicon, ...), # needed and used only for URLs with nonempty PATH_INFO our $base_url = $my_url; # When the script is used as DirectoryIndex, the URL does not contain the name # of the script file itself, and $cgi->url() fails to strip PATH_INFO, so we # have to do it ourselves. We make $path_info global because it's also used # later on. # # Another issue with the script being the DirectoryIndex is that the resulting # $my_url data is not the full script URL: this is good, because we want # generated links to keep implying the script name if it wasn't explicitly # indicated in the URL we're handling, but it means that $my_url cannot be used # as base URL. # Therefore, if we needed to strip PATH_INFO, then we know that we have # to build the base URL ourselves: our $path_info = $ENV{"PATH_INFO"}; if ($path_info) { if ($my_url =~ s,\Q$path_info\E$,, && $my_uri =~ s,\Q$path_info\E$,, && defined $ENV{'SCRIPT_NAME'}) { $base_url = $cgi->url(-base => 1) . $ENV{'SCRIPT_NAME'}; } } # core git executable to use # this can just be "git" if your webserver has a sensible PATH our $GIT = "/usr/bin/git"; # absolute fs-path which will be prepended to the project path #our $projectroot = "/pub/scm"; our $projectroot = "/var/www/pub/git"; # fs traversing limit for getting project list # the number is relative to the projectroot our $project_maxdepth = 2007; # target of the home link on top of all pages our $home_link = $my_uri || "/"; # string of the home link on top of all pages our $home_link_str = "projects"; # name of your site or organization to appear in page titles # replace this with something more descriptive for clearer bookmarks our $site_name = "" || ($ENV{'SERVER_NAME'} || "Untitled") . " Git"; # filename of html text to include at top of each page our $site_header = ""; # html text to include at home page our $home_text = "indextext.html"; # filename of html text to include at bottom of each page our $site_footer = ""; # URI of stylesheets our @stylesheets = ("gitweb.css"); # URI of a single stylesheet, which can be overridden in GITWEB_CONFIG. our $stylesheet = undef; # URI of GIT logo (72x27 size) our $logo = "git-logo.png"; # URI of GIT favicon, assumed to be image/png type our $favicon = "git-favicon.png"; # URI of gitweb.js (JavaScript code for gitweb) our $javascript = "gitweb.js"; # URI and label (title) of GIT logo link #our $logo_url = "http://www.kernel.org/pub/software/scm/git/docs/"; #our $logo_label = "git documentation"; our $logo_url = "http://git-scm.com/"; our $logo_label = "git homepage"; # source of projects list our $projects_list = ""; # the width (in characters) of the projects list "Description" column our $projects_list_description_width = 25; # default order of projects list # valid values are none, project, descr, owner, and age our $default_projects_order = "project"; # show repository only if this file exists # (only effective if this variable evaluates to true) our $export_ok = ""; # show repository only if this subroutine returns true # when given the path to the project, for example: # sub { return -e "$_[0]/git-daemon-export-ok"; } our $export_auth_hook = undef; # only allow viewing of repositories also shown on the overview page our $strict_export = ""; # list of git base URLs used for URL to where fetch project from, # i.e. full URL is "$git_base_url/$project" our @git_base_url_list = grep { $_ ne '' } (""); # default blob_plain mimetype and default charset for text/plain blob our $default_blob_plain_mimetype = 'text/plain'; our $default_text_plain_charset = undef; # file to use for guessing MIME types before trying /etc/mime.types # (relative to the current git repository) our $mimetypes_file = undef; # assume this charset if line contains non-UTF-8 characters; # it should be valid encoding (see Encoding::Supported(3pm) for list), # for which encoding all byte sequences are valid, for example # 'iso-8859-1' aka 'latin1' (it is decoded without checking, so it # could be even 'utf-8' for the old behavior) our $fallback_encoding = 'latin1'; # rename detection options for git-diff and git-diff-tree # - default is '-M', with the cost proportional to # (number of removed files) * (number of new files). # - more costly is '-C' (which implies '-M'), with the cost proportional to # (number of changed files + number of removed files) * (number of new files) # - even more costly is '-C', '--find-copies-harder' with cost # (number of files in the original tree) * (number of new files) # - one might want to include '-B' option, e.g. '-B', '-M' our @diff_opts = ('-M'); # taken from git_commit # Disables features that would allow repository owners to inject script into # the gitweb domain. our $prevent_xss = 0; # information about snapshot formats that gitweb is capable of serving our %known_snapshot_formats = ( # name => { # 'display' => display name, # 'type' => mime type, # 'suffix' => filename suffix, # 'format' => --format for git-archive, # 'compressor' => [compressor command and arguments] # (array reference, optional) # 'disabled' => boolean (optional)} # 'tgz' => { 'display' => 'tar.gz', 'type' => 'application/x-gzip', 'suffix' => '.tar.gz', 'format' => 'tar', 'compressor' => ['gzip']}, 'tbz2' => { 'display' => 'tar.bz2', 'type' => 'application/x-bzip2', 'suffix' => '.tar.bz2', 'format' => 'tar', 'compressor' => ['bzip2']}, 'txz' => { 'display' => 'tar.xz', 'type' => 'application/x-xz', 'suffix' => '.tar.xz', 'format' => 'tar', 'compressor' => ['xz'], 'disabled' => 1}, 'zip' => { 'display' => 'zip', 'type' => 'application/x-zip', 'suffix' => '.zip', 'format' => 'zip'}, ); # Aliases so we understand old gitweb.snapshot values in repository # configuration. our %known_snapshot_format_aliases = ( 'gzip' => 'tgz', 'bzip2' => 'tbz2', 'xz' => 'txz', # backward compatibility: legacy gitweb config support 'x-gzip' => undef, 'gz' => undef, 'x-bzip2' => undef, 'bz2' => undef, 'x-zip' => undef, '' => undef, ); # Pixel sizes for icons and avatars. If the default font sizes or lineheights # are changed, it may be appropriate to change these values too via # $GITWEB_CONFIG. our %avatar_size = ( 'default' => 16, 'double' => 32 ); # You define site-wide feature defaults here; override them with # $GITWEB_CONFIG as necessary. our %feature = ( # feature => { # 'sub' => feature-sub (subroutine), # 'override' => allow-override (boolean), # 'default' => [ default options...] (array reference)} # # if feature is overridable (it means that allow-override has true value), # then feature-sub will be called with default options as parameters; # return value of feature-sub indicates if to enable specified feature # # if there is no 'sub' key (no feature-sub), then feature cannot be # overriden # # use gitweb_get_feature() to retrieve the value # (an array) or gitweb_check_feature() to check if # is enabled # Enable the 'blame' blob view, showing the last commit that modified # each line in the file. This can be very CPU-intensive. # To enable system wide have in $GITWEB_CONFIG # $feature{'blame'}{'default'} = [1]; # To have project specific config enable override in $GITWEB_CONFIG # $feature{'blame'}{'override'} = 1; # and in project config gitweb.blame = 0|1; 'blame' => { 'sub' => sub { feature_bool('blame', @_) }, 'override' => 0, 'default' => [0]}, # Enable the 'snapshot' link, providing a compressed archive of any # tree. This can potentially generate high traffic if you have large # project. # Value is a list of formats defined in %known_snapshot_formats that # you wish to offer. # To disable system wide have in $GITWEB_CONFIG # $feature{'snapshot'}{'default'} = []; # To have project specific config enable override in $GITWEB_CONFIG # $feature{'snapshot'}{'override'} = 1; # and in project config, a comma-separated list of formats or "none" # to disable. Example: gitweb.snapshot = tbz2,zip; 'snapshot' => { 'sub' => \&feature_snapshot, 'override' => 0, 'default' => ['tgz']}, # Enable text search, which will list the commits which match author, # committer or commit text to a given string. Enabled by default. # Project specific override is not supported. 'search' => { 'override' => 0, 'default' => [1]}, # Enable grep search, which will list the files in currently selected # tree containing the given string. Enabled by default. This can be # potentially CPU-intensive, of course. # To enable system wide have in $GITWEB_CONFIG # $feature{'grep'}{'default'} = [1]; # To have project specific config enable override in $GITWEB_CONFIG # $feature{'grep'}{'override'} = 1; # and in project config gitweb.grep = 0|1; 'grep' => { 'sub' => sub { feature_bool('grep', @_) }, 'override' => 0, 'default' => [1]}, # Enable the pickaxe search, which will list the commits that modified # a given string in a file. This can be practical and quite faster # alternative to 'blame', but still potentially CPU-intensive. # To enable system wide have in $GITWEB_CONFIG # $feature{'pickaxe'}{'default'} = [1]; # To have project specific config enable override in $GITWEB_CONFIG # $feature{'pickaxe'}{'override'} = 1; # and in project config gitweb.pickaxe = 0|1; 'pickaxe' => { 'sub' => sub { feature_bool('pickaxe', @_) }, 'override' => 0, 'default' => [1]}, # Enable showing size of blobs in a 'tree' view, in a separate # column, similar to what 'ls -l' does. This cost a bit of IO. # To disable system wide have in $GITWEB_CONFIG # $feature{'show-sizes'}{'default'} = [0]; # To have project specific config enable override in $GITWEB_CONFIG # $feature{'show-sizes'}{'override'} = 1; # and in project config gitweb.showsizes = 0|1; 'show-sizes' => { 'sub' => sub { feature_bool('showsizes', @_) }, 'override' => 0, 'default' => [1]}, # Make gitweb use an alternative format of the URLs which can be # more readable and natural-looking: project name is embedded # directly in the path and the query string contains other # auxiliary information. All gitweb installations recognize # URL in either format; this configures in which formats gitweb # generates links. # To enable system wide have in $GITWEB_CONFIG # $feature{'pathinfo'}{'default'} = [1]; # Project specific override is not supported. # Note that you will need to change the default location of CSS, # favicon, logo and possibly other files to an absolute URL. Also, # if gitweb.cgi serves as your indexfile, you will need to force # $my_uri to contain the script name in your $GITWEB_CONFIG. 'pathinfo' => { 'override' => 0, 'default' => [0]}, # Make gitweb consider projects in project root subdirectories # to be forks of existing projects. Given project $projname.git, # projects matching $projname/*.git will not be shown in the main # projects list, instead a '+' mark will be added to $projname # there and a 'forks' view will be enabled for the project, listing # all the forks. If project list is taken from a file, forks have # to be listed after the main project. # To enable system wide have in $GITWEB_CONFIG # $feature{'forks'}{'default'} = [1]; # Project specific override is not supported. 'forks' => { 'override' => 0, 'default' => [0]}, # Insert custom links to the action bar of all project pages. # This enables you mainly to link to third-party scripts integrating # into gitweb; e.g. git-browser for graphical history representation # or custom web-based repository administration interface. # The 'default' value consists of a list of triplets in the form # (label, link, position) where position is the label after which # to insert the link and link is a format string where %n expands # to the project name, %f to the project path within the filesystem, # %h to the current hash (h gitweb parameter) and %b to the current # hash base (hb gitweb parameter); %% expands to %. # To enable system wide have in $GITWEB_CONFIG e.g. # $feature{'actions'}{'default'} = [('graphiclog', # '/git-browser/by-commit.html?r=%n', 'summary')]; # Project specific override is not supported. 'actions' => { 'override' => 0, 'default' => []}, # Allow gitweb scan project content tags described in ctags/ # of project repository, and display the popular Web 2.0-ish # "tag cloud" near the project list. Note that this is something # COMPLETELY different from the normal Git tags. # gitweb by itself can show existing tags, but it does not handle # tagging itself; you need an external application for that. # For an example script, check Girocco's cgi/tagproj.cgi. # You may want to install the HTML::TagCloud Perl module to get # a pretty tag cloud instead of just a list of tags. # To enable system wide have in $GITWEB_CONFIG # $feature{'ctags'}{'default'} = ['path_to_tag_script']; # Project specific override is not supported. 'ctags' => { 'override' => 0, 'default' => [0]}, # The maximum number of patches in a patchset generated in patch # view. Set this to 0 or undef to disable patch view, or to a # negative number to remove any limit. # To disable system wide have in $GITWEB_CONFIG # $feature{'patches'}{'default'} = [0]; # To have project specific config enable override in $GITWEB_CONFIG # $feature{'patches'}{'override'} = 1; # and in project config gitweb.patches = 0|n; # where n is the maximum number of patches allowed in a patchset. 'patches' => { 'sub' => \&feature_patches, 'override' => 0, 'default' => [16]}, # Avatar support. When this feature is enabled, views such as # shortlog or commit will display an avatar associated with # the email of the committer(s) and/or author(s). # Currently available providers are gravatar and picon. # If an unknown provider is specified, the feature is disabled. # Gravatar depends on Digest::MD5. # Picon currently relies on the indiana.edu database. # To enable system wide have in $GITWEB_CONFIG # $feature{'avatar'}{'default'} = ['']; # where is either gravatar or picon. # To have project specific config enable override in $GITWEB_CONFIG # $feature{'avatar'}{'override'} = 1; # and in project config gitweb.avatar = ; 'avatar' => { 'sub' => \&feature_avatar, 'override' => 0, 'default' => ['']}, # Enable displaying how much time and how many git commands # it took to generate and display page. Disabled by default. # Project specific override is not supported. 'timed' => { 'override' => 0, 'default' => [0]}, # Enable turning some links into links to actions which require # JavaScript to run (like 'blame_incremental'). Not enabled by # default. Project specific override is currently not supported. 'javascript-actions' => { 'override' => 0, 'default' => [0]}, ); sub gitweb_get_feature { my ($name) = @_; return unless exists $feature{$name}; my ($sub, $override, @defaults) = ( $feature{$name}{'sub'}, $feature{$name}{'override'}, @{$feature{$name}{'default'}}); if (!$override) { return @defaults; } if (!defined $sub) { warn "feature $name is not overridable"; return @defaults; } return $sub->(@defaults); } # A wrapper to check if a given feature is enabled. # With this, you can say # # my $bool_feat = gitweb_check_feature('bool_feat'); # gitweb_check_feature('bool_feat') or somecode; # # instead of # # my ($bool_feat) = gitweb_get_feature('bool_feat'); # (gitweb_get_feature('bool_feat'))[0] or somecode; # sub gitweb_check_feature { return (gitweb_get_feature(@_))[0]; } sub feature_bool { my $key = shift; my ($val) = git_get_project_config($key, '--bool'); if (!defined $val) { return ($_[0]); } elsif ($val eq 'true') { return (1); } elsif ($val eq 'false') { return (0); } } sub feature_snapshot { my (@fmts) = @_; my ($val) = git_get_project_config('snapshot'); if ($val) { @fmts = ($val eq 'none' ? () : split /\s*[,\s]\s*/, $val); } return @fmts; } sub feature_patches { my @val = (git_get_project_config('patches', '--int')); if (@val) { return @val; } return ($_[0]); } sub feature_avatar { my @val = (git_get_project_config('avatar')); return @val ? @val : @_; } # checking HEAD file with -e is fragile if the repository was # initialized long time ago (i.e. symlink HEAD) and was pack-ref'ed # and then pruned. sub check_head_link { my ($dir) = @_; my $headfile = "$dir/HEAD"; return ((-e $headfile) || (-l $headfile && readlink($headfile) =~ /^refs\/heads\//)); } sub check_export_ok { my ($dir) = @_; return (check_head_link($dir) && (!$export_ok || -e "$dir/$export_ok") && (!$export_auth_hook || $export_auth_hook->($dir))); } # process alternate names for backward compatibility # filter out unsupported (unknown) snapshot formats sub filter_snapshot_fmts { my @fmts = @_; @fmts = map { exists $known_snapshot_format_aliases{$_} ? $known_snapshot_format_aliases{$_} : $_} @fmts; @fmts = grep { exists $known_snapshot_formats{$_} && !$known_snapshot_formats{$_}{'disabled'}} @fmts; } our $GITWEB_CONFIG = $ENV{'GITWEB_CONFIG'} || "gitweb_config.perl"; if (-e $GITWEB_CONFIG) { do $GITWEB_CONFIG; } else { our $GITWEB_CONFIG_SYSTEM = $ENV{'GITWEB_CONFIG_SYSTEM'} || "/etc/gitweb.conf"; do $GITWEB_CONFIG_SYSTEM if -e $GITWEB_CONFIG_SYSTEM; } # version of the core git binary our $git_version = qx("$GIT" --version) =~ m/git version (.*)$/ ? $1 : "unknown"; $number_of_git_cmds++; $projects_list ||= $projectroot; # ====================================================================== # input validation and dispatch # input parameters can be collected from a variety of sources (presently, CGI # and PATH_INFO), so we define an %input_params hash that collects them all # together during validation: this allows subsequent uses (e.g. href()) to be # agnostic of the parameter origin our %input_params = (); # input parameters are stored with the long parameter name as key. This will # also be used in the href subroutine to convert parameters to their CGI # equivalent, and since the href() usage is the most frequent one, we store # the name -> CGI key mapping here, instead of the reverse. # # XXX: Warning: If you touch this, check the search form for updating, # too. our @cgi_param_mapping = ( project => "p", action => "a", file_name => "f", file_parent => "fp", hash => "h", hash_parent => "hp", hash_base => "hb", hash_parent_base => "hpb", page => "pg", order => "o", searchtext => "s", searchtype => "st", snapshot_format => "sf", extra_options => "opt", search_use_regexp => "sr", # this must be last entry (for manipulation from JavaScript) javascript => "js" ); our %cgi_param_mapping = @cgi_param_mapping; # we will also need to know the possible actions, for validation our %actions = ( "blame" => \&git_blame, "blame_incremental" => \&git_blame_incremental, "blame_data" => \&git_blame_data, "blobdiff" => \&git_blobdiff, "blobdiff_plain" => \&git_blobdiff_plain, "blob" => \&git_blob, "blob_plain" => \&git_blob_plain, "commitdiff" => \&git_commitdiff, "commitdiff_plain" => \&git_commitdiff_plain, "commit" => \&git_commit, "forks" => \&git_forks, "heads" => \&git_heads, "history" => \&git_history, "log" => \&git_log, "patch" => \&git_patch, "patches" => \&git_patches, "rss" => \&git_rss, "atom" => \&git_atom, "search" => \&git_search, "search_help" => \&git_search_help, "shortlog" => \&git_shortlog, "summary" => \&git_summary, "tag" => \&git_tag, "tags" => \&git_tags, "tree" => \&git_tree, "snapshot" => \&git_snapshot, "object" => \&git_object, # those below don't need $project "opml" => \&git_opml, "project_list" => \&git_project_list, "project_index" => \&git_project_index, ); # finally, we have the hash of allowed extra_options for the commands that # allow them our %allowed_options = ( "--no-merges" => [ qw(rss atom log shortlog history) ], ); # fill %input_params with the CGI parameters. All values except for 'opt' # should be single values, but opt can be an array. We should probably # build an array of parameters that can be multi-valued, but since for the time # being it's only this one, we just single it out while (my ($name, $symbol) = each %cgi_param_mapping) { if ($symbol eq 'opt') { $input_params{$name} = [ $cgi->param($symbol) ]; } else { $input_params{$name} = $cgi->param($symbol); } } # now read PATH_INFO and update the parameter list for missing parameters sub evaluate_path_info { return if defined $input_params{'project'}; return if !$path_info; $path_info =~ s,^/+,,; return if !$path_info; # find which part of PATH_INFO is project my $project = $path_info; $project =~ s,/+$,,; while ($project && !check_head_link("$projectroot/$project")) { $project =~ s,/*[^/]*$,,; } return unless $project; $input_params{'project'} = $project; # do not change any parameters if an action is given using the query string return if $input_params{'action'}; $path_info =~ s,^\Q$project\E/*,,; # next, check if we have an action my $action = $path_info; $action =~ s,/.*$,,; if (exists $actions{$action}) { $path_info =~ s,^$action/*,,; $input_params{'action'} = $action; } # list of actions that want hash_base instead of hash, but can have no # pathname (f) parameter my @wants_base = ( 'tree', 'history', ); # we want to catch # [$hash_parent_base[:$file_parent]..]$hash_parent[:$file_name] my ($parentrefname, $parentpathname, $refname, $pathname) = ($path_info =~ /^(?:(.+?)(?::(.+))?\.\.)?(.+?)(?::(.+))?$/); # first, analyze the 'current' part if (defined $pathname) { # we got "branch:filename" or "branch:dir/" # we could use git_get_type(branch:pathname), but: # - it needs $git_dir # - it does a git() call # - the convention of terminating directories with a slash # makes it superfluous # - embedding the action in the PATH_INFO would make it even # more superfluous $pathname =~ s,^/+,,; if (!$pathname || substr($pathname, -1) eq "/") { $input_params{'action'} ||= "tree"; $pathname =~ s,/$,,; } else { # the default action depends on whether we had parent info # or not if ($parentrefname) { $input_params{'action'} ||= "blobdiff_plain"; } else { $input_params{'action'} ||= "blob_plain"; } } $input_params{'hash_base'} ||= $refname; $input_params{'file_name'} ||= $pathname; } elsif (defined $refname) { # we got "branch". In this case we have to choose if we have to # set hash or hash_base. # # Most of the actions without a pathname only want hash to be # set, except for the ones specified in @wants_base that want # hash_base instead. It should also be noted that hand-crafted # links having 'history' as an action and no pathname or hash # set will fail, but that happens regardless of PATH_INFO. $input_params{'action'} ||= "shortlog"; if (grep { $_ eq $input_params{'action'} } @wants_base) { $input_params{'hash_base'} ||= $refname; } else { $input_params{'hash'} ||= $refname; } } # next, handle the 'parent' part, if present if (defined $parentrefname) { # a missing pathspec defaults to the 'current' filename, allowing e.g. # someproject/blobdiff/oldrev..newrev:/filename if ($parentpathname) { $parentpathname =~ s,^/+,,; $parentpathname =~ s,/$,,; $input_params{'file_parent'} ||= $parentpathname; } else { $input_params{'file_parent'} ||= $input_params{'file_name'}; } # we assume that hash_parent_base is wanted if a path was specified, # or if the action wants hash_base instead of hash if (defined $input_params{'file_parent'} || grep { $_ eq $input_params{'action'} } @wants_base) { $input_params{'hash_parent_base'} ||= $parentrefname; } else { $input_params{'hash_parent'} ||= $parentrefname; } } # for the snapshot action, we allow URLs in the form # $project/snapshot/$hash.ext # where .ext determines the snapshot and gets removed from the # passed $refname to provide the $hash. # # To be able to tell that $refname includes the format extension, we # require the following two conditions to be satisfied: # - the hash input parameter MUST have been set from the $refname part # of the URL (i.e. they must be equal) # - the snapshot format MUST NOT have been defined already (e.g. from # CGI parameter sf) # It's also useless to try any matching unless $refname has a dot, # so we check for that too if (defined $input_params{'action'} && $input_params{'action'} eq 'snapshot' && defined $refname && index($refname, '.') != -1 && $refname eq $input_params{'hash'} && !defined $input_params{'snapshot_format'}) { # We loop over the known snapshot formats, checking for # extensions. Allowed extensions are both the defined suffix # (which includes the initial dot already) and the snapshot # format key itself, with a prepended dot while (my ($fmt, $opt) = each %known_snapshot_formats) { my $hash = $refname; unless ($hash =~ s/(\Q$opt->{'suffix'}\E|\Q.$fmt\E)$//) { next; } my $sfx = $1; # a valid suffix was found, so set the snapshot format # and reset the hash parameter $input_params{'snapshot_format'} = $fmt; $input_params{'hash'} = $hash; # we also set the format suffix to the one requested # in the URL: this way a request for e.g. .tgz returns # a .tgz instead of a .tar.gz $known_snapshot_formats{$fmt}{'suffix'} = $sfx; last; } } } evaluate_path_info(); our $action = $input_params{'action'}; if (defined $action) { if (!validate_action($action)) { die_error(400, "Invalid action parameter"); } } # parameters which are pathnames our $project = $input_params{'project'}; if (defined $project) { if (!validate_project($project)) { undef $project; die_error(404, "No such project"); } } our $file_name = $input_params{'file_name'}; if (defined $file_name) { if (!validate_pathname($file_name)) { die_error(400, "Invalid file parameter"); } } our $file_parent = $input_params{'file_parent'}; if (defined $file_parent) { if (!validate_pathname($file_parent)) { die_error(400, "Invalid file parent parameter"); } } # parameters which are refnames our $hash = $input_params{'hash'}; if (defined $hash) { if (!validate_refname($hash)) { die_error(400, "Invalid hash parameter"); } } our $hash_parent = $input_params{'hash_parent'}; if (defined $hash_parent) { if (!validate_refname($hash_parent)) { die_error(400, "Invalid hash parent parameter"); } } our $hash_base = $input_params{'hash_base'}; if (defined $hash_base) { if (!validate_refname($hash_base)) { die_error(400, "Invalid hash base parameter"); } } our @extra_options = @{$input_params{'extra_options'}}; # @extra_options is always defined, since it can only be (currently) set from # CGI, and $cgi->param() returns the empty array in array context if the param # is not set foreach my $opt (@extra_options) { if (not exists $allowed_options{$opt}) { die_error(400, "Invalid option parameter"); } if (not grep(/^$action$/, @{$allowed_options{$opt}})) { die_error(400, "Invalid option parameter for this action"); } } our $hash_parent_base = $input_params{'hash_parent_base'}; if (defined $hash_parent_base) { if (!validate_refname($hash_parent_base)) { die_error(400, "Invalid hash parent base parameter"); } } # other parameters our $page = $input_params{'page'}; if (defined $page) { if ($page =~ m/[^0-9]/) { die_error(400, "Invalid page parameter"); } } our $searchtype = $input_params{'searchtype'}; if (defined $searchtype) { if ($searchtype =~ m/[^a-z]/) { die_error(400, "Invalid searchtype parameter"); } } our $search_use_regexp = $input_params{'search_use_regexp'}; our $searchtext = $input_params{'searchtext'}; our $search_regexp; if (defined $searchtext) { if (length($searchtext) < 2) { die_error(403, "At least two characters are required for search parameter"); } $search_regexp = $search_use_regexp ? $searchtext : quotemeta $searchtext; } # path to the current git repository our $git_dir; $git_dir = "$projectroot/$project" if $project; # list of supported snapshot formats our @snapshot_fmts = gitweb_get_feature('snapshot'); @snapshot_fmts = filter_snapshot_fmts(@snapshot_fmts); # check that the avatar feature is set to a known provider name, # and for each provider check if the dependencies are satisfied. # if the provider name is invalid or the dependencies are not met, # reset $git_avatar to the empty string. our ($git_avatar) = gitweb_get_feature('avatar'); if ($git_avatar eq 'gravatar') { $git_avatar = '' unless (eval { require Digest::MD5; 1; }); } elsif ($git_avatar eq 'picon') { # no dependencies } else { $git_avatar = ''; } # dispatch if (!defined $action) { if (defined $hash) { $action = git_get_type($hash); } elsif (defined $hash_base && defined $file_name) { $action = git_get_type("$hash_base:$file_name"); } elsif (defined $project) { $action = 'summary'; } else { $action = 'project_list'; } } if (!defined($actions{$action})) { die_error(400, "Unknown action"); } if ($action !~ m/^(?:opml|project_list|project_index)$/ && !$project) { die_error(400, "Project needed"); } $actions{$action}->(); exit; ## ====================================================================== ## action links sub href { my %params = @_; # default is to use -absolute url() i.e. $my_uri my $href = $params{-full} ? $my_url : $my_uri; $params{'project'} = $project unless exists $params{'project'}; if ($params{-replay}) { while (my ($name, $symbol) = each %cgi_param_mapping) { if (!exists $params{$name}) { $params{$name} = $input_params{$name}; } } } my $use_pathinfo = gitweb_check_feature('pathinfo'); if ($use_pathinfo and defined $params{'project'}) { # try to put as many parameters as possible in PATH_INFO: # - project name # - action # - hash_parent or hash_parent_base:/file_parent # - hash or hash_base:/filename # - the snapshot_format as an appropriate suffix # When the script is the root DirectoryIndex for the domain, # $href here would be something like http://gitweb.example.com/ # Thus, we strip any trailing / from $href, to spare us double # slashes in the final URL $href =~ s,/$,,; # Then add the project name, if present $href .= "/".esc_url($params{'project'}); delete $params{'project'}; # since we destructively absorb parameters, we keep this # boolean that remembers if we're handling a snapshot my $is_snapshot = $params{'action'} eq 'snapshot'; # Summary just uses the project path URL, any other action is # added to the URL if (defined $params{'action'}) { $href .= "/".esc_url($params{'action'}) unless $params{'action'} eq 'summary'; delete $params{'action'}; } # Next, we put hash_parent_base:/file_parent..hash_base:/file_name, # stripping nonexistent or useless pieces $href .= "/" if ($params{'hash_base'} || $params{'hash_parent_base'} || $params{'hash_parent'} || $params{'hash'}); if (defined $params{'hash_base'}) { if (defined $params{'hash_parent_base'}) { $href .= esc_url($params{'hash_parent_base'}); # skip the file_parent if it's the same as the file_name if (defined $params{'file_parent'}) { if (defined $params{'file_name'} && $params{'file_parent'} eq $params{'file_name'}) { delete $params{'file_parent'}; } elsif ($params{'file_parent'} !~ /\.\./) { $href .= ":/".esc_url($params{'file_parent'}); delete $params{'file_parent'}; } } $href .= ".."; delete $params{'hash_parent'}; delete $params{'hash_parent_base'}; } elsif (defined $params{'hash_parent'}) { $href .= esc_url($params{'hash_parent'}). ".."; delete $params{'hash_parent'}; } $href .= esc_url($params{'hash_base'}); if (defined $params{'file_name'} && $params{'file_name'} !~ /\.\./) { $href .= ":/".esc_url($params{'file_name'}); delete $params{'file_name'}; } delete $params{'hash'}; delete $params{'hash_base'}; } elsif (defined $params{'hash'}) { $href .= esc_url($params{'hash'}); delete $params{'hash'}; } # If the action was a snapshot, we can absorb the # snapshot_format parameter too if ($is_snapshot) { my $fmt = $params{'snapshot_format'}; # snapshot_format should always be defined when href() # is called, but just in case some code forgets, we # fall back to the default $fmt ||= $snapshot_fmts[0]; $href .= $known_snapshot_formats{$fmt}{'suffix'}; delete $params{'snapshot_format'}; } } # now encode the parameters explicitly my @result = (); for (my $i = 0; $i < @cgi_param_mapping; $i += 2) { my ($name, $symbol) = ($cgi_param_mapping[$i], $cgi_param_mapping[$i+1]); if (defined $params{$name}) { if (ref($params{$name}) eq "ARRAY") { foreach my $par (@{$params{$name}}) { push @result, $symbol . "=" . esc_param($par); } } else { push @result, $symbol . "=" . esc_param($params{$name}); } } } $href .= "?" . join(';', @result) if scalar @result; return $href; } ## ====================================================================== ## validation, quoting/unquoting and escaping sub validate_action { my $input = shift || return undef; return undef unless exists $actions{$input}; return $input; } sub validate_project { my $input = shift || return undef; if (!validate_pathname($input) || !(-d "$projectroot/$input") || !check_export_ok("$projectroot/$input") || ($strict_export && !project_in_list($input))) { return undef; } else { return $input; } } sub validate_pathname { my $input = shift || return undef; # no '.' or '..' as elements of path, i.e. no '.' nor '..' # at the beginning, at the end, and between slashes. # also this catches doubled slashes if ($input =~ m!(^|/)(|\.|\.\.)(/|$)!) { return undef; } # no null characters if ($input =~ m!\0!) { return undef; } return $input; } sub validate_refname { my $input = shift || return undef; # textual hashes are O.K. if ($input =~ m/^[0-9a-fA-F]{40}$/) { return $input; } # it must be correct pathname $input = validate_pathname($input) or return undef; # restrictions on ref name according to git-check-ref-format if ($input =~ m!(/\.|\.\.|[\000-\040\177 ~^:?*\[]|/$)!) { return undef; } return $input; } # decode sequences of octets in utf8 into Perl's internal form, # which is utf-8 with utf8 flag set if needed. gitweb writes out # in utf-8 thanks to "binmode STDOUT, ':utf8'" at beginning sub to_utf8 { my $str = shift; if (utf8::valid($str)) { utf8::decode($str); return $str; } else { return decode($fallback_encoding, $str, Encode::FB_DEFAULT); } } # quote unsafe chars, but keep the slash, even when it's not # correct, but quoted slashes look too horrible in bookmarks sub esc_param { my $str = shift; $str =~ s/([^A-Za-z0-9\-_.~()\/:@ ]+)/CGI::escape($1)/eg; $str =~ s/ /\+/g; return $str; } # quote unsafe chars in whole URL, so some charactrs cannot be quoted sub esc_url { my $str = shift; $str =~ s/([^A-Za-z0-9\-_.~();\/;?:@&=])/sprintf("%%%02X", ord($1))/eg; $str =~ s/\+/%2B/g; $str =~ s/ /\+/g; return $str; } # replace invalid utf8 character with SUBSTITUTION sequence sub esc_html { my $str = shift; my %opts = @_; $str = to_utf8($str); $str = $cgi->escapeHTML($str); if ($opts{'-nbsp'}) { $str =~ s/ / /g; } $str =~ s|([[:cntrl:]])|(($1 ne "\t") ? quot_cec($1) : $1)|eg; return $str; } # quote control characters and escape filename to HTML sub esc_path { my $str = shift; my %opts = @_; $str = to_utf8($str); $str = $cgi->escapeHTML($str); if ($opts{'-nbsp'}) { $str =~ s/ / /g; } $str =~ s|([[:cntrl:]])|quot_cec($1)|eg; return $str; } # Make control characters "printable", using character escape codes (CEC) sub quot_cec { my $cntrl = shift; my %opts = @_; my %es = ( # character escape codes, aka escape sequences "\t" => '\t', # tab (HT) "\n" => '\n', # line feed (LF) "\r" => '\r', # carrige return (CR) "\f" => '\f', # form feed (FF) "\b" => '\b', # backspace (BS) "\a" => '\a', # alarm (bell) (BEL) "\e" => '\e', # escape (ESC) "\013" => '\v', # vertical tab (VT) "\000" => '\0', # nul character (NUL) ); my $chr = ( (exists $es{$cntrl}) ? $es{$cntrl} : sprintf('\%2x', ord($cntrl)) ); if ($opts{-nohtml}) { return $chr; } else { return "$chr"; } } # Alternatively use unicode control pictures codepoints, # Unicode "printable representation" (PR) sub quot_upr { my $cntrl = shift; my %opts = @_; my $chr = sprintf('&#%04d;', 0x2400+ord($cntrl)); if ($opts{-nohtml}) { return $chr; } else { return "$chr"; } } # git may return quoted and escaped filenames sub unquote { my $str = shift; sub unq { my $seq = shift; my %es = ( # character escape codes, aka escape sequences 't' => "\t", # tab (HT, TAB) 'n' => "\n", # newline (NL) 'r' => "\r", # return (CR) 'f' => "\f", # form feed (FF) 'b' => "\b", # backspace (BS) 'a' => "\a", # alarm (bell) (BEL) 'e' => "\e", # escape (ESC) 'v' => "\013", # vertical tab (VT) ); if ($seq =~ m/^[0-7]{1,3}$/) { # octal char sequence return chr(oct($seq)); } elsif (exists $es{$seq}) { # C escape sequence, aka character escape code return $es{$seq}; } # quoted ordinary character return $seq; } if ($str =~ m/^"(.*)"$/) { # needs unquoting $str = $1; $str =~ s/\\([^0-7]|[0-7]{1,3})/unq($1)/eg; } return $str; } # escape tabs (convert tabs to spaces) sub untabify { my $line = shift; while ((my $pos = index($line, "\t")) != -1) { if (my $count = (8 - ($pos % 8))) { my $spaces = ' ' x $count; $line =~ s/\t/$spaces/; } } return $line; } sub project_in_list { my $project = shift; my @list = git_get_projects_list(); return @list && scalar(grep { $_->{'path'} eq $project } @list); } ## ---------------------------------------------------------------------- ## HTML aware string manipulation # Try to chop given string on a word boundary between position # $len and $len+$add_len. If there is no word boundary there, # chop at $len+$add_len. Do not chop if chopped part plus ellipsis # (marking chopped part) would be longer than given string. sub chop_str { my $str = shift; my $len = shift; my $add_len = shift || 10; my $where = shift || 'right'; # 'left' | 'center' | 'right' # Make sure perl knows it is utf8 encoded so we don't # cut in the middle of a utf8 multibyte char. $str = to_utf8($str); # allow only $len chars, but don't cut a word if it would fit in $add_len # if it doesn't fit, cut it if it's still longer than the dots we would add # remove chopped character entities entirely # when chopping in the middle, distribute $len into left and right part # return early if chopping wouldn't make string shorter if ($where eq 'center') { return $str if ($len + 5 >= length($str)); # filler is length 5 $len = int($len/2); } else { return $str if ($len + 4 >= length($str)); # filler is length 4 } # regexps: ending and beginning with word part up to $add_len my $endre = qr/.{$len}\w{0,$add_len}/; my $begre = qr/\w{0,$add_len}.{$len}/; if ($where eq 'left') { $str =~ m/^(.*?)($begre)$/; my ($lead, $body) = ($1, $2); if (length($lead) > 4) { $body =~ s/^[^;]*;// if ($lead =~ m/&[^;]*$/); $lead = " ..."; } return "$lead$body"; } elsif ($where eq 'center') { $str =~ m/^($endre)(.*)$/; my ($left, $str) = ($1, $2); $str =~ m/^(.*?)($begre)$/; my ($mid, $right) = ($1, $2); if (length($mid) > 5) { $left =~ s/&[^;]*$//; $right =~ s/^[^;]*;// if ($mid =~ m/&[^;]*$/); $mid = " ... "; } return "$left$mid$right"; } else { $str =~ m/^($endre)(.*)$/; my $body = $1; my $tail = $2; if (length($tail) > 4) { $body =~ s/&[^;]*$//; $tail = "... "; } return "$body$tail"; } } # takes the same arguments as chop_str, but also wraps a around the # result with a title attribute if it does get chopped. Additionally, the # string is HTML-escaped. sub chop_and_escape_str { my ($str) = @_; my $chopped = chop_str(@_); if ($chopped eq $str) { return esc_html($chopped); } else { $str =~ s/[[:cntrl:]]/?/g; return $cgi->span({-title=>$str}, esc_html($chopped)); } } ## ---------------------------------------------------------------------- ## functions returning short strings # CSS class for given age value (in seconds) sub age_class { my $age = shift; if (!defined $age) { return "noage"; } elsif ($age < 60*60*2) { return "age0"; } elsif ($age < 60*60*24*2) { return "age1"; } else { return "age2"; } } # convert age in seconds to "nn units ago" string sub age_string { my $age = shift; my $age_str; if ($age > 60*60*24*365*2) { $age_str = (int $age/60/60/24/365); $age_str .= " years ago"; } elsif ($age > 60*60*24*(365/12)*2) { $age_str = int $age/60/60/24/(365/12); $age_str .= " months ago"; } elsif ($age > 60*60*24*7*2) { $age_str = int $age/60/60/24/7; $age_str .= " weeks ago"; } elsif ($age > 60*60*24*2) { $age_str = int $age/60/60/24; $age_str .= " days ago"; } elsif ($age > 60*60*2) { $age_str = int $age/60/60; $age_str .= " hours ago"; } elsif ($age > 60*2) { $age_str = int $age/60; $age_str .= " min ago"; } elsif ($age > 2) { $age_str = int $age; $age_str .= " sec ago"; } else { $age_str .= " right now"; } return $age_str; } use constant { S_IFINVALID => 0030000, S_IFGITLINK => 0160000, }; # submodule/subproject, a commit object reference sub S_ISGITLINK { my $mode = shift; return (($mode & S_IFMT) == S_IFGITLINK) } # convert file mode in octal to symbolic file mode string sub mode_str { my $mode = oct shift; if (S_ISGITLINK($mode)) { return 'm---------'; } elsif (S_ISDIR($mode & S_IFMT)) { return 'drwxr-xr-x'; } elsif (S_ISLNK($mode)) { return 'lrwxrwxrwx'; } elsif (S_ISREG($mode)) { # git cares only about the executable bit if ($mode & S_IXUSR) { return '-rwxr-xr-x'; } else { return '-rw-r--r--'; }; } else { return '----------'; } } # convert file mode in octal to file type string sub file_type { my $mode = shift; if ($mode !~ m/^[0-7]+$/) { return $mode; } else { $mode = oct $mode; } if (S_ISGITLINK($mode)) { return "submodule"; } elsif (S_ISDIR($mode & S_IFMT)) { return "directory"; } elsif (S_ISLNK($mode)) { return "symlink"; } elsif (S_ISREG($mode)) { return "file"; } else { return "unknown"; } } # convert file mode in octal to file type description string sub file_type_long { my $mode = shift; if ($mode !~ m/^[0-7]+$/) { return $mode; } else { $mode = oct $mode; } if (S_ISGITLINK($mode)) { return "submodule"; } elsif (S_ISDIR($mode & S_IFMT)) { return "directory"; } elsif (S_ISLNK($mode)) { return "symlink"; } elsif (S_ISREG($mode)) { if ($mode & S_IXUSR) { return "executable"; } else { return "file"; }; } else { return "unknown"; } } ## ---------------------------------------------------------------------- ## functions returning short HTML fragments, or transforming HTML fragments ## which don't belong to other sections # format line of commit message. sub format_log_line_html { my $line = shift; $line = esc_html($line, -nbsp=>1); $line =~ s{\b([0-9a-fA-F]{8,40})\b}{ $cgi->a({-href => href(action=>"object", hash=>$1), -class => "text"}, $1); }eg; return $line; } # format marker of refs pointing to given object # the destination action is chosen based on object type and current context: # - for annotated tags, we choose the tag view unless it's the current view # already, in which case we go to shortlog view # - for other refs, we keep the current view if we're in history, shortlog or # log view, and select shortlog otherwise sub format_ref_marker { my ($refs, $id) = @_; my $markers = ''; if (defined $refs->{$id}) { foreach my $ref (@{$refs->{$id}}) { # this code exploits the fact that non-lightweight tags are the # only indirect objects, and that they are the only objects for which # we want to use tag instead of shortlog as action my ($type, $name) = qw(); my $indirect = ($ref =~ s/\^\{\}$//); # e.g. tags/v2.6.11 or heads/next if ($ref =~ m!^(.*?)s?/(.*)$!) { $type = $1; $name = $2; } else { $type = "ref"; $name = $ref; } my $class = $type; $class .= " indirect" if $indirect; my $dest_action = "shortlog"; if ($indirect) { $dest_action = "tag" unless $action eq "tag"; } elsif ($action =~ /^(history|(short)?log)$/) { $dest_action = $action; } my $dest = ""; $dest .= "refs/" unless $ref =~ m!^refs/!; $dest .= $ref; my $link = $cgi->a({ -href => href( action=>$dest_action, hash=>$dest )}, $name); $markers .= " " . $link . ""; } } if ($markers) { return ' '. $markers . ''; } else { return ""; } } # format, perhaps shortened and with markers, title line sub format_subject_html { my ($long, $short, $href, $extra) = @_; $extra = '' unless defined($extra); if (length($short) < length($long)) { $long =~ s/[[:cntrl:]]/?/g; return $cgi->a({-href => $href, -class => "list subject", -title => to_utf8($long)}, esc_html($short)) . $extra; } else { return $cgi->a({-href => $href, -class => "list subject"}, esc_html($long)) . $extra; } } # Rather than recomputing the url for an email multiple times, we cache it # after the first hit. This gives a visible benefit in views where the avatar # for the same email is used repeatedly (e.g. shortlog). # The cache is shared by all avatar engines (currently gravatar only), which # are free to use it as preferred. Since only one avatar engine is used for any # given page, there's no risk for cache conflicts. our %avatar_cache = (); # Compute the picon url for a given email, by using the picon search service over at # http://www.cs.indiana.edu/picons/search.html sub picon_url { my $email = lc shift; if (!$avatar_cache{$email}) { my ($user, $domain) = split('@', $email); $avatar_cache{$email} = "http://www.cs.indiana.edu/cgi-pub/kinzler/piconsearch.cgi/" . "$domain/$user/" . "users+domains+unknown/up/single"; } return $avatar_cache{$email}; } # Compute the gravatar url for a given email, if it's not in the cache already. # Gravatar stores only the part of the URL before the size, since that's the # one computationally more expensive. This also allows reuse of the cache for # different sizes (for this particular engine). sub gravatar_url { my $email = lc shift; my $size = shift; $avatar_cache{$email} ||= "http://www.gravatar.com/avatar/" . Digest::MD5::md5_hex($email) . "?s="; return $avatar_cache{$email} . $size; } # Insert an avatar for the given $email at the given $size if the feature # is enabled. sub git_get_avatar { my ($email, %opts) = @_; my $pre_white = ($opts{-pad_before} ? " " : ""); my $post_white = ($opts{-pad_after} ? " " : ""); $opts{-size} ||= 'default'; my $size = $avatar_size{$opts{-size}} || $avatar_size{'default'}; my $url = ""; if ($git_avatar eq 'gravatar') { $url = gravatar_url($email, $size); } elsif ($git_avatar eq 'picon') { $url = picon_url($email); } # Other providers can be added by extending the if chain, defining $url # as needed. If no variant puts something in $url, we assume avatars # are completely disabled/unavailable. if ($url) { return $pre_white . "" . $post_white; } else { return ""; } } sub format_search_author { my ($author, $searchtype, $displaytext) = @_; my $have_search = gitweb_check_feature('search'); if ($have_search) { my $performed = ""; if ($searchtype eq 'author') { $performed = "authored"; } elsif ($searchtype eq 'committer') { $performed = "committed"; } return $cgi->a({-href => href(action=>"search", hash=>$hash, searchtext=>$author, searchtype=>$searchtype), class=>"list", title=>"Search for commits $performed by $author"}, $displaytext); } else { return $displaytext; } } # format the author name of the given commit with the given tag # the author name is chopped and escaped according to the other # optional parameters (see chop_str). sub format_author_html { my $tag = shift; my $co = shift; my $author = chop_and_escape_str($co->{'author_name'}, @_); return "<$tag class=\"author\">" . format_search_author($co->{'author_name'}, "author", git_get_avatar($co->{'author_email'}, -pad_after => 1) . $author) . ""; } # format git diff header line, i.e. "diff --(git|combined|cc) ..." sub format_git_diff_header_line { my $line = shift; my $diffinfo = shift; my ($from, $to) = @_; if ($diffinfo->{'nparents'}) { # combined diff $line =~ s!^(diff (.*?) )"?.*$!$1!; if ($to->{'href'}) { $line .= $cgi->a({-href => $to->{'href'}, -class => "path"}, esc_path($to->{'file'})); } else { # file was deleted (no href) $line .= esc_path($to->{'file'}); } } else { # "ordinary" diff $line =~ s!^(diff (.*?) )"?a/.*$!$1!; if ($from->{'href'}) { $line .= $cgi->a({-href => $from->{'href'}, -class => "path"}, 'a/' . esc_path($from->{'file'})); } else { # file was added (no href) $line .= 'a/' . esc_path($from->{'file'}); } $line .= ' '; if ($to->{'href'}) { $line .= $cgi->a({-href => $to->{'href'}, -class => "path"}, 'b/' . esc_path($to->{'file'})); } else { # file was deleted $line .= 'b/' . esc_path($to->{'file'}); } } return "
    $line
    \n"; } # format extended diff header line, before patch itself sub format_extended_diff_header_line { my $line = shift; my $diffinfo = shift; my ($from, $to) = @_; # match if ($line =~ s!^((copy|rename) from ).*$!$1! && $from->{'href'}) { $line .= $cgi->a({-href=>$from->{'href'}, -class=>"path"}, esc_path($from->{'file'})); } if ($line =~ s!^((copy|rename) to ).*$!$1! && $to->{'href'}) { $line .= $cgi->a({-href=>$to->{'href'}, -class=>"path"}, esc_path($to->{'file'})); } # match single if ($line =~ m/\s(\d{6})$/) { $line .= ' (' . file_type_long($1) . ')'; } # match if ($line =~ m/^index [0-9a-fA-F]{40},[0-9a-fA-F]{40}/) { # can match only for combined diff $line = 'index '; for (my $i = 0; $i < $diffinfo->{'nparents'}; $i++) { if ($from->{'href'}[$i]) { $line .= $cgi->a({-href=>$from->{'href'}[$i], -class=>"hash"}, substr($diffinfo->{'from_id'}[$i],0,7)); } else { $line .= '0' x 7; } # separator $line .= ',' if ($i < $diffinfo->{'nparents'} - 1); } $line .= '..'; if ($to->{'href'}) { $line .= $cgi->a({-href=>$to->{'href'}, -class=>"hash"}, substr($diffinfo->{'to_id'},0,7)); } else { $line .= '0' x 7; } } elsif ($line =~ m/^index [0-9a-fA-F]{40}..[0-9a-fA-F]{40}/) { # can match only for ordinary diff my ($from_link, $to_link); if ($from->{'href'}) { $from_link = $cgi->a({-href=>$from->{'href'}, -class=>"hash"}, substr($diffinfo->{'from_id'},0,7)); } else { $from_link = '0' x 7; } if ($to->{'href'}) { $to_link = $cgi->a({-href=>$to->{'href'}, -class=>"hash"}, substr($diffinfo->{'to_id'},0,7)); } else { $to_link = '0' x 7; } my ($from_id, $to_id) = ($diffinfo->{'from_id'}, $diffinfo->{'to_id'}); $line =~ s!$from_id\.\.$to_id!$from_link..$to_link!; } return $line . "
    \n"; } # format from-file/to-file diff header sub format_diff_from_to_header { my ($from_line, $to_line, $diffinfo, $from, $to, @parents) = @_; my $line; my $result = ''; $line = $from_line; #assert($line =~ m/^---/) if DEBUG; # no extra formatting for "^--- /dev/null" if (! $diffinfo->{'nparents'}) { # ordinary (single parent) diff if ($line =~ m!^--- "?a/!) { if ($from->{'href'}) { $line = '--- a/' . $cgi->a({-href=>$from->{'href'}, -class=>"path"}, esc_path($from->{'file'})); } else { $line = '--- a/' . esc_path($from->{'file'}); } } $result .= qq!
    $line
    \n!; } else { # combined diff (merge commit) for (my $i = 0; $i < $diffinfo->{'nparents'}; $i++) { if ($from->{'href'}[$i]) { $line = '--- ' . $cgi->a({-href=>href(action=>"blobdiff", hash_parent=>$diffinfo->{'from_id'}[$i], hash_parent_base=>$parents[$i], file_parent=>$from->{'file'}[$i], hash=>$diffinfo->{'to_id'}, hash_base=>$hash, file_name=>$to->{'file'}), -class=>"path", -title=>"diff" . ($i+1)}, $i+1) . '/' . $cgi->a({-href=>$from->{'href'}[$i], -class=>"path"}, esc_path($from->{'file'}[$i])); } else { $line = '--- /dev/null'; } $result .= qq!
    $line
    \n!; } } $line = $to_line; #assert($line =~ m/^\+\+\+/) if DEBUG; # no extra formatting for "^+++ /dev/null" if ($line =~ m!^\+\+\+ "?b/!) { if ($to->{'href'}) { $line = '+++ b/' . $cgi->a({-href=>$to->{'href'}, -class=>"path"}, esc_path($to->{'file'})); } else { $line = '+++ b/' . esc_path($to->{'file'}); } } $result .= qq!
    $line
    \n!; return $result; } # create note for patch simplified by combined diff sub format_diff_cc_simplified { my ($diffinfo, @parents) = @_; my $result = ''; $result .= "
    " . "diff --cc "; if (!is_deleted($diffinfo)) { $result .= $cgi->a({-href => href(action=>"blob", hash_base=>$hash, hash=>$diffinfo->{'to_id'}, file_name=>$diffinfo->{'to_file'}), -class => "path"}, esc_path($diffinfo->{'to_file'})); } else { $result .= esc_path($diffinfo->{'to_file'}); } $result .= "
    \n" . # class="diff header" "
    " . "Simple merge" . "
    \n"; # class="diff nodifferences" return $result; } # format patch (diff) line (not to be used for diff headers) sub format_diff_line { my $line = shift; my ($from, $to) = @_; my $diff_class = ""; chomp $line; if ($from && $to && ref($from->{'href'}) eq "ARRAY") { # combined diff my $prefix = substr($line, 0, scalar @{$from->{'href'}}); if ($line =~ m/^\@{3}/) { $diff_class = " chunk_header"; } elsif ($line =~ m/^\\/) { $diff_class = " incomplete"; } elsif ($prefix =~ tr/+/+/) { $diff_class = " add"; } elsif ($prefix =~ tr/-/-/) { $diff_class = " rem"; } } else { # assume ordinary diff my $char = substr($line, 0, 1); if ($char eq '+') { $diff_class = " add"; } elsif ($char eq '-') { $diff_class = " rem"; } elsif ($char eq '@') { $diff_class = " chunk_header"; } elsif ($char eq "\\") { $diff_class = " incomplete"; } } $line = untabify($line); if ($from && $to && $line =~ m/^\@{2} /) { my ($from_text, $from_start, $from_lines, $to_text, $to_start, $to_lines, $section) = $line =~ m/^\@{2} (-(\d+)(?:,(\d+))?) (\+(\d+)(?:,(\d+))?) \@{2}(.*)$/; $from_lines = 0 unless defined $from_lines; $to_lines = 0 unless defined $to_lines; if ($from->{'href'}) { $from_text = $cgi->a({-href=>"$from->{'href'}#l$from_start", -class=>"list"}, $from_text); } if ($to->{'href'}) { $to_text = $cgi->a({-href=>"$to->{'href'}#l$to_start", -class=>"list"}, $to_text); } $line = "@@ $from_text $to_text @@" . "" . esc_html($section, -nbsp=>1) . ""; return "
    $line
    \n"; } elsif ($from && $to && $line =~ m/^\@{3}/) { my ($prefix, $ranges, $section) = $line =~ m/^(\@+) (.*?) \@+(.*)$/; my (@from_text, @from_start, @from_nlines, $to_text, $to_start, $to_nlines); @from_text = split(' ', $ranges); for (my $i = 0; $i < @from_text; ++$i) { ($from_start[$i], $from_nlines[$i]) = (split(',', substr($from_text[$i], 1)), 0); } $to_text = pop @from_text; $to_start = pop @from_start; $to_nlines = pop @from_nlines; $line = "$prefix "; for (my $i = 0; $i < @from_text; ++$i) { if ($from->{'href'}[$i]) { $line .= $cgi->a({-href=>"$from->{'href'}[$i]#l$from_start[$i]", -class=>"list"}, $from_text[$i]); } else { $line .= $from_text[$i]; } $line .= " "; } if ($to->{'href'}) { $line .= $cgi->a({-href=>"$to->{'href'}#l$to_start", -class=>"list"}, $to_text); } else { $line .= $to_text; } $line .= " $prefix" . "" . esc_html($section, -nbsp=>1) . ""; return "
    $line
    \n"; } return "
    " . esc_html($line, -nbsp=>1) . "
    \n"; } # Generates undef or something like "_snapshot_" or "snapshot (_tbz2_ _zip_)", # linked. Pass the hash of the tree/commit to snapshot. sub format_snapshot_links { my ($hash) = @_; my $num_fmts = @snapshot_fmts; if ($num_fmts > 1) { # A parenthesized list of links bearing format names. # e.g. "snapshot (_tar.gz_ _zip_)" return "snapshot (" . join(' ', map $cgi->a({ -href => href( action=>"snapshot", hash=>$hash, snapshot_format=>$_ ) }, $known_snapshot_formats{$_}{'display'}) , @snapshot_fmts) . ")"; } elsif ($num_fmts == 1) { # A single "snapshot" link whose tooltip bears the format name. # i.e. "_snapshot_" my ($fmt) = @snapshot_fmts; return $cgi->a({ -href => href( action=>"snapshot", hash=>$hash, snapshot_format=>$fmt ), -title => "in format: $known_snapshot_formats{$fmt}{'display'}" }, "snapshot"); } else { # $num_fmts == 0 return undef; } } ## ...................................................................... ## functions returning values to be passed, perhaps after some ## transformation, to other functions; e.g. returning arguments to href() # returns hash to be passed to href to generate gitweb URL # in -title key it returns description of link sub get_feed_info { my $format = shift || 'Atom'; my %res = (action => lc($format)); # feed links are possible only for project views return unless (defined $project); # some views should link to OPML, or to generic project feed, # or don't have specific feed yet (so they should use generic) return if ($action =~ /^(?:tags|heads|forks|tag|search)$/x); my $branch; # branches refs uses 'refs/heads/' prefix (fullname) to differentiate # from tag links; this also makes possible to detect branch links if ((defined $hash_base && $hash_base =~ m!^refs/heads/(.*)$!) || (defined $hash && $hash =~ m!^refs/heads/(.*)$!)) { $branch = $1; } # find log type for feed description (title) my $type = 'log'; if (defined $file_name) { $type = "history of $file_name"; $type .= "/" if ($action eq 'tree'); $type .= " on '$branch'" if (defined $branch); } else { $type = "log of $branch" if (defined $branch); } $res{-title} = $type; $res{'hash'} = (defined $branch ? "refs/heads/$branch" : undef); $res{'file_name'} = $file_name; return %res; } ## ---------------------------------------------------------------------- ## git utility subroutines, invoking git commands # returns path to the core git executable and the --git-dir parameter as list sub git_cmd { $number_of_git_cmds++; return $GIT, '--git-dir='.$git_dir; } # quote the given arguments for passing them to the shell # quote_command("command", "arg 1", "arg with ' and ! characters") # => "'command' 'arg 1' 'arg with '\'' and '\!' characters'" # Try to avoid using this function wherever possible. sub quote_command { return join(' ', map { my $a = $_; $a =~ s/(['!])/'\\$1'/g; "'$a'" } @_ ); } # get HEAD ref of given project as hash sub git_get_head_hash { return git_get_full_hash(shift, 'HEAD'); } sub git_get_full_hash { return git_get_hash(@_); } sub git_get_short_hash { return git_get_hash(@_, '--short=7'); } sub git_get_hash { my ($project, $hash, @options) = @_; my $o_git_dir = $git_dir; my $retval = undef; $git_dir = "$projectroot/$project"; if (open my $fd, '-|', git_cmd(), 'rev-parse', '--verify', '-q', @options, $hash) { $retval = <$fd>; chomp $retval if defined $retval; close $fd; } if (defined $o_git_dir) { $git_dir = $o_git_dir; } return $retval; } # get type of given object sub git_get_type { my $hash = shift; open my $fd, "-|", git_cmd(), "cat-file", '-t', $hash or return; my $type = <$fd>; close $fd or return; chomp $type; return $type; } # repository configuration our $config_file = ''; our %config; # store multiple values for single key as anonymous array reference # single values stored directly in the hash, not as [ ] sub hash_set_multi { my ($hash, $key, $value) = @_; if (!exists $hash->{$key}) { $hash->{$key} = $value; } elsif (!ref $hash->{$key}) { $hash->{$key} = [ $hash->{$key}, $value ]; } else { push @{$hash->{$key}}, $value; } } # return hash of git project configuration # optionally limited to some section, e.g. 'gitweb' sub git_parse_project_config { my $section_regexp = shift; my %config; local $/ = "\0"; open my $fh, "-|", git_cmd(), "config", '-z', '-l', or return; while (my $keyval = <$fh>) { chomp $keyval; my ($key, $value) = split(/\n/, $keyval, 2); hash_set_multi(\%config, $key, $value) if (!defined $section_regexp || $key =~ /^(?:$section_regexp)\./o); } close $fh; return %config; } # convert config value to boolean: 'true' or 'false' # no value, number > 0, 'true' and 'yes' values are true # rest of values are treated as false (never as error) sub config_to_bool { my $val = shift; return 1 if !defined $val; # section.key # strip leading and trailing whitespace $val =~ s/^\s+//; $val =~ s/\s+$//; return (($val =~ /^\d+$/ && $val) || # section.key = 1 ($val =~ /^(?:true|yes)$/i)); # section.key = true } # convert config value to simple decimal number # an optional value suffix of 'k', 'm', or 'g' will cause the value # to be multiplied by 1024, 1048576, or 1073741824 sub config_to_int { my $val = shift; # strip leading and trailing whitespace $val =~ s/^\s+//; $val =~ s/\s+$//; if (my ($num, $unit) = ($val =~ /^([0-9]*)([kmg])$/i)) { $unit = lc($unit); # unknown unit is treated as 1 return $num * ($unit eq 'g' ? 1073741824 : $unit eq 'm' ? 1048576 : $unit eq 'k' ? 1024 : 1); } return $val; } # convert config value to array reference, if needed sub config_to_multi { my $val = shift; return ref($val) ? $val : (defined($val) ? [ $val ] : []); } sub git_get_project_config { my ($key, $type) = @_; # key sanity check return unless ($key); $key =~ s/^gitweb\.//; return if ($key =~ m/\W/); # type sanity check if (defined $type) { $type =~ s/^--//; $type = undef unless ($type eq 'bool' || $type eq 'int'); } # get config if (!defined $config_file || $config_file ne "$git_dir/config") { %config = git_parse_project_config('gitweb'); $config_file = "$git_dir/config"; } # check if config variable (key) exists return unless exists $config{"gitweb.$key"}; # ensure given type if (!defined $type) { return $config{"gitweb.$key"}; } elsif ($type eq 'bool') { # backward compatibility: 'git config --bool' returns true/false return config_to_bool($config{"gitweb.$key"}) ? 'true' : 'false'; } elsif ($type eq 'int') { return config_to_int($config{"gitweb.$key"}); } return $config{"gitweb.$key"}; } # get hash of given path at given ref sub git_get_hash_by_path { my $base = shift; my $path = shift || return undef; my $type = shift; $path =~ s,/+$,,; open my $fd, "-|", git_cmd(), "ls-tree", $base, "--", $path or die_error(500, "Open git-ls-tree failed"); my $line = <$fd>; close $fd or return undef; if (!defined $line) { # there is no tree or hash given by $path at $base return undef; } #'100644 blob 0fa3f3a66fb6a137f6ec2c19351ed4d807070ffa panic.c' $line =~ m/^([0-9]+) (.+) ([0-9a-fA-F]{40})\t/; if (defined $type && $type ne $2) { # type doesn't match return undef; } return $3; } # get path of entry with given hash at given tree-ish (ref) # used to get 'from' filename for combined diff (merge commit) for renames sub git_get_path_by_hash { my $base = shift || return; my $hash = shift || return; local $/ = "\0"; open my $fd, "-|", git_cmd(), "ls-tree", '-r', '-t', '-z', $base or return undef; while (my $line = <$fd>) { chomp $line; #'040000 tree 595596a6a9117ddba9fe379b6b012b558bac8423 gitweb' #'100644 blob e02e90f0429be0d2a69b76571101f20b8f75530f gitweb/README' if ($line =~ m/(?:[0-9]+) (?:.+) $hash\t(.+)$/) { close $fd; return $1; } } close $fd; return undef; } ## ...................................................................... ## git utility functions, directly accessing git repository sub git_get_project_description { my $path = shift; $git_dir = "$projectroot/$path"; open my $fd, '<', "$git_dir/description" or return git_get_project_config('description'); my $descr = <$fd>; close $fd; if (defined $descr) { chomp $descr; } return $descr; } sub git_get_project_ctags { my $path = shift; my $ctags = {}; $git_dir = "$projectroot/$path"; opendir my $dh, "$git_dir/ctags" or return $ctags; foreach (grep { -f $_ } map { "$git_dir/ctags/$_" } readdir($dh)) { open my $ct, '<', $_ or next; my $val = <$ct>; chomp $val; close $ct; my $ctag = $_; $ctag =~ s#.*/##; $ctags->{$ctag} = $val; } closedir $dh; $ctags; } sub git_populate_project_tagcloud { my $ctags = shift; # First, merge different-cased tags; tags vote on casing my %ctags_lc; foreach (keys %$ctags) { $ctags_lc{lc $_}->{count} += $ctags->{$_}; if (not $ctags_lc{lc $_}->{topcount} or $ctags_lc{lc $_}->{topcount} < $ctags->{$_}) { $ctags_lc{lc $_}->{topcount} = $ctags->{$_}; $ctags_lc{lc $_}->{topname} = $_; } } my $cloud; if (eval { require HTML::TagCloud; 1; }) { $cloud = HTML::TagCloud->new; foreach (sort keys %ctags_lc) { # Pad the title with spaces so that the cloud looks # less crammed. my $title = $ctags_lc{$_}->{topname}; $title =~ s/ / /g; $title =~ s/^/ /g; $title =~ s/$/ /g; $cloud->add($title, $home_link."?by_tag=".$_, $ctags_lc{$_}->{count}); } } else { $cloud = \%ctags_lc; } $cloud; } sub git_show_project_tagcloud { my ($cloud, $count) = @_; print STDERR ref($cloud)."..\n"; if (ref $cloud eq 'HTML::TagCloud') { return $cloud->html_and_css($count); } else { my @tags = sort { $cloud->{$a}->{count} <=> $cloud->{$b}->{count} } keys %$cloud; return '

    ' . join (', ', map { "$cloud->{$_}->{topname}" } splice(@tags, 0, $count)) . '

    '; } } sub git_get_project_url_list { my $path = shift; $git_dir = "$projectroot/$path"; open my $fd, '<', "$git_dir/cloneurl" or return wantarray ? @{ config_to_multi(git_get_project_config('url')) } : config_to_multi(git_get_project_config('url')); my @git_project_url_list = map { chomp; $_ } <$fd>; close $fd; return wantarray ? @git_project_url_list : \@git_project_url_list; } sub git_get_projects_list { my ($filter) = @_; my @list; $filter ||= ''; $filter =~ s/\.git$//; my $check_forks = gitweb_check_feature('forks'); if (-d $projects_list) { # search in directory my $dir = $projects_list . ($filter ? "/$filter" : ''); # remove the trailing "/" $dir =~ s!/+$!!; my $pfxlen = length("$dir"); my $pfxdepth = ($dir =~ tr!/!!); File::Find::find({ follow_fast => 1, # follow symbolic links follow_skip => 2, # ignore duplicates dangling_symlinks => 0, # ignore dangling symlinks, silently wanted => sub { # skip project-list toplevel, if we get it. return if (m!^[/.]$!); # only directories can be git repositories return unless (-d $_); # don't traverse too deep (Find is super slow on os x) if (($File::Find::name =~ tr!/!!) - $pfxdepth > $project_maxdepth) { $File::Find::prune = 1; return; } my $subdir = substr($File::Find::name, $pfxlen + 1); # we check related file in $projectroot my $path = ($filter ? "$filter/" : '') . $subdir; if (check_export_ok("$projectroot/$path")) { push @list, { path => $path }; $File::Find::prune = 1; } }, }, "$dir"); } elsif (-f $projects_list) { # read from file(url-encoded): # 'git%2Fgit.git Linus+Torvalds' # 'libs%2Fklibc%2Fklibc.git H.+Peter+Anvin' # 'linux%2Fhotplug%2Fudev.git Greg+Kroah-Hartman' my %paths; open my $fd, '<', $projects_list or return; PROJECT: while (my $line = <$fd>) { chomp $line; my ($path, $owner) = split ' ', $line; $path = unescape($path); $owner = unescape($owner); if (!defined $path) { next; } if ($filter ne '') { # looking for forks; my $pfx = substr($path, 0, length($filter)); if ($pfx ne $filter) { next PROJECT; } my $sfx = substr($path, length($filter)); if ($sfx !~ /^\/.*\.git$/) { next PROJECT; } } elsif ($check_forks) { PATH: foreach my $filter (keys %paths) { # looking for forks; my $pfx = substr($path, 0, length($filter)); if ($pfx ne $filter) { next PATH; } my $sfx = substr($path, length($filter)); if ($sfx !~ /^\/.*\.git$/) { next PATH; } # is a fork, don't include it in # the list next PROJECT; } } if (check_export_ok("$projectroot/$path")) { my $pr = { path => $path, owner => to_utf8($owner), }; push @list, $pr; (my $forks_path = $path) =~ s/\.git$//; $paths{$forks_path}++; } } close $fd; } return @list; } our $gitweb_project_owner = undef; sub git_get_project_list_from_file { return if (defined $gitweb_project_owner); $gitweb_project_owner = {}; # read from file (url-encoded): # 'git%2Fgit.git Linus+Torvalds' # 'libs%2Fklibc%2Fklibc.git H.+Peter+Anvin' # 'linux%2Fhotplug%2Fudev.git Greg+Kroah-Hartman' if (-f $projects_list) { open(my $fd, '<', $projects_list); while (my $line = <$fd>) { chomp $line; my ($pr, $ow) = split ' ', $line; $pr = unescape($pr); $ow = unescape($ow); $gitweb_project_owner->{$pr} = to_utf8($ow); } close $fd; } } sub git_get_project_owner { my $project = shift; my $owner; return undef unless $project; $git_dir = "$projectroot/$project"; if (!defined $gitweb_project_owner) { git_get_project_list_from_file(); } if (exists $gitweb_project_owner->{$project}) { $owner = $gitweb_project_owner->{$project}; } if (!defined $owner){ $owner = git_get_project_config('owner'); } if (!defined $owner) { $owner = get_file_owner("$git_dir"); } return $owner; } sub git_get_last_activity { my ($path) = @_; my $fd; $git_dir = "$projectroot/$path"; open($fd, "-|", git_cmd(), 'for-each-ref', '--format=%(committer)', '--sort=-committerdate', '--count=1', 'refs/heads') or return; my $most_recent = <$fd>; close $fd or return; if (defined $most_recent && $most_recent =~ / (\d+) [-+][01]\d\d\d$/) { my $timestamp = $1; my $age = time - $timestamp; return ($age, age_string($age)); } return (undef, undef); } sub git_get_references { my $type = shift || ""; my %refs; # 5dc01c595e6c6ec9ccda4f6f69c131c0dd945f8c refs/tags/v2.6.11 # c39ae07f393806ccf406ef966e9a15afc43cc36a refs/tags/v2.6.11^{} open my $fd, "-|", git_cmd(), "show-ref", "--dereference", ($type ? ("--", "refs/$type") : ()) # use -- if $type or return; while (my $line = <$fd>) { chomp $line; if ($line =~ m!^([0-9a-fA-F]{40})\srefs/($type.*)$!) { if (defined $refs{$1}) { push @{$refs{$1}}, $2; } else { $refs{$1} = [ $2 ]; } } } close $fd or return; return \%refs; } sub git_get_rev_name_tags { my $hash = shift || return undef; open my $fd, "-|", git_cmd(), "name-rev", "--tags", $hash or return; my $name_rev = <$fd>; close $fd; if ($name_rev =~ m|^$hash tags/(.*)$|) { return $1; } else { # catches also '$hash undefined' output return undef; } } ## ---------------------------------------------------------------------- ## parse to hash functions sub parse_date { my $epoch = shift; my $tz = shift || "-0000"; my %date; my @months = ("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"); my @days = ("Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat"); my ($sec, $min, $hour, $mday, $mon, $year, $wday, $yday) = gmtime($epoch); $date{'hour'} = $hour; $date{'minute'} = $min; $date{'mday'} = $mday; $date{'day'} = $days[$wday]; $date{'month'} = $months[$mon]; $date{'rfc2822'} = sprintf "%s, %d %s %4d %02d:%02d:%02d +0000", $days[$wday], $mday, $months[$mon], 1900+$year, $hour ,$min, $sec; $date{'mday-time'} = sprintf "%d %s %02d:%02d", $mday, $months[$mon], $hour ,$min; $date{'iso-8601'} = sprintf "%04d-%02d-%02dT%02d:%02d:%02dZ", 1900+$year, 1+$mon, $mday, $hour ,$min, $sec; $tz =~ m/^([+\-][0-9][0-9])([0-9][0-9])$/; my $local = $epoch + ((int $1 + ($2/60)) * 3600); ($sec, $min, $hour, $mday, $mon, $year, $wday, $yday) = gmtime($local); $date{'hour_local'} = $hour; $date{'minute_local'} = $min; $date{'tz_local'} = $tz; $date{'iso-tz'} = sprintf("%04d-%02d-%02d %02d:%02d:%02d %s", 1900+$year, $mon+1, $mday, $hour, $min, $sec, $tz); return %date; } sub parse_tag { my $tag_id = shift; my %tag; my @comment; open my $fd, "-|", git_cmd(), "cat-file", "tag", $tag_id or return; $tag{'id'} = $tag_id; while (my $line = <$fd>) { chomp $line; if ($line =~ m/^object ([0-9a-fA-F]{40})$/) { $tag{'object'} = $1; } elsif ($line =~ m/^type (.+)$/) { $tag{'type'} = $1; } elsif ($line =~ m/^tag (.+)$/) { $tag{'name'} = $1; } elsif ($line =~ m/^tagger (.*) ([0-9]+) (.*)$/) { $tag{'author'} = $1; $tag{'author_epoch'} = $2; $tag{'author_tz'} = $3; if ($tag{'author'} =~ m/^([^<]+) <([^>]*)>/) { $tag{'author_name'} = $1; $tag{'author_email'} = $2; } else { $tag{'author_name'} = $tag{'author'}; } } elsif ($line =~ m/--BEGIN/) { push @comment, $line; last; } elsif ($line eq "") { last; } } push @comment, <$fd>; $tag{'comment'} = \@comment; close $fd or return; if (!defined $tag{'name'}) { return }; return %tag } sub parse_commit_text { my ($commit_text, $withparents) = @_; my @commit_lines = split '\n', $commit_text; my %co; pop @commit_lines; # Remove '\0' if (! @commit_lines) { return; } my $header = shift @commit_lines; if ($header !~ m/^[0-9a-fA-F]{40}/) { return; } ($co{'id'}, my @parents) = split ' ', $header; while (my $line = shift @commit_lines) { last if $line eq "\n"; if ($line =~ m/^tree ([0-9a-fA-F]{40})$/) { $co{'tree'} = $1; } elsif ((!defined $withparents) && ($line =~ m/^parent ([0-9a-fA-F]{40})$/)) { push @parents, $1; } elsif ($line =~ m/^author (.*) ([0-9]+) (.*)$/) { $co{'author'} = to_utf8($1); $co{'author_epoch'} = $2; $co{'author_tz'} = $3; if ($co{'author'} =~ m/^([^<]+) <([^>]*)>/) { $co{'author_name'} = $1; $co{'author_email'} = $2; } else { $co{'author_name'} = $co{'author'}; } } elsif ($line =~ m/^committer (.*) ([0-9]+) (.*)$/) { $co{'committer'} = to_utf8($1); $co{'committer_epoch'} = $2; $co{'committer_tz'} = $3; if ($co{'committer'} =~ m/^([^<]+) <([^>]*)>/) { $co{'committer_name'} = $1; $co{'committer_email'} = $2; } else { $co{'committer_name'} = $co{'committer'}; } } } if (!defined $co{'tree'}) { return; }; $co{'parents'} = \@parents; $co{'parent'} = $parents[0]; foreach my $title (@commit_lines) { $title =~ s/^ //; if ($title ne "") { $co{'title'} = chop_str($title, 80, 5); # remove leading stuff of merges to make the interesting part visible if (length($title) > 50) { $title =~ s/^Automatic //; $title =~ s/^merge (of|with) /Merge ... /i; if (length($title) > 50) { $title =~ s/(http|rsync):\/\///; } if (length($title) > 50) { $title =~ s/(master|www|rsync)\.//; } if (length($title) > 50) { $title =~ s/kernel.org:?//; } if (length($title) > 50) { $title =~ s/\/pub\/scm//; } } $co{'title_short'} = chop_str($title, 50, 5); last; } } if (! defined $co{'title'} || $co{'title'} eq "") { $co{'title'} = $co{'title_short'} = '(no commit message)'; } # remove added spaces foreach my $line (@commit_lines) { $line =~ s/^ //; } $co{'comment'} = \@commit_lines; my $age = time - $co{'committer_epoch'}; $co{'age'} = $age; $co{'age_string'} = age_string($age); my ($sec, $min, $hour, $mday, $mon, $year, $wday, $yday) = gmtime($co{'committer_epoch'}); if ($age > 60*60*24*7*2) { $co{'age_string_date'} = sprintf "%4i-%02u-%02i", 1900 + $year, $mon+1, $mday; $co{'age_string_age'} = $co{'age_string'}; } else { $co{'age_string_date'} = $co{'age_string'}; $co{'age_string_age'} = sprintf "%4i-%02u-%02i", 1900 + $year, $mon+1, $mday; } return %co; } sub parse_commit { my ($commit_id) = @_; my %co; local $/ = "\0"; open my $fd, "-|", git_cmd(), "rev-list", "--parents", "--header", "--max-count=1", $commit_id, "--", or die_error(500, "Open git-rev-list failed"); %co = parse_commit_text(<$fd>, 1); close $fd; return %co; } sub parse_commits { my ($commit_id, $maxcount, $skip, $filename, @args) = @_; my @cos; $maxcount ||= 1; $skip ||= 0; local $/ = "\0"; open my $fd, "-|", git_cmd(), "rev-list", "--header", @args, ("--max-count=" . $maxcount), ("--skip=" . $skip), @extra_options, $commit_id, "--", ($filename ? ($filename) : ()) or die_error(500, "Open git-rev-list failed"); while (my $line = <$fd>) { my %co = parse_commit_text($line); push @cos, \%co; } close $fd; return wantarray ? @cos : \@cos; } # parse line of git-diff-tree "raw" output sub parse_difftree_raw_line { my $line = shift; my %res; # ':100644 100644 03b218260e99b78c6df0ed378e59ed9205ccc96d 3b93d5e7cc7f7dd4ebed13a5cc1a4ad976fc94d8 M ls-files.c' # ':100644 100644 7f9281985086971d3877aca27704f2aaf9c448ce bc190ebc71bbd923f2b728e505408f5e54bd073a M rev-tree.c' if ($line =~ m/^:([0-7]{6}) ([0-7]{6}) ([0-9a-fA-F]{40}) ([0-9a-fA-F]{40}) (.)([0-9]{0,3})\t(.*)$/) { $res{'from_mode'} = $1; $res{'to_mode'} = $2; $res{'from_id'} = $3; $res{'to_id'} = $4; $res{'status'} = $5; $res{'similarity'} = $6; if ($res{'status'} eq 'R' || $res{'status'} eq 'C') { # renamed or copied ($res{'from_file'}, $res{'to_file'}) = map { unquote($_) } split("\t", $7); } else { $res{'from_file'} = $res{'to_file'} = $res{'file'} = unquote($7); } } # '::100755 100755 100755 60e79ca1b01bc8b057abe17ddab484699a7f5fdb 94067cc5f73388f33722d52ae02f44692bc07490 94067cc5f73388f33722d52ae02f44692bc07490 MR git-gui/git-gui.sh' # combined diff (for merge commit) elsif ($line =~ s/^(::+)((?:[0-7]{6} )+)((?:[0-9a-fA-F]{40} )+)([a-zA-Z]+)\t(.*)$//) { $res{'nparents'} = length($1); $res{'from_mode'} = [ split(' ', $2) ]; $res{'to_mode'} = pop @{$res{'from_mode'}}; $res{'from_id'} = [ split(' ', $3) ]; $res{'to_id'} = pop @{$res{'from_id'}}; $res{'status'} = [ split('', $4) ]; $res{'to_file'} = unquote($5); } # 'c512b523472485aef4fff9e57b229d9d243c967f' elsif ($line =~ m/^([0-9a-fA-F]{40})$/) { $res{'commit'} = $1; } return wantarray ? %res : \%res; } # wrapper: return parsed line of git-diff-tree "raw" output # (the argument might be raw line, or parsed info) sub parsed_difftree_line { my $line_or_ref = shift; if (ref($line_or_ref) eq "HASH") { # pre-parsed (or generated by hand) return $line_or_ref; } else { return parse_difftree_raw_line($line_or_ref); } } # parse line of git-ls-tree output sub parse_ls_tree_line { my $line = shift; my %opts = @_; my %res; if ($opts{'-l'}) { #'100644 blob 0fa3f3a66fb6a137f6ec2c19351ed4d807070ffa 16717 panic.c' $line =~ m/^([0-9]+) (.+) ([0-9a-fA-F]{40}) +(-|[0-9]+)\t(.+)$/s; $res{'mode'} = $1; $res{'type'} = $2; $res{'hash'} = $3; $res{'size'} = $4; if ($opts{'-z'}) { $res{'name'} = $5; } else { $res{'name'} = unquote($5); } } else { #'100644 blob 0fa3f3a66fb6a137f6ec2c19351ed4d807070ffa panic.c' $line =~ m/^([0-9]+) (.+) ([0-9a-fA-F]{40})\t(.+)$/s; $res{'mode'} = $1; $res{'type'} = $2; $res{'hash'} = $3; if ($opts{'-z'}) { $res{'name'} = $4; } else { $res{'name'} = unquote($4); } } return wantarray ? %res : \%res; } # generates _two_ hashes, references to which are passed as 2 and 3 argument sub parse_from_to_diffinfo { my ($diffinfo, $from, $to, @parents) = @_; if ($diffinfo->{'nparents'}) { # combined diff $from->{'file'} = []; $from->{'href'} = []; fill_from_file_info($diffinfo, @parents) unless exists $diffinfo->{'from_file'}; for (my $i = 0; $i < $diffinfo->{'nparents'}; $i++) { $from->{'file'}[$i] = defined $diffinfo->{'from_file'}[$i] ? $diffinfo->{'from_file'}[$i] : $diffinfo->{'to_file'}; if ($diffinfo->{'status'}[$i] ne "A") { # not new (added) file $from->{'href'}[$i] = href(action=>"blob", hash_base=>$parents[$i], hash=>$diffinfo->{'from_id'}[$i], file_name=>$from->{'file'}[$i]); } else { $from->{'href'}[$i] = undef; } } } else { # ordinary (not combined) diff $from->{'file'} = $diffinfo->{'from_file'}; if ($diffinfo->{'status'} ne "A") { # not new (added) file $from->{'href'} = href(action=>"blob", hash_base=>$hash_parent, hash=>$diffinfo->{'from_id'}, file_name=>$from->{'file'}); } else { delete $from->{'href'}; } } $to->{'file'} = $diffinfo->{'to_file'}; if (!is_deleted($diffinfo)) { # file exists in result $to->{'href'} = href(action=>"blob", hash_base=>$hash, hash=>$diffinfo->{'to_id'}, file_name=>$to->{'file'}); } else { delete $to->{'href'}; } } ## ...................................................................... ## parse to array of hashes functions sub git_get_heads_list { my $limit = shift; my @headslist; open my $fd, '-|', git_cmd(), 'for-each-ref', ($limit ? '--count='.($limit+1) : ()), '--sort=-committerdate', '--format=%(objectname) %(refname) %(subject)%00%(committer)', 'refs/heads' or return; while (my $line = <$fd>) { my %ref_item; chomp $line; my ($refinfo, $committerinfo) = split(/\0/, $line); my ($hash, $name, $title) = split(' ', $refinfo, 3); my ($committer, $epoch, $tz) = ($committerinfo =~ /^(.*) ([0-9]+) (.*)$/); $ref_item{'fullname'} = $name; $name =~ s!^refs/heads/!!; $ref_item{'name'} = $name; $ref_item{'id'} = $hash; $ref_item{'title'} = $title || '(no commit message)'; $ref_item{'epoch'} = $epoch; if ($epoch) { $ref_item{'age'} = age_string(time - $ref_item{'epoch'}); } else { $ref_item{'age'} = "unknown"; } push @headslist, \%ref_item; } close $fd; return wantarray ? @headslist : \@headslist; } sub git_get_tags_list { my $limit = shift; my @tagslist; open my $fd, '-|', git_cmd(), 'for-each-ref', ($limit ? '--count='.($limit+1) : ()), '--sort=-creatordate', '--format=%(objectname) %(objecttype) %(refname) '. '%(*objectname) %(*objecttype) %(subject)%00%(creator)', 'refs/tags' or return; while (my $line = <$fd>) { my %ref_item; chomp $line; my ($refinfo, $creatorinfo) = split(/\0/, $line); my ($id, $type, $name, $refid, $reftype, $title) = split(' ', $refinfo, 6); my ($creator, $epoch, $tz) = ($creatorinfo =~ /^(.*) ([0-9]+) (.*)$/); $ref_item{'fullname'} = $name; $name =~ s!^refs/tags/!!; $ref_item{'type'} = $type; $ref_item{'id'} = $id; $ref_item{'name'} = $name; if ($type eq "tag") { $ref_item{'subject'} = $title; $ref_item{'reftype'} = $reftype; $ref_item{'refid'} = $refid; } else { $ref_item{'reftype'} = $type; $ref_item{'refid'} = $id; } if ($type eq "tag" || $type eq "commit") { $ref_item{'epoch'} = $epoch; if ($epoch) { $ref_item{'age'} = age_string(time - $ref_item{'epoch'}); } else { $ref_item{'age'} = "unknown"; } } push @tagslist, \%ref_item; } close $fd; return wantarray ? @tagslist : \@tagslist; } ## ---------------------------------------------------------------------- ## filesystem-related functions sub get_file_owner { my $path = shift; my ($dev, $ino, $mode, $nlink, $st_uid, $st_gid, $rdev, $size) = stat($path); my ($name, $passwd, $uid, $gid, $quota, $comment, $gcos, $dir, $shell) = getpwuid($st_uid); if (!defined $gcos) { return undef; } my $owner = $gcos; $owner =~ s/[,;].*$//; return to_utf8($owner); } # assume that file exists sub insert_file { my $filename = shift; open my $fd, '<', $filename; print map { to_utf8($_) } <$fd>; close $fd; } ## ...................................................................... ## mimetype related functions sub mimetype_guess_file { my $filename = shift; my $mimemap = shift; -r $mimemap or return undef; my %mimemap; open(my $mh, '<', $mimemap) or return undef; while (<$mh>) { next if m/^#/; # skip comments my ($mimetype, $exts) = split(/\t+/); if (defined $exts) { my @exts = split(/\s+/, $exts); foreach my $ext (@exts) { $mimemap{$ext} = $mimetype; } } } close($mh); $filename =~ /\.([^.]*)$/; return $mimemap{$1}; } sub mimetype_guess { my $filename = shift; my $mime; $filename =~ /\./ or return undef; if ($mimetypes_file) { my $file = $mimetypes_file; if ($file !~ m!^/!) { # if it is relative path # it is relative to project $file = "$projectroot/$project/$file"; } $mime = mimetype_guess_file($filename, $file); } $mime ||= mimetype_guess_file($filename, '/etc/mime.types'); return $mime; } sub blob_mimetype { my $fd = shift; my $filename = shift; if ($filename) { my $mime = mimetype_guess($filename); $mime and return $mime; } # just in case return $default_blob_plain_mimetype unless $fd; if (-T $fd) { return 'text/plain'; } elsif (! $filename) { return 'application/octet-stream'; } elsif ($filename =~ m/\.png$/i) { return 'image/png'; } elsif ($filename =~ m/\.gif$/i) { return 'image/gif'; } elsif ($filename =~ m/\.jpe?g$/i) { return 'image/jpeg'; } else { return 'application/octet-stream'; } } sub blob_contenttype { my ($fd, $file_name, $type) = @_; $type ||= blob_mimetype($fd, $file_name); if ($type eq 'text/plain' && defined $default_text_plain_charset) { $type .= "; charset=$default_text_plain_charset"; } return $type; } ## ====================================================================== ## functions printing HTML: header, footer, error page sub git_header_html { my $status = shift || "200 OK"; my $expires = shift; my $title = "$site_name"; if (defined $project) { $title .= " - " . to_utf8($project); if (defined $action) { $title .= "/$action"; if (defined $file_name) { $title .= " - " . esc_path($file_name); if ($action eq "tree" && $file_name !~ m|/$|) { $title .= "/"; } } } } my $content_type; # require explicit support from the UA if we are to send the page as # 'application/xhtml+xml', otherwise send it as plain old 'text/html'. # we have to do this because MSIE sometimes globs '*/*', pretending to # support xhtml+xml but choking when it gets what it asked for. if (defined $cgi->http('HTTP_ACCEPT') && $cgi->http('HTTP_ACCEPT') =~ m/(,|;|\s|^)application\/xhtml\+xml(,|;|\s|$)/ && $cgi->Accept('application/xhtml+xml') != 0) { $content_type = 'application/xhtml+xml'; } else { $content_type = 'text/html'; } print $cgi->header(-type=>$content_type, -charset => 'utf-8', -status=> $status, -expires => $expires); my $mod_perl_version = $ENV{'MOD_PERL'} ? " $ENV{'MOD_PERL'}" : ''; print < $title EOF # the stylesheet, favicon etc urls won't work correctly with path_info # unless we set the appropriate base URL if ($ENV{'PATH_INFO'}) { print "\n"; } # print out each stylesheet that exist, providing backwards capability # for those people who defined $stylesheet in a config file if (defined $stylesheet) { print ''."\n"; } else { foreach my $stylesheet (@stylesheets) { next unless $stylesheet; print ''."\n"; } } if (defined $project) { my %href_params = get_feed_info(); if (!exists $href_params{'-title'}) { $href_params{'-title'} = 'log'; } foreach my $format qw(RSS Atom) { my $type = lc($format); my %link_attr = ( '-rel' => 'alternate', '-title' => "$project - $href_params{'-title'} - $format feed", '-type' => "application/$type+xml" ); $href_params{'action'} = $type; $link_attr{'-href'} = href(%href_params); print "\n"; $href_params{'extra_options'} = '--no-merges'; $link_attr{'-href'} = href(%href_params); $link_attr{'-title'} .= ' (no merges)'; print "\n"; } } else { printf(''."\n", $site_name, href(project=>undef, action=>"project_index")); printf(''."\n", $site_name, href(project=>undef, action=>"opml")); } if (defined $favicon) { print qq(\n); } print "\n" . "\n"; if (-f $site_header) { insert_file($site_header); } print "
    \n" . $cgi->a({-href => esc_url($logo_url), -title => $logo_label}, qq()); print $cgi->a({-href => esc_url($home_link)}, $home_link_str) . " / "; if (defined $project) { print $cgi->a({-href => href(action=>"summary")}, esc_html($project)); if (defined $action) { print " / $action"; } print "\n"; } print "
    \n"; my $have_search = gitweb_check_feature('search'); if (defined $project && $have_search) { if (!defined $searchtext) { $searchtext = ""; } my $search_hash; if (defined $hash_base) { $search_hash = $hash_base; } elsif (defined $hash) { $search_hash = $hash; } else { $search_hash = "HEAD"; } my $action = $my_uri; my $use_pathinfo = gitweb_check_feature('pathinfo'); if ($use_pathinfo) { $action .= "/".esc_url($project); } print $cgi->startform(-method => "get", -action => $action) . "
    \n" . (!$use_pathinfo && $cgi->input({-name=>"p", -value=>$project, -type=>"hidden"}) . "\n") . $cgi->input({-name=>"a", -value=>"search", -type=>"hidden"}) . "\n" . $cgi->input({-name=>"h", -value=>$search_hash, -type=>"hidden"}) . "\n" . $cgi->popup_menu(-name => 'st', -default => 'commit', -values => ['commit', 'grep', 'author', 'committer', 'pickaxe']) . $cgi->sup($cgi->a({-href => href(action=>"search_help")}, "?")) . " search:\n", $cgi->textfield(-name => "s", -value => $searchtext) . "\n" . "" . $cgi->checkbox(-name => 'sr', -value => 1, -label => 're', -checked => $search_use_regexp) . "" . "
    " . $cgi->end_form() . "\n"; } } sub git_footer_html { my $feed_class = 'rss_logo'; print "
    \n"; if (defined $project) { my $descr = git_get_project_description($project); if (defined $descr) { print "
    " . esc_html($descr) . "
    \n"; } my %href_params = get_feed_info(); if (!%href_params) { $feed_class .= ' generic'; } $href_params{'-title'} ||= 'log'; foreach my $format qw(RSS Atom) { $href_params{'action'} = lc($format); print $cgi->a({-href => href(%href_params), -title => "$href_params{'-title'} $format feed", -class => $feed_class}, $format)."\n"; } } else { print $cgi->a({-href => href(project=>undef, action=>"opml"), -class => $feed_class}, "OPML") . " "; print $cgi->a({-href => href(project=>undef, action=>"project_index"), -class => $feed_class}, "TXT") . "\n"; } print "
    \n"; # class="page_footer" if (defined $t0 && gitweb_check_feature('timed')) { print "
    \n"; print 'This page took '. ''. Time::HiRes::tv_interval($t0, [Time::HiRes::gettimeofday()]). ' seconds '. ' and '. ''. $number_of_git_cmds. ' git commands '. " to generate.\n"; print "
    \n"; # class="page_footer" } if (-f $site_footer) { insert_file($site_footer); } print qq!\n!; if ($action eq 'blame_incremental') { print qq!\n!; } elsif (gitweb_check_feature('javascript-actions')) { print qq!\n!; } print "\n" . ""; } # die_error(, ) # Example: die_error(404, 'Hash not found') # By convention, use the following status codes (as defined in RFC 2616): # 400: Invalid or missing CGI parameters, or # requested object exists but has wrong type. # 403: Requested feature (like "pickaxe" or "snapshot") not enabled on # this server or project. # 404: Requested object/revision/project doesn't exist. # 500: The server isn't configured properly, or # an internal error occurred (e.g. failed assertions caused by bugs), or # an unknown error occurred (e.g. the git binary died unexpectedly). sub die_error { my $status = shift || 500; my $error = shift || "Internal server error"; my %http_responses = (400 => '400 Bad Request', 403 => '403 Forbidden', 404 => '404 Not Found', 500 => '500 Internal Server Error'); git_header_html($http_responses{$status}); print <

    $status - $error
    EOF git_footer_html(); exit; } ## ---------------------------------------------------------------------- ## functions printing or outputting HTML: navigation sub git_print_page_nav { my ($current, $suppress, $head, $treehead, $treebase, $extra) = @_; $extra = '' if !defined $extra; # pager or formats my @navs = qw(summary shortlog log commit commitdiff tree); if ($suppress) { @navs = grep { $_ ne $suppress } @navs; } my %arg = map { $_ => {action=>$_} } @navs; if (defined $head) { for (qw(commit commitdiff)) { $arg{$_}{'hash'} = $head; } if ($current =~ m/^(tree | log | shortlog | commit | commitdiff | search)$/x) { for (qw(shortlog log)) { $arg{$_}{'hash'} = $head; } } } $arg{'tree'}{'hash'} = $treehead if defined $treehead; $arg{'tree'}{'hash_base'} = $treebase if defined $treebase; my @actions = gitweb_get_feature('actions'); my %repl = ( '%' => '%', 'n' => $project, # project name 'f' => $git_dir, # project path within filesystem 'h' => $treehead || '', # current hash ('h' parameter) 'b' => $treebase || '', # hash base ('hb' parameter) ); while (@actions) { my ($label, $link, $pos) = splice(@actions,0,3); # insert @navs = map { $_ eq $pos ? ($_, $label) : $_ } @navs; # munch munch $link =~ s/%([%nfhb])/$repl{$1}/g; $arg{$label}{'_href'} = $link; } print "
    \n" . (join " | ", map { $_ eq $current ? $_ : $cgi->a({-href => ($arg{$_}{_href} ? $arg{$_}{_href} : href(%{$arg{$_}}))}, "$_") } @navs); print "
    \n$extra
    \n" . "
    \n"; } sub format_paging_nav { my ($action, $page, $has_next_link) = @_; my $paging_nav; if ($page > 0) { $paging_nav .= $cgi->a({-href => href(-replay=>1, page=>undef)}, "first") . " ⋅ " . $cgi->a({-href => href(-replay=>1, page=>$page-1), -accesskey => "p", -title => "Alt-p"}, "prev"); } else { $paging_nav .= "first ⋅ prev"; } if ($has_next_link) { $paging_nav .= " ⋅ " . $cgi->a({-href => href(-replay=>1, page=>$page+1), -accesskey => "n", -title => "Alt-n"}, "next"); } else { $paging_nav .= " ⋅ next"; } return $paging_nav; } ## ...................................................................... ## functions printing or outputting HTML: div sub git_print_header_div { my ($action, $title, $hash, $hash_base) = @_; my %args = (); $args{'action'} = $action; $args{'hash'} = $hash if $hash; $args{'hash_base'} = $hash_base if $hash_base; print "
    \n" . $cgi->a({-href => href(%args), -class => "title"}, $title ? $title : $action) . "\n
    \n"; } sub print_local_time { my %date = @_; if ($date{'hour_local'} < 6) { printf(" (%02d:%02d %s)", $date{'hour_local'}, $date{'minute_local'}, $date{'tz_local'}); } else { printf(" (%02d:%02d %s)", $date{'hour_local'}, $date{'minute_local'}, $date{'tz_local'}); } } # Outputs the author name and date in long form sub git_print_authorship { my $co = shift; my %opts = @_; my $tag = $opts{-tag} || 'div'; my $author = $co->{'author_name'}; my %ad = parse_date($co->{'author_epoch'}, $co->{'author_tz'}); print "<$tag class=\"author_date\">" . format_search_author($author, "author", esc_html($author)) . " [$ad{'rfc2822'}"; print_local_time(%ad) if ($opts{-localtime}); print "]" . git_get_avatar($co->{'author_email'}, -pad_before => 1) . "\n"; } # Outputs table rows containing the full author or committer information, # in the format expected for 'commit' view (& similia). # Parameters are a commit hash reference, followed by the list of people # to output information for. If the list is empty it defalts to both # author and committer. sub git_print_authorship_rows { my $co = shift; # too bad we can't use @people = @_ || ('author', 'committer') my @people = @_; @people = ('author', 'committer') unless @people; foreach my $who (@people) { my %wd = parse_date($co->{"${who}_epoch"}, $co->{"${who}_tz"}); print "$who" . format_search_author($co->{"${who}_name"}, $who, esc_html($co->{"${who}_name"})) . " " . format_search_author($co->{"${who}_email"}, $who, esc_html("<" . $co->{"${who}_email"} . ">")) . "" . git_get_avatar($co->{"${who}_email"}, -size => 'double') . "\n" . "" . " $wd{'rfc2822'}"; print_local_time(%wd); print "" . "\n"; } } sub git_print_page_path { my $name = shift; my $type = shift; my $hb = shift; print "
    "; print $cgi->a({-href => href(action=>"tree", hash_base=>$hb), -title => 'tree root'}, to_utf8("[$project]")); print " / "; if (defined $name) { my @dirname = split '/', $name; my $basename = pop @dirname; my $fullname = ''; foreach my $dir (@dirname) { $fullname .= ($fullname ? '/' : '') . $dir; print $cgi->a({-href => href(action=>"tree", file_name=>$fullname, hash_base=>$hb), -title => $fullname}, esc_path($dir)); print " / "; } if (defined $type && $type eq 'blob') { print $cgi->a({-href => href(action=>"blob_plain", file_name=>$file_name, hash_base=>$hb), -title => $name}, esc_path($basename)); } elsif (defined $type && $type eq 'tree') { print $cgi->a({-href => href(action=>"tree", file_name=>$file_name, hash_base=>$hb), -title => $name}, esc_path($basename)); print " / "; } else { print esc_path($basename); } } print "
    \n"; } sub git_print_log { my $log = shift; my %opts = @_; if ($opts{'-remove_title'}) { # remove title, i.e. first line of log shift @$log; } # remove leading empty lines while (defined $log->[0] && $log->[0] eq "") { shift @$log; } # print log my $signoff = 0; my $empty = 0; foreach my $line (@$log) { if ($line =~ m/^ *(signed[ \-]off[ \-]by[ :]|acked[ \-]by[ :]|cc[ :])/i) { $signoff = 1; $empty = 0; if (! $opts{'-remove_signoff'}) { print "" . esc_html($line) . "
    \n"; next; } else { # remove signoff lines next; } } else { $signoff = 0; } # print only one empty line # do not print empty line after signoff if ($line eq "") { next if ($empty || $signoff); $empty = 1; } else { $empty = 0; } print format_log_line_html($line) . "
    \n"; } if ($opts{'-final_empty_line'}) { # end with single empty line print "
    \n" unless $empty; } } # return link target (what link points to) sub git_get_link_target { my $hash = shift; my $link_target; # read link open my $fd, "-|", git_cmd(), "cat-file", "blob", $hash or return; { local $/ = undef; $link_target = <$fd>; } close $fd or return; return $link_target; } # given link target, and the directory (basedir) the link is in, # return target of link relative to top directory (top tree); # return undef if it is not possible (including absolute links). sub normalize_link_target { my ($link_target, $basedir) = @_; # absolute symlinks (beginning with '/') cannot be normalized return if (substr($link_target, 0, 1) eq '/'); # normalize link target to path from top (root) tree (dir) my $path; if ($basedir) { $path = $basedir . '/' . $link_target; } else { # we are in top (root) tree (dir) $path = $link_target; } # remove //, /./, and /../ my @path_parts; foreach my $part (split('/', $path)) { # discard '.' and '' next if (!$part || $part eq '.'); # handle '..' if ($part eq '..') { if (@path_parts) { pop @path_parts; } else { # link leads outside repository (outside top dir) return; } } else { push @path_parts, $part; } } $path = join('/', @path_parts); return $path; } # print tree entry (row of git_tree), but without encompassing element sub git_print_tree_entry { my ($t, $basedir, $hash_base, $have_blame) = @_; my %base_key = (); $base_key{'hash_base'} = $hash_base if defined $hash_base; # The format of a table row is: mode list link. Where mode is # the mode of the entry, list is the name of the entry, an href, # and link is the action links of the entry. print "" . mode_str($t->{'mode'}) . "\n"; if (exists $t->{'size'}) { print "$t->{'size'}\n"; } if ($t->{'type'} eq "blob") { print "" . $cgi->a({-href => href(action=>"blob", hash=>$t->{'hash'}, file_name=>"$basedir$t->{'name'}", %base_key), -class => "list"}, esc_path($t->{'name'})); if (S_ISLNK(oct $t->{'mode'})) { my $link_target = git_get_link_target($t->{'hash'}); if ($link_target) { my $norm_target = normalize_link_target($link_target, $basedir); if (defined $norm_target) { print " -> " . $cgi->a({-href => href(action=>"object", hash_base=>$hash_base, file_name=>$norm_target), -title => $norm_target}, esc_path($link_target)); } else { print " -> " . esc_path($link_target); } } } print "\n"; print ""; print $cgi->a({-href => href(action=>"blob", hash=>$t->{'hash'}, file_name=>"$basedir$t->{'name'}", %base_key)}, "blob"); if ($have_blame) { print " | " . $cgi->a({-href => href(action=>"blame", hash=>$t->{'hash'}, file_name=>"$basedir$t->{'name'}", %base_key)}, "blame"); } if (defined $hash_base) { print " | " . $cgi->a({-href => href(action=>"history", hash_base=>$hash_base, hash=>$t->{'hash'}, file_name=>"$basedir$t->{'name'}")}, "history"); } print " | " . $cgi->a({-href => href(action=>"blob_plain", hash_base=>$hash_base, file_name=>"$basedir$t->{'name'}")}, "raw"); print "\n"; } elsif ($t->{'type'} eq "tree") { print ""; print $cgi->a({-href => href(action=>"tree", hash=>$t->{'hash'}, file_name=>"$basedir$t->{'name'}", %base_key)}, esc_path($t->{'name'})); print "\n"; print ""; print $cgi->a({-href => href(action=>"tree", hash=>$t->{'hash'}, file_name=>"$basedir$t->{'name'}", %base_key)}, "tree"); if (defined $hash_base) { print " | " . $cgi->a({-href => href(action=>"history", hash_base=>$hash_base, file_name=>"$basedir$t->{'name'}")}, "history"); } print "\n"; } else { # unknown object: we can only present history for it # (this includes 'commit' object, i.e. submodule support) print "" . esc_path($t->{'name'}) . "\n"; print ""; if (defined $hash_base) { print $cgi->a({-href => href(action=>"history", hash_base=>$hash_base, file_name=>"$basedir$t->{'name'}")}, "history"); } print "\n"; } } ## ...................................................................... ## functions printing large fragments of HTML # get pre-image filenames for merge (combined) diff sub fill_from_file_info { my ($diff, @parents) = @_; $diff->{'from_file'} = [ ]; $diff->{'from_file'}[$diff->{'nparents'} - 1] = undef; for (my $i = 0; $i < $diff->{'nparents'}; $i++) { if ($diff->{'status'}[$i] eq 'R' || $diff->{'status'}[$i] eq 'C') { $diff->{'from_file'}[$i] = git_get_path_by_hash($parents[$i], $diff->{'from_id'}[$i]); } } return $diff; } # is current raw difftree line of file deletion sub is_deleted { my $diffinfo = shift; return $diffinfo->{'to_id'} eq ('0' x 40); } # does patch correspond to [previous] difftree raw line # $diffinfo - hashref of parsed raw diff format # $patchinfo - hashref of parsed patch diff format # (the same keys as in $diffinfo) sub is_patch_split { my ($diffinfo, $patchinfo) = @_; return defined $diffinfo && defined $patchinfo && $diffinfo->{'to_file'} eq $patchinfo->{'to_file'}; } sub git_difftree_body { my ($difftree, $hash, @parents) = @_; my ($parent) = $parents[0]; my $have_blame = gitweb_check_feature('blame'); print "
    \n"; if ($#{$difftree} > 10) { print(($#{$difftree} + 1) . " files changed:\n"); } print "
    \n"; print " 1 ? "combined " : "") . "diff_tree\">\n"; # header only for combined diff in 'commitdiff' view my $has_header = @$difftree && @parents > 1 && $action eq 'commitdiff'; if ($has_header) { # table header print "\n" . "\n"; # filename, patchN link for (my $i = 0; $i < @parents; $i++) { my $par = $parents[$i]; print "\n"; } print "\n\n"; } my $alternate = 1; my $patchno = 0; foreach my $line (@{$difftree}) { my $diff = parsed_difftree_line($line); if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; if (exists $diff->{'nparents'}) { # combined diff fill_from_file_info($diff, @parents) unless exists $diff->{'from_file'}; if (!is_deleted($diff)) { # file exists in the result (child) commit print "\n"; } else { print "\n"; } if ($action eq 'commitdiff') { # link to patch $patchno++; print "\n"; } my $has_history = 0; my $not_deleted = 0; for (my $i = 0; $i < $diff->{'nparents'}; $i++) { my $hash_parent = $parents[$i]; my $from_hash = $diff->{'from_id'}[$i]; my $from_path = $diff->{'from_file'}[$i]; my $status = $diff->{'status'}[$i]; $has_history ||= ($status ne 'A'); $not_deleted ||= ($status ne 'D'); if ($status eq 'A') { print "\n"; } elsif ($status eq 'D') { print "\n"; } else { if ($diff->{'to_id'} eq $from_hash) { print "\n"; } } print "\n"; print "\n"; next; # instead of 'else' clause, to avoid extra indent } # else ordinary diff my ($to_mode_oct, $to_mode_str, $to_file_type); my ($from_mode_oct, $from_mode_str, $from_file_type); if ($diff->{'to_mode'} ne ('0' x 6)) { $to_mode_oct = oct $diff->{'to_mode'}; if (S_ISREG($to_mode_oct)) { # only for regular file $to_mode_str = sprintf("%04o", $to_mode_oct & 0777); # permission bits } $to_file_type = file_type($diff->{'to_mode'}); } if ($diff->{'from_mode'} ne ('0' x 6)) { $from_mode_oct = oct $diff->{'from_mode'}; if (S_ISREG($to_mode_oct)) { # only for regular file $from_mode_str = sprintf("%04o", $from_mode_oct & 0777); # permission bits } $from_file_type = file_type($diff->{'from_mode'}); } if ($diff->{'status'} eq "A") { # created my $mode_chng = "[new $to_file_type"; $mode_chng .= " with mode: $to_mode_str" if $to_mode_str; $mode_chng .= "]"; print "\n"; print "\n"; print "\n"; } elsif ($diff->{'status'} eq "D") { # deleted my $mode_chng = "[deleted $from_file_type]"; print "\n"; print "\n"; print "\n"; } elsif ($diff->{'status'} eq "M" || $diff->{'status'} eq "T") { # modified, or type changed my $mode_chnge = ""; if ($diff->{'from_mode'} != $diff->{'to_mode'}) { $mode_chnge = "[changed"; if ($from_file_type ne $to_file_type) { $mode_chnge .= " from $from_file_type to $to_file_type"; } if (($from_mode_oct & 0777) != ($to_mode_oct & 0777)) { if ($from_mode_str && $to_mode_str) { $mode_chnge .= " mode: $from_mode_str->$to_mode_str"; } elsif ($to_mode_str) { $mode_chnge .= " mode: $to_mode_str"; } } $mode_chnge .= "]\n"; } print "\n"; print "\n"; print "\n"; } elsif ($diff->{'status'} eq "R" || $diff->{'status'} eq "C") { # renamed or copied my %status_name = ('R' => 'moved', 'C' => 'copied'); my $nstatus = $status_name{$diff->{'status'}}; my $mode_chng = ""; if ($diff->{'from_mode'} != $diff->{'to_mode'}) { # mode also for directories, so we cannot use $to_mode_str $mode_chng = sprintf(", mode: %04o", $to_mode_oct & 0777); } print "\n" . "\n" . "\n"; } # we should not encounter Unmerged (U) or Unknown (X) status print "\n"; } print "" if $has_header; print "
    " . $cgi->a({-href => href(action=>"commitdiff", hash=>$hash, hash_parent=>$par), -title => 'commitdiff to parent number ' . ($i+1) . ': ' . substr($par,0,7)}, $i+1) . " 
    " . $cgi->a({-href => href(action=>"blob", hash=>$diff->{'to_id'}, file_name=>$diff->{'to_file'}, hash_base=>$hash), -class => "list"}, esc_path($diff->{'to_file'})) . "" . esc_path($diff->{'to_file'}) . "" . $cgi->a({-href => "#patch$patchno"}, "patch") . " | " . " | " . $cgi->a({-href => href(action=>"blob", hash_base=>$hash, hash=>$from_hash, file_name=>$from_path)}, "blob" . ($i+1)) . " | "; } else { print ""; } print $cgi->a({-href => href(action=>"blobdiff", hash=>$diff->{'to_id'}, hash_parent=>$from_hash, hash_base=>$hash, hash_parent_base=>$hash_parent, file_name=>$diff->{'to_file'}, file_parent=>$from_path)}, "diff" . ($i+1)) . " | "; if ($not_deleted) { print $cgi->a({-href => href(action=>"blob", hash=>$diff->{'to_id'}, file_name=>$diff->{'to_file'}, hash_base=>$hash)}, "blob"); print " | " if ($has_history); } if ($has_history) { print $cgi->a({-href => href(action=>"history", file_name=>$diff->{'to_file'}, hash_base=>$hash)}, "history"); } print "
    "; print $cgi->a({-href => href(action=>"blob", hash=>$diff->{'to_id'}, hash_base=>$hash, file_name=>$diff->{'file'}), -class => "list"}, esc_path($diff->{'file'})); print "$mode_chng"; if ($action eq 'commitdiff') { # link to patch $patchno++; print $cgi->a({-href => "#patch$patchno"}, "patch"); print " | "; } print $cgi->a({-href => href(action=>"blob", hash=>$diff->{'to_id'}, hash_base=>$hash, file_name=>$diff->{'file'})}, "blob"); print ""; print $cgi->a({-href => href(action=>"blob", hash=>$diff->{'from_id'}, hash_base=>$parent, file_name=>$diff->{'file'}), -class => "list"}, esc_path($diff->{'file'})); print "$mode_chng"; if ($action eq 'commitdiff') { # link to patch $patchno++; print $cgi->a({-href => "#patch$patchno"}, "patch"); print " | "; } print $cgi->a({-href => href(action=>"blob", hash=>$diff->{'from_id'}, hash_base=>$parent, file_name=>$diff->{'file'})}, "blob") . " | "; if ($have_blame) { print $cgi->a({-href => href(action=>"blame", hash_base=>$parent, file_name=>$diff->{'file'})}, "blame") . " | "; } print $cgi->a({-href => href(action=>"history", hash_base=>$parent, file_name=>$diff->{'file'})}, "history"); print ""; print $cgi->a({-href => href(action=>"blob", hash=>$diff->{'to_id'}, hash_base=>$hash, file_name=>$diff->{'file'}), -class => "list"}, esc_path($diff->{'file'})); print "$mode_chnge"; if ($action eq 'commitdiff') { # link to patch $patchno++; print $cgi->a({-href => "#patch$patchno"}, "patch") . " | "; } elsif ($diff->{'to_id'} ne $diff->{'from_id'}) { # "commit" view and modified file (not onlu mode changed) print $cgi->a({-href => href(action=>"blobdiff", hash=>$diff->{'to_id'}, hash_parent=>$diff->{'from_id'}, hash_base=>$hash, hash_parent_base=>$parent, file_name=>$diff->{'file'})}, "diff") . " | "; } print $cgi->a({-href => href(action=>"blob", hash=>$diff->{'to_id'}, hash_base=>$hash, file_name=>$diff->{'file'})}, "blob") . " | "; if ($have_blame) { print $cgi->a({-href => href(action=>"blame", hash_base=>$hash, file_name=>$diff->{'file'})}, "blame") . " | "; } print $cgi->a({-href => href(action=>"history", hash_base=>$hash, file_name=>$diff->{'file'})}, "history"); print "" . $cgi->a({-href => href(action=>"blob", hash_base=>$hash, hash=>$diff->{'to_id'}, file_name=>$diff->{'to_file'}), -class => "list"}, esc_path($diff->{'to_file'})) . "[$nstatus from " . $cgi->a({-href => href(action=>"blob", hash_base=>$parent, hash=>$diff->{'from_id'}, file_name=>$diff->{'from_file'}), -class => "list"}, esc_path($diff->{'from_file'})) . " with " . (int $diff->{'similarity'}) . "% similarity$mode_chng]"; if ($action eq 'commitdiff') { # link to patch $patchno++; print $cgi->a({-href => "#patch$patchno"}, "patch") . " | "; } elsif ($diff->{'to_id'} ne $diff->{'from_id'}) { # "commit" view and modified file (not only pure rename or copy) print $cgi->a({-href => href(action=>"blobdiff", hash=>$diff->{'to_id'}, hash_parent=>$diff->{'from_id'}, hash_base=>$hash, hash_parent_base=>$parent, file_name=>$diff->{'to_file'}, file_parent=>$diff->{'from_file'})}, "diff") . " | "; } print $cgi->a({-href => href(action=>"blob", hash=>$diff->{'to_id'}, hash_base=>$parent, file_name=>$diff->{'to_file'})}, "blob") . " | "; if ($have_blame) { print $cgi->a({-href => href(action=>"blame", hash_base=>$hash, file_name=>$diff->{'to_file'})}, "blame") . " | "; } print $cgi->a({-href => href(action=>"history", hash_base=>$hash, file_name=>$diff->{'to_file'})}, "history"); print "
    \n"; } sub git_patchset_body { my ($fd, $difftree, $hash, @hash_parents) = @_; my ($hash_parent) = $hash_parents[0]; my $is_combined = (@hash_parents > 1); my $patch_idx = 0; my $patch_number = 0; my $patch_line; my $diffinfo; my $to_name; my (%from, %to); print "
    \n"; # skip to first patch while ($patch_line = <$fd>) { chomp $patch_line; last if ($patch_line =~ m/^diff /); } PATCH: while ($patch_line) { # parse "git diff" header line if ($patch_line =~ m/^diff --git (\"(?:[^\\\"]*(?:\\.[^\\\"]*)*)\"|[^ "]*) (.*)$/) { # $1 is from_name, which we do not use $to_name = unquote($2); $to_name =~ s!^b/!!; } elsif ($patch_line =~ m/^diff --(cc|combined) ("?.*"?)$/) { # $1 is 'cc' or 'combined', which we do not use $to_name = unquote($2); } else { $to_name = undef; } # check if current patch belong to current raw line # and parse raw git-diff line if needed if (is_patch_split($diffinfo, { 'to_file' => $to_name })) { # this is continuation of a split patch print "
    \n"; } else { # advance raw git-diff output if needed $patch_idx++ if defined $diffinfo; # read and prepare patch information $diffinfo = parsed_difftree_line($difftree->[$patch_idx]); # compact combined diff output can have some patches skipped # find which patch (using pathname of result) we are at now; if ($is_combined) { while ($to_name ne $diffinfo->{'to_file'}) { print "
    \n" . format_diff_cc_simplified($diffinfo, @hash_parents) . "
    \n"; # class="patch" $patch_idx++; $patch_number++; last if $patch_idx > $#$difftree; $diffinfo = parsed_difftree_line($difftree->[$patch_idx]); } } # modifies %from, %to hashes parse_from_to_diffinfo($diffinfo, \%from, \%to, @hash_parents); # this is first patch for raw difftree line with $patch_idx index # we index @$difftree array from 0, but number patches from 1 print "
    \n"; } # git diff header #assert($patch_line =~ m/^diff /) if DEBUG; #assert($patch_line !~ m!$/$!) if DEBUG; # is chomp-ed $patch_number++; # print "git diff" header print format_git_diff_header_line($patch_line, $diffinfo, \%from, \%to); # print extended diff header print "
    \n"; EXTENDED_HEADER: while ($patch_line = <$fd>) { chomp $patch_line; last EXTENDED_HEADER if ($patch_line =~ m/^--- |^diff /); print format_extended_diff_header_line($patch_line, $diffinfo, \%from, \%to); } print "
    \n"; # class="diff extended_header" # from-file/to-file diff header if (! $patch_line) { print "
    \n"; # class="patch" last PATCH; } next PATCH if ($patch_line =~ m/^diff /); #assert($patch_line =~ m/^---/) if DEBUG; my $last_patch_line = $patch_line; $patch_line = <$fd>; chomp $patch_line; #assert($patch_line =~ m/^\+\+\+/) if DEBUG; print format_diff_from_to_header($last_patch_line, $patch_line, $diffinfo, \%from, \%to, @hash_parents); # the patch itself LINE: while ($patch_line = <$fd>) { chomp $patch_line; next PATCH if ($patch_line =~ m/^diff /); print format_diff_line($patch_line, \%from, \%to); } } continue { print "
    \n"; # class="patch" } # for compact combined (--cc) format, with chunk and patch simpliciaction # patchset might be empty, but there might be unprocessed raw lines for (++$patch_idx if $patch_number > 0; $patch_idx < @$difftree; ++$patch_idx) { # read and prepare patch information $diffinfo = parsed_difftree_line($difftree->[$patch_idx]); # generate anchor for "patch" links in difftree / whatchanged part print "
    \n" . format_diff_cc_simplified($diffinfo, @hash_parents) . "
    \n"; # class="patch" $patch_number++; } if ($patch_number == 0) { if (@hash_parents > 1) { print "
    Trivial merge
    \n"; } else { print "
    No differences found
    \n"; } } print "
    \n"; # class="patchset" } # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . # fills project list info (age, description, owner, forks) for each # project in the list, removing invalid projects from returned list # NOTE: modifies $projlist, but does not remove entries from it sub fill_project_list_info { my ($projlist, $check_forks) = @_; my @projects; my $show_ctags = gitweb_check_feature('ctags'); PROJECT: foreach my $pr (@$projlist) { my (@activity) = git_get_last_activity($pr->{'path'}); unless (@activity) { next PROJECT; } ($pr->{'age'}, $pr->{'age_string'}) = @activity; if (!defined $pr->{'descr'}) { my $descr = git_get_project_description($pr->{'path'}) || ""; $descr = to_utf8($descr); $pr->{'descr_long'} = $descr; $pr->{'descr'} = chop_str($descr, $projects_list_description_width, 5); } if (!defined $pr->{'owner'}) { $pr->{'owner'} = git_get_project_owner("$pr->{'path'}") || ""; } if ($check_forks) { my $pname = $pr->{'path'}; if (($pname =~ s/\.git$//) && ($pname !~ /\/$/) && (-d "$projectroot/$pname")) { $pr->{'forks'} = "-d $projectroot/$pname"; } else { $pr->{'forks'} = 0; } } $show_ctags and $pr->{'ctags'} = git_get_project_ctags($pr->{'path'}); push @projects, $pr; } return @projects; } # print 'sort by' element, generating 'sort by $name' replay link # if that order is not selected sub print_sort_th { my ($name, $order, $header) = @_; $header ||= ucfirst($name); if ($order eq $name) { print "$header\n"; } else { print "" . $cgi->a({-href => href(-replay=>1, order=>$name), -class => "header"}, $header) . "\n"; } } sub git_project_list_body { # actually uses global variable $project my ($projlist, $order, $from, $to, $extra, $no_header) = @_; my $check_forks = gitweb_check_feature('forks'); my @projects = fill_project_list_info($projlist, $check_forks); $order ||= $default_projects_order; $from = 0 unless defined $from; $to = $#projects if (!defined $to || $#projects < $to); my %order_info = ( project => { key => 'path', type => 'str' }, descr => { key => 'descr_long', type => 'str' }, owner => { key => 'owner', type => 'str' }, age => { key => 'age', type => 'num' } ); my $oi = $order_info{$order}; if ($oi->{'type'} eq 'str') { @projects = sort {$a->{$oi->{'key'}} cmp $b->{$oi->{'key'}}} @projects; } else { @projects = sort {$a->{$oi->{'key'}} <=> $b->{$oi->{'key'}}} @projects; } my $show_ctags = gitweb_check_feature('ctags'); if ($show_ctags) { my %ctags; foreach my $p (@projects) { foreach my $ct (keys %{$p->{'ctags'}}) { $ctags{$ct} += $p->{'ctags'}->{$ct}; } } my $cloud = git_populate_project_tagcloud(\%ctags); print git_show_project_tagcloud($cloud, 64); } print "\n"; unless ($no_header) { print "\n"; if ($check_forks) { print "\n"; } print_sort_th('project', $order, 'Project'); print_sort_th('descr', $order, 'Description'); print_sort_th('owner', $order, 'Owner'); print_sort_th('age', $order, 'Last Change'); print "\n" . # for links "\n"; } my $alternate = 1; my $tagfilter = $cgi->param('by_tag'); for (my $i = $from; $i <= $to; $i++) { my $pr = $projects[$i]; next if $tagfilter and $show_ctags and not grep { lc $_ eq lc $tagfilter } keys %{$pr->{'ctags'}}; next if $searchtext and not $pr->{'path'} =~ /$searchtext/ and not $pr->{'descr_long'} =~ /$searchtext/; # Weed out forks or non-matching entries of search if ($check_forks) { my $forkbase = $project; $forkbase ||= ''; $forkbase =~ s#\.git$#/#; $forkbase="^$forkbase" if $forkbase; next if not $searchtext and not $tagfilter and $show_ctags and $pr->{'path'} =~ m#$forkbase.*/.*#; # regexp-safe } if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; if ($check_forks) { print "\n"; } print "\n" . "\n" . "\n"; print "\n" . "\n" . "\n"; } if (defined $extra) { print "\n"; if ($check_forks) { print "\n"; } print "\n" . "\n"; } print "
    "; if ($pr->{'forks'}) { print "\n"; print $cgi->a({-href => href(project=>$pr->{'path'}, action=>"forks")}, "+"); } print "" . $cgi->a({-href => href(project=>$pr->{'path'}, action=>"summary"), -class => "list"}, esc_html($pr->{'path'})) . "" . $cgi->a({-href => href(project=>$pr->{'path'}, action=>"summary"), -class => "list", -title => $pr->{'descr_long'}}, esc_html($pr->{'descr'})) . "" . chop_and_escape_str($pr->{'owner'}, 15) . "{'age'}) . "\">" . (defined $pr->{'age_string'} ? $pr->{'age_string'} : "No commits") . "" . $cgi->a({-href => href(project=>$pr->{'path'}, action=>"summary")}, "summary") . " | " . $cgi->a({-href => href(project=>$pr->{'path'}, action=>"shortlog")}, "shortlog") . " | " . $cgi->a({-href => href(project=>$pr->{'path'}, action=>"log")}, "log") . " | " . $cgi->a({-href => href(project=>$pr->{'path'}, action=>"tree")}, "tree") . ($pr->{'forks'} ? " | " . $cgi->a({-href => href(project=>$pr->{'path'}, action=>"forks")}, "forks") : '') . "
    $extra
    \n"; } sub git_log_body { # uses global variable $project my ($commitlist, $from, $to, $refs, $extra) = @_; $from = 0 unless defined $from; $to = $#{$commitlist} if (!defined $to || $#{$commitlist} < $to); for (my $i = 0; $i <= $to; $i++) { my %co = %{$commitlist->[$i]}; next if !%co; my $commit = $co{'id'}; my $ref = format_ref_marker($refs, $commit); my %ad = parse_date($co{'author_epoch'}); git_print_header_div('commit', "$co{'age_string'}" . esc_html($co{'title'}) . $ref, $commit); print "
    \n" . "
    \n" . $cgi->a({-href => href(action=>"commit", hash=>$commit)}, "commit") . " | " . $cgi->a({-href => href(action=>"commitdiff", hash=>$commit)}, "commitdiff") . " | " . $cgi->a({-href => href(action=>"tree", hash=>$commit, hash_base=>$commit)}, "tree") . "
    \n" . "
    \n"; git_print_authorship(\%co, -tag => 'span'); print "
    \n
    \n"; print "
    \n"; git_print_log($co{'comment'}, -final_empty_line=> 1); print "
    \n"; } if ($extra) { print "
    \n"; print "$extra\n"; print "
    \n"; } } sub git_shortlog_body { # uses global variable $project my ($commitlist, $from, $to, $refs, $extra) = @_; $from = 0 unless defined $from; $to = $#{$commitlist} if (!defined $to || $#{$commitlist} < $to); print "\n"; my $alternate = 1; for (my $i = $from; $i <= $to; $i++) { my %co = %{$commitlist->[$i]}; my $commit = $co{'id'}; my $ref = format_ref_marker($refs, $commit); if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; # git_summary() used print "\n" . print "\n" . format_author_html('td', \%co, 10) . "\n" . "\n" . "\n"; } if (defined $extra) { print "\n" . "\n" . "\n"; } print "
    $co{'age_string'}$co{'age_string_date'}"; print format_subject_html($co{'title'}, $co{'title_short'}, href(action=>"commit", hash=>$commit), $ref); print "" . $cgi->a({-href => href(action=>"commit", hash=>$commit)}, "commit") . " | " . $cgi->a({-href => href(action=>"commitdiff", hash=>$commit)}, "commitdiff") . " | " . $cgi->a({-href => href(action=>"tree", hash=>$commit, hash_base=>$commit)}, "tree"); my $snapshot_links = format_snapshot_links($commit); if (defined $snapshot_links) { print " | " . $snapshot_links; } print "
    $extra
    \n"; } sub git_history_body { # Warning: assumes constant type (blob or tree) during history my ($commitlist, $from, $to, $refs, $extra, $file_name, $file_hash, $ftype) = @_; $from = 0 unless defined $from; $to = $#{$commitlist} unless (defined $to && $to <= $#{$commitlist}); print "\n"; my $alternate = 1; for (my $i = $from; $i <= $to; $i++) { my %co = %{$commitlist->[$i]}; if (!%co) { next; } my $commit = $co{'id'}; my $ref = format_ref_marker($refs, $commit); if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; print "\n" . # shortlog: format_author_html('td', \%co, 10) format_author_html('td', \%co, 15, 3) . "\n" . "\n" . "\n"; } if (defined $extra) { print "\n" . "\n" . "\n"; } print "
    $co{'age_string_date'}"; # originally git_history used chop_str($co{'title'}, 50) print format_subject_html($co{'title'}, $co{'title_short'}, href(action=>"commit", hash=>$commit), $ref); print "" . $cgi->a({-href => href(action=>$ftype, hash_base=>$commit, file_name=>$file_name)}, $ftype) . " | " . $cgi->a({-href => href(action=>"commitdiff", hash=>$commit)}, "commitdiff"); if ($ftype eq 'blob') { my $blob_current = $file_hash; my $blob_parent = git_get_hash_by_path($commit, $file_name); if (defined $blob_current && defined $blob_parent && $blob_current ne $blob_parent) { print " | " . $cgi->a({-href => href(action=>"blobdiff", hash=>$blob_current, hash_parent=>$blob_parent, hash_base=>$hash_base, hash_parent_base=>$commit, file_name=>$file_name)}, "diff to current"); } } print "
    $extra
    \n"; } sub git_tags_body { # uses global variable $project my ($taglist, $from, $to, $extra) = @_; $from = 0 unless defined $from; $to = $#{$taglist} if (!defined $to || $#{$taglist} < $to); print "\n"; my $alternate = 1; for (my $i = $from; $i <= $to; $i++) { my $entry = $taglist->[$i]; my %tag = %$entry; my $comment = $tag{'subject'}; my $comment_short; if (defined $comment) { $comment_short = chop_str($comment, 30, 5); } if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; if (defined $tag{'age'}) { print "\n"; } else { print "\n"; } print "\n" . "\n" . "\n" . "\n" . ""; } if (defined $extra) { print "\n" . "\n" . "\n"; } print "
    $tag{'age'}" . $cgi->a({-href => href(action=>$tag{'reftype'}, hash=>$tag{'refid'}), -class => "list name"}, esc_html($tag{'name'})) . ""; if (defined $comment) { print format_subject_html($comment, $comment_short, href(action=>"tag", hash=>$tag{'id'})); } print ""; if ($tag{'type'} eq "tag") { print $cgi->a({-href => href(action=>"tag", hash=>$tag{'id'})}, "tag"); } else { print " "; } print "" . " | " . $cgi->a({-href => href(action=>$tag{'reftype'}, hash=>$tag{'refid'})}, $tag{'reftype'}); if ($tag{'reftype'} eq "commit") { print " | " . $cgi->a({-href => href(action=>"shortlog", hash=>$tag{'fullname'})}, "shortlog") . " | " . $cgi->a({-href => href(action=>"log", hash=>$tag{'fullname'})}, "log"); } elsif ($tag{'reftype'} eq "blob") { print " | " . $cgi->a({-href => href(action=>"blob_plain", hash=>$tag{'refid'})}, "raw"); } print "
    $extra
    \n"; } sub git_heads_body { # uses global variable $project my ($headlist, $head, $from, $to, $extra) = @_; $from = 0 unless defined $from; $to = $#{$headlist} if (!defined $to || $#{$headlist} < $to); print "\n"; my $alternate = 1; for (my $i = $from; $i <= $to; $i++) { my $entry = $headlist->[$i]; my %ref = %$entry; my $curr = $ref{'id'} eq $head; if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; print "\n" . ($curr ? "\n" . "\n" . ""; } if (defined $extra) { print "\n" . "\n" . "\n"; } print "
    $ref{'age'}" : "") . $cgi->a({-href => href(action=>"shortlog", hash=>$ref{'fullname'}), -class => "list name"},esc_html($ref{'name'})) . "" . $cgi->a({-href => href(action=>"shortlog", hash=>$ref{'fullname'})}, "shortlog") . " | " . $cgi->a({-href => href(action=>"log", hash=>$ref{'fullname'})}, "log") . " | " . $cgi->a({-href => href(action=>"tree", hash=>$ref{'fullname'}, hash_base=>$ref{'name'})}, "tree") . "
    $extra
    \n"; } sub git_search_grep_body { my ($commitlist, $from, $to, $extra) = @_; $from = 0 unless defined $from; $to = $#{$commitlist} if (!defined $to || $#{$commitlist} < $to); print "\n"; my $alternate = 1; for (my $i = $from; $i <= $to; $i++) { my %co = %{$commitlist->[$i]}; if (!%co) { next; } my $commit = $co{'id'}; if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; print "\n" . format_author_html('td', \%co, 15, 5) . "\n" . "\n" . "\n"; } if (defined $extra) { print "\n" . "\n" . "\n"; } print "
    $co{'age_string_date'}" . $cgi->a({-href => href(action=>"commit", hash=>$co{'id'}), -class => "list subject"}, chop_and_escape_str($co{'title'}, 50) . "
    "); my $comment = $co{'comment'}; foreach my $line (@$comment) { if ($line =~ m/^(.*?)($search_regexp)(.*)$/i) { my ($lead, $match, $trail) = ($1, $2, $3); $match = chop_str($match, 70, 5, 'center'); my $contextlen = int((80 - length($match))/2); $contextlen = 30 if ($contextlen > 30); $lead = chop_str($lead, $contextlen, 10, 'left'); $trail = chop_str($trail, $contextlen, 10, 'right'); $lead = esc_html($lead); $match = esc_html($match); $trail = esc_html($trail); print "$lead$match$trail
    "; } } print "    		" . $cgi->a({-href => href(action=>"commit", hash=>$co{'id'})}, "commit") . " | " . $cgi->a({-href => href(action=>"commitdiff", hash=>$co{'id'})}, "commitdiff") . " | " . $cgi->a({-href => href(action=>"tree", hash=>$co{'tree'}, hash_base=>$co{'id'})}, "tree"); print "
    $extra
    \n"; } ## ====================================================================== ## ====================================================================== ## actions sub git_project_list { my $order = $input_params{'order'}; if (defined $order && $order !~ m/none|project|descr|owner|age/) { die_error(400, "Unknown order parameter"); } my @list = git_get_projects_list(); if (!@list) { die_error(404, "No projects found"); } git_header_html(); if (-f $home_text) { print "
    \n"; insert_file($home_text); print "
    \n"; } print $cgi->startform(-method => "get") . "

    Search:\n" . $cgi->textfield(-name => "s", -value => $searchtext) . "\n" . "

    " . $cgi->end_form() . "\n"; git_project_list_body(\@list, $order); git_footer_html(); } sub git_forks { my $order = $input_params{'order'}; if (defined $order && $order !~ m/none|project|descr|owner|age/) { die_error(400, "Unknown order parameter"); } my @list = git_get_projects_list($project); if (!@list) { die_error(404, "No forks found"); } git_header_html(); git_print_page_nav('',''); git_print_header_div('summary', "$project forks"); git_project_list_body(\@list, $order); git_footer_html(); } sub git_project_index { my @projects = git_get_projects_list($project); print $cgi->header( -type => 'text/plain', -charset => 'utf-8', -content_disposition => 'inline; filename="index.aux"'); foreach my $pr (@projects) { if (!exists $pr->{'owner'}) { $pr->{'owner'} = git_get_project_owner("$pr->{'path'}"); } my ($path, $owner) = ($pr->{'path'}, $pr->{'owner'}); # quote as in CGI::Util::encode, but keep the slash, and use '+' for ' ' $path =~ s/([^a-zA-Z0-9_.\-\/ ])/sprintf("%%%02X", ord($1))/eg; $owner =~ s/([^a-zA-Z0-9_.\-\/ ])/sprintf("%%%02X", ord($1))/eg; $path =~ s/ /\+/g; $owner =~ s/ /\+/g; print "$path $owner\n"; } } sub git_summary { my $descr = git_get_project_description($project) || "none"; my %co = parse_commit("HEAD"); my %cd = %co ? parse_date($co{'committer_epoch'}, $co{'committer_tz'}) : (); my $head = $co{'id'}; my $owner = git_get_project_owner($project); my $refs = git_get_references(); # These get_*_list functions return one more to allow us to see if # there are more ... my @taglist = git_get_tags_list(16); my @headlist = git_get_heads_list(16); my @forklist; my $check_forks = gitweb_check_feature('forks'); if ($check_forks) { @forklist = git_get_projects_list($project); } git_header_html(); git_print_page_nav('summary','', $head); print "
     
    \n"; print "\n" . "\n" . "\n"; if (defined $cd{'rfc2822'}) { print "\n"; } # use per project git URL list in $projectroot/$project/cloneurl # or make project git URL from git base URL and project name my $url_tag = "URL"; my @url_list = git_get_project_url_list($project); @url_list = map { "$_/$project" } @git_base_url_list unless @url_list; foreach my $git_url (@url_list) { next unless $git_url; print "\n"; $url_tag = ""; } # Tag cloud my $show_ctags = gitweb_check_feature('ctags'); if ($show_ctags) { my $ctags = git_get_project_ctags($project); my $cloud = git_populate_project_tagcloud($ctags); print "\n\n"; } print "
    description" . esc_html($descr) . "
    owner" . esc_html($owner) . "
    last change$cd{'rfc2822'}
    $url_tag$git_url
    Content tags:
    "; print "    		" unless %$ctags; print "
    Add:
    "; print "    		" if %$ctags; print git_show_project_tagcloud($cloud, 48); print "
    \n"; # If XSS prevention is on, we don't include README.html. # TODO: Allow a readme in some safe format. if (!$prevent_xss && -s "$projectroot/$project/README.html") { print "
    readme
    \n" . "
    \n"; insert_file("$projectroot/$project/README.html"); print "\n
    \n"; # class="readme" } # we need to request one more than 16 (0..15) to check if # those 16 are all my @commitlist = $head ? parse_commits($head, 17) : (); if (@commitlist) { git_print_header_div('shortlog'); git_shortlog_body(\@commitlist, 0, 15, $refs, $#commitlist <= 15 ? undef : $cgi->a({-href => href(action=>"shortlog")}, "...")); } if (@taglist) { git_print_header_div('tags'); git_tags_body(\@taglist, 0, 15, $#taglist <= 15 ? undef : $cgi->a({-href => href(action=>"tags")}, "...")); } if (@headlist) { git_print_header_div('heads'); git_heads_body(\@headlist, $head, 0, 15, $#headlist <= 15 ? undef : $cgi->a({-href => href(action=>"heads")}, "...")); } if (@forklist) { git_print_header_div('forks'); git_project_list_body(\@forklist, 'age', 0, 15, $#forklist <= 15 ? undef : $cgi->a({-href => href(action=>"forks")}, "..."), 'no_header'); } git_footer_html(); } sub git_tag { my $head = git_get_head_hash($project); git_header_html(); git_print_page_nav('','', $head,undef,$head); my %tag = parse_tag($hash); if (! %tag) { die_error(404, "Unknown tag object"); } git_print_header_div('commit', esc_html($tag{'name'}), $hash); print "
    \n" . "\n" . "\n" . "\n" . "\n" . "\n" . "\n"; if (defined($tag{'author'})) { git_print_authorship_rows(\%tag, 'author'); } print "
    object" . $cgi->a({-class => "list", -href => href(action=>$tag{'type'}, hash=>$tag{'object'})}, $tag{'object'}) . "" . $cgi->a({-href => href(action=>$tag{'type'}, hash=>$tag{'object'})}, $tag{'type'}) . "
    \n\n" . "
    \n"; print "
    "; my $comment = $tag{'comment'}; foreach my $line (@$comment) { chomp $line; print esc_html($line, -nbsp=>1) . "
    \n"; } print "
    \n"; git_footer_html(); } sub git_blame_common { my $format = shift || 'porcelain'; if ($format eq 'porcelain' && $cgi->param('js')) { $format = 'incremental'; $action = 'blame_incremental'; # for page title etc } # permissions gitweb_check_feature('blame') or die_error(403, "Blame view not allowed"); # error checking die_error(400, "No file name given") unless $file_name; $hash_base ||= git_get_head_hash($project); die_error(404, "Couldn't find base commit") unless $hash_base; my %co = parse_commit($hash_base) or die_error(404, "Commit not found"); my $ftype = "blob"; if (!defined $hash) { $hash = git_get_hash_by_path($hash_base, $file_name, "blob") or die_error(404, "Error looking up file"); } else { $ftype = git_get_type($hash); if ($ftype !~ "blob") { die_error(400, "Object is not a blob"); } } my $fd; if ($format eq 'incremental') { # get file contents (as base) open $fd, "-|", git_cmd(), 'cat-file', 'blob', $hash or die_error(500, "Open git-cat-file failed"); } elsif ($format eq 'data') { # run git-blame --incremental open $fd, "-|", git_cmd(), "blame", "--incremental", $hash_base, "--", $file_name or die_error(500, "Open git-blame --incremental failed"); } else { # run git-blame --porcelain open $fd, "-|", git_cmd(), "blame", '-p', $hash_base, '--', $file_name or die_error(500, "Open git-blame --porcelain failed"); } # incremental blame data returns early if ($format eq 'data') { print $cgi->header( -type=>"text/plain", -charset => "utf-8", -status=> "200 OK"); local $| = 1; # output autoflush print while <$fd>; close $fd or print "ERROR $!\n"; print 'END'; if (defined $t0 && gitweb_check_feature('timed')) { print ' '. Time::HiRes::tv_interval($t0, [Time::HiRes::gettimeofday()]). ' '.$number_of_git_cmds; } print "\n"; return; } # page header git_header_html(); my $formats_nav = $cgi->a({-href => href(action=>"blob", -replay=>1)}, "blob") . " | "; if ($format eq 'incremental') { $formats_nav .= $cgi->a({-href => href(action=>"blame", javascript=>0, -replay=>1)}, "blame") . " (non-incremental)"; } else { $formats_nav .= $cgi->a({-href => href(action=>"blame_incremental", -replay=>1)}, "blame") . " (incremental)"; } $formats_nav .= " | " . $cgi->a({-href => href(action=>"history", -replay=>1)}, "history") . " | " . $cgi->a({-href => href(action=>$action, file_name=>$file_name)}, "HEAD"); git_print_page_nav('','', $hash_base,$co{'tree'},$hash_base, $formats_nav); git_print_header_div('commit', esc_html($co{'title'}), $hash_base); git_print_page_path($file_name, $ftype, $hash_base); # page body if ($format eq 'incremental') { print "\n"; print qq!
    \n!; } print qq!
    \n!; print qq!
    ... / ...
    \n! if ($format eq 'incremental'); print qq!\n!. #qq!\n!. qq!\n!. qq!\n!. qq!\n!. qq!\n!; my @rev_color = qw(light dark); my $num_colors = scalar(@rev_color); my $current_color = 0; if ($format eq 'incremental') { my $color_class = $rev_color[$current_color]; #contents of a file my $linenr = 0; LINE: while (my $line = <$fd>) { chomp $line; $linenr++; print qq!!. qq!!. qq!!; print qq!\n"; print qq!\n!; } } else { # porcelain, i.e. ordinary blame my %metainfo = (); # saves information about commits # blame data LINE: while (my $line = <$fd>) { chomp $line; # the header: [] # no for subsequent lines in group of lines my ($full_rev, $orig_lineno, $lineno, $group_size) = ($line =~ /^([0-9a-f]{40}) (\d+) (\d+)(?: (\d+))?$/); if (!exists $metainfo{$full_rev}) { $metainfo{$full_rev} = { 'nprevious' => 0 }; } my $meta = $metainfo{$full_rev}; my $data; while ($data = <$fd>) { chomp $data; last if ($data =~ s/^\t//); # contents of line if ($data =~ /^(\S+)(?: (.*))?$/) { $meta->{$1} = $2 unless exists $meta->{$1}; } if ($data =~ /^previous /) { $meta->{'nprevious'}++; } } my $short_rev = substr($full_rev, 0, 8); my $author = $meta->{'author'}; my %date = parse_date($meta->{'author-time'}, $meta->{'author-tz'}); my $date = $date{'iso-tz'}; if ($group_size) { $current_color = ($current_color + 1) % $num_colors; } my $tr_class = $rev_color[$current_color]; $tr_class .= ' boundary' if (exists $meta->{'boundary'}); $tr_class .= ' no-previous' if ($meta->{'nprevious'} == 0); $tr_class .= ' multiple-previous' if ($meta->{'nprevious'} > 1); print "\n"; if ($group_size) { print "\n"; } # 'previous' if (exists $meta->{'previous'} && $meta->{'previous'} =~ /^([a-fA-F0-9]{40}) (.*)$/) { $meta->{'parent'} = $1; $meta->{'file_parent'} = unquote($2); } my $linenr_commit = exists($meta->{'parent'}) ? $meta->{'parent'} : $full_rev; my $linenr_filename = exists($meta->{'file_parent'}) ? $meta->{'file_parent'} : unquote($meta->{'filename'}); my $blamed = href(action => 'blame', file_name => $linenr_filename, hash_base => $linenr_commit); print ""; print "\n"; print "\n"; } # end while } # footer print "\n". "
    CommitLineData
    !. qq!$linenr! . esc_html($line) . "
    1); print ">"; print $cgi->a({-href => href(action=>"commit", hash=>$full_rev, file_name=>$file_name)}, esc_html($short_rev)); if ($group_size >= 2) { my @author_initials = ($author =~ /\b([[:upper:]])\B/g); if (@author_initials) { print "
    " . esc_html(join('', @author_initials)); # or join('.', ...) } } print "    		"; print $cgi->a({ -href => "$blamed#l$orig_lineno", -class => "linenr" }, esc_html($lineno)); print "" . esc_html($data) . "
    \n"; # class="blame" print "
    \n"; # class="blame_body" close $fd or print "Reading blob failed\n"; git_footer_html(); } sub git_blame { git_blame_common(); } sub git_blame_incremental { git_blame_common('incremental'); } sub git_blame_data { git_blame_common('data'); } sub git_tags { my $head = git_get_head_hash($project); git_header_html(); git_print_page_nav('','', $head,undef,$head); git_print_header_div('summary', $project); my @tagslist = git_get_tags_list(); if (@tagslist) { git_tags_body(\@tagslist); } git_footer_html(); } sub git_heads { my $head = git_get_head_hash($project); git_header_html(); git_print_page_nav('','', $head,undef,$head); git_print_header_div('summary', $project); my @headslist = git_get_heads_list(); if (@headslist) { git_heads_body(\@headslist, $head); } git_footer_html(); } sub git_blob_plain { my $type = shift; my $expires; if (!defined $hash) { if (defined $file_name) { my $base = $hash_base || git_get_head_hash($project); $hash = git_get_hash_by_path($base, $file_name, "blob") or die_error(404, "Cannot find file"); } else { die_error(400, "No file name defined"); } } elsif ($hash =~ m/^[0-9a-fA-F]{40}$/) { # blobs defined by non-textual hash id's can be cached $expires = "+1d"; } open my $fd, "-|", git_cmd(), "cat-file", "blob", $hash or die_error(500, "Open git-cat-file blob '$hash' failed"); # content-type (can include charset) $type = blob_contenttype($fd, $file_name, $type); # "save as" filename, even when no $file_name is given my $save_as = "$hash"; if (defined $file_name) { $save_as = $file_name; } elsif ($type =~ m/^text\//) { $save_as .= '.txt'; } # With XSS prevention on, blobs of all types except a few known safe # ones are served with "Content-Disposition: attachment" to make sure # they don't run in our security domain. For certain image types, # blob view writes an tag referring to blob_plain view, and we # want to be sure not to break that by serving the image as an # attachment (though Firefox 3 doesn't seem to care). my $sandbox = $prevent_xss && $type !~ m!^(?:text/plain|image/(?:gif|png|jpeg))$!; print $cgi->header( -type => $type, -expires => $expires, -content_disposition => ($sandbox ? 'attachment' : 'inline') . '; filename="' . $save_as . '"'); local $/ = undef; binmode STDOUT, ':raw'; print <$fd>; binmode STDOUT, ':utf8'; # as set at the beginning of gitweb.cgi close $fd; } sub git_blob { my $expires; if (!defined $hash) { if (defined $file_name) { my $base = $hash_base || git_get_head_hash($project); $hash = git_get_hash_by_path($base, $file_name, "blob") or die_error(404, "Cannot find file"); } else { die_error(400, "No file name defined"); } } elsif ($hash =~ m/^[0-9a-fA-F]{40}$/) { # blobs defined by non-textual hash id's can be cached $expires = "+1d"; } my $have_blame = gitweb_check_feature('blame'); open my $fd, "-|", git_cmd(), "cat-file", "blob", $hash or die_error(500, "Couldn't cat $file_name, $hash"); my $mimetype = blob_mimetype($fd, $file_name); if ($mimetype !~ m!^(?:text/|image/(?:gif|png|jpeg)$)! && -B $fd) { close $fd; return git_blob_plain($mimetype); } # we can have blame only for text/* mimetype $have_blame &&= ($mimetype =~ m!^text/!); git_header_html(undef, $expires); my $formats_nav = ''; if (defined $hash_base && (my %co = parse_commit($hash_base))) { if (defined $file_name) { if ($have_blame) { $formats_nav .= $cgi->a({-href => href(action=>"blame", -replay=>1)}, "blame") . " | "; } $formats_nav .= $cgi->a({-href => href(action=>"history", -replay=>1)}, "history") . " | " . $cgi->a({-href => href(action=>"blob_plain", -replay=>1)}, "raw") . " | " . $cgi->a({-href => href(action=>"blob", hash_base=>"HEAD", file_name=>$file_name)}, "HEAD"); } else { $formats_nav .= $cgi->a({-href => href(action=>"blob_plain", -replay=>1)}, "raw"); } git_print_page_nav('','', $hash_base,$co{'tree'},$hash_base, $formats_nav); git_print_header_div('commit', esc_html($co{'title'}), $hash_base); } else { print "
    \n" . "

    \n" . "
    $hash
    \n"; } git_print_page_path($file_name, "blob", $hash_base); print "
    \n"; if ($mimetype =~ m!^image/!) { print qq!$file_name$hash, hash_base=>$hash_base, file_name=>$file_name) . qq!" />\n!; } else { my $nr; while (my $line = <$fd>) { chomp $line; $nr++; $line = untabify($line); printf "
    1) . "#l%i\" class=\"linenr\">%4i %s
    \n", $nr, $nr, $nr, esc_html($line, -nbsp=>1); } } close $fd or print "Reading blob failed.\n"; print "
    "; git_footer_html(); } sub git_tree { if (!defined $hash_base) { $hash_base = "HEAD"; } if (!defined $hash) { if (defined $file_name) { $hash = git_get_hash_by_path($hash_base, $file_name, "tree"); } else { $hash = $hash_base; } } die_error(404, "No such tree") unless defined($hash); my $show_sizes = gitweb_check_feature('show-sizes'); my $have_blame = gitweb_check_feature('blame'); my @entries = (); { local $/ = "\0"; open my $fd, "-|", git_cmd(), "ls-tree", '-z', ($show_sizes ? '-l' : ()), @extra_options, $hash or die_error(500, "Open git-ls-tree failed"); @entries = map { chomp; $_ } <$fd>; close $fd or die_error(404, "Reading tree failed"); } my $refs = git_get_references(); my $ref = format_ref_marker($refs, $hash_base); git_header_html(); my $basedir = ''; if (defined $hash_base && (my %co = parse_commit($hash_base))) { my @views_nav = (); if (defined $file_name) { push @views_nav, $cgi->a({-href => href(action=>"history", -replay=>1)}, "history"), $cgi->a({-href => href(action=>"tree", hash_base=>"HEAD", file_name=>$file_name)}, "HEAD"), } my $snapshot_links = format_snapshot_links($hash); if (defined $snapshot_links) { # FIXME: Should be available when we have no hash base as well. push @views_nav, $snapshot_links; } git_print_page_nav('tree','', $hash_base, undef, undef, join(' | ', @views_nav)); git_print_header_div('commit', esc_html($co{'title'}) . $ref, $hash_base); } else { undef $hash_base; print "
    \n"; print "

    \n"; print "
    $hash
    \n"; } if (defined $file_name) { $basedir = $file_name; if ($basedir ne '' && substr($basedir, -1) ne '/') { $basedir .= '/'; } git_print_page_path($file_name, 'tree', $hash_base); } print "
    \n"; print "\n"; my $alternate = 1; # '..' (top directory) link if possible if (defined $hash_base && defined $file_name && $file_name =~ m![^/]+$!) { if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; my $up = $file_name; $up =~ s!/?[^/]+$!!; undef $up unless $up; # based on git_print_tree_entry print '\n"; print ''."\n" if $show_sizes; print '\n"; print "\n"; print "\n"; } foreach my $line (@entries) { my %t = parse_ls_tree_line($line, -z => 1, -l => $show_sizes); if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; git_print_tree_entry(\%t, $basedir, $hash_base, $have_blame); print "\n"; } print "
    ' . mode_str('040000') . " '; print $cgi->a({-href => href(action=>"tree", hash_base=>$hash_base, file_name=>$up)}, ".."); print "
    \n" . "
    "; git_footer_html(); } sub snapshot_name { my ($project, $hash) = @_; # path/to/project.git -> project # path/to/project/.git -> project my $name = to_utf8($project); $name =~ s,([^/])/*\.git$,$1,; $name = basename($name); # sanitize name $name =~ s/[[:cntrl:]]/?/g; my $ver = $hash; if ($hash =~ /^[0-9a-fA-F]+$/) { # shorten SHA-1 hash my $full_hash = git_get_full_hash($project, $hash); if ($full_hash =~ /^$hash/ && length($hash) > 7) { $ver = git_get_short_hash($project, $hash); } } elsif ($hash =~ m!^refs/tags/(.*)$!) { # tags don't need shortened SHA-1 hash $ver = $1; } else { # branches and other need shortened SHA-1 hash if ($hash =~ m!^refs/(?:heads|remotes)/(.*)$!) { $ver = $1; } $ver .= '-' . git_get_short_hash($project, $hash); } # in case of hierarchical branch names $ver =~ s!/!.!g; # name = project-version_string $name = "$name-$ver"; return wantarray ? ($name, $name) : $name; } sub git_snapshot { my $format = $input_params{'snapshot_format'}; if (!@snapshot_fmts) { die_error(403, "Snapshots not allowed"); } # default to first supported snapshot format $format ||= $snapshot_fmts[0]; if ($format !~ m/^[a-z0-9]+$/) { die_error(400, "Invalid snapshot format parameter"); } elsif (!exists($known_snapshot_formats{$format})) { die_error(400, "Unknown snapshot format"); } elsif ($known_snapshot_formats{$format}{'disabled'}) { die_error(403, "Snapshot format not allowed"); } elsif (!grep($_ eq $format, @snapshot_fmts)) { die_error(403, "Unsupported snapshot format"); } my $type = git_get_type("$hash^{}"); if (!$type) { die_error(404, 'Object does not exist'); } elsif ($type eq 'blob') { die_error(400, 'Object is not a tree-ish'); } my ($name, $prefix) = snapshot_name($project, $hash); my $filename = "$name$known_snapshot_formats{$format}{'suffix'}"; my $cmd = quote_command( git_cmd(), 'archive', "--format=$known_snapshot_formats{$format}{'format'}", "--prefix=$prefix/", $hash); if (exists $known_snapshot_formats{$format}{'compressor'}) { $cmd .= ' | ' . quote_command(@{$known_snapshot_formats{$format}{'compressor'}}); } $filename =~ s/(["\\])/\\$1/g; print $cgi->header( -type => $known_snapshot_formats{$format}{'type'}, -content_disposition => 'inline; filename="' . $filename . '"', -status => '200 OK'); open my $fd, "-|", $cmd or die_error(500, "Execute git-archive failed"); binmode STDOUT, ':raw'; print <$fd>; binmode STDOUT, ':utf8'; # as set at the beginning of gitweb.cgi close $fd; } sub git_log_generic { my ($fmt_name, $body_subr, $base, $parent, $file_name, $file_hash) = @_; my $head = git_get_head_hash($project); if (!defined $base) { $base = $head; } if (!defined $page) { $page = 0; } my $refs = git_get_references(); my $commit_hash = $base; if (defined $parent) { $commit_hash = "$parent..$base"; } my @commitlist = parse_commits($commit_hash, 101, (100 * $page), defined $file_name ? ($file_name, "--full-history") : ()); my $ftype; if (!defined $file_hash && defined $file_name) { # some commits could have deleted file in question, # and not have it in tree, but one of them has to have it for (my $i = 0; $i < @commitlist; $i++) { $file_hash = git_get_hash_by_path($commitlist[$i]{'id'}, $file_name); last if defined $file_hash; } } if (defined $file_hash) { $ftype = git_get_type($file_hash); } if (defined $file_name && !defined $ftype) { die_error(500, "Unknown type of object"); } my %co; if (defined $file_name) { %co = parse_commit($base) or die_error(404, "Unknown commit object"); } my $paging_nav = format_paging_nav($fmt_name, $page, $#commitlist >= 100); my $next_link = ''; if ($#commitlist >= 100) { $next_link = $cgi->a({-href => href(-replay=>1, page=>$page+1), -accesskey => "n", -title => "Alt-n"}, "next"); } my $patch_max = gitweb_get_feature('patches'); if ($patch_max && !defined $file_name) { if ($patch_max < 0 || @commitlist <= $patch_max) { $paging_nav .= " ⋅ " . $cgi->a({-href => href(action=>"patches", -replay=>1)}, "patches"); } } git_header_html(); git_print_page_nav($fmt_name,'', $hash,$hash,$hash, $paging_nav); if (defined $file_name) { git_print_header_div('commit', esc_html($co{'title'}), $base); } else { git_print_header_div('summary', $project) } git_print_page_path($file_name, $ftype, $hash_base) if (defined $file_name); $body_subr->(\@commitlist, 0, 99, $refs, $next_link, $file_name, $file_hash, $ftype); git_footer_html(); } sub git_log { git_log_generic('log', \&git_log_body, $hash, $hash_parent); } sub git_commit { $hash ||= $hash_base || "HEAD"; my %co = parse_commit($hash) or die_error(404, "Unknown commit object"); my $parent = $co{'parent'}; my $parents = $co{'parents'}; # listref # we need to prepare $formats_nav before any parameter munging my $formats_nav; if (!defined $parent) { # --root commitdiff $formats_nav .= '(initial)'; } elsif (@$parents == 1) { # single parent commit $formats_nav .= '(parent: ' . $cgi->a({-href => href(action=>"commit", hash=>$parent)}, esc_html(substr($parent, 0, 7))) . ')'; } else { # merge commit $formats_nav .= '(merge: ' . join(' ', map { $cgi->a({-href => href(action=>"commit", hash=>$_)}, esc_html(substr($_, 0, 7))); } @$parents ) . ')'; } if (gitweb_check_feature('patches') && @$parents <= 1) { $formats_nav .= " | " . $cgi->a({-href => href(action=>"patch", -replay=>1)}, "patch"); } if (!defined $parent) { $parent = "--root"; } my @difftree; open my $fd, "-|", git_cmd(), "diff-tree", '-r', "--no-commit-id", @diff_opts, (@$parents <= 1 ? $parent : '-c'), $hash, "--" or die_error(500, "Open git-diff-tree failed"); @difftree = map { chomp; $_ } <$fd>; close $fd or die_error(404, "Reading git-diff-tree failed"); # non-textual hash id's can be cached my $expires; if ($hash =~ m/^[0-9a-fA-F]{40}$/) { $expires = "+1d"; } my $refs = git_get_references(); my $ref = format_ref_marker($refs, $co{'id'}); git_header_html(undef, $expires); git_print_page_nav('commit', '', $hash, $co{'tree'}, $hash, $formats_nav); if (defined $co{'parent'}) { git_print_header_div('commitdiff', esc_html($co{'title'}) . $ref, $hash); } else { git_print_header_div('tree', esc_html($co{'title'}) . $ref, $co{'tree'}, $hash); } print "
    \n" . "\n"; git_print_authorship_rows(\%co); print "\n"; print "" . "" . "" . "" . "\n"; foreach my $par (@$parents) { print "" . "" . "" . "" . "\n"; } print "
    commit$co{'id'}
    tree" . $cgi->a({-href => href(action=>"tree", hash=>$co{'tree'}, hash_base=>$hash), class => "list"}, $co{'tree'}) . "" . $cgi->a({-href => href(action=>"tree", hash=>$co{'tree'}, hash_base=>$hash)}, "tree"); my $snapshot_links = format_snapshot_links($hash); if (defined $snapshot_links) { print " | " . $snapshot_links; } print "
    parent" . $cgi->a({-href => href(action=>"commit", hash=>$par), class => "list"}, $par) . "" . $cgi->a({-href => href(action=>"commit", hash=>$par)}, "commit") . " | " . $cgi->a({-href => href(action=>"commitdiff", hash=>$hash, hash_parent=>$par)}, "diff") . "
    ". "
    \n"; print "
    \n"; git_print_log($co{'comment'}); print "
    \n"; git_difftree_body(\@difftree, $hash, @$parents); git_footer_html(); } sub git_object { # object is defined by: # - hash or hash_base alone # - hash_base and file_name my $type; # - hash or hash_base alone if ($hash || ($hash_base && !defined $file_name)) { my $object_id = $hash || $hash_base; open my $fd, "-|", quote_command( git_cmd(), 'cat-file', '-t', $object_id) . ' 2> /dev/null' or die_error(404, "Object does not exist"); $type = <$fd>; chomp $type; close $fd or die_error(404, "Object does not exist"); # - hash_base and file_name } elsif ($hash_base && defined $file_name) { $file_name =~ s,/+$,,; system(git_cmd(), "cat-file", '-e', $hash_base) == 0 or die_error(404, "Base object does not exist"); # here errors should not hapen open my $fd, "-|", git_cmd(), "ls-tree", $hash_base, "--", $file_name or die_error(500, "Open git-ls-tree failed"); my $line = <$fd>; close $fd; #'100644 blob 0fa3f3a66fb6a137f6ec2c19351ed4d807070ffa panic.c' unless ($line && $line =~ m/^([0-9]+) (.+) ([0-9a-fA-F]{40})\t/) { die_error(404, "File or directory for given base does not exist"); } $type = $2; $hash = $3; } else { die_error(400, "Not enough information to find object"); } print $cgi->redirect(-uri => href(action=>$type, -full=>1, hash=>$hash, hash_base=>$hash_base, file_name=>$file_name), -status => '302 Found'); } sub git_blobdiff { my $format = shift || 'html'; my $fd; my @difftree; my %diffinfo; my $expires; # preparing $fd and %diffinfo for git_patchset_body # new style URI if (defined $hash_base && defined $hash_parent_base) { if (defined $file_name) { # read raw output open $fd, "-|", git_cmd(), "diff-tree", '-r', @diff_opts, $hash_parent_base, $hash_base, "--", (defined $file_parent ? $file_parent : ()), $file_name or die_error(500, "Open git-diff-tree failed"); @difftree = map { chomp; $_ } <$fd>; close $fd or die_error(404, "Reading git-diff-tree failed"); @difftree or die_error(404, "Blob diff not found"); } elsif (defined $hash && $hash =~ /[0-9a-fA-F]{40}/) { # try to find filename from $hash # read filtered raw output open $fd, "-|", git_cmd(), "diff-tree", '-r', @diff_opts, $hash_parent_base, $hash_base, "--" or die_error(500, "Open git-diff-tree failed"); @difftree = # ':100644 100644 03b21826... 3b93d5e7... M ls-files.c' # $hash == to_id grep { /^:[0-7]{6} [0-7]{6} [0-9a-fA-F]{40} $hash/ } map { chomp; $_ } <$fd>; close $fd or die_error(404, "Reading git-diff-tree failed"); @difftree or die_error(404, "Blob diff not found"); } else { die_error(400, "Missing one of the blob diff parameters"); } if (@difftree > 1) { die_error(400, "Ambiguous blob diff specification"); } %diffinfo = parse_difftree_raw_line($difftree[0]); $file_parent ||= $diffinfo{'from_file'} || $file_name; $file_name ||= $diffinfo{'to_file'}; $hash_parent ||= $diffinfo{'from_id'}; $hash ||= $diffinfo{'to_id'}; # non-textual hash id's can be cached if ($hash_base =~ m/^[0-9a-fA-F]{40}$/ && $hash_parent_base =~ m/^[0-9a-fA-F]{40}$/) { $expires = '+1d'; } # open patch output open $fd, "-|", git_cmd(), "diff-tree", '-r', @diff_opts, '-p', ($format eq 'html' ? "--full-index" : ()), $hash_parent_base, $hash_base, "--", (defined $file_parent ? $file_parent : ()), $file_name or die_error(500, "Open git-diff-tree failed"); } # old/legacy style URI -- not generated anymore since 1.4.3. if (!%diffinfo) { die_error('404 Not Found', "Missing one of the blob diff parameters") } # header if ($format eq 'html') { my $formats_nav = $cgi->a({-href => href(action=>"blobdiff_plain", -replay=>1)}, "raw"); git_header_html(undef, $expires); if (defined $hash_base && (my %co = parse_commit($hash_base))) { git_print_page_nav('','', $hash_base,$co{'tree'},$hash_base, $formats_nav); git_print_header_div('commit', esc_html($co{'title'}), $hash_base); } else { print "

    $formats_nav
    \n"; print "
    $hash vs $hash_parent
    \n"; } if (defined $file_name) { git_print_page_path($file_name, "blob", $hash_base); } else { print "
    \n"; } } elsif ($format eq 'plain') { print $cgi->header( -type => 'text/plain', -charset => 'utf-8', -expires => $expires, -content_disposition => 'inline; filename="' . "$file_name" . '.patch"'); print "X-Git-Url: " . $cgi->self_url() . "\n\n"; } else { die_error(400, "Unknown blobdiff format"); } # patch if ($format eq 'html') { print "
    \n"; git_patchset_body($fd, [ \%diffinfo ], $hash_base, $hash_parent_base); close $fd; print "
    \n"; # class="page_body" git_footer_html(); } else { while (my $line = <$fd>) { $line =~ s!a/($hash|$hash_parent)!'a/'.esc_path($diffinfo{'from_file'})!eg; $line =~ s!b/($hash|$hash_parent)!'b/'.esc_path($diffinfo{'to_file'})!eg; print $line; last if $line =~ m!^\+\+\+!; } local $/ = undef; print <$fd>; close $fd; } } sub git_blobdiff_plain { git_blobdiff('plain'); } sub git_commitdiff { my %params = @_; my $format = $params{-format} || 'html'; my ($patch_max) = gitweb_get_feature('patches'); if ($format eq 'patch') { die_error(403, "Patch view not allowed") unless $patch_max; } $hash ||= $hash_base || "HEAD"; my %co = parse_commit($hash) or die_error(404, "Unknown commit object"); # choose format for commitdiff for merge if (! defined $hash_parent && @{$co{'parents'}} > 1) { $hash_parent = '--cc'; } # we need to prepare $formats_nav before almost any parameter munging my $formats_nav; if ($format eq 'html') { $formats_nav = $cgi->a({-href => href(action=>"commitdiff_plain", -replay=>1)}, "raw"); if ($patch_max && @{$co{'parents'}} <= 1) { $formats_nav .= " | " . $cgi->a({-href => href(action=>"patch", -replay=>1)}, "patch"); } if (defined $hash_parent && $hash_parent ne '-c' && $hash_parent ne '--cc') { # commitdiff with two commits given my $hash_parent_short = $hash_parent; if ($hash_parent =~ m/^[0-9a-fA-F]{40}$/) { $hash_parent_short = substr($hash_parent, 0, 7); } $formats_nav .= ' (from'; for (my $i = 0; $i < @{$co{'parents'}}; $i++) { if ($co{'parents'}[$i] eq $hash_parent) { $formats_nav .= ' parent ' . ($i+1); last; } } $formats_nav .= ': ' . $cgi->a({-href => href(action=>"commitdiff", hash=>$hash_parent)}, esc_html($hash_parent_short)) . ')'; } elsif (!$co{'parent'}) { # --root commitdiff $formats_nav .= ' (initial)'; } elsif (scalar @{$co{'parents'}} == 1) { # single parent commit $formats_nav .= ' (parent: ' . $cgi->a({-href => href(action=>"commitdiff", hash=>$co{'parent'})}, esc_html(substr($co{'parent'}, 0, 7))) . ')'; } else { # merge commit if ($hash_parent eq '--cc') { $formats_nav .= ' | ' . $cgi->a({-href => href(action=>"commitdiff", hash=>$hash, hash_parent=>'-c')}, 'combined'); } else { # $hash_parent eq '-c' $formats_nav .= ' | ' . $cgi->a({-href => href(action=>"commitdiff", hash=>$hash, hash_parent=>'--cc')}, 'compact'); } $formats_nav .= ' (merge: ' . join(' ', map { $cgi->a({-href => href(action=>"commitdiff", hash=>$_)}, esc_html(substr($_, 0, 7))); } @{$co{'parents'}} ) . ')'; } } my $hash_parent_param = $hash_parent; if (!defined $hash_parent_param) { # --cc for multiple parents, --root for parentless $hash_parent_param = @{$co{'parents'}} > 1 ? '--cc' : $co{'parent'} || '--root'; } # read commitdiff my $fd; my @difftree; if ($format eq 'html') { open $fd, "-|", git_cmd(), "diff-tree", '-r', @diff_opts, "--no-commit-id", "--patch-with-raw", "--full-index", $hash_parent_param, $hash, "--" or die_error(500, "Open git-diff-tree failed"); while (my $line = <$fd>) { chomp $line; # empty line ends raw part of diff-tree output last unless $line; push @difftree, scalar parse_difftree_raw_line($line); } } elsif ($format eq 'plain') { open $fd, "-|", git_cmd(), "diff-tree", '-r', @diff_opts, '-p', $hash_parent_param, $hash, "--" or die_error(500, "Open git-diff-tree failed"); } elsif ($format eq 'patch') { # For commit ranges, we limit the output to the number of # patches specified in the 'patches' feature. # For single commits, we limit the output to a single patch, # diverging from the git-format-patch default. my @commit_spec = (); if ($hash_parent) { if ($patch_max > 0) { push @commit_spec, "-$patch_max"; } push @commit_spec, '-n', "$hash_parent..$hash"; } else { if ($params{-single}) { push @commit_spec, '-1'; } else { if ($patch_max > 0) { push @commit_spec, "-$patch_max"; } push @commit_spec, "-n"; } push @commit_spec, '--root', $hash; } open $fd, "-|", git_cmd(), "format-patch", '--encoding=utf8', '--stdout', @commit_spec or die_error(500, "Open git-format-patch failed"); } else { die_error(400, "Unknown commitdiff format"); } # non-textual hash id's can be cached my $expires; if ($hash =~ m/^[0-9a-fA-F]{40}$/) { $expires = "+1d"; } # write commit message if ($format eq 'html') { my $refs = git_get_references(); my $ref = format_ref_marker($refs, $co{'id'}); git_header_html(undef, $expires); git_print_page_nav('commitdiff','', $hash,$co{'tree'},$hash, $formats_nav); git_print_header_div('commit', esc_html($co{'title'}) . $ref, $hash); print "
    \n" . "\n"; git_print_authorship_rows(\%co); print "
    ". "
    \n"; print "
    \n"; if (@{$co{'comment'}} > 1) { print "
    \n"; git_print_log($co{'comment'}, -final_empty_line=> 1, -remove_title => 1); print "
    \n"; # class="log" } } elsif ($format eq 'plain') { my $refs = git_get_references("tags"); my $tagname = git_get_rev_name_tags($hash); my $filename = basename($project) . "-$hash.patch"; print $cgi->header( -type => 'text/plain', -charset => 'utf-8', -expires => $expires, -content_disposition => 'inline; filename="' . "$filename" . '"'); my %ad = parse_date($co{'author_epoch'}, $co{'author_tz'}); print "From: " . to_utf8($co{'author'}) . "\n"; print "Date: $ad{'rfc2822'} ($ad{'tz_local'})\n"; print "Subject: " . to_utf8($co{'title'}) . "\n"; print "X-Git-Tag: $tagname\n" if $tagname; print "X-Git-Url: " . $cgi->self_url() . "\n\n"; foreach my $line (@{$co{'comment'}}) { print to_utf8($line) . "\n"; } print "---\n\n"; } elsif ($format eq 'patch') { my $filename = basename($project) . "-$hash.patch"; print $cgi->header( -type => 'text/plain', -charset => 'utf-8', -expires => $expires, -content_disposition => 'inline; filename="' . "$filename" . '"'); } # write patch if ($format eq 'html') { my $use_parents = !defined $hash_parent || $hash_parent eq '-c' || $hash_parent eq '--cc'; git_difftree_body(\@difftree, $hash, $use_parents ? @{$co{'parents'}} : $hash_parent); print "
    \n"; git_patchset_body($fd, \@difftree, $hash, $use_parents ? @{$co{'parents'}} : $hash_parent); close $fd; print "
    \n"; # class="page_body" git_footer_html(); } elsif ($format eq 'plain') { local $/ = undef; print <$fd>; close $fd or print "Reading git-diff-tree failed\n"; } elsif ($format eq 'patch') { local $/ = undef; print <$fd>; close $fd or print "Reading git-format-patch failed\n"; } } sub git_commitdiff_plain { git_commitdiff(-format => 'plain'); } # format-patch-style patches sub git_patch { git_commitdiff(-format => 'patch', -single => 1); } sub git_patches { git_commitdiff(-format => 'patch'); } sub git_history { git_log_generic('history', \&git_history_body, $hash_base, $hash_parent_base, $file_name, $hash); } sub git_search { gitweb_check_feature('search') or die_error(403, "Search is disabled"); if (!defined $searchtext) { die_error(400, "Text field is empty"); } if (!defined $hash) { $hash = git_get_head_hash($project); } my %co = parse_commit($hash); if (!%co) { die_error(404, "Unknown commit object"); } if (!defined $page) { $page = 0; } $searchtype ||= 'commit'; if ($searchtype eq 'pickaxe') { # pickaxe may take all resources of your box and run for several minutes # with every query - so decide by yourself how public you make this feature gitweb_check_feature('pickaxe') or die_error(403, "Pickaxe is disabled"); } if ($searchtype eq 'grep') { gitweb_check_feature('grep') or die_error(403, "Grep is disabled"); } git_header_html(); if ($searchtype eq 'commit' or $searchtype eq 'author' or $searchtype eq 'committer') { my $greptype; if ($searchtype eq 'commit') { $greptype = "--grep="; } elsif ($searchtype eq 'author') { $greptype = "--author="; } elsif ($searchtype eq 'committer') { $greptype = "--committer="; } $greptype .= $searchtext; my @commitlist = parse_commits($hash, 101, (100 * $page), undef, $greptype, '--regexp-ignore-case', $search_use_regexp ? '--extended-regexp' : '--fixed-strings'); my $paging_nav = ''; if ($page > 0) { $paging_nav .= $cgi->a({-href => href(action=>"search", hash=>$hash, searchtext=>$searchtext, searchtype=>$searchtype)}, "first"); $paging_nav .= " ⋅ " . $cgi->a({-href => href(-replay=>1, page=>$page-1), -accesskey => "p", -title => "Alt-p"}, "prev"); } else { $paging_nav .= "first"; $paging_nav .= " ⋅ prev"; } my $next_link = ''; if ($#commitlist >= 100) { $next_link = $cgi->a({-href => href(-replay=>1, page=>$page+1), -accesskey => "n", -title => "Alt-n"}, "next"); $paging_nav .= " ⋅ $next_link"; } else { $paging_nav .= " ⋅ next"; } if ($#commitlist >= 100) { } git_print_page_nav('','', $hash,$co{'tree'},$hash, $paging_nav); git_print_header_div('commit', esc_html($co{'title'}), $hash); git_search_grep_body(\@commitlist, 0, 99, $next_link); } if ($searchtype eq 'pickaxe') { git_print_page_nav('','', $hash,$co{'tree'},$hash); git_print_header_div('commit', esc_html($co{'title'}), $hash); print "\n"; my $alternate = 1; local $/ = "\n"; open my $fd, '-|', git_cmd(), '--no-pager', 'log', @diff_opts, '--pretty=format:%H', '--no-abbrev', '--raw', "-S$searchtext", ($search_use_regexp ? '--pickaxe-regex' : ()); undef %co; my @files; while (my $line = <$fd>) { chomp $line; next unless $line; my %set = parse_difftree_raw_line($line); if (defined $set{'commit'}) { # finish previous commit if (%co) { print "\n" . "\n" . "\n"; } if ($alternate) { print "\n"; } else { print "\n"; } $alternate ^= 1; %co = parse_commit($set{'commit'}); my $author = chop_and_escape_str($co{'author_name'}, 15, 5); print "\n" . "\n" . "\n" . "\n" . "\n"; } print "
    " . $cgi->a({-href => href(action=>"commit", hash=>$co{'id'})}, "commit") . " | " . $cgi->a({-href => href(action=>"tree", hash=>$co{'tree'}, hash_base=>$co{'id'})}, "tree"); print "
    $co{'age_string_date'}$author" . $cgi->a({-href => href(action=>"commit", hash=>$co{'id'}), -class => "list subject"}, chop_and_escape_str($co{'title'}, 50) . "
    "); } elsif (defined $set{'to_id'}) { next if ($set{'to_id'} =~ m/^0{40}$/); print $cgi->a({-href => href(action=>"blob", hash_base=>$co{'id'}, hash=>$set{'to_id'}, file_name=>$set{'to_file'}), -class => "list"}, "" . esc_path($set{'file'}) . "") . "
    \n"; } } close $fd; # finish last commit (warning: repetition!) if (%co) { print "    		" . $cgi->a({-href => href(action=>"commit", hash=>$co{'id'})}, "commit") . " | " . $cgi->a({-href => href(action=>"tree", hash=>$co{'tree'}, hash_base=>$co{'id'})}, "tree"); print "
    \n"; } if ($searchtype eq 'grep') { git_print_page_nav('','', $hash,$co{'tree'},$hash); git_print_header_div('commit', esc_html($co{'title'}), $hash); print "\n"; my $alternate = 1; my $matches = 0; local $/ = "\n"; open my $fd, "-|", git_cmd(), 'grep', '-n', $search_use_regexp ? ('-E', '-i') : '-F', $searchtext, $co{'tree'}; my $lastfile = ''; while (my $line = <$fd>) { chomp $line; my ($file, $lno, $ltext, $binary); last if ($matches++ > 1000); if ($line =~ /^Binary file (.+) matches$/) { $file = $1; $binary = 1; } else { (undef, $file, $lno, $ltext) = split(/:/, $line, 4); } if ($file ne $lastfile) { $lastfile and print "\n"; if ($alternate++) { print "\n"; } else { print "\n"; } print "\n"; if ($matches > 1000) { print "
    Too many matches, listing trimmed
    \n"; } } else { print "
    No matches found
    \n"; } close $fd; print "
    ". $cgi->a({-href => href(action=>"blob", hash=>$co{'hash'}, file_name=>"$file"), -class => "list"}, esc_path($file)); print "\n"; $lastfile = $file; } if ($binary) { print "
    Binary file
    \n"; } else { $ltext = untabify($ltext); if ($ltext =~ m/^(.*)($search_regexp)(.*)$/i) { $ltext = esc_html($1, -nbsp=>1); $ltext .= ''; $ltext .= esc_html($2, -nbsp=>1); $ltext .= ''; $ltext .= esc_html($3, -nbsp=>1); } else { $ltext = esc_html($ltext, -nbsp=>1); } print "
    " . $cgi->a({-href => href(action=>"blob", hash=>$co{'hash'}, file_name=>"$file").'#l'.$lno, -class => "linenr"}, sprintf('%4i', $lno)) . ' ' . $ltext . "
    \n"; } } if ($lastfile) { print "
    \n"; } git_footer_html(); } sub git_search_help { git_header_html(); git_print_page_nav('','', $hash,$hash,$hash); print <Pattern is by default a normal string that is matched precisely (but without regard to case, except in the case of pickaxe). However, when you check the re checkbox, the pattern entered is recognized as the POSIX extended regular expression (also case insensitive).

    commit
    The commit messages and authorship information will be scanned for the given pattern.
    EOT my $have_grep = gitweb_check_feature('grep'); if ($have_grep) { print <grep
    All files in the currently selected tree (HEAD unless you are explicitly browsing a different one) are searched for the given pattern. On large trees, this search can take a while and put some strain on the server, so please use it with some consideration. Note that due to git-grep peculiarity, currently if regexp mode is turned off, the matches are case-sensitive.
    EOT } print <author
    Name and e-mail of the change author and date of birth of the patch will be scanned for the given pattern.
    committer
    Name and e-mail of the committer and date of commit will be scanned for the given pattern.
    EOT my $have_pickaxe = gitweb_check_feature('pickaxe'); if ($have_pickaxe) { print <pickaxe
    All commits that caused the string to appear or disappear from any file (changes that added, removed or "modified" the string) will be listed. This search can take a while and takes a lot of strain on the server, so please use it wisely. Note that since you may be interested even in changes just changing the case as well, this search is case sensitive.
    EOT } print "
    \n"; git_footer_html(); } sub git_shortlog { git_log_generic('shortlog', \&git_shortlog_body, $hash, $hash_parent); } ## ...................................................................... ## feeds (RSS, Atom; OPML) sub git_feed { my $format = shift || 'atom'; my $have_blame = gitweb_check_feature('blame'); # Atom: http://www.atomenabled.org/developers/syndication/ # RSS: http://www.notestips.com/80256B3A007F2692/1/NAMO5P9UPQ if ($format ne 'rss' && $format ne 'atom') { die_error(400, "Unknown web feed format"); } # log/feed of current (HEAD) branch, log of given branch, history of file/directory my $head = $hash || 'HEAD'; my @commitlist = parse_commits($head, 150, 0, $file_name); my %latest_commit; my %latest_date; my $content_type = "application/$format+xml"; if (defined $cgi->http('HTTP_ACCEPT') && $cgi->Accept('text/xml') > $cgi->Accept($content_type)) { # browser (feed reader) prefers text/xml $content_type = 'text/xml'; } if (defined($commitlist[0])) { %latest_commit = %{$commitlist[0]}; my $latest_epoch = $latest_commit{'committer_epoch'}; %latest_date = parse_date($latest_epoch); my $if_modified = $cgi->http('IF_MODIFIED_SINCE'); if (defined $if_modified) { my $since; if (eval { require HTTP::Date; 1; }) { $since = HTTP::Date::str2time($if_modified); } elsif (eval { require Time::ParseDate; 1; }) { $since = Time::ParseDate::parsedate($if_modified, GMT => 1); } if (defined $since && $latest_epoch <= $since) { print $cgi->header( -type => $content_type, -charset => 'utf-8', -last_modified => $latest_date{'rfc2822'}, -status => '304 Not Modified'); return; } } print $cgi->header( -type => $content_type, -charset => 'utf-8', -last_modified => $latest_date{'rfc2822'}); } else { print $cgi->header( -type => $content_type, -charset => 'utf-8'); } # Optimization: skip generating the body if client asks only # for Last-Modified date. return if ($cgi->request_method() eq 'HEAD'); # header variables my $title = "$site_name - $project/$action"; my $feed_type = 'log'; if (defined $hash) { $title .= " - '$hash'"; $feed_type = 'branch log'; if (defined $file_name) { $title .= " :: $file_name"; $feed_type = 'history'; } } elsif (defined $file_name) { $title .= " - $file_name"; $feed_type = 'history'; } $title .= " $feed_type"; my $descr = git_get_project_description($project); if (defined $descr) { $descr = esc_html($descr); } else { $descr = "$project " . ($format eq 'rss' ? 'RSS' : 'Atom') . " feed"; } my $owner = git_get_project_owner($project); $owner = esc_html($owner); #header my $alt_url; if (defined $file_name) { $alt_url = href(-full=>1, action=>"history", hash=>$hash, file_name=>$file_name); } elsif (defined $hash) { $alt_url = href(-full=>1, action=>"log", hash=>$hash); } else { $alt_url = href(-full=>1, action=>"summary"); } print qq!\n!; if ($format eq 'rss') { print < XML print "$title\n" . "$alt_url\n" . "$descr\n" . "en\n" . # project owner is responsible for 'editorial' content "$owner\n"; if (defined $logo || defined $favicon) { # prefer the logo to the favicon, since RSS # doesn't allow both my $img = esc_url($logo || $favicon); print "\n" . "$img\n" . "$title\n" . "$alt_url\n" . "\n"; } if (%latest_date) { print "$latest_date{'rfc2822'}\n"; print "$latest_date{'rfc2822'}\n"; } print "gitweb v.$version/$git_version\n"; } elsif ($format eq 'atom') { print < XML print "$title\n" . "$descr\n" . '' . "\n" . '' . "\n" . "" . href(-full=>1) . "\n" . # use project owner for feed author "$owner\n"; if (defined $favicon) { print "" . esc_url($favicon) . "\n"; } if (defined $logo_url) { # not twice as wide as tall: 72 x 27 pixels print "" . esc_url($logo) . "\n"; } if (! %latest_date) { # dummy date to keep the feed valid until commits trickle in: print "1970-01-01T00:00:00Z\n"; } else { print "$latest_date{'iso-8601'}\n"; } print "gitweb\n"; } # contents for (my $i = 0; $i <= $#commitlist; $i++) { my %co = %{$commitlist[$i]}; my $commit = $co{'id'}; # we read 150, we always show 30 and the ones more recent than 48 hours if (($i >= 20) && ((time - $co{'author_epoch'}) > 48*60*60)) { last; } my %cd = parse_date($co{'author_epoch'}); # get list of changed files open my $fd, "-|", git_cmd(), "diff-tree", '-r', @diff_opts, $co{'parent'} || "--root", $co{'id'}, "--", (defined $file_name ? $file_name : ()) or next; my @difftree = map { chomp; $_ } <$fd>; close $fd or next; # print element (entry, item) my $co_url = href(-full=>1, action=>"commitdiff", hash=>$commit); if ($format eq 'rss') { print "\n" . "" . esc_html($co{'title'}) . "\n" . "" . esc_html($co{'author'}) . "\n" . "$cd{'rfc2822'}\n" . "$co_url\n" . "$co_url\n" . "" . esc_html($co{'title'}) . "\n" . "" . "\n" . "" . esc_html($co{'title'}) . "\n" . "$cd{'iso-8601'}\n" . "\n" . " " . esc_html($co{'author_name'}) . "\n"; if ($co{'author_email'}) { print " " . esc_html($co{'author_email'}) . "\n"; } print "\n" . # use committer for contributor "\n" . " " . esc_html($co{'committer_name'}) . "\n"; if ($co{'committer_email'}) { print " " . esc_html($co{'committer_email'}) . "\n"; } print "\n" . "$cd{'iso-8601'}\n" . "\n" . "$co_url\n" . "\n" . "
    \n"; } my $comment = $co{'comment'}; print "
    \n";
		foreach my $line (@$comment) {
			$line = esc_html($line);
			print "$line\n";
		}
		print "
      \n"; foreach my $difftree_line (@difftree) { my %difftree = parse_difftree_raw_line($difftree_line); next if !$difftree{'from_id'}; my $file = $difftree{'file'} || $difftree{'to_file'}; print "
    • " . "[" . $cgi->a({-href => href(-full=>1, action=>"blobdiff", hash=>$difftree{'to_id'}, hash_parent=>$difftree{'from_id'}, hash_base=>$co{'id'}, hash_parent_base=>$co{'parent'}, file_name=>$file, file_parent=>$difftree{'from_file'}), -title => "diff"}, 'D'); if ($have_blame) { print $cgi->a({-href => href(-full=>1, action=>"blame", file_name=>$file, hash_base=>$commit), -title => "blame"}, 'B'); } # if this is not a feed of a file history if (!defined $file_name || $file_name ne $file) { print $cgi->a({-href => href(-full=>1, action=>"history", file_name=>$file, hash=>$commit), -title => "history"}, 'H'); } $file = esc_path($file); print "] ". "$file
      • \n"; } if ($format eq 'rss') { print "
    ]]>\n" . "\n" . "\n"; } elsif ($format eq 'atom') { print "\n
    \n" . "    \n" . "\n"; } } # end of feed if ($format eq 'rss') { print "    \n\n"; } elsif ($format eq 'atom') { print "\n"; } } sub git_rss { git_feed('rss'); } sub git_atom { git_feed('atom'); } sub git_opml { my @list = git_get_projects_list(); print $cgi->header( -type => 'text/xml', -charset => 'utf-8', -content_disposition => 'inline; filename="opml.xml"'); print < $site_name OPML Export XML foreach my $pr (@list) { my %proj = %$pr; my $head = git_get_head_hash($proj{'path'}); if (!defined $head) { next; } $git_dir = "$projectroot/$proj{'path'}"; my %co = parse_commit($head); if (!%co) { next; } my $path = esc_html(chop_str($proj{'path'}, 25, 5)); my $rss = href('project' => $proj{'path'}, 'action' => 'rss', -full => 1); my $html = href('project' => $proj{'path'}, 'action' => 'summary', -full => 1); print "\n"; } print < XML } genometools-1.5.1/www/genometools.org/htdocs/cgi-bin/gitweb.css000066400000000000000000000202731211610345200246040ustar00rootroot00000000000000body { font-family: sans-serif; font-size: small; border: solid #d9d8d1; border-width: 1px; margin: 10px; background-color: #ffffff; color: #000000; } a { color: #0000cc; } a:hover, a:visited, a:active { color: #880000; } span.cntrl { border: dashed #aaaaaa; border-width: 1px; padding: 0px 2px 0px 2px; margin: 0px 2px 0px 2px; } img.logo { float: right; border-width: 0px; } img.avatar { vertical-align: middle; } a.list img.avatar { border-style: none; } div.page_header { height: 25px; padding: 8px; font-size: 150%; font-weight: bold; background-color: #d9d8d1; } div.page_header a:visited, a.header { color: #0000cc; } div.page_header a:hover { color: #880000; } div.page_nav { padding: 8px; } div.page_nav a:visited { color: #0000cc; } div.page_path { padding: 8px; font-weight: bold; border: solid #d9d8d1; border-width: 0px 0px 1px; } div.page_footer { height: 17px; padding: 4px 8px; background-color: #d9d8d1; } div.page_footer_text { float: left; color: #555555; font-style: italic; } div#generating_info { margin: 4px; font-size: smaller; text-align: center; color: #505050; } div.page_body { padding: 8px; font-family: monospace; } div.title, a.title { display: block; padding: 6px 8px; font-weight: bold; background-color: #edece6; text-decoration: none; color: #000000; } div.readme { padding: 8px; } a.title:hover { background-color: #d9d8d1; } div.title_text { padding: 6px 0px; border: solid #d9d8d1; border-width: 0px 0px 1px; font-family: monospace; } div.log_body { padding: 8px 8px 8px 150px; } span.age { position: relative; float: left; width: 142px; font-style: italic; } span.signoff { color: #888888; } div.log_link { padding: 0px 8px; font-size: 70%; font-family: sans-serif; font-style: normal; position: relative; float: left; width: 136px; } div.list_head { padding: 6px 8px 4px; border: solid #d9d8d1; border-width: 1px 0px 0px; font-style: italic; } .author_date, .author { font-style: italic; } div.author_date { padding: 8px; border: solid #d9d8d1; border-width: 0px 0px 1px 0px; } a.list { text-decoration: none; color: #000000; } a.subject, a.name { font-weight: bold; } table.tags a.subject { font-weight: normal; } a.list:hover { text-decoration: underline; color: #880000; } a.text { text-decoration: none; color: #0000cc; } a.text:visited { text-decoration: none; color: #880000; } a.text:hover { text-decoration: underline; color: #880000; } table { padding: 8px 4px; border-spacing: 0; } table.diff_tree { font-family: monospace; } table.combined.diff_tree th { text-align: center; } table.combined.diff_tree td { padding-right: 24px; } table.combined.diff_tree th.link, table.combined.diff_tree td.link { padding: 0px 2px; } table.combined.diff_tree td.nochange a { color: #6666ff; } table.combined.diff_tree td.nochange a:hover, table.combined.diff_tree td.nochange a:visited { color: #d06666; } table.blame { border-collapse: collapse; } table.blame td { padding: 0px 5px; font-size: 100%; vertical-align: top; } th { padding: 2px 5px; font-size: 100%; text-align: left; } /* do not change row style on hover for 'blame' view */ tr.light, table.blame .light:hover { background-color: #ffffff; } tr.dark, table.blame .dark:hover { background-color: #f6f6f0; } /* currently both use the same, but it can change */ tr.light:hover, tr.dark:hover { background-color: #edece6; } /* boundary commits in 'blame' view */ /* and commits without "previous" */ tr.boundary td.sha1, tr.no-previous td.linenr { font-weight: bold; } /* for 'blame_incremental', during processing */ tr.color1 { background-color: #f6fff6; } tr.color2 { background-color: #f6f6ff; } tr.color3 { background-color: #fff6f6; } td { padding: 2px 5px; font-size: 100%; vertical-align: top; } td.link, td.selflink { padding: 2px 5px; font-family: sans-serif; font-size: 70%; } td.selflink { padding-right: 0px; } td.sha1 { font-family: monospace; } .error { color: red; background-color: yellow; } td.current_head { text-decoration: underline; } table.diff_tree span.file_status.new { color: #008000; } table.diff_tree span.file_status.deleted { color: #c00000; } table.diff_tree span.file_status.moved, table.diff_tree span.file_status.mode_chnge { color: #777777; } table.diff_tree span.file_status.copied { color: #70a070; } /* noage: "No commits" */ table.project_list td.noage { color: #808080; font-style: italic; } /* age2: 60*60*24*2 <= age */ table.project_list td.age2, table.blame td.age2 { font-style: italic; } /* age1: 60*60*2 <= age < 60*60*24*2 */ table.project_list td.age1 { color: #009900; font-style: italic; } table.blame td.age1 { color: #009900; background: transparent; } /* age0: age < 60*60*2 */ table.project_list td.age0 { color: #009900; font-style: italic; font-weight: bold; } table.blame td.age0 { color: #009900; background: transparent; font-weight: bold; } td.pre, div.pre, div.diff { font-family: monospace; font-size: 12px; white-space: pre; } td.mode { font-family: monospace; } /* progress of blame_interactive */ div#progress_bar { height: 2px; margin-bottom: -2px; background-color: #d8d9d0; } div#progress_info { float: right; text-align: right; } /* format of (optional) objects size in 'tree' view */ td.size { font-family: monospace; text-align: right; } /* styling of diffs (patchsets): commitdiff and blobdiff views */ div.diff.header, div.diff.extended_header { white-space: normal; } div.diff.header { font-weight: bold; background-color: #edece6; margin-top: 4px; padding: 4px 0px 2px 0px; border: solid #d9d8d1; border-width: 1px 0px 1px 0px; } div.diff.header a.path { text-decoration: underline; } div.diff.extended_header, div.diff.extended_header a.path, div.diff.extended_header a.hash { color: #777777; } div.diff.extended_header .info { color: #b0b0b0; } div.diff.extended_header { background-color: #f6f5ee; padding: 2px 0px 2px 0px; } div.diff a.list, div.diff a.path, div.diff a.hash { text-decoration: none; } div.diff a.list:hover, div.diff a.path:hover, div.diff a.hash:hover { text-decoration: underline; } div.diff.to_file a.path, div.diff.to_file { color: #007000; } div.diff.add { color: #008800; } div.diff.from_file a.path, div.diff.from_file { color: #aa0000; } div.diff.rem { color: #cc0000; } div.diff.chunk_header a, div.diff.chunk_header { color: #990099; } div.diff.chunk_header { border: dotted #ffe0ff; border-width: 1px 0px 0px 0px; margin-top: 2px; } div.diff.chunk_header span.chunk_info { background-color: #ffeeff; } div.diff.chunk_header span.section { color: #aa22aa; } div.diff.incomplete { color: #cccccc; } div.diff.nodifferences { font-weight: bold; color: #600000; } div.index_include { border: solid #d9d8d1; border-width: 0px 0px 1px; padding: 12px 8px; } div.search { font-size: 100%; font-weight: normal; margin: 4px 8px; float: right; top: 56px; right: 12px } p.projsearch { text-align: center; } td.linenr { text-align: right; } a.linenr { color: #999999; text-decoration: none } a.rss_logo { float: right; padding: 3px 0px; width: 35px; line-height: 10px; border: 1px solid; border-color: #fcc7a5 #7d3302 #3e1a01 #ff954e; color: #ffffff; background-color: #ff6600; font-weight: bold; font-family: sans-serif; font-size: 70%; text-align: center; text-decoration: none; } a.rss_logo:hover { background-color: #ee5500; } a.rss_logo.generic { background-color: #ff8800; } a.rss_logo.generic:hover { background-color: #ee7700; } span.refs span { padding: 0px 4px; font-size: 70%; font-weight: normal; border: 1px solid; background-color: #ffaaff; border-color: #ffccff #ff00ee #ff00ee #ffccff; } span.refs span a { text-decoration: none; color: inherit; } span.refs span a:hover { text-decoration: underline; } span.refs span.indirect { font-style: italic; } span.refs span.ref { background-color: #aaaaff; border-color: #ccccff #0033cc #0033cc #ccccff; } span.refs span.tag { background-color: #ffffaa; border-color: #ffffcc #ffee00 #ffee00 #ffffcc; } span.refs span.head { background-color: #aaffaa; border-color: #ccffcc #00cc33 #00cc33 #ccffcc; } span.atnight { color: #cc0000; } span.match { color: #e00000; } div.binary { font-style: italic; } genometools-1.5.1/www/genometools.org/htdocs/cgi-bin/gitweb.js000066400000000000000000000567641211610345200244460ustar00rootroot00000000000000// Copyright (C) 2007, Fredrik Kuivinen // 2007, Petr Baudis // 2008-2009, Jakub Narebski /** * @fileOverview JavaScript code for gitweb (git web interface). * @license GPLv2 or later */ /* ============================================================ */ /* functions for generic gitweb actions and views */ /** * used to check if link has 'js' query parameter already (at end), * and other reasons to not add 'js=1' param at the end of link * @constant */ var jsExceptionsRe = /[;?]js=[01]$/; /** * Add '?js=1' or ';js=1' to the end of every link in the document * that doesn't have 'js' query parameter set already. * * Links with 'js=1' lead to JavaScript version of given action, if it * exists (currently there is only 'blame_incremental' for 'blame') * * @globals jsExceptionsRe */ function fixLinks() { var allLinks = document.getElementsByTagName("a") || document.links; for (var i = 0, len = allLinks.length; i < len; i++) { var link = allLinks[i]; if (!jsExceptionsRe.test(link)) { // =~ /[;?]js=[01]$/; link.href += (link.href.indexOf('?') === -1 ? '?' : ';') + 'js=1'; } } } /* ============================================================ */ /* * This code uses DOM methods instead of (nonstandard) innerHTML * to modify page. * * innerHTML is non-standard IE extension, though supported by most * browsers; however Firefox up to version 1.5 didn't implement it in * a strict mode (application/xml+xhtml mimetype). * * Also my simple benchmarks show that using elem.firstChild.data = * 'content' is slightly faster than elem.innerHTML = 'content'. It * is however more fragile (text element fragment must exists), and * less feature-rich (we cannot add HTML). * * Note that DOM 2 HTML is preferred over generic DOM 2 Core; the * equivalent using DOM 2 Core is usually shown in comments. */ /* ============================================================ */ /* generic utility functions */ /** * pad number N with nonbreakable spaces on the left, to WIDTH characters * example: padLeftStr(12, 3, '\u00A0') == '\u00A012' * ('\u00A0' is nonbreakable space) * * @param {Number|String} input: number to pad * @param {Number} width: visible width of output * @param {String} str: string to prefix to string, e.g. '\u00A0' * @returns {String} INPUT prefixed with (WIDTH - INPUT.length) x STR */ function padLeftStr(input, width, str) { var prefix = ''; width -= input.toString().length; while (width > 0) { prefix += str; width--; } return prefix + input; } /** * Pad INPUT on the left to SIZE width, using given padding character CH, * for example padLeft('a', 3, '_') is '__a'. * * @param {String} input: input value converted to string. * @param {Number} width: desired length of output. * @param {String} ch: single character to prefix to string. * * @returns {String} Modified string, at least SIZE length. */ function padLeft(input, width, ch) { var s = input + ""; while (s.length < width) { s = ch + s; } return s; } /** * Create XMLHttpRequest object in cross-browser way * @returns XMLHttpRequest object, or null */ function createRequestObject() { try { return new XMLHttpRequest(); } catch (e) {} try { return window.createRequest(); } catch (e) {} try { return new ActiveXObject("Msxml2.XMLHTTP"); } catch (e) {} try { return new ActiveXObject("Microsoft.XMLHTTP"); } catch (e) {} return null; } /* ============================================================ */ /* utility/helper functions (and variables) */ var xhr; // XMLHttpRequest object var projectUrl; // partial query + separator ('?' or ';') // 'commits' is an associative map. It maps SHA1s to Commit objects. var commits = {}; /** * constructor for Commit objects, used in 'blame' * @class Represents a blamed commit * @param {String} sha1: SHA-1 identifier of a commit */ function Commit(sha1) { if (this instanceof Commit) { this.sha1 = sha1; this.nprevious = 0; /* number of 'previous', effective parents */ } else { return new Commit(sha1); } } /* ............................................................ */ /* progress info, timing, error reporting */ var blamedLines = 0; var totalLines = '???'; var div_progress_bar; var div_progress_info; /** * Detects how many lines does a blamed file have, * This information is used in progress info * * @returns {Number|String} Number of lines in file, or string '...' */ function countLines() { var table = document.getElementById('blame_table') || document.getElementsByTagName('table')[0]; if (table) { return table.getElementsByTagName('tr').length - 1; // for header } else { return '...'; } } /** * update progress info and length (width) of progress bar * * @globals div_progress_info, div_progress_bar, blamedLines, totalLines */ function updateProgressInfo() { if (!div_progress_info) { div_progress_info = document.getElementById('progress_info'); } if (!div_progress_bar) { div_progress_bar = document.getElementById('progress_bar'); } if (!div_progress_info && !div_progress_bar) { return; } var percentage = Math.floor(100.0*blamedLines/totalLines); if (div_progress_info) { div_progress_info.firstChild.data = blamedLines + ' / ' + totalLines + ' (' + padLeftStr(percentage, 3, '\u00A0') + '%)'; } if (div_progress_bar) { //div_progress_bar.setAttribute('style', 'width: '+percentage+'%;'); div_progress_bar.style.width = percentage + '%'; } } var t_interval_server = ''; var cmds_server = ''; var t0 = new Date(); /** * write how much it took to generate data, and to run script * * @globals t0, t_interval_server, cmds_server */ function writeTimeInterval() { var info_time = document.getElementById('generating_time'); if (!info_time || !t_interval_server) { return; } var t1 = new Date(); info_time.firstChild.data += ' + (' + t_interval_server + ' sec server blame_data / ' + (t1.getTime() - t0.getTime())/1000 + ' sec client JavaScript)'; var info_cmds = document.getElementById('generating_cmd'); if (!info_time || !cmds_server) { return; } info_cmds.firstChild.data += ' + ' + cmds_server; } /** * show an error message alert to user within page (in prohress info area) * @param {String} str: plain text error message (no HTML) * * @globals div_progress_info */ function errorInfo(str) { if (!div_progress_info) { div_progress_info = document.getElementById('progress_info'); } if (div_progress_info) { div_progress_info.className = 'error'; div_progress_info.firstChild.data = str; } } /* ............................................................ */ /* coloring rows during blame_data (git blame --incremental) run */ /** * used to extract N from 'colorN', where N is a number, * @constant */ var colorRe = /\bcolor([0-9]*)\b/; /** * return N if , otherwise return null * (some browsers require CSS class names to begin with letter) * * @param {HTMLElement} tr: table row element to check * @param {String} tr.className: 'class' attribute of tr element * @returns {Number|null} N if tr.className == 'colorN', otherwise null * * @globals colorRe */ function getColorNo(tr) { if (!tr) { return null; } var className = tr.className; if (className) { var match = colorRe.exec(className); if (match) { return parseInt(match[1], 10); } } return null; } var colorsFreq = [0, 0, 0]; /** * return one of given possible colors (currently least used one) * example: chooseColorNoFrom(2, 3) returns 2 or 3 * * @param {Number[]} arguments: one or more numbers * assumes that 1 <= arguments[i] <= colorsFreq.length * @returns {Number} Least used color number from arguments * @globals colorsFreq */ function chooseColorNoFrom() { // choose the color which is least used var colorNo = arguments[0]; for (var i = 1; i < arguments.length; i++) { if (colorsFreq[arguments[i]-1] < colorsFreq[colorNo-1]) { colorNo = arguments[i]; } } colorsFreq[colorNo-1]++; return colorNo; } /** * given two neigbour elements, find color which would be different * from color of both of neighbours; used to 3-color blame table * * @param {HTMLElement} tr_prev * @param {HTMLElement} tr_next * @returns {Number} color number N such that * colorN != tr_prev.className && colorN != tr_next.className */ function findColorNo(tr_prev, tr_next) { var color_prev = getColorNo(tr_prev); var color_next = getColorNo(tr_next); // neither of neighbours has color set // THEN we can use any of 3 possible colors if (!color_prev && !color_next) { return chooseColorNoFrom(1,2,3); } // either both neighbours have the same color, // or only one of neighbours have color set // THEN we can use any color except given var color; if (color_prev === color_next) { color = color_prev; // = color_next; } else if (!color_prev) { color = color_next; } else if (!color_next) { color = color_prev; } if (color) { return chooseColorNoFrom((color % 3) + 1, ((color+1) % 3) + 1); } // neighbours have different colors // THEN there is only one color left return (3 - ((color_prev + color_next) % 3)); } /* ............................................................ */ /* coloring rows like 'blame' after 'blame_data' finishes */ /** * returns true if given row element (tr) is first in commit group * to be used only after 'blame_data' finishes (after processing) * * @param {HTMLElement} tr: table row * @returns {Boolean} true if TR is first in commit group */ function isStartOfGroup(tr) { return tr.firstChild.className === 'sha1'; } /** * change colors to use zebra coloring (2 colors) instead of 3 colors * concatenate neighbour commit groups belonging to the same commit * * @globals colorRe */ function fixColorsAndGroups() { var colorClasses = ['light', 'dark']; var linenum = 1; var tr, prev_group; var colorClass = 0; var table = document.getElementById('blame_table') || document.getElementsByTagName('table')[0]; while ((tr = document.getElementById('l'+linenum))) { // index origin is 0, which is table header; start from 1 //while ((tr = table.rows[linenum])) { // <- it is slower if (isStartOfGroup(tr, linenum, document)) { if (prev_group && prev_group.firstChild.firstChild.href === tr.firstChild.firstChild.href) { // we have to concatenate groups var prev_rows = prev_group.firstChild.rowSpan || 1; var curr_rows = tr.firstChild.rowSpan || 1; prev_group.firstChild.rowSpan = prev_rows + curr_rows; //tr.removeChild(tr.firstChild); tr.deleteCell(0); // DOM2 HTML way } else { colorClass = (colorClass + 1) % 2; prev_group = tr; } } var tr_class = tr.className; tr.className = tr_class.replace(colorRe, colorClasses[colorClass]); linenum++; } } /* ............................................................ */ /* time and data */ /** * used to extract hours and minutes from timezone info, e.g '-0900' * @constant */ var tzRe = /^([+-][0-9][0-9])([0-9][0-9])$/; /** * return date in local time formatted in iso-8601 like format * 'yyyy-mm-dd HH:MM:SS +/-ZZZZ' e.g. '2005-08-07 21:49:46 +0200' * * @param {Number} epoch: seconds since '00:00:00 1970-01-01 UTC' * @param {String} timezoneInfo: numeric timezone '(+|-)HHMM' * @returns {String} date in local time in iso-8601 like format * * @globals tzRe */ function formatDateISOLocal(epoch, timezoneInfo) { var match = tzRe.exec(timezoneInfo); // date corrected by timezone var localDate = new Date(1000 * (epoch + (parseInt(match[1],10)*3600 + parseInt(match[2],10)*60))); var localDateStr = // e.g. '2005-08-07' localDate.getUTCFullYear() + '-' + padLeft(localDate.getUTCMonth()+1, 2, '0') + '-' + padLeft(localDate.getUTCDate(), 2, '0'); var localTimeStr = // e.g. '21:49:46' padLeft(localDate.getUTCHours(), 2, '0') + ':' + padLeft(localDate.getUTCMinutes(), 2, '0') + ':' + padLeft(localDate.getUTCSeconds(), 2, '0'); return localDateStr + ' ' + localTimeStr + ' ' + timezoneInfo; } /* ............................................................ */ /* unquoting/unescaping filenames */ /**#@+ * @constant */ var escCodeRe = /\\([^0-7]|[0-7]{1,3})/g; var octEscRe = /^[0-7]{1,3}$/; var maybeQuotedRe = /^\"(.*)\"$/; /**#@-*/ /** * unquote maybe git-quoted filename * e.g. 'aa' -> 'aa', '"a\ta"' -> 'a a' * * @param {String} str: git-quoted string * @returns {String} Unquoted and unescaped string * * @globals escCodeRe, octEscRe, maybeQuotedRe */ function unquote(str) { function unq(seq) { var es = { // character escape codes, aka escape sequences (from C) // replacements are to some extent JavaScript specific t: "\t", // tab (HT, TAB) n: "\n", // newline (NL) r: "\r", // return (CR) f: "\f", // form feed (FF) b: "\b", // backspace (BS) a: "\x07", // alarm (bell) (BEL) e: "\x1B", // escape (ESC) v: "\v" // vertical tab (VT) }; if (seq.search(octEscRe) !== -1) { // octal char sequence return String.fromCharCode(parseInt(seq, 8)); } else if (seq in es) { // C escape sequence, aka character escape code return es[seq]; } // quoted ordinary character return seq; } var match = str.match(maybeQuotedRe); if (match) { str = match[1]; // perhaps str = eval('"'+str+'"'); would be enough? str = str.replace(escCodeRe, function (substr, p1, offset, s) { return unq(p1); }); } return str; } /* ============================================================ */ /* main part: parsing response */ /** * Function called for each blame entry, as soon as it finishes. * It updates page via DOM manipulation, adding sha1 info, etc. * * @param {Commit} commit: blamed commit * @param {Object} group: object representing group of lines, * which blame the same commit (blame entry) * * @globals blamedLines */ function handleLine(commit, group) { /* This is the structure of the HTML fragment we are working with: 123 # times (my ext3 doesn't). */ var resline = group.resline; // format date and time string only once per commit if (!commit.info) { /* e.g. 'Kay Sievers, 2005-08-07 21:49:46 +0200' */ commit.info = commit.author + ', ' + formatDateISOLocal(commit.authorTime, commit.authorTimezone); } // color depends on group of lines, not only on blamed commit var colorNo = findColorNo( document.getElementById('l'+(resline-1)), document.getElementById('l'+(resline+group.numlines)) ); // loop over lines in commit group for (var i = 0; i < group.numlines; i++, resline++) { var tr = document.getElementById('l'+resline); if (!tr) { break; } /* 123 # times (my ext3 doesn't). */ var td_sha1 = tr.firstChild; var a_sha1 = td_sha1.firstChild; var a_linenr = td_sha1.nextSibling.firstChild; /* */ var tr_class = ''; if (colorNo !== null) { tr_class = 'color'+colorNo; } if (commit.boundary) { tr_class += ' boundary'; } if (commit.nprevious === 0) { tr_class += ' no-previous'; } else if (commit.nprevious > 1) { tr_class += ' multiple-previous'; } tr.className = tr_class; /* ? */ if (i === 0) { td_sha1.title = commit.info; td_sha1.rowSpan = group.numlines; a_sha1.href = projectUrl + 'a=commit;h=' + commit.sha1; if (a_sha1.firstChild) { a_sha1.firstChild.data = commit.sha1.substr(0, 8); } else { a_sha1.appendChild( document.createTextNode(commit.sha1.substr(0, 8))); } if (group.numlines >= 2) { var fragment = document.createDocumentFragment(); var br = document.createElement("br"); var match = commit.author.match(/\b([A-Z])\B/g); if (match) { var text = document.createTextNode( match.join('')); } if (br && text) { var elem = fragment || td_sha1; elem.appendChild(br); elem.appendChild(text); if (fragment) { td_sha1.appendChild(fragment); } } } } else { //tr.removeChild(td_sha1); // DOM2 Core way tr.deleteCell(0); // DOM2 HTML way } /* 123 */ var linenr_commit = ('previous' in commit ? commit.previous : commit.sha1); var linenr_filename = ('file_parent' in commit ? commit.file_parent : commit.filename); a_linenr.href = projectUrl + 'a=blame_incremental' + ';hb=' + linenr_commit + ';f=' + encodeURIComponent(linenr_filename) + '#l' + (group.srcline + i); blamedLines++; //updateProgressInfo(); } } // ---------------------------------------------------------------------- var inProgress = false; // are we processing response /**#@+ * @constant */ var sha1Re = /^([0-9a-f]{40}) ([0-9]+) ([0-9]+) ([0-9]+)/; var infoRe = /^([a-z-]+) ?(.*)/; var endRe = /^END ?([^ ]*) ?(.*)/; /**@-*/ var curCommit = new Commit(); var curGroup = {}; var pollTimer = null; /** * Parse output from 'git blame --incremental [...]', received via * XMLHttpRequest from server (blamedataUrl), and call handleLine * (which updates page) as soon as blame entry is completed. * * @param {String[]} lines: new complete lines from blamedata server * * @globals commits, curCommit, curGroup, t_interval_server, cmds_server * @globals sha1Re, infoRe, endRe */ function processBlameLines(lines) { var match; for (var i = 0, len = lines.length; i < len; i++) { if ((match = sha1Re.exec(lines[i]))) { var sha1 = match[1]; var srcline = parseInt(match[2], 10); var resline = parseInt(match[3], 10); var numlines = parseInt(match[4], 10); var c = commits[sha1]; if (!c) { c = new Commit(sha1); commits[sha1] = c; } curCommit = c; curGroup.srcline = srcline; curGroup.resline = resline; curGroup.numlines = numlines; } else if ((match = infoRe.exec(lines[i]))) { var info = match[1]; var data = match[2]; switch (info) { case 'filename': curCommit.filename = unquote(data); // 'filename' information terminates the entry handleLine(curCommit, curGroup); updateProgressInfo(); break; case 'author': curCommit.author = data; break; case 'author-time': curCommit.authorTime = parseInt(data, 10); break; case 'author-tz': curCommit.authorTimezone = data; break; case 'previous': curCommit.nprevious++; // store only first 'previous' header if (!'previous' in curCommit) { var parts = data.split(' ', 2); curCommit.previous = parts[0]; curCommit.file_parent = unquote(parts[1]); } break; case 'boundary': curCommit.boundary = true; break; } // end switch } else if ((match = endRe.exec(lines[i]))) { t_interval_server = match[1]; cmds_server = match[2]; } else if (lines[i] !== '') { // malformed line } // end if (match) } // end for (lines) } /** * Process new data and return pointer to end of processed part * * @param {String} unprocessed: new data (from nextReadPos) * @param {Number} nextReadPos: end of last processed data * @return {Number} end of processed data (new value for nextReadPos) */ function processData(unprocessed, nextReadPos) { var lastLineEnd = unprocessed.lastIndexOf('\n'); if (lastLineEnd !== -1) { var lines = unprocessed.substring(0, lastLineEnd).split('\n'); nextReadPos += lastLineEnd + 1 /* 1 == '\n'.length */; processBlameLines(lines); } // end if return nextReadPos; } /** * Handle XMLHttpRequest errors * * @param {XMLHttpRequest} xhr: XMLHttpRequest object * * @globals pollTimer, commits, inProgress */ function handleError(xhr) { errorInfo('Server error: ' + xhr.status + ' - ' + (xhr.statusText || 'Error contacting server')); clearInterval(pollTimer); commits = {}; // free memory inProgress = false; } /** * Called after XMLHttpRequest finishes (loads) * * @param {XMLHttpRequest} xhr: XMLHttpRequest object (unused) * * @globals pollTimer, commits, inProgress */ function responseLoaded(xhr) { clearInterval(pollTimer); fixColorsAndGroups(); writeTimeInterval(); commits = {}; // free memory inProgress = false; } /** * handler for XMLHttpRequest onreadystatechange event * @see startBlame * * @globals xhr, inProgress */ function handleResponse() { /* * xhr.readyState * * Value Constant (W3C) Description * ------------------------------------------------------------------- * 0 UNSENT open() has not been called yet. * 1 OPENED send() has not been called yet. * 2 HEADERS_RECEIVED send() has been called, and headers * and status are available. * 3 LOADING Downloading; responseText holds partial data. * 4 DONE The operation is complete. */ if (xhr.readyState !== 4 && xhr.readyState !== 3) { return; } // the server returned error if (xhr.readyState === 3 && xhr.status !== 200) { return; } if (xhr.readyState === 4 && xhr.status !== 200) { handleError(xhr); return; } // In konqueror xhr.responseText is sometimes null here... if (xhr.responseText === null) { return; } // in case we were called before finished processing if (inProgress) { return; } else { inProgress = true; } // extract new whole (complete) lines, and process them while (xhr.prevDataLength !== xhr.responseText.length) { if (xhr.readyState === 4 && xhr.prevDataLength === xhr.responseText.length) { break; } xhr.prevDataLength = xhr.responseText.length; var unprocessed = xhr.responseText.substring(xhr.nextReadPos); xhr.nextReadPos = processData(unprocessed, xhr.nextReadPos); } // end while // did we finish work? if (xhr.readyState === 4 && xhr.prevDataLength === xhr.responseText.length) { responseLoaded(xhr); } inProgress = false; } // ============================================================ // ------------------------------------------------------------ /** * Incrementally update line data in blame_incremental view in gitweb. * * @param {String} blamedataUrl: URL to server script generating blame data. * @param {String} bUrl: partial URL to project, used to generate links. * * Called from 'blame_incremental' view after loading table with * file contents, a base for blame view. * * @globals xhr, t0, projectUrl, div_progress_bar, totalLines, pollTimer */ function startBlame(blamedataUrl, bUrl) { xhr = createRequestObject(); if (!xhr) { errorInfo('ERROR: XMLHttpRequest not supported'); return; } t0 = new Date(); projectUrl = bUrl + (bUrl.indexOf('?') === -1 ? '?' : ';'); if ((div_progress_bar = document.getElementById('progress_bar'))) { //div_progress_bar.setAttribute('style', 'width: 100%;'); div_progress_bar.style.cssText = 'width: 100%;'; } totalLines = countLines(); updateProgressInfo(); /* add extra properties to xhr object to help processing response */ xhr.prevDataLength = -1; // used to detect if we have new data xhr.nextReadPos = 0; // where unread part of response starts xhr.onreadystatechange = handleResponse; //xhr.onreadystatechange = function () { handleResponse(xhr); }; xhr.open('GET', blamedataUrl); xhr.setRequestHeader('Accept', 'text/plain'); xhr.send(null); // not all browsers call onreadystatechange event on each server flush // poll response using timer every second to handle this issue pollTimer = setInterval(xhr.onreadystatechange, 1000); } // end of gitweb.js genometools-1.5.1/www/genometools.org/htdocs/customtracks.html000066400000000000000000000212621211610345200247100ustar00rootroot00000000000000 The AnnotationSketch module

    Custom tracks

    There are kinds of data which may be interesting to see together with annotation renderings, but that can not be expressed – or only in a complicated way – in GFF3 format. It may even be too difficult or counterintuitive to properly represent this data as typical AnnotationSketch box graphics. For example, this may be sequence data, numerical sequence analysis results, or other kinds of data which does not fit into the simple ‘genomic feature’ scheme. For an example, see Fig. 1.

    [Example custom track]

    Figure 1: Example AnnotationSketch output with a custom track at the bottom, displaying the GC content over a window size of 200 bp.

    With custom tracks, AnnotationSketch provides a mechanism to use the internal drawing functionality to create user-defined output which can be tailored to fit this kind of data. A custom track looks just like a normal AnnotationSketch track, but is completely in control of the developer. While native AnnotationSketch primitives such as boxes can of course be used, the author of a custom track is not restricted to the layout algorithm and can draw anything anywhere (as long as it is provided by the Graphics class), taking arbitrary external data into account.

    Anatomy of a custom track class

    Simply put, custom tracks are classes which are derived from a CustomTrack base class and must implement a set of mandatory methods:

    • get_height(): Returns the amount of vertical space (in pixels or points) the custom track will occupy in the final image. Must return a numeric value.
    • get_title(): Returns a title for the custom track which is displayed at the top of the track. Note that, unlike a track identifier string e.g. produced by a track selector function, the string returned by this function is not prepended by a file name.
    • render(graphics, ypos, range, style, error): Performs the actual rendering operations. As parameters, this function receives
      • a Graphics object to draw on,
      • the vertical offset ypos of the drawing area assigned to the custom track,
      • the Range of the sequence positions for which annotations are currently displayed,
      • a Style object which can be used to obtain style information specific to this custom track, and
      • an Error object which can be used to return an error message if the custom track needs to signal a problem.
      The render() method must return 0 if drawing was successful, or a negative value if an error occurred.
    Optionally, a free() method can be implemented if the subclass needs to clean up any private space allocated by itself. These methods are then called by the rendering code in AnnotationSketch when a Diagram containing a custom track is laid out and rendered. No other constraints apply on such a class besides that these methods are implemented (in the scripting language bindings, the parent classes' constructor must be called once).

    Writing an example custom track

    Let's suppose we are not satisfied with the display of single base features, such as transposable element insertion sites or SNPs. Instead of a single line denoting the feature location, we would like to have a small triangle pointing at the location. Suppose we also do not have this data in an annotation graph, so we cannot use the built-in rendering functions. It is straightforward to write a small custom track class which does this for us.
    This tutorial uses Python code for simplicity, but the general approach is common to all supported languages.

    First, we need to define a class inheriting from CustomTrack, call the parent constructor to register the functions and set instance variables for the triangle sidelength and a dictionary containing the feature positions and a description: 

    class CustomTrackInsertions(CustomTrack):
  def __init__(self, sidelength, data):
    super(CustomTrackInsertions, self).__init__()
    self.sidelength = sidelength
    self.data = data
    We define the height to be 20 pixels: 
      def get_height(self):
    return 20
    As a track title, we set "Insertion site": 
      def get_title(self):
    return "Insertion site"
    The rendering code then calculates the triangle coordinates and draws the respective lines: 
      def render(self, graphics, ypos, rng, style, error):
    height = (self.sidelength*math.sqrt(3))/2
    margins = graphics.get_xmargins()
    red = Color(1, 0, 0, 0.7)
    for pos, desc in self.data.iteritems():
      drawpos = margins + (float(pos)-rng.start)/(rng.end-rng.start+1)         \
                  * (graphics.get_image_width()-2*margins)
      graphics.draw_line(drawpos-self.sidelength/2, ypos + height,             \
                         drawpos, ypos,                                        \
                         red, 1)
      graphics.draw_line(drawpos, ypos,                                        \
                         drawpos+self.sidelength/2, ypos + height,             \
                         red, 1)
      graphics.draw_line(drawpos-self.sidelength/2, ypos + height,             \
                         drawpos+self.sidelength/2, ypos + height,             \
                         red, 1)
      graphics.draw_text_centered(drawpos, ypos + height + 13, str(desc))
    return 0
    For a Python custom track, that's it! No more code is necessary for this very simple custom track. We can now instantiate this class and attach the instance to a Diagram object: 
    ...
diagram = Diagram.from_index(feature_index, seqid, range, style)
...
ctt = CustomTrackInsertions(15, {2000:"foo", 4400:"bar", 8000:"baz"})
diagram.add_custom_track(ctt)
...
    Running layout and drawing functions on this diagram then produces the desired image:

    [Example custom track]

    Figure 2: The example insertion site custom track (at the bottom), displaying three sample data points.

    genometools-1.5.1/www/genometools.org/htdocs/design.html000066400000000000000000000370131211610345200234400ustar00rootroot00000000000000 The GenomeTools Design

    The GenomeTools design

    Major design goals of the GenomeTools system:

    • Correctness
      • built-in unit tests
      • extensive test suite
    • Portability
      • should run on every POSIX compliant UNIX system
      • depend only on a C/C++ compiler and the GNU Make build system
    • Efficiency
    • Minimalism (if in doubt, use the simpler solution)

    The GenomeTools C code is split into components plus the runtime and the main program. There are the following types of components:

    • classes
    • modules
    • unit tests
    • tools

    It is assumed that the reader is familiar with the terminology of object oriented software design.

    The runtime

    The runtime class gtr.h/gtr.c is the nucleus of the GenomeTools system. An object of this class is the place of execution in GenomeTools, like a process in an operating system. A new runtime object can be created with the gtr_new() function. gtr_register_components() registers all build in components to the runtime, and gtr_run() starts it.

    Rationale

    Having an explicit runtime class unifies the design — a runtime instance is just another object. In theory, this would allow to start multiple instances of the runtime class in parallel. For example, in threads.

    The runtime class is also the place were we start an embedded Lua script language interpreter.

    The main program

    The GenomeTools main program given in the file gt.c simply creates a new runtime object and starts it.

    Classes

    The central component type in GenomeTools is the class. Structuring the C code into classes and modules gives us a unified design approach which simplifies the thinking about design issues and avoids that the codebase becomes monolithic, a problem often encountered in C programs.

    Simple classes

    For most classes, a simple class suffices. A simple class is a class which does not inherit from other classes and from which no other classes inherit. Using mostly simple classes avoids the problems of large class hierarchies, namely the interdependence of classes which inherit from one another. The major advantage of simple classes over simple C structs is information hiding.

    Implementing simple classes

    We describe now how to implement a simple classes using the string class str.[ch] of GenomeTools as an example. The interface to a class is always given in the .h or _api.h header file (str_api.h in our example). To achieve information hiding the header file cannot contain implementation details of the class. The implementation can always be found in the corresponding .c file (str.c in our example). Therefore, we start with the following C construct to define our Str class in str.h: 

    typedef struct Str Str;

    This seldomly used feature of C introduces a new data type named Str which is a synonym for the struct Str data type, which needs not to be known at this point. In the scope of the header file, the new data type Str cannot be used, since it's size is unknown to the compiler at this point. Nevertheless, pointers of type Str can still be defined, because in C all pointers have the same size, regardless of it's type. Using this fact, we can define a constructor function: 

    Str*          str_new(void);

    which returns a new string object and a destructor function 

    void          str_free(Str*);

    which destroys a given string object. This gives us the basic structure of the string class header file: A new data type (which represents the class and it's objects), a constructor function, and a destructor function. 

    #ifndef STR_H
#define STR_H

/* the string class, string objects are strings which grow on demand */
typedef struct Str Str;

Str*          str_new(void);
void          str_free(Str*);

#endif

    Now we look at the implementation side of the story, which can be found in the str.c file. At first, we include the str.h header file to make sure that the newly defined data type is known: 

    #include "str.h"

    Then we define struct Str which contains the actual data of a string object (the member variables in OO lingo). 

    struct Str {
  char *cstr;           /* the actual string (always '\0' terminated) */
  unsigned long length; /* currently used length (without trailing '\0') */
  size_t allocated;     /* currently allocated memory */
};

    Finally, we code the constructor 

    Str* str_new(void)
{
  Str *s = xmalloc(sizeof(Str));      /* create new string object */
  s->cstr = xcalloc(1, sizeof(char)); /* init the string with '\0' */
  s->length = 0;                      /* set the initial length */
  s->allocated = 1;                   /* set the initially allocated space */
  return s;                           /* return the new string object */
}

    and the destructor 

    void str_free(Str *s)
{
  if (!s) return;           /* return without action if 's' is NULL */
  free(s->cstr);            /* free the stored the C string */
  free(s);                  /* free the actual string object */
}

    Our string class implementation so far looks like this 

    #include "str.h"
#include "xansi.h"

struct Str {
  char *cstr;           /* the actual string (always '\0' terminated) */
  unsigned long length; /* currently used length (without trailing '\0') */
  size_t allocated;     /* currently allocated memory */
};

Str* str_new(void)
{
  Str *s = xmalloc(sizeof(Str));      /* create new string object */
  s->cstr = xcalloc(1, sizeof(char)); /* init the string with '\0' */
  s->length = 0;                      /* set the initial length */
  s->allocated = 1;                   /* set the initially allocated space */
  return s;                           /* return the new string object */
}

void str_free(Str *s)
{
  if (!s) return;           /* return without action if 's' is NULL */
  free(s->cstr);            /* free the stored the C string */
  free(s);                  /* free the actual string object */
}

    Since this string objects are pretty much useless so far, we define a couple more (object) methods in the header file str_api.h.

    Because C does not allow the traditional object.methodname syntax often used in object-oriented programming, we use the convention to pass the object always as the first argument to the function (methodname(object, ...)). To make it clear that a function is a method of a particular class classname, we prefix the method name with classname_. That is, we get classname_methodname(object, ...) as the generic form of method names in C. The constructor is always called classname_new() and the destructor classname_free(). See str.c for examples.

    Reference counting

    Adding reference counting to our newly created string class is pretty simple. At first we add a new function to the header file, which returns a new reference to the given object: 

    Str*          str_ref(Str*);

    To implement this object, we add a new reference_count member variable in to the Str implementation 

    struct Str {
  char *cstr;           /* the actual string (always '\0' terminated) */
  unsigned long length; /* currently used length (without trailing '\0') */
  size_t allocated;     /* currently allocated memory */
  unsigned int reference_count;
};

    implement the str_ref() function 

    Str* str_ref(Str *s)
{
  if (!s) return NULL;
  s->reference_count++; /* increase the reference counter */
  return s;
}

    and finally modify the destructor to take care of reference counting: 

    void str_free(Str *s)
{
  if (!s) return;           /* return without action if 's' is NULL */
  if (s->reference_count) { /* there are multiple references to this string */
    s->reference_count--;   /* decrement the reference counter */
    return;                 /* return without freeing the object */
  }
  free(s->cstr);            /* free the stored the C string */
  free(s);                  /* free the actual string object */
}

    Modules

    Modules bundle related functions which do not belong to a class. Examples:

    • dynalloc.h, the low level module for dynamic allocation, e.g., used to implement arrays in array.c and the above-mentioned strings
    • sig.h, bundles signal related functions (high level)
    • xansi_api.h, contains wrappers for the standard ANSI C library
    • xposix.h, contains wrappers for POSIX functions we use

    When designing new code, it is not very often the case that one has to introduce new modules. Usually defining a new class is the better approach.

    The genometools.h header file

    The genometools.h header file includes all other header files of the GenomeTools library. That is, to write programs employing the library, it suffices to include the genometools.h header file.

    Unit tests

    Many classes and modules contain a *_unit_test(void) function which performs a unit test of the class/module and returns 0 in case of success and -1 in case of failure. The unit test components are loaded into the GenomeTools runtime in the function gtr_register_components() and can be executed on the command line with: 

    $ gt -test

    Tools

    A ``tool'' is the most high-level type of component GenomeTools has to offer. We consider the ``eval'' tool here as an example. It evaluates a gene prediction against a given annotation. In principle a tool could be compiled as a single binary linking against the ``libgenometools''. Therefore the header files gt_*.h for tools only contain a single function which resemble a main() function (see gt_eval.h) and the gt_*.c files include only the genometools.h header file (see gt_eval.c). All tools are linked into the single gt binary, though. They are also loaded into the runtime via the gtr_register_components() function. All tools can be called like the eval tool in the following example: 

    $ gt eval

    Getting started

    To get started with GenomeTools development yourself, we recommend the following:

    1. Install the Git version control system.
    2. Read the Git documentation.
    3. Clone the GenomeTools Git repository with: 
      $ git clone git://genometools.org/genometools.git
    4. Start hacking on your own feature branch: 
      $ cd genometools
$ git checkout -b my_feature_branch_name
    5. Have fun!

    Acknowledgment

    We want to thank Patrick Maaß for introducing us to some techniques described in this document.

    genometools-1.5.1/www/genometools.org/htdocs/documents/000077500000000000000000000000001211610345200232765ustar00rootroot00000000000000genometools-1.5.1/www/genometools.org/htdocs/documents/annotationsketch.pdf000066400000000000000000041120121211610345200273460ustar00rootroot00000000000000%PDF-1.4 % 1 0 obj << /S /GoTo /D (chapter.1) >> endobj 4 0 obj (AnnotationSketch) endobj 5 0 obj << /S /GoTo /D (section.1.1) >> endobj 8 0 obj (Overview) endobj 9 0 obj << /S /GoTo /D (subsection.1.1.1) >> endobj 12 0 obj (Phase 1: Feature selection) endobj 13 0 obj << /S /GoTo /D (subsection.1.1.2) >> endobj 16 0 obj (Phase 2: Layout) endobj 17 0 obj << /S /GoTo /D (subsection.1.1.3) >> endobj 20 0 obj (Phase 3: Rendering) endobj 21 0 obj << /S /GoTo /D (subsection.1.1.4) >> endobj 24 0 obj (Collapsing) endobj 25 0 obj << /S /GoTo /D (subsection.1.1.5) >> endobj 28 0 obj (Styles) endobj 29 0 obj << /S /GoTo /D (section.1.2) >> endobj 32 0 obj (The gt sketch tool) endobj 33 0 obj << /S /GoTo /D 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S{GXXlQR}%lh,듭?6hɬg\c}9 }I3 HgwI &'4ʋUɪcC$c4Gw_m46%y)Y~9{;Esx潃Mk 6ipr1l͙Atv 2hT&T{F![}.݁2Ef4Ӯu!īФ vvHը'ܴJL%AhI/d(.QeD?S`k@lEct{ף;F.r߶xQ[09Z.!5[yJYB?;j .WDђEV99gOڛ`漃 $"oѯ=#׏vzWU r1$/J)`C]ED8d9 xu_-j/sai$Rca"R3MT̀2[w!n⽑4}@̥hA|}uF!*h̲XRKe^AΛ>xPgZh(nUj+OBTb"dY]Ot8)X/lBfp^=% l@տ]jppccƵ(%NO,O%N$/3`MnqF{r9ʼS9h& DD?v\OuZkP 1ss||m,̱X 263 şwu_cz4c.n-:źK2g*-fE^|ΘK:0OH`8utaoD= ,P_.m(HLVr1P*OR=}҅)K^j(]ĺS@1+`fI(tt].>xZ~c\. u.<^#x`G OKʹHEٳX]#j5&6}`.#hJl@#mf%羠\?+4B,0Σ;n}ly% |:KYn޶B/F_\Uư%6_q}w_i( endstream endobj 824 0 obj << /Length1 1421 /Length2 5943 /Length3 0 /Length 6902 /Filter /FlateDecode >> stream xڍwT}? I ܄FwwJFlc4HwwJ7J#!t3y?}~W?7[ 쐶0U$Itt4 $ 88Xz #ᡄA82sA"]`! 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    AnnotationSketch code examples

    Using AnnotationSketch to draw annotations from a file

    The following code examples (in C and Lua) illustrate how to produce an image from a given GFF3 file using AnnotationSketch. The result is shown in Fig. 7. In essence, these code examples implement something like a simple version of the gt sketch tool from GenomeTools without most command-line options.

    [Example rendering from parsed GFF3 file]

    Figure 7: Example rendering of a GFF3 file with default style.

    C code

    (See src/examples/sketch_parsed.c in the source distribution.)

    Lua code

    (See gtscripts/sketch_parsed.lua in the source distribution. This example can be run by the command line gt gtscripts/sketch_parsed.lua <style_file> <PNG_file> <GFF3_file>)

    Ruby code

    (See gtruby/sketch_parsed.rb in the source distribution.)

    Python code

    (See gtpython/sketch_parsed.py in the source distribution.)

    Using AnnotationSketch to draw user-generated annotations

    The following C code example illustrates how to produce an image from annotation graphs created by user code. The result is shown in Fig. 8.

    [Example rendering from user-generated annotations]

    Figure 8: Example rendering of user-generated annotations with default style.

    C code

    (See src/examples/sketch_constructed.c in the source distribution.)

    Lua code

    (See gtscripts/sketch_constructed.lua in the source distribution. This example can be run by the command line gt gtscripts/sketch_constructed.lua <style_file> <PNG_file>)

    Ruby code

    (See gtruby/sketch_constructed.rb in the source distribution.)

    Python code

    (See gtpython/sketch_constructed.py in the source distribution.)
    genometools-1.5.1/www/genometools.org/htdocs/images/000077500000000000000000000000001211610345200225425ustar00rootroot00000000000000genometools-1.5.1/www/genometools.org/htdocs/images/annotation.gff3000066400000000000000000004117271211610345200254770ustar00rootroot00000000000000##gff-version 3 ##sequence-region chr16 4043 26056510 chr16 ENCODE gene 4043 9448 . - . ID=gene1;Name=Z84812.2-001;Name2=Z84812.2 chr16 ENCODE exon 4043 4511 . - . Parent=gene1 chr16 ENCODE CDS 4381 4511 . - . Parent=gene1 chr16 . intron 4512 4651 . - . Parent=gene1 chr16 ENCODE exon 4652 4720 . - . Parent=gene1 chr16 ENCODE CDS 4652 4720 . - . Parent=gene1 chr16 . intron 4721 5480 . - . Parent=gene1 chr16 ENCODE exon 5481 5633 . - . Parent=gene1 chr16 ENCODE CDS 5481 5633 . - . Parent=gene1 chr16 . intron 5634 6289 . - . Parent=gene1 chr16 ENCODE exon 6290 6448 . - . Parent=gene1 chr16 ENCODE CDS 6290 6448 . - . Parent=gene1 chr16 . intron 6449 6536 . - . Parent=gene1 chr16 ENCODE exon 6537 6738 . - . Parent=gene1 chr16 ENCODE CDS 6537 6738 . - . Parent=gene1 chr16 . intron 6739 6915 . - . Parent=gene1 chr16 ENCODE exon 6916 7051 . - . Parent=gene1 chr16 ENCODE CDS 6916 7051 . - . Parent=gene1 chr16 . intron 7052 7290 . - . Parent=gene1 chr16 ENCODE exon 7291 7427 . - . Parent=gene1 chr16 ENCODE CDS 7291 7427 . - . Parent=gene1 chr16 . intron 7428 7603 . - . Parent=gene1 chr16 ENCODE exon 7604 7750 . - . Parent=gene1 chr16 ENCODE CDS 7604 7750 . - . Parent=gene1 chr16 . intron 7751 7956 . - . Parent=gene1 chr16 ENCODE exon 7957 8068 . - . Parent=gene1 chr16 ENCODE CDS 7957 8068 . - . Parent=gene1 chr16 . intron 8069 8601 . - . Parent=gene1 chr16 ENCODE CDS 8602 8789 . - . Parent=gene1 chr16 ENCODE exon 8602 9448 . - . Parent=gene1 ### chr16 ENCODE gene 4085 6383 . - . ID=gene2;Name=Z84812.2-010;Name2=Z84812.2 chr16 ENCODE exon 4085 5633 . - . Parent=gene2 chr16 . intron 5634 6289 . - . Parent=gene2 chr16 ENCODE exon 6290 6383 . - . Parent=gene2 ### chr16 ENCODE gene 4085 7083 . - . ID=gene3;Name=Z84812.2-006;Name2=Z84812.2 chr16 ENCODE exon 4085 4720 . - . Parent=gene3 chr16 . intron 4721 5480 . - . Parent=gene3 chr16 ENCODE exon 5481 5633 . - . Parent=gene3 chr16 . intron 5634 6289 . - . Parent=gene3 chr16 ENCODE exon 6290 6448 . - . Parent=gene3 chr16 . intron 6449 6540 . - . Parent=gene3 chr16 ENCODE exon 6541 6738 . - . Parent=gene3 chr16 . intron 6739 6915 . - . Parent=gene3 chr16 ENCODE exon 6916 7083 . - . Parent=gene3 ### chr16 ENCODE gene 4085 8925 . - . ID=gene4;Name=Z84812.2-004;Name2=Z84812.2 chr16 ENCODE exon 4085 4511 . - . Parent=gene4 chr16 . intron 4512 4651 . - . Parent=gene4 chr16 ENCODE exon 4652 4720 . - . Parent=gene4 chr16 . intron 4721 5480 . - . Parent=gene4 chr16 ENCODE exon 5481 5633 . - . Parent=gene4 chr16 . intron 5634 6289 . - . Parent=gene4 chr16 ENCODE exon 6290 6448 . - . Parent=gene4 chr16 . intron 6449 6540 . - . Parent=gene4 chr16 ENCODE exon 6541 6738 . - . Parent=gene4 chr16 . intron 6739 6915 . - . Parent=gene4 chr16 ENCODE exon 6916 7427 . - . Parent=gene4 chr16 . intron 7428 7603 . - . Parent=gene4 chr16 ENCODE exon 7604 7750 . - . Parent=gene4 chr16 . intron 7751 7956 . - . Parent=gene4 chr16 ENCODE exon 7957 8058 . - . Parent=gene4 chr16 . intron 8059 8189 . - . Parent=gene4 chr16 ENCODE exon 8190 8243 . - . Parent=gene4 chr16 . intron 8244 8601 . - . Parent=gene4 chr16 ENCODE exon 8602 8925 . - . Parent=gene4 ### chr16 ENCODE gene 4085 9409 . - . ID=gene5;Name=Z84812.2-003;Name2=Z84812.2 chr16 ENCODE exon 4085 4511 . - . Parent=gene5 chr16 . intron 4512 4651 . - . Parent=gene5 chr16 ENCODE exon 4652 4720 . - . Parent=gene5 chr16 . intron 4721 5480 . - . Parent=gene5 chr16 ENCODE exon 5481 5633 . - . Parent=gene5 chr16 . intron 5634 6289 . - . Parent=gene5 chr16 ENCODE exon 6290 6448 . - . Parent=gene5 chr16 . intron 6449 6540 . - . Parent=gene5 chr16 ENCODE exon 6541 6738 . - . Parent=gene5 chr16 . intron 6739 6915 . - . Parent=gene5 chr16 ENCODE exon 6916 7427 . - . Parent=gene5 chr16 . intron 7428 7603 . - . Parent=gene5 chr16 ENCODE exon 7604 7750 . - . Parent=gene5 chr16 . intron 7751 7956 . - . Parent=gene5 chr16 ENCODE exon 7957 8055 . - . Parent=gene5 chr16 . intron 8056 8601 . - . Parent=gene5 chr16 ENCODE exon 8602 9409 . - . Parent=gene5 ### chr16 ENCODE gene 4085 9452 . - . ID=gene6;Name=Z84812.2-002;Name2=Z84812.2 chr16 ENCODE exon 4085 4511 . - . Parent=gene6 chr16 . intron 4512 4651 . - . Parent=gene6 chr16 ENCODE exon 4652 4720 . - . Parent=gene6 chr16 . intron 4721 5480 . - . Parent=gene6 chr16 ENCODE exon 5481 5633 . - . Parent=gene6 chr16 . intron 5634 6289 . - . Parent=gene6 chr16 ENCODE exon 6290 6448 . - . Parent=gene6 chr16 . intron 6449 6540 . - . Parent=gene6 chr16 ENCODE exon 6541 6738 . - . Parent=gene6 chr16 . intron 6739 6915 . - . Parent=gene6 chr16 ENCODE exon 6916 7051 . - . Parent=gene6 chr16 . intron 7052 7290 . - . Parent=gene6 chr16 ENCODE exon 7291 7427 . - . Parent=gene6 chr16 . intron 7428 7603 . - . Parent=gene6 chr16 ENCODE exon 7604 7750 . - . Parent=gene6 chr16 . intron 7751 7956 . - . Parent=gene6 chr16 ENCODE exon 7957 8055 . - . Parent=gene6 chr16 . intron 8056 8601 . - . Parent=gene6 chr16 ENCODE exon 8602 9452 . - . Parent=gene6 ### chr16 ENCODE gene 4088 8422 . - . ID=gene7;Name=Z84812.2-008;Name2=Z84812.2 chr16 ENCODE exon 4088 6448 . - . Parent=gene7 chr16 . intron 6449 6540 . - . Parent=gene7 chr16 ENCODE exon 6541 8422 . - . Parent=gene7 ### chr16 ENCODE gene 4117 6241 . - . ID=gene8;Name=Z84812.2-005;Name2=Z84812.2 chr16 ENCODE exon 4117 4720 . - . Parent=gene8 chr16 . intron 4721 5480 . - . Parent=gene8 chr16 ENCODE exon 5481 6241 . - . Parent=gene8 ### chr16 ENCODE gene 4256 5022 . - . ID=gene9;Name=Z84812.2-011;Name2=Z84812.2 chr16 ENCODE exon 4256 4511 . - . Parent=gene9 chr16 . intron 4512 4651 . - . Parent=gene9 chr16 ENCODE exon 4652 5022 . - . Parent=gene9 ### chr16 ENCODE gene 5739 6975 . - . ID=gene10;Name=Z84812.2-009;Name2=Z84812.2 chr16 ENCODE exon 5739 5993 . - . Parent=gene10 chr16 . intron 5994 6289 . - . Parent=gene10 chr16 ENCODE exon 6290 6448 . - . Parent=gene10 chr16 . intron 6449 6540 . - . Parent=gene10 chr16 ENCODE exon 6541 6738 . - . Parent=gene10 chr16 . intron 6739 6915 . - . Parent=gene10 chr16 ENCODE exon 6916 6975 . - . Parent=gene10 ### chr16 ENCODE gene 7711 8508 . - . ID=gene11;Name=Z84812.2-007;Name2=Z84812.2 chr16 ENCODE exon 7711 7750 . - . Parent=gene11 chr16 . intron 7751 7956 . - . Parent=gene11 chr16 ENCODE exon 7957 8508 . - . Parent=gene11 ### chr16 ENCODE gene 12910 15123 . + . ID=gene12;Name=Z84723.1-001;Name2=Z84723.1 chr16 ENCODE exon 12910 13085 . + . Parent=gene12 chr16 ENCODE CDS 12932 13085 . + . Parent=gene12 chr16 . intron 13086 14245 . + . Parent=gene12 chr16 ENCODE CDS 14246 14283 . + . Parent=gene12 chr16 ENCODE exon 14246 15123 . + . Parent=gene12 ### chr16 ENCODE gene 36407 43628 . - . ID=gene13;Name=Z69719.1-001;Name2=POLR3K chr16 ENCODE exon 36407 37557 . - . Parent=gene13 chr16 ENCODE CDS 37430 37557 . - . Parent=gene13 chr16 . intron 37558 41557 . - . Parent=gene13 chr16 ENCODE exon 41558 41645 . - . Parent=gene13 chr16 ENCODE CDS 41558 41645 . - . Parent=gene13 chr16 . intron 41646 43475 . - . Parent=gene13 chr16 ENCODE CDS 43476 43586 . - . Parent=gene13 chr16 ENCODE exon 43476 43628 . - . Parent=gene13 ### chr16 ENCODE gene 37236 42142 . - . ID=gene14;Name=Z69719.1-002;Name2=POLR3K chr16 ENCODE exon 37236 37557 . - . Parent=gene14 chr16 . intron 37558 41557 . - . Parent=gene14 chr16 ENCODE exon 41558 42142 . - . Parent=gene14 ### chr16 ENCODE gene 43010 47669 . + . ID=gene15;Name=Z69719.2-001;Name2=C16orf33 chr16 ENCODE exon 43010 44058 . + . Parent=gene15 chr16 ENCODE CDS 44017 44058 . + . Parent=gene15 chr16 . intron 44059 45458 . + . Parent=gene15 chr16 ENCODE exon 45459 45549 . + . Parent=gene15 chr16 ENCODE CDS 45459 45549 . + . Parent=gene15 chr16 . intron 45550 45776 . + . Parent=gene15 chr16 ENCODE exon 45777 45882 . + . Parent=gene15 chr16 ENCODE CDS 45777 45882 . + . Parent=gene15 chr16 . intron 45883 46538 . + . Parent=gene15 chr16 ENCODE exon 46539 46613 . + . Parent=gene15 chr16 ENCODE CDS 46539 46613 . + . Parent=gene15 chr16 . intron 46614 47085 . + . Parent=gene15 chr16 ENCODE CDS 47086 47143 . + . Parent=gene15 chr16 ENCODE exon 47086 47669 . + . Parent=gene15 ### chr16 ENCODE gene 43864 47467 . + . ID=gene16;Name=Z69719.2-003;Name2=C16orf33 chr16 ENCODE exon 43864 44058 . + . Parent=gene16 chr16 . intron 44059 45765 . + . Parent=gene16 chr16 ENCODE exon 45766 45882 . + . Parent=gene16 chr16 . intron 45883 46538 . + . Parent=gene16 chr16 ENCODE exon 46539 46613 . + . Parent=gene16 chr16 . intron 46614 47085 . + . Parent=gene16 chr16 ENCODE exon 47086 47467 . + . Parent=gene16 ### chr16 ENCODE gene 43887 47372 . + . ID=gene17;Name=Z69719.2-004;Name2=C16orf33 chr16 ENCODE exon 43887 44058 . + . Parent=gene17 chr16 . intron 44059 45458 . + . Parent=gene17 chr16 ENCODE exon 45459 45549 . + . Parent=gene17 chr16 . intron 45550 45776 . + . Parent=gene17 chr16 ENCODE exon 45777 45882 . + . Parent=gene17 chr16 . intron 45883 46320 . + . Parent=gene17 chr16 ENCODE exon 46321 46420 . + . Parent=gene17 chr16 . intron 46421 46538 . + . Parent=gene17 chr16 ENCODE exon 46539 46613 . + . Parent=gene17 chr16 . intron 46614 47085 . + . Parent=gene17 chr16 ENCODE exon 47086 47372 . + . Parent=gene17 ### chr16 ENCODE gene 44960 47444 . + . ID=gene18;Name=Z69719.2-002;Name2=C16orf33 chr16 ENCODE exon 44960 45549 . + . Parent=gene18 chr16 . intron 45550 45776 . + . Parent=gene18 chr16 ENCODE exon 45777 45882 . + . Parent=gene18 chr16 . intron 45883 46538 . + . Parent=gene18 chr16 ENCODE exon 46539 46613 . + . Parent=gene18 chr16 . intron 46614 47085 . + . Parent=gene18 chr16 ENCODE exon 47086 47444 . + . Parent=gene18 ### chr16 ENCODE gene 45495 47453 . + . ID=gene19;Name=Z69719.2-005;Name2=C16orf33 chr16 ENCODE exon 45495 45549 . + . Parent=gene19 chr16 . intron 45550 45776 . + . Parent=gene19 chr16 ENCODE exon 45777 46613 . + . Parent=gene19 chr16 . intron 46614 47085 . + . Parent=gene19 chr16 ENCODE exon 47086 47453 . + . Parent=gene19 ### chr16 ENCODE gene 48058 62629 . - . ID=gene20;Name=Z69719.3-001;Name2=RHBDF1 chr16 ENCODE exon 48058 48758 . - . Parent=gene20 chr16 ENCODE CDS 48339 48758 . - . Parent=gene20 chr16 . intron 48759 48971 . - . Parent=gene20 chr16 ENCODE exon 48972 49125 . - . Parent=gene20 chr16 ENCODE CDS 48972 49125 . - . Parent=gene20 chr16 . intron 49126 49246 . - . Parent=gene20 chr16 ENCODE exon 49247 49347 . - . Parent=gene20 chr16 ENCODE CDS 49247 49347 . - . Parent=gene20 chr16 . intron 49348 49416 . - . Parent=gene20 chr16 ENCODE exon 49417 49492 . - . Parent=gene20 chr16 ENCODE CDS 49417 49492 . - . Parent=gene20 chr16 . intron 49493 49729 . - . Parent=gene20 chr16 ENCODE exon 49730 49824 . - . Parent=gene20 chr16 ENCODE CDS 49730 49824 . - . Parent=gene20 chr16 . intron 49825 50213 . - . Parent=gene20 chr16 ENCODE exon 50214 50277 . - . Parent=gene20 chr16 ENCODE CDS 50214 50277 . - . Parent=gene20 chr16 . intron 50278 50436 . - . Parent=gene20 chr16 ENCODE exon 50437 50537 . - . Parent=gene20 chr16 ENCODE CDS 50437 50537 . - . Parent=gene20 chr16 . intron 50538 51117 . - . Parent=gene20 chr16 ENCODE exon 51118 51279 . - . Parent=gene20 chr16 ENCODE CDS 51118 51279 . - . Parent=gene20 chr16 . intron 51280 51382 . - . Parent=gene20 chr16 ENCODE exon 51383 51457 . - . Parent=gene20 chr16 ENCODE CDS 51383 51457 . - . Parent=gene20 chr16 . intron 51458 51582 . - . Parent=gene20 chr16 ENCODE exon 51583 51694 . - . Parent=gene20 chr16 ENCODE CDS 51583 51694 . - . Parent=gene20 chr16 . intron 51695 51795 . - . Parent=gene20 chr16 ENCODE exon 51796 52050 . - . Parent=gene20 chr16 ENCODE CDS 51796 52050 . - . Parent=gene20 chr16 . intron 52051 52535 . - . Parent=gene20 chr16 ENCODE exon 52536 52693 . - . Parent=gene20 chr16 ENCODE CDS 52536 52693 . - . Parent=gene20 chr16 . intron 52694 52772 . - . Parent=gene20 chr16 ENCODE exon 52773 52895 . - . Parent=gene20 chr16 ENCODE CDS 52773 52895 . - . Parent=gene20 chr16 . intron 52896 52970 . - . Parent=gene20 chr16 ENCODE exon 52971 53180 . - . Parent=gene20 chr16 ENCODE CDS 52971 53180 . - . Parent=gene20 chr16 . intron 53181 53584 . - . Parent=gene20 chr16 ENCODE exon 53585 53798 . - . Parent=gene20 chr16 ENCODE CDS 53585 53798 . - . Parent=gene20 chr16 . intron 53799 54696 . - . Parent=gene20 chr16 ENCODE exon 54697 54827 . - . Parent=gene20 chr16 ENCODE CDS 54697 54827 . - . Parent=gene20 chr16 . intron 54828 54896 . - . Parent=gene20 chr16 ENCODE CDS 54897 55013 . - . Parent=gene20 chr16 ENCODE exon 54897 55037 . - . Parent=gene20 chr16 . intron 55038 62510 . - . Parent=gene20 chr16 ENCODE exon 62511 62629 . - . Parent=gene20 ### chr16 ENCODE gene 48059 62593 . - . ID=gene21;Name=Z69719.3-002;Name2=RHBDF1 chr16 ENCODE exon 48059 48758 . - . Parent=gene21 chr16 . intron 48759 48971 . - . Parent=gene21 chr16 ENCODE exon 48972 49492 . - . Parent=gene21 chr16 . intron 49493 49729 . - . Parent=gene21 chr16 ENCODE exon 49730 50277 . - . Parent=gene21 chr16 . intron 50278 50436 . - . Parent=gene21 chr16 ENCODE exon 50437 51279 . - . Parent=gene21 chr16 . intron 51280 51382 . - . Parent=gene21 chr16 ENCODE exon 51383 51457 . - . Parent=gene21 chr16 . intron 51458 51582 . - . Parent=gene21 chr16 ENCODE exon 51583 51694 . - . Parent=gene21 chr16 . intron 51695 51795 . - . Parent=gene21 chr16 ENCODE exon 51796 52050 . - . Parent=gene21 chr16 . intron 52051 52535 . - . Parent=gene21 chr16 ENCODE exon 52536 52693 . - . Parent=gene21 chr16 . intron 52694 52772 . - . Parent=gene21 chr16 ENCODE exon 52773 52895 . - . Parent=gene21 chr16 . intron 52896 52970 . - . Parent=gene21 chr16 ENCODE exon 52971 53180 . - . Parent=gene21 chr16 . intron 53181 53584 . - . Parent=gene21 chr16 ENCODE exon 53585 53798 . - . Parent=gene21 chr16 . intron 53799 54696 . - . Parent=gene21 chr16 ENCODE exon 54697 54827 . - . Parent=gene21 chr16 . intron 54828 54929 . - . Parent=gene21 chr16 ENCODE exon 54930 55037 . - . Parent=gene21 chr16 . intron 55038 62510 . - . Parent=gene21 chr16 ENCODE exon 62511 62593 . - . Parent=gene21 ### chr16 ENCODE gene 48136 49760 . - . ID=gene22;Name=Z69719.3-008;Name2=RHBDF1 chr16 ENCODE exon 48136 48758 . - . Parent=gene22 chr16 ENCODE CDS 48339 48758 . - . Parent=gene22 chr16 . intron 48759 48971 . - . Parent=gene22 chr16 ENCODE exon 48972 49091 . - . Parent=gene22 chr16 ENCODE CDS 48972 49091 . - . Parent=gene22 chr16 . intron 49092 49296 . - . Parent=gene22 chr16 ENCODE exon 49297 49347 . - . Parent=gene22 chr16 ENCODE CDS 49297 49347 . - . Parent=gene22 chr16 . intron 49348 49416 . - . Parent=gene22 chr16 ENCODE exon 49417 49492 . - . Parent=gene22 chr16 ENCODE CDS 49417 49492 . - . Parent=gene22 chr16 . intron 49493 49729 . - . Parent=gene22 chr16 ENCODE exon 49730 49760 . - . Parent=gene22 chr16 ENCODE CDS 49730 49760 . - . Parent=gene22 ### chr16 ENCODE gene 48972 50191 . - . ID=gene23;Name=Z69719.3-007;Name2=RHBDF1 chr16 ENCODE exon 48972 49347 . - . Parent=gene23 chr16 . intron 49348 49416 . - . Parent=gene23 chr16 ENCODE exon 49417 49492 . - . Parent=gene23 chr16 . intron 49493 49729 . - . Parent=gene23 chr16 ENCODE exon 49730 50191 . - . Parent=gene23 ### chr16 ENCODE gene 49231 50678 . - . ID=gene24;Name=Z69719.3-006;Name2=RHBDF1 chr16 ENCODE exon 49231 49492 . - . Parent=gene24 chr16 . intron 49493 49729 . - . Parent=gene24 chr16 ENCODE exon 49730 50096 . - . Parent=gene24 chr16 . intron 50097 50213 . - . Parent=gene24 chr16 ENCODE exon 50214 50277 . - . Parent=gene24 chr16 . intron 50278 50436 . - . Parent=gene24 chr16 ENCODE exon 50437 50678 . - . Parent=gene24 ### chr16 ENCODE gene 51423 52204 . - . ID=gene25;Name=Z69719.3-009;Name2=RHBDF1 chr16 ENCODE exon 51423 51457 . - . Parent=gene25 chr16 . intron 51458 51582 . - . Parent=gene25 chr16 ENCODE exon 51583 51694 . - . Parent=gene25 chr16 . intron 51695 51795 . - . Parent=gene25 chr16 ENCODE exon 51796 52204 . - . Parent=gene25 ### chr16 ENCODE gene 52971 55035 . - . ID=gene26;Name=Z69719.3-005;Name2=RHBDF1 chr16 ENCODE exon 52971 53180 . - . Parent=gene26 chr16 . intron 53181 53584 . - . Parent=gene26 chr16 ENCODE exon 53585 53920 . - . Parent=gene26 chr16 . intron 53921 54696 . - . Parent=gene26 chr16 ENCODE exon 54697 54827 . - . Parent=gene26 chr16 . intron 54828 54896 . - . Parent=gene26 chr16 ENCODE exon 54897 55035 . - . Parent=gene26 ### chr16 ENCODE gene 53035 62619 . - . ID=gene27;Name=Z69719.3-003;Name2=RHBDF1 chr16 ENCODE exon 53035 53180 . - . Parent=gene27 chr16 . intron 53181 53584 . - . Parent=gene27 chr16 ENCODE exon 53585 55037 . - . Parent=gene27 chr16 . intron 55038 62510 . - . Parent=gene27 chr16 ENCODE exon 62511 62619 . - . Parent=gene27 ### chr16 ENCODE gene 53155 66354 . - . ID=gene28;Name=Z69719.3-010;Name2=RHBDF1 chr16 ENCODE exon 53155 53180 . - . Parent=gene28 chr16 ENCODE CDS 53155 53180 . - . Parent=gene28 chr16 . intron 53181 53584 . - . Parent=gene28 chr16 ENCODE exon 53585 53798 . - . Parent=gene28 chr16 ENCODE CDS 53585 53798 . - . Parent=gene28 chr16 . intron 53799 54696 . - . Parent=gene28 chr16 ENCODE exon 54697 54827 . - . Parent=gene28 chr16 ENCODE CDS 54697 54827 . - . Parent=gene28 chr16 . intron 54828 54896 . - . Parent=gene28 chr16 ENCODE CDS 54897 55013 . - . Parent=gene28 chr16 ENCODE exon 54897 55037 . - . Parent=gene28 chr16 . intron 55038 66251 . - . Parent=gene28 chr16 ENCODE exon 66252 66354 . - . Parent=gene28 ### chr16 ENCODE gene 53585 62566 . - . ID=gene29;Name=Z69719.3-004;Name2=RHBDF1 chr16 ENCODE exon 53585 53798 . - . Parent=gene29 chr16 ENCODE CDS 53585 53798 . - . Parent=gene29 chr16 . intron 53799 54330 . - . Parent=gene29 chr16 ENCODE exon 54331 54438 . - . Parent=gene29 chr16 ENCODE CDS 54331 54438 . - . Parent=gene29 chr16 . intron 54439 54696 . - . Parent=gene29 chr16 ENCODE exon 54697 54827 . - . Parent=gene29 chr16 ENCODE CDS 54697 54827 . - . Parent=gene29 chr16 . intron 54828 54896 . - . Parent=gene29 chr16 ENCODE CDS 54897 55013 . - . Parent=gene29 chr16 ENCODE exon 54897 55037 . - . Parent=gene29 chr16 . intron 55038 62513 . - . Parent=gene29 chr16 ENCODE exon 62514 62566 . - . Parent=gene29 ### chr16 ENCODE gene 54550 66340 . - . ID=gene30;Name=Z69719.3-011;Name2=RHBDF1 chr16 ENCODE exon 54550 55037 . - . Parent=gene30 chr16 . intron 55038 66251 . - . Parent=gene30 chr16 ENCODE exon 66252 66340 . - . Parent=gene30 ### chr16 ENCODE gene 67006 75683 . + . ID=gene31;Name=Z69720.1-004;Name2=MPG chr16 ENCODE exon 67006 67124 . + . Parent=gene31 chr16 . intron 67125 69423 . + . Parent=gene31 chr16 ENCODE exon 69424 69699 . + . Parent=gene31 chr16 ENCODE CDS 69436 69699 . + . Parent=gene31 chr16 . intron 69700 73050 . + . Parent=gene31 chr16 ENCODE exon 73051 73255 . + . Parent=gene31 chr16 ENCODE CDS 73051 73255 . + . Parent=gene31 chr16 . intron 73256 75399 . + . Parent=gene31 chr16 ENCODE exon 75400 75683 . + . Parent=gene31 chr16 ENCODE CDS 75400 75683 . + . Parent=gene31 ### chr16 ENCODE gene 68062 75852 . + . ID=gene32;Name=Z69720.1-002;Name2=MPG chr16 ENCODE exon 68062 68332 . + . Parent=gene32 chr16 ENCODE CDS 68309 68332 . + . Parent=gene32 chr16 . intron 68333 69423 . + . Parent=gene32 chr16 ENCODE exon 69424 69699 . + . Parent=gene32 chr16 ENCODE CDS 69424 69699 . + . Parent=gene32 chr16 . intron 69700 73050 . + . Parent=gene32 chr16 ENCODE exon 73051 73255 . + . Parent=gene32 chr16 ENCODE CDS 73051 73255 . + . Parent=gene32 chr16 . intron 73256 75399 . + . Parent=gene32 chr16 ENCODE CDS 75400 75776 . + . Parent=gene32 chr16 ENCODE exon 75400 75852 . + . Parent=gene32 ### chr16 ENCODE gene 68243 69843 . + . ID=gene33;Name=Z69720.1-003;Name2=MPG chr16 ENCODE exon 68243 68332 . + . Parent=gene33 chr16 . intron 68333 69423 . + . Parent=gene33 chr16 ENCODE exon 69424 69843 . + . Parent=gene33 ### chr16 ENCODE gene 68256 75841 . + . ID=gene34;Name=Z69720.1-001;Name2=MPG chr16 ENCODE exon 68256 68332 . + . Parent=gene34 chr16 . intron 68333 69137 . + . Parent=gene34 chr16 ENCODE exon 69138 69330 . + . Parent=gene34 chr16 ENCODE CDS 69292 69330 . + . Parent=gene34 chr16 . intron 69331 69423 . + . Parent=gene34 chr16 ENCODE exon 69424 69699 . + . Parent=gene34 chr16 ENCODE CDS 69424 69699 . + . Parent=gene34 chr16 . intron 69700 73050 . + . Parent=gene34 chr16 ENCODE exon 73051 73255 . + . Parent=gene34 chr16 ENCODE CDS 73051 73255 . + . Parent=gene34 chr16 . intron 73256 75399 . + . Parent=gene34 chr16 ENCODE CDS 75400 75776 . + . Parent=gene34 chr16 ENCODE exon 75400 75841 . + . Parent=gene34 ### chr16 ENCODE gene 74273 81084 . - . ID=gene35;Name=Z69666.1-005;Name2=C16orf35 chr16 ENCODE exon 74273 74594 . - . Parent=gene35 chr16 . intron 74595 76666 . - . Parent=gene35 chr16 ENCODE exon 76667 76869 . - . Parent=gene35 chr16 . intron 76870 78696 . - . Parent=gene35 chr16 ENCODE exon 78697 81084 . - . Parent=gene35 ### chr16 ENCODE gene 74273 128859 . - . ID=gene36;Name=Z69666.1-001;Name2=C16orf35 chr16 ENCODE exon 74273 74594 . - . Parent=gene36 chr16 . intron 74595 75819 . - . Parent=gene36 chr16 ENCODE exon 75820 76869 . - . Parent=gene36 chr16 . intron 76870 78696 . - . Parent=gene36 chr16 ENCODE exon 78697 78773 . - . Parent=gene36 chr16 . intron 78774 78775 . - . Parent=gene36 chr16 ENCODE exon 78776 78888 . - . Parent=gene36 chr16 . intron 78889 79710 . - . Parent=gene36 chr16 ENCODE exon 79711 79900 . - . Parent=gene36 chr16 . intron 79901 82593 . - . Parent=gene36 chr16 ENCODE exon 82594 82723 . - . Parent=gene36 chr16 . intron 82724 83216 . - . Parent=gene36 chr16 ENCODE exon 83217 83323 . - . Parent=gene36 chr16 . intron 83324 88142 . - . Parent=gene36 chr16 ENCODE exon 88143 88299 . - . Parent=gene36 chr16 . intron 88300 90369 . - . Parent=gene36 chr16 ENCODE exon 90370 90507 . - . Parent=gene36 chr16 . intron 90508 100522 . - . Parent=gene36 chr16 ENCODE exon 100523 100604 . - . Parent=gene36 chr16 . intron 100605 102620 . - . Parent=gene36 chr16 ENCODE exon 102621 102774 . - . Parent=gene36 chr16 . intron 102775 107299 . - . Parent=gene36 chr16 ENCODE exon 107300 107374 . - . Parent=gene36 chr16 . intron 107375 109124 . - . Parent=gene36 chr16 ENCODE exon 109125 109254 . - . Parent=gene36 chr16 . intron 109255 120520 . - . Parent=gene36 chr16 ENCODE exon 120521 120590 . - . Parent=gene36 chr16 . intron 120591 128148 . - . Parent=gene36 chr16 ENCODE exon 128149 128333 . - . Parent=gene36 chr16 . intron 128334 128640 . - . Parent=gene36 chr16 ENCODE exon 128641 128859 . - . Parent=gene36 ### chr16 ENCODE gene 75800 128511 . - . ID=gene37;Name=Z69666.1-003;Name2=C16orf35 chr16 ENCODE exon 75800 76869 . - . Parent=gene37 chr16 ENCODE CDS 76704 76869 . - . Parent=gene37 chr16 . intron 76870 78696 . - . Parent=gene37 chr16 ENCODE exon 78697 78773 . - . Parent=gene37 chr16 ENCODE CDS 78697 78773 . - . Parent=gene37 chr16 . intron 78774 78775 . - . Parent=gene37 chr16 ENCODE exon 78776 78888 . - . Parent=gene37 chr16 ENCODE CDS 78776 78888 . - . Parent=gene37 chr16 . intron 78889 79710 . - . Parent=gene37 chr16 ENCODE exon 79711 79900 . - . Parent=gene37 chr16 ENCODE CDS 79711 79900 . - . Parent=gene37 chr16 . intron 79901 82593 . - . Parent=gene37 chr16 ENCODE exon 82594 82723 . - . Parent=gene37 chr16 ENCODE CDS 82594 82723 . - . Parent=gene37 chr16 . intron 82724 83216 . - . Parent=gene37 chr16 ENCODE exon 83217 83323 . - . Parent=gene37 chr16 ENCODE CDS 83217 83323 . - . Parent=gene37 chr16 . intron 83324 88142 . - . Parent=gene37 chr16 ENCODE exon 88143 88299 . - . Parent=gene37 chr16 ENCODE CDS 88143 88299 . - . Parent=gene37 chr16 . intron 88300 90369 . - . Parent=gene37 chr16 ENCODE exon 90370 90507 . - . Parent=gene37 chr16 ENCODE CDS 90370 90507 . - . Parent=gene37 chr16 . intron 90508 100522 . - . Parent=gene37 chr16 ENCODE exon 100523 100604 . - . Parent=gene37 chr16 ENCODE CDS 100523 100604 . - . Parent=gene37 chr16 . intron 100605 102620 . - . Parent=gene37 chr16 ENCODE exon 102621 102774 . - . Parent=gene37 chr16 ENCODE CDS 102621 102774 . - . Parent=gene37 chr16 . intron 102775 109124 . - . Parent=gene37 chr16 ENCODE exon 109125 109254 . - . Parent=gene37 chr16 ENCODE CDS 109125 109254 . - . Parent=gene37 chr16 . intron 109255 120520 . - . Parent=gene37 chr16 ENCODE exon 120521 120590 . - . Parent=gene37 chr16 ENCODE CDS 120521 120590 . - . Parent=gene37 chr16 . intron 120591 128148 . - . Parent=gene37 chr16 ENCODE CDS 128149 128266 . - . Parent=gene37 chr16 ENCODE exon 128149 128511 . - . Parent=gene37 ### chr16 ENCODE gene 75800 128669 . - . ID=gene38;Name=Z69666.1-002;Name2=C16orf35 chr16 ENCODE exon 75800 76869 . - . Parent=gene38 chr16 . intron 76870 78696 . - . Parent=gene38 chr16 ENCODE exon 78697 78773 . - . Parent=gene38 chr16 . intron 78774 78775 . - . Parent=gene38 chr16 ENCODE exon 78776 78888 . - . Parent=gene38 chr16 . intron 78889 79710 . - . Parent=gene38 chr16 ENCODE exon 79711 79900 . - . Parent=gene38 chr16 . intron 79901 82593 . - . Parent=gene38 chr16 ENCODE exon 82594 82723 . - . Parent=gene38 chr16 . intron 82724 83216 . - . Parent=gene38 chr16 ENCODE exon 83217 83323 . - . Parent=gene38 chr16 . intron 83324 88142 . - . Parent=gene38 chr16 ENCODE exon 88143 88299 . - . Parent=gene38 chr16 . intron 88300 90369 . - . Parent=gene38 chr16 ENCODE exon 90370 90507 . - . Parent=gene38 chr16 . intron 90508 100522 . - . Parent=gene38 chr16 ENCODE exon 100523 100604 . - . Parent=gene38 chr16 . intron 100605 102620 . - . Parent=gene38 chr16 ENCODE exon 102621 102774 . - . Parent=gene38 chr16 . intron 102775 120520 . - . Parent=gene38 chr16 ENCODE exon 120521 120590 . - . Parent=gene38 chr16 . intron 120591 128148 . - . Parent=gene38 chr16 ENCODE exon 128149 128669 . - . Parent=gene38 ### chr16 ENCODE gene 76696 128268 . - . ID=gene39;Name=Z69666.1-004;Name2=C16orf35 chr16 ENCODE exon 76696 76869 . - . Parent=gene39 chr16 . intron 76870 78696 . - . Parent=gene39 chr16 ENCODE exon 78697 78888 . - . Parent=gene39 chr16 . intron 78889 79710 . - . Parent=gene39 chr16 ENCODE exon 79711 79900 . - . Parent=gene39 chr16 . intron 79901 82593 . - . Parent=gene39 chr16 ENCODE exon 82594 82723 . - . Parent=gene39 chr16 . intron 82724 83216 . - . Parent=gene39 chr16 ENCODE exon 83217 83323 . - . Parent=gene39 chr16 . intron 83324 88142 . - . Parent=gene39 chr16 ENCODE exon 88143 88299 . - . Parent=gene39 chr16 . intron 88300 90369 . - . Parent=gene39 chr16 ENCODE exon 90370 90507 . - . Parent=gene39 chr16 . intron 90508 100522 . - . Parent=gene39 chr16 ENCODE exon 100523 100604 . - . Parent=gene39 chr16 . intron 100605 102620 . - . Parent=gene39 chr16 ENCODE exon 102621 102774 . - . Parent=gene39 chr16 . intron 102775 107299 . - . Parent=gene39 chr16 ENCODE exon 107300 107374 . - . Parent=gene39 chr16 . intron 107375 120520 . - . Parent=gene39 chr16 ENCODE exon 120521 120590 . - . Parent=gene39 chr16 . intron 120591 128148 . - . Parent=gene39 chr16 ENCODE exon 128149 128268 . - . Parent=gene39 ### chr16 ENCODE gene 76704 128266 . - . ID=gene40;Name=Z69666.1-012;Name2=C16orf35 chr16 ENCODE exon 76704 76869 . - . Parent=gene40 chr16 ENCODE CDS 76704 76869 . - . Parent=gene40 chr16 . intron 76870 78696 . - . Parent=gene40 chr16 ENCODE exon 78697 78773 . - . Parent=gene40 chr16 ENCODE CDS 78697 78773 . - . Parent=gene40 chr16 . intron 78774 78775 . - . Parent=gene40 chr16 ENCODE exon 78776 78888 . - . Parent=gene40 chr16 ENCODE CDS 78776 78888 . - . Parent=gene40 chr16 . intron 78889 79710 . - . Parent=gene40 chr16 ENCODE exon 79711 79900 . - . Parent=gene40 chr16 ENCODE CDS 79711 79900 . - . Parent=gene40 chr16 . intron 79901 82593 . - . Parent=gene40 chr16 ENCODE exon 82594 82723 . - . Parent=gene40 chr16 ENCODE CDS 82594 82723 . - . Parent=gene40 chr16 . intron 82724 83216 . - . Parent=gene40 chr16 ENCODE exon 83217 83323 . - . Parent=gene40 chr16 ENCODE CDS 83217 83323 . - . Parent=gene40 chr16 . intron 83324 88142 . - . Parent=gene40 chr16 ENCODE exon 88143 88299 . - . Parent=gene40 chr16 ENCODE CDS 88143 88299 . - . Parent=gene40 chr16 . intron 88300 90369 . - . Parent=gene40 chr16 ENCODE exon 90370 90507 . - . Parent=gene40 chr16 ENCODE CDS 90370 90507 . - . Parent=gene40 chr16 . intron 90508 100522 . - . Parent=gene40 chr16 ENCODE exon 100523 100604 . - . Parent=gene40 chr16 ENCODE CDS 100523 100604 . - . Parent=gene40 chr16 . intron 100605 102620 . - . Parent=gene40 chr16 ENCODE exon 102621 102774 . - . Parent=gene40 chr16 ENCODE CDS 102621 102774 . - . Parent=gene40 chr16 . intron 102775 107299 . - . Parent=gene40 chr16 ENCODE exon 107300 107374 . - . Parent=gene40 chr16 ENCODE CDS 107300 107374 . - . Parent=gene40 chr16 . intron 107375 109124 . - . Parent=gene40 chr16 ENCODE exon 109125 109254 . - . Parent=gene40 chr16 ENCODE CDS 109125 109254 . - . Parent=gene40 chr16 . intron 109255 120520 . - . Parent=gene40 chr16 ENCODE exon 120521 120590 . - . Parent=gene40 chr16 ENCODE CDS 120521 120590 . - . Parent=gene40 chr16 . intron 120591 128148 . - . Parent=gene40 chr16 ENCODE exon 128149 128266 . - . Parent=gene40 chr16 ENCODE CDS 128149 128266 . - . Parent=gene40 ### chr16 ENCODE gene 82789 88158 . - . ID=gene41;Name=Z69666.1-009;Name2=C16orf35 chr16 ENCODE exon 82789 83323 . - . Parent=gene41 chr16 . intron 83324 88142 . - . Parent=gene41 chr16 ENCODE exon 88143 88158 . - . Parent=gene41 ### chr16 ENCODE gene 83257 109404 . - . ID=gene42;Name=Z69666.1-008;Name2=C16orf35 chr16 ENCODE exon 83257 83323 . - . Parent=gene42 chr16 . intron 83324 88142 . - . Parent=gene42 chr16 ENCODE exon 88143 88299 . - . Parent=gene42 chr16 . intron 88300 90369 . - . Parent=gene42 chr16 ENCODE exon 90370 90507 . - . Parent=gene42 chr16 . intron 90508 100522 . - . Parent=gene42 chr16 ENCODE exon 100523 100604 . - . Parent=gene42 chr16 . intron 100605 102620 . - . Parent=gene42 chr16 ENCODE exon 102621 102774 . - . Parent=gene42 chr16 . intron 102775 107299 . - . Parent=gene42 chr16 ENCODE exon 107300 107374 . - . Parent=gene42 chr16 . intron 107375 109124 . - . Parent=gene42 chr16 ENCODE exon 109125 109254 . - . Parent=gene42 chr16 . intron 109255 109352 . - . Parent=gene42 chr16 ENCODE exon 109353 109404 . - . Parent=gene42 ### chr16 ENCODE gene 88228 128665 . - . ID=gene43;Name=Z69666.1-010;Name2=C16orf35 chr16 ENCODE exon 88228 88299 . - . Parent=gene43 chr16 . intron 88300 90369 . - . Parent=gene43 chr16 ENCODE exon 90370 90507 . - . Parent=gene43 chr16 . intron 90508 100522 . - . Parent=gene43 chr16 ENCODE exon 100523 100604 . - . Parent=gene43 chr16 . intron 100605 102620 . - . Parent=gene43 chr16 ENCODE exon 102621 102774 . - . Parent=gene43 chr16 . intron 102775 107299 . - . Parent=gene43 chr16 ENCODE exon 107300 107374 . - . Parent=gene43 chr16 . intron 107375 109124 . - . Parent=gene43 chr16 ENCODE exon 109125 109254 . - . Parent=gene43 chr16 . intron 109255 113505 . - . Parent=gene43 chr16 ENCODE exon 113506 113544 . - . Parent=gene43 chr16 . intron 113545 114935 . - . Parent=gene43 chr16 ENCODE exon 114936 115072 . - . Parent=gene43 chr16 . intron 115073 120520 . - . Parent=gene43 chr16 ENCODE exon 120521 120590 . - . Parent=gene43 chr16 . intron 120591 128640 . - . Parent=gene43 chr16 ENCODE exon 128641 128665 . - . Parent=gene43 ### chr16 ENCODE gene 100523 128676 . - . ID=gene44;Name=Z69666.1-006;Name2=C16orf35 chr16 ENCODE exon 100523 100604 . - . Parent=gene44 chr16 . intron 100605 102620 . - . Parent=gene44 chr16 ENCODE exon 102621 102774 . - . Parent=gene44 chr16 . intron 102775 109124 . - . Parent=gene44 chr16 ENCODE exon 109125 109254 . - . Parent=gene44 chr16 . intron 109255 114935 . - . Parent=gene44 chr16 ENCODE exon 114936 115072 . - . Parent=gene44 chr16 . intron 115073 120520 . - . Parent=gene44 chr16 ENCODE exon 120521 120590 . - . Parent=gene44 chr16 . intron 120591 128148 . - . Parent=gene44 chr16 ENCODE exon 128149 128333 . - . Parent=gene44 chr16 . intron 128334 128640 . - . Parent=gene44 chr16 ENCODE exon 128641 128676 . - . Parent=gene44 ### chr16 ENCODE gene 102659 128334 . - . ID=gene45;Name=Z69666.1-011;Name2=C16orf35 chr16 ENCODE exon 102659 102774 . - . Parent=gene45 chr16 ENCODE CDS 102659 102774 . - . Parent=gene45 chr16 . intron 102775 107299 . - . Parent=gene45 chr16 ENCODE exon 107300 107374 . - . Parent=gene45 chr16 ENCODE CDS 107300 107374 . - . Parent=gene45 chr16 . intron 107375 109124 . - . Parent=gene45 chr16 ENCODE exon 109125 109254 . - . Parent=gene45 chr16 ENCODE CDS 109125 109254 . - . Parent=gene45 chr16 . intron 109255 113505 . - . Parent=gene45 chr16 ENCODE exon 113506 113544 . - . Parent=gene45 chr16 ENCODE CDS 113506 113544 . - . Parent=gene45 chr16 . intron 113545 120520 . - . Parent=gene45 chr16 ENCODE exon 120521 120590 . - . Parent=gene45 chr16 ENCODE CDS 120521 120590 . - . Parent=gene45 chr16 . intron 120591 128148 . - . Parent=gene45 chr16 ENCODE CDS 128149 128266 . - . Parent=gene45 chr16 ENCODE exon 128149 128334 . - . Parent=gene45 ### chr16 ENCODE gene 142686 144502 . + . ID=gene46;Name=Z84721.1-001;Name2=HBZ chr16 ENCODE exon 142686 143003 . + . Parent=gene46 chr16 ENCODE CDS 142909 143003 . + . Parent=gene46 chr16 . intron 143004 143890 . + . Parent=gene46 chr16 ENCODE exon 143891 144095 . + . Parent=gene46 chr16 ENCODE CDS 143891 144095 . + . Parent=gene46 chr16 . intron 144096 144270 . + . Parent=gene46 chr16 ENCODE CDS 144271 144399 . + . Parent=gene46 chr16 ENCODE exon 144271 144502 . + . Parent=gene46 ### chr16 ENCODE gene 143891 156760 . + . ID=gene47;Name=Z84721.3-003;Name2=HBM chr16 ENCODE exon 143891 144095 . + . Parent=gene47 chr16 . intron 144096 156266 . + . Parent=gene47 chr16 ENCODE exon 156267 156471 . + . Parent=gene47 chr16 . intron 156472 156578 . + . Parent=gene47 chr16 ENCODE exon 156579 156760 . + . Parent=gene47 ### chr16 ENCODE gene 154481 156760 . + . ID=gene48;Name=Z84721.3-002;Name2=HBM chr16 ENCODE exon 154481 154685 . + . Parent=gene48 chr16 . intron 154686 156266 . + . Parent=gene48 chr16 ENCODE exon 156267 156471 . + . Parent=gene48 chr16 . intron 156472 156578 . + . Parent=gene48 chr16 ENCODE exon 156579 156760 . + . Parent=gene48 ### chr16 ENCODE gene 155977 156767 . + . ID=gene49;Name=Z84721.3-001;Name2=HBM chr16 ENCODE exon 155977 156088 . + . Parent=gene49 chr16 ENCODE CDS 155997 156088 . + . Parent=gene49 chr16 . intron 156089 156266 . + . Parent=gene49 chr16 ENCODE exon 156267 156471 . + . Parent=gene49 chr16 ENCODE CDS 156267 156471 . + . Parent=gene49 chr16 . intron 156472 156578 . + . Parent=gene49 chr16 ENCODE CDS 156579 156707 . + . Parent=gene49 chr16 ENCODE exon 156579 156767 . + . Parent=gene49 ### chr16 ENCODE gene 162846 163709 . + . ID=gene50;Name=Z84721.5-001;Name2=HBA2 chr16 ENCODE exon 162846 163006 . + . Parent=gene50 chr16 ENCODE CDS 162912 163006 . + . Parent=gene50 chr16 . intron 163007 163123 . + . Parent=gene50 chr16 ENCODE exon 163124 163328 . + . Parent=gene50 chr16 ENCODE CDS 163124 163328 . + . Parent=gene50 chr16 . intron 163329 163470 . + . Parent=gene50 chr16 ENCODE CDS 163471 163599 . + . Parent=gene50 chr16 ENCODE exon 163471 163709 . + . Parent=gene50 ### chr16 ENCODE gene 162889 163709 . + . ID=gene51;Name=Z84721.5-002;Name2=HBA2 chr16 ENCODE exon 162889 162957 . + . Parent=gene51 chr16 . intron 162958 163123 . + . Parent=gene51 chr16 ENCODE exon 163124 163328 . + . Parent=gene51 chr16 ENCODE CDS 163125 163328 . + . Parent=gene51 chr16 . intron 163329 163470 . + . Parent=gene51 chr16 ENCODE CDS 163471 163599 . + . Parent=gene51 chr16 ENCODE exon 163471 163709 . + . Parent=gene51 ### chr16 ENCODE gene 162893 163674 . + . ID=gene52;Name=Z84721.5-003;Name2=HBA2 chr16 ENCODE exon 162893 163328 . + . Parent=gene52 chr16 . intron 163329 163470 . + . Parent=gene52 chr16 ENCODE exon 163471 163674 . + . Parent=gene52 ### chr16 ENCODE gene 162942 163655 . + . ID=gene53;Name=Z84721.5-005;Name2=HBA2 chr16 ENCODE exon 162942 163006 . + . Parent=gene53 chr16 . intron 163007 163123 . + . Parent=gene53 chr16 ENCODE exon 163124 163247 . + . Parent=gene53 chr16 . intron 163248 163307 . + . Parent=gene53 chr16 ENCODE exon 163308 163328 . + . Parent=gene53 chr16 . intron 163329 163470 . + . Parent=gene53 chr16 ENCODE exon 163471 163655 . + . Parent=gene53 ### chr16 ENCODE gene 162943 163462 . + . ID=gene54;Name=Z84721.5-006;Name2=HBA2 chr16 ENCODE exon 162943 163006 . + . Parent=gene54 chr16 . intron 163007 163123 . + . Parent=gene54 chr16 ENCODE exon 163124 163462 . + . Parent=gene54 ### chr16 ENCODE gene 166679 167521 . + . ID=gene55;Name=Z84721.6-001;Name2=HBA1 chr16 ENCODE exon 166679 166810 . + . Parent=gene55 chr16 ENCODE CDS 166716 166810 . + . Parent=gene55 chr16 . intron 166811 166927 . + . Parent=gene55 chr16 ENCODE exon 166928 167132 . + . Parent=gene55 chr16 ENCODE CDS 166928 167132 . + . Parent=gene55 chr16 . intron 167133 167281 . + . Parent=gene55 chr16 ENCODE CDS 167282 167410 . + . Parent=gene55 chr16 ENCODE exon 167282 167521 . + . Parent=gene55 ### chr16 ENCODE gene 166697 167519 . + . ID=gene56;Name=Z84721.6-002;Name2=HBA1 chr16 ENCODE exon 166697 167132 . + . Parent=gene56 chr16 . intron 167133 167281 . + . Parent=gene56 chr16 ENCODE exon 167282 167519 . + . Parent=gene56 ### chr16 ENCODE gene 166702 167488 . + . ID=gene57;Name=Z84721.6-003;Name2=HBA1 chr16 ENCODE exon 166702 166810 . + . Parent=gene57 chr16 . intron 166811 166927 . + . Parent=gene57 chr16 ENCODE exon 166928 166967 . + . Parent=gene57 chr16 . intron 166968 167120 . + . Parent=gene57 chr16 ENCODE exon 167121 167132 . + . Parent=gene57 chr16 . intron 167133 167281 . + . Parent=gene57 chr16 ENCODE exon 167282 167488 . + . Parent=gene57 ### chr16 ENCODE gene 166703 167521 . + . ID=gene58;Name=Z84721.6-006;Name2=HBA1 chr16 ENCODE exon 166703 166761 . + . Parent=gene58 chr16 . intron 166762 166927 . + . Parent=gene58 chr16 ENCODE exon 166928 167132 . + . Parent=gene58 chr16 ENCODE CDS 166929 167132 . + . Parent=gene58 chr16 . intron 167133 167281 . + . Parent=gene58 chr16 ENCODE CDS 167282 167410 . + . Parent=gene58 chr16 ENCODE exon 167282 167521 . + . Parent=gene58 ### chr16 ENCODE gene 166746 167498 . + . ID=gene59;Name=Z84721.6-004;Name2=HBA1 chr16 ENCODE exon 166746 166810 . + . Parent=gene59 chr16 . intron 166811 166927 . + . Parent=gene59 chr16 ENCODE exon 166928 167051 . + . Parent=gene59 chr16 . intron 167052 167111 . + . Parent=gene59 chr16 ENCODE exon 167112 167132 . + . Parent=gene59 chr16 . intron 167133 167281 . + . Parent=gene59 chr16 ENCODE exon 167282 167498 . + . Parent=gene59 ### chr16 ENCODE gene 166747 167273 . + . ID=gene60;Name=Z84721.6-005;Name2=HBA1 chr16 ENCODE exon 166747 166810 . + . Parent=gene60 chr16 . intron 166811 166927 . + . Parent=gene60 chr16 ENCODE exon 166928 167273 . + . Parent=gene60 ### chr16 ENCODE gene 170452 171180 . + . ID=gene61;Name=Z84721.7-001;Name2=HBQ1 chr16 ENCODE exon 170452 170580 . + . Parent=gene61 chr16 ENCODE CDS 170486 170580 . + . Parent=gene61 chr16 . intron 170581 170664 . + . Parent=gene61 chr16 ENCODE exon 170665 170869 . + . Parent=gene61 chr16 ENCODE CDS 170665 170869 . + . Parent=gene61 chr16 . intron 170870 170978 . + . Parent=gene61 chr16 ENCODE CDS 170979 171107 . + . Parent=gene61 chr16 ENCODE exon 170979 171180 . + . Parent=gene61 ### chr16 ENCODE gene 178969 219439 . - . ID=gene62;Name=LA16c-OS12.1-006;Name2=LUC7L chr16 ENCODE exon 178969 179339 . - . Parent=gene62 chr16 . intron 179340 179967 . - . Parent=gene62 chr16 ENCODE exon 179968 180135 . - . Parent=gene62 chr16 . intron 180136 180540 . - . Parent=gene62 chr16 ENCODE exon 180541 180570 . - . Parent=gene62 chr16 . intron 180571 182926 . - . Parent=gene62 chr16 ENCODE exon 182927 183015 . - . Parent=gene62 chr16 . intron 183016 189061 . - . Parent=gene62 chr16 ENCODE exon 189062 189238 . - . Parent=gene62 chr16 . intron 189239 196003 . - . Parent=gene62 chr16 ENCODE exon 196004 196147 . - . Parent=gene62 chr16 . intron 196148 198077 . - . Parent=gene62 chr16 ENCODE exon 198078 198188 . - . Parent=gene62 chr16 . intron 198189 210648 . - . Parent=gene62 chr16 ENCODE exon 210649 210747 . - . Parent=gene62 chr16 . intron 210748 217241 . - . Parent=gene62 chr16 ENCODE exon 217242 217336 . - . Parent=gene62 chr16 . intron 217337 217986 . - . Parent=gene62 chr16 ENCODE exon 217987 219439 . - . Parent=gene62 ### chr16 ENCODE gene 178969 219450 . - . ID=gene63;Name=LA16c-OS12.1-003;Name2=LUC7L chr16 ENCODE exon 178969 179339 . - . Parent=gene63 chr16 ENCODE CDS 179198 179339 . - . Parent=gene63 chr16 . intron 179340 179967 . - . Parent=gene63 chr16 ENCODE exon 179968 180135 . - . Parent=gene63 chr16 ENCODE CDS 179968 180135 . - . Parent=gene63 chr16 . intron 180136 180540 . - . Parent=gene63 chr16 ENCODE exon 180541 180570 . - . Parent=gene63 chr16 ENCODE CDS 180541 180570 . - . Parent=gene63 chr16 . intron 180571 182926 . - . Parent=gene63 chr16 ENCODE exon 182927 183015 . - . Parent=gene63 chr16 ENCODE CDS 182927 183015 . - . Parent=gene63 chr16 . intron 183016 189061 . - . Parent=gene63 chr16 ENCODE exon 189062 189238 . - . Parent=gene63 chr16 ENCODE CDS 189062 189238 . - . Parent=gene63 chr16 . intron 189239 196003 . - . Parent=gene63 chr16 ENCODE exon 196004 196147 . - . Parent=gene63 chr16 ENCODE CDS 196004 196147 . - . Parent=gene63 chr16 . intron 196148 198077 . - . Parent=gene63 chr16 ENCODE exon 198078 198188 . - . Parent=gene63 chr16 ENCODE CDS 198078 198188 . - . Parent=gene63 chr16 . intron 198189 210648 . - . Parent=gene63 chr16 ENCODE exon 210649 210747 . - . Parent=gene63 chr16 ENCODE CDS 210649 210747 . - . Parent=gene63 chr16 . intron 210748 217241 . - . Parent=gene63 chr16 ENCODE exon 217242 217336 . - . Parent=gene63 chr16 ENCODE CDS 217242 217336 . - . Parent=gene63 chr16 . intron 217337 219278 . - . Parent=gene63 chr16 ENCODE CDS 219279 219339 . - . Parent=gene63 chr16 ENCODE exon 219279 219450 . - . Parent=gene63 ### chr16 ENCODE gene 178969 219463 . - . ID=gene64;Name=LA16c-OS12.1-001;Name2=LUC7L chr16 ENCODE exon 178969 180135 . - . Parent=gene64 chr16 ENCODE CDS 179964 180135 . - . Parent=gene64 chr16 . intron 180136 180540 . - . Parent=gene64 chr16 ENCODE exon 180541 180570 . - . Parent=gene64 chr16 ENCODE CDS 180541 180570 . - . Parent=gene64 chr16 . intron 180571 182926 . - . Parent=gene64 chr16 ENCODE exon 182927 183015 . - . Parent=gene64 chr16 ENCODE CDS 182927 183015 . - . Parent=gene64 chr16 . intron 183016 189061 . - . Parent=gene64 chr16 ENCODE exon 189062 189238 . - . Parent=gene64 chr16 ENCODE CDS 189062 189238 . - . Parent=gene64 chr16 . intron 189239 196003 . - . Parent=gene64 chr16 ENCODE exon 196004 196147 . - . Parent=gene64 chr16 ENCODE CDS 196004 196147 . - . Parent=gene64 chr16 . intron 196148 198077 . - . Parent=gene64 chr16 ENCODE exon 198078 198188 . - . Parent=gene64 chr16 ENCODE CDS 198078 198188 . - . Parent=gene64 chr16 . intron 198189 210648 . - . Parent=gene64 chr16 ENCODE exon 210649 210747 . - . Parent=gene64 chr16 ENCODE CDS 210649 210747 . - . Parent=gene64 chr16 . intron 210748 217241 . - . Parent=gene64 chr16 ENCODE exon 217242 217336 . - . Parent=gene64 chr16 ENCODE CDS 217242 217336 . - . Parent=gene64 chr16 . intron 217337 219278 . - . Parent=gene64 chr16 ENCODE CDS 219279 219339 . - . Parent=gene64 chr16 ENCODE exon 219279 219463 . - . Parent=gene64 ### chr16 ENCODE gene 178971 219463 . - . ID=gene65;Name=LA16c-OS12.1-002;Name2=LUC7L chr16 ENCODE exon 178971 179339 . - . Parent=gene65 chr16 . intron 179340 179930 . - . Parent=gene65 chr16 ENCODE exon 179931 180135 . - . Parent=gene65 chr16 ENCODE CDS 179964 180135 . - . Parent=gene65 chr16 . intron 180136 180540 . - . Parent=gene65 chr16 ENCODE exon 180541 180570 . - . Parent=gene65 chr16 ENCODE CDS 180541 180570 . - . Parent=gene65 chr16 . intron 180571 182926 . - . Parent=gene65 chr16 ENCODE exon 182927 183015 . - . Parent=gene65 chr16 ENCODE CDS 182927 183015 . - . Parent=gene65 chr16 . intron 183016 189061 . - . Parent=gene65 chr16 ENCODE exon 189062 189238 . - . Parent=gene65 chr16 ENCODE CDS 189062 189238 . - . Parent=gene65 chr16 . intron 189239 196003 . - . Parent=gene65 chr16 ENCODE exon 196004 196147 . - . Parent=gene65 chr16 ENCODE CDS 196004 196147 . - . Parent=gene65 chr16 . intron 196148 198077 . - . Parent=gene65 chr16 ENCODE exon 198078 198188 . - . Parent=gene65 chr16 ENCODE CDS 198078 198188 . - . Parent=gene65 chr16 . intron 198189 210648 . - . Parent=gene65 chr16 ENCODE exon 210649 210747 . - . Parent=gene65 chr16 ENCODE CDS 210649 210747 . - . Parent=gene65 chr16 . intron 210748 217241 . - . Parent=gene65 chr16 ENCODE exon 217242 217336 . - . Parent=gene65 chr16 ENCODE CDS 217242 217336 . - . Parent=gene65 chr16 . intron 217337 219278 . - . Parent=gene65 chr16 ENCODE CDS 219279 219339 . - . Parent=gene65 chr16 ENCODE exon 219279 219463 . - . Parent=gene65 ### chr16 ENCODE gene 178990 180595 . - . ID=gene66;Name=LA16c-OS12.1-017;Name2=LUC7L chr16 ENCODE exon 178990 179339 . - . Parent=gene66 chr16 . intron 179340 179967 . - . Parent=gene66 chr16 ENCODE exon 179968 180135 . - . Parent=gene66 chr16 . intron 180136 180540 . - . Parent=gene66 chr16 ENCODE exon 180541 180595 . - . Parent=gene66 ### chr16 ENCODE gene 178990 196087 . - . ID=gene67;Name=LA16c-OS12.1-016;Name2=LUC7L chr16 ENCODE exon 178990 179339 . - . Parent=gene67 chr16 ENCODE CDS 179198 179339 . - . Parent=gene67 chr16 . intron 179340 179967 . - . Parent=gene67 chr16 ENCODE exon 179968 180135 . - . Parent=gene67 chr16 ENCODE CDS 179968 180135 . - . Parent=gene67 chr16 . intron 180136 180540 . - . Parent=gene67 chr16 ENCODE exon 180541 180570 . - . Parent=gene67 chr16 ENCODE CDS 180541 180570 . - . Parent=gene67 chr16 . intron 180571 182926 . - . Parent=gene67 chr16 ENCODE exon 182927 183015 . - . Parent=gene67 chr16 ENCODE CDS 182927 183015 . - . Parent=gene67 chr16 . intron 183016 196003 . - . Parent=gene67 chr16 ENCODE exon 196004 196087 . - . Parent=gene67 chr16 ENCODE CDS 196004 196087 . - . Parent=gene67 ### chr16 ENCODE gene 178990 219451 . - . ID=gene68;Name=LA16c-OS12.1-005;Name2=LUC7L chr16 ENCODE exon 178990 179339 . - . Parent=gene68 chr16 . intron 179340 179967 . - . Parent=gene68 chr16 ENCODE exon 179968 180135 . - . Parent=gene68 chr16 . intron 180136 180540 . - . Parent=gene68 chr16 ENCODE exon 180541 180570 . - . Parent=gene68 chr16 . intron 180571 180661 . - . Parent=gene68 chr16 ENCODE exon 180662 180802 . - . Parent=gene68 chr16 . intron 180803 182926 . - . Parent=gene68 chr16 ENCODE exon 182927 183015 . - . Parent=gene68 chr16 . intron 183016 189061 . - . Parent=gene68 chr16 ENCODE exon 189062 189238 . - . Parent=gene68 chr16 . intron 189239 196003 . - . Parent=gene68 chr16 ENCODE exon 196004 196147 . - . Parent=gene68 chr16 . intron 196148 198077 . - . Parent=gene68 chr16 ENCODE exon 198078 198188 . - . Parent=gene68 chr16 . intron 198189 210648 . - . Parent=gene68 chr16 ENCODE exon 210649 210747 . - . Parent=gene68 chr16 . intron 210748 217241 . - . Parent=gene68 chr16 ENCODE exon 217242 218402 . - . Parent=gene68 chr16 . intron 218403 219278 . - . Parent=gene68 chr16 ENCODE exon 219279 219451 . - . Parent=gene68 ### chr16 ENCODE gene 179098 199773 . - . ID=gene69;Name=LA16c-OS12.1-008;Name2=LUC7L chr16 ENCODE exon 179098 179339 . - . Parent=gene69 chr16 . intron 179340 179967 . - . Parent=gene69 chr16 ENCODE exon 179968 180135 . - . Parent=gene69 chr16 . intron 180136 180540 . - . Parent=gene69 chr16 ENCODE exon 180541 180570 . - . Parent=gene69 chr16 . intron 180571 182926 . - . Parent=gene69 chr16 ENCODE exon 182927 183015 . - . Parent=gene69 chr16 . intron 183016 189061 . - . Parent=gene69 chr16 ENCODE exon 189062 189238 . - . Parent=gene69 chr16 . intron 189239 196003 . - . Parent=gene69 chr16 ENCODE exon 196004 196147 . - . Parent=gene69 chr16 . intron 196148 198077 . - . Parent=gene69 chr16 ENCODE exon 198078 198188 . - . Parent=gene69 chr16 . intron 198189 198600 . - . Parent=gene69 chr16 ENCODE exon 198601 199773 . - . Parent=gene69 ### chr16 ENCODE gene 179115 180549 . - . ID=gene70;Name=LA16c-OS12.1-018;Name2=LUC7L chr16 ENCODE exon 179115 179339 . - . Parent=gene70 chr16 . intron 179340 179946 . - . Parent=gene70 chr16 ENCODE exon 179947 180135 . - . Parent=gene70 chr16 . intron 180136 180540 . - . Parent=gene70 chr16 ENCODE exon 180541 180549 . - . Parent=gene70 ### chr16 ENCODE gene 179896 217686 . - . ID=gene71;Name=LA16c-OS12.1-007;Name2=LUC7L chr16 ENCODE exon 179896 180135 . - . Parent=gene71 chr16 ENCODE CDS 179964 180135 . - . Parent=gene71 chr16 . intron 180136 180540 . - . Parent=gene71 chr16 ENCODE exon 180541 180570 . - . Parent=gene71 chr16 ENCODE CDS 180541 180570 . - . Parent=gene71 chr16 . intron 180571 182926 . - . Parent=gene71 chr16 ENCODE exon 182927 183015 . - . Parent=gene71 chr16 ENCODE CDS 182927 183015 . - . Parent=gene71 chr16 . intron 183016 189061 . - . Parent=gene71 chr16 ENCODE exon 189062 189238 . - . Parent=gene71 chr16 ENCODE CDS 189062 189238 . - . Parent=gene71 chr16 . intron 189239 196003 . - . Parent=gene71 chr16 ENCODE exon 196004 196147 . - . Parent=gene71 chr16 ENCODE CDS 196004 196147 . - . Parent=gene71 chr16 . intron 196148 198077 . - . Parent=gene71 chr16 ENCODE exon 198078 198188 . - . Parent=gene71 chr16 ENCODE CDS 198078 198188 . - . Parent=gene71 chr16 . intron 198189 210648 . - . Parent=gene71 chr16 ENCODE CDS 210649 210744 . - . Parent=gene71 chr16 ENCODE exon 210649 210747 . - . Parent=gene71 chr16 . intron 210748 217241 . - . Parent=gene71 chr16 ENCODE exon 217242 217686 . - . Parent=gene71 ### chr16 ENCODE gene 179896 219434 . - . ID=gene72;Name=LA16c-OS12.1-004;Name2=LUC7L chr16 ENCODE exon 179896 180135 . - . Parent=gene72 chr16 . intron 180136 180540 . - . Parent=gene72 chr16 ENCODE exon 180541 180570 . - . Parent=gene72 chr16 . intron 180571 182926 . - . Parent=gene72 chr16 ENCODE exon 182927 183015 . - . Parent=gene72 chr16 . intron 183016 189061 . - . Parent=gene72 chr16 ENCODE exon 189062 189238 . - . Parent=gene72 chr16 . intron 189239 196003 . - . Parent=gene72 chr16 ENCODE exon 196004 196147 . - . Parent=gene72 chr16 . intron 196148 198077 . - . Parent=gene72 chr16 ENCODE exon 198078 198188 . - . Parent=gene72 chr16 . intron 198189 210648 . - . Parent=gene72 chr16 ENCODE exon 210649 210747 . - . Parent=gene72 chr16 . intron 210748 217241 . - . Parent=gene72 chr16 ENCODE exon 217242 217336 . - . Parent=gene72 chr16 . intron 217337 218332 . - . Parent=gene72 chr16 ENCODE exon 218333 218402 . - . Parent=gene72 chr16 . intron 218403 219278 . - . Parent=gene72 chr16 ENCODE exon 219279 219434 . - . Parent=gene72 ### chr16 ENCODE gene 180001 198508 . - . ID=gene73;Name=LA16c-OS12.1-014;Name2=LUC7L chr16 ENCODE exon 180001 180135 . - . Parent=gene73 chr16 . intron 180136 180540 . - . Parent=gene73 chr16 ENCODE exon 180541 180570 . - . Parent=gene73 chr16 . intron 180571 182926 . - . Parent=gene73 chr16 ENCODE exon 182927 183015 . - . Parent=gene73 chr16 . intron 183016 189061 . - . Parent=gene73 chr16 ENCODE exon 189062 189238 . - . Parent=gene73 chr16 . intron 189239 196003 . - . Parent=gene73 chr16 ENCODE exon 196004 196147 . - . Parent=gene73 chr16 . intron 196148 198077 . - . Parent=gene73 chr16 ENCODE exon 198078 198508 . - . Parent=gene73 ### chr16 ENCODE gene 180122 219374 . - . ID=gene74;Name=LA16c-OS12.1-009;Name2=LUC7L chr16 ENCODE exon 180122 180135 . - . Parent=gene74 chr16 . intron 180136 180540 . - . Parent=gene74 chr16 ENCODE exon 180541 180570 . - . Parent=gene74 chr16 . intron 180571 182926 . - . Parent=gene74 chr16 ENCODE exon 182927 183015 . - . Parent=gene74 chr16 . intron 183016 189061 . - . Parent=gene74 chr16 ENCODE exon 189062 189238 . - . Parent=gene74 chr16 . intron 189239 196003 . - . Parent=gene74 chr16 ENCODE exon 196004 196147 . - . Parent=gene74 chr16 . intron 196148 198077 . - . Parent=gene74 chr16 ENCODE exon 198078 198188 . - . Parent=gene74 chr16 . intron 198189 198600 . - . Parent=gene74 chr16 ENCODE exon 198601 198664 . - . Parent=gene74 chr16 . intron 198665 210648 . - . Parent=gene74 chr16 ENCODE exon 210649 210747 . - . Parent=gene74 chr16 . intron 210748 217241 . - . Parent=gene74 chr16 ENCODE exon 217242 217336 . - . Parent=gene74 chr16 . intron 217337 218332 . - . Parent=gene74 chr16 ENCODE exon 218333 218402 . - . Parent=gene74 chr16 . intron 218403 219278 . - . Parent=gene74 chr16 ENCODE exon 219279 219374 . - . Parent=gene74 ### chr16 ENCODE gene 180541 219422 . - . ID=gene75;Name=LA16c-OS12.1-015;Name2=LUC7L chr16 ENCODE exon 180541 180570 . - . Parent=gene75 chr16 . intron 180571 182926 . - . Parent=gene75 chr16 ENCODE exon 182927 183015 . - . Parent=gene75 chr16 . intron 183016 189061 . - . Parent=gene75 chr16 ENCODE exon 189062 189238 . - . Parent=gene75 chr16 . intron 189239 196003 . - . Parent=gene75 chr16 ENCODE exon 196004 196147 . - . Parent=gene75 chr16 . intron 196148 198077 . - . Parent=gene75 chr16 ENCODE exon 198078 198188 . - . Parent=gene75 chr16 . intron 198189 219278 . - . Parent=gene75 chr16 ENCODE exon 219279 219422 . - . Parent=gene75 ### chr16 ENCODE gene 196004 217656 . - . ID=gene76;Name=LA16c-OS12.1-012;Name2=LUC7L chr16 ENCODE exon 196004 196147 . - . Parent=gene76 chr16 . intron 196148 198077 . - . Parent=gene76 chr16 ENCODE exon 198078 198188 . - . Parent=gene76 chr16 . intron 198189 198600 . - . Parent=gene76 chr16 ENCODE exon 198601 198664 . - . Parent=gene76 chr16 . intron 198665 210648 . - . Parent=gene76 chr16 ENCODE exon 210649 210747 . - . Parent=gene76 chr16 . intron 210748 217241 . - . Parent=gene76 chr16 ENCODE exon 217242 217656 . - . Parent=gene76 ### chr16 ENCODE gene 198633 219142 . - . ID=gene77;Name=LA16c-OS12.1-010;Name2=LUC7L chr16 ENCODE exon 198633 198664 . - . Parent=gene77 chr16 . intron 198665 210648 . - . Parent=gene77 chr16 ENCODE exon 210649 210747 . - . Parent=gene77 chr16 . intron 210748 217241 . - . Parent=gene77 chr16 ENCODE exon 217242 217336 . - . Parent=gene77 chr16 . intron 217337 218700 . - . Parent=gene77 chr16 ENCODE exon 218701 219142 . - . Parent=gene77 ### chr16 ENCODE gene 210171 217614 . - . ID=gene78;Name=LA16c-OS12.1-013;Name2=LUC7L chr16 ENCODE exon 210171 210747 . - . Parent=gene78 chr16 . intron 210748 217241 . - . Parent=gene78 chr16 ENCODE exon 217242 217614 . - . Parent=gene78 ### chr16 ENCODE gene 218124 218990 . - . ID=gene79;Name=LA16c-OS12.1-011;Name2=LUC7L chr16 ENCODE exon 218124 218402 . - . Parent=gene79 chr16 . intron 218403 218700 . - . Parent=gene79 chr16 ENCODE exon 218701 218990 . - . Parent=gene79 ### chr16 ENCODE gene 224546 256125 . + . ID=gene80;Name=AC004754.1-001;Name2=ITFG3 chr16 ENCODE exon 224546 224857 . + . Parent=gene80 chr16 . intron 224858 239548 . + . Parent=gene80 chr16 ENCODE exon 239549 239654 . + . Parent=gene80 chr16 . intron 239655 244380 . + . Parent=gene80 chr16 ENCODE exon 244381 244681 . + . Parent=gene80 chr16 ENCODE CDS 244414 244681 . + . Parent=gene80 chr16 . intron 244682 249482 . + . Parent=gene80 chr16 ENCODE exon 249483 249599 . + . Parent=gene80 chr16 ENCODE CDS 249483 249599 . + . Parent=gene80 chr16 . intron 249600 249968 . + . Parent=gene80 chr16 ENCODE exon 249969 250160 . + . Parent=gene80 chr16 ENCODE CDS 249969 250160 . + . Parent=gene80 chr16 . intron 250161 251383 . + . Parent=gene80 chr16 ENCODE exon 251384 251514 . + . Parent=gene80 chr16 ENCODE CDS 251384 251514 . + . Parent=gene80 chr16 . intron 251515 252092 . + . Parent=gene80 chr16 ENCODE exon 252093 252225 . + . Parent=gene80 chr16 ENCODE CDS 252093 252225 . + . Parent=gene80 chr16 . intron 252226 252423 . + . Parent=gene80 chr16 ENCODE exon 252424 252553 . + . Parent=gene80 chr16 ENCODE CDS 252424 252553 . + . Parent=gene80 chr16 . intron 252554 253261 . + . Parent=gene80 chr16 ENCODE exon 253262 253402 . + . Parent=gene80 chr16 ENCODE CDS 253262 253402 . + . Parent=gene80 chr16 . intron 253403 253699 . + . Parent=gene80 chr16 ENCODE exon 253700 253775 . + . Parent=gene80 chr16 ENCODE CDS 253700 253775 . + . Parent=gene80 chr16 . intron 253776 254015 . + . Parent=gene80 chr16 ENCODE exon 254016 254171 . + . Parent=gene80 chr16 ENCODE CDS 254016 254171 . + . Parent=gene80 chr16 . intron 254172 254613 . + . Parent=gene80 chr16 ENCODE exon 254614 254716 . + . Parent=gene80 chr16 ENCODE CDS 254614 254716 . + . Parent=gene80 chr16 . intron 254717 254810 . + . Parent=gene80 chr16 ENCODE CDS 254811 255022 . + . Parent=gene80 chr16 ENCODE exon 254811 256125 . + . Parent=gene80 ### chr16 ENCODE gene 224802 258971 . + . ID=gene81;Name=AC004754.1-002;Name2=ITFG3 chr16 ENCODE exon 224802 224857 . + . Parent=gene81 chr16 . intron 224858 239548 . + . Parent=gene81 chr16 ENCODE exon 239549 239654 . + . Parent=gene81 chr16 . intron 239655 244380 . + . Parent=gene81 chr16 ENCODE exon 244381 244681 . + . Parent=gene81 chr16 ENCODE CDS 244414 244681 . + . Parent=gene81 chr16 . intron 244682 249482 . + . Parent=gene81 chr16 ENCODE exon 249483 249599 . + . Parent=gene81 chr16 ENCODE CDS 249483 249599 . + . Parent=gene81 chr16 . intron 249600 249968 . + . Parent=gene81 chr16 ENCODE exon 249969 250160 . + . Parent=gene81 chr16 ENCODE CDS 249969 250160 . + . Parent=gene81 chr16 . intron 250161 251383 . + . Parent=gene81 chr16 ENCODE exon 251384 251514 . + . Parent=gene81 chr16 ENCODE CDS 251384 251514 . + . Parent=gene81 chr16 . intron 251515 252092 . + . Parent=gene81 chr16 ENCODE exon 252093 252225 . + . Parent=gene81 chr16 ENCODE CDS 252093 252225 . + . Parent=gene81 chr16 . intron 252226 252423 . + . Parent=gene81 chr16 ENCODE exon 252424 252553 . + . Parent=gene81 chr16 ENCODE CDS 252424 252553 . + . Parent=gene81 chr16 . intron 252554 253261 . + . Parent=gene81 chr16 ENCODE exon 253262 253402 . + . Parent=gene81 chr16 ENCODE CDS 253262 253402 . + . Parent=gene81 chr16 . intron 253403 253699 . + . Parent=gene81 chr16 ENCODE exon 253700 253775 . + . Parent=gene81 chr16 ENCODE CDS 253700 253775 . + . Parent=gene81 chr16 . intron 253776 254015 . + . Parent=gene81 chr16 ENCODE exon 254016 254171 . + . Parent=gene81 chr16 ENCODE CDS 254016 254171 . + . Parent=gene81 chr16 . intron 254172 254613 . + . Parent=gene81 chr16 ENCODE exon 254614 254716 . + . Parent=gene81 chr16 ENCODE CDS 254614 254716 . + . Parent=gene81 chr16 . intron 254717 254810 . + . Parent=gene81 chr16 ENCODE exon 254811 254908 . + . Parent=gene81 chr16 ENCODE CDS 254811 254908 . + . Parent=gene81 chr16 . intron 254909 258775 . + . Parent=gene81 chr16 ENCODE CDS 258776 258853 . + . Parent=gene81 chr16 ENCODE exon 258776 258971 . + . Parent=gene81 ### chr16 ENCODE gene 224818 249521 . + . ID=gene82;Name=AC004754.1-017;Name2=ITFG3 chr16 ENCODE exon 224818 224857 . + . Parent=gene82 chr16 . intron 224858 239548 . + . Parent=gene82 chr16 ENCODE exon 239549 239654 . + . Parent=gene82 chr16 . intron 239655 243832 . + . Parent=gene82 chr16 ENCODE exon 243833 243929 . + . Parent=gene82 chr16 . intron 243930 244380 . + . Parent=gene82 chr16 ENCODE exon 244381 244681 . + . Parent=gene82 chr16 ENCODE CDS 244414 244681 . + . Parent=gene82 chr16 . intron 244682 249482 . + . Parent=gene82 chr16 ENCODE CDS 249483 249504 . + . Parent=gene82 chr16 ENCODE exon 249483 249521 . + . Parent=gene82 ### chr16 ENCODE gene 224827 244565 . + . ID=gene83;Name=AC004754.1-005;Name2=ITFG3 chr16 ENCODE exon 224827 224857 . + . Parent=gene83 chr16 . intron 224858 239548 . + . Parent=gene83 chr16 ENCODE exon 239549 239654 . + . Parent=gene83 chr16 . intron 239655 244328 . + . Parent=gene83 chr16 ENCODE exon 244329 244565 . + . Parent=gene83 chr16 ENCODE CDS 244414 244565 . + . Parent=gene83 ### chr16 ENCODE gene 224829 250003 . + . ID=gene84;Name=AC004754.1-006;Name2=ITFG3 chr16 ENCODE exon 224829 224857 . + . Parent=gene84 chr16 . intron 224858 239548 . + . Parent=gene84 chr16 ENCODE exon 239549 239654 . + . Parent=gene84 chr16 . intron 239655 244387 . + . Parent=gene84 chr16 ENCODE exon 244388 244681 . + . Parent=gene84 chr16 ENCODE CDS 244414 244681 . + . Parent=gene84 chr16 . intron 244682 249482 . + . Parent=gene84 chr16 ENCODE exon 249483 249599 . + . Parent=gene84 chr16 ENCODE CDS 249483 249599 . + . Parent=gene84 chr16 . intron 249600 249995 . + . Parent=gene84 chr16 ENCODE exon 249996 250003 . + . Parent=gene84 chr16 ENCODE CDS 249996 250003 . + . Parent=gene84 ### chr16 ENCODE gene 224830 244674 . + . ID=gene85;Name=AC004754.1-007;Name2=ITFG3 chr16 ENCODE exon 224830 224857 . + . Parent=gene85 chr16 . intron 224858 239548 . + . Parent=gene85 chr16 ENCODE exon 239549 239658 . + . Parent=gene85 chr16 . intron 239659 244380 . + . Parent=gene85 chr16 ENCODE exon 244381 244674 . + . Parent=gene85 chr16 ENCODE CDS 244414 244674 . + . Parent=gene85 ### chr16 ENCODE gene 224834 251514 . + . ID=gene86;Name=AC004754.1-004;Name2=ITFG3 chr16 ENCODE exon 224834 224857 . + . Parent=gene86 chr16 . intron 224858 236956 . + . Parent=gene86 chr16 ENCODE exon 236957 237069 . + . Parent=gene86 chr16 . intron 237070 239548 . + . Parent=gene86 chr16 ENCODE exon 239549 239654 . + . Parent=gene86 chr16 . intron 239655 244380 . + . Parent=gene86 chr16 ENCODE exon 244381 244681 . + . Parent=gene86 chr16 ENCODE CDS 244414 244681 . + . Parent=gene86 chr16 . intron 244682 249482 . + . Parent=gene86 chr16 ENCODE exon 249483 249599 . + . Parent=gene86 chr16 ENCODE CDS 249483 249599 . + . Parent=gene86 chr16 . intron 249600 249968 . + . Parent=gene86 chr16 ENCODE exon 249969 250160 . + . Parent=gene86 chr16 ENCODE CDS 249969 250160 . + . Parent=gene86 chr16 . intron 250161 251383 . + . Parent=gene86 chr16 ENCODE exon 251384 251514 . + . Parent=gene86 chr16 ENCODE CDS 251384 251514 . + . Parent=gene86 ### chr16 ENCODE gene 224838 252139 . + . ID=gene87;Name=AC004754.1-010;Name2=ITFG3 chr16 ENCODE exon 224838 224857 . + . Parent=gene87 chr16 . intron 224858 239548 . + . Parent=gene87 chr16 ENCODE exon 239549 239654 . + . Parent=gene87 chr16 . intron 239655 244380 . + . Parent=gene87 chr16 ENCODE exon 244381 244681 . + . Parent=gene87 chr16 ENCODE CDS 244414 244681 . + . Parent=gene87 chr16 . intron 244682 249482 . + . Parent=gene87 chr16 ENCODE exon 249483 249599 . + . Parent=gene87 chr16 ENCODE CDS 249483 249599 . + . Parent=gene87 chr16 . intron 249600 249995 . + . Parent=gene87 chr16 ENCODE exon 249996 250160 . + . Parent=gene87 chr16 ENCODE CDS 249996 250160 . + . Parent=gene87 chr16 . intron 250161 251383 . + . Parent=gene87 chr16 ENCODE exon 251384 251514 . + . Parent=gene87 chr16 ENCODE CDS 251384 251514 . + . Parent=gene87 chr16 . intron 251515 252092 . + . Parent=gene87 chr16 ENCODE exon 252093 252139 . + . Parent=gene87 chr16 ENCODE CDS 252093 252139 . + . Parent=gene87 ### chr16 ENCODE gene 224844 251505 . + . ID=gene88;Name=AC004754.1-009;Name2=ITFG3 chr16 ENCODE exon 224844 224857 . + . Parent=gene88 chr16 . intron 224858 238243 . + . Parent=gene88 chr16 ENCODE exon 238244 238397 . + . Parent=gene88 chr16 . intron 238398 239548 . + . Parent=gene88 chr16 ENCODE exon 239549 239654 . + . Parent=gene88 chr16 . intron 239655 244380 . + . Parent=gene88 chr16 ENCODE exon 244381 244681 . + . Parent=gene88 chr16 ENCODE CDS 244414 244681 . + . Parent=gene88 chr16 . intron 244682 249482 . + . Parent=gene88 chr16 ENCODE exon 249483 249599 . + . Parent=gene88 chr16 ENCODE CDS 249483 249599 . + . Parent=gene88 chr16 . intron 249600 249968 . + . Parent=gene88 chr16 ENCODE exon 249969 250160 . + . Parent=gene88 chr16 ENCODE CDS 249969 250160 . + . Parent=gene88 chr16 . intron 250161 251383 . + . Parent=gene88 chr16 ENCODE exon 251384 251505 . + . Parent=gene88 chr16 ENCODE CDS 251384 251505 . + . Parent=gene88 ### chr16 ENCODE gene 224846 256120 . + . ID=gene89;Name=AC004754.1-003;Name2=ITFG3 chr16 ENCODE exon 224846 224857 . + . Parent=gene89 chr16 . intron 224858 239548 . + . Parent=gene89 chr16 ENCODE exon 239549 239654 . + . Parent=gene89 chr16 . intron 239655 244387 . + . Parent=gene89 chr16 ENCODE exon 244388 244681 . + . Parent=gene89 chr16 ENCODE CDS 244414 244681 . + . Parent=gene89 chr16 . intron 244682 249482 . + . Parent=gene89 chr16 ENCODE exon 249483 249599 . + . Parent=gene89 chr16 ENCODE CDS 249483 249599 . + . Parent=gene89 chr16 . intron 249600 249968 . + . Parent=gene89 chr16 ENCODE exon 249969 250160 . + . Parent=gene89 chr16 ENCODE CDS 249969 250160 . + . Parent=gene89 chr16 . intron 250161 251383 . + . Parent=gene89 chr16 ENCODE exon 251384 251514 . + . Parent=gene89 chr16 ENCODE CDS 251384 251514 . + . Parent=gene89 chr16 . intron 251515 252092 . + . Parent=gene89 chr16 ENCODE exon 252093 252225 . + . Parent=gene89 chr16 ENCODE CDS 252093 252225 . + . Parent=gene89 chr16 . intron 252226 252423 . + . Parent=gene89 chr16 ENCODE exon 252424 252553 . + . Parent=gene89 chr16 ENCODE CDS 252424 252553 . + . Parent=gene89 chr16 . intron 252554 253261 . + . Parent=gene89 chr16 ENCODE exon 253262 253402 . + . Parent=gene89 chr16 ENCODE CDS 253262 253402 . + . Parent=gene89 chr16 . intron 253403 253699 . + . Parent=gene89 chr16 ENCODE exon 253700 253775 . + . Parent=gene89 chr16 ENCODE CDS 253700 253775 . + . Parent=gene89 chr16 . intron 253776 254015 . + . Parent=gene89 chr16 ENCODE exon 254016 254171 . + . Parent=gene89 chr16 ENCODE CDS 254016 254171 . + . Parent=gene89 chr16 . intron 254172 254613 . + . Parent=gene89 chr16 ENCODE exon 254614 254716 . + . Parent=gene89 chr16 ENCODE CDS 254614 254716 . + . Parent=gene89 chr16 . intron 254717 254810 . + . Parent=gene89 chr16 ENCODE CDS 254811 255022 . + . Parent=gene89 chr16 ENCODE exon 254811 256120 . + . Parent=gene89 ### chr16 ENCODE gene 224847 250009 . + . ID=gene90;Name=AC004754.1-016;Name2=ITFG3 chr16 ENCODE exon 224847 224857 . + . Parent=gene90 chr16 . intron 224858 239548 . + . Parent=gene90 chr16 ENCODE exon 239549 239654 . + . Parent=gene90 chr16 . intron 239655 244380 . + . Parent=gene90 chr16 ENCODE exon 244381 244681 . + . Parent=gene90 chr16 ENCODE CDS 244414 244681 . + . Parent=gene90 chr16 . intron 244682 249968 . + . Parent=gene90 chr16 ENCODE exon 249969 250009 . + . Parent=gene90 chr16 ENCODE CDS 249969 250009 . + . Parent=gene90 ### chr16 ENCODE gene 230188 244619 . + . ID=gene91;Name=AC004754.1-008;Name2=ITFG3 chr16 ENCODE exon 230188 230276 . + . Parent=gene91 chr16 . intron 230277 239548 . + . Parent=gene91 chr16 ENCODE exon 239549 239654 . + . Parent=gene91 chr16 . intron 239655 243832 . + . Parent=gene91 chr16 ENCODE exon 243833 243929 . + . Parent=gene91 chr16 . intron 243930 244328 . + . Parent=gene91 chr16 ENCODE exon 244329 244619 . + . Parent=gene91 chr16 ENCODE CDS 244414 244619 . + . Parent=gene91 ### chr16 ENCODE gene 244122 249520 . + . ID=gene92;Name=AC004754.1-011;Name2=ITFG3 chr16 ENCODE exon 244122 244681 . + . Parent=gene92 chr16 . intron 244682 249482 . + . Parent=gene92 chr16 ENCODE exon 249483 249520 . + . Parent=gene92 ### chr16 ENCODE gene 244628 250788 . + . ID=gene93;Name=AC004754.1-013;Name2=ITFG3 chr16 ENCODE exon 244628 244681 . + . Parent=gene93 chr16 ENCODE CDS 244628 244681 . + . Parent=gene93 chr16 . intron 244682 249482 . + . Parent=gene93 chr16 ENCODE exon 249483 249599 . + . Parent=gene93 chr16 ENCODE CDS 249483 249599 . + . Parent=gene93 chr16 . intron 249600 249968 . + . Parent=gene93 chr16 ENCODE exon 249969 250160 . + . Parent=gene93 chr16 ENCODE CDS 249969 250160 . + . Parent=gene93 chr16 . intron 250161 250412 . + . Parent=gene93 chr16 ENCODE CDS 250413 250753 . + . Parent=gene93 chr16 ENCODE exon 250413 250788 . + . Parent=gene93 ### chr16 ENCODE gene 251205 252244 . + . ID=gene94;Name=AC004754.1-012;Name2=ITFG3 chr16 ENCODE exon 251205 251514 . + . Parent=gene94 chr16 . intron 251515 252092 . + . Parent=gene94 chr16 ENCODE exon 252093 252244 . + . Parent=gene94 ### chr16 ENCODE gene 252508 255090 . + . ID=gene95;Name=AC004754.1-014;Name2=ITFG3 chr16 ENCODE exon 252508 252553 . + . Parent=gene95 chr16 ENCODE CDS 252508 252553 . + . Parent=gene95 chr16 . intron 252554 253261 . + . Parent=gene95 chr16 ENCODE exon 253262 253402 . + . Parent=gene95 chr16 ENCODE CDS 253262 253402 . + . Parent=gene95 chr16 . intron 253403 253699 . + . Parent=gene95 chr16 ENCODE exon 253700 253775 . + . Parent=gene95 chr16 ENCODE CDS 253700 253775 . + . Parent=gene95 chr16 . intron 253776 254613 . + . Parent=gene95 chr16 ENCODE exon 254614 254716 . + . Parent=gene95 chr16 ENCODE CDS 254614 254716 . + . Parent=gene95 chr16 . intron 254717 254810 . + . Parent=gene95 chr16 ENCODE CDS 254811 255022 . + . Parent=gene95 chr16 ENCODE exon 254811 255090 . + . Parent=gene95 ### chr16 ENCODE gene 254624 256120 . + . ID=gene96;Name=AC004754.1-015;Name2=ITFG3 chr16 ENCODE exon 254624 254716 . + . Parent=gene96 chr16 . intron 254717 254810 . + . Parent=gene96 chr16 ENCODE exon 254811 254893 . + . Parent=gene96 chr16 . intron 254894 255941 . + . Parent=gene96 chr16 ENCODE exon 255942 256120 . + . Parent=gene96 ### chr16 ENCODE gene 258301 265930 . - . ID=gene97;Name=AC004754.2-001;Name2=RGS11 chr16 ENCODE exon 258301 259383 . - . Parent=gene97 chr16 ENCODE CDS 259269 259383 . - . Parent=gene97 chr16 . intron 259384 259502 . - . Parent=gene97 chr16 ENCODE exon 259503 259585 . - . Parent=gene97 chr16 ENCODE CDS 259503 259585 . - . Parent=gene97 chr16 . intron 259586 260522 . - . Parent=gene97 chr16 ENCODE exon 260523 260661 . - . Parent=gene97 chr16 ENCODE CDS 260523 260661 . - . Parent=gene97 chr16 . intron 260662 260743 . - . Parent=gene97 chr16 ENCODE exon 260744 260831 . - . Parent=gene97 chr16 ENCODE CDS 260744 260831 . - . Parent=gene97 chr16 . intron 260832 260983 . - . Parent=gene97 chr16 ENCODE exon 260984 261099 . - . Parent=gene97 chr16 ENCODE CDS 260984 261099 . - . Parent=gene97 chr16 . intron 261100 261201 . - . Parent=gene97 chr16 ENCODE exon 261202 261315 . - . Parent=gene97 chr16 ENCODE CDS 261202 261315 . - . Parent=gene97 chr16 . intron 261316 261398 . - . Parent=gene97 chr16 ENCODE exon 261399 261460 . - . Parent=gene97 chr16 ENCODE CDS 261399 261460 . - . Parent=gene97 chr16 . intron 261461 261539 . - . Parent=gene97 chr16 ENCODE exon 261540 261569 . - . Parent=gene97 chr16 ENCODE CDS 261540 261569 . - . Parent=gene97 chr16 . intron 261570 262862 . - . Parent=gene97 chr16 ENCODE exon 262863 262931 . - . Parent=gene97 chr16 ENCODE CDS 262863 262931 . - . Parent=gene97 chr16 . intron 262932 263475 . - . Parent=gene97 chr16 ENCODE exon 263476 263557 . - . Parent=gene97 chr16 ENCODE CDS 263476 263557 . - . Parent=gene97 chr16 . intron 263558 263760 . - . Parent=gene97 chr16 ENCODE exon 263761 263837 . - . Parent=gene97 chr16 ENCODE CDS 263761 263837 . - . Parent=gene97 chr16 . intron 263838 264043 . - . Parent=gene97 chr16 ENCODE exon 264044 264102 . - . Parent=gene97 chr16 ENCODE CDS 264044 264102 . - . Parent=gene97 chr16 . intron 264103 264214 . - . Parent=gene97 chr16 ENCODE exon 264215 264266 . - . Parent=gene97 chr16 ENCODE CDS 264215 264266 . - . Parent=gene97 chr16 . intron 264267 264976 . - . Parent=gene97 chr16 ENCODE exon 264977 265083 . - . Parent=gene97 chr16 ENCODE CDS 264977 265083 . - . Parent=gene97 chr16 . intron 265084 265283 . - . Parent=gene97 chr16 ENCODE exon 265284 265334 . - . Parent=gene97 chr16 ENCODE CDS 265284 265334 . - . Parent=gene97 chr16 . intron 265335 265402 . - . Parent=gene97 chr16 ENCODE exon 265403 265499 . - . Parent=gene97 chr16 ENCODE CDS 265403 265499 . - . Parent=gene97 chr16 . intron 265500 265849 . - . Parent=gene97 chr16 ENCODE CDS 265850 265912 . - . Parent=gene97 chr16 ENCODE exon 265850 265930 . - . Parent=gene97 ### chr16 ENCODE gene 258301 265941 . - . ID=gene98;Name=AC004754.2-002;Name2=RGS11 chr16 ENCODE exon 258301 259383 . - . Parent=gene98 chr16 . intron 259384 259502 . - . Parent=gene98 chr16 ENCODE exon 259503 259585 . - . Parent=gene98 chr16 . intron 259586 260522 . - . Parent=gene98 chr16 ENCODE exon 260523 260661 . - . Parent=gene98 chr16 . intron 260662 260743 . - . Parent=gene98 chr16 ENCODE exon 260744 260831 . - . Parent=gene98 chr16 . intron 260832 260983 . - . Parent=gene98 chr16 ENCODE exon 260984 261099 . - . Parent=gene98 chr16 . intron 261100 261201 . - . Parent=gene98 chr16 ENCODE exon 261202 261315 . - . Parent=gene98 chr16 . intron 261316 261398 . - . Parent=gene98 chr16 ENCODE exon 261399 261460 . - . Parent=gene98 chr16 . intron 261461 261539 . - . Parent=gene98 chr16 ENCODE exon 261540 261569 . - . Parent=gene98 chr16 . intron 261570 263475 . - . Parent=gene98 chr16 ENCODE exon 263476 263557 . - . Parent=gene98 chr16 . intron 263558 263760 . - . Parent=gene98 chr16 ENCODE exon 263761 263837 . - . Parent=gene98 chr16 . intron 263838 264043 . - . Parent=gene98 chr16 ENCODE exon 264044 264102 . - . Parent=gene98 chr16 . intron 264103 264214 . - . Parent=gene98 chr16 ENCODE exon 264215 264266 . - . Parent=gene98 chr16 . intron 264267 265283 . - . Parent=gene98 chr16 ENCODE exon 265284 265334 . - . Parent=gene98 chr16 . intron 265335 265402 . - . Parent=gene98 chr16 ENCODE exon 265403 265499 . - . Parent=gene98 chr16 . intron 265500 265838 . - . Parent=gene98 chr16 ENCODE exon 265839 265941 . - . Parent=gene98 ### chr16 ENCODE gene 258311 265915 . - . ID=gene99;Name=AC004754.2-003;Name2=RGS11 chr16 ENCODE exon 258311 259383 . - . Parent=gene99 chr16 ENCODE CDS 259269 259383 . - . Parent=gene99 chr16 . intron 259384 259502 . - . Parent=gene99 chr16 ENCODE exon 259503 259585 . - . Parent=gene99 chr16 ENCODE CDS 259503 259585 . - . Parent=gene99 chr16 . intron 259586 260522 . - . Parent=gene99 chr16 ENCODE exon 260523 260661 . - . Parent=gene99 chr16 ENCODE CDS 260523 260661 . - . Parent=gene99 chr16 . intron 260662 260743 . - . Parent=gene99 chr16 ENCODE exon 260744 260831 . - . Parent=gene99 chr16 ENCODE CDS 260744 260831 . - . Parent=gene99 chr16 . intron 260832 260983 . - . Parent=gene99 chr16 ENCODE exon 260984 261099 . - . Parent=gene99 chr16 ENCODE CDS 260984 261099 . - . Parent=gene99 chr16 . intron 261100 261201 . - . Parent=gene99 chr16 ENCODE exon 261202 261315 . - . Parent=gene99 chr16 ENCODE CDS 261202 261315 . - . Parent=gene99 chr16 . intron 261316 261398 . - . Parent=gene99 chr16 ENCODE exon 261399 261460 . - . Parent=gene99 chr16 ENCODE CDS 261399 261460 . - . Parent=gene99 chr16 . intron 261461 261539 . - . Parent=gene99 chr16 ENCODE exon 261540 261569 . - . Parent=gene99 chr16 ENCODE CDS 261540 261569 . - . Parent=gene99 chr16 . intron 261570 262862 . - . Parent=gene99 chr16 ENCODE exon 262863 262931 . - . Parent=gene99 chr16 ENCODE CDS 262863 262931 . - . Parent=gene99 chr16 . intron 262932 263475 . - . Parent=gene99 chr16 ENCODE exon 263476 263557 . - . Parent=gene99 chr16 ENCODE CDS 263476 263557 . - . Parent=gene99 chr16 . intron 263558 263760 . - . Parent=gene99 chr16 ENCODE exon 263761 263837 . - . Parent=gene99 chr16 ENCODE CDS 263761 263837 . - . Parent=gene99 chr16 . intron 263838 264043 . - . Parent=gene99 chr16 ENCODE exon 264044 264102 . - . Parent=gene99 chr16 ENCODE CDS 264044 264102 . - . Parent=gene99 chr16 . intron 264103 264214 . - . Parent=gene99 chr16 ENCODE exon 264215 264266 . - . Parent=gene99 chr16 ENCODE CDS 264215 264266 . - . Parent=gene99 chr16 . intron 264267 264976 . - . Parent=gene99 chr16 ENCODE exon 264977 265083 . - . Parent=gene99 chr16 ENCODE CDS 264977 265083 . - . Parent=gene99 chr16 . intron 265084 265283 . - . Parent=gene99 chr16 ENCODE exon 265284 265334 . - . Parent=gene99 chr16 ENCODE CDS 265284 265334 . - . Parent=gene99 chr16 . intron 265335 265402 . - . Parent=gene99 chr16 ENCODE exon 265403 265499 . - . Parent=gene99 chr16 ENCODE CDS 265403 265499 . - . Parent=gene99 chr16 . intron 265500 265838 . - . Parent=gene99 chr16 ENCODE exon 265839 265915 . - . Parent=gene99 ### chr16 ENCODE gene 258319 264957 . - . ID=gene100;Name=AC004754.2-008;Name2=RGS11 chr16 ENCODE exon 258319 259383 . - . Parent=gene100 chr16 . intron 259384 259502 . - . Parent=gene100 chr16 ENCODE exon 259503 259585 . - . Parent=gene100 chr16 . intron 259586 260522 . - . Parent=gene100 chr16 ENCODE exon 260523 260661 . - . Parent=gene100 chr16 . intron 260662 260743 . - . Parent=gene100 chr16 ENCODE exon 260744 260831 . - . Parent=gene100 chr16 . intron 260832 260983 . - . Parent=gene100 chr16 ENCODE exon 260984 261099 . - . Parent=gene100 chr16 . intron 261100 261201 . - . Parent=gene100 chr16 ENCODE exon 261202 262931 . - . Parent=gene100 chr16 . intron 262932 263475 . - . Parent=gene100 chr16 ENCODE exon 263476 263557 . - . Parent=gene100 chr16 . intron 263558 263760 . - . Parent=gene100 chr16 ENCODE exon 263761 263837 . - . Parent=gene100 chr16 . intron 263838 264043 . - . Parent=gene100 chr16 ENCODE exon 264044 264957 . - . Parent=gene100 ### chr16 ENCODE gene 258727 272085 . + . ID=gene101;Name=LA16c-314G4.1-006;Name2=ARHGDIG chr16 ENCODE exon 258727 259005 . + . Parent=gene101 chr16 ENCODE CDS 258727 259005 . + . Parent=gene101 chr16 . intron 259006 271746 . + . Parent=gene101 chr16 ENCODE exon 271747 271926 . + . Parent=gene101 chr16 ENCODE CDS 271747 271926 . + . Parent=gene101 chr16 . intron 271927 272025 . + . Parent=gene101 chr16 ENCODE exon 272026 272085 . + . Parent=gene101 chr16 ENCODE CDS 272026 272085 . + . Parent=gene101 ### chr16 ENCODE gene 258727 272085 . + . ID=gene102;Name=LA16c-314G4.1-005;Name2=ARHGDIG chr16 ENCODE exon 258727 259005 . + . Parent=gene102 chr16 ENCODE CDS 258727 259005 . + . Parent=gene102 chr16 . intron 259006 272025 . + . Parent=gene102 chr16 ENCODE exon 272026 272085 . + . Parent=gene102 chr16 ENCODE CDS 272026 272085 . + . Parent=gene102 ### chr16 ENCODE gene 258982 262183 . + . ID=gene103;Name=LA16c-314G4.1-007;Name2=ARHGDIG chr16 ENCODE exon 258982 259005 . + . Parent=gene103 chr16 . intron 259006 261881 . + . Parent=gene103 chr16 ENCODE exon 261882 262183 . + . Parent=gene103 ### chr16 ENCODE gene 259269 265912 . - . ID=gene104;Name=AC004754.2-004;Name2=RGS11 chr16 ENCODE exon 259269 259383 . - . Parent=gene104 chr16 ENCODE CDS 259269 259383 . - . Parent=gene104 chr16 . intron 259384 259502 . - . Parent=gene104 chr16 ENCODE exon 259503 259585 . - . Parent=gene104 chr16 ENCODE CDS 259503 259585 . - . Parent=gene104 chr16 . intron 259586 260522 . - . Parent=gene104 chr16 ENCODE exon 260523 260661 . - . Parent=gene104 chr16 ENCODE CDS 260523 260661 . - . Parent=gene104 chr16 . intron 260662 260743 . - . Parent=gene104 chr16 ENCODE exon 260744 260831 . - . Parent=gene104 chr16 ENCODE CDS 260744 260831 . - . Parent=gene104 chr16 . intron 260832 260983 . - . Parent=gene104 chr16 ENCODE exon 260984 261099 . - . Parent=gene104 chr16 ENCODE CDS 260984 261099 . - . Parent=gene104 chr16 . intron 261100 261201 . - . Parent=gene104 chr16 ENCODE exon 261202 261315 . - . Parent=gene104 chr16 ENCODE CDS 261202 261315 . - . Parent=gene104 chr16 . intron 261316 261398 . - . Parent=gene104 chr16 ENCODE exon 261399 261460 . - . Parent=gene104 chr16 ENCODE CDS 261399 261460 . - . Parent=gene104 chr16 . intron 261461 261539 . - . Parent=gene104 chr16 ENCODE exon 261540 261569 . - . Parent=gene104 chr16 ENCODE CDS 261540 261569 . - . Parent=gene104 chr16 . intron 261570 262862 . - . Parent=gene104 chr16 ENCODE exon 262863 262931 . - . Parent=gene104 chr16 ENCODE CDS 262863 262931 . - . Parent=gene104 chr16 . intron 262932 263475 . - . Parent=gene104 chr16 ENCODE exon 263476 263557 . - . Parent=gene104 chr16 ENCODE CDS 263476 263557 . - . Parent=gene104 chr16 . intron 263558 263760 . - . Parent=gene104 chr16 ENCODE exon 263761 263837 . - . Parent=gene104 chr16 ENCODE CDS 263761 263837 . - . Parent=gene104 chr16 . intron 263838 264043 . - . Parent=gene104 chr16 ENCODE exon 264044 264102 . - . Parent=gene104 chr16 ENCODE CDS 264044 264102 . - . Parent=gene104 chr16 . intron 264103 264957 . - . Parent=gene104 chr16 ENCODE exon 264958 265083 . - . Parent=gene104 chr16 ENCODE CDS 264958 265083 . - . Parent=gene104 chr16 . intron 265084 265283 . - . Parent=gene104 chr16 ENCODE exon 265284 265334 . - . Parent=gene104 chr16 ENCODE CDS 265284 265334 . - . Parent=gene104 chr16 . intron 265335 265402 . - . Parent=gene104 chr16 ENCODE exon 265403 265499 . - . Parent=gene104 chr16 ENCODE CDS 265403 265499 . - . Parent=gene104 chr16 . intron 265500 265849 . - . Parent=gene104 chr16 ENCODE exon 265850 265912 . - . Parent=gene104 chr16 ENCODE CDS 265850 265912 . - . Parent=gene104 ### chr16 ENCODE gene 260647 264274 . - . ID=gene105;Name=AC004754.2-007;Name2=RGS11 chr16 ENCODE exon 260647 260661 . - . Parent=gene105 chr16 . intron 260662 260743 . - . Parent=gene105 chr16 ENCODE exon 260744 260831 . - . Parent=gene105 chr16 . intron 260832 260983 . - . Parent=gene105 chr16 ENCODE exon 260984 261099 . - . Parent=gene105 chr16 . intron 261100 261201 . - . Parent=gene105 chr16 ENCODE exon 261202 261315 . - . Parent=gene105 chr16 . intron 261316 261398 . - . Parent=gene105 chr16 ENCODE exon 261399 261460 . - . Parent=gene105 chr16 . intron 261461 261539 . - . Parent=gene105 chr16 ENCODE exon 261540 261569 . - . Parent=gene105 chr16 . intron 261570 262862 . - . Parent=gene105 chr16 ENCODE exon 262863 262931 . - . Parent=gene105 chr16 . intron 262932 263475 . - . Parent=gene105 chr16 ENCODE exon 263476 263557 . - . Parent=gene105 chr16 . intron 263558 263760 . - . Parent=gene105 chr16 ENCODE exon 263761 263837 . - . Parent=gene105 chr16 . intron 263838 264043 . - . Parent=gene105 chr16 ENCODE exon 264044 264102 . - . Parent=gene105 chr16 . intron 264103 264214 . - . Parent=gene105 chr16 ENCODE exon 264215 264274 . - . Parent=gene105 ### chr16 ENCODE gene 261827 265981 . - . ID=gene106;Name=AC004754.2-005;Name2=RGS11 chr16 ENCODE exon 261827 262494 . - . Parent=gene106 chr16 . intron 262495 262862 . - . Parent=gene106 chr16 ENCODE exon 262863 262931 . - . Parent=gene106 chr16 . intron 262932 263475 . - . Parent=gene106 chr16 ENCODE exon 263476 263557 . - . Parent=gene106 chr16 . intron 263558 263760 . - . Parent=gene106 chr16 ENCODE exon 263761 263837 . - . Parent=gene106 chr16 . intron 263838 264043 . - . Parent=gene106 chr16 ENCODE exon 264044 264102 . - . Parent=gene106 chr16 . intron 264103 264214 . - . Parent=gene106 chr16 ENCODE exon 264215 265083 . - . Parent=gene106 chr16 . intron 265084 265283 . - . Parent=gene106 chr16 ENCODE exon 265284 265334 . - . Parent=gene106 chr16 . intron 265335 265402 . - . Parent=gene106 chr16 ENCODE exon 265403 265499 . - . Parent=gene106 chr16 . intron 265500 265849 . - . Parent=gene106 chr16 ENCODE exon 265850 265981 . - . Parent=gene106 ### chr16 ENCODE gene 264940 265568 . - . ID=gene107;Name=AC004754.2-006;Name2=RGS11 chr16 ENCODE exon 264940 265083 . - . Parent=gene107 chr16 . intron 265084 265283 . - . Parent=gene107 chr16 ENCODE exon 265284 265334 . - . Parent=gene107 chr16 . intron 265335 265402 . - . Parent=gene107 chr16 ENCODE exon 265403 265568 . - . Parent=gene107 ### chr16 ENCODE gene 270451 272689 . + . ID=gene108;Name=LA16c-314G4.1-004;Name2=ARHGDIG chr16 ENCODE exon 270451 270754 . + . Parent=gene108 chr16 ENCODE CDS 270682 270754 . + . Parent=gene108 chr16 . intron 270755 271746 . + . Parent=gene108 chr16 ENCODE exon 271747 271926 . + . Parent=gene108 chr16 ENCODE CDS 271747 271926 . + . Parent=gene108 chr16 . intron 271927 272025 . + . Parent=gene108 chr16 ENCODE exon 272026 272109 . + . Parent=gene108 chr16 ENCODE CDS 272026 272109 . + . Parent=gene108 chr16 . intron 272110 272297 . + . Parent=gene108 chr16 ENCODE exon 272298 272356 . + . Parent=gene108 chr16 ENCODE CDS 272298 272356 . + . Parent=gene108 chr16 . intron 272357 272467 . + . Parent=gene108 chr16 ENCODE exon 272468 272531 . + . Parent=gene108 chr16 ENCODE CDS 272468 272531 . + . Parent=gene108 chr16 . intron 272532 272615 . + . Parent=gene108 chr16 ENCODE exon 272616 272689 . + . Parent=gene108 chr16 ENCODE CDS 272616 272689 . + . Parent=gene108 ### chr16 ENCODE gene 270607 273004 . + . ID=gene109;Name=LA16c-314G4.1-001;Name2=ARHGDIG chr16 ENCODE exon 270607 270754 . + . Parent=gene109 chr16 ENCODE CDS 270682 270754 . + . Parent=gene109 chr16 . intron 270755 271746 . + . Parent=gene109 chr16 ENCODE exon 271747 271926 . + . Parent=gene109 chr16 ENCODE CDS 271747 271926 . + . Parent=gene109 chr16 . intron 271927 272025 . + . Parent=gene109 chr16 ENCODE exon 272026 272109 . + . Parent=gene109 chr16 ENCODE CDS 272026 272109 . + . Parent=gene109 chr16 . intron 272110 272297 . + . Parent=gene109 chr16 ENCODE exon 272298 272374 . + . Parent=gene109 chr16 ENCODE CDS 272298 272374 . + . Parent=gene109 chr16 . intron 272375 272467 . + . Parent=gene109 chr16 ENCODE exon 272468 272531 . + . Parent=gene109 chr16 ENCODE CDS 272468 272531 . + . Parent=gene109 chr16 . intron 272532 272615 . + . Parent=gene109 chr16 ENCODE CDS 272616 272815 . + . Parent=gene109 chr16 ENCODE exon 272616 273004 . + . Parent=gene109 ### chr16 ENCODE gene 270856 272811 . + . ID=gene110;Name=LA16c-314G4.1-002;Name2=ARHGDIG chr16 ENCODE exon 270856 270934 . + . Parent=gene110 chr16 ENCODE CDS 270856 270934 . + . Parent=gene110 chr16 . intron 270935 271746 . + . Parent=gene110 chr16 ENCODE exon 271747 271926 . + . Parent=gene110 chr16 ENCODE CDS 271747 271926 . + . Parent=gene110 chr16 . intron 271927 272025 . + . Parent=gene110 chr16 ENCODE exon 272026 272109 . + . Parent=gene110 chr16 ENCODE CDS 272026 272109 . + . Parent=gene110 chr16 . intron 272110 272297 . + . Parent=gene110 chr16 ENCODE exon 272298 272374 . + . Parent=gene110 chr16 ENCODE CDS 272298 272374 . + . Parent=gene110 chr16 . intron 272375 272467 . + . Parent=gene110 chr16 ENCODE exon 272468 272531 . + . Parent=gene110 chr16 ENCODE CDS 272468 272531 . + . Parent=gene110 chr16 . intron 272532 272615 . + . Parent=gene110 chr16 ENCODE exon 272616 272811 . + . Parent=gene110 chr16 ENCODE CDS 272616 272811 . + . Parent=gene110 ### chr16 ENCODE gene 271083 272841 . + . ID=gene111;Name=LA16c-314G4.1-003;Name2=ARHGDIG chr16 ENCODE exon 271083 271926 . + . Parent=gene111 chr16 . intron 271927 272048 . + . Parent=gene111 chr16 ENCODE exon 272049 272109 . + . Parent=gene111 chr16 . intron 272110 272297 . + . Parent=gene111 chr16 ENCODE exon 272298 272374 . + . Parent=gene111 chr16 . intron 272375 272467 . + . Parent=gene111 chr16 ENCODE exon 272468 272531 . + . Parent=gene111 chr16 . intron 272532 272615 . + . Parent=gene111 chr16 ENCODE exon 272616 272841 . + . Parent=gene111 ### chr16 ENCODE gene 273153 277216 . + . ID=gene112;Name=LA16c-314G4.2-001;Name2=PDIA2 chr16 ENCODE exon 273153 273369 . + . Parent=gene112 chr16 ENCODE CDS 273171 273369 . + . Parent=gene112 chr16 . intron 273370 274387 . + . Parent=gene112 chr16 ENCODE exon 274388 274594 . + . Parent=gene112 chr16 ENCODE CDS 274388 274594 . + . Parent=gene112 chr16 . intron 274595 274659 . + . Parent=gene112 chr16 ENCODE exon 274660 274793 . + . Parent=gene112 chr16 ENCODE CDS 274660 274793 . + . Parent=gene112 chr16 . intron 274794 274878 . + . Parent=gene112 chr16 ENCODE exon 274879 275016 . + . Parent=gene112 chr16 ENCODE CDS 274879 275016 . + . Parent=gene112 chr16 . intron 275017 275084 . + . Parent=gene112 chr16 ENCODE exon 275085 275201 . + . Parent=gene112 chr16 ENCODE CDS 275085 275201 . + . Parent=gene112 chr16 . intron 275202 275312 . + . Parent=gene112 chr16 ENCODE exon 275313 275438 . + . Parent=gene112 chr16 ENCODE CDS 275313 275438 . + . Parent=gene112 chr16 . intron 275439 275506 . + . Parent=gene112 chr16 ENCODE exon 275507 275704 . + . Parent=gene112 chr16 ENCODE CDS 275507 275704 . + . Parent=gene112 chr16 . intron 275705 276353 . + . Parent=gene112 chr16 ENCODE exon 276354 276474 . + . Parent=gene112 chr16 ENCODE CDS 276354 276474 . + . Parent=gene112 chr16 . intron 276475 276554 . + . Parent=gene112 chr16 ENCODE exon 276555 276736 . + . Parent=gene112 chr16 ENCODE CDS 276555 276736 . + . Parent=gene112 chr16 . intron 276737 276835 . + . Parent=gene112 chr16 ENCODE exon 276836 276946 . + . Parent=gene112 chr16 ENCODE CDS 276836 276946 . + . Parent=gene112 chr16 . intron 276947 277069 . + . Parent=gene112 chr16 ENCODE CDS 277070 277114 . + . Parent=gene112 chr16 ENCODE exon 277070 277216 . + . Parent=gene112 ### chr16 ENCODE gene 273165 277215 . + . ID=gene113;Name=LA16c-314G4.2-002;Name2=PDIA2 chr16 ENCODE exon 273165 273369 . + . Parent=gene113 chr16 . intron 273370 274387 . + . Parent=gene113 chr16 ENCODE exon 274388 274475 . + . Parent=gene113 chr16 . intron 274476 274512 . + . Parent=gene113 chr16 ENCODE exon 274513 274594 . + . Parent=gene113 chr16 . intron 274595 274659 . + . Parent=gene113 chr16 ENCODE exon 274660 274793 . + . Parent=gene113 chr16 . intron 274794 274878 . + . Parent=gene113 chr16 ENCODE exon 274879 275016 . + . Parent=gene113 chr16 . intron 275017 275084 . + . Parent=gene113 chr16 ENCODE exon 275085 275201 . + . Parent=gene113 chr16 . intron 275202 275312 . + . Parent=gene113 chr16 ENCODE exon 275313 275438 . + . Parent=gene113 chr16 . intron 275439 275506 . + . Parent=gene113 chr16 ENCODE exon 275507 275704 . + . Parent=gene113 chr16 . intron 275705 276353 . + . Parent=gene113 chr16 ENCODE exon 276354 276474 . + . Parent=gene113 chr16 . intron 276475 276554 . + . Parent=gene113 chr16 ENCODE exon 276555 276736 . + . Parent=gene113 chr16 . intron 276737 276835 . + . Parent=gene113 chr16 ENCODE exon 276836 276946 . + . Parent=gene113 chr16 . intron 276947 277069 . + . Parent=gene113 chr16 ENCODE exon 277070 277215 . + . Parent=gene113 ### chr16 ENCODE gene 273165 277215 . + . ID=gene114;Name=LA16c-314G4.2-003;Name2=PDIA2 chr16 ENCODE exon 273165 273369 . + . Parent=gene114 chr16 . intron 273370 274387 . + . Parent=gene114 chr16 ENCODE exon 274388 274793 . + . Parent=gene114 chr16 . intron 274794 274878 . + . Parent=gene114 chr16 ENCODE exon 274879 275016 . + . Parent=gene114 chr16 . intron 275017 275084 . + . Parent=gene114 chr16 ENCODE exon 275085 275201 . + . Parent=gene114 chr16 . intron 275202 275312 . + . Parent=gene114 chr16 ENCODE exon 275313 275438 . + . Parent=gene114 chr16 . intron 275439 275506 . + . Parent=gene114 chr16 ENCODE exon 275507 275704 . + . Parent=gene114 chr16 . intron 275705 276353 . + . Parent=gene114 chr16 ENCODE exon 276354 276474 . + . Parent=gene114 chr16 . intron 276475 276554 . + . Parent=gene114 chr16 ENCODE exon 276555 276736 . + . Parent=gene114 chr16 . intron 276737 276835 . + . Parent=gene114 chr16 ENCODE exon 276836 276946 . + . Parent=gene114 chr16 . intron 276947 277069 . + . Parent=gene114 chr16 ENCODE exon 277070 277215 . + . Parent=gene114 ### chr16 ENCODE gene 273181 275141 . + . ID=gene115;Name=LA16c-314G4.2-005;Name2=PDIA2 chr16 ENCODE exon 273181 273369 . + . Parent=gene115 chr16 ENCODE CDS 273181 273369 . + . Parent=gene115 chr16 . intron 273370 274387 . + . Parent=gene115 chr16 ENCODE exon 274388 274594 . + . Parent=gene115 chr16 ENCODE CDS 274388 274594 . + . Parent=gene115 chr16 . intron 274595 274659 . + . Parent=gene115 chr16 ENCODE exon 274660 274793 . + . Parent=gene115 chr16 ENCODE CDS 274660 274793 . + . Parent=gene115 chr16 . intron 274794 274923 . + . Parent=gene115 chr16 ENCODE exon 274924 275016 . + . Parent=gene115 chr16 ENCODE CDS 274924 275016 . + . Parent=gene115 chr16 . intron 275017 275084 . + . Parent=gene115 chr16 ENCODE exon 275085 275141 . + . Parent=gene115 chr16 ENCODE CDS 275085 275141 . + . Parent=gene115 ### chr16 ENCODE gene 274153 277209 . + . ID=gene116;Name=LA16c-314G4.2-004;Name2=PDIA2 chr16 ENCODE exon 274153 274594 . + . Parent=gene116 chr16 . intron 274595 274659 . + . Parent=gene116 chr16 ENCODE exon 274660 274793 . + . Parent=gene116 chr16 . intron 274794 274878 . + . Parent=gene116 chr16 ENCODE exon 274879 275704 . + . Parent=gene116 chr16 . intron 275705 276353 . + . Parent=gene116 chr16 ENCODE exon 276354 276474 . + . Parent=gene116 chr16 . intron 276475 276554 . + . Parent=gene116 chr16 ENCODE exon 276555 276736 . + . Parent=gene116 chr16 . intron 276737 276835 . + . Parent=gene116 chr16 ENCODE exon 276836 276946 . + . Parent=gene116 chr16 . intron 276947 277069 . + . Parent=gene116 chr16 ENCODE exon 277070 277209 . + . Parent=gene116 ### chr16 ENCODE gene 274876 275577 . + . ID=gene117;Name=LA16c-314G4.2-006;Name2=PDIA2 chr16 ENCODE exon 274876 275016 . + . Parent=gene117 chr16 . intron 275017 275084 . + . Parent=gene117 chr16 ENCODE exon 275085 275201 . + . Parent=gene117 chr16 . intron 275202 275312 . + . Parent=gene117 chr16 ENCODE exon 275313 275434 . + . Parent=gene117 chr16 . intron 275435 275506 . + . Parent=gene117 chr16 ENCODE exon 275507 275577 . + . Parent=gene117 ### chr16 ENCODE gene 275681 277216 . + . ID=gene118;Name=LA16c-314G4.2-007;Name2=PDIA2 chr16 ENCODE exon 275681 275704 . + . Parent=gene118 chr16 ENCODE CDS 275681 275704 . + . Parent=gene118 chr16 . intron 275705 276371 . + . Parent=gene118 chr16 ENCODE exon 276372 276474 . + . Parent=gene118 chr16 ENCODE CDS 276372 276474 . + . Parent=gene118 chr16 . intron 276475 276554 . + . Parent=gene118 chr16 ENCODE exon 276555 276736 . + . Parent=gene118 chr16 ENCODE CDS 276555 276736 . + . Parent=gene118 chr16 . intron 276737 276835 . + . Parent=gene118 chr16 ENCODE exon 276836 276946 . + . Parent=gene118 chr16 ENCODE CDS 276836 276946 . + . Parent=gene118 chr16 . intron 276947 277069 . + . Parent=gene118 chr16 ENCODE CDS 277070 277114 . + . Parent=gene118 chr16 ENCODE exon 277070 277216 . + . Parent=gene118 ### chr16 ENCODE gene 277441 283533 . - . ID=gene119;Name=LA16c-314G4.3-006;Name2=AXIN1 chr16 ENCODE exon 277441 277626 . - . Parent=gene119 chr16 . intron 277627 279464 . - . Parent=gene119 chr16 ENCODE exon 279465 279608 . - . Parent=gene119 chr16 . intron 279609 283488 . - . Parent=gene119 chr16 ENCODE exon 283489 283533 . - . Parent=gene119 ### chr16 ENCODE gene 277441 336323 . - . ID=gene120;Name=LA16c-314G4.3-007;Name2=AXIN1 chr16 ENCODE exon 277441 278249 . - . Parent=gene120 chr16 . intron 278250 279440 . - . Parent=gene120 chr16 ENCODE exon 279441 283719 . - . Parent=gene120 chr16 . intron 283720 287056 . - . Parent=gene120 chr16 ENCODE exon 287057 287227 . - . Parent=gene120 chr16 . intron 287228 287722 . - . Parent=gene120 chr16 ENCODE exon 287723 288252 . - . Parent=gene120 chr16 . intron 288253 294304 . - . Parent=gene120 chr16 ENCODE exon 294305 294442 . - . Parent=gene120 chr16 . intron 294443 299973 . - . Parent=gene120 chr16 ENCODE exon 299974 300070 . - . Parent=gene120 chr16 . intron 300071 304543 . - . Parent=gene120 chr16 ENCODE exon 304544 304684 . - . Parent=gene120 chr16 . intron 304685 336148 . - . Parent=gene120 chr16 ENCODE exon 336149 336323 . - . Parent=gene120 ### chr16 ENCODE gene 277441 342660 . - . ID=gene121;Name=LA16c-314G4.3-001;Name2=AXIN1 chr16 ENCODE exon 277441 278249 . - . Parent=gene121 chr16 ENCODE CDS 278123 278249 . - . Parent=gene121 chr16 . intron 278250 279440 . - . Parent=gene121 chr16 ENCODE exon 279441 279608 . - . Parent=gene121 chr16 ENCODE CDS 279441 279608 . - . Parent=gene121 chr16 . intron 279609 281190 . - . Parent=gene121 chr16 ENCODE exon 281191 281298 . - . Parent=gene121 chr16 ENCODE CDS 281191 281298 . - . Parent=gene121 chr16 . intron 281299 283488 . - . Parent=gene121 chr16 ENCODE exon 283489 283719 . - . Parent=gene121 chr16 ENCODE CDS 283489 283719 . - . Parent=gene121 chr16 . intron 283720 287056 . - . Parent=gene121 chr16 ENCODE exon 287057 287227 . - . Parent=gene121 chr16 ENCODE CDS 287057 287227 . - . Parent=gene121 chr16 . intron 287228 287722 . - . Parent=gene121 chr16 ENCODE exon 287723 288252 . - . Parent=gene121 chr16 ENCODE CDS 287723 288252 . - . Parent=gene121 chr16 . intron 288253 294304 . - . Parent=gene121 chr16 ENCODE exon 294305 294442 . - . Parent=gene121 chr16 ENCODE CDS 294305 294442 . - . Parent=gene121 chr16 . intron 294443 299973 . - . Parent=gene121 chr16 ENCODE exon 299974 300070 . - . Parent=gene121 chr16 ENCODE CDS 299974 300070 . - . Parent=gene121 chr16 . intron 300071 304543 . - . Parent=gene121 chr16 ENCODE exon 304544 304684 . - . Parent=gene121 chr16 ENCODE CDS 304544 304684 . - . Parent=gene121 chr16 . intron 304685 336148 . - . Parent=gene121 chr16 ENCODE CDS 336149 337026 . - . Parent=gene121 chr16 ENCODE exon 336149 337107 . - . Parent=gene121 chr16 . intron 337108 342369 . - . Parent=gene121 chr16 ENCODE exon 342370 342660 . - . Parent=gene121 ### chr16 ENCODE gene 277442 342450 . - . ID=gene122;Name=LA16c-314G4.3-002;Name2=AXIN1 chr16 ENCODE exon 277442 278249 . - . Parent=gene122 chr16 ENCODE CDS 278123 278249 . - . Parent=gene122 chr16 . intron 278250 279440 . - . Parent=gene122 chr16 ENCODE exon 279441 279608 . - . Parent=gene122 chr16 ENCODE CDS 279441 279608 . - . Parent=gene122 chr16 . intron 279609 283488 . - . Parent=gene122 chr16 ENCODE exon 283489 283719 . - . Parent=gene122 chr16 ENCODE CDS 283489 283719 . - . Parent=gene122 chr16 . intron 283720 287056 . - . Parent=gene122 chr16 ENCODE exon 287057 287227 . - . Parent=gene122 chr16 ENCODE CDS 287057 287227 . - . Parent=gene122 chr16 . intron 287228 287722 . - . Parent=gene122 chr16 ENCODE exon 287723 288252 . - . Parent=gene122 chr16 ENCODE CDS 287723 288252 . - . Parent=gene122 chr16 . intron 288253 294304 . - . Parent=gene122 chr16 ENCODE exon 294305 294442 . - . Parent=gene122 chr16 ENCODE CDS 294305 294442 . - . Parent=gene122 chr16 . intron 294443 299973 . - . Parent=gene122 chr16 ENCODE exon 299974 300070 . - . Parent=gene122 chr16 ENCODE CDS 299974 300070 . - . Parent=gene122 chr16 . intron 300071 304543 . - . Parent=gene122 chr16 ENCODE exon 304544 304684 . - . Parent=gene122 chr16 ENCODE CDS 304544 304684 . - . Parent=gene122 chr16 . intron 304685 336148 . - . Parent=gene122 chr16 ENCODE CDS 336149 337026 . - . Parent=gene122 chr16 ENCODE exon 336149 337107 . - . Parent=gene122 chr16 . intron 337108 342369 . - . Parent=gene122 chr16 ENCODE exon 342370 342450 . - . Parent=gene122 ### chr16 ENCODE gene 278191 283537 . - . ID=gene123;Name=LA16c-314G4.3-005;Name2=AXIN1 chr16 ENCODE exon 278191 278307 . - . Parent=gene123 chr16 . intron 278308 279440 . - . Parent=gene123 chr16 ENCODE exon 279441 279608 . - . Parent=gene123 chr16 . intron 279609 283488 . - . Parent=gene123 chr16 ENCODE exon 283489 283537 . - . Parent=gene123 ### chr16 ENCODE gene 287845 342674 . - . ID=gene124;Name=LA16c-314G4.3-004;Name2=AXIN1 chr16 ENCODE exon 287845 288252 . - . Parent=gene124 chr16 . intron 288253 294304 . - . Parent=gene124 chr16 ENCODE exon 294305 294442 . - . Parent=gene124 chr16 . intron 294443 299973 . - . Parent=gene124 chr16 ENCODE exon 299974 300070 . - . Parent=gene124 chr16 . intron 300071 304543 . - . Parent=gene124 chr16 ENCODE exon 304544 304684 . - . Parent=gene124 chr16 . intron 304685 342369 . - . Parent=gene124 chr16 ENCODE exon 342370 342674 . - . Parent=gene124 ### chr16 ENCODE gene 356928 360569 . - . ID=gene125;Name=Z97634.1-001;Name2=MRPL28 chr16 ENCODE exon 356928 357783 . - . Parent=gene125 chr16 ENCODE CDS 357676 357783 . - . Parent=gene125 chr16 . intron 357784 358328 . - . Parent=gene125 chr16 ENCODE exon 358329 358415 . - . Parent=gene125 chr16 ENCODE CDS 358329 358415 . - . Parent=gene125 chr16 . intron 358416 358501 . - . Parent=gene125 chr16 ENCODE exon 358502 358627 . - . Parent=gene125 chr16 ENCODE CDS 358502 358627 . - . Parent=gene125 chr16 . intron 358628 359059 . - . Parent=gene125 chr16 ENCODE exon 359060 359221 . - . Parent=gene125 chr16 ENCODE CDS 359060 359221 . - . Parent=gene125 chr16 . intron 359222 359931 . - . Parent=gene125 chr16 ENCODE CDS 359932 360219 . - . Parent=gene125 chr16 ENCODE exon 359932 360226 . - . Parent=gene125 chr16 . intron 360227 360499 . - . Parent=gene125 chr16 ENCODE exon 360500 360569 . - . Parent=gene125 ### chr16 ENCODE gene 357395 360510 . - . ID=gene126;Name=Z97634.1-004;Name2=MRPL28 chr16 ENCODE exon 357395 357783 . - . Parent=gene126 chr16 . intron 357784 358328 . - . Parent=gene126 chr16 ENCODE exon 358329 358415 . - . Parent=gene126 chr16 . intron 358416 358501 . - . Parent=gene126 chr16 ENCODE exon 358502 359221 . - . Parent=gene126 chr16 . intron 359222 359931 . - . Parent=gene126 chr16 ENCODE exon 359932 360226 . - . Parent=gene126 chr16 . intron 360227 360499 . - . Parent=gene126 chr16 ENCODE exon 360500 360510 . - . Parent=gene126 ### chr16 ENCODE gene 357395 360527 . - . ID=gene127;Name=Z97634.1-002;Name2=MRPL28 chr16 ENCODE exon 357395 357783 . - . Parent=gene127 chr16 . intron 357784 358328 . - . Parent=gene127 chr16 ENCODE exon 358329 358415 . - . Parent=gene127 chr16 . intron 358416 358501 . - . Parent=gene127 chr16 ENCODE exon 358502 360226 . - . Parent=gene127 chr16 . intron 360227 360499 . - . Parent=gene127 chr16 ENCODE exon 360500 360527 . - . Parent=gene127 ### chr16 ENCODE gene 357397 359804 . - . ID=gene128;Name=Z97634.1-012;Name2=MRPL28 chr16 ENCODE exon 357397 357496 . - . Parent=gene128 chr16 ENCODE CDS 357411 357496 . - . Parent=gene128 chr16 . intron 357497 359594 . - . Parent=gene128 chr16 ENCODE CDS 359595 359655 . - . Parent=gene128 chr16 ENCODE exon 359595 359804 . - . Parent=gene128 ### chr16 ENCODE gene 357397 360528 . - . ID=gene129;Name=Z97634.1-006;Name2=MRPL28 chr16 ENCODE exon 357397 357783 . - . Parent=gene129 chr16 ENCODE CDS 357676 357783 . - . Parent=gene129 chr16 . intron 357784 358328 . - . Parent=gene129 chr16 ENCODE exon 358329 358415 . - . Parent=gene129 chr16 ENCODE CDS 358329 358415 . - . Parent=gene129 chr16 . intron 358416 358501 . - . Parent=gene129 chr16 ENCODE exon 358502 358636 . - . Parent=gene129 chr16 ENCODE CDS 358502 358636 . - . Parent=gene129 chr16 . intron 358637 359068 . - . Parent=gene129 chr16 ENCODE exon 359069 359221 . - . Parent=gene129 chr16 ENCODE CDS 359069 359221 . - . Parent=gene129 chr16 . intron 359222 359931 . - . Parent=gene129 chr16 ENCODE CDS 359932 360219 . - . Parent=gene129 chr16 ENCODE exon 359932 360226 . - . Parent=gene129 chr16 . intron 360227 360499 . - . Parent=gene129 chr16 ENCODE exon 360500 360528 . - . Parent=gene129 ### chr16 ENCODE gene 357399 360226 . - . ID=gene130;Name=Z97634.1-007;Name2=MRPL28 chr16 ENCODE exon 357399 357783 . - . Parent=gene130 chr16 . intron 357784 358328 . - . Parent=gene130 chr16 ENCODE exon 358329 358415 . - . Parent=gene130 chr16 . intron 358416 358501 . - . Parent=gene130 chr16 ENCODE exon 358502 359212 . - . Parent=gene130 chr16 . intron 359213 359931 . - . Parent=gene130 chr16 ENCODE exon 359932 360226 . - . Parent=gene130 ### chr16 ENCODE gene 357410 360235 . - . ID=gene131;Name=Z97634.1-005;Name2=MRPL28 chr16 ENCODE exon 357410 357783 . - . Parent=gene131 chr16 ENCODE CDS 357676 357783 . - . Parent=gene131 chr16 . intron 357784 358328 . - . Parent=gene131 chr16 ENCODE exon 358329 358415 . - . Parent=gene131 chr16 ENCODE CDS 358329 358415 . - . Parent=gene131 chr16 . intron 358416 358501 . - . Parent=gene131 chr16 ENCODE exon 358502 358627 . - . Parent=gene131 chr16 ENCODE CDS 358502 358627 . - . Parent=gene131 chr16 . intron 358628 359059 . - . Parent=gene131 chr16 ENCODE exon 359060 359221 . - . Parent=gene131 chr16 ENCODE CDS 359060 359221 . - . Parent=gene131 chr16 . intron 359222 359931 . - . Parent=gene131 chr16 ENCODE CDS 359932 360219 . - . Parent=gene131 chr16 ENCODE exon 359932 360235 . - . Parent=gene131 ### chr16 ENCODE gene 357428 360235 . - . ID=gene132;Name=Z97634.1-003;Name2=MRPL28 chr16 ENCODE exon 357428 357783 . - . Parent=gene132 chr16 . intron 357784 358328 . - . Parent=gene132 chr16 ENCODE exon 358329 358415 . - . Parent=gene132 chr16 . intron 358416 358501 . - . Parent=gene132 chr16 ENCODE exon 358502 359221 . - . Parent=gene132 chr16 . intron 359222 359931 . - . Parent=gene132 chr16 ENCODE exon 359932 360235 . - . Parent=gene132 ### chr16 ENCODE gene 357614 360510 . - . ID=gene133;Name=Z97634.1-008;Name2=MRPL28 chr16 ENCODE exon 357614 357783 . - . Parent=gene133 chr16 ENCODE CDS 357676 357783 . - . Parent=gene133 chr16 . intron 357784 358328 . - . Parent=gene133 chr16 ENCODE exon 358329 358415 . - . Parent=gene133 chr16 ENCODE CDS 358329 358415 . - . Parent=gene133 chr16 . intron 358416 358501 . - . Parent=gene133 chr16 ENCODE exon 358502 358636 . - . Parent=gene133 chr16 ENCODE CDS 358502 358636 . - . Parent=gene133 chr16 . intron 358637 359068 . - . Parent=gene133 chr16 ENCODE exon 359069 359221 . - . Parent=gene133 chr16 ENCODE CDS 359069 359221 . - . Parent=gene133 chr16 . intron 359222 359931 . - . Parent=gene133 chr16 ENCODE CDS 359932 360219 . - . Parent=gene133 chr16 ENCODE exon 359932 360226 . - . Parent=gene133 chr16 . intron 360227 360485 . - . Parent=gene133 chr16 ENCODE exon 360486 360510 . - . Parent=gene133 ### chr16 ENCODE gene 357725 360433 . - . ID=gene134;Name=Z97634.1-010;Name2=MRPL28 chr16 ENCODE exon 357725 357783 . - . Parent=gene134 chr16 ENCODE CDS 357725 357783 . - . Parent=gene134 chr16 . intron 357784 358328 . - . Parent=gene134 chr16 ENCODE exon 358329 358415 . - . Parent=gene134 chr16 ENCODE CDS 358329 358415 . - . Parent=gene134 chr16 . intron 358416 358501 . - . Parent=gene134 chr16 ENCODE exon 358502 358636 . - . Parent=gene134 chr16 ENCODE CDS 358502 358636 . - . Parent=gene134 chr16 . intron 358637 359068 . - . Parent=gene134 chr16 ENCODE exon 359069 359221 . - . Parent=gene134 chr16 ENCODE CDS 359069 359221 . - . Parent=gene134 chr16 . intron 359222 359931 . - . Parent=gene134 chr16 ENCODE CDS 359932 360219 . - . Parent=gene134 chr16 ENCODE exon 359932 360226 . - . Parent=gene134 chr16 . intron 360227 360362 . - . Parent=gene134 chr16 ENCODE exon 360363 360433 . - . Parent=gene134 ### chr16 ENCODE gene 358336 360503 . - . ID=gene135;Name=Z97634.1-009;Name2=MRPL28 chr16 ENCODE exon 358336 358415 . - . Parent=gene135 chr16 ENCODE CDS 358336 358415 . - . Parent=gene135 chr16 . intron 358416 358501 . - . Parent=gene135 chr16 ENCODE exon 358502 358636 . - . Parent=gene135 chr16 ENCODE CDS 358502 358636 . - . Parent=gene135 chr16 . intron 358637 359068 . - . Parent=gene135 chr16 ENCODE exon 359069 359221 . - . Parent=gene135 chr16 ENCODE CDS 359069 359221 . - . Parent=gene135 chr16 . intron 359222 359931 . - . Parent=gene135 chr16 ENCODE CDS 359932 360219 . - . Parent=gene135 chr16 ENCODE exon 359932 360226 . - . Parent=gene135 chr16 . intron 360227 360444 . - . Parent=gene135 chr16 ENCODE exon 360445 360503 . - . Parent=gene135 ### chr16 ENCODE gene 358409 360339 . - . ID=gene136;Name=Z97634.1-011;Name2=MRPL28 chr16 ENCODE exon 358409 358415 . - . Parent=gene136 chr16 ENCODE CDS 358409 358415 . - . Parent=gene136 chr16 . intron 358416 358501 . - . Parent=gene136 chr16 ENCODE exon 358502 358636 . - . Parent=gene136 chr16 ENCODE CDS 358502 358636 . - . Parent=gene136 chr16 . intron 358637 359068 . - . Parent=gene136 chr16 ENCODE exon 359069 359221 . - . Parent=gene136 chr16 ENCODE CDS 359069 359221 . - . Parent=gene136 chr16 . intron 359222 359931 . - . Parent=gene136 chr16 ENCODE CDS 359932 360219 . - . Parent=gene136 chr16 ENCODE exon 359932 360226 . - . Parent=gene136 chr16 . intron 360227 360310 . - . Parent=gene136 chr16 ENCODE exon 360311 360339 . - . Parent=gene136 ### chr16 ENCODE gene 360774 371983 . - . ID=gene137;Name=Z97634.2-001;Name2=TMEM8 chr16 ENCODE exon 360774 362284 . - . Parent=gene137 chr16 ENCODE CDS 361988 362284 . - . Parent=gene137 chr16 . intron 362285 362611 . - . Parent=gene137 chr16 ENCODE exon 362612 362728 . - . Parent=gene137 chr16 ENCODE CDS 362612 362728 . - . Parent=gene137 chr16 . intron 362729 364005 . - . Parent=gene137 chr16 ENCODE exon 364006 364152 . - . Parent=gene137 chr16 ENCODE CDS 364006 364152 . - . Parent=gene137 chr16 . intron 364153 364221 . - . Parent=gene137 chr16 ENCODE exon 364222 364400 . - . Parent=gene137 chr16 ENCODE CDS 364222 364400 . - . Parent=gene137 chr16 . intron 364401 364756 . - . Parent=gene137 chr16 ENCODE exon 364757 364893 . - . Parent=gene137 chr16 ENCODE CDS 364757 364893 . - . Parent=gene137 chr16 . intron 364894 365133 . - . Parent=gene137 chr16 ENCODE exon 365134 365257 . - . Parent=gene137 chr16 ENCODE CDS 365134 365257 . - . Parent=gene137 chr16 . intron 365258 365345 . - . Parent=gene137 chr16 ENCODE exon 365346 365436 . - . Parent=gene137 chr16 ENCODE CDS 365346 365436 . - . Parent=gene137 chr16 . intron 365437 366136 . - . Parent=gene137 chr16 ENCODE exon 366137 366456 . - . Parent=gene137 chr16 ENCODE CDS 366137 366456 . - . Parent=gene137 chr16 . intron 366457 366544 . - . Parent=gene137 chr16 ENCODE exon 366545 366813 . - . Parent=gene137 chr16 ENCODE CDS 366545 366813 . - . Parent=gene137 chr16 . intron 366814 367037 . - . Parent=gene137 chr16 ENCODE exon 367038 367165 . - . Parent=gene137 chr16 ENCODE CDS 367038 367165 . - . Parent=gene137 chr16 . intron 367166 367378 . - . Parent=gene137 chr16 ENCODE exon 367379 367586 . - . Parent=gene137 chr16 ENCODE CDS 367379 367586 . - . Parent=gene137 chr16 . intron 367587 367671 . - . Parent=gene137 chr16 ENCODE exon 367672 367849 . - . Parent=gene137 chr16 ENCODE CDS 367672 367849 . - . Parent=gene137 chr16 . intron 367850 371701 . - . Parent=gene137 chr16 ENCODE CDS 371702 371822 . - . Parent=gene137 chr16 ENCODE exon 371702 371983 . - . Parent=gene137 ### chr16 ENCODE gene 361863 364852 . - . ID=gene138;Name=Z97634.2-005;Name2=TMEM8 chr16 ENCODE exon 361863 362284 . - . Parent=gene138 chr16 ENCODE CDS 361988 362284 . - . Parent=gene138 chr16 . intron 362285 364005 . - . Parent=gene138 chr16 ENCODE exon 364006 364152 . - . Parent=gene138 chr16 ENCODE CDS 364006 364152 . - . Parent=gene138 chr16 . intron 364153 364221 . - . Parent=gene138 chr16 ENCODE exon 364222 364400 . - . Parent=gene138 chr16 ENCODE CDS 364222 364400 . - . Parent=gene138 chr16 . intron 364401 364756 . - . Parent=gene138 chr16 ENCODE exon 364757 364852 . - . Parent=gene138 chr16 ENCODE CDS 364757 364852 . - . Parent=gene138 ### chr16 ENCODE gene 361865 371979 . - . ID=gene139;Name=Z97634.2-002;Name2=TMEM8 chr16 ENCODE exon 361865 362284 . - . Parent=gene139 chr16 . intron 362285 362611 . - . Parent=gene139 chr16 ENCODE exon 362612 362728 . - . Parent=gene139 chr16 . intron 362729 364005 . - . Parent=gene139 chr16 ENCODE exon 364006 364152 . - . Parent=gene139 chr16 . intron 364153 364221 . - . Parent=gene139 chr16 ENCODE exon 364222 364400 . - . Parent=gene139 chr16 . intron 364401 364756 . - . Parent=gene139 chr16 ENCODE exon 364757 364893 . - . Parent=gene139 chr16 . intron 364894 365133 . - . Parent=gene139 chr16 ENCODE exon 365134 365257 . - . Parent=gene139 chr16 . intron 365258 365345 . - . Parent=gene139 chr16 ENCODE exon 365346 365436 . - . Parent=gene139 chr16 . intron 365437 366136 . - . Parent=gene139 chr16 ENCODE exon 366137 366456 . - . Parent=gene139 chr16 . intron 366457 366544 . - . Parent=gene139 chr16 ENCODE exon 366545 366813 . - . Parent=gene139 chr16 . intron 366814 367037 . - . Parent=gene139 chr16 ENCODE exon 367038 367165 . - . Parent=gene139 chr16 . intron 367166 367378 . - . Parent=gene139 chr16 ENCODE exon 367379 367586 . - . Parent=gene139 chr16 . intron 367587 367671 . - . Parent=gene139 chr16 ENCODE exon 367672 367806 . - . Parent=gene139 chr16 . intron 367807 371908 . - . Parent=gene139 chr16 ENCODE exon 371909 371979 . - . Parent=gene139 ### chr16 ENCODE gene 362417 365216 . - . ID=gene140;Name=Z97634.2-006;Name2=TMEM8 chr16 ENCODE exon 362417 362728 . - . Parent=gene140 chr16 . intron 362729 364005 . - . Parent=gene140 chr16 ENCODE exon 364006 364152 . - . Parent=gene140 chr16 . intron 364153 364221 . - . Parent=gene140 chr16 ENCODE exon 364222 364400 . - . Parent=gene140 chr16 . intron 364401 364756 . - . Parent=gene140 chr16 ENCODE exon 364757 364893 . - . Parent=gene140 chr16 . intron 364894 365133 . - . Parent=gene140 chr16 ENCODE exon 365134 365216 . - . Parent=gene140 ### chr16 ENCODE gene 364006 365076 . - . ID=gene141;Name=Z97634.2-004;Name2=TMEM8 chr16 ENCODE exon 364006 364152 . - . Parent=gene141 chr16 . intron 364153 364221 . - . Parent=gene141 chr16 ENCODE exon 364222 364400 . - . Parent=gene141 chr16 . intron 364401 364756 . - . Parent=gene141 chr16 ENCODE exon 364757 365076 . - . Parent=gene141 ### chr16 ENCODE gene 364810 366476 . - . ID=gene142;Name=Z97634.2-003;Name2=TMEM8 chr16 ENCODE exon 364810 364893 . - . Parent=gene142 chr16 . intron 364894 365133 . - . Parent=gene142 chr16 ENCODE exon 365134 365257 . - . Parent=gene142 chr16 . intron 365258 365345 . - . Parent=gene142 chr16 ENCODE exon 365346 365436 . - . Parent=gene142 chr16 . intron 365437 366136 . - . Parent=gene142 chr16 ENCODE exon 366137 366476 . - . Parent=gene142 ### chr16 ENCODE gene 366807 377000 . - . ID=gene143;Name=Z97634.2-008;Name2=TMEM8 chr16 ENCODE exon 366807 366813 . - . Parent=gene143 chr16 . intron 366814 367037 . - . Parent=gene143 chr16 ENCODE exon 367038 367165 . - . Parent=gene143 chr16 . intron 367166 367378 . - . Parent=gene143 chr16 ENCODE exon 367379 367586 . - . Parent=gene143 chr16 . intron 367587 374256 . - . Parent=gene143 chr16 ENCODE exon 374257 374397 . - . Parent=gene143 chr16 . intron 374398 376897 . - . Parent=gene143 chr16 ENCODE exon 376898 377000 . - . Parent=gene143 ### chr16 ENCODE gene 367109 377114 . - . ID=gene144;Name=Z97634.2-007;Name2=TMEM8 chr16 ENCODE exon 367109 367165 . - . Parent=gene144 chr16 . intron 367166 367378 . - . Parent=gene144 chr16 ENCODE exon 367379 367586 . - . Parent=gene144 chr16 . intron 367587 367671 . - . Parent=gene144 chr16 ENCODE exon 367672 367849 . - . Parent=gene144 chr16 . intron 367850 374256 . - . Parent=gene144 chr16 ENCODE exon 374257 374397 . - . Parent=gene144 chr16 . intron 374398 376897 . - . Parent=gene144 chr16 ENCODE exon 376898 377114 . - . Parent=gene144 ### chr16 ENCODE gene 386726 390747 . + . ID=gene145;Name=Z97634.4-002;Name2=NME4 chr16 ENCODE exon 386726 387080 . + . Parent=gene145 chr16 . intron 387081 388990 . + . Parent=gene145 chr16 ENCODE exon 388991 389124 . + . Parent=gene145 chr16 ENCODE CDS 389110 389124 . + . Parent=gene145 chr16 . intron 389125 389379 . + . Parent=gene145 chr16 ENCODE exon 389380 389481 . + . Parent=gene145 chr16 ENCODE CDS 389380 389481 . + . Parent=gene145 chr16 . intron 389482 389627 . + . Parent=gene145 chr16 ENCODE exon 389628 389740 . + . Parent=gene145 chr16 ENCODE CDS 389628 389740 . + . Parent=gene145 chr16 . intron 389741 390219 . + . Parent=gene145 chr16 ENCODE CDS 390220 390343 . + . Parent=gene145 chr16 ENCODE exon 390220 390747 . + . Parent=gene145 ### chr16 ENCODE gene 386770 389475 . + . ID=gene146;Name=Z97634.4-005;Name2=NME4 chr16 ENCODE exon 386770 387080 . + . Parent=gene146 chr16 . intron 387081 388208 . + . Parent=gene146 chr16 ENCODE exon 388209 388386 . + . Parent=gene146 chr16 . intron 388387 388990 . + . Parent=gene146 chr16 ENCODE exon 388991 389124 . + . Parent=gene146 chr16 ENCODE CDS 389110 389124 . + . Parent=gene146 chr16 . intron 389125 389379 . + . Parent=gene146 chr16 ENCODE exon 389380 389475 . + . Parent=gene146 chr16 ENCODE CDS 389380 389475 . + . Parent=gene146 ### chr16 ENCODE gene 387200 390735 . + . ID=gene147;Name=Z97634.4-006;Name2=NME4 chr16 ENCODE exon 387200 387314 . + . Parent=gene147 chr16 . intron 387315 388208 . + . Parent=gene147 chr16 ENCODE exon 388209 388395 . + . Parent=gene147 chr16 . intron 388396 388990 . + . Parent=gene147 chr16 ENCODE exon 388991 389124 . + . Parent=gene147 chr16 . intron 389125 389379 . + . Parent=gene147 chr16 ENCODE exon 389380 389481 . + . Parent=gene147 chr16 . intron 389482 389627 . + . Parent=gene147 chr16 ENCODE exon 389628 389740 . + . Parent=gene147 chr16 . intron 389741 390219 . + . Parent=gene147 chr16 ENCODE exon 390220 390735 . + . Parent=gene147 ### chr16 ENCODE gene 387201 400368 . + . ID=gene148;Name=Z97634.4-0012;Name2=NME4 chr16 ENCODE exon 387201 387314 . + . Parent=gene148 chr16 . intron 387315 388990 . + . Parent=gene148 chr16 ENCODE exon 388991 389124 . + . Parent=gene148 chr16 . intron 389125 389379 . + . Parent=gene148 chr16 ENCODE exon 389380 389481 . + . Parent=gene148 chr16 . intron 389482 389627 . + . Parent=gene148 chr16 ENCODE exon 389628 389740 . + . Parent=gene148 chr16 . intron 389741 390219 . + . Parent=gene148 chr16 ENCODE exon 390220 390295 . + . Parent=gene148 chr16 . intron 390296 391947 . + . Parent=gene148 chr16 ENCODE exon 391948 392044 . + . Parent=gene148 chr16 . intron 392045 394956 . + . Parent=gene148 chr16 ENCODE exon 394957 395025 . + . Parent=gene148 chr16 . intron 395026 396346 . + . Parent=gene148 chr16 ENCODE exon 396347 396398 . + . Parent=gene148 chr16 . intron 396399 396685 . + . Parent=gene148 chr16 ENCODE exon 396686 396778 . + . Parent=gene148 chr16 . intron 396779 397425 . + . Parent=gene148 chr16 ENCODE exon 397426 397561 . + . Parent=gene148 chr16 . intron 397562 400243 . + . Parent=gene148 chr16 ENCODE exon 400244 400368 . + . Parent=gene148 ### chr16 ENCODE gene 387209 390588 . + . ID=gene149;Name=Z97634.4-007;Name2=NME4 chr16 ENCODE exon 387209 387314 . + . Parent=gene149 chr16 . intron 387315 388990 . + . Parent=gene149 chr16 ENCODE exon 388991 389012 . + . Parent=gene149 chr16 . intron 389013 389066 . + . Parent=gene149 chr16 ENCODE exon 389067 389124 . + . Parent=gene149 chr16 . intron 389125 389379 . + . Parent=gene149 chr16 ENCODE exon 389380 389481 . + . Parent=gene149 chr16 . intron 389482 389627 . + . Parent=gene149 chr16 ENCODE exon 389628 389740 . + . Parent=gene149 chr16 . intron 389741 390219 . + . Parent=gene149 chr16 ENCODE exon 390220 390588 . + . Parent=gene149 ### chr16 ENCODE gene 387209 390634 . + . ID=gene150;Name=Z97634.4-003;Name2=NME4 chr16 ENCODE exon 387209 387314 . + . Parent=gene150 chr16 . intron 387315 388208 . + . Parent=gene150 chr16 ENCODE exon 388209 389124 . + . Parent=gene150 chr16 . intron 389125 389379 . + . Parent=gene150 chr16 ENCODE exon 389380 389481 . + . Parent=gene150 chr16 . intron 389482 389627 . + . Parent=gene150 chr16 ENCODE exon 389628 389740 . + . Parent=gene150 chr16 . intron 389741 390219 . + . Parent=gene150 chr16 ENCODE exon 390220 390634 . + . Parent=gene150 ### chr16 ENCODE gene 387210 390507 . + . ID=gene151;Name=Z97634.4-011;Name2=NME4 chr16 ENCODE exon 387210 387314 . + . Parent=gene151 chr16 ENCODE CDS 387224 387314 . + . Parent=gene151 chr16 . intron 387315 387879 . + . Parent=gene151 chr16 ENCODE exon 387880 387903 . + . Parent=gene151 chr16 ENCODE CDS 387880 387903 . + . Parent=gene151 chr16 . intron 387904 388990 . + . Parent=gene151 chr16 ENCODE exon 388991 389124 . + . Parent=gene151 chr16 ENCODE CDS 388991 389124 . + . Parent=gene151 chr16 . intron 389125 389379 . + . Parent=gene151 chr16 ENCODE exon 389380 389481 . + . Parent=gene151 chr16 ENCODE CDS 389380 389481 . + . Parent=gene151 chr16 . intron 389482 389627 . + . Parent=gene151 chr16 ENCODE exon 389628 389740 . + . Parent=gene151 chr16 ENCODE CDS 389628 389740 . + . Parent=gene151 chr16 . intron 389741 390219 . + . Parent=gene151 chr16 ENCODE CDS 390220 390343 . + . Parent=gene151 chr16 ENCODE exon 390220 390507 . + . Parent=gene151 ### chr16 ENCODE gene 387210 390760 . + . ID=gene152;Name=Z97634.4-001;Name2=NME4 chr16 ENCODE exon 387210 387314 . + . Parent=gene152 chr16 ENCODE CDS 387224 387314 . + . Parent=gene152 chr16 . intron 387315 388990 . + . Parent=gene152 chr16 ENCODE exon 388991 389124 . + . Parent=gene152 chr16 ENCODE CDS 388991 389124 . + . Parent=gene152 chr16 . intron 389125 389379 . + . Parent=gene152 chr16 ENCODE exon 389380 389481 . + . Parent=gene152 chr16 ENCODE CDS 389380 389481 . + . Parent=gene152 chr16 . intron 389482 389627 . + . Parent=gene152 chr16 ENCODE exon 389628 389740 . + . Parent=gene152 chr16 ENCODE CDS 389628 389740 . + . Parent=gene152 chr16 . intron 389741 390219 . + . Parent=gene152 chr16 ENCODE CDS 390220 390343 . + . Parent=gene152 chr16 ENCODE exon 390220 390760 . + . Parent=gene152 ### chr16 ENCODE gene 387238 390649 . + . ID=gene153;Name=Z97634.4-009;Name2=NME4 chr16 ENCODE exon 387238 387314 . + . Parent=gene153 chr16 ENCODE CDS 387238 387314 . + . Parent=gene153 chr16 . intron 387315 388990 . + . Parent=gene153 chr16 ENCODE exon 388991 389124 . + . Parent=gene153 chr16 ENCODE CDS 388991 389124 . + . Parent=gene153 chr16 . intron 389125 389379 . + . Parent=gene153 chr16 ENCODE exon 389380 389481 . + . Parent=gene153 chr16 ENCODE CDS 389380 389481 . + . Parent=gene153 chr16 . intron 389482 389627 . + . Parent=gene153 chr16 ENCODE exon 389628 389740 . + . Parent=gene153 chr16 ENCODE CDS 389628 389740 . + . Parent=gene153 chr16 . intron 389741 390109 . + . Parent=gene153 chr16 ENCODE CDS 390110 390191 . + . Parent=gene153 chr16 ENCODE exon 390110 390649 . + . Parent=gene153 ### chr16 ENCODE gene 387743 390417 . + . ID=gene154;Name=Z97634.4-010;Name2=NME4 chr16 ENCODE exon 387743 388180 . + . Parent=gene154 chr16 . intron 388181 388990 . + . Parent=gene154 chr16 ENCODE exon 388991 389124 . + . Parent=gene154 chr16 . intron 389125 389379 . + . Parent=gene154 chr16 ENCODE exon 389380 389481 . + . Parent=gene154 chr16 . intron 389482 389627 . + . Parent=gene154 chr16 ENCODE exon 389628 389740 . + . Parent=gene154 chr16 . intron 389741 390219 . + . Parent=gene154 chr16 ENCODE exon 390220 390417 . + . Parent=gene154 ### chr16 ENCODE gene 387774 402488 . + . ID=gene155;Name=Z97634.4-0013;Name2=NME4 chr16 ENCODE exon 387774 387893 . + . Parent=gene155 chr16 . intron 387894 394985 . + . Parent=gene155 chr16 ENCODE exon 394986 395025 . + . Parent=gene155 chr16 . intron 395026 396346 . + . Parent=gene155 chr16 ENCODE exon 396347 396398 . + . Parent=gene155 chr16 . intron 396399 397425 . + . Parent=gene155 chr16 ENCODE exon 397426 397561 . + . Parent=gene155 chr16 . intron 397562 400243 . + . Parent=gene155 chr16 ENCODE exon 400244 400368 . + . Parent=gene155 chr16 . intron 400369 400691 . + . Parent=gene155 chr16 ENCODE exon 400692 400785 . + . Parent=gene155 chr16 . intron 400786 400972 . + . Parent=gene155 chr16 ENCODE exon 400973 401077 . + . Parent=gene155 chr16 . intron 401078 401361 . + . Parent=gene155 chr16 ENCODE exon 401362 401579 . + . Parent=gene155 chr16 . intron 401580 401890 . + . Parent=gene155 chr16 ENCODE exon 401891 402488 . + . Parent=gene155 ### chr16 ENCODE gene 388411 390750 . + . ID=gene156;Name=Z97634.4-004;Name2=NME4 chr16 ENCODE exon 388411 389740 . + . Parent=gene156 chr16 . intron 389741 390219 . + . Parent=gene156 chr16 ENCODE exon 390220 390750 . + . Parent=gene156 ### chr16 ENCODE gene 389048 389740 . + . ID=gene157;Name=Z97634.4-008;Name2=NME4 chr16 ENCODE exon 389048 389124 . + . Parent=gene157 chr16 . intron 389125 389295 . + . Parent=gene157 chr16 ENCODE exon 389296 389481 . + . Parent=gene157 chr16 . intron 389482 389627 . + . Parent=gene157 chr16 ENCODE exon 389628 389740 . + . Parent=gene157 ### chr16 ENCODE gene 391827 402488 . + . ID=gene158;Name=AL023881.1-001;Name2=DECR2 chr16 ENCODE exon 391827 392044 . + . Parent=gene158 chr16 ENCODE CDS 391965 392044 . + . Parent=gene158 chr16 . intron 392045 394956 . + . Parent=gene158 chr16 ENCODE exon 394957 395025 . + . Parent=gene158 chr16 ENCODE CDS 394957 395025 . + . Parent=gene158 chr16 . intron 395026 396346 . + . Parent=gene158 chr16 ENCODE exon 396347 396398 . + . Parent=gene158 chr16 ENCODE CDS 396347 396398 . + . Parent=gene158 chr16 . intron 396399 397425 . + . Parent=gene158 chr16 ENCODE exon 397426 397561 . + . Parent=gene158 chr16 ENCODE CDS 397426 397561 . + . Parent=gene158 chr16 . intron 397562 400243 . + . Parent=gene158 chr16 ENCODE exon 400244 400368 . + . Parent=gene158 chr16 ENCODE CDS 400244 400368 . + . Parent=gene158 chr16 . intron 400369 400691 . + . Parent=gene158 chr16 ENCODE exon 400692 400785 . + . Parent=gene158 chr16 ENCODE CDS 400692 400785 . + . Parent=gene158 chr16 . intron 400786 400972 . + . Parent=gene158 chr16 ENCODE exon 400973 401077 . + . Parent=gene158 chr16 ENCODE CDS 400973 401077 . + . Parent=gene158 chr16 . intron 401078 401361 . + . Parent=gene158 chr16 ENCODE exon 401362 401579 . + . Parent=gene158 chr16 ENCODE CDS 401362 401579 . + . Parent=gene158 chr16 . intron 401580 401890 . + . Parent=gene158 chr16 ENCODE exon 401891 402488 . + . Parent=gene158 ### chr16 ENCODE gene 391859 402371 . + . ID=gene159;Name=AL023881.1-005;Name2=DECR2 chr16 ENCODE exon 391859 392044 . + . Parent=gene159 chr16 . intron 392045 394956 . + . Parent=gene159 chr16 ENCODE exon 394957 395025 . + . Parent=gene159 chr16 . intron 395026 396346 . + . Parent=gene159 chr16 ENCODE exon 396347 396398 . + . Parent=gene159 chr16 . intron 396399 396685 . + . Parent=gene159 chr16 ENCODE exon 396686 397201 . + . Parent=gene159 chr16 . intron 397202 397295 . + . Parent=gene159 chr16 ENCODE exon 397296 397561 . + . Parent=gene159 chr16 . intron 397562 400243 . + . Parent=gene159 chr16 ENCODE exon 400244 400368 . + . Parent=gene159 chr16 . intron 400369 400691 . + . Parent=gene159 chr16 ENCODE exon 400692 400785 . + . Parent=gene159 chr16 . intron 400786 400972 . + . Parent=gene159 chr16 ENCODE exon 400973 401077 . + . Parent=gene159 chr16 . intron 401078 401361 . + . Parent=gene159 chr16 ENCODE exon 401362 401579 . + . Parent=gene159 chr16 . intron 401580 401890 . + . Parent=gene159 chr16 ENCODE exon 401891 402094 . + . Parent=gene159 chr16 . intron 402095 402120 . + . Parent=gene159 chr16 ENCODE exon 402121 402371 . + . Parent=gene159 ### chr16 ENCODE gene 391883 401977 . + . ID=gene160;Name=AL023881.1-008;Name2=DECR2 chr16 ENCODE exon 391883 392044 . + . Parent=gene160 chr16 ENCODE CDS 391965 392044 . + . Parent=gene160 chr16 . intron 392045 394956 . + . Parent=gene160 chr16 ENCODE exon 394957 395025 . + . Parent=gene160 chr16 ENCODE CDS 394957 395025 . + . Parent=gene160 chr16 . intron 395026 396346 . + . Parent=gene160 chr16 ENCODE exon 396347 396362 . + . Parent=gene160 chr16 ENCODE CDS 396347 396362 . + . Parent=gene160 chr16 . intron 396363 397425 . + . Parent=gene160 chr16 ENCODE exon 397426 397561 . + . Parent=gene160 chr16 ENCODE CDS 397426 397561 . + . Parent=gene160 chr16 . intron 397562 400243 . + . Parent=gene160 chr16 ENCODE exon 400244 400368 . + . Parent=gene160 chr16 ENCODE CDS 400244 400368 . + . Parent=gene160 chr16 . intron 400369 400691 . + . Parent=gene160 chr16 ENCODE exon 400692 400785 . + . Parent=gene160 chr16 ENCODE CDS 400692 400785 . + . Parent=gene160 chr16 . intron 400786 400972 . + . Parent=gene160 chr16 ENCODE exon 400973 401077 . + . Parent=gene160 chr16 ENCODE CDS 400973 401077 . + . Parent=gene160 chr16 . intron 401078 401361 . + . Parent=gene160 chr16 ENCODE exon 401362 401579 . + . Parent=gene160 chr16 ENCODE CDS 401362 401579 . + . Parent=gene160 chr16 . intron 401580 401890 . + . Parent=gene160 chr16 ENCODE exon 401891 401977 . + . Parent=gene160 ### chr16 ENCODE gene 391883 402467 . + . ID=gene161;Name=AL023881.1-004;Name2=DECR2 chr16 ENCODE exon 391883 392044 . + . Parent=gene161 chr16 . intron 392045 394956 . + . Parent=gene161 chr16 ENCODE exon 394957 395040 . + . Parent=gene161 chr16 . intron 395041 397425 . + . Parent=gene161 chr16 ENCODE exon 397426 397561 . + . Parent=gene161 chr16 . intron 397562 400243 . + . Parent=gene161 chr16 ENCODE exon 400244 400368 . + . Parent=gene161 chr16 . intron 400369 400691 . + . Parent=gene161 chr16 ENCODE exon 400692 400785 . + . Parent=gene161 chr16 . intron 400786 400972 . + . Parent=gene161 chr16 ENCODE exon 400973 401077 . + . Parent=gene161 chr16 . intron 401078 401361 . + . Parent=gene161 chr16 ENCODE exon 401362 401579 . + . Parent=gene161 chr16 . intron 401580 401890 . + . Parent=gene161 chr16 ENCODE exon 401891 402467 . + . Parent=gene161 ### chr16 ENCODE gene 391894 402371 . + . ID=gene162;Name=AL023881.1-003;Name2=DECR2 chr16 ENCODE exon 391894 392044 . + . Parent=gene162 chr16 . intron 392045 394956 . + . Parent=gene162 chr16 ENCODE exon 394957 395025 . + . Parent=gene162 chr16 . intron 395026 395513 . + . Parent=gene162 chr16 ENCODE exon 395514 395666 . + . Parent=gene162 chr16 . intron 395667 396346 . + . Parent=gene162 chr16 ENCODE exon 396347 396398 . + . Parent=gene162 chr16 . intron 396399 397425 . + . Parent=gene162 chr16 ENCODE exon 397426 397561 . + . Parent=gene162 chr16 . intron 397562 400209 . + . Parent=gene162 chr16 ENCODE exon 400210 400368 . + . Parent=gene162 chr16 . intron 400369 400691 . + . Parent=gene162 chr16 ENCODE exon 400692 400785 . + . Parent=gene162 chr16 . intron 400786 400972 . + . Parent=gene162 chr16 ENCODE exon 400973 401077 . + . Parent=gene162 chr16 . intron 401078 401361 . + . Parent=gene162 chr16 ENCODE exon 401362 401579 . + . Parent=gene162 chr16 . intron 401580 401890 . + . Parent=gene162 chr16 ENCODE exon 401891 402371 . + . Parent=gene162 ### chr16 ENCODE gene 391916 402488 . + . ID=gene163;Name=AL023881.1-006;Name2=DECR2 chr16 ENCODE exon 391916 392044 . + . Parent=gene163 chr16 . intron 392045 394956 . + . Parent=gene163 chr16 ENCODE exon 394957 395025 . + . Parent=gene163 chr16 . intron 395026 396346 . + . Parent=gene163 chr16 ENCODE exon 396347 396398 . + . Parent=gene163 chr16 . intron 396399 396685 . + . Parent=gene163 chr16 ENCODE exon 396686 396834 . + . Parent=gene163 chr16 . intron 396835 396890 . + . Parent=gene163 chr16 ENCODE exon 396891 396953 . + . Parent=gene163 chr16 . intron 396954 397425 . + . Parent=gene163 chr16 ENCODE exon 397426 397561 . + . Parent=gene163 chr16 . intron 397562 400243 . + . Parent=gene163 chr16 ENCODE exon 400244 400368 . + . Parent=gene163 chr16 . intron 400369 400691 . + . Parent=gene163 chr16 ENCODE exon 400692 400785 . + . Parent=gene163 chr16 . intron 400786 400972 . + . Parent=gene163 chr16 ENCODE exon 400973 401077 . + . Parent=gene163 chr16 . intron 401078 401361 . + . Parent=gene163 chr16 ENCODE exon 401362 401579 . + . Parent=gene163 chr16 . intron 401580 401890 . + . Parent=gene163 chr16 ENCODE exon 401891 402488 . + . Parent=gene163 ### chr16 ENCODE gene 391927 401472 . + . ID=gene164;Name=AL023881.1-009;Name2=DECR2 chr16 ENCODE exon 391927 392044 . + . Parent=gene164 chr16 . intron 392045 394956 . + . Parent=gene164 chr16 ENCODE exon 394957 395025 . + . Parent=gene164 chr16 . intron 395026 396346 . + . Parent=gene164 chr16 ENCODE exon 396347 396398 . + . Parent=gene164 chr16 . intron 396399 396685 . + . Parent=gene164 chr16 ENCODE exon 396686 396953 . + . Parent=gene164 chr16 . intron 396954 397425 . + . Parent=gene164 chr16 ENCODE exon 397426 397561 . + . Parent=gene164 chr16 . intron 397562 400243 . + . Parent=gene164 chr16 ENCODE exon 400244 400368 . + . Parent=gene164 chr16 . intron 400369 400691 . + . Parent=gene164 chr16 ENCODE exon 400692 400785 . + . Parent=gene164 chr16 . intron 400786 400972 . + . Parent=gene164 chr16 ENCODE exon 400973 401077 . + . Parent=gene164 chr16 . intron 401078 401361 . + . Parent=gene164 chr16 ENCODE exon 401362 401472 . + . Parent=gene164 ### chr16 ENCODE gene 392006 397172 . + . ID=gene165;Name=AL023881.1-010;Name2=DECR2 chr16 ENCODE exon 392006 392044 . + . Parent=gene165 chr16 . intron 392045 394956 . + . Parent=gene165 chr16 ENCODE exon 394957 395025 . + . Parent=gene165 chr16 . intron 395026 396346 . + . Parent=gene165 chr16 ENCODE exon 396347 396834 . + . Parent=gene165 chr16 . intron 396835 396890 . + . Parent=gene165 chr16 ENCODE exon 396891 397172 . + . Parent=gene165 ### chr16 ENCODE gene 396896 402488 . + . ID=gene166;Name=AL023881.1-015;Name2=DECR2 chr16 ENCODE exon 396896 396953 . + . Parent=gene166 chr16 . intron 396954 400243 . + . Parent=gene166 chr16 ENCODE exon 400244 400405 . + . Parent=gene166 chr16 . intron 400406 400691 . + . Parent=gene166 chr16 ENCODE exon 400692 400785 . + . Parent=gene166 chr16 . intron 400786 400972 . + . Parent=gene166 chr16 ENCODE exon 400973 401077 . + . Parent=gene166 chr16 . intron 401078 401890 . + . Parent=gene166 chr16 ENCODE exon 401891 402488 . + . Parent=gene166 ### chr16 ENCODE gene 396947 400296 . + . ID=gene167;Name=AL023881.1-012;Name2=DECR2 chr16 ENCODE exon 396947 397561 . + . Parent=gene167 chr16 . intron 397562 400209 . + . Parent=gene167 chr16 ENCODE exon 400210 400296 . + . Parent=gene167 ### chr16 ENCODE gene 397428 401929 . + . ID=gene168;Name=AL023881.1-014;Name2=DECR2 chr16 ENCODE exon 397428 397561 . + . Parent=gene168 chr16 . intron 397562 400243 . + . Parent=gene168 chr16 ENCODE exon 400244 400405 . + . Parent=gene168 chr16 . intron 400406 400691 . + . Parent=gene168 chr16 ENCODE exon 400692 400754 . + . Parent=gene168 chr16 . intron 400755 400972 . + . Parent=gene168 chr16 ENCODE exon 400973 401077 . + . Parent=gene168 chr16 . intron 401078 401361 . + . Parent=gene168 chr16 ENCODE exon 401362 401579 . + . Parent=gene168 chr16 . intron 401580 401890 . + . Parent=gene168 chr16 ENCODE exon 401891 401929 . + . Parent=gene168 ### chr16 ENCODE gene 399600 402482 . + . ID=gene169;Name=AL023881.1-007;Name2=DECR2 chr16 ENCODE exon 399600 400368 . + . Parent=gene169 chr16 . intron 400369 400691 . + . Parent=gene169 chr16 ENCODE exon 400692 400785 . + . Parent=gene169 chr16 . intron 400786 400972 . + . Parent=gene169 chr16 ENCODE exon 400973 401579 . + . Parent=gene169 chr16 . intron 401580 401890 . + . Parent=gene169 chr16 ENCODE exon 401891 402482 . + . Parent=gene169 ### chr16 ENCODE gene 400113 401051 . + . ID=gene170;Name=AL023881.1-013;Name2=DECR2 chr16 ENCODE exon 400113 400368 . + . Parent=gene170 chr16 . intron 400369 400691 . + . Parent=gene170 chr16 ENCODE exon 400692 401051 . + . Parent=gene170 ### chr16 ENCODE gene 415620 495628 . + . ID=gene171;Name=Z98882.1-001;Name2=RAB11FIP3 chr16 ENCODE exon 415620 416721 . + . Parent=gene171 chr16 . intron 416722 451404 . + . Parent=gene171 chr16 ENCODE exon 451405 451498 . + . Parent=gene171 chr16 . intron 451499 461295 . + . Parent=gene171 chr16 ENCODE exon 461296 461390 . + . Parent=gene171 chr16 . intron 461391 472525 . + . Parent=gene171 chr16 ENCODE exon 472526 472737 . + . Parent=gene171 chr16 . intron 472738 478851 . + . Parent=gene171 chr16 ENCODE exon 478852 479001 . + . Parent=gene171 chr16 . intron 479002 486824 . + . Parent=gene171 chr16 ENCODE exon 486825 486860 . + . Parent=gene171 chr16 . intron 486861 493004 . + . Parent=gene171 chr16 ENCODE exon 493005 493098 . + . Parent=gene171 chr16 . intron 493099 495524 . + . Parent=gene171 chr16 ENCODE exon 495525 495628 . + . Parent=gene171 ### chr16 ENCODE gene 464870 495606 . + . ID=gene172;Name=Z98882.1-002;Name2=RAB11FIP3 chr16 ENCODE exon 464870 465099 . + . Parent=gene172 chr16 . intron 465100 472525 . + . Parent=gene172 chr16 ENCODE exon 472526 472737 . + . Parent=gene172 chr16 ENCODE CDS 472553 472737 . + . Parent=gene172 chr16 . intron 472738 478851 . + . Parent=gene172 chr16 ENCODE exon 478852 479001 . + . Parent=gene172 chr16 ENCODE CDS 478852 479001 . + . Parent=gene172 chr16 . intron 479002 486824 . + . Parent=gene172 chr16 ENCODE exon 486825 486860 . + . Parent=gene172 chr16 ENCODE CDS 486825 486860 . + . Parent=gene172 chr16 . intron 486861 493004 . + . Parent=gene172 chr16 ENCODE exon 493005 493098 . + . Parent=gene172 chr16 ENCODE CDS 493005 493098 . + . Parent=gene172 chr16 . intron 493099 495524 . + . Parent=gene172 chr16 ENCODE exon 495525 495606 . + . Parent=gene172 chr16 ENCODE CDS 495525 495606 . + . Parent=gene172 ### chr16 ENCODE gene 464925 479102 . + . ID=gene173;Name=Z98882.1-008;Name2=RAB11FIP3 chr16 ENCODE exon 464925 465046 . + . Parent=gene173 chr16 . intron 465047 472525 . + . Parent=gene173 chr16 ENCODE exon 472526 472737 . + . Parent=gene173 chr16 . intron 472738 478851 . + . Parent=gene173 chr16 ENCODE exon 478852 479102 . + . Parent=gene173 ### chr16 ENCODE gene 464925 493064 . + . ID=gene174;Name=Z98882.1-009;Name2=RAB11FIP3 chr16 ENCODE exon 464925 465046 . + . Parent=gene174 chr16 ENCODE CDS 465032 465046 . + . Parent=gene174 chr16 . intron 465047 472525 . + . Parent=gene174 chr16 ENCODE exon 472526 472737 . + . Parent=gene174 chr16 ENCODE CDS 472526 472737 . + . Parent=gene174 chr16 . intron 472738 478851 . + . Parent=gene174 chr16 ENCODE exon 478852 479001 . + . Parent=gene174 chr16 ENCODE CDS 478852 479001 . + . Parent=gene174 chr16 . intron 479002 486824 . + . Parent=gene174 chr16 ENCODE exon 486825 486860 . + . Parent=gene174 chr16 ENCODE CDS 486825 486860 . + . Parent=gene174 chr16 . intron 486861 493004 . + . Parent=gene174 chr16 ENCODE exon 493005 493064 . + . Parent=gene174 chr16 ENCODE CDS 493005 493064 . + . Parent=gene174 ### chr16 ENCODE gene 472658 487449 . + . ID=gene175;Name=Z98882.1-004;Name2=RAB11FIP3 chr16 ENCODE exon 472658 472737 . + . Parent=gene175 chr16 . intron 472738 478851 . + . Parent=gene175 chr16 ENCODE exon 478852 479001 . + . Parent=gene175 chr16 . intron 479002 481134 . + . Parent=gene175 chr16 ENCODE exon 481135 481269 . + . Parent=gene175 chr16 . intron 481270 486824 . + . Parent=gene175 chr16 ENCODE exon 486825 486860 . + . Parent=gene175 chr16 . intron 486861 487292 . + . Parent=gene175 chr16 ENCODE exon 487293 487449 . + . Parent=gene175 ### chr16 ENCODE gene 478943 487159 . + . ID=gene176;Name=Z98882.1-003;Name2=RAB11FIP3 chr16 ENCODE exon 478943 479001 . + . Parent=gene176 chr16 . intron 479002 481134 . + . Parent=gene176 chr16 ENCODE exon 481135 481269 . + . Parent=gene176 chr16 . intron 481270 486824 . + . Parent=gene176 chr16 ENCODE exon 486825 487159 . + . Parent=gene176 ### chr16 ENCODE gene 492751 495628 . + . ID=gene177;Name=Z98882.1-005;Name2=RAB11FIP3 chr16 ENCODE exon 492751 493098 . + . Parent=gene177 chr16 . intron 493099 495524 . + . Parent=gene177 chr16 ENCODE exon 495525 495628 . + . Parent=gene177 ### chr16 ENCODE gene 25805568 26055029 . + . ID=gene178;Name=AC093511.1-002;Name2=HS3ST4 chr16 ENCODE exon 25805568 25805743 . + . Parent=gene178 chr16 . intron 25805744 26054433 . + . Parent=gene178 chr16 ENCODE exon 26054434 26055029 . + . Parent=gene178 ### chr16 ENCODE gene 26054434 26056510 . + . ID=gene179;Name=AC093511.1-001;Name2=HS3ST4 chr16 ENCODE exon 26054434 26056510 . + . 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!/@`B23t;},#B%G*$ RpIѿALǕ+Q >ߏxLBN!!""@@*px<{{{jd~~~ȑ&&&zyy1LII u k"hBa``P(h4ԨV5ٳI`hRT*&MMMIR٩j;;; .lٲœǨɓ'r477 hچ[IeNHHjIIIԞhyhw}8{_>SSSJ>999gǎOABJM6>|X7QOHS|>á3LTTTlݺ\ZZJW\I9I"tww3zOOϞvjLKKJyz0""bVI###΄6=44Ȍ10/ґ#GzzzZ[[ѓҘQQQQUUU,1B.]YYYǎUҬx XbqZZZppeƍXH)--U(\.Bh tGDDֲlIRѩ=flw͛7 ERnnn ̮.BP((.liF*x<RSSr\.NHTTTDǫb2hjlkk'O4by'LOO b,GeX剉vvveee&`3!!YRR"Hz{{322CccH$4{'''q8rj,((ذa5R5¯>'i6Zv!΋x+j666Y̒jƍn]SthZJu7LO2x]\\_,""ZQ < ފ ,)zԩӓP &FGGoݺ4DqDeBV4&_>;ptttwFdppkOwl2VjuGG0!>/n&&&:;;"¾O>d {_\"tww_>,%/Ϟ>ѵkJ4n֮]Kc !}h'`8::888*Db?p MWWWooo !>>>bH&+Dk{ժU666snքH[[ &i5bf(VEAٳsΩTC"S_xbR{RRRee\.LLLdV2yffK] >s\./))a%333..9...%%mwe,hNNٱccppR<<p ([n%$''Rcii)c0QB怹($Iww7ciooƴ4T訛ר IgfU놆Ȉ؟j:**b1Ƙⶶ☘BH[[ۥKz5++رcJ!ӕ.BXkliiٸq#!$66 r0tGDDֲlIRѩ=fldXB.;0T*Uv^nnn ̮.BP((.ciF*x<RSStpD":^'661FGGPPayNX=b&&&LgBBBuu5!;22D"fddPF[[[HTYYi4IONN.**p8̤kAA y"Y !!`̺jƍ|.s_h9`nԩ[Q < ظ,~._nwSNON:@XF'NT&$lE`Ν٨t,#ݻsm{~* Nwj O0D~}۟=}kהq,#BB+d GenomeTools

    GenomeTools

    The versatile open source genome analysis software

    [Genome Annotation]

    The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.

    If you are interested in gene prediction, have a look at GenomeThreader.

    Platforms

    GenomeTools has been designed to run on every POSIX compliant UNIX system. For example, Linux, Mac OS X, and OpenBSD. A Windows version which requires a Cygwin installation is available. Please report problems with it to our mailing list.

    Published software in GenomeTools

    The GenomeTools distribution includes several published software tools:

    • ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons.
      D. Ellinghaus, S. Kurtz, and U. Willhoeft.
      LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons.
      BMC Bioinformatics 2008, 9:18
    • tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
      S. Kurtz, A. Narechania, J.C. Stein, and D. Ware.
      A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
      BMC Genomics 2008, 9:517
    • uniquesub, a program for computing minimum unique substrings.
      S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek.
      Optimized design and assessment of whole genome tiling arrays.
      Bioinformatics 2007, 23(13):i195–i204
    • AnnotationSketch, a library for drawing genome annotations.
      S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz.
      AnnotationSketch: a genome annotation drawing library.
      Bioinformatics 2009, 25(4):533–534
    • ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons.
      S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz.
      Fine-grained annotation and classification of de novo predicted LTR retrotransposons.
      Nucleic Acids Research 2009, 37(21):7002–7013
    • MetaGenomeThreader, a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects.
      D.J. Schmitz-Hübsch and S. Kurtz.
      MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects.
      In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
    • GtEncseq, a compressed biosequence representation with many features.
      S. Steinbiss and S. Kurtz.
      A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.
      IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357
    • Readjoiner, a sequence assembler based on the assembly string graph framework.
      G. Gonnella and S. Kurtz.
      Readjoiner: a fast and memory efficient string graph-based sequence assembler.
      BMC Bioinformatics 2012, 13:82

    The following software tools are based on the GenomeTools library:

    • ParsEval, a tool for comparing genome annotations.
      D.S. Standage and V.P. Brendel.
      ParsEval: parallel comparison and analysis of gene structure annotations.
      BMC Bioinformatics 2012, 13:187
    • LTRsift, a graphical interface for working with LTR retrotransposon predictions.
      S. Steinbiss, S. Kastens and S. Kurtz.
      LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.
      Mobile DNA 2012, 3:18

    Contact

    The GenomeTools are being developed by:
    Gordon Gremme, Sascha Steinbiss, Stefan Kurtz and others
    Genome Informatics Research Group
    Center for Bioinformatics, University of Hamburg

    genometools-1.5.1/www/genometools.org/htdocs/license.html000066400000000000000000000070471211610345200236150ustar00rootroot00000000000000 GenomeTools License

    GenomeTools License

    /*
  Copyright (c) 2003-2013 G. Gremme, S. Steinbiss, S. Kurtz, and CONTRIBUTORS
  Copyright (c) 2003-2013 Center for Bioinformatics, University of Hamburg

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
*/

    Our copyright policy is modeled after the one of the OpenBSD operating system. We chose one of the most simple and free licenses, the ICS license. It is functionally equivalent to a two-term BSD copyright with language removed that is made unnecessary by the Berne convention.

    To ensure that GenomeTools remains absolutely free, we will only accept contributions which have been put under this license.

    We use external sources which are covered by their respective licenses. See LICENSE file for details.

    genometools-1.5.1/www/genometools.org/htdocs/manuals.html000066400000000000000000000057301211610345200236300ustar00rootroot00000000000000 GenomeTools manuals

    Manuals

    A general description of GenomeTools design guidelines and development best practices can be found in the following document:

    We also provide user manuals for some specific tools in the GenomeTools:

    genometools-1.5.1/www/genometools.org/htdocs/style.css000066400000000000000000000043271211610345200231550ustar00rootroot00000000000000body { font-family: Verdana, Geneva, Arial, sans-serif; } h1, h2, h3, h4, h5, h6 { color: gray; } #footer { font-size: 66%; text-align: center; margin-top: 20px; background-color: #DDDDDD; } img { border-style: solid; border-width: 1px; } #menu { float: left; clear: left; width: 180px; padding-right: 20px; } #menu li { list-style-type: none; margin-bottom: 10px; margin-left: -18px; } #menu li a { list-style-type: none; border : 1px solid black; display: block; padding: 4px 15px 4px 15px; text-decoration: none; } #menu li a:link { color: white; background: rgb(60%, 60%, 90%); } #menu li a:visited { color: white; background: rgb(60%, 60%, 90%); } #menu li a:hover { color: gray; background: rgb(90%, 90%, 20%); } #menu li a#current { color: gray; background: rgb(90%, 90%, 20%); } #menu ul.submenu li a { font-size: small; background: rgb(70%, 70%, 90%); } #menu ul.submenu li a:hover { color: black; } #main { margin-left: 220px; margin-right: 10%; line-height: 1.6em; } #main a:link { color: blue; text-decoration: none; border-bottom: thin dotted blue; } #main a:visited { color: gray; text-decoration: none; border-bottom: thin dotted gray; } #main a:hover { background: rgb(90%, 90%, 20%); } #examplesketch { text-align: center; } #examplesketch img { border: none; display: inline; margin: 5px 0px; } #examplesketch a:link, #examplesketch a:hover { text-decoration: none; border: none; background: none; } pre { line-height: 1.3em; } pre.code { line-height: 1.3em; background-color: #DDDDDD; padding: 15px; } /* Figure environment for library documentation. */ div.figure { position: relative; width: 650px; margin: 20px auto; background-color: white; line-height: 1em; } div.figure p { text-align: center; /* font-style: italic; */ font-size: smaller; text-indent: 0; margin:0px; } div.figure img { border: thin solid black; padding: 10px; margin: 0px; } div.figure img.noborder { border: none; padding: 0px; } div.figure div.subfigure { width: 300px; float: left; margin:12px; } div.ref { font-size: small; color: #444; line-height: 1.1em; } ul.pubs li { margin-top: 10px; line-height: 1.2em; } genometools-1.5.1/www/genometools.org/htdocs/style_options.html000066400000000000000000000343651211610345200251110ustar00rootroot00000000000000 The AnnotationSketch module

    Per-type settings

    These settings must be given for a specific type, e.g. for the gene type it could look like this: 

      gene = {
    stroke             = {red=0.0, green=0.0, blue=0.0, alpha = 1.0},
    stroke_marked      = {red=1.0, green=0.0, blue=0.0},
    fill               = {red=0.9, green=0.9, blue=1.0},
    style              = "box",
    collapse_to_parent = false,
    split_lines        = true,
    max_num_lines      = 10,
  },

    Color options

    These settings need to be set to a table with the red, blue, green and alpha keys. Alternatively, they can be set to a Lua function which returns such a table, given a FeatureNode object of the current element:

    fill = function(gn)
         if gn:get_score() then
           aval = gn:get_score()*1.0
         else
           aval = 0.0
         end
         return {red=1.0, green=0.0, blue=0.0, alpha=aval}
       end

    which would scale the transparency of the red element with the score value of the associated feature. The following settings are available:

    • stroke = {red=redval, green=greenval, blue=blueval, alpha=alphaval}
      Sets the outline color of elements of this type to the given RGBA color. All values must be decimal values between 0 and 1.
    • stroke_marked = {red=redval, green=greenval, blue=blueval, alpha=alphaval}
      Similar to stroke, but applies only to marked elements.
    • fill = {red=redval, green=greenval, blue=blueval, alpha=alphaval}
      Sets the fill color of all elements of this type to the given RGBA color.

    Drawing options

    • style = "box"/"line"/"rectangle"/"dashes"/"caret"
      Defines the visual style in which the elements of this type are drawn. Possible values are:
      • "box", which draws the elements as an box with arrowheads depending on their strand property.
      • "line", which draws the elements as straight lines with arrowheads depending on their strand property.
      • "rectangle", which draws the elements as a box without arrowheads.
      • "dashes", which draws the elements as straight lines with arrowheads depending on their strand property.
      • "caret", which draws the elements as a '^'-like glyph (often used for introns). Arrowheads are drawn depending on the strand property.
    • bar_height = value
      Sets the height of elements of this type to n pixels/points.
    • z_index = value
      Sets the z-index of the given type. The z-indices of collapsed types determine the order in which features are drawn on each other. Particularly, element with types with higher index numbers are drawn on top of elements with lower-numbered types. Elements whose types do not have a no z-index are always drawn below those with indices and their internal ordering is determined alphabetically.

    Track layout options

    • collapse_to_parent = true/false
      This boolean value determines whether the elements of this type should be drawn on top of their parent type's elements. This property can be used to recursively collapse feature trees by setting it in the parent type to true as well.

    Caption options

    • max_capt_show_width = value,
      This value determines up to which zoom width block captions are shown. If the width of the displayed sequence region (in characters) exceeds this value, then captions are omitted. If set to 0, captions are never shown for this type. If set to nil, then captions are always shown.
    • max_show_width = value,
      This value determines up to which zoom width blocks of this type are shown. It behaves just like max_capt_show_width.
    • block_caption = string/function
      This value determines how a block caption of a block of this top-level type should be generated. For example, it can be set to a Lua function which returns a string and receives a FeatureNode object of the top-level feature in the block: 
      block_caption = function(gn)
                  rng = gn:get_range()
                  return string.format("%s/%s (%dbp)",
                                       gn:get_attribute("Parent"),
                                       gn:get_attribute("ID"),
                                       rng:get_end() - rng:get_start() + 1)
                end,
      This function creates a block caption which consists of IDs of the parent feature and the feature itself followed by the length of the feature, for example: 
      gene1/mRNA1 (3400bp)

    Per-image settings

    Layout options

    • split_lines = true/false
      If this option set to false, all blocks per track are drawn in one line, instead of breaking lines if blocks overlap.
    • max_num_lines = value
      This value limits the number of lines per track. If the line breaker tries to create more tracks that set here (e.g. if many blocks overlap or if the displayed range is extremely wide), no more tracks are created. If the existing lines fill up, no more blocks will be drawn and the number of discarded blocks will be displayed next to the track title. This can be used to prevent the layouter from generating images of extreme height if a lot of features is packed at a very far zoom level.

    Ruler options

    • ruler_font_size = value
      Defines the font size (in pixels/points) of the top ruler.
    • ruler_space = value
      Defines the amount of vertical space (in pixels/points) between the ruler and the first track.

    Caption options

    • show_block_captions = true/false
      If set to false, no block captions are shown at all for all type tracks.
    • block_caption_font_size = value
      Defines the font size (in pixels/points) of the block captions.
    • block_caption_space = value
      Defines the amount of space (in pixels/points) between a block caption and the corresponding block.
    • show_track_captions = true/false
      If set to false, no track captions are shown at all.
    • track_caption_font_size = value
      Defines the font size (in pixels/points) of the track captions.
    • track_caption_space = value
      Defines the amount of space (in pixels/points) between a track caption and the lines in the track.
    • track_title_color = {red=redval, green=greenval, blue=blueval, alpha=alphaval}
      Defines the color in which track captions are drawn.

    Image options

    • background_color = {red=redval, green=greenval, blue=blueval, alpha=alphaval}
      Defines the background color of the image. If PNG output is used, this alpha value can be used to produce images with transparent backgrounds (e.g. for layering).
    • margins = value
      This value defines the amount of space left to the left and right of the diagram (in pixels/points).
    • bar_height = value
      Defines the default height of a single line (in pixels/points). Can be overridden by a per-type setting.
    • bar_vspace = value
      Defines the space left between lines (in pixels/points).
    • track_vspace = value
      Defines the space left between tracks (in pixels/points).
    • arrow_width = value
      Defines the width of an arrowhead in the "box", "dashes", "line" or "caret" element styles.
    • stroke_width = value
      Defines the width of the outline of an element.
    • stroke_marked_width = value
      Defines the width of the outline of a marked element.
    • default_stroke_color = {red=redval, green=greenval, blue=blueval, alpha=alphaval}
      Defines the default color of the outline of an element. Can be overidden by a per-type setting.
    • show_grid = true/false
      If set to true, then light vertical lines are drawn at minor ticks of the ruler for better orientation.
    • split_lines = true/false
      If this option set to false, all blocks for each type are drawn in one line per type track, instead of breaking lines if blocks overlap.
    • min_len_block = value
      Defines minimum pixel or point size of a block in which single collapsed elements are shown. If a block is more narrow then this threshold, only its outline will be drawn and its outline will be dashed. Set this to nil to always draw all elements in collapsed blocks.
    genometools-1.5.1/www/genometools.org/htdocs/trackselectors.html000066400000000000000000000167241211610345200252250ustar00rootroot00000000000000 The AnnotationSketch module

    Track selector functions

    This page explains how a special kind of function, called track selector function, can be used to customise the AnnotationSketch output by using arbitrary features of a block to assign blocks to tracks (and implicitly creating new tracks this way).

    Default: Top level type decides track membership

    By default, for each block in a Diagram, its source filename and/or the type attribute of its top level element decides into which track the block is finally inserted during the layout phase. So by default, an annotation graph parsed from the GFF3 input file ‘example.gff3’ with gene, mRNA and exon type nodes will be rendered into two separate tracks (exon→mRNA collapsing enabled, see Fig. 1):

    • example.gff3|gene and
    • example.gff3|mRNA
    We will call the second part (after the “|”) of these track titles track identifier strings in the rest of this document.

    [Basic drawing]

    Figure 1: Default AnnotationSketch output for a simple GFF3 file with simple exon→mRNA collapsing.

    While automatically determining tracks from the types actually present in the input annotations is convenient in many use cases, one could imagine cases in which more control about block handling may be desired. This leads to the question: How can one extract blocks with specific characteristics and assign them to a special track? The answer is simple: By overriding the default track identifier string, new tracks can be created and named on the fly as soon as a block satisfying user-defined rules is encountered.

    Track selector functions

    These rules take the form of track selector functions. Basically, a track selector function is a function which takes a block reference as an argument, and returns an appropriate track identifier string. For example, in Python the default track selector function would look like this: 

    def default_track_selector(block):
  return block.get_type()
    This function simply returns a string representation of the type of a block's top level element, creating the tracks just like depicted in Fig. 1.

    For a very simple example, let's assume that we want to create separate tracks for all mRNAs on the plus strand and for all mRNAs on the minus strand. The idea now is to change the strand identifier for blocks of the mRNA type to include the strand as additional information, thus creating different track identifiers for plus and minus strand features. In Python, this track selector function would construct a new string which contains both the type and the strand: 

    def strand_track_selector(block):
  if block.get_type() == "mRNA":
    return "%s (%s strand)" % (block.get_type(), block.get_strand())
  else:
    return block.get_type()
    Using this track selector function would produce the desired result of separate tracks for the mRNAs for each strand (see Fig. 2).

    [Strand Track Selector]

    Figure 2: AnnotationSketch output with strand_track_selector() track selector function. This image now shows separate tracks for plus and minus strand features.

    A track selector function can be set for a Diagram object using the diagram.set_track_selector_func() method. In C, its argument is a pointer to a function of the signature const char* (*GtTrackSelectorFunc)(GtBlock*, void*) where arbitrary data can be passed via the second void* argument. The Python set_track_selector_func() method directly accepts a Python function as an argument, while the Ruby version takes a Proc object: 

    ...
strand_track_selector = Proc.new { |block, data|
  "#{block.get_type} (#{block.get_strand} strand)"
}
...
diagram.set_track_selector_func(strand_track_selector)
...

    Note that in Python and Ruby, it is also possible to reference data declared outside of the track selector function. For example, this can be used to filter blocks by pulling blocks whose description matches a pattern into a separate track: 

    ...
interesting_genes = ["First test gene", "another gene"]

def filter_track_selector(block):
  if block.get_caption() in interesting_genes:
    return "interesting genes"
  else:
    return block.get_type()
...
diagram.set_track_selector_func(filter_track_selector)
...
    This code results in the following image (Fig. 3):

    [Filter Track Selector]

    Figure 3: AnnotationSketch output with filter_track_selector() track selector function. This image now shows a separate track for features with a specific caption.